Multiple sequence alignment - TraesCS3A01G392500

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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 TraesCS3A01G392500 chr3A 100.000 3554 0 0 1 3554 640390352 640393905 0.000000e+00 6564.0
1 TraesCS3A01G392500 chr3A 93.705 1652 86 7 960 2611 640497683 640499316 0.000000e+00 2459.0
2 TraesCS3A01G392500 chr3A 90.165 1576 142 8 1034 2603 640363379 640364947 0.000000e+00 2039.0
3 TraesCS3A01G392500 chr3A 95.497 755 24 5 215 966 640481721 640482468 0.000000e+00 1197.0
4 TraesCS3A01G392500 chr3A 91.061 358 31 1 3009 3366 640500973 640501329 1.920000e-132 483.0
5 TraesCS3A01G392500 chr3A 90.461 304 19 4 2608 2908 640500662 640500958 3.330000e-105 392.0
6 TraesCS3A01G392500 chr3A 94.444 198 7 2 3357 3554 640501641 640501834 5.770000e-78 302.0
7 TraesCS3A01G392500 chr3D 96.380 2928 86 9 1 2923 501033285 501030373 0.000000e+00 4802.0
8 TraesCS3A01G392500 chr3D 89.670 1578 150 8 1034 2605 501062278 501060708 0.000000e+00 1999.0
9 TraesCS3A01G392500 chr3D 95.312 192 6 1 3363 3554 501029690 501029502 5.770000e-78 302.0
10 TraesCS3A01G392500 chr3B 94.187 2219 77 18 713 2922 662480119 662477944 0.000000e+00 3336.0
11 TraesCS3A01G392500 chr3B 89.869 1599 148 9 1034 2626 662527924 662526334 0.000000e+00 2043.0
12 TraesCS3A01G392500 chr3B 84.524 420 56 5 2213 2626 662508554 662508138 1.190000e-109 407.0
13 TraesCS3A01G392500 chr3B 91.696 289 23 1 3009 3296 662477946 662477658 1.990000e-107 399.0
14 TraesCS3A01G392500 chr3B 88.673 309 32 3 1397 1705 461747723 461748028 1.200000e-99 374.0
15 TraesCS3A01G392500 chr3B 88.889 270 26 3 1 269 662481154 662480888 2.650000e-86 329.0
16 TraesCS3A01G392500 chr3B 92.708 192 11 1 3363 3554 662475696 662475508 1.260000e-69 274.0
17 TraesCS3A01G392500 chr3B 86.957 230 15 6 281 502 662480518 662480296 9.860000e-61 244.0
18 TraesCS3A01G392500 chr3B 86.747 83 11 0 3284 3366 662476223 662476141 3.780000e-15 93.5
19 TraesCS3A01G392500 chr3B 97.368 38 1 0 546 583 662480141 662480104 8.240000e-07 65.8
20 TraesCS3A01G392500 chr5D 89.347 291 30 1 1415 1705 47629231 47629520 7.250000e-97 364.0
21 TraesCS3A01G392500 chr1D 87.179 312 38 2 1395 1705 489787943 489788253 1.570000e-93 353.0
22 TraesCS3A01G392500 chr4D 81.481 108 8 8 2913 3011 234381190 234381294 1.060000e-10 78.7
23 TraesCS3A01G392500 chr4B 84.810 79 8 2 2936 3011 154020977 154020900 3.800000e-10 76.8
24 TraesCS3A01G392500 chr4B 95.000 40 1 1 576 615 316805767 316805729 1.070000e-05 62.1
25 TraesCS3A01G392500 chr4B 97.222 36 1 0 580 615 572045108 572045143 1.070000e-05 62.1
26 TraesCS3A01G392500 chr1B 85.000 80 6 4 2936 3011 160439681 160439604 3.800000e-10 76.8
27 TraesCS3A01G392500 chr1B 84.146 82 5 6 2936 3012 27581637 27581559 4.920000e-09 73.1
28 TraesCS3A01G392500 chr6B 83.721 86 7 5 2936 3016 36138916 36138999 1.370000e-09 75.0
29 TraesCS3A01G392500 chr6B 100.000 34 0 0 582 615 612853496 612853463 2.960000e-06 63.9
