Multiple sequence alignment - TraesCS2B01G357400

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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 TraesCS2B01G357400 chr2B 100.000 5339 0 0 1 5339 510399178 510404516 0.000000e+00 9860
1 TraesCS2B01G357400 chr2A 94.339 4858 189 33 1 4832 554824888 554820091 0.000000e+00 7369
2 TraesCS2B01G357400 chr2A 92.412 514 25 7 4833 5339 554820058 554819552 0.000000e+00 721
3 TraesCS2B01G357400 chr2D 92.909 4710 256 45 1 4670 431514318 431518989 0.000000e+00 6776
4 TraesCS2B01G357400 chr2D 89.744 117 8 2 5049 5161 431528794 431528910 4.310000e-31 147
5 TraesCS2B01G357400 chr2D 85.124 121 5 7 5228 5337 431531218 431531336 1.570000e-20 111


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 TraesCS2B01G357400 chr2B 510399178 510404516 5338 False 9860 9860 100.0000 1 5339 1 chr2B.!!$F1 5338
1 TraesCS2B01G357400 chr2A 554819552 554824888 5336 True 4045 7369 93.3755 1 5339 2 chr2A.!!$R1 5338
2 TraesCS2B01G357400 chr2D 431514318 431518989 4671 False 6776 6776 92.9090 1 4670 1 chr2D.!!$F1 4669

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
919 920 0.527565 CTTAAGCGCACCAAGCCAAT 59.472 50.0 11.47 0.0 41.38 3.16 F
2455 2481 0.040058 TAGTTGGGCGTGAGGGTCTA 59.960 55.0 0.00 0.0 0.00 2.59 F
3068 3103 0.331278 TGTCGGGCCTGGATTTTGAT 59.669 50.0 12.87 0.0 0.00 2.57 F
3949 3990 0.255890 TCTTAAGCTGGGTCCATGCC 59.744 55.0 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2845 2880 1.463056 CCACGAAGCTCATTACGCAAA 59.537 47.619 0.00 0.0 0.00 3.68 R
3930 3971 0.255890 GGCATGGACCCAGCTTAAGA 59.744 55.000 6.67 0.0 0.00 2.10 R
4214 4255 0.389166 CTGACTCTCAGGGTCGCAAC 60.389 60.000 0.00 0.0 40.71 4.17 R
4835 4893 1.065491 ACATAACGGATGCAGGCAGAA 60.065 47.619 0.00 0.0 39.39 3.02 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
25 26 3.504906 AGTGCATCCTGTCAAACAATCTG 59.495 43.478 0.00 0.00 0.00 2.90
100 101 3.891366 CCAAGTTTCTGTTCCTCACCATT 59.109 43.478 0.00 0.00 0.00 3.16
190 191 1.949525 GCAACACTCACCAATGTGACT 59.050 47.619 0.00 0.00 46.40 3.41
262 263 4.033709 CCTCCTTCCAGTCTCCATTCTTA 58.966 47.826 0.00 0.00 0.00 2.10
264 265 5.422214 TCCTTCCAGTCTCCATTCTTAAC 57.578 43.478 0.00 0.00 0.00 2.01
268 269 5.320549 TCCAGTCTCCATTCTTAACGTAC 57.679 43.478 0.00 0.00 0.00 3.67
310 311 2.158579 TGTAACCACACCCTTTTCCTCC 60.159 50.000 0.00 0.00 0.00 4.30
315 316 1.133792 CACACCCTTTTCCTCCACTGT 60.134 52.381 0.00 0.00 0.00 3.55
