Multiple sequence alignment - TraesCS6A01G302700

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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 TraesCS6A01G302700 chr6A 100.000 3533 0 0 1 3533 536025673 536022141 0.000000e+00 6525.0
1 TraesCS6A01G302700 chr6A 97.621 1261 24 2 1 1261 536032395 536031141 0.000000e+00 2158.0
2 TraesCS6A01G302700 chr6A 74.320 1690 271 95 691 2316 529559183 529560773 1.840000e-157 566.0
3 TraesCS6A01G302700 chr6A 73.290 1711 268 106 691 2316 529485077 529486683 1.500000e-123 453.0
4 TraesCS6A01G302700 chr6A 75.241 622 91 27 1910 2499 529288152 529288742 1.640000e-58 237.0
5 TraesCS6A01G302700 chr6D 89.345 2215 112 40 714 2864 389653357 389651203 0.000000e+00 2669.0
6 TraesCS6A01G302700 chr6D 74.242 1716 263 94 682 2316 385222483 385224100 3.980000e-154 555.0
7 TraesCS6A01G302700 chr6D 80.172 696 68 32 2866 3533 389651110 389650457 1.160000e-124 457.0
8 TraesCS6A01G302700 chr6D 73.348 1407 228 89 691 2049 385165057 385166364 5.530000e-103 385.0
9 TraesCS6A01G302700 chr6D 86.196 326 25 6 377 684 389653944 389653621 5.650000e-88 335.0
10 TraesCS6A01G302700 chr6D 86.567 201 21 4 111 308 385221718 385221915 2.140000e-52 217.0
11 TraesCS6A01G302700 chr6D 85.149 202 25 3 110 308 385163931 385164130 5.980000e-48 202.0
12 TraesCS6A01G302700 chr6D 100.000 36 0 0 683 718 389653585 389653550 2.280000e-07 67.6
13 TraesCS6A01G302700 chr6B 88.554 1293 60 29 1610 2866 583335484 583334244 0.000000e+00 1487.0
14 TraesCS6A01G302700 chr6B 90.527 929 34 27 683 1609 583336386 583335510 0.000000e+00 1179.0
15 TraesCS6A01G302700 chr6B 85.345 580 76 6 16 587 583337144 583336566 3.040000e-165 592.0
16 TraesCS6A01G302700 chr6B 74.620 1710 249 100 691 2316 575320977 575322585 1.830000e-162 582.0
17 TraesCS6A01G302700 chr6B 84.065 615 49 24 2936 3533 583334081 583333499 6.670000e-152 547.0
18 TraesCS6A01G302700 chr6B 73.609 1887 297 109 691 2499 575314461 575316224 1.120000e-149 540.0


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 TraesCS6A01G302700 chr6A 536022141 536025673 3532 True 6525.00 6525 100.00000 1 3533 1 chr6A.!!$R1 3532
1 TraesCS6A01G302700 chr6A 536031141 536032395 1254 True 2158.00 2158 97.62100 1 1261 1 chr6A.!!$R2 1260
2 TraesCS6A01G302700 chr6A 529559183 529560773 1590 False 566.00 566 74.32000 691 2316 1 chr6A.!!$F3 1625
3 TraesCS6A01G302700 chr6A 529485077 529486683 1606 False 453.00 453 73.29000 691 2316 1 chr6A.!!$F2 1625
4 TraesCS6A01G302700 chr6A 529288152 529288742 590 False 237.00 237 75.24100 1910 2499 1 chr6A.!!$F1 589
5 TraesCS6A01G302700 chr6D 389650457 389653944 3487 True 882.15 2669 88.92825 377 3533 4 chr6D.!!$R1 3156
