Multiple sequence alignment - TraesCS7D01G329400

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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 TraesCS7D01G329400 chr7D 100.000 4596 0 0 1 4596 421166058 421170653 0.000000e+00 8488.0
1 TraesCS7D01G329400 chr7B 94.294 3032 82 39 105 3089 437362463 437365450 0.000000e+00 4556.0
2 TraesCS7D01G329400 chr7B 94.541 1502 30 16 3104 4575 437365436 437366915 0.000000e+00 2272.0
3 TraesCS7D01G329400 chr7B 94.643 56 0 3 18 73 437362181 437362233 2.950000e-12 84.2
4 TraesCS7D01G329400 chr7A 91.574 2516 108 54 644 3092 511950754 511948276 0.000000e+00 3376.0
5 TraesCS7D01G329400 chr7A 87.847 1514 108 43 3104 4552 511948293 511946791 0.000000e+00 1707.0
6 TraesCS7D01G329400 chr7A 83.763 388 23 9 254 607 511951287 511950906 9.530000e-87 331.0
7 TraesCS7D01G329400 chr6A 77.524 307 47 18 1926 2218 558981583 558981881 1.020000e-36 165.0
8 TraesCS7D01G329400 chr6D 77.419 310 42 23 1926 2218 414000951 414001249 4.760000e-35 159.0
9 TraesCS7D01G329400 chr6B 76.087 322 52 21 1926 2232 623740567 623740878 1.330000e-30 145.0
10 TraesCS7D01G329400 chr3A 77.586 232 44 5 2009 2236 623777532 623777759 2.880000e-27 134.0
11 TraesCS7D01G329400 chr1D 91.071 56 5 0 437 492 21449044 21449099 4.930000e-10 76.8


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 TraesCS7D01G329400 chr7D 421166058 421170653 4595 False 8488.000000 8488 100.000000 1 4596 1 chr7D.!!$F1 4595
1 TraesCS7D01G329400 chr7B 437362181 437366915 4734 False 2304.066667 4556 94.492667 18 4575 3 chr7B.!!$F1 4557
2 TraesCS7D01G329400 chr7A 511946791 511951287 4496 True 1804.666667 3376 87.728000 254 4552 3 chr7A.!!$R1 4298

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
738 1120 0.106868 CCCGATTAACCCACTTCCCC 60.107 60.000 0.0 0.0 0.00 4.81 F
1087 1480 1.134007 TCTGCTCAGGTAATGCATGGG 60.134 52.381 0.0 0.0 36.07 4.00 F
2401 2820 1.133976 AGCTGTGAGAAAACTGGTGCT 60.134 47.619 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 2243 0.036388 GGCATCCACGTCAGAAAGGA 60.036 55.000 0.0 0.0 34.12 3.36 R
2486 2905 0.178967 TGGGGAACACACACATGCAT 60.179 50.000 0.0 0.0 0.00 3.96 R
3934 4428 1.073284 GGAGCCCCTTGTTAGTTGTGA 59.927 52.381 0.0 0.0 0.00 3.58 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
49 50 7.286546 TGAGGGAACAAACTCATATTTTTCACA 59.713 33.333 0.00 0.00 38.71 3.58
50 51 8.193953 AGGGAACAAACTCATATTTTTCACAT 57.806 30.769 0.00 0.00 0.00 3.21
