Multiple sequence alignment - TraesCS1A01G322400

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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 TraesCS1A01G322400 chr1A 100.000 3584 0 0 1 3584 512883787 512887370 0.000000e+00 6619.0
1 TraesCS1A01G322400 chr1B 93.395 3013 140 36 608 3584 561711379 561714368 0.000000e+00 4407.0
2 TraesCS1A01G322400 chr1B 85.012 427 24 12 1 416 561710854 561711251 7.210000e-107 398.0
3 TraesCS1A01G322400 chr1D 91.498 2223 114 40 515 2687 415421740 415423937 0.000000e+00 2988.0
4 TraesCS1A01G322400 chr1D 90.019 521 35 8 1 519 415421199 415421704 0.000000e+00 658.0
5 TraesCS1A01G322400 chr2B 86.567 67 7 2 3348 3414 753825753 753825817 4.960000e-09 73.1
6 TraesCS1A01G322400 chr2B 86.567 67 5 4 3348 3414 753768600 753768538 1.790000e-08 71.3
7 TraesCS1A01G322400 chr3D 86.364 66 8 1 3341 3406 495247919 495247855 1.790000e-08 71.3
8 TraesCS1A01G322400 chr3B 92.683 41 1 2 3343 3383 110231724 110231762 1.390000e-04 58.4


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 TraesCS1A01G322400 chr1A 512883787 512887370 3583 False 6619.0 6619 100.0000 1 3584 1 chr1A.!!$F1 3583
1 TraesCS1A01G322400 chr1B 561710854 561714368 3514 False 2402.5 4407 89.2035 1 3584 2 chr1B.!!$F1 3583
2 TraesCS1A01G322400 chr1D 415421199 415423937 2738 False 1823.0 2988 90.7585 1 2687 2 chr1D.!!$F1 2686

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
770 844 0.179078 GAGCAGATGAGGAGGCACAG 60.179 60.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2667 2777 0.036022 AGGAAAGAGCTCAGCACCAC 59.964 55.0 17.77 0.0 0.0 4.16 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
27 28 2.945440 GCCAATGCTGGGTATCTTGACA 60.945 50.000 0.00 0.00 43.74 3.58
78 79 3.005897 CGTACTCATCCACCATAGAAGGG 59.994 52.174 0.00 0.00 0.00 3.95
117 118 2.541547 CTTGCGAGGGATGGGCAGAA 62.542 60.000 0.00 0.00 38.04 3.02
142 143 1.701704 GGCTTTTGAACGCCAAGATG 58.298 50.000 6.39 0.00 45.59 2.90
143 144 1.000274 GGCTTTTGAACGCCAAGATGT 60.000 47.619 6.39 0.00 45.59 3.06
163 168 2.989840 GTCTTGCTGTAGCTGTGTAGTG 59.010 50.000 5.38 0.00 42.66 2.74
168 173 2.413453 GCTGTAGCTGTGTAGTGAAAGC 59.587 50.000 0.00 0.00 38.21 3.51
180 188 5.407387 GTGTAGTGAAAGCGATTAAACCAGA 59.593 40.000 0.00 0.00 0.00 3.86
213 221 1.873591 CAGAACCCAAAGTGAACCGAG 59.126 52.381 0.00 0.00 0.00 4.63
225 233 5.579564 AGTGAACCGAGTAGGAATAAGAC 57.420 43.478 0.00 0.00 45.00 3.01
226 234 4.096081 AGTGAACCGAGTAGGAATAAGACG 59.904 45.833 0.00 0.00 45.00 4.18
227 235 4.095483 GTGAACCGAGTAGGAATAAGACGA 59.905 45.833 0.00 0.00 45.00 4.20