30 TraesCS3A01G392500 chr5B 84.337 83 6 5 2936 3014 382074644 382074723 1.370000e-09 75.0
31 TraesCS3A01G392500 chr5B 84.146 82 5 6 2936 3012 654530301 654530379 4.920000e-09 73.1
32 TraesCS3A01G392500 chrUn 80.556 108 9 6 2919 3017 81701234 81701338 4.920000e-09 73.1
33 TraesCS3A01G392500 chr7A 81.373 102 5 7 2919 3010 138008556 138008459 1.770000e-08 71.3
34 TraesCS3A01G392500 chr2B 90.000 50 4 1 566 615 186376109 186376157 2.960000e-06 63.9
35 TraesCS3A01G392500 chr2B 94.872 39 2 0 577 615 59659699 59659737 1.070000e-05 62.1
36 TraesCS3A01G392500 chr2B 100.000 32 0 0 663 694 45609975 45610006 3.830000e-05 60.2
37 TraesCS3A01G392500 chr1A 90.385 52 0 3 569 615 311806734 311806683 2.960000e-06 63.9
38 TraesCS3A01G392500 chr5A 97.222 36 1 0 581 616 409331919 409331954 1.070000e-05 62.1


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 TraesCS3A01G392500 chr3A 640390352 640393905 3553 False 6564.000000 6564 100.000000 1 3554 1 chr3A.!!$F2 3553
1 TraesCS3A01G392500 chr3A 640363379 640364947 1568 False 2039.000000 2039 90.165000 1034 2603 1 chr3A.!!$F1 1569
2 TraesCS3A01G392500 chr3A 640481721 640482468 747 False 1197.000000 1197 95.497000 215 966 1 chr3A.!!$F3 751
3 TraesCS3A01G392500 chr3A 640497683 640501834 4151 False 909.000000 2459 92.417750 960 3554 4 chr3A.!!$F4 2594
4 TraesCS3A01G392500 chr3D 501029502 501033285 3783 True 2552.000000 4802 95.846000 1 3554 2 chr3D.!!$R2 3553
5 TraesCS3A01G392500 chr3D 501060708 501062278 1570 True 1999.000000 1999 89.670000 1034 2605 1 chr3D.!!$R1 1571
6 TraesCS3A01G392500 chr3B 662526334 662527924 1590 True 2043.000000 2043 89.869000 1034 2626 1 chr3B.!!$R2 1592
7 TraesCS3A01G392500 chr3B 662475508 662481154 5646 True 677.328571 3336 91.221714 1 3554 7 chr3B.!!$R3 3553

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
624 1105 0.253327 GGCAAGGGAGTTCGAATCCT 59.747 55.0 19.43 15.38 37.01 3.24 F
1107 1597 0.757188 AGCATCCTCACTACCTCGGG 60.757 60.0 0.00 0.00 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 2245 1.272490 ACGTTGCTCTCTCCATCGAAA 59.728 47.619 0.0 0.0 31.77 3.46 R
2923 4789 0.393077 AGACACTTGGAACGTGAGGG 59.607 55.000 0.0 0.0 36.29 4.30 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
114 115 5.970592 TCATTGTCTGATGAGTGTCTTAGG 58.029 41.667 0.00 0.00 32.50 2.69
193 195 0.257328 TCTGGGACACTTGGCAAACA 59.743 50.000 0.00 0.00 0.00 2.83
353 714 5.600484 ACCATTTGTGATGAAGGGTTTGTAA 59.400 36.000 0.00 0.00 37.89 2.41
624 1105 0.253327 GGCAAGGGAGTTCGAATCCT 59.747 55.000 19.43 15.38 37.01 3.24
703 1184 2.158842 GGGTGCTAGTGCTCATGATCTT 60.159 50.000 0.00 0.00 40.48 2.40
945 1431 8.950210 GGTAACAAGTTAAAATTAGGTAGGTCC 58.050 37.037 0.00 0.00 0.00 4.46
1062 1552 2.508526 ACACAGGAAGGTGCTTCAATC 58.491 47.619 0.00 0.00 41.77 2.67
1107 1597 0.757188 AGCATCCTCACTACCTCGGG 60.757 60.000 0.00 0.00 0.00 5.14
1281 1771 2.254350 CGCGACGTCCTTGAGACA 59.746 61.111 10.58 0.00 46.69 3.41
1296 1786 2.302733 TGAGACATGCAAGCAGAAGGTA 59.697 45.455 0.00 0.00 0.00 3.08
