Multiple sequence alignment - TraesCS1D01G217800

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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 TraesCS1D01G217800 chr1D 100.000 3172 0 0 1 3172 303292076 303295247 0.000000e+00 5858
1 TraesCS1D01G217800 chr1B 89.993 2788 110 57 6 2741 410666254 410668924 0.000000e+00 3446
2 TraesCS1D01G217800 chr1B 82.821 390 42 15 2767 3137 410668993 410669376 3.050000e-85 326
3 TraesCS1D01G217800 chr1A 89.641 2703 141 56 7 2638 380888644 380891278 0.000000e+00 3312
4 TraesCS1D01G217800 chr1A 76.170 235 37 13 2824 3058 380891277 380891492 4.330000e-19 106
5 TraesCS1D01G217800 chr4D 77.835 194 28 11 2927 3110 6829653 6829841 4.330000e-19 106


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 TraesCS1D01G217800 chr1D 303292076 303295247 3171 False 5858 5858 100.0000 1 3172 1 chr1D.!!$F1 3171
1 TraesCS1D01G217800 chr1B 410666254 410669376 3122 False 1886 3446 86.4070 6 3137 2 chr1B.!!$F1 3131
2 TraesCS1D01G217800 chr1A 380888644 380891492 2848 False 1709 3312 82.9055 7 3058 2 chr1A.!!$F1 3051

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
256 272 0.383949 GAGAGTCAAGAGCGCCTAGG 59.616 60.000 2.29 3.67 0.00 3.02 F
396 412 1.000171 GAGAACAACGACCCGGTTACT 60.000 52.381 0.00 0.00 0.00 2.24 F
665 701 1.336609 GGAGGCAGCAAAAGCTGAAAG 60.337 52.381 20.52 0.00 39.96 2.62 F
787 823 2.029666 CTCATCCGTCGCATCCCC 59.970 66.667 0.00 0.00 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1101 1185 0.259938 AATCCATGAACAGGGGAGGC 59.740 55.0 5.68 0.0 33.47 4.70 R
1479 1568 0.591741 CAGCCGGTCGATCTCGTTAC 60.592 60.0 1.90 0.0 40.80 2.50 R
1588 1677 0.681175 TCCGCCATCATCATCATCGT 59.319 50.0 0.00 0.0 0.00 3.73 R
2746 2907 0.321653 AACAGGCGTTCACCTCCATC 60.322 55.0 0.00 0.0 38.26 3.51 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
193 207 0.539051 ATAGATAGATGCTGCCCGCC 59.461 55.000 0.00 0.00 38.05 6.13
231 247 8.901748 CAAACGAACGAATGAACAGAATAAAAT 58.098 29.630 0.14 0.00 0.00 1.82
256 272 0.383949 GAGAGTCAAGAGCGCCTAGG 59.616 60.000 2.29 3.67 0.00 3.02
261 277 1.953138 CAAGAGCGCCTAGGCATCG 60.953 63.158 32.47 17.93 42.06 3.84
315 331 3.803340 TGGGAGTCCTTGGAAGTAGATT 58.197 45.455 9.58 0.00 0.00 2.40
316 332 4.175962 TGGGAGTCCTTGGAAGTAGATTT 58.824 43.478 9.58 0.00 0.00 2.17
317 333 5.347124 TGGGAGTCCTTGGAAGTAGATTTA 58.653 41.667 9.58 0.00 0.00 1.40
348 364 1.079750 GCAGAGGACCGAGGAACAC 60.080 63.158 0.00 0.00 0.00 3.32
395 411 1.269726 TGAGAACAACGACCCGGTTAC 60.270 52.381 0.00 0.00 0.00 2.50
