Multiple sequence alignment - TraesCS5A01G318900

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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 TraesCS5A01G318900 chr5A 100.000 2330 0 0 1 2330 529370134 529367805 0.000000e+00 4303.0
1 TraesCS5A01G318900 chr5A 91.892 111 6 3 710 818 521287938 521287829 4.010000e-33 152.0
2 TraesCS5A01G318900 chr5B 95.415 1505 58 9 831 2330 503327926 503326428 0.000000e+00 2386.0
3 TraesCS5A01G318900 chr5B 87.573 684 73 9 9 681 503328649 503327967 0.000000e+00 782.0
4 TraesCS5A01G318900 chr5D 95.455 1474 45 7 872 2330 416600914 416599448 0.000000e+00 2331.0
5 TraesCS5A01G318900 chr5D 83.766 308 26 11 3 290 416601641 416601338 1.060000e-68 270.0
6 TraesCS5A01G318900 chr1D 93.578 109 4 1 710 818 42271633 42271738 2.400000e-35 159.0
7 TraesCS5A01G318900 chr6A 92.661 109 6 2 710 818 64662295 64662401 3.100000e-34 156.0
8 TraesCS5A01G318900 chr6A 91.892 111 7 2 710 818 147256478 147256588 1.110000e-33 154.0
9 TraesCS5A01G318900 chr2A 91.892 111 7 2 710 818 194551901 194552011 1.110000e-33 154.0
10 TraesCS5A01G318900 chr2A 100.000 28 0 0 682 709 748215582 748215609 4.000000e-03 52.8
11 TraesCS5A01G318900 chr7A 91.743 109 9 0 710 818 84295795 84295687 4.010000e-33 152.0
12 TraesCS5A01G318900 chr7A 91.743 109 6 2 710 818 158656396 158656291 5.190000e-32 148.0
13 TraesCS5A01G318900 chr7A 91.071 112 6 4 710 818 536157839 536157729 5.190000e-32 148.0
14 TraesCS5A01G318900 chr1A 91.071 112 7 1 710 818 41071823 41071712 5.190000e-32 148.0
15 TraesCS5A01G318900 chrUn 84.906 53 7 1 657 709 345757019 345756968 4.000000e-03 52.8
16 TraesCS5A01G318900 chrUn 84.906 53 7 1 657 709 353376478 353376427 4.000000e-03 52.8
17 TraesCS5A01G318900 chrUn 84.906 53 7 1 657 709 353378695 353378644 4.000000e-03 52.8
18 TraesCS5A01G318900 chr3B 84.906 53 7 1 657 709 829904490 829904541 4.000000e-03 52.8
19 TraesCS5A01G318900 chr3B 84.906 53 7 1 657 709 830026789 830026840 4.000000e-03 52.8


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 TraesCS5A01G318900 chr5A 529367805 529370134 2329 True 4303.0 4303 100.0000 1 2330 1 chr5A.!!$R2 2329
1 TraesCS5A01G318900 chr5B 503326428 503328649 2221 True 1584.0 2386 91.4940 9 2330 2 chr5B.!!$R1 2321
2 TraesCS5A01G318900 chr5D 416599448 416601641 2193 True 1300.5 2331 89.6105 3 2330 2 chr5D.!!$R1 2327