6 TraesCS6A01G302700 chr6D 385221718 385224100 2382 False 386.00 555 80.40450 111 2316 2 chr6D.!!$F2 2205
7 TraesCS6A01G302700 chr6D 385163931 385166364 2433 False 293.50 385 79.24850 110 2049 2 chr6D.!!$F1 1939
8 TraesCS6A01G302700 chr6B 583333499 583337144 3645 True 951.25 1487 87.12275 16 3533 4 chr6B.!!$R1 3517
9 TraesCS6A01G302700 chr6B 575320977 575322585 1608 False 582.00 582 74.62000 691 2316 1 chr6B.!!$F2 1625
10 TraesCS6A01G302700 chr6B 575314461 575316224 1763 False 540.00 540 73.60900 691 2499 1 chr6B.!!$F1 1808

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
275 285 1.143889 TGTCAAGCCACATAACACCCA 59.856 47.619 0.00 0.0 0.00 4.51 F
1399 2324 0.252012 TCGCCCATGGGTTCCATTTT 60.252 50.000 31.58 0.0 42.23 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1403 2328 0.395862 TGCCACCGAAAAGGGACAAA 60.396 50.0 0.0 0.0 46.96 2.83 R
3249 4457 0.166597 TGAATCAAAAGCTGCTCGCG 59.833 50.0 1.0 0.0 45.59 5.87 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
275 285 1.143889 TGTCAAGCCACATAACACCCA 59.856 47.619 0.00 0.00 0.00 4.51
388 951 6.266558 CAGTTACCTTGATCTAGGCTAGTCAT 59.733 42.308 21.40 8.35 38.99 3.06
769 1645 4.002982 CCAAAAATCACCAGATCGACAGA 58.997 43.478 0.00 0.00 31.90 3.41
877 1768 2.198304 CTCCCCCAAAACCCCTCTCG 62.198 65.000 0.00 0.00 0.00 4.04
1350 2263 1.101331 CCTGCTTTCCCATTCTCTGC 58.899 55.000 0.00 0.00 0.00 4.26
1383 2308 1.136057 GGTGAAATCCTCGTGTTTCGC 60.136 52.381 5.88 5.88 41.63 4.70
1399 2324 0.252012 TCGCCCATGGGTTCCATTTT 60.252 50.000 31.58 0.00 42.23 1.82
1400 2325 0.612744 CGCCCATGGGTTCCATTTTT 59.387 50.000 31.58 0.00 42.23 1.94
1401 2326 1.405391 CGCCCATGGGTTCCATTTTTC 60.405 52.381 31.58 10.01 42.23 2.29
1402 2327 1.908619 GCCCATGGGTTCCATTTTTCT 59.091 47.619 31.58 0.00 42.23 2.52
1403 2328 2.305635 GCCCATGGGTTCCATTTTTCTT 59.694 45.455 31.58 0.00 42.23 2.52
1422 2347 0.395862 TTTGTCCCTTTTCGGTGGCA 60.396 50.000 0.00 0.00 0.00 4.92
1458 2383 1.227350 CAGGCGCCGATCAATCTCA 60.227 57.895 23.20 0.00 0.00 3.27
1459 2384 0.602106 CAGGCGCCGATCAATCTCAT 60.602 55.000 23.20 0.00 0.00 2.90
1460 2385 0.320247 AGGCGCCGATCAATCTCATC 60.320 55.000 23.20 0.00 0.00 2.92
1461 2386 0.320247 GGCGCCGATCAATCTCATCT 60.320 55.000 12.58 0.00 0.00 2.90
1462 2387 1.066914 GCGCCGATCAATCTCATCTC 58.933 55.000 0.00 0.00 0.00 2.75
1633 2583 3.691020 GCAAGGGGGTTATTCATGATCCA 60.691 47.826 0.00 0.00 0.00 3.41
1712 2673 1.278238 GCGGGTACTGATTTGACGAG 58.722 55.000 0.00 0.00 36.31 4.18
1749 2710 1.331756 GGTAATGCTGATTCCACGCTG 59.668 52.381 0.00 0.00 0.00 5.18
1753 2718 0.391130 TGCTGATTCCACGCTGGTAC 60.391 55.000 4.33 0.00 39.03 3.34
