Multiple sequence alignment - TraesCS1D01G051700

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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 TraesCS1D01G051700 chr1D 100.000 4582 0 0 1 4582 32478445 32483026 0.000000e+00 8462.0
1 TraesCS1D01G051700 chr1D 77.904 353 65 9 2259 2605 14484317 14483972 1.670000e-49 207.0
2 TraesCS1D01G051700 chr1D 74.317 366 64 17 2254 2615 210477520 210477859 1.340000e-25 128.0
3 TraesCS1D01G051700 chr1B 95.869 1743 56 10 528 2264 49933110 49934842 0.000000e+00 2806.0
4 TraesCS1D01G051700 chr1B 90.919 936 60 12 3404 4319 49937206 49938136 0.000000e+00 1234.0
5 TraesCS1D01G051700 chr1B 91.709 796 44 5 2603 3396 49934838 49935613 0.000000e+00 1085.0
6 TraesCS1D01G051700 chr1B 83.422 561 87 3 739 1293 685366084 685365524 2.440000e-142 516.0
7 TraesCS1D01G051700 chr1B 93.609 266 7 5 1 257 49932554 49932818 5.560000e-104 388.0
8 TraesCS1D01G051700 chr1B 84.030 263 13 13 290 524 49932818 49933079 4.610000e-55 226.0
9 TraesCS1D01G051700 chr1B 90.526 95 8 1 4356 4450 49938222 49938315 1.730000e-24 124.0
10 TraesCS1D01G051700 chr1A 92.428 1215 43 12 311 1478 31161080 31162292 0.000000e+00 1688.0
11 TraesCS1D01G051700 chr1A 94.480 942 43 3 2460 3396 31174660 31175597 0.000000e+00 1443.0
12 TraesCS1D01G051700 chr1A 93.496 492 23 4 3404 3893 31176044 31176528 0.000000e+00 723.0
13 TraesCS1D01G051700 chr1A 91.076 381 26 6 3942 4319 31176528 31176903 4.090000e-140 508.0
14 TraesCS1D01G051700 chr1A 95.349 258 8 1 1476 1733 31174412 31174665 1.530000e-109 407.0
15 TraesCS1D01G051700 chr1A 90.323 310 16 7 1 306 31160619 31160918 1.190000e-105 394.0
16 TraesCS1D01G051700 chr1A 92.135 267 19 1 4318 4582 31176965 31177231 4.330000e-100 375.0
17 TraesCS1D01G051700 chr1A 79.885 174 33 2 2312 2483 15433218 15433391 4.810000e-25 126.0
18 TraesCS1D01G051700 chr5B 81.720 558 93 5 739 1290 61369162 61369716 1.500000e-124 457.0
19 TraesCS1D01G051700 chr4B 82.184 348 60 2 2258 2604 486624536 486624190 9.640000e-77 298.0
20 TraesCS1D01G051700 chr4B 94.118 85 4 1 1363 1446 447451794 447451710 1.340000e-25 128.0
21 TraesCS1D01G051700 chr7D 78.857 350 63 10 2259 2604 24116185 24116527 4.610000e-55 226.0
22 TraesCS1D01G051700 chr3D 75.637 353 76 8 2256 2605 582229316 582228971 2.840000e-37 167.0
23 TraesCS1D01G051700 chr4D 75.482 363 62 13 2246 2604 38525499 38525838 7.940000e-33 152.0
24 TraesCS1D01G051700 chr3B 76.027 292 59 9 2256 2544 779196932 779197215 1.720000e-29 141.0
25 TraesCS1D01G051700 chr2D 74.862 362 64 13 2246 2604 452994109 452993772 6.180000e-29 139.0
26 TraesCS1D01G051700 chr7A 95.294 85 3 1 1363 1446 181833294 181833210 2.880000e-27 134.0
27 TraesCS1D01G051700 chr4A 82.667 150 25 1 2341 2489 697989543 697989394 1.030000e-26 132.0
28 TraesCS1D01G051700 chr4A 93.182 44 3 0 2440 2483 86703053 86703010 1.060000e-06 65.8
29 TraesCS1D01G051700 chr3A 91.489 94 6 2 1358 1449 57262242 57262149 1.340000e-25 128.0
30 TraesCS1D01G051700 chr2B 93.182 88 5 1 1360 1446 483452950 483453037 1.340000e-25 128.0
31 TraesCS1D01G051700 chr2B 92.857 42 2 1 2257 2298 414804100 414804140 4.950000e-05 60.2
32 TraesCS1D01G051700 chrUn 92.941 85 5 1 1363 1446 31863630 31863546 6.230000e-24 122.0
33 TraesCS1D01G051700 chr2A 91.954 87 6 1 1363 1448 96074910 96074996 2.240000e-23 121.0
34 TraesCS1D01G051700 chr2A 91.860 86 6 1 1362 1446 650624329 650624414 8.050000e-23 119.0
35 TraesCS1D01G051700 chr6A 100.000 50 0 0 3288 3337 490323130 490323081 4.880000e-15 93.5


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 TraesCS1D01G051700 chr1D 32478445 32483026 4581 False 8462.000000 8462 100.000000 1 4582 1 chr1D.!!$F1 4581
1 TraesCS1D01G051700 chr1B 49932554 49938315 5761 False 977.166667 2806 91.110333 1 4450 6 chr1B.!!$F1 4449
2 TraesCS1D01G051700 chr1B 685365524 685366084 560 True 516.000000 516 83.422000 739 1293 1 chr1B.!!$R1 554
3 TraesCS1D01G051700 chr1A 31160619 31162292 1673 False 1041.000000 1688 91.375500 1 1478 2 chr1A.!!$F2 1477
4 TraesCS1D01G051700 chr1A 31174412 31177231 2819 False 691.200000 1443 93.307200 1476 4582 5 chr1A.!!$F3 3106
5 TraesCS1D01G051700 chr5B 61369162 61369716 554 False 457.000000 457 81.720000 739 1290 1 chr5B.!!$F1 551

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
841 1086 0.113972 TGGGGAAACATGTGATGGCA 59.886 50.000 0.0 0.0 33.6 4.92 F
2078 2327 1.343142 AGTAACGATGCTGTGTGTCCA 59.657 47.619 0.0 0.0 0.0 4.02 F
2407 2656 0.106918 AGAGAAAACCCACCAACGCA 60.107 50.000 0.0 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2388 2637 0.106918 TGCGTTGGTGGGTTTTCTCT 60.107 50.0 0.00 0.00 0.00 3.10 R
3563 5476 0.098905 GTCAGTCGCGATCTGCAGTA 59.901 55.0 24.59 11.57 46.97 2.74 R
3923 5853 0.535335 TAGCCCAACGATGACACCTC 59.465 55.0 0.00 0.00 0.00 3.85 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
61 65 2.939103 CGTGGAGGAAGAAATAGCAAGG 59.061 50.000 0.00 0.00 0.00 3.61
211 224 3.131223 TGCTCTTCAGTACTGTAGATGGC 59.869 47.826 26.51 25.49 36.61 4.40
221 234 3.209410 ACTGTAGATGGCAAAGCATAGC 58.791 45.455 0.00 0.00 0.00 2.97