396 412 1.000171 GAGAACAACGACCCGGTTACT 60.000 52.381 0.00 0.00 0.00 2.24
397 413 2.228822 GAGAACAACGACCCGGTTACTA 59.771 50.000 0.00 0.00 0.00 1.82
400 416 4.096984 AGAACAACGACCCGGTTACTATAG 59.903 45.833 0.00 0.00 0.00 1.31
401 417 3.356290 ACAACGACCCGGTTACTATAGT 58.644 45.455 10.87 10.87 0.00 2.12
433 449 4.596180 GCAATGCGTCGATGGCCG 62.596 66.667 6.79 0.00 40.25 6.13
471 491 5.294306 CGTGTAGATCCAACAGCACAATAAT 59.706 40.000 0.00 0.00 0.00 1.28
472 492 6.478673 CGTGTAGATCCAACAGCACAATAATA 59.521 38.462 0.00 0.00 0.00 0.98
473 493 7.011016 CGTGTAGATCCAACAGCACAATAATAA 59.989 37.037 0.00 0.00 0.00 1.40
499 519 5.523438 AGGAAAGCGGTTAAAACATTTGA 57.477 34.783 0.00 0.00 0.00 2.69
500 520 5.528870 AGGAAAGCGGTTAAAACATTTGAG 58.471 37.500 0.00 0.00 0.00 3.02
501 521 4.149922 GGAAAGCGGTTAAAACATTTGAGC 59.850 41.667 0.00 0.00 0.00 4.26
505 531 4.048504 GCGGTTAAAACATTTGAGCTGTT 58.951 39.130 0.00 0.00 38.44 3.16
508 534 4.211164 GGTTAAAACATTTGAGCTGTTGGC 59.789 41.667 0.00 0.00 36.95 4.52
649 682 2.099098 GAGAGCGAGAGAAAAGAGGAGG 59.901 54.545 0.00 0.00 0.00 4.30
665 701 1.336609 GGAGGCAGCAAAAGCTGAAAG 60.337 52.381 20.52 0.00 39.96 2.62
702 738 2.656002 CCACCCTGATAAGACGAGAGA 58.344 52.381 0.00 0.00 0.00 3.10
787 823 2.029666 CTCATCCGTCGCATCCCC 59.970 66.667 0.00 0.00 0.00 4.81
788 824 3.848347 CTCATCCGTCGCATCCCCG 62.848 68.421 0.00 0.00 0.00 5.73
1110 1194 4.798344 CAGCAGCAGCCTCCCCTG 62.798 72.222 0.00 0.00 43.56 4.45
1128 1212 2.356125 CCTGTTCATGGATTTCTCCCGT 60.356 50.000 0.00 0.00 41.29 5.28
1210 1299 6.112734 TGTGATTGAGGCGATTAACTAACAT 58.887 36.000 0.00 0.00 0.00 2.71
1211 1300 6.037062 TGTGATTGAGGCGATTAACTAACATG 59.963 38.462 0.00 0.00 0.00 3.21
1213 1302 2.863740 TGAGGCGATTAACTAACATGCG 59.136 45.455 0.00 0.00 0.00 4.73
1442 1531 3.136123 CCTCGACGTCGCCCCTTA 61.136 66.667 32.19 13.67 39.60 2.69
1480 1569 4.373116 CAGTGCGGGCGGTACAGT 62.373 66.667 15.02 0.00 33.10 3.55
1582 1671 4.386867 TCGATCTACATGGAGGTTGTTC 57.613 45.455 4.74 0.00 0.00 3.18
1587 1676 5.089970 TCTACATGGAGGTTGTTCTGATG 57.910 43.478 4.74 0.00 0.00 3.07
1588 1677 4.777366 TCTACATGGAGGTTGTTCTGATGA 59.223 41.667 4.74 0.00 0.00 2.92
1589 1678 3.679389 ACATGGAGGTTGTTCTGATGAC 58.321 45.455 0.00 0.00 0.00 3.06
1590 1679 2.455674 TGGAGGTTGTTCTGATGACG 57.544 50.000 0.00 0.00 0.00 4.35
1591 1680 1.967779 TGGAGGTTGTTCTGATGACGA 59.032 47.619 0.00 0.00 0.00 4.20
1592 1681 2.567169 TGGAGGTTGTTCTGATGACGAT 59.433 45.455 0.00 0.00 0.00 3.73
1593 1682 2.932614 GGAGGTTGTTCTGATGACGATG 59.067 50.000 0.00 0.00 0.00 3.84
