Multiple sequence alignment - TraesCS1D01G069300

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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 TraesCS1D01G069300 chr1D 100.000 3732 0 0 1 3732 50191684 50195415 0.000000e+00 6892
1 TraesCS1D01G069300 chr1A 93.147 2291 67 28 187 2451 49360584 49362810 0.000000e+00 3278
2 TraesCS1D01G069300 chr1A 92.536 1179 53 10 2587 3732 49363207 49364383 0.000000e+00 1657
3 TraesCS1D01G069300 chr1A 95.541 157 5 1 1 155 49360429 49360585 2.230000e-62 250
4 TraesCS1D01G069300 chr1B 94.134 2165 93 14 342 2486 70706269 70708419 0.000000e+00 3264
5 TraesCS1D01G069300 chr1B 94.332 1041 53 6 2572 3609 70708699 70709736 0.000000e+00 1591
6 TraesCS1D01G069300 chr1B 93.248 311 8 8 1 303 70705831 70706136 2.640000e-121 446
7 TraesCS1D01G069300 chr1B 92.857 126 9 0 3607 3732 70709759 70709884 2.290000e-42 183


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 TraesCS1D01G069300 chr1D 50191684 50195415 3731 False 6892.000000 6892 100.000000 1 3732 1 chr1D.!!$F1 3731
1 TraesCS1D01G069300 chr1A 49360429 49364383 3954 False 1728.333333 3278 93.741333 1 3732 3 chr1A.!!$F1 3731
2 TraesCS1D01G069300 chr1B 70705831 70709884 4053 False 1371.000000 3264 93.642750 1 3732 4 chr1B.!!$F1 3731

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
411 549 0.673022 CTGTGGACTGGCTGAGCTTC 60.673 60.000 3.72 0.0 0.00 3.86 F
888 1048 1.003718 AGCCAAGAACACCGTAGCC 60.004 57.895 0.00 0.0 0.00 3.93 F
892 1052 1.003718 AAGAACACCGTAGCCAGCC 60.004 57.895 0.00 0.0 0.00 4.85 F
2528 2718 0.255033 GGCGGGGTGTTCCTTCTATT 59.745 55.000 0.00 0.0 35.33 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 2158 2.169144 CACCCAGACTGCATGATAGTGA 59.831 50.000 7.66 0.0 0.00 3.41 R
2509 2699 0.255033 AATAGAAGGAACACCCCGCC 59.745 55.000 0.00 0.0 34.66 6.13 R
2550 2740 1.159285 TGAAGAAGCACCGAAGCATG 58.841 50.000 2.02 0.0 36.85 4.06 R
3609 4062 4.555511 GCTGAGCTGTAAAGTGTTTCCTTG 60.556 45.833 0.00 0.0 0.00 3.61 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
65 73 3.891977 AGAAGAAAGAAAGAAAGGGCCAC 59.108 43.478 6.18 0.00 0.00 5.01
153 161 4.545706 TAAGCATCCGGGCAGCGG 62.546 66.667 0.00 0.00 35.83 5.52
157 165 4.545706 CATCCGGGCAGCGGCTAA 62.546 66.667 9.17 0.00 40.87 3.09
158 166 4.241555 ATCCGGGCAGCGGCTAAG 62.242 66.667 9.17 0.29 40.87 2.18
171 179 3.272334 CTAAGGCACCCGCGCATC 61.272 66.667 8.75 0.00 39.92 3.91
303 345 8.143193 ACAGACAGATATATGCTTCTCTCAAAG 58.857 37.037 0.00 0.00 0.00 2.77
305 347 8.359642 AGACAGATATATGCTTCTCTCAAAGAC 58.640 37.037 0.00 0.00 32.27 3.01
320 362 9.264653 TCTCTCAAAGACATATATATGATGCCT 57.735 33.333 26.05 14.68 37.15 4.75
321 363 9.315525 CTCTCAAAGACATATATATGATGCCTG 57.684 37.037 26.05 15.95 37.15 4.85
