Multiple sequence alignment - TraesCS5A01G085800

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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 TraesCS5A01G085800 chr5A 100.000 6492 0 0 1 6492 113716840 113723331 0.000000e+00 11989.0
1 TraesCS5A01G085800 chr5A 96.739 92 2 1 3249 3340 178391578 178391488 1.130000e-32 152.0
2 TraesCS5A01G085800 chr5A 90.526 95 7 2 6400 6492 165330902 165330808 2.460000e-24 124.0
3 TraesCS5A01G085800 chr5B 94.386 2779 112 22 3635 6404 119186480 119189223 0.000000e+00 4228.0
4 TraesCS5A01G085800 chr5B 96.048 2581 85 6 683 3250 119183429 119186005 0.000000e+00 4185.0
5 TraesCS5A01G085800 chr5B 94.498 309 15 2 3332 3638 119186004 119186312 5.890000e-130 475.0
6 TraesCS5A01G085800 chr5B 80.564 638 77 20 31 628 119180139 119180769 1.280000e-121 448.0
7 TraesCS5A01G085800 chr5B 93.814 97 5 1 3242 3338 142701504 142701409 1.890000e-30 145.0
8 TraesCS5A01G085800 chr5B 76.211 227 49 5 280 504 126127490 126127267 1.480000e-21 115.0
9 TraesCS5A01G085800 chr5D 96.157 2576 85 8 679 3250 108515292 108517857 0.000000e+00 4196.0
10 TraesCS5A01G085800 chr5D 91.376 1890 110 27 4282 6160 108519041 108520888 0.000000e+00 2538.0
11 TraesCS5A01G085800 chr5D 91.459 761 46 9 3536 4285 108518118 108518870 0.000000e+00 1027.0
12 TraesCS5A01G085800 chr5D 80.381 683 81 23 31 671 108505446 108506117 2.740000e-128 470.0
13 TraesCS5A01G085800 chr5D 94.800 250 11 2 6157 6404 108520990 108521239 7.890000e-104 388.0
14 TraesCS5A01G085800 chr5D 89.109 202 21 1 3336 3536 108517873 108518074 3.890000e-62 250.0
15 TraesCS5A01G085800 chr1B 85.437 618 43 13 4188 4797 152449753 152449175 3.350000e-167 599.0
16 TraesCS5A01G085800 chr1B 91.346 104 8 1 3235 3338 630905798 630905900 2.440000e-29 141.0
17 TraesCS5A01G085800 chr3B 78.599 257 37 13 281 525 527236216 527236466 3.130000e-33 154.0
18 TraesCS5A01G085800 chr3B 94.792 96 3 2 3244 3338 786722406 786722500 1.460000e-31 148.0
19 TraesCS5A01G085800 chr3B 92.157 102 7 1 3240 3341 421670492 421670592 6.790000e-30 143.0
20 TraesCS5A01G085800 chr3B 90.741 108 8 2 3240 3347 452550770 452550875 6.790000e-30 143.0
21 TraesCS5A01G085800 chr3B 82.946 129 20 2 285 411 267204773 267204645 1.480000e-21 115.0
22 TraesCS5A01G085800 chr7A 94.898 98 4 1 3248 3344 167268791 167268888 1.130000e-32 152.0
23 TraesCS5A01G085800 chr7A 93.333 90 2 1 6403 6492 93490683 93490598 5.280000e-26 130.0
24 TraesCS5A01G085800 chr7A 100.000 32 0 0 1 32 291671719 291671750 7.030000e-05 60.2
25 TraesCS5A01G085800 chr6B 96.667 90 3 0 3249 3338 216509758 216509847 4.050000e-32 150.0
26 TraesCS5A01G085800 chr4B 92.453 106 6 1 3249 3354 24837382 24837279 4.050000e-32 150.0
27 TraesCS5A01G085800 chr7D 97.674 86 2 0 3248 3333 557225429 557225514 1.460000e-31 148.0
28 TraesCS5A01G085800 chr7D 91.589 107 7 2 3230 3335 561960245 561960140 5.250000e-31 147.0
29 TraesCS5A01G085800 chr7D 100.000 33 0 0 1 33 446517722 446517690 1.950000e-05 62.1
30 TraesCS5A01G085800 chr7D 100.000 32 0 0 1 32 446525309 446525278 7.030000e-05 60.2
31 TraesCS5A01G085800 chr3D 96.629 89 3 0 3249 3337 219572181 219572269 1.460000e-31 148.0
32 TraesCS5A01G085800 chr3D 93.333 90 5 1 6403 6492 81841272 81841360 1.470000e-26 132.0
33 TraesCS5A01G085800 chr3D 83.810 105 14 3 284 386 554944217 554944114 5.360000e-16 97.1
34 TraesCS5A01G085800 chr1A 93.069 101 5 2 3236 3335 544367931 544367832 5.250000e-31 147.0
35 TraesCS5A01G085800 chr1A 93.333 90 6 0 6403 6492 350750801 350750712 4.080000e-27 134.0
36 TraesCS5A01G085800 chr1A 89.474 95 9 1 6398 6492 568118058 568118151 1.140000e-22 119.0
37 TraesCS5A01G085800 chr2B 92.157 102 7 1 3235 3336 682451004 682450904 6.790000e-30 143.0
38 TraesCS5A01G085800 chr2A 94.444 90 3 1 6403 6490 719525623 719525534 3.160000e-28 137.0
39 TraesCS5A01G085800 chr2D 93.333 90 6 0 6403 6492 194750242 194750331 4.080000e-27 134.0
40 TraesCS5A01G085800 chr4A 88.182 110 10 3 6383 6492 441498966 441499072 1.900000e-25 128.0
41 TraesCS5A01G085800 chr3A 93.182 88 5 1 6406 6492 196422009 196421922 1.900000e-25 128.0
42 TraesCS5A01G085800 chr3A 100.000 29 0 0 4 32 410889407 410889435 3.000000e-03 54.7


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 TraesCS5A01G085800 chr5A 113716840 113723331 6491 False 11989.0 11989 100.0000 1 6492 1 chr5A.!!$F1 6491
1 TraesCS5A01G085800 chr5B 119180139 119189223 9084 False 2334.0 4228 91.3740 31 6404 4 chr5B.!!$F1 6373
2 TraesCS5A01G085800 chr5D 108515292 108521239 5947 False 1679.8 4196 92.5802 679 6404 5 chr5D.!!$F2 5725
3 TraesCS5A01G085800 chr5D 108505446 108506117 671 False 470.0 470 80.3810 31 671 1 chr5D.!!$F1 640
4 TraesCS5A01G085800 chr1B 152449175 152449753 578 True 599.0 599 85.4370 4188 4797 1 chr1B.!!$R1 609

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
255 257 0.033601 AGATGAGCTCGTGGGACTCT 60.034 55.000 14.59 0.0 0.00 3.24 F
966 3637 0.325484 CCAGCCATCCAATCCCCAAA 60.325 55.000 0.00 0.0 0.00 3.28 F
1805 4489 0.955428 GCGACAGGGACAAATCTGCA 60.955 55.000 0.00 0.0 34.57 4.41 F
