Multiple sequence alignment - TraesCS5D01G091900

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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 TraesCS5D01G091900 chr5D 100.000 7555 0 0 1 7555 99915155 99922709 0.000000e+00 13952.0
1 TraesCS5D01G091900 chr5D 95.864 5367 166 21 733 6062 109807753 109813100 0.000000e+00 8630.0
2 TraesCS5D01G091900 chr5D 91.791 1072 44 20 6104 7159 109813094 109814137 0.000000e+00 1452.0
3 TraesCS5D01G091900 chr5D 89.730 779 42 16 6393 7162 112947746 112948495 0.000000e+00 961.0
4 TraesCS5D01G091900 chr5D 93.291 313 18 3 7240 7550 495363213 495363524 6.910000e-125 459.0
5 TraesCS5D01G091900 chr6B 96.429 6805 167 24 467 7239 184002951 184009711 0.000000e+00 11151.0
6 TraesCS5D01G091900 chr6B 90.021 481 36 6 1 469 184002382 184002862 5.010000e-171 612.0
7 TraesCS5D01G091900 chr6B 78.161 435 60 26 163 564 183996962 183997394 2.110000e-60 244.0
8 TraesCS5D01G091900 chr5A 97.548 4731 94 11 663 5377 102842118 102837394 0.000000e+00 8074.0
9 TraesCS5D01G091900 chr5A 96.508 2749 79 13 3272 6012 117507687 117504948 0.000000e+00 4529.0
10 TraesCS5D01G091900 chr5A 95.298 2467 103 9 718 3176 118345585 118348046 0.000000e+00 3901.0
11 TraesCS5D01G091900 chr5A 95.670 2448 55 13 4367 6779 118349080 118351511 0.000000e+00 3886.0
12 TraesCS5D01G091900 chr5A 95.320 2201 90 9 718 2910 117510315 117508120 0.000000e+00 3482.0
13 TraesCS5D01G091900 chr5A 89.754 2479 198 38 673 3142 298531915 298534346 0.000000e+00 3120.0
14 TraesCS5D01G091900 chr5A 95.003 1881 30 14 5376 7239 102837232 102835399 0.000000e+00 2894.0
15 TraesCS5D01G091900 chr5A 96.582 1024 30 5 3272 4294 118348047 118349066 0.000000e+00 1692.0
16 TraesCS5D01G091900 chr5A 92.041 1068 45 17 6110 7160 117504914 117503870 0.000000e+00 1465.0
17 TraesCS5D01G091900 chr5A 84.300 707 68 20 6459 7142 185645408 185646094 0.000000e+00 651.0
18 TraesCS5D01G091900 chr5A 90.249 482 35 6 3277 3750 298534359 298534836 2.990000e-173 619.0
19 TraesCS5D01G091900 chr5A 93.812 404 19 3 6098 6500 530380577 530380975 3.020000e-168 603.0
20 TraesCS5D01G091900 chr5A 83.383 668 66 24 2 647 102364740 102364096 1.830000e-160 577.0
21 TraesCS5D01G091900 chr5A 85.596 361 39 10 3767 4125 298535000 298535349 4.310000e-97 366.0
22 TraesCS5D01G091900 chr5A 96.875 32 1 0 4335 4366 652708902 652708933 4.000000e-03 54.7
23 TraesCS5D01G091900 chr5B 95.654 2646 89 20 3442 6074 122849849 122847217 0.000000e+00 4226.0
24 TraesCS5D01G091900 chr5B 95.921 2427 79 16 3645 6062 123688465 123690880 0.000000e+00 3916.0
25 TraesCS5D01G091900 chr5B 96.190 2257 84 2 923 3179 122852376 122850122 0.000000e+00 3690.0
26 TraesCS5D01G091900 chr5B 96.060 2259 82 3 923 3176 123685867 123688123 0.000000e+00 3672.0
27 TraesCS5D01G091900 chr5B 89.278 2453 196 36 711 3142 248756870 248759276 0.000000e+00 3011.0
28 TraesCS5D01G091900 chr5B 90.979 1164 59 23 6110 7236 122847229 122846075 0.000000e+00 1526.0
29 TraesCS5D01G091900 chr5B 90.926 1069 45 24 6104 7162 123690874 123691900 0.000000e+00 1389.0
30 TraesCS5D01G091900 chr5B 97.033 337 9 1 3272 3608 123688127 123688462 3.960000e-157 566.0
31 TraesCS5D01G091900 chr5B 86.885 488 39 12 3277 3750 248759289 248759765 2.420000e-144 523.0
32 TraesCS5D01G091900 chr5B 85.399 363 37 12 3767 4125 248759953 248760303 5.570000e-96 363.0
33 TraesCS5D01G091900 chr5B 80.519 462 42 23 460 909 122853012 122852587 2.050000e-80 311.0
34 TraesCS5D01G091900 chr5B 95.349 172 7 1 3272 3443 122850124 122849954 9.660000e-69 272.0
35 TraesCS5D01G091900 chr5B 79.321 324 27 19 460 778 123685358 123685646 2.780000e-44 191.0
36 TraesCS5D01G091900 chr5B 91.429 105 8 1 3167 3270 693583792 693583896 7.900000e-30 143.0
37 TraesCS5D01G091900 chr5B 96.154 52 1 1 718 768 122853823 122853772 4.860000e-12 84.2
38 TraesCS5D01G091900 chr7D 98.426 953 13 2 5007 5958 561633683 561632732 0.000000e+00 1676.0
39 TraesCS5D01G091900 chr7D 96.078 408 10 3 6094 6500 561632700 561632298 0.000000e+00 660.0
40 TraesCS5D01G091900 chr7D 93.125 320 17 4 7238 7554 62166769 62166452 1.480000e-126 464.0
41 TraesCS5D01G091900 chr1A 96.960 954 26 3 5007 5958 75199403 75200355 0.000000e+00 1598.0
42 TraesCS5D01G091900 chr1A 87.755 98 3 7 4309 4397 571581075 571581172 1.040000e-18 106.0
43 TraesCS5D01G091900 chr7B 96.957 953 25 3 5007 5958 641949496 641950445 0.000000e+00 1596.0
44 TraesCS5D01G091900 chr7A 94.175 412 18 3 6090 6500 210624377 210624783 2.310000e-174 623.0
45 TraesCS5D01G091900 chr7A 89.308 318 31 3 7238 7553 674505340 674505024 5.490000e-106 396.0
46 TraesCS5D01G091900 chr7A 83.750 80 6 5 4319 4397 612375619 612375692 1.360000e-07 69.4
47 TraesCS5D01G091900 chr3A 93.396 318 18 3 7238 7554 12633124 12633439 1.150000e-127 468.0
48 TraesCS5D01G091900 chr3A 82.500 80 7 6 4319 4397 712187269 712187196 6.330000e-06 63.9
49 TraesCS5D01G091900 chr3A 100.000 28 0 0 4340 4367 127963865 127963838 1.400000e-02 52.8
50 TraesCS5D01G091900 chr2A 93.269 312 18 3 7245 7554 690533517 690533207 2.480000e-124 457.0
51 TraesCS5D01G091900 chr2A 91.250 320 22 4 7238 7554 778637940 778638256 1.510000e-116 431.0
