Multiple sequence alignment - TraesCS2A01G182200

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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 TraesCS2A01G182200 chr2A 100.000 5317 0 0 1 5317 141494832 141500148 0.000000e+00 9819.0
1 TraesCS2A01G182200 chr2A 100.000 4058 0 0 5590 9647 141500421 141504478 0.000000e+00 7494.0
2 TraesCS2A01G182200 chr2B 96.016 3891 111 21 5780 9645 190016354 190020225 0.000000e+00 6287.0
3 TraesCS2A01G182200 chr2B 94.524 3232 104 21 2118 5317 190013100 190016290 0.000000e+00 4920.0
4 TraesCS2A01G182200 chr2B 89.290 831 60 12 384 1208 190011089 190011896 0.000000e+00 1014.0
5 TraesCS2A01G182200 chr2B 93.208 530 21 5 1232 1759 190012280 190012796 0.000000e+00 765.0
6 TraesCS2A01G182200 chr2B 90.349 373 23 10 1 363 189890495 189890864 2.440000e-130 477.0
7 TraesCS2A01G182200 chr2B 92.958 213 8 3 1759 1970 190012841 190013047 4.380000e-78 303.0
8 TraesCS2A01G182200 chr2B 97.778 45 0 1 5590 5634 190016313 190016356 1.040000e-09 76.8
9 TraesCS2A01G182200 chr2D 95.745 3925 109 28 5737 9645 133750539 133754421 0.000000e+00 6270.0
10 TraesCS2A01G182200 chr2D 95.262 3567 121 15 1759 5296 133745364 133748911 0.000000e+00 5607.0
11 TraesCS2A01G182200 chr2D 93.220 1770 95 17 1 1759 133743546 133745301 0.000000e+00 2580.0
12 TraesCS2A01G182200 chr2D 86.534 453 32 13 9208 9644 94090008 94089569 1.130000e-128 472.0
13 TraesCS2A01G182200 chr5D 85.013 1955 263 18 6839 8776 431911392 431909451 0.000000e+00 1960.0
14 TraesCS2A01G182200 chr5D 83.893 1341 174 21 6746 8072 413487745 413489057 0.000000e+00 1242.0
15 TraesCS2A01G182200 chr5D 79.061 1619 235 55 3709 5273 413454171 413455739 0.000000e+00 1016.0
16 TraesCS2A01G182200 chr5D 78.463 1444 197 61 3709 5101 431913808 431912428 0.000000e+00 839.0
17 TraesCS2A01G182200 chr5D 83.683 858 107 17 7537 8385 413611492 413612325 0.000000e+00 778.0
18 TraesCS2A01G182200 chr5D 86.593 455 32 13 9208 9645 140956422 140955980 8.770000e-130 475.0
19 TraesCS2A01G182200 chr5D 77.333 300 53 12 6243 6537 413478826 413479115 7.750000e-36 163.0
20 TraesCS2A01G182200 chr5A 85.458 1898 252 13 6827 8711 547040488 547038602 0.000000e+00 1954.0
21 TraesCS2A01G182200 chr5A 83.958 1228 157 22 6723 7945 525828001 525829193 0.000000e+00 1140.0
22 TraesCS2A01G182200 chr5A 83.957 1203 159 21 6746 7945 525916661 525917832 0.000000e+00 1122.0
23 TraesCS2A01G182200 chr5A 85.786 802 99 8 6827 7626 526289906 526290694 0.000000e+00 835.0
24 TraesCS2A01G182200 chr5A 78.431 1377 194 52 3781 5101 547044163 547042834 0.000000e+00 802.0
25 TraesCS2A01G182200 chr5A 78.934 1182 177 33 7488 8659 525718469 525719588 0.000000e+00 737.0
26 TraesCS2A01G182200 chr5A 77.865 1143 191 34 7537 8665 525936669 525937763 0.000000e+00 652.0
27 TraesCS2A01G182200 chr5A 77.033 1193 176 51 3949 5098 525715639 525716776 6.450000e-166 595.0
28 TraesCS2A01G182200 chr5A 81.431 657 97 16 7295 7945 525723110 525723747 1.860000e-141 514.0
29 TraesCS2A01G182200 chr5A 78.718 733 119 21 8019 8737 525913114 525913823 1.140000e-123 455.0
30 TraesCS2A01G182200 chr5A 85.463 454 36 13 9208 9644 27046462 27046022 6.870000e-121 446.0
31 TraesCS2A01G182200 chr5A 76.872 748 116 30 5786 6515 525935142 525935850 4.260000e-98 370.0
32 TraesCS2A01G182200 chr5A 76.751 714 86 35 4410 5098 525752970 525753628 9.340000e-85 326.0
33 TraesCS2A01G182200 chr5A 76.000 700 103 32 5834 6515 525753937 525754589 1.570000e-77 302.0
34 TraesCS2A01G182200 chr5A 79.339 242 45 4 6278 6515 525717665 525717905 2.160000e-36 165.0
35 TraesCS2A01G182200 chr5B 81.921 1499 194 47 6621 8075 498720505 498721970 0.000000e+00 1195.0
36 TraesCS2A01G182200 chr5B 78.514 1615 232 57 3709 5259 498273854 498275417 0.000000e+00 953.0
37 TraesCS2A01G182200 chr5B 85.661 802 102 7 6827 7626 498798622 498799412 0.000000e+00 832.0
38 TraesCS2A01G182200 chr5B 78.398 1361 194 51 3791 5098 524329432 524330745 0.000000e+00 793.0
39 TraesCS2A01G182200 chr5B 83.565 864 108 18 7537 8389 498799410 498800250 0.000000e+00 778.0
40 TraesCS2A01G182200 chr5B 80.038 1052 148 33 7703 8737 498716688 498717694 0.000000e+00 723.0
41 TraesCS2A01G182200 chr5B 82.407 864 110 25 7543 8389 498539577 498540415 0.000000e+00 715.0
42 TraesCS2A01G182200 chr5B 79.281 1057 143 33 7703 8737 498283642 498284644 0.000000e+00 669.0
43 TraesCS2A01G182200 chr5B 78.930 916 138 26 3709 4591 498715363 498716256 1.090000e-158 571.0
44 TraesCS2A01G182200 chr5B 76.853 1093 167 50 4035 5098 498537058 498538093 1.100000e-148 538.0
45 TraesCS2A01G182200 chr5B 76.819 742 113 36 5786 6515 498538355 498539049 7.120000e-96 363.0
46 TraesCS2A01G182200 chr6D 94.165 497 24 3 8432 8928 438545654 438545163 0.000000e+00 752.0
47 TraesCS2A01G182200 chr6D 87.033 455 30 12 9208 9645 297175042 297174600 4.050000e-133 486.0
48 TraesCS2A01G182200 chr6B 92.340 470 30 4 8463 8931 471226812 471227276 0.000000e+00 664.0
49 TraesCS2A01G182200 chr1A 86.414 449 37 13 9208 9645 340067449 340067884 4.080000e-128 470.0