1594 1683 3.368427 GGAGGTTGTTCTGATGACGATGA 60.368 47.826 0.00 0.00 0.00 2.92
1604 1693 3.332034 TGATGACGATGATGATGATGGC 58.668 45.455 0.00 0.00 0.00 4.40
1607 1696 0.681175 ACGATGATGATGATGGCGGA 59.319 50.000 0.00 0.00 0.00 5.54
2288 2399 2.650116 CGTGCTAGTGGGCTGGACT 61.650 63.158 0.00 0.00 0.00 3.85
2309 2421 2.974794 TGATTGATCCCTCCATGATCGT 59.025 45.455 0.00 0.00 41.22 3.73
2325 2437 4.637276 TGATCGTTTCACCTCTTTTGCTA 58.363 39.130 0.00 0.00 0.00 3.49
2326 2438 4.451096 TGATCGTTTCACCTCTTTTGCTAC 59.549 41.667 0.00 0.00 0.00 3.58
2329 2441 3.560068 CGTTTCACCTCTTTTGCTACTGT 59.440 43.478 0.00 0.00 0.00 3.55
2334 2446 5.539048 TCACCTCTTTTGCTACTGTTCTAC 58.461 41.667 0.00 0.00 0.00 2.59
2337 2449 6.586844 CACCTCTTTTGCTACTGTTCTACTAC 59.413 42.308 0.00 0.00 0.00 2.73
2338 2450 5.800941 CCTCTTTTGCTACTGTTCTACTACG 59.199 44.000 0.00 0.00 0.00 3.51
2343 2461 6.659361 TTGCTACTGTTCTACTACGACTAG 57.341 41.667 0.00 0.00 0.00 2.57
2370 2492 4.359971 TGATGATTTGAATCTTGCGTGG 57.640 40.909 5.42 0.00 36.39 4.94
2393 2515 2.875933 AGTTTTTACTGCTAGCAACGCA 59.124 40.909 19.86 0.27 35.80 5.24
2396 2518 3.740044 TTTACTGCTAGCAACGCATTC 57.260 42.857 19.86 0.00 36.70 2.67
2715 2841 0.520404 CATTCTGCTGCACTGGACAC 59.480 55.000 0.00 0.00 0.00 3.67
2727 2853 2.671145 TGGACACAGACAGGCTAGG 58.329 57.895 0.00 0.00 0.00 3.02
2730 2856 0.533032 GACACAGACAGGCTAGGTCC 59.467 60.000 1.66 0.00 35.89 4.46
2731 2857 0.115349 ACACAGACAGGCTAGGTCCT 59.885 55.000 0.00 0.00 35.89 3.85
2732 2858 0.820871 CACAGACAGGCTAGGTCCTC 59.179 60.000 0.00 0.00 35.89 3.71
2733 2859 0.681564 ACAGACAGGCTAGGTCCTCG 60.682 60.000 0.00 0.00 35.89 4.63
2734 2860 1.755008 AGACAGGCTAGGTCCTCGC 60.755 63.158 6.86 6.86 35.89 5.03
2735 2861 3.127352 GACAGGCTAGGTCCTCGCG 62.127 68.421 9.17 0.00 33.25 5.87
2736 2862 4.577246 CAGGCTAGGTCCTCGCGC 62.577 72.222 9.17 0.00 33.25 6.86
2757 2918 1.274703 GCCCCAGAGATGGAGGTGAA 61.275 60.000 0.00 0.00 0.00 3.18
2761 2922 0.460987 CAGAGATGGAGGTGAACGCC 60.461 60.000 0.00 0.00 39.86 5.68
2764 2925 1.194781 AGATGGAGGTGAACGCCTGT 61.195 55.000 11.79 0.00 40.14 4.00
2809 2978 1.484038 ATCTCACTCCAGCTGGACTC 58.516 55.000 32.00 0.00 39.78 3.36
2817 2986 1.665916 CAGCTGGACTCACCACACG 60.666 63.158 5.57 0.00 44.64 4.49
2840 3010 1.299926 CGCTATCCGGTACACCTGC 60.300 63.158 0.00 0.00 0.00 4.85
2846 3016 2.046314 CGGTACACCTGCCCTTGG 60.046 66.667 0.00 0.00 0.00 3.61
2858 3028 3.006728 CCTTGGGGTGCTACCGGA 61.007 66.667 9.46 0.00 39.83 5.14
2932 3102 8.889849 AAAAATTAGCGTGTACACAACATATC 57.110 30.769 24.98 5.37 41.10 1.63
