Multiple sequence alignment - TraesCS6B01G345300

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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 TraesCS6B01G345300 chr6B 100.000 3831 0 0 1 3831 608995331 608999161 0.000000e+00 7075.0
1 TraesCS6B01G345300 chr6A 90.718 2564 151 42 1 2505 551637649 551640184 0.000000e+00 3336.0
2 TraesCS6B01G345300 chr6A 96.431 1317 31 4 2529 3831 551640183 551641497 0.000000e+00 2158.0
3 TraesCS6B01G345300 chr6D 90.310 1744 73 32 1 1695 405081138 405082834 0.000000e+00 2196.0
4 TraesCS6B01G345300 chr6D 95.593 1316 44 2 2529 3831 405082983 405084297 0.000000e+00 2097.0
5 TraesCS6B01G345300 chr6D 95.597 159 7 0 2347 2505 405082826 405082984 4.910000e-64 255.0
6 TraesCS6B01G345300 chr2A 90.287 731 55 6 1599 2314 11922812 11922083 0.000000e+00 942.0
7 TraesCS6B01G345300 chr2A 82.081 346 37 10 1633 1967 778158981 778159312 4.880000e-69 272.0
8 TraesCS6B01G345300 chr7A 90.355 591 41 6 1596 2171 42642252 42641663 0.000000e+00 761.0
9 TraesCS6B01G345300 chr7A 92.208 77 5 1 1551 1627 46717063 46717138 1.460000e-19 108.0
10 TraesCS6B01G345300 chr1A 79.960 998 122 39 1233 2207 523120764 523121706 0.000000e+00 664.0
11 TraesCS6B01G345300 chr1A 82.305 729 85 22 1489 2206 525004787 525004092 3.300000e-165 592.0
12 TraesCS6B01G345300 chr1A 81.918 730 86 25 1489 2206 523125437 523126132 3.320000e-160 575.0
13 TraesCS6B01G345300 chr1A 100.000 33 0 0 2597 2629 523122957 523122989 1.150000e-05 62.1
14 TraesCS6B01G345300 chr1A 100.000 33 0 0 2597 2629 523124342 523124374 1.150000e-05 62.1
15 TraesCS6B01G345300 chr1A 100.000 33 0 0 2597 2629 523125352 523125384 1.150000e-05 62.1
16 TraesCS6B01G345300 chr5B 90.343 466 45 0 2596 3061 425667760 425668225 2.530000e-171 612.0
17 TraesCS6B01G345300 chr5B 89.957 468 45 2 2596 3061 264912595 264912128 1.520000e-168 603.0
18 TraesCS6B01G345300 chr5B 78.744 828 98 38 1154 1966 264913829 264913065 2.070000e-132 483.0
19 TraesCS6B01G345300 chr5B 84.726 419 52 6 1791 2207 439441995 439442403 3.560000e-110 409.0
20 TraesCS6B01G345300 chr5B 86.379 301 38 3 2206 2504 439442321 439442620 3.690000e-85 326.0
21 TraesCS6B01G345300 chr5B 80.930 430 43 14 1549 1966 425666887 425667289 1.730000e-78 303.0
22 TraesCS6B01G345300 chr5B 83.568 213 22 11 1199 1411 425666598 425666797 1.820000e-43 187.0
23 TraesCS6B01G345300 chr1B 90.343 466 45 0 2596 3061 656526669 656526204 2.530000e-171 612.0
24 TraesCS6B01G345300 chr1B 82.093 430 39 16 1549 1966 656527543 656527140 2.210000e-87 333.0
25 TraesCS6B01G345300 chr3B 88.841 466 52 0 2596 3061 174463768 174463303 1.190000e-159 573.0
26 TraesCS6B01G345300 chr3B 87.443 438 40 7 2628 3062 763474033 763473608 1.240000e-134 490.0
