Multiple sequence alignment - TraesCS5B01G217700

Loading Multiple Alignment...

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 TraesCS5B01G217700 chr5B 100.000 7453 0 0 1 7453 391751434 391758886 0.000000e+00 13764.0
1 TraesCS5B01G217700 chr5B 82.485 2221 322 45 1785 3982 440210934 440213110 0.000000e+00 1884.0
2 TraesCS5B01G217700 chr5B 80.207 773 109 25 3226 3984 440228354 440229096 2.370000e-149 540.0
3 TraesCS5B01G217700 chr5B 80.676 621 87 22 3381 3983 440186666 440187271 1.140000e-122 451.0
4 TraesCS5B01G217700 chr5B 82.524 515 72 10 4344 4855 440234861 440235360 3.190000e-118 436.0
5 TraesCS5B01G217700 chr5B 82.101 514 78 8 4344 4855 51858500 51857999 1.920000e-115 427.0
6 TraesCS5B01G217700 chr5B 81.343 402 69 5 5984 6384 51857220 51856824 9.330000e-84 322.0
7 TraesCS5B01G217700 chr5B 81.235 405 66 6 5986 6390 440214773 440215167 1.210000e-82 318.0
8 TraesCS5B01G217700 chr5B 100.000 39 0 0 772 810 391752167 391752205 1.040000e-08 73.1
9 TraesCS5B01G217700 chr5B 100.000 39 0 0 734 772 391752205 391752243 1.040000e-08 73.1
10 TraesCS5B01G217700 chr5D 97.012 5757 137 19 1592 7339 334890385 334896115 0.000000e+00 9646.0
11 TraesCS5B01G217700 chr5D 82.005 2145 326 37 1803 3934 49151298 49149201 0.000000e+00 1768.0
12 TraesCS5B01G217700 chr5D 85.556 1357 184 9 1803 3153 370838604 370839954 0.000000e+00 1410.0
13 TraesCS5B01G217700 chr5D 85.346 1358 193 6 1803 3157 370826821 370828175 0.000000e+00 1400.0
14 TraesCS5B01G217700 chr5D 95.455 814 30 5 772 1582 334889478 334890287 0.000000e+00 1291.0
15 TraesCS5B01G217700 chr5D 90.568 774 39 13 1 772 334888775 334889516 0.000000e+00 994.0
16 TraesCS5B01G217700 chr5D 81.169 770 112 24 3226 3984 370839985 370840732 8.330000e-164 588.0
17 TraesCS5B01G217700 chr5D 80.485 743 111 26 3207 3936 370828192 370828913 8.510000e-149 538.0
18 TraesCS5B01G217700 chr5D 84.615 468 57 9 4391 4855 370829165 370829620 1.140000e-122 451.0
19 TraesCS5B01G217700 chr5D 82.913 515 73 7 4344 4855 370841235 370841737 4.100000e-122 449.0
20 TraesCS5B01G217700 chr5D 81.518 514 81 9 4344 4855 49148879 49148378 1.940000e-110 411.0
21 TraesCS5B01G217700 chr5D 81.592 402 68 5 5984 6384 49147593 49147197 2.010000e-85 327.0
22 TraesCS5B01G217700 chr5D 78.208 491 90 13 5984 6471 370830369 370830845 1.570000e-76 298.0
23 TraesCS5B01G217700 chr5D 89.583 48 5 0 38 85 357513955 357514002 2.250000e-05 62.1
24 TraesCS5B01G217700 chr5A 96.383 5613 121 23 1768 7351 436286538 436292097 0.000000e+00 9166.0
25 TraesCS5B01G217700 chr5A 81.958 2145 310 45 1803 3934 38779129 38777049 0.000000e+00 1746.0
26 TraesCS5B01G217700 chr5A 85.041 1357 191 8 1803 3153 473619917 473621267 0.000000e+00 1371.0
27 TraesCS5B01G217700 chr5A 84.109 1353 205 9 1809 3156 473418085 473419432 0.000000e+00 1299.0
28 TraesCS5B01G217700 chr5A 82.814 1379 207 23 1803 3167 473457071 473458433 0.000000e+00 1206.0
29 TraesCS5B01G217700 chr5A 90.144 487 38 7 185 668 436283598 436284077 6.350000e-175 625.0
30 TraesCS5B01G217700 chr5A 80.779 770 112 26 3226 3984 473621298 473622042 3.020000e-158 569.0
31 TraesCS5B01G217700 chr5A 81.037 733 109 25 3207 3930 473419450 473420161 2.350000e-154 556.0
32 TraesCS5B01G217700 chr5A 94.311 334 12 1 991 1324 436284406 436284732 8.630000e-139 505.0
33 TraesCS5B01G217700 chr5A 83.301 515 71 7 4344 4855 473622724 473623226 1.890000e-125 460.0
34 TraesCS5B01G217700 chr5A 85.417 432 51 6 4424 4855 38776646 38776227 8.880000e-119 438.0
35 TraesCS5B01G217700 chr5A 83.974 468 59 10 4391 4855 473429168 473429622 1.150000e-117 435.0
36 TraesCS5B01G217700 chr5A 92.713 247 16 2 1338 1582 436286066 436286312 9.200000e-94 355.0
37 TraesCS5B01G217700 chr5A 78.455 492 87 15 5984 6471 473430329 473430805 3.380000e-78 303.0
38 TraesCS5B01G217700 chr5A 80.397 403 71 6 5984 6384 38775414 38775018 4.370000e-77 300.0
39 TraesCS5B01G217700 chr5A 89.778 225 20 3 1 225 436283095 436283316 1.220000e-72 285.0
40 TraesCS5B01G217700 chr5A 87.963 216 8 5 772 969 436284196 436284411 9.660000e-59 239.0
41 TraesCS5B01G217700 chr5A 94.656 131 4 2 1592 1720 436286412 436286541 4.560000e-47 200.0
42 TraesCS5B01G217700 chr5A 92.929 99 4 1 674 772 436284139 436284234 2.800000e-29 141.0
43 TraesCS5B01G217700 chr5A 98.148 54 0 1 176 229 436283633 436283685 7.960000e-15 93.5
44 TraesCS5B01G217700 chr5A 90.196 51 5 0 35 85 458687438 458687488 4.830000e-07 67.6
45 TraesCS5B01G217700 chr5A 94.737 38 2 0 1431 1468 436286108 436286145 8.080000e-05 60.2
46 TraesCS5B01G217700 chr6D 91.045 67 3 3 5114 5178 182993341 182993276 3.700000e-13 87.9
47 TraesCS5B01G217700 chr6A 91.045 67 3 3 5114 5178 578219287 578219222 3.700000e-13 87.9
