Multiple sequence alignment - TraesCS6B01G368100

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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 TraesCS6B01G368100 chr6B 100.000 2074 0 0 1 2074 642346720 642348793 0.000000e+00 3831.0
1 TraesCS6B01G368100 chr6B 100.000 599 0 0 2417 3015 642349136 642349734 0.000000e+00 1107.0
2 TraesCS6B01G368100 chr6B 89.024 164 15 3 362 523 642346964 642347126 1.830000e-47 200.0
3 TraesCS6B01G368100 chr6B 89.024 164 15 3 245 407 642347081 642347242 1.830000e-47 200.0
4 TraesCS6B01G368100 chr6B 93.043 115 6 2 1776 1889 642348437 642348550 1.860000e-37 167.0
5 TraesCS6B01G368100 chr6B 93.043 115 6 2 1718 1831 642348495 642348608 1.860000e-37 167.0
6 TraesCS6B01G368100 chr6B 100.000 40 0 0 785 824 642347467 642347506 1.160000e-09 75.0
7 TraesCS6B01G368100 chr6B 100.000 40 0 0 748 787 642347504 642347543 1.160000e-09 75.0
8 TraesCS6B01G368100 chr6A 96.844 1109 31 2 785 1889 571640080 571641188 0.000000e+00 1851.0
9 TraesCS6B01G368100 chr6A 93.647 787 35 3 1 787 571639348 571640119 0.000000e+00 1162.0
10 TraesCS6B01G368100 chr6A 94.314 510 24 4 2508 3015 571641654 571642160 0.000000e+00 776.0
11 TraesCS6B01G368100 chr6A 92.262 336 25 1 1719 2053 571641075 571641410 2.720000e-130 475.0
12 TraesCS6B01G368100 chr6A 92.593 162 11 1 362 523 571639579 571639739 6.500000e-57 231.0
13 TraesCS6B01G368100 chr6A 89.024 164 15 3 245 407 571639694 571639855 1.830000e-47 200.0
14 TraesCS6B01G368100 chr6A 93.913 115 6 1 1776 1889 571641016 571641130 4.000000e-39 172.0
15 TraesCS6B01G368100 chr6A 94.737 57 3 0 1833 1889 571641016 571641072 4.140000e-14 89.8
16 TraesCS6B01G368100 chr6A 100.000 35 0 0 2040 2074 571641422 571641456 6.980000e-07 65.8
17 TraesCS6B01G368100 chr6D 96.992 1064 28 2 785 1844 426884837 426885900 0.000000e+00 1784.0
18 TraesCS6B01G368100 chr6D 97.970 788 13 3 1 787 426884091 426884876 0.000000e+00 1363.0
19 TraesCS6B01G368100 chr6D 94.455 541 23 6 2478 3015 426886557 426887093 0.000000e+00 826.0
20 TraesCS6B01G368100 chr6D 93.050 259 7 6 1825 2074 426885926 426886182 4.750000e-98 368.0
21 TraesCS6B01G368100 chr6D 89.634 164 14 3 362 523 426884334 426884496 3.940000e-49 206.0
22 TraesCS6B01G368100 chr6D 89.634 164 14 3 245 407 426884451 426884612 3.940000e-49 206.0
23 TraesCS6B01G368100 chr6D 93.043 115 7 1 1776 1889 426885773 426885887 1.860000e-37 167.0
24 TraesCS6B01G368100 chr6D 91.304 69 1 2 1768 1831 426885926 426885994 4.140000e-14 89.8


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 TraesCS6B01G368100 chr6B 642346720 642349734 3014 False 727.750000 3831 95.516750 1 3015 8 chr6B.!!$F1 3014
1 TraesCS6B01G368100 chr6A 571639348 571642160 2812 False 558.066667 1851 94.148222 1 3015 9 chr6A.!!$F1 3014
2 TraesCS6B01G368100 chr6D 426884091 426887093 3002 False 626.225000 1784 93.260250 1 3015 8 chr6D.!!$F1 3014

