Multiple sequence alignment - TraesCS3D01G354900

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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 TraesCS3D01G354900 chr3D 100.000 3760 0 0 1 3760 465508059 465511818 0.000000e+00 6944
1 TraesCS3D01G354900 chr3D 95.211 522 24 1 1 522 590697299 590697819 0.000000e+00 824
2 TraesCS3D01G354900 chr3D 77.377 999 181 33 2017 2984 464808963 464807979 6.150000e-153 551
3 TraesCS3D01G354900 chr3D 100.000 203 0 0 4009 4211 465512067 465512269 3.970000e-100 375
4 TraesCS3D01G354900 chr3D 81.184 473 73 14 1449 1909 465027713 465027245 2.390000e-97 366
5 TraesCS3D01G354900 chr3D 84.375 256 33 5 1446 1696 464809978 464809725 1.170000e-60 244
6 TraesCS3D01G354900 chr3D 88.421 95 11 0 1217 1311 464810262 464810168 9.570000e-22 115
7 TraesCS3D01G354900 chr3A 93.503 3017 129 28 672 3636 608749794 608752795 0.000000e+00 4423
8 TraesCS3D01G354900 chr3A 75.627 997 202 28 2017 2984 608195761 608194777 1.380000e-124 457
9 TraesCS3D01G354900 chr3A 75.531 989 203 26 2024 2982 608347365 608346386 2.310000e-122 449
10 TraesCS3D01G354900 chr3A 90.272 257 23 2 1449 1704 608347931 608347676 6.750000e-88 335
11 TraesCS3D01G354900 chr3B 92.165 1940 90 27 1745 3634 618870372 618872299 0.000000e+00 2684
12 TraesCS3D01G354900 chr3B 92.681 1093 58 14 668 1748 618869004 618870086 0.000000e+00 1555
13 TraesCS3D01G354900 chr3B 76.052 998 196 30 2017 2984 618155769 618154785 2.950000e-131 479
14 TraesCS3D01G354900 chr3B 90.551 254 22 2 1449 1701 618442741 618442489 6.750000e-88 335
15 TraesCS3D01G354900 chr3B 84.375 256 33 5 1446 1696 618156816 618156563 1.170000e-60 244
16 TraesCS3D01G354900 chr3B 88.350 206 20 4 4009 4211 618872338 618872542 1.170000e-60 244
17 TraesCS3D01G354900 chr3B 87.368 95 12 0 1217 1311 618157106 618157012 4.450000e-20 110
18 TraesCS3D01G354900 chr7D 95.420 524 21 3 1 522 40617736 40617214 0.000000e+00 832
19 TraesCS3D01G354900 chr7D 74.197 996 206 35 2024 2983 149085144 149084164 6.650000e-98 368
20 TraesCS3D01G354900 chr7D 73.647 998 210 35 2024 2984 149181893 149182874 1.880000e-88 337
21 TraesCS3D01G354900 chr7D 85.141 249 33 4 1449 1695 149181430 149181676 6.990000e-63 252
22 TraesCS3D01G354900 chr7D 84.127 189 21 8 4018 4202 202059755 202059572 1.560000e-39 174
23 TraesCS3D01G354900 chr2D 95.385 520 22 2 1 520 384748926 384748409 0.000000e+00 826
24 TraesCS3D01G354900 chr2D 95.192 520 22 3 1 520 154199801 154200317 0.000000e+00 819
25 TraesCS3D01G354900 chr6D 95.211 522 23 2 1 522 107938222 107938741 0.000000e+00 824
26 TraesCS3D01G354900 chr6D 95.202 521 23 2 2 522 458332342 458332860 0.000000e+00 822
27 TraesCS3D01G354900 chr6D 93.913 115 6 1 3647 3760 447117 447231 5.600000e-39 172
28 TraesCS3D01G354900 chr1D 82.250 969 156 12 2024 2983 379911999 379911038 0.000000e+00 822
29 TraesCS3D01G354900 chr1D 82.323 198 26 6 4023 4211 28569573 28569376 3.370000e-36 163
30 TraesCS3D01G354900 chr1D 94.175 103 6 0 1208 1310 381019033 381019135 1.570000e-34 158
31 TraesCS3D01G354900 chr1D 93.243 74 4 1 3688 3760 41295050 41295123 1.600000e-19 108
32 TraesCS3D01G354900 chr5D 95.192 520 24 1 1 520 80439585 80439067 0.000000e+00 821
33 TraesCS3D01G354900 chr4D 95.029 523 22 3 1 523 487284799 487284281 0.000000e+00 819
34 TraesCS3D01G354900 chr1A 79.513 1191 204 31 2024 3196 480935160 480933992 0.000000e+00 811
35 TraesCS3D01G354900 chr1A 94.828 522 23 4 1 520 584504121 584504640 0.000000e+00 811
36 TraesCS3D01G354900 chr1A 95.146 103 5 0 1208 1310 481673981 481674083 3.370000e-36 163
37 TraesCS3D01G354900 chr1A 85.612 139 18 2 1226 1363 480935768 480935631 1.220000e-30 145
38 TraesCS3D01G354900 chr1B 81.959 970 157 13 2024 2983 509902338 509901377 0.000000e+00 806
39 TraesCS3D01G354900 chr1B 93.204 103 7 0 1208 1310 510808816 510808918 7.290000e-33 152
40 TraesCS3D01G354900 chr1B 83.893 149 22 2 1216 1363 509902963 509902816 1.580000e-29 141
41 TraesCS3D01G354900 chr7B 85.897 234 29 4 1449 1680 111942603 111942834 3.250000e-61 246
42 TraesCS3D01G354900 chr5A 91.346 104 7 2 3638 3739 359038022 359037919 1.580000e-29 141


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 TraesCS3D01G354900 chr3D 465508059 465512269 4210 False 3659.500000 6944 100.000000 1 4211 2 chr3D.!!$F2 4210
1 TraesCS3D01G354900 chr3D 590697299 590697819 520 False 824.000000 824 95.211000 1 522 1 chr3D.!!$F1 521
2 TraesCS3D01G354900 chr3D 464807979 464810262 2283 True 303.333333 551 83.391000 1217 2984 3 chr3D.!!$R2 1767
3 TraesCS3D01G354900 chr3A 608749794 608752795 3001 False 4423.000000 4423 93.503000 672 3636 1 chr3A.!!$F1 2964
4 TraesCS3D01G354900 chr3A 608194777 608195761 984 True 457.000000 457 75.627000 2017 2984 1 chr3A.!!$R1 967
5 TraesCS3D01G354900 chr3A 608346386 608347931 1545 True 392.000000 449 82.901500 1449 2982 2 chr3A.!!$R2 1533
6 TraesCS3D01G354900 chr3B 618869004 618872542 3538 False 1494.333333 2684 91.065333 668 4211 3 chr3B.!!$F1 3543
7 TraesCS3D01G354900 chr3B 618154785 618157106 2321 True 277.666667 479 82.598333 1217 2984 3 chr3B.!!$R2 1767
8 TraesCS3D01G354900 chr7D 40617214 40617736 522 True 832.000000 832 95.420000 1 522 1 chr7D.!!$R1 521
