Multiple sequence alignment - TraesCS1D01G307300

Loading Multiple Alignment...

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 TraesCS1D01G307300 chr1D 100.000 4587 0 0 1 4587 403723726 403719140 0.000000e+00 8471
1 TraesCS1D01G307300 chr1D 83.918 485 60 8 2827 3296 403720786 403720305 9.050000e-122 448
2 TraesCS1D01G307300 chr1D 83.918 485 60 8 2941 3422 403720900 403720431 9.050000e-122 448
3 TraesCS1D01G307300 chr1D 76.438 365 49 23 3627 3973 403719740 403719395 3.670000e-36 163
4 TraesCS1D01G307300 chr1D 76.438 365 49 23 3987 4332 403720100 403719754 3.670000e-36 163
5 TraesCS1D01G307300 chr1D 83.051 118 20 0 2828 2945 403720425 403720308 1.750000e-19 108
6 TraesCS1D01G307300 chr1D 83.051 118 20 0 3302 3419 403720899 403720782 1.750000e-19 108
7 TraesCS1D01G307300 chr1B 93.353 3355 178 17 552 3898 543084658 543081341 0.000000e+00 4918
8 TraesCS1D01G307300 chr1B 91.373 510 14 11 1 500 543085253 543084764 0.000000e+00 671
9 TraesCS1D01G307300 chr1B 89.937 477 30 5 4048 4517 543079540 543079075 2.360000e-167 599
10 TraesCS1D01G307300 chr1B 83.505 485 62 8 2827 3296 543082268 543081787 1.960000e-118 436
11 TraesCS1D01G307300 chr1B 83.230 483 67 6 2941 3422 543082382 543081913 9.120000e-117 431
12 TraesCS1D01G307300 chr1B 91.189 227 15 5 3886 4108 543079759 543079534 2.070000e-78 303
13 TraesCS1D01G307300 chr1B 81.773 203 25 8 3772 3973 543079451 543079260 4.750000e-35 159
14 TraesCS1D01G307300 chr1A 89.554 3743 292 43 765 4458 499441665 499437973 0.000000e+00 4654
15 TraesCS1D01G307300 chr1A 84.519 478 25 15 1 453 499442350 499441897 1.180000e-115 427
16 TraesCS1D01G307300 chr1A 82.680 485 66 8 2941 3422 499439579 499439110 9.180000e-112 414
17 TraesCS1D01G307300 chr1A 82.062 485 69 8 2827 3296 499439465 499438984 9.250000e-107 398
18 TraesCS1D01G307300 chr1A 90.110 91 8 1 553 643 499441762 499441673 2.900000e-22 117
19 TraesCS1D01G307300 chr1A 82.203 118 21 0 3302 3419 499439578 499439461 8.120000e-18 102


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 TraesCS1D01G307300 chr1D 403719140 403723726 4586 True 8471.000000 8471 100.000000 1 4587 1 chr1D.!!$R1 4586
1 TraesCS1D01G307300 chr1D 403719395 403720900 1505 True 239.666667 448 81.135667 2827 4332 6 chr1D.!!$R2 1505
2 TraesCS1D01G307300 chr1B 543079075 543085253 6178 True 1073.857143 4918 87.765714 1 4517 7 chr1B.!!$R1 4516
3 TraesCS1D01G307300 chr1A 499437973 499442350 4377 True 1018.666667 4654 85.188000 1 4458 6 chr1A.!!$R1 4457

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
750 848 0.251787 GGTTGGATTTGGCCTGGTCT 60.252 55.0 3.32 0.0 0.00 3.85 F
1009 1109 0.552848 AGGAGTGGCCATGGGTATTG 59.447 55.0 9.72 0.0 40.02 1.90 F
1243 1343 0.615331 GGGCACACATCTTCCTGAGA 59.385 55.0 0.00 0.0 39.13 3.27 F
