Multiple sequence alignment - TraesCS3A01G097100

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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 TraesCS3A01G097100 chr3A 100.000 5307 0 0 1 5307 63064558 63069864 0.000000e+00 9801.0
1 TraesCS3A01G097100 chr3B 90.517 3016 187 43 4 2970 79118976 79121941 0.000000e+00 3893.0
2 TraesCS3A01G097100 chr3B 96.522 1179 35 4 3008 4186 79121942 79123114 0.000000e+00 1945.0
3 TraesCS3A01G097100 chr3B 94.897 725 28 4 4585 5307 370553805 370553088 0.000000e+00 1125.0
4 TraesCS3A01G097100 chr3B 91.213 717 53 6 4588 5302 817821139 817820431 0.000000e+00 966.0
5 TraesCS3A01G097100 chr3B 90.571 350 18 4 4238 4587 79123392 79123726 2.920000e-122 449.0
6 TraesCS3A01G097100 chr3B 100.000 32 0 0 2666 2697 73587675 73587706 5.740000e-05 60.2
7 TraesCS3A01G097100 chr3D 95.660 2189 67 14 2412 4587 49639448 49641621 0.000000e+00 3491.0
8 TraesCS3A01G097100 chr3D 92.385 1983 92 27 454 2414 49637447 49639392 0.000000e+00 2771.0
9 TraesCS3A01G097100 chr3D 80.514 467 72 12 1772 2228 335214263 335214720 1.830000e-89 340.0
10 TraesCS3A01G097100 chr7A 97.517 725 12 1 4583 5307 702619787 702619069 0.000000e+00 1234.0
11 TraesCS3A01G097100 chr5A 97.095 723 13 1 4585 5307 237958418 237959132 0.000000e+00 1212.0
12 TraesCS3A01G097100 chr5A 95.978 721 23 2 4587 5307 416144920 416144206 0.000000e+00 1166.0
13 TraesCS3A01G097100 chr5A 100.000 31 0 0 2666 2696 706493266 706493236 2.060000e-04 58.4
14 TraesCS3A01G097100 chr6A 96.801 719 17 1 4589 5307 123505624 123506336 0.000000e+00 1195.0
15 TraesCS3A01G097100 chr7B 95.410 719 27 1 4589 5307 587653385 587654097 0.000000e+00 1140.0
16 TraesCS3A01G097100 chr7B 94.847 718 31 1 4590 5307 241774265 241773554 0.000000e+00 1116.0
17 TraesCS3A01G097100 chr2A 94.282 717 35 5 4591 5307 599426404 599425694 0.000000e+00 1092.0
18 TraesCS3A01G097100 chr1D 81.522 460 72 9 1772 2228 468031860 468032309 3.020000e-97 366.0
19 TraesCS3A01G097100 chr1D 86.061 165 17 6 1368 1530 109975939 109975779 7.070000e-39 172.0
20 TraesCS3A01G097100 chr1D 77.517 298 53 13 2483 2776 109974658 109974371 3.290000e-37 167.0
21 TraesCS3A01G097100 chr5D 80.702 456 70 12 1781 2228 69676738 69677183 6.580000e-89 339.0
22 TraesCS3A01G097100 chr5B 80.488 451 74 12 1773 2220 407321073 407320634 3.060000e-87 333.0
23 TraesCS3A01G097100 chr4A 80.488 451 75 11 1773 2220 638240065 638239625 3.060000e-87 333.0
24 TraesCS3A01G097100 chr4A 100.000 32 0 0 2666 2697 735595592 735595623 5.740000e-05 60.2
25 TraesCS3A01G097100 chr1A 79.915 468 73 12 1772 2228 163096403 163096860 1.840000e-84 324.0
26 TraesCS3A01G097100 chr1A 88.966 145 12 4 1368 1510 113861155 113861013 5.460000e-40 176.0
27 TraesCS3A01G097100 chr1A 77.627 295 55 10 2483 2776 113859890 113859606 9.140000e-38 169.0
28 TraesCS3A01G097100 chr1A 100.000 32 0 0 2666 2697 69993920 69993951 5.740000e-05 60.2
29 TraesCS3A01G097100 chr7D 79.657 467 75 13 1772 2228 573799087 573799543 8.580000e-83 318.0
30 TraesCS3A01G097100 chr1B 88.276 145 13 4 1368 1510 166594594 166594452 2.540000e-38 171.0
31 TraesCS3A01G097100 chr1B 76.846 298 55 13 2483 2776 166593286 166592999 7.120000e-34 156.0
32 TraesCS3A01G097100 chrUn 100.000 32 0 0 2666 2697 8833377 8833408 5.740000e-05 60.2
33 TraesCS3A01G097100 chr4D 100.000 32 0 0 2666 2697 73444234 73444265 5.740000e-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 TraesCS3A01G097100 chr3A 63064558 63069864 5306 False 9801.000000 9801 100.000000 1 5307 1 chr3A.!!$F1 5306
1 TraesCS3A01G097100 chr3B 79118976 79123726 4750 False 2095.666667 3893 92.536667 4 4587 3 chr3B.!!$F2 4583
2 TraesCS3A01G097100 chr3B 370553088 370553805 717 True 1125.000000 1125 94.897000 4585 5307 1 chr3B.!!$R1 722
3 TraesCS3A01G097100 chr3B 817820431 817821139 708 True 966.000000 966 91.213000 4588 5302 1 chr3B.!!$R2 714
4 TraesCS3A01G097100 chr3D 49637447 49641621 4174 False 3131.000000 3491 94.022500 454 4587 2 chr3D.!!$F2 4133
5 TraesCS3A01G097100 chr7A 702619069 702619787 718 True 1234.000000 1234 97.517000 4583 5307 1 chr7A.!!$R1 724
6 TraesCS3A01G097100 chr5A 237958418 237959132 714 False 1212.000000 1212 97.095000 4585 5307 1 chr5A.!!$F1 722