388 562 1.051812 AGCTGGCCTACGCTCATAAT 58.948 50.000 3.32 0.00 34.44 1.28
422 603 1.748493 TGTTTTGCACACCCAGAGAAC 59.252 47.619 0.00 0.00 0.00 3.01
425 606 0.546122 TTGCACACCCAGAGAACAGT 59.454 50.000 0.00 0.00 0.00 3.55
428 609 2.171659 TGCACACCCAGAGAACAGTTAA 59.828 45.455 0.00 0.00 0.00 2.01
429 610 3.211045 GCACACCCAGAGAACAGTTAAA 58.789 45.455 0.00 0.00 0.00 1.52
491 693 5.008415 TGCTGTTGTTTTTAAATTGGGCATG 59.992 36.000 0.00 0.00 0.00 4.06
706 941 7.453393 CCATATTAATTCTTGCTAGTGAGGGA 58.547 38.462 0.00 0.00 0.00 4.20
719 954 6.780522 TGCTAGTGAGGGAAATTAAGGTTTTT 59.219 34.615 0.00 0.00 0.00 1.94
765 1004 5.106948 GGTTCATGTGCATATTGAGATACCG 60.107 44.000 0.00 0.00 0.00 4.02
807 1046 1.538419 GCAAGGCTCGACTATGGTACC 60.538 57.143 4.43 4.43 0.00 3.34
841 1086 0.113972 TGGGGAAACATGTGATGGCA 59.886 50.000 0.00 0.00 33.60 4.92
1176 1421 1.590238 CGTGCTTGTCGAGATGATTCC 59.410 52.381 0.00 0.00 0.00 3.01
1377 1622 6.212791 AGCTGTGTTATACTCCCTCTGTAAAA 59.787 38.462 0.00 0.00 0.00 1.52
1447 1692 9.597681 TCTTATATTTCTTACGGAGGGAGTAAT 57.402 33.333 0.00 0.00 34.10 1.89
1680 1928 2.212812 TGCATGCCATGTCCAACTTA 57.787 45.000 16.68 0.00 0.00 2.24
1722 1970 5.192927 TGCTAACCCTTGGTATCTCAATTG 58.807 41.667 0.00 0.00 33.12 2.32
1838 2087 3.399440 TTCTTTTGCCGGAAATGCATT 57.601 38.095 5.05 5.99 38.76 3.56
1856 2105 8.774890 AATGCATTCAAACATACTGCAAAATA 57.225 26.923 5.99 0.00 45.03 1.40
1907 2156 3.435327 TGACGTGTCCTGATACAAAATGC 59.565 43.478 0.00 0.00 0.00 3.56
1926 2175 1.947456 GCGAAGGTGTTGTTTCTCCTT 59.053 47.619 0.00 0.00 41.87 3.36
1928 2177 3.059120 GCGAAGGTGTTGTTTCTCCTTAC 60.059 47.826 0.00 0.00 40.11 2.34
2069 2318 3.197766 TGGAGGATGAAAGTAACGATGCT 59.802 43.478 0.00 0.00 0.00 3.79
2078 2327 1.343142 AGTAACGATGCTGTGTGTCCA 59.657 47.619 0.00 0.00 0.00 4.02
2102 2351 3.683365 TGTCTATTCAGCTTCTGCACA 57.317 42.857 0.00 0.00 42.74 4.57
2114 2363 3.499918 GCTTCTGCACACTTTGTACATCT 59.500 43.478 0.00 0.00 39.41 2.90
2194 2443 7.506261 GGAGGTAGGAGAACTTTATCTCACATA 59.494 40.741 6.64 0.00 46.24 2.29
2272 2521 9.994017 ACTACTAATATATACTCCCTCCTTTCC 57.006 37.037 0.00 0.00 0.00 3.13
2273 2522 7.957992 ACTAATATATACTCCCTCCTTTCCG 57.042 40.000 0.00 0.00 0.00 4.30
2274 2523 6.896307 ACTAATATATACTCCCTCCTTTCCGG 59.104 42.308 0.00 0.00 0.00 5.14
2275 2524 3.632420 ATATACTCCCTCCTTTCCGGT 57.368 47.619 0.00 0.00 0.00 5.28
2276 2525 2.265526 ATACTCCCTCCTTTCCGGTT 57.734 50.000 0.00 0.00 0.00 4.44
2277 2526 2.034436 TACTCCCTCCTTTCCGGTTT 57.966 50.000 0.00 0.00 0.00 3.27
2278 2527 2.034436 ACTCCCTCCTTTCCGGTTTA 57.966 50.000 0.00 0.00 0.00 2.01
2279 2528 2.558974 ACTCCCTCCTTTCCGGTTTAT 58.441 47.619 0.00 0.00 0.00 1.40
2280 2529 3.727948 ACTCCCTCCTTTCCGGTTTATA 58.272 45.455 0.00 0.00 0.00 0.98
2281 2530 3.710165 ACTCCCTCCTTTCCGGTTTATAG 59.290 47.826 0.00 0.00 0.00 1.31
2282 2531 3.710165 CTCCCTCCTTTCCGGTTTATAGT 59.290 47.826 0.00 0.00 0.00 2.12
2283 2532 3.453353 TCCCTCCTTTCCGGTTTATAGTG 59.547 47.826 0.00 0.00 0.00 2.74
2284 2533 3.433173 CCCTCCTTTCCGGTTTATAGTGG 60.433 52.174 0.00 0.00 0.00 4.00
2285 2534 3.199289 CCTCCTTTCCGGTTTATAGTGGT 59.801 47.826 0.00 0.00 0.00 4.16
2286 2535 4.439968 CTCCTTTCCGGTTTATAGTGGTC 58.560 47.826 0.00 0.00 0.00 4.02
2287 2536 3.839490 TCCTTTCCGGTTTATAGTGGTCA 59.161 43.478 0.00 0.00 0.00 4.02
2288 2537 4.472108 TCCTTTCCGGTTTATAGTGGTCAT 59.528 41.667 0.00 0.00 0.00 3.06
2289 2538 4.814771 CCTTTCCGGTTTATAGTGGTCATC 59.185 45.833 0.00 0.00 0.00 2.92
2290 2539 5.396436 CCTTTCCGGTTTATAGTGGTCATCT 60.396 44.000 0.00 0.00 0.00 2.90
2291 2540 5.687166 TTCCGGTTTATAGTGGTCATCTT 57.313 39.130 0.00 0.00 0.00 2.40
2292 2541 6.795144 TTCCGGTTTATAGTGGTCATCTTA 57.205 37.500 0.00 0.00 0.00 2.10
2293 2542 6.795144 TCCGGTTTATAGTGGTCATCTTAA 57.205 37.500 0.00 0.00 0.00 1.85
2294 2543 7.185318 TCCGGTTTATAGTGGTCATCTTAAA 57.815 36.000 0.00 0.00 0.00 1.52
2295 2544 7.622713 TCCGGTTTATAGTGGTCATCTTAAAA 58.377 34.615 0.00 0.00 0.00 1.52
2296 2545 8.102047 TCCGGTTTATAGTGGTCATCTTAAAAA 58.898 33.333 0.00 0.00 0.00 1.94
2337 2586 9.587772 TTTATGAGTCTCAATTCTAGTACTTGC 57.412 33.333 6.64 0.00 0.00 4.01
2338 2587 5.967088 TGAGTCTCAATTCTAGTACTTGCC 58.033 41.667 0.00 0.00 0.00 4.52
2339 2588 5.717178 TGAGTCTCAATTCTAGTACTTGCCT 59.283 40.000 0.00 0.00 0.00 4.75
2340 2589 6.211584 TGAGTCTCAATTCTAGTACTTGCCTT 59.788 38.462 0.00 0.00 0.00 4.35
2341 2590 6.635755 AGTCTCAATTCTAGTACTTGCCTTC 58.364 40.000 0.00 0.00 0.00 3.46
2342 2591 6.211584 AGTCTCAATTCTAGTACTTGCCTTCA 59.788 38.462 0.00 0.00 0.00 3.02
2343 2592 6.311690 GTCTCAATTCTAGTACTTGCCTTCAC 59.688 42.308 0.00 0.00 0.00 3.18
2344 2593 6.014584 TCTCAATTCTAGTACTTGCCTTCACA 60.015 38.462 0.00 0.00 0.00 3.58
2345 2594 6.711277 TCAATTCTAGTACTTGCCTTCACAT 58.289 36.000 0.00 0.00 0.00 3.21
2346 2595 6.595326 TCAATTCTAGTACTTGCCTTCACATG 59.405 38.462 0.00 0.00 0.00 3.21
2347 2596 5.483685 TTCTAGTACTTGCCTTCACATGT 57.516 39.130 0.00 0.00 0.00 3.21
2348 2597 5.483685 TCTAGTACTTGCCTTCACATGTT 57.516 39.130 0.00 0.00 0.00 2.71