50 TraesCS2A01G182200 chr7B 86.123 454 33 14 9208 9644 610758435 610757995 6.830000e-126 462.0
51 TraesCS2A01G182200 chr7B 85.746 449 35 13 9214 9645 713324173 713323737 1.910000e-121 448.0
52 TraesCS2A01G182200 chr7B 85.022 454 38 14 9208 9644 611051375 611050935 1.490000e-117 435.0
53 TraesCS2A01G182200 chr7B 82.119 453 38 14 9208 9644 719314582 719314157 1.990000e-91 348.0
54 TraesCS2A01G182200 chr7A 86.123 454 33 14 9208 9644 734440000 734440440 6.830000e-126 462.0
55 TraesCS2A01G182200 chr3D 85.934 455 34 16 9208 9645 229431251 229430810 8.830000e-125 459.0
56 TraesCS2A01G182200 chr3D 91.228 171 7 5 9476 9645 37623858 37624021 9.750000e-55 226.0
57 TraesCS2A01G182200 chr7D 86.264 364 28 10 9299 9645 103537964 103538322 9.150000e-100 375.0


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 TraesCS2A01G182200 chr2A 141494832 141504478 9646 False 8656.500000 9819 100.000000 1 9647 2 chr2A.!!$F1 9646
1 TraesCS2A01G182200 chr2B 190011089 190020225 9136 False 2227.633333 6287 93.962333 384 9645 6 chr2B.!!$F2 9261
2 TraesCS2A01G182200 chr2D 133743546 133754421 10875 False 4819.000000 6270 94.742333 1 9645 3 chr2D.!!$F1 9644
3 TraesCS2A01G182200 chr5D 431909451 431913808 4357 True 1399.500000 1960 81.738000 3709 8776 2 chr5D.!!$R2 5067
4 TraesCS2A01G182200 chr5D 413487745 413489057 1312 False 1242.000000 1242 83.893000 6746 8072 1 chr5D.!!$F3 1326
5 TraesCS2A01G182200 chr5D 413454171 413455739 1568 False 1016.000000 1016 79.061000 3709 5273 1 chr5D.!!$F1 1564
6 TraesCS2A01G182200 chr5D 413611492 413612325 833 False 778.000000 778 83.683000 7537 8385 1 chr5D.!!$F4 848
7 TraesCS2A01G182200 chr5A 547038602 547044163 5561 True 1378.000000 1954 81.944500 3781 8711 2 chr5A.!!$R2 4930
8 TraesCS2A01G182200 chr5A 525828001 525829193 1192 False 1140.000000 1140 83.958000 6723 7945 1 chr5A.!!$F1 1222
9 TraesCS2A01G182200 chr5A 526289906 526290694 788 False 835.000000 835 85.786000 6827 7626 1 chr5A.!!$F2 799
10 TraesCS2A01G182200 chr5A 525913114 525917832 4718 False 788.500000 1122 81.337500 6746 8737 2 chr5A.!!$F5 1991
11 TraesCS2A01G182200 chr5A 525935142 525937763 2621 False 511.000000 652 77.368500 5786 8665 2 chr5A.!!$F6 2879
12 TraesCS2A01G182200 chr5A 525715639 525723747 8108 False 502.750000 737 79.184250 3949 8659 4 chr5A.!!$F3 4710
13 TraesCS2A01G182200 chr5A 525752970 525754589 1619 False 314.000000 326 76.375500 4410 6515 2 chr5A.!!$F4 2105
14 TraesCS2A01G182200 chr5B 498273854 498275417 1563 False 953.000000 953 78.514000 3709 5259 1 chr5B.!!$F1 1550
15 TraesCS2A01G182200 chr5B 498715363 498721970 6607 False 829.666667 1195 80.296333 3709 8737 3 chr5B.!!$F5 5028
16 TraesCS2A01G182200 chr5B 498798622 498800250 1628 False 805.000000 832 84.613000 6827 8389 2 chr5B.!!$F6 1562
17 TraesCS2A01G182200 chr5B 524329432 524330745 1313 False 793.000000 793 78.398000 3791 5098 1 chr5B.!!$F3 1307
18 TraesCS2A01G182200 chr5B 498283642 498284644 1002 False 669.000000 669 79.281000 7703 8737 1 chr5B.!!$F2 1034
19 TraesCS2A01G182200 chr5B 498537058 498540415 3357 False 538.666667 715 78.693000 4035 8389 3 chr5B.!!$F4 4354

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
488 491 0.179094 TTAGGACCATAAGTGCGCGG 60.179 55.000 8.83 0.00 42.70 6.46 F
532 535 1.164313 AATGGCATCCATCCCATCCT 58.836 50.000 0.00 0.00 44.40 3.24 F
1493 1862 0.723129 GCATTTGCGTTCGCGTTGTA 60.723 50.000 5.77 0.00 43.62 2.41 F
2434 2874 0.174845 TCCTGAAATCACGGCGTAGG 59.825 55.000 14.22 15.45 0.00 3.18 F
2877 3317 1.001641 AGTGCCAAGCTCCATGGTC 60.002 57.895 12.58 5.12 40.23 4.02 F
3322 3763 1.134401 GGCTAGCTGGCAGTATCAACA 60.134 52.381 24.41 0.00 41.37 3.33 F
4886 7943 1.815003 GCTCAATGTAGGTTGCAAGCT 59.185 47.619 31.64 31.64 40.36 3.74 F
5640 9486 0.179100 CTCATGTGGTGCTCCCTACG 60.179 60.000 1.59 0.00 0.00 3.51 F
5698 9544 0.475828 AACAGCTAGGTCTGGGGGTT 60.476 55.000 0.00 0.00 38.36 4.11 F
5699 9545 1.201429 ACAGCTAGGTCTGGGGGTTG 61.201 60.000 0.00 0.00 38.36 3.77 F
5700 9546 1.616628 AGCTAGGTCTGGGGGTTGG 60.617 63.158 0.00 0.00 0.00 3.77 F
5702 9548 2.001269 CTAGGTCTGGGGGTTGGGG 61.001 68.421 0.00 0.00 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 1722 1.805945 GATCACGTCACGTCCAGGC 60.806 63.158 0.00 0.00 38.32 4.85 R
1739 2112 2.480419 CCAAGAGCAAACTAGTCAACCG 59.520 50.000 0.00 0.00 0.00 4.44 R
2742 3182 0.606401 CACACTGGCCGAGGTCAATT 60.606 55.000 0.00 0.00 0.00 2.32 R
3299 3740 0.959553 GATACTGCCAGCTAGCCGTA 59.040 55.000 12.13 10.47 36.96 4.02 R
3774 4215 2.794103 TGCAGTGACCATTATGCAGTT 58.206 42.857 0.00 0.00 43.34 3.16 R
5018 8082 0.671781 ACTGGTGCACTCGCTTCATC 60.672 55.000 17.98 0.00 39.64 2.92 R
5729 9575 0.181350 CAGGTAATCTGCCCCCTCAC 59.819 60.000 0.00 0.00 36.60 3.51 R
7029 16378 2.629617 CAGAAAGTGGAAACCTGCCAAT 59.370 45.455 0.00 0.00 37.12 3.16 R
7327 16814 6.528321 TGTATCCAAGAAATAGGATGCTCAG 58.472 40.000 10.16 0.00 44.37 3.35 R
