Multiple sequence alignment - TraesCS4A01G072600

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 TraesCS4A01G072600 chr4A 100.000 7740 0 0 1 7740 70814719 70806980 0.000000e+00 14294.0
1 TraesCS4A01G072600 chr4A 96.840 633 20 0 4 636 132961261 132961893 0.000000e+00 1059.0
2 TraesCS4A01G072600 chr4A 81.132 477 84 6 6850 7323 664908366 664908839 2.040000e-100 377.0
3 TraesCS4A01G072600 chr4D 95.434 4774 133 31 2922 7645 389229153 389224415 0.000000e+00 7529.0
4 TraesCS4A01G072600 chr4D 94.764 2292 63 11 636 2921 389231445 389229205 0.000000e+00 3515.0
5 TraesCS4A01G072600 chr4D 80.882 476 87 4 6850 7323 327726186 327726659 9.480000e-99 372.0
6 TraesCS4A01G072600 chr4D 95.181 83 4 0 7658 7740 389224432 389224350 1.750000e-26 132.0
7 TraesCS4A01G072600 chr4D 90.385 52 3 1 3128 3177 40845339 40845288 5.010000e-07 67.6
8 TraesCS4A01G072600 chr4B 95.430 4530 120 27 3169 7646 479155283 479150789 0.000000e+00 7138.0
9 TraesCS4A01G072600 chr4B 95.129 1396 51 7 1542 2921 479157008 479155614 0.000000e+00 2185.0
10 TraesCS4A01G072600 chr4B 94.641 821 40 3 636 1455 479158352 479157535 0.000000e+00 1269.0
11 TraesCS4A01G072600 chr4B 95.109 184 9 0 2922 3105 479155510 479155327 2.730000e-74 291.0
12 TraesCS4A01G072600 chr4B 77.358 477 98 9 6850 7323 350461878 350461409 2.750000e-69 274.0
13 TraesCS4A01G072600 chr4B 96.386 83 3 0 7658 7740 479150807 479150725 3.770000e-28 137.0
14 TraesCS4A01G072600 chr7A 97.027 639 19 0 1 639 340940687 340941325 0.000000e+00 1075.0
15 TraesCS4A01G072600 chr7A 96.557 639 21 1 1 638 375072148 375072786 0.000000e+00 1057.0
16 TraesCS4A01G072600 chr5A 96.850 635 20 0 1 635 219670769 219671403 0.000000e+00 1062.0
17 TraesCS4A01G072600 chr5A 96.850 635 20 0 1 635 317041435 317042069 0.000000e+00 1062.0
18 TraesCS4A01G072600 chr5A 96.406 640 23 0 1 640 386901650 386902289 0.000000e+00 1055.0
19 TraesCS4A01G072600 chr1A 96.708 638 21 0 1 638 594088788 594089425 0.000000e+00 1062.0
20 TraesCS4A01G072600 chr1A 96.693 635 21 0 4 638 349401239 349400605 0.000000e+00 1057.0
21 TraesCS4A01G072600 chr3A 96.840 633 20 0 4 636 729105859 729105227 0.000000e+00 1059.0
22 TraesCS4A01G072600 chrUn 80.503 477 87 6 6850 7323 115107875 115107402 2.050000e-95 361.0
23 TraesCS4A01G072600 chr2D 80.042 476 89 5 6850 7323 249892466 249891995 1.600000e-91 348.0
24 TraesCS4A01G072600 chr2D 87.273 55 3 2 3128 3178 87242226 87242172 8.390000e-05 60.2
25 TraesCS4A01G072600 chr2D 100.000 31 0 0 3128 3158 348194641 348194671 3.020000e-04 58.4
26 TraesCS4A01G072600 chr5B 79.874 477 89 7 6850 7323 57124526 57124998 7.440000e-90 342.0
27 TraesCS4A01G072600 chr3B 79.455 477 92 6 6850 7323 327057895 327058368 4.480000e-87 333.0
28 TraesCS4A01G072600 chr3B 100.000 31 0 0 3128 3158 727790678 727790708 3.020000e-04 58.4
29 TraesCS4A01G072600 chr7D 92.000 50 4 0 3128 3177 592075610 592075561 3.870000e-08 71.3
