Multiple sequence alignment - TraesCS7A01G380500

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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 TraesCS7A01G380500 chr7A 100.000 4459 0 0 1 4459 555936130 555940588 0.000000e+00 8235.0
1 TraesCS7A01G380500 chr7A 90.330 455 42 2 1 454 98542804 98542351 2.970000e-166 595.0
2 TraesCS7A01G380500 chr7A 81.340 209 16 4 620 805 98542361 98542153 9.990000e-32 148.0
3 TraesCS7A01G380500 chr7A 86.555 119 12 3 3715 3832 270772579 270772694 1.300000e-25 128.0
4 TraesCS7A01G380500 chr7D 97.790 1403 28 3 2387 3788 488546189 488547589 0.000000e+00 2416.0
5 TraesCS7A01G380500 chr7D 92.583 1591 68 16 809 2388 488544589 488546140 0.000000e+00 2239.0
6 TraesCS7A01G380500 chr7D 90.980 255 16 2 4212 4459 488550687 488550941 1.990000e-88 337.0
7 TraesCS7A01G380500 chr7D 86.029 136 14 5 453 588 88455675 88455805 1.670000e-29 141.0
8 TraesCS7A01G380500 chr7D 87.395 119 11 3 3715 3832 250669805 250669690 2.800000e-27 134.0
9 TraesCS7A01G380500 chr7B 90.053 754 61 12 2392 3139 516792463 516793208 0.000000e+00 965.0
10 TraesCS7A01G380500 chr7B 86.682 856 91 14 1075 1920 516790922 516791764 0.000000e+00 928.0
11 TraesCS7A01G380500 chr7B 92.707 617 36 3 3851 4459 516794263 516794878 0.000000e+00 881.0
12 TraesCS7A01G380500 chr7B 89.907 535 43 10 3144 3675 516793712 516794238 0.000000e+00 678.0
13 TraesCS7A01G380500 chr7B 85.484 124 14 4 3715 3836 627984713 627984592 4.680000e-25 126.0
14 TraesCS7A01G380500 chr6B 92.967 455 31 1 1 454 213386323 213386777 0.000000e+00 662.0
15 TraesCS7A01G380500 chr6B 85.446 213 8 4 620 809 213386767 213386979 2.720000e-47 200.0
16 TraesCS7A01G380500 chr6B 100.000 28 0 0 623 650 159300165 159300192 8.000000e-03 52.8
17 TraesCS7A01G380500 chr6D 92.070 454 28 5 1 454 365587376 365586931 2.260000e-177 632.0
18 TraesCS7A01G380500 chr6D 84.507 213 10 4 620 809 365586941 365586729 5.890000e-44 189.0
19 TraesCS7A01G380500 chr6D 86.555 119 11 5 3716 3833 87598710 87598596 4.680000e-25 126.0
20 TraesCS7A01G380500 chr1D 91.429 455 31 4 1 454 318086658 318086211 6.340000e-173 617.0
21 TraesCS7A01G380500 chr1D 84.434 212 10 4 620 808 318086221 318086010 2.120000e-43 187.0
22 TraesCS7A01G380500 chr1D 87.603 121 13 2 3720 3839 465887257 465887138 6.010000e-29 139.0
23 TraesCS7A01G380500 chr3D 82.381 210 13 8 620 806 242130495 242130703 1.280000e-35 161.0
24 TraesCS7A01G380500 chr2B 86.992 123 14 2 1046 1166 152704523 152704645 2.160000e-28 137.0
25 TraesCS7A01G380500 chr4A 86.777 121 15 1 3720 3840 113861459 113861578 2.800000e-27 134.0
26 TraesCS7A01G380500 chr3B 81.481 189 10 6 644 807 704256308 704256496 1.010000e-26 132.0
27 TraesCS7A01G380500 chr3B 84.921 126 17 2 3709 3833 189413901 189414025 4.680000e-25 126.0
28 TraesCS7A01G380500 chr5D 85.246 122 17 1 3716 3837 308353351 308353471 1.680000e-24 124.0
29 TraesCS7A01G380500 chr4B 100.000 30 0 0 1049 1078 527334193 527334164 6.230000e-04 56.5


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 TraesCS7A01G380500 chr7A 555936130 555940588 4458 False 8235.0 8235 100.000000 1 4459 1 chr7A.!!$F2 4458
1 TraesCS7A01G380500 chr7A 98542153 98542804 651 True 371.5 595 85.835000 1 805 2 chr7A.!!$R1 804
2 TraesCS7A01G380500 chr7D 488544589 488550941 6352 False 1664.0 2416 93.784333 809 4459 3 chr7D.!!$F2 3650
3 TraesCS7A01G380500 chr7B 516790922 516794878 3956 False 863.0 965 89.837250 1075 4459 4 chr7B.!!$F1 3384
4 TraesCS7A01G380500 chr6B 213386323 213386979 656 False 431.0 662 89.206500 1 809 2 chr6B.!!$F2 808
5 TraesCS7A01G380500 chr6D 365586729 365587376 647 True 410.5 632 88.288500 1 809 2 chr6D.!!$R2 808
6 TraesCS7A01G380500 chr1D 318086010 318086658 648 True 402.0 617 87.931500 1 808 2 chr1D.!!$R2 807

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
981 1006 0.179134 CGCCGACCTCTCCTAAGTTG 60.179 60.0 0.00 0.0 0.00 3.16 F
1314 1343 0.105760 TTTGGGTGGGCATCACTGTT 60.106 50.0 8.90 0.0 45.38 3.16 F
1784 1817 0.263172 TTTTGTTCCTCCCAAGGCCA 59.737 50.0 5.01 0.0 43.02 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2399 2667 0.629596 TGGTTTGGGTTGTGGGTGTA 59.370 50.0 0.00 0.00 0.00 2.90 R
2910 3185 0.753111 GCATCGGGGCTTTCCAGAAT 60.753 55.0 0.00 0.00 42.81 2.40 R
3724 4500 0.643820 GCGACAAGTAATTCCGGACG 59.356 55.0 1.83 1.53 0.00 4.79 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 1.583054 GAGAACGTCCAAAGTGCAGT 58.417 50.000 0.00 0.00 0.00 4.40
