Multiple sequence alignment - TraesCS7A01G423400

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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 TraesCS7A01G423400 chr7A 100.000 3834 0 0 1 3834 615380329 615384162 0.000000e+00 7081.0
1 TraesCS7A01G423400 chr7A 100.000 1260 0 0 4172 5431 615384500 615385759 0.000000e+00 2327.0
2 TraesCS7A01G423400 chr7A 83.024 1402 177 26 835 2225 618192095 618190744 0.000000e+00 1214.0
3 TraesCS7A01G423400 chr7A 85.794 1077 142 5 2460 3526 618190683 618189608 0.000000e+00 1131.0
4 TraesCS7A01G423400 chr7A 84.502 271 33 5 3550 3812 618189610 618189341 5.400000e-65 259.0
5 TraesCS7A01G423400 chr7B 95.974 3800 112 13 42 3834 575423656 575427421 0.000000e+00 6131.0
6 TraesCS7A01G423400 chr7B 96.193 3467 114 10 383 3834 577184727 577188190 0.000000e+00 5655.0
7 TraesCS7A01G423400 chr7B 84.701 719 57 23 4738 5431 575428051 575428741 0.000000e+00 669.0
8 TraesCS7A01G423400 chr7B 83.193 714 68 32 4738 5431 577188824 577189505 1.670000e-169 606.0
9 TraesCS7A01G423400 chr7B 92.327 391 24 4 1 389 577184117 577184503 7.950000e-153 551.0
10 TraesCS7A01G423400 chr7B 96.371 248 9 0 4263 4510 575427490 575427737 5.060000e-110 409.0
11 TraesCS7A01G423400 chr7B 95.200 250 10 1 4263 4510 577188261 577188510 1.420000e-105 394.0
12 TraesCS7A01G423400 chr7B 92.818 181 13 0 4538 4718 575427883 575428063 4.170000e-66 263.0
13 TraesCS7A01G423400 chr7B 90.659 182 17 0 4538 4719 577188656 577188837 5.430000e-60 243.0
14 TraesCS7A01G423400 chr7B 90.625 64 5 1 4344 4407 577225453 577225515 3.490000e-12 84.2
15 TraesCS7A01G423400 chr7D 97.057 3432 95 4 402 3833 535410435 535413860 0.000000e+00 5773.0
16 TraesCS7A01G423400 chr7D 96.715 548 16 2 4172 4719 535413893 535414438 0.000000e+00 911.0
17 TraesCS7A01G423400 chr7D 96.154 390 12 3 3 389 535409750 535410139 7.670000e-178 634.0
18 TraesCS7A01G423400 chr7D 88.696 460 25 13 4982 5431 535414627 535415069 2.230000e-148 536.0
19 TraesCS7A01G423400 chr7D 91.623 191 10 2 4738 4922 535414425 535414615 5.400000e-65 259.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G423400 chr7A 615380329 615385759 5430 False 4704.0 7081 100.0000 1 5431 2 chr7A.!!$F1 5430
1 TraesCS7A01G423400 chr7A 618189341 618192095 2754 True 868.0 1214 84.4400 835 3812 3 chr7A.!!$R1 2977
2 TraesCS7A01G423400 chr7B 575423656 575428741 5085 False 1868.0 6131 92.4660 42 5431 4 chr7B.!!$F2 5389
