Multiple sequence alignment - TraesCS3A01G249700

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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 TraesCS3A01G249700 chr3A 100.000 2687 0 0 1 2687 468002317 468005003 0.000000e+00 4963.0
1 TraesCS3A01G249700 chr3A 84.848 627 72 7 995 1618 468317428 468316822 6.360000e-171 610.0
2 TraesCS3A01G249700 chr3D 90.000 1450 85 28 481 1906 349859969 349861382 0.000000e+00 1820.0
3 TraesCS3A01G249700 chr3D 88.462 754 61 15 1935 2678 349861803 349862540 0.000000e+00 887.0
4 TraesCS3A01G249700 chr3D 87.382 634 69 3 995 1618 350735956 350735324 0.000000e+00 717.0
5 TraesCS3A01G249700 chr3D 91.400 500 16 12 1 485 349855785 349856272 0.000000e+00 660.0
6 TraesCS3A01G249700 chr3B 91.524 1109 57 19 628 1724 448773238 448774321 0.000000e+00 1493.0
7 TraesCS3A01G249700 chr3B 87.719 627 74 1 995 1618 449156866 449156240 0.000000e+00 728.0
8 TraesCS3A01G249700 chr3B 86.567 469 44 13 1935 2392 448777584 448778044 1.440000e-137 499.0
9 TraesCS3A01G249700 chr3B 91.696 289 20 2 2394 2678 448778313 448778601 5.390000e-107 398.0
10 TraesCS3A01G249700 chr3B 92.460 252 10 6 1 250 448772996 448773240 4.260000e-93 351.0
11 TraesCS3A01G249700 chr7D 92.727 55 4 0 2403 2457 516979767 516979713 2.220000e-11 80.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G249700 chr3A 468002317 468005003 2686 False 4963.000000 4963 100.00000 1 2687 1 chr3A.!!$F1 2686
1 TraesCS3A01G249700 chr3A 468316822 468317428 606 True 610.000000 610 84.84800 995 1618 1 chr3A.!!$R1 623
2 TraesCS3A01G249700 chr3D 349855785 349862540 6755 False 1122.333333 1820 89.95400 1 2678 3 chr3D.!!$F1 2677
3 TraesCS3A01G249700 chr3D 350735324 350735956 632 True 717.000000 717 87.38200 995 1618 1 chr3D.!!$R1 623
4 TraesCS3A01G249700 chr3B 449156240 449156866 626 True 728.000000 728 87.71900 995 1618 1 chr3B.!!$R1 623
5 TraesCS3A01G249700 chr3B 448772996 448778601 5605 False 685.250000 1493 90.56175 1 2678 4 chr3B.!!$F1 2677

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
391 397 0.032217 ATCCATTTTGTGCCCCGGAT 60.032 50.0 0.73 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2308 9166 1.002033 CTCTTGCTTGCTGTTGACCAC 60.002 52.381 0.0 0.0 0.0 4.16 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
24 26 3.895656 TGGAGCCGACAAGCTTATATAGT 59.104 43.478 0.00 0.00 45.15 2.12
25 27 4.022242 TGGAGCCGACAAGCTTATATAGTC 60.022 45.833 0.00 0.76 45.15 2.59
26 28 4.022242 GGAGCCGACAAGCTTATATAGTCA 60.022 45.833 12.69 0.00 45.15 3.41
27 29 4.872664 AGCCGACAAGCTTATATAGTCAC 58.127 43.478 12.69 5.59 41.41 3.67
