Multiple sequence alignment - TraesCS3A01G211700

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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 TraesCS3A01G211700 chr3A 100.000 2378 0 0 1 2378 380680007 380682384 0.000000e+00 4392
1 TraesCS3A01G211700 chr3A 91.827 881 68 4 1 880 233137873 233138750 0.000000e+00 1225
2 TraesCS3A01G211700 chr3A 90.685 891 71 6 1 880 650254458 650255347 0.000000e+00 1175
3 TraesCS3A01G211700 chr3A 94.253 522 29 1 878 1399 369567901 369568421 0.000000e+00 797
4 TraesCS3A01G211700 chr2A 91.676 889 65 2 1 880 724933139 724934027 0.000000e+00 1223
5 TraesCS3A01G211700 chr2A 90.889 889 71 3 1 880 227247144 227248031 0.000000e+00 1184
6 TraesCS3A01G211700 chr2A 90.579 881 79 4 1 880 440684518 440683641 0.000000e+00 1164
7 TraesCS3A01G211700 chr2A 92.395 789 55 5 1592 2378 641239096 641239881 0.000000e+00 1120
8 TraesCS3A01G211700 chr2A 92.249 787 54 2 1592 2378 537097341 537098120 0.000000e+00 1109
9 TraesCS3A01G211700 chr2A 91.888 789 59 4 1592 2378 743447704 743446919 0.000000e+00 1098
10 TraesCS3A01G211700 chr2A 94.646 523 28 0 878 1400 150951979 150951457 0.000000e+00 811
11 TraesCS3A01G211700 chr2A 94.264 523 30 0 878 1400 437705176 437705698 0.000000e+00 800
12 TraesCS3A01G211700 chr2A 95.000 200 10 0 1393 1592 708849743 708849942 4.930000e-82 315
13 TraesCS3A01G211700 chr7A 91.451 889 64 5 1 880 102474286 102473401 0.000000e+00 1210
14 TraesCS3A01G211700 chr7A 92.415 791 51 9 1592 2378 718456762 718457547 0.000000e+00 1120
15 TraesCS3A01G211700 chr7A 93.881 523 32 0 878 1400 463221686 463222208 0.000000e+00 789
16 TraesCS3A01G211700 chr6D 91.226 889 68 3 1 881 74573220 74572334 0.000000e+00 1201
17 TraesCS3A01G211700 chr6D 92.172 792 54 7 1591 2378 354457546 354456759 0.000000e+00 1112
18 TraesCS3A01G211700 chr4A 91.226 889 69 4 1 880 369290014 369290902 0.000000e+00 1201
19 TraesCS3A01G211700 chr4A 91.143 892 66 6 1 880 73246332 73247222 0.000000e+00 1197
20 TraesCS3A01G211700 chr4A 93.881 523 32 0 878 1400 334602603 334603125 0.000000e+00 789
21 TraesCS3A01G211700 chr4A 94.975 199 10 0 1397 1595 24604184 24603986 1.770000e-81 313
22 TraesCS3A01G211700 chr4A 94.500 200 11 0 1393 1592 581741077 581741276 2.300000e-80 309
23 TraesCS3A01G211700 chr4A 95.337 193 9 0 1394 1586 95979840 95980032 8.260000e-80 307
24 TraesCS3A01G211700 chr5A 92.658 790 53 3 1592 2378 536552698 536551911 0.000000e+00 1133
25 TraesCS3A01G211700 chr5A 94.220 519 30 0 882 1400 258005244 258004726 0.000000e+00 793
26 TraesCS3A01G211700 chr5A 94.975 199 9 1 1394 1592 154649082 154649279 6.380000e-81 311
27 TraesCS3A01G211700 chr5D 92.640 788 51 4 1592 2378 233011810 233011029 0.000000e+00 1127
28 TraesCS3A01G211700 chr6A 92.005 788 56 4 1592 2378 107873780 107874561 0.000000e+00 1099
29 TraesCS3A01G211700 chr6A 94.472 199 11 0 1397 1595 118525406 118525208 8.260000e-80 307
30 TraesCS3A01G211700 chr6A 94.472 199 11 0 1397 1595 184669806 184669608 8.260000e-80 307
31 TraesCS3A01G211700 chr3D 91.834 796 54 7 1592 2378 368272495 368273288 0.000000e+00 1099
32 TraesCS3A01G211700 chr1A 94.073 523 28 1 878 1400 313211682 313212201 0.000000e+00 791
33 TraesCS3A01G211700 chr1A 93.881 523 32 0 878 1400 218131716 218132238 0.000000e+00 789
34 TraesCS3A01G211700 chr1A 94.975 199 10 0 1394 1592 448590892 448591090 1.770000e-81 313
35 TraesCS3A01G211700 chr1A 94.472 199 11 0 1397 1595 78221390 78221192 8.260000e-80 307
36 TraesCS3A01G211700 chr1D 93.870 522 32 0 881 1402 286497109 286496588 0.000000e+00 787


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 TraesCS3A01G211700 chr3A 380680007 380682384 2377 False 4392 4392 100.000 1 2378 1 chr3A.!!$F3 2377
1 TraesCS3A01G211700 chr3A 233137873 233138750 877 False 1225 1225 91.827 1 880 1 chr3A.!!$F1 879
2 TraesCS3A01G211700 chr3A 650254458 650255347 889 False 1175 1175 90.685 1 880 1 chr3A.!!$F4 879
3 TraesCS3A01G211700 chr3A 369567901 369568421 520 False 797 797 94.253 878 1399 1 chr3A.!!$F2 521
4 TraesCS3A01G211700 chr2A 724933139 724934027 888 False 1223 1223 91.676 1 880 1 chr2A.!!$F6 879
5 TraesCS3A01G211700 chr2A 227247144 227248031 887 False 1184 1184 90.889 1 880 1 chr2A.!!$F1 879
6 TraesCS3A01G211700 chr2A 440683641 440684518 877 True 1164 1164 90.579 1 880 1 chr2A.!!$R2 879
7 TraesCS3A01G211700 chr2A 641239096 641239881 785 False 1120 1120 92.395 1592 2378 1 chr2A.!!$F4 786
8 TraesCS3A01G211700 chr2A 537097341 537098120 779 False 1109 1109 92.249 1592 2378 1 chr2A.!!$F3 786
9 TraesCS3A01G211700 chr2A 743446919 743447704 785 True 1098 1098 91.888 1592 2378 1 chr2A.!!$R3 786
