Multiple sequence alignment - TraesCS6A01G359500

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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 TraesCS6A01G359500 chr6A 100.000 6775 0 0 1 6775 591012631 591019405 0.000000e+00 12512.0
1 TraesCS6A01G359500 chr6A 89.691 97 10 0 5645 5741 591018185 591018281 2.570000e-24 124.0
2 TraesCS6A01G359500 chr6A 89.691 97 10 0 5555 5651 591018275 591018371 2.570000e-24 124.0
3 TraesCS6A01G359500 chr6D 97.665 5397 84 12 889 6245 441745789 441751183 0.000000e+00 9230.0
4 TraesCS6A01G359500 chr6D 96.310 271 10 0 6247 6517 441751224 441751494 4.820000e-121 446.0
5 TraesCS6A01G359500 chr6D 93.773 273 4 5 6516 6775 441751654 441751926 1.370000e-106 398.0
6 TraesCS6A01G359500 chr6D 88.942 208 20 2 683 889 441743928 441744133 3.140000e-63 254.0
7 TraesCS6A01G359500 chr6D 90.722 97 9 0 5555 5651 441750583 441750679 5.510000e-26 130.0
8 TraesCS6A01G359500 chr6D 89.691 97 10 0 5645 5741 441750493 441750589 2.570000e-24 124.0
9 TraesCS6A01G359500 chr6B 98.231 2713 41 2 3539 6245 667774462 667777173 0.000000e+00 4737.0
10 TraesCS6A01G359500 chr6B 96.191 2704 63 14 839 3504 667771619 667774320 0.000000e+00 4386.0
11 TraesCS6A01G359500 chr6B 96.310 542 7 5 6247 6775 667777214 667777755 0.000000e+00 878.0
12 TraesCS6A01G359500 chr6B 83.033 666 93 9 1 653 348831654 348830996 2.720000e-163 586.0
13 TraesCS6A01G359500 chr6B 90.722 97 9 0 5555 5651 667776573 667776669 5.510000e-26 130.0
14 TraesCS6A01G359500 chr6B 89.691 97 10 0 5645 5741 667776483 667776579 2.570000e-24 124.0
15 TraesCS6A01G359500 chr6B 96.000 50 2 0 3502 3551 667774416 667774367 1.570000e-11 82.4
16 TraesCS6A01G359500 chr6B 81.522 92 13 4 6478 6567 557930412 557930323 9.430000e-09 73.1
17 TraesCS6A01G359500 chr7B 87.538 658 68 8 7 654 44870372 44871025 0.000000e+00 749.0
18 TraesCS6A01G359500 chr5D 83.109 669 89 13 1 657 383244452 383245108 7.570000e-164 588.0
19 TraesCS6A01G359500 chr5D 86.538 52 5 2 6478 6528 91340934 91340884 1.000000e-03 56.5
20 TraesCS6A01G359500 chr1D 82.132 666 91 15 2 650 464847743 464848397 4.620000e-151 545.0
21 TraesCS6A01G359500 chr1D 82.418 91 14 2 6475 6564 376862013 376862102 2.030000e-10 78.7
22 TraesCS6A01G359500 chr2A 81.682 666 94 21 7 648 17043118 17042457 4.650000e-146 529.0
23 TraesCS6A01G359500 chr7D 86.154 65 9 0 777 841 192670073 192670009 3.390000e-08 71.3