430 431 1.372499 GACAGCGTACGCCTGAACA 60.372 57.895 34.88 0.00 43.17 3.18
454 455 0.819666 GCCCTGTAGCCAAGGCATAC 60.820 60.000 14.40 12.54 45.89 2.39
888 889 2.512515 GGCCATTCGAGCTCGCTT 60.513 61.111 30.97 17.37 39.60 4.68
919 920 0.527565 CTTAAGCGCACCAAGCCAAT 59.472 50.000 11.47 0.00 41.38 3.16
937 938 2.113860 ATCGCTGCTTGCCTTTCTTA 57.886 45.000 0.00 0.00 38.78 2.10
966 968 2.031919 AGCAACCAATCCGTGCGA 59.968 55.556 0.00 0.00 0.00 5.10
1041 1044 0.396974 AGATCCGCCTCTCTGCTCTT 60.397 55.000 0.00 0.00 0.00 2.85
1088 1091 1.625818 GGCTTCTTCCTCTCCAACTCA 59.374 52.381 0.00 0.00 0.00 3.41
1197 1200 3.014538 TGGGTGGTGGATGCGGAT 61.015 61.111 0.00 0.00 0.00 4.18
1473 1476 2.501610 GACCTGCCCCTCATCGAC 59.498 66.667 0.00 0.00 0.00 4.20
1500 1503 1.472728 CGGGTAGGTGGTTGCTATCAC 60.473 57.143 2.64 2.64 0.00 3.06
1519 1522 3.004862 CACCGCTTTAAATAACCGAGGT 58.995 45.455 0.00 0.00 0.00 3.85
1520 1523 3.437741 CACCGCTTTAAATAACCGAGGTT 59.562 43.478 12.54 12.54 41.65 3.50
1521 1524 4.630940 CACCGCTTTAAATAACCGAGGTTA 59.369 41.667 16.09 16.09 43.56 2.85
1583 1586 4.142881 GGATTCCTGCGTTGTTCTAGTTTC 60.143 45.833 0.00 0.00 0.00 2.78
1609 1612 7.316544 ACTTGATGTCGGTATTAATCAAACC 57.683 36.000 0.00 0.00 38.27 3.27
1612 1615 7.315247 TGATGTCGGTATTAATCAAACCTTG 57.685 36.000 4.72 0.00 0.00 3.61
1656 1659 2.064014 GCAAGAAGCAATGGTCAAAGC 58.936 47.619 0.00 0.00 44.79 3.51
1871 1883 4.678509 GTGAACTGAACTTCACAACACA 57.321 40.909 7.10 0.00 46.38 3.72
1980 1996 9.499585 CATGAATCAATTTGTCTGTAGCTAAAG 57.500 33.333 4.35 4.35 0.00 1.85
1998 2014 6.668541 CTAAAGCAGCTGAAATTAGCACTA 57.331 37.500 20.43 0.00 46.07 2.74
2100 2116 0.465460 ACAAGGCTCGCCAAAGAACA 60.465 50.000 11.02 0.00 38.92 3.18
2206 2230 9.374838 GATCATTTTTGCTATTTCAGGAAATGT 57.625 29.630 15.61 0.00 43.23 2.71
2225 2250 7.542130 GGAAATGTCATCGCTCTTGTTTAAAAT 59.458 33.333 0.00 0.00 0.00 1.82
2455 2481 0.040058 TAGTTGGGCGTGAGGGTCTA 59.960 55.000 0.00 0.00 0.00 2.59
2534 2568 5.288804 CCAACCTGTATGTTTTTCTTGTGG 58.711 41.667 0.00 0.00 0.00 4.17
2666 2701 1.212935 AGGAAGTGGTGTCAGCTTTGT 59.787 47.619 3.30 0.00 0.00 2.83
2825 2860 3.305335 GGCAACAATGTTTAGGGACACAG 60.305 47.826 0.00 0.00 31.30 3.66
2845 2880 2.027745 AGAGAATGTTGTCGGCATGAGT 60.028 45.455 0.00 0.00 0.00 3.41
2951 2986 8.432013 TCATGCTATTGAGAAGGCTTTTCTATA 58.568 33.333 17.47 17.05 0.00 1.31
3068 3103 0.331278 TGTCGGGCCTGGATTTTGAT 59.669 50.000 12.87 0.00 0.00 2.57
3105 3140 1.960689 TGTCCCCAAAGCAAGTTAAGC 59.039 47.619 0.00 0.00 0.00 3.09
