Multiple sequence alignment - TraesCS1B01G055100

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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 TraesCS1B01G055100 chr1B 100.000 5058 0 0 1 5058 37573221 37568164 0.000000e+00 9341.0
1 TraesCS1B01G055100 chr1B 94.035 3621 148 36 584 4190 37317925 37321491 0.000000e+00 5428.0
2 TraesCS1B01G055100 chr1B 96.379 2016 54 8 2570 4581 38119419 38121419 0.000000e+00 3301.0
3 TraesCS1B01G055100 chr1B 91.138 1986 88 35 658 2624 38117530 38119446 0.000000e+00 2612.0
4 TraesCS1B01G055100 chr1B 98.925 279 3 0 4658 4936 660398567 660398845 2.720000e-137 499.0
5 TraesCS1B01G055100 chr1D 94.968 3617 118 33 852 4457 21885381 21888944 0.000000e+00 5613.0
6 TraesCS1B01G055100 chr1D 92.388 2601 149 25 240 2825 21929585 21927019 0.000000e+00 3661.0
7 TraesCS1B01G055100 chr1D 86.146 1855 197 32 2598 4407 21727990 21726151 0.000000e+00 1947.0
8 TraesCS1B01G055100 chr1D 96.343 793 16 8 2916 3705 21927016 21926234 0.000000e+00 1291.0
9 TraesCS1B01G055100 chr1D 89.839 807 61 9 1011 1796 21728993 21728187 0.000000e+00 1016.0
10 TraesCS1B01G055100 chr1D 92.857 490 28 4 3702 4190 21911631 21911148 0.000000e+00 704.0
11 TraesCS1B01G055100 chr1D 83.175 737 113 9 3393 4122 22102302 22103034 0.000000e+00 664.0
12 TraesCS1B01G055100 chr1D 88.358 335 36 3 240 572 21882489 21882822 2.840000e-107 399.0
13 TraesCS1B01G055100 chr1D 81.381 478 69 8 2056 2517 300672429 300671956 6.180000e-99 372.0
14 TraesCS1B01G055100 chr1D 84.857 350 28 12 584 929 21729324 21728996 3.780000e-86 329.0
15 TraesCS1B01G055100 chrUn 95.224 3371 105 22 865 4215 289137 285803 0.000000e+00 5282.0
16 TraesCS1B01G055100 chrUn 99.112 1126 10 0 3535 4660 258723 257598 0.000000e+00 2025.0
17 TraesCS1B01G055100 chrUn 84.521 2035 220 50 2598 4566 223066 225071 0.000000e+00 1925.0
18 TraesCS1B01G055100 chrUn 90.851 940 57 12 865 1796 221958 222876 0.000000e+00 1232.0
19 TraesCS1B01G055100 chrUn 90.957 575 40 3 1 574 289740 289177 0.000000e+00 763.0
20 TraesCS1B01G055100 chrUn 90.783 575 41 3 1 574 221355 221918 0.000000e+00 758.0
21 TraesCS1B01G055100 chrUn 87.429 350 41 3 240 588 291750 291403 2.840000e-107 399.0
22 TraesCS1B01G055100 chrUn 87.917 240 13 6 4410 4633 284312 284073 8.350000e-68 268.0
23 TraesCS1B01G055100 chrUn 94.479 163 7 1 4207 4369 284467 284307 3.020000e-62 250.0
24 TraesCS1B01G055100 chrUn 100.000 125 0 0 4934 5058 257600 257476 1.100000e-56 231.0
25 TraesCS1B01G055100 chrUn 93.750 112 7 0 1 112 258834 258723 8.710000e-38 169.0
26 TraesCS1B01G055100 chrUn 81.421 183 31 2 1819 1998 222866 223048 4.080000e-31 147.0
27 TraesCS1B01G055100 chr2B 98.925 279 3 0 4658 4936 198448733 198449011 2.720000e-137 499.0
28 TraesCS1B01G055100 chr5B 98.571 280 4 0 4658 4937 66293412 66293133 3.520000e-136 496.0
29 TraesCS1B01G055100 chr5B 98.208 279 5 0 4658 4936 487639387 487639109 5.890000e-134 488.0
30 TraesCS1B01G055100 chr5B 90.141 71 7 0 179 249 26393307 26393377 5.390000e-15 93.5
31 TraesCS1B01G055100 chr7B 98.909 275 3 0 4660 4934 709760111 709760385 4.550000e-135 492.0
32 TraesCS1B01G055100 chr7B 98.545 275 4 0 4660 4934 629872945 629873219 2.120000e-133 486.0
33 TraesCS1B01G055100 chr4B 98.214 280 5 0 4657 4936 595706117 595705838 1.640000e-134 490.0
34 TraesCS1B01G055100 chr4B 98.208 279 5 0 4658 4936 453049516 453049238 5.890000e-134 488.0
35 TraesCS1B01G055100 chr4B 98.208 279 5 0 4658 4936 590862205 590861927 5.890000e-134 488.0
36 TraesCS1B01G055100 chr4B 84.483 464 45 17 2045 2486 1247862 1247404 2.800000e-117 433.0
37 TraesCS1B01G055100 chr3D 85.386 479 55 7 2056 2521 264714473 264714949 2.740000e-132 483.0
38 TraesCS1B01G055100 chr4D 86.547 446 42 13 2057 2486 353045898 353046341 4.580000e-130 475.0
39 TraesCS1B01G055100 chr3A 84.375 480 57 8 2056 2521 325304575 325305050 5.970000e-124 455.0
40 TraesCS1B01G055100 chr6B 84.340 447 39 17 2056 2486 460084476 460084907 4.710000e-110 409.0
41 TraesCS1B01G055100 chr6B 90.141 71 7 0 179 249 522517049 522517119 5.390000e-15 93.5
42 TraesCS1B01G055100 chr5A 83.333 462 54 16 2056 2499 679497400 679497856 6.100000e-109 405.0
43 TraesCS1B01G055100 chr5A 86.345 249 27 6 1 246 293506365 293506609 1.080000e-66 265.0
44 TraesCS1B01G055100 chr7D 90.347 259 20 2 1 254 566210740 566210998 8.110000e-88 335.0
45 TraesCS1B01G055100 chr1A 87.938 257 22 6 1 249 67707477 67707732 1.380000e-75 294.0
46 TraesCS1B01G055100 chr5D 89.610 77 8 0 180 256 494689207 494689283 1.160000e-16 99.0
47 TraesCS1B01G055100 chr2A 88.158 76 7 2 179 253 4067002 4067076 6.970000e-14 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 TraesCS1B01G055100 chr1B 37568164 37573221 5057 True 9341.000000 9341 100.000000 1 5058 1 chr1B.!!$R1 5057
1 TraesCS1B01G055100 chr1B 37317925 37321491 3566 False 5428.000000 5428 94.035000 584 4190 1 chr1B.!!$F1 3606
2 TraesCS1B01G055100 chr1B 38117530 38121419 3889 False 2956.500000 3301 93.758500 658 4581 2 chr1B.!!$F3 3923
3 TraesCS1B01G055100 chr1D 21882489 21888944 6455 False 3006.000000 5613 91.663000 240 4457 2 chr1D.!!$F2 4217
4 TraesCS1B01G055100 chr1D 21926234 21929585 3351 True 2476.000000 3661 94.365500 240 3705 2 chr1D.!!$R4 3465