10 TraesCS3A01G211700 chr2A 150951457 150951979 522 True 811 811 94.646 878 1400 1 chr2A.!!$R1 522
11 TraesCS3A01G211700 chr2A 437705176 437705698 522 False 800 800 94.264 878 1400 1 chr2A.!!$F2 522
12 TraesCS3A01G211700 chr7A 102473401 102474286 885 True 1210 1210 91.451 1 880 1 chr7A.!!$R1 879
13 TraesCS3A01G211700 chr7A 718456762 718457547 785 False 1120 1120 92.415 1592 2378 1 chr7A.!!$F2 786
14 TraesCS3A01G211700 chr7A 463221686 463222208 522 False 789 789 93.881 878 1400 1 chr7A.!!$F1 522
15 TraesCS3A01G211700 chr6D 74572334 74573220 886 True 1201 1201 91.226 1 881 1 chr6D.!!$R1 880
16 TraesCS3A01G211700 chr6D 354456759 354457546 787 True 1112 1112 92.172 1591 2378 1 chr6D.!!$R2 787
17 TraesCS3A01G211700 chr4A 369290014 369290902 888 False 1201 1201 91.226 1 880 1 chr4A.!!$F4 879
18 TraesCS3A01G211700 chr4A 73246332 73247222 890 False 1197 1197 91.143 1 880 1 chr4A.!!$F1 879
19 TraesCS3A01G211700 chr4A 334602603 334603125 522 False 789 789 93.881 878 1400 1 chr4A.!!$F3 522
20 TraesCS3A01G211700 chr5A 536551911 536552698 787 True 1133 1133 92.658 1592 2378 1 chr5A.!!$R2 786
21 TraesCS3A01G211700 chr5A 258004726 258005244 518 True 793 793 94.220 882 1400 1 chr5A.!!$R1 518
22 TraesCS3A01G211700 chr5D 233011029 233011810 781 True 1127 1127 92.640 1592 2378 1 chr5D.!!$R1 786
23 TraesCS3A01G211700 chr6A 107873780 107874561 781 False 1099 1099 92.005 1592 2378 1 chr6A.!!$F1 786
24 TraesCS3A01G211700 chr3D 368272495 368273288 793 False 1099 1099 91.834 1592 2378 1 chr3D.!!$F1 786
25 TraesCS3A01G211700 chr1A 313211682 313212201 519 False 791 791 94.073 878 1400 1 chr1A.!!$F2 522
26 TraesCS3A01G211700 chr1A 218131716 218132238 522 False 789 789 93.881 878 1400 1 chr1A.!!$F1 522
27 TraesCS3A01G211700 chr1D 286496588 286497109 521 True 787 787 93.870 881 1402 1 chr1D.!!$R1 521

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
402 405 0.179234 TTCTGCGGTTCAGTCCACAA 59.821 50.0 0.0 0.0 43.32 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1432 0.101759 ACCGACATTACGCATACGCT 59.898 50.0 0.0 0.0 45.53 5.07 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
201 204 8.589701 ACTTAATAAAATACACCCTTCCAAGG 57.410 34.615 0.00 0.00 46.06 3.61
217 220 1.553248 CAAGGGACAGATACAACCCGA 59.447 52.381 0.00 0.00 46.13 5.14
242 245 2.282251 TCTCTCACAGGGCGACGT 60.282 61.111 0.00 0.00 0.00 4.34
253 256 3.458163 GCGACGTGGGGAGGATCA 61.458 66.667 0.00 0.00 36.25 2.92
290 293 6.013842 TGCTATACGATGATACTTGGTGAG 57.986 41.667 0.00 0.00 0.00 3.51
309 312 5.128008 GGTGAGCTTACCATCTACTCTCTTT 59.872 44.000 22.15 0.00 40.54 2.52
331 334 2.245159 TATGCTTCAAGATGGAGGCG 57.755 50.000 0.00 0.00 42.26 5.52
351 354 2.269172 GGCCAGAAGCGTAGTCTTTAC 58.731 52.381 0.00 0.00 45.17 2.01
389 392 2.547211 CCTCTTATTCTGGCATTCTGCG 59.453 50.000 0.00 0.00 46.21 5.18
402 405 0.179234 TTCTGCGGTTCAGTCCACAA 59.821 50.000 0.00 0.00 43.32 3.33
414 417 5.097742 TCAGTCCACAAATACTACCCATG 57.902 43.478 0.00 0.00 0.00 3.66
567 575 2.233431 GAGGATCCCGAGGATGATTCTG 59.767 54.545 8.55 0.00 43.27 3.02
615 623 4.748798 AGGTCCCAGGCAGGAGGG 62.749 72.222 0.00 0.00 46.90 4.30
717 725 1.502231 TGCTTTCGCTGACTCTTGTC 58.498 50.000 0.00 0.00 43.20 3.18
726 734 2.486203 GCTGACTCTTGTCTCTTCGAGA 59.514 50.000 0.00 0.00 43.29 4.04
904 921 2.776536 AGTCTAGGAAAGAGCATGGCAT 59.223 45.455 0.00 0.00 33.88 4.40
943 960 1.533731 ACATCGGCAAAGTTTACCACG 59.466 47.619 5.71 0.75 0.00 4.94
967 984 5.782925 AGGATCTTAAGGACACCATCTACT 58.217 41.667 1.85 0.00 0.00 2.57
975 992 6.597832 AAGGACACCATCTACTAGATATGC 57.402 41.667 0.00 0.00 32.12 3.14
1043 1060 0.179048 TCCATTGCAGCCTACATCCG 60.179 55.000 0.00 0.00 0.00 4.18
1121 1138 3.423539 CCTGAAGAAGGTGATGACCAA 57.576 47.619 3.51 0.00 45.98 3.67
1304 1321 4.456253 CGACACCGACTCCGACCG 62.456 72.222 0.00 0.00 38.22 4.79
1402 1419 6.862090 GTCGACCACCATATTATCAGTAGAAC 59.138 42.308 3.51 0.00 0.00 3.01
1403 1420 6.015688 TCGACCACCATATTATCAGTAGAACC 60.016 42.308 0.00 0.00 0.00 3.62
1404 1421 6.239204 CGACCACCATATTATCAGTAGAACCA 60.239 42.308 0.00 0.00 0.00 3.67
1405 1422 7.067496 ACCACCATATTATCAGTAGAACCAG 57.933 40.000 0.00 0.00 0.00 4.00
1406 1423 6.615726 ACCACCATATTATCAGTAGAACCAGT 59.384 38.462 0.00 0.00 0.00 4.00
1407 1424 7.155328 CCACCATATTATCAGTAGAACCAGTC 58.845 42.308 0.00 0.00 0.00 3.51
1408 1425 7.015682 CCACCATATTATCAGTAGAACCAGTCT 59.984 40.741 0.00 0.00 40.71 3.24
1409 1426 8.085296 CACCATATTATCAGTAGAACCAGTCTC 58.915 40.741 0.00 0.00 37.84 3.36
1410 1427 7.040340 ACCATATTATCAGTAGAACCAGTCTCG 60.040 40.741 0.00 0.00 37.84 4.04
