Multiple sequence alignment - TraesCS5D01G016700

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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 TraesCS5D01G016700 chr5D 100.000 6196 0 0 1 6196 9492495 9498690 0.000000e+00 11442.0
1 TraesCS5D01G016700 chr5D 92.308 52 4 0 2809 2860 445399269 445399320 2.400000e-09 75.0
2 TraesCS5D01G016700 chr5D 74.214 159 35 6 2817 2971 114355959 114356115 1.860000e-05 62.1
3 TraesCS5D01G016700 chr5B 94.927 3745 156 27 2470 6194 9504287 9508017 0.000000e+00 5832.0
4 TraesCS5D01G016700 chr5B 94.214 2385 100 18 1 2355 9501912 9504288 0.000000e+00 3605.0
5 TraesCS5D01G016700 chr5B 80.328 183 29 6 2809 2986 373527507 373527687 1.400000e-26 132.0
6 TraesCS5D01G016700 chr5A 90.128 1793 159 14 3843 5623 7631677 7633463 0.000000e+00 2314.0
7 TraesCS5D01G016700 chr5A 88.475 1475 157 11 3843 5308 7640321 7641791 0.000000e+00 1770.0
8 TraesCS5D01G016700 chr5A 91.281 562 38 8 5643 6196 7642680 7643238 0.000000e+00 756.0
9 TraesCS5D01G016700 chr5A 92.437 357 16 8 5300 5654 7642311 7642658 3.330000e-137 499.0
10 TraesCS5D01G016700 chr5A 82.212 208 25 8 1 198 7626688 7626893 1.070000e-37 169.0
11 TraesCS5D01G016700 chr1A 91.667 120 10 0 2353 2472 500974860 500974741 3.840000e-37 167.0
12 TraesCS5D01G016700 chr3D 90.833 120 11 0 2353 2472 168289826 168289945 1.790000e-35 161.0
13 TraesCS5D01G016700 chr3D 89.474 114 10 2 2829 2940 604669248 604669361 6.470000e-30 143.0
14 TraesCS5D01G016700 chr4D 90.678 118 11 0 2354 2471 503358032 503357915 2.310000e-34 158.0
15 TraesCS5D01G016700 chr1D 90.678 118 11 0 2354 2471 20996004 20995887 2.310000e-34 158.0
16 TraesCS5D01G016700 chr1D 90.909 66 6 0 2792 2857 357460911 357460976 8.550000e-14 89.8
17 TraesCS5D01G016700 chr1B 90.164 122 10 2 2352 2472 33990955 33991075 2.310000e-34 158.0
18 TraesCS5D01G016700 chr7B 89.344 122 13 0 2350 2471 383736126 383736247 2.990000e-33 154.0
19 TraesCS5D01G016700 chr3B 90.351 114 9 2 2829 2940 812340196 812340309 1.390000e-31 148.0
20 TraesCS5D01G016700 chr3B 87.402 127 13 2 2353 2479 545185560 545185437 6.470000e-30 143.0
21 TraesCS5D01G016700 chr4A 87.023 131 14 2 2351 2479 729078313 729078442 1.800000e-30 145.0
22 TraesCS5D01G016700 chr3A 85.612 139 17 3 2350 2487 607108186 607108050 6.470000e-30 143.0
23 TraesCS5D01G016700 chr3A 88.596 114 11 2 2829 2940 734786096 734786209 3.010000e-28 137.0
24 TraesCS5D01G016700 chr3A 82.707 133 19 4 2840 2970 615097338 615097208 1.410000e-21 115.0
25 TraesCS5D01G016700 chr2A 80.745 161 24 7 2816 2971 17751021 17751179 1.090000e-22 119.0
26 TraesCS5D01G016700 chr7A 77.246 167 26 8 2813 2976 195400720 195400563 3.080000e-13 87.9
27 TraesCS5D01G016700 chr4B 81.319 91 13 3 2899 2986 393165410 393165321 3.100000e-08 71.3
28 TraesCS5D01G016700 chr6A 100.000 29 0 0 6168 6196 564539668 564539696 3.000000e-03 54.7
29 TraesCS5D01G016700 chr6A 100.000 29 0 0 6168 6196 564583474 564583502 3.000000e-03 54.7


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 TraesCS5D01G016700 chr5D 9492495 9498690 6195 False 11442.000000 11442 100.0000 1 6196 1 chr5D.!!$F1 6195
1 TraesCS5D01G016700 chr5B 9501912 9508017 6105 False 4718.500000 5832 94.5705 1 6194 2 chr5B.!!$F2 6193
2 TraesCS5D01G016700 chr5A 7631677 7633463 1786 False 2314.000000 2314 90.1280 3843 5623 1 chr5A.!!$F2 1780
3 TraesCS5D01G016700 chr5A 7640321 7643238 2917 False 1008.333333 1770 90.7310 3843 6196 3 chr5A.!!$F3 2353

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
390 405 0.108992 GGCTTGCATGTGTGTGATGG 60.109 55.0 1.14 0.0 0.00 3.51 F
1426 1442 0.450583 TCGACATCGTGGCTGTACTC 59.549 55.0 0.54 0.0 40.80 2.59 F
2717 2749 0.857311 GCATGGCAAATCGAACGTCG 60.857 55.0 0.00 0.0 42.10 5.12 F
3429 3464 0.100325 CAACAAAACTGGCGCTGACA 59.900 50.0 7.64 0.0 0.00 3.58 F
3701 3736 0.305922 GGCTGAATGAAATCCGCTCG 59.694 55.0 0.00 0.0 31.15 5.03 F
4921 4962 0.323542 AAGATCCTCCTCCGTGACGT 60.324 55.0 3.64 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 2267 0.042431 TGCATTGGGGTTGCCCTTAT 59.958 50.0 4.02 0.00 44.66 1.73 R
2947 2981 0.447406 TGAGCATGGCAAATCGAACG 59.553 50.0 0.00 0.00 0.00 3.95 R
