Multiple sequence alignment - TraesCS2B01G332200

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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 TraesCS2B01G332200 chr2B 100.000 3034 0 0 1 3034 475302130 475299097 0.000000e+00 5603.0
1 TraesCS2B01G332200 chr2B 88.506 174 17 3 2232 2403 146768373 146768545 1.100000e-49 207.0
2 TraesCS2B01G332200 chr2B 85.143 175 20 6 2229 2400 4527579 4527408 1.120000e-39 174.0
3 TraesCS2B01G332200 chr2B 78.689 183 18 8 205 385 61289172 61289009 5.350000e-18 102.0
4 TraesCS2B01G332200 chr2B 77.717 184 20 9 205 386 61360696 61360532 3.220000e-15 93.5
5 TraesCS2B01G332200 chr2B 83.750 80 10 2 245 323 458106770 458106847 4.200000e-09 73.1
6 TraesCS2B01G332200 chr2D 91.401 2256 137 21 1 2225 401286560 401284331 0.000000e+00 3038.0
7 TraesCS2B01G332200 chr2D 90.781 640 48 7 2403 3034 401284343 401283707 0.000000e+00 845.0
8 TraesCS2B01G332200 chr2D 88.439 173 19 1 2232 2403 598010022 598009850 1.100000e-49 207.0
9 TraesCS2B01G332200 chr2A 90.353 1389 73 32 819 2179 537962935 537961580 0.000000e+00 1766.0
10 TraesCS2B01G332200 chr2A 86.645 307 22 9 2516 2822 537961423 537961136 3.770000e-84 322.0
11 TraesCS2B01G332200 chr2A 87.556 225 16 3 2818 3034 537952047 537951827 1.810000e-62 250.0
12 TraesCS2B01G332200 chr2A 89.231 65 3 3 2165 2225 537961566 537961502 9.020000e-11 78.7
13 TraesCS2B01G332200 chr6D 87.222 180 16 6 2229 2403 437151346 437151523 6.630000e-47 198.0
14 TraesCS2B01G332200 chr6D 85.311 177 19 7 2229 2402 17204440 17204268 3.110000e-40 176.0
15 TraesCS2B01G332200 chr7B 86.982 169 19 3 2240 2406 635021634 635021467 1.440000e-43 187.0
16 TraesCS2B01G332200 chr7B 79.508 122 15 6 292 409 687803432 687803317 9.020000e-11 78.7
17 TraesCS2B01G332200 chr3D 86.111 180 17 7 2230 2406 453100769 453100595 1.440000e-43 187.0
18 TraesCS2B01G332200 chr3D 84.536 97 14 1 2840 2935 362052337 362052433 8.950000e-16 95.3
19 TraesCS2B01G332200 chr3D 79.130 115 21 3 199 311 473740603 473740716 3.240000e-10 76.8
20 TraesCS2B01G332200 chr1A 85.965 171 17 6 2232 2400 11418241 11418406 3.110000e-40 176.0
21 TraesCS2B01G332200 chr3B 84.884 172 18 6 2233 2399 685896551 685896383 1.870000e-37 167.0
22 TraesCS2B01G332200 chr3B 83.495 103 13 3 210 310 654338990 654338890 3.220000e-15 93.5
23 TraesCS2B01G332200 chr4D 84.821 112 13 4 205 314 355853953 355853844 3.200000e-20 110.0
24 TraesCS2B01G332200 chr4B 84.821 112 13 4 205 314 439316276 439316167 3.200000e-20 110.0
25 TraesCS2B01G332200 chrUn 81.250 96 17 1 2841 2935 363304338 363304433 3.240000e-10 76.8
26 TraesCS2B01G332200 chr7D 81.053 95 13 3 224 317 47847801 47847711 1.510000e-08 71.3
27 TraesCS2B01G332200 chr3A 83.133 83 8 6 199 278 739148661 739148740 1.510000e-08 71.3
28 TraesCS2B01G332200 chr5D 93.182 44 3 0 1129 1172 520421800 520421757 7.020000e-07 65.8
29 TraesCS2B01G332200 chr5B 93.182 44 3 0 1129 1172 655701975 655701932 7.020000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G332200 chr2B 475299097 475302130 3033 True 5603.000000 5603 100.000 1 3034 1 chr2B.!!$R4 3033
1 TraesCS2B01G332200 chr2D 401283707 401286560 2853 True 1941.500000 3038 91.091 1 3034 2 chr2D.!!$R2 3033
2 TraesCS2B01G332200 chr2A 537961136 537962935 1799 True 722.233333 1766 88.743 819 2822 3 chr2A.!!$R2 2003

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
458 462 0.179137 TAAGATGCCAGAGACGCACG 60.179 55.0 0.0 0.0 39.49 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 2349 0.039617 TCGTTTTGATGCAAAGGCGG 60.04 50.0 14.16 0.23 45.35 6.13 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
103 104 8.493607 TGGAATAGTGTAAAGGATCATTCATCA 58.506 33.333 0.00 0.00 32.33 3.07
140 141 4.207891 ACGTAGCTCATTTGGATGTTCT 57.792 40.909 0.00 0.00 34.77 3.01
144 145 4.313020 AGCTCATTTGGATGTTCTTCCT 57.687 40.909 6.36 0.00 36.68 3.36
167 168 2.039084 CTCCCTTTCCTGTACAAGTGCT 59.961 50.000 0.00 0.00 0.00 4.40
202 203 8.328864 CAGTTTTTCGATTAATGGTCTACTAGC 58.671 37.037 0.00 0.00 0.00 3.42
207 208 6.062749 TCGATTAATGGTCTACTAGCAGTCT 58.937 40.000 0.00 0.00 39.39 3.24
210 211 1.475403 TGGTCTACTAGCAGTCTGCC 58.525 55.000 21.32 3.88 46.52 4.85
292 293 0.469917 AGCGGTACCCTCCATCATTG 59.530 55.000 6.25 0.00 0.00 2.82
317 318 4.460263 ACACAGGTCTTGTTGCAGATTTA 58.540 39.130 0.00 0.00 38.16 1.40
