Multiple sequence alignment - TraesCS5A01G254000

Loading Multiple Alignment...

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 TraesCS5A01G254000 chr5A 100.000 5113 0 0 1 5113 470032009 470037121 0.000000e+00 9443.0
1 TraesCS5A01G254000 chr5A 85.932 1315 174 5 932 2242 469898822 469900129 0.000000e+00 1393.0
2 TraesCS5A01G254000 chr5A 85.097 1295 175 6 951 2242 469906301 469907580 0.000000e+00 1306.0
3 TraesCS5A01G254000 chr5A 85.250 861 101 12 2738 3587 477377303 477378148 0.000000e+00 863.0
4 TraesCS5A01G254000 chr5A 82.139 879 108 26 3768 4621 477378340 477379194 0.000000e+00 708.0
5 TraesCS5A01G254000 chr5A 84.507 142 15 5 4254 4392 470047360 470047497 3.210000e-27 134.0
6 TraesCS5A01G254000 chr5D 95.767 3591 97 23 40 3598 367980287 367983854 0.000000e+00 5738.0
7 TraesCS5A01G254000 chr5D 86.400 1375 179 5 1020 2389 367996719 367998090 0.000000e+00 1496.0
8 TraesCS5A01G254000 chr5D 96.497 885 25 4 3605 4485 367983913 367984795 0.000000e+00 1458.0
9 TraesCS5A01G254000 chr5D 85.964 1318 174 6 932 2242 367812188 367813501 0.000000e+00 1399.0
10 TraesCS5A01G254000 chr5D 86.374 866 97 9 2727 3587 376353663 376354512 0.000000e+00 926.0
11 TraesCS5A01G254000 chr5D 82.653 882 108 27 3768 4627 376354704 376355562 0.000000e+00 739.0
12 TraesCS5A01G254000 chr5D 91.016 256 13 4 4859 5112 367986292 367986539 2.280000e-88 337.0
13 TraesCS5A01G254000 chr5D 94.737 133 4 1 4735 4867 367984815 367984944 2.410000e-48 204.0
14 TraesCS5A01G254000 chr5D 86.290 124 13 3 3640 3760 367998863 367998985 1.160000e-26 132.0
15 TraesCS5A01G254000 chr5D 84.028 144 14 7 4254 4392 367999579 367999718 4.150000e-26 130.0
16 TraesCS5A01G254000 chr5B 94.203 3088 113 25 58 3113 435942154 435945207 0.000000e+00 4650.0
17 TraesCS5A01G254000 chr5B 95.191 1123 41 7 3605 4717 435945819 435946938 0.000000e+00 1762.0
18 TraesCS5A01G254000 chr5B 83.889 1589 244 11 998 2579 436078297 436079880 0.000000e+00 1506.0
19 TraesCS5A01G254000 chr5B 83.468 1603 242 12 993 2579 435949610 435951205 0.000000e+00 1471.0
20 TraesCS5A01G254000 chr5B 85.769 1314 178 3 932 2242 435770550 435771857 0.000000e+00 1382.0
21 TraesCS5A01G254000 chr5B 97.452 471 11 1 3096 3566 435945266 435945735 0.000000e+00 802.0
22 TraesCS5A01G254000 chr5B 89.815 216 17 2 4883 5098 435948214 435948424 6.520000e-69 272.0
23 TraesCS5A01G254000 chr5B 91.892 111 4 3 4778 4886 435947953 435948060 3.190000e-32 150.0
24 TraesCS5A01G254000 chr5B 98.305 59 1 0 4724 4782 435947094 435947152 2.520000e-18 104.0
25 TraesCS5A01G254000 chr5B 90.789 76 6 1 3640 3715 435951696 435951770 3.260000e-17 100.0
26 TraesCS5A01G254000 chr5B 100.000 32 0 0 5081 5112 435948441 435948472 5.530000e-05 60.2


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 TraesCS5A01G254000 chr5A 470032009 470037121 5112 False 9443.000000 9443 100.000000 1 5113 1 chr5A.!!$F3 5112
1 TraesCS5A01G254000 chr5A 469898822 469900129 1307 False 1393.000000 1393 85.932000 932 2242 1 chr5A.!!$F1 1310
2 TraesCS5A01G254000 chr5A 469906301 469907580 1279 False 1306.000000 1306 85.097000 951 2242 1 chr5A.!!$F2 1291
3 TraesCS5A01G254000 chr5A 477377303 477379194 1891 False 785.500000 863 83.694500 2738 4621 2 chr5A.!!$F5 1883
4 TraesCS5A01G254000 chr5D 367980287 367986539 6252 False 1934.250000 5738 94.504250 40 5112 4 chr5D.!!$F2 5072
5 TraesCS5A01G254000 chr5D 367812188 367813501 1313 False 1399.000000 1399 85.964000 932 2242 1 chr5D.!!$F1 1310
6 TraesCS5A01G254000 chr5D 376353663 376355562 1899 False 832.500000 926 84.513500 2727 4627 2 chr5D.!!$F4 1900
7 TraesCS5A01G254000 chr5D 367996719 367999718 2999 False 586.000000 1496 85.572667 1020 4392 3 chr5D.!!$F3 3372
8 TraesCS5A01G254000 chr5B 436078297 436079880 1583 False 1506.000000 1506 83.889000 998 2579 1 chr5B.!!$F2 1581
9 TraesCS5A01G254000 chr5B 435770550 435771857 1307 False 1382.000000 1382 85.769000 932 2242 1 chr5B.!!$F1 1310
10 TraesCS5A01G254000 chr5B 435942154 435951770 9616 False 1041.244444 4650 93.457222 58 5112 9 chr5B.!!$F3 5054

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
32 33 0.179067 CTAACGGGCGCCAAATAGGA 60.179 55.000 30.85 5.04 41.22 2.94 F
33 34 0.252479 TAACGGGCGCCAAATAGGAA 59.748 50.000 30.85 1.22 41.22 3.36 F
935 975 0.313672 TTTTTGCGGGACTGCATCAC 59.686 50.000 6.65 0.00 45.78 3.06 F
974 1014 0.588252 CAGAGTGGTTTGGCAGTTCG 59.412 55.000 0.00 0.00 0.00 3.95 F
1032 1072 1.211190 GCCCGAAGCAAAGAAGCAG 59.789 57.895 0.00 0.00 42.97 4.24 F
3411 10142 1.209128 CGTGCACTTAATCTAGCGGG 58.791 55.000 16.19 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1101 1141 1.014352 ACGTCAACAAAGTGCTCACC 58.986 50.000 0.00 0.0 0.00 4.02 R
2164 8759 6.279882 GCACAATGCCAGCCTTTTTATATAA 58.720 36.000 0.00 0.0 37.42 0.98 R
2885 9584 2.878406 TGAGCCCTTTCTTTCAGTTTCG 59.122 45.455 0.00 0.0 0.00 3.46 R
3409 10140 8.458573 TCCATACAATGTAAAATATGTGACCC 57.541 34.615 0.00 0.0 0.00 4.46 R