4141 4182 0.393077 AGCAACACTCGGTAGCAAGT 59.607 50.0 0.00 0.00 0.00 3.16 R
4793 4834 0.039180 TCTCCTTCTCGGTAGCACCA 59.961 55.0 6.21 0.00 38.47 4.17 R
5120 5161 1.553690 CCTCCCTTTCCTTCCTCGCA 61.554 60.0 0.00 0.00 0.00 5.10 R
5742 6358 1.178276 CCCTAGCGAGGTATAGCAGG 58.822 60.0 12.29 1.67 41.95 4.85 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
58 59 8.623903 ACACGTCAGATGATTGCAATTATTTAT 58.376 29.630 16.90 5.21 0.00 1.40
122 127 6.676189 ACTTATCTTCCTCCAGAAATCTCCTT 59.324 38.462 0.00 0.00 32.88 3.36
123 128 7.183657 ACTTATCTTCCTCCAGAAATCTCCTTT 59.816 37.037 0.00 0.00 32.88 3.11
124 129 5.850046 TCTTCCTCCAGAAATCTCCTTTT 57.150 39.130 0.00 0.00 32.88 2.27
125 130 5.564550 TCTTCCTCCAGAAATCTCCTTTTG 58.435 41.667 0.00 0.00 32.88 2.44
126 131 5.073691 TCTTCCTCCAGAAATCTCCTTTTGT 59.926 40.000 0.00 0.00 32.88 2.83
157 162 6.276092 TCCTTATTTCCTAGGGTTCTTTTGGA 59.724 38.462 9.46 5.21 32.20 3.53
207 212 2.827921 AGGCTTTGTAAGGATGCTTTGG 59.172 45.455 4.26 0.00 0.00 3.28
250 255 1.945394 CCATTTCAATGCTCCCTCTCG 59.055 52.381 0.00 0.00 35.08 4.04
253 258 2.859165 TTCAATGCTCCCTCTCGTTT 57.141 45.000 0.00 0.00 0.00 3.60
380 395 1.751927 GAGGTGGAGGGCTTGCATG 60.752 63.158 0.00 0.00 0.00 4.06
390 405 0.108992 GGCTTGCATGTGTGTGATGG 60.109 55.000 1.14 0.00 0.00 3.51
404 419 2.601367 ATGGTGTGGGTGGCTTGC 60.601 61.111 0.00 0.00 0.00 4.01
561 576 9.698309 AATTGACGATCTAATAATACAGGTGAG 57.302 33.333 0.00 0.00 0.00 3.51
564 579 7.501225 TGACGATCTAATAATACAGGTGAGACA 59.499 37.037 0.00 0.00 0.00 3.41
590 605 0.824759 CCAGAAAGTCGGGACTAGGG 59.175 60.000 1.08 0.00 41.58 3.53
693 708 2.416162 GGAGACGAGAAGATCAAAGCGT 60.416 50.000 0.00 0.00 34.39 5.07
706 721 5.882557 AGATCAAAGCGTCCAATGAAAGTAT 59.117 36.000 0.00 0.00 0.00 2.12
720 735 4.892655 TGAAAGTATAGCGCAACATTTCG 58.107 39.130 11.47 0.00 0.00 3.46
725 740 4.570772 AGTATAGCGCAACATTTCGACATT 59.429 37.500 11.47 0.00 0.00 2.71
728 743 1.906966 GCGCAACATTTCGACATTGAG 59.093 47.619 0.30 0.00 0.00 3.02
738 753 9.722056 AACATTTCGACATTGAGCTTATTTATC 57.278 29.630 0.00 0.00 0.00 1.75
740 755 9.941664 CATTTCGACATTGAGCTTATTTATCTT 57.058 29.630 0.00 0.00 0.00 2.40
846 862 4.311816 CAACACCTCATTTCTTGTTGCT 57.688 40.909 0.73 0.00 41.60 3.91
886 902 3.575687 ACGTTTGGTACCAAGTAGCTAGT 59.424 43.478 25.74 15.71 37.41 2.57
914 930 4.039852 TGTCGCCTCTATATAAACCATGCA 59.960 41.667 0.00 0.00 0.00 3.96
917 933 6.816640 GTCGCCTCTATATAAACCATGCAATA 59.183 38.462 0.00 0.00 0.00 1.90
965 981 2.485426 TGCAAGCACAGAAGCAATACTC 59.515 45.455 0.00 0.00 36.85 2.59
972 988 3.034635 ACAGAAGCAATACTCGATCCCT 58.965 45.455 0.00 0.00 0.00 4.20
982 998 6.738731 GCAATACTCGATCCCTAACAAGATCA 60.739 42.308 0.00 0.00 39.09 2.92
991 1007 6.716934 TCCCTAACAAGATCAACTAGCTAG 57.283 41.667 19.44 19.44 0.00 3.42
1011 1027 1.752084 GCTAAGAAGATGGCCCTTGGG 60.752 57.143 0.00 0.32 0.00 4.12
1033 1049 4.561105 GAAGGTGACTCGATCAGTTTTCT 58.439 43.478 0.00 0.00 42.68 2.52
1045 1061 6.538742 TCGATCAGTTTTCTTCTTGTTGTTCT 59.461 34.615 0.00 0.00 0.00 3.01
1047 1063 7.164826 CGATCAGTTTTCTTCTTGTTGTTCTTG 59.835 37.037 0.00 0.00 0.00 3.02
1059 1075 7.206687 TCTTGTTGTTCTTGTTGTTCTTGTTT 58.793 30.769 0.00 0.00 0.00 2.83
1137 1153 3.838271 GGCGCTCCTGGATCACGA 61.838 66.667 7.64 0.00 0.00 4.35
1168 1184 4.693566 CACTTTGGTAACGAGATTAAGCCA 59.306 41.667 0.00 0.00 42.51 4.75
1188 1204 1.831580 AAGCTCACCTCTTTCCATGC 58.168 50.000 0.00 0.00 0.00 4.06
1206 1222 4.500887 CCATGCTTAATTTCCATGAGCCAG 60.501 45.833 11.82 0.00 38.84 4.85
1208 1224 2.223900 GCTTAATTTCCATGAGCCAGCC 60.224 50.000 0.00 0.00 0.00 4.85
1222 1238 1.459592 GCCAGCCTATTACGCGTATTG 59.540 52.381 21.30 12.57 0.00 1.90
1225 1241 2.729882 CAGCCTATTACGCGTATTGTCC 59.270 50.000 21.30 9.02 0.00 4.02
1227 1243 2.859806 GCCTATTACGCGTATTGTCCGT 60.860 50.000 21.30 3.38 38.84 4.69
1243 1259 5.643379 TGTCCGTCGTACCTAAATTAACT 57.357 39.130 0.00 0.00 0.00 2.24
1247 1263 5.047377 TCCGTCGTACCTAAATTAACTTGGT 60.047 40.000 0.00 0.00 35.05 3.67
1339 1355 4.388773 TGTGAGAAGACGCATAACATGTTC 59.611 41.667 15.85 0.00 0.00 3.18