27 TraesCS6B01G345300 chr3B 87.975 158 16 2 1199 1356 174464931 174464777 2.350000e-42 183.0
28 TraesCS6B01G345300 chr2B 80.024 836 100 35 1152 1976 779042647 779041868 1.200000e-154 556.0
29 TraesCS6B01G345300 chr2B 87.162 296 37 1 2206 2500 4576306 4576601 6.130000e-88 335.0
30 TraesCS6B01G345300 chr2B 86.777 242 30 2 2206 2446 779041756 779041516 6.310000e-68 268.0
31 TraesCS6B01G345300 chr1D 94.044 319 17 2 2626 2943 156285595 156285912 2.070000e-132 483.0
32 TraesCS6B01G345300 chr1D 93.730 319 18 2 2626 2943 11359482 11359799 9.630000e-131 477.0
33 TraesCS6B01G345300 chr3D 94.237 295 15 2 2650 2943 459882811 459882518 2.100000e-122 449.0
34 TraesCS6B01G345300 chr3D 83.047 466 42 21 1016 1463 353233742 353233296 4.640000e-104 388.0
35 TraesCS6B01G345300 chr3D 93.976 83 3 2 1549 1631 566655647 566655727 1.450000e-24 124.0
36 TraesCS6B01G345300 chr7B 84.726 419 52 6 1791 2207 98985013 98985421 3.560000e-110 409.0
37 TraesCS6B01G345300 chr7B 87.162 296 35 3 2206 2499 98985339 98985633 2.210000e-87 333.0
38 TraesCS6B01G345300 chr7D 88.754 329 34 3 1881 2207 77499546 77499219 2.140000e-107 399.0
39 TraesCS6B01G345300 chr7D 87.162 296 37 1 2206 2500 77499301 77499006 6.130000e-88 335.0
40 TraesCS6B01G345300 chr7D 85.811 296 41 1 2206 2500 147585793 147586088 2.870000e-81 313.0
41 TraesCS6B01G345300 chr5D 86.824 296 38 1 2206 2500 120935342 120935637 2.850000e-86 329.0
42 TraesCS6B01G345300 chr2D 93.671 79 4 1 1549 1627 264298253 264298330 2.420000e-22 117.0


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 TraesCS6B01G345300 chr6B 608995331 608999161 3830 False 7075.000000 7075 100.000000 1 3831 1 chr6B.!!$F1 3830
1 TraesCS6B01G345300 chr6A 551637649 551641497 3848 False 2747.000000 3336 93.574500 1 3831 2 chr6A.!!$F1 3830
2 TraesCS6B01G345300 chr6D 405081138 405084297 3159 False 1516.000000 2196 93.833333 1 3831 3 chr6D.!!$F1 3830
3 TraesCS6B01G345300 chr2A 11922083 11922812 729 True 942.000000 942 90.287000 1599 2314 1 chr2A.!!$R1 715
4 TraesCS6B01G345300 chr7A 42641663 42642252 589 True 761.000000 761 90.355000 1596 2171 1 chr7A.!!$R1 575
5 TraesCS6B01G345300 chr1A 525004092 525004787 695 True 592.000000 592 82.305000 1489 2206 1 chr1A.!!$R1 717
6 TraesCS6B01G345300 chr1A 523120764 523126132 5368 False 285.060000 664 92.375600 1233 2629 5 chr1A.!!$F1 1396
7 TraesCS6B01G345300 chr5B 264912128 264913829 1701 True 543.000000 603 84.350500 1154 3061 2 chr5B.!!$R1 1907
8 TraesCS6B01G345300 chr5B 439441995 439442620 625 False 367.500000 409 85.552500 1791 2504 2 chr5B.!!$F2 713
9 TraesCS6B01G345300 chr5B 425666598 425668225 1627 False 367.333333 612 84.947000 1199 3061 3 chr5B.!!$F1 1862