318 319 4.516698 ACACAGGTCTTGTTGCAGATTTAG 59.483 41.667 0.00 0.00 38.16 1.85
319 320 4.516698 CACAGGTCTTGTTGCAGATTTAGT 59.483 41.667 0.00 0.00 38.16 2.24
320 321 5.009010 CACAGGTCTTGTTGCAGATTTAGTT 59.991 40.000 0.00 0.00 38.16 2.24
378 380 5.493133 TCGCAACAGAAGTTTGTTACAAT 57.507 34.783 0.00 0.00 39.17 2.71
380 382 7.017498 TCGCAACAGAAGTTTGTTACAATTA 57.983 32.000 0.00 0.00 39.17 1.40
383 385 8.751335 CGCAACAGAAGTTTGTTACAATTATTT 58.249 29.630 0.00 0.00 39.17 1.40
409 412 9.545105 TTTTGTCTTCATCTTTTTGCAACATAT 57.455 25.926 0.00 0.00 0.00 1.78
446 450 2.994186 TAAGGGGAACGGTAAGATGC 57.006 50.000 0.00 0.00 0.00 3.91
450 454 0.539986 GGGAACGGTAAGATGCCAGA 59.460 55.000 0.00 0.00 33.32 3.86
455 459 0.872021 CGGTAAGATGCCAGAGACGC 60.872 60.000 0.00 0.00 0.00 5.19
458 462 0.179137 TAAGATGCCAGAGACGCACG 60.179 55.000 0.00 0.00 39.49 5.34
481 485 3.242706 ACACACGAAACACACATCACATG 60.243 43.478 0.00 0.00 0.00 3.21
482 486 3.002144 CACACGAAACACACATCACATGA 59.998 43.478 0.00 0.00 0.00 3.07
489 499 2.224042 ACACACATCACATGAGACACGT 60.224 45.455 0.00 0.00 0.00 4.49
497 507 3.254657 TCACATGAGACACGTGTCATACA 59.745 43.478 41.04 34.72 45.61 2.29
498 508 3.364920 CACATGAGACACGTGTCATACAC 59.635 47.826 41.04 27.43 45.61 2.90
546 556 0.902531 TCAGTCGGTTGAGGGGAATC 59.097 55.000 0.00 0.00 0.00 2.52
554 564 2.554564 GGTTGAGGGGAATCGTTTTCCT 60.555 50.000 15.99 9.72 38.61 3.36
559 569 3.939592 GAGGGGAATCGTTTTCCTTACTG 59.060 47.826 15.99 0.00 38.61 2.74
560 570 2.422479 GGGGAATCGTTTTCCTTACTGC 59.578 50.000 15.99 2.92 38.61 4.40
561 571 3.344515 GGGAATCGTTTTCCTTACTGCT 58.655 45.455 15.99 0.00 38.61 4.24
577 587 1.657594 CTGCTACATGTCACTGAAGCG 59.342 52.381 0.00 0.00 32.67 4.68
614 625 2.480845 GTCGCCAGTCACTAAAACAGT 58.519 47.619 0.00 0.00 38.32 3.55
680 691 2.658285 CCCTTGATGAGCTTGCCATTA 58.342 47.619 0.00 0.00 0.00 1.90
726 751 2.625737 CAGCACCACTCTCAATACCTG 58.374 52.381 0.00 0.00 0.00 4.00
753 778 5.184479 ACACCAAGTCAAGGATGAATGAATG 59.816 40.000 0.00 0.00 37.30 2.67
754 779 5.416639 CACCAAGTCAAGGATGAATGAATGA 59.583 40.000 0.00 0.00 37.30 2.57
755 780 6.012113 ACCAAGTCAAGGATGAATGAATGAA 58.988 36.000 0.00 0.00 37.30 2.57
756 781 6.666546 ACCAAGTCAAGGATGAATGAATGAAT 59.333 34.615 0.00 0.00 37.30 2.57
763 788 9.033711 TCAAGGATGAATGAATGAATAAACCAA 57.966 29.630 0.00 0.00 30.99 3.67
799 824 2.032681 GGAGCAAACGAGGCCACT 59.967 61.111 5.01 0.00 0.00 4.00
807 832 0.957395 AACGAGGCCACTGCAATCTG 60.957 55.000 5.01 0.00 40.13 2.90
840 865 2.165030 GGCACATGAAACAGATCAAGGG 59.835 50.000 0.00 0.00 32.06 3.95
866 891 5.821470 ACCTTTTGTGATATGATCTGCAGAG 59.179 40.000 22.96 4.79 0.00 3.35
1146 1199 2.202756 GTCGACGTCCTCATGGGC 60.203 66.667 10.58 0.00 34.39 5.36
1405 1458 1.200839 GCCGACGTGTGAGTTTTCG 59.799 57.895 0.00 0.00 0.00 3.46
1428 1482 5.437060 GTTTCTTCTCACCCCAATATGCTA 58.563 41.667 0.00 0.00 0.00 3.49
1439 1502 3.136763 CCAATATGCTAGCTGACCAGTG 58.863 50.000 17.23 5.79 0.00 3.66
1452 1515 2.290367 TGACCAGTGTGCTTCAATTTCG 59.710 45.455 0.00 0.00 0.00 3.46
1453 1516 2.290641 GACCAGTGTGCTTCAATTTCGT 59.709 45.455 0.00 0.00 0.00 3.85
1454 1517 3.472652 ACCAGTGTGCTTCAATTTCGTA 58.527 40.909 0.00 0.00 0.00 3.43
1462 1525 5.049954 TGTGCTTCAATTTCGTAGTACCAAC 60.050 40.000 0.00 0.00 0.00 3.77
1469 1532 6.211184 TCAATTTCGTAGTACCAACCCTTCTA 59.789 38.462 0.00 0.00 0.00 2.10
1474 1537 5.301045 TCGTAGTACCAACCCTTCTATGATG 59.699 44.000 0.00 0.00 0.00 3.07
1480 1543 4.042809 ACCAACCCTTCTATGATGTGTTCA 59.957 41.667 0.00 0.00 39.12 3.18
1550 1613 2.795297 GTCGACGAGAGGCTCAGG 59.205 66.667 18.26 10.23 36.51 3.86
1569 1632 0.716108 GCTCACCATCACGAACTTCG 59.284 55.000 9.68 9.68 46.93 3.79
1574 1637 0.673644 CCATCACGAACTTCGCCCTT 60.674 55.000 11.15 0.00 45.12 3.95
1616 1679 1.746322 TTTGCACCGACGTCTACCCA 61.746 55.000 14.70 2.96 0.00 4.51
1679 1742 1.731720 GCTTCCGTCTGAGCAAGAAT 58.268 50.000 0.00 0.00 36.40 2.40
1931 1994 2.102357 CCGGGTGACTCGACGATG 59.898 66.667 6.36 0.00 0.00 3.84
1954 2017 5.652452 TGGATTACGATCTGAAGTTCTCTCA 59.348 40.000 4.17 0.00 32.66 3.27
1994 2057 1.448540 CACCCAGGACGAGCATCAC 60.449 63.158 0.00 0.00 33.17 3.06
2037 2100 6.758886 GGTCTATTTCAGTTCATGGTAGTCTG 59.241 42.308 0.00 0.00 0.00 3.51
2094 2157 4.745649 CTGCTGTAAGTAGGAGTACAACC 58.254 47.826 0.00 0.00 43.53 3.77
2095 2158 4.154176 TGCTGTAAGTAGGAGTACAACCA 58.846 43.478 10.84 0.00 35.30 3.67
