Multiple sequence alignment - TraesCS3B01G487900

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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 TraesCS3B01G487900 chr3B 100.000 6444 0 0 1 6444 733878552 733884995 0.000000e+00 11900.0
1 TraesCS3B01G487900 chr3B 86.726 226 26 4 701 924 455067718 455067495 1.390000e-61 248.0
2 TraesCS3B01G487900 chr3B 86.486 222 28 2 701 921 455125826 455125606 6.460000e-60 243.0
3 TraesCS3B01G487900 chr3B 94.318 88 4 1 6358 6444 733895429 733895516 4.050000e-27 134.0
4 TraesCS3B01G487900 chr3B 97.561 41 0 1 5962 6002 733884480 733884519 1.160000e-07 69.4
5 TraesCS3B01G487900 chr3B 97.561 41 0 1 5929 5968 733884513 733884553 1.160000e-07 69.4
6 TraesCS3B01G487900 chr3A 93.919 2812 134 22 955 3745 689359219 689362014 0.000000e+00 4211.0
7 TraesCS3B01G487900 chr3A 95.667 2054 60 12 3746 5776 689362050 689364097 0.000000e+00 3273.0
8 TraesCS3B01G487900 chr3A 85.829 374 37 9 136 501 710054386 710054021 3.650000e-102 383.0
9 TraesCS3B01G487900 chr3A 89.286 224 22 2 695 917 401475245 401475467 4.920000e-71 279.0
10 TraesCS3B01G487900 chr3A 88.991 218 21 3 699 915 401530153 401530368 3.830000e-67 267.0
11 TraesCS3B01G487900 chr3A 94.118 102 6 0 27 128 641817387 641817488 8.650000e-34 156.0
12 TraesCS3B01G487900 chr3D 93.996 2798 126 18 976 3735 552955694 552958487 0.000000e+00 4198.0
13 TraesCS3B01G487900 chr3D 94.368 2042 69 19 3753 5776 552958543 552960556 0.000000e+00 3092.0
14 TraesCS3B01G487900 chr3D 93.403 576 32 4 4837 5407 553038430 553039004 0.000000e+00 848.0
15 TraesCS3B01G487900 chr3D 93.229 576 33 4 4837 5407 553076950 553077524 0.000000e+00 843.0
16 TraesCS3B01G487900 chr3D 90.836 371 26 7 5409 5776 553078639 553079004 2.090000e-134 490.0
17 TraesCS3B01G487900 chr3D 90.836 371 25 7 5409 5776 553040119 553040483 7.510000e-134 488.0
18 TraesCS3B01G487900 chr3D 88.601 193 16 6 5775 5967 553040510 553040696 5.030000e-56 230.0
19 TraesCS3B01G487900 chr3D 92.105 152 11 1 6294 6444 552963226 552963377 5.060000e-51 213.0
20 TraesCS3B01G487900 chr3D 88.652 141 16 0 5775 5915 553079031 553079171 8.590000e-39 172.0
21 TraesCS3B01G487900 chr3D 95.918 98 4 0 31 128 517878526 517878623 6.690000e-35 159.0
22 TraesCS3B01G487900 chr3D 91.781 73 3 2 6131 6200 553040892 553040964 1.480000e-16 99.0
23 TraesCS3B01G487900 chr3D 95.000 60 2 1 6385 6443 553041632 553041691 6.880000e-15 93.5
24 TraesCS3B01G487900 chr3D 93.333 60 3 1 6385 6443 553079542 553079601 3.200000e-13 87.9
25 TraesCS3B01G487900 chr5D 86.084 1660 134 30 1783 3376 82323815 82322187 0.000000e+00 1696.0
26 TraesCS3B01G487900 chr5D 87.014 1209 92 33 4351 5532 82319631 82318461 0.000000e+00 1303.0
27 TraesCS3B01G487900 chr5D 89.091 770 74 5 968 1736 82324653 82323893 0.000000e+00 948.0
28 TraesCS3B01G487900 chr5D 88.419 449 36 8 3846 4290 82320064 82319628 1.590000e-145 527.0
29 TraesCS3B01G487900 chr2B 95.765 921 39 0 1 921 244584541 244585461 0.000000e+00 1485.0
30 TraesCS3B01G487900 chr2B 84.950 598 46 15 1 596 727673533 727674088 3.370000e-157 566.0
31 TraesCS3B01G487900 chr2B 88.688 221 23 2 701 921 244581324 244581542 1.060000e-67 268.0
32 TraesCS3B01G487900 chr4B 93.381 559 33 3 1 559 626634123 626634677 0.000000e+00 824.0
33 TraesCS3B01G487900 chr4B 95.117 471 22 1 451 921 626630666 626631135 0.000000e+00 741.0
34 TraesCS3B01G487900 chr4B 94.692 471 21 3 451 921 626634525 626634991 0.000000e+00 728.0
35 TraesCS3B01G487900 chr4B 92.373 472 34 2 88 559 626630352 626630821 0.000000e+00 671.0
36 TraesCS3B01G487900 chr5A 93.501 477 29 2 1 476 670564716 670565191 0.000000e+00 708.0
37 TraesCS3B01G487900 chr5A 94.118 102 6 0 27 128 561677873 561677772 8.650000e-34 156.0
38 TraesCS3B01G487900 chr2A 85.377 424 40 11 136 544 740057007 740056591 2.780000e-113 420.0
39 TraesCS3B01G487900 chr2A 87.421 159 19 1 3091 3249 48255128 48255285 1.430000e-41 182.0
40 TraesCS3B01G487900 chr2A 95.000 100 5 0 27 126 740057156 740057057 2.410000e-34 158.0
41 TraesCS3B01G487900 chr7D 78.336 637 116 15 1792 2420 11021117 11021739 6.060000e-105 392.0