24 TraesCS6A01G359500 chr7A 94.872 39 2 0 6478 6516 288066223 288066261 2.040000e-05 62.1


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 TraesCS6A01G359500 chr6A 591012631 591019405 6774 False 4253.333333 12512 93.127333 1 6775 3 chr6A.!!$F1 6774
1 TraesCS6A01G359500 chr6D 441743928 441751926 7998 False 1763.666667 9230 92.850500 683 6775 6 chr6D.!!$F1 6092
2 TraesCS6A01G359500 chr6B 667771619 667777755 6136 False 2051.000000 4737 94.229000 839 6775 5 chr6B.!!$F1 5936
3 TraesCS6A01G359500 chr6B 348830996 348831654 658 True 586.000000 586 83.033000 1 653 1 chr6B.!!$R1 652
4 TraesCS6A01G359500 chr7B 44870372 44871025 653 False 749.000000 749 87.538000 7 654 1 chr7B.!!$F1 647
5 TraesCS6A01G359500 chr5D 383244452 383245108 656 False 588.000000 588 83.109000 1 657 1 chr5D.!!$F1 656
6 TraesCS6A01G359500 chr1D 464847743 464848397 654 False 545.000000 545 82.132000 2 650 1 chr1D.!!$F2 648
7 TraesCS6A01G359500 chr2A 17042457 17043118 661 True 529.000000 529 81.682000 7 648 1 chr2A.!!$R1 641

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
774 805 0.241749 ATCCTGTTGCAACGCACATG 59.758 50.000 23.79 5.23 38.71 3.21 F
776 807 1.008194 CTGTTGCAACGCACATGCT 60.008 52.632 23.79 0.00 44.14 3.79 F
781 812 1.207390 TGCAACGCACATGCTTTTTC 58.793 45.000 1.82 0.00 44.14 2.29 F
1822 3527 2.240667 ACATCAGGGATGCTTGCTACTT 59.759 45.455 6.15 0.00 43.15 2.24 F
2591 4301 3.381335 ACGTTATGTTCTAGATGGGGGT 58.619 45.455 0.00 0.00 0.00 4.95 F
2956 4667 5.006896 TGTTACTACAGGGAAGGAGAGAA 57.993 43.478 0.00 0.00 0.00 2.87 F
4155 6017 3.066621 GGTGTGACTTCATGAACTTTGCA 59.933 43.478 3.38 0.00 0.00 4.08 F
4364 6232 3.467803 ACGCCTGTGAATAAGAATAGCC 58.532 45.455 0.00 0.00 0.00 3.93 F
5236 7104 0.658897 GGTTCGAACAACCGCAGAAA 59.341 50.000 28.24 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2381 4091 2.016318 CAACGGCCTGCATCATTAAGA 58.984 47.619 0.00 0.00 0.00 2.10 R
2473 4183 4.202567 TGGACCAGTTTCCTTATCAGCTTT 60.203 41.667 0.00 0.00 36.51 3.51 R
2591 4301 8.078596 CACCCATTTTGTTTTTCTGTTTTTCAA 58.921 29.630 0.00 0.00 0.00 2.69 R
2903 4614 1.065926 TGGCAGAGCTCGATTCATTGT 60.066 47.619 8.37 0.00 0.00 2.71 R
3857 5718 1.402456 CGACGGTCTTCACGGATTTCT 60.402 52.381 6.57 0.00 35.23 2.52 R
4841 6709 2.039746 TCCAAAGAATTTCTCGGCCTCA 59.960 45.455 0.00 0.00 35.03 3.86 R