2096 2159 4.589798 TGCTGTAAGTAGGAGTACAACCAA 59.410 41.667 10.84 0.00 35.30 3.67
2097 2160 5.247564 TGCTGTAAGTAGGAGTACAACCAAT 59.752 40.000 10.84 0.00 35.30 3.16
2098 2161 5.581085 GCTGTAAGTAGGAGTACAACCAATG 59.419 44.000 10.84 0.00 35.30 2.82
2099 2162 6.573680 GCTGTAAGTAGGAGTACAACCAATGA 60.574 42.308 10.84 0.00 35.30 2.57
2100 2163 7.305813 TGTAAGTAGGAGTACAACCAATGAA 57.694 36.000 10.84 0.00 0.00 2.57
2101 2164 7.156673 TGTAAGTAGGAGTACAACCAATGAAC 58.843 38.462 10.84 5.09 0.00 3.18
2171 2236 1.006086 TTTGCCGACATGCTCATACG 58.994 50.000 0.00 0.00 0.00 3.06
2261 2354 2.447959 GGAGGTTATCCCCCGCCT 60.448 66.667 0.00 0.00 43.01 5.52
2262 2355 2.076803 GGAGGTTATCCCCCGCCTT 61.077 63.158 0.00 0.00 43.01 4.35
2263 2356 1.642513 GGAGGTTATCCCCCGCCTTT 61.643 60.000 0.00 0.00 43.01 3.11
2264 2357 0.465642 GAGGTTATCCCCCGCCTTTG 60.466 60.000 0.00 0.00 0.00 2.77
2265 2358 2.125326 GGTTATCCCCCGCCTTTGC 61.125 63.158 0.00 0.00 0.00 3.68
2266 2359 1.379309 GTTATCCCCCGCCTTTGCA 60.379 57.895 0.00 0.00 37.32 4.08
2267 2360 0.755327 GTTATCCCCCGCCTTTGCAT 60.755 55.000 0.00 0.00 37.32 3.96
2268 2361 0.467290 TTATCCCCCGCCTTTGCATC 60.467 55.000 0.00 0.00 37.32 3.91
2269 2362 1.640593 TATCCCCCGCCTTTGCATCA 61.641 55.000 0.00 0.00 37.32 3.07
2270 2363 2.512986 ATCCCCCGCCTTTGCATCAA 62.513 55.000 0.00 0.00 37.32 2.57
2271 2364 2.282039 CCCCCGCCTTTGCATCAAA 61.282 57.895 0.00 0.00 37.32 2.69
2272 2365 1.670590 CCCCGCCTTTGCATCAAAA 59.329 52.632 0.00 0.00 37.32 2.44
2273 2366 0.670239 CCCCGCCTTTGCATCAAAAC 60.670 55.000 0.00 0.00 37.32 2.43
2274 2367 1.008361 CCCGCCTTTGCATCAAAACG 61.008 55.000 0.00 7.14 37.32 3.60
2275 2368 0.039617 CCGCCTTTGCATCAAAACGA 60.040 50.000 12.79 0.00 36.05 3.85
2276 2369 1.402720 CCGCCTTTGCATCAAAACGAT 60.403 47.619 12.79 0.00 36.05 3.73
2285 2378 2.375110 CATCAAAACGATGCATACGGC 58.625 47.619 18.34 0.00 44.95 5.68
2286 2379 0.730265 TCAAAACGATGCATACGGCC 59.270 50.000 18.34 0.00 43.89 6.13
2287 2380 0.449786 CAAAACGATGCATACGGCCA 59.550 50.000 18.34 0.00 43.89 5.36
2288 2381 1.065401 CAAAACGATGCATACGGCCAT 59.935 47.619 18.34 0.00 43.89 4.40
2289 2382 2.248280 AAACGATGCATACGGCCATA 57.752 45.000 18.34 0.00 43.89 2.74
2290 2383 2.472695 AACGATGCATACGGCCATAT 57.527 45.000 18.34 0.00 43.89 1.78
2291 2384 2.472695 ACGATGCATACGGCCATATT 57.527 45.000 18.34 0.00 43.89 1.28
2292 2385 3.603158 ACGATGCATACGGCCATATTA 57.397 42.857 18.34 0.00 43.89 0.98
2293 2386 4.137116 ACGATGCATACGGCCATATTAT 57.863 40.909 18.34 0.00 43.89 1.28
2294 2387 4.513442 ACGATGCATACGGCCATATTATT 58.487 39.130 18.34 0.00 43.89 1.40
2295 2388 4.332543 ACGATGCATACGGCCATATTATTG 59.667 41.667 18.34 1.16 43.89 1.90
2296 2389 4.570369 CGATGCATACGGCCATATTATTGA 59.430 41.667 2.24 0.00 43.89 2.57
2297 2390 5.237127 CGATGCATACGGCCATATTATTGAT 59.763 40.000 2.24 0.00 43.89 2.57
2298 2391 6.423604 CGATGCATACGGCCATATTATTGATA 59.576 38.462 2.24 0.00 43.89 2.15
2299 2392 7.042119 CGATGCATACGGCCATATTATTGATAA 60.042 37.037 2.24 0.00 43.89 1.75
2300 2393 7.552458 TGCATACGGCCATATTATTGATAAG 57.448 36.000 2.24 0.00 43.89 1.73
2301 2394 6.038161 TGCATACGGCCATATTATTGATAAGC 59.962 38.462 2.24 0.00 43.89 3.09
2302 2395 6.038161 GCATACGGCCATATTATTGATAAGCA 59.962 38.462 2.24 0.00 36.11 3.91
2303 2396 7.415095 GCATACGGCCATATTATTGATAAGCAA 60.415 37.037 2.24 0.00 37.45 3.91
2304 2397 6.892658 ACGGCCATATTATTGATAAGCAAA 57.107 33.333 2.24 0.00 40.48 3.68
2305 2398 7.283625 ACGGCCATATTATTGATAAGCAAAA 57.716 32.000 2.24 0.00 40.48 2.44
2306 2399 7.370383 ACGGCCATATTATTGATAAGCAAAAG 58.630 34.615 2.24 0.00 40.48 2.27
2307 2400 6.808212 CGGCCATATTATTGATAAGCAAAAGG 59.192 38.462 2.24 0.00 40.48 3.11
2308 2401 7.523709 CGGCCATATTATTGATAAGCAAAAGGT 60.524 37.037 2.24 0.00 40.48 3.50
2309 2402 8.150296 GGCCATATTATTGATAAGCAAAAGGTT 58.850 33.333 0.00 0.00 40.48 3.50
2310 2403 9.546428 GCCATATTATTGATAAGCAAAAGGTTT 57.454 29.630 0.00 0.00 40.48 3.27
2318 2411 9.830975 ATTGATAAGCAAAAGGTTTAACAAAGT 57.169 25.926 0.00 0.00 38.05 2.66
2319 2412 8.865590 TGATAAGCAAAAGGTTTAACAAAGTC 57.134 30.769 0.00 0.00 0.00 3.01
2320 2413 8.691797 TGATAAGCAAAAGGTTTAACAAAGTCT 58.308 29.630 0.00 0.00 0.00 3.24
2321 2414 9.529325 GATAAGCAAAAGGTTTAACAAAGTCTT 57.471 29.630 0.00 0.00 0.00 3.01
2322 2415 7.595311 AAGCAAAAGGTTTAACAAAGTCTTG 57.405 32.000 0.00 0.00 38.61 3.02
