Multiple sequence alignment - TraesCS3B01G370100

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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 TraesCS3B01G370100 chr3B 100.000 9197 0 0 1 9197 581977105 581967909 0.000000e+00 16984.0
1 TraesCS3B01G370100 chr3B 81.407 597 65 24 4271 4829 581971601 581971013 6.550000e-121 446.0
2 TraesCS3B01G370100 chr3B 81.345 595 69 21 5505 6093 581972835 581972277 6.550000e-121 446.0
3 TraesCS3B01G370100 chr3B 79.375 640 98 16 2508 3130 581970021 581970643 3.970000e-113 420.0
4 TraesCS3B01G370100 chr3B 79.375 640 98 16 6463 7085 581973976 581974598 3.970000e-113 420.0
5 TraesCS3B01G370100 chr3B 79.310 464 70 18 5269 5719 581971387 581971837 1.500000e-77 302.0
6 TraesCS3B01G370100 chr3B 92.537 67 5 0 7332 7398 65192736 65192670 7.600000e-16 97.1
7 TraesCS3B01G370100 chr3B 97.778 45 1 0 7041 7085 581970021 581969977 2.750000e-10 78.7
8 TraesCS3B01G370100 chr3B 97.778 45 1 0 7085 7129 581970065 581970021 2.750000e-10 78.7
9 TraesCS3B01G370100 chr3B 87.931 58 5 2 5132 5187 581971278 581971335 5.960000e-07 67.6
10 TraesCS3B01G370100 chr3B 85.075 67 8 2 5759 5825 581971907 581971971 5.960000e-07 67.6
11 TraesCS3B01G370100 chr3A 93.768 2856 113 26 783 3605 585035184 585032361 0.000000e+00 4228.0
12 TraesCS3B01G370100 chr3A 94.893 1821 67 14 7194 8994 585028543 585026729 0.000000e+00 2824.0
13 TraesCS3B01G370100 chr3A 92.168 1647 73 22 5484 7085 585030298 585028663 0.000000e+00 2276.0
14 TraesCS3B01G370100 chr3A 93.264 861 34 6 4627 5487 585031168 585030332 0.000000e+00 1247.0
15 TraesCS3B01G370100 chr3A 93.992 749 35 4 1 745 585037448 585036706 0.000000e+00 1125.0
16 TraesCS3B01G370100 chr3A 95.942 345 12 2 3566 3909 585032359 585032016 8.070000e-155 558.0
17 TraesCS3B01G370100 chr3A 79.467 638 98 14 6463 7085 585032832 585033451 1.100000e-113 422.0
18 TraesCS3B01G370100 chr3A 97.487 199 5 0 7085 7283 585028707 585028509 3.180000e-89 340.0
19 TraesCS3B01G370100 chr3A 93.720 207 11 2 3935 4140 585031730 585031525 8.970000e-80 309.0
20 TraesCS3B01G370100 chr3A 82.432 370 38 13 4271 4615 585030277 585029910 1.940000e-76 298.0
21 TraesCS3B01G370100 chr3A 92.093 215 7 3 4403 4615 585031428 585031222 2.510000e-75 294.0
22 TraesCS3B01G370100 chr3A 76.101 636 97 30 4873 5490 585029678 585030276 1.960000e-71 281.0
23 TraesCS3B01G370100 chr3A 88.614 202 17 3 8996 9197 585026557 585026362 3.320000e-59 241.0
24 TraesCS3B01G370100 chr3A 77.419 248 36 15 5826 6065 585032124 585032359 7.490000e-26 130.0
25 TraesCS3B01G370100 chr3A 97.143 35 1 0 7249 7283 585028598 585028564 9.970000e-05 60.2
26 TraesCS3B01G370100 chr3D 94.577 1254 49 10 7716 8952 444063773 444062522 0.000000e+00 1921.0
27 TraesCS3B01G370100 chr3D 88.668 1456 78 30 783 2187 444073067 444071648 0.000000e+00 1694.0
28 TraesCS3B01G370100 chr3D 93.532 804 46 4 6285 7085 444067036 444066236 0.000000e+00 1192.0
29 TraesCS3B01G370100 chr3D 92.477 771 45 5 1 764 444074851 444074087 0.000000e+00 1090.0
30 TraesCS3B01G370100 chr3D 96.406 640 22 1 7085 7723 444066280 444065641 0.000000e+00 1053.0
31 TraesCS3B01G370100 chr3D 91.200 625 39 5 4873 5489 444069955 444069339 0.000000e+00 835.0
32 TraesCS3B01G370100 chr3D 92.222 450 31 4 5829 6274 444067541 444067092 1.300000e-177 634.0
33 TraesCS3B01G370100 chr3D 81.443 679 94 13 2469 3130 444066197 444066860 2.270000e-145 527.0
34 TraesCS3B01G370100 chr3D 79.919 742 105 23 2413 3137 444071130 444070416 1.070000e-138 505.0
35 TraesCS3B01G370100 chr3D 92.114 317 17 4 5484 5793 444069307 444068992 3.050000e-119 440.0
36 TraesCS3B01G370100 chr3D 95.152 165 8 0 2180 2344 445035556 445035720 2.550000e-65 261.0
37 TraesCS3B01G370100 chr3D 93.056 144 9 1 9054 9197 444062473 444062331 9.360000e-50 209.0
38 TraesCS3B01G370100 chr3D 82.743 226 24 9 4611 4821 444067506 444067281 4.380000e-43 187.0
39 TraesCS3B01G370100 chr3D 96.154 52 2 0 5777 5828 444067620 444067569 1.650000e-12 86.1
40 TraesCS3B01G370100 chr3D 97.143 35 1 0 7249 7283 444066171 444066137 9.970000e-05 60.2
41 TraesCS3B01G370100 chr4B 95.266 169 8 0 2180 2348 135218213 135218045 1.520000e-67 268.0
42 TraesCS3B01G370100 chr4D 95.181 166 8 0 2183 2348 12520301 12520136 7.080000e-66 263.0
43 TraesCS3B01G370100 chr4D 95.181 166 6 2 2180 2345 505988108 505987945 2.550000e-65 261.0
44 TraesCS3B01G370100 chr4D 87.654 81 9 1 7334 7414 388390962 388390883 9.830000e-15 93.5
45 TraesCS3B01G370100 chr4D 86.207 87 6 6 7334 7414 461433972 461434058 1.270000e-13 89.8
46 TraesCS3B01G370100 chr6B 94.611 167 9 0 2181 2347 720912054 720912220 9.160000e-65 259.0
47 TraesCS3B01G370100 chr6B 91.304 69 5 1 7334 7402 343030906 343030973 9.830000e-15 93.5