52 TraesCS5D01G091900 chr4A 92.114 317 20 3 7238 7553 21043138 21042826 6.960000e-120 442.0
53 TraesCS5D01G091900 chr4D 91.223 319 20 4 7238 7555 151987880 151987569 1.950000e-115 427.0
54 TraesCS5D01G091900 chr1D 89.538 325 25 5 7238 7554 89233048 89232725 3.280000e-108 403.0
55 TraesCS5D01G091900 chr1D 91.509 106 8 1 3173 3278 354519020 354518916 2.200000e-30 145.0
56 TraesCS5D01G091900 chr1D 90.476 84 3 2 4314 4397 12229784 12229706 1.040000e-18 106.0
57 TraesCS5D01G091900 chr4B 91.589 107 7 2 3178 3283 21198745 21198640 6.110000e-31 147.0
58 TraesCS5D01G091900 chr6D 92.233 103 6 2 3178 3280 419276463 419276563 2.200000e-30 145.0
59 TraesCS5D01G091900 chr6D 84.706 85 11 2 4314 4397 245495187 245495104 4.860000e-12 84.2
60 TraesCS5D01G091900 chr3D 92.157 102 8 0 3178 3279 197994392 197994493 2.200000e-30 145.0
61 TraesCS5D01G091900 chrUn 87.500 120 11 4 3170 3286 362465905 362465787 1.320000e-27 135.0


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 TraesCS5D01G091900 chr5D 99915155 99922709 7554 False 13952.000000 13952 100.000000 1 7555 1 chr5D.!!$F1 7554
1 TraesCS5D01G091900 chr5D 109807753 109814137 6384 False 5041.000000 8630 93.827500 733 7159 2 chr5D.!!$F4 6426
2 TraesCS5D01G091900 chr5D 112947746 112948495 749 False 961.000000 961 89.730000 6393 7162 1 chr5D.!!$F2 769
3 TraesCS5D01G091900 chr6B 184002382 184009711 7329 False 5881.500000 11151 93.225000 1 7239 2 chr6B.!!$F2 7238
4 TraesCS5D01G091900 chr5A 102835399 102842118 6719 True 5484.000000 8074 96.275500 663 7239 2 chr5A.!!$R2 6576
5 TraesCS5D01G091900 chr5A 118345585 118351511 5926 False 3159.666667 3901 95.850000 718 6779 3 chr5A.!!$F4 6061
6 TraesCS5D01G091900 chr5A 117503870 117510315 6445 True 3158.666667 4529 94.623000 718 7160 3 chr5A.!!$R3 6442
7 TraesCS5D01G091900 chr5A 298531915 298535349 3434 False 1368.333333 3120 88.533000 673 4125 3 chr5A.!!$F5 3452
8 TraesCS5D01G091900 chr5A 185645408 185646094 686 False 651.000000 651 84.300000 6459 7142 1 chr5A.!!$F1 683
9 TraesCS5D01G091900 chr5A 102364096 102364740 644 True 577.000000 577 83.383000 2 647 1 chr5A.!!$R1 645
10 TraesCS5D01G091900 chr5B 123685358 123691900 6542 False 1946.800000 3916 91.852200 460 7162 5 chr5B.!!$F2 6702
11 TraesCS5D01G091900 chr5B 122846075 122853823 7748 True 1684.866667 4226 92.474167 460 7236 6 chr5B.!!$R1 6776
12 TraesCS5D01G091900 chr5B 248756870 248760303 3433 False 1299.000000 3011 87.187333 711 4125 3 chr5B.!!$F3 3414
13 TraesCS5D01G091900 chr7D 561632298 561633683 1385 True 1168.000000 1676 97.252000 5007 6500 2 chr7D.!!$R2 1493
14 TraesCS5D01G091900 chr1A 75199403 75200355 952 False 1598.000000 1598 96.960000 5007 5958 1 chr1A.!!$F1 951
15 TraesCS5D01G091900 chr7B 641949496 641950445 949 False 1596.000000 1596 96.957000 5007 5958 1 chr7B.!!$F1 951

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
163 164 0.171903 CAAGGCGCCAATTGAGGAAG 59.828 55.000 31.54 0.0 0.0 3.46 F
802 1270 0.249280 GCCTCACCAAACCCAAAACG 60.249 55.000 0.00 0.0 0.0 3.60 F
1793 2620 0.669625 GCGGCAGTAAACTTCGACCT 60.670 55.000 0.00 0.0 0.0 3.85 F
2376 3208 1.071471 CCGCCAGTCTGACACCTTT 59.929 57.895 10.88 0.0 0.0 3.11 F
2521 3353 1.202330 CATCAGGGAGAAGCTGAGGT 58.798 55.000 0.00 0.0 0.0 3.85 F
3104 4109 2.185004 TTGCCCTAGTCTGCTTGTTC 57.815 50.000 0.00 0.0 0.0 3.18 F
4962 6436 2.105477 TCAAGTCCTTTGCAGAGCTTCT 59.895 45.455 0.00 0.0 36.7 2.85 F
5256 6730 2.368875 TCCCCTTGACACTGAGTTCTTC 59.631 50.000 0.00 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 2620 0.674581 CAAGGCAACCATGAGCGAGA 60.675 55.000 0.00 0.00 37.17 4.04 R
2376 3208 1.777878 TCCTGCACCCTTGGTAAAAGA 59.222 47.619 0.00 0.00 32.11 2.52 R
3104 4109 3.645212 TCCTCTGAATCAAGGAGGCATAG 59.355 47.826 12.26 0.00 44.39 2.23 R
3349 4475 3.847671 AGTGGCCTATAGGAAAAGAGC 57.152 47.619 23.61 4.67 37.39 4.09 R
3374 4500 4.991056 GGAAATTTTCCTTTGGAACTGAGC 59.009 41.667 19.01 0.00 46.57 4.26 R
5002 6476 1.142667 TGCAGACTTCCACAATGGTCA 59.857 47.619 0.00 0.00 39.03 4.02 R
6300 8000 0.732880 GCGAGCAAAGCAGACGTAGA 60.733 55.000 0.00 0.00 34.19 2.59 R
7255 9044 0.101219 GGAAAGCCCAATTAGCGCAG 59.899 55.000 11.47 0.00 34.64 5.18 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
39 40 1.407258 GGTGCTCAAGTCTCGCTATCT 59.593 52.381 0.00 0.00 0.00 1.98
83 84 0.250234 TGGTTCTCAATGAGAGGGCG 59.750 55.000 13.11 0.00 44.81 6.13
91 92 2.766263 TCAATGAGAGGGCGATGTTAGT 59.234 45.455 0.00 0.00 0.00 2.24
96 97 3.958147 TGAGAGGGCGATGTTAGTATTGA 59.042 43.478 0.00 0.00 0.00 2.57
144 145 4.317804 CGGAAGGCGTAAACTAAAAGAC 57.682 45.455 0.00 0.00 0.00 3.01
163 164 0.171903 CAAGGCGCCAATTGAGGAAG 59.828 55.000 31.54 0.00 0.00 3.46
183 184 3.555966 AGGCGGGAAAATCAAATAGAGG 58.444 45.455 0.00 0.00 0.00 3.69
200 201 1.152756 GGTGTGGGCTTCAAGTGGT 60.153 57.895 0.00 0.00 0.00 4.16
231 232 3.873952 GTGTTAGGCCATGAGCTAGAAAG 59.126 47.826 5.01 0.00 43.05 2.62
244 245 5.012664 TGAGCTAGAAAGTGGGTTATGTTGA 59.987 40.000 0.00 0.00 0.00 3.18
259 260 1.071605 GTTGATGTGAGTCGAGGCAC 58.928 55.000 9.92 9.92 35.63 5.01
281 282 5.405571 CACACACCGTTATAAGCCAGATATC 59.594 44.000 0.00 0.00 0.00 1.63