51 52 8.090214 AGGGAACAAACTCATATTTTTCACATG 58.910 33.333 0.00 0.00 0.00 3.21
91 302 0.747255 TGGAGCCACTAGATTCGAGC 59.253 55.000 0.00 0.00 0.00 5.03
92 303 0.318275 GGAGCCACTAGATTCGAGCG 60.318 60.000 0.00 0.00 0.00 5.03
93 304 0.382515 GAGCCACTAGATTCGAGCGT 59.617 55.000 0.00 0.00 0.00 5.07
94 305 0.382515 AGCCACTAGATTCGAGCGTC 59.617 55.000 0.00 0.00 0.00 5.19
95 306 0.930742 GCCACTAGATTCGAGCGTCG 60.931 60.000 0.00 1.67 42.10 5.12
96 307 0.930742 CCACTAGATTCGAGCGTCGC 60.931 60.000 9.80 9.80 40.21 5.19
97 308 0.930742 CACTAGATTCGAGCGTCGCC 60.931 60.000 14.86 4.55 40.21 5.54
98 309 1.096386 ACTAGATTCGAGCGTCGCCT 61.096 55.000 14.86 5.09 40.21 5.52
99 310 0.866427 CTAGATTCGAGCGTCGCCTA 59.134 55.000 14.86 6.05 40.21 3.93
100 311 0.866427 TAGATTCGAGCGTCGCCTAG 59.134 55.000 14.86 5.70 40.21 3.02
101 312 0.814410 AGATTCGAGCGTCGCCTAGA 60.814 55.000 14.86 8.21 40.21 2.43
102 313 0.238817 GATTCGAGCGTCGCCTAGAT 59.761 55.000 14.86 3.46 40.21 1.98
103 314 1.463831 GATTCGAGCGTCGCCTAGATA 59.536 52.381 14.86 3.17 40.21 1.98
104 315 1.302366 TTCGAGCGTCGCCTAGATAA 58.698 50.000 14.86 0.00 40.21 1.75
105 316 0.866427 TCGAGCGTCGCCTAGATAAG 59.134 55.000 14.86 0.00 40.21 1.73
106 317 0.866427 CGAGCGTCGCCTAGATAAGA 59.134 55.000 14.86 0.00 31.14 2.10
413 649 2.911484 AGTACCTAACTACCTCGGACG 58.089 52.381 0.00 0.00 36.36 4.79
429 665 2.723618 CGGACGATAAACAAAAGCACGG 60.724 50.000 0.00 0.00 0.00 4.94
544 780 2.327343 GGCATGAACTGTGCGCTCA 61.327 57.895 9.73 11.10 43.40 4.26
611 861 3.379445 GCACGAGGGAAGGGACGA 61.379 66.667 0.00 0.00 0.00 4.20
616 866 2.362632 AGGGAAGGGACGACGAGG 60.363 66.667 0.00 0.00 0.00 4.63
619 869 2.490685 GAAGGGACGACGAGGCTC 59.509 66.667 3.87 3.87 0.00 4.70
738 1120 0.106868 CCCGATTAACCCACTTCCCC 60.107 60.000 0.00 0.00 0.00 4.81
817 1205 6.792326 AGTAAAGTAAAGAATTATTGCCCGC 58.208 36.000 0.00 0.00 0.00 6.13
829 1218 2.029815 GCCCGCTTAGCCTAGCTC 59.970 66.667 0.00 0.00 40.44 4.09
830 1219 2.737830 CCCGCTTAGCCTAGCTCC 59.262 66.667 0.00 0.00 40.44 4.70
831 1220 2.737830 CCGCTTAGCCTAGCTCCC 59.262 66.667 0.00 0.00 40.44 4.30
832 1221 2.737830 CGCTTAGCCTAGCTCCCC 59.262 66.667 0.00 0.00 40.44 4.81
833 1222 2.873525 CGCTTAGCCTAGCTCCCCC 61.874 68.421 0.00 0.00 40.44 5.40
919 1308 6.698380 CCTGTCTATAAATACGCAATACCCT 58.302 40.000 0.00 0.00 0.00 4.34
962 1352 1.696884 CTCCTAGCTTCATTCCCTCCC 59.303 57.143 0.00 0.00 0.00 4.30
970 1360 2.286121 ATTCCCTCCCCGCTCCAA 60.286 61.111 0.00 0.00 0.00 3.53
