Multiple sequence alignment - TraesCS6A01G172200

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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 TraesCS6A01G172200 chr6A 100.000 5205 0 0 1 5205 183295282 183290078 0.000000e+00 9612.0
1 TraesCS6A01G172200 chr6A 94.613 297 13 2 1 294 582247862 582247566 1.710000e-124 457.0
2 TraesCS6A01G172200 chr6A 95.455 44 2 0 878 921 169505269 169505312 2.600000e-08 71.3
3 TraesCS6A01G172200 chr6A 80.460 87 16 1 835 921 459670657 459670572 1.210000e-06 65.8
4 TraesCS6A01G172200 chr6B 94.111 3549 148 22 1668 5185 239870916 239867398 0.000000e+00 5339.0
5 TraesCS6A01G172200 chr6B 91.910 754 42 6 928 1674 239871734 239870993 0.000000e+00 1037.0
6 TraesCS6A01G172200 chr6D 94.118 1802 77 19 2508 4288 140024973 140023180 0.000000e+00 2713.0
7 TraesCS6A01G172200 chr6D 95.809 859 31 3 1668 2521 140027495 140026637 0.000000e+00 1382.0
8 TraesCS6A01G172200 chr6D 92.175 754 43 3 922 1666 140028332 140027586 0.000000e+00 1051.0
9 TraesCS6A01G172200 chr6D 92.822 404 21 7 4286 4684 140023100 140022700 3.490000e-161 579.0
10 TraesCS6A01G172200 chr6D 86.982 507 39 10 4696 5200 140022411 140021930 3.540000e-151 545.0
11 TraesCS6A01G172200 chr5A 95.793 927 31 6 2 922 566655172 566656096 0.000000e+00 1489.0
12 TraesCS6A01G172200 chr3B 91.604 929 61 9 1 922 614996176 614995258 0.000000e+00 1267.0
13 TraesCS6A01G172200 chr3B 93.182 44 3 0 878 921 709516517 709516560 1.210000e-06 65.8
14 TraesCS6A01G172200 chr3B 83.333 60 10 0 215 274 486385940 486385999 7.280000e-04 56.5
15 TraesCS6A01G172200 chr2B 92.126 508 37 2 3 507 776307479 776307986 0.000000e+00 713.0
16 TraesCS6A01G172200 chr2B 88.206 407 35 8 516 918 776309615 776310012 1.700000e-129 473.0
17 TraesCS6A01G172200 chr2B 86.957 414 40 9 511 921 8195933 8196335 2.210000e-123 453.0
18 TraesCS6A01G172200 chr2B 86.715 414 41 9 511 921 8032052 8032454 1.030000e-121 448.0
19 TraesCS6A01G172200 chr2B 86.473 414 43 8 511 921 8147897 8148300 4.780000e-120 442.0
20 TraesCS6A01G172200 chr2B 86.684 383 39 7 511 890 8120996 8121369 1.040000e-111 414.0
21 TraesCS6A01G172200 chr2B 85.901 383 41 8 511 890 7952252 7952624 3.780000e-106 396.0
22 TraesCS6A01G172200 chr2B 85.901 383 41 8 511 890 7983221 7983593 3.780000e-106 396.0
23 TraesCS6A01G172200 chrUn 83.243 555 75 13 4657 5203 43290475 43291019 1.300000e-135 494.0
