Multiple sequence alignment - TraesCS2A01G379900

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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 TraesCS2A01G379900 chr2A 100.000 3864 0 0 1 3864 622854742 622850879 0.000000e+00 7136.0
1 TraesCS2A01G379900 chr2A 90.237 1096 85 11 543 1625 622748516 622747430 0.000000e+00 1411.0
2 TraesCS2A01G379900 chr2A 87.140 591 76 0 1030 1620 170602948 170603538 0.000000e+00 671.0
3 TraesCS2A01G379900 chr2A 79.677 620 83 28 2318 2916 622746500 622745903 1.290000e-109 407.0
4 TraesCS2A01G379900 chr2A 84.277 318 27 15 2004 2299 622746954 622746638 4.880000e-74 289.0
5 TraesCS2A01G379900 chr2A 100.000 75 0 0 3790 3864 189958832 189958758 5.210000e-29 139.0
6 TraesCS2A01G379900 chr2A 100.000 74 0 0 3791 3864 517649252 517649179 1.870000e-28 137.0
7 TraesCS2A01G379900 chr2A 97.468 79 2 0 3786 3864 188844670 188844748 6.730000e-28 135.0
8 TraesCS2A01G379900 chr2A 98.684 76 1 0 3789 3864 709508739 709508814 6.730000e-28 135.0
9 TraesCS2A01G379900 chr2A 98.649 74 1 0 3791 3864 134164775 134164702 8.710000e-27 132.0
10 TraesCS2A01G379900 chr2A 77.647 170 14 12 1724 1886 622747295 622747143 8.900000e-12 82.4
11 TraesCS2A01G379900 chr2D 89.173 2928 181 55 659 3501 480325868 480322992 0.000000e+00 3526.0
12 TraesCS2A01G379900 chr2D 91.317 1048 76 7 600 1639 480182076 480181036 0.000000e+00 1417.0
13 TraesCS2A01G379900 chr2D 86.971 591 77 0 1030 1620 159573843 159574433 0.000000e+00 665.0
14 TraesCS2A01G379900 chr2D 88.290 538 58 4 1 535 72627425 72626890 1.170000e-179 640.0
15 TraesCS2A01G379900 chr2D 88.104 538 59 3 1 535 72370580 72370045 5.450000e-178 634.0
16 TraesCS2A01G379900 chr2D 81.271 598 83 20 2342 2916 480180082 480179491 1.270000e-124 457.0
17 TraesCS2A01G379900 chr2D 84.713 314 21 17 2011 2298 480180560 480180248 4.880000e-74 289.0
18 TraesCS2A01G379900 chr2B 89.197 2092 168 32 1740 3792 563183890 563181818 0.000000e+00 2558.0
19 TraesCS2A01G379900 chr2B 93.727 1100 54 9 630 1718 563185336 563184241 0.000000e+00 1635.0
20 TraesCS2A01G379900 chr2B 89.155 1171 90 16 543 1687 563046903 563045744 0.000000e+00 1424.0
21 TraesCS2A01G379900 chr2B 87.352 593 71 3 1030 1620 216708490 216709080 0.000000e+00 676.0
22 TraesCS2A01G379900 chr2B 86.271 539 68 4 1 535 109075738 109075202 7.200000e-162 580.0
23 TraesCS2A01G379900 chr2B 86.502 526 63 5 1 521 53058750 53058228 4.330000e-159 571.0
24 TraesCS2A01G379900 chr2B 85.926 540 68 6 1 535 109788253 109787717 1.560000e-158 569.0
25 TraesCS2A01G379900 chr2B 79.839 620 84 25 2318 2916 563044397 563043798 7.720000e-112 414.0
26 TraesCS2A01G379900 chr2B 90.306 196 15 2 2011 2203 563045293 563045099 1.780000e-63 254.0
27 TraesCS2A01G379900 chr5D 86.620 568 73 2 1051 1618 128565428 128564864 3.280000e-175 625.0
28 TraesCS2A01G379900 chr3D 87.687 536 63 2 1 533 365333459 365333994 4.240000e-174 621.0
29 TraesCS2A01G379900 chr1D 86.085 539 67 5 1 535 315546222 315545688 1.200000e-159 573.0
30 TraesCS2A01G379900 chr5A 86.116 533 67 6 6 535 412911720 412911192 5.600000e-158 568.0
31 TraesCS2A01G379900 chr4D 85.981 535 69 3 1 535 323998107 323997579 5.600000e-158 568.0
32 TraesCS2A01G379900 chr7A 98.684 76 1 0 3789 3864 554615965 554616040 6.730000e-28 135.0
33 TraesCS2A01G379900 chr6A 98.684 76 1 0 3789 3864 229930600 229930675 6.730000e-28 135.0
34 TraesCS2A01G379900 chr6A 98.684 76 1 0 3789 3864 516031691 516031616 6.730000e-28 135.0
35 TraesCS2A01G379900 chr1A 95.294 85 1 3 3783 3864 373073771 373073687 8.710000e-27 132.0
36 TraesCS2A01G379900 chr7B 81.102 127 22 2 2014 2140 111269799 111269923 2.460000e-17 100.0


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 TraesCS2A01G379900 chr2A 622850879 622854742 3863 True 7136.000000 7136 100.000000 1 3864 1 chr2A.!!$R4 3863
1 TraesCS2A01G379900 chr2A 170602948 170603538 590 False 671.000000 671 87.140000 1030 1620 1 chr2A.!!$F1 590
2 TraesCS2A01G379900 chr2A 622745903 622748516 2613 True 547.350000 1411 82.959500 543 2916 4 chr2A.!!$R5 2373
3 TraesCS2A01G379900 chr2D 480322992 480325868 2876 True 3526.000000 3526 89.173000 659 3501 1 chr2D.!!$R3 2842
4 TraesCS2A01G379900 chr2D 480179491 480182076 2585 True 721.000000 1417 85.767000 600 2916 3 chr2D.!!$R4 2316
5 TraesCS2A01G379900 chr2D 159573843 159574433 590 False 665.000000 665 86.971000 1030 1620 1 chr2D.!!$F1 590
6 TraesCS2A01G379900 chr2D 72626890 72627425 535 True 640.000000 640 88.290000 1 535 1 chr2D.!!$R2 534
7 TraesCS2A01G379900 chr2D 72370045 72370580 535 True 634.000000 634 88.104000 1 535 1 chr2D.!!$R1 534
8 TraesCS2A01G379900 chr2B 563181818 563185336 3518 True 2096.500000 2558 91.462000 630 3792 2 chr2B.!!$R5 3162
9 TraesCS2A01G379900 chr2B 563043798 563046903 3105 True 697.333333 1424 86.433333 543 2916 3 chr2B.!!$R4 2373