2349 2598 5.479306 TCTAGTACTTGCCTTCACATGTTC 58.521 41.667 0.00 0.00 0.00 3.18
2350 2599 4.085357 AGTACTTGCCTTCACATGTTCA 57.915 40.909 0.00 0.00 0.00 3.18
2351 2600 4.067896 AGTACTTGCCTTCACATGTTCAG 58.932 43.478 0.00 0.00 0.00 3.02
2352 2601 3.213206 ACTTGCCTTCACATGTTCAGA 57.787 42.857 0.00 0.00 0.00 3.27
2353 2602 3.759581 ACTTGCCTTCACATGTTCAGAT 58.240 40.909 0.00 0.00 0.00 2.90
2354 2603 4.147321 ACTTGCCTTCACATGTTCAGATT 58.853 39.130 0.00 0.00 0.00 2.40
2355 2604 4.586001 ACTTGCCTTCACATGTTCAGATTT 59.414 37.500 0.00 0.00 0.00 2.17
2356 2605 4.771590 TGCCTTCACATGTTCAGATTTC 57.228 40.909 0.00 0.00 0.00 2.17
2357 2606 4.143543 TGCCTTCACATGTTCAGATTTCA 58.856 39.130 0.00 0.00 0.00 2.69
2358 2607 4.583907 TGCCTTCACATGTTCAGATTTCAA 59.416 37.500 0.00 0.00 0.00 2.69
2359 2608 5.159209 GCCTTCACATGTTCAGATTTCAAG 58.841 41.667 0.00 0.00 0.00 3.02
2360 2609 5.706916 CCTTCACATGTTCAGATTTCAAGG 58.293 41.667 0.00 0.00 0.00 3.61
2361 2610 5.242393 CCTTCACATGTTCAGATTTCAAGGT 59.758 40.000 0.00 0.00 0.00 3.50
2362 2611 5.694231 TCACATGTTCAGATTTCAAGGTG 57.306 39.130 0.00 0.00 0.00 4.00
2363 2612 4.022935 TCACATGTTCAGATTTCAAGGTGC 60.023 41.667 0.00 0.00 0.00 5.01
2364 2613 3.890756 ACATGTTCAGATTTCAAGGTGCA 59.109 39.130 0.00 0.00 0.00 4.57
2365 2614 4.525487 ACATGTTCAGATTTCAAGGTGCAT 59.475 37.500 0.00 0.00 0.00 3.96
2366 2615 5.011329 ACATGTTCAGATTTCAAGGTGCATT 59.989 36.000 0.00 0.00 0.00 3.56
2367 2616 6.209192 ACATGTTCAGATTTCAAGGTGCATTA 59.791 34.615 0.00 0.00 0.00 1.90
2368 2617 6.647334 TGTTCAGATTTCAAGGTGCATTAA 57.353 33.333 0.00 0.00 0.00 1.40
2369 2618 7.230849 TGTTCAGATTTCAAGGTGCATTAAT 57.769 32.000 0.00 0.00 0.00 1.40
2370 2619 7.315142 TGTTCAGATTTCAAGGTGCATTAATC 58.685 34.615 0.00 0.00 0.00 1.75
2371 2620 7.039853 TGTTCAGATTTCAAGGTGCATTAATCA 60.040 33.333 0.00 0.00 0.00 2.57
2372 2621 6.855836 TCAGATTTCAAGGTGCATTAATCAC 58.144 36.000 0.00 8.62 0.00 3.06
2373 2622 6.660521 TCAGATTTCAAGGTGCATTAATCACT 59.339 34.615 13.91 0.00 34.97 3.41
2374 2623 7.177216 TCAGATTTCAAGGTGCATTAATCACTT 59.823 33.333 13.91 7.16 34.97 3.16
2375 2624 7.487189 CAGATTTCAAGGTGCATTAATCACTTC 59.513 37.037 13.91 3.66 34.97 3.01
2376 2625 6.647334 TTTCAAGGTGCATTAATCACTTCA 57.353 33.333 13.91 0.90 34.97 3.02
2377 2626 6.839124 TTCAAGGTGCATTAATCACTTCAT 57.161 33.333 13.91 0.00 34.97 2.57
2378 2627 6.198650 TCAAGGTGCATTAATCACTTCATG 57.801 37.500 13.91 0.00 34.97 3.07
2379 2628 4.644103 AGGTGCATTAATCACTTCATGC 57.356 40.909 13.91 0.00 40.72 4.06
2380 2629 4.018490 AGGTGCATTAATCACTTCATGCA 58.982 39.130 13.91 1.57 45.23 3.96
2383 2632 5.001237 TGCATTAATCACTTCATGCAAGG 57.999 39.130 3.24 0.00 44.74 3.61
2384 2633 4.705991 TGCATTAATCACTTCATGCAAGGA 59.294 37.500 3.24 0.00 44.74 3.36
2385 2634 5.361571 TGCATTAATCACTTCATGCAAGGAT 59.638 36.000 3.24 6.51 44.74 3.24
2386 2635 5.919141 GCATTAATCACTTCATGCAAGGATC 59.081 40.000 0.00 0.00 40.27 3.36
2387 2636 6.460537 GCATTAATCACTTCATGCAAGGATCA 60.461 38.462 0.00 0.00 40.27 2.92
2388 2637 7.485810 CATTAATCACTTCATGCAAGGATCAA 58.514 34.615 0.00 3.77 36.26 2.57
2389 2638 5.578005 AATCACTTCATGCAAGGATCAAG 57.422 39.130 0.00 0.00 36.26 3.02
2390 2639 4.290711 TCACTTCATGCAAGGATCAAGA 57.709 40.909 0.00 0.00 36.26 3.02
2391 2640 4.259356 TCACTTCATGCAAGGATCAAGAG 58.741 43.478 0.00 0.00 36.26 2.85
2392 2641 4.019950 TCACTTCATGCAAGGATCAAGAGA 60.020 41.667 0.00 0.00 36.26 3.10
2393 2642 4.698780 CACTTCATGCAAGGATCAAGAGAA 59.301 41.667 0.00 0.00 36.26 2.87
2394 2643 5.182570 CACTTCATGCAAGGATCAAGAGAAA 59.817 40.000 0.00 0.00 36.26 2.52
2395 2644 5.771666 ACTTCATGCAAGGATCAAGAGAAAA 59.228 36.000 0.00 0.00 36.26 2.29
2396 2645 5.633830 TCATGCAAGGATCAAGAGAAAAC 57.366 39.130 0.00 0.00 0.00 2.43
2397 2646 4.460382 TCATGCAAGGATCAAGAGAAAACC 59.540 41.667 0.00 0.00 0.00 3.27
2398 2647 3.157087 TGCAAGGATCAAGAGAAAACCC 58.843 45.455 0.00 0.00 0.00 4.11
2399 2648 3.157087 GCAAGGATCAAGAGAAAACCCA 58.843 45.455 0.00 0.00 0.00 4.51
2400 2649 3.057245 GCAAGGATCAAGAGAAAACCCAC 60.057 47.826 0.00 0.00 0.00 4.61
2401 2650 3.441500 AGGATCAAGAGAAAACCCACC 57.558 47.619 0.00 0.00 0.00 4.61
2402 2651 2.716424 AGGATCAAGAGAAAACCCACCA 59.284 45.455 0.00 0.00 0.00 4.17
2403 2652 3.140144 AGGATCAAGAGAAAACCCACCAA 59.860 43.478 0.00 0.00 0.00 3.67
2404 2653 3.255888 GGATCAAGAGAAAACCCACCAAC 59.744 47.826 0.00 0.00 0.00 3.77
2405 2654 2.294074 TCAAGAGAAAACCCACCAACG 58.706 47.619 0.00 0.00 0.00 4.10
2406 2655 1.029681 AAGAGAAAACCCACCAACGC 58.970 50.000 0.00 0.00 0.00 4.84
2407 2656 0.106918 AGAGAAAACCCACCAACGCA 60.107 50.000 0.00 0.00 0.00 5.24
2408 2657 0.741915 GAGAAAACCCACCAACGCAA 59.258 50.000 0.00 0.00 0.00 4.85
2429 2678 8.150300 CGCAAGTTGAAGTTATTAGTCATTTG 57.850 34.615 7.16 0.00 0.00 2.32
2430 2679 7.271223 CGCAAGTTGAAGTTATTAGTCATTTGG 59.729 37.037 7.16 0.00 0.00 3.28
2431 2680 8.082242 GCAAGTTGAAGTTATTAGTCATTTGGT 58.918 33.333 7.16 0.00 0.00 3.67
2432 2681 9.398170 CAAGTTGAAGTTATTAGTCATTTGGTG 57.602 33.333 0.00 0.00 0.00 4.17
2433 2682 8.110860 AGTTGAAGTTATTAGTCATTTGGTGG 57.889 34.615 0.00 0.00 0.00 4.61
