Multiple sequence alignment - TraesCS3A01G263300

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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 TraesCS3A01G263300 chr3A 100.000 3110 0 0 1 3110 486930899 486927790 0.000000e+00 5744.0
1 TraesCS3A01G263300 chr3D 94.712 2307 91 12 812 3110 365054812 365052529 0.000000e+00 3555.0
2 TraesCS3A01G263300 chr3D 92.464 491 33 3 153 641 43563933 43564421 0.000000e+00 699.0
3 TraesCS3A01G263300 chr3D 91.700 494 38 2 149 641 156891102 156890611 0.000000e+00 682.0
4 TraesCS3A01G263300 chr3D 94.245 139 7 1 1 139 365055143 365055006 8.740000e-51 211.0
5 TraesCS3A01G263300 chr3B 94.170 1338 61 9 790 2125 475385782 475384460 0.000000e+00 2023.0
6 TraesCS3A01G263300 chr3B 88.552 725 35 20 2218 2935 475384538 475383855 0.000000e+00 835.0
7 TraesCS3A01G263300 chr3B 90.784 510 39 6 134 641 775734313 775734816 0.000000e+00 675.0
8 TraesCS3A01G263300 chr3B 100.000 177 0 0 2934 3110 475383741 475383565 8.320000e-86 327.0
9 TraesCS3A01G263300 chr3B 100.000 30 0 0 91 120 475386226 475386197 4.330000e-04 56.5
10 TraesCS3A01G263300 chr2D 92.110 507 35 5 137 641 429043042 429043545 0.000000e+00 710.0
11 TraesCS3A01G263300 chr7D 91.700 506 39 2 137 641 561806012 561805509 0.000000e+00 699.0
12 TraesCS3A01G263300 chr5D 91.287 505 39 3 138 641 62529900 62530400 0.000000e+00 684.0
13 TraesCS3A01G263300 chr5A 90.551 508 42 6 137 641 288257695 288258199 0.000000e+00 667.0
14 TraesCS3A01G263300 chr6D 90.514 506 40 5 138 641 5070215 5069716 0.000000e+00 662.0
15 TraesCS3A01G263300 chr6D 90.157 508 43 3 139 644 144144179 144144681 0.000000e+00 654.0
16 TraesCS3A01G263300 chr1A 79.954 863 148 19 1187 2032 550593553 550592699 2.050000e-171 612.0
17 TraesCS3A01G263300 chr1B 79.717 848 150 18 1191 2026 628499511 628498674 7.430000e-166 593.0


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 TraesCS3A01G263300 chr3A 486927790 486930899 3109 True 5744.000 5744 100.0000 1 3110 1 chr3A.!!$R1 3109
1 TraesCS3A01G263300 chr3D 365052529 365055143 2614 True 1883.000 3555 94.4785 1 3110 2 chr3D.!!$R2 3109
2 TraesCS3A01G263300 chr3B 475383565 475386226 2661 True 810.375 2023 95.6805 91 3110 4 chr3B.!!$R1 3019
3 TraesCS3A01G263300 chr3B 775734313 775734816 503 False 675.000 675 90.7840 134 641 1 chr3B.!!$F1 507
4 TraesCS3A01G263300 chr2D 429043042 429043545 503 False 710.000 710 92.1100 137 641 1 chr2D.!!$F1 504
5 TraesCS3A01G263300 chr7D 561805509 561806012 503 True 699.000 699 91.7000 137 641 1 chr7D.!!$R1 504
6 TraesCS3A01G263300 chr5D 62529900 62530400 500 False 684.000 684 91.2870 138 641 1 chr5D.!!$F1 503