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
213 214 0.033504 TGACTGACTGAAACCGGAGC 59.966 55.0 9.46 0.0 0.0 4.7 F
777 778 0.106015 AGCCCATATTCCCCAAGCAC 60.106 55.0 0.00 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 1352 0.526211 TGTCATCGTCGCTAGTGCTT 59.474 50.000 0.00 0.0 36.97 3.91 R
2752 2894 1.870901 CTACGCGTTACCGACAGGC 60.871 63.158 20.78 0.0 42.76 4.85 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
55 56 0.250234 TTCAGCTGCGCAGTCCTATT 59.750 50.000 35.80 13.86 0.00 1.73
213 214 0.033504 TGACTGACTGAAACCGGAGC 59.966 55.000 9.46 0.00 0.00 4.70
279 280 5.830457 AGAAGACATGAGATGGACGATTCTA 59.170 40.000 0.00 0.00 33.60 2.10
468 469 6.422776 AAGGATATGCTACAAAACAGAACG 57.577 37.500 0.00 0.00 0.00 3.95
502 503 4.982241 AGGGACAAAGAAGACATGAGAA 57.018 40.909 0.00 0.00 0.00 2.87
615 616 8.239038 TGGAATAATCCCTCGATAGATACATC 57.761 38.462 0.00 0.00 45.95 3.06
616 617 7.839200 TGGAATAATCCCTCGATAGATACATCA 59.161 37.037 0.00 0.00 45.95 3.07
617 618 8.356657 GGAATAATCCCTCGATAGATACATCAG 58.643 40.741 0.00 0.00 39.62 2.90
658 659 4.314740 TTTGGATTTTCAGTTTCCCACG 57.685 40.909 0.00 0.00 0.00 4.94
664 665 5.182380 GGATTTTCAGTTTCCCACGTGATAA 59.818 40.000 19.30 7.83 0.00 1.75
717 718 4.436998 CCACCGAGTCCAGCGTCC 62.437 72.222 0.00 0.00 0.00 4.79
774 775 2.895404 CAATCAGCCCATATTCCCCAAG 59.105 50.000 0.00 0.00 0.00 3.61
775 776 0.185901 TCAGCCCATATTCCCCAAGC 59.814 55.000 0.00 0.00 0.00 4.01
776 777 0.106066 CAGCCCATATTCCCCAAGCA 60.106 55.000 0.00 0.00 0.00 3.91
777 778 0.106015 AGCCCATATTCCCCAAGCAC 60.106 55.000 0.00 0.00 0.00 4.40
778 779 1.115326 GCCCATATTCCCCAAGCACC 61.115 60.000 0.00 0.00 0.00 5.01
779 780 0.261402 CCCATATTCCCCAAGCACCA 59.739 55.000 0.00 0.00 0.00 4.17
780 781 1.402787 CCATATTCCCCAAGCACCAC 58.597 55.000 0.00 0.00 0.00 4.16
781 782 1.402787 CATATTCCCCAAGCACCACC 58.597 55.000 0.00 0.00 0.00 4.61
782 783 1.006813 ATATTCCCCAAGCACCACCA 58.993 50.000 0.00 0.00 0.00 4.17
783 784 0.331278 TATTCCCCAAGCACCACCAG 59.669 55.000 0.00 0.00 0.00 4.00
784 785 1.434513 ATTCCCCAAGCACCACCAGA 61.435 55.000 0.00 0.00 0.00 3.86
785 786 2.282462 CCCCAAGCACCACCAGAC 60.282 66.667 0.00 0.00 0.00 3.51
786 787 2.282462 CCCAAGCACCACCAGACC 60.282 66.667 0.00 0.00 0.00 3.85
787 788 2.833913 CCCAAGCACCACCAGACCT 61.834 63.158 0.00 0.00 0.00 3.85
788 789 1.151450 CCAAGCACCACCAGACCTT 59.849 57.895 0.00 0.00 0.00 3.50
789 790 1.174712 CCAAGCACCACCAGACCTTG 61.175 60.000 0.00 0.00 34.26 3.61
790 791 1.529244 AAGCACCACCAGACCTTGC 60.529 57.895 0.00 0.00 0.00 4.01
791 792 2.203337 GCACCACCAGACCTTGCA 60.203 61.111 0.00 0.00 33.24 4.08
792 793 1.827789 GCACCACCAGACCTTGCAA 60.828 57.895 0.00 0.00 33.24 4.08
793 794 1.181098 GCACCACCAGACCTTGCAAT 61.181 55.000 0.00 0.00 33.24 3.56