2434 2683 7.724061 AGTTGAAGTTATTAGTCATTTGGTGGT 59.276 33.333 0.00 0.00 0.00 4.16
2435 2684 7.447374 TGAAGTTATTAGTCATTTGGTGGTG 57.553 36.000 0.00 0.00 0.00 4.17
2436 2685 7.227873 TGAAGTTATTAGTCATTTGGTGGTGA 58.772 34.615 0.00 0.00 0.00 4.02
2437 2686 7.888021 TGAAGTTATTAGTCATTTGGTGGTGAT 59.112 33.333 0.00 0.00 0.00 3.06
2438 2687 8.650143 AAGTTATTAGTCATTTGGTGGTGATT 57.350 30.769 0.00 0.00 0.00 2.57
2439 2688 8.281212 AGTTATTAGTCATTTGGTGGTGATTC 57.719 34.615 0.00 0.00 0.00 2.52
2440 2689 7.888021 AGTTATTAGTCATTTGGTGGTGATTCA 59.112 33.333 0.00 0.00 0.00 2.57
2441 2690 8.686334 GTTATTAGTCATTTGGTGGTGATTCAT 58.314 33.333 0.00 0.00 0.00 2.57
2442 2691 6.513806 TTAGTCATTTGGTGGTGATTCATG 57.486 37.500 0.00 0.00 0.00 3.07
2443 2692 3.194116 AGTCATTTGGTGGTGATTCATGC 59.806 43.478 0.00 0.00 0.00 4.06
2444 2693 3.056678 GTCATTTGGTGGTGATTCATGCA 60.057 43.478 0.00 0.00 0.00 3.96
2445 2694 3.770388 TCATTTGGTGGTGATTCATGCAT 59.230 39.130 0.00 0.00 0.00 3.96
2446 2695 3.596310 TTTGGTGGTGATTCATGCATG 57.404 42.857 21.07 21.07 0.00 4.06
2447 2696 0.818938 TGGTGGTGATTCATGCATGC 59.181 50.000 22.25 11.82 0.00 4.06
2448 2697 0.818938 GGTGGTGATTCATGCATGCA 59.181 50.000 25.04 25.04 0.00 3.96
2449 2698 1.470285 GGTGGTGATTCATGCATGCAC 60.470 52.381 25.37 21.56 0.00 4.57
2450 2699 1.475280 GTGGTGATTCATGCATGCACT 59.525 47.619 25.37 9.74 0.00 4.40
2451 2700 1.474879 TGGTGATTCATGCATGCACTG 59.525 47.619 25.37 20.99 0.00 3.66
2452 2701 1.475280 GGTGATTCATGCATGCACTGT 59.525 47.619 25.37 9.57 0.00 3.55
2453 2702 2.684374 GGTGATTCATGCATGCACTGTA 59.316 45.455 25.37 15.81 0.00 2.74
2454 2703 3.129113 GGTGATTCATGCATGCACTGTAA 59.871 43.478 25.37 14.80 0.00 2.41
2455 2704 4.202080 GGTGATTCATGCATGCACTGTAAT 60.202 41.667 25.37 18.74 0.00 1.89
2456 2705 5.345702 GTGATTCATGCATGCACTGTAATT 58.654 37.500 25.37 1.29 0.00 1.40
2457 2706 6.459985 GGTGATTCATGCATGCACTGTAATTA 60.460 38.462 25.37 13.40 0.00 1.40
2458 2707 6.974048 GTGATTCATGCATGCACTGTAATTAA 59.026 34.615 25.37 11.91 0.00 1.40
2459 2708 7.650504 GTGATTCATGCATGCACTGTAATTAAT 59.349 33.333 25.37 15.55 0.00 1.40
2460 2709 7.650104 TGATTCATGCATGCACTGTAATTAATG 59.350 33.333 25.37 13.33 0.00 1.90
2461 2710 5.283294 TCATGCATGCACTGTAATTAATGC 58.717 37.500 25.37 9.60 40.57 3.56
2466 2715 4.550577 TGCACTGTAATTAATGCATCGG 57.449 40.909 13.54 0.00 42.92 4.18
2471 2720 6.413818 GCACTGTAATTAATGCATCGGTAAAC 59.586 38.462 0.00 0.00 38.00 2.01
2515 2764 8.671384 TGAGTGTACTAATTAAGCACTTTTGT 57.329 30.769 13.80 0.00 40.06 2.83
2548 2797 9.201989 TGAAATGTATTCTACCACTCACTATCT 57.798 33.333 0.00 0.00 0.00 1.98
2563 2812 6.549364 ACTCACTATCTACCTTGATTGGAGAG 59.451 42.308 0.00 0.00 34.84 3.20
2588 2837 3.869065 TCCAAACTGAGCCCTATAAACG 58.131 45.455 0.00 0.00 0.00 3.60
3008 3261 8.740123 AGATCGCTATATATAAGATATCGGGG 57.260 38.462 9.22 0.00 0.00 5.73
3083 3336 8.028354 TGTAACTTTGCAATTGTTGGATATGAG 58.972 33.333 21.22 6.52 0.00 2.90
3131 3384 5.304101 GTGATATATTTTGCCCCCATTGTCA 59.696 40.000 0.00 0.00 0.00 3.58
3189 3442 2.359850 TTCAGACCGGGTGCATGC 60.360 61.111 11.82 11.82 0.00 4.06
3231 3484 1.395635 TACTTAGATGGGAAGCGCGA 58.604 50.000 12.10 0.00 0.00 5.87
3348 3601 3.547054 ACTCCAAAGGTAACGTGAACA 57.453 42.857 0.00 0.00 46.39 3.18
3396 3651 8.216423 AGATATCTGAGACAAGCAACCATAATT 58.784 33.333 3.89 0.00 0.00 1.40
3397 3652 6.690194 ATCTGAGACAAGCAACCATAATTC 57.310 37.500 0.00 0.00 0.00 2.17
3398 3653 4.631377 TCTGAGACAAGCAACCATAATTCG 59.369 41.667 0.00 0.00 0.00 3.34
3399 3654 4.323417 TGAGACAAGCAACCATAATTCGT 58.677 39.130 0.00 0.00 0.00 3.85
3400 3655 5.483811 TGAGACAAGCAACCATAATTCGTA 58.516 37.500 0.00 0.00 0.00 3.43
3401 3656 5.935206 TGAGACAAGCAACCATAATTCGTAA 59.065 36.000 0.00 0.00 0.00 3.18
3547 5460 2.079170 TCACAGCATTTTGGTCCCAA 57.921 45.000 0.00 0.00 0.00 4.12
3563 5476 0.899720 CCAAGGGATGCAAGCAACAT 59.100 50.000 0.00 0.00 0.00 2.71
3585 5498 2.161486 GCAGATCGCGACTGACACC 61.161 63.158 29.99 15.79 37.54 4.16
3594 5507 0.934901 CGACTGACACCGCGATATGG 60.935 60.000 8.23 0.00 0.00 2.74
3669 5582 0.512952 GCACCTCAACGCAACTACAG 59.487 55.000 0.00 0.00 0.00 2.74
3793 5710 1.625616 CGGCTTCTTGTACCGTAGTG 58.374 55.000 0.00 0.00 42.01 2.74
3800 5725 4.611310 TCTTGTACCGTAGTGAAGATCG 57.389 45.455 0.00 0.00 0.00 3.69
3803 5728 3.603532 TGTACCGTAGTGAAGATCGACT 58.396 45.455 0.00 1.47 0.00 4.18
3805 5730 1.132643 ACCGTAGTGAAGATCGACTGC 59.867 52.381 0.00 3.80 0.00 4.40
3829 5754 6.421202 GCGAAGTAGGATATTACAAAGGACTG 59.579 42.308 0.00 0.00 0.00 3.51
3933 5863 4.996976 ACACTGCGAGGTGTCATC 57.003 55.556 7.80 0.00 45.94 2.92
3945 5875 0.743345 GTGTCATCGTTGGGCTACCC 60.743 60.000 0.00 0.00 45.71 3.69
3965 5895 0.664224 ACTTACGCCCCGTTTGTTTG 59.336 50.000 0.00 0.00 41.54 2.93
3966 5896 0.662077 CTTACGCCCCGTTTGTTTGC 60.662 55.000 0.00 0.00 41.54 3.68
4021 5952 0.462581 GGCTCTGCCGATTGTCATGA 60.463 55.000 0.00 0.00 39.62 3.07
4069 6000 2.572290 GGATATGCCCGCTTACAAACT 58.428 47.619 0.00 0.00 0.00 2.66
4075 6006 1.608283 GCCCGCTTACAAACTCTCTGT 60.608 52.381 0.00 0.00 0.00 3.41
