Multiple sequence alignment - TraesCS5D01G056400

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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 TraesCS5D01G056400 chr5D 100.000 2540 0 0 1 2540 52328591 52326052 0.000000e+00 4691.0
1 TraesCS5D01G056400 chr5B 91.577 2315 131 29 35 2312 55505596 55503309 0.000000e+00 3136.0
2 TraesCS5D01G056400 chr1A 85.638 745 67 20 890 1607 6335241 6335972 0.000000e+00 747.0
3 TraesCS5D01G056400 chr1A 84.726 766 77 21 869 1607 4503539 4502787 0.000000e+00 730.0
4 TraesCS5D01G056400 chr1A 84.726 766 77 21 869 1607 5499038 5499790 0.000000e+00 730.0
5 TraesCS5D01G056400 chr1A 87.057 649 50 17 982 1607 5500631 5501268 0.000000e+00 702.0
6 TraesCS5D01G056400 chr1A 81.557 244 35 6 2055 2293 6336510 6336748 2.580000e-45 193.0
7 TraesCS5D01G056400 chr1A 88.194 144 17 0 2313 2456 4101481 4101624 3.360000e-39 172.0
8 TraesCS5D01G056400 chr1D 87.087 666 69 10 866 1522 3968756 3969413 0.000000e+00 737.0
9 TraesCS5D01G056400 chr1D 78.603 458 62 29 1327 1774 3618233 3617802 1.160000e-68 270.0
10 TraesCS5D01G056400 chr1D 81.304 230 19 4 2055 2270 3970089 3970308 5.620000e-37 165.0
11 TraesCS5D01G056400 chr1D 100.000 30 0 0 271 300 3967585 3967614 3.530000e-04 56.5
12 TraesCS5D01G056400 chr1B 86.727 663 71 10 869 1523 5760364 5759711 0.000000e+00 721.0
13 TraesCS5D01G056400 chr1B 85.414 665 76 13 869 1522 6481538 6482192 0.000000e+00 671.0
14 TraesCS5D01G056400 chr1B 84.571 175 16 7 2098 2269 6482824 6482990 2.020000e-36 163.0
15 TraesCS5D01G056400 chr1B 84.000 175 17 7 2098 2269 5759063 5758897 9.410000e-35 158.0
16 TraesCS5D01G056400 chr1B 82.162 185 13 10 2124 2293 7697699 7697878 9.470000e-30 141.0
17 TraesCS5D01G056400 chr1B 78.022 182 20 5 2127 2293 6286123 6285947 2.080000e-16 97.1
18 TraesCS5D01G056400 chr1B 88.889 72 8 0 2127 2198 7345268 7345197 3.480000e-14 89.8
19 TraesCS5D01G056400 chr3A 92.982 228 14 1 2312 2539 729708358 729708133 5.240000e-87 331.0
20 TraesCS5D01G056400 chr3A 92.070 227 16 1 2313 2539 720175184 720175408 4.080000e-83 318.0
21 TraesCS5D01G056400 chr3A 91.630 227 17 1 2313 2539 720146177 720146401 1.900000e-81 313.0
22 TraesCS5D01G056400 chr3B 92.952 227 14 1 2313 2539 816796570 816796794 1.880000e-86 329.0
23 TraesCS5D01G056400 chr4A 90.789 228 21 0 2313 2540 538220134 538220361 3.170000e-79 305.0
24 TraesCS5D01G056400 chr4A 92.982 171 12 0 2317 2487 620937023 620936853 1.510000e-62 250.0
25 TraesCS5D01G056400 chr2A 90.749 227 19 1 2313 2539 702948967 702949191 4.110000e-78 302.0
26 TraesCS5D01G056400 chr2B 93.617 188 11 1 2312 2499 797638591 797638405 1.920000e-71 279.0


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 TraesCS5D01G056400 chr5D 52326052 52328591 2539 True 4691.0 4691 100.000000 1 2540 1 chr5D.!!$R1 2539
1 TraesCS5D01G056400 chr5B 55503309 55505596 2287 True 3136.0 3136 91.577000 35 2312 1 chr5B.!!$R1 2277
2 TraesCS5D01G056400 chr1A 4502787 4503539 752 True 730.0 730 84.726000 869 1607 1 chr1A.!!$R1 738
3 TraesCS5D01G056400 chr1A 5499038 5501268 2230 False 716.0 730 85.891500 869 1607 2 chr1A.!!$F2 738
4 TraesCS5D01G056400 chr1A 6335241 6336748 1507 False 470.0 747 83.597500 890 2293 2 chr1A.!!$F3 1403
5 TraesCS5D01G056400 chr1D 3967585 3970308 2723 False 319.5 737 89.463667 271 2270 3 chr1D.!!$F1 1999
6 TraesCS5D01G056400 chr1B 5758897 5760364 1467 True 439.5 721 85.363500 869 2269 2 chr1B.!!$R3 1400
7 TraesCS5D01G056400 chr1B 6481538 6482990 1452 False 417.0 671 84.992500 869 2269 2 chr1B.!!$F2 1400

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
679 747 0.606401 AGCATTTGTGGGTGTCCTCG 60.606 55.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2501 3503 0.036858 TCGCAATCGACCAATGACCA 60.037 50.0 0.0 0.0 40.21 4.02 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
26 27 9.819267 CTAGGTAGGTTGTCTTTTAATCCTTAG 57.181 37.037 0.00 0.00 0.00 2.18
27 28 8.445361 AGGTAGGTTGTCTTTTAATCCTTAGA 57.555 34.615 0.00 0.00 0.00 2.10
28 29 8.541234 AGGTAGGTTGTCTTTTAATCCTTAGAG 58.459 37.037 0.00 0.00 0.00 2.43