1426 1442 0.450583 TCGACATCGTGGCTGTACTC 59.549 55.000 0.54 0.00 40.80 2.59
1585 1601 2.941064 CACATACATGTCTGAGCAAGGG 59.059 50.000 17.29 0.00 39.39 3.95
1698 1714 4.080356 CCCTTGACTTGGTGAATCTGGATA 60.080 45.833 0.00 0.00 0.00 2.59
1726 1742 1.271127 TGTGGTGGGCTAGCAGCATA 61.271 55.000 18.24 8.29 44.75 3.14
1774 1790 9.503427 GGAAATTTTACTCATTTTATGGACTCG 57.497 33.333 0.00 0.00 0.00 4.18
1782 1798 7.560368 ACTCATTTTATGGACTCGAGAAGATT 58.440 34.615 21.68 0.00 0.00 2.40
1786 1802 2.949451 TGGACTCGAGAAGATTCAGC 57.051 50.000 21.68 0.00 30.92 4.26
1804 1820 7.500559 AGATTCAGCTACAAAGAATTCATACCC 59.499 37.037 8.44 0.00 32.51 3.69
1871 1887 7.977853 ACATGATCTTGCAAATTAATCAAGACC 59.022 33.333 16.21 10.18 45.88 3.85
1889 1906 7.479980 TCAAGACCATTTTAATATTTCAGCGG 58.520 34.615 0.00 0.00 0.00 5.52
1929 1946 5.133941 TGCTTGTAGAACCATGGTTGTTAA 58.866 37.500 34.47 24.09 38.60 2.01
1944 1961 7.972832 TGGTTGTTAACTATGAAACACTAGG 57.027 36.000 7.22 0.00 35.43 3.02
1958 1975 8.117813 TGAAACACTAGGGAAATTTATGTTCC 57.882 34.615 0.00 0.00 43.35 3.62
2037 2054 8.877864 ACAAGATTTCATGTATGGAGGTTTTA 57.122 30.769 0.00 0.00 0.00 1.52
2038 2055 9.308000 ACAAGATTTCATGTATGGAGGTTTTAA 57.692 29.630 0.00 0.00 0.00 1.52
2328 2359 5.588246 TCAATGAACTCACTTGCTTTACACA 59.412 36.000 0.00 0.00 0.00 3.72
2347 2378 4.916870 CACATCTCCATGCATGTGTTTAG 58.083 43.478 24.58 13.29 43.33 1.85
2355 2386 7.657354 TCTCCATGCATGTGTTTAGACATATAC 59.343 37.037 24.58 0.00 35.69 1.47
2356 2387 7.508687 TCCATGCATGTGTTTAGACATATACT 58.491 34.615 24.58 0.00 35.69 2.12
2357 2388 7.657354 TCCATGCATGTGTTTAGACATATACTC 59.343 37.037 24.58 0.00 35.69 2.59
2358 2389 7.095060 CCATGCATGTGTTTAGACATATACTCC 60.095 40.741 24.58 0.00 35.69 3.85
2359 2390 6.288294 TGCATGTGTTTAGACATATACTCCC 58.712 40.000 0.00 0.00 35.69 4.30
2360 2391 6.099701 TGCATGTGTTTAGACATATACTCCCT 59.900 38.462 0.00 0.00 35.69 4.20
2361 2392 6.647067 GCATGTGTTTAGACATATACTCCCTC 59.353 42.308 0.00 0.00 35.69 4.30
2362 2393 6.726490 TGTGTTTAGACATATACTCCCTCC 57.274 41.667 0.00 0.00 38.23 4.30
2363 2394 5.301045 TGTGTTTAGACATATACTCCCTCCG 59.699 44.000 0.00 0.00 38.23 4.63
2364 2395 5.301298 GTGTTTAGACATATACTCCCTCCGT 59.699 44.000 0.00 0.00 38.23 4.69
2365 2396 5.533903 TGTTTAGACATATACTCCCTCCGTC 59.466 44.000 0.00 0.00 0.00 4.79
2366 2397 3.157750 AGACATATACTCCCTCCGTCC 57.842 52.381 0.00 0.00 0.00 4.79
2367 2398 1.811359 GACATATACTCCCTCCGTCCG 59.189 57.143 0.00 0.00 0.00 4.79
2368 2399 1.422781 ACATATACTCCCTCCGTCCGA 59.577 52.381 0.00 0.00 0.00 4.55
2369 2400 2.158564 ACATATACTCCCTCCGTCCGAA 60.159 50.000 0.00 0.00 0.00 4.30
2370 2401 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
2371 2402 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
2372 2403 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
2417 2448 8.307483 TCTTAAATGGATGTATCTAGCACTAGC 58.693 37.037 0.00 0.00 42.56 3.42
2432 2463 4.755411 GCACTAGCTTGGTGTTAGATACA 58.245 43.478 16.97 0.00 37.07 2.29
2433 2464 5.360591 GCACTAGCTTGGTGTTAGATACAT 58.639 41.667 16.97 0.00 37.10 2.29
2434 2465 5.463724 GCACTAGCTTGGTGTTAGATACATC 59.536 44.000 16.97 0.00 37.10 3.06
2435 2466 6.573434 CACTAGCTTGGTGTTAGATACATCA 58.427 40.000 10.24 0.00 46.01 3.07
2443 2474 7.864108 TGGTGTTAGATACATCAATTTGAGG 57.136 36.000 9.38 9.38 44.74 3.86
2444 2475 6.828273 TGGTGTTAGATACATCAATTTGAGGG 59.172 38.462 14.84 7.49 44.74 4.30
2445 2476 7.054124 GGTGTTAGATACATCAATTTGAGGGA 58.946 38.462 14.84 7.21 37.82 4.20
2446 2477 7.012421 GGTGTTAGATACATCAATTTGAGGGAC 59.988 40.741 14.84 6.24 37.82 4.46
2447 2478 7.552687 GTGTTAGATACATCAATTTGAGGGACA 59.447 37.037 14.84 7.10 39.39 4.02
2448 2479 8.106462 TGTTAGATACATCAATTTGAGGGACAA 58.894 33.333 14.84 0.44 31.56 3.18
2525 2556 6.218746 CACTAAACCTACGAAACCTACTTGT 58.781 40.000 0.00 0.00 0.00 3.16
2537 2568 7.148137 ACGAAACCTACTTGTTTTTCATCTTGT 60.148 33.333 0.00 0.00 38.51 3.16
2560 2592 8.148437 TGTTATTCTTACTGTACATACCCCAA 57.852 34.615 0.00 0.00 0.00 4.12
2562 2594 9.623000 GTTATTCTTACTGTACATACCCCAATT 57.377 33.333 0.00 0.00 0.00 2.32
2565 2597 9.623000 ATTCTTACTGTACATACCCCAATTTAC 57.377 33.333 0.00 0.00 0.00 2.01