268 276 3.258372 TGAGTGGGTCACTATCAGTCAAC 59.742 47.826 0.11 0.00 45.44 3.18
298 307 7.721286 AAATTAGCATCTCTACTACATGCAC 57.279 36.000 5.95 0.00 44.57 4.57
303 312 4.505922 GCATCTCTACTACATGCACAGTTC 59.494 45.833 3.06 0.00 42.18 3.01
306 315 5.654497 TCTCTACTACATGCACAGTTCATG 58.346 41.667 11.24 11.24 44.99 3.07
400 413 3.599343 GGCCAAAAGGATTCATTGGTTC 58.401 45.455 0.00 1.27 44.35 3.62
404 417 4.527816 CCAAAAGGATTCATTGGTTCAGGA 59.472 41.667 1.29 0.00 38.99 3.86
420 433 2.912956 TCAGGACCCTATTGCTTCTGTT 59.087 45.455 0.00 0.00 0.00 3.16
421 434 3.055094 TCAGGACCCTATTGCTTCTGTTC 60.055 47.826 0.00 0.00 0.00 3.18
424 437 4.783227 AGGACCCTATTGCTTCTGTTCTAA 59.217 41.667 0.00 0.00 0.00 2.10
495 509 7.750903 GGCAAAGATCTACACAAGAATTAACAC 59.249 37.037 0.00 0.00 37.89 3.32
532 586 1.367840 GACTGCGGTGCCCCTATAG 59.632 63.158 0.80 0.00 0.00 1.31
553 607 9.429359 CTATAGTTTGACAGAATCATGGGTATC 57.571 37.037 0.00 0.00 37.11 2.24
555 609 6.118170 AGTTTGACAGAATCATGGGTATCAG 58.882 40.000 0.00 0.00 37.11 2.90
556 610 4.077300 TGACAGAATCATGGGTATCAGC 57.923 45.455 0.00 0.00 29.99 4.26
572 626 6.258947 GGGTATCAGCAGAAACAAGAACTATC 59.741 42.308 0.00 0.00 0.00 2.08
574 628 8.198109 GGTATCAGCAGAAACAAGAACTATCTA 58.802 37.037 0.00 0.00 33.77 1.98
591 653 9.781834 GAACTATCTATATGTACATCAGACTGC 57.218 37.037 12.68 2.74 0.00 4.40
630 692 2.417933 CCAAGAACGCATCCTTCTGAAG 59.582 50.000 10.46 10.46 0.00 3.02
653 720 2.095364 GCATCCAAGACAGCACAAGAAG 60.095 50.000 0.00 0.00 0.00 2.85
659 730 4.260948 CCAAGACAGCACAAGAAGAAGAAC 60.261 45.833 0.00 0.00 0.00 3.01
692 763 3.330720 CACCTCACCCTGACCCCC 61.331 72.222 0.00 0.00 0.00 5.40
711 782 2.420687 CCCCTCCCGAAAGAAGATTCTG 60.421 54.545 0.00 0.00 37.65 3.02
732 806 4.683334 GTCACCTGCGCCGCAAAC 62.683 66.667 14.77 5.52 38.41 2.93
763 837 1.812525 GAGCACGAGCAGATGAGGA 59.187 57.895 7.77 0.00 45.49 3.71
764 838 0.248990 GAGCACGAGCAGATGAGGAG 60.249 60.000 7.77 0.00 45.49 3.69
765 839 1.227205 GCACGAGCAGATGAGGAGG 60.227 63.158 0.00 0.00 41.58 4.30
766 840 1.227205 CACGAGCAGATGAGGAGGC 60.227 63.158 0.00 0.00 0.00 4.70
767 841 1.683707 ACGAGCAGATGAGGAGGCA 60.684 57.895 0.00 0.00 0.00 4.75
768 842 1.227205 CGAGCAGATGAGGAGGCAC 60.227 63.158 0.00 0.00 0.00 5.01
769 843 1.903294 GAGCAGATGAGGAGGCACA 59.097 57.895 0.00 0.00 0.00 4.57
770 844 0.179078 GAGCAGATGAGGAGGCACAG 60.179 60.000 0.00 0.00 0.00 3.66
771 845 1.818785 GCAGATGAGGAGGCACAGC 60.819 63.158 0.00 0.00 0.00 4.40
790 864 1.300697 GGAATAGATTCGCGGCGGT 60.301 57.895 23.46 11.79 37.67 5.68
891 992 4.612259 GCATATCGTCTGGCTGCTATTTTG 60.612 45.833 0.00 0.00 0.00 2.44
