Multiple sequence alignment - TraesCS6A01G225500

Loading Multiple Alignment...

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 TraesCS6A01G225500 chr6A 100.000 2906 0 0 1 2906 424086505 424089410 0.000000e+00 5367.0
1 TraesCS6A01G225500 chr6A 78.846 104 18 3 2805 2905 262877542 262877440 1.870000e-07 67.6
2 TraesCS6A01G225500 chr6A 100.000 30 0 0 2744 2773 153831556 153831585 4.050000e-04 56.5
3 TraesCS6A01G225500 chr6D 93.755 2770 126 24 1 2754 296859799 296862537 0.000000e+00 4113.0
4 TraesCS6A01G225500 chr6D 91.538 130 11 0 2775 2904 196767425 196767296 2.300000e-41 180.0
5 TraesCS6A01G225500 chr6B 94.919 2165 67 22 612 2753 460092507 460090363 0.000000e+00 3349.0
6 TraesCS6A01G225500 chr6B 88.548 620 56 9 1 618 460093880 460093274 0.000000e+00 737.0
7 TraesCS6A01G225500 chr6B 90.909 132 12 0 2775 2906 286708588 286708457 8.280000e-41 178.0
8 TraesCS6A01G225500 chr3B 97.561 246 6 0 1791 2036 242897783 242897538 3.460000e-114 422.0
9 TraesCS6A01G225500 chr4B 97.872 188 4 0 1849 2036 241353741 241353928 2.790000e-85 326.0
10 TraesCS6A01G225500 chr4B 100.000 29 0 0 2744 2772 5732673 5732645 1.000000e-03 54.7
11 TraesCS6A01G225500 chr2A 97.872 188 4 0 1849 2036 135190494 135190307 2.790000e-85 326.0
12 TraesCS6A01G225500 chr2A 97.872 188 4 0 1849 2036 160160122 160160309 2.790000e-85 326.0
13 TraesCS6A01G225500 chr2A 98.361 183 3 0 1854 2036 135189496 135189314 3.610000e-84 322.0
14 TraesCS6A01G225500 chr2A 96.000 75 2 1 1962 2036 159927832 159927905 1.410000e-23 121.0
15 TraesCS6A01G225500 chr7D 89.542 153 15 1 2752 2904 102785148 102784997 2.960000e-45 193.0
16 TraesCS6A01G225500 chr7D 90.909 132 9 2 2775 2904 147465117 147465247 1.070000e-39 174.0
17 TraesCS6A01G225500 chr7D 90.769 130 11 1 2775 2904 111478847 111478719 3.850000e-39 172.0
18 TraesCS6A01G225500 chr1B 90.909 132 10 2 2774 2905 316020163 316020292 2.980000e-40 176.0
19 TraesCS6A01G225500 chr1B 87.195 164 8 6 2752 2904 51968841 51968680 1.070000e-39 174.0
20 TraesCS6A01G225500 chr4D 90.909 132 9 2 2775 2904 433364905 433364775 1.070000e-39 174.0
21 TraesCS6A01G225500 chr3D 90.152 132 13 0 2775 2906 56684683 56684552 3.850000e-39 172.0
22 TraesCS6A01G225500 chr2B 79.245 159 21 4 2744 2891 123278397 123278554 1.840000e-17 100.0
23 TraesCS6A01G225500 chr2D 77.714 175 25 6 2744 2905 289313265 289313092 8.570000e-16 95.3
24 TraesCS6A01G225500 chr5A 96.970 33 1 0 2744 2776 635952565 635952597 4.050000e-04 56.5
25 TraesCS6A01G225500 chr7B 96.875 32 1 0 579 610 636877600 636877631 1.000000e-03 54.7