1754 2719 0.391130 GCTGATTCCACGCTGGTACA 60.391 55.000 0.00 3.53 39.03 2.90
1755 2720 1.943968 GCTGATTCCACGCTGGTACAA 60.944 52.381 0.00 0.00 38.70 2.41
1756 2721 2.002586 CTGATTCCACGCTGGTACAAG 58.997 52.381 0.00 0.00 38.70 3.16
1757 2722 0.727398 GATTCCACGCTGGTACAAGC 59.273 55.000 12.63 12.63 38.70 4.01
1758 2723 0.036164 ATTCCACGCTGGTACAAGCA 59.964 50.000 22.05 2.22 38.70 3.91
1759 2724 0.602638 TTCCACGCTGGTACAAGCAG 60.603 55.000 22.05 16.01 45.86 4.24
1844 2824 7.572523 ATTTCTTTTCAGAATATGCCGATGA 57.427 32.000 0.00 0.00 38.89 2.92
1847 2827 5.987953 TCTTTTCAGAATATGCCGATGAGAG 59.012 40.000 0.00 0.00 0.00 3.20
1917 2922 8.292444 TGCTCTACCATGTTAATTATTTGCTT 57.708 30.769 0.00 0.00 0.00 3.91
2052 3105 8.962884 AAAATTATTGGGATGCATTTAGGTTC 57.037 30.769 0.00 0.00 0.00 3.62
2061 3114 6.152831 GGGATGCATTTAGGTTCAGTTTACTT 59.847 38.462 0.00 0.00 0.00 2.24
2078 3132 2.843701 ACTTGTCAAGAGTCAAGGCTG 58.156 47.619 19.53 0.00 42.66 4.85
2087 3141 2.304180 AGAGTCAAGGCTGCATACTGTT 59.696 45.455 0.50 0.00 0.00 3.16
2235 3299 5.647589 TGTCATCGACCACATAGACTTAAC 58.352 41.667 0.00 0.00 0.00 2.01
2330 3394 4.591929 TGTGACATTGTGACATGATGGAT 58.408 39.130 4.90 0.00 0.00 3.41
2356 3420 3.582647 TGCTGAATTCCCTTGTCTGTCTA 59.417 43.478 2.27 0.00 0.00 2.59
2414 3480 1.960250 GCAGGGAGCATCAGATCGC 60.960 63.158 0.00 0.00 44.79 4.58
2554 3620 1.609580 CGGGCGGCCATTAGCTTATTA 60.610 52.381 29.19 0.00 43.05 0.98
2555 3621 1.810755 GGGCGGCCATTAGCTTATTAC 59.189 52.381 25.33 0.00 43.05 1.89
2558 3624 4.258543 GGCGGCCATTAGCTTATTACATA 58.741 43.478 15.62 0.00 43.05 2.29
2559 3625 4.881850 GGCGGCCATTAGCTTATTACATAT 59.118 41.667 15.62 0.00 43.05 1.78
2560 3626 6.053005 GGCGGCCATTAGCTTATTACATATA 58.947 40.000 15.62 0.00 43.05 0.86
2561 3627 6.018180 GGCGGCCATTAGCTTATTACATATAC 60.018 42.308 15.62 0.00 43.05 1.47
2562 3628 6.761714 GCGGCCATTAGCTTATTACATATACT 59.238 38.462 2.24 0.00 43.05 2.12
2563 3629 7.924412 GCGGCCATTAGCTTATTACATATACTA 59.076 37.037 2.24 0.00 43.05 1.82
2621 3691 0.037160 ATGTTTAAACCGCCCGTCCT 59.963 50.000 15.59 0.00 0.00 3.85
2646 3716 0.456221 ACAGATCGAACTGGGTAGCG 59.544 55.000 24.36 0.40 41.59 4.26
2647 3717 0.738975 CAGATCGAACTGGGTAGCGA 59.261 55.000 14.48 0.00 37.17 4.93
2649 3719 0.030908 GATCGAACTGGGTAGCGAGG 59.969 60.000 8.85 0.00 36.12 4.63
2665 3738 1.268539 CGAGGAGTTGTTGTTGTTGGC 60.269 52.381 0.00 0.00 0.00 4.52
2811 3884 8.617290 ATCTTTTCGTAGTAATTCCTGTTTGT 57.383 30.769 0.00 0.00 0.00 2.83
2823 3896 0.594796 CTGTTTGTGCCTGGCGTTTC 60.595 55.000 14.98 5.20 0.00 2.78
2830 3903 3.726517 CCTGGCGTTTCCGTGCAG 61.727 66.667 0.00 0.00 37.80 4.41
2837 3910 0.784778 CGTTTCCGTGCAGTTCTCTC 59.215 55.000 0.00 0.00 0.00 3.20