30 TraesCS4A01G072600 chr6D 100.000 31 0 0 3128 3158 453809364 453809394 3.020000e-04 58.4
31 TraesCS4A01G072600 chr6D 100.000 30 0 0 3128 3157 461795552 461795523 1.000000e-03 56.5
32 TraesCS4A01G072600 chr6B 100.000 30 0 0 3128 3157 151608230 151608259 1.000000e-03 56.5


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 TraesCS4A01G072600 chr4A 70806980 70814719 7739 True 14294.000000 14294 100.000000 1 7740 1 chr4A.!!$R1 7739
1 TraesCS4A01G072600 chr4A 132961261 132961893 632 False 1059.000000 1059 96.840000 4 636 1 chr4A.!!$F1 632
2 TraesCS4A01G072600 chr4D 389224350 389231445 7095 True 3725.333333 7529 95.126333 636 7740 3 chr4D.!!$R2 7104
3 TraesCS4A01G072600 chr4B 479150725 479158352 7627 True 2204.000000 7138 95.339000 636 7740 5 chr4B.!!$R2 7104
4 TraesCS4A01G072600 chr7A 340940687 340941325 638 False 1075.000000 1075 97.027000 1 639 1 chr7A.!!$F1 638
5 TraesCS4A01G072600 chr7A 375072148 375072786 638 False 1057.000000 1057 96.557000 1 638 1 chr7A.!!$F2 637
6 TraesCS4A01G072600 chr5A 219670769 219671403 634 False 1062.000000 1062 96.850000 1 635 1 chr5A.!!$F1 634
7 TraesCS4A01G072600 chr5A 317041435 317042069 634 False 1062.000000 1062 96.850000 1 635 1 chr5A.!!$F2 634
8 TraesCS4A01G072600 chr5A 386901650 386902289 639 False 1055.000000 1055 96.406000 1 640 1 chr5A.!!$F3 639
9 TraesCS4A01G072600 chr1A 594088788 594089425 637 False 1062.000000 1062 96.708000 1 638 1 chr1A.!!$F1 637
10 TraesCS4A01G072600 chr1A 349400605 349401239 634 True 1057.000000 1057 96.693000 4 638 1 chr1A.!!$R1 634
11 TraesCS4A01G072600 chr3A 729105227 729105859 632 True 1059.000000 1059 96.840000 4 636 1 chr3A.!!$R1 632

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
269 270 0.043183 TCAGGCCCTCTTGATGGAGA 59.957 55.000 0.00 0.00 35.52 3.71 F
712 714 0.755698 AGAAGAGGATAAGCGGCCGA 60.756 55.000 33.48 8.89 0.00 5.54 F
1708 2153 0.248054 GATGCAATGTTACGCCGTGG 60.248 55.000 0.00 0.00 0.00 4.94 F
2802 3256 0.859232 CACGAAACTCCAAGGACACG 59.141 55.000 0.00 0.00 0.00 4.49 F
3178 3758 3.009033 TGTTTTGGGACAGAGGGAGTATG 59.991 47.826 0.00 0.00 42.39 2.39 F
3780 4365 0.394762 GACTCTTGCCCATGGATGCA 60.395 55.000 15.22 12.91 35.27 3.96 F
4206 4792 1.116308 TGACGACCCAGAACTTGTCA 58.884 50.000 0.00 0.00 34.27 3.58 F
5147 5740 2.361737 GGCTGGTTCTCCCTTGCC 60.362 66.667 0.00 0.00 42.93 4.52 F
6026 6619 2.111384 GACTTGGCTGGAGGAGATACA 58.889 52.381 0.00 0.00 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 1514 1.173913 GTTCAGGGGAACGAAATGGG 58.826 55.000 0.00 0.0 43.54 4.00 R
2673 3127 2.128771 TGAACCTTCAGGCTAATGGC 57.871 50.000 0.00 0.0 39.32 4.40 R
3280 3864 0.390860 CTCCTAGTCCCAAGCATCCG 59.609 60.000 0.00 0.0 0.00 4.18 R
3753 4338 0.835971 TGGGCAAGAGTCCTACTGCA 60.836 55.000 6.48 0.0 41.31 4.41 R
5147 5740 0.532573 TTAGTCCTGCCTCAAGCTCG 59.467 55.000 0.00 0.0 44.23 5.03 R
5689 6282 2.068519 CAAACGAGTCATAGCTGCACA 58.931 47.619 1.02 0.0 0.00 4.57 R