3134 3169 8.145767 TCATTTACTGGAAAGTTAGTCTTCGAA 58.854 33.333 0.00 0.00 35.02 3.71
3164 3199 4.200092 GGTATGGTTTCTCAGATGGAACC 58.800 47.826 0.26 0.26 0.00 3.62
3206 3241 0.682209 ATGATGCTTGTGGAGTGGCC 60.682 55.000 0.00 0.00 37.10 5.36
3209 3244 3.050275 GCTTGTGGAGTGGCCGTC 61.050 66.667 0.00 0.00 40.66 4.79
3332 3367 5.950965 ATCGTTATCTTACGTGCTTCTTG 57.049 39.130 0.00 0.00 42.01 3.02
3377 3412 0.704076 ATTGGGCTGTTTGGGCTCTA 59.296 50.000 0.00 0.00 0.00 2.43
3461 3496 5.155161 ACATGGGATTGGTATACAGCTAGA 58.845 41.667 5.01 0.00 0.00 2.43
3473 3508 2.266279 ACAGCTAGAAACCCCAGCTTA 58.734 47.619 0.00 0.00 42.95 3.09
3548 3587 3.388308 TCTCTGTATACCTAGCGACGTC 58.612 50.000 5.18 5.18 0.00 4.34
3598 3637 4.938080 TGCACATATTTGTCAAACCGTTT 58.062 34.783 0.00 0.00 32.34 3.60
3631 3670 3.511146 CCAACACATAAGCCTTTCATGGT 59.489 43.478 0.00 0.00 0.00 3.55
3679 3718 8.719648 CAGTATGCATTTATTGGCTTTCAAAAA 58.280 29.630 3.54 0.00 39.05 1.94
3750 3789 8.723942 ATGTAGTAGCCAAATAGTCAAGAAAG 57.276 34.615 0.00 0.00 0.00 2.62
3855 3896 1.949847 CTGCAGGTCCTGGTCTACCG 61.950 65.000 20.72 0.00 40.88 4.02
3876 3917 3.363970 CGAGCAGTCACAAACCATACAAC 60.364 47.826 0.00 0.00 0.00 3.32
3922 3963 1.621317 TCTGCGTGTTGGTGGAATCTA 59.379 47.619 0.00 0.00 0.00 1.98
3930 3971 4.454504 GTGTTGGTGGAATCTACGAATGTT 59.545 41.667 0.00 0.00 0.00 2.71
3945 3986 3.686016 GAATGTTCTTAAGCTGGGTCCA 58.314 45.455 0.00 0.00 0.00 4.02
3949 3990 0.255890 TCTTAAGCTGGGTCCATGCC 59.744 55.000 0.00 0.00 0.00 4.40
3982 4023 2.508663 GGAACTACACCTCCGCGC 60.509 66.667 0.00 0.00 0.00 6.86
4117 4158 3.758023 TGATTCAGGAATGCATGTTTCGT 59.242 39.130 0.00 0.00 0.00 3.85
4123 4164 2.095466 GGAATGCATGTTTCGTCCGAAA 60.095 45.455 10.55 10.55 41.22 3.46
4214 4255 2.027377 AGTGCCTGACTGAAGATCCAAG 60.027 50.000 0.00 0.00 31.75 3.61
4320 4361 4.048470 GGACCCTGGCCTCCAACC 62.048 72.222 3.32 0.00 30.80 3.77
4403 4444 1.338674 TGTTCAGGCCAATTCGACGAT 60.339 47.619 5.01 0.00 0.00 3.73
4414 4455 4.503007 CCAATTCGACGATCGTAATCTTGT 59.497 41.667 22.79 0.36 41.35 3.16
4455 4496 5.280945 GCAAAATGTCTGCAAGTTCACTTA 58.719 37.500 0.00 0.00 39.69 2.24
4494 4535 4.097286 TGTGTCACCCTTTAAGCACTTTTC 59.903 41.667 0.00 0.00 0.00 2.29
4540 4583 4.127907 TGTATGTTGCTTACGTTGTTGGA 58.872 39.130 0.00 0.00 0.00 3.53
4606 4663 5.180492 CCGTTGTTTGGTTGAGTATGTATGT 59.820 40.000 0.00 0.00 0.00 2.29
4613 4670 4.935205 TGGTTGAGTATGTATGTCACTTGC 59.065 41.667 0.00 0.00 0.00 4.01