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
474 504 0.866061 AATGCTACTACGTCGCTGCG 60.866 55.000 17.25 17.25 37.94 5.18 F
551 582 1.347707 AGCATCTTGGAGAACCGTCAA 59.652 47.619 0.00 0.00 39.42 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1326 1374 0.543749 CCTGAATCCTGGGGTCTCAC 59.456 60.000 0.0 0.0 0.00 3.51 R
1590 1641 1.680735 AGCATCTTTGGCGACACAAAA 59.319 42.857 0.0 0.0 42.67 2.44 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
48 50 8.827832 AAAATCATCAAGTTGATTGGAGGATA 57.172 30.769 15.85 0.00 43.73 2.59
58 60 4.560739 TGATTGGAGGATATGGTGTCTCT 58.439 43.478 0.00 0.00 0.00 3.10
64 66 5.905331 TGGAGGATATGGTGTCTCTGTAATT 59.095 40.000 0.00 0.00 0.00 1.40
77 79 9.534565 GTGTCTCTGTAATTATATGCTTCTTGA 57.465 33.333 0.00 0.00 0.00 3.02
82 84 9.317936 TCTGTAATTATATGCTTCTTGACACTG 57.682 33.333 0.00 0.00 0.00 3.66
84 86 9.317936 TGTAATTATATGCTTCTTGACACTGAG 57.682 33.333 0.00 0.00 0.00 3.35
115 136 3.118223 ACCTATGCAGCTACTTTTCCTCC 60.118 47.826 0.00 0.00 0.00 4.30
124 145 3.673866 GCTACTTTTCCTCCTCGACTCAC 60.674 52.174 0.00 0.00 0.00 3.51
125 146 2.317040 ACTTTTCCTCCTCGACTCACA 58.683 47.619 0.00 0.00 0.00 3.58
126 147 2.698797 ACTTTTCCTCCTCGACTCACAA 59.301 45.455 0.00 0.00 0.00 3.33
173 194 7.264373 ACAATAAAAGGAAAGGCATCTATCG 57.736 36.000 0.00 0.00 0.00 2.92
180 201 6.031751 AGGAAAGGCATCTATCGAAGTATC 57.968 41.667 0.00 0.00 0.00 2.24
184 205 4.411927 AGGCATCTATCGAAGTATCCACT 58.588 43.478 0.00 0.00 36.19 4.00
206 227 1.674221 GCAGTGATCCTTCGAAGCAGT 60.674 52.381 19.99 12.07 0.00 4.40
288 310 2.033151 GGTCGTTCGTGAAAGAAACTGG 60.033 50.000 0.00 0.00 31.08 4.00
290 312 3.798337 GTCGTTCGTGAAAGAAACTGGTA 59.202 43.478 0.00 0.00 31.08 3.25
293 315 5.005971 TCGTTCGTGAAAGAAACTGGTAAAG 59.994 40.000 0.00 0.00 0.00 1.85
295 317 3.246699 TCGTGAAAGAAACTGGTAAAGCG 59.753 43.478 0.00 0.00 0.00 4.68
302 324 2.467566 AACTGGTAAAGCGGGTACTG 57.532 50.000 0.00 0.00 38.10 2.74
328 352 2.103941 GGTGCTTAGAGATTCAGAGGGG 59.896 54.545 0.00 0.00 0.00 4.79
330 354 3.198853 GTGCTTAGAGATTCAGAGGGGTT 59.801 47.826 0.00 0.00 0.00 4.11
388 412 1.459450 TAATGCCCTCGAAGCCAAAC 58.541 50.000 4.76 0.00 0.00 2.93
389 413 1.250840 AATGCCCTCGAAGCCAAACC 61.251 55.000 4.76 0.00 0.00 3.27
401 425 3.059352 AGCCAAACCTAGTGTGATGAC 57.941 47.619 0.00 0.00 0.00 3.06
