Multiple sequence alignment - TraesCS4B01G028400

Loading Multiple Alignment...

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 TraesCS4B01G028400 chr4B 100.000 3461 0 0 1 3461 21182162 21185622 0.000000e+00 6392.0
1 TraesCS4B01G028400 chr4D 93.340 1937 83 22 667 2589 11289977 11291881 0.000000e+00 2820.0
2 TraesCS4B01G028400 chr4D 86.947 950 94 18 1161 2100 11217497 11218426 0.000000e+00 1040.0
3 TraesCS4B01G028400 chr4D 90.783 792 54 4 2669 3459 11361116 11361889 0.000000e+00 1040.0
4 TraesCS4B01G028400 chr4D 84.333 517 57 14 2096 2589 11280912 11281427 5.190000e-133 484.0
5 TraesCS4B01G028400 chr4D 85.664 286 28 12 1 284 11289379 11289653 4.370000e-74 289.0
6 TraesCS4B01G028400 chr4D 86.452 155 10 3 2596 2749 11360957 11361101 3.580000e-35 159.0
7 TraesCS4B01G028400 chr4D 97.959 49 1 0 282 330 11289685 11289733 6.150000e-13 86.1
8 TraesCS4B01G028400 chr4A 92.539 1796 92 23 820 2592 591072365 591070589 0.000000e+00 2536.0
9 TraesCS4B01G028400 chr4A 88.421 760 81 4 2702 3460 591000989 591000236 0.000000e+00 909.0
10 TraesCS4B01G028400 chr4A 85.866 283 21 9 3 284 591073776 591073512 2.030000e-72 283.0
11 TraesCS4B01G028400 chr4A 100.000 42 0 0 289 330 591073441 591073400 1.030000e-10 78.7
12 TraesCS4B01G028400 chr7A 90.300 866 68 7 2596 3460 620406747 620405897 0.000000e+00 1120.0
13 TraesCS4B01G028400 chr7B 90.909 605 53 2 2856 3460 3716297 3715695 0.000000e+00 811.0
14 TraesCS4B01G028400 chr7B 86.124 209 17 4 2618 2825 3716497 3716300 7.520000e-52 215.0
15 TraesCS4B01G028400 chr7B 93.519 108 7 0 536 643 23730807 23730914 9.940000e-36 161.0
16 TraesCS4B01G028400 chr7B 93.519 108 7 0 536 643 23791705 23791812 9.940000e-36 161.0
17 TraesCS4B01G028400 chr7B 93.458 107 7 0 537 643 75023844 75023950 3.580000e-35 159.0
18 TraesCS4B01G028400 chrUn 93.519 108 7 0 536 643 84603035 84602928 9.940000e-36 161.0
19 TraesCS4B01G028400 chrUn 93.519 108 7 0 536 643 320050246 320050139 9.940000e-36 161.0
20 TraesCS4B01G028400 chr6D 92.727 110 8 0 534 643 303338211 303338102 3.580000e-35 159.0
21 TraesCS4B01G028400 chr2A 93.458 107 7 0 537 643 412471542 412471648 3.580000e-35 159.0
22 TraesCS4B01G028400 chr1B 93.458 107 7 0 537 643 510795210 510795104 3.580000e-35 159.0
23 TraesCS4B01G028400 chr1D 91.964 112 8 1 533 643 464736341 464736230 4.620000e-34 156.0


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 TraesCS4B01G028400 chr4B 21182162 21185622 3460 False 6392.000000 6392 100.000000 1 3461 1 chr4B.!!$F1 3460
1 TraesCS4B01G028400 chr4D 11289379 11291881 2502 False 1065.033333 2820 92.321000 1 2589 3 chr4D.!!$F3 2588
2 TraesCS4B01G028400 chr4D 11217497 11218426 929 False 1040.000000 1040 86.947000 1161 2100 1 chr4D.!!$F1 939
3 TraesCS4B01G028400 chr4D 11360957 11361889 932 False 599.500000 1040 88.617500 2596 3459 2 chr4D.!!$F4 863
4 TraesCS4B01G028400 chr4D 11280912 11281427 515 False 484.000000 484 84.333000 2096 2589 1 chr4D.!!$F2 493
5 TraesCS4B01G028400 chr4A 591070589 591073776 3187 True 965.900000 2536 92.801667 3 2592 3 chr4A.!!$R2 2589
6 TraesCS4B01G028400 chr4A 591000236 591000989 753 True 909.000000 909 88.421000 2702 3460 1 chr4A.!!$R1 758
7 TraesCS4B01G028400 chr7A 620405897 620406747 850 True 1120.000000 1120 90.300000 2596 3460 1 chr7A.!!$R1 864
8 TraesCS4B01G028400 chr7B 3715695 3716497 802 True 513.000000 811 88.516500 2618 3460 2 chr7B.!!$R1 842

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
747 1616 0.323302 TCAGTTCCTGGCATGCGTAA 59.677 50.0 12.44 0.0 31.51 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2715 3634 0.915364 GGAGGTGAGGAAGCCTTCAT 59.085 55.0 6.8 0.0 34.81 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
24 25 2.972819 GCCCCTCGCCTTCCTCTTT 61.973 63.158 0.00 0.00 0.00 2.52
41 42 5.567138 CTCTTTGAGAGGTTTGTTGTTGT 57.433 39.130 0.00 0.00 38.67 3.32
42 43 5.954335 CTCTTTGAGAGGTTTGTTGTTGTT 58.046 37.500 0.00 0.00 38.67 2.83
43 44 5.949735 TCTTTGAGAGGTTTGTTGTTGTTC 58.050 37.500 0.00 0.00 0.00 3.18
44 45 4.712122 TTGAGAGGTTTGTTGTTGTTCC 57.288 40.909 0.00 0.00 0.00 3.62
45 46 3.963129 TGAGAGGTTTGTTGTTGTTCCT 58.037 40.909 0.00 0.00 0.00 3.36
46 47 3.694072 TGAGAGGTTTGTTGTTGTTCCTG 59.306 43.478 0.00 0.00 0.00 3.86
75 84 4.388499 TCGACGCCCCCTCTTTGC 62.388 66.667 0.00 0.00 0.00 3.68
149 158 7.282916 GCACAAAAGCAATAACATAACTTGTG 58.717 34.615 6.72 6.72 42.39 3.33
199 209 4.151867 GGTCGGCTAGTTTTGTTTGTAGAG 59.848 45.833 0.00 0.00 0.00 2.43
236 247 9.942850 TTTCCTTTCTCAAACAGAAAAGAAATT 57.057 25.926 13.31 0.00 46.97 1.82
332 409 3.971150 CTTGCATAGTTCGCTAGCTAGT 58.029 45.455 21.62 6.24 32.51 2.57
342 419 2.064762 CGCTAGCTAGTTGCATGATCC 58.935 52.381 21.62 0.50 45.94 3.36
345 422 1.516110 AGCTAGTTGCATGATCCCCT 58.484 50.000 0.00 0.00 45.94 4.79
346 423 2.694397 AGCTAGTTGCATGATCCCCTA 58.306 47.619 0.00 0.00 45.94 3.53
376 486 5.601662 TCTATCCTTCAACATAGAAAGCCG 58.398 41.667 0.00 0.00 30.18 5.52