9 TraesCS3D01G354900 chr7D 149084164 149085144 980 True 368.000000 368 74.197000 2024 2983 1 chr7D.!!$R2 959
10 TraesCS3D01G354900 chr7D 149181430 149182874 1444 False 294.500000 337 79.394000 1449 2984 2 chr7D.!!$F1 1535
11 TraesCS3D01G354900 chr2D 384748409 384748926 517 True 826.000000 826 95.385000 1 520 1 chr2D.!!$R1 519
12 TraesCS3D01G354900 chr2D 154199801 154200317 516 False 819.000000 819 95.192000 1 520 1 chr2D.!!$F1 519
13 TraesCS3D01G354900 chr6D 107938222 107938741 519 False 824.000000 824 95.211000 1 522 1 chr6D.!!$F2 521
14 TraesCS3D01G354900 chr6D 458332342 458332860 518 False 822.000000 822 95.202000 2 522 1 chr6D.!!$F3 520
15 TraesCS3D01G354900 chr1D 379911038 379911999 961 True 822.000000 822 82.250000 2024 2983 1 chr1D.!!$R2 959
16 TraesCS3D01G354900 chr5D 80439067 80439585 518 True 821.000000 821 95.192000 1 520 1 chr5D.!!$R1 519
17 TraesCS3D01G354900 chr4D 487284281 487284799 518 True 819.000000 819 95.029000 1 523 1 chr4D.!!$R1 522
18 TraesCS3D01G354900 chr1A 584504121 584504640 519 False 811.000000 811 94.828000 1 520 1 chr1A.!!$F2 519
19 TraesCS3D01G354900 chr1A 480933992 480935768 1776 True 478.000000 811 82.562500 1226 3196 2 chr1A.!!$R1 1970
20 TraesCS3D01G354900 chr1B 509901377 509902963 1586 True 473.500000 806 82.926000 1216 2983 2 chr1B.!!$R1 1767

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
664 670 0.035439 AGGTCCAAGCACATAACGGG 60.035 55.0 0.0 0.0 0.00 5.28 F
2017 2723 0.168788 ATGTCGGCAACTGAAATGCG 59.831 50.0 0.0 0.0 44.75 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 3001 0.104855 GATGAGCCGGAGCATGTACA 59.895 55.0 5.05 0.0 43.56 2.90 R
3329 4336 0.107214 TCCCAGGAAATCGGCACATC 60.107 55.0 0.00 0.0 0.00 3.06 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 1.141881 CATACAAGACGAGCGCCCT 59.858 57.895 2.29 0.00 0.00 5.19
343 348 8.828688 TTCATTTCACAATATGTTTGAATGCA 57.171 26.923 0.00 0.00 29.15 3.96
404 410 3.083848 ATATGGGTCGGCGCGTTGA 62.084 57.895 8.43 2.59 0.00 3.18
476 482 1.208535 ACCCAATCGGACAATAAGCGA 59.791 47.619 0.00 0.00 34.64 4.93
496 502 0.388391 ACGAAATCGCCGTCCGTTTA 60.388 50.000 2.15 0.00 44.43 2.01
523 529 1.439679 CCGTTGGAGTTGCTCTAACC 58.560 55.000 16.07 0.00 45.09 2.85
524 530 1.068474 CGTTGGAGTTGCTCTAACCG 58.932 55.000 16.07 9.78 45.09 4.44
525 531 1.439679 GTTGGAGTTGCTCTAACCGG 58.560 55.000 12.41 0.00 43.15 5.28
526 532 1.001633 GTTGGAGTTGCTCTAACCGGA 59.998 52.381 9.46 0.00 43.15 5.14
527 533 1.568504 TGGAGTTGCTCTAACCGGAT 58.431 50.000 9.46 0.00 40.24 4.18
528 534 2.742348 TGGAGTTGCTCTAACCGGATA 58.258 47.619 9.46 0.00 40.24 2.59
529 535 2.693591 TGGAGTTGCTCTAACCGGATAG 59.306 50.000 9.46 11.24 40.24 2.08
530 536 2.694109 GGAGTTGCTCTAACCGGATAGT 59.306 50.000 17.38 0.00 40.24 2.12
531 537 3.243468 GGAGTTGCTCTAACCGGATAGTC 60.243 52.174 17.38 11.43 40.24 2.59
532 538 3.633065 GAGTTGCTCTAACCGGATAGTCT 59.367 47.826 17.38 9.70 40.24 3.24
533 539 3.381908 AGTTGCTCTAACCGGATAGTCTG 59.618 47.826 17.38 10.55 40.24 3.51
537 543 2.885894 CTCTAACCGGATAGTCTGGGTC 59.114 54.545 17.38 0.00 38.93 4.46
538 544 1.962100 CTAACCGGATAGTCTGGGTCC 59.038 57.143 9.46 0.00 38.93 4.46
539 545 0.690077 AACCGGATAGTCTGGGTCCC 60.690 60.000 9.46 0.00 38.93 4.46
540 546 1.075525 CCGGATAGTCTGGGTCCCA 60.076 63.158 11.11 11.11 39.28 4.37
541 547 5.855729 TAACCGGATAGTCTGGGTCCCAG 62.856 56.522 29.86 29.86 38.93 4.45
555 561 2.038863 TCCCAGTAGGATGGTGTTGT 57.961 50.000 0.00 0.00 40.93 3.32
556 562 2.344592 TCCCAGTAGGATGGTGTTGTT 58.655 47.619 0.00 0.00 40.93 2.83
557 563 2.039746 TCCCAGTAGGATGGTGTTGTTG 59.960 50.000 0.00 0.00 40.93 3.33
558 564 2.039746 CCCAGTAGGATGGTGTTGTTGA 59.960 50.000 0.00 0.00 38.81 3.18
559 565 3.338249 CCAGTAGGATGGTGTTGTTGAG 58.662 50.000 0.00 0.00 36.89 3.02
560 566 3.007940 CCAGTAGGATGGTGTTGTTGAGA 59.992 47.826 0.00 0.00 36.89 3.27
561 567 4.323792 CCAGTAGGATGGTGTTGTTGAGAT 60.324 45.833 0.00 0.00 36.89 2.75
562 568 4.872691 CAGTAGGATGGTGTTGTTGAGATC 59.127 45.833 0.00 0.00 0.00 2.75
563 569 4.532126 AGTAGGATGGTGTTGTTGAGATCA 59.468 41.667 0.00 0.00 0.00 2.92
564 570 4.581309 AGGATGGTGTTGTTGAGATCAT 57.419 40.909 0.00 0.00 0.00 2.45
565 571 4.927049 AGGATGGTGTTGTTGAGATCATT 58.073 39.130 0.00 0.00 0.00 2.57
566 572 4.703575 AGGATGGTGTTGTTGAGATCATTG 59.296 41.667 0.00 0.00 0.00 2.82
567 573 4.142315 GGATGGTGTTGTTGAGATCATTGG 60.142 45.833 0.00 0.00 0.00 3.16
568 574 2.557924 TGGTGTTGTTGAGATCATTGGC 59.442 45.455 0.00 0.00 0.00 4.52
569 575 2.414559 GGTGTTGTTGAGATCATTGGCG 60.415 50.000 0.00 0.00 0.00 5.69
570 576 1.811965 TGTTGTTGAGATCATTGGCGG 59.188 47.619 0.00 0.00 0.00 6.13
571 577 1.812571 GTTGTTGAGATCATTGGCGGT 59.187 47.619 0.00 0.00 0.00 5.68
572 578 3.006940 GTTGTTGAGATCATTGGCGGTA 58.993 45.455 0.00 0.00 0.00 4.02
573 579 3.342377 TGTTGAGATCATTGGCGGTAA 57.658 42.857 0.00 0.00 0.00 2.85
574 580 3.270027 TGTTGAGATCATTGGCGGTAAG 58.730 45.455 0.00 0.00 0.00 2.34
575 581 3.055458 TGTTGAGATCATTGGCGGTAAGA 60.055 43.478 0.00 0.00 0.00 2.10
576 582 3.904800 TGAGATCATTGGCGGTAAGAA 57.095 42.857 0.00 0.00 0.00 2.52