24 TraesCS6A01G172200 chr5B 86.353 425 56 2 4780 5202 678705612 678706036 3.670000e-126 462.0
25 TraesCS6A01G172200 chr5B 89.091 55 6 0 867 921 101904901 101904847 9.350000e-08 69.4
26 TraesCS6A01G172200 chr7D 81.752 548 84 14 4655 5198 130174776 130175311 1.330000e-120 444.0
27 TraesCS6A01G172200 chr7D 82.653 490 73 11 4708 5190 478839726 478839242 1.730000e-114 424.0
28 TraesCS6A01G172200 chr7D 79.482 502 74 14 4707 5202 429485402 429485880 3.890000e-86 329.0
29 TraesCS6A01G172200 chr4A 82.186 494 65 16 4706 5185 705295708 705296192 2.260000e-108 403.0
30 TraesCS6A01G172200 chr4A 81.446 415 70 7 4715 5127 705471862 705471453 3.000000e-87 333.0
31 TraesCS6A01G172200 chr4D 79.817 545 89 12 4663 5201 490346501 490347030 1.370000e-100 377.0
32 TraesCS6A01G172200 chr1B 77.519 516 102 14 4664 5171 670210260 670210769 1.100000e-76 298.0
33 TraesCS6A01G172200 chr1B 86.364 66 5 3 858 921 583204616 583204553 9.350000e-08 69.4
34 TraesCS6A01G172200 chr1D 78.471 497 75 21 4714 5203 237333426 237332955 3.940000e-76 296.0


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 TraesCS6A01G172200 chr6A 183290078 183295282 5204 True 9612 9612 100.0000 1 5205 1 chr6A.!!$R1 5204
1 TraesCS6A01G172200 chr6B 239867398 239871734 4336 True 3188 5339 93.0105 928 5185 2 chr6B.!!$R1 4257
2 TraesCS6A01G172200 chr6D 140021930 140028332 6402 True 1254 2713 92.3812 922 5200 5 chr6D.!!$R1 4278
3 TraesCS6A01G172200 chr5A 566655172 566656096 924 False 1489 1489 95.7930 2 922 1 chr5A.!!$F1 920
4 TraesCS6A01G172200 chr3B 614995258 614996176 918 True 1267 1267 91.6040 1 922 1 chr3B.!!$R1 921
5 TraesCS6A01G172200 chr2B 776307479 776310012 2533 False 593 713 90.1660 3 918 2 chr2B.!!$F7 915
6 TraesCS6A01G172200 chrUn 43290475 43291019 544 False 494 494 83.2430 4657 5203 1 chrUn.!!$F1 546
7 TraesCS6A01G172200 chr7D 130174776 130175311 535 False 444 444 81.7520 4655 5198 1 chr7D.!!$F1 543
8 TraesCS6A01G172200 chr4D 490346501 490347030 529 False 377 377 79.8170 4663 5201 1 chr4D.!!$F1 538
9 TraesCS6A01G172200 chr1B 670210260 670210769 509 False 298 298 77.5190 4664 5171 1 chr1B.!!$F1 507

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
989 2632 0.976641 TCCACTTACACCTCTGCCAG 59.023 55.000 0.00 0.0 0.0 4.85 F
1342 2987 0.824109 GCCCTGCTTTCCCAATTACC 59.176 55.000 0.00 0.0 0.0 2.85 F
1693 3446 1.136197 TGCGTTTATGTGTAGCGTTGC 60.136 47.619 0.00 0.0 0.0 4.17 F