10 TraesCS2A01G379900 chr2B 216708490 216709080 590 False 676.000000 676 87.352000 1030 1620 1 chr2B.!!$F1 590
11 TraesCS2A01G379900 chr2B 109075202 109075738 536 True 580.000000 580 86.271000 1 535 1 chr2B.!!$R2 534
12 TraesCS2A01G379900 chr2B 53058228 53058750 522 True 571.000000 571 86.502000 1 521 1 chr2B.!!$R1 520
13 TraesCS2A01G379900 chr2B 109787717 109788253 536 True 569.000000 569 85.926000 1 535 1 chr2B.!!$R3 534
14 TraesCS2A01G379900 chr5D 128564864 128565428 564 True 625.000000 625 86.620000 1051 1618 1 chr5D.!!$R1 567
15 TraesCS2A01G379900 chr3D 365333459 365333994 535 False 621.000000 621 87.687000 1 533 1 chr3D.!!$F1 532
16 TraesCS2A01G379900 chr1D 315545688 315546222 534 True 573.000000 573 86.085000 1 535 1 chr1D.!!$R1 534
17 TraesCS2A01G379900 chr5A 412911192 412911720 528 True 568.000000 568 86.116000 6 535 1 chr5A.!!$R1 529
18 TraesCS2A01G379900 chr4D 323997579 323998107 528 True 568.000000 568 85.981000 1 535 1 chr4D.!!$R1 534

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
403 408 0.396417 AGGCTCAGACTATCGGCACT 60.396 55.0 0.0 0.0 0.00 4.40 F
625 630 0.465705 CATACACCCATCGCCAGACT 59.534 55.0 0.0 0.0 0.00 3.24 F
1065 1096 0.613853 CCAAGGACTACTCCGACCCA 60.614 60.0 0.0 0.0 42.22 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 1779 1.066787 GCAAGGGACTGGACTAGTGAC 60.067 57.143 0.00 0.00 40.53 3.67 R
2445 3682 0.181350 GGCTAATCAGTGGGGAGTGG 59.819 60.000 0.00 0.00 0.00 4.00 R
2869 4139 1.204704 GATCATCCATACATCGGCCGA 59.795 52.381 33.12 33.12 0.00 5.54 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
44 45 4.008933 AGCCTCGGAGGTGTGCAC 62.009 66.667 24.30 10.75 37.80 4.57
54 55 1.299926 GGTGTGCACGAACTCGAGT 60.300 57.895 13.58 13.58 43.02 4.18
76 77 1.202758 ACCAGCGGACAACATCTTTGA 60.203 47.619 1.50 0.00 0.00 2.69
103 104 3.065233 GCGGTGTTTCATCTTATGCATCA 59.935 43.478 0.19 0.00 0.00 3.07
123 124 2.761195 CGACTGTGGATCTCGGCGA 61.761 63.158 10.14 10.14 0.00 5.54
160 164 1.667756 GGCGTTCGATGTGTGTAGACA 60.668 52.381 0.00 0.00 0.00 3.41
169 173 0.516001 GTGTGTAGACAGACTCGCGA 59.484 55.000 9.26 9.26 37.20 5.87
200 204 3.207547 CTGTCTGGCGTCGTGGTGA 62.208 63.158 0.00 0.00 0.00 4.02
201 205 2.261671 GTCTGGCGTCGTGGTGAT 59.738 61.111 0.00 0.00 0.00 3.06
233 237 4.555709 TGGCAAGGTCGTGGCGTT 62.556 61.111 6.07 0.00 46.67 4.84
261 265 2.961062 TGCTCTGAAGATGGATCGATGA 59.039 45.455 0.54 0.00 0.00 2.92
300 304 0.667487 CTGTGAGTGCGTCGGATTGT 60.667 55.000 0.00 0.00 0.00 2.71
308 312 1.938125 CGTCGGATTGTTGTGTGCA 59.062 52.632 0.00 0.00 0.00 4.57
403 408 0.396417 AGGCTCAGACTATCGGCACT 60.396 55.000 0.00 0.00 0.00 4.40
412 417 1.338337 ACTATCGGCACTCCTTCATCG 59.662 52.381 0.00 0.00 0.00 3.84
424 429 4.339814 ACTCCTTCATCGAGTGGATAGAAC 59.660 45.833 0.00 0.00 39.14 3.01
435 440 5.564048 AGTGGATAGAACTAACGACAGAC 57.436 43.478 0.00 0.00 0.00 3.51
436 441 5.008331 AGTGGATAGAACTAACGACAGACA 58.992 41.667 0.00 0.00 0.00 3.41
440 445 6.071560 TGGATAGAACTAACGACAGACATTGT 60.072 38.462 0.00 0.00 44.55 2.71
560 565 3.863142 AAAGCAGGCAATTAAGCTGAG 57.137 42.857 0.00 0.00 37.41 3.35
584 589 2.609459 CGTATCTGCCATCACCTCAAAC 59.391 50.000 0.00 0.00 0.00 2.93
588 593 1.747355 CTGCCATCACCTCAAACCATC 59.253 52.381 0.00 0.00 0.00 3.51
592 597 2.874701 CCATCACCTCAAACCATCGATC 59.125 50.000 0.00 0.00 0.00 3.69
593 598 2.293677 TCACCTCAAACCATCGATCG 57.706 50.000 9.36 9.36 0.00 3.69
595 600 1.660607 CACCTCAAACCATCGATCGTG 59.339 52.381 15.94 12.28 0.00 4.35
596 601 1.275291 ACCTCAAACCATCGATCGTGT 59.725 47.619 15.94 8.35 0.00 4.49
597 602 2.494471 ACCTCAAACCATCGATCGTGTA 59.506 45.455 15.94 0.00 0.00 2.90
598 603 2.858344 CCTCAAACCATCGATCGTGTAC 59.142 50.000 15.94 0.00 0.00 2.90
602 607 3.976793 AACCATCGATCGTGTACGTAT 57.023 42.857 15.94 0.00 40.80 3.06
609 614 3.248125 TCGATCGTGTACGTATGTGCATA 59.752 43.478 15.94 1.83 42.79 3.14
615 620 2.496470 TGTACGTATGTGCATACACCCA 59.504 45.455 18.73 10.32 46.86 4.51
625 630 0.465705 CATACACCCATCGCCAGACT 59.534 55.000 0.00 0.00 0.00 3.24
626 631 1.686587 CATACACCCATCGCCAGACTA 59.313 52.381 0.00 0.00 0.00 2.59
627 632 1.855295 TACACCCATCGCCAGACTAA 58.145 50.000 0.00 0.00 0.00 2.24
628 633 1.204146 ACACCCATCGCCAGACTAAT 58.796 50.000 0.00 0.00 0.00 1.73
714 725 0.618680 TAGCTGCCCTGGAGTGATGT 60.619 55.000 0.00 0.00 0.00 3.06
720 731 2.092968 TGCCCTGGAGTGATGTAATGAC 60.093 50.000 0.00 0.00 0.00 3.06
721 732 2.746472 GCCCTGGAGTGATGTAATGACC 60.746 54.545 0.00 0.00 26.99 4.02
722 733 2.158755 CCCTGGAGTGATGTAATGACCC 60.159 54.545 0.00 0.00 26.99 4.46
812 828 7.228706 CCACTAATAAACCCAGCCACTAAATAG 59.771 40.741 0.00 0.00 0.00 1.73
958 986 1.333881 GCGCATTAGCATCTTGAGCAG 60.334 52.381 0.30 0.00 42.27 4.24
965 995 1.901159 AGCATCTTGAGCAGAGACACT 59.099 47.619 0.00 0.00 33.87 3.55
1065 1096 0.613853 CCAAGGACTACTCCGACCCA 60.614 60.000 0.00 0.00 42.22 4.51
1551 1582 1.337071 GAGATCATCGGCACCTTCGTA 59.663 52.381 0.00 0.00 0.00 3.43
