Multiple sequence alignment - TraesCS1D01G200600

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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 TraesCS1D01G200600 chr1D 100.000 4205 0 0 1 4205 283565000 283569204 0.000000e+00 7766.0
1 TraesCS1D01G200600 chr1D 100.000 45 0 0 151 195 483951372 483951416 2.690000e-12 84.2
2 TraesCS1D01G200600 chr1D 100.000 30 0 0 200 229 242173251 242173280 5.870000e-04 56.5
3 TraesCS1D01G200600 chr1B 91.844 2354 127 30 3 2331 385163242 385165555 0.000000e+00 3223.0
4 TraesCS1D01G200600 chr1B 91.089 808 47 11 2828 3626 385166149 385166940 0.000000e+00 1070.0
5 TraesCS1D01G200600 chr1B 92.825 446 24 4 2387 2829 385165571 385166011 1.270000e-179 640.0
6 TraesCS1D01G200600 chr1B 95.000 260 10 3 3949 4205 385170220 385170479 5.060000e-109 405.0
7 TraesCS1D01G200600 chr1B 92.829 251 12 4 3650 3897 385169974 385170221 4.000000e-95 359.0
8 TraesCS1D01G200600 chr1B 89.655 58 5 1 139 195 597265832 597265775 5.830000e-09 73.1
9 TraesCS1D01G200600 chr1A 91.471 1958 91 27 411 2335 355325917 355327831 0.000000e+00 2621.0
10 TraesCS1D01G200600 chr1A 93.248 1244 62 13 2387 3626 355327843 355329068 0.000000e+00 1812.0
11 TraesCS1D01G200600 chr1A 94.636 261 10 2 3949 4205 355330099 355330359 6.550000e-108 401.0
12 TraesCS1D01G200600 chr1A 88.889 270 21 4 3628 3897 355329840 355330100 1.460000e-84 324.0
13 TraesCS1D01G200600 chr1A 81.429 140 18 5 6 139 355325563 355325700 1.600000e-19 108.0
14 TraesCS1D01G200600 chr1A 100.000 45 0 0 151 195 580955824 580955868 2.690000e-12 84.2
15 TraesCS1D01G200600 chr1A 94.118 51 2 1 314 364 424016422 424016373 4.510000e-10 76.8
16 TraesCS1D01G200600 chr1A 95.745 47 2 0 314 360 424173282 424173236 4.510000e-10 76.8
17 TraesCS1D01G200600 chr3D 94.118 51 3 0 145 195 163135388 163135438 1.250000e-10 78.7
18 TraesCS1D01G200600 chr6B 90.164 61 2 3 136 195 82007374 82007431 4.510000e-10 76.8
19 TraesCS1D01G200600 chr6B 91.071 56 3 1 142 195 127605798 127605853 1.620000e-09 75.0
20 TraesCS1D01G200600 chr6B 96.774 31 1 0 3889 3919 191598098 191598128 8.000000e-03 52.8
21 TraesCS1D01G200600 chr5D 94.118 51 2 1 149 199 27354249 27354298 4.510000e-10 76.8
22 TraesCS1D01G200600 chr5D 100.000 30 0 0 200 229 51715586 51715557 5.870000e-04 56.5
23 TraesCS1D01G200600 chr2B 87.692 65 4 1 154 214 773129934 773129870 5.830000e-09 73.1
24 TraesCS1D01G200600 chr4A 92.157 51 3 1 314 364 607464308 607464259 2.100000e-08 71.3
25 TraesCS1D01G200600 chr4A 100.000 29 0 0 3893 3921 646776740 646776712 2.000000e-03 54.7
26 TraesCS1D01G200600 chr2D 92.157 51 3 1 314 364 591023828 591023877 2.100000e-08 71.3
27 TraesCS1D01G200600 chr2D 100.000 30 0 0 200 229 48711510 48711481 5.870000e-04 56.5
28 TraesCS1D01G200600 chr2D 100.000 30 0 0 200 229 397790446 397790417 5.870000e-04 56.5
29 TraesCS1D01G200600 chr2D 100.000 28 0 0 3892 3919 12630904 12630877 8.000000e-03 52.8
30 TraesCS1D01G200600 chr6D 92.000 50 3 1 315 364 346785004 346785052 7.540000e-08 69.4
31 TraesCS1D01G200600 chr6D 100.000 30 0 0 200 229 332875264 332875293 5.870000e-04 56.5
32 TraesCS1D01G200600 chr5A 95.122 41 2 0 314 354 690445901 690445941 9.760000e-07 65.8
33 TraesCS1D01G200600 chr5A 96.774 31 1 0 3889 3919 328445136 328445166 8.000000e-03 52.8
34 TraesCS1D01G200600 chr7A 89.583 48 3 2 314 360 221684190 221684144 4.540000e-05 60.2
35 TraesCS1D01G200600 chr3A 89.583 48 3 2 314 360 63527777 63527823 4.540000e-05 60.2
36 TraesCS1D01G200600 chr7D 100.000 30 0 0 200 229 489935659 489935688 5.870000e-04 56.5
37 TraesCS1D01G200600 chr7D 100.000 28 0 0 3892 3919 613869090 613869063 8.000000e-03 52.8
38 TraesCS1D01G200600 chr4D 100.000 30 0 0 200 229 307111283 307111312 5.870000e-04 56.5
39 TraesCS1D01G200600 chr7B 100.000 28 0 0 3892 3919 62852597 62852570 8.000000e-03 52.8
40 TraesCS1D01G200600 chr5B 100.000 28 0 0 3892 3919 126604602 126604629 8.000000e-03 52.8
41 TraesCS1D01G200600 chr5B 96.774 31 1 0 3889 3919 679686582 679686612 8.000000e-03 52.8
42 TraesCS1D01G200600 chr3B 100.000 28 0 0 3894 3921 499194094 499194121 8.000000e-03 52.8


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 TraesCS1D01G200600 chr1D 283565000 283569204 4204 False 7766.0 7766 100.0000 1 4205 1 chr1D.!!$F2 4204
1 TraesCS1D01G200600 chr1B 385163242 385170479 7237 False 1139.4 3223 92.7174 3 4205 5 chr1B.!!$F1 4202
2 TraesCS1D01G200600 chr1A 355325563 355330359 4796 False 1053.2 2621 89.9346 6 4205 5 chr1A.!!$F2 4199