2846 3919 3.033114 CAGTTCTCTCGCTGCTCTG 57.967 57.895 0.00 0.00 0.00 3.35
2869 3942 4.457834 ACGAAGTTCTCTGATAAGGTGG 57.542 45.455 0.56 0.00 37.78 4.61
2870 3943 3.195825 ACGAAGTTCTCTGATAAGGTGGG 59.804 47.826 0.56 0.00 37.78 4.61
2871 3944 3.536570 GAAGTTCTCTGATAAGGTGGGC 58.463 50.000 0.00 0.00 0.00 5.36
2893 4057 4.078537 CAGTGGAGAAGAAGAGACAGAGA 58.921 47.826 0.00 0.00 0.00 3.10
2897 4061 3.763897 GGAGAAGAAGAGACAGAGAAGCT 59.236 47.826 0.00 0.00 0.00 3.74
2928 4100 1.468340 GCGTGCGTGTTGTTTGTTCC 61.468 55.000 0.00 0.00 0.00 3.62
2977 4165 2.657237 GTGACCTGACCTCACCGG 59.343 66.667 0.00 0.00 33.23 5.28
3037 4225 1.364626 CTGCAGATCAGAACGTGGGC 61.365 60.000 8.42 0.00 45.72 5.36
3111 4303 3.561310 CCGTGCAGCTCATTGTATATTGT 59.439 43.478 0.00 0.00 0.00 2.71
3120 4312 7.859377 CAGCTCATTGTATATTGTTGTTCATCC 59.141 37.037 0.00 0.00 0.00 3.51
3123 4315 9.559732 CTCATTGTATATTGTTGTTCATCCCTA 57.440 33.333 0.00 0.00 0.00 3.53
3124 4316 9.337396 TCATTGTATATTGTTGTTCATCCCTAC 57.663 33.333 0.00 0.00 0.00 3.18
3126 4318 9.693739 ATTGTATATTGTTGTTCATCCCTACAA 57.306 29.630 0.00 0.00 33.73 2.41
3151 4343 2.908634 CACTCGATGTGTTTTCTGCAC 58.091 47.619 6.79 0.00 41.53 4.57
3156 4348 4.123506 TCGATGTGTTTTCTGCACTGTTA 58.876 39.130 0.00 0.00 37.70 2.41
3160 4352 5.378292 TGTGTTTTCTGCACTGTTACAAA 57.622 34.783 0.00 0.00 37.70 2.83
3178 4370 0.393808 AACGAACGGGGATTGGGATG 60.394 55.000 0.00 0.00 0.00 3.51
3202 4394 1.890876 AATACCACTGCAACGAAGCA 58.109 45.000 6.40 6.40 43.35 3.91
3205 4397 1.890876 ACCACTGCAACGAAGCAATA 58.109 45.000 7.81 0.00 45.13 1.90
3206 4398 1.535462 ACCACTGCAACGAAGCAATAC 59.465 47.619 7.81 0.00 45.13 1.89
3235 4442 1.153086 AATCCACGGATCTGCAGGC 60.153 57.895 15.13 6.41 33.08 4.85
3249 4457 0.871057 GCAGGCTGTTGTCAGAAGTC 59.129 55.000 17.16 0.00 43.76 3.01
3258 4466 2.126307 TCAGAAGTCGCGAGCAGC 60.126 61.111 10.24 0.00 43.95 5.25
3261 4469 1.005630 AGAAGTCGCGAGCAGCTTT 60.006 52.632 10.24 0.00 45.59 3.51
3262 4470 0.601311 AGAAGTCGCGAGCAGCTTTT 60.601 50.000 10.24 1.14 45.59 2.27
3263 4471 0.451792 GAAGTCGCGAGCAGCTTTTG 60.452 55.000 10.24 0.00 45.59 2.44
3264 4472 0.880278 AAGTCGCGAGCAGCTTTTGA 60.880 50.000 10.24 0.00 45.59 2.69
3273 4481 1.271656 AGCAGCTTTTGATTCACTGGC 59.728 47.619 0.00 1.41 0.00 4.85
3274 4482 1.973138 CAGCTTTTGATTCACTGGCG 58.027 50.000 0.00 0.00 0.00 5.69
3275 4483 1.267806 CAGCTTTTGATTCACTGGCGT 59.732 47.619 0.00 0.00 0.00 5.68
3286 4494 0.734942 CACTGGCGTAGTTGGTACCG 60.735 60.000 7.57 0.00 37.60 4.02
3296 4504 1.001887 TTGGTACCGGCAATGGTCC 60.002 57.895 7.57 1.74 42.62 4.46
3304 4512 1.361668 CGGCAATGGTCCGTCTTCTG 61.362 60.000 0.00 0.00 41.85 3.02