2584 6027 1.967319 TGGCAAGTTTCCAGTCAGAC 58.033 50.000 0.00 0.0 0.0 3.51 F
3354 6827 0.678048 ACCGCTTCCTGAATTCTGCC 60.678 55.000 7.05 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2131 3888 1.732917 CCGGTGCTGCAGAACAAAA 59.267 52.632 26.30 0.0 0.00 2.44 R
2584 6027 2.163613 GGGTATGCCTTGAAGGAAAACG 59.836 50.000 16.93 0.0 37.67 3.60 R
3354 6827 1.797320 ATGGGATTTTGGCCATCTGG 58.203 50.000 6.09 0.0 38.53 3.86 R
3561 7034 1.814394 GATGTGATCACTTTGCAGCCA 59.186 47.619 25.55 3.4 0.00 4.75 R
5080 8942 1.672854 CCCGGGCTCGTTGATGAGTA 61.673 60.000 8.08 0.0 38.28 2.59 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
36 37 1.273606 CTGGAACCAGAGAAAGAGCGA 59.726 52.381 14.94 0.00 46.30 4.93
55 56 3.009723 CGAAGGATACAAATGGTGCAGT 58.990 45.455 0.00 0.00 41.41 4.40
90 91 5.137551 ACAGTACCCAAAAATGCTACAACT 58.862 37.500 0.00 0.00 0.00 3.16
159 162 1.836604 AAAAGTTGTGGGCGGCCAT 60.837 52.632 35.05 15.83 0.00 4.40
635 2260 6.660521 TCAATGACAGATCTGCAACCTAAATT 59.339 34.615 22.83 8.02 0.00 1.82
665 2290 1.153549 GAGGTTCTTCGCCGAGCAT 60.154 57.895 0.00 0.00 0.00 3.79
739 2374 1.633852 GCAGCTTCTGTTCCTGCGAG 61.634 60.000 0.00 0.00 41.99 5.03
740 2375 1.018226 CAGCTTCTGTTCCTGCGAGG 61.018 60.000 0.00 0.00 36.46 4.63
741 2376 2.394563 GCTTCTGTTCCTGCGAGGC 61.395 63.158 0.00 0.00 34.61 4.70
742 2377 1.294780 CTTCTGTTCCTGCGAGGCT 59.705 57.895 0.00 0.00 34.61 4.58
743 2378 1.004560 TTCTGTTCCTGCGAGGCTG 60.005 57.895 0.00 0.00 34.61 4.85
744 2379 3.123620 CTGTTCCTGCGAGGCTGC 61.124 66.667 0.00 0.00 34.61 5.25
746 2381 4.742201 GTTCCTGCGAGGCTGCGA 62.742 66.667 9.91 0.00 34.61 5.10
747 2382 4.742201 TTCCTGCGAGGCTGCGAC 62.742 66.667 9.91 3.29 34.61 5.19
812 2447 4.773674 TGACCAGTATAAAGACGAGGGAAA 59.226 41.667 0.00 0.00 0.00 3.13
968 2606 1.227639 GAGTCGCTGATAGCCTACGA 58.772 55.000 0.00 0.00 38.18 3.43
977 2620 4.022242 GCTGATAGCCTACGATTCCACTTA 60.022 45.833 0.00 0.00 34.48 2.24
988 2631 1.429930 TTCCACTTACACCTCTGCCA 58.570 50.000 0.00 0.00 0.00 4.92
989 2632 0.976641 TCCACTTACACCTCTGCCAG 59.023 55.000 0.00 0.00 0.00 4.85
1053 2697 3.770040 CACCGCGTCTCCCCATCA 61.770 66.667 4.92 0.00 0.00 3.07
1058 2702 1.522092 GCGTCTCCCCATCACATCA 59.478 57.895 0.00 0.00 0.00 3.07
1132 2776 2.045926 CAGGGCTTCCTTCGTGGG 60.046 66.667 0.00 0.00 39.29 4.61
1237 2882 1.520787 GCATCGTTACAGTCGGGGG 60.521 63.158 0.00 0.00 0.00 5.40
1264 2909 1.079127 CTCCGTGGTGATCGGCTTT 60.079 57.895 0.00 0.00 46.49 3.51