4102 6033 2.573462 AGTGATGTACTGCTGTCCCATT 59.427 45.455 0.00 0.00 38.49 3.16
4160 6091 6.157994 ACCTCTAATTACTTATTGGTGAGCCA 59.842 38.462 0.00 0.00 44.38 4.75
4270 6203 4.010349 AGGCAGCCTACAAAGACAATTAC 58.990 43.478 14.18 0.00 28.47 1.89
4303 6236 4.780021 AGTGGCCGAATTCTCCTATATGAT 59.220 41.667 3.52 0.00 0.00 2.45
4304 6237 5.958380 AGTGGCCGAATTCTCCTATATGATA 59.042 40.000 3.52 0.00 0.00 2.15
4345 6355 2.391926 TATATTGTGGAGCGGAGGGA 57.608 50.000 0.00 0.00 0.00 4.20
4346 6356 1.051812 ATATTGTGGAGCGGAGGGAG 58.948 55.000 0.00 0.00 0.00 4.30
4347 6357 0.325296 TATTGTGGAGCGGAGGGAGT 60.325 55.000 0.00 0.00 0.00 3.85
4348 6358 0.325296 ATTGTGGAGCGGAGGGAGTA 60.325 55.000 0.00 0.00 0.00 2.59
4349 6359 0.543410 TTGTGGAGCGGAGGGAGTAA 60.543 55.000 0.00 0.00 0.00 2.24
4350 6360 1.255667 TGTGGAGCGGAGGGAGTAAC 61.256 60.000 0.00 0.00 0.00 2.50
4351 6361 0.971447 GTGGAGCGGAGGGAGTAACT 60.971 60.000 0.00 0.00 0.00 2.24
4352 6362 0.252103 TGGAGCGGAGGGAGTAACTT 60.252 55.000 0.00 0.00 0.00 2.66
4353 6363 0.903236 GGAGCGGAGGGAGTAACTTT 59.097 55.000 0.00 0.00 0.00 2.66
4354 6364 1.278413 GGAGCGGAGGGAGTAACTTTT 59.722 52.381 0.00 0.00 0.00 2.27
4355 6365 2.498885 GGAGCGGAGGGAGTAACTTTTA 59.501 50.000 0.00 0.00 0.00 1.52
4356 6366 3.430513 GGAGCGGAGGGAGTAACTTTTAG 60.431 52.174 0.00 0.00 0.00 1.85
4357 6367 3.171528 AGCGGAGGGAGTAACTTTTAGT 58.828 45.455 0.00 0.00 0.00 2.24
4358 6368 3.056035 AGCGGAGGGAGTAACTTTTAGTG 60.056 47.826 0.00 0.00 0.00 2.74
4371 6381 4.901868 ACTTTTAGTGCTCCCGTCATTTA 58.098 39.130 0.00 0.00 0.00 1.40
4473 6483 7.598493 ACACTATTTATTTGTTGTTGTGGATGC 59.402 33.333 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 65 2.115291 GTGAATCCCCGCCAGCTTC 61.115 63.158 0.00 0.00 0.00 3.86
221 234 4.662468 TTCCATGAAGCTAGCTACTCAG 57.338 45.455 19.70 12.05 0.00 3.35
260 273 8.740906 ACTACGGTGATCTAATATGGAATGTAG 58.259 37.037 0.00 0.00 0.00 2.74
388 562 5.929697 TGCAAAACACAACAAAAATGTCA 57.070 30.435 0.00 0.00 0.00 3.58
429 610 1.117142 AGCACAAAAGCAGGCATGGT 61.117 50.000 0.00 0.00 39.32 3.55
599 834 6.092122 TGTTTAAAATGACTATGCTGTCTCCG 59.908 38.462 0.00 0.00 37.79 4.63
637 872 2.418334 GGACATACCTGGAAAGACCGTC 60.418 54.545 0.00 0.00 42.61 4.79
765 1004 4.440802 GCCGAGACATCTATACCATCATCC 60.441 50.000 0.00 0.00 0.00 3.51
807 1046 6.868622 TGTTTCCCCATAATTTAATGTTCCG 58.131 36.000 0.00 0.00 0.00 4.30
841 1086 6.119536 TGTAAACAAGATTATCCGAGGCATT 58.880 36.000 0.00 0.00 0.00 3.56
1176 1421 6.481976 TCCTTGTAATTATAACATCAGGTGCG 59.518 38.462 0.00 0.00 30.22 5.34
1583 1828 3.103742 ACCCTCAGAACAAAGGCAAAAA 58.896 40.909 0.00 0.00 0.00 1.94
1584 1829 2.745968 ACCCTCAGAACAAAGGCAAAA 58.254 42.857 0.00 0.00 0.00 2.44
1701 1949 6.659242 ACAACAATTGAGATACCAAGGGTTAG 59.341 38.462 13.59 0.00 37.09 2.34
1770 2018 4.813027 TCGACACCTGTGAAGTAATAACC 58.187 43.478 3.94 0.00 0.00 2.85
1779 2028 3.311322 GTGACAAAATCGACACCTGTGAA 59.689 43.478 3.94 0.00 0.00 3.18
1838 2087 7.880105 TGACATGTATTTTGCAGTATGTTTGA 58.120 30.769 0.00 0.00 39.31 2.69
1856 2105 3.864789 ACAGTTCCTTCCTTGACATGT 57.135 42.857 0.00 0.00 0.00 3.21
1907 2156 4.124238 TGTAAGGAGAAACAACACCTTCG 58.876 43.478 0.00 0.00 40.29 3.79
1926 2175 5.123186 CCGCCAGAAGTGTTTTCAATATGTA 59.877 40.000 0.00 0.00 0.00 2.29
1928 2177 4.155826 TCCGCCAGAAGTGTTTTCAATATG 59.844 41.667 0.00 0.00 0.00 1.78
2069 2318 5.029807 TGAATAGACAACTTGGACACACA 57.970 39.130 0.00 0.00 0.00 3.72
2078 2327 4.453819 GTGCAGAAGCTGAATAGACAACTT 59.546 41.667 0.00 0.00 42.74 2.66
2102 2351 4.245660 CATGACGGTGAGATGTACAAAGT 58.754 43.478 0.00 0.00 0.00 2.66
2114 2363 0.250553 GTTTCCCCACATGACGGTGA 60.251 55.000 0.00 0.00 41.32 4.02
2220 2469 5.934781 TGAAACAGCCCCACAATTTAATTT 58.065 33.333 0.00 0.00 0.00 1.82
2221 2470 5.559148 TGAAACAGCCCCACAATTTAATT 57.441 34.783 0.00 0.00 0.00 1.40
2260 2509 3.710165 ACTATAAACCGGAAAGGAGGGAG 59.290 47.826 9.46 0.00 45.00 4.30
2261 2510 3.453353 CACTATAAACCGGAAAGGAGGGA 59.547 47.826 9.46 0.00 45.00 4.20
2262 2511 3.433173 CCACTATAAACCGGAAAGGAGGG 60.433 52.174 9.46 0.00 45.00 4.30
2263 2512 3.199289 ACCACTATAAACCGGAAAGGAGG 59.801 47.826 9.46 2.51 45.00 4.30
2264 2513 4.081309 TGACCACTATAAACCGGAAAGGAG 60.081 45.833 9.46 1.72 45.00 3.69
2265 2514 3.839490 TGACCACTATAAACCGGAAAGGA 59.161 43.478 9.46 0.00 45.00 3.36
2267 2516 5.671493 AGATGACCACTATAAACCGGAAAG 58.329 41.667 9.46 0.00 0.00 2.62
2268 2517 5.687166 AGATGACCACTATAAACCGGAAA 57.313 39.130 9.46 0.00 0.00 3.13
2269 2518 5.687166 AAGATGACCACTATAAACCGGAA 57.313 39.130 9.46 0.00 0.00 4.30
2270 2519 6.795144 TTAAGATGACCACTATAAACCGGA 57.205 37.500 9.46 0.00 0.00 5.14
2271 2520 7.852971 TTTTAAGATGACCACTATAAACCGG 57.147 36.000 0.00 0.00 0.00 5.28
2311 2560 9.587772 GCAAGTACTAGAATTGAGACTCATAAA 57.412 33.333 5.87 0.00 0.00 1.40
2312 2561 8.198109 GGCAAGTACTAGAATTGAGACTCATAA 58.802 37.037 5.87 0.00 0.00 1.90
2313 2562 7.561722 AGGCAAGTACTAGAATTGAGACTCATA 59.438 37.037 5.87 0.00 0.00 2.15
2314 2563 6.382570 AGGCAAGTACTAGAATTGAGACTCAT 59.617 38.462 5.87 0.00 0.00 2.90
