Multiple sequence alignment - TraesCS4A01G389800

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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 TraesCS4A01G389800 chr4A 100.000 3214 0 0 1 3214 667061511 667064724 0.000000e+00 5936.0
1 TraesCS4A01G389800 chr4A 87.796 1057 102 12 2073 3125 667003651 667004684 0.000000e+00 1212.0
2 TraesCS4A01G389800 chr4A 90.311 547 49 3 285 827 667092602 667093148 0.000000e+00 713.0
3 TraesCS4A01G389800 chr4A 85.630 341 48 1 2875 3214 667193517 667193177 1.100000e-94 357.0
4 TraesCS4A01G389800 chr4A 84.196 367 54 3 2850 3214 667002403 667002767 1.420000e-93 353.0
5 TraesCS4A01G389800 chr4A 80.909 330 52 9 2891 3214 667185885 667185561 1.910000e-62 250.0
6 TraesCS4A01G389800 chr4A 92.562 121 9 0 1 121 667107877 667107757 1.190000e-39 174.0
7 TraesCS4A01G389800 chr4A 78.065 310 39 14 1359 1643 667346005 667346310 5.510000e-38 169.0
8 TraesCS4A01G389800 chr4A 91.589 107 9 0 1379 1485 667105088 667104982 7.180000e-32 148.0
9 TraesCS4A01G389800 chr4A 83.230 161 19 5 1359 1512 667330919 667331078 1.200000e-29 141.0
10 TraesCS4A01G389800 chr4A 81.098 164 23 5 1010 1167 667345335 667345496 1.210000e-24 124.0
11 TraesCS4A01G389800 chr7D 89.407 944 80 6 2289 3214 52522938 52523879 0.000000e+00 1171.0
12 TraesCS4A01G389800 chr7D 86.946 835 80 13 1 827 52408831 52409644 0.000000e+00 911.0
13 TraesCS4A01G389800 chr7D 85.030 501 65 7 336 827 52512609 52513108 4.790000e-138 501.0
14 TraesCS4A01G389800 chr7D 90.411 365 34 1 2851 3214 53331519 53331155 2.240000e-131 479.0
15 TraesCS4A01G389800 chr7D 81.260 603 42 35 1033 1608 52258148 52258706 3.830000e-114 422.0
16 TraesCS4A01G389800 chr7D 86.416 346 45 2 2505 2849 53333031 53332687 8.420000e-101 377.0
17 TraesCS4A01G389800 chr7D 81.760 466 51 24 1837 2294 52520089 52520528 3.050000e-95 359.0
18 TraesCS4A01G389800 chr7D 86.127 346 29 10 1241 1582 53333397 53333067 3.940000e-94 355.0
19 TraesCS4A01G389800 chr7D 84.337 332 31 11 1171 1487 52513581 52513906 4.030000e-79 305.0
20 TraesCS4A01G389800 chr7D 88.073 218 24 2 2501 2717 52258722 52258938 1.140000e-64 257.0
21 TraesCS4A01G389800 chr7D 82.456 285 44 4 2935 3214 52528559 52528842 8.910000e-61 244.0
22 TraesCS4A01G389800 chr7D 81.013 316 36 12 1359 1656 53268785 53268476 2.490000e-56 230.0
23 TraesCS4A01G389800 chr7D 88.950 181 5 5 1033 1205 53333942 53333769 3.250000e-50 209.0
24 TraesCS4A01G389800 chr7D 98.889 90 0 1 821 910 52422669 52422757 3.320000e-35 159.0
25 TraesCS4A01G389800 chr7D 84.615 169 10 7 1013 1175 52513293 52513451 1.540000e-33 154.0
26 TraesCS4A01G389800 chr7D 85.484 124 15 2 1044 1166 53374415 53374294 3.370000e-25 126.0
27 TraesCS4A01G389800 chr7D 80.137 146 19 6 958 1098 53269705 53269565 2.040000e-17 100.0
28 TraesCS4A01G389800 chr7D 93.617 47 3 0 1067 1113 52453210 52453256 1.600000e-08 71.3
29 TraesCS4A01G389800 chr7D 97.500 40 1 0 1131 1170 53374287 53374248 5.750000e-08 69.4
30 TraesCS4A01G389800 chr7A 89.676 833 83 3 1 831 54923499 54924330 0.000000e+00 1059.0
31 TraesCS4A01G389800 chr7A 84.809 994 106 33 1524 2507 54898337 54899295 0.000000e+00 957.0
32 TraesCS4A01G389800 chr7A 83.206 786 80 24 1976 2730 54925793 54926557 0.000000e+00 673.0
33 TraesCS4A01G389800 chr7A 88.854 323 31 4 361 679 54896928 54897249 3.010000e-105 392.0
34 TraesCS4A01G389800 chr7A 85.965 342 40 5 2846 3180 54927760 54928100 3.050000e-95 359.0
35 TraesCS4A01G389800 chr7A 86.136 339 29 13 1241 1576 54938369 54938692 1.830000e-92 350.0
36 TraesCS4A01G389800 chr7A 84.971 346 43 6 2502 2843 54938731 54939071 3.070000e-90 342.0
37 TraesCS4A01G389800 chr7A 88.889 270 19 5 907 1175 54924505 54924764 4.000000e-84 322.0
38 TraesCS4A01G389800 chr7A 83.533 334 50 5 2882 3212 54987262 54987593 1.120000e-79 307.0
39 TraesCS4A01G389800 chr7A 92.708 96 7 0 1359 1454 54943462 54943367 4.320000e-29 139.0
40 TraesCS4A01G389800 chr7A 91.667 96 8 0 1359 1454 54962230 54962135 2.010000e-27 134.0
41 TraesCS4A01G389800 chr7A 79.290 169 20 12 1013 1177 54963231 54963074 1.580000e-18 104.0
42 TraesCS4A01G389800 chr5D 79.924 264 46 7 2475 2735 385964206 385963947 1.520000e-43 187.0
43 TraesCS4A01G389800 chr6D 78.922 204 30 10 2515 2714 392509687 392509881 3.370000e-25 126.0


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 TraesCS4A01G389800 chr4A 667061511 667064724 3213 False 5936.00 5936 100.000000 1 3214 1 chr4A.!!$F1 3213
1 TraesCS4A01G389800 chr4A 667002403 667004684 2281 False 782.50 1212 85.996000 2073 3214 2 chr4A.!!$F4 1141
2 TraesCS4A01G389800 chr4A 667092602 667093148 546 False 713.00 713 90.311000 285 827 1 chr4A.!!$F2 542
3 TraesCS4A01G389800 chr7D 52408831 52409644 813 False 911.00 911 86.946000 1 827 1 chr7D.!!$F1 826