7918 17527 2.158959 CAGTTCCTACGGCGCTTCG 61.159 63.158 6.90 5.82 0.00 3.79 R
8481 18111 5.563842 GGTATGACTTCTTTCTTGAATGCG 58.436 41.667 0.00 0.00 0.00 4.73 R
8891 18534 0.258484 CACATAGGTGGGGGCAATGA 59.742 55.000 0.00 0.00 41.45 2.57 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
19 20 0.625849 AAGTCCATGGTGATGACCCC 59.374 55.000 12.58 0.00 42.34 4.95
45 46 1.604604 CTCCGCACCAAAAAGGAAGA 58.395 50.000 0.00 0.00 41.22 2.87
50 51 2.476241 CGCACCAAAAAGGAAGAAATGC 59.524 45.455 0.00 0.00 41.22 3.56
70 71 9.669353 GAAATGCTATTTGACCATGTATTACAG 57.331 33.333 2.53 0.00 0.00 2.74
174 175 9.573133 CAACAAATGATCTTACTGGAAAATACC 57.427 33.333 0.00 0.00 0.00 2.73
175 176 8.877864 ACAAATGATCTTACTGGAAAATACCA 57.122 30.769 0.00 0.00 38.33 3.25
191 192 2.364972 ACCAGAACCAAAGACCCAAG 57.635 50.000 0.00 0.00 0.00 3.61
205 206 7.550906 CCAAAGACCCAAGAGATAGAGTTTAAG 59.449 40.741 0.00 0.00 0.00 1.85
223 224 3.848978 AAGACCTAGGTCACCTAAGGT 57.151 47.619 37.27 19.55 46.76 3.50
262 263 7.379750 CAACCTAGGCCTTATAACTATCTCAC 58.620 42.308 12.58 0.00 0.00 3.51
270 272 6.448006 CCTTATAACTATCTCACCCAACTCG 58.552 44.000 0.00 0.00 0.00 4.18
487 490 1.202371 TCTTAGGACCATAAGTGCGCG 60.202 52.381 0.00 0.00 42.70 6.86
488 491 0.179094 TTAGGACCATAAGTGCGCGG 60.179 55.000 8.83 0.00 42.70 6.46
498 501 2.746277 GTGCGCGGGAGATGGTTT 60.746 61.111 8.83 0.00 0.00 3.27
532 535 1.164313 AATGGCATCCATCCCATCCT 58.836 50.000 0.00 0.00 44.40 3.24
543 546 2.605825 TCCCATCCTTCCCCAAGTAT 57.394 50.000 0.00 0.00 0.00 2.12
544 547 2.871796 TCCCATCCTTCCCCAAGTATT 58.128 47.619 0.00 0.00 0.00 1.89
558 561 4.511082 CCCAAGTATTGTTGCACCTTTTTG 59.489 41.667 0.00 0.00 46.99 2.44
567 570 3.518634 TGCACCTTTTTGAGAAACACC 57.481 42.857 0.00 0.00 0.00 4.16
570 573 3.428316 GCACCTTTTTGAGAAACACCGAA 60.428 43.478 0.00 0.00 0.00 4.30
590 594 7.438160 CACCGAATACATATAGACACACACAAT 59.562 37.037 0.00 0.00 0.00 2.71
616 622 8.857098 TGACTACTAAAGACTATAATTGCGGAT 58.143 33.333 0.00 0.00 0.00 4.18
737 743 8.634335 TTTAAGATCAATGAAATCACCACTGA 57.366 30.769 0.00 0.00 0.00 3.41
813 819 7.867445 ATGAAACAGTAAATAGCCAAAAACG 57.133 32.000 0.00 0.00 0.00 3.60
814 820 6.797454 TGAAACAGTAAATAGCCAAAAACGT 58.203 32.000 0.00 0.00 0.00 3.99
815 821 6.913673 TGAAACAGTAAATAGCCAAAAACGTC 59.086 34.615 0.00 0.00 0.00 4.34
816 822 5.025986 ACAGTAAATAGCCAAAAACGTCG 57.974 39.130 0.00 0.00 0.00 5.12
817 823 4.512571 ACAGTAAATAGCCAAAAACGTCGT 59.487 37.500 0.00 0.00 0.00 4.34
861 867 4.150980 CGCATTAACGAGACAGTAAACCAA 59.849 41.667 0.00 0.00 34.06 3.67
863 869 5.049954 GCATTAACGAGACAGTAAACCAACA 60.050 40.000 0.00 0.00 0.00 3.33
888 896 2.990479 GGCTCTCCAACCCACGAT 59.010 61.111 0.00 0.00 0.00 3.73
894 902 2.695666 CTCTCCAACCCACGATATCAGT 59.304 50.000 3.12 0.00 0.00 3.41
902 910 1.541889 CCACGATATCAGTGCTGGCAT 60.542 52.381 17.06 0.00 38.22 4.40
905 913 2.067013 CGATATCAGTGCTGGCATCTG 58.933 52.381 3.12 14.36 0.00 2.90
947 955 6.755141 TCGCCTCGCAATAAATAATATCCTAC 59.245 38.462 0.00 0.00 0.00 3.18
949 957 7.254117 CGCCTCGCAATAAATAATATCCTACAG 60.254 40.741 0.00 0.00 0.00 2.74
1214 1223 2.436824 GCCGCTTTCCCAGTCCTC 60.437 66.667 0.00 0.00 0.00 3.71
1215 1224 2.960688 GCCGCTTTCCCAGTCCTCT 61.961 63.158 0.00 0.00 0.00 3.69
1216 1225 1.219393 CCGCTTTCCCAGTCCTCTC 59.781 63.158 0.00 0.00 0.00 3.20
1338 1707 1.694133 CCTCTGGTGAGCATCCTCCC 61.694 65.000 0.00 0.00 38.93 4.30
1493 1862 0.723129 GCATTTGCGTTCGCGTTGTA 60.723 50.000 5.77 0.00 43.62 2.41
1563 1932 3.246880 GTCAGGGTTGGACGGGGT 61.247 66.667 0.00 0.00 0.00 4.95
1755 2128 8.556213 TTAATATTTCGGTTGACTAGTTTGCT 57.444 30.769 0.00 0.00 0.00 3.91
1844 2281 5.069501 AGTCGGAAGAAATACCACTGTAC 57.930 43.478 0.00 0.00 45.01 2.90
1845 2282 4.771054 AGTCGGAAGAAATACCACTGTACT 59.229 41.667 0.00 0.00 45.01 2.73
1846 2283 5.948162 AGTCGGAAGAAATACCACTGTACTA 59.052 40.000 0.00 0.00 45.01 1.82
1896 2333 7.454260 GAAACTCAGTTTCCATTTCCTGTAT 57.546 36.000 18.27 0.00 44.04 2.29
1899 2336 7.016153 ACTCAGTTTCCATTTCCTGTATGTA 57.984 36.000 0.00 0.00 0.00 2.29
1923 2360 2.722094 TGCACCCTAAATCGATGCTTT 58.278 42.857 0.00 0.00 37.20 3.51
1970 2407 9.019656 AGAATGGTGTGTGCTTATAATTTGTAA 57.980 29.630 0.00 0.00 0.00 2.41
1971 2408 9.632807 GAATGGTGTGTGCTTATAATTTGTAAA 57.367 29.630 0.00 0.00 0.00 2.01
1972 2409 9.988815 AATGGTGTGTGCTTATAATTTGTAAAA 57.011 25.926 0.00 0.00 0.00 1.52
1973 2410 9.988815 ATGGTGTGTGCTTATAATTTGTAAAAA 57.011 25.926 0.00 0.00 0.00 1.94
1974 2411 9.469807 TGGTGTGTGCTTATAATTTGTAAAAAG 57.530 29.630 0.00 0.00 0.00 2.27
1975 2412 9.685828 GGTGTGTGCTTATAATTTGTAAAAAGA 57.314 29.630 0.00 0.00 0.00 2.52
2069 2506 7.444183 CCACTTGGTTACTCATTTTGACTCTTA 59.556 37.037 0.00 0.00 0.00 2.10
2125 2562 2.833794 ACAGTTAGCGTTCTCTGCAAA 58.166 42.857 0.00 0.00 33.85 3.68
2127 2564 3.187227 ACAGTTAGCGTTCTCTGCAAATG 59.813 43.478 0.00 0.00 33.85 2.32
2263 2701 7.039363 TGACATTGAAGTTTAGGTTATTTGGGG 60.039 37.037 0.00 0.00 0.00 4.96
2273 2711 2.536066 GTTATTTGGGGCCTCACCTTT 58.464 47.619 3.60 0.00 39.10 3.11