794 795 0.883833 CACCACCAGACCTTGCAATC 59.116 55.000 0.00 0.00 0.00 2.67
795 796 0.478072 ACCACCAGACCTTGCAATCA 59.522 50.000 0.00 0.00 0.00 2.57
796 797 1.171308 CCACCAGACCTTGCAATCAG 58.829 55.000 0.00 0.00 0.00 2.90
797 798 0.524862 CACCAGACCTTGCAATCAGC 59.475 55.000 0.00 0.00 45.96 4.26
798 799 0.610232 ACCAGACCTTGCAATCAGCC 60.610 55.000 0.00 0.00 44.83 4.85
799 800 1.318158 CCAGACCTTGCAATCAGCCC 61.318 60.000 0.00 0.00 44.83 5.19
800 801 0.609957 CAGACCTTGCAATCAGCCCA 60.610 55.000 0.00 0.00 44.83 5.36
801 802 0.333993 AGACCTTGCAATCAGCCCAT 59.666 50.000 0.00 0.00 44.83 4.00
802 803 1.565759 AGACCTTGCAATCAGCCCATA 59.434 47.619 0.00 0.00 44.83 2.74
803 804 2.176364 AGACCTTGCAATCAGCCCATAT 59.824 45.455 0.00 0.00 44.83 1.78
804 805 2.961062 GACCTTGCAATCAGCCCATATT 59.039 45.455 0.00 0.00 44.83 1.28
805 806 2.961062 ACCTTGCAATCAGCCCATATTC 59.039 45.455 0.00 0.00 44.83 1.75
806 807 2.298163 CCTTGCAATCAGCCCATATTCC 59.702 50.000 0.00 0.00 44.83 3.01
807 808 1.999648 TGCAATCAGCCCATATTCCC 58.000 50.000 0.00 0.00 44.83 3.97
808 809 1.260544 GCAATCAGCCCATATTCCCC 58.739 55.000 0.00 0.00 37.23 4.81
809 810 1.481055 GCAATCAGCCCATATTCCCCA 60.481 52.381 0.00 0.00 37.23 4.96
810 811 2.961510 CAATCAGCCCATATTCCCCAA 58.038 47.619 0.00 0.00 0.00 4.12
1111 1112 3.370231 ACGAAAACCGCCATGGCC 61.370 61.111 30.79 14.48 43.94 5.36
1192 1193 1.212375 TATCCATGGTGACCTGGGTG 58.788 55.000 12.58 5.42 33.13 4.61
1194 1195 2.759114 CATGGTGACCTGGGTGCT 59.241 61.111 2.11 0.00 0.00 4.40
1351 1352 1.080093 GAACGGTGCTCGATCCACA 60.080 57.895 15.50 0.00 42.43 4.17
1360 1361 1.565305 CTCGATCCACAAGCACTAGC 58.435 55.000 0.00 0.00 42.56 3.42
1412 1413 0.378962 TGTGGCTTTTACACACGCAC 59.621 50.000 0.00 0.00 43.35 5.34
1516 1517 6.595682 TCAATGTGAAAAGGAAGAAGAGAGT 58.404 36.000 0.00 0.00 0.00 3.24
1534 1535 1.068474 GTGACGTCGCACTGCTTAAT 58.932 50.000 23.67 0.00 35.91 1.40
1538 1539 3.930229 TGACGTCGCACTGCTTAATAATT 59.070 39.130 11.62 0.00 0.00 1.40
1539 1540 4.390603 TGACGTCGCACTGCTTAATAATTT 59.609 37.500 11.62 0.00 0.00 1.82
1540 1541 5.577554 TGACGTCGCACTGCTTAATAATTTA 59.422 36.000 11.62 0.00 0.00 1.40
1697 1701 1.276844 GTCGTGTGTTGCTGCTGAC 59.723 57.895 0.00 0.29 0.00 3.51
1721 1725 5.920273 CGAAAGTGGCTTAATCATGTTTGTT 59.080 36.000 0.00 0.00 0.00 2.83
1729 1733 7.125113 GGCTTAATCATGTTTGTTTTTGTGTG 58.875 34.615 0.00 0.00 0.00 3.82
1775 1779 8.874744 TGGTACTAGTAACTTATCAAGTCACT 57.125 34.615 18.57 0.79 42.58 3.41
1806 1869 8.541133 TTTGTAATTAAGGTATTTGCCAAAGC 57.459 30.769 0.00 0.00 40.48 3.51
1871 1983 2.165641 GGTATTTGCCAAAGCTGGTACC 59.834 50.000 4.43 4.43 45.53 3.34
1964 2076 8.905702 GCTATTATGCAAGCAACATAATTACAC 58.094 33.333 18.21 7.47 44.44 2.90
1965 2077 9.949174 CTATTATGCAAGCAACATAATTACACA 57.051 29.630 18.21 5.48 44.44 3.72
1972 2084 7.009540 GCAAGCAACATAATTACACATTCCTTC 59.990 37.037 0.00 0.00 0.00 3.46