6026 6619 3.788227 TCAGCACAAGGATTACCAAGT 57.212 42.857 0.00 0.0 38.94 3.16 R
6399 6992 0.679505 TGGGTGGAAGAACTGAGTCG 59.320 55.000 0.00 0.0 0.00 4.18 R
7450 8113 0.255890 ATGCGTGCAAGGGTTAGGAT 59.744 50.000 0.79 0.0 0.00 3.24 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
243 244 2.752903 GGCAGGGAACACGATGTTTTAT 59.247 45.455 0.00 0.00 41.28 1.40
269 270 0.043183 TCAGGCCCTCTTGATGGAGA 59.957 55.000 0.00 0.00 35.52 3.71
353 354 2.832129 ACGAGATCAAGGAGGCTAAACA 59.168 45.455 0.00 0.00 0.00 2.83
354 355 3.452627 ACGAGATCAAGGAGGCTAAACAT 59.547 43.478 0.00 0.00 0.00 2.71
487 488 7.227512 GGTTACAATGGTAGGAGATCTTGAATG 59.772 40.741 0.00 0.00 0.00 2.67
489 490 6.725364 ACAATGGTAGGAGATCTTGAATGTT 58.275 36.000 0.00 0.00 0.00 2.71
520 521 1.600636 CTTGCCTTCCACGCCAAGA 60.601 57.895 0.00 0.00 0.00 3.02
527 528 2.222027 CTTCCACGCCAAGAAAAGTCT 58.778 47.619 0.00 0.00 34.72 3.24
590 591 1.984570 CCAGGAGTCCGGCTGAAGA 60.985 63.158 2.76 0.00 0.00 2.87
642 643 1.075896 GGACTCCCTCAGGGACGAT 60.076 63.158 9.06 0.00 46.17 3.73
654 655 1.084370 GGGACGATGAGGTCAAAGCG 61.084 60.000 0.00 0.00 38.70 4.68
677 678 3.804036 CGGTGAGGAAAATATGTGGCTA 58.196 45.455 0.00 0.00 0.00 3.93
712 714 0.755698 AGAAGAGGATAAGCGGCCGA 60.756 55.000 33.48 8.89 0.00 5.54
717 719 2.358737 GATAAGCGGCCGATGGGG 60.359 66.667 33.48 0.00 39.58 4.96
727 729 2.517414 CGATGGGGCCCACATGAT 59.483 61.111 31.54 12.45 35.80 2.45
728 730 1.760527 CGATGGGGCCCACATGATA 59.239 57.895 31.54 2.20 35.80 2.15
762 764 3.197766 AGGGATGCGACTGATTTGTCTAA 59.802 43.478 0.00 0.00 35.00 2.10
792 794 3.491276 CCGGTTGGTTTAAACACTTTCCC 60.491 47.826 19.57 9.02 0.00 3.97
798 800 7.439955 GGTTGGTTTAAACACTTTCCCTAATTG 59.560 37.037 19.57 0.00 0.00 2.32
801 803 7.982354 TGGTTTAAACACTTTCCCTAATTGTTG 59.018 33.333 19.57 0.00 38.30 3.33
900 902 4.487714 TGAGCGTGGATATTCCTCTTTT 57.512 40.909 0.00 0.00 37.46 2.27
901 903 4.843728 TGAGCGTGGATATTCCTCTTTTT 58.156 39.130 0.00 0.00 37.46 1.94
936 938 4.636206 GCAGTAGTGTATTTTCCCCTTCTG 59.364 45.833 0.00 0.00 0.00 3.02
940 942 7.711339 CAGTAGTGTATTTTCCCCTTCTGTATC 59.289 40.741 0.00 0.00 0.00 2.24
980 983 3.376540 GAATACAACACCGCAGCAAAAA 58.623 40.909 0.00 0.00 0.00 1.94
1131 1136 2.290514 TGGCAACAGATCCCTCTTTCAG 60.291 50.000 0.00 0.00 46.17 3.02
1252 1257 1.154205 ATCGAAATCTTCTGGCGGCG 61.154 55.000 0.51 0.51 0.00 6.46
1431 1436 1.203523 GTGTGAAGAGATGAGTCCGCT 59.796 52.381 0.00 0.00 0.00 5.52
1463 1468 1.179152 TGATTTGCCAGATGCCACTG 58.821 50.000 0.00 0.00 40.16 3.66
1486 1491 3.781770 CTCTGCGTCCGATCCCAGC 62.782 68.421 0.00 0.00 0.00 4.85
1509 1514 1.070134 GAAGCCTGGTTTGTTTTCCCC 59.930 52.381 0.00 0.00 0.00 4.81
1571 2016 2.995466 TTCCTGATCTTTTTGCGCTG 57.005 45.000 9.73 0.00 0.00 5.18
1708 2153 0.248054 GATGCAATGTTACGCCGTGG 60.248 55.000 0.00 0.00 0.00 4.94
2486 2933 1.096416 AGACGCTACACCTAGAGCAC 58.904 55.000 0.00 0.00 38.69 4.40
2610 3064 1.463444 GCTTTGTCCTCGCGTATTGTT 59.537 47.619 5.77 0.00 0.00 2.83