2935 3105 4.450082 AGCGTGTACACAACATATCTCA 57.550 40.909 24.98 0.00 41.10 3.27
2937 3107 4.864806 AGCGTGTACACAACATATCTCAAG 59.135 41.667 24.98 5.67 41.10 3.02
2948 3118 6.207221 ACAACATATCTCAAGCATGTCACAAA 59.793 34.615 0.00 0.00 31.82 2.83
2999 3173 7.809331 TGAGAATCAATACAACAAATTCAGCAC 59.191 33.333 0.00 0.00 45.97 4.40
3047 3221 9.487442 AATTTATGGCCCAATCTAAAAAGAGTA 57.513 29.630 0.00 0.00 0.00 2.59
3049 3223 5.514500 TGGCCCAATCTAAAAAGAGTACT 57.486 39.130 0.00 0.00 0.00 2.73
3050 3224 6.630203 TGGCCCAATCTAAAAAGAGTACTA 57.370 37.500 0.00 0.00 0.00 1.82
3052 3226 7.639378 TGGCCCAATCTAAAAAGAGTACTATT 58.361 34.615 0.00 0.00 0.00 1.73
3053 3227 7.556275 TGGCCCAATCTAAAAAGAGTACTATTG 59.444 37.037 2.98 3.88 0.00 1.90
3054 3228 7.773690 GGCCCAATCTAAAAAGAGTACTATTGA 59.226 37.037 2.98 0.00 0.00 2.57
3055 3229 9.343539 GCCCAATCTAAAAAGAGTACTATTGAT 57.656 33.333 2.98 0.00 0.00 2.57
3092 3280 9.538508 TTTTTGTTTCTAGAGTTGTAGGTCTAC 57.461 33.333 1.43 1.43 36.63 2.59
3106 3294 9.654663 GTTGTAGGTCTACTTTGTATCTGAATT 57.345 33.333 9.24 0.00 37.00 2.17
3112 3300 7.755373 GGTCTACTTTGTATCTGAATTTTTGGC 59.245 37.037 0.00 0.00 0.00 4.52
3118 3306 6.078202 TGTATCTGAATTTTTGGCGAAACA 57.922 33.333 0.00 0.00 0.00 2.83
3119 3307 6.148948 TGTATCTGAATTTTTGGCGAAACAG 58.851 36.000 0.00 4.84 0.00 3.16
3128 3316 6.811253 TTTTTGGCGAAACAGTAGATGTAT 57.189 33.333 0.00 0.00 43.00 2.29
3137 3325 7.010183 GCGAAACAGTAGATGTATGTTATGTGT 59.990 37.037 0.00 0.00 43.00 3.72
3138 3326 8.321005 CGAAACAGTAGATGTATGTTATGTGTG 58.679 37.037 0.00 0.00 43.00 3.82
3139 3327 7.539712 AACAGTAGATGTATGTTATGTGTGC 57.460 36.000 0.00 0.00 43.00 4.57
3140 3328 5.748630 ACAGTAGATGTATGTTATGTGTGCG 59.251 40.000 0.00 0.00 41.60 5.34
3141 3329 5.748630 CAGTAGATGTATGTTATGTGTGCGT 59.251 40.000 0.00 0.00 0.00 5.24
3142 3330 5.748630 AGTAGATGTATGTTATGTGTGCGTG 59.251 40.000 0.00 0.00 0.00 5.34
3143 3331 4.503910 AGATGTATGTTATGTGTGCGTGT 58.496 39.130 0.00 0.00 0.00 4.49
3144 3332 4.329801 AGATGTATGTTATGTGTGCGTGTG 59.670 41.667 0.00 0.00 0.00 3.82
3145 3333 2.158645 TGTATGTTATGTGTGCGTGTGC 59.841 45.455 0.00 0.00 43.20 4.57
3158 3346 3.648179 GCGTGTGCAAAATTGTTTTCA 57.352 38.095 0.00 0.00 42.15 2.69
3159 3347 4.194381 GCGTGTGCAAAATTGTTTTCAT 57.806 36.364 0.00 0.00 42.15 2.57
3160 3348 5.321983 GCGTGTGCAAAATTGTTTTCATA 57.678 34.783 0.00 0.00 42.15 2.15
3161 3349 5.914746 GCGTGTGCAAAATTGTTTTCATAT 58.085 33.333 0.00 0.00 42.15 1.78
3162 3350 6.361899 GCGTGTGCAAAATTGTTTTCATATT 58.638 32.000 0.00 0.00 42.15 1.28
