Multiple sequence alignment - TraesCS6A01G047800

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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 TraesCS6A01G047800 chr6A 100.000 4513 0 0 1 4513 24067505 24072017 0.000000e+00 8335.0
1 TraesCS6A01G047800 chr6A 95.714 140 3 2 4377 4513 109488698 109488559 5.880000e-54 222.0
2 TraesCS6A01G047800 chr6D 93.783 1898 85 17 2509 4386 26251200 26253084 0.000000e+00 2820.0
3 TraesCS6A01G047800 chr6D 92.216 1516 114 2 979 2491 26249702 26251216 0.000000e+00 2143.0
4 TraesCS6A01G047800 chr6D 94.808 443 18 3 1 440 26244894 26245334 0.000000e+00 686.0
5 TraesCS6A01G047800 chr6D 90.037 271 20 5 643 912 26246011 26246275 1.200000e-90 344.0
6 TraesCS6A01G047800 chr6B 89.530 1853 95 45 2509 4324 42506760 42508550 0.000000e+00 2255.0
7 TraesCS6A01G047800 chr6B 93.528 618 38 1 1876 2491 42506159 42506776 0.000000e+00 918.0
8 TraesCS6A01G047800 chr6B 93.440 564 37 0 1042 1605 42505591 42506154 0.000000e+00 837.0
9 TraesCS6A01G047800 chr6B 93.103 406 21 5 1 402 42500207 42500609 5.030000e-164 588.0
10 TraesCS6A01G047800 chr7D 91.557 379 20 7 4019 4385 555860315 555859937 3.110000e-141 512.0
11 TraesCS6A01G047800 chr7D 91.293 379 21 7 4019 4385 91413197 91413575 1.450000e-139 507.0
12 TraesCS6A01G047800 chr7D 91.293 379 20 8 4019 4384 273497957 273497579 5.210000e-139 505.0
13 TraesCS6A01G047800 chr7D 90.501 379 21 9 4019 4385 278469540 278469165 1.890000e-133 486.0
14 TraesCS6A01G047800 chr7D 97.101 138 2 2 4377 4513 459392103 459391967 9.760000e-57 231.0
15 TraesCS6A01G047800 chr7D 80.333 300 42 11 1023 1318 594130607 594130893 1.270000e-50 211.0
16 TraesCS6A01G047800 chr7D 77.075 253 47 8 651 899 207608368 207608123 7.870000e-28 135.0
17 TraesCS6A01G047800 chr3D 91.293 379 21 7 4019 4385 542180991 542181369 1.450000e-139 507.0
18 TraesCS6A01G047800 chr3D 97.727 132 3 0 4382 4513 217587550 217587681 1.260000e-55 228.0
19 TraesCS6A01G047800 chr5D 74.513 1232 256 40 994 2211 441239198 441238011 2.440000e-132 483.0
20 TraesCS6A01G047800 chr5D 72.211 1533 331 66 997 2470 441358665 441357169 2.550000e-102 383.0
21 TraesCS6A01G047800 chr5D 72.510 1215 282 40 997 2197 441163651 441162475 3.340000e-91 346.0
22 TraesCS6A01G047800 chr5B 73.602 1288 278 44 994 2260 536910893 536909647 5.360000e-119 438.0
23 TraesCS6A01G047800 chr5B 72.670 1266 292 41 997 2237 537536404 537535168 5.510000e-99 372.0
24 TraesCS6A01G047800 chr5B 72.179 1276 293 46 997 2260 536852722 536851497 2.600000e-87 333.0
25 TraesCS6A01G047800 chr5B 94.776 134 7 0 518 651 660144711 660144578 4.570000e-50 209.0
26 TraesCS6A01G047800 chr5A 97.778 135 2 1 4379 4513 290391685 290391818 9.760000e-57 231.0
27 TraesCS6A01G047800 chr5A 96.094 128 5 0 519 646 46616188 46616315 4.570000e-50 209.0
28 TraesCS6A01G047800 chr2B 99.219 128 1 0 4386 4513 149836963 149837090 9.760000e-57 231.0
29 TraesCS6A01G047800 chr1B 97.744 133 2 1 4381 4513 117848610 117848479 1.260000e-55 228.0
30 TraesCS6A01G047800 chr7A 95.714 140 3 3 4374 4513 541437976 541438112 5.880000e-54 222.0
31 TraesCS6A01G047800 chr3A 97.674 129 3 0 518 646 430794946 430795074 5.880000e-54 222.0
32 TraesCS6A01G047800 chr4B 94.444 144 5 3 4372 4513 551079894 551080036 7.600000e-53 219.0
33 TraesCS6A01G047800 chr4B 92.157 51 4 0 3897 3947 626000348 626000298 6.260000e-09 73.1
34 TraesCS6A01G047800 chr1A 94.406 143 6 2 4371 4513 66898379 66898519 7.600000e-53 219.0
35 TraesCS6A01G047800 chr4A 96.124 129 5 0 517 645 200095982 200095854 1.270000e-50 211.0
36 TraesCS6A01G047800 chrUn 94.737 133 7 0 516 648 17025388 17025256 1.650000e-49 207.0
37 TraesCS6A01G047800 chrUn 94.737 133 7 0 516 648 17027621 17027489 1.650000e-49 207.0
38 TraesCS6A01G047800 chrUn 94.737 133 7 0 516 648 292131058 292131190 1.650000e-49 207.0
39 TraesCS6A01G047800 chrUn 94.737 133 7 0 516 648 302852128 302852260 1.650000e-49 207.0
40 TraesCS6A01G047800 chrUn 94.737 133 7 0 516 648 302859427 302859295 1.650000e-49 207.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G047800 chr6A 24067505 24072017 4512 False 8335.000000 8335 100.000 1 4513 1 chr6A.!!$F1 4512
1 TraesCS6A01G047800 chr6D 26244894 26253084 8190 False 1498.250000 2820 92.711 1 4386 4 chr6D.!!$F1 4385
2 TraesCS6A01G047800 chr6B 42505591 42508550 2959 False 1336.666667 2255 92.166 1042 4324 3 chr6B.!!$F2 3282
3 TraesCS6A01G047800 chr5D 441238011 441239198 1187 True 483.000000 483 74.513 994 2211 1 chr5D.!!$R2 1217
4 TraesCS6A01G047800 chr5D 441357169 441358665 1496 True 383.000000 383 72.211 997 2470 1 chr5D.!!$R3 1473
5 TraesCS6A01G047800 chr5D 441162475 441163651 1176 True 346.000000 346 72.510 997 2197 1 chr5D.!!$R1 1200
6 TraesCS6A01G047800 chr5B 536909647 536910893 1246 True 438.000000 438 73.602 994 2260 1 chr5B.!!$R2 1266
7 TraesCS6A01G047800 chr5B 537535168 537536404 1236 True 372.000000 372 72.670 997 2237 1 chr5B.!!$R3 1240