3 TraesCS7A01G423400 chr7B 577184117 577189505 5388 False 1489.8 5655 91.5144 1 5431 5 chr7B.!!$F3 5430
4 TraesCS7A01G423400 chr7D 535409750 535415069 5319 False 1622.6 5773 94.0490 3 5431 5 chr7D.!!$F1 5428

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
618 931 0.390492 CATGATCGTGCAGCTCCCTA 59.610 55.000 1.07 0.0 0.00 3.53 F
845 1170 0.895559 GTAACCTGCTGGCCTTTGCT 60.896 55.000 9.95 0.0 37.74 3.91 F
1107 1440 1.375908 GGCAGCATCGGTTCTGACA 60.376 57.895 0.00 0.0 38.22 3.58 F
2546 2881 2.159476 GCGATGCATGTCTGATTGTTGT 60.159 45.455 2.46 0.0 0.00 3.32 F
3103 3447 1.835494 AGACCTACTTACGCAGCTCA 58.165 50.000 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1442 1775 0.041238 TAGTGTGCTACTCCTGCCCT 59.959 55.000 0.00 0.0 40.89 5.19 R
1916 2249 2.748532 ACTAGCACTCTACTTCCACGAC 59.251 50.000 0.00 0.0 0.00 4.34 R
2973 3317 3.071023 TCCTTTCTTGAACATCGTGGAGT 59.929 43.478 0.00 0.0 0.00 3.85 R
3735 4079 2.303022 ACCTGCTTCAGAATCGAAGGAA 59.697 45.455 13.57 0.0 41.97 3.36 R
4946 5457 0.486879 AAGGGGCCATTTCAGGTTCA 59.513 50.000 4.39 0.0 0.00 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
82 84 3.866582 GCCCTAGCCTCACGCCAT 61.867 66.667 0.00 0.00 38.78 4.40
242 244 2.383338 ACAAATTCCCATTCCCCTCTGT 59.617 45.455 0.00 0.00 0.00 3.41
287 290 0.717224 GAAATCGTTCGCCGTAGCAA 59.283 50.000 0.00 0.00 39.83 3.91
407 717 5.521735 GTGTACTAGATGTGATGCTTTCCTG 59.478 44.000 0.00 0.00 0.00 3.86
424 734 0.536260 CTGCAGTCCAGAGGAAGAGG 59.464 60.000 5.25 0.00 44.64 3.69
450 760 6.208988 GAACTCCTTTCTGTTCCTGTTTTT 57.791 37.500 0.00 0.00 37.26 1.94
569 882 5.414454 TCATCAGTAAAAGCCACACCATAAC 59.586 40.000 0.00 0.00 0.00 1.89
578 891 2.292292 GCCACACCATAACGAAACACTT 59.708 45.455 0.00 0.00 0.00 3.16
579 892 3.499157 GCCACACCATAACGAAACACTTA 59.501 43.478 0.00 0.00 0.00 2.24
582 895 5.334569 CCACACCATAACGAAACACTTAAGG 60.335 44.000 7.53 0.00 0.00 2.69
618 931 0.390492 CATGATCGTGCAGCTCCCTA 59.610 55.000 1.07 0.00 0.00 3.53
648 961 3.723260 TGCTTCACATGACACGTAGAAA 58.277 40.909 0.00 0.00 0.00 2.52
660 974 4.726416 ACACGTAGAAATACAGTACACCG 58.274 43.478 0.00 0.00 0.00 4.94
668 991 5.417894 AGAAATACAGTACACCGATGTCTCA 59.582 40.000 0.00 0.00 40.48 3.27
687 1010 8.698973 TGTCTCAATATCTTAGTAGCTTAGCT 57.301 34.615 12.67 12.67 43.41 3.32
690 1013 6.692486 TCAATATCTTAGTAGCTTAGCTGCC 58.308 40.000 17.97 7.29 42.06 4.85
775 1098 7.550906 AGGTTGCTGAGAAGATAAATTCACTAC 59.449 37.037 0.00 0.00 0.00 2.73
