Multiple sequence alignment - TraesCS3A01G104500

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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 TraesCS3A01G104500 chr3A 100.000 3987 0 0 1 3987 67910073 67914059 0.000000e+00 7363.0
1 TraesCS3A01G104500 chr3A 82.328 481 57 16 1590 2047 164279270 164278795 3.740000e-105 392.0
2 TraesCS3A01G104500 chr3B 93.261 1855 88 15 2105 3932 94667436 94669280 0.000000e+00 2699.0
3 TraesCS3A01G104500 chr3B 92.605 1217 51 18 865 2048 94666228 94667438 0.000000e+00 1712.0
4 TraesCS3A01G104500 chr3B 89.474 114 5 3 679 790 94663803 94663911 1.930000e-28 137.0
5 TraesCS3A01G104500 chr3D 93.482 1657 64 19 2105 3737 58756078 58757714 0.000000e+00 2422.0
6 TraesCS3A01G104500 chr3D 92.426 1360 68 19 696 2048 58754749 58756080 0.000000e+00 1908.0
7 TraesCS3A01G104500 chr3D 90.950 221 11 4 3766 3977 58757711 58757931 5.040000e-74 289.0
8 TraesCS3A01G104500 chr3D 85.000 140 16 5 3824 3959 167049467 167049605 1.930000e-28 137.0
9 TraesCS3A01G104500 chr3D 87.603 121 9 5 3845 3959 389633130 389633010 6.950000e-28 135.0
10 TraesCS3A01G104500 chr2B 94.081 321 14 4 275 592 472883524 472883206 2.150000e-132 483.0
11 TraesCS3A01G104500 chr2B 91.698 265 19 3 2 264 34301992 34301729 8.140000e-97 364.0
12 TraesCS3A01G104500 chr2B 91.532 248 10 3 2 239 472883773 472883527 8.260000e-87 331.0
13 TraesCS3A01G104500 chr2B 91.781 73 2 1 2043 2111 321689905 321689833 9.120000e-17 99.0
14 TraesCS3A01G104500 chr2B 91.304 46 3 1 551 595 16301615 16301570 1.200000e-05 62.1
15 TraesCS3A01G104500 chrUn 85.942 313 21 6 2716 3007 3120879 3120569 2.990000e-81 313.0
16 TraesCS3A01G104500 chr6D 86.826 167 12 8 3809 3966 48675890 48676055 1.140000e-40 178.0
17 TraesCS3A01G104500 chr7B 88.356 146 13 3 3817 3959 477814825 477814969 5.300000e-39 172.0
18 TraesCS3A01G104500 chr5B 84.247 146 16 7 3818 3959 290386640 290386498 6.950000e-28 135.0
19 TraesCS3A01G104500 chr5B 95.238 63 2 1 2046 2107 370194767 370194705 9.120000e-17 99.0
20 TraesCS3A01G104500 chr5B 95.238 63 2 1 2046 2107 370239627 370239565 9.120000e-17 99.0
21 TraesCS3A01G104500 chr1D 83.562 146 15 8 3817 3956 395850789 395850931 1.160000e-25 128.0
22 TraesCS3A01G104500 chr1D 96.491 57 2 0 2045 2101 351255384 351255328 1.180000e-15 95.3
23 TraesCS3A01G104500 chr1B 83.582 134 16 5 3832 3959 211627043 211626910 1.950000e-23 121.0
24 TraesCS3A01G104500 chr5D 94.030 67 3 1 2042 2107 22401350 22401416 2.540000e-17 100.0
25 TraesCS3A01G104500 chr5D 90.909 44 3 1 549 592 521183140 521183182 1.550000e-04 58.4
26 TraesCS3A01G104500 chr5A 94.030 67 3 1 2042 2107 15866761 15866827 2.540000e-17 100.0
27 TraesCS3A01G104500 chr5A 85.965 57 6 2 538 592 474317501 474317445 4.300000e-05 60.2
28 TraesCS3A01G104500 chr5A 85.714 56 6 2 538 592 474052077 474052023 1.550000e-04 58.4
29 TraesCS3A01G104500 chr5A 85.965 57 5 3 538 592 474185554 474185499 1.550000e-04 58.4
30 TraesCS3A01G104500 chr5A 85.455 55 6 2 538 591 474379208 474379155 5.570000e-04 56.5
31 TraesCS3A01G104500 chr6A 96.610 59 2 0 2043 2101 573510876 573510818 9.120000e-17 99.0
32 TraesCS3A01G104500 chr4A 96.429 56 2 0 2046 2101 6936614 6936559 4.240000e-15 93.5
33 TraesCS3A01G104500 chr4A 97.297 37 1 0 559 595 731667331 731667295 3.330000e-06 63.9
34 TraesCS3A01G104500 chr4A 82.857 70 8 4 538 605 552889315 552889382 4.300000e-05 60.2
35 TraesCS3A01G104500 chr7D 91.045 67 3 2 2043 2106 72175871 72175937 1.970000e-13 87.9


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 TraesCS3A01G104500 chr3A 67910073 67914059 3986 False 7363.000000 7363 100.0000 1 3987 1 chr3A.!!$F1 3986
1 TraesCS3A01G104500 chr3B 94663803 94669280 5477 False 1516.000000 2699 91.7800 679 3932 3 chr3B.!!$F1 3253
2 TraesCS3A01G104500 chr3D 58754749 58757931 3182 False 1539.666667 2422 92.2860 696 3977 3 chr3D.!!$F2 3281
3 TraesCS3A01G104500 chr2B 472883206 472883773 567 True 407.000000 483 92.8065 2 592 2 chr2B.!!$R4 590

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
454 465 0.179040 GGACGGTGAACACAAGGGAA 60.179 55.0 7.25 0.0 0.00 3.97 F
1207 3501 0.177141 TTCTCGCTTGTTATCCCCCG 59.823 55.0 0.00 0.0 0.00 5.73 F
2056 4381 0.113776 TGTGGAACTACTCCCTCCGT 59.886 55.0 0.00 0.0 44.69 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 3919 0.178975 TTGGCCCGAACTCAAACCAT 60.179 50.000 0.0 0.0 0.00 3.55 R
2092 4417 1.340568 GCCTTCATACTACTCCGTCCC 59.659 57.143 0.0 0.0 0.00 4.46 R
3677 6027 0.762842 TGCGTGAGGCCCCAGTATAT 60.763 55.000 0.0 0.0 42.61 0.86 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
126 136 7.543172 CAGACTAATTTTCCACACATCCAAATG 59.457 37.037 0.00 0.00 38.93 2.32
148 158 6.662414 TGGCATAATAAACTTTCTGTCTCG 57.338 37.500 0.00 0.00 0.00 4.04
153 163 9.851043 GCATAATAAACTTTCTGTCTCGATAAC 57.149 33.333 0.00 0.00 0.00 1.89
217 228 1.528129 CCCAGAAGTCTCAACCAAGC 58.472 55.000 0.00 0.00 0.00 4.01
218 229 1.202806 CCCAGAAGTCTCAACCAAGCA 60.203 52.381 0.00 0.00 0.00 3.91
226 237 6.541641 AGAAGTCTCAACCAAGCATATCATTC 59.458 38.462 0.00 0.00 0.00 2.67
239 250 4.495472 GCATATCATTCGTTTCGTTGTTGG 59.505 41.667 0.00 0.00 0.00 3.77
241 252 3.326733 TCATTCGTTTCGTTGTTGGTG 57.673 42.857 0.00 0.00 0.00 4.17
