Multiple sequence alignment - TraesCS4D01G354200

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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 TraesCS4D01G354200 chr4D 100.000 3167 0 0 1 3167 504179295 504176129 0.000000e+00 5849.0
1 TraesCS4D01G354200 chr4D 84.563 583 59 17 897 1462 504116022 504115454 1.660000e-152 549.0
2 TraesCS4D01G354200 chr4B 87.140 1563 84 37 658 2155 650707281 650705771 0.000000e+00 1664.0
3 TraesCS4D01G354200 chr4B 84.965 572 46 18 897 1462 650702454 650701917 7.730000e-151 544.0
4 TraesCS4D01G354200 chr4B 91.736 242 9 3 1 242 650708391 650708161 3.050000e-85 326.0
5 TraesCS4D01G354200 chr4B 88.060 67 4 4 212 276 340637053 340636989 3.390000e-10 76.8
6 TraesCS4D01G354200 chr5A 88.339 1355 97 24 897 2242 688841243 688839941 0.000000e+00 1570.0
7 TraesCS4D01G354200 chr5A 87.114 939 68 14 2240 3167 688837241 688836345 0.000000e+00 1014.0
8 TraesCS4D01G354200 chr5A 89.911 783 56 8 2240 3021 688838500 688837740 0.000000e+00 987.0
9 TraesCS4D01G354200 chr5A 88.931 786 64 6 2241 3024 688839768 688839004 0.000000e+00 948.0
10 TraesCS4D01G354200 chr5A 87.109 512 44 8 897 1402 688832178 688831683 7.670000e-156 560.0
11 TraesCS4D01G354200 chr5A 76.319 891 130 48 1603 2461 688831443 688830602 4.920000e-108 401.0
12 TraesCS4D01G354200 chr5A 87.000 300 21 6 1947 2244 688838953 688838670 3.940000e-84 322.0
13 TraesCS4D01G354200 chr5A 92.045 176 11 3 681 854 688841427 688841253 8.770000e-61 244.0
14 TraesCS4D01G354200 chr7D 86.364 418 47 5 1140 1557 561520907 561521314 6.230000e-122 448.0
15 TraesCS4D01G354200 chr3B 86.246 349 45 2 1069 1417 72478138 72477793 2.980000e-100 375.0
16 TraesCS4D01G354200 chr3D 85.960 349 46 1 1069 1417 46471865 46471520 1.390000e-98 370.0
17 TraesCS4D01G354200 chr3A 86.707 331 41 1 1069 1399 57886850 57886523 6.460000e-97 364.0
18 TraesCS4D01G354200 chr3A 74.499 349 50 26 1594 1912 57886307 57885968 7.180000e-22 115.0
19 TraesCS4D01G354200 chr3A 89.394 66 3 4 212 274 50721850 50721914 2.620000e-11 80.5
20 TraesCS4D01G354200 chr7A 85.333 75 9 2 205 277 708552539 708552465 3.390000e-10 76.8
21 TraesCS4D01G354200 chr5B 88.060 67 4 4 212 275 534344287 534344222 3.390000e-10 76.8
22 TraesCS4D01G354200 chr4A 85.135 74 9 2 205 276 684524458 684524385 1.220000e-09 75.0
23 TraesCS4D01G354200 chr2A 86.111 72 6 3 207 275 547446973 547447043 1.220000e-09 75.0
24 TraesCS4D01G354200 chr2A 82.716 81 10 3 207 284 567348879 567348800 5.670000e-08 69.4
25 TraesCS4D01G354200 chr7B 86.567 67 7 2 212 276 477623519 477623453 4.380000e-09 73.1
26 TraesCS4D01G354200 chr2D 84.932 73 8 3 205 275 314567889 314567818 1.580000e-08 71.3


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 TraesCS4D01G354200 chr4D 504176129 504179295 3166 True 5849.000000 5849 100.000 1 3167 1 chr4D.!!$R2 3166
1 TraesCS4D01G354200 chr4D 504115454 504116022 568 True 549.000000 549 84.563 897 1462 1 chr4D.!!$R1 565
2 TraesCS4D01G354200 chr4B 650701917 650708391 6474 True 844.666667 1664 87.947 1 2155 3 chr4B.!!$R2 2154
3 TraesCS4D01G354200 chr5A 688836345 688841427 5082 True 847.500000 1570 88.890 681 3167 6 chr5A.!!$R2 2486
4 TraesCS4D01G354200 chr5A 688830602 688832178 1576 True 480.500000 560 81.714 897 2461 2 chr5A.!!$R1 1564
5 TraesCS4D01G354200 chr3A 57885968 57886850 882 True 239.500000 364 80.603 1069 1912 2 chr3A.!!$R1 843

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
380 381 0.038159 ACTGGCACTACAGCGACTTC 60.038 55.0 0.00 0.0 42.21 3.01 F
860 1372 0.256464 TTTTGGAACCCACGGTGAGT 59.744 50.0 10.28 0.0 35.34 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 2297 0.961358 ACGACGACTCCCTCCTCTTG 60.961 60.0 0.0 0.0 0.0 3.02 R
2792 5048 0.459411 ACAACCAACTTTTGCCGCAC 60.459 50.0 0.0 0.0 0.0 5.34 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
78 79 0.881796 ACGACAGATGCTCGTTCTCA 59.118 50.000 0.00 0.00 41.58 3.27
97 98 6.187727 TCTCAGTCCAAGGTTGATAAAACT 57.812 37.500 0.00 0.00 0.00 2.66
121 122 1.968050 CTAAGGTGTAGTGGGCCGGG 61.968 65.000 2.18 0.00 0.00 5.73