1362 1855 1.578206 GGTTCGAGGAACAAGCAGGC 61.578 60.000 10.32 0.00 43.54 4.85
1383 1876 4.626081 GCTGTGGTCGCTGTGGGT 62.626 66.667 0.00 0.00 0.00 4.51
1920 2413 2.959484 CGTGGACACCATGAGGGCT 61.959 63.158 4.18 0.00 42.73 5.19
2019 2512 2.176055 CTCCACGTCGACGACCTG 59.824 66.667 41.52 28.60 43.02 4.00
2665 4510 1.480137 GTGAGGTGATGAGGTGAGAGG 59.520 57.143 0.00 0.00 0.00 3.69
2667 4512 1.142748 GGTGATGAGGTGAGAGGCG 59.857 63.158 0.00 0.00 0.00 5.52
2682 4527 2.699321 AGAGGCGGGGAAGAAAGTATAC 59.301 50.000 0.00 0.00 0.00 1.47
2691 4536 7.321153 CGGGGAAGAAAGTATACCTACATATG 58.679 42.308 0.00 0.00 0.00 1.78
2692 4537 7.578955 CGGGGAAGAAAGTATACCTACATATGG 60.579 44.444 7.80 0.00 0.00 2.74
2693 4538 7.311109 GGGGAAGAAAGTATACCTACATATGGG 60.311 44.444 7.80 1.92 0.00 4.00
2694 4539 7.456902 GGGAAGAAAGTATACCTACATATGGGA 59.543 40.741 7.80 0.00 0.00 4.37
2695 4540 9.047947 GGAAGAAAGTATACCTACATATGGGAT 57.952 37.037 7.80 0.00 32.00 3.85
2731 4590 2.831565 AGAGAAGCTCACAGGAGGATT 58.168 47.619 0.00 0.00 41.67 3.01
2732 4591 3.987745 AGAGAAGCTCACAGGAGGATTA 58.012 45.455 0.00 0.00 41.67 1.75
2734 4593 4.344679 AGAGAAGCTCACAGGAGGATTATG 59.655 45.833 0.00 0.00 41.67 1.90
2735 4594 2.926778 AGCTCACAGGAGGATTATGC 57.073 50.000 0.00 0.00 41.67 3.14
2736 4595 1.069823 AGCTCACAGGAGGATTATGCG 59.930 52.381 0.00 0.00 41.67 4.73
2737 4596 1.202580 GCTCACAGGAGGATTATGCGT 60.203 52.381 0.00 0.00 41.67 5.24
2738 4597 2.035961 GCTCACAGGAGGATTATGCGTA 59.964 50.000 0.00 0.00 41.67 4.42
2739 4598 3.858877 GCTCACAGGAGGATTATGCGTAG 60.859 52.174 0.00 0.00 41.67 3.51
2740 4599 3.562182 TCACAGGAGGATTATGCGTAGA 58.438 45.455 0.00 0.00 0.00 2.59
2741 4600 3.570125 TCACAGGAGGATTATGCGTAGAG 59.430 47.826 0.00 0.00 0.00 2.43
2742 4601 2.894126 ACAGGAGGATTATGCGTAGAGG 59.106 50.000 0.00 0.00 0.00 3.69
2743 4602 3.157881 CAGGAGGATTATGCGTAGAGGA 58.842 50.000 0.00 0.00 0.00 3.71
2744 4603 3.766591 CAGGAGGATTATGCGTAGAGGAT 59.233 47.826 0.00 0.00 34.41 3.24
2745 4604 3.766591 AGGAGGATTATGCGTAGAGGATG 59.233 47.826 0.00 0.00 31.61 3.51
2746 4605 3.511934 GGAGGATTATGCGTAGAGGATGT 59.488 47.826 0.00 0.00 31.61 3.06
2747 4606 4.021016 GGAGGATTATGCGTAGAGGATGTT 60.021 45.833 0.00 0.00 31.61 2.71
2748 4607 5.140747 AGGATTATGCGTAGAGGATGTTC 57.859 43.478 0.00 0.00 31.61 3.18
2749 4608 4.588951 AGGATTATGCGTAGAGGATGTTCA 59.411 41.667 0.00 0.00 31.61 3.18
2750 4609 5.070446 AGGATTATGCGTAGAGGATGTTCAA 59.930 40.000 0.00 0.00 31.61 2.69
2751 4610 5.406780 GGATTATGCGTAGAGGATGTTCAAG 59.593 44.000 0.00 0.00 31.61 3.02
2752 4611 2.672961 TGCGTAGAGGATGTTCAAGG 57.327 50.000 0.00 0.00 0.00 3.61
2753 4612 1.899814 TGCGTAGAGGATGTTCAAGGT 59.100 47.619 0.00 0.00 0.00 3.50
2754 4613 3.093814 TGCGTAGAGGATGTTCAAGGTA 58.906 45.455 0.00 0.00 0.00 3.08
2845 4704 9.221775 CGCTTGACAATTTTTGTATAGGTATTC 57.778 33.333 0.00 0.00 45.52 1.75
2928 4794 8.431910 AAGAAAGTGTAAATACTACTCCCTCA 57.568 34.615 0.00 0.00 0.00 3.86