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
796 934 0.604511 GAGGACGGCGGGAAAAGAAA 60.605 55.0 13.24 0.0 0.00 2.52 F
797 935 0.605589 AGGACGGCGGGAAAAGAAAG 60.606 55.0 13.24 0.0 0.00 2.62 F
798 936 0.604511 GGACGGCGGGAAAAGAAAGA 60.605 55.0 13.24 0.0 0.00 2.52 F
2221 2380 0.258484 CAATCCAGGTGCATGGGGTA 59.742 55.0 6.50 0.0 41.01 3.69 F
2223 2382 0.552848 ATCCAGGTGCATGGGGTAAG 59.447 55.0 6.50 0.0 41.01 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2158 0.248784 GCCATTTTCTCGCCTCATGC 60.249 55.0 0.00 0.0 0.00 4.06 R
2202 2361 0.258484 TACCCCATGCACCTGGATTG 59.742 55.0 7.97 0.0 38.69 2.67 R
2480 2641 0.537188 AGGGTAAGAGGTGCGTCATG 59.463 55.0 0.00 0.0 0.00 3.07 R
3040 3341 0.035458 AGCTCTACTTGTTTGCGCCT 59.965 50.0 4.18 0.0 0.00 5.52 R
3438 3744 0.110056 CTGCTTGCACCAAGTTAGCG 60.110 55.0 6.80 0.0 42.77 4.26 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
162 167 9.109246 TCATCATCAATCAAATATACTCCCTCT 57.891 33.333 0.00 0.00 0.00 3.69
172 177 9.225682 TCAAATATACTCCCTCTGTTCCTAAAT 57.774 33.333 0.00 0.00 0.00 1.40
214 219 7.827819 TTTCAGTGTCTTATATTCAGGAACG 57.172 36.000 0.00 0.00 0.00 3.95
230 235 2.619147 GAACGGAGGGAGTAGAAAAGC 58.381 52.381 0.00 0.00 0.00 3.51
283 400 4.743057 TCGTCCAGTACACTAGTAGCTA 57.257 45.455 0.00 0.00 0.00 3.32
298 415 9.239551 CACTAGTAGCTACTCTCTCTCTCTATA 57.760 40.741 29.28 6.81 37.73 1.31
449 569 1.741706 GCATGATCGAAGGCCATATGG 59.258 52.381 18.07 18.07 38.53 2.74
591 716 6.547880 TGGGAAAACACTCAACTAATAAAGCA 59.452 34.615 0.00 0.00 0.00 3.91
599 724 7.880195 ACACTCAACTAATAAAGCAGACTGAAT 59.120 33.333 6.65 0.00 0.00 2.57
612 737 2.032030 AGACTGAATTTTGGTTCGTGCG 60.032 45.455 0.00 0.00 0.00 5.34
629 754 1.498865 GCGGGTTGGTCATATCTGCG 61.499 60.000 0.00 0.00 0.00 5.18
721 858 1.269166 GCATCTCGTCAACGTACCTG 58.731 55.000 2.09 0.00 40.80 4.00
722 859 1.269166 CATCTCGTCAACGTACCTGC 58.731 55.000 2.09 0.00 40.80 4.85
747 884 1.913317 TGAACAGCGAGACGATGATG 58.087 50.000 15.71 1.44 46.56 3.07
795 933 1.004200 GAGGACGGCGGGAAAAGAA 60.004 57.895 13.24 0.00 0.00 2.52
796 934 0.604511 GAGGACGGCGGGAAAAGAAA 60.605 55.000 13.24 0.00 0.00 2.52
797 935 0.605589 AGGACGGCGGGAAAAGAAAG 60.606 55.000 13.24 0.00 0.00 2.62
798 936 0.604511 GGACGGCGGGAAAAGAAAGA 60.605 55.000 13.24 0.00 0.00 2.52
799 937 1.450025 GACGGCGGGAAAAGAAAGAT 58.550 50.000 13.24 0.00 0.00 2.40
800 938 1.130561 GACGGCGGGAAAAGAAAGATG 59.869 52.381 13.24 0.00 0.00 2.90
802 940 0.887933 GGCGGGAAAAGAAAGATGCA 59.112 50.000 0.00 0.00 0.00 3.96
879 1017 1.810755 CATCGCCATGATTGATCTGGG 59.189 52.381 0.00 5.05 34.13 4.45
913 1051 2.223066 CCGACCGACTCGCTCATATATC 60.223 54.545 0.00 0.00 41.46 1.63
953 1091 2.125147 ATATGCGTGCGTGCCAGT 60.125 55.556 0.00 0.00 0.00 4.00
991 1132 2.464865 CACATTAGTCACTAGCTCGCC 58.535 52.381 0.00 0.00 0.00 5.54
992 1133 1.065701 ACATTAGTCACTAGCTCGCCG 59.934 52.381 0.00 0.00 0.00 6.46
995 1136 4.874977 GTCACTAGCTCGCCGGCC 62.875 72.222 23.46 7.02 0.00 6.13
1323 1479 1.658686 CCCACGTCTTCCTCCTCTCG 61.659 65.000 0.00 0.00 0.00 4.04
1632 1788 1.103398 TCTGCGAGATGCTCATCGGA 61.103 55.000 4.41 3.73 46.63 4.55
1755 1911 0.711184 ACAGAGGCCTACAGGTACCT 59.289 55.000 9.21 9.21 37.57 3.08
1878 2035 1.665679 ACCAAGATTCGCGCAAGTATG 59.334 47.619 8.75 0.00 41.68 2.39
2117 2276 2.932614 CACGGATGAACAGATTCTGGAC 59.067 50.000 17.66 11.04 35.51 4.02
2148 2307 8.437360 TTTGACACTCATAATTGCAGGTATAG 57.563 34.615 0.00 0.00 0.00 1.31
2151 2310 9.088987 TGACACTCATAATTGCAGGTATAGATA 57.911 33.333 0.00 0.00 0.00 1.98
2162 2321 8.650143 TTGCAGGTATAGATATATGTCAGTCA 57.350 34.615 2.04 0.00 0.00 3.41
2180 2339 9.337396 TGTCAGTCATAATTCAGTTGTTAACTT 57.663 29.630 7.22 0.00 40.46 2.66
2181 2340 9.599322 GTCAGTCATAATTCAGTTGTTAACTTG 57.401 33.333 7.22 3.39 40.46 3.16
2182 2341 8.289618 TCAGTCATAATTCAGTTGTTAACTTGC 58.710 33.333 7.22 0.00 40.46 4.01
2185 2344 9.243637 GTCATAATTCAGTTGTTAACTTGCAAA 57.756 29.630 7.22 0.00 40.46 3.68
2204 2363 8.994429 TTGCAAAGACTTAGTTGAAATTTCAA 57.006 26.923 26.01 26.01 44.31 2.69
2214 2373 4.952071 TTGAAATTTCAATCCAGGTGCA 57.048 36.364 26.01 3.89 41.88 4.57
2215 2374 5.486735 TTGAAATTTCAATCCAGGTGCAT 57.513 34.783 26.01 0.00 41.88 3.96
2216 2375 4.823157 TGAAATTTCAATCCAGGTGCATG 58.177 39.130 18.45 0.00 33.55 4.06
2217 2376 3.899052 AATTTCAATCCAGGTGCATGG 57.101 42.857 0.00 0.00 42.11 3.66
2218 2377 1.559368 TTTCAATCCAGGTGCATGGG 58.441 50.000 6.50 0.83 41.01 4.00
2219 2378 0.324552 TTCAATCCAGGTGCATGGGG 60.325 55.000 6.50 0.46 41.01 4.96