5 TraesCS1B01G055100 chr1D 21726151 21729324 3173 True 1097.333333 1947 86.947333 584 4407 3 chr1D.!!$R3 3823
6 TraesCS1B01G055100 chr1D 22102302 22103034 732 False 664.000000 664 83.175000 3393 4122 1 chr1D.!!$F1 729
7 TraesCS1B01G055100 chrUn 284073 291750 7677 True 1392.400000 5282 91.201200 1 4633 5 chrUn.!!$R2 4632
8 TraesCS1B01G055100 chrUn 221355 225071 3716 False 1015.500000 1925 86.894000 1 4566 4 chrUn.!!$F1 4565
9 TraesCS1B01G055100 chrUn 257476 258834 1358 True 808.333333 2025 97.620667 1 5058 3 chrUn.!!$R1 5057

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
368 2380 0.031449 GCGAGAGGTGCCATCTAGTC 59.969 60.000 0.00 0.00 0.00 2.59 F
948 5290 0.763604 TAACCTGTCCCGACCCAACA 60.764 55.000 0.00 0.00 0.00 3.33 F
1414 5775 0.689080 AGGAGGGCAGTGATGACGAT 60.689 55.000 0.00 0.00 0.00 3.73 F
1555 5947 0.770590 CGATTATGAAGACGACGGCG 59.229 55.000 10.39 10.39 44.79 6.46 F
2326 6778 2.519013 GAAGAATTGGTTGGGCAGAGT 58.481 47.619 0.00 0.00 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 5754 1.326213 CGTCATCACTGCCCTCCTCT 61.326 60.000 0.00 0.0 0.00 3.69 R
2016 6467 1.598882 TGGTTTCATAGCAACGCACA 58.401 45.000 0.00 0.0 0.00 4.57 R
3044 7543 2.373169 TGAGAACTGGTCTGATGGCTTT 59.627 45.455 0.00 0.0 36.41 3.51 R
3167 7676 5.086058 CCGTCTTAATTGCACATGTGTAAC 58.914 41.667 28.27 15.9 37.97 2.50 R
4241 10139 2.095415 GGCCACATAAAAGTCAACGGTC 60.095 50.000 0.00 0.0 0.00 4.79 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
26 2037 0.611340 AAGAAGACGTAGAGGCCGGT 60.611 55.000 1.90 0.00 0.00 5.28
41 2052 1.598924 GCCGGTAGAACTAATCGACGG 60.599 57.143 1.90 0.00 42.43 4.79
85 2096 3.118261 GCAGATGGGTCTACATGGAAAGA 60.118 47.826 0.00 0.00 32.09 2.52
95 2106 1.281867 ACATGGAAAGATGGAAGCGGA 59.718 47.619 0.00 0.00 0.00 5.54
99 2110 1.066143 GGAAAGATGGAAGCGGAGACA 60.066 52.381 0.00 0.00 0.00 3.41
106 2117 1.347707 TGGAAGCGGAGACAGTTCATT 59.652 47.619 0.00 0.00 0.00 2.57
149 2161 5.163864 ACACGTGTCATTATGCATGTTGTAG 60.164 40.000 17.22 3.48 33.10 2.74
198 2210 4.885907 CACTTGATGATGTGGATAGGCTTT 59.114 41.667 0.00 0.00 0.00 3.51
348 2360 5.999205 TTGCAACAGATTCCCACAATAAT 57.001 34.783 0.00 0.00 0.00 1.28
359 2371 1.331756 CCACAATAATGCGAGAGGTGC 59.668 52.381 0.00 0.00 0.00 5.01
368 2380 0.031449 GCGAGAGGTGCCATCTAGTC 59.969 60.000 0.00 0.00 0.00 2.59
438 2451 2.863132 ACCAACAAGCGGTATTACCA 57.137 45.000 13.22 0.00 38.47 3.25
445 2458 4.083565 ACAAGCGGTATTACCACCAAAAT 58.916 39.130 13.22 0.00 38.47 1.82
448 2461 4.532834 AGCGGTATTACCACCAAAATGAT 58.467 39.130 13.22 0.00 38.47 2.45
494 2508 9.213799 GGCTATTCTATTTTGATCAAGGACTAG 57.786 37.037 8.41 12.82 0.00 2.57
512 2526 6.522946 GGACTAGTTCCACAAGAGTAAACTT 58.477 40.000 0.00 0.00 45.10 2.66
587 3872 5.856126 TGATTGAGCGAGTCGTTAAAAAT 57.144 34.783 15.08 8.97 0.00 1.82
588 3873 6.954616 TGATTGAGCGAGTCGTTAAAAATA 57.045 33.333 15.08 0.00 0.00 1.40
589 3874 7.534085 TGATTGAGCGAGTCGTTAAAAATAT 57.466 32.000 15.08 0.00 0.00 1.28
590 3875 7.398746 TGATTGAGCGAGTCGTTAAAAATATG 58.601 34.615 15.08 0.00 0.00 1.78
592 3877 6.715344 TGAGCGAGTCGTTAAAAATATGTT 57.285 33.333 15.08 0.00 0.00 2.71
593 3878 6.758149 TGAGCGAGTCGTTAAAAATATGTTC 58.242 36.000 15.08 0.00 0.00 3.18
594 3879 6.366604 TGAGCGAGTCGTTAAAAATATGTTCA 59.633 34.615 15.08 0.00 0.00 3.18
596 3881 7.399523 AGCGAGTCGTTAAAAATATGTTCATC 58.600 34.615 15.08 0.00 0.00 2.92
647 3933 6.143118 TGAAATCGCGAACATTTTTCGAATTT 59.857 30.769 15.24 11.90 43.97 1.82
648 3934 4.859941 TCGCGAACATTTTTCGAATTTG 57.140 36.364 6.20 0.00 43.97 2.32
711 3997 6.347725 CGTGATTCCGAGAATCAGAACTTTTT 60.348 38.462 21.95 0.00 33.78 1.94
843 5172 3.064271 CCACGTTTATAACCCGTTCCATG 59.936 47.826 6.63 0.00 31.46 3.66
870 5212 6.768861 TCCATGTACCTCGAAAGAAAAAGAAA 59.231 34.615 0.00 0.00 41.32 2.52
871 5213 7.283580 TCCATGTACCTCGAAAGAAAAAGAAAA 59.716 33.333 0.00 0.00 41.32 2.29
872 5214 7.918562 CCATGTACCTCGAAAGAAAAAGAAAAA 59.081 33.333 0.00 0.00 41.32 1.94
873 5215 8.958043 CATGTACCTCGAAAGAAAAAGAAAAAG 58.042 33.333 0.00 0.00 41.32 2.27
874 5216 8.271312 TGTACCTCGAAAGAAAAAGAAAAAGA 57.729 30.769 0.00 0.00 41.32 2.52
875 5217 8.732531 TGTACCTCGAAAGAAAAAGAAAAAGAA 58.267 29.630 0.00 0.00 41.32 2.52
876 5218 9.563898 GTACCTCGAAAGAAAAAGAAAAAGAAA 57.436 29.630 0.00 0.00 41.32 2.52
878 5220 9.483916 ACCTCGAAAGAAAAAGAAAAAGAAAAA 57.516 25.926 0.00 0.00 41.32 1.94
879 5221 9.958285 CCTCGAAAGAAAAAGAAAAAGAAAAAG 57.042 29.630 0.00 0.00 41.32 2.27
948 5290 0.763604 TAACCTGTCCCGACCCAACA 60.764 55.000 0.00 0.00 0.00 3.33
1009 5358 3.101209 CCGTGTTGATGGCATCGG 58.899 61.111 21.65 15.56 0.00 4.18
1137 5486 3.961414 GGGGTGGAGGTTGCCGAA 61.961 66.667 0.00 0.00 0.00 4.30
1198 5547 2.475155 TCATGCATCTCCACTCTTCCT 58.525 47.619 0.00 0.00 0.00 3.36
1199 5548 2.433604 TCATGCATCTCCACTCTTCCTC 59.566 50.000 0.00 0.00 0.00 3.71
1200 5549 2.244486 TGCATCTCCACTCTTCCTCT 57.756 50.000 0.00 0.00 0.00 3.69
1201 5550 1.829849 TGCATCTCCACTCTTCCTCTG 59.170 52.381 0.00 0.00 0.00 3.35
1202 5551 1.830477 GCATCTCCACTCTTCCTCTGT 59.170 52.381 0.00 0.00 0.00 3.41
1203 5552 2.235898 GCATCTCCACTCTTCCTCTGTT 59.764 50.000 0.00 0.00 0.00 3.16