93 94 3.127352 GAGAGGACTCGCCGCGAAT 62.127 63.158 17.53 6.70 41.97 3.34
230 232 1.228124 CGGTGGGGCAGTTCTTTGA 60.228 57.895 0.00 0.00 0.00 2.69
231 233 0.821711 CGGTGGGGCAGTTCTTTGAA 60.822 55.000 0.00 0.00 0.00 2.69
241 243 4.441356 GGCAGTTCTTTGAAACCACAATGA 60.441 41.667 0.00 0.00 34.02 2.57
251 253 6.951062 TGAAACCACAATGACAAGTTCATA 57.049 33.333 0.00 0.00 44.86 2.15
256 258 4.456911 CCACAATGACAAGTTCATAGCTGT 59.543 41.667 0.00 0.00 44.86 4.40
316 318 2.553602 CAACAGAGGCAATTGCAGTACA 59.446 45.455 30.32 0.00 44.36 2.90
345 347 5.350365 GGAATGAATCTAGCACGTACAACAA 59.650 40.000 0.00 0.00 0.00 2.83
387 389 7.782168 AGATCAACTCAGATAGTATGGAAGTGA 59.218 37.037 0.00 0.00 37.50 3.41
402 404 7.609097 ATGGAAGTGATAGAAGCTCTAATGA 57.391 36.000 0.00 0.00 31.96 2.57
405 407 7.343057 TGGAAGTGATAGAAGCTCTAATGAAGA 59.657 37.037 0.00 0.00 31.96 2.87
446 448 4.692625 GCTAGTGCCATATTCGATGATTGT 59.307 41.667 0.00 0.00 0.00 2.71
447 449 5.180117 GCTAGTGCCATATTCGATGATTGTT 59.820 40.000 0.00 0.00 0.00 2.83
448 450 6.368791 GCTAGTGCCATATTCGATGATTGTTA 59.631 38.462 0.00 0.00 0.00 2.41
449 451 7.065085 GCTAGTGCCATATTCGATGATTGTTAT 59.935 37.037 0.00 0.00 0.00 1.89
450 452 7.750229 AGTGCCATATTCGATGATTGTTATT 57.250 32.000 0.00 0.00 0.00 1.40
451 453 8.169977 AGTGCCATATTCGATGATTGTTATTT 57.830 30.769 0.00 0.00 0.00 1.40
452 454 8.292448 AGTGCCATATTCGATGATTGTTATTTC 58.708 33.333 0.00 0.00 0.00 2.17
453 455 8.075574 GTGCCATATTCGATGATTGTTATTTCA 58.924 33.333 0.00 0.00 0.00 2.69
454 456 8.628280 TGCCATATTCGATGATTGTTATTTCAA 58.372 29.630 0.00 0.00 0.00 2.69
455 457 9.630098 GCCATATTCGATGATTGTTATTTCAAT 57.370 29.630 0.00 0.00 40.20 2.57
504 506 8.722342 TTTTTAAAAACGTCACATCTATGCTC 57.278 30.769 9.31 0.00 0.00 4.26
505 507 4.946784 AAAAACGTCACATCTATGCTCC 57.053 40.909 0.00 0.00 0.00 4.70
506 508 2.604046 AACGTCACATCTATGCTCCC 57.396 50.000 0.00 0.00 0.00 4.30
507 509 1.485124 ACGTCACATCTATGCTCCCA 58.515 50.000 0.00 0.00 0.00 4.37
508 510 2.042464 ACGTCACATCTATGCTCCCAT 58.958 47.619 0.00 0.00 35.44 4.00
509 511 3.230976 ACGTCACATCTATGCTCCCATA 58.769 45.455 0.00 0.00 32.85 2.74
510 512 3.641436 ACGTCACATCTATGCTCCCATAA 59.359 43.478 0.00 0.00 33.72 1.90
511 513 4.100963 ACGTCACATCTATGCTCCCATAAA 59.899 41.667 0.00 0.00 33.72 1.40
512 514 5.221722 ACGTCACATCTATGCTCCCATAAAT 60.222 40.000 0.00 0.00 33.72 1.40
513 515 6.014584 ACGTCACATCTATGCTCCCATAAATA 60.015 38.462 0.00 0.00 33.72 1.40
514 516 7.044181 CGTCACATCTATGCTCCCATAAATAT 58.956 38.462 0.00 0.00 33.72 1.28
515 517 8.197439 CGTCACATCTATGCTCCCATAAATATA 58.803 37.037 0.00 0.00 33.72 0.86
578 580 8.871686 AAAAATAGACCACAAACAGAATGAAC 57.128 30.769 0.00 0.00 39.69 3.18
579 581 7.581213 AAATAGACCACAAACAGAATGAACA 57.419 32.000 0.00 0.00 39.69 3.18
580 582 7.765695 AATAGACCACAAACAGAATGAACAT 57.234 32.000 0.00 0.00 39.69 2.71
581 583 5.695851 AGACCACAAACAGAATGAACATC 57.304 39.130 0.00 0.00 39.69 3.06
582 584 5.132502 AGACCACAAACAGAATGAACATCA 58.867 37.500 0.00 0.00 39.69 3.07
583 585 5.240183 AGACCACAAACAGAATGAACATCAG 59.760 40.000 0.00 0.00 39.69 2.90
584 586 4.889409 ACCACAAACAGAATGAACATCAGT 59.111 37.500 0.00 0.00 39.69 3.41
585 587 5.360714 ACCACAAACAGAATGAACATCAGTT 59.639 36.000 0.00 0.00 39.69 3.16
586 588 6.127366 ACCACAAACAGAATGAACATCAGTTT 60.127 34.615 0.00 0.00 39.69 2.66
587 589 7.068103 ACCACAAACAGAATGAACATCAGTTTA 59.932 33.333 0.00 0.00 39.69 2.01
588 590 8.084073 CCACAAACAGAATGAACATCAGTTTAT 58.916 33.333 0.00 0.00 39.69 1.40
589 591 8.908678 CACAAACAGAATGAACATCAGTTTATG 58.091 33.333 0.00 0.00 39.69 1.90
590 592 8.632679 ACAAACAGAATGAACATCAGTTTATGT 58.367 29.630 0.00 0.00 39.93 2.29
591 593 9.121517 CAAACAGAATGAACATCAGTTTATGTC 57.878 33.333 0.00 0.00 38.24 3.06
592 594 7.984422 ACAGAATGAACATCAGTTTATGTCA 57.016 32.000 0.00 0.00 38.24 3.58
593 595 7.810658 ACAGAATGAACATCAGTTTATGTCAC 58.189 34.615 0.00 0.00 38.24 3.67
594 596 7.445096 ACAGAATGAACATCAGTTTATGTCACA 59.555 33.333 0.00 0.00 38.24 3.58
595 597 8.456471 CAGAATGAACATCAGTTTATGTCACAT 58.544 33.333 0.00 0.00 39.16 3.21
596 598 8.671921 AGAATGAACATCAGTTTATGTCACATC 58.328 33.333 0.00 0.00 39.16 3.06
597 599 8.571461 AATGAACATCAGTTTATGTCACATCT 57.429 30.769 0.00 0.00 39.16 2.90
598 600 9.671279 AATGAACATCAGTTTATGTCACATCTA 57.329 29.630 0.00 0.00 39.16 1.98
599 601 8.707938 TGAACATCAGTTTATGTCACATCTAG 57.292 34.615 0.00 0.00 39.16 2.43
600 602 8.531146 TGAACATCAGTTTATGTCACATCTAGA 58.469 33.333 0.00 0.00 39.16 2.43