410 434 3.056107 CCTAGTGTGATGACGGAAAGGAA 60.056 47.826 0.00 0.00 0.00 3.36
419 443 3.334691 TGACGGAAAGGAATGCACTAAG 58.665 45.455 0.00 0.00 0.00 2.18
440 464 5.102953 AGCCTACAACAATCATAGCTTCA 57.897 39.130 0.00 0.00 0.00 3.02
458 487 7.187244 AGCTTCATGATCTAATCGAACAATG 57.813 36.000 0.00 0.00 0.00 2.82
474 504 0.866061 AATGCTACTACGTCGCTGCG 60.866 55.000 17.25 17.25 37.94 5.18
547 578 2.813754 TCAAAAGCATCTTGGAGAACCG 59.186 45.455 0.00 0.00 39.42 4.44
549 580 2.100605 AAGCATCTTGGAGAACCGTC 57.899 50.000 0.00 0.00 39.42 4.79
551 582 1.347707 AGCATCTTGGAGAACCGTCAA 59.652 47.619 0.00 0.00 39.42 3.18
588 619 7.331440 TGAAAATTGCACGCAATCAAAATAGAT 59.669 29.630 17.06 0.00 44.86 1.98
624 655 2.032549 GCTAATCTACGGCGTTACGAGA 60.033 50.000 21.24 15.86 37.61 4.04
656 687 1.387295 TTGGTTGCGTCATGTGCCAA 61.387 50.000 9.60 0.00 34.12 4.52
672 703 3.938334 GTGCCAAACAATGTTTCTTTGGT 59.062 39.130 8.59 0.00 44.00 3.67
681 712 9.804758 AAACAATGTTTCTTTGGTCGTATTTAA 57.195 25.926 5.41 0.00 0.00 1.52
682 713 9.804758 AACAATGTTTCTTTGGTCGTATTTAAA 57.195 25.926 0.00 0.00 0.00 1.52
683 714 9.804758 ACAATGTTTCTTTGGTCGTATTTAAAA 57.195 25.926 0.00 0.00 0.00 1.52
685 716 9.804758 AATGTTTCTTTGGTCGTATTTAAAACA 57.195 25.926 0.00 0.00 38.15 2.83
686 717 8.844441 TGTTTCTTTGGTCGTATTTAAAACAG 57.156 30.769 0.00 0.00 32.26 3.16
687 718 8.460428 TGTTTCTTTGGTCGTATTTAAAACAGT 58.540 29.630 0.00 0.00 32.26 3.55
688 719 9.292846 GTTTCTTTGGTCGTATTTAAAACAGTT 57.707 29.630 0.00 0.00 0.00 3.16
689 720 9.857957 TTTCTTTGGTCGTATTTAAAACAGTTT 57.142 25.926 0.00 0.00 0.00 2.66
690 721 9.857957 TTCTTTGGTCGTATTTAAAACAGTTTT 57.142 25.926 15.58 15.58 36.67 2.43
691 722 9.291664 TCTTTGGTCGTATTTAAAACAGTTTTG 57.708 29.630 19.77 3.73 34.19 2.44
692 723 7.452630 TTGGTCGTATTTAAAACAGTTTTGC 57.547 32.000 19.77 5.59 34.19 3.68
693 724 6.797454 TGGTCGTATTTAAAACAGTTTTGCT 58.203 32.000 19.77 7.85 34.19 3.91
694 725 7.928103 TGGTCGTATTTAAAACAGTTTTGCTA 58.072 30.769 19.77 6.64 34.19 3.49
695 726 8.404000 TGGTCGTATTTAAAACAGTTTTGCTAA 58.596 29.630 19.77 11.80 34.19 3.09
696 727 9.235537 GGTCGTATTTAAAACAGTTTTGCTAAA 57.764 29.630 19.77 13.01 34.19 1.85
698 729 8.960075 TCGTATTTAAAACAGTTTTGCTAAAGC 58.040 29.630 19.77 9.42 42.50 3.51
716 747 7.586747 GCTAAAGCACGTCTAGATATCTAAGT 58.413 38.462 13.41 10.62 41.59 2.24
