Multiple sequence alignment - TraesCS2B01G372500

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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 TraesCS2B01G372500 chr2B 100.000 3325 0 0 1 3325 531052021 531055345 0.000000e+00 6141.0
1 TraesCS2B01G372500 chr2A 88.654 3358 222 61 21 3325 598643558 598640307 0.000000e+00 3943.0
2 TraesCS2B01G372500 chr2D 90.794 2759 140 53 21 2705 450917114 450919832 0.000000e+00 3583.0
3 TraesCS2B01G372500 chr2D 80.035 571 65 22 2774 3325 450920838 450921378 8.710000e-101 377.0
4 TraesCS2B01G372500 chr6A 85.827 635 79 7 12 638 524758023 524758654 0.000000e+00 664.0
5 TraesCS2B01G372500 chr4D 84.772 637 84 12 12 638 445089390 445088757 7.830000e-176 627.0
6 TraesCS2B01G372500 chr4D 84.028 144 21 2 1079 1221 81666364 81666222 1.610000e-28 137.0
7 TraesCS2B01G372500 chr4D 85.526 76 9 2 1143 1217 394379266 394379192 9.890000e-11 78.7
8 TraesCS2B01G372500 chr5D 85.072 623 82 8 23 638 353461980 353462598 2.820000e-175 625.0
9 TraesCS2B01G372500 chr5D 84.541 621 85 8 24 638 284118578 284119193 3.670000e-169 604.0
10 TraesCS2B01G372500 chr5D 82.828 99 17 0 1423 1521 393801803 393801705 4.570000e-14 89.8
11 TraesCS2B01G372500 chr1A 84.530 627 82 13 21 638 38736685 38737305 1.020000e-169 606.0
12 TraesCS2B01G372500 chr1A 87.356 87 11 0 1414 1500 107485269 107485183 2.110000e-17 100.0
13 TraesCS2B01G372500 chr1D 84.893 609 80 9 37 638 37416049 37415446 3.670000e-169 604.0
14 TraesCS2B01G372500 chr1D 86.667 90 12 0 1411 1500 104543991 104544080 2.110000e-17 100.0
15 TraesCS2B01G372500 chr6D 84.355 620 88 8 24 638 138970777 138970162 1.710000e-167 599.0
16 TraesCS2B01G372500 chr7A 84.219 621 91 5 24 638 245605784 245605165 6.140000e-167 597.0
17 TraesCS2B01G372500 chr7A 89.286 84 9 0 1420 1503 646585032 646584949 4.540000e-19 106.0
18 TraesCS2B01G372500 chr1B 88.506 87 10 0 1414 1500 162005913 162005827 4.540000e-19 106.0
19 TraesCS2B01G372500 chr7D 86.905 84 11 0 1420 1503 561757818 561757735 9.820000e-16 95.3
20 TraesCS2B01G372500 chr7B 86.905 84 11 0 1420 1503 610737355 610737272 9.820000e-16 95.3
21 TraesCS2B01G372500 chr7B 100.000 28 0 0 1 28 618505953 618505926 6.000000e-03 52.8
22 TraesCS2B01G372500 chr4A 80.374 107 15 6 1124 1227 75843224 75843121 3.560000e-10 76.8
23 TraesCS2B01G372500 chr5B 83.333 72 6 2 2959 3030 691995688 691995623 9.960000e-06 62.1
24 TraesCS2B01G372500 chr5B 94.286 35 2 0 1190 1224 428963176 428963142 2.000000e-03 54.7
25 TraesCS2B01G372500 chr5A 94.286 35 2 0 1190 1224 463765908 463765874 2.000000e-03 54.7
26 TraesCS2B01G372500 chr3A 100.000 28 0 0 1 28 625248681 625248654 6.000000e-03 52.8


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 TraesCS2B01G372500 chr2B 531052021 531055345 3324 False 6141 6141 100.0000 1 3325 1 chr2B.!!$F1 3324
1 TraesCS2B01G372500 chr2A 598640307 598643558 3251 True 3943 3943 88.6540 21 3325 1 chr2A.!!$R1 3304