577 583 3.797039 TGAGATCATTGGCGGTAAGAAG 58.203 45.455 0.00 0.00 0.00 2.85
578 584 3.450817 TGAGATCATTGGCGGTAAGAAGA 59.549 43.478 0.00 0.00 0.00 2.87
579 585 4.054671 GAGATCATTGGCGGTAAGAAGAG 58.945 47.826 0.00 0.00 0.00 2.85
580 586 2.691409 TCATTGGCGGTAAGAAGAGG 57.309 50.000 0.00 0.00 0.00 3.69
581 587 2.184533 TCATTGGCGGTAAGAAGAGGA 58.815 47.619 0.00 0.00 0.00 3.71
582 588 2.569853 TCATTGGCGGTAAGAAGAGGAA 59.430 45.455 0.00 0.00 0.00 3.36
583 589 2.762535 TTGGCGGTAAGAAGAGGAAG 57.237 50.000 0.00 0.00 0.00 3.46
584 590 0.249398 TGGCGGTAAGAAGAGGAAGC 59.751 55.000 0.00 0.00 0.00 3.86
585 591 0.249398 GGCGGTAAGAAGAGGAAGCA 59.751 55.000 0.00 0.00 0.00 3.91
586 592 1.134371 GGCGGTAAGAAGAGGAAGCAT 60.134 52.381 0.00 0.00 0.00 3.79
587 593 2.205911 GCGGTAAGAAGAGGAAGCATC 58.794 52.381 0.00 0.00 0.00 3.91
588 594 2.159028 GCGGTAAGAAGAGGAAGCATCT 60.159 50.000 0.00 0.00 0.00 2.90
589 595 3.712187 CGGTAAGAAGAGGAAGCATCTC 58.288 50.000 0.00 0.00 0.00 2.75
590 596 3.491792 CGGTAAGAAGAGGAAGCATCTCC 60.492 52.174 0.00 0.00 35.51 3.71
591 597 3.181459 GGTAAGAAGAGGAAGCATCTCCC 60.181 52.174 0.00 0.00 35.95 4.30
592 598 2.566708 AGAAGAGGAAGCATCTCCCT 57.433 50.000 0.00 0.00 35.95 4.20
593 599 2.844369 AGAAGAGGAAGCATCTCCCTT 58.156 47.619 0.00 0.00 35.95 3.95
594 600 2.504996 AGAAGAGGAAGCATCTCCCTTG 59.495 50.000 7.49 0.00 35.95 3.61
595 601 0.545646 AGAGGAAGCATCTCCCTTGC 59.454 55.000 0.00 0.00 40.45 4.01
596 602 0.254178 GAGGAAGCATCTCCCTTGCA 59.746 55.000 0.00 0.00 42.62 4.08
597 603 0.700564 AGGAAGCATCTCCCTTGCAA 59.299 50.000 0.00 0.00 42.62 4.08
598 604 1.076024 AGGAAGCATCTCCCTTGCAAA 59.924 47.619 0.00 0.00 42.62 3.68
599 605 1.895131 GGAAGCATCTCCCTTGCAAAA 59.105 47.619 0.00 0.00 42.62 2.44
600 606 2.299867 GGAAGCATCTCCCTTGCAAAAA 59.700 45.455 0.00 0.00 42.62 1.94
601 607 3.320626 GAAGCATCTCCCTTGCAAAAAC 58.679 45.455 0.00 0.00 42.62 2.43
602 608 2.601905 AGCATCTCCCTTGCAAAAACT 58.398 42.857 0.00 0.00 42.62 2.66
603 609 2.967887 AGCATCTCCCTTGCAAAAACTT 59.032 40.909 0.00 0.00 42.62 2.66
604 610 4.151883 AGCATCTCCCTTGCAAAAACTTA 58.848 39.130 0.00 0.00 42.62 2.24
605 611 4.588528 AGCATCTCCCTTGCAAAAACTTAA 59.411 37.500 0.00 0.00 42.62 1.85
606 612 5.246883 AGCATCTCCCTTGCAAAAACTTAAT 59.753 36.000 0.00 0.00 42.62 1.40
607 613 6.437162 AGCATCTCCCTTGCAAAAACTTAATA 59.563 34.615 0.00 0.00 42.62 0.98
608 614 6.531594 GCATCTCCCTTGCAAAAACTTAATAC 59.468 38.462 0.00 0.00 39.90 1.89
609 615 7.577616 GCATCTCCCTTGCAAAAACTTAATACT 60.578 37.037 0.00 0.00 39.90 2.12
610 616 8.956426 CATCTCCCTTGCAAAAACTTAATACTA 58.044 33.333 0.00 0.00 0.00 1.82
611 617 8.561738 TCTCCCTTGCAAAAACTTAATACTAG 57.438 34.615 0.00 0.00 0.00 2.57
612 618 7.120726 TCTCCCTTGCAAAAACTTAATACTAGC 59.879 37.037 0.00 0.00 0.00 3.42
613 619 6.152154 TCCCTTGCAAAAACTTAATACTAGCC 59.848 38.462 0.00 0.00 0.00 3.93
614 620 6.152831 CCCTTGCAAAAACTTAATACTAGCCT 59.847 38.462 0.00 0.00 0.00 4.58
615 621 7.338449 CCCTTGCAAAAACTTAATACTAGCCTA 59.662 37.037 0.00 0.00 0.00 3.93
616 622 8.182227 CCTTGCAAAAACTTAATACTAGCCTAC 58.818 37.037 0.00 0.00 0.00 3.18
617 623 7.298507 TGCAAAAACTTAATACTAGCCTACG 57.701 36.000 0.00 0.00 0.00 3.51
618 624 6.875195 TGCAAAAACTTAATACTAGCCTACGT 59.125 34.615 0.00 0.00 0.00 3.57
619 625 7.148540 TGCAAAAACTTAATACTAGCCTACGTG 60.149 37.037 0.00 0.00 0.00 4.49
620 626 7.675637 GCAAAAACTTAATACTAGCCTACGTGG 60.676 40.741 0.00 0.00 39.35 4.94
629 635 4.192000 CCTACGTGGCAAGCTCAG 57.808 61.111 0.00 0.00 0.00 3.35
630 636 1.293498 CCTACGTGGCAAGCTCAGT 59.707 57.895 0.00 0.00 0.00 3.41
631 637 0.320771 CCTACGTGGCAAGCTCAGTT 60.321 55.000 0.00 0.00 0.00 3.16
632 638 1.067142 CCTACGTGGCAAGCTCAGTTA 60.067 52.381 0.00 0.00 0.00 2.24
633 639 2.263077 CTACGTGGCAAGCTCAGTTAG 58.737 52.381 0.00 0.00 0.00 2.34
647 653 5.998454 CTCAGTTAGCATTGGAATGTAGG 57.002 43.478 1.49 0.00 38.65 3.18
648 654 5.431765 CTCAGTTAGCATTGGAATGTAGGT 58.568 41.667 1.49 0.00 38.65 3.08
649 655 5.428253 TCAGTTAGCATTGGAATGTAGGTC 58.572 41.667 1.49 0.00 38.65 3.85
650 656 4.576463 CAGTTAGCATTGGAATGTAGGTCC 59.424 45.833 1.49 0.00 38.65 4.46
651 657 4.227300 AGTTAGCATTGGAATGTAGGTCCA 59.773 41.667 1.49 0.00 43.57 4.02
656 662 2.489938 TGGAATGTAGGTCCAAGCAC 57.510 50.000 0.00 0.00 42.29 4.40
657 663 1.702401 TGGAATGTAGGTCCAAGCACA 59.298 47.619 0.00 0.00 42.29 4.57
658 664 2.308570 TGGAATGTAGGTCCAAGCACAT 59.691 45.455 0.00 0.00 42.29 3.21
659 665 3.521531 TGGAATGTAGGTCCAAGCACATA 59.478 43.478 0.00 0.00 42.29 2.29
660 666 4.018870 TGGAATGTAGGTCCAAGCACATAA 60.019 41.667 0.00 0.00 42.29 1.90
661 667 4.335594 GGAATGTAGGTCCAAGCACATAAC 59.664 45.833 0.00 0.00 35.05 1.89
662 668 2.967362 TGTAGGTCCAAGCACATAACG 58.033 47.619 0.00 0.00 0.00 3.18
663 669 2.277084 GTAGGTCCAAGCACATAACGG 58.723 52.381 0.00 0.00 0.00 4.44
664 670 0.035439 AGGTCCAAGCACATAACGGG 60.035 55.000 0.00 0.00 0.00 5.28
665 671 1.654023 GGTCCAAGCACATAACGGGC 61.654 60.000 0.00 0.00 0.00 6.13
666 672 0.958382 GTCCAAGCACATAACGGGCA 60.958 55.000 0.00 0.00 0.00 5.36
667 673 0.250945 TCCAAGCACATAACGGGCAA 60.251 50.000 0.00 0.00 0.00 4.52
668 674 0.817013 CCAAGCACATAACGGGCAAT 59.183 50.000 0.00 0.00 0.00 3.56