139 140 1.143073 GGGCCTTGGGGATAGTTGTAG 59.857 57.143 0.84 0.00 33.58 2.74
239 240 4.220821 GTCACAATCTGAGAGTTGGGAGTA 59.779 45.833 8.97 0.00 38.34 2.59
241 242 5.485353 TCACAATCTGAGAGTTGGGAGTAAT 59.515 40.000 5.76 0.00 33.11 1.89
242 243 6.667848 TCACAATCTGAGAGTTGGGAGTAATA 59.332 38.462 5.76 0.00 33.11 0.98
243 244 7.345653 TCACAATCTGAGAGTTGGGAGTAATAT 59.654 37.037 5.76 0.00 33.11 1.28
244 245 7.989741 CACAATCTGAGAGTTGGGAGTAATATT 59.010 37.037 8.66 0.00 30.31 1.28
245 246 7.989741 ACAATCTGAGAGTTGGGAGTAATATTG 59.010 37.037 0.00 0.00 0.00 1.90
246 247 5.918608 TCTGAGAGTTGGGAGTAATATTGC 58.081 41.667 0.00 0.00 0.00 3.56
247 248 5.425217 TCTGAGAGTTGGGAGTAATATTGCA 59.575 40.000 6.31 0.00 0.00 4.08
248 249 6.061022 TGAGAGTTGGGAGTAATATTGCAA 57.939 37.500 0.00 0.00 0.00 4.08
249 250 6.480763 TGAGAGTTGGGAGTAATATTGCAAA 58.519 36.000 1.71 0.00 0.00 3.68
250 251 6.599244 TGAGAGTTGGGAGTAATATTGCAAAG 59.401 38.462 1.71 0.00 0.00 2.77
251 252 6.721318 AGAGTTGGGAGTAATATTGCAAAGA 58.279 36.000 1.71 0.00 0.00 2.52
252 253 6.825721 AGAGTTGGGAGTAATATTGCAAAGAG 59.174 38.462 1.71 0.00 0.00 2.85
253 254 6.485171 AGTTGGGAGTAATATTGCAAAGAGT 58.515 36.000 1.71 0.00 0.00 3.24
254 255 7.630082 AGTTGGGAGTAATATTGCAAAGAGTA 58.370 34.615 1.71 0.00 0.00 2.59
255 256 7.553044 AGTTGGGAGTAATATTGCAAAGAGTAC 59.447 37.037 1.71 8.64 38.71 2.73
268 269 8.547967 TTGCAAAGAGTACTCCTTAATTAGTG 57.452 34.615 19.38 8.08 0.00 2.74
269 270 7.903145 TGCAAAGAGTACTCCTTAATTAGTGA 58.097 34.615 19.38 0.00 0.00 3.41
270 271 8.540388 TGCAAAGAGTACTCCTTAATTAGTGAT 58.460 33.333 19.38 0.00 0.00 3.06
271 272 9.384764 GCAAAGAGTACTCCTTAATTAGTGATT 57.615 33.333 19.38 0.00 0.00 2.57
274 275 9.804758 AAGAGTACTCCTTAATTAGTGATTTCG 57.195 33.333 19.38 0.00 0.00 3.46
275 276 8.414778 AGAGTACTCCTTAATTAGTGATTTCGG 58.585 37.037 19.38 0.00 0.00 4.30
276 277 7.498443 AGTACTCCTTAATTAGTGATTTCGGG 58.502 38.462 0.00 0.00 0.00 5.14
277 278 5.681639 ACTCCTTAATTAGTGATTTCGGGG 58.318 41.667 0.00 0.00 0.00 5.73
278 279 5.191124 ACTCCTTAATTAGTGATTTCGGGGT 59.809 40.000 0.00 0.00 29.61 4.95
279 280 5.677567 TCCTTAATTAGTGATTTCGGGGTC 58.322 41.667 0.00 0.00 0.00 4.46
280 281 4.510340 CCTTAATTAGTGATTTCGGGGTCG 59.490 45.833 0.00 0.00 37.82 4.79
318 319 1.001745 GCGTCAAATGGCCGTTGTTC 61.002 55.000 11.94 8.49 0.00 3.18
363 364 4.722193 CCCATTGGCGACTCAACT 57.278 55.556 0.00 0.00 0.00 3.16
364 365 2.174334 CCCATTGGCGACTCAACTG 58.826 57.895 0.00 0.00 0.00 3.16
366 367 1.503542 CATTGGCGACTCAACTGGC 59.496 57.895 0.00 0.00 0.00 4.85
380 381 0.038159 ACTGGCACTACAGCGACTTC 60.038 55.000 0.00 0.00 42.21 3.01
409 410 1.337823 ACTGCAGCGACTTTACCGAAT 60.338 47.619 15.27 0.00 0.00 3.34
416 417 3.308866 AGCGACTTTACCGAATATTGTGC 59.691 43.478 0.00 0.00 0.00 4.57
422 423 7.413219 CGACTTTACCGAATATTGTGCCTAAAA 60.413 37.037 0.00 0.00 0.00 1.52
448 449 6.801539 TTTTAGCAACTTGACTGGATACTG 57.198 37.500 0.00 0.00 42.06 2.74
461 462 2.034685 TGGATACTGTAGCGAGCACATC 59.965 50.000 0.00 0.00 37.61 3.06
464 465 2.751166 ACTGTAGCGAGCACATCTTT 57.249 45.000 0.00 0.00 0.00 2.52
466 467 2.996621 ACTGTAGCGAGCACATCTTTTC 59.003 45.455 0.00 0.00 0.00 2.29
590 605 7.890763 ACACTAACATTTTTAAAGTGTTTGCG 58.109 30.769 20.34 15.42 46.38 4.85
599 614 9.833182 ATTTTTAAAGTGTTTGCGAACATTTTT 57.167 22.222 32.63 27.97 46.85 1.94
600 615 8.867248 TTTTAAAGTGTTTGCGAACATTTTTC 57.133 26.923 32.63 17.46 46.85 2.29
601 616 5.463499 AAAGTGTTTGCGAACATTTTTCC 57.537 34.783 26.27 12.85 46.85 3.13
602 617 3.112580 AGTGTTTGCGAACATTTTTCCG 58.887 40.909 22.15 0.00 46.63 4.30
605 620 4.031878 GTGTTTGCGAACATTTTTCCGAAA 59.968 37.500 22.15 0.00 46.63 3.46
607 622 3.422417 TGCGAACATTTTTCCGAAACA 57.578 38.095 0.00 0.00 0.00 2.83
608 623 3.109619 TGCGAACATTTTTCCGAAACAC 58.890 40.909 0.00 0.00 0.00 3.32
610 625 3.179599 GCGAACATTTTTCCGAAACACAG 59.820 43.478 0.00 0.00 0.00 3.66
626 641 7.594758 CCGAAACACAGACATTTTATGAAACAT 59.405 33.333 0.00 0.00 0.00 2.71
627 642 8.419435 CGAAACACAGACATTTTATGAAACATG 58.581 33.333 0.00 0.00 0.00 3.21