4 TraesCS4A01G389800 chr7D 52520089 52523879 3790 False 765.00 1171 85.583500 1837 3214 2 chr7D.!!$F7 1377
5 TraesCS4A01G389800 chr7D 53331155 53333942 2787 True 355.00 479 87.976000 1033 3214 4 chr7D.!!$R2 2181
6 TraesCS4A01G389800 chr7D 52258148 52258938 790 False 339.50 422 84.666500 1033 2717 2 chr7D.!!$F5 1684
7 TraesCS4A01G389800 chr7D 52512609 52513906 1297 False 320.00 501 84.660667 336 1487 3 chr7D.!!$F6 1151
8 TraesCS4A01G389800 chr7A 54896928 54899295 2367 False 674.50 957 86.831500 361 2507 2 chr7A.!!$F2 2146
9 TraesCS4A01G389800 chr7A 54923499 54928100 4601 False 603.25 1059 86.934000 1 3180 4 chr7A.!!$F3 3179
10 TraesCS4A01G389800 chr7A 54938369 54939071 702 False 346.00 350 85.553500 1241 2843 2 chr7A.!!$F4 1602

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
390 396 0.171903 ACGGGTTATTCCACGACTCG 59.828 55.0 0.00 0.00 42.65 4.18 F
1544 2765 0.038251 TCTCTCGTGTCCATGTGCAC 60.038 55.0 10.75 10.75 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 3597 0.039074 GTCGTCTGTCTGTCCAGTGG 60.039 60.0 1.40 1.40 34.02 4.00 R
2702 6887 0.116940 AGACATTGTTGGGCCCCAAT 59.883 50.0 20.32 19.62 45.80 3.16 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
43 45 4.526650 TCTCTATTGTAATCGGGCTATGCA 59.473 41.667 0.00 0.00 0.00 3.96
59 61 1.226295 GCATAAGCCGCCGTGTTTC 60.226 57.895 0.00 0.00 33.58 2.78
106 108 7.508977 ACTTTCCCTTTTGATTTGGAGTGAATA 59.491 33.333 0.00 0.00 0.00 1.75
113 115 4.803452 TGATTTGGAGTGAATATTCCCCC 58.197 43.478 12.90 10.97 31.98 5.40
167 170 4.844085 TCTTTCTCTAGAAACCACCATCCA 59.156 41.667 1.00 0.00 38.94 3.41
184 187 7.122948 CCACCATCCATACTAGTTAGATCCTAC 59.877 44.444 0.00 0.00 0.00 3.18
214 217 3.083997 GGCCTCCATGAGTCCCGT 61.084 66.667 0.00 0.00 0.00 5.28
230 233 1.293179 CGTGACCTGCACCTCATCA 59.707 57.895 0.00 0.00 44.85 3.07
233 236 0.543277 TGACCTGCACCTCATCATCC 59.457 55.000 0.00 0.00 0.00 3.51
280 283 1.519455 CCGCGGAAGATGTGGTCTC 60.519 63.158 24.07 0.00 35.67 3.36
326 329 0.320771 AGTACAGCTCCAACTTGGCG 60.321 55.000 2.52 0.00 37.47 5.69
354 357 1.999648 TTGTGGCTTCAAGCAGGAAT 58.000 45.000 12.53 0.00 44.75 3.01
357 360 2.305635 TGTGGCTTCAAGCAGGAATCTA 59.694 45.455 12.53 0.00 44.75 1.98
390 396 0.171903 ACGGGTTATTCCACGACTCG 59.828 55.000 0.00 0.00 42.65 4.18
405 411 2.798283 CGACTCGAGAGCTCTAGGTTAG 59.202 54.545 21.68 12.44 0.00 2.34
573 580 9.046296 CCAACTTCTTGAATATACATAGGTGAC 57.954 37.037 0.00 0.00 0.00 3.67
622 631 5.278071 CGCGATCTAAGAGACTTGGAATACT 60.278 44.000 0.00 0.00 0.00 2.12
827 902 7.198390 CCTCACATGCCTTTAATACAATTCTG 58.802 38.462 0.00 0.00 0.00 3.02
831 906 3.181491 TGCCTTTAATACAATTCTGCGCC 60.181 43.478 4.18 0.00 0.00 6.53
833 908 4.789802 GCCTTTAATACAATTCTGCGCCTC 60.790 45.833 4.18 0.00 0.00 4.70
836 1434 1.959042 ATACAATTCTGCGCCTCTGG 58.041 50.000 4.18 0.00 0.00 3.86
851 1449 1.410517 CTCTGGATGCTGTCACCGTAT 59.589 52.381 0.00 0.00 0.00 3.06
857 1455 3.308866 GGATGCTGTCACCGTATTTACAC 59.691 47.826 0.00 0.00 0.00 2.90
861 1459 3.120786 GCTGTCACCGTATTTACACACAC 60.121 47.826 0.00 0.00 0.00 3.82
863 1461 4.439968 TGTCACCGTATTTACACACACAA 58.560 39.130 0.00 0.00 0.00 3.33
865 1463 4.508861 GTCACCGTATTTACACACACAAGT 59.491 41.667 0.00 0.00 0.00 3.16
868 1466 6.421501 TCACCGTATTTACACACACAAGTTAG 59.578 38.462 0.00 0.00 0.00 2.34
869 1467 5.697633 ACCGTATTTACACACACAAGTTAGG 59.302 40.000 0.00 0.00 0.00 2.69
873 1471 7.544566 CGTATTTACACACACAAGTTAGGAGAT 59.455 37.037 0.00 0.00 0.00 2.75
877 1475 6.859112 ACACACACAAGTTAGGAGATATCT 57.141 37.500 4.47 4.47 0.00 1.98
882 1480 7.982354 ACACACAAGTTAGGAGATATCTAAAGC 59.018 37.037 4.89 0.00 0.00 3.51
888 1486 7.242359 AGTTAGGAGATATCTAAAGCTAGCCA 58.758 38.462 12.13 0.00 0.00 4.75
889 1487 7.730784 AGTTAGGAGATATCTAAAGCTAGCCAA 59.269 37.037 12.13 0.00 0.00 4.52
894 1492 7.003402 AGATATCTAAAGCTAGCCAAAGAGG 57.997 40.000 12.13 0.00 41.84 3.69
896 1494 4.473477 TCTAAAGCTAGCCAAAGAGGAC 57.527 45.455 12.13 0.00 41.22 3.85
898 1496 3.508845 AAAGCTAGCCAAAGAGGACAA 57.491 42.857 12.13 0.00 41.22 3.18
905 1503 3.749226 AGCCAAAGAGGACAAAAGAGAG 58.251 45.455 0.00 0.00 41.22 3.20
906 1504 2.816672 GCCAAAGAGGACAAAAGAGAGG 59.183 50.000 0.00 0.00 41.22 3.69
907 1505 3.496870 GCCAAAGAGGACAAAAGAGAGGA 60.497 47.826 0.00 0.00 41.22 3.71
908 1506 4.718961 CCAAAGAGGACAAAAGAGAGGAA 58.281 43.478 0.00 0.00 41.22 3.36
929 1527 6.070538 AGGAACAAGATATACAAGCACTGAGT 60.071 38.462 0.00 0.00 0.00 3.41
930 1528 6.595716 GGAACAAGATATACAAGCACTGAGTT 59.404 38.462 0.00 0.00 0.00 3.01
944 1542 4.051922 CACTGAGTTCGTAGCTCACTTTT 58.948 43.478 0.00 0.00 37.98 2.27
1000 1598 7.987458 TGGAGGCTAATTAGTCTTGTAATCTTG 59.013 37.037 20.23 0.00 38.61 3.02
1007 1605 8.480643 AATTAGTCTTGTAATCTTGTTCCTCG 57.519 34.615 0.00 0.00 0.00 4.63
1018 1616 0.389296 TGTTCCTCGCCATACACACG 60.389 55.000 0.00 0.00 0.00 4.49
