Multiple sequence alignment - TraesCS7A01G117800

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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 TraesCS7A01G117800 chr7A 100.000 3020 0 0 1 3020 76187166 76190185 0.000000e+00 5578
1 TraesCS7A01G117800 chr7A 80.738 244 35 6 2784 3020 76498252 76498490 2.390000e-41 180
2 TraesCS7A01G117800 chr7D 93.138 2288 114 21 21 2275 69642012 69644289 0.000000e+00 3315
3 TraesCS7A01G117800 chr7D 94.197 517 24 4 2507 3020 69658126 69658639 0.000000e+00 784
4 TraesCS7A01G117800 chr7D 89.944 179 7 4 2266 2436 69644697 69644872 1.410000e-53 220
5 TraesCS7A01G117800 chr7D 90.604 149 12 1 2802 2948 71349601 71349453 2.380000e-46 196
6 TraesCS7A01G117800 chr7D 80.258 233 34 5 2795 3020 69868720 69868947 6.700000e-37 165
7 TraesCS7A01G117800 chr7B 91.856 1670 87 22 744 2386 12179162 12180809 0.000000e+00 2285
8 TraesCS7A01G117800 chr7B 81.713 432 59 17 2509 2931 12180988 12181408 2.880000e-90 342
9 TraesCS7A01G117800 chr7B 95.726 117 4 1 2815 2931 13872893 13873008 1.430000e-43 187
10 TraesCS7A01G117800 chrUn 90.604 149 12 1 2802 2948 82524378 82524526 2.380000e-46 196
11 TraesCS7A01G117800 chrUn 89.103 156 10 3 2802 2950 84244851 84245006 1.430000e-43 187
12 TraesCS7A01G117800 chr2B 89.933 149 13 1 2802 2948 723398813 723398961 1.110000e-44 191


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 TraesCS7A01G117800 chr7A 76187166 76190185 3019 False 5578.0 5578 100.0000 1 3020 1 chr7A.!!$F1 3019
1 TraesCS7A01G117800 chr7D 69642012 69644872 2860 False 1767.5 3315 91.5410 21 2436 2 chr7D.!!$F3 2415
2 TraesCS7A01G117800 chr7D 69658126 69658639 513 False 784.0 784 94.1970 2507 3020 1 chr7D.!!$F1 513
3 TraesCS7A01G117800 chr7B 12179162 12181408 2246 False 1313.5 2285 86.7845 744 2931 2 chr7B.!!$F2 2187

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
465 476 0.038526 CTAGGTTGTCGTTGCCTCGT 60.039 55.0 0.0 0.0 34.07 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2247 1.400846 CATGCAGTGAGATGTTGCTCC 59.599 52.381 0.0 0.0 38.6 4.7 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
50 51 1.134753 TGTGGATCATGGCATTTTCGC 59.865 47.619 0.00 0.00 0.00 4.70
51 52 1.134753 GTGGATCATGGCATTTTCGCA 59.865 47.619 0.00 0.00 0.00 5.10
57 58 1.584761 CATGGCATTTTCGCATGAACG 59.415 47.619 0.00 0.00 32.71 3.95
68 69 1.523758 GCATGAACGTTTGGAGGACT 58.476 50.000 0.46 0.00 0.00 3.85
198 209 2.742372 CGTCCCCACTTTCGCTGG 60.742 66.667 0.00 0.00 0.00 4.85