398 508 1.539827 ACAATTAGCTTTGTGGCCGAC 59.460 47.619 2.97 0.00 38.37 4.79
432 543 6.015434 GCCTATGTCCTGAAAAAGAAAAAGGA 60.015 38.462 0.00 0.00 34.65 3.36
437 548 7.102993 TGTCCTGAAAAAGAAAAAGGAAAAGG 58.897 34.615 0.00 0.00 38.73 3.11
487 598 6.032251 CGCGTTACTACTACTTCAGTTCTTTC 59.968 42.308 0.00 0.00 38.80 2.62
502 614 6.603201 TCAGTTCTTTCAAGTTGACTTTGGAT 59.397 34.615 4.68 0.00 33.11 3.41
512 624 4.875536 AGTTGACTTTGGATTGCAAAAACC 59.124 37.500 1.71 8.45 0.00 3.27
538 1407 3.513209 CCCCCACAATCCCACATAC 57.487 57.895 0.00 0.00 0.00 2.39
539 1408 0.926293 CCCCCACAATCCCACATACT 59.074 55.000 0.00 0.00 0.00 2.12
542 1411 2.654863 CCCACAATCCCACATACTTCC 58.345 52.381 0.00 0.00 0.00 3.46
544 1413 3.545703 CCACAATCCCACATACTTCCTC 58.454 50.000 0.00 0.00 0.00 3.71
545 1414 3.545703 CACAATCCCACATACTTCCTCC 58.454 50.000 0.00 0.00 0.00 4.30
546 1415 2.170607 ACAATCCCACATACTTCCTCCG 59.829 50.000 0.00 0.00 0.00 4.63
547 1416 2.170607 CAATCCCACATACTTCCTCCGT 59.829 50.000 0.00 0.00 0.00 4.69
548 1417 1.946984 TCCCACATACTTCCTCCGTT 58.053 50.000 0.00 0.00 0.00 4.44
549 1418 1.829222 TCCCACATACTTCCTCCGTTC 59.171 52.381 0.00 0.00 0.00 3.95
550 1419 1.553248 CCCACATACTTCCTCCGTTCA 59.447 52.381 0.00 0.00 0.00 3.18
551 1420 2.418746 CCCACATACTTCCTCCGTTCAG 60.419 54.545 0.00 0.00 0.00 3.02
552 1421 2.496070 CCACATACTTCCTCCGTTCAGA 59.504 50.000 0.00 0.00 0.00 3.27
553 1422 3.056107 CCACATACTTCCTCCGTTCAGAA 60.056 47.826 0.00 0.00 0.00 3.02
554 1423 4.383118 CCACATACTTCCTCCGTTCAGAAT 60.383 45.833 0.00 0.00 0.00 2.40
555 1424 5.178797 CACATACTTCCTCCGTTCAGAATT 58.821 41.667 0.00 0.00 0.00 2.17
556 1425 6.338146 CACATACTTCCTCCGTTCAGAATTA 58.662 40.000 0.00 0.00 0.00 1.40
557 1426 6.255887 CACATACTTCCTCCGTTCAGAATTAC 59.744 42.308 0.00 0.00 0.00 1.89
558 1427 6.154706 ACATACTTCCTCCGTTCAGAATTACT 59.845 38.462 0.00 0.00 0.00 2.24
559 1428 5.485209 ACTTCCTCCGTTCAGAATTACTT 57.515 39.130 0.00 0.00 0.00 2.24
560 1429 5.238583 ACTTCCTCCGTTCAGAATTACTTG 58.761 41.667 0.00 0.00 0.00 3.16
561 1430 4.884668 TCCTCCGTTCAGAATTACTTGT 57.115 40.909 0.00 0.00 0.00 3.16
562 1431 5.223449 TCCTCCGTTCAGAATTACTTGTT 57.777 39.130 0.00 0.00 0.00 2.83
563 1432 4.994852 TCCTCCGTTCAGAATTACTTGTTG 59.005 41.667 0.00 0.00 0.00 3.33
564 1433 4.755123 CCTCCGTTCAGAATTACTTGTTGT 59.245 41.667 0.00 0.00 0.00 3.32
565 1434 5.929992 CCTCCGTTCAGAATTACTTGTTGTA 59.070 40.000 0.00 0.00 0.00 2.41
566 1435 6.090898 CCTCCGTTCAGAATTACTTGTTGTAG 59.909 42.308 0.00 0.00 32.08 2.74
567 1436 6.751157 TCCGTTCAGAATTACTTGTTGTAGA 58.249 36.000 0.00 0.00 32.08 2.59
568 1437 7.211573 TCCGTTCAGAATTACTTGTTGTAGAA 58.788 34.615 0.00 0.00 32.08 2.10
569 1438 7.711772 TCCGTTCAGAATTACTTGTTGTAGAAA 59.288 33.333 0.00 0.00 32.08 2.52
570 1439 8.504005 CCGTTCAGAATTACTTGTTGTAGAAAT 58.496 33.333 0.00 0.00 32.08 2.17
571 1440 9.318041 CGTTCAGAATTACTTGTTGTAGAAATG 57.682 33.333 0.00 0.00 32.08 2.32
572 1441 9.612620 GTTCAGAATTACTTGTTGTAGAAATGG 57.387 33.333 0.00 0.00 32.08 3.16
573 1442 8.335532 TCAGAATTACTTGTTGTAGAAATGGG 57.664 34.615 0.00 0.00 32.08 4.00
574 1443 7.942341 TCAGAATTACTTGTTGTAGAAATGGGT 59.058 33.333 0.00 0.00 32.08 4.51
575 1444 8.023128 CAGAATTACTTGTTGTAGAAATGGGTG 58.977 37.037 0.00 0.00 32.08 4.61
576 1445 7.724061 AGAATTACTTGTTGTAGAAATGGGTGT 59.276 33.333 0.00 0.00 32.08 4.16
577 1446 8.927675 AATTACTTGTTGTAGAAATGGGTGTA 57.072 30.769 0.00 0.00 32.08 2.90
578 1447 9.528489 AATTACTTGTTGTAGAAATGGGTGTAT 57.472 29.630 0.00 0.00 32.08 2.29
579 1448 8.556213 TTACTTGTTGTAGAAATGGGTGTATC 57.444 34.615 0.00 0.00 32.08 2.24
580 1449 6.779860 ACTTGTTGTAGAAATGGGTGTATCT 58.220 36.000 0.00 0.00 0.00 1.98
581 1450 7.913789 ACTTGTTGTAGAAATGGGTGTATCTA 58.086 34.615 0.00 0.00 0.00 1.98
582 1451 8.041323 ACTTGTTGTAGAAATGGGTGTATCTAG 58.959 37.037 0.00 0.00 0.00 2.43
583 1452 7.727578 TGTTGTAGAAATGGGTGTATCTAGA 57.272 36.000 0.00 0.00 0.00 2.43
584 1453 8.319057 TGTTGTAGAAATGGGTGTATCTAGAT 57.681 34.615 10.73 10.73 0.00 1.98
585 1454 8.204160 TGTTGTAGAAATGGGTGTATCTAGATG 58.796 37.037 15.79 0.00 0.00 2.90
586 1455 6.759272 TGTAGAAATGGGTGTATCTAGATGC 58.241 40.000 15.79 14.54 0.00 3.91
587 1456 5.894298 AGAAATGGGTGTATCTAGATGCA 57.106 39.130 18.36 18.36 0.00 3.96
588 1457 6.445451 AGAAATGGGTGTATCTAGATGCAT 57.555 37.500 23.86 9.10 35.92 3.96
589 1458 6.845908 AGAAATGGGTGTATCTAGATGCATT 58.154 36.000 23.86 14.74 35.92 3.56
590 1459 7.293073 AGAAATGGGTGTATCTAGATGCATTT 58.707 34.615 23.86 19.27 35.92 2.32
591 1460 7.781693 AGAAATGGGTGTATCTAGATGCATTTT 59.218 33.333 23.86 19.31 35.92 1.82
592 1461 8.995027 AAATGGGTGTATCTAGATGCATTTTA 57.005 30.769 23.86 12.70 35.92 1.52
593 1462 8.627208 AATGGGTGTATCTAGATGCATTTTAG 57.373 34.615 23.86 6.74 35.92 1.85
594 1463 5.997746 TGGGTGTATCTAGATGCATTTTAGC 59.002 40.000 23.86 11.45 35.92 3.09
595 1464 6.183361 TGGGTGTATCTAGATGCATTTTAGCT 60.183 38.462 23.86 0.98 35.92 3.32