1031 1629 4.275689 CCATACACACGCATAATGGTCATT 59.724 41.667 1.65 1.65 33.81 2.57
1106 1710 5.594725 TCAGAACAGAACACTCAACTAGACT 59.405 40.000 0.00 0.00 0.00 3.24
1116 1720 5.654650 ACACTCAACTAGACTAGGAATCCTG 59.345 44.000 12.96 4.65 34.61 3.86
1118 1722 5.889289 ACTCAACTAGACTAGGAATCCTGTC 59.111 44.000 12.96 16.20 34.61 3.51
1119 1723 5.202004 TCAACTAGACTAGGAATCCTGTCC 58.798 45.833 20.48 7.93 34.55 4.02
1120 1724 4.187506 ACTAGACTAGGAATCCTGTCCC 57.812 50.000 20.48 6.51 38.59 4.46
1121 1725 3.794971 ACTAGACTAGGAATCCTGTCCCT 59.205 47.826 20.48 11.95 38.59 4.20
1122 1726 3.039252 AGACTAGGAATCCTGTCCCTG 57.961 52.381 20.48 5.81 38.59 4.45
1123 1727 2.316372 AGACTAGGAATCCTGTCCCTGT 59.684 50.000 20.48 8.24 38.59 4.00
1124 1728 2.432510 GACTAGGAATCCTGTCCCTGTG 59.567 54.545 12.96 0.00 38.59 3.66
1125 1729 2.225650 ACTAGGAATCCTGTCCCTGTGT 60.226 50.000 12.96 0.00 38.59 3.72
1126 1730 2.642171 AGGAATCCTGTCCCTGTGTA 57.358 50.000 0.00 0.00 38.59 2.90
1127 1731 2.188817 AGGAATCCTGTCCCTGTGTAC 58.811 52.381 0.00 0.00 38.59 2.90
1128 1732 1.906574 GGAATCCTGTCCCTGTGTACA 59.093 52.381 0.00 0.00 0.00 2.90
1129 1733 2.354805 GGAATCCTGTCCCTGTGTACAC 60.355 54.545 19.36 19.36 0.00 2.90
1130 1734 2.024176 ATCCTGTCCCTGTGTACACA 57.976 50.000 26.37 26.37 39.32 3.72
1131 1735 1.796017 TCCTGTCCCTGTGTACACAA 58.204 50.000 27.66 12.21 41.33 3.33
1132 1736 2.120312 TCCTGTCCCTGTGTACACAAA 58.880 47.619 27.66 14.43 41.33 2.83
1133 1737 2.104111 TCCTGTCCCTGTGTACACAAAG 59.896 50.000 27.66 21.07 41.33 2.77
1176 1793 3.031013 ACCACCCAGAGAAAAACAAAGG 58.969 45.455 0.00 0.00 0.00 3.11
1219 2327 8.635765 TCTTTTCTCAGCCTATAAAACAACAT 57.364 30.769 0.00 0.00 0.00 2.71
1220 2328 8.730680 TCTTTTCTCAGCCTATAAAACAACATC 58.269 33.333 0.00 0.00 0.00 3.06
1221 2329 7.391148 TTTCTCAGCCTATAAAACAACATCC 57.609 36.000 0.00 0.00 0.00 3.51
1225 2333 3.053917 AGCCTATAAAACAACATCCCCGT 60.054 43.478 0.00 0.00 0.00 5.28
1226 2334 3.314357 GCCTATAAAACAACATCCCCGTC 59.686 47.826 0.00 0.00 0.00 4.79
1230 2338 2.185004 AAACAACATCCCCGTCTCTG 57.815 50.000 0.00 0.00 0.00 3.35
1255 2363 1.175983 TGTTCCAATCCCACAACGCC 61.176 55.000 0.00 0.00 0.00 5.68
1256 2364 1.969064 TTCCAATCCCACAACGCCG 60.969 57.895 0.00 0.00 0.00 6.46
1257 2365 2.359354 CCAATCCCACAACGCCGA 60.359 61.111 0.00 0.00 0.00 5.54
1258 2366 2.398554 CCAATCCCACAACGCCGAG 61.399 63.158 0.00 0.00 0.00 4.63
1260 2368 0.953471 CAATCCCACAACGCCGAGAA 60.953 55.000 0.00 0.00 0.00 2.87
1261 2369 0.250553 AATCCCACAACGCCGAGAAA 60.251 50.000 0.00 0.00 0.00 2.52
1262 2370 0.250553 ATCCCACAACGCCGAGAAAA 60.251 50.000 0.00 0.00 0.00 2.29
1266 2374 0.512952 CACAACGCCGAGAAAAGAGG 59.487 55.000 0.00 0.00 0.00 3.69
1299 2412 5.733373 GCAGAGCGGAAAAGAAAGAAAGAAA 60.733 40.000 0.00 0.00 0.00 2.52
1328 2449 6.403878 TGCTAGTTGTTCTTCCATAGTAACC 58.596 40.000 0.00 0.00 0.00 2.85
1330 2451 5.836024 AGTTGTTCTTCCATAGTAACCCA 57.164 39.130 0.00 0.00 0.00 4.51
1331 2452 5.557866 AGTTGTTCTTCCATAGTAACCCAC 58.442 41.667 0.00 0.00 0.00 4.61
1334 2455 3.502051 TCTTCCATAGTAACCCACCCT 57.498 47.619 0.00 0.00 0.00 4.34
1337 2458 5.352264 TCTTCCATAGTAACCCACCCTTTA 58.648 41.667 0.00 0.00 0.00 1.85
1338 2459 5.190330 TCTTCCATAGTAACCCACCCTTTAC 59.810 44.000 0.00 0.00 0.00 2.01
1339 2460 4.437023 TCCATAGTAACCCACCCTTTACA 58.563 43.478 0.00 0.00 31.66 2.41
1340 2461 4.850963 TCCATAGTAACCCACCCTTTACAA 59.149 41.667 0.00 0.00 31.66 2.41
1341 2462 5.312708 TCCATAGTAACCCACCCTTTACAAA 59.687 40.000 0.00 0.00 31.66 2.83
1342 2463 5.416639 CCATAGTAACCCACCCTTTACAAAC 59.583 44.000 0.00 0.00 31.66 2.93
1343 2464 4.523168 AGTAACCCACCCTTTACAAACA 57.477 40.909 0.00 0.00 31.66 2.83
1344 2465 4.869451 AGTAACCCACCCTTTACAAACAA 58.131 39.130 0.00 0.00 31.66 2.83
1488 2629 3.947841 CGCTCGCTCTCCCTCTCG 61.948 72.222 0.00 0.00 0.00 4.04
1498 2639 0.391793 CTCCCTCTCGCTGGGTTTTC 60.392 60.000 7.01 0.00 44.84 2.29
1506 2647 1.301677 CGCTGGGTTTTCCTCTGCTC 61.302 60.000 0.00 0.00 40.46 4.26
1507 2648 0.250901 GCTGGGTTTTCCTCTGCTCA 60.251 55.000 0.00 0.00 40.46 4.26
1540 2761 4.116747 GAGAAATCTCTCGTGTCCATGT 57.883 45.455 3.16 0.00 38.91 3.21
1542 2763 2.015736 AATCTCTCGTGTCCATGTGC 57.984 50.000 0.00 0.00 0.00 4.57
1543 2764 0.897621 ATCTCTCGTGTCCATGTGCA 59.102 50.000 0.00 0.00 0.00 4.57
1544 2765 0.038251 TCTCTCGTGTCCATGTGCAC 60.038 55.000 10.75 10.75 0.00 4.57
1547 2768 2.281414 CGTGTCCATGTGCACCCA 60.281 61.111 15.69 0.00 32.40 4.51
1585 3295 5.364778 CGAGAGAGAGATAAGACTCTTCCA 58.635 45.833 0.00 0.00 45.69 3.53
1592 3302 5.598005 AGAGATAAGACTCTTCCACCATCTG 59.402 44.000 5.95 0.00 43.62 2.90
1596 3306 5.511386 AAGACTCTTCCACCATCTGAAAT 57.489 39.130 0.00 0.00 0.00 2.17
1608 3318 6.000219 CACCATCTGAAATATCCTCGGAAAT 59.000 40.000 1.50 0.00 32.04 2.17
1612 3322 8.043113 CCATCTGAAATATCCTCGGAAATATCA 58.957 37.037 1.50 0.00 32.04 2.15