7 TraesCS3A01G097100 chr5A 416144206 416144920 714 True 1166.000000 1166 95.978000 4587 5307 1 chr5A.!!$R1 720
8 TraesCS3A01G097100 chr6A 123505624 123506336 712 False 1195.000000 1195 96.801000 4589 5307 1 chr6A.!!$F1 718
9 TraesCS3A01G097100 chr7B 587653385 587654097 712 False 1140.000000 1140 95.410000 4589 5307 1 chr7B.!!$F1 718
10 TraesCS3A01G097100 chr7B 241773554 241774265 711 True 1116.000000 1116 94.847000 4590 5307 1 chr7B.!!$R1 717
11 TraesCS3A01G097100 chr2A 599425694 599426404 710 True 1092.000000 1092 94.282000 4591 5307 1 chr2A.!!$R1 716

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
491 497 0.030773 CCGGTCATCGTCATCGTCAT 59.969 55.0 0.00 0.00 38.33 3.06 F
778 784 0.250124 TGATCGACCAAACGCCAACT 60.250 50.0 0.00 0.00 0.00 3.16 F
1180 1191 0.460987 CTCCGAGCGCTTGGATTTCT 60.461 55.0 40.03 2.75 42.06 2.52 F
1678 1709 0.040204 CCAGTGGAAATCTTGGGCCT 59.960 55.0 1.68 0.00 0.00 5.19 F
2311 2361 0.893270 TGCTTTGGATGGGACGTTGG 60.893 55.0 0.00 0.00 0.00 3.77 F
2739 2848 0.108424 CTGTGCTGTCTCTACTGGCC 60.108 60.0 0.00 0.00 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 1683 0.038744 AGATTTCCACTGGCCACTGG 59.961 55.000 22.00 22.00 0.0 4.00 R
1656 1687 0.251742 CCCAAGATTTCCACTGGCCA 60.252 55.000 4.71 4.71 0.0 5.36 R
2337 2387 0.673644 GGGACACTACTGCATGCGTT 60.674 55.000 14.09 4.51 0.0 4.84 R
2493 2601 0.746659 GTGCAGGGAATAATGGCCAC 59.253 55.000 8.16 0.00 0.0 5.01 R
3884 3999 0.253327 AAGGGTCTGATTCGCCTTCC 59.747 55.000 0.00 0.00 0.0 3.46 R
4512 4865 1.006519 TGGGACCCAAGAGAGAGAGAG 59.993 57.143 12.05 0.00 0.0 3.20 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
52 53 3.963383 ACGAAGCAGAAATGTCGTTTT 57.037 38.095 0.00 0.00 43.78 2.43
62 63 0.309612 ATGTCGTTTTCGTGGTTGCC 59.690 50.000 0.00 0.00 44.46 4.52
64 65 2.188161 TCGTTTTCGTGGTTGCCCC 61.188 57.895 0.00 0.00 44.46 5.80
72 73 1.817209 GTGGTTGCCCCGTTGAAAA 59.183 52.632 0.00 0.00 35.15 2.29
74 75 1.365999 GGTTGCCCCGTTGAAAAGG 59.634 57.895 0.00 0.00 0.00 3.11
84 85 2.035832 CCGTTGAAAAGGGTCATTTGCT 59.964 45.455 0.00 0.00 46.38 3.91
85 86 3.492482 CCGTTGAAAAGGGTCATTTGCTT 60.492 43.478 0.00 0.00 46.38 3.91
86 87 3.735746 CGTTGAAAAGGGTCATTTGCTTC 59.264 43.478 0.00 0.00 0.00 3.86
91 92 5.363580 TGAAAAGGGTCATTTGCTTCTTCTT 59.636 36.000 0.00 0.00 0.00 2.52
113 114 2.308347 TTTGCTTGTGTTACGCGATG 57.692 45.000 15.93 0.00 0.00 3.84
128 129 3.736252 ACGCGATGTATTGCTTCTGTATC 59.264 43.478 15.93 0.00 34.99 2.24
134 135 4.298626 TGTATTGCTTCTGTATCCCCTCT 58.701 43.478 0.00 0.00 0.00 3.69
137 138 0.249657 GCTTCTGTATCCCCTCTGCG 60.250 60.000 0.00 0.00 0.00 5.18
144 145 2.632996 TGTATCCCCTCTGCGAATAAGG 59.367 50.000 0.00 0.00 0.00 2.69
149 150 2.632996 CCCCTCTGCGAATAAGGTCATA 59.367 50.000 0.00 0.00 0.00 2.15
161 162 7.587757 GCGAATAAGGTCATATAACTTTGCAAG 59.412 37.037 0.00 0.00 0.00 4.01
166 167 5.358160 AGGTCATATAACTTTGCAAGAAGGC 59.642 40.000 0.00 0.00 0.00 4.35
171 172 1.286880 CTTTGCAAGAAGGCCACCG 59.713 57.895 5.01 0.00 0.00 4.94
172 173 2.753931 CTTTGCAAGAAGGCCACCGC 62.754 60.000 5.01 5.30 0.00 5.68
194 195 5.210715 GCCATCATAGCAAATTCTTTCTCG 58.789 41.667 0.00 0.00 0.00 4.04
195 196 5.008019 GCCATCATAGCAAATTCTTTCTCGA 59.992 40.000 0.00 0.00 0.00 4.04
198 199 8.777413 CCATCATAGCAAATTCTTTCTCGATTA 58.223 33.333 0.00 0.00 0.00 1.75
204 205 7.103641 AGCAAATTCTTTCTCGATTAGTACCA 58.896 34.615 0.00 0.00 0.00 3.25
207 208 8.552034 CAAATTCTTTCTCGATTAGTACCATCC 58.448 37.037 0.00 0.00 0.00 3.51
208 209 5.434352 TCTTTCTCGATTAGTACCATCCG 57.566 43.478 0.00 0.00 0.00 4.18
212 213 3.572682 TCTCGATTAGTACCATCCGCAAT 59.427 43.478 0.00 0.00 0.00 3.56
260 261 4.025401 CCAACGCCAACGCTCACC 62.025 66.667 0.00 0.00 45.53 4.02
261 262 2.972505 CAACGCCAACGCTCACCT 60.973 61.111 0.00 0.00 45.53 4.00
262 263 2.665185 AACGCCAACGCTCACCTC 60.665 61.111 0.00 0.00 45.53 3.85
263 264 4.681978 ACGCCAACGCTCACCTCC 62.682 66.667 0.00 0.00 45.53 4.30
264 265 4.680237 CGCCAACGCTCACCTCCA 62.680 66.667 0.00 0.00 0.00 3.86
265 266 3.050275 GCCAACGCTCACCTCCAC 61.050 66.667 0.00 0.00 0.00 4.02
266 267 2.425592 CCAACGCTCACCTCCACA 59.574 61.111 0.00 0.00 0.00 4.17
267 268 1.003355 CCAACGCTCACCTCCACAT 60.003 57.895 0.00 0.00 0.00 3.21