2620 2652 5.767816 AGCGGTGTGTCTTAAATTTTTCT 57.232 34.783 0.00 0.00 0.00 2.52
2671 2703 8.244113 TCAGTGCTACATACATATAGGATTTCG 58.756 37.037 0.00 0.00 0.00 3.46
2674 2706 8.188799 GTGCTACATACATATAGGATTTCGCTA 58.811 37.037 0.00 0.00 0.00 4.26
2675 2707 8.914011 TGCTACATACATATAGGATTTCGCTAT 58.086 33.333 0.00 0.00 0.00 2.97
2676 2708 9.186323 GCTACATACATATAGGATTTCGCTATG 57.814 37.037 0.00 0.00 0.00 2.23
2704 2736 2.353579 ACGTCGGTTTTATAAGCATGGC 59.646 45.455 0.00 0.00 0.00 4.40
2713 2745 6.019881 GGTTTTATAAGCATGGCAAATCGAAC 60.020 38.462 0.00 0.00 0.00 3.95
2717 2749 0.857311 GCATGGCAAATCGAACGTCG 60.857 55.000 0.00 0.00 42.10 5.12
2733 2765 4.724074 ACGTCGGAGGTGAATTATGTAA 57.276 40.909 2.02 0.00 0.00 2.41
2734 2766 5.272283 ACGTCGGAGGTGAATTATGTAAT 57.728 39.130 2.02 0.00 0.00 1.89
2739 2771 6.537301 GTCGGAGGTGAATTATGTAATGAACA 59.463 38.462 0.00 0.00 43.86 3.18
2799 2831 9.241919 AGGTGGTTTTCAAAAGAAAAATCAAAT 57.758 25.926 5.10 0.00 38.17 2.32
2801 2833 9.838975 GTGGTTTTCAAAAGAAAAATCAAATGT 57.161 25.926 5.10 0.00 38.17 2.71
2806 2838 7.928908 TCAAAAGAAAAATCAAATGTCCGAG 57.071 32.000 0.00 0.00 0.00 4.63
2825 2857 4.578516 CCGAGGTGGCAAATTATATTGTCA 59.421 41.667 0.00 0.00 42.26 3.58
2847 2879 7.237173 GTCACGAGGATGACAATTTTCTTTAG 58.763 38.462 1.08 0.00 46.89 1.85
2860 2892 4.540359 TTTCTTTAGCAAGCATGGCAAT 57.460 36.364 0.00 0.00 37.68 3.56
2947 2981 5.575218 CGACAACATAATTTGCCTAAAACCC 59.425 40.000 0.00 0.00 0.00 4.11
2988 3022 7.377131 GCTCAAAAATCTAATGTCGGATTTAGC 59.623 37.037 0.00 0.00 40.06 3.09
3173 3208 5.112129 TCTTCAAGGAAACTATTAGCCCC 57.888 43.478 0.00 0.00 42.68 5.80
3184 3219 0.178990 ATTAGCCCCGATTTCCCAGC 60.179 55.000 0.00 0.00 0.00 4.85
3185 3220 1.567208 TTAGCCCCGATTTCCCAGCA 61.567 55.000 0.00 0.00 0.00 4.41
3251 3286 3.148279 ATCGCCGACCAGACCTCC 61.148 66.667 0.00 0.00 0.00 4.30
3369 3404 1.381872 ATCACCCTCGGGACTCCTG 60.382 63.158 9.43 0.00 38.96 3.86
3371 3406 2.037527 ACCCTCGGGACTCCTGAC 59.962 66.667 9.43 0.00 33.41 3.51
3425 3460 2.498056 CCCCAACAAAACTGGCGCT 61.498 57.895 7.64 0.00 32.10 5.92
3429 3464 0.100325 CAACAAAACTGGCGCTGACA 59.900 50.000 7.64 0.00 0.00 3.58
3470 3505 1.154301 CAACAACATGTACGCCGGC 60.154 57.895 19.07 19.07 0.00 6.13
3527 3562 2.037136 CACGAAGGAGGGCAAGCAG 61.037 63.158 0.00 0.00 0.00 4.24
3529 3564 1.003355 CGAAGGAGGGCAAGCAGAA 60.003 57.895 0.00 0.00 0.00 3.02
3596 3631 2.117156 GCAGCTGGCCGACATTGAT 61.117 57.895 17.12 0.00 36.11 2.57
3701 3736 0.305922 GGCTGAATGAAATCCGCTCG 59.694 55.000 0.00 0.00 31.15 5.03
3740 3775 0.807275 TCGCACGGATCAATCAGCTG 60.807 55.000 7.63 7.63 0.00 4.24
3980 4015 1.909302 ACCACCATGGACGATCTCTTT 59.091 47.619 21.47 0.00 40.96 2.52
4071 4112 2.250237 GCTGCCGCTGCTAATCCTC 61.250 63.158 14.47 0.00 38.71 3.71
4074 4115 1.301322 GCCGCTGCTAATCCTCCTC 60.301 63.158 0.00 0.00 33.53 3.71
4107 4148 5.076057 TCCTACTACTAGATGGGGAAAGG 57.924 47.826 0.00 0.00 0.00 3.11
4266 4307 1.226686 GCTGCAGTATCCCATGCTCG 61.227 60.000 16.64 0.00 42.98 5.03
4273 4314 0.829990 TATCCCATGCTCGCAGACAA 59.170 50.000 0.00 0.00 0.00 3.18
4505 4546 3.532155 ATCGGAGACCAGCGCCTC 61.532 66.667 2.29 2.79 42.51 4.70
4631 4672 1.517257 GATCCACGCACTCGGTGAG 60.517 63.158 8.04 7.13 40.69 3.51
4633 4674 4.662961 CCACGCACTCGGTGAGCA 62.663 66.667 8.04 0.00 36.85 4.26
4709 4750 3.094572 CCTCCAGATTGCTTCAACCATT 58.905 45.455 0.00 0.00 0.00 3.16
4745 4786 2.487086 CCTCAACACCATGACACTCCAA 60.487 50.000 0.00 0.00 0.00 3.53
4793 4834 2.416432 GGAGCGCCTAGGACGACTT 61.416 63.158 23.94 11.66 0.00 3.01
4921 4962 0.323542 AAGATCCTCCTCCGTGACGT 60.324 55.000 3.64 0.00 0.00 4.34
4931 4972 0.675837 TCCGTGACGTCGAGAAGGAT 60.676 55.000 11.62 0.00 0.00 3.24
4998 5039 2.430248 TCAGCTCAACCATGATGCAT 57.570 45.000 0.00 0.00 34.37 3.96
5025 5066 3.316308 GGTATATGCTTCAGTTGCCAAGG 59.684 47.826 0.00 0.00 0.00 3.61
5120 5161 2.618709 GGACACTTTGCTTACAAGTGCT 59.381 45.455 11.78 1.40 37.92 4.40
5155 5196 1.486726 GGAGGTGAAATCCCTGATCGT 59.513 52.381 0.00 0.00 30.60 3.73
5221 5263 3.906720 TCCCGAGAATAAAGGTCAAGG 57.093 47.619 0.00 0.00 0.00 3.61
5239 5281 6.096846 GGTCAAGGCAATGGATAATTGTAAGT 59.903 38.462 0.51 0.00 46.37 2.24