242 253 2.032302 TCATTCGTTTCGTTGTTGGTGG 59.968 45.455 0.00 0.00 0.00 4.61
243 254 1.451067 TTCGTTTCGTTGTTGGTGGT 58.549 45.000 0.00 0.00 0.00 4.16
244 255 0.727970 TCGTTTCGTTGTTGGTGGTG 59.272 50.000 0.00 0.00 0.00 4.17
245 256 0.863957 CGTTTCGTTGTTGGTGGTGC 60.864 55.000 0.00 0.00 0.00 5.01
246 257 0.454196 GTTTCGTTGTTGGTGGTGCT 59.546 50.000 0.00 0.00 0.00 4.40
247 258 1.135228 GTTTCGTTGTTGGTGGTGCTT 60.135 47.619 0.00 0.00 0.00 3.91
248 259 1.178276 TTCGTTGTTGGTGGTGCTTT 58.822 45.000 0.00 0.00 0.00 3.51
249 260 0.453793 TCGTTGTTGGTGGTGCTTTG 59.546 50.000 0.00 0.00 0.00 2.77
250 261 0.527385 CGTTGTTGGTGGTGCTTTGG 60.527 55.000 0.00 0.00 0.00 3.28
251 262 0.820871 GTTGTTGGTGGTGCTTTGGA 59.179 50.000 0.00 0.00 0.00 3.53
252 263 0.820871 TTGTTGGTGGTGCTTTGGAC 59.179 50.000 0.00 0.00 0.00 4.02
253 264 0.323816 TGTTGGTGGTGCTTTGGACA 60.324 50.000 0.00 0.00 0.00 4.02
254 265 0.820871 GTTGGTGGTGCTTTGGACAA 59.179 50.000 0.00 0.00 0.00 3.18
255 266 1.205893 GTTGGTGGTGCTTTGGACAAA 59.794 47.619 0.00 0.00 0.00 2.83
256 267 1.786937 TGGTGGTGCTTTGGACAAAT 58.213 45.000 0.00 0.00 0.00 2.32
257 268 1.411977 TGGTGGTGCTTTGGACAAATG 59.588 47.619 0.00 0.00 0.00 2.32
258 269 1.686052 GGTGGTGCTTTGGACAAATGA 59.314 47.619 0.00 0.00 0.00 2.57
259 270 2.299867 GGTGGTGCTTTGGACAAATGAT 59.700 45.455 0.00 0.00 0.00 2.45
260 271 3.578688 GTGGTGCTTTGGACAAATGATC 58.421 45.455 0.00 0.00 0.00 2.92
261 272 3.256631 GTGGTGCTTTGGACAAATGATCT 59.743 43.478 0.00 0.00 0.00 2.75
262 273 3.507233 TGGTGCTTTGGACAAATGATCTC 59.493 43.478 0.00 0.00 0.00 2.75
263 274 3.760684 GGTGCTTTGGACAAATGATCTCT 59.239 43.478 0.00 0.00 0.00 3.10
264 275 4.943705 GGTGCTTTGGACAAATGATCTCTA 59.056 41.667 0.00 0.00 0.00 2.43
265 276 5.163713 GGTGCTTTGGACAAATGATCTCTAC 60.164 44.000 0.00 0.00 0.00 2.59
266 277 5.412594 GTGCTTTGGACAAATGATCTCTACA 59.587 40.000 0.00 0.00 0.00 2.74
267 278 5.645067 TGCTTTGGACAAATGATCTCTACAG 59.355 40.000 0.00 0.00 0.00 2.74
268 279 5.645497 GCTTTGGACAAATGATCTCTACAGT 59.355 40.000 0.00 0.00 0.00 3.55
269 280 6.402983 GCTTTGGACAAATGATCTCTACAGTG 60.403 42.308 0.00 0.00 0.00 3.66
270 281 4.507710 TGGACAAATGATCTCTACAGTGC 58.492 43.478 0.00 0.00 0.00 4.40
271 282 3.873952 GGACAAATGATCTCTACAGTGCC 59.126 47.826 0.00 0.00 0.00 5.01
272 283 4.507710 GACAAATGATCTCTACAGTGCCA 58.492 43.478 0.00 0.00 0.00 4.92
273 284 4.511527 ACAAATGATCTCTACAGTGCCAG 58.488 43.478 0.00 0.00 0.00 4.85
289 300 2.334023 GCCAGACCCTTAGATGGAGAT 58.666 52.381 0.00 0.00 34.60 2.75
334 345 9.239551 GGACTAAAGATTTATGTTAGGGTTTGT 57.760 33.333 0.00 0.00 0.00 2.83
343 354 5.722021 ATGTTAGGGTTTGTTGACCATTC 57.278 39.130 0.00 0.00 41.65 2.67
358 369 5.301555 TGACCATTCGTACAAAAGTCATCA 58.698 37.500 0.05 0.00 0.00 3.07
368 379 8.139350 TCGTACAAAAGTCATCAGAACTAAAGA 58.861 33.333 0.00 0.00 0.00 2.52
369 380 8.761497 CGTACAAAAGTCATCAGAACTAAAGAA 58.239 33.333 0.00 0.00 0.00 2.52
439 450 1.213094 AACACACGCGAGAAAGGACG 61.213 55.000 15.93 0.00 0.00 4.79
443 454 2.257371 CGCGAGAAAGGACGGTGA 59.743 61.111 0.00 0.00 0.00 4.02
454 465 0.179040 GGACGGTGAACACAAGGGAA 60.179 55.000 7.25 0.00 0.00 3.97
474 485 3.870633 ACGAAGAACCTCATACTGGTC 57.129 47.619 0.00 0.00 36.69 4.02
478 489 4.617530 CGAAGAACCTCATACTGGTCGAAA 60.618 45.833 0.00 0.00 36.69 3.46
583 597 4.776647 GGCAACGCACGGGCATTC 62.777 66.667 11.77 0.00 41.24 2.67
592 606 1.269621 GCACGGGCATTCGACTAGTAT 60.270 52.381 3.77 0.00 40.72 2.12
593 607 2.662700 CACGGGCATTCGACTAGTATC 58.337 52.381 0.00 0.00 0.00 2.24
594 608 2.034179 CACGGGCATTCGACTAGTATCA 59.966 50.000 0.00 0.00 0.00 2.15
595 609 2.293677 ACGGGCATTCGACTAGTATCAG 59.706 50.000 0.00 0.00 0.00 2.90
596 610 2.552743 CGGGCATTCGACTAGTATCAGA 59.447 50.000 0.00 0.00 0.00 3.27
597 611 3.191581 CGGGCATTCGACTAGTATCAGAT 59.808 47.826 0.00 0.00 0.00 2.90
598 612 4.489810 GGGCATTCGACTAGTATCAGATG 58.510 47.826 0.00 0.00 0.00 2.90
599 613 4.218635 GGGCATTCGACTAGTATCAGATGA 59.781 45.833 0.00 0.00 0.00 2.92
600 614 5.105554 GGGCATTCGACTAGTATCAGATGAT 60.106 44.000 0.00 0.31 38.51 2.45
601 615 5.804473 GGCATTCGACTAGTATCAGATGATG 59.196 44.000 5.58 0.00 36.05 3.07
602 616 5.804473 GCATTCGACTAGTATCAGATGATGG 59.196 44.000 5.58 0.00 36.05 3.51
603 617 5.378292 TTCGACTAGTATCAGATGATGGC 57.622 43.478 5.58 0.00 36.05 4.40
604 618 4.398319 TCGACTAGTATCAGATGATGGCA 58.602 43.478 5.58 0.00 36.05 4.92
605 619 4.457257 TCGACTAGTATCAGATGATGGCAG 59.543 45.833 5.58 2.58 36.05 4.85
606 620 4.493547 GACTAGTATCAGATGATGGCAGC 58.506 47.826 5.58 0.00 36.05 5.25
607 621 2.452295 AGTATCAGATGATGGCAGCG 57.548 50.000 5.58 0.00 35.08 5.18
608 622 1.001746 AGTATCAGATGATGGCAGCGG 59.998 52.381 5.58 0.00 35.08 5.52
609 623 0.321034 TATCAGATGATGGCAGCGGC 60.321 55.000 0.00 0.00 35.08 6.53
610 624 3.646976 CAGATGATGGCAGCGGCG 61.647 66.667 0.51 0.51 42.47 6.46
611 625 4.923942 AGATGATGGCAGCGGCGG 62.924 66.667 9.78 0.00 42.47 6.13
626 640 4.137872 CGGCGCGAGAAACCCCTA 62.138 66.667 12.10 0.00 0.00 3.53
627 641 2.504519 GGCGCGAGAAACCCCTAT 59.495 61.111 12.10 0.00 0.00 2.57
628 642 1.887707 GGCGCGAGAAACCCCTATG 60.888 63.158 12.10 0.00 0.00 2.23
629 643 2.534903 GCGCGAGAAACCCCTATGC 61.535 63.158 12.10 0.00 0.00 3.14
630 644 2.237751 CGCGAGAAACCCCTATGCG 61.238 63.158 0.00 0.00 35.73 4.73