669 675 1.204467 CCAAGCACATAACGGGCAATT 59.796 47.619 0.00 0.00 0.00 2.32
670 676 2.353605 CCAAGCACATAACGGGCAATTT 60.354 45.455 0.00 0.00 0.00 1.82
715 721 9.646427 GTGGCACAAATTAACTAAAATTGGATA 57.354 29.630 13.86 0.00 44.16 2.59
825 837 1.154225 CAACGGACGAGCAAATGGC 60.154 57.895 0.00 0.00 45.30 4.40
849 861 4.178540 CAATGCCAAGTTTTGCTATGGAG 58.821 43.478 0.00 0.00 34.82 3.86
861 873 0.392998 CTATGGAGCCGCACCAACTT 60.393 55.000 13.88 0.14 40.93 2.66
923 935 3.799753 GCACGAAGCGATCATGGT 58.200 55.556 0.00 0.00 0.00 3.55
1005 1017 0.603439 CCAAGCCACACAAAATGGGC 60.603 55.000 0.00 0.00 42.16 5.36
1014 1026 2.040544 CAAAATGGGCGCTCCTCGT 61.041 57.895 3.94 0.00 41.07 4.18
1140 1158 2.613730 ATGTACTCACGACGTCTGTG 57.386 50.000 24.81 24.81 38.70 3.66
1141 1159 1.302366 TGTACTCACGACGTCTGTGT 58.698 50.000 27.40 23.23 38.48 3.72
1142 1160 1.672363 TGTACTCACGACGTCTGTGTT 59.328 47.619 27.40 21.03 38.48 3.32
1143 1161 2.871633 TGTACTCACGACGTCTGTGTTA 59.128 45.455 27.40 20.36 38.48 2.41
1156 1174 6.153067 ACGTCTGTGTTATCTTCTTGAAGAG 58.847 40.000 16.66 3.92 31.48 2.85
1164 1182 6.641314 TGTTATCTTCTTGAAGAGTGAACGAC 59.359 38.462 16.66 8.78 31.48 4.34
1378 1450 0.526211 CTGGTGAGGAACGACATCGA 59.474 55.000 8.54 0.00 43.02 3.59
1420 1513 6.626623 CGGTGCTGTATGATCTATGATGATGA 60.627 42.308 0.00 0.00 0.00 2.92
1421 1514 7.273712 GGTGCTGTATGATCTATGATGATGAT 58.726 38.462 0.00 0.00 0.00 2.45
1437 1530 5.147330 TGATGATGTTTCAGTAACGGTCT 57.853 39.130 0.00 0.00 39.72 3.85
1439 1532 5.995282 TGATGATGTTTCAGTAACGGTCTTT 59.005 36.000 0.00 0.00 39.72 2.52
1440 1533 6.485313 TGATGATGTTTCAGTAACGGTCTTTT 59.515 34.615 0.00 0.00 39.72 2.27
1637 1730 1.532794 CTCTCCTCATCCTCCCCGG 60.533 68.421 0.00 0.00 0.00 5.73
1755 2198 0.465097 AGGGGATGCTCAATTGCTCG 60.465 55.000 0.00 0.00 0.00 5.03
1940 2400 3.949754 TCTCTCCCAAATCATCAACATGC 59.050 43.478 0.00 0.00 0.00 4.06
2017 2723 0.168788 ATGTCGGCAACTGAAATGCG 59.831 50.000 0.00 0.00 44.75 4.73
2334 3285 2.034532 TCCTCCAGTACGACGCCA 59.965 61.111 0.00 0.00 0.00 5.69
2366 3340 4.649705 TCCGCCCAGAACCTCCCA 62.650 66.667 0.00 0.00 0.00 4.37
3156 4162 4.077184 TGGATGGTGGACGACGGC 62.077 66.667 0.00 0.00 0.00 5.68
3207 4213 1.470979 CCGTCCGATCTTCCGAAATGT 60.471 52.381 0.00 0.00 0.00 2.71
3221 4227 3.551890 CCGAAATGTTGATGACTCCTACG 59.448 47.826 0.00 0.00 0.00 3.51
3302 4309 1.891150 ACGTACCAACTACCACTCCTG 59.109 52.381 0.00 0.00 0.00 3.86
3313 4320 1.646447 ACCACTCCTGGATCTGGACTA 59.354 52.381 21.67 0.00 40.55 2.59
3318 4325 5.545723 CCACTCCTGGATCTGGACTATTTAT 59.454 44.000 13.11 0.00 40.55 1.40
3325 4332 9.799106 CCTGGATCTGGACTATTTATTTTGTAT 57.201 33.333 0.00 0.00 0.00 2.29
3342 4349 5.984233 TTGTATACTGATGTGCCGATTTC 57.016 39.130 4.17 0.00 0.00 2.17
3354 4361 1.408822 GCCGATTTCCTGGGAAGTCAT 60.409 52.381 19.75 5.50 39.73 3.06
3417 4426 6.751157 TCCGAATAAGAAGTGACACTGTTTA 58.249 36.000 9.33 11.06 0.00 2.01
3437 4446 8.754991 TGTTTATTCTTGGACACCTTTTCTTA 57.245 30.769 0.00 0.00 0.00 2.10
3438 4447 8.626526 TGTTTATTCTTGGACACCTTTTCTTAC 58.373 33.333 0.00 0.00 0.00 2.34
3451 4460 4.202430 CCTTTTCTTACTGTGTACACCCCT 60.202 45.833 22.91 7.85 0.00 4.79
3470 4479 5.489637 ACCCCTTGTAATATGAGTTACCACA 59.510 40.000 0.00 0.00 34.43 4.17
3491 4500 7.565398 ACCACATCTTGATCACTTATAGTACCT 59.435 37.037 0.00 0.00 0.00 3.08
3505 4514 7.776969 ACTTATAGTACCTCAAACATCCGACTA 59.223 37.037 0.00 0.00 0.00 2.59
3636 4645 7.880195 AGACATGGATAATTAGATTGCTGGTAC 59.120 37.037 0.00 0.00 0.00 3.34
3639 4648 6.455647 TGGATAATTAGATTGCTGGTACGAG 58.544 40.000 0.00 0.00 0.00 4.18
3640 4649 5.869888 GGATAATTAGATTGCTGGTACGAGG 59.130 44.000 7.03 0.00 0.00 4.63
3641 4650 2.596904 TTAGATTGCTGGTACGAGGC 57.403 50.000 7.03 1.99 0.00 4.70
3644 4653 0.175760 GATTGCTGGTACGAGGCAGA 59.824 55.000 7.03 0.43 37.28 4.26
3645 4654 0.613260 ATTGCTGGTACGAGGCAGAA 59.387 50.000 7.03 0.00 37.28 3.02
3647 4656 0.394938 TGCTGGTACGAGGCAGAAAA 59.605 50.000 7.03 0.00 0.00 2.29
3648 4657 1.202710 TGCTGGTACGAGGCAGAAAAA 60.203 47.619 7.03 0.00 0.00 1.94
3665 4674 1.480789 AAAAATGTATCACCGGGGCC 58.519 50.000 6.32 0.00 0.00 5.80
3666 4675 0.333312 AAAATGTATCACCGGGGCCA 59.667 50.000 6.32 0.00 0.00 5.36
3667 4676 0.333312 AAATGTATCACCGGGGCCAA 59.667 50.000 6.32 0.00 0.00 4.52
3668 4677 0.106719 AATGTATCACCGGGGCCAAG 60.107 55.000 6.32 0.00 0.00 3.61
3669 4678 1.279025 ATGTATCACCGGGGCCAAGT 61.279 55.000 6.32 0.00 0.00 3.16
3671 4680 3.338275 TATCACCGGGGCCAAGTGC 62.338 63.158 17.72 0.00 40.16 4.40
3675 4684 4.974721 CCGGGGCCAAGTGCTGTT 62.975 66.667 4.39 0.00 40.92 3.16
3676 4685 2.033448 CGGGGCCAAGTGCTGTTA 59.967 61.111 4.39 0.00 40.92 2.41
3677 4686 1.602323 CGGGGCCAAGTGCTGTTAA 60.602 57.895 4.39 0.00 40.92 2.01
3678 4687 1.175983 CGGGGCCAAGTGCTGTTAAA 61.176 55.000 4.39 0.00 40.92 1.52
3679 4688 1.044611 GGGGCCAAGTGCTGTTAAAA 58.955 50.000 4.39 0.00 40.92 1.52
3680 4689 1.270094 GGGGCCAAGTGCTGTTAAAAC 60.270 52.381 4.39 0.00 40.92 2.43
3681 4690 1.686587 GGGCCAAGTGCTGTTAAAACT 59.313 47.619 4.39 0.00 40.92 2.66
3682 4691 2.545742 GGGCCAAGTGCTGTTAAAACTG 60.546 50.000 4.39 0.00 40.92 3.16
3683 4692 2.360801 GGCCAAGTGCTGTTAAAACTGA 59.639 45.455 0.00 0.00 40.92 3.41