29 30 8.537858 GGTAGGTTGTCTTTTAATCCTTAGAGA 58.462 37.037 0.00 0.00 0.00 3.10
30 31 9.939802 GTAGGTTGTCTTTTAATCCTTAGAGAA 57.060 33.333 0.00 0.00 0.00 2.87
31 32 8.850007 AGGTTGTCTTTTAATCCTTAGAGAAC 57.150 34.615 0.00 0.00 39.08 3.01
32 33 8.041829 GGTTGTCTTTTAATCCTTAGAGAACC 57.958 38.462 12.35 12.35 46.77 3.62
33 34 7.120873 GGTTGTCTTTTAATCCTTAGAGAACCC 59.879 40.741 15.31 2.81 46.91 4.11
55 56 3.706086 CAGAACCCTCCCCAAAATAATGG 59.294 47.826 0.00 0.00 40.35 3.16
68 69 6.996282 CCCAAAATAATGGTAGGACGTAGATT 59.004 38.462 0.00 0.00 38.91 2.40
73 74 9.847224 AAATAATGGTAGGACGTAGATTGAAAT 57.153 29.630 0.00 0.00 0.00 2.17
91 92 4.579753 TGAAATGTTGTGCATCTCTTGTCA 59.420 37.500 0.00 0.00 36.67 3.58
97 98 3.593096 TGTGCATCTCTTGTCATCTGTC 58.407 45.455 0.00 0.00 0.00 3.51
143 158 2.591715 GCTGGTGCGTGTTGTCCT 60.592 61.111 0.00 0.00 0.00 3.85
154 169 1.954382 GTGTTGTCCTTCCCCTGTTTC 59.046 52.381 0.00 0.00 0.00 2.78
159 174 3.173965 TGTCCTTCCCCTGTTTCTAGAG 58.826 50.000 0.00 0.00 0.00 2.43
185 208 2.898181 CAATGTCAGTGCATTGCGTA 57.102 45.000 19.99 0.00 45.84 4.42
229 252 3.047695 TCTGGTATCCCTTCTCCTTCC 57.952 52.381 0.00 0.00 0.00 3.46
230 253 2.317900 TCTGGTATCCCTTCTCCTTCCA 59.682 50.000 0.00 0.00 0.00 3.53
236 259 1.135960 CCCTTCTCCTTCCATCCCTC 58.864 60.000 0.00 0.00 0.00 4.30
267 290 1.493022 ACGGCAGATCTCTCTACCTCT 59.507 52.381 0.00 0.00 33.28 3.69
373 429 3.555139 CCAATTTGTCGCTGAGAGATCTC 59.445 47.826 15.29 15.29 43.15 2.75
403 462 4.278419 GCCTTATCCTTGTGTTGTGAAGTT 59.722 41.667 0.00 0.00 0.00 2.66
444 503 2.334307 GCAGTCAGCTTGCTTTCCA 58.666 52.632 1.51 0.00 41.15 3.53
520 579 2.536997 AATAGCGGCCACCAGGTGAC 62.537 60.000 22.37 9.69 35.23 3.67
601 665 8.355913 TGCTTATCTATGTCTGTAACATCTGAG 58.644 37.037 0.00 0.00 45.78 3.35
631 695 7.909267 TGAGAATAAAATGTTGATCGTGCTAG 58.091 34.615 0.00 0.00 0.00 3.42
679 747 0.606401 AGCATTTGTGGGTGTCCTCG 60.606 55.000 0.00 0.00 0.00 4.63
709 777 2.610433 TGTAGAATTCTGTGCAGAGCG 58.390 47.619 18.47 0.00 38.88 5.03
749 1421 3.004315 ACGCAACACTTTAACAGGAATGG 59.996 43.478 0.00 0.00 0.00 3.16
822 1494 4.764308 TGTTTGCTCATACTGTTATTGCCA 59.236 37.500 0.00 0.00 0.00 4.92
825 1497 3.194861 GCTCATACTGTTATTGCCACGA 58.805 45.455 0.00 0.00 0.00 4.35
878 1550 6.257411 CACTGTACTAGAAAGCATTCAGGATG 59.743 42.308 4.27 0.00 38.06 3.51
956 1634 8.761575 ACATCCATAACACTTGCTTTTTAATG 57.238 30.769 0.00 0.00 0.00 1.90
1048 1726 0.108472 CAGCTTGATCGACCAGCTCA 60.108 55.000 11.04 0.00 33.09 4.26
1050 1728 0.390340 GCTTGATCGACCAGCTCACA 60.390 55.000 5.30 0.00 0.00 3.58
1112 1793 1.801913 CGAAGAAGGTCGTGGAGCG 60.802 63.158 0.00 0.00 43.01 5.03
1138 1819 1.452833 GAGCCTCAGGACAATGGCC 60.453 63.158 0.00 0.00 45.94 5.36
1241 1922 4.270153 TGCTCCTCCACCACCCCT 62.270 66.667 0.00 0.00 0.00 4.79
1260 1941 1.678970 GCCGGCAATCCAGGAAGTT 60.679 57.895 24.80 0.00 0.00 2.66
1274 1955 2.070783 GGAAGTTGAAACCATACGCGA 58.929 47.619 15.93 0.00 0.00 5.87
1349 2030 0.176680 ATGCGTGAGGAGCTTACCAG 59.823 55.000 0.00 0.00 35.28 4.00
1388 2069 1.875576 CGACAAGGAGTTCAAGCTGCT 60.876 52.381 0.00 0.00 38.85 4.24
1461 2142 2.671070 CGGAGCAACACCCAGGAT 59.329 61.111 0.00 0.00 0.00 3.24
1596 2336 2.577606 TGGTTTGTCGGGATGATTGT 57.422 45.000 0.00 0.00 0.00 2.71
1600 2340 5.746284 TGGTTTGTCGGGATGATTGTATAA 58.254 37.500 0.00 0.00 0.00 0.98
1601 2341 5.587043 TGGTTTGTCGGGATGATTGTATAAC 59.413 40.000 0.00 0.00 0.00 1.89
1602 2342 5.008316 GGTTTGTCGGGATGATTGTATAACC 59.992 44.000 0.00 0.00 0.00 2.85
1603 2343 5.623956 TTGTCGGGATGATTGTATAACCT 57.376 39.130 0.00 0.00 0.00 3.50
1604 2344 4.956085 TGTCGGGATGATTGTATAACCTG 58.044 43.478 0.00 0.00 0.00 4.00
1605 2345 4.651962 TGTCGGGATGATTGTATAACCTGA 59.348 41.667 0.00 0.00 0.00 3.86
1606 2346 5.129650 TGTCGGGATGATTGTATAACCTGAA 59.870 40.000 0.00 0.00 35.11 3.02
1607 2347 6.053005 GTCGGGATGATTGTATAACCTGAAA 58.947 40.000 0.00 0.00 35.11 2.69
1608 2348 6.540914 GTCGGGATGATTGTATAACCTGAAAA 59.459 38.462 0.00 0.00 35.11 2.29
1609 2349 7.228706 GTCGGGATGATTGTATAACCTGAAAAT 59.771 37.037 0.00 0.00 35.11 1.82