2323 2416 6.930731 AGCAAAAGGTTTAACAAAGTCTTGA 58.069 32.000 0.00 0.00 36.33 3.02
2324 2417 7.035612 AGCAAAAGGTTTAACAAAGTCTTGAG 58.964 34.615 0.00 0.00 36.33 3.02
2325 2418 6.255670 GCAAAAGGTTTAACAAAGTCTTGAGG 59.744 38.462 0.00 0.00 36.33 3.86
2326 2419 7.320399 CAAAAGGTTTAACAAAGTCTTGAGGT 58.680 34.615 0.00 0.00 36.33 3.85
2327 2420 6.694877 AAGGTTTAACAAAGTCTTGAGGTC 57.305 37.500 0.00 0.00 36.33 3.85
2328 2421 6.002653 AGGTTTAACAAAGTCTTGAGGTCT 57.997 37.500 0.00 0.00 36.33 3.85
2329 2422 6.056236 AGGTTTAACAAAGTCTTGAGGTCTC 58.944 40.000 0.00 0.00 36.33 3.36
2330 2423 5.820947 GGTTTAACAAAGTCTTGAGGTCTCA 59.179 40.000 0.00 0.00 36.33 3.27
2331 2424 6.486993 GGTTTAACAAAGTCTTGAGGTCTCAT 59.513 38.462 1.16 0.00 39.64 2.90
2332 2425 7.660208 GGTTTAACAAAGTCTTGAGGTCTCATA 59.340 37.037 1.16 0.00 39.64 2.15
2333 2426 9.052759 GTTTAACAAAGTCTTGAGGTCTCATAA 57.947 33.333 1.16 0.00 39.64 1.90
2334 2427 8.833231 TTAACAAAGTCTTGAGGTCTCATAAG 57.167 34.615 1.16 0.00 39.64 1.73
2335 2428 5.799213 ACAAAGTCTTGAGGTCTCATAAGG 58.201 41.667 1.16 0.00 39.64 2.69
2336 2429 5.181748 CAAAGTCTTGAGGTCTCATAAGGG 58.818 45.833 1.16 0.00 39.64 3.95
2337 2430 4.338795 AGTCTTGAGGTCTCATAAGGGA 57.661 45.455 1.16 0.00 39.64 4.20
2338 2431 4.689062 AGTCTTGAGGTCTCATAAGGGAA 58.311 43.478 1.16 0.00 39.64 3.97
2339 2432 5.094387 AGTCTTGAGGTCTCATAAGGGAAA 58.906 41.667 1.16 0.00 39.64 3.13
2340 2433 5.548056 AGTCTTGAGGTCTCATAAGGGAAAA 59.452 40.000 1.16 0.00 39.64 2.29
2341 2434 6.044404 AGTCTTGAGGTCTCATAAGGGAAAAA 59.956 38.462 1.16 0.00 39.64 1.94
2369 2462 7.385668 CTCACATAGAGCAAAAACACAAAAG 57.614 36.000 0.00 0.00 37.59 2.27
2370 2463 7.094508 TCACATAGAGCAAAAACACAAAAGA 57.905 32.000 0.00 0.00 0.00 2.52
2371 2464 7.542890 TCACATAGAGCAAAAACACAAAAGAA 58.457 30.769 0.00 0.00 0.00 2.52
2372 2465 7.487829 TCACATAGAGCAAAAACACAAAAGAAC 59.512 33.333 0.00 0.00 0.00 3.01
2373 2466 6.472163 ACATAGAGCAAAAACACAAAAGAACG 59.528 34.615 0.00 0.00 0.00 3.95
2374 2467 4.173256 AGAGCAAAAACACAAAAGAACGG 58.827 39.130 0.00 0.00 0.00 4.44
2375 2468 3.258228 AGCAAAAACACAAAAGAACGGG 58.742 40.909 0.00 0.00 0.00 5.28
2376 2469 3.056465 AGCAAAAACACAAAAGAACGGGA 60.056 39.130 0.00 0.00 0.00 5.14
2377 2470 3.868661 GCAAAAACACAAAAGAACGGGAT 59.131 39.130 0.00 0.00 0.00 3.85
2378 2471 5.044558 GCAAAAACACAAAAGAACGGGATA 58.955 37.500 0.00 0.00 0.00 2.59
2379 2472 5.174943 GCAAAAACACAAAAGAACGGGATAG 59.825 40.000 0.00 0.00 0.00 2.08
2380 2473 4.499037 AAACACAAAAGAACGGGATAGC 57.501 40.909 0.00 0.00 0.00 2.97
2381 2474 2.433436 ACACAAAAGAACGGGATAGCC 58.567 47.619 0.00 0.00 0.00 3.93
2382 2475 2.224670 ACACAAAAGAACGGGATAGCCA 60.225 45.455 0.00 0.00 35.15 4.75
2383 2476 2.161609 CACAAAAGAACGGGATAGCCAC 59.838 50.000 0.00 0.00 35.15 5.01
2384 2477 2.224670 ACAAAAGAACGGGATAGCCACA 60.225 45.455 0.00 0.00 35.15 4.17
2385 2478 2.817258 CAAAAGAACGGGATAGCCACAA 59.183 45.455 0.00 0.00 35.15 3.33
2386 2479 2.109425 AAGAACGGGATAGCCACAAC 57.891 50.000 0.00 0.00 35.15 3.32
2387 2480 0.252197 AGAACGGGATAGCCACAACC 59.748 55.000 0.00 0.00 35.15 3.77
2390 2483 4.534401 GGGATAGCCACAACCGAC 57.466 61.111 0.00 0.00 35.15 4.79
2391 2484 1.600107 GGGATAGCCACAACCGACA 59.400 57.895 0.00 0.00 35.15 4.35
2392 2485 0.462047 GGGATAGCCACAACCGACAG 60.462 60.000 0.00 0.00 35.15 3.51
2393 2486 0.462047 GGATAGCCACAACCGACAGG 60.462 60.000 0.00 0.00 45.13 4.00
2396 2489 2.904866 GCCACAACCGACAGGCAA 60.905 61.111 0.00 0.00 46.26 4.52
2397 2490 2.485795 GCCACAACCGACAGGCAAA 61.486 57.895 0.00 0.00 46.26 3.68
2398 2491 2.010582 GCCACAACCGACAGGCAAAA 62.011 55.000 0.00 0.00 46.26 2.44
2399 2492 0.457851 CCACAACCGACAGGCAAAAA 59.542 50.000 0.00 0.00 42.76 1.94
2400 2493 1.535860 CCACAACCGACAGGCAAAAAG 60.536 52.381 0.00 0.00 42.76 2.27
2401 2494 1.403679 CACAACCGACAGGCAAAAAGA 59.596 47.619 0.00 0.00 42.76 2.52
2402 2495 2.096248 ACAACCGACAGGCAAAAAGAA 58.904 42.857 0.00 0.00 42.76 2.52
2407 2500 6.207810 ACAACCGACAGGCAAAAAGAATATTA 59.792 34.615 0.00 0.00 42.76 0.98
2486 2583 5.004361 TGACTCCCCCAATTTCATTAACA 57.996 39.130 0.00 0.00 0.00 2.41
2505 2602 7.536895 TTAACAAAACTAGCGTCAACTACAA 57.463 32.000 0.00 0.00 0.00 2.41
2553 2651 0.530650 GTCCACGCGATCACCATCAT 60.531 55.000 15.93 0.00 0.00 2.45
2556 2654 1.069765 ACGCGATCACCATCATCCC 59.930 57.895 15.93 0.00 0.00 3.85
2648 2751 0.035056 AAAAGACCAGGGGCATCTCG 60.035 55.000 0.00 0.00 0.00 4.04