2 TraesCS2B01G372500 chr2D 450917114 450921378 4264 False 1980 3583 85.4145 21 3325 2 chr2D.!!$F1 3304
3 TraesCS2B01G372500 chr6A 524758023 524758654 631 False 664 664 85.8270 12 638 1 chr6A.!!$F1 626
4 TraesCS2B01G372500 chr4D 445088757 445089390 633 True 627 627 84.7720 12 638 1 chr4D.!!$R3 626
5 TraesCS2B01G372500 chr5D 353461980 353462598 618 False 625 625 85.0720 23 638 1 chr5D.!!$F2 615
6 TraesCS2B01G372500 chr5D 284118578 284119193 615 False 604 604 84.5410 24 638 1 chr5D.!!$F1 614
7 TraesCS2B01G372500 chr1A 38736685 38737305 620 False 606 606 84.5300 21 638 1 chr1A.!!$F1 617
8 TraesCS2B01G372500 chr1D 37415446 37416049 603 True 604 604 84.8930 37 638 1 chr1D.!!$R1 601
9 TraesCS2B01G372500 chr6D 138970162 138970777 615 True 599 599 84.3550 24 638 1 chr6D.!!$R1 614
10 TraesCS2B01G372500 chr7A 245605165 245605784 619 True 597 597 84.2190 24 638 1 chr7A.!!$R1 614

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
219 222 0.027194 TCGTATCGCTGACACGCTAC 59.973 55.0 4.82 0.0 35.70 3.58 F
1225 1275 0.038801 CTGCTTCGTCAGAGTGAGCA 60.039 55.0 0.00 0.0 36.19 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1285 1337 0.249676 ATCACTCACTGCAGGCTCTG 59.750 55.0 19.93 7.22 34.12 3.35 R
3049 4111 0.249238 GCAGATCTCGATGCCGAACT 60.249 55.0 0.00 0.00 45.04 3.01 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
99 100 0.108615 TTCGTAGGCAGAAGCAGAGC 60.109 55.000 0.00 0.00 44.61 4.09
219 222 0.027194 TCGTATCGCTGACACGCTAC 59.973 55.000 4.82 0.00 35.70 3.58
223 226 0.381089 ATCGCTGACACGCTACCTAC 59.619 55.000 0.00 0.00 0.00 3.18
287 291 3.451004 GGTGGCCATTGCATGCGA 61.451 61.111 9.72 10.79 40.13 5.10
416 421 3.506398 TGTATCACAAGACAGAGGGACA 58.494 45.455 0.00 0.00 0.00 4.02
421 426 4.019858 TCACAAGACAGAGGGACAGATAG 58.980 47.826 0.00 0.00 0.00 2.08
459 464 0.323725 GGATGAAGCTGAAGGGGCAA 60.324 55.000 0.00 0.00 0.00 4.52
463 470 3.386932 TGAAGCTGAAGGGGCAATATT 57.613 42.857 0.00 0.00 0.00 1.28
570 586 3.822594 TGTTACGTGTGGATGATTTGC 57.177 42.857 0.00 0.00 0.00 3.68
638 655 6.704819 TGAGTTTCGTTCGGTTAGTTAAAAC 58.295 36.000 0.00 0.00 0.00 2.43
683 718 2.141517 CCAGCCAGCTGATTAGAATCG 58.858 52.381 21.01 0.00 46.30 3.34
722 758 0.842030 ATGGCCTCCTCACAGAACCA 60.842 55.000 3.32 0.00 0.00 3.67
756 792 1.303398 TTCGGGCTGAGACGTCTCT 60.303 57.895 37.63 12.15 43.25 3.10
775 813 0.609151 TTCCGACACGCCCTTAATCA 59.391 50.000 0.00 0.00 0.00 2.57
781 819 0.999406 CACGCCCTTAATCACGTCTG 59.001 55.000 0.00 0.00 36.45 3.51
782 820 0.606604 ACGCCCTTAATCACGTCTGT 59.393 50.000 0.00 0.00 32.37 3.41
785 823 3.050619 CGCCCTTAATCACGTCTGTATC 58.949 50.000 0.00 0.00 0.00 2.24
786 824 3.391049 GCCCTTAATCACGTCTGTATCC 58.609 50.000 0.00 0.00 0.00 2.59
787 825 3.639538 CCCTTAATCACGTCTGTATCCG 58.360 50.000 0.00 0.00 0.00 4.18
875 913 2.362120 GCCAGCAGTGCCCAGATT 60.362 61.111 12.58 0.00 0.00 2.40
876 914 1.077501 GCCAGCAGTGCCCAGATTA 60.078 57.895 12.58 0.00 0.00 1.75