2274 2712 3.564790 GGTTATTTGGGGCCTCACCTTTA 60.565 47.826 3.60 0.00 39.10 1.85
2394 2834 7.056635 AGATGTTTTTGCTAGTGTATGGCTAT 58.943 34.615 0.00 0.00 36.12 2.97
2434 2874 0.174845 TCCTGAAATCACGGCGTAGG 59.825 55.000 14.22 15.45 0.00 3.18
2444 2884 2.140717 CACGGCGTAGGTTTTCTTCTT 58.859 47.619 14.22 0.00 0.00 2.52
2449 2889 4.316645 GGCGTAGGTTTTCTTCTTCTTCT 58.683 43.478 0.00 0.00 0.00 2.85
2565 3005 2.179424 TCCTAGTCTCCACTTATCCCCC 59.821 54.545 0.00 0.00 33.62 5.40
2576 3016 1.048724 TTATCCCCCGTCTCCTGCAG 61.049 60.000 6.78 6.78 0.00 4.41
2578 3018 3.322466 CCCCCGTCTCCTGCAGTT 61.322 66.667 13.81 0.00 0.00 3.16
2618 3058 4.621068 TTTTTGATCCATGCTCATCGTC 57.379 40.909 0.00 0.00 0.00 4.20
2637 3077 2.440385 CTTGCTCGACACCCTGCTCA 62.440 60.000 0.00 0.00 0.00 4.26
2742 3182 1.896660 GGCTGTCAACGCCAAGGAA 60.897 57.895 9.95 0.00 46.77 3.36
2802 3242 2.049433 CCGGCGTGAAGTTCTCGT 60.049 61.111 23.66 0.00 35.98 4.18
2877 3317 1.001641 AGTGCCAAGCTCCATGGTC 60.002 57.895 12.58 5.12 40.23 4.02
2926 3366 5.189180 CAGAGTTGGAAGAGAATTAAGGGG 58.811 45.833 0.00 0.00 0.00 4.79
3060 3500 5.650266 TGGACTTGTATAATCAAATTGGCGT 59.350 36.000 0.00 0.00 0.00 5.68
3069 3509 5.895636 AATCAAATTGGCGTTCATACTCA 57.104 34.783 0.00 0.00 0.00 3.41
3152 3592 7.869937 TGGAAATTTCAATACTCAAATTTGCGA 59.130 29.630 19.49 2.43 45.80 5.10
3226 3666 1.460504 CATGCATGAGAACCAGCAGT 58.539 50.000 22.59 0.00 40.71 4.40
3299 3740 2.612567 TTCGCGCGCAATCCTTTGT 61.613 52.632 32.61 0.00 35.17 2.83
3322 3763 1.134401 GGCTAGCTGGCAGTATCAACA 60.134 52.381 24.41 0.00 41.37 3.33
3377 3818 3.308473 GGAGGGAAATTAGAGGCAAGTGT 60.308 47.826 0.00 0.00 0.00 3.55
3924 4380 7.172875 ACAGAATAGCAGATGAATATTGCTGAC 59.827 37.037 8.75 1.75 46.78 3.51
3991 4450 9.764363 CATCTATCTTTGTACTTTGTAGGCATA 57.236 33.333 0.00 0.00 0.00 3.14
4476 4963 9.928618 TTTAATGAATCAGTATCATTTACCCCA 57.071 29.630 7.03 0.00 43.19 4.96
4540 5030 2.379972 AGACCTGAGGAGGAACGTATG 58.620 52.381 4.99 0.00 42.93 2.39
4611 5388 8.663025 CGAACTTCTACTTCTACACACTGTATA 58.337 37.037 0.00 0.00 31.66 1.47
4661 7700 6.929049 CCGACAAGCTAATCTATGGTATCAAA 59.071 38.462 0.00 0.00 0.00 2.69
4886 7943 1.815003 GCTCAATGTAGGTTGCAAGCT 59.185 47.619 31.64 31.64 40.36 3.74
5018 8082 9.333497 CAAGAAAAAGAAAAAGAAAAGGCAAAG 57.667 29.630 0.00 0.00 0.00 2.77
5312 9158 1.953686 GAACTGCTTTGCACAAGGGTA 59.046 47.619 9.63 0.00 33.79 3.69
5634 9480 0.322975 ACAGGACTCATGTGGTGCTC 59.677 55.000 11.09 0.00 33.24 4.26
5636 9482 1.078143 GGACTCATGTGGTGCTCCC 60.078 63.158 1.59 0.00 0.00 4.30
5637 9483 1.557269 GGACTCATGTGGTGCTCCCT 61.557 60.000 1.59 0.00 0.00 4.20
5638 9484 1.195115 GACTCATGTGGTGCTCCCTA 58.805 55.000 1.59 0.00 0.00 3.53
5639 9485 0.905357 ACTCATGTGGTGCTCCCTAC 59.095 55.000 1.59 0.00 0.00 3.18
5640 9486 0.179100 CTCATGTGGTGCTCCCTACG 60.179 60.000 1.59 0.00 0.00 3.51
5641 9487 0.902984 TCATGTGGTGCTCCCTACGT 60.903 55.000 1.59 0.00 0.00 3.57
5642 9488 0.740868 CATGTGGTGCTCCCTACGTG 60.741 60.000 0.00 2.93 0.00 4.49
5643 9489 1.899437 ATGTGGTGCTCCCTACGTGG 61.899 60.000 0.00 0.00 0.00 4.94
5644 9490 3.702048 TGGTGCTCCCTACGTGGC 61.702 66.667 0.00 0.00 0.00 5.01
5645 9491 3.702048 GGTGCTCCCTACGTGGCA 61.702 66.667 0.00 0.00 0.00 4.92
5646 9492 2.584608 GTGCTCCCTACGTGGCAT 59.415 61.111 0.00 0.00 37.05 4.40
5647 9493 1.521681 GTGCTCCCTACGTGGCATC 60.522 63.158 0.00 0.00 37.05 3.91
5649 9495 2.731571 GCTCCCTACGTGGCATCCA 61.732 63.158 0.00 0.00 0.00 3.41
5657 9503 4.073052 GTGGCATCCACGGTTCAA 57.927 55.556 0.00 0.00 44.95 2.69
5658 9504 1.579429 GTGGCATCCACGGTTCAAC 59.421 57.895 0.00 0.00 44.95 3.18
5659 9505 0.889186 GTGGCATCCACGGTTCAACT 60.889 55.000 0.00 0.00 44.95 3.16
5660 9506 0.888736 TGGCATCCACGGTTCAACTG 60.889 55.000 0.00 0.00 0.00 3.16
5661 9507 0.889186 GGCATCCACGGTTCAACTGT 60.889 55.000 0.00 0.00 38.46 3.55
5668 9514 3.991605 CACGGTTCAACTGTGCTATAC 57.008 47.619 16.59 0.00 46.96 1.47
5669 9515 2.671396 CACGGTTCAACTGTGCTATACC 59.329 50.000 16.59 0.00 46.96 2.73
5670 9516 1.924524 CGGTTCAACTGTGCTATACCG 59.075 52.381 0.00 0.00 40.68 4.02
5672 9518 2.354403 GGTTCAACTGTGCTATACCGGT 60.354 50.000 13.98 13.98 0.00 5.28
5673 9519 2.665649 TCAACTGTGCTATACCGGTG 57.334 50.000 19.93 0.56 33.03 4.94
5674 9520 2.172679 TCAACTGTGCTATACCGGTGA 58.827 47.619 19.93 3.75 37.81 4.02
5675 9521 2.563620 TCAACTGTGCTATACCGGTGAA 59.436 45.455 19.93 3.60 37.30 3.18
5676 9522 2.667473 ACTGTGCTATACCGGTGAAC 57.333 50.000 19.93 5.88 0.00 3.18
5677 9523 1.897133 ACTGTGCTATACCGGTGAACA 59.103 47.619 19.93 10.92 0.00 3.18
5678 9524 2.094182 ACTGTGCTATACCGGTGAACAG 60.094 50.000 23.67 23.67 39.49 3.16
5679 9525 2.165641 CTGTGCTATACCGGTGAACAGA 59.834 50.000 21.77 10.93 36.51 3.41
5680 9526 2.563620 TGTGCTATACCGGTGAACAGAA 59.436 45.455 19.93 0.00 0.00 3.02
5681 9527 2.928116 GTGCTATACCGGTGAACAGAAC 59.072 50.000 19.93 9.52 0.00 3.01
5682 9528 2.563620 TGCTATACCGGTGAACAGAACA 59.436 45.455 19.93 1.46 0.00 3.18
5683 9529 3.187700 GCTATACCGGTGAACAGAACAG 58.812 50.000 19.93 0.00 0.00 3.16