10 TraesCS6B01G345300 chr1B 656526204 656527543 1339 True 472.500000 612 86.218000 1549 3061 2 chr1B.!!$R1 1512
11 TraesCS6B01G345300 chr3B 174463303 174464931 1628 True 378.000000 573 88.408000 1199 3061 2 chr3B.!!$R2 1862
12 TraesCS6B01G345300 chr2B 779041516 779042647 1131 True 412.000000 556 83.400500 1152 2446 2 chr2B.!!$R1 1294
13 TraesCS6B01G345300 chr7B 98985013 98985633 620 False 371.000000 409 85.944000 1791 2499 2 chr7B.!!$F1 708
14 TraesCS6B01G345300 chr7D 77499006 77499546 540 True 367.000000 399 87.958000 1881 2500 2 chr7D.!!$R1 619

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
356 365 0.035152 ACACACATCACCGCATCCAT 60.035 50.0 0.00 0.0 0.00 3.41 F
480 496 0.949105 AATCCGAACCAGTGTCGTGC 60.949 55.0 2.89 0.0 0.00 5.34 F
1846 5439 0.035881 CATGGCAGACCTCCGCATAT 59.964 55.0 0.00 0.0 36.63 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 3899 0.322816 TGCCTTCCTGCCATGAGAAC 60.323 55.000 0.00 0.00 0.00 3.01 R
2060 5665 2.517875 AATGCGAGCATGGAGGGC 60.518 61.111 11.64 0.00 36.68 5.19 R
3573 7731 1.365633 CGGGTCTAGCAGGCTGATC 59.634 63.158 20.86 0.47 0.00 2.92 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
20 21 0.036010 CCTCCTCATTTGTCGTGGCT 60.036 55.000 0.00 0.00 0.00 4.75
32 33 1.208870 CGTGGCTTGCGCAATGTTA 59.791 52.632 25.26 7.84 38.10 2.41
37 38 1.985684 GGCTTGCGCAATGTTAGTTTC 59.014 47.619 25.26 2.19 38.10 2.78
38 39 1.643810 GCTTGCGCAATGTTAGTTTCG 59.356 47.619 25.26 8.83 35.78 3.46
39 40 2.664424 GCTTGCGCAATGTTAGTTTCGA 60.664 45.455 25.26 0.00 35.78 3.71
45 46 4.523813 CGCAATGTTAGTTTCGAAGTGTT 58.476 39.130 0.00 0.00 0.00 3.32
87 90 4.202060 TGCCACGAAAGAAATTTTGTAGCA 60.202 37.500 9.26 9.26 39.46 3.49
90 93 5.977129 CCACGAAAGAAATTTTGTAGCAACT 59.023 36.000 0.00 0.00 0.00 3.16
176 181 5.994668 GGCACCCAAATCTTGTGAAATTTTA 59.005 36.000 0.00 0.00 31.66 1.52
177 182 6.147656 GGCACCCAAATCTTGTGAAATTTTAG 59.852 38.462 0.00 0.00 31.66 1.85
178 183 6.705825 GCACCCAAATCTTGTGAAATTTTAGT 59.294 34.615 0.00 0.00 31.66 2.24
179 184 7.095649 GCACCCAAATCTTGTGAAATTTTAGTC 60.096 37.037 0.00 0.00 31.66 2.59
180 185 8.143835 CACCCAAATCTTGTGAAATTTTAGTCT 58.856 33.333 0.00 0.00 31.66 3.24
181 186 8.704668 ACCCAAATCTTGTGAAATTTTAGTCTT 58.295 29.630 0.00 0.00 0.00 3.01
186 191 9.588096 AATCTTGTGAAATTTTAGTCTTACCCT 57.412 29.630 0.00 0.00 0.00 4.34
188 193 7.386848 TCTTGTGAAATTTTAGTCTTACCCTCG 59.613 37.037 0.00 0.00 0.00 4.63
189 194 6.527423 TGTGAAATTTTAGTCTTACCCTCGT 58.473 36.000 0.00 0.00 0.00 4.18
205 211 9.204570 CTTACCCTCGTATCCATTTATTACAAG 57.795 37.037 0.00 0.00 0.00 3.16
253 259 7.064866 ACACAATCACCATGATATTCTCCATT 58.935 34.615 0.00 0.00 35.76 3.16