1204 5553 3.678529 GCATCTCCACTCTTCCTCTGTTC 60.679 52.174 0.00 0.00 0.00 3.18
1205 5554 3.244887 TCTCCACTCTTCCTCTGTTCA 57.755 47.619 0.00 0.00 0.00 3.18
1206 5555 3.784178 TCTCCACTCTTCCTCTGTTCAT 58.216 45.455 0.00 0.00 0.00 2.57
1207 5556 3.513119 TCTCCACTCTTCCTCTGTTCATG 59.487 47.826 0.00 0.00 0.00 3.07
1208 5557 2.027745 TCCACTCTTCCTCTGTTCATGC 60.028 50.000 0.00 0.00 0.00 4.06
1209 5558 2.354259 CACTCTTCCTCTGTTCATGCC 58.646 52.381 0.00 0.00 0.00 4.40
1414 5775 0.689080 AGGAGGGCAGTGATGACGAT 60.689 55.000 0.00 0.00 0.00 3.73
1447 5811 4.838986 GGTAGCCAATTCTCCCTACAGATA 59.161 45.833 0.00 0.00 33.55 1.98
1448 5812 5.046950 GGTAGCCAATTCTCCCTACAGATAG 60.047 48.000 0.00 0.00 33.55 2.08
1449 5813 4.820775 AGCCAATTCTCCCTACAGATAGA 58.179 43.478 0.00 0.00 0.00 1.98
1450 5814 5.410602 AGCCAATTCTCCCTACAGATAGAT 58.589 41.667 0.00 0.00 0.00 1.98
1451 5815 5.248020 AGCCAATTCTCCCTACAGATAGATG 59.752 44.000 0.00 0.00 0.00 2.90
1452 5816 5.012561 GCCAATTCTCCCTACAGATAGATGT 59.987 44.000 0.00 0.00 37.19 3.06
1555 5947 0.770590 CGATTATGAAGACGACGGCG 59.229 55.000 10.39 10.39 44.79 6.46
1805 6208 9.163899 CTGGGAGTTTATGATGATGATTATGAG 57.836 37.037 0.00 0.00 0.00 2.90
2042 6493 5.861251 TGCGTTGCTATGAAACCATAAAAAG 59.139 36.000 0.00 0.00 0.00 2.27
2214 6666 4.098914 TGGAACATAGGATAATGGGCAC 57.901 45.455 0.00 0.00 0.00 5.01
2326 6778 2.519013 GAAGAATTGGTTGGGCAGAGT 58.481 47.619 0.00 0.00 0.00 3.24
2439 6891 7.094118 GGGTAGCAGTGTATTTGTTTATTTGGA 60.094 37.037 0.00 0.00 0.00 3.53
3015 7508 6.366877 CCATGTTCAAAAGGTCTGCTTTTATG 59.633 38.462 0.00 0.00 33.32 1.90
3306 7830 5.046910 AGCAATTGATAAAACGGACACAG 57.953 39.130 10.34 0.00 0.00 3.66
3460 8005 4.513442 TGCTAATGTATGTGGAAGTGGAC 58.487 43.478 0.00 0.00 0.00 4.02
3464 8009 6.765989 GCTAATGTATGTGGAAGTGGACATTA 59.234 38.462 0.00 0.00 38.24 1.90
3974 8525 6.507023 ACTTTTCAAGATGAACATGTTGGAC 58.493 36.000 17.58 6.60 41.00 4.02
4241 10139 6.650372 CCTTAAACTCGTGAAAACAAGAGAG 58.350 40.000 16.83 8.06 35.26 3.20
4374 10352 4.789012 GGATGAATCCTTGTTCTTTGCA 57.211 40.909 1.86 0.00 43.73 4.08
4375 10353 5.334724 GGATGAATCCTTGTTCTTTGCAT 57.665 39.130 1.86 0.00 43.73 3.96
4376 10354 5.107133 GGATGAATCCTTGTTCTTTGCATG 58.893 41.667 1.86 0.00 43.73 4.06
4377 10355 4.524316 TGAATCCTTGTTCTTTGCATGG 57.476 40.909 0.00 0.00 33.86 3.66
4378 10356 3.896888 TGAATCCTTGTTCTTTGCATGGT 59.103 39.130 0.00 0.00 34.13 3.55
4379 10357 3.947910 ATCCTTGTTCTTTGCATGGTG 57.052 42.857 0.00 0.00 34.13 4.17
4380 10358 2.665165 TCCTTGTTCTTTGCATGGTGT 58.335 42.857 0.00 0.00 34.13 4.16
4381 10359 2.361757 TCCTTGTTCTTTGCATGGTGTG 59.638 45.455 0.00 0.00 34.13 3.82
4382 10360 2.101249 CCTTGTTCTTTGCATGGTGTGT 59.899 45.455 0.00 0.00 0.00 3.72
4383 10361 3.430651 CCTTGTTCTTTGCATGGTGTGTT 60.431 43.478 0.00 0.00 0.00 3.32
4384 10362 3.435105 TGTTCTTTGCATGGTGTGTTC 57.565 42.857 0.00 0.00 0.00 3.18
4385 10363 3.023119 TGTTCTTTGCATGGTGTGTTCT 58.977 40.909 0.00 0.00 0.00 3.01
4386 10364 4.203226 TGTTCTTTGCATGGTGTGTTCTA 58.797 39.130 0.00 0.00 0.00 2.10
4387 10365 4.036262 TGTTCTTTGCATGGTGTGTTCTAC 59.964 41.667 0.00 0.00 0.00 2.59
4388 10366 4.085357 TCTTTGCATGGTGTGTTCTACT 57.915 40.909 0.00 0.00 0.00 2.57
4389 10367 4.460263 TCTTTGCATGGTGTGTTCTACTT 58.540 39.130 0.00 0.00 0.00 2.24
4390 10368 5.616270 TCTTTGCATGGTGTGTTCTACTTA 58.384 37.500 0.00 0.00 0.00 2.24
4391 10369 5.700832 TCTTTGCATGGTGTGTTCTACTTAG 59.299 40.000 0.00 0.00 0.00 2.18
4392 10370 4.882842 TGCATGGTGTGTTCTACTTAGA 57.117 40.909 0.00 0.00 0.00 2.10
4393 10371 5.420725 TGCATGGTGTGTTCTACTTAGAT 57.579 39.130 0.00 0.00 31.40 1.98
4394 10372 6.538945 TGCATGGTGTGTTCTACTTAGATA 57.461 37.500 0.00 0.00 31.40 1.98
4395 10373 6.941857 TGCATGGTGTGTTCTACTTAGATAA 58.058 36.000 0.00 0.00 31.40 1.75
4396 10374 7.041721 TGCATGGTGTGTTCTACTTAGATAAG 58.958 38.462 0.00 0.00 39.18 1.73
4397 10375 6.480320 GCATGGTGTGTTCTACTTAGATAAGG 59.520 42.308 4.71 0.00 37.62 2.69
4398 10376 7.632898 GCATGGTGTGTTCTACTTAGATAAGGA 60.633 40.741 4.71 0.00 37.62 3.36
4399 10377 7.973048 TGGTGTGTTCTACTTAGATAAGGAT 57.027 36.000 4.71 0.00 37.62 3.24
4400 10378 9.656323 ATGGTGTGTTCTACTTAGATAAGGATA 57.344 33.333 4.71 0.00 37.62 2.59
4401 10379 9.656323 TGGTGTGTTCTACTTAGATAAGGATAT 57.344 33.333 4.71 0.00 37.62 1.63
4558 10537 9.387123 GTAATAAAGCAGAAGTTGAAACAGAAG 57.613 33.333 0.00 0.00 0.00 2.85
4660 10655 3.608474 GCTTGGTGGCTGTAACGTTTTAG 60.608 47.826 5.91 6.62 0.00 1.85
4661 10656 2.496111 TGGTGGCTGTAACGTTTTAGG 58.504 47.619 5.91 0.00 0.00 2.69
4662 10657 1.198408 GGTGGCTGTAACGTTTTAGGC 59.802 52.381 22.65 22.65 36.39 3.93
4663 10658 2.148768 GTGGCTGTAACGTTTTAGGCT 58.851 47.619 26.55 0.00 36.75 4.58
4664 10659 2.095919 GTGGCTGTAACGTTTTAGGCTG 60.096 50.000 26.55 11.57 36.75 4.85
4665 10660 1.467342 GGCTGTAACGTTTTAGGCTGG 59.533 52.381 22.34 3.31 33.44 4.85
4666 10661 2.148768 GCTGTAACGTTTTAGGCTGGT 58.851 47.619 5.91 0.00 0.00 4.00
4667 10662 2.551032 GCTGTAACGTTTTAGGCTGGTT 59.449 45.455 5.91 0.00 0.00 3.67
4668 10663 3.608474 GCTGTAACGTTTTAGGCTGGTTG 60.608 47.826 5.91 0.00 0.00 3.77
4669 10664 3.543665 TGTAACGTTTTAGGCTGGTTGT 58.456 40.909 5.91 0.00 0.00 3.32
4670 10665 4.701765 TGTAACGTTTTAGGCTGGTTGTA 58.298 39.130 5.91 0.00 0.00 2.41
