Multiple sequence alignment - TraesCS4A01G139200

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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 TraesCS4A01G139200 chr4A 100.000 2441 0 0 1 2441 209413708 209416148 0.000000e+00 4508.0
1 TraesCS4A01G139200 chr4A 90.823 1057 95 2 649 1703 209433356 209434412 0.000000e+00 1413.0
2 TraesCS4A01G139200 chr4A 84.748 813 94 27 1629 2427 362170705 362169909 0.000000e+00 787.0
3 TraesCS4A01G139200 chr4A 83.373 842 115 21 1606 2440 331370886 331371709 0.000000e+00 756.0
4 TraesCS4A01G139200 chr4A 89.668 542 44 3 1 530 209425869 209426410 0.000000e+00 680.0
5 TraesCS4A01G139200 chr4A 86.384 448 56 3 566 1011 221647434 221646990 3.650000e-133 484.0
6 TraesCS4A01G139200 chr4A 86.456 443 57 3 566 1006 399949931 399949490 1.310000e-132 483.0
7 TraesCS4A01G139200 chr4A 93.237 207 14 0 566 772 355351144 355350938 3.050000e-79 305.0
8 TraesCS4A01G139200 chr4A 89.623 212 21 1 567 778 329606570 329606780 4.000000e-68 268.0
9 TraesCS4A01G139200 chr4A 75.390 577 82 37 1 526 526177664 526177097 8.780000e-55 224.0
10 TraesCS4A01G139200 chr4A 76.798 431 55 30 1 405 331982040 331982451 1.480000e-47 200.0
11 TraesCS4A01G139200 chr4A 91.971 137 11 0 394 530 276257610 276257746 2.480000e-45 193.0
12 TraesCS4A01G139200 chr4A 91.971 137 11 0 394 530 276266026 276266162 2.480000e-45 193.0
13 TraesCS4A01G139200 chr4A 91.304 138 10 2 394 530 368551815 368551951 1.150000e-43 187.0
14 TraesCS4A01G139200 chr4A 84.416 77 10 2 931 1007 250257368 250257442 9.360000e-10 75.0
15 TraesCS4A01G139200 chr4A 84.416 77 10 2 931 1007 250278098 250278172 9.360000e-10 75.0
16 TraesCS4A01G139200 chr2A 92.867 729 49 3 1662 2390 263575552 263576277 0.000000e+00 1055.0
17 TraesCS4A01G139200 chr2A 81.156 398 58 14 1 390 233303758 233303370 1.100000e-78 303.0
18 TraesCS4A01G139200 chr2A 90.741 108 10 0 1075 1182 632672960 632673067 7.030000e-31 145.0
19 TraesCS4A01G139200 chr2A 77.075 253 33 19 1 237 445839573 445839816 3.300000e-24 122.0
20 TraesCS4A01G139200 chr2A 78.421 190 28 7 1 178 264108189 264108001 7.130000e-21 111.0
21 TraesCS4A01G139200 chr7B 84.104 843 107 23 1606 2440 187459512 187460335 0.000000e+00 789.0
22 TraesCS4A01G139200 chr2B 83.829 841 111 21 1606 2440 610303862 610304683 0.000000e+00 776.0
23 TraesCS4A01G139200 chr3A 83.768 844 107 27 1609 2440 416868628 416869453 0.000000e+00 773.0
24 TraesCS4A01G139200 chr3A 91.057 123 9 2 1075 1195 258408150 258408028 5.400000e-37 165.0
25 TraesCS4A01G139200 chr3A 90.598 117 11 0 1103 1219 105364679 105364563 3.250000e-34 156.0
26 TraesCS4A01G139200 chr3A 85.714 77 9 2 931 1007 475268063 475268137 2.010000e-11 80.5
27 TraesCS4A01G139200 chr3A 93.182 44 3 0 870 913 589116826 589116783 5.630000e-07 65.8
28 TraesCS4A01G139200 chr3B 83.610 842 109 25 1609 2440 261161425 261160603 0.000000e+00 763.0
29 TraesCS4A01G139200 chr6B 83.432 845 111 24 1605 2440 115366161 115365337 0.000000e+00 758.0
30 TraesCS4A01G139200 chr7A 83.372 854 105 29 1605 2440 632784617 632783783 0.000000e+00 756.0
31 TraesCS4A01G139200 chr7A 90.521 211 20 0 566 776 403206751 403206541 1.850000e-71 279.0
32 TraesCS4A01G139200 chr7A 88.626 211 24 0 566 776 403212913 403212703 8.660000e-65 257.0
33 TraesCS4A01G139200 chr6A 84.597 409 49 12 133 530 206268728 206269133 6.330000e-106 394.0
34 TraesCS4A01G139200 chr6A 82.160 426 53 17 2 409 537995603 537996023 6.460000e-91 344.0
35 TraesCS4A01G139200 chr6A 81.840 424 57 18 2 409 537928026 537927607 3.010000e-89 339.0
36 TraesCS4A01G139200 chr6A 78.014 423 65 23 1 404 461293353 461293766 8.720000e-60 241.0
37 TraesCS4A01G139200 chr6A 77.358 424 66 24 1 404 461342951 461343364 8.780000e-55 224.0
38 TraesCS4A01G139200 chr6A 94.068 118 7 0 1075 1192 303196453 303196336 1.930000e-41 180.0
39 TraesCS4A01G139200 chr6A 89.130 138 15 0 388 525 378263093 378262956 3.230000e-39 172.0
40 TraesCS4A01G139200 chr6A 87.013 154 14 5 372 525 309029438 309029585 4.170000e-38 169.0
41 TraesCS4A01G139200 chr6A 88.636 132 15 0 399 530 378280657 378280526 6.980000e-36 161.0
42 TraesCS4A01G139200 chr6A 85.714 77 9 2 931 1007 190052223 190052149 2.010000e-11 80.5
43 TraesCS4A01G139200 chr4D 83.554 377 54 7 38 408 199782716 199782342 1.800000e-91 346.0
44 TraesCS4A01G139200 chr4D 76.224 572 66 36 1 524 193255322 193254773 3.140000e-59 239.0
45 TraesCS4A01G139200 chr4D 75.703 498 71 24 66 524 348204276 348204762 1.140000e-48 204.0