809 1132 3.837731 TCCTACACATGGTTCTCACATGA 59.162 43.478 11.87 0.00 46.60 3.07
810 1133 4.081476 TCCTACACATGGTTCTCACATGAG 60.081 45.833 11.87 2.24 46.60 2.90
832 1157 2.638363 GAGTTCCAGGAACAGGTAACCT 59.362 50.000 30.40 10.30 44.11 3.50
845 1170 0.895559 GTAACCTGCTGGCCTTTGCT 60.896 55.000 9.95 0.00 37.74 3.91
990 1323 2.557924 TGCTGTGCTAACATTTTGAGGG 59.442 45.455 0.00 0.00 35.22 4.30
1107 1440 1.375908 GGCAGCATCGGTTCTGACA 60.376 57.895 0.00 0.00 38.22 3.58
1341 1674 3.550437 TTCCATCAGGCTAAGAGCTTC 57.450 47.619 0.00 0.00 41.99 3.86
1442 1775 6.816640 CGTTATGGAATTTCTGTAGGAGAACA 59.183 38.462 0.00 0.00 40.60 3.18
1916 2249 6.771076 TGAAGCGTGCACTTGTAATAAATAG 58.229 36.000 16.19 0.00 0.00 1.73
2546 2881 2.159476 GCGATGCATGTCTGATTGTTGT 60.159 45.455 2.46 0.00 0.00 3.32
2588 2923 4.570772 TGTCGTATACGGTAACTCTGGTAC 59.429 45.833 24.18 11.14 40.29 3.34
2972 3316 7.969536 AATTGAGGCATCTGTATGTATACAC 57.030 36.000 7.96 0.00 38.28 2.90
2973 3317 6.478512 TTGAGGCATCTGTATGTATACACA 57.521 37.500 7.96 1.72 38.28 3.72
3103 3447 1.835494 AGACCTACTTACGCAGCTCA 58.165 50.000 0.00 0.00 0.00 4.26
3249 3593 6.545298 GCAAGGATGAGGTTCTTAATCTGATT 59.455 38.462 8.14 8.14 0.00 2.57
3596 3940 7.762159 GGAGATTGTTGGTCTAAAGAGTCTAAG 59.238 40.741 0.00 0.00 0.00 2.18
3646 3990 7.332926 ACATTAAGACACTACAGAAGATGCTTG 59.667 37.037 0.00 0.00 0.00 4.01
3735 4079 4.647564 ACCTGACATCCAGAGTTTTGAT 57.352 40.909 0.00 0.00 45.78 2.57
3789 4141 5.801531 TGTACACTGTGAATACCTTGAGT 57.198 39.130 15.86 0.00 0.00 3.41
3821 4173 8.357402 GTGGTTATGGTCAGTTTAGTTTTTCAT 58.643 33.333 0.00 0.00 0.00 2.57
4229 4581 3.251487 ACAAATTTGCTTGCAATGGAAGC 59.749 39.130 28.59 28.59 45.12 3.86
4303 4655 3.930634 AATCTCCTTTGACTTGCTTGC 57.069 42.857 0.00 0.00 0.00 4.01
4539 5011 3.478509 ACAACCTTAACCGTGCAATGTA 58.521 40.909 0.00 0.00 0.00 2.29
4555 5027 4.262079 GCAATGTAGGTAGATACGCTTCCT 60.262 45.833 0.00 0.00 45.34 3.36
4556 5028 5.223382 CAATGTAGGTAGATACGCTTCCTG 58.777 45.833 0.00 0.00 43.47 3.86
4609 5081 0.176449 GGGCTGTTTGGATCATTGCC 59.824 55.000 0.00 0.00 38.28 4.52
4617 5089 0.982852 TGGATCATTGCCCCGAGACT 60.983 55.000 0.00 0.00 0.00 3.24
4668 5140 0.174162 GTGGTGCTCATTTGGATGGC 59.826 55.000 0.00 0.00 33.93 4.40
4704 5176 3.782443 CCCACCCCTCCGTAGCAC 61.782 72.222 0.00 0.00 0.00 4.40
4705 5177 3.782443 CCACCCCTCCGTAGCACC 61.782 72.222 0.00 0.00 0.00 5.01
4706 5178 2.683933 CACCCCTCCGTAGCACCT 60.684 66.667 0.00 0.00 0.00 4.00