48 TraesCS3B01G370100 chr5D 94.578 166 9 0 2179 2344 230416996 230416831 3.290000e-64 257.0
49 TraesCS3B01G370100 chr5D 90.278 72 7 0 7332 7403 89377612 89377541 2.730000e-15 95.3
50 TraesCS3B01G370100 chr2D 93.642 173 9 2 2183 2354 362930969 362930798 3.290000e-64 257.0
51 TraesCS3B01G370100 chr2D 93.605 172 10 1 2173 2344 624881776 624881946 1.190000e-63 255.0
52 TraesCS3B01G370100 chr7B 86.585 82 10 1 7334 7415 210161536 210161456 1.270000e-13 89.8
53 TraesCS3B01G370100 chr5B 86.585 82 10 1 7334 7414 223689827 223689908 1.270000e-13 89.8


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 TraesCS3B01G370100 chr3B 581967909 581977105 9196 True 16984.000000 16984 100.000000 1 9197 1 chr3B.!!$R2 9196
1 TraesCS3B01G370100 chr3B 581969977 581972835 2858 True 262.350000 446 89.577000 4271 7129 4 chr3B.!!$R3 2858
2 TraesCS3B01G370100 chr3B 581970021 581974598 4577 False 255.440000 420 82.213200 2508 7085 5 chr3B.!!$F1 4577
3 TraesCS3B01G370100 chr3A 585026362 585037448 11086 True 1150.016667 4228 92.959667 1 9197 12 chr3A.!!$R1 9196
4 TraesCS3B01G370100 chr3A 585029678 585033451 3773 False 277.666667 422 77.662333 4873 7085 3 chr3A.!!$F1 2212
5 TraesCS3B01G370100 chr3D 444062331 444074851 12520 True 762.023077 1921 91.554692 1 9197 13 chr3D.!!$R1 9196
6 TraesCS3B01G370100 chr3D 444066197 444066860 663 False 527.000000 527 81.443000 2469 3130 1 chr3D.!!$F1 661

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
583 590 0.534203 TGCCTCAGACGTTTGGAACC 60.534 55.0 6.21 0.00 0.00 3.62 F
1196 2729 0.554792 CAATCCCAGCCCTCATCCTT 59.445 55.0 0.00 0.00 0.00 3.36 F
1726 3260 0.317160 CCTGAACTGACCGTAGCACA 59.683 55.0 0.00 0.00 0.00 4.57 F
3023 5046 0.248661 CAATCTGGAGCGACGACGAT 60.249 55.0 12.29 4.03 42.66 3.73 F
3783 5912 0.772124 TGCCCTTTCCTCCTCAACCT 60.772 55.0 0.00 0.00 0.00 3.50 F
4255 6670 0.319728 CATAGTAGCAGCGCTGGGAT 59.680 55.0 36.47 15.29 40.10 3.85 F
4256 6671 0.319728 ATAGTAGCAGCGCTGGGATG 59.680 55.0 36.47 14.52 40.10 3.51 F
7461 13346 0.815734 CCGTCCTGTCGTATGAAGGT 59.184 55.0 10.90 0.00 32.59 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 3238 0.889306 GCTACGGTCAGTTCAGGACT 59.111 55.000 0.0 0.0 39.89 3.85 R
3005 5028 0.248661 CATCGTCGTCGCTCCAGATT 60.249 55.000 0.0 0.0 36.96 2.40 R
3262 5338 1.746470 TCGAGTCCGTCAAGCATCTA 58.254 50.000 0.0 0.0 37.05 1.98 R
4207 6622 0.038744 CCTTCTGAGGTGGGCATTGT 59.961 55.000 0.0 0.0 38.32 2.71 R
7199 13029 6.603201 ACTTTGTCAGATATGGTTGTATTGGG 59.397 38.462 0.0 0.0 0.00 4.12 R
7441 13326 0.527817 CCTTCATACGACAGGACGGC 60.528 60.000 0.0 0.0 37.61 5.68 R
7469 13354 5.906073 AGCTGCTTCACAAGTTTGTATTTT 58.094 33.333 0.0 0.0 39.91 1.82 R
9120 17079 0.526524 CCGAGACCGAGTGAATGAGC 60.527 60.000 0.0 0.0 38.22 4.26 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
24 25 1.722011 ACCGAGTTATCAGTTTGGCG 58.278 50.000 0.00 0.00 0.00 5.69
46 47 4.201666 CGTTCACATGGGTTGTTTGTTTTG 60.202 41.667 0.00 0.00 36.00 2.44
165 166 2.404693 CGTTGATTTGAACATGTTGCCG 59.595 45.455 17.58 2.53 0.00 5.69
181 182 1.221840 CCGTTCTGGCATGGCTACT 59.778 57.895 21.08 0.00 0.00 2.57
194 195 4.154918 GCATGGCTACTGGTTTATAGATGC 59.845 45.833 0.00 0.00 0.00 3.91
199 200 4.040461 GCTACTGGTTTATAGATGCCCTCA 59.960 45.833 0.00 0.00 0.00 3.86
201 202 4.978099 ACTGGTTTATAGATGCCCTCATG 58.022 43.478 0.00 0.00 31.96 3.07
208 209 0.846693 AGATGCCCTCATGTAACCCC 59.153 55.000 0.00 0.00 31.96 4.95
213 214 1.522900 CCCTCATGTAACCCCCTCAT 58.477 55.000 0.00 0.00 0.00 2.90
218 219 2.771943 TCATGTAACCCCCTCATCAGAC 59.228 50.000 0.00 0.00 0.00 3.51
226 227 2.224305 CCCCCTCATCAGACGGTTAATC 60.224 54.545 0.00 0.00 0.00 1.75
227 228 2.434336 CCCCTCATCAGACGGTTAATCA 59.566 50.000 0.00 0.00 0.00 2.57
228 229 3.493350 CCCCTCATCAGACGGTTAATCAG 60.493 52.174 0.00 0.00 0.00 2.90
229 230 3.133003 CCCTCATCAGACGGTTAATCAGT 59.867 47.826 0.00 0.00 0.00 3.41
343 344 5.568685 TGAGGAAGAGATGACTAACTTCG 57.431 43.478 0.00 0.00 39.39 3.79
359 360 0.889186 TTCGCCCACTCCAAGAAAGC 60.889 55.000 0.00 0.00 0.00 3.51
376 377 2.464459 GCCGAATCCGACAGGCTTG 61.464 63.158 0.00 0.00 45.67 4.01
410 411 3.439857 ACATAACACATCAAGCAGGGT 57.560 42.857 0.00 0.00 0.00 4.34
571 578 8.360390 TGTTGTATACTGTATTATCTGCCTCAG 58.640 37.037 5.52 0.00 0.00 3.35
583 590 0.534203 TGCCTCAGACGTTTGGAACC 60.534 55.000 6.21 0.00 0.00 3.62
636 643 4.154195 GCTCGCTTAGGATCTTTGTTTGAA 59.846 41.667 0.00 0.00 0.00 2.69
647 654 7.182930 AGGATCTTTGTTTGAATAGTCTAGGGT 59.817 37.037 0.00 0.00 0.00 4.34
708 716 9.440761 ACTGATCTTACTAAATGGTCTCCTATT 57.559 33.333 0.00 0.00 0.00 1.73
728 736 3.907894 TTTAGTTGGTGATTGGTTCGC 57.092 42.857 0.00 0.00 0.00 4.70
736 744 3.055458 TGGTGATTGGTTCGCTCAGATTA 60.055 43.478 0.00 0.00 35.11 1.75
