Multiple sequence alignment - TraesCS3A01G440800

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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 TraesCS3A01G440800 chr3A 100.000 4642 0 0 1 4642 683255365 683250724 0.000000e+00 8573.0
1 TraesCS3A01G440800 chr3A 78.697 399 85 0 1957 2355 683188768 683188370 2.750000e-67 267.0
2 TraesCS3A01G440800 chr3A 89.041 73 8 0 3579 3651 683193431 683193359 1.780000e-14 91.6
3 TraesCS3A01G440800 chr3A 96.226 53 2 0 4351 4403 716884769 716884821 2.300000e-13 87.9
4 TraesCS3A01G440800 chr3D 92.121 3541 159 48 496 3989 546478682 546475215 0.000000e+00 4883.0
5 TraesCS3A01G440800 chr3D 90.168 417 35 2 1 412 546479105 546478690 5.280000e-149 538.0
6 TraesCS3A01G440800 chr3D 90.179 224 20 1 1 224 546484382 546484161 1.630000e-74 291.0
7 TraesCS3A01G440800 chr3D 79.500 400 80 2 1957 2355 546332624 546332226 2.730000e-72 283.0
8 TraesCS3A01G440800 chr3B 92.041 2802 143 32 1784 4536 723507686 723504916 0.000000e+00 3866.0
9 TraesCS3A01G440800 chr3B 87.043 1150 60 44 496 1633 723508826 723507754 0.000000e+00 1216.0
10 TraesCS3A01G440800 chr3B 92.704 233 17 0 1 233 723509421 723509189 2.070000e-88 337.0
11 TraesCS3A01G440800 chr3B 80.702 399 77 0 1957 2355 723445400 723445002 1.250000e-80 311.0
12 TraesCS3A01G440800 chr3B 88.832 197 12 1 226 412 723509030 723508834 2.790000e-57 233.0
13 TraesCS3A01G440800 chr3B 91.250 80 2 1 4568 4642 723504918 723504839 2.280000e-18 104.0
14 TraesCS3A01G440800 chr2B 75.626 878 185 22 2771 3642 435156423 435157277 4.320000e-110 409.0
15 TraesCS3A01G440800 chr2A 78.203 523 112 2 3121 3642 495958341 495958862 2.680000e-87 333.0


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 TraesCS3A01G440800 chr3A 683250724 683255365 4641 True 8573.0 8573 100.0000 1 4642 1 chr3A.!!$R3 4641
1 TraesCS3A01G440800 chr3D 546475215 546479105 3890 True 2710.5 4883 91.1445 1 3989 2 chr3D.!!$R3 3988
2 TraesCS3A01G440800 chr3B 723504839 723509421 4582 True 1151.2 3866 90.3740 1 4642 5 chr3B.!!$R2 4641
3 TraesCS3A01G440800 chr2B 435156423 435157277 854 False 409.0 409 75.6260 2771 3642 1 chr2B.!!$F1 871
4 TraesCS3A01G440800 chr2A 495958341 495958862 521 False 333.0 333 78.2030 3121 3642 1 chr2A.!!$F1 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
414 596 0.038166 TGATTTGGGCCCACAGACTC 59.962 55.0 28.70 14.84 0.00 3.36 F
1048 1236 0.100861 GGTCTCGGCGTAGGAAGAAG 59.899 60.0 6.85 0.00 0.00 2.85 F
1239 1431 0.035630 CAGAGAGAGGGGCAGGTTTG 60.036 60.0 0.00 0.00 0.00 2.93 F
1396 1595 0.035915 GAGGGGCCTTGTCTTGACTC 60.036 60.0 0.84 0.00 0.00 3.36 F
1928 2134 0.665369 CTTTGCTCTGCTTTTGGGCG 60.665 55.0 0.00 0.00 34.52 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1238 1430 0.326143 TCATCTTCCCGATCCCCACA 60.326 55.000 0.00 0.0 0.00 4.17 R
2175 2381 1.080366 GTCGCATGTCGGGTACACA 60.080 57.895 9.16 0.0 42.09 3.72 R
2973 3210 2.552599 TTGCCGGTGTCATAGAACAA 57.447 45.000 1.90 0.0 0.00 2.83 R
3272 3509 2.279037 AAACCACGGCTTCCACCAGT 62.279 55.000 0.00 0.0 0.00 4.00 R
3701 3939 1.884235 AGGCGCAAAGTATATCAGGC 58.116 50.000 10.83 0.0 0.00 4.85 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
51 52 2.718731 CGTCGGTTTTGGCTTGCA 59.281 55.556 0.00 0.00 0.00 4.08
95 96 2.452600 TTTGGCTCTTCCACCACTTT 57.547 45.000 0.00 0.00 46.55 2.66
161 167 8.090214 GGTATAATTTTCATTCATCCCATGTGG 58.910 37.037 0.00 0.00 0.00 4.17
196 202 7.865706 ATTCAAATTACTATGGAGAAAGCGT 57.134 32.000 0.00 0.00 0.00 5.07
220 226 6.089685 GTCTTTTCTCATAGACGTGGAAGAAC 59.910 42.308 0.00 0.00 32.31 3.01
230 402 1.927174 CGTGGAAGAACGATCATGACC 59.073 52.381 0.00 0.00 46.49 4.02
336 518 1.190984 CGATCGTCGGCTGAAATGATG 59.809 52.381 7.03 1.77 36.00 3.07
350 532 5.483811 TGAAATGATGTGAGCCGTTAGTTA 58.516 37.500 0.00 0.00 0.00 2.24
361 543 1.422662 GTTAGTTACGGCTTGCGGC 59.577 57.895 0.00 0.00 40.90 6.53
412 594 0.890683 CTTGATTTGGGCCCACAGAC 59.109 55.000 28.70 17.08 0.00 3.51
413 595 0.482446 TTGATTTGGGCCCACAGACT 59.518 50.000 28.70 3.65 0.00 3.24
414 596 0.038166 TGATTTGGGCCCACAGACTC 59.962 55.000 28.70 14.84 0.00 3.36
415 597 0.681243 GATTTGGGCCCACAGACTCC 60.681 60.000 28.70 5.82 0.00 3.85
416 598 1.142688 ATTTGGGCCCACAGACTCCT 61.143 55.000 28.70 0.00 0.00 3.69
417 599 1.360393 TTTGGGCCCACAGACTCCTT 61.360 55.000 28.70 0.00 0.00 3.36
418 600 0.474854 TTGGGCCCACAGACTCCTTA 60.475 55.000 28.70 1.58 0.00 2.69
419 601 0.909610 TGGGCCCACAGACTCCTTAG 60.910 60.000 24.45 0.00 0.00 2.18
420 602 1.222113 GGCCCACAGACTCCTTAGC 59.778 63.158 0.00 0.00 0.00 3.09
421 603 1.153549 GCCCACAGACTCCTTAGCG 60.154 63.158 0.00 0.00 0.00 4.26
422 604 1.889530 GCCCACAGACTCCTTAGCGT 61.890 60.000 0.00 0.00 0.00 5.07
423 605 0.173708 CCCACAGACTCCTTAGCGTC 59.826 60.000 0.00 0.00 0.00 5.19
424 606 1.178276 CCACAGACTCCTTAGCGTCT 58.822 55.000 0.00 0.00 40.92 4.18
425 607 1.133407 CCACAGACTCCTTAGCGTCTC 59.867 57.143 0.55 0.00 38.37 3.36