46 TraesCS4A01G139200 chr1A 81.327 407 52 17 1 390 447938780 447939179 2.360000e-80 309.0
47 TraesCS4A01G139200 chr1A 90.995 211 19 0 566 776 436482513 436482303 3.970000e-73 285.0
48 TraesCS4A01G139200 chr1A 89.100 211 23 0 566 776 436531723 436531513 1.860000e-66 263.0
49 TraesCS4A01G139200 chr1A 75.991 429 63 31 1 405 351720826 351721238 4.140000e-43 185.0
50 TraesCS4A01G139200 chr1A 93.519 108 5 2 418 524 226628851 226628957 2.510000e-35 159.0
51 TraesCS4A01G139200 chr1A 89.256 121 13 0 1075 1195 119635954 119635834 4.200000e-33 152.0
52 TraesCS4A01G139200 chr1A 90.741 108 8 2 418 524 226648672 226648778 2.530000e-30 143.0
53 TraesCS4A01G139200 chr1A 81.119 143 19 8 397 533 297475220 297475080 9.230000e-20 108.0
54 TraesCS4A01G139200 chr1A 81.667 120 8 8 1 108 401280451 401280334 1.200000e-13 87.9
55 TraesCS4A01G139200 chr1A 97.778 45 1 0 1 45 302959760 302959716 7.240000e-11 78.7
56 TraesCS4A01G139200 chr7D 81.102 381 58 11 36 409 116204447 116204074 2.370000e-75 292.0
57 TraesCS4A01G139200 chr3D 80.047 426 59 13 1 409 435256594 435257010 2.370000e-75 292.0
58 TraesCS4A01G139200 chr5A 89.100 211 23 0 566 776 422423039 422422829 1.860000e-66 263.0
59 TraesCS4A01G139200 chr5A 89.655 116 11 1 1075 1190 60375000 60375114 1.960000e-31 147.0
60 TraesCS4A01G139200 chr5D 86.364 132 17 1 394 524 157164218 157164087 2.530000e-30 143.0
61 TraesCS4A01G139200 chr1D 87.755 98 11 1 394 490 253156274 253156177 1.980000e-21 113.0
62 TraesCS4A01G139200 chr4B 85.714 105 8 6 386 486 324110910 324111011 1.190000e-18 104.0
63 TraesCS4A01G139200 chrUn 86.250 80 9 2 931 1010 301026895 301026818 4.320000e-13 86.1
64 TraesCS4A01G139200 chrUn 84.416 77 10 2 931 1007 325166390 325166316 9.360000e-10 75.0


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 TraesCS4A01G139200 chr4A 209413708 209416148 2440 False 4508 4508 100.000 1 2441 1 chr4A.!!$F1 2440
1 TraesCS4A01G139200 chr4A 209433356 209434412 1056 False 1413 1413 90.823 649 1703 1 chr4A.!!$F3 1054
2 TraesCS4A01G139200 chr4A 362169909 362170705 796 True 787 787 84.748 1629 2427 1 chr4A.!!$R3 798
3 TraesCS4A01G139200 chr4A 331370886 331371709 823 False 756 756 83.373 1606 2440 1 chr4A.!!$F9 834
4 TraesCS4A01G139200 chr4A 209425869 209426410 541 False 680 680 89.668 1 530 1 chr4A.!!$F2 529
5 TraesCS4A01G139200 chr4A 526177097 526177664 567 True 224 224 75.390 1 526 1 chr4A.!!$R5 525
6 TraesCS4A01G139200 chr2A 263575552 263576277 725 False 1055 1055 92.867 1662 2390 1 chr2A.!!$F1 728
7 TraesCS4A01G139200 chr7B 187459512 187460335 823 False 789 789 84.104 1606 2440 1 chr7B.!!$F1 834
8 TraesCS4A01G139200 chr2B 610303862 610304683 821 False 776 776 83.829 1606 2440 1 chr2B.!!$F1 834
9 TraesCS4A01G139200 chr3A 416868628 416869453 825 False 773 773 83.768 1609 2440 1 chr3A.!!$F1 831
10 TraesCS4A01G139200 chr3B 261160603 261161425 822 True 763 763 83.610 1609 2440 1 chr3B.!!$R1 831
11 TraesCS4A01G139200 chr6B 115365337 115366161 824 True 758 758 83.432 1605 2440 1 chr6B.!!$R1 835
12 TraesCS4A01G139200 chr7A 632783783 632784617 834 True 756 756 83.372 1605 2440 1 chr7A.!!$R3 835
13 TraesCS4A01G139200 chr4D 193254773 193255322 549 True 239 239 76.224 1 524 1 chr4D.!!$R1 523

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
592 646 0.095245 CTTGGCGCGTCATTGTGTAG 59.905 55.0 16.97 3.23 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1593 0.03563 GAGAGTGTGCAGGGCTTCAT 60.036 55.0 0.0 0.0 0.0 2.57 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
31 32 2.158928 TCATGATGCGGATGACATGTGA 60.159 45.455 1.15 0.00 40.32 3.58
51 63 9.866936 CATGTGAAAGTTTTATGAAAATGTTGG 57.133 29.630 0.00 0.00 32.22 3.77
94 109 2.018515 GTCACCGTGGTGGAAAGAAAA 58.981 47.619 18.47 0.00 45.43 2.29
95 110 2.621526 GTCACCGTGGTGGAAAGAAAAT 59.378 45.455 18.47 0.00 45.43 1.82
218 236 1.078708 ATAAACGGTGGGGTGCTCG 60.079 57.895 0.00 0.00 0.00 5.03
257 275 0.893727 ATGACGGTGGCAAGGAAACC 60.894 55.000 0.00 0.00 0.00 3.27
287 305 2.026641 CAAGGATCAATTCGGGCATGT 58.973 47.619 0.00 0.00 0.00 3.21
356 378 3.344064 GTCGTTCCGGCGGTTATAA 57.656 52.632 27.32 10.06 0.00 0.98
360 382 2.425312 TCGTTCCGGCGGTTATAACTTA 59.575 45.455 27.32 10.43 0.00 2.24
375 399 8.182227 GGTTATAACTTACAAGGTTGCATTCTC 58.818 37.037 15.05 0.00 0.00 2.87
378 402 3.244422 ACTTACAAGGTTGCATTCTCGGA 60.244 43.478 0.00 0.00 0.00 4.55
405 458 5.510349 GGTTCGGTTTGTAGAGGAAGTAGTT 60.510 44.000 0.00 0.00 0.00 2.24