896 1000 4.941263 TCGTCTGGCTGCTATTTTGTTTAT 59.059 37.500 0.00 0.00 0.00 1.40
902 1006 5.359576 TGGCTGCTATTTTGTTTATCCGATT 59.640 36.000 0.00 0.00 0.00 3.34
911 1015 2.158928 TGTTTATCCGATTACACCCCGG 60.159 50.000 0.00 0.00 44.22 5.73
950 1054 0.183014 TTTGCCCCCTCAACGTGTTA 59.817 50.000 0.00 0.00 0.00 2.41
954 1058 1.368579 CCCCTCAACGTGTTACGGT 59.631 57.895 6.31 0.00 45.77 4.83
955 1059 0.602562 CCCCTCAACGTGTTACGGTA 59.397 55.000 6.31 0.00 41.04 4.02
959 1063 3.383761 CCTCAACGTGTTACGGTAAGTT 58.616 45.455 0.00 0.00 41.04 2.66
960 1064 4.545610 CCTCAACGTGTTACGGTAAGTTA 58.454 43.478 0.00 0.00 41.04 2.24
961 1065 4.382754 CCTCAACGTGTTACGGTAAGTTAC 59.617 45.833 4.32 4.32 41.04 2.50
962 1066 3.971871 TCAACGTGTTACGGTAAGTTACG 59.028 43.478 20.89 20.89 41.04 3.18
963 1067 3.119463 CAACGTGTTACGGTAAGTTACGG 59.881 47.826 23.77 16.59 41.04 4.02
1226 1333 0.035915 TTCGATGAAATGCCCGACCA 60.036 50.000 0.00 0.00 0.00 4.02
1449 1556 1.215647 GCCGGACATGTTCGTCTCT 59.784 57.895 24.43 0.00 36.12 3.10
1461 1568 0.888619 TCGTCTCTACCCAGCTTGTG 59.111 55.000 0.00 0.00 0.00 3.33
1481 1588 4.790962 AGTCTACGGGGAGCGCGA 62.791 66.667 12.10 0.00 42.31 5.87
1546 1653 4.980805 GTGCCGTCGCCTGGAACA 62.981 66.667 0.00 0.00 34.89 3.18
1608 1715 1.079503 CGTACCAGCTCTTTCTTGCC 58.920 55.000 0.00 0.00 0.00 4.52
1767 1874 1.148273 GTCCACTGTCCTTGGTGCA 59.852 57.895 0.00 0.00 35.42 4.57
1770 1877 0.538057 CCACTGTCCTTGGTGCATGT 60.538 55.000 0.00 0.00 32.68 3.21
1772 1879 0.538057 ACTGTCCTTGGTGCATGTGG 60.538 55.000 0.00 0.00 0.00 4.17
1971 2078 4.141597 TGGACAACAGTGATTTGTGGACTA 60.142 41.667 4.00 0.00 37.31 2.59
2088 2195 2.358615 GCGTGTGCACATGGAGGA 60.359 61.111 33.97 3.84 42.15 3.71
2194 2301 3.411418 GATCTTCTCGGCCGCGTCA 62.411 63.158 23.51 1.03 0.00 4.35
2265 2372 0.773644 ACATGGTGATATGGGGAGCC 59.226 55.000 0.00 0.00 32.32 4.70
2382 2489 2.874701 GGTGATGATGTCCAGCATGTAC 59.125 50.000 2.28 2.47 43.71 2.90
2441 2548 0.962356 AGGGAAATGAACAGCCTGCG 60.962 55.000 0.00 0.00 0.00 5.18
2451 2558 0.036732 ACAGCCTGCGGATGAAGAAA 59.963 50.000 17.52 0.00 42.34 2.52
2505 2612 1.181098 AGGTGCATGAGTTTGTGGCC 61.181 55.000 0.00 0.00 0.00 5.36
2555 2662 3.668447 AGATTTGTACTGTGCTGGAGTG 58.332 45.455 0.00 0.00 0.00 3.51
2559 2666 1.484653 TGTACTGTGCTGGAGTGTGTT 59.515 47.619 0.00 0.00 0.00 3.32
2608 2715 1.174712 GCAAAGCTCTTGTGCTGGGA 61.175 55.000 9.40 0.00 43.24 4.37
2636 2746 1.351017 CAGGTGGAGCTAAGGGTGAAA 59.649 52.381 0.00 0.00 0.00 2.69
2642 2752 5.479027 GGTGGAGCTAAGGGTGAAAATTTAA 59.521 40.000 0.00 0.00 0.00 1.52
2646 2756 7.619302 TGGAGCTAAGGGTGAAAATTTAATGAT 59.381 33.333 0.00 0.00 0.00 2.45