7 TraesCS3A01G263300 chr5A 288257695 288258199 504 False 667.000 667 90.5510 137 641 1 chr5A.!!$F1 504
8 TraesCS3A01G263300 chr6D 144144179 144144681 502 False 654.000 654 90.1570 139 644 1 chr6D.!!$F1 505
9 TraesCS3A01G263300 chr1A 550592699 550593553 854 True 612.000 612 79.9540 1187 2032 1 chr1A.!!$R1 845
10 TraesCS3A01G263300 chr1B 628498674 628499511 837 True 593.000 593 79.7170 1191 2026 1 chr1B.!!$R1 835

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
854 963 0.391661 ATACCAGCCGTGCAAGACTG 60.392 55.0 8.92 8.92 0.00 3.51 F
2044 2165 0.036577 CAGCCAAGGACTGTCCAGAG 60.037 60.0 27.48 15.92 39.61 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2197 0.729116 CATGGCATTGTCTCCGTGTC 59.271 55.0 0.0 0.0 35.25 3.67 R
2932 3175 5.951747 CCCTCAGGAATATTTTCAAACCAGA 59.048 40.0 0.0 0.0 33.23 3.86 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
42 43 8.573885 TCCTATGAATTAGTAGAACACATACCG 58.426 37.037 0.00 0.00 0.00 4.02
50 51 6.737254 AGTAGAACACATACCGAATTTTGG 57.263 37.500 0.75 0.75 0.00 3.28
129 130 2.104792 TCACAACTCCCCTATGCTATGC 59.895 50.000 0.00 0.00 0.00 3.14
130 131 2.105477 CACAACTCCCCTATGCTATGCT 59.895 50.000 0.00 0.00 0.00 3.79
132 133 1.650528 ACTCCCCTATGCTATGCTCC 58.349 55.000 0.00 0.00 0.00 4.70
133 134 1.150986 ACTCCCCTATGCTATGCTCCT 59.849 52.381 0.00 0.00 0.00 3.69
135 136 3.030291 CTCCCCTATGCTATGCTCCTAG 58.970 54.545 0.00 0.00 0.00 3.02
236 238 4.508551 TCTATGTCCGTAGACCACCTAA 57.491 45.455 0.00 0.00 42.81 2.69
440 442 5.049749 TCCAATTTGTAGACACATGAACACG 60.050 40.000 0.00 0.00 33.76 4.49
497 499 1.740296 CAAACGCCGACCGAATCCT 60.740 57.895 0.00 0.00 41.02 3.24
508 510 0.747255 CCGAATCCTGTGAGATCCGT 59.253 55.000 0.00 0.00 0.00 4.69
595 598 4.949856 GGGAAGAACCTTATTCATCAGCAA 59.050 41.667 0.00 0.00 38.98 3.91
641 644 1.002544 CTGAGGAGGACACAAACCCTC 59.997 57.143 0.00 0.00 46.29 4.30
646 649 3.140325 GAGGACACAAACCCTCAATGA 57.860 47.619 0.00 0.00 46.28 2.57
647 650 3.486383 GAGGACACAAACCCTCAATGAA 58.514 45.455 0.00 0.00 46.28 2.57
648 651 3.222603 AGGACACAAACCCTCAATGAAC 58.777 45.455 0.00 0.00 0.00 3.18
649 652 2.955660 GGACACAAACCCTCAATGAACA 59.044 45.455 0.00 0.00 0.00 3.18
650 653 3.383185 GGACACAAACCCTCAATGAACAA 59.617 43.478 0.00 0.00 0.00 2.83
651 654 4.142049 GGACACAAACCCTCAATGAACAAA 60.142 41.667 0.00 0.00 0.00 2.83
652 655 4.754322 ACACAAACCCTCAATGAACAAAC 58.246 39.130 0.00 0.00 0.00 2.93
653 656 3.796178 CACAAACCCTCAATGAACAAACG 59.204 43.478 0.00 0.00 0.00 3.60
654 657 3.697045 ACAAACCCTCAATGAACAAACGA 59.303 39.130 0.00 0.00 0.00 3.85
655 658 3.982576 AACCCTCAATGAACAAACGAC 57.017 42.857 0.00 0.00 0.00 4.34