1624 3334 7.063593 CCTCGGAAATATCATAGAGATAGGGA 58.936 42.308 0.00 0.00 42.26 4.20
1668 3378 5.250543 TCTTCCCCTAGTTCATGTCAATTCA 59.749 40.000 0.00 0.00 0.00 2.57
1671 3381 5.887598 TCCCCTAGTTCATGTCAATTCATTG 59.112 40.000 0.00 0.00 39.10 2.82
1672 3382 5.450965 CCCCTAGTTCATGTCAATTCATTGC 60.451 44.000 0.00 0.00 37.68 3.56
1679 3390 5.771469 TCATGTCAATTCATTGCGTTCTTT 58.229 33.333 0.00 0.00 37.68 2.52
1681 3392 6.363088 TCATGTCAATTCATTGCGTTCTTTTC 59.637 34.615 0.00 0.00 37.68 2.29
1686 3397 2.898746 TCATTGCGTTCTTTTCGTTCG 58.101 42.857 0.00 0.00 0.00 3.95
1705 3416 9.550406 TTCGTTCGTCCCTTCATAATATTATTT 57.450 29.630 5.18 0.00 0.00 1.40
1727 3438 4.703897 TGTTCTTCCGTTTCTGATTCTGT 58.296 39.130 0.00 0.00 0.00 3.41
1729 3440 5.588648 TGTTCTTCCGTTTCTGATTCTGTTT 59.411 36.000 0.00 0.00 0.00 2.83
1740 3451 6.672266 TCTGATTCTGTTTCTCTACCAAGT 57.328 37.500 0.00 0.00 0.00 3.16
1748 3459 6.431543 TCTGTTTCTCTACCAAGTAGTCTCTG 59.568 42.308 1.94 0.00 37.41 3.35
1777 3488 4.826733 TGTGTGTGATTGACTGGCTATTTT 59.173 37.500 0.00 0.00 0.00 1.82
1794 3505 0.743688 TTTGGTTGCAGCGTGTTCAT 59.256 45.000 0.00 0.00 0.00 2.57
1796 3507 1.081242 GGTTGCAGCGTGTTCATGG 60.081 57.895 0.00 0.00 0.00 3.66
1822 3533 2.663358 CTGCTTCTGCTGCTACGAG 58.337 57.895 0.00 0.00 40.48 4.18
1861 3572 3.903616 CTGCCTCTGCTGCTGCTGT 62.904 63.158 17.00 0.00 40.48 4.40
1870 3581 3.070018 CTGCTGCTGCTGTAACTAAACT 58.930 45.455 17.00 0.00 40.48 2.66
1882 3597 0.463833 ACTAAACTAGCCATGGCCGC 60.464 55.000 33.14 8.89 43.17 6.53
1885 3600 3.995506 AACTAGCCATGGCCGCCAC 62.996 63.158 33.14 4.73 43.17 5.01
1901 3617 0.039074 CCACTGGACAGACAGACGAC 60.039 60.000 6.29 0.00 40.97 4.34
1905 3621 0.608308 TGGACAGACAGACGACGGAT 60.608 55.000 0.00 0.00 0.00 4.18
1931 3647 4.530857 GCCGAGATCCACCACCGG 62.531 72.222 0.00 0.00 42.74 5.28
1933 3649 4.530857 CGAGATCCACCACCGGCC 62.531 72.222 0.00 0.00 0.00 6.13
1936 3652 3.083997 GATCCACCACCGGCCTCT 61.084 66.667 0.00 0.00 0.00 3.69
1937 3653 2.610859 ATCCACCACCGGCCTCTT 60.611 61.111 0.00 0.00 0.00 2.85
1938 3654 2.595009 GATCCACCACCGGCCTCTTC 62.595 65.000 0.00 0.00 0.00 2.87
1954 3670 4.882427 GCCTCTTCTGTCTTTAATTACCCC 59.118 45.833 0.00 0.00 0.00 4.95
1967 3683 7.449086 TCTTTAATTACCCCGACAGTTTTTGAT 59.551 33.333 0.00 0.00 0.00 2.57
2010 3726 4.156922 TGTGTCTAGCTCTCAACTTAGCTC 59.843 45.833 0.00 0.00 45.92 4.09
2015 3731 3.020274 AGCTCTCAACTTAGCTCGATGA 58.980 45.455 0.00 0.00 45.92 2.92
2017 3733 3.181491 GCTCTCAACTTAGCTCGATGAGT 60.181 47.826 17.15 0.00 38.83 3.41
2026 3742 2.736978 AGCTCGATGAGTGCTTTATCG 58.263 47.619 8.81 8.81 46.35 2.92
2027 3743 2.359214 AGCTCGATGAGTGCTTTATCGA 59.641 45.455 14.42 14.42 46.35 3.59
2032 3748 6.934561 TCGATGAGTGCTTTATCGATATTG 57.065 37.500 5.84 3.58 45.22 1.90
2033 3749 5.346011 TCGATGAGTGCTTTATCGATATTGC 59.654 40.000 17.79 17.79 45.22 3.56
2034 3750 5.119125 CGATGAGTGCTTTATCGATATTGCA 59.881 40.000 21.30 21.30 44.64 4.08
2035 3751 6.346838 CGATGAGTGCTTTATCGATATTGCAA 60.347 38.462 24.62 0.00 44.64 4.08
2036 3752 6.866010 TGAGTGCTTTATCGATATTGCAAT 57.134 33.333 24.62 23.98 32.10 3.56
2037 3753 7.961325 TGAGTGCTTTATCGATATTGCAATA 57.039 32.000 24.62 20.95 32.10 1.90
2038 3754 8.021955 TGAGTGCTTTATCGATATTGCAATAG 57.978 34.615 24.62 11.55 32.10 1.73
2039 3755 7.657354 TGAGTGCTTTATCGATATTGCAATAGT 59.343 33.333 24.62 12.01 32.10 2.12
2040 3756 9.140286 GAGTGCTTTATCGATATTGCAATAGTA 57.860 33.333 24.62 11.84 32.10 1.82
2041 3757 9.144747 AGTGCTTTATCGATATTGCAATAGTAG 57.855 33.333 24.62 15.99 32.10 2.57
2053 3769 9.838339 ATATTGCAATAGTAGTATTATCTGCCC 57.162 33.333 22.76 0.00 0.00 5.36
2054 3770 6.049955 TGCAATAGTAGTATTATCTGCCCC 57.950 41.667 2.44 0.00 0.00 5.80
2055 3771 5.045869 TGCAATAGTAGTATTATCTGCCCCC 60.046 44.000 2.44 0.00 0.00 5.40
2056 3772 5.661458 CAATAGTAGTATTATCTGCCCCCG 58.339 45.833 2.44 0.00 0.00 5.73
2058 3774 3.163467 AGTAGTATTATCTGCCCCCGAC 58.837 50.000 0.00 0.00 0.00 4.79
2059 3775 2.097110 AGTATTATCTGCCCCCGACA 57.903 50.000 0.00 0.00 0.00 4.35
2061 3777 2.368875 AGTATTATCTGCCCCCGACAAG 59.631 50.000 0.00 0.00 0.00 3.16
2062 3778 1.507140 ATTATCTGCCCCCGACAAGA 58.493 50.000 0.00 0.00 0.00 3.02
2063 3779 0.539986 TTATCTGCCCCCGACAAGAC 59.460 55.000 0.00 0.00 0.00 3.01
2065 3781 0.325296 ATCTGCCCCCGACAAGACTA 60.325 55.000 0.00 0.00 0.00 2.59
2066 3782 0.325296 TCTGCCCCCGACAAGACTAT 60.325 55.000 0.00 0.00 0.00 2.12
2069 3785 0.179081 GCCCCCGACAAGACTATCAC 60.179 60.000 0.00 0.00 0.00 3.06
2071 3787 1.137086 CCCCCGACAAGACTATCACTG 59.863 57.143 0.00 0.00 0.00 3.66
2072 3788 1.825474 CCCCGACAAGACTATCACTGT 59.175 52.381 0.00 0.00 0.00 3.55
2073 3789 3.021695 CCCCGACAAGACTATCACTGTA 58.978 50.000 0.00 0.00 0.00 2.74
2074 3790 3.446161 CCCCGACAAGACTATCACTGTAA 59.554 47.826 0.00 0.00 0.00 2.41
2075 3791 4.099573 CCCCGACAAGACTATCACTGTAAT 59.900 45.833 0.00 0.00 0.00 1.89