28 30 3.669122 GCCGACAAGCTTATATAGTCACG 59.331 47.826 12.69 4.79 0.00 4.35
29 31 4.556104 GCCGACAAGCTTATATAGTCACGA 60.556 45.833 12.69 0.00 0.00 4.35
30 32 4.910456 CCGACAAGCTTATATAGTCACGAC 59.090 45.833 12.69 0.00 0.00 4.34
97 99 1.276421 CCGAACTTCACATCTCCCTGT 59.724 52.381 0.00 0.00 0.00 4.00
125 128 4.020573 TGTGTCAATTTGAGACCCGTAGAT 60.021 41.667 20.29 0.00 39.62 1.98
197 200 2.024871 GTCGATCACCGGAGCTCG 59.975 66.667 17.41 17.41 39.14 5.03
209 212 0.532573 GGAGCTCGATGTTCTGGACA 59.467 55.000 7.83 0.00 43.71 4.02
233 236 1.514443 GACGAGCAGAGCGGTGTAC 60.514 63.158 0.00 0.00 0.00 2.90
264 267 3.089784 CATACGAAGCACGCCACC 58.910 61.111 0.00 0.00 46.94 4.61
265 268 1.739929 CATACGAAGCACGCCACCA 60.740 57.895 0.00 0.00 46.94 4.17
266 269 1.447838 ATACGAAGCACGCCACCAG 60.448 57.895 0.00 0.00 46.94 4.00
267 270 1.884075 ATACGAAGCACGCCACCAGA 61.884 55.000 0.00 0.00 46.94 3.86
268 271 2.758770 TACGAAGCACGCCACCAGAC 62.759 60.000 0.00 0.00 46.94 3.51
317 322 5.936956 ACAAATCTGCTTCTTCTTCTACCTG 59.063 40.000 0.00 0.00 0.00 4.00
329 335 3.650298 CTACCTGGTCGGGTCCGGA 62.650 68.421 0.63 0.00 40.48 5.14
391 397 0.032217 ATCCATTTTGTGCCCCGGAT 60.032 50.000 0.73 0.00 0.00 4.18
397 403 2.119484 TTTGTGCCCCGGATCGAAGT 62.119 55.000 0.73 0.00 0.00 3.01
401 407 1.221021 GCCCCGGATCGAAGTCTTT 59.779 57.895 0.73 0.00 0.00 2.52
403 409 0.535335 CCCCGGATCGAAGTCTTTGA 59.465 55.000 0.73 4.95 0.00 2.69
410 416 1.139989 TCGAAGTCTTTGAAGCAGCG 58.860 50.000 0.00 0.00 0.00 5.18
462 478 1.180029 GGGCATGCTCTGTTTGTCAT 58.820 50.000 18.92 0.00 0.00 3.06
591 4308 2.261729 AGGAAGAGGAAACCTGGAGAC 58.738 52.381 0.00 0.00 31.76 3.36
615 4332 6.620253 GAGTTTCTCGACTGAATCTTGTAC 57.380 41.667 1.01 0.00 0.00 2.90
616 4333 6.334102 AGTTTCTCGACTGAATCTTGTACT 57.666 37.500 0.00 0.00 0.00 2.73
617 4334 7.450124 AGTTTCTCGACTGAATCTTGTACTA 57.550 36.000 0.00 0.00 0.00 1.82
618 4335 7.883217 AGTTTCTCGACTGAATCTTGTACTAA 58.117 34.615 0.00 0.00 0.00 2.24
619 4336 8.524487 AGTTTCTCGACTGAATCTTGTACTAAT 58.476 33.333 0.00 0.00 0.00 1.73
620 4337 9.784680 GTTTCTCGACTGAATCTTGTACTAATA 57.215 33.333 0.00 0.00 0.00 0.98
621 4338 9.784680 TTTCTCGACTGAATCTTGTACTAATAC 57.215 33.333 0.00 0.00 0.00 1.89
710 4440 0.037303 GATGGTCCATGGCATCCGAT 59.963 55.000 9.76 10.89 0.00 4.18
711 4441 0.037303 ATGGTCCATGGCATCCGATC 59.963 55.000 6.96 0.00 0.00 3.69
712 4442 1.669115 GGTCCATGGCATCCGATCG 60.669 63.158 6.96 8.51 0.00 3.69
713 4443 1.669115 GTCCATGGCATCCGATCGG 60.669 63.158 28.62 28.62 0.00 4.18
742 4472 2.871096 TCCCAGCCGTTATTTGAGTT 57.129 45.000 0.00 0.00 0.00 3.01
743 4473 2.432444 TCCCAGCCGTTATTTGAGTTG 58.568 47.619 0.00 0.00 0.00 3.16