3315 4523 1.668337 CCGTCTTCTGTCACTGCAGAG 60.668 57.143 23.35 13.75 45.03 3.35
3357 4566 1.836383 AATTTAGCTACGCCGTCGAG 58.164 50.000 0.00 0.00 39.41 4.04
3380 4589 4.437959 CGTGCGCGCCGATGAAAA 62.438 61.111 30.77 3.44 0.00 2.29
3381 4590 2.574212 GTGCGCGCCGATGAAAAG 60.574 61.111 30.77 0.00 0.00 2.27
3388 4598 1.465187 GCGCCGATGAAAAGTAACACC 60.465 52.381 0.00 0.00 0.00 4.16
3394 4604 4.235360 CGATGAAAAGTAACACCGAGACT 58.765 43.478 0.00 0.00 0.00 3.24
3396 4606 4.659111 TGAAAAGTAACACCGAGACTCA 57.341 40.909 2.82 0.00 0.00 3.41
3407 4617 1.082300 GAGACTCAACGTGACGCGA 60.082 57.895 15.93 0.50 44.77 5.87
3408 4618 1.328685 GAGACTCAACGTGACGCGAC 61.329 60.000 15.93 7.62 44.77 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
275 285 5.367945 TTCCGGGAGCACTTTTAATAGAT 57.632 39.130 0.00 0.00 0.00 1.98
308 318 3.926616 AGACACGTCAGATTTGGGTTAG 58.073 45.455 0.00 0.00 0.00 2.34
508 1074 4.049186 ACATTACTATGATCCGCGTTGAC 58.951 43.478 4.92 0.00 35.65 3.18
769 1645 1.826921 ACACGAGACACCTGGACGT 60.827 57.895 0.00 0.00 37.68 4.34
877 1768 0.463620 GAGAGAGACTGGATGGTGGC 59.536 60.000 0.00 0.00 0.00 5.01
1109 2016 1.281960 CTGTCCTTGTCGTCGTCGT 59.718 57.895 1.33 0.00 38.33 4.34
1110 2017 1.442184 CCTGTCCTTGTCGTCGTCG 60.442 63.158 0.00 0.00 38.55 5.12
1111 2018 1.733399 GCCTGTCCTTGTCGTCGTC 60.733 63.158 0.00 0.00 0.00 4.20
1112 2019 2.338984 GCCTGTCCTTGTCGTCGT 59.661 61.111 0.00 0.00 0.00 4.34
1113 2020 1.734477 CTGCCTGTCCTTGTCGTCG 60.734 63.158 0.00 0.00 0.00 5.12
1114 2021 1.374758 CCTGCCTGTCCTTGTCGTC 60.375 63.158 0.00 0.00 0.00 4.20
1115 2022 2.743718 CCTGCCTGTCCTTGTCGT 59.256 61.111 0.00 0.00 0.00 4.34
1116 2023 2.743928 GCCTGCCTGTCCTTGTCG 60.744 66.667 0.00 0.00 0.00 4.35
1117 2024 2.743928 CGCCTGCCTGTCCTTGTC 60.744 66.667 0.00 0.00 0.00 3.18
1383 2308 4.639078 AAAGAAAAATGGAACCCATGGG 57.361 40.909 30.23 30.23 44.40 4.00
1399 2324 2.691011 CCACCGAAAAGGGACAAAAGAA 59.309 45.455 0.00 0.00 46.96 2.52
1400 2325 2.303175 CCACCGAAAAGGGACAAAAGA 58.697 47.619 0.00 0.00 46.96 2.52
1401 2326 1.269569 GCCACCGAAAAGGGACAAAAG 60.270 52.381 0.00 0.00 46.96 2.27
1402 2327 0.747852 GCCACCGAAAAGGGACAAAA 59.252 50.000 0.00 0.00 46.96 2.44
1403 2328 0.395862 TGCCACCGAAAAGGGACAAA 60.396 50.000 0.00 0.00 46.96 2.83
1422 2347 1.218854 GGCCAAAAATCGCCAGCAT 59.781 52.632 0.00 0.00 45.01 3.79
1458 2383 0.792640 CGCAAAGCAACACGAGAGAT 59.207 50.000 0.00 0.00 0.00 2.75
1459 2384 1.221466 CCGCAAAGCAACACGAGAGA 61.221 55.000 0.00 0.00 0.00 3.10
1460 2385 1.205064 CCGCAAAGCAACACGAGAG 59.795 57.895 0.00 0.00 0.00 3.20
1461 2386 1.522806 ACCGCAAAGCAACACGAGA 60.523 52.632 0.00 0.00 0.00 4.04