2929 4795 7.838884 AGAAAGTGTAAATACTACTCCCTCAC 58.161 38.462 0.00 0.00 0.00 3.51
2930 4796 5.831702 AGTGTAAATACTACTCCCTCACG 57.168 43.478 0.00 0.00 0.00 4.35
2931 4797 5.259632 AGTGTAAATACTACTCCCTCACGT 58.740 41.667 0.00 0.00 0.00 4.49
2932 4798 5.713861 AGTGTAAATACTACTCCCTCACGTT 59.286 40.000 0.00 0.00 0.00 3.99
2933 4799 6.032717 GTGTAAATACTACTCCCTCACGTTC 58.967 44.000 0.00 0.00 0.00 3.95
2934 4800 4.732672 AAATACTACTCCCTCACGTTCC 57.267 45.455 0.00 0.00 0.00 3.62
2935 4801 2.885135 TACTACTCCCTCACGTTCCA 57.115 50.000 0.00 0.00 0.00 3.53
2936 4802 2.005370 ACTACTCCCTCACGTTCCAA 57.995 50.000 0.00 0.00 0.00 3.53
2937 4803 1.893801 ACTACTCCCTCACGTTCCAAG 59.106 52.381 0.00 0.00 0.00 3.61
2938 4804 1.893801 CTACTCCCTCACGTTCCAAGT 59.106 52.381 0.00 0.00 0.00 3.16
2939 4805 0.393077 ACTCCCTCACGTTCCAAGTG 59.607 55.000 0.00 0.00 40.71 3.16
2940 4806 0.393077 CTCCCTCACGTTCCAAGTGT 59.607 55.000 0.00 0.00 40.28 3.55
2941 4807 0.391597 TCCCTCACGTTCCAAGTGTC 59.608 55.000 0.00 0.00 40.28 3.67
2942 4808 0.393077 CCCTCACGTTCCAAGTGTCT 59.607 55.000 0.00 0.00 40.28 3.41
2943 4809 1.605712 CCCTCACGTTCCAAGTGTCTC 60.606 57.143 0.00 0.00 40.28 3.36
2944 4810 1.068588 CCTCACGTTCCAAGTGTCTCA 59.931 52.381 0.00 0.00 40.28 3.27
2945 4811 2.483013 CCTCACGTTCCAAGTGTCTCAA 60.483 50.000 0.00 0.00 40.28 3.02
2946 4812 2.797156 CTCACGTTCCAAGTGTCTCAAG 59.203 50.000 0.00 0.00 40.28 3.02
2947 4813 1.261619 CACGTTCCAAGTGTCTCAAGC 59.738 52.381 0.00 0.00 35.08 4.01
2948 4814 1.139058 ACGTTCCAAGTGTCTCAAGCT 59.861 47.619 0.00 0.00 0.00 3.74
2949 4815 2.213499 CGTTCCAAGTGTCTCAAGCTT 58.787 47.619 0.00 0.00 0.00 3.74
2950 4816 3.181469 ACGTTCCAAGTGTCTCAAGCTTA 60.181 43.478 0.00 0.00 0.00 3.09
2951 4817 3.430218 CGTTCCAAGTGTCTCAAGCTTAG 59.570 47.826 0.00 0.00 0.00 2.18
2952 4818 4.381411 GTTCCAAGTGTCTCAAGCTTAGT 58.619 43.478 0.00 0.00 0.00 2.24
2953 4819 3.995199 TCCAAGTGTCTCAAGCTTAGTG 58.005 45.455 0.00 0.00 0.00 2.74
2954 4820 2.481952 CCAAGTGTCTCAAGCTTAGTGC 59.518 50.000 0.00 0.00 43.29 4.40
2973 4839 2.856398 GCTTTGCACTAAGCTTAGCAC 58.144 47.619 29.39 22.14 45.50 4.40
2974 4840 2.485814 GCTTTGCACTAAGCTTAGCACT 59.514 45.455 29.39 10.94 45.50 4.40
2975 4841 3.684788 GCTTTGCACTAAGCTTAGCACTA 59.315 43.478 29.39 17.13 45.50 2.74
2976 4842 4.154195 GCTTTGCACTAAGCTTAGCACTAA 59.846 41.667 29.39 21.89 45.50 2.24
2977 4843 5.672321 GCTTTGCACTAAGCTTAGCACTAAG 60.672 44.000 29.39 28.16 45.50 2.18
2993 4859 6.487689 GCACTAAGCTTGAGACACTTATTT 57.512 37.500 9.86 0.00 41.15 1.40
2994 4860 6.903419 GCACTAAGCTTGAGACACTTATTTT 58.097 36.000 9.86 0.00 41.15 1.82
2995 4861 6.798959 GCACTAAGCTTGAGACACTTATTTTG 59.201 38.462 9.86 0.00 41.15 2.44
2996 4862 7.307989 GCACTAAGCTTGAGACACTTATTTTGA 60.308 37.037 9.86 0.00 41.15 2.69
2997 4863 8.226448 CACTAAGCTTGAGACACTTATTTTGAG 58.774 37.037 9.86 0.00 0.00 3.02
2998 4864 8.150945 ACTAAGCTTGAGACACTTATTTTGAGA 58.849 33.333 9.86 0.00 0.00 3.27
2999 4865 7.992754 AAGCTTGAGACACTTATTTTGAGAT 57.007 32.000 0.00 0.00 0.00 2.75