737 745 4.130118 GGTGATTGGTTCGCTCAGATTAT 58.870 43.478 0.00 0.00 35.11 1.28
742 750 2.139118 GGTTCGCTCAGATTATGCTCC 58.861 52.381 0.00 0.00 0.00 4.70
745 753 1.342496 TCGCTCAGATTATGCTCCTGG 59.658 52.381 0.00 0.00 0.00 4.45
746 754 1.342496 CGCTCAGATTATGCTCCTGGA 59.658 52.381 0.00 0.00 0.00 3.86
750 873 5.177326 GCTCAGATTATGCTCCTGGATTAG 58.823 45.833 0.00 0.00 0.00 1.73
764 2245 4.220602 CCTGGATTAGGTTTTTGGGTTCAG 59.779 45.833 0.00 0.00 42.00 3.02
792 2273 3.182967 CAGTACTGCAGATCGAAAGTCC 58.817 50.000 23.35 0.00 0.00 3.85
793 2274 2.826128 AGTACTGCAGATCGAAAGTCCA 59.174 45.455 23.35 0.00 0.00 4.02
931 2464 4.587684 GCATAGCCTACCTACCTTTCTACA 59.412 45.833 0.00 0.00 0.00 2.74
963 2496 1.744368 CTCTGTTGCTGCATCCGCT 60.744 57.895 1.84 0.00 39.64 5.52
1193 2726 1.152368 CCCAATCCCAGCCCTCATC 59.848 63.158 0.00 0.00 0.00 2.92
1194 2727 1.152368 CCAATCCCAGCCCTCATCC 59.848 63.158 0.00 0.00 0.00 3.51
1195 2728 1.358830 CCAATCCCAGCCCTCATCCT 61.359 60.000 0.00 0.00 0.00 3.24
1196 2729 0.554792 CAATCCCAGCCCTCATCCTT 59.445 55.000 0.00 0.00 0.00 3.36
1197 2730 0.849417 AATCCCAGCCCTCATCCTTC 59.151 55.000 0.00 0.00 0.00 3.46
1198 2731 1.064824 ATCCCAGCCCTCATCCTTCC 61.065 60.000 0.00 0.00 0.00 3.46
1199 2732 2.761465 CCCAGCCCTCATCCTTCCC 61.761 68.421 0.00 0.00 0.00 3.97
1200 2733 2.761465 CCAGCCCTCATCCTTCCCC 61.761 68.421 0.00 0.00 0.00 4.81
1256 2789 1.938585 TCCCTCTACAGGACCAAGTG 58.061 55.000 0.00 0.00 43.65 3.16
1273 2806 2.114411 GGTTTTCCGTCCCTGCCA 59.886 61.111 0.00 0.00 0.00 4.92
1327 2861 3.038417 GCGCGTGACTTGTGCTCT 61.038 61.111 8.43 0.00 39.67 4.09
1399 2933 4.051167 TGTACGAGGCGGAGGGGA 62.051 66.667 0.00 0.00 0.00 4.81
1467 3001 2.352032 CGCCGAGGGGGATAGGATC 61.352 68.421 0.00 0.00 37.91 3.36
1519 3053 1.889530 GAGGGTCAGGTCGGTTCTGG 61.890 65.000 0.00 0.00 33.36 3.86
1527 3061 0.613777 GGTCGGTTCTGGTTCCTCAT 59.386 55.000 0.00 0.00 0.00 2.90
1544 3078 5.545588 TCCTCATCTGTGTTTCTTCTTCTG 58.454 41.667 0.00 0.00 0.00 3.02
1583 3117 8.189709 TCTTGATGCTATAAATCATATGCGAC 57.810 34.615 0.00 0.00 34.14 5.19
1665 3199 3.487544 GGAATTATCTGAAGTTGGCACGC 60.488 47.826 0.00 0.00 0.00 5.34
1666 3200 1.448985 TTATCTGAAGTTGGCACGCC 58.551 50.000 0.00 0.00 0.00 5.68
1725 3259 0.601558 TCCTGAACTGACCGTAGCAC 59.398 55.000 0.00 0.00 0.00 4.40
1726 3260 0.317160 CCTGAACTGACCGTAGCACA 59.683 55.000 0.00 0.00 0.00 4.57
1791 3325 4.902443 TCCATTGAGCTACTTCTCTACG 57.098 45.455 0.00 0.00 34.29 3.51
2026 3570 2.586425 CTGCCTTTGGACCTGAAAAGA 58.414 47.619 4.70 0.00 35.79 2.52
2036 3580 9.987272 CTTTGGACCTGAAAAGAGAAAATTATT 57.013 29.630 0.00 0.00 35.79 1.40
2192 3738 2.258109 GGAACAGTTGTACTCCCTCCT 58.742 52.381 0.00 0.00 0.00 3.69
2380 3927 1.000270 TGGCCTGTTGTGGTTGTGT 60.000 52.632 3.32 0.00 0.00 3.72
2444 4444 2.502130 TGGGTAGTGTTGAGTTGTCACA 59.498 45.455 0.00 0.00 34.94 3.58
2626 4632 4.938832 TGGTAATTAGAACCATGTCAACCG 59.061 41.667 0.00 0.00 42.10 4.44
2678 4684 4.007644 CTGTCACCAGCGAGGGCA 62.008 66.667 3.26 0.00 43.89 5.36
2808 4830 2.756283 CCGCCTCCTCTTCGGTCT 60.756 66.667 0.00 0.00 38.47 3.85
2809 4831 2.776913 CCGCCTCCTCTTCGGTCTC 61.777 68.421 0.00 0.00 38.47 3.36
2815 4837 0.322636 TCCTCTTCGGTCTCGCTCTT 60.323 55.000 0.00 0.00 36.13 2.85
2822 4844 1.375268 GGTCTCGCTCTTTGCTGCT 60.375 57.895 0.00 0.00 40.11 4.24
2915 4937 4.276926 GCTCTTGACAACACCAATTTCTCT 59.723 41.667 0.00 0.00 0.00 3.10
2959 4981 1.136305 GTTACTCAGCCGCTACCATGA 59.864 52.381 0.00 0.00 0.00 3.07
2964 4986 3.573491 GCCGCTACCATGAACGCC 61.573 66.667 0.00 0.00 0.00 5.68
3005 5028 1.480954 GTTGACCGGCTCTCTAATCCA 59.519 52.381 0.00 0.00 0.00 3.41
3023 5046 0.248661 CAATCTGGAGCGACGACGAT 60.249 55.000 12.29 4.03 42.66 3.73
3122 5160 3.331889 ACACAATTTGGACTCTCCTCCAT 59.668 43.478 0.78 0.00 40.18 3.41
3128 5166 3.019799 TGGACTCTCCTCCATGAGTAC 57.980 52.381 0.00 0.00 42.79 2.73
3129 5167 2.583101 TGGACTCTCCTCCATGAGTACT 59.417 50.000 0.00 0.00 42.86 2.73
3130 5168 3.011821 TGGACTCTCCTCCATGAGTACTT 59.988 47.826 0.00 0.00 42.86 2.24
3262 5338 3.748048 CAGCTACTGCACACTTACATTGT 59.252 43.478 0.00 0.00 42.74 2.71
3320 5396 0.947244 GCCGCGATTCTCCAATTGAT 59.053 50.000 8.23 0.00 0.00 2.57
3348 5424 3.562176 CCCTGCCTACCTTTGTTCAAGAT 60.562 47.826 0.00 0.00 33.80 2.40
3366 5442 6.003326 TCAAGATTGTTCATGCCTTGTTCTA 58.997 36.000 0.00 0.00 36.53 2.10
3384 5460 3.242867 TCTAGCCGGAATCTCCATCAAT 58.757 45.455 5.05 0.00 35.91 2.57
3386 5462 3.692257 AGCCGGAATCTCCATCAATAG 57.308 47.619 5.05 0.00 35.91 1.73
3495 5571 4.256180 GGCGATCGGGCTCCCAAT 62.256 66.667 18.30 0.00 38.40 3.16
3620 5741 4.802051 CCCCGCACACCCTGGATG 62.802 72.222 0.00 0.00 0.00 3.51
3783 5912 0.772124 TGCCCTTTCCTCCTCAACCT 60.772 55.000 0.00 0.00 0.00 3.50
3898 6027 2.039327 TATCGTTGTTGGCAAAACGC 57.961 45.000 27.31 9.76 46.60 4.84