2436 2576 2.466846 GGGGGTGCTTTATGGATTTGT 58.533 47.619 0.00 0.00 0.00 2.83
2437 2577 3.637769 GGGGGTGCTTTATGGATTTGTA 58.362 45.455 0.00 0.00 0.00 2.41
2438 2578 4.223144 GGGGGTGCTTTATGGATTTGTAT 58.777 43.478 0.00 0.00 0.00 2.29
2439 2579 5.390387 GGGGGTGCTTTATGGATTTGTATA 58.610 41.667 0.00 0.00 0.00 1.47
2440 2580 5.243060 GGGGGTGCTTTATGGATTTGTATAC 59.757 44.000 0.00 0.00 0.00 1.47
2441 2581 5.243060 GGGGTGCTTTATGGATTTGTATACC 59.757 44.000 0.00 0.00 0.00 2.73
2442 2582 5.830991 GGGTGCTTTATGGATTTGTATACCA 59.169 40.000 0.00 0.00 38.09 3.25
2443 2583 6.493458 GGGTGCTTTATGGATTTGTATACCAT 59.507 38.462 0.00 0.00 44.94 3.55
2444 2584 7.370383 GGTGCTTTATGGATTTGTATACCATG 58.630 38.462 0.00 0.00 43.15 3.66
2445 2585 7.370383 GTGCTTTATGGATTTGTATACCATGG 58.630 38.462 11.19 11.19 43.15 3.66
2446 2586 7.014230 GTGCTTTATGGATTTGTATACCATGGT 59.986 37.037 23.55 23.55 43.15 3.55
2447 2587 7.563188 TGCTTTATGGATTTGTATACCATGGTT 59.437 33.333 25.38 13.40 43.15 3.67
2448 2588 8.421002 GCTTTATGGATTTGTATACCATGGTTT 58.579 33.333 25.38 18.40 43.15 3.27
2449 2589 9.748708 CTTTATGGATTTGTATACCATGGTTTG 57.251 33.333 25.38 0.00 43.15 2.93
2450 2590 9.480861 TTTATGGATTTGTATACCATGGTTTGA 57.519 29.630 25.38 5.28 43.15 2.69
2451 2591 7.587037 ATGGATTTGTATACCATGGTTTGAG 57.413 36.000 25.38 0.00 41.96 3.02
2452 2592 6.489603 TGGATTTGTATACCATGGTTTGAGT 58.510 36.000 25.38 7.15 0.00 3.41
2453 2593 6.601613 TGGATTTGTATACCATGGTTTGAGTC 59.398 38.462 25.38 12.41 0.00 3.36
2454 2594 6.601613 GGATTTGTATACCATGGTTTGAGTCA 59.398 38.462 25.38 11.17 0.00 3.41
2455 2595 7.122055 GGATTTGTATACCATGGTTTGAGTCAA 59.878 37.037 25.38 16.02 0.00 3.18
2456 2596 7.447374 TTTGTATACCATGGTTTGAGTCAAG 57.553 36.000 25.38 0.00 0.00 3.02
2457 2597 6.121776 TGTATACCATGGTTTGAGTCAAGT 57.878 37.500 25.38 2.26 0.00 3.16
2458 2598 6.539173 TGTATACCATGGTTTGAGTCAAGTT 58.461 36.000 25.38 0.00 0.00 2.66
2459 2599 6.653320 TGTATACCATGGTTTGAGTCAAGTTC 59.347 38.462 25.38 1.50 0.00 3.01
2460 2600 3.897239 ACCATGGTTTGAGTCAAGTTCA 58.103 40.909 13.00 6.51 0.00 3.18
2461 2601 4.277476 ACCATGGTTTGAGTCAAGTTCAA 58.723 39.130 13.00 0.00 33.00 2.69
2462 2602 4.339247 ACCATGGTTTGAGTCAAGTTCAAG 59.661 41.667 13.00 3.66 36.07 3.02
2463 2603 4.293415 CATGGTTTGAGTCAAGTTCAAGC 58.707 43.478 5.56 1.38 36.07 4.01
2464 2604 3.620488 TGGTTTGAGTCAAGTTCAAGCT 58.380 40.909 5.56 0.00 36.43 3.74
2465 2605 3.627577 TGGTTTGAGTCAAGTTCAAGCTC 59.372 43.478 5.56 0.00 36.43 4.09
2466 2606 3.627577 GGTTTGAGTCAAGTTCAAGCTCA 59.372 43.478 5.56 0.00 36.43 4.26
2467 2607 4.276926 GGTTTGAGTCAAGTTCAAGCTCAT 59.723 41.667 5.56 0.00 36.43 2.90
2468 2608 5.447573 GTTTGAGTCAAGTTCAAGCTCATC 58.552 41.667 5.56 0.00 36.07 2.92
2469 2609 4.613925 TGAGTCAAGTTCAAGCTCATCT 57.386 40.909 0.00 0.00 32.09 2.90