3000 4866 7.375106 AGCTTGAGACACTTATTTTGAGATG 57.625 36.000 0.00 0.00 0.00 2.90
3001 4867 6.373774 AGCTTGAGACACTTATTTTGAGATGG 59.626 38.462 0.00 0.00 0.00 3.51
3002 4868 6.372659 GCTTGAGACACTTATTTTGAGATGGA 59.627 38.462 0.00 0.00 0.00 3.41
3003 4869 7.413877 GCTTGAGACACTTATTTTGAGATGGAG 60.414 40.741 0.00 0.00 0.00 3.86
3004 4870 6.409704 TGAGACACTTATTTTGAGATGGAGG 58.590 40.000 0.00 0.00 0.00 4.30
3005 4871 5.749462 AGACACTTATTTTGAGATGGAGGG 58.251 41.667 0.00 0.00 0.00 4.30
3006 4872 5.488919 AGACACTTATTTTGAGATGGAGGGA 59.511 40.000 0.00 0.00 0.00 4.20
3007 4873 5.749462 ACACTTATTTTGAGATGGAGGGAG 58.251 41.667 0.00 0.00 0.00 4.30
3008 4874 5.251700 ACACTTATTTTGAGATGGAGGGAGT 59.748 40.000 0.00 0.00 0.00 3.85
3009 4875 6.443849 ACACTTATTTTGAGATGGAGGGAGTA 59.556 38.462 0.00 0.00 0.00 2.59
3010 4876 6.763610 CACTTATTTTGAGATGGAGGGAGTAC 59.236 42.308 0.00 0.00 0.00 2.73
3011 4877 6.674419 ACTTATTTTGAGATGGAGGGAGTACT 59.326 38.462 0.00 0.00 0.00 2.73
3038 4904 7.640616 TTACACTGCAAATGTGATGATTTTG 57.359 32.000 11.19 0.00 38.65 2.44
3044 4910 9.357652 ACTGCAAATGTGATGATTTTGTTATAC 57.642 29.630 0.00 0.00 33.83 1.47
3119 4985 5.487488 TCCATGAGTGTGGTTTAGAATACCT 59.513 40.000 0.00 0.00 40.27 3.08
3136 5002 7.454225 AGAATACCTACTAAATCCAGCCATTC 58.546 38.462 0.00 0.00 0.00 2.67
3148 5014 3.633525 TCCAGCCATTCATATTGAAGTGC 59.366 43.478 5.94 5.94 40.05 4.40
3150 5016 4.357142 CAGCCATTCATATTGAAGTGCAC 58.643 43.478 9.40 9.40 40.05 4.57
3185 5051 6.214205 TGTATTTCGTGTTCGTTTAACCTC 57.786 37.500 0.00 0.00 37.27 3.85
3263 5140 0.388659 TATTGCCCAATTCGCCATGC 59.611 50.000 0.00 0.00 32.50 4.06
3358 6682 7.741785 TGATCTTGTGTTTCTTCTTACCCTTA 58.258 34.615 0.00 0.00 0.00 2.69
3360 6684 7.133133 TCTTGTGTTTCTTCTTACCCTTAGT 57.867 36.000 0.00 0.00 0.00 2.24
3444 7218 3.425525 CGATAACTAGGTATGCACTTGCG 59.574 47.826 4.64 0.00 45.83 4.85
3483 7257 2.287915 GCCACTATAAGCATGGTCGTTG 59.712 50.000 0.00 0.00 35.79 4.10
3484 7258 3.531538 CCACTATAAGCATGGTCGTTGT 58.468 45.455 0.00 0.00 0.00 3.32
3485 7259 3.938963 CCACTATAAGCATGGTCGTTGTT 59.061 43.478 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 1.898938 AATCAACATGCATGCGTTCG 58.101 45.000 26.53 10.42 0.00 3.95
320 681 6.362283 CCTTCATCACAAATGGTTTACGAAAC 59.638 38.462 0.00 0.00 40.65 2.78
353 714 2.491693 CCGGTGGTGTGCAAAATTCTAT 59.508 45.455 0.00 0.00 0.00 1.98
461 830 4.525100 ACAAACCCATATAGGCGTGTTTTT 59.475 37.500 0.00 0.00 30.02 1.94
462 831 4.083565 ACAAACCCATATAGGCGTGTTTT 58.916 39.130 0.00 0.00 30.02 2.43
463 832 3.692593 GACAAACCCATATAGGCGTGTTT 59.307 43.478 0.00 0.00 31.85 2.83
464 833 3.054655 AGACAAACCCATATAGGCGTGTT 60.055 43.478 0.00 0.00 35.39 3.32
465 834 2.504175 AGACAAACCCATATAGGCGTGT 59.496 45.455 0.00 0.00 35.39 4.49
479 848 4.351131 AGAAACAACCGTTGAGACAAAC 57.649 40.909 18.19 2.68 34.86 2.93
624 1105 1.202879 ACCAGAAATTTGCTCCCGACA 60.203 47.619 0.00 0.00 0.00 4.35
712 1193 7.029563 GCACGAAATAAATCACCTCTTCAATT 58.970 34.615 0.00 0.00 0.00 2.32