2647 2757 8.478066 GGAGCTAAGGGTGAAAATTTAATGATT 58.522 33.333 0.00 0.00 0.00 2.57
2648 2758 9.875691 GAGCTAAGGGTGAAAATTTAATGATTT 57.124 29.630 0.00 0.00 0.00 2.17
2667 2777 7.572523 TGATTTATTGAGCCTTTCAGTATGG 57.427 36.000 0.00 0.00 37.07 2.74
2668 2778 7.118723 TGATTTATTGAGCCTTTCAGTATGGT 58.881 34.615 0.00 0.00 37.07 3.55
2670 2780 2.787473 TGAGCCTTTCAGTATGGTGG 57.213 50.000 0.00 0.00 36.16 4.61
2671 2781 1.985159 TGAGCCTTTCAGTATGGTGGT 59.015 47.619 0.00 0.00 36.16 4.16
2672 2782 2.290260 TGAGCCTTTCAGTATGGTGGTG 60.290 50.000 0.00 0.00 36.16 4.17
2673 2783 0.811281 GCCTTTCAGTATGGTGGTGC 59.189 55.000 0.00 0.00 36.16 5.01
2676 2793 2.290260 CCTTTCAGTATGGTGGTGCTGA 60.290 50.000 0.00 0.00 38.75 4.26
2681 2798 0.539051 GTATGGTGGTGCTGAGCTCT 59.461 55.000 16.19 0.00 0.00 4.09
2692 2809 2.158769 TGCTGAGCTCTTTCCTTTGTGA 60.159 45.455 16.19 0.00 0.00 3.58
2708 2825 0.826715 GTGAGCCAGCATACAGAGGA 59.173 55.000 0.00 0.00 0.00 3.71
2709 2826 1.117994 TGAGCCAGCATACAGAGGAG 58.882 55.000 0.00 0.00 0.00 3.69
2710 2827 0.392336 GAGCCAGCATACAGAGGAGG 59.608 60.000 0.00 0.00 0.00 4.30
2711 2828 1.053264 AGCCAGCATACAGAGGAGGG 61.053 60.000 0.00 0.00 0.00 4.30
2712 2829 1.449353 CCAGCATACAGAGGAGGGC 59.551 63.158 0.00 0.00 0.00 5.19
2713 2830 1.449353 CAGCATACAGAGGAGGGCC 59.551 63.158 0.00 0.00 0.00 5.80
2796 2913 3.498397 CACCGAGTAAATGTTGAAGCTGT 59.502 43.478 0.00 0.00 0.00 4.40
2800 2917 4.905866 CGAGTAAATGTTGAAGCTGTTGTG 59.094 41.667 0.00 0.00 0.00 3.33
2833 2950 4.216257 CACTTCAATTCAGAATCCCGTTGT 59.784 41.667 0.00 0.00 0.00 3.32
2839 2956 3.695830 TCAGAATCCCGTTGTTAAGCT 57.304 42.857 0.00 0.00 0.00 3.74
2841 2958 5.155278 TCAGAATCCCGTTGTTAAGCTAA 57.845 39.130 0.00 0.00 0.00 3.09
2842 2959 5.175859 TCAGAATCCCGTTGTTAAGCTAAG 58.824 41.667 0.00 0.00 0.00 2.18
2843 2960 5.046878 TCAGAATCCCGTTGTTAAGCTAAGA 60.047 40.000 0.00 0.00 0.00 2.10
2844 2961 5.642063 CAGAATCCCGTTGTTAAGCTAAGAA 59.358 40.000 0.00 0.00 0.00 2.52
2859 2976 2.125773 AAGAATGCCTGAGCTGGAAG 57.874 50.000 0.00 0.00 40.80 3.46
2903 3020 4.458989 TCCTACATTCTTGCACCAATGTTC 59.541 41.667 21.72 0.00 39.69 3.18
2938 3055 2.159014 GCCGTGGTATTGTCAGTGGATA 60.159 50.000 0.00 0.00 0.00 2.59
2941 3058 3.981416 CGTGGTATTGTCAGTGGATATCG 59.019 47.826 0.00 0.00 0.00 2.92
2960 3077 1.106285 GCCAACCAATCATCCCTGTC 58.894 55.000 0.00 0.00 0.00 3.51
3000 3117 0.379316 ACTGTATATCGCGACGCACA 59.621 50.000 21.35 14.43 0.00 4.57
3007 3124 2.542211 ATCGCGACGCACACTCATGA 62.542 55.000 21.35 6.45 0.00 3.07
3044 3161 4.292178 CGAGATGGAGAGGGCGCC 62.292 72.222 21.18 21.18 34.13 6.53