1610 2350 7.444183 TCGGGATGATTGTATAACCTGAAAATC 59.556 37.037 0.00 0.00 31.14 2.17
1611 2351 7.571244 CGGGATGATTGTATAACCTGAAAATCG 60.571 40.741 0.00 0.00 0.00 3.34
1612 2352 7.308589 GGGATGATTGTATAACCTGAAAATCGG 60.309 40.741 0.00 0.00 0.00 4.18
1613 2353 7.228706 GGATGATTGTATAACCTGAAAATCGGT 59.771 37.037 0.00 0.00 34.27 4.69
1614 2354 7.931578 TGATTGTATAACCTGAAAATCGGTT 57.068 32.000 10.06 10.06 45.06 4.44
1615 2355 8.343168 TGATTGTATAACCTGAAAATCGGTTT 57.657 30.769 10.33 0.00 43.02 3.27
1616 2356 8.240682 TGATTGTATAACCTGAAAATCGGTTTG 58.759 33.333 0.00 0.00 43.02 2.93
1617 2357 7.513371 TTGTATAACCTGAAAATCGGTTTGT 57.487 32.000 0.00 0.00 43.02 2.83
1618 2358 7.136289 TGTATAACCTGAAAATCGGTTTGTC 57.864 36.000 0.00 0.00 43.02 3.18
1619 2359 3.619233 AACCTGAAAATCGGTTTGTCG 57.381 42.857 0.00 0.00 40.47 4.35
1620 2360 1.877443 ACCTGAAAATCGGTTTGTCGG 59.123 47.619 0.00 0.00 0.00 4.79
1621 2361 1.199097 CCTGAAAATCGGTTTGTCGGG 59.801 52.381 13.34 13.34 31.15 5.14
1622 2362 2.147958 CTGAAAATCGGTTTGTCGGGA 58.852 47.619 0.00 0.00 0.00 5.14
1665 2413 3.485463 TTTCGGTGAGACCTGAAACAT 57.515 42.857 0.00 0.00 36.56 2.71
1682 2430 8.362860 CTGAAACATCATCAGGTGTAGATTAG 57.637 38.462 0.00 0.00 40.48 1.73
1692 2440 6.878317 TCAGGTGTAGATTAGAATTCTGGTG 58.122 40.000 18.47 1.24 0.00 4.17
1696 2444 6.127026 GGTGTAGATTAGAATTCTGGTGAGGT 60.127 42.308 18.47 0.00 0.00 3.85
1698 2446 7.921745 GTGTAGATTAGAATTCTGGTGAGGTAC 59.078 40.741 18.47 10.15 0.00 3.34
1819 2577 6.597832 TGGTTTGAATTAATGTTTCCCGAT 57.402 33.333 0.00 0.00 0.00 4.18
1857 2615 0.104671 TGGCTGCTTTTCCTTGCAAC 59.895 50.000 0.00 0.00 38.81 4.17
1859 2617 1.551503 GCTGCTTTTCCTTGCAACGC 61.552 55.000 0.00 0.00 38.81 4.84
1861 2619 1.664649 GCTTTTCCTTGCAACGCCC 60.665 57.895 0.00 0.00 0.00 6.13
1873 2631 0.109319 CAACGCCCTGGCATGTTTAC 60.109 55.000 9.17 0.00 42.06 2.01
1874 2632 0.538516 AACGCCCTGGCATGTTTACA 60.539 50.000 9.17 0.00 42.06 2.41
1883 2642 6.512297 CCCTGGCATGTTTACATAAATAACC 58.488 40.000 0.00 0.00 34.26 2.85
1897 2657 6.147492 ACATAAATAACCGTGCTCGTTTGTTA 59.853 34.615 7.47 8.81 35.01 2.41
1949 2824 3.423539 TTTAGCTTCAGATGCACCTGT 57.576 42.857 8.25 0.00 35.71 4.00
1962 2837 2.984155 CCTGTTGCTGCTGCTGCT 60.984 61.111 27.67 0.00 40.48 4.24
2231 3227 1.401670 CCGACACTTCTCGACCAAGAG 60.402 57.143 6.40 1.81 39.52 2.85
2241 3237 1.446966 GACCAAGAGCAGAGCGACC 60.447 63.158 0.00 0.00 0.00 4.79
2284 3286 2.756760 AGCAATAACAGCCATTCCACTG 59.243 45.455 0.00 0.00 39.86 3.66
2312 3314 0.329596 ACAATCAAGGACCAGGCCTC 59.670 55.000 0.00 0.00 37.26 4.70
2313 3315 0.329261 CAATCAAGGACCAGGCCTCA 59.671 55.000 0.00 0.00 37.26 3.86
2314 3316 0.622665 AATCAAGGACCAGGCCTCAG 59.377 55.000 0.00 0.00 37.26 3.35
2315 3317 1.277580 ATCAAGGACCAGGCCTCAGG 61.278 60.000 0.00 4.49 37.26 3.86
2316 3318 2.612115 AAGGACCAGGCCTCAGGG 60.612 66.667 13.51 9.95 37.26 4.45
2317 3319 4.748798 AGGACCAGGCCTCAGGGG 62.749 72.222 13.51 9.58 30.76 4.79
2327 3329 1.754234 CCTCAGGGGCGAAATTGGG 60.754 63.158 0.00 0.00 0.00 4.12
2328 3330 2.362375 TCAGGGGCGAAATTGGGC 60.362 61.111 0.00 0.00 0.00 5.36
2334 3336 1.828224 GGCGAAATTGGGCCTAGGG 60.828 63.158 11.72 0.00 45.93 3.53
2345 3347 3.017581 CCTAGGGCAACTGGGGCT 61.018 66.667 0.00 0.00 43.73 5.19
2347 3349 1.062488 CCTAGGGCAACTGGGGCTAT 61.062 60.000 0.00 0.00 43.73 2.97
2348 3350 1.729586 CTAGGGCAACTGGGGCTATA 58.270 55.000 0.00 0.00 0.00 1.31
2349 3351 1.625818 CTAGGGCAACTGGGGCTATAG 59.374 57.143 0.00 0.00 0.00 1.31
2372 3374 2.746277 GGCGTGGCCCAACTAGTG 60.746 66.667 0.00 0.00 44.06 2.74
2373 3375 3.431725 GCGTGGCCCAACTAGTGC 61.432 66.667 0.00 0.00 0.00 4.40
2374 3376 2.746277 CGTGGCCCAACTAGTGCC 60.746 66.667 14.34 14.34 45.56 5.01
2379 3381 2.364972 GGCCCAACTAGTGCCATTAT 57.635 50.000 15.91 0.00 44.70 1.28
2380 3382 3.502123 GGCCCAACTAGTGCCATTATA 57.498 47.619 15.91 0.00 44.70 0.98
2381 3383 4.034285 GGCCCAACTAGTGCCATTATAT 57.966 45.455 15.91 0.00 44.70 0.86
2382 3384 4.010349 GGCCCAACTAGTGCCATTATATC 58.990 47.826 15.91 0.00 44.70 1.63