426 608 2.088423 CACAGACTCCTTAGCGTCTCT 58.912 52.381 0.55 0.00 38.37 3.10
427 609 3.271729 CACAGACTCCTTAGCGTCTCTA 58.728 50.000 0.55 0.00 38.37 2.43
428 610 3.064271 CACAGACTCCTTAGCGTCTCTAC 59.936 52.174 0.55 0.00 38.37 2.59
429 611 3.054948 ACAGACTCCTTAGCGTCTCTACT 60.055 47.826 0.55 0.00 38.37 2.57
430 612 3.558418 CAGACTCCTTAGCGTCTCTACTC 59.442 52.174 0.55 0.00 38.37 2.59
431 613 2.540931 GACTCCTTAGCGTCTCTACTCG 59.459 54.545 0.00 0.00 0.00 4.18
432 614 2.168106 ACTCCTTAGCGTCTCTACTCGA 59.832 50.000 0.00 0.00 0.00 4.04
433 615 2.540931 CTCCTTAGCGTCTCTACTCGAC 59.459 54.545 0.00 0.00 0.00 4.20
434 616 1.598601 CCTTAGCGTCTCTACTCGACC 59.401 57.143 0.00 0.00 0.00 4.79
435 617 2.553086 CTTAGCGTCTCTACTCGACCT 58.447 52.381 0.00 0.00 0.00 3.85
436 618 3.492309 CCTTAGCGTCTCTACTCGACCTA 60.492 52.174 0.00 0.00 0.00 3.08
437 619 2.687700 AGCGTCTCTACTCGACCTAA 57.312 50.000 0.00 0.00 0.00 2.69
438 620 2.983229 AGCGTCTCTACTCGACCTAAA 58.017 47.619 0.00 0.00 0.00 1.85
439 621 3.341823 AGCGTCTCTACTCGACCTAAAA 58.658 45.455 0.00 0.00 0.00 1.52
440 622 3.946558 AGCGTCTCTACTCGACCTAAAAT 59.053 43.478 0.00 0.00 0.00 1.82
441 623 4.036352 GCGTCTCTACTCGACCTAAAATG 58.964 47.826 0.00 0.00 0.00 2.32
442 624 4.599047 CGTCTCTACTCGACCTAAAATGG 58.401 47.826 0.00 0.00 0.00 3.16
443 625 4.334759 CGTCTCTACTCGACCTAAAATGGA 59.665 45.833 0.00 0.00 0.00 3.41
444 626 5.580661 GTCTCTACTCGACCTAAAATGGAC 58.419 45.833 0.00 0.00 0.00 4.02
445 627 4.643784 TCTCTACTCGACCTAAAATGGACC 59.356 45.833 0.00 0.00 0.00 4.46
446 628 2.667473 ACTCGACCTAAAATGGACCG 57.333 50.000 0.00 0.00 0.00 4.79
447 629 1.206371 ACTCGACCTAAAATGGACCGG 59.794 52.381 0.00 0.00 0.00 5.28
448 630 1.206371 CTCGACCTAAAATGGACCGGT 59.794 52.381 6.92 6.92 0.00 5.28
449 631 1.066716 TCGACCTAAAATGGACCGGTG 60.067 52.381 14.63 0.00 0.00 4.94
450 632 1.746470 GACCTAAAATGGACCGGTGG 58.254 55.000 14.63 6.84 0.00 4.61
451 633 1.279846 GACCTAAAATGGACCGGTGGA 59.720 52.381 14.63 0.00 0.00 4.02
452 634 1.003928 ACCTAAAATGGACCGGTGGAC 59.996 52.381 14.63 1.94 0.00 4.02
453 635 1.280998 CCTAAAATGGACCGGTGGACT 59.719 52.381 14.63 0.00 0.00 3.85
454 636 2.290705 CCTAAAATGGACCGGTGGACTT 60.291 50.000 14.63 0.79 0.00 3.01
455 637 2.375014 AAAATGGACCGGTGGACTTT 57.625 45.000 14.63 3.40 0.00 2.66
456 638 1.616159 AAATGGACCGGTGGACTTTG 58.384 50.000 14.63 0.00 0.00 2.77
457 639 0.768622 AATGGACCGGTGGACTTTGA 59.231 50.000 14.63 0.00 0.00 2.69
458 640 0.768622 ATGGACCGGTGGACTTTGAA 59.231 50.000 14.63 0.00 0.00 2.69
459 641 0.107831 TGGACCGGTGGACTTTGAAG 59.892 55.000 14.63 0.00 0.00 3.02
460 642 0.605589 GGACCGGTGGACTTTGAAGG 60.606 60.000 14.63 0.00 0.00 3.46
461 643 0.395312 GACCGGTGGACTTTGAAGGA 59.605 55.000 14.63 0.00 0.00 3.36
462 644 1.003233 GACCGGTGGACTTTGAAGGAT 59.997 52.381 14.63 0.00 0.00 3.24
463 645 1.003233 ACCGGTGGACTTTGAAGGATC 59.997 52.381 6.12 0.00 0.00 3.36
464 646 1.003118 CCGGTGGACTTTGAAGGATCA 59.997 52.381 0.00 0.00 0.00 2.92
465 647 2.350522 CGGTGGACTTTGAAGGATCAG 58.649 52.381 0.00 0.00 36.78 2.90
466 648 2.716217 GGTGGACTTTGAAGGATCAGG 58.284 52.381 0.00 0.00 36.78 3.86
467 649 2.305927 GGTGGACTTTGAAGGATCAGGA 59.694 50.000 0.00 0.00 36.78 3.86
468 650 3.244911 GGTGGACTTTGAAGGATCAGGAA 60.245 47.826 0.00 0.00 36.78 3.36
469 651 4.006319 GTGGACTTTGAAGGATCAGGAAG 58.994 47.826 0.00 0.00 36.78 3.46
470 652 3.909995 TGGACTTTGAAGGATCAGGAAGA 59.090 43.478 0.00 0.00 36.78 2.87
471 653 4.019860 TGGACTTTGAAGGATCAGGAAGAG 60.020 45.833 0.00 0.00 36.78 2.85
472 654 4.223923 GGACTTTGAAGGATCAGGAAGAGA 59.776 45.833 0.00 0.00 36.78 3.10
473 655 5.280215 GGACTTTGAAGGATCAGGAAGAGAA 60.280 44.000 0.00 0.00 36.78 2.87
474 656 5.803552 ACTTTGAAGGATCAGGAAGAGAAG 58.196 41.667 0.00 0.00 36.78 2.85
475 657 3.902881 TGAAGGATCAGGAAGAGAAGC 57.097 47.619 0.00 0.00 0.00 3.86
476 658 3.176411 TGAAGGATCAGGAAGAGAAGCA 58.824 45.455 0.00 0.00 0.00 3.91
477 659 3.779183 TGAAGGATCAGGAAGAGAAGCAT 59.221 43.478 0.00 0.00 0.00 3.79
478 660 4.141756 TGAAGGATCAGGAAGAGAAGCATC 60.142 45.833 0.00 0.00 0.00 3.91
479 661 3.656496 AGGATCAGGAAGAGAAGCATCT 58.344 45.455 0.00 0.00 39.10 2.90
480 662 3.388676 AGGATCAGGAAGAGAAGCATCTG 59.611 47.826 0.00 0.00 35.54 2.90
481 663 3.387374 GGATCAGGAAGAGAAGCATCTGA 59.613 47.826 0.00 0.00 35.54 3.27
482 664 4.501915 GGATCAGGAAGAGAAGCATCTGAG 60.502 50.000 0.00 0.00 35.54 3.35
483 665 2.168106 TCAGGAAGAGAAGCATCTGAGC 59.832 50.000 0.00 0.00 35.54 4.26
484 666 1.485895 AGGAAGAGAAGCATCTGAGCC 59.514 52.381 0.00 0.00 35.54 4.70
485 667 1.209019 GGAAGAGAAGCATCTGAGCCA 59.791 52.381 0.00 0.00 35.54 4.75
486 668 2.278854 GAAGAGAAGCATCTGAGCCAC 58.721 52.381 0.00 0.00 35.54 5.01
487 669 0.540923 AGAGAAGCATCTGAGCCACC 59.459 55.000 0.00 0.00 35.54 4.61
488 670 0.540923 GAGAAGCATCTGAGCCACCT 59.459 55.000 0.00 0.00 35.54 4.00
591 773 7.557719 CAGAGGACCCAAATACAGTATCAATTT 59.442 37.037 0.00 0.00 0.00 1.82