877 915 0.680921 GCCAGCAGTGCCCAGATTAA 60.681 55.000 12.58 0.00 0.00 1.40
921 959 1.949525 CCTCATTTATGCAACTCCCCG 59.050 52.381 0.00 0.00 0.00 5.73
993 1031 1.248101 TGTGCTAGCTGCCGTGTCTA 61.248 55.000 17.23 0.00 42.00 2.59
1225 1275 0.038801 CTGCTTCGTCAGAGTGAGCA 60.039 55.000 0.00 0.00 36.19 4.26
1283 1335 0.684479 TCGATGTCAGGGTAGCAGCT 60.684 55.000 0.00 0.00 0.00 4.24
1284 1336 0.529337 CGATGTCAGGGTAGCAGCTG 60.529 60.000 10.11 10.11 0.00 4.24
1285 1337 0.813210 GATGTCAGGGTAGCAGCTGC 60.813 60.000 31.53 31.53 42.49 5.25
1286 1338 1.556373 ATGTCAGGGTAGCAGCTGCA 61.556 55.000 38.24 22.31 45.16 4.41
1287 1339 1.449246 GTCAGGGTAGCAGCTGCAG 60.449 63.158 38.24 20.30 45.16 4.41
1288 1340 1.610379 TCAGGGTAGCAGCTGCAGA 60.610 57.895 38.24 24.02 45.16 4.26
1289 1341 1.153409 CAGGGTAGCAGCTGCAGAG 60.153 63.158 38.24 18.42 45.16 3.35
1290 1342 2.513435 GGGTAGCAGCTGCAGAGC 60.513 66.667 38.24 31.39 46.64 4.09
1317 1369 1.202639 TGAGTGATTCAAGTGCGTGGT 60.203 47.619 0.00 0.00 31.34 4.16
1524 1580 1.737838 AGCCATGGTACGTCATGTTG 58.262 50.000 14.67 3.69 42.02 3.33
1574 1630 3.377439 CACGCTGTGTTTGTCTGTAGTA 58.623 45.455 0.00 0.00 0.00 1.82
2120 2184 1.153369 CATCCTCCGCAACATCCGT 60.153 57.895 0.00 0.00 0.00 4.69
2299 2363 3.518998 CGGCGAGATCAGGGACGT 61.519 66.667 0.00 0.00 0.00 4.34
2300 2364 2.184830 CGGCGAGATCAGGGACGTA 61.185 63.158 0.00 0.00 0.00 3.57
2338 2402 0.992072 AACTGATCGACGCGTCATTG 59.008 50.000 35.71 21.39 0.00 2.82
2345 2409 2.799871 TCGACGCGTCATTGCTATAAA 58.200 42.857 35.71 7.31 0.00 1.40
2346 2410 3.180613 TCGACGCGTCATTGCTATAAAA 58.819 40.909 35.71 2.25 0.00 1.52
2358 2422 9.546909 GTCATTGCTATAAAATCATACGAATGG 57.453 33.333 0.00 0.00 33.61 3.16
2374 2438 3.725740 CGAATGGTCGCATTCAAATTAGC 59.274 43.478 13.80 0.00 41.08 3.09
2409 2473 4.108699 TGCGGAAACATGAATTCATTCC 57.891 40.909 21.82 21.82 35.97 3.01
2410 2474 3.763360 TGCGGAAACATGAATTCATTCCT 59.237 39.130 25.88 12.80 35.97 3.36
2411 2475 4.142403 TGCGGAAACATGAATTCATTCCTC 60.142 41.667 25.88 21.58 35.97 3.71
2413 2477 5.393461 GCGGAAACATGAATTCATTCCTCTT 60.393 40.000 25.88 13.77 35.97 2.85
2414 2478 6.624423 CGGAAACATGAATTCATTCCTCTTT 58.376 36.000 25.88 15.79 35.97 2.52
2416 2480 8.408601 CGGAAACATGAATTCATTCCTCTTTAT 58.591 33.333 25.88 2.29 35.97 1.40
2473 2561 7.049754 GGTGGGATTAAGATTGCATTTTCATT 58.950 34.615 0.00 0.00 0.00 2.57
2499 2587 4.525411 AAACGGACGAGTTGTTAACAAG 57.475 40.909 21.12 12.23 36.39 3.16
2500 2588 3.169355 ACGGACGAGTTGTTAACAAGT 57.831 42.857 25.17 25.17 41.81 3.16
2501 2589 4.305989 ACGGACGAGTTGTTAACAAGTA 57.694 40.909 24.99 1.44 39.43 2.24
2502 2590 4.681744 ACGGACGAGTTGTTAACAAGTAA 58.318 39.130 24.99 1.07 39.43 2.24
2503 2591 4.504097 ACGGACGAGTTGTTAACAAGTAAC 59.496 41.667 24.99 18.35 39.43 2.50
2568 2656 4.639310 TGTGCAATGCAAAGGAAACAAAAT 59.361 33.333 10.44 0.00 41.47 1.82
2598 2691 6.671779 AGAAAAGATGAGAATGGGAGTACTCT 59.328 38.462 21.88 2.22 0.00 3.24