2667 2770 4.080469 TCTCGTATCACACCTAGGAAGAGT 60.080 45.833 17.98 5.44 0.00 3.24
2689 2792 0.182299 TCCAACACACACATCCAGCA 59.818 50.000 0.00 0.00 0.00 4.41
2691 2794 1.614903 CCAACACACACATCCAGCAAT 59.385 47.619 0.00 0.00 0.00 3.56
2749 2852 1.425448 AGCTAACCCAAGCCACTCTTT 59.575 47.619 0.00 0.00 43.86 2.52
2848 2951 3.099905 CCTCACTTGGTGGATCTCAGTA 58.900 50.000 0.00 0.00 33.87 2.74
2856 2959 2.480416 GGTGGATCTCAGTAGCAACTCG 60.480 54.545 0.00 0.00 31.97 4.18
2872 2975 1.229428 CTCGCTCCAGAAGTTTTGCA 58.771 50.000 0.00 0.00 0.00 4.08
2877 2980 1.002468 CTCCAGAAGTTTTGCACACCG 60.002 52.381 0.00 0.00 0.00 4.94
2888 2991 2.325082 GCACACCGCTACAACCCAG 61.325 63.158 0.00 0.00 37.77 4.45
2890 2993 0.534203 CACACCGCTACAACCCAGTT 60.534 55.000 0.00 0.00 0.00 3.16
2914 3017 4.120755 CCTCCCTCCCCTGCAAGC 62.121 72.222 0.00 0.00 0.00 4.01
2956 3059 6.183360 CCAAAATGAAACTCTGAACAGAACCT 60.183 38.462 6.01 0.00 36.94 3.50
2971 3074 2.240493 AACCTCACTTGGTTCGACAG 57.760 50.000 0.00 0.00 46.37 3.51
2977 3080 1.608590 CACTTGGTTCGACAGCCATTT 59.391 47.619 3.75 0.00 34.37 2.32
2979 3082 2.693074 ACTTGGTTCGACAGCCATTTTT 59.307 40.909 3.75 0.00 34.37 1.94
3011 3115 4.475944 CAAGGTTACGAGCTTTCCAAATG 58.524 43.478 0.00 0.00 41.44 2.32
3025 3129 4.454728 TCCAAATGCTCCAAATAACTGC 57.545 40.909 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.671279 AGAATGATCATATAAACAACAGTGTCA 57.329 29.630 9.04 0.00 36.80 3.58
109 110 8.902540 TCCAAATGAGCTACGTATCAAATTAT 57.097 30.769 3.15 0.00 0.00 1.28
117 118 5.918608 AGAACATCCAAATGAGCTACGTAT 58.081 37.500 0.00 0.00 36.67 3.06
121 122 5.189180 AGGAAGAACATCCAAATGAGCTAC 58.811 41.667 0.00 0.00 42.27 3.58
140 141 2.158066 TGTACAGGAAAGGGAGGAGGAA 60.158 50.000 0.00 0.00 0.00 3.36
144 145 2.637872 CACTTGTACAGGAAAGGGAGGA 59.362 50.000 12.54 0.00 0.00 3.71
167 168 8.286800 CCATTAATCGAAAAACTGTCTACAACA 58.713 33.333 0.00 0.00 36.18 3.33
202 203 0.392193 AAAGATCAGCCGGCAGACTG 60.392 55.000 31.54 18.66 35.15 3.51
207 208 3.823873 TCTTTTAAAAAGATCAGCCGGCA 59.176 39.130 31.54 9.64 0.00 5.69
250 251 3.260483 GCTCGATGCGCCACTCTG 61.260 66.667 4.18 0.00 0.00 3.35
383 385 7.846644 ATGTTGCAAAAAGATGAAGACAAAA 57.153 28.000 0.00 0.00 0.00 2.44
425 429 3.434596 GGCATCTTACCGTTCCCCTTAAT 60.435 47.826 0.00 0.00 0.00 1.40
437 441 0.175760 TGCGTCTCTGGCATCTTACC 59.824 55.000 0.00 0.00 35.04 2.85
443 447 2.125912 GTCGTGCGTCTCTGGCAT 60.126 61.111 0.00 0.00 43.19 4.40
446 450 2.016704 GTGTGTCGTGCGTCTCTGG 61.017 63.158 0.00 0.00 0.00 3.86
450 454 1.226745 TTTCGTGTGTCGTGCGTCT 60.227 52.632 0.00 0.00 40.80 4.18
455 459 0.716666 TGTGTGTTTCGTGTGTCGTG 59.283 50.000 0.00 0.00 40.80 4.35
458 462 2.350192 TGTGATGTGTGTTTCGTGTGTC 59.650 45.455 0.00 0.00 0.00 3.67
514 524 1.153147 GACTGATTTCTCGGCCCCC 60.153 63.158 0.00 0.00 0.00 5.40
536 546 3.585732 AGTAAGGAAAACGATTCCCCTCA 59.414 43.478 17.27 0.00 39.39 3.86
546 556 4.688879 TGACATGTAGCAGTAAGGAAAACG 59.311 41.667 0.00 0.00 0.00 3.60
554 564 4.245660 GCTTCAGTGACATGTAGCAGTAA 58.754 43.478 10.47 0.00 41.63 2.24
559 569 1.002366 CCGCTTCAGTGACATGTAGC 58.998 55.000 0.00 1.61 39.44 3.58
560 570 2.370281 ACCGCTTCAGTGACATGTAG 57.630 50.000 0.00 0.00 0.00 2.74
561 571 2.831685 AACCGCTTCAGTGACATGTA 57.168 45.000 0.00 0.00 0.00 2.29
585 595 1.149361 TGACTGGCGACGTCAACAAC 61.149 55.000 17.16 10.42 39.61 3.32
596 607 3.963383 AAACTGTTTTAGTGACTGGCG 57.037 42.857 0.00 0.00 40.26 5.69
680 691 3.533105 TGGTCGAGGTGTGCACGT 61.533 61.111 13.13 0.00 0.00 4.49
706 717 2.625737 CAGGTATTGAGAGTGGTGCTG 58.374 52.381 0.00 0.00 0.00 4.41
710 721 3.195825 GTGTAGCAGGTATTGAGAGTGGT 59.804 47.826 0.00 0.00 0.00 4.16
711 722 3.430929 GGTGTAGCAGGTATTGAGAGTGG 60.431 52.174 0.00 0.00 0.00 4.00
712 723 3.195610 TGGTGTAGCAGGTATTGAGAGTG 59.804 47.826 0.00 0.00 0.00 3.51
713 724 3.441101 TGGTGTAGCAGGTATTGAGAGT 58.559 45.455 0.00 0.00 0.00 3.24
726 751 3.334583 TCATCCTTGACTTGGTGTAGC 57.665 47.619 0.00 0.00 0.00 3.58
753 778 5.048991 AGGATGTTGACACGTTGGTTTATTC 60.049 40.000 0.00 0.00 0.00 1.75
754 779 4.825085 AGGATGTTGACACGTTGGTTTATT 59.175 37.500 0.00 0.00 0.00 1.40
755 780 4.215399 CAGGATGTTGACACGTTGGTTTAT 59.785 41.667 0.00 0.00 0.00 1.40
756 781 3.562141 CAGGATGTTGACACGTTGGTTTA 59.438 43.478 0.00 0.00 0.00 2.01
763 788 0.667487 CGCTCAGGATGTTGACACGT 60.667 55.000 0.00 0.00 37.40 4.49