3601 10339 2.028748 GCAACTACTCCCTCCGTTTACA 60.029 50.000 0.00 0.0 0.00 2.41 R
4957 13288 0.249826 AAGGTTGGTTTTGCATGCCG 60.250 50.000 16.68 0.0 0.00 5.69 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
20 21 2.088423 TGCAAAATGCCTACTAACGGG 58.912 47.619 0.00 0.00 44.23 5.28
21 22 3.775331 TGCAAAATGCCTACTAACGGGC 61.775 50.000 0.00 0.00 44.23 6.13
25 26 4.151582 GCCTACTAACGGGCGCCA 62.152 66.667 30.85 6.35 38.91 5.69
26 27 2.580276 CCTACTAACGGGCGCCAA 59.420 61.111 30.85 9.42 0.00 4.52
27 28 1.078988 CCTACTAACGGGCGCCAAA 60.079 57.895 30.85 9.02 0.00 3.28
28 29 0.463116 CCTACTAACGGGCGCCAAAT 60.463 55.000 30.85 15.64 0.00 2.32
29 30 1.202557 CCTACTAACGGGCGCCAAATA 60.203 52.381 30.85 15.95 0.00 1.40
30 31 2.132762 CTACTAACGGGCGCCAAATAG 58.867 52.381 30.85 25.75 0.00 1.73
31 32 0.463116 ACTAACGGGCGCCAAATAGG 60.463 55.000 30.85 15.31 41.84 2.57
32 33 0.179067 CTAACGGGCGCCAAATAGGA 60.179 55.000 30.85 5.04 41.22 2.94
33 34 0.252479 TAACGGGCGCCAAATAGGAA 59.748 50.000 30.85 1.22 41.22 3.36
34 35 0.609681 AACGGGCGCCAAATAGGAAA 60.610 50.000 30.85 0.00 41.22 3.13
35 36 1.310216 ACGGGCGCCAAATAGGAAAC 61.310 55.000 30.85 5.23 41.22 2.78
36 37 1.431845 GGGCGCCAAATAGGAAACG 59.568 57.895 30.85 0.00 41.22 3.60
37 38 1.226575 GGCGCCAAATAGGAAACGC 60.227 57.895 24.80 0.00 43.11 4.84
38 39 1.226575 GCGCCAAATAGGAAACGCC 60.227 57.895 0.00 0.00 39.54 5.68
43 44 1.102978 CAAATAGGAAACGCCCCCTG 58.897 55.000 0.00 0.00 37.37 4.45
53 54 2.690510 GCCCCCTGCTCTTCCTCT 60.691 66.667 0.00 0.00 36.87 3.69
145 150 9.601217 CACTACTCTACCATATAATTAATGCCC 57.399 37.037 0.00 0.00 0.00 5.36
146 151 8.769359 ACTACTCTACCATATAATTAATGCCCC 58.231 37.037 0.00 0.00 0.00 5.80
148 153 8.232098 ACTCTACCATATAATTAATGCCCCTT 57.768 34.615 0.00 0.00 0.00 3.95
150 155 8.463055 TCTACCATATAATTAATGCCCCTTCT 57.537 34.615 0.00 0.00 0.00 2.85
151 156 8.900802 TCTACCATATAATTAATGCCCCTTCTT 58.099 33.333 0.00 0.00 0.00 2.52
152 157 9.178758 CTACCATATAATTAATGCCCCTTCTTC 57.821 37.037 0.00 0.00 0.00 2.87
153 158 6.954102 ACCATATAATTAATGCCCCTTCTTCC 59.046 38.462 0.00 0.00 0.00 3.46
154 159 6.381133 CCATATAATTAATGCCCCTTCTTCCC 59.619 42.308 0.00 0.00 0.00 3.97
155 160 5.686535 ATAATTAATGCCCCTTCTTCCCT 57.313 39.130 0.00 0.00 0.00 4.20
160 165 1.715785 TGCCCCTTCTTCCCTTTTTG 58.284 50.000 0.00 0.00 0.00 2.44
238 248 0.811616 CGCTAAAGGCAGCCGAGAAT 60.812 55.000 5.55 0.00 41.91 2.40
374 398 3.027170 GCGCCCGTGATTGTGAGTG 62.027 63.158 0.00 0.00 0.00 3.51
392 416 2.283966 CTCCACTCCCCTCCGTGT 60.284 66.667 0.00 0.00 0.00 4.49
399 423 0.905337 CTCCCCTCCGTGTCCTCTTT 60.905 60.000 0.00 0.00 0.00 2.52
401 425 0.321653 CCCCTCCGTGTCCTCTTTTG 60.322 60.000 0.00 0.00 0.00 2.44
402 426 0.955919 CCCTCCGTGTCCTCTTTTGC 60.956 60.000 0.00 0.00 0.00 3.68
430 454 1.079057 GGCTGTTTCCTCCTCCGAC 60.079 63.158 0.00 0.00 0.00 4.79
431 455 1.446272 GCTGTTTCCTCCTCCGACG 60.446 63.158 0.00 0.00 0.00 5.12
432 456 1.874345 GCTGTTTCCTCCTCCGACGA 61.874 60.000 0.00 0.00 0.00 4.20
545 569 1.728490 GGGAGGGCGCATGATTGTTC 61.728 60.000 10.83 0.00 0.00 3.18
556 581 4.186159 GCATGATTGTTCCTTGGATTTGG 58.814 43.478 0.00 0.00 0.00 3.28
643 680 4.096382 ACCGCAAGATTATGCTTTTGGTAG 59.904 41.667 0.00 0.00 44.21 3.18
687 724 4.387862 TGGAGACGAAAGAAGCGAATTTAC 59.612 41.667 0.00 0.00 0.00 2.01
724 761 2.253758 GGACGCTGCAACAGAGCAA 61.254 57.895 0.00 0.00 45.13 3.91
750 787 5.664294 TTTTTAGATGCCGTCAGTACCTA 57.336 39.130 0.00 0.00 0.00 3.08
752 789 1.400737 AGATGCCGTCAGTACCTACC 58.599 55.000 0.00 0.00 0.00 3.18
836 876 4.229876 GTTTCATCTTCTTTCTTTGCCGG 58.770 43.478 0.00 0.00 0.00 6.13
855 895 6.402222 TGCCGGCAAAATAATTTTAATGACT 58.598 32.000 30.74 0.00 0.00 3.41
857 897 6.704819 CCGGCAAAATAATTTTAATGACTGC 58.295 36.000 0.00 0.00 0.00 4.40
917 957 7.338800 CAGTATGCCCTGTATCATTTTTCTT 57.661 36.000 0.00 0.00 0.00 2.52
935 975 0.313672 TTTTTGCGGGACTGCATCAC 59.686 50.000 6.65 0.00 45.78 3.06
949 989 4.142315 ACTGCATCACTAATTGGAATGTGC 60.142 41.667 0.00 1.58 0.00 4.57
968 1008 0.594796 CGTTTGCAGAGTGGTTTGGC 60.595 55.000 0.00 0.00 0.00 4.52
974 1014 0.588252 CAGAGTGGTTTGGCAGTTCG 59.412 55.000 0.00 0.00 0.00 3.95
1032 1072 1.211190 GCCCGAAGCAAAGAAGCAG 59.789 57.895 0.00 0.00 42.97 4.24
2083 8678 5.240891 TCGAGATTGATTTGAGCAAGAAGT 58.759 37.500 0.00 0.00 0.00 3.01
2308 8903 5.505173 ACATGAGCATGCCTTATTTGTAC 57.495 39.130 15.66 0.00 42.39 2.90
2339 8934 6.381801 CAAACTGTTATTAGCCTTCAACCTG 58.618 40.000 0.00 0.00 0.00 4.00
2363 8958 8.378115 TGGATGAATGTTCCTTATTTTGGAAT 57.622 30.769 0.00 0.00 44.27 3.01
2595 9282 4.743057 AAAAAGATCCATAAGGCAAGGC 57.257 40.909 0.00 0.00 33.74 4.35
2596 9283 3.386932 AAAGATCCATAAGGCAAGGCA 57.613 42.857 0.00 0.00 33.74 4.75
2651 9348 1.466856 TGCATCTTGATGCCTTGACC 58.533 50.000 26.48 4.65 46.43 4.02
2749 9446 4.004314 CCGGACATACATTACAACCAACA 58.996 43.478 0.00 0.00 0.00 3.33
2801 9498 4.428615 AGTGCGTTAACAAGTGTTTTGT 57.571 36.364 6.39 0.00 39.31 2.83