3684 4693 3.005791 GGCCAAGTGCTGTTAAAACTGAT 59.994 43.478 0.00 0.00 40.92 2.90
3685 4694 4.501400 GGCCAAGTGCTGTTAAAACTGATT 60.501 41.667 0.00 0.00 40.92 2.57
3686 4695 5.278758 GGCCAAGTGCTGTTAAAACTGATTA 60.279 40.000 0.00 0.00 40.92 1.75
3687 4696 5.858581 GCCAAGTGCTGTTAAAACTGATTAG 59.141 40.000 4.15 0.00 36.87 1.73
3688 4697 6.381801 CCAAGTGCTGTTAAAACTGATTAGG 58.618 40.000 4.15 0.00 0.00 2.69
3689 4698 6.381801 CAAGTGCTGTTAAAACTGATTAGGG 58.618 40.000 4.15 0.00 0.00 3.53
3690 4699 5.876357 AGTGCTGTTAAAACTGATTAGGGA 58.124 37.500 4.15 0.00 0.00 4.20
3691 4700 5.940470 AGTGCTGTTAAAACTGATTAGGGAG 59.060 40.000 4.15 0.00 0.00 4.30
3692 4701 5.123979 GTGCTGTTAAAACTGATTAGGGAGG 59.876 44.000 4.15 0.00 0.00 4.30
3693 4702 4.640647 GCTGTTAAAACTGATTAGGGAGGG 59.359 45.833 4.15 0.00 0.00 4.30
3694 4703 4.595986 TGTTAAAACTGATTAGGGAGGGC 58.404 43.478 0.00 0.00 0.00 5.19
3695 4704 2.828661 AAAACTGATTAGGGAGGGCC 57.171 50.000 0.00 0.00 0.00 5.80
3696 4705 1.681229 AAACTGATTAGGGAGGGCCA 58.319 50.000 6.18 0.00 35.15 5.36
3697 4706 1.681229 AACTGATTAGGGAGGGCCAA 58.319 50.000 6.18 0.00 35.15 4.52
3698 4707 1.681229 ACTGATTAGGGAGGGCCAAA 58.319 50.000 6.18 0.00 35.15 3.28
3699 4708 1.285078 ACTGATTAGGGAGGGCCAAAC 59.715 52.381 6.18 0.00 35.15 2.93
3700 4709 0.629058 TGATTAGGGAGGGCCAAACC 59.371 55.000 6.18 4.43 35.15 3.27
3701 4710 0.629058 GATTAGGGAGGGCCAAACCA 59.371 55.000 6.18 0.00 42.05 3.67
3702 4711 1.217942 GATTAGGGAGGGCCAAACCAT 59.782 52.381 6.18 6.56 42.05 3.55
3703 4712 1.089123 TTAGGGAGGGCCAAACCATT 58.911 50.000 6.18 1.48 42.05 3.16
3704 4713 0.334676 TAGGGAGGGCCAAACCATTG 59.665 55.000 6.18 0.00 42.05 2.82
3705 4714 1.078347 GGGAGGGCCAAACCATTGA 59.922 57.895 6.18 0.00 42.05 2.57
3706 4715 0.544120 GGGAGGGCCAAACCATTGAA 60.544 55.000 6.18 0.00 42.05 2.69
3707 4716 1.347062 GGAGGGCCAAACCATTGAAA 58.653 50.000 6.18 0.00 42.05 2.69
3708 4717 1.696884 GGAGGGCCAAACCATTGAAAA 59.303 47.619 6.18 0.00 42.05 2.29
3709 4718 2.549992 GGAGGGCCAAACCATTGAAAAC 60.550 50.000 6.18 0.00 42.05 2.43
3710 4719 2.368548 GAGGGCCAAACCATTGAAAACT 59.631 45.455 6.18 0.00 42.05 2.66
3711 4720 2.104622 AGGGCCAAACCATTGAAAACTG 59.895 45.455 6.18 0.00 42.05 3.16
3712 4721 2.158827 GGGCCAAACCATTGAAAACTGT 60.159 45.455 4.39 0.00 42.05 3.55
3713 4722 3.540617 GGCCAAACCATTGAAAACTGTT 58.459 40.909 0.00 0.00 38.94 3.16
3714 4723 3.944650 GGCCAAACCATTGAAAACTGTTT 59.055 39.130 0.00 0.00 38.94 2.83
3715 4724 4.397730 GGCCAAACCATTGAAAACTGTTTT 59.602 37.500 17.71 17.71 38.94 2.43
3716 4725 5.105957 GGCCAAACCATTGAAAACTGTTTTT 60.106 36.000 18.58 1.71 38.94 1.94
4048 5057 6.207417 ACGATGATTGTTTCTTCCTTTGTCAT 59.793 34.615 0.00 0.00 0.00 3.06
4065 5074 7.805071 CCTTTGTCATGAGTTTAGTGATGTTTC 59.195 37.037 0.00 0.00 0.00 2.78
4086 5095 3.596046 TCCATTGATTTTGTCCTAGGGGT 59.404 43.478 9.46 0.00 0.00 4.95
4091 5100 1.080638 TTTTGTCCTAGGGGTGCCAT 58.919 50.000 9.46 0.00 0.00 4.40
4095 5104 1.774254 TGTCCTAGGGGTGCCATTATG 59.226 52.381 9.46 0.00 0.00 1.90
4096 5105 1.073923 GTCCTAGGGGTGCCATTATGG 59.926 57.143 9.46 6.92 41.55 2.74
4097 5106 1.149101 CCTAGGGGTGCCATTATGGT 58.851 55.000 13.28 0.00 40.46 3.55
4101 5110 0.760189 GGGGTGCCATTATGGTGCAT 60.760 55.000 13.28 0.00 40.46 3.96
4109 5118 6.462207 GGTGCCATTATGGTGCATATGTTTTA 60.462 38.462 13.28 0.00 40.46 1.52
4110 5119 6.642131 GTGCCATTATGGTGCATATGTTTTAG 59.358 38.462 13.28 0.00 40.46 1.85
4111 5120 5.634859 GCCATTATGGTGCATATGTTTTAGC 59.365 40.000 13.28 0.00 40.46 3.09
4112 5121 6.517194 GCCATTATGGTGCATATGTTTTAGCT 60.517 38.462 13.28 0.00 40.46 3.32
4113 5122 7.309133 GCCATTATGGTGCATATGTTTTAGCTA 60.309 37.037 13.28 0.00 40.46 3.32
4114 5123 8.023128 CCATTATGGTGCATATGTTTTAGCTAC 58.977 37.037 2.48 0.00 31.35 3.58
4115 5124 8.786898 CATTATGGTGCATATGTTTTAGCTACT 58.213 33.333 4.29 0.00 0.00 2.57
4118 5127 7.786178 TGGTGCATATGTTTTAGCTACTAAG 57.214 36.000 4.29 0.00 0.00 2.18
4119 5128 7.335627 TGGTGCATATGTTTTAGCTACTAAGT 58.664 34.615 4.29 0.00 0.00 2.24
4120 5129 7.494625 TGGTGCATATGTTTTAGCTACTAAGTC 59.505 37.037 4.29 0.00 0.00 3.01
4121 5130 7.041984 GGTGCATATGTTTTAGCTACTAAGTCC 60.042 40.741 4.29 0.00 0.00 3.85
4133 5145 6.811954 AGCTACTAAGTCCAAGAATTCTAGC 58.188 40.000 8.75 9.67 31.78 3.42
4138 5150 4.936685 AGTCCAAGAATTCTAGCCCTTT 57.063 40.909 8.75 0.00 0.00 3.11
4174 5186 4.216472 GGAACCTCCTGAATTTCTTGTGTC 59.784 45.833 0.00 0.00 32.53 3.67
4181 5193 5.471116 TCCTGAATTTCTTGTGTCTGTCATG 59.529 40.000 0.00 0.00 0.00 3.07
4188 5200 4.512484 TCTTGTGTCTGTCATGTCAAACA 58.488 39.130 0.00 0.00 0.00 2.83
4196 5208 5.853282 GTCTGTCATGTCAAACAATGTAAGC 59.147 40.000 0.00 0.00 0.00 3.09
4200 5212 5.339611 GTCATGTCAAACAATGTAAGCGTTC 59.660 40.000 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.048222 TTCAGGGCGCTCGTCTTG 60.048 61.111 7.64 0.00 0.00 3.02
41 42 1.882623 CACCCTGAAACTGAAAGCCTC 59.117 52.381 0.00 0.00 37.60 4.70
343 348 4.394610 GCCGCCCAATTTTACATTGATTTT 59.605 37.500 0.00 0.00 0.00 1.82
462 468 2.350899 TTCGTTCGCTTATTGTCCGA 57.649 45.000 0.00 0.00 0.00 4.55
476 482 1.223417 AAACGGACGGCGATTTCGTT 61.223 50.000 16.62 19.23 44.34 3.85
523 529 4.699192 TGGGACCCAGACTATCCG 57.301 61.111 9.95 0.00 32.90 4.18