717 748 7.747357 GCTAAAGCACGTCTAGATATCTAAGTC 59.253 40.741 13.41 6.25 41.59 3.01
718 749 7.569639 AAAGCACGTCTAGATATCTAAGTCA 57.430 36.000 13.41 0.00 0.00 3.41
719 750 7.753309 AAGCACGTCTAGATATCTAAGTCAT 57.247 36.000 13.41 3.25 0.00 3.06
720 751 8.850007 AAGCACGTCTAGATATCTAAGTCATA 57.150 34.615 13.41 0.00 0.00 2.15
721 752 9.456147 AAGCACGTCTAGATATCTAAGTCATAT 57.544 33.333 13.41 0.00 0.00 1.78
746 777 7.809226 ATCATTGATCTTACATCGAGATTCG 57.191 36.000 0.00 0.00 42.10 3.34
747 778 6.739112 TCATTGATCTTACATCGAGATTCGT 58.261 36.000 0.00 0.00 41.35 3.85
748 779 6.638468 TCATTGATCTTACATCGAGATTCGTG 59.362 38.462 0.00 0.05 41.35 4.35
749 780 5.500645 TGATCTTACATCGAGATTCGTGT 57.499 39.130 0.00 10.04 41.35 4.49
751 782 4.957759 TCTTACATCGAGATTCGTGTGA 57.042 40.909 13.14 7.32 41.35 3.58
757 788 8.642908 TTACATCGAGATTCGTGTGAATATTT 57.357 30.769 13.14 0.00 44.79 1.40
759 790 7.974675 ACATCGAGATTCGTGTGAATATTTTT 58.025 30.769 11.35 0.00 44.79 1.94
796 827 7.876936 ATGCTTGATTCACTCATTTAGATGT 57.123 32.000 0.00 0.00 34.77 3.06
797 828 7.080353 TGCTTGATTCACTCATTTAGATGTG 57.920 36.000 0.00 0.00 34.77 3.21
798 829 5.970023 GCTTGATTCACTCATTTAGATGTGC 59.030 40.000 0.00 0.00 34.77 4.57
799 830 6.403964 GCTTGATTCACTCATTTAGATGTGCA 60.404 38.462 0.00 0.00 34.77 4.57
800 831 7.451501 TTGATTCACTCATTTAGATGTGCAA 57.548 32.000 0.00 0.00 34.77 4.08
801 832 7.634671 TGATTCACTCATTTAGATGTGCAAT 57.365 32.000 0.00 0.00 34.77 3.56
802 833 8.735692 TGATTCACTCATTTAGATGTGCAATA 57.264 30.769 0.00 0.00 34.77 1.90
803 834 9.176460 TGATTCACTCATTTAGATGTGCAATAA 57.824 29.630 0.00 0.00 34.77 1.40
804 835 9.443283 GATTCACTCATTTAGATGTGCAATAAC 57.557 33.333 0.00 0.00 34.77 1.89
805 836 8.565896 TTCACTCATTTAGATGTGCAATAACT 57.434 30.769 0.00 0.00 34.77 2.24
806 837 9.665719 TTCACTCATTTAGATGTGCAATAACTA 57.334 29.630 0.00 0.00 34.77 2.24
807 838 9.317936 TCACTCATTTAGATGTGCAATAACTAG 57.682 33.333 0.00 0.00 34.77 2.57
808 839 9.317936 CACTCATTTAGATGTGCAATAACTAGA 57.682 33.333 0.00 0.00 34.77 2.43
809 840 9.539825 ACTCATTTAGATGTGCAATAACTAGAG 57.460 33.333 0.00 0.00 34.77 2.43
810 841 8.370493 TCATTTAGATGTGCAATAACTAGAGC 57.630 34.615 0.00 0.00 34.77 4.09
811 842 7.986889 TCATTTAGATGTGCAATAACTAGAGCA 59.013 33.333 0.00 0.00 34.77 4.26
826 857 6.168270 ACTAGAGCACATCTAATTCCTTCC 57.832 41.667 0.00 0.00 40.06 3.46