4671 10666 5.121811 TGTAACGTTTTAGGCTGGTTGTAA 58.878 37.500 5.91 0.00 0.00 2.41
4672 10667 5.764192 TGTAACGTTTTAGGCTGGTTGTAAT 59.236 36.000 5.91 0.00 0.00 1.89
4673 10668 4.759516 ACGTTTTAGGCTGGTTGTAATG 57.240 40.909 0.00 0.00 0.00 1.90
4674 10669 3.504520 ACGTTTTAGGCTGGTTGTAATGG 59.495 43.478 0.00 0.00 0.00 3.16
4675 10670 3.119637 CGTTTTAGGCTGGTTGTAATGGG 60.120 47.826 0.00 0.00 0.00 4.00
4676 10671 4.083565 GTTTTAGGCTGGTTGTAATGGGA 58.916 43.478 0.00 0.00 0.00 4.37
4677 10672 3.644966 TTAGGCTGGTTGTAATGGGAG 57.355 47.619 0.00 0.00 0.00 4.30
4678 10673 1.372501 AGGCTGGTTGTAATGGGAGT 58.627 50.000 0.00 0.00 0.00 3.85
4679 10674 2.557869 AGGCTGGTTGTAATGGGAGTA 58.442 47.619 0.00 0.00 0.00 2.59
4680 10675 3.123273 AGGCTGGTTGTAATGGGAGTAT 58.877 45.455 0.00 0.00 0.00 2.12
4681 10676 3.136626 AGGCTGGTTGTAATGGGAGTATC 59.863 47.826 0.00 0.00 0.00 2.24
4682 10677 3.118038 GGCTGGTTGTAATGGGAGTATCA 60.118 47.826 0.00 0.00 36.25 2.15
4683 10678 4.446311 GGCTGGTTGTAATGGGAGTATCAT 60.446 45.833 0.00 0.00 36.25 2.45
4684 10679 5.221843 GGCTGGTTGTAATGGGAGTATCATA 60.222 44.000 0.00 0.00 36.25 2.15
4685 10680 5.934625 GCTGGTTGTAATGGGAGTATCATAG 59.065 44.000 0.00 0.00 36.25 2.23
4686 10681 5.865085 TGGTTGTAATGGGAGTATCATAGC 58.135 41.667 0.00 0.00 36.25 2.97
4687 10682 5.606749 TGGTTGTAATGGGAGTATCATAGCT 59.393 40.000 0.00 0.00 36.25 3.32
4688 10683 6.785466 TGGTTGTAATGGGAGTATCATAGCTA 59.215 38.462 0.00 0.00 36.25 3.32
4689 10684 7.039011 TGGTTGTAATGGGAGTATCATAGCTAG 60.039 40.741 0.00 0.00 36.25 3.42
4690 10685 7.038941 GGTTGTAATGGGAGTATCATAGCTAGT 60.039 40.741 0.00 0.00 36.25 2.57
4691 10686 9.021807 GTTGTAATGGGAGTATCATAGCTAGTA 57.978 37.037 0.00 0.00 36.25 1.82
4692 10687 9.769677 TTGTAATGGGAGTATCATAGCTAGTAT 57.230 33.333 0.00 0.00 36.25 2.12
4693 10688 9.409918 TGTAATGGGAGTATCATAGCTAGTATC 57.590 37.037 0.00 0.00 36.25 2.24
4694 10689 9.409918 GTAATGGGAGTATCATAGCTAGTATCA 57.590 37.037 0.00 0.00 36.25 2.15
4696 10691 7.888250 TGGGAGTATCATAGCTAGTATCATG 57.112 40.000 0.00 0.00 36.25 3.07
4697 10692 6.322456 TGGGAGTATCATAGCTAGTATCATGC 59.678 42.308 0.00 0.00 36.25 4.06
4698 10693 6.322456 GGGAGTATCATAGCTAGTATCATGCA 59.678 42.308 0.00 0.00 36.25 3.96
4699 10694 7.015098 GGGAGTATCATAGCTAGTATCATGCAT 59.985 40.741 0.00 0.00 36.25 3.96
4700 10695 7.866898 GGAGTATCATAGCTAGTATCATGCATG 59.133 40.741 21.07 21.07 36.25 4.06
4701 10696 7.208777 AGTATCATAGCTAGTATCATGCATGC 58.791 38.462 22.25 11.82 0.00 4.06
4702 10697 4.763073 TCATAGCTAGTATCATGCATGCC 58.237 43.478 22.25 11.72 0.00 4.40
4703 10698 4.223477 TCATAGCTAGTATCATGCATGCCA 59.777 41.667 22.25 8.84 0.00 4.92
4704 10699 3.497103 AGCTAGTATCATGCATGCCAA 57.503 42.857 22.25 5.34 0.00 4.52
4705 10700 3.144506 AGCTAGTATCATGCATGCCAAC 58.855 45.455 22.25 17.59 0.00 3.77
4706 10701 3.144506 GCTAGTATCATGCATGCCAACT 58.855 45.455 22.25 22.78 0.00 3.16
4707 10702 4.040829 AGCTAGTATCATGCATGCCAACTA 59.959 41.667 22.25 22.70 0.00 2.24
4708 10703 4.391216 GCTAGTATCATGCATGCCAACTAG 59.609 45.833 32.38 32.38 37.27 2.57
4709 10704 3.748083 AGTATCATGCATGCCAACTAGG 58.252 45.455 22.25 0.00 41.84 3.02
4727 10722 3.800628 GCAACTTTGATGAGGTGGC 57.199 52.632 0.00 0.00 34.87 5.01
4728 10723 0.961019 GCAACTTTGATGAGGTGGCA 59.039 50.000 0.00 0.00 34.87 4.92
4729 10724 1.547372 GCAACTTTGATGAGGTGGCAT 59.453 47.619 0.00 0.00 34.87 4.40
4730 10725 2.754552 GCAACTTTGATGAGGTGGCATA 59.245 45.455 0.00 0.00 34.87 3.14
4731 10726 3.181493 GCAACTTTGATGAGGTGGCATAG 60.181 47.826 0.00 0.00 34.87 2.23
4732 10727 4.264253 CAACTTTGATGAGGTGGCATAGA 58.736 43.478 0.00 0.00 30.59 1.98
4733 10728 4.574674 ACTTTGATGAGGTGGCATAGAA 57.425 40.909 0.00 0.00 0.00 2.10
4734 10729 5.121380 ACTTTGATGAGGTGGCATAGAAT 57.879 39.130 0.00 0.00 0.00 2.40
4735 10730 5.513233 ACTTTGATGAGGTGGCATAGAATT 58.487 37.500 0.00 0.00 0.00 2.17
4736 10731 6.662755 ACTTTGATGAGGTGGCATAGAATTA 58.337 36.000 0.00 0.00 0.00 1.40
4737 10732 7.118723 ACTTTGATGAGGTGGCATAGAATTAA 58.881 34.615 0.00 0.00 0.00 1.40
4738 10733 7.615365 ACTTTGATGAGGTGGCATAGAATTAAA 59.385 33.333 0.00 0.00 0.00 1.52
4739 10734 8.537728 TTTGATGAGGTGGCATAGAATTAAAT 57.462 30.769 0.00 0.00 0.00 1.40
4740 10735 7.514784 TGATGAGGTGGCATAGAATTAAATG 57.485 36.000 0.00 0.00 0.00 2.32
4741 10736 7.289310 TGATGAGGTGGCATAGAATTAAATGA 58.711 34.615 0.00 0.00 0.00 2.57
4742 10737 7.779326 TGATGAGGTGGCATAGAATTAAATGAA 59.221 33.333 0.00 0.00 0.00 2.57
4743 10738 7.572523 TGAGGTGGCATAGAATTAAATGAAG 57.427 36.000 0.00 0.00 0.00 3.02
4744 10739 7.118723 TGAGGTGGCATAGAATTAAATGAAGT 58.881 34.615 0.00 0.00 0.00 3.01
4745 10740 8.271458 TGAGGTGGCATAGAATTAAATGAAGTA 58.729 33.333 0.00 0.00 0.00 2.24
4746 10741 9.120538 GAGGTGGCATAGAATTAAATGAAGTAA 57.879 33.333 0.00 0.00 0.00 2.24
4747 10742 9.125026 AGGTGGCATAGAATTAAATGAAGTAAG 57.875 33.333 0.00 0.00 0.00 2.34
4748 10743 9.120538 GGTGGCATAGAATTAAATGAAGTAAGA 57.879 33.333 0.00 0.00 0.00 2.10
4756 10751 9.454859 AGAATTAAATGAAGTAAGAGAGGGTTG 57.545 33.333 0.00 0.00 0.00 3.77
4757 10752 9.449719 GAATTAAATGAAGTAAGAGAGGGTTGA 57.550 33.333 0.00 0.00 0.00 3.18
4758 10753 9.454859 AATTAAATGAAGTAAGAGAGGGTTGAG 57.545 33.333 0.00 0.00 0.00 3.02