42 TraesCS3B01G487900 chr7D 75.793 599 94 30 4488 5054 11022815 11023394 8.290000e-64 255.0
43 TraesCS3B01G487900 chr7D 87.195 164 15 4 3080 3243 11022299 11022456 1.430000e-41 182.0
44 TraesCS3B01G487900 chr7A 78.315 641 115 13 1789 2420 10193502 10194127 6.060000e-105 392.0
45 TraesCS3B01G487900 chr7A 76.014 592 99 29 4488 5054 10195203 10195776 3.830000e-67 267.0
46 TraesCS3B01G487900 chr7A 87.195 164 15 4 3080 3243 10194689 10194846 1.430000e-41 182.0
47 TraesCS3B01G487900 chr7A 95.098 102 5 0 27 128 671209124 671209023 1.860000e-35 161.0
48 TraesCS3B01G487900 chr4A 77.900 638 117 14 1792 2420 727117301 727116679 6.100000e-100 375.0
49 TraesCS3B01G487900 chr4A 88.435 147 14 3 3080 3226 727116118 727115975 2.390000e-39 174.0
50 TraesCS3B01G487900 chr2D 78.342 591 59 39 27 596 620496658 620497200 1.040000e-82 318.0
51 TraesCS3B01G487900 chr1A 86.909 275 31 4 136 410 61355121 61355390 2.920000e-78 303.0
52 TraesCS3B01G487900 chr5B 88.745 231 22 4 693 921 606976648 606976876 4.920000e-71 279.0
53 TraesCS3B01G487900 chrUn 93.056 72 3 1 6131 6200 357387609 357387538 3.180000e-18 104.0
54 TraesCS3B01G487900 chrUn 93.056 72 3 1 6131 6200 464995776 464995705 3.180000e-18 104.0
55 TraesCS3B01G487900 chrUn 93.333 60 3 1 6385 6443 241685438 241685379 3.200000e-13 87.9
56 TraesCS3B01G487900 chrUn 93.333 60 3 1 6385 6443 357386870 357386811 3.200000e-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 TraesCS3B01G487900 chr3B 733878552 733884995 6443 False 4012.933333 11900 98.374000 1 6444 3 chr3B.!!$F2 6443
1 TraesCS3B01G487900 chr3A 689359219 689364097 4878 False 3742.000000 4211 94.793000 955 5776 2 chr3A.!!$F4 4821
2 TraesCS3B01G487900 chr3D 552955694 552963377 7683 False 2501.000000 4198 93.489667 976 6444 3 chr3D.!!$F2 5468
3 TraesCS3B01G487900 chr3D 553076950 553079601 2651 False 398.225000 843 91.512500 4837 6443 4 chr3D.!!$F4 1606
4 TraesCS3B01G487900 chr3D 553038430 553041691 3261 False 351.700000 848 91.924200 4837 6443 5 chr3D.!!$F3 1606
5 TraesCS3B01G487900 chr5D 82318461 82324653 6192 True 1118.500000 1696 87.652000 968 5532 4 chr5D.!!$R1 4564
6 TraesCS3B01G487900 chr2B 244581324 244585461 4137 False 876.500000 1485 92.226500 1 921 2 chr2B.!!$F2 920
7 TraesCS3B01G487900 chr2B 727673533 727674088 555 False 566.000000 566 84.950000 1 596 1 chr2B.!!$F1 595
8 TraesCS3B01G487900 chr4B 626630352 626634991 4639 False 741.000000 824 93.890750 1 921 4 chr4B.!!$F1 920
9 TraesCS3B01G487900 chr2A 740056591 740057156 565 True 289.000000 420 90.188500 27 544 2 chr2A.!!$R1 517
10 TraesCS3B01G487900 chr7D 11021117 11023394 2277 False 276.333333 392 80.441333 1792 5054 3 chr7D.!!$F1 3262
11 TraesCS3B01G487900 chr7A 10193502 10195776 2274 False 280.333333 392 80.508000 1789 5054 3 chr7A.!!$F1 3265
12 TraesCS3B01G487900 chr4A 727115975 727117301 1326 True 274.500000 375 83.167500 1792 3226 2 chr4A.!!$R1 1434
13 TraesCS3B01G487900 chr2D 620496658 620497200 542 False 318.000000 318 78.342000 27 596 1 chr2D.!!$F1 569

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
942 4849 0.254178 AAGCCAGATGCCGATGTCTT 59.746 50.000 0.00 0.0 42.71 3.01 F
943 4850 0.254178 AGCCAGATGCCGATGTCTTT 59.746 50.000 0.00 0.0 42.71 2.52 F
1173 5081 0.529378 AGTTATTCGCCTCCGTCGTT 59.471 50.000 0.00 0.0 35.54 3.85 F
2233 6187 1.017387 GAAGATAGCAAAGGCCACGG 58.983 55.000 5.01 0.0 42.56 4.94 F
3033 7052 1.533756 CCGTGGCGCTTATTTGGAATG 60.534 52.381 7.64 0.0 0.00 2.67 F
3505 9083 0.756903 AAGTGACGGTGCAGTTACCT 59.243 50.000 0.00 0.0 38.62 3.08 F
3679 9263 1.122227 TGCTGCCCTTTCTTTGCTTT 58.878 45.000 0.00 0.0 0.00 3.51 F
4456 10311 1.480545 GCAACTTGTGGGTCTTGGTTT 59.519 47.619 0.00 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 5922 0.107268 TGTCATCGGCATCAGATGGG 59.893 55.000 12.54 0.00 44.04 4.00 R
2803 6789 0.700564 AAGCCCATGTGACATCAGGT 59.299 50.000 11.59 2.35 0.00 4.00 R
3007 7026 0.814010 AATAAGCGCCACGGATGTCC 60.814 55.000 2.29 0.00 0.00 4.02 R
3505 9083 0.039256 GCTGATGTCGCAAAGGCAAA 60.039 50.000 0.00 0.00 38.34 3.68 R
4952 10845 2.241160 TGCATCCAAATCAACAGTGCT 58.759 42.857 0.00 0.00 32.67 4.40 R