713 1194 6.150976 TGCACGAAATAAATCACCTCTTCAAT 59.849 34.615 0.00 0.00 0.00 2.57
725 1208 7.849804 ACTCACTCTAATGCACGAAATAAAT 57.150 32.000 0.00 0.00 0.00 1.40
790 1276 9.569167 CTCGTCTAAAACAATGTCTCTGTTATA 57.431 33.333 0.00 0.00 35.98 0.98
1062 1552 6.689241 CGTAGTCTAGTTCTTGATTAGTGCAG 59.311 42.308 0.00 0.00 0.00 4.41
1107 1597 0.318275 CGAGCGCTACCTCCTCAATC 60.318 60.000 11.50 0.00 0.00 2.67
1281 1771 1.407989 GCCTCTACCTTCTGCTTGCAT 60.408 52.381 0.00 0.00 0.00 3.96
1362 1855 4.363990 ACAGCGACCACAGCCTCG 62.364 66.667 0.00 0.00 34.64 4.63
1752 2245 1.272490 ACGTTGCTCTCTCCATCGAAA 59.728 47.619 0.00 0.00 31.77 3.46
2274 2767 4.908687 AACTGCTCCACACGCGCA 62.909 61.111 5.73 0.00 0.00 6.09
2665 4510 3.385755 TGTAGGTATACTTTCTTCCCCGC 59.614 47.826 2.25 0.00 32.75 6.13
2667 4512 7.311109 CCCATATGTAGGTATACTTTCTTCCCC 60.311 44.444 2.25 0.00 32.75 4.81
2682 4527 5.768980 ATCCACTCAATCCCATATGTAGG 57.231 43.478 1.24 0.00 0.00 3.18
2691 4536 8.980481 TTCTCTTTATTTATCCACTCAATCCC 57.020 34.615 0.00 0.00 0.00 3.85
2692 4537 8.563732 GCTTCTCTTTATTTATCCACTCAATCC 58.436 37.037 0.00 0.00 0.00 3.01
2693 4538 9.336171 AGCTTCTCTTTATTTATCCACTCAATC 57.664 33.333 0.00 0.00 0.00 2.67
2694 4539 9.336171 GAGCTTCTCTTTATTTATCCACTCAAT 57.664 33.333 0.00 0.00 0.00 2.57
2695 4540 8.321353 TGAGCTTCTCTTTATTTATCCACTCAA 58.679 33.333 0.00 0.00 0.00 3.02
2696 4541 7.766278 GTGAGCTTCTCTTTATTTATCCACTCA 59.234 37.037 0.00 0.00 0.00 3.41
2731 4590 3.704566 ACCTTGAACATCCTCTACGCATA 59.295 43.478 0.00 0.00 0.00 3.14
2732 4591 2.501723 ACCTTGAACATCCTCTACGCAT 59.498 45.455 0.00 0.00 0.00 4.73
2734 4593 2.674796 ACCTTGAACATCCTCTACGC 57.325 50.000 0.00 0.00 0.00 4.42
2735 4594 7.749570 CGTAATATACCTTGAACATCCTCTACG 59.250 40.741 0.00 0.00 0.00 3.51
2736 4595 8.574737 ACGTAATATACCTTGAACATCCTCTAC 58.425 37.037 0.00 0.00 0.00 2.59
2737 4596 8.573885 CACGTAATATACCTTGAACATCCTCTA 58.426 37.037 0.00 0.00 0.00 2.43
2738 4597 7.069578 ACACGTAATATACCTTGAACATCCTCT 59.930 37.037 0.00 0.00 0.00 3.69
2739 4598 7.169308 CACACGTAATATACCTTGAACATCCTC 59.831 40.741 0.00 0.00 0.00 3.71
2740 4599 6.984474 CACACGTAATATACCTTGAACATCCT 59.016 38.462 0.00 0.00 0.00 3.24
2741 4600 6.292703 GCACACGTAATATACCTTGAACATCC 60.293 42.308 0.00 0.00 0.00 3.51
2742 4601 6.479001 AGCACACGTAATATACCTTGAACATC 59.521 38.462 0.00 0.00 0.00 3.06
2743 4602 6.346096 AGCACACGTAATATACCTTGAACAT 58.654 36.000 0.00 0.00 0.00 2.71
2744 4603 5.726397 AGCACACGTAATATACCTTGAACA 58.274 37.500 0.00 0.00 0.00 3.18
2745 4604 6.311935 TCAAGCACACGTAATATACCTTGAAC 59.688 38.462 0.00 0.00 35.77 3.18
2746 4605 6.399743 TCAAGCACACGTAATATACCTTGAA 58.600 36.000 0.00 0.00 35.77 2.69
2747 4606 5.968254 TCAAGCACACGTAATATACCTTGA 58.032 37.500 0.00 0.00 36.18 3.02
2748 4607 6.091577 TGTTCAAGCACACGTAATATACCTTG 59.908 38.462 0.00 0.00 0.00 3.61
2749 4608 6.091713 GTGTTCAAGCACACGTAATATACCTT 59.908 38.462 0.00 0.00 37.90 3.50
2750 4609 5.579511 GTGTTCAAGCACACGTAATATACCT 59.420 40.000 0.00 0.00 37.90 3.08
