Multiple sequence alignment - TraesCS7A01G365800

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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 TraesCS7A01G365800 chr7A 100.000 2426 0 0 1 2426 539652970 539655395 0.000000e+00 4481.0
1 TraesCS7A01G365800 chr7A 78.548 606 102 20 1835 2421 569444890 569444294 8.190000e-100 374.0
2 TraesCS7A01G365800 chr7A 77.686 605 101 24 1843 2421 569450042 569449446 2.990000e-89 339.0
3 TraesCS7A01G365800 chr7D 93.478 644 24 10 1 639 459872582 459871952 0.000000e+00 941.0
4 TraesCS7A01G365800 chr7D 86.649 764 73 14 1674 2426 459871640 459870895 0.000000e+00 819.0
5 TraesCS7A01G365800 chr7D 78.846 312 36 22 642 931 109016491 109016794 1.480000e-42 183.0
6 TraesCS7A01G365800 chr7B 93.189 646 24 9 1 639 482175001 482174369 0.000000e+00 931.0
7 TraesCS7A01G365800 chr7B 86.277 685 71 14 750 1416 63627247 63627926 0.000000e+00 723.0
8 TraesCS7A01G365800 chr7B 83.279 616 63 17 1849 2426 482173728 482173115 4.590000e-147 531.0
9 TraesCS7A01G365800 chr7B 77.311 595 109 20 1845 2421 15073097 15073683 6.470000e-86 327.0
10 TraesCS7A01G365800 chr7B 81.579 152 17 6 785 926 63632275 63632425 5.480000e-22 115.0
11 TraesCS7A01G365800 chr7B 93.182 44 1 2 638 680 63627136 63627178 2.010000e-06 63.9
12 TraesCS7A01G365800 chr7B 97.059 34 1 0 647 680 63632131 63632164 9.370000e-05 58.4
13 TraesCS7A01G365800 chr6B 87.158 584 54 14 751 1317 716104857 716104278 0.000000e+00 643.0
14 TraesCS7A01G365800 chr5A 87.857 560 52 6 859 1416 544456529 544457074 0.000000e+00 643.0
15 TraesCS7A01G365800 chr6D 86.472 547 67 7 867 1410 19623808 19623266 5.780000e-166 593.0
16 TraesCS7A01G365800 chr1D 88.727 479 48 6 859 1335 484721588 484721114 4.500000e-162 580.0
17 TraesCS7A01G365800 chr1D 77.573 379 85 0 1033 1411 24583860 24583482 1.880000e-56 230.0
18 TraesCS7A01G365800 chr3A 82.238 563 93 7 857 1416 142956430 142955872 1.690000e-131 479.0
19 TraesCS7A01G365800 chr3A 85.526 304 21 13 647 927 31787287 31787590 1.820000e-76 296.0
20 TraesCS7A01G365800 chr5B 78.678 605 107 14 1835 2421 645915397 645914797 1.360000e-102 383.0
21 TraesCS7A01G365800 chr6A 78.702 601 97 22 1843 2421 592347594 592347003 2.950000e-99 372.0
22 TraesCS7A01G365800 chr1B 86.000 350 42 4 1067 1409 674871821 674871472 3.810000e-98 368.0
23 TraesCS7A01G365800 chr1A 77.686 605 114 14 1835 2421 440774119 440773518 1.380000e-92 350.0
24 TraesCS7A01G365800 chr1A 78.040 551 97 21 1848 2381 515619499 515620042 2.330000e-85 326.0
25 TraesCS7A01G365800 chr4D 82.768 383 62 4 1030 1410 76233207 76233587 2.990000e-89 339.0
26 TraesCS7A01G365800 chr4D 82.286 175 27 4 864 1036 76199495 76199667 5.400000e-32 148.0
27 TraesCS7A01G365800 chr3B 88.382 241 22 5 693 927 39140238 39140478 3.950000e-73 285.0
28 TraesCS7A01G365800 chr2D 74.953 527 109 14 903 1411 623445558 623445037 1.130000e-53 220.0
29 TraesCS7A01G365800 chr2D 90.000 60 3 3 1712 1769 561877854 561877796 9.300000e-10 75.0
30 TraesCS7A01G365800 chr2A 90.411 73 7 0 1696 1768 660948767 660948695 1.990000e-16 97.1
31 TraesCS7A01G365800 chr2B 85.333 75 9 2 1696 1769 670856907 670856834 2.590000e-10 76.8


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 TraesCS7A01G365800 chr7A 539652970 539655395 2425 False 4481.00 4481 100.0000 1 2426 1 chr7A.!!$F1 2425
1 TraesCS7A01G365800 chr7A 569444294 569444890 596 True 374.00 374 78.5480 1835 2421 1 chr7A.!!$R1 586
2 TraesCS7A01G365800 chr7A 569449446 569450042 596 True 339.00 339 77.6860 1843 2421 1 chr7A.!!$R2 578
3 TraesCS7A01G365800 chr7D 459870895 459872582 1687 True 880.00 941 90.0635 1 2426 2 chr7D.!!$R1 2425
4 TraesCS7A01G365800 chr7B 482173115 482175001 1886 True 731.00 931 88.2340 1 2426 2 chr7B.!!$R1 2425
5 TraesCS7A01G365800 chr7B 63627136 63627926 790 False 393.45 723 89.7295 638 1416 2 chr7B.!!$F2 778
6 TraesCS7A01G365800 chr7B 15073097 15073683 586 False 327.00 327 77.3110 1845 2421 1 chr7B.!!$F1 576
7 TraesCS7A01G365800 chr6B 716104278 716104857 579 True 643.00 643 87.1580 751 1317 1 chr6B.!!$R1 566
8 TraesCS7A01G365800 chr5A 544456529 544457074 545 False 643.00 643 87.8570 859 1416 1 chr5A.!!$F1 557
9 TraesCS7A01G365800 chr6D 19623266 19623808 542 True 593.00 593 86.4720 867 1410 1 chr6D.!!$R1 543
10 TraesCS7A01G365800 chr3A 142955872 142956430 558 True 479.00 479 82.2380 857 1416 1 chr3A.!!$R1 559
11 TraesCS7A01G365800 chr5B 645914797 645915397 600 True 383.00 383 78.6780 1835 2421 1 chr5B.!!$R1 586
12 TraesCS7A01G365800 chr6A 592347003 592347594 591 True 372.00 372 78.7020 1843 2421 1 chr6A.!!$R1 578
13 TraesCS7A01G365800 chr1A 440773518 440774119 601 True 350.00 350 77.6860 1835 2421 1 chr1A.!!$R1 586
14 TraesCS7A01G365800 chr1A 515619499 515620042 543 False 326.00 326 78.0400 1848 2381 1 chr1A.!!$F1 533
15 TraesCS7A01G365800 chr2D 623445037 623445558 521 True 220.00 220 74.9530 903 1411 1 chr2D.!!$R2 508

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
684 695 0.03918 TTACAGAGGAGGAGGCGTCA 59.961 55.0 8.91 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1540 1638 0.39034 TCACATCTTGCTGTCGAGGC 60.39 55.0 3.64 3.64 0.0 4.7 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
65 66 3.450115 GGCTGTACGCGGAGGAGT 61.450 66.667 12.47 0.00 40.44 3.85
169 170 2.094442 CCAGAGGAAGTTCGAGAAGGAC 60.094 54.545 0.00 0.00 0.00 3.85
214 215 1.663739 GTACGTCACCAGGCTCACA 59.336 57.895 0.00 0.00 0.00 3.58