631 645 1.143183 GCGAGAAACCCCTATGCGA 59.857 57.895 0.00 0.00 0.00 5.10
632 646 0.461339 GCGAGAAACCCCTATGCGAA 60.461 55.000 0.00 0.00 0.00 4.70
633 647 1.571919 CGAGAAACCCCTATGCGAAG 58.428 55.000 0.00 0.00 0.00 3.79
647 661 4.373116 GAAGCGTGGCTGGGTCGA 62.373 66.667 0.00 0.00 39.62 4.20
648 662 4.379243 AAGCGTGGCTGGGTCGAG 62.379 66.667 0.00 0.00 39.62 4.04
651 665 3.461773 CGTGGCTGGGTCGAGGAT 61.462 66.667 0.00 0.00 0.00 3.24
652 666 2.187946 GTGGCTGGGTCGAGGATG 59.812 66.667 0.00 0.00 0.00 3.51
653 667 2.038813 TGGCTGGGTCGAGGATGA 59.961 61.111 0.00 0.00 0.00 2.92
654 668 2.060383 TGGCTGGGTCGAGGATGAG 61.060 63.158 0.00 0.00 0.00 2.90
655 669 2.107953 GCTGGGTCGAGGATGAGC 59.892 66.667 0.00 0.00 35.66 4.26
659 673 3.309582 GGTCGAGGATGAGCCCAA 58.690 61.111 0.00 0.00 37.37 4.12
660 674 1.153349 GGTCGAGGATGAGCCCAAC 60.153 63.158 0.00 0.00 37.37 3.77
661 675 1.617947 GGTCGAGGATGAGCCCAACT 61.618 60.000 0.00 0.00 37.37 3.16
662 676 0.250513 GTCGAGGATGAGCCCAACTT 59.749 55.000 0.00 0.00 37.37 2.66
663 677 0.984230 TCGAGGATGAGCCCAACTTT 59.016 50.000 0.00 0.00 37.37 2.66
664 678 1.089920 CGAGGATGAGCCCAACTTTG 58.910 55.000 0.00 0.00 37.37 2.77
665 679 1.339055 CGAGGATGAGCCCAACTTTGA 60.339 52.381 0.00 0.00 37.37 2.69
666 680 2.363683 GAGGATGAGCCCAACTTTGAG 58.636 52.381 0.00 0.00 37.37 3.02
667 681 1.707427 AGGATGAGCCCAACTTTGAGT 59.293 47.619 0.00 0.00 37.37 3.41
668 682 2.087646 GGATGAGCCCAACTTTGAGTC 58.912 52.381 0.00 0.00 0.00 3.36
669 683 2.290577 GGATGAGCCCAACTTTGAGTCT 60.291 50.000 0.00 0.00 0.00 3.24
670 684 3.055094 GGATGAGCCCAACTTTGAGTCTA 60.055 47.826 0.00 0.00 0.00 2.59
671 685 3.402628 TGAGCCCAACTTTGAGTCTAC 57.597 47.619 0.00 0.00 0.00 2.59
672 686 2.972713 TGAGCCCAACTTTGAGTCTACT 59.027 45.455 0.00 0.00 0.00 2.57
673 687 4.157246 TGAGCCCAACTTTGAGTCTACTA 58.843 43.478 0.00 0.00 0.00 1.82
674 688 4.777896 TGAGCCCAACTTTGAGTCTACTAT 59.222 41.667 0.00 0.00 0.00 2.12
675 689 5.955959 TGAGCCCAACTTTGAGTCTACTATA 59.044 40.000 0.00 0.00 0.00 1.31
676 690 6.439375 TGAGCCCAACTTTGAGTCTACTATAA 59.561 38.462 0.00 0.00 0.00 0.98
677 691 6.879400 AGCCCAACTTTGAGTCTACTATAAG 58.121 40.000 0.00 3.43 0.00 1.73
678 692 5.524281 GCCCAACTTTGAGTCTACTATAAGC 59.476 44.000 0.00 0.00 0.00 3.09
679 693 5.749109 CCCAACTTTGAGTCTACTATAAGCG 59.251 44.000 0.00 0.00 0.00 4.68
680 694 6.331061 CCAACTTTGAGTCTACTATAAGCGT 58.669 40.000 0.00 0.00 0.00 5.07
681 695 6.253727 CCAACTTTGAGTCTACTATAAGCGTG 59.746 42.308 0.00 3.89 0.00 5.34
682 696 6.754702 ACTTTGAGTCTACTATAAGCGTGA 57.245 37.500 0.00 0.00 0.00 4.35
687 701 8.672823 TTGAGTCTACTATAAGCGTGAATAGA 57.327 34.615 6.94 0.00 31.44 1.98
710 724 6.656693 AGAAATAGCTCAATTAACACACTGCT 59.343 34.615 0.00 0.00 0.00 4.24
711 725 6.824305 AATAGCTCAATTAACACACTGCTT 57.176 33.333 0.00 0.00 0.00 3.91
812 827 0.317854 GCCGCACTCACCAACTTTTC 60.318 55.000 0.00 0.00 0.00 2.29
814 829 1.308998 CGCACTCACCAACTTTTCCT 58.691 50.000 0.00 0.00 0.00 3.36
815 830 1.676006 CGCACTCACCAACTTTTCCTT 59.324 47.619 0.00 0.00 0.00 3.36
816 831 2.099098 CGCACTCACCAACTTTTCCTTT 59.901 45.455 0.00 0.00 0.00 3.11
817 832 3.447742 GCACTCACCAACTTTTCCTTTG 58.552 45.455 0.00 0.00 0.00 2.77
818 833 3.447742 CACTCACCAACTTTTCCTTTGC 58.552 45.455 0.00 0.00 0.00 3.68
819 834 3.131046 CACTCACCAACTTTTCCTTTGCT 59.869 43.478 0.00 0.00 0.00 3.91
820 835 3.131046 ACTCACCAACTTTTCCTTTGCTG 59.869 43.478 0.00 0.00 0.00 4.41
821 836 2.430332 TCACCAACTTTTCCTTTGCTGG 59.570 45.455 0.00 0.00 0.00 4.85
842 858 1.967319 TTGTTCTCTTGCGCTTTCCT 58.033 45.000 9.73 0.00 0.00 3.36
919 3204 2.502080 GTCACGACTCCACGAGCG 60.502 66.667 0.00 0.00 36.12 5.03
1016 3307 4.537433 GATGGCGGCGGAGAAGCT 62.537 66.667 9.78 0.00 37.29 3.74
1207 3501 0.177141 TTCTCGCTTGTTATCCCCCG 59.823 55.000 0.00 0.00 0.00 5.73
1236 3530 1.982938 GCCTACCCTGTGTCGGTCT 60.983 63.158 0.00 0.00 34.66 3.85
1250 3544 0.318275 CGGTCTCGCTCTCTAATGCC 60.318 60.000 0.00 0.00 0.00 4.40
1272 3566 2.136728 CGTGTGGTGGTTCGTTTGATA 58.863 47.619 0.00 0.00 0.00 2.15
1299 3593 1.276145 GCGGCGATGATAAGGACGTC 61.276 60.000 12.98 7.13 33.93 4.34
1380 3675 1.542492 CAGGTTTGCATGAGCTCCTT 58.458 50.000 12.15 0.00 42.74 3.36
1381 3676 1.201647 CAGGTTTGCATGAGCTCCTTG 59.798 52.381 12.15 10.25 42.74 3.61
1404 3720 6.235664 TGCTTGTCTAAACCTAAAACTAGGG 58.764 40.000 3.35 0.00 41.51 3.53
1407 3723 7.094890 GCTTGTCTAAACCTAAAACTAGGGAAC 60.095 40.741 3.35 0.00 41.51 3.62
1409 3725 5.349817 GTCTAAACCTAAAACTAGGGAACGC 59.650 44.000 3.35 0.00 41.51 4.84
1412 3728 2.094338 ACCTAAAACTAGGGAACGCTCG 60.094 50.000 3.35 0.00 41.51 5.03
1427 3745 1.791555 CGCTCGGTCAAATTGATGTGC 60.792 52.381 0.00 7.00 0.00 4.57
1485 3803 0.250338 AAGAGGTGAAACGACTGCCC 60.250 55.000 0.00 0.00 38.12 5.36
1539 3861 4.614555 TTGCACACTTTACACAGTTCAG 57.385 40.909 0.00 0.00 0.00 3.02
1544 3866 5.163754 GCACACTTTACACAGTTCAGTTTCT 60.164 40.000 0.00 0.00 0.00 2.52
1547 3869 7.491372 CACACTTTACACAGTTCAGTTTCTAGA 59.509 37.037 0.00 0.00 0.00 2.43
1560 3882 8.612619 GTTCAGTTTCTAGATGTTTGACTTCAA 58.387 33.333 0.00 0.00 0.00 2.69
1579 3901 4.211125 TCAACCCTAGATGCTAGTCTGAG 58.789 47.826 0.00 0.00 0.00 3.35
1632 3954 3.609853 GGCCAATGTAGAATGTCTGTCA 58.390 45.455 0.00 0.00 0.00 3.58