2751 4610 5.792631 GTGTTCAAGCACACGTAATATACC 58.207 41.667 0.00 0.00 37.90 2.73
2845 4704 6.875726 TGAAAGGAATTATATCGATCAGCCAG 59.124 38.462 0.00 0.00 0.00 4.85
2923 4789 0.393077 AGACACTTGGAACGTGAGGG 59.607 55.000 0.00 0.00 36.29 4.30
2924 4790 1.068588 TGAGACACTTGGAACGTGAGG 59.931 52.381 0.00 0.00 36.29 3.86
2925 4791 2.509052 TGAGACACTTGGAACGTGAG 57.491 50.000 0.00 0.00 36.29 3.51
2926 4792 2.821546 CTTGAGACACTTGGAACGTGA 58.178 47.619 0.00 0.00 36.29 4.35
2927 4793 1.261619 GCTTGAGACACTTGGAACGTG 59.738 52.381 0.00 0.00 38.32 4.49
2928 4794 1.139058 AGCTTGAGACACTTGGAACGT 59.861 47.619 0.00 0.00 0.00 3.99
2929 4795 1.871080 AGCTTGAGACACTTGGAACG 58.129 50.000 0.00 0.00 0.00 3.95
2930 4796 4.212214 CACTAAGCTTGAGACACTTGGAAC 59.788 45.833 9.86 0.00 0.00 3.62
2931 4797 4.380531 CACTAAGCTTGAGACACTTGGAA 58.619 43.478 9.86 0.00 0.00 3.53
2932 4798 3.803715 GCACTAAGCTTGAGACACTTGGA 60.804 47.826 9.86 0.00 41.15 3.53
2933 4799 2.481952 GCACTAAGCTTGAGACACTTGG 59.518 50.000 9.86 0.00 41.15 3.61
2934 4800 3.802722 GCACTAAGCTTGAGACACTTG 57.197 47.619 9.86 0.00 41.15 3.16
2954 4820 5.862811 CTTAGTGCTAAGCTTAGTGCAAAG 58.137 41.667 29.42 22.82 45.94 2.77
2955 4821 5.862924 CTTAGTGCTAAGCTTAGTGCAAA 57.137 39.130 29.42 18.99 45.94 3.68
2970 4836 6.487689 AAATAAGTGTCTCAAGCTTAGTGC 57.512 37.500 0.00 0.00 43.29 4.40
2971 4837 8.087982 TCAAAATAAGTGTCTCAAGCTTAGTG 57.912 34.615 0.00 0.00 0.00 2.74
2972 4838 8.150945 TCTCAAAATAAGTGTCTCAAGCTTAGT 58.849 33.333 0.00 0.00 0.00 2.24
2973 4839 8.539770 TCTCAAAATAAGTGTCTCAAGCTTAG 57.460 34.615 0.00 0.00 0.00 2.18
2974 4840 8.939929 CATCTCAAAATAAGTGTCTCAAGCTTA 58.060 33.333 0.00 0.00 0.00 3.09
2975 4841 7.094463 CCATCTCAAAATAAGTGTCTCAAGCTT 60.094 37.037 0.00 0.00 0.00 3.74
2976 4842 6.373774 CCATCTCAAAATAAGTGTCTCAAGCT 59.626 38.462 0.00 0.00 0.00 3.74
2977 4843 6.372659 TCCATCTCAAAATAAGTGTCTCAAGC 59.627 38.462 0.00 0.00 0.00 4.01
2978 4844 7.065563 CCTCCATCTCAAAATAAGTGTCTCAAG 59.934 40.741 0.00 0.00 0.00 3.02
2979 4845 6.881065 CCTCCATCTCAAAATAAGTGTCTCAA 59.119 38.462 0.00 0.00 0.00 3.02
2980 4846 6.409704 CCTCCATCTCAAAATAAGTGTCTCA 58.590 40.000 0.00 0.00 0.00 3.27
2981 4847 5.819901 CCCTCCATCTCAAAATAAGTGTCTC 59.180 44.000 0.00 0.00 0.00 3.36
2982 4848 5.488919 TCCCTCCATCTCAAAATAAGTGTCT 59.511 40.000 0.00 0.00 0.00 3.41
2983 4849 5.745227 TCCCTCCATCTCAAAATAAGTGTC 58.255 41.667 0.00 0.00 0.00 3.67
2984 4850 5.251700 ACTCCCTCCATCTCAAAATAAGTGT 59.748 40.000 0.00 0.00 0.00 3.55
2985 4851 5.749462 ACTCCCTCCATCTCAAAATAAGTG 58.251 41.667 0.00 0.00 0.00 3.16
2986 4852 6.674419 AGTACTCCCTCCATCTCAAAATAAGT 59.326 38.462 0.00 0.00 0.00 2.24
2987 4853 7.130681 AGTACTCCCTCCATCTCAAAATAAG 57.869 40.000 0.00 0.00 0.00 1.73
2988 4854 7.510675 AAGTACTCCCTCCATCTCAAAATAA 57.489 36.000 0.00 0.00 0.00 1.40
2989 4855 7.510675 AAAGTACTCCCTCCATCTCAAAATA 57.489 36.000 0.00 0.00 0.00 1.40
2990 4856 6.394345 AAAGTACTCCCTCCATCTCAAAAT 57.606 37.500 0.00 0.00 0.00 1.82