596 1465 6.370166 GGGTGTATCTAGATGCATTTTAGCTC 59.630 42.308 23.86 8.54 35.92 4.09
597 1466 7.158021 GGTGTATCTAGATGCATTTTAGCTCT 58.842 38.462 23.86 0.00 35.92 4.09
598 1467 8.307483 GGTGTATCTAGATGCATTTTAGCTCTA 58.693 37.037 23.86 0.00 35.92 2.43
599 1468 9.352784 GTGTATCTAGATGCATTTTAGCTCTAG 57.647 37.037 23.86 6.29 40.16 2.43
600 1469 9.301897 TGTATCTAGATGCATTTTAGCTCTAGA 57.698 33.333 18.36 18.47 44.96 2.43
604 1473 9.301897 TCTAGATGCATTTTAGCTCTAGATACA 57.698 33.333 14.19 0.00 41.25 2.29
607 1476 8.040132 AGATGCATTTTAGCTCTAGATACATCC 58.960 37.037 0.00 0.00 34.99 3.51
608 1477 7.066307 TGCATTTTAGCTCTAGATACATCCA 57.934 36.000 0.00 0.00 34.99 3.41
609 1478 7.683578 TGCATTTTAGCTCTAGATACATCCAT 58.316 34.615 0.00 0.00 34.99 3.41
610 1479 8.159447 TGCATTTTAGCTCTAGATACATCCATT 58.841 33.333 0.00 0.00 34.99 3.16
611 1480 9.007901 GCATTTTAGCTCTAGATACATCCATTT 57.992 33.333 0.00 0.00 0.00 2.32
616 1485 9.770097 TTAGCTCTAGATACATCCATTTTCAAG 57.230 33.333 0.00 0.00 0.00 3.02
617 1486 8.027524 AGCTCTAGATACATCCATTTTCAAGA 57.972 34.615 0.00 0.00 0.00 3.02
618 1487 7.930865 AGCTCTAGATACATCCATTTTCAAGAC 59.069 37.037 0.00 0.00 0.00 3.01
619 1488 7.712639 GCTCTAGATACATCCATTTTCAAGACA 59.287 37.037 0.00 0.00 0.00 3.41
620 1489 9.605275 CTCTAGATACATCCATTTTCAAGACAA 57.395 33.333 0.00 0.00 0.00 3.18
621 1490 9.605275 TCTAGATACATCCATTTTCAAGACAAG 57.395 33.333 0.00 0.00 0.00 3.16
622 1491 9.388506 CTAGATACATCCATTTTCAAGACAAGT 57.611 33.333 0.00 0.00 0.00 3.16
624 1493 9.739276 AGATACATCCATTTTCAAGACAAGTAA 57.261 29.630 0.00 0.00 0.00 2.24
628 1497 9.082313 ACATCCATTTTCAAGACAAGTAATTCT 57.918 29.630 0.00 0.00 0.00 2.40
629 1498 9.350357 CATCCATTTTCAAGACAAGTAATTCTG 57.650 33.333 0.00 0.00 0.00 3.02
630 1499 8.690203 TCCATTTTCAAGACAAGTAATTCTGA 57.310 30.769 0.00 0.00 0.00 3.27
631 1500 9.130661 TCCATTTTCAAGACAAGTAATTCTGAA 57.869 29.630 0.00 0.00 0.00 3.02
632 1501 9.185192 CCATTTTCAAGACAAGTAATTCTGAAC 57.815 33.333 0.00 0.00 0.00 3.18
633 1502 8.895845 CATTTTCAAGACAAGTAATTCTGAACG 58.104 33.333 0.00 0.00 0.00 3.95
634 1503 6.539649 TTCAAGACAAGTAATTCTGAACGG 57.460 37.500 0.00 0.00 0.00 4.44
635 1504 5.849510 TCAAGACAAGTAATTCTGAACGGA 58.150 37.500 0.00 0.00 0.00 4.69
636 1505 5.926542 TCAAGACAAGTAATTCTGAACGGAG 59.073 40.000 0.00 0.00 0.00 4.63
637 1506 4.822026 AGACAAGTAATTCTGAACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
638 1507 3.933332 GACAAGTAATTCTGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
639 1508 3.581332 ACAAGTAATTCTGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
640 1509 4.184629 CAAGTAATTCTGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
641 1510 3.442076 AGTAATTCTGAACGGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
642 1511 4.607239 AGTAATTCTGAACGGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
643 1512 3.889520 AATTCTGAACGGAGGGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
644 1513 1.553706 TTCTGAACGGAGGGAGTACC 58.446 55.000 0.00 0.00 40.67 3.34
645 1514 0.406750 TCTGAACGGAGGGAGTACCA 59.593 55.000 0.00 0.00 43.89 3.25
646 1515 0.818296 CTGAACGGAGGGAGTACCAG 59.182 60.000 0.00 0.00 43.89 4.00
647 1516 0.406750 TGAACGGAGGGAGTACCAGA 59.593 55.000 0.00 0.00 43.89 3.86
648 1517 1.006758 TGAACGGAGGGAGTACCAGAT 59.993 52.381 0.00 0.00 43.89 2.90
649 1518 2.242965 TGAACGGAGGGAGTACCAGATA 59.757 50.000 0.00 0.00 43.89 1.98
650 1519 3.117246 TGAACGGAGGGAGTACCAGATAT 60.117 47.826 0.00 0.00 43.89 1.63
651 1520 3.157750 ACGGAGGGAGTACCAGATATC 57.842 52.381 0.00 0.00 43.89 1.63
652 1521 2.225066 ACGGAGGGAGTACCAGATATCC 60.225 54.545 0.00 0.00 43.89 2.59
653 1522 2.041891 CGGAGGGAGTACCAGATATCCT 59.958 54.545 0.00 0.00 43.89 3.24
654 1523 3.266254 CGGAGGGAGTACCAGATATCCTA 59.734 52.174 0.00 0.00 43.89 2.94
655 1524 4.263816 CGGAGGGAGTACCAGATATCCTAA 60.264 50.000 0.00 0.00 43.89 2.69
656 1525 5.018149 GGAGGGAGTACCAGATATCCTAAC 58.982 50.000 0.00 0.00 43.89 2.34
657 1526 5.013258 AGGGAGTACCAGATATCCTAACC 57.987 47.826 0.00 0.00 43.89 2.85
658 1527 4.675550 AGGGAGTACCAGATATCCTAACCT 59.324 45.833 0.00 0.00 43.89 3.50
659 1528 5.138123 AGGGAGTACCAGATATCCTAACCTT 59.862 44.000 0.00 0.00 43.89 3.50
662 1531 7.443477 GGAGTACCAGATATCCTAACCTTTTC 58.557 42.308 0.00 0.00 35.97 2.29
663 1532 7.376335 AGTACCAGATATCCTAACCTTTTCC 57.624 40.000 0.00 0.00 0.00 3.13
665 1534 6.502074 ACCAGATATCCTAACCTTTTCCTC 57.498 41.667 0.00 0.00 0.00 3.71
668 1537 7.184753 ACCAGATATCCTAACCTTTTCCTCTTT 59.815 37.037 0.00 0.00 0.00 2.52
691 1560 9.606631 CTTTTAAGAGAGCCACATATCTTAACT 57.393 33.333 5.90 0.00 41.51 2.24
692 1561 8.948631 TTTAAGAGAGCCACATATCTTAACTG 57.051 34.615 5.90 0.00 41.51 3.16
693 1562 5.543507 AGAGAGCCACATATCTTAACTGG 57.456 43.478 0.00 0.00 0.00 4.00
712 1581 7.865706 AACTGGAAAAGACGATATTGCTTAT 57.134 32.000 0.00 0.00 0.00 1.73
717 1586 6.018994 GGAAAAGACGATATTGCTTATGACGT 60.019 38.462 0.00 0.00 34.10 4.34
