Multiple sequence alignment - TraesCS2D01G216200

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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 TraesCS2D01G216200 chr2D 100.000 5073 0 0 1 5073 179130938 179136010 0.000000e+00 9369.0
1 TraesCS2D01G216200 chr2A 93.114 2338 124 18 2350 4670 193706384 193708701 0.000000e+00 3391.0
2 TraesCS2D01G216200 chr2A 90.399 1229 51 26 391 1569 193704367 193705578 0.000000e+00 1554.0
3 TraesCS2D01G216200 chr2A 93.369 377 14 6 4665 5036 193708729 193709099 9.600000e-152 547.0
4 TraesCS2D01G216200 chr2A 89.231 390 26 4 1 375 193703991 193704379 1.650000e-129 473.0
5 TraesCS2D01G216200 chr2A 88.406 414 14 5 1881 2283 193705998 193706388 7.690000e-128 468.0
6 TraesCS2D01G216200 chr2A 92.763 304 16 1 1580 1877 193705648 193705951 7.800000e-118 435.0
7 TraesCS2D01G216200 chr2A 97.500 40 1 0 5034 5073 193724538 193724577 9.110000e-08 69.4
8 TraesCS2D01G216200 chr2B 91.887 2305 114 27 2348 4620 236046546 236048809 0.000000e+00 3153.0
9 TraesCS2D01G216200 chr2B 90.025 1223 58 26 391 1571 236044540 236045740 0.000000e+00 1524.0
10 TraesCS2D01G216200 chr2B 95.062 324 11 4 4674 4997 236048882 236049200 5.860000e-139 505.0
11 TraesCS2D01G216200 chr2B 90.390 385 32 4 1882 2266 236046155 236046534 7.580000e-138 501.0
12 TraesCS2D01G216200 chr2B 85.166 391 31 9 1 375 236044173 236044552 4.800000e-100 375.0
13 TraesCS2D01G216200 chr2B 85.993 307 27 5 1573 1865 236045798 236046102 1.060000e-81 315.0
14 TraesCS2D01G216200 chr5D 82.775 209 14 9 4322 4525 422035226 422035417 3.140000e-37 167.0
15 TraesCS2D01G216200 chr5D 100.000 68 0 0 2285 2352 277724115 277724048 5.330000e-25 126.0
16 TraesCS2D01G216200 chr3B 98.507 67 1 0 2286 2352 252592219 252592285 8.920000e-23 119.0
17 TraesCS2D01G216200 chr3B 100.000 29 0 0 1540 1568 4423667 4423639 3.000000e-03 54.7
18 TraesCS2D01G216200 chr6D 97.143 70 1 1 2284 2352 2480788 2480719 3.210000e-22 117.0
19 TraesCS2D01G216200 chr6D 97.059 68 2 0 2285 2352 17236990 17237057 1.150000e-21 115.0
20 TraesCS2D01G216200 chr7B 97.059 68 2 0 2285 2352 512330520 512330453 1.150000e-21 115.0
21 TraesCS2D01G216200 chr4A 97.101 69 1 1 2285 2352 708545133 708545201 1.150000e-21 115.0
22 TraesCS2D01G216200 chr3D 97.059 68 2 0 2285 2352 36157506 36157439 1.150000e-21 115.0
23 TraesCS2D01G216200 chr1B 97.059 68 2 0 2285 2352 683588643 683588576 1.150000e-21 115.0
24 TraesCS2D01G216200 chr1D 97.015 67 2 0 2285 2351 35867262 35867328 4.150000e-21 113.0


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 TraesCS2D01G216200 chr2D 179130938 179136010 5072 False 9369.000000 9369 100.000000 1 5073 1 chr2D.!!$F1 5072
1 TraesCS2D01G216200 chr2A 193703991 193709099 5108 False 1144.666667 3391 91.213667 1 5036 6 chr2A.!!$F2 5035
2 TraesCS2D01G216200 chr2B 236044173 236049200 5027 False 1062.166667 3153 89.753833 1 4997 6 chr2B.!!$F1 4996

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
368 388 0.036483 AAACCCAAATGATTGCCCGC 60.036 50.0 0.00 0.00 35.10 6.13 F
450 470 0.037046 CCTTGGGGCTGCACAATTTC 60.037 55.0 3.46 0.00 0.00 2.17 F
1298 1376 0.808060 GAGCTAACTCTTGGCCGCTC 60.808 60.0 8.89 8.89 40.03 5.03 F
2342 2562 0.105778 TCAATCGATGCATACGGCCA 59.894 50.0 2.24 0.00 43.89 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2332 0.102300 AACTGGTTTTGCGTGCTTCC 59.898 50.0 0.00 0.00 0.00 3.46 R
2323 2543 0.105778 TGGCCGTATGCATCGATTGA 59.894 50.0 16.69 0.00 43.89 2.57 R
2654 2874 0.250858 TGTGAACAGGGCAGGATGTG 60.251 55.0 0.00 0.00 39.31 3.21 R
4178 4433 0.037326 GAATCGCCGGGCTGATGATA 60.037 55.0 21.21 0.81 0.00 2.15 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 62 1.039785 GCTTTCTCTCCCAATGCCCC 61.040 60.000 0.00 0.00 0.00 5.80
125 142 2.604046 ATCGCCACGAGCTAAAATCT 57.396 45.000 0.00 0.00 39.91 2.40
131 148 4.328983 CGCCACGAGCTAAAATCTTTAGAA 59.671 41.667 9.77 0.00 40.39 2.10
210 227 5.648092 TCACATGAGACTGAGAGATAAACGA 59.352 40.000 0.00 0.00 0.00 3.85
214 231 8.037758 ACATGAGACTGAGAGATAAACGAAAAT 58.962 33.333 0.00 0.00 0.00 1.82