2610 2706 6.088541 TGGGAGTACTCTGGATTAAGTAGT 57.911 41.667 21.88 0.00 34.98 2.73
2611 2707 7.217028 TGGGAGTACTCTGGATTAAGTAGTA 57.783 40.000 21.88 0.00 32.96 1.82
2612 2708 7.645942 TGGGAGTACTCTGGATTAAGTAGTAA 58.354 38.462 21.88 0.00 32.96 2.24
2636 2732 4.327357 CGTGTTGGTTTGAGCTGTCTATAG 59.673 45.833 0.00 0.00 0.00 1.31
2830 3870 0.973632 TGGCGGTGAGTGAGTGTATT 59.026 50.000 0.00 0.00 0.00 1.89
2843 3883 7.753580 TGAGTGAGTGTATTGTTACTATTGACG 59.246 37.037 0.00 0.00 0.00 4.35
2844 3884 7.600065 AGTGAGTGTATTGTTACTATTGACGT 58.400 34.615 0.00 0.00 0.00 4.34
2845 3885 8.733458 AGTGAGTGTATTGTTACTATTGACGTA 58.267 33.333 0.00 0.00 0.00 3.57
2846 3886 8.792538 GTGAGTGTATTGTTACTATTGACGTAC 58.207 37.037 0.00 0.00 0.00 3.67
2847 3887 8.733458 TGAGTGTATTGTTACTATTGACGTACT 58.267 33.333 0.00 0.00 0.00 2.73
2848 3888 9.219497 GAGTGTATTGTTACTATTGACGTACTC 57.781 37.037 0.00 0.00 0.00 2.59
2849 3889 8.954350 AGTGTATTGTTACTATTGACGTACTCT 58.046 33.333 0.00 0.00 0.00 3.24
2850 3890 9.565213 GTGTATTGTTACTATTGACGTACTCTT 57.435 33.333 0.00 0.00 0.00 2.85
2854 3894 7.928307 TGTTACTATTGACGTACTCTTACCT 57.072 36.000 0.00 0.00 0.00 3.08
2855 3895 7.978982 TGTTACTATTGACGTACTCTTACCTC 58.021 38.462 0.00 0.00 0.00 3.85
2856 3896 7.066284 TGTTACTATTGACGTACTCTTACCTCC 59.934 40.741 0.00 0.00 0.00 4.30
2857 3897 4.574013 ACTATTGACGTACTCTTACCTCCG 59.426 45.833 0.00 0.00 0.00 4.63
2858 3898 1.742761 TGACGTACTCTTACCTCCGG 58.257 55.000 0.00 0.00 0.00 5.14
2859 3899 0.380024 GACGTACTCTTACCTCCGGC 59.620 60.000 0.00 0.00 0.00 6.13
2860 3900 1.354506 CGTACTCTTACCTCCGGCG 59.645 63.158 0.00 0.00 0.00 6.46
2861 3901 1.732308 GTACTCTTACCTCCGGCGG 59.268 63.158 22.51 22.51 0.00 6.13
2862 3902 1.034292 GTACTCTTACCTCCGGCGGT 61.034 60.000 27.32 21.94 41.10 5.68
2863 3903 1.033746 TACTCTTACCTCCGGCGGTG 61.034 60.000 26.53 23.68 37.93 4.94
2864 3904 2.036098 TCTTACCTCCGGCGGTGA 59.964 61.111 26.53 17.36 37.93 4.02
2865 3905 2.005960 CTCTTACCTCCGGCGGTGAG 62.006 65.000 25.45 25.45 40.85 3.51
2866 3906 2.283388 TTACCTCCGGCGGTGAGT 60.283 61.111 26.53 23.42 37.93 3.41
2867 3907 1.001020 TTACCTCCGGCGGTGAGTA 60.001 57.895 26.53 22.50 37.93 2.59
2868 3908 1.315257 TTACCTCCGGCGGTGAGTAC 61.315 60.000 26.53 0.00 37.93 2.73
2869 3909 3.834799 CCTCCGGCGGTGAGTACC 61.835 72.222 27.97 0.00 43.89 3.34
2917 3972 3.886123 TCTGCCTCCAGCTAAAAATACC 58.114 45.455 0.00 0.00 44.23 2.73
2920 3975 2.612672 GCCTCCAGCTAAAAATACCGAC 59.387 50.000 0.00 0.00 38.99 4.79
2932 3993 6.494666 AAAAATACCGACTAGATCCATCCA 57.505 37.500 0.00 0.00 0.00 3.41
2946 4007 7.543359 AGATCCATCCAAAAACTTCATGAAA 57.457 32.000 9.88 0.00 0.00 2.69
3049 4111 2.092049 TCCTACGGATCAGAACCTAGCA 60.092 50.000 0.00 0.00 0.00 3.49
3050 4112 2.294791 CCTACGGATCAGAACCTAGCAG 59.705 54.545 0.00 0.00 0.00 4.24
3059 4129 1.291132 GAACCTAGCAGTTCGGCATC 58.709 55.000 0.00 0.00 37.04 3.91
3089 4159 5.987098 TGCCAAAATTTGCATGGTGTATAT 58.013 33.333 8.76 0.00 36.57 0.86