26 TraesCS6A01G225500 chr1D 100.000 29 0 0 2748 2776 248109112 248109084 1.000000e-03 54.7
27 TraesCS6A01G225500 chr1D 100.000 29 0 0 2748 2776 248199586 248199558 1.000000e-03 54.7


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 TraesCS6A01G225500 chr6A 424086505 424089410 2905 False 5367 5367 100.0000 1 2906 1 chr6A.!!$F2 2905
1 TraesCS6A01G225500 chr6D 296859799 296862537 2738 False 4113 4113 93.7550 1 2754 1 chr6D.!!$F1 2753
2 TraesCS6A01G225500 chr6B 460090363 460093880 3517 True 2043 3349 91.7335 1 2753 2 chr6B.!!$R2 2752
3 TraesCS6A01G225500 chr2A 135189314 135190494 1180 True 324 326 98.1165 1849 2036 2 chr2A.!!$R1 187

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
379 382 0.514691 CTCGCACAAGAAACAGCTCC 59.485 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2375 3160 0.107508 CCCCGACTGATTGAGCACAT 60.108 55.0 0.0 0.0 0.0 3.21 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
56 57 1.600023 CCCACTAGCGTCACCAAAAA 58.400 50.000 0.00 0.00 0.00 1.94
75 76 7.226523 ACCAAAAACATTTGAAAGTTATGCCTC 59.773 33.333 3.00 0.00 33.95 4.70
76 77 7.307930 CCAAAAACATTTGAAAGTTATGCCTCC 60.308 37.037 3.00 0.00 33.95 4.30
197 198 5.005094 CCCCATAAACCGTTTTTACAGAGA 58.995 41.667 0.96 0.00 0.00 3.10
307 310 9.167311 GGTATTATGTGTGAACTCTCTTGAAAT 57.833 33.333 0.00 0.00 0.00 2.17
343 346 8.903820 AGCATTTTAGAAAACTTTATATCCGCT 58.096 29.630 0.00 0.00 0.00 5.52
379 382 0.514691 CTCGCACAAGAAACAGCTCC 59.485 55.000 0.00 0.00 0.00 4.70
425 428 3.786516 TCGTCGCTTATTCACCACATA 57.213 42.857 0.00 0.00 0.00 2.29
492 495 4.035792 ACGTCGACATTTCCAAATTCACAA 59.964 37.500 17.16 0.00 0.00 3.33
678 1453 2.650116 CGTGCCAGCTAGGTGGAGT 61.650 63.158 38.78 0.00 40.44 3.85
1209 1990 1.153647 CTGCATCGTCGCCCTTGTA 60.154 57.895 0.00 0.00 0.00 2.41
1251 2032 1.737236 CTGAATTTGGCCATCGACGAA 59.263 47.619 6.09 0.00 0.00 3.85
1413 2194 0.823460 CGCCAATTTGCCATACCCTT 59.177 50.000 0.00 0.00 0.00 3.95
1596 2377 3.335534 GTTCTTGTGGCGTCGCGT 61.336 61.111 11.75 0.00 0.00 6.01
1710 2491 5.350504 ACTCCTGTAGACTCCATTTGATG 57.649 43.478 0.00 0.00 0.00 3.07
1812 2593 2.470781 CGTCGTTTTCATCTCGCTTGTC 60.471 50.000 0.00 0.00 0.00 3.18
1917 2698 4.959596 AACTGAATGAATAGCAGCACTG 57.040 40.909 0.00 0.00 33.03 3.66
2073 2854 2.231964 TGGCTCTAAATGCTTGGCAAAG 59.768 45.455 0.00 0.00 43.62 2.77
2075 2856 3.505836 GCTCTAAATGCTTGGCAAAGTC 58.494 45.455 2.03 0.00 43.62 3.01
2105 2886 1.550524 GCACTCTGGTCTGGTGATGTA 59.449 52.381 0.00 0.00 33.32 2.29