1692 1749 2.749076 TGCTTTGCATGGACATACAGAC 59.251 45.455 0.00 0.00 31.71 3.51
1700 1758 1.893137 TGGACATACAGACGAAGCAGT 59.107 47.619 0.00 0.00 0.00 4.40
1718 1779 7.591057 CGAAGCAGTTCTCTGAATATTCTCTAG 59.409 40.741 16.24 10.48 43.76 2.43
1819 2227 5.556382 CGCTTGTGATTAACGCTATACAAGG 60.556 44.000 14.42 4.00 43.00 3.61
1865 2273 4.156008 GGGACATAGTGCGAAAGTCAAAAT 59.844 41.667 0.00 0.00 0.00 1.82
1940 2356 5.048224 AGCCATCTTTATCAAGCATGCATAC 60.048 40.000 21.98 0.00 0.00 2.39
1976 2402 4.337274 GTCTTCTTCCTAGACAGCTCTACC 59.663 50.000 0.00 0.00 41.29 3.18
2018 2593 7.167801 GGTTTTGAATTTGTTGCAATGAATTGG 59.832 33.333 20.74 0.00 38.21 3.16
2190 2771 1.637934 CGCCACACACTATCGCATG 59.362 57.895 0.00 0.00 0.00 4.06
2213 2794 8.902806 CATGTCTCTGCTAATTTAATGGGTTAA 58.097 33.333 0.00 0.00 0.00 2.01
2253 3310 4.321750 GGTCACAATCACCTCGAAGACTAA 60.322 45.833 0.00 0.00 0.00 2.24
2257 3314 5.696724 CACAATCACCTCGAAGACTAAAACT 59.303 40.000 0.00 0.00 0.00 2.66
2293 3364 1.597663 GAACTTGTGTGGTGTTCCTCG 59.402 52.381 0.00 0.00 35.41 4.63
2516 3764 9.175060 GTAGCTAATGTATATATGACATCTGCG 57.825 37.037 0.00 0.00 38.91 5.18
2588 3838 3.282021 CACTCCCAACTACCATCCAATG 58.718 50.000 0.00 0.00 0.00 2.82
2592 3842 2.288666 CCAACTACCATCCAATGACGG 58.711 52.381 0.00 0.00 0.00 4.79
2631 3889 5.809051 GCTGTAACGTGCCTAACTAGTTAAT 59.191 40.000 15.95 0.00 0.00 1.40
2632 3890 6.974622 GCTGTAACGTGCCTAACTAGTTAATA 59.025 38.462 15.95 3.41 0.00 0.98
2661 3919 8.253810 GCTATCTTCTTCTACATACATATGCCA 58.746 37.037 1.58 0.00 37.19 4.92
2662 3920 9.579768 CTATCTTCTTCTACATACATATGCCAC 57.420 37.037 1.58 0.00 37.19 5.01
2663 3921 6.447162 TCTTCTTCTACATACATATGCCACG 58.553 40.000 1.58 0.00 37.19 4.94
2668 3929 5.676552 TCTACATACATATGCCACGGTTTT 58.323 37.500 1.58 0.00 37.19 2.43
2673 3934 6.600032 ACATACATATGCCACGGTTTTTAGAA 59.400 34.615 1.58 0.00 37.19 2.10
2740 4010 3.472652 ACTTACTTTTGCGGTCATGTCA 58.527 40.909 0.00 0.00 0.00 3.58
2869 4139 2.196925 CGGCAGGAGCTAGATCGGT 61.197 63.158 1.16 0.00 41.70 4.69
2898 4175 2.433970 TGTATGGATGATCGGAAGCACA 59.566 45.455 0.00 0.00 0.00 4.57
2906 4183 2.560981 TGATCGGAAGCACAGACAGTAA 59.439 45.455 0.00 0.00 0.00 2.24
2955 4232 0.093026 GTATTGTGCACGCGTCTGTC 59.907 55.000 9.86 0.52 0.00 3.51
3071 4349 2.160205 GGTACAGAAGGACCCAAAAGC 58.840 52.381 0.00 0.00 0.00 3.51
3098 4380 6.763135 GCATTAACTAGAAGTGGATCACATCA 59.237 38.462 0.00 0.00 34.97 3.07
3100 4382 8.986847 CATTAACTAGAAGTGGATCACATCATC 58.013 37.037 0.00 0.00 34.97 2.92
3103 4385 6.580788 ACTAGAAGTGGATCACATCATCTTG 58.419 40.000 0.00 5.22 34.97 3.02
3104 4386 5.432680 AGAAGTGGATCACATCATCTTGT 57.567 39.130 6.15 0.00 34.97 3.16
3116 4398 5.809562 CACATCATCTTGTAACAGGACTCTC 59.190 44.000 0.00 0.00 0.00 3.20
3117 4399 4.703645 TCATCTTGTAACAGGACTCTCG 57.296 45.455 0.00 0.00 0.00 4.04
3124 4406 4.868067 TGTAACAGGACTCTCGAAGAAAC 58.132 43.478 2.28 0.00 34.09 2.78
3127 4409 3.223435 ACAGGACTCTCGAAGAAACAGA 58.777 45.455 2.28 0.00 34.09 3.41
3128 4410 3.004944 ACAGGACTCTCGAAGAAACAGAC 59.995 47.826 2.28 0.00 34.09 3.51
3130 4412 3.829601 AGGACTCTCGAAGAAACAGACAT 59.170 43.478 2.28 0.00 34.09 3.06
3139 4422 6.943981 TCGAAGAAACAGACATAACAAACTG 58.056 36.000 0.00 0.00 36.58 3.16
3142 4425 6.619801 AGAAACAGACATAACAAACTGGTC 57.380 37.500 0.00 0.00 35.08 4.02
3145 4428 3.137544 ACAGACATAACAAACTGGTCCCA 59.862 43.478 0.00 0.00 35.08 4.37
3147 4430 3.650942 AGACATAACAAACTGGTCCCAGA 59.349 43.478 19.95 0.00 46.30 3.86
3148 4431 3.751518 ACATAACAAACTGGTCCCAGAC 58.248 45.455 19.95 0.00 46.30 3.51
3165 4448 4.717280 CCCAGACTATTACAAAGAGGACCT 59.283 45.833 0.00 0.00 0.00 3.85
3172 4455 7.339482 ACTATTACAAAGAGGACCTCCAAATC 58.661 38.462 18.32 0.00 38.89 2.17
3181 4465 4.750941 AGGACCTCCAAATCCATTGAAAA 58.249 39.130 0.00 0.00 41.85 2.29
3189 4473 5.811613 TCCAAATCCATTGAAAATCGCAATC 59.188 36.000 0.00 0.00 41.85 2.67
3191 4475 5.515982 CAAATCCATTGAAAATCGCAATCGA 59.484 36.000 0.00 0.00 44.57 3.59
3206 4497 1.786937 ATCGAGTCCTTGGCATCTCT 58.213 50.000 0.00 0.00 0.00 3.10
3210 4501 2.038659 GAGTCCTTGGCATCTCTAGCT 58.961 52.381 0.00 0.00 0.00 3.32
3223 4514 5.181245 GCATCTCTAGCTCGAATCTAGTCTT 59.819 44.000 16.42 4.97 36.00 3.01
3233 4524 4.099120 CGAATCTAGTCTTGTCTTCACCG 58.901 47.826 0.00 0.00 0.00 4.94
3299 4590 4.816385 GCCATGAATTCCAAGACGAAGATA 59.184 41.667 2.27 0.00 0.00 1.98
3309 4600 4.038042 CCAAGACGAAGATATAGTGCCTCA 59.962 45.833 0.00 0.00 0.00 3.86
3343 4634 1.074566 CTGGGAGGAAGAAGCAAGGTT 59.925 52.381 0.00 0.00 0.00 3.50
3352 4643 2.711542 AGAAGCAAGGTTACCATTCGG 58.288 47.619 3.51 0.00 38.77 4.30
3354 4645 0.328258 AGCAAGGTTACCATTCGGCT 59.672 50.000 3.51 1.85 34.57 5.52
3355 4646 0.451783 GCAAGGTTACCATTCGGCTG 59.548 55.000 3.51 0.00 34.57 4.85
3359 4650 1.559682 AGGTTACCATTCGGCTGACAT 59.440 47.619 3.51 0.00 34.57 3.06