972 1362 3.864983 TTCCCTCCCCGCTCCAACT 62.865 63.158 0.00 0.00 0.00 3.16
987 1377 2.225727 TCCAACTATCGGATCGATCGTG 59.774 50.000 18.81 13.73 43.45 4.35
988 1378 2.031069 CCAACTATCGGATCGATCGTGT 60.031 50.000 18.81 9.39 43.45 4.49
1087 1480 1.134007 TCTGCTCAGGTAATGCATGGG 60.134 52.381 0.00 0.00 36.07 4.00
1125 1524 2.107041 ATTCAGTTGGCCGGACGTCA 62.107 55.000 18.91 0.00 0.00 4.35
1764 2168 1.544246 GCCGACCCAGCAAAGTAATTT 59.456 47.619 0.00 0.00 0.00 1.82
1775 2179 8.306761 CCCAGCAAAGTAATTTCTCTTTAACAT 58.693 33.333 0.00 0.00 33.38 2.71
1825 2243 1.748647 CGTCAGCACACGTGTCGTTT 61.749 55.000 20.49 1.29 38.32 3.60
2262 2681 4.764336 TACAACGTCGGCCTCGCG 62.764 66.667 15.29 0.00 40.03 5.87
2354 2773 4.333649 TGCCGCTCATTCTTCTTAATTCTG 59.666 41.667 0.00 0.00 0.00 3.02
2399 2818 1.605710 CCAGCTGTGAGAAAACTGGTG 59.394 52.381 13.81 6.47 42.42 4.17
2401 2820 1.133976 AGCTGTGAGAAAACTGGTGCT 60.134 47.619 0.00 0.00 0.00 4.40
2402 2821 1.265365 GCTGTGAGAAAACTGGTGCTC 59.735 52.381 0.00 0.00 0.00 4.26
2406 2825 3.244078 TGTGAGAAAACTGGTGCTCGTAT 60.244 43.478 0.00 0.00 0.00 3.06
2461 2880 6.920758 CCTTTTTCGGTCAGTCAGAGATATAG 59.079 42.308 0.00 0.00 0.00 1.31
2462 2881 7.406031 TTTTTCGGTCAGTCAGAGATATAGT 57.594 36.000 0.00 0.00 0.00 2.12
2463 2882 6.621316 TTTCGGTCAGTCAGAGATATAGTC 57.379 41.667 0.00 0.00 0.00 2.59
2464 2883 5.291905 TCGGTCAGTCAGAGATATAGTCA 57.708 43.478 0.00 0.00 0.00 3.41
2465 2884 5.870706 TCGGTCAGTCAGAGATATAGTCAT 58.129 41.667 0.00 0.00 0.00 3.06
2467 2886 6.874664 TCGGTCAGTCAGAGATATAGTCATAC 59.125 42.308 0.00 0.00 0.00 2.39
2484 2903 7.672983 AGTCATACACAGTGGTAAAGATTTG 57.327 36.000 5.31 0.00 0.00 2.32
2485 2904 6.149474 AGTCATACACAGTGGTAAAGATTTGC 59.851 38.462 5.31 0.00 0.00 3.68
2486 2905 6.000840 TCATACACAGTGGTAAAGATTTGCA 58.999 36.000 5.31 0.00 0.00 4.08
2493 2912 4.221262 AGTGGTAAAGATTTGCATGCATGT 59.779 37.500 26.79 13.33 0.00 3.21
2494 2913 4.327898 GTGGTAAAGATTTGCATGCATGTG 59.672 41.667 26.79 5.68 0.00 3.21
2576 2995 4.806247 CCAAGCTGGACTTTACTAGAATCG 59.194 45.833 0.00 0.00 40.96 3.34
2577 2996 5.411781 CAAGCTGGACTTTACTAGAATCGT 58.588 41.667 0.00 0.00 36.04 3.73
2578 2997 6.405508 CCAAGCTGGACTTTACTAGAATCGTA 60.406 42.308 0.00 0.00 40.96 3.43
2579 2998 6.134040 AGCTGGACTTTACTAGAATCGTAC 57.866 41.667 0.00 0.00 0.00 3.67
2600 3025 6.417044 CGTACTACTATGCAAAAGTCGCTTAT 59.583 38.462 8.24 0.00 0.00 1.73
2601 3026 7.588854 CGTACTACTATGCAAAAGTCGCTTATA 59.411 37.037 8.24 0.00 0.00 0.98