2623 3077 5.405873 TCGCGTATTGTTTTACAGATCACAA 59.594 36.000 5.77 0.00 33.78 3.33
2673 3127 6.419710 TGAACCAGCGAATATATTGTACTTCG 59.580 38.462 1.78 7.97 42.41 3.79
2684 3138 2.309528 TGTACTTCGCCATTAGCCTG 57.690 50.000 0.00 0.00 38.78 4.85
2802 3256 0.859232 CACGAAACTCCAAGGACACG 59.141 55.000 0.00 0.00 0.00 4.49
3028 3592 7.871853 ACCTACAAATCATGCGGTATATTTTC 58.128 34.615 0.00 0.00 35.16 2.29
3079 3643 7.921745 GGTATTAGTGTTTAGGAGCTAGAACTG 59.078 40.741 0.00 0.00 0.00 3.16
3105 3669 7.067494 GTGAGGCCTTTATAGATCAATTGTGTT 59.933 37.037 6.77 0.00 0.00 3.32
3106 3670 7.615365 TGAGGCCTTTATAGATCAATTGTGTTT 59.385 33.333 6.77 0.00 0.00 2.83
3108 3672 9.125026 AGGCCTTTATAGATCAATTGTGTTTAG 57.875 33.333 0.00 0.00 0.00 1.85
3109 3673 8.352942 GGCCTTTATAGATCAATTGTGTTTAGG 58.647 37.037 5.13 5.09 0.00 2.69
3110 3674 9.120538 GCCTTTATAGATCAATTGTGTTTAGGA 57.879 33.333 5.13 0.00 0.00 2.94
3157 3734 9.912634 AAATGTAAGACCATTTTTGACACTATG 57.087 29.630 0.00 0.00 41.11 2.23
3178 3758 3.009033 TGTTTTGGGACAGAGGGAGTATG 59.991 47.826 0.00 0.00 42.39 2.39
3280 3864 6.142818 TGCATAATAACAATAACTGGGTGC 57.857 37.500 0.00 0.00 0.00 5.01
3313 3897 4.443621 GACTAGGAGGGTGCTTATTGTTC 58.556 47.826 0.00 0.00 0.00 3.18
3314 3898 3.844211 ACTAGGAGGGTGCTTATTGTTCA 59.156 43.478 0.00 0.00 0.00 3.18
3337 3921 4.970662 ATATTGACACGCAAAATGCTCT 57.029 36.364 0.43 0.00 42.25 4.09
3652 4237 8.691661 TCCTATTTTATAGGGAAATCAACTGC 57.308 34.615 11.74 0.00 35.45 4.40
3660 4245 9.920946 TTATAGGGAAATCAACTGCTAAAAGAT 57.079 29.630 0.00 0.00 0.00 2.40
3702 4287 8.460759 GAAAGTGTTCACTAGGGGATACACGT 62.461 46.154 15.48 11.84 40.44 4.49
3753 4338 6.294955 GCAAGACTCCAGGAAATCAATCTTTT 60.295 38.462 3.65 0.00 0.00 2.27
3780 4365 0.394762 GACTCTTGCCCATGGATGCA 60.395 55.000 15.22 12.91 35.27 3.96
3941 4526 8.347771 TGATCACTTCTTTTCATCTGTTTTGAG 58.652 33.333 0.00 0.00 0.00 3.02
4206 4792 1.116308 TGACGACCCAGAACTTGTCA 58.884 50.000 0.00 0.00 34.27 3.58
4754 5347 7.445096 TCTTTTCTCATATTCTCAAACAGCACA 59.555 33.333 0.00 0.00 0.00 4.57
4942 5535 3.247173 GTGCTCATCAAGAGGATTTAGCG 59.753 47.826 0.00 0.00 46.90 4.26
5147 5740 2.361737 GGCTGGTTCTCCCTTGCC 60.362 66.667 0.00 0.00 42.93 4.52
5689 6282 8.457261 CAAAAATCCTCTTTTCGATGAGAATCT 58.543 33.333 10.81 0.00 38.86 2.40
5978 6571 4.664188 TCAACAAGTTTTTACCTGTTCGC 58.336 39.130 0.00 0.00 0.00 4.70
5982 6575 2.927028 AGTTTTTACCTGTTCGCCACT 58.073 42.857 0.00 0.00 0.00 4.00
6026 6619 2.111384 GACTTGGCTGGAGGAGATACA 58.889 52.381 0.00 0.00 0.00 2.29
6028 6621 2.114616 CTTGGCTGGAGGAGATACACT 58.885 52.381 0.00 0.00 0.00 3.55
6399 6992 3.181546 CGTTCTTCGTGTCCGATAACAAC 60.182 47.826 9.80 0.00 43.80 3.32
6936 7531 8.680903 GTGATGTTGATGAAGATAAGAACCATT 58.319 33.333 0.00 0.00 0.00 3.16
6947 7542 7.707624 AGATAAGAACCATTGAATCAAAGCA 57.292 32.000 0.00 0.00 0.00 3.91
6963 7558 0.773644 AGCAGGTTGGATGAAGTGGT 59.226 50.000 0.00 0.00 0.00 4.16