1724 4049 1.202348 GCAACAAGCGCAAGTGTGTC 61.202 55.000 11.47 2.81 35.81 3.67
1793 4118 5.588648 ACTGTTTGCAGCTAGTGAAGTAAAA 59.411 36.000 0.00 0.00 46.30 1.52
1858 4183 5.449553 TGTTCTGTAGATGCTAGATCCAGA 58.550 41.667 0.00 1.37 0.00 3.86
1876 4201 0.250467 GACTTGAGCTGAACCTGCCA 60.250 55.000 0.00 0.00 0.00 4.92
1921 4246 8.588290 ATGTTTGCTATTAAGGTTGGACATAA 57.412 30.769 0.00 0.00 0.00 1.90
2038 4363 6.036083 CGGTTGTCAAGGTAATCAGTTATCTG 59.964 42.308 0.00 0.00 42.54 2.90
2048 4373 7.620094 AGGTAATCAGTTATCTGTGGAACTACT 59.380 37.037 0.83 0.00 41.91 2.57
2049 4374 7.921745 GGTAATCAGTTATCTGTGGAACTACTC 59.078 40.741 0.83 0.00 41.91 2.59
2050 4375 5.916661 TCAGTTATCTGTGGAACTACTCC 57.083 43.478 0.83 0.00 41.29 3.85
2051 4376 4.710375 TCAGTTATCTGTGGAACTACTCCC 59.290 45.833 0.83 0.00 40.74 4.30
2052 4377 4.712337 CAGTTATCTGTGGAACTACTCCCT 59.288 45.833 0.00 0.00 36.73 4.20
2053 4378 4.957327 AGTTATCTGTGGAACTACTCCCTC 59.043 45.833 0.00 0.00 44.69 4.30
2054 4379 2.233305 TCTGTGGAACTACTCCCTCC 57.767 55.000 0.00 0.00 44.69 4.30
2055 4380 0.818296 CTGTGGAACTACTCCCTCCG 59.182 60.000 0.00 0.00 44.69 4.63
2056 4381 0.113776 TGTGGAACTACTCCCTCCGT 59.886 55.000 0.00 0.00 44.69 4.69
2057 4382 0.816373 GTGGAACTACTCCCTCCGTC 59.184 60.000 0.00 0.00 44.69 4.79
2058 4383 0.324091 TGGAACTACTCCCTCCGTCC 60.324 60.000 0.00 0.00 44.69 4.79
2059 4384 1.042003 GGAACTACTCCCTCCGTCCC 61.042 65.000 0.00 0.00 38.44 4.46
2060 4385 0.324091 GAACTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
2061 4386 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2062 4387 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2063 4388 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2064 4389 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2065 4390 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2066 4391 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2067 4392 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2068 4393 2.563179 CTCCCTCCGTCCCATAATGTAG 59.437 54.545 0.00 0.00 0.00 2.74
2069 4394 2.090943 TCCCTCCGTCCCATAATGTAGT 60.091 50.000 0.00 0.00 0.00 2.73
2070 4395 2.037251 CCCTCCGTCCCATAATGTAGTG 59.963 54.545 0.00 0.00 0.00 2.74
2071 4396 2.698797 CCTCCGTCCCATAATGTAGTGT 59.301 50.000 0.00 0.00 0.00 3.55
2072 4397 3.243771 CCTCCGTCCCATAATGTAGTGTC 60.244 52.174 0.00 0.00 0.00 3.67
2073 4398 3.367321 TCCGTCCCATAATGTAGTGTCA 58.633 45.455 0.00 0.00 0.00 3.58
2074 4399 3.964688 TCCGTCCCATAATGTAGTGTCAT 59.035 43.478 0.00 0.00 0.00 3.06
2075 4400 5.141910 TCCGTCCCATAATGTAGTGTCATA 58.858 41.667 0.00 0.00 0.00 2.15
2076 4401 5.599242 TCCGTCCCATAATGTAGTGTCATAA 59.401 40.000 0.00 0.00 0.00 1.90
2077 4402 6.098552 TCCGTCCCATAATGTAGTGTCATAAA 59.901 38.462 0.00 0.00 0.00 1.40
2078 4403 6.764085 CCGTCCCATAATGTAGTGTCATAAAA 59.236 38.462 0.00 0.00 0.00 1.52
2079 4404 7.254658 CCGTCCCATAATGTAGTGTCATAAAAC 60.255 40.741 0.00 0.00 0.00 2.43
2080 4405 7.516155 CGTCCCATAATGTAGTGTCATAAAACG 60.516 40.741 0.00 0.00 0.00 3.60
2081 4406 7.279313 GTCCCATAATGTAGTGTCATAAAACGT 59.721 37.037 0.00 0.00 0.00 3.99
2082 4407 7.493320 TCCCATAATGTAGTGTCATAAAACGTC 59.507 37.037 0.00 0.00 0.00 4.34
2083 4408 7.494625 CCCATAATGTAGTGTCATAAAACGTCT 59.505 37.037 0.00 0.00 0.00 4.18
2084 4409 8.879759 CCATAATGTAGTGTCATAAAACGTCTT 58.120 33.333 0.00 0.00 0.00 3.01
2087 4412 8.821147 AATGTAGTGTCATAAAACGTCTTACA 57.179 30.769 0.00 0.00 0.00 2.41
2088 4413 8.997621 ATGTAGTGTCATAAAACGTCTTACAT 57.002 30.769 0.00 0.00 0.00 2.29
2089 4414 8.821147 TGTAGTGTCATAAAACGTCTTACATT 57.179 30.769 0.00 0.00 0.00 2.71
2090 4415 9.911138 TGTAGTGTCATAAAACGTCTTACATTA 57.089 29.630 0.00 0.00 0.00 1.90
2093 4418 8.879759 AGTGTCATAAAACGTCTTACATTATGG 58.120 33.333 0.00 0.00 35.62 2.74
2094 4419 8.120465 GTGTCATAAAACGTCTTACATTATGGG 58.880 37.037 0.00 0.00 35.62 4.00
2095 4420 8.041919 TGTCATAAAACGTCTTACATTATGGGA 58.958 33.333 0.00 0.00 35.62 4.37
2096 4421 8.333186 GTCATAAAACGTCTTACATTATGGGAC 58.667 37.037 0.00 1.75 35.62 4.46
2099 4424 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
2100 4425 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2132 4457 6.025749 AGGCTTTTAGTGTTTCATTTAGGC 57.974 37.500 0.00 0.00 0.00 3.93
2254 4582 4.581824 AGCTACATGGCCTGATGTAATTTG 59.418 41.667 14.87 6.61 38.15 2.32
2305 4633 5.355071 ACATGTCATGTATGCTTTCATCGTT 59.645 36.000 16.99 0.00 42.78 3.85
2352 4680 2.761559 TCATTCGGTTTCACATCACGT 58.238 42.857 0.00 0.00 0.00 4.49
2394 4723 9.179909 TCTTTGCGGTAATGATTTAAGGAAATA 57.820 29.630 0.00 0.00 35.33 1.40
2415 4744 9.620259 GAAATACAAATCAGTAATCTCCTTCCT 57.380 33.333 0.00 0.00 0.00 3.36
2503 4835 2.918712 ATAGGAATGGAGAGCAACCG 57.081 50.000 0.00 0.00 0.00 4.44
2554 4886 7.880195 AGTTGGTGCTTACATGGATAATAGATC 59.120 37.037 0.00 0.00 0.00 2.75
2557 4889 8.385491 TGGTGCTTACATGGATAATAGATCATT 58.615 33.333 0.00 0.00 0.00 2.57
2749 5082 4.225942 ACTGTGGCTATTCTGGATCTCAAA 59.774 41.667 0.00 0.00 0.00 2.69
2809 5142 3.832276 TCTGATGTTATGTTTTTGCGGC 58.168 40.909 0.00 0.00 0.00 6.53
2888 5224 7.763172 ATCTGATTAAAGTTAGCAAGACTCG 57.237 36.000 0.00 0.00 0.00 4.18
3022 5358 0.035056 AGGCAATACACCAGTGGAGC 60.035 55.000 18.40 9.28 34.19 4.70
3088 5424 2.676748 TGCCTGTCAAATGGGTTCTTT 58.323 42.857 0.00 0.00 0.00 2.52