2220 2379 1.000739 CAATCCAGGTGCATGGGGT 59.999 57.895 6.50 0.00 41.01 4.95
2221 2380 0.258484 CAATCCAGGTGCATGGGGTA 59.742 55.000 6.50 0.00 41.01 3.69
2222 2381 1.006813 AATCCAGGTGCATGGGGTAA 58.993 50.000 6.50 0.00 41.01 2.85
2223 2382 0.552848 ATCCAGGTGCATGGGGTAAG 59.447 55.000 6.50 0.00 41.01 2.34
2224 2383 0.844661 TCCAGGTGCATGGGGTAAGT 60.845 55.000 6.50 0.00 41.01 2.24
2265 2424 0.592247 GGCAAGTGACAACAGCAACG 60.592 55.000 0.00 0.00 32.89 4.10
2307 2466 1.961277 CCTGGGCGACAACACAGAC 60.961 63.158 0.00 0.00 32.86 3.51
2320 2479 4.141390 ACAACACAGACCTCCAAGAGAAAT 60.141 41.667 0.00 0.00 0.00 2.17
2335 2494 6.593382 CCAAGAGAAATTAAGAGTGAGTGAGG 59.407 42.308 0.00 0.00 0.00 3.86
2336 2495 7.382110 CAAGAGAAATTAAGAGTGAGTGAGGA 58.618 38.462 0.00 0.00 0.00 3.71
2337 2496 6.930731 AGAGAAATTAAGAGTGAGTGAGGAC 58.069 40.000 0.00 0.00 0.00 3.85
2338 2497 6.723977 AGAGAAATTAAGAGTGAGTGAGGACT 59.276 38.462 0.00 0.00 33.98 3.85
2339 2498 6.696411 AGAAATTAAGAGTGAGTGAGGACTG 58.304 40.000 0.00 0.00 30.16 3.51
2340 2499 6.495181 AGAAATTAAGAGTGAGTGAGGACTGA 59.505 38.462 0.00 0.00 30.16 3.41
2341 2500 5.913137 ATTAAGAGTGAGTGAGGACTGAG 57.087 43.478 0.00 0.00 30.16 3.35
2342 2501 2.214376 AGAGTGAGTGAGGACTGAGG 57.786 55.000 0.00 0.00 30.16 3.86
2343 2502 1.707989 AGAGTGAGTGAGGACTGAGGA 59.292 52.381 0.00 0.00 30.16 3.71
2344 2503 2.091541 GAGTGAGTGAGGACTGAGGAG 58.908 57.143 0.00 0.00 30.16 3.69
2345 2504 1.427368 AGTGAGTGAGGACTGAGGAGT 59.573 52.381 0.00 0.00 30.16 3.85
2362 2521 4.952071 GGAGTCATTCCATCTCATCTGA 57.048 45.455 0.00 0.00 46.01 3.27
2363 2522 5.486735 GGAGTCATTCCATCTCATCTGAT 57.513 43.478 0.00 0.00 46.01 2.90
2364 2523 5.481105 GGAGTCATTCCATCTCATCTGATC 58.519 45.833 0.00 0.00 46.01 2.92
2365 2524 5.246656 GGAGTCATTCCATCTCATCTGATCT 59.753 44.000 0.00 0.00 46.01 2.75
2366 2525 6.436847 GGAGTCATTCCATCTCATCTGATCTA 59.563 42.308 0.00 0.00 46.01 1.98
2367 2526 7.039152 GGAGTCATTCCATCTCATCTGATCTAA 60.039 40.741 0.00 0.00 46.01 2.10
2368 2527 7.669427 AGTCATTCCATCTCATCTGATCTAAC 58.331 38.462 0.00 0.00 0.00 2.34
2369 2528 6.873076 GTCATTCCATCTCATCTGATCTAACC 59.127 42.308 0.00 0.00 0.00 2.85
2370 2529 6.556116 TCATTCCATCTCATCTGATCTAACCA 59.444 38.462 0.00 0.00 0.00 3.67
2371 2530 7.237055 TCATTCCATCTCATCTGATCTAACCAT 59.763 37.037 0.00 0.00 0.00 3.55
2372 2531 6.602410 TCCATCTCATCTGATCTAACCATC 57.398 41.667 0.00 0.00 0.00 3.51
2373 2532 6.321321 TCCATCTCATCTGATCTAACCATCT 58.679 40.000 0.00 0.00 0.00 2.90
2374 2533 6.786461 TCCATCTCATCTGATCTAACCATCTT 59.214 38.462 0.00 0.00 0.00 2.40
2375 2534 7.952368 TCCATCTCATCTGATCTAACCATCTTA 59.048 37.037 0.00 0.00 0.00 2.10
2376 2535 8.034215 CCATCTCATCTGATCTAACCATCTTAC 58.966 40.741 0.00 0.00 0.00 2.34
2377 2536 7.531857 TCTCATCTGATCTAACCATCTTACC 57.468 40.000 0.00 0.00 0.00 2.85
2378 2537 6.495181 TCTCATCTGATCTAACCATCTTACCC 59.505 42.308 0.00 0.00 0.00 3.69
2379 2538 6.143206 TCATCTGATCTAACCATCTTACCCA 58.857 40.000 0.00 0.00 0.00 4.51
2380 2539 6.789457 TCATCTGATCTAACCATCTTACCCAT 59.211 38.462 0.00 0.00 0.00 4.00
2381 2540 7.955750 TCATCTGATCTAACCATCTTACCCATA 59.044 37.037 0.00 0.00 0.00 2.74
2382 2541 7.540474 TCTGATCTAACCATCTTACCCATAC 57.460 40.000 0.00 0.00 0.00 2.39
2383 2542 7.073208 TCTGATCTAACCATCTTACCCATACA 58.927 38.462 0.00 0.00 0.00 2.29
2384 2543 7.734865 TCTGATCTAACCATCTTACCCATACAT 59.265 37.037 0.00 0.00 0.00 2.29
2385 2544 8.966155 TGATCTAACCATCTTACCCATACATA 57.034 34.615 0.00 0.00 0.00 2.29
2405 2564 5.824624 ACATAGCCCATGTATGAAGAACAAG 59.175 40.000 8.39 0.00 46.34 3.16
2434 2593 9.017509 ACTTCATTTCTTGATTGCAATTCTCTA 57.982 29.630 14.33 0.00 33.34 2.43
2453 2614 7.823745 TCTCTATCTACATGTATGCAGTCAA 57.176 36.000 5.91 0.00 0.00 3.18
2480 2641 1.105759 GGATCTGGCATCCAAGCACC 61.106 60.000 2.21 0.00 38.09 5.01
2485 2646 0.966875 TGGCATCCAAGCACCATGAC 60.967 55.000 0.00 0.00 35.83 3.06
2536 2697 3.430236 CCATGGACTACGCATACAAGACA 60.430 47.826 5.56 0.00 0.00 3.41
2637 2799 7.407337 GGTAACTAAACCTCGCTGATTTTATG 58.593 38.462 0.00 0.00 36.53 1.90
2716 2878 4.782691 TCCACATTAAGAAGGACTGGATCA 59.217 41.667 0.00 0.00 0.00 2.92
2769 2931 1.072173 CCGGCCATCTATGACAATCCA 59.928 52.381 2.24 0.00 0.00 3.41
2773 2935 2.031682 GCCATCTATGACAATCCAACGC 60.032 50.000 0.00 0.00 0.00 4.84
2885 3186 2.778299 TGTTGTTGCTATGGACAGGAC 58.222 47.619 0.00 0.00 0.00 3.85
2912 3213 2.409948 AGCCATACAGCTTCTTGGTC 57.590 50.000 7.27 1.46 41.41 4.02
2948 3249 1.572415 AGAACATGCCTGGGGATGAAT 59.428 47.619 24.17 13.88 45.01 2.57