744 4474 1.135402 CCCAGCCGTTATTTGAGTTGC 60.135 52.381 0.00 0.00 0.00 4.17
745 4475 1.539388 CCAGCCGTTATTTGAGTTGCA 59.461 47.619 0.00 0.00 0.00 4.08
746 4476 2.414559 CCAGCCGTTATTTGAGTTGCAG 60.415 50.000 0.00 0.00 0.00 4.41
747 4477 2.483877 CAGCCGTTATTTGAGTTGCAGA 59.516 45.455 0.00 0.00 0.00 4.26
748 4478 3.127548 CAGCCGTTATTTGAGTTGCAGAT 59.872 43.478 0.00 0.00 0.00 2.90
749 4479 4.332543 CAGCCGTTATTTGAGTTGCAGATA 59.667 41.667 0.00 0.00 0.00 1.98
750 4480 5.008019 CAGCCGTTATTTGAGTTGCAGATAT 59.992 40.000 0.00 0.00 0.00 1.63
751 4481 5.008019 AGCCGTTATTTGAGTTGCAGATATG 59.992 40.000 0.00 0.00 0.00 1.78
752 4482 5.220854 GCCGTTATTTGAGTTGCAGATATGT 60.221 40.000 0.00 0.00 0.00 2.29
753 4483 6.422223 CCGTTATTTGAGTTGCAGATATGTC 58.578 40.000 0.00 0.00 0.00 3.06
754 4484 6.258727 CCGTTATTTGAGTTGCAGATATGTCT 59.741 38.462 0.00 0.00 34.14 3.41
767 4497 4.507021 CAGATATGTCTGTGCAACTAGCAG 59.493 45.833 11.11 0.00 45.03 4.24
782 4512 3.361443 GCAGTTCGCTTGTAAACCG 57.639 52.632 0.00 0.00 37.77 4.44
784 4514 0.584396 CAGTTCGCTTGTAAACCGCA 59.416 50.000 0.00 0.00 0.00 5.69
785 4515 1.196808 CAGTTCGCTTGTAAACCGCAT 59.803 47.619 0.00 0.00 0.00 4.73
789 4519 2.623535 TCGCTTGTAAACCGCATACAT 58.376 42.857 0.00 0.00 33.55 2.29
790 4520 2.350192 TCGCTTGTAAACCGCATACATG 59.650 45.455 0.00 0.00 33.55 3.21
791 4521 2.538737 CGCTTGTAAACCGCATACATGG 60.539 50.000 0.00 0.00 33.55 3.66
792 4522 2.680841 GCTTGTAAACCGCATACATGGA 59.319 45.455 0.00 0.00 33.55 3.41
793 4523 3.315191 GCTTGTAAACCGCATACATGGAT 59.685 43.478 0.00 0.00 33.55 3.41
794 4524 4.202010 GCTTGTAAACCGCATACATGGATT 60.202 41.667 0.00 0.00 33.55 3.01
795 4525 5.008217 GCTTGTAAACCGCATACATGGATTA 59.992 40.000 0.00 0.00 33.55 1.75
796 4526 6.293955 GCTTGTAAACCGCATACATGGATTAT 60.294 38.462 0.00 0.00 33.55 1.28
802 4532 7.553881 AACCGCATACATGGATTATATTAGC 57.446 36.000 0.00 0.00 0.00 3.09
806 4536 6.697455 CGCATACATGGATTATATTAGCGTCT 59.303 38.462 8.06 0.00 36.06 4.18
819 4549 0.788995 AGCGTCTACGTATCGATCGG 59.211 55.000 16.41 0.89 42.22 4.18
849 4579 2.665519 CGTGGCACAAATAGCACAAGAC 60.666 50.000 19.09 0.00 44.16 3.01
851 4581 2.293122 TGGCACAAATAGCACAAGACAC 59.707 45.455 0.00 0.00 31.92 3.67
853 4583 3.243367 GGCACAAATAGCACAAGACACAA 60.243 43.478 0.00 0.00 0.00 3.33
855 4585 4.383649 GCACAAATAGCACAAGACACAATG 59.616 41.667 0.00 0.00 0.00 2.82
856 4586 5.522456 CACAAATAGCACAAGACACAATGT 58.478 37.500 0.00 0.00 0.00 2.71
896 4631 0.697079 AGAGACGTACCAGGTCAGGA 59.303 55.000 0.00 0.00 35.60 3.86
906 4641 1.155390 AGGTCAGGAGACGGTTCCA 59.845 57.895 9.73 0.00 45.92 3.53