294 302 3.319755 TCCGAGATTACAAAACGGTGTC 58.680 45.455 0.00 0.00 43.36 3.67
297 305 3.367025 CGAGATTACAAAACGGTGTCTCC 59.633 47.826 0.00 0.00 33.73 3.71
338 347 6.292328 GCAAGAAAATAAGCCAAGAAACACAC 60.292 38.462 0.00 0.00 0.00 3.82
339 348 6.463995 AGAAAATAAGCCAAGAAACACACA 57.536 33.333 0.00 0.00 0.00 3.72
340 349 6.273071 AGAAAATAAGCCAAGAAACACACAC 58.727 36.000 0.00 0.00 0.00 3.82
341 350 5.590530 AAATAAGCCAAGAAACACACACA 57.409 34.783 0.00 0.00 0.00 3.72
342 351 2.939460 AAGCCAAGAAACACACACAC 57.061 45.000 0.00 0.00 0.00 3.82
343 352 1.832883 AGCCAAGAAACACACACACA 58.167 45.000 0.00 0.00 0.00 3.72
344 353 2.378038 AGCCAAGAAACACACACACAT 58.622 42.857 0.00 0.00 0.00 3.21
345 354 2.358898 AGCCAAGAAACACACACACATC 59.641 45.455 0.00 0.00 0.00 3.06
346 355 2.098934 GCCAAGAAACACACACACATCA 59.901 45.455 0.00 0.00 0.00 3.07
347 356 3.694734 CCAAGAAACACACACACATCAC 58.305 45.455 0.00 0.00 0.00 3.06
348 357 3.489059 CCAAGAAACACACACACATCACC 60.489 47.826 0.00 0.00 0.00 4.02
349 358 1.939934 AGAAACACACACACATCACCG 59.060 47.619 0.00 0.00 0.00 4.94
350 359 0.380378 AAACACACACACATCACCGC 59.620 50.000 0.00 0.00 0.00 5.68
351 360 0.746204 AACACACACACATCACCGCA 60.746 50.000 0.00 0.00 0.00 5.69
352 361 0.534877 ACACACACACATCACCGCAT 60.535 50.000 0.00 0.00 0.00 4.73
353 362 0.166597 CACACACACATCACCGCATC 59.833 55.000 0.00 0.00 0.00 3.91
356 365 0.035152 ACACACATCACCGCATCCAT 60.035 50.000 0.00 0.00 0.00 3.41
363 372 2.998316 TCACCGCATCCATCACATAA 57.002 45.000 0.00 0.00 0.00 1.90
364 373 3.490439 TCACCGCATCCATCACATAAT 57.510 42.857 0.00 0.00 0.00 1.28
368 384 3.565482 ACCGCATCCATCACATAATTCAC 59.435 43.478 0.00 0.00 0.00 3.18
382 398 9.524106 TCACATAATTCACATTACTAACCTACG 57.476 33.333 0.00 0.00 0.00 3.51
383 399 9.309516 CACATAATTCACATTACTAACCTACGT 57.690 33.333 0.00 0.00 0.00 3.57
387 403 8.693542 AATTCACATTACTAACCTACGTACAC 57.306 34.615 0.00 0.00 0.00 2.90
389 405 5.030295 CACATTACTAACCTACGTACACCG 58.970 45.833 0.00 0.00 44.03 4.94
405 421 2.591915 CCGGAGGCCAGTCTAGAAA 58.408 57.895 5.01 0.00 46.14 2.52
411 427 1.552792 AGGCCAGTCTAGAAACAGAGC 59.447 52.381 5.01 0.00 0.00 4.09
414 430 2.676463 GCCAGTCTAGAAACAGAGCAGG 60.676 54.545 0.00 0.00 0.00 4.85
468 484 4.142047 GCGCACGCGAAATCCGAA 62.142 61.111 15.93 0.00 42.83 4.30
480 496 0.949105 AATCCGAACCAGTGTCGTGC 60.949 55.000 2.89 0.00 0.00 5.34
757 787 5.605534 CTCCACTTGAGAAGAAGAAGAACA 58.394 41.667 0.00 0.00 44.42 3.18
884 940 1.583054 ATCGGGAGTAAATTCGCAGC 58.417 50.000 0.00 0.00 0.00 5.25
971 1035 1.683385 GCTCATTAACCCAGCATTCCC 59.317 52.381 0.00 0.00 33.06 3.97
1191 1288 4.082523 CACCCCGTGCAGTCCGAT 62.083 66.667 0.00 0.00 0.00 4.18
