Multiple sequence alignment - TraesCS2D01G182300

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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 TraesCS2D01G182300 chr2D 100.000 2303 0 0 1 2303 126957167 126959469 0.000000e+00 4253
1 TraesCS2D01G182300 chr2D 75.588 893 156 42 1374 2232 126947559 126948423 3.590000e-103 385
2 TraesCS2D01G182300 chr2D 76.957 677 131 19 1448 2103 126946654 126947326 1.680000e-96 363
3 TraesCS2D01G182300 chr2D 97.222 72 2 0 2232 2303 593406782 593406711 3.110000e-24 122
4 TraesCS2D01G182300 chr2D 97.143 70 2 0 2234 2303 35317373 35317304 4.020000e-23 119
5 TraesCS2D01G182300 chr6D 99.247 1328 7 2 1 1328 60313526 60314850 0.000000e+00 2394
6 TraesCS2D01G182300 chr6D 98.794 1327 14 2 1 1327 132391944 132393268 0.000000e+00 2361
7 TraesCS2D01G182300 chr4D 99.014 1318 13 0 1 1318 337468943 337467626 0.000000e+00 2362
8 TraesCS2D01G182300 chr4D 98.644 1327 17 1 1 1327 28465723 28464398 0.000000e+00 2350
9 TraesCS2D01G182300 chr3D 98.718 1326 16 1 1 1326 264599522 264600846 0.000000e+00 2353
10 TraesCS2D01G182300 chr3D 98.420 1329 19 2 1 1328 569380519 569381846 0.000000e+00 2337
11 TraesCS2D01G182300 chr3D 95.833 72 3 0 2232 2303 104815026 104815097 1.450000e-22 117
12 TraesCS2D01G182300 chr1D 97.816 1328 27 2 1 1327 163481530 163480204 0.000000e+00 2290
13 TraesCS2D01G182300 chr1D 97.362 1327 32 3 1 1326 360147420 360146096 0.000000e+00 2254
14 TraesCS2D01G182300 chr1D 97.143 70 2 0 2234 2303 421873412 421873481 4.020000e-23 119
15 TraesCS2D01G182300 chr5B 97.739 1327 29 1 1 1327 521395031 521396356 0.000000e+00 2283
16 TraesCS2D01G182300 chr2B 92.874 842 50 7 1388 2225 180546196 180547031 0.000000e+00 1214
17 TraesCS2D01G182300 chr2B 77.071 676 131 16 1448 2103 180539921 180540592 3.610000e-98 368
18 TraesCS2D01G182300 chr2A 92.687 670 45 3 1410 2078 133484869 133485535 0.000000e+00 963
19 TraesCS2D01G182300 chr2A 75.889 900 140 49 1374 2232 133474008 133474871 2.770000e-104 388
20 TraesCS2D01G182300 chr2A 76.471 680 130 20 1448 2103 133473118 133473791 2.190000e-90 342
21 TraesCS2D01G182300 chr2A 93.793 145 9 0 2081 2225 133488490 133488634 3.850000e-53 219
22 TraesCS2D01G182300 chr7D 95.122 82 4 0 2222 2303 423695534 423695453 1.860000e-26 130
23 TraesCS2D01G182300 chr5D 98.571 70 1 0 2234 2303 390346514 390346445 8.640000e-25 124
24 TraesCS2D01G182300 chr5D 97.183 71 2 0 2233 2303 421145526 421145596 1.120000e-23 121
25 TraesCS2D01G182300 chr3B 97.101 69 2 0 2235 2303 822797662 822797594 1.450000e-22 117
26 TraesCS2D01G182300 chr6A 95.775 71 3 0 2233 2303 617983913 617983843 5.200000e-22 115


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 TraesCS2D01G182300 chr2D 126957167 126959469 2302 False 4253 4253 100.0000 1 2303 1 chr2D.!!$F1 2302