1892 4576 0.242017 AGCTTTTGACTGCCGCAATC 59.758 50.000 0.00 0.0 0.00 2.67 F
2974 5658 1.274167 TGGCAAGTCTAAGGTACACGG 59.726 52.381 0.00 0.0 0.00 4.94 F
3528 6226 2.813754 TGTGCTGAATTGTACTGGAAGC 59.186 45.455 0.00 0.0 37.60 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 4354 1.146041 AACACGGAGCAGCTTGTCA 59.854 52.632 0.00 0.0 0.00 3.58 R
1868 4552 1.799258 CGGCAGTCAAAAGCTTGCCT 61.799 55.000 19.80 3.0 40.02 4.75 R
2974 5658 2.093235 CCAACTTCAGGATCCTCCTCAC 60.093 54.545 12.69 0.0 45.66 3.51 R
3862 6786 0.391228 TACAGCGACTGCAAGAACCA 59.609 50.000 6.74 0.0 46.23 3.67 R
3946 6870 0.906066 TAAGGAGCCCATACGCAACA 59.094 50.000 0.00 0.0 0.00 3.33 R
5515 8634 0.806102 ACGAAGCGACAATCCATCGG 60.806 55.000 0.00 0.0 39.99 4.18 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
22 23 4.531332 GGTTACTGTAGCGTAGTTATCCG 58.469 47.826 0.00 0.00 0.00 4.18
23 24 4.531332 GTTACTGTAGCGTAGTTATCCGG 58.469 47.826 0.00 0.00 0.00 5.14
24 25 1.952296 ACTGTAGCGTAGTTATCCGGG 59.048 52.381 0.00 0.00 0.00 5.73
25 26 0.670162 TGTAGCGTAGTTATCCGGGC 59.330 55.000 0.00 0.00 0.00 6.13
26 27 0.386478 GTAGCGTAGTTATCCGGGCG 60.386 60.000 0.00 0.00 0.00 6.13
27 28 0.819259 TAGCGTAGTTATCCGGGCGT 60.819 55.000 0.00 0.00 0.00 5.68
28 29 1.659644 GCGTAGTTATCCGGGCGTC 60.660 63.158 0.00 0.00 0.00 5.19
29 30 1.729276 CGTAGTTATCCGGGCGTCA 59.271 57.895 0.00 0.00 0.00 4.35
90 91 3.333189 CGGCCGACATGAGCATCG 61.333 66.667 24.07 0.00 38.61 3.84
94 95 1.083806 GCCGACATGAGCATCGTCAA 61.084 55.000 0.00 0.00 38.61 3.18
101 102 0.737367 TGAGCATCGTCAAGGCTTCG 60.737 55.000 0.00 0.00 38.15 3.79
125 127 2.126189 CGTCGGTCGGTTTCTCCC 60.126 66.667 0.00 0.00 35.71 4.30
126 128 2.922950 CGTCGGTCGGTTTCTCCCA 61.923 63.158 0.00 0.00 35.71 4.37
128 130 1.532316 TCGGTCGGTTTCTCCCACT 60.532 57.895 0.00 0.00 0.00 4.00
129 131 1.117142 TCGGTCGGTTTCTCCCACTT 61.117 55.000 0.00 0.00 0.00 3.16
133 135 2.380410 CGGTTTCTCCCACTTCGCG 61.380 63.158 0.00 0.00 0.00 5.87
172 174 7.732025 ACGAAATTCCCTCAAGGTAAAAATTT 58.268 30.769 0.00 2.78 36.75 1.82
186 188 7.053498 AGGTAAAAATTTGCACAAACTTGGAT 58.947 30.769 0.00 0.00 32.51 3.41
187 189 7.555914 AGGTAAAAATTTGCACAAACTTGGATT 59.444 29.630 0.00 0.00 32.51 3.01
228 230 4.223032 AGATGTAGTTTGACGGTGATTCCT 59.777 41.667 0.00 0.00 0.00 3.36
249 251 4.320861 CCTCTATTGTAGATGAGCTCGTGG 60.321 50.000 14.59 0.00 33.66 4.94
255 257 0.033601 AGATGAGCTCGTGGGACTCT 60.034 55.000 14.59 0.00 0.00 3.24
273 275 6.349694 GGGACTCTTCTTTTGTGGATGATTTC 60.350 42.308 0.00 0.00 0.00 2.17
309 335 6.071108 AGGACATTGATATGCTAGTAGCGATT 60.071 38.462 17.16 7.38 46.26 3.34
311 337 6.102663 ACATTGATATGCTAGTAGCGATTCC 58.897 40.000 17.16 6.13 46.26 3.01
312 338 5.984695 TTGATATGCTAGTAGCGATTCCT 57.015 39.130 17.16 0.00 46.26 3.36
314 340 6.685527 TGATATGCTAGTAGCGATTCCTAG 57.314 41.667 17.16 3.47 46.26 3.02
353 379 2.041686 GCGGTTCCGTATTTGGCCA 61.042 57.895 0.00 0.00 0.00 5.36
362 388 3.135712 TCCGTATTTGGCCATGAGTACAT 59.864 43.478 6.09 0.00 37.19 2.29
381 408 4.891566 CGAAGAGACGGGTTGAGG 57.108 61.111 0.00 0.00 0.00 3.86
395 422 2.545113 GGTTGAGGCGCACGATAGATTA 60.545 50.000 10.83 0.00 41.38 1.75
399 426 2.069273 AGGCGCACGATAGATTAATGC 58.931 47.619 10.83 0.00 41.38 3.56
406 433 6.211664 GCACGATAGATTAATGCGTAACTT 57.788 37.500 0.00 0.00 41.38 2.66
450 477 4.572985 TTCAAAGAGGTACTTTCGTCGA 57.427 40.909 0.00 0.00 45.66 4.20
458 485 6.860080 AGAGGTACTTTCGTCGATGATTTAA 58.140 36.000 8.43 0.00 41.55 1.52
469 496 5.748630 CGTCGATGATTTAAGATGTCCAAGA 59.251 40.000 0.00 0.00 0.00 3.02
526 561 3.077556 TTCGGGCAGAGGAGGAGC 61.078 66.667 0.00 0.00 0.00 4.70
527 562 3.608759 TTCGGGCAGAGGAGGAGCT 62.609 63.158 0.00 0.00 0.00 4.09
528 563 3.847602 CGGGCAGAGGAGGAGCTG 61.848 72.222 0.00 0.00 35.28 4.24
531 566 4.527583 GCAGAGGAGGAGCTGCGG 62.528 72.222 0.00 0.00 46.66 5.69
532 567 3.073735 CAGAGGAGGAGCTGCGGT 61.074 66.667 0.00 0.00 0.00 5.68
572 607 2.093306 TTACATCACCTGTTGGAGCG 57.907 50.000 0.00 0.00 39.39 5.03
573 608 1.262417 TACATCACCTGTTGGAGCGA 58.738 50.000 0.00 0.00 39.39 4.93
577 612 4.003788 ACCTGTTGGAGCGACGGG 62.004 66.667 0.00 0.00 46.84 5.28
593 634 2.817834 GGCGCACGGCTGATGTAA 60.818 61.111 10.83 0.00 42.94 2.41
622 663 5.183522 TCCGTTGAAGTTAGGTGTTTTTGTT 59.816 36.000 0.00 0.00 0.00 2.83
623 664 5.287513 CCGTTGAAGTTAGGTGTTTTTGTTG 59.712 40.000 0.00 0.00 0.00 3.33
624 665 5.859648 CGTTGAAGTTAGGTGTTTTTGTTGT 59.140 36.000 0.00 0.00 0.00 3.32
626 667 7.537991 CGTTGAAGTTAGGTGTTTTTGTTGTAA 59.462 33.333 0.00 0.00 0.00 2.41
628 669 9.760077 TTGAAGTTAGGTGTTTTTGTTGTAAAA 57.240 25.926 0.00 0.00 0.00 1.52
632 673 9.078753 AGTTAGGTGTTTTTGTTGTAAAATTCG 57.921 29.630 0.00 0.00 30.44 3.34
758 3429 1.536418 CTCCCACAGACCTCCACCA 60.536 63.158 0.00 0.00 0.00 4.17
792 3463 2.825836 GGCCACCTCGAATGCCAG 60.826 66.667 0.00 0.00 43.46 4.85
966 3637 0.325484 CCAGCCATCCAATCCCCAAA 60.325 55.000 0.00 0.00 0.00 3.28
1073 3744 3.093278 CGGGAGCGATCTTGTTGC 58.907 61.111 0.00 0.00 37.51 4.17