2687 3124 1.947013 CATGCATGGACGGATGAGC 59.053 57.895 19.40 0.00 36.90 4.26
2735 3179 9.463443 AAGTAAAGAAATTAATCAGCAACACAC 57.537 29.630 0.00 0.00 0.00 3.82
2979 3430 2.029288 CATGCACCACGACGCTTCT 61.029 57.895 0.00 0.00 0.00 2.85
3020 3476 4.651778 TGGAGGAAACTTCACGAATCAAT 58.348 39.130 0.00 0.00 42.58 2.57
3021 3477 4.695455 TGGAGGAAACTTCACGAATCAATC 59.305 41.667 0.00 0.00 42.58 2.67
3022 3478 4.695455 GGAGGAAACTTCACGAATCAATCA 59.305 41.667 0.00 0.00 44.43 2.57
3023 3479 5.181245 GGAGGAAACTTCACGAATCAATCAA 59.819 40.000 0.00 0.00 44.43 2.57
3024 3480 6.246420 AGGAAACTTCACGAATCAATCAAG 57.754 37.500 0.00 0.00 37.44 3.02
3025 3481 5.765182 AGGAAACTTCACGAATCAATCAAGT 59.235 36.000 0.00 0.00 37.44 3.16
3081 3539 2.771943 GTCATCCCATCACCAAGGAGTA 59.228 50.000 0.00 0.00 31.94 2.59
3082 3540 3.041211 TCATCCCATCACCAAGGAGTAG 58.959 50.000 0.00 0.00 31.94 2.57
3083 3541 2.940514 TCCCATCACCAAGGAGTAGA 57.059 50.000 0.00 0.00 0.00 2.59
3084 3542 2.752030 TCCCATCACCAAGGAGTAGAG 58.248 52.381 0.00 0.00 0.00 2.43
3085 3543 2.314852 TCCCATCACCAAGGAGTAGAGA 59.685 50.000 0.00 0.00 0.00 3.10
3086 3544 3.051803 TCCCATCACCAAGGAGTAGAGAT 60.052 47.826 0.00 0.00 0.00 2.75
3087 3545 3.713764 CCCATCACCAAGGAGTAGAGATT 59.286 47.826 0.00 0.00 0.00 2.40
3088 3546 4.164988 CCCATCACCAAGGAGTAGAGATTT 59.835 45.833 0.00 0.00 0.00 2.17
3089 3547 5.339530 CCCATCACCAAGGAGTAGAGATTTT 60.340 44.000 0.00 0.00 0.00 1.82
3090 3548 6.183347 CCATCACCAAGGAGTAGAGATTTTT 58.817 40.000 0.00 0.00 0.00 1.94
3188 3646 3.703286 AAGTGTTCCTTTTTGGTACGC 57.297 42.857 0.00 0.00 43.95 4.42
3533 3997 1.518367 TGTTGGGAAGGACTTGACCT 58.482 50.000 0.00 0.00 42.69 3.85
3608 4072 1.106285 GGGATAGCAAAAGCACCCAG 58.894 55.000 0.00 0.00 37.50 4.45
3934 4428 2.689983 CTGAAAGCCTGAAACACTTGGT 59.310 45.455 0.00 0.00 0.00 3.67
3961 4462 0.860457 AACAAGGGGCTCCTCCTTTT 59.140 50.000 5.00 0.00 44.07 2.27
4136 4646 3.814268 GCGCGCACACATGGGATT 61.814 61.111 29.10 0.00 41.24 3.01
4330 4863 6.106673 TCTTTTATTTGTTCTAGGCTCGGAG 58.893 40.000 0.00 0.00 0.00 4.63
4366 4899 0.463654 TGATCAGTTGGTATGCGGGC 60.464 55.000 0.00 0.00 0.00 6.13
4426 4959 7.031975 CAGAGTATATTATGATTCTCGCTGCA 58.968 38.462 0.00 0.00 0.00 4.41
4481 5015 3.555518 GGCGAAATTCGGATTAAGATGC 58.444 45.455 17.49 0.00 40.84 3.91
4504 5040 1.533129 GCCCTTGTTGTTGTTGTCGTC 60.533 52.381 0.00 0.00 0.00 4.20
4505 5041 1.064952 CCCTTGTTGTTGTTGTCGTCC 59.935 52.381 0.00 0.00 0.00 4.79