907 4642 0.900647 AGGTCAGGAGACGGTTCCAG 60.901 60.000 9.73 2.44 45.92 3.86
908 4643 1.079750 GTCAGGAGACGGTTCCAGC 60.080 63.158 9.73 0.00 39.84 4.85
909 4644 2.125912 CAGGAGACGGTTCCAGCG 60.126 66.667 9.73 0.00 45.69 5.18
951 4687 3.243068 GCCTACATATTCGCAAAACAGGG 60.243 47.826 0.00 0.00 0.00 4.45
962 4698 2.698803 CAAAACAGGGGCAAAATAGGC 58.301 47.619 0.00 0.00 0.00 3.93
1095 4831 1.048601 TCTTCTGGATACCCATCGGC 58.951 55.000 0.00 0.00 42.59 5.54
1138 4874 1.301293 CTGCCTCCCAAGTTCTCCC 59.699 63.158 0.00 0.00 0.00 4.30
1152 4888 0.898789 TCTCCCTTCAGGTCACCGAC 60.899 60.000 0.00 0.00 36.75 4.79
1175 4911 2.683933 GAGTCCCGAAGCTCCCCA 60.684 66.667 0.00 0.00 0.00 4.96
1209 4954 4.459089 GACCCCGTCTCCAGCAGC 62.459 72.222 0.00 0.00 0.00 5.25
1222 4967 4.043200 GCAGCACCGCCTTCAACC 62.043 66.667 0.00 0.00 0.00 3.77
1233 4978 0.038744 CCTTCAACCTCACCCTGCAT 59.961 55.000 0.00 0.00 0.00 3.96
1599 5344 1.343069 AGAACTGGGCCTCGGATATC 58.657 55.000 4.53 0.00 0.00 1.63
1642 5387 1.789523 TATGGCCTCTGGGTGTAGTC 58.210 55.000 3.32 0.00 34.45 2.59
1664 5409 1.128507 GCTCGAAACGATTGTGCATGA 59.871 47.619 0.00 0.00 34.61 3.07
1723 5471 5.645056 TGTGGATCATATGTAATGTGGGT 57.355 39.130 1.90 0.00 35.96 4.51
1726 5489 6.894654 TGTGGATCATATGTAATGTGGGTTTT 59.105 34.615 1.90 0.00 35.96 2.43
1727 5490 7.068103 TGTGGATCATATGTAATGTGGGTTTTC 59.932 37.037 1.90 0.00 35.96 2.29
1733 5496 5.705609 ATGTAATGTGGGTTTTCACTGTC 57.294 39.130 0.00 0.00 38.40 3.51
1734 5497 4.787551 TGTAATGTGGGTTTTCACTGTCT 58.212 39.130 0.00 0.00 38.40 3.41
1735 5498 4.578516 TGTAATGTGGGTTTTCACTGTCTG 59.421 41.667 0.00 0.00 38.40 3.51
1741 5504 3.214328 GGGTTTTCACTGTCTGTGTGAT 58.786 45.455 9.41 0.00 46.27 3.06
1747 5510 2.054363 CACTGTCTGTGTGATCGTGTC 58.946 52.381 1.84 0.00 41.53 3.67
1749 5512 2.030717 ACTGTCTGTGTGATCGTGTCTC 60.031 50.000 0.00 0.00 0.00 3.36
1751 5514 2.623416 TGTCTGTGTGATCGTGTCTCTT 59.377 45.455 0.00 0.00 0.00 2.85
1821 8265 9.689976 TTCATGTTTAATAAATTGACTGTGTGG 57.310 29.630 0.00 0.00 0.00 4.17
1822 8266 8.303156 TCATGTTTAATAAATTGACTGTGTGGG 58.697 33.333 0.00 0.00 0.00 4.61
1823 8267 6.451393 TGTTTAATAAATTGACTGTGTGGGC 58.549 36.000 0.00 0.00 0.00 5.36
1825 8269 1.917872 TAAATTGACTGTGTGGGCCC 58.082 50.000 17.59 17.59 0.00 5.80
1863 8307 4.675114 CGGACTCCGTTTTCAAGAAAAATG 59.325 41.667 9.51 5.86 42.73 2.32
1869 8313 8.410141 ACTCCGTTTTCAAGAAAAATGAATGTA 58.590 29.630 9.35 0.00 43.63 2.29
1950 8796 0.527385 GCGAGAGTCATGCAGAGGTC 60.527 60.000 0.00 0.00 0.00 3.85
1977 8823 7.862873 ACTCATACACTCATTATGTGTCGTATG 59.137 37.037 23.98 23.98 44.24 2.39