1169 3853 1.134848 GCGAGAGATTGGAGAAGCTGT 60.135 52.381 0.00 0.00 0.00 4.40
1177 3861 2.435372 TGGAGAAGCTGTTTGGTTGT 57.565 45.000 0.00 0.00 36.40 3.32
1264 3948 1.683319 GGAGGAAGGAAGGTGATTGCC 60.683 57.143 0.00 0.00 0.00 4.52
1613 4297 3.591835 AAGCGCAACAACCGTGGG 61.592 61.111 11.47 0.00 0.00 4.61
1685 4369 1.146041 TGTTGACAAGCTGCTCCGT 59.854 52.632 1.00 3.12 0.00 4.69
1697 4381 2.671070 CTCCGTGTTGCCCCTGAT 59.329 61.111 0.00 0.00 0.00 2.90
1746 4430 2.124942 CTTTCCGGGGAGAGCTGC 60.125 66.667 0.00 0.00 0.00 5.25
1799 4483 2.342279 CTCGGCGACAGGGACAAA 59.658 61.111 4.99 0.00 0.00 2.83
1805 4489 0.955428 GCGACAGGGACAAATCTGCA 60.955 55.000 0.00 0.00 34.57 4.41
1806 4490 1.081892 CGACAGGGACAAATCTGCAG 58.918 55.000 7.63 7.63 34.57 4.41
1836 4520 1.672356 GAGGTGTTCCACGCTGCAT 60.672 57.895 0.00 0.00 34.83 3.96
1868 4552 1.295792 GCAATGGCTCCGTCGATAAA 58.704 50.000 0.00 0.00 36.96 1.40
1883 4567 4.072131 TCGATAAAGGCAAGCTTTTGACT 58.928 39.130 11.76 0.00 43.40 3.41
1892 4576 0.242017 AGCTTTTGACTGCCGCAATC 59.758 50.000 0.00 0.00 0.00 2.67
2219 4903 2.975851 CAATTCACTTCTTTCTGCGTGC 59.024 45.455 0.00 0.00 0.00 5.34
2269 4953 4.153986 CGTGCTGTCTTTGATGAAATGAC 58.846 43.478 0.00 0.00 41.25 3.06
2420 5104 8.703604 ATGTTGTTACATACAGTACACTGATC 57.296 34.615 16.05 0.00 43.46 2.92
2546 5230 3.139077 GGCTATTTATGTGAAGACCGGG 58.861 50.000 6.32 0.00 0.00 5.73
2762 5446 2.368655 ATTCAAAAGCGGGAATGCAC 57.631 45.000 0.00 0.00 37.31 4.57
2915 5599 7.616528 TGATATGACTGAGATGGGTATCAAA 57.383 36.000 0.00 0.00 35.70 2.69
2974 5658 1.274167 TGGCAAGTCTAAGGTACACGG 59.726 52.381 0.00 0.00 0.00 4.94
3212 5896 7.362056 GCTTGCAGGTACATCTTGATTTCTTTA 60.362 37.037 0.00 0.00 0.00 1.85
3252 5936 8.900983 ATGCCAAATCTCTCTAATTCTTACTC 57.099 34.615 0.00 0.00 0.00 2.59
3253 5937 7.275920 TGCCAAATCTCTCTAATTCTTACTCC 58.724 38.462 0.00 0.00 0.00 3.85
3254 5938 6.708502 GCCAAATCTCTCTAATTCTTACTCCC 59.291 42.308 0.00 0.00 0.00 4.30
3255 5939 7.419634 GCCAAATCTCTCTAATTCTTACTCCCT 60.420 40.741 0.00 0.00 0.00 4.20
3256 5940 8.147704 CCAAATCTCTCTAATTCTTACTCCCTC 58.852 40.741 0.00 0.00 0.00 4.30
3257 5941 8.923270 CAAATCTCTCTAATTCTTACTCCCTCT 58.077 37.037 0.00 0.00 0.00 3.69
3258 5942 8.477419 AATCTCTCTAATTCTTACTCCCTCTG 57.523 38.462 0.00 0.00 0.00 3.35
3259 5943 6.975949 TCTCTCTAATTCTTACTCCCTCTGT 58.024 40.000 0.00 0.00 0.00 3.41
3260 5944 7.057894 TCTCTCTAATTCTTACTCCCTCTGTC 58.942 42.308 0.00 0.00 0.00 3.51
3261 5945 6.130569 TCTCTAATTCTTACTCCCTCTGTCC 58.869 44.000 0.00 0.00 0.00 4.02
3262 5946 5.209659 TCTAATTCTTACTCCCTCTGTCCC 58.790 45.833 0.00 0.00 0.00 4.46
3263 5947 3.491766 ATTCTTACTCCCTCTGTCCCA 57.508 47.619 0.00 0.00 0.00 4.37
3264 5948 3.491766 TTCTTACTCCCTCTGTCCCAT 57.508 47.619 0.00 0.00 0.00 4.00
3265 5949 4.620086 TTCTTACTCCCTCTGTCCCATA 57.380 45.455 0.00 0.00 0.00 2.74
3266 5950 4.620086 TCTTACTCCCTCTGTCCCATAA 57.380 45.455 0.00 0.00 0.00 1.90
3267 5951 5.157770 TCTTACTCCCTCTGTCCCATAAT 57.842 43.478 0.00 0.00 0.00 1.28
3268 5952 6.289482 TCTTACTCCCTCTGTCCCATAATA 57.711 41.667 0.00 0.00 0.00 0.98
3269 5953 6.875469 TCTTACTCCCTCTGTCCCATAATAT 58.125 40.000 0.00 0.00 0.00 1.28
3270 5954 8.008104 TCTTACTCCCTCTGTCCCATAATATA 57.992 38.462 0.00 0.00 0.00 0.86
3271 5955 8.461854 TCTTACTCCCTCTGTCCCATAATATAA 58.538 37.037 0.00 0.00 0.00 0.98
3272 5956 8.666129 TTACTCCCTCTGTCCCATAATATAAG 57.334 38.462 0.00 0.00 0.00 1.73
3273 5957 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
3274 5958 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
3275 5959 5.721960 TCCCTCTGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
3276 5960 5.394663 CCCTCTGTCCCATAATATAAGAGCG 60.395 48.000 0.00 0.00 0.00 5.03
3277 5961 5.186021 CCTCTGTCCCATAATATAAGAGCGT 59.814 44.000 0.00 0.00 0.00 5.07
3278 5962 6.295349 CCTCTGTCCCATAATATAAGAGCGTT 60.295 42.308 0.00 0.00 0.00 4.84
3279 5963 7.062749 TCTGTCCCATAATATAAGAGCGTTT 57.937 36.000 0.00 0.00 0.00 3.60
3280 5964 7.506114 TCTGTCCCATAATATAAGAGCGTTTT 58.494 34.615 0.00 0.00 0.00 2.43
3281 5965 7.990886 TCTGTCCCATAATATAAGAGCGTTTTT 59.009 33.333 0.00 0.00 0.00 1.94
3308 5992 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
3309 5993 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
3310 5994 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
3311 5995 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
3312 5996 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
3313 5997 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
3314 5998 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
3320 6004 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
3321 6005 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
3322 6006 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
3354 6051 7.067421 AGTAGTATTCTACCACTGGATGCTTA 58.933 38.462 0.71 0.00 45.36 3.09
3528 6226 2.813754 TGTGCTGAATTGTACTGGAAGC 59.186 45.455 0.00 0.00 37.60 3.86
3546 6288 6.311735 TGGAAGCTAATTACCTTTTTCCTGT 58.688 36.000 0.00 0.00 34.98 4.00
