Multiple sequence alignment - TraesCS4B01G349800

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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 TraesCS4B01G349800 chr4B 100.000 4269 0 0 1 4269 642745578 642749846 0.000000e+00 7884.0
1 TraesCS4B01G349800 chr4B 87.019 701 85 6 3570 4269 642778798 642779493 0.000000e+00 785.0
2 TraesCS4B01G349800 chr4B 88.908 586 62 2 3683 4268 642965251 642964669 0.000000e+00 719.0
3 TraesCS4B01G349800 chr4B 80.866 277 53 0 1039 1315 642775700 642775976 7.190000e-53 219.0
4 TraesCS4B01G349800 chr4B 80.150 267 46 5 1042 1306 642458720 642458459 4.360000e-45 193.0
5 TraesCS4B01G349800 chr4B 94.382 89 5 0 3585 3673 642965990 642965902 2.070000e-28 137.0
6 TraesCS4B01G349800 chr5A 89.055 1535 121 23 1455 2950 680660237 680661763 0.000000e+00 1860.0
7 TraesCS4B01G349800 chr5A 87.560 1254 105 27 906 2125 680764437 680763201 0.000000e+00 1404.0
8 TraesCS4B01G349800 chr5A 88.346 798 86 5 2127 2921 680753158 680752365 0.000000e+00 952.0
9 TraesCS4B01G349800 chr5A 89.601 702 71 2 3568 4269 680750659 680749960 0.000000e+00 891.0
10 TraesCS4B01G349800 chr5A 88.269 699 76 6 3572 4269 680695274 680695967 0.000000e+00 832.0
11 TraesCS4B01G349800 chr5A 93.878 245 15 0 1071 1315 680659857 680660101 1.880000e-98 370.0
12 TraesCS4B01G349800 chr5A 90.795 239 20 2 3086 3323 680661822 680662059 6.890000e-83 318.0
13 TraesCS4B01G349800 chr5A 85.016 307 40 2 3674 3977 680662501 680662804 1.490000e-79 307.0
14 TraesCS4B01G349800 chr5A 84.173 278 44 0 1039 1316 680692582 680692859 1.960000e-68 270.0
15 TraesCS4B01G349800 chr5A 78.409 264 49 8 1052 1314 624967427 624967171 9.500000e-37 165.0
16 TraesCS4B01G349800 chr5A 93.182 44 3 0 2980 3023 680661764 680661807 9.910000e-07 65.8
17 TraesCS4B01G349800 chr4D 91.680 1262 103 2 1767 3027 499697817 499696557 0.000000e+00 1748.0
18 TraesCS4B01G349800 chr4D 90.883 702 62 1 3568 4269 499696050 499695351 0.000000e+00 941.0
19 TraesCS4B01G349800 chr4D 88.193 703 74 9 3570 4269 499711342 499712038 0.000000e+00 830.0
20 TraesCS4B01G349800 chr4D 86.974 737 61 19 1020 1724 499698687 499697954 0.000000e+00 797.0
21 TraesCS4B01G349800 chr4D 84.706 595 82 7 3674 4264 499700386 499700975 1.710000e-163 586.0
22 TraesCS4B01G349800 chr4D 90.591 372 32 3 3568 3938 499834015 499833646 1.380000e-134 490.0
23 TraesCS4B01G349800 chr4D 88.952 353 38 1 3917 4269 499831352 499831001 6.560000e-118 435.0
24 TraesCS4B01G349800 chr4D 94.094 254 12 3 3073 3323 499696561 499696308 2.410000e-102 383.0
25 TraesCS4B01G349800 chr4D 92.395 263 20 0 2659 2921 499835273 499835011 4.030000e-100 375.0
26 TraesCS4B01G349800 chr4D 83.394 277 46 0 1039 1315 499707818 499708094 1.520000e-64 257.0
27 TraesCS4B01G349800 chr4D 79.775 267 47 6 1042 1306 499504574 499504313 2.030000e-43 187.0
28 TraesCS4B01G349800 chr4D 96.667 60 1 1 924 982 499698749 499698690 9.770000e-17 99.0
29 TraesCS4B01G349800 chr7D 97.204 465 13 0 338 802 499613340 499612876 0.000000e+00 787.0
30 TraesCS4B01G349800 chr7D 98.529 340 4 1 1 339 499613712 499613373 2.200000e-167 599.0
31 TraesCS4B01G349800 chr7D 95.154 227 11 0 3343 3569 598726743 598726969 4.060000e-95 359.0
32 TraesCS4B01G349800 chr7D 94.248 226 13 0 3343 3568 45518494 45518719 3.160000e-91 346.0
33 TraesCS4B01G349800 chr2B 94.861 467 18 3 338 802 30314342 30313880 0.000000e+00 725.0
34 TraesCS4B01G349800 chr2B 96.830 347 3 1 1 339 30314721 30314375 1.330000e-159 573.0
35 TraesCS4B01G349800 chr2B 93.013 229 16 0 3343 3571 5810107 5809879 6.840000e-88 335.0
36 TraesCS4B01G349800 chr5B 97.052 407 12 0 391 797 649422146 649421740 0.000000e+00 686.0
37 TraesCS4B01G349800 chr5B 95.870 339 12 1 1 339 649424140 649423804 8.070000e-152 547.0
38 TraesCS4B01G349800 chr5B 94.248 226 13 0 3343 3568 396146587 396146362 3.160000e-91 346.0
39 TraesCS4B01G349800 chr5B 98.276 58 1 0 338 395 649423773 649423716 7.550000e-18 102.0
40 TraesCS4B01G349800 chr3A 93.103 464 31 1 336 798 53412639 53413102 0.000000e+00 678.0
41 TraesCS4B01G349800 chr3A 90.343 466 42 2 336 798 54861644 54861179 3.650000e-170 608.0
42 TraesCS4B01G349800 chr3A 92.308 195 11 3 20 212 53412436 53412628 1.510000e-69 274.0
43 TraesCS4B01G349800 chr3A 90.306 196 18 1 20 215 54861846 54861652 5.480000e-64 255.0
44 TraesCS4B01G349800 chr3A 83.333 78 9 4 726 802 594814263 594814337 7.660000e-08 69.4
45 TraesCS4B01G349800 chrUn 89.201 463 47 3 336 797 32165856 32166316 3.700000e-160 575.0
46 TraesCS4B01G349800 chrUn 89.970 329 22 5 20 339 32165499 32165825 8.540000e-112 414.0
47 TraesCS4B01G349800 chr6B 95.175 228 11 0 3343 3570 100904488 100904261 1.130000e-95 361.0
48 TraesCS4B01G349800 chr2D 94.273 227 13 0 3343 3569 43970637 43970863 8.790000e-92 348.0
49 TraesCS4B01G349800 chr7B 94.248 226 13 0 3343 3568 743678387 743678162 3.160000e-91 346.0
50 TraesCS4B01G349800 chr5D 93.103 232 15 1 3343 3574 7038561 7038331 5.290000e-89 339.0
51 TraesCS4B01G349800 chr5D 78.599 257 47 8 1042 1297 500681074 500681323 3.420000e-36 163.0