5236 7104 1.002430 TCTCTGAGCCAAAAGATGCGT 59.998 47.619 0.00 0.00 0.00 5.24 R
5459 7327 1.153549 GTCCCCACTAGCGCTTCTG 60.154 63.158 18.68 11.39 0.00 3.02 R
6245 8113 3.591789 AGGGAGCCTATTATGCAAGAGA 58.408 45.455 0.00 0.00 28.47 3.10 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
23 24 1.734163 CGGTTTAAGACAAGGGCGAT 58.266 50.000 0.00 0.00 0.00 4.58
27 28 0.393808 TTAAGACAAGGGCGATGGGC 60.394 55.000 0.00 0.00 42.51 5.36
225 226 4.351938 CCGGACCGAGAACACGCA 62.352 66.667 17.49 0.00 0.00 5.24
337 349 2.671619 CGGCACCACGACCCAAAT 60.672 61.111 0.00 0.00 35.47 2.32
348 360 3.068064 CCCAAATGGTGCCGGGTC 61.068 66.667 2.18 0.00 33.67 4.46
358 371 2.050350 TGCCGGGTCCGTAAGAGAG 61.050 63.158 2.18 0.00 43.02 3.20
391 404 3.275088 TCGAAGGCGACTCCAGAC 58.725 61.111 0.00 0.00 42.51 3.51
405 418 3.795688 TCCAGACAGGAAAGAAGCAAT 57.204 42.857 0.00 0.00 45.65 3.56
485 504 3.304721 GCATGGCAGGGCACACAA 61.305 61.111 0.00 0.00 0.00 3.33
491 510 2.784356 GCAGGGCACACAACAGCAA 61.784 57.895 0.00 0.00 0.00 3.91
494 513 0.684153 AGGGCACACAACAGCAAAGT 60.684 50.000 0.00 0.00 0.00 2.66
495 514 0.249031 GGGCACACAACAGCAAAGTC 60.249 55.000 0.00 0.00 0.00 3.01
506 525 2.030562 CAAAGTCGTCCGGGCTGT 59.969 61.111 3.66 0.00 0.00 4.40
591 619 4.113617 CGGAGGTGGAGTGGAGAA 57.886 61.111 0.00 0.00 0.00 2.87
592 620 1.893786 CGGAGGTGGAGTGGAGAAG 59.106 63.158 0.00 0.00 0.00 2.85
634 664 4.003788 CCCAACGAGTCGCCAGGT 62.004 66.667 13.59 0.00 0.00 4.00
659 689 4.222847 GGGAGCCCGTCATCCGTC 62.223 72.222 0.00 0.00 36.38 4.79
660 690 3.148279 GGAGCCCGTCATCCGTCT 61.148 66.667 0.00 0.00 33.66 4.18
661 691 2.722201 GGAGCCCGTCATCCGTCTT 61.722 63.158 0.00 0.00 33.66 3.01
662 692 1.218316 GAGCCCGTCATCCGTCTTT 59.782 57.895 0.00 0.00 33.66 2.52
663 693 0.806492 GAGCCCGTCATCCGTCTTTC 60.806 60.000 0.00 0.00 33.66 2.62
664 694 1.218316 GCCCGTCATCCGTCTTTCT 59.782 57.895 0.00 0.00 33.66 2.52
665 695 0.391263 GCCCGTCATCCGTCTTTCTT 60.391 55.000 0.00 0.00 33.66 2.52
666 696 1.944430 GCCCGTCATCCGTCTTTCTTT 60.944 52.381 0.00 0.00 33.66 2.52
667 697 2.000447 CCCGTCATCCGTCTTTCTTTC 59.000 52.381 0.00 0.00 33.66 2.62
668 698 2.000447 CCGTCATCCGTCTTTCTTTCC 59.000 52.381 0.00 0.00 33.66 3.13
669 699 2.000447 CGTCATCCGTCTTTCTTTCCC 59.000 52.381 0.00 0.00 0.00 3.97
670 700 2.353803 CGTCATCCGTCTTTCTTTCCCT 60.354 50.000 0.00 0.00 0.00 4.20
671 701 3.263261 GTCATCCGTCTTTCTTTCCCTC 58.737 50.000 0.00 0.00 0.00 4.30