3610 6353 6.294508 GCACTGGTTAAATTTTAGCCTTCAGA 60.295 38.462 19.05 2.43 0.00 3.27
3839 6762 4.018870 TCCAACCTGCAAATCTGGTATACA 60.019 41.667 5.01 0.00 45.00 2.29
3946 6870 7.573096 CGCTTGTTTGATAACTTTGTCTATGGT 60.573 37.037 0.00 0.00 35.24 3.55
4101 7025 1.050988 GGCCAGGTAGGATCTGCTCA 61.051 60.000 0.00 0.00 41.22 4.26
4357 7468 6.432783 CCTTGGTGTAGTGGATTTTGTCATTA 59.567 38.462 0.00 0.00 0.00 1.90
4482 7593 7.148306 ACGTAGTCTATTGGCATTTTTGGTTAG 60.148 37.037 0.00 0.00 29.74 2.34
4498 7609 7.659652 TTTGGTTAGTTTGGAAGTTGTTTTG 57.340 32.000 0.00 0.00 0.00 2.44
4504 7615 9.366216 GTTAGTTTGGAAGTTGTTTTGAGATTT 57.634 29.630 0.00 0.00 0.00 2.17
4593 7704 6.589523 CCATCTTCATATGTAGAGTAGCAAGC 59.410 42.308 16.02 0.00 0.00 4.01
4657 7768 5.303589 CACAGGGCTAATCCATTTGATGAAT 59.696 40.000 0.00 0.00 36.21 2.57
4811 7927 0.109412 GTGCAGCTCAAGCAATGGTC 60.109 55.000 4.59 0.00 44.64 4.02
4901 8017 7.277981 AGGTACTCGATGCTACAACTTATTTTG 59.722 37.037 0.00 0.00 0.00 2.44
4938 8054 5.818857 ACATTTACGGTAGTTTTGTGTCTGT 59.181 36.000 0.00 0.00 0.00 3.41
4939 8055 5.721876 TTTACGGTAGTTTTGTGTCTGTG 57.278 39.130 0.00 0.00 0.00 3.66
4982 8098 5.964477 ACTTTTCCTCCCATCTGTATCTGTA 59.036 40.000 0.00 0.00 0.00 2.74
4983 8099 6.617371 ACTTTTCCTCCCATCTGTATCTGTAT 59.383 38.462 0.00 0.00 0.00 2.29
4984 8100 7.789831 ACTTTTCCTCCCATCTGTATCTGTATA 59.210 37.037 0.00 0.00 0.00 1.47
5197 8313 1.064463 AGAATCCGGCACCATCAACAT 60.064 47.619 0.00 0.00 0.00 2.71
5210 8326 4.718774 ACCATCAACATGATACTCCTCAGT 59.281 41.667 0.00 0.00 34.28 3.41
5351 8469 3.914312 TCTCCTTAGTTTGTCTTCTGCG 58.086 45.455 0.00 0.00 0.00 5.18
5374 8492 5.398711 CGTTTCAGAAGACTGTGTAGTGTAC 59.601 44.000 0.00 0.00 43.81 2.90
5463 8581 5.065914 TCAAGTTCCAACTCCTTTCATCAG 58.934 41.667 0.00 0.00 38.57 2.90
5471 8590 1.211457 CTCCTTTCATCAGGGGTGGAG 59.789 57.143 0.00 0.00 34.24 3.86
5476 8595 3.893753 TTCATCAGGGGTGGAGAAAAA 57.106 42.857 0.00 0.00 0.00 1.94
5515 8634 2.597903 GATTGGCTCCCCTGTCCC 59.402 66.667 0.00 0.00 0.00 4.46
5563 8682 1.617947 GGACCGGGAATCACTGCTCT 61.618 60.000 6.32 0.00 0.00 4.09
5582 8701 0.906282 TCAGAGGGTCATCTGCAGCA 60.906 55.000 9.47 0.00 45.25 4.41
5621 8740 3.823281 TCTTGTTTTGGTACTCGTCCA 57.177 42.857 0.00 0.00 0.00 4.02
5644 8763 1.069978 GAAGGCAGATACCTGGAGCTC 59.930 57.143 4.71 4.71 39.93 4.09
5645 8764 0.264359 AGGCAGATACCTGGAGCTCT 59.736 55.000 14.64 0.00 39.13 4.09
5646 8765 1.127343 GGCAGATACCTGGAGCTCTT 58.873 55.000 14.64 0.00 40.72 2.85
5647 8766 1.488393 GGCAGATACCTGGAGCTCTTT 59.512 52.381 14.64 0.00 40.72 2.52
5648 8767 2.092699 GGCAGATACCTGGAGCTCTTTT 60.093 50.000 14.64 0.00 40.72 2.27
5649 8768 2.941720 GCAGATACCTGGAGCTCTTTTG 59.058 50.000 14.64 2.71 40.72 2.44
5650 8769 2.941720 CAGATACCTGGAGCTCTTTTGC 59.058 50.000 14.64 0.00 36.77 3.68
5651 8770 6.967097 GCAGATACCTGGAGCTCTTTTGCT 62.967 50.000 14.64 0.22 42.30 3.91
5736 8856 2.475187 GCTCGTGATGCTGCTTTACAAG 60.475 50.000 10.30 3.28 0.00 3.16
5737 8857 2.995939 CTCGTGATGCTGCTTTACAAGA 59.004 45.455 10.30 7.47 0.00 3.02
5738 8858 3.599343 TCGTGATGCTGCTTTACAAGAT 58.401 40.909 10.30 0.00 0.00 2.40
5739 8859 4.754322 TCGTGATGCTGCTTTACAAGATA 58.246 39.130 10.30 0.00 0.00 1.98
5740 8860 4.566759 TCGTGATGCTGCTTTACAAGATAC 59.433 41.667 10.30 0.00 0.00 2.24
5741 8861 4.329801 CGTGATGCTGCTTTACAAGATACA 59.670 41.667 10.30 0.00 0.00 2.29
5742 8862 5.163864 CGTGATGCTGCTTTACAAGATACAA 60.164 40.000 10.30 0.00 0.00 2.41
5759 8879 2.522185 ACAAGATGCCATCAGCTTTGT 58.478 42.857 7.56 5.89 45.72 2.83
5784 8904 3.122850 GCAAATGGCATCTCCCCG 58.877 61.111 0.00 0.00 43.97 5.73
5901 9021 2.544685 GAGATGAGCGCAATGTGTAGT 58.455 47.619 11.47 0.00 0.00 2.73
5905 9025 0.371645 GAGCGCAATGTGTAGTCTGC 59.628 55.000 11.47 0.00 0.00 4.26
5906 9026 0.036952 AGCGCAATGTGTAGTCTGCT 60.037 50.000 11.47 0.00 32.52 4.24
5907 9027 0.095935 GCGCAATGTGTAGTCTGCTG 59.904 55.000 0.30 0.00 32.52 4.41
5908 9028 1.713597 CGCAATGTGTAGTCTGCTGA 58.286 50.000 0.00 0.00 32.52 4.26
5911 9032 3.242220 CGCAATGTGTAGTCTGCTGATTC 60.242 47.826 0.00 0.00 32.52 2.52
5925 9046 6.691818 GTCTGCTGATTCATTCATTCATTCAC 59.308 38.462 0.00 0.00 32.72 3.18
5935 9056 3.433343 TCATTCATTCACTTGCCATGGT 58.567 40.909 14.67 0.00 0.00 3.55
6017 9139 7.716799 AAAATTGGCTGGAAACTGTATATCA 57.283 32.000 0.00 0.00 0.00 2.15
6023 9145 4.679639 GCTGGAAACTGTATATCACCGACA 60.680 45.833 0.00 0.00 0.00 4.35
6026 9148 2.486951 ACTGTATATCACCGACACGC 57.513 50.000 0.00 0.00 0.00 5.34
6028 9150 1.003223 CTGTATATCACCGACACGCGA 60.003 52.381 15.93 0.00 44.57 5.87
6080 9202 5.208463 ACATTTAATGGTTGGTTCGCTTT 57.792 34.783 9.88 0.00 33.60 3.51
6086 9208 0.869730 GGTTGGTTCGCTTTTCGCTA 59.130 50.000 0.00 0.00 38.27 4.26
6106 9228 5.692204 CGCTATCATCGGTATTTGACTTCTT 59.308 40.000 0.00 0.00 0.00 2.52
6107 9229 6.129062 CGCTATCATCGGTATTTGACTTCTTC 60.129 42.308 0.00 0.00 0.00 2.87
6108 9230 6.146347 GCTATCATCGGTATTTGACTTCTTCC 59.854 42.308 0.00 0.00 0.00 3.46
6295 9524 3.804786 TCGGTAAATGATCGGTTAGCA 57.195 42.857 14.25 3.47 30.29 3.49
6300 9529 5.464057 CGGTAAATGATCGGTTAGCATTGTA 59.536 40.000 14.25 0.00 43.30 2.41