2470 2610 4.965814 TGAGTCAAGTTCAAGCTCATCTT 58.034 39.130 0.00 0.00 32.09 2.40
2471 2611 4.993584 TGAGTCAAGTTCAAGCTCATCTTC 59.006 41.667 0.00 0.00 32.09 2.87
2472 2612 4.322567 AGTCAAGTTCAAGCTCATCTTCC 58.677 43.478 0.00 0.00 31.27 3.46
2473 2613 4.041444 AGTCAAGTTCAAGCTCATCTTCCT 59.959 41.667 0.00 0.00 31.27 3.36
2474 2614 4.391523 GTCAAGTTCAAGCTCATCTTCCTC 59.608 45.833 0.00 0.00 31.27 3.71
2475 2615 4.285517 TCAAGTTCAAGCTCATCTTCCTCT 59.714 41.667 0.00 0.00 31.27 3.69
2476 2616 4.906747 AGTTCAAGCTCATCTTCCTCTT 57.093 40.909 0.00 0.00 31.27 2.85
2558 2698 8.717821 CGAGTATCAACAAAAGTTCTTTATGGA 58.282 33.333 0.00 0.00 33.17 3.41
2561 2701 7.839680 ATCAACAAAAGTTCTTTATGGAGGT 57.160 32.000 0.00 0.00 0.00 3.85
2641 2783 5.406649 TGAAATTTATAAGCCGCAAACTGG 58.593 37.500 0.00 0.00 0.00 4.00
2660 2802 4.263462 ACTGGATAGTGGCAAAATCACTCA 60.263 41.667 11.22 1.86 43.55 3.41
2727 2869 3.081133 CATCGTGTACGCAGCACC 58.919 61.111 7.29 0.00 39.60 5.01
2752 2894 0.459237 AAGATTCTCTCGTGCCTGCG 60.459 55.000 0.00 0.00 0.00 5.18
2796 2938 2.981859 AACCTATCATGTCGTGTCCC 57.018 50.000 0.00 0.00 0.00 4.46
2870 3012 2.416547 CTCTGCCTTTAACCGTGTGATG 59.583 50.000 0.00 0.00 0.00 3.07
2882 3024 5.034852 ACCGTGTGATGATTTGATATGGA 57.965 39.130 0.00 0.00 0.00 3.41
2883 3025 5.436175 ACCGTGTGATGATTTGATATGGAA 58.564 37.500 0.00 0.00 0.00 3.53
2957 3100 1.956477 GTTTCCTTGGCTTGCAAGAGA 59.044 47.619 30.39 12.10 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 0.114954 AGGAGCAAAGCAATGGGGAA 59.885 50.000 0.00 0.00 0.00 3.97
213 214 4.641541 TGATTGATGAAGCATGTTGTAGGG 59.358 41.667 0.00 0.00 0.00 3.53
279 280 2.095263 CGATGTGTTCGGGAAGCAATTT 60.095 45.455 0.00 0.00 44.28 1.82
502 503 3.216800 TGAAGCAATTCAGCAGTGTTCT 58.783 40.909 0.00 0.00 36.85 3.01
642 643 6.834168 ATTATCACGTGGGAAACTGAAAAT 57.166 33.333 17.00 0.00 0.00 1.82
693 694 2.007608 GCTGGACTCGGTGGAATTTAC 58.992 52.381 0.00 0.00 0.00 2.01
717 718 3.548745 TGGTGGCTCTACATCATTCTG 57.451 47.619 0.00 0.00 0.00 3.02
774 775 1.181098 ATTGCAAGGTCTGGTGGTGC 61.181 55.000 4.94 0.00 35.75 5.01
775 776 0.883833 GATTGCAAGGTCTGGTGGTG 59.116 55.000 4.94 0.00 0.00 4.17
776 777 0.478072 TGATTGCAAGGTCTGGTGGT 59.522 50.000 4.94 0.00 0.00 4.16
777 778 1.171308 CTGATTGCAAGGTCTGGTGG 58.829 55.000 4.94 0.00 0.00 4.61
778 779 0.524862 GCTGATTGCAAGGTCTGGTG 59.475 55.000 4.94 0.00 42.31 4.17
779 780 0.610232 GGCTGATTGCAAGGTCTGGT 60.610 55.000 4.94 0.00 45.15 4.00
780 781 1.318158 GGGCTGATTGCAAGGTCTGG 61.318 60.000 4.94 0.00 45.15 3.86
781 782 0.609957 TGGGCTGATTGCAAGGTCTG 60.610 55.000 4.94 3.96 45.15 3.51
782 783 0.333993 ATGGGCTGATTGCAAGGTCT 59.666 50.000 4.94 0.00 45.15 3.85
783 784 2.057137 TATGGGCTGATTGCAAGGTC 57.943 50.000 4.94 0.00 45.15 3.85
784 785 2.761786 ATATGGGCTGATTGCAAGGT 57.238 45.000 4.94 0.00 45.15 3.50