219 230 2.562298 GGAACCCAACATGCATTCTCAA 59.438 45.455 0.00 0.00 0.00 3.02
244 255 7.710676 TTTATTTCGGATGATCCCTCAAAAA 57.289 32.000 5.78 0.00 34.37 1.94
245 256 7.896383 TTATTTCGGATGATCCCTCAAAAAT 57.104 32.000 5.78 7.14 34.37 1.82
250 261 7.896383 TCGGATGATCCCTCAAAAATAAAAT 57.104 32.000 5.78 0.00 34.37 1.82
251 262 8.305046 TCGGATGATCCCTCAAAAATAAAATT 57.695 30.769 5.78 0.00 34.37 1.82
253 264 9.034544 CGGATGATCCCTCAAAAATAAAATTTC 57.965 33.333 5.78 0.00 34.37 2.17
254 265 9.889128 GGATGATCCCTCAAAAATAAAATTTCA 57.111 29.630 0.00 0.00 34.37 2.69
307 318 1.102154 CATATGGCGCAAACCTCCAA 58.898 50.000 10.83 0.00 33.04 3.53
316 327 2.536066 GCAAACCTCCAAACCCCTATT 58.464 47.619 0.00 0.00 0.00 1.73
321 332 4.692523 ACCTCCAAACCCCTATTTCATT 57.307 40.909 0.00 0.00 0.00 2.57
331 342 6.699575 ACCCCTATTTCATTTTCTTCATCG 57.300 37.500 0.00 0.00 0.00 3.84
333 344 6.095440 ACCCCTATTTCATTTTCTTCATCGTG 59.905 38.462 0.00 0.00 0.00 4.35
346 357 2.969827 TCGTGAGAGATTGGCGCA 59.030 55.556 10.83 0.00 34.84 6.09
368 379 5.741673 GCATACCTTCTTCTTCCTCATCCTC 60.742 48.000 0.00 0.00 0.00 3.71
377 388 1.117749 TCCTCATCCTCCTCGCCATG 61.118 60.000 0.00 0.00 0.00 3.66
395 406 3.549794 CATGTCATTCTTTCCCTCCTCC 58.450 50.000 0.00 0.00 0.00 4.30
396 407 2.921221 TGTCATTCTTTCCCTCCTCCT 58.079 47.619 0.00 0.00 0.00 3.69
397 408 2.840651 TGTCATTCTTTCCCTCCTCCTC 59.159 50.000 0.00 0.00 0.00 3.71
405 416 3.629142 TTCCCTCCTCCTCGATTTTTC 57.371 47.619 0.00 0.00 0.00 2.29
412 423 2.094182 CCTCCTCGATTTTTCGGTCTCA 60.094 50.000 0.00 0.00 0.00 3.27
434 445 0.877071 AGCGTCAAGTCAAGGCATTG 59.123 50.000 4.34 4.34 37.80 2.82
456 467 2.736721 CCACATTGTCACTAGGTTGTCG 59.263 50.000 0.00 0.00 0.00 4.35
465 476 0.038526 CTAGGTTGTCGTTGCCTCGT 60.039 55.000 0.00 0.00 34.07 4.18
477 488 0.945265 TGCCTCGTTAACGGTTTCGG 60.945 55.000 26.51 18.58 41.39 4.30
499 510 2.612251 CTCCCCTCCCTCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
508 519 0.324830 CCCTCTCCTCCTTCCTCGTT 60.325 60.000 0.00 0.00 0.00 3.85
524 535 2.558795 CTCGTTCTCCTTCCTTCACTCA 59.441 50.000 0.00 0.00 0.00 3.41
526 537 3.056536 TCGTTCTCCTTCCTTCACTCATG 60.057 47.826 0.00 0.00 0.00 3.07
528 539 2.544721 TCTCCTTCCTTCACTCATGCT 58.455 47.619 0.00 0.00 0.00 3.79
544 556 3.129462 TCATGCTCTTCTCCACTAGTTCG 59.871 47.826 0.00 0.00 0.00 3.95
547 559 0.809385 TCTTCTCCACTAGTTCGCGG 59.191 55.000 6.13 0.00 0.00 6.46
583 595 4.152526 CAAGACTAGAGACTGAACGTTCG 58.847 47.826 22.48 18.51 0.00 3.95
584 596 3.401182 AGACTAGAGACTGAACGTTCGT 58.599 45.455 22.48 21.29 0.00 3.85