2229 3012 8.484641 TCTAGCAACACTGATTATTTTCTCTG 57.515 34.615 0.00 0.00 0.00 3.35
2230 3013 8.097038 TCTAGCAACACTGATTATTTTCTCTGT 58.903 33.333 0.00 0.00 0.00 3.41
2264 3048 5.777802 TGGCGATTTTTCTTGCATTTTAGA 58.222 33.333 0.00 0.00 0.00 2.10
2314 3098 6.685657 TGCTGTATTCATTTGTATGTTTGCA 58.314 32.000 0.00 0.00 33.34 4.08
2340 3124 3.788227 TGAACTGCAACTCAACCCTAT 57.212 42.857 0.00 0.00 0.00 2.57
2375 3160 0.770499 TGGTTGGCTCCACAATCTCA 59.230 50.000 0.00 0.00 32.71 3.27
2390 3175 4.634883 ACAATCTCATGTGCTCAATCAGTC 59.365 41.667 0.00 0.00 30.82 3.51
2473 3260 2.025887 ACCATCAGGCCTAAAGGAACTG 60.026 50.000 20.04 12.44 40.68 3.16
2495 3282 2.203001 CCCACGCACACACACTCA 60.203 61.111 0.00 0.00 0.00 3.41
2554 3352 1.017387 GAGGGCCACGCAAATCTTAG 58.983 55.000 6.18 0.00 0.00 2.18
2557 3355 1.679032 GGGCCACGCAAATCTTAGAGT 60.679 52.381 4.39 0.00 0.00 3.24
2608 3410 6.600032 TCAGAGGAGTCTAAGACATGAACTAC 59.400 42.308 0.00 0.00 34.60 2.73
2609 3411 6.375736 CAGAGGAGTCTAAGACATGAACTACA 59.624 42.308 0.00 0.00 34.60 2.74
2636 3438 3.010420 GACATCACTTTAGAACAGCCCC 58.990 50.000 0.00 0.00 0.00 5.80
2728 3531 4.347453 CAGCCGCCAAACACCAGC 62.347 66.667 0.00 0.00 0.00 4.85
2740 3544 0.980231 ACACCAGCTCTCCATCCCTC 60.980 60.000 0.00 0.00 0.00 4.30
2747 3551 1.075301 TCTCCATCCCTCCGATGCA 60.075 57.895 0.00 0.00 46.17 3.96
2754 3558 0.398522 TCCCTCCGATGCATGGTACT 60.399 55.000 2.46 0.00 0.00 2.73
2755 3559 0.034059 CCCTCCGATGCATGGTACTC 59.966 60.000 2.46 0.00 0.00 2.59
2756 3560 0.034059 CCTCCGATGCATGGTACTCC 59.966 60.000 2.46 0.00 0.00 3.85
2757 3561 0.034059 CTCCGATGCATGGTACTCCC 59.966 60.000 2.46 0.00 0.00 4.30
2758 3562 0.398522 TCCGATGCATGGTACTCCCT 60.399 55.000 2.46 0.00 0.00 4.20
2759 3563 0.034059 CCGATGCATGGTACTCCCTC 59.966 60.000 2.46 0.00 0.00 4.30
2760 3564 0.034059 CGATGCATGGTACTCCCTCC 59.966 60.000 2.46 0.00 0.00 4.30
2761 3565 0.034059 GATGCATGGTACTCCCTCCG 59.966 60.000 2.46 0.00 0.00 4.63
2762 3566 0.691078 ATGCATGGTACTCCCTCCGT 60.691 55.000 0.00 0.00 0.00 4.69
2763 3567 0.907704 TGCATGGTACTCCCTCCGTT 60.908 55.000 0.00 0.00 0.00 4.44
2764 3568 0.179081 GCATGGTACTCCCTCCGTTC 60.179 60.000 0.00 0.00 0.00 3.95
2765 3569 0.464452 CATGGTACTCCCTCCGTTCC 59.536 60.000 0.00 0.00 0.00 3.62
2766 3570 0.338814 ATGGTACTCCCTCCGTTCCT 59.661 55.000 0.00 0.00 0.00 3.36
2767 3571 1.002069 TGGTACTCCCTCCGTTCCTA 58.998 55.000 0.00 0.00 0.00 2.94
2768 3572 1.358787 TGGTACTCCCTCCGTTCCTAA 59.641 52.381 0.00 0.00 0.00 2.69
2769 3573 2.225343 TGGTACTCCCTCCGTTCCTAAA 60.225 50.000 0.00 0.00 0.00 1.85