268 269 1.300971 CCAACGCTCACCTCCACATG 61.301 60.000 0.00 0.00 0.00 3.21
269 270 1.003355 AACGCTCACCTCCACATGG 60.003 57.895 0.00 0.00 0.00 3.66
270 271 2.821366 CGCTCACCTCCACATGGC 60.821 66.667 0.00 0.00 34.44 4.40
272 273 1.001641 GCTCACCTCCACATGGCTT 60.002 57.895 0.00 0.00 34.44 4.35
275 276 1.004044 CTCACCTCCACATGGCTTTCT 59.996 52.381 0.00 0.00 34.44 2.52
277 278 0.036010 ACCTCCACATGGCTTTCTCG 60.036 55.000 0.00 0.00 34.44 4.04
283 284 3.004315 TCCACATGGCTTTCTCGTTTTTC 59.996 43.478 0.00 0.00 34.44 2.29
285 286 4.499696 CCACATGGCTTTCTCGTTTTTCTT 60.500 41.667 0.00 0.00 0.00 2.52
286 287 4.442073 CACATGGCTTTCTCGTTTTTCTTG 59.558 41.667 0.00 0.00 0.00 3.02
287 288 4.097892 ACATGGCTTTCTCGTTTTTCTTGT 59.902 37.500 0.00 0.00 0.00 3.16
289 290 5.066968 TGGCTTTCTCGTTTTTCTTGTTT 57.933 34.783 0.00 0.00 0.00 2.83
290 291 5.099575 TGGCTTTCTCGTTTTTCTTGTTTC 58.900 37.500 0.00 0.00 0.00 2.78
291 292 4.204370 GGCTTTCTCGTTTTTCTTGTTTCG 59.796 41.667 0.00 0.00 0.00 3.46
299 305 5.579511 TCGTTTTTCTTGTTTCGTCTCTCTT 59.420 36.000 0.00 0.00 0.00 2.85
301 307 6.408325 CGTTTTTCTTGTTTCGTCTCTCTTTC 59.592 38.462 0.00 0.00 0.00 2.62
308 314 5.175859 TGTTTCGTCTCTCTTTCTGTTGTT 58.824 37.500 0.00 0.00 0.00 2.83
311 317 2.726760 CGTCTCTCTTTCTGTTGTTCCG 59.273 50.000 0.00 0.00 0.00 4.30
335 341 2.810274 CCTACTTTGATCGATGCCATGG 59.190 50.000 7.63 7.63 0.00 3.66
337 343 1.064463 ACTTTGATCGATGCCATGGGT 60.064 47.619 15.13 0.00 0.00 4.51
357 363 3.349006 CGTGAGCAGCACCCACAC 61.349 66.667 11.50 0.00 44.85 3.82
360 366 2.113986 GAGCAGCACCCACACCTT 59.886 61.111 0.00 0.00 0.00 3.50
373 379 2.305927 CCACACCTTGACCAACCTATCT 59.694 50.000 0.00 0.00 0.00 1.98
384 390 3.270877 CCAACCTATCTTTCAAGTCCCG 58.729 50.000 0.00 0.00 0.00 5.14
431 437 0.098728 GTCGTTGTTGCTGCTGTGTT 59.901 50.000 0.00 0.00 0.00 3.32
442 448 1.338973 CTGCTGTGTTGCAACCTCATT 59.661 47.619 26.14 0.00 42.83 2.57
474 480 2.470821 CTCTTATCGTTGCTAACCCCG 58.529 52.381 0.00 0.00 0.00 5.73
487 493 2.027605 CCCCGGTCATCGTCATCG 59.972 66.667 0.00 0.00 37.11 3.84
488 494 2.782222 CCCCGGTCATCGTCATCGT 61.782 63.158 0.00 0.00 38.33 3.73
489 495 1.299165 CCCGGTCATCGTCATCGTC 60.299 63.158 0.00 0.00 38.33 4.20
490 496 1.431845 CCGGTCATCGTCATCGTCA 59.568 57.895 0.00 0.00 38.33 4.35
491 497 0.030773 CCGGTCATCGTCATCGTCAT 59.969 55.000 0.00 0.00 38.33 3.06
492 498 1.399572 CGGTCATCGTCATCGTCATC 58.600 55.000 0.00 0.00 38.33 2.92
510 516 0.697511 TCCATCCCCACCAATCCGAT 60.698 55.000 0.00 0.00 0.00 4.18
513 519 1.768684 ATCCCCACCAATCCGATCCG 61.769 60.000 0.00 0.00 0.00 4.18
515 521 2.591715 CCACCAATCCGATCCGCC 60.592 66.667 0.00 0.00 0.00 6.13
544 550 2.742348 TCTCCTTCACCCGTGCTTATA 58.258 47.619 0.00 0.00 0.00 0.98
547 553 3.035363 TCCTTCACCCGTGCTTATATCA 58.965 45.455 0.00 0.00 0.00 2.15
553 559 1.497991 CCGTGCTTATATCACACCCG 58.502 55.000 6.49 0.00 34.27 5.28
554 560 1.497991 CGTGCTTATATCACACCCGG 58.502 55.000 0.00 0.00 34.27 5.73
565 571 2.111878 CACCCGGAGCCCATCATC 59.888 66.667 0.73 0.00 0.00 2.92
573 579 2.611473 CGGAGCCCATCATCTACACATC 60.611 54.545 0.00 0.00 0.00 3.06
576 582 2.984604 AGCCCATCATCTACACATCCAT 59.015 45.455 0.00 0.00 0.00 3.41
577 583 3.079578 GCCCATCATCTACACATCCATG 58.920 50.000 0.00 0.00 0.00 3.66
598 604 4.407818 TGCGTTAGGTTATTCATTTTGCG 58.592 39.130 0.00 0.00 0.00 4.85
686 692 6.116711 TCACTTTTGCACCACCTAATACTA 57.883 37.500 0.00 0.00 0.00 1.82
687 693 5.935789 TCACTTTTGCACCACCTAATACTAC 59.064 40.000 0.00 0.00 0.00 2.73
688 694 5.938125 CACTTTTGCACCACCTAATACTACT 59.062 40.000 0.00 0.00 0.00 2.57
690 696 7.604927 CACTTTTGCACCACCTAATACTACTAA 59.395 37.037 0.00 0.00 0.00 2.24
695 701 6.893554 TGCACCACCTAATACTACTAAAGAGA 59.106 38.462 0.00 0.00 0.00 3.10
778 784 0.250124 TGATCGACCAAACGCCAACT 60.250 50.000 0.00 0.00 0.00 3.16
815 821 4.555709 TCACACACGTGGCCACCC 62.556 66.667 29.95 6.81 43.79 4.61
841 847 6.507900 CACCTACTGCGTACTACTACTACTA 58.492 44.000 0.00 0.00 0.00 1.82
859 865 5.713861 ACTACTACTAATCAAACACGTCCCT 59.286 40.000 0.00 0.00 0.00 4.20
897 903 1.410850 CCCCCTGCGGTGTCTGATAT 61.411 60.000 0.00 0.00 0.00 1.63
959 965 2.359354 CACCGGGCGGAAATGTCA 60.359 61.111 6.32 0.00 38.96 3.58