3363 4654 4.213482 GGTTACCATTCGGCTGACATATTC 59.787 45.833 0.00 0.00 34.57 1.75
3389 4680 2.162921 GATGATTGGCATCGACCGCG 62.163 60.000 0.00 0.00 43.57 6.46
3406 4697 2.908073 CGGCAGTGGACACCAAAGC 61.908 63.158 0.00 0.00 34.18 3.51
3457 4748 5.678583 CACAAACACCATCTAGATCTCCAT 58.321 41.667 1.03 0.00 0.00 3.41
3465 4756 4.224818 CCATCTAGATCTCCATCTTTCCCC 59.775 50.000 1.03 0.00 40.18 4.81
3486 4778 0.596577 CTTCTCCTTCACGACCACGA 59.403 55.000 0.00 0.00 42.66 4.35
3492 4784 1.203994 CCTTCACGACCACGATAACCT 59.796 52.381 0.00 0.00 42.66 3.50
3494 4786 3.119388 CCTTCACGACCACGATAACCTTA 60.119 47.826 0.00 0.00 42.66 2.69
3498 4790 4.699735 TCACGACCACGATAACCTTACTAA 59.300 41.667 0.00 0.00 42.66 2.24
3505 4797 3.387050 ACGATAACCTTACTAAGCAGGGG 59.613 47.826 0.00 0.00 34.02 4.79
3532 4824 1.146982 AGGACCTCCTCTAGATCAGGC 59.853 57.143 14.50 8.95 44.77 4.85
3533 4825 1.243902 GACCTCCTCTAGATCAGGCG 58.756 60.000 14.50 0.00 0.00 5.52
3535 4827 0.178975 CCTCCTCTAGATCAGGCGGT 60.179 60.000 4.54 0.00 31.94 5.68
3545 4837 4.170062 CAGGCGGTCATGCAAGCG 62.170 66.667 5.65 5.65 42.74 4.68
3549 4841 1.714899 GGCGGTCATGCAAGCGTATT 61.715 55.000 11.23 0.00 41.92 1.89
3550 4842 0.316196 GCGGTCATGCAAGCGTATTC 60.316 55.000 11.23 0.00 41.92 1.75
3551 4843 1.006086 CGGTCATGCAAGCGTATTCA 58.994 50.000 1.90 0.00 35.53 2.57
3553 4845 2.009774 GGTCATGCAAGCGTATTCACT 58.990 47.619 0.00 0.00 0.00 3.41
3554 4846 3.194861 GGTCATGCAAGCGTATTCACTA 58.805 45.455 0.00 0.00 0.00 2.74
3563 4855 1.396815 GCGTATTCACTAAATCGCCGC 60.397 52.381 0.00 0.00 37.65 6.53
3606 4898 0.390860 AGCTCCCAACTAGCATAGCG 59.609 55.000 0.00 0.00 44.39 4.26
3611 4903 1.269831 CCCAACTAGCATAGCGAGGAC 60.270 57.143 4.25 0.00 44.39 3.85
3614 4906 2.060050 ACTAGCATAGCGAGGACTGT 57.940 50.000 4.25 0.00 44.39 3.55
3617 4909 1.323412 AGCATAGCGAGGACTGTAGG 58.677 55.000 0.00 0.00 0.00 3.18
3620 4912 1.033574 ATAGCGAGGACTGTAGGTGC 58.966 55.000 0.00 0.00 36.48 5.01
3631 4923 2.682136 TAGGTGCCGCTAGCCACA 60.682 61.111 21.02 12.24 42.71 4.17
3637 4929 2.185350 CCGCTAGCCACAGACCAG 59.815 66.667 9.66 0.00 0.00 4.00
3639 4931 1.446792 CGCTAGCCACAGACCAGTG 60.447 63.158 9.66 0.00 39.21 3.66
3646 4938 1.339055 GCCACAGACCAGTGCTCAATA 60.339 52.381 0.00 0.00 38.18 1.90
3648 4940 3.614092 CCACAGACCAGTGCTCAATAAT 58.386 45.455 0.00 0.00 38.18 1.28
3652 4944 2.025981 AGACCAGTGCTCAATAATGGCA 60.026 45.455 0.00 0.00 34.24 4.92
3667 4959 2.661866 GCAACGACGTGCTCCACT 60.662 61.111 0.00 0.00 41.51 4.00
3674 4966 0.179073 GACGTGCTCCACTATGGCAT 60.179 55.000 4.88 4.88 37.47 4.40
3676 4968 1.694150 ACGTGCTCCACTATGGCATAT 59.306 47.619 7.81 0.00 37.47 1.78
3677 4969 2.289072 ACGTGCTCCACTATGGCATATC 60.289 50.000 7.81 0.00 37.47 1.63
3678 4970 2.289010 CGTGCTCCACTATGGCATATCA 60.289 50.000 7.81 0.00 37.47 2.15
3679 4971 3.070018 GTGCTCCACTATGGCATATCAC 58.930 50.000 7.81 6.14 37.47 3.06
3684 4976 4.717877 TCCACTATGGCATATCACCAAAG 58.282 43.478 7.81 0.00 41.49 2.77
3693 4985 1.367346 TATCACCAAAGGCCACAGGA 58.633 50.000 5.01 0.00 0.00 3.86
3695 4987 2.116125 ACCAAAGGCCACAGGAGC 59.884 61.111 5.01 0.00 0.00 4.70
3700 4992 1.504275 AAAGGCCACAGGAGCAGGAT 61.504 55.000 5.01 0.00 0.00 3.24
3713 5005 1.008938 AGCAGGATGGAACCTAGACCT 59.991 52.381 0.00 0.00 38.32 3.85
3714 5006 1.139853 GCAGGATGGAACCTAGACCTG 59.860 57.143 0.00 0.00 45.01 4.00
3723 5015 6.303903 TGGAACCTAGACCTGGTATTTTAC 57.696 41.667 0.00 0.00 36.69 2.01
3745 5037 1.140312 GGATACTCCATGCCCCTTCA 58.860 55.000 0.00 0.00 36.28 3.02
3747 5039 1.771255 GATACTCCATGCCCCTTCACT 59.229 52.381 0.00 0.00 0.00 3.41
3750 5042 0.329261 CTCCATGCCCCTTCACTTCA 59.671 55.000 0.00 0.00 0.00 3.02
3754 5046 0.329596 ATGCCCCTTCACTTCACTCC 59.670 55.000 0.00 0.00 0.00 3.85
3770 5062 4.347453 CCAGCTTGCAACACCGCC 62.347 66.667 0.00 0.00 0.00 6.13
3772 5064 3.289834 AGCTTGCAACACCGCCAG 61.290 61.111 0.00 0.00 0.00 4.85
3781 5073 0.609131 AACACCGCCAGGGAAGATTG 60.609 55.000 0.00 0.00 43.47 2.67
3792 5084 0.179018 GGAAGATTGGGGATCGGGTG 60.179 60.000 0.00 0.00 39.85 4.61
3793 5085 0.546598 GAAGATTGGGGATCGGGTGT 59.453 55.000 0.00 0.00 39.85 4.16
3794 5086 0.255890 AAGATTGGGGATCGGGTGTG 59.744 55.000 0.00 0.00 39.85 3.82
3795 5087 1.152963 GATTGGGGATCGGGTGTGG 60.153 63.158 0.00 0.00 0.00 4.17
3796 5088 3.358932 ATTGGGGATCGGGTGTGGC 62.359 63.158 0.00 0.00 0.00 5.01
3799 5091 4.832608 GGGATCGGGTGTGGCGAC 62.833 72.222 0.00 0.00 0.00 5.19
3800 5092 4.832608 GGATCGGGTGTGGCGACC 62.833 72.222 0.00 0.00 34.96 4.79
3813 5105 3.454573 CGACCCGACCCGAATGGA 61.455 66.667 0.00 0.00 37.49 3.41
3814 5106 2.792947 CGACCCGACCCGAATGGAT 61.793 63.158 0.00 0.00 37.49 3.41
3815 5107 1.069258 GACCCGACCCGAATGGATC 59.931 63.158 0.00 0.00 37.49 3.36
3816 5108 1.682451 GACCCGACCCGAATGGATCA 61.682 60.000 0.00 0.00 37.49 2.92
3817 5109 1.268992 ACCCGACCCGAATGGATCAA 61.269 55.000 0.00 0.00 37.49 2.57