585 597 4.564041 AGACTAGAGACTGAACGTTCGTA 58.436 43.478 22.48 5.99 0.00 3.43
595 607 9.229784 GAGACTGAACGTTCGTATGATAAAATA 57.770 33.333 22.48 0.15 0.00 1.40
671 683 5.163884 GCCCGTGTACATTCTTCTTAAACTC 60.164 44.000 0.00 0.00 0.00 3.01
674 686 6.530534 CCGTGTACATTCTTCTTAAACTCGAT 59.469 38.462 0.00 0.00 0.00 3.59
675 687 7.253684 CCGTGTACATTCTTCTTAAACTCGATC 60.254 40.741 0.00 0.00 0.00 3.69
676 688 7.485277 CGTGTACATTCTTCTTAAACTCGATCT 59.515 37.037 0.00 0.00 0.00 2.75
677 689 9.141400 GTGTACATTCTTCTTAAACTCGATCTT 57.859 33.333 0.00 0.00 0.00 2.40
678 690 9.706691 TGTACATTCTTCTTAAACTCGATCTTT 57.293 29.630 0.00 0.00 0.00 2.52
714 729 9.757227 TTAAAATCCTGTAAAACTTGTTCATGG 57.243 29.630 0.00 0.00 0.00 3.66
715 730 4.846779 TCCTGTAAAACTTGTTCATGGC 57.153 40.909 0.00 0.00 0.00 4.40
735 750 6.618287 TGGCACATAGAAATAAGTGTATGC 57.382 37.500 0.00 0.00 34.59 3.14
737 752 5.236478 GGCACATAGAAATAAGTGTATGCGT 59.764 40.000 0.00 0.00 34.59 5.24
738 753 6.129393 GCACATAGAAATAAGTGTATGCGTG 58.871 40.000 0.00 0.00 34.59 5.34
741 756 7.222805 CACATAGAAATAAGTGTATGCGTGTCT 59.777 37.037 0.00 0.00 0.00 3.41
742 757 7.222805 ACATAGAAATAAGTGTATGCGTGTCTG 59.777 37.037 0.00 0.00 0.00 3.51
753 768 0.732880 GCGTGTCTGTGCGTCTGTAT 60.733 55.000 0.00 0.00 0.00 2.29
760 775 3.985279 GTCTGTGCGTCTGTATTGTGTTA 59.015 43.478 0.00 0.00 0.00 2.41
1368 1396 2.794166 CGCGTCGACGTCGTCTTT 60.794 61.111 35.48 0.00 42.22 2.52
1378 1406 1.615107 CGTCGTCTTTGAGCGGTTCC 61.615 60.000 0.00 0.00 0.00 3.62
1392 1423 1.079057 GTTCCTCGGCAACTCCTCC 60.079 63.158 0.00 0.00 0.00 4.30
2065 2096 4.741342 CCGTCTGGTTTAACTAGGTGTAG 58.259 47.826 8.55 0.00 0.00 2.74
2200 2247 6.280643 TGTACATCGAAATAGGTCATCTTGG 58.719 40.000 0.00 0.00 0.00 3.61
2225 2272 3.425892 GCAACATCTCACTGCATGTTCTC 60.426 47.826 0.00 0.00 40.52 2.87
2230 2277 2.233186 TCTCACTGCATGTTCTCTGAGG 59.767 50.000 4.59 0.00 0.00 3.86
2264 2313 6.149973 CAGATTGCAATGGACTTTCTACTTCA 59.850 38.462 18.59 0.00 0.00 3.02
2268 2317 6.913170 TGCAATGGACTTTCTACTTCATTTC 58.087 36.000 0.00 0.00 0.00 2.17
2311 2777 1.202330 CTTCTGATGCTCCCTCCACT 58.798 55.000 0.00 0.00 0.00 4.00
2323 2789 1.827969 CCCTCCACTTCCAGTACAGAG 59.172 57.143 0.00 0.00 0.00 3.35
2325 2791 0.888619 TCCACTTCCAGTACAGAGCG 59.111 55.000 0.00 0.00 0.00 5.03
2343 2809 3.964909 AGCGAAACTCAAAATTGTGACC 58.035 40.909 0.00 0.00 0.00 4.02
2357 2823 6.707440 AATTGTGACCGAAATATAATGCCA 57.293 33.333 0.00 0.00 0.00 4.92