409 462 5.756833 CGGTTTGTAGAGGAAGTAGTTGTTT 59.243 40.000 0.00 0.00 0.00 2.83
439 493 1.469335 ATGTTCGGGGTCACGACACT 61.469 55.000 0.00 0.00 43.37 3.55
440 494 0.822944 TGTTCGGGGTCACGACACTA 60.823 55.000 0.00 0.00 43.37 2.74
530 584 3.640029 TCGGTAGAGGAACTTGACACTTT 59.360 43.478 0.00 0.00 41.55 2.66
531 585 3.741344 CGGTAGAGGAACTTGACACTTTG 59.259 47.826 0.00 0.00 41.55 2.77
532 586 4.500887 CGGTAGAGGAACTTGACACTTTGA 60.501 45.833 0.00 0.00 41.55 2.69
533 587 5.552178 GGTAGAGGAACTTGACACTTTGAT 58.448 41.667 0.00 0.00 41.55 2.57
534 588 5.409826 GGTAGAGGAACTTGACACTTTGATG 59.590 44.000 0.00 0.00 41.55 3.07
535 589 4.392940 AGAGGAACTTGACACTTTGATGG 58.607 43.478 0.00 0.00 41.55 3.51
536 590 4.137543 GAGGAACTTGACACTTTGATGGT 58.862 43.478 0.00 0.00 41.55 3.55
537 591 5.071788 AGAGGAACTTGACACTTTGATGGTA 59.928 40.000 0.00 0.00 41.55 3.25
538 592 5.690865 AGGAACTTGACACTTTGATGGTAA 58.309 37.500 0.00 0.00 27.25 2.85
539 593 6.306987 AGGAACTTGACACTTTGATGGTAAT 58.693 36.000 0.00 0.00 27.25 1.89
540 594 6.207417 AGGAACTTGACACTTTGATGGTAATG 59.793 38.462 0.00 0.00 27.25 1.90
541 595 5.964958 ACTTGACACTTTGATGGTAATGG 57.035 39.130 0.00 0.00 0.00 3.16
542 596 5.385198 ACTTGACACTTTGATGGTAATGGT 58.615 37.500 0.00 0.00 0.00 3.55
543 597 6.539173 ACTTGACACTTTGATGGTAATGGTA 58.461 36.000 0.00 0.00 0.00 3.25
544 598 6.430000 ACTTGACACTTTGATGGTAATGGTAC 59.570 38.462 0.00 0.00 0.00 3.34
561 615 5.708736 TGGTACATATCATGGTGGAACTT 57.291 39.130 0.00 0.00 36.74 2.66
562 616 5.436175 TGGTACATATCATGGTGGAACTTG 58.564 41.667 0.00 0.00 36.74 3.16
563 617 4.821805 GGTACATATCATGGTGGAACTTGG 59.178 45.833 0.00 0.00 36.74 3.61
564 618 4.591321 ACATATCATGGTGGAACTTGGT 57.409 40.909 0.00 0.00 36.74 3.67
565 619 4.272489 ACATATCATGGTGGAACTTGGTG 58.728 43.478 0.00 0.00 36.74 4.17
566 620 4.018506 ACATATCATGGTGGAACTTGGTGA 60.019 41.667 0.00 0.00 36.74 4.02
567 621 2.566833 TCATGGTGGAACTTGGTGAG 57.433 50.000 0.00 0.00 36.74 3.51
568 622 1.073763 TCATGGTGGAACTTGGTGAGG 59.926 52.381 0.00 0.00 36.74 3.86
569 623 0.405585 ATGGTGGAACTTGGTGAGGG 59.594 55.000 0.00 0.00 36.74 4.30
570 624 1.074951 GGTGGAACTTGGTGAGGGG 59.925 63.158 0.00 0.00 36.74 4.79
571 625 1.423794 GGTGGAACTTGGTGAGGGGA 61.424 60.000 0.00 0.00 36.74 4.81
572 626 0.476771 GTGGAACTTGGTGAGGGGAA 59.523 55.000 0.00 0.00 0.00 3.97
573 627 0.476771 TGGAACTTGGTGAGGGGAAC 59.523 55.000 0.00 0.00 0.00 3.62
574 628 0.771755 GGAACTTGGTGAGGGGAACT 59.228 55.000 0.00 0.00 0.00 3.01
575 629 1.145119 GGAACTTGGTGAGGGGAACTT 59.855 52.381 0.00 0.00 0.00 2.66
576 630 2.230660 GAACTTGGTGAGGGGAACTTG 58.769 52.381 0.00 0.00 0.00 3.16
577 631 0.478507 ACTTGGTGAGGGGAACTTGG 59.521 55.000 0.00 0.00 0.00 3.61
578 632 0.895559 CTTGGTGAGGGGAACTTGGC 60.896 60.000 0.00 0.00 0.00 4.52
579 633 2.359975 GGTGAGGGGAACTTGGCG 60.360 66.667 0.00 0.00 0.00 5.69
580 634 3.056328 GTGAGGGGAACTTGGCGC 61.056 66.667 0.00 0.00 0.00 6.53
581 635 4.697756 TGAGGGGAACTTGGCGCG 62.698 66.667 0.00 0.00 0.00 6.86
582 636 4.699522 GAGGGGAACTTGGCGCGT 62.700 66.667 8.43 0.00 0.00 6.01
583 637 4.699522 AGGGGAACTTGGCGCGTC 62.700 66.667 2.29 2.29 0.00 5.19
585 639 2.746277 GGGAACTTGGCGCGTCAT 60.746 61.111 16.97 0.00 0.00 3.06
586 640 2.332654 GGGAACTTGGCGCGTCATT 61.333 57.895 16.97 6.78 0.00 2.57
587 641 1.154225 GGAACTTGGCGCGTCATTG 60.154 57.895 16.97 13.74 0.00 2.82
588 642 1.574428 GAACTTGGCGCGTCATTGT 59.426 52.632 16.97 14.49 0.00 2.71
589 643 0.725784 GAACTTGGCGCGTCATTGTG 60.726 55.000 16.97 8.14 0.00 3.33
590 644 1.444119 AACTTGGCGCGTCATTGTGT 61.444 50.000 16.97 8.85 0.00 3.72
591 645 0.601576 ACTTGGCGCGTCATTGTGTA 60.602 50.000 16.97 0.00 0.00 2.90
592 646 0.095245 CTTGGCGCGTCATTGTGTAG 59.905 55.000 16.97 3.23 0.00 2.74
593 647 0.601576 TTGGCGCGTCATTGTGTAGT 60.602 50.000 16.97 0.00 0.00 2.73
594 648 1.011968 TGGCGCGTCATTGTGTAGTC 61.012 55.000 10.57 0.00 0.00 2.59
595 649 1.340465 GCGCGTCATTGTGTAGTCG 59.660 57.895 8.43 0.00 0.00 4.18
596 650 1.342082 GCGCGTCATTGTGTAGTCGT 61.342 55.000 8.43 0.00 0.00 4.34
597 651 1.886037 CGCGTCATTGTGTAGTCGTA 58.114 50.000 0.00 0.00 0.00 3.43
598 652 1.576246 CGCGTCATTGTGTAGTCGTAC 59.424 52.381 0.00 0.00 0.00 3.67
599 653 2.587956 GCGTCATTGTGTAGTCGTACA 58.412 47.619 0.00 0.00 36.78 2.90
600 654 3.176708 GCGTCATTGTGTAGTCGTACAT 58.823 45.455 0.00 0.00 41.29 2.29
601 655 3.239941 GCGTCATTGTGTAGTCGTACATC 59.760 47.826 0.00 0.00 41.29 3.06