2770 3574 3.036819 GGTACTCCCTCCGTTCCTAAAT 58.963 50.000 0.00 0.00 0.00 1.40
2771 3575 4.218312 GGTACTCCCTCCGTTCCTAAATA 58.782 47.826 0.00 0.00 0.00 1.40
2772 3576 4.038522 GGTACTCCCTCCGTTCCTAAATAC 59.961 50.000 0.00 0.00 0.00 1.89
2773 3577 3.716431 ACTCCCTCCGTTCCTAAATACA 58.284 45.455 0.00 0.00 0.00 2.29
2774 3578 4.098894 ACTCCCTCCGTTCCTAAATACAA 58.901 43.478 0.00 0.00 0.00 2.41
2775 3579 4.161754 ACTCCCTCCGTTCCTAAATACAAG 59.838 45.833 0.00 0.00 0.00 3.16
2776 3580 4.355549 TCCCTCCGTTCCTAAATACAAGA 58.644 43.478 0.00 0.00 0.00 3.02
2777 3581 4.404715 TCCCTCCGTTCCTAAATACAAGAG 59.595 45.833 0.00 0.00 0.00 2.85
2778 3582 4.404715 CCCTCCGTTCCTAAATACAAGAGA 59.595 45.833 0.00 0.00 0.00 3.10
2779 3583 5.070580 CCCTCCGTTCCTAAATACAAGAGAT 59.929 44.000 0.00 0.00 0.00 2.75
2780 3584 6.408206 CCCTCCGTTCCTAAATACAAGAGATT 60.408 42.308 0.00 0.00 0.00 2.40
2781 3585 7.048512 CCTCCGTTCCTAAATACAAGAGATTT 58.951 38.462 0.00 0.00 0.00 2.17
2782 3586 7.224949 CCTCCGTTCCTAAATACAAGAGATTTC 59.775 40.741 0.00 0.00 0.00 2.17
2783 3587 7.617225 TCCGTTCCTAAATACAAGAGATTTCA 58.383 34.615 0.00 0.00 0.00 2.69
2784 3588 7.548075 TCCGTTCCTAAATACAAGAGATTTCAC 59.452 37.037 0.00 0.00 0.00 3.18
2785 3589 7.549488 CCGTTCCTAAATACAAGAGATTTCACT 59.451 37.037 0.00 0.00 0.00 3.41
2786 3590 9.582431 CGTTCCTAAATACAAGAGATTTCACTA 57.418 33.333 0.00 0.00 0.00 2.74
2795 3599 7.482169 ACAAGAGATTTCACTATAGACCACA 57.518 36.000 6.78 0.00 0.00 4.17
2796 3600 8.083828 ACAAGAGATTTCACTATAGACCACAT 57.916 34.615 6.78 0.00 0.00 3.21
2797 3601 9.201989 ACAAGAGATTTCACTATAGACCACATA 57.798 33.333 6.78 0.00 0.00 2.29
2814 3618 8.970020 AGACCACATATAAAGCAAAATGAATGA 58.030 29.630 0.00 0.00 0.00 2.57
2815 3619 9.585099 GACCACATATAAAGCAAAATGAATGAA 57.415 29.630 0.00 0.00 0.00 2.57
2824 3628 8.976986 AAAGCAAAATGAATGAATCTACACTC 57.023 30.769 0.00 0.00 0.00 3.51
2825 3629 7.934855 AGCAAAATGAATGAATCTACACTCT 57.065 32.000 0.00 0.00 0.00 3.24
2826 3630 7.759465 AGCAAAATGAATGAATCTACACTCTG 58.241 34.615 0.00 0.00 0.00 3.35
2827 3631 7.609146 AGCAAAATGAATGAATCTACACTCTGA 59.391 33.333 0.00 0.00 0.00 3.27
2828 3632 8.239314 GCAAAATGAATGAATCTACACTCTGAA 58.761 33.333 0.00 0.00 0.00 3.02
2832 3636 7.312657 TGAATGAATCTACACTCTGAAATGC 57.687 36.000 0.00 0.00 0.00 3.56
2833 3637 6.880529 TGAATGAATCTACACTCTGAAATGCA 59.119 34.615 0.00 0.00 0.00 3.96
2834 3638 7.555195 TGAATGAATCTACACTCTGAAATGCAT 59.445 33.333 0.00 0.00 0.00 3.96
2835 3639 6.915544 TGAATCTACACTCTGAAATGCATC 57.084 37.500 0.00 0.00 0.00 3.91