48 TraesCS5B01G217700 chr6A 91.045 67 3 3 5114 5178 597231518 597231583 3.700000e-13 87.9
49 TraesCS5B01G217700 chr6A 89.831 59 3 3 20 77 154445853 154445797 1.040000e-08 73.1
50 TraesCS5B01G217700 chr6A 88.710 62 3 4 18 77 480245018 480244959 1.040000e-08 73.1
51 TraesCS5B01G217700 chr4A 91.045 67 3 3 5114 5178 295266177 295266112 3.700000e-13 87.9
52 TraesCS5B01G217700 chr4A 90.909 44 3 1 4089 4132 534781615 534781573 2.900000e-04 58.4
53 TraesCS5B01G217700 chr3B 91.045 67 3 3 5114 5178 201595210 201595275 3.700000e-13 87.9
54 TraesCS5B01G217700 chr3B 93.182 44 3 0 4089 4132 684251660 684251703 1.740000e-06 65.8
55 TraesCS5B01G217700 chr1B 84.211 95 8 6 7346 7434 84362779 84362686 1.330000e-12 86.1
56 TraesCS5B01G217700 chr1B 87.838 74 5 4 5114 5184 668813366 668813438 4.790000e-12 84.2
57 TraesCS5B01G217700 chrUn 87.671 73 6 3 5108 5178 282365200 282365271 1.720000e-11 82.4
58 TraesCS5B01G217700 chr2B 83.871 93 7 6 7350 7434 798381473 798381565 1.720000e-11 82.4
59 TraesCS5B01G217700 chr2B 91.667 48 3 1 5700 5747 775028720 775028674 1.740000e-06 65.8
60 TraesCS5B01G217700 chr2A 83.696 92 7 8 7350 7434 733869497 733869587 6.200000e-11 80.5
61 TraesCS5B01G217700 chr4B 89.831 59 3 3 20 77 554049638 554049694 1.040000e-08 73.1
62 TraesCS5B01G217700 chr4B 95.455 44 1 1 4089 4132 91337719 91337761 1.340000e-07 69.4
63 TraesCS5B01G217700 chr3D 92.308 52 2 2 5695 5745 266427019 266427069 1.040000e-08 73.1
64 TraesCS5B01G217700 chr3A 92.308 52 2 2 5695 5745 301143303 301143353 1.040000e-08 73.1
65 TraesCS5B01G217700 chr7D 97.561 41 1 0 5700 5740 141356416 141356376 3.730000e-08 71.3
66 TraesCS5B01G217700 chr7D 89.091 55 3 2 5694 5745 127000927 127000981 1.740000e-06 65.8
67 TraesCS5B01G217700 chr6B 91.837 49 4 0 4084 4132 664222689 664222737 1.340000e-07 69.4
68 TraesCS5B01G217700 chr1D 95.349 43 1 1 5696 5738 22976619 22976578 4.830000e-07 67.6
69 TraesCS5B01G217700 chr2D 93.333 45 2 1 5695 5739 35799968 35800011 1.740000e-06 65.8


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 TraesCS5B01G217700 chr5B 391751434 391758886 7452 False 13764.000000 13764 100.000000 1 7453 1 chr5B.!!$F1 7452
1 TraesCS5B01G217700 chr5B 440210934 440215167 4233 False 1101.000000 1884 81.860000 1785 6390 2 chr5B.!!$F6 4605
2 TraesCS5B01G217700 chr5B 440228354 440229096 742 False 540.000000 540 80.207000 3226 3984 1 chr5B.!!$F3 758
3 TraesCS5B01G217700 chr5B 440186666 440187271 605 False 451.000000 451 80.676000 3381 3983 1 chr5B.!!$F2 602
4 TraesCS5B01G217700 chr5B 51856824 51858500 1676 True 374.500000 427 81.722000 4344 6384 2 chr5B.!!$R1 2040
5 TraesCS5B01G217700 chr5D 334888775 334896115 7340 False 3977.000000 9646 94.345000 1 7339 3 chr5D.!!$F2 7338
6 TraesCS5B01G217700 chr5D 49147197 49151298 4101 True 835.333333 1768 81.705000 1803 6384 3 chr5D.!!$R1 4581
7 TraesCS5B01G217700 chr5D 370838604 370841737 3133 False 815.666667 1410 83.212667 1803 4855 3 chr5D.!!$F4 3052
8 TraesCS5B01G217700 chr5D 370826821 370830845 4024 False 671.750000 1400 82.163500 1803 6471 4 chr5D.!!$F3 4668
9 TraesCS5B01G217700 chr5A 473457071 473458433 1362 False 1206.000000 1206 82.814000 1803 3167 1 chr5A.!!$F2 1364
10 TraesCS5B01G217700 chr5A 436283095 436292097 9002 False 1166.970000 9166 93.176200 1 7351 10 chr5A.!!$F3 7350
11 TraesCS5B01G217700 chr5A 473418085 473420161 2076 False 927.500000 1299 82.573000 1809 3930 2 chr5A.!!$F4 2121
12 TraesCS5B01G217700 chr5A 38775018 38779129 4111 True 828.000000 1746 82.590667 1803 6384 3 chr5A.!!$R1 4581
13 TraesCS5B01G217700 chr5A 473619917 473623226 3309 False 800.000000 1371 83.040333 1803 4855 3 chr5A.!!$F6 3052
14 TraesCS5B01G217700 chr5A 473429168 473430805 1637 False 369.000000 435 81.214500 4391 6471 2 chr5A.!!$F5 2080

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
27 28 0.098200 GCACGCGAAGATTTTACCCC 59.902 55.000 15.93 0.00 0.00 4.95 F
1117 1523 0.105593 CCATGTGGGAGTGATCCTCG 59.894 60.000 0.00 0.00 41.46 4.63 F
1588 3316 0.037605 ATAACCTACATAGCGGCCGC 60.038 55.000 42.34 42.34 42.33 6.53 F
1589 3317 2.091102 TAACCTACATAGCGGCCGCC 62.091 60.000 44.47 27.39 43.17 6.13 F
2812 4638 1.611491 TCCCGGCAGTTGAATCAAAAC 59.389 47.619 0.00 0.00 0.00 2.43 F
3753 5624 0.324943 TTGCCTGGCTTCTGGAGTAC 59.675 55.000 21.03 0.00 0.00 2.73 F
4370 6696 1.135431 TGGAACGTTATGCATTGCAGC 60.135 47.619 17.52 8.73 43.65 5.25 F
5164 7558 0.179100 CTCACTGACCGCACCCTATG 60.179 60.000 0.00 0.00 0.00 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 3310 0.100503 CTTTTATCCTTTGGCGGCCG 59.899 55.000 24.05 24.05 0.00 6.13 R
2794 4620 1.665735 CCGTTTTGATTCAACTGCCGG 60.666 52.381 0.00 0.00 0.00 6.13 R
2812 4638 2.487762 TGATCCTGCTGTTTTTAAGCCG 59.512 45.455 0.00 0.00 40.06 5.52 R