3168 5504 3.947834 GGTGTTCTAATTACTGCTGGCAT 59.052 43.478 0.00 0.00 0.00 4.40
3220 5557 2.947532 CGAGTTCCTCCTGCAGGCA 61.948 63.158 28.91 15.63 43.08 4.75
3348 5685 1.846007 AGTAGTGCTCCAGTCTCCTG 58.154 55.000 0.00 0.00 38.50 3.86
3400 5737 5.095490 GTGTTACTTTGTATTGCATCCAGC 58.905 41.667 0.00 0.00 45.96 4.85
3559 5906 6.606796 TCATGAATTAGTGTGGCCATGTAATT 59.393 34.615 21.16 21.16 34.63 1.40
3563 5910 9.634021 TGAATTAGTGTGGCCATGTAATTATTA 57.366 29.630 21.09 12.77 29.49 0.98
3630 5977 0.258774 AACTTGTTGCTGTGGTCCCT 59.741 50.000 0.00 0.00 0.00 4.20
3651 5998 8.523658 GTCCCTAGCTGATTTGTTCTTTAATTT 58.476 33.333 0.00 0.00 0.00 1.82
3702 6052 2.597510 GGGCCTCACGCAAGGTTT 60.598 61.111 0.84 0.00 46.39 3.27
3746 6096 0.839946 CCCTGGCACTATTGTAGGCT 59.160 55.000 0.00 0.00 31.42 4.58
3752 6102 2.280628 GCACTATTGTAGGCTGACACC 58.719 52.381 0.00 0.00 0.00 4.16
3756 6106 2.667473 ATTGTAGGCTGACACCGTAC 57.333 50.000 0.00 0.00 33.69 3.67
3758 6108 0.599558 TGTAGGCTGACACCGTACAC 59.400 55.000 0.00 0.00 33.69 2.90
3759 6109 0.599558 GTAGGCTGACACCGTACACA 59.400 55.000 0.00 0.00 33.69 3.72
3865 6221 4.681025 CCAACTTTTTGTGAATCGGATGTG 59.319 41.667 0.00 0.00 0.00 3.21
3869 6225 4.481930 TTTTGTGAATCGGATGTGTGTC 57.518 40.909 0.00 0.00 0.00 3.67
3870 6226 2.093306 TGTGAATCGGATGTGTGTCC 57.907 50.000 0.00 0.00 34.82 4.02
3959 6319 5.365605 TCATATTTGTGAACGGAGGGAGTAT 59.634 40.000 0.00 0.00 0.00 2.12
3966 6326 6.312529 TGTGAACGGAGGGAGTATCTTATAT 58.687 40.000 0.00 0.00 33.73 0.86
3970 6330 8.967918 TGAACGGAGGGAGTATCTTATATTATG 58.032 37.037 0.00 0.00 33.73 1.90
3977 6337 9.047947 AGGGAGTATCTTATATTATGGGTTGAC 57.952 37.037 0.00 0.00 33.73 3.18
3978 6338 9.047947 GGGAGTATCTTATATTATGGGTTGACT 57.952 37.037 0.00 0.00 33.73 3.41
3979 6339 9.877178 GGAGTATCTTATATTATGGGTTGACTG 57.123 37.037 0.00 0.00 33.73 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.671302 TCATAGCTTCCACCTAGATTGTTATC 58.329 38.462 0.00 0.00 0.00 1.75
101 111 7.309990 CCATTTGGATGTGTGGAAAATTAGTCT 60.310 37.037 0.00 0.00 37.39 3.24
126 136 6.903883 TCGAGACAGAAAGTTTATTATGCC 57.096 37.500 0.00 0.00 0.00 4.40
174 184 9.181061 GGGGTAAAGACATATTGTTTTTAGCTA 57.819 33.333 21.63 0.00 46.04 3.32
217 228 5.507876 CACCAACAACGAAACGAATGATATG 59.492 40.000 0.00 0.00 0.00 1.78
218 229 5.391523 CCACCAACAACGAAACGAATGATAT 60.392 40.000 0.00 0.00 0.00 1.63
226 237 0.863957 GCACCACCAACAACGAAACG 60.864 55.000 0.00 0.00 0.00 3.60
239 250 3.256631 AGATCATTTGTCCAAAGCACCAC 59.743 43.478 0.00 0.00 33.32 4.16
241 252 3.760684 AGAGATCATTTGTCCAAAGCACC 59.239 43.478 0.00 0.00 33.32 5.01
242 253 5.412594 TGTAGAGATCATTTGTCCAAAGCAC 59.587 40.000 0.00 0.00 33.32 4.40
243 254 5.559770 TGTAGAGATCATTTGTCCAAAGCA 58.440 37.500 0.00 0.00 33.32 3.91
244 255 5.645497 ACTGTAGAGATCATTTGTCCAAAGC 59.355 40.000 0.00 0.00 33.32 3.51
245 256 6.402983 GCACTGTAGAGATCATTTGTCCAAAG 60.403 42.308 0.00 0.00 33.32 2.77
246 257 5.412594 GCACTGTAGAGATCATTTGTCCAAA 59.587 40.000 0.00 0.00 34.46 3.28
247 258 4.937620 GCACTGTAGAGATCATTTGTCCAA 59.062 41.667 0.00 0.00 0.00 3.53
248 259 4.507710 GCACTGTAGAGATCATTTGTCCA 58.492 43.478 0.00 0.00 0.00 4.02
249 260 3.873952 GGCACTGTAGAGATCATTTGTCC 59.126 47.826 0.00 0.00 0.00 4.02
250 261 4.507710 TGGCACTGTAGAGATCATTTGTC 58.492 43.478 0.00 0.00 0.00 3.18
251 262 4.223700 TCTGGCACTGTAGAGATCATTTGT 59.776 41.667 0.00 0.00 0.00 2.83
252 263 4.569966 GTCTGGCACTGTAGAGATCATTTG 59.430 45.833 0.00 0.00 0.00 2.32
253 264 4.383552 GGTCTGGCACTGTAGAGATCATTT 60.384 45.833 0.00 0.00 0.00 2.32
254 265 3.133721 GGTCTGGCACTGTAGAGATCATT 59.866 47.826 0.00 0.00 0.00 2.57
255 266 2.697751 GGTCTGGCACTGTAGAGATCAT 59.302 50.000 0.00 0.00 0.00 2.45
256 267 2.103373 GGTCTGGCACTGTAGAGATCA 58.897 52.381 0.00 0.00 0.00 2.92
257 268 1.410882 GGGTCTGGCACTGTAGAGATC 59.589 57.143 0.00 0.00 0.00 2.75
258 269 1.007721 AGGGTCTGGCACTGTAGAGAT 59.992 52.381 0.00 0.00 0.00 2.75
259 270 0.409876 AGGGTCTGGCACTGTAGAGA 59.590 55.000 0.00 0.00 0.00 3.10
260 271 1.270907 AAGGGTCTGGCACTGTAGAG 58.729 55.000 0.00 0.00 0.00 2.43
261 272 2.042569 TCTAAGGGTCTGGCACTGTAGA 59.957 50.000 0.00 0.00 0.00 2.59
262 273 2.457598 TCTAAGGGTCTGGCACTGTAG 58.542 52.381 0.00 0.00 0.00 2.74
263 274 2.615986 TCTAAGGGTCTGGCACTGTA 57.384 50.000 0.00 0.00 0.00 2.74
264 275 1.556911 CATCTAAGGGTCTGGCACTGT 59.443 52.381 0.00 0.00 0.00 3.55
265 276 1.134280 CCATCTAAGGGTCTGGCACTG 60.134 57.143 0.00 0.00 0.00 3.66
266 277 1.207791 CCATCTAAGGGTCTGGCACT 58.792 55.000 0.00 0.00 0.00 4.40
267 278 1.139853 CTCCATCTAAGGGTCTGGCAC 59.860 57.143 0.00 0.00 0.00 5.01
268 279 1.008327 TCTCCATCTAAGGGTCTGGCA 59.992 52.381 0.00 0.00 0.00 4.92
269 280 1.794714 TCTCCATCTAAGGGTCTGGC 58.205 55.000 0.00 0.00 0.00 4.85
270 281 5.545723 ACATAATCTCCATCTAAGGGTCTGG 59.454 44.000 0.00 0.00 0.00 3.86
271 282 6.678568 ACATAATCTCCATCTAAGGGTCTG 57.321 41.667 0.00 0.00 0.00 3.51
272 283 7.698163 AAACATAATCTCCATCTAAGGGTCT 57.302 36.000 0.00 0.00 0.00 3.85
273 284 8.652290 AGTAAACATAATCTCCATCTAAGGGTC 58.348 37.037 0.00 0.00 0.00 4.46
334 345 5.760743 TGATGACTTTTGTACGAATGGTCAA 59.239 36.000 23.78 13.42 36.16 3.18
343 354 8.294341 TCTTTAGTTCTGATGACTTTTGTACG 57.706 34.615 0.00 0.00 0.00 3.67