1375 1472 2.030893 TCCAATCGTCGTTTACTCGTGT 60.031 45.455 0.00 0.00 0.00 4.49
1631 3829 7.655328 CCTTCCTGTAAGTCTTATCATCATCAC 59.345 40.741 0.00 0.00 32.89 3.06
1691 3899 4.590222 CCCTTTAATCATGGAGGAATTGGG 59.410 45.833 0.00 0.00 0.00 4.12
1846 5439 0.035881 CATGGCAGACCTCCGCATAT 59.964 55.000 0.00 0.00 36.63 1.78
1847 5440 1.276138 CATGGCAGACCTCCGCATATA 59.724 52.381 0.00 0.00 36.63 0.86
1848 5441 0.679505 TGGCAGACCTCCGCATATAC 59.320 55.000 0.00 0.00 36.63 1.47
1857 5458 3.116300 CCTCCGCATATACATACATCGC 58.884 50.000 0.00 0.00 0.00 4.58
1943 5548 0.447801 CAAATTCTGCGTTCGAGGGG 59.552 55.000 0.00 0.00 0.00 4.79
1945 5550 0.323629 AATTCTGCGTTCGAGGGGAA 59.676 50.000 0.00 0.00 0.00 3.97
2060 5665 3.179010 GCAAATTCAATGATCATGACGCG 59.821 43.478 9.46 3.53 0.00 6.01
2258 5906 6.169800 TCGATCAATGTGTTAAACCAGATCA 58.830 36.000 0.00 0.00 32.85 2.92
2259 5907 6.823182 TCGATCAATGTGTTAAACCAGATCAT 59.177 34.615 0.00 0.00 32.85 2.45
2260 5908 7.336679 TCGATCAATGTGTTAAACCAGATCATT 59.663 33.333 0.00 0.00 32.85 2.57
2381 6029 2.420642 TCAGAGATTGCTGCAAGTGTC 58.579 47.619 20.72 15.40 35.86 3.67
2446 6127 3.146847 GGGCTACAACTACTTGCAAGTT 58.853 45.455 35.20 20.18 40.37 2.66
2476 6157 2.757868 AGGTAGTGATCAGCTCAGTGTC 59.242 50.000 0.00 0.00 38.06 3.67
2530 6211 2.349376 CCCCCACACGCACATACA 59.651 61.111 0.00 0.00 0.00 2.29
2535 6216 2.029470 CCCCACACGCACATACAAAATT 60.029 45.455 0.00 0.00 0.00 1.82
2569 6250 1.005347 GCAATGATGCGCTTGAATTGC 60.005 47.619 24.85 24.85 43.83 3.56
3062 7205 3.866651 CATGCTAAGCTGTTAGTGTCCT 58.133 45.455 0.00 0.00 38.38 3.85
3136 7279 4.085733 GAGATGAGAGCTCTATTGCCCTA 58.914 47.826 18.25 0.00 0.00 3.53
3166 7310 7.827236 TGTATTTCGGTTCCATATTCAGTTTCT 59.173 33.333 0.00 0.00 0.00 2.52
3320 7465 9.467796 TTGTTGTTCCATTTTATTTCCCTTTTT 57.532 25.926 0.00 0.00 0.00 1.94
3393 7538 4.569719 ACCCAATCCTTTATTCGTCACT 57.430 40.909 0.00 0.00 0.00 3.41
3514 7659 3.359695 TCCTTACAAGTGCATTACCCC 57.640 47.619 0.00 0.00 0.00 4.95
3522 7667 3.297134 AGTGCATTACCCCTTACCATG 57.703 47.619 0.00 0.00 0.00 3.66
3541 7686 6.342906 ACCATGTGATTTGGAGCATAATTTG 58.657 36.000 0.00 0.00 37.69 2.32
3573 7731 1.418334 AGTAGCACTGATGGCCCTAG 58.582 55.000 0.00 0.00 0.00 3.02
3634 7792 7.105588 TGTTGAATACTGTAGTGCAATCTGAT 58.894 34.615 0.00 0.00 0.00 2.90
3677 7835 4.681744 TCACAAACCTGCATTTGAAGTTC 58.318 39.130 17.47 0.00 41.28 3.01
3684 7842 3.760151 CCTGCATTTGAAGTTCCATCTCA 59.240 43.478 0.00 0.00 0.00 3.27
3784 7942 2.163412 TGTCGGATTTGCTAATGCCAAC 59.837 45.455 6.79 6.29 38.71 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.002862 ACTTCGAAACTAACATTGCGCAA 59.997 39.130 27.24 27.24 0.00 4.85
32 33 4.269363 CGTAAGGAACAACACTTCGAAACT 59.731 41.667 0.00 0.00 0.00 2.66