601 603 9.539825 GAACATCAGTTTATGTCACATCTAGAT 57.460 33.333 0.00 0.00 39.16 1.98
602 604 8.883954 ACATCAGTTTATGTCACATCTAGATG 57.116 34.615 27.63 27.63 38.95 2.90
603 605 8.699130 ACATCAGTTTATGTCACATCTAGATGA 58.301 33.333 34.16 15.19 36.91 2.92
604 606 9.538508 CATCAGTTTATGTCACATCTAGATGAA 57.461 33.333 34.16 20.50 41.20 2.57
606 608 9.755804 TCAGTTTATGTCACATCTAGATGAATC 57.244 33.333 34.16 22.58 41.20 2.52
607 609 8.986847 CAGTTTATGTCACATCTAGATGAATCC 58.013 37.037 34.16 19.75 41.20 3.01
608 610 8.932610 AGTTTATGTCACATCTAGATGAATCCT 58.067 33.333 34.16 18.96 41.20 3.24
611 613 9.813826 TTATGTCACATCTAGATGAATCCTAGA 57.186 33.333 34.16 17.69 44.50 2.43
613 615 9.987726 ATGTCACATCTAGATGAATCCTAGATA 57.012 33.333 34.16 18.22 46.55 1.98
614 616 9.460019 TGTCACATCTAGATGAATCCTAGATAG 57.540 37.037 34.16 7.87 46.55 2.08
615 617 9.679661 GTCACATCTAGATGAATCCTAGATAGA 57.320 37.037 34.16 13.27 46.55 1.98
618 620 9.866655 ACATCTAGATGAATCCTAGATAGATCC 57.133 37.037 34.16 0.00 46.55 3.36
621 623 9.919416 TCTAGATGAATCCTAGATAGATCCTTG 57.081 37.037 0.00 0.00 38.08 3.61
693 695 3.880490 AGAGAGAGTAATGTGGTAGCTCG 59.120 47.826 0.00 0.00 0.00 5.03
708 719 4.201724 GGTAGCTCGTGAGTTTGCTAAATG 60.202 45.833 0.00 0.00 37.29 2.32
726 751 4.910458 AATGTTCTACTACTGGTTGCCT 57.090 40.909 0.00 0.00 0.00 4.75
762 787 2.422276 GTTGCTTGGAAACGATGCTT 57.578 45.000 0.00 0.00 0.00 3.91
961 986 2.446282 CAAACACACACTAAACACCGC 58.554 47.619 0.00 0.00 0.00 5.68
977 1002 3.145551 GCCGCCGACCTCTCCTAA 61.146 66.667 0.00 0.00 0.00 2.69
981 1006 0.179134 CGCCGACCTCTCCTAAGTTG 60.179 60.000 0.00 0.00 0.00 3.16
982 1007 0.896226 GCCGACCTCTCCTAAGTTGT 59.104 55.000 0.00 0.00 0.00 3.32
1029 1054 4.789075 GCTTCGTCGGTAGCGCCA 62.789 66.667 9.99 0.00 36.97 5.69
1050 1075 1.392853 GTTCTCGTCATCTGCTTGCTG 59.607 52.381 0.00 0.00 0.00 4.41
1058 1083 2.038164 TCATCTGCTTGCTGTCTCTTGT 59.962 45.455 0.00 0.00 0.00 3.16
1066 1091 4.630111 CTTGCTGTCTCTTGTTCTCTTCT 58.370 43.478 0.00 0.00 0.00 2.85
1077 1102 5.365605 TCTTGTTCTCTTCTTCCACAGGTTA 59.634 40.000 0.00 0.00 0.00 2.85
1080 1105 2.231478 TCTCTTCTTCCACAGGTTAGCG 59.769 50.000 0.00 0.00 0.00 4.26
1081 1106 1.968493 TCTTCTTCCACAGGTTAGCGT 59.032 47.619 0.00 0.00 0.00 5.07
1082 1107 3.159472 TCTTCTTCCACAGGTTAGCGTA 58.841 45.455 0.00 0.00 0.00 4.42
1128 1153 1.702957 TGAACCTTTGGGGATCTCGTT 59.297 47.619 0.00 0.00 37.71 3.85
1146 1171 3.812609 TCGTTTGCTGAATTAAGTGCTGA 59.187 39.130 0.00 0.00 0.00 4.26
1183 1208 4.832266 TCTTAGCCTTTCTTTGCCATGAAA 59.168 37.500 0.00 0.00 0.00 2.69
1197 1222 5.177326 TGCCATGAAAATGTTAGATTTGCC 58.823 37.500 0.00 0.00 0.00 4.52
1247 1272 4.108886 GAGCAAGATTTCGCTCGTAATC 57.891 45.455 11.85 11.85 44.68 1.75
1248 1273 3.521560 AGCAAGATTTCGCTCGTAATCA 58.478 40.909 18.80 0.00 35.34 2.57
1249 1274 4.122776 AGCAAGATTTCGCTCGTAATCAT 58.877 39.130 18.80 8.38 35.34 2.45
1250 1275 4.210120 AGCAAGATTTCGCTCGTAATCATC 59.790 41.667 18.80 10.10 35.34 2.92
1285 1314 1.065928 CACCCCTACGCTCGCTTAG 59.934 63.158 0.00 0.00 0.00 2.18
1308 1337 3.565307 TGAGATAATTTGGGTGGGCATC 58.435 45.455 0.00 0.00 0.00 3.91
1312 1341 1.269012 AATTTGGGTGGGCATCACTG 58.731 50.000 8.90 0.00 45.38 3.66
1314 1343 0.105760 TTTGGGTGGGCATCACTGTT 60.106 50.000 8.90 0.00 45.38 3.16
1315 1344 0.539438 TTGGGTGGGCATCACTGTTC 60.539 55.000 8.90 0.00 45.38 3.18
1334 1363 3.604875 TCTAAACGTTCTTGGGGCTAG 57.395 47.619 0.00 0.00 0.00 3.42
1351 1384 3.274288 GCTAGCCTTGTTACTGCAATCT 58.726 45.455 2.29 0.00 0.00 2.40
1369 1402 4.931661 ATCTAATCGAAGCCGGTTTCTA 57.068 40.909 25.87 17.49 40.08 2.10
1386 1419 3.650281 TCTATTCAGGGATGCTTTGCA 57.350 42.857 0.00 0.00 44.86 4.08
1457 1490 5.791336 TGTGTAATCTGAGTCTGAACTGT 57.209 39.130 3.62 0.00 35.28 3.55
1479 1512 7.067008 ACTGTATGCCTTGGTGTGTAATTAATC 59.933 37.037 0.00 0.00 0.00 1.75
1498 1531 3.241530 AGGTGCCGGAGCTGTGAA 61.242 61.111 5.05 0.00 40.80 3.18
1509 1542 0.982704 AGCTGTGAAGCTGTGGAGAT 59.017 50.000 0.00 0.00 44.44 2.75
1561 1594 4.075963 TGGTTTGTCTGGTAACTACACC 57.924 45.455 0.00 0.00 39.20 4.16
1654 1687 3.295973 AGAGAGGGCATCACTCTTCTAC 58.704 50.000 0.58 0.00 44.89 2.59
1671 1704 0.387565 TACGCTGAGCATGCCGATAA 59.612 50.000 15.66 0.00 0.00 1.75
1740 1773 7.533900 CCGTATGTTTTGTTCTAAAGACATGTG 59.466 37.037 1.15 0.00 0.00 3.21
1741 1774 8.067784 CGTATGTTTTGTTCTAAAGACATGTGT 58.932 33.333 1.15 0.00 0.00 3.72
1742 1775 9.169468 GTATGTTTTGTTCTAAAGACATGTGTG 57.831 33.333 1.15 0.00 0.00 3.82
1748 1781 7.151999 TGTTCTAAAGACATGTGTGTTTTGT 57.848 32.000 1.15 0.00 41.07 2.83