650 665 9.588774 CATGATATTTTTCAAAAGCACAAACAG 57.411 29.630 0.00 0.00 0.00 3.16
656 671 7.532682 TTTTCAAAAGCACAAACAGTATTCC 57.467 32.000 0.00 0.00 0.00 3.01
661 1169 7.604164 TCAAAAGCACAAACAGTATTCCAAAAA 59.396 29.630 0.00 0.00 0.00 1.94
690 1198 1.604593 GACAACCTGCCTGCACCAT 60.605 57.895 0.00 0.00 0.00 3.55
699 1210 1.372683 CCTGCACCATATCCCTCCG 59.627 63.158 0.00 0.00 0.00 4.63
701 1212 1.383943 TGCACCATATCCCTCCGGT 60.384 57.895 0.00 0.00 0.00 5.28
734 1246 2.581409 GGATGTCGCGTACCACGG 60.581 66.667 5.77 0.00 42.82 4.94
830 1342 5.053145 TGTTTGCACGCTAAAATCCATTTT 58.947 33.333 2.92 2.92 42.21 1.82
831 1343 5.176590 TGTTTGCACGCTAAAATCCATTTTC 59.823 36.000 0.45 0.00 40.24 2.29
833 1345 5.132897 TGCACGCTAAAATCCATTTTCTT 57.867 34.783 0.45 0.00 40.24 2.52
834 1346 4.922692 TGCACGCTAAAATCCATTTTCTTG 59.077 37.500 0.45 0.00 40.24 3.02
837 1349 6.073819 GCACGCTAAAATCCATTTTCTTGTTT 60.074 34.615 0.45 0.00 40.24 2.83
838 1350 7.501515 CACGCTAAAATCCATTTTCTTGTTTC 58.498 34.615 0.45 0.00 40.24 2.78
839 1351 6.645003 ACGCTAAAATCCATTTTCTTGTTTCC 59.355 34.615 0.45 0.00 40.24 3.13
840 1352 6.090763 CGCTAAAATCCATTTTCTTGTTTCCC 59.909 38.462 0.45 0.00 40.24 3.97
843 1355 9.559732 CTAAAATCCATTTTCTTGTTTCCCTTT 57.440 29.630 0.45 0.00 40.24 3.11
844 1356 8.821686 AAAATCCATTTTCTTGTTTCCCTTTT 57.178 26.923 0.00 0.00 35.18 2.27
854 1366 4.911901 TCCCTTTTGGAACCCACG 57.088 55.556 0.00 0.00 41.40 4.94
855 1367 1.151908 TCCCTTTTGGAACCCACGG 59.848 57.895 0.00 0.00 41.40 4.94
857 1369 1.460273 CCCTTTTGGAACCCACGGTG 61.460 60.000 0.00 0.00 44.07 4.94
858 1370 0.466555 CCTTTTGGAACCCACGGTGA 60.467 55.000 10.28 0.00 44.07 4.02
859 1371 0.951558 CTTTTGGAACCCACGGTGAG 59.048 55.000 10.28 0.00 35.34 3.51
860 1372 0.256464 TTTTGGAACCCACGGTGAGT 59.744 50.000 10.28 0.00 35.34 3.41
879 1391 3.088532 AGTGATCGCTCTATCCATCTCC 58.911 50.000 2.02 0.00 0.00 3.71
880 1392 2.165437 GTGATCGCTCTATCCATCTCCC 59.835 54.545 0.00 0.00 0.00 4.30
881 1393 2.042297 TGATCGCTCTATCCATCTCCCT 59.958 50.000 0.00 0.00 0.00 4.20
882 1394 2.208132 TCGCTCTATCCATCTCCCTC 57.792 55.000 0.00 0.00 0.00 4.30
883 1395 1.181786 CGCTCTATCCATCTCCCTCC 58.818 60.000 0.00 0.00 0.00 4.30
884 1396 1.567357 GCTCTATCCATCTCCCTCCC 58.433 60.000 0.00 0.00 0.00 4.30
885 1397 1.078656 GCTCTATCCATCTCCCTCCCT 59.921 57.143 0.00 0.00 0.00 4.20
886 1398 2.888069 GCTCTATCCATCTCCCTCCCTC 60.888 59.091 0.00 0.00 0.00 4.30
887 1399 1.719378 TCTATCCATCTCCCTCCCTCC 59.281 57.143 0.00 0.00 0.00 4.30
888 1400 0.793617 TATCCATCTCCCTCCCTCCC 59.206 60.000 0.00 0.00 0.00 4.30
889 1401 1.015131 ATCCATCTCCCTCCCTCCCT 61.015 60.000 0.00 0.00 0.00 4.20
890 1402 1.152139 CCATCTCCCTCCCTCCCTC 60.152 68.421 0.00 0.00 0.00 4.30
891 1403 1.152139 CATCTCCCTCCCTCCCTCC 60.152 68.421 0.00 0.00 0.00 4.30
892 1404 2.416923 ATCTCCCTCCCTCCCTCCC 61.417 68.421 0.00 0.00 0.00 4.30
893 1405 2.929738 ATCTCCCTCCCTCCCTCCCT 62.930 65.000 0.00 0.00 0.00 4.20
894 1406 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
975 1487 1.075536 CTACAAAACCCTCCTGCCCTT 59.924 52.381 0.00 0.00 0.00 3.95
977 1489 0.900182 CAAAACCCTCCTGCCCTTCC 60.900 60.000 0.00 0.00 0.00 3.46
978 1490 2.094170 AAAACCCTCCTGCCCTTCCC 62.094 60.000 0.00 0.00 0.00 3.97
1015 1527 2.359850 CCCACACCACCATCACCG 60.360 66.667 0.00 0.00 0.00 4.94
1022 1534 2.747460 CACCATCACCGCCACCAG 60.747 66.667 0.00 0.00 0.00 4.00
1023 1535 4.722700 ACCATCACCGCCACCAGC 62.723 66.667 0.00 0.00 38.52 4.85
1041 1558 3.540211 CTCACCGGAGCAACAAGAT 57.460 52.632 9.46 0.00 33.67 2.40
1042 1559 2.672961 CTCACCGGAGCAACAAGATA 57.327 50.000 9.46 0.00 33.67 1.98
1043 1560 2.972625 CTCACCGGAGCAACAAGATAA 58.027 47.619 9.46 0.00 33.67 1.75
1044 1561 3.334691 CTCACCGGAGCAACAAGATAAA 58.665 45.455 9.46 0.00 33.67 1.40
1045 1562 3.071479 TCACCGGAGCAACAAGATAAAC 58.929 45.455 9.46 0.00 0.00 2.01
1046 1563 2.161609 CACCGGAGCAACAAGATAAACC 59.838 50.000 9.46 0.00 0.00 3.27
1047 1564 2.039879 ACCGGAGCAACAAGATAAACCT 59.960 45.455 9.46 0.00 0.00 3.50
1601 2230 4.753662 CCACGAGGGGGAGTCCGA 62.754 72.222 2.26 0.00 36.01 4.55