656 659 2.227194 ACCCTCAATGAACAAACGACC 58.773 47.619 0.00 0.00 0.00 4.79
657 660 1.539827 CCCTCAATGAACAAACGACCC 59.460 52.381 0.00 0.00 0.00 4.46
658 661 2.504367 CCTCAATGAACAAACGACCCT 58.496 47.619 0.00 0.00 0.00 4.34
659 662 2.884639 CCTCAATGAACAAACGACCCTT 59.115 45.455 0.00 0.00 0.00 3.95
660 663 3.317993 CCTCAATGAACAAACGACCCTTT 59.682 43.478 0.00 0.00 0.00 3.11
661 664 4.290155 CTCAATGAACAAACGACCCTTTG 58.710 43.478 0.00 0.00 37.20 2.77
662 665 3.067461 TCAATGAACAAACGACCCTTTGG 59.933 43.478 0.00 0.00 35.73 3.28
673 676 3.354678 CCTTTGGGAACTGGTGCG 58.645 61.111 0.00 0.00 33.58 5.34
674 677 2.268076 CCTTTGGGAACTGGTGCGG 61.268 63.158 0.00 0.00 33.58 5.69
675 678 2.203422 TTTGGGAACTGGTGCGGG 60.203 61.111 0.00 0.00 0.00 6.13
676 679 2.976494 CTTTGGGAACTGGTGCGGGT 62.976 60.000 0.00 0.00 0.00 5.28
677 680 2.575455 TTTGGGAACTGGTGCGGGTT 62.575 55.000 0.00 0.00 0.00 4.11
678 681 2.203437 GGGAACTGGTGCGGGTTT 60.203 61.111 0.00 0.00 0.00 3.27
679 682 1.830847 GGGAACTGGTGCGGGTTTT 60.831 57.895 0.00 0.00 0.00 2.43
680 683 1.658114 GGAACTGGTGCGGGTTTTC 59.342 57.895 0.00 0.00 0.00 2.29
681 684 1.658114 GAACTGGTGCGGGTTTTCC 59.342 57.895 0.00 0.00 39.75 3.13
682 685 0.822121 GAACTGGTGCGGGTTTTCCT 60.822 55.000 0.00 0.00 40.46 3.36
689 692 2.255252 CGGGTTTTCCTGCTTGCG 59.745 61.111 0.00 0.00 39.73 4.85
690 693 2.551912 CGGGTTTTCCTGCTTGCGT 61.552 57.895 0.00 0.00 39.73 5.24
691 694 1.739667 GGGTTTTCCTGCTTGCGTT 59.260 52.632 0.00 0.00 40.46 4.84
692 695 0.597377 GGGTTTTCCTGCTTGCGTTG 60.597 55.000 0.00 0.00 40.46 4.10
693 696 1.215014 GGTTTTCCTGCTTGCGTTGC 61.215 55.000 0.00 0.00 36.94 4.17
694 697 0.527385 GTTTTCCTGCTTGCGTTGCA 60.527 50.000 0.00 0.00 38.81 4.08
701 704 3.667282 CTTGCGTTGCAGGCAGCT 61.667 61.111 13.26 0.00 45.94 4.24
702 705 3.606065 CTTGCGTTGCAGGCAGCTC 62.606 63.158 13.26 0.00 45.94 4.09
703 706 4.933563 TGCGTTGCAGGCAGCTCA 62.934 61.111 10.11 1.68 45.94 4.26
704 707 4.395583 GCGTTGCAGGCAGCTCAC 62.396 66.667 2.86 0.00 45.94 3.51
705 708 2.974148 CGTTGCAGGCAGCTCACA 60.974 61.111 2.86 0.00 45.94 3.58
706 709 2.330372 CGTTGCAGGCAGCTCACAT 61.330 57.895 2.86 0.00 45.94 3.21
707 710 1.211969 GTTGCAGGCAGCTCACATG 59.788 57.895 2.86 0.00 45.94 3.21
708 711 1.228337 TTGCAGGCAGCTCACATGT 60.228 52.632 2.86 0.00 45.94 3.21
709 712 0.824595 TTGCAGGCAGCTCACATGTT 60.825 50.000 2.86 0.00 45.94 2.71
710 713 1.239296 TGCAGGCAGCTCACATGTTC 61.239 55.000 2.86 0.00 45.94 3.18
711 714 1.930908 GCAGGCAGCTCACATGTTCC 61.931 60.000 0.00 0.00 41.15 3.62
712 715 1.001641 AGGCAGCTCACATGTTCCC 60.002 57.895 0.00 0.00 0.00 3.97
713 716 2.401766 GGCAGCTCACATGTTCCCG 61.402 63.158 0.00 0.00 0.00 5.14