2885 9584 1.244019 AAGTTGATGGCCCGTTCAGC 61.244 55.000 0.00 3.09 0.00 4.26
3409 10140 1.588404 CACCGTGCACTTAATCTAGCG 59.412 52.381 16.19 0.00 0.00 4.26
3411 10142 1.209128 CGTGCACTTAATCTAGCGGG 58.791 55.000 16.19 0.00 0.00 6.13
3427 10158 6.588204 TCTAGCGGGTCACATATTTTACATT 58.412 36.000 0.00 0.00 0.00 2.71
3598 10336 5.337652 GCCTTGTCTAGTACTCACTCCATTT 60.338 44.000 0.00 0.00 36.14 2.32
3599 10337 6.702329 CCTTGTCTAGTACTCACTCCATTTT 58.298 40.000 0.00 0.00 36.14 1.82
3600 10338 6.814146 CCTTGTCTAGTACTCACTCCATTTTC 59.186 42.308 0.00 0.00 36.14 2.29
3601 10339 7.310113 CCTTGTCTAGTACTCACTCCATTTTCT 60.310 40.741 0.00 0.00 36.14 2.52
3602 10340 6.925211 TGTCTAGTACTCACTCCATTTTCTG 58.075 40.000 0.00 0.00 36.14 3.02
3603 10341 6.493802 TGTCTAGTACTCACTCCATTTTCTGT 59.506 38.462 0.00 0.00 36.14 3.41
3607 10397 7.964604 AGTACTCACTCCATTTTCTGTAAAC 57.035 36.000 0.00 0.00 0.00 2.01
3615 10405 3.689649 CCATTTTCTGTAAACGGAGGGAG 59.310 47.826 0.00 0.00 32.05 4.30
3995 10947 2.672961 TGGGATGAAGTAGCGAACAG 57.327 50.000 0.00 0.00 0.00 3.16
4027 10982 9.822185 TGTATTTGATATCCTGATCCATATTCG 57.178 33.333 0.00 0.00 0.00 3.34
4047 11002 3.013921 CGCTTTTGGCAGGGTAAATCTA 58.986 45.455 0.00 0.00 41.91 1.98
4085 11043 1.281867 TCTTCCATTGCCCGTCTTGAT 59.718 47.619 0.00 0.00 0.00 2.57
4268 11228 0.174389 TCTCGCTCCATCAGTTGCTC 59.826 55.000 0.00 0.00 0.00 4.26
4486 11449 5.228665 AGTTCTCACGATATGCATCTGATG 58.771 41.667 13.26 13.26 0.00 3.07
4492 11455 4.271776 CACGATATGCATCTGATGTTGTGT 59.728 41.667 18.19 7.75 0.00 3.72
4493 11456 4.271776 ACGATATGCATCTGATGTTGTGTG 59.728 41.667 18.19 8.12 0.00 3.82
4495 11458 2.565046 TGCATCTGATGTTGTGTGGA 57.435 45.000 18.19 0.00 0.00 4.02
4496 11459 2.153645 TGCATCTGATGTTGTGTGGAC 58.846 47.619 18.19 0.10 0.00 4.02
4497 11460 2.224597 TGCATCTGATGTTGTGTGGACT 60.225 45.455 18.19 0.00 0.00 3.85
4498 11461 3.007831 TGCATCTGATGTTGTGTGGACTA 59.992 43.478 18.19 0.00 0.00 2.59
4500 11463 4.637534 GCATCTGATGTTGTGTGGACTAAT 59.362 41.667 18.19 0.00 0.00 1.73
4509 11472 3.146066 TGTGTGGACTAATCTGCCAAAC 58.854 45.455 0.00 0.00 39.79 2.93
4511 11474 3.189287 GTGTGGACTAATCTGCCAAACTG 59.811 47.826 0.00 0.00 37.04 3.16
4513 11476 3.437049 GTGGACTAATCTGCCAAACTGTC 59.563 47.826 0.00 0.00 32.68 3.51
4516 11479 3.935828 GACTAATCTGCCAAACTGTCTCC 59.064 47.826 0.00 0.00 0.00 3.71
4517 11480 2.957402 AATCTGCCAAACTGTCTCCA 57.043 45.000 0.00 0.00 0.00 3.86
4518 11481 2.957402 ATCTGCCAAACTGTCTCCAA 57.043 45.000 0.00 0.00 0.00 3.53
4519 11482 1.967319 TCTGCCAAACTGTCTCCAAC 58.033 50.000 0.00 0.00 0.00 3.77
4521 11484 0.257328 TGCCAAACTGTCTCCAACCA 59.743 50.000 0.00 0.00 0.00 3.67
4524 11499 2.223805 GCCAAACTGTCTCCAACCAAAG 60.224 50.000 0.00 0.00 0.00 2.77
4530 11505 5.048846 ACTGTCTCCAACCAAAGTATGTT 57.951 39.130 0.00 0.00 0.00 2.71
4544 11519 7.440856 ACCAAAGTATGTTTTCGAATGCAAAAT 59.559 29.630 0.00 0.00 0.00 1.82
4545 11520 7.741216 CCAAAGTATGTTTTCGAATGCAAAATG 59.259 33.333 0.00 0.00 0.00 2.32
4548 11523 2.805099 TGTTTTCGAATGCAAAATGGGC 59.195 40.909 0.00 0.00 0.00 5.36
4550 11525 2.367030 TTCGAATGCAAAATGGGCTG 57.633 45.000 0.00 0.00 0.00 4.85
4577 11552 3.257393 GTGCATTAGTGTCCTCTGAGTG 58.743 50.000 3.66 0.00 0.00 3.51
4578 11553 3.056536 GTGCATTAGTGTCCTCTGAGTGA 60.057 47.826 3.66 0.00 0.00 3.41
4579 11554 3.194329 TGCATTAGTGTCCTCTGAGTGAG 59.806 47.826 3.66 0.00 42.30 3.51
4580 11555 3.779759 CATTAGTGTCCTCTGAGTGAGC 58.220 50.000 3.66 0.00 41.35 4.26
4603 11578 1.886542 AGGGCGAAAACATTCTGGAAC 59.113 47.619 0.00 0.00 0.00 3.62
4605 11580 1.265905 GGCGAAAACATTCTGGAACGT 59.734 47.619 0.00 0.00 0.00 3.99
4623 11598 2.159627 ACGTCTGAAGGCTAAAAATGCG 59.840 45.455 0.00 0.00 0.00 4.73
4627 11602 1.615883 TGAAGGCTAAAAATGCGCCAA 59.384 42.857 4.18 0.00 46.14 4.52
4628 11603 1.992667 GAAGGCTAAAAATGCGCCAAC 59.007 47.619 4.18 0.00 46.14 3.77
4629 11604 0.246360 AGGCTAAAAATGCGCCAACC 59.754 50.000 4.18 0.00 46.14 3.77
4630 11605 0.246360 GGCTAAAAATGCGCCAACCT 59.754 50.000 4.18 0.00 43.25 3.50
4631 11606 1.349234 GCTAAAAATGCGCCAACCTG 58.651 50.000 4.18 0.00 0.00 4.00
4632 11607 1.994916 CTAAAAATGCGCCAACCTGG 58.005 50.000 4.18 0.00 41.55 4.45
4633 11608 1.543802 CTAAAAATGCGCCAACCTGGA 59.456 47.619 4.18 0.00 40.96 3.86
4634 11609 0.755686 AAAAATGCGCCAACCTGGAA 59.244 45.000 4.18 0.00 40.96 3.53
4635 11610 0.033366 AAAATGCGCCAACCTGGAAC 59.967 50.000 4.18 0.00 40.96 3.62
4636 11611 2.141122 AAATGCGCCAACCTGGAACG 62.141 55.000 4.18 0.00 40.96 3.95
4637 11612 3.545124 ATGCGCCAACCTGGAACGA 62.545 57.895 4.18 0.00 40.96 3.85
4638 11613 2.975799 GCGCCAACCTGGAACGAA 60.976 61.111 0.00 0.00 40.96 3.85
4639 11614 2.332654 GCGCCAACCTGGAACGAAT 61.333 57.895 0.00 0.00 40.96 3.34
4640 11615 1.501741 CGCCAACCTGGAACGAATG 59.498 57.895 0.00 0.00 40.96 2.67
4641 11616 1.212751 GCCAACCTGGAACGAATGC 59.787 57.895 0.00 0.00 40.96 3.56
4642 11617 1.501741 CCAACCTGGAACGAATGCG 59.498 57.895 0.00 0.00 40.96 4.73