1656 2297 4.395583 GCGCTGGCAGACAAGCAC 62.396 66.667 20.86 0.00 39.62 4.40
1663 2304 0.250467 GGCAGACAAGCACAAGAGGA 60.250 55.000 0.00 0.00 35.83 3.71
1665 2306 1.805869 CAGACAAGCACAAGAGGAGG 58.194 55.000 0.00 0.00 0.00 4.30
1788 2450 4.154347 CTGGAGCTCACCCTCGGC 62.154 72.222 17.19 0.00 32.57 5.54
1939 2621 1.292223 GTCCTTCGTACTGCTGGCA 59.708 57.895 0.00 0.00 0.00 4.92
1994 2703 3.975670 GGATCATCGTTCGTGTCATACTC 59.024 47.826 0.00 0.00 0.00 2.59
1995 2704 3.047613 TCATCGTTCGTGTCATACTCG 57.952 47.619 0.00 0.00 36.55 4.18
2009 2718 2.973694 TACTCGCACCTTTGGGATAC 57.026 50.000 0.00 0.00 43.30 2.24
2202 4196 3.779444 TGAAGACTATGTGTGAGAGGGT 58.221 45.455 0.00 0.00 0.00 4.34
2224 4218 5.689068 GGTAGTGAATACAATAGCGTGTACC 59.311 44.000 0.00 0.00 36.83 3.34
2233 4227 2.062971 TAGCGTGTACCCCTTAGAGG 57.937 55.000 0.00 0.00 34.30 3.69
2246 4414 5.189145 ACCCCTTAGAGGTACATGTACTTTG 59.811 44.000 29.89 16.16 35.24 2.77
2274 4442 5.105756 GGTGGATCGAAATTTCATGAACCTT 60.106 40.000 17.99 4.23 0.00 3.50
2329 4497 3.699067 GCATGATTCAACCAAATCCGAG 58.301 45.455 0.00 0.00 35.23 4.63
2356 4524 0.620556 AACCTTCACGCATCCTCCAT 59.379 50.000 0.00 0.00 0.00 3.41
2391 4560 3.204827 CCCAATCCGAGGCAAGCG 61.205 66.667 0.00 0.00 0.00 4.68
2407 4576 0.984995 AGCGGGATAGGGCCTTATTC 59.015 55.000 13.45 6.73 0.00 1.75
2424 4593 6.520272 CCTTATTCCAACTCTAGGATGTGAG 58.480 44.000 0.00 0.00 34.56 3.51
2434 4603 2.951745 GATGTGAGCGCCTCGTCG 60.952 66.667 2.29 0.00 32.35 5.12
2449 4618 4.680237 TCGCCCCAAGCAGACACG 62.680 66.667 0.00 0.00 44.04 4.49
2461 4630 3.931824 AGCAGACACGAAACGTAAAAAC 58.068 40.909 0.00 0.00 38.32 2.43
2469 4638 8.124199 AGACACGAAACGTAAAAACAAATGTAT 58.876 29.630 0.00 0.00 38.32 2.29
2477 4646 5.285134 CGTAAAAACAAATGTATTCCTGCCG 59.715 40.000 0.00 0.00 0.00 5.69
2534 4703 1.529948 CTGGCGGGGCATCATGATT 60.530 57.895 5.16 0.00 0.00 2.57
2611 4867 4.864247 CACTAAGTTGCAGCAAAAGTTGTT 59.136 37.500 10.11 0.00 0.00 2.83
2642 4898 9.585099 TTAGCAATTCACCAAGCTTTATTAATG 57.415 29.630 0.00 0.00 38.47 1.90
2663 4919 5.136068 TGAGAAGAGGTGGTCATAGAGAT 57.864 43.478 0.00 0.00 0.00 2.75
2665 4921 6.065374 TGAGAAGAGGTGGTCATAGAGATAC 58.935 44.000 0.00 0.00 0.00 2.24
2673 4929 6.498651 AGGTGGTCATAGAGATACATAAAGGG 59.501 42.308 0.00 0.00 0.00 3.95
2689 4945 1.444933 AGGGTCATGAGGAACACCAA 58.555 50.000 0.00 0.00 33.68 3.67
2700 4956 4.038042 TGAGGAACACCAAGCTATAGATCG 59.962 45.833 3.21 0.00 0.00 3.69
2701 4957 3.060602 GGAACACCAAGCTATAGATCGC 58.939 50.000 3.21 0.00 0.00 4.58
2711 4967 0.881796 TATAGATCGCGACCCTGCAG 59.118 55.000 12.93 6.78 34.15 4.41
2746 5002 2.243478 TGGCAAGGTTATGGGCTTCATA 59.757 45.455 0.00 0.00 37.30 2.15
2752 5008 6.736794 GCAAGGTTATGGGCTTCATAATTCAG 60.737 42.308 13.28 7.98 46.37 3.02
2756 5012 2.564771 TGGGCTTCATAATTCAGCTCG 58.435 47.619 0.00 0.00 36.76 5.03
2821 5077 6.262049 GGCAAAAGTTGGTTGTATTTGGAAAT 59.738 34.615 0.00 0.00 32.91 2.17
2826 5082 7.130681 AGTTGGTTGTATTTGGAAATTTGGA 57.869 32.000 0.00 0.00 0.00 3.53
2833 5089 9.271828 GTTGTATTTGGAAATTTGGAAATGAGT 57.728 29.630 0.00 0.00 0.00 3.41
2874 5130 0.609131 ACTGAAATGAACCTGGGCCG 60.609 55.000 0.00 0.00 0.00 6.13
2888 5144 2.595655 GCCGGAAGTTGGGCCTAT 59.404 61.111 5.05 0.00 43.64 2.57
2900 5156 4.110493 GCCTATGCCGACTCACAC 57.890 61.111 0.00 0.00 0.00 3.82
2910 5166 1.080434 GACTCACACAGCCGACCTC 60.080 63.158 0.00 0.00 0.00 3.85
2932 5188 2.726792 ATCGAGGTATCCCCGTCCCC 62.727 65.000 0.00 0.00 38.74 4.81
2934 5190 3.745761 GAGGTATCCCCGTCCCCGT 62.746 68.421 0.00 0.00 38.74 5.28
2935 5191 3.229501 GGTATCCCCGTCCCCGTC 61.230 72.222 0.00 0.00 0.00 4.79
3021 5338 0.599204 ACCGACCACTAGTTGCAACG 60.599 55.000 23.21 12.97 0.00 4.10
3023 5340 0.944311 CGACCACTAGTTGCAACGCT 60.944 55.000 23.21 10.16 0.00 5.07
3046 7264 1.823169 TACCAAGTCACTGTCGCCCC 61.823 60.000 0.00 0.00 0.00 5.80
3047 7265 2.358737 CAAGTCACTGTCGCCCCC 60.359 66.667 0.00 0.00 0.00 5.40
3076 7294 3.004315 TGTCTTCCGTTCCTTGAATTTGC 59.996 43.478 0.00 0.00 0.00 3.68