4707 5179 2.363925 ACCCCTCCGTAGCACCTC 60.364 66.667 0.00 0.00 0.00 3.85
4708 5180 2.363795 CCCCTCCGTAGCACCTCA 60.364 66.667 0.00 0.00 0.00 3.86
4709 5181 1.762460 CCCCTCCGTAGCACCTCAT 60.762 63.158 0.00 0.00 0.00 2.90
4710 5182 0.469331 CCCCTCCGTAGCACCTCATA 60.469 60.000 0.00 0.00 0.00 2.15
4711 5183 0.962489 CCCTCCGTAGCACCTCATAG 59.038 60.000 0.00 0.00 0.00 2.23
4712 5184 1.693627 CCTCCGTAGCACCTCATAGT 58.306 55.000 0.00 0.00 0.00 2.12
4713 5185 2.032620 CCTCCGTAGCACCTCATAGTT 58.967 52.381 0.00 0.00 0.00 2.24
4714 5186 2.223829 CCTCCGTAGCACCTCATAGTTG 60.224 54.545 0.00 0.00 0.00 3.16
4715 5187 2.427453 CTCCGTAGCACCTCATAGTTGT 59.573 50.000 0.00 0.00 0.00 3.32
4716 5188 2.829720 TCCGTAGCACCTCATAGTTGTT 59.170 45.455 0.00 0.00 0.00 2.83
4717 5189 2.930040 CCGTAGCACCTCATAGTTGTTG 59.070 50.000 0.00 0.00 0.00 3.33
4718 5190 3.585862 CGTAGCACCTCATAGTTGTTGT 58.414 45.455 0.00 0.00 0.00 3.32
4719 5191 4.381185 CCGTAGCACCTCATAGTTGTTGTA 60.381 45.833 0.00 0.00 0.00 2.41
4720 5192 4.561606 CGTAGCACCTCATAGTTGTTGTAC 59.438 45.833 0.00 0.00 0.00 2.90
4721 5193 3.939066 AGCACCTCATAGTTGTTGTACC 58.061 45.455 0.00 0.00 0.00 3.34
4722 5194 3.007635 GCACCTCATAGTTGTTGTACCC 58.992 50.000 0.00 0.00 0.00 3.69
4723 5195 3.606687 CACCTCATAGTTGTTGTACCCC 58.393 50.000 0.00 0.00 0.00 4.95
4724 5196 3.263425 CACCTCATAGTTGTTGTACCCCT 59.737 47.826 0.00 0.00 0.00 4.79
4725 5197 3.518303 ACCTCATAGTTGTTGTACCCCTC 59.482 47.826 0.00 0.00 0.00 4.30
4726 5198 3.517901 CCTCATAGTTGTTGTACCCCTCA 59.482 47.826 0.00 0.00 0.00 3.86
4727 5199 4.019681 CCTCATAGTTGTTGTACCCCTCAA 60.020 45.833 0.00 0.00 0.00 3.02
4728 5200 5.514136 CCTCATAGTTGTTGTACCCCTCAAA 60.514 44.000 0.00 0.00 0.00 2.69
4729 5201 5.942961 TCATAGTTGTTGTACCCCTCAAAA 58.057 37.500 0.00 0.00 0.00 2.44
4730 5202 6.366340 TCATAGTTGTTGTACCCCTCAAAAA 58.634 36.000 0.00 0.00 0.00 1.94
4758 5230 1.350684 TCATAGTTCTTGTGCAGGGCA 59.649 47.619 0.00 0.00 35.60 5.36
4878 5389 9.897744 TGTAGCAAAATTTGAATCTCTTTACAG 57.102 29.630 10.26 0.00 0.00 2.74
4879 5390 9.899226 GTAGCAAAATTTGAATCTCTTTACAGT 57.101 29.630 10.26 0.00 0.00 3.55
4880 5391 8.807667 AGCAAAATTTGAATCTCTTTACAGTG 57.192 30.769 10.26 0.00 0.00 3.66
4881 5392 8.416329 AGCAAAATTTGAATCTCTTTACAGTGT 58.584 29.630 10.26 0.00 0.00 3.55
4882 5393 9.677567 GCAAAATTTGAATCTCTTTACAGTGTA 57.322 29.630 10.26 0.00 0.00 2.90
4885 5396 9.878599 AAATTTGAATCTCTTTACAGTGTAACG 57.121 29.630 15.31 13.60 45.86 3.18