1013 1019 2.306847 GGTTAGCAGGAGAGAGAGAGG 58.693 57.143 0.00 0.00 0.00 3.69
1179 1190 2.009888 CTCCGAGCGCTTGGATTTC 58.990 57.895 40.03 13.48 42.06 2.17
1180 1191 0.460987 CTCCGAGCGCTTGGATTTCT 60.461 55.000 40.03 2.75 42.06 2.52
1181 1192 0.740868 TCCGAGCGCTTGGATTTCTG 60.741 55.000 37.62 14.62 38.21 3.02
1201 1218 2.983725 AAGAGGTTGGTGGTGCTGCC 62.984 60.000 0.00 0.00 37.90 4.85
1223 1244 4.038080 GGTTGCTTTGACCGGCCG 62.038 66.667 21.04 21.04 0.00 6.13
1224 1245 4.038080 GTTGCTTTGACCGGCCGG 62.038 66.667 42.17 42.17 42.03 6.13
1345 1375 2.873288 CTGCTTCTTGCTTCCCGC 59.127 61.111 0.00 0.00 43.37 6.13
1356 1386 4.143333 TTCCCGCGCTCTGTAGCC 62.143 66.667 5.56 0.00 46.68 3.93
1551 1581 4.475135 GCCCCGCTCCTTGTCCTC 62.475 72.222 0.00 0.00 0.00 3.71
1577 1608 3.764160 CTTCGCCTCCCTGGATGCC 62.764 68.421 7.72 0.00 38.35 4.40
1603 1634 4.143333 ATGCTTCGCCCGCGTAGT 62.143 61.111 15.58 0.00 38.71 2.73
1624 1655 0.589229 CTCGTAGACGTGCGATGTCC 60.589 60.000 0.00 0.00 40.24 4.02
1650 1681 1.375523 GTTAGGGTCGTGGGCAGTG 60.376 63.158 0.00 0.00 0.00 3.66
1651 1682 2.589157 TTAGGGTCGTGGGCAGTGG 61.589 63.158 0.00 0.00 0.00 4.00
1677 1708 1.607801 GCCAGTGGAAATCTTGGGCC 61.608 60.000 15.20 0.00 33.93 5.80
1678 1709 0.040204 CCAGTGGAAATCTTGGGCCT 59.960 55.000 1.68 0.00 0.00 5.19
1692 1723 2.238521 TGGGCCTGTGAGAATTTTGTC 58.761 47.619 4.53 0.00 0.00 3.18
1698 1729 4.378874 GCCTGTGAGAATTTTGTCTACTGC 60.379 45.833 0.00 0.00 0.00 4.40
1793 1830 2.292267 GGGTTGGCACATCATGACTAG 58.708 52.381 0.00 0.00 39.30 2.57
1840 1877 6.963805 GCTCAACTTGAATGAATTACAGCTAC 59.036 38.462 0.00 0.00 0.00 3.58
1842 1879 8.032952 TCAACTTGAATGAATTACAGCTACTG 57.967 34.615 0.00 0.00 37.52 2.74
1874 1911 4.641989 GGTGACTTGCTGGAATGAATATGT 59.358 41.667 0.00 0.00 0.00 2.29
1876 1913 5.587844 GTGACTTGCTGGAATGAATATGTCT 59.412 40.000 0.00 0.00 0.00 3.41
1916 1953 2.224744 TGAGCTTACATCCTGCCAAACA 60.225 45.455 0.00 0.00 0.00 2.83
1983 2023 7.885009 AGTAAAACAAAAAGCAGGTAGGTTA 57.115 32.000 0.00 0.00 36.83 2.85
2261 2311 7.959651 CCAGAACTTTTCAAGATTTCATAGTCG 59.040 37.037 0.00 0.00 0.00 4.18
2311 2361 0.893270 TGCTTTGGATGGGACGTTGG 60.893 55.000 0.00 0.00 0.00 3.77
2337 2387 8.293867 GGTGTGCATAAAATTAGTGTGACTTTA 58.706 33.333 0.00 0.00 0.00 1.85
2478 2586 7.998753 GCTCATGCTAAAAATGCTCTTTATT 57.001 32.000 0.00 0.00 36.03 1.40
2493 2601 6.151648 TGCTCTTTATTTCCAGATGACAAAGG 59.848 38.462 0.00 0.00 0.00 3.11
2556 2664 2.851195 TCAGGAAGAAGTTCAGGTTGC 58.149 47.619 5.50 0.00 33.93 4.17
2580 2688 5.902613 ATTTTGATACACCATGTCCACTG 57.097 39.130 0.00 0.00 0.00 3.66
2582 2690 4.365514 TTGATACACCATGTCCACTGTT 57.634 40.909 0.00 0.00 0.00 3.16
2583 2691 5.491323 TTGATACACCATGTCCACTGTTA 57.509 39.130 0.00 0.00 0.00 2.41
2585 2693 6.800072 TGATACACCATGTCCACTGTTATA 57.200 37.500 0.00 0.00 0.00 0.98
2587 2695 7.801104 TGATACACCATGTCCACTGTTATATT 58.199 34.615 0.00 0.00 0.00 1.28
2588 2696 7.714813 TGATACACCATGTCCACTGTTATATTG 59.285 37.037 0.00 0.00 0.00 1.90
2589 2697 5.192927 ACACCATGTCCACTGTTATATTGG 58.807 41.667 0.00 0.00 0.00 3.16
2590 2698 5.045213 ACACCATGTCCACTGTTATATTGGA 60.045 40.000 0.00 0.00 35.91 3.53
2594 2702 6.706270 CCATGTCCACTGTTATATTGGAGTAC 59.294 42.308 0.00 0.00 38.64 2.73
2637 2746 5.386958 TTCTATCTTTACTGTGCAGTCGT 57.613 39.130 8.23 0.00 42.54 4.34
2649 2758 1.002366 GCAGTCGTTACATCCAGCTG 58.998 55.000 6.78 6.78 0.00 4.24
2731 2840 2.547642 GCTATGGGATCTGTGCTGTCTC 60.548 54.545 0.00 0.00 0.00 3.36
2739 2848 0.108424 CTGTGCTGTCTCTACTGGCC 60.108 60.000 0.00 0.00 0.00 5.36
2776 2885 7.917505 CCTGTATTGCTCAAATTGTATCCTTTC 59.082 37.037 0.00 0.00 0.00 2.62
2784 2893 7.852945 GCTCAAATTGTATCCTTTCGACAATAG 59.147 37.037 0.28 0.00 41.71 1.73
2927 3042 3.459710 AGTGACTCCCTACAGCTACTT 57.540 47.619 0.00 0.00 0.00 2.24
2937 3052 5.763204 TCCCTACAGCTACTTTGTTTTCTTG 59.237 40.000 0.00 0.00 0.00 3.02
2963 3078 5.067805 CAGCCACTTTGTTTCTACTTTCCTT 59.932 40.000 0.00 0.00 0.00 3.36
2964 3079 5.299531 AGCCACTTTGTTTCTACTTTCCTTC 59.700 40.000 0.00 0.00 0.00 3.46
2973 3088 8.658499 TGTTTCTACTTTCCTTCTGAACTTAC 57.342 34.615 0.00 0.00 31.05 2.34
3034 3149 4.892934 ACCTCTTGGTTACAATGCTGAAAA 59.107 37.500 0.00 0.00 46.05 2.29