226 243 8.934507 AGATAAACGAAAATTTGTTTCCAACA 57.065 26.923 13.38 0.00 42.28 3.33
246 263 5.964958 ACAATGTGTGTTTAATGGGAGAG 57.035 39.130 0.00 0.00 37.01 3.20
336 355 2.420568 AAAGCATGATGCCCGCCAG 61.421 57.895 14.72 0.00 46.52 4.85
367 387 2.470983 AAAACCCAAATGATTGCCCG 57.529 45.000 0.00 0.00 35.10 6.13
368 388 0.036483 AAACCCAAATGATTGCCCGC 60.036 50.000 0.00 0.00 35.10 6.13
369 389 1.898330 AACCCAAATGATTGCCCGCC 61.898 55.000 0.00 0.00 35.10 6.13
370 390 2.357575 CCCAAATGATTGCCCGCCA 61.358 57.895 0.00 0.00 35.10 5.69
371 391 1.595882 CCAAATGATTGCCCGCCAA 59.404 52.632 0.00 0.00 37.94 4.52
372 392 0.460635 CCAAATGATTGCCCGCCAAG 60.461 55.000 0.00 0.00 36.76 3.61
373 393 0.247185 CAAATGATTGCCCGCCAAGT 59.753 50.000 0.00 0.00 36.76 3.16
374 394 0.975887 AAATGATTGCCCGCCAAGTT 59.024 45.000 0.00 0.00 36.76 2.66
375 395 0.975887 AATGATTGCCCGCCAAGTTT 59.024 45.000 0.00 0.00 36.76 2.66
376 396 0.975887 ATGATTGCCCGCCAAGTTTT 59.024 45.000 0.00 0.00 36.76 2.43
377 397 0.755686 TGATTGCCCGCCAAGTTTTT 59.244 45.000 0.00 0.00 36.76 1.94
378 398 1.270041 TGATTGCCCGCCAAGTTTTTC 60.270 47.619 0.00 0.00 36.76 2.29
379 399 1.000843 GATTGCCCGCCAAGTTTTTCT 59.999 47.619 0.00 0.00 36.76 2.52
380 400 0.827368 TTGCCCGCCAAGTTTTTCTT 59.173 45.000 0.00 0.00 36.75 2.52
381 401 0.827368 TGCCCGCCAAGTTTTTCTTT 59.173 45.000 0.00 0.00 33.63 2.52
382 402 1.208293 TGCCCGCCAAGTTTTTCTTTT 59.792 42.857 0.00 0.00 33.63 2.27
383 403 2.285083 GCCCGCCAAGTTTTTCTTTTT 58.715 42.857 0.00 0.00 33.63 1.94
384 404 2.031560 GCCCGCCAAGTTTTTCTTTTTG 59.968 45.455 0.00 0.00 33.63 2.44
385 405 3.526534 CCCGCCAAGTTTTTCTTTTTGA 58.473 40.909 0.00 0.00 33.63 2.69
386 406 3.555547 CCCGCCAAGTTTTTCTTTTTGAG 59.444 43.478 0.00 0.00 33.63 3.02
387 407 3.555547 CCGCCAAGTTTTTCTTTTTGAGG 59.444 43.478 0.00 0.00 33.63 3.86
388 408 3.555547 CGCCAAGTTTTTCTTTTTGAGGG 59.444 43.478 0.00 0.00 33.63 4.30
389 409 3.876914 GCCAAGTTTTTCTTTTTGAGGGG 59.123 43.478 0.00 0.00 33.63 4.79
424 444 1.618861 GCGTCAGCAGTACTACAGTG 58.381 55.000 0.00 0.00 44.35 3.66
434 454 1.900486 GTACTACAGTGCCTGTCCCTT 59.100 52.381 10.60 0.00 41.21 3.95
444 464 4.284550 TGTCCCTTGGGGCTGCAC 62.285 66.667 11.92 0.00 43.94 4.57
450 470 0.037046 CCTTGGGGCTGCACAATTTC 60.037 55.000 3.46 0.00 0.00 2.17
474 495 1.598685 CACGTTTTAGGTGCCCCGT 60.599 57.895 0.00 0.00 35.12 5.28
656 695 3.128349 ACGTTATTATTAGCAGCCACGG 58.872 45.455 0.00 0.00 0.00 4.94
679 718 3.702330 GCTAATTGCCCGATTTAACCAC 58.298 45.455 0.00 0.00 35.15 4.16
731 770 4.096003 CGTGTTCCCCGGCATCCT 62.096 66.667 0.00 0.00 0.00 3.24
758 797 1.070786 GCGTGGGACCTCTTGACAA 59.929 57.895 0.00 0.00 0.00 3.18
923 981 1.972795 ACGGGACCAAGTAGTAGCAAA 59.027 47.619 0.00 0.00 0.00 3.68
956 1014 4.698304 ACGAAACAAAAACTTCAGGACAGA 59.302 37.500 0.00 0.00 0.00 3.41
965 1023 2.903135 ACTTCAGGACAGAAAGAGGGAG 59.097 50.000 0.00 0.00 0.00 4.30
1224 1302 3.009115 ATGTGGGAGGGGGACGTG 61.009 66.667 0.00 0.00 0.00 4.49
1227 1305 3.603080 TGGGAGGGGGACGTGGTA 61.603 66.667 0.00 0.00 0.00 3.25
1298 1376 0.808060 GAGCTAACTCTTGGCCGCTC 60.808 60.000 8.89 8.89 40.03 5.03
1470 1555 5.406780 GTCTTTATGCCAACTCGATATGGAG 59.593 44.000 18.09 12.73 39.12 3.86
1473 1558 4.527509 ATGCCAACTCGATATGGAGTAG 57.472 45.455 19.27 14.80 46.21 2.57
1481 1566 7.095144 CCAACTCGATATGGAGTAGTAGTACTG 60.095 44.444 19.27 11.53 46.21 2.74
1485 1572 8.743085 TCGATATGGAGTAGTAGTACTGTTTT 57.257 34.615 15.07 0.59 39.78 2.43
1486 1573 8.618677 TCGATATGGAGTAGTAGTACTGTTTTG 58.381 37.037 15.07 0.00 39.78 2.44
1487 1574 7.378995 CGATATGGAGTAGTAGTACTGTTTTGC 59.621 40.741 15.07 0.00 39.78 3.68
1605 1756 2.497675 ACTTCTTCCTAGCTGCAATCGA 59.502 45.455 1.02 0.00 0.00 3.59
1661 1814 3.797039 TGCCTAATTAGTGCTAGCTGTG 58.203 45.455 17.23 0.00 0.00 3.66
1748 1901 8.768501 AGGTTTAGTTTCTCTCTTGGATTTTT 57.231 30.769 0.00 0.00 0.00 1.94
1877 2042 2.157738 CCCTTCTGAACTTCTGCCTTG 58.842 52.381 0.00 0.00 0.00 3.61
1878 2043 2.487986 CCCTTCTGAACTTCTGCCTTGT 60.488 50.000 0.00 0.00 0.00 3.16