2384 3386 4.506625 GCCCAACTAGTGCCATTATATCCA 60.507 45.833 0.00 0.00 0.00 3.41
2388 3390 7.099764 CCAACTAGTGCCATTATATCCAGTAG 58.900 42.308 0.00 0.00 37.29 2.57
2389 3391 7.039011 CCAACTAGTGCCATTATATCCAGTAGA 60.039 40.741 0.00 0.00 35.69 2.59
2390 3392 8.367911 CAACTAGTGCCATTATATCCAGTAGAA 58.632 37.037 0.00 0.00 35.69 2.10
2391 3393 8.492415 ACTAGTGCCATTATATCCAGTAGAAA 57.508 34.615 0.00 0.00 35.69 2.52
2392 3394 8.934697 ACTAGTGCCATTATATCCAGTAGAAAA 58.065 33.333 0.00 0.00 35.69 2.29
2395 3397 9.646522 AGTGCCATTATATCCAGTAGAAAATTT 57.353 29.630 0.00 0.00 0.00 1.82
2419 3421 7.935338 TTCAGATTTTCACATTCAAAGAAGC 57.065 32.000 0.00 0.00 0.00 3.86
2420 3422 6.449698 TCAGATTTTCACATTCAAAGAAGCC 58.550 36.000 0.00 0.00 0.00 4.35
2421 3423 5.636543 CAGATTTTCACATTCAAAGAAGCCC 59.363 40.000 0.00 0.00 0.00 5.19
2422 3424 5.305128 AGATTTTCACATTCAAAGAAGCCCA 59.695 36.000 0.00 0.00 0.00 5.36
2423 3425 4.589216 TTTCACATTCAAAGAAGCCCAG 57.411 40.909 0.00 0.00 0.00 4.45
2426 3428 0.533951 CATTCAAAGAAGCCCAGCCC 59.466 55.000 0.00 0.00 0.00 5.19
2427 3429 0.615827 ATTCAAAGAAGCCCAGCCCC 60.616 55.000 0.00 0.00 0.00 5.80
2428 3430 2.017668 TTCAAAGAAGCCCAGCCCCA 62.018 55.000 0.00 0.00 0.00 4.96
2429 3431 1.980772 CAAAGAAGCCCAGCCCCAG 60.981 63.158 0.00 0.00 0.00 4.45
2430 3432 3.229659 AAAGAAGCCCAGCCCCAGG 62.230 63.158 0.00 0.00 0.00 4.45
2441 3443 2.927056 CCCCAGGCCTGAATACCC 59.073 66.667 34.91 0.00 0.00 3.69
2442 3444 2.006415 CCCCAGGCCTGAATACCCA 61.006 63.158 34.91 0.00 0.00 4.51
2443 3445 1.533711 CCCAGGCCTGAATACCCAG 59.466 63.158 34.91 14.22 0.00 4.45
2444 3446 1.152881 CCAGGCCTGAATACCCAGC 60.153 63.158 34.91 0.00 32.97 4.85
2445 3447 1.152881 CAGGCCTGAATACCCAGCC 60.153 63.158 29.88 0.00 32.97 4.85
2447 3449 2.689691 GGCCTGAATACCCAGCCCA 61.690 63.158 0.00 0.00 32.35 5.36
2449 3451 0.753111 GCCTGAATACCCAGCCCAAG 60.753 60.000 0.00 0.00 32.97 3.61
2468 3470 3.365265 CCTCAACGGCAGCCCAAC 61.365 66.667 5.63 0.00 0.00 3.77
2469 3471 2.281761 CTCAACGGCAGCCCAACT 60.282 61.111 5.63 0.00 0.00 3.16
2470 3472 1.003839 CTCAACGGCAGCCCAACTA 60.004 57.895 5.63 0.00 0.00 2.24
2472 3474 0.887387 TCAACGGCAGCCCAACTAAC 60.887 55.000 5.63 0.00 0.00 2.34
2473 3475 0.889186 CAACGGCAGCCCAACTAACT 60.889 55.000 5.63 0.00 0.00 2.24
2474 3476 0.688487 AACGGCAGCCCAACTAACTA 59.312 50.000 5.63 0.00 0.00 2.24
2475 3477 0.249398 ACGGCAGCCCAACTAACTAG 59.751 55.000 5.63 0.00 0.00 2.57
2476 3478 1.090052 CGGCAGCCCAACTAACTAGC 61.090 60.000 5.63 0.00 0.00 3.42
2477 3479 0.253327 GGCAGCCCAACTAACTAGCT 59.747 55.000 0.00 0.00 0.00 3.32
2478 3480 1.657822 GCAGCCCAACTAACTAGCTC 58.342 55.000 0.00 0.00 0.00 4.09
2479 3481 1.066143 GCAGCCCAACTAACTAGCTCA 60.066 52.381 0.00 0.00 0.00 4.26
2480 3482 2.898705 CAGCCCAACTAACTAGCTCAG 58.101 52.381 0.00 0.00 0.00 3.35
2481 3483 1.208293 AGCCCAACTAACTAGCTCAGC 59.792 52.381 0.00 0.00 0.00 4.26
2482 3484 1.066143 GCCCAACTAACTAGCTCAGCA 60.066 52.381 0.00 0.00 0.00 4.41
2483 3485 2.898705 CCCAACTAACTAGCTCAGCAG 58.101 52.381 0.00 0.00 0.00 4.24
2484 3486 2.419297 CCCAACTAACTAGCTCAGCAGG 60.419 54.545 0.00 0.00 0.00 4.85
2485 3487 2.497675 CCAACTAACTAGCTCAGCAGGA 59.502 50.000 0.00 0.00 0.00 3.86
2487 3489 3.878160 ACTAACTAGCTCAGCAGGAAC 57.122 47.619 0.00 0.00 0.00 3.62
2489 3491 0.615850 AACTAGCTCAGCAGGAACCC 59.384 55.000 0.00 0.00 0.00 4.11
2490 3492 0.545309 ACTAGCTCAGCAGGAACCCA 60.545 55.000 0.00 0.00 0.00 4.51
2491 3493 0.835941 CTAGCTCAGCAGGAACCCAT 59.164 55.000 0.00 0.00 0.00 4.00
2492 3494 0.543277 TAGCTCAGCAGGAACCCATG 59.457 55.000 0.00 0.00 0.00 3.66
2493 3495 2.413142 GCTCAGCAGGAACCCATGC 61.413 63.158 0.00 0.00 42.87 4.06
2494 3496 1.751927 CTCAGCAGGAACCCATGCC 60.752 63.158 0.00 0.00 43.60 4.40
2495 3497 2.757099 CAGCAGGAACCCATGCCC 60.757 66.667 0.00 0.00 43.60 5.36
2497 3499 3.070576 GCAGGAACCCATGCCCAC 61.071 66.667 0.00 0.00 36.41 4.61
2498 3500 2.751436 CAGGAACCCATGCCCACG 60.751 66.667 0.00 0.00 0.00 4.94
2499 3501 3.256960 AGGAACCCATGCCCACGT 61.257 61.111 0.00 0.00 0.00 4.49