3818 5110 0.532862 CCCGACCCGAATGGATCAAG 60.533 60.000 0.00 0.00 37.49 3.02
3819 5111 0.178068 CCGACCCGAATGGATCAAGT 59.822 55.000 0.00 0.00 37.49 3.16
3820 5112 1.571919 CGACCCGAATGGATCAAGTC 58.428 55.000 0.00 0.00 37.49 3.01
3821 5113 1.137086 CGACCCGAATGGATCAAGTCT 59.863 52.381 0.00 0.00 37.49 3.24
3822 5114 2.361119 CGACCCGAATGGATCAAGTCTA 59.639 50.000 0.00 0.00 37.49 2.59
3823 5115 3.718815 GACCCGAATGGATCAAGTCTAC 58.281 50.000 0.00 0.00 37.49 2.59
3824 5116 3.375699 ACCCGAATGGATCAAGTCTACT 58.624 45.455 0.00 0.00 37.49 2.57
3825 5117 3.133003 ACCCGAATGGATCAAGTCTACTG 59.867 47.826 0.00 0.00 37.49 2.74
3826 5118 3.133003 CCCGAATGGATCAAGTCTACTGT 59.867 47.826 0.00 0.00 37.49 3.55
3827 5119 4.115516 CCGAATGGATCAAGTCTACTGTG 58.884 47.826 0.00 0.00 37.49 3.66
3828 5120 3.553511 CGAATGGATCAAGTCTACTGTGC 59.446 47.826 0.00 0.00 0.00 4.57
3829 5121 4.679106 CGAATGGATCAAGTCTACTGTGCT 60.679 45.833 0.00 0.00 0.00 4.40
3830 5122 3.876274 TGGATCAAGTCTACTGTGCTC 57.124 47.619 0.00 0.00 0.00 4.26
3831 5123 2.497675 TGGATCAAGTCTACTGTGCTCC 59.502 50.000 0.00 7.59 0.00 4.70
3832 5124 2.480416 GGATCAAGTCTACTGTGCTCCG 60.480 54.545 0.00 0.00 0.00 4.63
3833 5125 0.888619 TCAAGTCTACTGTGCTCCGG 59.111 55.000 0.00 0.00 0.00 5.14
3834 5126 0.603569 CAAGTCTACTGTGCTCCGGT 59.396 55.000 0.00 0.00 36.38 5.28
3835 5127 0.603569 AAGTCTACTGTGCTCCGGTG 59.396 55.000 0.00 0.00 33.63 4.94
3836 5128 0.539901 AGTCTACTGTGCTCCGGTGT 60.540 55.000 0.00 0.00 33.63 4.16
3837 5129 0.109226 GTCTACTGTGCTCCGGTGTC 60.109 60.000 0.00 0.00 33.63 3.67
3838 5130 0.538746 TCTACTGTGCTCCGGTGTCA 60.539 55.000 0.00 2.40 33.63 3.58
3839 5131 0.532573 CTACTGTGCTCCGGTGTCAT 59.467 55.000 0.00 0.00 33.63 3.06
3840 5132 0.530744 TACTGTGCTCCGGTGTCATC 59.469 55.000 0.00 0.00 33.63 2.92
3841 5133 1.448540 CTGTGCTCCGGTGTCATCC 60.449 63.158 0.00 0.00 0.00 3.51
3842 5134 2.125106 GTGCTCCGGTGTCATCCC 60.125 66.667 0.00 0.00 0.00 3.85
3843 5135 2.284625 TGCTCCGGTGTCATCCCT 60.285 61.111 0.00 0.00 0.00 4.20
3844 5136 2.187946 GCTCCGGTGTCATCCCTG 59.812 66.667 0.00 0.00 0.00 4.45
3845 5137 2.903357 CTCCGGTGTCATCCCTGG 59.097 66.667 0.00 0.00 0.00 4.45
3846 5138 1.685765 CTCCGGTGTCATCCCTGGA 60.686 63.158 0.00 0.00 0.00 3.86
3847 5139 1.002921 TCCGGTGTCATCCCTGGAT 59.997 57.895 0.00 0.00 34.81 3.41
3848 5140 1.048724 TCCGGTGTCATCCCTGGATC 61.049 60.000 0.00 0.00 31.62 3.36
3849 5141 1.337384 CCGGTGTCATCCCTGGATCA 61.337 60.000 0.00 0.00 31.62 2.92
3850 5142 0.105593 CGGTGTCATCCCTGGATCAG 59.894 60.000 0.00 0.00 31.62 2.90
3851 5143 1.207791 GGTGTCATCCCTGGATCAGT 58.792 55.000 0.00 0.00 31.62 3.41
3852 5144 2.398588 GGTGTCATCCCTGGATCAGTA 58.601 52.381 0.00 0.00 31.62 2.74
3853 5145 2.771943 GGTGTCATCCCTGGATCAGTAA 59.228 50.000 0.00 0.00 31.62 2.24
3854 5146 3.392616 GGTGTCATCCCTGGATCAGTAAT 59.607 47.826 0.00 0.00 31.62 1.89
3855 5147 4.384056 GTGTCATCCCTGGATCAGTAATG 58.616 47.826 0.00 0.00 31.62 1.90
3856 5148 3.181451 TGTCATCCCTGGATCAGTAATGC 60.181 47.826 0.00 0.00 31.62 3.56
3857 5149 3.072184 GTCATCCCTGGATCAGTAATGCT 59.928 47.826 0.00 0.00 31.62 3.79
3858 5150 3.072038 TCATCCCTGGATCAGTAATGCTG 59.928 47.826 0.00 0.00 46.34 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.220999 TTCGTGCACACCTCCGAGG 62.221 63.158 18.64 13.31 42.49 4.63
32 33 2.022129 GAGTTCGTGCACACCTCCG 61.022 63.158 18.64 1.10 0.00 4.63
44 45 1.797933 CGCTGGTCACTCGAGTTCG 60.798 63.158 17.26 5.88 41.45 3.95
54 55 0.396435 AAGATGTTGTCCGCTGGTCA 59.604 50.000 0.00 0.00 0.00 4.02
76 77 2.496899 AAGATGAAACACCGCTCCAT 57.503 45.000 0.00 0.00 0.00 3.41
103 104 1.215647 GCCGAGATCCACAGTCGTT 59.784 57.895 1.33 0.00 31.65 3.85
129 133 2.126031 GAACGCCGAGACTCCACC 60.126 66.667 0.00 0.00 0.00 4.61
160 164 1.388065 CCATCCTCCTTCGCGAGTCT 61.388 60.000 9.59 0.00 0.00 3.24
169 173 1.992277 AGACAGCGCCATCCTCCTT 60.992 57.895 2.29 0.00 0.00 3.36
200 204 1.524002 CCAGGTCTGCCATCGACAT 59.476 57.895 0.00 0.00 37.19 3.06
201 205 2.981302 CCAGGTCTGCCATCGACA 59.019 61.111 0.00 0.00 37.19 4.35
233 237 4.251103 TCCATCTTCAGAGCAGGTACTA 57.749 45.455 0.00 0.00 36.02 1.82
284 288 0.249699 ACAACAATCCGACGCACTCA 60.250 50.000 0.00 0.00 0.00 3.41
300 304 1.152984 CCTGGTCTGGTGCACACAA 60.153 57.895 20.43 0.41 0.00 3.33
308 312 2.439507 CAAGCCATATACCTGGTCTGGT 59.560 50.000 18.68 4.96 43.66 4.00
403 408 4.537751 AGTTCTATCCACTCGATGAAGGA 58.462 43.478 0.00 0.00 31.92 3.36
412 417 5.123502 TGTCTGTCGTTAGTTCTATCCACTC 59.876 44.000 0.00 0.00 0.00 3.51
435 440 2.743664 TGAAGCGACCATCTTGACAATG 59.256 45.455 0.00 0.00 0.00 2.82
436 441 3.005554 CTGAAGCGACCATCTTGACAAT 58.994 45.455 0.00 0.00 0.00 2.71
440 445 1.895798 AGTCTGAAGCGACCATCTTGA 59.104 47.619 0.00 0.00 34.46 3.02
491 496 9.664332 TGCATGCAACCACTTTATTAATTATTT 57.336 25.926 20.30 0.00 0.00 1.40
538 543 4.562143 CCTCAGCTTAATTGCCTGCTTTTT 60.562 41.667 0.00 0.00 33.03 1.94