785 786 2.298163 GGAATATGGGCTGATTGCAAGG 59.702 50.000 4.94 0.00 45.15 3.61
786 787 2.298163 GGGAATATGGGCTGATTGCAAG 59.702 50.000 4.94 0.00 45.15 4.01
787 788 2.318908 GGGAATATGGGCTGATTGCAA 58.681 47.619 0.00 0.00 45.15 4.08
788 789 1.481055 GGGGAATATGGGCTGATTGCA 60.481 52.381 0.00 0.00 45.15 4.08
789 790 1.260544 GGGGAATATGGGCTGATTGC 58.739 55.000 0.00 0.00 41.94 3.56
790 791 2.681319 TGGGGAATATGGGCTGATTG 57.319 50.000 0.00 0.00 0.00 2.67
791 792 2.757606 GCTTGGGGAATATGGGCTGATT 60.758 50.000 0.00 0.00 0.00 2.57
792 793 1.203100 GCTTGGGGAATATGGGCTGAT 60.203 52.381 0.00 0.00 0.00 2.90
793 794 0.185901 GCTTGGGGAATATGGGCTGA 59.814 55.000 0.00 0.00 0.00 4.26
794 795 0.106066 TGCTTGGGGAATATGGGCTG 60.106 55.000 0.00 0.00 0.00 4.85
795 796 0.106015 GTGCTTGGGGAATATGGGCT 60.106 55.000 0.00 0.00 0.00 5.19
796 797 1.115326 GGTGCTTGGGGAATATGGGC 61.115 60.000 0.00 0.00 0.00 5.36
797 798 0.261402 TGGTGCTTGGGGAATATGGG 59.739 55.000 0.00 0.00 0.00 4.00
798 799 1.402787 GTGGTGCTTGGGGAATATGG 58.597 55.000 0.00 0.00 0.00 2.74
799 800 1.341877 TGGTGGTGCTTGGGGAATATG 60.342 52.381 0.00 0.00 0.00 1.78
800 801 1.006813 TGGTGGTGCTTGGGGAATAT 58.993 50.000 0.00 0.00 0.00 1.28
801 802 0.331278 CTGGTGGTGCTTGGGGAATA 59.669 55.000 0.00 0.00 0.00 1.75
802 803 1.077265 CTGGTGGTGCTTGGGGAAT 59.923 57.895 0.00 0.00 0.00 3.01
803 804 2.081787 TCTGGTGGTGCTTGGGGAA 61.082 57.895 0.00 0.00 0.00 3.97
804 805 2.449518 TCTGGTGGTGCTTGGGGA 60.450 61.111 0.00 0.00 0.00 4.81
805 806 2.282462 GTCTGGTGGTGCTTGGGG 60.282 66.667 0.00 0.00 0.00 4.96
806 807 2.282462 GGTCTGGTGGTGCTTGGG 60.282 66.667 0.00 0.00 0.00 4.12
807 808 0.962356 GATGGTCTGGTGGTGCTTGG 60.962 60.000 0.00 0.00 0.00 3.61
808 809 0.250858 TGATGGTCTGGTGGTGCTTG 60.251 55.000 0.00 0.00 0.00 4.01
809 810 0.250901 GTGATGGTCTGGTGGTGCTT 60.251 55.000 0.00 0.00 0.00 3.91
810 811 1.376466 GTGATGGTCTGGTGGTGCT 59.624 57.895 0.00 0.00 0.00 4.40
1130 1131 0.679321 GCTTTGGAGAAGGCCTGGAG 60.679 60.000 5.69 0.00 0.00 3.86
1192 1193 2.369870 GCAAGAACATGCATGCAGC 58.630 52.632 26.69 17.60 45.70 5.25
1351 1352 0.526211 TGTCATCGTCGCTAGTGCTT 59.474 50.000 0.00 0.00 36.97 3.91
1360 1361 2.723143 CACAGCATCTATGTCATCGTCG 59.277 50.000 0.00 0.00 0.00 5.12
1363 1364 3.055591 GACCACAGCATCTATGTCATCG 58.944 50.000 0.00 0.00 0.00 3.84
1412 1413 1.093159 GCAGCATGGGTCTCTTTGAG 58.907 55.000 0.00 0.00 35.86 3.02
1516 1517 2.640346 TATTAAGCAGTGCGACGTCA 57.360 45.000 17.16 0.00 0.00 4.35
1697 1701 5.460646 ACAAACATGATTAAGCCACTTTCG 58.539 37.500 0.00 0.00 0.00 3.46
1729 1733 7.640597 ACCAGCTTTGGTAAATACCTTAATC 57.359 36.000 10.77 2.20 46.58 1.75
1742 1746 5.820404 AAGTTACTAGTACCAGCTTTGGT 57.180 39.130 0.91 2.83 45.46 3.67
1761 1765 7.391148 ACAAAACACAAGTGACTTGATAAGT 57.609 32.000 30.03 18.55 43.42 2.24
1775 1779 9.262358 GGCAAATACCTTAATTACAAAACACAA 57.738 29.630 0.00 0.00 0.00 3.33