791 816 0.251354 TCTCAGATTGCAGTGGCCTC 59.749 55.000 3.32 0.00 40.13 4.70
795 820 3.278668 AATCCTCTCAGATTGCAGTGG 57.721 47.619 0.00 0.00 35.15 4.00
799 824 4.202441 GCCTAAAATCCTCTCAGATTGCA 58.798 43.478 0.00 0.00 36.59 4.08
807 832 5.415701 TGTTTCATGTGCCTAAAATCCTCTC 59.584 40.000 0.00 0.00 0.00 3.20
864 889 1.193426 GTCACGTTTCTTCTGCTGCTC 59.807 52.381 0.00 0.00 0.00 4.26
866 891 0.111089 CGTCACGTTTCTTCTGCTGC 60.111 55.000 0.00 0.00 0.00 5.25
907 932 4.889995 GGAATGGTGGAATTAGAAGGAAGG 59.110 45.833 0.00 0.00 0.00 3.46
908 933 5.358160 GTGGAATGGTGGAATTAGAAGGAAG 59.642 44.000 0.00 0.00 0.00 3.46
909 934 5.261216 GTGGAATGGTGGAATTAGAAGGAA 58.739 41.667 0.00 0.00 0.00 3.36
1405 1458 4.273318 AGCATATTGGGGTGAGAAGAAAC 58.727 43.478 0.00 0.00 0.00 2.78
1428 1482 0.181114 TTGAAGCACACTGGTCAGCT 59.819 50.000 0.00 0.00 39.37 4.24
1439 1502 5.379827 GTTGGTACTACGAAATTGAAGCAC 58.620 41.667 0.00 0.00 0.00 4.40
1452 1515 6.127140 ACACATCATAGAAGGGTTGGTACTAC 60.127 42.308 0.00 0.00 0.00 2.73
1453 1516 5.962031 ACACATCATAGAAGGGTTGGTACTA 59.038 40.000 0.00 0.00 0.00 1.82
1454 1517 4.783227 ACACATCATAGAAGGGTTGGTACT 59.217 41.667 0.00 0.00 0.00 2.73
1474 1537 0.676782 AGGCGCCCTGTAATGAACAC 60.677 55.000 26.15 0.00 33.45 3.32
1550 1613 0.716108 CGAAGTTCGTGATGGTGAGC 59.284 55.000 17.16 0.00 34.72 4.26
1569 1632 2.588989 CAGCTCCTCCAGAAGGGC 59.411 66.667 0.00 0.00 46.23 5.19
1679 1742 2.288666 GTGTTCCACTTGCAGAACTGA 58.711 47.619 15.17 0.00 42.32 3.41
1826 1889 0.753479 AGTGGCGGATGTCGAGAGAT 60.753 55.000 0.00 0.00 45.19 2.75
1918 1981 2.031314 TCGTAATCCATCGTCGAGTCAC 59.969 50.000 0.00 0.00 0.00 3.67
1931 1994 5.974751 GTGAGAGAACTTCAGATCGTAATCC 59.025 44.000 0.00 0.00 31.78 3.01
1994 2057 0.518636 CCAACTCGTGCCAATCACAG 59.481 55.000 0.00 0.00 45.92 3.66
2037 2100 0.320374 TAGCTGCACACCAGTACACC 59.680 55.000 1.02 0.00 43.71 4.16
2094 2157 4.556592 AACCCATCCATTTGGTTCATTG 57.443 40.909 0.00 0.00 37.88 2.82
2095 2158 6.889595 ATTAACCCATCCATTTGGTTCATT 57.110 33.333 0.00 0.00 41.34 2.57
2096 2159 7.986553 TTATTAACCCATCCATTTGGTTCAT 57.013 32.000 0.00 0.00 41.34 2.57
2097 2160 7.147585 CCATTATTAACCCATCCATTTGGTTCA 60.148 37.037 0.00 0.00 41.34 3.18
2098 2161 7.216494 CCATTATTAACCCATCCATTTGGTTC 58.784 38.462 0.00 0.00 41.34 3.62
2099 2162 6.409120 GCCATTATTAACCCATCCATTTGGTT 60.409 38.462 0.00 0.00 44.31 3.67
2100 2163 5.071653 GCCATTATTAACCCATCCATTTGGT 59.928 40.000 0.00 0.00 34.77 3.67
2101 2164 5.071519 TGCCATTATTAACCCATCCATTTGG 59.928 40.000 0.00 0.00 36.46 3.28
2141 2204 1.002251 TGTCGGCAAAATCAACGAACC 60.002 47.619 0.00 0.00 37.08 3.62
2143 2206 2.920227 GCATGTCGGCAAAATCAACGAA 60.920 45.455 0.00 0.00 37.08 3.85
2145 2208 0.984109 GCATGTCGGCAAAATCAACG 59.016 50.000 0.00 0.00 0.00 4.10
2146 2209 2.253603 GAGCATGTCGGCAAAATCAAC 58.746 47.619 0.00 0.00 35.83 3.18
2171 2236 0.039618 TGGAGAGGGGTGAAAATGGC 59.960 55.000 0.00 0.00 0.00 4.40
2245 2338 0.465642 CAAAGGCGGGGGATAACCTC 60.466 60.000 0.00 0.00 40.03 3.85
2246 2339 1.613061 CAAAGGCGGGGGATAACCT 59.387 57.895 0.00 0.00 40.03 3.50
2247 2340 2.125326 GCAAAGGCGGGGGATAACC 61.125 63.158 0.00 0.00 39.11 2.85
2248 2341 0.755327 ATGCAAAGGCGGGGGATAAC 60.755 55.000 0.00 0.00 45.35 1.89
2249 2342 0.467290 GATGCAAAGGCGGGGGATAA 60.467 55.000 0.00 0.00 45.35 1.75
2250 2343 1.150536 GATGCAAAGGCGGGGGATA 59.849 57.895 0.00 0.00 45.35 2.59
2251 2344 2.123726 GATGCAAAGGCGGGGGAT 60.124 61.111 0.00 0.00 45.35 3.85
2252 2345 2.721803 TTTGATGCAAAGGCGGGGGA 62.722 55.000 0.00 0.00 45.35 4.81
2253 2346 1.825281 TTTTGATGCAAAGGCGGGGG 61.825 55.000 0.00 0.00 45.35 5.40
2254 2347 0.670239 GTTTTGATGCAAAGGCGGGG 60.670 55.000 0.00 0.00 45.35 5.73
2255 2348 1.008361 CGTTTTGATGCAAAGGCGGG 61.008 55.000 0.00 0.00 45.35 6.13
2256 2349 0.039617 TCGTTTTGATGCAAAGGCGG 60.040 50.000 14.16 0.23 45.35 6.13
2257 2350 1.981254 ATCGTTTTGATGCAAAGGCG 58.019 45.000 0.00 0.00 45.35 5.52
2266 2359 1.333619 GGCCGTATGCATCGTTTTGAT 59.666 47.619 0.19 0.00 43.89 2.57
2267 2360 0.730265 GGCCGTATGCATCGTTTTGA 59.270 50.000 0.19 0.00 43.89 2.69
2268 2361 0.449786 TGGCCGTATGCATCGTTTTG 59.550 50.000 0.19 0.00 43.89 2.44
2269 2362 1.388547 ATGGCCGTATGCATCGTTTT 58.611 45.000 0.19 0.00 43.89 2.43
2270 2363 2.248280 TATGGCCGTATGCATCGTTT 57.752 45.000 0.19 0.00 43.89 3.60