1750 1783 7.753132 TGTTCTAAAGACATGTGTGTTTTGTTC 59.247 33.333 1.15 9.17 41.07 3.18
1753 1786 9.168451 TCTAAAGACATGTGTGTTTTGTTCTAA 57.832 29.630 1.15 0.00 41.07 2.10
1754 1787 9.781834 CTAAAGACATGTGTGTTTTGTTCTAAA 57.218 29.630 1.15 0.00 41.07 1.85
1755 1788 8.687824 AAAGACATGTGTGTTTTGTTCTAAAG 57.312 30.769 1.15 0.00 38.17 1.85
1756 1789 7.624360 AGACATGTGTGTTTTGTTCTAAAGA 57.376 32.000 1.15 0.00 39.09 2.52
1757 1790 7.472543 AGACATGTGTGTTTTGTTCTAAAGAC 58.527 34.615 1.15 0.00 39.09 3.01
1758 1791 7.120579 AGACATGTGTGTTTTGTTCTAAAGACA 59.879 33.333 1.15 5.86 38.49 3.41
1759 1792 7.771183 ACATGTGTGTTTTGTTCTAAAGACAT 58.229 30.769 0.00 0.00 41.44 3.06
1760 1793 7.701924 ACATGTGTGTTTTGTTCTAAAGACATG 59.298 33.333 0.00 0.00 41.44 3.21
1761 1794 7.151999 TGTGTGTTTTGTTCTAAAGACATGT 57.848 32.000 0.00 0.00 41.44 3.21
1762 1795 7.026562 TGTGTGTTTTGTTCTAAAGACATGTG 58.973 34.615 1.15 0.00 41.44 3.21
1777 1810 2.693074 ACATGTGTGTTTTGTTCCTCCC 59.307 45.455 0.00 0.00 34.01 4.30
1784 1817 0.263172 TTTTGTTCCTCCCAAGGCCA 59.737 50.000 5.01 0.00 43.02 5.36
1787 1820 1.139498 TGTTCCTCCCAAGGCCATGA 61.139 55.000 10.18 0.00 43.02 3.07
1844 1877 7.631717 ACCTAATTCCTGAGCTAAATTTGTC 57.368 36.000 0.00 0.00 0.00 3.18
1865 1898 7.009179 TGTCTCTTCAGTTTCTTGGTATGAT 57.991 36.000 0.00 0.00 0.00 2.45
1867 1900 8.035394 TGTCTCTTCAGTTTCTTGGTATGATAC 58.965 37.037 0.00 0.00 0.00 2.24
1955 2150 7.916914 TCAGATGATTGATATATGTGGCAAG 57.083 36.000 0.00 0.00 0.00 4.01
1958 2153 4.081406 TGATTGATATATGTGGCAAGGGC 58.919 43.478 0.00 0.00 40.13 5.19
2081 2276 7.064016 GTGATTAGGAGTGTTCTGTGAAGAATC 59.936 40.741 0.00 0.00 0.00 2.52
2256 2465 7.548196 TTAACTTACAAGTTCCAACTCAGTG 57.452 36.000 10.51 0.00 45.65 3.66
2279 2495 8.432013 AGTGATCTATAGCCAAATCAACATGTA 58.568 33.333 0.00 0.00 30.45 2.29
2399 2667 0.326264 AACCTTCAGCCGCTTCTGAT 59.674 50.000 5.75 0.00 42.12 2.90
2411 2679 2.084546 GCTTCTGATACACCCACAACC 58.915 52.381 0.00 0.00 0.00 3.77
2464 2732 1.021202 TAAGCATGCCCACATTACGC 58.979 50.000 15.66 0.00 32.87 4.42
2565 2834 1.064017 TCCCCACCTGAATATGTTGCC 60.064 52.381 0.00 0.00 0.00 4.52
2662 2931 5.830912 TGAACTGATGCAACAAAAAGGTAG 58.169 37.500 0.00 0.00 0.00 3.18
2673 2942 6.672147 CAACAAAAAGGTAGATTGGAGACAG 58.328 40.000 0.00 0.00 44.54 3.51
2705 2974 2.905736 TGTGACATGAGGAGGTTGATCA 59.094 45.455 0.00 0.00 0.00 2.92
2724 2993 7.099266 TGATCAACATTCTTGAACACTTTGT 57.901 32.000 0.00 0.00 31.55 2.83
2840 3113 6.923012 AGTACTATCATGCTAATCTGCTCTG 58.077 40.000 0.00 0.00 0.00 3.35
2910 3185 2.371841 AGTGGTCCAGTTTGTGCTATGA 59.628 45.455 0.00 0.00 0.00 2.15
3169 3943 9.933723 TGTGATCCATGTCTCATAACATATTAG 57.066 33.333 0.00 0.00 37.78 1.73
3317 4091 0.679002 ATTCACCGCAATCTGCAGCT 60.679 50.000 9.47 0.00 45.36 4.24
3675 4451 3.618594 CCATCTAACTGATTGTGTGTCCG 59.381 47.826 0.00 0.00 32.05 4.79
3724 4500 3.264964 TGTCCCAGTTAAATACACCCTCC 59.735 47.826 0.00 0.00 0.00 4.30
3738 4514 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
3802 4578 8.783833 AAGATACATCCATTTCTATCCATTCG 57.216 34.615 0.00 0.00 0.00 3.34
3805 4581 4.516698 ACATCCATTTCTATCCATTCGTGC 59.483 41.667 0.00 0.00 0.00 5.34
3806 4582 4.422073 TCCATTTCTATCCATTCGTGCT 57.578 40.909 0.00 0.00 0.00 4.40
3807 4583 4.129380 TCCATTTCTATCCATTCGTGCTG 58.871 43.478 0.00 0.00 0.00 4.41
3808 4584 3.304257 CCATTTCTATCCATTCGTGCTGC 60.304 47.826 0.00 0.00 0.00 5.25
3809 4585 2.689553 TTCTATCCATTCGTGCTGCA 57.310 45.000 0.00 0.00 0.00 4.41
3810 4586 2.229675 TCTATCCATTCGTGCTGCAG 57.770 50.000 10.11 10.11 0.00 4.41
3811 4587 1.202568 TCTATCCATTCGTGCTGCAGG 60.203 52.381 17.12 15.70 0.00 4.85
3812 4588 0.541392 TATCCATTCGTGCTGCAGGT 59.459 50.000 20.27 4.43 0.00 4.00
3813 4589 0.541392 ATCCATTCGTGCTGCAGGTA 59.459 50.000 20.27 12.63 0.00 3.08
3815 4591 1.065491 TCCATTCGTGCTGCAGGTAAT 60.065 47.619 20.27 15.20 0.00 1.89
3816 4592 1.745087 CCATTCGTGCTGCAGGTAATT 59.255 47.619 20.27 3.39 0.00 1.40
3817 4593 2.223340 CCATTCGTGCTGCAGGTAATTC 60.223 50.000 20.27 0.00 0.00 2.17
3818 4594 2.472695 TTCGTGCTGCAGGTAATTCT 57.527 45.000 20.27 0.00 0.00 2.40
3820 4596 0.729116 CGTGCTGCAGGTAATTCTGG 59.271 55.000 17.12 0.00 35.43 3.86
3821 4597 1.675714 CGTGCTGCAGGTAATTCTGGA 60.676 52.381 17.12 0.00 35.43 3.86
3823 4599 1.009829 GCTGCAGGTAATTCTGGACG 58.990 55.000 17.12 0.00 35.43 4.79
3824 4600 1.656652 CTGCAGGTAATTCTGGACGG 58.343 55.000 5.57 0.00 35.43 4.79
3825 4601 0.251916 TGCAGGTAATTCTGGACGGG 59.748 55.000 0.00 0.00 35.43 5.28