1276 2921 4.133796 GGCTTTGTGCGGATGCCC 62.134 66.667 0.00 0.00 44.05 5.36
1284 2929 2.336809 GCGGATGCCCTCTCGTAG 59.663 66.667 0.00 0.00 33.98 3.51
1289 2934 1.576356 GATGCCCTCTCGTAGCTTTG 58.424 55.000 0.00 0.00 0.00 2.77
1293 2938 1.206371 GCCCTCTCGTAGCTTTGGTTA 59.794 52.381 0.00 0.00 0.00 2.85
1321 2966 6.207614 GCCAGAGAAGGACTAAACATTTTTCT 59.792 38.462 0.00 0.00 0.00 2.52
1337 2982 1.072266 TTCTAGCCCTGCTTTCCCAA 58.928 50.000 0.00 0.00 40.44 4.12
1338 2983 1.298953 TCTAGCCCTGCTTTCCCAAT 58.701 50.000 0.00 0.00 40.44 3.16
1339 2984 1.640670 TCTAGCCCTGCTTTCCCAATT 59.359 47.619 0.00 0.00 40.44 2.32
1340 2985 2.849943 TCTAGCCCTGCTTTCCCAATTA 59.150 45.455 0.00 0.00 40.44 1.40
1341 2986 1.852633 AGCCCTGCTTTCCCAATTAC 58.147 50.000 0.00 0.00 33.89 1.89
1342 2987 0.824109 GCCCTGCTTTCCCAATTACC 59.176 55.000 0.00 0.00 0.00 2.85
1343 2988 1.894978 GCCCTGCTTTCCCAATTACCA 60.895 52.381 0.00 0.00 0.00 3.25
1347 2992 3.099141 CTGCTTTCCCAATTACCATGGT 58.901 45.455 23.55 23.55 36.14 3.55
1444 3097 2.052782 AGTTCCGTTCCAAGTTTGCT 57.947 45.000 0.00 0.00 0.00 3.91
1475 3128 3.507622 CCTGGATTTTGAGTCTGTTTCCC 59.492 47.826 0.00 0.00 0.00 3.97
1489 3142 5.347907 GTCTGTTTCCCTTGTATACGAGTTG 59.652 44.000 17.25 9.29 0.00 3.16
1505 3158 5.898174 ACGAGTTGACATATATTGTTCGGA 58.102 37.500 0.00 0.00 38.54 4.55
1581 3234 5.636123 TGTGAATTGGGCTTACCTTTCTAA 58.364 37.500 0.00 0.00 41.11 2.10
1592 3245 8.188799 GGGCTTACCTTTCTAAAATAATGTGAC 58.811 37.037 0.00 0.00 35.85 3.67
1666 3319 8.467598 TGAACTAGTTTAAGTCTGCGAAGATAT 58.532 33.333 10.02 0.00 0.00 1.63
1688 3441 3.757745 ATGGTTGCGTTTATGTGTAGC 57.242 42.857 0.00 0.00 0.00 3.58
1693 3446 1.136197 TGCGTTTATGTGTAGCGTTGC 60.136 47.619 0.00 0.00 0.00 4.17
1904 3658 9.620259 ATTTCCTACTCCTTACATCTTGATTTC 57.380 33.333 0.00 0.00 0.00 2.17
1905 3659 7.733773 TCCTACTCCTTACATCTTGATTTCA 57.266 36.000 0.00 0.00 0.00 2.69
2005 3762 8.664211 CCTTTTAGGTATCTCTGGTTGTATTC 57.336 38.462 0.00 0.00 0.00 1.75
2075 3832 3.195471 TGAAATCCGTTGTGTGTACCA 57.805 42.857 0.00 0.00 0.00 3.25
2105 3862 5.331069 ACACTACTCTTAGCAGTCCCTTTA 58.669 41.667 0.00 0.00 0.00 1.85
2338 4095 4.521130 TCTCATTACTCTTGCACTCGTT 57.479 40.909 0.00 0.00 0.00 3.85
2349 4113 5.294356 TCTTGCACTCGTTGTAGTTAATGT 58.706 37.500 0.00 0.00 0.00 2.71
2584 6027 1.967319 TGGCAAGTTTCCAGTCAGAC 58.033 50.000 0.00 0.00 0.00 3.51