2394 2518 0.390472 CTGAGGTGGAAAGGAGTCGC 60.390 60.0 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 1690 0.181350 ATGGATCTTTGGACTCCCGC 59.819 55.000 0.0 0.0 34.29 6.13 R
2104 2225 1.135199 CATTGGAGCAACATCAGCCAC 60.135 52.381 0.0 0.0 0.00 5.01 R
2775 2899 1.167851 CATCCAGCACGAAACATGGT 58.832 50.000 0.0 0.0 34.32 3.55 R
4057 5780 0.673985 GGAACAACTTCACAAGGCCC 59.326 55.000 0.0 0.0 0.00 5.80 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
105 106 1.170290 ACAACGCGGGAAAGGGAAAG 61.170 55.000 12.47 0.00 0.00 2.62
264 271 4.810191 ACTACCAACAGAAGAGATGGTC 57.190 45.455 0.00 0.00 44.73 4.02
312 319 2.417516 CCCACTACCAGCGATCGG 59.582 66.667 18.30 2.45 0.00 4.18
313 320 2.279517 CCACTACCAGCGATCGGC 60.280 66.667 18.30 9.32 44.05 5.54
390 427 2.159043 TCTTGAGCTCGGATCACCATTC 60.159 50.000 9.64 0.00 35.59 2.67
420 458 2.779506 TCGCTCCCCTTTTTCTTTCTC 58.220 47.619 0.00 0.00 0.00 2.87
508 546 4.685026 CCGGCGATCGACCTAGCG 62.685 72.222 21.57 1.94 42.43 4.26
512 550 2.716244 CGATCGACCTAGCGTGCT 59.284 61.111 10.26 0.00 0.00 4.40
614 712 2.892425 CCCATCGCCGTCAGCTTC 60.892 66.667 0.00 0.00 40.39 3.86
622 720 1.352156 GCCGTCAGCTTCAAGGTACG 61.352 60.000 10.02 10.02 38.99 3.67
648 746 5.009710 ACTTCTGATGCTACCGATCGATTAA 59.990 40.000 18.66 0.00 0.00 1.40
655 753 8.343366 TGATGCTACCGATCGATTAATCTATAC 58.657 37.037 18.66 2.67 0.00 1.47
686 784 7.487509 TGTGATTGTGACATTTTAATTATGCCG 59.512 33.333 0.00 0.00 0.00 5.69
719 817 6.347859 AGGGTCTTAGAGATTAATTAGCCG 57.652 41.667 0.00 0.00 0.00 5.52
750 848 0.251787 GGTTGGATTTGGCCTGGTCT 60.252 55.000 3.32 0.00 0.00 3.85
1006 1106 0.691078 GAGAGGAGTGGCCATGGGTA 60.691 60.000 9.72 0.00 40.02 3.69
1009 1109 0.552848 AGGAGTGGCCATGGGTATTG 59.447 55.000 9.72 0.00 40.02 1.90
1014 1114 1.229927 GGCCATGGGTATTGAGGCA 59.770 57.895 15.13 0.00 46.96 4.75
1027 1127 4.644103 ATTGAGGCAAAGCATGATACAC 57.356 40.909 0.00 0.00 0.00 2.90
1041 1141 5.704515 GCATGATACACTAGGCATCAAGAAT 59.295 40.000 0.00 0.00 32.73 2.40
1049 1149 6.072286 ACACTAGGCATCAAGAATGTTTTGAG 60.072 38.462 0.00 0.00 37.91 3.02
1052 1152 4.219288 AGGCATCAAGAATGTTTTGAGGTC 59.781 41.667 0.00 0.00 40.21 3.85
1056 1156 4.065088 TCAAGAATGTTTTGAGGTCCTCG 58.935 43.478 14.34 0.00 32.35 4.63
1090 1190 3.550437 ATAGATGTGCCTCTGAACACC 57.450 47.619 7.72 0.00 35.90 4.16
1110 1210 1.479709 GGGCTCTCTTCAGTCTAGCA 58.520 55.000 0.00 0.00 34.85 3.49
1111 1211 2.038659 GGGCTCTCTTCAGTCTAGCAT 58.961 52.381 0.00 0.00 34.85 3.79
1114 1214 4.283212 GGGCTCTCTTCAGTCTAGCATTAT 59.717 45.833 0.00 0.00 34.85 1.28
1225 1325 3.638160 TGGTATACTGCTAAGTTACGGGG 59.362 47.826 2.25 0.00 37.88 5.73
1243 1343 0.615331 GGGCACACATCTTCCTGAGA 59.385 55.000 0.00 0.00 39.13 3.27
1245 1345 1.277557 GGCACACATCTTCCTGAGACT 59.722 52.381 0.00 0.00 37.17 3.24