52 TraesCS4B01G349800 chr3D 93.778 225 14 0 3345 3569 600514371 600514147 5.290000e-89 339.0
53 TraesCS4B01G349800 chr3D 86.567 67 9 0 732 798 560859602 560859536 1.650000e-09 75.0
54 TraesCS4B01G349800 chr6D 86.765 68 9 0 732 799 436876813 436876746 4.580000e-10 76.8
55 TraesCS4B01G349800 chr2A 84.507 71 10 1 498 568 117181656 117181587 7.660000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G349800 chr4B 642745578 642749846 4268 False 7884.000000 7884 100.0000 1 4269 1 chr4B.!!$F1 4268
1 TraesCS4B01G349800 chr4B 642775700 642779493 3793 False 502.000000 785 83.9425 1039 4269 2 chr4B.!!$F2 3230
2 TraesCS4B01G349800 chr4B 642964669 642965990 1321 True 428.000000 719 91.6450 3585 4268 2 chr4B.!!$R2 683
3 TraesCS4B01G349800 chr5A 680763201 680764437 1236 True 1404.000000 1404 87.5600 906 2125 1 chr5A.!!$R2 1219
4 TraesCS4B01G349800 chr5A 680749960 680753158 3198 True 921.500000 952 88.9735 2127 4269 2 chr5A.!!$R3 2142
5 TraesCS4B01G349800 chr5A 680659857 680662804 2947 False 584.160000 1860 90.3852 1071 3977 5 chr5A.!!$F1 2906
6 TraesCS4B01G349800 chr5A 680692582 680695967 3385 False 551.000000 832 86.2210 1039 4269 2 chr5A.!!$F2 3230
7 TraesCS4B01G349800 chr4D 499695351 499698749 3398 True 793.600000 1748 92.0596 924 4269 5 chr4D.!!$R2 3345
8 TraesCS4B01G349800 chr4D 499700386 499700975 589 False 586.000000 586 84.7060 3674 4264 1 chr4D.!!$F1 590
9 TraesCS4B01G349800 chr4D 499707818 499712038 4220 False 543.500000 830 85.7935 1039 4269 2 chr4D.!!$F2 3230
10 TraesCS4B01G349800 chr4D 499831001 499835273 4272 True 433.333333 490 90.6460 2659 4269 3 chr4D.!!$R3 1610
11 TraesCS4B01G349800 chr7D 499612876 499613712 836 True 693.000000 787 97.8665 1 802 2 chr7D.!!$R1 801
12 TraesCS4B01G349800 chr2B 30313880 30314721 841 True 649.000000 725 95.8455 1 802 2 chr2B.!!$R2 801
13 TraesCS4B01G349800 chr5B 649421740 649424140 2400 True 445.000000 686 97.0660 1 797 3 chr5B.!!$R2 796
14 TraesCS4B01G349800 chr3A 53412436 53413102 666 False 476.000000 678 92.7055 20 798 2 chr3A.!!$F2 778
15 TraesCS4B01G349800 chr3A 54861179 54861846 667 True 431.500000 608 90.3245 20 798 2 chr3A.!!$R1 778
16 TraesCS4B01G349800 chrUn 32165499 32166316 817 False 494.500000 575 89.5855 20 797 2 chrUn.!!$F1 777

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
507 2167 0.532573 TCTCAAGATGGAGACCGTGC 59.467 55.0 0.00 0.00 38.95 5.34 F
1212 2875 0.957888 GGCTGCCTGACAAACCTCTC 60.958 60.0 12.43 0.00 0.00 3.20 F
2228 5192 0.810648 TGGTCGGATCAAGCAATTGC 59.189 50.0 23.05 23.05 42.49 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1586 3345 0.101219 TCACCAGATCGTCGCTGATG 59.899 55.0 1.88 0.0 35.39 3.07 R
2434 5398 0.319900 GCCTCTCGTTTGCTGACAGA 60.320 55.0 6.65 0.0 0.00 3.41 R
3514 7545 0.172578 CCTACGCTCGACACCATTGA 59.827 55.0 0.00 0.0 0.00 2.57 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 9.582648 AGATAAGTACACCTTTTGTATTGGTTT 57.417 29.630 0.00 0.00 42.82 3.27
468 2127 0.537188 CCTCGTGACCCTACTGCATT 59.463 55.000 0.00 0.00 0.00 3.56
507 2167 0.532573 TCTCAAGATGGAGACCGTGC 59.467 55.000 0.00 0.00 38.95 5.34
641 2303 4.595762 AAGCTTGTGCATGAATCAAGTT 57.404 36.364 18.74 13.63 42.74 2.66
688 2350 6.885918 TGCTGACCAATCTGAAATGAAGAATA 59.114 34.615 0.00 0.00 0.00 1.75
798 2460 2.283351 CGCACGGGCATTTTACTAGTAC 59.717 50.000 11.77 0.00 41.24 2.73
803 2465 6.311723 CACGGGCATTTTACTAGTACTTTTG 58.688 40.000 0.00 0.02 0.00 2.44
804 2466 5.999600 ACGGGCATTTTACTAGTACTTTTGT 59.000 36.000 0.00 0.80 0.00 2.83
805 2467 7.118101 CACGGGCATTTTACTAGTACTTTTGTA 59.882 37.037 0.00 0.00 0.00 2.41
806 2468 7.661027 ACGGGCATTTTACTAGTACTTTTGTAA 59.339 33.333 0.00 6.24 36.56 2.41
807 2469 7.959109 CGGGCATTTTACTAGTACTTTTGTAAC 59.041 37.037 0.00 0.00 36.56 2.50
808 2470 8.785946 GGGCATTTTACTAGTACTTTTGTAACA 58.214 33.333 0.00 3.00 36.56 2.41
809 2471 9.603298 GGCATTTTACTAGTACTTTTGTAACAC 57.397 33.333 0.00 0.00 36.56 3.32
813 2475 9.579768 TTTTACTAGTACTTTTGTAACACACGA 57.420 29.630 0.00 0.00 36.56 4.35
814 2476 9.579768 TTTACTAGTACTTTTGTAACACACGAA 57.420 29.630 0.00 0.00 36.56 3.85
815 2477 7.455331 ACTAGTACTTTTGTAACACACGAAC 57.545 36.000 0.00 0.00 36.56 3.95
816 2478 7.260603 ACTAGTACTTTTGTAACACACGAACT 58.739 34.615 0.00 0.00 36.56 3.01
817 2479 6.973229 AGTACTTTTGTAACACACGAACTT 57.027 33.333 0.00 0.00 36.56 2.66
818 2480 7.368480 AGTACTTTTGTAACACACGAACTTT 57.632 32.000 0.00 0.00 36.56 2.66
819 2481 7.809665 AGTACTTTTGTAACACACGAACTTTT 58.190 30.769 0.00 0.00 36.56 2.27
820 2482 8.291740 AGTACTTTTGTAACACACGAACTTTTT 58.708 29.630 0.00 0.00 36.56 1.94
873 2535 5.548706 TTTGAACGTAATTCGGTAATGGG 57.451 39.130 0.00 0.00 40.67 4.00
874 2536 2.937799 TGAACGTAATTCGGTAATGGGC 59.062 45.455 0.00 0.00 40.67 5.36
875 2537 1.957668 ACGTAATTCGGTAATGGGCC 58.042 50.000 0.00 0.00 44.69 5.80
881 2543 3.520402 CGGTAATGGGCCGCAATT 58.480 55.556 0.00 0.00 42.82 2.32
882 2544 1.813192 CGGTAATGGGCCGCAATTT 59.187 52.632 0.00 0.00 42.82 1.82