2386 2852 7.312154 TGCACATTATTTGGTGTCACTAAATC 58.688 34.615 25.28 13.66 38.36 2.17
2450 2987 2.972625 TCGAGCAGGGTTACAGATTTG 58.027 47.619 0.00 0.00 0.00 2.32
2451 2988 2.565391 TCGAGCAGGGTTACAGATTTGA 59.435 45.455 0.00 0.00 0.00 2.69
2452 2989 3.007506 TCGAGCAGGGTTACAGATTTGAA 59.992 43.478 0.00 0.00 0.00 2.69
2453 2990 3.372206 CGAGCAGGGTTACAGATTTGAAG 59.628 47.826 0.00 0.00 0.00 3.02
2454 2991 4.327680 GAGCAGGGTTACAGATTTGAAGT 58.672 43.478 0.00 0.00 0.00 3.01
2455 2992 4.729868 AGCAGGGTTACAGATTTGAAGTT 58.270 39.130 0.00 0.00 0.00 2.66
2456 2993 4.762251 AGCAGGGTTACAGATTTGAAGTTC 59.238 41.667 0.00 0.00 0.00 3.01
2457 2994 4.762251 GCAGGGTTACAGATTTGAAGTTCT 59.238 41.667 4.17 0.00 0.00 3.01
2458 2995 5.241728 GCAGGGTTACAGATTTGAAGTTCTT 59.758 40.000 4.17 0.00 0.00 2.52
2459 2996 6.568653 GCAGGGTTACAGATTTGAAGTTCTTC 60.569 42.308 4.17 5.70 0.00 2.87
2460 2997 6.004574 AGGGTTACAGATTTGAAGTTCTTCC 58.995 40.000 4.17 0.00 0.00 3.46
2461 2998 5.183331 GGGTTACAGATTTGAAGTTCTTCCC 59.817 44.000 4.17 0.00 0.00 3.97
2462 2999 5.768164 GGTTACAGATTTGAAGTTCTTCCCA 59.232 40.000 4.17 0.00 0.00 4.37
2463 3000 6.264518 GGTTACAGATTTGAAGTTCTTCCCAA 59.735 38.462 4.17 4.08 0.00 4.12
2464 3001 7.039714 GGTTACAGATTTGAAGTTCTTCCCAAT 60.040 37.037 4.17 7.99 0.00 3.16
2465 3002 6.983906 ACAGATTTGAAGTTCTTCCCAATT 57.016 33.333 4.17 0.00 0.00 2.32
2467 3004 7.886338 ACAGATTTGAAGTTCTTCCCAATTAC 58.114 34.615 4.17 0.20 0.00 1.89
2469 3006 8.025445 CAGATTTGAAGTTCTTCCCAATTACTG 58.975 37.037 4.17 8.47 0.00 2.74
2472 3009 7.979444 TTGAAGTTCTTCCCAATTACTGTAG 57.021 36.000 4.17 0.00 0.00 2.74
2477 3014 7.162082 AGTTCTTCCCAATTACTGTAGACTTG 58.838 38.462 0.00 0.00 0.00 3.16
2481 3018 8.258007 TCTTCCCAATTACTGTAGACTTGTATG 58.742 37.037 0.00 0.00 0.00 2.39
2482 3019 6.346096 TCCCAATTACTGTAGACTTGTATGC 58.654 40.000 0.00 0.00 0.00 3.14
2486 3023 7.549134 CCAATTACTGTAGACTTGTATGCTTGA 59.451 37.037 0.00 0.00 0.00 3.02
2495 3032 4.081406 ACTTGTATGCTTGATTGCTGGAA 58.919 39.130 0.00 0.00 0.00 3.53
2497 3034 2.419673 TGTATGCTTGATTGCTGGAACG 59.580 45.455 0.00 0.00 0.00 3.95
2500 3037 0.449388 GCTTGATTGCTGGAACGAGG 59.551 55.000 0.00 0.00 0.00 4.63
2503 3040 1.808411 TGATTGCTGGAACGAGGAAC 58.192 50.000 0.00 0.00 0.00 3.62
2505 3042 2.565391 TGATTGCTGGAACGAGGAACTA 59.435 45.455 0.00 0.00 41.55 2.24
2579 3117 8.234546 CGGTCAACAAATAATAAGCTAAACTGT 58.765 33.333 0.00 0.00 0.00 3.55
2634 3172 7.961326 ACATAACTAAAAGAATCCAGGCAAT 57.039 32.000 0.00 0.00 0.00 3.56
2668 3207 3.181499 GGCACTGCATCTTCTTCAGATTG 60.181 47.826 2.82 0.00 40.67 2.67