4621 4678 0.322456 TATGTCACTTGCTGGCCACC 60.322 55.000 0.00 0.00 0.00 4.61
4638 4695 1.258445 ACCGAGGCAGTCTAGGGTTG 61.258 60.000 6.10 0.00 41.84 3.77
4693 4750 3.561143 GTGAGGAGGAGATAGAGCTTGA 58.439 50.000 0.00 0.00 0.00 3.02
4694 4751 3.957497 GTGAGGAGGAGATAGAGCTTGAA 59.043 47.826 0.00 0.00 0.00 2.69
4695 4752 4.037923 GTGAGGAGGAGATAGAGCTTGAAG 59.962 50.000 0.00 0.00 0.00 3.02
4696 4753 4.079500 TGAGGAGGAGATAGAGCTTGAAGA 60.080 45.833 0.00 0.00 0.00 2.87
4697 4754 4.877773 AGGAGGAGATAGAGCTTGAAGAA 58.122 43.478 0.00 0.00 0.00 2.52
4698 4755 5.276440 AGGAGGAGATAGAGCTTGAAGAAA 58.724 41.667 0.00 0.00 0.00 2.52
4699 4756 5.723887 AGGAGGAGATAGAGCTTGAAGAAAA 59.276 40.000 0.00 0.00 0.00 2.29
4700 4757 6.214412 AGGAGGAGATAGAGCTTGAAGAAAAA 59.786 38.462 0.00 0.00 0.00 1.94
4701 4758 6.538381 GGAGGAGATAGAGCTTGAAGAAAAAG 59.462 42.308 0.00 0.00 0.00 2.27
4702 4759 6.413892 AGGAGATAGAGCTTGAAGAAAAAGG 58.586 40.000 0.00 0.00 0.00 3.11
4703 4760 6.214412 AGGAGATAGAGCTTGAAGAAAAAGGA 59.786 38.462 0.00 0.00 0.00 3.36
4704 4761 6.881602 GGAGATAGAGCTTGAAGAAAAAGGAA 59.118 38.462 0.00 0.00 0.00 3.36
4705 4762 7.065683 GGAGATAGAGCTTGAAGAAAAAGGAAG 59.934 40.741 0.00 0.00 0.00 3.46
4706 4763 6.883756 AGATAGAGCTTGAAGAAAAAGGAAGG 59.116 38.462 0.00 0.00 0.00 3.46
4707 4764 3.571828 AGAGCTTGAAGAAAAAGGAAGGC 59.428 43.478 0.00 0.00 0.00 4.35
4708 4765 2.294512 AGCTTGAAGAAAAAGGAAGGCG 59.705 45.455 0.00 0.00 0.00 5.52
4709 4766 2.034685 GCTTGAAGAAAAAGGAAGGCGT 59.965 45.455 0.00 0.00 0.00 5.68
4710 4767 3.490933 GCTTGAAGAAAAAGGAAGGCGTT 60.491 43.478 0.00 0.00 0.00 4.84
4711 4768 4.682787 CTTGAAGAAAAAGGAAGGCGTTT 58.317 39.130 0.00 0.00 33.86 3.60
4717 4774 4.099419 AGAAAAAGGAAGGCGTTTCACAAT 59.901 37.500 0.00 0.00 37.54 2.71
4783 4841 6.748333 TTATTCAGCTGAATGACAAGGAAG 57.252 37.500 39.83 1.91 43.90 3.46
4807 4865 5.682212 GCAAACTCAAACCAAACTGAATCCT 60.682 40.000 0.00 0.00 0.00 3.24
4821 4879 6.356186 ACTGAATCCTAAAGAACCTAACGT 57.644 37.500 0.00 0.00 0.00 3.99
4851 4941 1.327303 TTTTTCTGCCTGCATCCGTT 58.673 45.000 0.00 0.00 0.00 4.44
4854 4944 1.667236 TTCTGCCTGCATCCGTTATG 58.333 50.000 0.00 0.00 38.74 1.90
4928 5018 2.099141 TTGAAGGACGAGATTGCCTG 57.901 50.000 0.00 0.00 31.06 4.85
4935 5025 0.463295 ACGAGATTGCCTGGCATGAG 60.463 55.000 24.03 14.33 38.76 2.90
4938 5028 0.106819 AGATTGCCTGGCATGAGGAC 60.107 55.000 24.03 10.16 38.76 3.85
5028 5120 4.457949 AGGATTGGATTACGGTTGAAACAC 59.542 41.667 0.00 0.00 0.00 3.32
5047 5139 6.747659 AACACAAAATTCACGCTGTTAATC 57.252 33.333 0.00 0.00 0.00 1.75