322 364 8.262933 TCTCAAAGACATATATATGATGCCTGG 58.737 37.037 26.05 12.37 37.15 4.45
325 367 9.404848 CAAAGACATATATATGATGCCTGGAAT 57.595 33.333 26.05 0.00 37.15 3.01
327 369 9.624373 AAGACATATATATGATGCCTGGAATTC 57.376 33.333 26.05 10.52 37.15 2.17
328 370 9.000978 AGACATATATATGATGCCTGGAATTCT 57.999 33.333 26.05 12.31 37.15 2.40
329 371 9.270640 GACATATATATGATGCCTGGAATTCTC 57.729 37.037 26.05 7.00 37.15 2.87
330 372 8.775151 ACATATATATGATGCCTGGAATTCTCA 58.225 33.333 26.05 0.24 37.15 3.27
331 373 9.053840 CATATATATGATGCCTGGAATTCTCAC 57.946 37.037 16.44 0.00 35.75 3.51
332 374 2.028420 TGATGCCTGGAATTCTCACG 57.972 50.000 5.23 0.00 0.00 4.35
333 375 1.303309 GATGCCTGGAATTCTCACGG 58.697 55.000 5.23 6.70 0.00 4.94
334 376 0.749454 ATGCCTGGAATTCTCACGGC 60.749 55.000 18.95 18.95 38.01 5.68
335 377 1.377202 GCCTGGAATTCTCACGGCA 60.377 57.895 19.87 6.26 37.48 5.69
336 378 1.372087 GCCTGGAATTCTCACGGCAG 61.372 60.000 19.87 12.70 37.48 4.85
337 379 1.372087 CCTGGAATTCTCACGGCAGC 61.372 60.000 5.23 0.00 0.00 5.25
411 549 0.673022 CTGTGGACTGGCTGAGCTTC 60.673 60.000 3.72 0.00 0.00 3.86
421 561 1.404391 GGCTGAGCTTCAATGGATGTG 59.596 52.381 3.72 0.00 0.00 3.21
422 562 1.404391 GCTGAGCTTCAATGGATGTGG 59.596 52.381 0.00 0.00 0.00 4.17
449 589 2.887151 AAATGGCAGTGCTTCCTACT 57.113 45.000 16.11 0.00 0.00 2.57
452 592 3.760580 ATGGCAGTGCTTCCTACTATC 57.239 47.619 16.11 0.00 0.00 2.08
712 862 1.575922 CATTGCAGGGACACACACG 59.424 57.895 0.00 0.00 0.00 4.49
858 1015 6.041296 AGAGTGAGACAAGCCAAATCAAATTT 59.959 34.615 0.00 0.00 0.00 1.82
888 1048 1.003718 AGCCAAGAACACCGTAGCC 60.004 57.895 0.00 0.00 0.00 3.93
892 1052 1.003718 AAGAACACCGTAGCCAGCC 60.004 57.895 0.00 0.00 0.00 4.85
893 1053 2.781595 AAGAACACCGTAGCCAGCCG 62.782 60.000 0.00 0.00 0.00 5.52
989 1160 2.187424 CTGAGCAGGAGCAGGAGC 59.813 66.667 0.00 0.00 45.49 4.70
992 1163 3.388703 GAGCAGGAGCAGGAGCAGG 62.389 68.421 0.00 0.00 45.49 4.85
993 1164 3.397439 GCAGGAGCAGGAGCAGGA 61.397 66.667 0.00 0.00 45.49 3.86
994 1165 2.964310 GCAGGAGCAGGAGCAGGAA 61.964 63.158 0.00 0.00 45.49 3.36
996 1167 2.124778 GGAGCAGGAGCAGGAAGC 60.125 66.667 0.00 0.00 45.49 3.86
1062 1235 2.125106 GGCTACCTCAACCTGGCG 60.125 66.667 0.00 0.00 0.00 5.69
1549 1722 3.627577 CACCGGTCCATTTTCTTCCATAG 59.372 47.826 2.59 0.00 0.00 2.23
1571 1744 2.621338 TGCTCCTCTTGCTATTTGTCG 58.379 47.619 0.00 0.00 0.00 4.35
1577 1750 3.521560 CTCTTGCTATTTGTCGCCACTA 58.478 45.455 0.00 0.00 0.00 2.74
1814 1991 6.609616 ACCAAGATTCAAAACCCAGTAAAGAA 59.390 34.615 0.00 0.00 0.00 2.52
1823 2000 4.021102 ACCCAGTAAAGAATGTGACCTG 57.979 45.455 0.00 0.00 0.00 4.00
1837 2014 2.618709 GTGACCTGAGGACAAAGTTTGG 59.381 50.000 19.45 2.65 34.12 3.28