1879 2044 3.244561 CCCTTCTGAACTTCTGCCTTGTA 60.245 47.826 0.00 0.00 0.00 2.41
1890 2099 8.438676 AACTTCTGCCTTGTATACAACATATC 57.561 34.615 14.35 3.23 38.10 1.63
1972 2181 2.292828 ACTACTTGCAGTTGCCCATT 57.707 45.000 1.06 0.00 41.18 3.16
2050 2259 5.846714 AGGTACAGATAATACCCTGAGCAAT 59.153 40.000 0.00 0.00 42.80 3.56
2070 2279 2.863401 TTATGACCATGTCTCGTCCG 57.137 50.000 0.00 0.00 33.15 4.79
2082 2291 1.067974 TCTCGTCCGTTTCTTGCTTGA 59.932 47.619 0.00 0.00 0.00 3.02
2103 2312 5.486526 TGACATTTTTCTGTGCCAAAAGTT 58.513 33.333 0.00 0.00 0.00 2.66
2110 2319 5.906113 TTCTGTGCCAAAAGTTTAGTCAA 57.094 34.783 0.00 0.00 0.00 3.18
2123 2332 6.560253 AGTTTAGTCAAATTGCTGTGTAGG 57.440 37.500 0.00 0.00 0.00 3.18
2124 2333 5.473504 AGTTTAGTCAAATTGCTGTGTAGGG 59.526 40.000 0.00 0.00 0.00 3.53
2125 2334 3.788227 AGTCAAATTGCTGTGTAGGGA 57.212 42.857 0.00 0.00 0.00 4.20
2126 2335 4.098914 AGTCAAATTGCTGTGTAGGGAA 57.901 40.909 0.00 0.00 0.00 3.97
2127 2336 4.074970 AGTCAAATTGCTGTGTAGGGAAG 58.925 43.478 0.00 0.00 0.00 3.46
2236 2451 8.125978 TCCAGTATCAAATGCAGAATTTCTTT 57.874 30.769 0.00 0.00 36.28 2.52
2282 2502 8.950208 AAAGTAGACTTCTTGATATAGTTGCC 57.050 34.615 0.00 0.00 34.61 4.52
2283 2503 7.056844 AGTAGACTTCTTGATATAGTTGCCC 57.943 40.000 0.00 0.00 0.00 5.36
2284 2504 6.841755 AGTAGACTTCTTGATATAGTTGCCCT 59.158 38.462 0.00 0.00 0.00 5.19
2285 2505 6.567602 AGACTTCTTGATATAGTTGCCCTT 57.432 37.500 0.00 0.00 0.00 3.95
2286 2506 6.963322 AGACTTCTTGATATAGTTGCCCTTT 58.037 36.000 0.00 0.00 0.00 3.11
2287 2507 7.406104 AGACTTCTTGATATAGTTGCCCTTTT 58.594 34.615 0.00 0.00 0.00 2.27
2288 2508 7.890655 AGACTTCTTGATATAGTTGCCCTTTTT 59.109 33.333 0.00 0.00 0.00 1.94
2317 2537 2.441959 GGTTAAAACCCCCGGCCT 59.558 61.111 0.00 0.00 43.43 5.19
2318 2538 1.679977 GGTTAAAACCCCCGGCCTC 60.680 63.158 0.00 0.00 43.43 4.70
2319 2539 1.381463 GTTAAAACCCCCGGCCTCT 59.619 57.895 0.00 0.00 0.00 3.69
2320 2540 0.963856 GTTAAAACCCCCGGCCTCTG 60.964 60.000 0.00 0.00 0.00 3.35
2321 2541 2.774687 TTAAAACCCCCGGCCTCTGC 62.775 60.000 0.00 0.00 0.00 4.26
2326 2546 4.113815 CCCCGGCCTCTGCATCAA 62.114 66.667 0.00 0.00 40.13 2.57
2327 2547 2.194056 CCCGGCCTCTGCATCAAT 59.806 61.111 0.00 0.00 40.13 2.57
2328 2548 1.895707 CCCGGCCTCTGCATCAATC 60.896 63.158 0.00 0.00 40.13 2.67
2329 2549 2.249535 CCGGCCTCTGCATCAATCG 61.250 63.158 0.00 0.00 40.13 3.34
2330 2550 1.227350 CGGCCTCTGCATCAATCGA 60.227 57.895 0.00 0.00 40.13 3.59
2331 2551 0.602106 CGGCCTCTGCATCAATCGAT 60.602 55.000 0.00 0.00 40.13 3.59
2340 2560 2.515641 CATCAATCGATGCATACGGC 57.484 50.000 15.33 0.00 42.54 5.68
2341 2561 1.129251 CATCAATCGATGCATACGGCC 59.871 52.381 15.33 0.00 42.54 6.13
2342 2562 0.105778 TCAATCGATGCATACGGCCA 59.894 50.000 2.24 0.00 43.89 5.36
2343 2563 1.159285 CAATCGATGCATACGGCCAT 58.841 50.000 2.24 0.00 43.89 4.40
2344 2564 1.129251 CAATCGATGCATACGGCCATC 59.871 52.381 2.24 0.00 43.89 3.51
2345 2565 0.610174 ATCGATGCATACGGCCATCT 59.390 50.000 2.24 0.00 43.89 2.90
2346 2566 0.392706 TCGATGCATACGGCCATCTT 59.607 50.000 2.24 0.00 43.89 2.40
2347 2567 1.202639 TCGATGCATACGGCCATCTTT 60.203 47.619 2.24 0.00 43.89 2.52
2348 2568 2.036604 TCGATGCATACGGCCATCTTTA 59.963 45.455 2.24 0.00 43.89 1.85
2349 2569 3.002791 CGATGCATACGGCCATCTTTAT 58.997 45.455 2.24 0.00 43.89 1.40
2350 2570 3.436704 CGATGCATACGGCCATCTTTATT 59.563 43.478 2.24 0.00 43.89 1.40
2351 2571 4.083324 CGATGCATACGGCCATCTTTATTT 60.083 41.667 2.24 0.00 43.89 1.40
2469 2689 8.406297 GGTGGAATATTTTGTTAGAATGTCTCC 58.594 37.037 0.00 0.00 0.00 3.71
2541 2761 7.445402 AGTCAAAAATAGCAAAGCTGTCTTCTA 59.555 33.333 1.04 0.00 40.10 2.10
2586 2806 9.851686 AAGATAATGCATAGGATGTTTGACTTA 57.148 29.630 0.00 0.00 0.00 2.24
2633 2853 6.039270 TGGATAATTCTGTATTCTTTTGGGCG 59.961 38.462 0.00 0.00 0.00 6.13
2654 2874 2.191128 AGACCTGGTCAACATGAAGC 57.809 50.000 27.48 0.00 34.60 3.86
2718 2938 5.324784 AGTATAACGTGCAGTCTCATTCA 57.675 39.130 0.00 0.00 0.00 2.57
2778 3004 3.778075 TCCTTTAGGGTATGCACAAGCTA 59.222 43.478 0.00 0.00 37.79 3.32