744 1613 1.642037 CTGTCAGTTCCTGGCATGCG 61.642 60.000 12.44 0.00 45.31 4.73
746 1615 0.391130 GTCAGTTCCTGGCATGCGTA 60.391 55.000 12.44 2.02 35.96 4.42
747 1616 0.323302 TCAGTTCCTGGCATGCGTAA 59.677 50.000 12.44 0.00 31.51 3.18
748 1617 1.065491 TCAGTTCCTGGCATGCGTAAT 60.065 47.619 12.44 0.00 31.51 1.89
749 1618 1.331756 CAGTTCCTGGCATGCGTAATC 59.668 52.381 12.44 0.00 0.00 1.75
750 1619 0.663153 GTTCCTGGCATGCGTAATCC 59.337 55.000 12.44 0.00 0.00 3.01
760 1629 3.254166 GCATGCGTAATCCAATCCTTGAT 59.746 43.478 0.00 0.00 0.00 2.57
871 1740 7.360269 GCCTTGTCATTTCAATACACCATTTTG 60.360 37.037 0.00 0.00 0.00 2.44
920 1797 1.336795 GGCAGTGCCGTTGCTAATTTT 60.337 47.619 20.55 0.00 39.62 1.82
937 1814 6.524586 GCTAATTTTTCATTTCCTGACTGACG 59.475 38.462 0.00 0.00 32.17 4.35
1096 1980 1.830587 TTGAGGACACGAGGCATGCT 61.831 55.000 18.92 3.20 0.00 3.79
1143 2027 1.443872 CACTCGTGCGTACTGTCCC 60.444 63.158 1.24 0.00 0.00 4.46
1144 2028 1.900016 ACTCGTGCGTACTGTCCCA 60.900 57.895 1.24 0.00 0.00 4.37
1145 2029 1.287815 CTCGTGCGTACTGTCCCAA 59.712 57.895 1.24 0.00 0.00 4.12
1146 2030 0.732880 CTCGTGCGTACTGTCCCAAG 60.733 60.000 1.24 0.00 0.00 3.61
1148 2032 0.108804 CGTGCGTACTGTCCCAAGAT 60.109 55.000 1.24 0.00 0.00 2.40
1149 2033 1.133598 CGTGCGTACTGTCCCAAGATA 59.866 52.381 1.24 0.00 0.00 1.98
1151 2035 3.592059 GTGCGTACTGTCCCAAGATAAA 58.408 45.455 0.00 0.00 0.00 1.40
1152 2036 3.370061 GTGCGTACTGTCCCAAGATAAAC 59.630 47.826 0.00 0.00 0.00 2.01
1332 2220 1.630148 GTACTCGTCCTGACATGCAC 58.370 55.000 0.00 0.00 0.00 4.57
1333 2221 0.530744 TACTCGTCCTGACATGCACC 59.469 55.000 0.00 0.00 0.00 5.01
1364 2252 3.935872 GTGCGCAACGTGACAGCA 61.936 61.111 14.00 0.00 35.27 4.41
1365 2253 3.198489 TGCGCAACGTGACAGCAA 61.198 55.556 8.16 0.00 34.66 3.91
1366 2254 2.252260 GCGCAACGTGACAGCAAT 59.748 55.556 0.30 0.00 0.00 3.56
1401 2289 2.742760 TCGTCGACGAGCTGAGCT 60.743 61.111 34.97 6.69 44.22 4.09
1514 2402 1.677633 GGGGGAACAATGGTGGTCG 60.678 63.158 0.00 0.00 42.96 4.79
1579 2467 1.248785 TGCTGAGGTCCCGTACTCAC 61.249 60.000 0.00 0.00 38.71 3.51
1580 2468 1.248785 GCTGAGGTCCCGTACTCACA 61.249 60.000 0.00 0.00 38.71 3.58
1583 2471 0.957395 GAGGTCCCGTACTCACACGA 60.957 60.000 0.00 0.00 44.69 4.35
1746 2634 3.061006 CGCTTCACTTCAACATTTGCAAC 60.061 43.478 0.00 0.00 0.00 4.17
1763 2651 2.813754 GCAACTGCTTCACCTCAACATA 59.186 45.455 0.00 0.00 38.21 2.29
1924 2812 1.845205 AAGTGGGACCTGCAGCTCT 60.845 57.895 8.66 0.00 0.00 4.09
1932 2820 0.037232 ACCTGCAGCTCTTAACCGTC 60.037 55.000 8.66 0.00 0.00 4.79
1938 2826 2.223525 GCAGCTCTTAACCGTCGTCTAT 60.224 50.000 0.00 0.00 0.00 1.98
1941 2829 3.693085 AGCTCTTAACCGTCGTCTATTCA 59.307 43.478 0.00 0.00 0.00 2.57
2078 2974 1.125093 TTGGTCCTCATGTCGTGGGT 61.125 55.000 0.00 0.00 0.00 4.51
2139 3035 1.663379 CCCTCACGATGGTAGCGACA 61.663 60.000 0.00 0.00 0.00 4.35
2205 3101 1.099689 GGTGAGCTAGCTTCTCGACT 58.900 55.000 20.42 0.00 33.41 4.18
2258 3155 8.255111 AGTCCAGATATGTATGTCAATCTCAA 57.745 34.615 0.00 0.00 0.00 3.02
2377 3287 3.850923 CGCTAACGAAGAACGCCA 58.149 55.556 0.00 0.00 46.94 5.69
2389 3299 2.417719 AGAACGCCAGTGAGAATGAAC 58.582 47.619 0.00 0.00 0.00 3.18
2456 3366 1.206745 CGTCGCGGCGATGAAATAGT 61.207 55.000 34.31 0.00 44.49 2.12
2522 3440 7.361127 CGGTCACTTACATTAGAACTATCGAT 58.639 38.462 2.16 2.16 0.00 3.59
2593 3511 9.715121 ATTTGTTCAATGAGCATTTAATTCAGT 57.285 25.926 0.00 0.00 0.00 3.41
2594 3512 8.523523 TTGTTCAATGAGCATTTAATTCAGTG 57.476 30.769 0.00 1.95 38.03 3.66
2602 3520 6.985645 TGAGCATTTAATTCAGTGTTGCTTTT 59.014 30.769 0.00 0.00 38.93 2.27
2655 3574 7.927092 GTCCCCTCTTTTAGCTAGTTAACTATG 59.073 40.741 15.57 10.79 0.00 2.23
2668 3587 2.185004 AACTATGGAGCGTTGCAACT 57.815 45.000 26.09 9.60 0.00 3.16
2669 3588 2.185004 ACTATGGAGCGTTGCAACTT 57.815 45.000 26.09 14.82 0.00 2.66
2670 3589 1.806542 ACTATGGAGCGTTGCAACTTG 59.193 47.619 26.09 13.47 0.00 3.16
2671 3590 0.521291 TATGGAGCGTTGCAACTTGC 59.479 50.000 26.09 21.98 45.29 4.01
2720 3639 6.981762 AGAGTTCATTCAGCTTGTATGAAG 57.018 37.500 12.71 0.00 42.20 3.02
2805 3819 2.363788 TCAAGCTCGCGAAGTATGTT 57.636 45.000 11.33 0.00 0.00 2.71
2806 3820 3.497297 TCAAGCTCGCGAAGTATGTTA 57.503 42.857 11.33 0.00 0.00 2.41
2807 3821 3.176708 TCAAGCTCGCGAAGTATGTTAC 58.823 45.455 11.33 0.00 0.00 2.50
2808 3822 1.823828 AGCTCGCGAAGTATGTTACG 58.176 50.000 11.33 0.00 0.00 3.18
2906 3920 0.614812 TCTTATCACCAGCTGCAGCA 59.385 50.000 38.24 19.65 45.16 4.41
2914 3928 1.673337 CAGCTGCAGCACAAGCCTA 60.673 57.895 38.24 0.00 45.16 3.93
2915 3929 1.673665 AGCTGCAGCACAAGCCTAC 60.674 57.895 38.24 7.01 45.16 3.18
2918 3932 1.357258 CTGCAGCACAAGCCTACTCG 61.357 60.000 0.00 0.00 43.56 4.18
2923 3937 2.860735 CAGCACAAGCCTACTCGATAAC 59.139 50.000 0.00 0.00 43.56 1.89
2926 3940 3.307242 GCACAAGCCTACTCGATAACTTG 59.693 47.826 10.44 10.44 40.19 3.16
2976 3990 0.107897 TTCATACTGCCGGCATCGTT 60.108 50.000 32.87 17.03 33.95 3.85