313 314 5.297547 CGATCCCTTCCGAATCTTCAATTA 58.702 41.667 0.00 0.00 0.00 1.40
315 316 6.428159 CGATCCCTTCCGAATCTTCAATTATT 59.572 38.462 0.00 0.00 0.00 1.40
360 367 9.817809 ACTCAAAGATTCGTGTATGTATTATGT 57.182 29.630 0.00 0.00 0.00 2.29
395 402 3.159213 TGAGTAGTCTACGGGGTTCAA 57.841 47.619 4.34 0.00 0.00 2.69
396 403 3.087031 TGAGTAGTCTACGGGGTTCAAG 58.913 50.000 4.34 0.00 0.00 3.02
426 433 3.671716 CCCTGTAGGTTGTTCTTGTACC 58.328 50.000 0.00 0.00 0.00 3.34
469 476 3.753434 CGACGCAGAGGCCAGAGT 61.753 66.667 5.01 1.52 36.38 3.24
472 479 3.385384 CGCAGAGGCCAGAGTGGA 61.385 66.667 5.01 0.00 40.96 4.02
473 480 2.729479 CGCAGAGGCCAGAGTGGAT 61.729 63.158 5.01 0.00 40.96 3.41
474 481 1.153208 GCAGAGGCCAGAGTGGATG 60.153 63.158 5.01 0.00 40.96 3.51
475 482 1.620739 GCAGAGGCCAGAGTGGATGA 61.621 60.000 5.01 0.00 40.96 2.92
476 483 0.177604 CAGAGGCCAGAGTGGATGAC 59.822 60.000 5.01 0.00 40.96 3.06
477 484 1.142748 GAGGCCAGAGTGGATGACG 59.857 63.158 5.01 0.00 40.96 4.35
478 485 2.187946 GGCCAGAGTGGATGACGG 59.812 66.667 0.00 0.00 40.96 4.79
479 486 2.359169 GGCCAGAGTGGATGACGGA 61.359 63.158 0.00 0.00 40.96 4.69
480 487 1.153549 GCCAGAGTGGATGACGGAC 60.154 63.158 0.00 0.00 40.96 4.79
486 493 1.133407 GAGTGGATGACGGACAGAGAC 59.867 57.143 0.00 0.00 0.00 3.36
523 530 3.995636 AGGTCATCCTGCTTACTTAGGA 58.004 45.455 0.00 0.00 46.43 2.94
545 552 2.528127 TGGAGGGCCCGACAGAAA 60.528 61.111 18.44 0.00 37.93 2.52
553 560 1.503542 CCCGACAGAAAGCATGCAC 59.496 57.895 21.98 10.82 0.00 4.57
583 590 3.009143 AGAGGGCCGAGACTAATTTGTTT 59.991 43.478 0.00 0.00 0.00 2.83
585 592 4.913784 AGGGCCGAGACTAATTTGTTTAA 58.086 39.130 0.00 0.00 0.00 1.52
586 593 4.698780 AGGGCCGAGACTAATTTGTTTAAC 59.301 41.667 0.00 0.00 0.00 2.01
588 595 4.389687 GGCCGAGACTAATTTGTTTAACGA 59.610 41.667 0.00 0.00 0.00 3.85
590 597 6.402875 GGCCGAGACTAATTTGTTTAACGATT 60.403 38.462 0.00 2.94 0.00 3.34
591 598 6.464834 GCCGAGACTAATTTGTTTAACGATTG 59.535 38.462 0.00 0.00 0.00 2.67
651 662 6.117911 TCAACTTTCTACATGTGTGTGTTG 57.882 37.500 9.11 15.58 39.39 3.33
680 691 4.636249 CAATATGTTACAGAGGAGGAGGC 58.364 47.826 0.00 0.00 0.00 4.70
682 693 0.251653 TGTTACAGAGGAGGAGGCGT 60.252 55.000 0.00 0.00 0.00 5.68
684 695 0.039180 TTACAGAGGAGGAGGCGTCA 59.961 55.000 8.91 0.00 0.00 4.35
685 696 0.259065 TACAGAGGAGGAGGCGTCAT 59.741 55.000 8.91 0.00 0.00 3.06
686 697 0.616111 ACAGAGGAGGAGGCGTCATT 60.616 55.000 8.91 0.00 0.00 2.57
687 698 0.179089 CAGAGGAGGAGGCGTCATTG 60.179 60.000 8.91 0.00 0.00 2.82
688 699 0.324738 AGAGGAGGAGGCGTCATTGA 60.325 55.000 8.91 0.00 0.00 2.57
689 700 0.179097 GAGGAGGAGGCGTCATTGAC 60.179 60.000 8.91 6.73 0.00 3.18
697 711 1.154413 GCGTCATTGACACTTGGCG 60.154 57.895 16.61 7.11 43.45 5.69
722 736 1.941812 CACCCTTGACGTGCTTGAC 59.058 57.895 0.00 0.00 0.00 3.18
730 744 2.928361 CGTGCTTGACGTGGTGAC 59.072 61.111 0.00 0.00 43.50 3.67
733 747 1.137513 GTGCTTGACGTGGTGACTAC 58.862 55.000 0.00 0.00 0.00 2.73
734 748 1.037493 TGCTTGACGTGGTGACTACT 58.963 50.000 0.00 0.00 0.00 2.57
735 749 1.000607 TGCTTGACGTGGTGACTACTC 60.001 52.381 0.00 0.00 0.00 2.59
736 750 1.269998 GCTTGACGTGGTGACTACTCT 59.730 52.381 0.00 0.00 0.00 3.24
737 751 2.486982 GCTTGACGTGGTGACTACTCTA 59.513 50.000 0.00 0.00 0.00 2.43
738 752 3.426426 GCTTGACGTGGTGACTACTCTAG 60.426 52.174 0.00 2.46 0.00 2.43
739 753 2.082231 TGACGTGGTGACTACTCTAGC 58.918 52.381 0.00 0.00 0.00 3.42
740 754 1.062294 GACGTGGTGACTACTCTAGCG 59.938 57.143 0.00 0.00 0.00 4.26
741 755 1.085091 CGTGGTGACTACTCTAGCGT 58.915 55.000 0.00 0.00 0.00 5.07
742 756 2.274437 CGTGGTGACTACTCTAGCGTA 58.726 52.381 0.00 0.00 0.00 4.42
743 757 2.284684 CGTGGTGACTACTCTAGCGTAG 59.715 54.545 16.60 16.60 41.98 3.51
744 758 2.613133 GTGGTGACTACTCTAGCGTAGG 59.387 54.545 20.96 6.38 40.87 3.18
745 759 1.603326 GGTGACTACTCTAGCGTAGGC 59.397 57.143 20.96 19.26 44.18 3.93
757 771 1.079503 GCGTAGGCTTTCTGTTGAGG 58.920 55.000 0.00 0.00 35.83 3.86
771 785 7.540474 TTCTGTTGAGGTTGTTAGAGATAGT 57.460 36.000 0.00 0.00 0.00 2.12
844 865 2.280628 GTTAGGCAATCTTCACCGAGG 58.719 52.381 0.00 0.00 0.00 4.63
851 872 3.535561 CAATCTTCACCGAGGCTTGTAT 58.464 45.455 0.12 0.00 0.00 2.29
862 893 3.367806 CGAGGCTTGTATCCATCGATCAT 60.368 47.826 0.00 0.00 32.13 2.45
909 945 3.096852 TCGTGTATGAGGGTTGAGACAT 58.903 45.455 0.00 0.00 0.00 3.06
971 1013 5.772672 TCCATCTCATCTAGCTAGTTCTTCC 59.227 44.000 20.10 0.00 0.00 3.46
973 1015 6.071952 CCATCTCATCTAGCTAGTTCTTCCTC 60.072 46.154 20.10 0.00 0.00 3.71
974 1016 6.007485 TCTCATCTAGCTAGTTCTTCCTCA 57.993 41.667 20.10 0.00 0.00 3.86
976 1018 6.320164 TCTCATCTAGCTAGTTCTTCCTCAAC 59.680 42.308 20.10 0.00 0.00 3.18
977 1019 6.191315 TCATCTAGCTAGTTCTTCCTCAACT 58.809 40.000 20.10 0.00 37.80 3.16
978 1020 6.320164 TCATCTAGCTAGTTCTTCCTCAACTC 59.680 42.308 20.10 0.00 35.63 3.01
979 1021 5.822204 TCTAGCTAGTTCTTCCTCAACTCT 58.178 41.667 20.10 0.00 35.63 3.24
980 1022 6.249951 TCTAGCTAGTTCTTCCTCAACTCTT 58.750 40.000 20.10 0.00 35.63 2.85
981 1023 5.400066 AGCTAGTTCTTCCTCAACTCTTC 57.600 43.478 0.00 0.00 35.63 2.87
982 1024 4.835615 AGCTAGTTCTTCCTCAACTCTTCA 59.164 41.667 0.00 0.00 35.63 3.02
983 1025 4.926832 GCTAGTTCTTCCTCAACTCTTCAC 59.073 45.833 0.00 0.00 35.63 3.18
1031 1129 1.379710 CCGCACCCATCCAATCCAA 60.380 57.895 0.00 0.00 0.00 3.53
1048 1146 2.506231 TCCAACCTCAACTACAACACCA 59.494 45.455 0.00 0.00 0.00 4.17