3090 4160 7.069208 TCTGCCAAAATTTGCATGGTGTATATA 59.931 33.333 8.76 0.00 36.79 0.86
3091 4161 7.733969 TGCCAAAATTTGCATGGTGTATATAT 58.266 30.769 8.76 0.00 36.57 0.86
3092 4162 8.864087 TGCCAAAATTTGCATGGTGTATATATA 58.136 29.630 8.76 0.00 36.57 0.86
3124 4194 9.874205 TTATCCAAAGATTTGAATTCCACATTC 57.126 29.630 6.87 0.00 40.55 2.67
3128 4198 9.880157 CCAAAGATTTGAATTCCACATTCTAAT 57.120 29.630 6.87 4.57 40.55 1.73
3143 4213 9.003658 CCACATTCTAATCTAAATCCCATACAC 57.996 37.037 0.00 0.00 0.00 2.90
3190 4260 6.814506 AAGTCACTGAAATCTTTCTCCATG 57.185 37.500 4.46 0.00 38.02 3.66
3197 4267 6.013379 ACTGAAATCTTTCTCCATGTAGACCA 60.013 38.462 4.46 0.00 38.02 4.02
3218 4288 2.499205 CAATCGCTAGCCACCGGA 59.501 61.111 9.46 0.00 0.00 5.14
3247 4317 3.062639 CCATTGACGGATGTTTCTCTTCG 59.937 47.826 0.00 0.00 0.00 3.79
3274 4344 1.967066 ACCACATCATCGAGATCCTCC 59.033 52.381 0.00 0.00 33.72 4.30
3275 4345 2.246469 CCACATCATCGAGATCCTCCT 58.754 52.381 0.00 0.00 33.72 3.69
3276 4346 2.632028 CCACATCATCGAGATCCTCCTT 59.368 50.000 0.00 0.00 33.72 3.36
3278 4348 2.036992 ACATCATCGAGATCCTCCTTGC 59.963 50.000 0.00 0.00 33.72 4.01
3280 4350 0.319383 CATCGAGATCCTCCTTGCGG 60.319 60.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.927936 AGTACTCCCTTCGTTTCTTTTTAGTC 59.072 38.462 0.00 0.00 0.00 2.59
3 4 7.440255 TCAAGTACTCCCTTCGTTTCTTTTTAG 59.560 37.037 0.00 0.00 0.00 1.85
4 5 7.225341 GTCAAGTACTCCCTTCGTTTCTTTTTA 59.775 37.037 0.00 0.00 0.00 1.52
6 7 5.526479 GTCAAGTACTCCCTTCGTTTCTTTT 59.474 40.000 0.00 0.00 0.00 2.27
7 8 5.055144 GTCAAGTACTCCCTTCGTTTCTTT 58.945 41.667 0.00 0.00 0.00 2.52
8 9 4.100498 TGTCAAGTACTCCCTTCGTTTCTT 59.900 41.667 0.00 0.00 0.00 2.52
9 10 3.640029 TGTCAAGTACTCCCTTCGTTTCT 59.360 43.478 0.00 0.00 0.00 2.52
12 13 4.315803 CATTGTCAAGTACTCCCTTCGTT 58.684 43.478 0.00 0.00 0.00 3.85
13 14 3.306780 CCATTGTCAAGTACTCCCTTCGT 60.307 47.826 0.00 0.00 0.00 3.85
14 15 3.056107 TCCATTGTCAAGTACTCCCTTCG 60.056 47.826 0.00 0.00 0.00 3.79
15 16 4.508662 CTCCATTGTCAAGTACTCCCTTC 58.491 47.826 0.00 0.00 0.00 3.46
16 17 3.264450 CCTCCATTGTCAAGTACTCCCTT 59.736 47.826 0.00 0.00 0.00 3.95
17 18 2.840651 CCTCCATTGTCAAGTACTCCCT 59.159 50.000 0.00 0.00 0.00 4.20
18 19 2.838202 TCCTCCATTGTCAAGTACTCCC 59.162 50.000 0.00 0.00 0.00 4.30
19 20 4.162320 TCATCCTCCATTGTCAAGTACTCC 59.838 45.833 0.00 0.00 0.00 3.85
20 21 5.105146 ACTCATCCTCCATTGTCAAGTACTC 60.105 44.000 0.00 0.00 0.00 2.59
21 22 4.780021 ACTCATCCTCCATTGTCAAGTACT 59.220 41.667 0.00 0.00 0.00 2.73
22 23 5.091261 ACTCATCCTCCATTGTCAAGTAC 57.909 43.478 0.00 0.00 0.00 2.73
91 92 0.980231 AGAAGGGATCCGCTCTGCTT 60.980 55.000 12.28 5.99 0.00 3.91
156 159 6.544564 TGGTTGAGTGATATACATGTCGTAGA 59.455 38.462 0.00 0.00 32.28 2.59
169 172 2.741517 CACATTGCGTGGTTGAGTGATA 59.258 45.455 0.00 0.00 42.34 2.15
174 177 1.603802 ACTTCACATTGCGTGGTTGAG 59.396 47.619 0.00 0.00 46.36 3.02
219 222 1.066858 ACTTGGTGACGCTGATGTAGG 60.067 52.381 0.00 0.00 0.00 3.18