6301 9530 6.018588 CGGTAAATGATCGGTTAGCATTGTAA 60.019 38.462 14.25 0.00 43.30 2.41
6312 9541 8.181573 TCGGTTAGCATTGTAAGATTGATTTTC 58.818 33.333 0.00 0.00 0.00 2.29
6335 9564 5.477984 TCTCTTTGTGGGAAGAAATCAATGG 59.522 40.000 0.00 0.00 35.38 3.16
6391 9621 3.140325 TGGCCGAGAAGTTTGAAGATT 57.860 42.857 0.00 0.00 0.00 2.40
6406 9637 9.875691 AGTTTGAAGATTAAATAAATTCAGGCC 57.124 29.630 0.00 0.00 31.23 5.19
6407 9638 9.875691 GTTTGAAGATTAAATAAATTCAGGCCT 57.124 29.630 0.00 0.00 31.23 5.19
6409 9640 8.237811 TGAAGATTAAATAAATTCAGGCCTCC 57.762 34.615 0.00 0.00 0.00 4.30
6410 9641 8.061304 TGAAGATTAAATAAATTCAGGCCTCCT 58.939 33.333 0.00 0.00 0.00 3.69
6411 9642 8.844865 AAGATTAAATAAATTCAGGCCTCCTT 57.155 30.769 0.00 0.00 0.00 3.36
6412 9643 8.844865 AGATTAAATAAATTCAGGCCTCCTTT 57.155 30.769 0.00 5.58 0.00 3.11
6413 9644 8.699130 AGATTAAATAAATTCAGGCCTCCTTTG 58.301 33.333 0.00 0.00 0.00 2.77
6414 9645 5.682234 AAATAAATTCAGGCCTCCTTTGG 57.318 39.130 0.00 0.00 0.00 3.28
6415 9646 2.702270 AAATTCAGGCCTCCTTTGGT 57.298 45.000 0.00 0.00 0.00 3.67
6416 9647 2.702270 AATTCAGGCCTCCTTTGGTT 57.298 45.000 0.00 0.00 0.00 3.67
6417 9648 2.702270 ATTCAGGCCTCCTTTGGTTT 57.298 45.000 0.00 0.00 0.00 3.27
6418 9649 3.825908 ATTCAGGCCTCCTTTGGTTTA 57.174 42.857 0.00 0.00 0.00 2.01
6419 9650 2.879103 TCAGGCCTCCTTTGGTTTAG 57.121 50.000 0.00 0.00 0.00 1.85
6420 9651 2.344592 TCAGGCCTCCTTTGGTTTAGA 58.655 47.619 0.00 0.00 0.00 2.10
6421 9652 2.305927 TCAGGCCTCCTTTGGTTTAGAG 59.694 50.000 0.00 0.00 0.00 2.43
6430 9661 7.709149 CTCCTTTGGTTTAGAGGAATTTCAT 57.291 36.000 0.00 0.00 39.00 2.57
6431 9662 8.807948 CTCCTTTGGTTTAGAGGAATTTCATA 57.192 34.615 0.00 0.00 39.00 2.15
6432 9663 9.243105 CTCCTTTGGTTTAGAGGAATTTCATAA 57.757 33.333 0.00 0.00 39.00 1.90
6433 9664 9.594936 TCCTTTGGTTTAGAGGAATTTCATAAA 57.405 29.630 0.00 0.00 36.67 1.40
6444 9675 8.975295 AGAGGAATTTCATAAAAATTCTGGAGG 58.025 33.333 17.82 0.00 42.94 4.30
6445 9676 8.899887 AGGAATTTCATAAAAATTCTGGAGGA 57.100 30.769 17.82 0.00 42.94 3.71
6446 9677 9.498039 AGGAATTTCATAAAAATTCTGGAGGAT 57.502 29.630 17.82 0.00 42.94 3.24
6474 9705 3.895704 TTTCCTTTAGAGCCCTTTGGT 57.104 42.857 0.00 0.00 0.00 3.67
6475 9706 3.895704 TTCCTTTAGAGCCCTTTGGTT 57.104 42.857 0.00 0.00 0.00 3.67
6476 9707 3.434940 TCCTTTAGAGCCCTTTGGTTC 57.565 47.619 0.00 0.00 41.91 3.62
6477 9708 2.714250 TCCTTTAGAGCCCTTTGGTTCA 59.286 45.455 0.00 0.00 43.89 3.18
6478 9709 3.333680 TCCTTTAGAGCCCTTTGGTTCAT 59.666 43.478 0.00 0.00 43.89 2.57
6479 9710 4.538490 TCCTTTAGAGCCCTTTGGTTCATA 59.462 41.667 0.00 0.00 43.89 2.15
6480 9711 4.884164 CCTTTAGAGCCCTTTGGTTCATAG 59.116 45.833 0.00 0.00 43.89 2.23
6481 9712 4.503714 TTAGAGCCCTTTGGTTCATAGG 57.496 45.455 0.00 0.00 43.89 2.57
6482 9713 2.562296 AGAGCCCTTTGGTTCATAGGA 58.438 47.619 6.07 0.00 43.89 2.94
6483 9714 2.919602 AGAGCCCTTTGGTTCATAGGAA 59.080 45.455 6.07 0.00 43.89 3.36
6484 9715 3.529319 AGAGCCCTTTGGTTCATAGGAAT 59.471 43.478 6.07 0.00 43.89 3.01
6485 9716 3.633986 GAGCCCTTTGGTTCATAGGAATG 59.366 47.826 6.07 0.00 41.28 2.67
6486 9717 2.695147 GCCCTTTGGTTCATAGGAATGG 59.305 50.000 6.07 0.00 35.14 3.16
6487 9718 3.627237 GCCCTTTGGTTCATAGGAATGGA 60.627 47.826 6.07 0.00 35.14 3.41
6488 9719 4.808042 CCCTTTGGTTCATAGGAATGGAT 58.192 43.478 6.07 0.00 35.14 3.41
6489 9720 5.211201 CCCTTTGGTTCATAGGAATGGATT 58.789 41.667 6.07 0.00 35.14 3.01
6490 9721 5.302823 CCCTTTGGTTCATAGGAATGGATTC 59.697 44.000 6.07 0.00 35.14 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.531332 CGGATAACTACGCTACAGTAACC 58.469 47.826 0.00 0.00 0.00 2.85
1 2 4.531332 CCGGATAACTACGCTACAGTAAC 58.469 47.826 0.00 0.00 0.00 2.50
2 3 3.565482 CCCGGATAACTACGCTACAGTAA 59.435 47.826 0.73 0.00 0.00 2.24
3 4 3.141398 CCCGGATAACTACGCTACAGTA 58.859 50.000 0.73 0.00 0.00 2.74
4 5 1.952296 CCCGGATAACTACGCTACAGT 59.048 52.381 0.73 0.00 0.00 3.55
5 6 1.335689 GCCCGGATAACTACGCTACAG 60.336 57.143 0.73 0.00 0.00 2.74
6 7 0.670162 GCCCGGATAACTACGCTACA 59.330 55.000 0.73 0.00 0.00 2.74
7 8 0.386478 CGCCCGGATAACTACGCTAC 60.386 60.000 0.73 0.00 0.00 3.58
8 9 0.819259 ACGCCCGGATAACTACGCTA 60.819 55.000 0.73 0.00 0.00 4.26
9 10 2.068277 GACGCCCGGATAACTACGCT 62.068 60.000 0.73 0.00 0.00 5.07
10 11 1.659644 GACGCCCGGATAACTACGC 60.660 63.158 0.73 0.00 0.00 4.42
11 12 0.593263 GTGACGCCCGGATAACTACG 60.593 60.000 0.73 0.00 0.00 3.51
12 13 0.457035 TGTGACGCCCGGATAACTAC 59.543 55.000 0.73 0.00 0.00 2.73
13 14 0.742505 CTGTGACGCCCGGATAACTA 59.257 55.000 0.73 0.00 0.00 2.24
14 15 1.515954 CTGTGACGCCCGGATAACT 59.484 57.895 0.73 0.00 0.00 2.24
15 16 2.171725 GCTGTGACGCCCGGATAAC 61.172 63.158 0.73 0.00 0.00 1.89
16 17 2.185867 GCTGTGACGCCCGGATAA 59.814 61.111 0.73 0.00 0.00 1.75
17 18 3.845259 GGCTGTGACGCCCGGATA 61.845 66.667 0.73 0.00 44.41 2.59
23 24 4.980805 TTGGACGGCTGTGACGCC 62.981 66.667 0.80 8.11 46.68 5.68
24 25 3.414700 CTTGGACGGCTGTGACGC 61.415 66.667 0.80 0.00 37.73 5.19
25 26 2.738521 CCTTGGACGGCTGTGACG 60.739 66.667 0.80 0.00 41.40 4.35