3287 3402 7.064728 GGTAAGTATTGAACTAGGCTGTGAAAG 59.935 40.741 0.00 0.00 37.50 2.62
3426 3541 2.239654 TGTGATTGGGAAGACATCTCCC 59.760 50.000 0.64 0.64 43.82 4.30
3659 3774 2.030540 TCATTGTGCTTTGAGCTCTTGC 60.031 45.455 16.19 15.84 42.97 4.01
3719 3834 6.641314 CGACGTGATTAAGGAGTAAGCATAAT 59.359 38.462 0.00 0.00 40.11 1.28
3720 3835 7.169308 CGACGTGATTAAGGAGTAAGCATAATT 59.831 37.037 0.00 0.00 40.11 1.40
3772 3887 9.740710 GTCCACTTTATAAGCCCTATCAATTAT 57.259 33.333 0.00 0.00 0.00 1.28
3811 3926 1.555075 GTAGCTGGATGGTGGTTCTCA 59.445 52.381 0.00 0.00 0.00 3.27
3825 3940 1.483004 GTTCTCAGCCCCTCTTACCTC 59.517 57.143 0.00 0.00 0.00 3.85
3935 4050 2.047655 TTGAACGCCGCCGAGAAT 60.048 55.556 0.00 0.00 38.29 2.40
3938 4053 4.077184 AACGCCGCCGAGAATGGA 62.077 61.111 0.00 0.00 38.29 3.41
3941 4056 4.537433 GCCGCCGAGAATGGAGCT 62.537 66.667 0.00 0.00 0.00 4.09
3948 4063 1.022982 CGAGAATGGAGCTGCTGCAA 61.023 55.000 27.28 11.45 42.74 4.08
3995 4110 2.571757 TGGAGCTCCAAGTACGCG 59.428 61.111 33.41 3.53 44.35 6.01
4178 4293 4.755123 CCTGAGTGTAATGAACGTTCCTTT 59.245 41.667 24.78 19.36 0.00 3.11
4236 4573 3.347958 TTGCTTCTGTTTTGGCTTACG 57.652 42.857 0.00 0.00 0.00 3.18
4263 4604 3.348119 TGTGGTGCTGTTGTAAAAGTGA 58.652 40.909 0.00 0.00 0.00 3.41
4337 4688 7.243604 AGATACAAAATTTCAATTGCTGGGA 57.756 32.000 0.00 0.00 0.00 4.37
4464 4816 5.749596 TTGTACAAGTGTTCAGTGAATGG 57.250 39.130 9.18 0.00 0.00 3.16
4513 4866 9.399797 TCAGTTTGTGATATAAGATGCATTTCT 57.600 29.630 0.00 0.00 0.00 2.52
4514 4867 9.661187 CAGTTTGTGATATAAGATGCATTTCTC 57.339 33.333 0.00 0.00 0.00 2.87
4559 4912 3.249559 CCAGTTGCTGAAGACAAGACTTC 59.750 47.826 5.53 5.53 44.31 3.01
4690 5043 3.222603 ACAAAGCCCTCAAACTCGAAAT 58.777 40.909 0.00 0.00 0.00 2.17
4691 5044 3.636764 ACAAAGCCCTCAAACTCGAAATT 59.363 39.130 0.00 0.00 0.00 1.82
4692 5045 4.825085 ACAAAGCCCTCAAACTCGAAATTA 59.175 37.500 0.00 0.00 0.00 1.40
4693 5046 5.048713 ACAAAGCCCTCAAACTCGAAATTAG 60.049 40.000 0.00 0.00 0.00 1.73
4694 5047 4.553330 AGCCCTCAAACTCGAAATTAGA 57.447 40.909 0.00 0.00 0.00 2.10
4695 5048 4.508662 AGCCCTCAAACTCGAAATTAGAG 58.491 43.478 1.53 1.53 41.27 2.43
4887 5240 7.936950 GCAGAAGAAATCAGCTAAAACTTTT 57.063 32.000 0.00 0.00 37.56 2.27
4989 5343 2.110967 CGGCTGGCTGATGTTGAGG 61.111 63.158 0.00 0.00 0.00 3.86
5218 5574 3.819337 CGGTCCCGTGATAAGAAGATCTA 59.181 47.826 0.00 0.00 34.35 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.699839 AGCTTTCGGTGTTTATCATTGTTC 58.300 37.500 0.00 0.00 0.00 3.18
1 2 5.705609 AGCTTTCGGTGTTTATCATTGTT 57.294 34.783 0.00 0.00 0.00 2.83
2 3 5.699839 GAAGCTTTCGGTGTTTATCATTGT 58.300 37.500 0.00 0.00 0.00 2.71
43 44 0.309612 GGCAACCACGAAAACGACAT 59.690 50.000 0.00 0.00 0.00 3.06
62 63 2.866065 GCAAATGACCCTTTTCAACGGG 60.866 50.000 0.00 0.00 46.26 5.28
64 65 3.369546 AGCAAATGACCCTTTTCAACG 57.630 42.857 0.00 0.00 0.00 4.10
72 73 5.876651 AAAAAGAAGAAGCAAATGACCCT 57.123 34.783 0.00 0.00 0.00 4.34
98 99 3.062099 AGCAATACATCGCGTAACACAAG 59.938 43.478 5.77 0.00 32.59 3.16
102 103 3.305897 CAGAAGCAATACATCGCGTAACA 59.694 43.478 5.77 0.00 32.59 2.41
113 114 4.636249 CAGAGGGGATACAGAAGCAATAC 58.364 47.826 0.00 0.00 39.74 1.89
128 129 0.830648 TGACCTTATTCGCAGAGGGG 59.169 55.000 0.00 0.00 38.43 4.79
134 135 6.540551 TGCAAAGTTATATGACCTTATTCGCA 59.459 34.615 0.00 0.00 0.00 5.10
144 145 5.125417 TGGCCTTCTTGCAAAGTTATATGAC 59.875 40.000 3.32 0.00 46.34 3.06
149 150 2.562738 GGTGGCCTTCTTGCAAAGTTAT 59.437 45.455 3.32 0.00 46.34 1.89
166 167 1.321474 ATTTGCTATGATGGCGGTGG 58.679 50.000 0.00 0.00 0.00 4.61
171 172 5.008019 TCGAGAAAGAATTTGCTATGATGGC 59.992 40.000 0.00 0.00 39.27 4.40
172 173 6.609237 TCGAGAAAGAATTTGCTATGATGG 57.391 37.500 0.00 0.00 39.27 3.51
180 181 7.303634 TGGTACTAATCGAGAAAGAATTTGC 57.696 36.000 0.00 0.00 39.27 3.68
181 182 8.552034 GGATGGTACTAATCGAGAAAGAATTTG 58.448 37.037 0.00 0.00 39.27 2.32
208 209 4.722855 AAAGCGGCGCACCATTGC 62.723 61.111 35.02 0.80 46.21 3.56
248 249 3.050275 GTGGAGGTGAGCGTTGGC 61.050 66.667 0.00 0.00 40.37 4.52
251 252 1.003355 CCATGTGGAGGTGAGCGTT 60.003 57.895 0.00 0.00 37.39 4.84
254 255 0.610232 AAAGCCATGTGGAGGTGAGC 60.610 55.000 2.55 0.00 37.39 4.26