1871 1983 5.447279 GCACATTTGACTTGATAAGGTACCG 60.447 44.000 6.18 0.00 0.00 4.02
1964 2076 6.955963 CGAAAGTCGAACATAAAGAAGGAATG 59.044 38.462 0.00 0.00 43.74 2.67
1965 2077 6.872020 TCGAAAGTCGAACATAAAGAAGGAAT 59.128 34.615 0.00 0.00 46.90 3.01
2416 2556 2.466846 ACAAATCCATAAAGCACCCCC 58.533 47.619 0.00 0.00 0.00 5.40
2417 2557 5.243060 GGTATACAAATCCATAAAGCACCCC 59.757 44.000 5.01 0.00 0.00 4.95
2418 2558 5.830991 TGGTATACAAATCCATAAAGCACCC 59.169 40.000 5.01 0.00 0.00 4.61
2419 2559 6.952773 TGGTATACAAATCCATAAAGCACC 57.047 37.500 5.01 0.00 0.00 5.01
2420 2560 7.014230 ACCATGGTATACAAATCCATAAAGCAC 59.986 37.037 18.10 0.00 39.57 4.40
2421 2561 7.066142 ACCATGGTATACAAATCCATAAAGCA 58.934 34.615 18.10 0.00 39.57 3.91
2422 2562 7.524717 ACCATGGTATACAAATCCATAAAGC 57.475 36.000 18.10 0.00 39.57 3.51
2423 2563 9.748708 CAAACCATGGTATACAAATCCATAAAG 57.251 33.333 20.12 0.00 39.57 1.85
2424 2564 9.480861 TCAAACCATGGTATACAAATCCATAAA 57.519 29.630 20.12 0.00 39.57 1.40
2425 2565 9.130661 CTCAAACCATGGTATACAAATCCATAA 57.869 33.333 20.12 0.00 39.57 1.90
2426 2566 8.278639 ACTCAAACCATGGTATACAAATCCATA 58.721 33.333 20.12 0.00 39.57 2.74
2427 2567 7.125391 ACTCAAACCATGGTATACAAATCCAT 58.875 34.615 20.12 0.00 41.88 3.41
2428 2568 6.489603 ACTCAAACCATGGTATACAAATCCA 58.510 36.000 20.12 0.00 35.64 3.41
2429 2569 6.601613 TGACTCAAACCATGGTATACAAATCC 59.398 38.462 20.12 3.16 0.00 3.01
2430 2570 7.624360 TGACTCAAACCATGGTATACAAATC 57.376 36.000 20.12 10.72 0.00 2.17
2431 2571 7.669722 ACTTGACTCAAACCATGGTATACAAAT 59.330 33.333 20.12 6.56 0.00 2.32
2432 2572 7.001674 ACTTGACTCAAACCATGGTATACAAA 58.998 34.615 20.12 6.50 0.00 2.83
2433 2573 6.539173 ACTTGACTCAAACCATGGTATACAA 58.461 36.000 20.12 16.26 0.00 2.41
2434 2574 6.121776 ACTTGACTCAAACCATGGTATACA 57.878 37.500 20.12 10.05 0.00 2.29
2435 2575 6.653320 TGAACTTGACTCAAACCATGGTATAC 59.347 38.462 20.12 7.55 0.00 1.47
2436 2576 6.774673 TGAACTTGACTCAAACCATGGTATA 58.225 36.000 20.12 5.66 0.00 1.47
2437 2577 5.630121 TGAACTTGACTCAAACCATGGTAT 58.370 37.500 20.12 5.74 0.00 2.73
2438 2578 5.042463 TGAACTTGACTCAAACCATGGTA 57.958 39.130 20.12 0.84 0.00 3.25
2439 2579 3.897239 TGAACTTGACTCAAACCATGGT 58.103 40.909 13.00 13.00 0.00 3.55
2440 2580 4.794003 GCTTGAACTTGACTCAAACCATGG 60.794 45.833 11.19 11.19 32.57 3.66
2441 2581 4.037208 AGCTTGAACTTGACTCAAACCATG 59.963 41.667 0.00 0.00 32.57 3.66
2442 2582 4.210331 AGCTTGAACTTGACTCAAACCAT 58.790 39.130 0.00 0.00 32.57 3.55
2443 2583 3.620488 AGCTTGAACTTGACTCAAACCA 58.380 40.909 0.00 0.00 32.57 3.67
2444 2584 3.627577 TGAGCTTGAACTTGACTCAAACC 59.372 43.478 0.00 0.00 34.59 3.27
2445 2585 4.882671 TGAGCTTGAACTTGACTCAAAC 57.117 40.909 0.00 0.00 34.59 2.93
2446 2586 5.371526 AGATGAGCTTGAACTTGACTCAAA 58.628 37.500 0.00 0.00 40.49 2.69