3909 6038 2.368655 GCAAAACGCCTTCCAATCAT 57.631 45.000 0.00 0.00 32.94 2.45
3910 6039 2.687370 GCAAAACGCCTTCCAATCATT 58.313 42.857 0.00 0.00 32.94 2.57
3911 6040 2.412770 GCAAAACGCCTTCCAATCATTG 59.587 45.455 0.00 0.00 32.94 2.82
3912 6041 4.711397 GCAAAACGCCTTCCAATCATTGG 61.711 47.826 10.56 10.56 43.31 3.16
3914 6043 7.794542 GCAAAACGCCTTCCAATCATTGGTA 62.795 44.000 16.42 5.91 42.81 3.25
3920 6049 3.494850 CCAATCATTGGTACCGGCT 57.505 52.632 8.44 0.00 45.93 5.52
3921 6050 1.308998 CCAATCATTGGTACCGGCTC 58.691 55.000 8.44 0.00 45.93 4.70
3922 6051 1.408127 CCAATCATTGGTACCGGCTCA 60.408 52.381 8.44 0.00 45.93 4.26
3973 6369 9.974980 TCCCAATCTTGTCAAAAATTAGTTTAC 57.025 29.630 0.00 0.00 0.00 2.01
4004 6401 7.962918 GCAAATTTACTCGTGACAATCTATGTT 59.037 33.333 0.00 0.00 44.12 2.71
4026 6423 5.186996 TCAGTTGAGTTTCATCCTTTTGC 57.813 39.130 0.00 0.00 0.00 3.68
4038 6435 1.202359 TCCTTTTGCCTTTTGCGTGAC 60.202 47.619 0.00 0.00 45.60 3.67
4075 6472 3.195396 GGGCAAATCTTCAATAGCCACAA 59.805 43.478 0.00 0.00 43.72 3.33
4093 6491 6.535508 AGCCACAACGACTTATATTTCTTCTC 59.464 38.462 0.00 0.00 0.00 2.87
4133 6531 3.610040 TCATCATTAGCACTCACCGTT 57.390 42.857 0.00 0.00 0.00 4.44
4176 6591 3.829026 TCGATTCTGCTACTATGGCTCAT 59.171 43.478 0.00 0.00 0.00 2.90
4177 6592 4.281941 TCGATTCTGCTACTATGGCTCATT 59.718 41.667 0.00 0.00 0.00 2.57
4179 6594 5.468072 CGATTCTGCTACTATGGCTCATTTT 59.532 40.000 0.00 0.00 0.00 1.82
4181 6596 3.879295 TCTGCTACTATGGCTCATTTTGC 59.121 43.478 0.00 0.00 0.00 3.68
4182 6597 3.881688 CTGCTACTATGGCTCATTTTGCT 59.118 43.478 0.00 0.00 0.00 3.91
4183 6598 4.272489 TGCTACTATGGCTCATTTTGCTT 58.728 39.130 0.00 0.00 0.00 3.91
4186 6601 2.684881 ACTATGGCTCATTTTGCTTCGG 59.315 45.455 0.00 0.00 0.00 4.30
4187 6602 1.838112 ATGGCTCATTTTGCTTCGGA 58.162 45.000 0.00 0.00 0.00 4.55
4188 6603 1.838112 TGGCTCATTTTGCTTCGGAT 58.162 45.000 0.00 0.00 0.00 4.18
4189 6604 2.170166 TGGCTCATTTTGCTTCGGATT 58.830 42.857 0.00 0.00 0.00 3.01
4190 6605 2.562298 TGGCTCATTTTGCTTCGGATTT 59.438 40.909 0.00 0.00 0.00 2.17
4193 6608 5.167845 GGCTCATTTTGCTTCGGATTTTTA 58.832 37.500 0.00 0.00 0.00 1.52
4196 6611 6.753744 GCTCATTTTGCTTCGGATTTTTATCT 59.246 34.615 0.00 0.00 0.00 1.98
4197 6612 7.276438 GCTCATTTTGCTTCGGATTTTTATCTT 59.724 33.333 0.00 0.00 0.00 2.40
4198 6613 8.464770 TCATTTTGCTTCGGATTTTTATCTTG 57.535 30.769 0.00 0.00 0.00 3.02
4201 6616 9.921637 ATTTTGCTTCGGATTTTTATCTTGTAA 57.078 25.926 0.00 0.00 0.00 2.41
4202 6617 9.921637 TTTTGCTTCGGATTTTTATCTTGTAAT 57.078 25.926 0.00 0.00 0.00 1.89
4216 6631 8.815565 TTATCTTGTAATAAGAACAATGCCCA 57.184 30.769 0.00 0.00 36.33 5.36
4217 6632 6.509418 TCTTGTAATAAGAACAATGCCCAC 57.491 37.500 0.00 0.00 36.33 4.61
4218 6633 5.417580 TCTTGTAATAAGAACAATGCCCACC 59.582 40.000 0.00 0.00 36.33 4.61
4219 6634 4.929479 TGTAATAAGAACAATGCCCACCT 58.071 39.130 0.00 0.00 0.00 4.00
4220 6635 4.947388 TGTAATAAGAACAATGCCCACCTC 59.053 41.667 0.00 0.00 0.00 3.85
4221 6636 3.737559 ATAAGAACAATGCCCACCTCA 57.262 42.857 0.00 0.00 0.00 3.86
4222 6637 1.915141 AAGAACAATGCCCACCTCAG 58.085 50.000 0.00 0.00 0.00 3.35
4223 6638 1.067295 AGAACAATGCCCACCTCAGA 58.933 50.000 0.00 0.00 0.00 3.27
4224 6639 1.425066 AGAACAATGCCCACCTCAGAA 59.575 47.619 0.00 0.00 0.00 3.02
4225 6640 1.815003 GAACAATGCCCACCTCAGAAG 59.185 52.381 0.00 0.00 0.00 2.85
4241 6656 5.435291 CTCAGAAGGAAAATGAGCCATAGT 58.565 41.667 0.00 0.00 34.55 2.12
4242 6657 6.408548 CCTCAGAAGGAAAATGAGCCATAGTA 60.409 42.308 0.00 0.00 46.67 1.82
4243 6658 6.586344 TCAGAAGGAAAATGAGCCATAGTAG 58.414 40.000 0.00 0.00 0.00 2.57
4244 6659 5.238214 CAGAAGGAAAATGAGCCATAGTAGC 59.762 44.000 0.00 0.00 0.00 3.58
4245 6660 4.778213 AGGAAAATGAGCCATAGTAGCA 57.222 40.909 0.00 0.00 0.00 3.49
4246 6661 4.712476 AGGAAAATGAGCCATAGTAGCAG 58.288 43.478 0.00 0.00 0.00 4.24
4247 6662 3.251972 GGAAAATGAGCCATAGTAGCAGC 59.748 47.826 0.00 0.00 0.00 5.25
4248 6663 2.160822 AATGAGCCATAGTAGCAGCG 57.839 50.000 0.00 0.00 0.00 5.18
4249 6664 0.320247 ATGAGCCATAGTAGCAGCGC 60.320 55.000 0.00 0.00 0.00 5.92
4250 6665 1.365633 GAGCCATAGTAGCAGCGCT 59.634 57.895 2.64 2.64 43.41 5.92
4251 6666 0.943359 GAGCCATAGTAGCAGCGCTG 60.943 60.000 32.83 32.83 40.10 5.18
4252 6667 1.958205 GCCATAGTAGCAGCGCTGG 60.958 63.158 36.47 20.53 40.10 4.85
4253 6668 1.301244 CCATAGTAGCAGCGCTGGG 60.301 63.158 36.47 23.56 40.10 4.45
4254 6669 1.742146 CATAGTAGCAGCGCTGGGA 59.258 57.895 36.47 0.00 40.10 4.37
4255 6670 0.319728 CATAGTAGCAGCGCTGGGAT 59.680 55.000 36.47 15.29 40.10 3.85
4256 6671 0.319728 ATAGTAGCAGCGCTGGGATG 59.680 55.000 36.47 14.52 40.10 3.51
4257 6672 1.748329 TAGTAGCAGCGCTGGGATGG 61.748 60.000 36.47 12.81 40.10 3.51
4258 6673 4.552365 TAGCAGCGCTGGGATGGC 62.552 66.667 36.47 22.24 40.10 4.40