5685 9531 1.045407 TACCGGTGAACAGAACAGCT 58.955 50.000 19.93 0.00 34.23 4.24
5687 9533 1.000955 ACCGGTGAACAGAACAGCTAG 59.999 52.381 6.12 0.00 34.23 3.42
5689 9535 1.000955 CGGTGAACAGAACAGCTAGGT 59.999 52.381 0.00 0.00 34.23 3.08
5690 9536 2.689646 GGTGAACAGAACAGCTAGGTC 58.310 52.381 0.00 0.00 33.71 3.85
5695 9541 2.998493 AGAACAGCTAGGTCTGGGG 58.002 57.895 3.32 0.00 44.48 4.96
5696 9542 0.618968 AGAACAGCTAGGTCTGGGGG 60.619 60.000 3.32 0.00 44.48 5.40
5697 9543 0.910088 GAACAGCTAGGTCTGGGGGT 60.910 60.000 0.00 0.00 38.36 4.95
5698 9544 0.475828 AACAGCTAGGTCTGGGGGTT 60.476 55.000 0.00 0.00 38.36 4.11
5699 9545 1.201429 ACAGCTAGGTCTGGGGGTTG 61.201 60.000 0.00 0.00 38.36 3.77
5700 9546 1.616628 AGCTAGGTCTGGGGGTTGG 60.617 63.158 0.00 0.00 0.00 3.77
5702 9548 2.001269 CTAGGTCTGGGGGTTGGGG 61.001 68.421 0.00 0.00 0.00 4.96
5721 9567 3.917988 GGGGGTAGATATAAACGGTTCG 58.082 50.000 0.00 0.00 0.00 3.95
5722 9568 3.573967 GGGGGTAGATATAAACGGTTCGA 59.426 47.826 0.00 0.00 0.00 3.71
5723 9569 4.321527 GGGGGTAGATATAAACGGTTCGAG 60.322 50.000 0.00 0.00 0.00 4.04
5725 9571 5.010012 GGGGTAGATATAAACGGTTCGAGAA 59.990 44.000 0.00 0.00 0.00 2.87
5726 9572 6.294955 GGGGTAGATATAAACGGTTCGAGAAT 60.295 42.308 0.00 0.00 0.00 2.40
5727 9573 7.094205 GGGGTAGATATAAACGGTTCGAGAATA 60.094 40.741 0.00 0.00 0.00 1.75
5728 9574 7.967303 GGGTAGATATAAACGGTTCGAGAATAG 59.033 40.741 0.00 0.00 0.00 1.73
5729 9575 7.967303 GGTAGATATAAACGGTTCGAGAATAGG 59.033 40.741 0.00 0.00 0.00 2.57
5730 9576 7.521871 AGATATAAACGGTTCGAGAATAGGT 57.478 36.000 0.00 0.00 0.00 3.08
5732 9578 3.947910 AAACGGTTCGAGAATAGGTGA 57.052 42.857 0.00 0.00 0.00 4.02
5733 9579 3.505464 AACGGTTCGAGAATAGGTGAG 57.495 47.619 0.00 0.00 0.00 3.51
5766 10801 3.519510 ACCTGGTTAAATGAGCTCAGCTA 59.480 43.478 22.96 12.56 39.88 3.32
5854 10889 8.363390 TCTTCATTTGTGTTGTTTGCCATAATA 58.637 29.630 0.00 0.00 0.00 0.98
6024 11061 3.106827 TGTGAGAAGGGCTGACATGATA 58.893 45.455 0.00 0.00 35.74 2.15
6469 11690 8.649973 AACTTTTCTAGTATAGCACACATAGC 57.350 34.615 0.00 0.00 38.99 2.97
6493 11714 9.107177 AGCTGTTATTTTCTGATCTTCAGTATG 57.893 33.333 4.56 0.00 44.58 2.39
7029 16378 4.552355 CAAAGCAAATGAGAGCACATCAA 58.448 39.130 0.00 0.00 0.00 2.57
7071 16420 6.249192 TCTGGTGAAGAATCTAGTCTCTGAA 58.751 40.000 0.00 0.00 29.54 3.02
7837 17434 5.716979 TCTTAGATGAACTACCTGGCCTAT 58.283 41.667 3.32 0.00 0.00 2.57
7918 17527 7.391833 AGTTGGAATCCTATGAGAAGTTCAAAC 59.608 37.037 5.50 0.00 39.77 2.93
8820 18463 0.746063 TTTTCTGCTGCAGGGTGTTG 59.254 50.000 27.79 3.06 31.51 3.33
8891 18534 1.109323 GGGTTTTCTGCTGCCTGTGT 61.109 55.000 0.00 0.00 0.00 3.72
8932 18575 1.646912 TCCATCCGGTGACCTGTTTA 58.353 50.000 0.00 0.00 0.00 2.01
8958 18601 2.355363 TGCCGACGACTTTGGACG 60.355 61.111 0.00 0.00 36.75 4.79
9023 18666 2.436173 GACTTCCAGGGCTAGCAGTTAT 59.564 50.000 18.24 0.00 0.00 1.89
9059 18702 7.555639 TTTACCTTTTCGCGAAACAATAATG 57.444 32.000 32.32 16.92 0.00 1.90
9126 18777 6.315642 GCACTCTGTTATCTAGGGTAAAAACC 59.684 42.308 0.00 0.00 0.00 3.27
9129 18780 6.633856 TCTGTTATCTAGGGTAAAAACCGAC 58.366 40.000 0.00 0.00 0.00 4.79
9212 18863 2.042762 TGGGCTATCAGGGGTGCT 59.957 61.111 0.00 0.00 0.00 4.40
9264 18915 2.344592 TGTTTGGAGTGAGGGGTATGT 58.655 47.619 0.00 0.00 0.00 2.29
9279 18930 1.953686 GTATGTGTGGGTTTGCTGTGT 59.046 47.619 0.00 0.00 0.00 3.72
9294 18945 5.384063 TGCTGTGTGTTTGGTTATATTGG 57.616 39.130 0.00 0.00 0.00 3.16
9315 18966 1.202290 GCTTGTGTGTTGGTCTGGTTG 60.202 52.381 0.00 0.00 0.00 3.77
9320 18971 0.395173 GTGTTGGTCTGGTTGGTGGT 60.395 55.000 0.00 0.00 0.00 4.16
9342 18994 3.118408 TGTGTTTACCTGCTCTTGTGAGT 60.118 43.478 0.00 0.00 42.13 3.41
9348 19000 2.360475 GCTCTTGTGAGTGGGGCC 60.360 66.667 0.00 0.00 42.13 5.80
9389 19042 6.233434 TCTGAACCTGATGTTATGCCATATC 58.767 40.000 0.00 0.00 37.29 1.63
9421 19074 2.435372 TGGATGGCCAAGTGAATACC 57.565 50.000 10.96 4.17 42.49 2.73
9454 19109 2.079170 TGCACCCATGAAACCAGAAA 57.921 45.000 0.00 0.00 0.00 2.52
9467 19122 9.154847 CATGAAACCAGAAATTTATTTCCCTTC 57.845 33.333 10.71 9.13 45.52 3.46
9471 19126 7.100458 ACCAGAAATTTATTTCCCTTCGATG 57.900 36.000 10.71 0.00 45.52 3.84
9472 19127 6.889722 ACCAGAAATTTATTTCCCTTCGATGA 59.110 34.615 10.71 0.00 45.52 2.92
9473 19128 7.396055 ACCAGAAATTTATTTCCCTTCGATGAA 59.604 33.333 10.71 0.00 45.52 2.57
9487 19155 1.760192 GATGAATCTTGTGCTGGCCT 58.240 50.000 3.32 0.00 0.00 5.19
9489 19157 2.408271 TGAATCTTGTGCTGGCCTAG 57.592 50.000 3.32 0.34 0.00 3.02
9533 19201 1.450531 CTGCCCATGATCCGGCTTTC 61.451 60.000 14.56 0.00 45.90 2.62
9537 19205 2.027192 GCCCATGATCCGGCTTTCTATA 60.027 50.000 0.00 0.00 42.21 1.31
9543 19211 6.207417 CCATGATCCGGCTTTCTATATTTTGT 59.793 38.462 0.00 0.00 0.00 2.83
9645 22411 8.939929 AGCTATAATGGAATTACATGATTCACG 58.060 33.333 5.78 0.00 42.43 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 9.189156 ACTGTAATACATGGTCAAATAGCATTT 57.811 29.630 0.00 0.00 43.83 2.32
174 175 3.492102 TCTCTTGGGTCTTTGGTTCTG 57.508 47.619 0.00 0.00 0.00 3.02