4535 5071 1.768684 GCACACCACAGAGGAAGGGA 61.769 60.000 0.00 0.00 41.22 4.20
4558 5094 3.320626 TCAAGAGAAGTTGATGCACTCG 58.679 45.455 0.00 0.00 31.31 4.18
4570 5106 4.183865 TGATGCACTCGGATTAAACTCTG 58.816 43.478 0.00 0.00 0.00 3.35
4575 5111 3.619038 CACTCGGATTAAACTCTGCTTCC 59.381 47.826 0.00 0.00 0.00 3.46
4576 5112 3.515901 ACTCGGATTAAACTCTGCTTCCT 59.484 43.478 0.00 0.00 0.00 3.36
4577 5113 3.861840 TCGGATTAAACTCTGCTTCCTG 58.138 45.455 0.00 0.00 0.00 3.86
4578 5114 3.513912 TCGGATTAAACTCTGCTTCCTGA 59.486 43.478 0.00 0.00 0.00 3.86
4579 5115 4.020573 TCGGATTAAACTCTGCTTCCTGAA 60.021 41.667 0.00 0.00 0.00 3.02
4580 5116 4.331168 CGGATTAAACTCTGCTTCCTGAAG 59.669 45.833 2.48 2.48 41.24 3.02
4581 5117 5.249420 GGATTAAACTCTGCTTCCTGAAGT 58.751 41.667 8.57 0.00 40.45 3.01
4582 5118 6.407202 GGATTAAACTCTGCTTCCTGAAGTA 58.593 40.000 8.57 3.37 40.45 2.24
4583 5119 6.879458 GGATTAAACTCTGCTTCCTGAAGTAA 59.121 38.462 8.57 0.00 40.45 2.24
4584 5120 7.390718 GGATTAAACTCTGCTTCCTGAAGTAAA 59.609 37.037 8.57 0.00 40.45 2.01
4585 5121 8.870075 ATTAAACTCTGCTTCCTGAAGTAAAT 57.130 30.769 8.57 0.00 40.45 1.40
4586 5122 8.691661 TTAAACTCTGCTTCCTGAAGTAAATT 57.308 30.769 8.57 0.92 40.45 1.82
4587 5123 6.566197 AACTCTGCTTCCTGAAGTAAATTG 57.434 37.500 8.57 0.00 40.45 2.32
4588 5124 5.006386 ACTCTGCTTCCTGAAGTAAATTGG 58.994 41.667 8.57 0.00 40.45 3.16
4589 5125 4.985538 TCTGCTTCCTGAAGTAAATTGGT 58.014 39.130 8.57 0.00 40.45 3.67
4590 5126 5.385198 TCTGCTTCCTGAAGTAAATTGGTT 58.615 37.500 8.57 0.00 40.45 3.67
4591 5127 5.473504 TCTGCTTCCTGAAGTAAATTGGTTC 59.526 40.000 8.57 0.00 40.45 3.62
4592 5128 4.522789 TGCTTCCTGAAGTAAATTGGTTCC 59.477 41.667 8.57 0.00 40.45 3.62
4593 5129 4.379499 GCTTCCTGAAGTAAATTGGTTCCG 60.379 45.833 8.57 0.00 40.45 4.30
4594 5130 3.681593 TCCTGAAGTAAATTGGTTCCGG 58.318 45.455 0.00 0.00 0.00 5.14
4595 5131 3.073356 TCCTGAAGTAAATTGGTTCCGGT 59.927 43.478 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.111916 AGTTGCCGAACAGTTTTCATTTG 58.888 39.130 0.00 0.00 34.17 2.32
1 2 4.385358 AGTTGCCGAACAGTTTTCATTT 57.615 36.364 0.00 0.00 34.17 2.32
2 3 4.111916 CAAGTTGCCGAACAGTTTTCATT 58.888 39.130 0.00 0.00 34.17 2.57
3 4 3.380004 TCAAGTTGCCGAACAGTTTTCAT 59.620 39.130 0.00 0.00 34.17 2.57
4 5 2.750166 TCAAGTTGCCGAACAGTTTTCA 59.250 40.909 0.00 0.00 34.17 2.69
5 6 3.363178 CTCAAGTTGCCGAACAGTTTTC 58.637 45.455 0.00 0.00 34.17 2.29
6 7 2.099098 CCTCAAGTTGCCGAACAGTTTT 59.901 45.455 0.00 0.00 34.17 2.43