672 702 3.055747 GTCATCCGTCTTTCTTTCCCTCT 60.056 47.826 0.00 0.00 0.00 3.69
673 703 3.195825 TCATCCGTCTTTCTTTCCCTCTC 59.804 47.826 0.00 0.00 0.00 3.20
674 704 1.900486 TCCGTCTTTCTTTCCCTCTCC 59.100 52.381 0.00 0.00 0.00 3.71
675 705 1.066071 CCGTCTTTCTTTCCCTCTCCC 60.066 57.143 0.00 0.00 0.00 4.30
676 706 1.903183 CGTCTTTCTTTCCCTCTCCCT 59.097 52.381 0.00 0.00 0.00 4.20
677 707 2.354203 CGTCTTTCTTTCCCTCTCCCTG 60.354 54.545 0.00 0.00 0.00 4.45
678 708 2.026729 GTCTTTCTTTCCCTCTCCCTGG 60.027 54.545 0.00 0.00 0.00 4.45
679 709 1.988846 CTTTCTTTCCCTCTCCCTGGT 59.011 52.381 0.00 0.00 0.00 4.00
680 710 2.133858 TTCTTTCCCTCTCCCTGGTT 57.866 50.000 0.00 0.00 0.00 3.67
681 711 1.362224 TCTTTCCCTCTCCCTGGTTG 58.638 55.000 0.00 0.00 0.00 3.77
723 753 9.180678 CATTAAAGTTAATATGTTCCGAATGGC 57.819 33.333 0.00 0.00 32.39 4.40
732 762 4.448537 TGTTCCGAATGGCTTAATTTGG 57.551 40.909 7.07 7.07 41.02 3.28
734 764 4.157656 TGTTCCGAATGGCTTAATTTGGAG 59.842 41.667 12.89 0.00 46.33 3.86
757 788 8.771766 GGAGTCGTAATTTTGTTATCCCTTATC 58.228 37.037 0.00 0.00 0.00 1.75
759 790 8.491958 AGTCGTAATTTTGTTATCCCTTATCCT 58.508 33.333 0.00 0.00 0.00 3.24
766 797 5.186256 TGTTATCCCTTATCCTGTTGCAA 57.814 39.130 0.00 0.00 0.00 4.08
772 803 1.535028 CTTATCCTGTTGCAACGCACA 59.465 47.619 23.79 6.94 38.71 4.57
773 804 1.819928 TATCCTGTTGCAACGCACAT 58.180 45.000 23.79 14.82 38.71 3.21
774 805 0.241749 ATCCTGTTGCAACGCACATG 59.758 50.000 23.79 5.23 38.71 3.21
776 807 1.008194 CTGTTGCAACGCACATGCT 60.008 52.632 23.79 0.00 44.14 3.79
781 812 1.207390 TGCAACGCACATGCTTTTTC 58.793 45.000 1.82 0.00 44.14 2.29
812 843 3.008375 AGTTGTAATTCAGCTGCTCCAGA 59.992 43.478 9.47 0.00 36.30 3.86
824 855 5.236047 CAGCTGCTCCAGAGACAAATATTAC 59.764 44.000 0.00 0.00 32.44 1.89
827 858 4.161565 TGCTCCAGAGACAAATATTACGGT 59.838 41.667 0.00 0.00 0.00 4.83
853 884 8.990163 ACAGAGGGAGTAATTGTTAAAAGAAA 57.010 30.769 0.00 0.00 0.00 2.52
854 885 9.416284 ACAGAGGGAGTAATTGTTAAAAGAAAA 57.584 29.630 0.00 0.00 0.00 2.29
910 2597 4.101448 CAGGGCTCCAACCTCCGG 62.101 72.222 0.00 0.00 35.78 5.14
1370 3072 4.131088 GACGGTCGGACAGGAGGC 62.131 72.222 12.76 0.00 0.00 4.70
1407 3109 4.498520 ACCATGAGCGTCGCGGAG 62.499 66.667 12.30 1.03 0.00 4.63
1536 3238 3.003763 GACCAGGAGTCCCGCCTT 61.004 66.667 5.25 0.00 39.84 4.35