372 385 2.344592 TCTAGCTTTCAACCTCCCCAA 58.655 47.619 0.00 0.00 0.00 4.12
385 398 3.339742 ACCTCCCCAACCCTAATTTGAAT 59.660 43.478 0.00 0.00 0.00 2.57
386 399 4.202890 ACCTCCCCAACCCTAATTTGAATT 60.203 41.667 0.00 0.00 0.00 2.17
387 400 4.782691 CCTCCCCAACCCTAATTTGAATTT 59.217 41.667 0.00 0.00 0.00 1.82
394 407 6.147000 CCAACCCTAATTTGAATTTTTCACCG 59.853 38.462 0.00 0.00 39.87 4.94
406 419 6.258947 TGAATTTTTCACCGAAAATTTGTCCC 59.741 34.615 11.81 2.37 44.74 4.46
415 428 4.869861 CCGAAAATTTGTCCCAAATCCATC 59.130 41.667 2.92 2.40 0.00 3.51
437 450 3.499737 CGGCGGCAAGGATGTGAC 61.500 66.667 10.53 0.00 0.00 3.67
491 937 4.154195 TCTCGCTTAGGAATGAAAGCAAAC 59.846 41.667 7.71 0.00 38.11 2.93
548 997 2.295070 ACCCAAAACATGCTACCGTTTC 59.705 45.455 0.00 0.00 34.32 2.78
636 1087 1.068741 GGAGTACCGAACTGGCCATAG 59.931 57.143 5.51 0.00 43.94 2.23
657 1108 2.604079 TACGGCTTCGTTCCCCCA 60.604 61.111 0.00 0.00 45.87 4.96
676 1135 2.126071 GAGCCACGAGTAGCGCAA 60.126 61.111 11.47 0.00 46.04 4.85
706 1165 3.433740 GGTCTGGTCTTCCAAGTCAAGTT 60.434 47.826 0.00 0.00 43.81 2.66
759 1220 4.625742 CCACGCTGAATATAAATACCTCCG 59.374 45.833 0.00 0.00 0.00 4.63
802 1270 0.249280 GCCTCACCAAACCCAAAACG 60.249 55.000 0.00 0.00 0.00 3.60
1781 2608 2.356313 CGTGTCTCAAGCGGCAGT 60.356 61.111 1.45 0.00 0.00 4.40
1793 2620 0.669625 GCGGCAGTAAACTTCGACCT 60.670 55.000 0.00 0.00 0.00 3.85
2304 3136 5.771469 CTGCAGTCACTTATAGATCCAGAG 58.229 45.833 5.25 0.00 0.00 3.35
2376 3208 1.071471 CCGCCAGTCTGACACCTTT 59.929 57.895 10.88 0.00 0.00 3.11
2521 3353 1.202330 CATCAGGGAGAAGCTGAGGT 58.798 55.000 0.00 0.00 0.00 3.85
2623 3455 4.446994 TCACTGTTCTGCTGATAGTGAG 57.553 45.455 24.47 10.80 39.56 3.51
3104 4109 2.185004 TTGCCCTAGTCTGCTTGTTC 57.815 50.000 0.00 0.00 0.00 3.18
3374 4500 2.325583 TTCCTATAGGCCACTTTGCG 57.674 50.000 14.50 0.00 34.44 4.85
3737 4975 4.102210 TCATTGGGCAATCTGAAAAACCAA 59.898 37.500 8.86 8.86 40.37 3.67
4190 5602 9.959721 AAAACATAGATGTGGTATCTTACACTT 57.040 29.630 0.00 0.00 41.61 3.16
4479 5930 9.659830 GTGTGTAAAGTATTGACCTAAAAACAG 57.340 33.333 0.00 0.00 0.00 3.16
4551 6002 5.331906 TGAATTCCTGGTGAATCAATTCCA 58.668 37.500 2.27 0.00 42.97 3.53
4585 6036 5.841957 AACTTTTGCTTCTGAGATTGTGT 57.158 34.783 0.00 0.00 0.00 3.72
4603 6054 5.437289 TGTGTCCACAATTCTCATTGAAC 57.563 39.130 0.00 0.00 42.35 3.18
4962 6436 2.105477 TCAAGTCCTTTGCAGAGCTTCT 59.895 45.455 0.00 0.00 36.70 2.85
5256 6730 2.368875 TCCCCTTGACACTGAGTTCTTC 59.631 50.000 0.00 0.00 0.00 2.87
5449 7089 2.925724 TGGTTGACGTTCATGACCTTT 58.074 42.857 0.00 0.00 30.51 3.11
5539 7179 6.692486 TCTAAGACTGAAGCAAGGTTCTTAG 58.308 40.000 12.54 13.96 37.69 2.18
5605 7246 5.067805 CCTGGTTCAAATTGCCTAGGTTATC 59.932 44.000 11.31 0.00 0.00 1.75
5855 7500 6.013689 GTCGCTGAGTTCTTTTTATAAACGG 58.986 40.000 0.00 0.00 0.00 4.44
6192 7891 5.076873 TCTGGTTACTTAATTTGCCTGCTT 58.923 37.500 0.00 0.00 0.00 3.91
6193 7892 5.538433 TCTGGTTACTTAATTTGCCTGCTTT 59.462 36.000 0.00 0.00 0.00 3.51
6300 8000 3.007074 CAGATCTGCTATGCTGATGACCT 59.993 47.826 10.38 5.37 44.82 3.85
6407 8107 2.614057 GTTGATCAAGGCCCTGTATTCG 59.386 50.000 8.80 0.00 0.00 3.34
6424 8124 6.607689 TGTATTCGTTCTTGTAGCCATTTTG 58.392 36.000 0.00 0.00 0.00 2.44
6898 8634 3.137728 TGATGCATCACCATCAGGAATCT 59.862 43.478 25.42 0.00 44.79 2.40
6928 8664 7.220741 AGGCTGTTTTTATTTCCTTTCTCTC 57.779 36.000 0.00 0.00 0.00 3.20
6929 8665 6.072452 AGGCTGTTTTTATTTCCTTTCTCTCG 60.072 38.462 0.00 0.00 0.00 4.04
6930 8666 6.072673 GGCTGTTTTTATTTCCTTTCTCTCGA 60.073 38.462 0.00 0.00 0.00 4.04
6931 8667 7.018235 GCTGTTTTTATTTCCTTTCTCTCGAG 58.982 38.462 5.93 5.93 0.00 4.04
6940 8676 4.632153 TCCTTTCTCTCGAGTTTCCTTTG 58.368 43.478 13.13 0.00 0.00 2.77
6941 8677 4.101119 TCCTTTCTCTCGAGTTTCCTTTGT 59.899 41.667 13.13 0.00 0.00 2.83
7078 8841 8.431593 CGTGTTTGAGAAGAAAAATTGTTTCAA 58.568 29.630 2.26 3.55 0.00 2.69
7255 9044 9.956720 ATCAATAAAAATACTTATCAGTGCAGC 57.043 29.630 0.00 0.00 34.06 5.25
7256 9045 9.177608 TCAATAAAAATACTTATCAGTGCAGCT 57.822 29.630 0.00 0.00 34.06 4.24
7257 9046 9.229784 CAATAAAAATACTTATCAGTGCAGCTG 57.770 33.333 10.11 10.11 46.34 4.24
7258 9047 4.889832 AAATACTTATCAGTGCAGCTGC 57.110 40.909 31.89 31.89 44.66 5.25
7259 9048 1.926561 TACTTATCAGTGCAGCTGCG 58.073 50.000 32.11 19.09 44.66 5.18
7267 9056 3.189921 TGCAGCTGCGCTAATTGG 58.810 55.556 32.11 0.00 45.83 3.16
7268 9057 2.409055 TGCAGCTGCGCTAATTGGG 61.409 57.895 32.11 0.00 45.83 4.12
7285 9074 2.721231 GCTTTCCAAGCGCACACA 59.279 55.556 11.47 0.00 45.74 3.72
7286 9075 1.658409 GCTTTCCAAGCGCACACAC 60.658 57.895 11.47 0.00 45.74 3.82
7287 9076 2.024918 CTTTCCAAGCGCACACACT 58.975 52.632 11.47 0.00 0.00 3.55
7288 9077 1.225855 CTTTCCAAGCGCACACACTA 58.774 50.000 11.47 0.00 0.00 2.74
7289 9078 1.806542 CTTTCCAAGCGCACACACTAT 59.193 47.619 11.47 0.00 0.00 2.12
7290 9079 1.155889 TTCCAAGCGCACACACTATG 58.844 50.000 11.47 0.00 0.00 2.23
7291 9080 1.135315 CCAAGCGCACACACTATGC 59.865 57.895 11.47 0.00 39.81 3.14
7298 9087 2.679355 GCACACACTATGCGACAAAA 57.321 45.000 0.00 0.00 32.45 2.44
7299 9088 2.993545 GCACACACTATGCGACAAAAA 58.006 42.857 0.00 0.00 32.45 1.94