2725 6169 8.692110 TGCATCTAAACTGCATTAGATTTTTG 57.308 30.769 16.51 10.37 45.78 2.44
2727 6171 9.787532 GCATCTAAACTGCATTAGATTTTTGTA 57.212 29.630 16.51 0.00 45.78 2.41
2765 6209 8.959548 TGCAATATTTGTCTAAGATGTGTTGAT 58.040 29.630 0.00 0.00 0.00 2.57
2771 6215 5.550290 TGTCTAAGATGTGTTGATGAAGCA 58.450 37.500 0.00 0.00 0.00 3.91
2801 6245 9.612066 GATGAAAGTAGGATCTTCTCTTGAAAT 57.388 33.333 0.00 0.00 0.00 2.17
2832 6276 6.035220 GCCACAACACAAACTTAAGTAAAACC 59.965 38.462 8.92 0.00 0.00 3.27
3224 6697 5.770162 AGTGAACAAGGGGTTATTCTTCTTG 59.230 40.000 0.00 0.00 40.63 3.02
3237 6710 9.481340 GGTTATTCTTCTTGCTCAATTTCTTTT 57.519 29.630 0.00 0.00 0.00 2.27
3354 6827 0.678048 ACCGCTTCCTGAATTCTGCC 60.678 55.000 7.05 0.00 0.00 4.85
3423 6896 4.084013 AGCGTACTTATTCAAACTGTGTGC 60.084 41.667 0.00 0.00 0.00 4.57
3561 7034 2.309755 TCCATCTTTGCCAGAACCATCT 59.690 45.455 0.00 0.00 34.16 2.90
3602 7075 4.283337 TCATCCATACCGGTAAAGTCTCA 58.717 43.478 20.22 0.00 35.57 3.27
3606 7079 4.283978 TCCATACCGGTAAAGTCTCAACAA 59.716 41.667 20.22 0.00 35.57 2.83
3655 7128 1.926511 GCCGAATGCACTCACCAAGG 61.927 60.000 0.00 0.00 40.77 3.61
3869 7342 4.166725 TGGAATGCTCAGTGGGATATCTTT 59.833 41.667 2.05 0.00 0.00 2.52
3924 7397 2.544486 CGACGAGATGATGCTCATTGGA 60.544 50.000 0.00 0.00 37.20 3.53
4148 7630 4.493547 TGCTCAAACACTTTTCAACCTTG 58.506 39.130 0.00 0.00 0.00 3.61
4210 7693 1.985895 CCTGTCCCTTACTGAAACCCT 59.014 52.381 0.00 0.00 0.00 4.34
4249 7732 4.211164 TGCAGAATACACGTGAACAAAGAG 59.789 41.667 25.01 5.96 0.00 2.85
4344 7909 2.231964 TGCAGAAATCATTTGGAGCCAC 59.768 45.455 0.00 0.00 0.00 5.01
4424 7990 6.323996 ACTCTAGTTTGCTGCACATATACCTA 59.676 38.462 0.00 0.00 0.00 3.08
4425 7991 6.513180 TCTAGTTTGCTGCACATATACCTAC 58.487 40.000 0.00 0.00 0.00 3.18
4426 7992 5.359194 AGTTTGCTGCACATATACCTACT 57.641 39.130 0.00 0.00 0.00 2.57
4486 8053 3.002965 CCTTTTCTAAACGAGGTTTGCGT 59.997 43.478 4.11 0.00 44.94 5.24
4515 8082 4.174009 GACGAAAGCTATGTGTTGCTCTA 58.826 43.478 0.00 0.00 38.75 2.43
4603 8172 4.334759 CGAGTTAGAGATCTTTACGGACCA 59.665 45.833 0.00 0.00 0.00 4.02
4630 8199 2.829120 ACCCAAAATAAATGTCCCCACG 59.171 45.455 0.00 0.00 0.00 4.94
4684 8253 9.213799 GAAGGATCAAAGATGTAGATAATGTCC 57.786 37.037 0.00 0.00 0.00 4.02
4692 8282 9.647918 AAAGATGTAGATAATGTCCACTAGAGA 57.352 33.333 0.00 0.00 0.00 3.10
4694 8284 8.664992 AGATGTAGATAATGTCCACTAGAGAGA 58.335 37.037 0.00 0.00 0.00 3.10