4759 10754 6.441088 AAATGAAGTAAGAGAGGGTTGAGT 57.559 37.500 0.00 0.00 0.00 3.41
4760 10755 7.554959 AAATGAAGTAAGAGAGGGTTGAGTA 57.445 36.000 0.00 0.00 0.00 2.59
4761 10756 7.741554 AATGAAGTAAGAGAGGGTTGAGTAT 57.258 36.000 0.00 0.00 0.00 2.12
4762 10757 6.777213 TGAAGTAAGAGAGGGTTGAGTATC 57.223 41.667 0.00 0.00 0.00 2.24
4799 10794 9.856488 ACCGTATCATAATAAATGCTACACTAG 57.144 33.333 0.00 0.00 0.00 2.57
4800 10795 9.856488 CCGTATCATAATAAATGCTACACTAGT 57.144 33.333 0.00 0.00 0.00 2.57
4810 10805 7.776933 AAATGCTACACTAGTATGTGTCATG 57.223 36.000 3.46 0.00 46.90 3.07
4811 10806 4.682787 TGCTACACTAGTATGTGTCATGC 58.317 43.478 3.46 8.05 46.90 4.06
4812 10807 4.159506 TGCTACACTAGTATGTGTCATGCA 59.840 41.667 3.46 10.15 46.90 3.96
4813 10808 5.163416 TGCTACACTAGTATGTGTCATGCAT 60.163 40.000 3.46 0.00 46.90 3.96
4814 10809 5.176406 GCTACACTAGTATGTGTCATGCATG 59.824 44.000 21.07 21.07 46.90 4.06
4815 10810 4.445453 ACACTAGTATGTGTCATGCATGG 58.555 43.478 25.97 8.61 46.90 3.66
4816 10811 3.249320 CACTAGTATGTGTCATGCATGGC 59.751 47.826 24.40 24.40 33.61 4.40
4817 10812 2.423446 AGTATGTGTCATGCATGGCA 57.577 45.000 29.45 29.45 44.86 4.92
4818 10813 2.725637 AGTATGTGTCATGCATGGCAA 58.274 42.857 34.01 23.37 44.94 4.52
4819 10814 3.293337 AGTATGTGTCATGCATGGCAAT 58.707 40.909 34.01 27.34 44.94 3.56
4820 10815 4.463070 AGTATGTGTCATGCATGGCAATA 58.537 39.130 34.01 26.44 44.94 1.90
4821 10816 4.888823 AGTATGTGTCATGCATGGCAATAA 59.111 37.500 34.01 22.53 44.94 1.40
4822 10817 4.739587 ATGTGTCATGCATGGCAATAAA 57.260 36.364 34.01 20.14 44.94 1.40
4823 10818 4.739587 TGTGTCATGCATGGCAATAAAT 57.260 36.364 34.01 0.00 44.94 1.40
4824 10819 5.848833 TGTGTCATGCATGGCAATAAATA 57.151 34.783 34.01 14.13 44.94 1.40
4825 10820 6.218108 TGTGTCATGCATGGCAATAAATAA 57.782 33.333 34.01 7.61 44.94 1.40
4826 10821 6.637657 TGTGTCATGCATGGCAATAAATAAA 58.362 32.000 34.01 6.82 44.94 1.40
4827 10822 6.757478 TGTGTCATGCATGGCAATAAATAAAG 59.243 34.615 34.01 0.00 44.94 1.85
4828 10823 6.757947 GTGTCATGCATGGCAATAAATAAAGT 59.242 34.615 34.01 0.00 44.94 2.66
4829 10824 6.979817 TGTCATGCATGGCAATAAATAAAGTC 59.020 34.615 30.82 0.00 43.62 3.01
4830 10825 6.979817 GTCATGCATGGCAATAAATAAAGTCA 59.020 34.615 26.04 0.00 43.62 3.41
4831 10826 7.654520 GTCATGCATGGCAATAAATAAAGTCAT 59.345 33.333 26.04 0.00 43.62 3.06
4832 10827 7.868922 TCATGCATGGCAATAAATAAAGTCATC 59.131 33.333 25.97 0.00 43.62 2.92
4833 10828 7.350744 TGCATGGCAATAAATAAAGTCATCT 57.649 32.000 0.00 0.00 34.76 2.90
4834 10829 8.462589 TGCATGGCAATAAATAAAGTCATCTA 57.537 30.769 0.00 0.00 34.76 1.98
4835 10830 9.081204 TGCATGGCAATAAATAAAGTCATCTAT 57.919 29.630 0.00 0.00 34.76 1.98
4836 10831 9.350357 GCATGGCAATAAATAAAGTCATCTATG 57.650 33.333 0.00 0.00 0.00 2.23
4865 10860 9.715119 ACTACCATATGATACTATGCATTAGGA 57.285 33.333 3.54 0.00 31.68 2.94
4868 10863 8.489489 ACCATATGATACTATGCATTAGGAAGG 58.511 37.037 3.54 0.00 31.68 3.46
4869 10864 8.489489 CCATATGATACTATGCATTAGGAAGGT 58.511 37.037 3.54 0.00 31.68 3.50
4872 10867 8.671987 ATGATACTATGCATTAGGAAGGTAGT 57.328 34.615 3.54 0.88 31.68 2.73
4873 10868 9.769677 ATGATACTATGCATTAGGAAGGTAGTA 57.230 33.333 3.54 3.44 31.68 1.82
4874 10869 9.769677 TGATACTATGCATTAGGAAGGTAGTAT 57.230 33.333 3.54 8.56 36.89 2.12
4876 10871 9.769677 ATACTATGCATTAGGAAGGTAGTATCA 57.230 33.333 3.54 0.00 31.70 2.15
4877 10872 8.671987 ACTATGCATTAGGAAGGTAGTATCAT 57.328 34.615 3.54 0.00 31.68 2.45
4878 10873 9.769677 ACTATGCATTAGGAAGGTAGTATCATA 57.230 33.333 3.54 0.00 31.68 2.15
4880 10875 7.849322 TGCATTAGGAAGGTAGTATCATACA 57.151 36.000 0.00 0.00 0.00 2.29
4881 10876 7.667557 TGCATTAGGAAGGTAGTATCATACAC 58.332 38.462 0.00 0.00 0.00 2.90
4882 10877 7.509318 TGCATTAGGAAGGTAGTATCATACACT 59.491 37.037 0.00 0.00 0.00 3.55
4883 10878 9.021807 GCATTAGGAAGGTAGTATCATACACTA 57.978 37.037 0.00 0.00 0.00 2.74
4888 10883 9.962809 AGGAAGGTAGTATCATACACTAGTATC 57.037 37.037 0.00 0.00 38.88 2.24
4889 10884 9.736414 GGAAGGTAGTATCATACACTAGTATCA 57.264 37.037 0.00 0.00 38.88 2.15
4931 10926 9.640963 CTTATGATACTACCTATTACAACCAGC 57.359 37.037 0.00 0.00 0.00 4.85
4932 10927 6.415206 TGATACTACCTATTACAACCAGCC 57.585 41.667 0.00 0.00 0.00 4.85
4933 10928 6.141083 TGATACTACCTATTACAACCAGCCT 58.859 40.000 0.00 0.00 0.00 4.58
4934 10929 6.614087 TGATACTACCTATTACAACCAGCCTT 59.386 38.462 0.00 0.00 0.00 4.35
4935 10930 7.785985 TGATACTACCTATTACAACCAGCCTTA 59.214 37.037 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 2037 3.287867 ACTCCCCGTCGATTAGTTCTA 57.712 47.619 0.00 0.00 0.00 2.10
41 2052 2.754946 TCGTCCACACAATTACTCCC 57.245 50.000 0.00 0.00 0.00 4.30
85 2096 0.976641 TGAACTGTCTCCGCTTCCAT 59.023 50.000 0.00 0.00 0.00 3.41
106 2117 4.386049 CGTGTGTTTGGTAAGCAACAAAAA 59.614 37.500 0.00 0.00 38.20 1.94
149 2161 0.520404 CTGTGCCACATGAGCAACTC 59.480 55.000 15.09 5.89 43.02 3.01
219 2231 7.707467 ATATACTTAAGAAGTTCACCCCCAT 57.293 36.000 10.09 0.00 42.81 4.00
222 2234 8.488308 TCCTATATACTTAAGAAGTTCACCCC 57.512 38.462 10.09 0.00 42.81 4.95
318 2330 7.744733 TGTGGGAATCTGTTGCAATATATCTA 58.255 34.615 0.59 0.00 0.00 1.98
320 2332 6.882610 TGTGGGAATCTGTTGCAATATATC 57.117 37.500 0.59 0.00 0.00 1.63