5153 11051 0.107654 GGCTGCTTCGTCCACCTAAT 60.108 55.000 0.00 0.00 0.00 1.73 R
5295 11194 0.529378 GTACCTGTTCCGACACCGAT 59.471 55.000 0.00 0.00 38.22 4.18 R
5457 12469 1.064463 CCAAGGCACCCAGATACATGT 60.064 52.381 2.69 2.69 0.00 3.21 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
208 4035 0.605589 TGAGAGGAAGAGACGTGCGA 60.606 55.000 0.00 0.00 0.00 5.10
269 4098 4.153330 GAGGAGGCCGACCCCCTA 62.153 72.222 16.41 0.00 35.25 3.53
298 4150 4.602259 CCACGCCGCGTCCCATAT 62.602 66.667 17.16 0.00 38.32 1.78
306 4158 4.293648 CGTCCCATATGCCGCCGA 62.294 66.667 0.00 0.00 0.00 5.54
672 4579 3.755628 GACCGCACGCTCACCCTA 61.756 66.667 0.00 0.00 0.00 3.53
921 4828 8.397957 AGGAGCTTCTATTCTTATCTCTGGATA 58.602 37.037 0.00 0.00 33.71 2.59
922 4829 9.200817 GGAGCTTCTATTCTTATCTCTGGATAT 57.799 37.037 0.00 0.00 34.78 1.63
928 4835 9.997172 TCTATTCTTATCTCTGGATATAAGCCA 57.003 33.333 9.46 0.00 36.20 4.75
935 4842 2.768253 TGGATATAAGCCAGATGCCG 57.232 50.000 0.00 0.00 42.71 5.69
936 4843 2.256306 TGGATATAAGCCAGATGCCGA 58.744 47.619 0.00 0.00 42.71 5.54
937 4844 2.840038 TGGATATAAGCCAGATGCCGAT 59.160 45.455 0.00 0.00 42.71 4.18
938 4845 3.201290 GGATATAAGCCAGATGCCGATG 58.799 50.000 0.00 0.00 42.71 3.84
939 4846 3.369892 GGATATAAGCCAGATGCCGATGT 60.370 47.826 0.00 0.00 42.71 3.06
940 4847 2.175878 ATAAGCCAGATGCCGATGTC 57.824 50.000 0.00 0.00 42.71 3.06
941 4848 1.123077 TAAGCCAGATGCCGATGTCT 58.877 50.000 0.00 0.00 42.71 3.41
942 4849 0.254178 AAGCCAGATGCCGATGTCTT 59.746 50.000 0.00 0.00 42.71 3.01
943 4850 0.254178 AGCCAGATGCCGATGTCTTT 59.746 50.000 0.00 0.00 42.71 2.52
944 4851 0.659957 GCCAGATGCCGATGTCTTTC 59.340 55.000 0.00 0.00 0.00 2.62
945 4852 0.933097 CCAGATGCCGATGTCTTTCG 59.067 55.000 0.00 0.00 38.83 3.46
946 4853 1.645034 CAGATGCCGATGTCTTTCGT 58.355 50.000 0.00 0.00 37.42 3.85
947 4854 2.002586 CAGATGCCGATGTCTTTCGTT 58.997 47.619 0.00 0.00 37.42 3.85
948 4855 2.002586 AGATGCCGATGTCTTTCGTTG 58.997 47.619 0.00 0.00 37.42 4.10
949 4856 1.999735 GATGCCGATGTCTTTCGTTGA 59.000 47.619 0.00 0.00 37.42 3.18
950 4857 1.428448 TGCCGATGTCTTTCGTTGAG 58.572 50.000 0.00 0.00 37.42 3.02
951 4858 0.721718 GCCGATGTCTTTCGTTGAGG 59.278 55.000 0.00 0.00 37.42 3.86
952 4859 1.671850 GCCGATGTCTTTCGTTGAGGA 60.672 52.381 0.00 0.00 37.42 3.71
953 4860 2.683968 CCGATGTCTTTCGTTGAGGAA 58.316 47.619 0.00 0.00 37.42 3.36
954 4861 3.064207 CCGATGTCTTTCGTTGAGGAAA 58.936 45.455 0.00 0.00 37.42 3.13
955 4862 3.496884 CCGATGTCTTTCGTTGAGGAAAA 59.503 43.478 1.24 0.00 37.42 2.29
956 4863 4.024387 CCGATGTCTTTCGTTGAGGAAAAA 60.024 41.667 1.24 0.00 37.42 1.94
1173 5081 0.529378 AGTTATTCGCCTCCGTCGTT 59.471 50.000 0.00 0.00 35.54 3.85
1197 5105 3.242291 GCCATCCCCTCCCTACCG 61.242 72.222 0.00 0.00 0.00 4.02
1375 5292 1.189524 ATCCAAACGAGACCCCGACA 61.190 55.000 0.00 0.00 0.00 4.35
1479 5396 1.818674 GGGGTAATGTTTGCTGACCTG 59.181 52.381 0.00 0.00 0.00 4.00
1499 5416 2.125106 GGGCATGGAGTCGGTGAC 60.125 66.667 0.00 0.00 0.00 3.67
1745 5662 5.126779 TGCACCAAGTTTGTGTAATACTCA 58.873 37.500 8.71 0.00 0.00 3.41
1751 5668 8.426489 ACCAAGTTTGTGTAATACTCACTCTTA 58.574 33.333 0.00 0.00 36.83 2.10
1803 5751 1.981256 TTGTTCTTGCAGGAGGTTCC 58.019 50.000 0.00 0.00 36.58 3.62
1884 5832 9.588774 GTATTTATAGACGAGATAGATGCGATC 57.411 37.037 0.00 0.00 0.00 3.69
1974 5922 4.907879 GGATGAATTCCACCAGAACATC 57.092 45.455 2.27 0.00 44.74 3.06
2127 6081 6.349363 GGTTTGATCGGGAAATATATCTTGGC 60.349 42.308 0.00 0.00 0.00 4.52
2233 6187 1.017387 GAAGATAGCAAAGGCCACGG 58.983 55.000 5.01 0.00 42.56 4.94
2353 6313 3.409570 GAAGGAAACAACCTGGACTACC 58.590 50.000 0.00 0.00 40.49 3.18
2386 6346 5.221185 CCTTTGGATAAACATGAGATGCAGG 60.221 44.000 0.00 0.00 0.00 4.85
2397 6357 3.856900 TGAGATGCAGGGCCTAAGTATA 58.143 45.455 5.28 0.00 0.00 1.47
2431 6391 6.148811 TGACTTTGAGGTAATTAAGCTTTCCG 59.851 38.462 3.20 0.00 35.60 4.30
2442 6402 3.850122 AAGCTTTCCGCCTTTTACATC 57.150 42.857 0.00 0.00 40.39 3.06
2461 6421 8.582657 TTACATCTACATCCCTAGCTAGAATC 57.417 38.462 22.70 0.00 0.00 2.52
2467 6427 4.767928 ACATCCCTAGCTAGAATCCTTACG 59.232 45.833 22.70 1.70 0.00 3.18
2592 6576 3.056749 GTCTAAGTTGACGTGGATGGTCT 60.057 47.826 0.00 0.00 35.45 3.85