1 TraesCS2D01G182300 chr2D 126946654 126948423 1769 False 374 385 76.2725 1374 2232 2 chr2D.!!$F2 858
2 TraesCS2D01G182300 chr6D 60313526 60314850 1324 False 2394 2394 99.2470 1 1328 1 chr6D.!!$F1 1327
3 TraesCS2D01G182300 chr6D 132391944 132393268 1324 False 2361 2361 98.7940 1 1327 1 chr6D.!!$F2 1326
4 TraesCS2D01G182300 chr4D 337467626 337468943 1317 True 2362 2362 99.0140 1 1318 1 chr4D.!!$R2 1317
5 TraesCS2D01G182300 chr4D 28464398 28465723 1325 True 2350 2350 98.6440 1 1327 1 chr4D.!!$R1 1326
6 TraesCS2D01G182300 chr3D 264599522 264600846 1324 False 2353 2353 98.7180 1 1326 1 chr3D.!!$F2 1325
7 TraesCS2D01G182300 chr3D 569380519 569381846 1327 False 2337 2337 98.4200 1 1328 1 chr3D.!!$F3 1327
8 TraesCS2D01G182300 chr1D 163480204 163481530 1326 True 2290 2290 97.8160 1 1327 1 chr1D.!!$R1 1326
9 TraesCS2D01G182300 chr1D 360146096 360147420 1324 True 2254 2254 97.3620 1 1326 1 chr1D.!!$R2 1325
10 TraesCS2D01G182300 chr5B 521395031 521396356 1325 False 2283 2283 97.7390 1 1327 1 chr5B.!!$F1 1326
11 TraesCS2D01G182300 chr2B 180546196 180547031 835 False 1214 1214 92.8740 1388 2225 1 chr2B.!!$F2 837
12 TraesCS2D01G182300 chr2B 180539921 180540592 671 False 368 368 77.0710 1448 2103 1 chr2B.!!$F1 655
13 TraesCS2D01G182300 chr2A 133484869 133488634 3765 False 591 963 93.2400 1410 2225 2 chr2A.!!$F2 815
14 TraesCS2D01G182300 chr2A 133473118 133474871 1753 False 365 388 76.1800 1374 2232 2 chr2A.!!$F1 858

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
362 363 2.302733 CCTGCCCAGCAAAGGTAAAAAT 59.697 45.455 0.0 0.0 38.41 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1366 1370 0.036388 ATGCGTTGTGGTGGAGGTAG 60.036 55.0 0.0 0.0 0.0 3.18 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
362 363 2.302733 CCTGCCCAGCAAAGGTAAAAAT 59.697 45.455 0.00 0.00 38.41 1.82
1341 1345 2.936928 AAAAACTCCTAACCGCCGG 58.063 52.632 0.00 0.00 0.00 6.13
1342 1346 1.239296 AAAAACTCCTAACCGCCGGC 61.239 55.000 19.07 19.07 0.00 6.13
1343 1347 2.120737 AAAACTCCTAACCGCCGGCT 62.121 55.000 26.68 8.66 0.00 5.52
1344 1348 2.517484 AAACTCCTAACCGCCGGCTC 62.517 60.000 26.68 0.00 0.00 4.70
1345 1349 3.458163 CTCCTAACCGCCGGCTCA 61.458 66.667 26.68 5.37 0.00 4.26
1346 1350 2.762459 TCCTAACCGCCGGCTCAT 60.762 61.111 26.68 12.46 0.00 2.90
1347 1351 2.588877 CCTAACCGCCGGCTCATG 60.589 66.667 26.68 12.63 0.00 3.07
1348 1352 2.499205 CTAACCGCCGGCTCATGA 59.501 61.111 26.68 4.73 0.00 3.07
1349 1353 1.153449 CTAACCGCCGGCTCATGAA 60.153 57.895 26.68 3.80 0.00 2.57
1350 1354 0.742990 CTAACCGCCGGCTCATGAAA 60.743 55.000 26.68 2.08 0.00 2.69
1351 1355 0.742990 TAACCGCCGGCTCATGAAAG 60.743 55.000 26.68 5.71 0.00 2.62