1706 3411 6.795144 TGGCTTATCAATGGATTGTTTGAT 57.205 33.333 3.89 3.89 43.22 2.57
1743 3448 5.675575 GCATGAATGTGAGAGTTGAATGTCC 60.676 44.000 0.00 0.00 0.00 4.02
1822 3527 2.240667 ACATCAGGGATGCTTGCTACTT 59.759 45.455 6.15 0.00 43.15 2.24
1983 3688 4.217334 TCTTGCTGGAATTATTTTGTCGCA 59.783 37.500 0.00 0.00 0.00 5.10
2237 3942 8.995027 ACAGAGGGCAATTATAATGTATTTGA 57.005 30.769 0.00 0.00 0.00 2.69
2323 4029 3.432252 CAGACAAACTGGTATTCGTGTCC 59.568 47.826 0.00 0.00 42.39 4.02
2338 4044 6.854496 TTCGTGTCCAAAGGTATATATTGC 57.146 37.500 0.00 0.00 0.00 3.56
2473 4183 4.527509 TCCAAAAGTTGTGTTTTCTGCA 57.472 36.364 0.00 0.00 0.00 4.41
2591 4301 3.381335 ACGTTATGTTCTAGATGGGGGT 58.619 45.455 0.00 0.00 0.00 4.95
2903 4614 5.785423 TCTGAAGGAAAATCACCCTCTTCTA 59.215 40.000 0.00 0.00 33.77 2.10
2956 4667 5.006896 TGTTACTACAGGGAAGGAGAGAA 57.993 43.478 0.00 0.00 0.00 2.87
3155 4909 6.799925 CCTTTTTGAACATTGGATACGTGTAC 59.200 38.462 0.00 0.00 37.08 2.90
3542 5296 5.867716 GTGACTGTTACATACCCACAACTAG 59.132 44.000 0.00 0.00 0.00 2.57
3857 5718 4.398044 GGAGAACAAACCACTTCTCAAACA 59.602 41.667 9.10 0.00 42.90 2.83
4155 6017 3.066621 GGTGTGACTTCATGAACTTTGCA 59.933 43.478 3.38 0.00 0.00 4.08
4310 6172 6.148480 GCAGTTTCCTAGTATGCCTCATATTG 59.852 42.308 0.00 0.00 0.00 1.90
4338 6206 7.765819 TCACATCCATGTTTGTTATCTGTCTAG 59.234 37.037 0.00 0.00 39.39 2.43
4364 6232 3.467803 ACGCCTGTGAATAAGAATAGCC 58.532 45.455 0.00 0.00 0.00 3.93
4377 6245 9.160496 GAATAAGAATAGCCTGGTATCTGATTG 57.840 37.037 0.00 0.00 0.00 2.67
4703 6571 3.482783 GCTCGCAAGCCTGACGTC 61.483 66.667 9.11 9.11 43.10 4.34
4788 6656 5.787953 TGAGTTTGCTGATTCATCCAAAA 57.212 34.783 11.77 0.00 0.00 2.44
4979 6847 6.039493 ACGAAGAGGACGATATTGACAGTTAT 59.961 38.462 0.00 0.00 34.70 1.89
5186 7054 6.405286 CCTCCCTAAGATCTAGTCATATTGCG 60.405 46.154 0.00 0.00 0.00 4.85
5236 7104 0.658897 GGTTCGAACAACCGCAGAAA 59.341 50.000 28.24 0.00 0.00 2.52
5459 7327 5.817816 TGCCAGAAGCTCTAACTTAAATAGC 59.182 40.000 0.00 0.00 44.23 2.97
5705 7573 4.022849 AGAGGTTCGCAAAGAAATGAAAGG 60.023 41.667 0.00 0.00 41.10 3.11
5880 7748 0.415429 ACTGGATCCTGAGACCCTGT 59.585 55.000 24.13 0.00 0.00 4.00
5982 7850 8.249638 TGTTACATCATGGAATTTGGTATGTTG 58.750 33.333 0.00 0.00 0.00 3.33
6245 8113 9.410556 CGGAAAATTTGTTCTGAAACTATTGAT 57.589 29.630 0.00 0.00 36.17 2.57
6304 8211 3.844211 AGGTTTGGTAGTCATTGGCTAGA 59.156 43.478 0.00 0.00 0.00 2.43
