Multiple sequence alignment - TraesCS2D01G219700

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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 TraesCS2D01G219700 chr2D 100.000 5973 0 0 1 5973 186965310 186959338 0.000000e+00 11031
1 TraesCS2D01G219700 chr2D 95.604 91 4 0 1 91 410240078 410239988 4.820000e-31 147
2 TraesCS2D01G219700 chr2D 93.407 91 6 0 1 91 528075730 528075640 1.040000e-27 135
3 TraesCS2D01G219700 chr2D 80.488 164 28 2 488 650 351977476 351977316 8.130000e-24 122
4 TraesCS2D01G219700 chr2A 95.302 2618 89 13 721 3320 199586942 199584341 0.000000e+00 4122
5 TraesCS2D01G219700 chr2A 95.299 1489 46 4 4450 5937 199583148 199581683 0.000000e+00 2340
6 TraesCS2D01G219700 chr2A 95.280 1144 33 11 3319 4452 199584313 199583181 0.000000e+00 1794
7 TraesCS2D01G219700 chr2A 89.735 302 31 0 1138 1439 88668725 88668424 2.610000e-103 387
8 TraesCS2D01G219700 chr2B 97.591 1370 26 3 724 2088 240319430 240318063 0.000000e+00 2340
9 TraesCS2D01G219700 chr2B 93.429 1400 37 11 4450 5827 240309651 240308285 0.000000e+00 2025
10 TraesCS2D01G219700 chr2B 96.716 1218 34 6 2081 3293 240317303 240316087 0.000000e+00 2023
11 TraesCS2D01G219700 chr2B 94.167 480 23 3 3791 4270 240310537 240310063 0.000000e+00 726
12 TraesCS2D01G219700 chr2B 93.878 490 15 5 3321 3795 240315921 240315432 0.000000e+00 725
13 TraesCS2D01G219700 chr2B 92.105 190 9 4 4263 4452 240309867 240309684 4.590000e-66 263
14 TraesCS2D01G219700 chr2B 94.631 149 4 1 5791 5939 240308268 240308124 1.670000e-55 228
15 TraesCS2D01G219700 chr2B 76.780 323 33 17 377 659 744191100 744190780 6.240000e-30 143
16 TraesCS2D01G219700 chr2B 93.023 86 3 2 653 735 240319544 240319459 8.130000e-24 122
17 TraesCS2D01G219700 chr1A 84.321 574 53 16 89 628 95493674 95494244 1.470000e-145 527
18 TraesCS2D01G219700 chr3B 83.003 606 57 12 89 650 241670045 241670648 1.920000e-139 507
19 TraesCS2D01G219700 chr3B 84.901 404 51 8 89 486 713992881 713992482 3.350000e-107 399
20 TraesCS2D01G219700 chr3B 86.275 357 40 4 89 437 254762209 254761854 4.370000e-101 379
21 TraesCS2D01G219700 chr4D 89.516 372 30 4 89 453 299779752 299779383 4.220000e-126 462
22 TraesCS2D01G219700 chr4D 80.976 594 75 26 89 650 363565527 363566114 2.560000e-118 436
23 TraesCS2D01G219700 chr4D 93.407 91 6 0 1 91 299780758 299780668 1.040000e-27 135
24 TraesCS2D01G219700 chr5A 88.172 372 36 3 89 453 529099440 529099070 2.560000e-118 436
25 TraesCS2D01G219700 chr3A 88.076 369 35 4 89 450 517761145 517761511 4.280000e-116 429
26 TraesCS2D01G219700 chr3A 86.275 102 14 0 489 590 517761592 517761693 1.760000e-20 111
27 TraesCS2D01G219700 chr1D 85.714 406 45 8 89 486 424734114 424734514 3.330000e-112 416
28 TraesCS2D01G219700 chr7A 87.534 369 33 9 89 450 292817749 292818111 1.200000e-111 414
29 TraesCS2D01G219700 chr5D 80.201 596 73 29 89 650 205129537 205130121 7.210000e-109 405
30 TraesCS2D01G219700 chr5D 94.505 91 5 0 1 91 565324066 565323976 2.240000e-29 141
31 TraesCS2D01G219700 chr7D 85.876 354 40 5 89 433 45397996 45397644 9.460000e-98 368
32 TraesCS2D01G219700 chr7D 94.505 91 5 0 1 91 161135576 161135486 2.240000e-29 141
33 TraesCS2D01G219700 chr7D 93.407 91 6 0 1 91 4239134 4239044 1.040000e-27 135
34 TraesCS2D01G219700 chr7D 93.407 91 6 0 1 91 488767909 488767999 1.040000e-27 135
35 TraesCS2D01G219700 chr7D 93.407 91 6 0 1 91 536461606 536461516 1.040000e-27 135
36 TraesCS2D01G219700 chr6B 89.961 259 25 1 1152 1410 59900526 59900783 3.450000e-87 333
37 TraesCS2D01G219700 chr5B 85.065 154 19 2 232 385 531554324 531554473 2.880000e-33 154
38 TraesCS2D01G219700 chr6A 94.505 91 5 0 1 91 553094908 553094818 2.240000e-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 TraesCS2D01G219700 chr2D 186959338 186965310 5972 True 11031.0 11031 100.000000 1 5973 1 chr2D.!!$R1 5972
1 TraesCS2D01G219700 chr2A 199581683 199586942 5259 True 2752.0 4122 95.293667 721 5937 3 chr2A.!!$R2 5216
2 TraesCS2D01G219700 chr2B 240315432 240319544 4112 True 1302.5 2340 95.302000 653 3795 4 chr2B.!!$R3 3142
3 TraesCS2D01G219700 chr2B 240308124 240310537 2413 True 810.5 2025 93.583000 3791 5939 4 chr2B.!!$R2 2148
4 TraesCS2D01G219700 chr1A 95493674 95494244 570 False 527.0 527 84.321000 89 628 1 chr1A.!!$F1 539
5 TraesCS2D01G219700 chr3B 241670045 241670648 603 False 507.0 507 83.003000 89 650 1 chr3B.!!$F1 561
6 TraesCS2D01G219700 chr4D 363565527 363566114 587 False 436.0 436 80.976000 89 650 1 chr4D.!!$F1 561