1411 1428 7.040340 CCATATTATCAGTAGAACCAGTCTCGT 60.040 40.741 0.00 0.00 37.84 4.18
1412 1429 5.562506 TTATCAGTAGAACCAGTCTCGTG 57.437 43.478 0.00 0.00 37.84 4.35
1413 1430 2.860009 TCAGTAGAACCAGTCTCGTGT 58.140 47.619 0.00 0.00 37.84 4.49
1414 1431 4.011966 TCAGTAGAACCAGTCTCGTGTA 57.988 45.455 0.00 0.00 37.84 2.90
1415 1432 4.392047 TCAGTAGAACCAGTCTCGTGTAA 58.608 43.478 0.00 0.00 37.84 2.41
1416 1433 4.454847 TCAGTAGAACCAGTCTCGTGTAAG 59.545 45.833 0.00 0.00 37.84 2.34
1417 1434 2.726832 AGAACCAGTCTCGTGTAAGC 57.273 50.000 0.00 0.00 0.00 3.09
1418 1435 1.068472 AGAACCAGTCTCGTGTAAGCG 60.068 52.381 0.00 0.00 0.00 4.68
1419 1436 0.672342 AACCAGTCTCGTGTAAGCGT 59.328 50.000 0.00 0.00 0.00 5.07
1420 1437 1.527034 ACCAGTCTCGTGTAAGCGTA 58.473 50.000 0.00 0.00 0.00 4.42
1421 1438 2.089980 ACCAGTCTCGTGTAAGCGTAT 58.910 47.619 0.00 0.00 0.00 3.06
1422 1439 2.159421 ACCAGTCTCGTGTAAGCGTATG 60.159 50.000 0.00 0.00 0.00 2.39
1423 1440 1.846782 CAGTCTCGTGTAAGCGTATGC 59.153 52.381 0.00 0.00 43.24 3.14
1434 1451 2.585263 GCGTATGCGTAATGTCGGT 58.415 52.632 4.81 0.00 40.81 4.69
1435 1452 0.501435 GCGTATGCGTAATGTCGGTC 59.499 55.000 4.81 0.00 40.81 4.79
1436 1453 1.862815 GCGTATGCGTAATGTCGGTCT 60.863 52.381 4.81 0.00 40.81 3.85
1437 1454 1.779157 CGTATGCGTAATGTCGGTCTG 59.221 52.381 0.00 0.00 0.00 3.51
1438 1455 2.124903 GTATGCGTAATGTCGGTCTGG 58.875 52.381 0.00 0.00 0.00 3.86
1439 1456 0.821517 ATGCGTAATGTCGGTCTGGA 59.178 50.000 0.00 0.00 0.00 3.86
1440 1457 0.108992 TGCGTAATGTCGGTCTGGAC 60.109 55.000 0.00 0.00 37.45 4.02
1449 1466 4.522971 GGTCTGGACCGCTTCATC 57.477 61.111 3.88 0.00 42.29 2.92
1450 1467 1.153349 GGTCTGGACCGCTTCATCC 60.153 63.158 3.88 0.00 42.29 3.51
1451 1468 1.596934 GTCTGGACCGCTTCATCCA 59.403 57.895 0.00 0.00 42.88 3.41
1453 1470 2.268920 TGGACCGCTTCATCCAGC 59.731 61.111 0.00 0.00 40.17 4.85
1454 1471 2.268920 GGACCGCTTCATCCAGCA 59.731 61.111 0.00 0.00 40.09 4.41
1455 1472 1.377202 GGACCGCTTCATCCAGCAA 60.377 57.895 0.00 0.00 40.09 3.91
1456 1473 0.749454 GGACCGCTTCATCCAGCAAT 60.749 55.000 0.00 0.00 40.09 3.56
1457 1474 1.475034 GGACCGCTTCATCCAGCAATA 60.475 52.381 0.00 0.00 40.09 1.90
1458 1475 1.599542 GACCGCTTCATCCAGCAATAC 59.400 52.381 0.00 0.00 40.09 1.89
1459 1476 0.947244 CCGCTTCATCCAGCAATACC 59.053 55.000 0.00 0.00 40.09 2.73
1460 1477 0.583438 CGCTTCATCCAGCAATACCG 59.417 55.000 0.00 0.00 40.09 4.02
1461 1478 1.668419 GCTTCATCCAGCAATACCGT 58.332 50.000 0.00 0.00 39.83 4.83
1462 1479 1.599542 GCTTCATCCAGCAATACCGTC 59.400 52.381 0.00 0.00 39.83 4.79
1463 1480 1.860950 CTTCATCCAGCAATACCGTCG 59.139 52.381 0.00 0.00 0.00 5.12
1464 1481 1.107945 TCATCCAGCAATACCGTCGA 58.892 50.000 0.00 0.00 0.00 4.20
1465 1482 1.478916 TCATCCAGCAATACCGTCGAA 59.521 47.619 0.00 0.00 0.00 3.71
1466 1483 2.102420 TCATCCAGCAATACCGTCGAAT 59.898 45.455 0.00 0.00 0.00 3.34
1467 1484 2.218953 TCCAGCAATACCGTCGAATC 57.781 50.000 0.00 0.00 0.00 2.52
1468 1485 1.478916 TCCAGCAATACCGTCGAATCA 59.521 47.619 0.00 0.00 0.00 2.57
1469 1486 2.102420 TCCAGCAATACCGTCGAATCAT 59.898 45.455 0.00 0.00 0.00 2.45
1470 1487 2.221749 CCAGCAATACCGTCGAATCATG 59.778 50.000 0.00 0.00 0.00 3.07
1471 1488 3.123050 CAGCAATACCGTCGAATCATGA 58.877 45.455 0.00 0.00 0.00 3.07
1472 1489 3.555547 CAGCAATACCGTCGAATCATGAA 59.444 43.478 0.00 0.00 0.00 2.57
1473 1490 4.212004 CAGCAATACCGTCGAATCATGAAT 59.788 41.667 0.00 0.00 0.00 2.57
1474 1491 4.449068 AGCAATACCGTCGAATCATGAATC 59.551 41.667 0.00 0.00 0.00 2.52
1475 1492 4.211164 GCAATACCGTCGAATCATGAATCA 59.789 41.667 11.26 0.00 0.00 2.57
1476 1493 5.277297 GCAATACCGTCGAATCATGAATCAA 60.277 40.000 11.26 0.00 0.00 2.57
1477 1494 5.907197 ATACCGTCGAATCATGAATCAAC 57.093 39.130 11.26 1.68 0.00 3.18
1478 1495 3.861840 ACCGTCGAATCATGAATCAACT 58.138 40.909 11.26 0.00 0.00 3.16
1479 1496 5.006153 ACCGTCGAATCATGAATCAACTA 57.994 39.130 11.26 0.00 0.00 2.24
1480 1497 5.043903 ACCGTCGAATCATGAATCAACTAG 58.956 41.667 11.26 0.29 0.00 2.57
1481 1498 5.043903 CCGTCGAATCATGAATCAACTAGT 58.956 41.667 11.26 0.00 0.00 2.57
1482 1499 5.051441 CCGTCGAATCATGAATCAACTAGTG 60.051 44.000 11.26 0.00 0.00 2.74
1483 1500 5.743872 CGTCGAATCATGAATCAACTAGTGA 59.256 40.000 11.26 0.00 41.67 3.41
1484 1501 6.291322 CGTCGAATCATGAATCAACTAGTGAC 60.291 42.308 11.26 7.01 39.72 3.67
1485 1502 5.743872 TCGAATCATGAATCAACTAGTGACG 59.256 40.000 11.26 0.00 39.72 4.35
1486 1503 5.051441 CGAATCATGAATCAACTAGTGACGG 60.051 44.000 11.26 0.00 39.72 4.79
1487 1504 3.521560 TCATGAATCAACTAGTGACGGC 58.478 45.455 0.00 0.00 39.72 5.68
1488 1505 3.056179 TCATGAATCAACTAGTGACGGCA 60.056 43.478 0.00 0.00 39.72 5.69