4761 8611 5.767168 AGTTGCTTTTTAGAGTCAAGAGCAT 59.233 36.000 8.63 0.00 38.32 3.79
4914 8768 4.993705 AAAAGTGGTGGAGACAAGGATA 57.006 40.909 0.00 0.00 46.06 2.59
4952 8806 2.238646 CACTTGGGGGTGTGCTAATCTA 59.761 50.000 0.00 0.00 33.04 1.98
4998 8856 1.670674 GCTCCCACGACAACGAATGTA 60.671 52.381 0.00 0.00 44.12 2.29
5080 8942 0.918983 TCTTGGGGCGAGATCCAAAT 59.081 50.000 0.00 0.00 41.83 2.32
5087 8949 3.330267 GGGCGAGATCCAAATACTCATC 58.670 50.000 0.00 0.00 0.00 2.92
5185 9051 6.127619 CCCAAGAGTAAAAAGATTTGCTAGGG 60.128 42.308 0.00 8.51 40.91 3.53
5192 9058 4.640771 AAAGATTTGCTAGGGTCTCACA 57.359 40.909 0.00 0.00 0.00 3.58
5203 9069 1.676014 GGGTCTCACAGGGAATCAACG 60.676 57.143 0.00 0.00 0.00 4.10
5204 9070 1.275291 GGTCTCACAGGGAATCAACGA 59.725 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.227300 TCCTACTGCACCATTTGTATCCTT 59.773 41.667 0.00 0.00 0.00 3.36
55 56 1.278127 GGGTACTGTTTGCAGCTCCTA 59.722 52.381 0.00 0.00 46.30 2.94
90 91 2.029649 GTGGTAGCTTCCTTACACGACA 60.030 50.000 11.05 0.00 0.00 4.35
159 162 2.939756 TGTAGCTTTTCAGTTTGTGCGA 59.060 40.909 0.00 0.00 0.00 5.10
163 166 3.066203 CCGGTTGTAGCTTTTCAGTTTGT 59.934 43.478 0.00 0.00 0.00 2.83
635 2260 1.682684 GAACCTCTCCCCGCTCTCA 60.683 63.158 0.00 0.00 0.00 3.27
812 2447 3.380479 TCGTCTCTCACATCGGTTTTT 57.620 42.857 0.00 0.00 0.00 1.94
816 2451 2.492088 TGATTTCGTCTCTCACATCGGT 59.508 45.455 0.00 0.00 0.00 4.69
817 2452 3.111838 CTGATTTCGTCTCTCACATCGG 58.888 50.000 0.00 0.00 0.00 4.18
825 2463 1.135257 CAGCCGTCTGATTTCGTCTCT 60.135 52.381 0.00 0.00 42.95 3.10
827 2465 0.603569 ACAGCCGTCTGATTTCGTCT 59.396 50.000 0.00 0.00 42.95 4.18
968 2606 1.985159 TGGCAGAGGTGTAAGTGGAAT 59.015 47.619 0.00 0.00 0.00 3.01
977 2620 0.472734 AGGAGAACTGGCAGAGGTGT 60.473 55.000 23.66 4.14 0.00 4.16
988 2631 2.066999 GGGCCATCGGAGGAGAACT 61.067 63.158 4.39 0.00 0.00 3.01
989 2632 2.367202 TGGGCCATCGGAGGAGAAC 61.367 63.158 0.00 0.00 0.00 3.01
1050 2694 0.179100 CGAGGAACGGCTGATGTGAT 60.179 55.000 0.00 0.00 38.46 3.06
1053 2697 2.125512 GCGAGGAACGGCTGATGT 60.126 61.111 0.00 0.00 42.83 3.06
1058 2702 0.951040 CTTCAAAGCGAGGAACGGCT 60.951 55.000 0.00 0.00 42.83 5.52
1165 2809 1.429148 CGCTACAAACCTGCCCGATC 61.429 60.000 0.00 0.00 0.00 3.69
1271 2916 0.179000 CCAAAGCTACGAGAGGGCAT 59.821 55.000 0.00 0.00 36.64 4.40
1276 2921 2.924290 GCACTAACCAAAGCTACGAGAG 59.076 50.000 0.00 0.00 0.00 3.20