1309 1409 6.916360 AGTTTGGATGCTTTTCCAGAAATA 57.084 33.333 4.24 0.00 46.22 1.40
1326 1426 7.814107 TCCAGAAATATTCATTTTGAAGCACAC 59.186 33.333 0.00 0.00 40.05 3.82
1353 1453 4.082026 GGATTTTCTGTGCCTGCAGTTAAT 60.082 41.667 13.81 0.40 37.70 1.40
1364 1464 4.479619 CCTGCAGTTAATGAGAACAAAGC 58.520 43.478 13.81 0.00 0.00 3.51
1421 1542 1.344803 TGGCAAGGAGAGGGATGAGAT 60.345 52.381 0.00 0.00 0.00 2.75
1504 1625 1.143305 CGCTGAGGTGTTCACTTCTG 58.857 55.000 14.28 14.21 0.00 3.02
1569 1690 8.503458 AGGAATTCATGAAGACTAAACATGAG 57.497 34.615 14.54 0.00 46.63 2.90
1619 1740 8.140628 CAGCAATGATAAGAGTACTGAGTATGT 58.859 37.037 0.00 0.00 0.00 2.29
1668 1789 1.480137 AGAGTTGATGAGAAGGAGGCG 59.520 52.381 0.00 0.00 0.00 5.52
1673 1794 1.410517 TGATGAGAAGGAGGCGACATC 59.589 52.381 0.00 0.00 35.96 3.06
1676 1797 1.107114 GAGAAGGAGGCGACATCTGA 58.893 55.000 0.00 0.00 0.00 3.27
1688 1809 4.274459 GGCGACATCTGAATTATGCTCTTT 59.726 41.667 0.00 0.00 0.00 2.52
1719 1840 5.835113 ATGATAGGGAAAATGGTGAAACG 57.165 39.130 0.00 0.00 38.12 3.60
1735 1856 3.637229 TGAAACGGTGGCAAAGGAAAATA 59.363 39.130 0.00 0.00 0.00 1.40
1739 1860 3.006430 ACGGTGGCAAAGGAAAATAAAGG 59.994 43.478 0.00 0.00 0.00 3.11
1914 2035 5.887598 TGTTGATGTAAGCAGCCAAATAGAT 59.112 36.000 0.00 0.00 30.07 1.98
2053 2174 4.159321 TGCTCGATGATATTGATCCTCCTC 59.841 45.833 0.00 0.00 0.00 3.71
2104 2225 6.219417 AGAGTTCCTCTTGTGATATCACTG 57.781 41.667 30.67 23.52 37.60 3.66
2154 2275 4.786425 AGATTGATCCTCCTTTAGGCAAC 58.214 43.478 0.00 0.00 46.10 4.17
2162 2283 3.343617 CTCCTTTAGGCAACGAATTCCA 58.656 45.455 0.00 0.00 46.39 3.53
2197 2318 1.405872 TGGCAATGATGATTCTGGCC 58.594 50.000 0.00 0.00 40.29 5.36
2198 2319 1.063492 TGGCAATGATGATTCTGGCCT 60.063 47.619 3.32 0.00 40.51 5.19
2199 2320 2.037144 GGCAATGATGATTCTGGCCTT 58.963 47.619 3.32 0.00 37.00 4.35
2200 2321 2.433239 GGCAATGATGATTCTGGCCTTT 59.567 45.455 3.32 0.00 37.00 3.11
2201 2322 3.492137 GGCAATGATGATTCTGGCCTTTC 60.492 47.826 3.32 0.00 37.00 2.62
2202 2323 3.131577 GCAATGATGATTCTGGCCTTTCA 59.868 43.478 3.32 1.89 0.00 2.69
2204 2325 5.289595 CAATGATGATTCTGGCCTTTCATG 58.710 41.667 3.32 0.00 0.00 3.07
2205 2326 3.972133 TGATGATTCTGGCCTTTCATGT 58.028 40.909 3.32 0.00 0.00 3.21
2206 2327 3.949754 TGATGATTCTGGCCTTTCATGTC 59.050 43.478 3.32 0.00 0.00 3.06
2208 2329 3.765381 TGATTCTGGCCTTTCATGTCAA 58.235 40.909 3.32 0.00 0.00 3.18
2209 2330 4.151121 TGATTCTGGCCTTTCATGTCAAA 58.849 39.130 3.32 0.00 0.00 2.69
2210 2331 4.588106 TGATTCTGGCCTTTCATGTCAAAA 59.412 37.500 3.32 0.00 0.00 2.44
2211 2332 5.246656 TGATTCTGGCCTTTCATGTCAAAAT 59.753 36.000 3.32 0.00 0.00 1.82
2212 2333 6.436847 TGATTCTGGCCTTTCATGTCAAAATA 59.563 34.615 3.32 0.00 0.00 1.40
2213 2334 6.662865 TTCTGGCCTTTCATGTCAAAATAA 57.337 33.333 3.32 0.00 0.00 1.40