5328 5900 2.155279 GGCCAGACCACTCTCTTTTTC 58.845 52.381 0.00 0.00 38.86 2.29
5403 5976 0.874390 TCAGTTTGCTTCATGGACGC 59.126 50.000 0.00 0.00 0.00 5.19
5414 5988 2.639065 TCATGGACGCTTGGGAATAAC 58.361 47.619 0.00 0.00 0.00 1.89
5428 6002 8.311109 GCTTGGGAATAACAAAGAAGGAAATAA 58.689 33.333 0.00 0.00 0.00 1.40
5627 6209 6.219417 ACATACATTCTCTCAAGAGGACAG 57.781 41.667 7.17 0.00 42.30 3.51
5656 6272 9.949174 AAAAAGGAAATGAACATTTTTACATGC 57.051 25.926 12.91 0.82 40.77 4.06
5660 6276 8.584157 AGGAAATGAACATTTTTACATGCACTA 58.416 29.630 12.91 0.00 40.77 2.74
5774 6390 7.910999 ATACCTCGCTAGGGATATTGATCCTAG 60.911 44.444 10.28 10.37 45.54 3.02
5850 6469 4.141937 GGGATTTTTGCATAGGAAAGGGAC 60.142 45.833 0.00 0.00 0.00 4.46
5933 6552 3.910170 GGATTCGTTTCGGTTTTTACTGC 59.090 43.478 0.00 0.00 0.00 4.40
5974 6594 6.262273 TGCTGTTCTTTAACCTGTTTTCTAGG 59.738 38.462 0.00 0.00 41.22 3.02
6020 6643 9.817809 GTTATTTTCTTTTTCAAGAACTTCCCT 57.182 29.630 0.00 0.00 46.71 4.20
6025 6648 8.771920 TTCTTTTTCAAGAACTTCCCTTTTTC 57.228 30.769 0.00 0.00 42.99 2.29
6026 6649 7.902087 TCTTTTTCAAGAACTTCCCTTTTTCA 58.098 30.769 0.00 0.00 35.99 2.69
6031 6655 8.716646 TTCAAGAACTTCCCTTTTTCAAAATC 57.283 30.769 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.047274 AGTTGACCATGCCGACGG 60.047 61.111 10.29 10.29 0.00 4.79
11 12 3.027170 GCAGTTGACCATGCCGACG 62.027 63.158 0.00 0.00 36.41 5.12
122 127 7.116736 CCCTAGGAAATAAGGAGCTAAACAAA 58.883 38.462 11.48 0.00 34.58 2.83
123 128 6.216868 ACCCTAGGAAATAAGGAGCTAAACAA 59.783 38.462 11.48 0.00 34.58 2.83
124 129 5.729718 ACCCTAGGAAATAAGGAGCTAAACA 59.270 40.000 11.48 0.00 34.58 2.83
125 130 6.249911 ACCCTAGGAAATAAGGAGCTAAAC 57.750 41.667 11.48 0.00 34.58 2.01
126 131 6.677076 AGAACCCTAGGAAATAAGGAGCTAAA 59.323 38.462 11.48 0.00 34.58 1.85
157 162 7.797121 AACAATCCTTATCCATGGACTTTTT 57.203 32.000 18.99 2.79 34.90 1.94
207 212 5.177696 GGTTGTATCTAAACATCCGATCAGC 59.822 44.000 0.00 0.00 31.42 4.26
282 287 7.379529 ACTCGTATTTCATTGCTCAAACTTTTG 59.620 33.333 0.00 0.00 39.48 2.44
287 292 6.086765 CACAACTCGTATTTCATTGCTCAAAC 59.913 38.462 0.00 0.00 0.00 2.93
290 295 4.754618 ACACAACTCGTATTTCATTGCTCA 59.245 37.500 0.00 0.00 0.00 4.26
291 296 5.082059 CACACAACTCGTATTTCATTGCTC 58.918 41.667 0.00 0.00 0.00 4.26
342 347 7.220683 CCACCTCATTTTTATTTATCAGCAACG 59.779 37.037 0.00 0.00 0.00 4.10
351 356 5.837829 AGCCCTCCACCTCATTTTTATTTA 58.162 37.500 0.00 0.00 0.00 1.40
355 360 3.430453 CAAGCCCTCCACCTCATTTTTA 58.570 45.455 0.00 0.00 0.00 1.52
380 395 1.172180 CCACCCACACCATCACACAC 61.172 60.000 0.00 0.00 0.00 3.82
390 405 0.600782 CATTTGCAAGCCACCCACAC 60.601 55.000 0.00 0.00 0.00 3.82
444 459 5.452078 TTAGGGATCTTGCAAACACAAAG 57.548 39.130 0.00 0.00 0.00 2.77
549 564 9.429109 TCTGGTTTATATGTCTCACCTGTATTA 57.571 33.333 0.00 0.00 0.00 0.98
559 574 5.753921 CCCGACTTTCTGGTTTATATGTCTC 59.246 44.000 0.00 0.00 0.00 3.36
561 576 5.522824 GTCCCGACTTTCTGGTTTATATGTC 59.477 44.000 0.00 0.00 0.00 3.06
564 579 5.952347 AGTCCCGACTTTCTGGTTTATAT 57.048 39.130 0.00 0.00 38.83 0.86
590 605 5.122396 GGCGTTGATCCCATAGATTGTATTC 59.878 44.000 0.00 0.00 34.42 1.75
693 708 4.257731 TGTTGCGCTATACTTTCATTGGA 58.742 39.130 9.73 0.00 0.00 3.53
706 721 2.739379 TCAATGTCGAAATGTTGCGCTA 59.261 40.909 9.73 0.00 0.00 4.26
725 740 9.407380 TGCCTTTCATAAAGATAAATAAGCTCA 57.593 29.630 0.99 0.00 41.02 4.26
758 773 3.380320 ACTCTTGGGTTGTTGCTTTGTAC 59.620 43.478 0.00 0.00 0.00 2.90
846 862 7.288389 ACCAAACGTCCTCACCAATATACTATA 59.712 37.037 0.00 0.00 0.00 1.31
860 876 2.538512 ACTTGGTACCAAACGTCCTC 57.461 50.000 26.90 0.00 35.33 3.71
914 930 3.999663 GTGTGCTCTGAGCTTGAAGTATT 59.000 43.478 28.04 0.00 42.97 1.89
917 933 1.415659 AGTGTGCTCTGAGCTTGAAGT 59.584 47.619 28.04 12.21 42.97 3.01
965 981 4.985409 GCTAGTTGATCTTGTTAGGGATCG 59.015 45.833 0.00 0.00 40.63 3.69
972 988 8.521170 TCTTAGCTAGCTAGTTGATCTTGTTA 57.479 34.615 23.03 4.37 0.00 2.41
982 998 4.039852 GGCCATCTTCTTAGCTAGCTAGTT 59.960 45.833 23.03 18.30 0.00 2.24
991 1007 1.685148 CCAAGGGCCATCTTCTTAGC 58.315 55.000 6.18 0.00 0.00 3.09