2076 3792 5.043903 CCCGACAAGACTATCACTGTAATG 58.956 45.833 0.00 0.00 0.00 1.90
2080 3796 6.638873 CGACAAGACTATCACTGTAATGATCC 59.361 42.308 0.00 0.00 39.97 3.36
2089 3805 5.291971 TCACTGTAATGATCCATCATCGTG 58.708 41.667 2.47 8.13 46.22 4.35
2212 3931 2.041485 TGAAGGTTGGAATGGAGCATGA 59.959 45.455 0.00 0.00 0.00 3.07
2220 3944 3.713248 TGGAATGGAGCATGAGTCACTAT 59.287 43.478 0.00 0.00 0.00 2.12
2268 4015 5.742453 GCAGATGTTTGTTGAGCAGATTATG 59.258 40.000 0.00 0.00 0.00 1.90
2287 4034 1.000896 ACCTGCCATACCAACTGCC 60.001 57.895 0.00 0.00 0.00 4.85
2301 6463 1.597854 CTGCCAGCAGACGGTTCAA 60.598 57.895 14.54 0.00 46.30 2.69
2328 6490 4.454504 ACCGTCAACATGATACACCTTTTC 59.545 41.667 0.00 0.00 0.00 2.29
2336 6498 5.253096 ACATGATACACCTTTTCCCTAACCT 59.747 40.000 0.00 0.00 0.00 3.50
2389 6551 7.944729 AGGCATTAGTTCAACTGTCAATAAT 57.055 32.000 0.00 0.00 0.00 1.28
2446 6608 0.315869 CGTTCGTGGTTGTGCACTTC 60.316 55.000 19.41 10.61 0.00 3.01
2595 6768 7.280356 AGACCAAGACAAGTACTGTAATTGTT 58.720 34.615 27.68 15.74 45.65 2.83
2613 6798 2.098934 TGTTTGTGCAGGTGTTGATCAC 59.901 45.455 0.00 0.00 45.47 3.06
2643 6828 3.074538 AGTCCAAATACTCCTGCTGGTTT 59.925 43.478 9.73 0.00 34.23 3.27
2717 6902 1.132554 TGCAATTGGGGCCCAACAAT 61.133 50.000 39.23 24.98 46.95 2.71
2718 6903 0.677414 GCAATTGGGGCCCAACAATG 60.677 55.000 39.23 33.40 46.95 2.82
2723 6908 0.039035 TGGGGCCCAACAATGTCTAC 59.961 55.000 26.55 0.98 0.00 2.59
2735 6920 7.106239 CCAACAATGTCTACAATAGAGGAAGT 58.894 38.462 0.00 0.00 35.04 3.01
2861 8221 1.416401 CACCATCGTGGGGCTACTAAT 59.584 52.381 8.57 0.00 43.37 1.73
2864 8224 2.548067 CCATCGTGGGGCTACTAATGAC 60.548 54.545 0.00 0.00 32.67 3.06
2883 8243 3.843619 TGACTGAATCCCCACACAGAATA 59.156 43.478 0.00 0.00 34.88 1.75
2895 8255 3.511146 CACACAGAATACCCATTTGGCTT 59.489 43.478 0.00 0.00 37.83 4.35
2926 8286 3.542969 AATAAAAGGACCAGGTGGCTT 57.457 42.857 0.00 0.00 39.32 4.35
2957 8324 6.672266 TCTCACTTCCATCTACTCTTTGTT 57.328 37.500 0.00 0.00 0.00 2.83
2990 8357 5.155161 TCCCTAATGCCTCTCAAGCTTATA 58.845 41.667 0.00 0.00 0.00 0.98
3022 8389 9.599866 CATTCAAATAAGATGTGGTCACTACTA 57.400 33.333 2.66 0.00 0.00 1.82
3027 8394 9.959721 AAATAAGATGTGGTCACTACTAATTGT 57.040 29.630 2.66 0.00 0.00 2.71
3071 8442 3.839323 TTACTAGAGGAACTGGACCCA 57.161 47.619 0.00 0.00 41.55 4.51
3154 8526 4.913335 AGCTCACTGGATTGCATTTATG 57.087 40.909 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.564550 ACAATAGAGATGGCTTCAACACTT 58.435 37.500 3.03 0.00 0.00 3.16
43 45 3.481661 CGAAACACGGCGGCTTAT 58.518 55.556 13.24 0.00 38.46 1.73
59 61 4.708386 TAGGGTTTGTGCCGGCCG 62.708 66.667 26.77 21.04 0.00 6.13
63 65 0.249398 AGTAGCTAGGGTTTGTGCCG 59.751 55.000 0.00 0.00 0.00 5.69
106 108 5.104109 TCGAATAGATGAACTTTGGGGGAAT 60.104 40.000 0.00 0.00 0.00 3.01
140 142 6.187727 TGGTGGTTTCTAGAGAAAGAATGT 57.812 37.500 4.94 0.00 43.82 2.71
143 145 5.309543 TGGATGGTGGTTTCTAGAGAAAGAA 59.690 40.000 4.94 0.00 43.82 2.52
153 156 6.901300 TCTAACTAGTATGGATGGTGGTTTCT 59.099 38.462 0.00 0.00 0.00 2.52
154 157 7.120923 TCTAACTAGTATGGATGGTGGTTTC 57.879 40.000 0.00 0.00 0.00 2.78
156 159 6.270231 GGATCTAACTAGTATGGATGGTGGTT 59.730 42.308 0.00 0.00 0.00 3.67
184 187 1.832912 GAGGCCATGTACCTCCAGG 59.167 63.158 17.44 0.00 46.81 4.45
214 217 0.543277 GGATGATGAGGTGCAGGTCA 59.457 55.000 0.50 0.50 0.00 4.02
263 266 1.519455 GGAGACCACATCTTCCGCG 60.519 63.158 0.00 0.00 38.00 6.46
268 271 1.296715 GTGCCGGAGACCACATCTT 59.703 57.895 5.05 0.00 38.00 2.40
280 283 4.738998 TCCCATTGCAGGTGCCGG 62.739 66.667 0.00 0.00 41.18 6.13
326 329 3.568538 CTTGAAGCCACAATAGTTGCAC 58.431 45.455 0.00 0.00 38.77 4.57
354 357 1.629013 CGTCTTCAGCGCAACATAGA 58.371 50.000 11.47 1.59 0.00 1.98
357 360 2.034879 CCCGTCTTCAGCGCAACAT 61.035 57.895 11.47 0.00 0.00 2.71
390 396 8.251721 TGTATTTTTCACTAACCTAGAGCTCTC 58.748 37.037 22.17 0.00 0.00 3.20
573 580 6.485830 TCCTCTAGTGATGGTGAATAAAGG 57.514 41.667 0.00 0.00 0.00 3.11
747 819 9.305925 CATAAAAGGGAAAGATAGCAAATGAAC 57.694 33.333 0.00 0.00 0.00 3.18
827 902 2.894387 GACAGCATCCAGAGGCGC 60.894 66.667 0.00 0.00 43.74 6.53
831 906 0.817654 TACGGTGACAGCATCCAGAG 59.182 55.000 5.35 0.00 0.00 3.35
833 908 2.315925 AATACGGTGACAGCATCCAG 57.684 50.000 5.35 0.00 0.00 3.86
836 1434 3.930229 TGTGTAAATACGGTGACAGCATC 59.070 43.478 5.35 0.00 0.00 3.91
851 1449 8.812972 AGATATCTCCTAACTTGTGTGTGTAAA 58.187 33.333 0.00 0.00 0.00 2.01
857 1455 8.200792 AGCTTTAGATATCTCCTAACTTGTGTG 58.799 37.037 8.95 0.00 0.00 3.82
861 1459 8.032451 GGCTAGCTTTAGATATCTCCTAACTTG 58.968 40.741 15.72 4.51 0.00 3.16
863 1461 7.242359 TGGCTAGCTTTAGATATCTCCTAACT 58.758 38.462 15.72 4.66 0.00 2.24
865 1463 8.492415 TTTGGCTAGCTTTAGATATCTCCTAA 57.508 34.615 15.72 2.38 0.00 2.69
868 1466 6.998802 TCTTTGGCTAGCTTTAGATATCTCC 58.001 40.000 15.72 2.15 0.00 3.71