4656 11631 3.940303 CGAATGCGTATTTTGCTAAGCT 58.060 40.909 0.00 0.00 0.00 3.74
4657 11632 4.342772 CGAATGCGTATTTTGCTAAGCTT 58.657 39.130 3.48 3.48 0.00 3.74
4658 11633 4.793216 CGAATGCGTATTTTGCTAAGCTTT 59.207 37.500 3.20 0.00 0.00 3.51
4659 11634 5.286082 CGAATGCGTATTTTGCTAAGCTTTT 59.714 36.000 3.20 0.00 0.00 2.27
4660 11635 6.183359 CGAATGCGTATTTTGCTAAGCTTTTT 60.183 34.615 3.20 0.00 0.00 1.94
4661 11636 6.632171 ATGCGTATTTTGCTAAGCTTTTTC 57.368 33.333 3.20 0.00 0.00 2.29
4662 11637 5.768317 TGCGTATTTTGCTAAGCTTTTTCT 58.232 33.333 3.20 0.00 0.00 2.52
4663 11638 6.212955 TGCGTATTTTGCTAAGCTTTTTCTT 58.787 32.000 3.20 0.00 0.00 2.52
4664 11639 6.699642 TGCGTATTTTGCTAAGCTTTTTCTTT 59.300 30.769 3.20 0.00 0.00 2.52
4665 11640 7.096230 TGCGTATTTTGCTAAGCTTTTTCTTTC 60.096 33.333 3.20 0.00 0.00 2.62
4666 11641 7.114953 GCGTATTTTGCTAAGCTTTTTCTTTCT 59.885 33.333 3.20 0.00 0.00 2.52
4667 11642 8.968242 CGTATTTTGCTAAGCTTTTTCTTTCTT 58.032 29.630 3.20 0.00 0.00 2.52
4670 11645 9.992910 ATTTTGCTAAGCTTTTTCTTTCTTTTG 57.007 25.926 3.20 0.00 0.00 2.44
4671 11646 7.538303 TTGCTAAGCTTTTTCTTTCTTTTGG 57.462 32.000 3.20 0.00 0.00 3.28
4672 11647 6.048509 TGCTAAGCTTTTTCTTTCTTTTGGG 58.951 36.000 3.20 0.00 0.00 4.12
4673 11648 5.050091 GCTAAGCTTTTTCTTTCTTTTGGGC 60.050 40.000 3.20 0.00 0.00 5.36
4674 11649 3.808728 AGCTTTTTCTTTCTTTTGGGCC 58.191 40.909 0.00 0.00 0.00 5.80
4675 11650 2.543848 GCTTTTTCTTTCTTTTGGGCCG 59.456 45.455 0.00 0.00 0.00 6.13
4676 11651 3.739830 GCTTTTTCTTTCTTTTGGGCCGA 60.740 43.478 0.00 0.00 0.00 5.54
4677 11652 3.726291 TTTTCTTTCTTTTGGGCCGAG 57.274 42.857 0.00 0.00 0.00 4.63
4678 11653 2.649531 TTCTTTCTTTTGGGCCGAGA 57.350 45.000 0.00 0.00 0.00 4.04
4679 11654 2.649531 TCTTTCTTTTGGGCCGAGAA 57.350 45.000 11.38 11.38 0.00 2.87
4680 11655 3.154827 TCTTTCTTTTGGGCCGAGAAT 57.845 42.857 14.87 0.00 30.26 2.40
4681 11656 2.819608 TCTTTCTTTTGGGCCGAGAATG 59.180 45.455 14.87 15.98 30.26 2.67
4682 11657 0.887933 TTCTTTTGGGCCGAGAATGC 59.112 50.000 11.38 0.00 0.00 3.56
4690 11665 2.841442 GGCCGAGAATGCCTAGTTAT 57.159 50.000 0.00 0.00 45.70 1.89
4691 11666 2.689646 GGCCGAGAATGCCTAGTTATC 58.310 52.381 0.00 0.00 45.70 1.75
4692 11667 2.329379 GCCGAGAATGCCTAGTTATCG 58.671 52.381 2.57 2.57 39.30 2.92
4693 11668 2.030185 GCCGAGAATGCCTAGTTATCGA 60.030 50.000 9.42 0.00 41.35 3.59
4694 11669 3.827625 CCGAGAATGCCTAGTTATCGAG 58.172 50.000 9.42 0.00 41.35 4.04
4695 11670 3.253677 CCGAGAATGCCTAGTTATCGAGT 59.746 47.826 9.42 0.00 41.35 4.18
4696 11671 4.261656 CCGAGAATGCCTAGTTATCGAGTT 60.262 45.833 9.42 0.00 41.35 3.01
4697 11672 5.048921 CCGAGAATGCCTAGTTATCGAGTTA 60.049 44.000 9.42 0.00 41.35 2.24
4698 11673 6.436261 CGAGAATGCCTAGTTATCGAGTTAA 58.564 40.000 3.29 0.00 41.35 2.01
4699 11674 7.085116 CGAGAATGCCTAGTTATCGAGTTAAT 58.915 38.462 3.29 0.00 41.35 1.40
4700 11675 7.061210 CGAGAATGCCTAGTTATCGAGTTAATG 59.939 40.741 3.29 0.00 41.35 1.90
4701 11676 7.155328 AGAATGCCTAGTTATCGAGTTAATGG 58.845 38.462 0.00 0.00 0.00 3.16
4702 11677 5.864418 TGCCTAGTTATCGAGTTAATGGT 57.136 39.130 0.00 0.00 0.00 3.55
4703 11678 5.597806 TGCCTAGTTATCGAGTTAATGGTG 58.402 41.667 0.00 0.00 0.00 4.17
4704 11679 5.128171 TGCCTAGTTATCGAGTTAATGGTGT 59.872 40.000 0.00 0.00 0.00 4.16
4705 11680 6.047231 GCCTAGTTATCGAGTTAATGGTGTT 58.953 40.000 0.00 0.00 0.00 3.32
4706 11681 6.537660 GCCTAGTTATCGAGTTAATGGTGTTT 59.462 38.462 0.00 0.00 0.00 2.83
4707 11682 7.254353 GCCTAGTTATCGAGTTAATGGTGTTTC 60.254 40.741 0.00 0.00 0.00 2.78
4708 11683 6.980051 AGTTATCGAGTTAATGGTGTTTCC 57.020 37.500 0.00 0.00 0.00 3.13
4709 11684 5.878669 AGTTATCGAGTTAATGGTGTTTCCC 59.121 40.000 0.00 0.00 34.77 3.97
4710 11685 4.569719 ATCGAGTTAATGGTGTTTCCCT 57.430 40.909 0.00 0.00 34.77 4.20
4711 11686 4.360951 TCGAGTTAATGGTGTTTCCCTT 57.639 40.909 0.00 0.00 34.77 3.95
4712 11687 4.721132 TCGAGTTAATGGTGTTTCCCTTT 58.279 39.130 0.00 0.00 34.77 3.11
4713 11688 5.134661 TCGAGTTAATGGTGTTTCCCTTTT 58.865 37.500 0.00 0.00 34.77 2.27
4714 11689 5.009210 TCGAGTTAATGGTGTTTCCCTTTTG 59.991 40.000 0.00 0.00 34.77 2.44
4715 11690 5.221165 CGAGTTAATGGTGTTTCCCTTTTGT 60.221 40.000 0.00 0.00 34.77 2.83
4716 11691 6.016943 CGAGTTAATGGTGTTTCCCTTTTGTA 60.017 38.462 0.00 0.00 34.77 2.41
4717 11692 7.046292 AGTTAATGGTGTTTCCCTTTTGTAC 57.954 36.000 0.00 0.00 34.77 2.90
4718 11693 6.837048 AGTTAATGGTGTTTCCCTTTTGTACT 59.163 34.615 0.00 0.00 34.77 2.73
4719 11694 5.529581 AATGGTGTTTCCCTTTTGTACTG 57.470 39.130 0.00 0.00 34.77 2.74
4720 11695 3.292460 TGGTGTTTCCCTTTTGTACTGG 58.708 45.455 0.00 0.00 34.77 4.00
4721 11696 2.626266 GGTGTTTCCCTTTTGTACTGGG 59.374 50.000 0.00 1.07 42.20 4.45
4722 11697 3.293337 GTGTTTCCCTTTTGTACTGGGT 58.707 45.455 11.53 0.00 41.58 4.51
4723 11698 4.463070 GTGTTTCCCTTTTGTACTGGGTA 58.537 43.478 11.53 2.75 41.58 3.69
4724 11699 4.888823 GTGTTTCCCTTTTGTACTGGGTAA 59.111 41.667 11.53 7.39 41.58 2.85
4725 11700 5.009310 GTGTTTCCCTTTTGTACTGGGTAAG 59.991 44.000 11.53 0.00 41.58 2.34