1011 1027 4.561105 AGAAAACTGATCGAGTCACCTTC 58.439 43.478 0.00 0.00 31.73 3.46
1033 1049 6.744112 ACAAGAACAACAAGAACAACAAGAA 58.256 32.000 0.00 0.00 0.00 2.52
1045 1061 7.816995 ACATGCTAAGAAAAACAAGAACAACAA 59.183 29.630 0.00 0.00 0.00 2.83
1047 1063 7.755582 ACATGCTAAGAAAAACAAGAACAAC 57.244 32.000 0.00 0.00 0.00 3.32
1168 1184 2.165998 GCATGGAAAGAGGTGAGCTTT 58.834 47.619 0.00 0.00 38.22 3.51
1188 1204 3.294214 AGGCTGGCTCATGGAAATTAAG 58.706 45.455 0.00 0.00 0.00 1.85
1206 1222 1.717645 CGGACAATACGCGTAATAGGC 59.282 52.381 24.55 17.22 0.00 3.93
1208 1224 2.648897 CGACGGACAATACGCGTAATAG 59.351 50.000 24.55 17.43 34.00 1.73
1222 1238 5.289434 CCAAGTTAATTTAGGTACGACGGAC 59.711 44.000 0.10 0.10 0.00 4.79
1225 1241 6.710692 AACCAAGTTAATTTAGGTACGACG 57.289 37.500 0.00 0.00 31.10 5.12
1227 1243 7.546667 CAGCTAACCAAGTTAATTTAGGTACGA 59.453 37.037 0.00 0.00 32.43 3.43
1406 1422 1.065701 GAGTACAGCCACGATGTCGAT 59.934 52.381 9.67 0.00 43.02 3.59
1408 1424 0.861866 CGAGTACAGCCACGATGTCG 60.862 60.000 0.11 0.11 46.33 4.35
1411 1427 0.170339 TGTCGAGTACAGCCACGATG 59.830 55.000 0.00 0.00 37.14 3.84
1426 1442 2.107750 ATGCTCCCGCTGATGTCG 59.892 61.111 0.00 0.00 36.97 4.35
1447 1463 2.853542 TGCTCCAGCTTGTCCCCA 60.854 61.111 0.00 0.00 42.66 4.96
1698 1714 1.298953 AGCCCACCACACCAATATCT 58.701 50.000 0.00 0.00 0.00 1.98
1747 1763 9.503427 GAGTCCATAAAATGAGTAAAATTTCCG 57.497 33.333 0.00 0.00 0.00 4.30
1758 1774 7.708322 TGAATCTTCTCGAGTCCATAAAATGAG 59.292 37.037 13.13 0.00 35.93 2.90
1768 1784 3.378742 TGTAGCTGAATCTTCTCGAGTCC 59.621 47.826 13.13 0.00 35.93 3.85
1774 1790 8.261492 TGAATTCTTTGTAGCTGAATCTTCTC 57.739 34.615 7.05 0.00 31.03 2.87
1782 1798 5.116180 CGGGTATGAATTCTTTGTAGCTGA 58.884 41.667 7.05 0.00 0.00 4.26
1786 1802 3.564225 GGCCGGGTATGAATTCTTTGTAG 59.436 47.826 2.18 0.00 0.00 2.74
1804 1820 2.094659 GTGTGTGATCGTCTGGCCG 61.095 63.158 0.00 0.00 0.00 6.13
1835 1851 6.816134 TTGCAAGATCATGTAAGTTGCTTA 57.184 33.333 18.60 9.41 43.18 3.09
1868 1884 6.791303 TGACCGCTGAAATATTAAAATGGTC 58.209 36.000 16.37 16.37 41.86 4.02
1871 1887 9.950680 AACTATGACCGCTGAAATATTAAAATG 57.049 29.630 0.00 0.00 0.00 2.32
1889 1906 8.248945 TCTACAAGCAACTTACCTAACTATGAC 58.751 37.037 0.00 0.00 0.00 3.06
1899 1916 4.156008 CCATGGTTCTACAAGCAACTTACC 59.844 45.833 2.57 0.00 43.15 2.85
1929 1946 9.975218 ACATAAATTTCCCTAGTGTTTCATAGT 57.025 29.630 0.00 0.00 0.00 2.12
1942 1959 6.246163 AGTCTTTCGGAACATAAATTTCCCT 58.754 36.000 0.00 0.00 39.65 4.20
1944 1961 6.806739 CCAAGTCTTTCGGAACATAAATTTCC 59.193 38.462 0.00 0.00 39.45 3.13
1957 1974 7.277319 GTCTAAAATAGTACCCAAGTCTTTCGG 59.723 40.741 0.00 0.00 0.00 4.30
1958 1975 7.277319 GGTCTAAAATAGTACCCAAGTCTTTCG 59.723 40.741 0.00 0.00 0.00 3.46
2201 2232 5.779241 TGGGGATGTCTAAAGTTCTTCAT 57.221 39.130 0.00 0.00 0.00 2.57
2233 2264 1.756538 CATTGGGGTTGCCCTTATGTC 59.243 52.381 4.02 0.00 44.66 3.06
2236 2267 0.042431 TGCATTGGGGTTGCCCTTAT 59.958 50.000 4.02 0.00 44.66 1.73
2328 2359 4.847198 TGTCTAAACACATGCATGGAGAT 58.153 39.130 29.41 14.03 0.00 2.75
2347 2378 1.811359 CGGACGGAGGGAGTATATGTC 59.189 57.143 0.00 0.00 0.00 3.06
2391 2422 8.307483 GCTAGTGCTAGATACATCCATTTAAGA 58.693 37.037 10.17 0.00 35.21 2.10
2392 2423 8.472683 GCTAGTGCTAGATACATCCATTTAAG 57.527 38.462 10.17 0.00 35.21 1.85
2406 2437 8.286404 TGTATCTAACACCAAGCTAGTGCTAGA 61.286 40.741 22.39 22.39 43.39 2.43
2407 2438 6.183360 TGTATCTAACACCAAGCTAGTGCTAG 60.183 42.308 14.95 15.52 40.24 3.42
2408 2439 5.655090 TGTATCTAACACCAAGCTAGTGCTA 59.345 40.000 14.95 7.91 40.24 3.49
2409 2440 4.466370 TGTATCTAACACCAAGCTAGTGCT 59.534 41.667 14.95 7.22 41.95 4.40
2410 2441 4.755411 TGTATCTAACACCAAGCTAGTGC 58.245 43.478 14.95 0.57 38.87 4.40
2411 2442 6.573434 TGATGTATCTAACACCAAGCTAGTG 58.427 40.000 13.76 13.76 42.09 2.74
2412 2443 6.791867 TGATGTATCTAACACCAAGCTAGT 57.208 37.500 0.00 0.00 42.09 2.57
2413 2444 8.668510 AATTGATGTATCTAACACCAAGCTAG 57.331 34.615 0.00 0.00 44.99 3.42
2414 2445 8.892723 CAAATTGATGTATCTAACACCAAGCTA 58.107 33.333 0.00 0.00 44.99 3.32
2415 2446 7.611467 TCAAATTGATGTATCTAACACCAAGCT 59.389 33.333 0.00 0.00 44.99 3.74