8 TraesCS6A01G047800 chr5B 536851497 536852722 1225 True 333.000000 333 72.179 997 2260 1 chr5B.!!$R1 1263
9 TraesCS6A01G047800 chrUn 17025256 17027621 2365 True 207.000000 207 94.737 516 648 2 chrUn.!!$R2 132

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
977 4957 0.033228 CCTTTCAACAATGCGCCCAA 59.967 50.0 4.18 0.0 0.00 4.12 F
1773 6939 0.030101 CCTCGAGCTTCTCCACGATC 59.970 60.0 6.99 0.0 34.41 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 7531 0.897863 TGATCCAAAGGCCAAACGGG 60.898 55.000 5.01 0.0 40.85 5.28 R
3576 9105 1.153549 GCCCACTACTGCTCTTCCG 60.154 63.158 0.00 0.0 0.00 4.30 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.023452 ACTGTCAGTCCACAAGGTATATGA 58.977 41.667 0.00 0.00 35.89 2.15
28 29 6.609616 TGTCAGTCCACAAGGTATATGATGTA 59.390 38.462 0.00 0.00 35.89 2.29
34 35 6.269769 TCCACAAGGTATATGATGTATCAGCA 59.730 38.462 0.74 0.00 36.84 4.41
71 72 0.958382 ATTCGCGCCCTTTGCACTTA 60.958 50.000 0.00 0.00 41.33 2.24
82 83 1.508632 TTGCACTTACTCGAACTGGC 58.491 50.000 0.00 0.00 0.00 4.85
127 128 0.107312 CCTTCCTGCCATCTCCAGTG 60.107 60.000 0.00 0.00 0.00 3.66
176 177 2.813908 GCACGTGTTAGCTCCCCG 60.814 66.667 18.38 0.00 0.00 5.73
188 189 1.680207 AGCTCCCCGTATTTACTCGAC 59.320 52.381 0.00 0.00 0.00 4.20
193 194 3.763360 TCCCCGTATTTACTCGACAAAGA 59.237 43.478 0.00 0.00 0.00 2.52
223 224 1.806542 GAATGCCTGAGAAGCGTCAAA 59.193 47.619 1.61 0.00 0.00 2.69
231 232 2.802816 TGAGAAGCGTCAAAGAAGAAGC 59.197 45.455 1.61 0.00 42.24 3.86
252 253 3.505386 CTCCAGTAGGATATGAGGCTGT 58.495 50.000 0.00 0.00 44.70 4.40
263 264 2.680312 TGAGGCTGTGATGTCTTAGC 57.320 50.000 0.00 0.00 35.49 3.09
300 301 4.905866 CACACTCGCATTGTTGTCTTAAAG 59.094 41.667 0.00 0.00 0.00 1.85
313 314 3.646162 TGTCTTAAAGAGGGACTTGCAGA 59.354 43.478 0.00 0.00 41.55 4.26
372 376 6.218019 TCAAACTTTGAGGAATTTCTGCATG 58.782 36.000 0.00 0.00 34.08 4.06
408 412 2.916702 AGCATGGTATGATTCGCTGA 57.083 45.000 0.00 0.00 0.00 4.26
418 422 5.406780 GGTATGATTCGCTGAACTAATCTGG 59.593 44.000 0.00 0.00 32.89 3.86
442 446 9.342308 TGGATTCTTATAATGTCTTGTTGATCC 57.658 33.333 0.00 0.00 0.00 3.36
443 447 9.342308 GGATTCTTATAATGTCTTGTTGATCCA 57.658 33.333 0.00 0.00 0.00 3.41
446 450 8.213518 TCTTATAATGTCTTGTTGATCCAAGC 57.786 34.615 6.80 4.04 41.29 4.01
447 451 8.049117 TCTTATAATGTCTTGTTGATCCAAGCT 58.951 33.333 6.80 0.00 41.29 3.74
448 452 9.330063 CTTATAATGTCTTGTTGATCCAAGCTA 57.670 33.333 6.80 0.54 41.29 3.32
450 454 3.338249 TGTCTTGTTGATCCAAGCTAGC 58.662 45.455 6.62 6.62 41.29 3.42
451 455 3.008375 TGTCTTGTTGATCCAAGCTAGCT 59.992 43.478 12.68 12.68 41.29 3.32
452 456 3.620821 GTCTTGTTGATCCAAGCTAGCTC 59.379 47.826 19.65 5.78 41.29 4.09
453 457 3.261643 TCTTGTTGATCCAAGCTAGCTCA 59.738 43.478 19.65 8.73 41.29 4.26
454 458 3.701205 TGTTGATCCAAGCTAGCTCAA 57.299 42.857 19.65 14.65 0.00 3.02
455 459 3.338249 TGTTGATCCAAGCTAGCTCAAC 58.662 45.455 27.36 27.36 43.67 3.18
468 567 1.009675 CTCAACTTGTGCGTGTGCC 60.010 57.895 0.00 0.00 41.78 5.01
489 588 2.620112 CCAACAGACAAGGCGCCAG 61.620 63.158 31.54 23.15 0.00 4.85
502 1105 1.798735 CGCCAGTTGATCCAAGCAG 59.201 57.895 0.00 0.00 0.00 4.24
512 1115 3.730761 CCAAGCAGGTGCACGCTC 61.731 66.667 17.91 6.26 45.16 5.03
542 1145 2.034124 CCCTCCGTCCGGAAATACTTA 58.966 52.381 5.23 0.00 44.66 2.24
606 1209 7.979444 TCAGTTCTAGATACAACCCTTTTTG 57.021 36.000 0.00 0.00 0.00 2.44
608 1211 7.660208 TCAGTTCTAGATACAACCCTTTTTGTC 59.340 37.037 0.00 0.00 40.29 3.18
616 1219 4.522114 ACAACCCTTTTTGTCCATTTTGG 58.478 39.130 0.00 0.00 34.48 3.28
706 1309 8.821147 AAACTGATACTTGTCATACGTGTAAA 57.179 30.769 0.00 0.00 0.00 2.01
726 1330 9.221775 GTGTAAATTGTTATTTCATCGTGATCC 57.778 33.333 0.00 0.00 35.61 3.36
739 1343 5.633601 TCATCGTGATCCGTATTGAAATAGC 59.366 40.000 3.97 0.00 37.94 2.97
744 1348 6.562270 CGTGATCCGTATTGAAATAGCTGTTC 60.562 42.308 0.00 0.13 0.00 3.18
746 1350 6.257849 TGATCCGTATTGAAATAGCTGTTCAC 59.742 38.462 12.72 4.31 34.78 3.18
832 1436 8.671384 AATATGAAATTGGAATGGCTGAAATG 57.329 30.769 0.00 0.00 0.00 2.32
844 1448 7.818930 GGAATGGCTGAAATGACATTTTAAAGA 59.181 33.333 14.46 1.02 44.85 2.52
879 2293 7.122650 TCCTTGATCTCACCCATTTGAAATAAC 59.877 37.037 0.00 0.00 0.00 1.89
889 2303 6.326323 ACCCATTTGAAATAACCAGTTTCACT 59.674 34.615 1.17 0.00 43.16 3.41
912 2326 1.674359 TTTGTGGTGTGCGAGATTGT 58.326 45.000 0.00 0.00 0.00 2.71
913 2327 1.674359 TTGTGGTGTGCGAGATTGTT 58.326 45.000 0.00 0.00 0.00 2.83
915 2329 2.139917 TGTGGTGTGCGAGATTGTTAC 58.860 47.619 0.00 0.00 0.00 2.50
916 2330 1.126113 GTGGTGTGCGAGATTGTTACG 59.874 52.381 0.00 0.00 0.00 3.18
918 2332 1.389106 GGTGTGCGAGATTGTTACGTC 59.611 52.381 0.00 0.00 0.00 4.34
919 2333 1.389106 GTGTGCGAGATTGTTACGTCC 59.611 52.381 0.00 0.00 0.00 4.79
920 2334 1.000052 TGTGCGAGATTGTTACGTCCA 60.000 47.619 0.00 0.00 0.00 4.02