6393 8300 0.829990 TCAATACGCCTGCTGATCCA 59.170 50.000 0.00 0.00 0.00 3.41
6605 8674 7.822334 TGATTTACCATTCGTTACATCAAGTCT 59.178 33.333 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.225376 TGTTACTGCTTCCGTTGCCG 61.225 55.000 0.00 0.00 0.00 5.69
32 33 1.005394 CCGGTGTTACTGCTTCCGT 60.005 57.895 0.00 0.00 39.62 4.69
34 35 0.250597 AACCCGGTGTTACTGCTTCC 60.251 55.000 0.00 0.00 34.69 3.46
37 38 1.072505 CCAACCCGGTGTTACTGCT 59.927 57.895 0.00 0.00 34.69 4.24
118 119 3.083997 GTCCATGCCTCCCTCCGT 61.084 66.667 0.00 0.00 0.00 4.69
211 212 3.103911 CCGTGCGTGTTCTCGGTC 61.104 66.667 0.00 0.00 38.45 4.79
225 226 1.670083 GCGGTTCAGGTTAAGCCGT 60.670 57.895 0.00 0.00 43.78 5.68
230 231 1.225376 CTGCGTGCGGTTCAGGTTAA 61.225 55.000 0.00 0.00 33.35 2.01
267 271 0.255318 TCCTCCCTCCTGTCGTACTC 59.745 60.000 0.00 0.00 0.00 2.59
337 349 3.697747 CTTACGGACCCGGCACCA 61.698 66.667 13.43 0.00 44.69 4.17
347 359 1.341778 GGAGTTCCCCTCTCTTACGGA 60.342 57.143 0.00 0.00 40.30 4.69
348 360 1.112950 GGAGTTCCCCTCTCTTACGG 58.887 60.000 0.00 0.00 40.30 4.02
358 371 3.082055 GACCCCTCGGAGTTCCCC 61.082 72.222 4.02 0.00 0.00 4.81
391 404 3.057736 CCTGTGTCATTGCTTCTTTCCTG 60.058 47.826 0.00 0.00 0.00 3.86
405 418 4.680237 CCTTCCGCGCCTGTGTCA 62.680 66.667 0.00 0.00 0.00 3.58
471 487 2.519063 CTGTTGTGTGCCCTGCCA 60.519 61.111 0.00 0.00 0.00 4.92
480 496 1.014352 GGACGACTTTGCTGTTGTGT 58.986 50.000 0.00 0.00 34.94 3.72
482 498 1.157870 CCGGACGACTTTGCTGTTGT 61.158 55.000 0.00 0.00 37.28 3.32
485 504 2.030562 CCCGGACGACTTTGCTGT 59.969 61.111 0.73 0.00 0.00 4.40
491 510 4.003788 CCACAGCCCGGACGACTT 62.004 66.667 0.73 0.00 0.00 3.01
574 593 1.608717 CCTTCTCCACTCCACCTCCG 61.609 65.000 0.00 0.00 0.00 4.63
620 650 2.143594 GACTCACCTGGCGACTCGTT 62.144 60.000 0.00 0.00 0.00 3.85
650 680 3.055747 AGAGGGAAAGAAAGACGGATGAC 60.056 47.826 0.00 0.00 0.00 3.06
657 687 2.026729 CCAGGGAGAGGGAAAGAAAGAC 60.027 54.545 0.00 0.00 0.00 3.01
658 688 2.269940 CCAGGGAGAGGGAAAGAAAGA 58.730 52.381 0.00 0.00 0.00 2.52
659 689 1.988846 ACCAGGGAGAGGGAAAGAAAG 59.011 52.381 0.00 0.00 0.00 2.62
660 690 2.108250 CAACCAGGGAGAGGGAAAGAAA 59.892 50.000 0.00 0.00 0.00 2.52
661 691 1.705186 CAACCAGGGAGAGGGAAAGAA 59.295 52.381 0.00 0.00 0.00 2.52
662 692 1.362224 CAACCAGGGAGAGGGAAAGA 58.638 55.000 0.00 0.00 0.00 2.52
663 693 1.068121 ACAACCAGGGAGAGGGAAAG 58.932 55.000 0.00 0.00 0.00 2.62