597 779 9.131791 ACCCAAATACAGTATCAATTTATCACC 57.868 33.333 0.00 0.00 0.00 4.02
663 845 5.711976 TGCTAAAGAATGAGGGAAAAAGAGG 59.288 40.000 0.00 0.00 0.00 3.69
695 877 5.163764 TGACAGTTGACAAGTTGACATGTTC 60.164 40.000 10.54 7.07 0.00 3.18
703 885 4.704540 ACAAGTTGACATGTTCAAGGTGAA 59.295 37.500 10.54 0.00 45.23 3.18
730 912 1.550524 TGAGAGGTCGAATGTCCAAGG 59.449 52.381 0.00 0.00 0.00 3.61
741 923 0.991355 TGTCCAAGGTGGGTGAGGTT 60.991 55.000 0.00 0.00 38.32 3.50
823 1006 1.266786 CGCCGCGTTAGACTAATCCG 61.267 60.000 4.92 4.63 0.00 4.18
930 1117 4.459089 GCGGACAGCTCTCCCACC 62.459 72.222 1.99 0.00 44.04 4.61
932 1119 2.284995 GGACAGCTCTCCCACCCT 60.285 66.667 0.00 0.00 0.00 4.34
934 1121 2.284995 ACAGCTCTCCCACCCTCC 60.285 66.667 0.00 0.00 0.00 4.30
936 1123 3.288381 AGCTCTCCCACCCTCCCT 61.288 66.667 0.00 0.00 0.00 4.20
957 1144 0.967887 CCTCCTCGTCTCTCAGCCAA 60.968 60.000 0.00 0.00 0.00 4.52
975 1162 3.750922 GCCAACAGTATTAATCCCCTCCC 60.751 52.174 0.00 0.00 0.00 4.30
995 1183 0.846870 CCCCTTCCCTCCCTTGAAGT 60.847 60.000 0.00 0.00 36.98 3.01
996 1184 0.621082 CCCTTCCCTCCCTTGAAGTC 59.379 60.000 0.00 0.00 36.98 3.01
1020 1208 2.105006 TGAGCAGCTCTGATTGTTCC 57.895 50.000 23.15 0.00 0.00 3.62
1031 1219 1.347707 TGATTGTTCCTCAAGCTCGGT 59.652 47.619 0.00 0.00 42.20 4.69
1044 1232 2.046023 TCGGTCTCGGCGTAGGAA 60.046 61.111 6.85 0.00 36.95 3.36
1045 1233 2.049475 CTCGGTCTCGGCGTAGGAAG 62.049 65.000 6.85 0.00 36.95 3.46
1046 1234 2.110967 CGGTCTCGGCGTAGGAAGA 61.111 63.158 6.85 0.00 0.00 2.87
1047 1235 1.651240 CGGTCTCGGCGTAGGAAGAA 61.651 60.000 6.85 0.00 0.00 2.52
1048 1236 0.100861 GGTCTCGGCGTAGGAAGAAG 59.899 60.000 6.85 0.00 0.00 2.85
1049 1237 1.093159 GTCTCGGCGTAGGAAGAAGA 58.907 55.000 6.85 0.00 0.00 2.87
1050 1238 1.471684 GTCTCGGCGTAGGAAGAAGAA 59.528 52.381 6.85 0.00 0.00 2.52
1051 1239 2.094854 GTCTCGGCGTAGGAAGAAGAAA 60.095 50.000 6.85 0.00 0.00 2.52
1052 1240 2.163815 TCTCGGCGTAGGAAGAAGAAAG 59.836 50.000 6.85 0.00 0.00 2.62
1053 1241 1.203994 TCGGCGTAGGAAGAAGAAAGG 59.796 52.381 6.85 0.00 0.00 3.11
1054 1242 1.739371 CGGCGTAGGAAGAAGAAAGGG 60.739 57.143 0.00 0.00 0.00 3.95
1055 1243 1.553704 GGCGTAGGAAGAAGAAAGGGA 59.446 52.381 0.00 0.00 0.00 4.20
1056 1244 2.027469 GGCGTAGGAAGAAGAAAGGGAA 60.027 50.000 0.00 0.00 0.00 3.97
1057 1245 3.263261 GCGTAGGAAGAAGAAAGGGAAG 58.737 50.000 0.00 0.00 0.00 3.46
1058 1246 3.263261 CGTAGGAAGAAGAAAGGGAAGC 58.737 50.000 0.00 0.00 0.00 3.86
1059 1247 2.889170 AGGAAGAAGAAAGGGAAGCC 57.111 50.000 0.00 0.00 0.00 4.35
1060 1248 2.353349 AGGAAGAAGAAAGGGAAGCCT 58.647 47.619 0.00 0.00 0.00 4.58
1061 1249 3.532102 AGGAAGAAGAAAGGGAAGCCTA 58.468 45.455 0.00 0.00 0.00 3.93
1062 1250 3.521531 AGGAAGAAGAAAGGGAAGCCTAG 59.478 47.826 0.00 0.00 0.00 3.02
1063 1251 3.371059 GGAAGAAGAAAGGGAAGCCTAGG 60.371 52.174 3.67 3.67 0.00 3.02
1064 1252 3.207044 AGAAGAAAGGGAAGCCTAGGA 57.793 47.619 14.75 0.00 0.00 2.94
1065 1253 3.741955 AGAAGAAAGGGAAGCCTAGGAT 58.258 45.455 14.75 1.88 0.00 3.24
1116 1308 1.460255 CTTCTTGGTGGGGCAAGGA 59.540 57.895 0.00 0.00 0.00 3.36
1117 1309 0.178964 CTTCTTGGTGGGGCAAGGAA 60.179 55.000 0.00 0.00 0.00 3.36
1118 1310 0.178964 TTCTTGGTGGGGCAAGGAAG 60.179 55.000 0.00 0.00 0.00 3.46
1119 1311 1.607467 CTTGGTGGGGCAAGGAAGG 60.607 63.158 0.00 0.00 0.00 3.46
1139 1331 1.133216 GAATTGCCGGAAAAGCCTCTC 59.867 52.381 5.05 0.00 0.00 3.20
1147 1339 1.854507 AAAAGCCTCTCCCCTGCCT 60.855 57.895 0.00 0.00 0.00 4.75
1200 1392 3.739519 CGATTGCCTAGAGGTTCAGAAGG 60.740 52.174 0.00 0.00 37.57 3.46
1201 1393 1.573108 TGCCTAGAGGTTCAGAAGGG 58.427 55.000 0.00 0.00 37.57 3.95
1202 1394 0.179234 GCCTAGAGGTTCAGAAGGGC 59.821 60.000 0.00 0.00 37.57 5.19
1203 1395 1.573108 CCTAGAGGTTCAGAAGGGCA 58.427 55.000 0.00 0.00 0.00 5.36
1204 1396 1.484240 CCTAGAGGTTCAGAAGGGCAG 59.516 57.143 0.00 0.00 0.00 4.85
1205 1397 2.461695 CTAGAGGTTCAGAAGGGCAGA 58.538 52.381 0.00 0.00 0.00 4.26
1206 1398 1.274712 AGAGGTTCAGAAGGGCAGAG 58.725 55.000 0.00 0.00 0.00 3.35
1207 1399 0.392327 GAGGTTCAGAAGGGCAGAGC 60.392 60.000 0.00 0.00 0.00 4.09
1209 1401 2.046892 TTCAGAAGGGCAGAGCGC 60.047 61.111 0.00 0.00 41.91 5.92
1227 1419 2.438614 CGGAGCCGGACAGAGAGA 60.439 66.667 5.05 0.00 35.56 3.10
1228 1420 2.477176 CGGAGCCGGACAGAGAGAG 61.477 68.421 5.05 0.00 35.56 3.20
1230 1422 2.043450 AGCCGGACAGAGAGAGGG 60.043 66.667 5.05 0.00 0.00 4.30
1231 1423 3.151022 GCCGGACAGAGAGAGGGG 61.151 72.222 5.05 0.00 0.00 4.79
1232 1424 3.151022 CCGGACAGAGAGAGGGGC 61.151 72.222 0.00 0.00 0.00 5.80
1233 1425 2.363018 CGGACAGAGAGAGGGGCA 60.363 66.667 0.00 0.00 0.00 5.36
1234 1426 2.422231 CGGACAGAGAGAGGGGCAG 61.422 68.421 0.00 0.00 0.00 4.85
1235 1427 2.063378 GGACAGAGAGAGGGGCAGG 61.063 68.421 0.00 0.00 0.00 4.85
1236 1428 1.305718 GACAGAGAGAGGGGCAGGT 60.306 63.158 0.00 0.00 0.00 4.00
1237 1429 0.907230 GACAGAGAGAGGGGCAGGTT 60.907 60.000 0.00 0.00 0.00 3.50
1238 1430 0.474660 ACAGAGAGAGGGGCAGGTTT 60.475 55.000 0.00 0.00 0.00 3.27