1352 1356 2.125147 CCGCCGGCTCATGAAAGA 60.125 61.111 26.68 0.00 0.00 2.52
1353 1357 2.176273 CCGCCGGCTCATGAAAGAG 61.176 63.158 26.68 4.04 38.68 2.85
1354 1358 1.448540 CGCCGGCTCATGAAAGAGT 60.449 57.895 26.68 0.00 37.94 3.24
1355 1359 1.021390 CGCCGGCTCATGAAAGAGTT 61.021 55.000 26.68 0.00 37.94 3.01
1356 1360 0.449388 GCCGGCTCATGAAAGAGTTG 59.551 55.000 22.15 0.00 37.94 3.16
1357 1361 1.089920 CCGGCTCATGAAAGAGTTGG 58.910 55.000 0.00 0.00 37.94 3.77
1358 1362 1.339055 CCGGCTCATGAAAGAGTTGGA 60.339 52.381 0.00 0.00 37.94 3.53
1359 1363 2.636830 CGGCTCATGAAAGAGTTGGAT 58.363 47.619 0.00 0.00 37.94 3.41
1360 1364 2.611292 CGGCTCATGAAAGAGTTGGATC 59.389 50.000 0.00 0.00 37.94 3.36
1361 1365 2.611292 GGCTCATGAAAGAGTTGGATCG 59.389 50.000 0.00 0.00 37.94 3.69
1362 1366 3.525537 GCTCATGAAAGAGTTGGATCGA 58.474 45.455 0.00 0.00 37.94 3.59
1363 1367 3.935203 GCTCATGAAAGAGTTGGATCGAA 59.065 43.478 0.00 0.00 37.94 3.71
1364 1368 4.201763 GCTCATGAAAGAGTTGGATCGAAC 60.202 45.833 12.27 12.27 37.94 3.95
1365 1369 4.253685 TCATGAAAGAGTTGGATCGAACC 58.746 43.478 16.02 4.46 0.00 3.62
1366 1370 3.053831 TGAAAGAGTTGGATCGAACCC 57.946 47.619 16.02 5.51 0.00 4.11
1367 1371 2.637872 TGAAAGAGTTGGATCGAACCCT 59.362 45.455 16.02 7.85 0.00 4.34
1368 1372 3.835978 TGAAAGAGTTGGATCGAACCCTA 59.164 43.478 16.02 0.00 0.00 3.53
1369 1373 3.889520 AAGAGTTGGATCGAACCCTAC 57.110 47.619 16.02 10.85 0.00 3.18
1370 1374 2.108970 AGAGTTGGATCGAACCCTACC 58.891 52.381 16.02 5.92 31.26 3.18
1371 1375 2.108970 GAGTTGGATCGAACCCTACCT 58.891 52.381 16.02 0.00 31.26 3.08
1372 1376 2.101082 GAGTTGGATCGAACCCTACCTC 59.899 54.545 16.02 5.45 31.26 3.85
1373 1377 1.138464 GTTGGATCGAACCCTACCTCC 59.862 57.143 9.50 0.00 0.00 4.30
1374 1378 0.337082 TGGATCGAACCCTACCTCCA 59.663 55.000 9.50 2.45 0.00 3.86
1375 1379 0.751452 GGATCGAACCCTACCTCCAC 59.249 60.000 0.00 0.00 0.00 4.02
1376 1380 0.751452 GATCGAACCCTACCTCCACC 59.249 60.000 0.00 0.00 0.00 4.61
1377 1381 0.042131 ATCGAACCCTACCTCCACCA 59.958 55.000 0.00 0.00 0.00 4.17
1378 1382 0.901580 TCGAACCCTACCTCCACCAC 60.902 60.000 0.00 0.00 0.00 4.16
1379 1383 1.189524 CGAACCCTACCTCCACCACA 61.190 60.000 0.00 0.00 0.00 4.17
1380 1384 1.061546 GAACCCTACCTCCACCACAA 58.938 55.000 0.00 0.00 0.00 3.33
1381 1385 0.769247 AACCCTACCTCCACCACAAC 59.231 55.000 0.00 0.00 0.00 3.32
1382 1386 1.295423 CCCTACCTCCACCACAACG 59.705 63.158 0.00 0.00 0.00 4.10
1383 1387 1.375523 CCTACCTCCACCACAACGC 60.376 63.158 0.00 0.00 0.00 4.84
1384 1388 1.369692 CTACCTCCACCACAACGCA 59.630 57.895 0.00 0.00 0.00 5.24
1385 1389 0.036388 CTACCTCCACCACAACGCAT 60.036 55.000 0.00 0.00 0.00 4.73
1386 1390 0.036765 TACCTCCACCACAACGCATC 60.037 55.000 0.00 0.00 0.00 3.91