3055 4881 4.360563 CCAGGTACTCATAAGTAAGTGCG 58.639 47.826 0.00 0.00 39.66 5.34 R
4732 7061 3.737559 AGGGGATTTCATGTACAAGCA 57.262 42.857 0.00 0.00 0.00 3.91 R
5164 7558 3.515602 AGCTTACATTGATGATCCCCC 57.484 47.619 0.00 0.00 0.00 5.40 R
6167 8910 2.346803 TCAAAAGTGATAGCGCCTGAC 58.653 47.619 2.29 0.00 0.00 3.51 R
7023 9781 0.388778 TCGCGAATGTGCTACCGAAA 60.389 50.000 6.20 0.00 0.00 3.46 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
27 28 0.098200 GCACGCGAAGATTTTACCCC 59.902 55.000 15.93 0.00 0.00 4.95
29 30 0.741927 ACGCGAAGATTTTACCCCGG 60.742 55.000 15.93 0.00 0.00 5.73
30 31 1.433837 CGCGAAGATTTTACCCCGGG 61.434 60.000 15.80 15.80 0.00 5.73
86 87 3.385314 TGCTTGGATTGGATTGATGGA 57.615 42.857 0.00 0.00 0.00 3.41
93 94 4.231658 TGGATTGGATTGATGGAAAGGGTA 59.768 41.667 0.00 0.00 0.00 3.69
110 111 1.694696 GGTACCATGTGAGAGGGGATC 59.305 57.143 7.15 0.00 0.00 3.36
131 132 6.995091 GGATCACAATGGAGAATAGTAAGCTT 59.005 38.462 3.48 3.48 0.00 3.74
153 154 9.771534 AGCTTTATCAAGAGTATTAGATTGGAC 57.228 33.333 0.00 0.00 30.57 4.02
252 573 4.595350 GTCTTATAAAGGAGGAGGATGCCT 59.405 45.833 0.00 0.00 42.17 4.75
369 691 5.854338 ACGCTCCACAAAATATTTTAACGTG 59.146 36.000 12.98 15.43 0.00 4.49
371 693 6.248420 CGCTCCACAAAATATTTTAACGTGAG 59.752 38.462 22.18 18.10 0.00 3.51
397 719 0.260230 TTTGCACAAGTCCCCAAGGA 59.740 50.000 0.00 0.00 41.08 3.36
437 759 7.292292 TCGTTTATTGGAACAGACAAATTACG 58.708 34.615 0.00 0.00 42.39 3.18
447 769 9.274065 GGAACAGACAAATTACGAATCAAATAC 57.726 33.333 0.00 0.00 0.00 1.89
448 770 9.820229 GAACAGACAAATTACGAATCAAATACA 57.180 29.630 0.00 0.00 0.00 2.29
449 771 9.825972 AACAGACAAATTACGAATCAAATACAG 57.174 29.630 0.00 0.00 0.00 2.74
450 772 8.999431 ACAGACAAATTACGAATCAAATACAGT 58.001 29.630 0.00 0.00 0.00 3.55
481 809 2.872245 CACGCCACCCTTATGTAGATTG 59.128 50.000 0.00 0.00 0.00 2.67
576 905 6.238402 GGTTTTCAGGTCTTCAGTTTGACTAC 60.238 42.308 0.00 0.00 34.01 2.73
617 946 9.540431 CAAATTAAAAATCTAAAAACCCATGCG 57.460 29.630 0.00 0.00 0.00 4.73
770 1155 4.878397 ACACCAAAGTCAAGAGAGAAACAG 59.122 41.667 0.00 0.00 0.00 3.16
771 1156 4.878397 CACCAAAGTCAAGAGAGAAACAGT 59.122 41.667 0.00 0.00 0.00 3.55
772 1157 5.355350 CACCAAAGTCAAGAGAGAAACAGTT 59.645 40.000 0.00 0.00 0.00 3.16
773 1158 6.538742 CACCAAAGTCAAGAGAGAAACAGTTA 59.461 38.462 0.00 0.00 0.00 2.24
774 1159 6.763610 ACCAAAGTCAAGAGAGAAACAGTTAG 59.236 38.462 0.00 0.00 0.00 2.34
775 1160 6.293135 CCAAAGTCAAGAGAGAAACAGTTAGC 60.293 42.308 0.00 0.00 0.00 3.09
776 1161 5.799827 AGTCAAGAGAGAAACAGTTAGCT 57.200 39.130 0.00 0.00 0.00 3.32
778 1163 4.151512 GTCAAGAGAGAAACAGTTAGCTGC 59.848 45.833 6.48 0.00 46.30 5.25
779 1164 4.060900 CAAGAGAGAAACAGTTAGCTGCA 58.939 43.478 6.48 0.00 46.30 4.41
780 1165 4.342862 AGAGAGAAACAGTTAGCTGCAA 57.657 40.909 6.48 0.00 46.30 4.08
781 1166 4.708177 AGAGAGAAACAGTTAGCTGCAAA 58.292 39.130 6.48 0.00 46.30 3.68
782 1167 5.312079 AGAGAGAAACAGTTAGCTGCAAAT 58.688 37.500 6.48 0.00 46.30 2.32
783 1168 5.180868 AGAGAGAAACAGTTAGCTGCAAATG 59.819 40.000 6.48 6.57 46.30 2.32
784 1169 5.065914 AGAGAAACAGTTAGCTGCAAATGA 58.934 37.500 6.48 0.00 46.30 2.57
785 1170 5.532406 AGAGAAACAGTTAGCTGCAAATGAA 59.468 36.000 6.48 0.00 46.30 2.57
786 1171 5.523369 AGAAACAGTTAGCTGCAAATGAAC 58.477 37.500 6.48 6.37 46.30 3.18
787 1172 4.916983 AACAGTTAGCTGCAAATGAACA 57.083 36.364 6.48 0.00 46.30 3.18
788 1173 4.228912 ACAGTTAGCTGCAAATGAACAC 57.771 40.909 6.48 0.00 46.30 3.32
789 1174 3.004734 ACAGTTAGCTGCAAATGAACACC 59.995 43.478 6.48 0.00 46.30 4.16
790 1175 3.004629 CAGTTAGCTGCAAATGAACACCA 59.995 43.478 1.02 0.00 35.77 4.17
791 1176 3.636300 AGTTAGCTGCAAATGAACACCAA 59.364 39.130 1.02 0.00 0.00 3.67
792 1177 4.099266 AGTTAGCTGCAAATGAACACCAAA 59.901 37.500 1.02 0.00 0.00 3.28
793 1178 3.102052 AGCTGCAAATGAACACCAAAG 57.898 42.857 1.02 0.00 0.00 2.77
794 1179 2.431782 AGCTGCAAATGAACACCAAAGT 59.568 40.909 1.02 0.00 0.00 2.66
795 1180 2.796593 GCTGCAAATGAACACCAAAGTC 59.203 45.455 0.00 0.00 0.00 3.01
796 1181 3.737663 GCTGCAAATGAACACCAAAGTCA 60.738 43.478 0.00 0.00 0.00 3.41
797 1182 4.431809 CTGCAAATGAACACCAAAGTCAA 58.568 39.130 0.00 0.00 0.00 3.18
798 1183 4.431809 TGCAAATGAACACCAAAGTCAAG 58.568 39.130 0.00 0.00 0.00 3.02
799 1184 4.159321 TGCAAATGAACACCAAAGTCAAGA 59.841 37.500 0.00 0.00 0.00 3.02
800 1185 4.741676 GCAAATGAACACCAAAGTCAAGAG 59.258 41.667 0.00 0.00 0.00 2.85
801 1186 5.450412 GCAAATGAACACCAAAGTCAAGAGA 60.450 40.000 0.00 0.00 0.00 3.10
802 1187 6.204359 CAAATGAACACCAAAGTCAAGAGAG 58.796 40.000 0.00 0.00 0.00 3.20
803 1188 4.753516 TGAACACCAAAGTCAAGAGAGA 57.246 40.909 0.00 0.00 0.00 3.10
804 1189 5.097742 TGAACACCAAAGTCAAGAGAGAA 57.902 39.130 0.00 0.00 0.00 2.87