921 2335 2.268298 GTGCGAGATTGTTACGTCCAT 58.732 47.619 0.00 0.00 0.00 3.41
922 2336 2.281762 GTGCGAGATTGTTACGTCCATC 59.718 50.000 0.00 0.00 0.00 3.51
923 2337 1.517276 GCGAGATTGTTACGTCCATCG 59.483 52.381 0.00 0.00 46.00 3.84
924 2338 2.117137 CGAGATTGTTACGTCCATCGG 58.883 52.381 0.00 0.00 44.69 4.18
925 2339 2.470821 GAGATTGTTACGTCCATCGGG 58.529 52.381 0.00 0.00 44.69 5.14
926 2340 1.829222 AGATTGTTACGTCCATCGGGT 59.171 47.619 0.00 0.00 44.69 5.28
927 2341 2.235402 AGATTGTTACGTCCATCGGGTT 59.765 45.455 0.00 0.00 44.69 4.11
929 2343 2.083167 TGTTACGTCCATCGGGTTTC 57.917 50.000 0.00 0.00 44.69 2.78
944 4924 1.001706 GGTTTCTTTCGTCCACCTTGC 60.002 52.381 0.00 0.00 0.00 4.01
958 4938 0.464554 CCTTGCTCGATCCCCTTTCC 60.465 60.000 0.00 0.00 0.00 3.13
959 4939 0.464554 CTTGCTCGATCCCCTTTCCC 60.465 60.000 0.00 0.00 0.00 3.97
960 4940 0.914417 TTGCTCGATCCCCTTTCCCT 60.914 55.000 0.00 0.00 0.00 4.20
961 4941 0.914417 TGCTCGATCCCCTTTCCCTT 60.914 55.000 0.00 0.00 0.00 3.95
962 4942 0.256177 GCTCGATCCCCTTTCCCTTT 59.744 55.000 0.00 0.00 0.00 3.11
963 4943 1.747552 GCTCGATCCCCTTTCCCTTTC 60.748 57.143 0.00 0.00 0.00 2.62
964 4944 1.559682 CTCGATCCCCTTTCCCTTTCA 59.440 52.381 0.00 0.00 0.00 2.69
965 4945 1.989586 TCGATCCCCTTTCCCTTTCAA 59.010 47.619 0.00 0.00 0.00 2.69
966 4946 2.092323 CGATCCCCTTTCCCTTTCAAC 58.908 52.381 0.00 0.00 0.00 3.18
967 4947 2.554344 CGATCCCCTTTCCCTTTCAACA 60.554 50.000 0.00 0.00 0.00 3.33
968 4948 3.506398 GATCCCCTTTCCCTTTCAACAA 58.494 45.455 0.00 0.00 0.00 2.83
969 4949 3.628832 TCCCCTTTCCCTTTCAACAAT 57.371 42.857 0.00 0.00 0.00 2.71
970 4950 3.238597 TCCCCTTTCCCTTTCAACAATG 58.761 45.455 0.00 0.00 0.00 2.82
971 4951 2.289631 CCCCTTTCCCTTTCAACAATGC 60.290 50.000 0.00 0.00 0.00 3.56
972 4952 2.610232 CCCTTTCCCTTTCAACAATGCG 60.610 50.000 0.00 0.00 0.00 4.73
973 4953 2.061028 CTTTCCCTTTCAACAATGCGC 58.939 47.619 0.00 0.00 0.00 6.09
974 4954 0.316841 TTCCCTTTCAACAATGCGCC 59.683 50.000 4.18 0.00 0.00 6.53
975 4955 1.079888 CCCTTTCAACAATGCGCCC 60.080 57.895 4.18 0.00 0.00 6.13
976 4956 1.664873 CCTTTCAACAATGCGCCCA 59.335 52.632 4.18 0.00 0.00 5.36
977 4957 0.033228 CCTTTCAACAATGCGCCCAA 59.967 50.000 4.18 0.00 0.00 4.12
984 4964 2.203625 AATGCGCCCAAACCCACT 60.204 55.556 4.18 0.00 0.00 4.00
989 4969 2.022240 GCGCCCAAACCCACTGAAAA 62.022 55.000 0.00 0.00 0.00 2.29
1095 6035 1.228184 GGAGATCCTCCTCCGCGTA 60.228 63.158 4.92 0.00 46.41 4.42
1335 6281 3.061429 GCTTCAGCTTCGACATCTACAAC 59.939 47.826 0.00 0.00 38.21 3.32
1340 6286 0.604073 TTCGACATCTACAACGGCCA 59.396 50.000 2.24 0.00 0.00 5.36
1341 6287 0.604073 TCGACATCTACAACGGCCAA 59.396 50.000 2.24 0.00 0.00 4.52
1346 6292 2.091541 CATCTACAACGGCCAATTGGT 58.908 47.619 25.19 7.28 37.57 3.67
1445 6596 4.459089 GCTGTGCCCTCGGAGACC 62.459 72.222 6.58 0.00 0.00 3.85
1656 6822 0.679002 CTCCCTTGGACATGCACCAG 60.679 60.000 11.20 7.00 38.70 4.00
1682 6848 0.108615 CGTCCACTACTCCAGCCAAG 60.109 60.000 0.00 0.00 0.00 3.61
1683 6849 0.250513 GTCCACTACTCCAGCCAAGG 59.749 60.000 0.00 0.00 0.00 3.61
1747 6913 3.553597 GACATCGTCGTCCTGGATC 57.446 57.895 0.00 0.00 0.00 3.36
1761 6927 2.026879 GATCTGACGGCCTCGAGC 59.973 66.667 6.99 2.33 40.11 5.03
1773 6939 0.030101 CCTCGAGCTTCTCCACGATC 59.970 60.000 6.99 0.00 34.41 3.69
1845 7014 3.567797 GCTCACGATGCTTCCGGC 61.568 66.667 0.00 0.00 42.22 6.13
1935 7104 0.249238 TGGACACCATTTGTTTGCGC 60.249 50.000 0.00 0.00 39.17 6.09
1949 7118 2.887568 GCGCGAGATGTGTCCTGG 60.888 66.667 12.10 0.00 0.00 4.45
1986 7155 1.900351 CACGGCTGAGGATGAGGAA 59.100 57.895 0.00 0.00 0.00 3.36
2016 7185 1.489230 GTCATAAGACGGGTGGGGAAT 59.511 52.381 0.00 0.00 34.60 3.01
2082 7251 1.144057 GGATACCAGGTGCAGGACG 59.856 63.158 0.76 0.00 0.00 4.79
2163 7332 0.107268 TGATGATCTGGCATCCCACG 59.893 55.000 0.00 0.00 43.10 4.94
2197 7531 1.478105 GGGGTGATCATGCAAGGTTTC 59.522 52.381 0.00 0.00 0.00 2.78
2200 7534 1.133025 GTGATCATGCAAGGTTTCCCG 59.867 52.381 0.00 0.00 35.12 5.14
2302 7679 3.130869 TGGCAATAGATGTGGAATTGTGC 59.869 43.478 0.00 0.00 33.96 4.57
2324 7701 7.879677 TGTGCTAGGTATATGATTGATTCCTTG 59.120 37.037 0.00 0.00 0.00 3.61
2473 7871 2.137528 TGTCCCTTGCGTGTCCTCA 61.138 57.895 0.00 0.00 0.00 3.86
2476 7874 1.191489 TCCCTTGCGTGTCCTCATGA 61.191 55.000 0.00 0.00 32.78 3.07
2477 7875 0.742281 CCCTTGCGTGTCCTCATGAG 60.742 60.000 16.24 16.24 32.78 2.90
2478 7876 0.036952 CCTTGCGTGTCCTCATGAGT 60.037 55.000 21.11 0.00 32.78 3.41
2479 7877 1.073964 CTTGCGTGTCCTCATGAGTG 58.926 55.000 21.11 12.59 32.78 3.51
2480 7878 0.950555 TTGCGTGTCCTCATGAGTGC 60.951 55.000 21.11 15.67 32.78 4.40
2481 7879 1.079543 GCGTGTCCTCATGAGTGCT 60.080 57.895 21.11 0.00 32.78 4.40
2482 7880 0.671781 GCGTGTCCTCATGAGTGCTT 60.672 55.000 21.11 0.00 32.78 3.91
2483 7881 1.073964 CGTGTCCTCATGAGTGCTTG 58.926 55.000 21.11 5.81 32.78 4.01
2484 7882 1.337167 CGTGTCCTCATGAGTGCTTGA 60.337 52.381 21.11 8.14 32.78 3.02