1387 1391 2.390599 CCTCCACCACAACGCATCG 61.391 63.158 0.00 0.00 0.00 3.84
1388 1392 1.374125 CTCCACCACAACGCATCGA 60.374 57.895 0.00 0.00 0.00 3.59
1389 1393 0.740868 CTCCACCACAACGCATCGAT 60.741 55.000 0.00 0.00 0.00 3.59
1390 1394 0.321210 TCCACCACAACGCATCGATT 60.321 50.000 0.00 0.00 0.00 3.34
1391 1395 0.179192 CCACCACAACGCATCGATTG 60.179 55.000 0.00 0.00 0.00 2.67
1392 1396 0.795698 CACCACAACGCATCGATTGA 59.204 50.000 0.00 0.00 0.00 2.57
1393 1397 1.398041 CACCACAACGCATCGATTGAT 59.602 47.619 0.00 0.00 34.28 2.57
1394 1398 2.083774 ACCACAACGCATCGATTGATT 58.916 42.857 0.00 0.00 30.49 2.57
1395 1399 2.095853 ACCACAACGCATCGATTGATTC 59.904 45.455 0.00 0.00 30.49 2.52
1396 1400 2.352651 CCACAACGCATCGATTGATTCT 59.647 45.455 0.00 0.00 30.49 2.40
1413 1417 4.404394 TGATTCTTCAGATAGGGTTACGCA 59.596 41.667 1.60 0.00 0.00 5.24
1519 1523 2.261671 CCGTGGGAGGTTCTGTCG 59.738 66.667 0.00 0.00 0.00 4.35
1541 1545 3.474570 CCTCCTCAAGGGCCTCCG 61.475 72.222 6.46 0.47 42.03 4.63
1787 2786 1.522569 GGTCTATGGCGGCTGTCTT 59.477 57.895 11.43 0.00 0.00 3.01
1850 2849 0.391597 TCGACGCAAAGAAGAACCCT 59.608 50.000 0.00 0.00 0.00 4.34
1984 3007 2.668550 GTTTGGCGGCCTCTTCGT 60.669 61.111 21.46 0.00 0.00 3.85
2012 3035 0.118144 AGGAGGAGAAGAAGCCCAGT 59.882 55.000 0.00 0.00 0.00 4.00
2078 3104 2.280389 CCTCCGGTGCCATCATCG 60.280 66.667 0.00 0.00 45.88 3.84
2082 6057 2.969238 CGGTGCCATCATCGGAGC 60.969 66.667 0.00 0.00 42.79 4.70
2157 6132 4.351874 TCTTTCACTCGGTTTCAGGAAT 57.648 40.909 0.00 0.00 0.00 3.01
2217 6192 0.471211 ACTTTCACGGGAGGAGGTGA 60.471 55.000 5.30 0.00 41.13 4.02
2225 6200 3.386726 CACGGGAGGAGGTGACAATTATA 59.613 47.826 0.00 0.00 36.25 0.98
2226 6201 3.641906 ACGGGAGGAGGTGACAATTATAG 59.358 47.826 0.00 0.00 0.00 1.31
2232 6207 7.256835 GGGAGGAGGTGACAATTATAGATTGAT 60.257 40.741 5.82 0.00 33.51 2.57
2233 6208 8.160106 GGAGGAGGTGACAATTATAGATTGATT 58.840 37.037 5.82 0.00 33.51 2.57
2234 6209 9.566432 GAGGAGGTGACAATTATAGATTGATTT 57.434 33.333 5.82 0.00 33.51 2.17
2235 6210 9.347240 AGGAGGTGACAATTATAGATTGATTTG 57.653 33.333 5.82 0.00 33.51 2.32
2236 6211 9.342308 GGAGGTGACAATTATAGATTGATTTGA 57.658 33.333 5.82 0.00 33.51 2.69
2239 6214 9.903682 GGTGACAATTATAGATTGATTTGATGG 57.096 33.333 5.82 0.00 33.51 3.51
2250 6225 8.362464 AGATTGATTTGATGGATTATGGATGG 57.638 34.615 0.00 0.00 0.00 3.51
2251 6226 6.921486 TTGATTTGATGGATTATGGATGGG 57.079 37.500 0.00 0.00 0.00 4.00
2252 6227 4.773674 TGATTTGATGGATTATGGATGGGC 59.226 41.667 0.00 0.00 0.00 5.36
2253 6228 4.474303 TTTGATGGATTATGGATGGGCT 57.526 40.909 0.00 0.00 0.00 5.19
2254 6229 4.474303 TTGATGGATTATGGATGGGCTT 57.526 40.909 0.00 0.00 0.00 4.35
2255 6230 5.597430 TTGATGGATTATGGATGGGCTTA 57.403 39.130 0.00 0.00 0.00 3.09