223 226 2.653890 CAAAACTTGGTGACGCTGATG 58.346 47.619 0.00 0.00 0.00 3.07
391 396 4.964897 TCCCTCTGTCTTGTGATACATCAT 59.035 41.667 0.00 0.00 39.30 2.45
416 421 5.954296 ACAGTGTGTGTACGTAACTATCT 57.046 39.130 0.00 0.00 37.75 1.98
421 426 3.446799 TCCAACAGTGTGTGTACGTAAC 58.553 45.455 0.00 0.00 39.03 2.50
459 464 9.177608 CAACGGATCATGTTATCCCATAAATAT 57.822 33.333 7.64 0.00 42.21 1.28
463 470 6.181206 TCAACGGATCATGTTATCCCATAA 57.819 37.500 7.64 0.00 42.21 1.90
570 586 8.282592 TCATCGAAATTTGGATAGAAAATAGCG 58.717 33.333 14.41 0.65 0.00 4.26
638 655 2.047274 AGGACGCCACATTCCGTG 60.047 61.111 0.00 0.00 45.92 4.94
683 718 7.765819 AGGCCATATTTCTTATTTGCAGAAAAC 59.234 33.333 5.01 0.00 42.23 2.43
703 738 0.842030 TGGTTCTGTGAGGAGGCCAT 60.842 55.000 5.01 0.00 0.00 4.40
722 758 0.748005 CGAACCGGAATGAAGCCCAT 60.748 55.000 9.46 0.00 36.99 4.00
756 792 0.609151 TGATTAAGGGCGTGTCGGAA 59.391 50.000 0.00 0.00 0.00 4.30
775 813 0.606604 AAGTTGGCGGATACAGACGT 59.393 50.000 0.00 0.00 0.00 4.34
781 819 1.733360 TGCGTTTAAGTTGGCGGATAC 59.267 47.619 0.00 0.00 0.00 2.24
782 820 2.096220 TGCGTTTAAGTTGGCGGATA 57.904 45.000 0.00 0.00 0.00 2.59
785 823 1.613270 GAATGCGTTTAAGTTGGCGG 58.387 50.000 0.00 0.00 0.00 6.13
786 824 1.246970 CGAATGCGTTTAAGTTGGCG 58.753 50.000 0.00 0.00 0.00 5.69
921 959 1.751924 ACTCGGGATAGAGCAAGTGAC 59.248 52.381 0.00 0.00 41.77 3.67
993 1031 4.096003 CCGTCGGCCATTCCTGGT 62.096 66.667 2.24 0.00 45.10 4.00
1225 1275 1.142465 CCATTCAGCCCAGCTATCTGT 59.858 52.381 8.35 0.00 36.40 3.41
1285 1337 0.249676 ATCACTCACTGCAGGCTCTG 59.750 55.000 19.93 7.22 34.12 3.35
1286 1338 0.982704 AATCACTCACTGCAGGCTCT 59.017 50.000 19.93 0.00 0.00 4.09
1287 1339 1.338484 TGAATCACTCACTGCAGGCTC 60.338 52.381 19.93 3.03 0.00 4.70
1288 1340 0.689055 TGAATCACTCACTGCAGGCT 59.311 50.000 19.93 0.00 0.00 4.58
1289 1341 1.467734 CTTGAATCACTCACTGCAGGC 59.532 52.381 19.93 0.00 32.21 4.85
1290 1342 2.483106 CACTTGAATCACTCACTGCAGG 59.517 50.000 19.93 7.28 32.21 4.85
1291 1343 2.095869 GCACTTGAATCACTCACTGCAG 60.096 50.000 13.48 13.48 37.69 4.41
1292 1344 1.875514 GCACTTGAATCACTCACTGCA 59.124 47.619 0.00 0.00 37.69 4.41
1293 1345 1.136141 CGCACTTGAATCACTCACTGC 60.136 52.381 0.00 0.00 35.73 4.40
1294 1346 2.096565 CACGCACTTGAATCACTCACTG 60.097 50.000 0.00 0.00 32.21 3.66
1403 1455 1.380302 GTCAACCACATCCAGGCCT 59.620 57.895 0.00 0.00 0.00 5.19
1412 1464 4.858680 TTGGCGCGGTCAACCACA 62.859 61.111 8.83 0.00 35.14 4.17
1524 1580 0.725118 CGAGTCGAACACCTCGTGTC 60.725 60.000 6.73 0.00 46.79 3.67
1574 1630 2.007049 GCATCACGAGTTCCCGACAAT 61.007 52.381 0.00 0.00 0.00 2.71
1741 1801 1.267574 GGAGCACCTGGATGGAGTCA 61.268 60.000 0.00 0.00 39.71 3.41
1781 1841 4.719369 GTCGCGGTCGTTGAGGCT 62.719 66.667 6.13 0.00 36.96 4.58
1826 1886 2.674852 TGTCGCGGAGTACTAGTAAGTG 59.325 50.000 6.13 4.00 36.36 3.16
1827 1887 2.977914 TGTCGCGGAGTACTAGTAAGT 58.022 47.619 6.13 0.00 39.91 2.24