2500 3502 2.282887 GGAACCCATGCCCACGTT 60.283 61.111 0.00 0.00 0.00 3.99
2501 3503 1.906333 GGAACCCATGCCCACGTTT 60.906 57.895 0.00 0.00 0.00 3.60
2502 3504 1.288752 GAACCCATGCCCACGTTTG 59.711 57.895 0.00 0.00 0.00 2.93
2504 3506 2.600173 CCCATGCCCACGTTTGGT 60.600 61.111 3.01 0.00 42.10 3.67
2505 3507 2.635443 CCCATGCCCACGTTTGGTC 61.635 63.158 3.01 0.00 42.10 4.02
2506 3508 1.900981 CCATGCCCACGTTTGGTCA 60.901 57.895 3.01 2.51 42.10 4.02
2507 3509 1.250154 CCATGCCCACGTTTGGTCAT 61.250 55.000 3.01 4.46 42.45 3.06
2508 3510 0.602562 CATGCCCACGTTTGGTCATT 59.397 50.000 3.01 0.00 38.36 2.57
2509 3511 0.602562 ATGCCCACGTTTGGTCATTG 59.397 50.000 3.01 0.00 38.36 2.82
2510 3512 1.288752 GCCCACGTTTGGTCATTGG 59.711 57.895 3.01 0.00 42.10 3.16
2511 3513 1.460273 GCCCACGTTTGGTCATTGGT 61.460 55.000 3.01 0.00 42.10 3.67
2512 3514 0.596082 CCCACGTTTGGTCATTGGTC 59.404 55.000 0.00 0.00 42.10 4.02
2513 3515 0.237235 CCACGTTTGGTCATTGGTCG 59.763 55.000 0.00 0.00 38.23 4.79
2514 3516 1.222300 CACGTTTGGTCATTGGTCGA 58.778 50.000 0.00 0.00 0.00 4.20
2515 3517 1.804151 CACGTTTGGTCATTGGTCGAT 59.196 47.619 0.00 0.00 0.00 3.59
2516 3518 2.225491 CACGTTTGGTCATTGGTCGATT 59.775 45.455 0.00 0.00 0.00 3.34
2517 3519 2.225491 ACGTTTGGTCATTGGTCGATTG 59.775 45.455 0.00 0.00 0.00 2.67
2518 3520 2.595386 GTTTGGTCATTGGTCGATTGC 58.405 47.619 0.00 0.00 0.00 3.56
2519 3521 0.801872 TTGGTCATTGGTCGATTGCG 59.198 50.000 0.00 0.00 39.35 4.85
2520 3522 0.036858 TGGTCATTGGTCGATTGCGA 60.037 50.000 0.00 0.00 45.71 5.10
2530 3532 2.107950 TCGATTGCGATTCCAAAGGT 57.892 45.000 0.00 0.00 42.51 3.50
2531 3533 3.254470 TCGATTGCGATTCCAAAGGTA 57.746 42.857 0.00 0.00 42.51 3.08
2532 3534 3.804036 TCGATTGCGATTCCAAAGGTAT 58.196 40.909 0.00 0.00 42.51 2.73
2533 3535 3.807622 TCGATTGCGATTCCAAAGGTATC 59.192 43.478 0.00 0.00 42.51 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.819267 CTAAGGATTAAAAGACAACCTACCTAG 57.181 37.037 0.00 0.00 0.00 3.02
1 2 9.551339 TCTAAGGATTAAAAGACAACCTACCTA 57.449 33.333 0.00 0.00 0.00 3.08
2 3 8.445361 TCTAAGGATTAAAAGACAACCTACCT 57.555 34.615 0.00 0.00 0.00 3.08
3 4 8.537858 TCTCTAAGGATTAAAAGACAACCTACC 58.462 37.037 0.00 0.00 0.00 3.18
4 5 9.939802 TTCTCTAAGGATTAAAAGACAACCTAC 57.060 33.333 0.00 0.00 0.00 3.18
5 6 9.939802 GTTCTCTAAGGATTAAAAGACAACCTA 57.060 33.333 0.00 0.00 0.00 3.08
6 7 7.883833 GGTTCTCTAAGGATTAAAAGACAACCT 59.116 37.037 0.00 0.00 35.41 3.50
7 8 7.120873 GGGTTCTCTAAGGATTAAAAGACAACC 59.879 40.741 0.00 0.00 36.71 3.77
8 9 7.664318 TGGGTTCTCTAAGGATTAAAAGACAAC 59.336 37.037 0.00 0.00 0.00 3.32
9 10 7.751646 TGGGTTCTCTAAGGATTAAAAGACAA 58.248 34.615 0.00 0.00 0.00 3.18
10 11 7.236847 TCTGGGTTCTCTAAGGATTAAAAGACA 59.763 37.037 0.00 0.00 0.00 3.41
11 12 7.621796 TCTGGGTTCTCTAAGGATTAAAAGAC 58.378 38.462 0.00 0.00 0.00 3.01
12 13 7.808279 TCTGGGTTCTCTAAGGATTAAAAGA 57.192 36.000 0.00 0.00 0.00 2.52
13 14 7.337184 GGTTCTGGGTTCTCTAAGGATTAAAAG 59.663 40.741 0.00 0.00 0.00 2.27
14 15 7.173032 GGTTCTGGGTTCTCTAAGGATTAAAA 58.827 38.462 0.00 0.00 0.00 1.52
15 16 6.296836 GGGTTCTGGGTTCTCTAAGGATTAAA 60.297 42.308 0.00 0.00 0.00 1.52
16 17 5.191124 GGGTTCTGGGTTCTCTAAGGATTAA 59.809 44.000 0.00 0.00 0.00 1.40
17 18 4.720273 GGGTTCTGGGTTCTCTAAGGATTA 59.280 45.833 0.00 0.00 0.00 1.75
18 19 3.523972 GGGTTCTGGGTTCTCTAAGGATT 59.476 47.826 0.00 0.00 0.00 3.01
19 20 3.116174 GGGTTCTGGGTTCTCTAAGGAT 58.884 50.000 0.00 0.00 0.00 3.24
20 21 2.113777 AGGGTTCTGGGTTCTCTAAGGA 59.886 50.000 0.00 0.00 0.00 3.36
21 22 2.502130 GAGGGTTCTGGGTTCTCTAAGG 59.498 54.545 0.00 0.00 0.00 2.69
22 23 2.502130 GGAGGGTTCTGGGTTCTCTAAG 59.498 54.545 0.00 0.00 0.00 2.18
23 24 2.547990 GGAGGGTTCTGGGTTCTCTAA 58.452 52.381 0.00 0.00 0.00 2.10
24 25 1.273666 GGGAGGGTTCTGGGTTCTCTA 60.274 57.143 0.00 0.00 0.00 2.43
25 26 0.547954 GGGAGGGTTCTGGGTTCTCT 60.548 60.000 0.00 0.00 0.00 3.10
26 27 1.563577 GGGGAGGGTTCTGGGTTCTC 61.564 65.000 0.00 0.00 0.00 2.87
27 28 1.541620 GGGGAGGGTTCTGGGTTCT 60.542 63.158 0.00 0.00 0.00 3.01