4886 5397 7.416154 TTTGAATCTCTTTACAGTGTAACGG 57.584 36.000 15.31 11.15 45.86 4.44
4887 5398 4.927425 TGAATCTCTTTACAGTGTAACGGC 59.073 41.667 15.31 2.59 45.86 5.68
4888 5399 4.530710 ATCTCTTTACAGTGTAACGGCA 57.469 40.909 15.31 4.80 45.86 5.69
4889 5400 4.325028 TCTCTTTACAGTGTAACGGCAA 57.675 40.909 15.31 0.00 45.86 4.52
4890 5401 4.890088 TCTCTTTACAGTGTAACGGCAAT 58.110 39.130 15.31 0.00 45.86 3.56
4935 5446 2.014068 GCTCTACATTCCACCCTGCAC 61.014 57.143 0.00 0.00 0.00 4.57
4938 5449 1.278985 CTACATTCCACCCTGCACAGA 59.721 52.381 0.00 0.00 0.00 3.41
4939 5450 0.250901 ACATTCCACCCTGCACAGAC 60.251 55.000 0.00 0.00 0.00 3.51
4940 5451 0.962356 CATTCCACCCTGCACAGACC 60.962 60.000 0.00 0.00 0.00 3.85
4941 5452 1.136329 ATTCCACCCTGCACAGACCT 61.136 55.000 0.00 0.00 0.00 3.85
4942 5453 1.352622 TTCCACCCTGCACAGACCTT 61.353 55.000 0.00 0.00 0.00 3.50
4943 5454 0.472925 TCCACCCTGCACAGACCTTA 60.473 55.000 0.00 0.00 0.00 2.69
4944 5455 0.400213 CCACCCTGCACAGACCTTAA 59.600 55.000 0.00 0.00 0.00 1.85
4945 5456 1.202879 CCACCCTGCACAGACCTTAAA 60.203 52.381 0.00 0.00 0.00 1.52
4946 5457 2.555227 CCACCCTGCACAGACCTTAAAT 60.555 50.000 0.00 0.00 0.00 1.40
4947 5458 2.489329 CACCCTGCACAGACCTTAAATG 59.511 50.000 0.00 0.00 0.00 2.32
4948 5459 2.375174 ACCCTGCACAGACCTTAAATGA 59.625 45.455 0.00 0.00 0.00 2.57
5007 5529 5.178067 CCAGCAAGCTTTATTGTTTTGAAGG 59.822 40.000 0.00 0.00 32.56 3.46
5119 5642 6.047870 TGCTGTTACATTGAGTTTGCAAAAT 58.952 32.000 14.67 13.64 0.00 1.82
5182 5729 2.076100 TGCTTGGTCGCACATTTCTAG 58.924 47.619 0.00 0.00 34.44 2.43
5258 5806 7.497579 TGCATAAAGAATCAGCGGTCTTATAAA 59.502 33.333 0.00 0.00 32.90 1.40
5273 5821 7.065324 CGGTCTTATAAACTGTTAAGCCATTGA 59.935 37.037 0.00 0.00 0.00 2.57
5277 5825 6.840780 ATAAACTGTTAAGCCATTGAAGCT 57.159 33.333 0.00 0.00 44.19 3.74
5290 5839 2.284263 TGAAGCTCACACTATCGCTG 57.716 50.000 0.00 0.00 32.22 5.18
5321 5870 9.372369 AGCTACATTACTATCAAAAGTTCAGAC 57.628 33.333 0.00 0.00 0.00 3.51
5325 5874 7.117812 ACATTACTATCAAAAGTTCAGACACCG 59.882 37.037 0.00 0.00 0.00 4.94
5383 5940 3.845781 ATAATCGTGCATCAGAGGGTT 57.154 42.857 0.00 0.00 0.00 4.11
5401 5958 6.541278 AGAGGGTTGTTGTTTAGTTTGTACTC 59.459 38.462 0.00 0.00 35.78 2.59
5403 5960 5.504392 GGTTGTTGTTTAGTTTGTACTCCG 58.496 41.667 0.00 0.00 35.78 4.63
5404 5961 5.065090 GGTTGTTGTTTAGTTTGTACTCCGT 59.935 40.000 0.00 0.00 35.78 4.69