7319 9108 3.844577 AAACTCACATTGCATCTGAGC 57.155 42.857 13.18 0.00 35.75 4.26
7320 9109 2.484742 ACTCACATTGCATCTGAGCA 57.515 45.000 13.18 0.00 43.99 4.26
7321 9110 2.357075 ACTCACATTGCATCTGAGCAG 58.643 47.619 13.18 0.00 46.54 4.24
7322 9111 2.027469 ACTCACATTGCATCTGAGCAGA 60.027 45.455 13.18 2.23 46.54 4.26
7323 9112 2.352034 CTCACATTGCATCTGAGCAGAC 59.648 50.000 1.71 0.00 46.54 3.51
7324 9113 1.400846 CACATTGCATCTGAGCAGACC 59.599 52.381 1.71 0.00 46.54 3.85
7325 9114 1.281287 ACATTGCATCTGAGCAGACCT 59.719 47.619 1.71 0.00 46.54 3.85
7326 9115 1.671328 CATTGCATCTGAGCAGACCTG 59.329 52.381 1.71 0.00 46.54 4.00
7327 9116 0.689055 TTGCATCTGAGCAGACCTGT 59.311 50.000 1.71 0.00 46.54 4.00
7328 9117 0.248565 TGCATCTGAGCAGACCTGTC 59.751 55.000 1.71 0.00 40.75 3.51
7329 9118 0.248565 GCATCTGAGCAGACCTGTCA 59.751 55.000 1.71 1.59 40.75 3.58
7330 9119 1.134461 GCATCTGAGCAGACCTGTCAT 60.134 52.381 1.71 0.00 40.75 3.06
7331 9120 2.102084 GCATCTGAGCAGACCTGTCATA 59.898 50.000 1.71 0.00 40.75 2.15
7332 9121 3.431346 GCATCTGAGCAGACCTGTCATAA 60.431 47.826 1.71 0.00 40.75 1.90
7333 9122 4.763073 CATCTGAGCAGACCTGTCATAAA 58.237 43.478 1.71 0.00 40.75 1.40
7334 9123 4.462508 TCTGAGCAGACCTGTCATAAAG 57.537 45.455 0.00 0.00 31.41 1.85
7335 9124 3.196469 TCTGAGCAGACCTGTCATAAAGG 59.804 47.826 0.00 0.00 40.93 3.11
7336 9125 2.237143 TGAGCAGACCTGTCATAAAGGG 59.763 50.000 0.00 0.00 39.30 3.95
7337 9126 2.237392 GAGCAGACCTGTCATAAAGGGT 59.763 50.000 0.00 0.00 39.30 4.34
7338 9127 2.026822 AGCAGACCTGTCATAAAGGGTG 60.027 50.000 0.00 0.00 39.30 4.61
7339 9128 2.290323 GCAGACCTGTCATAAAGGGTGT 60.290 50.000 0.00 0.00 39.30 4.16
7340 9129 3.338249 CAGACCTGTCATAAAGGGTGTG 58.662 50.000 0.00 0.00 39.30 3.82
7341 9130 2.979678 AGACCTGTCATAAAGGGTGTGT 59.020 45.455 0.00 0.00 39.30 3.72
7342 9131 3.074412 GACCTGTCATAAAGGGTGTGTG 58.926 50.000 0.00 0.00 39.30 3.82
7343 9132 2.441750 ACCTGTCATAAAGGGTGTGTGT 59.558 45.455 0.00 0.00 39.30 3.72
7344 9133 3.074412 CCTGTCATAAAGGGTGTGTGTC 58.926 50.000 0.00 0.00 0.00 3.67
7345 9134 3.495983 CCTGTCATAAAGGGTGTGTGTCA 60.496 47.826 0.00 0.00 0.00 3.58
7346 9135 4.326826 CTGTCATAAAGGGTGTGTGTCAT 58.673 43.478 0.00 0.00 0.00 3.06
7347 9136 4.323417 TGTCATAAAGGGTGTGTGTCATC 58.677 43.478 0.00 0.00 0.00 2.92
7348 9137 4.202409 TGTCATAAAGGGTGTGTGTCATCA 60.202 41.667 0.00 0.00 0.00 3.07
7349 9138 4.943705 GTCATAAAGGGTGTGTGTCATCAT 59.056 41.667 0.00 0.00 0.00 2.45
7350 9139 5.415701 GTCATAAAGGGTGTGTGTCATCATT 59.584 40.000 0.00 0.00 32.25 2.57
7351 9140 6.597672 GTCATAAAGGGTGTGTGTCATCATTA 59.402 38.462 0.00 0.00 29.45 1.90
7352 9141 6.597672 TCATAAAGGGTGTGTGTCATCATTAC 59.402 38.462 0.00 0.00 29.45 1.89
7353 9142 4.365514 AAGGGTGTGTGTCATCATTACA 57.634 40.909 0.00 0.00 28.95 2.41
7354 9143 3.942829 AGGGTGTGTGTCATCATTACAG 58.057 45.455 0.00 0.00 0.00 2.74
7355 9144 3.327757 AGGGTGTGTGTCATCATTACAGT 59.672 43.478 0.00 0.00 0.00 3.55
7356 9145 4.530553 AGGGTGTGTGTCATCATTACAGTA 59.469 41.667 0.00 0.00 0.00 2.74
7357 9146 4.630069 GGGTGTGTGTCATCATTACAGTAC 59.370 45.833 0.00 0.00 0.00 2.73
7358 9147 4.630069 GGTGTGTGTCATCATTACAGTACC 59.370 45.833 0.00 0.00 0.00 3.34
7359 9148 5.234752 GTGTGTGTCATCATTACAGTACCA 58.765 41.667 0.00 0.00 0.00 3.25
7360 9149 5.699001 GTGTGTGTCATCATTACAGTACCAA 59.301 40.000 0.00 0.00 0.00 3.67
7361 9150 6.203915 GTGTGTGTCATCATTACAGTACCAAA 59.796 38.462 0.00 0.00 0.00 3.28
7362 9151 6.768381 TGTGTGTCATCATTACAGTACCAAAA 59.232 34.615 0.00 0.00 0.00 2.44
7363 9152 7.283354 TGTGTGTCATCATTACAGTACCAAAAA 59.717 33.333 0.00 0.00 0.00 1.94
7364 9153 7.803189 GTGTGTCATCATTACAGTACCAAAAAG 59.197 37.037 0.00 0.00 0.00 2.27
7365 9154 7.717436 TGTGTCATCATTACAGTACCAAAAAGA 59.283 33.333 0.00 0.00 0.00 2.52
7366 9155 8.564574 GTGTCATCATTACAGTACCAAAAAGAA 58.435 33.333 0.00 0.00 0.00 2.52
7367 9156 9.126151 TGTCATCATTACAGTACCAAAAAGAAA 57.874 29.630 0.00 0.00 0.00 2.52
7368 9157 9.959749 GTCATCATTACAGTACCAAAAAGAAAA 57.040 29.630 0.00 0.00 0.00 2.29
7369 9158 9.959749 TCATCATTACAGTACCAAAAAGAAAAC 57.040 29.630 0.00 0.00 0.00 2.43
7370 9159 9.965824 CATCATTACAGTACCAAAAAGAAAACT 57.034 29.630 0.00 0.00 0.00 2.66
7376 9165 8.166422 ACAGTACCAAAAAGAAAACTATCTGG 57.834 34.615 0.00 0.00 0.00 3.86
7377 9166 7.778382 ACAGTACCAAAAAGAAAACTATCTGGT 59.222 33.333 0.00 0.00 0.00 4.00
7378 9167 8.290325 CAGTACCAAAAAGAAAACTATCTGGTC 58.710 37.037 0.00 0.00 0.00 4.02
7379 9168 6.650427 ACCAAAAAGAAAACTATCTGGTCC 57.350 37.500 0.00 0.00 0.00 4.46
7380 9169 6.133356 ACCAAAAAGAAAACTATCTGGTCCA 58.867 36.000 0.00 0.00 0.00 4.02
7381 9170 6.040504 ACCAAAAAGAAAACTATCTGGTCCAC 59.959 38.462 0.00 0.00 0.00 4.02
7382 9171 5.941948 AAAAGAAAACTATCTGGTCCACG 57.058 39.130 0.00 0.00 0.00 4.94
7383 9172 4.618920 AAGAAAACTATCTGGTCCACGT 57.381 40.909 0.00 0.00 0.00 4.49
7384 9173 4.189639 AGAAAACTATCTGGTCCACGTC 57.810 45.455 0.00 0.00 0.00 4.34
7385 9174 3.056035 AGAAAACTATCTGGTCCACGTCC 60.056 47.826 0.00 0.00 0.00 4.79
7386 9175 1.192428 AACTATCTGGTCCACGTCCC 58.808 55.000 0.00 0.00 0.00 4.46
7387 9176 0.040646 ACTATCTGGTCCACGTCCCA 59.959 55.000 0.00 0.00 0.00 4.37