6973 7568 4.072131 TGGATGAAGTGGTGCTAAGTTTC 58.928 43.478 0.00 0.00 0.00 2.78
7060 7680 4.213270 CGACTCACAATGTTGTATGGTGTT 59.787 41.667 0.00 0.00 39.91 3.32
7061 7681 5.437289 ACTCACAATGTTGTATGGTGTTG 57.563 39.130 0.00 0.00 39.91 3.33
7062 7682 5.129634 ACTCACAATGTTGTATGGTGTTGA 58.870 37.500 0.00 0.00 39.91 3.18
7063 7683 5.239306 ACTCACAATGTTGTATGGTGTTGAG 59.761 40.000 0.00 1.97 39.91 3.02
7064 7684 5.129634 TCACAATGTTGTATGGTGTTGAGT 58.870 37.500 0.00 0.00 39.91 3.41
7065 7685 5.008514 TCACAATGTTGTATGGTGTTGAGTG 59.991 40.000 0.00 0.00 39.91 3.51
7066 7686 4.887071 ACAATGTTGTATGGTGTTGAGTGT 59.113 37.500 0.00 0.00 40.16 3.55
7067 7687 5.359576 ACAATGTTGTATGGTGTTGAGTGTT 59.640 36.000 0.00 0.00 40.16 3.32
7068 7688 6.544197 ACAATGTTGTATGGTGTTGAGTGTTA 59.456 34.615 0.00 0.00 40.16 2.41
7069 7689 6.801539 ATGTTGTATGGTGTTGAGTGTTAG 57.198 37.500 0.00 0.00 0.00 2.34
7070 7690 4.513692 TGTTGTATGGTGTTGAGTGTTAGC 59.486 41.667 0.00 0.00 0.00 3.09
7071 7691 4.617253 TGTATGGTGTTGAGTGTTAGCT 57.383 40.909 0.00 0.00 0.00 3.32
7072 7692 4.314961 TGTATGGTGTTGAGTGTTAGCTG 58.685 43.478 0.00 0.00 0.00 4.24
7073 7693 3.769739 ATGGTGTTGAGTGTTAGCTGA 57.230 42.857 0.00 0.00 0.00 4.26
7074 7694 3.769739 TGGTGTTGAGTGTTAGCTGAT 57.230 42.857 0.00 0.00 0.00 2.90
7075 7695 4.882842 TGGTGTTGAGTGTTAGCTGATA 57.117 40.909 0.00 0.00 0.00 2.15
7076 7696 5.222079 TGGTGTTGAGTGTTAGCTGATAA 57.778 39.130 0.00 0.00 0.00 1.75
7077 7697 5.616270 TGGTGTTGAGTGTTAGCTGATAAA 58.384 37.500 0.00 0.00 0.00 1.40
7078 7698 6.058833 TGGTGTTGAGTGTTAGCTGATAAAA 58.941 36.000 0.00 0.00 0.00 1.52
7079 7699 6.544197 TGGTGTTGAGTGTTAGCTGATAAAAA 59.456 34.615 0.00 0.00 0.00 1.94
7080 7700 7.230510 TGGTGTTGAGTGTTAGCTGATAAAAAT 59.769 33.333 0.00 0.00 0.00 1.82
7081 7701 7.538678 GGTGTTGAGTGTTAGCTGATAAAAATG 59.461 37.037 0.00 0.00 0.00 2.32
7082 7702 8.076178 GTGTTGAGTGTTAGCTGATAAAAATGT 58.924 33.333 0.00 0.00 0.00 2.71
7251 7894 4.218200 TGAGTTGGTTTGGACATATGCAAG 59.782 41.667 1.58 0.00 37.47 4.01
7292 7935 4.154375 TCAATGCATAGCGAACGGTTAAAA 59.846 37.500 0.00 0.00 0.00 1.52
7293 7936 4.893424 ATGCATAGCGAACGGTTAAAAT 57.107 36.364 0.00 0.00 0.00 1.82
7310 7954 8.849490 CGGTTAAAATGTGTTGATAATGTCAAG 58.151 33.333 0.00 0.00 46.99 3.02
7330 7974 0.408700 AGAGGTCGGGGTCAACTACT 59.591 55.000 0.00 0.00 0.00 2.57
7364 8009 2.509964 ACCAAGGCCCCTTTAGATAGTG 59.490 50.000 0.00 0.00 33.42 2.74
7421 8084 5.355910 GCTGATTTCCAATTTGGCATCAATT 59.644 36.000 21.35 6.63 36.86 2.32
7450 8113 0.414629 TCCTCTCCCCCTTCGGTTTA 59.585 55.000 0.00 0.00 0.00 2.01
7462 8125 4.196971 CCTTCGGTTTATCCTAACCCTTG 58.803 47.826 0.00 0.00 43.81 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 244 1.151810 AAGAGGGCCTGAACCTGGA 60.152 57.895 12.95 0.00 38.79 3.86
269 270 3.262405 TCAAGCAGGACGTAGGGTTTTAT 59.738 43.478 0.00 0.00 0.00 1.40
310 311 7.733969 TCGTGGTAGATCTACTCTTGTACTAT 58.266 38.462 27.68 0.00 36.36 2.12