5048 5140 5.826586 ACACAAAATTCACGCTGTTAATCA 58.173 33.333 0.00 0.00 0.00 2.57
5049 5141 6.269315 ACACAAAATTCACGCTGTTAATCAA 58.731 32.000 0.00 0.00 0.00 2.57
5050 5142 6.922957 ACACAAAATTCACGCTGTTAATCAAT 59.077 30.769 0.00 0.00 0.00 2.57
5059 5151 6.752815 TCACGCTGTTAATCAATTATACGACA 59.247 34.615 0.00 0.00 0.00 4.35
5062 5154 8.114290 ACGCTGTTAATCAATTATACGACAAAG 58.886 33.333 0.00 0.00 0.00 2.77
5113 5209 9.387123 GTAACAAATCTCTTGTGATGAGAAAAC 57.613 33.333 0.00 0.00 42.84 2.43
5141 5237 3.936372 TCGTTCGATGGAAAAGAGTCT 57.064 42.857 0.00 0.00 33.05 3.24
5145 5241 4.921515 CGTTCGATGGAAAAGAGTCTTACA 59.078 41.667 5.65 6.56 33.05 2.41
5209 5306 0.827507 GGACCTGGCCATGTGTGTTT 60.828 55.000 19.24 0.00 0.00 2.83
5219 5316 2.166254 CCATGTGTGTTTAGCATTCCCC 59.834 50.000 0.00 0.00 0.00 4.81
5283 5380 2.243736 TGAACAGGAAGGAAACCCACTT 59.756 45.455 0.00 0.00 0.00 3.16
5318 5415 1.393539 CAATTACCACGTCTCGCCTTG 59.606 52.381 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.301987 GAGAACTTGATAAGGCGCGC 59.698 55.000 25.94 25.94 0.00 6.86
100 101 3.452627 GAGTTTATGCAGAGGAGAAGGGA 59.547 47.826 0.00 0.00 0.00 4.20
190 191 2.562298 GGTTCAGGCACCATTTGATGAA 59.438 45.455 0.00 0.00 36.73 2.57
262 263 0.313043 CGATGATAGCGGGGTACGTT 59.687 55.000 0.00 0.00 46.52 3.99
268 269 1.021390 GGAATGCGATGATAGCGGGG 61.021 60.000 0.00 0.00 37.44 5.73
337 338 3.315142 GAGCTGTGGGGATGTCGCA 62.315 63.158 0.00 0.00 35.87 5.10
338 339 2.512515 GAGCTGTGGGGATGTCGC 60.513 66.667 0.00 0.00 0.00 5.19
342 343 3.076258 TACGCGAGCTGTGGGGATG 62.076 63.158 15.93 0.00 0.00 3.51
430 431 3.612247 CTTGGCTACAGGGCGCAGT 62.612 63.158 10.83 7.22 44.11 4.40
691 692 4.914420 CTCGAGGCTACCGCGCTG 62.914 72.222 5.56 0.00 45.89 5.18
937 938 2.584835 TGGTTGCTGCTTGGATAAGT 57.415 45.000 0.00 0.00 36.27 2.24
987 989 3.391296 GGTATGACATGTGGGACCACTAT 59.609 47.826 21.05 10.85 46.30 2.12
989 991 1.559682 GGTATGACATGTGGGACCACT 59.440 52.381 21.05 2.27 46.30 4.00
994 996 5.458451 TTAAATGGGTATGACATGTGGGA 57.542 39.130 1.15 0.00 0.00 4.37
1007 1009 3.886123 CGGATCTGGAGTTTAAATGGGT 58.114 45.455 0.00 0.00 0.00 4.51
1041 1044 0.490017 TTACTGGGACTGGGACTGGA 59.510 55.000 0.00 0.00 0.00 3.86
1431 1434 0.463116 GGTCTGGGTTGTTGACACGT 60.463 55.000 0.00 0.00 32.95 4.49
1473 1476 2.103339 AACCACCTACCCGGAACACG 62.103 60.000 0.73 0.00 43.80 4.49
1500 1503 5.996669 ATAACCTCGGTTATTTAAAGCGG 57.003 39.130 14.11 1.41 45.70 5.52