4262 6677 4.809496 AGCGCTGGGATGGCCAAG 62.809 66.667 10.96 2.94 38.37 3.61
4264 6679 2.361610 CGCTGGGATGGCCAAGTT 60.362 61.111 10.96 0.00 37.56 2.66
4265 6680 2.703798 CGCTGGGATGGCCAAGTTG 61.704 63.158 10.96 0.00 37.56 3.16
4266 6681 3.010413 GCTGGGATGGCCAAGTTGC 62.010 63.158 10.96 7.48 37.56 4.17
7199 13029 2.287915 ACGTGACAACTCAACATTCAGC 59.712 45.455 0.00 0.00 0.00 4.26
7313 13198 5.251932 TGACCCCTTCACCAATTCTTACATA 59.748 40.000 0.00 0.00 0.00 2.29
7441 13326 2.099431 GCTTCAGTGGCTCGAGCTG 61.099 63.158 34.46 25.19 41.70 4.24
7461 13346 0.815734 CCGTCCTGTCGTATGAAGGT 59.184 55.000 10.90 0.00 32.59 3.50
7469 13354 4.556233 CTGTCGTATGAAGGTGACAAGAA 58.444 43.478 0.00 0.00 40.50 2.52
7537 13422 5.252969 ACAATGCTTATGAATGCAATCGT 57.747 34.783 1.40 1.40 42.74 3.73
7538 13423 5.038683 ACAATGCTTATGAATGCAATCGTG 58.961 37.500 6.75 0.00 42.74 4.35
7584 13470 9.944376 ATTGATGTCTTAACATACTTGTACAGT 57.056 29.630 0.00 0.00 46.20 3.55
7629 13517 5.303971 AGTTCAGCAGGCAATAAGCTATAG 58.696 41.667 0.00 0.00 44.79 1.31
7701 13589 0.250901 TTCTCAGCCAGGGAAACTGC 60.251 55.000 0.00 0.00 46.14 4.40
7994 15769 7.334421 ACAAGAATGCTTACGTATGTGATCTTT 59.666 33.333 9.88 0.00 31.81 2.52
8020 15795 9.342308 TGATTTTGGTAAAATTGCAAATGGTTA 57.658 25.926 1.71 0.00 40.97 2.85
8053 15829 4.695455 GCCTCACTATAGTTGTGCTTTTGA 59.305 41.667 1.56 0.00 35.58 2.69
8055 15831 6.676456 GCCTCACTATAGTTGTGCTTTTGATG 60.676 42.308 1.56 0.00 35.58 3.07
8094 15871 5.350091 GGAGAAGCTCAAGTTGAATGAGTAC 59.650 44.000 7.06 0.00 44.88 2.73
8115 15892 0.610174 AGGAAGCATTGAGACGAGCA 59.390 50.000 0.00 0.00 0.00 4.26
8137 15914 8.418597 AGCAAAATATCATCCTATGCAGAATT 57.581 30.769 0.00 0.00 34.89 2.17
8197 15974 5.992217 GCAAAGAGGAAGAGACTGAAGTAAA 59.008 40.000 0.00 0.00 0.00 2.01
8239 16017 2.507407 TCATTTGCCTCAAGGTACCC 57.493 50.000 8.74 0.00 37.57 3.69
8244 16022 2.047769 TGCCTCAAGGTACCCCTAAA 57.952 50.000 8.74 0.00 41.56 1.85
8343 16121 3.676873 GCATTCATCCTCGGCACATTTTT 60.677 43.478 0.00 0.00 0.00 1.94
8372 16150 5.929058 AGATAGAAGAGCATTGTGTCTCA 57.071 39.130 0.00 0.00 0.00 3.27
8457 16236 0.825410 TATGCGGCCTTTCGGAACTA 59.175 50.000 0.00 0.00 33.58 2.24
8497 16277 4.370364 TTCTTCAACCTTTTGTGCAGAC 57.630 40.909 0.00 0.00 34.02 3.51
8619 16402 1.348250 GCACATGATGTACGTGGCG 59.652 57.895 0.00 0.00 39.59 5.69
8648 16432 4.437930 CCTTTCCAGCAGAATGAACGAATC 60.438 45.833 0.00 0.00 39.69 2.52
8711 16495 2.295253 TTTCTTTTGGCGGCGAAAAA 57.705 40.000 23.09 15.35 0.00 1.94
8714 16498 0.873743 CTTTTGGCGGCGAAAAAGCA 60.874 50.000 25.00 3.16 36.79 3.91
8751 16535 3.118629 TGCTGCCGAGAGAATGTTATTCT 60.119 43.478 3.86 3.86 0.00 2.40
8847 16632 2.664851 TGCTTGGCCGTCACGAAG 60.665 61.111 0.00 0.00 0.00 3.79
8864 16649 2.280592 GTTGTGGGCGGTCGACTT 60.281 61.111 16.46 0.00 0.00 3.01
8923 16712 0.588252 CAGCTGACCGTTGGTTTCTG 59.412 55.000 8.42 0.00 35.25 3.02
8925 16714 1.515521 GCTGACCGTTGGTTTCTGGG 61.516 60.000 0.00 0.00 35.25 4.45
8965 16754 0.036732 TTGGCTCGGTGCTCTTCATT 59.963 50.000 1.77 0.00 42.39 2.57
8975 16764 1.687660 TGCTCTTCATTTTGCCTTGCA 59.312 42.857 0.00 0.00 36.47 4.08
8994 16783 2.231235 GCATTTCGGGTTTGGAGATGTT 59.769 45.455 0.00 0.00 30.88 2.71
9010 16969 8.217131 TGGAGATGTTCTCATTCATTTGTATG 57.783 34.615 6.83 0.00 45.12 2.39
9028 16987 4.641541 TGTATGCTAGTACTAAGCGGTCAA 59.358 41.667 3.76 0.00 0.00 3.18
9032 16991 4.334759 TGCTAGTACTAAGCGGTCAACTAG 59.665 45.833 3.76 15.56 39.46 2.57
9033 16992 3.779271 AGTACTAAGCGGTCAACTAGC 57.221 47.619 0.00 0.00 0.00 3.42
9042 17001 2.159558 GCGGTCAACTAGCCTTAAAAGC 60.160 50.000 0.00 0.00 0.00 3.51
9056 17015 1.755179 AAAAGCATCCTCGTCCATGG 58.245 50.000 4.97 4.97 0.00 3.66
9106 17065 8.360390 ACCTTTTGTGACTCTTAATTTGGATTC 58.640 33.333 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.932200 TCAAAACAAACAACCCATGTGAAC 59.068 37.500 0.00 0.00 42.99 3.18
46 47 1.197721 CTGACGAAATGCCAACCTGTC 59.802 52.381 0.00 0.00 0.00 3.51
165 166 0.035056 ACCAGTAGCCATGCCAGAAC 60.035 55.000 0.00 0.00 0.00 3.01
181 182 6.296026 GTTACATGAGGGCATCTATAAACCA 58.704 40.000 0.00 0.00 30.68 3.67
194 195 1.421646 GATGAGGGGGTTACATGAGGG 59.578 57.143 0.00 0.00 0.00 4.30
199 200 1.762957 CGTCTGATGAGGGGGTTACAT 59.237 52.381 0.00 0.00 0.00 2.29
201 202 0.464452 CCGTCTGATGAGGGGGTTAC 59.536 60.000 0.00 0.00 42.71 2.50
208 209 4.115516 CACTGATTAACCGTCTGATGAGG 58.884 47.826 0.00 0.00 0.00 3.86
213 214 4.219725 TCATGTCACTGATTAACCGTCTGA 59.780 41.667 0.00 0.00 0.00 3.27
218 219 5.512788 GCAAATTCATGTCACTGATTAACCG 59.487 40.000 0.00 0.00 0.00 4.44
226 227 3.928727 ACCTGCAAATTCATGTCACTG 57.071 42.857 0.00 0.00 0.00 3.66
227 228 5.948162 AGATAACCTGCAAATTCATGTCACT 59.052 36.000 0.00 0.00 0.00 3.41