175 176 5.094387 TCTATCTCTTGGGTCTTTGGTTCT 58.906 41.667 0.00 0.00 0.00 3.01
191 192 7.013559 GGTGACCTAGGTCTTAAACTCTATCTC 59.986 44.444 35.83 12.26 44.80 2.75
270 272 8.268738 GCATTGTTTCATTCTCTTACAACAAAC 58.731 33.333 0.00 0.00 37.59 2.93
318 320 8.962884 ATCGAGCAATAATGTATGCCAATATA 57.037 30.769 0.00 0.00 43.57 0.86
319 321 7.870509 ATCGAGCAATAATGTATGCCAATAT 57.129 32.000 0.00 0.00 43.57 1.28
320 322 8.962884 ATATCGAGCAATAATGTATGCCAATA 57.037 30.769 0.00 0.00 43.57 1.90
321 323 7.870509 ATATCGAGCAATAATGTATGCCAAT 57.129 32.000 0.00 0.00 43.57 3.16
367 370 2.480419 AGTTGTGTTGCTGATTCGCTAC 59.520 45.455 7.63 7.63 36.43 3.58
425 428 8.964476 TCATAGGTTAAGAAAATGGACTGATC 57.036 34.615 0.00 0.00 0.00 2.92
487 490 3.536956 TCGTGTGATAAACCATCTCCC 57.463 47.619 0.00 0.00 34.46 4.30
488 491 4.504858 ACTTCGTGTGATAAACCATCTCC 58.495 43.478 0.00 0.00 34.46 3.71
532 535 2.158385 AGGTGCAACAATACTTGGGGAA 60.158 45.455 3.64 0.00 39.98 3.97
543 546 4.688413 GTGTTTCTCAAAAAGGTGCAACAA 59.312 37.500 3.64 0.00 39.98 2.83
544 547 4.241681 GTGTTTCTCAAAAAGGTGCAACA 58.758 39.130 3.64 0.00 39.98 3.33
558 561 7.919091 TGTGTCTATATGTATTCGGTGTTTCTC 59.081 37.037 0.00 0.00 0.00 2.87
567 570 8.480066 GTCATTGTGTGTGTCTATATGTATTCG 58.520 37.037 0.00 0.00 0.00 3.34
570 573 9.967346 GTAGTCATTGTGTGTGTCTATATGTAT 57.033 33.333 0.00 0.00 0.00 2.29
590 594 8.229253 TCCGCAATTATAGTCTTTAGTAGTCA 57.771 34.615 0.00 0.00 0.00 3.41
737 743 2.418628 CGTTTTGTTGACAGTGAGGTGT 59.581 45.455 0.00 0.00 0.00 4.16
793 799 5.007921 ACGACGTTTTTGGCTATTTACTGTT 59.992 36.000 0.00 0.00 0.00 3.16
803 809 2.011222 TGAAAGACGACGTTTTTGGCT 58.989 42.857 19.77 0.00 0.00 4.75
846 852 5.510323 GTGTTTTTGTTGGTTTACTGTCTCG 59.490 40.000 0.00 0.00 0.00 4.04
861 867 1.404035 GTTGGAGAGCCGTGTTTTTGT 59.596 47.619 0.00 0.00 36.79 2.83
863 869 1.029681 GGTTGGAGAGCCGTGTTTTT 58.970 50.000 0.00 0.00 36.79 1.94
888 896 1.499368 TCCAGATGCCAGCACTGATA 58.501 50.000 17.94 7.80 34.07 2.15
894 902 1.153309 CGACATCCAGATGCCAGCA 60.153 57.895 7.56 0.00 42.39 4.41
902 910 1.611977 ACGTTTCTGTCGACATCCAGA 59.388 47.619 20.40 10.04 35.97 3.86
947 955 5.505780 TGGATTTAACCTCCACCATTACTG 58.494 41.667 2.44 0.00 37.87 2.74
949 957 6.126409 TCATGGATTTAACCTCCACCATTAC 58.874 40.000 7.88 0.00 45.27 1.89
952 960 4.879295 TCATGGATTTAACCTCCACCAT 57.121 40.909 7.88 0.00 45.27 3.55
953 961 4.535781 CATCATGGATTTAACCTCCACCA 58.464 43.478 7.88 0.00 45.27 4.17
954 962 3.891366 CCATCATGGATTTAACCTCCACC 59.109 47.826 0.00 0.00 45.27 4.61
955 963 4.792068 TCCATCATGGATTTAACCTCCAC 58.208 43.478 0.66 0.00 45.27 4.02
1210 1219 2.015726 GGAGGGGAGGAGGAGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
1350 1719 2.910479 ACGTCACGTCCAGGCAGA 60.910 61.111 0.00 0.00 33.69 4.26
1353 1722 1.805945 GATCACGTCACGTCCAGGC 60.806 63.158 0.00 0.00 38.32 4.85
1443 1812 3.001939 CCCTATTTATGCCGACACGAAAC 59.998 47.826 0.00 0.00 0.00 2.78
1449 1818 3.717842 GGCCCTATTTATGCCGACA 57.282 52.632 0.00 0.00 35.08 4.35
1493 1862 2.941583 GCCCAACCCCTCTTCCCT 60.942 66.667 0.00 0.00 0.00 4.20
1563 1932 2.852449 TGGTGGTACGCAATCTTTCAA 58.148 42.857 0.00 0.00 43.02 2.69
1739 2112 2.480419 CCAAGAGCAAACTAGTCAACCG 59.520 50.000 0.00 0.00 0.00 4.44
1755 2128 3.149196 GACAAAGAGTTGCCATCCAAGA 58.851 45.455 0.00 0.00 38.39 3.02
1846 2283 9.490379 CCTAGAGTTGTGTTTCAGTAAACTATT 57.510 33.333 0.00 0.00 44.44 1.73
1896 2333 4.681074 TCGATTTAGGGTGCATGATACA 57.319 40.909 0.00 0.00 0.00 2.29
1899 2336 2.816087 GCATCGATTTAGGGTGCATGAT 59.184 45.455 0.00 0.00 35.93 2.45
1970 2407 7.169813 GCCTCTTCGAATGACAAATTTTCTTTT 59.830 33.333 0.00 0.00 0.00 2.27
1971 2408 6.642540 GCCTCTTCGAATGACAAATTTTCTTT 59.357 34.615 0.00 0.00 0.00 2.52
1972 2409 6.015940 AGCCTCTTCGAATGACAAATTTTCTT 60.016 34.615 0.00 0.00 0.00 2.52
1973 2410 5.474876 AGCCTCTTCGAATGACAAATTTTCT 59.525 36.000 0.00 0.00 0.00 2.52
1974 2411 5.703876 AGCCTCTTCGAATGACAAATTTTC 58.296 37.500 0.00 0.00 0.00 2.29
1975 2412 5.712152 AGCCTCTTCGAATGACAAATTTT 57.288 34.783 0.00 0.00 0.00 1.82
1976 2413 5.712152 AAGCCTCTTCGAATGACAAATTT 57.288 34.783 0.00 0.00 0.00 1.82
1977 2414 6.599244 TCATAAGCCTCTTCGAATGACAAATT 59.401 34.615 0.00 0.00 0.00 1.82
1978 2415 6.115446 TCATAAGCCTCTTCGAATGACAAAT 58.885 36.000 0.00 0.00 0.00 2.32
1979 2416 5.487433 TCATAAGCCTCTTCGAATGACAAA 58.513 37.500 0.00 0.00 0.00 2.83
1982 2419 6.481644 AGAAATCATAAGCCTCTTCGAATGAC 59.518 38.462 0.00 0.00 0.00 3.06
2125 2562 3.582208 TCCAAACAGGCTTAAAATGGCAT 59.418 39.130 0.00 0.00 37.29 4.40
2127 2564 3.588955 CTCCAAACAGGCTTAAAATGGC 58.411 45.455 0.00 0.00 37.29 4.40
2263 2701 7.210174 AGAAAAGAAAAACATAAAGGTGAGGC 58.790 34.615 0.00 0.00 0.00 4.70
2273 2711 9.052759 AGAGCGACTAAAGAAAAGAAAAACATA 57.947 29.630 0.00 0.00 0.00 2.29
2274 2712 7.931275 AGAGCGACTAAAGAAAAGAAAAACAT 58.069 30.769 0.00 0.00 0.00 2.71
2394 2834 5.104360 AGGAACAGAGGATGCATAAAGCTAA 60.104 40.000 0.00 0.00 45.94 3.09
2449 2889 4.219507 TGCACCTTCTTTCACTGAAAAACA 59.780 37.500 5.72 0.00 30.84 2.83