827 858 5.902431 ACTAGAGCACATCTAATTCCTTCCT 59.098 40.000 0.00 0.00 40.06 3.36
833 868 8.829373 AGCACATCTAATTCCTTCCTAATTTT 57.171 30.769 0.00 0.00 0.00 1.82
851 886 3.984838 TTTTTGTCCATGGCAGTGC 57.015 47.368 6.96 6.55 0.00 4.40
900 936 3.041940 CGCCGTGTGTGTTCCCTC 61.042 66.667 0.00 0.00 0.00 4.30
1080 1116 2.134287 GCGCCCTCTCATCCACCTA 61.134 63.158 0.00 0.00 0.00 3.08
1326 1374 3.483922 CCGACGAGAAGAAGATCAAATCG 59.516 47.826 0.00 0.00 35.00 3.34
1480 1528 4.554586 CGTGTATGCTGCAATTTGTACTTG 59.445 41.667 6.36 0.00 0.00 3.16
1518 1566 0.038166 GTGACCAAAGATGCCCCTGA 59.962 55.000 0.00 0.00 0.00 3.86
1539 1590 8.624776 CCCTGATTATGAATACAAGTTCCTTTC 58.375 37.037 0.00 0.00 0.00 2.62
1562 1613 5.241285 TCTGCAGCAGTTCAATTCATGTTTA 59.759 36.000 22.10 0.00 32.61 2.01
1590 1641 5.473066 ACTTGCTGCTAAAATTGGTCAAT 57.527 34.783 0.00 0.00 0.00 2.57
1621 1672 3.889815 CCAAAGATGCTCCTGGTTATCA 58.110 45.455 0.00 0.00 0.00 2.15
1633 1684 7.051000 GCTCCTGGTTATCAAATAGAAGTTCT 58.949 38.462 10.87 10.87 0.00 3.01
1713 1767 7.151999 TGGTGCGACAAAATATTATTTCACT 57.848 32.000 13.34 0.00 0.00 3.41
1812 1866 2.400399 TCGTTTGTTCTCATGACCGAC 58.600 47.619 0.00 0.00 0.00 4.79
1828 1882 1.441016 GACGACGACACCGGTACAC 60.441 63.158 6.87 0.08 40.78 2.90
1855 1909 5.938322 ACAAAGGTGTTACTTATTCATGCG 58.062 37.500 0.00 0.00 32.58 4.73
2092 2146 1.269998 GCTCTGTACTTGGACGTGACT 59.730 52.381 0.00 0.00 0.00 3.41
2296 2350 3.089284 AGATGGTCTCATGTCGTACACA 58.911 45.455 0.00 0.00 40.18 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 50 8.654997 AGAAGCATATAATTACAGAGACACCAT 58.345 33.333 0.00 0.00 0.00 3.55
58 60 9.317936 CTCAGTGTCAAGAAGCATATAATTACA 57.682 33.333 0.00 0.00 0.00 2.41
64 66 5.422012 TCACCTCAGTGTCAAGAAGCATATA 59.578 40.000 0.00 0.00 44.83 0.86
77 79 4.100189 GCATAGGTAATCTCACCTCAGTGT 59.900 45.833 0.00 0.00 46.34 3.55
82 84 3.323403 AGCTGCATAGGTAATCTCACCTC 59.677 47.826 1.02 0.00 46.34 3.85
84 86 3.760580 AGCTGCATAGGTAATCTCACC 57.239 47.619 1.02 0.00 39.02 4.02
97 118 2.419297 CGAGGAGGAAAAGTAGCTGCAT 60.419 50.000 4.12 0.00 0.00 3.96
115 136 2.985809 CTGCTTCTCTTTGTGAGTCGAG 59.014 50.000 0.00 0.00 43.13 4.04
125 146 9.998106 TGTACTTTTAATAGACTGCTTCTCTTT 57.002 29.630 0.00 0.00 35.55 2.52
126 147 9.998106 TTGTACTTTTAATAGACTGCTTCTCTT 57.002 29.630 0.00 0.00 35.55 2.85