2416 2447 7.761409 TCAAATTGATGTATCTAACACCAAGC 58.239 34.615 0.00 0.00 44.99 4.01
2417 2448 8.400947 CCTCAAATTGATGTATCTAACACCAAG 58.599 37.037 0.00 0.00 44.99 3.61
2418 2449 7.339212 CCCTCAAATTGATGTATCTAACACCAA 59.661 37.037 0.00 0.00 45.86 3.67
2419 2450 6.828273 CCCTCAAATTGATGTATCTAACACCA 59.172 38.462 0.00 0.00 42.09 4.17
2420 2451 7.012421 GTCCCTCAAATTGATGTATCTAACACC 59.988 40.741 0.00 0.00 42.09 4.16
2421 2452 7.552687 TGTCCCTCAAATTGATGTATCTAACAC 59.447 37.037 0.00 0.00 42.09 3.32
2422 2453 7.629157 TGTCCCTCAAATTGATGTATCTAACA 58.371 34.615 0.00 0.00 43.86 2.41
2423 2454 8.506168 TTGTCCCTCAAATTGATGTATCTAAC 57.494 34.615 0.00 0.00 32.64 2.34
2451 2482 3.007506 TGCTACTCCATCCGTCTGAAAAA 59.992 43.478 0.00 0.00 0.00 1.94
2452 2483 2.565391 TGCTACTCCATCCGTCTGAAAA 59.435 45.455 0.00 0.00 0.00 2.29
2453 2484 2.094182 GTGCTACTCCATCCGTCTGAAA 60.094 50.000 0.00 0.00 0.00 2.69
2454 2485 1.476891 GTGCTACTCCATCCGTCTGAA 59.523 52.381 0.00 0.00 0.00 3.02
2455 2486 1.103803 GTGCTACTCCATCCGTCTGA 58.896 55.000 0.00 0.00 0.00 3.27
2456 2487 0.817654 TGTGCTACTCCATCCGTCTG 59.182 55.000 0.00 0.00 0.00 3.51
2457 2488 1.781786 ATGTGCTACTCCATCCGTCT 58.218 50.000 0.00 0.00 0.00 4.18
2458 2489 3.579709 CATATGTGCTACTCCATCCGTC 58.420 50.000 0.00 0.00 0.00 4.79
2459 2490 2.300152 CCATATGTGCTACTCCATCCGT 59.700 50.000 1.24 0.00 0.00 4.69
2460 2491 2.562738 TCCATATGTGCTACTCCATCCG 59.437 50.000 1.24 0.00 0.00 4.18
2461 2492 4.284490 TCTTCCATATGTGCTACTCCATCC 59.716 45.833 1.24 0.00 0.00 3.51
2462 2493 5.011533 AGTCTTCCATATGTGCTACTCCATC 59.988 44.000 1.24 0.00 0.00 3.51
2463 2494 4.904251 AGTCTTCCATATGTGCTACTCCAT 59.096 41.667 1.24 0.00 0.00 3.41
2464 2495 4.290093 AGTCTTCCATATGTGCTACTCCA 58.710 43.478 1.24 0.00 0.00 3.86
2465 2496 4.946478 AGTCTTCCATATGTGCTACTCC 57.054 45.455 1.24 0.00 0.00 3.85
2466 2497 8.144478 TCAATAAGTCTTCCATATGTGCTACTC 58.856 37.037 1.24 0.00 0.00 2.59
2467 2498 8.023021 TCAATAAGTCTTCCATATGTGCTACT 57.977 34.615 1.24 0.00 0.00 2.57
2468 2499 8.662781 TTCAATAAGTCTTCCATATGTGCTAC 57.337 34.615 1.24 0.00 0.00 3.58
2469 2500 9.679661 TTTTCAATAAGTCTTCCATATGTGCTA 57.320 29.630 1.24 0.00 0.00 3.49
2470 2501 8.579850 TTTTCAATAAGTCTTCCATATGTGCT 57.420 30.769 1.24 0.00 0.00 4.40
2560 2592 6.183347 AGCAGGCACTTGATTAAGAGTAAAT 58.817 36.000 3.94 0.00 34.60 1.40
2562 2594 5.165961 AGCAGGCACTTGATTAAGAGTAA 57.834 39.130 3.94 0.00 34.60 2.24
2565 2597 5.423015 TCTTAGCAGGCACTTGATTAAGAG 58.577 41.667 3.94 0.00 34.60 2.85
2620 2652 9.645059 GATCGATCATTGATAGAACAAATAGGA 57.355 33.333 20.52 0.00 33.44 2.94
2671 2703 5.713822 AAAACCGACGTTCTATTCATAGC 57.286 39.130 0.00 0.00 0.00 2.97
2674 2706 7.493320 TGCTTATAAAACCGACGTTCTATTCAT 59.507 33.333 0.00 0.00 0.00 2.57
2675 2707 6.812656 TGCTTATAAAACCGACGTTCTATTCA 59.187 34.615 0.00 0.00 0.00 2.57
2676 2708 7.225523 TGCTTATAAAACCGACGTTCTATTC 57.774 36.000 0.00 0.00 0.00 1.75
2704 2736 0.713883 CACCTCCGACGTTCGATTTG 59.286 55.000 8.63 0.00 43.74 2.32
2713 2745 5.286438 TCATTACATAATTCACCTCCGACG 58.714 41.667 0.00 0.00 0.00 5.12
2717 2749 9.520204 CAATTGTTCATTACATAATTCACCTCC 57.480 33.333 0.00 0.00 36.44 4.30
2782 2814 6.922957 CCTCGGACATTTGATTTTTCTTTTGA 59.077 34.615 0.00 0.00 0.00 2.69
2783 2815 6.701400 ACCTCGGACATTTGATTTTTCTTTTG 59.299 34.615 0.00 0.00 0.00 2.44
2784 2816 6.701400 CACCTCGGACATTTGATTTTTCTTTT 59.299 34.615 0.00 0.00 0.00 2.27
2785 2817 6.215845 CACCTCGGACATTTGATTTTTCTTT 58.784 36.000 0.00 0.00 0.00 2.52
2788 2820 4.485163 CCACCTCGGACATTTGATTTTTC 58.515 43.478 0.00 0.00 36.56 2.29
2799 2831 2.799126 ATAATTTGCCACCTCGGACA 57.201 45.000 0.00 0.00 36.56 4.02
2801 2833 4.787551 ACAATATAATTTGCCACCTCGGA 58.212 39.130 0.00 0.00 36.56 4.55
2806 2838 5.493133 TCGTGACAATATAATTTGCCACC 57.507 39.130 1.42 0.00 36.85 4.61
2825 2857 5.705441 TGCTAAAGAAAATTGTCATCCTCGT 59.295 36.000 0.00 0.00 0.00 4.18
2914 2948 5.572211 CAAATTATGTTGTCGTGAGGATGG 58.428 41.667 0.00 0.00 0.00 3.51
2947 2981 0.447406 TGAGCATGGCAAATCGAACG 59.553 50.000 0.00 0.00 0.00 3.95
3023 3057 2.147958 TGGACGGAAGAATTTGTTCGG 58.852 47.619 10.93 10.93 0.00 4.30