2979 3993 1.151777 ATACTGCCGGCATCGTTTCG 61.152 55.000 32.87 19.14 33.95 3.46
2994 4008 3.749088 TCGTTTCGTATTCTGTGGCAATT 59.251 39.130 0.00 0.00 0.00 2.32
3017 4031 0.756294 TCAGCTTGAAGACGGACCAA 59.244 50.000 0.00 0.00 0.00 3.67
3032 4046 1.269206 GACCAACAGTGCACAATGGTG 60.269 52.381 32.66 24.99 44.12 4.17
3089 4103 1.906574 AGGGAAAGTATCTCGCCAACA 59.093 47.619 0.00 0.00 31.91 3.33
3106 4120 0.393402 ACATGCATCAGCCACGACAT 60.393 50.000 0.00 0.00 41.13 3.06
3164 4179 7.724061 TCCCCTTTTATTATCATAAGTGAAGGC 59.276 37.037 8.81 0.00 38.01 4.35
3181 4196 0.526211 GGCAACTCCTTTTAAGCCCG 59.474 55.000 0.00 0.00 36.17 6.13
3203 4218 5.090757 CGGATCAACAAGTTCACAATCATG 58.909 41.667 0.00 0.00 0.00 3.07
3235 4250 1.657751 GAAGGCCGCCATTTGTCCTC 61.658 60.000 13.15 0.00 0.00 3.71
3236 4251 2.044946 GGCCGCCATTTGTCCTCT 60.045 61.111 3.91 0.00 0.00 3.69
3268 4283 5.009610 GTGGTGAAGGAAAAGTGCTCAAATA 59.990 40.000 0.00 0.00 0.00 1.40
3282 4297 3.133691 CTCAAATAGCCATAGCGCTTCA 58.866 45.455 18.68 0.00 46.67 3.02
3303 4319 0.537653 TGAAATCGCCCATGACGGTA 59.462 50.000 8.02 0.00 0.00 4.02
3304 4320 1.066071 TGAAATCGCCCATGACGGTAA 60.066 47.619 8.02 0.00 0.00 2.85
3325 4341 4.996788 AATGGCAAATCTGACTTGGATC 57.003 40.909 0.72 0.00 0.00 3.36
3331 4347 4.142513 GCAAATCTGACTTGGATCTCAACC 60.143 45.833 0.72 0.00 0.00 3.77
3338 4354 0.250234 TTGGATCTCAACCGCCTCAG 59.750 55.000 0.00 0.00 0.00 3.35
3391 4407 3.500448 TTGGCTCTCCATACACACAAA 57.500 42.857 0.00 0.00 43.05 2.83
3415 4431 2.599645 ATCTCCATGTCACAGCGGCC 62.600 60.000 0.00 0.00 0.00 6.13
3454 4470 2.751806 TGCATCAATGTGCCGTTCATTA 59.248 40.909 5.61 0.00 44.43 1.90
3460 4476 4.940654 TCAATGTGCCGTTCATTAAGATCA 59.059 37.500 0.00 0.00 34.34 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.567138 ACAACAACAAACCTCTCAAAGAG 57.433 39.130 0.00 0.00 41.96 2.85
24 25 3.694072 CAGGAACAACAACAAACCTCTCA 59.306 43.478 0.00 0.00 0.00 3.27
37 38 3.286751 TGCGCAGGCAGGAACAAC 61.287 61.111 5.66 0.00 46.21 3.32
57 62 2.434359 CAAAGAGGGGGCGTCGAC 60.434 66.667 5.18 5.18 0.00 4.20
75 84 6.331369 AGCAGAATTAGCTAGCTAGAGAAG 57.669 41.667 25.15 15.45 41.32 2.85
87 96 7.611213 TTTGTTACCTCTAAGCAGAATTAGC 57.389 36.000 0.00 0.00 33.57 3.09
88 97 8.616076 CCATTTGTTACCTCTAAGCAGAATTAG 58.384 37.037 0.00 0.00 34.63 1.73
90 99 6.948309 ACCATTTGTTACCTCTAAGCAGAATT 59.052 34.615 0.00 0.00 0.00 2.17
91 100 6.485171 ACCATTTGTTACCTCTAAGCAGAAT 58.515 36.000 0.00 0.00 0.00 2.40
92 101 5.876357 ACCATTTGTTACCTCTAAGCAGAA 58.124 37.500 0.00 0.00 0.00 3.02
93 102 5.499004 ACCATTTGTTACCTCTAAGCAGA 57.501 39.130 0.00 0.00 0.00 4.26
94 103 5.940470 AGAACCATTTGTTACCTCTAAGCAG 59.060 40.000 0.00 0.00 37.29 4.24
95 104 5.705441 CAGAACCATTTGTTACCTCTAAGCA 59.295 40.000 0.00 0.00 37.29 3.91
96 105 5.705905 ACAGAACCATTTGTTACCTCTAAGC 59.294 40.000 0.00 0.00 37.29 3.09
155 164 6.480320 CGACCGAAGAAGAAAATAATGGAGAT 59.520 38.462 0.00 0.00 0.00 2.75
244 255 6.089685 TGTTCGTCGATTAATTTCACGATTGA 59.910 34.615 14.50 7.67 39.12 2.57
261 272 9.831054 GAAACTTATGTCTTATAATGTTCGTCG 57.169 33.333 0.00 0.00 0.00 5.12
329 406 3.384168 AGTGTAGGGGATCATGCAACTA 58.616 45.455 0.00 0.00 0.00 2.24
330 407 2.200081 AGTGTAGGGGATCATGCAACT 58.800 47.619 0.00 0.00 0.00 3.16
331 408 2.717639 AGTGTAGGGGATCATGCAAC 57.282 50.000 0.00 0.00 0.00 4.17
332 409 4.660303 AGATAAGTGTAGGGGATCATGCAA 59.340 41.667 0.00 0.00 0.00 4.08
342 419 7.361457 TGTTGAAGGATAGATAAGTGTAGGG 57.639 40.000 0.00 0.00 0.00 3.53
376 486 1.135402 CGGCCACAAAGCTAATTGTCC 60.135 52.381 2.24 0.75 41.44 4.02
398 508 2.628178 TCAGGACATAGGCTACAATCCG 59.372 50.000 12.48 9.11 0.00 4.18
450 561 8.624776 AGTAGTAGTAACGCGGAGTAATTAAAT 58.375 33.333 12.47 0.00 0.00 1.40
451 562 7.985476 AGTAGTAGTAACGCGGAGTAATTAAA 58.015 34.615 12.47 0.00 0.00 1.52
452 563 7.553881 AGTAGTAGTAACGCGGAGTAATTAA 57.446 36.000 12.47 0.00 0.00 1.40
453 564 7.279981 TGAAGTAGTAGTAACGCGGAGTAATTA 59.720 37.037 12.47 0.00 0.00 1.40
463 574 6.860023 TGAAAGAACTGAAGTAGTAGTAACGC 59.140 38.462 0.00 0.00 39.18 4.84
487 598 6.250089 GTTTTTGCAATCCAAAGTCAACTTG 58.750 36.000 0.00 0.00 43.77 3.16
537 1406 5.221661 ACAAGTAATTCTGAACGGAGGAAGT 60.222 40.000 0.00 0.00 0.00 3.01
538 1407 5.238583 ACAAGTAATTCTGAACGGAGGAAG 58.761 41.667 0.00 0.00 0.00 3.46
539 1408 5.223449 ACAAGTAATTCTGAACGGAGGAA 57.777 39.130 0.00 0.00 0.00 3.36
542 1411 5.924475 ACAACAAGTAATTCTGAACGGAG 57.076 39.130 0.00 0.00 0.00 4.63
544 1413 7.416154 TTCTACAACAAGTAATTCTGAACGG 57.584 36.000 0.00 0.00 30.92 4.44
545 1414 9.318041 CATTTCTACAACAAGTAATTCTGAACG 57.682 33.333 0.00 0.00 30.92 3.95
546 1415 9.612620 CCATTTCTACAACAAGTAATTCTGAAC 57.387 33.333 0.00 0.00 30.92 3.18
547 1416 8.792633 CCCATTTCTACAACAAGTAATTCTGAA 58.207 33.333 0.00 0.00 30.92 3.02
548 1417 7.942341 ACCCATTTCTACAACAAGTAATTCTGA 59.058 33.333 0.00 0.00 30.92 3.27
549 1418 8.023128 CACCCATTTCTACAACAAGTAATTCTG 58.977 37.037 0.00 0.00 30.92 3.02