7388 9177 1.343075 ACTATCTGGTCCACGTCCCAT 60.343 52.381 0.00 0.00 0.00 4.00
7389 9178 1.341531 CTATCTGGTCCACGTCCCATC 59.658 57.143 0.00 0.00 0.00 3.51
7390 9179 1.338136 ATCTGGTCCACGTCCCATCC 61.338 60.000 0.00 0.00 0.00 3.51
7391 9180 3.371097 CTGGTCCACGTCCCATCCG 62.371 68.421 0.00 0.00 0.00 4.18
7392 9181 3.072468 GGTCCACGTCCCATCCGA 61.072 66.667 0.00 0.00 0.00 4.55
7393 9182 2.652095 GGTCCACGTCCCATCCGAA 61.652 63.158 0.00 0.00 0.00 4.30
7394 9183 1.447314 GTCCACGTCCCATCCGAAC 60.447 63.158 0.00 0.00 0.00 3.95
7395 9184 1.909287 TCCACGTCCCATCCGAACA 60.909 57.895 0.00 0.00 0.00 3.18
7396 9185 1.740296 CCACGTCCCATCCGAACAC 60.740 63.158 0.00 0.00 0.00 3.32
7397 9186 1.005512 CACGTCCCATCCGAACACA 60.006 57.895 0.00 0.00 0.00 3.72
7398 9187 0.601576 CACGTCCCATCCGAACACAA 60.602 55.000 0.00 0.00 0.00 3.33
7399 9188 0.320421 ACGTCCCATCCGAACACAAG 60.320 55.000 0.00 0.00 0.00 3.16
7400 9189 0.320421 CGTCCCATCCGAACACAAGT 60.320 55.000 0.00 0.00 0.00 3.16
7401 9190 1.439679 GTCCCATCCGAACACAAGTC 58.560 55.000 0.00 0.00 0.00 3.01
7402 9191 1.052617 TCCCATCCGAACACAAGTCA 58.947 50.000 0.00 0.00 0.00 3.41
7403 9192 1.418264 TCCCATCCGAACACAAGTCAA 59.582 47.619 0.00 0.00 0.00 3.18
7404 9193 2.158740 TCCCATCCGAACACAAGTCAAA 60.159 45.455 0.00 0.00 0.00 2.69
7405 9194 2.621055 CCCATCCGAACACAAGTCAAAA 59.379 45.455 0.00 0.00 0.00 2.44
7406 9195 3.067461 CCCATCCGAACACAAGTCAAAAA 59.933 43.478 0.00 0.00 0.00 1.94
7439 9228 9.477484 AAATACGTGCATTTATTTGGTTTTACA 57.523 25.926 12.38 0.00 0.00 2.41
7440 9229 9.477484 AATACGTGCATTTATTTGGTTTTACAA 57.523 25.926 0.00 0.00 0.00 2.41
7441 9230 7.772332 ACGTGCATTTATTTGGTTTTACAAA 57.228 28.000 0.00 0.00 43.69 2.83
7442 9231 8.197988 ACGTGCATTTATTTGGTTTTACAAAA 57.802 26.923 0.00 0.00 42.91 2.44
7443 9232 8.831550 ACGTGCATTTATTTGGTTTTACAAAAT 58.168 25.926 0.00 0.00 42.91 1.82
7444 9233 9.657121 CGTGCATTTATTTGGTTTTACAAAATT 57.343 25.926 0.00 0.00 42.91 1.82
7494 9283 8.712285 AGTATCGGAATTTAGATTCGTTTTCA 57.288 30.769 0.28 0.00 42.12 2.69
7495 9284 8.601476 AGTATCGGAATTTAGATTCGTTTTCAC 58.399 33.333 0.28 0.00 42.12 3.18
7496 9285 6.173191 TCGGAATTTAGATTCGTTTTCACC 57.827 37.500 0.28 0.00 42.12 4.02
7497 9286 5.701750 TCGGAATTTAGATTCGTTTTCACCA 59.298 36.000 0.28 0.00 42.12 4.17
7498 9287 6.373216 TCGGAATTTAGATTCGTTTTCACCAT 59.627 34.615 0.28 0.00 42.12 3.55
7499 9288 7.027161 CGGAATTTAGATTCGTTTTCACCATT 58.973 34.615 0.28 0.00 42.12 3.16
7500 9289 7.008266 CGGAATTTAGATTCGTTTTCACCATTG 59.992 37.037 0.28 0.00 42.12 2.82
7501 9290 7.275560 GGAATTTAGATTCGTTTTCACCATTGG 59.724 37.037 0.00 0.00 42.12 3.16
7502 9291 5.637006 TTAGATTCGTTTTCACCATTGGG 57.363 39.130 7.78 0.00 41.29 4.12
7513 9302 3.209266 CCATTGGGTTTTTCACGGC 57.791 52.632 0.00 0.00 0.00 5.68
7514 9303 0.665972 CCATTGGGTTTTTCACGGCG 60.666 55.000 4.80 4.80 0.00 6.46
7515 9304 0.312416 CATTGGGTTTTTCACGGCGA 59.688 50.000 16.62 0.00 0.00 5.54
7516 9305 0.596082 ATTGGGTTTTTCACGGCGAG 59.404 50.000 16.62 5.72 0.00 5.03
7517 9306 0.748729 TTGGGTTTTTCACGGCGAGT 60.749 50.000 16.62 0.00 0.00 4.18
7518 9307 0.748729 TGGGTTTTTCACGGCGAGTT 60.749 50.000 16.62 0.00 0.00 3.01
7519 9308 0.040692 GGGTTTTTCACGGCGAGTTC 60.041 55.000 16.62 0.00 0.00 3.01
7520 9309 0.942252 GGTTTTTCACGGCGAGTTCT 59.058 50.000 16.62 0.00 0.00 3.01
7521 9310 1.332686 GGTTTTTCACGGCGAGTTCTT 59.667 47.619 16.62 0.00 0.00 2.52
7522 9311 2.601504 GGTTTTTCACGGCGAGTTCTTC 60.602 50.000 16.62 0.00 0.00 2.87
7523 9312 1.942677 TTTTCACGGCGAGTTCTTCA 58.057 45.000 16.62 0.00 0.00 3.02
7524 9313 1.942677 TTTCACGGCGAGTTCTTCAA 58.057 45.000 16.62 0.00 0.00 2.69
7525 9314 1.942677 TTCACGGCGAGTTCTTCAAA 58.057 45.000 16.62 0.00 0.00 2.69
7526 9315 1.942677 TCACGGCGAGTTCTTCAAAA 58.057 45.000 16.62 0.00 0.00 2.44
7527 9316 1.595794 TCACGGCGAGTTCTTCAAAAC 59.404 47.619 16.62 0.00 0.00 2.43
7528 9317 1.597663 CACGGCGAGTTCTTCAAAACT 59.402 47.619 16.62 0.00 42.10 2.66
7529 9318 2.798283 CACGGCGAGTTCTTCAAAACTA 59.202 45.455 16.62 0.00 39.55 2.24
7530 9319 3.057734 ACGGCGAGTTCTTCAAAACTAG 58.942 45.455 16.62 0.00 39.55 2.57
7531 9320 3.243636 ACGGCGAGTTCTTCAAAACTAGA 60.244 43.478 16.62 0.00 39.55 2.43
7532 9321 3.927142 CGGCGAGTTCTTCAAAACTAGAT 59.073 43.478 0.00 0.00 39.55 1.98
7533 9322 4.031878 CGGCGAGTTCTTCAAAACTAGATC 59.968 45.833 0.00 0.00 39.55 2.75
7534 9323 4.330347 GGCGAGTTCTTCAAAACTAGATCC 59.670 45.833 0.00 0.00 39.55 3.36
7535 9324 4.330347 GCGAGTTCTTCAAAACTAGATCCC 59.670 45.833 0.00 0.00 39.55 3.85
7536 9325 5.479306 CGAGTTCTTCAAAACTAGATCCCA 58.521 41.667 0.00 0.00 39.55 4.37
7537 9326 6.109359 CGAGTTCTTCAAAACTAGATCCCAT 58.891 40.000 0.00 0.00 39.55 4.00
7538 9327 7.265673 CGAGTTCTTCAAAACTAGATCCCATA 58.734 38.462 0.00 0.00 39.55 2.74
7539 9328 7.928706 CGAGTTCTTCAAAACTAGATCCCATAT 59.071 37.037 0.00 0.00 39.55 1.78
7540 9329 8.970859 AGTTCTTCAAAACTAGATCCCATATG 57.029 34.615 0.00 0.00 37.71 1.78
7541 9330 7.995488 AGTTCTTCAAAACTAGATCCCATATGG 59.005 37.037 15.41 15.41 37.71 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.490490 TGAGCACCTGATAATCCACCC 59.510 52.381 0.00 0.00 0.00 4.61
9 10 3.776969 AGACTTGAGCACCTGATAATCCA 59.223 43.478 0.00 0.00 0.00 3.41