7 8 1.676006 CCTCAAGTTGCCGAACAGTTT 59.324 47.619 0.00 0.00 34.17 2.66
8 9 1.308998 CCTCAAGTTGCCGAACAGTT 58.691 50.000 0.00 0.00 34.17 3.16
9 10 0.535102 CCCTCAAGTTGCCGAACAGT 60.535 55.000 0.00 0.00 34.17 3.55
10 11 0.250295 TCCCTCAAGTTGCCGAACAG 60.250 55.000 0.00 0.00 34.17 3.16
11 12 0.181587 TTCCCTCAAGTTGCCGAACA 59.818 50.000 0.00 0.00 34.17 3.18
12 13 0.591659 GTTCCCTCAAGTTGCCGAAC 59.408 55.000 11.34 11.34 0.00 3.95
13 14 0.181587 TGTTCCCTCAAGTTGCCGAA 59.818 50.000 0.00 0.00 0.00 4.30
14 15 0.181587 TTGTTCCCTCAAGTTGCCGA 59.818 50.000 0.00 0.00 0.00 5.54
15 16 1.028905 TTTGTTCCCTCAAGTTGCCG 58.971 50.000 0.00 0.00 0.00 5.69
16 17 2.031870 AGTTTGTTCCCTCAAGTTGCC 58.968 47.619 0.00 0.00 0.00 4.52
57 58 2.623416 GGCTCCAACTACTTTGCTTGTT 59.377 45.455 0.00 0.00 33.34 2.83
59 60 2.030805 GTGGCTCCAACTACTTTGCTTG 60.031 50.000 0.00 0.00 33.34 4.01
62 273 1.897560 AGTGGCTCCAACTACTTTGC 58.102 50.000 0.00 0.00 33.34 3.68
67 278 3.380637 TCGAATCTAGTGGCTCCAACTAC 59.619 47.826 0.00 0.00 0.00 2.73
91 302 2.219458 TGGTCTCTTATCTAGGCGACG 58.781 52.381 0.00 0.00 0.00 5.12
92 303 3.191791 GGATGGTCTCTTATCTAGGCGAC 59.808 52.174 0.00 0.00 0.00 5.19
93 304 3.181433 TGGATGGTCTCTTATCTAGGCGA 60.181 47.826 0.00 0.00 0.00 5.54
94 305 3.157881 TGGATGGTCTCTTATCTAGGCG 58.842 50.000 0.00 0.00 0.00 5.52
95 306 3.513515 CCTGGATGGTCTCTTATCTAGGC 59.486 52.174 0.00 0.00 42.58 3.93
97 308 6.528537 CATCCTGGATGGTCTCTTATCTAG 57.471 45.833 25.84 0.00 36.51 2.43
124 335 5.053145 ACTGTATCCATTTTCTGCGAGATC 58.947 41.667 0.00 0.00 0.00 2.75
131 342 5.480073 TGGGGAAAACTGTATCCATTTTCTG 59.520 40.000 12.83 0.00 40.56 3.02
204 416 4.953667 TCGCTCTGAATCTTTGCTATGAT 58.046 39.130 0.00 0.00 0.00 2.45
210 422 1.201965 CCGTTCGCTCTGAATCTTTGC 60.202 52.381 0.00 0.00 39.21 3.68
221 433 2.262471 TTCGACTAGGCCGTTCGCTC 62.262 60.000 16.21 0.00 37.74 5.03
375 607 4.263068 GGTACTACTCCATATGCAGGCATT 60.263 45.833 12.54 0.00 37.82 3.56
380 612 6.902771 AGTTAGGTACTACTCCATATGCAG 57.097 41.667 0.00 0.00 42.67 4.41
544 780 1.602605 GGCGGGTTACTTGTTGGCT 60.603 57.895 0.00 0.00 0.00 4.75
738 1120 2.897350 GGGCCTTCTTCATCGGCG 60.897 66.667 0.84 0.00 44.68 6.46
919 1308 2.693017 GGAGGGAGAGAGGCAGGA 59.307 66.667 0.00 0.00 0.00 3.86
972 1362 1.197036 GCTGACACGATCGATCCGATA 59.803 52.381 24.34 2.30 47.00 2.92
987 1377 2.181021 GCCATTGCTGCTGCTGAC 59.819 61.111 17.00 2.73 40.48 3.51
988 1378 3.436924 CGCCATTGCTGCTGCTGA 61.437 61.111 17.00 5.95 40.48 4.26