2485 7883 2.676176 CGTGTCCTCATGAGTGCTTGAT 60.676 50.000 21.11 0.00 32.78 2.57
2486 7884 3.341823 GTGTCCTCATGAGTGCTTGATT 58.658 45.455 21.11 0.00 0.00 2.57
2487 7885 3.126514 GTGTCCTCATGAGTGCTTGATTG 59.873 47.826 21.11 2.94 0.00 2.67
2488 7886 2.681848 GTCCTCATGAGTGCTTGATTGG 59.318 50.000 21.11 3.06 0.00 3.16
2489 7887 1.404391 CCTCATGAGTGCTTGATTGGC 59.596 52.381 21.11 0.00 0.00 4.52
2490 7888 2.366533 CTCATGAGTGCTTGATTGGCT 58.633 47.619 14.95 0.00 0.00 4.75
2491 7889 2.753452 CTCATGAGTGCTTGATTGGCTT 59.247 45.455 14.95 0.00 0.00 4.35
2492 7890 3.159472 TCATGAGTGCTTGATTGGCTTT 58.841 40.909 0.00 0.00 0.00 3.51
2493 7891 3.575256 TCATGAGTGCTTGATTGGCTTTT 59.425 39.130 0.00 0.00 0.00 2.27
2494 7892 4.039488 TCATGAGTGCTTGATTGGCTTTTT 59.961 37.500 0.00 0.00 0.00 1.94
2543 7941 2.863137 GCTAGTTGAGAAGGAAGATGCG 59.137 50.000 0.00 0.00 0.00 4.73
2587 7986 1.120530 TCGTCTTAGGGAAGGATGGC 58.879 55.000 0.00 0.00 33.09 4.40
2610 8009 5.621329 GCGGTGTATTTCTTGGTTGCTAAAT 60.621 40.000 0.00 0.00 0.00 1.40
2682 8081 4.159506 GGCAAATAATCTGCTTGGGTACAA 59.840 41.667 0.00 0.00 39.82 2.41
2910 8329 2.439156 GGGCAGACCACTCCATGC 60.439 66.667 0.00 0.00 39.85 4.06
3181 8689 8.861033 CAAATGTCCCATATTTGTATGTTGAG 57.139 34.615 0.00 0.00 39.49 3.02
3185 8693 4.887071 TCCCATATTTGTATGTTGAGGCAC 59.113 41.667 0.00 0.00 0.00 5.01
3204 8729 6.488715 AGGCACAGAGGATTCTAAATTTCTT 58.511 36.000 0.00 0.00 30.73 2.52
3205 8730 7.633789 AGGCACAGAGGATTCTAAATTTCTTA 58.366 34.615 0.00 0.00 30.73 2.10
3206 8731 8.277918 AGGCACAGAGGATTCTAAATTTCTTAT 58.722 33.333 0.00 0.00 30.73 1.73
3207 8732 8.348507 GGCACAGAGGATTCTAAATTTCTTATG 58.651 37.037 0.00 0.00 30.73 1.90
3208 8733 7.859875 GCACAGAGGATTCTAAATTTCTTATGC 59.140 37.037 0.00 0.00 30.73 3.14
3209 8734 8.896744 CACAGAGGATTCTAAATTTCTTATGCA 58.103 33.333 0.00 0.00 30.73 3.96
3210 8735 9.638176 ACAGAGGATTCTAAATTTCTTATGCAT 57.362 29.630 3.79 3.79 30.73 3.96
3291 8816 4.013728 TGATAGCGGGTAATTTGTGCTTT 58.986 39.130 0.00 0.00 37.12 3.51
3320 8845 7.124750 TGTCATTTGTCCTTCTATGATCAGAGA 59.875 37.037 15.98 15.98 30.51 3.10
3364 8889 5.550232 TGCAGACTGTATAATGCAAAGTG 57.450 39.130 3.99 0.00 45.09 3.16
3390 8915 5.645056 TGTCTGGGATATGAAGCCATTTA 57.355 39.130 0.00 0.00 34.31 1.40
3391 8916 6.012337 TGTCTGGGATATGAAGCCATTTAA 57.988 37.500 0.00 0.00 34.31 1.52
3392 8917 6.613699 TGTCTGGGATATGAAGCCATTTAAT 58.386 36.000 0.00 0.00 34.31 1.40
3393 8918 7.068702 TGTCTGGGATATGAAGCCATTTAATT 58.931 34.615 0.00 0.00 34.31 1.40
3394 8919 7.564660 TGTCTGGGATATGAAGCCATTTAATTT 59.435 33.333 0.00 0.00 34.31 1.82
3576 9105 0.107312 AGTGATCAGGGCAGCATCAC 60.107 55.000 13.36 13.36 44.61 3.06
3629 9158 7.332430 GTCTAGTACGTGATAGACTGATAGCAT 59.668 40.741 23.99 0.00 42.96 3.79
3637 9166 7.327275 CGTGATAGACTGATAGCATTTCTAACC 59.673 40.741 4.17 1.73 0.00 2.85
3730 9259 3.777465 GAGCACGTACTCCTATGTGAA 57.223 47.619 4.30 0.00 40.95 3.18
3732 9261 4.683832 GAGCACGTACTCCTATGTGAATT 58.316 43.478 4.30 0.00 40.95 2.17
3796 9325 6.149640 TGAGTAGTTATCTCGTCTGATATGCC 59.850 42.308 0.00 0.00 34.99 4.40
3822 9351 3.489785 GTGTAAGTCTTGTGGTTCGACTG 59.510 47.826 0.00 0.00 38.00 3.51
3827 9356 1.272490 TCTTGTGGTTCGACTGCTAGG 59.728 52.381 0.00 0.00 0.00 3.02
3838 9367 5.339008 TCGACTGCTAGGATGTTTGTTAT 57.661 39.130 0.00 0.00 0.00 1.89
3839 9368 5.109210 TCGACTGCTAGGATGTTTGTTATG 58.891 41.667 0.00 0.00 0.00 1.90
3970 9499 3.391296 AGTTTCTTTGAGGCCACAGTCTA 59.609 43.478 5.01 0.00 0.00 2.59
3971 9500 3.402628 TTCTTTGAGGCCACAGTCTAC 57.597 47.619 5.01 0.00 0.00 2.59
4059 9596 6.255596 TGTAGTTGTGCTAGTTCAGAGTAG 57.744 41.667 0.00 0.00 32.85 2.57
4302 9844 2.768253 TGGACATGAACGCTTCAGAT 57.232 45.000 0.00 0.00 43.98 2.90
4317 9859 6.201044 ACGCTTCAGATAAATTAATCGACAGG 59.799 38.462 0.00 0.00 0.00 4.00
4386 9928 7.882791 TGACATGGACAACAGAACATAATAAGT 59.117 33.333 0.00 0.00 0.00 2.24
4387 9929 8.635765 ACATGGACAACAGAACATAATAAGTT 57.364 30.769 0.00 0.00 0.00 2.66
4388 9930 9.733556 ACATGGACAACAGAACATAATAAGTTA 57.266 29.630 0.00 0.00 0.00 2.24
4401 9943 8.350852 ACATAATAAGTTATCTACTCCCTCCG 57.649 38.462 0.00 0.00 35.54 4.63
4402 9944 7.949006 ACATAATAAGTTATCTACTCCCTCCGT 59.051 37.037 0.00 0.00 35.54 4.69
4403 9945 8.804204 CATAATAAGTTATCTACTCCCTCCGTT 58.196 37.037 0.00 0.00 35.54 4.44
4404 9946 6.897706 ATAAGTTATCTACTCCCTCCGTTC 57.102 41.667 0.00 0.00 35.54 3.95
4405 9947 3.564264 AGTTATCTACTCCCTCCGTTCC 58.436 50.000 0.00 0.00 28.23 3.62
4406 9948 3.204831 AGTTATCTACTCCCTCCGTTCCT 59.795 47.826 0.00 0.00 28.23 3.36
4407 9949 4.414846 AGTTATCTACTCCCTCCGTTCCTA 59.585 45.833 0.00 0.00 28.23 2.94
4408 9950 3.967467 ATCTACTCCCTCCGTTCCTAA 57.033 47.619 0.00 0.00 0.00 2.69
4409 9951 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
4410 9952 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
4411 9953 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