717 720 1.745489 GCTCACATGTTCCCGTCCC 60.745 63.158 0.00 0.00 0.00 4.46
724 727 3.128589 CACATGTTCCCGTCCCAAAATAG 59.871 47.826 0.00 0.00 0.00 1.73
730 733 1.816224 CCCGTCCCAAAATAGGTGTTG 59.184 52.381 0.00 0.00 0.00 3.33
731 734 1.201414 CCGTCCCAAAATAGGTGTTGC 59.799 52.381 0.00 0.00 0.00 4.17
733 736 2.294791 CGTCCCAAAATAGGTGTTGCAA 59.705 45.455 0.00 0.00 0.00 4.08
742 745 8.921670 CCAAAATAGGTGTTGCAATTTTAGTAC 58.078 33.333 0.59 0.00 31.97 2.73
749 752 7.491048 AGGTGTTGCAATTTTAGTACAACTTTG 59.509 33.333 0.59 0.00 40.88 2.77
750 753 7.254286 GGTGTTGCAATTTTAGTACAACTTTGG 60.254 37.037 0.59 0.00 40.88 3.28
752 755 7.489757 TGTTGCAATTTTAGTACAACTTTGGAC 59.510 33.333 0.59 0.00 42.46 4.02
854 963 0.391661 ATACCAGCCGTGCAAGACTG 60.392 55.000 8.92 8.92 0.00 3.51
918 1027 2.482664 CGTGGCACTCTCAGCTGATATT 60.483 50.000 18.63 0.82 0.00 1.28
958 1067 3.724914 GAGTCCCCGCTGCTACTGC 62.725 68.421 0.00 0.00 40.20 4.40
992 1101 4.778143 GGGTGCGCGGGATTGAGT 62.778 66.667 8.83 0.00 0.00 3.41
1006 1115 3.516615 GATTGAGTCGCCTATATGAGCC 58.483 50.000 0.00 0.00 0.00 4.70
1019 1128 2.894387 GAGCCGCCTCATCAGCAC 60.894 66.667 0.00 0.00 38.03 4.40
1089 1198 4.536687 GGCGGCACACATAAGCGC 62.537 66.667 3.07 0.00 0.00 5.92
1166 1275 2.391389 GCTGTAGCGGCACCAAGAC 61.391 63.158 1.45 0.00 35.55 3.01
1302 1411 1.666189 GACAAGATCCAGCTTTACCGC 59.334 52.381 0.00 0.00 0.00 5.68
1761 1882 2.499205 CGCAAGGCCATCGGAGTA 59.501 61.111 5.01 0.00 0.00 2.59
2044 2165 0.036577 CAGCCAAGGACTGTCCAGAG 60.037 60.000 27.48 15.92 39.61 3.35
2058 2179 3.786586 AGAGACGACGACGCCGAC 61.787 66.667 11.37 3.89 43.96 4.79
2339 2460 7.707774 TTTTCGGGTTCAAAATTTTCTGATC 57.292 32.000 0.00 0.00 0.00 2.92
2486 2609 1.134250 GGGGCTGTGAATTCTCTCTCC 60.134 57.143 7.05 5.42 0.00 3.71
2523 2648 1.608590 CTGGATCGAGAGGCTCTTCTC 59.391 57.143 19.80 14.64 40.16 2.87
2524 2649 0.958822 GGATCGAGAGGCTCTTCTCC 59.041 60.000 19.80 19.29 40.39 3.71
2525 2650 1.478654 GGATCGAGAGGCTCTTCTCCT 60.479 57.143 19.80 2.14 40.39 3.69
2526 2651 2.306847 GATCGAGAGGCTCTTCTCCTT 58.693 52.381 19.80 0.85 40.39 3.36
2527 2652 1.757682 TCGAGAGGCTCTTCTCCTTC 58.242 55.000 19.80 2.91 40.39 3.46
2528 2653 0.744281 CGAGAGGCTCTTCTCCTTCC 59.256 60.000 19.80 1.82 40.39 3.46
2537 2662 3.428862 GCTCTTCTCCTTCCTCTTCTTCG 60.429 52.174 0.00 0.00 0.00 3.79
2559 2684 3.977134 TCTTCAGAATCTGCTCTGCTT 57.023 42.857 5.18 0.00 42.25 3.91
2589 2714 0.179468 ACCACACCACACCACTGTAC 59.821 55.000 0.00 0.00 0.00 2.90
2615 2740 0.898320 ACAGTGCAATCTAGTCCGCT 59.102 50.000 0.00 0.00 0.00 5.52
2673 2798 3.120060 GCTGCCTATCTTGAACAGTGTTG 60.120 47.826 14.57 0.00 0.00 3.33