805 1190 5.496556 TGAACACCAAAGTCAAGAGAGAAA 58.503 37.500 0.00 0.00 0.00 2.52
806 1191 5.354234 TGAACACCAAAGTCAAGAGAGAAAC 59.646 40.000 0.00 0.00 0.00 2.78
807 1192 4.843728 ACACCAAAGTCAAGAGAGAAACA 58.156 39.130 0.00 0.00 0.00 2.83
831 1216 1.920574 CACGACGAAAGATGCTGGTAG 59.079 52.381 0.00 0.00 0.00 3.18
922 1324 4.209112 GTTAAGCCGAAAAGTCTTCAACG 58.791 43.478 0.00 0.00 0.00 4.10
925 1327 1.865340 GCCGAAAAGTCTTCAACGAGT 59.135 47.619 0.00 0.00 0.00 4.18
982 1385 3.190535 TCAGCGCCAAAGAATCTAAAACC 59.809 43.478 2.29 0.00 0.00 3.27
984 1387 3.826729 AGCGCCAAAGAATCTAAAACCTT 59.173 39.130 2.29 0.00 0.00 3.50
985 1388 3.920412 GCGCCAAAGAATCTAAAACCTTG 59.080 43.478 0.00 0.00 0.00 3.61
986 1389 3.920412 CGCCAAAGAATCTAAAACCTTGC 59.080 43.478 0.00 0.00 0.00 4.01
987 1390 4.245660 GCCAAAGAATCTAAAACCTTGCC 58.754 43.478 0.00 0.00 0.00 4.52
988 1391 4.485163 CCAAAGAATCTAAAACCTTGCCG 58.515 43.478 0.00 0.00 0.00 5.69
989 1392 4.022329 CCAAAGAATCTAAAACCTTGCCGT 60.022 41.667 0.00 0.00 0.00 5.68
990 1393 4.766404 AAGAATCTAAAACCTTGCCGTG 57.234 40.909 0.00 0.00 0.00 4.94
992 1395 1.904287 ATCTAAAACCTTGCCGTGCA 58.096 45.000 0.00 0.00 36.47 4.57
993 1396 1.234821 TCTAAAACCTTGCCGTGCAG 58.765 50.000 0.00 0.00 40.61 4.41
1104 1510 1.800805 AAGCAGACGAGTTCCATGTG 58.199 50.000 0.00 0.00 0.00 3.21
1117 1523 0.105593 CCATGTGGGAGTGATCCTCG 59.894 60.000 0.00 0.00 41.46 4.63
1144 1550 0.535102 CTCGCTGGTGGGAAAAGTGT 60.535 55.000 0.00 0.00 34.69 3.55
1162 1568 2.226437 GTGTCACGAACCAGCATTTCAT 59.774 45.455 0.00 0.00 0.00 2.57
1171 1577 0.523968 CAGCATTTCATTGGCCGTCG 60.524 55.000 0.00 0.00 0.00 5.12
1534 3262 7.010923 CCAAGCAGAGTCTATAAAATCACAGAC 59.989 40.741 0.00 0.00 38.13 3.51
1551 3279 8.594881 ATCACAGACCGAGAAAATATATGTTC 57.405 34.615 7.47 7.47 0.00 3.18
1555 3283 9.396022 ACAGACCGAGAAAATATATGTTCATTT 57.604 29.630 16.40 0.00 0.00 2.32
1582 3310 5.828299 TTGCAAACCATAACCTACATAGC 57.172 39.130 0.00 0.00 0.00 2.97
1584 3312 3.250040 GCAAACCATAACCTACATAGCGG 59.750 47.826 0.00 0.00 0.00 5.52
1586 3314 1.346722 ACCATAACCTACATAGCGGCC 59.653 52.381 0.00 0.00 0.00 6.13
1587 3315 1.671850 CCATAACCTACATAGCGGCCG 60.672 57.143 24.05 24.05 0.00 6.13
1588 3316 0.037605 ATAACCTACATAGCGGCCGC 60.038 55.000 42.34 42.34 42.33 6.53
1589 3317 2.091102 TAACCTACATAGCGGCCGCC 62.091 60.000 44.47 27.39 43.17 6.13
1590 3318 3.923864 CCTACATAGCGGCCGCCA 61.924 66.667 44.47 34.90 43.17 5.69
1625 3443 6.482973 AGCAGTCTTAGTTATAGGAGTCGTAC 59.517 42.308 0.00 0.00 0.00 3.67
1634 3452 6.776603 AGTTATAGGAGTCGTACAAGGCTTAT 59.223 38.462 0.00 0.00 0.00 1.73
1640 3458 4.261801 AGTCGTACAAGGCTTATGCAAAT 58.738 39.130 0.00 0.00 41.91 2.32
1753 3573 8.785329 TGTTATGTGCTATGATGTTGTTTCTA 57.215 30.769 0.00 0.00 0.00 2.10
1755 3575 8.664798 GTTATGTGCTATGATGTTGTTTCTACA 58.335 33.333 0.00 0.00 0.00 2.74
1756 3576 7.870509 ATGTGCTATGATGTTGTTTCTACAT 57.129 32.000 0.00 0.00 38.86 2.29
1822 3642 5.938322 TCAAAAGCGATTGAATTACTGGAC 58.062 37.500 4.95 0.00 36.42 4.02
1894 3714 6.049149 TGTATTCATCTCCAAGATCGGAAAC 58.951 40.000 0.00 0.00 31.32 2.78
1901 3721 4.224147 TCTCCAAGATCGGAAACATAACCA 59.776 41.667 0.00 0.00 33.65 3.67
2259 4079 5.472137 CCACGATGACTTCCCTTCTTTTTAA 59.528 40.000 0.00 0.00 0.00 1.52
2604 4424 4.333926 GTCCATTAAGAACTCCACATGCTC 59.666 45.833 0.00 0.00 0.00 4.26
2794 4620 3.315470 GGAGTGTGAAAAGTGGACTTTCC 59.685 47.826 5.26 0.00 44.69 3.13
2812 4638 1.611491 TCCCGGCAGTTGAATCAAAAC 59.389 47.619 0.00 0.00 0.00 2.43
2842 4668 2.121948 ACAGCAGGATCAGCCTCAATA 58.878 47.619 5.84 0.00 46.97 1.90
2968 4794 6.603940 AGCAATTGCCCAGAGTTTATAAAA 57.396 33.333 26.45 0.00 43.38 1.52
3055 4881 4.527944 AGGCAATAAAGAGGCTACCTTTC 58.472 43.478 4.62 0.00 39.04 2.62
3753 5624 0.324943 TTGCCTGGCTTCTGGAGTAC 59.675 55.000 21.03 0.00 0.00 2.73
4355 6681 2.879103 TCCCAATCAAGTCCTGGAAC 57.121 50.000 0.00 0.00 31.38 3.62
4370 6696 1.135431 TGGAACGTTATGCATTGCAGC 60.135 47.619 17.52 8.73 43.65 5.25
4732 7061 1.274167 CAAAGATGGTGGCATTGCTGT 59.726 47.619 8.82 0.00 0.00 4.40
4857 7187 7.373493 TGTAAGTTTAACTACACTCACTAGGC 58.627 38.462 0.00 0.00 0.00 3.93
4881 7211 7.148689 GGCTGCTTTGTTTTAATCTCTTGAATG 60.149 37.037 0.00 0.00 0.00 2.67
4883 7213 8.801715 TGCTTTGTTTTAATCTCTTGAATGAC 57.198 30.769 0.00 0.00 0.00 3.06
4926 7257 8.105097 TGCTACAAGTCAAGCAAAATGTTATA 57.895 30.769 0.00 0.00 45.36 0.98
5164 7558 0.179100 CTCACTGACCGCACCCTATG 60.179 60.000 0.00 0.00 0.00 2.23
6167 8910 7.350744 TCAACATGAGGATAAAATTGATGGG 57.649 36.000 0.00 0.00 0.00 4.00
6345 9095 2.029020 GGGCAACAAGGAGAAAATGGAC 60.029 50.000 0.00 0.00 39.74 4.02
6479 9234 4.451435 GCTACCAGAACAGTAAGAACAACC 59.549 45.833 0.00 0.00 0.00 3.77