1239 1431 0.035630 CAGAGAGAGGGGCAGGTTTG 60.036 60.000 0.00 0.00 0.00 2.93
1249 1441 2.046285 GCAGGTTTGTGGGGATCGG 61.046 63.158 0.00 0.00 0.00 4.18
1252 1444 1.137594 AGGTTTGTGGGGATCGGGAA 61.138 55.000 0.00 0.00 0.00 3.97
1396 1595 0.035915 GAGGGGCCTTGTCTTGACTC 60.036 60.000 0.84 0.00 0.00 3.36
1411 1610 3.868757 TGACTCTTGACTTGATACCCG 57.131 47.619 0.00 0.00 0.00 5.28
1595 1796 4.973168 TGATTGCTTGTGGTTAGACTTCT 58.027 39.130 0.00 0.00 0.00 2.85
1609 1810 2.909006 AGACTTCTCCAGCCTGAATTCA 59.091 45.455 8.12 8.12 0.00 2.57
1624 1825 3.826157 TGAATTCACAGGTCCCATTTCAC 59.174 43.478 3.38 0.00 0.00 3.18
1634 1835 3.382546 GGTCCCATTTCACAATCAGATGG 59.617 47.826 0.00 0.00 37.57 3.51
1644 1845 3.630769 CACAATCAGATGGGACTGGATTG 59.369 47.826 10.21 10.21 38.99 2.67
1651 1852 4.102210 CAGATGGGACTGGATTGTACAGAT 59.898 45.833 0.00 0.00 39.24 2.90
1656 1857 4.202264 GGGACTGGATTGTACAGATAGGTG 60.202 50.000 0.00 0.00 39.24 4.00
1677 1878 4.338400 GTGGAATGGGGTAGTTTCTATTGC 59.662 45.833 0.00 0.00 0.00 3.56
1748 1954 9.807649 ACTATCTTTTATTGAACATCCAAATGC 57.192 29.630 0.00 0.00 36.26 3.56
1782 1988 7.124901 ACCTCAGTTCATATAGTCAAGACATGT 59.875 37.037 0.00 0.00 0.00 3.21
1790 1996 2.688507 AGTCAAGACATGTACCTTGCG 58.311 47.619 18.09 1.72 39.53 4.85
1852 2058 9.649316 AGAGTATTAGAGTTAGACCTTGCTTAT 57.351 33.333 0.00 0.00 0.00 1.73
1853 2059 9.902196 GAGTATTAGAGTTAGACCTTGCTTATC 57.098 37.037 0.00 0.00 0.00 1.75
1928 2134 0.665369 CTTTGCTCTGCTTTTGGGCG 60.665 55.000 0.00 0.00 34.52 6.13
2175 2381 1.338769 GCGGATTGGTTCTACACACCT 60.339 52.381 0.00 0.00 35.07 4.00
2319 2525 3.426695 GGGCAGATCATTTCTTTGTCACG 60.427 47.826 0.00 0.00 29.93 4.35
2453 2685 4.881273 AGTACATGTGTTTTGAACAGCTGA 59.119 37.500 23.35 0.00 43.10 4.26
2459 2691 3.319122 GTGTTTTGAACAGCTGAGGGATT 59.681 43.478 23.35 2.90 43.10 3.01
2491 2723 2.057137 ACAAAGCATGTGGACAGTGT 57.943 45.000 0.00 0.00 41.93 3.55
2559 2791 7.368833 GCAACTCTGACTTAAGTACTTCAGTA 58.631 38.462 19.83 6.59 37.38 2.74
2687 2923 2.732844 TGCCAATCTGCCATGTCATA 57.267 45.000 0.00 0.00 0.00 2.15
2697 2933 4.398988 TCTGCCATGTCATACCATGTTTTC 59.601 41.667 0.00 0.00 40.50 2.29
2745 2982 5.221402 TGCTTATTCCAGCACAATTTTGTCA 60.221 36.000 0.00 0.00 45.14 3.58
2756 2993 7.222417 CAGCACAATTTTGTCATTCTGTAACAA 59.778 33.333 0.00 0.00 39.91 2.83
2759 2996 9.467258 CACAATTTTGTCATTCTGTAACAAGAT 57.533 29.630 0.00 0.00 39.91 2.40
2795 3032 3.424703 TCAGGAAGAGAAAGCAATTGGG 58.575 45.455 7.72 0.00 0.00 4.12
2933 3170 6.894103 AGAAAATGCAGAATCACCTTATTCCT 59.106 34.615 0.00 0.00 36.68 3.36
2936 3173 2.620585 GCAGAATCACCTTATTCCTGGC 59.379 50.000 0.00 0.00 36.68 4.85
2959 3196 1.005630 CCCCTCGATCCATCTTCGC 60.006 63.158 0.00 0.00 36.56 4.70
2973 3210 1.274167 TCTTCGCATACTTCCGTGGTT 59.726 47.619 0.00 0.00 0.00 3.67
3017 3254 1.625818 CCTGAGGGTGGATACTATGCC 59.374 57.143 0.00 0.00 37.61 4.40
3024 3261 3.587506 GGGTGGATACTATGCCAGGTAAT 59.412 47.826 0.00 0.00 34.22 1.89
3051 3288 3.433274 TGTCTGTCGAAAACTGATGCATC 59.567 43.478 20.14 20.14 38.02 3.91
3084 3321 5.848921 AGATCCTGCTATTCCCTCTTATTGT 59.151 40.000 0.00 0.00 0.00 2.71
3091 3328 9.125026 CTGCTATTCCCTCTTATTGTATTGTTT 57.875 33.333 0.00 0.00 0.00 2.83
3092 3329 9.474313 TGCTATTCCCTCTTATTGTATTGTTTT 57.526 29.630 0.00 0.00 0.00 2.43
3380 3617 0.034896 AGATCGGCGTGTTTGTTCCT 59.965 50.000 6.85 0.00 0.00 3.36
3425 3662 1.848388 AGCATCCTGACATCCATTCCA 59.152 47.619 0.00 0.00 0.00 3.53
3545 3782 1.940613 CAGATACTTAACGGGCTTGCC 59.059 52.381 2.49 2.49 0.00 4.52
3825 4078 6.789959 AGTATACCATAGAGCTTCATCCCTTT 59.210 38.462 0.00 0.00 0.00 3.11
3880 4133 3.374220 AATGTGTCAACCATTGTGCAG 57.626 42.857 0.00 0.00 31.52 4.41
3887 4140 3.551485 GTCAACCATTGTGCAGTTTGTTC 59.449 43.478 0.00 0.00 0.00 3.18
3903 4156 7.798516 GCAGTTTGTTCGTTATATGTGGATATG 59.201 37.037 0.00 0.00 0.00 1.78
3934 4187 8.601546 TGGAAATTGCAAGATTTAAACCCTATT 58.398 29.630 4.94 0.00 29.75 1.73
3950 4203 4.142004 ACCCTATTGACCGTCTGATGTTAC 60.142 45.833 0.00 0.00 0.00 2.50
3976 4236 1.094073 ACATGCTTGCGATCTCCAGC 61.094 55.000 1.93 1.93 0.00 4.85
3978 4238 0.755079 ATGCTTGCGATCTCCAGCTA 59.245 50.000 9.84 0.00 0.00 3.32
4027 4287 2.496899 TCATCCCCTCTCTGTTTTGC 57.503 50.000 0.00 0.00 0.00 3.68
4057 4317 5.232610 CTGATGAACAGGAGAGAAATTGC 57.767 43.478 0.00 0.00 42.39 3.56
4058 4318 3.686241 TGATGAACAGGAGAGAAATTGCG 59.314 43.478 0.00 0.00 0.00 4.85
4061 4321 3.748048 TGAACAGGAGAGAAATTGCGAAG 59.252 43.478 0.00 0.00 0.00 3.79
4063 4323 3.070018 ACAGGAGAGAAATTGCGAAGTG 58.930 45.455 0.00 0.00 0.00 3.16
4064 4324 2.417933 CAGGAGAGAAATTGCGAAGTGG 59.582 50.000 0.00 0.00 0.00 4.00
4095 4355 3.940221 GCATTGCTATCTCATCTGGATCC 59.060 47.826 4.20 4.20 0.00 3.36
4110 4374 2.972021 TGGATCCTGTCAGTTTGAGTGA 59.028 45.455 14.23 0.00 0.00 3.41
4111 4375 3.244215 TGGATCCTGTCAGTTTGAGTGAC 60.244 47.826 14.23 8.58 46.17 3.67