2674 2799 4.067896 CTGCCTATCTTGAACAGTGTTGT 58.932 43.478 14.57 0.00 39.87 3.32
2686 2811 0.178068 AGTGTTGTTGAGGAGCGTGT 59.822 50.000 0.00 0.00 0.00 4.49
2703 2828 0.539051 TGTGGTTTTTGTTGGGGCTG 59.461 50.000 0.00 0.00 0.00 4.85
2741 2866 2.363683 CCTCCTTTTCCTCTGCATCAC 58.636 52.381 0.00 0.00 0.00 3.06
2756 2881 2.481969 GCATCACAGATTGGCGTCTCTA 60.482 50.000 0.00 0.00 0.00 2.43
2757 2882 3.379240 CATCACAGATTGGCGTCTCTAG 58.621 50.000 0.00 0.00 0.00 2.43
2770 2895 3.340034 CGTCTCTAGAGTCTGGACAAGT 58.660 50.000 19.21 0.00 0.00 3.16
2813 2938 2.106477 TCTTGCATGTTATGTGCCGA 57.894 45.000 0.00 0.00 41.83 5.54
2826 2951 2.720915 TGTGCCGATTGATCATTTGGA 58.279 42.857 22.83 9.08 0.00 3.53
2870 2997 4.215399 ACCATGTTATGTTGGTCGTTTCTG 59.785 41.667 0.00 0.00 42.61 3.02
2883 3011 4.379499 GGTCGTTTCTGGTTGATTCATTCC 60.379 45.833 0.00 0.00 0.00 3.01
2891 3019 6.546484 TCTGGTTGATTCATTCCTCTTCTTT 58.454 36.000 8.97 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.055675 TCATCGGACTACCAAAATTCGGT 60.056 43.478 4.99 4.99 40.73 4.69
83 84 7.093354 AGCAAGGATATAGTTCATACATGACG 58.907 38.462 0.00 0.00 36.36 4.35
168 169 8.185506 TCTTTGTACTACCTTGACAGTTGATA 57.814 34.615 0.00 0.00 0.00 2.15
211 213 3.243434 GGTGGTCTACGGACATAGATGTG 60.243 52.174 0.00 0.00 43.77 3.21
219 221 1.167851 CGTTAGGTGGTCTACGGACA 58.832 55.000 0.00 0.00 43.77 4.02
236 238 0.039437 CCAGTGCAAGTAGTCGTCGT 60.039 55.000 0.00 0.00 0.00 4.34
283 285 1.907739 CTTCGATGAGGAAGGGGCA 59.092 57.895 0.00 0.00 39.76 5.36
319 321 1.130749 CGACTTCCCGACTGTCTACTG 59.869 57.143 6.21 0.00 0.00 2.74
422 424 3.386486 GTCCGTGTTCATGTGTCTACAA 58.614 45.455 0.00 0.00 40.84 2.41
440 442 2.260481 GGATCTTGTCTTCGTTCGTCC 58.740 52.381 0.00 0.00 0.00 4.79
497 499 0.322187 TGTCTCCGACGGATCTCACA 60.322 55.000 18.71 14.47 34.95 3.58
607 610 2.826287 TCAGAGAGGCGAGGCGAG 60.826 66.667 0.00 0.00 0.00 5.03
608 611 2.826287 CTCAGAGAGGCGAGGCGA 60.826 66.667 0.00 0.00 0.00 5.54
641 644 3.380142 CCAAAGGGTCGTTTGTTCATTG 58.620 45.455 12.96 0.00 35.93 2.82
642 645 2.364002 CCCAAAGGGTCGTTTGTTCATT 59.636 45.455 12.96 0.00 38.25 2.57
644 647 1.064611 TCCCAAAGGGTCGTTTGTTCA 60.065 47.619 12.96 0.00 44.74 3.18
645 648 1.682740 TCCCAAAGGGTCGTTTGTTC 58.317 50.000 12.96 0.00 44.74 3.18
646 649 1.752498 GTTCCCAAAGGGTCGTTTGTT 59.248 47.619 12.96 0.00 44.74 2.83
647 650 1.064240 AGTTCCCAAAGGGTCGTTTGT 60.064 47.619 12.96 0.00 44.74 2.83
648 651 1.336755 CAGTTCCCAAAGGGTCGTTTG 59.663 52.381 1.36 8.61 44.74 2.93
649 652 1.687563 CAGTTCCCAAAGGGTCGTTT 58.312 50.000 1.36 0.00 44.74 3.60
650 653 0.179001 CCAGTTCCCAAAGGGTCGTT 60.179 55.000 1.36 0.00 44.74 3.85