3163 3351 6.850317 GCGTGTGCAAAATTGTTTTCATATTT 59.150 30.769 0.00 0.00 42.15 1.40
3164 3352 7.375544 GCGTGTGCAAAATTGTTTTCATATTTT 59.624 29.630 0.00 0.00 42.15 1.82
3165 3353 9.219497 CGTGTGCAAAATTGTTTTCATATTTTT 57.781 25.926 0.00 0.00 33.17 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
193 207 1.264288 GTTCGTTTGGTCAAGCCTCAG 59.736 52.381 0.00 0.00 38.35 3.35
231 247 0.238553 CGCTCTTGACTCTCGTGTCA 59.761 55.000 5.00 5.00 44.17 3.58
256 272 5.176407 CTAGTATAGTAGGCATCCGATGC 57.824 47.826 22.92 22.92 44.10 3.91
261 277 3.354467 ACGGCTAGTATAGTAGGCATCC 58.646 50.000 30.13 16.28 44.04 3.51
315 331 5.104652 GGTCCTCTGCCCAAGTAAGTAATAA 60.105 44.000 0.00 0.00 0.00 1.40
316 332 4.407945 GGTCCTCTGCCCAAGTAAGTAATA 59.592 45.833 0.00 0.00 0.00 0.98
317 333 3.200165 GGTCCTCTGCCCAAGTAAGTAAT 59.800 47.826 0.00 0.00 0.00 1.89
348 364 5.294799 TCGTATTAATTGGACATTTGGACGG 59.705 40.000 0.00 0.00 0.00 4.79
397 413 8.221100 CGCATTGCACGTAGATTAATTTACTAT 58.779 33.333 9.69 0.80 0.00 2.12
400 416 6.189567 ACGCATTGCACGTAGATTAATTTAC 58.810 36.000 9.69 6.15 43.02 2.01
401 417 6.352682 ACGCATTGCACGTAGATTAATTTA 57.647 33.333 9.69 0.00 43.02 1.40
422 438 2.579787 GTCAGACGGCCATCGACG 60.580 66.667 2.24 0.00 42.43 5.12
433 449 2.420372 TCTACACGCAGATGAGTCAGAC 59.580 50.000 0.00 0.00 0.00 3.51
471 491 4.574013 TGTTTTAACCGCTTTCCTTCGTTA 59.426 37.500 0.00 0.00 0.00 3.18
472 492 3.377798 TGTTTTAACCGCTTTCCTTCGTT 59.622 39.130 0.00 0.00 0.00 3.85
473 493 2.944349 TGTTTTAACCGCTTTCCTTCGT 59.056 40.909 0.00 0.00 0.00 3.85
500 520 2.644992 CCGTCCAAAGCCAACAGC 59.355 61.111 0.00 0.00 44.25 4.40
501 521 2.268076 CCCCGTCCAAAGCCAACAG 61.268 63.158 0.00 0.00 0.00 3.16
505 531 2.493273 GAATCCCCCGTCCAAAGCCA 62.493 60.000 0.00 0.00 0.00 4.75
508 534 1.004277 TGAAGAATCCCCCGTCCAAAG 59.996 52.381 0.00 0.00 0.00 2.77
575 601 3.186047 CGGCTTTCCCTACGTGCG 61.186 66.667 0.00 0.00 0.00 5.34
702 738 1.129058 AACTGTTCCTTCCACCGTCT 58.871 50.000 0.00 0.00 0.00 4.18
739 775 4.293648 GGGGTGGGCAACGCAAAC 62.294 66.667 11.54 0.00 43.40 2.93
808 858 1.226311 GGGAGGAGTTGGATGGGAAT 58.774 55.000 0.00 0.00 0.00 3.01
809 859 0.919289 GGGGAGGAGTTGGATGGGAA 60.919 60.000 0.00 0.00 0.00 3.97
967 1037 3.132139 CTCGGAGCGGAAGTCGGA 61.132 66.667 0.00 0.00 39.69 4.55
1101 1185 0.259938 AATCCATGAACAGGGGAGGC 59.740 55.000 5.68 0.00 33.47 4.70
1110 1194 1.933853 CGACGGGAGAAATCCATGAAC 59.066 52.381 0.00 0.00 0.00 3.18
1128 1212 1.386533 GTCGGTTACCTCCATCTCGA 58.613 55.000 0.00 0.00 0.00 4.04