2822 3048 3.234630 TTGACCAGGTCGAAGCCCG 62.235 63.158 15.24 0.00 34.95 6.13
2893 3119 9.109533 CAAATTAGTTGTCACGTATTTTGGTAC 57.890 33.333 0.00 0.00 32.08 3.34
2894 3120 8.611654 AATTAGTTGTCACGTATTTTGGTACT 57.388 30.769 0.00 0.00 0.00 2.73
2909 3147 5.829062 TTGGTACTGTGGGTTTATGTAGT 57.171 39.130 0.00 0.00 0.00 2.73
2910 3148 5.410355 TGGTACTGTGGGTTTATGTAGTC 57.590 43.478 0.00 0.00 0.00 2.59
2911 3149 4.839550 TGGTACTGTGGGTTTATGTAGTCA 59.160 41.667 0.00 0.00 0.00 3.41
2912 3150 5.173664 GGTACTGTGGGTTTATGTAGTCAC 58.826 45.833 0.00 0.00 0.00 3.67
2913 3151 4.967084 ACTGTGGGTTTATGTAGTCACA 57.033 40.909 0.00 0.00 39.52 3.58
2914 3152 5.298989 ACTGTGGGTTTATGTAGTCACAA 57.701 39.130 0.00 0.00 38.42 3.33
3034 3282 1.064017 TCTGTTTTCCTGCCCTGTTGT 60.064 47.619 0.00 0.00 0.00 3.32
3141 3390 4.320494 CCATTGGTTTACTTGAGCTGTGTC 60.320 45.833 0.00 0.00 0.00 3.67
3269 3518 5.569059 CAGCTTAATTGCCTTTTCTGTAACG 59.431 40.000 0.00 0.00 0.00 3.18
3271 3520 6.016610 AGCTTAATTGCCTTTTCTGTAACGAA 60.017 34.615 0.00 0.00 0.00 3.85
3326 3575 7.930865 GGTTCTGTTCTCTTGATAGCAATCTAT 59.069 37.037 0.00 0.00 38.19 1.98
3483 3732 4.260170 GTGCCTGTCTTCTCTTGAATCAT 58.740 43.478 0.00 0.00 0.00 2.45
3523 3772 7.471721 TGTGGCTTTAATCGAATGAACAATAG 58.528 34.615 0.00 0.00 0.00 1.73
3529 3778 9.430838 CTTTAATCGAATGAACAATAGCTGAAG 57.569 33.333 0.00 0.00 0.00 3.02
3558 3807 7.604927 TGTTTTGAGTTAATATTGGTAGCTCGT 59.395 33.333 0.00 0.00 33.00 4.18
3740 3990 5.430886 TCCATCTGATATGTCCTTGTTGTG 58.569 41.667 0.00 0.00 0.00 3.33
3742 3992 3.261580 TCTGATATGTCCTTGTTGTGCG 58.738 45.455 0.00 0.00 0.00 5.34
3765 4015 4.152402 GCTGTGCCAGGTTATATACATTCG 59.848 45.833 4.65 0.00 31.21 3.34
3859 4111 2.166270 GCAGGAGGCGAGAACTTTG 58.834 57.895 0.00 0.00 0.00 2.77
4145 4399 4.142687 CCTGCGTGTTATCGAAAGGAAAAT 60.143 41.667 0.00 0.00 37.96 1.82
4148 4402 6.900189 TGCGTGTTATCGAAAGGAAAATAAA 58.100 32.000 0.00 0.00 0.00 1.40
4151 4405 6.964934 CGTGTTATCGAAAGGAAAATAAAGGG 59.035 38.462 0.00 0.00 0.00 3.95
4178 4433 1.455773 TGGATCCCTCTGCGACGAT 60.456 57.895 9.90 0.00 0.00 3.73
4190 4445 1.073216 GCGACGATATCATCAGCCCG 61.073 60.000 0.00 0.00 0.00 6.13
4236 4491 7.054124 TGTATCAAGTCTGAAGAACTGGTTTT 58.946 34.615 0.00 0.00 34.49 2.43
4245 4500 1.824230 AGAACTGGTTTTGCAGCAACA 59.176 42.857 7.54 0.00 30.60 3.33
4462 4724 4.561735 TTCTTGTAAAACTTGCCTTCCG 57.438 40.909 0.00 0.00 0.00 4.30
4463 4725 2.882137 TCTTGTAAAACTTGCCTTCCGG 59.118 45.455 0.00 0.00 0.00 5.14
4490 4752 6.986817 GCTCTCTGCTAACATCATTTACCTTA 59.013 38.462 0.00 0.00 38.95 2.69
4521 4783 6.202331 TCCTCTGGGAACTGATGATTACTTA 58.798 40.000 0.00 0.00 38.93 2.24
4577 4839 7.024340 AGCATAGCACATAACAAAAGAGATG 57.976 36.000 0.00 0.00 0.00 2.90
4583 4845 3.941483 ACATAACAAAAGAGATGCTCGGG 59.059 43.478 0.00 0.00 35.36 5.14
4584 4846 2.568623 AACAAAAGAGATGCTCGGGT 57.431 45.000 0.00 0.00 35.36 5.28
4586 4848 1.072331 ACAAAAGAGATGCTCGGGTGT 59.928 47.619 0.00 0.00 35.36 4.16
4612 4878 8.728088 ATCAAAATTTCTGTGTTTAGCTTACG 57.272 30.769 0.00 0.00 0.00 3.18
4621 4887 6.370442 TCTGTGTTTAGCTTACGCAAATACAT 59.630 34.615 13.67 0.00 37.48 2.29
4623 4889 8.203937 TGTGTTTAGCTTACGCAAATACATAT 57.796 30.769 11.20 0.00 35.57 1.78
4624 4890 9.315525 TGTGTTTAGCTTACGCAAATACATATA 57.684 29.630 11.20 0.00 35.57 0.86
4633 4899 3.367932 CGCAAATACATATAGCCGTGGAG 59.632 47.826 0.00 0.00 0.00 3.86
4651 4917 1.602237 GGAAGCAATCCGGGAGACA 59.398 57.895 0.00 0.00 38.79 3.41
4670 4936 3.620488 ACAATTCCATTCGCCAGTACAT 58.380 40.909 0.00 0.00 0.00 2.29
4671 4937 3.378112 ACAATTCCATTCGCCAGTACATG 59.622 43.478 0.00 0.00 0.00 3.21
4684 4986 5.235305 CCAGTACATGGCTTTGTTATGAC 57.765 43.478 0.00 0.00 43.83 3.06
4751 5053 7.761249 CCTTCTTTTCCAATGTATAAAGCCTTG 59.239 37.037 0.00 0.00 0.00 3.61
4891 5193 1.457267 TGTGCACCACCTTTGCCAT 60.457 52.632 15.69 0.00 39.39 4.40
5018 5325 8.750416 CAACTATTCTACTTTCTGATGATCACG 58.250 37.037 0.00 0.00 0.00 4.35
5027 5334 0.394216 TGATGATCACGGCCCAAAGG 60.394 55.000 0.00 0.00 0.00 3.11