39 40 0.840288 TCCCCAGGCTTGTGCTTCTA 60.840 55.000 0.00 0.00 39.59 2.10
73 74 4.588951 TCAATACTAACATCGCCCTCTCAT 59.411 41.667 0.00 0.00 0.00 2.90
91 92 8.510243 TTAACCTAGTCACAGTATCGTCAATA 57.490 34.615 0.00 0.00 0.00 1.90
144 145 0.171903 CTTCCTCAATTGGCGCCTTG 59.828 55.000 29.70 24.01 0.00 3.61
163 164 3.066760 CACCTCTATTTGATTTTCCCGCC 59.933 47.826 0.00 0.00 0.00 6.13
183 184 1.111277 AAACCACTTGAAGCCCACAC 58.889 50.000 0.00 0.00 0.00 3.82
200 201 1.769026 TGGCCTAACACACTGCAAAA 58.231 45.000 3.32 0.00 0.00 2.44
231 232 3.370978 CGACTCACATCAACATAACCCAC 59.629 47.826 0.00 0.00 0.00 4.61
244 245 0.319900 GTGTGTGCCTCGACTCACAT 60.320 55.000 15.41 0.00 43.53 3.21
259 260 4.621460 CGATATCTGGCTTATAACGGTGTG 59.379 45.833 0.34 0.00 0.00 3.82
281 282 6.892310 TCATTGATGATTCTCACTTACACG 57.108 37.500 0.00 0.00 0.00 4.49
303 304 9.995957 GAAAGAGGCTTAGACTAATTTCATTTC 57.004 33.333 16.05 8.73 31.05 2.17
322 323 1.063806 CGACACGAGCAAGAAAGAGG 58.936 55.000 0.00 0.00 0.00 3.69
372 385 6.658188 TCGGTGAAAAATTCAAATTAGGGT 57.342 33.333 0.00 0.00 42.15 4.34
385 398 5.086104 TGGGACAAATTTTCGGTGAAAAA 57.914 34.783 8.59 0.00 39.27 1.94
386 399 4.737855 TGGGACAAATTTTCGGTGAAAA 57.262 36.364 7.12 7.12 39.80 2.29
406 419 1.082561 CGCCGCATCGATGGATTTG 60.083 57.895 26.00 2.01 0.00 2.32
437 450 1.640428 AATCGACATGTGCGGTACTG 58.360 50.000 1.15 0.00 0.00 2.74
491 937 6.211587 TCATACTCATTGGGATTTGCTTTG 57.788 37.500 0.00 0.00 0.00 2.77
548 997 1.538047 CCCCTGTGACAGTGATTTGG 58.462 55.000 12.15 4.15 0.00 3.28
657 1108 4.477975 GCGCTACTCGTGGCTCGT 62.478 66.667 8.94 0.00 41.07 4.18
676 1135 1.550976 GGAAGACCAGACCACGAAGAT 59.449 52.381 0.00 0.00 35.97 2.40
706 1165 1.534697 GTGGTGGAAAGGGTGGTGA 59.465 57.895 0.00 0.00 0.00 4.02
802 1270 4.267503 GGGATCGACGAGGCGGTC 62.268 72.222 2.47 2.47 40.54 4.79
1793 2620 0.674581 CAAGGCAACCATGAGCGAGA 60.675 55.000 0.00 0.00 37.17 4.04
2304 3136 7.502226 TCATCCTGTGATGTATTTTCCCAATAC 59.498 37.037 2.77 0.00 46.96 1.89
2376 3208 1.777878 TCCTGCACCCTTGGTAAAAGA 59.222 47.619 0.00 0.00 32.11 2.52
2521 3353 6.148811 GTGCTAAGTGTATCTTTAGGCAACAA 59.851 38.462 0.00 0.00 37.02 2.83
2623 3455 7.420800 CAAGCCAATCATTAGTCTGATAAACC 58.579 38.462 0.00 0.00 34.79 3.27
3104 4109 3.645212 TCCTCTGAATCAAGGAGGCATAG 59.355 47.826 12.26 0.00 44.39 2.23
3349 4475 3.847671 AGTGGCCTATAGGAAAAGAGC 57.152 47.619 23.61 4.67 37.39 4.09
3374 4500 4.991056 GGAAATTTTCCTTTGGAACTGAGC 59.009 41.667 19.01 0.00 46.57 4.26
3430 4556 7.334921 AGCATGCAACAACATATTTGCTAATTT 59.665 29.630 21.98 0.00 46.83 1.82
3737 4975 7.613801 TGCACACATACAAAGGAAATTATAGGT 59.386 33.333 0.00 0.00 0.00 3.08
4045 5456 6.293244 GGTTTACATACTCTGCTTTCACGTTT 60.293 38.462 0.00 0.00 0.00 3.60
4551 6002 2.837591 AGCAAAAGTTTTCCCAACCTGT 59.162 40.909 0.00 0.00 0.00 4.00
4585 6036 4.143543 TGCAGTTCAATGAGAATTGTGGA 58.856 39.130 0.00 0.00 43.60 4.02
4603 6054 5.319139 CGAACAAGTTTCTGACATATGCAG 58.681 41.667 16.45 16.45 34.71 4.41
4962 6436 5.411361 CGAAACTGTTCATCCAATAGAACCA 59.589 40.000 0.00 0.00 42.57 3.67
5002 6476 1.142667 TGCAGACTTCCACAATGGTCA 59.857 47.619 0.00 0.00 39.03 4.02
5605 7246 3.986277 AGAAGCAAAATGCCTTGTCAAG 58.014 40.909 5.53 5.53 46.52 3.02
5855 7500 4.215399 TCTTCAACCGTTCAATCAATGGAC 59.785 41.667 0.00 0.00 43.35 4.02
5958 7603 6.303839 AGGCCATTTCCTATTCGCTATAAAA 58.696 36.000 5.01 0.00 33.95 1.52
6192 7891 5.123820 GGAGTGACTTGCTTGCATATGTAAA 59.876 40.000 7.66 0.84 0.00 2.01
6193 7892 4.635765 GGAGTGACTTGCTTGCATATGTAA 59.364 41.667 6.07 6.07 0.00 2.41
6300 8000 0.732880 GCGAGCAAAGCAGACGTAGA 60.733 55.000 0.00 0.00 34.19 2.59
6407 8107 8.135529 AGTTAAGAACAAAATGGCTACAAGAAC 58.864 33.333 0.00 0.00 0.00 3.01
6424 8124 6.198966 CACCAACAAATCAGCAAGTTAAGAAC 59.801 38.462 0.00 0.00 0.00 3.01
6898 8634 8.700439 AAAGGAAATAAAAACAGCCTACAGTA 57.300 30.769 0.00 0.00 0.00 2.74
6928 8664 4.153655 GCCTACCTTAACAAAGGAAACTCG 59.846 45.833 11.04 0.00 42.68 4.18
6929 8665 5.314529 AGCCTACCTTAACAAAGGAAACTC 58.685 41.667 11.04 0.00 42.68 3.01
6931 8667 5.314529 AGAGCCTACCTTAACAAAGGAAAC 58.685 41.667 11.04 0.00 42.62 2.78
6940 8676 3.069872 GGAAGCCTAGAGCCTACCTTAAC 59.930 52.174 0.00 0.00 45.47 2.01
6941 8677 3.306613 GGAAGCCTAGAGCCTACCTTAA 58.693 50.000 0.00 0.00 45.47 1.85
7078 8841 5.522097 GGGTCGACATTTTCAACAACAAAAT 59.478 36.000 18.91 0.00 34.42 1.82
7254 9043 3.798712 GGAAAGCCCAATTAGCGCAGC 62.799 57.143 11.47 0.00 45.81 5.25
7255 9044 0.101219 GGAAAGCCCAATTAGCGCAG 59.899 55.000 11.47 0.00 34.64 5.18
7256 9045 0.610509 TGGAAAGCCCAATTAGCGCA 60.611 50.000 11.47 0.00 43.29 6.09
7257 9046 2.188912 TGGAAAGCCCAATTAGCGC 58.811 52.632 0.00 0.00 43.29 5.92
7270 9059 1.535028 CATAGTGTGTGCGCTTGGAAA 59.465 47.619 9.73 0.00 36.72 3.13
7271 9060 1.155889 CATAGTGTGTGCGCTTGGAA 58.844 50.000 9.73 0.00 36.72 3.53
7272 9061 1.298157 GCATAGTGTGTGCGCTTGGA 61.298 55.000 9.73 0.00 36.72 3.53
7273 9062 1.135315 GCATAGTGTGTGCGCTTGG 59.865 57.895 9.73 0.00 36.72 3.61
7274 9063 4.751539 GCATAGTGTGTGCGCTTG 57.248 55.556 9.73 0.00 36.72 4.01
7279 9068 2.679355 TTTTGTCGCATAGTGTGTGC 57.321 45.000 0.00 0.00 38.23 4.57