1062 1160 1.424638 ACACCACTGAGCCACTTACT 58.575 50.000 0.00 0.00 0.00 2.24
1065 1163 0.888619 CCACTGAGCCACTTACTCGA 59.111 55.000 0.00 0.00 36.94 4.04
1126 1224 2.457743 AATGGGCGTCGGCTTGTACA 62.458 55.000 19.00 7.92 39.81 2.90
1127 1225 2.357760 GGGCGTCGGCTTGTACAA 60.358 61.111 19.00 8.28 39.81 2.41
1157 1255 0.036010 AACACCATTGAGGAGCCTCG 60.036 55.000 11.64 0.42 45.48 4.63
1194 1292 1.594331 AAGACAAAGACGGCAAGGAC 58.406 50.000 0.00 0.00 0.00 3.85
1211 1309 1.465188 ACCAGGTCATCCCCAACCA 60.465 57.895 0.00 0.00 38.06 3.67
1323 1421 1.995484 CTTGAGACGTCACATGCGATT 59.005 47.619 19.50 0.00 30.10 3.34
1330 1428 1.196581 CGTCACATGCGATTTGGACAA 59.803 47.619 0.00 0.00 0.00 3.18
1350 1448 0.967380 CCTTGGCCACCATGTTCTCC 60.967 60.000 3.88 0.00 31.53 3.71
1406 1504 4.760047 GCACACGGACGCCCAGAT 62.760 66.667 0.00 0.00 0.00 2.90
1418 1516 2.839098 CCAGATGGGCGCCCTAAT 59.161 61.111 43.34 31.09 36.94 1.73
1419 1517 1.151450 CCAGATGGGCGCCCTAATT 59.849 57.895 43.34 26.31 36.94 1.40
1420 1518 0.468029 CCAGATGGGCGCCCTAATTT 60.468 55.000 43.34 23.77 36.94 1.82
1421 1519 1.402787 CAGATGGGCGCCCTAATTTT 58.597 50.000 43.34 22.00 36.94 1.82
1422 1520 1.756538 CAGATGGGCGCCCTAATTTTT 59.243 47.619 43.34 20.24 36.94 1.94
1450 1548 9.763465 AACGATTATTTTAAGGTTTATCGTGTG 57.237 29.630 0.00 0.00 43.79 3.82
1451 1549 8.938906 ACGATTATTTTAAGGTTTATCGTGTGT 58.061 29.630 0.00 0.00 43.19 3.72
1452 1550 9.763465 CGATTATTTTAAGGTTTATCGTGTGTT 57.237 29.630 0.00 0.00 31.48 3.32
1459 1557 9.896263 TTTAAGGTTTATCGTGTGTTTATTTCC 57.104 29.630 0.00 0.00 0.00 3.13
1460 1558 7.513371 AAGGTTTATCGTGTGTTTATTTCCA 57.487 32.000 0.00 0.00 0.00 3.53
1461 1559 7.696992 AGGTTTATCGTGTGTTTATTTCCAT 57.303 32.000 0.00 0.00 0.00 3.41
1462 1560 8.117813 AGGTTTATCGTGTGTTTATTTCCATT 57.882 30.769 0.00 0.00 0.00 3.16
1463 1561 8.581578 AGGTTTATCGTGTGTTTATTTCCATTT 58.418 29.630 0.00 0.00 0.00 2.32
1464 1562 9.198837 GGTTTATCGTGTGTTTATTTCCATTTT 57.801 29.630 0.00 0.00 0.00 1.82
1470 1568 9.967346 TCGTGTGTTTATTTCCATTTTATTTCA 57.033 25.926 0.00 0.00 0.00 2.69
1480 1578 9.844257 ATTTCCATTTTATTTCAACTTTCCACA 57.156 25.926 0.00 0.00 0.00 4.17
1481 1579 9.844257 TTTCCATTTTATTTCAACTTTCCACAT 57.156 25.926 0.00 0.00 0.00 3.21
1482 1580 8.830201 TCCATTTTATTTCAACTTTCCACATG 57.170 30.769 0.00 0.00 0.00 3.21
1483 1581 8.428063 TCCATTTTATTTCAACTTTCCACATGT 58.572 29.630 0.00 0.00 0.00 3.21
1484 1582 8.711457 CCATTTTATTTCAACTTTCCACATGTC 58.289 33.333 0.00 0.00 0.00 3.06
1485 1583 9.480053 CATTTTATTTCAACTTTCCACATGTCT 57.520 29.630 0.00 0.00 0.00 3.41
1487 1585 9.959749 TTTTATTTCAACTTTCCACATGTCTAC 57.040 29.630 0.00 0.00 0.00 2.59
1488 1586 8.684386 TTATTTCAACTTTCCACATGTCTACA 57.316 30.769 0.00 0.00 0.00 2.74
1489 1587 6.618287 TTTCAACTTTCCACATGTCTACAG 57.382 37.500 0.00 0.00 0.00 2.74
1490 1588 5.290493 TCAACTTTCCACATGTCTACAGT 57.710 39.130 0.00 0.00 0.00 3.55
1491 1589 5.680619 TCAACTTTCCACATGTCTACAGTT 58.319 37.500 0.00 0.00 0.00 3.16
1492 1590 6.119536 TCAACTTTCCACATGTCTACAGTTT 58.880 36.000 0.00 0.00 0.00 2.66
1493 1591 6.601613 TCAACTTTCCACATGTCTACAGTTTT 59.398 34.615 0.00 0.00 0.00 2.43
1494 1592 6.619801 ACTTTCCACATGTCTACAGTTTTC 57.380 37.500 0.00 0.00 0.00 2.29
1495 1593 5.531287 ACTTTCCACATGTCTACAGTTTTCC 59.469 40.000 0.00 0.00 0.00 3.13
1496 1594 4.698201 TCCACATGTCTACAGTTTTCCA 57.302 40.909 0.00 0.00 0.00 3.53
1497 1595 4.385825 TCCACATGTCTACAGTTTTCCAC 58.614 43.478 0.00 0.00 0.00 4.02
1498 1596 4.133820 CCACATGTCTACAGTTTTCCACA 58.866 43.478 0.00 0.00 0.00 4.17
1499 1597 4.761739 CCACATGTCTACAGTTTTCCACAT 59.238 41.667 0.00 0.00 0.00 3.21
1500 1598 5.335113 CCACATGTCTACAGTTTTCCACATG 60.335 44.000 0.00 8.04 44.37 3.21
1501 1599 4.216257 ACATGTCTACAGTTTTCCACATGC 59.784 41.667 9.26 0.00 43.19 4.06
1502 1600 2.805671 TGTCTACAGTTTTCCACATGCG 59.194 45.455 0.00 0.00 0.00 4.73
1503 1601 3.064207 GTCTACAGTTTTCCACATGCGA 58.936 45.455 0.00 0.00 0.00 5.10
1504 1602 3.496884 GTCTACAGTTTTCCACATGCGAA 59.503 43.478 0.00 0.00 0.00 4.70
1505 1603 4.024387 GTCTACAGTTTTCCACATGCGAAA 60.024 41.667 4.81 4.81 0.00 3.46
1506 1604 3.791973 ACAGTTTTCCACATGCGAAAA 57.208 38.095 14.25 14.25 36.98 2.29
1507 1605 4.116747 ACAGTTTTCCACATGCGAAAAA 57.883 36.364 18.03 8.59 40.04 1.94
1540 1638 9.634163 GTTAGAAATAAGGTTGTTATTGTTGGG 57.366 33.333 0.00 0.00 0.00 4.12
1541 1639 6.697395 AGAAATAAGGTTGTTATTGTTGGGC 58.303 36.000 0.00 0.00 0.00 5.36
1542 1640 5.414789 AATAAGGTTGTTATTGTTGGGCC 57.585 39.130 0.00 0.00 0.00 5.80
1543 1641 2.694616 AGGTTGTTATTGTTGGGCCT 57.305 45.000 4.53 0.00 0.00 5.19
1544 1642 2.525368 AGGTTGTTATTGTTGGGCCTC 58.475 47.619 4.53 0.00 0.00 4.70
1545 1643 1.201414 GGTTGTTATTGTTGGGCCTCG 59.799 52.381 4.53 0.00 0.00 4.63
1546 1644 2.156098 GTTGTTATTGTTGGGCCTCGA 58.844 47.619 4.53 0.00 0.00 4.04
1547 1645 1.816074 TGTTATTGTTGGGCCTCGAC 58.184 50.000 4.53 3.49 0.00 4.20
1548 1646 1.072489 TGTTATTGTTGGGCCTCGACA 59.928 47.619 4.53 6.44 37.96 4.35
1549 1647 1.737793 GTTATTGTTGGGCCTCGACAG 59.262 52.381 4.53 0.00 40.58 3.51
1550 1648 0.392461 TATTGTTGGGCCTCGACAGC 60.392 55.000 4.53 0.00 40.58 4.40
1551 1649 2.410322 ATTGTTGGGCCTCGACAGCA 62.410 55.000 4.53 0.00 40.58 4.41
1552 1650 2.281484 GTTGGGCCTCGACAGCAA 60.281 61.111 4.53 0.00 0.00 3.91
1553 1651 2.032528 TTGGGCCTCGACAGCAAG 59.967 61.111 4.53 0.00 0.00 4.01
1554 1652 2.515979 TTGGGCCTCGACAGCAAGA 61.516 57.895 4.53 0.00 0.00 3.02