5036 5343 1.866853 CGGCCCAAAGGAGCAGAAAC 61.867 60.000 0.00 0.00 33.47 2.78
5037 5344 1.536073 GGCCCAAAGGAGCAGAAACC 61.536 60.000 0.00 0.00 33.47 3.27
5038 5345 0.540597 GCCCAAAGGAGCAGAAACCT 60.541 55.000 0.00 0.00 38.23 3.50
5039 5346 1.539157 CCCAAAGGAGCAGAAACCTC 58.461 55.000 0.00 0.00 35.25 3.85
5048 5355 4.786425 GGAGCAGAAACCTCCATAATTCT 58.214 43.478 2.70 0.00 46.51 2.40
5049 5356 5.930135 GGAGCAGAAACCTCCATAATTCTA 58.070 41.667 2.70 0.00 46.51 2.10
5050 5357 6.357367 GGAGCAGAAACCTCCATAATTCTAA 58.643 40.000 2.70 0.00 46.51 2.10
5051 5358 6.261158 GGAGCAGAAACCTCCATAATTCTAAC 59.739 42.308 2.70 0.00 46.51 2.34
5052 5359 6.963322 AGCAGAAACCTCCATAATTCTAACT 58.037 36.000 0.00 0.00 31.25 2.24
5053 5360 7.406104 AGCAGAAACCTCCATAATTCTAACTT 58.594 34.615 0.00 0.00 31.25 2.66
5054 5361 8.548877 AGCAGAAACCTCCATAATTCTAACTTA 58.451 33.333 0.00 0.00 31.25 2.24
5055 5362 8.831550 GCAGAAACCTCCATAATTCTAACTTAG 58.168 37.037 0.00 0.00 31.25 2.18
5056 5363 9.331282 CAGAAACCTCCATAATTCTAACTTAGG 57.669 37.037 0.00 0.00 31.25 2.69
5057 5364 7.993758 AGAAACCTCCATAATTCTAACTTAGGC 59.006 37.037 0.00 0.00 30.69 3.93
5058 5365 6.189036 ACCTCCATAATTCTAACTTAGGCC 57.811 41.667 0.00 0.00 0.00 5.19
5059 5366 5.911766 ACCTCCATAATTCTAACTTAGGCCT 59.088 40.000 11.78 11.78 0.00 5.19
5060 5367 6.043358 ACCTCCATAATTCTAACTTAGGCCTC 59.957 42.308 9.68 0.00 0.00 4.70
5061 5368 6.043243 CCTCCATAATTCTAACTTAGGCCTCA 59.957 42.308 9.68 0.00 0.00 3.86
5062 5369 7.256835 CCTCCATAATTCTAACTTAGGCCTCAT 60.257 40.741 9.68 0.00 0.00 2.90
5063 5370 8.045720 TCCATAATTCTAACTTAGGCCTCATT 57.954 34.615 9.68 4.71 0.00 2.57
5064 5371 8.502738 TCCATAATTCTAACTTAGGCCTCATTT 58.497 33.333 9.68 0.50 0.00 2.32
5065 5372 8.571336 CCATAATTCTAACTTAGGCCTCATTTG 58.429 37.037 9.68 3.47 0.00 2.32
5066 5373 8.571336 CATAATTCTAACTTAGGCCTCATTTGG 58.429 37.037 9.68 0.32 0.00 3.28
5067 5374 5.514500 TTCTAACTTAGGCCTCATTTGGT 57.486 39.130 9.68 0.00 0.00 3.67
5068 5375 5.514500 TCTAACTTAGGCCTCATTTGGTT 57.486 39.130 9.68 9.15 0.00 3.67
5069 5376 5.497474 TCTAACTTAGGCCTCATTTGGTTC 58.503 41.667 9.68 0.00 0.00 3.62
5070 5377 3.806949 ACTTAGGCCTCATTTGGTTCA 57.193 42.857 9.68 0.00 0.00 3.18
5071 5378 4.322057 ACTTAGGCCTCATTTGGTTCAT 57.678 40.909 9.68 0.00 0.00 2.57
5072 5379 5.450818 ACTTAGGCCTCATTTGGTTCATA 57.549 39.130 9.68 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 142 8.728833 TCGTAGGTTTTCTTTTGTTGTTCTAAA 58.271 29.630 0.00 0.00 0.00 1.85
131 148 5.826208 AGGATCGTAGGTTTTCTTTTGTTGT 59.174 36.000 0.00 0.00 0.00 3.32
226 243 3.440173 CGCTCTCCCATTAAACACACATT 59.560 43.478 0.00 0.00 0.00 2.71
232 249 4.020573 TCTCTTTCGCTCTCCCATTAAACA 60.021 41.667 0.00 0.00 0.00 2.83
236 253 3.428999 CGTTCTCTTTCGCTCTCCCATTA 60.429 47.826 0.00 0.00 0.00 1.90
246 263 0.097150 GAATGGCCGTTCTCTTTCGC 59.903 55.000 27.38 1.79 0.00 4.70
270 287 1.600023 TAGTTGTTCGGCCAAACCTG 58.400 50.000 3.59 0.00 35.61 4.00
271 288 1.951602 GTTAGTTGTTCGGCCAAACCT 59.048 47.619 3.59 0.00 35.61 3.50
319 338 2.831742 CTGGCGGGCATCATGCTT 60.832 61.111 10.11 0.00 44.28 3.91
352 371 1.897225 TTGGCGGGCAATCATTTGGG 61.897 55.000 13.46 0.00 33.22 4.12
362 382 0.827368 AAAGAAAAACTTGGCGGGCA 59.173 45.000 0.00 0.00 38.98 5.36
363 383 1.948104 AAAAGAAAAACTTGGCGGGC 58.052 45.000 0.00 0.00 38.98 6.13
364 384 3.526534 TCAAAAAGAAAAACTTGGCGGG 58.473 40.909 0.00 0.00 38.98 6.13
365 385 3.555547 CCTCAAAAAGAAAAACTTGGCGG 59.444 43.478 0.00 0.00 38.98 6.13
366 386 3.555547 CCCTCAAAAAGAAAAACTTGGCG 59.444 43.478 0.00 0.00 38.98 5.69
367 387 3.876914 CCCCTCAAAAAGAAAAACTTGGC 59.123 43.478 0.00 0.00 38.98 4.52
368 388 4.875536 CACCCCTCAAAAAGAAAAACTTGG 59.124 41.667 0.00 0.00 38.98 3.61
369 389 4.332543 GCACCCCTCAAAAAGAAAAACTTG 59.667 41.667 0.00 0.00 38.98 3.16
370 390 4.513442 GCACCCCTCAAAAAGAAAAACTT 58.487 39.130 0.00 0.00 40.98 2.66
371 391 3.118408 GGCACCCCTCAAAAAGAAAAACT 60.118 43.478 0.00 0.00 0.00 2.66
372 392 3.202906 GGCACCCCTCAAAAAGAAAAAC 58.797 45.455 0.00 0.00 0.00 2.43
373 393 3.552132 GGCACCCCTCAAAAAGAAAAA 57.448 42.857 0.00 0.00 0.00 1.94