4726 11701 5.104024 TGTTTCCCTTTTGTACTGGGTAAGA 60.104 40.000 11.53 6.41 41.58 2.10
4727 11702 5.853572 TTCCCTTTTGTACTGGGTAAGAT 57.146 39.130 11.53 0.00 41.58 2.40
4728 11703 5.174037 TCCCTTTTGTACTGGGTAAGATG 57.826 43.478 11.53 0.00 41.58 2.90
4729 11704 4.847512 TCCCTTTTGTACTGGGTAAGATGA 59.152 41.667 11.53 0.00 41.58 2.92
4730 11705 5.491078 TCCCTTTTGTACTGGGTAAGATGAT 59.509 40.000 11.53 0.00 41.58 2.45
4731 11706 5.590259 CCCTTTTGTACTGGGTAAGATGATG 59.410 44.000 0.00 0.00 36.32 3.07
4732 11707 5.066505 CCTTTTGTACTGGGTAAGATGATGC 59.933 44.000 0.00 0.00 0.00 3.91
4733 11708 4.835284 TTGTACTGGGTAAGATGATGCA 57.165 40.909 0.00 0.00 0.00 3.96
4802 11777 4.798882 AGACTCTTCCTACTATGGTCCAG 58.201 47.826 0.00 0.00 0.00 3.86
4810 11785 3.324846 CCTACTATGGTCCAGCTATTGCA 59.675 47.826 1.12 0.00 42.74 4.08
4818 11793 5.260424 TGGTCCAGCTATTGCATCTTTTTA 58.740 37.500 1.12 0.00 42.74 1.52
4890 13221 8.278729 TGTATCTGACATCTATCTATCTGCTG 57.721 38.462 0.00 0.00 31.20 4.41
4891 13222 5.641783 TCTGACATCTATCTATCTGCTGC 57.358 43.478 0.00 0.00 0.00 5.25
4903 13234 1.629013 TCTGCTGCTATGTTCGAACG 58.371 50.000 22.48 10.25 0.00 3.95
4922 13253 1.403647 CGTCTGAACCGACTATTGCCA 60.404 52.381 0.00 0.00 0.00 4.92
4975 13306 1.112315 TCGGCATGCAAAACCAACCT 61.112 50.000 21.36 0.00 0.00 3.50
4976 13307 0.249826 CGGCATGCAAAACCAACCTT 60.250 50.000 21.36 0.00 0.00 3.50
4977 13308 1.228533 GGCATGCAAAACCAACCTTG 58.771 50.000 21.36 0.00 0.00 3.61
4978 13309 1.474855 GGCATGCAAAACCAACCTTGT 60.475 47.619 21.36 0.00 0.00 3.16
5019 13350 5.904984 TGCCTCCCATACTAATGTTATGT 57.095 39.130 0.00 0.00 0.00 2.29
5075 13407 5.132502 TCTGAAGAAAATCACTCAAGGCAA 58.867 37.500 0.00 0.00 0.00 4.52
5076 13408 5.771666 TCTGAAGAAAATCACTCAAGGCAAT 59.228 36.000 0.00 0.00 0.00 3.56
5112 13445 6.506147 TGTCATCTTTGCATTATACCATTGC 58.494 36.000 0.00 0.00 36.91 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.844122 CCCGTTAGTAGGCATTTTGC 57.156 50.000 0.00 0.00 44.08 3.68
8 9 3.668980 TTGGCGCCCGTTAGTAGGC 62.669 63.158 26.77 0.00 46.17 3.93
9 10 0.463116 ATTTGGCGCCCGTTAGTAGG 60.463 55.000 26.77 0.00 0.00 3.18
10 11 2.132762 CTATTTGGCGCCCGTTAGTAG 58.867 52.381 26.77 13.24 0.00 2.57
11 12 1.202557 CCTATTTGGCGCCCGTTAGTA 60.203 52.381 26.77 0.00 0.00 1.82
12 13 0.463116 CCTATTTGGCGCCCGTTAGT 60.463 55.000 26.77 6.53 0.00 2.24
13 14 0.179067 TCCTATTTGGCGCCCGTTAG 60.179 55.000 26.77 20.01 35.26 2.34
14 15 0.252479 TTCCTATTTGGCGCCCGTTA 59.748 50.000 26.77 11.49 35.26 3.18
15 16 0.609681 TTTCCTATTTGGCGCCCGTT 60.610 50.000 26.77 10.86 35.26 4.44
16 17 1.001887 TTTCCTATTTGGCGCCCGT 60.002 52.632 26.77 12.48 35.26 5.28
17 18 1.431845 GTTTCCTATTTGGCGCCCG 59.568 57.895 26.77 6.90 35.26 6.13
18 19 1.431845 CGTTTCCTATTTGGCGCCC 59.568 57.895 26.77 6.44 35.26 6.13
19 20 1.226575 GCGTTTCCTATTTGGCGCC 60.227 57.895 22.73 22.73 38.37 6.53
20 21 1.226575 GGCGTTTCCTATTTGGCGC 60.227 57.895 0.00 0.00 41.79 6.53
21 22 1.431845 GGGCGTTTCCTATTTGGCG 59.568 57.895 0.00 0.00 35.26 5.69
22 23 1.672854 GGGGGCGTTTCCTATTTGGC 61.673 60.000 0.00 0.00 35.26 4.52
23 24 0.033503 AGGGGGCGTTTCCTATTTGG 60.034 55.000 0.00 0.00 34.39 3.28
24 25 1.102978 CAGGGGGCGTTTCCTATTTG 58.897 55.000 0.00 0.00 34.39 2.32
25 26 0.683179 GCAGGGGGCGTTTCCTATTT 60.683 55.000 0.00 0.00 34.39 1.40
26 27 1.076995 GCAGGGGGCGTTTCCTATT 60.077 57.895 0.00 0.00 34.39 1.73
27 28 2.595655 GCAGGGGGCGTTTCCTAT 59.404 61.111 0.00 0.00 34.39 2.57
36 37 0.983378 TTAGAGGAAGAGCAGGGGGC 60.983 60.000 0.00 0.00 45.30 5.80
37 38 0.833949 GTTAGAGGAAGAGCAGGGGG 59.166 60.000 0.00 0.00 0.00 5.40
38 39 1.872773 AGTTAGAGGAAGAGCAGGGG 58.127 55.000 0.00 0.00 0.00 4.79
43 44 1.996191 CGTGCAAGTTAGAGGAAGAGC 59.004 52.381 0.00 0.00 0.00 4.09
137 142 3.845109 AAAGGGAAGAAGGGGCATTAA 57.155 42.857 0.00 0.00 0.00 1.40
141 146 1.062505 ACAAAAAGGGAAGAAGGGGCA 60.063 47.619 0.00 0.00 0.00 5.36
142 147 1.717032 ACAAAAAGGGAAGAAGGGGC 58.283 50.000 0.00 0.00 0.00 5.80
143 148 4.771114 AAAACAAAAAGGGAAGAAGGGG 57.229 40.909 0.00 0.00 0.00 4.79
179 184 2.421619 GCAGGAAGGAACAGAACAGAG 58.578 52.381 0.00 0.00 0.00 3.35
225 235 2.739996 CCTCCATTCTCGGCTGCCT 61.740 63.158 17.92 0.00 0.00 4.75
238 248 3.717294 GCCGCTCTTTCCCCTCCA 61.717 66.667 0.00 0.00 0.00 3.86
374 398 3.775654 CACGGAGGGGAGTGGAGC 61.776 72.222 0.00 0.00 34.93 4.70
392 416 0.311790 CGCAAGCAAGCAAAAGAGGA 59.688 50.000 1.32 0.00 0.00 3.71
399 423 3.980989 CAGCCCGCAAGCAAGCAA 61.981 61.111 6.15 0.00 34.23 3.91
401 425 3.504524 AAACAGCCCGCAAGCAAGC 62.505 57.895 0.00 0.00 34.23 4.01
402 426 1.372128 GAAACAGCCCGCAAGCAAG 60.372 57.895 0.00 0.00 34.23 4.01
501 525 0.807667 CGCCTCAATCCCTCAACTCG 60.808 60.000 0.00 0.00 0.00 4.18
545 569 3.012518 CAGACTAGTGCCAAATCCAAGG 58.987 50.000 0.00 0.00 0.00 3.61
556 581 0.737715 CCCGAACTGCAGACTAGTGC 60.738 60.000 23.35 0.00 44.27 4.40
643 680 6.375377 TCCACGCTAAAACAATGTTATCAAC 58.625 36.000 0.00 0.00 0.00 3.18