2987 3288 4.569943 TGCTAATATTCCTTCATCGCCTC 58.430 43.478 0.00 0.00 0.00 4.70
2988 3289 4.040339 TGCTAATATTCCTTCATCGCCTCA 59.960 41.667 0.00 0.00 0.00 3.86
3004 3305 3.426695 CGCCTCATCACAAATTTCAGGTC 60.427 47.826 0.00 0.00 0.00 3.85
3008 3309 5.123502 CCTCATCACAAATTTCAGGTCTCAG 59.876 44.000 0.00 0.00 0.00 3.35
3017 3318 5.753721 ATTTCAGGTCTCAGCTCTAAAGT 57.246 39.130 0.00 0.00 0.00 2.66
3039 3340 9.598517 AAAGTCAAGTTTCTTTATTTTGATGCA 57.401 25.926 0.00 0.00 33.00 3.96
3040 3341 9.598517 AAGTCAAGTTTCTTTATTTTGATGCAA 57.401 25.926 0.00 0.00 31.28 4.08
3041 3342 9.252962 AGTCAAGTTTCTTTATTTTGATGCAAG 57.747 29.630 0.00 0.00 31.28 4.01
3042 3343 8.490355 GTCAAGTTTCTTTATTTTGATGCAAGG 58.510 33.333 0.00 0.00 31.28 3.61
3043 3344 7.171337 TCAAGTTTCTTTATTTTGATGCAAGGC 59.829 33.333 0.00 0.00 0.00 4.35
3065 3367 2.999355 GCAAACAAGTAGAGCTGGAGAG 59.001 50.000 0.00 0.00 0.00 3.20
3078 3380 7.913674 AGAGCTGGAGAGTAAAACTAAAATG 57.086 36.000 0.00 0.00 0.00 2.32
3123 3426 1.927895 CAGACCACGATACAAGCCTC 58.072 55.000 0.00 0.00 0.00 4.70
3144 3447 2.230992 CGAGAAATGGGCAATGTTTCCA 59.769 45.455 0.00 0.00 33.46 3.53
3150 3453 0.037046 GGGCAATGTTTCCAAGGCTG 60.037 55.000 0.00 0.00 0.00 4.85
3170 3473 0.819582 AAGAATGGCTGCCCAATTCG 59.180 50.000 17.53 0.00 46.14 3.34
3308 3611 7.205297 ACTCCAACAGATGAAACAAATTCTTG 58.795 34.615 0.00 0.00 38.92 3.02
3417 3721 5.709631 TGCTGCTGGTCTTTGTGATATTTTA 59.290 36.000 0.00 0.00 0.00 1.52
3440 3746 2.305252 CATGTATGCATGCAGTACGC 57.695 50.000 26.69 13.53 44.87 4.42
3481 3787 5.368145 GGCAAACCCTCAGAAATTTCTTTT 58.632 37.500 18.16 12.52 34.74 2.27
3511 3817 8.912988 AGTTGAGATGAATTAAAACCAACAGAA 58.087 29.630 0.00 0.00 36.18 3.02
3588 3899 9.311916 CATACAAGAAATGAAAACTGACCAAAA 57.688 29.630 0.00 0.00 0.00 2.44
3597 3908 5.656416 TGAAAACTGACCAAAACTGGAATCT 59.344 36.000 0.00 0.00 0.00 2.40
3599 3910 6.635030 AAACTGACCAAAACTGGAATCTAC 57.365 37.500 0.00 0.00 0.00 2.59
3626 3937 5.857845 AGCATAGTTTCCCTCCCCTATTTAT 59.142 40.000 0.00 0.00 0.00 1.40
3699 7113 8.750515 TGCTGGATGTCATTATCTAAATTTCA 57.249 30.769 0.00 0.00 0.00 2.69
3742 7156 5.951494 GCACACGTTTTGATTTCAGTTTTTC 59.049 36.000 0.00 0.00 0.00 2.29
3753 7167 4.829064 TTCAGTTTTTCCCATTGAGACG 57.171 40.909 0.00 0.00 0.00 4.18
3757 7171 3.564225 AGTTTTTCCCATTGAGACGTCAC 59.436 43.478 19.50 12.69 30.10 3.67
3780 7194 8.370940 TCACTTTCTAGATTTCACAGATTCTGT 58.629 33.333 13.61 13.61 46.51 3.41
3809 7223 3.476552 TGGTTTTTCGCTCATGAAGACT 58.523 40.909 0.00 0.00 0.00 3.24
3904 7321 7.793948 ACTACACTTACAAAATACTCCCTCT 57.206 36.000 0.00 0.00 0.00 3.69
3905 7322 7.612677 ACTACACTTACAAAATACTCCCTCTG 58.387 38.462 0.00 0.00 0.00 3.35
3906 7323 6.435292 ACACTTACAAAATACTCCCTCTGT 57.565 37.500 0.00 0.00 0.00 3.41
3907 7324 6.465084 ACACTTACAAAATACTCCCTCTGTC 58.535 40.000 0.00 0.00 0.00 3.51
3908 7325 5.875359 CACTTACAAAATACTCCCTCTGTCC 59.125 44.000 0.00 0.00 0.00 4.02
3909 7326 5.045797 ACTTACAAAATACTCCCTCTGTCCC 60.046 44.000 0.00 0.00 0.00 4.46
3910 7327 3.256704 ACAAAATACTCCCTCTGTCCCA 58.743 45.455 0.00 0.00 0.00 4.37
3911 7328 3.852578 ACAAAATACTCCCTCTGTCCCAT 59.147 43.478 0.00 0.00 0.00 4.00
3912 7329 5.036916 ACAAAATACTCCCTCTGTCCCATA 58.963 41.667 0.00 0.00 0.00 2.74
3913 7330 5.491078 ACAAAATACTCCCTCTGTCCCATAA 59.509 40.000 0.00 0.00 0.00 1.90
3914 7331 6.160459 ACAAAATACTCCCTCTGTCCCATAAT 59.840 38.462 0.00 0.00 0.00 1.28
3915 7332 5.832539 AATACTCCCTCTGTCCCATAATG 57.167 43.478 0.00 0.00 0.00 1.90
3916 7333 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
3917 7334 4.280789 ACTCCCTCTGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
3918 7335 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
3919 7336 5.036916 ACTCCCTCTGTCCCATAATGTAAA 58.963 41.667 0.00 0.00 0.00 2.01
3920 7337 5.491078 ACTCCCTCTGTCCCATAATGTAAAA 59.509 40.000 0.00 0.00 0.00 1.52
3921 7338 6.011981 ACTCCCTCTGTCCCATAATGTAAAAA 60.012 38.462 0.00 0.00 0.00 1.94
3922 7339 6.184789 TCCCTCTGTCCCATAATGTAAAAAC 58.815 40.000 0.00 0.00 0.00 2.43
3923 7340 5.065988 CCCTCTGTCCCATAATGTAAAAACG 59.934 44.000 0.00 0.00 0.00 3.60
3924 7341 5.448632 CCTCTGTCCCATAATGTAAAAACGC 60.449 44.000 0.00 0.00 0.00 4.84
3925 7342 4.396790 TCTGTCCCATAATGTAAAAACGCC 59.603 41.667 0.00 0.00 0.00 5.68
3926 7343 4.337145 TGTCCCATAATGTAAAAACGCCT 58.663 39.130 0.00 0.00 0.00 5.52
3927 7344 4.767928 TGTCCCATAATGTAAAAACGCCTT 59.232 37.500 0.00 0.00 0.00 4.35