28 29 1.432023 TTGGGGAGGGTTCTGGGTTC 61.432 60.000 0.00 0.00 0.00 3.62
29 30 1.002242 TTTGGGGAGGGTTCTGGGTT 61.002 55.000 0.00 0.00 0.00 4.11
30 31 1.002242 TTTTGGGGAGGGTTCTGGGT 61.002 55.000 0.00 0.00 0.00 4.51
31 32 0.413434 ATTTTGGGGAGGGTTCTGGG 59.587 55.000 0.00 0.00 0.00 4.45
32 33 3.466395 TTATTTTGGGGAGGGTTCTGG 57.534 47.619 0.00 0.00 0.00 3.86
33 34 3.706086 CCATTATTTTGGGGAGGGTTCTG 59.294 47.826 0.00 0.00 32.80 3.02
55 56 6.672357 GCACAACATTTCAATCTACGTCCTAC 60.672 42.308 0.00 0.00 0.00 3.18
68 69 4.579753 TGACAAGAGATGCACAACATTTCA 59.420 37.500 0.00 0.00 41.33 2.69
73 74 3.749609 CAGATGACAAGAGATGCACAACA 59.250 43.478 0.00 0.00 0.00 3.33
109 110 2.627699 CCAGCCTGAGGAGAAGAGATAC 59.372 54.545 0.65 0.00 0.00 2.24
143 158 1.286248 GGGCTCTAGAAACAGGGGAA 58.714 55.000 0.00 0.00 0.00 3.97
154 169 3.875727 CACTGACATTGATTGGGCTCTAG 59.124 47.826 0.00 0.00 0.00 2.43
159 174 0.889994 TGCACTGACATTGATTGGGC 59.110 50.000 0.00 0.00 0.00 5.36
182 205 1.178276 AGCAGTGGAGAAGAGGTACG 58.822 55.000 0.00 0.00 0.00 3.67
185 208 0.036022 GCAAGCAGTGGAGAAGAGGT 59.964 55.000 0.00 0.00 0.00 3.85
215 238 1.299629 AGGGATGGAAGGAGAAGGGAT 59.700 52.381 0.00 0.00 0.00 3.85
229 252 1.196808 CGTGGAAACAAACGAGGGATG 59.803 52.381 0.00 0.00 46.06 3.51
230 253 1.519408 CGTGGAAACAAACGAGGGAT 58.481 50.000 0.00 0.00 46.06 3.85
236 259 0.591170 ATCTGCCGTGGAAACAAACG 59.409 50.000 0.00 0.00 46.06 3.60
373 429 2.821969 ACACAAGGATAAGGCAGCAAAG 59.178 45.455 0.00 0.00 0.00 2.77
454 513 2.089980 CTTGTTTCAGAGGCTGATGGG 58.910 52.381 0.00 0.00 40.39 4.00
520 579 3.005050 TGCATCTTTCAAGAAACAGCAGG 59.995 43.478 7.36 0.00 38.77 4.85
601 665 7.427606 CACGATCAACATTTTATTCTCAAGCTC 59.572 37.037 0.00 0.00 0.00 4.09
631 695 4.846779 TCCCAGTTAAAATGTCAGCAAC 57.153 40.909 0.00 0.00 0.00 4.17
660 728 0.606401 CGAGGACACCCACAAATGCT 60.606 55.000 0.00 0.00 33.88 3.79
679 747 8.256611 TGCACAGAATTCTACATTAAGAAGAC 57.743 34.615 7.86 0.00 38.81 3.01
709 777 7.686938 GTGTTGCGTAACAGAATGAATAAGTAC 59.313 37.037 19.76 0.00 46.75 2.73
749 1421 8.126700 TCCAGTTAGAATTTTGAAAGTTTCGTC 58.873 33.333 10.92 3.68 0.00 4.20
788 1460 7.811236 ACAGTATGAGCAAACAAATTCAGAATG 59.189 33.333 0.00 0.00 39.69 2.67
822 1494 9.787532 CCACATGTTAAATAGAATGAATTTCGT 57.212 29.630 0.00 0.00 39.46 3.85
862 1534 2.357569 GGACCCATCCTGAATGCTTTCT 60.358 50.000 12.96 0.00 42.45 2.52
878 1550 6.441088 AAGTAGAATGAATATCTGGGACCC 57.559 41.667 2.45 2.45 0.00 4.46
956 1634 2.613691 CATGGCAATCAAAAGTCAGGC 58.386 47.619 0.00 0.00 0.00 4.85
1048 1726 1.154016 CCTTCTCGTCATCGCGTGT 60.154 57.895 5.77 0.00 36.96 4.49
1050 1728 1.154016 CACCTTCTCGTCATCGCGT 60.154 57.895 5.77 0.00 36.96 6.01
1112 1793 0.534873 GTCCTGAGGCTCCTCTTGTC 59.465 60.000 12.86 3.01 43.12 3.18
1138 1819 2.391389 GCTCGCTTGGAAGTTCCCG 61.391 63.158 19.42 15.05 35.03 5.14
1241 1922 2.045045 CTTCCTGGATTGCCGGCA 60.045 61.111 29.03 29.03 39.39 5.69
1260 1941 1.009903 CCACGTCGCGTATGGTTTCA 61.010 55.000 5.77 0.00 38.32 2.69
1323 2004 3.402691 CTCCTCACGCATCGTCGCT 62.403 63.158 0.00 0.00 38.32 4.93
1349 2030 4.811364 GCAGCTCCTTGGCCCTCC 62.811 72.222 0.00 0.00 0.00 4.30
1388 2069 1.684734 GGCGAGGGGTTCTGGTAGA 60.685 63.158 0.00 0.00 0.00 2.59
1454 2135 1.153289 CACTTGAGCGGATCCTGGG 60.153 63.158 10.75 0.00 0.00 4.45
1488 2169 3.802418 AACGCACGCCTCGAACCTT 62.802 57.895 0.00 0.00 0.00 3.50
1600 2340 1.877443 CCGACAAACCGATTTTCAGGT 59.123 47.619 0.00 0.00 43.68 4.00
1601 2341 1.199097 CCCGACAAACCGATTTTCAGG 59.801 52.381 0.00 0.00 0.00 3.86
1602 2342 2.147958 TCCCGACAAACCGATTTTCAG 58.852 47.619 0.00 0.00 0.00 3.02
1603 2343 2.257691 TCCCGACAAACCGATTTTCA 57.742 45.000 0.00 0.00 0.00 2.69
1604 2344 2.745281 TCATCCCGACAAACCGATTTTC 59.255 45.455 0.00 0.00 0.00 2.29
1605 2345 2.785562 TCATCCCGACAAACCGATTTT 58.214 42.857 0.00 0.00 0.00 1.82
1606 2346 2.483014 TCATCCCGACAAACCGATTT 57.517 45.000 0.00 0.00 0.00 2.17
1607 2347 2.682856 CAATCATCCCGACAAACCGATT 59.317 45.455 0.00 0.00 0.00 3.34
1608 2348 2.093181 TCAATCATCCCGACAAACCGAT 60.093 45.455 0.00 0.00 0.00 4.18