228 229 6.199937 AGATAACCTGCAAATTCATGTCAC 57.800 37.500 0.00 0.00 0.00 3.67
229 230 6.127647 GGAAGATAACCTGCAAATTCATGTCA 60.128 38.462 0.00 0.00 0.00 3.58
343 344 2.335712 CGGCTTTCTTGGAGTGGGC 61.336 63.158 0.00 0.00 0.00 5.36
359 360 2.464459 GCAAGCCTGTCGGATTCGG 61.464 63.158 0.00 0.00 36.62 4.30
376 377 3.670055 GTGTTATGTTTGTCATGCTGTGC 59.330 43.478 0.00 0.00 37.91 4.57
410 411 1.207089 CCGGAGCATTCTACACCTCAA 59.793 52.381 0.00 0.00 0.00 3.02
571 578 0.814812 TTCACCGGGTTCCAAACGTC 60.815 55.000 6.32 0.00 0.00 4.34
583 590 0.957395 AGCTCTGCATGTTTCACCGG 60.957 55.000 0.00 0.00 0.00 5.28
614 621 5.862924 TTCAAACAAAGATCCTAAGCGAG 57.137 39.130 0.00 0.00 0.00 5.03
636 643 6.043938 TCTGTTTTGTTCCAACCCTAGACTAT 59.956 38.462 0.00 0.00 0.00 2.12
647 654 6.522625 TGACAAATCTCTGTTTTGTTCCAA 57.477 33.333 3.59 0.00 44.90 3.53
663 671 9.848710 AGATCAGTCAAATATCAGATGACAAAT 57.151 29.630 7.75 1.14 44.55 2.32
664 672 9.676861 AAGATCAGTCAAATATCAGATGACAAA 57.323 29.630 7.75 0.00 44.55 2.83
708 716 3.482436 AGCGAACCAATCACCAACTAAA 58.518 40.909 0.00 0.00 0.00 1.85
742 750 5.048013 GTCTGAACCCAAAAACCTAATCCAG 60.048 44.000 0.00 0.00 0.00 3.86
745 753 5.386958 GGTCTGAACCCAAAAACCTAATC 57.613 43.478 0.00 0.00 39.93 1.75
771 2252 3.182967 GGACTTTCGATCTGCAGTACTG 58.817 50.000 18.93 18.93 0.00 2.74
784 2265 3.674423 GAATGAGCGATTTGGACTTTCG 58.326 45.455 0.00 0.00 36.02 3.46
785 2266 3.125316 ACGAATGAGCGATTTGGACTTTC 59.875 43.478 0.00 0.00 34.83 2.62
788 2269 2.002586 CACGAATGAGCGATTTGGACT 58.997 47.619 0.00 0.00 34.83 3.85
789 2270 1.062587 CCACGAATGAGCGATTTGGAC 59.937 52.381 0.00 0.00 34.83 4.02
790 2271 1.368641 CCACGAATGAGCGATTTGGA 58.631 50.000 0.00 0.00 34.83 3.53
791 2272 0.378257 CCCACGAATGAGCGATTTGG 59.622 55.000 0.00 0.00 34.83 3.28
792 2273 1.062587 GTCCCACGAATGAGCGATTTG 59.937 52.381 0.00 0.00 34.83 2.32
793 2274 1.369625 GTCCCACGAATGAGCGATTT 58.630 50.000 0.00 0.00 34.83 2.17
816 2310 1.750399 CCAAATCGGTCCCTGCCAG 60.750 63.158 0.00 0.00 0.00 4.85
817 2311 2.354729 CCAAATCGGTCCCTGCCA 59.645 61.111 0.00 0.00 0.00 4.92
842 2337 2.856720 GCGAGCTAGAGAAATCAGGACG 60.857 54.545 0.00 0.00 0.00 4.79
878 2374 3.494336 CTTCGCTGCAGGCCTTCG 61.494 66.667 17.12 10.15 37.74 3.79
942 2475 2.413142 GGATGCAGCAACAGAGGCC 61.413 63.158 3.51 0.00 0.00 5.19
1008 2541 2.518587 TCGTCGGGCAGATCGGAT 60.519 61.111 0.00 0.00 0.00 4.18
1152 2685 2.756283 AAGTCGCGGGAGAGGAGG 60.756 66.667 6.13 0.00 0.00 4.30
1193 2726 1.045911 CGAAGAGGAGGAGGGGAAGG 61.046 65.000 0.00 0.00 0.00 3.46
1194 2727 1.681486 GCGAAGAGGAGGAGGGGAAG 61.681 65.000 0.00 0.00 0.00 3.46
1195 2728 1.686110 GCGAAGAGGAGGAGGGGAA 60.686 63.158 0.00 0.00 0.00 3.97
1196 2729 2.042843 GCGAAGAGGAGGAGGGGA 60.043 66.667 0.00 0.00 0.00 4.81
1197 2730 2.364317 TGCGAAGAGGAGGAGGGG 60.364 66.667 0.00 0.00 0.00 4.79
1198 2731 3.087666 GCTGCGAAGAGGAGGAGGG 62.088 68.421 0.00 0.00 38.88 4.30
1199 2732 2.354401 TGCTGCGAAGAGGAGGAGG 61.354 63.158 0.00 0.00 38.88 4.30
1200 2733 3.292656 TGCTGCGAAGAGGAGGAG 58.707 61.111 0.00 0.00 38.88 3.69
1256 2789 2.114411 TGGCAGGGACGGAAAACC 59.886 61.111 0.00 0.00 0.00 3.27
1303 2837 2.429236 AAGTCACGCGCTCTGACG 60.429 61.111 22.21 3.18 42.52 4.35
1304 2838 1.661821 ACAAGTCACGCGCTCTGAC 60.662 57.895 21.42 21.42 38.70 3.51
1305 2839 1.661509 CACAAGTCACGCGCTCTGA 60.662 57.895 5.73 0.00 0.00 3.27
1306 2840 2.849007 CACAAGTCACGCGCTCTG 59.151 61.111 5.73 0.00 0.00 3.35
1307 2841 3.038417 GCACAAGTCACGCGCTCT 61.038 61.111 5.73 0.00 0.00 4.09
1327 2861 2.659016 CCTCTCGAACCTGCAGCA 59.341 61.111 8.66 0.00 0.00 4.41
1519 3053 5.994668 AGAAGAAGAAACACAGATGAGGAAC 59.005 40.000 0.00 0.00 0.00 3.62
1527 3061 4.405680 TCACTCCAGAAGAAGAAACACAGA 59.594 41.667 0.00 0.00 0.00 3.41
1544 3078 3.486542 GCATCAAGAGCGAATTTCACTCC 60.487 47.826 10.14 0.00 0.00 3.85
1583 3117 7.321034 GGTAATTTGTTGTTTTCGGTTACTACG 59.679 37.037 0.00 0.00 0.00 3.51
1594 3128 7.582667 AGCTAGTCAGGTAATTTGTTGTTTT 57.417 32.000 0.00 0.00 0.00 2.43
1665 3199 5.789643 AATTGGATAATTGTCATTCCCGG 57.210 39.130 4.48 0.00 35.26 5.73
1666 3200 7.362920 GGGATAATTGGATAATTGTCATTCCCG 60.363 40.741 4.48 0.00 42.70 5.14
1704 3238 0.889306 GCTACGGTCAGTTCAGGACT 59.111 55.000 0.00 0.00 39.89 3.85
1725 3259 6.467677 AGCAATACCTACTGTTGCCTATATG 58.532 40.000 5.77 0.00 45.71 1.78
1726 3260 6.270000 TGAGCAATACCTACTGTTGCCTATAT 59.730 38.462 5.77 0.00 45.71 0.86
1791 3325 3.539604 ACAATCTCAGTCCAGCTTATGC 58.460 45.455 0.00 0.00 40.05 3.14
2014 3558 9.411801 GTGAAATAATTTTCTCTTTTCAGGTCC 57.588 33.333 0.00 0.00 41.54 4.46
2036 3580 5.255687 ACAACCATAGAGCATTGATGTGAA 58.744 37.500 0.00 0.00 0.00 3.18
2444 4444 6.864685 CAGAAACAATAACACATGTGCAGAAT 59.135 34.615 25.68 10.87 0.00 2.40
2626 4632 3.403558 GGAGGAGTGAGTGGGGCC 61.404 72.222 0.00 0.00 0.00 5.80