1555 1653 1.841302 TTGGGCCTCGACAGCAAGAT 61.841 55.000 4.53 0.00 0.00 2.40
1556 1654 1.817099 GGGCCTCGACAGCAAGATG 60.817 63.158 0.84 0.00 0.00 2.90
1557 1655 1.078848 GGCCTCGACAGCAAGATGT 60.079 57.895 0.00 0.00 35.68 3.06
1558 1656 1.364626 GGCCTCGACAGCAAGATGTG 61.365 60.000 0.00 0.00 32.25 3.21
1559 1657 0.390340 GCCTCGACAGCAAGATGTGA 60.390 55.000 0.00 0.00 32.25 3.58
1560 1658 1.741732 GCCTCGACAGCAAGATGTGAT 60.742 52.381 0.00 0.00 32.25 3.06
1574 1672 2.702898 TGTGATGCACAAATTCACCG 57.297 45.000 13.39 0.00 41.69 4.94
1575 1673 2.225467 TGTGATGCACAAATTCACCGA 58.775 42.857 13.39 0.00 41.69 4.69
1576 1674 2.031245 TGTGATGCACAAATTCACCGAC 60.031 45.455 13.39 0.00 41.69 4.79
1577 1675 2.031245 GTGATGCACAAATTCACCGACA 60.031 45.455 6.17 0.00 34.95 4.35
1578 1676 2.031245 TGATGCACAAATTCACCGACAC 60.031 45.455 0.00 0.00 0.00 3.67
1579 1677 1.383523 TGCACAAATTCACCGACACA 58.616 45.000 0.00 0.00 0.00 3.72
1580 1678 1.745653 TGCACAAATTCACCGACACAA 59.254 42.857 0.00 0.00 0.00 3.33
1581 1679 2.116366 GCACAAATTCACCGACACAAC 58.884 47.619 0.00 0.00 0.00 3.32
1582 1680 2.478709 GCACAAATTCACCGACACAACA 60.479 45.455 0.00 0.00 0.00 3.33
1583 1681 3.105203 CACAAATTCACCGACACAACAC 58.895 45.455 0.00 0.00 0.00 3.32
1584 1682 2.750166 ACAAATTCACCGACACAACACA 59.250 40.909 0.00 0.00 0.00 3.72
1585 1683 3.380004 ACAAATTCACCGACACAACACAT 59.620 39.130 0.00 0.00 0.00 3.21
1586 1684 4.576873 ACAAATTCACCGACACAACACATA 59.423 37.500 0.00 0.00 0.00 2.29
1587 1685 5.240623 ACAAATTCACCGACACAACACATAT 59.759 36.000 0.00 0.00 0.00 1.78
1588 1686 4.944962 ATTCACCGACACAACACATATG 57.055 40.909 0.00 0.00 0.00 1.78
1589 1687 2.073056 TCACCGACACAACACATATGC 58.927 47.619 1.58 0.00 0.00 3.14
1590 1688 1.803555 CACCGACACAACACATATGCA 59.196 47.619 1.58 0.00 0.00 3.96
1591 1689 2.225255 CACCGACACAACACATATGCAA 59.775 45.455 1.58 0.00 0.00 4.08
1592 1690 2.881513 ACCGACACAACACATATGCAAA 59.118 40.909 1.58 0.00 0.00 3.68
1593 1691 3.233578 CCGACACAACACATATGCAAAC 58.766 45.455 1.58 0.00 0.00 2.93
1594 1692 3.304324 CCGACACAACACATATGCAAACA 60.304 43.478 1.58 0.00 0.00 2.83
1595 1693 4.286101 CGACACAACACATATGCAAACAA 58.714 39.130 1.58 0.00 0.00 2.83
1596 1694 4.146271 CGACACAACACATATGCAAACAAC 59.854 41.667 1.58 0.00 0.00 3.32
1597 1695 4.367450 ACACAACACATATGCAAACAACC 58.633 39.130 1.58 0.00 0.00 3.77
1598 1696 3.740321 CACAACACATATGCAAACAACCC 59.260 43.478 1.58 0.00 0.00 4.11
1599 1697 3.640967 ACAACACATATGCAAACAACCCT 59.359 39.130 1.58 0.00 0.00 4.34
1600 1698 4.236935 CAACACATATGCAAACAACCCTC 58.763 43.478 1.58 0.00 0.00 4.30
1607 1705 2.733956 TGCAAACAACCCTCTTCACTT 58.266 42.857 0.00 0.00 0.00 3.16
1608 1706 3.096092 TGCAAACAACCCTCTTCACTTT 58.904 40.909 0.00 0.00 0.00 2.66
1655 1753 3.070590 ACCAACTAGTAAGCAACGTTCCT 59.929 43.478 0.00 0.00 0.00 3.36
1657 1755 4.514066 CCAACTAGTAAGCAACGTTCCTTT 59.486 41.667 10.24 1.91 0.00 3.11
1658 1756 5.333875 CCAACTAGTAAGCAACGTTCCTTTC 60.334 44.000 10.24 5.06 0.00 2.62
1660 1758 4.989168 ACTAGTAAGCAACGTTCCTTTCAG 59.011 41.667 10.24 7.55 0.00 3.02
1661 1759 4.067972 AGTAAGCAACGTTCCTTTCAGA 57.932 40.909 10.24 0.00 0.00 3.27
1662 1760 4.448210 AGTAAGCAACGTTCCTTTCAGAA 58.552 39.130 10.24 0.00 0.00 3.02
1663 1761 4.879545 AGTAAGCAACGTTCCTTTCAGAAA 59.120 37.500 10.24 0.00 0.00 2.52
1664 1762 3.971032 AGCAACGTTCCTTTCAGAAAG 57.029 42.857 15.18 15.18 38.24 2.62
1665 1763 3.541632 AGCAACGTTCCTTTCAGAAAGA 58.458 40.909 22.55 7.55 41.02 2.52
1666 1764 3.945285 AGCAACGTTCCTTTCAGAAAGAA 59.055 39.130 22.55 12.49 41.02 2.52
1667 1765 4.398044 AGCAACGTTCCTTTCAGAAAGAAA 59.602 37.500 22.55 7.49 43.71 2.52
1668 1766 5.099575 GCAACGTTCCTTTCAGAAAGAAAA 58.900 37.500 22.55 13.71 45.11 2.29
1669 1767 5.575218 GCAACGTTCCTTTCAGAAAGAAAAA 59.425 36.000 22.55 11.54 45.11 1.94
1755 1853 7.348956 CACATGTGACACTTAATTTAACGTGA 58.651 34.615 21.64 0.00 0.00 4.35
1756 1854 7.853437 CACATGTGACACTTAATTTAACGTGAA 59.147 33.333 21.64 0.00 0.00 3.18
1757 1855 8.399425 ACATGTGACACTTAATTTAACGTGAAA 58.601 29.630 17.81 0.00 0.00 2.69
1758 1856 9.227490 CATGTGACACTTAATTTAACGTGAAAA 57.773 29.630 17.81 0.22 0.00 2.29
1759 1857 9.790389 ATGTGACACTTAATTTAACGTGAAAAA 57.210 25.926 17.81 0.00 0.00 1.94
1760 1858 9.063739 TGTGACACTTAATTTAACGTGAAAAAC 57.936 29.630 17.81 12.57 0.00 2.43
1761 1859 8.525876 GTGACACTTAATTTAACGTGAAAAACC 58.474 33.333 17.81 0.00 0.00 3.27
1762 1860 8.242053 TGACACTTAATTTAACGTGAAAAACCA 58.758 29.630 17.81 0.00 0.00 3.67
1763 1861 8.397215 ACACTTAATTTAACGTGAAAAACCAC 57.603 30.769 17.81 0.00 0.00 4.16
1764 1862 7.488792 ACACTTAATTTAACGTGAAAAACCACC 59.511 33.333 17.81 0.00 33.67 4.61
1765 1863 7.703197 CACTTAATTTAACGTGAAAAACCACCT 59.297 33.333 1.27 0.00 33.67 4.00
1766 1864 7.916977 ACTTAATTTAACGTGAAAAACCACCTC 59.083 33.333 1.27 0.00 33.67 3.85
1773 1871 4.021807 ACGTGAAAAACCACCTCAAAAACT 60.022 37.500 0.00 0.00 33.67 2.66
1776 1874 6.624204 CGTGAAAAACCACCTCAAAAACTACT 60.624 38.462 0.00 0.00 33.67 2.57
1785 1883 3.243401 CCTCAAAAACTACTGTTGTGGCC 60.243 47.826 0.00 0.00 36.39 5.36
1807 1905 3.502211 CCACACAACTTCACCATTAGGAC 59.498 47.826 0.00 0.00 38.69 3.85
1821 1919 3.947910 TTAGGACGGTGAGTACAAAGG 57.052 47.619 0.00 0.00 35.65 3.11
1923 2194 5.705441 ACACAACTTCTGTCTGTTTCTGAAA 59.295 36.000 0.00 0.00 35.47 2.69
1934 2205 7.542890 TGTCTGTTTCTGAAATTTGCAAACTA 58.457 30.769 15.41 0.26 0.00 2.24