2836 3640 6.647229 TGAATCTACACTCTGAAATGCATCT 58.353 36.000 0.00 0.00 0.00 2.90
2837 3641 7.785033 TGAATCTACACTCTGAAATGCATCTA 58.215 34.615 0.00 0.00 0.00 1.98
2838 3642 8.427276 TGAATCTACACTCTGAAATGCATCTAT 58.573 33.333 0.00 0.00 0.00 1.98
2839 3643 9.920133 GAATCTACACTCTGAAATGCATCTATA 57.080 33.333 0.00 0.00 0.00 1.31
2841 3645 9.872721 ATCTACACTCTGAAATGCATCTATATG 57.127 33.333 0.00 0.00 36.09 1.78
2858 3662 9.555727 CATCTATATGCATCCATATGTGATTCA 57.444 33.333 0.19 5.63 42.94 2.57
2863 3667 7.625828 ATGCATCCATATGTGATTCATAGTG 57.374 36.000 13.51 2.84 41.55 2.74
2864 3668 6.771573 TGCATCCATATGTGATTCATAGTGA 58.228 36.000 1.24 0.00 41.55 3.41
2865 3669 7.225725 TGCATCCATATGTGATTCATAGTGAA 58.774 34.615 1.24 0.00 41.55 3.18
2866 3670 7.720515 TGCATCCATATGTGATTCATAGTGAAA 59.279 33.333 1.24 0.00 41.55 2.69
2867 3671 8.737175 GCATCCATATGTGATTCATAGTGAAAT 58.263 33.333 1.24 0.00 41.55 2.17
2870 3674 9.716531 TCCATATGTGATTCATAGTGAAATCTC 57.283 33.333 1.24 0.00 40.12 2.75
2871 3675 9.722184 CCATATGTGATTCATAGTGAAATCTCT 57.278 33.333 1.24 0.00 40.12 3.10
2874 3678 8.809159 ATGTGATTCATAGTGAAATCTCTACG 57.191 34.615 0.00 0.00 40.12 3.51
2875 3679 7.996385 TGTGATTCATAGTGAAATCTCTACGA 58.004 34.615 0.00 0.00 40.12 3.43
2876 3680 8.466798 TGTGATTCATAGTGAAATCTCTACGAA 58.533 33.333 4.23 4.23 40.12 3.85
2877 3681 8.963130 GTGATTCATAGTGAAATCTCTACGAAG 58.037 37.037 7.00 0.00 40.12 3.79
2878 3682 8.903820 TGATTCATAGTGAAATCTCTACGAAGA 58.096 33.333 7.00 0.00 40.12 2.87
2879 3683 9.176181 GATTCATAGTGAAATCTCTACGAAGAC 57.824 37.037 7.00 2.22 40.12 3.01
2880 3684 7.867305 TCATAGTGAAATCTCTACGAAGACT 57.133 36.000 0.00 0.00 0.00 3.24
2881 3685 8.282455 TCATAGTGAAATCTCTACGAAGACTT 57.718 34.615 0.00 0.00 0.00 3.01
2882 3686 9.392259 TCATAGTGAAATCTCTACGAAGACTTA 57.608 33.333 0.00 0.00 0.00 2.24
2895 3699 9.941664 TCTACGAAGACTTATATTTAGAAACGG 57.058 33.333 0.00 0.00 0.00 4.44
2896 3700 9.941664 CTACGAAGACTTATATTTAGAAACGGA 57.058 33.333 0.00 0.00 0.00 4.69
2897 3701 8.853469 ACGAAGACTTATATTTAGAAACGGAG 57.147 34.615 0.00 0.00 0.00 4.63
2898 3702 7.919621 ACGAAGACTTATATTTAGAAACGGAGG 59.080 37.037 0.00 0.00 0.00 4.30
2899 3703 7.381678 CGAAGACTTATATTTAGAAACGGAGGG 59.618 40.741 0.00 0.00 0.00 4.30
2900 3704 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
2901 3705 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
2902 3706 7.564292 AGACTTATATTTAGAAACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
2903 3707 8.773033 ACTTATATTTAGAAACGGAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