1489 1506 3.394674 TGAATCAACTAGTGACGGCAA 57.605 42.857 0.00 0.00 39.72 4.52
1490 1507 3.325870 TGAATCAACTAGTGACGGCAAG 58.674 45.455 0.00 0.00 39.72 4.01
1491 1508 1.726853 ATCAACTAGTGACGGCAAGC 58.273 50.000 0.00 0.00 39.72 4.01
1492 1509 0.391228 TCAACTAGTGACGGCAAGCA 59.609 50.000 0.00 0.00 0.00 3.91
1493 1510 1.202592 TCAACTAGTGACGGCAAGCAA 60.203 47.619 0.00 0.00 0.00 3.91
1494 1511 1.806542 CAACTAGTGACGGCAAGCAAT 59.193 47.619 0.00 0.00 0.00 3.56
1495 1512 3.000041 CAACTAGTGACGGCAAGCAATA 59.000 45.455 0.00 0.00 0.00 1.90
1496 1513 3.543680 ACTAGTGACGGCAAGCAATAT 57.456 42.857 0.00 0.00 0.00 1.28
1497 1514 3.198068 ACTAGTGACGGCAAGCAATATG 58.802 45.455 0.00 0.00 0.00 1.78
1498 1515 2.113860 AGTGACGGCAAGCAATATGT 57.886 45.000 0.00 0.00 0.00 2.29
1499 1516 3.260475 AGTGACGGCAAGCAATATGTA 57.740 42.857 0.00 0.00 0.00 2.29
1500 1517 3.808728 AGTGACGGCAAGCAATATGTAT 58.191 40.909 0.00 0.00 0.00 2.29
1501 1518 4.956085 AGTGACGGCAAGCAATATGTATA 58.044 39.130 0.00 0.00 0.00 1.47
1502 1519 5.551233 AGTGACGGCAAGCAATATGTATAT 58.449 37.500 0.00 0.00 0.00 0.86
1503 1520 6.697395 AGTGACGGCAAGCAATATGTATATA 58.303 36.000 0.00 0.00 0.00 0.86
1504 1521 6.590292 AGTGACGGCAAGCAATATGTATATAC 59.410 38.462 5.89 5.89 0.00 1.47
1505 1522 5.872617 TGACGGCAAGCAATATGTATATACC 59.127 40.000 10.38 0.00 0.00 2.73
1506 1523 5.183228 ACGGCAAGCAATATGTATATACCC 58.817 41.667 10.38 0.00 0.00 3.69
1507 1524 5.182487 CGGCAAGCAATATGTATATACCCA 58.818 41.667 10.38 0.00 0.00 4.51
1508 1525 5.064707 CGGCAAGCAATATGTATATACCCAC 59.935 44.000 10.38 0.00 0.00 4.61
1509 1526 5.064707 GGCAAGCAATATGTATATACCCACG 59.935 44.000 10.38 0.00 0.00 4.94
1510 1527 5.447279 GCAAGCAATATGTATATACCCACGC 60.447 44.000 10.38 6.81 0.00 5.34
1511 1528 4.766375 AGCAATATGTATATACCCACGCC 58.234 43.478 10.38 0.00 0.00 5.68
1512 1529 3.875134 GCAATATGTATATACCCACGCCC 59.125 47.826 10.38 0.00 0.00 6.13
1513 1530 4.624364 GCAATATGTATATACCCACGCCCA 60.624 45.833 10.38 0.00 0.00 5.36
1514 1531 4.748277 ATATGTATATACCCACGCCCAC 57.252 45.455 10.38 0.00 0.00 4.61
1515 1532 1.790818 TGTATATACCCACGCCCACA 58.209 50.000 10.38 0.00 0.00 4.17
1516 1533 2.117051 TGTATATACCCACGCCCACAA 58.883 47.619 10.38 0.00 0.00 3.33
1517 1534 2.158928 TGTATATACCCACGCCCACAAC 60.159 50.000 10.38 0.00 0.00 3.32
1518 1535 1.209621 ATATACCCACGCCCACAACT 58.790 50.000 0.00 0.00 0.00 3.16
1519 1536 0.538118 TATACCCACGCCCACAACTC 59.462 55.000 0.00 0.00 0.00 3.01
1520 1537 2.193087 ATACCCACGCCCACAACTCC 62.193 60.000 0.00 0.00 0.00 3.85
1521 1538 3.953775 CCCACGCCCACAACTCCT 61.954 66.667 0.00 0.00 0.00 3.69
1522 1539 2.113139 CCACGCCCACAACTCCTT 59.887 61.111 0.00 0.00 0.00 3.36
1523 1540 1.528309 CCACGCCCACAACTCCTTT 60.528 57.895 0.00 0.00 0.00 3.11
1524 1541 1.654220 CACGCCCACAACTCCTTTG 59.346 57.895 0.00 0.00 41.49 2.77
1535 1552 3.940303 CAACTCCTTTGTGTTCAACTCG 58.060 45.455 0.00 0.00 32.93 4.18
1536 1553 3.261981 ACTCCTTTGTGTTCAACTCGT 57.738 42.857 0.00 0.00 32.93 4.18
1537 1554 2.936498 ACTCCTTTGTGTTCAACTCGTG 59.064 45.455 0.00 0.00 32.93 4.35
1538 1555 1.668751 TCCTTTGTGTTCAACTCGTGC 59.331 47.619 0.00 0.00 32.93 5.34
1539 1556 1.400142 CCTTTGTGTTCAACTCGTGCA 59.600 47.619 0.00 0.00 32.93 4.57
1540 1557 2.033299 CCTTTGTGTTCAACTCGTGCAT 59.967 45.455 0.00 0.00 32.93 3.96
1541 1558 3.249799 CCTTTGTGTTCAACTCGTGCATA 59.750 43.478 0.00 0.00 32.93 3.14
1542 1559 4.083324 CCTTTGTGTTCAACTCGTGCATAT 60.083 41.667 0.00 0.00 32.93 1.78
1543 1560 5.121611 CCTTTGTGTTCAACTCGTGCATATA 59.878 40.000 0.00 0.00 32.93 0.86
1544 1561 6.348132 CCTTTGTGTTCAACTCGTGCATATAA 60.348 38.462 0.00 0.00 32.93 0.98
1545 1562 5.524511 TGTGTTCAACTCGTGCATATAAC 57.475 39.130 0.00 0.00 0.00 1.89
1546 1563 4.991687 TGTGTTCAACTCGTGCATATAACA 59.008 37.500 0.00 0.00 0.00 2.41
1547 1564 5.641636 TGTGTTCAACTCGTGCATATAACAT 59.358 36.000 0.00 0.00 0.00 2.71
1548 1565 6.183360 TGTGTTCAACTCGTGCATATAACATC 60.183 38.462 0.00 0.00 0.00 3.06
1549 1566 6.036083 GTGTTCAACTCGTGCATATAACATCT 59.964 38.462 0.00 0.00 0.00 2.90
1550 1567 7.222031 GTGTTCAACTCGTGCATATAACATCTA 59.778 37.037 0.00 0.00 0.00 1.98
1551 1568 7.222031 TGTTCAACTCGTGCATATAACATCTAC 59.778 37.037 0.00 0.00 0.00 2.59
1552 1569 5.912955 TCAACTCGTGCATATAACATCTACG 59.087 40.000 0.00 0.00 0.00 3.51
1553 1570 4.227538 ACTCGTGCATATAACATCTACGC 58.772 43.478 0.00 0.00 0.00 4.42
1554 1571 3.231160 TCGTGCATATAACATCTACGCG 58.769 45.455 3.53 3.53 0.00 6.01
1555 1572 2.977829 CGTGCATATAACATCTACGCGT 59.022 45.455 19.17 19.17 0.00 6.01
1556 1573 4.083908 TCGTGCATATAACATCTACGCGTA 60.084 41.667 19.40 19.40 0.00 4.42
1557 1574 4.259964 CGTGCATATAACATCTACGCGTAG 59.740 45.833 34.93 34.93 34.56 3.51