7303 9092 2.353323 GTCTGCTCAGATGCAATGTGA 58.647 47.619 2.62 2.91 45.20 3.58
7304 9093 1.400846 GGTCTGCTCAGATGCAATGTG 59.599 52.381 2.62 0.00 42.83 3.21
7305 9094 1.281287 AGGTCTGCTCAGATGCAATGT 59.719 47.619 2.62 0.00 42.83 2.71
7306 9095 1.671328 CAGGTCTGCTCAGATGCAATG 59.329 52.381 2.62 0.00 42.83 2.82
7307 9096 1.281287 ACAGGTCTGCTCAGATGCAAT 59.719 47.619 2.62 0.00 42.83 3.56
7308 9097 0.689055 ACAGGTCTGCTCAGATGCAA 59.311 50.000 2.62 0.00 42.83 4.08
7309 9098 0.248565 GACAGGTCTGCTCAGATGCA 59.751 55.000 2.62 0.00 39.97 3.96
7310 9099 0.248565 TGACAGGTCTGCTCAGATGC 59.751 55.000 2.62 0.00 39.97 3.91
7311 9100 2.983907 ATGACAGGTCTGCTCAGATG 57.016 50.000 2.62 1.35 39.97 2.90
7312 9101 4.141756 CCTTTATGACAGGTCTGCTCAGAT 60.142 45.833 2.62 0.00 39.97 2.90
7313 9102 3.196469 CCTTTATGACAGGTCTGCTCAGA 59.804 47.826 0.65 0.00 34.56 3.27
7314 9103 3.529533 CCTTTATGACAGGTCTGCTCAG 58.470 50.000 0.65 0.00 0.00 3.35
7315 9104 2.237143 CCCTTTATGACAGGTCTGCTCA 59.763 50.000 0.65 2.50 0.00 4.26
7316 9105 2.237392 ACCCTTTATGACAGGTCTGCTC 59.763 50.000 0.65 0.00 0.00 4.26
7317 9106 2.026822 CACCCTTTATGACAGGTCTGCT 60.027 50.000 0.65 0.00 0.00 4.24
7318 9107 2.290323 ACACCCTTTATGACAGGTCTGC 60.290 50.000 0.65 0.00 0.00 4.26
7319 9108 3.244561 ACACACCCTTTATGACAGGTCTG 60.245 47.826 0.65 0.00 0.00 3.51
7320 9109 2.979678 ACACACCCTTTATGACAGGTCT 59.020 45.455 0.65 0.00 0.00 3.85
7321 9110 3.074412 CACACACCCTTTATGACAGGTC 58.926 50.000 0.00 0.00 0.00 3.85
7322 9111 2.441750 ACACACACCCTTTATGACAGGT 59.558 45.455 0.00 0.00 0.00 4.00
7323 9112 3.074412 GACACACACCCTTTATGACAGG 58.926 50.000 0.00 0.00 0.00 4.00
7324 9113 3.738982 TGACACACACCCTTTATGACAG 58.261 45.455 0.00 0.00 0.00 3.51
7325 9114 3.847671 TGACACACACCCTTTATGACA 57.152 42.857 0.00 0.00 0.00 3.58
7326 9115 4.323417 TGATGACACACACCCTTTATGAC 58.677 43.478 0.00 0.00 0.00 3.06
7327 9116 4.632327 TGATGACACACACCCTTTATGA 57.368 40.909 0.00 0.00 0.00 2.15
7328 9117 5.902613 AATGATGACACACACCCTTTATG 57.097 39.130 0.00 0.00 0.00 1.90
7329 9118 6.480763 TGTAATGATGACACACACCCTTTAT 58.519 36.000 0.00 0.00 0.00 1.40
7330 9119 5.870706 TGTAATGATGACACACACCCTTTA 58.129 37.500 0.00 0.00 0.00 1.85
7331 9120 4.724399 TGTAATGATGACACACACCCTTT 58.276 39.130 0.00 0.00 0.00 3.11
7332 9121 4.202461 ACTGTAATGATGACACACACCCTT 60.202 41.667 0.00 0.00 0.00 3.95
7333 9122 3.327757 ACTGTAATGATGACACACACCCT 59.672 43.478 0.00 0.00 0.00 4.34
7334 9123 3.674997 ACTGTAATGATGACACACACCC 58.325 45.455 0.00 0.00 0.00 4.61
7335 9124 4.630069 GGTACTGTAATGATGACACACACC 59.370 45.833 0.00 0.00 0.00 4.16
7336 9125 5.234752 TGGTACTGTAATGATGACACACAC 58.765 41.667 0.00 0.00 0.00 3.82
7337 9126 5.476091 TGGTACTGTAATGATGACACACA 57.524 39.130 0.00 0.00 0.00 3.72
7338 9127 6.795098 TTTGGTACTGTAATGATGACACAC 57.205 37.500 0.00 0.00 0.00 3.82
7339 9128 7.717436 TCTTTTTGGTACTGTAATGATGACACA 59.283 33.333 0.00 0.00 0.00 3.72
7340 9129 8.094798 TCTTTTTGGTACTGTAATGATGACAC 57.905 34.615 0.00 0.00 0.00 3.67
7341 9130 8.684386 TTCTTTTTGGTACTGTAATGATGACA 57.316 30.769 0.00 0.00 0.00 3.58
7342 9131 9.959749 TTTTCTTTTTGGTACTGTAATGATGAC 57.040 29.630 0.00 0.00 0.00 3.06
7343 9132 9.959749 GTTTTCTTTTTGGTACTGTAATGATGA 57.040 29.630 0.00 0.00 0.00 2.92
7344 9133 9.965824 AGTTTTCTTTTTGGTACTGTAATGATG 57.034 29.630 0.00 0.00 0.00 3.07
7350 9139 9.280174 CCAGATAGTTTTCTTTTTGGTACTGTA 57.720 33.333 0.00 0.00 31.78 2.74
7351 9140 7.778382 ACCAGATAGTTTTCTTTTTGGTACTGT 59.222 33.333 0.00 0.00 41.71 3.55
7352 9141 8.166422 ACCAGATAGTTTTCTTTTTGGTACTG 57.834 34.615 0.00 0.00 41.71 2.74
7353 9142 7.447545 GGACCAGATAGTTTTCTTTTTGGTACT 59.552 37.037 0.00 0.00 42.82 2.73
7354 9143 7.229907 TGGACCAGATAGTTTTCTTTTTGGTAC 59.770 37.037 0.00 4.53 42.82 3.34
7355 9144 7.229907 GTGGACCAGATAGTTTTCTTTTTGGTA 59.770 37.037 0.00 0.00 42.82 3.25
7356 9145 6.040504 GTGGACCAGATAGTTTTCTTTTTGGT 59.959 38.462 0.00 0.00 44.40 3.67
7357 9146 6.447162 GTGGACCAGATAGTTTTCTTTTTGG 58.553 40.000 0.00 0.00 38.45 3.28
7358 9147 6.142817 CGTGGACCAGATAGTTTTCTTTTTG 58.857 40.000 0.00 0.00 0.00 2.44
7359 9148 5.826208 ACGTGGACCAGATAGTTTTCTTTTT 59.174 36.000 0.00 0.00 0.00 1.94
7360 9149 5.374071 ACGTGGACCAGATAGTTTTCTTTT 58.626 37.500 0.00 0.00 0.00 2.27
7361 9150 4.969484 ACGTGGACCAGATAGTTTTCTTT 58.031 39.130 0.00 0.00 0.00 2.52
7362 9151 4.562963 GGACGTGGACCAGATAGTTTTCTT 60.563 45.833 0.00 0.00 0.00 2.52
7363 9152 3.056035 GGACGTGGACCAGATAGTTTTCT 60.056 47.826 0.00 0.00 0.00 2.52
7364 9153 3.259902 GGACGTGGACCAGATAGTTTTC 58.740 50.000 0.00 0.00 0.00 2.29
7365 9154 2.027469 GGGACGTGGACCAGATAGTTTT 60.027 50.000 0.00 0.00 0.00 2.43
7366 9155 1.553704 GGGACGTGGACCAGATAGTTT 59.446 52.381 0.00 0.00 0.00 2.66
7367 9156 1.192428 GGGACGTGGACCAGATAGTT 58.808 55.000 0.00 0.00 0.00 2.24
7368 9157 0.040646 TGGGACGTGGACCAGATAGT 59.959 55.000 0.00 0.00 31.92 2.12
7369 9158 1.341531 GATGGGACGTGGACCAGATAG 59.658 57.143 0.00 0.00 40.67 2.08
7370 9159 1.410004 GATGGGACGTGGACCAGATA 58.590 55.000 0.00 0.00 40.67 1.98
7371 9160 1.338136 GGATGGGACGTGGACCAGAT 61.338 60.000 0.00 0.00 40.67 2.90
7372 9161 1.987855 GGATGGGACGTGGACCAGA 60.988 63.158 0.00 0.00 40.67 3.86