389 409 4.043200 GCTCAACTTGGCGGGCAC 62.043 66.667 2.73 0.00 0.00 5.01
434 454 1.186917 CCTGAAATTGTGCAGCCCCA 61.187 55.000 0.00 0.00 0.00 4.96
444 464 3.980775 CCTAAAACGTGCACCTGAAATTG 59.019 43.478 12.15 0.00 0.00 2.32
474 495 2.609610 AGAAAGGGGGTGCCGCTA 60.610 61.111 5.28 0.00 46.26 4.26
544 573 4.694021 CTGCTTCAGAGTCCAGACTGGAT 61.694 52.174 26.78 15.52 40.48 3.41
800 839 1.687494 CTGTTCGCACTCGCTTAGGC 61.687 60.000 0.00 0.00 35.30 3.93
803 842 0.883153 TACCTGTTCGCACTCGCTTA 59.117 50.000 0.00 0.00 35.30 3.09
822 861 1.072965 GCATCTCCGATTGGGATTCCT 59.927 52.381 2.01 0.00 46.04 3.36
923 981 6.051646 AGTTTTTGTTTCGTACTATTGCGT 57.948 33.333 0.00 0.00 31.89 5.24
956 1014 1.162951 TCTCCCTCCCCTCCCTCTTT 61.163 60.000 0.00 0.00 0.00 2.52
965 1023 2.520741 CTCGCTCTCTCCCTCCCC 60.521 72.222 0.00 0.00 0.00 4.81
1197 1275 1.153489 CTCCCACATCCTCTGCACG 60.153 63.158 0.00 0.00 0.00 5.34
1224 1302 3.381590 GGTCCTCCAAGCAATCAATTACC 59.618 47.826 0.00 0.00 0.00 2.85
1227 1305 2.094675 CGGTCCTCCAAGCAATCAATT 58.905 47.619 0.00 0.00 0.00 2.32
1298 1376 7.037438 CCAATACAGGTTTGATGAATGAAAGG 58.963 38.462 0.00 0.00 0.00 3.11
1326 1404 2.567985 GAAAACAGGTCCTTCCGAACA 58.432 47.619 0.00 0.00 41.99 3.18
1470 1555 3.611549 GCGAGGCAAAACAGTACTACTAC 59.388 47.826 0.00 0.00 0.00 2.73
1473 1558 2.409975 TGCGAGGCAAAACAGTACTAC 58.590 47.619 0.00 0.00 34.76 2.73
1481 1566 3.429085 CAGTATTCATGCGAGGCAAAAC 58.571 45.455 0.00 0.00 43.62 2.43
1485 1572 2.694065 GCAGTATTCATGCGAGGCA 58.306 52.632 0.00 0.00 44.86 4.75
1569 1656 5.582665 AGGAAGAAGTAACAAGCGATGAATC 59.417 40.000 0.00 0.00 0.00 2.52
1571 1658 4.894784 AGGAAGAAGTAACAAGCGATGAA 58.105 39.130 0.00 0.00 0.00 2.57
1577 1719 3.372514 GCAGCTAGGAAGAAGTAACAAGC 59.627 47.826 0.00 0.00 0.00 4.01
1578 1720 4.569943 TGCAGCTAGGAAGAAGTAACAAG 58.430 43.478 0.00 0.00 0.00 3.16
1605 1756 1.611936 GCGAAGGCCTTTCTTCTTCCT 60.612 52.381 21.54 0.00 40.56 3.36
1661 1814 5.061853 TCAGAGATGAAATATGCTCCAAGC 58.938 41.667 0.00 0.00 42.82 4.01
1673 1826 4.082026 TGCGAGTCTTCATCAGAGATGAAA 60.082 41.667 19.41 10.49 37.55 2.69
1718 1871 5.180304 CCAAGAGAGAAACTAAACCTTGAGC 59.820 44.000 0.00 0.00 32.18 4.26
1748 1901 2.030007 CGGTACTCGAGTTAACCAACCA 60.030 50.000 28.54 6.56 42.43 3.67
1879 2044 9.177608 ACAGTTGCACATTAAGATATGTTGTAT 57.822 29.630 0.00 0.00 36.64 2.29
1890 2099 8.801715 AAGTTTAATCACAGTTGCACATTAAG 57.198 30.769 0.00 0.00 0.00 1.85
1972 2181 4.640201 GCATGTTCTTGCCAAACCTATAGA 59.360 41.667 0.00 0.00 36.60 1.98
2050 2259 2.494471 ACGGACGAGACATGGTCATAAA 59.506 45.455 0.00 0.00 35.98 1.40
2070 2279 6.699063 CACAGAAAAATGTCAAGCAAGAAAC 58.301 36.000 0.00 0.00 0.00 2.78
2082 2291 7.102993 ACTAAACTTTTGGCACAGAAAAATGT 58.897 30.769 0.00 0.00 42.39 2.71
2103 2312 5.235850 TCCCTACACAGCAATTTGACTAA 57.764 39.130 0.00 0.00 0.00 2.24
2110 2319 2.162681 GTGCTTCCCTACACAGCAATT 58.837 47.619 0.00 0.00 44.99 2.32
2123 2332 0.102300 AACTGGTTTTGCGTGCTTCC 59.898 50.000 0.00 0.00 0.00 3.46
2124 2333 1.199624 CAACTGGTTTTGCGTGCTTC 58.800 50.000 0.00 0.00 0.00 3.86
2125 2334 0.814457 TCAACTGGTTTTGCGTGCTT 59.186 45.000 0.00 0.00 0.00 3.91
2126 2335 0.381801 CTCAACTGGTTTTGCGTGCT 59.618 50.000 0.00 0.00 0.00 4.40
2127 2336 0.594796 CCTCAACTGGTTTTGCGTGC 60.595 55.000 0.00 0.00 0.00 5.34
2212 2424 8.767478 AAAAGAAATTCTGCATTTGATACTGG 57.233 30.769 0.00 0.00 35.02 4.00
2215 2427 9.860898 ACCTAAAAGAAATTCTGCATTTGATAC 57.139 29.630 0.00 0.00 35.02 2.24
2218 2433 7.950512 TGACCTAAAAGAAATTCTGCATTTGA 58.049 30.769 0.00 0.00 35.02 2.69
2301 2521 0.963856 CAGAGGCCGGGGGTTTTAAC 60.964 60.000 2.18 0.00 0.00 2.01
2302 2522 1.381076 CAGAGGCCGGGGGTTTTAA 59.619 57.895 2.18 0.00 0.00 1.52
2303 2523 3.083386 CAGAGGCCGGGGGTTTTA 58.917 61.111 2.18 0.00 0.00 1.52
2304 2524 4.678743 GCAGAGGCCGGGGGTTTT 62.679 66.667 2.18 0.00 0.00 2.43
2309 2529 3.426309 ATTGATGCAGAGGCCGGGG 62.426 63.158 2.18 0.00 40.13 5.73
2310 2530 1.895707 GATTGATGCAGAGGCCGGG 60.896 63.158 2.18 0.00 40.13 5.73