4122 4386 1.801242 TTGAGTGACTGGGGACTTGA 58.199 50.000 0.00 0.00 0.00 3.02
4124 4388 0.610687 GAGTGACTGGGGACTTGAGG 59.389 60.000 0.00 0.00 0.00 3.86
4130 4394 4.410400 GGGGACTTGAGGGTGGCG 62.410 72.222 0.00 0.00 0.00 5.69
4135 4399 1.065709 GGACTTGAGGGTGGCGATTAA 60.066 52.381 0.00 0.00 0.00 1.40
4162 4429 4.878971 TGTAGCTGCAGTCTTTGTGTAAAA 59.121 37.500 16.64 0.00 0.00 1.52
4163 4430 5.530915 TGTAGCTGCAGTCTTTGTGTAAAAT 59.469 36.000 16.64 0.00 0.00 1.82
4164 4431 6.708502 TGTAGCTGCAGTCTTTGTGTAAAATA 59.291 34.615 16.64 0.00 0.00 1.40
4165 4432 6.824305 AGCTGCAGTCTTTGTGTAAAATAT 57.176 33.333 16.64 0.00 0.00 1.28
4166 4433 7.921786 AGCTGCAGTCTTTGTGTAAAATATA 57.078 32.000 16.64 0.00 0.00 0.86
4168 4435 8.616076 AGCTGCAGTCTTTGTGTAAAATATATC 58.384 33.333 16.64 0.00 0.00 1.63
4209 4476 1.067974 TGTTCAGACGTGTGACCGAAT 59.932 47.619 15.88 0.00 0.00 3.34
4219 4486 0.240945 GTGACCGAATTGGCCAACAG 59.759 55.000 23.27 14.74 43.94 3.16
4249 4516 3.415212 TGGCTCTTCTGAAGTTTGGATG 58.585 45.455 16.43 2.45 0.00 3.51
4253 4520 4.805609 GCTCTTCTGAAGTTTGGATGTCCT 60.806 45.833 16.43 0.00 36.82 3.85
4256 4523 2.373169 TCTGAAGTTTGGATGTCCTGCT 59.627 45.455 0.09 0.00 36.82 4.24
4257 4524 3.152341 CTGAAGTTTGGATGTCCTGCTT 58.848 45.455 0.09 2.50 36.82 3.91
4258 4525 2.886523 TGAAGTTTGGATGTCCTGCTTG 59.113 45.455 0.09 0.00 36.82 4.01
4259 4526 2.664402 AGTTTGGATGTCCTGCTTGT 57.336 45.000 0.09 0.00 36.82 3.16
4270 4539 3.249805 TGCTTGTTGGCAGAGGGA 58.750 55.556 0.00 0.00 37.29 4.20
4302 4579 1.202927 CCAACAGTCCACACCCATCTT 60.203 52.381 0.00 0.00 0.00 2.40
4319 4596 1.005450 TCTTAATGGGCCTGGGTGAAC 59.995 52.381 4.53 0.00 0.00 3.18
4336 4613 0.841289 AACGTTGTCCAAGGGGAGAA 59.159 50.000 0.00 0.00 46.12 2.87
4437 4716 2.165301 CCGACCGAATCCGCTGTTC 61.165 63.158 0.00 0.00 0.00 3.18
4484 4763 2.790791 CGCGGGGAGAAGCAGATCT 61.791 63.158 0.00 0.00 0.00 2.75
4528 4807 1.918609 GAGCACACGAGGTAAATCGAC 59.081 52.381 2.78 0.00 45.56 4.20
4536 4815 3.754766 GGTAAATCGACCTCGGCTT 57.245 52.632 0.00 0.00 40.29 4.35
4537 4816 2.019948 GGTAAATCGACCTCGGCTTT 57.980 50.000 0.00 0.00 40.29 3.51
4538 4817 1.664151 GGTAAATCGACCTCGGCTTTG 59.336 52.381 0.00 0.00 40.29 2.77
4539 4818 1.664151 GTAAATCGACCTCGGCTTTGG 59.336 52.381 0.00 0.00 40.29 3.28
4540 4819 0.676782 AAATCGACCTCGGCTTTGGG 60.677 55.000 0.00 0.00 40.29 4.12
4541 4820 1.838073 AATCGACCTCGGCTTTGGGT 61.838 55.000 0.00 0.00 40.29 4.51
4542 4821 2.240162 ATCGACCTCGGCTTTGGGTC 62.240 60.000 0.00 0.00 44.16 4.46
4543 4822 2.046217 GACCTCGGCTTTGGGTCC 60.046 66.667 0.00 0.00 42.45 4.46
4544 4823 2.529389 ACCTCGGCTTTGGGTCCT 60.529 61.111 0.00 0.00 0.00 3.85
4545 4824 2.045926 CCTCGGCTTTGGGTCCTG 60.046 66.667 0.00 0.00 0.00 3.86
4546 4825 2.045926 CTCGGCTTTGGGTCCTGG 60.046 66.667 0.00 0.00 0.00 4.45
4547 4826 4.344865 TCGGCTTTGGGTCCTGGC 62.345 66.667 0.00 0.00 0.00 4.85
4602 4881 1.078759 CTCTGTTTAGGCGCCACGAG 61.079 60.000 31.54 21.91 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.084370 GTTTCCAGTGGCGATCGGAG 61.084 60.000 18.30 0.00 0.00 4.63
51 52 2.906389 TGAGTATCAGCAAACCCACTCT 59.094 45.455 0.00 0.00 42.56 3.24
95 96 1.554617 TGAATCAAGCGGGACTGATCA 59.445 47.619 0.00 0.00 0.00 2.92
177 183 7.824779 AGAAAAGACGCTTTCTCCATAGTAATT 59.175 33.333 5.51 0.00 40.84 1.40
196 202 5.977489 TCTTCCACGTCTATGAGAAAAGA 57.023 39.130 0.00 0.00 0.00 2.52
217 223 1.278238 GTCGTGGGTCATGATCGTTC 58.722 55.000 0.00 0.00 31.77 3.95
220 226 0.999406 GTTGTCGTGGGTCATGATCG 59.001 55.000 0.00 2.58 31.77 3.69
246 418 0.814010 ACGCGGCATTGGGAAGATAC 60.814 55.000 12.47 0.00 0.00 2.24
327 509 3.937814 ACTAACGGCTCACATCATTTCA 58.062 40.909 0.00 0.00 0.00 2.69
361 543 3.377172 GTGGAAGGTATTGGAAATCCGTG 59.623 47.826 0.00 0.00 39.43 4.94
412 594 2.540931 GTCGAGTAGAGACGCTAAGGAG 59.459 54.545 0.00 0.00 0.00 3.69
413 595 2.548875 GTCGAGTAGAGACGCTAAGGA 58.451 52.381 0.00 0.00 0.00 3.36
414 596 1.598601 GGTCGAGTAGAGACGCTAAGG 59.401 57.143 0.00 0.00 39.38 2.69
415 597 2.553086 AGGTCGAGTAGAGACGCTAAG 58.447 52.381 0.00 0.00 39.38 2.18
416 598 2.687700 AGGTCGAGTAGAGACGCTAA 57.312 50.000 0.00 0.00 39.38 3.09
417 599 3.808466 TTAGGTCGAGTAGAGACGCTA 57.192 47.619 0.00 0.00 39.38 4.26
418 600 2.687700 TTAGGTCGAGTAGAGACGCT 57.312 50.000 0.00 0.00 39.38 5.07
419 601 3.754188 TTTTAGGTCGAGTAGAGACGC 57.246 47.619 0.00 0.00 39.38 5.19
420 602 4.334759 TCCATTTTAGGTCGAGTAGAGACG 59.665 45.833 0.00 0.00 39.38 4.18
421 603 5.450274 GGTCCATTTTAGGTCGAGTAGAGAC 60.450 48.000 0.00 0.00 37.86 3.36
422 604 4.643784 GGTCCATTTTAGGTCGAGTAGAGA 59.356 45.833 0.00 0.00 0.00 3.10
423 605 4.497674 CGGTCCATTTTAGGTCGAGTAGAG 60.498 50.000 0.00 0.00 0.00 2.43
424 606 3.379372 CGGTCCATTTTAGGTCGAGTAGA 59.621 47.826 0.00 0.00 0.00 2.59
425 607 3.490419 CCGGTCCATTTTAGGTCGAGTAG 60.490 52.174 0.00 0.00 0.00 2.57
426 608 2.428171 CCGGTCCATTTTAGGTCGAGTA 59.572 50.000 0.00 0.00 0.00 2.59
427 609 1.206371 CCGGTCCATTTTAGGTCGAGT 59.794 52.381 0.00 0.00 0.00 4.18