883 2545 1.025812 CGGTAATGGGCCGCAATTTA 58.974 50.000 0.00 0.00 42.82 1.40
884 2546 1.268845 CGGTAATGGGCCGCAATTTAC 60.269 52.381 0.00 3.27 42.82 2.01
885 2547 1.268845 GGTAATGGGCCGCAATTTACG 60.269 52.381 0.00 0.00 0.00 3.18
894 2556 1.647084 GCAATTTACGGCGCCTAGG 59.353 57.895 26.68 12.04 0.00 3.02
895 2557 1.647084 CAATTTACGGCGCCTAGGC 59.353 57.895 26.68 24.75 42.76 3.93
923 2585 4.785453 CTCCCCGCTGCAACCCTC 62.785 72.222 0.00 0.00 0.00 4.30
1002 2665 3.411351 GTCGCCGCACGTGTCATT 61.411 61.111 18.38 0.00 44.19 2.57
1017 2680 0.975556 TCATTGCTCGCTCCTACCCA 60.976 55.000 0.00 0.00 0.00 4.51
1084 2747 2.665185 GTGGTGGACAGGTCGTGC 60.665 66.667 0.00 0.00 36.27 5.34
1107 2770 3.112075 CGTGCTGTTCGCCGACAT 61.112 61.111 0.00 0.00 38.05 3.06
1212 2875 0.957888 GGCTGCCTGACAAACCTCTC 60.958 60.000 12.43 0.00 0.00 3.20
1288 2951 1.591703 CACGCTTCTCAGGCCTACA 59.408 57.895 3.98 0.00 0.00 2.74
1319 3004 6.426937 CGATGAATTTGGGTCCGTATCTTAAT 59.573 38.462 0.00 0.00 0.00 1.40
1320 3005 7.041372 CGATGAATTTGGGTCCGTATCTTAATT 60.041 37.037 0.00 0.00 0.00 1.40
1321 3006 9.280174 GATGAATTTGGGTCCGTATCTTAATTA 57.720 33.333 0.00 0.00 0.00 1.40
1370 3114 2.991190 CCAAATCTTGCTGTCAATGTGC 59.009 45.455 0.00 0.00 0.00 4.57
1372 3116 4.052608 CAAATCTTGCTGTCAATGTGCAA 58.947 39.130 0.00 9.54 43.25 4.08
1378 3122 2.030628 TGCTGTCAATGTGCAAGTCATG 60.031 45.455 0.00 0.00 33.48 3.07
1414 3167 2.871182 TTCTATGCTCGCAGGTACAG 57.129 50.000 0.00 0.00 0.00 2.74
1416 3169 2.927028 TCTATGCTCGCAGGTACAGTA 58.073 47.619 0.00 0.00 0.00 2.74
1421 3174 2.180769 CGCAGGTACAGTAGCGCA 59.819 61.111 11.47 0.00 43.80 6.09
1447 3200 1.227823 CAGGGTGCACTCCGTTCAA 60.228 57.895 14.62 0.00 0.00 2.69
1503 3259 2.519302 AGTGTGGTTGCAGGTGCC 60.519 61.111 0.00 0.00 41.18 5.01
1525 3284 2.203266 GGTCATGGCTAGGCTGGC 60.203 66.667 15.25 15.25 0.00 4.85
1534 3293 2.436469 TAGGCTGGCGCATGTGTG 60.436 61.111 10.83 0.21 38.10 3.82
1559 3318 1.014352 AAACAACACGCACAGAGGTC 58.986 50.000 0.00 0.00 0.00 3.85
1586 3345 3.060602 CAAGTGGAAAGAGAGGTTCGTC 58.939 50.000 0.00 0.00 0.00 4.20
1749 4630 5.774690 TGTCTACATTTCTTTGGCCTGAATT 59.225 36.000 3.32 0.07 0.00 2.17
1760 4646 7.520798 TCTTTGGCCTGAATTCATACTGATAT 58.479 34.615 8.96 0.00 0.00 1.63
1788 4705 7.546358 TGATGCTATAAATTTCAGGTGGTTTG 58.454 34.615 0.00 0.00 0.00 2.93
1890 4840 3.501062 ACATCAGTGCTCACAATTCACAG 59.499 43.478 2.63 0.00 33.44 3.66
1891 4841 3.198409 TCAGTGCTCACAATTCACAGT 57.802 42.857 2.63 0.00 33.44 3.55
1913 4863 1.161563 TCGGCGTCAAGAAACCAACC 61.162 55.000 6.85 0.00 0.00 3.77
1916 4866 1.135333 GGCGTCAAGAAACCAACCAAA 59.865 47.619 0.00 0.00 0.00 3.28
2101 5063 4.024048 CACGGCTTCAACAATCTTTACAGT 60.024 41.667 0.00 0.00 0.00 3.55
2177 5141 1.153369 GCACGCTGCTGGATCCTAA 60.153 57.895 14.23 0.00 40.96 2.69
2196 5160 5.991606 TCCTAATATTGCTCCGTTGAAGATG 59.008 40.000 0.00 0.00 0.00 2.90
2206 5170 4.695993 TGAAGATGCACGGCGCCA 62.696 61.111 28.98 7.02 41.33 5.69
2209 5173 2.270297 GAAGATGCACGGCGCCAATT 62.270 55.000 28.98 6.84 41.33 2.32
2228 5192 0.810648 TGGTCGGATCAAGCAATTGC 59.189 50.000 23.05 23.05 42.49 3.56
2319 5283 2.816204 TGTTCGATCCGGTGTTTGTA 57.184 45.000 0.00 0.00 0.00 2.41
2353 5317 0.961857 TGTGGTAGCCGACGAGCTTA 60.962 55.000 14.55 2.18 41.41 3.09
2433 5397 6.402222 GGATAATGTAGTGGAGATGGACATC 58.598 44.000 4.15 4.15 38.09 3.06
2482 5452 9.784531 GTTATCTATATATACATGCCTTGGCAT 57.215 33.333 20.26 20.26 0.00 4.40
2582 5552 1.447838 GCAGGCTGTTGCGCTACTA 60.448 57.895 22.01 8.46 40.82 1.82
2608 5578 3.854666 CGGTGATCAATTCAGAGACTGT 58.145 45.455 0.00 0.00 34.17 3.55
2613 5583 3.758755 TCAATTCAGAGACTGTGCTGT 57.241 42.857 0.00 0.00 33.90 4.40
2629 5599 1.941209 GCTGTCAGATGCGTTCAAGGA 60.941 52.381 3.32 0.00 0.00 3.36
2637 5607 1.593196 TGCGTTCAAGGAGAGGTTTG 58.407 50.000 0.00 0.00 0.00 2.93
2653 5623 2.719376 TTGAGCAGGAAGCACAACC 58.281 52.632 0.00 0.00 46.56 3.77
2748 5727 0.608130 CGAGACCATCACCCTTGACA 59.392 55.000 0.00 0.00 33.38 3.58
2806 5785 0.849417 ATCCAGATGAAGGGGAAGCC 59.151 55.000 0.00 0.00 33.73 4.35
2870 5849 1.639635 ATCCATGGACCCTGGCTGAC 61.640 60.000 18.99 0.00 33.56 3.51
2882 5861 0.038599 TGGCTGACTGTGGCATTCAT 59.961 50.000 0.00 0.00 35.04 2.57
3040 6388 3.627395 TTTTCATGAGCGTCATAGGGT 57.373 42.857 0.00 0.00 34.28 4.34
3041 6389 2.602257 TTCATGAGCGTCATAGGGTG 57.398 50.000 0.00 0.00 34.28 4.61
3042 6390 0.752658 TCATGAGCGTCATAGGGTGG 59.247 55.000 0.00 0.00 34.28 4.61
3043 6391 0.882042 CATGAGCGTCATAGGGTGGC 60.882 60.000 0.00 0.00 34.28 5.01
3044 6392 1.337384 ATGAGCGTCATAGGGTGGCA 61.337 55.000 0.00 0.00 34.88 4.92
3048 6396 1.441729 CGTCATAGGGTGGCATCGT 59.558 57.895 0.00 0.00 30.99 3.73
3049 6397 0.671796 CGTCATAGGGTGGCATCGTA 59.328 55.000 2.23 2.23 30.99 3.43
3050 6398 1.335964 CGTCATAGGGTGGCATCGTAG 60.336 57.143 6.32 0.00 30.99 3.51
3051 6399 1.687123 GTCATAGGGTGGCATCGTAGT 59.313 52.381 6.32 0.00 30.99 2.73
3053 6401 1.412710 CATAGGGTGGCATCGTAGTGT 59.587 52.381 6.32 0.00 0.00 3.55
3054 6402 1.563924 TAGGGTGGCATCGTAGTGTT 58.436 50.000 0.00 0.00 0.00 3.32