2723 6709 4.675063 AGTGGGACCCATTTCTAACATT 57.325 40.909 18.51 0.00 35.28 2.71
2752 6738 3.944087 ACTTCAATCGCTAAAGGAAGCT 58.056 40.909 0.00 0.00 40.49 3.74
3007 7026 7.487509 CAGTATGGACAGCTAATCGAATCATAG 59.512 40.741 0.00 0.00 0.00 2.23
3033 7052 1.533756 CCGTGGCGCTTATTTGGAATG 60.534 52.381 7.64 0.00 0.00 2.67
3049 7069 6.601741 TTGGAATGTTGTTTTCAAGCAATC 57.398 33.333 0.00 0.00 40.74 2.67
3327 7408 6.035843 TCATTCAAAAGAGTGTTGCTTGTTC 58.964 36.000 0.00 0.00 0.00 3.18
3407 8975 3.251487 ACTCCGTCGGTTAAATGGTTTTG 59.749 43.478 11.88 0.00 0.00 2.44
3505 9083 0.756903 AAGTGACGGTGCAGTTACCT 59.243 50.000 0.00 0.00 38.62 3.08
3549 9131 4.722220 TGGCTTCTAATGATTCTGGATGG 58.278 43.478 0.00 0.00 0.00 3.51
3679 9263 1.122227 TGCTGCCCTTTCTTTGCTTT 58.878 45.000 0.00 0.00 0.00 3.51
3738 9330 4.495422 AGAATCGCATCATCCGGTAATAC 58.505 43.478 0.00 0.00 0.00 1.89
3761 9388 4.651778 TGTTGATTCGGAATCTTGGTTCT 58.348 39.130 26.15 0.00 38.72 3.01
3919 9720 3.810386 GGACCTTCTGTTCAACTGAGTTC 59.190 47.826 0.00 0.00 0.00 3.01
3942 9743 2.439409 GGTAGTTTTGGCATTACCGGT 58.561 47.619 13.98 13.98 43.94 5.28
4040 9844 9.567848 AATTGAGTTTTACAATGCTAAATACGG 57.432 29.630 0.00 0.00 37.89 4.02
4281 10089 6.644181 ACGAGGTAAAGTTTCTGTTTAGCTAC 59.356 38.462 7.16 0.00 44.35 3.58
4401 10256 5.241506 TGGCTCAGTCTCTTAACAAATTTGG 59.758 40.000 21.74 4.61 0.00 3.28
4456 10311 1.480545 GCAACTTGTGGGTCTTGGTTT 59.519 47.619 0.00 0.00 0.00 3.27
4645 10529 2.098614 TGTTTGTTCCTTTGCTCAGCA 58.901 42.857 0.00 0.00 36.47 4.41
4824 10717 2.837498 TCATGTATGGTGCAGAATCGG 58.163 47.619 0.00 0.00 0.00 4.18
4952 10845 5.306937 TGTTCTCAGAGAAAACCTGTATCCA 59.693 40.000 14.77 1.90 35.75 3.41
5083 10981 6.256757 CGTTAGAAAATTTTCAAAGTGGGCAA 59.743 34.615 28.00 8.52 39.61 4.52
5153 11051 4.261572 GCAACTCACAAACATGCTTCCTTA 60.262 41.667 0.00 0.00 34.29 2.69
5232 11131 5.964958 ATGGGGCATTATCAATAAGTTCG 57.035 39.130 0.00 0.00 0.00 3.95
5249 11148 3.190535 AGTTCGTTGTGTTCAGTTGCTTT 59.809 39.130 0.00 0.00 0.00 3.51
5295 11194 5.106157 GCAAGCTCTGTCTAAAATAAAGCCA 60.106 40.000 0.00 0.00 0.00 4.75
5456 12468 3.316308 GGCAATGTAACTGATCCATCACC 59.684 47.826 0.00 0.00 32.50 4.02
5457 12469 3.947196 GCAATGTAACTGATCCATCACCA 59.053 43.478 0.00 0.00 32.50 4.17
5503 12515 6.319048 ACCATCTTGATGTCTAAATGAGGT 57.681 37.500 9.41 0.00 0.00 3.85
5575 12589 5.837586 TGCCTTCAAATTGCGTTATTTTC 57.162 34.783 0.00 0.00 0.00 2.29
5622 12636 3.684788 GCGGGTATGCAAGGATATTACAG 59.315 47.826 0.00 0.00 34.15 2.74
5639 12653 9.916397 GATATTACAGTTTTCAATGGTCTAACG 57.084 33.333 0.00 0.00 0.00 3.18
5640 12654 7.739498 ATTACAGTTTTCAATGGTCTAACGT 57.261 32.000 0.00 0.00 0.00 3.99
5641 12655 5.668558 ACAGTTTTCAATGGTCTAACGTC 57.331 39.130 0.00 0.00 0.00 4.34
5642 12656 5.120399 ACAGTTTTCAATGGTCTAACGTCA 58.880 37.500 0.00 0.00 0.00 4.35
5647 12662 7.331193 AGTTTTCAATGGTCTAACGTCAGATAC 59.669 37.037 0.00 0.00 0.00 2.24
5683 12701 2.365293 GGTCCTTGTGTTGCATTCCTTT 59.635 45.455 0.00 0.00 0.00 3.11
5684 12702 3.181466 GGTCCTTGTGTTGCATTCCTTTT 60.181 43.478 0.00 0.00 0.00 2.27
5685 12703 4.051237 GTCCTTGTGTTGCATTCCTTTTC 58.949 43.478 0.00 0.00 0.00 2.29
5710 12728 4.886247 TTTACCTTCACAAAGTCCGTTG 57.114 40.909 0.00 0.00 34.52 4.10
5729 12748 7.220683 GTCCGTTGATTCCACAAAATGATAATG 59.779 37.037 0.00 0.00 0.00 1.90
5762 12782 7.581213 TGAAACAGAAGCCTTCTCAAAATAA 57.419 32.000 3.39 0.00 38.11 1.40
5764 12784 8.641541 TGAAACAGAAGCCTTCTCAAAATAATT 58.358 29.630 3.39 0.00 38.11 1.40
5765 12785 8.822652 AAACAGAAGCCTTCTCAAAATAATTG 57.177 30.769 3.39 0.00 38.11 2.32
5843 12891 8.017373 GGTTTAATTGTCGGATGTGATCATATG 58.983 37.037 9.97 0.00 34.06 1.78
5844 12892 8.773645 GTTTAATTGTCGGATGTGATCATATGA 58.226 33.333 9.97 8.10 34.06 2.15
5856 12904 9.317936 GATGTGATCATATGACAACACTAAAGA 57.682 33.333 25.53 14.40 34.06 2.52
5865 12913 9.911788 ATATGACAACACTAAAGAATTGGATCT 57.088 29.630 0.00 0.00 0.00 2.75
5869 12917 8.048534 ACAACACTAAAGAATTGGATCTCATG 57.951 34.615 0.00 0.00 0.00 3.07
5899 14386 4.523083 TGAAGTTAAGCTCCTTGTGTTGT 58.477 39.130 0.00 0.00 0.00 3.32
5908 14397 3.935828 GCTCCTTGTGTTGTATTCCTCTC 59.064 47.826 0.00 0.00 0.00 3.20