4412 9954 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
4413 9955 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
4414 9956 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4415 9957 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4416 9958 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4417 9959 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4418 9960 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4419 9961 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4420 9962 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4421 9963 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
4422 9964 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
4423 9965 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
4424 9966 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
4425 9967 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
4438 9980 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
4439 9981 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
4440 9982 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
4441 9983 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
4442 9984 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
4443 9985 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
4444 9986 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
4445 9987 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
4446 9988 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
4448 9990 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
4449 9991 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
4450 9992 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
4451 9993 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
4452 9994 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
4453 9995 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
4454 9996 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
4455 9997 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
4456 9998 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
4457 9999 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
4458 10000 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
4459 10001 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
4460 10002 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
4461 10003 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
4462 10004 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
4463 10005 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
4464 10006 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
4465 10007 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
4466 10008 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
4467 10009 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
4468 10010 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
4469 10011 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
4470 10012 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
4471 10013 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
4472 10014 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
4505 10047 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
4507 10049 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
4508 10050 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
4509 10051 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
4510 10052 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
4511 10053 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
4512 10054 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 2.521105 AAACGTTAGCCAGTTCGAGT 57.479 45.000 0.00 0.00 0.00 4.18
82 83 7.639945 AGAAGGAAACAATGAGAAAACGTTAG 58.360 34.615 0.00 0.00 0.00 2.34
176 177 7.793902 TCTGCTTTTCTTTGTCGAGTAAATAC 58.206 34.615 0.00 0.00 0.00 1.89
188 189 4.625742 CAGGCATTCATCTGCTTTTCTTTG 59.374 41.667 0.00 0.00 41.95 2.77
193 194 3.693807 TCTCAGGCATTCATCTGCTTTT 58.306 40.909 0.00 0.00 41.95 2.27
223 224 5.710646 TCATATCCTACTGGAGCTTCTTCT 58.289 41.667 0.00 0.00 46.91 2.85
231 232 3.257873 CACAGCCTCATATCCTACTGGAG 59.742 52.174 0.00 0.00 46.91 3.86
252 253 2.967599 ATGCAGACGCTAAGACATCA 57.032 45.000 0.00 0.00 39.64 3.07
263 264 3.469629 CGAGTGTGTAAAAATGCAGACG 58.530 45.455 0.00 0.00 34.60 4.18
300 301 3.149196 TGTGAAAATCTGCAAGTCCCTC 58.851 45.455 0.00 0.00 33.76 4.30
342 346 8.758715 CAGAAATTCCTCAAAGTTTGAATGTTC 58.241 33.333 18.55 15.63 39.58 3.18
443 447 1.151668 CGCACAAGTTGAGCTAGCTT 58.848 50.000 20.42 0.00 31.68 3.74
445 449 0.164647 CACGCACAAGTTGAGCTAGC 59.835 55.000 20.67 6.62 31.68 3.42
446 450 1.193203 CACACGCACAAGTTGAGCTAG 59.807 52.381 20.67 15.26 31.68 3.42
447 451 1.217001 CACACGCACAAGTTGAGCTA 58.783 50.000 20.67 0.00 31.68 3.32
448 452 2.016961 CACACGCACAAGTTGAGCT 58.983 52.632 20.67 7.40 31.68 4.09