1828 1888 3.848917 GCATGTCGCGGAGTACTAGTAAG 60.849 52.174 6.13 0.00 0.00 2.34
1883 1947 3.641492 GCATATGCATGTCGCGGA 58.359 55.556 22.84 0.00 46.97 5.54
1922 1986 3.000080 GACGAAGAAGCACGCCGTG 62.000 63.158 13.95 13.95 36.51 4.94
2087 2151 1.825474 AGGATGGAGTCGTCGAATGTT 59.175 47.619 0.00 0.00 0.00 2.71
2228 2292 1.314534 TGATCATGGCGCCCACAAAG 61.315 55.000 26.77 7.27 35.80 2.77
2285 2349 0.955178 AGCATACGTCCCTGATCTCG 59.045 55.000 0.00 0.00 0.00 4.04
2294 2358 2.202703 AACGCCGAGCATACGTCC 60.203 61.111 0.00 0.00 39.49 4.79
2299 2363 1.348538 CGTGTTGAACGCCGAGCATA 61.349 55.000 2.97 0.00 46.99 3.14
2300 2364 2.667318 CGTGTTGAACGCCGAGCAT 61.667 57.895 2.97 0.00 46.99 3.79
2330 2394 6.817396 TCGTATGATTTTATAGCAATGACGC 58.183 36.000 0.00 0.00 0.00 5.19
2358 2422 4.083581 ACAGTGCTAATTTGAATGCGAC 57.916 40.909 0.00 0.00 0.00 5.19
2372 2436 2.028112 TCCGCAAGAGATTTACAGTGCT 60.028 45.455 0.00 0.00 43.02 4.40
2373 2437 2.346803 TCCGCAAGAGATTTACAGTGC 58.653 47.619 0.00 0.00 43.02 4.40
2374 2438 4.213270 TGTTTCCGCAAGAGATTTACAGTG 59.787 41.667 0.00 0.00 43.02 3.66
2388 2452 3.763360 AGGAATGAATTCATGTTTCCGCA 59.237 39.130 23.95 0.00 37.52 5.69
2425 2513 9.435688 CACCACCATTCTCGATTATCAATATTA 57.564 33.333 0.00 0.00 0.00 0.98
2442 2530 3.706086 GCAATCTTAATCCCACCACCATT 59.294 43.478 0.00 0.00 0.00 3.16
2445 2533 2.733956 TGCAATCTTAATCCCACCACC 58.266 47.619 0.00 0.00 0.00 4.61
2473 2561 3.389925 AACAACTCGTCCGTTTATCCA 57.610 42.857 0.00 0.00 0.00 3.41
2479 2567 3.524541 ACTTGTTAACAACTCGTCCGTT 58.475 40.909 17.01 0.00 0.00 4.44
2499 2587 6.849305 CCACTAGAAATCAAACACGTTGTTAC 59.151 38.462 0.00 0.00 40.14 2.50
2500 2588 6.512091 GCCACTAGAAATCAAACACGTTGTTA 60.512 38.462 0.00 0.00 40.14 2.41
2501 2589 5.732247 GCCACTAGAAATCAAACACGTTGTT 60.732 40.000 0.00 0.00 43.41 2.83
2502 2590 4.261031 GCCACTAGAAATCAAACACGTTGT 60.261 41.667 0.00 0.00 38.47 3.32
2503 2591 4.219033 GCCACTAGAAATCAAACACGTTG 58.781 43.478 0.00 0.00 38.71 4.10
2504 2592 3.880490 TGCCACTAGAAATCAAACACGTT 59.120 39.130 0.00 0.00 0.00 3.99
2505 2593 3.472652 TGCCACTAGAAATCAAACACGT 58.527 40.909 0.00 0.00 0.00 4.49
2568 2656 3.691118 CCCATTCTCATCTTTTCTGCGAA 59.309 43.478 0.00 0.00 0.00 4.70
2598 2691 6.100404 ACCAACACGTTACTACTTAATCCA 57.900 37.500 0.00 0.00 0.00 3.41
2610 2706 2.610374 GACAGCTCAAACCAACACGTTA 59.390 45.455 0.00 0.00 0.00 3.18
2611 2707 1.400494 GACAGCTCAAACCAACACGTT 59.600 47.619 0.00 0.00 0.00 3.99
2612 2708 1.014352 GACAGCTCAAACCAACACGT 58.986 50.000 0.00 0.00 0.00 4.49
2738 3520 1.846782 GCGATGCGAGTAACACAGTAG 59.153 52.381 0.00 0.00 0.00 2.57
2809 3849 0.530744 TACACTCACTCACCGCCATC 59.469 55.000 0.00 0.00 0.00 3.51
2830 3870 7.066284 GGAGGTAAGAGTACGTCAATAGTAACA 59.934 40.741 0.00 0.00 43.77 2.41
2852 3892 3.834799 GGTACTCACCGCCGGAGG 61.835 72.222 24.18 24.18 43.75 4.30
2860 3900 5.070580 AGGCAGATACTATTTGGTACTCACC 59.929 44.000 0.00 0.00 46.00 4.02
2861 3901 6.163135 AGGCAGATACTATTTGGTACTCAC 57.837 41.667 0.00 0.00 0.00 3.51