602 656 3.477446 CGTCATTGTGTAGTCGTACATCG 59.523 47.826 0.00 0.00 41.29 3.84
603 657 4.655027 GTCATTGTGTAGTCGTACATCGA 58.345 43.478 0.00 0.00 46.83 3.59
611 665 3.867549 TCGTACATCGAGGTCCTCA 57.132 52.632 19.15 6.59 44.01 3.86
612 666 2.343484 TCGTACATCGAGGTCCTCAT 57.657 50.000 19.15 8.58 44.01 2.90
613 667 1.947456 TCGTACATCGAGGTCCTCATG 59.053 52.381 19.15 20.16 44.01 3.07
614 668 1.600663 CGTACATCGAGGTCCTCATGC 60.601 57.143 19.15 8.58 42.86 4.06
615 669 1.409064 GTACATCGAGGTCCTCATGCA 59.591 52.381 19.15 9.32 0.00 3.96
616 670 0.176680 ACATCGAGGTCCTCATGCAC 59.823 55.000 19.15 0.00 0.00 4.57
617 671 0.463204 CATCGAGGTCCTCATGCACT 59.537 55.000 19.15 0.00 0.00 4.40
618 672 1.134580 CATCGAGGTCCTCATGCACTT 60.135 52.381 19.15 0.00 0.00 3.16
619 673 0.976641 TCGAGGTCCTCATGCACTTT 59.023 50.000 19.15 0.00 0.00 2.66
620 674 1.081892 CGAGGTCCTCATGCACTTTG 58.918 55.000 19.15 0.00 0.00 2.77
621 675 1.338105 CGAGGTCCTCATGCACTTTGA 60.338 52.381 19.15 0.00 0.00 2.69
622 676 2.679059 CGAGGTCCTCATGCACTTTGAT 60.679 50.000 19.15 0.00 0.00 2.57
623 677 2.681848 GAGGTCCTCATGCACTTTGATG 59.318 50.000 14.46 0.00 0.00 3.07
624 678 2.306805 AGGTCCTCATGCACTTTGATGA 59.693 45.455 0.00 0.00 0.00 2.92
625 679 2.421424 GGTCCTCATGCACTTTGATGAC 59.579 50.000 12.97 12.97 37.76 3.06
626 680 3.341823 GTCCTCATGCACTTTGATGACT 58.658 45.455 13.70 0.00 36.44 3.41
627 681 3.373439 GTCCTCATGCACTTTGATGACTC 59.627 47.826 13.70 0.00 36.44 3.36
628 682 3.262660 TCCTCATGCACTTTGATGACTCT 59.737 43.478 0.00 0.00 0.00 3.24
629 683 3.374367 CCTCATGCACTTTGATGACTCTG 59.626 47.826 0.00 0.00 0.00 3.35
630 684 3.340928 TCATGCACTTTGATGACTCTGG 58.659 45.455 0.00 0.00 0.00 3.86
631 685 3.008266 TCATGCACTTTGATGACTCTGGA 59.992 43.478 0.00 0.00 0.00 3.86
632 686 2.771089 TGCACTTTGATGACTCTGGAC 58.229 47.619 0.00 0.00 0.00 4.02
633 687 1.728971 GCACTTTGATGACTCTGGACG 59.271 52.381 0.00 0.00 0.00 4.79
634 688 2.610479 GCACTTTGATGACTCTGGACGA 60.610 50.000 0.00 0.00 0.00 4.20
635 689 3.249091 CACTTTGATGACTCTGGACGAG 58.751 50.000 0.00 0.00 45.56 4.18
636 690 2.232452 ACTTTGATGACTCTGGACGAGG 59.768 50.000 0.00 0.00 44.33 4.63
637 691 2.215942 TTGATGACTCTGGACGAGGA 57.784 50.000 0.00 0.00 44.33 3.71
638 692 2.215942 TGATGACTCTGGACGAGGAA 57.784 50.000 0.00 0.00 44.33 3.36
639 693 1.819288 TGATGACTCTGGACGAGGAAC 59.181 52.381 0.00 0.00 44.33 3.62
640 694 2.096248 GATGACTCTGGACGAGGAACT 58.904 52.381 0.00 0.00 44.33 3.01
641 695 1.996798 TGACTCTGGACGAGGAACTT 58.003 50.000 0.00 0.00 44.33 2.66
643 697 0.969894 ACTCTGGACGAGGAACTTGG 59.030 55.000 0.00 0.00 46.15 3.61
665 719 1.219522 CCCACGGTCTTGACGTCAAC 61.220 60.000 26.53 18.44 43.58 3.18
696 750 2.661566 CGGAGAGCACGCACAACAG 61.662 63.158 0.00 0.00 0.00 3.16
713 767 3.365265 GGGCACGGCAGAAGTTGG 61.365 66.667 0.00 0.00 0.00 3.77
719 773 3.365265 GGCAGAAGTTGGGCACGG 61.365 66.667 0.00 0.00 0.00 4.94
743 797 1.057851 AACGGGTCACCCAAAGGAGA 61.058 55.000 15.17 0.00 45.83 3.71
744 798 0.840722 ACGGGTCACCCAAAGGAGAT 60.841 55.000 15.17 0.00 45.83 2.75
759 813 2.740055 GATAGAGGCCATGGCGCG 60.740 66.667 29.90 0.00 43.06 6.86
785 839 3.264897 GCGGCAGCTGTGTATCCG 61.265 66.667 21.14 21.14 42.68 4.18
789 843 0.807667 GGCAGCTGTGTATCCGAGTG 60.808 60.000 16.64 0.00 0.00 3.51
791 845 1.404181 GCAGCTGTGTATCCGAGTGAA 60.404 52.381 16.64 0.00 0.00 3.18
792 846 2.930887 GCAGCTGTGTATCCGAGTGAAA 60.931 50.000 16.64 0.00 0.00 2.69
805 859 1.139853 GAGTGAAAGGATGGCGGATCT 59.860 52.381 0.00 0.00 0.00 2.75
806 860 1.134280 AGTGAAAGGATGGCGGATCTG 60.134 52.381 0.00 0.00 0.00 2.90
831 886 1.811266 CACGACAAGGGCTGATCCG 60.811 63.158 0.00 0.00 34.94 4.18
833 888 2.721167 CGACAAGGGCTGATCCGGA 61.721 63.158 6.61 6.61 34.94 5.14
835 890 2.202932 CAAGGGCTGATCCGGACG 60.203 66.667 6.12 0.00 34.94 4.79
903 958 3.680786 CACCAGGAGACGGCGTGA 61.681 66.667 21.19 0.00 31.83 4.35
956 1011 0.543749 AAGCCACTGATGTAGAGGGC 59.456 55.000 0.00 0.00 44.87 5.19
975 1030 2.125512 GTGCGGTGCGGAGAAGAT 60.126 61.111 0.00 0.00 0.00 2.40
979 1034 1.299165 CGGTGCGGAGAAGATACGG 60.299 63.158 0.00 0.00 0.00 4.02
987 1042 1.614413 GGAGAAGATACGGGTAGCAGG 59.386 57.143 0.00 0.00 0.00 4.85
988 1043 2.584236 GAGAAGATACGGGTAGCAGGA 58.416 52.381 0.00 0.00 0.00 3.86
1012 1067 4.570663 GGAGGATGGCCGACGTCG 62.571 72.222 30.33 30.33 39.96 5.12
1059 1114 1.278127 CGACAGAATTGGGGTGTAGGT 59.722 52.381 0.00 0.00 0.00 3.08
1062 1117 1.004745 CAGAATTGGGGTGTAGGTGCT 59.995 52.381 0.00 0.00 0.00 4.40