2271 2364 2.472695 ATATGGCCGTATGCATCGTT 57.527 45.000 16.99 0.00 43.89 3.85
2272 2365 2.472695 AATATGGCCGTATGCATCGT 57.527 45.000 18.38 0.00 43.89 3.73
2273 2366 4.570369 TCAATAATATGGCCGTATGCATCG 59.430 41.667 18.38 7.03 43.89 3.84
2274 2367 6.624352 ATCAATAATATGGCCGTATGCATC 57.376 37.500 18.38 0.00 43.89 3.91
2275 2368 7.255242 GCTTATCAATAATATGGCCGTATGCAT 60.255 37.037 18.38 11.61 43.89 3.96
2276 2369 6.038161 GCTTATCAATAATATGGCCGTATGCA 59.962 38.462 18.38 9.81 43.89 3.96
2277 2370 6.038161 TGCTTATCAATAATATGGCCGTATGC 59.962 38.462 18.38 13.44 40.16 3.14
2278 2371 7.552458 TGCTTATCAATAATATGGCCGTATG 57.448 36.000 18.38 7.57 0.00 2.39
2279 2372 8.574251 TTTGCTTATCAATAATATGGCCGTAT 57.426 30.769 11.98 11.98 34.12 3.06
2280 2373 7.987750 TTTGCTTATCAATAATATGGCCGTA 57.012 32.000 7.25 7.25 34.12 4.02
2281 2374 6.892658 TTTGCTTATCAATAATATGGCCGT 57.107 33.333 1.35 1.35 34.12 5.68
2282 2375 6.808212 CCTTTTGCTTATCAATAATATGGCCG 59.192 38.462 0.00 0.00 34.12 6.13
2283 2376 7.670364 ACCTTTTGCTTATCAATAATATGGCC 58.330 34.615 0.00 0.00 34.12 5.36
2284 2377 9.546428 AAACCTTTTGCTTATCAATAATATGGC 57.454 29.630 0.00 0.00 34.12 4.40
2292 2385 9.830975 ACTTTGTTAAACCTTTTGCTTATCAAT 57.169 25.926 0.00 0.00 34.12 2.57
2293 2386 9.308318 GACTTTGTTAAACCTTTTGCTTATCAA 57.692 29.630 0.00 0.00 0.00 2.57
2294 2387 8.691797 AGACTTTGTTAAACCTTTTGCTTATCA 58.308 29.630 0.00 0.00 0.00 2.15
2295 2388 9.529325 AAGACTTTGTTAAACCTTTTGCTTATC 57.471 29.630 0.00 0.00 0.00 1.75
2296 2389 9.313118 CAAGACTTTGTTAAACCTTTTGCTTAT 57.687 29.630 0.00 0.00 0.00 1.73
2297 2390 8.524487 TCAAGACTTTGTTAAACCTTTTGCTTA 58.476 29.630 0.00 0.00 35.73 3.09
2298 2391 7.382898 TCAAGACTTTGTTAAACCTTTTGCTT 58.617 30.769 0.00 0.00 35.73 3.91
2299 2392 6.930731 TCAAGACTTTGTTAAACCTTTTGCT 58.069 32.000 0.00 0.00 35.73 3.91
2300 2393 6.255670 CCTCAAGACTTTGTTAAACCTTTTGC 59.744 38.462 0.00 0.00 35.73 3.68
2301 2394 7.320399 ACCTCAAGACTTTGTTAAACCTTTTG 58.680 34.615 0.00 0.00 35.73 2.44
2302 2395 7.396339 AGACCTCAAGACTTTGTTAAACCTTTT 59.604 33.333 0.00 0.00 35.73 2.27
2303 2396 6.890268 AGACCTCAAGACTTTGTTAAACCTTT 59.110 34.615 0.00 0.00 35.73 3.11
2304 2397 6.424032 AGACCTCAAGACTTTGTTAAACCTT 58.576 36.000 0.00 0.00 35.73 3.50
2305 2398 6.002653 AGACCTCAAGACTTTGTTAAACCT 57.997 37.500 0.00 0.00 35.73 3.50
2306 2399 5.820947 TGAGACCTCAAGACTTTGTTAAACC 59.179 40.000 0.00 0.00 36.53 3.27
2307 2400 6.920569 TGAGACCTCAAGACTTTGTTAAAC 57.079 37.500 0.00 0.00 36.53 2.01
2308 2401 9.273016 CTTATGAGACCTCAAGACTTTGTTAAA 57.727 33.333 3.62 0.00 43.58 1.52
2309 2402 7.878127 CCTTATGAGACCTCAAGACTTTGTTAA 59.122 37.037 3.62 0.00 43.58 2.01
2310 2403 7.386851 CCTTATGAGACCTCAAGACTTTGTTA 58.613 38.462 3.62 0.00 43.58 2.41
2311 2404 6.234177 CCTTATGAGACCTCAAGACTTTGTT 58.766 40.000 3.62 0.00 43.58 2.83
2312 2405 5.280215 CCCTTATGAGACCTCAAGACTTTGT 60.280 44.000 3.62 0.00 43.58 2.83
2313 2406 5.046304 TCCCTTATGAGACCTCAAGACTTTG 60.046 44.000 3.62 0.00 43.58 2.77
2314 2407 5.094387 TCCCTTATGAGACCTCAAGACTTT 58.906 41.667 3.62 0.00 43.58 2.66
2315 2408 4.689062 TCCCTTATGAGACCTCAAGACTT 58.311 43.478 3.62 0.00 43.58 3.01
2316 2409 4.338795 TCCCTTATGAGACCTCAAGACT 57.661 45.455 3.62 0.00 43.58 3.24
2317 2410 5.422214 TTTCCCTTATGAGACCTCAAGAC 57.578 43.478 3.62 0.00 43.58 3.01
2318 2411 6.448369 TTTTTCCCTTATGAGACCTCAAGA 57.552 37.500 3.62 0.00 43.58 3.02
2345 2438 7.195646 TCTTTTGTGTTTTTGCTCTATGTGAG 58.804 34.615 0.00 0.00 45.33 3.51
2346 2439 7.094508 TCTTTTGTGTTTTTGCTCTATGTGA 57.905 32.000 0.00 0.00 0.00 3.58
2347 2440 7.513505 CGTTCTTTTGTGTTTTTGCTCTATGTG 60.514 37.037 0.00 0.00 0.00 3.21
2348 2441 6.472163 CGTTCTTTTGTGTTTTTGCTCTATGT 59.528 34.615 0.00 0.00 0.00 2.29
2349 2442 6.074888 CCGTTCTTTTGTGTTTTTGCTCTATG 60.075 38.462 0.00 0.00 0.00 2.23
2350 2443 5.977129 CCGTTCTTTTGTGTTTTTGCTCTAT 59.023 36.000 0.00 0.00 0.00 1.98
2351 2444 5.336744 CCGTTCTTTTGTGTTTTTGCTCTA 58.663 37.500 0.00 0.00 0.00 2.43
2352 2445 4.173256 CCGTTCTTTTGTGTTTTTGCTCT 58.827 39.130 0.00 0.00 0.00 4.09
2353 2446 3.305897 CCCGTTCTTTTGTGTTTTTGCTC 59.694 43.478 0.00 0.00 0.00 4.26
2354 2447 3.056465 TCCCGTTCTTTTGTGTTTTTGCT 60.056 39.130 0.00 0.00 0.00 3.91
2355 2448 3.254892 TCCCGTTCTTTTGTGTTTTTGC 58.745 40.909 0.00 0.00 0.00 3.68
2356 2449 5.174943 GCTATCCCGTTCTTTTGTGTTTTTG 59.825 40.000 0.00 0.00 0.00 2.44