5405 5962 6.257630 GGTTGTTGTTTAGTTTGTACTCCGTA 59.742 38.462 0.00 0.00 35.78 4.02
5407 5964 8.337532 GTTGTTGTTTAGTTTGTACTCCGTATT 58.662 33.333 0.00 0.00 35.78 1.89
5408 5965 7.853524 TGTTGTTTAGTTTGTACTCCGTATTG 58.146 34.615 0.00 0.00 35.78 1.90
5410 5967 8.977505 GTTGTTTAGTTTGTACTCCGTATTGTA 58.022 33.333 0.00 0.00 35.78 2.41
5411 5968 8.519492 TGTTTAGTTTGTACTCCGTATTGTAC 57.481 34.615 0.00 0.00 39.37 2.90
5416 5976 5.918426 TTGTACTCCGTATTGTACATGGA 57.082 39.130 0.00 1.47 45.35 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 84 4.517934 CTCGACCCCTCCCGGCTA 62.518 72.222 0.00 0.00 0.00 3.93
287 290 3.181418 ACCCAAAACAAGATGATCCAGGT 60.181 43.478 0.00 0.00 0.00 4.00
407 717 0.248843 CACCTCTTCCTCTGGACTGC 59.751 60.000 0.00 0.00 0.00 4.40
525 838 7.167535 TGATGAAGTTTCACCATGTATCTCAA 58.832 34.615 0.00 0.00 40.49 3.02
538 851 5.592282 TGTGGCTTTTACTGATGAAGTTTCA 59.408 36.000 0.00 0.00 40.56 2.69
569 882 1.202031 GCCGCATCCTTAAGTGTTTCG 60.202 52.381 0.97 0.00 0.00 3.46
578 891 2.813754 GCATGAATTAGCCGCATCCTTA 59.186 45.455 0.00 0.00 0.00 2.69
579 892 1.610522 GCATGAATTAGCCGCATCCTT 59.389 47.619 0.00 0.00 0.00 3.36
582 895 2.227149 TCATGCATGAATTAGCCGCATC 59.773 45.455 26.87 0.00 41.19 3.91
648 961 5.854010 ATTGAGACATCGGTGTACTGTAT 57.146 39.130 0.00 0.00 39.09 2.29
660 974 9.567848 GCTAAGCTACTAAGATATTGAGACATC 57.432 37.037 0.00 0.00 0.00 3.06
668 991 6.459923 GTGGCAGCTAAGCTACTAAGATATT 58.540 40.000 5.42 0.00 42.03 1.28
690 1013 6.674760 CATGATTGCATCTGACACTAACAGTG 60.675 42.308 4.79 4.79 41.51 3.66
775 1098 7.169158 ACCATGTGTAGGATTGTTAAATTGG 57.831 36.000 0.00 0.00 0.00 3.16
783 1106 4.041567 TGTGAGAACCATGTGTAGGATTGT 59.958 41.667 0.00 0.00 0.00 2.71
785 1108 4.908601 TGTGAGAACCATGTGTAGGATT 57.091 40.909 0.00 0.00 0.00 3.01
809 1132 2.638363 GTTACCTGTTCCTGGAACTCCT 59.362 50.000 32.85 19.82 42.39 3.69
810 1133 2.290134 GGTTACCTGTTCCTGGAACTCC 60.290 54.545 32.85 21.87 42.39 3.85
832 1157 2.195411 TCACAGCAAAGGCCAGCA 59.805 55.556 5.01 0.00 42.56 4.41
845 1170 4.405680 CAGGGATAAGTATCACAGGTCACA 59.594 45.833 3.49 0.00 38.58 3.58
939 1267 5.448360 GCACTACATCATTGAAGAAGCTTCC 60.448 44.000 22.81 9.23 0.00 3.46
990 1323 2.042831 GTCTGCCATGTGTGCTCCC 61.043 63.158 0.00 0.00 0.00 4.30
1107 1440 2.336945 TCATGCCATGCTCGAAATCT 57.663 45.000 0.00 0.00 0.00 2.40
1442 1775 0.041238 TAGTGTGCTACTCCTGCCCT 59.959 55.000 0.00 0.00 40.89 5.19
1806 2139 3.884091 GGTAGCTCTGAAGTTCCTCGATA 59.116 47.826 0.00 0.00 0.00 2.92