353 354 7.986553 ATCATACCATAGGCTAGCTTCTAAT 57.013 36.000 15.72 0.00 0.00 1.73
354 355 7.235606 ACAATCATACCATAGGCTAGCTTCTAA 59.764 37.037 15.72 0.00 0.00 2.10
487 488 1.512734 CAAGCTTGGCGATGCGAAC 60.513 57.895 19.14 0.00 0.00 3.95
489 490 3.803082 GCAAGCTTGGCGATGCGA 61.803 61.111 27.10 0.00 36.80 5.10
520 521 2.080286 CGTGTCCGGATGAGACTTTT 57.920 50.000 7.81 0.00 35.16 2.27
555 556 7.118496 ACTCCTGGACTATGAAGATACAAAG 57.882 40.000 0.00 0.00 0.00 2.77
556 557 6.098409 GGACTCCTGGACTATGAAGATACAAA 59.902 42.308 0.00 0.00 0.00 2.83
590 591 2.165998 GTTCGGGTAGCCGGACTATAT 58.834 52.381 32.69 0.00 38.53 0.86
642 643 3.936203 ACCGCCGCTTTGACCTCA 61.936 61.111 0.00 0.00 0.00 3.86
654 655 1.676006 CCACATATTTTCCTCACCGCC 59.324 52.381 0.00 0.00 0.00 6.13
677 678 2.504585 TCTTCTCTCCATGCAGCTTCAT 59.495 45.455 0.00 0.00 0.00 2.57
683 684 4.800249 GCTTATCCTCTTCTCTCCATGCAG 60.800 50.000 0.00 0.00 0.00 4.41
712 714 1.160702 ACATATCATGTGGGCCCCAT 58.839 50.000 22.27 19.34 43.01 4.00
727 729 0.809636 CATCCCTCGCGCAACACATA 60.810 55.000 8.75 0.00 0.00 2.29
728 730 2.108514 CATCCCTCGCGCAACACAT 61.109 57.895 8.75 0.00 0.00 3.21
749 751 4.393062 CGGCTGATGTTTAGACAAATCAGT 59.607 41.667 14.90 0.00 41.63 3.41
762 764 2.279935 TAAACCAACCGGCTGATGTT 57.720 45.000 6.38 0.00 34.57 2.71
792 794 4.378616 GTGCTACGCAACAACAACAATTAG 59.621 41.667 0.00 0.00 41.47 1.73
798 800 2.765814 CGTGCTACGCAACAACAAC 58.234 52.632 0.00 0.00 41.47 3.32
884 886 9.838339 TTCTATCTCAAAAAGAGGAATATCCAC 57.162 33.333 0.00 0.00 44.81 4.02
900 902 4.353777 ACACTACTGCCCTTCTATCTCAA 58.646 43.478 0.00 0.00 0.00 3.02
901 903 3.982516 ACACTACTGCCCTTCTATCTCA 58.017 45.455 0.00 0.00 0.00 3.27
936 938 7.875327 TCCTATTGTTAGCTTTTTGGGATAC 57.125 36.000 0.00 0.00 0.00 2.24
940 942 8.062065 TGTATTCCTATTGTTAGCTTTTTGGG 57.938 34.615 0.00 0.00 0.00 4.12
980 983 0.916086 TCCCCTTGCAATACCACGAT 59.084 50.000 0.00 0.00 0.00 3.73
1040 1045 2.195096 CAAACAACCTACGACGTCACA 58.805 47.619 17.16 0.75 0.00 3.58
1041 1046 1.523934 CCAAACAACCTACGACGTCAC 59.476 52.381 17.16 0.00 0.00 3.67
1131 1136 5.065731 AGGAATGAAAGATGAGAACAATCGC 59.934 40.000 0.00 0.00 0.00 4.58
1339 1344 2.743636 AGATTTCACGCGAGAGGAAA 57.256 45.000 15.93 16.70 40.21 3.13
1342 1347 1.855360 GCTTAGATTTCACGCGAGAGG 59.145 52.381 15.93 0.00 0.00 3.69
1509 1514 1.173913 GTTCAGGGGAACGAAATGGG 58.826 55.000 0.00 0.00 43.54 4.00
1571 2016 6.024049 CCTTTTTCGCTATCAAGATGAACAC 58.976 40.000 0.00 0.00 0.00 3.32
1708 2153 7.435068 TCTATCAACTAAGCAGTTTGGAAAC 57.565 36.000 0.00 0.00 42.51 2.78
1868 2314 4.759782 ACGGTCTCAGATGTATTTTCCTG 58.240 43.478 0.00 0.00 0.00 3.86
2028 2474 3.134804 GGGATAGTGGTGCTATGTGAACT 59.865 47.826 0.00 0.00 40.30 3.01
2251 2698 4.448537 TGAAGTTGTCCAACCACAAAAG 57.551 40.909 6.55 0.00 42.06 2.27
2610 3064 9.725019 AATTATGTCAGACTTGTGATCTGTAAA 57.275 29.630 1.31 0.00 43.47 2.01
2656 3110 7.391786 GCTAATGGCGAAGTACAATATATTCG 58.608 38.462 7.97 7.97 45.44 3.34