1558 1575 5.388111 GTGCATATAACATCTACGCGTAGA 58.612 41.667 41.51 41.51 45.24 2.59
1559 1576 5.283247 GTGCATATAACATCTACGCGTAGAC 59.717 44.000 42.16 28.30 44.11 2.59
1560 1577 4.792189 GCATATAACATCTACGCGTAGACC 59.208 45.833 42.16 21.27 44.11 3.85
1561 1578 5.391736 GCATATAACATCTACGCGTAGACCT 60.392 44.000 42.16 31.24 44.11 3.85
1562 1579 2.846039 AACATCTACGCGTAGACCTG 57.154 50.000 42.16 36.96 44.11 4.00
1563 1580 1.022735 ACATCTACGCGTAGACCTGG 58.977 55.000 42.16 32.37 44.11 4.45
1564 1581 0.317938 CATCTACGCGTAGACCTGGC 60.318 60.000 42.16 0.00 44.11 4.85
1565 1582 0.465824 ATCTACGCGTAGACCTGGCT 60.466 55.000 42.16 26.92 44.11 4.75
1566 1583 1.094073 TCTACGCGTAGACCTGGCTC 61.094 60.000 37.98 0.00 37.28 4.70
1567 1584 2.376231 CTACGCGTAGACCTGGCTCG 62.376 65.000 36.87 10.28 35.21 5.03
1568 1585 4.554363 CGCGTAGACCTGGCTCGG 62.554 72.222 0.00 0.00 0.00 4.63
1569 1586 3.138798 GCGTAGACCTGGCTCGGA 61.139 66.667 0.00 0.00 0.00 4.55
1570 1587 2.491022 GCGTAGACCTGGCTCGGAT 61.491 63.158 0.00 0.00 0.00 4.18
1571 1588 1.360551 CGTAGACCTGGCTCGGATG 59.639 63.158 0.00 0.00 0.00 3.51
1572 1589 1.068250 GTAGACCTGGCTCGGATGC 59.932 63.158 0.00 0.00 0.00 3.91
1580 1597 3.181367 GCTCGGATGCCACTGTTG 58.819 61.111 0.00 0.00 0.00 3.33
1582 1599 1.746615 CTCGGATGCCACTGTTGGG 60.747 63.158 0.00 0.00 44.15 4.12
1583 1600 2.751436 CGGATGCCACTGTTGGGG 60.751 66.667 0.00 0.00 44.15 4.96
1584 1601 2.763215 GGATGCCACTGTTGGGGA 59.237 61.111 0.00 0.00 44.15 4.81
1585 1602 1.076549 GGATGCCACTGTTGGGGAA 59.923 57.895 0.00 0.00 44.15 3.97
1586 1603 1.250840 GGATGCCACTGTTGGGGAAC 61.251 60.000 0.00 0.00 44.15 3.62
1587 1604 1.586154 GATGCCACTGTTGGGGAACG 61.586 60.000 0.00 0.00 44.15 3.95
1588 1605 3.670377 GCCACTGTTGGGGAACGC 61.670 66.667 0.00 0.00 44.15 4.84
1711 1729 1.809133 TGGGACTAACCTGTTGACCA 58.191 50.000 0.00 0.00 38.98 4.02
1783 1802 6.472887 AGAAAAGGAATATCAAACGGAGTCA 58.527 36.000 0.00 0.00 45.00 3.41
1799 1818 3.316868 GGAGTCAAAACGGAATGAAACCA 59.683 43.478 0.00 0.00 0.00 3.67
1944 1966 4.052518 CCCTTGTGGCTCCCCTGG 62.053 72.222 0.00 0.00 0.00 4.45
1994 2020 0.538584 ACCCTAAAACGATCGGGGAC 59.461 55.000 26.92 0.00 41.11 4.46
2097 2127 1.689582 GGGAATCCCTCTCCGGTGT 60.690 63.158 11.95 0.00 41.34 4.16
2199 2235 3.351740 TGCGTTTGATCTCTCTCTCTCT 58.648 45.455 0.00 0.00 0.00 3.10
2200 2236 3.376859 TGCGTTTGATCTCTCTCTCTCTC 59.623 47.826 0.00 0.00 0.00 3.20
2228 2270 4.765339 TCTCTCGTGTTCTTGAGGTGATAA 59.235 41.667 0.00 0.00 33.00 1.75
2271 2313 8.614469 AGCTTTGCTATTATAGTTGGATCTTC 57.386 34.615 0.94 0.00 36.99 2.87
2336 2378 9.244292 GAGTTTCCCCTTTGAAGTTATCTTATT 57.756 33.333 0.00 0.00 33.64 1.40
2339 2381 6.431722 TCCCCTTTGAAGTTATCTTATTGGG 58.568 40.000 0.00 0.00 33.64 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 0.175073 AGGGACACGGCTATTCGAAC 59.825 55.000 0.00 0.00 0.00 3.95
201 204 3.654414 GATCATCGGGTTGTATCTGTCC 58.346 50.000 0.00 0.00 0.00 4.02
203 206 2.545952 GCGATCATCGGGTTGTATCTGT 60.546 50.000 9.59 0.00 40.84 3.41
217 220 1.039068 CCCTGTGAGAGAGCGATCAT 58.961 55.000 2.38 0.00 0.00 2.45
242 245 2.599139 CTACCCGGTGATCCTCCCCA 62.599 65.000 0.00 0.00 0.00 4.96
253 256 3.698040 CGTATAGCATAATCCTACCCGGT 59.302 47.826 0.00 0.00 0.00 5.28
290 293 9.145865 GCATATAAAAGAGAGTAGATGGTAAGC 57.854 37.037 0.00 0.00 0.00 3.09
309 312 4.318332 CGCCTCCATCTTGAAGCATATAA 58.682 43.478 0.00 0.00 0.00 0.98
331 334 2.094130 AGTAAAGACTACGCTTCTGGCC 60.094 50.000 0.00 0.00 33.52 5.36
351 354 2.923629 AGAGGGGGATAGCTAGTCCTAG 59.076 54.545 16.79 0.00 36.00 3.02
389 392 4.259356 GGGTAGTATTTGTGGACTGAACC 58.741 47.826 0.00 0.00 0.00 3.62
402 405 7.387265 TGGTATCAATGACATGGGTAGTATT 57.613 36.000 0.00 0.00 0.00 1.89
567 575 0.784778 CTCGAAGTCAAACTCCACGC 59.215 55.000 0.00 0.00 0.00 5.34
615 623 1.606606 CAACGATCAAAAAGGCGAGC 58.393 50.000 0.00 0.00 0.00 5.03
726 734 3.545703 CCAGAGGGCTCGAATACAAATT 58.454 45.455 0.00 0.00 34.09 1.82
779 796 3.702330 TCACAACACAACTCTAGACACG 58.298 45.455 0.00 0.00 0.00 4.49
904 921 1.264045 TGTCCCATGGCGATGTGAGA 61.264 55.000 6.09 0.00 0.00 3.27
931 948 6.013984 TCCTTAAGATCCTCGTGGTAAACTTT 60.014 38.462 3.36 0.00 34.23 2.66
943 960 5.836358 AGTAGATGGTGTCCTTAAGATCCTC 59.164 44.000 3.36 1.79 0.00 3.71
1043 1060 2.955660 TGAATGTGTTGGTTCAACTCCC 59.044 45.455 11.36 1.96 43.85 4.30
1121 1138 3.987745 TCCTCTTCTAGCTCCATGTTCT 58.012 45.455 0.00 0.00 0.00 3.01
1304 1321 8.008279 CGTCTTCATAATCATCATCATTGTCAC 58.992 37.037 0.00 0.00 0.00 3.67
1402 1419 2.451132 CATACGCTTACACGAGACTGG 58.549 52.381 0.00 0.00 36.70 4.00
1403 1420 1.846782 GCATACGCTTACACGAGACTG 59.153 52.381 0.00 0.00 36.70 3.51