1916 2249 2.748532 ACTAGCACTCTACTTCCACGAC 59.251 50.000 0.00 0.00 0.00 4.34
2023 2356 5.885912 GGAATGCCTTTTGACAGAATAGGTA 59.114 40.000 0.00 0.00 0.00 3.08
2546 2881 4.745125 CGACAGCAAACTTCTCTCTGTTTA 59.255 41.667 0.00 0.00 38.03 2.01
2588 2923 4.065789 GACTTCAGAGTTAACCTGGGTTG 58.934 47.826 14.53 11.32 36.15 3.77
2972 3316 3.187227 CCTTTCTTGAACATCGTGGAGTG 59.813 47.826 0.00 0.00 0.00 3.51
2973 3317 3.071023 TCCTTTCTTGAACATCGTGGAGT 59.929 43.478 0.00 0.00 0.00 3.85
3249 3593 5.296780 CAGATTTCGCAAGGGCTTTATCTTA 59.703 40.000 0.00 0.00 38.10 2.10
3646 3990 5.810587 TGAACTCCTTTCGCATATCTGTTAC 59.189 40.000 0.00 0.00 36.97 2.50
3735 4079 2.303022 ACCTGCTTCAGAATCGAAGGAA 59.697 45.455 13.57 0.00 41.97 3.36
3789 4141 4.354893 AACTGACCATAACCACGGTTTA 57.645 40.909 6.80 0.00 39.31 2.01
4184 4536 8.574251 TGTGCACTATGTTGGATAGTATTTTT 57.426 30.769 19.41 0.00 33.45 1.94
4229 4581 5.221422 TGTTTGCTTATTGACCAAAGAAGGG 60.221 40.000 8.75 0.00 0.00 3.95
4303 4655 9.734620 CAGTGAGTCAGAAGAGATATCTTTTAG 57.265 37.037 6.70 4.40 0.00 1.85
4539 5011 3.014304 TGTCAGGAAGCGTATCTACCT 57.986 47.619 0.00 0.00 0.00 3.08
4555 5027 3.119388 GCCTGCAGCTTATGAAAATGTCA 60.119 43.478 8.66 0.00 38.62 3.58
4556 5028 3.119388 TGCCTGCAGCTTATGAAAATGTC 60.119 43.478 8.66 0.00 44.23 3.06
4609 5081 2.124507 TTTTGGCAGGGAGTCTCGGG 62.125 60.000 0.00 0.00 0.00 5.14
4648 5120 1.548081 CCATCCAAATGAGCACCACA 58.452 50.000 0.00 0.00 34.61 4.17
4704 5176 3.517901 TGAGGGGTACAACAACTATGAGG 59.482 47.826 0.00 0.00 0.00 3.86
4705 5177 4.819105 TGAGGGGTACAACAACTATGAG 57.181 45.455 0.00 0.00 0.00 2.90
4706 5178 5.570205 TTTGAGGGGTACAACAACTATGA 57.430 39.130 0.00 0.00 0.00 2.15
4707 5179 6.642707 TTTTTGAGGGGTACAACAACTATG 57.357 37.500 0.00 0.00 0.00 2.23
4732 5204 5.010012 CCCTGCACAAGAACTATGAGTTTTT 59.990 40.000 0.00 0.00 38.80 1.94
4733 5205 4.520492 CCCTGCACAAGAACTATGAGTTTT 59.480 41.667 0.00 0.00 38.80 2.43
4734 5206 4.074970 CCCTGCACAAGAACTATGAGTTT 58.925 43.478 0.00 0.00 38.80 2.66
4735 5207 3.679389 CCCTGCACAAGAACTATGAGTT 58.321 45.455 0.00 0.00 41.95 3.01
4736 5208 2.616510 GCCCTGCACAAGAACTATGAGT 60.617 50.000 0.00 0.00 0.00 3.41
4838 5310 1.235724 GCTACAACACTCCCCACAAC 58.764 55.000 0.00 0.00 0.00 3.32
4878 5389 3.581755 TCTACAGTGATTGCCGTTACAC 58.418 45.455 0.00 0.00 0.00 2.90
4879 5390 3.945981 TCTACAGTGATTGCCGTTACA 57.054 42.857 0.00 0.00 0.00 2.41