6488 9243 5.681639 ACAGTAAGAACAACCATATAGGCC 58.318 41.667 0.00 0.00 43.14 5.19
6505 9260 1.335872 GGCCGTGGATTCACACAAAAG 60.336 52.381 4.68 0.00 43.79 2.27
6520 9275 2.108700 CAAAAGAACAAGGCAACGTCG 58.891 47.619 0.00 0.00 46.39 5.12
6529 9284 2.658707 GGCAACGTCGCTGACTCAC 61.659 63.158 0.00 0.00 0.00 3.51
6538 9293 1.354337 CGCTGACTCACATTGGTCCG 61.354 60.000 0.00 0.00 0.00 4.79
6556 9311 1.293179 GCAAACCATTCACAGGGGC 59.707 57.895 0.00 0.00 0.00 5.80
6568 9323 0.763035 ACAGGGGCGACAAAAGTAGT 59.237 50.000 0.00 0.00 0.00 2.73
6573 9328 3.770933 AGGGGCGACAAAAGTAGTATGTA 59.229 43.478 0.00 0.00 0.00 2.29
6577 9332 6.457799 GGGGCGACAAAAGTAGTATGTAATTG 60.458 42.308 0.00 0.00 0.00 2.32
6672 9427 1.377229 CCCGGCAGAACTTTGGGTA 59.623 57.895 0.00 0.00 35.05 3.69
6701 9456 4.376340 CTTCCTATGGATGCAAAACACC 57.624 45.455 0.00 0.00 0.00 4.16
6702 9457 3.448093 TCCTATGGATGCAAAACACCA 57.552 42.857 0.00 0.00 35.05 4.17
6703 9458 3.772387 TCCTATGGATGCAAAACACCAA 58.228 40.909 0.00 0.00 34.50 3.67
6704 9459 4.155709 TCCTATGGATGCAAAACACCAAA 58.844 39.130 0.00 0.00 34.50 3.28
6722 9477 6.756542 ACACCAAAATCAAGTAAAGTTTCAGC 59.243 34.615 0.00 0.00 0.00 4.26
6731 9486 7.224297 TCAAGTAAAGTTTCAGCCTGTCTTAT 58.776 34.615 0.00 0.00 0.00 1.73
6732 9487 7.719633 TCAAGTAAAGTTTCAGCCTGTCTTATT 59.280 33.333 0.00 0.00 0.00 1.40
6733 9488 8.999431 CAAGTAAAGTTTCAGCCTGTCTTATTA 58.001 33.333 0.00 0.00 0.00 0.98
6767 9522 1.327690 GGGCATCACCTGTCTCGGTA 61.328 60.000 0.00 0.00 39.10 4.02
6774 9529 5.405797 CATCACCTGTCTCGGTATATCATG 58.594 45.833 0.00 0.00 34.94 3.07
6779 9534 5.473846 ACCTGTCTCGGTATATCATGTACTG 59.526 44.000 0.00 0.00 34.94 2.74
6780 9535 5.473846 CCTGTCTCGGTATATCATGTACTGT 59.526 44.000 0.68 0.00 31.77 3.55
6785 9540 7.802251 GTCTCGGTATATCATGTACTGTTGTAC 59.198 40.741 0.68 0.00 46.74 2.90
6984 9742 0.747255 CAGTATCCGTCTGTCCCCAG 59.253 60.000 0.00 0.00 40.25 4.45
6995 9753 2.305927 TCTGTCCCCAGAAATCTCAACC 59.694 50.000 0.00 0.00 44.67 3.77
7017 9775 3.120546 CCACATCAAACTAGTGTTCTGCG 60.121 47.826 0.00 0.00 34.96 5.18
7023 9781 6.371809 TCAAACTAGTGTTCTGCGAAATTT 57.628 33.333 0.00 0.00 34.96 1.82
7024 9782 6.791303 TCAAACTAGTGTTCTGCGAAATTTT 58.209 32.000 0.00 0.00 34.96 1.82
7025 9783 7.254852 TCAAACTAGTGTTCTGCGAAATTTTT 58.745 30.769 0.00 0.00 34.96 1.94
7051 9809 1.651099 CACATTCGCGAACGCATATG 58.349 50.000 26.00 19.28 42.06 1.78
7057 9815 0.318360 CGCGAACGCATATGGTAGGA 60.318 55.000 18.69 0.00 42.06 2.94
7058 9816 1.860676 GCGAACGCATATGGTAGGAA 58.139 50.000 14.26 0.00 41.49 3.36
7059 9817 1.525619 GCGAACGCATATGGTAGGAAC 59.474 52.381 14.26 0.00 41.49 3.62
7152 9916 1.460504 ATCTCGACGTACCTTGCTGA 58.539 50.000 0.00 0.00 0.00 4.26
7268 10047 4.689549 TGGAAGGCGGAGGACGGA 62.690 66.667 0.00 0.00 44.51 4.69
7351 10130 2.930040 GCATAGCTGCTCAACGTTAAGA 59.070 45.455 4.91 0.00 45.32 2.10
7352 10131 3.000724 GCATAGCTGCTCAACGTTAAGAG 59.999 47.826 4.91 6.96 45.32 2.85
7367 10146 2.280052 GAGCATCTCCAGCCGAGC 60.280 66.667 0.00 0.00 38.62 5.03
7368 10147 3.805891 GAGCATCTCCAGCCGAGCC 62.806 68.421 0.00 0.00 38.62 4.70
7369 10148 4.925861 GCATCTCCAGCCGAGCCC 62.926 72.222 0.00 0.00 38.62 5.19
7370 10149 4.247380 CATCTCCAGCCGAGCCCC 62.247 72.222 0.00 0.00 38.62 5.80
7371 10150 4.804420 ATCTCCAGCCGAGCCCCA 62.804 66.667 0.00 0.00 38.62 4.96
7387 10166 4.096003 CACGGCCCCCACTCGATT 62.096 66.667 0.00 0.00 0.00 3.34
7388 10167 3.327404 ACGGCCCCCACTCGATTT 61.327 61.111 0.00 0.00 0.00 2.17
7389 10168 2.045340 CGGCCCCCACTCGATTTT 60.045 61.111 0.00 0.00 0.00 1.82
7390 10169 1.677633 CGGCCCCCACTCGATTTTT 60.678 57.895 0.00 0.00 0.00 1.94
7423 10202 2.898343 AAAAACGGCCAGTCGCGT 60.898 55.556 5.77 0.00 38.94 6.01
7424 10203 2.888998 AAAAACGGCCAGTCGCGTC 61.889 57.895 5.77 0.00 38.94 5.19
7431 10210 4.135153 CCAGTCGCGTCCCAGGAG 62.135 72.222 5.77 0.00 0.00 3.69
7432 10211 4.803426 CAGTCGCGTCCCAGGAGC 62.803 72.222 5.77 0.00 0.00 4.70
7436 10215 4.394712 CGCGTCCCAGGAGCCTTT 62.395 66.667 0.00 0.00 0.00 3.11
7437 10216 2.034221 GCGTCCCAGGAGCCTTTT 59.966 61.111 0.00 0.00 0.00 2.27
7438 10217 1.603739 GCGTCCCAGGAGCCTTTTT 60.604 57.895 0.00 0.00 0.00 1.94
7439 10218 1.587043 GCGTCCCAGGAGCCTTTTTC 61.587 60.000 0.00 0.00 0.00 2.29
7440 10219 1.298859 CGTCCCAGGAGCCTTTTTCG 61.299 60.000 0.00 0.00 0.00 3.46
7441 10220 0.250770 GTCCCAGGAGCCTTTTTCGT 60.251 55.000 0.00 0.00 0.00 3.85
7442 10221 0.036306 TCCCAGGAGCCTTTTTCGTC 59.964 55.000 0.00 0.00 0.00 4.20
7443 10222 1.298859 CCCAGGAGCCTTTTTCGTCG 61.299 60.000 0.00 0.00 0.00 5.12
7444 10223 1.298859 CCAGGAGCCTTTTTCGTCGG 61.299 60.000 0.00 0.00 0.00 4.79
7445 10224 1.671379 AGGAGCCTTTTTCGTCGGC 60.671 57.895 0.00 0.00 44.09 5.54
7448 10227 4.533566 GCCTTTTTCGTCGGCTTG 57.466 55.556 0.00 0.00 40.62 4.01