1404 1421 1.531264 CGCATACGCTTACACGAGACT 60.531 52.381 0.00 0.00 36.70 3.24
1405 1422 0.838229 CGCATACGCTTACACGAGAC 59.162 55.000 0.00 0.00 36.70 3.36
1406 1423 0.448990 ACGCATACGCTTACACGAGA 59.551 50.000 0.00 0.00 45.53 4.04
1407 1424 2.095384 TACGCATACGCTTACACGAG 57.905 50.000 0.00 0.00 45.53 4.18
1408 1425 2.541055 TTACGCATACGCTTACACGA 57.459 45.000 0.00 0.00 45.53 4.35
1409 1426 2.532723 ACATTACGCATACGCTTACACG 59.467 45.455 0.00 0.00 45.53 4.49
1410 1427 3.360384 CGACATTACGCATACGCTTACAC 60.360 47.826 0.00 0.00 45.53 2.90
1411 1428 2.784928 CGACATTACGCATACGCTTACA 59.215 45.455 0.00 0.00 45.53 2.41
1412 1429 2.152489 CCGACATTACGCATACGCTTAC 59.848 50.000 0.00 0.00 45.53 2.34
1413 1430 2.223548 ACCGACATTACGCATACGCTTA 60.224 45.455 0.00 0.00 45.53 3.09
1414 1431 1.205657 CCGACATTACGCATACGCTT 58.794 50.000 0.00 0.00 45.53 4.68
1415 1432 0.101759 ACCGACATTACGCATACGCT 59.898 50.000 0.00 0.00 45.53 5.07
1416 1433 0.501435 GACCGACATTACGCATACGC 59.499 55.000 0.00 0.00 45.53 4.42
1418 1435 2.124903 CCAGACCGACATTACGCATAC 58.875 52.381 0.00 0.00 0.00 2.39
1419 1436 2.025898 TCCAGACCGACATTACGCATA 58.974 47.619 0.00 0.00 0.00 3.14
1420 1437 0.821517 TCCAGACCGACATTACGCAT 59.178 50.000 0.00 0.00 0.00 4.73
1421 1438 0.108992 GTCCAGACCGACATTACGCA 60.109 55.000 0.00 0.00 32.74 5.24
1422 1439 0.804933 GGTCCAGACCGACATTACGC 60.805 60.000 0.05 0.00 42.29 4.42
1423 1440 3.340727 GGTCCAGACCGACATTACG 57.659 57.895 0.05 0.00 42.29 3.18
1433 1450 1.596934 TGGATGAAGCGGTCCAGAC 59.403 57.895 0.00 0.00 39.51 3.51
1434 1451 4.128580 TGGATGAAGCGGTCCAGA 57.871 55.556 0.00 0.00 39.51 3.86
1436 1453 2.123248 TTGCTGGATGAAGCGGTCCA 62.123 55.000 0.00 0.00 46.65 4.02
1437 1454 0.749454 ATTGCTGGATGAAGCGGTCC 60.749 55.000 0.00 0.00 46.65 4.46
1438 1455 1.599542 GTATTGCTGGATGAAGCGGTC 59.400 52.381 0.00 0.00 46.65 4.79
1439 1456 1.668419 GTATTGCTGGATGAAGCGGT 58.332 50.000 0.00 0.00 46.65 5.68
1440 1457 0.947244 GGTATTGCTGGATGAAGCGG 59.053 55.000 0.00 0.00 46.65 5.52
1441 1458 0.583438 CGGTATTGCTGGATGAAGCG 59.417 55.000 0.00 0.00 46.65 4.68
1442 1459 1.599542 GACGGTATTGCTGGATGAAGC 59.400 52.381 0.00 0.00 43.82 3.86
1443 1460 1.860950 CGACGGTATTGCTGGATGAAG 59.139 52.381 0.00 0.00 0.00 3.02
1444 1461 1.478916 TCGACGGTATTGCTGGATGAA 59.521 47.619 0.00 0.00 0.00 2.57
1445 1462 1.107945 TCGACGGTATTGCTGGATGA 58.892 50.000 0.00 0.00 0.00 2.92
1446 1463 1.934589 TTCGACGGTATTGCTGGATG 58.065 50.000 0.00 0.00 0.00 3.51
1447 1464 2.102420 TGATTCGACGGTATTGCTGGAT 59.898 45.455 0.00 0.00 0.00 3.41
1448 1465 1.478916 TGATTCGACGGTATTGCTGGA 59.521 47.619 0.00 0.00 0.00 3.86
1449 1466 1.934589 TGATTCGACGGTATTGCTGG 58.065 50.000 0.00 0.00 0.00 4.85
1450 1467 3.123050 TCATGATTCGACGGTATTGCTG 58.877 45.455 0.00 0.00 0.00 4.41
1451 1468 3.452755 TCATGATTCGACGGTATTGCT 57.547 42.857 0.00 0.00 0.00 3.91
1452 1469 4.211164 TGATTCATGATTCGACGGTATTGC 59.789 41.667 11.83 0.00 0.00 3.56
1453 1470 5.905480 TGATTCATGATTCGACGGTATTG 57.095 39.130 11.83 0.00 0.00 1.90
1454 1471 6.049149 AGTTGATTCATGATTCGACGGTATT 58.951 36.000 23.11 10.02 32.89 1.89
1455 1472 5.601662 AGTTGATTCATGATTCGACGGTAT 58.398 37.500 23.11 10.29 32.89 2.73
1456 1473 5.006153 AGTTGATTCATGATTCGACGGTA 57.994 39.130 23.11 2.00 32.89 4.02
1457 1474 3.861840 AGTTGATTCATGATTCGACGGT 58.138 40.909 23.11 11.08 32.89 4.83
1458 1475 5.043903 ACTAGTTGATTCATGATTCGACGG 58.956 41.667 23.11 21.43 32.89 4.79
1459 1476 5.743872 TCACTAGTTGATTCATGATTCGACG 59.256 40.000 23.11 16.20 32.89 5.12
1460 1477 6.291322 CGTCACTAGTTGATTCATGATTCGAC 60.291 42.308 22.43 22.43 36.32 4.20
1461 1478 5.743872 CGTCACTAGTTGATTCATGATTCGA 59.256 40.000 11.83 8.01 36.32 3.71
1462 1479 5.051441 CCGTCACTAGTTGATTCATGATTCG 60.051 44.000 11.83 1.78 36.32 3.34
1463 1480 5.277058 GCCGTCACTAGTTGATTCATGATTC 60.277 44.000 10.10 10.10 36.32 2.52
1464 1481 4.572389 GCCGTCACTAGTTGATTCATGATT 59.428 41.667 0.00 0.00 36.32 2.57
1465 1482 4.122776 GCCGTCACTAGTTGATTCATGAT 58.877 43.478 0.00 0.00 36.32 2.45
1466 1483 3.056179 TGCCGTCACTAGTTGATTCATGA 60.056 43.478 0.00 0.00 36.32 3.07
1467 1484 3.261580 TGCCGTCACTAGTTGATTCATG 58.738 45.455 0.00 0.00 36.32 3.07
1468 1485 3.610040 TGCCGTCACTAGTTGATTCAT 57.390 42.857 0.00 0.00 36.32 2.57
1469 1486 3.325870 CTTGCCGTCACTAGTTGATTCA 58.674 45.455 0.00 0.00 36.32 2.57
1470 1487 2.094417 GCTTGCCGTCACTAGTTGATTC 59.906 50.000 0.00 0.00 36.32 2.52
1471 1488 2.076863 GCTTGCCGTCACTAGTTGATT 58.923 47.619 0.00 0.00 36.32 2.57
1472 1489 1.001974 TGCTTGCCGTCACTAGTTGAT 59.998 47.619 0.00 0.00 36.32 2.57