4880 5391 5.143916 CAATCTACAGTGATTGCCGTTAC 57.856 43.478 0.00 0.00 44.21 2.50
4935 5446 6.624423 CCATTTCAGGTTCATTTAAGGTCTG 58.376 40.000 0.00 0.00 0.00 3.51
4938 5449 4.222810 GGCCATTTCAGGTTCATTTAAGGT 59.777 41.667 0.00 0.00 0.00 3.50
4939 5450 4.383010 GGGCCATTTCAGGTTCATTTAAGG 60.383 45.833 4.39 0.00 0.00 2.69
4940 5451 4.383010 GGGGCCATTTCAGGTTCATTTAAG 60.383 45.833 4.39 0.00 0.00 1.85
4941 5452 3.517500 GGGGCCATTTCAGGTTCATTTAA 59.482 43.478 4.39 0.00 0.00 1.52
4942 5453 3.103742 GGGGCCATTTCAGGTTCATTTA 58.896 45.455 4.39 0.00 0.00 1.40
4943 5454 1.908619 GGGGCCATTTCAGGTTCATTT 59.091 47.619 4.39 0.00 0.00 2.32
4944 5455 1.079323 AGGGGCCATTTCAGGTTCATT 59.921 47.619 4.39 0.00 0.00 2.57
4945 5456 0.712380 AGGGGCCATTTCAGGTTCAT 59.288 50.000 4.39 0.00 0.00 2.57
4946 5457 0.486879 AAGGGGCCATTTCAGGTTCA 59.513 50.000 4.39 0.00 0.00 3.18
4947 5458 1.186200 GAAGGGGCCATTTCAGGTTC 58.814 55.000 4.31 0.00 0.00 3.62
4948 5459 0.486879 TGAAGGGGCCATTTCAGGTT 59.513 50.000 16.05 0.00 0.00 3.50
5119 5642 8.348285 AGCCTAAACTGATGCACTTTTATTTA 57.652 30.769 0.00 0.00 0.00 1.40
5123 5646 6.446318 CAAAGCCTAAACTGATGCACTTTTA 58.554 36.000 0.00 0.00 0.00 1.52
5128 5651 2.094545 CCCAAAGCCTAAACTGATGCAC 60.095 50.000 0.00 0.00 0.00 4.57
5182 5729 8.810652 TCCAAAATTATGTGCAACTTTAGTTC 57.189 30.769 0.00 0.00 38.04 3.01
5258 5806 3.503748 GTGAGCTTCAATGGCTTAACAGT 59.496 43.478 0.00 0.00 40.40 3.55
5273 5821 0.247460 TGCAGCGATAGTGTGAGCTT 59.753 50.000 0.00 0.00 37.94 3.74
5277 5825 1.713597 CTTGTGCAGCGATAGTGTGA 58.286 50.000 0.00 0.00 39.35 3.58
5290 5839 7.752695 ACTTTTGATAGTAATGTAGCTTGTGC 58.247 34.615 0.00 0.00 40.05 4.57
5321 5870 0.603065 TCCACTCACATCAGACGGTG 59.397 55.000 0.00 0.00 36.36 4.94
5325 5874 3.393089 AAGTGTCCACTCACATCAGAC 57.607 47.619 0.00 0.00 41.58 3.51
5401 5958 2.987149 GCGATCTCCATGTACAATACGG 59.013 50.000 0.00 0.00 0.00 4.02
5403 5960 5.050490 ACTTGCGATCTCCATGTACAATAC 58.950 41.667 0.00 0.00 0.00 1.89
5404 5961 5.049828 CACTTGCGATCTCCATGTACAATA 58.950 41.667 0.00 0.00 0.00 1.90
5405 5962 3.873361 CACTTGCGATCTCCATGTACAAT 59.127 43.478 0.00 0.00 0.00 2.71
5407 5964 2.418609 CCACTTGCGATCTCCATGTACA 60.419 50.000 0.00 0.00 0.00 2.90
5408 5965 2.205074 CCACTTGCGATCTCCATGTAC 58.795 52.381 0.00 0.00 0.00 2.90
5410 5967 0.615331 ACCACTTGCGATCTCCATGT 59.385 50.000 0.00 0.00 0.00 3.21
5411 5968 1.012086 CACCACTTGCGATCTCCATG 58.988 55.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.