1980 2157 9.456147 TGCTGCTAAAATTACTAATGGAACTAA 57.544 29.630 0.00 0.00 0.00 2.24
2294 2471 1.453155 ACCGCATGTCCAAGATCAAC 58.547 50.000 0.00 0.00 0.00 3.18
2393 2570 3.068560 TGCTGCTTTTCATTGGCATTTC 58.931 40.909 0.00 0.00 35.37 2.17
2437 2614 2.638855 TCAGCCCCAAAAATGCATTTCT 59.361 40.909 24.28 8.84 0.00 2.52
2438 2615 3.837146 TCAGCCCCAAAAATGCATTTCTA 59.163 39.130 24.28 3.98 0.00 2.10
2451 2630 7.493743 AATGCATTTCTACAGTCTCATGATC 57.506 36.000 5.99 0.00 0.00 2.92
2504 2694 7.445096 TCTGAATAGTGCTCATTCAACAGAAAA 59.555 33.333 11.82 0.00 40.81 2.29
2505 2695 7.587629 TGAATAGTGCTCATTCAACAGAAAAG 58.412 34.615 9.61 0.00 38.98 2.27
2506 2696 4.843220 AGTGCTCATTCAACAGAAAAGG 57.157 40.909 0.00 0.00 0.00 3.11
2507 2697 3.571401 AGTGCTCATTCAACAGAAAAGGG 59.429 43.478 0.00 0.00 0.00 3.95
2508 2698 2.892852 TGCTCATTCAACAGAAAAGGGG 59.107 45.455 0.00 0.00 0.00 4.79
2509 2699 2.232208 GCTCATTCAACAGAAAAGGGGG 59.768 50.000 0.00 0.00 0.00 5.40
2524 2714 4.735358 GGGGCGGGGTGTTCCTTC 62.735 72.222 0.00 0.00 35.33 3.46
2525 2715 3.647771 GGGCGGGGTGTTCCTTCT 61.648 66.667 0.00 0.00 35.33 2.85
2526 2716 2.295602 GGGCGGGGTGTTCCTTCTA 61.296 63.158 0.00 0.00 35.33 2.10
2527 2717 1.632965 GGGCGGGGTGTTCCTTCTAT 61.633 60.000 0.00 0.00 35.33 1.98
2528 2718 0.255033 GGCGGGGTGTTCCTTCTATT 59.745 55.000 0.00 0.00 35.33 1.73
2529 2719 1.664873 GCGGGGTGTTCCTTCTATTC 58.335 55.000 0.00 0.00 35.33 1.75
2530 2720 1.209747 GCGGGGTGTTCCTTCTATTCT 59.790 52.381 0.00 0.00 35.33 2.40
2531 2721 2.906354 CGGGGTGTTCCTTCTATTCTG 58.094 52.381 0.00 0.00 35.33 3.02
2532 2722 2.236395 CGGGGTGTTCCTTCTATTCTGT 59.764 50.000 0.00 0.00 35.33 3.41
2533 2723 3.307480 CGGGGTGTTCCTTCTATTCTGTT 60.307 47.826 0.00 0.00 35.33 3.16
2534 2724 4.663334 GGGGTGTTCCTTCTATTCTGTTT 58.337 43.478 0.00 0.00 35.33 2.83
2535 2725 5.077564 GGGGTGTTCCTTCTATTCTGTTTT 58.922 41.667 0.00 0.00 35.33 2.43
2536 2726 5.183331 GGGGTGTTCCTTCTATTCTGTTTTC 59.817 44.000 0.00 0.00 35.33 2.29
2537 2727 5.768164 GGGTGTTCCTTCTATTCTGTTTTCA 59.232 40.000 0.00 0.00 0.00 2.69
2538 2728 6.294010 GGGTGTTCCTTCTATTCTGTTTTCAC 60.294 42.308 0.00 0.00 0.00 3.18
2539 2729 6.262273 GGTGTTCCTTCTATTCTGTTTTCACA 59.738 38.462 0.00 0.00 0.00 3.58
2540 2730 7.201785 GGTGTTCCTTCTATTCTGTTTTCACAA 60.202 37.037 0.00 0.00 30.36 3.33
2541 2731 7.644157 GTGTTCCTTCTATTCTGTTTTCACAAC 59.356 37.037 0.00 0.00 30.36 3.32
2542 2732 7.556275 TGTTCCTTCTATTCTGTTTTCACAACT 59.444 33.333 0.00 0.00 30.36 3.16
2543 2733 7.496529 TCCTTCTATTCTGTTTTCACAACTG 57.503 36.000 0.00 0.00 30.36 3.16
2544 2734 6.017109 TCCTTCTATTCTGTTTTCACAACTGC 60.017 38.462 0.00 0.00 30.36 4.40
2545 2735 6.238731 CCTTCTATTCTGTTTTCACAACTGCA 60.239 38.462 0.00 0.00 30.36 4.41
2546 2736 6.882610 TCTATTCTGTTTTCACAACTGCAT 57.117 33.333 0.00 0.00 30.36 3.96