2227 2351 7.630242 TGTCAAAATAATCAGGATCCTCAAC 57.370 36.000 12.69 0.00 0.00 3.18
2262 2386 6.927294 AATAACAACAAGCCTGATACTAGC 57.073 37.500 0.00 0.00 0.00 3.42
2267 2391 4.826274 ACAAGCCTGATACTAGCAAAGA 57.174 40.909 0.00 0.00 0.00 2.52
2394 2518 0.390472 CTGAGGTGGAAAGGAGTCGC 60.390 60.000 0.00 0.00 0.00 5.19
2397 2521 1.376037 GGTGGAAAGGAGTCGCAGG 60.376 63.158 0.00 0.00 0.00 4.85
2427 2551 5.131594 TCATGATGGCTAAGAGAAGATCG 57.868 43.478 0.00 0.00 0.00 3.69
2445 2569 9.921637 AGAAGATCGAGGAAGAACATAATATTC 57.078 33.333 0.00 0.00 0.00 1.75
2499 2623 4.578601 CAGATAGATTTTCACGTTTCCGC 58.421 43.478 0.00 0.00 37.70 5.54
2520 2644 3.688272 CATGCAAGTTCAGCCTATTTCG 58.312 45.455 0.00 0.00 0.00 3.46
2775 2899 5.048224 AGAGAGACACCGTTCTCGATTTAAA 60.048 40.000 0.00 0.00 45.87 1.52
4057 5780 4.359971 TGCCATTTTCTGAACATCGATG 57.640 40.909 23.68 23.68 0.00 3.84
4334 6121 0.096976 CGGTTGGAAGCAAGCATACG 59.903 55.000 0.00 0.00 33.25 3.06
4349 6142 3.112580 GCATACGAGCTCTTCTTCAGAC 58.887 50.000 12.85 0.00 0.00 3.51
4397 6199 2.543012 CACAGACAGCTTCAGTGACAAG 59.457 50.000 12.73 0.00 42.91 3.16
4399 6201 3.058450 CAGACAGCTTCAGTGACAAGAG 58.942 50.000 0.00 0.00 0.00 2.85
4460 6263 3.134623 AGAAGAAAGCCCCCAAAACAAAG 59.865 43.478 0.00 0.00 0.00 2.77
4480 6283 7.869800 ACAAAGCAAAACAAAAACAATCTTGA 58.130 26.923 0.00 0.00 0.00 3.02
4481 6284 8.513774 ACAAAGCAAAACAAAAACAATCTTGAT 58.486 25.926 0.00 0.00 0.00 2.57
4500 6303 2.911439 TTTGCGTCAGTTGCGTGCAC 62.911 55.000 6.82 6.82 34.90 4.57
4517 6320 2.951745 CGATCGACTGACTGCCGC 60.952 66.667 10.26 0.00 0.00 6.53
4518 6321 2.181777 GATCGACTGACTGCCGCA 59.818 61.111 0.00 0.00 0.00 5.69
4519 6322 1.227089 GATCGACTGACTGCCGCAT 60.227 57.895 0.00 0.00 0.00 4.73
4520 6323 1.485838 GATCGACTGACTGCCGCATG 61.486 60.000 0.00 0.00 0.00 4.06
4521 6324 2.230994 ATCGACTGACTGCCGCATGT 62.231 55.000 0.00 0.00 0.00 3.21
4522 6325 2.447887 CGACTGACTGCCGCATGTC 61.448 63.158 13.09 13.09 0.00 3.06
4523 6326 2.433145 ACTGACTGCCGCATGTCG 60.433 61.111 14.32 12.12 36.10 4.35
4524 6327 3.857854 CTGACTGCCGCATGTCGC 61.858 66.667 14.32 0.00 36.10 5.19
4535 6338 1.495878 GCATGTCGCGATCAGATTCT 58.504 50.000 14.06 0.00 0.00 2.40
4536 6339 1.863454 GCATGTCGCGATCAGATTCTT 59.137 47.619 14.06 0.00 0.00 2.52
4537 6340 2.097007 GCATGTCGCGATCAGATTCTTC 60.097 50.000 14.06 0.00 0.00 2.87
4538 6341 3.379240 CATGTCGCGATCAGATTCTTCT 58.621 45.455 14.06 0.00 0.00 2.85
4552 6355 6.306643 AGATTCTTCTGAACTTTCTAGGGG 57.693 41.667 0.00 0.00 34.71 4.79
4553 6356 3.983044 TCTTCTGAACTTTCTAGGGGC 57.017 47.619 0.00 0.00 0.00 5.80
4554 6357 3.248024 TCTTCTGAACTTTCTAGGGGCA 58.752 45.455 0.00 0.00 0.00 5.36
4555 6358 3.261897 TCTTCTGAACTTTCTAGGGGCAG 59.738 47.826 0.00 0.00 0.00 4.85
4556 6359 2.902608 TCTGAACTTTCTAGGGGCAGA 58.097 47.619 0.00 0.00 0.00 4.26