3077 7295 3.004315 GTCTTCCGTTCCTTGAATTTGCA 59.996 43.478 0.00 0.00 0.00 4.08
3082 7300 3.119849 CCGTTCCTTGAATTTGCAGGTAG 60.120 47.826 0.00 0.00 0.00 3.18
3086 7304 4.585879 TCCTTGAATTTGCAGGTAGGTAC 58.414 43.478 0.00 0.00 0.00 3.34
3097 8678 0.754587 GGTAGGTACGTCCTCCCCAG 60.755 65.000 9.44 0.00 44.42 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.607198 TGTCATCTTCCTCCTCTTTTGTTTTT 59.393 34.615 0.00 0.00 0.00 1.94
78 79 8.203681 AGTACTAGTTTTATCAACCTTGGACT 57.796 34.615 0.00 0.00 0.00 3.85
97 98 3.635591 GGCCCACTACACCTTAGTACTA 58.364 50.000 0.00 0.00 0.00 1.82
121 122 1.477014 GCCTACAACTATCCCCAAGGC 60.477 57.143 0.00 0.00 41.06 4.35
160 161 5.523552 TGTCACACTGCATATTATGTGCTAC 59.476 40.000 14.57 4.90 41.78 3.58
162 163 4.516323 TGTCACACTGCATATTATGTGCT 58.484 39.130 14.57 0.00 41.78 4.40
170 171 3.005554 GAGCAACTGTCACACTGCATAT 58.994 45.455 9.32 0.00 37.26 1.78
171 172 2.224257 TGAGCAACTGTCACACTGCATA 60.224 45.455 9.32 0.00 37.26 3.14
172 173 1.233019 GAGCAACTGTCACACTGCAT 58.767 50.000 9.32 0.00 37.26 3.96
216 217 3.007398 ACTCCCAACTCTCAGATTGTGAC 59.993 47.826 0.00 0.00 0.00 3.67
217 218 3.242867 ACTCCCAACTCTCAGATTGTGA 58.757 45.455 0.00 0.00 0.00 3.58
218 219 3.692257 ACTCCCAACTCTCAGATTGTG 57.308 47.619 0.00 0.00 0.00 3.33
219 220 7.682787 ATATTACTCCCAACTCTCAGATTGT 57.317 36.000 0.00 0.00 0.00 2.71
220 221 7.041508 GCAATATTACTCCCAACTCTCAGATTG 60.042 40.741 0.00 0.00 0.00 2.67
227 228 6.721318 TCTTTGCAATATTACTCCCAACTCT 58.279 36.000 0.00 0.00 0.00 3.24
242 243 9.167311 CACTAATTAAGGAGTACTCTTTGCAAT 57.833 33.333 25.81 16.96 31.18 3.56
243 244 8.372459 TCACTAATTAAGGAGTACTCTTTGCAA 58.628 33.333 25.81 15.63 31.18 4.08
244 245 7.903145 TCACTAATTAAGGAGTACTCTTTGCA 58.097 34.615 25.81 14.91 31.18 4.08
245 246 8.950208 ATCACTAATTAAGGAGTACTCTTTGC 57.050 34.615 25.81 9.27 31.18 3.68
248 249 9.804758 CGAAATCACTAATTAAGGAGTACTCTT 57.195 33.333 21.88 12.52 0.00 2.85
249 250 8.414778 CCGAAATCACTAATTAAGGAGTACTCT 58.585 37.037 21.88 6.36 0.00 3.24
250 251 7.652507 CCCGAAATCACTAATTAAGGAGTACTC 59.347 40.741 14.87 14.87 0.00 2.59
251 252 7.418712 CCCCGAAATCACTAATTAAGGAGTACT 60.419 40.741 0.00 0.00 0.00 2.73
252 253 6.704937 CCCCGAAATCACTAATTAAGGAGTAC 59.295 42.308 0.00 0.00 0.00 2.73
253 254 6.384886 ACCCCGAAATCACTAATTAAGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
254 255 5.191124 ACCCCGAAATCACTAATTAAGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
255 256 5.681639 ACCCCGAAATCACTAATTAAGGAG 58.318 41.667 0.00 0.00 0.00 3.69
256 257 5.677567 GACCCCGAAATCACTAATTAAGGA 58.322 41.667 0.00 0.00 0.00 3.36
257 258 4.510340 CGACCCCGAAATCACTAATTAAGG 59.490 45.833 0.00 0.00 38.22 2.69
258 259 5.114081 ACGACCCCGAAATCACTAATTAAG 58.886 41.667 0.00 0.00 39.50 1.85
259 260 5.088680 ACGACCCCGAAATCACTAATTAA 57.911 39.130 0.00 0.00 39.50 1.40
260 261 4.441913 GGACGACCCCGAAATCACTAATTA 60.442 45.833 0.00 0.00 39.50 1.40
261 262 3.528532 GACGACCCCGAAATCACTAATT 58.471 45.455 0.00 0.00 39.50 1.40
262 263 2.159000 GGACGACCCCGAAATCACTAAT 60.159 50.000 0.00 0.00 39.50 1.73
263 264 1.205417 GGACGACCCCGAAATCACTAA 59.795 52.381 0.00 0.00 39.50 2.24
264 265 0.819582 GGACGACCCCGAAATCACTA 59.180 55.000 0.00 0.00 39.50 2.74
265 266 0.903454 AGGACGACCCCGAAATCACT 60.903 55.000 0.00 0.00 39.50 3.41
266 267 0.819582 TAGGACGACCCCGAAATCAC 59.180 55.000 0.00 0.00 39.50 3.06
267 268 1.784358 ATAGGACGACCCCGAAATCA 58.216 50.000 0.00 0.00 39.50 2.57
268 269 2.870411 CAAATAGGACGACCCCGAAATC 59.130 50.000 0.00 0.00 39.50 2.17
269 270 2.502538 TCAAATAGGACGACCCCGAAAT 59.497 45.455 0.00 0.00 39.50 2.17
270 271 1.901159 TCAAATAGGACGACCCCGAAA 59.099 47.619 0.00 0.00 39.50 3.46
271 272 1.205417 GTCAAATAGGACGACCCCGAA 59.795 52.381 0.00 0.00 39.50 4.30
272 273 0.819582 GTCAAATAGGACGACCCCGA 59.180 55.000 0.00 0.00 39.50 5.14
273 274 3.357504 GTCAAATAGGACGACCCCG 57.642 57.895 0.00 0.00 42.50 5.73
280 281 3.676646 ACGCTAAACACGTCAAATAGGAC 59.323 43.478 0.00 0.00 40.28 3.85
293 294 0.519519 CGGCCATTTGACGCTAAACA 59.480 50.000 2.24 0.00 0.00 2.83