2315 2564 5.717178 AGGCAAGTACTAGAATTGAGACTCA 59.283 40.000 0.00 0.00 0.00 3.41
2316 2565 6.215495 AGGCAAGTACTAGAATTGAGACTC 57.785 41.667 0.00 0.00 0.00 3.36
2317 2566 6.211584 TGAAGGCAAGTACTAGAATTGAGACT 59.788 38.462 0.00 0.00 0.00 3.24
2318 2567 6.311690 GTGAAGGCAAGTACTAGAATTGAGAC 59.688 42.308 0.00 0.00 0.00 3.36
2319 2568 6.014584 TGTGAAGGCAAGTACTAGAATTGAGA 60.015 38.462 0.00 0.00 0.00 3.27
2320 2569 6.166279 TGTGAAGGCAAGTACTAGAATTGAG 58.834 40.000 0.00 0.00 0.00 3.02
2321 2570 6.109156 TGTGAAGGCAAGTACTAGAATTGA 57.891 37.500 0.00 0.00 0.00 2.57
2322 2571 6.372659 ACATGTGAAGGCAAGTACTAGAATTG 59.627 38.462 0.00 0.00 0.00 2.32
2323 2572 6.476378 ACATGTGAAGGCAAGTACTAGAATT 58.524 36.000 0.00 0.00 0.00 2.17
2324 2573 6.054860 ACATGTGAAGGCAAGTACTAGAAT 57.945 37.500 0.00 0.00 0.00 2.40
2325 2574 5.483685 ACATGTGAAGGCAAGTACTAGAA 57.516 39.130 0.00 0.00 0.00 2.10
2326 2575 5.011635 TGAACATGTGAAGGCAAGTACTAGA 59.988 40.000 0.00 0.00 0.00 2.43
2327 2576 5.237815 TGAACATGTGAAGGCAAGTACTAG 58.762 41.667 0.00 0.00 0.00 2.57
2328 2577 5.011635 TCTGAACATGTGAAGGCAAGTACTA 59.988 40.000 0.00 0.00 0.00 1.82
2329 2578 4.067896 CTGAACATGTGAAGGCAAGTACT 58.932 43.478 0.00 0.00 0.00 2.73
2330 2579 4.065088 TCTGAACATGTGAAGGCAAGTAC 58.935 43.478 0.00 0.00 0.00 2.73
2331 2580 4.350368 TCTGAACATGTGAAGGCAAGTA 57.650 40.909 0.00 0.00 0.00 2.24
2332 2581 3.213206 TCTGAACATGTGAAGGCAAGT 57.787 42.857 0.00 0.00 0.00 3.16
2333 2582 4.778534 AATCTGAACATGTGAAGGCAAG 57.221 40.909 0.00 0.00 0.00 4.01
2334 2583 4.583907 TGAAATCTGAACATGTGAAGGCAA 59.416 37.500 0.00 0.00 0.00 4.52
2335 2584 4.143543 TGAAATCTGAACATGTGAAGGCA 58.856 39.130 0.00 0.00 0.00 4.75
2336 2585 4.771590 TGAAATCTGAACATGTGAAGGC 57.228 40.909 0.00 0.00 0.00 4.35
2337 2586 5.242393 ACCTTGAAATCTGAACATGTGAAGG 59.758 40.000 0.00 0.00 33.82 3.46
2338 2587 6.147581 CACCTTGAAATCTGAACATGTGAAG 58.852 40.000 0.00 0.00 0.00 3.02
2339 2588 5.507817 GCACCTTGAAATCTGAACATGTGAA 60.508 40.000 0.00 0.00 0.00 3.18
2340 2589 4.022935 GCACCTTGAAATCTGAACATGTGA 60.023 41.667 0.00 0.00 0.00 3.58
2341 2590 4.232221 GCACCTTGAAATCTGAACATGTG 58.768 43.478 0.00 0.00 0.00 3.21
2342 2591 3.890756 TGCACCTTGAAATCTGAACATGT 59.109 39.130 0.00 0.00 0.00 3.21
2343 2592 4.508461 TGCACCTTGAAATCTGAACATG 57.492 40.909 0.00 0.00 0.00 3.21
2344 2593 5.733620 AATGCACCTTGAAATCTGAACAT 57.266 34.783 0.00 0.00 0.00 2.71
2345 2594 6.647334 TTAATGCACCTTGAAATCTGAACA 57.353 33.333 0.00 0.00 0.00 3.18
2346 2595 7.274250 GTGATTAATGCACCTTGAAATCTGAAC 59.726 37.037 0.00 0.00 0.00 3.18
2347 2596 7.177216 AGTGATTAATGCACCTTGAAATCTGAA 59.823 33.333 11.86 0.00 36.95 3.02
2348 2597 6.660521 AGTGATTAATGCACCTTGAAATCTGA 59.339 34.615 11.86 0.00 36.95 3.27
2349 2598 6.860080 AGTGATTAATGCACCTTGAAATCTG 58.140 36.000 11.86 0.00 36.95 2.90
2350 2599 7.177216 TGAAGTGATTAATGCACCTTGAAATCT 59.823 33.333 11.86 0.00 36.95 2.40
2351 2600 7.315142 TGAAGTGATTAATGCACCTTGAAATC 58.685 34.615 11.86 0.00 36.95 2.17
2352 2601 7.230849 TGAAGTGATTAATGCACCTTGAAAT 57.769 32.000 11.86 0.00 36.95 2.17
2353 2602 6.647334 TGAAGTGATTAATGCACCTTGAAA 57.353 33.333 11.86 0.00 36.95 2.69
2354 2603 6.623486 CATGAAGTGATTAATGCACCTTGAA 58.377 36.000 11.86 0.00 36.95 2.69
2355 2604 5.393352 GCATGAAGTGATTAATGCACCTTGA 60.393 40.000 0.00 4.48 43.84 3.02
2356 2605 4.802039 GCATGAAGTGATTAATGCACCTTG 59.198 41.667 0.00 8.64 43.84 3.61
2357 2606 5.002464 GCATGAAGTGATTAATGCACCTT 57.998 39.130 0.00 7.72 43.84 3.50
2358 2607 4.644103 GCATGAAGTGATTAATGCACCT 57.356 40.909 0.00 2.99 43.84 4.00
2362 2611 5.252969 TCCTTGCATGAAGTGATTAATGC 57.747 39.130 0.00 3.74 44.49 3.56
2363 2612 7.034685 TGATCCTTGCATGAAGTGATTAATG 57.965 36.000 0.00 0.00 0.00 1.90
2364 2613 7.558807 TCTTGATCCTTGCATGAAGTGATTAAT 59.441 33.333 0.00 0.00 0.00 1.40
2365 2614 6.885918 TCTTGATCCTTGCATGAAGTGATTAA 59.114 34.615 0.00 5.54 0.00 1.40
2366 2615 6.417258 TCTTGATCCTTGCATGAAGTGATTA 58.583 36.000 0.00 0.00 0.00 1.75
2367 2616 5.258841 TCTTGATCCTTGCATGAAGTGATT 58.741 37.500 0.00 0.00 0.00 2.57
2368 2617 4.851843 TCTTGATCCTTGCATGAAGTGAT 58.148 39.130 0.00 3.34 0.00 3.06
2369 2618 4.019950 TCTCTTGATCCTTGCATGAAGTGA 60.020 41.667 0.00 1.17 0.00 3.41
2370 2619 4.259356 TCTCTTGATCCTTGCATGAAGTG 58.741 43.478 0.00 0.00 0.00 3.16
2371 2620 4.564782 TCTCTTGATCCTTGCATGAAGT 57.435 40.909 0.00 0.00 0.00 3.01
2372 2621 5.892160 TTTCTCTTGATCCTTGCATGAAG 57.108 39.130 0.00 0.00 0.00 3.02
2373 2622 5.047802 GGTTTTCTCTTGATCCTTGCATGAA 60.048 40.000 0.00 0.00 0.00 2.57
2374 2623 4.460382 GGTTTTCTCTTGATCCTTGCATGA 59.540 41.667 0.00 0.00 0.00 3.07
2375 2624 4.381292 GGGTTTTCTCTTGATCCTTGCATG 60.381 45.833 0.00 0.00 0.00 4.06
2376 2625 3.766051 GGGTTTTCTCTTGATCCTTGCAT 59.234 43.478 0.00 0.00 0.00 3.96
2377 2626 3.157087 GGGTTTTCTCTTGATCCTTGCA 58.843 45.455 0.00 0.00 0.00 4.08
2378 2627 3.057245 GTGGGTTTTCTCTTGATCCTTGC 60.057 47.826 0.00 0.00 0.00 4.01
2379 2628 3.507622 GGTGGGTTTTCTCTTGATCCTTG 59.492 47.826 0.00 0.00 0.00 3.61
2380 2629 3.140144 TGGTGGGTTTTCTCTTGATCCTT 59.860 43.478 0.00 0.00 0.00 3.36