1064 1119 0.035439 AATTGGGGTGTAGGTGCTCG 60.035 55.000 0.00 0.00 0.00 5.03
1065 1120 1.198759 ATTGGGGTGTAGGTGCTCGT 61.199 55.000 0.00 0.00 0.00 4.18
1071 1126 1.839747 TGTAGGTGCTCGTGGGGTT 60.840 57.895 0.00 0.00 0.00 4.11
1107 1162 1.626654 CTTGGTCGACGATGGTGCAC 61.627 60.000 8.80 8.80 0.00 4.57
1123 1178 3.129792 CACGGGAGAAGAAGTGCTC 57.870 57.895 0.00 0.00 0.00 4.26
1231 1286 2.359404 GAGAGGTGGGAGTCGGGA 59.641 66.667 0.00 0.00 0.00 5.14
1239 1294 3.839432 GGAGTCGGGAAGGAGGCG 61.839 72.222 0.00 0.00 0.00 5.52
1261 1316 2.579684 GAAGTGGAGGCGGCGATCTT 62.580 60.000 12.98 7.36 0.00 2.40
1266 1321 2.125512 AGGCGGCGATCTTGTGAC 60.126 61.111 12.98 0.00 0.00 3.67
1340 1395 1.079256 CAGAGGGAGGAGGTGGTGA 59.921 63.158 0.00 0.00 0.00 4.02
1353 1408 0.669625 GTGGTGACGCTAGGTGGAAC 60.670 60.000 0.00 0.00 38.02 3.62
1367 1422 1.693103 GGAACGAGGGGAAGGGGAT 60.693 63.158 0.00 0.00 0.00 3.85
1371 1426 0.542232 ACGAGGGGAAGGGGATATCG 60.542 60.000 0.00 0.00 35.00 2.92
1378 1433 2.292587 GGGAAGGGGATATCGAGGAGAT 60.293 54.545 0.00 0.00 43.19 2.75
1383 1438 1.480137 GGGATATCGAGGAGATGGCTG 59.520 57.143 0.00 0.00 40.40 4.85
1415 1470 0.106217 GAGGTGGAGGAGAGGGAGAG 60.106 65.000 0.00 0.00 0.00 3.20
1542 1597 2.268920 GGCTGCGACTGGGATGAA 59.731 61.111 0.00 0.00 0.00 2.57
1561 1616 0.835543 AGCCCTGCACACTCTCTCTT 60.836 55.000 0.00 0.00 0.00 2.85
1575 1630 4.411212 ACTCTCTCTTACTCTCCCCTAGAC 59.589 50.000 0.00 0.00 0.00 2.59
1585 1640 3.660669 CTCTCCCCTAGACTATTCTCCCT 59.339 52.174 0.00 0.00 32.75 4.20
1658 1715 0.597568 TGAGCAGGACGCCAATTTTG 59.402 50.000 0.00 0.00 44.04 2.44
1709 1768 4.934356 AGAAAATTAGGAGTGGGCATGAA 58.066 39.130 0.00 0.00 0.00 2.57
1887 1952 1.866601 GGCATGGGATTATTTTTGCGC 59.133 47.619 0.00 0.00 0.00 6.09
2153 2234 1.958288 ATAGCTGGAAGACACCTGGT 58.042 50.000 0.00 0.00 41.17 4.00
2157 2238 0.179020 CTGGAAGACACCTGGTGCAA 60.179 55.000 26.20 2.94 36.98 4.08
2158 2239 0.478072 TGGAAGACACCTGGTGCAAT 59.522 50.000 26.20 12.32 36.98 3.56
2184 2265 0.322187 GGGGCGTTACAACACTCCAT 60.322 55.000 0.00 0.00 0.00 3.41
2292 2375 6.713762 TCTTTGACAAATGAGTGAAACCAT 57.286 33.333 0.05 0.00 37.80 3.55
2427 2511 8.002459 AGGTTGAAAGACATAAGAAAAGGGTTA 58.998 33.333 0.00 0.00 0.00 2.85
2428 2512 8.803235 GGTTGAAAGACATAAGAAAAGGGTTAT 58.197 33.333 0.00 0.00 0.00 1.89
2429 2513 9.626045 GTTGAAAGACATAAGAAAAGGGTTATG 57.374 33.333 0.00 0.00 40.85 1.90
2440 2524 6.183347 AGAAAAGGGTTATGATGGACAAGAG 58.817 40.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 109 1.003839 ATTCGTCACCGTGGCACAT 60.004 52.632 19.09 1.44 44.52 3.21
95 110 1.666553 GATTCGTCACCGTGGCACA 60.667 57.895 19.09 0.00 35.01 4.57
115 130 7.143340 CGATATGTTTTCATGGCATCATTCTT 58.857 34.615 0.00 0.00 41.09 2.52
152 167 2.020131 GCACCAGCATCTCAATCGG 58.980 57.895 0.00 0.00 41.58 4.18
218 236 2.046604 GGGACACCCGGTTACTGC 60.047 66.667 0.00 0.00 32.13 4.40
257 275 1.522668 TTGATCCTTGCACGTTCCTG 58.477 50.000 0.00 0.00 0.00 3.86
287 305 0.821301 TGAGATGCCCGTGTTTGCAA 60.821 50.000 0.00 0.00 41.50 4.08
296 314 2.022764 TGTGTTGTATGAGATGCCCG 57.977 50.000 0.00 0.00 0.00 6.13
356 378 3.074412 CCGAGAATGCAACCTTGTAAGT 58.926 45.455 0.00 0.00 0.00 2.24
360 382 1.813513 CTCCGAGAATGCAACCTTGT 58.186 50.000 0.00 0.00 0.00 3.16
375 399 1.349259 CTACAAACCGAACCGCTCCG 61.349 60.000 0.00 0.00 0.00 4.63
378 402 0.037605 CCTCTACAAACCGAACCGCT 60.038 55.000 0.00 0.00 0.00 5.52
405 458 5.416083 CCCGAACATCTACAGACATAAACA 58.584 41.667 0.00 0.00 0.00 2.83
409 462 3.635373 GACCCCGAACATCTACAGACATA 59.365 47.826 0.00 0.00 0.00 2.29
530 584 7.167535 CACCATGATATGTACCATTACCATCA 58.832 38.462 0.00 0.00 35.08 3.07
531 585 6.599244 CCACCATGATATGTACCATTACCATC 59.401 42.308 0.00 0.00 0.00 3.51
532 586 6.274436 TCCACCATGATATGTACCATTACCAT 59.726 38.462 0.00 0.00 0.00 3.55
533 587 5.608860 TCCACCATGATATGTACCATTACCA 59.391 40.000 0.00 0.00 0.00 3.25
534 588 6.121776 TCCACCATGATATGTACCATTACC 57.878 41.667 0.00 0.00 0.00 2.85
535 589 7.224297 AGTTCCACCATGATATGTACCATTAC 58.776 38.462 0.00 0.00 0.00 1.89
536 590 7.387265 AGTTCCACCATGATATGTACCATTA 57.613 36.000 0.00 0.00 0.00 1.90
537 591 6.266131 AGTTCCACCATGATATGTACCATT 57.734 37.500 0.00 0.00 0.00 3.16
538 592 5.912149 AGTTCCACCATGATATGTACCAT 57.088 39.130 0.00 0.00 0.00 3.55
539 593 5.436175 CAAGTTCCACCATGATATGTACCA 58.564 41.667 0.00 0.00 0.00 3.25
540 594 4.821805 CCAAGTTCCACCATGATATGTACC 59.178 45.833 0.00 0.00 0.00 3.34
541 595 5.296780 CACCAAGTTCCACCATGATATGTAC 59.703 44.000 0.00 0.00 0.00 2.90