1050 1443 0.932955 AGAGGAGGATGCAGAGGAGA 59.067 55.000 0.00 0.00 0.00 3.71
1097 1490 1.715585 CCAACTGAATTCGCGCGAT 59.284 52.632 35.21 20.94 0.00 4.58
1125 1524 5.923204 AGAAAATCTTGTCAGTCACACTCT 58.077 37.500 0.00 0.00 33.41 3.24
1482 1886 1.509370 CTCGTCGTCGTCGGTGAAG 60.509 63.158 11.74 0.00 38.33 3.02
1793 2211 3.126171 TGTGCTGACGTGGCATATTTAAC 59.874 43.478 14.47 2.90 41.86 2.01
1825 2243 0.036388 GGCATCCACGTCAGAAAGGA 60.036 55.000 0.00 0.00 34.12 3.36
2262 2681 3.418068 GACGTGGTCTGCTGCTGC 61.418 66.667 8.89 8.89 40.20 5.25
2328 2747 4.465632 TTAAGAAGAATGAGCGGCACTA 57.534 40.909 1.45 0.00 0.00 2.74
2399 2818 8.144155 TGATAGATATGCTGTACTATACGAGC 57.856 38.462 0.00 0.00 35.13 5.03
2401 2820 8.483758 TCCTGATAGATATGCTGTACTATACGA 58.516 37.037 0.00 0.00 0.00 3.43
2402 2821 8.664211 TCCTGATAGATATGCTGTACTATACG 57.336 38.462 0.00 0.00 0.00 3.06
2406 2825 7.281100 CGTGATCCTGATAGATATGCTGTACTA 59.719 40.741 0.00 0.00 0.00 1.82
2461 2880 6.072728 TGCAAATCTTTACCACTGTGTATGAC 60.073 38.462 7.08 0.00 0.00 3.06
2462 2881 6.000840 TGCAAATCTTTACCACTGTGTATGA 58.999 36.000 7.08 0.88 0.00 2.15
2463 2882 6.252967 TGCAAATCTTTACCACTGTGTATG 57.747 37.500 7.08 0.00 0.00 2.39
2464 2883 6.625740 GCATGCAAATCTTTACCACTGTGTAT 60.626 38.462 14.21 0.00 0.00 2.29
2465 2884 5.335583 GCATGCAAATCTTTACCACTGTGTA 60.336 40.000 14.21 0.00 0.00 2.90
2467 2886 3.922240 GCATGCAAATCTTTACCACTGTG 59.078 43.478 14.21 0.00 0.00 3.66
2484 2903 0.388907 GGGAACACACACATGCATGC 60.389 55.000 26.53 11.82 0.00 4.06
2485 2904 0.244450 GGGGAACACACACATGCATG 59.756 55.000 25.09 25.09 0.00 4.06
2486 2905 0.178967 TGGGGAACACACACATGCAT 60.179 50.000 0.00 0.00 0.00 3.96
2567 2986 8.684520 ACTTTTGCATAGTAGTACGATTCTAGT 58.315 33.333 0.46 0.00 0.00 2.57
2569 2988 7.854422 CGACTTTTGCATAGTAGTACGATTCTA 59.146 37.037 2.30 0.00 0.00 2.10
2571 2990 6.559886 GCGACTTTTGCATAGTAGTACGATTC 60.560 42.308 10.49 0.00 0.00 2.52
2573 2992 4.738740 GCGACTTTTGCATAGTAGTACGAT 59.261 41.667 10.49 0.00 0.00 3.73
2574 2993 4.100529 GCGACTTTTGCATAGTAGTACGA 58.899 43.478 10.49 0.00 0.00 3.43
2576 2995 7.695869 ATAAGCGACTTTTGCATAGTAGTAC 57.304 36.000 10.00 0.00 33.85 2.73
2577 2996 9.622004 GATATAAGCGACTTTTGCATAGTAGTA 57.378 33.333 10.00 0.00 33.85 1.82
2578 2997 8.361139 AGATATAAGCGACTTTTGCATAGTAGT 58.639 33.333 10.00 2.04 33.85 2.73
2579 2998 8.749841 AGATATAAGCGACTTTTGCATAGTAG 57.250 34.615 2.30 4.10 33.85 2.57
2600 3025 6.040166 GGACCACTACCACTTTCGATTAGATA 59.960 42.308 2.41 0.00 0.00 1.98