4557 6360 2.834549 TCTGAACTTTCTAGGGGCAGAG 59.165 50.000 0.00 0.00 0.00 3.35
4558 6361 1.909302 TGAACTTTCTAGGGGCAGAGG 59.091 52.381 0.00 0.00 0.00 3.69
4559 6362 0.621082 AACTTTCTAGGGGCAGAGGC 59.379 55.000 0.00 0.00 40.13 4.70
4560 6363 0.252927 ACTTTCTAGGGGCAGAGGCT 60.253 55.000 0.00 0.00 40.87 4.58
4561 6364 0.179936 CTTTCTAGGGGCAGAGGCTG 59.820 60.000 0.00 0.00 40.87 4.85
4562 6365 1.274703 TTTCTAGGGGCAGAGGCTGG 61.275 60.000 0.00 0.00 40.87 4.85
4569 6372 3.896479 GCAGAGGCTGGCTTGTAC 58.104 61.111 4.82 0.00 36.96 2.90
4570 6373 1.298014 GCAGAGGCTGGCTTGTACT 59.702 57.895 4.82 0.00 36.96 2.73
4571 6374 1.023513 GCAGAGGCTGGCTTGTACTG 61.024 60.000 4.82 9.11 36.96 2.74
4572 6375 0.392193 CAGAGGCTGGCTTGTACTGG 60.392 60.000 4.82 0.00 0.00 4.00
4573 6376 0.838122 AGAGGCTGGCTTGTACTGGT 60.838 55.000 4.82 0.00 0.00 4.00
4574 6377 0.902531 GAGGCTGGCTTGTACTGGTA 59.097 55.000 4.82 0.00 0.00 3.25
4575 6378 0.905357 AGGCTGGCTTGTACTGGTAG 59.095 55.000 0.00 0.00 0.00 3.18
4576 6379 0.744771 GGCTGGCTTGTACTGGTAGC 60.745 60.000 0.00 0.00 0.00 3.58
4581 6384 1.726853 GCTTGTACTGGTAGCCTGTG 58.273 55.000 7.77 0.00 36.40 3.66
4582 6385 1.726853 CTTGTACTGGTAGCCTGTGC 58.273 55.000 7.77 7.05 38.22 4.57
4583 6386 1.001974 CTTGTACTGGTAGCCTGTGCA 59.998 52.381 10.71 10.71 43.42 4.57
4584 6387 1.052617 TGTACTGGTAGCCTGTGCAA 58.947 50.000 11.94 0.00 42.57 4.08
4585 6388 1.418264 TGTACTGGTAGCCTGTGCAAA 59.582 47.619 11.94 0.00 42.57 3.68
4586 6389 2.076863 GTACTGGTAGCCTGTGCAAAG 58.923 52.381 0.00 0.00 41.13 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 250 4.221703 CAGACCATCTCTTCTGTTGGTAGT 59.778 45.833 0.00 0.00 42.41 2.73
244 251 4.464244 TCAGACCATCTCTTCTGTTGGTAG 59.536 45.833 0.00 0.00 42.41 3.18
245 252 4.416516 TCAGACCATCTCTTCTGTTGGTA 58.583 43.478 0.00 0.00 42.41 3.25
291 298 1.306654 ATCGCTGGTAGTGGGGGAA 60.307 57.895 0.00 0.00 0.00 3.97
390 427 1.222113 GGGGAGCGAAGGAAAGGAG 59.778 63.158 0.00 0.00 0.00 3.69
463 501 3.261951 CAGATGTAACGCCGGCCG 61.262 66.667 23.46 21.04 44.21 6.13
464 502 3.573491 GCAGATGTAACGCCGGCC 61.573 66.667 23.46 7.25 0.00 6.13
501 539 0.613777 AAAAGGCTAGCACGCTAGGT 59.386 50.000 23.77 0.00 44.48 3.08
502 540 1.134670 AGAAAAGGCTAGCACGCTAGG 60.135 52.381 23.77 9.03 44.48 3.02
508 546 4.275936 TCAAGAACAAGAAAAGGCTAGCAC 59.724 41.667 18.24 6.06 0.00 4.40
512 550 5.182001 GCAGATCAAGAACAAGAAAAGGCTA 59.818 40.000 0.00 0.00 0.00 3.93
614 712 3.589988 AGCATCAGAAGTTCGTACCTTG 58.410 45.455 0.00 0.00 0.00 3.61
622 720 3.046390 CGATCGGTAGCATCAGAAGTTC 58.954 50.000 7.38 0.00 0.00 3.01
648 746 5.105106 TGTCACAATCACAACGGGTATAGAT 60.105 40.000 0.00 0.00 0.00 1.98
655 753 3.641437 AAATGTCACAATCACAACGGG 57.359 42.857 0.00 0.00 0.00 5.28