3928 7345 5.944599 TGTCCCATAATGTAAAAACGCCTTA 59.055 36.000 0.00 0.00 0.00 2.69
3929 7346 6.433404 TGTCCCATAATGTAAAAACGCCTTAA 59.567 34.615 0.00 0.00 0.00 1.85
3930 7347 7.039923 TGTCCCATAATGTAAAAACGCCTTAAA 60.040 33.333 0.00 0.00 0.00 1.52
3931 7348 7.977293 GTCCCATAATGTAAAAACGCCTTAAAT 59.023 33.333 0.00 0.00 0.00 1.40
3932 7349 8.532819 TCCCATAATGTAAAAACGCCTTAAATT 58.467 29.630 0.00 0.00 0.00 1.82
3933 7350 9.804758 CCCATAATGTAAAAACGCCTTAAATTA 57.195 29.630 0.00 0.00 0.00 1.40
3937 7354 8.710835 AATGTAAAAACGCCTTAAATTATGGG 57.289 30.769 7.00 0.00 0.00 4.00
3938 7355 6.631962 TGTAAAAACGCCTTAAATTATGGGG 58.368 36.000 16.75 16.75 40.41 4.96
3939 7356 3.812156 AAACGCCTTAAATTATGGGGC 57.188 42.857 17.81 10.55 38.85 5.80
3942 7359 1.989706 GCCTTAAATTATGGGGCGGA 58.010 50.000 7.00 0.00 33.30 5.54
3943 7360 1.886542 GCCTTAAATTATGGGGCGGAG 59.113 52.381 7.00 0.00 33.30 4.63
3944 7361 2.514803 CCTTAAATTATGGGGCGGAGG 58.485 52.381 0.00 0.00 0.00 4.30
3945 7362 2.514803 CTTAAATTATGGGGCGGAGGG 58.485 52.381 0.00 0.00 0.00 4.30
3946 7363 1.822425 TAAATTATGGGGCGGAGGGA 58.178 50.000 0.00 0.00 0.00 4.20
3947 7364 0.478507 AAATTATGGGGCGGAGGGAG 59.521 55.000 0.00 0.00 0.00 4.30
3948 7365 0.697854 AATTATGGGGCGGAGGGAGT 60.698 55.000 0.00 0.00 0.00 3.85
3949 7366 0.192566 ATTATGGGGCGGAGGGAGTA 59.807 55.000 0.00 0.00 0.00 2.59
4150 7570 4.460382 CCAATCAAGTCCTACAGCACAATT 59.540 41.667 0.00 0.00 0.00 2.32
4159 7579 6.016777 AGTCCTACAGCACAATTCAGAAAAAG 60.017 38.462 0.00 0.00 0.00 2.27
4168 7588 7.440255 AGCACAATTCAGAAAAAGGAAAAGATG 59.560 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 101 8.047310 TCATCTGATTAATGAGCTATCATGCAT 58.953 33.333 0.00 0.00 45.67 3.96
188 193 8.543774 CGTTCCTGAATATAAGACACTGAAATC 58.456 37.037 0.00 0.00 0.00 2.17
195 200 5.290386 CCTCCGTTCCTGAATATAAGACAC 58.710 45.833 0.00 0.00 0.00 3.67
197 202 4.587684 TCCCTCCGTTCCTGAATATAAGAC 59.412 45.833 0.00 0.00 0.00 3.01
207 212 1.848652 TTCTACTCCCTCCGTTCCTG 58.151 55.000 0.00 0.00 0.00 3.86
214 219 1.471851 GCTCGCTTTTCTACTCCCTCC 60.472 57.143 0.00 0.00 0.00 4.30
298 415 5.575157 TCCCGCAAAGAGAGAGAGATATAT 58.425 41.667 0.00 0.00 0.00 0.86
302 419 2.151502 TCCCGCAAAGAGAGAGAGAT 57.848 50.000 0.00 0.00 0.00 2.75
304 421 2.615869 CTTTCCCGCAAAGAGAGAGAG 58.384 52.381 0.00 0.00 44.02 3.20
305 422 1.276421 CCTTTCCCGCAAAGAGAGAGA 59.724 52.381 6.65 0.00 44.02 3.10
306 423 1.276421 TCCTTTCCCGCAAAGAGAGAG 59.724 52.381 6.65 0.00 44.02 3.20
307 424 1.348064 TCCTTTCCCGCAAAGAGAGA 58.652 50.000 6.65 0.00 44.02 3.10
308 425 1.807142 GTTCCTTTCCCGCAAAGAGAG 59.193 52.381 6.65 0.00 44.02 3.20
449 569 1.224592 CCCGCATATCTATGGGCCC 59.775 63.158 17.59 17.59 43.03 5.80
537 657 0.532862 CGGCCGCATATTCTGGTCTT 60.533 55.000 14.67 0.00 0.00 3.01
591 716 2.032030 CGCACGAACCAAAATTCAGTCT 60.032 45.455 0.00 0.00 0.00 3.24
599 724 1.433879 CAACCCGCACGAACCAAAA 59.566 52.632 0.00 0.00 0.00 2.44
612 737 1.299541 CACGCAGATATGACCAACCC 58.700 55.000 0.00 0.00 0.00 4.11
721 858 0.179205 GTCTCGCTGTTCATGCAAGC 60.179 55.000 0.00 0.00 0.00 4.01
722 859 0.094216 CGTCTCGCTGTTCATGCAAG 59.906 55.000 0.00 0.00 0.00 4.01
776 914 1.477685 TTCTTTTCCCGCCGTCCTCT 61.478 55.000 0.00 0.00 0.00 3.69
795 933 1.202222 GCGCTAGTTGCATTGCATCTT 60.202 47.619 23.29 10.46 43.06 2.40
796 934 0.379669 GCGCTAGTTGCATTGCATCT 59.620 50.000 22.13 22.13 43.06 2.90
797 935 0.099259 TGCGCTAGTTGCATTGCATC 59.901 50.000 12.95 11.86 43.06 3.91
798 936 0.527113 TTGCGCTAGTTGCATTGCAT 59.473 45.000 12.95 0.58 42.84 3.96
799 937 0.109643 CTTGCGCTAGTTGCATTGCA 60.110 50.000 9.73 7.38 42.84 4.08
800 938 0.109597 ACTTGCGCTAGTTGCATTGC 60.110 50.000 18.92 0.46 42.84 3.56
802 940 0.109597 GCACTTGCGCTAGTTGCATT 60.110 50.000 27.18 6.57 42.84 3.56
953 1091 3.286751 GTTTCACTGGCGCTGGCA 61.287 61.111 7.64 0.00 42.47 4.92
991 1132 2.147315 ATCGACATCATCTCCGGCCG 62.147 60.000 21.04 21.04 0.00 6.13
992 1133 0.668706 CATCGACATCATCTCCGGCC 60.669 60.000 0.00 0.00 0.00 6.13
995 1136 1.264288 TCGACATCGACATCATCTCCG 59.736 52.381 0.00 0.00 44.22 4.63
1084 1240 1.829096 GGAGGAGGAGGTAGGCGAC 60.829 68.421 0.00 0.00 0.00 5.19
1116 1272 2.527951 CTTCCTGCCGGAGTTGGGAG 62.528 65.000 5.05 0.35 46.23 4.30
1119 1275 2.045926 CCTTCCTGCCGGAGTTGG 60.046 66.667 5.05 0.01 41.25 3.77
1632 1788 1.583556 TATGTGCATCCTCCTGTGGT 58.416 50.000 0.00 0.00 0.00 4.16
1848 2005 4.799678 CGCGAATCTTGGTATCTAGTGAT 58.200 43.478 0.00 0.00 36.74 3.06
1849 2006 3.550233 GCGCGAATCTTGGTATCTAGTGA 60.550 47.826 12.10 0.00 0.00 3.41