2256 6231 5.183530 TGATGGATTATGGATGGGCTTAG 57.816 43.478 0.00 0.00 0.00 2.18
2257 6232 4.018141 TGATGGATTATGGATGGGCTTAGG 60.018 45.833 0.00 0.00 0.00 2.69
2258 6233 2.041620 TGGATTATGGATGGGCTTAGGC 59.958 50.000 0.00 0.00 37.82 3.93
2277 6252 9.549078 GCTTAGGCCTATATAAGACAATAATCC 57.451 37.037 14.74 0.00 31.87 3.01
2279 6254 9.799223 TTAGGCCTATATAAGACAATAATCCCT 57.201 33.333 14.74 0.00 0.00 4.20
2281 6256 9.440761 AGGCCTATATAAGACAATAATCCCTAG 57.559 37.037 1.29 0.00 0.00 3.02
2282 6257 9.214962 GGCCTATATAAGACAATAATCCCTAGT 57.785 37.037 0.00 0.00 0.00 2.57
2290 6265 8.625467 AAGACAATAATCCCTAGTTAACCTCT 57.375 34.615 0.88 0.00 0.00 3.69
2291 6266 9.725206 AAGACAATAATCCCTAGTTAACCTCTA 57.275 33.333 0.88 0.00 0.00 2.43
2292 6267 9.725206 AGACAATAATCCCTAGTTAACCTCTAA 57.275 33.333 0.88 0.00 0.00 2.10
2293 6268 9.984190 GACAATAATCCCTAGTTAACCTCTAAG 57.016 37.037 0.88 0.00 0.00 2.18
2294 6269 8.935741 ACAATAATCCCTAGTTAACCTCTAAGG 58.064 37.037 0.88 2.21 42.49 2.69
2295 6270 5.890752 AATCCCTAGTTAACCTCTAAGGC 57.109 43.478 0.88 0.00 39.63 4.35
2296 6271 3.650948 TCCCTAGTTAACCTCTAAGGCC 58.349 50.000 0.88 0.00 39.63 5.19
2297 6272 2.704596 CCCTAGTTAACCTCTAAGGCCC 59.295 54.545 0.00 0.00 39.63 5.80
2298 6273 3.381335 CCTAGTTAACCTCTAAGGCCCA 58.619 50.000 0.00 0.00 39.63 5.36
2299 6274 3.974642 CCTAGTTAACCTCTAAGGCCCAT 59.025 47.826 0.00 0.00 39.63 4.00
2300 6275 3.933861 AGTTAACCTCTAAGGCCCATG 57.066 47.619 0.00 0.00 39.63 3.66
2301 6276 2.092375 AGTTAACCTCTAAGGCCCATGC 60.092 50.000 0.00 0.00 39.63 4.06
2302 6277 1.590591 TAACCTCTAAGGCCCATGCA 58.409 50.000 0.00 0.00 39.63 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
362 363 7.013369 TGCCATGTAATGTACGCCATATAAAAA 59.987 33.333 0.00 0.00 44.81 1.94
1327 1331 3.459063 GAGCCGGCGGTTAGGAGT 61.459 66.667 28.82 0.00 0.00 3.85
1328 1332 2.797278 ATGAGCCGGCGGTTAGGAG 61.797 63.158 28.82 0.00 0.00 3.69
1329 1333 2.762459 ATGAGCCGGCGGTTAGGA 60.762 61.111 28.82 9.48 0.00 2.94
1330 1334 2.587322 TTCATGAGCCGGCGGTTAGG 62.587 60.000 28.82 15.44 0.00 2.69
1331 1335 0.742990 TTTCATGAGCCGGCGGTTAG 60.743 55.000 28.82 14.89 0.00 2.34
1332 1336 0.742990 CTTTCATGAGCCGGCGGTTA 60.743 55.000 28.82 14.45 0.00 2.85
1333 1337 2.033448 TTTCATGAGCCGGCGGTT 59.967 55.556 28.82 23.64 0.00 4.44
1334 1338 2.436646 CTTTCATGAGCCGGCGGT 60.437 61.111 28.82 14.51 0.00 5.68
1335 1339 2.125147 TCTTTCATGAGCCGGCGG 60.125 61.111 24.35 24.35 0.00 6.13
1336 1340 1.021390 AACTCTTTCATGAGCCGGCG 61.021 55.000 23.20 6.78 37.58 6.46
1337 1341 0.449388 CAACTCTTTCATGAGCCGGC 59.551 55.000 21.89 21.89 37.58 6.13
1338 1342 1.089920 CCAACTCTTTCATGAGCCGG 58.910 55.000 0.00 0.00 37.58 6.13
1339 1343 2.099141 TCCAACTCTTTCATGAGCCG 57.901 50.000 0.00 0.00 37.58 5.52