3054 3089 5.398169 CCGCAAAATCTAGCATAACAACAA 58.602 37.500 0.00 0.00 0.00 2.83
3173 3208 0.606401 AGGTGTGTGCTGGGAAATCG 60.606 55.000 0.00 0.00 0.00 3.34
3184 3219 1.741525 CCCAAGCCAAAGGTGTGTG 59.258 57.895 0.00 0.00 0.00 3.82
3185 3220 2.133641 GCCCAAGCCAAAGGTGTGT 61.134 57.895 0.00 0.00 0.00 3.72
3251 3286 1.513586 GACGAAGGAGTACGTGCCG 60.514 63.158 0.00 0.00 42.74 5.69
3257 3292 3.655276 TCCTTGTTGACGAAGGAGTAC 57.345 47.619 0.00 0.00 43.39 2.73
3369 3404 1.001597 GGACGATATGAGGACACCGTC 60.002 57.143 0.00 0.00 43.65 4.79
3371 3406 1.029681 TGGACGATATGAGGACACCG 58.970 55.000 0.00 0.00 0.00 4.94
3437 3472 3.353029 TTGATGTGCACGGTGCCG 61.353 61.111 28.57 9.29 44.23 5.69
3470 3505 6.633634 GGTAGACGATGAAGTTCTTCTTATCG 59.366 42.308 22.02 22.02 40.70 2.92
3473 3508 6.127703 CCAGGTAGACGATGAAGTTCTTCTTA 60.128 42.308 14.75 4.59 36.40 2.10
3512 3547 0.679321 CCTTCTGCTTGCCCTCCTTC 60.679 60.000 0.00 0.00 0.00 3.46
3542 3577 2.124736 CCATGGTACTGGCCACCG 60.125 66.667 0.00 0.00 41.94 4.94
3660 3695 2.765250 TTCACCCGTGCGAGCTCTTC 62.765 60.000 12.85 3.99 0.00 2.87
3701 3736 1.140652 AGCTCTTCTGCCTCATAAGCC 59.859 52.381 0.00 0.00 0.00 4.35
3740 3775 2.893489 AGAAAGTGAACCATTGGCCTTC 59.107 45.455 3.32 0.00 0.00 3.46
4071 4112 3.680777 AGTAGGAGAAGGAGAAGGAGG 57.319 52.381 0.00 0.00 0.00 4.30
4074 4115 6.503560 TCTAGTAGTAGGAGAAGGAGAAGG 57.496 45.833 4.74 0.00 0.00 3.46
4107 4148 0.449388 CTCTTTGCCCTTGCGATGAC 59.551 55.000 0.00 0.00 41.78 3.06
4133 4174 2.761208 ACTCGGTAGCAAGTAAGAGCAT 59.239 45.455 0.00 0.00 0.00 3.79
4141 4182 0.393077 AGCAACACTCGGTAGCAAGT 59.607 50.000 0.00 0.00 0.00 3.16
4266 4307 1.536766 TGCAGCATAGTTGTTGTCTGC 59.463 47.619 0.00 5.21 40.96 4.26
4273 4314 1.039233 GGCCCATGCAGCATAGTTGT 61.039 55.000 7.82 0.00 40.13 3.32
4395 4436 2.105821 CCGGGATAGCTTGGTAAATGGA 59.894 50.000 0.00 0.00 0.00 3.41
4505 4546 1.537814 TTTGCAGCTTGGCATCCCTG 61.538 55.000 0.00 0.00 44.48 4.45
4631 4672 1.068250 GTAGGGCTCCTCGATGTGC 59.932 63.158 6.24 6.24 34.61 4.57
4633 4674 1.043673 GGTGTAGGGCTCCTCGATGT 61.044 60.000 0.00 0.00 34.61 3.06
4709 4750 1.301716 GAGGTCGCCAAACTGCTCA 60.302 57.895 0.00 0.00 0.00 4.26
4745 4786 1.271840 TGAGCCGCCCAATAACCTCT 61.272 55.000 0.00 0.00 0.00 3.69
4793 4834 0.039180 TCTCCTTCTCGGTAGCACCA 59.961 55.000 6.21 0.00 38.47 4.17
4921 4962 6.100004 GTCAACAACTCATTATCCTTCTCGA 58.900 40.000 0.00 0.00 0.00 4.04
4931 4972 3.073678 AGCATGCGTCAACAACTCATTA 58.926 40.909 13.01 0.00 30.90 1.90
4998 5039 4.199310 GCAACTGAAGCATATACCTTGGA 58.801 43.478 0.00 0.00 0.00 3.53
5120 5161 1.553690 CCTCCCTTTCCTTCCTCGCA 61.554 60.000 0.00 0.00 0.00 5.10
5155 5196 1.872952 CATTGTCACCGTGAGCTTCAA 59.127 47.619 0.08 3.19 0.00 2.69
5221 5263 8.466798 AGGTAAACACTTACAATTATCCATTGC 58.533 33.333 0.00 0.00 45.74 3.56
5239 5281 2.240160 ACACCAGTTGACCAGGTAAACA 59.760 45.455 20.68 0.00 29.69 2.83
5328 5900 1.897802 AGTAGGGTGGAAACTGTACCG 59.102 52.381 0.00 0.00 35.31 4.02
5428 6002 7.108841 AGAGCACTGCATTGATCATTTTATT 57.891 32.000 22.16 0.00 34.19 1.40
5474 6048 6.486248 GCGTTGCTAAACAATATCTCATTCA 58.514 36.000 0.00 0.00 41.27 2.57
5656 6272 5.335661 GGCAGGACCAAATAAGTTTGTAGTG 60.336 44.000 0.00 0.00 42.50 2.74
5660 6276 3.826729 GAGGCAGGACCAAATAAGTTTGT 59.173 43.478 0.00 0.00 42.50 2.83
5678 6294 1.673665 CACTGAACTGGGCTGAGGC 60.674 63.158 0.00 0.00 37.82 4.70
5742 6358 1.178276 CCCTAGCGAGGTATAGCAGG 58.822 60.000 12.29 1.67 41.95 4.85
5850 6469 1.638133 CTGAAGCCACGATCACTCAG 58.362 55.000 0.00 0.00 0.00 3.35
5994 6617 9.817809 AGGGAAGTTCTTGAAAAAGAAAATAAC 57.182 29.630 2.25 0.00 40.15 1.89
5997 6620 9.739276 AAAAGGGAAGTTCTTGAAAAAGAAAAT 57.261 25.926 2.25 0.00 40.15 1.82
6153 6778 8.611757 GTTAACAAAATTTGAAAACAGAGCCAT 58.388 29.630 13.19 0.00 32.80 4.40
6154 6779 7.604164 TGTTAACAAAATTTGAAAACAGAGCCA 59.396 29.630 13.19 0.00 35.52 4.75
6155 6780 7.969314 TGTTAACAAAATTTGAAAACAGAGCC 58.031 30.769 13.19 0.00 35.52 4.70
6156 6781 9.818796 TTTGTTAACAAAATTTGAAAACAGAGC 57.181 25.926 27.26 4.39 42.26 4.09


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

AutoCloner maintained by Alex Coulton.