5911 14400 5.551233 TCCTTGTGTTGTATTCCTCTCTTG 58.449 41.667 0.00 0.00 0.00 3.02
5915 14404 7.444183 CCTTGTGTTGTATTCCTCTCTTGTTTA 59.556 37.037 0.00 0.00 0.00 2.01
5916 14405 8.918202 TTGTGTTGTATTCCTCTCTTGTTTAT 57.082 30.769 0.00 0.00 0.00 1.40
5917 14406 8.918202 TGTGTTGTATTCCTCTCTTGTTTATT 57.082 30.769 0.00 0.00 0.00 1.40
5918 14407 8.999431 TGTGTTGTATTCCTCTCTTGTTTATTC 58.001 33.333 0.00 0.00 0.00 1.75
5938 14427 4.650754 TCTACCTTCATAAAGTCCGCTC 57.349 45.455 0.00 0.00 0.00 5.03
5951 14440 2.554032 AGTCCGCTCATTCCACAAAAAG 59.446 45.455 0.00 0.00 0.00 2.27
5954 14443 3.826157 TCCGCTCATTCCACAAAAAGAAT 59.174 39.130 0.00 0.00 32.95 2.40
5956 14445 5.652014 TCCGCTCATTCCACAAAAAGAATAT 59.348 36.000 0.00 0.00 31.55 1.28
5957 14446 5.745294 CCGCTCATTCCACAAAAAGAATATG 59.255 40.000 0.00 0.00 31.55 1.78
5958 14447 6.404623 CCGCTCATTCCACAAAAAGAATATGA 60.405 38.462 0.00 0.00 31.55 2.15
5959 14448 7.198390 CGCTCATTCCACAAAAAGAATATGAT 58.802 34.615 0.00 0.00 31.55 2.45
5960 14449 8.344831 CGCTCATTCCACAAAAAGAATATGATA 58.655 33.333 0.00 0.00 31.55 2.15
5970 14459 9.301153 ACAAAAAGAATATGATAAAATGTCCGC 57.699 29.630 0.00 0.00 0.00 5.54
5971 14460 9.520204 CAAAAAGAATATGATAAAATGTCCGCT 57.480 29.630 0.00 0.00 0.00 5.52
5972 14461 9.736023 AAAAAGAATATGATAAAATGTCCGCTC 57.264 29.630 0.00 0.00 0.00 5.03
5973 14462 8.450578 AAAGAATATGATAAAATGTCCGCTCA 57.549 30.769 0.00 0.00 0.00 4.26
5974 14463 8.627208 AAGAATATGATAAAATGTCCGCTCAT 57.373 30.769 0.00 0.00 0.00 2.90
5975 14464 8.627208 AGAATATGATAAAATGTCCGCTCATT 57.373 30.769 0.00 0.00 39.35 2.57
5976 14465 8.725148 AGAATATGATAAAATGTCCGCTCATTC 58.275 33.333 4.31 0.00 37.09 2.67
5977 14466 5.695851 ATGATAAAATGTCCGCTCATTCC 57.304 39.130 4.31 0.00 37.09 3.01
5978 14467 4.522114 TGATAAAATGTCCGCTCATTCCA 58.478 39.130 4.31 0.00 37.09 3.53
5979 14468 4.335315 TGATAAAATGTCCGCTCATTCCAC 59.665 41.667 4.31 0.00 37.09 4.02
5980 14469 2.198827 AAATGTCCGCTCATTCCACA 57.801 45.000 4.31 0.00 37.09 4.17
5981 14470 2.198827 AATGTCCGCTCATTCCACAA 57.801 45.000 0.00 0.00 33.43 3.33
5982 14471 2.198827 ATGTCCGCTCATTCCACAAA 57.801 45.000 0.00 0.00 0.00 2.83
5983 14472 1.974265 TGTCCGCTCATTCCACAAAA 58.026 45.000 0.00 0.00 0.00 2.44
5984 14473 2.302260 TGTCCGCTCATTCCACAAAAA 58.698 42.857 0.00 0.00 0.00 1.94
5985 14474 2.293122 TGTCCGCTCATTCCACAAAAAG 59.707 45.455 0.00 0.00 0.00 2.27
5986 14475 2.552315 GTCCGCTCATTCCACAAAAAGA 59.448 45.455 0.00 0.00 0.00 2.52
5987 14476 3.004315 GTCCGCTCATTCCACAAAAAGAA 59.996 43.478 0.00 0.00 0.00 2.52
5988 14477 3.826157 TCCGCTCATTCCACAAAAAGAAT 59.174 39.130 0.00 0.00 32.95 2.40
6010 14499 9.669353 AGAATATGATAAAATGTCGCATCAAAC 57.331 29.630 0.00 0.00 31.59 2.93
6013 14502 5.639757 TGATAAAATGTCGCATCAAACTGG 58.360 37.500 0.00 0.00 0.00 4.00
6033 14524 6.435164 ACTGGCACCCTTATCAAAATAATCT 58.565 36.000 0.00 0.00 0.00 2.40
6065 14760 3.220674 AGAAATCCTCCAATAGCTGGC 57.779 47.619 0.00 0.00 45.98 4.85
6067 14762 0.480252 AATCCTCCAATAGCTGGCCC 59.520 55.000 0.00 0.00 45.98 5.80
6068 14763 0.698886 ATCCTCCAATAGCTGGCCCA 60.699 55.000 0.00 0.00 45.98 5.36
6070 14765 0.186873 CCTCCAATAGCTGGCCCAAT 59.813 55.000 0.00 0.00 45.98 3.16
6073 14768 2.887152 CTCCAATAGCTGGCCCAATAAC 59.113 50.000 0.00 0.00 45.98 1.89
6098 14793 3.582444 GCTATTGCTCACGAAGATGTG 57.418 47.619 0.00 0.00 41.28 3.21
6111 14806 4.035324 ACGAAGATGTGACCTACGACATAG 59.965 45.833 0.00 0.00 32.85 2.23
6112 14807 4.272748 CGAAGATGTGACCTACGACATAGA 59.727 45.833 0.00 0.00 32.85 1.98
6113 14808 5.220796 CGAAGATGTGACCTACGACATAGAA 60.221 44.000 0.00 0.00 32.85 2.10
6129 15080 7.766278 ACGACATAGAAAATTATCACTCAAGCT 59.234 33.333 0.00 0.00 0.00 3.74
6164 15183 1.069823 CAGCAGACTCCCGAAGCATAT 59.930 52.381 0.00 0.00 0.00 1.78
6207 15229 9.169468 CACAAATGAGTGTTGAACAACTAATAC 57.831 33.333 16.70 8.08 41.67 1.89
6245 15277 3.781965 TCTCAAATCATCCTCATGGTCCA 59.218 43.478 0.00 0.00 34.23 4.02
6264 15296 7.158697 TGGTCCATGATTGGTTCTAATATACG 58.841 38.462 0.00 0.00 44.06 3.06
6284 15567 5.599999 ACGATAGAGTAATCCTTGTGCTT 57.400 39.130 0.00 0.00 41.38 3.91