3051 3168 2.514824 GAGAGGGCGCCACAATCC 60.515 66.667 30.85 9.73 0.00 3.01
3052 3169 3.011517 AGAGGGCGCCACAATCCT 61.012 61.111 30.85 15.26 0.00 3.24
3144 3268 9.877178 GGATACTGACGAATTATATGGATTCTT 57.123 33.333 0.00 3.49 32.60 2.52
3152 3276 7.596248 ACGAATTATATGGATTCTTTGCATTGC 59.404 33.333 0.46 0.46 37.58 3.56
3154 3278 8.827177 AATTATATGGATTCTTTGCATTGCTG 57.173 30.769 10.49 0.68 37.58 4.41
3188 3312 8.281194 GCATATTGTCATCTATCAAACAGTCAG 58.719 37.037 0.00 0.00 0.00 3.51
3214 3338 0.036022 TGTCCAATCGTGATGTGGCA 59.964 50.000 0.00 0.00 32.10 4.92
3260 3384 4.148825 CGCCCCCTCCTCTGTTCG 62.149 72.222 0.00 0.00 0.00 3.95
3496 3625 9.562752 GACATTTAAAAAGAAATTGTACAACGC 57.437 29.630 11.22 3.30 0.00 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.385755 AGTCCAAGCTGTTGCAAGAATTT 59.614 39.130 0.00 0.00 42.74 1.82
78 79 1.685148 GATTGCCTTCAGGGATGGAC 58.315 55.000 2.63 0.00 34.74 4.02
142 143 2.989840 CACTACACAGCTACAGCAAGAC 59.010 50.000 3.70 0.00 45.16 3.01
143 144 2.890945 TCACTACACAGCTACAGCAAGA 59.109 45.455 3.70 0.00 45.16 3.02
152 153 2.751166 ATCGCTTTCACTACACAGCT 57.249 45.000 0.00 0.00 0.00 4.24
163 168 5.123979 AGTTCCATCTGGTTTAATCGCTTTC 59.876 40.000 0.00 0.00 36.34 2.62
168 173 4.882671 CCAGTTCCATCTGGTTTAATCG 57.117 45.455 4.75 0.00 46.92 3.34
180 188 0.610232 GGTTCTGCAGCCAGTTCCAT 60.610 55.000 9.47 0.00 40.09 3.41
192 200 0.310854 CGGTTCACTTTGGGTTCTGC 59.689 55.000 0.00 0.00 0.00 4.26
213 221 4.278669 TCTGCCTCATCGTCTTATTCCTAC 59.721 45.833 0.00 0.00 0.00 3.18
225 233 1.000385 GGATCTCAGTCTGCCTCATCG 60.000 57.143 0.00 0.00 0.00 3.84
226 234 2.036217 CAGGATCTCAGTCTGCCTCATC 59.964 54.545 0.00 0.00 0.00 2.92
227 235 2.040939 CAGGATCTCAGTCTGCCTCAT 58.959 52.381 0.00 0.00 0.00 2.90
298 307 2.933495 CATGCCTTGGACATGAACTG 57.067 50.000 14.48 0.00 46.33 3.16
400 413 3.054802 AGAACAGAAGCAATAGGGTCCTG 60.055 47.826 0.00 0.00 0.00 3.86
404 417 6.963322 AGAATTAGAACAGAAGCAATAGGGT 58.037 36.000 0.00 0.00 0.00 4.34
495 509 3.007398 AGTCCTCAACTTGCTCCAGTTAG 59.993 47.826 0.00 0.00 35.10 2.34
501 515 1.294659 CGCAGTCCTCAACTTGCTCC 61.295 60.000 0.00 0.00 35.45 4.70
532 586 5.220931 GCTGATACCCATGATTCTGTCAAAC 60.221 44.000 0.00 0.00 40.97 2.93
553 607 9.539825 ACATATAGATAGTTCTTGTTTCTGCTG 57.460 33.333 0.00 0.00 33.17 4.41
572 626 7.922811 TCTGTTTGCAGTCTGATGTACATATAG 59.077 37.037 8.71 10.47 43.05 1.31
574 628 6.536582 GTCTGTTTGCAGTCTGATGTACATAT 59.463 38.462 8.71 0.00 43.05 1.78
576 630 4.692625 GTCTGTTTGCAGTCTGATGTACAT 59.307 41.667 8.43 8.43 43.05 2.29
577 631 4.058124 GTCTGTTTGCAGTCTGATGTACA 58.942 43.478 3.32 0.00 43.05 2.90