1462 2387 1.369209 CACCGCAAAGCAACACGAG 60.369 57.895 0.00 0.00 0.00 4.18
1712 2673 5.504173 GCATTACCTTTCTAATGAACGAGGC 60.504 44.000 0.00 0.00 36.56 4.70
1749 2710 1.270839 TGGACTGCTTCTGCTTGTACC 60.271 52.381 0.00 0.00 40.48 3.34
1753 2718 1.817357 TGATGGACTGCTTCTGCTTG 58.183 50.000 0.00 0.00 40.48 4.01
1754 2719 2.574006 TTGATGGACTGCTTCTGCTT 57.426 45.000 0.00 0.00 40.48 3.91
1755 2720 2.803030 ATTGATGGACTGCTTCTGCT 57.197 45.000 0.00 0.00 40.48 4.24
1756 2721 3.015327 AGAATTGATGGACTGCTTCTGC 58.985 45.455 0.00 0.00 40.20 4.26
1757 2722 6.748333 TTAAGAATTGATGGACTGCTTCTG 57.252 37.500 0.00 0.00 0.00 3.02
1758 2723 7.951347 AATTAAGAATTGATGGACTGCTTCT 57.049 32.000 0.00 0.00 0.00 2.85
1759 2724 8.897752 ACTAATTAAGAATTGATGGACTGCTTC 58.102 33.333 0.00 0.00 32.38 3.86
1799 2776 8.953665 AGAAATACAGGAGGGAATAAGATTCAT 58.046 33.333 1.90 0.00 0.00 2.57
1800 2777 8.337118 AGAAATACAGGAGGGAATAAGATTCA 57.663 34.615 1.90 0.00 0.00 2.57
1801 2778 9.634021 AAAGAAATACAGGAGGGAATAAGATTC 57.366 33.333 0.00 0.00 0.00 2.52
1802 2779 9.997172 AAAAGAAATACAGGAGGGAATAAGATT 57.003 29.630 0.00 0.00 0.00 2.40
1917 2922 5.976458 TGCATCAACAGTACATGTCTGATA 58.024 37.500 23.48 12.95 43.00 2.15
1967 2975 7.001674 GGGACCAAAATTAAACAGGGATTTTT 58.998 34.615 0.00 0.00 0.00 1.94
1968 2976 6.331572 AGGGACCAAAATTAAACAGGGATTTT 59.668 34.615 0.00 0.00 0.00 1.82
1970 2978 5.248248 CAGGGACCAAAATTAAACAGGGATT 59.752 40.000 0.00 0.00 0.00 3.01
1971 2979 4.777366 CAGGGACCAAAATTAAACAGGGAT 59.223 41.667 0.00 0.00 0.00 3.85
1972 2980 4.140900 TCAGGGACCAAAATTAAACAGGGA 60.141 41.667 0.00 0.00 0.00 4.20
1973 2981 4.156477 TCAGGGACCAAAATTAAACAGGG 58.844 43.478 0.00 0.00 0.00 4.45
1974 2982 5.799827 TTCAGGGACCAAAATTAAACAGG 57.200 39.130 0.00 0.00 0.00 4.00
1975 2983 6.991938 TGATTCAGGGACCAAAATTAAACAG 58.008 36.000 0.00 0.00 0.00 3.16
1976 2984 6.985653 TGATTCAGGGACCAAAATTAAACA 57.014 33.333 0.00 0.00 0.00 2.83
1977 2985 7.386059 ACATGATTCAGGGACCAAAATTAAAC 58.614 34.615 0.00 0.00 0.00 2.01
2052 3105 5.277538 GCCTTGACTCTTGACAAGTAAACTG 60.278 44.000 14.75 3.70 41.81 3.16
2061 3114 0.469494 TGCAGCCTTGACTCTTGACA 59.531 50.000 0.00 0.00 0.00 3.58
2078 3132 2.170607 TGCTTAGGGGAGAACAGTATGC 59.829 50.000 0.00 0.00 42.53 3.14
2087 3141 1.681229 AATGGGTTGCTTAGGGGAGA 58.319 50.000 0.00 0.00 0.00 3.71
2119 3177 2.575532 ACAACTCATATGATTGGCCGG 58.424 47.619 21.51 0.00 0.00 6.13
2303 3367 3.809279 TCATGTCACAATGTCACAGACAC 59.191 43.478 6.45 0.00 45.65 3.67
2330 3394 3.760151 CAGACAAGGGAATTCAGCATCAA 59.240 43.478 7.93 0.00 0.00 2.57
2356 3420 4.457496 CTCGCCCCTGCACGACAT 62.457 66.667 0.00 0.00 37.32 3.06