664 694 1.982958 GTACAACCAGGGAGAGGGAAA 59.017 52.381 0.00 0.00 0.00 3.13
665 695 1.132657 TGTACAACCAGGGAGAGGGAA 60.133 52.381 0.00 0.00 0.00 3.97
666 696 0.490017 TGTACAACCAGGGAGAGGGA 59.510 55.000 0.00 0.00 0.00 4.20
667 697 1.584724 ATGTACAACCAGGGAGAGGG 58.415 55.000 0.00 0.00 0.00 4.30
668 698 5.373812 AATAATGTACAACCAGGGAGAGG 57.626 43.478 0.00 0.00 0.00 3.69
669 699 6.180472 ACAAATAATGTACAACCAGGGAGAG 58.820 40.000 0.00 0.00 41.63 3.20
670 700 6.134535 ACAAATAATGTACAACCAGGGAGA 57.865 37.500 0.00 0.00 41.63 3.71
671 701 6.834168 AACAAATAATGTACAACCAGGGAG 57.166 37.500 0.00 0.00 42.99 4.30
672 702 7.287927 TGAAAACAAATAATGTACAACCAGGGA 59.712 33.333 0.00 0.00 42.99 4.20
673 703 7.437748 TGAAAACAAATAATGTACAACCAGGG 58.562 34.615 0.00 0.00 42.99 4.45
674 704 9.487790 AATGAAAACAAATAATGTACAACCAGG 57.512 29.630 0.00 0.00 42.99 4.45
705 735 9.743057 CAAATTAAGCCATTCGGAACATATTAA 57.257 29.630 0.00 0.00 0.00 1.40
708 738 6.549364 TCCAAATTAAGCCATTCGGAACATAT 59.451 34.615 0.00 0.00 0.00 1.78
709 739 5.888724 TCCAAATTAAGCCATTCGGAACATA 59.111 36.000 0.00 0.00 0.00 2.29
716 746 3.374058 ACGACTCCAAATTAAGCCATTCG 59.626 43.478 0.00 0.00 0.00 3.34
732 762 8.771766 GGATAAGGGATAACAAAATTACGACTC 58.228 37.037 0.00 0.00 0.00 3.36
734 764 8.557029 CAGGATAAGGGATAACAAAATTACGAC 58.443 37.037 0.00 0.00 0.00 4.34
757 788 2.017783 GCATGTGCGTTGCAACAGG 61.018 57.895 28.01 13.06 41.47 4.00
772 803 6.313744 ACAACTAAACTAGCGAAAAAGCAT 57.686 33.333 0.00 0.00 40.15 3.79
773 804 5.744666 ACAACTAAACTAGCGAAAAAGCA 57.255 34.783 0.00 0.00 40.15 3.91
774 805 8.723777 AATTACAACTAAACTAGCGAAAAAGC 57.276 30.769 0.00 0.00 37.41 3.51
776 807 9.872757 CTGAATTACAACTAAACTAGCGAAAAA 57.127 29.630 0.00 0.00 0.00 1.94
781 812 6.470160 CAGCTGAATTACAACTAAACTAGCG 58.530 40.000 8.42 0.00 33.05 4.26
812 843 5.895534 TCCCTCTGTACCGTAATATTTGTCT 59.104 40.000 0.00 0.00 0.00 3.41
824 855 4.467198 AACAATTACTCCCTCTGTACCG 57.533 45.455 0.00 0.00 0.00 4.02
910 2597 0.670854 GAGCTCCTCGTGGGTTGTTC 60.671 60.000 0.87 0.00 36.25 3.18
1122 2809 4.798682 TTCGAGGAGGAGGGGGCC 62.799 72.222 0.00 0.00 0.00 5.80
1706 3411 4.809958 CACATTCATGCCAAAGTGTTTTCA 59.190 37.500 0.00 0.00 0.00 2.69
1743 3448 3.610911 CAGGCCCTTTACAAGTCTAAGG 58.389 50.000 0.00 0.00 38.51 2.69
2235 3940 9.225436 TGTATGCATAGTATTCACTGTTTTTCA 57.775 29.630 6.67 0.00 36.14 2.69