2815 4837 4.269523 AAGGGTCGGCAGCAGCAA 62.270 61.111 2.65 0.00 44.61 3.91
2822 4844 2.683933 GAGGAGGAAGGGTCGGCA 60.684 66.667 0.00 0.00 0.00 5.69
2915 4937 2.378445 TGATGAAAGAACGCCATCGA 57.622 45.000 0.00 0.00 39.48 3.59
2959 4981 2.034066 CCTGGATGTGGTGGCGTT 59.966 61.111 0.00 0.00 0.00 4.84
3005 5028 0.248661 CATCGTCGTCGCTCCAGATT 60.249 55.000 0.00 0.00 36.96 2.40
3122 5160 4.345257 ACTCCTGCTTCAAAGAAGTACTCA 59.655 41.667 0.00 0.00 28.94 3.41
3128 5166 3.433615 CCGTAACTCCTGCTTCAAAGAAG 59.566 47.826 2.48 2.48 0.00 2.85
3129 5167 3.399330 CCGTAACTCCTGCTTCAAAGAA 58.601 45.455 0.00 0.00 0.00 2.52
3130 5168 2.870435 GCCGTAACTCCTGCTTCAAAGA 60.870 50.000 0.00 0.00 0.00 2.52
3262 5338 1.746470 TCGAGTCCGTCAAGCATCTA 58.254 50.000 0.00 0.00 37.05 1.98
3320 5396 2.758852 AAAGGTAGGCAGGGGGACGA 62.759 60.000 0.00 0.00 0.00 4.20
3348 5424 2.819608 GGCTAGAACAAGGCATGAACAA 59.180 45.455 0.00 0.00 41.51 2.83
3366 5442 2.304180 CCTATTGATGGAGATTCCGGCT 59.696 50.000 0.00 0.00 40.17 5.52
3408 5484 2.186826 GTGGACGGCAAGCAACTGT 61.187 57.895 0.00 0.00 0.00 3.55
3483 5559 2.609299 TCACCATTGGGAGCCCGA 60.609 61.111 7.78 0.00 39.42 5.14
3620 5741 2.293955 GACCCTAGTAGAGTTGGATCGC 59.706 54.545 0.00 0.00 0.00 4.58
3742 5871 1.081242 CGTGGCTTGGTGCAACATC 60.081 57.895 4.62 0.00 45.76 3.06
3783 5912 1.004628 CCCATGTCCATGAACCACTCA 59.995 52.381 8.82 0.00 41.20 3.41
3909 6038 3.324108 GGGGTGAGCCGGTACCAA 61.324 66.667 21.00 0.00 38.74 3.67
3912 6041 3.468140 GAGGGGGTGAGCCGGTAC 61.468 72.222 1.90 0.00 34.97 3.34
3930 6059 0.175989 GGAGAGATGGAACGGTCACC 59.824 60.000 1.31 0.00 0.00 4.02
3931 6060 0.175989 GGGAGAGATGGAACGGTCAC 59.824 60.000 1.31 0.00 0.00 3.67
3973 6369 1.388768 TCACGAGTAAATTTGCGAGCG 59.611 47.619 14.13 14.05 0.00 5.03
4004 6401 4.037923 GGCAAAAGGATGAAACTCAACTGA 59.962 41.667 0.00 0.00 0.00 3.41
4026 6423 0.320073 TAGGTCCGTCACGCAAAAGG 60.320 55.000 0.00 0.00 0.00 3.11
4038 6435 2.987125 CCCTGGTTGGTAGGTCCG 59.013 66.667 0.00 0.00 39.52 4.79
4093 6491 5.242069 TGATGCACCGTTATTATTGTTGG 57.758 39.130 0.00 0.00 0.00 3.77
4148 6563 4.279671 CCATAGTAGCAGAATCGAGAAGGT 59.720 45.833 0.00 0.00 0.00 3.50
4157 6572 5.009410 GCAAAATGAGCCATAGTAGCAGAAT 59.991 40.000 0.00 0.00 0.00 2.40
4176 6591 9.921637 ATTACAAGATAAAAATCCGAAGCAAAA 57.078 25.926 0.00 0.00 0.00 2.44
4190 6605 9.249053 TGGGCATTGTTCTTATTACAAGATAAA 57.751 29.630 0.00 0.00 38.74 1.40
4193 6608 6.096846 GGTGGGCATTGTTCTTATTACAAGAT 59.903 38.462 0.00 0.00 38.74 2.40
4196 6611 5.329399 AGGTGGGCATTGTTCTTATTACAA 58.671 37.500 0.00 0.00 39.58 2.41
4197 6612 4.929479 AGGTGGGCATTGTTCTTATTACA 58.071 39.130 0.00 0.00 0.00 2.41
4198 6613 4.947388 TGAGGTGGGCATTGTTCTTATTAC 59.053 41.667 0.00 0.00 0.00 1.89
4201 6616 3.266772 TCTGAGGTGGGCATTGTTCTTAT 59.733 43.478 0.00 0.00 0.00 1.73
4202 6617 2.642311 TCTGAGGTGGGCATTGTTCTTA 59.358 45.455 0.00 0.00 0.00 2.10
4203 6618 1.425066 TCTGAGGTGGGCATTGTTCTT 59.575 47.619 0.00 0.00 0.00 2.52
4204 6619 1.067295 TCTGAGGTGGGCATTGTTCT 58.933 50.000 0.00 0.00 0.00 3.01
4205 6620 1.815003 CTTCTGAGGTGGGCATTGTTC 59.185 52.381 0.00 0.00 0.00 3.18
4206 6621 1.548582 CCTTCTGAGGTGGGCATTGTT 60.549 52.381 0.00 0.00 38.32 2.83
4207 6622 0.038744 CCTTCTGAGGTGGGCATTGT 59.961 55.000 0.00 0.00 38.32 2.71
4208 6623 0.329261 TCCTTCTGAGGTGGGCATTG 59.671 55.000 0.00 0.00 43.97 2.82
4209 6624 1.075601 TTCCTTCTGAGGTGGGCATT 58.924 50.000 0.00 0.00 43.97 3.56
4210 6625 1.075601 TTTCCTTCTGAGGTGGGCAT 58.924 50.000 0.00 0.00 43.97 4.40
4211 6626 0.850100 TTTTCCTTCTGAGGTGGGCA 59.150 50.000 0.00 0.00 43.97 5.36
4212 6627 1.821136 CATTTTCCTTCTGAGGTGGGC 59.179 52.381 0.00 0.00 43.97 5.36
4213 6628 3.350833 CTCATTTTCCTTCTGAGGTGGG 58.649 50.000 0.00 0.00 43.97 4.61
4214 6629 2.751806 GCTCATTTTCCTTCTGAGGTGG 59.248 50.000 0.00 0.00 43.97 4.61
4215 6630 2.751806 GGCTCATTTTCCTTCTGAGGTG 59.248 50.000 0.00 0.00 43.97 4.00
4216 6631 2.376518 TGGCTCATTTTCCTTCTGAGGT 59.623 45.455 0.00 0.00 43.97 3.85
4217 6632 3.077484 TGGCTCATTTTCCTTCTGAGG 57.923 47.619 0.00 0.00 45.02 3.86
4218 6633 5.435291 ACTATGGCTCATTTTCCTTCTGAG 58.565 41.667 0.00 0.00 39.50 3.35
4219 6634 5.441718 ACTATGGCTCATTTTCCTTCTGA 57.558 39.130 0.00 0.00 0.00 3.27
4220 6635 5.238214 GCTACTATGGCTCATTTTCCTTCTG 59.762 44.000 0.00 0.00 0.00 3.02
4221 6636 5.104360 TGCTACTATGGCTCATTTTCCTTCT 60.104 40.000 0.00 0.00 0.00 2.85
4222 6637 5.126067 TGCTACTATGGCTCATTTTCCTTC 58.874 41.667 0.00 0.00 0.00 3.46
4223 6638 5.116084 TGCTACTATGGCTCATTTTCCTT 57.884 39.130 0.00 0.00 0.00 3.36
4224 6639 4.712476 CTGCTACTATGGCTCATTTTCCT 58.288 43.478 0.00 0.00 0.00 3.36
4225 6640 3.251972 GCTGCTACTATGGCTCATTTTCC 59.748 47.826 0.00 0.00 0.00 3.13