450 454 1.009675 GGCACACGCACAAGTTGAG 60.010 57.895 10.54 2.31 41.24 3.02
451 455 1.308783 TTGGCACACGCACAAGTTGA 61.309 50.000 10.54 0.00 39.29 3.18
452 456 1.138459 TTGGCACACGCACAAGTTG 59.862 52.632 0.00 0.00 39.29 3.16
453 457 1.138671 GTTGGCACACGCACAAGTT 59.861 52.632 0.00 0.00 39.29 2.66
454 458 2.770589 GGTTGGCACACGCACAAGT 61.771 57.895 0.00 0.00 39.29 3.16
455 459 2.026014 GGTTGGCACACGCACAAG 59.974 61.111 0.00 0.00 39.29 3.16
468 567 1.008538 GCGCCTTGTCTGTTGGTTG 60.009 57.895 0.00 0.00 0.00 3.77
489 588 0.242017 GTGCACCTGCTTGGATCAAC 59.758 55.000 5.22 0.00 42.66 3.18
502 1105 2.027625 GTACCAGTGAGCGTGCACC 61.028 63.158 12.15 4.10 39.59 5.01
512 1115 1.321074 GGACGGAGGGAGTACCAGTG 61.321 65.000 0.00 0.00 43.89 3.66
583 1186 7.094762 GGACAAAAAGGGTTGTATCTAGAACTG 60.095 40.741 0.00 0.00 41.78 3.16
597 1200 3.777522 TCACCAAAATGGACAAAAAGGGT 59.222 39.130 2.85 0.00 40.96 4.34
606 1209 6.362283 CGAAAATACTTGTCACCAAAATGGAC 59.638 38.462 2.85 0.00 40.96 4.02
608 1211 5.633182 CCGAAAATACTTGTCACCAAAATGG 59.367 40.000 0.00 0.00 45.02 3.16
616 1219 3.319755 TCCGTCCGAAAATACTTGTCAC 58.680 45.455 0.00 0.00 0.00 3.67
678 1281 6.586463 ACACGTATGACAAGTATCAGTTTCAG 59.414 38.462 0.00 0.00 30.46 3.02
699 1302 8.820628 ATCACGATGAAATAACAATTTACACG 57.179 30.769 0.00 0.00 0.00 4.49
719 1323 8.835798 TGAACAGCTATTTCAATACGGATCACG 61.836 40.741 7.35 0.00 38.10 4.35
844 1448 4.958581 GGGTGAGATCAAGGATTCCAATTT 59.041 41.667 5.29 0.00 0.00 1.82
854 2268 5.927281 ATTTCAAATGGGTGAGATCAAGG 57.073 39.130 0.00 0.00 0.00 3.61
855 2269 7.093814 TGGTTATTTCAAATGGGTGAGATCAAG 60.094 37.037 0.00 0.00 0.00 3.02
861 2275 5.982890 ACTGGTTATTTCAAATGGGTGAG 57.017 39.130 0.00 0.00 0.00 3.51
899 2313 1.389106 GGACGTAACAATCTCGCACAC 59.611 52.381 0.00 0.00 0.00 3.82
912 2326 3.328505 GAAAGAAACCCGATGGACGTAA 58.671 45.455 0.00 0.00 40.78 3.18
913 2327 2.671914 CGAAAGAAACCCGATGGACGTA 60.672 50.000 0.00 0.00 40.78 3.57
915 2329 0.719465 CGAAAGAAACCCGATGGACG 59.281 55.000 0.00 0.00 42.18 4.79
916 2330 1.730612 GACGAAAGAAACCCGATGGAC 59.269 52.381 0.00 0.00 34.81 4.02
918 2332 1.084289 GGACGAAAGAAACCCGATGG 58.916 55.000 0.00 0.00 37.80 3.51
919 2333 1.463444 GTGGACGAAAGAAACCCGATG 59.537 52.381 0.00 0.00 0.00 3.84
920 2334 1.609841 GGTGGACGAAAGAAACCCGAT 60.610 52.381 0.00 0.00 0.00 4.18
921 2335 0.249996 GGTGGACGAAAGAAACCCGA 60.250 55.000 0.00 0.00 0.00 5.14
922 2336 0.250166 AGGTGGACGAAAGAAACCCG 60.250 55.000 0.00 0.00 33.81 5.28
923 2337 1.607148 CAAGGTGGACGAAAGAAACCC 59.393 52.381 0.00 0.00 33.81 4.11
924 2338 1.001706 GCAAGGTGGACGAAAGAAACC 60.002 52.381 0.00 0.00 0.00 3.27
925 2339 1.947456 AGCAAGGTGGACGAAAGAAAC 59.053 47.619 0.00 0.00 0.00 2.78
926 2340 2.218603 GAGCAAGGTGGACGAAAGAAA 58.781 47.619 0.00 0.00 0.00 2.52
927 2341 1.872237 CGAGCAAGGTGGACGAAAGAA 60.872 52.381 0.00 0.00 0.00 2.52
929 2343 0.319555 TCGAGCAAGGTGGACGAAAG 60.320 55.000 0.00 0.00 0.00 2.62
944 4924 1.559682 TGAAAGGGAAAGGGGATCGAG 59.440 52.381 0.00 0.00 0.00 4.04
958 4938 0.033228 TTGGGCGCATTGTTGAAAGG 59.967 50.000 10.83 0.00 0.00 3.11
959 4939 1.526464 GTTTGGGCGCATTGTTGAAAG 59.474 47.619 10.83 0.00 0.00 2.62
960 4940 1.576356 GTTTGGGCGCATTGTTGAAA 58.424 45.000 10.83 0.00 0.00 2.69
961 4941 0.249657 GGTTTGGGCGCATTGTTGAA 60.250 50.000 10.83 0.00 0.00 2.69
962 4942 1.365633 GGTTTGGGCGCATTGTTGA 59.634 52.632 10.83 0.00 0.00 3.18
963 4943 1.667510 GGGTTTGGGCGCATTGTTG 60.668 57.895 10.83 0.00 0.00 3.33
964 4944 2.136878 TGGGTTTGGGCGCATTGTT 61.137 52.632 10.83 0.00 0.00 2.83
965 4945 2.522923 TGGGTTTGGGCGCATTGT 60.523 55.556 10.83 0.00 0.00 2.71
966 4946 2.048316 GTGGGTTTGGGCGCATTG 60.048 61.111 10.83 0.00 33.93 2.82
967 4947 2.203625 AGTGGGTTTGGGCGCATT 60.204 55.556 10.83 0.00 33.93 3.56
968 4948 2.990967 CAGTGGGTTTGGGCGCAT 60.991 61.111 10.83 0.00 33.93 4.73
969 4949 3.723097 TTCAGTGGGTTTGGGCGCA 62.723 57.895 10.83 0.00 0.00 6.09
970 4950 2.022240 TTTTCAGTGGGTTTGGGCGC 62.022 55.000 0.00 0.00 0.00 6.53
971 4951 0.249280 GTTTTCAGTGGGTTTGGGCG 60.249 55.000 0.00 0.00 0.00 6.13
972 4952 0.827368 TGTTTTCAGTGGGTTTGGGC 59.173 50.000 0.00 0.00 0.00 5.36
973 4953 2.234908 TGTTGTTTTCAGTGGGTTTGGG 59.765 45.455 0.00 0.00 0.00 4.12
974 4954 3.258228 GTGTTGTTTTCAGTGGGTTTGG 58.742 45.455 0.00 0.00 0.00 3.28
975 4955 3.919216 TGTGTTGTTTTCAGTGGGTTTG 58.081 40.909 0.00 0.00 0.00 2.93
976 4956 3.829601 TCTGTGTTGTTTTCAGTGGGTTT 59.170 39.130 0.00 0.00 0.00 3.27
977 4957 3.426615 TCTGTGTTGTTTTCAGTGGGTT 58.573 40.909 0.00 0.00 0.00 4.11
984 4964 4.099266 CCCTCCATTTCTGTGTTGTTTTCA 59.901 41.667 0.00 0.00 0.00 2.69
989 4969 1.620822 GCCCTCCATTTCTGTGTTGT 58.379 50.000 0.00 0.00 0.00 3.32
1179 6119 4.785453 GGGTGGAGCTTGCGGGAG 62.785 72.222 0.00 0.00 0.00 4.30
1335 6281 1.103398 GGATCTGGACCAATTGGCCG 61.103 60.000 24.79 19.23 39.32 6.13
1340 6286 1.909302 AGTCGTGGATCTGGACCAATT 59.091 47.619 0.00 0.00 39.22 2.32