255 256 1.004044 AGAAAGCCATGTGGAGGTGAG 59.996 52.381 2.55 0.00 37.39 3.51
256 257 1.003580 GAGAAAGCCATGTGGAGGTGA 59.996 52.381 2.55 0.00 37.39 4.02
260 261 1.813513 AACGAGAAAGCCATGTGGAG 58.186 50.000 2.55 0.00 37.39 3.86
261 262 2.270352 AAACGAGAAAGCCATGTGGA 57.730 45.000 2.55 0.00 37.39 4.02
262 263 3.004734 AGAAAAACGAGAAAGCCATGTGG 59.995 43.478 0.00 0.00 38.53 4.17
263 264 4.228912 AGAAAAACGAGAAAGCCATGTG 57.771 40.909 0.00 0.00 0.00 3.21
264 265 4.097892 ACAAGAAAAACGAGAAAGCCATGT 59.902 37.500 0.00 0.00 0.00 3.21
265 266 4.610945 ACAAGAAAAACGAGAAAGCCATG 58.389 39.130 0.00 0.00 0.00 3.66
266 267 4.918810 ACAAGAAAAACGAGAAAGCCAT 57.081 36.364 0.00 0.00 0.00 4.40
267 268 4.712122 AACAAGAAAAACGAGAAAGCCA 57.288 36.364 0.00 0.00 0.00 4.75
268 269 4.204370 CGAAACAAGAAAAACGAGAAAGCC 59.796 41.667 0.00 0.00 0.00 4.35
269 270 4.791676 ACGAAACAAGAAAAACGAGAAAGC 59.208 37.500 0.00 0.00 0.00 3.51
270 271 6.248631 AGACGAAACAAGAAAAACGAGAAAG 58.751 36.000 0.00 0.00 0.00 2.62
272 273 5.579511 AGAGACGAAACAAGAAAAACGAGAA 59.420 36.000 0.00 0.00 0.00 2.87
275 276 5.107133 AGAGAGACGAAACAAGAAAAACGA 58.893 37.500 0.00 0.00 0.00 3.85
277 278 7.426743 CAGAAAGAGAGACGAAACAAGAAAAAC 59.573 37.037 0.00 0.00 0.00 2.43
283 284 5.292101 ACAACAGAAAGAGAGACGAAACAAG 59.708 40.000 0.00 0.00 0.00 3.16
285 286 4.755411 ACAACAGAAAGAGAGACGAAACA 58.245 39.130 0.00 0.00 0.00 2.83
286 287 5.276915 GGAACAACAGAAAGAGAGACGAAAC 60.277 44.000 0.00 0.00 0.00 2.78
287 288 4.809426 GGAACAACAGAAAGAGAGACGAAA 59.191 41.667 0.00 0.00 0.00 3.46
289 290 3.550233 CGGAACAACAGAAAGAGAGACGA 60.550 47.826 0.00 0.00 0.00 4.20
290 291 2.726760 CGGAACAACAGAAAGAGAGACG 59.273 50.000 0.00 0.00 0.00 4.18
291 292 2.476997 GCGGAACAACAGAAAGAGAGAC 59.523 50.000 0.00 0.00 0.00 3.36
299 305 0.035739 GTAGGGGCGGAACAACAGAA 59.964 55.000 0.00 0.00 0.00 3.02
301 307 0.036306 AAGTAGGGGCGGAACAACAG 59.964 55.000 0.00 0.00 0.00 3.16
308 314 0.685131 TCGATCAAAGTAGGGGCGGA 60.685 55.000 0.00 0.00 0.00 5.54
311 317 1.230324 GCATCGATCAAAGTAGGGGC 58.770 55.000 0.00 0.00 0.00 5.80
348 354 1.454847 TTGGTCAAGGTGTGGGTGC 60.455 57.895 0.00 0.00 0.00 5.01
350 356 1.229076 GGTTGGTCAAGGTGTGGGT 59.771 57.895 0.00 0.00 0.00 4.51
357 363 5.316987 ACTTGAAAGATAGGTTGGTCAAGG 58.683 41.667 13.90 0.00 43.93 3.61
360 366 4.263331 GGGACTTGAAAGATAGGTTGGTCA 60.263 45.833 0.00 0.00 0.00 4.02
400 406 3.966218 GCAACAACGACATTTACAGTGTC 59.034 43.478 0.00 0.00 41.91 3.67
401 407 3.625764 AGCAACAACGACATTTACAGTGT 59.374 39.130 0.00 0.00 0.00 3.55
403 409 3.548014 GCAGCAACAACGACATTTACAGT 60.548 43.478 0.00 0.00 0.00 3.55
404 410 2.973224 GCAGCAACAACGACATTTACAG 59.027 45.455 0.00 0.00 0.00 2.74
417 423 1.888736 TTGCAACACAGCAGCAACA 59.111 47.368 0.00 0.00 46.54 3.33
442 448 1.134401 CGATAAGAGGAGGCAAAGGCA 60.134 52.381 0.00 0.00 43.71 4.75
448 454 1.195115 AGCAACGATAAGAGGAGGCA 58.805 50.000 0.00 0.00 0.00 4.75
474 480 1.067060 TGGATGACGATGACGATGACC 59.933 52.381 0.00 0.00 42.66 4.02
487 493 1.479389 GGATTGGTGGGGATGGATGAC 60.479 57.143 0.00 0.00 0.00 3.06
488 494 0.852842 GGATTGGTGGGGATGGATGA 59.147 55.000 0.00 0.00 0.00 2.92
489 495 0.538057 CGGATTGGTGGGGATGGATG 60.538 60.000 0.00 0.00 0.00 3.51
490 496 0.697511 TCGGATTGGTGGGGATGGAT 60.698 55.000 0.00 0.00 0.00 3.41
491 497 0.697511 ATCGGATTGGTGGGGATGGA 60.698 55.000 0.00 0.00 0.00 3.41
492 498 0.250901 GATCGGATTGGTGGGGATGG 60.251 60.000 0.00 0.00 0.00 3.51
510 516 2.042843 GAGAAGAGGGGAGGCGGA 60.043 66.667 0.00 0.00 0.00 5.54
513 519 0.618968 TGAAGGAGAAGAGGGGAGGC 60.619 60.000 0.00 0.00 0.00 4.70
515 521 1.199615 GGTGAAGGAGAAGAGGGGAG 58.800 60.000 0.00 0.00 0.00 4.30
544 550 2.692368 ATGGGCTCCGGGTGTGAT 60.692 61.111 0.00 0.00 0.00 3.06
547 553 2.692368 ATGATGGGCTCCGGGTGT 60.692 61.111 0.00 0.00 0.00 4.16
553 559 2.289945 GGATGTGTAGATGATGGGCTCC 60.290 54.545 0.00 0.00 0.00 4.70
554 560 2.369860 TGGATGTGTAGATGATGGGCTC 59.630 50.000 0.00 0.00 0.00 4.70
573 579 5.231991 GCAAAATGAATAACCTAACGCATGG 59.768 40.000 0.00 0.00 0.00 3.66
576 582 4.154375 TCGCAAAATGAATAACCTAACGCA 59.846 37.500 0.00 0.00 0.00 5.24
577 583 4.654015 TCGCAAAATGAATAACCTAACGC 58.346 39.130 0.00 0.00 0.00 4.84