308 309 3.587933 TTGTGCGGAACAACGGCC 61.588 61.111 0.00 0.00 43.96 6.13
352 353 1.014564 GTAGTGCCAGTTGAGTCGCC 61.015 60.000 0.00 0.00 0.00 5.54
363 364 0.319555 GTGAAGTCGCTGTAGTGCCA 60.320 55.000 0.00 0.00 0.00 4.92
364 365 1.014564 GGTGAAGTCGCTGTAGTGCC 61.015 60.000 0.00 0.00 0.00 5.01
366 367 0.732880 CCGGTGAAGTCGCTGTAGTG 60.733 60.000 0.00 0.00 0.00 2.74
397 398 6.913873 TTAGGCACAATATTCGGTAAAGTC 57.086 37.500 0.00 0.00 0.00 3.01
416 417 9.573133 CCAGTCAAGTTGCTAAAATATTTTAGG 57.427 33.333 33.56 22.26 46.03 2.69
422 423 9.113838 CAGTATCCAGTCAAGTTGCTAAAATAT 57.886 33.333 0.00 0.00 0.00 1.28
432 433 3.762288 TCGCTACAGTATCCAGTCAAGTT 59.238 43.478 0.00 0.00 0.00 2.66
448 449 2.996621 ACTGAAAAGATGTGCTCGCTAC 59.003 45.455 0.00 0.00 0.00 3.58
589 604 4.436523 GTCTGTGTTTCGGAAAAATGTTCG 59.563 41.667 4.46 0.00 32.76 3.95
590 605 5.336744 TGTCTGTGTTTCGGAAAAATGTTC 58.663 37.500 4.46 0.00 32.76 3.18
599 614 6.869315 TTCATAAAATGTCTGTGTTTCGGA 57.131 33.333 0.00 0.00 0.00 4.55
600 615 6.915300 TGTTTCATAAAATGTCTGTGTTTCGG 59.085 34.615 0.00 0.00 0.00 4.30
601 616 7.906611 TGTTTCATAAAATGTCTGTGTTTCG 57.093 32.000 0.00 0.00 0.00 3.46
602 617 9.462174 TCATGTTTCATAAAATGTCTGTGTTTC 57.538 29.630 0.00 0.00 0.00 2.78
626 641 8.715191 ACTGTTTGTGCTTTTGAAAAATATCA 57.285 26.923 0.00 0.00 0.00 2.15
661 1169 2.952310 GGCAGGTTGTCTGTCTTTTCTT 59.048 45.455 0.00 0.00 44.34 2.52
675 1183 0.106519 GGATATGGTGCAGGCAGGTT 60.107 55.000 0.00 0.00 0.00 3.50
724 1236 2.506438 GAGTGCTCCGTGGTACGC 60.506 66.667 0.00 0.00 40.91 4.42
734 1246 0.238553 GCGGTTTTCTTGGAGTGCTC 59.761 55.000 0.00 0.00 0.00 4.26
763 1275 2.317609 CGGTGGAGTTTCTGTGCGG 61.318 63.158 0.00 0.00 0.00 5.69
837 1349 1.151908 CCGTGGGTTCCAAAAGGGA 59.848 57.895 0.00 0.00 46.61 4.20
838 1350 1.152631 ACCGTGGGTTCCAAAAGGG 60.153 57.895 8.47 2.69 34.18 3.95
839 1351 0.466555 TCACCGTGGGTTCCAAAAGG 60.467 55.000 0.00 0.00 34.18 3.11
840 1352 0.951558 CTCACCGTGGGTTCCAAAAG 59.048 55.000 0.00 0.00 34.18 2.27
843 1355 1.147376 CACTCACCGTGGGTTCCAA 59.853 57.895 0.00 0.00 40.02 3.53
844 1356 1.125093 ATCACTCACCGTGGGTTCCA 61.125 55.000 0.00 0.00 43.94 3.53
854 1366 1.957177 TGGATAGAGCGATCACTCACC 59.043 52.381 13.07 12.36 39.26 4.02
855 1367 3.505680 AGATGGATAGAGCGATCACTCAC 59.494 47.826 13.07 4.26 39.26 3.51
857 1369 3.128589 GGAGATGGATAGAGCGATCACTC 59.871 52.174 2.38 2.33 36.91 3.51
858 1370 3.088532 GGAGATGGATAGAGCGATCACT 58.911 50.000 2.38 0.00 0.00 3.41
859 1371 2.165437 GGGAGATGGATAGAGCGATCAC 59.835 54.545 2.38 0.00 0.00 3.06
860 1372 2.042297 AGGGAGATGGATAGAGCGATCA 59.958 50.000 2.38 0.00 0.00 2.92
861 1373 2.687935 GAGGGAGATGGATAGAGCGATC 59.312 54.545 0.00 0.00 0.00 3.69
862 1374 2.622977 GGAGGGAGATGGATAGAGCGAT 60.623 54.545 0.00 0.00 0.00 4.58
863 1375 1.272203 GGAGGGAGATGGATAGAGCGA 60.272 57.143 0.00 0.00 0.00 4.93
864 1376 1.181786 GGAGGGAGATGGATAGAGCG 58.818 60.000 0.00 0.00 0.00 5.03
865 1377 1.078656 AGGGAGGGAGATGGATAGAGC 59.921 57.143 0.00 0.00 0.00 4.09
866 1378 2.292192 GGAGGGAGGGAGATGGATAGAG 60.292 59.091 0.00 0.00 0.00 2.43
867 1379 1.719378 GGAGGGAGGGAGATGGATAGA 59.281 57.143 0.00 0.00 0.00 1.98
879 1391 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
880 1392 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
881 1393 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
882 1394 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
883 1395 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
884 1396 2.277126 AATGGGAGGGAGGGAGGGAG 62.277 65.000 0.00 0.00 0.00 4.30
885 1397 2.272170 AATGGGAGGGAGGGAGGGA 61.272 63.158 0.00 0.00 0.00 4.20
886 1398 2.081161 CAATGGGAGGGAGGGAGGG 61.081 68.421 0.00 0.00 0.00 4.30
887 1399 0.921256 AACAATGGGAGGGAGGGAGG 60.921 60.000 0.00 0.00 0.00 4.30
888 1400 1.002857 AAACAATGGGAGGGAGGGAG 58.997 55.000 0.00 0.00 0.00 4.30
889 1401 1.077005 CAAAACAATGGGAGGGAGGGA 59.923 52.381 0.00 0.00 0.00 4.20
890 1402 1.560505 CAAAACAATGGGAGGGAGGG 58.439 55.000 0.00 0.00 0.00 4.30
891 1403 1.560505 CCAAAACAATGGGAGGGAGG 58.439 55.000 0.00 0.00 36.79 4.30