2547 2737 7.977789 TCTATTCTGTTTTCACAACTGCATA 57.022 32.000 0.00 0.00 30.36 3.14
2548 2738 8.389779 TCTATTCTGTTTTCACAACTGCATAA 57.610 30.769 0.00 0.00 30.36 1.90
2549 2739 9.013229 TCTATTCTGTTTTCACAACTGCATAAT 57.987 29.630 0.00 0.00 30.36 1.28
2550 2740 9.282247 CTATTCTGTTTTCACAACTGCATAATC 57.718 33.333 0.00 0.00 30.36 1.75
2551 2741 6.631971 TCTGTTTTCACAACTGCATAATCA 57.368 33.333 0.00 0.00 30.36 2.57
2552 2742 7.218228 TCTGTTTTCACAACTGCATAATCAT 57.782 32.000 0.00 0.00 30.36 2.45
2553 2743 7.085746 TCTGTTTTCACAACTGCATAATCATG 58.914 34.615 0.00 0.00 31.51 3.07
2554 2744 6.183360 CTGTTTTCACAACTGCATAATCATGC 60.183 38.462 0.00 0.00 44.45 4.06
2555 2745 8.263218 CTGTTTTCACAACTGCATAATCATGCT 61.263 37.037 1.73 0.00 44.47 3.79
2564 2754 3.976793 CATAATCATGCTTCGGTGCTT 57.023 42.857 0.00 0.00 0.00 3.91
2565 2755 3.881795 CATAATCATGCTTCGGTGCTTC 58.118 45.455 0.00 0.00 0.00 3.86
2566 2756 2.119801 AATCATGCTTCGGTGCTTCT 57.880 45.000 0.00 0.00 0.00 2.85
2567 2757 2.119801 ATCATGCTTCGGTGCTTCTT 57.880 45.000 0.00 0.00 0.00 2.52
2568 2758 1.442769 TCATGCTTCGGTGCTTCTTC 58.557 50.000 0.00 0.00 0.00 2.87
2569 2759 1.159285 CATGCTTCGGTGCTTCTTCA 58.841 50.000 2.64 0.00 0.00 3.02
2570 2760 1.741706 CATGCTTCGGTGCTTCTTCAT 59.258 47.619 2.64 0.00 0.00 2.57
2647 3087 3.328505 CAATTTCAGTTTGTGGCCATCC 58.671 45.455 9.72 0.00 0.00 3.51
2660 3100 1.068127 GGCCATCCATTTGCTGTGATC 59.932 52.381 0.00 0.00 0.00 2.92
2671 3112 6.402983 CCATTTGCTGTGATCTTCTAACACTC 60.403 42.308 0.00 0.00 35.83 3.51
2679 3120 8.134202 TGTGATCTTCTAACACTCCTTTATGA 57.866 34.615 0.00 0.00 35.83 2.15
2925 3369 6.262944 CCAGTATTGGTAGAATGCTTTGCATA 59.737 38.462 5.43 0.00 43.09 3.14
3045 3489 6.704493 TGTACTGTTGGTGTGACTTCTATTTC 59.296 38.462 0.00 0.00 0.00 2.17
3101 3545 2.298610 TCAGTAGACCCATAGACTGCG 58.701 52.381 0.00 0.00 39.33 5.18
3156 3600 1.143183 ATGGCATGGACCGTCGTAC 59.857 57.895 0.00 0.00 0.00 3.67
3174 3618 6.902948 CGTCGTACTTTGAAGTGATTTGAAAA 59.097 34.615 6.64 0.00 40.07 2.29
3328 3776 8.715998 CAGTGATCATCTACAATTAGTATTGGC 58.284 37.037 0.00 0.00 44.42 4.52
3372 3820 6.727231 TGTTAACCTTTCTCCACTATGGTAGA 59.273 38.462 2.48 0.00 39.03 2.59
3445 3893 7.415592 AAGAGAAGTGATGTCATGTCTATCA 57.584 36.000 0.00 0.00 0.00 2.15
3457 3905 8.722480 TGTCATGTCTATCAAGTAAAATCCAG 57.278 34.615 0.00 0.00 0.00 3.86
3471 3921 8.540507 AGTAAAATCCAGAGAGTCAGCTATAA 57.459 34.615 0.00 0.00 0.00 0.98
3648 4126 3.603532 CTCAGCAATAGTTCAGAAGGCA 58.396 45.455 0.00 0.00 0.00 4.75
3651 4129 3.126514 CAGCAATAGTTCAGAAGGCACTG 59.873 47.826 5.56 5.56 40.86 3.66
3678 4156 5.811399 TTCAAGGCAGAATAATGTAACGG 57.189 39.130 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 9.627123 TTTCTTTCTTTCTTCTCCTTACATCAA 57.373 29.630 0.00 0.00 0.00 2.57