26 27 2.358737 CCCTTGGACGGCTGTGAC 60.359 66.667 0.80 0.00 0.00 3.67
27 28 4.329545 GCCCTTGGACGGCTGTGA 62.330 66.667 0.80 0.00 43.48 3.58
44 45 1.513836 GGCGGCTAGGTCTACTACGG 61.514 65.000 0.00 0.00 0.00 4.02
90 91 3.567473 GCTGGTCGAAGCCTTGAC 58.433 61.111 0.00 0.00 37.20 3.18
114 115 1.005394 GCGAAGTGGGAGAAACCGA 60.005 57.895 0.00 0.00 40.11 4.69
121 123 2.664851 TTGTGCGCGAAGTGGGAG 60.665 61.111 12.10 0.00 39.19 4.30
125 127 2.423517 CACGTTGTGCGCGAAGTG 60.424 61.111 17.33 17.33 46.11 3.16
126 128 2.356093 GAACACGTTGTGCGCGAAGT 62.356 55.000 12.10 0.00 46.11 3.01
128 130 2.321740 GAACACGTTGTGCGCGAA 59.678 55.556 12.10 0.00 46.11 4.70
129 131 3.978764 CGAACACGTTGTGCGCGA 61.979 61.111 12.10 0.00 43.10 5.87
158 160 7.148340 CCAAGTTTGTGCAAATTTTTACCTTGA 60.148 33.333 16.46 0.00 31.64 3.02
196 198 3.678548 GTCAAACTACATCTTCACGTCCC 59.321 47.826 0.00 0.00 0.00 4.46
207 209 4.223032 AGAGGAATCACCGTCAAACTACAT 59.777 41.667 0.00 0.00 44.74 2.29
228 230 3.570125 CCCACGAGCTCATCTACAATAGA 59.430 47.826 15.40 0.00 39.50 1.98
249 251 6.432472 AGAAATCATCCACAAAAGAAGAGTCC 59.568 38.462 0.00 0.00 0.00 3.85
255 257 7.233144 TCCAATGAGAAATCATCCACAAAAGAA 59.767 33.333 0.00 0.00 0.00 2.52
273 275 6.127980 GCATATCAATGTCCTCATCCAATGAG 60.128 42.308 9.50 9.50 44.05 2.90
309 335 2.526888 TCGGCTTCTTCCTTCTAGGA 57.473 50.000 0.00 0.00 44.10 2.94
311 337 2.093973 TGCTTCGGCTTCTTCCTTCTAG 60.094 50.000 0.00 0.00 42.37 2.43
312 338 1.899814 TGCTTCGGCTTCTTCCTTCTA 59.100 47.619 0.00 0.00 42.37 2.10
314 340 0.799393 GTGCTTCGGCTTCTTCCTTC 59.201 55.000 0.00 0.00 42.37 3.46
341 367 2.912771 TGTACTCATGGCCAAATACGG 58.087 47.619 10.96 0.00 0.00 4.02
342 368 3.498397 GGATGTACTCATGGCCAAATACG 59.502 47.826 10.96 0.00 34.06 3.06
345 371 2.172505 TCGGATGTACTCATGGCCAAAT 59.827 45.455 10.96 0.00 34.06 2.32
353 379 3.972950 CGTCTCTTCGGATGTACTCAT 57.027 47.619 0.00 0.00 36.95 2.90
406 433 3.512219 AATGGGTCGGAGTACCAAAAA 57.488 42.857 0.00 0.00 41.67 1.94
488 515 0.674895 GCTCTGCCTCACGGAATTGT 60.675 55.000 0.00 0.00 31.65 2.71
541 576 2.099098 GGTGATGTAAAAAGGGCCATCG 59.901 50.000 6.18 0.00 0.00 3.84
577 612 0.316196 GATTTACATCAGCCGTGCGC 60.316 55.000 0.00 0.00 37.98 6.09
593 634 4.906618 ACACCTAACTTCAACGGATGATT 58.093 39.130 0.00 0.00 38.03 2.57
601 642 8.745464 TTACAACAAAAACACCTAACTTCAAC 57.255 30.769 0.00 0.00 0.00 3.18
610 651 6.103330 AGCGAATTTTACAACAAAAACACCT 58.897 32.000 0.00 0.00 31.50 4.00
639 680 6.135290 GCTAGATGCAAATTTACATCACCA 57.865 37.500 26.03 13.83 44.16 4.17
671 712 6.259387 TGCTGTGTTTATTAGAGCAGATGATG 59.741 38.462 0.00 0.00 39.21 3.07
672 713 6.259608 GTGCTGTGTTTATTAGAGCAGATGAT 59.740 38.462 0.00 0.00 43.84 2.45
673 714 5.582269 GTGCTGTGTTTATTAGAGCAGATGA 59.418 40.000 0.00 0.00 43.84 2.92
675 716 4.878397 GGTGCTGTGTTTATTAGAGCAGAT 59.122 41.667 0.00 0.00 43.84 2.90
676 717 4.253685 GGTGCTGTGTTTATTAGAGCAGA 58.746 43.478 0.00 0.00 43.84 4.26
677 718 4.002982 TGGTGCTGTGTTTATTAGAGCAG 58.997 43.478 0.00 0.00 43.84 4.24
689 3357 2.111878 GAGCTGGTGGTGCTGTGT 59.888 61.111 0.00 0.00 41.30 3.72
714 3385 2.043248 GGGGCTGACTAGGTCCGA 60.043 66.667 0.00 0.00 0.00 4.55
792 3463 2.044946 GTCCATGACCTGTGGGGC 60.045 66.667 0.00 0.00 42.24 5.80
845 3516 8.986929 AGAATTATTTCCGGAAGATTTCTCAT 57.013 30.769 17.97 7.94 28.35 2.90
846 3517 8.267894 AGAGAATTATTTCCGGAAGATTTCTCA 58.732 33.333 34.16 19.08 42.61 3.27
923 3594 2.437359 AAGATCGCACCAGGCTGC 60.437 61.111 9.56 0.00 41.67 5.25
924 3595 1.817099 GGAAGATCGCACCAGGCTG 60.817 63.158 7.75 7.75 41.67 4.85
966 3637 5.491982 GTGATAAGATTGGATTAGGCGGAT 58.508 41.667 0.00 0.00 0.00 4.18
1073 3744 5.129485 AGTCAGGATATTTATATGGCCGGAG 59.871 44.000 5.05 0.00 0.00 4.63
1169 3853 3.133721 CCAAATCCTTCCACACAACCAAA 59.866 43.478 0.00 0.00 0.00 3.28
1177 3861 2.348472 ACTCCTCCAAATCCTTCCACA 58.652 47.619 0.00 0.00 0.00 4.17
1220 3904 2.440065 TCCCGGCACCGTACGTAT 60.440 61.111 15.21 0.00 37.81 3.06
1550 4234 3.993535 CTGAACTCAGGGCCAAGC 58.006 61.111 6.18 0.00 40.20 4.01
1583 4267 1.442769 TGCGCTTGGAGATGTTCTTC 58.557 50.000 9.73 0.00 0.00 2.87
1670 4354 1.146041 AACACGGAGCAGCTTGTCA 59.854 52.632 0.00 0.00 0.00 3.58
1685 4369 2.350895 CGGTCATCAGGGGCAACA 59.649 61.111 0.00 0.00 39.74 3.33
1746 4430 3.209410 GGCAGTAATCATCAGGACCAAG 58.791 50.000 0.00 0.00 0.00 3.61
1805 4489 3.616721 ACCTCAAGCGCACGGACT 61.617 61.111 11.47 0.00 0.00 3.85
1806 4490 3.414700 CACCTCAAGCGCACGGAC 61.415 66.667 11.47 0.00 0.00 4.79
1868 4552 1.799258 CGGCAGTCAAAAGCTTGCCT 61.799 55.000 19.80 3.00 40.02 4.75
1925 4609 3.005050 CAGCATCAAAACCTCTTCTTGCA 59.995 43.478 0.00 0.00 0.00 4.08
2239 4923 2.410322 AAAGACAGCACGGGCATCCA 62.410 55.000 14.57 0.00 44.61 3.41
2750 5434 2.735772 ATCTCCGTGCATTCCCGCT 61.736 57.895 0.00 0.00 0.00 5.52
2753 5437 3.425422 GCATCTCCGTGCATTCCC 58.575 61.111 0.00 0.00 44.43 3.97
2762 5446 9.208022 TCTAAATAGACATTAAATGCATCTCCG 57.792 33.333 0.00 0.00 0.00 4.63
2816 5500 3.309682 TGAAAGAGCTGAACAGAACAACG 59.690 43.478 5.97 0.00 0.00 4.10