1519 1522 5.431731 TCTTGGCTTCTCAGGGGATAAATAA 59.568 40.000 0.00 0.00 0.00 1.40
1520 1523 4.975147 TCTTGGCTTCTCAGGGGATAAATA 59.025 41.667 0.00 0.00 0.00 1.40
1521 1524 3.788142 TCTTGGCTTCTCAGGGGATAAAT 59.212 43.478 0.00 0.00 0.00 1.40
1522 1525 3.189606 TCTTGGCTTCTCAGGGGATAAA 58.810 45.455 0.00 0.00 0.00 1.40
1612 1615 8.450964 TGCACTTTGAATACTAGCTAAATGAAC 58.549 33.333 0.00 0.00 0.00 3.18
1812 1824 6.425114 ACTCTAGCAGCAACAAATATATTCCG 59.575 38.462 0.00 0.00 0.00 4.30
1813 1825 7.579726 CACTCTAGCAGCAACAAATATATTCC 58.420 38.462 0.00 0.00 0.00 3.01
1980 1996 6.324819 TCAAAATAGTGCTAATTTCAGCTGC 58.675 36.000 9.47 0.00 42.30 5.25
2009 2025 6.377327 TTGGACTTCTGAAGCAAGTTTTAG 57.623 37.500 17.00 0.00 34.10 1.85
2100 2116 6.899892 AAGAGAAAAGAAGGATACCCTGAT 57.100 37.500 0.00 0.00 43.48 2.90
2206 2230 8.946085 AGACAATATTTTAAACAAGAGCGATGA 58.054 29.630 0.00 0.00 0.00 2.92
2225 2250 6.601613 AGTGGCGAATAAAATGGAAGACAATA 59.398 34.615 0.00 0.00 0.00 1.90
2455 2481 3.334280 AGCTAACTAGATACCTCCCCGAT 59.666 47.826 0.00 0.00 0.00 4.18
2534 2568 3.259902 GTTTAGCCTGGTACTAGTGTGC 58.740 50.000 5.39 1.86 0.00 4.57
2542 2577 4.575885 TCACTTCATGTTTAGCCTGGTAC 58.424 43.478 0.00 0.00 0.00 3.34
2666 2701 4.835284 TGACCATAATACTGTTGCTGGA 57.165 40.909 0.00 0.00 0.00 3.86
2737 2772 3.073798 TGTCTCCAAAGAAGCCATTACCA 59.926 43.478 0.00 0.00 31.93 3.25
2825 2860 2.350522 ACTCATGCCGACAACATTCTC 58.649 47.619 0.00 0.00 0.00 2.87
2845 2880 1.463056 CCACGAAGCTCATTACGCAAA 59.537 47.619 0.00 0.00 0.00 3.68
3068 3103 3.833070 GGGACAAGAAGGAGAGACTGTTA 59.167 47.826 0.00 0.00 0.00 2.41
3105 3140 8.608844 AAGACTAACTTTCCAGTAAATGACAG 57.391 34.615 0.00 0.00 34.94 3.51
3134 3169 4.012374 CTGAGAAACCATACCAATGCTGT 58.988 43.478 0.00 0.00 0.00 4.40
3164 3199 3.951775 TGGTTCCAATTTTCCCAATCG 57.048 42.857 0.00 0.00 0.00 3.34
3332 3367 2.977914 TCCATTTCAGCTGCTACACTC 58.022 47.619 9.47 0.00 0.00 3.51
3377 3412 6.469533 CCTCCCTGATATAGTAACTCCCTTCT 60.470 46.154 0.00 0.00 0.00 2.85
3461 3496 4.488770 TCCTTTCAATTAAGCTGGGGTTT 58.511 39.130 0.00 0.00 0.00 3.27
3491 3526 4.038271 ACCTTGAAATGGAGATTGCAGA 57.962 40.909 0.00 0.00 34.70 4.26
3557 3596 4.252073 TGCAACAGACAGCACAAATTTTT 58.748 34.783 0.00 0.00 35.51 1.94
3598 3637 4.736168 GCTTATGTGTTGGTTCAGCAAACA 60.736 41.667 4.63 1.99 38.62 2.83
3702 3741 7.820872 ACATATATCATCATCGAAGTGCATCAA 59.179 33.333 0.00 0.00 0.00 2.57
3703 3742 7.325694 ACATATATCATCATCGAAGTGCATCA 58.674 34.615 0.00 0.00 0.00 3.07