1609 2349 1.276705 TCAATCATCCCGACAAACCGA 59.723 47.619 0.00 0.00 0.00 4.69
1610 2350 1.732941 TCAATCATCCCGACAAACCG 58.267 50.000 0.00 0.00 0.00 4.44
1611 2351 5.828299 TTATTCAATCATCCCGACAAACC 57.172 39.130 0.00 0.00 0.00 3.27
1612 2352 7.012327 TCAGATTATTCAATCATCCCGACAAAC 59.988 37.037 0.65 0.00 42.66 2.93
1613 2353 7.053498 TCAGATTATTCAATCATCCCGACAAA 58.947 34.615 0.65 0.00 42.66 2.83
1614 2354 6.591001 TCAGATTATTCAATCATCCCGACAA 58.409 36.000 0.65 0.00 42.66 3.18
1615 2355 6.173427 TCAGATTATTCAATCATCCCGACA 57.827 37.500 0.65 0.00 42.66 4.35
1616 2356 7.361542 CCATTCAGATTATTCAATCATCCCGAC 60.362 40.741 0.65 0.00 42.66 4.79
1617 2357 6.656270 CCATTCAGATTATTCAATCATCCCGA 59.344 38.462 0.65 0.00 42.66 5.14
1618 2358 6.656270 TCCATTCAGATTATTCAATCATCCCG 59.344 38.462 0.65 0.00 42.66 5.14
1619 2359 8.591114 ATCCATTCAGATTATTCAATCATCCC 57.409 34.615 0.65 0.00 42.66 3.85
1665 2413 7.345653 ACCAGAATTCTAATCTACACCTGATGA 59.654 37.037 7.86 0.00 0.00 2.92
1672 2420 6.879400 ACCTCACCAGAATTCTAATCTACAC 58.121 40.000 7.86 0.00 0.00 2.90
1682 2430 3.003480 GTGCAGTACCTCACCAGAATTC 58.997 50.000 0.00 0.00 0.00 2.17
1779 2535 5.177142 TCAAACCATGCAAATTCATGTTTCG 59.823 36.000 0.00 0.00 41.60 3.46
1819 2577 8.217799 AGCAGCCATTTTACCTAAATATACTCA 58.782 33.333 0.00 0.00 34.69 3.41
1857 2615 1.674359 TATGTAAACATGCCAGGGCG 58.326 50.000 5.74 0.00 45.51 6.13
1859 2617 6.512297 GGTTATTTATGTAAACATGCCAGGG 58.488 40.000 5.85 0.00 37.15 4.45
1861 2619 6.690957 CACGGTTATTTATGTAAACATGCCAG 59.309 38.462 5.85 0.28 37.15 4.85
1883 2642 1.393539 CATCCCTAACAAACGAGCACG 59.606 52.381 0.76 0.76 45.75 5.34
1897 2657 9.799106 CTATAATGGTTATTCAAACTCATCCCT 57.201 33.333 0.00 0.00 0.00 4.20
1949 2824 1.593209 GCAAAAGCAGCAGCAGCAA 60.593 52.632 12.92 0.00 45.49 3.91
2125 3103 2.867624 TCTTGATCTGGTTTGCTGCTT 58.132 42.857 0.00 0.00 0.00 3.91
2241 3237 2.413796 TCTACAACTTAAATGTGCCGCG 59.586 45.455 0.00 0.00 32.27 6.46
2250 3246 7.229707 TGGCTGTTATTGCTTCTACAACTTAAA 59.770 33.333 0.00 0.00 31.03 1.52
2284 3286 1.200948 GTCCTTGATTGTTGCTCTGCC 59.799 52.381 0.00 0.00 0.00 4.85
2312 3314 3.460868 GGCCCAATTTCGCCCCTG 61.461 66.667 0.00 0.00 39.39 4.45
2316 3318 1.828224 CCCTAGGCCCAATTTCGCC 60.828 63.158 2.05 4.61 46.09 5.54
2317 3319 2.490148 GCCCTAGGCCCAATTTCGC 61.490 63.158 2.05 0.00 44.06 4.70
2318 3320 3.841870 GCCCTAGGCCCAATTTCG 58.158 61.111 2.05 0.00 44.06 3.46
2328 3330 1.062488 ATAGCCCCAGTTGCCCTAGG 61.062 60.000 0.06 0.06 0.00 3.02
2329 3331 1.625818 CTATAGCCCCAGTTGCCCTAG 59.374 57.143 0.00 0.00 0.00 3.02
2330 3332 1.729586 CTATAGCCCCAGTTGCCCTA 58.270 55.000 0.00 0.00 0.00 3.53
2332 3334 1.228276 GCTATAGCCCCAGTTGCCC 60.228 63.158 14.13 0.00 34.31 5.36
2364 3366 7.896811 TCTACTGGATATAATGGCACTAGTTG 58.103 38.462 0.00 0.00 0.00 3.16
2365 3367 8.492415 TTCTACTGGATATAATGGCACTAGTT 57.508 34.615 0.00 0.00 0.00 2.24
2366 3368 8.492415 TTTCTACTGGATATAATGGCACTAGT 57.508 34.615 0.00 0.00 0.00 2.57
2367 3369 9.950496 ATTTTCTACTGGATATAATGGCACTAG 57.050 33.333 0.00 0.00 0.00 2.57
2369 3371 9.646522 AAATTTTCTACTGGATATAATGGCACT 57.353 29.630 0.00 0.00 0.00 4.40
2395 3397 6.925165 GGCTTCTTTGAATGTGAAAATCTGAA 59.075 34.615 0.00 0.00 0.00 3.02
2396 3398 6.449698 GGCTTCTTTGAATGTGAAAATCTGA 58.550 36.000 0.00 0.00 0.00 3.27
2397 3399 5.636543 GGGCTTCTTTGAATGTGAAAATCTG 59.363 40.000 0.00 0.00 0.00 2.90
2398 3400 5.305128 TGGGCTTCTTTGAATGTGAAAATCT 59.695 36.000 0.00 0.00 0.00 2.40
2400 3402 5.544650 CTGGGCTTCTTTGAATGTGAAAAT 58.455 37.500 0.00 0.00 0.00 1.82
2401 3403 4.740334 GCTGGGCTTCTTTGAATGTGAAAA 60.740 41.667 0.00 0.00 0.00 2.29
2404 3406 1.888512 GCTGGGCTTCTTTGAATGTGA 59.111 47.619 0.00 0.00 0.00 3.58
2405 3407 1.067354 GGCTGGGCTTCTTTGAATGTG 60.067 52.381 0.00 0.00 0.00 3.21
2406 3408 1.260544 GGCTGGGCTTCTTTGAATGT 58.739 50.000 0.00 0.00 0.00 2.71
2407 3409 0.533951 GGGCTGGGCTTCTTTGAATG 59.466 55.000 0.00 0.00 0.00 2.67
2408 3410 0.615827 GGGGCTGGGCTTCTTTGAAT 60.616 55.000 0.00 0.00 0.00 2.57
2410 3412 2.430704 CTGGGGCTGGGCTTCTTTGA 62.431 60.000 0.00 0.00 0.00 2.69