686 784 2.627699 CTCTAAGACCCTCCATCTCAGC 59.372 54.545 0.00 0.00 0.00 4.26
719 817 0.676782 ATCCAACCGTGTAAGCAGGC 60.677 55.000 0.00 0.00 0.00 4.85
1006 1106 4.275810 AGTGTATCATGCTTTGCCTCAAT 58.724 39.130 0.00 0.00 0.00 2.57
1009 1109 3.812053 CCTAGTGTATCATGCTTTGCCTC 59.188 47.826 0.00 0.00 0.00 4.70
1014 1114 5.039920 TGATGCCTAGTGTATCATGCTTT 57.960 39.130 7.54 0.00 40.61 3.51
1027 1127 5.416952 ACCTCAAAACATTCTTGATGCCTAG 59.583 40.000 0.00 0.00 39.47 3.02
1041 1141 2.897326 TCTGATCGAGGACCTCAAAACA 59.103 45.455 21.49 11.91 0.00 2.83
1049 1149 2.243810 AGCCTATTCTGATCGAGGACC 58.756 52.381 0.00 0.00 0.00 4.46
1052 1152 6.545666 ACATCTATAGCCTATTCTGATCGAGG 59.454 42.308 0.00 0.00 0.00 4.63
1056 1156 6.279882 GGCACATCTATAGCCTATTCTGATC 58.720 44.000 0.00 0.00 44.92 2.92
1090 1190 0.383949 GCTAGACTGAAGAGAGCCCG 59.616 60.000 0.00 0.00 0.00 6.13
1110 1210 6.414732 TCTGTACAGCAGGTAAAGCAATAAT 58.585 36.000 18.45 0.00 45.08 1.28
1111 1211 5.800296 TCTGTACAGCAGGTAAAGCAATAA 58.200 37.500 18.45 0.00 45.08 1.40
1114 1214 3.762407 TCTGTACAGCAGGTAAAGCAA 57.238 42.857 18.45 0.00 45.08 3.91
1225 1325 1.277557 AGTCTCAGGAAGATGTGTGCC 59.722 52.381 0.00 0.00 36.11 5.01
1243 1343 2.040178 AGTCTTCCGGTCTTCAACAGT 58.960 47.619 0.00 0.00 0.00 3.55
1245 1345 2.036387 TCAGTCTTCCGGTCTTCAACA 58.964 47.619 0.00 0.00 0.00 3.33
1271 1371 2.430332 CCAAACTTGGGAGCTGAACAAA 59.570 45.455 0.00 0.00 44.70 2.83
1309 1409 3.007182 CCCTGGTGTGCTTCAAAATGAAT 59.993 43.478 0.00 0.00 35.59 2.57
1326 1426 1.180029 CAGGCACAGAAAATCCCTGG 58.820 55.000 0.00 0.00 39.45 4.45
1353 1453 2.346766 TGAAGCCAGCTTTGTTCTCA 57.653 45.000 6.31 0.00 36.26 3.27
1364 1464 3.967332 ATTCCCAACATTTGAAGCCAG 57.033 42.857 0.00 0.00 0.00 4.85
1421 1542 5.060427 TGATCCCTTCAAAAGAGGAACAA 57.940 39.130 0.00 0.00 36.33 2.83
1504 1625 2.213499 CAGTGTCACCACAGAAGGAAC 58.787 52.381 0.00 0.00 44.39 3.62
1569 1690 0.181350 ATGGATCTTTGGACTCCCGC 59.819 55.000 0.00 0.00 34.29 6.13
1619 1740 4.019792 TCAGCATCCTCAAACAAGCTAA 57.980 40.909 0.00 0.00 0.00 3.09
1676 1797 8.749026 ATCATTCTCACTGAAAGAGCATAATT 57.251 30.769 0.00 0.00 36.10 1.40
1688 1809 6.069440 ACCATTTTCCCTATCATTCTCACTGA 60.069 38.462 0.00 0.00 0.00 3.41
1719 1840 4.617253 ACCTTTATTTTCCTTTGCCACC 57.383 40.909 0.00 0.00 0.00 4.61
1735 1856 6.042781 TGTGAATCTGTTACCACTCTACCTTT 59.957 38.462 0.00 0.00 0.00 3.11
1739 1860 6.929606 ACTTTGTGAATCTGTTACCACTCTAC 59.070 38.462 0.00 0.00 0.00 2.59
1897 2018 6.765512 AGAGAAGAATCTATTTGGCTGCTTAC 59.234 38.462 0.00 0.00 35.54 2.34
1899 2020 5.753716 AGAGAAGAATCTATTTGGCTGCTT 58.246 37.500 0.00 0.00 35.54 3.91
1914 2035 4.997395 GCACATGGTGAAACTAGAGAAGAA 59.003 41.667 0.00 0.00 35.23 2.52
2053 2174 7.938715 AGCTTAAAAGAATCATCATTGCCTAG 58.061 34.615 0.00 0.00 0.00 3.02
2104 2225 1.135199 CATTGGAGCAACATCAGCCAC 60.135 52.381 0.00 0.00 0.00 5.01