3827 4603 0.180406 CAGGTAATTCTGGACGGGGG 59.820 60.000 0.00 0.00 0.00 5.40
3848 4624 7.029053 GGGGGAGTATATAATTGGCTTTACT 57.971 40.000 0.00 0.00 0.00 2.24
3849 4625 6.884836 GGGGGAGTATATAATTGGCTTTACTG 59.115 42.308 0.00 0.00 0.00 2.74
3935 4711 9.781834 TTATCAAAAACTGTCACTTGTTAGTTG 57.218 29.630 0.00 0.00 33.95 3.16
3946 4970 5.534278 TCACTTGTTAGTTGATGGAATGCAA 59.466 36.000 0.00 0.00 30.26 4.08
3949 4973 5.627499 TGTTAGTTGATGGAATGCAAGTC 57.373 39.130 0.00 0.00 0.00 3.01
3968 4992 3.713248 AGTCCAGATGCAGTAATCCATGA 59.287 43.478 0.00 0.00 0.00 3.07
3996 5020 1.690352 AGAACAAAGCTGCCATTTGCT 59.310 42.857 12.58 2.83 40.54 3.91
4004 7019 4.119442 AGCTGCCATTTGCTGAAAATAG 57.881 40.909 0.00 0.00 41.11 1.73
4025 7040 4.458397 AGCATGCTTGAGTAACAGCATAT 58.542 39.130 16.30 0.00 39.44 1.78
4072 7469 5.416947 AGTATTTTACCAGCGGTTCAGTAG 58.583 41.667 5.57 0.00 37.09 2.57
4097 7494 0.323629 TTACAAAGGGTGAGGCCGAG 59.676 55.000 0.00 0.00 38.44 4.63
4135 7532 1.679944 GCAGGTGCAGGCTTGATCTTA 60.680 52.381 0.00 0.00 41.59 2.10
4170 7567 7.519032 TTGTAAGGAAACATGTAGGGAAAAG 57.481 36.000 0.00 0.00 0.00 2.27
4176 7573 6.940867 AGGAAACATGTAGGGAAAAGTAAGAC 59.059 38.462 0.00 0.00 0.00 3.01
4201 7598 6.745450 CGCAAAAGATGTGTACGGAAAATTAT 59.255 34.615 0.00 0.00 34.75 1.28
4205 7602 6.604735 AGATGTGTACGGAAAATTATCAGC 57.395 37.500 0.00 0.00 0.00 4.26
4232 7685 7.883391 TGAGTTAGAAGTACCCTGATAGAAG 57.117 40.000 0.00 0.00 0.00 2.85
4303 7756 5.183713 CCCACAATCAATGCTTACTTGAAGA 59.816 40.000 0.00 0.00 37.33 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 5.241506 CCTCTCACAACCAAGCTTATTTGAA 59.758 40.000 20.63 10.54 0.00 2.69
93 94 7.546358 CCTTAGGTGTGCATGAAATAATGAAA 58.454 34.615 0.00 0.00 0.00 2.69
163 164 4.759693 ACCAGCATCGACATTCAGTTTAAA 59.240 37.500 0.00 0.00 0.00 1.52
177 178 2.333926 TCTACGTCAAAACCAGCATCG 58.666 47.619 0.00 0.00 0.00 3.84
230 232 5.536161 AGCTATGAACTTGTCATTGTGGTTT 59.464 36.000 0.00 0.00 45.13 3.27
231 233 5.048504 CAGCTATGAACTTGTCATTGTGGTT 60.049 40.000 0.00 0.00 45.13 3.67
241 243 2.766313 TCGCAACAGCTATGAACTTGT 58.234 42.857 2.99 0.00 0.00 3.16
251 253 4.022935 TCAATCTTTTCATTCGCAACAGCT 60.023 37.500 0.00 0.00 0.00 4.24
289 291 3.636300 TGCAATTGCCTCTGTTGTAAACT 59.364 39.130 26.94 0.00 44.02 2.66
297 299 2.566833 TGTACTGCAATTGCCTCTGT 57.433 45.000 26.94 20.36 41.18 3.41
316 318 6.597672 TGTACGTGCTAGATTCATTCCAAATT 59.402 34.615 4.97 0.00 0.00 1.82
323 325 5.351465 CCTTGTTGTACGTGCTAGATTCATT 59.649 40.000 4.97 0.00 0.00 2.57
345 347 4.471904 TGATCTCGATTTTGCTACACCT 57.528 40.909 0.00 0.00 0.00 4.00
405 407 6.047870 CACTAGCAATTGATGAAGAGTAGCT 58.952 40.000 10.34 0.00 0.00 3.32
420 422 4.898320 TCATCGAATATGGCACTAGCAAT 58.102 39.130 0.00 0.00 44.61 3.56
479 481 7.806014 GGAGCATAGATGTGACGTTTTTAAAAA 59.194 33.333 9.31 9.31 0.00 1.94
480 482 7.302524 GGAGCATAGATGTGACGTTTTTAAAA 58.697 34.615 0.00 0.00 0.00 1.52
481 483 6.128117 GGGAGCATAGATGTGACGTTTTTAAA 60.128 38.462 0.00 0.00 0.00 1.52
482 484 5.353123 GGGAGCATAGATGTGACGTTTTTAA 59.647 40.000 0.00 0.00 0.00 1.52
483 485 4.873827 GGGAGCATAGATGTGACGTTTTTA 59.126 41.667 0.00 0.00 0.00 1.52
484 486 3.689649 GGGAGCATAGATGTGACGTTTTT 59.310 43.478 0.00 0.00 0.00 1.94
485 487 3.270877 GGGAGCATAGATGTGACGTTTT 58.729 45.455 0.00 0.00 0.00 2.43
486 488 2.236146 TGGGAGCATAGATGTGACGTTT 59.764 45.455 0.00 0.00 0.00 3.60
487 489 1.831106 TGGGAGCATAGATGTGACGTT 59.169 47.619 0.00 0.00 0.00 3.99
488 490 1.485124 TGGGAGCATAGATGTGACGT 58.515 50.000 0.00 0.00 0.00 4.34
489 491 2.827800 ATGGGAGCATAGATGTGACG 57.172 50.000 0.00 0.00 0.00 4.35
553 555 8.474025 TGTTCATTCTGTTTGTGGTCTATTTTT 58.526 29.630 0.00 0.00 0.00 1.94
554 556 8.006298 TGTTCATTCTGTTTGTGGTCTATTTT 57.994 30.769 0.00 0.00 0.00 1.82
555 557 7.581213 TGTTCATTCTGTTTGTGGTCTATTT 57.419 32.000 0.00 0.00 0.00 1.40
556 558 7.448161 TGATGTTCATTCTGTTTGTGGTCTATT 59.552 33.333 0.00 0.00 0.00 1.73
557 559 6.942005 TGATGTTCATTCTGTTTGTGGTCTAT 59.058 34.615 0.00 0.00 0.00 1.98
558 560 6.295249 TGATGTTCATTCTGTTTGTGGTCTA 58.705 36.000 0.00 0.00 0.00 2.59
559 561 5.132502 TGATGTTCATTCTGTTTGTGGTCT 58.867 37.500 0.00 0.00 0.00 3.85
560 562 5.009010 ACTGATGTTCATTCTGTTTGTGGTC 59.991 40.000 0.00 0.00 0.00 4.02
561 563 4.889409 ACTGATGTTCATTCTGTTTGTGGT 59.111 37.500 0.00 0.00 0.00 4.16
562 564 5.443185 ACTGATGTTCATTCTGTTTGTGG 57.557 39.130 0.00 0.00 0.00 4.17
563 565 8.908678 CATAAACTGATGTTCATTCTGTTTGTG 58.091 33.333 14.83 14.31 42.07 3.33