1850 2007 2.726760 GCGCGAATCTTGGTATCTAGTG 59.273 50.000 12.10 0.00 0.00 2.74
1851 2008 2.361119 TGCGCGAATCTTGGTATCTAGT 59.639 45.455 12.10 0.00 0.00 2.57
1852 2009 3.013276 TGCGCGAATCTTGGTATCTAG 57.987 47.619 12.10 0.00 0.00 2.43
1853 2010 3.181479 ACTTGCGCGAATCTTGGTATCTA 60.181 43.478 12.10 0.00 0.00 1.98
1854 2011 2.205074 CTTGCGCGAATCTTGGTATCT 58.795 47.619 12.10 0.00 0.00 1.98
1855 2012 1.933853 ACTTGCGCGAATCTTGGTATC 59.066 47.619 12.10 0.00 0.00 2.24
1889 2046 7.739498 TCCCTTCTTGTGAATTTGTAGTAAC 57.261 36.000 0.00 0.00 0.00 2.50
1920 2077 3.706594 TCCACACCAAGAATCTAGCTAGG 59.293 47.826 20.58 6.16 0.00 3.02
1999 2158 0.248784 GCCATTTTCTCGCCTCATGC 60.249 55.000 0.00 0.00 0.00 4.06
2117 2276 7.148705 CCTGCAATTATGAGTGTCAAAATGTTG 60.149 37.037 0.00 0.00 35.95 3.33
2156 2315 8.289618 GCAAGTTAACAACTGAATTATGACTGA 58.710 33.333 8.61 0.00 41.91 3.41
2157 2316 8.075574 TGCAAGTTAACAACTGAATTATGACTG 58.924 33.333 8.61 0.00 41.91 3.51
2162 2321 9.463443 GTCTTTGCAAGTTAACAACTGAATTAT 57.537 29.630 8.61 0.00 41.91 1.28
2168 2327 7.472543 ACTAAGTCTTTGCAAGTTAACAACTG 58.527 34.615 8.61 3.36 41.91 3.16
2173 2332 8.905103 TTTCAACTAAGTCTTTGCAAGTTAAC 57.095 30.769 0.00 0.00 0.00 2.01
2193 2352 8.699717 CCCATGCACCTGGATTGAAATTTCAA 62.700 42.308 30.27 30.27 40.49 2.69
2197 2356 2.502538 CCCATGCACCTGGATTGAAATT 59.497 45.455 7.97 0.00 38.69 1.82
2198 2357 2.112998 CCCATGCACCTGGATTGAAAT 58.887 47.619 7.97 0.00 38.69 2.17
2201 2360 1.307309 CCCCATGCACCTGGATTGA 59.693 57.895 7.97 0.00 38.69 2.57
2202 2361 0.258484 TACCCCATGCACCTGGATTG 59.742 55.000 7.97 0.00 38.69 2.67
2203 2362 1.006813 TTACCCCATGCACCTGGATT 58.993 50.000 7.97 0.00 38.69 3.01
2204 2363 0.552848 CTTACCCCATGCACCTGGAT 59.447 55.000 7.97 0.00 38.69 3.41
2205 2364 0.844661 ACTTACCCCATGCACCTGGA 60.845 55.000 7.97 0.00 38.69 3.86
2207 2366 0.620556 AGACTTACCCCATGCACCTG 59.379 55.000 0.00 0.00 0.00 4.00
2209 2368 1.271926 ACAAGACTTACCCCATGCACC 60.272 52.381 0.00 0.00 0.00 5.01
2210 2369 2.200373 ACAAGACTTACCCCATGCAC 57.800 50.000 0.00 0.00 0.00 4.57
2211 2370 2.890311 CAAACAAGACTTACCCCATGCA 59.110 45.455 0.00 0.00 0.00 3.96
2212 2371 2.890945 ACAAACAAGACTTACCCCATGC 59.109 45.455 0.00 0.00 0.00 4.06
2213 2372 5.768164 AGTTACAAACAAGACTTACCCCATG 59.232 40.000 0.00 0.00 0.00 3.66
2214 2373 5.768164 CAGTTACAAACAAGACTTACCCCAT 59.232 40.000 0.00 0.00 0.00 4.00
2215 2374 5.104444 TCAGTTACAAACAAGACTTACCCCA 60.104 40.000 0.00 0.00 0.00 4.96
2216 2375 5.370679 TCAGTTACAAACAAGACTTACCCC 58.629 41.667 0.00 0.00 0.00 4.95
2217 2376 6.018180 CACTCAGTTACAAACAAGACTTACCC 60.018 42.308 0.00 0.00 0.00 3.69
2218 2377 6.511282 GCACTCAGTTACAAACAAGACTTACC 60.511 42.308 0.00 0.00 0.00 2.85
2219 2378 6.036735 TGCACTCAGTTACAAACAAGACTTAC 59.963 38.462 0.00 0.00 0.00 2.34
2220 2379 6.110033 TGCACTCAGTTACAAACAAGACTTA 58.890 36.000 0.00 0.00 0.00 2.24
2221 2380 4.941263 TGCACTCAGTTACAAACAAGACTT 59.059 37.500 0.00 0.00 0.00 3.01
2222 2381 4.513442 TGCACTCAGTTACAAACAAGACT 58.487 39.130 0.00 0.00 0.00 3.24
2223 2382 4.260784 CCTGCACTCAGTTACAAACAAGAC 60.261 45.833 0.00 0.00 38.66 3.01
2224 2383 3.876914 CCTGCACTCAGTTACAAACAAGA 59.123 43.478 0.00 0.00 38.66 3.02
2265 2424 3.701040 ACTTGACCATCCATGTAATTGCC 59.299 43.478 0.00 0.00 0.00 4.52
2307 2466 6.593382 CACTCACTCTTAATTTCTCTTGGAGG 59.407 42.308 0.00 0.00 0.00 4.30
2320 2479 4.082845 CCTCAGTCCTCACTCACTCTTAA 58.917 47.826 0.00 0.00 0.00 1.85
2336 2495 3.717576 TGAGATGGAATGACTCCTCAGT 58.282 45.455 0.00 0.00 45.64 3.41
2337 2496 4.589798 AGATGAGATGGAATGACTCCTCAG 59.410 45.833 0.00 0.00 45.64 3.35
2338 2497 4.344390 CAGATGAGATGGAATGACTCCTCA 59.656 45.833 0.00 0.00 45.64 3.86
2339 2498 4.588106 TCAGATGAGATGGAATGACTCCTC 59.412 45.833 0.00 0.00 45.64 3.71
2340 2499 4.554683 TCAGATGAGATGGAATGACTCCT 58.445 43.478 0.00 0.00 45.64 3.69
2341 2500 4.952071 TCAGATGAGATGGAATGACTCC 57.048 45.455 0.00 0.00 45.64 3.85
2342 2501 6.349243 AGATCAGATGAGATGGAATGACTC 57.651 41.667 0.00 0.00 0.00 3.36
2343 2502 7.256261 GGTTAGATCAGATGAGATGGAATGACT 60.256 40.741 0.00 0.00 0.00 3.41
2344 2503 6.873076 GGTTAGATCAGATGAGATGGAATGAC 59.127 42.308 0.00 0.00 0.00 3.06
2345 2504 6.556116 TGGTTAGATCAGATGAGATGGAATGA 59.444 38.462 0.00 0.00 0.00 2.57
2346 2505 6.766429 TGGTTAGATCAGATGAGATGGAATG 58.234 40.000 0.00 0.00 0.00 2.67
2347 2506 7.458488 AGATGGTTAGATCAGATGAGATGGAAT 59.542 37.037 0.00 0.00 0.00 3.01
2348 2507 6.786461 AGATGGTTAGATCAGATGAGATGGAA 59.214 38.462 0.00 0.00 0.00 3.53