2381 2630 2.716424 TGGTGGGTTTTCTCTTGATCCT 59.284 45.455 0.00 0.00 0.00 3.24
2382 2631 3.154827 TGGTGGGTTTTCTCTTGATCC 57.845 47.619 0.00 0.00 0.00 3.36
2383 2632 3.058224 CGTTGGTGGGTTTTCTCTTGATC 60.058 47.826 0.00 0.00 0.00 2.92
2384 2633 2.884639 CGTTGGTGGGTTTTCTCTTGAT 59.115 45.455 0.00 0.00 0.00 2.57
2385 2634 2.294074 CGTTGGTGGGTTTTCTCTTGA 58.706 47.619 0.00 0.00 0.00 3.02
2386 2635 1.269051 GCGTTGGTGGGTTTTCTCTTG 60.269 52.381 0.00 0.00 0.00 3.02
2387 2636 1.029681 GCGTTGGTGGGTTTTCTCTT 58.970 50.000 0.00 0.00 0.00 2.85
2388 2637 0.106918 TGCGTTGGTGGGTTTTCTCT 60.107 50.000 0.00 0.00 0.00 3.10
2389 2638 0.741915 TTGCGTTGGTGGGTTTTCTC 59.258 50.000 0.00 0.00 0.00 2.87
2390 2639 0.744281 CTTGCGTTGGTGGGTTTTCT 59.256 50.000 0.00 0.00 0.00 2.52
2391 2640 0.458260 ACTTGCGTTGGTGGGTTTTC 59.542 50.000 0.00 0.00 0.00 2.29
2392 2641 0.899019 AACTTGCGTTGGTGGGTTTT 59.101 45.000 0.00 0.00 30.67 2.43
2393 2642 0.174617 CAACTTGCGTTGGTGGGTTT 59.825 50.000 0.00 0.00 45.28 3.27
2394 2643 1.813192 CAACTTGCGTTGGTGGGTT 59.187 52.632 0.00 0.00 45.28 4.11
2395 2644 3.520402 CAACTTGCGTTGGTGGGT 58.480 55.556 0.00 0.00 45.28 4.51
2402 2651 6.854496 TGACTAATAACTTCAACTTGCGTT 57.146 33.333 0.00 3.01 0.00 4.84
2403 2652 7.435068 AATGACTAATAACTTCAACTTGCGT 57.565 32.000 0.00 0.00 0.00 5.24
2404 2653 7.271223 CCAAATGACTAATAACTTCAACTTGCG 59.729 37.037 0.00 0.00 0.00 4.85
2405 2654 8.082242 ACCAAATGACTAATAACTTCAACTTGC 58.918 33.333 0.00 0.00 0.00 4.01
2406 2655 9.398170 CACCAAATGACTAATAACTTCAACTTG 57.602 33.333 0.00 0.00 0.00 3.16
2407 2656 8.576442 CCACCAAATGACTAATAACTTCAACTT 58.424 33.333 0.00 0.00 0.00 2.66
2408 2657 7.724061 ACCACCAAATGACTAATAACTTCAACT 59.276 33.333 0.00 0.00 0.00 3.16
2409 2658 7.807907 CACCACCAAATGACTAATAACTTCAAC 59.192 37.037 0.00 0.00 0.00 3.18
2410 2659 7.721842 TCACCACCAAATGACTAATAACTTCAA 59.278 33.333 0.00 0.00 0.00 2.69
2411 2660 7.227873 TCACCACCAAATGACTAATAACTTCA 58.772 34.615 0.00 0.00 0.00 3.02
2412 2661 7.681939 TCACCACCAAATGACTAATAACTTC 57.318 36.000 0.00 0.00 0.00 3.01
2413 2662 8.650143 AATCACCACCAAATGACTAATAACTT 57.350 30.769 0.00 0.00 0.00 2.66
2414 2663 7.888021 TGAATCACCACCAAATGACTAATAACT 59.112 33.333 0.00 0.00 0.00 2.24
2415 2664 8.050778 TGAATCACCACCAAATGACTAATAAC 57.949 34.615 0.00 0.00 0.00 1.89
2416 2665 8.685427 CATGAATCACCACCAAATGACTAATAA 58.315 33.333 0.00 0.00 0.00 1.40
2417 2666 7.201812 GCATGAATCACCACCAAATGACTAATA 60.202 37.037 0.00 0.00 0.00 0.98
2418 2667 6.406177 GCATGAATCACCACCAAATGACTAAT 60.406 38.462 0.00 0.00 0.00 1.73
2419 2668 5.105797 GCATGAATCACCACCAAATGACTAA 60.106 40.000 0.00 0.00 0.00 2.24
2420 2669 4.398988 GCATGAATCACCACCAAATGACTA 59.601 41.667 0.00 0.00 0.00 2.59
2421 2670 3.194116 GCATGAATCACCACCAAATGACT 59.806 43.478 0.00 0.00 0.00 3.41
2422 2671 3.056678 TGCATGAATCACCACCAAATGAC 60.057 43.478 0.00 0.00 0.00 3.06
2423 2672 3.163467 TGCATGAATCACCACCAAATGA 58.837 40.909 0.00 0.00 0.00 2.57
2424 2673 3.596310 TGCATGAATCACCACCAAATG 57.404 42.857 0.00 0.00 0.00 2.32
2425 2674 3.680475 GCATGCATGAATCACCACCAAAT 60.680 43.478 30.64 0.00 0.00 2.32
2426 2675 2.353903 GCATGCATGAATCACCACCAAA 60.354 45.455 30.64 0.00 0.00 3.28
2427 2676 1.205179 GCATGCATGAATCACCACCAA 59.795 47.619 30.64 0.00 0.00 3.67
2428 2677 0.818938 GCATGCATGAATCACCACCA 59.181 50.000 30.64 0.00 0.00 4.17
2429 2678 0.818938 TGCATGCATGAATCACCACC 59.181 50.000 30.64 9.40 0.00 4.61
2430 2679 1.475280 AGTGCATGCATGAATCACCAC 59.525 47.619 30.64 23.94 0.00 4.16
2431 2680 1.474879 CAGTGCATGCATGAATCACCA 59.525 47.619 30.64 14.19 0.00 4.17
2432 2681 1.475280 ACAGTGCATGCATGAATCACC 59.525 47.619 30.64 11.62 0.00 4.02
2433 2682 2.933495 ACAGTGCATGCATGAATCAC 57.067 45.000 30.64 25.28 0.00 3.06
2434 2683 5.585820 AATTACAGTGCATGCATGAATCA 57.414 34.783 30.64 15.69 0.00 2.57
2435 2684 7.358931 GCATTAATTACAGTGCATGCATGAATC 60.359 37.037 30.64 17.57 37.54 2.52
2436 2685 6.422701 GCATTAATTACAGTGCATGCATGAAT 59.577 34.615 30.64 15.99 37.54 2.57
2437 2686 5.749588 GCATTAATTACAGTGCATGCATGAA 59.250 36.000 30.64 18.49 37.54 2.57
2438 2687 5.163540 TGCATTAATTACAGTGCATGCATGA 60.164 36.000 30.64 12.48 41.52 3.07
2439 2688 5.044558 TGCATTAATTACAGTGCATGCATG 58.955 37.500 25.64 22.70 41.52 4.06
2440 2689 5.265350 TGCATTAATTACAGTGCATGCAT 57.735 34.783 25.64 10.90 41.52 3.96
2441 2690 4.715527 TGCATTAATTACAGTGCATGCA 57.284 36.364 18.46 18.46 43.56 3.96
2446 2695 4.552166 ACCGATGCATTAATTACAGTGC 57.448 40.909 0.00 8.86 38.05 4.40
2447 2696 7.428183 GTGTTTACCGATGCATTAATTACAGTG 59.572 37.037 0.00 0.00 0.00 3.66
2448 2697 7.119992 TGTGTTTACCGATGCATTAATTACAGT 59.880 33.333 0.00 0.00 0.00 3.55
2449 2698 7.468441 TGTGTTTACCGATGCATTAATTACAG 58.532 34.615 0.00 0.00 0.00 2.74
2450 2699 7.379098 TGTGTTTACCGATGCATTAATTACA 57.621 32.000 0.00 2.14 0.00 2.41
2451 2700 7.966204 AGTTGTGTTTACCGATGCATTAATTAC 59.034 33.333 0.00 0.00 0.00 1.89
2452 2701 8.046294 AGTTGTGTTTACCGATGCATTAATTA 57.954 30.769 0.00 0.00 0.00 1.40
2453 2702 6.919721 AGTTGTGTTTACCGATGCATTAATT 58.080 32.000 0.00 0.00 0.00 1.40