7449 10228 1.081442 GCCTTTTTCGTCGGCTTGG 60.081 57.895 0.00 0.00 40.62 3.61
7450 10229 1.579429 CCTTTTTCGTCGGCTTGGG 59.421 57.895 0.00 0.00 0.00 4.12
7451 10230 1.081442 CTTTTTCGTCGGCTTGGGC 60.081 57.895 0.00 0.00 37.82 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.393402 ACCCGGGGTAAAATCTTCGC 60.393 55.000 27.92 0.00 32.11 4.70
29 30 1.044790 CCATCATGAGGGCCCAAACC 61.045 60.000 27.56 10.65 0.00 3.27
30 31 0.033208 TCCATCATGAGGGCCCAAAC 60.033 55.000 27.56 15.59 31.15 2.93
65 66 3.710724 TCCATCAATCCAATCCAAGCAA 58.289 40.909 0.00 0.00 0.00 3.91
86 87 1.916181 CCCTCTCACATGGTACCCTTT 59.084 52.381 10.07 0.00 0.00 3.11
93 94 1.207791 GTGATCCCCTCTCACATGGT 58.792 55.000 0.00 0.00 42.08 3.55
110 111 9.330063 TGATAAAGCTTACTATTCTCCATTGTG 57.670 33.333 0.00 0.00 0.00 3.33
131 132 7.722363 TGCGTCCAATCTAATACTCTTGATAA 58.278 34.615 0.00 0.00 0.00 1.75
153 154 1.066303 CTAGCCTAGAGACACCTTGCG 59.934 57.143 0.00 0.00 0.00 4.85
252 573 6.655930 ACACTGAAACTCTTTGTAACCCTAA 58.344 36.000 0.00 0.00 0.00 2.69
369 691 3.234386 GGACTTGTGCAAATAAACGCTC 58.766 45.455 0.00 0.00 0.00 5.03
371 693 2.324860 GGGACTTGTGCAAATAAACGC 58.675 47.619 0.00 0.00 0.00 4.84
437 759 7.149015 CGTGCCTACGTATACTGTATTTGATTC 60.149 40.741 5.52 0.00 44.99 2.52
508 837 4.211584 CGGATGAAGAGAGCAGAATGAATG 59.788 45.833 0.00 0.00 39.69 2.67
770 1155 3.641437 TGGTGTTCATTTGCAGCTAAC 57.359 42.857 0.00 0.00 34.57 2.34
771 1156 4.099266 ACTTTGGTGTTCATTTGCAGCTAA 59.901 37.500 0.00 0.00 34.57 3.09
772 1157 3.636300 ACTTTGGTGTTCATTTGCAGCTA 59.364 39.130 0.00 0.00 34.57 3.32
773 1158 2.431782 ACTTTGGTGTTCATTTGCAGCT 59.568 40.909 0.00 0.00 34.57 4.24
774 1159 2.796593 GACTTTGGTGTTCATTTGCAGC 59.203 45.455 0.00 0.00 0.00 5.25
775 1160 4.044336 TGACTTTGGTGTTCATTTGCAG 57.956 40.909 0.00 0.00 0.00 4.41
776 1161 4.159321 TCTTGACTTTGGTGTTCATTTGCA 59.841 37.500 0.00 0.00 0.00 4.08
777 1162 4.681744 TCTTGACTTTGGTGTTCATTTGC 58.318 39.130 0.00 0.00 0.00 3.68
778 1163 6.038603 TCTCTCTTGACTTTGGTGTTCATTTG 59.961 38.462 0.00 0.00 0.00 2.32
779 1164 6.122277 TCTCTCTTGACTTTGGTGTTCATTT 58.878 36.000 0.00 0.00 0.00 2.32
780 1165 5.684704 TCTCTCTTGACTTTGGTGTTCATT 58.315 37.500 0.00 0.00 0.00 2.57
781 1166 5.296151 TCTCTCTTGACTTTGGTGTTCAT 57.704 39.130 0.00 0.00 0.00 2.57
782 1167 4.753516 TCTCTCTTGACTTTGGTGTTCA 57.246 40.909 0.00 0.00 0.00 3.18
783 1168 5.354234 TGTTTCTCTCTTGACTTTGGTGTTC 59.646 40.000 0.00 0.00 0.00 3.18
784 1169 5.253330 TGTTTCTCTCTTGACTTTGGTGTT 58.747 37.500 0.00 0.00 0.00 3.32
785 1170 4.843728 TGTTTCTCTCTTGACTTTGGTGT 58.156 39.130 0.00 0.00 0.00 4.16
786 1171 4.878397 ACTGTTTCTCTCTTGACTTTGGTG 59.122 41.667 0.00 0.00 0.00 4.17
787 1172 5.104259 ACTGTTTCTCTCTTGACTTTGGT 57.896 39.130 0.00 0.00 0.00 3.67
788 1173 6.018669 GTGTACTGTTTCTCTCTTGACTTTGG 60.019 42.308 0.00 0.00 0.00 3.28
789 1174 6.291849 CGTGTACTGTTTCTCTCTTGACTTTG 60.292 42.308 0.00 0.00 0.00 2.77
790 1175 5.749109 CGTGTACTGTTTCTCTCTTGACTTT 59.251 40.000 0.00 0.00 0.00 2.66
791 1176 5.067413 TCGTGTACTGTTTCTCTCTTGACTT 59.933 40.000 0.00 0.00 0.00 3.01
792 1177 4.579340 TCGTGTACTGTTTCTCTCTTGACT 59.421 41.667 0.00 0.00 0.00 3.41
793 1178 4.676018 GTCGTGTACTGTTTCTCTCTTGAC 59.324 45.833 0.00 0.00 0.00 3.18
794 1179 4.554134 CGTCGTGTACTGTTTCTCTCTTGA 60.554 45.833 0.00 0.00 0.00 3.02
795 1180 3.664486 CGTCGTGTACTGTTTCTCTCTTG 59.336 47.826 0.00 0.00 0.00 3.02
796 1181 3.562973 TCGTCGTGTACTGTTTCTCTCTT 59.437 43.478 0.00 0.00 0.00 2.85
797 1182 3.136763 TCGTCGTGTACTGTTTCTCTCT 58.863 45.455 0.00 0.00 0.00 3.10
798 1183 3.532892 TCGTCGTGTACTGTTTCTCTC 57.467 47.619 0.00 0.00 0.00 3.20
799 1184 3.976793 TTCGTCGTGTACTGTTTCTCT 57.023 42.857 0.00 0.00 0.00 3.10
800 1185 4.285292 TCTTTCGTCGTGTACTGTTTCTC 58.715 43.478 0.00 0.00 0.00 2.87
801 1186 4.297299 TCTTTCGTCGTGTACTGTTTCT 57.703 40.909 0.00 0.00 0.00 2.52
802 1187 4.663389 GCATCTTTCGTCGTGTACTGTTTC 60.663 45.833 0.00 0.00 0.00 2.78
803 1188 3.183775 GCATCTTTCGTCGTGTACTGTTT 59.816 43.478 0.00 0.00 0.00 2.83
804 1189 2.729882 GCATCTTTCGTCGTGTACTGTT 59.270 45.455 0.00 0.00 0.00 3.16
805 1190 2.030185 AGCATCTTTCGTCGTGTACTGT 60.030 45.455 0.00 0.00 0.00 3.55
806 1191 2.342651 CAGCATCTTTCGTCGTGTACTG 59.657 50.000 0.00 0.00 0.00 2.74
807 1192 2.596452 CAGCATCTTTCGTCGTGTACT 58.404 47.619 0.00 0.00 0.00 2.73
831 1216 5.574830 CAGCTGTGACAGATTAGTTGTCTAC 59.425 44.000 18.18 0.00 44.08 2.59
875 1260 3.270027 TGTGTCACTGGTCAAACTGAAG 58.730 45.455 4.27 0.00 0.00 3.02
922 1324 5.740513 GCACCCTCTTATGTAGGATTCACTC 60.741 48.000 0.00 0.00 36.08 3.51
925 1327 4.037222 TGCACCCTCTTATGTAGGATTCA 58.963 43.478 0.00 0.00 36.08 2.57
965 1368 4.245660 GGCAAGGTTTTAGATTCTTTGGC 58.754 43.478 4.85 4.85 36.83 4.52