6290 15573 2.554032 AGTAATCCTTGTGCTTGCACAC 59.446 45.455 25.44 13.52 41.10 3.82
6296 15585 2.212652 CTTGTGCTTGCACACTGACTA 58.787 47.619 25.44 10.91 41.30 2.59
6344 15633 4.570772 CCACCCACATCTAAAACACGATAG 59.429 45.833 0.00 0.00 46.19 2.08
6378 15667 7.325660 TCTCACATCTAATTTTGCTCCATTC 57.674 36.000 0.00 0.00 0.00 2.67
6398 15928 5.873179 TTCCTCTAATTTTGCGTAACTGG 57.127 39.130 0.00 0.00 0.00 4.00
6406 15936 5.761165 ATTTTGCGTAACTGGTACAAACT 57.239 34.783 3.47 0.00 38.70 2.66
6436 15966 5.335504 GCCTCTAATTTGCTGCATTCCTATC 60.336 44.000 1.84 0.00 0.00 2.08
6438 15968 3.996150 AATTTGCTGCATTCCTATCCG 57.004 42.857 1.84 0.00 0.00 4.18
6439 15969 2.708216 TTTGCTGCATTCCTATCCGA 57.292 45.000 1.84 0.00 0.00 4.55
6440 15970 2.245159 TTGCTGCATTCCTATCCGAG 57.755 50.000 1.84 0.00 0.00 4.63
6441 15971 1.123077 TGCTGCATTCCTATCCGAGT 58.877 50.000 0.00 0.00 0.00 4.18
6443 15973 1.869767 GCTGCATTCCTATCCGAGTTG 59.130 52.381 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 3870 2.092291 GCATTGTCTTCGTCGCCGA 61.092 57.895 0.00 0.00 42.41 5.54
189 4016 0.605589 TCGCACGTCTCTTCCTCTCA 60.606 55.000 0.00 0.00 0.00 3.27
298 4150 4.947147 AAGGCAAAGTCGGCGGCA 62.947 61.111 16.23 0.00 36.37 5.69
306 4158 2.985847 GGCGAGGCAAGGCAAAGT 60.986 61.111 0.00 0.00 0.00 2.66
434 4292 0.114560 TTCTCCTCCTTCCCTGTCGT 59.885 55.000 0.00 0.00 0.00 4.34
879 4786 1.764054 CCTCTCCCGGCTCCTCAAT 60.764 63.158 0.00 0.00 0.00 2.57
880 4787 2.364317 CCTCTCCCGGCTCCTCAA 60.364 66.667 0.00 0.00 0.00 3.02
921 4828 1.696336 AGACATCGGCATCTGGCTTAT 59.304 47.619 2.10 0.00 44.01 1.73
922 4829 1.123077 AGACATCGGCATCTGGCTTA 58.877 50.000 2.10 0.00 44.01 3.09
923 4830 0.254178 AAGACATCGGCATCTGGCTT 59.746 50.000 2.10 0.00 44.01 4.35
924 4831 0.254178 AAAGACATCGGCATCTGGCT 59.746 50.000 2.10 0.00 44.01 4.75
925 4832 0.659957 GAAAGACATCGGCATCTGGC 59.340 55.000 0.00 0.00 43.74 4.85
926 4833 0.933097 CGAAAGACATCGGCATCTGG 59.067 55.000 0.00 0.00 39.12 3.86
927 4834 1.645034 ACGAAAGACATCGGCATCTG 58.355 50.000 1.59 0.00 46.82 2.90
928 4835 2.002586 CAACGAAAGACATCGGCATCT 58.997 47.619 1.59 0.00 46.82 2.90
929 4836 1.999735 TCAACGAAAGACATCGGCATC 59.000 47.619 1.59 0.00 46.82 3.91
930 4837 2.002586 CTCAACGAAAGACATCGGCAT 58.997 47.619 1.59 0.00 46.82 4.40
931 4838 1.428448 CTCAACGAAAGACATCGGCA 58.572 50.000 1.59 0.00 46.82 5.69
932 4839 0.721718 CCTCAACGAAAGACATCGGC 59.278 55.000 1.59 0.00 46.82 5.54
933 4840 2.363788 TCCTCAACGAAAGACATCGG 57.636 50.000 1.59 0.00 46.82 4.18
957 4864 3.707611 GGGTAGGGTTTGGTGTTCTTTTT 59.292 43.478 0.00 0.00 0.00 1.94
958 4865 3.302161 GGGTAGGGTTTGGTGTTCTTTT 58.698 45.455 0.00 0.00 0.00 2.27
959 4866 2.245287 TGGGTAGGGTTTGGTGTTCTTT 59.755 45.455 0.00 0.00 0.00 2.52
960 4867 1.854280 TGGGTAGGGTTTGGTGTTCTT 59.146 47.619 0.00 0.00 0.00 2.52
961 4868 1.144298 GTGGGTAGGGTTTGGTGTTCT 59.856 52.381 0.00 0.00 0.00 3.01
962 4869 1.612676 GTGGGTAGGGTTTGGTGTTC 58.387 55.000 0.00 0.00 0.00 3.18
963 4870 0.186630 GGTGGGTAGGGTTTGGTGTT 59.813 55.000 0.00 0.00 0.00 3.32
964 4871 1.722110 GGGTGGGTAGGGTTTGGTGT 61.722 60.000 0.00 0.00 0.00 4.16
965 4872 1.076014 GGGTGGGTAGGGTTTGGTG 59.924 63.158 0.00 0.00 0.00 4.17
966 4873 2.531601 CGGGTGGGTAGGGTTTGGT 61.532 63.158 0.00 0.00 0.00 3.67
1262 5173 4.451150 TGGAGGACGATGTGGCGC 62.451 66.667 0.00 0.00 33.86 6.53
1375 5292 0.969917 ATCTCGAGCTGCTGGTCAGT 60.970 55.000 20.64 2.76 44.66 3.41
1499 5416 0.105224 CTCCATCCTCAGCTGCTCTG 59.895 60.000 9.47 3.71 44.21 3.35
1511 5428 2.680370 GGGACCACCACCTCCATCC 61.680 68.421 0.00 0.00 39.85 3.51
1513 5430 3.009115 CGGGACCACCACCTCCAT 61.009 66.667 0.00 0.00 40.22 3.41
1575 5492 4.032452 TGCAGCAGAATCCCGGCA 62.032 61.111 0.00 0.00 38.49 5.69
1803 5751 3.257393 CAAGGTTCTGATGTTCTCCTCG 58.743 50.000 0.00 0.00 0.00 4.63
1888 5836 2.005451 CTGCATATCATCCCGCTTAGC 58.995 52.381 0.00 0.00 0.00 3.09
1890 5838 1.672737 CGCTGCATATCATCCCGCTTA 60.673 52.381 0.00 0.00 0.00 3.09
1974 5922 0.107268 TGTCATCGGCATCAGATGGG 59.893 55.000 12.54 0.00 44.04 4.00
2019 5973 3.274095 ACATAGCCAGGCTTCTTCTTC 57.726 47.619 22.26 0.00 40.44 2.87
2127 6081 1.303309 GGGCATTCTCATCTGGAACG 58.697 55.000 0.00 0.00 0.00 3.95