542 596 5.190726 TCACCAAGTTCCACCATGATATGTA 59.809 40.000 0.00 0.00 0.00 2.29
543 597 4.018506 TCACCAAGTTCCACCATGATATGT 60.019 41.667 0.00 0.00 0.00 2.29
544 598 4.525996 TCACCAAGTTCCACCATGATATG 58.474 43.478 0.00 0.00 0.00 1.78
545 599 4.385643 CCTCACCAAGTTCCACCATGATAT 60.386 45.833 0.00 0.00 0.00 1.63
546 600 3.054434 CCTCACCAAGTTCCACCATGATA 60.054 47.826 0.00 0.00 0.00 2.15
547 601 2.291153 CCTCACCAAGTTCCACCATGAT 60.291 50.000 0.00 0.00 0.00 2.45
548 602 1.073763 CCTCACCAAGTTCCACCATGA 59.926 52.381 0.00 0.00 0.00 3.07
549 603 1.538047 CCTCACCAAGTTCCACCATG 58.462 55.000 0.00 0.00 0.00 3.66
550 604 0.405585 CCCTCACCAAGTTCCACCAT 59.594 55.000 0.00 0.00 0.00 3.55
551 605 1.715019 CCCCTCACCAAGTTCCACCA 61.715 60.000 0.00 0.00 0.00 4.17
552 606 1.074951 CCCCTCACCAAGTTCCACC 59.925 63.158 0.00 0.00 0.00 4.61
553 607 0.476771 TTCCCCTCACCAAGTTCCAC 59.523 55.000 0.00 0.00 0.00 4.02
554 608 0.476771 GTTCCCCTCACCAAGTTCCA 59.523 55.000 0.00 0.00 0.00 3.53
555 609 0.771755 AGTTCCCCTCACCAAGTTCC 59.228 55.000 0.00 0.00 0.00 3.62
556 610 2.230660 CAAGTTCCCCTCACCAAGTTC 58.769 52.381 0.00 0.00 0.00 3.01
557 611 1.133482 CCAAGTTCCCCTCACCAAGTT 60.133 52.381 0.00 0.00 0.00 2.66
558 612 0.478507 CCAAGTTCCCCTCACCAAGT 59.521 55.000 0.00 0.00 0.00 3.16
559 613 0.895559 GCCAAGTTCCCCTCACCAAG 60.896 60.000 0.00 0.00 0.00 3.61
560 614 1.152830 GCCAAGTTCCCCTCACCAA 59.847 57.895 0.00 0.00 0.00 3.67
561 615 2.843545 GCCAAGTTCCCCTCACCA 59.156 61.111 0.00 0.00 0.00 4.17
562 616 2.359975 CGCCAAGTTCCCCTCACC 60.360 66.667 0.00 0.00 0.00 4.02
563 617 3.056328 GCGCCAAGTTCCCCTCAC 61.056 66.667 0.00 0.00 0.00 3.51
564 618 4.697756 CGCGCCAAGTTCCCCTCA 62.698 66.667 0.00 0.00 0.00 3.86
565 619 4.699522 ACGCGCCAAGTTCCCCTC 62.700 66.667 5.73 0.00 0.00 4.30
566 620 4.699522 GACGCGCCAAGTTCCCCT 62.700 66.667 5.73 0.00 0.00 4.79
568 622 2.332654 AATGACGCGCCAAGTTCCC 61.333 57.895 5.73 0.00 0.00 3.97
569 623 1.154225 CAATGACGCGCCAAGTTCC 60.154 57.895 5.73 0.00 0.00 3.62
570 624 0.725784 CACAATGACGCGCCAAGTTC 60.726 55.000 5.73 0.00 0.00 3.01
571 625 1.282570 CACAATGACGCGCCAAGTT 59.717 52.632 5.73 0.00 0.00 2.66
572 626 0.601576 TACACAATGACGCGCCAAGT 60.602 50.000 5.73 1.21 0.00 3.16
573 627 0.095245 CTACACAATGACGCGCCAAG 59.905 55.000 5.73 0.44 0.00 3.61
574 628 0.601576 ACTACACAATGACGCGCCAA 60.602 50.000 5.73 0.00 0.00 4.52
575 629 1.005512 ACTACACAATGACGCGCCA 60.006 52.632 5.73 0.00 0.00 5.69
576 630 1.708027 GACTACACAATGACGCGCC 59.292 57.895 5.73 0.00 0.00 6.53
577 631 1.340465 CGACTACACAATGACGCGC 59.660 57.895 5.73 0.00 0.00 6.86
578 632 1.576246 GTACGACTACACAATGACGCG 59.424 52.381 3.53 3.53 0.00 6.01
579 633 2.587956 TGTACGACTACACAATGACGC 58.412 47.619 0.00 0.00 0.00 5.19
580 634 3.477446 CGATGTACGACTACACAATGACG 59.523 47.826 0.00 0.00 45.77 4.35
581 635 4.655027 TCGATGTACGACTACACAATGAC 58.345 43.478 0.00 0.00 46.45 3.06
582 636 4.201881 CCTCGATGTACGACTACACAATGA 60.202 45.833 0.00 0.00 46.45 2.57
583 637 4.035684 CCTCGATGTACGACTACACAATG 58.964 47.826 0.00 0.00 46.45 2.82
584 638 3.693085 ACCTCGATGTACGACTACACAAT 59.307 43.478 0.00 0.00 46.45 2.71
585 639 3.076621 ACCTCGATGTACGACTACACAA 58.923 45.455 0.00 0.00 46.45 3.33
586 640 2.674852 GACCTCGATGTACGACTACACA 59.325 50.000 0.00 0.00 46.45 3.72
587 641 2.031437 GGACCTCGATGTACGACTACAC 59.969 54.545 0.00 0.00 46.45 2.90
588 642 2.093288 AGGACCTCGATGTACGACTACA 60.093 50.000 0.00 0.00 46.45 2.74
589 643 2.543430 GAGGACCTCGATGTACGACTAC 59.457 54.545 5.55 0.00 46.45 2.73
590 644 2.169144 TGAGGACCTCGATGTACGACTA 59.831 50.000 16.81 0.00 46.45 2.59
591 645 1.065636 TGAGGACCTCGATGTACGACT 60.066 52.381 16.81 0.00 46.45 4.18
592 646 1.376543 TGAGGACCTCGATGTACGAC 58.623 55.000 16.81 0.00 46.45 4.34
594 648 1.600663 GCATGAGGACCTCGATGTACG 60.601 57.143 23.49 8.89 44.09 3.67
595 649 1.409064 TGCATGAGGACCTCGATGTAC 59.591 52.381 23.49 14.53 32.35 2.90
596 650 1.409064 GTGCATGAGGACCTCGATGTA 59.591 52.381 23.49 19.73 32.35 2.29
597 651 0.176680 GTGCATGAGGACCTCGATGT 59.823 55.000 23.49 0.00 32.35 3.06
598 652 0.463204 AGTGCATGAGGACCTCGATG 59.537 55.000 16.81 19.26 36.65 3.84
599 653 1.198713 AAGTGCATGAGGACCTCGAT 58.801 50.000 16.81 8.56 36.65 3.59
600 654 0.976641 AAAGTGCATGAGGACCTCGA 59.023 50.000 16.81 6.56 36.65 4.04
601 655 1.081892 CAAAGTGCATGAGGACCTCG 58.918 55.000 16.81 4.56 36.65 4.63
602 656 2.479566 TCAAAGTGCATGAGGACCTC 57.520 50.000 15.13 15.13 36.65 3.85