2162 2283 2.311854 CCAATGGGACCAGGGCTCT 61.312 63.158 0.00 0.00 35.59 4.09
2171 2292 3.640029 AGAATCATCATTGCCAATGGGAC 59.360 43.478 16.96 5.39 39.38 4.46
2197 2318 8.910944 AGGATCCTGATTATTTTGACATGAAAG 58.089 33.333 15.29 0.00 0.00 2.62
2198 2319 8.827832 AGGATCCTGATTATTTTGACATGAAA 57.172 30.769 15.29 0.00 0.00 2.69
2199 2320 8.054572 TGAGGATCCTGATTATTTTGACATGAA 58.945 33.333 22.02 0.00 0.00 2.57
2200 2321 7.576403 TGAGGATCCTGATTATTTTGACATGA 58.424 34.615 22.02 0.00 0.00 3.07
2201 2322 7.812690 TGAGGATCCTGATTATTTTGACATG 57.187 36.000 22.02 0.00 0.00 3.21
2202 2323 8.057623 AGTTGAGGATCCTGATTATTTTGACAT 58.942 33.333 22.02 0.00 0.00 3.06
2204 2325 7.201767 CCAGTTGAGGATCCTGATTATTTTGAC 60.202 40.741 22.02 2.85 0.00 3.18
2205 2326 6.830324 CCAGTTGAGGATCCTGATTATTTTGA 59.170 38.462 22.02 0.00 0.00 2.69
2206 2327 6.830324 TCCAGTTGAGGATCCTGATTATTTTG 59.170 38.462 22.02 6.38 31.23 2.44
2208 2329 6.581388 TCCAGTTGAGGATCCTGATTATTT 57.419 37.500 22.02 0.00 31.23 1.40
2209 2330 6.776887 ATCCAGTTGAGGATCCTGATTATT 57.223 37.500 22.02 0.00 45.16 1.40
2210 2331 7.021873 ACTATCCAGTTGAGGATCCTGATTAT 58.978 38.462 22.02 5.92 45.16 1.28
2211 2332 6.268617 CACTATCCAGTTGAGGATCCTGATTA 59.731 42.308 22.02 0.00 45.16 1.75
2212 2333 5.071519 CACTATCCAGTTGAGGATCCTGATT 59.928 44.000 22.02 1.01 45.16 2.57
2213 2334 4.592351 CACTATCCAGTTGAGGATCCTGAT 59.408 45.833 22.02 16.40 45.16 2.90
2227 2351 6.038271 GGCTTGTTGTTATTACCACTATCCAG 59.962 42.308 0.00 0.00 0.00 3.86
2232 2356 6.116711 TCAGGCTTGTTGTTATTACCACTA 57.883 37.500 0.00 0.00 0.00 2.74
2262 2386 5.726397 TCCTTGGCATCATTTTCATCTTTG 58.274 37.500 0.00 0.00 0.00 2.77
2267 2391 4.291792 TCCATCCTTGGCATCATTTTCAT 58.708 39.130 0.00 0.00 43.29 2.57
2394 2518 1.747355 GCCATCATGAACTCCAACCTG 59.253 52.381 0.00 0.00 0.00 4.00
2397 2521 4.517285 TCTTAGCCATCATGAACTCCAAC 58.483 43.478 0.00 0.00 0.00 3.77
2427 2551 9.698309 TCAAGATCGAATATTATGTTCTTCCTC 57.302 33.333 0.00 0.00 0.00 3.71
2445 2569 5.212934 CAAGCATCATTTCCATCAAGATCG 58.787 41.667 0.00 0.00 0.00 3.69
2499 2623 3.488047 CCGAAATAGGCTGAACTTGCATG 60.488 47.826 0.00 0.00 0.00 4.06
2520 2644 3.653835 AAAGGGCTTCTCCTTGATACC 57.346 47.619 0.00 0.00 45.67 2.73
2775 2899 1.167851 CATCCAGCACGAAACATGGT 58.832 50.000 0.00 0.00 34.32 3.55
4057 5780 0.673985 GGAACAACTTCACAAGGCCC 59.326 55.000 0.00 0.00 0.00 5.80
4480 6283 1.370414 GCACGCAACTGACGCAAAT 60.370 52.632 0.00 0.00 0.00 2.32
4481 6284 2.024022 GCACGCAACTGACGCAAA 59.976 55.556 0.00 0.00 0.00 3.68
4485 6288 2.534264 GATCGTGCACGCAACTGACG 62.534 60.000 33.63 7.86 39.60 4.35
4517 6320 3.379240 AGAAGAATCTGATCGCGACATG 58.621 45.455 12.93 4.08 33.59 3.21
4518 6321 3.724508 AGAAGAATCTGATCGCGACAT 57.275 42.857 12.93 0.00 33.59 3.06