2233 6187 0.955428 TCTGCACCAACGAATCCTGC 60.955 55.000 0.00 0.00 0.00 4.85
2386 6346 7.483580 AGTCATCCATAGTTATACTTAGGCC 57.516 40.000 0.00 0.00 0.00 5.19
2431 6391 4.998033 GCTAGGGATGTAGATGTAAAAGGC 59.002 45.833 0.00 0.00 0.00 4.35
2442 6402 6.094325 CGTAAGGATTCTAGCTAGGGATGTAG 59.906 46.154 20.58 0.00 0.00 2.74
2723 6709 5.642063 CCTTTAGCGATTGAAGTAACAAGGA 59.358 40.000 0.00 0.00 33.22 3.36
2803 6789 0.700564 AAGCCCATGTGACATCAGGT 59.299 50.000 11.59 2.35 0.00 4.00
3007 7026 0.814010 AATAAGCGCCACGGATGTCC 60.814 55.000 2.29 0.00 0.00 4.02
3033 7052 8.406172 TGTTAAAGAGATTGCTTGAAAACAAC 57.594 30.769 0.00 0.00 30.04 3.32
3243 7313 3.779444 TGGAAGGAGTGTACTGACTGAT 58.221 45.455 0.00 0.00 0.00 2.90
3327 7408 6.639212 CAATCAATTCCGTTTTTGACTGTTG 58.361 36.000 0.00 0.00 34.87 3.33
3505 9083 0.039256 GCTGATGTCGCAAAGGCAAA 60.039 50.000 0.00 0.00 38.34 3.68
3679 9263 1.174783 GTGTCGAGAGTAGCAAGGGA 58.825 55.000 0.00 0.00 0.00 4.20
3738 9330 4.697352 AGAACCAAGATTCCGAATCAACAG 59.303 41.667 20.71 10.22 40.42 3.16
3761 9388 1.808531 GCTTCATGCACTGGCCAACA 61.809 55.000 7.01 6.00 42.31 3.33
3919 9720 2.422127 CGGTAATGCCAAAACTACCCTG 59.578 50.000 0.00 0.00 36.97 4.45
4281 10089 2.676342 CCGAACGGAGGGAATACAAAAG 59.324 50.000 7.53 0.00 37.50 2.27
4456 10311 6.660521 ACATATGATGAGAAAAGCACCTTCAA 59.339 34.615 10.38 0.00 0.00 2.69
4588 10450 5.945155 TCTCGGTATTTTGCCAAACATAAC 58.055 37.500 0.00 0.00 0.00 1.89
4645 10529 7.268586 ACTGCGATCAGAACAAGTAGAATAAT 58.731 34.615 0.00 0.00 42.95 1.28
4824 10717 5.855925 CGTAGAAGAGCATCATCTATCACAC 59.144 44.000 0.00 0.00 45.74 3.82
4952 10845 2.241160 TGCATCCAAATCAACAGTGCT 58.759 42.857 0.00 0.00 32.67 4.40
5083 10981 9.582431 CATGCTTCATCACAAAGAATTAAAGAT 57.418 29.630 0.00 0.00 0.00 2.40
5153 11051 0.107654 GGCTGCTTCGTCCACCTAAT 60.108 55.000 0.00 0.00 0.00 1.73
5232 11131 5.101628 TCAATCAAAGCAACTGAACACAAC 58.898 37.500 0.00 0.00 0.00 3.32
5249 11148 5.123661 TGCTCAAAGTGCGATAATTCAATCA 59.876 36.000 0.00 0.00 0.00 2.57
5295 11194 0.529378 GTACCTGTTCCGACACCGAT 59.471 55.000 0.00 0.00 38.22 4.18
5456 12468 2.019249 CAAGGCACCCAGATACATGTG 58.981 52.381 9.11 0.00 0.00 3.21
5457 12469 1.064463 CCAAGGCACCCAGATACATGT 60.064 52.381 2.69 2.69 0.00 3.21
5575 12589 2.029110 ACAAAGGTGCATTCGGAAATGG 60.029 45.455 0.00 0.00 42.18 3.16
5599 12613 2.949177 AATATCCTTGCATACCCGCA 57.051 45.000 0.00 0.00 41.03 5.69
5622 12636 5.917541 TCTGACGTTAGACCATTGAAAAC 57.082 39.130 5.85 0.00 0.00 2.43
5639 12653 6.159988 CCTCCCTTTTATGATCGTATCTGAC 58.840 44.000 0.00 0.00 0.00 3.51
5640 12654 5.839063 ACCTCCCTTTTATGATCGTATCTGA 59.161 40.000 0.00 0.00 0.00 3.27
5641 12655 6.102897 ACCTCCCTTTTATGATCGTATCTG 57.897 41.667 0.00 0.00 0.00 2.90
5642 12656 5.246429 GGACCTCCCTTTTATGATCGTATCT 59.754 44.000 0.00 0.00 0.00 1.98
5710 12728 9.545611 GCAAAAACATTATCATTTTGTGGAATC 57.454 29.630 10.70 0.00 42.89 2.52
5729 12748 4.122046 AGGCTTCTGTTTCATGCAAAAAC 58.878 39.130 16.92 16.92 37.18 2.43
5744 12763 9.252635 AGATTCAATTATTTTGAGAAGGCTTCT 57.747 29.630 28.94 28.94 44.21 2.85
5762 12782 6.165700 AGCACAAAGGTTTGAAGATTCAAT 57.834 33.333 9.42 0.00 45.65 2.57
5764 12784 5.592282 TGTAGCACAAAGGTTTGAAGATTCA 59.408 36.000 9.42 2.34 40.55 2.57
5765 12785 6.072112 TGTAGCACAAAGGTTTGAAGATTC 57.928 37.500 9.42 0.05 40.55 2.52
5822 12870 6.290605 TGTCATATGATCACATCCGACAATT 58.709 36.000 9.02 0.00 40.98 2.32
5828 12876 5.052481 AGTGTTGTCATATGATCACATCCG 58.948 41.667 25.55 0.00 37.87 4.18
5843 12891 7.672983 TGAGATCCAATTCTTTAGTGTTGTC 57.327 36.000 0.00 0.00 0.00 3.18
5844 12892 7.884877 TCATGAGATCCAATTCTTTAGTGTTGT 59.115 33.333 0.00 0.00 0.00 3.32
5856 12904 9.032624 ACTTCAAAAATCTCATGAGATCCAATT 57.967 29.630 33.00 22.36 46.75 2.32
5859 12907 9.519191 TTAACTTCAAAAATCTCATGAGATCCA 57.481 29.630 33.00 15.61 46.75 3.41
5865 12913 7.667219 AGGAGCTTAACTTCAAAAATCTCATGA 59.333 33.333 0.00 0.00 0.00 3.07
5869 12917 7.592903 CACAAGGAGCTTAACTTCAAAAATCTC 59.407 37.037 0.00 0.00 0.00 2.75
5873 12921 6.524101 ACACAAGGAGCTTAACTTCAAAAA 57.476 33.333 0.00 0.00 0.00 1.94
5876 12924 4.947388 ACAACACAAGGAGCTTAACTTCAA 59.053 37.500 0.00 0.00 0.00 2.69