2447 2587 4.965814 AGATGAGCTTGAACTTGACTCAA 58.034 39.130 0.00 0.00 40.49 3.02
2448 2588 4.613925 AGATGAGCTTGAACTTGACTCA 57.386 40.909 0.00 0.00 41.28 3.41
2449 2589 4.391523 GGAAGATGAGCTTGAACTTGACTC 59.608 45.833 0.00 0.00 36.83 3.36
2450 2590 4.041444 AGGAAGATGAGCTTGAACTTGACT 59.959 41.667 0.00 0.00 36.83 3.41
2451 2591 4.322567 AGGAAGATGAGCTTGAACTTGAC 58.677 43.478 0.00 0.00 36.83 3.18
2452 2592 4.285517 AGAGGAAGATGAGCTTGAACTTGA 59.714 41.667 0.00 0.00 36.83 3.02
2453 2593 4.577875 AGAGGAAGATGAGCTTGAACTTG 58.422 43.478 0.00 0.00 36.83 3.16
2454 2594 4.906747 AGAGGAAGATGAGCTTGAACTT 57.093 40.909 0.00 0.00 36.83 2.66
2455 2595 4.906747 AAGAGGAAGATGAGCTTGAACT 57.093 40.909 0.00 0.00 36.83 3.01
2456 2596 6.652900 ACTTAAAGAGGAAGATGAGCTTGAAC 59.347 38.462 0.00 0.00 36.83 3.18
2457 2597 6.773638 ACTTAAAGAGGAAGATGAGCTTGAA 58.226 36.000 0.00 0.00 36.83 2.69
2458 2598 6.365970 ACTTAAAGAGGAAGATGAGCTTGA 57.634 37.500 0.00 0.00 36.83 3.02
2459 2599 6.878389 AGAACTTAAAGAGGAAGATGAGCTTG 59.122 38.462 0.00 0.00 36.83 4.01
2460 2600 7.014988 AGAACTTAAAGAGGAAGATGAGCTT 57.985 36.000 0.00 0.00 40.25 3.74
2461 2601 6.619329 AGAACTTAAAGAGGAAGATGAGCT 57.381 37.500 0.00 0.00 0.00 4.09
2462 2602 8.038351 AGTAAGAACTTAAAGAGGAAGATGAGC 58.962 37.037 0.00 0.00 29.00 4.26
2463 2603 9.581099 GAGTAAGAACTTAAAGAGGAAGATGAG 57.419 37.037 0.00 0.00 35.56 2.90
2464 2604 9.090103 TGAGTAAGAACTTAAAGAGGAAGATGA 57.910 33.333 0.00 0.00 35.56 2.92
2465 2605 9.712305 TTGAGTAAGAACTTAAAGAGGAAGATG 57.288 33.333 0.00 0.00 35.56 2.90
2467 2607 9.930693 GATTGAGTAAGAACTTAAAGAGGAAGA 57.069 33.333 0.00 0.00 35.14 2.87
2468 2608 9.936759 AGATTGAGTAAGAACTTAAAGAGGAAG 57.063 33.333 0.00 0.00 35.14 3.46
2469 2609 9.930693 GAGATTGAGTAAGAACTTAAAGAGGAA 57.069 33.333 0.00 0.00 35.14 3.36
2470 2610 9.090103 TGAGATTGAGTAAGAACTTAAAGAGGA 57.910 33.333 0.00 0.00 35.14 3.71
2471 2611 9.364989 CTGAGATTGAGTAAGAACTTAAAGAGG 57.635 37.037 0.00 0.00 35.14 3.69
2472 2612 9.921637 ACTGAGATTGAGTAAGAACTTAAAGAG 57.078 33.333 0.00 0.00 35.14 2.85
2585 2727 5.444122 GTTCATTCGAGTTTGTTCCTGAAG 58.556 41.667 0.00 0.00 0.00 3.02
2641 2783 4.641989 ACCATGAGTGATTTTGCCACTATC 59.358 41.667 0.00 0.00 44.14 2.08
2752 2894 1.870901 CTACGCGTTACCGACAGGC 60.871 63.158 20.78 0.00 42.76 4.85
2796 2938 4.998788 TCTCTTGACTGTTACCATGATCG 58.001 43.478 0.00 0.00 0.00 3.69
2847 2989 0.396811 ACACGGTTAAAGGCAGAGCT 59.603 50.000 0.00 0.00 0.00 4.09
2860 3002 5.034852 TCCATATCAAATCATCACACGGT 57.965 39.130 0.00 0.00 0.00 4.83
2870 3012 7.661847 AGGTACTCGGATTTTCCATATCAAATC 59.338 37.037 0.00 0.00 38.27 2.17
2882 3024 2.168728 GAGCTCCAGGTACTCGGATTTT 59.831 50.000 0.87 0.00 34.60 1.82
2883 3025 1.757699 GAGCTCCAGGTACTCGGATTT 59.242 52.381 0.87 0.00 34.60 2.17
2957 3100 0.606401 CCATCGCCAGAAACCACACT 60.606 55.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.