1988 2259 1.959282 TGGCATGCAAACATACACACA 59.041 42.857 21.36 0.00 33.67 3.72
1995 2266 4.626042 TGCAAACATACACACAAATTCCC 58.374 39.130 0.00 0.00 0.00 3.97
2009 2280 4.215109 CAAATTCCCGACATCCCCTAAAT 58.785 43.478 0.00 0.00 0.00 1.40
2010 2281 4.536295 AATTCCCGACATCCCCTAAATT 57.464 40.909 0.00 0.00 0.00 1.82
2011 2282 4.536295 ATTCCCGACATCCCCTAAATTT 57.464 40.909 0.00 0.00 0.00 1.82
2054 2325 4.157656 TGTTTGCTTACCCAATCTATGCAC 59.842 41.667 0.00 0.00 0.00 4.57
2061 2332 2.706190 ACCCAATCTATGCACCTCCTAC 59.294 50.000 0.00 0.00 0.00 3.18
2147 2420 1.075374 TGACCCAATCCTCAAACCAGG 59.925 52.381 0.00 0.00 34.40 4.45
2160 2433 2.742053 CAAACCAGGTAACCACATCGAG 59.258 50.000 0.00 0.00 37.17 4.04
2177 2451 7.364200 CACATCGAGATACCTAAAGTAAGGAG 58.636 42.308 0.00 0.00 39.15 3.69
2216 2496 1.615384 GGTCAATCCAAGCAAGCCTCT 60.615 52.381 0.00 0.00 35.97 3.69
2246 2526 5.934625 CCAGCTTAAACATTGTCTAGTCAGT 59.065 40.000 0.00 0.00 0.00 3.41
2249 2529 6.992715 AGCTTAAACATTGTCTAGTCAGTTGT 59.007 34.615 0.00 0.00 0.00 3.32
2283 2590 3.181412 ACAGAACCTCTCTCCTCCTTCTT 60.181 47.826 0.00 0.00 29.07 2.52
2296 2603 4.770010 TCCTCCTTCTTTCTCTCTCTCAAC 59.230 45.833 0.00 0.00 0.00 3.18
2298 2605 4.145807 TCCTTCTTTCTCTCTCTCAACGT 58.854 43.478 0.00 0.00 0.00 3.99
2342 2664 4.645535 TCTTTCACTCTCACAATGGAAGG 58.354 43.478 0.00 0.00 30.96 3.46
2351 2673 0.827507 ACAATGGAAGGCACCACCAC 60.828 55.000 5.63 0.00 43.03 4.16
2384 2709 3.329814 TGACTAGGGTTTTCTTCTTCCCC 59.670 47.826 0.00 0.00 40.70 4.81
2395 2721 2.904434 TCTTCTTCCCCCACTTCACTAC 59.096 50.000 0.00 0.00 0.00 2.73
2399 2725 1.946984 TCCCCCACTTCACTACGAAT 58.053 50.000 0.00 0.00 31.69 3.34
2404 2730 3.446161 CCCCACTTCACTACGAATCACTA 59.554 47.826 0.00 0.00 31.69 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 0.471211 ACCCAGTTCTTCCACTCCGA 60.471 55.000 0.00 0.00 0.00 4.55
169 170 3.740128 CTTGGGCGGGATGAGGTCG 62.740 68.421 0.00 0.00 0.00 4.79
313 314 9.598517 TTGAGTAAAAGAATTGAACAAAGCAAT 57.401 25.926 0.00 0.00 37.56 3.56
315 316 8.994429 TTTGAGTAAAAGAATTGAACAAAGCA 57.006 26.923 0.00 0.00 0.00 3.91
358 365 9.696572 AGACTACTCAAATGTCCTAGTAATACA 57.303 33.333 0.00 0.00 0.00 2.29
361 368 8.838365 CGTAGACTACTCAAATGTCCTAGTAAT 58.162 37.037 10.82 0.00 0.00 1.89
362 369 7.281774 CCGTAGACTACTCAAATGTCCTAGTAA 59.718 40.741 10.82 0.00 0.00 2.24
426 433 2.780643 CTGACACGGCGAATGCAG 59.219 61.111 16.62 11.46 45.35 4.41
458 465 1.326213 CGTCATCCACTCTGGCCTCT 61.326 60.000 3.32 0.00 37.47 3.69
463 470 0.174389 CTGTCCGTCATCCACTCTGG 59.826 60.000 0.00 0.00 39.43 3.86
464 471 1.133982 CTCTGTCCGTCATCCACTCTG 59.866 57.143 0.00 0.00 0.00 3.35
466 473 1.133407 GTCTCTGTCCGTCATCCACTC 59.867 57.143 0.00 0.00 0.00 3.51
467 474 1.178276 GTCTCTGTCCGTCATCCACT 58.822 55.000 0.00 0.00 0.00 4.00
468 475 0.888619 TGTCTCTGTCCGTCATCCAC 59.111 55.000 0.00 0.00 0.00 4.02
469 476 1.272490 GTTGTCTCTGTCCGTCATCCA 59.728 52.381 0.00 0.00 0.00 3.41
472 479 2.300152 ACATGTTGTCTCTGTCCGTCAT 59.700 45.455 0.00 0.00 0.00 3.06
473 480 1.686587 ACATGTTGTCTCTGTCCGTCA 59.313 47.619 0.00 0.00 0.00 4.35
474 481 2.440539 ACATGTTGTCTCTGTCCGTC 57.559 50.000 0.00 0.00 0.00 4.79
475 482 2.910688 AACATGTTGTCTCTGTCCGT 57.089 45.000 11.07 0.00 0.00 4.69
476 483 3.185188 CAGAAACATGTTGTCTCTGTCCG 59.815 47.826 22.46 5.45 0.00 4.79
477 484 4.130118 ACAGAAACATGTTGTCTCTGTCC 58.870 43.478 27.38 6.42 32.31 4.02
478 485 5.053145 AGACAGAAACATGTTGTCTCTGTC 58.947 41.667 37.09 37.09 46.24 3.51
479 486 5.028549 AGACAGAAACATGTTGTCTCTGT 57.971 39.130 30.76 30.76 46.24 3.41
480 487 5.636965 CCTAGACAGAAACATGTTGTCTCTG 59.363 44.000 27.01 26.68 46.24 3.35
486 493 5.352569 GGATGACCTAGACAGAAACATGTTG 59.647 44.000 12.82 2.82 32.25 3.33
545 552 3.220110 CCCTCTTCAATATGTGCATGCT 58.780 45.455 20.33 0.40 0.00 3.79
553 560 2.366916 AGTCTCGGCCCTCTTCAATATG 59.633 50.000 0.00 0.00 0.00 1.78
583 590 9.206870 AGACGATAAACCTTAAAACAATCGTTA 57.793 29.630 8.61 0.00 45.46 3.18
586 593 7.515643 ACAGACGATAAACCTTAAAACAATCG 58.484 34.615 0.00 0.00 40.28 3.34
641 652 3.797451 ATTGCATGTTCAACACACACA 57.203 38.095 0.00 0.00 38.61 3.72
642 653 5.221880 ACATATTGCATGTTCAACACACAC 58.778 37.500 0.00 0.00 38.61 3.82
651 662 6.017605 CCTCCTCTGTAACATATTGCATGTTC 60.018 42.308 7.42 1.94 41.81 3.18
680 691 0.110688 CACGCCAAGTGTCAATGACG 60.111 55.000 9.00 0.00 45.51 4.35
704 718 1.831389 CGTCAAGCACGTCAAGGGTG 61.831 60.000 0.00 0.00 44.07 4.61
705 719 1.594293 CGTCAAGCACGTCAAGGGT 60.594 57.895 0.00 0.00 44.07 4.34
714 728 1.137513 GTAGTCACCACGTCAAGCAC 58.862 55.000 0.00 0.00 0.00 4.40
715 729 1.000607 GAGTAGTCACCACGTCAAGCA 60.001 52.381 0.00 0.00 0.00 3.91
718 732 2.486982 GCTAGAGTAGTCACCACGTCAA 59.513 50.000 0.00 0.00 0.00 3.18
719 733 2.082231 GCTAGAGTAGTCACCACGTCA 58.918 52.381 0.00 0.00 0.00 4.35
720 734 1.062294 CGCTAGAGTAGTCACCACGTC 59.938 57.143 0.00 0.00 0.00 4.34
722 736 1.085091 ACGCTAGAGTAGTCACCACG 58.915 55.000 0.00 0.99 0.00 4.94
723 737 2.613133 CCTACGCTAGAGTAGTCACCAC 59.387 54.545 25.90 0.00 41.76 4.16
724 738 2.915349 CCTACGCTAGAGTAGTCACCA 58.085 52.381 25.90 0.00 41.76 4.17
725 739 1.603326 GCCTACGCTAGAGTAGTCACC 59.397 57.143 25.90 11.88 41.76 4.02
726 740 2.563702 AGCCTACGCTAGAGTAGTCAC 58.436 52.381 25.90 17.22 46.08 3.67
738 752 1.079503 CCTCAACAGAAAGCCTACGC 58.920 55.000 0.00 0.00 0.00 4.42
739 753 2.457366 ACCTCAACAGAAAGCCTACG 57.543 50.000 0.00 0.00 0.00 3.51