1164 1248 4.467198 ACCGTCATCGAGAAAGGTAATT 57.533 40.909 5.78 0.00 37.64 1.40
1210 1299 2.434185 GCATCGACCCAAGACGCA 60.434 61.111 0.00 0.00 0.00 5.24
1211 1300 2.434185 TGCATCGACCCAAGACGC 60.434 61.111 0.00 0.00 0.00 5.19
1213 1302 2.755929 GACTGCATCGACCCAAGAC 58.244 57.895 0.00 0.00 0.00 3.01
1288 1377 2.124778 GCCTGCAGGGAGAAGAGC 60.125 66.667 33.46 13.09 37.23 4.09
1426 1515 1.008767 GATAAGGGGCGACGTCGAG 60.009 63.158 39.74 14.27 43.02 4.04
1436 1525 3.626924 CTCGCCGGGGATAAGGGG 61.627 72.222 22.85 5.16 41.23 4.79
1479 1568 0.591741 CAGCCGGTCGATCTCGTTAC 60.592 60.000 1.90 0.00 40.80 2.50
1480 1569 1.725665 CAGCCGGTCGATCTCGTTA 59.274 57.895 1.90 0.00 40.80 3.18
1574 1663 3.961480 TCATCGTCATCAGAACAACCT 57.039 42.857 0.00 0.00 0.00 3.50
1582 1671 3.371285 GCCATCATCATCATCGTCATCAG 59.629 47.826 0.00 0.00 0.00 2.90
1587 1676 1.073964 CCGCCATCATCATCATCGTC 58.926 55.000 0.00 0.00 0.00 4.20
1588 1677 0.681175 TCCGCCATCATCATCATCGT 59.319 50.000 0.00 0.00 0.00 3.73
1589 1678 2.019948 ATCCGCCATCATCATCATCG 57.980 50.000 0.00 0.00 0.00 3.84
1590 1679 2.350804 CGAATCCGCCATCATCATCATC 59.649 50.000 0.00 0.00 0.00 2.92
1591 1680 2.289882 ACGAATCCGCCATCATCATCAT 60.290 45.455 0.00 0.00 39.95 2.45
1592 1681 1.070601 ACGAATCCGCCATCATCATCA 59.929 47.619 0.00 0.00 39.95 3.07
1593 1682 1.800805 ACGAATCCGCCATCATCATC 58.199 50.000 0.00 0.00 39.95 2.92
1594 1683 2.146342 GAACGAATCCGCCATCATCAT 58.854 47.619 0.00 0.00 39.95 2.45
1604 1693 4.842139 CTACAAAGGAAGAACGAATCCG 57.158 45.455 0.00 0.00 40.78 4.18
1709 1798 4.779733 ATCTCCCTGACCCGCCGT 62.780 66.667 0.00 0.00 0.00 5.68
2288 2399 2.974794 ACGATCATGGAGGGATCAATCA 59.025 45.455 0.00 0.00 40.93 2.57
2309 2421 5.437060 AGAACAGTAGCAAAAGAGGTGAAA 58.563 37.500 0.00 0.00 0.00 2.69
2325 2437 9.224267 TCAAATTACTAGTCGTAGTAGAACAGT 57.776 33.333 0.00 0.00 41.75 3.55
2343 2461 8.316046 CACGCAAGATTCAAATCATCAAATTAC 58.684 33.333 5.59 0.00 43.62 1.89
2396 2518 4.791163 CGCGGTAACAAAATTCACCTAATG 59.209 41.667 0.00 0.00 0.00 1.90
2454 2576 3.225798 GCAACTGCCCCAACTGCA 61.226 61.111 0.00 0.00 37.17 4.41
2674 2800 3.125316 GGTGATGATCAAAGACGGAACAC 59.875 47.826 0.00 0.00 0.00 3.32
2675 2801 3.244387 TGGTGATGATCAAAGACGGAACA 60.244 43.478 0.00 0.00 0.00 3.18
2715 2841 2.010582 GCGAGGACCTAGCCTGTCTG 62.011 65.000 15.26 0.00 38.73 3.51
2735 2861 4.247380 CTCCATCTCTGGGGCCGC 62.247 72.222 14.01 14.01 43.34 6.53
2736 2862 3.554342 CCTCCATCTCTGGGGCCG 61.554 72.222 0.00 0.00 42.29 6.13
2741 2902 0.460987 GCGTTCACCTCCATCTCTGG 60.461 60.000 0.00 0.00 44.64 3.86