439 450 1.602377 CTTCGTTCCCTTGTGTTCACC 59.398 52.381 0.37 0.00 0.00 4.02
443 454 2.092592 AGGTTCTTCGTTCCCTTGTGTT 60.093 45.455 0.00 0.00 0.00 3.32
454 465 2.163815 CGACCAGTATGAGGTTCTTCGT 59.836 50.000 0.00 0.00 40.09 3.85
474 485 7.306283 CGTCCTAAGATGCTCTCTTTAATTTCG 60.306 40.741 7.30 3.72 41.60 3.46
478 489 6.096987 TGTCGTCCTAAGATGCTCTCTTTAAT 59.903 38.462 7.30 0.00 41.60 1.40
545 558 4.321230 GCCACGGACAAAGAAAGATTTCAT 60.321 41.667 7.97 0.00 39.61 2.57
546 559 3.004315 GCCACGGACAAAGAAAGATTTCA 59.996 43.478 7.97 0.00 39.61 2.69
547 560 3.004315 TGCCACGGACAAAGAAAGATTTC 59.996 43.478 0.00 0.00 37.45 2.17
548 561 2.955660 TGCCACGGACAAAGAAAGATTT 59.044 40.909 0.00 0.00 0.00 2.17
554 568 2.018544 CGTTGCCACGGACAAAGAA 58.981 52.632 1.68 0.00 43.16 2.52
583 597 4.731720 CTGCCATCATCTGATACTAGTCG 58.268 47.826 0.00 0.00 32.63 4.18
592 606 2.203112 GCCGCTGCCATCATCTGA 60.203 61.111 0.00 0.00 0.00 3.27
593 607 3.646976 CGCCGCTGCCATCATCTG 61.647 66.667 0.00 0.00 0.00 2.90
594 608 4.923942 CCGCCGCTGCCATCATCT 62.924 66.667 0.00 0.00 0.00 2.90
609 623 3.441011 ATAGGGGTTTCTCGCGCCG 62.441 63.158 0.00 0.00 42.84 6.46
610 624 1.887707 CATAGGGGTTTCTCGCGCC 60.888 63.158 0.00 0.00 38.99 6.53
611 625 2.534903 GCATAGGGGTTTCTCGCGC 61.535 63.158 0.00 0.00 0.00 6.86
612 626 2.237751 CGCATAGGGGTTTCTCGCG 61.238 63.158 0.00 0.00 34.27 5.87
613 627 0.461339 TTCGCATAGGGGTTTCTCGC 60.461 55.000 0.00 0.00 0.00 5.03
614 628 1.571919 CTTCGCATAGGGGTTTCTCG 58.428 55.000 0.00 0.00 0.00 4.04
615 629 1.300481 GCTTCGCATAGGGGTTTCTC 58.700 55.000 0.00 0.00 0.00 2.87
616 630 0.462047 CGCTTCGCATAGGGGTTTCT 60.462 55.000 0.00 0.00 0.00 2.52
617 631 0.743345 ACGCTTCGCATAGGGGTTTC 60.743 55.000 4.51 0.00 32.78 2.78
618 632 1.024579 CACGCTTCGCATAGGGGTTT 61.025 55.000 4.51 0.00 32.78 3.27
619 633 1.449601 CACGCTTCGCATAGGGGTT 60.450 57.895 4.51 0.00 32.78 4.11
620 634 2.186903 CACGCTTCGCATAGGGGT 59.813 61.111 4.51 0.00 32.78 4.95
621 635 2.588877 CCACGCTTCGCATAGGGG 60.589 66.667 4.51 0.00 32.78 4.79
622 636 3.272334 GCCACGCTTCGCATAGGG 61.272 66.667 0.00 0.00 0.00 3.53
623 637 2.202932 AGCCACGCTTCGCATAGG 60.203 61.111 0.00 0.00 33.89 2.57
624 638 2.528743 CCAGCCACGCTTCGCATAG 61.529 63.158 0.00 0.00 36.40 2.23
625 639 2.511373 CCAGCCACGCTTCGCATA 60.511 61.111 0.00 0.00 36.40 3.14
630 644 4.373116 TCGACCCAGCCACGCTTC 62.373 66.667 0.00 0.00 36.40 3.86
631 645 4.379243 CTCGACCCAGCCACGCTT 62.379 66.667 0.00 0.00 36.40 4.68
634 648 3.461773 ATCCTCGACCCAGCCACG 61.462 66.667 0.00 0.00 0.00 4.94
635 649 2.187946 CATCCTCGACCCAGCCAC 59.812 66.667 0.00 0.00 0.00 5.01
636 650 2.038813 TCATCCTCGACCCAGCCA 59.961 61.111 0.00 0.00 0.00 4.75
637 651 2.818132 CTCATCCTCGACCCAGCC 59.182 66.667 0.00 0.00 0.00 4.85
638 652 2.107953 GCTCATCCTCGACCCAGC 59.892 66.667 0.00 0.00 0.00 4.85
639 653 2.801631 GGGCTCATCCTCGACCCAG 61.802 68.421 0.30 0.00 40.52 4.45
640 654 2.764128 GGGCTCATCCTCGACCCA 60.764 66.667 0.30 0.00 40.52 4.51
641 655 2.367202 TTGGGCTCATCCTCGACCC 61.367 63.158 0.00 0.00 41.24 4.46
642 656 1.153349 GTTGGGCTCATCCTCGACC 60.153 63.158 0.00 0.00 34.39 4.79
643 657 0.250513 AAGTTGGGCTCATCCTCGAC 59.749 55.000 0.00 0.00 34.39 4.20
644 658 0.984230 AAAGTTGGGCTCATCCTCGA 59.016 50.000 0.00 0.00 34.39 4.04
645 659 1.089920 CAAAGTTGGGCTCATCCTCG 58.910 55.000 0.00 0.00 34.39 4.63
646 660 2.290577 ACTCAAAGTTGGGCTCATCCTC 60.291 50.000 0.00 0.00 34.39 3.71
647 661 1.707427 ACTCAAAGTTGGGCTCATCCT 59.293 47.619 0.00 0.00 34.39 3.24
648 662 2.087646 GACTCAAAGTTGGGCTCATCC 58.912 52.381 0.00 0.00 29.59 3.51
649 663 3.064900 AGACTCAAAGTTGGGCTCATC 57.935 47.619 0.00 0.00 29.59 2.92
650 664 3.584848 AGTAGACTCAAAGTTGGGCTCAT 59.415 43.478 0.00 0.00 29.59 2.90
651 665 2.972713 AGTAGACTCAAAGTTGGGCTCA 59.027 45.455 0.00 0.00 29.59 4.26
652 666 3.686916 AGTAGACTCAAAGTTGGGCTC 57.313 47.619 0.00 0.00 29.59 4.70
653 667 6.630638 GCTTATAGTAGACTCAAAGTTGGGCT 60.631 42.308 0.00 0.00 29.59 5.19
654 668 5.524281 GCTTATAGTAGACTCAAAGTTGGGC 59.476 44.000 0.00 0.00 29.59 5.36
655 669 5.749109 CGCTTATAGTAGACTCAAAGTTGGG 59.251 44.000 0.00 0.00 33.95 4.12
656 670 6.253727 CACGCTTATAGTAGACTCAAAGTTGG 59.746 42.308 6.05 0.00 0.00 3.77
657 671 7.027760 TCACGCTTATAGTAGACTCAAAGTTG 58.972 38.462 6.05 0.00 0.00 3.16
658 672 7.154435 TCACGCTTATAGTAGACTCAAAGTT 57.846 36.000 6.05 0.00 0.00 2.66
659 673 6.754702 TCACGCTTATAGTAGACTCAAAGT 57.245 37.500 6.05 0.00 0.00 2.66
660 674 9.388346 CTATTCACGCTTATAGTAGACTCAAAG 57.612 37.037 0.00 0.00 0.00 2.77
661 675 9.117183 TCTATTCACGCTTATAGTAGACTCAAA 57.883 33.333 0.00 0.00 0.00 2.69
662 676 8.672823 TCTATTCACGCTTATAGTAGACTCAA 57.327 34.615 0.00 0.00 0.00 3.02
663 677 8.672823 TTCTATTCACGCTTATAGTAGACTCA 57.327 34.615 0.00 0.00 0.00 3.41
670 684 8.577296 TGAGCTATTTCTATTCACGCTTATAGT 58.423 33.333 0.00 0.00 0.00 2.12
671 685 8.972262 TGAGCTATTTCTATTCACGCTTATAG 57.028 34.615 0.00 0.00 0.00 1.31
672 686 9.929180 ATTGAGCTATTTCTATTCACGCTTATA 57.071 29.630 0.00 0.00 0.00 0.98
673 687 8.839310 ATTGAGCTATTTCTATTCACGCTTAT 57.161 30.769 0.00 0.00 0.00 1.73
674 688 8.662781 AATTGAGCTATTTCTATTCACGCTTA 57.337 30.769 0.00 0.00 0.00 3.09
675 689 7.559590 AATTGAGCTATTTCTATTCACGCTT 57.440 32.000 0.00 0.00 0.00 4.68