537 543 2.039746 TCAACAACACCATCCTACTGGG 59.960 50.000 0.00 0.00 40.85 4.45
538 544 3.007940 TCTCAACAACACCATCCTACTGG 59.992 47.826 0.00 0.00 42.35 4.00
539 545 4.271696 TCTCAACAACACCATCCTACTG 57.728 45.455 0.00 0.00 0.00 2.74
540 546 4.532126 TGATCTCAACAACACCATCCTACT 59.468 41.667 0.00 0.00 0.00 2.57
541 547 4.832248 TGATCTCAACAACACCATCCTAC 58.168 43.478 0.00 0.00 0.00 3.18
542 548 5.698741 ATGATCTCAACAACACCATCCTA 57.301 39.130 0.00 0.00 0.00 2.94
543 549 4.581309 ATGATCTCAACAACACCATCCT 57.419 40.909 0.00 0.00 0.00 3.24
544 550 4.142315 CCAATGATCTCAACAACACCATCC 60.142 45.833 0.00 0.00 0.00 3.51
545 551 4.676196 GCCAATGATCTCAACAACACCATC 60.676 45.833 0.00 0.00 0.00 3.51
546 552 3.194116 GCCAATGATCTCAACAACACCAT 59.806 43.478 0.00 0.00 0.00 3.55
547 553 2.557924 GCCAATGATCTCAACAACACCA 59.442 45.455 0.00 0.00 0.00 4.17
548 554 2.414559 CGCCAATGATCTCAACAACACC 60.415 50.000 0.00 0.00 0.00 4.16
549 555 2.414559 CCGCCAATGATCTCAACAACAC 60.415 50.000 0.00 0.00 0.00 3.32
550 556 1.811965 CCGCCAATGATCTCAACAACA 59.188 47.619 0.00 0.00 0.00 3.33
551 557 1.812571 ACCGCCAATGATCTCAACAAC 59.187 47.619 0.00 0.00 0.00 3.32
552 558 2.198827 ACCGCCAATGATCTCAACAA 57.801 45.000 0.00 0.00 0.00 2.83
553 559 3.055458 TCTTACCGCCAATGATCTCAACA 60.055 43.478 0.00 0.00 0.00 3.33
554 560 3.531538 TCTTACCGCCAATGATCTCAAC 58.468 45.455 0.00 0.00 0.00 3.18
555 561 3.904800 TCTTACCGCCAATGATCTCAA 57.095 42.857 0.00 0.00 0.00 3.02
556 562 3.450817 TCTTCTTACCGCCAATGATCTCA 59.549 43.478 0.00 0.00 0.00 3.27
557 563 4.054671 CTCTTCTTACCGCCAATGATCTC 58.945 47.826 0.00 0.00 0.00 2.75
558 564 3.181461 CCTCTTCTTACCGCCAATGATCT 60.181 47.826 0.00 0.00 0.00 2.75
559 565 3.134458 CCTCTTCTTACCGCCAATGATC 58.866 50.000 0.00 0.00 0.00 2.92
560 566 2.771943 TCCTCTTCTTACCGCCAATGAT 59.228 45.455 0.00 0.00 0.00 2.45
561 567 2.184533 TCCTCTTCTTACCGCCAATGA 58.815 47.619 0.00 0.00 0.00 2.57
562 568 2.691409 TCCTCTTCTTACCGCCAATG 57.309 50.000 0.00 0.00 0.00 2.82
563 569 2.681097 GCTTCCTCTTCTTACCGCCAAT 60.681 50.000 0.00 0.00 0.00 3.16
564 570 1.338769 GCTTCCTCTTCTTACCGCCAA 60.339 52.381 0.00 0.00 0.00 4.52
565 571 0.249398 GCTTCCTCTTCTTACCGCCA 59.751 55.000 0.00 0.00 0.00 5.69
566 572 0.249398 TGCTTCCTCTTCTTACCGCC 59.751 55.000 0.00 0.00 0.00 6.13
567 573 2.159028 AGATGCTTCCTCTTCTTACCGC 60.159 50.000 0.00 0.00 0.00 5.68
568 574 3.491792 GGAGATGCTTCCTCTTCTTACCG 60.492 52.174 0.00 0.00 34.27 4.02
569 575 3.181459 GGGAGATGCTTCCTCTTCTTACC 60.181 52.174 0.00 0.00 37.40 2.85
570 576 3.709141 AGGGAGATGCTTCCTCTTCTTAC 59.291 47.826 0.00 0.00 33.33 2.34
571 577 4.000928 AGGGAGATGCTTCCTCTTCTTA 57.999 45.455 0.00 0.00 33.33 2.10
572 578 2.844369 AGGGAGATGCTTCCTCTTCTT 58.156 47.619 0.00 0.00 33.33 2.52
573 579 2.504996 CAAGGGAGATGCTTCCTCTTCT 59.495 50.000 0.00 0.00 38.83 2.85
574 580 2.916640 CAAGGGAGATGCTTCCTCTTC 58.083 52.381 0.00 0.00 38.83 2.87
575 581 1.064832 GCAAGGGAGATGCTTCCTCTT 60.065 52.381 0.00 0.00 38.83 2.85
576 582 0.545646 GCAAGGGAGATGCTTCCTCT 59.454 55.000 0.00 0.00 38.83 3.69
577 583 0.254178 TGCAAGGGAGATGCTTCCTC 59.746 55.000 0.00 0.00 38.83 3.71
578 584 0.700564 TTGCAAGGGAGATGCTTCCT 59.299 50.000 0.00 0.00 42.24 3.36
579 585 1.549203 TTTGCAAGGGAGATGCTTCC 58.451 50.000 0.00 0.00 44.14 3.46
580 586 3.006217 AGTTTTTGCAAGGGAGATGCTTC 59.994 43.478 0.00 0.00 44.14 3.86
581 587 2.967887 AGTTTTTGCAAGGGAGATGCTT 59.032 40.909 0.00 0.00 44.14 3.91
582 588 2.601905 AGTTTTTGCAAGGGAGATGCT 58.398 42.857 0.00 0.00 44.14 3.79
583 589 3.391506 AAGTTTTTGCAAGGGAGATGC 57.608 42.857 0.00 0.00 44.08 3.91
584 590 7.830739 AGTATTAAGTTTTTGCAAGGGAGATG 58.169 34.615 0.00 0.00 0.00 2.90
585 591 9.178758 CTAGTATTAAGTTTTTGCAAGGGAGAT 57.821 33.333 0.00 0.00 0.00 2.75
586 592 7.120726 GCTAGTATTAAGTTTTTGCAAGGGAGA 59.879 37.037 0.00 0.00 0.00 3.71
587 593 7.251281 GCTAGTATTAAGTTTTTGCAAGGGAG 58.749 38.462 0.00 0.00 0.00 4.30
588 594 6.152154 GGCTAGTATTAAGTTTTTGCAAGGGA 59.848 38.462 0.00 0.00 0.00 4.20
589 595 6.152831 AGGCTAGTATTAAGTTTTTGCAAGGG 59.847 38.462 0.00 0.00 0.00 3.95
590 596 7.158099 AGGCTAGTATTAAGTTTTTGCAAGG 57.842 36.000 0.00 0.00 0.00 3.61
591 597 7.903431 CGTAGGCTAGTATTAAGTTTTTGCAAG 59.097 37.037 0.00 0.00 0.00 4.01
592 598 7.388500 ACGTAGGCTAGTATTAAGTTTTTGCAA 59.612 33.333 0.00 0.00 0.00 4.08
593 599 6.875195 ACGTAGGCTAGTATTAAGTTTTTGCA 59.125 34.615 0.00 0.00 0.00 4.08
594 600 7.178074 CACGTAGGCTAGTATTAAGTTTTTGC 58.822 38.462 0.00 0.00 0.00 3.68
595 601 7.681903 CCACGTAGGCTAGTATTAAGTTTTTG 58.318 38.462 0.00 0.00 0.00 2.44
596 602 7.838771 CCACGTAGGCTAGTATTAAGTTTTT 57.161 36.000 0.00 0.00 0.00 1.94
612 618 0.320771 AACTGAGCTTGCCACGTAGG 60.321 55.000 0.00 0.00 41.84 3.18
613 619 2.263077 CTAACTGAGCTTGCCACGTAG 58.737 52.381 0.00 0.00 0.00 3.51
614 620 2.363788 CTAACTGAGCTTGCCACGTA 57.636 50.000 0.00 0.00 0.00 3.57
615 621 3.217242 CTAACTGAGCTTGCCACGT 57.783 52.632 0.00 0.00 0.00 4.49
625 631 5.431765 ACCTACATTCCAATGCTAACTGAG 58.568 41.667 0.00 0.00 40.04 3.35
626 632 5.428253 GACCTACATTCCAATGCTAACTGA 58.572 41.667 0.00 0.00 40.04 3.41
627 633 4.576463 GGACCTACATTCCAATGCTAACTG 59.424 45.833 0.00 0.00 40.04 3.16