672 709 9.052759 TGACTAGAAAAGTAAATTCGCTTCTTT 57.947 29.630 0.00 0.00 39.07 2.52
687 724 6.918022 AGCGTCCAAAATTTTGACTAGAAAAG 59.082 34.615 28.44 11.10 40.55 2.27
750 787 1.978617 CCAATGCGCCAAGGAAGGT 60.979 57.895 4.18 0.00 0.00 3.50
752 789 2.182537 GCCAATGCGCCAAGGAAG 59.817 61.111 4.18 0.00 0.00 3.46
855 895 9.120538 ACTTGAAAAATTACTAGACAGAAAGCA 57.879 29.630 0.00 0.00 0.00 3.91
917 957 0.537143 AGTGATGCAGTCCCGCAAAA 60.537 50.000 0.00 0.00 46.87 2.44
935 975 3.573598 TGCAAACGCACATTCCAATTAG 58.426 40.909 0.00 0.00 33.43 1.73
949 989 0.594796 GCCAAACCACTCTGCAAACG 60.595 55.000 0.00 0.00 0.00 3.60
987 1027 0.953471 TAACCATGGTGAGCACGCAC 60.953 55.000 20.60 0.00 38.05 5.34
999 1039 1.207089 TCGGGCTCTTCAGTAACCATG 59.793 52.381 0.00 0.00 0.00 3.66
1032 1072 7.752239 CGGTTTATGATGCATTCCTCATTTATC 59.248 37.037 0.00 0.00 34.14 1.75
1101 1141 1.014352 ACGTCAACAAAGTGCTCACC 58.986 50.000 0.00 0.00 0.00 4.02
2164 8759 6.279882 GCACAATGCCAGCCTTTTTATATAA 58.720 36.000 0.00 0.00 37.42 0.98
2308 8903 3.498082 GCTAATAACAGTTTGGCCAACG 58.502 45.455 20.35 12.48 40.75 4.10
2363 8958 3.440228 GCAAGTTAGCGGTTGTCAAAAA 58.560 40.909 0.00 0.00 0.00 1.94
2502 9189 4.407296 AGAATCACCTGACTTGGACTATCC 59.593 45.833 0.00 0.00 36.96 2.59
2507 9194 3.971245 AGAGAATCACCTGACTTGGAC 57.029 47.619 0.00 0.00 37.82 4.02
2673 9370 6.100668 GGTCAGTTGTTTAGCCTAGTCTTAG 58.899 44.000 0.00 0.00 0.00 2.18
2685 9382 5.092554 TGTCTTGAGTGGTCAGTTGTTTA 57.907 39.130 0.00 0.00 32.98 2.01
2749 9446 8.308207 ACAACACACTTAAAATAGTTTTGTGGT 58.692 29.630 18.08 11.90 37.32 4.16
2801 9498 5.423931 GGGGACTTTGGCTATTGGAAAATTA 59.576 40.000 0.00 0.00 0.00 1.40
2885 9584 2.878406 TGAGCCCTTTCTTTCAGTTTCG 59.122 45.455 0.00 0.00 0.00 3.46
3409 10140 8.458573 TCCATACAATGTAAAATATGTGACCC 57.541 34.615 0.00 0.00 0.00 4.46
3598 10336 3.771216 ACTACTCCCTCCGTTTACAGAA 58.229 45.455 0.00 0.00 0.00 3.02
3599 10337 3.446442 ACTACTCCCTCCGTTTACAGA 57.554 47.619 0.00 0.00 0.00 3.41
3600 10338 3.846360 CAACTACTCCCTCCGTTTACAG 58.154 50.000 0.00 0.00 0.00 2.74
3601 10339 2.028748 GCAACTACTCCCTCCGTTTACA 60.029 50.000 0.00 0.00 0.00 2.41
3602 10340 2.614779 GCAACTACTCCCTCCGTTTAC 58.385 52.381 0.00 0.00 0.00 2.01
3603 10341 1.551883 GGCAACTACTCCCTCCGTTTA 59.448 52.381 0.00 0.00 0.00 2.01
3738 10530 7.360353 CCATTATAGTTACTGATGCACAATCCG 60.360 40.741 0.00 0.00 34.00 4.18
3739 10531 7.661437 TCCATTATAGTTACTGATGCACAATCC 59.339 37.037 0.00 0.00 34.00 3.01
3995 10947 9.342308 TGGATCAGGATATCAAATACAAGAAAC 57.658 33.333 4.83 0.00 0.00 2.78
4027 10982 4.017126 AGTAGATTTACCCTGCCAAAAGC 58.983 43.478 0.00 0.00 44.14 3.51
4085 11043 6.678568 ATGTTCTCTTCTTCCTTCTTCTCA 57.321 37.500 0.00 0.00 0.00 3.27
4268 11228 5.211454 TGAAAGTGCAATGTAATGACAACG 58.789 37.500 0.00 0.00 39.59 4.10
4316 11277 3.481024 CAAGCGGCATTTTGCGCC 61.481 61.111 4.18 0.00 46.21 6.53
4486 11449 2.778299 TGGCAGATTAGTCCACACAAC 58.222 47.619 0.00 0.00 0.00 3.32
4492 11455 3.327757 AGACAGTTTGGCAGATTAGTCCA 59.672 43.478 0.00 0.00 0.00 4.02
4493 11456 3.935828 GAGACAGTTTGGCAGATTAGTCC 59.064 47.826 0.00 0.00 0.00 3.85
4495 11458 3.327757 TGGAGACAGTTTGGCAGATTAGT 59.672 43.478 0.00 0.00 35.01 2.24
4496 11459 3.942829 TGGAGACAGTTTGGCAGATTAG 58.057 45.455 0.00 0.00 35.01 1.73
4497 11460 4.072131 GTTGGAGACAGTTTGGCAGATTA 58.928 43.478 0.00 0.00 44.54 1.75
4498 11461 2.887152 GTTGGAGACAGTTTGGCAGATT 59.113 45.455 0.00 0.00 44.54 2.40
4500 11463 1.476833 GGTTGGAGACAGTTTGGCAGA 60.477 52.381 0.00 0.00 44.54 4.26
4509 11472 6.391227 AAAACATACTTTGGTTGGAGACAG 57.609 37.500 0.00 0.00 44.54 3.51
4511 11474 5.237779 TCGAAAACATACTTTGGTTGGAGAC 59.762 40.000 0.00 0.00 34.73 3.36
4513 11476 5.682943 TCGAAAACATACTTTGGTTGGAG 57.317 39.130 0.00 0.00 34.73 3.86
4516 11479 5.689514 TGCATTCGAAAACATACTTTGGTTG 59.310 36.000 0.00 0.00 34.73 3.77
4517 11480 5.837437 TGCATTCGAAAACATACTTTGGTT 58.163 33.333 0.00 0.00 36.59 3.67
4518 11481 5.446143 TGCATTCGAAAACATACTTTGGT 57.554 34.783 0.00 0.00 0.00 3.67
4519 11482 6.761731 TTTGCATTCGAAAACATACTTTGG 57.238 33.333 0.00 0.00 0.00 3.28
4521 11484 7.095271 CCCATTTTGCATTCGAAAACATACTTT 60.095 33.333 0.00 0.00 0.00 2.66
4524 11499 5.445806 GCCCATTTTGCATTCGAAAACATAC 60.446 40.000 0.00 0.00 0.00 2.39
4530 11505 2.036992 ACAGCCCATTTTGCATTCGAAA 59.963 40.909 0.00 0.00 0.00 3.46
4577 11552 1.131315 GAATGTTTTCGCCCTCTGCTC 59.869 52.381 0.00 0.00 38.05 4.26
4578 11553 1.168714 GAATGTTTTCGCCCTCTGCT 58.831 50.000 0.00 0.00 38.05 4.24
4579 11554 1.135575 CAGAATGTTTTCGCCCTCTGC 60.136 52.381 0.00 0.00 36.93 4.26
4580 11555 1.470098 CCAGAATGTTTTCGCCCTCTG 59.530 52.381 0.00 0.00 36.93 3.35
4588 11563 5.418310 TTCAGACGTTCCAGAATGTTTTC 57.582 39.130 6.70 0.00 40.35 2.29
4603 11578 2.774007 CGCATTTTTAGCCTTCAGACG 58.226 47.619 0.00 0.00 0.00 4.18
4605 11580 1.472480 GGCGCATTTTTAGCCTTCAGA 59.528 47.619 10.83 0.00 46.83 3.27
4623 11598 1.212751 GCATTCGTTCCAGGTTGGC 59.787 57.895 0.00 0.00 37.47 4.52