2974 5658 2.093235 CCAACTTCAGGATCCTCCTCAC 60.093 54.545 12.69 0.00 45.66 3.51
3212 5896 7.679783 AGATTTGGCATTAAAAGGCTTAAGTT 58.320 30.769 0.00 0.00 35.75 2.66
3285 5969 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
3286 5970 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
3287 5971 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
3294 5978 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
3295 5979 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
3296 5980 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
3297 5981 9.451002 TGTCCCATAATATAAGAACGTTTTTGA 57.549 29.630 13.87 2.81 0.00 2.69
3298 5982 9.716507 CTGTCCCATAATATAAGAACGTTTTTG 57.283 33.333 13.87 0.00 0.00 2.44
3299 5983 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
3300 5984 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
3301 5985 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
3302 5986 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
3303 5987 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
3304 5988 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
3305 5989 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
3306 5990 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
3307 5991 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
3308 5992 7.896496 ACTACTCCCTCTGTCCCATAATATAAG 59.104 40.741 0.00 0.00 0.00 1.73
3309 5993 7.776745 ACTACTCCCTCTGTCCCATAATATAA 58.223 38.462 0.00 0.00 0.00 0.98
3310 5994 7.358255 ACTACTCCCTCTGTCCCATAATATA 57.642 40.000 0.00 0.00 0.00 0.86
3311 5995 6.234404 ACTACTCCCTCTGTCCCATAATAT 57.766 41.667 0.00 0.00 0.00 1.28
3312 5996 5.681494 ACTACTCCCTCTGTCCCATAATA 57.319 43.478 0.00 0.00 0.00 0.98
3313 5997 4.561254 ACTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
3314 5998 5.681494 ATACTACTCCCTCTGTCCCATAA 57.319 43.478 0.00 0.00 0.00 1.90
3315 5999 5.375956 AGAATACTACTCCCTCTGTCCCATA 59.624 44.000 0.00 0.00 0.00 2.74
3316 6000 4.171044 AGAATACTACTCCCTCTGTCCCAT 59.829 45.833 0.00 0.00 0.00 4.00
3317 6001 3.532232 AGAATACTACTCCCTCTGTCCCA 59.468 47.826 0.00 0.00 0.00 4.37
3318 6002 4.187506 AGAATACTACTCCCTCTGTCCC 57.812 50.000 0.00 0.00 0.00 4.46
3319 6003 5.072055 GGTAGAATACTACTCCCTCTGTCC 58.928 50.000 0.00 0.00 45.70 4.02
3320 6004 5.692928 TGGTAGAATACTACTCCCTCTGTC 58.307 45.833 0.00 0.00 45.70 3.51
3321 6005 5.728937 TGGTAGAATACTACTCCCTCTGT 57.271 43.478 0.00 0.00 45.70 3.41
3331 6015 7.950684 AGATAAGCATCCAGTGGTAGAATACTA 59.049 37.037 9.54 0.00 42.51 1.82
3332 6016 6.784969 AGATAAGCATCCAGTGGTAGAATACT 59.215 38.462 9.54 0.00 42.51 2.12
3514 6212 8.879427 AAAGGTAATTAGCTTCCAGTACAATT 57.121 30.769 25.71 7.54 42.60 2.32
3610 6353 7.750229 ATTTTCCATACGCAGATCATGTATT 57.250 32.000 0.00 0.00 0.00 1.89
3660 6581 5.885912 ACACTCTTTTCTAGAACCAGCAAAA 59.114 36.000 4.18 0.00 30.91 2.44
3839 6762 9.662947 ACCAAATTAAAGCGTAGAGTTAGTTAT 57.337 29.630 0.00 0.00 0.00 1.89
3862 6786 0.391228 TACAGCGACTGCAAGAACCA 59.609 50.000 6.74 0.00 46.23 3.67
3863 6787 1.508632 TTACAGCGACTGCAAGAACC 58.491 50.000 6.74 0.00 46.23 3.62
3946 6870 0.906066 TAAGGAGCCCATACGCAACA 59.094 50.000 0.00 0.00 0.00 3.33
4039 6963 7.495934 TCAGTAAGAGCATTATAAAAGGCAGAC 59.504 37.037 9.05 3.08 44.73 3.51
4137 7061 5.459762 ACATCACAAAATCTCTGTTTTTGCG 59.540 36.000 8.38 0.89 44.22 4.85
4202 7126 9.131791 TGAGAATAAAAATTACCCCTAAGCATC 57.868 33.333 0.00 0.00 0.00 3.91
4325 7424 5.994416 ATCCACTACACCAAGGGAATATT 57.006 39.130 0.00 0.00 0.00 1.28
4326 7425 5.994416 AATCCACTACACCAAGGGAATAT 57.006 39.130 0.00 0.00 0.00 1.28
4469 7580 6.315144 ACAACTTCCAAACTAACCAAAAATGC 59.685 34.615 0.00 0.00 0.00 3.56
4475 7586 6.994221 TCAAAACAACTTCCAAACTAACCAA 58.006 32.000 0.00 0.00 0.00 3.67
4482 7593 7.595311 ACAAATCTCAAAACAACTTCCAAAC 57.405 32.000 0.00 0.00 0.00 2.93
4498 7609 9.141400 CAGGACAGTTTAACTACTACAAATCTC 57.859 37.037 0.00 0.00 0.00 2.75
4504 7615 9.268268 CAAATTCAGGACAGTTTAACTACTACA 57.732 33.333 0.00 0.00 0.00 2.74
4527 7638 5.626142 TCAAGCTGTCCAGTAAATACCAAA 58.374 37.500 0.00 0.00 0.00 3.28
4593 7704 5.229887 GGAACATTTTACATAGCATGCAACG 59.770 40.000 21.98 9.60 0.00 4.10
4657 7768 5.850557 AGGAACACACATTTGTCATTCAA 57.149 34.783 7.48 0.00 32.65 2.69
4901 8017 5.275494 ACCGTAAATGTAACAAACACAAGC 58.725 37.500 0.00 0.00 42.09 4.01
4939 8055 3.392882 AGTTAACAGCCTTTGCATTTGC 58.607 40.909 8.61 0.00 41.13 3.68
4956 8072 6.443849 ACAGATACAGATGGGAGGAAAAGTTA 59.556 38.462 0.00 0.00 0.00 2.24
4982 8098 8.654997 AGATATACAGAGCATGGTTTCAGTTAT 58.345 33.333 0.00 0.00 0.00 1.89
4983 8099 7.928167 CAGATATACAGAGCATGGTTTCAGTTA 59.072 37.037 0.00 0.00 0.00 2.24
4984 8100 6.765036 CAGATATACAGAGCATGGTTTCAGTT 59.235 38.462 0.00 0.00 0.00 3.16
5197 8313 2.017782 GCTCGTCACTGAGGAGTATCA 58.982 52.381 23.37 0.00 43.71 2.15
5351 8469 6.505272 AGTACACTACACAGTCTTCTGAAAC 58.495 40.000 0.00 0.00 43.76 2.78
5374 8492 2.356382 CTCCTATTCGGCGAGCCTATAG 59.644 54.545 10.46 13.89 32.72 1.31
5476 8595 5.566469 TCGGGTGGATTCTCATTAAACTTT 58.434 37.500 0.00 0.00 0.00 2.66