1284 2929 2.185004 TCTCTGGCACTAACCAAAGC 57.815 50.000 0.00 0.00 39.86 3.51
1289 2934 1.903183 AGTCCTTCTCTGGCACTAACC 59.097 52.381 0.00 0.00 0.00 2.85
1293 2938 2.972713 TGTTTAGTCCTTCTCTGGCACT 59.027 45.455 0.00 0.00 0.00 4.40
1321 2966 2.357777 GGTAATTGGGAAAGCAGGGCTA 60.358 50.000 0.00 0.00 38.25 3.93
1337 2982 5.332743 ACAAATTCACTGGACCATGGTAAT 58.667 37.500 19.80 10.02 0.00 1.89
1338 2983 4.735369 ACAAATTCACTGGACCATGGTAA 58.265 39.130 19.80 7.77 0.00 2.85
1339 2984 4.380843 ACAAATTCACTGGACCATGGTA 57.619 40.909 19.80 1.42 0.00 3.25
1340 2985 3.243359 ACAAATTCACTGGACCATGGT 57.757 42.857 19.89 19.89 0.00 3.55
1341 2986 3.573538 TGAACAAATTCACTGGACCATGG 59.426 43.478 11.19 11.19 40.01 3.66
1342 2987 4.279169 ACTGAACAAATTCACTGGACCATG 59.721 41.667 0.00 0.00 40.01 3.66
1343 2988 4.473444 ACTGAACAAATTCACTGGACCAT 58.527 39.130 0.00 0.00 40.01 3.55
1347 2992 4.022935 GCATGACTGAACAAATTCACTGGA 60.023 41.667 0.00 0.00 40.01 3.86
1444 3097 2.892852 CTCAAAATCCAGGGCACTTCAA 59.107 45.455 0.00 0.00 0.00 2.69
1505 3158 6.855763 TCCAATTCAGCAACCTTTATCAAT 57.144 33.333 0.00 0.00 0.00 2.57
1615 3268 8.665685 CATCTTACCAGGACAAACTTACATTAC 58.334 37.037 0.00 0.00 0.00 1.89
1628 3281 8.312564 ACTTAAACTAGTTCATCTTACCAGGAC 58.687 37.037 8.95 0.00 0.00 3.85
1666 3319 4.201734 CGCTACACATAAACGCAACCATAA 60.202 41.667 0.00 0.00 0.00 1.90
1688 3441 0.917259 GAGCTCACGATACAGCAACG 59.083 55.000 9.40 0.00 38.18 4.10
1904 3658 4.191033 TGCAGTTATTTCAAGCCCAATG 57.809 40.909 0.00 0.00 0.00 2.82
1905 3659 6.736110 ATATGCAGTTATTTCAAGCCCAAT 57.264 33.333 0.00 0.00 0.00 3.16
2075 3832 4.589374 ACTGCTAAGAGTAGTGTTGGTCTT 59.411 41.667 0.00 0.00 39.72 3.01
2131 3888 1.732917 CCGGTGCTGCAGAACAAAA 59.267 52.632 26.30 0.00 0.00 2.44
2338 4095 5.238868 TGCGCTAACCAAAACATTAACTACA 59.761 36.000 9.73 0.00 0.00 2.74
2349 4113 3.067461 AGACAATTGTGCGCTAACCAAAA 59.933 39.130 17.58 0.00 0.00 2.44
2584 6027 2.163613 GGGTATGCCTTGAAGGAAAACG 59.836 50.000 16.93 0.00 37.67 3.60
2725 6169 9.884465 GACAAATATTGCACTGATAGGAATTAC 57.116 33.333 0.00 0.00 0.00 1.89
2727 6171 8.757982 AGACAAATATTGCACTGATAGGAATT 57.242 30.769 0.00 0.00 0.00 2.17
2733 6177 9.836864 ACATCTTAGACAAATATTGCACTGATA 57.163 29.630 0.00 0.00 0.00 2.15
2740 6184 9.229784 CATCAACACATCTTAGACAAATATTGC 57.770 33.333 0.00 0.00 0.00 3.56
2765 6209 7.114754 AGATCCTACTTTCATCAATTGCTTCA 58.885 34.615 0.00 0.00 0.00 3.02