628 634 4.227300 TGGACCTACATTCCAATGCTAACT 59.773 41.667 0.00 0.00 40.35 2.24
629 635 4.523083 TGGACCTACATTCCAATGCTAAC 58.477 43.478 0.00 0.00 40.35 2.34
630 636 4.853468 TGGACCTACATTCCAATGCTAA 57.147 40.909 0.00 0.00 40.35 3.09
631 637 4.853468 TTGGACCTACATTCCAATGCTA 57.147 40.909 0.00 0.00 46.23 3.49
632 638 3.737559 TTGGACCTACATTCCAATGCT 57.262 42.857 0.00 0.00 46.23 3.79
637 643 1.702401 TGTGCTTGGACCTACATTCCA 59.298 47.619 0.00 0.00 41.64 3.53
638 644 2.489938 TGTGCTTGGACCTACATTCC 57.510 50.000 0.00 0.00 0.00 3.01
639 645 4.034048 CGTTATGTGCTTGGACCTACATTC 59.966 45.833 8.71 4.42 35.55 2.67
640 646 3.938963 CGTTATGTGCTTGGACCTACATT 59.061 43.478 8.71 0.00 35.55 2.71
641 647 3.531538 CGTTATGTGCTTGGACCTACAT 58.468 45.455 0.00 1.69 37.51 2.29
642 648 2.354303 CCGTTATGTGCTTGGACCTACA 60.354 50.000 0.00 0.00 0.00 2.74
643 649 2.277084 CCGTTATGTGCTTGGACCTAC 58.723 52.381 0.00 0.00 0.00 3.18
644 650 1.208535 CCCGTTATGTGCTTGGACCTA 59.791 52.381 0.00 0.00 0.00 3.08
645 651 0.035439 CCCGTTATGTGCTTGGACCT 60.035 55.000 0.00 0.00 0.00 3.85
646 652 1.654023 GCCCGTTATGTGCTTGGACC 61.654 60.000 0.00 0.00 0.00 4.46
647 653 0.958382 TGCCCGTTATGTGCTTGGAC 60.958 55.000 0.00 0.00 0.00 4.02
648 654 0.250945 TTGCCCGTTATGTGCTTGGA 60.251 50.000 0.00 0.00 0.00 3.53
649 655 0.817013 ATTGCCCGTTATGTGCTTGG 59.183 50.000 0.00 0.00 0.00 3.61
650 656 2.652941 AATTGCCCGTTATGTGCTTG 57.347 45.000 0.00 0.00 0.00 4.01
651 657 3.676291 AAAATTGCCCGTTATGTGCTT 57.324 38.095 0.00 0.00 0.00 3.91
652 658 3.676291 AAAAATTGCCCGTTATGTGCT 57.324 38.095 0.00 0.00 0.00 4.40
670 676 6.040729 GTGCCACTAACTACCCCTTTTAAAAA 59.959 38.462 1.66 0.00 0.00 1.94
731 737 9.216117 GTGACACAAAATACCTCATTTAGTAGT 57.784 33.333 0.00 0.00 35.74 2.73
825 837 3.264104 CATAGCAAAACTTGGCATTGGG 58.736 45.455 1.19 0.00 0.00 4.12
849 861 2.480555 CGATCAAGTTGGTGCGGC 59.519 61.111 2.34 0.00 0.00 6.53
851 863 2.480555 GCCGATCAAGTTGGTGCG 59.519 61.111 2.34 4.67 33.42 5.34
861 873 1.195442 TGGTAGTGGTTGGCCGATCA 61.195 55.000 0.12 0.12 37.67 2.92
893 905 0.740868 TTCGTGCTCTGCATGGTAGC 60.741 55.000 11.20 0.00 44.68 3.58
923 935 6.398655 AATGAGTACGGGGTCTATATAGGA 57.601 41.667 9.89 0.00 0.00 2.94
1140 1158 6.183359 CGTCGTTCACTCTTCAAGAAGATAAC 60.183 42.308 12.50 14.43 45.40 1.89
1141 1159 5.856986 CGTCGTTCACTCTTCAAGAAGATAA 59.143 40.000 12.50 5.84 45.40 1.75
1142 1160 5.391449 CGTCGTTCACTCTTCAAGAAGATA 58.609 41.667 12.50 0.32 45.40 1.98
1143 1161 4.230657 CGTCGTTCACTCTTCAAGAAGAT 58.769 43.478 12.50 1.89 45.40 2.40
1156 1174 1.296145 CGATGCATGCGTCGTTCAC 60.296 57.895 40.73 17.03 46.64 3.18
1164 1182 0.168788 AAGGAACAACGATGCATGCG 59.831 50.000 14.09 10.48 0.00 4.73
1177 1196 1.004292 CAACACGAACGGTCAAGGAAC 60.004 52.381 0.00 0.00 0.00 3.62
1326 1345 2.562912 CGGCTCATGTGGTTGTGC 59.437 61.111 0.00 0.00 35.82 4.57
1420 1513 5.355910 ACACAAAAGACCGTTACTGAAACAT 59.644 36.000 0.00 0.00 38.03 2.71
1421 1514 4.696402 ACACAAAAGACCGTTACTGAAACA 59.304 37.500 0.00 0.00 38.03 2.83
1437 1530 2.780094 CCCGTGCCTGCACACAAAA 61.780 57.895 21.01 0.00 46.47 2.44
1755 2198 2.036992 TGCCAACAACATCCATTCCAAC 59.963 45.455 0.00 0.00 0.00 3.77
1957 2417 7.685594 AGTAGACGAATTGCTTTATTAACTGC 58.314 34.615 0.00 0.00 0.00 4.40
2059 3001 0.104855 GATGAGCCGGAGCATGTACA 59.895 55.000 5.05 0.00 43.56 2.90
2474 3448 0.968901 TGAATAGGACGTGCCGGTCT 60.969 55.000 2.38 0.00 43.43 3.85
2489 3463 4.143333 CCGAGGCCGACGGTGAAT 62.143 66.667 27.75 0.00 44.57 2.57
3156 4162 0.252193 TCTTTTGATTGGGCAGGGGG 60.252 55.000 0.00 0.00 0.00 5.40
3159 4165 3.592059 CAACATCTTTTGATTGGGCAGG 58.408 45.455 0.00 0.00 36.97 4.85
3207 4213 1.776662 CCCCTCGTAGGAGTCATCAA 58.223 55.000 11.31 0.00 37.67 2.57
3221 4227 2.279784 CGCAGATCTTCGCCCCTC 60.280 66.667 0.89 0.00 0.00 4.30
3313 4320 8.445275 TCGGCACATCAGTATACAAAATAAAT 57.555 30.769 5.50 0.00 0.00 1.40
3318 4325 6.183360 GGAAATCGGCACATCAGTATACAAAA 60.183 38.462 5.50 0.00 0.00 2.44
3325 4332 2.419990 CCAGGAAATCGGCACATCAGTA 60.420 50.000 0.00 0.00 0.00 2.74
3326 4333 1.679944 CCAGGAAATCGGCACATCAGT 60.680 52.381 0.00 0.00 0.00 3.41
3327 4334 1.019673 CCAGGAAATCGGCACATCAG 58.980 55.000 0.00 0.00 0.00 2.90
3329 4336 0.107214 TCCCAGGAAATCGGCACATC 60.107 55.000 0.00 0.00 0.00 3.06
3330 4337 0.331278 TTCCCAGGAAATCGGCACAT 59.669 50.000 0.00 0.00 0.00 3.21
3336 4343 2.684881 CCAATGACTTCCCAGGAAATCG 59.315 50.000 3.65 0.00 33.62 3.34
3354 4361 0.749818 TGCGTGGAAGCAAAGTCCAA 60.750 50.000 0.00 0.00 46.66 3.53
3364 4371 1.200020 GGGAATTCAAGTGCGTGGAAG 59.800 52.381 7.93 0.00 0.00 3.46
3417 4426 6.263168 CACAGTAAGAAAAGGTGTCCAAGAAT 59.737 38.462 0.00 0.00 0.00 2.40
3437 4446 5.486063 TCATATTACAAGGGGTGTACACAGT 59.514 40.000 26.51 17.29 42.56 3.55
3438 4447 5.984725 TCATATTACAAGGGGTGTACACAG 58.015 41.667 26.51 12.88 42.56 3.66
3491 4500 7.557724 TGGTTATAATGTAGTCGGATGTTTGA 58.442 34.615 0.00 0.00 0.00 2.69
3571 4580 3.192001 AGTTCATTCTTCGCACAATGCAT 59.808 39.130 0.00 0.00 45.36 3.96
3619 4628 4.100344 TGCCTCGTACCAGCAATCTAATTA 59.900 41.667 0.00 0.00 32.56 1.40
3627 4636 0.394938 TTTCTGCCTCGTACCAGCAA 59.605 50.000 1.38 0.00 35.79 3.91