2454 2703 6.509418 AGTTGTGTTTACCGATGCATTAAT 57.491 33.333 0.00 0.00 0.00 1.40
2455 2704 5.950758 AGTTGTGTTTACCGATGCATTAA 57.049 34.783 0.00 0.00 0.00 1.40
2456 2705 5.950758 AAGTTGTGTTTACCGATGCATTA 57.049 34.783 0.00 0.00 0.00 1.90
2457 2706 4.846779 AAGTTGTGTTTACCGATGCATT 57.153 36.364 0.00 0.00 0.00 3.56
2458 2707 4.846779 AAAGTTGTGTTTACCGATGCAT 57.153 36.364 0.00 0.00 0.00 3.96
2459 2708 4.640789 AAAAGTTGTGTTTACCGATGCA 57.359 36.364 0.00 0.00 0.00 3.96
2460 2709 4.801516 ACAAAAAGTTGTGTTTACCGATGC 59.198 37.500 0.00 0.00 46.40 3.91
2490 2739 8.671384 ACAAAAGTGCTTAATTAGTACACTCA 57.329 30.769 14.01 0.00 41.45 3.41
2517 2766 9.250624 GTGAGTGGTAGAATACATTTCATAGTC 57.749 37.037 0.00 0.00 45.43 2.59
2522 2771 9.201989 AGATAGTGAGTGGTAGAATACATTTCA 57.798 33.333 0.00 0.00 45.43 2.69
2539 2788 6.775142 TCTCTCCAATCAAGGTAGATAGTGAG 59.225 42.308 0.00 0.00 0.00 3.51
2563 2812 6.458342 CGTTTATAGGGCTCAGTTTGGAAATC 60.458 42.308 0.00 0.00 0.00 2.17
2588 2837 1.700186 GTGGATACTCCCTCCATTCCC 59.300 57.143 0.00 0.00 44.34 3.97
2712 2961 5.709594 TCCTCTTCATCATAGTCATCCAGA 58.290 41.667 0.00 0.00 0.00 3.86
3005 3258 1.670811 CACGTCATCTTATTGCACCCC 59.329 52.381 0.00 0.00 0.00 4.95
3008 3261 3.366724 TCGAACACGTCATCTTATTGCAC 59.633 43.478 0.00 0.00 0.00 4.57
3083 3336 5.444663 AAAAGAGAACTCACCTGAAATGC 57.555 39.130 4.64 0.00 0.00 3.56
3131 3384 9.102757 CTTCTTTGTCAAGGCGCATATATATAT 57.897 33.333 10.83 0.00 0.00 0.86
3201 3454 3.008049 CCCATCTAAGTATTTCCTCCCGG 59.992 52.174 0.00 0.00 0.00 5.73
3215 3468 1.138069 TCATTCGCGCTTCCCATCTAA 59.862 47.619 5.56 0.00 0.00 2.10
3231 3484 1.659035 GCCCCCTCCCTGGATTCATT 61.659 60.000 0.00 0.00 38.35 2.57
3396 3651 2.264813 GAGGCGTTTGTGCTATTACGA 58.735 47.619 0.00 0.00 36.16 3.43
3397 3652 1.996898 TGAGGCGTTTGTGCTATTACG 59.003 47.619 0.00 0.00 37.09 3.18
3398 3653 3.621268 TCATGAGGCGTTTGTGCTATTAC 59.379 43.478 0.00 0.00 34.52 1.89
3399 3654 3.867857 TCATGAGGCGTTTGTGCTATTA 58.132 40.909 0.00 0.00 34.52 0.98
3400 3655 2.710377 TCATGAGGCGTTTGTGCTATT 58.290 42.857 0.00 0.00 34.52 1.73
3401 3656 2.401583 TCATGAGGCGTTTGTGCTAT 57.598 45.000 0.00 0.00 34.52 2.97
3547 5460 2.372264 CAGTATGTTGCTTGCATCCCT 58.628 47.619 0.00 0.00 0.00 4.20
3563 5476 0.098905 GTCAGTCGCGATCTGCAGTA 59.901 55.000 24.59 11.57 46.97 2.74
3585 5498 2.047844 CCTCTGGCCCATATCGCG 60.048 66.667 0.00 0.00 0.00 5.87
3669 5582 3.569701 TCATGAGCAGAACCTTTGGAAAC 59.430 43.478 0.00 0.00 0.00 2.78
3793 5710 2.355132 TCCTACTTCGCAGTCGATCTTC 59.645 50.000 0.00 0.00 45.04 2.87
3800 5725 6.421202 CCTTTGTAATATCCTACTTCGCAGTC 59.579 42.308 0.00 0.00 34.06 3.51
3803 5728 6.097839 AGTCCTTTGTAATATCCTACTTCGCA 59.902 38.462 0.00 0.00 0.00 5.10
3805 5730 7.713750 TCAGTCCTTTGTAATATCCTACTTCG 58.286 38.462 0.00 0.00 0.00 3.79
3819 5744 8.717717 TGATATAATTCCTCATCAGTCCTTTGT 58.282 33.333 0.00 0.00 0.00 2.83
3923 5853 0.535335 TAGCCCAACGATGACACCTC 59.465 55.000 0.00 0.00 0.00 3.85
3925 5855 0.743345 GGTAGCCCAACGATGACACC 60.743 60.000 0.00 0.00 0.00 4.16
3945 5875 0.664224 AAACAAACGGGGCGTAAGTG 59.336 50.000 0.00 0.00 39.99 3.16
3966 5896 4.813526 CGTCCTCACGCTCGACCG 62.814 72.222 0.00 0.00 39.69 4.79
4013 5944 4.777366 TCAATCCAGTAGAGGTCATGACAA 59.223 41.667 26.47 6.75 0.00 3.18
4014 5945 4.352893 TCAATCCAGTAGAGGTCATGACA 58.647 43.478 26.47 3.72 0.00 3.58
4075 6006 3.344515 ACAGCAGTACATCACTCTCGTA 58.655 45.455 0.00 0.00 34.26 3.43
4093 6024 8.768957 CTATGTGAATCATAGTAATGGGACAG 57.231 38.462 6.68 0.00 45.41 3.51
4211 6142 6.017026 TTTGTACGCAAAAGAATGATGGTACA 60.017 34.615 0.00 0.00 41.87 2.90
4270 6203 3.821421 ATTCGGCCACTACCTCTAAAG 57.179 47.619 2.24 0.00 0.00 1.85
4337 6333 3.259902 CACTAAAAGTTACTCCCTCCGC 58.740 50.000 0.00 0.00 0.00 5.54
4345 6355 3.322828 TGACGGGAGCACTAAAAGTTACT 59.677 43.478 0.00 0.00 0.00 2.24
4346 6356 3.656559 TGACGGGAGCACTAAAAGTTAC 58.343 45.455 0.00 0.00 0.00 2.50
4347 6357 4.546829 ATGACGGGAGCACTAAAAGTTA 57.453 40.909 0.00 0.00 0.00 2.24
4348 6358 2.922740 TGACGGGAGCACTAAAAGTT 57.077 45.000 0.00 0.00 0.00 2.66
4349 6359 3.418684 AATGACGGGAGCACTAAAAGT 57.581 42.857 0.00 0.00 0.00 2.66
4350 6360 5.873179 TTAAATGACGGGAGCACTAAAAG 57.127 39.130 0.00 0.00 0.00 2.27
4351 6361 7.925043 TTATTAAATGACGGGAGCACTAAAA 57.075 32.000 0.00 0.00 0.00 1.52
4352 6362 7.554835 ACATTATTAAATGACGGGAGCACTAAA 59.445 33.333 5.18 0.00 44.50 1.85
4353 6363 7.051623 ACATTATTAAATGACGGGAGCACTAA 58.948 34.615 5.18 0.00 44.50 2.24
4354 6364 6.588204 ACATTATTAAATGACGGGAGCACTA 58.412 36.000 5.18 0.00 44.50 2.74
4355 6365 5.437060 ACATTATTAAATGACGGGAGCACT 58.563 37.500 5.18 0.00 44.50 4.40
4356 6366 5.751243 ACATTATTAAATGACGGGAGCAC 57.249 39.130 5.18 0.00 44.50 4.40
4357 6367 6.481976 CACTACATTATTAAATGACGGGAGCA 59.518 38.462 5.18 0.00 44.50 4.26
4358 6368 6.482308 ACACTACATTATTAAATGACGGGAGC 59.518 38.462 5.18 0.00 44.50 4.70
4551 6563 9.467258 CTGAGAATTCAAAACTCAAGCAAATAA 57.533 29.630 8.44 0.00 39.60 1.40


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

AutoCloner maintained by Alex Coulton.