3055 6403 1.563924 AGGGTGGCATCGTAGTGTTA 58.436 50.000 0.00 0.00 0.00 2.41
3056 6404 2.116238 AGGGTGGCATCGTAGTGTTAT 58.884 47.619 0.00 0.00 0.00 1.89
3057 6405 2.158957 AGGGTGGCATCGTAGTGTTATG 60.159 50.000 0.00 0.00 0.00 1.90
3059 6407 3.181473 GGGTGGCATCGTAGTGTTATGTA 60.181 47.826 0.00 0.00 0.00 2.29
3060 6408 4.502604 GGGTGGCATCGTAGTGTTATGTAT 60.503 45.833 0.00 0.00 0.00 2.29
3062 6410 5.176958 GGTGGCATCGTAGTGTTATGTATTC 59.823 44.000 0.00 0.00 0.00 1.75
3063 6411 5.751509 GTGGCATCGTAGTGTTATGTATTCA 59.248 40.000 0.00 0.00 0.00 2.57
3064 6412 5.983118 TGGCATCGTAGTGTTATGTATTCAG 59.017 40.000 0.00 0.00 0.00 3.02
3065 6413 5.983720 GGCATCGTAGTGTTATGTATTCAGT 59.016 40.000 0.00 0.00 0.00 3.41
3066 6414 6.074302 GGCATCGTAGTGTTATGTATTCAGTG 60.074 42.308 0.00 0.00 0.00 3.66
3067 6415 6.475727 GCATCGTAGTGTTATGTATTCAGTGT 59.524 38.462 0.00 0.00 0.00 3.55
3068 6416 7.646526 GCATCGTAGTGTTATGTATTCAGTGTA 59.353 37.037 0.00 0.00 0.00 2.90
3071 6419 9.563898 TCGTAGTGTTATGTATTCAGTGTAAAG 57.436 33.333 0.00 0.00 0.00 1.85
3072 6420 9.350357 CGTAGTGTTATGTATTCAGTGTAAAGT 57.650 33.333 0.00 0.00 0.00 2.66
3075 6423 9.998106 AGTGTTATGTATTCAGTGTAAAGTTCT 57.002 29.630 0.00 0.00 0.00 3.01
3109 6457 0.527565 GCAACGAGGCCATGTCATTT 59.472 50.000 5.01 0.00 0.00 2.32
3281 7200 7.707774 AAAATCAATAAACGAAAACCCACTG 57.292 32.000 0.00 0.00 0.00 3.66
3338 7369 5.901413 AGACCACTGGATCATACAATCAT 57.099 39.130 0.71 0.00 0.00 2.45
3339 7370 6.257994 AGACCACTGGATCATACAATCATT 57.742 37.500 0.71 0.00 0.00 2.57
3343 7374 6.483307 ACCACTGGATCATACAATCATTAACG 59.517 38.462 0.71 0.00 0.00 3.18
3345 7376 7.226523 CCACTGGATCATACAATCATTAACGAA 59.773 37.037 0.00 0.00 0.00 3.85
3349 7380 8.425703 TGGATCATACAATCATTAACGAACCTA 58.574 33.333 0.00 0.00 0.00 3.08
3354 7385 6.920569 ACAATCATTAACGAACCTATGGTC 57.079 37.500 0.00 0.00 33.12 4.02
3355 7386 6.650120 ACAATCATTAACGAACCTATGGTCT 58.350 36.000 0.00 0.00 33.12 3.85
3356 7387 7.788026 ACAATCATTAACGAACCTATGGTCTA 58.212 34.615 0.00 0.00 33.12 2.59
3359 7390 7.356089 TCATTAACGAACCTATGGTCTATGT 57.644 36.000 0.00 0.00 33.12 2.29
3360 7391 7.431249 TCATTAACGAACCTATGGTCTATGTC 58.569 38.462 0.00 0.00 33.12 3.06
3361 7392 6.778834 TTAACGAACCTATGGTCTATGTCA 57.221 37.500 0.00 0.00 33.12 3.58
3362 7393 5.871396 AACGAACCTATGGTCTATGTCAT 57.129 39.130 0.00 0.00 33.12 3.06
3363 7394 6.971726 AACGAACCTATGGTCTATGTCATA 57.028 37.500 0.00 0.00 33.12 2.15
3364 7395 6.328641 ACGAACCTATGGTCTATGTCATAC 57.671 41.667 0.00 0.00 33.12 2.39
3365 7396 5.048921 ACGAACCTATGGTCTATGTCATACG 60.049 44.000 0.00 0.00 33.12 3.06
3368 7399 7.540474 AACCTATGGTCTATGTCATACGATT 57.460 36.000 0.00 0.00 33.12 3.34
3369 7400 7.540474 ACCTATGGTCTATGTCATACGATTT 57.460 36.000 0.00 0.00 0.00 2.17
3370 7401 8.645814 ACCTATGGTCTATGTCATACGATTTA 57.354 34.615 0.00 0.00 0.00 1.40
3371 7402 9.085645 ACCTATGGTCTATGTCATACGATTTAA 57.914 33.333 0.00 0.00 0.00 1.52
3372 7403 9.355215 CCTATGGTCTATGTCATACGATTTAAC 57.645 37.037 0.00 0.00 0.00 2.01
3373 7404 9.908152 CTATGGTCTATGTCATACGATTTAACA 57.092 33.333 0.00 0.00 0.00 2.41
3375 7406 8.812147 TGGTCTATGTCATACGATTTAACATC 57.188 34.615 0.00 0.00 33.01 3.06
3376 7407 7.870954 TGGTCTATGTCATACGATTTAACATCC 59.129 37.037 0.00 0.00 33.01 3.51
3377 7408 8.088981 GGTCTATGTCATACGATTTAACATCCT 58.911 37.037 0.00 0.00 33.01 3.24
3382 7413 9.909644 ATGTCATACGATTTAACATCCTACTAC 57.090 33.333 0.00 0.00 0.00 2.73
3383 7414 8.905850 TGTCATACGATTTAACATCCTACTACA 58.094 33.333 0.00 0.00 0.00 2.74
3385 7416 9.908152 TCATACGATTTAACATCCTACTACATG 57.092 33.333 0.00 0.00 0.00 3.21
3387 7418 9.692749 ATACGATTTAACATCCTACTACATGTG 57.307 33.333 9.11 0.93 33.38 3.21
3388 7419 6.984474 ACGATTTAACATCCTACTACATGTGG 59.016 38.462 9.11 8.41 33.38 4.17
3395 7426 4.736126 TCCTACTACATGTGGATGTGTG 57.264 45.455 16.98 4.28 43.03 3.82
3397 7428 4.159693 TCCTACTACATGTGGATGTGTGAC 59.840 45.833 16.98 0.00 43.03 3.67
3398 7429 4.081697 CCTACTACATGTGGATGTGTGACA 60.082 45.833 16.98 0.00 43.03 3.58
3399 7430 4.558226 ACTACATGTGGATGTGTGACAT 57.442 40.909 16.98 0.00 43.03 3.06
3400 7431 4.910195 ACTACATGTGGATGTGTGACATT 58.090 39.130 16.98 0.00 43.03 2.71
3401 7432 4.937620 ACTACATGTGGATGTGTGACATTC 59.062 41.667 16.98 0.00 43.03 2.67
3403 7434 4.338012 ACATGTGGATGTGTGACATTCAT 58.662 39.130 0.00 0.00 45.15 2.57
3405 7436 2.488937 TGTGGATGTGTGACATTCATGC 59.511 45.455 1.06 1.60 45.15 4.06
3409 7440 3.504863 GATGTGTGACATTCATGCCAAC 58.495 45.455 0.00 0.00 39.27 3.77
3410 7441 2.585330 TGTGTGACATTCATGCCAACT 58.415 42.857 0.00 0.00 0.00 3.16
3411 7442 2.293955 TGTGTGACATTCATGCCAACTG 59.706 45.455 0.00 0.00 0.00 3.16
3412 7443 1.270274 TGTGACATTCATGCCAACTGC 59.730 47.619 0.00 0.00 41.77 4.40
3449 7480 5.819825 CATGCATGGATCCTCATGAATAG 57.180 43.478 24.98 10.24 45.30 1.73
3450 7481 5.497474 CATGCATGGATCCTCATGAATAGA 58.503 41.667 24.98 0.00 45.30 1.98
3451 7482 4.903054 TGCATGGATCCTCATGAATAGAC 58.097 43.478 14.23 0.00 45.30 2.59