869 1467 7.039363 TCCTCTTTGGCTAGCTTTAGATATCTC 60.039 40.741 15.72 0.00 35.26 2.75
873 1471 5.661312 TGTCCTCTTTGGCTAGCTTTAGATA 59.339 40.000 15.72 3.77 35.26 1.98
877 1475 4.634012 TTGTCCTCTTTGGCTAGCTTTA 57.366 40.909 15.72 0.00 35.26 1.85
882 1480 4.899502 TCTCTTTTGTCCTCTTTGGCTAG 58.100 43.478 0.00 0.00 35.26 3.42
888 1486 5.373812 TGTTCCTCTCTTTTGTCCTCTTT 57.626 39.130 0.00 0.00 0.00 2.52
889 1487 5.131142 TCTTGTTCCTCTCTTTTGTCCTCTT 59.869 40.000 0.00 0.00 0.00 2.85
894 1492 9.436957 TTGTATATCTTGTTCCTCTCTTTTGTC 57.563 33.333 0.00 0.00 0.00 3.18
896 1494 8.394121 GCTTGTATATCTTGTTCCTCTCTTTTG 58.606 37.037 0.00 0.00 0.00 2.44
898 1496 7.550906 GTGCTTGTATATCTTGTTCCTCTCTTT 59.449 37.037 0.00 0.00 0.00 2.52
905 1503 6.109359 ACTCAGTGCTTGTATATCTTGTTCC 58.891 40.000 0.00 0.00 0.00 3.62
906 1504 7.463383 CGAACTCAGTGCTTGTATATCTTGTTC 60.463 40.741 0.00 0.00 0.00 3.18
907 1505 6.311445 CGAACTCAGTGCTTGTATATCTTGTT 59.689 38.462 0.00 0.00 0.00 2.83
908 1506 5.807520 CGAACTCAGTGCTTGTATATCTTGT 59.192 40.000 0.00 0.00 0.00 3.16
929 1527 3.744426 GTGCCTAAAAAGTGAGCTACGAA 59.256 43.478 0.00 0.00 0.00 3.85
930 1528 3.323243 GTGCCTAAAAAGTGAGCTACGA 58.677 45.455 0.00 0.00 0.00 3.43
944 1542 7.870954 CCACTAATACTAATCAATCGTGCCTAA 59.129 37.037 0.00 0.00 0.00 2.69
1000 1598 1.693083 GCGTGTGTATGGCGAGGAAC 61.693 60.000 0.00 0.00 0.00 3.62
1007 1605 1.946768 ACCATTATGCGTGTGTATGGC 59.053 47.619 0.00 0.00 39.46 4.40
1018 1616 3.553508 GCATGGACCAATGACCATTATGC 60.554 47.826 0.00 10.01 43.21 3.14
1106 1710 2.642171 ACACAGGGACAGGATTCCTA 57.358 50.000 4.51 0.00 35.76 2.94
1116 1720 4.196971 ACTTTCTTTGTGTACACAGGGAC 58.803 43.478 26.52 0.17 42.94 4.46
1118 1722 4.196193 TGACTTTCTTTGTGTACACAGGG 58.804 43.478 26.52 21.81 42.94 4.45
1119 1723 4.273480 CCTGACTTTCTTTGTGTACACAGG 59.727 45.833 26.52 22.12 42.94 4.00
1120 1724 5.116180 TCCTGACTTTCTTTGTGTACACAG 58.884 41.667 26.52 17.30 42.94 3.66
1121 1725 5.092554 TCCTGACTTTCTTTGTGTACACA 57.907 39.130 24.62 24.62 39.98 3.72
1122 1726 6.260050 TGAATCCTGACTTTCTTTGTGTACAC 59.740 38.462 19.36 19.36 0.00 2.90
1123 1727 6.260050 GTGAATCCTGACTTTCTTTGTGTACA 59.740 38.462 0.00 0.00 0.00 2.90
1124 1728 6.260050 TGTGAATCCTGACTTTCTTTGTGTAC 59.740 38.462 0.00 0.00 0.00 2.90
1125 1729 6.353323 TGTGAATCCTGACTTTCTTTGTGTA 58.647 36.000 0.00 0.00 0.00 2.90
1126 1730 5.192927 TGTGAATCCTGACTTTCTTTGTGT 58.807 37.500 0.00 0.00 0.00 3.72
1127 1731 5.756195 TGTGAATCCTGACTTTCTTTGTG 57.244 39.130 0.00 0.00 0.00 3.33
1128 1732 5.067805 GGTTGTGAATCCTGACTTTCTTTGT 59.932 40.000 0.00 0.00 0.00 2.83
1129 1733 5.067674 TGGTTGTGAATCCTGACTTTCTTTG 59.932 40.000 0.00 0.00 0.00 2.77
1130 1734 5.200483 TGGTTGTGAATCCTGACTTTCTTT 58.800 37.500 0.00 0.00 0.00 2.52
1131 1735 4.792068 TGGTTGTGAATCCTGACTTTCTT 58.208 39.130 0.00 0.00 0.00 2.52
1132 1736 4.437682 TGGTTGTGAATCCTGACTTTCT 57.562 40.909 0.00 0.00 0.00 2.52
1133 1737 5.281727 GTTTGGTTGTGAATCCTGACTTTC 58.718 41.667 0.00 0.00 0.00 2.62
1201 2309 4.532834 GGGGATGTTGTTTTATAGGCTGA 58.467 43.478 0.00 0.00 0.00 4.26
1219 2327 1.984570 CAGGAAGCAGAGACGGGGA 60.985 63.158 0.00 0.00 0.00 4.81
1220 2328 1.831652 AACAGGAAGCAGAGACGGGG 61.832 60.000 0.00 0.00 0.00 5.73
1221 2329 0.390472 GAACAGGAAGCAGAGACGGG 60.390 60.000 0.00 0.00 0.00 5.28
1225 2333 2.026822 GGATTGGAACAGGAAGCAGAGA 60.027 50.000 0.00 0.00 42.39 3.10
1226 2334 2.363683 GGATTGGAACAGGAAGCAGAG 58.636 52.381 0.00 0.00 42.39 3.35
1230 2338 1.177401 GTGGGATTGGAACAGGAAGC 58.823 55.000 0.00 0.00 42.39 3.86
1255 2363 2.735126 GCTCTGCTCTCCTCTTTTCTCG 60.735 54.545 0.00 0.00 0.00 4.04
1256 2364 2.233431 TGCTCTGCTCTCCTCTTTTCTC 59.767 50.000 0.00 0.00 0.00 2.87
1257 2365 2.234414 CTGCTCTGCTCTCCTCTTTTCT 59.766 50.000 0.00 0.00 0.00 2.52
1258 2366 2.233431 TCTGCTCTGCTCTCCTCTTTTC 59.767 50.000 0.00 0.00 0.00 2.29
1260 2368 1.826720 CTCTGCTCTGCTCTCCTCTTT 59.173 52.381 0.00 0.00 0.00 2.52
1261 2369 1.477553 CTCTGCTCTGCTCTCCTCTT 58.522 55.000 0.00 0.00 0.00 2.85
1262 2370 1.039233 GCTCTGCTCTGCTCTCCTCT 61.039 60.000 0.00 0.00 0.00 3.69
1266 2374 1.943116 TTCCGCTCTGCTCTGCTCTC 61.943 60.000 0.00 0.00 0.00 3.20
1299 2412 2.441750 TGGAAGAACAACTAGCAAGGGT 59.558 45.455 0.00 0.00 0.00 4.34
1328 2449 5.694458 GCTTTGTATTGTTTGTAAAGGGTGG 59.306 40.000 0.00 0.00 0.00 4.61
1330 2451 5.508320 CGGCTTTGTATTGTTTGTAAAGGGT 60.508 40.000 0.00 0.00 0.00 4.34
1331 2452 4.920927 CGGCTTTGTATTGTTTGTAAAGGG 59.079 41.667 0.00 0.00 0.00 3.95
1334 2455 4.299978 GCCGGCTTTGTATTGTTTGTAAA 58.700 39.130 22.15 0.00 0.00 2.01
1337 2458 1.000394 GGCCGGCTTTGTATTGTTTGT 60.000 47.619 28.56 0.00 0.00 2.83
1338 2459 1.000283 TGGCCGGCTTTGTATTGTTTG 60.000 47.619 28.56 0.00 0.00 2.93
1339 2460 1.333177 TGGCCGGCTTTGTATTGTTT 58.667 45.000 28.56 0.00 0.00 2.83