65 73 2.809601 CGGCTTTCTGGACGACCG 60.810 66.667 0.00 0.00 40.66 4.79
154 162 3.272334 GATGCGCGGGTGCCTTAG 61.272 66.667 8.83 0.00 38.08 2.18
174 182 4.961511 TATGGCGCGGCATCGTCC 62.962 66.667 45.44 20.09 38.89 4.79
175 183 1.841663 AATTATGGCGCGGCATCGTC 61.842 55.000 45.44 10.51 38.89 4.20
176 184 1.841663 GAATTATGGCGCGGCATCGT 61.842 55.000 45.44 32.62 38.89 3.73
177 185 1.154413 GAATTATGGCGCGGCATCG 60.154 57.895 45.44 0.00 39.81 3.84
178 186 1.210155 GGAATTATGGCGCGGCATC 59.790 57.895 45.44 33.05 0.00 3.91
179 187 2.616330 CGGAATTATGGCGCGGCAT 61.616 57.895 43.14 43.14 0.00 4.40
180 188 3.276091 CGGAATTATGGCGCGGCA 61.276 61.111 37.91 37.91 0.00 5.69
181 189 2.325082 ATCGGAATTATGGCGCGGC 61.325 57.895 27.61 27.61 0.00 6.53
182 190 1.497278 CATCGGAATTATGGCGCGG 59.503 57.895 8.83 0.00 0.00 6.46
183 191 1.154413 GCATCGGAATTATGGCGCG 60.154 57.895 0.00 0.00 0.00 6.86
184 192 0.593128 AAGCATCGGAATTATGGCGC 59.407 50.000 0.00 0.00 0.00 6.53
185 193 3.354089 AAAAGCATCGGAATTATGGCG 57.646 42.857 0.00 0.00 0.00 5.69
259 301 6.503524 TGTCTGTTTTCTTATTTGCTGGAAC 58.496 36.000 0.00 0.00 0.00 3.62
303 345 9.270640 GAGAATTCCAGGCATCATATATATGTC 57.729 37.037 19.78 11.45 35.26 3.06
305 347 9.053840 GTGAGAATTCCAGGCATCATATATATG 57.946 37.037 15.47 15.47 35.04 1.78
309 351 5.482006 CGTGAGAATTCCAGGCATCATATA 58.518 41.667 0.65 0.00 0.00 0.86
310 352 4.321718 CGTGAGAATTCCAGGCATCATAT 58.678 43.478 0.65 0.00 0.00 1.78
311 353 3.494924 CCGTGAGAATTCCAGGCATCATA 60.495 47.826 0.65 0.00 0.00 2.15
312 354 2.569059 CGTGAGAATTCCAGGCATCAT 58.431 47.619 0.65 0.00 0.00 2.45
313 355 1.407299 CCGTGAGAATTCCAGGCATCA 60.407 52.381 0.65 0.00 0.00 3.07
314 356 1.303309 CCGTGAGAATTCCAGGCATC 58.697 55.000 0.65 0.00 0.00 3.91
315 357 0.749454 GCCGTGAGAATTCCAGGCAT 60.749 55.000 19.63 0.00 41.61 4.40
316 358 1.377202 GCCGTGAGAATTCCAGGCA 60.377 57.895 19.63 5.37 41.61 4.75
318 360 1.372087 GCTGCCGTGAGAATTCCAGG 61.372 60.000 0.65 5.84 0.00 4.45
320 362 0.250684 TTGCTGCCGTGAGAATTCCA 60.251 50.000 0.65 0.00 0.00 3.53
321 363 1.098050 ATTGCTGCCGTGAGAATTCC 58.902 50.000 0.65 0.00 0.00 3.01
322 364 3.058639 GGATATTGCTGCCGTGAGAATTC 60.059 47.826 0.00 0.00 0.00 2.17
325 367 1.486310 AGGATATTGCTGCCGTGAGAA 59.514 47.619 0.00 0.00 0.00 2.87
327 369 1.600957 CAAGGATATTGCTGCCGTGAG 59.399 52.381 0.00 0.00 33.78 3.51
328 370 1.065491 ACAAGGATATTGCTGCCGTGA 60.065 47.619 0.00 0.00 35.55 4.35
329 371 1.382522 ACAAGGATATTGCTGCCGTG 58.617 50.000 0.00 0.00 37.23 4.94
330 372 2.128771 AACAAGGATATTGCTGCCGT 57.871 45.000 0.00 0.00 0.00 5.68
331 373 4.836125 ATAAACAAGGATATTGCTGCCG 57.164 40.909 0.00 0.00 0.00 5.69