603 657 2.306805 TCATCAAAGTGCATGAGGACCT 59.693 45.455 0.00 0.00 36.65 3.85
604 658 2.715046 TCATCAAAGTGCATGAGGACC 58.285 47.619 0.00 0.00 36.65 4.46
605 659 3.754188 GTCATCAAAGTGCATGAGGAC 57.246 47.619 15.37 15.37 46.91 3.85
606 660 3.262660 AGAGTCATCAAAGTGCATGAGGA 59.737 43.478 0.00 0.00 35.46 3.71
607 661 3.374367 CAGAGTCATCAAAGTGCATGAGG 59.626 47.826 0.00 0.00 29.46 3.86
608 662 3.374367 CCAGAGTCATCAAAGTGCATGAG 59.626 47.826 0.00 0.00 29.46 2.90
609 663 3.008266 TCCAGAGTCATCAAAGTGCATGA 59.992 43.478 0.00 0.00 0.00 3.07
610 664 3.126514 GTCCAGAGTCATCAAAGTGCATG 59.873 47.826 0.00 0.00 0.00 4.06
611 665 3.341823 GTCCAGAGTCATCAAAGTGCAT 58.658 45.455 0.00 0.00 0.00 3.96
612 666 2.771089 GTCCAGAGTCATCAAAGTGCA 58.229 47.619 0.00 0.00 0.00 4.57
613 667 1.728971 CGTCCAGAGTCATCAAAGTGC 59.271 52.381 0.00 0.00 0.00 4.40
614 668 3.249091 CTCGTCCAGAGTCATCAAAGTG 58.751 50.000 0.00 0.00 41.99 3.16
615 669 2.232452 CCTCGTCCAGAGTCATCAAAGT 59.768 50.000 0.00 0.00 45.44 2.66
616 670 2.493675 TCCTCGTCCAGAGTCATCAAAG 59.506 50.000 0.00 0.00 45.44 2.77
617 671 2.525368 TCCTCGTCCAGAGTCATCAAA 58.475 47.619 0.00 0.00 45.44 2.69
618 672 2.215942 TCCTCGTCCAGAGTCATCAA 57.784 50.000 0.00 0.00 45.44 2.57
619 673 1.819288 GTTCCTCGTCCAGAGTCATCA 59.181 52.381 0.00 0.00 45.44 3.07
620 674 2.096248 AGTTCCTCGTCCAGAGTCATC 58.904 52.381 0.00 0.00 45.44 2.92
621 675 2.223803 AGTTCCTCGTCCAGAGTCAT 57.776 50.000 0.00 0.00 45.44 3.06
622 676 1.613925 CAAGTTCCTCGTCCAGAGTCA 59.386 52.381 0.00 0.00 45.44 3.41
623 677 1.067495 CCAAGTTCCTCGTCCAGAGTC 60.067 57.143 0.00 0.00 45.44 3.36
624 678 0.969894 CCAAGTTCCTCGTCCAGAGT 59.030 55.000 0.00 0.00 45.44 3.24
625 679 0.390472 GCCAAGTTCCTCGTCCAGAG 60.390 60.000 0.00 0.00 46.44 3.35
626 680 1.118965 TGCCAAGTTCCTCGTCCAGA 61.119 55.000 0.00 0.00 0.00 3.86
627 681 0.951040 GTGCCAAGTTCCTCGTCCAG 60.951 60.000 0.00 0.00 0.00 3.86
628 682 1.070786 GTGCCAAGTTCCTCGTCCA 59.929 57.895 0.00 0.00 0.00 4.02
629 683 1.671379 GGTGCCAAGTTCCTCGTCC 60.671 63.158 0.00 0.00 0.00 4.79
630 684 1.671379 GGGTGCCAAGTTCCTCGTC 60.671 63.158 0.00 0.00 0.00 4.20
631 685 2.430367 GGGTGCCAAGTTCCTCGT 59.570 61.111 0.00 0.00 0.00 4.18
632 686 1.966451 GTGGGTGCCAAGTTCCTCG 60.966 63.158 0.00 0.00 34.18 4.63
633 687 1.966451 CGTGGGTGCCAAGTTCCTC 60.966 63.158 0.00 0.00 34.18 3.71
634 688 2.113139 CGTGGGTGCCAAGTTCCT 59.887 61.111 0.00 0.00 34.18 3.36
635 689 2.983592 CCGTGGGTGCCAAGTTCC 60.984 66.667 0.00 0.00 34.18 3.62
636 690 2.203294 ACCGTGGGTGCCAAGTTC 60.203 61.111 0.00 0.00 34.18 3.01
637 691 2.203294 GACCGTGGGTGCCAAGTT 60.203 61.111 0.00 0.00 35.25 2.66
638 692 2.752807 AAGACCGTGGGTGCCAAGT 61.753 57.895 0.00 0.00 35.25 3.16
639 693 2.113139 AAGACCGTGGGTGCCAAG 59.887 61.111 0.00 0.00 35.25 3.61
640 694 2.203280 CAAGACCGTGGGTGCCAA 60.203 61.111 0.00 0.00 35.25 4.52
641 695 3.164977 TCAAGACCGTGGGTGCCA 61.165 61.111 0.00 0.00 35.25 4.92
642 696 2.668550 GTCAAGACCGTGGGTGCC 60.669 66.667 0.00 0.00 35.25 5.01
643 697 3.041940 CGTCAAGACCGTGGGTGC 61.042 66.667 0.00 0.00 35.25 5.01
644 698 1.663702 GACGTCAAGACCGTGGGTG 60.664 63.158 11.55 0.00 38.92 4.61
645 699 1.678598 TTGACGTCAAGACCGTGGGT 61.679 55.000 26.53 0.00 38.92 4.51
646 700 1.068417 TTGACGTCAAGACCGTGGG 59.932 57.895 26.53 0.00 38.92 4.61
647 701 0.528901 TGTTGACGTCAAGACCGTGG 60.529 55.000 30.38 0.00 38.92 4.94
696 750 3.365265 CCAACTTCTGCCGTGCCC 61.365 66.667 0.00 0.00 0.00 5.36
703 757 4.043200 GCCGTGCCCAACTTCTGC 62.043 66.667 0.00 0.00 0.00 4.26
743 797 2.721971 CTTCGCGCCATGGCCTCTAT 62.722 60.000 30.79 0.00 37.98 1.98
744 798 3.445518 CTTCGCGCCATGGCCTCTA 62.446 63.158 30.79 12.13 37.98 2.43
759 813 2.178890 CAGCTGCCGCTCATCCTTC 61.179 63.158 0.00 0.00 45.15 3.46
770 824 0.807667 CACTCGGATACACAGCTGCC 60.808 60.000 15.27 5.34 0.00 4.85
773 827 2.093973 CCTTTCACTCGGATACACAGCT 60.094 50.000 0.00 0.00 0.00 4.24
785 839 1.139853 AGATCCGCCATCCTTTCACTC 59.860 52.381 0.00 0.00 30.71 3.51
789 843 1.169034 GCCAGATCCGCCATCCTTTC 61.169 60.000 0.00 0.00 30.71 2.62
791 845 2.074948 AGCCAGATCCGCCATCCTT 61.075 57.895 0.00 0.00 30.71 3.36
792 846 2.447379 AGCCAGATCCGCCATCCT 60.447 61.111 0.00 0.00 30.71 3.24
805 859 4.641645 CCTTGTCGTGCCCAGCCA 62.642 66.667 0.00 0.00 0.00 4.75
831 886 3.048941 CTTCGTCCCGACTCCGTCC 62.049 68.421 0.00 0.00 34.89 4.79
833 888 3.060615 CCTTCGTCCCGACTCCGT 61.061 66.667 0.00 0.00 34.89 4.69
835 890 4.493747 CGCCTTCGTCCCGACTCC 62.494 72.222 0.00 0.00 34.89 3.85