564 566 8.632679 ACATAAACTGATGTTCATTCTGTTTGT 58.367 29.630 14.83 8.45 41.96 2.83
565 567 9.121517 GACATAAACTGATGTTCATTCTGTTTG 57.878 33.333 14.83 6.38 41.96 2.93
566 568 8.849168 TGACATAAACTGATGTTCATTCTGTTT 58.151 29.630 11.58 11.58 43.34 2.83
567 569 8.292448 GTGACATAAACTGATGTTCATTCTGTT 58.708 33.333 0.00 0.00 40.18 3.16
568 570 7.445096 TGTGACATAAACTGATGTTCATTCTGT 59.555 33.333 0.00 0.00 40.18 3.41
569 571 7.809665 TGTGACATAAACTGATGTTCATTCTG 58.190 34.615 0.00 0.00 40.18 3.02
570 572 7.984422 TGTGACATAAACTGATGTTCATTCT 57.016 32.000 0.00 0.00 40.18 2.40
571 573 8.671921 AGATGTGACATAAACTGATGTTCATTC 58.328 33.333 0.00 0.00 40.18 2.67
572 574 8.571461 AGATGTGACATAAACTGATGTTCATT 57.429 30.769 0.00 0.00 40.18 2.57
573 575 9.322773 CTAGATGTGACATAAACTGATGTTCAT 57.677 33.333 0.00 0.00 40.18 2.57
574 576 8.531146 TCTAGATGTGACATAAACTGATGTTCA 58.469 33.333 0.00 0.00 40.18 3.18
575 577 8.932945 TCTAGATGTGACATAAACTGATGTTC 57.067 34.615 0.00 0.00 40.18 3.18
576 578 9.322773 CATCTAGATGTGACATAAACTGATGTT 57.677 33.333 22.42 0.00 35.87 2.71
577 579 8.699130 TCATCTAGATGTGACATAAACTGATGT 58.301 33.333 27.80 0.00 39.93 3.06
578 580 9.538508 TTCATCTAGATGTGACATAAACTGATG 57.461 33.333 27.80 8.68 39.72 3.07
580 582 9.755804 GATTCATCTAGATGTGACATAAACTGA 57.244 33.333 27.80 6.22 39.72 3.41
581 583 8.986847 GGATTCATCTAGATGTGACATAAACTG 58.013 37.037 27.80 3.94 39.72 3.16
582 584 8.932610 AGGATTCATCTAGATGTGACATAAACT 58.067 33.333 27.80 14.86 39.72 2.66
585 587 9.813826 TCTAGGATTCATCTAGATGTGACATAA 57.186 33.333 27.80 16.29 38.50 1.90
586 588 9.987726 ATCTAGGATTCATCTAGATGTGACATA 57.012 33.333 27.80 19.61 46.72 2.29
587 589 8.898303 ATCTAGGATTCATCTAGATGTGACAT 57.102 34.615 27.80 19.56 46.72 3.06
595 597 9.919416 CAAGGATCTATCTAGGATTCATCTAGA 57.081 37.037 0.00 0.00 44.78 2.43
596 598 9.699410 ACAAGGATCTATCTAGGATTCATCTAG 57.301 37.037 0.00 0.00 36.46 2.43
598 600 8.971032 AACAAGGATCTATCTAGGATTCATCT 57.029 34.615 0.00 0.00 0.00 2.90
609 611 8.943085 AGGACATGAAATAACAAGGATCTATCT 58.057 33.333 0.00 0.00 0.00 1.98
610 612 9.566432 AAGGACATGAAATAACAAGGATCTATC 57.434 33.333 0.00 0.00 0.00 2.08
613 615 8.772250 TCTAAGGACATGAAATAACAAGGATCT 58.228 33.333 0.00 0.00 0.00 2.75
614 616 8.964476 TCTAAGGACATGAAATAACAAGGATC 57.036 34.615 0.00 0.00 0.00 3.36
615 617 9.927081 AATCTAAGGACATGAAATAACAAGGAT 57.073 29.630 0.00 0.00 0.00 3.24
616 618 9.753674 AAATCTAAGGACATGAAATAACAAGGA 57.246 29.630 0.00 0.00 0.00 3.36
693 695 8.436200 CAGTAGTAGAACATTTAGCAAACTCAC 58.564 37.037 0.00 0.00 0.00 3.51
708 719 3.368531 CCAGAGGCAACCAGTAGTAGAAC 60.369 52.174 0.00 0.00 37.17 3.01
751 776 4.089065 GCATCAAAACAGAAGCATCGTTTC 59.911 41.667 10.63 0.00 33.95 2.78
762 787 7.309377 CCTCCTTTATTCAAGCATCAAAACAGA 60.309 37.037 0.00 0.00 0.00 3.41
825 850 2.749441 GCACCTGCTGCTTCTCCC 60.749 66.667 0.00 0.00 43.33 4.30
895 920 5.276440 ACAGTAGATTGAAGAGGATCAGGT 58.724 41.667 0.00 0.00 37.82 4.00
961 986 1.321074 AACTTAGGAGAGGTCGGCGG 61.321 60.000 7.21 0.00 0.00 6.13
981 1006 0.970937 TCTCCGGTGAGATGGGACAC 60.971 60.000 0.00 0.00 42.73 3.67
982 1007 1.386550 TCTCCGGTGAGATGGGACA 59.613 57.895 0.00 0.00 42.73 4.02
1029 1054 1.274728 AGCAAGCAGATGACGAGAACT 59.725 47.619 0.00 0.00 0.00 3.01
1050 1075 4.950050 TGTGGAAGAAGAGAACAAGAGAC 58.050 43.478 0.00 0.00 0.00 3.36
1058 1083 3.306088 CGCTAACCTGTGGAAGAAGAGAA 60.306 47.826 0.00 0.00 0.00 2.87
1066 1091 3.181463 ACAAGTTACGCTAACCTGTGGAA 60.181 43.478 9.74 0.00 40.68 3.53
1077 1102 6.022163 AGTACATGTAGAACAAGTTACGCT 57.978 37.500 5.62 0.00 31.92 5.07
1080 1105 7.828712 AGAGGAGTACATGTAGAACAAGTTAC 58.171 38.462 5.62 0.00 31.92 2.50
1081 1106 9.175312 CTAGAGGAGTACATGTAGAACAAGTTA 57.825 37.037 5.62 0.00 31.92 2.24
1082 1107 6.919775 AGAGGAGTACATGTAGAACAAGTT 57.080 37.500 5.62 0.00 31.92 2.66
1128 1153 4.456911 CCTCTTCAGCACTTAATTCAGCAA 59.543 41.667 0.00 0.00 0.00 3.91
1146 1171 1.492599 GCTAAGAAGCCATCCCCTCTT 59.507 52.381 0.00 0.00 43.40 2.85
1176 1201 4.805192 CCGGCAAATCTAACATTTTCATGG 59.195 41.667 0.00 0.00 34.27 3.66
1183 1208 4.887071 TGCTAATCCGGCAAATCTAACATT 59.113 37.500 0.00 0.00 36.71 2.71
1242 1267 0.693049 AGGATGCCGGGGATGATTAC 59.307 55.000 5.50 0.00 0.00 1.89
1246 1271 3.233980 CGAGGATGCCGGGGATGA 61.234 66.667 5.50 0.00 0.00 2.92
1247 1272 4.320456 CCGAGGATGCCGGGGATG 62.320 72.222 5.50 0.00 43.05 3.51
1271 1300 1.400846 TCTCAACTAAGCGAGCGTAGG 59.599 52.381 19.03 5.73 33.40 3.18