3647 4656 0.333312 TGGCCCCGGTGATACATTTT 59.667 50.000 0.00 0.00 0.00 1.82
3648 4657 0.333312 TTGGCCCCGGTGATACATTT 59.667 50.000 0.00 0.00 0.00 2.32
3650 4659 1.279025 ACTTGGCCCCGGTGATACAT 61.279 55.000 0.00 0.00 0.00 2.29
3652 4661 1.451387 CACTTGGCCCCGGTGATAC 60.451 63.158 12.60 0.00 33.32 2.24
3653 4662 2.994699 CACTTGGCCCCGGTGATA 59.005 61.111 12.60 0.00 33.32 2.15
3654 4663 4.740822 GCACTTGGCCCCGGTGAT 62.741 66.667 19.49 0.00 36.11 3.06
3658 4667 3.561120 TAACAGCACTTGGCCCCGG 62.561 63.158 0.00 0.00 46.50 5.73
3659 4668 1.175983 TTTAACAGCACTTGGCCCCG 61.176 55.000 0.00 0.00 46.50 5.73
3660 4669 1.044611 TTTTAACAGCACTTGGCCCC 58.955 50.000 0.00 0.00 46.50 5.80
3661 4670 1.686587 AGTTTTAACAGCACTTGGCCC 59.313 47.619 0.00 0.00 46.50 5.80
3662 4671 2.360801 TCAGTTTTAACAGCACTTGGCC 59.639 45.455 0.00 0.00 46.50 5.36
3663 4672 3.708563 TCAGTTTTAACAGCACTTGGC 57.291 42.857 0.00 0.00 45.30 4.52
3665 4674 6.206634 TCCCTAATCAGTTTTAACAGCACTTG 59.793 38.462 0.00 0.00 0.00 3.16
3666 4675 6.303839 TCCCTAATCAGTTTTAACAGCACTT 58.696 36.000 0.00 0.00 0.00 3.16
3667 4676 5.876357 TCCCTAATCAGTTTTAACAGCACT 58.124 37.500 0.00 0.00 0.00 4.40
3668 4677 5.123979 CCTCCCTAATCAGTTTTAACAGCAC 59.876 44.000 0.00 0.00 0.00 4.40
3669 4678 5.253330 CCTCCCTAATCAGTTTTAACAGCA 58.747 41.667 0.00 0.00 0.00 4.41
3671 4680 4.640647 GCCCTCCCTAATCAGTTTTAACAG 59.359 45.833 0.00 0.00 0.00 3.16
3672 4681 4.569015 GGCCCTCCCTAATCAGTTTTAACA 60.569 45.833 0.00 0.00 0.00 2.41
3673 4682 3.952323 GGCCCTCCCTAATCAGTTTTAAC 59.048 47.826 0.00 0.00 0.00 2.01
3674 4683 3.594232 TGGCCCTCCCTAATCAGTTTTAA 59.406 43.478 0.00 0.00 0.00 1.52
3675 4684 3.194620 TGGCCCTCCCTAATCAGTTTTA 58.805 45.455 0.00 0.00 0.00 1.52
3676 4685 2.000048 TGGCCCTCCCTAATCAGTTTT 59.000 47.619 0.00 0.00 0.00 2.43
3677 4686 1.681229 TGGCCCTCCCTAATCAGTTT 58.319 50.000 0.00 0.00 0.00 2.66
3678 4687 1.681229 TTGGCCCTCCCTAATCAGTT 58.319 50.000 0.00 0.00 0.00 3.16
3679 4688 1.285078 GTTTGGCCCTCCCTAATCAGT 59.715 52.381 0.00 0.00 31.07 3.41
3680 4689 1.410224 GGTTTGGCCCTCCCTAATCAG 60.410 57.143 0.00 0.00 30.83 2.90
3681 4690 0.629058 GGTTTGGCCCTCCCTAATCA 59.371 55.000 0.00 0.00 30.83 2.57
3682 4691 0.629058 TGGTTTGGCCCTCCCTAATC 59.371 55.000 0.00 0.00 36.04 1.75
3683 4692 1.318934 ATGGTTTGGCCCTCCCTAAT 58.681 50.000 0.00 0.00 36.04 1.73
3684 4693 1.089123 AATGGTTTGGCCCTCCCTAA 58.911 50.000 0.00 0.00 36.04 2.69
3685 4694 0.334676 CAATGGTTTGGCCCTCCCTA 59.665 55.000 0.00 0.00 36.04 3.53
3686 4695 1.079073 CAATGGTTTGGCCCTCCCT 59.921 57.895 0.00 0.00 36.04 4.20
3687 4696 0.544120 TTCAATGGTTTGGCCCTCCC 60.544 55.000 0.00 0.00 36.04 4.30
3688 4697 1.347062 TTTCAATGGTTTGGCCCTCC 58.653 50.000 0.00 0.00 36.04 4.30
3689 4698 2.368548 AGTTTTCAATGGTTTGGCCCTC 59.631 45.455 0.00 0.00 36.04 4.30
3690 4699 2.104622 CAGTTTTCAATGGTTTGGCCCT 59.895 45.455 0.00 0.00 36.04 5.19
3691 4700 2.158827 ACAGTTTTCAATGGTTTGGCCC 60.159 45.455 0.00 0.00 36.04 5.80
3692 4701 3.192541 ACAGTTTTCAATGGTTTGGCC 57.807 42.857 0.00 0.00 33.44 5.36
3693 4702 5.559427 AAAACAGTTTTCAATGGTTTGGC 57.441 34.783 5.37 0.00 35.09 4.52
4065 5074 3.701040 CACCCCTAGGACAAAATCAATGG 59.299 47.826 11.48 0.03 36.73 3.16
4086 5095 5.611128 AAAACATATGCACCATAATGGCA 57.389 34.783 1.58 0.00 42.67 4.92
4091 5100 9.839817 TTAGTAGCTAAAACATATGCACCATAA 57.160 29.630 1.58 0.00 29.74 1.90
4095 5104 7.041984 GGACTTAGTAGCTAAAACATATGCACC 60.042 40.741 1.58 0.00 0.00 5.01
4096 5105 7.494625 TGGACTTAGTAGCTAAAACATATGCAC 59.505 37.037 1.58 0.00 0.00 4.57
4097 5106 7.561251 TGGACTTAGTAGCTAAAACATATGCA 58.439 34.615 1.58 0.00 0.00 3.96
4109 5118 6.183360 GGCTAGAATTCTTGGACTTAGTAGCT 60.183 42.308 14.36 0.00 0.00 3.32
4110 5119 5.986741 GGCTAGAATTCTTGGACTTAGTAGC 59.013 44.000 14.36 11.65 0.00 3.58
4111 5120 6.325286 AGGGCTAGAATTCTTGGACTTAGTAG 59.675 42.308 14.36 1.75 0.00 2.57
4112 5121 6.203072 AGGGCTAGAATTCTTGGACTTAGTA 58.797 40.000 14.36 0.00 0.00 1.82
4113 5122 5.033522 AGGGCTAGAATTCTTGGACTTAGT 58.966 41.667 14.36 0.00 0.00 2.24
4114 5123 5.622346 AGGGCTAGAATTCTTGGACTTAG 57.378 43.478 14.36 4.02 0.00 2.18
4115 5124 6.388619 AAAGGGCTAGAATTCTTGGACTTA 57.611 37.500 14.36 0.00 0.00 2.24
4116 5125 4.936685 AAGGGCTAGAATTCTTGGACTT 57.063 40.909 14.36 10.65 0.00 3.01
4118 5127 4.767409 ACAAAAGGGCTAGAATTCTTGGAC 59.233 41.667 14.36 9.21 0.00 4.02
4119 5128 4.998051 ACAAAAGGGCTAGAATTCTTGGA 58.002 39.130 14.36 0.00 0.00 3.53
4120 5129 5.728637 AACAAAAGGGCTAGAATTCTTGG 57.271 39.130 14.36 8.39 0.00 3.61
4121 5130 5.928264 CCAAACAAAAGGGCTAGAATTCTTG 59.072 40.000 14.36 13.01 0.00 3.02
4133 5145 2.038659 TCCTCTTGCCAAACAAAAGGG 58.961 47.619 0.00 0.00 45.32 3.95
4138 5150 2.306847 GAGGTTCCTCTTGCCAAACAA 58.693 47.619 11.20 0.00 36.62 2.83
4164 5176 5.414144 TGTTTGACATGACAGACACAAGAAA 59.586 36.000 15.54 0.00 31.63 2.52
4174 5186 4.847757 CGCTTACATTGTTTGACATGACAG 59.152 41.667 0.00 0.00 0.00 3.51
4181 5193 3.664025 GCAGAACGCTTACATTGTTTGAC 59.336 43.478 0.00 0.00 37.77 3.18
4188 5200 4.513442 TCATAAGGCAGAACGCTTACATT 58.487 39.130 0.00 0.00 41.91 2.71


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

AutoCloner maintained by Alex Coulton.