550 1419 7.724061 ACACCCATTTCTACAACAAGTAATTCT 59.276 33.333 0.00 0.00 30.92 2.40
551 1420 7.882179 ACACCCATTTCTACAACAAGTAATTC 58.118 34.615 0.00 0.00 30.92 2.17
552 1421 7.833285 ACACCCATTTCTACAACAAGTAATT 57.167 32.000 0.00 0.00 30.92 1.40
553 1422 9.174166 GATACACCCATTTCTACAACAAGTAAT 57.826 33.333 0.00 0.00 30.92 1.89
554 1423 8.380099 AGATACACCCATTTCTACAACAAGTAA 58.620 33.333 0.00 0.00 30.92 2.24
555 1424 7.913789 AGATACACCCATTTCTACAACAAGTA 58.086 34.615 0.00 0.00 0.00 2.24
556 1425 6.779860 AGATACACCCATTTCTACAACAAGT 58.220 36.000 0.00 0.00 0.00 3.16
557 1426 8.258007 TCTAGATACACCCATTTCTACAACAAG 58.742 37.037 0.00 0.00 0.00 3.16
558 1427 8.141298 TCTAGATACACCCATTTCTACAACAA 57.859 34.615 0.00 0.00 0.00 2.83
559 1428 7.727578 TCTAGATACACCCATTTCTACAACA 57.272 36.000 0.00 0.00 0.00 3.33
560 1429 7.171678 GCATCTAGATACACCCATTTCTACAAC 59.828 40.741 4.54 0.00 0.00 3.32
561 1430 7.147567 TGCATCTAGATACACCCATTTCTACAA 60.148 37.037 4.54 0.00 0.00 2.41
562 1431 6.326323 TGCATCTAGATACACCCATTTCTACA 59.674 38.462 4.54 0.00 0.00 2.74
563 1432 6.759272 TGCATCTAGATACACCCATTTCTAC 58.241 40.000 4.54 0.00 0.00 2.59
564 1433 6.994421 TGCATCTAGATACACCCATTTCTA 57.006 37.500 4.54 0.00 0.00 2.10
565 1434 5.894298 TGCATCTAGATACACCCATTTCT 57.106 39.130 4.54 0.00 0.00 2.52
566 1435 7.516198 AAATGCATCTAGATACACCCATTTC 57.484 36.000 7.83 0.00 28.73 2.17
567 1436 7.902920 AAAATGCATCTAGATACACCCATTT 57.097 32.000 7.83 12.41 34.29 2.32
568 1437 7.175641 GCTAAAATGCATCTAGATACACCCATT 59.824 37.037 7.83 7.95 0.00 3.16
569 1438 6.656693 GCTAAAATGCATCTAGATACACCCAT 59.343 38.462 7.83 2.77 0.00 4.00
570 1439 5.997746 GCTAAAATGCATCTAGATACACCCA 59.002 40.000 7.83 0.62 0.00 4.51
571 1440 6.234177 AGCTAAAATGCATCTAGATACACCC 58.766 40.000 7.83 0.00 34.99 4.61
572 1441 7.158021 AGAGCTAAAATGCATCTAGATACACC 58.842 38.462 7.83 0.00 34.99 4.16
573 1442 9.352784 CTAGAGCTAAAATGCATCTAGATACAC 57.647 37.037 7.83 0.63 39.84 2.90
574 1443 9.301897 TCTAGAGCTAAAATGCATCTAGATACA 57.698 33.333 14.19 8.11 40.48 2.29
578 1447 9.301897 TGTATCTAGAGCTAAAATGCATCTAGA 57.698 33.333 18.47 18.47 44.10 2.43
581 1450 8.040132 GGATGTATCTAGAGCTAAAATGCATCT 58.960 37.037 19.00 0.00 38.62 2.90
582 1451 7.821359 TGGATGTATCTAGAGCTAAAATGCATC 59.179 37.037 0.00 14.85 38.17 3.91
583 1452 7.683578 TGGATGTATCTAGAGCTAAAATGCAT 58.316 34.615 0.00 0.00 34.99 3.96
584 1453 7.066307 TGGATGTATCTAGAGCTAAAATGCA 57.934 36.000 0.00 0.00 34.99 3.96
585 1454 8.558973 AATGGATGTATCTAGAGCTAAAATGC 57.441 34.615 0.00 0.00 0.00 3.56
590 1459 9.770097 CTTGAAAATGGATGTATCTAGAGCTAA 57.230 33.333 0.00 0.00 0.00 3.09
591 1460 9.147732 TCTTGAAAATGGATGTATCTAGAGCTA 57.852 33.333 0.00 0.00 0.00 3.32
592 1461 7.930865 GTCTTGAAAATGGATGTATCTAGAGCT 59.069 37.037 0.00 0.00 0.00 4.09
593 1462 7.712639 TGTCTTGAAAATGGATGTATCTAGAGC 59.287 37.037 0.00 0.00 0.00 4.09
594 1463 9.605275 TTGTCTTGAAAATGGATGTATCTAGAG 57.395 33.333 0.00 0.00 0.00 2.43
595 1464 9.605275 CTTGTCTTGAAAATGGATGTATCTAGA 57.395 33.333 0.00 0.00 0.00 2.43
596 1465 9.388506 ACTTGTCTTGAAAATGGATGTATCTAG 57.611 33.333 0.00 0.00 0.00 2.43
598 1467 9.739276 TTACTTGTCTTGAAAATGGATGTATCT 57.261 29.630 0.00 0.00 0.00 1.98
602 1471 9.082313 AGAATTACTTGTCTTGAAAATGGATGT 57.918 29.630 0.00 0.00 0.00 3.06
603 1472 9.350357 CAGAATTACTTGTCTTGAAAATGGATG 57.650 33.333 0.00 0.00 0.00 3.51
604 1473 9.300681 TCAGAATTACTTGTCTTGAAAATGGAT 57.699 29.630 0.00 0.00 0.00 3.41
605 1474 8.690203 TCAGAATTACTTGTCTTGAAAATGGA 57.310 30.769 0.00 0.00 0.00 3.41
606 1475 9.185192 GTTCAGAATTACTTGTCTTGAAAATGG 57.815 33.333 0.00 0.00 0.00 3.16
607 1476 8.895845 CGTTCAGAATTACTTGTCTTGAAAATG 58.104 33.333 0.00 0.00 0.00 2.32
608 1477 8.076178 CCGTTCAGAATTACTTGTCTTGAAAAT 58.924 33.333 0.00 0.00 0.00 1.82
609 1478 7.281324 TCCGTTCAGAATTACTTGTCTTGAAAA 59.719 33.333 0.00 0.00 0.00 2.29
610 1479 6.764085 TCCGTTCAGAATTACTTGTCTTGAAA 59.236 34.615 0.00 0.00 0.00 2.69
611 1480 6.285224 TCCGTTCAGAATTACTTGTCTTGAA 58.715 36.000 0.00 0.00 0.00 2.69
612 1481 5.849510 TCCGTTCAGAATTACTTGTCTTGA 58.150 37.500 0.00 0.00 0.00 3.02
613 1482 5.120830 CCTCCGTTCAGAATTACTTGTCTTG 59.879 44.000 0.00 0.00 0.00 3.02
614 1483 5.238583 CCTCCGTTCAGAATTACTTGTCTT 58.761 41.667 0.00 0.00 0.00 3.01
615 1484 4.322801 CCCTCCGTTCAGAATTACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
616 1485 3.933332 CCCTCCGTTCAGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
617 1486 3.581332 TCCCTCCGTTCAGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
618 1487 4.184629 CTCCCTCCGTTCAGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
619 1488 3.838903 ACTCCCTCCGTTCAGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
620 1489 3.442076 ACTCCCTCCGTTCAGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
621 1490 3.889520 ACTCCCTCCGTTCAGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