7 TraesCS2D01G219700 chr4D 299779383 299780758 1375 True 298.5 462 91.461500 1 453 2 chr4D.!!$R1 452
8 TraesCS2D01G219700 chr3A 517761145 517761693 548 False 270.0 429 87.175500 89 590 2 chr3A.!!$F1 501
9 TraesCS2D01G219700 chr5D 205129537 205130121 584 False 405.0 405 80.201000 89 650 1 chr5D.!!$F1 561

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
59 60 0.179181 GACGAAGGCATACACGACGA 60.179 55.0 0.00 0.0 0.00 4.20 F
651 1624 0.596577 ACGCGTTAGAGTTGCTCTGA 59.403 50.0 5.58 0.0 41.37 3.27 F
1637 2658 0.902516 GCTGGAGACTCAGGTGGTCT 60.903 60.0 4.53 0.0 45.37 3.85 F
2301 4092 0.616395 TTCCGGTCCCTGTGATAGCA 60.616 55.0 0.00 0.0 0.00 3.49 F
2466 4257 0.882042 AGTCTGGTGAAAGTGCTGCG 60.882 55.0 0.00 0.0 0.00 5.18 F
4035 5991 1.288350 CAATGAGAGCGAAGAGGCAG 58.712 55.0 0.00 0.0 34.64 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 2658 0.753479 GACCTCTCCATCTCAGGCGA 60.753 60.000 0.00 0.00 0.00 5.54 R
1780 2801 1.075536 GGTTCCACACCCTTCTCCATT 59.924 52.381 0.00 0.00 40.19 3.16 R
3349 5297 1.602377 ACGGCAAGCTAGTGACAAAAC 59.398 47.619 0.00 0.00 0.00 2.43 R
4069 6025 0.761187 GCCCATCTAGCAGTCCATCA 59.239 55.000 0.00 0.00 0.00 3.07 R
4070 6026 1.055040 AGCCCATCTAGCAGTCCATC 58.945 55.000 0.00 0.00 0.00 3.51 R
5678 7895 0.321919 CCTTCTAGTGCTTGCTGGCA 60.322 55.000 0.33 0.33 40.15 4.92 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
39 40 2.949106 GAAGCGCAAGAGCAAGCA 59.051 55.556 11.47 0.00 42.27 3.91
44 45 2.023771 CGCAAGAGCAAGCAGACGA 61.024 57.895 0.00 0.00 42.27 4.20
56 57 0.457853 GCAGACGAAGGCATACACGA 60.458 55.000 0.00 0.00 0.00 4.35
59 60 0.179181 GACGAAGGCATACACGACGA 60.179 55.000 0.00 0.00 0.00 4.20
168 1087 3.330267 CAAGGCGAAAGAAGTAGCTCTT 58.670 45.455 0.00 0.00 37.24 2.85
185 1104 1.482182 TCTTGCTAGCATGATGACGGT 59.518 47.619 24.97 0.00 0.00 4.83
225 1150 3.379445 ACCGTGTCGCCGAGGAAT 61.379 61.111 0.00 0.00 0.00 3.01
237 1162 1.133792 CCGAGGAATAGGCCATGGTTT 60.134 52.381 14.67 4.41 0.00 3.27
247 1172 2.042162 AGGCCATGGTTTGAGAAGATGT 59.958 45.455 14.67 0.00 0.00 3.06
307 1233 1.275856 TGGCATGCACCATCCTTTTTC 59.724 47.619 21.36 0.00 33.75 2.29
438 1368 7.441157 CAGTAAGACTGTGTGATGGTCTTTTTA 59.559 37.037 11.81 0.00 44.63 1.52
450 1380 2.424956 GGTCTTTTTAGAGGCTGGCATG 59.575 50.000 3.38 0.00 0.00 4.06
453 1383 1.838112 TTTTAGAGGCTGGCATGGTG 58.162 50.000 3.38 0.00 0.00 4.17
454 1384 0.680921 TTTAGAGGCTGGCATGGTGC 60.681 55.000 3.38 0.00 44.08 5.01
501 1474 1.064952 CCGCTACGGGCCTTTTAAATG 59.935 52.381 0.84 0.00 44.15 2.32
554 1527 2.355363 CGCACGACCGACCAGAAA 60.355 61.111 0.00 0.00 0.00 2.52
555 1528 1.952133 CGCACGACCGACCAGAAAA 60.952 57.895 0.00 0.00 0.00 2.29
556 1529 1.860078 GCACGACCGACCAGAAAAG 59.140 57.895 0.00 0.00 0.00 2.27
557 1530 0.599204 GCACGACCGACCAGAAAAGA 60.599 55.000 0.00 0.00 0.00 2.52
558 1531 1.860676 CACGACCGACCAGAAAAGAA 58.139 50.000 0.00 0.00 0.00 2.52
559 1532 2.206750 CACGACCGACCAGAAAAGAAA 58.793 47.619 0.00 0.00 0.00 2.52
560 1533 2.610374 CACGACCGACCAGAAAAGAAAA 59.390 45.455 0.00 0.00 0.00 2.29
561 1534 2.610833 ACGACCGACCAGAAAAGAAAAC 59.389 45.455 0.00 0.00 0.00 2.43
562 1535 2.870411 CGACCGACCAGAAAAGAAAACT 59.130 45.455 0.00 0.00 0.00 2.66
563 1536 3.303132 CGACCGACCAGAAAAGAAAACTG 60.303 47.826 0.00 0.00 0.00 3.16
570 1543 5.665916 CCAGAAAAGAAAACTGGGCATAT 57.334 39.130 0.00 0.00 44.96 1.78
571 1544 5.413499 CCAGAAAAGAAAACTGGGCATATG 58.587 41.667 0.00 0.00 44.96 1.78
572 1545 4.866486 CAGAAAAGAAAACTGGGCATATGC 59.134 41.667 19.79 19.79 41.14 3.14
573 1546 4.774200 AGAAAAGAAAACTGGGCATATGCT 59.226 37.500 26.12 5.32 41.70 3.79
574 1547 4.460948 AAAGAAAACTGGGCATATGCTG 57.539 40.909 26.12 18.10 41.70 4.41
575 1548 3.370840 AGAAAACTGGGCATATGCTGA 57.629 42.857 26.12 12.52 41.70 4.26
576 1549 3.285484 AGAAAACTGGGCATATGCTGAG 58.715 45.455 26.12 22.05 41.70 3.35
577 1550 1.396653 AAACTGGGCATATGCTGAGC 58.603 50.000 26.12 10.17 41.70 4.26
578 1551 0.816825 AACTGGGCATATGCTGAGCG 60.817 55.000 26.12 13.01 41.70 5.03
579 1552 1.964891 CTGGGCATATGCTGAGCGG 60.965 63.158 26.12 8.13 41.70 5.52
580 1553 2.670934 GGGCATATGCTGAGCGGG 60.671 66.667 26.12 0.00 41.70 6.13
581 1554 2.111878 GGCATATGCTGAGCGGGT 59.888 61.111 26.12 0.00 41.70 5.28
582 1555 2.256591 GGCATATGCTGAGCGGGTG 61.257 63.158 26.12 0.00 41.70 4.61
583 1556 2.256591 GCATATGCTGAGCGGGTGG 61.257 63.158 20.64 0.00 38.21 4.61
584 1557 2.111878 ATATGCTGAGCGGGTGGC 59.888 61.111 0.00 0.00 44.05 5.01