4635 11610 3.940303 AGCTTAGCAAAATACGCATTCG 58.060 40.909 7.07 0.00 42.43 3.34
4636 11611 6.632171 AAAAGCTTAGCAAAATACGCATTC 57.368 33.333 7.07 0.00 0.00 2.67
4637 11612 6.868339 AGAAAAAGCTTAGCAAAATACGCATT 59.132 30.769 7.07 0.00 0.00 3.56
4638 11613 6.389906 AGAAAAAGCTTAGCAAAATACGCAT 58.610 32.000 7.07 0.00 0.00 4.73
4639 11614 5.768317 AGAAAAAGCTTAGCAAAATACGCA 58.232 33.333 7.07 0.00 0.00 5.24
4640 11615 6.690704 AAGAAAAAGCTTAGCAAAATACGC 57.309 33.333 7.07 0.00 0.00 4.42
4641 11616 8.507470 AGAAAGAAAAAGCTTAGCAAAATACG 57.493 30.769 7.07 0.00 0.00 3.06
4644 11619 9.992910 CAAAAGAAAGAAAAAGCTTAGCAAAAT 57.007 25.926 7.07 0.00 0.00 1.82
4645 11620 8.450180 CCAAAAGAAAGAAAAAGCTTAGCAAAA 58.550 29.630 7.07 0.00 0.00 2.44
4646 11621 7.065683 CCCAAAAGAAAGAAAAAGCTTAGCAAA 59.934 33.333 7.07 0.00 0.00 3.68
4647 11622 6.538381 CCCAAAAGAAAGAAAAAGCTTAGCAA 59.462 34.615 7.07 0.00 0.00 3.91
4648 11623 6.048509 CCCAAAAGAAAGAAAAAGCTTAGCA 58.951 36.000 7.07 0.00 0.00 3.49
4649 11624 5.050091 GCCCAAAAGAAAGAAAAAGCTTAGC 60.050 40.000 0.00 0.00 0.00 3.09
4650 11625 5.466728 GGCCCAAAAGAAAGAAAAAGCTTAG 59.533 40.000 0.00 0.00 0.00 2.18
4651 11626 5.364778 GGCCCAAAAGAAAGAAAAAGCTTA 58.635 37.500 0.00 0.00 0.00 3.09
4652 11627 4.199310 GGCCCAAAAGAAAGAAAAAGCTT 58.801 39.130 0.00 0.00 0.00 3.74
4653 11628 3.741075 CGGCCCAAAAGAAAGAAAAAGCT 60.741 43.478 0.00 0.00 0.00 3.74
4654 11629 2.543848 CGGCCCAAAAGAAAGAAAAAGC 59.456 45.455 0.00 0.00 0.00 3.51
4655 11630 4.051237 CTCGGCCCAAAAGAAAGAAAAAG 58.949 43.478 0.00 0.00 0.00 2.27
4656 11631 3.702045 TCTCGGCCCAAAAGAAAGAAAAA 59.298 39.130 0.00 0.00 0.00 1.94
4657 11632 3.292460 TCTCGGCCCAAAAGAAAGAAAA 58.708 40.909 0.00 0.00 0.00 2.29
4658 11633 2.938838 TCTCGGCCCAAAAGAAAGAAA 58.061 42.857 0.00 0.00 0.00 2.52
4659 11634 2.649531 TCTCGGCCCAAAAGAAAGAA 57.350 45.000 0.00 0.00 0.00 2.52
4660 11635 2.649531 TTCTCGGCCCAAAAGAAAGA 57.350 45.000 0.00 0.00 0.00 2.52
4661 11636 2.672195 GCATTCTCGGCCCAAAAGAAAG 60.672 50.000 0.00 0.05 33.10 2.62
4662 11637 1.272212 GCATTCTCGGCCCAAAAGAAA 59.728 47.619 0.00 0.00 33.10 2.52
4663 11638 0.887933 GCATTCTCGGCCCAAAAGAA 59.112 50.000 0.00 1.83 33.83 2.52
4664 11639 0.965363 GGCATTCTCGGCCCAAAAGA 60.965 55.000 0.00 0.00 45.87 2.52
4665 11640 1.512694 GGCATTCTCGGCCCAAAAG 59.487 57.895 0.00 0.00 45.87 2.27
4666 11641 3.693411 GGCATTCTCGGCCCAAAA 58.307 55.556 0.00 0.00 45.87 2.44
4672 11647 2.030185 TCGATAACTAGGCATTCTCGGC 60.030 50.000 0.00 0.00 0.00 5.54
4673 11648 3.253677 ACTCGATAACTAGGCATTCTCGG 59.746 47.826 0.00 0.00 0.00 4.63
4674 11649 4.491234 ACTCGATAACTAGGCATTCTCG 57.509 45.455 0.00 0.00 0.00 4.04
4675 11650 7.329717 CCATTAACTCGATAACTAGGCATTCTC 59.670 40.741 0.00 0.00 0.00 2.87
4676 11651 7.155328 CCATTAACTCGATAACTAGGCATTCT 58.845 38.462 0.00 0.00 0.00 2.40
4677 11652 6.929606 ACCATTAACTCGATAACTAGGCATTC 59.070 38.462 0.00 0.00 0.00 2.67
4678 11653 6.706270 CACCATTAACTCGATAACTAGGCATT 59.294 38.462 0.00 0.00 0.00 3.56
4679 11654 6.183360 ACACCATTAACTCGATAACTAGGCAT 60.183 38.462 0.00 0.00 0.00 4.40
4680 11655 5.128171 ACACCATTAACTCGATAACTAGGCA 59.872 40.000 0.00 0.00 0.00 4.75
4681 11656 5.598769 ACACCATTAACTCGATAACTAGGC 58.401 41.667 0.00 0.00 0.00 3.93
4682 11657 7.224167 GGAAACACCATTAACTCGATAACTAGG 59.776 40.741 0.00 0.00 38.79 3.02
4683 11658 7.224167 GGGAAACACCATTAACTCGATAACTAG 59.776 40.741 0.00 0.00 41.20 2.57
4684 11659 7.043565 GGGAAACACCATTAACTCGATAACTA 58.956 38.462 0.00 0.00 41.20 2.24
4685 11660 5.878669 GGGAAACACCATTAACTCGATAACT 59.121 40.000 0.00 0.00 41.20 2.24
4686 11661 5.878669 AGGGAAACACCATTAACTCGATAAC 59.121 40.000 0.00 0.00 41.20 1.89
4687 11662 6.057321 AGGGAAACACCATTAACTCGATAA 57.943 37.500 0.00 0.00 41.20 1.75
4688 11663 5.687166 AGGGAAACACCATTAACTCGATA 57.313 39.130 0.00 0.00 41.20 2.92
4689 11664 4.569719 AGGGAAACACCATTAACTCGAT 57.430 40.909 0.00 0.00 41.20 3.59
4690 11665 4.360951 AAGGGAAACACCATTAACTCGA 57.639 40.909 0.00 0.00 41.10 4.04
4691 11666 5.219633 CAAAAGGGAAACACCATTAACTCG 58.780 41.667 0.00 0.00 42.12 4.18
4692 11667 6.156748 ACAAAAGGGAAACACCATTAACTC 57.843 37.500 0.00 0.00 42.12 3.01
4693 11668 6.837048 AGTACAAAAGGGAAACACCATTAACT 59.163 34.615 0.00 0.00 42.12 2.24
4694 11669 6.921307 CAGTACAAAAGGGAAACACCATTAAC 59.079 38.462 0.00 0.00 42.12 2.01
4695 11670 6.041069 CCAGTACAAAAGGGAAACACCATTAA 59.959 38.462 0.00 0.00 42.12 1.40
4696 11671 5.536916 CCAGTACAAAAGGGAAACACCATTA 59.463 40.000 0.00 0.00 42.12 1.90
4697 11672 4.343814 CCAGTACAAAAGGGAAACACCATT 59.656 41.667 0.00 0.00 45.03 3.16
4698 11673 3.895041 CCAGTACAAAAGGGAAACACCAT 59.105 43.478 0.00 0.00 41.20 3.55
4699 11674 3.292460 CCAGTACAAAAGGGAAACACCA 58.708 45.455 0.00 0.00 41.20 4.17
4700 11675 2.626266 CCCAGTACAAAAGGGAAACACC 59.374 50.000 6.83 0.00 45.80 4.16
4701 11676 3.293337 ACCCAGTACAAAAGGGAAACAC 58.707 45.455 16.59 0.00 45.80 3.32
4702 11677 3.673543 ACCCAGTACAAAAGGGAAACA 57.326 42.857 16.59 0.00 45.80 2.83