332 374 5.163416 ACCAATAAACAAGGATATTGCTGCC 60.163 40.000 0.00 0.00 37.90 4.85
333 375 5.906073 ACCAATAAACAAGGATATTGCTGC 58.094 37.500 0.00 0.00 37.90 5.25
411 549 5.583061 CCATTTTCACATTCCACATCCATTG 59.417 40.000 0.00 0.00 0.00 2.82
421 561 2.028748 AGCACTGCCATTTTCACATTCC 60.029 45.455 0.00 0.00 0.00 3.01
422 562 3.308438 AGCACTGCCATTTTCACATTC 57.692 42.857 0.00 0.00 0.00 2.67
480 624 4.202264 GCCTTAGCAGCCTATTTCTGTCTA 60.202 45.833 0.00 0.00 39.53 2.59
484 628 1.869767 CGCCTTAGCAGCCTATTTCTG 59.130 52.381 0.00 0.00 39.83 3.02
493 637 0.109735 GTGTTTTCCGCCTTAGCAGC 60.110 55.000 0.00 0.00 39.83 5.25
523 667 1.126113 CGCGCTACGTGTTTGATTTCT 59.874 47.619 5.56 0.00 36.87 2.52
663 813 2.240921 TGTGGGTATTCTAATGCTGGCA 59.759 45.455 0.00 0.00 0.00 4.92
712 862 3.349006 CCTGGTGACTGTGCGTGC 61.349 66.667 0.00 0.00 0.00 5.34
888 1048 5.529430 TGGTTTGGTTTATATGATACGGCTG 59.471 40.000 0.00 0.00 0.00 4.85
892 1052 6.915843 GCCTTTGGTTTGGTTTATATGATACG 59.084 38.462 0.00 0.00 0.00 3.06
893 1053 7.147811 TGGCCTTTGGTTTGGTTTATATGATAC 60.148 37.037 3.32 0.00 0.00 2.24
986 1157 1.396301 CGTTCATCTTGCTTCCTGCTC 59.604 52.381 0.00 0.00 43.37 4.26
989 1160 0.449388 GCCGTTCATCTTGCTTCCTG 59.551 55.000 0.00 0.00 0.00 3.86
992 1163 1.470098 ACATGCCGTTCATCTTGCTTC 59.530 47.619 0.00 0.00 31.79 3.86
993 1164 1.538047 ACATGCCGTTCATCTTGCTT 58.462 45.000 0.00 0.00 31.79 3.91
994 1165 2.009774 GTACATGCCGTTCATCTTGCT 58.990 47.619 0.00 0.00 31.79 3.91
996 1167 3.555956 GGTAGTACATGCCGTTCATCTTG 59.444 47.826 2.06 0.00 31.79 3.02
997 1168 3.431766 GGGTAGTACATGCCGTTCATCTT 60.432 47.826 2.06 0.00 33.68 2.40
1335 1508 3.680196 TCCCTGTACGGCCTCCCT 61.680 66.667 0.00 0.00 0.00 4.20
1440 1613 3.951769 CTTGGGGCAGGCCTTGGAG 62.952 68.421 13.81 0.00 36.10 3.86
1549 1722 3.181516 CGACAAATAGCAAGAGGAGCAAC 60.182 47.826 0.00 0.00 0.00 4.17
1571 1744 2.222027 ACAAGTGCTGAAAGTAGTGGC 58.778 47.619 0.00 0.00 30.51 5.01
1577 1750 5.671493 ACTACAACTACAAGTGCTGAAAGT 58.329 37.500 0.00 0.00 35.30 2.66
1612 1785 4.627467 GTGCCGGCTATACTTCAGATTATG 59.373 45.833 29.70 0.00 0.00 1.90
1623 1796 3.623960 TGTTATGTTTGTGCCGGCTATAC 59.376 43.478 29.70 18.50 0.00 1.47
1681 1858 7.094205 ACTGGTGAACTGGATCAATAATTTGTC 60.094 37.037 0.00 0.00 34.32 3.18
1686 1863 5.126061 GCAACTGGTGAACTGGATCAATAAT 59.874 40.000 0.00 0.00 0.00 1.28
1814 1991 3.864789 AACTTTGTCCTCAGGTCACAT 57.135 42.857 0.00 0.00 0.00 3.21
1823 2000 2.358322 TGGGTCCAAACTTTGTCCTC 57.642 50.000 0.88 0.00 0.00 3.71
1837 2014 9.974980 TTTGTTTAGTTTATCTGAAAATGGGTC 57.025 29.630 0.00 0.00 0.00 4.46
1980 2157 3.044156 ACCCAGACTGCATGATAGTGAT 58.956 45.455 7.66 0.00 0.00 3.06
1981 2158 2.169144 CACCCAGACTGCATGATAGTGA 59.831 50.000 7.66 0.00 0.00 3.41
2393 2570 7.483307 TGAAACCAAACATCTGAAGAGAAAAG 58.517 34.615 0.00 0.00 0.00 2.27