2323 4029 7.498900 TCTGTTGGAGTGCAATATATACCTTTG 59.501 37.037 0.00 0.00 0.00 2.77
2381 4091 2.016318 CAACGGCCTGCATCATTAAGA 58.984 47.619 0.00 0.00 0.00 2.10
2473 4183 4.202567 TGGACCAGTTTCCTTATCAGCTTT 60.203 41.667 0.00 0.00 36.51 3.51
2591 4301 8.078596 CACCCATTTTGTTTTTCTGTTTTTCAA 58.921 29.630 0.00 0.00 0.00 2.69
2903 4614 1.065926 TGGCAGAGCTCGATTCATTGT 60.066 47.619 8.37 0.00 0.00 2.71
2982 4693 2.393271 AGCAGATCTGGGAAAGAACG 57.607 50.000 23.89 0.00 38.79 3.95
3155 4909 4.935702 TGCCATTGTTCAAAGTGAGAAAG 58.064 39.130 0.00 0.00 0.00 2.62
3378 5132 1.068083 CGCAGACCTATCACGCCAT 59.932 57.895 0.00 0.00 0.00 4.40
3542 5296 6.619801 ACTGTTGAGAGATGTTTTGGTAAC 57.380 37.500 0.00 0.00 0.00 2.50
3711 5572 6.331845 TGAGCATGAATTTCGCAAATTACAT 58.668 32.000 0.00 8.75 40.97 2.29
3857 5718 1.402456 CGACGGTCTTCACGGATTTCT 60.402 52.381 6.57 0.00 35.23 2.52
4056 5917 7.506328 AAATTACAGGTGAGACAGGTTAAAC 57.494 36.000 0.00 0.00 0.00 2.01
4310 6172 7.281774 AGACAGATAACAAACATGGATGTGATC 59.718 37.037 16.99 16.99 41.61 2.92
4338 6206 2.695359 TCTTATTCACAGGCGTGTTCC 58.305 47.619 9.81 0.00 44.02 3.62
4364 6232 8.503458 AATGAAGAAAGACAATCAGATACCAG 57.497 34.615 0.00 0.00 0.00 4.00
4468 6336 6.040278 TCAAATGTGCACTGTTTCCTTTATCA 59.960 34.615 19.41 0.00 0.00 2.15
4703 6571 3.997021 AGTCAAAGTTCCACGCATTAGAG 59.003 43.478 0.00 0.00 0.00 2.43
4788 6656 2.040939 CACAGATGAGCTCTCCCTGAT 58.959 52.381 25.93 9.09 35.06 2.90
4841 6709 2.039746 TCCAAAGAATTTCTCGGCCTCA 59.960 45.455 0.00 0.00 35.03 3.86
4979 6847 4.202141 CCACCTTTTGACAAATCAAGCTCA 60.202 41.667 0.50 0.00 45.54 4.26
5186 7054 3.157087 TCTGGTTTTCTGCCAAGAATCC 58.843 45.455 0.00 0.00 42.04 3.01
5236 7104 1.002430 TCTCTGAGCCAAAAGATGCGT 59.998 47.619 0.00 0.00 0.00 5.24
5459 7327 1.153549 GTCCCCACTAGCGCTTCTG 60.154 63.158 18.68 11.39 0.00 3.02
5705 7573 4.890581 TCACTACTTCTATCCCAGCTTCTC 59.109 45.833 0.00 0.00 0.00 2.87
5880 7748 6.070424 ACACTTCCTAAAACATCCCTTATCGA 60.070 38.462 0.00 0.00 0.00 3.59
5982 7850 8.932945 AGGAAAAAGTTCTTTCACAAAATCTC 57.067 30.769 10.59 0.00 37.09 2.75
6024 7892 3.814283 CCTTGAGAAGATTATGAGGCAGC 59.186 47.826 0.00 0.00 0.00 5.25
6245 8113 3.591789 AGGGAGCCTATTATGCAAGAGA 58.408 45.455 0.00 0.00 28.47 3.10
6452 8360 7.227873 TGTTTACATGTATGAAAGAACTCCCA 58.772 34.615 6.36 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.