184 205 1.270785 TGCTTCGAAGGATCACTGCAA 60.271 47.619 25.77 0.00 0.00 4.08
206 227 2.398588 CCATGTGGGGCTCTACTTAGA 58.601 52.381 0.37 0.00 0.00 2.10
288 310 2.285977 CCATTCCAGTACCCGCTTTAC 58.714 52.381 0.00 0.00 0.00 2.01
290 312 0.696501 ACCATTCCAGTACCCGCTTT 59.303 50.000 0.00 0.00 0.00 3.51
293 315 2.112815 GCACCATTCCAGTACCCGC 61.113 63.158 0.00 0.00 0.00 6.13
295 317 2.504175 TCTAAGCACCATTCCAGTACCC 59.496 50.000 0.00 0.00 0.00 3.69
302 324 5.028549 TCTGAATCTCTAAGCACCATTCC 57.971 43.478 0.00 0.00 0.00 3.01
328 352 7.722795 ATTTGTAAGCCAAAATGGTTACAAC 57.277 32.000 21.28 9.69 44.15 3.32
330 354 8.738645 AAAATTTGTAAGCCAAAATGGTTACA 57.261 26.923 10.69 10.69 45.72 2.41
365 389 1.064758 TGGCTTCGAGGGCATTATTGT 60.065 47.619 20.13 0.00 36.85 2.71
388 412 2.496070 TCCTTTCCGTCATCACACTAGG 59.504 50.000 0.00 0.00 0.00 3.02
389 413 3.868757 TCCTTTCCGTCATCACACTAG 57.131 47.619 0.00 0.00 0.00 2.57
401 425 1.401905 GGCTTAGTGCATTCCTTTCCG 59.598 52.381 0.00 0.00 45.15 4.30
410 434 4.588899 TGATTGTTGTAGGCTTAGTGCAT 58.411 39.130 0.00 0.00 45.15 3.96
419 443 5.528690 TCATGAAGCTATGATTGTTGTAGGC 59.471 40.000 0.00 0.00 32.39 3.93
440 464 7.539022 CGTAGTAGCATTGTTCGATTAGATCAT 59.461 37.037 0.00 0.00 0.00 2.45
474 504 2.359900 CTCCATGACTGGTTGGTTAGC 58.640 52.381 0.00 0.00 43.61 3.09
522 553 5.184671 GGTTCTCCAAGATGCTTTTGATCTT 59.815 40.000 0.00 0.00 40.16 2.40
547 578 9.091255 GTGCAATTTTCAACGAAATAAATTGAC 57.909 29.630 22.17 16.75 44.64 3.18
549 580 7.201058 GCGTGCAATTTTCAACGAAATAAATTG 60.201 33.333 17.64 17.64 44.65 2.32
551 582 6.074088 TGCGTGCAATTTTCAACGAAATAAAT 60.074 30.769 0.00 0.00 31.34 1.40
588 619 7.494625 CCGTAGATTAGCAAGGTAATGAGAAAA 59.505 37.037 9.04 0.00 0.00 2.29
598 629 0.822164 ACGCCGTAGATTAGCAAGGT 59.178 50.000 0.00 0.00 0.00 3.50
624 655 0.881118 CAACCAACAAGCGGTGCTAT 59.119 50.000 0.00 0.00 38.25 2.97
646 677 4.669206 AGAAACATTGTTTGGCACATGA 57.331 36.364 19.03 0.00 39.30 3.07
656 687 9.804758 TTTAAATACGACCAAAGAAACATTGTT 57.195 25.926 0.00 0.00 0.00 2.83
672 703 8.960075 GCTTTAGCAAAACTGTTTTAAATACGA 58.040 29.630 17.31 2.04 41.59 3.43
691 722 7.586747 ACTTAGATATCTAGACGTGCTTTAGC 58.413 38.462 12.16 0.00 42.50 3.09
692 723 8.775527 TGACTTAGATATCTAGACGTGCTTTAG 58.224 37.037 12.16 6.01 0.00 1.85
693 724 8.672823 TGACTTAGATATCTAGACGTGCTTTA 57.327 34.615 12.16 0.00 0.00 1.85