539 544 3.056322 CCTCAGCTTAATTGCCTGCTTTT 60.056 43.478 0.00 0.00 33.03 2.27
540 545 2.494870 CCTCAGCTTAATTGCCTGCTTT 59.505 45.455 0.00 0.00 33.03 3.51
541 546 2.097825 CCTCAGCTTAATTGCCTGCTT 58.902 47.619 0.00 0.00 33.03 3.91
560 565 0.753262 AGGTGATGGCAGATACGTCC 59.247 55.000 0.00 0.00 0.00 4.79
584 589 2.971261 CACATACGTACACGATCGATGG 59.029 50.000 24.34 13.03 43.02 3.51
588 593 1.817609 TGCACATACGTACACGATCG 58.182 50.000 14.88 14.88 43.02 3.69
595 600 3.167921 TGGGTGTATGCACATACGTAC 57.832 47.619 16.11 8.83 46.95 3.67
596 601 3.551250 CGATGGGTGTATGCACATACGTA 60.551 47.826 16.11 0.00 46.95 3.57
597 602 2.801699 CGATGGGTGTATGCACATACGT 60.802 50.000 16.11 6.60 46.95 3.57
598 603 1.792367 CGATGGGTGTATGCACATACG 59.208 52.381 16.11 10.98 46.95 3.06
602 607 1.451207 GGCGATGGGTGTATGCACA 60.451 57.895 16.11 0.00 46.95 4.57
609 614 1.204146 ATTAGTCTGGCGATGGGTGT 58.796 50.000 0.00 0.00 0.00 4.16
615 620 4.451900 CCCAGTTTAATTAGTCTGGCGAT 58.548 43.478 22.14 0.00 44.06 4.58
702 713 2.483714 CGGGTCATTACATCACTCCAGG 60.484 54.545 0.00 0.00 0.00 4.45
714 725 2.675242 CCCACAGCCCGGGTCATTA 61.675 63.158 24.63 0.00 39.05 1.90
812 828 4.318831 CGCTCGCTTTGGGATTAATTAGTC 60.319 45.833 0.00 0.00 0.00 2.59
885 905 3.720002 GGGGGAAGGTGAGGTATTTATGA 59.280 47.826 0.00 0.00 0.00 2.15
958 986 1.896465 ACAAGCTAGGGTGAGTGTCTC 59.104 52.381 0.00 0.00 0.00 3.36
965 995 1.751351 CTGATCGACAAGCTAGGGTGA 59.249 52.381 0.00 0.00 0.00 4.02
995 1026 0.842635 GATGTCCTTGGCCATCCTCT 59.157 55.000 6.09 0.00 33.00 3.69
998 1029 0.533755 CTCGATGTCCTTGGCCATCC 60.534 60.000 6.09 0.00 35.17 3.51
1428 1459 3.322466 CCCTTGACGAGCCCCACT 61.322 66.667 0.00 0.00 0.00 4.00
1551 1582 2.075338 GAGAAGACGGTGTAGACGAGT 58.925 52.381 0.00 0.00 34.93 4.18
1684 1734 3.856521 CAGAGAACTGCTTCGTCTGTATG 59.143 47.826 0.00 0.00 37.33 2.39
1689 1739 3.951775 ATTCAGAGAACTGCTTCGTCT 57.048 42.857 0.00 0.00 43.17 4.18
1692 1749 6.272318 AGAGAATATTCAGAGAACTGCTTCG 58.728 40.000 17.56 0.00 43.17 3.79
1718 1779 1.066787 GCAAGGGACTGGACTAGTGAC 60.067 57.143 0.00 0.00 40.53 3.67
1765 2173 3.517100 ACCTCACAGCTGAGTTGATACAT 59.483 43.478 23.35 0.00 42.36 2.29
1766 2174 2.899900 ACCTCACAGCTGAGTTGATACA 59.100 45.455 23.35 0.00 42.36 2.29
1819 2227 3.677190 TCTAGAGAATCGAACGTGCTC 57.323 47.619 0.00 0.00 42.67 4.26
1940 2356 4.697352 AGGAAGAAGACATGAATGTTTCCG 59.303 41.667 14.53 0.00 43.58 4.30
2018 2593 2.267324 GAGGAGCCAGCACCTGAC 59.733 66.667 13.63 0.00 37.16 3.51
2190 2771 9.343539 AGATTAACCCATTAAATTAGCAGAGAC 57.656 33.333 0.00 0.00 33.98 3.36
2293 3364 9.654663 GTTTGATAAGGTATATAGTCCATGGAC 57.345 37.037 33.72 33.72 44.86 4.02
2445 3682 0.181350 GGCTAATCAGTGGGGAGTGG 59.819 60.000 0.00 0.00 0.00 4.00
2496 3741 8.831715 TTGTTCGCAGATGTCATATATACATT 57.168 30.769 4.78 0.00 37.69 2.71
2501 3746 7.792374 AGTTTTGTTCGCAGATGTCATATAT 57.208 32.000 0.00 0.00 35.04 0.86
2503 3748 7.792374 ATAGTTTTGTTCGCAGATGTCATAT 57.208 32.000 0.00 0.00 35.04 1.78
2504 3749 7.119116 ACAATAGTTTTGTTCGCAGATGTCATA 59.881 33.333 0.00 0.00 35.04 2.15
2516 3764 5.043248 ACTGCTGCAACAATAGTTTTGTTC 58.957 37.500 8.52 5.56 40.30 3.18
2588 3838 3.307242 CAGCTAGTAGATTTTGTGCCGTC 59.693 47.826 0.00 0.00 0.00 4.79
2592 3842 5.347907 ACGTTACAGCTAGTAGATTTTGTGC 59.652 40.000 0.00 0.00 33.43 4.57
2661 3919 6.263617 TCCTAATTGCACTTTCTAAAAACCGT 59.736 34.615 0.00 0.00 0.00 4.83
2662 3920 6.674066 TCCTAATTGCACTTTCTAAAAACCG 58.326 36.000 0.00 0.00 0.00 4.44
2663 3921 7.039993 TCCTCCTAATTGCACTTTCTAAAAACC 60.040 37.037 0.00 0.00 0.00 3.27
2668 3929 6.620877 TCTCCTCCTAATTGCACTTTCTAA 57.379 37.500 0.00 0.00 0.00 2.10
2673 3934 8.055181 TGAATTAATCTCCTCCTAATTGCACTT 58.945 33.333 0.00 0.00 0.00 3.16
2709 3976 5.995897 ACCGCAAAAGTAAGTAAGATGTCTT 59.004 36.000 0.45 0.45 39.85 3.01
2740 4010 1.637553 ACCCAGAAGATCCACTGCAAT 59.362 47.619 10.18 0.00 33.40 3.56
2788 4058 2.038329 TACTGGTGGTAGGCGGCT 59.962 61.111 18.33 18.33 0.00 5.52
2869 4139 1.204704 GATCATCCATACATCGGCCGA 59.795 52.381 33.12 33.12 0.00 5.54
2876 4146 3.071457 TGTGCTTCCGATCATCCATACAT 59.929 43.478 0.00 0.00 0.00 2.29
2877 4147 2.433970 TGTGCTTCCGATCATCCATACA 59.566 45.455 0.00 0.00 0.00 2.29
2955 4232 4.023193 ACACCCAAATGCGTCTAAGAAAAG 60.023 41.667 0.00 0.00 0.00 2.27
3067 4345 5.560724 TCCACTTCTAGTTAATGCAGCTTT 58.439 37.500 0.00 0.00 0.00 3.51
3071 4349 6.108687 TGTGATCCACTTCTAGTTAATGCAG 58.891 40.000 0.00 0.00 35.11 4.41
3098 4380 5.010933 TCTTCGAGAGTCCTGTTACAAGAT 58.989 41.667 0.00 0.00 0.00 2.40
3100 4382 4.768130 TCTTCGAGAGTCCTGTTACAAG 57.232 45.455 0.00 0.00 0.00 3.16
3103 4385 4.868067 TGTTTCTTCGAGAGTCCTGTTAC 58.132 43.478 0.00 0.00 0.00 2.50
3104 4386 4.825634 TCTGTTTCTTCGAGAGTCCTGTTA 59.174 41.667 0.00 0.00 0.00 2.41
3116 4398 6.136071 CCAGTTTGTTATGTCTGTTTCTTCG 58.864 40.000 0.00 0.00 0.00 3.79
3117 4399 7.027778 ACCAGTTTGTTATGTCTGTTTCTTC 57.972 36.000 0.00 0.00 0.00 2.87