651 654 1.350310 ACCAGTTCCCAAAGGGTCGT 61.350 55.000 1.36 0.00 44.74 4.34
652 655 0.889186 CACCAGTTCCCAAAGGGTCG 60.889 60.000 1.36 0.00 44.74 4.79
653 656 1.179174 GCACCAGTTCCCAAAGGGTC 61.179 60.000 1.36 0.00 44.74 4.46
654 657 1.152546 GCACCAGTTCCCAAAGGGT 60.153 57.895 1.36 0.00 44.74 4.34
655 658 2.268076 CGCACCAGTTCCCAAAGGG 61.268 63.158 0.00 0.00 46.11 3.95
656 659 2.268076 CCGCACCAGTTCCCAAAGG 61.268 63.158 0.00 0.00 0.00 3.11
657 660 2.268076 CCCGCACCAGTTCCCAAAG 61.268 63.158 0.00 0.00 0.00 2.77
658 661 2.203422 CCCGCACCAGTTCCCAAA 60.203 61.111 0.00 0.00 0.00 3.28
659 662 2.575455 AAACCCGCACCAGTTCCCAA 62.575 55.000 0.00 0.00 0.00 4.12
660 663 2.575455 AAAACCCGCACCAGTTCCCA 62.575 55.000 0.00 0.00 0.00 4.37
661 664 1.802337 GAAAACCCGCACCAGTTCCC 61.802 60.000 0.00 0.00 0.00 3.97
662 665 1.658114 GAAAACCCGCACCAGTTCC 59.342 57.895 0.00 0.00 0.00 3.62
663 666 0.822121 AGGAAAACCCGCACCAGTTC 60.822 55.000 0.00 0.00 40.87 3.01
664 667 1.106944 CAGGAAAACCCGCACCAGTT 61.107 55.000 0.00 0.00 40.87 3.16
665 668 1.528309 CAGGAAAACCCGCACCAGT 60.528 57.895 0.00 0.00 40.87 4.00
666 669 2.919494 GCAGGAAAACCCGCACCAG 61.919 63.158 0.00 0.00 40.87 4.00
667 670 2.909965 GCAGGAAAACCCGCACCA 60.910 61.111 0.00 0.00 40.87 4.17
668 671 2.200337 AAGCAGGAAAACCCGCACC 61.200 57.895 0.00 0.00 40.87 5.01
669 672 1.007387 CAAGCAGGAAAACCCGCAC 60.007 57.895 0.00 0.00 40.87 5.34
670 673 2.855514 GCAAGCAGGAAAACCCGCA 61.856 57.895 0.00 0.00 40.87 5.69
671 674 2.049156 GCAAGCAGGAAAACCCGC 60.049 61.111 0.00 0.00 40.87 6.13
672 675 2.070654 AACGCAAGCAGGAAAACCCG 62.071 55.000 0.00 0.00 45.62 5.28
673 676 0.597377 CAACGCAAGCAGGAAAACCC 60.597 55.000 0.00 0.00 45.62 4.11
674 677 1.215014 GCAACGCAAGCAGGAAAACC 61.215 55.000 0.00 0.00 45.62 3.27
675 678 0.527385 TGCAACGCAAGCAGGAAAAC 60.527 50.000 0.00 0.00 45.62 2.43
676 679 1.812525 TGCAACGCAAGCAGGAAAA 59.187 47.368 0.00 0.00 45.62 2.29
677 680 3.519202 TGCAACGCAAGCAGGAAA 58.481 50.000 0.00 0.00 45.62 3.13
684 687 3.606065 GAGCTGCCTGCAACGCAAG 62.606 63.158 9.24 5.42 45.94 4.01
685 688 3.663176 GAGCTGCCTGCAACGCAA 61.663 61.111 9.24 0.00 45.94 4.85
686 689 4.933563 TGAGCTGCCTGCAACGCA 62.934 61.111 7.81 7.81 45.94 5.24
687 690 4.395583 GTGAGCTGCCTGCAACGC 62.396 66.667 0.00 0.00 45.94 4.84
688 691 2.330372 ATGTGAGCTGCCTGCAACG 61.330 57.895 0.00 0.00 45.94 4.10
689 692 1.211969 CATGTGAGCTGCCTGCAAC 59.788 57.895 0.00 0.00 45.94 4.17
690 693 0.824595 AACATGTGAGCTGCCTGCAA 60.825 50.000 0.00 0.00 45.94 4.08
691 694 1.228337 AACATGTGAGCTGCCTGCA 60.228 52.632 0.00 0.00 45.94 4.41
692 695 1.505353 GAACATGTGAGCTGCCTGC 59.495 57.895 0.00 0.00 43.29 4.85