2862 3902 6.382859 TGAAGGCAGATACTATTTGGTACTCA 59.617 38.462 0.00 0.00 0.00 3.41
2863 3903 6.817184 TGAAGGCAGATACTATTTGGTACTC 58.183 40.000 0.00 0.00 0.00 2.59
2864 3904 6.808321 TGAAGGCAGATACTATTTGGTACT 57.192 37.500 0.00 0.00 0.00 2.73
2865 3905 7.217200 TGATGAAGGCAGATACTATTTGGTAC 58.783 38.462 0.00 0.00 0.00 3.34
2866 3906 7.071196 ACTGATGAAGGCAGATACTATTTGGTA 59.929 37.037 0.00 0.00 36.86 3.25
2867 3907 6.126652 ACTGATGAAGGCAGATACTATTTGGT 60.127 38.462 0.00 0.00 36.86 3.67
2868 3908 6.294473 ACTGATGAAGGCAGATACTATTTGG 58.706 40.000 0.00 0.00 36.86 3.28
2869 3909 7.798596 AACTGATGAAGGCAGATACTATTTG 57.201 36.000 0.00 0.00 36.86 2.32
2871 3911 9.717942 GATTAACTGATGAAGGCAGATACTATT 57.282 33.333 0.00 0.00 36.86 1.73
2872 3912 9.099071 AGATTAACTGATGAAGGCAGATACTAT 57.901 33.333 0.00 0.00 36.86 2.12
2873 3913 8.484214 AGATTAACTGATGAAGGCAGATACTA 57.516 34.615 0.00 0.00 36.86 1.82
2874 3914 7.372260 AGATTAACTGATGAAGGCAGATACT 57.628 36.000 0.00 0.00 36.86 2.12
2917 3972 5.874810 TGAAGTTTTTGGATGGATCTAGTCG 59.125 40.000 0.00 0.00 0.00 4.18
2920 3975 7.870509 TCATGAAGTTTTTGGATGGATCTAG 57.129 36.000 0.00 0.00 0.00 2.43
3031 4093 3.014304 ACTGCTAGGTTCTGATCCGTA 57.986 47.619 0.00 0.00 0.00 4.02
3033 4095 2.796383 CGAACTGCTAGGTTCTGATCCG 60.796 54.545 9.35 0.00 42.20 4.18
3049 4111 0.249238 GCAGATCTCGATGCCGAACT 60.249 55.000 0.00 0.00 45.04 3.01
3050 4112 2.220761 GCAGATCTCGATGCCGAAC 58.779 57.895 0.00 0.00 45.04 3.95
3059 4129 3.220507 TGCAAATTTTGGCAGATCTCG 57.779 42.857 10.96 0.00 34.58 4.04
3117 4187 9.003658 GTGTATGGGATTTAGATTAGAATGTGG 57.996 37.037 0.00 0.00 0.00 4.17
3118 4188 9.784531 AGTGTATGGGATTTAGATTAGAATGTG 57.215 33.333 0.00 0.00 0.00 3.21
3124 4194 9.896645 ATGCATAGTGTATGGGATTTAGATTAG 57.103 33.333 0.00 0.00 36.68 1.73
3128 4198 7.078249 ACATGCATAGTGTATGGGATTTAGA 57.922 36.000 0.00 0.00 43.41 2.10
3140 4210 8.109705 TGATTTTACAAGAACATGCATAGTGT 57.890 30.769 0.00 2.14 0.00 3.55
3146 4216 7.978414 TGACTTTTGATTTTACAAGAACATGCA 59.022 29.630 0.00 0.00 0.00 3.96
3147 4217 8.268738 GTGACTTTTGATTTTACAAGAACATGC 58.731 33.333 0.00 0.00 0.00 4.06
3163 4233 6.828273 TGGAGAAAGATTTCAGTGACTTTTGA 59.172 34.615 7.97 0.00 39.61 2.69
3169 4239 7.064016 GTCTACATGGAGAAAGATTTCAGTGAC 59.936 40.741 9.89 0.00 39.61 3.67
3190 4260 2.221981 GCTAGCGATTGCAATGGTCTAC 59.778 50.000 18.59 11.33 46.23 2.59
3197 4267 2.408333 GGTGGCTAGCGATTGCAAT 58.592 52.632 12.83 12.83 46.23 3.56
3227 4297 3.926616 ACGAAGAGAAACATCCGTCAAT 58.073 40.909 0.00 0.00 0.00 2.57
3229 4299 3.057019 CAACGAAGAGAAACATCCGTCA 58.943 45.455 0.00 0.00 0.00 4.35
3247 4317 3.849911 TCTCGATGATGTGGTCTTCAAC 58.150 45.455 0.00 0.00 32.81 3.18
3274 4344 3.474570 AGGCTAGGGCTCCGCAAG 61.475 66.667 0.00 0.00 38.73 4.01
3282 4352 2.235898 CCTATGATGAAGAGGCTAGGGC 59.764 54.545 0.00 0.00 37.82 5.19


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

AutoCloner maintained by Alex Coulton.