659 665 2.456577 AGGTGGTGCAAAAGTGAGTTT 58.543 42.857 0.00 0.00 0.00 2.66
660 666 2.143876 AGGTGGTGCAAAAGTGAGTT 57.856 45.000 0.00 0.00 0.00 3.01
661 667 3.290948 TTAGGTGGTGCAAAAGTGAGT 57.709 42.857 0.00 0.00 0.00 3.41
703 709 9.421806 TGAAATTGCTTTGGTGATTAGTTTATG 57.578 29.630 0.00 0.00 0.00 1.90
778 784 6.599244 GTGTGAATGAGAGGGATTTTGTGATA 59.401 38.462 0.00 0.00 0.00 2.15
841 847 2.635915 TCCAGGGACGTGTTTGATTAGT 59.364 45.455 0.00 0.00 0.00 2.24
853 859 2.464459 GCGATTTGCTCCAGGGACG 61.464 63.158 0.00 0.00 41.73 4.79
859 865 2.751436 GGCTGGCGATTTGCTCCA 60.751 61.111 0.00 0.00 45.43 3.86
890 896 2.362397 GGACCTGAGCGTGAATATCAGA 59.638 50.000 3.09 0.00 42.48 3.27
891 897 2.546795 GGGACCTGAGCGTGAATATCAG 60.547 54.545 0.00 0.00 40.13 2.90
897 903 2.583441 CCAGGGACCTGAGCGTGAA 61.583 63.158 19.65 0.00 46.30 3.18
917 923 3.977244 GTTTGGTGGTGGGCGCTG 61.977 66.667 7.64 0.00 0.00 5.18
959 965 6.888088 AGACAGGGGCTTTTATATAAAAACGT 59.112 34.615 18.74 11.85 35.04 3.99
1013 1019 2.760385 CCTCCACCCGTCCTCTCC 60.760 72.222 0.00 0.00 0.00 3.71
1169 1180 3.192212 CCAACCTCTTCAGAAATCCAAGC 59.808 47.826 0.00 0.00 0.00 4.01
1179 1190 0.109342 AGCACCACCAACCTCTTCAG 59.891 55.000 0.00 0.00 0.00 3.02
1180 1191 0.179020 CAGCACCACCAACCTCTTCA 60.179 55.000 0.00 0.00 0.00 3.02
1181 1192 1.518903 GCAGCACCACCAACCTCTTC 61.519 60.000 0.00 0.00 0.00 2.87
1201 1218 4.038080 GGTCAAAGCAACCGGGCG 62.038 66.667 6.32 0.00 39.27 6.13
1302 1323 2.747686 GAGCTTCCCACCGAACCA 59.252 61.111 0.00 0.00 0.00 3.67
1303 1324 2.434359 CGAGCTTCCCACCGAACC 60.434 66.667 0.00 0.00 0.00 3.62
1304 1325 1.737008 GACGAGCTTCCCACCGAAC 60.737 63.158 0.00 0.00 0.00 3.95
1305 1326 2.654877 GACGAGCTTCCCACCGAA 59.345 61.111 0.00 0.00 0.00 4.30
1306 1327 3.744719 CGACGAGCTTCCCACCGA 61.745 66.667 0.00 0.00 0.00 4.69
1309 1330 4.070552 AGCCGACGAGCTTCCCAC 62.071 66.667 0.00 0.00 41.41 4.61
1310 1331 4.069232 CAGCCGACGAGCTTCCCA 62.069 66.667 7.92 0.00 42.61 4.37
1620 1651 1.829222 GACCCTAACCGAATCTGGACA 59.171 52.381 0.00 0.00 0.00 4.02
1624 1655 1.470979 CCACGACCCTAACCGAATCTG 60.471 57.143 0.00 0.00 0.00 2.90
1652 1683 0.038744 AGATTTCCACTGGCCACTGG 59.961 55.000 22.00 22.00 0.00 4.00
1653 1684 1.542915 CAAGATTTCCACTGGCCACTG 59.457 52.381 0.00 2.66 0.00 3.66
1654 1685 1.548582 CCAAGATTTCCACTGGCCACT 60.549 52.381 0.00 0.00 0.00 4.00
1655 1686 0.890683 CCAAGATTTCCACTGGCCAC 59.109 55.000 0.00 0.00 0.00 5.01
1656 1687 0.251742 CCCAAGATTTCCACTGGCCA 60.252 55.000 4.71 4.71 0.00 5.36
1660 1691 1.180029 CAGGCCCAAGATTTCCACTG 58.820 55.000 0.00 0.00 0.00 3.66
1677 1708 4.686091 TCGCAGTAGACAAAATTCTCACAG 59.314 41.667 0.00 0.00 0.00 3.66
1678 1709 4.627058 TCGCAGTAGACAAAATTCTCACA 58.373 39.130 0.00 0.00 0.00 3.58
1840 1877 2.012673 GCAAGTCACCCTAAGCATCAG 58.987 52.381 0.00 0.00 0.00 2.90
1842 1879 2.012673 CAGCAAGTCACCCTAAGCATC 58.987 52.381 0.00 0.00 0.00 3.91
1874 1911 3.137544 CACTCTAGCTCCCTTCTCCTAGA 59.862 52.174 0.00 0.00 36.02 2.43
1876 1913 3.124066 TCACTCTAGCTCCCTTCTCCTA 58.876 50.000 0.00 0.00 0.00 2.94
1906 1943 5.183713 TCTTCTCAACATATTGTTTGGCAGG 59.816 40.000 0.00 0.00 38.77 4.85
1907 1944 6.258230 TCTTCTCAACATATTGTTTGGCAG 57.742 37.500 0.00 0.00 38.77 4.85
1916 1953 9.442047 CCACTACTCTTTTCTTCTCAACATATT 57.558 33.333 0.00 0.00 0.00 1.28
1959 1997 6.785337 AACCTACCTGCTTTTTGTTTTACT 57.215 33.333 0.00 0.00 0.00 2.24
1963 2001 5.524971 GGTAACCTACCTGCTTTTTGTTT 57.475 39.130 0.00 0.00 45.52 2.83
1980 2020 4.214119 GGTTGAGTAAAACTTCGGGGTAAC 59.786 45.833 0.00 0.00 0.00 2.50
1983 2023 2.440627 AGGTTGAGTAAAACTTCGGGGT 59.559 45.455 0.00 0.00 28.44 4.95
2261 2311 7.220030 TGCCATTCTAGATAAGGAACTGAATC 58.780 38.462 9.19 0.00 40.86 2.52
2311 2361 6.254281 AGTCACACTAATTTTATGCACACC 57.746 37.500 0.00 0.00 0.00 4.16
2337 2387 0.673644 GGGACACTACTGCATGCGTT 60.674 55.000 14.09 4.51 0.00 4.84
2367 2417 2.223340 CCTAAGATGTCGTTTGCCATGC 60.223 50.000 0.00 0.00 0.00 4.06
2478 2586 1.547675 GGCCACCTTTGTCATCTGGAA 60.548 52.381 0.00 0.00 0.00 3.53
2493 2601 0.746659 GTGCAGGGAATAATGGCCAC 59.253 55.000 8.16 0.00 0.00 5.01
2556 2664 6.599244 ACAGTGGACATGGTGTATCAAAATAG 59.401 38.462 0.00 0.00 0.00 1.73
2587 2695 8.996651 TCAGTCAGATGATAATTAGTACTCCA 57.003 34.615 0.00 0.00 0.00 3.86