585 1558 3.482232 ATATGCTGAGCGGGTGGCC 62.482 63.158 0.00 0.00 45.17 5.36
605 1578 2.943843 GACCTGAACGGACGAAAAAG 57.056 50.000 0.00 0.00 36.31 2.27
606 1579 1.529865 GACCTGAACGGACGAAAAAGG 59.470 52.381 0.00 2.70 36.31 3.11
607 1580 1.139455 ACCTGAACGGACGAAAAAGGA 59.861 47.619 0.00 0.00 36.31 3.36
608 1581 1.529865 CCTGAACGGACGAAAAAGGAC 59.470 52.381 0.00 0.00 33.16 3.85
609 1582 2.206750 CTGAACGGACGAAAAAGGACA 58.793 47.619 0.00 0.00 0.00 4.02
610 1583 2.610374 CTGAACGGACGAAAAAGGACAA 59.390 45.455 0.00 0.00 0.00 3.18
611 1584 3.207778 TGAACGGACGAAAAAGGACAAT 58.792 40.909 0.00 0.00 0.00 2.71
612 1585 4.378774 TGAACGGACGAAAAAGGACAATA 58.621 39.130 0.00 0.00 0.00 1.90
613 1586 4.998672 TGAACGGACGAAAAAGGACAATAT 59.001 37.500 0.00 0.00 0.00 1.28
614 1587 5.121142 TGAACGGACGAAAAAGGACAATATC 59.879 40.000 0.00 0.00 0.00 1.63
615 1588 4.571919 ACGGACGAAAAAGGACAATATCA 58.428 39.130 0.00 0.00 0.00 2.15
616 1589 5.183228 ACGGACGAAAAAGGACAATATCAT 58.817 37.500 0.00 0.00 0.00 2.45
617 1590 5.064707 ACGGACGAAAAAGGACAATATCATG 59.935 40.000 0.00 0.00 0.00 3.07
618 1591 5.504010 CGGACGAAAAAGGACAATATCATGG 60.504 44.000 0.00 0.00 0.00 3.66
619 1592 5.357032 GGACGAAAAAGGACAATATCATGGT 59.643 40.000 0.00 0.00 0.00 3.55
620 1593 6.436843 ACGAAAAAGGACAATATCATGGTC 57.563 37.500 0.00 0.00 0.00 4.02
626 1599 4.552166 GGACAATATCATGGTCCGTTTG 57.448 45.455 2.80 0.00 41.43 2.93
627 1600 3.315191 GGACAATATCATGGTCCGTTTGG 59.685 47.826 2.80 0.00 41.43 3.28
628 1601 3.287222 ACAATATCATGGTCCGTTTGGG 58.713 45.455 0.00 0.00 35.24 4.12
629 1602 3.287222 CAATATCATGGTCCGTTTGGGT 58.713 45.455 0.00 0.00 37.00 4.51
630 1603 3.662759 ATATCATGGTCCGTTTGGGTT 57.337 42.857 0.00 0.00 37.00 4.11
631 1604 4.781775 ATATCATGGTCCGTTTGGGTTA 57.218 40.909 0.00 0.00 37.00 2.85
632 1605 2.953284 TCATGGTCCGTTTGGGTTAA 57.047 45.000 0.00 0.00 37.00 2.01
633 1606 2.506444 TCATGGTCCGTTTGGGTTAAC 58.494 47.619 0.00 0.00 37.00 2.01
640 1613 2.215874 CGTTTGGGTTAACGCGTTAG 57.784 50.000 28.48 13.05 43.51 2.34
641 1614 1.791785 CGTTTGGGTTAACGCGTTAGA 59.208 47.619 28.48 18.00 43.51 2.10
642 1615 2.159934 CGTTTGGGTTAACGCGTTAGAG 60.160 50.000 28.48 12.78 43.51 2.43
643 1616 2.802247 GTTTGGGTTAACGCGTTAGAGT 59.198 45.455 28.48 8.76 0.00 3.24
644 1617 2.818130 TGGGTTAACGCGTTAGAGTT 57.182 45.000 28.48 7.98 42.81 3.01
645 1618 2.406130 TGGGTTAACGCGTTAGAGTTG 58.594 47.619 28.48 0.00 40.53 3.16
646 1619 1.127397 GGGTTAACGCGTTAGAGTTGC 59.873 52.381 28.48 16.09 40.53 4.17
647 1620 2.064014 GGTTAACGCGTTAGAGTTGCT 58.936 47.619 28.48 5.65 40.53 3.91
648 1621 2.091744 GGTTAACGCGTTAGAGTTGCTC 59.908 50.000 28.48 13.62 40.53 4.26
649 1622 2.985139 GTTAACGCGTTAGAGTTGCTCT 59.015 45.455 28.48 4.33 43.83 4.09
650 1623 1.419374 AACGCGTTAGAGTTGCTCTG 58.581 50.000 25.38 0.00 41.37 3.35
651 1624 0.596577 ACGCGTTAGAGTTGCTCTGA 59.403 50.000 5.58 0.00 41.37 3.27
664 1637 5.126067 AGTTGCTCTGAGTAGCTTTCAAAA 58.874 37.500 6.32 0.00 43.19 2.44
675 1648 9.905713 TGAGTAGCTTTCAAAATATTATGGAGT 57.094 29.630 0.00 0.00 0.00 3.85
710 1683 4.578871 CATTATGGACGCATTATGGAGGA 58.421 43.478 0.00 0.00 0.00 3.71
713 1686 3.961480 TGGACGCATTATGGAGGATAG 57.039 47.619 0.00 0.00 0.00 2.08
714 1687 2.567169 TGGACGCATTATGGAGGATAGG 59.433 50.000 0.00 0.00 0.00 2.57
715 1688 2.832129 GGACGCATTATGGAGGATAGGA 59.168 50.000 0.00 0.00 0.00 2.94
716 1689 3.452627 GGACGCATTATGGAGGATAGGAT 59.547 47.826 0.00 0.00 0.00 3.24
717 1690 4.649674 GGACGCATTATGGAGGATAGGATA 59.350 45.833 0.00 0.00 0.00 2.59
718 1691 5.305644 GGACGCATTATGGAGGATAGGATAT 59.694 44.000 0.00 0.00 0.00 1.63
719 1692 6.166984 ACGCATTATGGAGGATAGGATATG 57.833 41.667 0.00 0.00 0.00 1.78
721 1694 6.183360 ACGCATTATGGAGGATAGGATATGTC 60.183 42.308 0.00 0.00 0.00 3.06
722 1695 6.183360 CGCATTATGGAGGATAGGATATGTCA 60.183 42.308 0.00 0.00 0.00 3.58
1119 2140 1.791695 TTCCCCAAACCCTAACCCCG 61.792 60.000 0.00 0.00 0.00 5.73
1637 2658 0.902516 GCTGGAGACTCAGGTGGTCT 60.903 60.000 4.53 0.00 45.37 3.85
1706 2727 0.904865 TGCCATCGAGAGACCAAGGT 60.905 55.000 0.00 0.00 46.97 3.50
1769 2790 3.532102 AGGTCAGTTGGATTAAGAGGGT 58.468 45.455 0.00 0.00 0.00 4.34
1780 2801 0.759959 TAAGAGGGTTGGACGTTGCA 59.240 50.000 0.00 0.00 0.00 4.08
2241 4032 4.156008 GGTTCACTATGACATGGTGGAAAC 59.844 45.833 26.09 22.55 41.49 2.78
2301 4092 0.616395 TTCCGGTCCCTGTGATAGCA 60.616 55.000 0.00 0.00 0.00 3.49
2310 4101 3.264193 TCCCTGTGATAGCAAGTGTCATT 59.736 43.478 0.00 0.00 0.00 2.57