1340 2461 1.204467 CATGGCCGGCTTTGTATTGTT 59.796 47.619 28.56 0.00 0.00 2.83
1341 2462 0.817013 CATGGCCGGCTTTGTATTGT 59.183 50.000 28.56 0.00 0.00 2.71
1342 2463 0.817013 ACATGGCCGGCTTTGTATTG 59.183 50.000 28.56 14.97 0.00 1.90
1343 2464 2.021457 GTACATGGCCGGCTTTGTATT 58.979 47.619 30.78 16.15 0.00 1.89
1344 2465 1.675552 GTACATGGCCGGCTTTGTAT 58.324 50.000 30.78 16.69 0.00 2.29
1417 2558 0.619832 AGATGCAGCCCTTCTCCTCA 60.620 55.000 0.00 0.00 0.00 3.86
1488 2629 0.250901 TGAGCAGAGGAAAACCCAGC 60.251 55.000 0.00 0.00 37.41 4.85
1498 2639 0.106335 ATCGGCAAGATGAGCAGAGG 59.894 55.000 0.00 0.00 39.43 3.69
1506 2647 4.815308 AGAGATTTCTCAATCGGCAAGATG 59.185 41.667 10.07 0.00 45.21 2.90
1507 2648 5.033589 AGAGATTTCTCAATCGGCAAGAT 57.966 39.130 10.07 0.00 45.21 2.40
1532 2753 1.073025 GACTGGGTGCACATGGACA 59.927 57.895 20.43 8.08 38.19 4.02
1533 2754 2.034879 CGACTGGGTGCACATGGAC 61.035 63.158 20.43 5.88 35.50 4.02
1534 2755 1.552799 ATCGACTGGGTGCACATGGA 61.553 55.000 20.43 7.90 0.00 3.41
1535 2756 1.078214 ATCGACTGGGTGCACATGG 60.078 57.895 20.43 9.75 0.00 3.66
1536 2757 1.985447 GCATCGACTGGGTGCACATG 61.985 60.000 20.43 12.56 38.68 3.21
1537 2758 1.746615 GCATCGACTGGGTGCACAT 60.747 57.895 20.43 0.00 38.68 3.21
1540 2761 2.046988 CTGCATCGACTGGGTGCA 60.047 61.111 10.03 10.03 45.69 4.57
1542 2763 1.153489 CCTCTGCATCGACTGGGTG 60.153 63.158 0.00 0.00 0.00 4.61
1543 2764 3.023949 GCCTCTGCATCGACTGGGT 62.024 63.158 0.00 0.00 37.47 4.51
1544 2765 2.202987 GCCTCTGCATCGACTGGG 60.203 66.667 0.00 0.00 37.47 4.45
1547 2768 2.755876 TCGGCCTCTGCATCGACT 60.756 61.111 0.00 0.00 40.13 4.18
1585 3295 5.630415 TTTCCGAGGATATTTCAGATGGT 57.370 39.130 0.00 0.00 0.00 3.55
1596 3306 9.800572 CCTATCTCTATGATATTTCCGAGGATA 57.199 37.037 0.00 0.00 37.07 2.59
1612 3322 7.189203 TCCAGGATATTCCTTCCCTATCTCTAT 59.811 40.741 0.00 0.00 46.91 1.98
1619 3329 4.907875 CAGTTCCAGGATATTCCTTCCCTA 59.092 45.833 0.00 0.00 46.91 3.53
1624 3334 4.375313 AGACCAGTTCCAGGATATTCCTT 58.625 43.478 0.00 0.00 46.91 3.36
1643 3353 4.553330 TTGACATGAACTAGGGGAAGAC 57.447 45.455 0.00 0.00 0.00 3.01
1668 3378 2.349155 GGACGAACGAAAAGAACGCAAT 60.349 45.455 0.14 0.00 0.00 3.56
1671 3381 0.110956 GGGACGAACGAAAAGAACGC 60.111 55.000 0.14 0.00 0.00 4.84
1672 3382 1.494824 AGGGACGAACGAAAAGAACG 58.505 50.000 0.14 0.00 0.00 3.95
1679 3390 9.550406 AAATAATATTATGAAGGGACGAACGAA 57.450 29.630 8.74 0.00 0.00 3.85
1681 3392 8.770828 ACAAATAATATTATGAAGGGACGAACG 58.229 33.333 8.74 0.00 0.00 3.95
1705 3416 4.703897 ACAGAATCAGAAACGGAAGAACA 58.296 39.130 0.00 0.00 0.00 3.18
1718 3429 7.607250 ACTACTTGGTAGAGAAACAGAATCAG 58.393 38.462 11.08 0.00 38.29 2.90
1727 3438 4.463186 GCCAGAGACTACTTGGTAGAGAAA 59.537 45.833 11.08 0.00 38.29 2.52
1729 3440 3.267291 AGCCAGAGACTACTTGGTAGAGA 59.733 47.826 11.08 0.00 38.29 3.10
1740 3451 2.039418 ACACACACAAGCCAGAGACTA 58.961 47.619 0.00 0.00 0.00 2.59
1748 3459 1.949525 AGTCAATCACACACACAAGCC 59.050 47.619 0.00 0.00 0.00 4.35
1777 3488 1.653667 CATGAACACGCTGCAACCA 59.346 52.632 0.00 0.00 0.00 3.67
1794 3505 2.595463 AGAAGCAGCAAAGCGCCA 60.595 55.556 2.29 0.00 44.04 5.69
1796 3507 2.804090 GCAGAAGCAGCAAAGCGC 60.804 61.111 0.00 0.00 41.58 5.92
1820 3531 2.813042 GCAGCACTCGCAGGTCTC 60.813 66.667 0.00 0.00 42.27 3.36
1822 3533 4.385405 AGGCAGCACTCGCAGGTC 62.385 66.667 0.00 0.00 42.27 3.85
1861 3572 2.743838 GCGGCCATGGCTAGTTTAGTTA 60.744 50.000 34.70 0.00 41.60 2.24
1870 3581 4.488136 CAGTGGCGGCCATGGCTA 62.488 66.667 34.70 16.78 41.60 3.93
1882 3597 0.039074 GTCGTCTGTCTGTCCAGTGG 60.039 60.000 1.40 1.40 34.02 4.00
1885 3600 1.210413 CCGTCGTCTGTCTGTCCAG 59.790 63.158 0.00 0.00 0.00 3.86
1905 3621 2.279252 GATCTCGGCGCGCCTTTA 60.279 61.111 43.60 29.48 0.00 1.85
1917 3633 3.083997 AGGCCGGTGGTGGATCTC 61.084 66.667 1.90 0.00 0.00 2.75
1924 3640 2.526873 ACAGAAGAGGCCGGTGGT 60.527 61.111 1.90 0.00 0.00 4.16
1929 3645 4.571176 GGTAATTAAAGACAGAAGAGGCCG 59.429 45.833 0.00 0.00 0.00 6.13
1931 3647 4.882427 GGGGTAATTAAAGACAGAAGAGGC 59.118 45.833 0.00 0.00 0.00 4.70
1933 3649 5.811100 GTCGGGGTAATTAAAGACAGAAGAG 59.189 44.000 0.00 0.00 0.00 2.85
1936 3652 5.486735 TGTCGGGGTAATTAAAGACAGAA 57.513 39.130 8.54 0.00 34.24 3.02
1974 3690 9.319143 GAGAGCTAGACACACATGTTTATTATT 57.681 33.333 0.00 0.00 39.95 1.40
1982 3698 3.576118 AGTTGAGAGCTAGACACACATGT 59.424 43.478 0.00 0.00 43.71 3.21
2010 3726 5.119125 TGCAATATCGATAAAGCACTCATCG 59.881 40.000 23.28 7.81 42.18 3.84
2015 3731 7.969536 ACTATTGCAATATCGATAAAGCACT 57.030 32.000 25.55 22.99 0.00 4.40
2027 3743 9.838339 GGGCAGATAATACTACTATTGCAATAT 57.162 33.333 19.17 11.87 0.00 1.28
2028 3744 8.265055 GGGGCAGATAATACTACTATTGCAATA 58.735 37.037 17.94 17.94 0.00 1.90
2029 3745 7.112779 GGGGCAGATAATACTACTATTGCAAT 58.887 38.462 17.56 17.56 0.00 3.56