428 610 1.206371 ACCGGTCCATTTTAGGTCGAG 59.794 52.381 0.00 0.00 0.00 4.04
429 611 1.066716 CACCGGTCCATTTTAGGTCGA 60.067 52.381 2.59 0.00 32.04 4.20
430 612 1.365699 CACCGGTCCATTTTAGGTCG 58.634 55.000 2.59 0.00 32.04 4.79
431 613 1.279846 TCCACCGGTCCATTTTAGGTC 59.720 52.381 2.59 0.00 32.04 3.85
432 614 1.003928 GTCCACCGGTCCATTTTAGGT 59.996 52.381 2.59 0.00 35.24 3.08
433 615 1.280998 AGTCCACCGGTCCATTTTAGG 59.719 52.381 2.59 0.00 0.00 2.69
434 616 2.781681 AGTCCACCGGTCCATTTTAG 57.218 50.000 2.59 0.00 0.00 1.85
435 617 3.150767 CAAAGTCCACCGGTCCATTTTA 58.849 45.455 2.59 0.00 0.00 1.52
436 618 1.960689 CAAAGTCCACCGGTCCATTTT 59.039 47.619 2.59 0.00 0.00 1.82
437 619 1.144093 TCAAAGTCCACCGGTCCATTT 59.856 47.619 2.59 0.36 0.00 2.32
438 620 0.768622 TCAAAGTCCACCGGTCCATT 59.231 50.000 2.59 0.00 0.00 3.16
439 621 0.768622 TTCAAAGTCCACCGGTCCAT 59.231 50.000 2.59 0.00 0.00 3.41
440 622 0.107831 CTTCAAAGTCCACCGGTCCA 59.892 55.000 2.59 0.00 0.00 4.02
441 623 0.605589 CCTTCAAAGTCCACCGGTCC 60.606 60.000 2.59 0.00 0.00 4.46
442 624 0.395312 TCCTTCAAAGTCCACCGGTC 59.605 55.000 2.59 0.00 0.00 4.79
443 625 1.003233 GATCCTTCAAAGTCCACCGGT 59.997 52.381 0.00 0.00 0.00 5.28
444 626 1.003118 TGATCCTTCAAAGTCCACCGG 59.997 52.381 0.00 0.00 0.00 5.28
445 627 2.350522 CTGATCCTTCAAAGTCCACCG 58.649 52.381 0.00 0.00 0.00 4.94
446 628 2.305927 TCCTGATCCTTCAAAGTCCACC 59.694 50.000 0.00 0.00 0.00 4.61
447 629 3.703001 TCCTGATCCTTCAAAGTCCAC 57.297 47.619 0.00 0.00 0.00 4.02
448 630 3.909995 TCTTCCTGATCCTTCAAAGTCCA 59.090 43.478 0.00 0.00 0.00 4.02
449 631 4.223923 TCTCTTCCTGATCCTTCAAAGTCC 59.776 45.833 0.00 0.00 0.00 3.85
450 632 5.413309 TCTCTTCCTGATCCTTCAAAGTC 57.587 43.478 0.00 0.00 0.00 3.01
451 633 5.802821 GCTTCTCTTCCTGATCCTTCAAAGT 60.803 44.000 0.00 0.00 0.00 2.66
452 634 4.635324 GCTTCTCTTCCTGATCCTTCAAAG 59.365 45.833 0.00 0.00 0.00 2.77
453 635 4.042062 TGCTTCTCTTCCTGATCCTTCAAA 59.958 41.667 0.00 0.00 0.00 2.69
454 636 3.584406 TGCTTCTCTTCCTGATCCTTCAA 59.416 43.478 0.00 0.00 0.00 2.69
455 637 3.176411 TGCTTCTCTTCCTGATCCTTCA 58.824 45.455 0.00 0.00 0.00 3.02
456 638 3.902881 TGCTTCTCTTCCTGATCCTTC 57.097 47.619 0.00 0.00 0.00 3.46
457 639 4.039339 AGATGCTTCTCTTCCTGATCCTT 58.961 43.478 0.00 0.00 0.00 3.36
458 640 3.388676 CAGATGCTTCTCTTCCTGATCCT 59.611 47.826 0.00 0.00 0.00 3.24
459 641 3.387374 TCAGATGCTTCTCTTCCTGATCC 59.613 47.826 0.00 0.00 0.00 3.36
460 642 4.624015 CTCAGATGCTTCTCTTCCTGATC 58.376 47.826 0.00 0.00 0.00 2.92
461 643 3.181463 GCTCAGATGCTTCTCTTCCTGAT 60.181 47.826 0.00 0.00 0.00 2.90
462 644 2.168106 GCTCAGATGCTTCTCTTCCTGA 59.832 50.000 0.00 0.00 0.00 3.86
463 645 2.553086 GCTCAGATGCTTCTCTTCCTG 58.447 52.381 0.00 0.00 0.00 3.86
464 646 1.485895 GGCTCAGATGCTTCTCTTCCT 59.514 52.381 0.00 0.00 0.00 3.36
465 647 1.209019 TGGCTCAGATGCTTCTCTTCC 59.791 52.381 0.00 2.01 0.00 3.46
466 648 2.278854 GTGGCTCAGATGCTTCTCTTC 58.721 52.381 0.00 0.00 0.00 2.87
467 649 1.065564 GGTGGCTCAGATGCTTCTCTT 60.066 52.381 0.00 0.00 0.00 2.85
468 650 0.540923 GGTGGCTCAGATGCTTCTCT 59.459 55.000 0.00 0.00 0.00 3.10
469 651 0.540923 AGGTGGCTCAGATGCTTCTC 59.459 55.000 0.00 0.00 0.00 2.87
470 652 0.540923 GAGGTGGCTCAGATGCTTCT 59.459 55.000 0.00 0.00 0.00 2.85
471 653 0.251354 TGAGGTGGCTCAGATGCTTC 59.749 55.000 0.00 0.00 0.00 3.86
472 654 2.380365 TGAGGTGGCTCAGATGCTT 58.620 52.632 0.00 0.00 0.00 3.91
473 655 4.142045 TGAGGTGGCTCAGATGCT 57.858 55.556 0.00 0.00 0.00 3.79
483 665 0.620556 ATACCAAGTGCCTGAGGTGG 59.379 55.000 0.00 1.85 35.62 4.61
484 666 3.627395 TTATACCAAGTGCCTGAGGTG 57.373 47.619 0.00 0.00 35.62 4.00
485 667 4.862641 AATTATACCAAGTGCCTGAGGT 57.137 40.909 0.00 0.00 38.14 3.85
486 668 4.580580 GGAAATTATACCAAGTGCCTGAGG 59.419 45.833 0.00 0.00 0.00 3.86
487 669 5.192927 TGGAAATTATACCAAGTGCCTGAG 58.807 41.667 0.00 0.00 32.93 3.35
488 670 5.186256 TGGAAATTATACCAAGTGCCTGA 57.814 39.130 0.00 0.00 32.93 3.86
492 674 6.294731 GGATGGATGGAAATTATACCAAGTGC 60.295 42.308 0.00 0.00 39.69 4.40
494 676 6.125919 TGGGATGGATGGAAATTATACCAAGT 60.126 38.462 0.00 0.00 39.69 3.16
663 845 2.910688 TGTCAACTGTCAAGTCCTCC 57.089 50.000 0.00 0.00 34.77 4.30
695 877 3.181461 ACCTCTCACTTGTCTTCACCTTG 60.181 47.826 0.00 0.00 0.00 3.61
703 885 2.894126 ACATTCGACCTCTCACTTGTCT 59.106 45.455 0.00 0.00 0.00 3.41
730 912 1.842381 CTCCCCTCAACCTCACCCAC 61.842 65.000 0.00 0.00 0.00 4.61
741 923 1.352352 CTTTCTTTCCTGCTCCCCTCA 59.648 52.381 0.00 0.00 0.00 3.86
864 1047 1.308783 CCTGCGGCTTTCCTTCCTTC 61.309 60.000 0.00 0.00 0.00 3.46
865 1048 1.303643 CCTGCGGCTTTCCTTCCTT 60.304 57.895 0.00 0.00 0.00 3.36
866 1049 1.779061 TTCCTGCGGCTTTCCTTCCT 61.779 55.000 0.00 0.00 0.00 3.36
867 1050 1.303317 TTCCTGCGGCTTTCCTTCC 60.303 57.895 0.00 0.00 0.00 3.46
930 1117 2.123640 GACGAGGAGGGAGGGAGG 60.124 72.222 0.00 0.00 0.00 4.30
932 1119 1.619975 AGAGACGAGGAGGGAGGGA 60.620 63.158 0.00 0.00 0.00 4.20