2466 4257 0.882042 AGTCTGGTGAAAGTGCTGCG 60.882 55.000 0.00 0.00 0.00 5.18
2502 4293 6.095440 ACACAGTGTTTAGCTTCTCATTTTGT 59.905 34.615 0.00 0.00 0.00 2.83
2592 4383 8.102800 TGCTGTAAATTGGCTCATATCTATTG 57.897 34.615 0.00 0.00 0.00 1.90
2600 4391 8.818622 ATTGGCTCATATCTATTGCATGTTAT 57.181 30.769 0.00 0.00 0.00 1.89
2614 4405 8.861033 ATTGCATGTTATTGTCATTGTCATAC 57.139 30.769 0.00 0.00 0.00 2.39
2784 4578 6.748333 TGCACTACGTGTATTCTAACTACT 57.252 37.500 0.00 0.00 35.75 2.57
2820 4614 6.096846 AGGCAGATCAAAATAACACCCAATAC 59.903 38.462 0.00 0.00 0.00 1.89
2833 4629 3.117888 CACCCAATACTCTAGGCCATGTT 60.118 47.826 5.01 0.00 0.00 2.71
2971 4767 6.419413 GTGTCACTGTTTTTCTGTTTGACAAA 59.581 34.615 3.24 0.00 34.97 2.83
3127 4929 1.785353 TAGGAACCACAAGGCCACCC 61.785 60.000 5.01 0.00 39.06 4.61
3144 4946 3.576982 CCACCCGCTATGGAGAAGTATTA 59.423 47.826 0.00 0.00 42.00 0.98
3145 4947 4.557205 CACCCGCTATGGAGAAGTATTAC 58.443 47.826 0.00 0.00 42.00 1.89
3198 5001 3.951663 AGTAGAATGGTACTTTGGTGCC 58.048 45.455 0.00 0.00 46.34 5.01
3220 5023 6.693545 TGCCGTTTTCTGTTATTTGTTTACAG 59.306 34.615 0.00 0.00 40.42 2.74
3268 5071 8.149647 AGAATGTTTAGAATCATTGTTTTGGCA 58.850 29.630 3.81 0.00 34.92 4.92
3307 5110 7.219726 GCTGAATTTCTTAGCAACTCAATAAGC 59.780 37.037 4.35 0.00 37.40 3.09
3349 5297 5.721232 AGTTCATTTACCGGTAGAGAAGTG 58.279 41.667 22.04 14.68 0.00 3.16
3361 5309 5.629849 CGGTAGAGAAGTGTTTTGTCACTAG 59.370 44.000 0.00 0.00 46.25 2.57
3495 5443 2.091541 CCGGGAACAAGTATGTGCATT 58.908 47.619 0.00 0.00 40.46 3.56
3517 5465 6.500684 TTTGCTTTCTTACATCCACTCATC 57.499 37.500 0.00 0.00 0.00 2.92
3857 5813 5.293319 TGTTGCTGTTACCTAGTTAACCA 57.707 39.130 7.62 0.00 0.00 3.67
3910 5866 2.218603 GGGTTCCAGTGTATTATGCCG 58.781 52.381 0.00 0.00 0.00 5.69
4035 5991 1.288350 CAATGAGAGCGAAGAGGCAG 58.712 55.000 0.00 0.00 34.64 4.85
4042 5998 1.600916 GCGAAGAGGCAGGGTTGTT 60.601 57.895 0.00 0.00 0.00 2.83
4068 6024 7.108841 TGGTAGCCTACAGTTACAGAATTAG 57.891 40.000 3.95 0.00 0.00 1.73
4069 6025 6.666546 TGGTAGCCTACAGTTACAGAATTAGT 59.333 38.462 3.95 0.00 0.00 2.24
4070 6026 6.979238 GGTAGCCTACAGTTACAGAATTAGTG 59.021 42.308 3.95 0.00 0.00 2.74
4071 6027 6.852420 AGCCTACAGTTACAGAATTAGTGA 57.148 37.500 0.00 0.00 0.00 3.41
4072 6028 7.425224 AGCCTACAGTTACAGAATTAGTGAT 57.575 36.000 0.00 0.00 0.00 3.06
4084 6040 6.326064 ACAGAATTAGTGATGGACTGCTAGAT 59.674 38.462 0.00 0.00 35.96 1.98
4089 6045 1.055040 GATGGACTGCTAGATGGGCT 58.945 55.000 0.00 0.00 0.00 5.19
4101 6057 3.567478 AGATGGGCTTTCGCTCTTAAT 57.433 42.857 0.00 0.00 37.58 1.40
4102 6058 4.689612 AGATGGGCTTTCGCTCTTAATA 57.310 40.909 0.00 0.00 37.58 0.98
4103 6059 5.036117 AGATGGGCTTTCGCTCTTAATAA 57.964 39.130 0.00 0.00 37.58 1.40
4108 6064 6.769512 TGGGCTTTCGCTCTTAATAAGATAT 58.230 36.000 2.87 0.00 37.58 1.63
4144 6100 3.874543 TCGTATGCTGTTGACAACACTTT 59.125 39.130 17.02 7.07 36.25 2.66
4207 6163 2.200081 AGGCCTGGAAAGCTAGATTCA 58.800 47.619 3.11 0.00 0.00 2.57
4317 6476 8.717717 AGTGTCAAGGAAGGATATTGATTATGA 58.282 33.333 0.00 0.00 35.56 2.15
4402 6561 8.465273 ACTTGTTATGCTTCTTTTTCCTAAGT 57.535 30.769 0.00 0.00 0.00 2.24
4403 6562 9.569122 ACTTGTTATGCTTCTTTTTCCTAAGTA 57.431 29.630 0.00 0.00 0.00 2.24
4404 6563 9.827411 CTTGTTATGCTTCTTTTTCCTAAGTAC 57.173 33.333 0.00 0.00 0.00 2.73
4444 6603 8.966868 TCTTTTCTGTGGAGTTTAATTTTCTGT 58.033 29.630 0.00 0.00 0.00 3.41
4878 7072 2.011122 AGTCCAAGAGTTCCTCCGAA 57.989 50.000 0.00 0.00 0.00 4.30
4879 7073 1.896465 AGTCCAAGAGTTCCTCCGAAG 59.104 52.381 0.00 0.00 0.00 3.79
5058 7252 3.251729 AGCACAGTCACTGCTTTACATTG 59.748 43.478 4.13 0.00 42.54 2.82
5141 7336 7.647715 TGCTAGTCTCATTTTTAGCAAACAAAC 59.352 33.333 2.82 0.00 43.81 2.93
5363 7558 6.994421 ACACCCTCTTACCAAAATGATTTT 57.006 33.333 0.00 0.00 0.00 1.82
5392 7587 9.624697 TGTGATTTCATCAGCAAAGTTAATTAC 57.375 29.630 0.00 0.00 40.53 1.89
5414 7631 6.712241 ACGAGTGAAGATTGTACAATTCTG 57.288 37.500 21.63 12.15 0.00 3.02
5428 7645 8.334263 TGTACAATTCTGTCATGATTTGCTTA 57.666 30.769 0.00 0.00 36.96 3.09
5504 7721 3.935828 GCAGAGTACAGTTGGATTTCTCC 59.064 47.826 0.00 0.00 42.45 3.71
5505 7722 4.177026 CAGAGTACAGTTGGATTTCTCCG 58.823 47.826 0.00 0.00 45.37 4.63
5506 7723 3.833070 AGAGTACAGTTGGATTTCTCCGT 59.167 43.478 0.00 0.00 45.37 4.69
5540 7757 2.683362 CCTATTTTCCGAAACTGGCTCC 59.317 50.000 0.00 0.00 0.00 4.70
5562 7779 4.942852 CAAGTATTGCTTTTGTGGAACCA 58.057 39.130 0.00 0.00 40.39 3.67