5515 8634 0.806102 ACGAAGCGACAATCCATCGG 60.806 55.000 0.00 0.00 39.99 4.18
5563 8682 0.906282 TGCTGCAGATGACCCTCTGA 60.906 55.000 20.43 0.00 44.48 3.27
5582 8701 4.917906 AGAACTCAAGGCATCTTAACCT 57.082 40.909 0.00 0.00 38.14 3.50
5621 8740 2.114616 CTCCAGGTATCTGCCTTCACT 58.885 52.381 0.00 0.00 39.61 3.41
5644 8763 2.490328 TGCCGAAACAAGAGCAAAAG 57.510 45.000 0.00 0.00 30.97 2.27
5645 8764 2.949451 TTGCCGAAACAAGAGCAAAA 57.051 40.000 0.00 0.00 41.93 2.44
5736 8856 4.337555 ACAAAGCTGATGGCATCTTGTATC 59.662 41.667 26.49 10.14 44.79 2.24
5737 8857 4.275810 ACAAAGCTGATGGCATCTTGTAT 58.724 39.130 26.49 9.07 44.79 2.29
5738 8858 3.689347 ACAAAGCTGATGGCATCTTGTA 58.311 40.909 26.49 7.03 44.79 2.41
5739 8859 2.522185 ACAAAGCTGATGGCATCTTGT 58.478 42.857 26.49 23.24 44.79 3.16
5740 8860 3.057104 TCAACAAAGCTGATGGCATCTTG 60.057 43.478 26.49 22.66 44.79 3.02
5741 8861 3.159472 TCAACAAAGCTGATGGCATCTT 58.841 40.909 26.49 11.41 44.79 2.40
5742 8862 2.799017 TCAACAAAGCTGATGGCATCT 58.201 42.857 26.49 5.46 44.79 2.90
5784 8904 2.686405 TGCTTGCTCATCATTCATGGAC 59.314 45.455 0.00 0.00 32.64 4.02
5810 8930 1.525535 GAGCTGCCCACATAGCCAG 60.526 63.158 0.00 0.00 40.76 4.85
5816 8936 1.303888 CCACTTGAGCTGCCCACAT 60.304 57.895 0.00 0.00 0.00 3.21
5863 8983 0.889186 TCCTCCACGCCTTTTTGCTC 60.889 55.000 0.00 0.00 0.00 4.26
5901 9021 6.602009 AGTGAATGAATGAATGAATCAGCAGA 59.398 34.615 0.00 0.00 42.53 4.26
5905 9025 6.475727 GGCAAGTGAATGAATGAATGAATCAG 59.524 38.462 0.00 0.00 42.53 2.90
5906 9026 6.071278 TGGCAAGTGAATGAATGAATGAATCA 60.071 34.615 0.00 0.00 43.67 2.57
5907 9027 6.334989 TGGCAAGTGAATGAATGAATGAATC 58.665 36.000 0.00 0.00 0.00 2.52
5908 9028 6.288941 TGGCAAGTGAATGAATGAATGAAT 57.711 33.333 0.00 0.00 0.00 2.57
5911 9032 4.808895 CCATGGCAAGTGAATGAATGAATG 59.191 41.667 0.00 0.00 0.00 2.67
5925 9046 2.517959 TCAGAAAGGAACCATGGCAAG 58.482 47.619 13.04 0.00 0.00 4.01
5935 9056 4.584325 CAGGTCCAATTGTTCAGAAAGGAA 59.416 41.667 4.43 0.00 0.00 3.36
6017 9139 2.999739 AAAATGGGTCGCGTGTCGGT 63.000 55.000 5.77 0.00 39.05 4.69
6067 9189 4.221873 GCGAAAAGCGAACCAACC 57.778 55.556 0.00 0.00 44.57 3.77
6080 9202 5.196341 AGTCAAATACCGATGATAGCGAA 57.804 39.130 0.00 0.00 0.00 4.70
6086 9208 6.240549 AGGAAGAAGTCAAATACCGATGAT 57.759 37.500 0.00 0.00 0.00 2.45
6106 9228 2.122989 GGGGGTATGCGAGGAGGA 60.123 66.667 0.00 0.00 0.00 3.71
6107 9229 1.766461 AAGGGGGTATGCGAGGAGG 60.766 63.158 0.00 0.00 0.00 4.30
6108 9230 1.447643 CAAGGGGGTATGCGAGGAG 59.552 63.158 0.00 0.00 0.00 3.69
6257 9486 1.165270 GATCCCGTGACCAAAACCAG 58.835 55.000 0.00 0.00 0.00 4.00
6295 9524 9.918630 CCACAAAGAGAAAATCAATCTTACAAT 57.081 29.630 0.00 0.00 33.05 2.71
6300 9529 7.506938 TCTTCCCACAAAGAGAAAATCAATCTT 59.493 33.333 0.00 0.00 34.81 2.40
6301 9530 7.006509 TCTTCCCACAAAGAGAAAATCAATCT 58.993 34.615 0.00 0.00 31.71 2.40
6312 9541 5.244626 ACCATTGATTTCTTCCCACAAAGAG 59.755 40.000 0.00 0.00 36.66 2.85
6335 9564 4.790810 AAAAAGAGAGAAAACGACGGAC 57.209 40.909 0.00 0.00 0.00 4.79
6391 9621 6.260663 ACCAAAGGAGGCCTGAATTTATTTA 58.739 36.000 12.00 0.00 32.13 1.40
6404 9635 3.434940 TTCCTCTAAACCAAAGGAGGC 57.565 47.619 0.00 0.00 43.46 4.70
6405 9636 6.010219 TGAAATTCCTCTAAACCAAAGGAGG 58.990 40.000 0.00 0.00 44.69 4.30
6406 9637 7.709149 ATGAAATTCCTCTAAACCAAAGGAG 57.291 36.000 0.00 0.00 40.21 3.69
6407 9638 9.594936 TTTATGAAATTCCTCTAAACCAAAGGA 57.405 29.630 0.00 0.00 37.42 3.36
6418 9649 8.975295 CCTCCAGAATTTTTATGAAATTCCTCT 58.025 33.333 18.12 5.13 43.88 3.69
6419 9650 8.971073 TCCTCCAGAATTTTTATGAAATTCCTC 58.029 33.333 18.12 3.51 43.88 3.71
6420 9651 8.899887 TCCTCCAGAATTTTTATGAAATTCCT 57.100 30.769 18.12 8.84 43.88 3.36
6452 9683 4.552674 ACCAAAGGGCTCTAAAGGAAAAA 58.447 39.130 5.94 0.00 37.90 1.94
6453 9684 4.193240 ACCAAAGGGCTCTAAAGGAAAA 57.807 40.909 5.94 0.00 37.90 2.29
6454 9685 3.895704 ACCAAAGGGCTCTAAAGGAAA 57.104 42.857 5.94 0.00 37.90 3.13
6455 9686 3.139397 TGAACCAAAGGGCTCTAAAGGAA 59.861 43.478 5.94 0.00 37.90 3.36
6456 9687 2.714250 TGAACCAAAGGGCTCTAAAGGA 59.286 45.455 5.94 0.00 37.90 3.36
6457 9688 3.154827 TGAACCAAAGGGCTCTAAAGG 57.845 47.619 0.00 0.00 37.90 3.11
6458 9689 4.884164 CCTATGAACCAAAGGGCTCTAAAG 59.116 45.833 0.00 0.00 37.90 1.85
6459 9690 4.538490 TCCTATGAACCAAAGGGCTCTAAA 59.462 41.667 0.00 0.00 37.90 1.85
6460 9691 4.108570 TCCTATGAACCAAAGGGCTCTAA 58.891 43.478 0.00 0.00 37.90 2.10
6461 9692 3.731431 TCCTATGAACCAAAGGGCTCTA 58.269 45.455 0.00 0.00 37.90 2.43
6462 9693 2.562296 TCCTATGAACCAAAGGGCTCT 58.438 47.619 0.00 0.00 37.90 4.09
6463 9694 3.366052 TTCCTATGAACCAAAGGGCTC 57.634 47.619 0.00 0.00 37.90 4.70
6464 9695 3.628257 CCATTCCTATGAACCAAAGGGCT 60.628 47.826 0.00 0.00 33.50 5.19
6465 9696 2.695147 CCATTCCTATGAACCAAAGGGC 59.305 50.000 0.00 0.00 33.50 5.19
6466 9697 4.249638 TCCATTCCTATGAACCAAAGGG 57.750 45.455 0.00 0.00 35.37 3.95
6467 9698 6.396829 GAATCCATTCCTATGAACCAAAGG 57.603 41.667 0.00 0.00 33.37 3.11


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

AutoCloner maintained by Alex Coulton.