740 754 3.477530 ACAACCTCAACAGAAAGCCTAC 58.522 45.455 0.00 0.00 0.00 3.18
741 755 3.857157 ACAACCTCAACAGAAAGCCTA 57.143 42.857 0.00 0.00 0.00 3.93
742 756 2.736670 ACAACCTCAACAGAAAGCCT 57.263 45.000 0.00 0.00 0.00 4.58
743 757 4.134563 TCTAACAACCTCAACAGAAAGCC 58.865 43.478 0.00 0.00 0.00 4.35
744 758 5.057149 TCTCTAACAACCTCAACAGAAAGC 58.943 41.667 0.00 0.00 0.00 3.51
745 759 8.091449 ACTATCTCTAACAACCTCAACAGAAAG 58.909 37.037 0.00 0.00 0.00 2.62
746 760 7.963532 ACTATCTCTAACAACCTCAACAGAAA 58.036 34.615 0.00 0.00 0.00 2.52
747 761 7.540474 ACTATCTCTAACAACCTCAACAGAA 57.460 36.000 0.00 0.00 0.00 3.02
748 762 7.451877 AGAACTATCTCTAACAACCTCAACAGA 59.548 37.037 0.00 0.00 0.00 3.41
795 816 3.265995 GGGAGGTTACAGGGAGAATCAAA 59.734 47.826 0.00 0.00 36.25 2.69
797 818 2.478292 GGGAGGTTACAGGGAGAATCA 58.522 52.381 0.00 0.00 36.25 2.57
805 826 2.506065 CGAGAGGGGAGGTTACAGG 58.494 63.158 0.00 0.00 0.00 4.00
851 872 5.963214 ATATTGATGGGATGATCGATGGA 57.037 39.130 0.54 0.00 30.39 3.41
862 893 4.685848 GCCCGCATGTATATATTGATGGGA 60.686 45.833 19.63 0.00 32.35 4.37
971 1013 3.760580 AGGGTTGAGTGAAGAGTTGAG 57.239 47.619 0.00 0.00 0.00 3.02
973 1015 4.078639 AGAAGGGTTGAGTGAAGAGTTG 57.921 45.455 0.00 0.00 0.00 3.16
974 1016 4.164221 TGAAGAAGGGTTGAGTGAAGAGTT 59.836 41.667 0.00 0.00 0.00 3.01
976 1018 4.342862 TGAAGAAGGGTTGAGTGAAGAG 57.657 45.455 0.00 0.00 0.00 2.85
977 1019 4.347876 TGATGAAGAAGGGTTGAGTGAAGA 59.652 41.667 0.00 0.00 0.00 2.87
978 1020 4.645535 TGATGAAGAAGGGTTGAGTGAAG 58.354 43.478 0.00 0.00 0.00 3.02
979 1021 4.705110 TGATGAAGAAGGGTTGAGTGAA 57.295 40.909 0.00 0.00 0.00 3.18
980 1022 4.042062 ACATGATGAAGAAGGGTTGAGTGA 59.958 41.667 0.00 0.00 0.00 3.41
981 1023 4.330250 ACATGATGAAGAAGGGTTGAGTG 58.670 43.478 0.00 0.00 0.00 3.51
982 1024 4.566488 GGACATGATGAAGAAGGGTTGAGT 60.566 45.833 0.00 0.00 0.00 3.41
983 1025 3.944015 GGACATGATGAAGAAGGGTTGAG 59.056 47.826 0.00 0.00 0.00 3.02
1031 1129 2.769663 TCAGTGGTGTTGTAGTTGAGGT 59.230 45.455 0.00 0.00 0.00 3.85
1048 1146 1.068472 CGTTCGAGTAAGTGGCTCAGT 60.068 52.381 0.00 0.00 33.45 3.41
1062 1160 4.823157 TCCAAAGGACATAATTCGTTCGA 58.177 39.130 0.00 0.00 0.00 3.71
1065 1163 5.336451 GGCTTTCCAAAGGACATAATTCGTT 60.336 40.000 1.32 0.00 36.53 3.85
1115 1213 2.488937 TCGATGTAGTTGTACAAGCCGA 59.511 45.455 8.98 8.80 42.54 5.54
1126 1224 4.637276 TCAATGGTGTTGTCGATGTAGTT 58.363 39.130 0.00 0.00 0.00 2.24
1127 1225 4.245660 CTCAATGGTGTTGTCGATGTAGT 58.754 43.478 0.00 0.00 0.00 2.73
1157 1255 3.084039 TCTTTGGTGGTGATGATCTTGC 58.916 45.455 0.00 0.00 0.00 4.01
1194 1292 0.396139 CATGGTTGGGGATGACCTGG 60.396 60.000 0.00 0.00 40.03 4.45
1221 1319 2.915869 TGATCCTGGACAAACTAGGGT 58.084 47.619 0.00 0.00 45.63 4.34
1226 1324 5.126061 GCAATATGTTGATCCTGGACAAACT 59.874 40.000 18.79 10.47 37.53 2.66
1228 1326 4.402155 GGCAATATGTTGATCCTGGACAAA 59.598 41.667 6.35 0.00 37.53 2.83
1323 1421 1.456705 GGTGGCCAAGGTTGTCCAA 60.457 57.895 7.24 0.00 35.89 3.53
1330 1428 0.251341 GAGAACATGGTGGCCAAGGT 60.251 55.000 7.24 0.00 36.95 3.50
1391 1489 4.082523 CCATCTGGGCGTCCGTGT 62.083 66.667 0.00 0.00 35.24 4.49
1424 1522 9.763465 CACACGATAAACCTTAAAATAATCGTT 57.237 29.630 4.85 0.00 39.73 3.85
1425 1523 8.938906 ACACACGATAAACCTTAAAATAATCGT 58.061 29.630 0.00 0.00 41.96 3.73
1426 1524 9.763465 AACACACGATAAACCTTAAAATAATCG 57.237 29.630 0.00 0.00 35.46 3.34
1433 1531 9.896263 GGAAATAAACACACGATAAACCTTAAA 57.104 29.630 0.00 0.00 0.00 1.52
1434 1532 9.064706 TGGAAATAAACACACGATAAACCTTAA 57.935 29.630 0.00 0.00 0.00 1.85
1435 1533 8.618702 TGGAAATAAACACACGATAAACCTTA 57.381 30.769 0.00 0.00 0.00 2.69
1436 1534 7.513371 TGGAAATAAACACACGATAAACCTT 57.487 32.000 0.00 0.00 0.00 3.50
1437 1535 7.696992 ATGGAAATAAACACACGATAAACCT 57.303 32.000 0.00 0.00 0.00 3.50
1438 1536 8.751302 AAATGGAAATAAACACACGATAAACC 57.249 30.769 0.00 0.00 0.00 3.27
1444 1542 9.967346 TGAAATAAAATGGAAATAAACACACGA 57.033 25.926 0.00 0.00 0.00 4.35
1454 1552 9.844257 TGTGGAAAGTTGAAATAAAATGGAAAT 57.156 25.926 0.00 0.00 0.00 2.17
1455 1553 9.844257 ATGTGGAAAGTTGAAATAAAATGGAAA 57.156 25.926 0.00 0.00 0.00 3.13
1456 1554 9.270640 CATGTGGAAAGTTGAAATAAAATGGAA 57.729 29.630 0.00 0.00 0.00 3.53
1457 1555 8.428063 ACATGTGGAAAGTTGAAATAAAATGGA 58.572 29.630 0.00 0.00 0.00 3.41
1458 1556 8.606040 ACATGTGGAAAGTTGAAATAAAATGG 57.394 30.769 0.00 0.00 0.00 3.16
1459 1557 9.480053 AGACATGTGGAAAGTTGAAATAAAATG 57.520 29.630 1.15 0.00 0.00 2.32
1461 1559 9.959749 GTAGACATGTGGAAAGTTGAAATAAAA 57.040 29.630 1.15 0.00 0.00 1.52
1462 1560 9.126151 TGTAGACATGTGGAAAGTTGAAATAAA 57.874 29.630 1.15 0.00 0.00 1.40
1463 1561 8.684386 TGTAGACATGTGGAAAGTTGAAATAA 57.316 30.769 1.15 0.00 0.00 1.40
1464 1562 7.936847 ACTGTAGACATGTGGAAAGTTGAAATA 59.063 33.333 1.15 0.00 0.00 1.40
1465 1563 6.772716 ACTGTAGACATGTGGAAAGTTGAAAT 59.227 34.615 1.15 0.00 0.00 2.17
1466 1564 6.119536 ACTGTAGACATGTGGAAAGTTGAAA 58.880 36.000 1.15 0.00 0.00 2.69
1467 1565 5.680619 ACTGTAGACATGTGGAAAGTTGAA 58.319 37.500 1.15 0.00 0.00 2.69
1468 1566 5.290493 ACTGTAGACATGTGGAAAGTTGA 57.710 39.130 1.15 0.00 0.00 3.18
1469 1567 6.377327 AAACTGTAGACATGTGGAAAGTTG 57.623 37.500 1.15 0.00 0.00 3.16
1470 1568 6.039382 GGAAAACTGTAGACATGTGGAAAGTT 59.961 38.462 1.15 4.65 0.00 2.66
1471 1569 5.531287 GGAAAACTGTAGACATGTGGAAAGT 59.469 40.000 1.15 0.00 0.00 2.66