591 653 1.610038 TGGATTGCTGCTGTCTGTTTG 59.390 47.619 0.00 0.00 0.00 2.93
598 660 0.877071 CGTTCTTGGATTGCTGCTGT 59.123 50.000 0.00 0.00 0.00 4.40
599 661 0.455633 GCGTTCTTGGATTGCTGCTG 60.456 55.000 0.00 0.00 0.00 4.41
600 662 0.890542 TGCGTTCTTGGATTGCTGCT 60.891 50.000 0.00 0.00 0.00 4.24
647 714 8.811378 GTTCTTGGATTTTTGTTCTTCTTCTTG 58.189 33.333 0.00 0.00 0.00 3.02
653 720 5.040635 TGCGTTCTTGGATTTTTGTTCTTC 58.959 37.500 0.00 0.00 0.00 2.87
659 730 3.243367 TGAGGTGCGTTCTTGGATTTTTG 60.243 43.478 0.00 0.00 0.00 2.44
692 763 2.420687 CCCAGAATCTTCTTTCGGGAGG 60.421 54.545 7.70 0.00 41.74 4.30
693 764 2.501723 TCCCAGAATCTTCTTTCGGGAG 59.498 50.000 10.86 0.00 41.74 4.30
698 769 4.019771 AGGTGACTCCCAGAATCTTCTTTC 60.020 45.833 0.00 0.00 32.90 2.62
743 817 1.138459 CTCATCTGCTCGTGCTCGT 59.862 57.895 11.19 0.00 40.48 4.18
753 827 1.818785 GCTGTGCCTCCTCATCTGC 60.819 63.158 0.00 0.00 0.00 4.26
758 832 0.975556 TATTCCGCTGTGCCTCCTCA 60.976 55.000 0.00 0.00 0.00 3.86
763 837 1.539065 CGAATCTATTCCGCTGTGCCT 60.539 52.381 0.00 0.00 33.28 4.75
764 838 0.861837 CGAATCTATTCCGCTGTGCC 59.138 55.000 0.00 0.00 33.28 5.01
765 839 0.233332 GCGAATCTATTCCGCTGTGC 59.767 55.000 0.00 0.00 35.24 4.57
766 840 0.504384 CGCGAATCTATTCCGCTGTG 59.496 55.000 0.00 0.00 35.62 3.66
767 841 0.597637 CCGCGAATCTATTCCGCTGT 60.598 55.000 8.23 0.00 35.62 4.40
768 842 1.891060 GCCGCGAATCTATTCCGCTG 61.891 60.000 8.23 0.00 35.62 5.18
769 843 1.664965 GCCGCGAATCTATTCCGCT 60.665 57.895 8.23 0.00 35.62 5.52
770 844 2.853914 GCCGCGAATCTATTCCGC 59.146 61.111 8.23 0.00 34.98 5.54
771 845 2.372690 CCGCCGCGAATCTATTCCG 61.373 63.158 15.93 2.79 33.28 4.30
891 992 2.158914 ACCGGGGTGTAATCGGATAAAC 60.159 50.000 6.32 0.00 45.96 2.01
896 1000 3.301070 CACCGGGGTGTAATCGGA 58.699 61.111 6.32 0.00 45.96 4.55
911 1015 6.183359 GGCAAATCGTAAATGATGAAACACAC 60.183 38.462 0.00 0.00 0.00 3.82
950 1054 1.201414 CCCGTAACCGTAACTTACCGT 59.799 52.381 0.00 0.00 0.00 4.83
952 1056 1.739035 GCCCCGTAACCGTAACTTACC 60.739 57.143 0.00 0.00 0.00 2.85
953 1057 1.204704 AGCCCCGTAACCGTAACTTAC 59.795 52.381 0.00 0.00 0.00 2.34
954 1058 1.476488 GAGCCCCGTAACCGTAACTTA 59.524 52.381 0.00 0.00 0.00 2.24
955 1059 0.247460 GAGCCCCGTAACCGTAACTT 59.753 55.000 0.00 0.00 0.00 2.66
959 1063 3.825611 GCGAGCCCCGTAACCGTA 61.826 66.667 0.00 0.00 41.15 4.02
1449 1556 2.310779 AGACTCTCACAAGCTGGGTA 57.689 50.000 0.00 0.00 0.00 3.69
1461 1568 2.836793 GCGCTCCCCGTAGACTCTC 61.837 68.421 0.00 0.00 39.71 3.20
1546 1653 2.239402 TGACATACTGATGCACCATGGT 59.761 45.455 13.00 13.00 36.43 3.55