2904 3708 8.637099 ACTTATATTTAGAAACGGAGGGAGTAC 58.363 37.037 0.00 0.00 0.00 2.73
2905 3709 8.537728 TTATATTTAGAAACGGAGGGAGTACA 57.462 34.615 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 4.677182 AGGGAGGCATAACTTTCAAATGT 58.323 39.130 0.00 0.00 0.00 2.71
75 76 2.396590 TGCTAGGCGTAAAAGAAGGG 57.603 50.000 0.00 0.00 0.00 3.95
76 77 3.798202 AGATGCTAGGCGTAAAAGAAGG 58.202 45.455 0.00 0.00 0.00 3.46
210 212 8.246180 GGCCACTTATAATCAATTGACATATGG 58.754 37.037 11.07 15.64 0.00 2.74
221 223 3.275143 CGGTGTGGCCACTTATAATCAA 58.725 45.455 34.75 10.14 41.53 2.57
254 257 7.826260 ACCGGCACAAATAATTCTTTTATTG 57.174 32.000 0.00 0.00 0.00 1.90
285 288 8.675705 TTCATTTCAAGAGAGTTCACACATAA 57.324 30.769 0.00 0.00 0.00 1.90
343 346 2.991190 GCGAGTGGATTTTAGACGAACA 59.009 45.455 0.00 0.00 0.00 3.18
520 523 8.149973 TCTTAGTTTCATTTCGTAACTTTGCT 57.850 30.769 0.00 0.00 36.68 3.91
569 572 7.329499 TGTAACTTTATTTATACCAGCGACCA 58.671 34.615 0.00 0.00 0.00 4.02
570 573 7.775397 TGTAACTTTATTTATACCAGCGACC 57.225 36.000 0.00 0.00 0.00 4.79
690 1465 2.598394 GCAGGGCTGGCTCAAACA 60.598 61.111 0.00 0.00 0.00 2.83
898 1679 1.810030 GATTCGCCGTGGTCACTCC 60.810 63.158 0.00 0.00 0.00 3.85
1209 1990 3.250744 CGTATGTGTCCATGTCGAAACT 58.749 45.455 0.00 0.00 34.22 2.66
1251 2032 5.152623 TGTCGAATTTCAGGAGAGTGATT 57.847 39.130 0.00 0.00 0.00 2.57
1413 2194 3.184382 TCTGAACTGATGGACCTGGTA 57.816 47.619 0.00 0.00 0.00 3.25
1602 2383 0.877071 CAAAGACGTGCAGCCAAGAT 59.123 50.000 0.00 0.00 0.00 2.40
1710 2491 3.006247 GACCATGAGAGCAAAGGAGAAC 58.994 50.000 0.00 0.00 0.00 3.01
1917 2698 5.066505 CACATGTAACTTCCTGATTAAGCCC 59.933 44.000 0.00 0.00 0.00 5.19
2105 2886 2.424956 GCCTTGAATGCCTCGAGAAAAT 59.575 45.455 15.71 1.03 37.74 1.82
2270 3054 2.418368 TAAGATGCACAGGCCGATTT 57.582 45.000 0.00 0.00 40.13 2.17
2273 3057 3.384816 CATAAGATGCACAGGCCGA 57.615 52.632 0.00 0.00 40.13 5.54
2314 3098 3.319122 GGTTGAGTTGCAGTTCATTTCCT 59.681 43.478 3.44 0.00 0.00 3.36
2340 3124 2.880268 CAACCATCAACAGAGTGCAGAA 59.120 45.455 0.00 0.00 0.00 3.02
2375 3160 0.107508 CCCCGACTGATTGAGCACAT 60.108 55.000 0.00 0.00 0.00 3.21
2464 3251 0.744281 CGTGGGTTTGCAGTTCCTTT 59.256 50.000 0.00 0.00 0.00 3.11
2473 3260 2.278531 GTGTGTGCGTGGGTTTGC 60.279 61.111 0.00 0.00 0.00 3.68
2495 3282 4.931661 TTGTCTCGACTGTCTTAGGTTT 57.068 40.909 6.21 0.00 0.00 3.27
2546 3344 5.589192 CGTGATCCGGTAACTCTAAGATTT 58.411 41.667 0.00 0.00 0.00 2.17
2554 3352 0.527817 CCTGCGTGATCCGGTAACTC 60.528 60.000 0.00 0.00 36.94 3.01