2663 3117 3.118408 TCAGGCTAATGGCGAAGTACAAT 60.118 43.478 0.00 0.00 44.18 2.71
2673 3127 2.128771 TGAACCTTCAGGCTAATGGC 57.871 50.000 0.00 0.00 39.32 4.40
2933 3497 9.390795 CAGAAATATATAGCACAGAAACATTGC 57.609 33.333 0.00 0.00 36.45 3.56
2970 3534 4.908601 TCCAAAGTTCAAGCATCCTAGA 57.091 40.909 0.00 0.00 0.00 2.43
2977 3541 6.240894 AGAATGACTATCCAAAGTTCAAGCA 58.759 36.000 0.00 0.00 0.00 3.91
3028 3592 2.357009 GAGGTGTAATCTGCATTGCTGG 59.643 50.000 14.55 5.89 0.00 4.85
3079 3643 6.543831 ACACAATTGATCTATAAAGGCCTCAC 59.456 38.462 13.59 0.00 0.00 3.51
3105 3669 5.105269 GGGGAAAACAACAAAACACTCCTAA 60.105 40.000 0.00 0.00 0.00 2.69
3106 3670 4.403113 GGGGAAAACAACAAAACACTCCTA 59.597 41.667 0.00 0.00 0.00 2.94
3108 3672 3.055747 TGGGGAAAACAACAAAACACTCC 60.056 43.478 0.00 0.00 0.00 3.85
3109 3673 4.195225 TGGGGAAAACAACAAAACACTC 57.805 40.909 0.00 0.00 0.00 3.51
3110 3674 4.625607 TTGGGGAAAACAACAAAACACT 57.374 36.364 0.00 0.00 0.00 3.55
3111 3675 5.690997 TTTTGGGGAAAACAACAAAACAC 57.309 34.783 0.00 0.00 37.74 3.32
3113 3677 6.260870 ACATTTTGGGGAAAACAACAAAAC 57.739 33.333 0.00 0.00 43.12 2.43
3155 3732 2.065799 ACTCCCTCTGTCCCAAAACAT 58.934 47.619 0.00 0.00 0.00 2.71
3156 3733 1.518367 ACTCCCTCTGTCCCAAAACA 58.482 50.000 0.00 0.00 0.00 2.83
3157 3734 3.263425 TCATACTCCCTCTGTCCCAAAAC 59.737 47.826 0.00 0.00 0.00 2.43
3178 3758 7.865707 AGTCAGAACAGAAAACATACAATGTC 58.134 34.615 0.00 0.00 44.07 3.06
3247 3827 6.720112 ATTGTTATTATGCAATGCAGGAGT 57.280 33.333 14.98 3.67 43.65 3.85
3280 3864 0.390860 CTCCTAGTCCCAAGCATCCG 59.609 60.000 0.00 0.00 0.00 4.18
3605 4189 6.660521 AGGATATGTTGCATGAGAAACAGAAA 59.339 34.615 12.60 4.35 46.22 2.52
3660 4245 8.488651 AACACTTTCTTCTCGTTCTTTTTCTA 57.511 30.769 0.00 0.00 0.00 2.10
3702 4287 8.138928 TGAGAACTGGAGATGAAGAAGATAAA 57.861 34.615 0.00 0.00 0.00 1.40
3753 4338 0.835971 TGGGCAAGAGTCCTACTGCA 60.836 55.000 6.48 0.00 41.31 4.41
3780 4365 1.607148 GCTCCTTTGCTACCGTTTTGT 59.393 47.619 0.00 0.00 0.00 2.83
3941 4526 5.244851 TGAGTGAGGCTAAGGATACATCATC 59.755 44.000 0.00 0.00 41.41 2.92
4963 5556 2.038952 AGCCACTGCAACAGTATCTTGA 59.961 45.455 0.00 0.00 43.43 3.02
5147 5740 0.532573 TTAGTCCTGCCTCAAGCTCG 59.467 55.000 0.00 0.00 44.23 5.03
5689 6282 2.068519 CAAACGAGTCATAGCTGCACA 58.931 47.619 1.02 0.00 0.00 4.57
5978 6571 7.190871 ACAACAAGAACGTAAATTAACAGTGG 58.809 34.615 0.00 0.00 0.00 4.00
5982 6575 8.550376 GTCCTACAACAAGAACGTAAATTAACA 58.450 33.333 0.00 0.00 0.00 2.41
6026 6619 3.788227 TCAGCACAAGGATTACCAAGT 57.212 42.857 0.00 0.00 38.94 3.16
6028 6621 4.299586 TCATCAGCACAAGGATTACCAA 57.700 40.909 0.00 0.00 38.94 3.67
6399 6992 0.679505 TGGGTGGAAGAACTGAGTCG 59.320 55.000 0.00 0.00 0.00 4.18
6604 7197 6.594937 GGAACAACCCGATTTACATAGTACAA 59.405 38.462 0.00 0.00 0.00 2.41
6936 7531 3.765381 TCATCCAACCTGCTTTGATTCA 58.235 40.909 0.00 0.00 0.00 2.57
6947 7542 0.773644 AGCACCACTTCATCCAACCT 59.226 50.000 0.00 0.00 0.00 3.50