892 1404 0.897621 GCCAAAACAATGGGAGGGAG 59.102 55.000 0.00 0.00 41.01 4.30
893 1405 0.189574 TGCCAAAACAATGGGAGGGA 59.810 50.000 0.00 0.00 41.01 4.20
894 1406 2.757313 TGCCAAAACAATGGGAGGG 58.243 52.632 0.00 0.00 41.01 4.30
927 1439 3.712287 CCATGGTTTTGGGAGGGC 58.288 61.111 2.57 0.00 32.80 5.19
952 1464 1.203013 GGCAGGAGGGTTTTGTAGGTT 60.203 52.381 0.00 0.00 0.00 3.50
977 1489 1.768077 GGTGGAGAGGAGATGGGGG 60.768 68.421 0.00 0.00 0.00 5.40
978 1490 2.136878 CGGTGGAGAGGAGATGGGG 61.137 68.421 0.00 0.00 0.00 4.96
979 1491 1.381872 ACGGTGGAGAGGAGATGGG 60.382 63.158 0.00 0.00 0.00 4.00
980 1492 1.395826 GGACGGTGGAGAGGAGATGG 61.396 65.000 0.00 0.00 0.00 3.51
981 1493 1.395826 GGGACGGTGGAGAGGAGATG 61.396 65.000 0.00 0.00 0.00 2.90
982 1494 1.075896 GGGACGGTGGAGAGGAGAT 60.076 63.158 0.00 0.00 0.00 2.75
983 1495 2.359404 GGGACGGTGGAGAGGAGA 59.641 66.667 0.00 0.00 0.00 3.71
984 1496 2.037367 TGGGACGGTGGAGAGGAG 59.963 66.667 0.00 0.00 0.00 3.69
985 1497 2.283676 GTGGGACGGTGGAGAGGA 60.284 66.667 0.00 0.00 0.00 3.71
986 1498 2.603473 TGTGGGACGGTGGAGAGG 60.603 66.667 0.00 0.00 0.00 3.69
987 1499 2.657237 GTGTGGGACGGTGGAGAG 59.343 66.667 0.00 0.00 0.00 3.20
993 1505 2.852075 ATGGTGGTGTGGGACGGT 60.852 61.111 0.00 0.00 0.00 4.83
1015 1527 4.767255 CTCCGGTGAGCTGGTGGC 62.767 72.222 0.00 0.00 41.89 5.01
1023 1535 2.672961 TATCTTGTTGCTCCGGTGAG 57.327 50.000 7.92 0.00 41.84 3.51
1036 1553 6.924060 CGAGGTGGTTCTATAGGTTTATCTTG 59.076 42.308 0.00 0.00 0.00 3.02
1040 1557 5.303845 GGTCGAGGTGGTTCTATAGGTTTAT 59.696 44.000 0.00 0.00 0.00 1.40
1041 1558 4.646492 GGTCGAGGTGGTTCTATAGGTTTA 59.354 45.833 0.00 0.00 0.00 2.01
1042 1559 3.450096 GGTCGAGGTGGTTCTATAGGTTT 59.550 47.826 0.00 0.00 0.00 3.27
1043 1560 3.029570 GGTCGAGGTGGTTCTATAGGTT 58.970 50.000 0.00 0.00 0.00 3.50
1044 1561 2.664015 GGTCGAGGTGGTTCTATAGGT 58.336 52.381 0.00 0.00 0.00 3.08
1045 1562 1.607628 CGGTCGAGGTGGTTCTATAGG 59.392 57.143 0.00 0.00 0.00 2.57
1046 1563 2.290093 GTCGGTCGAGGTGGTTCTATAG 59.710 54.545 0.00 0.00 0.00 1.31
1047 1564 2.292267 GTCGGTCGAGGTGGTTCTATA 58.708 52.381 0.00 0.00 0.00 1.31
1462 2025 1.906574 GATGCCGTCCTTGGGGATATA 59.093 52.381 0.00 0.00 44.33 0.86
1543 2130 4.821589 CGCCGAACAGGAGGAGGC 62.822 72.222 0.00 0.00 45.00 4.70
1656 2297 0.961358 ACGACGACTCCCTCCTCTTG 60.961 60.000 0.00 0.00 0.00 3.02
1663 2304 3.117171 CGACGACGACGACTCCCT 61.117 66.667 15.32 0.00 42.66 4.20
1665 2306 3.081159 CTCCGACGACGACGACTCC 62.081 68.421 20.63 0.00 42.66 3.85
1755 2402 2.750237 AGCCCAATTTCGCCGTCC 60.750 61.111 0.00 0.00 0.00 4.79
1840 2517 3.114616 CTCGGTGCTCAAGGTGCG 61.115 66.667 0.00 0.00 0.00 5.34
1844 2521 2.125912 CGGACTCGGTGCTCAAGG 60.126 66.667 0.00 0.00 0.00 3.61
1939 2621 4.287067 TGCCATTTTTGTCTCTCTCTACCT 59.713 41.667 0.00 0.00 0.00 3.08
1942 2624 5.489792 ACTGCCATTTTTGTCTCTCTCTA 57.510 39.130 0.00 0.00 0.00 2.43
1994 2703 2.332063 ATCTGTATCCCAAAGGTGCG 57.668 50.000 0.00 0.00 0.00 5.34
1995 2704 5.012561 AGAGATATCTGTATCCCAAAGGTGC 59.987 44.000 10.74 0.00 37.94 5.01
2071 2791 9.671279 AGACAAAAAGGTTTCTTGATTTGATTT 57.329 25.926 9.08 0.00 35.69 2.17
2072 2792 9.317936 GAGACAAAAAGGTTTCTTGATTTGATT 57.682 29.630 9.08 0.55 35.69 2.57
2073 2793 8.699130 AGAGACAAAAAGGTTTCTTGATTTGAT 58.301 29.630 9.08 0.97 35.69 2.57
2074 2794 7.975616 CAGAGACAAAAAGGTTTCTTGATTTGA 59.024 33.333 9.08 0.00 35.69 2.69
2075 2795 7.254218 GCAGAGACAAAAAGGTTTCTTGATTTG 60.254 37.037 0.00 0.00 37.03 2.32
2191 4185 5.401531 TTGTATTCACTACCCTCTCACAC 57.598 43.478 0.00 0.00 0.00 3.82
2202 4196 5.221303 GGGGTACACGCTATTGTATTCACTA 60.221 44.000 0.00 0.00 34.50 2.74
2224 4218 5.396436 CCCAAAGTACATGTACCTCTAAGGG 60.396 48.000 28.29 24.40 40.58 3.95
2233 4227 3.262405 TCCACCTCCCAAAGTACATGTAC 59.738 47.826 25.51 25.51 36.35 2.90
2246 4414 2.999331 TGAAATTTCGATCCACCTCCC 58.001 47.619 13.34 0.00 0.00 4.30
2274 4442 4.961511 GTCGGTGCCGCTGTGTCA 62.962 66.667 5.64 0.00 39.59 3.58
2329 4497 1.816074 TGCGTGAAGGTTATGTTCCC 58.184 50.000 0.00 0.00 0.00 3.97