37 38 2.155155 GCTCGTAAGGAACAACACTTCG 59.845 50.000 0.00 0.00 38.47 3.79
38 39 2.155155 CGCTCGTAAGGAACAACACTTC 59.845 50.000 0.00 0.00 38.47 3.01
39 40 2.132762 CGCTCGTAAGGAACAACACTT 58.867 47.619 0.00 0.00 38.47 3.16
45 46 2.343101 CAAATCCGCTCGTAAGGAACA 58.657 47.619 0.32 0.00 40.32 3.18
87 90 6.795399 AGTTTGTGATTTTCGTGATTCAGTT 58.205 32.000 0.00 0.00 0.00 3.16
90 93 9.743057 AAATTAGTTTGTGATTTTCGTGATTCA 57.257 25.926 0.00 0.00 0.00 2.57
176 181 7.613551 AATAAATGGATACGAGGGTAAGACT 57.386 36.000 0.00 0.00 42.51 3.24
177 182 8.362639 TGTAATAAATGGATACGAGGGTAAGAC 58.637 37.037 0.00 0.00 42.51 3.01
178 183 8.481492 TGTAATAAATGGATACGAGGGTAAGA 57.519 34.615 0.00 0.00 42.51 2.10
179 184 9.204570 CTTGTAATAAATGGATACGAGGGTAAG 57.795 37.037 0.00 0.00 42.51 2.34
180 185 8.152246 CCTTGTAATAAATGGATACGAGGGTAA 58.848 37.037 9.62 0.00 43.26 2.85
181 186 7.510001 TCCTTGTAATAAATGGATACGAGGGTA 59.490 37.037 15.17 0.00 45.45 3.69
182 187 6.328148 TCCTTGTAATAAATGGATACGAGGGT 59.672 38.462 15.17 0.00 45.45 4.34
185 190 6.929049 TGCTCCTTGTAATAAATGGATACGAG 59.071 38.462 0.00 0.00 42.51 4.18
186 191 6.822442 TGCTCCTTGTAATAAATGGATACGA 58.178 36.000 0.00 0.00 42.51 3.43
188 193 8.677148 TCTTGCTCCTTGTAATAAATGGATAC 57.323 34.615 0.00 0.00 0.00 2.24
189 194 9.693739 TTTCTTGCTCCTTGTAATAAATGGATA 57.306 29.630 0.00 0.00 0.00 2.59
205 211 4.823790 TTTACGGTTTCTTTCTTGCTCC 57.176 40.909 0.00 0.00 0.00 4.70
253 259 9.788889 TCTCGGAGATCTTTACTTGTATATGTA 57.211 33.333 2.97 0.00 33.89 2.29
265 272 6.755141 CCGTTTTGTAATCTCGGAGATCTTTA 59.245 38.462 20.15 8.04 43.22 1.85
294 302 1.200020 GCGAAACAAACATGGGAGGAG 59.800 52.381 0.00 0.00 0.00 3.69
297 305 2.293122 TCTTGCGAAACAAACATGGGAG 59.707 45.455 0.00 0.00 37.96 4.30
318 327 5.810074 GTGTGTGTGTTTCTTGGCTTATTTT 59.190 36.000 0.00 0.00 0.00 1.82
338 347 0.659427 GATGGATGCGGTGATGTGTG 59.341 55.000 0.00 0.00 0.00 3.82
339 348 0.252761 TGATGGATGCGGTGATGTGT 59.747 50.000 0.00 0.00 0.00 3.72
340 349 0.659427 GTGATGGATGCGGTGATGTG 59.341 55.000 0.00 0.00 0.00 3.21
341 350 0.252761 TGTGATGGATGCGGTGATGT 59.747 50.000 0.00 0.00 0.00 3.06
342 351 1.601166 ATGTGATGGATGCGGTGATG 58.399 50.000 0.00 0.00 0.00 3.07
343 352 3.490439 TTATGTGATGGATGCGGTGAT 57.510 42.857 0.00 0.00 0.00 3.06
344 353 2.998316 TTATGTGATGGATGCGGTGA 57.002 45.000 0.00 0.00 0.00 4.02
345 354 3.565063 TGAATTATGTGATGGATGCGGTG 59.435 43.478 0.00 0.00 0.00 4.94
346 355 3.565482 GTGAATTATGTGATGGATGCGGT 59.435 43.478 0.00 0.00 0.00 5.68
347 356 3.565063 TGTGAATTATGTGATGGATGCGG 59.435 43.478 0.00 0.00 0.00 5.69
348 357 4.816786 TGTGAATTATGTGATGGATGCG 57.183 40.909 0.00 0.00 0.00 4.73