2734 3279 0.455815 GATCCAAACATGCCCGTTCC 59.544 55.000 0.00 0.00 0.00 3.62
2744 3289 1.971695 GCCCGTTCCCTGAAACTGG 60.972 63.158 0.00 0.00 36.80 4.00
2786 3331 7.178712 AGAAACTGATTCTTGAACAGTAACG 57.821 36.000 14.19 0.00 46.39 3.18
2835 3380 2.236741 TCAGTTCGATGTGTACGACG 57.763 50.000 0.00 0.00 39.46 5.12
2888 3433 4.104383 TCCTTCAGTTTCCATGAGCTTT 57.896 40.909 0.00 0.00 0.00 3.51
2889 3434 5.241403 TCCTTCAGTTTCCATGAGCTTTA 57.759 39.130 0.00 0.00 0.00 1.85
2931 3476 2.304180 ACTCTCCCTGGAAGTGTTCATG 59.696 50.000 0.00 0.00 0.00 3.07
2940 3485 4.507710 TGGAAGTGTTCATGTAGCTCATC 58.492 43.478 0.00 0.00 34.09 2.92
2944 3489 4.502016 AGTGTTCATGTAGCTCATCAGTG 58.498 43.478 0.00 0.00 34.09 3.66
2951 3496 5.363580 TCATGTAGCTCATCAGTGTGGAATA 59.636 40.000 0.00 0.00 34.09 1.75
2987 3532 3.009033 TGCAGTCCTAATAAGTTGGCAGT 59.991 43.478 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.776107 TGATCCACAATGAACAAGTACAAAAA 58.224 30.769 0.00 0.00 0.00 1.94
14 15 7.340122 TGATCCACAATGAACAAGTACAAAA 57.660 32.000 0.00 0.00 0.00 2.44
15 16 6.951062 TGATCCACAATGAACAAGTACAAA 57.049 33.333 0.00 0.00 0.00 2.83
16 17 6.072008 CCATGATCCACAATGAACAAGTACAA 60.072 38.462 0.00 0.00 0.00 2.41
17 18 5.415389 CCATGATCCACAATGAACAAGTACA 59.585 40.000 0.00 0.00 0.00 2.90
18 19 5.677091 GCCATGATCCACAATGAACAAGTAC 60.677 44.000 0.00 0.00 0.00 2.73
19 20 4.398988 GCCATGATCCACAATGAACAAGTA 59.601 41.667 0.00 0.00 0.00 2.24
36 37 2.731654 CGTTCATGCGAAAATGCCATGA 60.732 45.455 0.00 0.00 33.59 3.07
50 51 3.138304 TGAAGTCCTCCAAACGTTCATG 58.862 45.455 0.00 0.00 0.00 3.07
51 52 3.485463 TGAAGTCCTCCAAACGTTCAT 57.515 42.857 0.00 0.00 0.00 2.57
57 58 4.821805 TCTGAACAATGAAGTCCTCCAAAC 59.178 41.667 0.00 0.00 0.00 2.93
186 197 1.971695 GGGTTCCCAGCGAAAGTGG 60.972 63.158 2.59 0.00 34.52 4.00
198 209 2.170166 TGAGAATGCATGTTGGGTTCC 58.830 47.619 0.00 0.00 0.00 3.62
219 230 7.896383 TTTTGAGGGATCATCCGAAATAAAT 57.104 32.000 0.00 0.00 37.43 1.40
244 255 9.927081 ACATTCTAGTCCCATCTGAAATTTTAT 57.073 29.630 0.00 0.00 0.00 1.40
245 256 9.753674 AACATTCTAGTCCCATCTGAAATTTTA 57.246 29.630 0.00 0.00 0.00 1.52
250 261 4.943705 GCAACATTCTAGTCCCATCTGAAA 59.056 41.667 0.00 0.00 0.00 2.69
251 262 4.019411 TGCAACATTCTAGTCCCATCTGAA 60.019 41.667 0.00 0.00 0.00 3.02
253 264 3.877559 TGCAACATTCTAGTCCCATCTG 58.122 45.455 0.00 0.00 0.00 2.90
254 265 4.785346 ATGCAACATTCTAGTCCCATCT 57.215 40.909 0.00 0.00 0.00 2.90
295 306 0.250989 TAGGGGTTTGGAGGTTTGCG 60.251 55.000 0.00 0.00 0.00 4.85