2637 2746 3.197766 CACTAAGGGACAGCTGGATGTAA 59.802 47.826 19.93 0.00 32.25 2.41
2649 2758 2.861147 AAAGGAGCACACTAAGGGAC 57.139 50.000 0.00 0.00 0.00 4.46
2731 2840 1.359848 GTTGTGACGATGGCCAGTAG 58.640 55.000 13.05 7.52 0.00 2.57
2739 2848 3.002791 AGCAATACAGGTTGTGACGATG 58.997 45.455 0.00 0.00 0.00 3.84
2776 2885 6.145048 ACGGTAGAAGAAAACAACTATTGTCG 59.855 38.462 0.00 0.00 44.59 4.35
2784 2893 8.900511 AAAGTTTTACGGTAGAAGAAAACAAC 57.099 30.769 14.93 0.00 41.88 3.32
2860 2973 6.668541 ATACTGACAAACTACATGATGTGC 57.331 37.500 8.61 0.00 0.00 4.57
2927 3042 4.021544 ACAAAGTGGCTGTCAAGAAAACAA 60.022 37.500 0.00 0.00 0.00 2.83
2937 3052 5.500645 AAAGTAGAAACAAAGTGGCTGTC 57.499 39.130 0.00 0.00 0.00 3.51
2963 3078 9.696572 ATCTACAGTACCTATTGTAAGTTCAGA 57.303 33.333 0.00 0.00 29.75 3.27
3034 3149 9.825972 CAAACATAATACTCAATCGTGAAGTTT 57.174 29.630 0.00 0.00 31.88 2.66
3287 3402 4.226761 CCGTGTCAAAAATCAAGGTAAGC 58.773 43.478 0.00 0.00 0.00 3.09
3772 3887 7.252708 CAGCTACATATGAAGCACATCAAAAA 58.747 34.615 10.38 0.00 41.32 1.94
3811 3926 0.337428 TAACCGAGGTAAGAGGGGCT 59.663 55.000 0.00 0.00 0.00 5.19
3825 3940 5.997385 ACAAGAAAATTGTAGCAGTAACCG 58.003 37.500 0.00 0.00 0.00 4.44
3884 3999 0.253327 AAGGGTCTGATTCGCCTTCC 59.747 55.000 0.00 0.00 0.00 3.46
3935 4050 2.595463 GTGGTTGCAGCAGCTCCA 60.595 61.111 9.34 12.62 42.74 3.86
3938 4053 4.254709 TCGGTGGTTGCAGCAGCT 62.255 61.111 9.34 0.00 41.44 4.24
3941 4056 4.228567 TCGTCGGTGGTTGCAGCA 62.229 61.111 2.05 0.00 0.00 4.41
3948 4063 3.374402 CAGAGGCTCGTCGGTGGT 61.374 66.667 9.22 0.00 0.00 4.16
4218 4334 3.492313 CATCGTAAGCCAAAACAGAAGC 58.508 45.455 0.00 0.00 37.18 3.86
4236 4573 1.174712 ACAACAGCACCACAGGCATC 61.175 55.000 0.00 0.00 0.00 3.91
4263 4604 2.649312 TGGAGTCATTTGGGGTGAGATT 59.351 45.455 0.00 0.00 0.00 2.40
4271 4622 1.901159 TGCCATTTGGAGTCATTTGGG 59.099 47.619 0.00 0.00 37.39 4.12
4272 4623 2.827322 TCTGCCATTTGGAGTCATTTGG 59.173 45.455 0.00 0.00 37.39 3.28
4273 4624 4.401519 AGATCTGCCATTTGGAGTCATTTG 59.598 41.667 0.00 0.00 37.39 2.32
4274 4625 4.607239 AGATCTGCCATTTGGAGTCATTT 58.393 39.130 0.00 0.00 37.39 2.32
4275 4626 4.246712 AGATCTGCCATTTGGAGTCATT 57.753 40.909 0.00 0.00 37.39 2.57
4276 4627 3.947612 AGATCTGCCATTTGGAGTCAT 57.052 42.857 0.00 0.00 37.39 3.06
4277 4628 3.118261 GGTAGATCTGCCATTTGGAGTCA 60.118 47.826 23.58 0.00 37.39 3.41
4278 4629 3.135530 AGGTAGATCTGCCATTTGGAGTC 59.864 47.826 28.90 0.86 37.85 3.36
4279 4630 3.118531 AGGTAGATCTGCCATTTGGAGT 58.881 45.455 28.90 5.45 37.85 3.85
4280 4631 3.853355 AGGTAGATCTGCCATTTGGAG 57.147 47.619 28.90 0.00 37.85 3.86
4454 4806 2.046292 TCACCACAGACCATTCACTGA 58.954 47.619 0.00 0.00 37.54 3.41
4457 4809 3.340814 AGATCACCACAGACCATTCAC 57.659 47.619 0.00 0.00 0.00 3.18
4460 4812 4.728772 TCAAAAGATCACCACAGACCATT 58.271 39.130 0.00 0.00 0.00 3.16
4464 4816 3.406764 AGCTCAAAAGATCACCACAGAC 58.593 45.455 0.00 0.00 0.00 3.51
4512 4865 1.006519 TGGGACCCAAGAGAGAGAGAG 59.993 57.143 12.05 0.00 0.00 3.20
4513 4866 1.084866 TGGGACCCAAGAGAGAGAGA 58.915 55.000 12.05 0.00 0.00 3.10
4514 4867 2.173126 ATGGGACCCAAGAGAGAGAG 57.827 55.000 19.58 0.00 36.95 3.20
4559 4912 7.672983 TTCTTCAACAATGACTAGCCTAAAG 57.327 36.000 0.00 0.00 34.61 1.85
4653 5006 5.106475 GGGCTTTGTAATTCATGTTGTACGA 60.106 40.000 0.00 0.00 0.00 3.43
4690 5043 8.604184 TGTAGTTTCTCTCCTCTCTAACTCTAA 58.396 37.037 0.00 0.00 0.00 2.10
4691 5044 8.148437 TGTAGTTTCTCTCCTCTCTAACTCTA 57.852 38.462 0.00 0.00 0.00 2.43
4692 5045 7.023171 TGTAGTTTCTCTCCTCTCTAACTCT 57.977 40.000 0.00 0.00 0.00 3.24
4693 5046 6.317893 CCTGTAGTTTCTCTCCTCTCTAACTC 59.682 46.154 0.00 0.00 0.00 3.01
4694 5047 6.184789 CCTGTAGTTTCTCTCCTCTCTAACT 58.815 44.000 0.00 0.00 0.00 2.24
4695 5048 5.358725 CCCTGTAGTTTCTCTCCTCTCTAAC 59.641 48.000 0.00 0.00 0.00 2.34
4887 5240 2.023404 TGCTACCCCTTGGACTATCAGA 60.023 50.000 0.00 0.00 34.81 3.27
4989 5343 3.182182 GGCTGCAAAAGTAGCTAAATGC 58.818 45.455 0.50 12.04 39.80 3.56
5218 5574 2.625790 TGCAGGGACAAACGCTTAAATT 59.374 40.909 0.00 0.00 39.79 1.82
5254 5610 7.691993 ACTCCAGTTGTATCTTAACCCATAT 57.308 36.000 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.