2746 2907 0.321653 AACAGGCGTTCACCTCCATC 60.322 55.000 0.00 0.00 38.26 3.51
2750 2911 0.788391 CGTAAACAGGCGTTCACCTC 59.212 55.000 0.00 0.00 38.26 3.85
2757 2918 1.547372 AGTGTATCCGTAAACAGGCGT 59.453 47.619 0.00 0.00 0.00 5.68
2761 2922 5.165676 TGCAAGTAGTGTATCCGTAAACAG 58.834 41.667 0.00 0.00 0.00 3.16
2809 2978 1.079405 ATAGCGTTCCCGTGTGGTG 60.079 57.895 0.00 0.00 36.15 4.17
2817 2986 0.249197 GTGTACCGGATAGCGTTCCC 60.249 60.000 9.46 0.00 31.61 3.97
2858 3028 1.098050 GATTTCGGATGGCTGTTGCT 58.902 50.000 0.00 0.00 39.59 3.91
2862 3032 3.845781 ATAGTGATTTCGGATGGCTGT 57.154 42.857 0.00 0.00 0.00 4.40
2909 3079 7.547722 TGAGATATGTTGTGTACACGCTAATTT 59.452 33.333 20.61 7.32 40.19 1.82
2910 3080 7.039270 TGAGATATGTTGTGTACACGCTAATT 58.961 34.615 20.61 4.88 40.19 1.40
2911 3081 6.569780 TGAGATATGTTGTGTACACGCTAAT 58.430 36.000 20.61 13.39 40.19 1.73
2912 3082 5.956642 TGAGATATGTTGTGTACACGCTAA 58.043 37.500 20.61 7.30 40.19 3.09
2913 3083 5.570234 TGAGATATGTTGTGTACACGCTA 57.430 39.130 20.61 9.60 40.19 4.26
2914 3084 4.450082 TGAGATATGTTGTGTACACGCT 57.550 40.909 20.61 8.88 40.19 5.07
2916 3086 4.625311 TGCTTGAGATATGTTGTGTACACG 59.375 41.667 20.61 3.21 40.19 4.49
2920 3090 6.313658 GTGACATGCTTGAGATATGTTGTGTA 59.686 38.462 6.60 0.00 35.35 2.90
2924 3094 5.806366 TGTGACATGCTTGAGATATGTTG 57.194 39.130 6.60 0.00 35.35 3.33
2961 3131 9.844790 TTGTATTGATTCTCAAGCTGTAATTTG 57.155 29.630 0.00 0.00 40.05 2.32
2983 3156 7.987750 TGGTATAAGTGCTGAATTTGTTGTA 57.012 32.000 0.00 0.00 0.00 2.41
3064 3238 8.483758 AGACCTACAACTCTAGAAACAAAAAGA 58.516 33.333 0.00 0.00 0.00 2.52
3065 3239 8.664211 AGACCTACAACTCTAGAAACAAAAAG 57.336 34.615 0.00 0.00 0.00 2.27
3068 3256 8.474710 AGTAGACCTACAACTCTAGAAACAAA 57.525 34.615 9.56 0.00 38.48 2.83
3092 3280 7.168972 TGTTTCGCCAAAAATTCAGATACAAAG 59.831 33.333 0.00 0.00 0.00 2.77
3106 3294 5.703592 ACATACATCTACTGTTTCGCCAAAA 59.296 36.000 0.00 0.00 39.39 2.44
3112 3300 8.321005 CACACATAACATACATCTACTGTTTCG 58.679 37.037 0.00 0.00 39.39 3.46
3118 3306 5.748630 CACGCACACATAACATACATCTACT 59.251 40.000 0.00 0.00 0.00 2.57
3119 3307 5.518847 ACACGCACACATAACATACATCTAC 59.481 40.000 0.00 0.00 0.00 2.59
3128 3316 2.695314 TGCACACGCACACATAACA 58.305 47.368 0.00 0.00 45.36 2.41
3138 3326 3.648179 TGAAAACAATTTTGCACACGC 57.352 38.095 0.00 0.00 39.24 5.34
3139 3327 8.765044 AAAATATGAAAACAATTTTGCACACG 57.235 26.923 0.00 0.00 32.68 4.49


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

AutoCloner maintained by Alex Coulton.