3452 7483 4.348754 TGCATGGATCCTCATGAATAGACA 59.651 41.667 14.23 0.00 45.30 3.41
3453 7484 5.013808 TGCATGGATCCTCATGAATAGACAT 59.986 40.000 14.23 0.00 45.30 3.06
3454 7485 5.354513 GCATGGATCCTCATGAATAGACATG 59.645 44.000 14.23 17.94 45.30 3.21
3455 7486 4.903054 TGGATCCTCATGAATAGACATGC 58.097 43.478 14.23 0.00 44.79 4.06
3456 7487 4.348754 TGGATCCTCATGAATAGACATGCA 59.651 41.667 14.23 0.00 44.79 3.96
3457 7488 5.013808 TGGATCCTCATGAATAGACATGCAT 59.986 40.000 14.23 0.00 44.79 3.96
3458 7489 5.354513 GGATCCTCATGAATAGACATGCATG 59.645 44.000 25.09 25.09 46.18 4.06
3503 7534 5.819825 CATGCATGGATCCTCATGAATAG 57.180 43.478 24.98 10.24 45.30 1.73
3505 7536 4.648651 TGCATGGATCCTCATGAATAGTG 58.351 43.478 14.23 0.00 45.30 2.74
3507 7538 4.694509 GCATGGATCCTCATGAATAGTGTC 59.305 45.833 14.23 0.00 45.30 3.67
3508 7539 5.512749 GCATGGATCCTCATGAATAGTGTCT 60.513 44.000 14.23 0.00 45.30 3.41
3511 7542 6.614657 TGGATCCTCATGAATAGTGTCTAGA 58.385 40.000 14.23 0.00 0.00 2.43
3512 7543 7.069344 TGGATCCTCATGAATAGTGTCTAGAA 58.931 38.462 14.23 0.00 0.00 2.10
3513 7544 7.565029 TGGATCCTCATGAATAGTGTCTAGAAA 59.435 37.037 14.23 0.00 0.00 2.52
3514 7545 8.592809 GGATCCTCATGAATAGTGTCTAGAAAT 58.407 37.037 3.84 0.00 0.00 2.17
3518 7549 9.775854 CCTCATGAATAGTGTCTAGAAATCAAT 57.224 33.333 0.00 0.00 0.00 2.57
3521 7552 9.334947 CATGAATAGTGTCTAGAAATCAATGGT 57.665 33.333 0.00 0.00 0.00 3.55
3522 7553 8.722480 TGAATAGTGTCTAGAAATCAATGGTG 57.278 34.615 0.00 0.00 0.00 4.17
3523 7554 8.321353 TGAATAGTGTCTAGAAATCAATGGTGT 58.679 33.333 0.00 0.00 0.00 4.16
3525 7556 5.171476 AGTGTCTAGAAATCAATGGTGTCG 58.829 41.667 0.00 0.00 0.00 4.35
3527 7558 5.289675 GTGTCTAGAAATCAATGGTGTCGAG 59.710 44.000 0.00 0.00 0.00 4.04
3528 7559 4.268884 GTCTAGAAATCAATGGTGTCGAGC 59.731 45.833 0.00 0.00 0.00 5.03
3529 7560 2.002586 AGAAATCAATGGTGTCGAGCG 58.997 47.619 0.00 0.00 0.00 5.03
3531 7562 2.665649 AATCAATGGTGTCGAGCGTA 57.334 45.000 0.00 0.00 0.00 4.42
3532 7563 2.209838 ATCAATGGTGTCGAGCGTAG 57.790 50.000 0.00 0.00 0.00 3.51
3536 7567 0.172803 ATGGTGTCGAGCGTAGGTTC 59.827 55.000 0.00 0.00 39.88 3.62
3537 7568 1.513586 GGTGTCGAGCGTAGGTTCG 60.514 63.158 14.47 14.47 46.64 3.95
3538 7569 1.513586 GTGTCGAGCGTAGGTTCGG 60.514 63.158 19.24 3.89 45.52 4.30
3539 7570 2.578981 GTCGAGCGTAGGTTCGGC 60.579 66.667 19.24 15.13 45.52 5.54
3540 7571 3.818787 TCGAGCGTAGGTTCGGCC 61.819 66.667 19.24 0.00 45.52 6.13
3552 7583 1.918868 GTTCGGCCGAACCATGGTTC 61.919 60.000 46.28 37.56 46.21 3.62
3561 7592 2.496111 GAACCATGGTTCCGTACAACA 58.504 47.619 37.55 0.00 46.21 3.33
3562 7593 2.871096 ACCATGGTTCCGTACAACAT 57.129 45.000 13.00 0.00 0.00 2.71
3565 7596 3.892588 ACCATGGTTCCGTACAACATTTT 59.107 39.130 13.00 0.00 0.00 1.82
3566 7597 4.022676 ACCATGGTTCCGTACAACATTTTC 60.023 41.667 13.00 0.00 0.00 2.29
3580 8278 4.729227 ACATTTTCGGACAAACTTGGTT 57.271 36.364 0.00 0.00 0.00 3.67
3583 8281 6.037726 ACATTTTCGGACAAACTTGGTTAAC 58.962 36.000 0.00 0.00 0.00 2.01
3591 8289 3.253921 ACAAACTTGGTTAACGGGCATAC 59.746 43.478 0.00 0.00 0.00 2.39
3617 8315 7.148738 CGAAAGGAAATGTATGTCTCCATATCG 60.149 40.741 0.00 0.00 36.02 2.92
3798 9145 2.487775 AGCAATGGTAGGGTGGTATCA 58.512 47.619 0.00 0.00 0.00 2.15
3865 9212 3.490419 GCGGTTCCGTACAGAACATCTAT 60.490 47.826 20.65 0.00 46.52 1.98
3944 11606 9.429359 AGAACAAGAATATCTTCAGTAGTTGTG 57.571 33.333 0.00 0.00 33.78 3.33
3980 11642 8.035394 TGAAAATACACAGGTCTATTCTCACTC 58.965 37.037 0.00 0.00 0.00 3.51
3981 11643 5.759506 ATACACAGGTCTATTCTCACTCG 57.240 43.478 0.00 0.00 0.00 4.18
4100 11762 1.661112 GCTCTCAATACACTTGCGGTC 59.339 52.381 0.00 0.00 0.00 4.79
4123 11788 7.221452 GGTCATGTTTGCATCAACAAGATTATC 59.779 37.037 11.19 1.18 33.72 1.75
4130 11795 7.868906 TGCATCAACAAGATTATCATTCAGA 57.131 32.000 0.00 0.00 33.72 3.27
4131 11796 7.927048 TGCATCAACAAGATTATCATTCAGAG 58.073 34.615 0.00 0.00 33.72 3.35
4157 11822 3.018856 TGCTATCTCCATTGCCAAACAG 58.981 45.455 0.00 0.00 30.36 3.16
4201 11867 1.219646 TCCGTGCTTCCAAACGTAAC 58.780 50.000 0.00 0.00 38.11 2.50
4205 11871 1.944709 GTGCTTCCAAACGTAACCACT 59.055 47.619 0.00 0.00 0.00 4.00
4247 11914 2.867368 CTCATGAGACAGATGCTTCAGC 59.133 50.000 18.34 0.00 42.50 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 0.960364 GCTTCACCCGAGGAATTGCA 60.960 55.000 0.00 0.00 0.00 4.08
507 2167 1.078426 GGTCCACGGGAATGGTGAG 60.078 63.158 0.00 0.00 40.95 3.51
641 2303 7.011994 AGCAATATGATCCATCCACCAATAAA 58.988 34.615 0.00 0.00 0.00 1.40
688 2350 4.942761 AGTGAACAAAATCATGGCTTGT 57.057 36.364 0.00 0.00 34.81 3.16
756 2418 1.301401 GCTACGGGCCATAATGCGA 60.301 57.895 4.39 0.00 34.27 5.10
847 2509 8.347035 CCCATTACCGAATTACGTTCAAAATAT 58.653 33.333 0.00 0.00 40.78 1.28
848 2510 7.679164 GCCCATTACCGAATTACGTTCAAAATA 60.679 37.037 0.00 0.00 40.78 1.40
849 2511 6.557110 CCCATTACCGAATTACGTTCAAAAT 58.443 36.000 0.00 0.00 40.78 1.82
850 2512 5.619533 GCCCATTACCGAATTACGTTCAAAA 60.620 40.000 0.00 0.00 40.78 2.44
851 2513 4.142643 GCCCATTACCGAATTACGTTCAAA 60.143 41.667 0.00 0.00 40.78 2.69