1340 1344 2.611292 CGATCCAACTCTTTCATGAGCC 59.389 50.000 0.00 0.00 37.58 4.70
1341 1345 3.525537 TCGATCCAACTCTTTCATGAGC 58.474 45.455 0.00 0.00 37.58 4.26
1342 1346 4.331168 GGTTCGATCCAACTCTTTCATGAG 59.669 45.833 7.68 0.00 39.78 2.90
1343 1347 4.253685 GGTTCGATCCAACTCTTTCATGA 58.746 43.478 7.68 0.00 0.00 3.07
1344 1348 3.375299 GGGTTCGATCCAACTCTTTCATG 59.625 47.826 14.36 0.00 0.00 3.07
1345 1349 3.264450 AGGGTTCGATCCAACTCTTTCAT 59.736 43.478 14.36 0.00 32.81 2.57
1346 1350 2.637872 AGGGTTCGATCCAACTCTTTCA 59.362 45.455 14.36 0.00 32.81 2.69
1347 1351 3.336138 AGGGTTCGATCCAACTCTTTC 57.664 47.619 14.36 0.00 32.81 2.62
1348 1352 3.055312 GGTAGGGTTCGATCCAACTCTTT 60.055 47.826 11.05 0.00 38.17 2.52
1349 1353 2.500504 GGTAGGGTTCGATCCAACTCTT 59.499 50.000 11.05 0.00 38.17 2.85
1350 1354 2.108970 GGTAGGGTTCGATCCAACTCT 58.891 52.381 10.60 10.60 40.41 3.24
1351 1355 2.101082 GAGGTAGGGTTCGATCCAACTC 59.899 54.545 14.36 8.26 0.00 3.01
1352 1356 2.108970 GAGGTAGGGTTCGATCCAACT 58.891 52.381 14.36 2.61 0.00 3.16
1353 1357 1.138464 GGAGGTAGGGTTCGATCCAAC 59.862 57.143 14.36 10.88 0.00 3.77
1354 1358 1.273381 TGGAGGTAGGGTTCGATCCAA 60.273 52.381 14.36 0.00 34.02 3.53
1355 1359 0.337082 TGGAGGTAGGGTTCGATCCA 59.663 55.000 14.36 5.47 34.54 3.41
1356 1360 0.751452 GTGGAGGTAGGGTTCGATCC 59.249 60.000 3.76 3.76 0.00 3.36
1357 1361 0.751452 GGTGGAGGTAGGGTTCGATC 59.249 60.000 0.00 0.00 0.00 3.69
1358 1362 0.042131 TGGTGGAGGTAGGGTTCGAT 59.958 55.000 0.00 0.00 0.00 3.59
1359 1363 0.901580 GTGGTGGAGGTAGGGTTCGA 60.902 60.000 0.00 0.00 0.00 3.71
1360 1364 1.189524 TGTGGTGGAGGTAGGGTTCG 61.190 60.000 0.00 0.00 0.00 3.95
1361 1365 1.061546 TTGTGGTGGAGGTAGGGTTC 58.938 55.000 0.00 0.00 0.00 3.62
1362 1366 0.769247 GTTGTGGTGGAGGTAGGGTT 59.231 55.000 0.00 0.00 0.00 4.11
1363 1367 1.477685 CGTTGTGGTGGAGGTAGGGT 61.478 60.000 0.00 0.00 0.00 4.34
1364 1368 1.295423 CGTTGTGGTGGAGGTAGGG 59.705 63.158 0.00 0.00 0.00 3.53
1365 1369 1.375523 GCGTTGTGGTGGAGGTAGG 60.376 63.158 0.00 0.00 0.00 3.18
1366 1370 0.036388 ATGCGTTGTGGTGGAGGTAG 60.036 55.000 0.00 0.00 0.00 3.18
1367 1371 0.036765 GATGCGTTGTGGTGGAGGTA 60.037 55.000 0.00 0.00 0.00 3.08
1368 1372 1.302511 GATGCGTTGTGGTGGAGGT 60.303 57.895 0.00 0.00 0.00 3.85
1369 1373 2.390599 CGATGCGTTGTGGTGGAGG 61.391 63.158 0.00 0.00 0.00 4.30
1370 1374 0.740868 ATCGATGCGTTGTGGTGGAG 60.741 55.000 0.00 0.00 0.00 3.86
1371 1375 0.321210 AATCGATGCGTTGTGGTGGA 60.321 50.000 0.00 0.00 0.00 4.02
1372 1376 0.179192 CAATCGATGCGTTGTGGTGG 60.179 55.000 0.00 0.00 0.00 4.61
1373 1377 0.795698 TCAATCGATGCGTTGTGGTG 59.204 50.000 0.00 0.00 0.00 4.17
1374 1378 1.737838 ATCAATCGATGCGTTGTGGT 58.262 45.000 0.00 0.00 0.00 4.16