676 690 8.552034 GTTAATTGAGCTATTTCTATTCACGCT 58.448 33.333 0.00 0.00 0.00 5.07
677 691 8.335356 TGTTAATTGAGCTATTTCTATTCACGC 58.665 33.333 0.00 0.00 0.00 5.34
678 692 9.638300 GTGTTAATTGAGCTATTTCTATTCACG 57.362 33.333 0.00 0.00 0.00 4.35
687 701 6.824305 AGCAGTGTGTTAATTGAGCTATTT 57.176 33.333 0.00 0.00 0.00 1.40
694 708 4.651778 AGGCTAAGCAGTGTGTTAATTGA 58.348 39.130 0.00 0.00 0.00 2.57
745 759 2.203938 AGCCCAGGAGTTTCCGGA 60.204 61.111 0.00 0.00 42.75 5.14
748 762 0.332972 AATCCAGCCCAGGAGTTTCC 59.667 55.000 0.00 0.00 41.90 3.13
802 817 2.466846 ACCAGCAAAGGAAAAGTTGGT 58.533 42.857 0.00 0.00 41.23 3.67
812 827 3.709987 CAAGAGAACAAACCAGCAAAGG 58.290 45.455 0.00 0.00 0.00 3.11
814 829 2.479389 CGCAAGAGAACAAACCAGCAAA 60.479 45.455 0.00 0.00 43.02 3.68
815 830 1.065401 CGCAAGAGAACAAACCAGCAA 59.935 47.619 0.00 0.00 43.02 3.91
816 831 0.662619 CGCAAGAGAACAAACCAGCA 59.337 50.000 0.00 0.00 43.02 4.41
817 832 0.661483 GCGCAAGAGAACAAACCAGC 60.661 55.000 0.30 0.00 43.02 4.85
818 833 0.947244 AGCGCAAGAGAACAAACCAG 59.053 50.000 11.47 0.00 43.02 4.00
819 834 1.388547 AAGCGCAAGAGAACAAACCA 58.611 45.000 11.47 0.00 43.02 3.67
820 835 2.385315 GAAAGCGCAAGAGAACAAACC 58.615 47.619 11.47 0.00 43.02 3.27
821 836 2.033424 AGGAAAGCGCAAGAGAACAAAC 59.967 45.455 11.47 0.00 43.02 2.93
842 858 1.132201 TCTCCCCCTTTCCTCCTTTCA 60.132 52.381 0.00 0.00 0.00 2.69
883 3168 1.270625 ACGGATTTGGTTCTGCTCGAA 60.271 47.619 0.00 0.00 0.00 3.71
919 3204 3.426568 GTGTTGCCCTGCTCGAGC 61.427 66.667 30.42 30.42 42.50 5.03
1172 3463 2.294791 CGAGAAGGCTAGGTAGGTCATG 59.705 54.545 0.00 0.00 0.00 3.07
1173 3464 2.588620 CGAGAAGGCTAGGTAGGTCAT 58.411 52.381 0.00 0.00 0.00 3.06
1207 3501 0.108472 AGGGTAGGCGTAAACGAAGC 60.108 55.000 6.71 0.62 43.02 3.86
1250 3544 2.815298 AAACGAACCACCACACGCG 61.815 57.895 3.53 3.53 0.00 6.01
1272 3566 0.392706 TATCATCGCCGCCTTCACAT 59.607 50.000 0.00 0.00 0.00 3.21
1378 3673 7.094762 CCCTAGTTTTAGGTTTAGACAAGCAAG 60.095 40.741 0.37 0.00 44.32 4.01
1380 3675 6.043474 TCCCTAGTTTTAGGTTTAGACAAGCA 59.957 38.462 0.37 0.00 44.32 3.91
1381 3676 6.470278 TCCCTAGTTTTAGGTTTAGACAAGC 58.530 40.000 0.37 0.00 44.32 4.01
1404 3720 2.159627 ACATCAATTTGACCGAGCGTTC 59.840 45.455 0.15 0.00 0.00 3.95
1407 3723 1.791555 GCACATCAATTTGACCGAGCG 60.792 52.381 0.15 0.00 0.00 5.03
1409 3725 2.485426 ACAGCACATCAATTTGACCGAG 59.515 45.455 0.15 0.00 0.00 4.63
1412 3728 3.648339 ACACAGCACATCAATTTGACC 57.352 42.857 0.15 0.00 0.00 4.02
1427 3745 2.859981 GCACCCCCTGCAAACACAG 61.860 63.158 0.00 0.00 46.29 3.66
1485 3803 0.667993 TTTTCTTGAGCTTGCCACCG 59.332 50.000 0.00 0.00 0.00 4.94
1491 3809 4.050852 AGCAACCTTTTTCTTGAGCTTG 57.949 40.909 0.00 0.00 0.00 4.01
1511 3829 3.380004 TGTGTAAAGTGTGCAAAGGGAAG 59.620 43.478 0.00 0.00 0.00 3.46
1539 3861 6.486993 AGGGTTGAAGTCAAACATCTAGAAAC 59.513 38.462 11.05 0.00 45.01 2.78
1544 3866 6.928348 TCTAGGGTTGAAGTCAAACATCTA 57.072 37.500 11.05 3.78 45.01 1.98
1547 3869 4.702131 GCATCTAGGGTTGAAGTCAAACAT 59.298 41.667 11.05 6.46 45.01 2.71
1560 3882 4.740154 ATCTCAGACTAGCATCTAGGGT 57.260 45.455 5.92 0.00 0.00 4.34
1597 3919 0.178975 TTGGCCCGAACTCAAACCAT 60.179 50.000 0.00 0.00 0.00 3.55
1632 3954 4.328536 ACATTGGCATTCAAACATTGCAT 58.671 34.783 0.00 0.00 39.05 3.96
1724 4049 1.174712 CCAGGCCTTTCACCACAGTG 61.175 60.000 0.00 0.00 46.00 3.66
1858 4183 0.403271 ATGGCAGGTTCAGCTCAAGT 59.597 50.000 0.00 0.00 0.00 3.16
1921 4246 9.226606 TCAGGAAACAAACACGATCTATTAAAT 57.773 29.630 0.00 0.00 0.00 1.40
2048 4373 2.090943 ACTACATTATGGGACGGAGGGA 60.091 50.000 0.00 0.00 0.00 4.20
2049 4374 2.037251 CACTACATTATGGGACGGAGGG 59.963 54.545 0.00 0.00 0.00 4.30
2050 4375 2.698797 ACACTACATTATGGGACGGAGG 59.301 50.000 0.00 0.00 0.00 4.30
2051 4376 3.383505 TGACACTACATTATGGGACGGAG 59.616 47.826 0.00 0.00 0.00 4.63
2052 4377 3.367321 TGACACTACATTATGGGACGGA 58.633 45.455 0.00 0.00 0.00 4.69
2053 4378 3.812156 TGACACTACATTATGGGACGG 57.188 47.619 0.00 0.00 0.00 4.79
2054 4379 7.516155 CGTTTTATGACACTACATTATGGGACG 60.516 40.741 0.00 0.00 0.00 4.79
2055 4380 7.279313 ACGTTTTATGACACTACATTATGGGAC 59.721 37.037 0.00 0.00 0.00 4.46
2056 4381 7.332557 ACGTTTTATGACACTACATTATGGGA 58.667 34.615 0.00 0.00 0.00 4.37
2057 4382 7.494625 AGACGTTTTATGACACTACATTATGGG 59.505 37.037 0.00 0.00 0.00 4.00
2058 4383 8.420374 AGACGTTTTATGACACTACATTATGG 57.580 34.615 0.00 0.00 0.00 2.74
2061 4386 9.911138 TGTAAGACGTTTTATGACACTACATTA 57.089 29.630 1.49 0.00 0.00 1.90
2062 4387 8.821147 TGTAAGACGTTTTATGACACTACATT 57.179 30.769 1.49 0.00 0.00 2.71
2063 4388 8.997621 ATGTAAGACGTTTTATGACACTACAT 57.002 30.769 1.49 0.00 0.00 2.29
2064 4389 8.821147 AATGTAAGACGTTTTATGACACTACA 57.179 30.769 1.49 0.00 0.00 2.74
2067 4392 8.879759 CCATAATGTAAGACGTTTTATGACACT 58.120 33.333 1.49 0.00 33.93 3.55
2068 4393 8.120465 CCCATAATGTAAGACGTTTTATGACAC 58.880 37.037 1.49 0.00 33.93 3.67
2069 4394 8.041919 TCCCATAATGTAAGACGTTTTATGACA 58.958 33.333 1.49 0.00 33.93 3.58
2070 4395 8.333186 GTCCCATAATGTAAGACGTTTTATGAC 58.667 37.037 1.49 0.00 33.93 3.06
2071 4396 7.223193 CGTCCCATAATGTAAGACGTTTTATGA 59.777 37.037 1.49 0.00 43.89 2.15
2072 4397 7.342194 CGTCCCATAATGTAAGACGTTTTATG 58.658 38.462 1.49 0.00 43.89 1.90