1472 1570 5.530915 TGGAAAACTGTAGACATGTGGAAAG 59.469 40.000 1.15 0.00 0.00 2.62
1473 1571 5.298276 GTGGAAAACTGTAGACATGTGGAAA 59.702 40.000 1.15 0.00 0.00 3.13
1474 1572 4.819630 GTGGAAAACTGTAGACATGTGGAA 59.180 41.667 1.15 0.00 0.00 3.53
1475 1573 4.141597 TGTGGAAAACTGTAGACATGTGGA 60.142 41.667 1.15 0.00 0.00 4.02
1476 1574 4.133820 TGTGGAAAACTGTAGACATGTGG 58.866 43.478 1.15 0.00 0.00 4.17
1477 1575 5.692814 CATGTGGAAAACTGTAGACATGTG 58.307 41.667 1.15 0.00 0.00 3.21
1478 1576 4.216257 GCATGTGGAAAACTGTAGACATGT 59.784 41.667 0.00 0.00 0.00 3.21
1479 1577 4.669965 CGCATGTGGAAAACTGTAGACATG 60.670 45.833 0.00 0.00 0.00 3.21
1480 1578 3.436704 CGCATGTGGAAAACTGTAGACAT 59.563 43.478 0.00 0.00 0.00 3.06
1481 1579 2.805671 CGCATGTGGAAAACTGTAGACA 59.194 45.455 0.00 0.00 0.00 3.41
1482 1580 3.064207 TCGCATGTGGAAAACTGTAGAC 58.936 45.455 6.39 0.00 0.00 2.59
1483 1581 3.394674 TCGCATGTGGAAAACTGTAGA 57.605 42.857 6.39 0.00 0.00 2.59
1484 1582 4.481930 TTTCGCATGTGGAAAACTGTAG 57.518 40.909 6.39 0.00 30.91 2.74
1485 1583 4.902443 TTTTCGCATGTGGAAAACTGTA 57.098 36.364 10.35 0.00 38.18 2.74
1486 1584 3.791973 TTTTCGCATGTGGAAAACTGT 57.208 38.095 10.35 0.00 38.18 3.55
1514 1612 9.634163 CCCAACAATAACAACCTTATTTCTAAC 57.366 33.333 0.00 0.00 0.00 2.34
1515 1613 8.308207 GCCCAACAATAACAACCTTATTTCTAA 58.692 33.333 0.00 0.00 0.00 2.10
1516 1614 7.093684 GGCCCAACAATAACAACCTTATTTCTA 60.094 37.037 0.00 0.00 0.00 2.10
1517 1615 6.295632 GGCCCAACAATAACAACCTTATTTCT 60.296 38.462 0.00 0.00 0.00 2.52
1518 1616 5.872617 GGCCCAACAATAACAACCTTATTTC 59.127 40.000 0.00 0.00 0.00 2.17
1519 1617 5.546110 AGGCCCAACAATAACAACCTTATTT 59.454 36.000 0.00 0.00 0.00 1.40
1520 1618 5.090845 AGGCCCAACAATAACAACCTTATT 58.909 37.500 0.00 0.00 0.00 1.40
1521 1619 4.683643 AGGCCCAACAATAACAACCTTAT 58.316 39.130 0.00 0.00 0.00 1.73
1522 1620 4.083565 GAGGCCCAACAATAACAACCTTA 58.916 43.478 0.00 0.00 0.00 2.69
1523 1621 2.897326 GAGGCCCAACAATAACAACCTT 59.103 45.455 0.00 0.00 0.00 3.50
1524 1622 2.525368 GAGGCCCAACAATAACAACCT 58.475 47.619 0.00 0.00 0.00 3.50
1525 1623 1.201414 CGAGGCCCAACAATAACAACC 59.799 52.381 0.00 0.00 0.00 3.77
1526 1624 2.095415 GTCGAGGCCCAACAATAACAAC 60.095 50.000 0.00 0.00 0.00 3.32
1527 1625 2.156098 GTCGAGGCCCAACAATAACAA 58.844 47.619 0.00 0.00 0.00 2.83
1528 1626 1.072489 TGTCGAGGCCCAACAATAACA 59.928 47.619 0.00 0.00 0.00 2.41
1529 1627 1.737793 CTGTCGAGGCCCAACAATAAC 59.262 52.381 0.00 0.00 0.00 1.89
1530 1628 1.948611 GCTGTCGAGGCCCAACAATAA 60.949 52.381 0.00 0.00 0.00 1.40
1531 1629 0.392461 GCTGTCGAGGCCCAACAATA 60.392 55.000 0.00 0.00 0.00 1.90
1532 1630 1.675641 GCTGTCGAGGCCCAACAAT 60.676 57.895 0.00 0.00 0.00 2.71
1533 1631 2.281484 GCTGTCGAGGCCCAACAA 60.281 61.111 0.00 0.00 0.00 2.83
1534 1632 3.113514 TTGCTGTCGAGGCCCAACA 62.114 57.895 0.00 0.00 0.00 3.33
1535 1633 2.281484 TTGCTGTCGAGGCCCAAC 60.281 61.111 0.00 0.00 0.00 3.77
1536 1634 1.841302 ATCTTGCTGTCGAGGCCCAA 61.841 55.000 0.00 0.00 0.00 4.12
1537 1635 2.293318 ATCTTGCTGTCGAGGCCCA 61.293 57.895 0.00 0.00 0.00 5.36
1538 1636 1.817099 CATCTTGCTGTCGAGGCCC 60.817 63.158 0.00 0.00 0.00 5.80
1539 1637 1.078848 ACATCTTGCTGTCGAGGCC 60.079 57.895 0.00 0.00 0.00 5.19
1540 1638 0.390340 TCACATCTTGCTGTCGAGGC 60.390 55.000 3.64 3.64 0.00 4.70
1541 1639 1.931841 CATCACATCTTGCTGTCGAGG 59.068 52.381 0.00 0.00 0.00 4.63
1542 1640 1.326852 GCATCACATCTTGCTGTCGAG 59.673 52.381 0.00 0.00 35.95 4.04
1543 1641 1.338011 TGCATCACATCTTGCTGTCGA 60.338 47.619 0.00 0.00 39.60 4.20
1544 1642 1.081094 TGCATCACATCTTGCTGTCG 58.919 50.000 0.00 0.00 39.60 4.35
1545 1643 1.808343 TGTGCATCACATCTTGCTGTC 59.192 47.619 0.00 0.00 39.62 3.51
1546 1644 1.900245 TGTGCATCACATCTTGCTGT 58.100 45.000 0.00 0.00 39.62 4.40
1547 1645 3.291809 TTTGTGCATCACATCTTGCTG 57.708 42.857 0.11 0.00 44.16 4.41
1548 1646 4.021807 TGAATTTGTGCATCACATCTTGCT 60.022 37.500 0.11 0.00 44.16 3.91
1549 1647 4.090930 GTGAATTTGTGCATCACATCTTGC 59.909 41.667 11.58 0.00 44.16 4.01
1550 1648 4.624024 GGTGAATTTGTGCATCACATCTTG 59.376 41.667 16.85 0.00 44.16 3.02
1551 1649 4.616604 CGGTGAATTTGTGCATCACATCTT 60.617 41.667 16.85 0.00 44.16 2.40
1552 1650 3.119743 CGGTGAATTTGTGCATCACATCT 60.120 43.478 16.85 0.00 44.16 2.90
1553 1651 3.119884 TCGGTGAATTTGTGCATCACATC 60.120 43.478 16.85 2.93 44.16 3.06
1554 1652 2.819019 TCGGTGAATTTGTGCATCACAT 59.181 40.909 16.85 1.83 44.16 3.21
1555 1653 2.031245 GTCGGTGAATTTGTGCATCACA 60.031 45.455 16.85 0.00 44.05 3.58
1556 1654 2.031245 TGTCGGTGAATTTGTGCATCAC 60.031 45.455 8.57 8.57 42.08 3.06
1557 1655 2.031245 GTGTCGGTGAATTTGTGCATCA 60.031 45.455 0.00 0.00 0.00 3.07
1558 1656 2.031245 TGTGTCGGTGAATTTGTGCATC 60.031 45.455 0.00 0.00 0.00 3.91
1559 1657 1.952990 TGTGTCGGTGAATTTGTGCAT 59.047 42.857 0.00 0.00 0.00 3.96
1560 1658 1.383523 TGTGTCGGTGAATTTGTGCA 58.616 45.000 0.00 0.00 0.00 4.57
1561 1659 2.116366 GTTGTGTCGGTGAATTTGTGC 58.884 47.619 0.00 0.00 0.00 4.57
1562 1660 3.105203 GTGTTGTGTCGGTGAATTTGTG 58.895 45.455 0.00 0.00 0.00 3.33
1563 1661 2.750166 TGTGTTGTGTCGGTGAATTTGT 59.250 40.909 0.00 0.00 0.00 2.83
1564 1662 3.412981 TGTGTTGTGTCGGTGAATTTG 57.587 42.857 0.00 0.00 0.00 2.32
1565 1663 5.698832 CATATGTGTTGTGTCGGTGAATTT 58.301 37.500 0.00 0.00 0.00 1.82
1566 1664 4.379394 GCATATGTGTTGTGTCGGTGAATT 60.379 41.667 4.29 0.00 0.00 2.17
1567 1665 3.126858 GCATATGTGTTGTGTCGGTGAAT 59.873 43.478 4.29 0.00 0.00 2.57