2557 3355 0.387929 GATCCTGCGTGATCCGGTAA 59.612 55.000 0.00 0.00 36.04 2.85
2608 3410 6.634436 GCTGTTCTAAAGTGATGTCTTTTGTG 59.366 38.462 0.00 0.00 38.40 3.33
2609 3411 6.238759 GGCTGTTCTAAAGTGATGTCTTTTGT 60.239 38.462 0.00 0.00 38.40 2.83
2636 3438 4.497006 GCTGCCTATGCTGTTTCATACTTG 60.497 45.833 0.00 0.00 38.57 3.16
2719 3522 0.329596 GGGATGGAGAGCTGGTGTTT 59.670 55.000 0.00 0.00 0.00 2.83
2723 3526 1.383803 GGAGGGATGGAGAGCTGGT 60.384 63.158 0.00 0.00 0.00 4.00
2740 3544 0.034059 GAGGGAGTACCATGCATCGG 59.966 60.000 12.06 12.06 43.89 4.18
2747 3551 0.338814 AGGAACGGAGGGAGTACCAT 59.661 55.000 0.00 0.00 43.89 3.55
2754 3558 4.355549 TCTTGTATTTAGGAACGGAGGGA 58.644 43.478 0.00 0.00 0.00 4.20
2755 3559 4.404715 TCTCTTGTATTTAGGAACGGAGGG 59.595 45.833 0.00 0.00 0.00 4.30
2756 3560 5.593679 TCTCTTGTATTTAGGAACGGAGG 57.406 43.478 0.00 0.00 0.00 4.30
2757 3561 7.764443 TGAAATCTCTTGTATTTAGGAACGGAG 59.236 37.037 0.00 0.00 0.00 4.63
2758 3562 7.548075 GTGAAATCTCTTGTATTTAGGAACGGA 59.452 37.037 0.00 0.00 0.00 4.69
2759 3563 7.549488 AGTGAAATCTCTTGTATTTAGGAACGG 59.451 37.037 0.00 0.00 0.00 4.44
2760 3564 8.480643 AGTGAAATCTCTTGTATTTAGGAACG 57.519 34.615 0.00 0.00 0.00 3.95
2769 3573 9.201989 TGTGGTCTATAGTGAAATCTCTTGTAT 57.798 33.333 0.00 0.00 0.00 2.29
2770 3574 8.589701 TGTGGTCTATAGTGAAATCTCTTGTA 57.410 34.615 0.00 0.00 0.00 2.41
2771 3575 7.482169 TGTGGTCTATAGTGAAATCTCTTGT 57.518 36.000 0.00 0.00 0.00 3.16
2788 3592 8.970020 TCATTCATTTTGCTTTATATGTGGTCT 58.030 29.630 0.00 0.00 0.00 3.85
2789 3593 9.585099 TTCATTCATTTTGCTTTATATGTGGTC 57.415 29.630 0.00 0.00 0.00 4.02
2799 3603 8.800332 AGAGTGTAGATTCATTCATTTTGCTTT 58.200 29.630 0.00 0.00 0.00 3.51
2800 3604 8.242053 CAGAGTGTAGATTCATTCATTTTGCTT 58.758 33.333 0.00 0.00 0.00 3.91
2801 3605 7.609146 TCAGAGTGTAGATTCATTCATTTTGCT 59.391 33.333 0.00 0.00 0.00 3.91
2802 3606 7.755591 TCAGAGTGTAGATTCATTCATTTTGC 58.244 34.615 0.00 0.00 0.00 3.68
2806 3610 8.404000 GCATTTCAGAGTGTAGATTCATTCATT 58.596 33.333 0.00 0.00 0.00 2.57
2807 3611 7.555195 TGCATTTCAGAGTGTAGATTCATTCAT 59.445 33.333 0.00 0.00 0.00 2.57
2808 3612 6.880529 TGCATTTCAGAGTGTAGATTCATTCA 59.119 34.615 0.00 0.00 0.00 2.57
2809 3613 7.312657 TGCATTTCAGAGTGTAGATTCATTC 57.687 36.000 0.00 0.00 0.00 2.67
2810 3614 7.774157 AGATGCATTTCAGAGTGTAGATTCATT 59.226 33.333 0.00 0.00 0.00 2.57
2811 3615 7.281098 AGATGCATTTCAGAGTGTAGATTCAT 58.719 34.615 0.00 0.00 0.00 2.57
2812 3616 6.647229 AGATGCATTTCAGAGTGTAGATTCA 58.353 36.000 0.00 0.00 0.00 2.57