622 1491 3.703052 GGTACTCCCTCCGTTCAGAATTA 59.297 47.826 0.00 0.00 0.00 1.40
623 1492 2.500504 GGTACTCCCTCCGTTCAGAATT 59.499 50.000 0.00 0.00 0.00 2.17
624 1493 2.108970 GGTACTCCCTCCGTTCAGAAT 58.891 52.381 0.00 0.00 0.00 2.40
625 1494 1.203087 TGGTACTCCCTCCGTTCAGAA 60.203 52.381 0.00 0.00 0.00 3.02
626 1495 0.406750 TGGTACTCCCTCCGTTCAGA 59.593 55.000 0.00 0.00 0.00 3.27
627 1496 0.818296 CTGGTACTCCCTCCGTTCAG 59.182 60.000 0.00 0.00 0.00 3.02
628 1497 0.406750 TCTGGTACTCCCTCCGTTCA 59.593 55.000 0.00 0.00 0.00 3.18
629 1498 1.777941 ATCTGGTACTCCCTCCGTTC 58.222 55.000 0.00 0.00 0.00 3.95
630 1499 3.498334 GATATCTGGTACTCCCTCCGTT 58.502 50.000 0.00 0.00 0.00 4.44
631 1500 2.225066 GGATATCTGGTACTCCCTCCGT 60.225 54.545 2.05 0.00 0.00 4.69
632 1501 2.041891 AGGATATCTGGTACTCCCTCCG 59.958 54.545 2.05 0.00 0.00 4.63
633 1502 3.837399 AGGATATCTGGTACTCCCTCC 57.163 52.381 2.05 0.00 0.00 4.30
634 1503 5.018149 GGTTAGGATATCTGGTACTCCCTC 58.982 50.000 2.05 0.00 0.00 4.30
635 1504 4.675550 AGGTTAGGATATCTGGTACTCCCT 59.324 45.833 2.05 0.00 0.00 4.20
636 1505 5.013258 AGGTTAGGATATCTGGTACTCCC 57.987 47.826 2.05 0.00 0.00 4.30
637 1506 6.997942 AAAGGTTAGGATATCTGGTACTCC 57.002 41.667 2.05 0.00 0.00 3.85
638 1507 7.290481 AGGAAAAGGTTAGGATATCTGGTACTC 59.710 40.741 2.05 0.00 0.00 2.59
639 1508 7.140304 AGGAAAAGGTTAGGATATCTGGTACT 58.860 38.462 2.05 0.00 0.00 2.73
640 1509 7.290481 AGAGGAAAAGGTTAGGATATCTGGTAC 59.710 40.741 2.05 0.00 0.00 3.34
641 1510 7.371043 AGAGGAAAAGGTTAGGATATCTGGTA 58.629 38.462 2.05 0.00 0.00 3.25
642 1511 6.213525 AGAGGAAAAGGTTAGGATATCTGGT 58.786 40.000 2.05 0.00 0.00 4.00
643 1512 6.755542 AGAGGAAAAGGTTAGGATATCTGG 57.244 41.667 2.05 0.00 0.00 3.86
665 1534 9.606631 AGTTAAGATATGTGGCTCTCTTAAAAG 57.393 33.333 9.61 0.00 40.17 2.27
668 1537 7.344612 TCCAGTTAAGATATGTGGCTCTCTTAA 59.655 37.037 5.78 5.78 37.68 1.85
691 1560 6.019075 CGTCATAAGCAATATCGTCTTTTCCA 60.019 38.462 0.00 0.00 0.00 3.53
692 1561 6.018994 ACGTCATAAGCAATATCGTCTTTTCC 60.019 38.462 0.00 0.00 0.00 3.13
693 1562 6.934210 ACGTCATAAGCAATATCGTCTTTTC 58.066 36.000 0.00 0.00 0.00 2.29
712 1581 4.304110 GAACTGACAGATAACCAACGTCA 58.696 43.478 10.08 0.00 35.44 4.35
744 1613 9.487790 TTTGTTTTCAATCAAGGATTGGATTAC 57.512 29.630 16.43 10.78 46.43 1.89
746 1615 8.431222 TCTTTGTTTTCAATCAAGGATTGGATT 58.569 29.630 16.43 0.00 46.43 3.01
747 1616 7.965718 TCTTTGTTTTCAATCAAGGATTGGAT 58.034 30.769 16.43 0.00 46.43 3.41
748 1617 7.358770 TCTTTGTTTTCAATCAAGGATTGGA 57.641 32.000 16.43 7.38 46.43 3.53
749 1618 9.709495 TTATCTTTGTTTTCAATCAAGGATTGG 57.291 29.630 16.43 1.59 46.43 3.16
780 1649 4.149221 CGCATTCGACTGTGTTTTGTACTA 59.851 41.667 8.07 0.00 38.10 1.82
782 1651 3.215244 CGCATTCGACTGTGTTTTGTAC 58.785 45.455 8.07 0.00 38.10 2.90
783 1652 2.222213 CCGCATTCGACTGTGTTTTGTA 59.778 45.455 14.27 0.00 38.10 2.41
784 1653 1.002900 CCGCATTCGACTGTGTTTTGT 60.003 47.619 14.27 0.00 38.10 2.83
785 1654 1.002900 ACCGCATTCGACTGTGTTTTG 60.003 47.619 14.27 2.84 38.10 2.44
788 1657 2.066262 CTTACCGCATTCGACTGTGTT 58.934 47.619 14.27 3.76 38.10 3.32
798 1667 3.134804 AGACCATCTTAGCTTACCGCATT 59.865 43.478 0.00 0.00 42.61 3.56
810 1679 4.901197 TGGTGCAAACTAGACCATCTTA 57.099 40.909 0.00 0.00 34.75 2.10
839 1708 2.157834 TGAAATGACAAGGCGTACGT 57.842 45.000 17.90 0.00 0.00 3.57
840 1709 3.740044 ATTGAAATGACAAGGCGTACG 57.260 42.857 11.84 11.84 33.22 3.67
841 1710 5.321516 GTGTATTGAAATGACAAGGCGTAC 58.678 41.667 0.00 0.00 33.22 3.67
842 1711 4.393680 GGTGTATTGAAATGACAAGGCGTA 59.606 41.667 0.00 0.00 33.22 4.42
871 1740 0.531974 TCACTGGGAACGTTGAGTGC 60.532 55.000 19.72 1.94 36.55 4.40
937 1814 2.961526 TTCCTGCGAGATAAGGTGAC 57.038 50.000 0.00 0.00 34.94 3.67
1059 1936 1.948508 ACGCGTCTGTACCGTGTTA 59.051 52.632 5.58 0.00 45.80 2.41
1060 1937 2.723746 ACGCGTCTGTACCGTGTT 59.276 55.556 5.58 0.00 45.80 3.32
1062 1939 1.334992 CTCAACGCGTCTGTACCGTG 61.335 60.000 14.44 4.26 41.34 4.94
1064 1941 1.800315 CCTCAACGCGTCTGTACCG 60.800 63.158 14.44 0.00 0.00 4.02
1066 1943 0.039798 TGTCCTCAACGCGTCTGTAC 60.040 55.000 14.44 8.48 0.00 2.90
1067 1944 0.039798 GTGTCCTCAACGCGTCTGTA 60.040 55.000 14.44 0.00 0.00 2.74
1068 1945 1.299926 GTGTCCTCAACGCGTCTGT 60.300 57.895 14.44 0.00 0.00 3.41
1074 1958 3.112709 GCCTCGTGTCCTCAACGC 61.113 66.667 0.00 0.00 34.92 4.84
1096 1980 3.749226 TGAGTGTACAATGTTGCCATCA 58.251 40.909 0.00 0.00 0.00 3.07
1103 1987 4.340666 TGGCATGTTTGAGTGTACAATGTT 59.659 37.500 0.00 0.00 0.00 2.71
1106 1990 4.144297 AGTGGCATGTTTGAGTGTACAAT 58.856 39.130 0.00 0.00 0.00 2.71
1144 2028 9.892130 CAAGGTAATAGAGTCCAAGTTTATCTT 57.108 33.333 0.00 0.00 36.75 2.40
1145 2029 9.268282 TCAAGGTAATAGAGTCCAAGTTTATCT 57.732 33.333 0.00 0.00 0.00 1.98
1146 2030 9.315525 GTCAAGGTAATAGAGTCCAAGTTTATC 57.684 37.037 0.00 0.00 0.00 1.75
1148 2032 7.236019 TGGTCAAGGTAATAGAGTCCAAGTTTA 59.764 37.037 0.00 0.00 0.00 2.01