694 725 7.569639 TGACTTAGATATCTAGACGTGCTTT 57.430 36.000 12.16 0.00 0.00 3.51
695 726 7.753309 ATGACTTAGATATCTAGACGTGCTT 57.247 36.000 12.16 3.40 0.00 3.91
720 751 9.513727 CGAATCTCGATGTAAGATCAATGATAT 57.486 33.333 0.00 0.00 43.74 1.63
721 752 8.515414 ACGAATCTCGATGTAAGATCAATGATA 58.485 33.333 2.59 0.00 43.74 2.15
722 753 7.328005 CACGAATCTCGATGTAAGATCAATGAT 59.672 37.037 2.59 0.00 43.74 2.45
723 754 6.638468 CACGAATCTCGATGTAAGATCAATGA 59.362 38.462 2.59 0.00 43.74 2.57
724 755 6.419116 ACACGAATCTCGATGTAAGATCAATG 59.581 38.462 2.59 0.00 43.74 2.82
725 756 6.419116 CACACGAATCTCGATGTAAGATCAAT 59.581 38.462 2.59 0.00 43.74 2.57
726 757 5.743872 CACACGAATCTCGATGTAAGATCAA 59.256 40.000 2.59 0.00 43.74 2.57
727 758 5.065988 TCACACGAATCTCGATGTAAGATCA 59.934 40.000 2.59 0.00 43.74 2.92
728 759 5.511571 TCACACGAATCTCGATGTAAGATC 58.488 41.667 2.59 0.00 43.74 2.75
729 760 5.500645 TCACACGAATCTCGATGTAAGAT 57.499 39.130 2.59 0.00 43.74 2.40
730 761 4.957759 TCACACGAATCTCGATGTAAGA 57.042 40.909 2.59 0.00 43.74 2.10
731 762 7.859613 ATATTCACACGAATCTCGATGTAAG 57.140 36.000 2.59 0.00 43.74 2.34
732 763 8.642908 AAATATTCACACGAATCTCGATGTAA 57.357 30.769 2.59 1.56 43.74 2.41
733 764 8.642908 AAAATATTCACACGAATCTCGATGTA 57.357 30.769 2.59 0.00 43.74 2.29
734 765 7.539712 AAAATATTCACACGAATCTCGATGT 57.460 32.000 2.59 1.35 43.74 3.06
771 802 8.833493 CACATCTAAATGAGTGAATCAAGCATA 58.167 33.333 0.00 0.00 42.53 3.14
773 804 6.403964 GCACATCTAAATGAGTGAATCAAGCA 60.404 38.462 0.00 0.00 42.53 3.91
775 806 7.080353 TGCACATCTAAATGAGTGAATCAAG 57.920 36.000 0.00 0.00 42.53 3.02
778 809 9.443283 GTTATTGCACATCTAAATGAGTGAATC 57.557 33.333 0.00 0.00 36.67 2.52
781 812 9.317936 CTAGTTATTGCACATCTAAATGAGTGA 57.682 33.333 0.00 0.00 36.67 3.41
783 814 9.539825 CTCTAGTTATTGCACATCTAAATGAGT 57.460 33.333 0.00 0.00 36.67 3.41
785 816 7.986889 TGCTCTAGTTATTGCACATCTAAATGA 59.013 33.333 0.00 0.00 36.67 2.57
796 827 7.442364 GGAATTAGATGTGCTCTAGTTATTGCA 59.558 37.037 0.00 0.00 36.75 4.08
797 828 7.659390 AGGAATTAGATGTGCTCTAGTTATTGC 59.341 37.037 0.00 0.00 36.75 3.56
798 829 9.553064 AAGGAATTAGATGTGCTCTAGTTATTG 57.447 33.333 0.00 0.00 36.75 1.90
799 830 9.771534 GAAGGAATTAGATGTGCTCTAGTTATT 57.228 33.333 0.00 0.00 36.75 1.40
800 831 8.371699 GGAAGGAATTAGATGTGCTCTAGTTAT 58.628 37.037 0.00 0.00 36.75 1.89