1995 8841 7.119116 TGTCGTATGTCTTTGATGCTATTGTTT 59.881 33.333 0.00 0.00 0.00 2.83
1996 8842 7.426456 GTCGTATGTCTTTGATGCTATTGTTTG 59.574 37.037 0.00 0.00 0.00 2.93
1997 8843 7.333174 TCGTATGTCTTTGATGCTATTGTTTGA 59.667 33.333 0.00 0.00 0.00 2.69
1998 8844 7.637519 CGTATGTCTTTGATGCTATTGTTTGAG 59.362 37.037 0.00 0.00 0.00 3.02
2001 8847 7.715657 TGTCTTTGATGCTATTGTTTGAGTTT 58.284 30.769 0.00 0.00 0.00 2.66
2003 8849 9.677567 GTCTTTGATGCTATTGTTTGAGTTTAA 57.322 29.630 0.00 0.00 0.00 1.52
2054 8903 8.682710 ACACTATTTAAATGGCGAATGTTACAT 58.317 29.630 11.05 0.00 0.00 2.29
2062 8911 7.581011 AATGGCGAATGTTACATTTTTCTTC 57.419 32.000 12.13 0.00 29.89 2.87
2063 8912 6.078202 TGGCGAATGTTACATTTTTCTTCA 57.922 33.333 12.13 3.45 0.00 3.02
2068 8917 7.998212 GCGAATGTTACATTTTTCTTCAAACTG 59.002 33.333 12.13 0.00 32.51 3.16
2119 8968 3.261981 ACACTCGGTTGTGACTTTCTT 57.738 42.857 10.18 0.00 40.12 2.52
2129 8978 6.202954 CGGTTGTGACTTTCTTAAGAAGTGAT 59.797 38.462 17.05 5.36 35.21 3.06
2234 9085 0.042731 TCCTCTTCCCGACCTCCATT 59.957 55.000 0.00 0.00 0.00 3.16
2239 9090 1.131303 TTCCCGACCTCCATTGGTGT 61.131 55.000 1.86 1.44 41.00 4.16
2285 9143 0.182775 ACTCCCACCACAACTGAACC 59.817 55.000 0.00 0.00 0.00 3.62
2286 9144 0.182537 CTCCCACCACAACTGAACCA 59.817 55.000 0.00 0.00 0.00 3.67
2287 9145 0.626382 TCCCACCACAACTGAACCAA 59.374 50.000 0.00 0.00 0.00 3.67
2298 9156 3.446442 ACTGAACCAATTCTCTGCCAT 57.554 42.857 0.00 0.00 35.69 4.40
2317 9175 1.227943 GAGGCTGCAGTGGTCAACA 60.228 57.895 16.64 0.00 0.00 3.33
2340 9198 0.320247 AGCAAGAGGAGCGACAGTTG 60.320 55.000 0.00 0.00 37.01 3.16
2354 9212 0.321564 CAGTTGGCAACGGGATCTCA 60.322 55.000 23.47 0.00 42.51 3.27
2369 9227 4.443598 GGGATCTCATGGGTGAAGTAGAAC 60.444 50.000 0.00 0.00 33.05 3.01
2401 9526 6.226787 AGCCATCAATACAGACTAAGCATAC 58.773 40.000 0.00 0.00 0.00 2.39
2412 9537 5.845953 CAGACTAAGCATACGTGTTGTTTTG 59.154 40.000 0.00 4.25 0.00 2.44
2460 9585 5.902613 TCAAATGGTGAATTAAGAGCTGG 57.097 39.130 0.00 0.00 31.51 4.85
2580 9705 7.672351 TTATTTTTGTGTCGATGTGTTCAAC 57.328 32.000 0.00 0.00 0.00 3.18
2669 9798 7.201702 AGAAATAGAAGGAGAAGGGGTAAAG 57.798 40.000 0.00 0.00 0.00 1.85
2673 9802 4.449389 AGAAGGAGAAGGGGTAAAGGAAT 58.551 43.478 0.00 0.00 0.00 3.01
2678 9807 2.100197 GAAGGGGTAAAGGAATGTGGC 58.900 52.381 0.00 0.00 0.00 5.01
2679 9808 1.382914 AGGGGTAAAGGAATGTGGCT 58.617 50.000 0.00 0.00 0.00 4.75
2680 9809 1.716503 AGGGGTAAAGGAATGTGGCTT 59.283 47.619 0.00 0.00 0.00 4.35
2681 9810 2.111792 AGGGGTAAAGGAATGTGGCTTT 59.888 45.455 0.00 0.00 0.00 3.51
2682 9811 2.903784 GGGGTAAAGGAATGTGGCTTTT 59.096 45.455 0.00 0.00 0.00 2.27