4529 6332 5.338789 GCCCCTAGAAAGTTCAGAAGAATCT 60.339 44.000 0.00 0.00 35.92 2.40
4530 6333 4.878971 GCCCCTAGAAAGTTCAGAAGAATC 59.121 45.833 0.00 0.00 35.92 2.52
4531 6334 4.289672 TGCCCCTAGAAAGTTCAGAAGAAT 59.710 41.667 0.00 0.00 35.92 2.40
4532 6335 3.650942 TGCCCCTAGAAAGTTCAGAAGAA 59.349 43.478 0.00 0.00 0.00 2.52
4533 6336 3.248024 TGCCCCTAGAAAGTTCAGAAGA 58.752 45.455 0.00 0.00 0.00 2.87
4534 6337 3.261897 TCTGCCCCTAGAAAGTTCAGAAG 59.738 47.826 0.00 0.00 0.00 2.85
4535 6338 3.248024 TCTGCCCCTAGAAAGTTCAGAA 58.752 45.455 0.00 0.00 0.00 3.02
4536 6339 2.834549 CTCTGCCCCTAGAAAGTTCAGA 59.165 50.000 0.00 0.00 0.00 3.27
4537 6340 2.093235 CCTCTGCCCCTAGAAAGTTCAG 60.093 54.545 0.00 0.00 0.00 3.02
4538 6341 1.909302 CCTCTGCCCCTAGAAAGTTCA 59.091 52.381 0.00 0.00 0.00 3.18
4539 6342 1.407575 GCCTCTGCCCCTAGAAAGTTC 60.408 57.143 0.00 0.00 0.00 3.01
4540 6343 0.621082 GCCTCTGCCCCTAGAAAGTT 59.379 55.000 0.00 0.00 0.00 2.66
4541 6344 0.252927 AGCCTCTGCCCCTAGAAAGT 60.253 55.000 0.00 0.00 38.69 2.66
4542 6345 0.179936 CAGCCTCTGCCCCTAGAAAG 59.820 60.000 0.00 0.00 38.69 2.62
4543 6346 1.274703 CCAGCCTCTGCCCCTAGAAA 61.275 60.000 0.00 0.00 38.69 2.52
4544 6347 1.690633 CCAGCCTCTGCCCCTAGAA 60.691 63.158 0.00 0.00 38.69 2.10
4545 6348 2.041508 CCAGCCTCTGCCCCTAGA 60.042 66.667 0.00 0.00 38.69 2.43
4546 6349 3.871395 GCCAGCCTCTGCCCCTAG 61.871 72.222 0.00 0.00 38.69 3.02
4547 6350 3.950861 AAGCCAGCCTCTGCCCCTA 62.951 63.158 0.00 0.00 38.69 3.53
4550 6353 2.971598 TACAAGCCAGCCTCTGCCC 61.972 63.158 0.00 0.00 38.69 5.36
4551 6354 1.746991 GTACAAGCCAGCCTCTGCC 60.747 63.158 0.00 0.00 38.69 4.85
4552 6355 1.023513 CAGTACAAGCCAGCCTCTGC 61.024 60.000 0.00 0.00 37.95 4.26
4553 6356 0.392193 CCAGTACAAGCCAGCCTCTG 60.392 60.000 0.00 0.00 0.00 3.35
4554 6357 0.838122 ACCAGTACAAGCCAGCCTCT 60.838 55.000 0.00 0.00 0.00 3.69
4555 6358 0.902531 TACCAGTACAAGCCAGCCTC 59.097 55.000 0.00 0.00 0.00 4.70
4556 6359 0.905357 CTACCAGTACAAGCCAGCCT 59.095 55.000 0.00 0.00 0.00 4.58
4557 6360 0.744771 GCTACCAGTACAAGCCAGCC 60.745 60.000 0.00 0.00 0.00 4.85
4558 6361 2.768834 GCTACCAGTACAAGCCAGC 58.231 57.895 0.00 0.00 0.00 4.85
4562 6365 1.726853 CACAGGCTACCAGTACAAGC 58.273 55.000 0.00 0.00 35.47 4.01
4563 6366 1.001974 TGCACAGGCTACCAGTACAAG 59.998 52.381 0.00 0.00 41.91 3.16
4564 6367 1.052617 TGCACAGGCTACCAGTACAA 58.947 50.000 0.00 0.00 41.91 2.41
4565 6368 1.052617 TTGCACAGGCTACCAGTACA 58.947 50.000 0.00 0.00 41.91 2.90
4566 6369 2.076863 CTTTGCACAGGCTACCAGTAC 58.923 52.381 0.00 0.00 41.91 2.73
4567 6370 2.472695 CTTTGCACAGGCTACCAGTA 57.527 50.000 0.00 0.00 41.91 2.74
4568 6371 3.329300 CTTTGCACAGGCTACCAGT 57.671 52.632 0.00 0.00 41.91 4.00


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

AutoCloner maintained by Alex Coulton.