5585 7802 1.024271 CGACCAAATCATGCGGGATT 58.976 50.000 0.00 0.00 39.11 3.01
5593 7810 4.900635 AATCATGCGGGATTACAAGAAC 57.099 40.909 1.19 0.00 35.79 3.01
5596 7813 1.448985 TGCGGGATTACAAGAACTGC 58.551 50.000 0.00 0.00 0.00 4.40
5600 7817 2.739913 CGGGATTACAAGAACTGCGAAA 59.260 45.455 0.00 0.00 0.00 3.46
5682 7899 7.012661 ACATAGATATTCACATGAGATGCCA 57.987 36.000 0.00 0.00 0.00 4.92
5683 7900 7.104290 ACATAGATATTCACATGAGATGCCAG 58.896 38.462 0.00 0.00 0.00 4.85
5684 7901 4.325119 AGATATTCACATGAGATGCCAGC 58.675 43.478 0.00 0.00 0.00 4.85
5685 7902 2.430248 ATTCACATGAGATGCCAGCA 57.570 45.000 0.00 0.00 0.00 4.41
5757 7974 1.867233 CACAAACACAGAGAGGGTTCG 59.133 52.381 0.00 0.00 44.99 3.95
5816 8033 3.349006 CACACCACCACAGCGAGC 61.349 66.667 0.00 0.00 0.00 5.03
5846 8112 1.214062 CGCTCAGAAGAGGAACGCT 59.786 57.895 0.00 0.00 43.09 5.07
5939 8205 3.578282 CAGTTTTAGGGGCACAAGGAATT 59.422 43.478 0.00 0.00 0.00 2.17
5940 8206 3.832490 AGTTTTAGGGGCACAAGGAATTC 59.168 43.478 0.00 0.00 0.00 2.17
5941 8207 3.534357 TTTAGGGGCACAAGGAATTCA 57.466 42.857 7.93 0.00 0.00 2.57
5942 8208 3.534357 TTAGGGGCACAAGGAATTCAA 57.466 42.857 7.93 0.00 0.00 2.69
5943 8209 2.629017 AGGGGCACAAGGAATTCAAT 57.371 45.000 7.93 0.00 0.00 2.57
5945 8211 3.250617 AGGGGCACAAGGAATTCAATTT 58.749 40.909 7.93 0.00 0.00 1.82
5947 8213 4.843516 AGGGGCACAAGGAATTCAATTTTA 59.156 37.500 7.93 0.00 0.00 1.52
5948 8214 5.046376 AGGGGCACAAGGAATTCAATTTTAG 60.046 40.000 7.93 0.00 0.00 1.85
5949 8215 5.178061 GGGCACAAGGAATTCAATTTTAGG 58.822 41.667 7.93 0.00 0.00 2.69
5950 8216 5.178061 GGCACAAGGAATTCAATTTTAGGG 58.822 41.667 7.93 0.00 0.00 3.53
5951 8217 5.046663 GGCACAAGGAATTCAATTTTAGGGA 60.047 40.000 7.93 0.00 0.00 4.20
5952 8218 5.869344 GCACAAGGAATTCAATTTTAGGGAC 59.131 40.000 7.93 0.00 0.00 4.46
5953 8219 6.518200 GCACAAGGAATTCAATTTTAGGGACA 60.518 38.462 7.93 0.00 0.00 4.02
5954 8220 7.441017 CACAAGGAATTCAATTTTAGGGACAA 58.559 34.615 7.93 0.00 0.00 3.18
5955 8221 7.384932 CACAAGGAATTCAATTTTAGGGACAAC 59.615 37.037 7.93 0.00 0.00 3.32
5956 8222 7.070571 ACAAGGAATTCAATTTTAGGGACAACA 59.929 33.333 7.93 0.00 0.00 3.33
5957 8223 7.610580 AGGAATTCAATTTTAGGGACAACAA 57.389 32.000 7.93 0.00 0.00 2.83
5958 8224 8.206126 AGGAATTCAATTTTAGGGACAACAAT 57.794 30.769 7.93 0.00 0.00 2.71
5959 8225 8.314021 AGGAATTCAATTTTAGGGACAACAATC 58.686 33.333 7.93 0.00 0.00 2.67
5960 8226 8.314021 GGAATTCAATTTTAGGGACAACAATCT 58.686 33.333 7.93 0.00 0.00 2.40
5961 8227 9.143631 GAATTCAATTTTAGGGACAACAATCTG 57.856 33.333 0.00 0.00 0.00 2.90
5962 8228 6.024552 TCAATTTTAGGGACAACAATCTGC 57.975 37.500 0.00 0.00 0.00 4.26
5963 8229 5.774690 TCAATTTTAGGGACAACAATCTGCT 59.225 36.000 0.00 0.00 0.00 4.24
5964 8230 6.267471 TCAATTTTAGGGACAACAATCTGCTT 59.733 34.615 0.00 0.00 0.00 3.91
5965 8231 5.452078 TTTTAGGGACAACAATCTGCTTG 57.548 39.130 0.00 0.00 40.90 4.01
5966 8232 1.915141 AGGGACAACAATCTGCTTGG 58.085 50.000 0.00 0.00 39.30 3.61
5967 8233 1.425066 AGGGACAACAATCTGCTTGGA 59.575 47.619 0.00 0.00 39.30 3.53
5968 8234 2.158475 AGGGACAACAATCTGCTTGGAA 60.158 45.455 0.00 0.00 39.30 3.53
5969 8235 2.827921 GGGACAACAATCTGCTTGGAAT 59.172 45.455 0.00 0.00 39.30 3.01
5970 8236 3.367703 GGGACAACAATCTGCTTGGAATG 60.368 47.826 0.00 0.00 39.30 2.67
5971 8237 3.248266 GACAACAATCTGCTTGGAATGC 58.752 45.455 0.00 0.00 39.30 3.56
5972 8238 2.629137 ACAACAATCTGCTTGGAATGCA 59.371 40.909 0.00 0.00 45.42 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.076296 CTCTTGCGCTTCGGCTTCG 62.076 63.158 9.73 0.00 39.13 3.79
39 40 0.179171 CGTCGTGTATGCCTTCGTCT 60.179 55.000 0.00 0.00 0.00 4.18
44 45 1.153901 CGGTCGTCGTGTATGCCTT 60.154 57.895 0.00 0.00 0.00 4.35
56 57 2.637383 GGAGCTTGTCCTCGGTCGT 61.637 63.158 0.00 0.00 42.99 4.34
168 1087 0.179076 CCACCGTCATCATGCTAGCA 60.179 55.000 21.85 21.85 0.00 3.49
185 1104 1.561076 CCACCTTCATGATCTCCACCA 59.439 52.381 0.00 0.00 0.00 4.17
225 1150 3.266772 ACATCTTCTCAAACCATGGCCTA 59.733 43.478 13.04 0.00 0.00 3.93
237 1162 1.847328 TGTCGGCCTACATCTTCTCA 58.153 50.000 5.89 0.00 0.00 3.27
247 1172 0.613260 AACTTGAGCATGTCGGCCTA 59.387 50.000 0.00 0.00 0.00 3.93
450 1380 1.080569 CCAAAGTTCATGCGGCACC 60.081 57.895 4.03 0.00 0.00 5.01
453 1383 2.125952 GCCCAAAGTTCATGCGGC 60.126 61.111 0.00 0.00 0.00 6.53
454 1384 2.179018 CGCCCAAAGTTCATGCGG 59.821 61.111 0.00 0.00 41.42 5.69
455 1385 2.179018 CCGCCCAAAGTTCATGCG 59.821 61.111 0.00 0.00 44.47 4.73
486 1442 2.485038 CGTACACATTTAAAAGGCCCGT 59.515 45.455 0.00 0.00 0.00 5.28