2357 2450 5.286438 GCTATCCCGTTCTTTTGTGTTTTT 58.714 37.500 0.00 0.00 0.00 1.94
2358 2451 4.261867 GGCTATCCCGTTCTTTTGTGTTTT 60.262 41.667 0.00 0.00 0.00 2.43
2359 2452 3.254903 GGCTATCCCGTTCTTTTGTGTTT 59.745 43.478 0.00 0.00 0.00 2.83
2360 2453 2.817844 GGCTATCCCGTTCTTTTGTGTT 59.182 45.455 0.00 0.00 0.00 3.32
2361 2454 2.224670 TGGCTATCCCGTTCTTTTGTGT 60.225 45.455 0.00 0.00 35.87 3.72
2362 2455 2.161609 GTGGCTATCCCGTTCTTTTGTG 59.838 50.000 0.00 0.00 35.87 3.33
2363 2456 2.224670 TGTGGCTATCCCGTTCTTTTGT 60.225 45.455 0.00 0.00 35.87 2.83
2364 2457 2.432444 TGTGGCTATCCCGTTCTTTTG 58.568 47.619 0.00 0.00 35.87 2.44
2365 2458 2.817844 GTTGTGGCTATCCCGTTCTTTT 59.182 45.455 0.00 0.00 35.87 2.27
2366 2459 2.433436 GTTGTGGCTATCCCGTTCTTT 58.567 47.619 0.00 0.00 35.87 2.52
2367 2460 1.339727 GGTTGTGGCTATCCCGTTCTT 60.340 52.381 0.00 0.00 35.87 2.52
2368 2461 0.252197 GGTTGTGGCTATCCCGTTCT 59.748 55.000 0.00 0.00 35.87 3.01
2369 2462 1.087771 CGGTTGTGGCTATCCCGTTC 61.088 60.000 0.00 0.00 35.87 3.95
2370 2463 1.078708 CGGTTGTGGCTATCCCGTT 60.079 57.895 0.00 0.00 35.87 4.44
2371 2464 1.985662 TCGGTTGTGGCTATCCCGT 60.986 57.895 0.00 0.00 39.62 5.28
2372 2465 1.520787 GTCGGTTGTGGCTATCCCG 60.521 63.158 0.00 0.00 39.98 5.14
2373 2466 0.462047 CTGTCGGTTGTGGCTATCCC 60.462 60.000 0.00 0.00 0.00 3.85
2374 2467 0.462047 CCTGTCGGTTGTGGCTATCC 60.462 60.000 0.00 0.00 0.00 2.59
2375 2468 1.090052 GCCTGTCGGTTGTGGCTATC 61.090 60.000 0.00 0.00 41.92 2.08
2376 2469 1.078426 GCCTGTCGGTTGTGGCTAT 60.078 57.895 0.00 0.00 41.92 2.97
2377 2470 2.046009 TTGCCTGTCGGTTGTGGCTA 62.046 55.000 0.00 0.00 45.11 3.93
2378 2471 2.902423 TTTGCCTGTCGGTTGTGGCT 62.902 55.000 0.00 0.00 45.11 4.75
2379 2472 2.010582 TTTTGCCTGTCGGTTGTGGC 62.011 55.000 0.00 0.00 45.10 5.01
2380 2473 0.457851 TTTTTGCCTGTCGGTTGTGG 59.542 50.000 0.00 0.00 0.00 4.17
2381 2474 1.403679 TCTTTTTGCCTGTCGGTTGTG 59.596 47.619 0.00 0.00 0.00 3.33
2382 2475 1.757682 TCTTTTTGCCTGTCGGTTGT 58.242 45.000 0.00 0.00 0.00 3.32
2383 2476 2.861462 TTCTTTTTGCCTGTCGGTTG 57.139 45.000 0.00 0.00 0.00 3.77
2384 2477 5.722021 AATATTCTTTTTGCCTGTCGGTT 57.278 34.783 0.00 0.00 0.00 4.44
2385 2478 7.404671 AATAATATTCTTTTTGCCTGTCGGT 57.595 32.000 0.00 0.00 0.00 4.69
2386 2479 9.450807 CTAAATAATATTCTTTTTGCCTGTCGG 57.549 33.333 4.37 0.00 0.00 4.79
2460 2557 2.287584 TGAAATTGGGGGAGTCATCCT 58.712 47.619 0.00 0.00 45.85 3.24
2486 2583 4.444536 TGGTTGTAGTTGACGCTAGTTTT 58.555 39.130 0.00 0.00 0.00 2.43
2505 2602 2.372172 TGGTGTGTTTTGGGTTTTTGGT 59.628 40.909 0.00 0.00 0.00 3.67
2543 2641 1.911454 TTGGAGGGGATGATGGTGAT 58.089 50.000 0.00 0.00 0.00 3.06
2633 2736 0.318762 GATACGAGATGCCCCTGGTC 59.681 60.000 0.00 0.00 0.00 4.02
2634 2737 0.398522 TGATACGAGATGCCCCTGGT 60.399 55.000 0.00 0.00 0.00 4.00
2640 2743 2.029828 CCTAGGTGTGATACGAGATGCC 60.030 54.545 0.00 0.00 0.00 4.40
2648 2751 6.107343 GGAAAACTCTTCCTAGGTGTGATAC 58.893 44.000 9.08 0.00 35.73 2.24
2667 2770 2.100584 GCTGGATGTGTGTGTTGGAAAA 59.899 45.455 0.00 0.00 0.00 2.29
2706 2809 2.890766 TTGGGGTTCAGGAGTCCGC 61.891 63.158 2.76 0.00 35.26 5.54
2749 2852 1.062880 GCGGTCTTGTCGTGTGAAAAA 59.937 47.619 0.00 0.00 0.00 1.94
2754 2857 0.455464 TATCGCGGTCTTGTCGTGTG 60.455 55.000 6.13 0.00 38.95 3.82
2756 2859 0.179171 AGTATCGCGGTCTTGTCGTG 60.179 55.000 6.13 0.00 39.20 4.35
2768 2871 3.182572 GGTTGATCATCGACAAGTATCGC 59.817 47.826 7.37 0.00 41.97 4.58
2807 2910 2.665185 AAGCTGGGCGTCGTGAAC 60.665 61.111 0.00 0.00 0.00 3.18
2856 2959 1.269257 GGTGTGCAAAACTTCTGGAGC 60.269 52.381 0.00 0.00 0.00 4.70
2872 2975 0.181824 AAACTGGGTTGTAGCGGTGT 59.818 50.000 0.00 0.00 0.00 4.16
2877 2980 0.666374 ACGCAAAACTGGGTTGTAGC 59.334 50.000 0.00 0.00 0.00 3.58
2888 2991 1.674651 GGGAGGGAGGACGCAAAAC 60.675 63.158 0.00 0.00 0.00 2.43
2890 2993 3.327404 GGGGAGGGAGGACGCAAA 61.327 66.667 0.00 0.00 0.00 3.68
2914 3017 7.784037 TCATTTTGGATTAATGATTGGAGTGG 58.216 34.615 0.00 0.00 37.15 4.00
2956 3059 0.396435 ATGGCTGTCGAACCAAGTGA 59.604 50.000 7.12 0.00 39.96 3.41
2977 3080 7.878036 AGCTCGTAACCTTGCTTATTTAAAAA 58.122 30.769 0.00 0.00 30.96 1.94
2979 3082 7.443259 AAGCTCGTAACCTTGCTTATTTAAA 57.557 32.000 0.00 0.00 42.94 1.52
2982 3085 5.106277 GGAAAGCTCGTAACCTTGCTTATTT 60.106 40.000 0.00 0.00 43.80 1.40


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

AutoCloner maintained by Alex Coulton.