2437 2614 4.718940 TCGCTTTGATCATGAGACTGTA 57.281 40.909 0.09 0.00 0.00 2.74
2438 2615 3.599730 TCGCTTTGATCATGAGACTGT 57.400 42.857 0.09 0.00 0.00 3.55
2507 2697 4.735358 GAAGGAACACCCCGCCCC 62.735 72.222 0.00 0.00 34.66 5.80
2508 2698 1.632965 ATAGAAGGAACACCCCGCCC 61.633 60.000 0.00 0.00 34.66 6.13
2509 2699 0.255033 AATAGAAGGAACACCCCGCC 59.745 55.000 0.00 0.00 34.66 6.13
2510 2700 1.209747 AGAATAGAAGGAACACCCCGC 59.790 52.381 0.00 0.00 34.66 6.13
2511 2701 2.236395 ACAGAATAGAAGGAACACCCCG 59.764 50.000 0.00 0.00 34.66 5.73
2512 2702 4.302559 AACAGAATAGAAGGAACACCCC 57.697 45.455 0.00 0.00 34.66 4.95
2513 2703 5.768164 TGAAAACAGAATAGAAGGAACACCC 59.232 40.000 0.00 0.00 0.00 4.61
2514 2704 6.262273 TGTGAAAACAGAATAGAAGGAACACC 59.738 38.462 0.00 0.00 0.00 4.16
2515 2705 7.259290 TGTGAAAACAGAATAGAAGGAACAC 57.741 36.000 0.00 0.00 0.00 3.32
2516 2706 7.556275 AGTTGTGAAAACAGAATAGAAGGAACA 59.444 33.333 0.00 0.00 0.00 3.18
2517 2707 7.857885 CAGTTGTGAAAACAGAATAGAAGGAAC 59.142 37.037 0.00 0.00 0.00 3.62
2518 2708 7.468631 GCAGTTGTGAAAACAGAATAGAAGGAA 60.469 37.037 0.00 0.00 0.00 3.36
2519 2709 6.017109 GCAGTTGTGAAAACAGAATAGAAGGA 60.017 38.462 0.00 0.00 0.00 3.36
2520 2710 6.145535 GCAGTTGTGAAAACAGAATAGAAGG 58.854 40.000 0.00 0.00 0.00 3.46
2521 2711 6.728200 TGCAGTTGTGAAAACAGAATAGAAG 58.272 36.000 0.00 0.00 0.00 2.85
2522 2712 6.691754 TGCAGTTGTGAAAACAGAATAGAA 57.308 33.333 0.00 0.00 0.00 2.10
2523 2713 6.882610 ATGCAGTTGTGAAAACAGAATAGA 57.117 33.333 0.00 0.00 0.00 1.98
2524 2714 9.282247 GATTATGCAGTTGTGAAAACAGAATAG 57.718 33.333 0.00 0.00 0.00 1.73
2525 2715 8.791675 TGATTATGCAGTTGTGAAAACAGAATA 58.208 29.630 0.00 0.00 0.00 1.75
2526 2716 7.660112 TGATTATGCAGTTGTGAAAACAGAAT 58.340 30.769 0.00 0.00 0.00 2.40
2527 2717 7.036996 TGATTATGCAGTTGTGAAAACAGAA 57.963 32.000 0.00 0.00 0.00 3.02
2528 2718 6.631971 TGATTATGCAGTTGTGAAAACAGA 57.368 33.333 0.00 0.00 0.00 3.41
2529 2719 7.273188 CATGATTATGCAGTTGTGAAAACAG 57.727 36.000 0.00 0.00 0.00 3.16
2544 2734 3.562973 AGAAGCACCGAAGCATGATTATG 59.437 43.478 0.00 0.00 36.85 1.90
2545 2735 3.813443 AGAAGCACCGAAGCATGATTAT 58.187 40.909 0.00 0.00 36.85 1.28
2546 2736 3.266510 AGAAGCACCGAAGCATGATTA 57.733 42.857 0.00 0.00 36.85 1.75
2547 2737 2.119801 AGAAGCACCGAAGCATGATT 57.880 45.000 0.00 0.00 36.85 2.57
2548 2738 2.012673 GAAGAAGCACCGAAGCATGAT 58.987 47.619 0.00 0.00 36.85 2.45
2549 2739 1.270785 TGAAGAAGCACCGAAGCATGA 60.271 47.619 0.00 0.00 36.85 3.07
2550 2740 1.159285 TGAAGAAGCACCGAAGCATG 58.841 50.000 2.02 0.00 36.85 4.06
2551 2741 2.119801 ATGAAGAAGCACCGAAGCAT 57.880 45.000 2.02 0.00 36.85 3.79
2552 2742 1.896220 AATGAAGAAGCACCGAAGCA 58.104 45.000 2.02 0.00 36.85 3.91