4703 11678 5.379187 TCTTACCCAGTACAAAAGGGAAAC 58.621 41.667 16.59 0.00 45.80 2.78
4704 11679 5.649970 TCTTACCCAGTACAAAAGGGAAA 57.350 39.130 16.59 4.75 45.80 3.13
4705 11680 5.311121 TCATCTTACCCAGTACAAAAGGGAA 59.689 40.000 16.59 4.35 45.80 3.97
4706 11681 4.847512 TCATCTTACCCAGTACAAAAGGGA 59.152 41.667 16.59 0.00 45.80 4.20
4708 11683 5.066505 GCATCATCTTACCCAGTACAAAAGG 59.933 44.000 0.00 0.00 0.00 3.11
4709 11684 5.647658 TGCATCATCTTACCCAGTACAAAAG 59.352 40.000 0.00 0.00 0.00 2.27
4710 11685 5.565509 TGCATCATCTTACCCAGTACAAAA 58.434 37.500 0.00 0.00 0.00 2.44
4711 11686 5.172687 TGCATCATCTTACCCAGTACAAA 57.827 39.130 0.00 0.00 0.00 2.83
4712 11687 4.835284 TGCATCATCTTACCCAGTACAA 57.165 40.909 0.00 0.00 0.00 2.41
4713 11688 4.835284 TTGCATCATCTTACCCAGTACA 57.165 40.909 0.00 0.00 0.00 2.90
4714 11689 4.335594 GGTTTGCATCATCTTACCCAGTAC 59.664 45.833 0.00 0.00 0.00 2.73
4715 11690 4.227300 AGGTTTGCATCATCTTACCCAGTA 59.773 41.667 0.00 0.00 0.00 2.74
4716 11691 3.010584 AGGTTTGCATCATCTTACCCAGT 59.989 43.478 0.00 0.00 0.00 4.00
4717 11692 3.379372 CAGGTTTGCATCATCTTACCCAG 59.621 47.826 0.00 0.00 0.00 4.45
4718 11693 3.355378 CAGGTTTGCATCATCTTACCCA 58.645 45.455 0.00 0.00 0.00 4.51
4719 11694 2.689983 CCAGGTTTGCATCATCTTACCC 59.310 50.000 0.00 0.00 0.00 3.69
4720 11695 2.689983 CCCAGGTTTGCATCATCTTACC 59.310 50.000 0.00 0.00 0.00 2.85
4721 11696 3.378427 GTCCCAGGTTTGCATCATCTTAC 59.622 47.826 0.00 0.00 0.00 2.34
4722 11697 3.266772 AGTCCCAGGTTTGCATCATCTTA 59.733 43.478 0.00 0.00 0.00 2.10
4723 11698 2.042162 AGTCCCAGGTTTGCATCATCTT 59.958 45.455 0.00 0.00 0.00 2.40
4724 11699 1.637553 AGTCCCAGGTTTGCATCATCT 59.362 47.619 0.00 0.00 0.00 2.90
4725 11700 2.134789 AGTCCCAGGTTTGCATCATC 57.865 50.000 0.00 0.00 0.00 2.92
4726 11701 2.173519 CAAGTCCCAGGTTTGCATCAT 58.826 47.619 0.00 0.00 0.00 2.45
4727 11702 1.144708 TCAAGTCCCAGGTTTGCATCA 59.855 47.619 0.00 0.00 0.00 3.07
4728 11703 1.815003 CTCAAGTCCCAGGTTTGCATC 59.185 52.381 0.00 0.00 0.00 3.91
4729 11704 1.425066 TCTCAAGTCCCAGGTTTGCAT 59.575 47.619 0.00 0.00 0.00 3.96
4730 11705 0.843309 TCTCAAGTCCCAGGTTTGCA 59.157 50.000 0.00 0.00 0.00 4.08
4731 11706 1.609072 GTTCTCAAGTCCCAGGTTTGC 59.391 52.381 0.00 0.00 0.00 3.68
4732 11707 3.214696 AGTTCTCAAGTCCCAGGTTTG 57.785 47.619 0.00 0.00 0.00 2.93
4733 11708 3.953542 AAGTTCTCAAGTCCCAGGTTT 57.046 42.857 0.00 0.00 0.00 3.27
4793 11768 4.712051 AAGATGCAATAGCTGGACCATA 57.288 40.909 0.00 0.00 42.74 2.74
4794 11769 3.589951 AAGATGCAATAGCTGGACCAT 57.410 42.857 0.00 0.00 42.74 3.55
4795 11770 3.370840 AAAGATGCAATAGCTGGACCA 57.629 42.857 0.00 0.00 42.74 4.02
4802 11777 4.574828 TCGGGACTAAAAAGATGCAATAGC 59.425 41.667 0.00 0.00 42.57 2.97
4810 11785 4.636206 GCAATCACTCGGGACTAAAAAGAT 59.364 41.667 0.00 0.00 0.00 2.40
4818 11793 0.461961 GCTAGCAATCACTCGGGACT 59.538 55.000 10.63 0.00 0.00 3.85
4847 11822 5.599656 AGATACATAAACCACCGGCTTACTA 59.400 40.000 0.00 0.00 0.00 1.82
4883 13214 2.196749 CGTTCGAACATAGCAGCAGAT 58.803 47.619 26.71 0.00 0.00 2.90
4884 13215 1.067846 ACGTTCGAACATAGCAGCAGA 60.068 47.619 26.71 0.00 0.00 4.26
4885 13216 1.321743 GACGTTCGAACATAGCAGCAG 59.678 52.381 26.71 10.32 0.00 4.24
4886 13217 1.067846 AGACGTTCGAACATAGCAGCA 60.068 47.619 26.71 0.00 0.00 4.41
4887 13218 1.321743 CAGACGTTCGAACATAGCAGC 59.678 52.381 26.71 8.17 0.00 5.25
4888 13219 2.863739 TCAGACGTTCGAACATAGCAG 58.136 47.619 26.71 12.38 0.00 4.24
4889 13220 2.984471 GTTCAGACGTTCGAACATAGCA 59.016 45.455 26.71 5.69 40.97 3.49
4890 13221 2.344741 GGTTCAGACGTTCGAACATAGC 59.655 50.000 26.71 12.72 42.67 2.97
4891 13222 2.592897 CGGTTCAGACGTTCGAACATAG 59.407 50.000 26.71 13.78 42.67 2.23
4903 13234 2.000447 GTGGCAATAGTCGGTTCAGAC 59.000 52.381 0.00 0.00 41.23 3.51
4947 13278 1.014044 TTGCATGCCGAGACGTTCTC 61.014 55.000 16.68 0.00 40.06 2.87
4953 13284 0.313672 TTGGTTTTGCATGCCGAGAC 59.686 50.000 16.68 9.12 0.00 3.36
4957 13288 0.249826 AAGGTTGGTTTTGCATGCCG 60.250 50.000 16.68 0.00 0.00 5.69
4959 13290 1.952193 ACAAGGTTGGTTTTGCATGC 58.048 45.000 11.82 11.82 0.00 4.06
4961 13292 3.688673 CACAAACAAGGTTGGTTTTGCAT 59.311 39.130 2.59 0.00 35.55 3.96
4975 13306 6.293298 GGCAATTGTAATTCATGCACAAACAA 60.293 34.615 7.40 0.00 35.91 2.83
4976 13307 5.178996 GGCAATTGTAATTCATGCACAAACA 59.821 36.000 7.40 0.00 35.91 2.83
4977 13308 5.409214 AGGCAATTGTAATTCATGCACAAAC 59.591 36.000 7.40 0.00 35.91 2.93
4978 13309 5.549347 AGGCAATTGTAATTCATGCACAAA 58.451 33.333 7.40 0.00 35.91 2.83
5019 13350 6.321181 ACACTGCTTCTCAAATTGGAAACTTA 59.679 34.615 0.00 0.00 0.00 2.24
5066 13398 3.604875 AATTGCTTCCATTGCCTTGAG 57.395 42.857 0.00 0.00 0.00 3.02
5075 13407 6.127281 TGCAAAGATGACATAATTGCTTCCAT 60.127 34.615 25.82 0.00 44.95 3.41
5076 13408 5.185442 TGCAAAGATGACATAATTGCTTCCA 59.815 36.000 25.82 12.15 44.95 3.53


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

AutoCloner maintained by Alex Coulton.