307 318 6.663523 ACGATGAAGAAAATGAAATAGGGGTT 59.336 34.615 0.00 0.00 0.00 4.11
316 327 7.148356 CCAATCTCTCACGATGAAGAAAATGAA 60.148 37.037 0.00 0.00 0.00 2.57
321 332 3.935203 GCCAATCTCTCACGATGAAGAAA 59.065 43.478 0.00 0.00 0.00 2.52
331 342 1.202580 AGGTATGCGCCAATCTCTCAC 60.203 52.381 4.18 0.00 0.00 3.51
333 344 2.139118 GAAGGTATGCGCCAATCTCTC 58.861 52.381 4.18 0.00 0.00 3.20
339 350 2.356135 GAAGAAGAAGGTATGCGCCAA 58.644 47.619 4.18 0.00 0.00 4.52
346 357 4.904853 GGAGGATGAGGAAGAAGAAGGTAT 59.095 45.833 0.00 0.00 0.00 2.73
368 379 1.672881 GGAAAGAATGACATGGCGAGG 59.327 52.381 0.00 0.00 0.00 4.63
377 388 2.159028 CGAGGAGGAGGGAAAGAATGAC 60.159 54.545 0.00 0.00 0.00 3.06
395 406 2.668457 CTGGTGAGACCGAAAAATCGAG 59.332 50.000 0.00 0.00 42.58 4.04
396 407 2.683968 CTGGTGAGACCGAAAAATCGA 58.316 47.619 0.00 0.00 42.58 3.59
397 408 1.128692 GCTGGTGAGACCGAAAAATCG 59.871 52.381 0.00 0.00 42.58 3.34
405 416 1.734477 CTTGACGCTGGTGAGACCG 60.734 63.158 0.00 0.00 42.58 4.79
412 423 1.598130 GCCTTGACTTGACGCTGGT 60.598 57.895 0.00 0.00 0.00 4.00
434 445 2.484264 GACAACCTAGTGACAATGTGGC 59.516 50.000 0.00 0.00 0.00 5.01
437 448 3.746045 ACGACAACCTAGTGACAATGT 57.254 42.857 0.00 0.00 0.00 2.71
438 449 3.363970 GCAACGACAACCTAGTGACAATG 60.364 47.826 0.00 0.00 0.00 2.82
440 451 2.206750 GCAACGACAACCTAGTGACAA 58.793 47.619 0.00 0.00 0.00 3.18
443 454 1.000506 GAGGCAACGACAACCTAGTGA 59.999 52.381 0.00 0.00 46.39 3.41
456 467 1.397567 CGAAACCGTTAACGAGGCAAC 60.398 52.381 28.79 13.09 43.02 4.17
465 476 2.612721 GGGAGCTAACCGAAACCGTTAA 60.613 50.000 0.00 0.00 0.00 2.01
477 488 0.761323 GGAGAGGGAGGGGAGCTAAC 60.761 65.000 0.00 0.00 0.00 2.34
499 510 2.563179 TGAAGGAAGGAGAACGAGGAAG 59.437 50.000 0.00 0.00 0.00 3.46
508 519 2.499289 GAGCATGAGTGAAGGAAGGAGA 59.501 50.000 0.00 0.00 0.00 3.71
524 535 2.159170 GCGAACTAGTGGAGAAGAGCAT 60.159 50.000 0.00 0.00 0.00 3.79
526 537 1.795889 CGCGAACTAGTGGAGAAGAGC 60.796 57.143 0.00 0.00 0.00 4.09
528 539 0.809385 CCGCGAACTAGTGGAGAAGA 59.191 55.000 8.23 0.00 44.18 2.87
544 556 3.497031 GGTGGCTAACGCTTCCGC 61.497 66.667 0.00 0.00 38.22 5.54
547 559 0.796927 GTCTTGGTGGCTAACGCTTC 59.203 55.000 0.00 0.00 36.09 3.86
555 567 2.175202 CAGTCTCTAGTCTTGGTGGCT 58.825 52.381 0.00 0.00 0.00 4.75
556 568 2.171840 TCAGTCTCTAGTCTTGGTGGC 58.828 52.381 0.00 0.00 0.00 5.01
595 607 9.445973 AACTCCTAAAGATGAGATTAGAGGAAT 57.554 33.333 0.00 0.00 32.10 3.01
633 645 4.490899 ACACGGGCCATGTAAAACTATA 57.509 40.909 1.98 0.00 0.00 1.31