2991 4857 5.843019 AAAGTACTCCCTCCATCTCAAAA 57.157 39.130 0.00 0.00 0.00 2.44
2992 4858 5.843019 AAAAGTACTCCCTCCATCTCAAA 57.157 39.130 0.00 0.00 0.00 2.69
2993 4859 5.843019 AAAAAGTACTCCCTCCATCTCAA 57.157 39.130 0.00 0.00 0.00 3.02
2994 4860 5.783360 TGTAAAAAGTACTCCCTCCATCTCA 59.217 40.000 0.00 0.00 0.00 3.27
2995 4861 6.070710 AGTGTAAAAAGTACTCCCTCCATCTC 60.071 42.308 0.00 0.00 0.00 2.75
2996 4862 5.785940 AGTGTAAAAAGTACTCCCTCCATCT 59.214 40.000 0.00 0.00 0.00 2.90
2997 4863 5.875359 CAGTGTAAAAAGTACTCCCTCCATC 59.125 44.000 0.00 0.00 0.00 3.51
2998 4864 5.803470 GCAGTGTAAAAAGTACTCCCTCCAT 60.803 44.000 0.00 0.00 0.00 3.41
2999 4865 4.504340 GCAGTGTAAAAAGTACTCCCTCCA 60.504 45.833 0.00 0.00 0.00 3.86
3000 4866 4.001652 GCAGTGTAAAAAGTACTCCCTCC 58.998 47.826 0.00 0.00 0.00 4.30
3001 4867 4.638304 TGCAGTGTAAAAAGTACTCCCTC 58.362 43.478 0.00 0.00 0.00 4.30
3002 4868 4.699925 TGCAGTGTAAAAAGTACTCCCT 57.300 40.909 0.00 0.00 0.00 4.20
3003 4869 5.761165 TTTGCAGTGTAAAAAGTACTCCC 57.239 39.130 3.69 0.00 0.00 4.30
3004 4870 6.636850 CACATTTGCAGTGTAAAAAGTACTCC 59.363 38.462 10.53 0.00 32.44 3.85
3005 4871 7.414436 TCACATTTGCAGTGTAAAAAGTACTC 58.586 34.615 10.53 0.00 38.16 2.59
3006 4872 7.328277 TCACATTTGCAGTGTAAAAAGTACT 57.672 32.000 10.53 0.00 38.16 2.73
3007 4873 7.860373 TCATCACATTTGCAGTGTAAAAAGTAC 59.140 33.333 10.53 0.00 38.16 2.73
3008 4874 7.935520 TCATCACATTTGCAGTGTAAAAAGTA 58.064 30.769 10.53 0.00 38.16 2.24
3009 4875 6.804677 TCATCACATTTGCAGTGTAAAAAGT 58.195 32.000 10.53 9.41 38.16 2.66
3010 4876 7.878477 ATCATCACATTTGCAGTGTAAAAAG 57.122 32.000 10.53 8.82 38.16 2.27
3011 4877 8.659925 AAATCATCACATTTGCAGTGTAAAAA 57.340 26.923 10.53 0.78 38.16 1.94
3038 4904 7.192232 ACTCAAAGATAACCGAGACGTATAAC 58.808 38.462 0.00 0.00 0.00 1.89
3044 4910 5.840940 AAAACTCAAAGATAACCGAGACG 57.159 39.130 0.00 0.00 0.00 4.18
3119 4985 9.288576 CTTCAATATGAATGGCTGGATTTAGTA 57.711 33.333 0.00 0.00 35.59 1.82
3175 5041 4.879598 ACTTAGTGGACAGAGGTTAAACG 58.120 43.478 0.00 0.00 0.00 3.60
3215 5085 9.319143 CCTCTAGATTAATGTTCAACAGTTAGG 57.681 37.037 0.00 0.00 0.00 2.69
3276 5153 2.353323 GCTAGTTTTACCTTCCGTGGG 58.647 52.381 0.00 0.00 0.00 4.61
3280 5157 2.950433 TCACGCTAGTTTTACCTTCCG 58.050 47.619 0.00 0.00 0.00 4.30
3311 6635 9.288576 GATCATAAAATACTGGTGATCCAATCA 57.711 33.333 0.00 0.00 43.81 2.57
3337 6661 6.293462 GCACTAAGGGTAAGAAGAAACACAAG 60.293 42.308 0.00 0.00 0.00 3.16
3358 6682 1.608590 CGGTTGAGACCAATTTGCACT 59.391 47.619 0.00 0.00 46.91 4.40
3360 6684 1.974265 TCGGTTGAGACCAATTTGCA 58.026 45.000 0.00 0.00 46.91 4.08
3444 7218 1.596727 GGCATCATCGTTCTCTCTTGC 59.403 52.381 0.00 0.00 0.00 4.01
3483 7257 6.908870 ATTGAACTTCTTTTTGGCAAGAAC 57.091 33.333 0.00 0.00 37.77 3.01
3484 7258 9.612066 ATTAATTGAACTTCTTTTTGGCAAGAA 57.388 25.926 0.00 0.82 39.91 2.52
3517 7291 7.928873 AGAGATTTTATTTGTTACTCCCTCCA 58.071 34.615 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.