1341 6287 1.208052 CAGTCGTGGATCTGGACCAAT 59.792 52.381 0.00 0.00 39.22 3.16
1346 6292 2.710902 CGGCAGTCGTGGATCTGGA 61.711 63.158 0.00 0.00 32.94 3.86
1609 6775 0.252479 AGCCAGAGACCATCTTGCAG 59.748 55.000 4.09 0.00 46.68 4.41
1656 6822 1.385756 GGAGTAGTGGACGAGGGAGC 61.386 65.000 0.00 0.00 0.00 4.70
1699 6865 0.668535 GCCGGCATGTAAATTCTCCC 59.331 55.000 24.80 0.00 0.00 4.30
1700 6866 0.307760 CGCCGGCATGTAAATTCTCC 59.692 55.000 28.98 0.00 0.00 3.71
1701 6867 0.307760 CCGCCGGCATGTAAATTCTC 59.692 55.000 28.98 0.00 0.00 2.87
1747 6913 2.202676 GAAGCTCGAGGCCGTCAG 60.203 66.667 15.58 0.00 43.05 3.51
1761 6927 1.134670 GGGAGTTGGATCGTGGAGAAG 60.135 57.143 0.00 0.00 0.00 2.85
1833 7002 1.151777 AATACACGCCGGAAGCATCG 61.152 55.000 5.05 0.00 44.04 3.84
1874 7043 2.068821 TGGAGCCAGATGAGGAGCC 61.069 63.158 0.00 0.00 0.00 4.70
1935 7104 2.341257 CTCAAACCAGGACACATCTCG 58.659 52.381 0.00 0.00 0.00 4.04
1949 7118 1.960689 TGCAGCCTAAAACCCTCAAAC 59.039 47.619 0.00 0.00 0.00 2.93
1986 7155 3.306780 CCCGTCTTATGACAAGACCACTT 60.307 47.826 10.65 0.00 42.68 3.16
2016 7185 2.551032 CAAGAGCACAAACTCAGCATCA 59.449 45.455 0.00 0.00 39.26 3.07
2082 7251 0.931005 GCTCATACACCTTACGCAGC 59.069 55.000 0.00 0.00 0.00 5.25
2197 7531 0.897863 TGATCCAAAGGCCAAACGGG 60.898 55.000 5.01 0.00 40.85 5.28
2200 7534 2.827921 ACAGATGATCCAAAGGCCAAAC 59.172 45.455 5.01 0.00 0.00 2.93
2302 7679 8.043710 GTCCCAAGGAATCAATCATATACCTAG 58.956 40.741 0.00 0.00 31.38 3.02
2324 7701 5.869649 AGGCAATATGGTTAAAATGTCCC 57.130 39.130 0.00 0.00 0.00 4.46
2473 7871 4.612264 AAAAAGCCAATCAAGCACTCAT 57.388 36.364 0.00 0.00 0.00 2.90
2495 7893 5.614308 TCAAGCACTCATCTCTCTCAAAAA 58.386 37.500 0.00 0.00 0.00 1.94
2496 7894 5.219343 TCAAGCACTCATCTCTCTCAAAA 57.781 39.130 0.00 0.00 0.00 2.44
2497 7895 4.879197 TCAAGCACTCATCTCTCTCAAA 57.121 40.909 0.00 0.00 0.00 2.69
2498 7896 5.176592 CAATCAAGCACTCATCTCTCTCAA 58.823 41.667 0.00 0.00 0.00 3.02
2499 7897 4.382793 CCAATCAAGCACTCATCTCTCTCA 60.383 45.833 0.00 0.00 0.00 3.27
2500 7898 4.121317 CCAATCAAGCACTCATCTCTCTC 58.879 47.826 0.00 0.00 0.00 3.20
2501 7899 3.682155 GCCAATCAAGCACTCATCTCTCT 60.682 47.826 0.00 0.00 0.00 3.10
2502 7900 2.613133 GCCAATCAAGCACTCATCTCTC 59.387 50.000 0.00 0.00 0.00 3.20
2503 7901 2.239150 AGCCAATCAAGCACTCATCTCT 59.761 45.455 0.00 0.00 0.00 3.10
2504 7902 2.641305 AGCCAATCAAGCACTCATCTC 58.359 47.619 0.00 0.00 0.00 2.75
2505 7903 2.803030 AGCCAATCAAGCACTCATCT 57.197 45.000 0.00 0.00 0.00 2.90
2506 7904 3.539604 ACTAGCCAATCAAGCACTCATC 58.460 45.455 0.00 0.00 0.00 2.92
2507 7905 3.641434 ACTAGCCAATCAAGCACTCAT 57.359 42.857 0.00 0.00 0.00 2.90
2508 7906 3.076621 CAACTAGCCAATCAAGCACTCA 58.923 45.455 0.00 0.00 0.00 3.41
2509 7907 3.338249 TCAACTAGCCAATCAAGCACTC 58.662 45.455 0.00 0.00 0.00 3.51
2510 7908 3.008375 TCTCAACTAGCCAATCAAGCACT 59.992 43.478 0.00 0.00 0.00 4.40
2587 7986 5.365403 TTTAGCAACCAAGAAATACACCG 57.635 39.130 0.00 0.00 0.00 4.94
2624 8023 9.573133 CCATCATGTTTGTCTATTTAAAAGGAC 57.427 33.333 13.55 13.55 0.00 3.85
2848 8251 9.668497 AGTATATGTCTAGCAATCGACACTATA 57.332 33.333 0.00 0.00 42.32 1.31
2910 8329 6.359617 CACAAGCGTTAGAAAAGTAACCATTG 59.640 38.462 0.00 0.00 34.28 2.82
3181 8689 6.765915 AAGAAATTTAGAATCCTCTGTGCC 57.234 37.500 0.00 0.00 32.70 5.01
3204 8729 7.512130 ACATCTGACTCAGGAAATTATGCATA 58.488 34.615 1.16 1.16 31.51 3.14
3205 8730 6.363065 ACATCTGACTCAGGAAATTATGCAT 58.637 36.000 3.79 3.79 31.51 3.96
3206 8731 5.748402 ACATCTGACTCAGGAAATTATGCA 58.252 37.500 6.20 0.00 31.51 3.96
3207 8732 7.976135 ATACATCTGACTCAGGAAATTATGC 57.024 36.000 6.20 0.00 31.51 3.14
3211 8736 8.543774 ACTGTAATACATCTGACTCAGGAAATT 58.456 33.333 6.20 4.70 31.51 1.82
3212 8737 7.984050 CACTGTAATACATCTGACTCAGGAAAT 59.016 37.037 6.20 0.00 31.51 2.17
3213 8738 7.178451 TCACTGTAATACATCTGACTCAGGAAA 59.822 37.037 6.20 0.00 31.51 3.13
3214 8739 6.663523 TCACTGTAATACATCTGACTCAGGAA 59.336 38.462 6.20 0.00 31.51 3.36
3215 8740 6.187682 TCACTGTAATACATCTGACTCAGGA 58.812 40.000 6.20 0.00 31.51 3.86
3216 8741 6.456795 TCACTGTAATACATCTGACTCAGG 57.543 41.667 6.20 0.00 31.51 3.86
3291 8816 7.167535 TGATCATAGAAGGACAAATGACACAA 58.832 34.615 0.00 0.00 31.56 3.33
3320 8845 6.876257 TGCAGTCCAGTAAAACAAAAACAAAT 59.124 30.769 0.00 0.00 0.00 2.32
3364 8889 2.157738 GCTTCATATCCCAGACATGCC 58.842 52.381 0.00 0.00 0.00 4.40
3400 8925 9.968870 ACAAGTAGCTAGTACAAGAATAATAGC 57.031 33.333 0.35 4.52 45.01 2.97
3409 8934 6.924060 ACACAAAGACAAGTAGCTAGTACAAG 59.076 38.462 0.35 0.00 33.55 3.16
3461 8986 2.191128 ACAAAGGTCAGCATGGAGAC 57.809 50.000 0.00 0.00 36.16 3.36
3576 9105 1.153549 GCCCACTACTGCTCTTCCG 60.154 63.158 0.00 0.00 0.00 4.30
3792 9321 3.141398 CACAAGACTTACACACAGGCAT 58.859 45.455 0.00 0.00 0.00 4.40
3796 9325 3.245284 CGAACCACAAGACTTACACACAG 59.755 47.826 0.00 0.00 0.00 3.66
3822 9351 4.794003 GCCATGCATAACAAACATCCTAGC 60.794 45.833 0.00 0.00 0.00 3.42