2683 9812 3.326588 GGGGTAAAGGAATGTGGCTTTTT 59.673 43.478 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.496571 GTGAGTCGTGACTATATAAGCTTGT 58.503 40.000 9.86 4.77 42.66 3.16
24 26 2.416893 CTCAATCTCTCGTGAGTCGTGA 59.583 50.000 13.77 13.33 40.98 4.35
25 27 2.416893 TCTCAATCTCTCGTGAGTCGTG 59.583 50.000 13.77 10.32 41.69 4.35
26 28 2.701107 TCTCAATCTCTCGTGAGTCGT 58.299 47.619 13.77 0.13 41.69 4.34
27 29 3.486708 CCTTCTCAATCTCTCGTGAGTCG 60.487 52.174 13.77 4.70 41.69 4.18
28 30 3.692101 TCCTTCTCAATCTCTCGTGAGTC 59.308 47.826 13.77 0.00 41.69 3.36
29 31 3.691575 TCCTTCTCAATCTCTCGTGAGT 58.308 45.455 13.77 0.00 41.69 3.41
30 32 4.261572 GGATCCTTCTCAATCTCTCGTGAG 60.262 50.000 3.84 8.20 42.23 3.51
97 99 4.036262 CGGGTCTCAAATTGACACAAAAGA 59.964 41.667 3.94 0.00 37.69 2.52
209 212 2.103934 GCTCTGCTCGTCGCTGAT 59.896 61.111 8.76 0.00 44.19 2.90
233 236 0.934901 CGTATGCACTGGACGGATCG 60.935 60.000 0.00 0.00 33.01 3.69
264 267 1.153939 CGAGCAAGGGTCTCGTCTG 60.154 63.158 4.44 0.00 45.86 3.51
265 268 3.279183 CGAGCAAGGGTCTCGTCT 58.721 61.111 4.44 0.00 45.86 4.18
329 335 3.560251 ACCAGCAGCAACCGACCT 61.560 61.111 0.00 0.00 0.00 3.85
331 337 3.357079 CCACCAGCAGCAACCGAC 61.357 66.667 0.00 0.00 0.00 4.79
391 397 1.139989 CGCTGCTTCAAAGACTTCGA 58.860 50.000 0.00 0.00 0.00 3.71
397 403 0.603707 CAGGTCCGCTGCTTCAAAGA 60.604 55.000 0.00 0.00 0.00 2.52
401 407 1.301716 GTTCAGGTCCGCTGCTTCA 60.302 57.895 0.00 0.00 0.00 3.02
403 409 1.302033 CTGTTCAGGTCCGCTGCTT 60.302 57.895 0.00 0.00 0.00 3.91
410 416 1.073199 CCACCCACTGTTCAGGTCC 59.927 63.158 4.82 0.00 0.00 4.46
462 478 0.628522 AGACTCAGAGCAGCCTAGGA 59.371 55.000 14.75 0.00 0.00 2.94
510 4227 1.417517 TGCAGTCTTCTTGAGCTCCAA 59.582 47.619 12.15 4.89 0.00 3.53
535 4252 2.728922 GTCCTACGCTCGGTCATAAAG 58.271 52.381 0.00 0.00 0.00 1.85
613 4330 9.445878 CCGGTCTCTCATGTTATAGTATTAGTA 57.554 37.037 0.00 0.00 0.00 1.82
614 4331 8.162085 TCCGGTCTCTCATGTTATAGTATTAGT 58.838 37.037 0.00 0.00 0.00 2.24
615 4332 8.452534 GTCCGGTCTCTCATGTTATAGTATTAG 58.547 40.741 0.00 0.00 0.00 1.73
616 4333 7.940688 TGTCCGGTCTCTCATGTTATAGTATTA 59.059 37.037 0.00 0.00 0.00 0.98
617 4334 6.776116 TGTCCGGTCTCTCATGTTATAGTATT 59.224 38.462 0.00 0.00 0.00 1.89
618 4335 6.304624 TGTCCGGTCTCTCATGTTATAGTAT 58.695 40.000 0.00 0.00 0.00 2.12
619 4336 5.687780 TGTCCGGTCTCTCATGTTATAGTA 58.312 41.667 0.00 0.00 0.00 1.82
620 4337 4.533815 TGTCCGGTCTCTCATGTTATAGT 58.466 43.478 0.00 0.00 0.00 2.12
621 4338 4.580995 ACTGTCCGGTCTCTCATGTTATAG 59.419 45.833 0.00 0.00 0.00 1.31
710 4440 3.264574 CTGGGAAAATCCAAGCCGA 57.735 52.632 0.00 0.00 38.64 5.54