1273 1302 4.888038 TTATCTCAACTAAGCGAGCGTA 57.112 40.909 0.00 0.00 0.00 4.42
1274 1303 3.777465 TTATCTCAACTAAGCGAGCGT 57.223 42.857 0.00 0.00 0.00 5.07
1285 1314 3.096092 TGCCCACCCAAATTATCTCAAC 58.904 45.455 0.00 0.00 0.00 3.18
1308 1337 3.250040 CCCCAAGAACGTTTAGAACAGTG 59.750 47.826 0.46 0.00 0.00 3.66
1312 1341 2.501261 AGCCCCAAGAACGTTTAGAAC 58.499 47.619 0.46 0.00 0.00 3.01
1314 1343 2.354403 GCTAGCCCCAAGAACGTTTAGA 60.354 50.000 2.29 0.00 0.00 2.10
1315 1344 2.007608 GCTAGCCCCAAGAACGTTTAG 58.992 52.381 2.29 0.00 0.00 1.85
1334 1363 4.570772 TCGATTAGATTGCAGTAACAAGGC 59.429 41.667 0.00 0.00 31.96 4.35
1351 1384 5.013568 TGAATAGAAACCGGCTTCGATTA 57.986 39.130 21.23 6.69 32.75 1.75
1369 1402 1.203052 CGTTGCAAAGCATCCCTGAAT 59.797 47.619 0.00 0.00 38.76 2.57
1386 1419 0.472352 TCCCCACAACTACCTCCGTT 60.472 55.000 0.00 0.00 0.00 4.44
1401 1434 0.919710 ACTACAGGCATTTCCTCCCC 59.080 55.000 0.00 0.00 45.52 4.81
1457 1490 6.427441 TGGATTAATTACACACCAAGGCATA 58.573 36.000 0.00 0.00 0.00 3.14
1498 1531 2.748132 CGTCCTCTCTATCTCCACAGCT 60.748 54.545 0.00 0.00 0.00 4.24
1509 1542 0.738975 CATCGCCAACGTCCTCTCTA 59.261 55.000 0.00 0.00 41.18 2.43
1632 1665 3.678965 AGAAGAGTGATGCCCTCTCTA 57.321 47.619 7.82 0.00 42.93 2.43
1654 1687 0.657312 TTTTATCGGCATGCTCAGCG 59.343 50.000 18.92 12.71 0.00 5.18
1671 1704 3.817647 CACTAGGCTGTTGAAGAAGCTTT 59.182 43.478 0.00 0.00 39.46 3.51
1740 1773 7.027161 ACACACATGTCTTTAGAACAAAACAC 58.973 34.615 0.00 0.00 31.55 3.32
1741 1774 7.151999 ACACACATGTCTTTAGAACAAAACA 57.848 32.000 0.00 0.00 31.55 2.83
1742 1775 8.460831 AAACACACATGTCTTTAGAACAAAAC 57.539 30.769 0.00 0.00 38.45 2.43
1748 1781 7.122055 AGGAACAAAACACACATGTCTTTAGAA 59.878 33.333 0.00 0.00 38.45 2.10
1750 1783 6.795399 AGGAACAAAACACACATGTCTTTAG 58.205 36.000 0.00 0.00 38.45 1.85
1753 1786 4.097892 GGAGGAACAAAACACACATGTCTT 59.902 41.667 0.00 0.00 38.45 3.01
1754 1787 3.632145 GGAGGAACAAAACACACATGTCT 59.368 43.478 0.00 0.00 38.45 3.41
1755 1788 3.243401 GGGAGGAACAAAACACACATGTC 60.243 47.826 0.00 0.00 38.45 3.06
1756 1789 2.693074 GGGAGGAACAAAACACACATGT 59.307 45.455 0.00 0.00 42.46 3.21
1757 1790 2.692557 TGGGAGGAACAAAACACACATG 59.307 45.455 0.00 0.00 0.00 3.21
1758 1791 3.025322 TGGGAGGAACAAAACACACAT 57.975 42.857 0.00 0.00 0.00 3.21
1759 1792 2.516227 TGGGAGGAACAAAACACACA 57.484 45.000 0.00 0.00 0.00 3.72
1760 1793 2.100749 CCTTGGGAGGAACAAAACACAC 59.899 50.000 0.00 0.00 46.74 3.82
1761 1794 2.383855 CCTTGGGAGGAACAAAACACA 58.616 47.619 0.00 0.00 46.74 3.72
1762 1795 1.068588 GCCTTGGGAGGAACAAAACAC 59.931 52.381 0.00 0.00 46.74 3.32
1777 1810 4.748277 ATCAAATTTCCTCATGGCCTTG 57.252 40.909 12.41 12.41 0.00 3.61
1784 1817 6.384886 AGGTGGCATTAATCAAATTTCCTCAT 59.615 34.615 0.00 0.00 0.00 2.90
1787 1820 5.960202 AGAGGTGGCATTAATCAAATTTCCT 59.040 36.000 0.00 0.00 0.00 3.36
1844 1877 8.777865 TTGTATCATACCAAGAAACTGAAGAG 57.222 34.615 0.00 0.00 0.00 2.85
1923 1957 8.926374 ACATATATCAATCATCTGATCTCCTCC 58.074 37.037 0.00 0.00 37.27 4.30
2081 2276 2.288825 TGACTCCTAAGCACCAAGTTCG 60.289 50.000 0.00 0.00 0.00 3.95
2399 2667 0.629596 TGGTTTGGGTTGTGGGTGTA 59.370 50.000 0.00 0.00 0.00 2.90
2411 2679 2.422127 ACGAACACTCTGTTTGGTTTGG 59.578 45.455 7.18 0.00 44.15 3.28
2464 2732 1.185315 ATGTCCAATTTTGCTCGGGG 58.815 50.000 0.00 0.00 0.00 5.73
2565 2834 2.194201 ATACTCCACACCGGTTTTGG 57.806 50.000 21.78 21.78 35.57 3.28
2662 2931 4.024556 CAGTTCACAACACTGTCTCCAATC 60.025 45.833 0.00 0.00 37.47 2.67
2673 2942 3.002656 CCTCATGTCACAGTTCACAACAC 59.997 47.826 0.00 0.00 0.00 3.32
2705 2974 6.515272 AGTGACAAAGTGTTCAAGAATGTT 57.485 33.333 0.00 0.00 0.00 2.71
2724 2993 2.518112 TTGGGCAGCGCAAAGTGA 60.518 55.556 21.81 0.00 33.52 3.41
2797 3067 7.992180 AGTACTCAAATGCAAACAAGAAAAG 57.008 32.000 0.00 0.00 0.00 2.27
2798 3068 9.677567 GATAGTACTCAAATGCAAACAAGAAAA 57.322 29.630 0.00 0.00 0.00 2.29
2840 3113 1.399791 GTCAGAGGCTGCTTTGTATGC 59.600 52.381 0.00 0.00 0.00 3.14
2910 3185 0.753111 GCATCGGGGCTTTCCAGAAT 60.753 55.000 0.00 0.00 42.81 2.40
3169 3943 3.187432 GCAAGAGTTAGGTTCAAGCTCAC 59.813 47.826 0.00 0.00 0.00 3.51
3317 4091 6.684686 TCCGAAGAAAAACGAAATCTCTCTA 58.315 36.000 0.00 0.00 0.00 2.43
3395 4169 5.902613 TCATGGTCAGAAAATTCATGGTC 57.097 39.130 0.00 0.00 36.72 4.02
3688 4464 4.023291 ACTGGGACACACAATCAGTTTTT 58.977 39.130 0.00 0.00 35.44 1.94
3724 4500 0.643820 GCGACAAGTAATTCCGGACG 59.356 55.000 1.83 1.53 0.00 4.79
3738 4514 6.310467 GTCTAGTTACATTCATTTCTGCGACA 59.690 38.462 0.00 0.00 0.00 4.35