2771 6215 9.393512 CAAGAGAAGATCCTACTTTCATCAATT 57.606 33.333 0.00 0.00 0.00 2.32
2832 6276 9.261180 TCTGCAATCTATAGGAAATAAAGTTCG 57.739 33.333 0.00 0.00 0.00 3.95
3224 6697 9.140286 GGACCATTACTTAAAAAGAAATTGAGC 57.860 33.333 0.00 0.00 0.00 4.26
3237 6710 7.942341 ACTGATGAAGTTTGGACCATTACTTAA 59.058 33.333 17.78 13.31 34.57 1.85
3354 6827 1.797320 ATGGGATTTTGGCCATCTGG 58.203 50.000 6.09 0.00 38.53 3.86
3423 6896 4.424061 TCCTTGAGAACATTTTGATGCG 57.576 40.909 0.00 0.00 0.00 4.73
3528 7001 4.161333 GCAAAGATGGACTTTCAATGACG 58.839 43.478 0.00 0.00 45.66 4.35
3561 7034 1.814394 GATGTGATCACTTTGCAGCCA 59.186 47.619 25.55 3.40 0.00 4.75
3602 7075 5.526846 ACATTTTTCATGACCGCAAATTGTT 59.473 32.000 0.00 0.00 0.00 2.83
3606 7079 6.928492 AGTTTACATTTTTCATGACCGCAAAT 59.072 30.769 0.00 0.00 0.00 2.32
3655 7128 2.558359 CACCATTTTCCTCACCTTCCAC 59.442 50.000 0.00 0.00 0.00 4.02
3869 7342 3.516586 TCCTGGACACTCACATTCCTTA 58.483 45.455 0.00 0.00 0.00 2.69
3924 7397 4.956075 ACAGGTTTGACAAGAATTCCACTT 59.044 37.500 0.65 0.00 0.00 3.16
4045 7527 5.537188 TGGAGTTTGCAATAAACCATGAAC 58.463 37.500 0.00 0.00 0.00 3.18
4057 7539 3.826524 TGGTAGATGTTGGAGTTTGCAA 58.173 40.909 0.00 0.00 0.00 4.08
4148 7630 4.081198 ACCAGATCTCATGTCCTCAAGAAC 60.081 45.833 0.00 0.00 0.00 3.01
4344 7909 3.189287 GGCATAAGGTTGACACACAAGAG 59.811 47.826 0.00 0.00 39.30 2.85
4424 7990 4.096682 GCCTCGTCTCTACACTTCAATAGT 59.903 45.833 0.00 0.00 37.68 2.12
4425 7991 4.336993 AGCCTCGTCTCTACACTTCAATAG 59.663 45.833 0.00 0.00 0.00 1.73
4426 7992 4.270834 AGCCTCGTCTCTACACTTCAATA 58.729 43.478 0.00 0.00 0.00 1.90
4486 8053 7.279981 AGCAACACATAGCTTTCGTCATATTAA 59.720 33.333 0.00 0.00 38.01 1.40
4603 8172 4.041075 GGGACATTTATTTTGGGTGTTGGT 59.959 41.667 0.00 0.00 0.00 3.67
4770 8620 4.946157 CACCCAGTTGCATTTCTAGAGAAT 59.054 41.667 0.00 0.00 33.54 2.40
4836 8687 4.228912 ACTTGCTTGTGTGTTATCTTGC 57.771 40.909 0.00 0.00 0.00 4.01
4841 8692 7.316640 TGTTGTTTTACTTGCTTGTGTGTTAT 58.683 30.769 0.00 0.00 0.00 1.89
4914 8768 5.181245 CCCAAGTGTGTGAACTTCGAATTAT 59.819 40.000 0.00 0.00 38.34 1.28
4952 8806 3.370527 CGTTGTTCCCCACTCTCCAATAT 60.371 47.826 0.00 0.00 0.00 1.28
4998 8856 2.498078 GGTTCTCGGAGAAGAAGGTGAT 59.502 50.000 20.23 0.00 34.42 3.06
5080 8942 1.672854 CCCGGGCTCGTTGATGAGTA 61.673 60.000 8.08 0.00 38.28 2.59
5185 9051 2.743636 TCGTTGATTCCCTGTGAGAC 57.256 50.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.