2414 3480 0.173481 TTCCATGAGCTCGTCCTTCG 59.827 55.000 5.16 0.00 41.41 3.79
2554 3620 5.775195 TGGCACATCACTAGCTAGTATATGT 59.225 40.000 30.38 30.38 40.12 2.29
2555 3621 6.096036 GTGGCACATCACTAGCTAGTATATG 58.904 44.000 29.50 29.50 44.52 1.78
2558 3624 3.960755 TGTGGCACATCACTAGCTAGTAT 59.039 43.478 25.63 15.87 44.52 2.12
2559 3625 3.361786 TGTGGCACATCACTAGCTAGTA 58.638 45.455 25.63 14.40 44.52 1.82
2560 3626 2.179427 TGTGGCACATCACTAGCTAGT 58.821 47.619 20.95 20.95 44.52 2.57
2561 3627 2.967599 TGTGGCACATCACTAGCTAG 57.032 50.000 17.96 19.44 44.52 3.42
2562 3628 6.857437 ATATATGTGGCACATCACTAGCTA 57.143 37.500 34.48 16.40 44.52 3.32
2563 3629 5.752036 ATATATGTGGCACATCACTAGCT 57.248 39.130 34.48 13.58 44.52 3.32
2621 3691 5.221185 GCTACCCAGTTCGATCTGTATACAA 60.221 44.000 19.45 0.00 34.02 2.41
2646 3716 1.268539 CGCCAACAACAACAACTCCTC 60.269 52.381 0.00 0.00 0.00 3.71
2647 3717 0.738389 CGCCAACAACAACAACTCCT 59.262 50.000 0.00 0.00 0.00 3.69
2649 3719 2.384382 CATCGCCAACAACAACAACTC 58.616 47.619 0.00 0.00 0.00 3.01
2720 3793 2.269241 GGGCAGGAGAGGAAACCG 59.731 66.667 0.00 0.00 0.00 4.44
2823 3896 2.091112 CAGCGAGAGAACTGCACGG 61.091 63.158 0.00 0.00 0.00 4.94
2830 3903 0.457681 GTCCAGAGCAGCGAGAGAAC 60.458 60.000 0.00 0.00 0.00 3.01
2837 3910 1.347817 GAACTTCGTCCAGAGCAGCG 61.348 60.000 0.00 0.00 0.00 5.18
2846 3919 4.425520 CACCTTATCAGAGAACTTCGTCC 58.574 47.826 0.00 0.00 0.00 4.79
2868 3941 1.066502 GTCTCTTCTTCTCCACTGCCC 60.067 57.143 0.00 0.00 0.00 5.36
2869 3942 1.620819 TGTCTCTTCTTCTCCACTGCC 59.379 52.381 0.00 0.00 0.00 4.85
2870 3943 2.560542 TCTGTCTCTTCTTCTCCACTGC 59.439 50.000 0.00 0.00 0.00 4.40
2871 3944 4.078537 TCTCTGTCTCTTCTTCTCCACTG 58.921 47.826 0.00 0.00 0.00 3.66
2893 4057 2.564975 GCATGCGCTTGACAGCTT 59.435 55.556 25.77 0.00 44.85 3.74
2897 4061 4.388080 GCACGCATGCGCTTGACA 62.388 61.111 38.15 0.00 43.33 3.58
2911 4075 1.131504 TCTGGAACAAACAACACGCAC 59.868 47.619 0.00 0.00 38.70 5.34
2912 4076 1.131504 GTCTGGAACAAACAACACGCA 59.868 47.619 0.00 0.00 38.70 5.24
2977 4165 2.170166 TGGGTTTGATTGCATCAGGAC 58.830 47.619 0.00 0.00 40.94 3.85
3090 4282 4.801147 ACAATATACAATGAGCTGCACG 57.199 40.909 1.02 0.00 0.00 5.34
3095 4287 7.013655 GGGATGAACAACAATATACAATGAGCT 59.986 37.037 0.00 0.00 0.00 4.09
3111 4303 3.810941 GTGTCGTTTGTAGGGATGAACAA 59.189 43.478 0.00 0.00 0.00 2.83
3120 4312 2.661675 CACATCGAGTGTCGTTTGTAGG 59.338 50.000 6.79 0.00 43.40 3.18
3143 4335 4.654015 GTTCGTTTGTAACAGTGCAGAAA 58.346 39.130 0.00 0.00 0.00 2.52
3151 4343 1.868469 TCCCCGTTCGTTTGTAACAG 58.132 50.000 0.00 0.00 0.00 3.16
3156 4348 0.891904 CCCAATCCCCGTTCGTTTGT 60.892 55.000 0.00 0.00 0.00 2.83