1580 1687 4.082523 GCTGGTACGCAGCCTCCA 62.083 66.667 19.74 0.00 39.61 3.86
1602 1709 2.586245 CTCCTCGGCATGGCAAGA 59.414 61.111 20.37 10.98 0.00 3.02
1608 1715 1.227764 CACATCCCTCCTCGGCATG 60.228 63.158 0.00 0.00 0.00 4.06
1767 1874 2.072874 AACACCCTGCAGCTCCACAT 62.073 55.000 8.66 0.00 0.00 3.21
1770 1877 1.529010 CAAACACCCTGCAGCTCCA 60.529 57.895 8.66 0.00 0.00 3.86
1772 1879 1.228245 TCCAAACACCCTGCAGCTC 60.228 57.895 8.66 0.00 0.00 4.09
1971 2078 3.197790 GCACGACCATGCATCGCT 61.198 61.111 15.24 3.25 45.39 4.93
2088 2195 0.693049 CAAGGCCTTGGTCCACTAGT 59.307 55.000 34.08 0.00 36.95 2.57
2194 2301 1.699054 TATGCCTCTGCCAATCGCCT 61.699 55.000 0.00 0.00 36.24 5.52
2203 2310 6.760770 GTCTTTATCATCCTATATGCCTCTGC 59.239 42.308 0.00 0.00 38.26 4.26
2265 2372 0.179171 CTTTGCATGCGCTCAGGAAG 60.179 55.000 14.09 3.99 39.64 3.46
2441 2548 3.084786 CACCCTGGAGTTTTCTTCATCC 58.915 50.000 0.00 0.00 34.53 3.51
2451 2558 2.753029 GAGCTGCACCCTGGAGTT 59.247 61.111 1.02 0.00 38.17 3.01
2555 2662 1.230635 ATGTGACTGCGCCTCAACAC 61.231 55.000 4.18 9.01 34.72 3.32
2559 2666 0.108662 CTGTATGTGACTGCGCCTCA 60.109 55.000 4.18 2.20 0.00 3.86
2618 2728 2.579410 TTTTCACCCTTAGCTCCACC 57.421 50.000 0.00 0.00 0.00 4.61
2620 2730 6.951198 TCATTAAATTTTCACCCTTAGCTCCA 59.049 34.615 0.00 0.00 0.00 3.86
2642 2752 7.781693 ACCATACTGAAAGGCTCAATAAATCAT 59.218 33.333 0.00 0.00 39.30 2.45
2646 2756 5.652014 CCACCATACTGAAAGGCTCAATAAA 59.348 40.000 0.00 0.00 39.30 1.40
2647 2757 5.192927 CCACCATACTGAAAGGCTCAATAA 58.807 41.667 0.00 0.00 39.30 1.40
2648 2758 4.227300 ACCACCATACTGAAAGGCTCAATA 59.773 41.667 0.00 0.00 39.30 1.90
2649 2759 3.010584 ACCACCATACTGAAAGGCTCAAT 59.989 43.478 0.00 0.00 39.30 2.57
2652 2762 2.359900 CACCACCATACTGAAAGGCTC 58.640 52.381 0.00 0.00 39.30 4.70
2653 2763 1.614317 GCACCACCATACTGAAAGGCT 60.614 52.381 0.00 0.00 39.30 4.58
2665 2775 0.250467 GAAAGAGCTCAGCACCACCA 60.250 55.000 17.77 0.00 0.00 4.17
2667 2777 0.036022 AGGAAAGAGCTCAGCACCAC 59.964 55.000 17.77 0.00 0.00 4.16
2668 2778 0.767375 AAGGAAAGAGCTCAGCACCA 59.233 50.000 17.77 0.00 0.00 4.17
2670 2780 2.031333 CACAAAGGAAAGAGCTCAGCAC 60.031 50.000 17.77 3.37 0.00 4.40
2671 2781 2.158769 TCACAAAGGAAAGAGCTCAGCA 60.159 45.455 17.77 0.00 0.00 4.41
2672 2782 2.483491 CTCACAAAGGAAAGAGCTCAGC 59.517 50.000 17.77 4.15 0.00 4.26
2681 2798 1.999648 ATGCTGGCTCACAAAGGAAA 58.000 45.000 0.00 0.00 0.00 3.13
2692 2809 1.053264 CCCTCCTCTGTATGCTGGCT 61.053 60.000 0.00 0.00 0.00 4.75
2723 2840 5.895636 TCGCATTATGACCAACTGAAATT 57.104 34.783 0.00 0.00 0.00 1.82