2565 3005 3.305398 AGTAGAAAACTGCAGGAGACG 57.695 47.619 19.93 0.00 36.93 4.18
2601 3041 2.830104 CAAGACGATGAGCATGGATCA 58.170 47.619 0.00 0.00 30.86 2.92
2618 3058 1.739562 GAGCAGGGTGTCGAGCAAG 60.740 63.158 0.00 0.00 0.00 4.01
2637 3077 1.893808 CCACACCAACGAGCAAGCT 60.894 57.895 0.00 0.00 0.00 3.74
2742 3182 0.606401 CACACTGGCCGAGGTCAATT 60.606 55.000 0.00 0.00 0.00 2.32
2817 3257 2.748647 TCACGCCGGATCGAGACA 60.749 61.111 5.05 0.00 0.00 3.41
2923 3363 1.278413 GACTAAGAGTGTTCCACCCCC 59.722 57.143 0.00 0.00 34.49 5.40
2926 3366 3.498777 GCTTTGACTAAGAGTGTTCCACC 59.501 47.826 0.49 0.00 35.80 4.61
3085 3525 6.347061 AATTTGAAGGGAGGGATTAGATGT 57.653 37.500 0.00 0.00 0.00 3.06
3152 3592 6.369615 GGCACTGATTAAAAACATTGCTTCAT 59.630 34.615 12.64 0.00 40.65 2.57
3163 3603 6.309980 CGTTGCATTATGGCACTGATTAAAAA 59.690 34.615 0.00 0.00 44.86 1.94
3226 3666 2.741985 CATGCAACCCTCGTCGCA 60.742 61.111 0.00 0.00 39.01 5.10
3281 3722 1.292571 TACAAAGGATTGCGCGCGAA 61.293 50.000 37.18 24.32 40.34 4.70
3299 3740 0.959553 GATACTGCCAGCTAGCCGTA 59.040 55.000 12.13 10.47 36.96 4.02
3377 3818 1.915228 GCCCCTGCTAATCTCACCA 59.085 57.895 0.00 0.00 33.53 4.17
3396 3837 3.594603 TTCGTTGATCTGGACTCCTTC 57.405 47.619 0.00 0.00 0.00 3.46
3586 4027 2.257409 ATCCATGGTGCTGACCGGTC 62.257 60.000 28.17 28.17 46.62 4.79
3774 4215 2.794103 TGCAGTGACCATTATGCAGTT 58.206 42.857 0.00 0.00 43.34 3.16
3924 4380 7.693969 ACAAGAGAGAGGAAATAAATTGGTG 57.306 36.000 0.00 0.00 0.00 4.17
3991 4450 6.494059 AGGCTTCCTTTTTCTGTGGTAATAT 58.506 36.000 0.00 0.00 0.00 1.28
4476 4963 6.533730 TCAAACTGAACTGATGGTTGATAGT 58.466 36.000 0.00 0.00 38.41 2.12
4540 5030 4.000331 AGTACATACAGCCAGATCATGC 58.000 45.455 0.00 0.00 0.00 4.06
4611 5388 4.339247 ACAAGCATGTAGAGCAAAACAACT 59.661 37.500 0.00 0.00 38.24 3.16
4886 7943 2.708216 TCTGCCATTTTCTCCGCATA 57.292 45.000 0.00 0.00 0.00 3.14
5018 8082 0.671781 ACTGGTGCACTCGCTTCATC 60.672 55.000 17.98 0.00 39.64 2.92
5589 9435 0.106419 AACGGGTGGATGGTGTGTTT 60.106 50.000 0.00 0.00 0.00 2.83
5590 9436 0.536460 GAACGGGTGGATGGTGTGTT 60.536 55.000 0.00 0.00 0.00 3.32
5591 9437 1.072505 GAACGGGTGGATGGTGTGT 59.927 57.895 0.00 0.00 0.00 3.72
5592 9438 1.072332 TGAACGGGTGGATGGTGTG 59.928 57.895 0.00 0.00 0.00 3.82
5593 9439 1.072505 GTGAACGGGTGGATGGTGT 59.927 57.895 0.00 0.00 0.00 4.16
5594 9440 1.674322 GGTGAACGGGTGGATGGTG 60.674 63.158 0.00 0.00 0.00 4.17
5595 9441 2.754375 GGTGAACGGGTGGATGGT 59.246 61.111 0.00 0.00 0.00 3.55
5596 9442 2.045340 GGGTGAACGGGTGGATGG 60.045 66.667 0.00 0.00 0.00 3.51
5597 9443 1.074072 TTGGGTGAACGGGTGGATG 59.926 57.895 0.00 0.00 0.00 3.51
5598 9444 1.074248 GTTGGGTGAACGGGTGGAT 59.926 57.895 0.00 0.00 0.00 3.41
5599 9445 2.332312 CTGTTGGGTGAACGGGTGGA 62.332 60.000 0.00 0.00 37.30 4.02
5641 9487 0.888736 CAGTTGAACCGTGGATGCCA 60.889 55.000 0.00 0.00 0.00 4.92
5642 9488 0.889186 ACAGTTGAACCGTGGATGCC 60.889 55.000 0.00 0.00 0.00 4.40
5643 9489 0.238289 CACAGTTGAACCGTGGATGC 59.762 55.000 3.80 0.00 0.00 3.91
5644 9490 0.238289 GCACAGTTGAACCGTGGATG 59.762 55.000 13.01 0.00 0.00 3.51
5645 9491 0.108585 AGCACAGTTGAACCGTGGAT 59.891 50.000 13.01 0.00 0.00 3.41
5646 9492 0.753867 TAGCACAGTTGAACCGTGGA 59.246 50.000 13.01 0.00 0.00 4.02
5647 9493 1.808411 ATAGCACAGTTGAACCGTGG 58.192 50.000 13.01 0.00 0.00 4.94
5649 9495 2.673043 CGGTATAGCACAGTTGAACCGT 60.673 50.000 2.37 0.00 42.50 4.83
5653 9499 2.563620 TCACCGGTATAGCACAGTTGAA 59.436 45.455 6.87 0.00 0.00 2.69
5655 9501 2.665649 TCACCGGTATAGCACAGTTG 57.334 50.000 6.87 0.00 0.00 3.16
5656 9502 2.300723 TGTTCACCGGTATAGCACAGTT 59.699 45.455 6.87 0.00 0.00 3.16
5657 9503 1.897133 TGTTCACCGGTATAGCACAGT 59.103 47.619 6.87 0.00 0.00 3.55
5658 9504 2.165641 TCTGTTCACCGGTATAGCACAG 59.834 50.000 6.87 11.88 33.00 3.66
5659 9505 2.172679 TCTGTTCACCGGTATAGCACA 58.827 47.619 6.87 0.49 0.00 4.57
5660 9506 2.928116 GTTCTGTTCACCGGTATAGCAC 59.072 50.000 6.87 0.00 0.00 4.40
5661 9507 2.563620 TGTTCTGTTCACCGGTATAGCA 59.436 45.455 6.87 6.10 0.00 3.49
5662 9508 3.187700 CTGTTCTGTTCACCGGTATAGC 58.812 50.000 6.87 0.64 0.00 2.97
5664 9510 2.829720 AGCTGTTCTGTTCACCGGTATA 59.170 45.455 6.87 0.00 0.00 1.47
5665 9511 1.623811 AGCTGTTCTGTTCACCGGTAT 59.376 47.619 6.87 0.00 0.00 2.73
5666 9512 1.045407 AGCTGTTCTGTTCACCGGTA 58.955 50.000 6.87 0.00 0.00 4.02
5667 9513 1.000955 CTAGCTGTTCTGTTCACCGGT 59.999 52.381 0.00 0.00 0.00 5.28
5668 9514 1.673033 CCTAGCTGTTCTGTTCACCGG 60.673 57.143 0.00 0.00 0.00 5.28
5669 9515 1.000955 ACCTAGCTGTTCTGTTCACCG 59.999 52.381 0.00 0.00 0.00 4.94
5670 9516 2.300437 AGACCTAGCTGTTCTGTTCACC 59.700 50.000 0.00 0.00 0.00 4.02
5672 9518 2.300152 CCAGACCTAGCTGTTCTGTTCA 59.700 50.000 15.82 0.00 34.06 3.18
5673 9519 2.354203 CCCAGACCTAGCTGTTCTGTTC 60.354 54.545 15.82 0.00 34.06 3.18
5674 9520 1.625818 CCCAGACCTAGCTGTTCTGTT 59.374 52.381 15.82 0.00 34.06 3.16
5675 9521 1.270907 CCCAGACCTAGCTGTTCTGT 58.729 55.000 15.82 0.00 34.06 3.41