852 2514 3.374678 GCCCATTACCGAATTACGTTCAA 59.625 43.478 0.00 0.00 40.78 2.69
853 2515 2.937799 GCCCATTACCGAATTACGTTCA 59.062 45.455 0.00 0.00 40.78 3.18
854 2516 2.288729 GGCCCATTACCGAATTACGTTC 59.711 50.000 0.00 0.00 40.78 3.95
855 2517 2.291365 GGCCCATTACCGAATTACGTT 58.709 47.619 0.00 0.00 40.78 3.99
856 2518 1.957668 GGCCCATTACCGAATTACGT 58.042 50.000 0.00 0.00 40.78 3.57
865 2527 1.268845 CGTAAATTGCGGCCCATTACC 60.269 52.381 0.00 0.00 0.00 2.85
866 2528 1.268845 CCGTAAATTGCGGCCCATTAC 60.269 52.381 9.92 2.80 42.82 1.89
867 2529 1.025812 CCGTAAATTGCGGCCCATTA 58.974 50.000 9.92 0.00 42.82 1.90
868 2530 1.813192 CCGTAAATTGCGGCCCATT 59.187 52.632 9.92 0.00 42.82 3.16
869 2531 3.520402 CCGTAAATTGCGGCCCAT 58.480 55.556 9.92 0.00 42.82 4.00
876 2538 1.647084 CCTAGGCGCCGTAAATTGC 59.353 57.895 23.20 0.00 0.00 3.56
877 2539 1.647084 GCCTAGGCGCCGTAAATTG 59.353 57.895 23.20 7.77 0.00 2.32
878 2540 4.136250 GCCTAGGCGCCGTAAATT 57.864 55.556 23.20 4.49 0.00 1.82
992 2655 1.417592 GAGCGAGCAATGACACGTG 59.582 57.895 15.48 15.48 0.00 4.49
1002 2665 1.295423 GTTTGGGTAGGAGCGAGCA 59.705 57.895 0.00 0.00 0.00 4.26
1017 2680 0.822121 GCCGACTGAGGTTTGGGTTT 60.822 55.000 0.00 0.00 0.00 3.27
1288 2951 0.608035 ACCCAAATTCATCGGCGTGT 60.608 50.000 6.85 0.00 0.00 4.49
1319 3004 6.348498 TCTTGCGATCTGATCAAATTCCTAA 58.652 36.000 17.19 0.76 0.00 2.69
1320 3005 5.917462 TCTTGCGATCTGATCAAATTCCTA 58.083 37.500 17.19 0.00 0.00 2.94
1321 3006 4.774124 TCTTGCGATCTGATCAAATTCCT 58.226 39.130 17.19 0.00 0.00 3.36
1345 3085 4.458295 ACATTGACAGCAAGATTTGGAGAG 59.542 41.667 0.00 0.00 37.45 3.20
1350 3090 3.644823 TGCACATTGACAGCAAGATTTG 58.355 40.909 0.00 0.00 37.45 2.32
1351 3091 4.325028 TTGCACATTGACAGCAAGATTT 57.675 36.364 10.30 0.00 42.71 2.17
1370 3114 4.648651 TCCTCATGGATATGCATGACTTG 58.351 43.478 29.64 21.45 37.46 3.16
1372 3116 4.987963 TTCCTCATGGATATGCATGACT 57.012 40.909 29.64 0.00 42.81 3.41
1378 3122 6.602406 AGCATAGAAATTCCTCATGGATATGC 59.398 38.462 14.69 14.69 46.42 3.14
1421 3174 4.684134 GTGCACCCTGGGCATGGT 62.684 66.667 14.08 0.00 44.11 3.55
1447 3200 0.984230 TGGAGTCGGATGCTTTTCCT 59.016 50.000 0.00 0.00 33.30 3.36
1503 3259 3.142393 CCTAGCCATGACCTCCCG 58.858 66.667 0.00 0.00 0.00 5.14
1534 3293 1.937362 GTGCGTGTTGTTTGGTCGC 60.937 57.895 0.00 0.00 45.70 5.19
1536 3295 0.730265 TCTGTGCGTGTTGTTTGGTC 59.270 50.000 0.00 0.00 0.00 4.02
1559 3318 3.326297 ACCTCTCTTTCCACTTGGAGAAG 59.674 47.826 0.00 6.08 46.36 2.85
1586 3345 0.101219 TCACCAGATCGTCGCTGATG 59.899 55.000 1.88 0.00 35.39 3.07
1622 3381 3.746045 AGAAAAGACAAGACCGTGCTA 57.254 42.857 0.00 0.00 0.00 3.49
1628 3387 3.815962 GACCCTGAAGAAAAGACAAGACC 59.184 47.826 0.00 0.00 0.00 3.85
1760 4646 8.995027 ACCACCTGAAATTTATAGCATCATAA 57.005 30.769 0.00 0.00 0.00 1.90
1767 4653 5.965922 AGCAAACCACCTGAAATTTATAGC 58.034 37.500 0.00 0.00 0.00 2.97
1882 4829 0.389948 GACGCCGAGGACTGTGAATT 60.390 55.000 0.00 0.00 0.00 2.17
1890 4840 1.289800 GGTTTCTTGACGCCGAGGAC 61.290 60.000 0.00 0.00 0.00 3.85
1891 4841 1.005394 GGTTTCTTGACGCCGAGGA 60.005 57.895 0.00 0.00 0.00 3.71
1913 4863 2.608970 ATCTGCGGATCGGGGGTTTG 62.609 60.000 0.90 0.00 0.00 2.93
1916 4866 3.550431 CATCTGCGGATCGGGGGT 61.550 66.667 4.63 0.00 0.00 4.95
2038 5000 1.457346 CCAGGTTCTTGAGGATGCAC 58.543 55.000 0.00 0.00 0.00 4.57
2065 5027 2.048503 CCGTGGAACCGGTGAGAC 60.049 66.667 8.52 3.69 43.07 3.36
2101 5063 1.174078 TGTTGAGACCGTCGGCACTA 61.174 55.000 12.28 0.00 0.00 2.74
2177 5141 3.313526 GTGCATCTTCAACGGAGCAATAT 59.686 43.478 0.00 0.00 33.37 1.28
2196 5160 4.776647 GACCAATTGGCGCCGTGC 62.777 66.667 24.79 4.30 45.38 5.34
2206 5170 3.676873 GCAATTGCTTGATCCGACCAATT 60.677 43.478 23.21 0.00 36.77 2.32
2209 5173 0.810648 GCAATTGCTTGATCCGACCA 59.189 50.000 23.21 0.00 38.21 4.02
2228 5192 1.000283 GGCAGAGATGATACCACTCCG 60.000 57.143 0.00 0.00 0.00 4.63
2273 5237 3.734902 GCATGACCTTTTATCCTTTGCGG 60.735 47.826 0.00 0.00 0.00 5.69
2340 5304 2.569059 TGTATACTAAGCTCGTCGGCT 58.431 47.619 4.17 2.81 45.30 5.52
2342 5306 4.744136 TGATGTATACTAAGCTCGTCGG 57.256 45.455 4.17 0.00 0.00 4.79
2353 5317 1.344763 GGCCGGAGCTTGATGTATACT 59.655 52.381 5.05 0.00 39.73 2.12
2433 5397 1.707632 CCTCTCGTTTGCTGACAGAG 58.292 55.000 6.65 0.00 0.00 3.35
2434 5398 0.319900 GCCTCTCGTTTGCTGACAGA 60.320 55.000 6.65 0.00 0.00 3.41
2582 5552 1.204704 TCTGAATTGATCACCGCTCGT 59.795 47.619 0.00 0.00 33.47 4.18
2608 5578 1.150827 CTTGAACGCATCTGACAGCA 58.849 50.000 0.00 0.00 0.00 4.41
2613 5583 1.205655 CCTCTCCTTGAACGCATCTGA 59.794 52.381 0.00 0.00 0.00 3.27
2629 5599 0.767375 TGCTTCCTGCTCAAACCTCT 59.233 50.000 0.00 0.00 43.37 3.69
2637 5607 2.970974 GCGGTTGTGCTTCCTGCTC 61.971 63.158 0.00 0.00 43.37 4.26
2653 5623 1.207593 CTTTTCGAAGGTGGCAGCG 59.792 57.895 11.51 1.84 0.00 5.18
2655 5625 2.977405 CTTCTTTTCGAAGGTGGCAG 57.023 50.000 0.00 0.00 44.37 4.85
2748 5727 2.434884 CGTGTCGGAGCTTGCCAT 60.435 61.111 0.00 0.00 0.00 4.40
2806 5785 2.086869 CTAACCCACAGTCAGCCATTG 58.913 52.381 0.00 0.00 0.00 2.82