988 1391 1.364626 CTCTCCATTCCGTGCTGCAC 61.365 60.000 22.38 22.38 0.00 4.57
989 1392 1.078918 CTCTCCATTCCGTGCTGCA 60.079 57.895 0.00 0.00 0.00 4.41
990 1393 0.391661 TTCTCTCCATTCCGTGCTGC 60.392 55.000 0.00 0.00 0.00 5.25
992 1395 0.976641 TGTTCTCTCCATTCCGTGCT 59.023 50.000 0.00 0.00 0.00 4.40
993 1396 1.079503 GTGTTCTCTCCATTCCGTGC 58.920 55.000 0.00 0.00 0.00 5.34
1074 1477 2.193536 GTCTGCTTTGCCGGTGGTT 61.194 57.895 1.90 0.00 0.00 3.67
1075 1478 2.594592 GTCTGCTTTGCCGGTGGT 60.595 61.111 1.90 0.00 0.00 4.16
1076 1479 3.726517 CGTCTGCTTTGCCGGTGG 61.727 66.667 1.90 0.00 0.00 4.61
1104 1510 0.965439 CCAGATCGAGGATCACTCCC 59.035 60.000 8.21 0.00 43.21 4.30
1117 1523 2.202987 CACCAGCGAGCCCAGATC 60.203 66.667 0.00 0.00 0.00 2.75
1144 1550 2.228582 CCAATGAAATGCTGGTTCGTGA 59.771 45.455 0.00 0.00 0.00 4.35
1162 1568 1.068055 GTAGAAGTCTTCGACGGCCAA 60.068 52.381 9.69 0.00 37.67 4.52
1171 1577 0.524862 TGGACCGCGTAGAAGTCTTC 59.475 55.000 4.92 4.26 32.71 2.87
1215 1621 3.117398 CCATGGAATCCCTGAAATGGAGA 60.117 47.826 5.56 0.00 35.40 3.71
1501 3227 1.889545 AGACTCTGCTTGGCTTCAAC 58.110 50.000 0.00 0.00 0.00 3.18
1503 3229 5.420725 TTTATAGACTCTGCTTGGCTTCA 57.579 39.130 0.00 0.00 0.00 3.02
1551 3279 7.437793 AGGTTATGGTTTGCAATTGAAAATG 57.562 32.000 14.72 0.00 0.00 2.32
1555 3283 6.656632 TGTAGGTTATGGTTTGCAATTGAA 57.343 33.333 10.34 0.00 0.00 2.69
1582 3310 0.100503 CTTTTATCCTTTGGCGGCCG 59.899 55.000 24.05 24.05 0.00 6.13
1584 3312 0.530288 TGCTTTTATCCTTTGGCGGC 59.470 50.000 0.00 0.00 0.00 6.53
1586 3314 2.749621 AGACTGCTTTTATCCTTTGGCG 59.250 45.455 0.00 0.00 0.00 5.69
1587 3315 4.790765 AAGACTGCTTTTATCCTTTGGC 57.209 40.909 0.00 0.00 0.00 4.52
1588 3316 7.454260 AACTAAGACTGCTTTTATCCTTTGG 57.546 36.000 0.00 0.00 35.56 3.28
1625 3443 4.398988 TGACACCTATTTGCATAAGCCTTG 59.601 41.667 0.00 0.00 41.13 3.61
1634 3452 6.433716 TCTTGATCATTTGACACCTATTTGCA 59.566 34.615 0.00 0.00 0.00 4.08
1640 3458 9.958180 TCTATTTTCTTGATCATTTGACACCTA 57.042 29.630 0.00 0.00 0.00 3.08
1719 3539 9.506018 ACATCATAGCACATAACAAAGCATATA 57.494 29.630 0.00 0.00 0.00 0.86
1720 3540 8.400184 ACATCATAGCACATAACAAAGCATAT 57.600 30.769 0.00 0.00 0.00 1.78
1729 3549 8.664798 TGTAGAAACAACATCATAGCACATAAC 58.335 33.333 0.00 0.00 30.91 1.89
1753 3573 9.131791 GGTCAGATGGTATTGGTTTAATAATGT 57.868 33.333 0.00 0.00 33.22 2.71
1755 3575 8.215050 TCGGTCAGATGGTATTGGTTTAATAAT 58.785 33.333 0.00 0.00 33.22 1.28
1756 3576 7.566569 TCGGTCAGATGGTATTGGTTTAATAA 58.433 34.615 0.00 0.00 33.22 1.40
1765 3585 5.590259 AGGAAATTTCGGTCAGATGGTATTG 59.410 40.000 11.95 0.00 0.00 1.90
1767 3587 5.373812 AGGAAATTTCGGTCAGATGGTAT 57.626 39.130 11.95 0.00 0.00 2.73
1822 3642 4.558178 TGATGGCTTGCAGTTTGTAATTG 58.442 39.130 0.00 0.00 0.00 2.32
1894 3714 3.154827 ACTGTGGGGACTTTGGTTATG 57.845 47.619 0.00 0.00 0.00 1.90
2604 4424 2.890945 GGGGAAATAACCATGGATTCCG 59.109 50.000 21.47 0.00 40.34 4.30
2794 4620 1.665735 CCGTTTTGATTCAACTGCCGG 60.666 52.381 0.00 0.00 0.00 6.13
2812 4638 2.487762 TGATCCTGCTGTTTTTAAGCCG 59.512 45.455 0.00 0.00 40.06 5.52
2842 4668 7.068716 GGCCAAATTACAGGATTTAGATCAAGT 59.931 37.037 0.00 0.00 33.77 3.16
2968 4794 7.667219 ACATTTGTAACAGGATCTCTGAATGTT 59.333 33.333 15.51 9.14 46.18 2.71
3055 4881 4.360563 CCAGGTACTCATAAGTAAGTGCG 58.639 47.826 0.00 0.00 39.66 5.34
3753 5624 6.206395 TGTACATGTTGATTGCCATTTAGG 57.794 37.500 2.30 0.00 41.84 2.69
4370 6696 4.326504 AACAAACTTGAAAGCTGGGATG 57.673 40.909 0.00 0.00 0.00 3.51
4732 7061 3.737559 AGGGGATTTCATGTACAAGCA 57.262 42.857 0.00 0.00 0.00 3.91
4857 7187 8.909671 GTCATTCAAGAGATTAAAACAAAGCAG 58.090 33.333 0.00 0.00 0.00 4.24
4881 7211 3.737774 GCAAACTTCAAGGCAGAATTGTC 59.262 43.478 0.00 0.00 0.00 3.18
4883 7213 3.986277 AGCAAACTTCAAGGCAGAATTG 58.014 40.909 0.00 0.00 0.00 2.32
4886 7216 3.550820 TGTAGCAAACTTCAAGGCAGAA 58.449 40.909 0.00 0.00 0.00 3.02
4926 7257 5.495926 AGAATTGAAGGAGACACATGAGT 57.504 39.130 0.00 0.00 0.00 3.41
5035 7391 8.607459 CAGTCAACTGGAAGATACATTATTCAC 58.393 37.037 2.08 0.00 40.20 3.18
5164 7558 3.515602 AGCTTACATTGATGATCCCCC 57.484 47.619 0.00 0.00 0.00 5.40
6167 8910 2.346803 TCAAAAGTGATAGCGCCTGAC 58.653 47.619 2.29 0.00 0.00 3.51
6345 9095 4.645535 TCTCCTTGTTCTTCCTGTGAATG 58.354 43.478 0.00 0.00 0.00 2.67
6479 9234 3.067106 GTGTGAATCCACGGCCTATATG 58.933 50.000 0.00 0.00 46.06 1.78
6488 9243 4.285807 TGTTCTTTTGTGTGAATCCACG 57.714 40.909 0.00 0.00 46.06 4.94
6505 9260 1.082756 CAGCGACGTTGCCTTGTTC 60.083 57.895 24.15 0.00 34.65 3.18
6520 9275 1.639298 GCGGACCAATGTGAGTCAGC 61.639 60.000 0.00 0.00 44.65 4.26
6538 9293 1.293179 GCCCCTGTGAATGGTTTGC 59.707 57.895 0.00 0.00 0.00 3.68
6556 9311 8.380644 CCACTCAATTACATACTACTTTTGTCG 58.619 37.037 0.00 0.00 0.00 4.35