3124 4406 3.750371 TGGGACCAGTTTGTTATGTCTG 58.250 45.455 0.00 0.00 0.00 3.51
3127 4409 3.394606 AGTCTGGGACCAGTTTGTTATGT 59.605 43.478 17.34 0.00 43.96 2.29
3128 4410 4.021102 AGTCTGGGACCAGTTTGTTATG 57.979 45.455 17.34 0.00 43.96 1.90
3130 4412 5.836024 AATAGTCTGGGACCAGTTTGTTA 57.164 39.130 17.34 5.65 43.96 2.41
3139 4422 4.715297 TCCTCTTTGTAATAGTCTGGGACC 59.285 45.833 0.00 0.00 32.18 4.46
3142 4425 4.717280 AGGTCCTCTTTGTAATAGTCTGGG 59.283 45.833 0.00 0.00 0.00 4.45
3145 4428 5.590818 TGGAGGTCCTCTTTGTAATAGTCT 58.409 41.667 18.58 0.00 36.82 3.24
3146 4429 5.934402 TGGAGGTCCTCTTTGTAATAGTC 57.066 43.478 18.58 0.00 36.82 2.59
3147 4430 6.697641 TTTGGAGGTCCTCTTTGTAATAGT 57.302 37.500 18.58 0.00 36.82 2.12
3148 4431 6.768381 GGATTTGGAGGTCCTCTTTGTAATAG 59.232 42.308 18.58 0.00 36.82 1.73
3165 4448 4.797800 TGCGATTTTCAATGGATTTGGA 57.202 36.364 0.00 0.00 35.92 3.53
3172 4455 4.019919 ACTCGATTGCGATTTTCAATGG 57.980 40.909 0.00 0.00 46.80 3.16
3181 4465 0.811616 GCCAAGGACTCGATTGCGAT 60.812 55.000 0.00 0.00 46.80 4.58
3189 4473 1.269517 GCTAGAGATGCCAAGGACTCG 60.270 57.143 0.00 0.00 34.98 4.18
3191 4475 2.038659 GAGCTAGAGATGCCAAGGACT 58.961 52.381 0.00 0.00 0.00 3.85
3196 4480 2.961741 AGATTCGAGCTAGAGATGCCAA 59.038 45.455 0.00 0.00 0.00 4.52
3206 4497 5.880887 TGAAGACAAGACTAGATTCGAGCTA 59.119 40.000 0.00 0.00 0.00 3.32
3210 4501 4.142665 CGGTGAAGACAAGACTAGATTCGA 60.143 45.833 0.00 0.00 0.00 3.71
3223 4514 1.003839 GTCATGCCCGGTGAAGACA 60.004 57.895 0.00 0.00 0.00 3.41
3233 4524 3.607163 CCATGTGGTGTCATGCCC 58.393 61.111 0.00 0.00 42.44 5.36
3267 4558 1.963515 GGAATTCATGGCATGGTACCC 59.036 52.381 26.15 17.91 0.00 3.69
3275 4566 2.488204 TCGTCTTGGAATTCATGGCA 57.512 45.000 7.93 0.00 0.00 4.92
3284 4575 4.649674 AGGCACTATATCTTCGTCTTGGAA 59.350 41.667 0.00 0.00 36.02 3.53
3309 4600 1.210204 TCCCAGCCAAGAGCCAGATT 61.210 55.000 0.00 0.00 45.47 2.40
3343 4634 4.681074 TGAATATGTCAGCCGAATGGTA 57.319 40.909 0.00 0.00 37.67 3.25
3352 4643 3.499537 TCATCGCCATTGAATATGTCAGC 59.500 43.478 0.00 0.00 37.61 4.26
3354 4645 5.048573 CCAATCATCGCCATTGAATATGTCA 60.049 40.000 3.23 0.00 33.69 3.58
3355 4646 5.396484 CCAATCATCGCCATTGAATATGTC 58.604 41.667 3.23 0.00 33.69 3.06
3359 4650 3.220940 TGCCAATCATCGCCATTGAATA 58.779 40.909 3.23 0.00 33.69 1.75
3363 4654 2.060326 GATGCCAATCATCGCCATTG 57.940 50.000 0.00 0.00 41.82 2.82
3389 4680 2.564721 GGCTTTGGTGTCCACTGCC 61.565 63.158 12.76 12.76 42.01 4.85
3397 4688 1.528309 CGTGGAAGGGCTTTGGTGT 60.528 57.895 0.00 0.00 0.00 4.16
3399 4690 2.115266 CCGTGGAAGGGCTTTGGT 59.885 61.111 0.00 0.00 33.71 3.67
3441 4732 4.843516 GGGAAAGATGGAGATCTAGATGGT 59.156 45.833 10.74 0.00 38.03 3.55
3457 4748 0.613777 GAAGGAGAAGCGGGGAAAGA 59.386 55.000 0.00 0.00 0.00 2.52
3465 4756 1.009389 GTGGTCGTGAAGGAGAAGCG 61.009 60.000 0.00 0.00 0.00 4.68
3486 4778 5.670361 TGATTCCCCTGCTTAGTAAGGTTAT 59.330 40.000 11.84 0.00 0.00 1.89
3492 4784 3.711704 CCTCTGATTCCCCTGCTTAGTAA 59.288 47.826 0.00 0.00 0.00 2.24
3494 4786 2.122768 CCTCTGATTCCCCTGCTTAGT 58.877 52.381 0.00 0.00 0.00 2.24
3498 4790 0.985490 GGTCCTCTGATTCCCCTGCT 60.985 60.000 0.00 0.00 0.00 4.24
3525 4817 2.020131 CTTGCATGACCGCCTGATC 58.980 57.895 0.00 0.00 0.00 2.92
3530 4822 1.714899 AATACGCTTGCATGACCGCC 61.715 55.000 3.33 0.00 0.00 6.13
3532 4824 1.006086 TGAATACGCTTGCATGACCG 58.994 50.000 3.33 1.04 0.00 4.79
3533 4825 2.009774 AGTGAATACGCTTGCATGACC 58.990 47.619 3.33 0.00 32.53 4.02
3535 4827 5.276820 CGATTTAGTGAATACGCTTGCATGA 60.277 40.000 3.33 0.00 37.97 3.07
3545 4837 1.191647 CGGCGGCGATTTAGTGAATAC 59.808 52.381 29.19 0.00 0.00 1.89
3549 4841 1.517694 GTCGGCGGCGATTTAGTGA 60.518 57.895 36.75 9.45 0.00 3.41
3550 4842 2.856346 CGTCGGCGGCGATTTAGTG 61.856 63.158 36.75 17.87 0.00 2.74
3551 4843 2.581409 CGTCGGCGGCGATTTAGT 60.581 61.111 36.75 0.00 0.00 2.24
3553 4845 4.798026 TGCGTCGGCGGCGATTTA 62.798 61.111 39.40 21.89 44.10 1.40
3563 4855 2.507102 ATGCGAAGAGTGCGTCGG 60.507 61.111 0.00 0.00 44.44 4.79
3567 4859 1.011463 GATGCATGCGAAGAGTGCG 60.011 57.895 14.09 0.00 41.21 5.34
3574 4866 0.250038 GGGAGCTAGATGCATGCGAA 60.250 55.000 14.09 0.00 45.94 4.70
3577 4869 0.950116 GTTGGGAGCTAGATGCATGC 59.050 55.000 11.82 11.82 45.94 4.06
3606 4898 1.035932 TAGCGGCACCTACAGTCCTC 61.036 60.000 1.45 0.00 0.00 3.71
3611 4903 2.107141 GGCTAGCGGCACCTACAG 59.893 66.667 9.00 0.00 44.01 2.74
3620 4912 2.185350 CTGGTCTGTGGCTAGCGG 59.815 66.667 9.00 0.00 0.00 5.52
3631 4923 2.025981 TGCCATTATTGAGCACTGGTCT 60.026 45.455 9.57 0.00 0.00 3.85
3637 4929 2.785679 GTCGTTGCCATTATTGAGCAC 58.214 47.619 0.00 0.00 35.96 4.40
3639 4931 1.396996 ACGTCGTTGCCATTATTGAGC 59.603 47.619 0.00 0.00 0.00 4.26
3646 4938 2.325082 GGAGCACGTCGTTGCCATT 61.325 57.895 13.70 0.00 44.14 3.16
3648 4940 4.228567 TGGAGCACGTCGTTGCCA 62.229 61.111 13.70 10.29 44.14 4.92