2813 3617 8.830201 ATAGATGCATTTCAGAGTGTAGATTC 57.170 34.615 0.00 0.00 0.00 2.52
2815 3619 9.872721 CATATAGATGCATTTCAGAGTGTAGAT 57.127 33.333 0.00 0.00 0.00 1.98
2832 3636 9.555727 TGAATCACATATGGATGCATATAGATG 57.444 33.333 23.16 18.87 36.43 2.90
2837 3641 9.338622 CACTATGAATCACATATGGATGCATAT 57.661 33.333 22.46 13.50 40.69 1.78
2838 3642 8.542080 TCACTATGAATCACATATGGATGCATA 58.458 33.333 21.64 21.64 40.64 3.14
2839 3643 7.399634 TCACTATGAATCACATATGGATGCAT 58.600 34.615 21.70 21.70 42.41 3.96
2840 3644 6.771573 TCACTATGAATCACATATGGATGCA 58.228 36.000 13.95 13.95 40.18 3.96
2841 3645 7.677454 TTCACTATGAATCACATATGGATGC 57.323 36.000 7.80 6.46 40.18 3.91
2844 3648 9.716531 GAGATTTCACTATGAATCACATATGGA 57.283 33.333 7.80 2.05 40.18 3.41
2845 3649 9.722184 AGAGATTTCACTATGAATCACATATGG 57.278 33.333 7.80 0.00 40.18 2.74
2848 3652 9.899226 CGTAGAGATTTCACTATGAATCACATA 57.101 33.333 0.00 0.00 36.11 2.29
2849 3653 8.633561 TCGTAGAGATTTCACTATGAATCACAT 58.366 33.333 4.96 0.00 36.11 3.21
2850 3654 7.996385 TCGTAGAGATTTCACTATGAATCACA 58.004 34.615 4.96 0.00 36.11 3.58
2851 3655 8.858003 TTCGTAGAGATTTCACTATGAATCAC 57.142 34.615 12.69 0.00 38.89 3.06
2852 3656 8.903820 TCTTCGTAGAGATTTCACTATGAATCA 58.096 33.333 15.46 7.11 41.10 2.57
2853 3657 9.176181 GTCTTCGTAGAGATTTCACTATGAATC 57.824 37.037 15.46 10.58 41.10 2.52
2854 3658 8.908903 AGTCTTCGTAGAGATTTCACTATGAAT 58.091 33.333 15.46 4.15 41.10 2.57
2855 3659 8.282455 AGTCTTCGTAGAGATTTCACTATGAA 57.718 34.615 14.74 14.74 40.33 2.57
2856 3660 7.867305 AGTCTTCGTAGAGATTTCACTATGA 57.133 36.000 0.00 3.68 38.43 2.15
2869 3673 9.941664 CCGTTTCTAAATATAAGTCTTCGTAGA 57.058 33.333 0.00 0.00 0.00 2.59
2870 3674 9.941664 TCCGTTTCTAAATATAAGTCTTCGTAG 57.058 33.333 0.00 0.00 0.00 3.51
2871 3675 9.941664 CTCCGTTTCTAAATATAAGTCTTCGTA 57.058 33.333 0.00 0.00 0.00 3.43
2872 3676 7.919621 CCTCCGTTTCTAAATATAAGTCTTCGT 59.080 37.037 0.00 0.00 0.00 3.85
2873 3677 7.381678 CCCTCCGTTTCTAAATATAAGTCTTCG 59.618 40.741 0.00 0.00 0.00 3.79
2874 3678 8.419442 TCCCTCCGTTTCTAAATATAAGTCTTC 58.581 37.037 0.00 0.00 0.00 2.87
2875 3679 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
2876 3680 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
2877 3681 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
2878 3682 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
2879 3683 8.636213 TGTACTCCCTCCGTTTCTAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
2880 3684 8.537728 TGTACTCCCTCCGTTTCTAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.