341 2353 1.065491 TGGCACCTCTCGCATTATTGT 60.065 47.619 0.00 0.00 0.00 2.71
348 2360 0.684479 ACTAGATGGCACCTCTCGCA 60.684 55.000 0.00 0.00 0.00 5.10
445 2458 8.918116 AGCCGATAATCTAGCTAATATTGATCA 58.082 33.333 10.03 0.00 32.73 2.92
468 2481 9.213799 CTAGTCCTTGATCAAAATAGAATAGCC 57.786 37.037 9.88 0.00 0.00 3.93
497 2511 9.268268 TGACATTACTAAAGTTTACTCTTGTGG 57.732 33.333 0.00 0.00 0.00 4.17
613 3898 4.865776 TGTTCGCGATTTCAAAAGGAATT 58.134 34.783 10.88 0.00 34.91 2.17
618 3903 5.773570 CGAAAAATGTTCGCGATTTCAAAAG 59.226 36.000 24.00 10.11 35.05 2.27
647 3933 5.355630 TCACCGAATTCAAAAACAGTTCTCA 59.644 36.000 6.22 0.00 0.00 3.27
648 3934 5.816919 TCACCGAATTCAAAAACAGTTCTC 58.183 37.500 6.22 0.00 0.00 2.87
843 5172 5.934935 TTTTCTTTCGAGGTACATGGAAC 57.065 39.130 4.38 0.00 0.00 3.62
1009 5358 1.448717 GGAAGACTTGCTCCTCCGC 60.449 63.158 0.00 0.00 0.00 5.54
1137 5486 4.101448 GCCGGCTGGTCATGGAGT 62.101 66.667 22.15 0.00 37.67 3.85
1168 5517 2.600420 GGAGATGCATGATATACGCACG 59.400 50.000 2.46 0.00 38.73 5.34
1198 5547 1.351076 TCCAGTGAGGCATGAACAGA 58.649 50.000 0.00 0.00 37.29 3.41
1199 5548 2.189594 TTCCAGTGAGGCATGAACAG 57.810 50.000 0.00 0.00 37.29 3.16
1200 5549 2.885135 ATTCCAGTGAGGCATGAACA 57.115 45.000 0.00 0.00 37.29 3.18
1201 5550 2.424956 GGAATTCCAGTGAGGCATGAAC 59.575 50.000 20.04 0.00 37.29 3.18
1202 5551 2.309755 AGGAATTCCAGTGAGGCATGAA 59.690 45.455 26.22 0.00 38.89 2.57
1203 5552 1.918262 AGGAATTCCAGTGAGGCATGA 59.082 47.619 26.22 0.00 38.89 3.07
1204 5553 2.092538 AGAGGAATTCCAGTGAGGCATG 60.093 50.000 26.22 0.00 38.89 4.06
1205 5554 2.203584 AGAGGAATTCCAGTGAGGCAT 58.796 47.619 26.22 1.77 38.89 4.40
1206 5555 1.661463 AGAGGAATTCCAGTGAGGCA 58.339 50.000 26.22 0.00 38.89 4.75
1207 5556 2.797177 AAGAGGAATTCCAGTGAGGC 57.203 50.000 26.22 6.44 38.89 4.70
1208 5557 4.467795 TCAGTAAGAGGAATTCCAGTGAGG 59.532 45.833 26.22 9.93 38.89 3.86
1209 5558 5.667539 TCAGTAAGAGGAATTCCAGTGAG 57.332 43.478 26.22 9.66 38.89 3.51
1390 5751 2.430610 ATCACTGCCCTCCTCTCGC 61.431 63.158 0.00 0.00 0.00 5.03
1393 5754 1.326213 CGTCATCACTGCCCTCCTCT 61.326 60.000 0.00 0.00 0.00 3.69
1414 5775 4.922206 AGAATTGGCTACCTTGTTCATCA 58.078 39.130 0.00 0.00 0.00 3.07
1447 5811 9.386122 AGGATCTATGGATACTTAACAACATCT 57.614 33.333 0.00 0.00 40.01 2.90
1481 5857 5.433051 TCCCCTCCTACAGAATCAATCAATT 59.567 40.000 0.00 0.00 0.00 2.32
1805 6208 8.775527 GGAGCATCATCATCATCATAATCATAC 58.224 37.037 0.00 0.00 36.25 2.39
2016 6467 1.598882 TGGTTTCATAGCAACGCACA 58.401 45.000 0.00 0.00 0.00 4.57
2042 6493 5.402398 GCAAAACACCAGTAATTCCTCATC 58.598 41.667 0.00 0.00 0.00 2.92
2214 6666 8.131455 ACGATATTGTGCATTCAACTTACTAG 57.869 34.615 0.00 0.00 0.00 2.57
2481 6933 5.608437 TGGGACTAGCAATATTCCAAGAGAT 59.392 40.000 0.00 0.00 0.00 2.75
2493 6945 2.425143 CCACATGTGGGACTAGCAAT 57.575 50.000 33.56 0.00 46.81 3.56
3044 7543 2.373169 TGAGAACTGGTCTGATGGCTTT 59.627 45.455 0.00 0.00 36.41 3.51
3167 7676 5.086058 CCGTCTTAATTGCACATGTGTAAC 58.914 41.667 28.27 15.90 37.97 2.50
3974 8525 3.999663 GAGTCATCAGGAGAAACAACAGG 59.000 47.826 0.00 0.00 0.00 4.00
4241 10139 2.095415 GGCCACATAAAAGTCAACGGTC 60.095 50.000 0.00 0.00 0.00 4.79
4369 10347 5.616270 TCTAAGTAGAACACACCATGCAAA 58.384 37.500 0.00 0.00 0.00 3.68
4370 10348 5.222079 TCTAAGTAGAACACACCATGCAA 57.778 39.130 0.00 0.00 0.00 4.08
4371 10349 4.882842 TCTAAGTAGAACACACCATGCA 57.117 40.909 0.00 0.00 0.00 3.96
4372 10350 6.480320 CCTTATCTAAGTAGAACACACCATGC 59.520 42.308 0.00 0.00 35.69 4.06
4373 10351 7.782049 TCCTTATCTAAGTAGAACACACCATG 58.218 38.462 0.00 0.00 35.69 3.66
4374 10352 7.973048 TCCTTATCTAAGTAGAACACACCAT 57.027 36.000 0.00 0.00 35.69 3.55
4375 10353 7.973048 ATCCTTATCTAAGTAGAACACACCA 57.027 36.000 0.00 0.00 35.69 4.17
4394 10372 8.869109 TGATTTGAACAAAACAAGGATATCCTT 58.131 29.630 28.25 28.25 44.21 3.36
4395 10373 8.421249 TGATTTGAACAAAACAAGGATATCCT 57.579 30.769 19.18 19.18 40.04 3.24
4404 10382 8.147642 ACAAACACTTGATTTGAACAAAACAA 57.852 26.923 17.24 17.24 39.60 2.83
4405 10383 7.721286 ACAAACACTTGATTTGAACAAAACA 57.279 28.000 4.12 5.27 39.01 2.83
4558 10537 9.573133 CAGGTTTATATTGTTGAGAATTTCCAC 57.427 33.333 0.00 0.00 0.00 4.02
4641 10636 2.496111 CCTAAAACGTTACAGCCACCA 58.504 47.619 0.00 0.00 0.00 4.17
4660 10655 3.118038 TGATACTCCCATTACAACCAGCC 60.118 47.826 0.00 0.00 0.00 4.85
4661 10656 4.150897 TGATACTCCCATTACAACCAGC 57.849 45.455 0.00 0.00 0.00 4.85
4662 10657 5.934625 GCTATGATACTCCCATTACAACCAG 59.065 44.000 0.00 0.00 0.00 4.00
4663 10658 5.606749 AGCTATGATACTCCCATTACAACCA 59.393 40.000 0.00 0.00 0.00 3.67
4664 10659 6.115448 AGCTATGATACTCCCATTACAACC 57.885 41.667 0.00 0.00 0.00 3.77
4665 10660 7.897864 ACTAGCTATGATACTCCCATTACAAC 58.102 38.462 0.00 0.00 0.00 3.32
4666 10661 9.769677 ATACTAGCTATGATACTCCCATTACAA 57.230 33.333 0.00 0.00 0.00 2.41
4667 10662 9.409918 GATACTAGCTATGATACTCCCATTACA 57.590 37.037 0.00 0.00 0.00 2.41
4668 10663 9.409918 TGATACTAGCTATGATACTCCCATTAC 57.590 37.037 0.00 0.00 0.00 1.89
4670 10665 8.922237 CATGATACTAGCTATGATACTCCCATT 58.078 37.037 0.00 0.00 0.00 3.16
4671 10666 7.015098 GCATGATACTAGCTATGATACTCCCAT 59.985 40.741 0.00 0.00 0.00 4.00
4672 10667 6.322456 GCATGATACTAGCTATGATACTCCCA 59.678 42.308 0.00 0.00 0.00 4.37