2816 5795 1.337447 CCACCGTACACTAACCCACAG 60.337 57.143 0.00 0.00 0.00 3.66
2870 5849 2.877168 GGCTTCTCTATGAATGCCACAG 59.123 50.000 0.00 0.00 42.81 3.66
2882 5861 3.051940 AGATGGATGGTGGCTTCTCTA 57.948 47.619 0.00 0.00 0.00 2.43
2985 6333 5.240844 TGCATCATAATGATTCTCAAGCCTG 59.759 40.000 0.00 0.00 34.28 4.85
3027 6375 0.601311 GATGCCACCCTATGACGCTC 60.601 60.000 0.00 0.00 0.00 5.03
3029 6377 1.956170 CGATGCCACCCTATGACGC 60.956 63.158 0.00 0.00 0.00 5.19
3030 6378 0.671796 TACGATGCCACCCTATGACG 59.328 55.000 0.00 0.00 0.00 4.35
3033 6381 1.412710 ACACTACGATGCCACCCTATG 59.587 52.381 0.00 0.00 0.00 2.23
3035 6383 1.563924 AACACTACGATGCCACCCTA 58.436 50.000 0.00 0.00 0.00 3.53
3037 6385 2.210116 CATAACACTACGATGCCACCC 58.790 52.381 0.00 0.00 0.00 4.61
3038 6386 2.901249 ACATAACACTACGATGCCACC 58.099 47.619 0.00 0.00 0.00 4.61
3039 6387 5.751509 TGAATACATAACACTACGATGCCAC 59.248 40.000 0.00 0.00 0.00 5.01
3040 6388 5.908341 TGAATACATAACACTACGATGCCA 58.092 37.500 0.00 0.00 0.00 4.92
3041 6389 5.983720 ACTGAATACATAACACTACGATGCC 59.016 40.000 0.00 0.00 0.00 4.40
3042 6390 6.475727 ACACTGAATACATAACACTACGATGC 59.524 38.462 0.00 0.00 0.00 3.91
3043 6391 7.987268 ACACTGAATACATAACACTACGATG 57.013 36.000 0.00 0.00 0.00 3.84
3049 6397 9.998106 AGAACTTTACACTGAATACATAACACT 57.002 29.630 0.00 0.00 0.00 3.55
3065 6413 8.823818 GCCTTTCGCTATTATAAGAACTTTACA 58.176 33.333 0.00 0.00 0.00 2.41
3066 6414 8.823818 TGCCTTTCGCTATTATAAGAACTTTAC 58.176 33.333 0.00 0.00 38.78 2.01
3067 6415 8.951787 TGCCTTTCGCTATTATAAGAACTTTA 57.048 30.769 0.00 0.00 38.78 1.85
3068 6416 7.859325 TGCCTTTCGCTATTATAAGAACTTT 57.141 32.000 0.00 0.00 38.78 2.66
3070 6418 6.018994 CGTTGCCTTTCGCTATTATAAGAACT 60.019 38.462 0.00 0.00 38.78 3.01
3071 6419 6.019318 TCGTTGCCTTTCGCTATTATAAGAAC 60.019 38.462 0.00 0.00 38.78 3.01
3072 6420 6.044046 TCGTTGCCTTTCGCTATTATAAGAA 58.956 36.000 0.00 0.00 38.78 2.52
3073 6421 5.593968 TCGTTGCCTTTCGCTATTATAAGA 58.406 37.500 0.00 0.00 38.78 2.10
3074 6422 5.107453 CCTCGTTGCCTTTCGCTATTATAAG 60.107 44.000 0.00 0.00 38.78 1.73
3075 6423 4.748102 CCTCGTTGCCTTTCGCTATTATAA 59.252 41.667 0.00 0.00 38.78 0.98
3076 6424 4.304110 CCTCGTTGCCTTTCGCTATTATA 58.696 43.478 0.00 0.00 38.78 0.98
3077 6425 3.131396 CCTCGTTGCCTTTCGCTATTAT 58.869 45.455 0.00 0.00 38.78 1.28
3078 6426 2.546778 CCTCGTTGCCTTTCGCTATTA 58.453 47.619 0.00 0.00 38.78 0.98
3079 6427 1.369625 CCTCGTTGCCTTTCGCTATT 58.630 50.000 0.00 0.00 38.78 1.73
3080 6428 1.090052 GCCTCGTTGCCTTTCGCTAT 61.090 55.000 0.00 0.00 38.78 2.97
3081 6429 1.740296 GCCTCGTTGCCTTTCGCTA 60.740 57.895 0.00 0.00 38.78 4.26
3082 6430 3.050275 GCCTCGTTGCCTTTCGCT 61.050 61.111 0.00 0.00 38.78 4.93
3109 6457 4.161377 TGATGATCATCGACCCAAGTTACA 59.839 41.667 26.52 6.07 40.63 2.41
3281 7200 9.612620 CCGCTTAAAAGAATAATTGTATGATCC 57.387 33.333 0.00 0.00 0.00 3.36
3324 7243 7.730364 AGGTTCGTTAATGATTGTATGATCC 57.270 36.000 0.00 0.00 0.00 3.36
3326 7245 9.219603 CCATAGGTTCGTTAATGATTGTATGAT 57.780 33.333 15.63 0.00 0.00 2.45
3327 7246 8.208224 ACCATAGGTTCGTTAATGATTGTATGA 58.792 33.333 15.63 0.00 27.29 2.15
3338 7369 6.778834 TGACATAGACCATAGGTTCGTTAA 57.221 37.500 0.00 0.00 35.25 2.01
3339 7370 6.971726 ATGACATAGACCATAGGTTCGTTA 57.028 37.500 0.00 0.00 35.25 3.18
3343 7374 6.570672 TCGTATGACATAGACCATAGGTTC 57.429 41.667 0.00 0.00 35.25 3.62
3345 7376 7.540474 AAATCGTATGACATAGACCATAGGT 57.460 36.000 0.00 0.00 39.44 3.08
3349 7380 9.424319 GATGTTAAATCGTATGACATAGACCAT 57.576 33.333 0.00 0.00 31.59 3.55
3356 7387 9.909644 GTAGTAGGATGTTAAATCGTATGACAT 57.090 33.333 0.00 0.00 33.93 3.06
3359 7390 9.908152 CATGTAGTAGGATGTTAAATCGTATGA 57.092 33.333 0.00 0.00 0.00 2.15
3360 7391 9.692749 ACATGTAGTAGGATGTTAAATCGTATG 57.307 33.333 0.00 0.00 27.94 2.39
3361 7392 9.692749 CACATGTAGTAGGATGTTAAATCGTAT 57.307 33.333 0.00 0.00 30.14 3.06
3362 7393 8.139350 CCACATGTAGTAGGATGTTAAATCGTA 58.861 37.037 0.00 0.00 30.14 3.43
3363 7394 6.984474 CCACATGTAGTAGGATGTTAAATCGT 59.016 38.462 0.00 0.00 30.14 3.73
3364 7395 7.207383 TCCACATGTAGTAGGATGTTAAATCG 58.793 38.462 0.00 0.00 30.14 3.34
3365 7396 8.993121 CATCCACATGTAGTAGGATGTTAAATC 58.007 37.037 24.77 0.00 43.44 2.17
3373 7404 4.962362 TCACACATCCACATGTAGTAGGAT 59.038 41.667 9.15 9.15 41.69 3.24
3374 7405 4.159693 GTCACACATCCACATGTAGTAGGA 59.840 45.833 0.00 0.75 41.69 2.94
3375 7406 4.081697 TGTCACACATCCACATGTAGTAGG 60.082 45.833 0.00 0.00 41.69 3.18
3376 7407 5.072040 TGTCACACATCCACATGTAGTAG 57.928 43.478 0.00 0.00 41.69 2.57
3377 7408 5.675684 ATGTCACACATCCACATGTAGTA 57.324 39.130 0.00 0.00 41.69 1.82
3378 7409 4.558226 ATGTCACACATCCACATGTAGT 57.442 40.909 0.00 0.00 41.69 2.73
3379 7410 4.937015 TGAATGTCACACATCCACATGTAG 59.063 41.667 0.00 0.00 41.69 2.74
3380 7411 4.904241 TGAATGTCACACATCCACATGTA 58.096 39.130 0.00 0.00 41.69 2.29
3381 7412 3.753815 TGAATGTCACACATCCACATGT 58.246 40.909 0.00 0.00 44.72 3.21
3382 7413 4.668289 CATGAATGTCACACATCCACATG 58.332 43.478 12.50 12.50 37.97 3.21