855 910 2.885644 CAAGTCCCGTCGCCGATG 60.886 66.667 0.00 0.00 35.63 3.84
856 911 4.143333 CCAAGTCCCGTCGCCGAT 62.143 66.667 0.00 0.00 35.63 4.18
899 954 2.353030 TGCACACTCGACGTCACG 60.353 61.111 17.16 7.95 0.00 4.35
901 956 2.335011 CCTGCACACTCGACGTCA 59.665 61.111 17.16 1.87 0.00 4.35
907 962 2.125952 TCATCGCCTGCACACTCG 60.126 61.111 0.00 0.00 0.00 4.18
909 964 2.435586 GCTCATCGCCTGCACACT 60.436 61.111 0.00 0.00 0.00 3.55
911 966 2.435410 CTGCTCATCGCCTGCACA 60.435 61.111 0.00 0.00 38.05 4.57
912 967 2.125391 TCTGCTCATCGCCTGCAC 60.125 61.111 0.00 0.00 38.05 4.57
933 988 1.135915 CTCTACATCAGTGGCTTCGCT 59.864 52.381 0.00 0.00 0.00 4.93
944 999 2.900273 GCACGGCCCTCTACATCA 59.100 61.111 0.00 0.00 0.00 3.07
971 1026 1.041437 GCTCCTGCTACCCGTATCTT 58.959 55.000 0.00 0.00 36.03 2.40
975 1030 2.831742 CCGCTCCTGCTACCCGTA 60.832 66.667 0.00 0.00 36.97 4.02
979 1034 4.537433 CCTGCCGCTCCTGCTACC 62.537 72.222 0.00 0.00 36.97 3.18
987 1042 4.925861 GCCATCCTCCTGCCGCTC 62.926 72.222 0.00 0.00 0.00 5.03
1005 1060 3.207669 CCTACCTCCCCGACGTCG 61.208 72.222 30.33 30.33 39.44 5.12
1007 1062 4.371417 TGCCTACCTCCCCGACGT 62.371 66.667 0.00 0.00 0.00 4.34
1012 1067 3.155167 CGGAGTGCCTACCTCCCC 61.155 72.222 0.00 0.00 33.93 4.81
1019 1074 4.753662 ACCTCGCCGGAGTGCCTA 62.754 66.667 5.05 0.00 38.70 3.93
1032 1087 1.026718 CCCAATTCTGTCGCCACCTC 61.027 60.000 0.00 0.00 0.00 3.85
1040 1095 2.711542 CACCTACACCCCAATTCTGTC 58.288 52.381 0.00 0.00 0.00 3.51
1043 1098 1.282157 GAGCACCTACACCCCAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
1059 1114 2.594303 CAGCAAACCCCACGAGCA 60.594 61.111 0.00 0.00 0.00 4.26
1062 1117 2.203280 CACCAGCAAACCCCACGA 60.203 61.111 0.00 0.00 0.00 4.35
1064 1119 2.521708 AGCACCAGCAAACCCCAC 60.522 61.111 0.00 0.00 45.49 4.61
1065 1120 2.521465 CAGCACCAGCAAACCCCA 60.521 61.111 0.00 0.00 45.49 4.96
1071 1126 2.665008 AAGTCGAGCAGCACCAGCAA 62.665 55.000 0.00 0.00 45.49 3.91
1100 1155 1.371183 CTTCTTCTCCCGTGCACCA 59.629 57.895 12.15 0.00 0.00 4.17
1107 1162 1.153745 CGGAGCACTTCTTCTCCCG 60.154 63.158 3.01 0.00 44.61 5.14
1163 1218 3.787001 CTTGAGTCCGAGGGCCCC 61.787 72.222 21.43 9.47 0.00 5.80
1167 1222 1.079543 CACTGCTTGAGTCCGAGGG 60.080 63.158 0.00 0.00 29.75 4.30
1169 1224 1.739562 GCCACTGCTTGAGTCCGAG 60.740 63.158 0.00 0.00 29.75 4.63
1207 1262 4.779733 TCCCACCTCTCCGCCTCC 62.780 72.222 0.00 0.00 0.00 4.30
1231 1286 4.394712 CCACTTCGCCGCCTCCTT 62.395 66.667 0.00 0.00 0.00 3.36
1261 1316 2.661537 CTTCTGCACCGCGTCACA 60.662 61.111 4.92 0.00 0.00 3.58
1266 1321 1.515952 CTCTCTCTTCTGCACCGCG 60.516 63.158 0.00 0.00 0.00 6.46
1340 1395 2.348888 CCCTCGTTCCACCTAGCGT 61.349 63.158 0.00 0.00 0.00 5.07
1353 1408 0.251653 TCGATATCCCCTTCCCCTCG 60.252 60.000 0.00 0.00 0.00 4.63
1367 1422 1.202989 AGAGCAGCCATCTCCTCGATA 60.203 52.381 0.00 0.00 0.00 2.92
1371 1426 1.446791 CCAGAGCAGCCATCTCCTC 59.553 63.158 0.00 0.00 0.00 3.71
1395 1450 1.454847 CTCCCTCTCCTCCACCTCG 60.455 68.421 0.00 0.00 0.00 4.63
1403 1458 0.699577 TCGATCCCTCTCCCTCTCCT 60.700 60.000 0.00 0.00 0.00 3.69
1415 1470 0.948678 CGACCTCTTCTCTCGATCCC 59.051 60.000 0.00 0.00 0.00 3.85
1426 1481 0.337428 TAACCCTAGGCCGACCTCTT 59.663 55.000 2.05 0.00 46.34 2.85
1433 1488 1.837499 CCCTCCTAACCCTAGGCCG 60.837 68.421 2.05 0.00 44.13 6.13
1518 1573 4.320456 CAGTCGCAGCCCACCACT 62.320 66.667 0.00 0.00 0.00 4.00
1538 1593 0.035630 GAGAGTGTGCAGGGCTTCAT 60.036 55.000 0.00 0.00 0.00 2.57
1542 1597 0.835543 AAGAGAGAGTGTGCAGGGCT 60.836 55.000 0.00 0.00 0.00 5.19
1561 1616 4.602732 GGGAGAATAGTCTAGGGGAGAGTA 59.397 50.000 0.00 0.00 42.99 2.59
1600 1655 6.072064 TCCCTCTCTACTTTCTTTACTCGTTG 60.072 42.308 0.00 0.00 0.00 4.10
1602 1657 5.568392 TCCCTCTCTACTTTCTTTACTCGT 58.432 41.667 0.00 0.00 0.00 4.18
1658 1715 5.473504 TCAAGCTCCTTTTTATGAGTCCAAC 59.526 40.000 0.00 0.00 0.00 3.77
1986 2059 3.899052 TCGGTCCATTTAAATCGAGGT 57.101 42.857 0.00 0.00 0.00 3.85
2153 2234 4.776322 CGCCCCGAGACCATTGCA 62.776 66.667 0.00 0.00 0.00 4.08
2157 2238 1.546589 TTGTAACGCCCCGAGACCAT 61.547 55.000 0.00 0.00 0.00 3.55
2158 2239 2.208619 TTGTAACGCCCCGAGACCA 61.209 57.895 0.00 0.00 0.00 4.02
2184 2265 3.280295 GGACGAGATCCTCTTGTAGTGA 58.720 50.000 0.00 0.00 41.04 3.41
2334 2418 8.306761 AGAGTGTTTTCAACTTTGTTCATCTTT 58.693 29.630 0.00 0.00 0.00 2.52
2366 2450 8.857694 TCGTAATATTCCTTGTTCCTCTTTTT 57.142 30.769 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.