771 4501 2.680841 TCCATGTATGCGGTTTACAAGC 59.319 45.455 0.00 0.00 33.55 4.01
776 4506 9.104965 GCTAATATAATCCATGTATGCGGTTTA 57.895 33.333 0.00 0.00 0.00 2.01
777 4507 7.201609 CGCTAATATAATCCATGTATGCGGTTT 60.202 37.037 0.00 0.00 35.76 3.27
780 4510 5.753438 ACGCTAATATAATCCATGTATGCGG 59.247 40.000 0.00 0.00 42.23 5.69
781 4511 6.697455 AGACGCTAATATAATCCATGTATGCG 59.303 38.462 0.00 0.00 43.31 4.73
782 4512 8.969267 GTAGACGCTAATATAATCCATGTATGC 58.031 37.037 0.00 0.00 0.00 3.14
784 4514 8.900781 ACGTAGACGCTAATATAATCCATGTAT 58.099 33.333 1.14 0.00 44.43 2.29
785 4515 8.272545 ACGTAGACGCTAATATAATCCATGTA 57.727 34.615 1.14 0.00 44.43 2.29
789 4519 7.492344 TCGATACGTAGACGCTAATATAATCCA 59.508 37.037 16.45 0.00 44.43 3.41
790 4520 7.845483 TCGATACGTAGACGCTAATATAATCC 58.155 38.462 16.45 0.00 44.43 3.01
791 4521 9.514822 GATCGATACGTAGACGCTAATATAATC 57.485 37.037 16.45 9.93 44.43 1.75
792 4522 8.213153 CGATCGATACGTAGACGCTAATATAAT 58.787 37.037 10.26 5.93 44.43 1.28
793 4523 7.306225 CCGATCGATACGTAGACGCTAATATAA 60.306 40.741 18.66 2.15 44.43 0.98
794 4524 6.142958 CCGATCGATACGTAGACGCTAATATA 59.857 42.308 18.66 2.72 44.43 0.86
795 4525 5.051173 CCGATCGATACGTAGACGCTAATAT 60.051 44.000 18.66 7.56 44.43 1.28
796 4526 4.266265 CCGATCGATACGTAGACGCTAATA 59.734 45.833 18.66 3.84 44.43 0.98
802 4532 1.143305 ACCCGATCGATACGTAGACG 58.857 55.000 18.66 15.52 46.33 4.18
806 4536 3.003275 GGTTGTTACCCGATCGATACGTA 59.997 47.826 18.66 8.32 38.60 3.57
819 4549 0.739561 TTTGTGCCACGGTTGTTACC 59.260 50.000 0.00 0.00 41.33 2.85
873 4603 3.199677 CTGACCTGGTACGTCTCTCTAG 58.800 54.545 0.00 0.00 0.00 2.43
896 4631 2.776370 TAGTCCCGCTGGAACCGTCT 62.776 60.000 0.00 0.00 44.07 4.18
906 4641 1.706305 ACCTAGCTAGATAGTCCCGCT 59.294 52.381 22.70 0.00 34.88 5.52
907 4642 2.086094 GACCTAGCTAGATAGTCCCGC 58.914 57.143 22.70 0.00 0.00 6.13
908 4643 3.340034 CTGACCTAGCTAGATAGTCCCG 58.660 54.545 22.70 10.43 0.00 5.14
962 4698 1.442526 GGCTTCTCGGTGATGCATGG 61.443 60.000 2.46 0.00 44.64 3.66
1059 4795 1.904440 AGAAGAGGGGCATCCAGATT 58.096 50.000 0.00 0.00 38.24 2.40
1138 4874 2.432628 GGCGTCGGTGACCTGAAG 60.433 66.667 0.00 2.67 0.00 3.02
1209 4954 1.966451 GGTGAGGTTGAAGGCGGTG 60.966 63.158 0.00 0.00 0.00 4.94
1222 4967 2.821366 GACGGCATGCAGGGTGAG 60.821 66.667 21.96 5.17 0.00 3.51
1283 5028 2.010582 GAGGCCGGAGTAGAGCACAG 62.011 65.000 5.05 0.00 0.00 3.66
1503 5248 3.313007 CTTGCACCGCATCCACGTG 62.313 63.158 9.08 9.08 38.76 4.49
1599 5344 2.203139 TGCATCCAATACGGGCCG 60.203 61.111 27.06 27.06 34.36 6.13
1642 5387 1.225745 GCACAATCGTTTCGAGCCG 60.226 57.895 0.00 0.00 39.91 5.52