3838 9367 1.546923 CACTTCTCCAAATGCCATGCA 59.453 47.619 0.00 0.00 44.86 3.96
3839 9368 1.547372 ACACTTCTCCAAATGCCATGC 59.453 47.619 0.00 0.00 0.00 4.06
3970 9499 4.229304 TCATCCATTTACCGTCCATTGT 57.771 40.909 0.00 0.00 0.00 2.71
3971 9500 4.397730 TGTTCATCCATTTACCGTCCATTG 59.602 41.667 0.00 0.00 0.00 2.82
4048 9585 0.325765 GGCCTCCCCTACTCTGAACT 60.326 60.000 0.00 0.00 0.00 3.01
4317 9859 9.409918 TCAATCTGCTACCACTACTATATATCC 57.590 37.037 0.00 0.00 0.00 2.59
4386 9928 3.967467 AGGAACGGAGGGAGTAGATAA 57.033 47.619 0.00 0.00 0.00 1.75
4387 9929 5.393068 TTTAGGAACGGAGGGAGTAGATA 57.607 43.478 0.00 0.00 0.00 1.98
4388 9930 3.967467 TTAGGAACGGAGGGAGTAGAT 57.033 47.619 0.00 0.00 0.00 1.98
4389 9931 3.744940 TTTAGGAACGGAGGGAGTAGA 57.255 47.619 0.00 0.00 0.00 2.59
4390 9932 6.667558 AATATTTAGGAACGGAGGGAGTAG 57.332 41.667 0.00 0.00 0.00 2.57
4391 9933 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
4392 9934 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
4393 9935 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4394 9936 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
4395 9937 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
4396 9938 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
4397 9939 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
4398 9940 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
4399 9941 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
4412 9954 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
4413 9955 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
4414 9956 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
4415 9957 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
4416 9958 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
4417 9959 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
4418 9960 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
4419 9961 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
4420 9962 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
4421 9963 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
4422 9964 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
4423 9965 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
4424 9966 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
4425 9967 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
4426 9968 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
4427 9969 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
4428 9970 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
4429 9971 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
4430 9972 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
4431 9973 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
4432 9974 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
4433 9975 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
4434 9976 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
4435 9977 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
4436 9978 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
4437 9979 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
4438 9980 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
4439 9981 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
4440 9982 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
4441 9983 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
4442 9984 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
4443 9985 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
4444 9986 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
4445 9987 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
4446 9988 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
4447 9989 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
4448 9990 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
4449 9991 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
4450 9992 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
4479 10021 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
4481 10023 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
4482 10024 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
4483 10025 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
4484 10026 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
4485 10027 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
4486 10028 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
4487 10029 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
4488 10030 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
4489 10031 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
4490 10032 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29


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

AutoCloner maintained by Alex Coulton.