3741 3780 8.776680 TTTGCGTAAATTTAGTCTTTCTTGAC 57.223 30.769 0.00 0.00 37.23 3.18
3742 3781 8.617809 ACTTTGCGTAAATTTAGTCTTTCTTGA 58.382 29.630 0.00 0.00 0.00 3.02
3827 3868 3.261897 ACCAGGACCTGCAGTATATATGC 59.738 47.826 16.72 6.06 44.11 3.14
3855 3896 3.363970 CGTTGTATGGTTTGTGACTGCTC 60.364 47.826 0.00 0.00 0.00 4.26
3876 3917 5.867716 CCCGGTTAGAGGATGAAATATTACG 59.132 44.000 0.00 0.00 0.00 3.18
3922 3963 3.335579 GACCCAGCTTAAGAACATTCGT 58.664 45.455 6.67 0.00 0.00 3.85
3930 3971 0.255890 GGCATGGACCCAGCTTAAGA 59.744 55.000 6.67 0.00 0.00 2.10
3945 3986 1.064505 CAAGCGTTCGATTCATGGCAT 59.935 47.619 0.00 0.00 0.00 4.40
3949 3990 2.416547 AGTTCCAAGCGTTCGATTCATG 59.583 45.455 0.00 0.00 0.00 3.07
4117 4158 4.383770 GGTCCCATTCTTAGTGATTTCGGA 60.384 45.833 0.00 0.00 0.00 4.55
4123 4164 4.163078 CACTCTGGTCCCATTCTTAGTGAT 59.837 45.833 0.00 0.00 36.13 3.06
4214 4255 0.389166 CTGACTCTCAGGGTCGCAAC 60.389 60.000 0.00 0.00 40.71 4.17
4320 4361 0.924090 GCTACCGCGATGAACTTGAG 59.076 55.000 8.23 0.00 0.00 3.02
4403 4444 4.466370 ACTTCCCAGATCACAAGATTACGA 59.534 41.667 0.00 0.00 33.72 3.43
4414 4455 1.621317 TGCGTGTAACTTCCCAGATCA 59.379 47.619 0.00 0.00 31.75 2.92
4455 4496 6.127423 GGGTGACACATTATACACACTAGAGT 60.127 42.308 8.08 0.00 34.38 3.24
4494 4535 7.290118 CAAGTGGTTTGTTTTGACAGAAAAAG 58.710 34.615 0.00 0.00 29.93 2.27
4606 4663 3.535629 CTCGGTGGCCAGCAAGTGA 62.536 63.158 32.71 20.60 0.00 3.41
4621 4678 0.970937 TCCAACCCTAGACTGCCTCG 60.971 60.000 0.00 0.00 0.00 4.63
4626 4683 2.697751 CCTCAGATCCAACCCTAGACTG 59.302 54.545 0.00 0.00 0.00 3.51
4638 4695 1.667724 CACGATTGCAACCTCAGATCC 59.332 52.381 0.00 0.00 0.00 3.36
4693 4750 3.445805 TGTGAAACGCCTTCCTTTTTCTT 59.554 39.130 0.00 0.00 42.39 2.52
4694 4751 3.020984 TGTGAAACGCCTTCCTTTTTCT 58.979 40.909 0.00 0.00 42.39 2.52
4695 4752 3.430333 TGTGAAACGCCTTCCTTTTTC 57.570 42.857 0.00 0.00 42.39 2.29
4696 4753 3.878160 TTGTGAAACGCCTTCCTTTTT 57.122 38.095 0.00 0.00 42.39 1.94
4697 4754 4.400529 AATTGTGAAACGCCTTCCTTTT 57.599 36.364 0.00 0.00 42.39 2.27
4698 4755 4.400529 AAATTGTGAAACGCCTTCCTTT 57.599 36.364 0.00 0.00 42.39 3.11
4699 4756 4.400529 AAAATTGTGAAACGCCTTCCTT 57.599 36.364 0.00 0.00 42.39 3.36
4700 4757 4.099419 AGAAAAATTGTGAAACGCCTTCCT 59.901 37.500 0.00 0.00 42.39 3.36
4701 4758 4.368315 AGAAAAATTGTGAAACGCCTTCC 58.632 39.130 0.00 0.00 42.39 3.46
4702 4759 5.290885 ACAAGAAAAATTGTGAAACGCCTTC 59.709 36.000 0.00 0.00 41.76 3.46