4673 10668 6.322456 TGCATGATACTAGCTATGATACTCCC 59.678 42.308 0.00 0.00 0.00 4.30
4674 10669 7.340122 TGCATGATACTAGCTATGATACTCC 57.660 40.000 0.00 0.00 0.00 3.85
4675 10670 7.381948 GCATGCATGATACTAGCTATGATACTC 59.618 40.741 30.64 1.38 0.00 2.59
4676 10671 7.208777 GCATGCATGATACTAGCTATGATACT 58.791 38.462 30.64 0.00 0.00 2.12
4677 10672 6.423302 GGCATGCATGATACTAGCTATGATAC 59.577 42.308 30.64 5.71 0.00 2.24
4678 10673 6.098695 TGGCATGCATGATACTAGCTATGATA 59.901 38.462 30.64 0.00 0.00 2.15
4679 10674 5.104652 TGGCATGCATGATACTAGCTATGAT 60.105 40.000 30.64 0.00 0.00 2.45
4680 10675 4.223477 TGGCATGCATGATACTAGCTATGA 59.777 41.667 30.64 0.00 0.00 2.15
4681 10676 4.510571 TGGCATGCATGATACTAGCTATG 58.489 43.478 30.64 0.23 0.00 2.23
4682 10677 4.831674 TGGCATGCATGATACTAGCTAT 57.168 40.909 30.64 0.00 0.00 2.97
4683 10678 4.040829 AGTTGGCATGCATGATACTAGCTA 59.959 41.667 30.64 7.90 0.00 3.32
4684 10679 3.144506 GTTGGCATGCATGATACTAGCT 58.855 45.455 30.64 0.00 0.00 3.32
4685 10680 3.144506 AGTTGGCATGCATGATACTAGC 58.855 45.455 30.64 12.56 0.00 3.42
4686 10681 4.934001 CCTAGTTGGCATGCATGATACTAG 59.066 45.833 31.40 31.40 36.03 2.57
4687 10682 4.898320 CCTAGTTGGCATGCATGATACTA 58.102 43.478 30.64 25.87 0.00 1.82
4688 10683 3.748083 CCTAGTTGGCATGCATGATACT 58.252 45.455 30.64 26.11 0.00 2.12
4701 10696 3.441572 CCTCATCAAAGTTGCCTAGTTGG 59.558 47.826 0.00 0.00 39.35 3.77
4702 10697 4.074970 ACCTCATCAAAGTTGCCTAGTTG 58.925 43.478 0.00 0.00 0.00 3.16
4703 10698 4.074970 CACCTCATCAAAGTTGCCTAGTT 58.925 43.478 0.00 0.00 0.00 2.24
4704 10699 3.560025 CCACCTCATCAAAGTTGCCTAGT 60.560 47.826 0.00 0.00 0.00 2.57
4705 10700 3.012518 CCACCTCATCAAAGTTGCCTAG 58.987 50.000 0.00 0.00 0.00 3.02
4706 10701 2.879756 GCCACCTCATCAAAGTTGCCTA 60.880 50.000 0.00 0.00 0.00 3.93
4707 10702 1.915141 CCACCTCATCAAAGTTGCCT 58.085 50.000 0.00 0.00 0.00 4.75
4708 10703 0.244721 GCCACCTCATCAAAGTTGCC 59.755 55.000 0.00 0.00 0.00 4.52
4709 10704 0.961019 TGCCACCTCATCAAAGTTGC 59.039 50.000 0.00 0.00 0.00 4.17
4710 10705 4.264253 TCTATGCCACCTCATCAAAGTTG 58.736 43.478 0.00 0.00 0.00 3.16
4711 10706 4.574674 TCTATGCCACCTCATCAAAGTT 57.425 40.909 0.00 0.00 0.00 2.66
4712 10707 4.574674 TTCTATGCCACCTCATCAAAGT 57.425 40.909 0.00 0.00 0.00 2.66
4713 10708 7.572523 TTAATTCTATGCCACCTCATCAAAG 57.427 36.000 0.00 0.00 0.00 2.77
4714 10709 7.953005 TTTAATTCTATGCCACCTCATCAAA 57.047 32.000 0.00 0.00 0.00 2.69
4715 10710 7.779326 TCATTTAATTCTATGCCACCTCATCAA 59.221 33.333 0.00 0.00 0.00 2.57
4716 10711 7.289310 TCATTTAATTCTATGCCACCTCATCA 58.711 34.615 0.00 0.00 0.00 3.07
4717 10712 7.750229 TCATTTAATTCTATGCCACCTCATC 57.250 36.000 0.00 0.00 0.00 2.92
4718 10713 7.781693 ACTTCATTTAATTCTATGCCACCTCAT 59.218 33.333 0.00 0.00 0.00 2.90
4719 10714 7.118723 ACTTCATTTAATTCTATGCCACCTCA 58.881 34.615 0.00 0.00 0.00 3.86
4720 10715 7.573968 ACTTCATTTAATTCTATGCCACCTC 57.426 36.000 0.00 0.00 0.00 3.85
4721 10716 9.125026 CTTACTTCATTTAATTCTATGCCACCT 57.875 33.333 0.00 0.00 0.00 4.00
4722 10717 9.120538 TCTTACTTCATTTAATTCTATGCCACC 57.879 33.333 0.00 0.00 0.00 4.61
4730 10725 9.454859 CAACCCTCTCTTACTTCATTTAATTCT 57.545 33.333 0.00 0.00 0.00 2.40
4731 10726 9.449719 TCAACCCTCTCTTACTTCATTTAATTC 57.550 33.333 0.00 0.00 0.00 2.17
4732 10727 9.454859 CTCAACCCTCTCTTACTTCATTTAATT 57.545 33.333 0.00 0.00 0.00 1.40
4733 10728 8.606830 ACTCAACCCTCTCTTACTTCATTTAAT 58.393 33.333 0.00 0.00 0.00 1.40
4734 10729 7.974504 ACTCAACCCTCTCTTACTTCATTTAA 58.025 34.615 0.00 0.00 0.00 1.52
4735 10730 7.554959 ACTCAACCCTCTCTTACTTCATTTA 57.445 36.000 0.00 0.00 0.00 1.40
4736 10731 6.441088 ACTCAACCCTCTCTTACTTCATTT 57.559 37.500 0.00 0.00 0.00 2.32
4737 10732 7.400339 TGATACTCAACCCTCTCTTACTTCATT 59.600 37.037 0.00 0.00 0.00 2.57
4738 10733 6.897966 TGATACTCAACCCTCTCTTACTTCAT 59.102 38.462 0.00 0.00 0.00 2.57
4739 10734 6.253758 TGATACTCAACCCTCTCTTACTTCA 58.746 40.000 0.00 0.00 0.00 3.02
4740 10735 6.777213 TGATACTCAACCCTCTCTTACTTC 57.223 41.667 0.00 0.00 0.00 3.01
4741 10736 9.084533 GATATGATACTCAACCCTCTCTTACTT 57.915 37.037 0.00 0.00 0.00 2.24
4742 10737 8.228206 TGATATGATACTCAACCCTCTCTTACT 58.772 37.037 0.00 0.00 0.00 2.24
4743 10738 8.410673 TGATATGATACTCAACCCTCTCTTAC 57.589 38.462 0.00 0.00 0.00 2.34
4744 10739 9.029368 CATGATATGATACTCAACCCTCTCTTA 57.971 37.037 0.00 0.00 0.00 2.10
4745 10740 7.732140 TCATGATATGATACTCAACCCTCTCTT 59.268 37.037 0.00 0.00 33.59 2.85
4746 10741 7.244558 TCATGATATGATACTCAACCCTCTCT 58.755 38.462 0.00 0.00 33.59 3.10
4747 10742 7.473735 TCATGATATGATACTCAACCCTCTC 57.526 40.000 0.00 0.00 33.59 3.20
4773 10768 9.856488 CTAGTGTAGCATTTATTATGATACGGT 57.144 33.333 8.18 0.00 42.05 4.83
4774 10769 9.856488 ACTAGTGTAGCATTTATTATGATACGG 57.144 33.333 0.00 2.94 42.05 4.02
4791 10786 9.976056 TGCCATGCATGACACATACTAGTGTAG 62.976 44.444 28.31 5.81 42.57 2.74
4792 10787 8.307927 TGCCATGCATGACACATACTAGTGTA 62.308 42.308 28.31 2.94 42.57 2.90
4793 10788 7.601456 TGCCATGCATGACACATACTAGTGT 62.601 44.000 28.31 0.00 44.07 3.55
4794 10789 3.249320 GCCATGCATGACACATACTAGTG 59.751 47.826 28.31 7.28 44.93 2.74
4795 10790 3.118298 TGCCATGCATGACACATACTAGT 60.118 43.478 28.31 0.00 31.71 2.57