5911 14400 7.494952 AGCGGACTTTATGAAGGTAGAATAAAC 59.505 37.037 1.95 0.00 37.19 2.01
5915 14404 5.128827 TGAGCGGACTTTATGAAGGTAGAAT 59.871 40.000 1.95 0.00 37.19 2.40
5916 14405 4.464951 TGAGCGGACTTTATGAAGGTAGAA 59.535 41.667 1.95 0.00 37.19 2.10
5917 14406 4.021229 TGAGCGGACTTTATGAAGGTAGA 58.979 43.478 1.95 0.00 37.19 2.59
5918 14407 4.386867 TGAGCGGACTTTATGAAGGTAG 57.613 45.455 1.95 0.00 37.19 3.18
5951 14440 7.965107 GGAATGAGCGGACATTTTATCATATTC 59.035 37.037 7.87 0.00 40.03 1.75
5954 14443 6.204688 GTGGAATGAGCGGACATTTTATCATA 59.795 38.462 7.87 0.00 40.03 2.15
5956 14445 4.335315 GTGGAATGAGCGGACATTTTATCA 59.665 41.667 7.87 0.00 40.03 2.15
5957 14446 4.335315 TGTGGAATGAGCGGACATTTTATC 59.665 41.667 7.87 0.00 40.03 1.75
5958 14447 4.269183 TGTGGAATGAGCGGACATTTTAT 58.731 39.130 7.87 0.00 40.03 1.40
5959 14448 3.680490 TGTGGAATGAGCGGACATTTTA 58.320 40.909 7.87 0.40 40.03 1.52
5960 14449 2.513753 TGTGGAATGAGCGGACATTTT 58.486 42.857 7.87 0.00 40.03 1.82
5962 14451 2.198827 TTGTGGAATGAGCGGACATT 57.801 45.000 6.54 6.54 42.19 2.71
5963 14452 2.198827 TTTGTGGAATGAGCGGACAT 57.801 45.000 0.00 0.00 0.00 3.06
5964 14453 1.974265 TTTTGTGGAATGAGCGGACA 58.026 45.000 0.00 0.00 0.00 4.02
5965 14454 2.552315 TCTTTTTGTGGAATGAGCGGAC 59.448 45.455 0.00 0.00 0.00 4.79
5966 14455 2.857483 TCTTTTTGTGGAATGAGCGGA 58.143 42.857 0.00 0.00 0.00 5.54
5967 14456 3.641437 TTCTTTTTGTGGAATGAGCGG 57.359 42.857 0.00 0.00 0.00 5.52
5968 14457 6.554419 TCATATTCTTTTTGTGGAATGAGCG 58.446 36.000 0.00 0.00 34.52 5.03
5978 14467 9.853555 TGCGACATTTTATCATATTCTTTTTGT 57.146 25.926 0.00 0.00 0.00 2.83
5984 14473 9.669353 GTTTGATGCGACATTTTATCATATTCT 57.331 29.630 0.00 0.00 30.45 2.40
5985 14474 9.669353 AGTTTGATGCGACATTTTATCATATTC 57.331 29.630 0.00 0.00 30.45 1.75
5986 14475 9.454585 CAGTTTGATGCGACATTTTATCATATT 57.545 29.630 0.00 0.00 30.45 1.28
5987 14476 8.077991 CCAGTTTGATGCGACATTTTATCATAT 58.922 33.333 0.00 0.00 30.45 1.78
5988 14477 7.416817 CCAGTTTGATGCGACATTTTATCATA 58.583 34.615 0.00 0.00 30.45 2.15
6001 14490 1.526575 AAGGGTGCCAGTTTGATGCG 61.527 55.000 0.00 0.00 0.00 4.73
6010 14499 6.966534 AGATTATTTTGATAAGGGTGCCAG 57.033 37.500 0.00 0.00 0.00 4.85
6033 14524 8.884124 ATTGGAGGATTTCTTGAACAAGATTA 57.116 30.769 16.29 9.37 45.78 1.75
6098 14793 9.182933 GAGTGATAATTTTCTATGTCGTAGGTC 57.817 37.037 0.00 0.00 0.00 3.85
6111 14806 7.359514 GCACCAAAAGCTTGAGTGATAATTTTC 60.360 37.037 21.54 4.03 36.56 2.29
6112 14807 6.424812 GCACCAAAAGCTTGAGTGATAATTTT 59.575 34.615 21.54 0.00 36.56 1.82
6113 14808 5.928264 GCACCAAAAGCTTGAGTGATAATTT 59.072 36.000 21.54 0.00 36.56 1.82
6129 15080 3.023119 TCTGCTGAAAAGAGCACCAAAA 58.977 40.909 0.00 0.00 44.16 2.44
6164 15183 1.838396 TGTCTGCACTCTCCAGGCA 60.838 57.895 0.00 0.00 42.15 4.75
6221 15243 5.103813 TGGACCATGAGGATGATTTGAGATT 60.104 40.000 0.00 0.00 38.69 2.40
6222 15244 4.414514 TGGACCATGAGGATGATTTGAGAT 59.585 41.667 0.00 0.00 38.69 2.75
6223 15245 3.781965 TGGACCATGAGGATGATTTGAGA 59.218 43.478 0.00 0.00 38.69 3.27
6224 15246 4.160642 TGGACCATGAGGATGATTTGAG 57.839 45.455 0.00 0.00 38.69 3.02
6225 15247 4.166531 TCATGGACCATGAGGATGATTTGA 59.833 41.667 29.67 7.43 44.60 2.69
6226 15248 4.466827 TCATGGACCATGAGGATGATTTG 58.533 43.478 29.67 5.08 44.60 2.32
6227 15249 4.801521 TCATGGACCATGAGGATGATTT 57.198 40.909 29.67 0.00 44.60 2.17
6264 15296 5.007136 GTGCAAGCACAAGGATTACTCTATC 59.993 44.000 19.47 0.00 45.53 2.08
6284 15567 8.352942 CACTAGTATATCATTAGTCAGTGTGCA 58.647 37.037 0.00 0.00 27.70 4.57
6323 15612 5.416271 ACTATCGTGTTTTAGATGTGGGT 57.584 39.130 0.00 0.00 0.00 4.51
6345 15634 9.212641 GCAAAATTAGATGTGAGAGCTATCATA 57.787 33.333 15.19 12.67 0.00 2.15
6356 15645 6.189859 AGGAATGGAGCAAAATTAGATGTGA 58.810 36.000 0.00 0.00 0.00 3.58
6366 15655 6.165577 GCAAAATTAGAGGAATGGAGCAAAA 58.834 36.000 0.00 0.00 0.00 2.44
6378 15667 5.640357 TGTACCAGTTACGCAAAATTAGAGG 59.360 40.000 0.00 0.00 32.71 3.69
6398 15928 6.743575 AATTAGAGGCATGTCAGTTTGTAC 57.256 37.500 0.00 0.00 0.00 2.90
6406 15936 2.424601 GCAGCAAATTAGAGGCATGTCA 59.575 45.455 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.