801 832 7.565398 AGGAAGGAATTAGATGTGCTCTAGTTA 59.435 37.037 0.00 0.00 36.75 2.24
802 833 6.385467 AGGAAGGAATTAGATGTGCTCTAGTT 59.615 38.462 0.00 0.00 38.65 2.24
803 834 5.902431 AGGAAGGAATTAGATGTGCTCTAGT 59.098 40.000 0.00 0.00 37.75 2.57
804 835 6.418057 AGGAAGGAATTAGATGTGCTCTAG 57.582 41.667 0.00 0.00 37.75 2.43
805 836 7.914427 TTAGGAAGGAATTAGATGTGCTCTA 57.086 36.000 0.00 0.00 35.28 2.43
806 837 6.814954 TTAGGAAGGAATTAGATGTGCTCT 57.185 37.500 0.00 0.00 38.06 4.09
807 838 8.457238 AAATTAGGAAGGAATTAGATGTGCTC 57.543 34.615 0.00 0.00 0.00 4.26
808 839 8.829373 AAAATTAGGAAGGAATTAGATGTGCT 57.171 30.769 0.00 0.00 0.00 4.40
833 868 1.412079 AGCACTGCCATGGACAAAAA 58.588 45.000 18.40 0.00 0.00 1.94
838 873 3.255642 TCTTAAAAAGCACTGCCATGGAC 59.744 43.478 18.40 7.64 0.00 4.02
839 874 3.495331 TCTTAAAAAGCACTGCCATGGA 58.505 40.909 18.40 0.00 0.00 3.41
938 974 2.420022 CGATTGGTTGGCTGGAGTTTAG 59.580 50.000 0.00 0.00 0.00 1.85
939 975 2.432444 CGATTGGTTGGCTGGAGTTTA 58.568 47.619 0.00 0.00 0.00 2.01
1278 1323 3.664025 CTTGTCGCCGCTGGGATCA 62.664 63.158 0.00 0.00 35.70 2.92
1326 1374 0.543749 CCTGAATCCTGGGGTCTCAC 59.456 60.000 0.00 0.00 0.00 3.51
1480 1528 3.189910 TCACACAAAGAATGATGAGCAGC 59.810 43.478 0.00 0.00 0.00 5.25
1539 1590 3.570926 ACATGAATTGAACTGCTGCAG 57.429 42.857 27.02 27.02 37.52 4.41
1562 1613 5.243730 ACCAATTTTAGCAGCAAGTATGTGT 59.756 36.000 0.00 0.00 0.00 3.72
1590 1641 1.680735 AGCATCTTTGGCGACACAAAA 59.319 42.857 0.00 0.00 42.67 2.44
1633 1684 7.433708 TGAATTGAAGAGTCGCAATAGAAAA 57.566 32.000 12.62 0.00 33.87 2.29
1639 1691 5.396484 CAACATGAATTGAAGAGTCGCAAT 58.604 37.500 0.00 8.03 36.35 3.56
1640 1692 4.786507 CAACATGAATTGAAGAGTCGCAA 58.213 39.130 0.00 4.34 0.00 4.85
1644 1696 5.618056 TCTGCAACATGAATTGAAGAGTC 57.382 39.130 0.00 0.00 39.03 3.36
1647 1699 7.080353 CAGTATCTGCAACATGAATTGAAGA 57.920 36.000 8.74 8.74 46.25 2.87
1713 1767 7.418712 GGGCTTCTTGGCTAGAGTTTTACTATA 60.419 40.741 0.00 0.00 41.48 1.31
1812 1866 1.727022 GTGTGTACCGGTGTCGTCG 60.727 63.158 19.93 0.00 33.95 5.12
1828 1882 7.962918 GCATGAATAAGTAACACCTTTGTAGTG 59.037 37.037 0.00 0.00 41.15 2.74
2092 2146 2.033448 GTCACCAATGTCGGCCCA 59.967 61.111 0.00 0.00 0.00 5.36
2296 2350 2.113986 GCTGCACACCCTGGTCTT 59.886 61.111 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.