2311 2531 2.249535 CGATTGATGCAGAGGCCGG 61.250 63.158 0.00 0.00 40.13 6.13
2312 2532 0.602106 ATCGATTGATGCAGAGGCCG 60.602 55.000 0.00 0.00 40.13 6.13
2313 2533 0.873054 CATCGATTGATGCAGAGGCC 59.127 55.000 10.05 0.00 45.06 5.19
2322 2542 1.270785 TGGCCGTATGCATCGATTGAT 60.271 47.619 16.69 0.00 43.89 2.57
2323 2543 0.105778 TGGCCGTATGCATCGATTGA 59.894 50.000 16.69 0.00 43.89 2.57
2324 2544 1.129251 GATGGCCGTATGCATCGATTG 59.871 52.381 16.69 0.00 43.89 2.67
2325 2545 1.002430 AGATGGCCGTATGCATCGATT 59.998 47.619 16.69 0.00 43.89 3.34
2326 2546 0.610174 AGATGGCCGTATGCATCGAT 59.390 50.000 16.69 0.00 43.89 3.59
2327 2547 0.392706 AAGATGGCCGTATGCATCGA 59.607 50.000 16.69 0.00 43.89 3.59
2328 2548 1.229428 AAAGATGGCCGTATGCATCG 58.771 50.000 0.19 7.03 43.89 3.84
2329 2549 5.376854 AAATAAAGATGGCCGTATGCATC 57.623 39.130 0.19 0.00 43.89 3.91
2330 2550 4.218417 GGAAATAAAGATGGCCGTATGCAT 59.782 41.667 3.79 3.79 43.89 3.96
2331 2551 3.568007 GGAAATAAAGATGGCCGTATGCA 59.432 43.478 0.00 0.00 43.89 3.96
2332 2552 3.057526 GGGAAATAAAGATGGCCGTATGC 60.058 47.826 0.00 0.00 40.16 3.14
2333 2553 4.216257 CAGGGAAATAAAGATGGCCGTATG 59.784 45.833 0.00 0.00 0.00 2.39
2334 2554 4.104102 TCAGGGAAATAAAGATGGCCGTAT 59.896 41.667 0.00 0.00 0.00 3.06
2335 2555 3.456644 TCAGGGAAATAAAGATGGCCGTA 59.543 43.478 0.00 0.00 0.00 4.02
2336 2556 2.241176 TCAGGGAAATAAAGATGGCCGT 59.759 45.455 0.00 0.00 0.00 5.68
2337 2557 2.930950 TCAGGGAAATAAAGATGGCCG 58.069 47.619 0.00 0.00 0.00 6.13
2338 2558 5.187772 ACTTTTCAGGGAAATAAAGATGGCC 59.812 40.000 0.00 0.00 31.34 5.36
2339 2559 6.286240 ACTTTTCAGGGAAATAAAGATGGC 57.714 37.500 0.00 0.00 31.34 4.40
2340 2560 8.802267 TGTTACTTTTCAGGGAAATAAAGATGG 58.198 33.333 0.00 0.00 31.34 3.51
2343 2563 9.807921 AGATGTTACTTTTCAGGGAAATAAAGA 57.192 29.630 0.00 0.00 31.34 2.52
2348 2568 9.588096 AGTTAAGATGTTACTTTTCAGGGAAAT 57.412 29.630 0.00 0.00 31.34 2.17
2349 2569 8.990163 AGTTAAGATGTTACTTTTCAGGGAAA 57.010 30.769 0.00 0.00 0.00 3.13
2350 2570 8.990163 AAGTTAAGATGTTACTTTTCAGGGAA 57.010 30.769 0.00 0.00 0.00 3.97
2351 2571 8.437575 AGAAGTTAAGATGTTACTTTTCAGGGA 58.562 33.333 0.00 0.00 0.00 4.20
2427 2647 2.178764 TCCACCTCTCTAGCATCAGGAT 59.821 50.000 0.00 0.00 0.00 3.24
2432 2652 6.995091 ACAAAATATTCCACCTCTCTAGCATC 59.005 38.462 0.00 0.00 0.00 3.91
2469 2689 8.025243 AGCATTCATTTCAACAAATTTAGCAG 57.975 30.769 0.00 0.00 28.97 4.24
2586 2806 4.961438 AGCAAATCCTTTTCACATTGGT 57.039 36.364 0.00 0.00 0.00 3.67
2633 2853 3.003480 GCTTCATGTTGACCAGGTCTAC 58.997 50.000 23.19 23.19 38.40 2.59
2654 2874 0.250858 TGTGAACAGGGCAGGATGTG 60.251 55.000 0.00 0.00 39.31 3.21
2753 2979 4.757149 GCTTGTGCATACCCTAAAGGATAG 59.243 45.833 0.00 0.00 37.95 2.08
2822 3048 6.012658 TGTCATGGTAAGTCAAATTCTTGC 57.987 37.500 0.00 0.00 32.14 4.01
2893 3119 5.937540 TGATTGTGACTACATAAACCCACAG 59.062 40.000 0.00 0.00 36.53 3.66
2894 3120 5.703592 GTGATTGTGACTACATAAACCCACA 59.296 40.000 0.00 0.00 36.53 4.17
2909 3147 5.427378 TGAGAGAACTGTTTGTGATTGTGA 58.573 37.500 0.00 0.00 0.00 3.58
2910 3148 5.739752 TGAGAGAACTGTTTGTGATTGTG 57.260 39.130 0.00 0.00 0.00 3.33
2911 3149 6.204301 CAGATGAGAGAACTGTTTGTGATTGT 59.796 38.462 0.00 0.00 0.00 2.71
2912 3150 6.204301 ACAGATGAGAGAACTGTTTGTGATTG 59.796 38.462 0.00 0.00 41.21 2.67
2913 3151 6.204301 CACAGATGAGAGAACTGTTTGTGATT 59.796 38.462 10.59 0.00 41.93 2.57
2914 3152 5.699915 CACAGATGAGAGAACTGTTTGTGAT 59.300 40.000 10.59 0.00 41.93 3.06
3168 3417 9.133627 CATATTGTATCAGAAGAGTGAATACGG 57.866 37.037 0.00 0.00 0.00 4.02
3523 3772 8.642020 CAATATTAACTCAAAACAAGCTTCAGC 58.358 33.333 0.00 0.00 42.49 4.26
3529 3778 8.244113 AGCTACCAATATTAACTCAAAACAAGC 58.756 33.333 0.00 0.00 0.00 4.01
3558 3807 5.650266 CACATACAAACTGGCAAGGGTATAA 59.350 40.000 0.00 0.00 0.00 0.98
3765 4015 0.105401 TTTTGGTTCCAAGGGGGTCC 60.105 55.000 4.44 0.00 38.11 4.46
3817 4069 9.230122 TGCTTATTCAAAATGACAACTATGAGA 57.770 29.630 0.00 0.00 0.00 3.27
3822 4074 7.121168 CCTCCTGCTTATTCAAAATGACAACTA 59.879 37.037 0.00 0.00 0.00 2.24