2724 2841 5.647658 TCTTCGCATTATGACCAACTGAAAT 59.352 36.000 0.00 0.00 0.00 2.17
2725 2842 5.000591 TCTTCGCATTATGACCAACTGAAA 58.999 37.500 0.00 0.00 0.00 2.69
2726 2843 4.574892 TCTTCGCATTATGACCAACTGAA 58.425 39.130 0.00 0.00 0.00 3.02
2742 2859 6.902417 GCTTATTAACTTCATGAGTTCTTCGC 59.098 38.462 12.05 7.90 45.40 4.70
2796 2913 0.388659 GAAGTGCACAATGGCCACAA 59.611 50.000 21.04 0.00 0.00 3.33
2800 2917 2.288948 TGAATTGAAGTGCACAATGGCC 60.289 45.455 21.04 0.00 37.89 5.36
2839 2956 2.681976 GCTTCCAGCTCAGGCATTCTTA 60.682 50.000 0.00 0.00 41.70 2.10
2841 2958 0.394080 GCTTCCAGCTCAGGCATTCT 60.394 55.000 0.00 0.00 41.70 2.40
2842 2959 1.382692 GGCTTCCAGCTCAGGCATTC 61.383 60.000 5.91 0.00 41.99 2.67
2843 2960 1.379576 GGCTTCCAGCTCAGGCATT 60.380 57.895 5.91 0.00 41.99 3.56
2844 2961 2.274760 GGCTTCCAGCTCAGGCAT 59.725 61.111 5.91 0.00 41.99 4.40
2859 2976 0.678048 ATTCAACTCCGCTTCCAGGC 60.678 55.000 0.00 0.00 0.00 4.85
2860 2977 2.691409 TATTCAACTCCGCTTCCAGG 57.309 50.000 0.00 0.00 0.00 4.45
2903 3020 2.338015 ACGGCTTGGCTGATGCAAG 61.338 57.895 5.30 0.00 41.91 4.01
2926 3043 2.627945 GTTGGCGATATCCACTGACAA 58.372 47.619 0.00 0.00 35.50 3.18
2938 3055 0.552848 AGGGATGATTGGTTGGCGAT 59.447 50.000 0.00 0.00 0.00 4.58
2941 3058 1.106285 GACAGGGATGATTGGTTGGC 58.894 55.000 0.00 0.00 0.00 4.52
2960 3077 5.748152 CAGTTAGGTTGTGTTTGGTTTGATG 59.252 40.000 0.00 0.00 0.00 3.07
3007 3124 5.417894 TCTCGATAACCATGACACACTAAGT 59.582 40.000 0.00 0.00 0.00 2.24
3015 3132 4.215109 TCTCCATCTCGATAACCATGACA 58.785 43.478 0.00 0.00 0.00 3.58
3044 3161 2.672961 TTCCTGCGACTAGGATTGTG 57.327 50.000 4.63 0.00 45.85 3.33
3051 3168 6.646653 TCATAGCAAATAATTCCTGCGACTAG 59.353 38.462 0.00 0.00 41.05 2.57
3052 3169 6.521162 TCATAGCAAATAATTCCTGCGACTA 58.479 36.000 0.00 0.00 41.05 2.59
3065 3185 6.827586 AACTTTTCCGGTTCATAGCAAATA 57.172 33.333 0.00 0.00 0.00 1.40
3144 3268 1.940883 GCTAGCTGCCAGCAATGCAA 61.941 55.000 20.53 0.00 45.56 4.08
3145 3269 2.412323 GCTAGCTGCCAGCAATGCA 61.412 57.895 20.53 0.00 45.56 3.96
3152 3276 2.842457 TGACAATATGCTAGCTGCCAG 58.158 47.619 17.23 5.92 42.00 4.85
3154 3278 3.672808 AGATGACAATATGCTAGCTGCC 58.327 45.455 17.23 0.00 42.00 4.85
3188 3312 6.201517 CCACATCACGATTGGACAAAATATC 58.798 40.000 0.00 0.00 31.39 1.63
3214 3338 1.305219 AATTGCATAGGCGCACACGT 61.305 50.000 10.83 0.00 42.87 4.49
3216 3340 1.270971 CAAATTGCATAGGCGCACAC 58.729 50.000 10.83 0.00 42.87 3.82
3496 3625 6.542574 TTCAAACCATGCTAGCAATTTTTG 57.457 33.333 26.82 26.82 0.00 2.44


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

AutoCloner maintained by Alex Coulton.