1149 2033 6.043938 TGGTCAAGGTAATAGAGTCCAAGTTT 59.956 38.462 0.00 0.00 0.00 2.66
1151 2035 5.091552 TGGTCAAGGTAATAGAGTCCAAGT 58.908 41.667 0.00 0.00 0.00 3.16
1152 2036 5.677319 TGGTCAAGGTAATAGAGTCCAAG 57.323 43.478 0.00 0.00 0.00 3.61
1165 2053 4.892934 TGTTAGCAGAAAAATGGTCAAGGT 59.107 37.500 0.00 0.00 32.19 3.50
1332 2220 1.673760 CGCACGTGAAGATTTGTTGG 58.326 50.000 22.23 0.00 0.00 3.77
1333 2221 1.044725 GCGCACGTGAAGATTTGTTG 58.955 50.000 22.23 0.00 0.00 3.33
1404 2292 4.787280 ACCAGAGAGGAGGCCGGG 62.787 72.222 2.18 0.00 41.22 5.73
1405 2293 2.685380 AACCAGAGAGGAGGCCGG 60.685 66.667 0.00 0.00 41.22 6.13
1406 2294 1.671901 GAGAACCAGAGAGGAGGCCG 61.672 65.000 0.00 0.00 41.22 6.13
1407 2295 1.334384 GGAGAACCAGAGAGGAGGCC 61.334 65.000 0.00 0.00 41.22 5.19
1408 2296 0.616111 TGGAGAACCAGAGAGGAGGC 60.616 60.000 0.00 0.00 41.77 4.70
1409 2297 3.699798 TGGAGAACCAGAGAGGAGG 57.300 57.895 0.00 0.00 41.77 4.30
1450 2338 3.675228 GCTTCATCTTTCCATGCCACTTG 60.675 47.826 0.00 0.00 0.00 3.16
1724 2612 2.730069 TGCAAATGTTGAAGTGAAGCG 58.270 42.857 0.00 0.00 0.00 4.68
1746 2634 4.082625 TGCAAATATGTTGAGGTGAAGCAG 60.083 41.667 0.00 0.00 0.00 4.24
1788 2676 4.270317 AGATGGGAATACCTTGGCAATT 57.730 40.909 0.00 0.00 41.11 2.32
1789 2677 3.979501 AGATGGGAATACCTTGGCAAT 57.020 42.857 0.00 0.00 41.11 3.56
1841 2729 1.228956 AATGCTTGCAGGCTTCCCA 60.229 52.632 22.31 0.74 0.00 4.37
1924 2812 6.149308 TGTCTTACTGAATAGACGACGGTTAA 59.851 38.462 0.00 0.00 42.88 2.01
1932 2820 5.352284 AGCCAATGTCTTACTGAATAGACG 58.648 41.667 0.00 0.00 42.88 4.18
1938 2826 4.640771 AGGAAGCCAATGTCTTACTGAA 57.359 40.909 0.00 0.00 33.65 3.02
1941 2829 3.944087 GACAGGAAGCCAATGTCTTACT 58.056 45.455 0.00 0.00 40.14 2.24
2139 3035 2.165234 CAGTGTCGAGTCCATGATCACT 59.835 50.000 0.00 0.00 35.49 3.41
2232 3128 8.940397 TGAGATTGACATACATATCTGGACTA 57.060 34.615 0.00 0.00 31.65 2.59
2258 3155 5.202765 TGCTGTTGATGGTATCATGGAAAT 58.797 37.500 0.00 0.00 39.39 2.17
2270 3167 3.748048 CGTCCCTATTATGCTGTTGATGG 59.252 47.826 0.00 0.00 0.00 3.51
2377 3287 2.304180 CTCCAGGGTGTTCATTCTCACT 59.696 50.000 0.00 0.00 35.26 3.41
2589 3507 2.844946 TCCATCGAAAAGCAACACTGA 58.155 42.857 0.00 0.00 0.00 3.41
2715 3634 0.915364 GGAGGTGAGGAAGCCTTCAT 59.085 55.000 6.80 0.00 34.81 2.57
2720 3639 1.208293 CAGTAAGGAGGTGAGGAAGCC 59.792 57.143 0.00 0.00 0.00 4.35
2764 3778 1.137513 CGGTCCGTTCTGAACTGAAC 58.862 55.000 16.98 16.98 41.91 3.18
2805 3819 2.396601 CAGTCGCAAGTTTGGTACGTA 58.603 47.619 0.00 0.00 39.48 3.57
2806 3820 1.214367 CAGTCGCAAGTTTGGTACGT 58.786 50.000 0.00 0.00 39.48 3.57
2807 3821 0.110823 GCAGTCGCAAGTTTGGTACG 60.111 55.000 0.00 0.00 38.36 3.67
2808 3822 3.748021 GCAGTCGCAAGTTTGGTAC 57.252 52.632 0.00 0.00 38.36 3.34
2827 3841 1.680735 TGAAATCGTTGCAAGCTTGGT 59.319 42.857 27.10 0.00 0.00 3.67
2906 3920 4.495422 CACAAGTTATCGAGTAGGCTTGT 58.505 43.478 13.88 13.88 44.70 3.16
2914 3928 4.323417 TGATTTGCCACAAGTTATCGAGT 58.677 39.130 0.00 0.00 0.00 4.18
2915 3929 4.631377 TCTGATTTGCCACAAGTTATCGAG 59.369 41.667 0.00 0.00 0.00 4.04
2918 3932 4.651994 CGTCTGATTTGCCACAAGTTATC 58.348 43.478 0.00 0.00 0.00 1.75
2923 3937 3.389741 GCGTCTGATTTGCCACAAG 57.610 52.632 0.00 0.00 0.00 3.16
2976 3990 5.471797 TGAGAAAATTGCCACAGAATACGAA 59.528 36.000 0.00 0.00 0.00 3.85
2979 3993 5.098211 GCTGAGAAAATTGCCACAGAATAC 58.902 41.667 0.00 0.00 0.00 1.89
2994 4008 2.548067 GGTCCGTCTTCAAGCTGAGAAA 60.548 50.000 3.77 0.00 0.00 2.52
3017 4031 1.888215 CTCTCACCATTGTGCACTGT 58.112 50.000 19.41 7.21 42.46 3.55
3032 4046 6.690194 AACACATTATTTCCTCATGCTCTC 57.310 37.500 0.00 0.00 0.00 3.20
3089 4103 0.107557 TCATGTCGTGGCTGATGCAT 60.108 50.000 0.00 0.00 41.91 3.96
3106 4120 0.532573 GTCAAGGTGAGGCTCGATCA 59.467 55.000 10.42 0.00 0.00 2.92
3164 4179 2.194201 TCCGGGCTTAAAAGGAGTTG 57.806 50.000 0.00 0.00 0.00 3.16
3174 4189 2.039216 TGAACTTGTTGATCCGGGCTTA 59.961 45.455 0.00 0.00 0.00 3.09
3181 4196 6.258230 TCATGATTGTGAACTTGTTGATCC 57.742 37.500 0.00 0.00 0.00 3.36
3203 4218 1.524849 GCCTTCCGAGATGCCCTTC 60.525 63.158 0.00 0.00 0.00 3.46
3223 4238 1.137086 TCGAGCTAGAGGACAAATGGC 59.863 52.381 0.00 0.00 0.00 4.40
3231 4246 0.618981 TCACCACTCGAGCTAGAGGA 59.381 55.000 25.16 11.65 42.31 3.71
3235 4250 1.464734 TCCTTCACCACTCGAGCTAG 58.535 55.000 13.61 3.68 0.00 3.42
3236 4251 1.919240 TTCCTTCACCACTCGAGCTA 58.081 50.000 13.61 0.00 0.00 3.32
3282 4297 0.744414 CCGTCATGGGCGATTTCAGT 60.744 55.000 11.19 0.00 0.00 3.41
3303 4319 5.021458 AGATCCAAGTCAGATTTGCCATTT 58.979 37.500 0.00 0.00 0.00 2.32
3304 4320 4.607239 AGATCCAAGTCAGATTTGCCATT 58.393 39.130 0.00 0.00 0.00 3.16
3325 4341 0.946221 GACACACTGAGGCGGTTGAG 60.946 60.000 0.00 0.00 0.00 3.02
3391 4407 3.525537 CGCTGTGACATGGAGATTAACT 58.474 45.455 0.00 0.00 0.00 2.24
3415 4431 3.138930 ATGCGTGGGATCGTCTCCG 62.139 63.158 1.59 0.00 46.01 4.63


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

AutoCloner maintained by Alex Coulton.