2349 2508 6.321321 AGATGGTTAGATCAGATGAGATGGA 58.679 40.000 0.00 0.00 0.00 3.41
2350 2509 6.608539 AGATGGTTAGATCAGATGAGATGG 57.391 41.667 0.00 0.00 0.00 3.51
2351 2510 8.034215 GGTAAGATGGTTAGATCAGATGAGATG 58.966 40.741 0.00 0.00 0.00 2.90
2352 2511 7.180051 GGGTAAGATGGTTAGATCAGATGAGAT 59.820 40.741 0.00 0.00 0.00 2.75
2353 2512 6.495181 GGGTAAGATGGTTAGATCAGATGAGA 59.505 42.308 0.00 0.00 0.00 3.27
2354 2513 6.268617 TGGGTAAGATGGTTAGATCAGATGAG 59.731 42.308 0.00 0.00 0.00 2.90
2355 2514 6.143206 TGGGTAAGATGGTTAGATCAGATGA 58.857 40.000 0.00 0.00 0.00 2.92
2356 2515 6.425210 TGGGTAAGATGGTTAGATCAGATG 57.575 41.667 0.00 0.00 0.00 2.90
2357 2516 7.734865 TGTATGGGTAAGATGGTTAGATCAGAT 59.265 37.037 0.00 0.00 0.00 2.90
2358 2517 7.073208 TGTATGGGTAAGATGGTTAGATCAGA 58.927 38.462 0.00 0.00 0.00 3.27
2359 2518 7.303182 TGTATGGGTAAGATGGTTAGATCAG 57.697 40.000 0.00 0.00 0.00 2.90
2360 2519 7.872061 ATGTATGGGTAAGATGGTTAGATCA 57.128 36.000 0.00 0.00 0.00 2.92
2361 2520 7.982354 GCTATGTATGGGTAAGATGGTTAGATC 59.018 40.741 0.00 0.00 0.00 2.75
2362 2521 7.092846 GGCTATGTATGGGTAAGATGGTTAGAT 60.093 40.741 0.00 0.00 0.00 1.98
2363 2522 6.212791 GGCTATGTATGGGTAAGATGGTTAGA 59.787 42.308 0.00 0.00 0.00 2.10
2364 2523 6.407202 GGCTATGTATGGGTAAGATGGTTAG 58.593 44.000 0.00 0.00 0.00 2.34
2365 2524 5.249852 GGGCTATGTATGGGTAAGATGGTTA 59.750 44.000 0.00 0.00 0.00 2.85
2366 2525 4.042934 GGGCTATGTATGGGTAAGATGGTT 59.957 45.833 0.00 0.00 0.00 3.67
2367 2526 3.587506 GGGCTATGTATGGGTAAGATGGT 59.412 47.826 0.00 0.00 0.00 3.55
2368 2527 3.587061 TGGGCTATGTATGGGTAAGATGG 59.413 47.826 0.00 0.00 0.00 3.51
2369 2528 4.908601 TGGGCTATGTATGGGTAAGATG 57.091 45.455 0.00 0.00 0.00 2.90
2370 2529 5.441718 CATGGGCTATGTATGGGTAAGAT 57.558 43.478 2.19 0.00 31.92 2.40
2371 2530 4.908601 CATGGGCTATGTATGGGTAAGA 57.091 45.455 2.19 0.00 31.92 2.10
2382 2541 5.824624 ACTTGTTCTTCATACATGGGCTATG 59.175 40.000 9.52 9.52 42.68 2.23
2383 2542 6.006275 ACTTGTTCTTCATACATGGGCTAT 57.994 37.500 0.00 0.00 0.00 2.97
2384 2543 5.435686 ACTTGTTCTTCATACATGGGCTA 57.564 39.130 0.00 0.00 0.00 3.93
2385 2544 4.307032 ACTTGTTCTTCATACATGGGCT 57.693 40.909 0.00 0.00 0.00 5.19
2402 2561 8.578308 TTGCAATCAAGAAATGAAGTAACTTG 57.422 30.769 0.00 0.00 42.54 3.16
2405 2564 9.415544 AGAATTGCAATCAAGAAATGAAGTAAC 57.584 29.630 13.38 0.00 42.54 2.50
2434 2593 6.204301 GCTGAATTGACTGCATACATGTAGAT 59.796 38.462 11.91 0.00 42.19 1.98
2436 2595 5.526479 AGCTGAATTGACTGCATACATGTAG 59.474 40.000 11.91 5.85 44.64 2.74
2439 2598 4.497507 CCAGCTGAATTGACTGCATACATG 60.498 45.833 17.39 0.00 37.23 3.21
2453 2614 1.202903 GGATGCCAGATCCAGCTGAAT 60.203 52.381 17.39 0.00 38.14 2.57
2480 2641 0.537188 AGGGTAAGAGGTGCGTCATG 59.463 55.000 0.00 0.00 0.00 3.07
2485 2646 1.274167 TGTTGTAGGGTAAGAGGTGCG 59.726 52.381 0.00 0.00 0.00 5.34
2687 2849 6.126768 CCAGTCCTTCTTAATGTGGAATCCTA 60.127 42.308 0.00 0.00 0.00 2.94
2716 2878 2.034179 TGGATCTCGCGTCGACATTTAT 59.966 45.455 17.16 1.73 0.00 1.40
2769 2931 2.154462 CTGGAAGGATCAAACAGCGTT 58.846 47.619 0.00 0.00 0.00 4.84
2844 3145 4.389992 ACATCAATCTGTCGACATCACAAC 59.610 41.667 20.40 0.00 0.00 3.32
2854 3155 3.818961 AGCAACAACATCAATCTGTCG 57.181 42.857 0.00 0.00 0.00 4.35
2912 3213 0.892358 TTCTGCTGCCTGCTCCAAAG 60.892 55.000 0.00 0.00 43.37 2.77
2948 3249 9.524496 AATATTAGCATCATAATCTTGGCAAGA 57.476 29.630 30.29 30.29 42.69 3.02
2987 3288 4.458295 AGCTGAGACCTGAAATTTGTGATG 59.542 41.667 0.00 0.00 0.00 3.07
2988 3289 4.660168 AGCTGAGACCTGAAATTTGTGAT 58.340 39.130 0.00 0.00 0.00 3.06
3004 3305 7.489574 AAAGAAACTTGACTTTAGAGCTGAG 57.510 36.000 0.00 0.00 35.07 3.35
3017 3318 7.171337 GCCTTGCATCAAAATAAAGAAACTTGA 59.829 33.333 0.00 0.00 0.00 3.02
3037 3338 0.591170 TCTACTTGTTTGCGCCTTGC 59.409 50.000 4.18 0.00 46.70 4.01
3038 3339 1.400242 GCTCTACTTGTTTGCGCCTTG 60.400 52.381 4.18 0.00 0.00 3.61
3039 3340 0.875059 GCTCTACTTGTTTGCGCCTT 59.125 50.000 4.18 0.00 0.00 4.35
3040 3341 0.035458 AGCTCTACTTGTTTGCGCCT 59.965 50.000 4.18 0.00 0.00 5.52
3041 3342 0.166814 CAGCTCTACTTGTTTGCGCC 59.833 55.000 4.18 0.00 0.00 6.53
3042 3343 0.166814 CCAGCTCTACTTGTTTGCGC 59.833 55.000 0.00 0.00 0.00 6.09
3043 3344 1.728971 CTCCAGCTCTACTTGTTTGCG 59.271 52.381 0.00 0.00 0.00 4.85
3051 3352 7.778185 TTTAGTTTTACTCTCCAGCTCTACT 57.222 36.000 0.00 0.00 0.00 2.57
3052 3353 8.874816 CATTTTAGTTTTACTCTCCAGCTCTAC 58.125 37.037 0.00 0.00 0.00 2.59
3123 3426 2.230992 TGGAAACATTGCCCATTTCTCG 59.769 45.455 0.00 0.00 33.68 4.04