1473 1490 0.391228 TGCTTGCCGTCACTAGTTGA 59.609 50.000 0.00 0.00 0.00 3.18
1474 1491 1.225855 TTGCTTGCCGTCACTAGTTG 58.774 50.000 0.00 0.00 0.00 3.16
1475 1492 2.185004 ATTGCTTGCCGTCACTAGTT 57.815 45.000 0.00 0.00 0.00 2.24
1476 1493 3.198068 CATATTGCTTGCCGTCACTAGT 58.802 45.455 0.00 0.00 0.00 2.57
1477 1494 3.198068 ACATATTGCTTGCCGTCACTAG 58.802 45.455 0.00 0.00 0.00 2.57
1478 1495 3.260475 ACATATTGCTTGCCGTCACTA 57.740 42.857 0.00 0.00 0.00 2.74
1479 1496 2.113860 ACATATTGCTTGCCGTCACT 57.886 45.000 0.00 0.00 0.00 3.41
1480 1497 5.862924 ATATACATATTGCTTGCCGTCAC 57.137 39.130 0.00 0.00 0.00 3.67
1481 1498 5.872617 GGTATATACATATTGCTTGCCGTCA 59.127 40.000 14.70 0.00 0.00 4.35
1482 1499 5.293569 GGGTATATACATATTGCTTGCCGTC 59.706 44.000 14.70 0.00 0.00 4.79
1483 1500 5.183228 GGGTATATACATATTGCTTGCCGT 58.817 41.667 14.70 0.00 0.00 5.68
1484 1501 5.064707 GTGGGTATATACATATTGCTTGCCG 59.935 44.000 14.70 0.00 0.00 5.69
1485 1502 5.064707 CGTGGGTATATACATATTGCTTGCC 59.935 44.000 14.70 3.37 0.00 4.52
1486 1503 5.447279 GCGTGGGTATATACATATTGCTTGC 60.447 44.000 14.70 2.62 0.00 4.01
1487 1504 5.064707 GGCGTGGGTATATACATATTGCTTG 59.935 44.000 14.70 0.00 0.00 4.01
1488 1505 5.183228 GGCGTGGGTATATACATATTGCTT 58.817 41.667 14.70 0.00 0.00 3.91
1489 1506 4.383770 GGGCGTGGGTATATACATATTGCT 60.384 45.833 14.70 0.00 0.00 3.91
1490 1507 3.875134 GGGCGTGGGTATATACATATTGC 59.125 47.826 14.70 10.52 0.00 3.56
1491 1508 4.873827 GTGGGCGTGGGTATATACATATTG 59.126 45.833 14.70 1.86 0.00 1.90
1492 1509 4.532916 TGTGGGCGTGGGTATATACATATT 59.467 41.667 14.70 0.00 0.00 1.28
1493 1510 4.098155 TGTGGGCGTGGGTATATACATAT 58.902 43.478 14.70 0.00 0.00 1.78
1494 1511 3.508426 TGTGGGCGTGGGTATATACATA 58.492 45.455 14.70 0.07 0.00 2.29
1495 1512 2.331166 TGTGGGCGTGGGTATATACAT 58.669 47.619 14.70 0.00 0.00 2.29
1496 1513 1.790818 TGTGGGCGTGGGTATATACA 58.209 50.000 14.70 0.00 0.00 2.29
1497 1514 2.103601 AGTTGTGGGCGTGGGTATATAC 59.896 50.000 4.14 4.14 0.00 1.47
1498 1515 2.366266 GAGTTGTGGGCGTGGGTATATA 59.634 50.000 0.00 0.00 0.00 0.86
1499 1516 1.140252 GAGTTGTGGGCGTGGGTATAT 59.860 52.381 0.00 0.00 0.00 0.86
1500 1517 0.538118 GAGTTGTGGGCGTGGGTATA 59.462 55.000 0.00 0.00 0.00 1.47
1501 1518 1.298667 GAGTTGTGGGCGTGGGTAT 59.701 57.895 0.00 0.00 0.00 2.73
1502 1519 2.745037 GAGTTGTGGGCGTGGGTA 59.255 61.111 0.00 0.00 0.00 3.69
1503 1520 4.265056 GGAGTTGTGGGCGTGGGT 62.265 66.667 0.00 0.00 0.00 4.51
1504 1521 2.976494 AAAGGAGTTGTGGGCGTGGG 62.976 60.000 0.00 0.00 0.00 4.61
1505 1522 1.528309 AAAGGAGTTGTGGGCGTGG 60.528 57.895 0.00 0.00 0.00 4.94
1506 1523 1.654220 CAAAGGAGTTGTGGGCGTG 59.346 57.895 0.00 0.00 32.08 5.34
1507 1524 4.157607 CAAAGGAGTTGTGGGCGT 57.842 55.556 0.00 0.00 32.08 5.68
1514 1531 3.374058 ACGAGTTGAACACAAAGGAGTTG 59.626 43.478 0.00 0.00 43.43 3.16
1515 1532 3.374058 CACGAGTTGAACACAAAGGAGTT 59.626 43.478 0.00 0.00 0.00 3.01
1516 1533 2.936498 CACGAGTTGAACACAAAGGAGT 59.064 45.455 0.00 0.00 0.00 3.85
1517 1534 2.286418 GCACGAGTTGAACACAAAGGAG 60.286 50.000 0.00 0.00 0.00 3.69
1518 1535 1.668751 GCACGAGTTGAACACAAAGGA 59.331 47.619 0.00 0.00 0.00 3.36
1519 1536 1.400142 TGCACGAGTTGAACACAAAGG 59.600 47.619 0.00 0.00 0.00 3.11
1520 1537 2.823196 TGCACGAGTTGAACACAAAG 57.177 45.000 0.00 0.00 0.00 2.77
1521 1538 6.017852 TGTTATATGCACGAGTTGAACACAAA 60.018 34.615 0.00 0.00 0.00 2.83
1522 1539 5.467063 TGTTATATGCACGAGTTGAACACAA 59.533 36.000 0.00 0.00 0.00 3.33
1523 1540 4.991687 TGTTATATGCACGAGTTGAACACA 59.008 37.500 0.00 0.00 0.00 3.72
1524 1541 5.524511 TGTTATATGCACGAGTTGAACAC 57.475 39.130 0.00 0.00 0.00 3.32
1525 1542 6.106003 AGATGTTATATGCACGAGTTGAACA 58.894 36.000 0.00 0.00 0.00 3.18
1526 1543 6.589830 AGATGTTATATGCACGAGTTGAAC 57.410 37.500 0.00 0.00 0.00 3.18
1527 1544 6.416750 CGTAGATGTTATATGCACGAGTTGAA 59.583 38.462 0.00 0.00 0.00 2.69
1528 1545 5.912955 CGTAGATGTTATATGCACGAGTTGA 59.087 40.000 0.00 0.00 0.00 3.18
1529 1546 5.387444 GCGTAGATGTTATATGCACGAGTTG 60.387 44.000 0.00 0.00 35.62 3.16
1530 1547 4.680110 GCGTAGATGTTATATGCACGAGTT 59.320 41.667 0.00 0.00 35.62 3.01
1531 1548 4.227538 GCGTAGATGTTATATGCACGAGT 58.772 43.478 0.00 0.00 35.62 4.18
1532 1549 3.298239 CGCGTAGATGTTATATGCACGAG 59.702 47.826 0.00 0.00 35.33 4.18
1533 1550 3.231160 CGCGTAGATGTTATATGCACGA 58.769 45.455 0.00 0.00 35.33 4.35
1534 1551 2.977829 ACGCGTAGATGTTATATGCACG 59.022 45.455 11.67 0.00 35.33 5.34
1535 1552 5.283247 GTCTACGCGTAGATGTTATATGCAC 59.717 44.000 41.73 25.34 43.32 4.57
1536 1553 5.388111 GTCTACGCGTAGATGTTATATGCA 58.612 41.667 41.73 19.49 43.32 3.96
1537 1554 4.792189 GGTCTACGCGTAGATGTTATATGC 59.208 45.833 41.73 27.94 43.32 3.14