1708 5456 7.121168 AGACAGTGAAAACCCACATTACATATG 59.879 37.037 0.00 0.00 39.42 1.78
1839 8283 9.742570 TTCATTTTTCTTGAAAACGGAGTCCGG 62.743 40.741 33.69 16.85 45.00 5.14
1841 8285 5.827666 TCATTTTTCTTGAAAACGGAGTCC 58.172 37.500 7.90 0.00 45.00 3.85
1919 8742 3.838120 TGACTCTCGCATACAGTTGAAG 58.162 45.455 0.00 0.00 0.00 3.02
1927 8750 2.392821 CTCTGCATGACTCTCGCATAC 58.607 52.381 0.00 0.00 34.63 2.39
1977 8823 9.677567 TTAAACTCAAACAATAGCATCAAAGAC 57.322 29.630 0.00 0.00 0.00 3.01
2029 8875 9.515020 AATGTAACATTCGCCATTTAAATAGTG 57.485 29.630 0.00 0.32 0.00 2.74
2035 8884 9.482627 AAGAAAAATGTAACATTCGCCATTTAA 57.517 25.926 0.00 0.00 36.72 1.52
2042 8891 7.998212 CAGTTTGAAGAAAAATGTAACATTCGC 59.002 33.333 0.00 0.00 38.68 4.70
2043 8892 7.998212 GCAGTTTGAAGAAAAATGTAACATTCG 59.002 33.333 0.00 0.00 43.96 3.34
2054 8903 6.866480 AGTCATTCTGCAGTTTGAAGAAAAA 58.134 32.000 14.67 0.00 44.65 1.94
2059 8908 3.496130 ACGAGTCATTCTGCAGTTTGAAG 59.504 43.478 14.67 13.61 0.00 3.02
2062 8911 2.545526 ACACGAGTCATTCTGCAGTTTG 59.454 45.455 14.67 12.48 0.00 2.93
2063 8912 2.545526 CACACGAGTCATTCTGCAGTTT 59.454 45.455 14.67 0.00 0.00 2.66
2068 8917 1.783284 TGACACACGAGTCATTCTGC 58.217 50.000 6.12 0.00 43.18 4.26
2119 8968 4.487714 GGTCCATCACCATCACTTCTTA 57.512 45.455 0.00 0.00 45.98 2.10
2183 9032 4.899239 GATGAGAGCGGCGGTGGG 62.899 72.222 19.47 0.00 0.00 4.61
2186 9035 3.842923 CAGGATGAGAGCGGCGGT 61.843 66.667 13.08 13.08 39.69 5.68
2234 9085 3.441101 ACAGATAGCTTGTCCTACACCA 58.559 45.455 0.00 0.00 0.00 4.17
2298 9156 1.227943 GTTGACCACTGCAGCCTCA 60.228 57.895 15.27 9.05 0.00 3.86
2308 9166 1.002033 CTCTTGCTTGCTGTTGACCAC 60.002 52.381 0.00 0.00 0.00 4.16
2309 9167 1.311859 CTCTTGCTTGCTGTTGACCA 58.688 50.000 0.00 0.00 0.00 4.02
2317 9175 1.375268 GTCGCTCCTCTTGCTTGCT 60.375 57.895 0.00 0.00 0.00 3.91
2340 9198 1.526917 CCCATGAGATCCCGTTGCC 60.527 63.158 0.00 0.00 0.00 4.52
2354 9212 2.305927 CCACCAGTTCTACTTCACCCAT 59.694 50.000 0.00 0.00 0.00 4.00
2369 9227 2.947652 CTGTATTGATGGCTTCCACCAG 59.052 50.000 0.00 0.00 44.71 4.00
2401 9526 4.574527 TTCAAACATGCAAAACAACACG 57.425 36.364 0.00 0.00 0.00 4.49
2412 9537 3.119779 CCATTTTGGCCATTCAAACATGC 60.120 43.478 6.09 0.00 36.49 4.06
2460 9585 6.313658 TCCAATATGCATAGTGTCATAATCGC 59.686 38.462 27.12 0.00 0.00 4.58
2527 9652 9.447157 GAGACTATGACTACGGTTATATACCTT 57.553 37.037 0.00 0.00 45.40 3.50
2570 9695 4.908601 TCAGATGGGTAGTTGAACACAT 57.091 40.909 0.00 0.00 46.16 3.21
2645 9774 6.158871 CCTTTACCCCTTCTCCTTCTATTTCT 59.841 42.308 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.