2370 4538 3.936772 TTGCCTCGGATTGGGTGGC 62.937 63.158 0.00 0.00 43.49 5.01
2391 4560 2.716969 AGTTGGAATAAGGCCCTATCCC 59.283 50.000 0.00 0.00 0.00 3.85
2395 4564 4.078219 TCCTAGAGTTGGAATAAGGCCCTA 60.078 45.833 0.00 0.00 0.00 3.53
2407 4576 1.804372 GCGCTCACATCCTAGAGTTGG 60.804 57.143 0.00 0.00 34.39 3.77
2434 4603 1.896660 TTTCGTGTCTGCTTGGGGC 60.897 57.895 0.00 0.00 42.22 5.80
2441 4610 3.672310 TGTTTTTACGTTTCGTGTCTGC 58.328 40.909 0.00 0.00 41.39 4.26
2444 4613 6.543187 ACATTTGTTTTTACGTTTCGTGTC 57.457 33.333 0.00 0.00 41.39 3.67
2449 4618 8.211838 GCAGGAATACATTTGTTTTTACGTTTC 58.788 33.333 0.00 0.00 0.00 2.78
2529 4698 0.464036 TTAGAGGTGCGGCGAATCAT 59.536 50.000 12.98 0.00 0.00 2.45
2534 4703 1.269723 CATATCTTAGAGGTGCGGCGA 59.730 52.381 12.98 0.00 0.00 5.54
2579 4835 3.126000 GCTGCAACTTAGTGGATGACTTC 59.874 47.826 0.00 0.00 35.96 3.01
2583 4839 2.857186 TGCTGCAACTTAGTGGATGA 57.143 45.000 0.00 0.00 0.00 2.92
2618 4874 7.839907 TCATTAATAAAGCTTGGTGAATTGCT 58.160 30.769 0.00 0.00 37.37 3.91
2619 4875 7.975616 TCTCATTAATAAAGCTTGGTGAATTGC 59.024 33.333 0.00 0.00 0.00 3.56
2620 4876 9.859427 TTCTCATTAATAAAGCTTGGTGAATTG 57.141 29.630 0.00 0.00 0.00 2.32
2622 4878 9.466497 TCTTCTCATTAATAAAGCTTGGTGAAT 57.534 29.630 0.00 0.00 0.00 2.57
2623 4879 8.862325 TCTTCTCATTAATAAAGCTTGGTGAA 57.138 30.769 0.00 0.00 0.00 3.18
2625 4881 7.337942 ACCTCTTCTCATTAATAAAGCTTGGTG 59.662 37.037 0.00 0.00 0.00 4.17
2626 4882 7.337942 CACCTCTTCTCATTAATAAAGCTTGGT 59.662 37.037 0.00 0.00 0.00 3.67
2627 4883 7.201767 CCACCTCTTCTCATTAATAAAGCTTGG 60.202 40.741 0.00 0.00 0.00 3.61
2628 4884 7.337942 ACCACCTCTTCTCATTAATAAAGCTTG 59.662 37.037 0.00 0.00 0.00 4.01
2631 4887 6.823689 TGACCACCTCTTCTCATTAATAAAGC 59.176 38.462 0.00 0.00 0.00 3.51
2642 4898 6.065374 TGTATCTCTATGACCACCTCTTCTC 58.935 44.000 0.00 0.00 0.00 2.87
2663 4919 5.338871 GGTGTTCCTCATGACCCTTTATGTA 60.339 44.000 0.00 0.00 0.00 2.29
2665 4921 3.947834 GGTGTTCCTCATGACCCTTTATG 59.052 47.826 0.00 0.00 0.00 1.90
2673 4929 2.191128 AGCTTGGTGTTCCTCATGAC 57.809 50.000 0.00 0.00 34.23 3.06
2689 4945 1.169577 CAGGGTCGCGATCTATAGCT 58.830 55.000 20.42 4.10 0.00 3.32
2700 4956 3.655810 CTCTCCACTGCAGGGTCGC 62.656 68.421 19.93 0.00 0.00 5.19
2701 4957 1.943116 CTCTCTCCACTGCAGGGTCG 61.943 65.000 19.93 7.05 0.00 4.79
2711 4967 2.421619 CTTGCCAAGTTCTCTCTCCAC 58.578 52.381 0.00 0.00 0.00 4.02
2715 4971 4.566488 CCATAACCTTGCCAAGTTCTCTCT 60.566 45.833 3.37 0.00 0.00 3.10
2746 5002 2.161855 TCAAATGGTGCGAGCTGAATT 58.838 42.857 0.00 0.00 0.00 2.17
2752 5008 3.552604 TTAGTTTCAAATGGTGCGAGC 57.447 42.857 0.00 0.00 0.00 5.03
2756 5012 7.224557 AGTTGTGATTTTAGTTTCAAATGGTGC 59.775 33.333 0.00 0.00 0.00 5.01
2792 5048 0.459411 ACAACCAACTTTTGCCGCAC 60.459 50.000 0.00 0.00 0.00 5.34
2821 5077 9.308000 ACCTAACATATTTCACTCATTTCCAAA 57.692 29.630 0.00 0.00 0.00 3.28
2826 5082 9.614792 GACCTACCTAACATATTTCACTCATTT 57.385 33.333 0.00 0.00 0.00 2.32
2833 5089 7.181305 TCAGTTGGACCTACCTAACATATTTCA 59.819 37.037 2.15 0.00 39.86 2.69
2839 5095 5.836024 TTTCAGTTGGACCTACCTAACAT 57.164 39.130 2.15 0.00 39.86 2.71
2844 5100 4.506802 GGTTCATTTCAGTTGGACCTACCT 60.507 45.833 2.15 0.00 39.34 3.08
2888 5144 4.662961 CGGCTGTGTGAGTCGGCA 62.663 66.667 0.00 0.00 46.54 5.69
2900 5156 1.358402 CTCGATCTGAGGTCGGCTG 59.642 63.158 15.85 2.47 41.29 4.85
3021 5338 1.801178 GACAGTGACTTGGTAGCAAGC 59.199 52.381 29.70 22.63 35.70 4.01
3023 5340 1.872237 GCGACAGTGACTTGGTAGCAA 60.872 52.381 7.22 7.22 34.02 3.91
3027 5344 1.669440 GGGCGACAGTGACTTGGTA 59.331 57.895 0.00 0.00 0.00 3.25
3030 5347 2.358737 GGGGGCGACAGTGACTTG 60.359 66.667 0.00 0.00 0.00 3.16
3046 7264 3.886123 AGGAACGGAAGACAAATATGGG 58.114 45.455 0.00 0.00 0.00 4.00
3047 7265 4.941263 TCAAGGAACGGAAGACAAATATGG 59.059 41.667 0.00 0.00 0.00 2.74
3061 7279 3.119849 CCTACCTGCAAATTCAAGGAACG 60.120 47.826 7.76 0.00 0.00 3.95
3082 7300 3.468140 GGCTGGGGAGGACGTACC 61.468 72.222 0.00 0.00 39.35 3.34


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

AutoCloner maintained by Alex Coulton.