3144 3447 0.969409 GGCAGCCATTCTTCAGCCTT 60.969 55.000 6.55 0.00 39.02 4.35
3150 3453 1.202336 CGAATTGGGCAGCCATTCTTC 60.202 52.381 15.19 9.22 0.00 2.87
3388 3692 0.595095 CAAAGACCAGCAGCACTTCC 59.405 55.000 0.00 0.00 0.00 3.46
3438 3744 0.110056 CTGCTTGCACCAAGTTAGCG 60.110 55.000 6.80 0.00 42.77 4.26
3440 3746 0.883833 CCCTGCTTGCACCAAGTTAG 59.116 55.000 6.80 5.86 42.77 2.34
3481 3787 8.567948 GTTGGTTTTAATTCATCTCAACTCTGA 58.432 33.333 0.00 0.00 32.93 3.27
3487 3793 8.690884 TGTTCTGTTGGTTTTAATTCATCTCAA 58.309 29.630 0.00 0.00 0.00 3.02
3511 3817 6.705302 TCTGAATTAGCTGAGACTTTGATGT 58.295 36.000 0.00 0.00 0.00 3.06
3597 3908 2.124411 GGAGGGAAACTATGCTGGGTA 58.876 52.381 0.00 0.00 0.00 3.69
3599 3910 0.183731 GGGAGGGAAACTATGCTGGG 59.816 60.000 0.00 0.00 0.00 4.45
3698 7112 4.207635 GTGCAAACACACACAGAATTGATG 59.792 41.667 0.00 0.00 46.61 3.07
3699 7113 4.362279 GTGCAAACACACACAGAATTGAT 58.638 39.130 0.00 0.00 46.61 2.57
3742 7156 3.045601 AGAAAGTGACGTCTCAATGGG 57.954 47.619 17.92 0.00 0.00 4.00
3753 7167 8.655092 CAGAATCTGTGAAATCTAGAAAGTGAC 58.345 37.037 1.31 0.00 0.00 3.67
3757 7171 8.040132 AGGACAGAATCTGTGAAATCTAGAAAG 58.960 37.037 21.81 0.00 45.44 2.62
3780 7194 2.073816 GAGCGAAAAACCATCGAAGGA 58.926 47.619 14.76 0.00 42.76 3.36
3868 7285 9.964303 TTTTGTAAGTGTAGTATTACGTTGAGA 57.036 29.630 0.00 0.00 35.16 3.27
3905 7322 4.976224 AGGCGTTTTTACATTATGGGAC 57.024 40.909 0.00 0.00 0.00 4.46
3906 7323 7.463961 TTTAAGGCGTTTTTACATTATGGGA 57.536 32.000 0.00 0.00 0.00 4.37
3907 7324 8.710835 AATTTAAGGCGTTTTTACATTATGGG 57.289 30.769 0.00 0.00 0.00 4.00
3911 7328 9.804758 CCCATAATTTAAGGCGTTTTTACATTA 57.195 29.630 0.00 0.00 0.00 1.90
3912 7329 7.766738 CCCCATAATTTAAGGCGTTTTTACATT 59.233 33.333 0.00 0.00 0.00 2.71
3913 7330 7.269316 CCCCATAATTTAAGGCGTTTTTACAT 58.731 34.615 0.00 0.00 0.00 2.29
3914 7331 6.631962 CCCCATAATTTAAGGCGTTTTTACA 58.368 36.000 0.00 0.00 0.00 2.41
3915 7332 5.521010 GCCCCATAATTTAAGGCGTTTTTAC 59.479 40.000 0.00 0.00 33.18 2.01
3916 7333 5.662456 GCCCCATAATTTAAGGCGTTTTTA 58.338 37.500 0.00 0.00 33.18 1.52
3917 7334 4.509616 GCCCCATAATTTAAGGCGTTTTT 58.490 39.130 0.00 0.00 33.18 1.94
3918 7335 4.131649 GCCCCATAATTTAAGGCGTTTT 57.868 40.909 0.00 0.00 33.18 2.43
3919 7336 3.812156 GCCCCATAATTTAAGGCGTTT 57.188 42.857 0.00 0.00 33.18 3.60
3923 7340 1.886542 CTCCGCCCCATAATTTAAGGC 59.113 52.381 5.74 5.74 40.33 4.35
3924 7341 2.514803 CCTCCGCCCCATAATTTAAGG 58.485 52.381 0.00 0.00 0.00 2.69
3925 7342 2.107552 TCCCTCCGCCCCATAATTTAAG 59.892 50.000 0.00 0.00 0.00 1.85
3926 7343 2.107552 CTCCCTCCGCCCCATAATTTAA 59.892 50.000 0.00 0.00 0.00 1.52
3927 7344 1.702957 CTCCCTCCGCCCCATAATTTA 59.297 52.381 0.00 0.00 0.00 1.40
3928 7345 0.478507 CTCCCTCCGCCCCATAATTT 59.521 55.000 0.00 0.00 0.00 1.82
3929 7346 0.697854 ACTCCCTCCGCCCCATAATT 60.698 55.000 0.00 0.00 0.00 1.40
3930 7347 0.192566 TACTCCCTCCGCCCCATAAT 59.807 55.000 0.00 0.00 0.00 1.28
3931 7348 0.471211 CTACTCCCTCCGCCCCATAA 60.471 60.000 0.00 0.00 0.00 1.90
3932 7349 1.155390 CTACTCCCTCCGCCCCATA 59.845 63.158 0.00 0.00 0.00 2.74
3933 7350 2.122813 CTACTCCCTCCGCCCCAT 60.123 66.667 0.00 0.00 0.00 4.00
3935 7352 4.862823 AGCTACTCCCTCCGCCCC 62.863 72.222 0.00 0.00 0.00 5.80
3936 7353 3.541713 CAGCTACTCCCTCCGCCC 61.542 72.222 0.00 0.00 0.00 6.13
3937 7354 2.442272 TCAGCTACTCCCTCCGCC 60.442 66.667 0.00 0.00 0.00 6.13
3938 7355 0.465824 TACTCAGCTACTCCCTCCGC 60.466 60.000 0.00 0.00 0.00 5.54
3939 7356 2.054232 TTACTCAGCTACTCCCTCCG 57.946 55.000 0.00 0.00 0.00 4.63
3940 7357 5.386924 TCTTATTACTCAGCTACTCCCTCC 58.613 45.833 0.00 0.00 0.00 4.30
3941 7358 5.048294 GCTCTTATTACTCAGCTACTCCCTC 60.048 48.000 0.00 0.00 0.00 4.30
3942 7359 4.830600 GCTCTTATTACTCAGCTACTCCCT 59.169 45.833 0.00 0.00 0.00 4.20
3943 7360 4.585162 TGCTCTTATTACTCAGCTACTCCC 59.415 45.833 0.00 0.00 32.76 4.30
3944 7361 5.300792 ACTGCTCTTATTACTCAGCTACTCC 59.699 44.000 0.00 0.00 32.76 3.85
3945 7362 6.385649 ACTGCTCTTATTACTCAGCTACTC 57.614 41.667 0.00 0.00 32.76 2.59
3946 7363 7.883391 TTACTGCTCTTATTACTCAGCTACT 57.117 36.000 0.00 0.00 32.76 2.57
3947 7364 8.407064 TCTTTACTGCTCTTATTACTCAGCTAC 58.593 37.037 0.00 0.00 32.76 3.58
3948 7365 8.521170 TCTTTACTGCTCTTATTACTCAGCTA 57.479 34.615 0.00 0.00 32.76 3.32
3949 7366 7.411486 TCTTTACTGCTCTTATTACTCAGCT 57.589 36.000 0.00 0.00 32.76 4.24
4150 7570 8.840321 CAAGTAGTCATCTTTTCCTTTTTCTGA 58.160 33.333 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.