5676 9522 0.539051 CCCCAGACCTAGCTGTTCTG 59.461 60.000 12.04 12.04 34.06 3.02
5677 9523 0.618968 CCCCCAGACCTAGCTGTTCT 60.619 60.000 0.00 0.00 34.06 3.01
5678 9524 0.910088 ACCCCCAGACCTAGCTGTTC 60.910 60.000 0.00 0.00 34.06 3.18
5679 9525 0.475828 AACCCCCAGACCTAGCTGTT 60.476 55.000 0.00 0.00 34.06 3.16
5680 9526 1.161113 AACCCCCAGACCTAGCTGT 59.839 57.895 0.00 0.00 34.06 4.40
5681 9527 1.604378 CAACCCCCAGACCTAGCTG 59.396 63.158 0.00 0.00 35.66 4.24
5682 9528 1.616628 CCAACCCCCAGACCTAGCT 60.617 63.158 0.00 0.00 0.00 3.32
5683 9529 2.680370 CCCAACCCCCAGACCTAGC 61.680 68.421 0.00 0.00 0.00 3.42
5685 9531 2.126372 CCCCAACCCCCAGACCTA 59.874 66.667 0.00 0.00 0.00 3.08
5700 9546 3.573967 TCGAACCGTTTATATCTACCCCC 59.426 47.826 0.00 0.00 0.00 5.40
5702 9548 5.695851 TCTCGAACCGTTTATATCTACCC 57.304 43.478 0.00 0.00 0.00 3.69
5705 9551 8.509690 CACCTATTCTCGAACCGTTTATATCTA 58.490 37.037 0.00 0.00 0.00 1.98
5706 9552 7.230108 TCACCTATTCTCGAACCGTTTATATCT 59.770 37.037 0.00 0.00 0.00 1.98
5708 9554 7.281040 TCACCTATTCTCGAACCGTTTATAT 57.719 36.000 0.00 0.00 0.00 0.86
5710 9556 5.451520 CCTCACCTATTCTCGAACCGTTTAT 60.452 44.000 0.00 0.00 0.00 1.40
5711 9557 4.142315 CCTCACCTATTCTCGAACCGTTTA 60.142 45.833 0.00 0.00 0.00 2.01
5712 9558 3.368116 CCTCACCTATTCTCGAACCGTTT 60.368 47.826 0.00 0.00 0.00 3.60
5713 9559 2.165845 CCTCACCTATTCTCGAACCGTT 59.834 50.000 0.00 0.00 0.00 4.44
5714 9560 1.749634 CCTCACCTATTCTCGAACCGT 59.250 52.381 0.00 0.00 0.00 4.83
5715 9561 1.067212 CCCTCACCTATTCTCGAACCG 59.933 57.143 0.00 0.00 0.00 4.44
5718 9564 1.789523 CCCCCTCACCTATTCTCGAA 58.210 55.000 0.00 0.00 0.00 3.71
5719 9565 0.759436 GCCCCCTCACCTATTCTCGA 60.759 60.000 0.00 0.00 0.00 4.04
5720 9566 1.048724 TGCCCCCTCACCTATTCTCG 61.049 60.000 0.00 0.00 0.00 4.04
5721 9567 0.761802 CTGCCCCCTCACCTATTCTC 59.238 60.000 0.00 0.00 0.00 2.87
5722 9568 0.343372 TCTGCCCCCTCACCTATTCT 59.657 55.000 0.00 0.00 0.00 2.40
5723 9569 1.439543 ATCTGCCCCCTCACCTATTC 58.560 55.000 0.00 0.00 0.00 1.75
5725 9571 2.339769 GTAATCTGCCCCCTCACCTAT 58.660 52.381 0.00 0.00 0.00 2.57
5726 9572 1.694693 GGTAATCTGCCCCCTCACCTA 60.695 57.143 0.00 0.00 0.00 3.08
5727 9573 0.988678 GGTAATCTGCCCCCTCACCT 60.989 60.000 0.00 0.00 0.00 4.00
5728 9574 0.988678 AGGTAATCTGCCCCCTCACC 60.989 60.000 0.00 0.00 0.00 4.02
5729 9575 0.181350 CAGGTAATCTGCCCCCTCAC 59.819 60.000 0.00 0.00 36.60 3.51
5730 9576 0.988145 CCAGGTAATCTGCCCCCTCA 60.988 60.000 0.00 0.00 42.05 3.86
5732 9578 0.552615 AACCAGGTAATCTGCCCCCT 60.553 55.000 0.00 0.00 42.05 4.79
5733 9579 1.218844 TAACCAGGTAATCTGCCCCC 58.781 55.000 0.00 0.00 42.05 5.40
7029 16378 2.629617 CAGAAAGTGGAAACCTGCCAAT 59.370 45.455 0.00 0.00 37.12 3.16
7327 16814 6.528321 TGTATCCAAGAAATAGGATGCTCAG 58.472 40.000 10.16 0.00 44.37 3.35
7918 17527 2.158959 CAGTTCCTACGGCGCTTCG 61.159 63.158 6.90 5.82 0.00 3.79
8481 18111 5.563842 GGTATGACTTCTTTCTTGAATGCG 58.436 41.667 0.00 0.00 0.00 4.73
8891 18534 0.258484 CACATAGGTGGGGGCAATGA 59.742 55.000 0.00 0.00 41.45 2.57
8932 18575 1.747709 AGTCGTCGGCACATACTACT 58.252 50.000 0.00 0.00 0.00 2.57
8958 18601 5.072464 AGGATCAGTTCCCTAGCTAATTTCC 59.928 44.000 0.00 0.00 46.81 3.13
9023 18666 7.487189 TCGCGAAAAGGTAAAAATAAACAAACA 59.513 29.630 6.20 0.00 0.00 2.83
9126 18777 1.369209 CCGCAGCAAACACTTGTCG 60.369 57.895 0.00 0.00 34.79 4.35
9129 18780 0.317269 CTGTCCGCAGCAAACACTTG 60.317 55.000 0.00 0.00 35.77 3.16
9152 18803 0.875059 AGCAAAAAGAGTACCTGCGC 59.125 50.000 0.00 0.00 38.07 6.09
9212 18863 2.068821 GCATGAGAGGCCCTGAGGA 61.069 63.158 0.00 0.00 33.47 3.71
9264 18915 1.067283 CAAACACACAGCAAACCCACA 60.067 47.619 0.00 0.00 0.00 4.17
9279 18930 4.835615 ACACAAGCCCAATATAACCAAACA 59.164 37.500 0.00 0.00 0.00 2.83
9294 18945 0.751643 ACCAGACCAACACACAAGCC 60.752 55.000 0.00 0.00 0.00 4.35
9315 18966 1.202770 AGAGCAGGTAAACACACCACC 60.203 52.381 0.00 0.00 41.40 4.61
9320 18971 3.118408 ACTCACAAGAGCAGGTAAACACA 60.118 43.478 0.00 0.00 46.09 3.72
9342 18994 3.569210 CAGTGACACAGGGCCCCA 61.569 66.667 21.43 5.71 0.00 4.96
9348 19000 3.732212 TCAGAAACATCAGTGACACAGG 58.268 45.455 8.59 0.00 0.00 4.00
9436 19089 3.683365 AATTTCTGGTTTCATGGGTGC 57.317 42.857 0.00 0.00 0.00 5.01
9454 19109 8.408601 CACAAGATTCATCGAAGGGAAATAAAT 58.591 33.333 0.00 0.00 0.00 1.40
9467 19122 0.379669 GGCCAGCACAAGATTCATCG 59.620 55.000 0.00 0.00 0.00 3.84
9471 19126 2.169352 TCTCTAGGCCAGCACAAGATTC 59.831 50.000 5.01 0.00 0.00 2.52
9472 19127 2.191400 TCTCTAGGCCAGCACAAGATT 58.809 47.619 5.01 0.00 0.00 2.40
9473 19128 1.871418 TCTCTAGGCCAGCACAAGAT 58.129 50.000 5.01 0.00 0.00 2.40
9489 19157 9.587772 AGCCATATAACGATATTACAACATCTC 57.412 33.333 0.00 0.00 0.00 2.75
9526 19194 6.293955 CCATACCCACAAAATATAGAAAGCCG 60.294 42.308 0.00 0.00 0.00 5.52
9533 19201 7.765695 AGAATGCCATACCCACAAAATATAG 57.234 36.000 0.00 0.00 0.00 1.31
9537 19205 5.760484 AAAGAATGCCATACCCACAAAAT 57.240 34.783 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.