4703 4760 5.175127 ACAAGAAAAATTGTGAAACGCCTT 58.825 33.333 0.00 0.00 41.76 4.35
4704 4761 4.754322 ACAAGAAAAATTGTGAAACGCCT 58.246 34.783 0.00 0.00 41.76 5.52
4705 4762 5.463499 AACAAGAAAAATTGTGAAACGCC 57.537 34.783 0.00 0.00 42.49 5.68
4742 4799 9.914131 GCTGAATAAAGGTAATCAGTTTTTCTT 57.086 29.630 0.00 0.00 38.86 2.52
4743 4800 9.301897 AGCTGAATAAAGGTAATCAGTTTTTCT 57.698 29.630 0.00 0.00 38.86 2.52
4744 4801 9.346725 CAGCTGAATAAAGGTAATCAGTTTTTC 57.653 33.333 8.42 0.00 38.86 2.29
4745 4802 9.077885 TCAGCTGAATAAAGGTAATCAGTTTTT 57.922 29.630 15.67 0.00 38.86 1.94
4753 4810 8.579850 TTGTCATTCAGCTGAATAAAGGTAAT 57.420 30.769 35.25 13.83 42.41 1.89
4783 4841 4.507756 GGATTCAGTTTGGTTTGAGTTTGC 59.492 41.667 0.00 0.00 0.00 3.68
4832 4890 1.327303 AACGGATGCAGGCAGAAAAA 58.673 45.000 0.00 0.00 0.00 1.94
4833 4891 2.192664 TAACGGATGCAGGCAGAAAA 57.807 45.000 0.00 0.00 0.00 2.29
4834 4892 2.016318 CATAACGGATGCAGGCAGAAA 58.984 47.619 0.00 0.00 0.00 2.52
4835 4893 1.065491 ACATAACGGATGCAGGCAGAA 60.065 47.619 0.00 0.00 39.39 3.02
4846 4936 3.427573 TCAGTTCTGAGGACATAACGGA 58.572 45.455 0.00 0.00 37.89 4.69
4854 4944 9.418045 GCTATTAGATAATTCAGTTCTGAGGAC 57.582 37.037 2.77 0.00 0.00 3.85
4890 4980 6.293626 CCTTCAATTTATGATTGGACGGCTAG 60.294 42.308 0.00 0.00 38.03 3.42
4928 5018 4.016444 TGTTAAATTCTGGTCCTCATGCC 58.984 43.478 0.00 0.00 0.00 4.40
4935 5025 8.836413 TCGAATATCAATGTTAAATTCTGGTCC 58.164 33.333 0.00 0.00 0.00 4.46
4991 5082 2.369860 CCAATCCTGTGCTAGCATCCTA 59.630 50.000 22.51 7.95 0.00 2.94
4992 5083 1.142465 CCAATCCTGTGCTAGCATCCT 59.858 52.381 22.51 1.50 0.00 3.24
4993 5084 1.141657 TCCAATCCTGTGCTAGCATCC 59.858 52.381 22.51 9.70 0.00 3.51
5006 5097 4.216687 TGTGTTTCAACCGTAATCCAATCC 59.783 41.667 0.00 0.00 0.00 3.01
5083 5175 8.096414 TCTCATCACAAGAGATTTGTTACATGA 58.904 33.333 0.00 0.00 37.22 3.07
5113 5209 4.725556 TTTCCATCGAACGAAGAAACAG 57.274 40.909 16.09 0.00 30.64 3.16
5123 5219 6.780706 TTGTAAGACTCTTTTCCATCGAAC 57.219 37.500 0.00 0.00 0.00 3.95
5141 5237 5.576563 TGGAGGTCTGGATCTTTTTGTAA 57.423 39.130 0.00 0.00 0.00 2.41
5145 5241 4.537688 TGAGATGGAGGTCTGGATCTTTTT 59.462 41.667 0.00 0.00 0.00 1.94
5209 5306 4.080243 TGGACGAAATTAAGGGGAATGCTA 60.080 41.667 0.00 0.00 0.00 3.49
5283 5380 3.758554 GGTAATTGAGCAAGCAGAGGAAA 59.241 43.478 0.00 0.00 0.00 3.13
5318 5415 2.983229 TGAGCTGAGGAAGAGCAAATC 58.017 47.619 0.00 0.00 39.05 2.17


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

AutoCloner maintained by Alex Coulton.