2411 3413 1.980772 CTGGGGCTGGGCTTCTTTG 60.981 63.158 0.00 0.00 0.00 2.77
2413 3415 3.665971 CCTGGGGCTGGGCTTCTT 61.666 66.667 0.00 0.00 0.00 2.52
2426 3428 1.152881 GCTGGGTATTCAGGCCTGG 60.153 63.158 32.23 14.58 35.43 4.45
2427 3429 4.567318 GCTGGGTATTCAGGCCTG 57.433 61.111 27.87 27.87 35.43 4.85
2431 3433 0.106519 CCTTGGGCTGGGTATTCAGG 60.107 60.000 0.00 0.00 35.43 3.86
2432 3434 0.753111 GCCTTGGGCTGGGTATTCAG 60.753 60.000 0.80 0.00 46.69 3.02
2433 3435 1.306296 GCCTTGGGCTGGGTATTCA 59.694 57.895 0.80 0.00 46.69 2.57
2434 3436 4.259952 GCCTTGGGCTGGGTATTC 57.740 61.111 0.80 0.00 46.69 1.75
2451 3453 2.463589 TAGTTGGGCTGCCGTTGAGG 62.464 60.000 13.40 0.00 44.97 3.86
2453 3455 0.887387 GTTAGTTGGGCTGCCGTTGA 60.887 55.000 13.40 0.00 0.00 3.18
2454 3456 0.889186 AGTTAGTTGGGCTGCCGTTG 60.889 55.000 13.40 0.00 0.00 4.10
2457 3459 1.090052 GCTAGTTAGTTGGGCTGCCG 61.090 60.000 13.40 0.00 0.00 5.69
2458 3460 0.253327 AGCTAGTTAGTTGGGCTGCC 59.747 55.000 11.05 11.05 31.68 4.85
2459 3461 1.066143 TGAGCTAGTTAGTTGGGCTGC 60.066 52.381 0.00 0.00 33.13 5.25
2460 3462 2.898705 CTGAGCTAGTTAGTTGGGCTG 58.101 52.381 0.00 0.00 33.13 4.85
2462 3464 1.066143 TGCTGAGCTAGTTAGTTGGGC 60.066 52.381 5.83 0.00 0.00 5.36
2463 3465 2.419297 CCTGCTGAGCTAGTTAGTTGGG 60.419 54.545 5.83 0.00 0.00 4.12
2465 3467 3.876274 TCCTGCTGAGCTAGTTAGTTG 57.124 47.619 5.83 0.00 0.00 3.16
2466 3468 3.055747 GGTTCCTGCTGAGCTAGTTAGTT 60.056 47.826 5.83 0.00 0.00 2.24
2467 3469 2.498078 GGTTCCTGCTGAGCTAGTTAGT 59.502 50.000 5.83 0.00 0.00 2.24
2468 3470 2.159028 GGGTTCCTGCTGAGCTAGTTAG 60.159 54.545 5.83 0.00 0.00 2.34
2469 3471 1.831736 GGGTTCCTGCTGAGCTAGTTA 59.168 52.381 5.83 0.00 0.00 2.24
2470 3472 0.615850 GGGTTCCTGCTGAGCTAGTT 59.384 55.000 5.83 0.00 0.00 2.24
2472 3474 0.835941 ATGGGTTCCTGCTGAGCTAG 59.164 55.000 5.83 1.28 0.00 3.42
2473 3475 0.543277 CATGGGTTCCTGCTGAGCTA 59.457 55.000 5.83 0.00 0.00 3.32
2474 3476 1.302285 CATGGGTTCCTGCTGAGCT 59.698 57.895 5.83 0.00 0.00 4.09
2475 3477 2.413142 GCATGGGTTCCTGCTGAGC 61.413 63.158 0.00 0.00 35.49 4.26
2476 3478 1.751927 GGCATGGGTTCCTGCTGAG 60.752 63.158 0.00 0.00 38.45 3.35
2477 3479 2.356278 GGCATGGGTTCCTGCTGA 59.644 61.111 0.00 0.00 38.45 4.26
2478 3480 2.757099 GGGCATGGGTTCCTGCTG 60.757 66.667 0.00 0.00 38.45 4.41
2479 3481 3.267233 TGGGCATGGGTTCCTGCT 61.267 61.111 0.00 0.00 38.45 4.24
2480 3482 3.070576 GTGGGCATGGGTTCCTGC 61.071 66.667 0.00 0.00 37.66 4.85
2481 3483 2.751436 CGTGGGCATGGGTTCCTG 60.751 66.667 0.00 0.00 0.00 3.86
2482 3484 2.366153 AAACGTGGGCATGGGTTCCT 62.366 55.000 0.00 0.00 0.00 3.36
2483 3485 1.906333 AAACGTGGGCATGGGTTCC 60.906 57.895 0.00 0.00 0.00 3.62
2484 3486 1.288752 CAAACGTGGGCATGGGTTC 59.711 57.895 0.00 0.00 0.00 3.62
2485 3487 2.206536 CCAAACGTGGGCATGGGTT 61.207 57.895 0.00 0.00 41.77 4.11
2495 3497 1.222300 TCGACCAATGACCAAACGTG 58.778 50.000 0.00 0.00 0.00 4.49
2497 3499 2.850321 CAATCGACCAATGACCAAACG 58.150 47.619 0.00 0.00 0.00 3.60
2498 3500 2.595386 GCAATCGACCAATGACCAAAC 58.405 47.619 0.00 0.00 0.00 2.93
2499 3501 1.198867 CGCAATCGACCAATGACCAAA 59.801 47.619 0.00 0.00 38.10 3.28
2500 3502 0.801872 CGCAATCGACCAATGACCAA 59.198 50.000 0.00 0.00 38.10 3.67
2501 3503 0.036858 TCGCAATCGACCAATGACCA 60.037 50.000 0.00 0.00 40.21 4.02
2502 3504 2.762360 TCGCAATCGACCAATGACC 58.238 52.632 0.00 0.00 40.21 4.02
2512 3514 3.362986 CGATACCTTTGGAATCGCAATCG 60.363 47.826 0.00 0.00 36.46 3.34
2513 3515 3.807622 TCGATACCTTTGGAATCGCAATC 59.192 43.478 0.00 0.00 41.66 2.67
2514 3516 3.804036 TCGATACCTTTGGAATCGCAAT 58.196 40.909 0.00 0.00 41.66 3.56
2515 3517 3.254470 TCGATACCTTTGGAATCGCAA 57.746 42.857 0.00 0.00 41.66 4.85
2516 3518 2.971660 TCGATACCTTTGGAATCGCA 57.028 45.000 0.00 0.00 41.66 5.10
2517 3519 2.408704 CGATCGATACCTTTGGAATCGC 59.591 50.000 10.26 0.00 41.66 4.58
2518 3520 2.408704 GCGATCGATACCTTTGGAATCG 59.591 50.000 21.57 0.00 42.90 3.34


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

AutoCloner maintained by Alex Coulton.