934 1121 0.465460 CTGAGAGACGAGGAGGGAGG 60.465 65.000 0.00 0.00 0.00 4.30
936 1123 1.077357 GCTGAGAGACGAGGAGGGA 60.077 63.158 0.00 0.00 0.00 4.20
957 1144 2.714808 GGGGGAGGGGATTAATACTGT 58.285 52.381 0.00 0.00 0.00 3.55
975 1162 1.543896 TTCAAGGGAGGGAAGGGGG 60.544 63.158 0.00 0.00 0.00 5.40
995 1183 1.201424 ATCAGAGCTGCTCATGTGGA 58.799 50.000 29.49 18.18 32.06 4.02
996 1184 1.671328 CAATCAGAGCTGCTCATGTGG 59.329 52.381 29.49 13.21 32.06 4.17
1020 1208 2.202676 GCCGAGACCGAGCTTGAG 60.203 66.667 1.22 0.00 38.22 3.02
1031 1219 1.830279 TTCTTCTTCCTACGCCGAGA 58.170 50.000 0.00 0.00 0.00 4.04
1044 1232 3.207044 TCCTAGGCTTCCCTTTCTTCT 57.793 47.619 2.96 0.00 42.87 2.85
1045 1233 4.041075 CCTATCCTAGGCTTCCCTTTCTTC 59.959 50.000 2.96 0.00 42.87 2.87
1046 1234 3.977326 CCTATCCTAGGCTTCCCTTTCTT 59.023 47.826 2.96 0.00 42.87 2.52
1047 1235 3.592865 CCTATCCTAGGCTTCCCTTTCT 58.407 50.000 2.96 0.00 42.87 2.52
1059 1247 0.972883 GTGAGCAGGGCCTATCCTAG 59.027 60.000 5.28 0.00 34.92 3.02
1060 1248 0.471971 GGTGAGCAGGGCCTATCCTA 60.472 60.000 5.28 0.00 34.92 2.94
1061 1249 1.768077 GGTGAGCAGGGCCTATCCT 60.768 63.158 5.28 2.43 37.71 3.24
1062 1250 1.348775 AAGGTGAGCAGGGCCTATCC 61.349 60.000 5.28 4.61 31.43 2.59
1063 1251 0.107643 GAAGGTGAGCAGGGCCTATC 59.892 60.000 5.28 8.50 31.43 2.08
1064 1252 1.348775 GGAAGGTGAGCAGGGCCTAT 61.349 60.000 5.28 0.00 31.43 2.57
1065 1253 1.995626 GGAAGGTGAGCAGGGCCTA 60.996 63.158 5.28 0.00 31.43 3.93
1116 1308 0.608130 GGCTTTTCCGGCAATTCCTT 59.392 50.000 0.00 0.00 0.00 3.36
1117 1309 0.251787 AGGCTTTTCCGGCAATTCCT 60.252 50.000 0.00 0.00 40.77 3.36
1118 1310 0.173481 GAGGCTTTTCCGGCAATTCC 59.827 55.000 0.00 0.00 40.77 3.01
1119 1311 1.133216 GAGAGGCTTTTCCGGCAATTC 59.867 52.381 0.00 0.00 40.77 2.17
1139 1331 3.787001 GAGAACGGGAGGCAGGGG 61.787 72.222 0.00 0.00 0.00 4.79
1147 1339 5.803237 AGTTAAAGAAGAAGAGAACGGGA 57.197 39.130 0.00 0.00 0.00 5.14
1189 1381 1.682257 GCTCTGCCCTTCTGAACCT 59.318 57.895 0.00 0.00 0.00 3.50
1221 1413 0.474660 ACAAACCTGCCCCTCTCTCT 60.475 55.000 0.00 0.00 0.00 3.10
1227 1419 3.914713 CCCCACAAACCTGCCCCT 61.915 66.667 0.00 0.00 0.00 4.79
1228 1420 3.238197 ATCCCCACAAACCTGCCCC 62.238 63.158 0.00 0.00 0.00 5.80
1230 1422 2.046285 CGATCCCCACAAACCTGCC 61.046 63.158 0.00 0.00 0.00 4.85
1231 1423 2.046285 CCGATCCCCACAAACCTGC 61.046 63.158 0.00 0.00 0.00 4.85
1232 1424 1.378514 CCCGATCCCCACAAACCTG 60.379 63.158 0.00 0.00 0.00 4.00
1233 1425 1.137594 TTCCCGATCCCCACAAACCT 61.138 55.000 0.00 0.00 0.00 3.50
1234 1426 0.679960 CTTCCCGATCCCCACAAACC 60.680 60.000 0.00 0.00 0.00 3.27
1235 1427 0.326927 TCTTCCCGATCCCCACAAAC 59.673 55.000 0.00 0.00 0.00 2.93
1236 1428 1.064758 CATCTTCCCGATCCCCACAAA 60.065 52.381 0.00 0.00 0.00 2.83
1237 1429 0.546122 CATCTTCCCGATCCCCACAA 59.454 55.000 0.00 0.00 0.00 3.33
1238 1430 0.326143 TCATCTTCCCGATCCCCACA 60.326 55.000 0.00 0.00 0.00 4.17
1239 1431 1.059913 ATCATCTTCCCGATCCCCAC 58.940 55.000 0.00 0.00 0.00 4.61
1249 1441 1.958205 CGCCTCGCCATCATCTTCC 60.958 63.158 0.00 0.00 0.00 3.46
1252 1444 3.933722 CCCGCCTCGCCATCATCT 61.934 66.667 0.00 0.00 0.00 2.90
1270 1462 2.098426 AACCGCAATGGCAACCAAGG 62.098 55.000 0.00 0.00 43.94 3.61
1396 1595 6.594159 ACAAAGATTACGGGTATCAAGTCAAG 59.406 38.462 0.00 0.00 0.00 3.02
1595 1796 3.963733 CCTGTGAATTCAGGCTGGA 57.036 52.632 15.73 6.22 46.53 3.86
1609 1810 3.074390 TCTGATTGTGAAATGGGACCTGT 59.926 43.478 0.00 0.00 0.00 4.00
1618 1819 4.018141 TCCAGTCCCATCTGATTGTGAAAT 60.018 41.667 0.00 0.00 37.61 2.17
1624 1825 3.894759 ACAATCCAGTCCCATCTGATTG 58.105 45.455 8.53 8.53 38.02 2.67
1634 1835 4.202264 CCACCTATCTGTACAATCCAGTCC 60.202 50.000 0.00 0.00 0.00 3.85
1635 1836 4.649674 TCCACCTATCTGTACAATCCAGTC 59.350 45.833 0.00 0.00 0.00 3.51
1644 1845 3.046374 ACCCCATTCCACCTATCTGTAC 58.954 50.000 0.00 0.00 0.00 2.90
1651 1852 3.810623 AGAAACTACCCCATTCCACCTA 58.189 45.455 0.00 0.00 0.00 3.08
1656 1857 3.889538 GGCAATAGAAACTACCCCATTCC 59.110 47.826 0.00 0.00 0.00 3.01
1677 1878 4.219725 ACAAATTATTTGGAGGTGGAACGG 59.780 41.667 20.00 0.00 44.81 4.44
1748 1954 8.797438 TGACTATATGAACTGAGGTGCTAATAG 58.203 37.037 0.00 0.00 0.00 1.73
1768 1974 4.081642 ACGCAAGGTACATGTCTTGACTAT 60.082 41.667 24.20 8.50 41.94 2.12
1770 1976 2.037251 ACGCAAGGTACATGTCTTGACT 59.963 45.455 24.20 10.00 41.94 3.41
1790 1996 3.057033 GGCATGAATCATGATTGCCCTAC 60.057 47.826 28.57 14.54 43.81 3.18
1826 2032 7.964666 AAGCAAGGTCTAACTCTAATACTCT 57.035 36.000 0.00 0.00 0.00 3.24
1827 2033 9.902196 GATAAGCAAGGTCTAACTCTAATACTC 57.098 37.037 0.00 0.00 0.00 2.59
1828 2034 9.422681 TGATAAGCAAGGTCTAACTCTAATACT 57.577 33.333 0.00 0.00 0.00 2.12
1852 2058 7.177216 AGCACTTTGATTGAAAGGATTGTATGA 59.823 33.333 0.72 0.00 44.85 2.15
1853 2059 7.318141 AGCACTTTGATTGAAAGGATTGTATG 58.682 34.615 0.72 0.00 44.85 2.39
1928 2134 4.367450 GCCAGAAGACATCTATGAGTGTC 58.633 47.826 0.00 0.00 43.85 3.67