501 1474 1.062002 CCATTTCATGTCCGCGTACAC 59.938 52.381 6.68 0.00 30.75 2.90
550 1523 4.774200 AGCATATGCCCAGTTTTCTTTTCT 59.226 37.500 23.96 0.00 43.38 2.52
551 1524 4.866486 CAGCATATGCCCAGTTTTCTTTTC 59.134 41.667 23.96 0.00 43.38 2.29
553 1526 4.088634 TCAGCATATGCCCAGTTTTCTTT 58.911 39.130 23.96 0.00 43.38 2.52
554 1527 3.698040 CTCAGCATATGCCCAGTTTTCTT 59.302 43.478 23.96 0.00 43.38 2.52
555 1528 3.285484 CTCAGCATATGCCCAGTTTTCT 58.715 45.455 23.96 0.00 43.38 2.52
556 1529 2.223665 GCTCAGCATATGCCCAGTTTTC 60.224 50.000 23.96 3.99 43.38 2.29
557 1530 1.753073 GCTCAGCATATGCCCAGTTTT 59.247 47.619 23.96 0.36 43.38 2.43
558 1531 1.396653 GCTCAGCATATGCCCAGTTT 58.603 50.000 23.96 1.16 43.38 2.66
559 1532 0.816825 CGCTCAGCATATGCCCAGTT 60.817 55.000 23.96 1.96 43.38 3.16
560 1533 1.227764 CGCTCAGCATATGCCCAGT 60.228 57.895 23.96 2.38 43.38 4.00
561 1534 1.964891 CCGCTCAGCATATGCCCAG 60.965 63.158 23.96 19.46 43.38 4.45
562 1535 2.111669 CCGCTCAGCATATGCCCA 59.888 61.111 23.96 9.91 43.38 5.36
563 1536 2.670934 CCCGCTCAGCATATGCCC 60.671 66.667 23.96 9.30 43.38 5.36
564 1537 2.111878 ACCCGCTCAGCATATGCC 59.888 61.111 23.96 7.81 43.38 4.40
565 1538 2.256591 CCACCCGCTCAGCATATGC 61.257 63.158 20.36 20.36 42.49 3.14
566 1539 2.256591 GCCACCCGCTCAGCATATG 61.257 63.158 0.00 0.00 0.00 1.78
567 1540 2.111878 GCCACCCGCTCAGCATAT 59.888 61.111 0.00 0.00 0.00 1.78
568 1541 4.175337 GGCCACCCGCTCAGCATA 62.175 66.667 0.00 0.00 37.74 3.14
580 1553 3.998672 TCCGTTCAGGTCGGCCAC 61.999 66.667 9.71 0.00 46.49 5.01
581 1554 3.998672 GTCCGTTCAGGTCGGCCA 61.999 66.667 9.71 0.00 46.49 5.36
586 1559 1.529865 CCTTTTTCGTCCGTTCAGGTC 59.470 52.381 0.00 0.00 41.99 3.85
587 1560 1.139455 TCCTTTTTCGTCCGTTCAGGT 59.861 47.619 0.00 0.00 41.99 4.00
588 1561 1.529865 GTCCTTTTTCGTCCGTTCAGG 59.470 52.381 0.00 0.00 42.97 3.86
589 1562 2.206750 TGTCCTTTTTCGTCCGTTCAG 58.793 47.619 0.00 0.00 0.00 3.02
590 1563 2.312722 TGTCCTTTTTCGTCCGTTCA 57.687 45.000 0.00 0.00 0.00 3.18
591 1564 3.891056 ATTGTCCTTTTTCGTCCGTTC 57.109 42.857 0.00 0.00 0.00 3.95
592 1565 4.998672 TGATATTGTCCTTTTTCGTCCGTT 59.001 37.500 0.00 0.00 0.00 4.44
593 1566 4.571919 TGATATTGTCCTTTTTCGTCCGT 58.428 39.130 0.00 0.00 0.00 4.69
594 1567 5.501715 CATGATATTGTCCTTTTTCGTCCG 58.498 41.667 0.00 0.00 0.00 4.79
595 1568 5.357032 ACCATGATATTGTCCTTTTTCGTCC 59.643 40.000 0.00 0.00 0.00 4.79
596 1569 6.436843 ACCATGATATTGTCCTTTTTCGTC 57.563 37.500 0.00 0.00 0.00 4.20
597 1570 5.357032 GGACCATGATATTGTCCTTTTTCGT 59.643 40.000 9.99 0.00 44.17 3.85
598 1571 5.504010 CGGACCATGATATTGTCCTTTTTCG 60.504 44.000 13.94 0.00 45.13 3.46
599 1572 5.357032 ACGGACCATGATATTGTCCTTTTTC 59.643 40.000 13.94 0.00 45.13 2.29
600 1573 5.261216 ACGGACCATGATATTGTCCTTTTT 58.739 37.500 13.94 0.00 45.13 1.94
601 1574 4.855340 ACGGACCATGATATTGTCCTTTT 58.145 39.130 13.94 0.00 45.13 2.27
602 1575 4.503714 ACGGACCATGATATTGTCCTTT 57.496 40.909 13.94 1.48 45.13 3.11
603 1576 4.503714 AACGGACCATGATATTGTCCTT 57.496 40.909 13.94 4.41 45.13 3.36
604 1577 4.199310 CAAACGGACCATGATATTGTCCT 58.801 43.478 13.94 2.00 45.13 3.85
605 1578 3.315191 CCAAACGGACCATGATATTGTCC 59.685 47.826 7.76 7.76 44.12 4.02
606 1579 3.315191 CCCAAACGGACCATGATATTGTC 59.685 47.826 0.00 0.00 0.00 3.18
607 1580 3.287222 CCCAAACGGACCATGATATTGT 58.713 45.455 0.00 0.00 0.00 2.71
608 1581 3.287222 ACCCAAACGGACCATGATATTG 58.713 45.455 0.00 0.00 34.64 1.90
609 1582 3.662759 ACCCAAACGGACCATGATATT 57.337 42.857 0.00 0.00 34.64 1.28
610 1583 3.662759 AACCCAAACGGACCATGATAT 57.337 42.857 0.00 0.00 34.64 1.63
611 1584 4.263435 GTTAACCCAAACGGACCATGATA 58.737 43.478 0.00 0.00 34.64 2.15
612 1585 3.086282 GTTAACCCAAACGGACCATGAT 58.914 45.455 0.00 0.00 34.64 2.45
613 1586 2.506444 GTTAACCCAAACGGACCATGA 58.494 47.619 0.00 0.00 34.64 3.07
614 1587 1.198178 CGTTAACCCAAACGGACCATG 59.802 52.381 0.00 0.00 46.47 3.66
615 1588 1.525941 CGTTAACCCAAACGGACCAT 58.474 50.000 0.00 0.00 46.47 3.55
616 1589 3.003740 CGTTAACCCAAACGGACCA 57.996 52.632 0.00 0.00 46.47 4.02
622 1595 2.802247 ACTCTAACGCGTTAACCCAAAC 59.198 45.455 29.58 0.00 0.00 2.93
623 1596 3.110447 ACTCTAACGCGTTAACCCAAA 57.890 42.857 29.58 10.47 0.00 3.28
624 1597 2.801679 CAACTCTAACGCGTTAACCCAA 59.198 45.455 29.58 11.20 0.00 4.12
625 1598 2.406130 CAACTCTAACGCGTTAACCCA 58.594 47.619 29.58 11.94 0.00 4.51
626 1599 1.127397 GCAACTCTAACGCGTTAACCC 59.873 52.381 29.58 12.89 0.00 4.11