6963 7558 2.037251 AGAGAACGCCAGAAACTTAGCA 59.963 45.455 0.00 0.00 0.00 3.49
6973 7568 2.478134 CTCTTTTCACAGAGAACGCCAG 59.522 50.000 0.00 0.00 42.81 4.85
7017 7612 1.399440 GAATCGCCGTCCTTAAAACCC 59.601 52.381 0.00 0.00 0.00 4.11
7060 7680 7.977789 TCACATTTTTATCAGCTAACACTCA 57.022 32.000 0.00 0.00 0.00 3.41
7078 7698 9.905713 ACACCTAACTATTGAACATATCACATT 57.094 29.630 0.00 0.00 37.92 2.71
7079 7699 9.905713 AACACCTAACTATTGAACATATCACAT 57.094 29.630 0.00 0.00 37.92 3.21
7080 7700 9.161629 CAACACCTAACTATTGAACATATCACA 57.838 33.333 0.00 0.00 37.92 3.58
7081 7701 9.162764 ACAACACCTAACTATTGAACATATCAC 57.837 33.333 0.00 0.00 37.92 3.06
7082 7702 9.161629 CACAACACCTAACTATTGAACATATCA 57.838 33.333 0.00 0.00 35.85 2.15
7094 7714 4.562757 GCACATCTCCACAACACCTAACTA 60.563 45.833 0.00 0.00 0.00 2.24
7125 7745 4.352009 TCTTTTGTGGCCATACATCCATT 58.648 39.130 9.72 0.00 34.47 3.16
7134 7754 3.509442 TGATCCTTTCTTTTGTGGCCAT 58.491 40.909 9.72 0.00 0.00 4.40
7178 7798 2.171840 TGGTGCTACCTCAACTCTCTC 58.828 52.381 6.83 0.00 39.58 3.20
7292 7935 6.715280 ACCTCTCTTGACATTATCAACACAT 58.285 36.000 0.00 0.00 42.62 3.21
7293 7936 6.114187 ACCTCTCTTGACATTATCAACACA 57.886 37.500 0.00 0.00 42.62 3.72
7310 7954 0.816373 GTAGTTGACCCCGACCTCTC 59.184 60.000 0.00 0.00 0.00 3.20
7330 7974 2.685897 GGCCTTGGTTACGATGCATTTA 59.314 45.455 0.00 0.00 0.00 1.40
7398 8061 6.596106 TGAATTGATGCCAAATTGGAAATCAG 59.404 34.615 17.47 0.00 40.69 2.90
7405 8068 4.131596 GGGATGAATTGATGCCAAATTGG 58.868 43.478 10.54 7.84 41.55 3.16
7450 8113 0.255890 ATGCGTGCAAGGGTTAGGAT 59.744 50.000 0.79 0.00 0.00 3.24
7462 8125 2.206815 TAATTCATTGCCATGCGTGC 57.793 45.000 0.00 0.00 0.00 5.34
7559 8225 6.710295 TCTTAGTACCTCGTGTTAGTGTGTTA 59.290 38.462 0.00 0.00 0.00 2.41
7560 8226 5.532406 TCTTAGTACCTCGTGTTAGTGTGTT 59.468 40.000 0.00 0.00 0.00 3.32
7561 8227 5.065914 TCTTAGTACCTCGTGTTAGTGTGT 58.934 41.667 0.00 0.00 0.00 3.72
7659 8325 9.566432 GTGTCTCCTCAAGGATCAAAATATTAT 57.434 33.333 0.00 0.00 44.46 1.28
7660 8326 8.772250 AGTGTCTCCTCAAGGATCAAAATATTA 58.228 33.333 0.00 0.00 44.46 0.98
7661 8327 7.637511 AGTGTCTCCTCAAGGATCAAAATATT 58.362 34.615 0.00 0.00 44.46 1.28
7662 8328 7.205515 AGTGTCTCCTCAAGGATCAAAATAT 57.794 36.000 0.00 0.00 44.46 1.28
7663 8329 6.352222 GGAGTGTCTCCTCAAGGATCAAAATA 60.352 42.308 8.38 0.00 46.41 1.40
7664 8330 5.495640 GAGTGTCTCCTCAAGGATCAAAAT 58.504 41.667 0.00 0.00 44.46 1.82
7665 8331 4.263068 GGAGTGTCTCCTCAAGGATCAAAA 60.263 45.833 8.38 0.00 46.41 2.44
7666 8332 3.261897 GGAGTGTCTCCTCAAGGATCAAA 59.738 47.826 8.38 0.00 46.41 2.69
7667 8333 2.834549 GGAGTGTCTCCTCAAGGATCAA 59.165 50.000 8.38 0.00 46.41 2.57
7668 8334 2.461695 GGAGTGTCTCCTCAAGGATCA 58.538 52.381 8.38 0.08 46.41 2.92
7712 8378 8.239038 AGAATCGAATATCTCAACAGAGGTTA 57.761 34.615 0.00 0.00 34.87 2.85


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

AutoCloner maintained by Alex Coulton.