349 358 7.879070 AGTAATGTGAATTATGTGATGGATGC 58.121 34.615 0.00 0.00 0.00 3.91
352 361 9.337396 GGTTAGTAATGTGAATTATGTGATGGA 57.663 33.333 0.00 0.00 0.00 3.41
353 362 9.342308 AGGTTAGTAATGTGAATTATGTGATGG 57.658 33.333 0.00 0.00 0.00 3.51
356 365 9.524106 CGTAGGTTAGTAATGTGAATTATGTGA 57.476 33.333 0.00 0.00 0.00 3.58
363 372 7.260603 GGTGTACGTAGGTTAGTAATGTGAAT 58.739 38.462 0.00 0.00 0.00 2.57
364 373 6.620678 GGTGTACGTAGGTTAGTAATGTGAA 58.379 40.000 0.00 0.00 0.00 3.18
368 384 4.335315 TCCGGTGTACGTAGGTTAGTAATG 59.665 45.833 0.00 0.00 42.24 1.90
381 397 3.352338 GACTGGCCTCCGGTGTACG 62.352 68.421 3.32 0.00 44.10 3.67
382 398 0.682209 TAGACTGGCCTCCGGTGTAC 60.682 60.000 3.32 0.00 44.10 2.90
383 399 0.395311 CTAGACTGGCCTCCGGTGTA 60.395 60.000 3.32 1.96 44.10 2.90
384 400 1.682684 CTAGACTGGCCTCCGGTGT 60.683 63.158 3.32 0.72 44.10 4.16
385 401 0.970937 TTCTAGACTGGCCTCCGGTG 60.971 60.000 3.32 0.00 44.10 4.94
387 403 0.175989 GTTTCTAGACTGGCCTCCGG 59.824 60.000 3.32 0.00 35.68 5.14
389 405 2.167487 CTCTGTTTCTAGACTGGCCTCC 59.833 54.545 3.32 0.00 0.00 4.30
395 411 3.951775 ACCTGCTCTGTTTCTAGACTG 57.048 47.619 0.00 0.00 0.00 3.51
405 421 6.374417 TCCTTTCTTATTTACCTGCTCTGT 57.626 37.500 0.00 0.00 0.00 3.41
411 427 7.114388 GCGTTTGTTTCCTTTCTTATTTACCTG 59.886 37.037 0.00 0.00 0.00 4.00
414 430 7.096353 GGTGCGTTTGTTTCCTTTCTTATTTAC 60.096 37.037 0.00 0.00 0.00 2.01
745 775 2.225467 GCCTGCTGTGTTCTTCTTCTT 58.775 47.619 0.00 0.00 0.00 2.52
757 787 2.071778 TTCCTTTTTCTGCCTGCTGT 57.928 45.000 0.00 0.00 0.00 4.40
884 940 0.528684 GCCGAATCCCTCGTCTCTTG 60.529 60.000 0.00 0.00 46.65 3.02
930 994 3.002246 GCAATCAATAAACCGATGCGAGA 59.998 43.478 0.00 0.00 0.00 4.04
931 995 3.002656 AGCAATCAATAAACCGATGCGAG 59.997 43.478 0.00 0.00 0.00 5.03
971 1035 4.183686 CCAAGAATGGCAGCGGCG 62.184 66.667 0.51 0.51 40.58 6.46
986 1055 0.842030 AACCATGCTGACTCCTCCCA 60.842 55.000 0.00 0.00 0.00 4.37
1663 3861 7.607615 ATTCCTCCATGATTAAAGGGATTTG 57.392 36.000 0.00 0.00 0.00 2.32
1691 3899 0.322816 TGCCTTCCTGCCATGAGAAC 60.323 55.000 0.00 0.00 0.00 3.01
1846 5439 5.339008 AGAACCTTTCAGCGATGTATGTA 57.661 39.130 0.00 0.00 0.00 2.29
1847 5440 4.207891 AGAACCTTTCAGCGATGTATGT 57.792 40.909 0.00 0.00 0.00 2.29
1848 5441 5.352569 AGAAAGAACCTTTCAGCGATGTATG 59.647 40.000 18.20 0.00 0.00 2.39
1937 5540 3.054655 TCCTTTTTATGGTCTTCCCCTCG 60.055 47.826 0.00 0.00 0.00 4.63
1943 5548 5.196695 AGCTCCATCCTTTTTATGGTCTTC 58.803 41.667 0.00 0.00 43.72 2.87
1945 5550 4.870021 AGCTCCATCCTTTTTATGGTCT 57.130 40.909 0.00 0.00 43.72 3.85
2060 5665 2.517875 AATGCGAGCATGGAGGGC 60.518 61.111 11.64 0.00 36.68 5.19
2275 5923 5.146460 CCGCCAAATTATACACATTGATCG 58.854 41.667 0.00 0.00 0.00 3.69