627 1600 2.064014 AGCAACTCTAACGCGTTAACC 58.936 47.619 29.58 15.00 0.00 2.85
628 1601 2.985139 AGAGCAACTCTAACGCGTTAAC 59.015 45.455 29.58 15.70 39.28 2.01
629 1602 2.984471 CAGAGCAACTCTAACGCGTTAA 59.016 45.455 29.58 19.52 38.99 2.01
630 1603 2.227149 TCAGAGCAACTCTAACGCGTTA 59.773 45.455 28.34 28.34 38.99 3.18
631 1604 1.000607 TCAGAGCAACTCTAACGCGTT 60.001 47.619 29.27 29.27 38.99 4.84
632 1605 0.596577 TCAGAGCAACTCTAACGCGT 59.403 50.000 5.58 5.58 38.99 6.01
633 1606 1.263776 CTCAGAGCAACTCTAACGCG 58.736 55.000 3.53 3.53 38.99 6.01
634 1607 2.355717 ACTCAGAGCAACTCTAACGC 57.644 50.000 0.00 0.00 38.99 4.84
635 1608 3.127895 AGCTACTCAGAGCAACTCTAACG 59.872 47.826 0.00 0.00 45.43 3.18
636 1609 4.712122 AGCTACTCAGAGCAACTCTAAC 57.288 45.455 0.00 0.00 45.43 2.34
637 1610 5.243954 TGAAAGCTACTCAGAGCAACTCTAA 59.756 40.000 0.00 0.00 45.43 2.10
638 1611 4.767409 TGAAAGCTACTCAGAGCAACTCTA 59.233 41.667 0.00 0.00 45.43 2.43
639 1612 3.576118 TGAAAGCTACTCAGAGCAACTCT 59.424 43.478 0.00 0.00 45.43 3.24
640 1613 3.919216 TGAAAGCTACTCAGAGCAACTC 58.081 45.455 0.00 0.00 45.43 3.01
641 1614 4.342862 TTGAAAGCTACTCAGAGCAACT 57.657 40.909 0.00 0.00 45.43 3.16
642 1615 5.424121 TTTTGAAAGCTACTCAGAGCAAC 57.576 39.130 0.00 0.00 45.43 4.17
643 1616 7.928307 ATATTTTGAAAGCTACTCAGAGCAA 57.072 32.000 0.00 0.00 45.43 3.91
644 1617 7.928307 AATATTTTGAAAGCTACTCAGAGCA 57.072 32.000 0.00 0.00 45.43 4.26
645 1618 9.875675 CATAATATTTTGAAAGCTACTCAGAGC 57.124 33.333 0.00 0.00 43.19 4.09
649 1622 9.905713 ACTCCATAATATTTTGAAAGCTACTCA 57.094 29.630 7.40 0.00 0.00 3.41
710 1683 5.150715 TCTGCTGGAGTTGACATATCCTAT 58.849 41.667 7.70 0.00 34.04 2.57
713 1686 3.726607 CTCTGCTGGAGTTGACATATCC 58.273 50.000 0.00 0.46 37.30 2.59
746 1762 4.095185 TGAGGGTTGTTTGTAAAACGACTG 59.905 41.667 18.15 0.00 35.42 3.51
794 1811 0.320160 ACTTTGGGTAACTCGCGTCC 60.320 55.000 5.77 2.31 0.00 4.79
1119 2140 4.112341 CGGTGAGGGGTCGTCGAC 62.112 72.222 17.16 17.16 0.00 4.20
1240 2261 4.516195 GAGGAAGCGGCGGGAGTC 62.516 72.222 9.78 0.00 0.00 3.36
1637 2658 0.753479 GACCTCTCCATCTCAGGCGA 60.753 60.000 0.00 0.00 0.00 5.54
1706 2727 1.181741 AGCTCTCTCACAGCCAACGA 61.182 55.000 0.00 0.00 37.63 3.85
1769 2790 1.879380 CTTCTCCATTGCAACGTCCAA 59.121 47.619 0.00 4.37 0.00 3.53
1780 2801 1.075536 GGTTCCACACCCTTCTCCATT 59.924 52.381 0.00 0.00 40.19 3.16
2123 3913 6.313519 TCTCCTATATGGTTTGCAAACTCT 57.686 37.500 34.39 25.15 38.89 3.24
2241 4032 5.447624 AACCACCACGGAAAAAGATTAAG 57.552 39.130 0.00 0.00 38.63 1.85
2301 4092 3.864789 ACCTCAACCTGAATGACACTT 57.135 42.857 0.00 0.00 0.00 3.16
2310 4101 3.855255 TCATGAACAACCTCAACCTGA 57.145 42.857 0.00 0.00 0.00 3.86
2466 4257 4.338379 AAACACTGTGTACCTCTCCTTC 57.662 45.455 14.69 0.00 0.00 3.46
2502 4293 8.076178 GCAAAGCAAATAGAGAAGTTACAAGAA 58.924 33.333 0.00 0.00 0.00 2.52
2540 4331 9.160496 AGCAACAAACAATCAAGTTAAAAATGA 57.840 25.926 0.00 0.00 0.00 2.57
2592 4383 6.794374 TGGTATGACAATGACAATAACATGC 58.206 36.000 0.00 0.00 0.00 4.06
2600 4391 7.625469 TGGTAGTTATGGTATGACAATGACAA 58.375 34.615 0.00 0.00 0.00 3.18
2620 4413 8.902540 TTGAGCAGGTTATAAATGTATGGTAG 57.097 34.615 0.00 0.00 0.00 3.18
2717 4511 3.847542 TGCATCAAAGTTGCGCATATTT 58.152 36.364 12.75 12.89 43.10 1.40
2784 4578 2.407562 TGATCTGCCTACCAGCCATTA 58.592 47.619 0.00 0.00 41.50 1.90
2820 4614 6.655003 TGTAAAAAGAGAAACATGGCCTAGAG 59.345 38.462 3.32 0.00 0.00 2.43
2833 4629 6.770785 ACTACATGCCAACTGTAAAAAGAGAA 59.229 34.615 0.00 0.00 0.00 2.87
3079 4875 8.234136 TCCAAATCAGAACTATGATACGTACT 57.766 34.615 0.00 0.00 39.00 2.73
3198 5001 7.672351 TGCTGTAAACAAATAACAGAAAACG 57.328 32.000 5.91 0.00 42.59 3.60
3220 5023 3.160269 CAGAAATAAGGGATGGGGATGC 58.840 50.000 0.00 0.00 0.00 3.91
3268 5071 9.988815 CTAAGAAATTCAGCACCAGTATATAGT 57.011 33.333 0.00 0.00 0.00 2.12
3307 5110 2.810274 ACTAGGCATTGCATATTGCTCG 59.190 45.455 11.39 0.00 45.31 5.03
3349 5297 1.602377 ACGGCAAGCTAGTGACAAAAC 59.398 47.619 0.00 0.00 0.00 2.43
3361 5309 3.560826 TTGCAAAACTACGGCAAGC 57.439 47.368 0.00 0.00 42.12 4.01
3426 5374 5.297029 GGCCTAATAGATTGGACAACAAGAC 59.703 44.000 0.00 0.00 43.48 3.01
3495 5443 5.645067 CAGATGAGTGGATGTAAGAAAGCAA 59.355 40.000 0.00 0.00 0.00 3.91
3517 5465 9.405587 CATAAAATAACACACCACTAAAACCAG 57.594 33.333 0.00 0.00 0.00 4.00
3574 5522 6.462207 CGATCTCTGAGAACCTGGTTTCATAT 60.462 42.308 14.28 11.69 0.00 1.78
3700 5651 7.880160 TGCCTTGACAATGCTAGTAATAATT 57.120 32.000 15.22 0.00 0.00 1.40