2030 3746 6.472887 GGGGCAGATAATACTACTATTGCAA 58.527 40.000 0.00 0.00 0.00 4.08
2032 3748 5.429130 GGGGGCAGATAATACTACTATTGC 58.571 45.833 0.00 0.00 0.00 3.56
2033 3749 5.421056 TCGGGGGCAGATAATACTACTATTG 59.579 44.000 0.00 0.00 0.00 1.90
2034 3750 5.421374 GTCGGGGGCAGATAATACTACTATT 59.579 44.000 0.00 0.00 0.00 1.73
2035 3751 4.954826 GTCGGGGGCAGATAATACTACTAT 59.045 45.833 0.00 0.00 0.00 2.12
2036 3752 4.202599 TGTCGGGGGCAGATAATACTACTA 60.203 45.833 0.00 0.00 0.00 1.82
2037 3753 3.163467 GTCGGGGGCAGATAATACTACT 58.837 50.000 0.00 0.00 0.00 2.57
2038 3754 2.895404 TGTCGGGGGCAGATAATACTAC 59.105 50.000 0.00 0.00 0.00 2.73
2039 3755 3.247948 TGTCGGGGGCAGATAATACTA 57.752 47.619 0.00 0.00 0.00 1.82
2040 3756 2.097110 TGTCGGGGGCAGATAATACT 57.903 50.000 0.00 0.00 0.00 2.12
2041 3757 2.367567 TCTTGTCGGGGGCAGATAATAC 59.632 50.000 0.00 0.00 0.00 1.89
2043 3759 1.141053 GTCTTGTCGGGGGCAGATAAT 59.859 52.381 0.00 0.00 0.00 1.28
2046 3762 0.325296 TAGTCTTGTCGGGGGCAGAT 60.325 55.000 0.00 0.00 0.00 2.90
2048 3764 0.105039 GATAGTCTTGTCGGGGGCAG 59.895 60.000 0.00 0.00 0.00 4.85
2050 3766 0.179081 GTGATAGTCTTGTCGGGGGC 60.179 60.000 0.00 0.00 0.00 5.80
2051 3767 1.137086 CAGTGATAGTCTTGTCGGGGG 59.863 57.143 0.00 0.00 0.00 5.40
2053 3769 4.713824 TTACAGTGATAGTCTTGTCGGG 57.286 45.455 0.00 0.00 0.00 5.14
2054 3770 5.891451 TCATTACAGTGATAGTCTTGTCGG 58.109 41.667 0.00 0.00 0.00 4.79
2055 3771 6.638873 GGATCATTACAGTGATAGTCTTGTCG 59.361 42.308 0.00 0.00 38.88 4.35
2056 3772 7.492524 TGGATCATTACAGTGATAGTCTTGTC 58.507 38.462 0.00 0.00 38.88 3.18
2058 3774 8.146412 TGATGGATCATTACAGTGATAGTCTTG 58.854 37.037 0.00 0.00 38.88 3.02
2059 3775 8.255111 TGATGGATCATTACAGTGATAGTCTT 57.745 34.615 0.00 0.00 38.88 3.01
2061 3777 7.487509 CGATGATGGATCATTACAGTGATAGTC 59.512 40.741 0.00 0.00 46.84 2.59
2062 3778 7.039434 ACGATGATGGATCATTACAGTGATAGT 60.039 37.037 0.00 0.00 46.84 2.12
2063 3779 7.275123 CACGATGATGGATCATTACAGTGATAG 59.725 40.741 15.60 0.00 46.84 2.08
2065 3781 5.930569 CACGATGATGGATCATTACAGTGAT 59.069 40.000 15.60 0.00 46.84 3.06
2066 3782 5.163416 ACACGATGATGGATCATTACAGTGA 60.163 40.000 21.59 0.00 46.84 3.41
2069 3785 6.037500 ACAAACACGATGATGGATCATTACAG 59.962 38.462 3.65 0.33 46.84 2.74
2071 3787 6.363577 ACAAACACGATGATGGATCATTAC 57.636 37.500 3.65 0.00 46.84 1.89
2072 3788 6.677675 GCAACAAACACGATGATGGATCATTA 60.678 38.462 3.65 0.00 46.84 1.90
2073 3789 5.643664 CAACAAACACGATGATGGATCATT 58.356 37.500 3.65 0.00 46.84 2.57
2075 3791 3.119884 GCAACAAACACGATGATGGATCA 60.120 43.478 0.00 0.00 41.70 2.92
2076 3792 3.119884 TGCAACAAACACGATGATGGATC 60.120 43.478 0.00 0.00 0.00 3.36
2080 3796 4.087510 AGATGCAACAAACACGATGATG 57.912 40.909 0.00 0.00 0.00 3.07
2268 4015 1.032114 GGCAGTTGGTATGGCAGGTC 61.032 60.000 0.00 0.00 42.45 3.85
2287 4034 2.105323 GTTTGTTGAACCGTCTGCTG 57.895 50.000 0.00 0.00 31.85 4.41
2301 6463 3.500680 GGTGTATCATGTTGACGGTTTGT 59.499 43.478 0.00 0.00 0.00 2.83
2359 6521 6.076981 ACAGTTGAACTAATGCCTTCTTTG 57.923 37.500 0.00 0.00 0.00 2.77
2389 6551 6.840527 TCCAAATCTTGTCCATGCTCATATA 58.159 36.000 0.00 0.00 0.00 0.86
2393 6555 3.438216 TCCAAATCTTGTCCATGCTCA 57.562 42.857 0.00 0.00 0.00 4.26
2400 6562 9.378551 ACTTTTTAAACTTTCCAAATCTTGTCC 57.621 29.630 0.00 0.00 0.00 4.02
2503 6673 5.806654 ACAAAGGATTAATGCAACCTGTT 57.193 34.783 9.81 0.00 32.73 3.16
2613 6798 5.510520 GCAGGAGTATTTGGACTAGGATCAG 60.511 48.000 0.00 0.00 0.00 2.90
2665 6850 5.683681 AGGCAAACAACAATTTTCCTCAAT 58.316 33.333 0.00 0.00 0.00 2.57
2702 6887 0.116940 AGACATTGTTGGGCCCCAAT 59.883 50.000 20.32 19.62 45.80 3.16
2717 6902 3.130516 CCGCACTTCCTCTATTGTAGACA 59.869 47.826 0.00 0.00 0.00 3.41
2718 6903 3.707793 CCGCACTTCCTCTATTGTAGAC 58.292 50.000 0.00 0.00 0.00 2.59
2723 6908 1.154205 CGGCCGCACTTCCTCTATTG 61.154 60.000 14.67 0.00 0.00 1.90
2807 6993 0.679505 GGGCAGCTACATCACCGATA 59.320 55.000 0.00 0.00 0.00 2.92
2861 8221 1.728323 TCTGTGTGGGGATTCAGTCA 58.272 50.000 0.00 0.00 0.00 3.41
2864 8224 3.545703 GGTATTCTGTGTGGGGATTCAG 58.454 50.000 0.00 0.00 0.00 3.02
2895 8255 7.036863 ACCTGGTCCTTTTATTTCTTCCATAGA 60.037 37.037 0.00 0.00 0.00 1.98
2926 8286 8.871125 AGAGTAGATGGAAGTGAGAACTTTTTA 58.129 33.333 0.00 0.00 0.00 1.52
2957 8324 5.665701 AGAGGCATTAGGGATTATCCTACA 58.334 41.667 11.40 0.00 38.97 2.74
2990 8357 7.448161 TGACCACATCTTATTTGAATGAGTTGT 59.552 33.333 6.46 6.46 36.17 3.32
3041 8412 7.732140 TCCAGTTCCTCTAGTAATGATGATGAT 59.268 37.037 0.00 0.00 0.00 2.45
3071 8442 2.299326 AGTTGCATTCCAAGCCTCTT 57.701 45.000 0.00 0.00 33.21 2.85
3142 8514 3.853475 GCATAGGCCCATAAATGCAATC 58.147 45.455 15.67 0.00 43.30 2.67
3172 8544 4.338012 TCATGTGCTGAAATTGGAGACAT 58.662 39.130 0.00 0.00 42.32 3.06


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

AutoCloner maintained by Alex Coulton.