3160 4352 1.223487 CATCCCAATCCCCGTTCGT 59.777 57.895 0.00 0.00 0.00 3.85
3189 4381 1.459592 GTCGTATTGCTTCGTTGCAGT 59.540 47.619 5.42 5.66 44.27 4.40
3202 4394 2.434702 GTGGATTCTGGAGGGTCGTATT 59.565 50.000 0.00 0.00 0.00 1.89
3205 4397 1.605058 CGTGGATTCTGGAGGGTCGT 61.605 60.000 0.00 0.00 0.00 4.34
3206 4398 1.141881 CGTGGATTCTGGAGGGTCG 59.858 63.158 0.00 0.00 0.00 4.79
3235 4442 1.056103 CTCGCGACTTCTGACAACAG 58.944 55.000 3.71 0.00 44.66 3.16
3249 4457 0.166597 TGAATCAAAAGCTGCTCGCG 59.833 50.000 1.00 0.00 45.59 5.87
3258 4466 4.466828 CAACTACGCCAGTGAATCAAAAG 58.533 43.478 0.00 0.00 37.63 2.27
3261 4469 2.224426 ACCAACTACGCCAGTGAATCAA 60.224 45.455 0.00 0.00 37.63 2.57
3262 4470 1.346395 ACCAACTACGCCAGTGAATCA 59.654 47.619 0.00 0.00 37.63 2.57
3263 4471 2.094762 ACCAACTACGCCAGTGAATC 57.905 50.000 0.00 0.00 37.63 2.52
3264 4472 2.354403 GGTACCAACTACGCCAGTGAAT 60.354 50.000 7.15 0.00 37.63 2.57
3273 4481 1.003851 CATTGCCGGTACCAACTACG 58.996 55.000 13.54 0.00 0.00 3.51
3274 4482 1.339342 ACCATTGCCGGTACCAACTAC 60.339 52.381 13.54 0.00 37.57 2.73
3275 4483 0.985760 ACCATTGCCGGTACCAACTA 59.014 50.000 13.54 0.00 37.57 2.24
3286 4494 0.321653 ACAGAAGACGGACCATTGCC 60.322 55.000 0.00 0.00 0.00 4.52
3296 4504 1.695813 CTCTGCAGTGACAGAAGACG 58.304 55.000 14.67 3.99 45.72 4.18
3304 4512 1.571460 CCGTTTGCTCTGCAGTGAC 59.429 57.895 19.61 10.88 40.61 3.67
3315 4523 2.126110 CCCGAAATGGCCGTTTGC 60.126 61.111 27.54 16.59 40.16 3.68
3370 4579 2.070783 TCGGTGTTACTTTTCATCGGC 58.929 47.619 0.00 0.00 38.49 5.54
3371 4580 3.367025 GTCTCGGTGTTACTTTTCATCGG 59.633 47.826 0.00 0.00 38.49 4.18
3372 4581 4.235360 AGTCTCGGTGTTACTTTTCATCG 58.765 43.478 0.00 0.00 39.18 3.84
3373 4582 5.227908 TGAGTCTCGGTGTTACTTTTCATC 58.772 41.667 0.00 0.00 0.00 2.92
3374 4583 5.209818 TGAGTCTCGGTGTTACTTTTCAT 57.790 39.130 0.00 0.00 0.00 2.57
3375 4584 4.659111 TGAGTCTCGGTGTTACTTTTCA 57.341 40.909 0.00 0.00 0.00 2.69
3376 4585 4.085210 CGTTGAGTCTCGGTGTTACTTTTC 60.085 45.833 0.00 0.00 0.00 2.29
3378 4587 3.181483 ACGTTGAGTCTCGGTGTTACTTT 60.181 43.478 11.51 0.00 0.00 2.66
3379 4588 2.360165 ACGTTGAGTCTCGGTGTTACTT 59.640 45.455 11.51 0.00 0.00 2.24
3380 4589 1.952296 ACGTTGAGTCTCGGTGTTACT 59.048 47.619 11.51 0.00 0.00 2.24
3381 4590 2.049228 CACGTTGAGTCTCGGTGTTAC 58.951 52.381 11.51 0.00 0.00 2.50
3388 4598 2.418333 CGCGTCACGTTGAGTCTCG 61.418 63.158 0.00 6.72 36.87 4.04
3509 4720 2.594962 GGTGTTGTCGCCGTCACAG 61.595 63.158 0.00 0.00 34.40 3.66
3510 4721 2.586635 GGTGTTGTCGCCGTCACA 60.587 61.111 0.00 0.00 34.40 3.58


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

AutoCloner maintained by Alex Coulton.