3788 4564 3.544684 TGCAGCACGAATGGATAGAAAT 58.455 40.909 0.00 0.00 0.00 2.17
3789 4565 2.938451 CTGCAGCACGAATGGATAGAAA 59.062 45.455 0.00 0.00 0.00 2.52
3792 4568 1.224075 CCTGCAGCACGAATGGATAG 58.776 55.000 8.66 0.00 0.00 2.08
3793 4569 0.541392 ACCTGCAGCACGAATGGATA 59.459 50.000 8.66 0.00 0.00 2.59
3794 4570 0.541392 TACCTGCAGCACGAATGGAT 59.459 50.000 8.66 0.00 0.00 3.41
3795 4571 0.323302 TTACCTGCAGCACGAATGGA 59.677 50.000 8.66 0.00 0.00 3.41
3796 4572 1.382522 ATTACCTGCAGCACGAATGG 58.617 50.000 8.66 0.00 0.00 3.16
3797 4573 2.679837 AGAATTACCTGCAGCACGAATG 59.320 45.455 8.66 0.00 0.00 2.67
3798 4574 2.679837 CAGAATTACCTGCAGCACGAAT 59.320 45.455 8.66 1.55 0.00 3.34
3799 4575 2.076100 CAGAATTACCTGCAGCACGAA 58.924 47.619 8.66 0.00 0.00 3.85
3800 4576 1.675714 CCAGAATTACCTGCAGCACGA 60.676 52.381 8.66 0.00 32.97 4.35
3801 4577 0.729116 CCAGAATTACCTGCAGCACG 59.271 55.000 8.66 0.00 32.97 5.34
3802 4578 1.740025 GTCCAGAATTACCTGCAGCAC 59.260 52.381 8.66 0.00 32.97 4.40
3805 4581 1.656652 CCGTCCAGAATTACCTGCAG 58.343 55.000 6.78 6.78 32.97 4.41
3806 4582 0.251916 CCCGTCCAGAATTACCTGCA 59.748 55.000 0.00 0.00 32.97 4.41
3807 4583 0.463833 CCCCGTCCAGAATTACCTGC 60.464 60.000 0.00 0.00 32.97 4.85
3808 4584 0.180406 CCCCCGTCCAGAATTACCTG 59.820 60.000 0.00 0.00 0.00 4.00
3809 4585 2.616489 CCCCCGTCCAGAATTACCT 58.384 57.895 0.00 0.00 0.00 3.08
3824 4600 6.884836 CAGTAAAGCCAATTATATACTCCCCC 59.115 42.308 0.00 0.00 0.00 5.40
3825 4601 6.884836 CCAGTAAAGCCAATTATATACTCCCC 59.115 42.308 0.00 0.00 0.00 4.81
3835 4611 9.487442 AGGATTTTTATCCAGTAAAGCCAATTA 57.513 29.630 6.92 0.00 43.14 1.40
3836 4612 8.379428 AGGATTTTTATCCAGTAAAGCCAATT 57.621 30.769 6.92 0.00 43.14 2.32
3837 4613 7.978099 AGGATTTTTATCCAGTAAAGCCAAT 57.022 32.000 6.92 0.00 43.14 3.16
3838 4614 8.912988 CATAGGATTTTTATCCAGTAAAGCCAA 58.087 33.333 6.92 0.00 43.14 4.52
3839 4615 7.505585 CCATAGGATTTTTATCCAGTAAAGCCA 59.494 37.037 6.92 0.00 43.14 4.75
3841 4617 7.505923 ACCCATAGGATTTTTATCCAGTAAAGC 59.494 37.037 6.92 0.00 43.14 3.51
3842 4618 8.996651 ACCCATAGGATTTTTATCCAGTAAAG 57.003 34.615 6.92 0.00 43.14 1.85
3843 4619 9.777008 AAACCCATAGGATTTTTATCCAGTAAA 57.223 29.630 6.92 0.00 43.14 2.01
3844 4620 9.777008 AAAACCCATAGGATTTTTATCCAGTAA 57.223 29.630 6.92 0.00 43.14 2.24
3847 4623 9.640952 TCTAAAACCCATAGGATTTTTATCCAG 57.359 33.333 6.92 0.00 43.14 3.86
3848 4624 9.998752 TTCTAAAACCCATAGGATTTTTATCCA 57.001 29.630 6.92 0.00 43.14 3.41
3875 4651 3.052082 CAAGCCAGTCAGCACGGG 61.052 66.667 0.00 0.00 40.69 5.28
3876 4652 2.031012 TCAAGCCAGTCAGCACGG 59.969 61.111 0.00 0.00 34.23 4.94
3877 4653 2.320587 GGTCAAGCCAGTCAGCACG 61.321 63.158 0.00 0.00 37.17 5.34
3878 4654 1.227943 TGGTCAAGCCAGTCAGCAC 60.228 57.895 0.00 0.00 43.61 4.40
3879 4655 3.239464 TGGTCAAGCCAGTCAGCA 58.761 55.556 0.00 0.00 43.61 4.41
3922 4698 5.069318 TGCATTCCATCAACTAACAAGTGA 58.931 37.500 0.00 0.00 0.00 3.41
3935 4711 2.034305 GCATCTGGACTTGCATTCCATC 59.966 50.000 16.02 5.01 42.43 3.51
3946 4970 3.713248 TCATGGATTACTGCATCTGGACT 59.287 43.478 0.00 0.00 29.89 3.85
3949 4973 3.072038 TCCTCATGGATTACTGCATCTGG 59.928 47.826 0.00 0.00 37.46 3.86
3968 4992 1.546548 GCAGCTTTGTTCTCCCTTCCT 60.547 52.381 0.00 0.00 0.00 3.36
3996 5020 6.623549 GCTGTTACTCAAGCATGCTATTTTCA 60.624 38.462 23.00 13.03 0.00 2.69
4004 7019 4.825546 ATATGCTGTTACTCAAGCATGC 57.174 40.909 17.92 10.51 46.00 4.06
4025 7040 4.020751 ACTCTTGAATCTACAGCAGAGCAA 60.021 41.667 0.00 0.00 36.48 3.91
4072 7469 2.779506 CCTCACCCTTTGTAACCAGAC 58.220 52.381 0.00 0.00 0.00 3.51
4097 7494 1.751927 CACAAGCTGGATGGGGCTC 60.752 63.158 0.00 0.00 37.87 4.70
4170 7567 4.433805 CCGTACACATCTTTTGCGTCTTAC 60.434 45.833 0.00 0.00 0.00 2.34
4176 7573 3.529634 TTTCCGTACACATCTTTTGCG 57.470 42.857 0.00 0.00 0.00 4.85
4191 7588 5.409643 AACTCATCGCTGATAATTTTCCG 57.590 39.130 0.00 0.00 0.00 4.30
4201 7598 3.380637 GGGTACTTCTAACTCATCGCTGA 59.619 47.826 0.00 0.00 0.00 4.26
4205 7602 5.776173 ATCAGGGTACTTCTAACTCATCG 57.224 43.478 0.00 0.00 0.00 3.84
4232 7685 7.830739 ACAAAGATCATCCATAAGACCAAAAC 58.169 34.615 0.00 0.00 0.00 2.43
4303 7756 2.083774 CGGCACAATTGGACTACACAT 58.916 47.619 10.83 0.00 0.00 3.21
4409 7869 9.216087 CACAATTTTATGTCGCGTATATTGAAA 57.784 29.630 5.77 5.21 0.00 2.69
4419 7879 9.858247 AGTATAATAACACAATTTTATGTCGCG 57.142 29.630 0.00 0.00 0.00 5.87


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

AutoCloner maintained by Alex Coulton.