1375 1379 2.352651 AGAATCAATCGATGCGTTGTGG 59.647 45.455 0.00 0.00 31.60 4.17
1376 1380 3.663464 AGAATCAATCGATGCGTTGTG 57.337 42.857 0.00 0.00 31.60 3.33
1377 1381 3.684305 TGAAGAATCAATCGATGCGTTGT 59.316 39.130 0.00 0.00 31.60 3.32
1378 1382 4.033243 TCTGAAGAATCAATCGATGCGTTG 59.967 41.667 0.00 0.00 34.49 4.10
1379 1383 4.183865 TCTGAAGAATCAATCGATGCGTT 58.816 39.130 0.00 0.00 34.49 4.84
1380 1384 3.785486 TCTGAAGAATCAATCGATGCGT 58.215 40.909 0.00 0.00 34.49 5.24
1381 1385 4.986875 ATCTGAAGAATCAATCGATGCG 57.013 40.909 0.00 0.00 34.49 4.73
1382 1386 5.350914 CCCTATCTGAAGAATCAATCGATGC 59.649 44.000 0.00 0.00 34.49 3.91
1383 1387 6.462500 ACCCTATCTGAAGAATCAATCGATG 58.538 40.000 0.00 0.00 34.49 3.84
1384 1388 6.678568 ACCCTATCTGAAGAATCAATCGAT 57.321 37.500 0.00 0.00 34.49 3.59
1385 1389 6.485830 AACCCTATCTGAAGAATCAATCGA 57.514 37.500 0.00 0.00 34.49 3.59
1386 1390 6.363626 CGTAACCCTATCTGAAGAATCAATCG 59.636 42.308 0.00 0.00 34.49 3.34
1387 1391 6.146347 GCGTAACCCTATCTGAAGAATCAATC 59.854 42.308 0.00 0.00 34.49 2.67
1388 1392 5.992217 GCGTAACCCTATCTGAAGAATCAAT 59.008 40.000 0.00 0.00 34.49 2.57
1389 1393 5.105106 TGCGTAACCCTATCTGAAGAATCAA 60.105 40.000 0.00 0.00 34.49 2.57
1390 1394 4.404394 TGCGTAACCCTATCTGAAGAATCA 59.596 41.667 0.00 0.00 0.00 2.57
1391 1395 4.945246 TGCGTAACCCTATCTGAAGAATC 58.055 43.478 0.00 0.00 0.00 2.52
1392 1396 4.740934 GCTGCGTAACCCTATCTGAAGAAT 60.741 45.833 0.00 0.00 0.00 2.40
1393 1397 3.430374 GCTGCGTAACCCTATCTGAAGAA 60.430 47.826 0.00 0.00 0.00 2.52
1394 1398 2.100916 GCTGCGTAACCCTATCTGAAGA 59.899 50.000 0.00 0.00 0.00 2.87
1395 1399 2.101582 AGCTGCGTAACCCTATCTGAAG 59.898 50.000 0.00 0.00 0.00 3.02
1396 1400 2.108168 AGCTGCGTAACCCTATCTGAA 58.892 47.619 0.00 0.00 0.00 3.02
1519 1523 2.671682 GCCCTTGAGGAGGTGGAC 59.328 66.667 0.00 0.00 44.71 4.02
1807 2806 1.078708 CGGTTTACCATGAGGGCGT 60.079 57.895 0.00 0.00 42.05 5.68
1946 2969 2.838225 CTACCCCCACCGCTCGAT 60.838 66.667 0.00 0.00 0.00 3.59
1984 3007 2.003830 TCTTCTCCTCCTCCTCCTTGA 58.996 52.381 0.00 0.00 0.00 3.02
2012 3035 2.431683 GACTTGCCCTCACTGCCA 59.568 61.111 0.00 0.00 0.00 4.92
2020 3043 3.829601 CTCTAATATCTCCGACTTGCCCT 59.170 47.826 0.00 0.00 0.00 5.19
2021 3044 3.827302 TCTCTAATATCTCCGACTTGCCC 59.173 47.826 0.00 0.00 0.00 5.36
2078 3104 2.952310 ACCTTCTTTTCACTTGTGCTCC 59.048 45.455 0.00 0.00 0.00 4.70
2082 6057 2.719798 CGCACCTTCTTTTCACTTGTG 58.280 47.619 0.00 0.00 0.00 3.33
2179 6154 4.004196 AGTAGAAGAAACAAGGAACGGG 57.996 45.455 0.00 0.00 0.00 5.28
2225 6200 7.399191 CCCATCCATAATCCATCAAATCAATCT 59.601 37.037 0.00 0.00 0.00 2.40
2226 6201 7.553334 CCCATCCATAATCCATCAAATCAATC 58.447 38.462 0.00 0.00 0.00 2.67