2073 4398 6.480981 CCGTCCCATAATGTAAGACGTTTTAT 59.519 38.462 1.49 0.00 46.62 1.40
2074 4399 5.811613 CCGTCCCATAATGTAAGACGTTTTA 59.188 40.000 9.63 0.00 46.62 1.52
2075 4400 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2076 4401 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2077 4402 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2078 4403 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2080 4405 4.667519 ACTCCGTCCCATAATGTAAGAC 57.332 45.455 0.00 0.00 0.00 3.01
2081 4406 5.452255 ACTACTCCGTCCCATAATGTAAGA 58.548 41.667 0.00 0.00 0.00 2.10
2082 4407 5.786264 ACTACTCCGTCCCATAATGTAAG 57.214 43.478 0.00 0.00 0.00 2.34
2083 4408 7.005902 TCATACTACTCCGTCCCATAATGTAA 58.994 38.462 0.00 0.00 0.00 2.41
2084 4409 6.545567 TCATACTACTCCGTCCCATAATGTA 58.454 40.000 0.00 0.00 0.00 2.29
2085 4410 5.391256 TCATACTACTCCGTCCCATAATGT 58.609 41.667 0.00 0.00 0.00 2.71
2086 4411 5.977489 TCATACTACTCCGTCCCATAATG 57.023 43.478 0.00 0.00 0.00 1.90
2087 4412 5.480772 CCTTCATACTACTCCGTCCCATAAT 59.519 44.000 0.00 0.00 0.00 1.28
2088 4413 4.831155 CCTTCATACTACTCCGTCCCATAA 59.169 45.833 0.00 0.00 0.00 1.90
2089 4414 4.404640 CCTTCATACTACTCCGTCCCATA 58.595 47.826 0.00 0.00 0.00 2.74
2090 4415 3.231818 CCTTCATACTACTCCGTCCCAT 58.768 50.000 0.00 0.00 0.00 4.00
2091 4416 2.662866 CCTTCATACTACTCCGTCCCA 58.337 52.381 0.00 0.00 0.00 4.37
2092 4417 1.340568 GCCTTCATACTACTCCGTCCC 59.659 57.143 0.00 0.00 0.00 4.46
2093 4418 2.308690 AGCCTTCATACTACTCCGTCC 58.691 52.381 0.00 0.00 0.00 4.79
2094 4419 4.388378 AAAGCCTTCATACTACTCCGTC 57.612 45.455 0.00 0.00 0.00 4.79
2095 4420 4.820894 AAAAGCCTTCATACTACTCCGT 57.179 40.909 0.00 0.00 0.00 4.69
2096 4421 5.749109 CACTAAAAGCCTTCATACTACTCCG 59.251 44.000 0.00 0.00 0.00 4.63
2097 4422 6.641474 ACACTAAAAGCCTTCATACTACTCC 58.359 40.000 0.00 0.00 0.00 3.85
2098 4423 8.549338 AAACACTAAAAGCCTTCATACTACTC 57.451 34.615 0.00 0.00 0.00 2.59
2099 4424 8.154856 TGAAACACTAAAAGCCTTCATACTACT 58.845 33.333 0.00 0.00 0.00 2.57
2100 4425 8.319143 TGAAACACTAAAAGCCTTCATACTAC 57.681 34.615 0.00 0.00 0.00 2.73
2101 4426 9.515226 AATGAAACACTAAAAGCCTTCATACTA 57.485 29.630 0.00 0.00 33.53 1.82
2102 4427 8.409358 AATGAAACACTAAAAGCCTTCATACT 57.591 30.769 0.00 0.00 33.53 2.12
2105 4430 8.306761 CCTAAATGAAACACTAAAAGCCTTCAT 58.693 33.333 0.00 0.00 35.56 2.57
2106 4431 7.657336 CCTAAATGAAACACTAAAAGCCTTCA 58.343 34.615 0.00 0.00 0.00 3.02
2132 4457 7.095017 GGAACACAAAGAGAGAATTAGACAAGG 60.095 40.741 0.00 0.00 0.00 3.61
2254 4582 6.471146 ACCATAATAAGATGCAGAGATGGAC 58.529 40.000 14.04 0.00 36.82 4.02
2305 4633 5.997129 TGTCAAGTTGATCAGAATGCTAACA 59.003 36.000 9.18 0.00 34.76 2.41
2352 4680 4.631377 CGCAAAGATAACATCAGTCTTCCA 59.369 41.667 0.00 0.00 31.37 3.53
2415 4744 7.556275 ACTTTCATAGTTTCACTTTCTTGGTCA 59.444 33.333 0.00 0.00 31.29 4.02
2484 4816 2.119495 ACGGTTGCTCTCCATTCCTAT 58.881 47.619 0.00 0.00 0.00 2.57
2503 4835 2.284190 GCCAGATCTCCACAAAGCTAC 58.716 52.381 0.00 0.00 0.00 3.58
2554 4886 3.091545 ACACCATTGAGCTAACCCAATG 58.908 45.455 15.52 15.52 45.45 2.82
2557 4889 2.969821 AACACCATTGAGCTAACCCA 57.030 45.000 0.00 0.00 0.00 4.51
2714 5047 7.064134 CAGAATAGCCACAGTATTACGAAACAA 59.936 37.037 0.00 0.00 0.00 2.83
2749 5082 7.741554 AGTCTAAAGTAGAATGAATCCTGGT 57.258 36.000 0.00 0.00 36.40 4.00
2888 5224 4.095334 AGGAGTAACCAACGTGAACAAAAC 59.905 41.667 0.00 0.00 42.04 2.43
3077 5413 5.494706 TGGGAGTAAGGATAAAGAACCCATT 59.505 40.000 0.00 0.00 39.65 3.16
3088 5424 5.091552 AGTTGTGTCTTGGGAGTAAGGATA 58.908 41.667 0.00 0.00 0.00 2.59
3152 5488 2.032549 GCGACATGCCAGCAGTAATTAG 60.033 50.000 0.00 0.00 37.76 1.73
3156 5492 3.889227 GCGACATGCCAGCAGTAA 58.111 55.556 0.00 0.00 37.76 2.24
3168 5504 1.749063 AGATGATACACGAAGGCGACA 59.251 47.619 0.00 0.00 41.64 4.35
3348 5685 3.686726 CCAGACTGTTCCTATGAAAGCAC 59.313 47.826 0.93 0.00 30.79 4.40
3421 5758 2.358267 ACACCGACAACGATCTATCTCC 59.642 50.000 0.00 0.00 42.66 3.71
3584 5931 6.015603 TGTGAACAAGTTTAATGATCATGGCA 60.016 34.615 9.46 0.00 33.10 4.92
3586 5933 7.819644 TCTGTGAACAAGTTTAATGATCATGG 58.180 34.615 9.46 0.00 33.10 3.66
3674 6024 3.028850 GCGTGAGGCCCCAGTATATATA 58.971 50.000 0.00 0.00 34.80 0.86
3675 6025 1.831736 GCGTGAGGCCCCAGTATATAT 59.168 52.381 0.00 0.00 34.80 0.86
3676 6026 1.263356 GCGTGAGGCCCCAGTATATA 58.737 55.000 0.00 0.00 34.80 0.86
3677 6027 0.762842 TGCGTGAGGCCCCAGTATAT 60.763 55.000 0.00 0.00 42.61 0.86
3702 6052 5.278315 CGTGATATAATGTCTCCTTCGGACA 60.278 44.000 0.00 0.00 45.84 4.02
3716 6066 1.699634 AGTGCCAGGGCGTGATATAAT 59.300 47.619 9.09 0.00 45.51 1.28
3746 6096 3.069016 AGTGAAGATTGTGTACGGTGTCA 59.931 43.478 0.00 0.00 0.00 3.58
3752 6102 6.887368 TGATGAAAAGTGAAGATTGTGTACG 58.113 36.000 0.00 0.00 0.00 3.67
3756 6106 6.564709 TCCTGATGAAAAGTGAAGATTGTG 57.435 37.500 0.00 0.00 0.00 3.33
3758 6108 7.600065 ACAATCCTGATGAAAAGTGAAGATTG 58.400 34.615 0.00 0.00 42.23 2.67
3759 6109 7.668886 AGACAATCCTGATGAAAAGTGAAGATT 59.331 33.333 0.00 0.00 0.00 2.40
3865 6221 5.575019 AGAACAAACACATTAAACGGACAC 58.425 37.500 0.00 0.00 0.00 3.67
3869 6225 9.458374 AAATTAGAGAACAAACACATTAAACGG 57.542 29.630 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.