4796 10791 3.469739 TGCCATGCATGACACATACTAG 58.530 45.455 28.31 8.01 31.71 2.57
4797 10792 3.557228 TGCCATGCATGACACATACTA 57.443 42.857 28.31 0.00 31.71 1.82
4798 10793 2.423446 TGCCATGCATGACACATACT 57.577 45.000 28.31 0.00 31.71 2.12
4799 10794 3.720949 ATTGCCATGCATGACACATAC 57.279 42.857 28.31 8.36 38.76 2.39
4800 10795 5.848833 TTTATTGCCATGCATGACACATA 57.151 34.783 28.31 17.78 38.76 2.29
4801 10796 4.739587 TTTATTGCCATGCATGACACAT 57.260 36.364 28.31 18.68 38.76 3.21
4802 10797 4.739587 ATTTATTGCCATGCATGACACA 57.260 36.364 28.31 18.81 38.76 3.72
4803 10798 6.757947 ACTTTATTTATTGCCATGCATGACAC 59.242 34.615 28.31 16.49 38.76 3.67
4804 10799 6.876155 ACTTTATTTATTGCCATGCATGACA 58.124 32.000 28.31 20.53 38.76 3.58
4805 10800 6.979817 TGACTTTATTTATTGCCATGCATGAC 59.020 34.615 28.31 17.77 38.76 3.06
4806 10801 7.110043 TGACTTTATTTATTGCCATGCATGA 57.890 32.000 28.31 8.76 38.76 3.07
4807 10802 7.870954 AGATGACTTTATTTATTGCCATGCATG 59.129 33.333 20.19 20.19 38.76 4.06
4808 10803 7.959175 AGATGACTTTATTTATTGCCATGCAT 58.041 30.769 0.00 0.00 38.76 3.96
4809 10804 7.350744 AGATGACTTTATTTATTGCCATGCA 57.649 32.000 0.00 0.00 36.47 3.96
4810 10805 9.350357 CATAGATGACTTTATTTATTGCCATGC 57.650 33.333 0.00 0.00 0.00 4.06
4839 10834 9.715119 TCCTAATGCATAGTATCATATGGTAGT 57.285 33.333 8.39 8.39 34.35 2.73
4842 10837 8.489489 CCTTCCTAATGCATAGTATCATATGGT 58.511 37.037 0.00 0.00 34.35 3.55
4843 10838 8.489489 ACCTTCCTAATGCATAGTATCATATGG 58.511 37.037 0.00 0.00 34.35 2.74
4846 10841 9.769677 ACTACCTTCCTAATGCATAGTATCATA 57.230 33.333 0.00 0.00 0.00 2.15
4847 10842 8.671987 ACTACCTTCCTAATGCATAGTATCAT 57.328 34.615 0.00 0.00 0.00 2.45
4848 10843 9.769677 ATACTACCTTCCTAATGCATAGTATCA 57.230 33.333 0.00 0.00 31.76 2.15
4850 10845 9.769677 TGATACTACCTTCCTAATGCATAGTAT 57.230 33.333 11.08 11.08 37.18 2.12
4851 10846 9.769677 ATGATACTACCTTCCTAATGCATAGTA 57.230 33.333 0.00 0.81 0.00 1.82
4852 10847 8.671987 ATGATACTACCTTCCTAATGCATAGT 57.328 34.615 0.00 0.00 0.00 2.12
4854 10849 9.541884 TGTATGATACTACCTTCCTAATGCATA 57.458 33.333 0.00 0.00 0.00 3.14
4855 10850 8.314751 GTGTATGATACTACCTTCCTAATGCAT 58.685 37.037 4.03 0.00 0.00 3.96
4856 10851 7.509318 AGTGTATGATACTACCTTCCTAATGCA 59.491 37.037 4.03 0.00 0.00 3.96
4857 10852 7.897864 AGTGTATGATACTACCTTCCTAATGC 58.102 38.462 4.03 0.00 0.00 3.56
4862 10857 9.962809 GATACTAGTGTATGATACTACCTTCCT 57.037 37.037 5.39 0.00 39.29 3.36
4863 10858 9.736414 TGATACTAGTGTATGATACTACCTTCC 57.264 37.037 5.39 0.00 39.29 3.46
4905 10900 9.640963 GCTGGTTGTAATAGGTAGTATCATAAG 57.359 37.037 0.00 0.00 0.00 1.73
4906 10901 8.591072 GGCTGGTTGTAATAGGTAGTATCATAA 58.409 37.037 0.00 0.00 0.00 1.90
4907 10902 7.954056 AGGCTGGTTGTAATAGGTAGTATCATA 59.046 37.037 0.00 0.00 0.00 2.15
4908 10903 6.787957 AGGCTGGTTGTAATAGGTAGTATCAT 59.212 38.462 0.00 0.00 0.00 2.45
4909 10904 6.141083 AGGCTGGTTGTAATAGGTAGTATCA 58.859 40.000 0.00 0.00 0.00 2.15
4910 10905 6.667558 AGGCTGGTTGTAATAGGTAGTATC 57.332 41.667 0.00 0.00 0.00 2.24
4911 10906 7.788385 AGTAAGGCTGGTTGTAATAGGTAGTAT 59.212 37.037 0.00 0.00 0.00 2.12
4912 10907 7.128077 AGTAAGGCTGGTTGTAATAGGTAGTA 58.872 38.462 0.00 0.00 0.00 1.82
4913 10908 5.962641 AGTAAGGCTGGTTGTAATAGGTAGT 59.037 40.000 0.00 0.00 0.00 2.73
4914 10909 6.481434 AGTAAGGCTGGTTGTAATAGGTAG 57.519 41.667 0.00 0.00 0.00 3.18
4915 10910 6.896860 TGTAGTAAGGCTGGTTGTAATAGGTA 59.103 38.462 0.00 0.00 0.00 3.08
4916 10911 5.722923 TGTAGTAAGGCTGGTTGTAATAGGT 59.277 40.000 0.00 0.00 0.00 3.08
4917 10912 6.229936 TGTAGTAAGGCTGGTTGTAATAGG 57.770 41.667 0.00 0.00 0.00 2.57
4918 10913 8.556213 TTTTGTAGTAAGGCTGGTTGTAATAG 57.444 34.615 0.00 0.00 0.00 1.73
4919 10914 8.377034 TCTTTTGTAGTAAGGCTGGTTGTAATA 58.623 33.333 0.00 0.00 0.00 0.98
4920 10915 7.228590 TCTTTTGTAGTAAGGCTGGTTGTAAT 58.771 34.615 0.00 0.00 0.00 1.89
4921 10916 6.593807 TCTTTTGTAGTAAGGCTGGTTGTAA 58.406 36.000 0.00 0.00 0.00 2.41
4922 10917 6.177310 TCTTTTGTAGTAAGGCTGGTTGTA 57.823 37.500 0.00 0.00 0.00 2.41
4923 10918 5.043737 TCTTTTGTAGTAAGGCTGGTTGT 57.956 39.130 0.00 0.00 0.00 3.32
4924 10919 5.562890 GCTTCTTTTGTAGTAAGGCTGGTTG 60.563 44.000 0.00 0.00 0.00 3.77
4925 10920 4.519350 GCTTCTTTTGTAGTAAGGCTGGTT 59.481 41.667 0.00 0.00 0.00 3.67
4926 10921 4.072839 GCTTCTTTTGTAGTAAGGCTGGT 58.927 43.478 0.00 0.00 0.00 4.00
4927 10922 4.072131 TGCTTCTTTTGTAGTAAGGCTGG 58.928 43.478 0.00 0.00 0.00 4.85
4928 10923 5.689383 TTGCTTCTTTTGTAGTAAGGCTG 57.311 39.130 0.00 0.00 0.00 4.85
4929 10924 6.901081 ATTTGCTTCTTTTGTAGTAAGGCT 57.099 33.333 0.00 0.00 0.00 4.58
4930 10925 6.923508 ACAATTTGCTTCTTTTGTAGTAAGGC 59.076 34.615 0.00 0.00 30.89 4.35
4931 10926 8.134895 TCACAATTTGCTTCTTTTGTAGTAAGG 58.865 33.333 0.00 0.00 31.45 2.69
4932 10927 9.173939 CTCACAATTTGCTTCTTTTGTAGTAAG 57.826 33.333 0.00 0.00 31.45 2.34
4933 10928 8.898761 TCTCACAATTTGCTTCTTTTGTAGTAA 58.101 29.630 0.00 0.00 31.45 2.24
4934 10929 8.342634 GTCTCACAATTTGCTTCTTTTGTAGTA 58.657 33.333 0.00 0.00 31.45 1.82
4935 10930 7.196331 GTCTCACAATTTGCTTCTTTTGTAGT 58.804 34.615 0.00 0.00 31.45 2.73


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

AutoCloner maintained by Alex Coulton.