2232 6207 4.474303 AGCCCATCCATAATCCATCAAA 57.526 40.909 0.00 0.00 0.00 2.69
2233 6208 4.474303 AAGCCCATCCATAATCCATCAA 57.526 40.909 0.00 0.00 0.00 2.57
2234 6209 4.018141 CCTAAGCCCATCCATAATCCATCA 60.018 45.833 0.00 0.00 0.00 3.07
2235 6210 4.530875 CCTAAGCCCATCCATAATCCATC 58.469 47.826 0.00 0.00 0.00 3.51
2236 6211 3.309410 GCCTAAGCCCATCCATAATCCAT 60.309 47.826 0.00 0.00 0.00 3.41
2237 6212 2.041620 GCCTAAGCCCATCCATAATCCA 59.958 50.000 0.00 0.00 0.00 3.41
2238 6213 2.728007 GCCTAAGCCCATCCATAATCC 58.272 52.381 0.00 0.00 0.00 3.01
2251 6226 9.549078 GGATTATTGTCTTATATAGGCCTAAGC 57.451 37.037 18.42 8.29 38.76 3.09
2253 6228 9.799223 AGGGATTATTGTCTTATATAGGCCTAA 57.201 33.333 18.42 6.84 0.00 2.69
2255 6230 9.440761 CTAGGGATTATTGTCTTATATAGGCCT 57.559 37.037 11.78 11.78 0.00 5.19
2256 6231 9.214962 ACTAGGGATTATTGTCTTATATAGGCC 57.785 37.037 0.00 0.00 0.00 5.19
2264 6239 9.725206 AGAGGTTAACTAGGGATTATTGTCTTA 57.275 33.333 5.42 0.00 0.00 2.10
2265 6240 8.625467 AGAGGTTAACTAGGGATTATTGTCTT 57.375 34.615 5.42 0.00 0.00 3.01
2266 6241 9.725206 TTAGAGGTTAACTAGGGATTATTGTCT 57.275 33.333 5.42 0.00 0.00 3.41
2267 6242 9.984190 CTTAGAGGTTAACTAGGGATTATTGTC 57.016 37.037 5.42 0.00 0.00 3.18
2268 6243 8.935741 CCTTAGAGGTTAACTAGGGATTATTGT 58.064 37.037 5.42 0.00 38.73 2.71
2269 6244 7.878644 GCCTTAGAGGTTAACTAGGGATTATTG 59.121 40.741 5.42 0.00 38.73 1.90
2270 6245 7.017353 GGCCTTAGAGGTTAACTAGGGATTATT 59.983 40.741 5.42 0.00 38.73 1.40
2271 6246 6.501102 GGCCTTAGAGGTTAACTAGGGATTAT 59.499 42.308 5.42 0.00 38.73 1.28
2272 6247 5.842874 GGCCTTAGAGGTTAACTAGGGATTA 59.157 44.000 5.42 0.00 38.73 1.75
2273 6248 4.659368 GGCCTTAGAGGTTAACTAGGGATT 59.341 45.833 5.42 0.00 38.73 3.01
2274 6249 4.232909 GGCCTTAGAGGTTAACTAGGGAT 58.767 47.826 5.42 0.00 38.73 3.85
2275 6250 3.631865 GGGCCTTAGAGGTTAACTAGGGA 60.632 52.174 0.84 0.00 38.73 4.20
2276 6251 2.704596 GGGCCTTAGAGGTTAACTAGGG 59.295 54.545 0.84 1.64 37.80 3.53
2277 6252 3.381335 TGGGCCTTAGAGGTTAACTAGG 58.619 50.000 4.53 6.29 37.80 3.02
2278 6253 4.743955 GCATGGGCCTTAGAGGTTAACTAG 60.744 50.000 4.53 0.00 37.80 2.57
2279 6254 3.135895 GCATGGGCCTTAGAGGTTAACTA 59.864 47.826 4.53 0.00 37.80 2.24
2280 6255 2.092375 GCATGGGCCTTAGAGGTTAACT 60.092 50.000 4.53 0.00 37.80 2.24
2281 6256 2.298610 GCATGGGCCTTAGAGGTTAAC 58.701 52.381 4.53 0.00 37.80 2.01
2282 6257 1.919654 TGCATGGGCCTTAGAGGTTAA 59.080 47.619 4.53 0.00 37.80 2.01
2283 6258 1.590591 TGCATGGGCCTTAGAGGTTA 58.409 50.000 4.53 0.00 37.80 2.85
2284 6259 2.397815 TGCATGGGCCTTAGAGGTT 58.602 52.632 4.53 0.00 37.80 3.50
2285 6260 4.169452 TGCATGGGCCTTAGAGGT 57.831 55.556 4.53 0.00 37.80 3.85


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

AutoCloner maintained by Alex Coulton.