2553 2743 3.725010 CGTTAATGAAGAAGCACCGAAGC 60.725 47.826 0.00 0.00 0.00 3.86
2554 2744 3.678072 TCGTTAATGAAGAAGCACCGAAG 59.322 43.478 0.00 0.00 0.00 3.79
2555 2745 3.655486 TCGTTAATGAAGAAGCACCGAA 58.345 40.909 0.00 0.00 0.00 4.30
2556 2746 3.306917 TCGTTAATGAAGAAGCACCGA 57.693 42.857 0.00 0.00 0.00 4.69
2557 2747 4.398549 TTTCGTTAATGAAGAAGCACCG 57.601 40.909 9.94 0.00 0.00 4.94
2558 2748 6.612306 AGAATTTCGTTAATGAAGAAGCACC 58.388 36.000 9.94 0.00 0.00 5.01
2559 2749 8.420189 CAAAGAATTTCGTTAATGAAGAAGCAC 58.580 33.333 9.94 2.03 35.03 4.40
2560 2750 7.114811 GCAAAGAATTTCGTTAATGAAGAAGCA 59.885 33.333 9.94 0.00 35.03 3.91
2561 2751 7.114811 TGCAAAGAATTTCGTTAATGAAGAAGC 59.885 33.333 9.94 9.17 35.03 3.86
2562 2752 8.420189 GTGCAAAGAATTTCGTTAATGAAGAAG 58.580 33.333 9.94 0.65 35.03 2.85
2563 2753 7.918033 TGTGCAAAGAATTTCGTTAATGAAGAA 59.082 29.630 9.94 0.00 35.03 2.52
2564 2754 7.378461 GTGTGCAAAGAATTTCGTTAATGAAGA 59.622 33.333 9.94 3.20 35.03 2.87
2565 2755 7.167302 TGTGTGCAAAGAATTTCGTTAATGAAG 59.833 33.333 9.94 0.00 35.03 3.02
2566 2756 6.975197 TGTGTGCAAAGAATTTCGTTAATGAA 59.025 30.769 6.00 6.00 35.03 2.57
2567 2757 6.499172 TGTGTGCAAAGAATTTCGTTAATGA 58.501 32.000 0.00 0.00 35.03 2.57
2568 2758 6.746104 TGTGTGCAAAGAATTTCGTTAATG 57.254 33.333 0.00 0.00 35.03 1.90
2569 2759 9.469807 TTTATGTGTGCAAAGAATTTCGTTAAT 57.530 25.926 0.00 0.00 35.03 1.40
2570 2760 8.858003 TTTATGTGTGCAAAGAATTTCGTTAA 57.142 26.923 0.00 0.00 35.03 2.01
2647 3087 6.402983 GGAGTGTTAGAAGATCACAGCAAATG 60.403 42.308 0.00 0.00 34.94 2.32
2660 3100 7.905493 GCGAAAATCATAAAGGAGTGTTAGAAG 59.095 37.037 0.00 0.00 0.00 2.85
2671 3112 5.220854 CCACCTGTAGCGAAAATCATAAAGG 60.221 44.000 0.00 0.00 0.00 3.11
2776 3217 2.350458 CCAACCCCTCGGCCATTTG 61.350 63.158 2.24 0.00 0.00 2.32
2865 3306 1.815003 CCTTCCACTTCACCATCTTGC 59.185 52.381 0.00 0.00 0.00 4.01
3101 3545 4.502431 GGAGAGCCTGTCTTAGATTTAGCC 60.502 50.000 0.00 0.00 34.71 3.93
3174 3618 6.607600 TGAGCTGTATCCACTATCTAAAGTGT 59.392 38.462 0.00 0.00 44.45 3.55
3347 3795 5.836024 ACCATAGTGGAGAAAGGTTAACA 57.164 39.130 8.10 0.00 40.96 2.41
3348 3796 7.040494 GTCTACCATAGTGGAGAAAGGTTAAC 58.960 42.308 2.45 0.00 40.96 2.01
3445 3893 5.753721 AGCTGACTCTCTGGATTTTACTT 57.246 39.130 0.00 0.00 0.00 2.24
3457 3905 8.612619 GCTGATATAGTCTTATAGCTGACTCTC 58.387 40.741 7.65 5.34 41.92 3.20
3471 3921 6.968263 ACAGTACATGTGCTGATATAGTCT 57.032 37.500 39.60 19.12 44.51 3.24
3609 4062 4.555511 GCTGAGCTGTAAAGTGTTTCCTTG 60.556 45.833 0.00 0.00 0.00 3.61
3651 4129 7.587757 CGTTACATTATTCTGCCTTGAATTAGC 59.412 37.037 0.00 0.00 37.73 3.09
3678 4156 6.643770 TCGTTCTTATCAGGTGTTTGTCTTAC 59.356 38.462 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.