7373 9162 2.584608 GGATGGGACGTGGACCAG 59.415 66.667 0.00 0.00 40.67 4.00
7374 9163 3.387091 CGGATGGGACGTGGACCA 61.387 66.667 0.00 0.00 41.76 4.02
7375 9164 2.652095 TTCGGATGGGACGTGGACC 61.652 63.158 0.00 0.00 0.00 4.46
7376 9165 1.447314 GTTCGGATGGGACGTGGAC 60.447 63.158 0.00 0.00 0.00 4.02
7377 9166 1.909287 TGTTCGGATGGGACGTGGA 60.909 57.895 0.00 0.00 0.00 4.02
7378 9167 1.740296 GTGTTCGGATGGGACGTGG 60.740 63.158 0.00 0.00 0.00 4.94
7379 9168 0.601576 TTGTGTTCGGATGGGACGTG 60.602 55.000 0.00 0.00 0.00 4.49
7380 9169 0.320421 CTTGTGTTCGGATGGGACGT 60.320 55.000 0.00 0.00 0.00 4.34
7381 9170 0.320421 ACTTGTGTTCGGATGGGACG 60.320 55.000 0.00 0.00 0.00 4.79
7382 9171 1.270625 TGACTTGTGTTCGGATGGGAC 60.271 52.381 0.00 0.00 0.00 4.46
7383 9172 1.052617 TGACTTGTGTTCGGATGGGA 58.947 50.000 0.00 0.00 0.00 4.37
7384 9173 1.890876 TTGACTTGTGTTCGGATGGG 58.109 50.000 0.00 0.00 0.00 4.00
7385 9174 3.980646 TTTTGACTTGTGTTCGGATGG 57.019 42.857 0.00 0.00 0.00 3.51
7413 9202 9.477484 TGTAAAACCAAATAAATGCACGTATTT 57.523 25.926 9.59 9.59 34.78 1.40
7414 9203 9.477484 TTGTAAAACCAAATAAATGCACGTATT 57.523 25.926 0.00 0.00 0.00 1.89
7415 9204 9.477484 TTTGTAAAACCAAATAAATGCACGTAT 57.523 25.926 0.00 0.00 29.67 3.06
7416 9205 8.867112 TTTGTAAAACCAAATAAATGCACGTA 57.133 26.923 0.00 0.00 29.67 3.57
7417 9206 7.772332 TTTGTAAAACCAAATAAATGCACGT 57.228 28.000 0.00 0.00 29.67 4.49
7418 9207 9.657121 AATTTTGTAAAACCAAATAAATGCACG 57.343 25.926 0.00 0.00 34.50 5.34
7462 9251 9.338291 CGAATCTAAATTCCGATACTCGAATAA 57.662 33.333 0.00 0.00 40.30 1.40
7463 9252 8.509690 ACGAATCTAAATTCCGATACTCGAATA 58.490 33.333 13.48 0.00 40.30 1.75
7464 9253 7.368833 ACGAATCTAAATTCCGATACTCGAAT 58.631 34.615 13.48 0.00 40.30 3.34
7465 9254 6.732154 ACGAATCTAAATTCCGATACTCGAA 58.268 36.000 13.48 0.00 40.30 3.71
7466 9255 6.309712 ACGAATCTAAATTCCGATACTCGA 57.690 37.500 13.48 0.00 40.30 4.04
7467 9256 6.988109 AACGAATCTAAATTCCGATACTCG 57.012 37.500 0.00 8.37 38.46 4.18
7468 9257 8.814235 TGAAAACGAATCTAAATTCCGATACTC 58.186 33.333 0.00 0.00 38.46 2.59
7469 9258 8.601476 GTGAAAACGAATCTAAATTCCGATACT 58.399 33.333 0.00 0.00 38.46 2.12
7470 9259 7.849515 GGTGAAAACGAATCTAAATTCCGATAC 59.150 37.037 0.00 0.00 38.46 2.24
7471 9260 7.549842 TGGTGAAAACGAATCTAAATTCCGATA 59.450 33.333 0.00 0.00 38.46 2.92
7472 9261 6.373216 TGGTGAAAACGAATCTAAATTCCGAT 59.627 34.615 0.00 0.00 38.46 4.18
7473 9262 5.701750 TGGTGAAAACGAATCTAAATTCCGA 59.298 36.000 0.00 0.00 38.46 4.55
7474 9263 5.933790 TGGTGAAAACGAATCTAAATTCCG 58.066 37.500 0.00 0.00 38.46 4.30
7475 9264 7.275560 CCAATGGTGAAAACGAATCTAAATTCC 59.724 37.037 0.00 0.00 38.46 3.01
7476 9265 7.275560 CCCAATGGTGAAAACGAATCTAAATTC 59.724 37.037 0.00 0.00 38.34 2.17
7477 9266 7.096551 CCCAATGGTGAAAACGAATCTAAATT 58.903 34.615 0.00 0.00 0.00 1.82
7478 9267 6.210584 ACCCAATGGTGAAAACGAATCTAAAT 59.789 34.615 0.00 0.00 45.58 1.40
7479 9268 5.536916 ACCCAATGGTGAAAACGAATCTAAA 59.463 36.000 0.00 0.00 45.58 1.85
7480 9269 5.074115 ACCCAATGGTGAAAACGAATCTAA 58.926 37.500 0.00 0.00 45.58 2.10
7481 9270 4.658063 ACCCAATGGTGAAAACGAATCTA 58.342 39.130 0.00 0.00 45.58 1.98
7482 9271 3.496331 ACCCAATGGTGAAAACGAATCT 58.504 40.909 0.00 0.00 45.58 2.40
7483 9272 3.934457 ACCCAATGGTGAAAACGAATC 57.066 42.857 0.00 0.00 45.58 2.52
7495 9284 0.665972 CGCCGTGAAAAACCCAATGG 60.666 55.000 0.00 0.00 37.80 3.16
7496 9285 0.312416 TCGCCGTGAAAAACCCAATG 59.688 50.000 0.00 0.00 0.00 2.82
7497 9286 0.596082 CTCGCCGTGAAAAACCCAAT 59.404 50.000 0.00 0.00 0.00 3.16
7498 9287 0.748729 ACTCGCCGTGAAAAACCCAA 60.749 50.000 0.00 0.00 0.00 4.12
7499 9288 0.748729 AACTCGCCGTGAAAAACCCA 60.749 50.000 0.00 0.00 0.00 4.51
7500 9289 0.040692 GAACTCGCCGTGAAAAACCC 60.041 55.000 0.00 0.00 0.00 4.11
7501 9290 0.942252 AGAACTCGCCGTGAAAAACC 59.058 50.000 0.00 0.00 0.00 3.27
7502 9291 2.031191 TGAAGAACTCGCCGTGAAAAAC 59.969 45.455 0.00 0.00 0.00 2.43
7503 9292 2.281517 TGAAGAACTCGCCGTGAAAAA 58.718 42.857 0.00 0.00 0.00 1.94
7504 9293 1.942677 TGAAGAACTCGCCGTGAAAA 58.057 45.000 0.00 0.00 0.00 2.29
7505 9294 1.942677 TTGAAGAACTCGCCGTGAAA 58.057 45.000 0.00 0.00 0.00 2.69
7506 9295 1.942677 TTTGAAGAACTCGCCGTGAA 58.057 45.000 0.00 0.00 0.00 3.18
7507 9296 1.595794 GTTTTGAAGAACTCGCCGTGA 59.404 47.619 0.00 0.00 0.00 4.35
7508 9297 1.597663 AGTTTTGAAGAACTCGCCGTG 59.402 47.619 0.00 0.00 34.94 4.94
7509 9298 1.949465 AGTTTTGAAGAACTCGCCGT 58.051 45.000 0.00 0.00 34.94 5.68
7510 9299 3.314553 TCTAGTTTTGAAGAACTCGCCG 58.685 45.455 0.00 0.00 40.24 6.46
7511 9300 4.330347 GGATCTAGTTTTGAAGAACTCGCC 59.670 45.833 0.00 0.00 40.24 5.54
7512 9301 4.330347 GGGATCTAGTTTTGAAGAACTCGC 59.670 45.833 0.00 0.00 40.24 5.03
7513 9302 5.479306 TGGGATCTAGTTTTGAAGAACTCG 58.521 41.667 0.00 0.00 40.24 4.18
7514 9303 9.050601 CATATGGGATCTAGTTTTGAAGAACTC 57.949 37.037 0.00 0.00 40.24 3.01
7515 9304 7.995488 CCATATGGGATCTAGTTTTGAAGAACT 59.005 37.037 14.52 0.00 40.17 3.01
7516 9305 8.159344 CCATATGGGATCTAGTTTTGAAGAAC 57.841 38.462 14.52 0.00 40.01 3.01


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

AutoCloner maintained by Alex Coulton.