2175 2381 1.080366 GTCGCATGTCGGGTACACA 60.080 57.895 9.16 0.00 42.09 3.72
2404 2636 7.172532 TCCAGTACTAAACAACTGCTTAACATG 59.827 37.037 0.00 0.00 0.00 3.21
2453 2685 3.700538 TGTGCTGCAATTAGAAATCCCT 58.299 40.909 2.77 0.00 0.00 4.20
2459 2691 4.239304 CATGCTTTGTGCTGCAATTAGAA 58.761 39.130 2.77 0.00 42.74 2.10
2515 2747 5.421693 AGTTGCCCATTGATAAGTGCAAATA 59.578 36.000 0.00 0.00 40.03 1.40
2560 2792 5.756195 TCTGAAACAAAGGACAGAACATG 57.244 39.130 0.00 0.00 36.63 3.21
2561 2793 8.517878 CATTATCTGAAACAAAGGACAGAACAT 58.482 33.333 0.00 0.00 41.57 2.71
2562 2794 7.719193 TCATTATCTGAAACAAAGGACAGAACA 59.281 33.333 0.00 0.00 41.57 3.18
2563 2795 8.099364 TCATTATCTGAAACAAAGGACAGAAC 57.901 34.615 0.00 0.00 41.57 3.01
2564 2796 8.868522 ATCATTATCTGAAACAAAGGACAGAA 57.131 30.769 0.00 0.00 41.57 3.02
2615 2851 7.771826 ACTGTAGATCTAAAGAGTAGTCAGACC 59.228 40.741 24.22 0.00 0.00 3.85
2644 2880 8.028938 GCATGTAGTTATTTTCAATTGGACAGT 58.971 33.333 5.42 0.00 0.00 3.55
2687 2923 4.576463 GTGTCAGTCAGAAGAAAACATGGT 59.424 41.667 0.00 0.00 0.00 3.55
2697 2933 7.465647 GCATCAAGATAATGTGTCAGTCAGAAG 60.466 40.741 0.00 0.00 0.00 2.85
2973 3210 2.552599 TTGCCGGTGTCATAGAACAA 57.447 45.000 1.90 0.00 0.00 2.83
3046 3283 4.837298 AGCAGGATCTATAAGACTGATGCA 59.163 41.667 0.00 0.00 32.22 3.96
3047 3284 5.404466 AGCAGGATCTATAAGACTGATGC 57.596 43.478 0.00 0.00 0.00 3.91
3051 3288 6.667414 AGGGAATAGCAGGATCTATAAGACTG 59.333 42.308 0.00 0.00 0.00 3.51
3060 3297 5.848921 ACAATAAGAGGGAATAGCAGGATCT 59.151 40.000 0.00 0.00 0.00 2.75
3112 3349 6.096423 ACGAGCACCTCTGTAAAATACATAGA 59.904 38.462 0.00 0.00 38.15 1.98
3122 3359 3.726548 AGATGCACGAGCACCTCTGTAA 61.727 50.000 10.42 0.00 42.44 2.41
3272 3509 2.279037 AAACCACGGCTTCCACCAGT 62.279 55.000 0.00 0.00 0.00 4.00
3425 3662 3.196685 GCTTCCTCAGTATGTCCTCTGTT 59.803 47.826 0.00 0.00 37.40 3.16
3518 3755 3.808174 GCCCGTTAAGTATCTGATGGAAC 59.192 47.826 0.00 0.00 0.00 3.62
3701 3939 1.884235 AGGCGCAAAGTATATCAGGC 58.116 50.000 10.83 0.00 0.00 4.85
3776 4014 6.749923 AGCTATCAGCAAAGAAGGTAAAAG 57.250 37.500 0.38 0.00 45.56 2.27
3778 4016 6.947464 ACTAGCTATCAGCAAAGAAGGTAAA 58.053 36.000 0.00 0.00 45.56 2.01
3780 4018 7.841282 ATACTAGCTATCAGCAAAGAAGGTA 57.159 36.000 0.00 0.00 45.56 3.08
3781 4019 6.739331 ATACTAGCTATCAGCAAAGAAGGT 57.261 37.500 0.00 0.00 45.56 3.50
3782 4020 7.093992 GGTATACTAGCTATCAGCAAAGAAGG 58.906 42.308 2.25 0.00 45.56 3.46
3934 4187 1.068125 CGGTGTAACATCAGACGGTCA 60.068 52.381 11.27 0.00 39.98 4.02
3950 4203 4.764336 CGCAAGCATGTGCCGGTG 62.764 66.667 1.90 0.00 41.73 4.94
3999 4259 3.054139 CAGAGAGGGGATGAAAATCACCA 60.054 47.826 9.58 0.00 46.55 4.17
4047 4307 1.537202 GCACCACTTCGCAATTTCTCT 59.463 47.619 0.00 0.00 0.00 3.10
4084 4344 3.840078 TCAAACTGACAGGATCCAGATGA 59.160 43.478 15.82 9.64 34.65 2.92
4095 4355 2.487934 CCCAGTCACTCAAACTGACAG 58.512 52.381 0.00 0.00 45.64 3.51
4110 4374 1.847968 CCACCCTCAAGTCCCCAGT 60.848 63.158 0.00 0.00 0.00 4.00
4111 4375 3.081554 CCACCCTCAAGTCCCCAG 58.918 66.667 0.00 0.00 0.00 4.45
4122 4386 3.807209 GCTACATGATTAATCGCCACCCT 60.807 47.826 10.80 0.00 0.00 4.34
4124 4388 3.187227 CAGCTACATGATTAATCGCCACC 59.813 47.826 10.80 0.00 0.00 4.61
4130 4394 6.857777 AAGACTGCAGCTACATGATTAATC 57.142 37.500 15.27 8.60 0.00 1.75
4135 4399 3.688185 CACAAAGACTGCAGCTACATGAT 59.312 43.478 15.27 0.00 0.00 2.45
4164 4431 9.388506 CATTATTCCTTAGGAAATCAGCGATAT 57.611 33.333 18.34 0.00 45.41 1.63
4165 4432 8.375506 ACATTATTCCTTAGGAAATCAGCGATA 58.624 33.333 18.34 0.24 45.41 2.92
4166 4433 7.227156 ACATTATTCCTTAGGAAATCAGCGAT 58.773 34.615 18.34 1.25 45.41 4.58
4168 4435 6.867662 ACATTATTCCTTAGGAAATCAGCG 57.132 37.500 18.34 7.28 45.41 5.18
4209 4476 1.412079 AACAAGCATCTGTTGGCCAA 58.588 45.000 16.05 16.05 38.12 4.52
4219 4486 2.430465 TCAGAAGAGCCAACAAGCATC 58.570 47.619 0.00 0.00 34.23 3.91
4253 4520 0.106268 TTTCCCTCTGCCAACAAGCA 60.106 50.000 0.00 0.00 41.46 3.91
4256 4523 0.260230 TGGTTTCCCTCTGCCAACAA 59.740 50.000 0.00 0.00 0.00 2.83
4257 4524 0.467290 GTGGTTTCCCTCTGCCAACA 60.467 55.000 0.00 0.00 32.26 3.33
4258 4525 0.467290 TGTGGTTTCCCTCTGCCAAC 60.467 55.000 0.00 0.00 32.26 3.77
4259 4526 0.178992 CTGTGGTTTCCCTCTGCCAA 60.179 55.000 0.00 0.00 32.26 4.52
4265 4534 1.056660 TGGAGTCTGTGGTTTCCCTC 58.943 55.000 0.00 0.00 0.00 4.30
4270 4539 2.919228 GACTGTTGGAGTCTGTGGTTT 58.081 47.619 0.00 0.00 46.85 3.27
4285 4554 3.955471 CATTAAGATGGGTGTGGACTGT 58.045 45.455 0.00 0.00 0.00 3.55
4302 4579 1.301623 CGTTCACCCAGGCCCATTA 59.698 57.895 0.00 0.00 0.00 1.90
4311 4588 0.464735 CCTTGGACAACGTTCACCCA 60.465 55.000 14.95 11.75 0.00 4.51
4319 4596 0.107831 TGTTCTCCCCTTGGACAACG 59.892 55.000 0.00 0.00 41.12 4.10
4336 4613 1.266178 GGCTTTGCCCTACCATTTGT 58.734 50.000 0.00 0.00 44.06 2.83
4528 4807 2.045926 CAGGACCCAAAGCCGAGG 60.046 66.667 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.