1538 1555 6.022208 CAGGTCTACGCGTAGATGTTATATG 58.978 44.000 41.73 28.30 43.32 1.78
1539 1556 5.123502 CCAGGTCTACGCGTAGATGTTATAT 59.876 44.000 41.73 23.58 43.32 0.86
1540 1557 4.453478 CCAGGTCTACGCGTAGATGTTATA 59.547 45.833 41.73 21.99 43.32 0.98
1541 1558 3.252701 CCAGGTCTACGCGTAGATGTTAT 59.747 47.826 41.73 26.17 43.32 1.89
1542 1559 2.615447 CCAGGTCTACGCGTAGATGTTA 59.385 50.000 41.73 23.35 43.32 2.41
1543 1560 1.404391 CCAGGTCTACGCGTAGATGTT 59.596 52.381 41.73 29.27 43.32 2.71
1544 1561 1.022735 CCAGGTCTACGCGTAGATGT 58.977 55.000 41.73 31.07 43.32 3.06
1545 1562 0.317938 GCCAGGTCTACGCGTAGATG 60.318 60.000 41.73 35.35 43.32 2.90
1546 1563 0.465824 AGCCAGGTCTACGCGTAGAT 60.466 55.000 41.73 28.96 43.32 1.98
1547 1564 1.077930 AGCCAGGTCTACGCGTAGA 60.078 57.895 37.98 37.98 39.67 2.59
1548 1565 1.355916 GAGCCAGGTCTACGCGTAG 59.644 63.158 34.93 34.93 34.56 3.51
1549 1566 2.466982 CGAGCCAGGTCTACGCGTA 61.467 63.158 19.40 19.40 0.00 4.42
1550 1567 3.812019 CGAGCCAGGTCTACGCGT 61.812 66.667 19.17 19.17 0.00 6.01
1551 1568 4.554363 CCGAGCCAGGTCTACGCG 62.554 72.222 3.53 3.53 0.00 6.01
1552 1569 2.491022 ATCCGAGCCAGGTCTACGC 61.491 63.158 0.00 0.00 0.00 4.42
1553 1570 1.360551 CATCCGAGCCAGGTCTACG 59.639 63.158 0.00 0.00 0.00 3.51
1554 1571 1.068250 GCATCCGAGCCAGGTCTAC 59.932 63.158 0.00 0.00 0.00 2.59
1555 1572 3.538614 GCATCCGAGCCAGGTCTA 58.461 61.111 0.00 0.00 0.00 2.59
1563 1580 2.401766 CCAACAGTGGCATCCGAGC 61.402 63.158 0.00 0.00 38.35 5.03
1564 1581 1.746615 CCCAACAGTGGCATCCGAG 60.747 63.158 0.00 0.00 44.46 4.63
1565 1582 2.350895 CCCAACAGTGGCATCCGA 59.649 61.111 0.00 0.00 44.46 4.55
1566 1583 2.751436 CCCCAACAGTGGCATCCG 60.751 66.667 0.00 0.00 44.46 4.18
1567 1584 1.076549 TTCCCCAACAGTGGCATCC 59.923 57.895 0.00 0.00 44.46 3.51
1568 1585 1.586154 CGTTCCCCAACAGTGGCATC 61.586 60.000 0.00 0.00 44.46 3.91
1569 1586 1.603455 CGTTCCCCAACAGTGGCAT 60.603 57.895 0.00 0.00 44.46 4.40
1570 1587 2.203280 CGTTCCCCAACAGTGGCA 60.203 61.111 0.00 0.00 44.46 4.92
1571 1588 3.670377 GCGTTCCCCAACAGTGGC 61.670 66.667 0.00 0.00 44.46 5.01
1572 1589 2.203280 TGCGTTCCCCAACAGTGG 60.203 61.111 0.00 0.00 45.53 4.00
1573 1590 1.525995 ACTGCGTTCCCCAACAGTG 60.526 57.895 0.00 0.00 41.63 3.66
1574 1591 1.525995 CACTGCGTTCCCCAACAGT 60.526 57.895 0.00 0.00 43.92 3.55
1575 1592 0.606401 ATCACTGCGTTCCCCAACAG 60.606 55.000 0.00 0.00 36.22 3.16
1576 1593 0.687920 TATCACTGCGTTCCCCAACA 59.312 50.000 0.00 0.00 32.14 3.33
1577 1594 1.084289 GTATCACTGCGTTCCCCAAC 58.916 55.000 0.00 0.00 0.00 3.77
1578 1595 0.390603 CGTATCACTGCGTTCCCCAA 60.391 55.000 0.00 0.00 0.00 4.12
1579 1596 1.216977 CGTATCACTGCGTTCCCCA 59.783 57.895 0.00 0.00 0.00 4.96
1580 1597 0.804933 GACGTATCACTGCGTTCCCC 60.805 60.000 0.00 0.00 44.02 4.81
1581 1598 0.172803 AGACGTATCACTGCGTTCCC 59.827 55.000 0.00 0.00 44.02 3.97
1582 1599 1.546834 GAGACGTATCACTGCGTTCC 58.453 55.000 5.07 0.00 44.02 3.62
1583 1600 1.135489 TGGAGACGTATCACTGCGTTC 60.135 52.381 12.92 0.00 44.02 3.95
1584 1601 0.885879 TGGAGACGTATCACTGCGTT 59.114 50.000 12.92 0.00 44.02 4.84
1585 1602 0.885879 TTGGAGACGTATCACTGCGT 59.114 50.000 12.92 0.00 46.75 5.24
1586 1603 1.269166 GTTGGAGACGTATCACTGCG 58.731 55.000 12.92 0.00 36.47 5.18
1587 1604 1.269166 CGTTGGAGACGTATCACTGC 58.731 55.000 12.92 0.00 46.49 4.40
1704 1722 1.518903 GCACTGGGCTCTTGGTCAAC 61.519 60.000 0.00 0.00 40.25 3.18
1711 1729 1.004440 GAACTCGCACTGGGCTCTT 60.004 57.895 0.00 0.00 41.67 2.85
1783 1802 6.472887 TCTCTAGATGGTTTCATTCCGTTTT 58.527 36.000 0.00 0.00 32.98 2.43
1994 2020 3.113260 GGAACTCCCGATCTATTGTGG 57.887 52.381 0.00 0.00 0.00 4.17
2018 2044 2.058595 GGCTACGGAGGCTTCTGGA 61.059 63.158 15.23 0.00 44.83 3.86
2097 2127 1.417517 CACCGGGATGATGAAGATGGA 59.582 52.381 6.32 0.00 0.00 3.41
2153 2183 1.952621 ACTGGTACATACCCACAGCT 58.047 50.000 5.62 0.00 45.87 4.24
2158 2188 3.576982 GCATAGCTACTGGTACATACCCA 59.423 47.826 5.62 0.00 45.87 4.51
2180 2210 5.118990 AGAGAGAGAGAGAGAGATCAAACG 58.881 45.833 0.00 0.00 0.00 3.60
2199 2235 4.000325 CTCAAGAACACGAGAGAGAGAGA 59.000 47.826 0.00 0.00 0.00 3.10
2200 2236 3.126858 CCTCAAGAACACGAGAGAGAGAG 59.873 52.174 0.00 0.00 0.00 3.20
2228 2270 2.556189 AGCTCGCGATACATCAAGATCT 59.444 45.455 10.36 0.00 0.00 2.75
2271 2313 3.728385 AGAGGGGGAAGAAAACATCAG 57.272 47.619 0.00 0.00 0.00 2.90
2336 2378 7.287061 TCTCAAATCTTTAAAGACTCAACCCA 58.713 34.615 19.94 0.00 37.98 4.51
2339 2381 9.439537 GTGTTCTCAAATCTTTAAAGACTCAAC 57.560 33.333 19.94 15.38 37.98 3.18


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

AutoCloner maintained by Alex Coulton.