693 696 1.310933 GGGAACATGTGAGCTGCCTG 61.311 60.000 0.00 0.00 0.00 4.85
694 697 1.001641 GGGAACATGTGAGCTGCCT 60.002 57.895 0.00 0.00 0.00 4.75
695 698 2.401766 CGGGAACATGTGAGCTGCC 61.402 63.158 0.00 0.00 0.00 4.85
696 699 1.639298 GACGGGAACATGTGAGCTGC 61.639 60.000 0.00 0.00 0.00 5.25
697 700 1.021390 GGACGGGAACATGTGAGCTG 61.021 60.000 0.00 0.00 0.00 4.24
698 701 1.296715 GGACGGGAACATGTGAGCT 59.703 57.895 0.00 0.00 0.00 4.09
699 702 1.745489 GGGACGGGAACATGTGAGC 60.745 63.158 0.00 0.00 0.00 4.26
700 703 0.036164 TTGGGACGGGAACATGTGAG 59.964 55.000 0.00 0.00 0.00 3.51
701 704 0.474614 TTTGGGACGGGAACATGTGA 59.525 50.000 0.00 0.00 0.00 3.58
702 705 1.323412 TTTTGGGACGGGAACATGTG 58.677 50.000 0.00 0.00 0.00 3.21
703 706 2.302587 ATTTTGGGACGGGAACATGT 57.697 45.000 0.00 0.00 0.00 3.21
704 707 2.687935 CCTATTTTGGGACGGGAACATG 59.312 50.000 0.00 0.00 0.00 3.21
705 708 2.310647 ACCTATTTTGGGACGGGAACAT 59.689 45.455 0.00 0.00 0.00 2.71
706 709 1.706305 ACCTATTTTGGGACGGGAACA 59.294 47.619 0.00 0.00 0.00 3.18
707 710 2.089201 CACCTATTTTGGGACGGGAAC 58.911 52.381 0.00 0.00 0.00 3.62
708 711 1.706305 ACACCTATTTTGGGACGGGAA 59.294 47.619 0.00 0.00 0.00 3.97
709 712 1.364269 ACACCTATTTTGGGACGGGA 58.636 50.000 0.00 0.00 0.00 5.14
710 713 1.816224 CAACACCTATTTTGGGACGGG 59.184 52.381 0.00 0.00 0.00 5.28
711 714 1.201414 GCAACACCTATTTTGGGACGG 59.799 52.381 0.00 0.00 0.00 4.79
712 715 1.883275 TGCAACACCTATTTTGGGACG 59.117 47.619 0.00 0.00 0.00 4.79
713 716 4.535526 ATTGCAACACCTATTTTGGGAC 57.464 40.909 0.00 0.00 0.00 4.46
717 720 9.469807 TGTACTAAAATTGCAACACCTATTTTG 57.530 29.630 0.00 2.19 34.02 2.44
724 727 7.254286 CCAAAGTTGTACTAAAATTGCAACACC 60.254 37.037 0.00 0.00 41.07 4.16
730 733 9.177304 GTTAGTCCAAAGTTGTACTAAAATTGC 57.823 33.333 9.87 0.00 39.98 3.56
796 904 2.555325 ACAGTGTCATTGCCAGTTCATG 59.445 45.455 0.00 0.00 0.00 3.07
822 931 2.618709 GGCTGGTATCTGTATTTGTGCC 59.381 50.000 0.00 0.00 0.00 5.01
958 1067 2.258591 CCACCAGTCACCTCGTCG 59.741 66.667 0.00 0.00 0.00 5.12
960 1069 2.923035 CCCCACCAGTCACCTCGT 60.923 66.667 0.00 0.00 0.00 4.18
1006 1115 2.298629 CGATCGTGCTGATGAGGCG 61.299 63.158 7.03 0.00 37.47 5.52
1070 1179 4.536687 GCTTATGTGTGCCGCCGC 62.537 66.667 0.00 0.00 0.00 6.53
1108 1217 1.734465 GACTCTTGTCCTTTCCATGCG 59.266 52.381 0.00 0.00 37.24 4.73
1166 1275 4.760047 CCCCACGTTCTGCCTCCG 62.760 72.222 0.00 0.00 0.00 4.63
1262 1371 2.047274 CGTTCACCACCTCGCCAT 60.047 61.111 0.00 0.00 0.00 4.40
1659 1777 1.533219 CATGCCCTCACCCAGCATA 59.467 57.895 0.00 0.00 45.16 3.14
2044 2165 4.724697 TTCGTCGGCGTCGTCGTC 62.725 66.667 26.20 12.95 45.17 4.20