3796 5752 8.003784 GCTTCCAGAAAACAAATCAAAATTACG 58.996 33.333 0.00 0.00 0.00 3.18
3843 5799 4.258543 GCAGCACATGGTTAACTAGGTAA 58.741 43.478 9.00 0.00 0.00 2.85
4020 5976 1.893919 AACCCTGCCTCTTCGCTCTC 61.894 60.000 0.00 0.00 0.00 3.20
4035 5991 2.817844 CTGTAGGCTACCAAAACAACCC 59.182 50.000 21.34 0.00 0.00 4.11
4042 5998 5.811796 TTCTGTAACTGTAGGCTACCAAA 57.188 39.130 21.34 2.65 0.00 3.28
4068 6024 1.542108 GCCCATCTAGCAGTCCATCAC 60.542 57.143 0.00 0.00 0.00 3.06
4069 6025 0.761187 GCCCATCTAGCAGTCCATCA 59.239 55.000 0.00 0.00 0.00 3.07
4070 6026 1.055040 AGCCCATCTAGCAGTCCATC 58.945 55.000 0.00 0.00 0.00 3.51
4071 6027 1.516110 AAGCCCATCTAGCAGTCCAT 58.484 50.000 0.00 0.00 0.00 3.41
4072 6028 1.210478 GAAAGCCCATCTAGCAGTCCA 59.790 52.381 0.00 0.00 0.00 4.02
4108 6064 9.388346 CAACAGCATACGATTTGTAACTTTTAA 57.612 29.630 0.00 0.00 36.44 1.52
4144 6100 3.368427 CCTGATAGAAACAGCGTCAAGGA 60.368 47.826 0.00 0.00 34.47 3.36
4207 6163 7.739498 AGCTTCAAATGCATTCAAAGAAAAT 57.261 28.000 26.13 12.73 0.00 1.82
4352 6511 7.992180 AAAGTTGCTACTGAAAAGTGAAATG 57.008 32.000 0.36 0.00 34.01 2.32
4353 6512 8.903820 AGTAAAGTTGCTACTGAAAAGTGAAAT 58.096 29.630 0.36 0.00 34.01 2.17
4402 6561 6.043938 ACAGAAAAGAACATTCCCCACTAGTA 59.956 38.462 0.00 0.00 0.00 1.82
4403 6562 5.163088 ACAGAAAAGAACATTCCCCACTAGT 60.163 40.000 0.00 0.00 0.00 2.57
4404 6563 5.182001 CACAGAAAAGAACATTCCCCACTAG 59.818 44.000 0.00 0.00 0.00 2.57
4552 6746 3.876914 CTCTGTGACCAACTGCAAAACTA 59.123 43.478 0.00 0.00 0.00 2.24
5058 7252 1.269257 GGAACAACTGAACAAGGCTGC 60.269 52.381 0.00 0.00 0.00 5.25
5141 7336 2.806244 CCACCAACTTACAAGAGGAACG 59.194 50.000 10.64 0.00 0.00 3.95
5392 7587 6.366061 TGACAGAATTGTACAATCTTCACTCG 59.634 38.462 21.02 11.84 37.76 4.18
5414 7631 8.337532 GGGCAAATAAAATAAGCAAATCATGAC 58.662 33.333 0.00 0.00 0.00 3.06
5428 7645 7.763985 CGGAAAAATACAGAGGGCAAATAAAAT 59.236 33.333 0.00 0.00 0.00 1.82
5451 7668 2.103094 GTCATTCATCCCTGTGATCGGA 59.897 50.000 0.00 0.00 0.00 4.55
5453 7670 2.103771 AGGTCATTCATCCCTGTGATCG 59.896 50.000 0.00 0.00 0.00 3.69
5504 7721 1.535833 ATAGGATAGCAGGACCGACG 58.464 55.000 0.00 0.00 0.00 5.12
5505 7722 4.308265 GAAAATAGGATAGCAGGACCGAC 58.692 47.826 0.00 0.00 0.00 4.79
5506 7723 3.323979 GGAAAATAGGATAGCAGGACCGA 59.676 47.826 0.00 0.00 0.00 4.69
5540 7757 4.942852 TGGTTCCACAAAAGCAATACTTG 58.057 39.130 0.00 0.00 39.09 3.16
5556 7773 1.304134 ATTTGGTCGGCCTGGTTCC 60.304 57.895 7.97 0.00 35.27 3.62
5562 7779 2.114670 CGCATGATTTGGTCGGCCT 61.115 57.895 7.97 0.00 35.27 5.19
5605 7822 2.738964 GCGCCTCTCTTTAGATCGGTTT 60.739 50.000 0.00 0.00 31.89 3.27
5606 7823 1.202428 GCGCCTCTCTTTAGATCGGTT 60.202 52.381 0.00 0.00 31.89 4.44
5607 7824 0.386113 GCGCCTCTCTTTAGATCGGT 59.614 55.000 0.00 0.00 31.89 4.69
5608 7825 0.385751 TGCGCCTCTCTTTAGATCGG 59.614 55.000 4.18 0.00 31.89 4.18
5634 7851 1.533625 TGTTTCGGCTTCCATCCAAG 58.466 50.000 0.00 0.00 0.00 3.61
5678 7895 0.321919 CCTTCTAGTGCTTGCTGGCA 60.322 55.000 0.33 0.33 40.15 4.92
5682 7899 3.988976 TGATTCCTTCTAGTGCTTGCT 57.011 42.857 0.00 0.00 0.00 3.91
5683 7900 5.605534 TCTATGATTCCTTCTAGTGCTTGC 58.394 41.667 0.00 0.00 0.00 4.01
5684 7901 6.202570 GCTTCTATGATTCCTTCTAGTGCTTG 59.797 42.308 0.00 0.00 0.00 4.01
5685 7902 6.126940 TGCTTCTATGATTCCTTCTAGTGCTT 60.127 38.462 0.00 0.00 0.00 3.91
5816 8033 3.819920 TGAGCGAGCTCAGGCGAG 61.820 66.667 22.28 0.00 46.80 5.03
5939 8205 5.774690 AGCAGATTGTTGTCCCTAAAATTGA 59.225 36.000 0.00 0.00 0.00 2.57
5940 8206 6.029346 AGCAGATTGTTGTCCCTAAAATTG 57.971 37.500 0.00 0.00 0.00 2.32
5941 8207 6.458210 CAAGCAGATTGTTGTCCCTAAAATT 58.542 36.000 0.00 0.00 33.95 1.82
5942 8208 5.047092 CCAAGCAGATTGTTGTCCCTAAAAT 60.047 40.000 0.00 0.00 37.17 1.82
5943 8209 4.280677 CCAAGCAGATTGTTGTCCCTAAAA 59.719 41.667 0.00 0.00 37.17 1.52
5945 8211 3.073798 TCCAAGCAGATTGTTGTCCCTAA 59.926 43.478 0.00 0.00 37.17 2.69
5947 8213 1.425066 TCCAAGCAGATTGTTGTCCCT 59.575 47.619 0.00 0.00 37.17 4.20
5948 8214 1.909700 TCCAAGCAGATTGTTGTCCC 58.090 50.000 0.00 0.00 37.17 4.46
5949 8215 3.841643 CATTCCAAGCAGATTGTTGTCC 58.158 45.455 0.00 0.00 37.17 4.02
5950 8216 3.248266 GCATTCCAAGCAGATTGTTGTC 58.752 45.455 0.00 0.00 37.17 3.18
5951 8217 2.629137 TGCATTCCAAGCAGATTGTTGT 59.371 40.909 0.00 0.00 37.02 3.32
5952 8218 3.306917 TGCATTCCAAGCAGATTGTTG 57.693 42.857 0.00 0.00 37.02 3.33


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

AutoCloner maintained by Alex Coulton.