3383 7414 3.129813 GCATGAATGTCACACATCCACAT 59.870 43.478 0.00 0.00 37.97 3.21
3385 7416 2.159338 GGCATGAATGTCACACATCCAC 60.159 50.000 0.00 0.00 37.97 4.02
3387 7418 2.093890 TGGCATGAATGTCACACATCC 58.906 47.619 0.00 0.00 37.97 3.51
3388 7419 3.192001 AGTTGGCATGAATGTCACACATC 59.808 43.478 0.00 0.00 42.90 3.06
3391 7422 2.923605 GCAGTTGGCATGAATGTCACAC 60.924 50.000 0.00 0.48 42.90 3.82
3392 7423 1.270274 GCAGTTGGCATGAATGTCACA 59.730 47.619 0.00 0.00 42.90 3.58
3393 7424 1.986698 GCAGTTGGCATGAATGTCAC 58.013 50.000 0.00 0.00 42.90 3.67
3427 7458 5.354513 GTCTATTCATGAGGATCCATGCATG 59.645 44.000 24.86 24.86 42.63 4.06
3428 7459 5.013808 TGTCTATTCATGAGGATCCATGCAT 59.986 40.000 15.82 11.45 42.63 3.96
3429 7460 4.348754 TGTCTATTCATGAGGATCCATGCA 59.651 41.667 15.82 9.47 42.63 3.96
3430 7461 4.903054 TGTCTATTCATGAGGATCCATGC 58.097 43.478 15.82 3.29 42.63 4.06
3431 7462 5.354513 GCATGTCTATTCATGAGGATCCATG 59.645 44.000 15.82 10.15 45.41 3.66
3432 7463 5.013808 TGCATGTCTATTCATGAGGATCCAT 59.986 40.000 15.82 0.00 45.41 3.41
3433 7464 4.348754 TGCATGTCTATTCATGAGGATCCA 59.651 41.667 15.82 0.00 45.41 3.41
3434 7465 4.903054 TGCATGTCTATTCATGAGGATCC 58.097 43.478 2.48 2.48 45.41 3.36
3435 7466 5.938710 ACATGCATGTCTATTCATGAGGATC 59.061 40.000 26.61 0.00 45.41 3.36
3436 7467 5.877491 ACATGCATGTCTATTCATGAGGAT 58.123 37.500 26.61 0.00 45.41 3.24
3437 7468 5.300411 ACATGCATGTCTATTCATGAGGA 57.700 39.130 26.61 0.00 45.41 3.71
3489 7520 9.638239 GATTTCTAGACACTATTCATGAGGATC 57.362 37.037 0.00 0.00 0.00 3.36
3495 7526 9.334947 ACCATTGATTTCTAGACACTATTCATG 57.665 33.333 0.00 0.00 0.00 3.07
3501 7532 6.152154 TCGACACCATTGATTTCTAGACACTA 59.848 38.462 0.00 0.00 0.00 2.74
3503 7534 5.168569 TCGACACCATTGATTTCTAGACAC 58.831 41.667 0.00 0.00 0.00 3.67
3505 7536 4.268884 GCTCGACACCATTGATTTCTAGAC 59.731 45.833 0.00 0.00 0.00 2.59
3507 7538 3.243877 CGCTCGACACCATTGATTTCTAG 59.756 47.826 0.00 0.00 0.00 2.43
3508 7539 3.186909 CGCTCGACACCATTGATTTCTA 58.813 45.455 0.00 0.00 0.00 2.10
3511 7542 1.808411 ACGCTCGACACCATTGATTT 58.192 45.000 0.00 0.00 0.00 2.17
3512 7543 2.540515 CTACGCTCGACACCATTGATT 58.459 47.619 0.00 0.00 0.00 2.57
3513 7544 1.202417 CCTACGCTCGACACCATTGAT 60.202 52.381 0.00 0.00 0.00 2.57
3514 7545 0.172578 CCTACGCTCGACACCATTGA 59.827 55.000 0.00 0.00 0.00 2.57
3518 7549 1.582968 GAACCTACGCTCGACACCA 59.417 57.895 0.00 0.00 0.00 4.17
3521 7552 2.872557 CCGAACCTACGCTCGACA 59.127 61.111 0.00 0.00 37.23 4.35
3522 7553 2.578981 GCCGAACCTACGCTCGAC 60.579 66.667 0.00 0.00 37.23 4.20
3523 7554 3.818787 GGCCGAACCTACGCTCGA 61.819 66.667 0.00 0.00 37.23 4.04
3525 7556 3.346631 TTCGGCCGAACCTACGCTC 62.347 63.158 35.81 0.00 35.61 5.03
3527 7558 3.184003 GTTCGGCCGAACCTACGC 61.184 66.667 46.28 28.81 46.21 4.42
3545 7576 4.155449 CGAAAATGTTGTACGGAACCATG 58.845 43.478 0.00 0.00 0.00 3.66
3547 7578 2.548904 CCGAAAATGTTGTACGGAACCA 59.451 45.455 0.00 0.00 45.31 3.67
3548 7579 3.191735 CCGAAAATGTTGTACGGAACC 57.808 47.619 0.00 0.00 45.31 3.62
3552 7583 3.881780 TTGTCCGAAAATGTTGTACGG 57.118 42.857 0.00 0.00 44.09 4.02
3553 7584 4.839796 AGTTTGTCCGAAAATGTTGTACG 58.160 39.130 0.00 0.00 0.00 3.67
3554 7585 5.457473 CCAAGTTTGTCCGAAAATGTTGTAC 59.543 40.000 0.00 0.00 0.00 2.90
3558 7589 4.729227 ACCAAGTTTGTCCGAAAATGTT 57.271 36.364 0.00 0.00 0.00 2.71
3560 7591 5.172411 CGTTAACCAAGTTTGTCCGAAAATG 59.828 40.000 0.00 0.00 0.00 2.32
3561 7592 5.275494 CGTTAACCAAGTTTGTCCGAAAAT 58.725 37.500 0.00 0.00 0.00 1.82
3562 7593 4.438472 CCGTTAACCAAGTTTGTCCGAAAA 60.438 41.667 0.00 0.00 0.00 2.29
3565 7596 2.211806 CCGTTAACCAAGTTTGTCCGA 58.788 47.619 0.00 0.00 0.00 4.55
3566 7597 1.264826 CCCGTTAACCAAGTTTGTCCG 59.735 52.381 0.00 0.00 0.00 4.79
3580 8278 3.331478 TTTCCTTTCGTATGCCCGTTA 57.669 42.857 0.00 0.00 0.00 3.18
3583 8281 2.014128 ACATTTCCTTTCGTATGCCCG 58.986 47.619 0.00 0.00 0.00 6.13
3659 8361 8.732746 AATGTAAGTCTTGTAAACTCTTGTGT 57.267 30.769 0.00 0.00 0.00 3.72
3699 9043 5.473931 CCCTCTGATGAATGGTATTAGACG 58.526 45.833 0.00 0.00 0.00 4.18
3798 9145 2.579860 AGGTCCTTGCATGGAAATCTCT 59.420 45.455 21.99 11.83 37.93 3.10
3865 9212 3.627237 GGAAGTTCCCAAGATAATGGCCA 60.627 47.826 8.56 8.56 39.26 5.36
3944 11606 4.244862 CTGTGTATTTTCAACCAATGGGC 58.755 43.478 3.55 0.00 37.90 5.36
3980 11642 1.091771 AGCATCCGCATGAACTTCCG 61.092 55.000 0.00 0.00 42.27 4.30
3981 11643 0.659957 GAGCATCCGCATGAACTTCC 59.340 55.000 0.00 0.00 42.27 3.46
4093 11755 0.957362 TGATGCAAACATGACCGCAA 59.043 45.000 0.00 0.00 38.01 4.85
4100 11762 8.642908 ATGATAATCTTGTTGATGCAAACATG 57.357 30.769 4.85 7.61 39.68 3.21
4130 11795 3.393609 TGGCAATGGAGATAGCAGAATCT 59.606 43.478 0.00 0.00 38.95 2.40
4131 11796 3.748083 TGGCAATGGAGATAGCAGAATC 58.252 45.455 0.00 0.00 0.00 2.52
4157 11822 2.045926 ATGCACCCGAGGCTTGTC 60.046 61.111 0.12 0.00 0.00 3.18
4247 11914 4.955925 TGGAACAACACACACTTTAGTG 57.044 40.909 8.29 8.29 44.16 2.74


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

AutoCloner maintained by Alex Coulton.