2381 6029 2.806198 CCAAATGCGGCAAGTGCG 60.806 61.111 6.82 0.00 43.26 5.34
2446 6127 6.070824 TGAGCTGATCACTACCTTGTTTATGA 60.071 38.462 0.00 0.00 31.12 2.15
2476 6157 5.394115 GGGGCAAATGGTTTAGTAAGTGATG 60.394 44.000 0.00 0.00 0.00 3.07
2513 6194 0.891449 TTTGTATGTGCGTGTGGGGG 60.891 55.000 0.00 0.00 0.00 5.40
2514 6195 0.955178 TTTTGTATGTGCGTGTGGGG 59.045 50.000 0.00 0.00 0.00 4.96
2515 6196 2.985809 CAATTTTGTATGTGCGTGTGGG 59.014 45.455 0.00 0.00 0.00 4.61
2516 6197 3.637432 ACAATTTTGTATGTGCGTGTGG 58.363 40.909 0.00 0.00 40.16 4.17
2517 6198 5.116377 GGTTACAATTTTGTATGTGCGTGTG 59.884 40.000 4.12 0.00 42.66 3.82
2518 6199 5.009210 AGGTTACAATTTTGTATGTGCGTGT 59.991 36.000 4.12 0.00 42.66 4.49
2519 6200 5.341993 CAGGTTACAATTTTGTATGTGCGTG 59.658 40.000 4.12 4.48 42.66 5.34
2520 6201 5.009210 ACAGGTTACAATTTTGTATGTGCGT 59.991 36.000 4.12 0.00 42.66 5.24
2521 6202 5.457140 ACAGGTTACAATTTTGTATGTGCG 58.543 37.500 4.12 0.00 42.66 5.34
2522 6203 8.804688 TTTACAGGTTACAATTTTGTATGTGC 57.195 30.769 14.17 3.83 42.66 4.57
2524 6205 9.418045 GCATTTACAGGTTACAATTTTGTATGT 57.582 29.630 11.05 11.05 42.66 2.29
2525 6206 9.416794 TGCATTTACAGGTTACAATTTTGTATG 57.583 29.630 4.12 3.22 42.66 2.39
2526 6207 9.988815 TTGCATTTACAGGTTACAATTTTGTAT 57.011 25.926 4.12 0.00 42.66 2.29
2527 6208 9.988815 ATTGCATTTACAGGTTACAATTTTGTA 57.011 25.926 0.00 0.00 42.35 2.41
2528 6209 8.772705 CATTGCATTTACAGGTTACAATTTTGT 58.227 29.630 1.08 1.08 44.86 2.83
2529 6210 8.986847 TCATTGCATTTACAGGTTACAATTTTG 58.013 29.630 0.00 0.00 0.00 2.44
2530 6211 9.723601 ATCATTGCATTTACAGGTTACAATTTT 57.276 25.926 0.00 0.00 0.00 1.82
2569 6250 8.738645 AAGAGGTATTTAGGCAAATGAAGTAG 57.261 34.615 5.52 0.00 35.88 2.57
3062 7205 2.224137 GCCTACACTAGCATGCATCTCA 60.224 50.000 21.98 0.00 0.00 3.27
3136 7279 8.966868 ACTGAATATGGAACCGAAATACAAAAT 58.033 29.630 0.00 0.00 0.00 1.82
3166 7310 1.899142 GCCCTTGCCCAAAGTTCATTA 59.101 47.619 0.00 0.00 33.66 1.90
3320 7465 9.280174 TCACGACATAATAGTAGACATCACATA 57.720 33.333 0.00 0.00 0.00 2.29
3321 7466 8.166422 TCACGACATAATAGTAGACATCACAT 57.834 34.615 0.00 0.00 0.00 3.21
3343 7488 3.829948 CACAGTTGCAATCAAGGATCAC 58.170 45.455 0.59 0.00 31.93 3.06
3514 7659 6.698008 TTATGCTCCAAATCACATGGTAAG 57.302 37.500 0.00 0.00 39.09 2.34
3522 7667 7.398834 GCATACAAATTATGCTCCAAATCAC 57.601 36.000 8.67 0.00 44.93 3.06
3546 7691 4.372656 GCCATCAGTGCTACTAACCTTAG 58.627 47.826 0.00 0.00 36.82 2.18
3573 7731 1.365633 CGGGTCTAGCAGGCTGATC 59.634 63.158 20.86 0.47 0.00 2.92
3784 7942 7.176589 AGGTTTAATAGTTCCTCAGTCAGAG 57.823 40.000 0.00 0.00 44.31 3.35


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

AutoCloner maintained by Alex Coulton.