690 705 6.705825 GCCATGAACAAGTTTTACAGGATTTT 59.294 34.615 0.00 0.00 0.00 1.82
704 719 7.699391 CACTTATTTCTATGTGCCATGAACAAG 59.301 37.037 0.00 0.29 0.00 3.16
714 729 6.129393 CACGCATACACTTATTTCTATGTGC 58.871 40.000 0.00 0.00 36.80 4.57
715 730 7.222805 AGACACGCATACACTTATTTCTATGTG 59.777 37.037 0.00 0.00 38.39 3.21
726 741 1.148310 GCACAGACACGCATACACTT 58.852 50.000 0.00 0.00 0.00 3.16
735 750 1.386748 CAATACAGACGCACAGACACG 59.613 52.381 0.00 0.00 0.00 4.49
737 752 2.223947 ACACAATACAGACGCACAGACA 60.224 45.455 0.00 0.00 0.00 3.41
738 753 2.404215 ACACAATACAGACGCACAGAC 58.596 47.619 0.00 0.00 0.00 3.51
741 756 5.736486 TTTTAACACAATACAGACGCACA 57.264 34.783 0.00 0.00 0.00 4.57
1368 1396 3.621805 TTGCCGAGGAACCGCTCA 61.622 61.111 0.00 0.00 0.00 4.26
1378 1406 2.896443 GGAGGAGGAGTTGCCGAG 59.104 66.667 0.00 0.00 43.43 4.63
1980 2011 2.043450 CTCCCGTCCTCCAGCTCT 60.043 66.667 0.00 0.00 0.00 4.09
2193 2233 2.681848 GTGAGATGTTGCTCCCAAGATG 59.318 50.000 0.00 0.00 35.33 2.90
2200 2247 1.400846 CATGCAGTGAGATGTTGCTCC 59.599 52.381 0.00 0.00 38.60 4.70
2225 2272 3.382865 TGCAATCTGCTACTAGTCCTCAG 59.617 47.826 0.00 5.66 45.31 3.35
2230 2277 4.509600 GTCCATTGCAATCTGCTACTAGTC 59.490 45.833 9.53 0.00 45.31 2.59
2311 2777 2.626266 TGAGTTTCGCTCTGTACTGGAA 59.374 45.455 0.00 0.00 44.41 3.53
2323 2789 2.719046 CGGTCACAATTTTGAGTTTCGC 59.281 45.455 0.00 0.00 0.00 4.70
2325 2791 8.742554 ATATTTCGGTCACAATTTTGAGTTTC 57.257 30.769 0.00 0.00 0.00 2.78
2343 2809 8.692110 AATGTGCATATTGGCATTATATTTCG 57.308 30.769 8.00 0.00 46.92 3.46
2357 2823 7.408756 AGTGACACCAAATAATGTGCATATT 57.591 32.000 13.54 13.54 35.90 1.28
2450 2987 7.387643 AGTCTACAGTAATTGGGAAGAACTTC 58.612 38.462 6.06 6.06 38.80 3.01
2451 2988 7.317722 AGTCTACAGTAATTGGGAAGAACTT 57.682 36.000 0.00 0.00 0.00 2.66
2452 2989 6.936968 AGTCTACAGTAATTGGGAAGAACT 57.063 37.500 0.00 0.00 0.00 3.01
2453 2990 6.935208 ACAAGTCTACAGTAATTGGGAAGAAC 59.065 38.462 0.00 0.00 0.00 3.01
2454 2991 7.074653 ACAAGTCTACAGTAATTGGGAAGAA 57.925 36.000 0.00 0.00 0.00 2.52
2455 2992 6.681729 ACAAGTCTACAGTAATTGGGAAGA 57.318 37.500 0.00 0.00 0.00 2.87
2456 2993 7.011482 GCATACAAGTCTACAGTAATTGGGAAG 59.989 40.741 0.00 0.00 0.00 3.46
2457 2994 6.821665 GCATACAAGTCTACAGTAATTGGGAA 59.178 38.462 0.00 0.00 0.00 3.97
2458 2995 6.156256 AGCATACAAGTCTACAGTAATTGGGA 59.844 38.462 0.00 0.00 0.00 4.37
2459 2996 6.349300 AGCATACAAGTCTACAGTAATTGGG 58.651 40.000 0.00 0.00 0.00 4.12