1568 1666 2.482336 GCATATGTGTTGTGTCGGTGAA 59.518 45.455 4.29 0.00 0.00 3.18
1569 1667 2.073056 GCATATGTGTTGTGTCGGTGA 58.927 47.619 4.29 0.00 0.00 4.02
1570 1668 1.803555 TGCATATGTGTTGTGTCGGTG 59.196 47.619 4.29 0.00 0.00 4.94
1571 1669 2.177394 TGCATATGTGTTGTGTCGGT 57.823 45.000 4.29 0.00 0.00 4.69
1572 1670 3.233578 GTTTGCATATGTGTTGTGTCGG 58.766 45.455 4.29 0.00 0.00 4.79
1573 1671 3.882982 TGTTTGCATATGTGTTGTGTCG 58.117 40.909 4.29 0.00 0.00 4.35
1574 1672 4.444056 GGTTGTTTGCATATGTGTTGTGTC 59.556 41.667 4.29 0.00 0.00 3.67
1575 1673 4.367450 GGTTGTTTGCATATGTGTTGTGT 58.633 39.130 4.29 0.00 0.00 3.72
1576 1674 3.740321 GGGTTGTTTGCATATGTGTTGTG 59.260 43.478 4.29 0.00 0.00 3.33
1577 1675 3.640967 AGGGTTGTTTGCATATGTGTTGT 59.359 39.130 4.29 0.00 0.00 3.32
1578 1676 4.022068 AGAGGGTTGTTTGCATATGTGTTG 60.022 41.667 4.29 0.00 0.00 3.33
1579 1677 4.151883 AGAGGGTTGTTTGCATATGTGTT 58.848 39.130 4.29 0.00 0.00 3.32
1580 1678 3.766545 AGAGGGTTGTTTGCATATGTGT 58.233 40.909 4.29 0.00 0.00 3.72
1581 1679 4.218200 TGAAGAGGGTTGTTTGCATATGTG 59.782 41.667 4.29 0.00 0.00 3.21
1582 1680 4.218417 GTGAAGAGGGTTGTTTGCATATGT 59.782 41.667 4.29 0.00 0.00 2.29
1583 1681 4.460382 AGTGAAGAGGGTTGTTTGCATATG 59.540 41.667 0.00 0.00 0.00 1.78
1584 1682 4.666512 AGTGAAGAGGGTTGTTTGCATAT 58.333 39.130 0.00 0.00 0.00 1.78
1585 1683 4.098914 AGTGAAGAGGGTTGTTTGCATA 57.901 40.909 0.00 0.00 0.00 3.14
1586 1684 2.949447 AGTGAAGAGGGTTGTTTGCAT 58.051 42.857 0.00 0.00 0.00 3.96
1587 1685 2.435372 AGTGAAGAGGGTTGTTTGCA 57.565 45.000 0.00 0.00 0.00 4.08
1588 1686 3.801114 AAAGTGAAGAGGGTTGTTTGC 57.199 42.857 0.00 0.00 0.00 3.68
1589 1687 6.451064 ACTAAAAGTGAAGAGGGTTGTTTG 57.549 37.500 0.00 0.00 0.00 2.93
1607 1705 8.754991 TGAACCTAACCTCAAAATTCACTAAA 57.245 30.769 0.00 0.00 0.00 1.85
1608 1706 8.626526 GTTGAACCTAACCTCAAAATTCACTAA 58.373 33.333 0.00 0.00 33.52 2.24
1624 1722 6.177310 TGCTTACTAGTTGGTTGAACCTAA 57.823 37.500 16.33 5.58 39.58 2.69
1628 1726 4.271776 ACGTTGCTTACTAGTTGGTTGAAC 59.728 41.667 0.00 0.00 34.40 3.18
1638 1736 5.227908 TCTGAAAGGAACGTTGCTTACTAG 58.772 41.667 31.37 26.26 37.91 2.57
1643 1741 3.945285 TCTTTCTGAAAGGAACGTTGCTT 59.055 39.130 26.94 26.94 40.77 3.91
1710 1808 6.825284 TGTGCATGTTGTTTGAGTTTATTG 57.175 33.333 0.00 0.00 0.00 1.90
1755 1853 6.599356 ACAGTAGTTTTTGAGGTGGTTTTT 57.401 33.333 0.00 0.00 0.00 1.94
1756 1854 6.014925 ACAACAGTAGTTTTTGAGGTGGTTTT 60.015 34.615 0.00 0.00 35.28 2.43
1757 1855 5.479027 ACAACAGTAGTTTTTGAGGTGGTTT 59.521 36.000 0.00 0.00 35.28 3.27
1758 1856 5.014202 ACAACAGTAGTTTTTGAGGTGGTT 58.986 37.500 0.00 0.00 35.28 3.67
1759 1857 4.398044 CACAACAGTAGTTTTTGAGGTGGT 59.602 41.667 0.00 0.00 35.28 4.16
1760 1858 4.202010 CCACAACAGTAGTTTTTGAGGTGG 60.202 45.833 0.00 0.00 35.28 4.61
1761 1859 4.733523 GCCACAACAGTAGTTTTTGAGGTG 60.734 45.833 6.87 0.00 35.28 4.00
1762 1860 3.380320 GCCACAACAGTAGTTTTTGAGGT 59.620 43.478 6.87 0.00 35.28 3.85
1763 1861 3.243401 GGCCACAACAGTAGTTTTTGAGG 60.243 47.826 0.00 0.00 35.28 3.86
1764 1862 3.243401 GGGCCACAACAGTAGTTTTTGAG 60.243 47.826 4.39 0.00 35.28 3.02
1765 1863 2.691011 GGGCCACAACAGTAGTTTTTGA 59.309 45.455 4.39 0.00 35.28 2.69
1766 1864 2.428890 TGGGCCACAACAGTAGTTTTTG 59.571 45.455 0.00 0.00 35.28 2.44
1773 1871 4.889807 GTGTGGGCCACAACAGTA 57.110 55.556 39.03 14.79 46.28 2.74
1785 1883 3.502211 GTCCTAATGGTGAAGTTGTGTGG 59.498 47.826 0.00 0.00 34.23 4.17
1807 1905 2.093973 AGAGATGCCTTTGTACTCACCG 60.094 50.000 0.00 0.00 0.00 4.94
1814 1912 3.961408 GAGGTCCTAGAGATGCCTTTGTA 59.039 47.826 0.00 0.00 0.00 2.41
1821 1919 3.640967 ACATTGAGAGGTCCTAGAGATGC 59.359 47.826 0.00 0.00 0.00 3.91
1923 2194 6.277605 AGCGGTTTAAAAGTAGTTTGCAAAT 58.722 32.000 16.21 7.20 0.00 2.32
1934 2205 7.760340 TGTTGTTTGATTTAGCGGTTTAAAAGT 59.240 29.630 0.00 0.00 0.00 2.66
1988 2259 4.536295 ATTTAGGGGATGTCGGGAATTT 57.464 40.909 0.00 0.00 0.00 1.82
2011 2282 3.886505 ACAATGTCGGGTCAAGCTAAAAA 59.113 39.130 0.00 0.00 0.00 1.94
2020 2291 1.686355 AAGCAAACAATGTCGGGTCA 58.314 45.000 0.00 0.00 0.00 4.02
2021 2292 2.095415 GGTAAGCAAACAATGTCGGGTC 60.095 50.000 0.00 0.00 0.00 4.46
2061 2332 7.215568 CGTTGTAGTTTCAACACAAAGTAGTTG 59.784 37.037 9.60 0.00 45.28 3.16
2147 2420 6.803642 ACTTTAGGTATCTCGATGTGGTTAC 58.196 40.000 0.00 0.00 0.00 2.50
2160 2433 5.712004 GGATCGCTCCTTACTTTAGGTATC 58.288 45.833 0.00 0.00 38.65 2.24
2177 2451 3.222603 ACCCCAAATTTGATAGGATCGC 58.777 45.455 19.86 0.00 0.00 4.58
2216 2496 5.381757 AGACAATGTTTAAGCTGGTGGTTA 58.618 37.500 0.00 0.00 35.36 2.85
2246 2526 2.622942 GTTCTGTCCAGATTTGCCACAA 59.377 45.455 0.00 0.00 37.29 3.33
2249 2529 1.425066 AGGTTCTGTCCAGATTTGCCA 59.575 47.619 0.00 0.00 37.29 4.92
2283 2590 4.386867 ACACAAACGTTGAGAGAGAGAA 57.613 40.909 0.00 0.00 0.00 2.87
2296 2603 4.597079 AGCACACAATAAGAACACAAACG 58.403 39.130 0.00 0.00 0.00 3.60
2298 2605 5.822519 AGAGAGCACACAATAAGAACACAAA 59.177 36.000 0.00 0.00 0.00 2.83
2351 2673 1.272760 ACCCTAGTCACTCCACTCAGG 60.273 57.143 0.00 0.00 39.47 3.86
2384 2709 5.466819 TGTTAGTGATTCGTAGTGAAGTGG 58.533 41.667 0.00 0.00 40.65 4.00
2395 2721 6.037062 TGCATCCAACTATTGTTAGTGATTCG 59.963 38.462 0.00 0.00 38.69 3.34
2399 2725 7.537715 CATTTGCATCCAACTATTGTTAGTGA 58.462 34.615 0.00 0.00 38.69 3.41


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

AutoCloner maintained by Alex Coulton.