2601 3026 5.163437 GGACCACTACCACTTTCGATTAGAT 60.163 44.000 2.41 0.00 0.00 1.98
2687 3124 0.452987 CAAGGGTGCCATGTTGATCG 59.547 55.000 0.00 0.00 0.00 3.69
2995 3450 3.830744 TTCGTGAAGTTTCCTCCAAGA 57.169 42.857 0.00 0.00 0.00 3.02
3015 3471 5.870978 GCCTTGCATACAAAACTTGATTGAT 59.129 36.000 0.00 0.00 34.74 2.57
3020 3476 2.030363 CGGCCTTGCATACAAAACTTGA 60.030 45.455 0.00 0.00 34.74 3.02
3021 3477 2.288152 ACGGCCTTGCATACAAAACTTG 60.288 45.455 0.00 0.00 34.74 3.16
3022 3478 1.960689 ACGGCCTTGCATACAAAACTT 59.039 42.857 0.00 0.00 34.74 2.66
3023 3479 1.616159 ACGGCCTTGCATACAAAACT 58.384 45.000 0.00 0.00 34.74 2.66
3024 3480 2.324860 GAACGGCCTTGCATACAAAAC 58.675 47.619 0.00 0.00 34.74 2.43
3025 3481 1.068885 CGAACGGCCTTGCATACAAAA 60.069 47.619 0.00 0.00 34.74 2.44
3092 3550 3.576982 TCTCTACTCCTTCCTCGCAAAAA 59.423 43.478 0.00 0.00 0.00 1.94
3093 3551 3.162666 TCTCTACTCCTTCCTCGCAAAA 58.837 45.455 0.00 0.00 0.00 2.44
3094 3552 2.803956 TCTCTACTCCTTCCTCGCAAA 58.196 47.619 0.00 0.00 0.00 3.68
3095 3553 2.509166 TCTCTACTCCTTCCTCGCAA 57.491 50.000 0.00 0.00 0.00 4.85
3096 3554 2.738587 ATCTCTACTCCTTCCTCGCA 57.261 50.000 0.00 0.00 0.00 5.10
3097 3555 3.634910 AGAAATCTCTACTCCTTCCTCGC 59.365 47.826 0.00 0.00 0.00 5.03
3098 3556 6.945938 TTAGAAATCTCTACTCCTTCCTCG 57.054 41.667 0.00 0.00 33.73 4.63
3188 3646 5.401674 GGAATACTAAACCGCACGATAAGAG 59.598 44.000 0.00 0.00 0.00 2.85
3189 3647 5.284079 GGAATACTAAACCGCACGATAAGA 58.716 41.667 0.00 0.00 0.00 2.10
3934 4428 1.073284 GGAGCCCCTTGTTAGTTGTGA 59.927 52.381 0.00 0.00 0.00 3.58
4047 4548 4.329545 CCCACCACACCCCACGAG 62.330 72.222 0.00 0.00 0.00 4.18
4136 4646 2.603473 CCCCGCATATCTCCCGGA 60.603 66.667 0.73 0.00 44.55 5.14
4211 4726 1.203237 GGCACAAAGGGGGCATAAAT 58.797 50.000 0.00 0.00 0.00 1.40
4366 4899 4.876107 AGTTATTTACATCAACGCCCAGAG 59.124 41.667 0.00 0.00 0.00 3.35
4481 5015 0.823460 ACAACAACAACAAGGGCTGG 59.177 50.000 0.00 0.00 0.00 4.85
4504 5040 2.159128 TGTGGTGTGCAGTTTCATTTGG 60.159 45.455 0.00 0.00 0.00 3.28
4505 5041 3.117794 CTGTGGTGTGCAGTTTCATTTG 58.882 45.455 0.00 0.00 0.00 2.32
4535 5071 4.314121 GAGTGCATCAACTTCTCTTGAGT 58.686 43.478 0.00 0.00 33.65 3.41
4558 5094 5.249420 ACTTCAGGAAGCAGAGTTTAATCC 58.751 41.667 8.89 0.00 41.99 3.01
4570 5106 4.379499 CGGAACCAATTTACTTCAGGAAGC 60.379 45.833 8.89 0.00 41.99 3.86


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

AutoCloner maintained by Alex Coulton.