4226 6641 3.059325 CGCTGCTACTATGGCTCATTTTC 60.059 47.826 0.00 0.00 0.00 2.29
4241 6656 4.552365 GCCATCCCAGCGCTGCTA 62.552 66.667 31.96 21.12 36.40 3.49
4245 6660 4.809496 CTTGGCCATCCCAGCGCT 62.809 66.667 6.09 2.64 46.39 5.92
4247 6662 2.361610 AACTTGGCCATCCCAGCG 60.362 61.111 6.09 0.00 46.39 5.18
4248 6663 3.010413 GCAACTTGGCCATCCCAGC 62.010 63.158 6.09 3.85 46.39 4.85
4249 6664 3.291611 GCAACTTGGCCATCCCAG 58.708 61.111 6.09 2.68 46.39 4.45
4257 6672 1.383456 TATGGCATCGGCAACTTGGC 61.383 55.000 1.65 5.24 42.43 4.52
4258 6673 0.664761 CTATGGCATCGGCAACTTGG 59.335 55.000 1.65 0.00 42.43 3.61
4259 6674 0.664761 CCTATGGCATCGGCAACTTG 59.335 55.000 1.65 0.00 42.43 3.16
4260 6675 0.255890 ACCTATGGCATCGGCAACTT 59.744 50.000 17.29 0.00 42.43 2.66
4261 6676 0.179045 GACCTATGGCATCGGCAACT 60.179 55.000 17.29 0.00 42.43 3.16
4262 6677 0.179045 AGACCTATGGCATCGGCAAC 60.179 55.000 17.29 9.53 42.43 4.17
4263 6678 0.546122 AAGACCTATGGCATCGGCAA 59.454 50.000 17.29 0.00 42.43 4.52
4264 6679 0.179048 CAAGACCTATGGCATCGGCA 60.179 55.000 17.29 0.00 43.71 5.69
4265 6680 1.510480 GCAAGACCTATGGCATCGGC 61.510 60.000 17.29 10.42 40.13 5.54
4266 6681 1.224069 CGCAAGACCTATGGCATCGG 61.224 60.000 15.93 15.93 43.02 4.18
4267 6682 0.249447 TCGCAAGACCTATGGCATCG 60.249 55.000 1.65 0.00 45.01 3.84
4268 6683 1.506493 CTCGCAAGACCTATGGCATC 58.494 55.000 1.65 0.00 45.01 3.91
4269 6684 0.107456 CCTCGCAAGACCTATGGCAT 59.893 55.000 4.88 4.88 45.01 4.40
7199 13029 6.603201 ACTTTGTCAGATATGGTTGTATTGGG 59.397 38.462 0.00 0.00 0.00 4.12
7441 13326 0.527817 CCTTCATACGACAGGACGGC 60.528 60.000 0.00 0.00 37.61 5.68
7461 13346 9.352784 CTTCACAAGTTTGTATTTTTCTTGTCA 57.647 29.630 5.99 0.00 44.11 3.58
7469 13354 5.906073 AGCTGCTTCACAAGTTTGTATTTT 58.094 33.333 0.00 0.00 39.91 1.82
7574 13460 5.985911 ACCTTGTCTTAACACTGTACAAGT 58.014 37.500 16.25 0.00 43.42 3.16
7590 13476 8.398665 CCTGCTGAACTATAAATAAACCTTGTC 58.601 37.037 0.00 0.00 0.00 3.18
7629 13517 6.995091 AGGTGAGCAGATAATGGAGTATTTTC 59.005 38.462 0.00 0.00 0.00 2.29
7994 15769 7.814264 ACCATTTGCAATTTTACCAAAATCA 57.186 28.000 0.00 0.00 40.05 2.57
8053 15829 4.292186 TCTCCTTGTTCTAGCAAAGCAT 57.708 40.909 0.00 0.00 0.00 3.79
8055 15831 3.120025 GCTTCTCCTTGTTCTAGCAAAGC 60.120 47.826 0.00 0.00 0.00 3.51
8094 15871 1.554392 CTCGTCTCAATGCTTCCTCG 58.446 55.000 0.00 0.00 0.00 4.63
8137 15914 1.548719 AGGTGCGCTTGTATCACTACA 59.451 47.619 9.73 0.00 36.06 2.74
8197 15974 2.577606 TCCGATGGTGAACAATGGTT 57.422 45.000 0.00 0.00 40.76 3.67
8239 16017 7.434492 TCAAGAGATACGGAAAGCTATTTAGG 58.566 38.462 0.00 0.00 0.00 2.69
8244 16022 6.350612 GGCTATCAAGAGATACGGAAAGCTAT 60.351 42.308 0.00 0.00 35.67 2.97
8343 16121 7.164122 ACACAATGCTCTTCTATCTTGAAAGA 58.836 34.615 0.00 0.00 39.78 2.52
8405 16183 2.034558 GCCGGTTATCCATTCCAACATG 59.965 50.000 1.90 0.00 0.00 3.21
8442 16221 7.849447 TACTGTGAATAGTTCCGAAAGGCCG 62.849 48.000 0.00 0.00 40.72 6.13
8497 16277 2.180017 GCACTGCGGATGCCTTTG 59.820 61.111 0.00 0.00 41.78 2.77
8619 16402 3.569701 TCATTCTGCTGGAAAGGAACAAC 59.430 43.478 0.00 0.00 37.49 3.32
8648 16432 2.290514 TGGAAGGGATCAGTTGAGCTTG 60.291 50.000 0.00 0.00 0.00 4.01
8714 16498 2.552809 GGCAGCAATTGGTGGGAAAATT 60.553 45.455 32.32 0.00 43.24 1.82
8751 16535 1.067495 TGCACGGTACACATTCGATGA 60.067 47.619 0.00 0.00 0.00 2.92
8836 16621 2.604174 CCCACAACTTCGTGACGGC 61.604 63.158 4.70 0.00 39.34 5.68
8847 16632 1.441732 AAAAGTCGACCGCCCACAAC 61.442 55.000 13.01 0.00 0.00 3.32
8864 16649 2.891580 AGTCGTCCTTCTGCTGTAGAAA 59.108 45.455 9.45 0.00 44.47 2.52
8923 16712 2.167900 AGTTTCATACAGTACGCTCCCC 59.832 50.000 0.00 0.00 0.00 4.81
8925 16714 3.846360 ACAGTTTCATACAGTACGCTCC 58.154 45.455 0.00 0.00 0.00 4.70
8965 16754 0.755686 AACCCGAAATGCAAGGCAAA 59.244 45.000 0.00 0.00 43.62 3.68
8975 16764 4.010349 GAGAACATCTCCAAACCCGAAAT 58.990 43.478 0.00 0.00 37.55 2.17
9010 16969 3.779271 AGTTGACCGCTTAGTACTAGC 57.221 47.619 2.23 8.21 0.00 3.42
9028 16987 3.197983 ACGAGGATGCTTTTAAGGCTAGT 59.802 43.478 0.02 0.00 0.00 2.57
9032 16991 1.671328 GGACGAGGATGCTTTTAAGGC 59.329 52.381 0.00 0.00 0.00 4.35
9033 16992 2.985896 TGGACGAGGATGCTTTTAAGG 58.014 47.619 0.00 0.00 0.00 2.69
9042 17001 2.814604 TCGCCATGGACGAGGATG 59.185 61.111 22.05 0.56 33.96 3.51
9056 17015 1.882167 GAGGCTGCTCATCACTCGC 60.882 63.158 0.00 0.00 0.00 5.03
9077 17036 7.978975 TCCAAATTAAGAGTCACAAAAGGTTTG 59.021 33.333 0.00 0.00 0.00 2.93
9106 17065 5.809562 AGTGAATGAGCGATCTTAAGTCAAG 59.190 40.000 0.90 0.00 35.38 3.02
9120 17079 0.526524 CCGAGACCGAGTGAATGAGC 60.527 60.000 0.00 0.00 38.22 4.26
9172 17131 3.118261 AGCTCTTTGGTCAACTGACTGAA 60.118 43.478 9.60 4.56 44.20 3.02


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

AutoCloner maintained by Alex Coulton.