2460 2997 7.549134 TCAAGCATACAAGTCTACAGTAATTGG 59.451 37.037 0.00 0.00 0.00 3.16
2461 2998 8.479313 TCAAGCATACAAGTCTACAGTAATTG 57.521 34.615 0.00 0.00 0.00 2.32
2462 2999 9.672673 AATCAAGCATACAAGTCTACAGTAATT 57.327 29.630 0.00 0.00 0.00 1.40
2463 3000 9.102757 CAATCAAGCATACAAGTCTACAGTAAT 57.897 33.333 0.00 0.00 0.00 1.89
2464 3001 7.064609 GCAATCAAGCATACAAGTCTACAGTAA 59.935 37.037 0.00 0.00 0.00 2.24
2465 3002 6.535150 GCAATCAAGCATACAAGTCTACAGTA 59.465 38.462 0.00 0.00 0.00 2.74
2467 3004 5.583854 AGCAATCAAGCATACAAGTCTACAG 59.416 40.000 0.00 0.00 36.85 2.74
2469 3006 5.220739 CCAGCAATCAAGCATACAAGTCTAC 60.221 44.000 0.00 0.00 36.85 2.59
2472 3009 3.691118 TCCAGCAATCAAGCATACAAGTC 59.309 43.478 0.00 0.00 36.85 3.01
2477 3014 2.677836 TCGTTCCAGCAATCAAGCATAC 59.322 45.455 0.00 0.00 36.85 2.39
2481 3018 0.449388 CCTCGTTCCAGCAATCAAGC 59.551 55.000 0.00 0.00 0.00 4.01
2482 3019 2.099141 TCCTCGTTCCAGCAATCAAG 57.901 50.000 0.00 0.00 0.00 3.02
2486 3023 3.914426 ATAGTTCCTCGTTCCAGCAAT 57.086 42.857 0.00 0.00 0.00 3.56
2495 3032 4.770795 CAAATCCCAGAATAGTTCCTCGT 58.229 43.478 0.00 0.00 0.00 4.18
2497 3034 4.786425 AGCAAATCCCAGAATAGTTCCTC 58.214 43.478 0.00 0.00 0.00 3.71
2500 3037 5.189180 ACAGAGCAAATCCCAGAATAGTTC 58.811 41.667 0.00 0.00 0.00 3.01
2503 3040 5.188434 TGAACAGAGCAAATCCCAGAATAG 58.812 41.667 0.00 0.00 0.00 1.73
2504 3041 5.178096 TGAACAGAGCAAATCCCAGAATA 57.822 39.130 0.00 0.00 0.00 1.75
2505 3042 4.015084 CTGAACAGAGCAAATCCCAGAAT 58.985 43.478 0.00 0.00 0.00 2.40
2615 3153 6.928520 CAGAAATTGCCTGGATTCTTTTAGT 58.071 36.000 0.00 0.00 30.01 2.24
2634 3172 1.202915 TGCAGTGCCATCTTCCAGAAA 60.203 47.619 13.72 0.00 0.00 2.52
2668 3207 4.202441 TCCAGAGGAGCTCATTTATTTGC 58.798 43.478 17.19 0.00 32.06 3.68
2734 3279 5.308825 AGATGTACAAGAACCAGTTTCAGG 58.691 41.667 0.00 0.00 36.57 3.86
2744 3289 6.367422 CAGTTTCTCTGGAGATGTACAAGAAC 59.633 42.308 0.00 1.30 40.23 3.01
2770 3315 3.128349 ACGTGCGTTACTGTTCAAGAAT 58.872 40.909 0.00 0.00 0.00 2.40
2835 3380 2.475487 GCAAACTGGTGAACGAGTACTC 59.525 50.000 13.18 13.18 33.72 2.59
2888 3433 8.280084 AGAGTAGTGGAGTATGACAAACCTATA 58.720 37.037 0.00 0.00 0.00 1.31
2889 3434 7.126733 AGAGTAGTGGAGTATGACAAACCTAT 58.873 38.462 0.00 0.00 0.00 2.57
2931 3476 6.985188 TTTTATTCCACACTGATGAGCTAC 57.015 37.500 0.00 0.00 0.00 3.58
2987 3532 9.607988 ATGAATGACGGTATGTTTGTCTTATTA 57.392 29.630 0.00 0.00 33.81 0.98


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

AutoCloner maintained by Alex Coulton.