2058 2179 1.397692 GTCACTACTCCGTCCTCTTCG 59.602 57.143 0.00 0.00 0.00 3.79
2076 2197 0.729116 CATGGCATTGTCTCCGTGTC 59.271 55.000 0.00 0.00 35.25 3.67
2339 2460 3.876198 CTCCAAAATCGGCGGCGG 61.876 66.667 31.73 14.57 0.00 6.13
2416 2538 2.050714 TCCGTGTTCTGTCGTCGC 60.051 61.111 0.00 0.00 0.00 5.19
2423 2545 2.509052 TGTCTTGTCTCCGTGTTCTG 57.491 50.000 0.00 0.00 0.00 3.02
2490 2613 2.687909 GATCCAGGGAGGGAGGGAGG 62.688 70.000 0.00 0.00 41.08 4.30
2501 2626 0.758685 AAGAGCCTCTCGATCCAGGG 60.759 60.000 0.00 0.00 35.36 4.45
2523 2648 4.021894 TCTGAAGAACGAAGAAGAGGAAGG 60.022 45.833 0.00 0.00 0.00 3.46
2524 2649 5.127693 TCTGAAGAACGAAGAAGAGGAAG 57.872 43.478 0.00 0.00 0.00 3.46
2525 2650 5.531122 TTCTGAAGAACGAAGAAGAGGAA 57.469 39.130 0.00 0.00 0.00 3.36
2526 2651 5.478679 AGATTCTGAAGAACGAAGAAGAGGA 59.521 40.000 0.00 0.00 36.80 3.71
2527 2652 5.576384 CAGATTCTGAAGAACGAAGAAGAGG 59.424 44.000 8.00 0.00 36.80 3.69
2528 2653 5.062058 GCAGATTCTGAAGAACGAAGAAGAG 59.938 44.000 17.87 0.00 36.80 2.85
2537 2662 3.598299 AGCAGAGCAGATTCTGAAGAAC 58.402 45.455 17.87 3.45 45.95 3.01
2559 2684 0.896479 TGGTGTGGTGTCGCTAGCTA 60.896 55.000 13.93 0.00 0.00 3.32
2567 2692 1.095228 CAGTGGTGTGGTGTGGTGTC 61.095 60.000 0.00 0.00 0.00 3.67
2589 2714 5.687730 CGGACTAGATTGCACTGTAGTATTG 59.312 44.000 12.97 3.94 0.00 1.90
2602 2727 6.662414 TTTTGAACATAGCGGACTAGATTG 57.338 37.500 0.00 0.00 0.00 2.67
2656 2781 5.991606 TCCTCAACAACACTGTTCAAGATAG 59.008 40.000 0.00 0.00 44.15 2.08
2657 2782 5.924356 TCCTCAACAACACTGTTCAAGATA 58.076 37.500 0.00 0.00 44.15 1.98
2673 2798 1.021968 AAAACCACACGCTCCTCAAC 58.978 50.000 0.00 0.00 0.00 3.18
2674 2799 1.403679 CAAAAACCACACGCTCCTCAA 59.596 47.619 0.00 0.00 0.00 3.02
2675 2800 1.021202 CAAAAACCACACGCTCCTCA 58.979 50.000 0.00 0.00 0.00 3.86
2681 2806 0.808060 CCCCAACAAAAACCACACGC 60.808 55.000 0.00 0.00 0.00 5.34
2686 2811 1.977293 GCCAGCCCCAACAAAAACCA 61.977 55.000 0.00 0.00 0.00 3.67
2703 2828 1.004560 GGCCAGCAAAGGAAAAGCC 60.005 57.895 0.00 0.00 0.00 4.35
2741 2866 2.948979 AGACTCTAGAGACGCCAATCTG 59.051 50.000 26.57 0.00 0.00 2.90
2756 2881 3.155897 AGGCACTTGTCCAGACTCT 57.844 52.632 0.00 0.00 27.25 3.24
2793 2918 2.642427 TCGGCACATAACATGCAAGAT 58.358 42.857 0.00 0.00 45.27 2.40
2807 2932 2.542411 GCTCCAAATGATCAATCGGCAC 60.542 50.000 0.00 0.00 0.00 5.01
2813 2938 6.555463 AAAATCTGGCTCCAAATGATCAAT 57.445 33.333 0.00 0.00 0.00 2.57
2826 2951 4.324331 GGTAGGGTGAAGTAAAATCTGGCT 60.324 45.833 0.00 0.00 0.00 4.75
2932 3175 5.951747 CCCTCAGGAATATTTTCAAACCAGA 59.048 40.000 0.00 0.00 33.23 3.86


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

AutoCloner maintained by Alex Coulton.