3859 4111 4.818546 CCACACTGGACATTATTCATCTCC 59.181 45.833 0.00 0.00 40.96 3.71
4145 4399 3.716872 GGGATCCACTGATTCTCCCTTTA 59.283 47.826 15.23 0.00 32.30 1.85
4148 4402 1.296523 AGGGATCCACTGATTCTCCCT 59.703 52.381 15.23 2.55 37.82 4.20
4151 4405 2.224257 GCAGAGGGATCCACTGATTCTC 60.224 54.545 29.81 18.62 43.27 2.87
4178 4433 0.037326 GAATCGCCGGGCTGATGATA 60.037 55.000 21.21 0.81 0.00 2.15
4245 4500 1.890573 GCCCACCACCAACATACATGT 60.891 52.381 2.69 2.69 44.20 3.21
4257 4512 2.706834 GGCCAATTACGCCCACCAC 61.707 63.158 0.00 0.00 40.78 4.16
4293 4548 4.452114 GGTGCATGATGAACATTATCGCTA 59.548 41.667 5.81 0.00 37.07 4.26
4297 4552 3.814842 TCCGGTGCATGATGAACATTATC 59.185 43.478 5.81 0.00 37.07 1.75
4387 4642 1.134521 TGCCGAATCTCGCCAACTATT 60.135 47.619 0.00 0.00 38.82 1.73
4403 4659 5.808540 AGAACATTTGATTTCATTCATGCCG 59.191 36.000 0.00 0.00 0.00 5.69
4504 4766 9.330063 TGATTGACATAAGTAATCATCAGTTCC 57.670 33.333 0.00 0.00 36.28 3.62
4521 4783 4.274978 TGCATCTTCCATGTGATTGACAT 58.725 39.130 0.00 0.00 46.98 3.06
4556 4818 6.018425 CGAGCATCTCTTTTGTTATGTGCTAT 60.018 38.462 0.00 0.00 41.29 2.97
4557 4819 5.291858 CGAGCATCTCTTTTGTTATGTGCTA 59.708 40.000 0.00 0.00 41.29 3.49
4558 4820 4.093998 CGAGCATCTCTTTTGTTATGTGCT 59.906 41.667 0.00 0.00 43.62 4.40
4559 4821 4.337763 CGAGCATCTCTTTTGTTATGTGC 58.662 43.478 0.00 0.00 0.00 4.57
4560 4822 4.201851 CCCGAGCATCTCTTTTGTTATGTG 60.202 45.833 0.00 0.00 0.00 3.21
4577 4839 4.156008 ACAGAAATTTTGATACACCCGAGC 59.844 41.667 0.00 0.00 0.00 5.03
4583 4845 9.463443 AAGCTAAACACAGAAATTTTGATACAC 57.537 29.630 0.00 0.00 0.00 2.90
4586 4848 9.820229 CGTAAGCTAAACACAGAAATTTTGATA 57.180 29.630 0.00 0.00 0.00 2.15
4612 4878 3.684788 CCTCCACGGCTATATGTATTTGC 59.315 47.826 0.00 0.00 0.00 3.68
4621 4887 1.491668 TTGCTTCCTCCACGGCTATA 58.508 50.000 0.00 0.00 0.00 1.31
4623 4889 0.178068 GATTGCTTCCTCCACGGCTA 59.822 55.000 0.00 0.00 0.00 3.93
4624 4890 1.078143 GATTGCTTCCTCCACGGCT 60.078 57.895 0.00 0.00 0.00 5.52
4633 4899 0.035439 TTGTCTCCCGGATTGCTTCC 60.035 55.000 0.73 0.00 41.59 3.46
4651 4917 2.951642 CCATGTACTGGCGAATGGAATT 59.048 45.455 2.21 0.00 41.84 2.17
4681 4983 4.640364 TGTGAGTATGCATCACTTTGTCA 58.360 39.130 17.40 6.30 45.87 3.58
4684 4986 6.185852 TGATTGTGAGTATGCATCACTTTG 57.814 37.500 17.40 0.00 45.87 2.77
4891 5193 7.278135 AGACACGTATAGACATTCTAGTGGTA 58.722 38.462 0.00 0.00 31.67 3.25
4999 5301 3.181475 GGCCGTGATCATCAGAAAGTAGA 60.181 47.826 0.00 0.00 0.00 2.59
5007 5314 1.019673 CTTTGGGCCGTGATCATCAG 58.980 55.000 0.00 0.00 0.00 2.90
5010 5317 0.107017 CTCCTTTGGGCCGTGATCAT 60.107 55.000 0.00 0.00 0.00 2.45
5018 5325 1.536073 GGTTTCTGCTCCTTTGGGCC 61.536 60.000 0.00 0.00 0.00 5.80
5027 5334 7.051000 AGTTAGAATTATGGAGGTTTCTGCTC 58.949 38.462 0.00 0.00 32.15 4.26
5036 5343 6.043243 TGAGGCCTAAGTTAGAATTATGGAGG 59.957 42.308 4.42 0.00 0.00 4.30
5037 5344 7.067496 TGAGGCCTAAGTTAGAATTATGGAG 57.933 40.000 4.42 0.00 0.00 3.86
5038 5345 7.633018 ATGAGGCCTAAGTTAGAATTATGGA 57.367 36.000 4.42 0.00 0.00 3.41
5039 5346 8.571336 CAAATGAGGCCTAAGTTAGAATTATGG 58.429 37.037 4.42 0.00 0.00 2.74
5040 5347 8.571336 CCAAATGAGGCCTAAGTTAGAATTATG 58.429 37.037 4.42 0.00 0.00 1.90
5041 5348 8.282256 ACCAAATGAGGCCTAAGTTAGAATTAT 58.718 33.333 4.42 0.00 0.00 1.28
5042 5349 7.639378 ACCAAATGAGGCCTAAGTTAGAATTA 58.361 34.615 4.42 0.00 0.00 1.40
5043 5350 6.494059 ACCAAATGAGGCCTAAGTTAGAATT 58.506 36.000 4.42 1.32 0.00 2.17
5044 5351 6.079712 ACCAAATGAGGCCTAAGTTAGAAT 57.920 37.500 4.42 0.00 0.00 2.40
5045 5352 5.514500 ACCAAATGAGGCCTAAGTTAGAA 57.486 39.130 4.42 0.00 0.00 2.10
5046 5353 5.013704 TGAACCAAATGAGGCCTAAGTTAGA 59.986 40.000 4.42 0.00 0.00 2.10
5047 5354 5.253330 TGAACCAAATGAGGCCTAAGTTAG 58.747 41.667 4.42 0.00 0.00 2.34
5048 5355 5.249780 TGAACCAAATGAGGCCTAAGTTA 57.750 39.130 4.42 0.00 0.00 2.24
5049 5356 4.112634 TGAACCAAATGAGGCCTAAGTT 57.887 40.909 4.42 0.00 0.00 2.66
5050 5357 3.806949 TGAACCAAATGAGGCCTAAGT 57.193 42.857 4.42 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.