3652 4944 0.108804 CCATAGTGGAGCACGTCGTT 60.109 55.000 0.00 0.00 40.96 3.85
3667 4959 2.176581 TGGCCTTTGGTGATATGCCATA 59.823 45.455 3.32 0.00 43.49 2.74
3674 4966 1.281867 CTCCTGTGGCCTTTGGTGATA 59.718 52.381 3.32 0.00 0.00 2.15
3676 4968 1.455849 CTCCTGTGGCCTTTGGTGA 59.544 57.895 3.32 0.00 0.00 4.02
3677 4969 2.270986 GCTCCTGTGGCCTTTGGTG 61.271 63.158 3.32 5.29 0.00 4.17
3678 4970 2.116125 GCTCCTGTGGCCTTTGGT 59.884 61.111 3.32 0.00 0.00 3.67
3679 4971 1.975407 CTGCTCCTGTGGCCTTTGG 60.975 63.158 3.32 2.92 0.00 3.28
3684 4976 2.124403 CATCCTGCTCCTGTGGCC 60.124 66.667 0.00 0.00 0.00 5.36
3693 4985 1.008938 AGGTCTAGGTTCCATCCTGCT 59.991 52.381 0.00 0.00 38.41 4.24
3695 4987 1.765314 CCAGGTCTAGGTTCCATCCTG 59.235 57.143 0.00 0.00 41.17 3.86
3700 4992 5.786457 TGTAAAATACCAGGTCTAGGTTCCA 59.214 40.000 0.00 0.00 40.54 3.53
3728 5020 1.898863 AGTGAAGGGGCATGGAGTAT 58.101 50.000 0.00 0.00 0.00 2.12
3730 5022 0.329596 GAAGTGAAGGGGCATGGAGT 59.670 55.000 0.00 0.00 0.00 3.85
3739 5031 0.689623 AGCTGGAGTGAAGTGAAGGG 59.310 55.000 0.00 0.00 0.00 3.95
3745 5037 1.312815 GTTGCAAGCTGGAGTGAAGT 58.687 50.000 0.00 0.00 0.00 3.01
3747 5039 1.024271 GTGTTGCAAGCTGGAGTGAA 58.976 50.000 0.00 0.00 0.00 3.18
3750 5042 1.893808 CGGTGTTGCAAGCTGGAGT 60.894 57.895 0.00 0.00 0.00 3.85
3754 5046 3.547249 CTGGCGGTGTTGCAAGCTG 62.547 63.158 0.00 2.07 36.28 4.24
3770 5062 0.109342 CCGATCCCCAATCTTCCCTG 59.891 60.000 0.00 0.00 31.68 4.45
3772 5064 1.353394 ACCCGATCCCCAATCTTCCC 61.353 60.000 0.00 0.00 31.68 3.97
3796 5088 2.694829 GATCCATTCGGGTCGGGTCG 62.695 65.000 0.00 0.00 31.02 4.79
3797 5089 1.069258 GATCCATTCGGGTCGGGTC 59.931 63.158 0.00 0.00 31.02 4.46
3798 5090 1.268992 TTGATCCATTCGGGTCGGGT 61.269 55.000 0.00 0.00 46.61 5.28
3799 5091 0.532862 CTTGATCCATTCGGGTCGGG 60.533 60.000 0.00 0.00 46.61 5.14
3800 5092 0.178068 ACTTGATCCATTCGGGTCGG 59.822 55.000 0.00 0.00 46.61 4.79
3801 5093 1.137086 AGACTTGATCCATTCGGGTCG 59.863 52.381 0.00 0.00 46.61 4.79
3802 5094 2.990066 AGACTTGATCCATTCGGGTC 57.010 50.000 0.00 0.00 43.54 4.46
3803 5095 3.133003 CAGTAGACTTGATCCATTCGGGT 59.867 47.826 0.00 0.00 38.11 5.28
3804 5096 3.133003 ACAGTAGACTTGATCCATTCGGG 59.867 47.826 0.00 0.00 38.37 5.14
3805 5097 4.115516 CACAGTAGACTTGATCCATTCGG 58.884 47.826 0.00 0.00 0.00 4.30
3806 5098 3.553511 GCACAGTAGACTTGATCCATTCG 59.446 47.826 0.00 0.00 0.00 3.34
3807 5099 4.764172 AGCACAGTAGACTTGATCCATTC 58.236 43.478 0.00 0.00 0.00 2.67
3808 5100 4.383552 GGAGCACAGTAGACTTGATCCATT 60.384 45.833 17.06 0.00 43.87 3.16
3809 5101 3.133721 GGAGCACAGTAGACTTGATCCAT 59.866 47.826 17.06 0.00 43.87 3.41
3810 5102 2.497675 GGAGCACAGTAGACTTGATCCA 59.502 50.000 17.06 0.00 43.87 3.41
3811 5103 2.480416 CGGAGCACAGTAGACTTGATCC 60.480 54.545 14.16 14.16 41.52 3.36
3812 5104 2.480416 CCGGAGCACAGTAGACTTGATC 60.480 54.545 0.00 0.00 0.00 2.92
3813 5105 1.478510 CCGGAGCACAGTAGACTTGAT 59.521 52.381 0.00 0.00 0.00 2.57
3814 5106 0.888619 CCGGAGCACAGTAGACTTGA 59.111 55.000 0.00 0.00 0.00 3.02
3815 5107 0.603569 ACCGGAGCACAGTAGACTTG 59.396 55.000 9.46 0.00 0.00 3.16
3816 5108 0.603569 CACCGGAGCACAGTAGACTT 59.396 55.000 9.46 0.00 0.00 3.01
3817 5109 0.539901 ACACCGGAGCACAGTAGACT 60.540 55.000 9.46 0.00 0.00 3.24
3818 5110 0.109226 GACACCGGAGCACAGTAGAC 60.109 60.000 9.46 0.00 0.00 2.59
3819 5111 0.538746 TGACACCGGAGCACAGTAGA 60.539 55.000 9.46 0.00 0.00 2.59
3820 5112 0.532573 ATGACACCGGAGCACAGTAG 59.467 55.000 9.46 0.00 0.00 2.57
3821 5113 0.530744 GATGACACCGGAGCACAGTA 59.469 55.000 9.46 0.00 0.00 2.74
3822 5114 1.293498 GATGACACCGGAGCACAGT 59.707 57.895 9.46 0.00 0.00 3.55
3823 5115 1.448540 GGATGACACCGGAGCACAG 60.449 63.158 9.46 0.00 0.00 3.66
3824 5116 2.662596 GGATGACACCGGAGCACA 59.337 61.111 9.46 4.98 0.00 4.57
3825 5117 2.125106 GGGATGACACCGGAGCAC 60.125 66.667 9.46 0.00 0.00 4.40
3826 5118 2.284625 AGGGATGACACCGGAGCA 60.285 61.111 9.46 3.05 0.00 4.26
3827 5119 2.187946 CAGGGATGACACCGGAGC 59.812 66.667 9.46 0.00 0.00 4.70
3828 5120 1.050988 ATCCAGGGATGACACCGGAG 61.051 60.000 9.46 1.26 35.34 4.63
3829 5121 1.002921 ATCCAGGGATGACACCGGA 59.997 57.895 9.46 0.00 35.96 5.14
3830 5122 1.337384 TGATCCAGGGATGACACCGG 61.337 60.000 5.35 0.00 34.60 5.28
3831 5123 0.105593 CTGATCCAGGGATGACACCG 59.894 60.000 5.35 0.00 34.60 4.94
3832 5124 1.207791 ACTGATCCAGGGATGACACC 58.792 55.000 5.35 0.00 35.51 4.16
3833 5125 4.384056 CATTACTGATCCAGGGATGACAC 58.616 47.826 5.35 0.00 35.51 3.67
3834 5126 3.181451 GCATTACTGATCCAGGGATGACA 60.181 47.826 5.35 0.00 35.51 3.58
3835 5127 3.072184 AGCATTACTGATCCAGGGATGAC 59.928 47.826 5.35 0.00 35.51 3.06
3836 5128 3.321039 AGCATTACTGATCCAGGGATGA 58.679 45.455 5.35 0.00 35.51 2.92
3837 5129 3.784511 AGCATTACTGATCCAGGGATG 57.215 47.619 5.35 0.00 35.51 3.51


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

AutoCloner maintained by Alex Coulton.