6568 9323 8.023021 ACTAGCTTGATCCACTCAATTACATA 57.977 34.615 1.04 0.00 42.87 2.29
6573 9328 5.189180 GGAACTAGCTTGATCCACTCAATT 58.811 41.667 17.42 0.00 42.87 2.32
6577 9332 3.895232 TGGAACTAGCTTGATCCACTC 57.105 47.619 20.31 0.00 37.05 3.51
6656 9411 1.468520 CACATACCCAAAGTTCTGCCG 59.531 52.381 0.00 0.00 0.00 5.69
6660 9415 2.644798 AGCTCCACATACCCAAAGTTCT 59.355 45.455 0.00 0.00 0.00 3.01
6672 9427 2.224719 GCATCCATAGGAAGCTCCACAT 60.225 50.000 6.05 0.00 42.34 3.21
6697 9452 6.756542 GCTGAAACTTTACTTGATTTTGGTGT 59.243 34.615 0.00 0.00 0.00 4.16
6698 9453 6.200854 GGCTGAAACTTTACTTGATTTTGGTG 59.799 38.462 0.00 0.00 0.00 4.17
6699 9454 6.098266 AGGCTGAAACTTTACTTGATTTTGGT 59.902 34.615 0.00 0.00 0.00 3.67
6700 9455 6.421801 CAGGCTGAAACTTTACTTGATTTTGG 59.578 38.462 9.42 0.00 0.00 3.28
6701 9456 6.980397 ACAGGCTGAAACTTTACTTGATTTTG 59.020 34.615 23.66 0.00 0.00 2.44
6702 9457 7.068716 AGACAGGCTGAAACTTTACTTGATTTT 59.931 33.333 23.66 0.00 0.00 1.82
6703 9458 6.547510 AGACAGGCTGAAACTTTACTTGATTT 59.452 34.615 23.66 0.00 0.00 2.17
6704 9459 6.064717 AGACAGGCTGAAACTTTACTTGATT 58.935 36.000 23.66 0.00 0.00 2.57
6722 9477 5.041191 AGGGTGAAGCATAATAAGACAGG 57.959 43.478 0.00 0.00 0.00 4.00
6767 9522 9.383519 CTGGAAAAGTACAACAGTACATGATAT 57.616 33.333 0.00 0.00 40.41 1.63
6774 9529 6.930667 TTTCCTGGAAAAGTACAACAGTAC 57.069 37.500 19.14 0.00 38.69 2.73
6779 9534 7.438160 CCTTGATTTTTCCTGGAAAAGTACAAC 59.562 37.037 27.89 16.73 41.55 3.32
6780 9535 7.496747 CCTTGATTTTTCCTGGAAAAGTACAA 58.503 34.615 27.89 27.64 41.55 2.41
6785 9540 5.219343 AGCCTTGATTTTTCCTGGAAAAG 57.781 39.130 27.89 18.76 41.55 2.27
6847 9605 6.523201 CGTGTGAAAACCTGAATGTATAAAGC 59.477 38.462 0.00 0.00 0.00 3.51
6905 9663 1.136502 CAGCTCGCGAAAAGAAGTGAC 60.137 52.381 11.33 0.00 0.00 3.67
6984 9742 5.712152 AGTTTGATGTGGGTTGAGATTTC 57.288 39.130 0.00 0.00 0.00 2.17
6989 9747 4.389374 ACACTAGTTTGATGTGGGTTGAG 58.611 43.478 0.00 0.00 36.16 3.02
6990 9748 4.431416 ACACTAGTTTGATGTGGGTTGA 57.569 40.909 0.00 0.00 36.16 3.18
6995 9753 3.120546 CGCAGAACACTAGTTTGATGTGG 60.121 47.826 0.00 0.00 38.30 4.17
7017 9775 4.030195 GCGAATGTGCTACCGAAAAATTTC 59.970 41.667 0.00 0.00 0.00 2.17
7023 9781 0.388778 TCGCGAATGTGCTACCGAAA 60.389 50.000 6.20 0.00 0.00 3.46
7024 9782 0.388778 TTCGCGAATGTGCTACCGAA 60.389 50.000 19.38 0.00 33.05 4.30
7025 9783 1.074319 GTTCGCGAATGTGCTACCGA 61.074 55.000 26.23 0.00 0.00 4.69
7051 9809 4.056092 AGATCGAAATTCGGTTCCTACC 57.944 45.455 15.76 0.00 40.88 3.18
7057 9815 5.116882 CCTCCTTAAGATCGAAATTCGGTT 58.883 41.667 15.76 9.22 40.88 4.44
7058 9816 4.443034 CCCTCCTTAAGATCGAAATTCGGT 60.443 45.833 15.76 8.47 40.88 4.69
7059 9817 4.058817 CCCTCCTTAAGATCGAAATTCGG 58.941 47.826 15.76 0.00 40.88 4.30
7351 10130 3.859414 GGCTCGGCTGGAGATGCT 61.859 66.667 9.12 0.00 46.23 3.79
7352 10131 4.925861 GGGCTCGGCTGGAGATGC 62.926 72.222 9.12 0.00 46.23 3.91
7353 10132 4.247380 GGGGCTCGGCTGGAGATG 62.247 72.222 9.12 0.00 46.23 2.90
7354 10133 4.804420 TGGGGCTCGGCTGGAGAT 62.804 66.667 9.12 0.00 46.23 2.75
7370 10149 3.622060 AAATCGAGTGGGGGCCGTG 62.622 63.158 0.00 0.00 0.00 4.94
7371 10150 2.420466 AAAAATCGAGTGGGGGCCGT 62.420 55.000 0.00 0.00 0.00 5.68
7372 10151 1.677633 AAAAATCGAGTGGGGGCCG 60.678 57.895 0.00 0.00 0.00 6.13
7373 10152 4.434483 AAAAATCGAGTGGGGGCC 57.566 55.556 0.00 0.00 0.00 5.80
7406 10185 2.888998 GACGCGACTGGCCGTTTTT 61.889 57.895 15.93 0.00 38.94 1.94
7407 10186 3.343421 GACGCGACTGGCCGTTTT 61.343 61.111 15.93 0.00 38.94 2.43
7414 10193 4.135153 CTCCTGGGACGCGACTGG 62.135 72.222 15.93 15.71 0.00 4.00
7415 10194 4.803426 GCTCCTGGGACGCGACTG 62.803 72.222 15.93 6.62 0.00 3.51
7419 10198 3.901797 AAAAGGCTCCTGGGACGCG 62.902 63.158 3.53 3.53 0.00 6.01
7420 10199 1.587043 GAAAAAGGCTCCTGGGACGC 61.587 60.000 0.00 0.00 0.00 5.19
7421 10200 1.298859 CGAAAAAGGCTCCTGGGACG 61.299 60.000 0.00 0.00 0.00 4.79
7422 10201 0.250770 ACGAAAAAGGCTCCTGGGAC 60.251 55.000 0.00 0.00 0.00 4.46
7423 10202 0.036306 GACGAAAAAGGCTCCTGGGA 59.964 55.000 0.00 0.00 0.00 4.37
7424 10203 1.298859 CGACGAAAAAGGCTCCTGGG 61.299 60.000 0.00 0.00 0.00 4.45
7425 10204 1.298859 CCGACGAAAAAGGCTCCTGG 61.299 60.000 0.00 0.00 0.00 4.45
7426 10205 1.912371 GCCGACGAAAAAGGCTCCTG 61.912 60.000 0.00 0.00 46.83 3.86
7427 10206 1.671379 GCCGACGAAAAAGGCTCCT 60.671 57.895 0.00 0.00 46.83 3.69
7428 10207 2.868196 GCCGACGAAAAAGGCTCC 59.132 61.111 0.00 0.00 46.83 4.70
7432 10211 1.579429 CCCAAGCCGACGAAAAAGG 59.421 57.895 0.00 0.00 0.00 3.11
7433 10212 1.081442 GCCCAAGCCGACGAAAAAG 60.081 57.895 0.00 0.00 0.00 2.27
7434 10213 3.035727 GCCCAAGCCGACGAAAAA 58.964 55.556 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.