Multiple sequence alignment - TraesCS4A01G364200

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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 TraesCS4A01G364200 chr4A 100.000 5482 0 0 1 5482 637741945 637736464 0.000000e+00 10124.0
1 TraesCS4A01G364200 chr4A 80.074 2158 359 46 976 3105 637896818 637894704 0.000000e+00 1537.0
2 TraesCS4A01G364200 chr5D 93.874 4750 171 36 388 5071 534090688 534095383 0.000000e+00 7049.0
3 TraesCS4A01G364200 chr5D 80.705 2156 346 49 976 3105 534027674 534029785 0.000000e+00 1613.0
4 TraesCS4A01G364200 chr5D 92.718 412 27 2 5072 5481 534095635 534096045 4.730000e-165 592.0
5 TraesCS4A01G364200 chr5D 79.811 530 74 19 3485 3987 534030147 534030670 6.750000e-94 355.0
6 TraesCS4A01G364200 chr5D 87.097 310 13 16 1 291 534090025 534090326 5.300000e-85 326.0
7 TraesCS4A01G364200 chr5D 84.887 311 47 0 4160 4470 532550067 532549757 1.150000e-81 315.0
8 TraesCS4A01G364200 chr5D 87.023 131 14 1 3605 3735 532550224 532550097 1.590000e-30 145.0
9 TraesCS4A01G364200 chr5D 100.000 30 0 0 3724 3753 532550096 532550067 7.670000e-04 56.5
10 TraesCS4A01G364200 chr5B 95.399 4390 120 30 1166 5482 674492138 674496518 0.000000e+00 6913.0
11 TraesCS4A01G364200 chr5B 81.234 1929 313 34 975 2890 674337367 674339259 0.000000e+00 1511.0
12 TraesCS4A01G364200 chr5B 82.255 1206 65 52 1 1133 674491006 674492135 0.000000e+00 904.0
13 TraesCS4A01G364200 chr5B 81.783 516 65 19 4270 4782 672268769 672268280 6.610000e-109 405.0
14 TraesCS4A01G364200 chr5B 87.786 131 13 2 3605 3735 672614109 672613982 3.420000e-32 150.0
15 TraesCS4A01G364200 chr5B 100.000 30 0 0 3724 3753 672613981 672613952 7.670000e-04 56.5
16 TraesCS4A01G364200 chrUn 97.403 385 10 0 2601 2985 480256529 480256145 0.000000e+00 656.0
17 TraesCS4A01G364200 chr4D 87.042 355 21 11 340 687 35613303 35613639 1.440000e-100 377.0


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 TraesCS4A01G364200 chr4A 637736464 637741945 5481 True 10124.000000 10124 100.000000 1 5482 1 chr4A.!!$R1 5481
1 TraesCS4A01G364200 chr4A 637894704 637896818 2114 True 1537.000000 1537 80.074000 976 3105 1 chr4A.!!$R2 2129
2 TraesCS4A01G364200 chr5D 534090025 534096045 6020 False 2655.666667 7049 91.229667 1 5481 3 chr5D.!!$F2 5480
3 TraesCS4A01G364200 chr5D 534027674 534030670 2996 False 984.000000 1613 80.258000 976 3987 2 chr5D.!!$F1 3011
4 TraesCS4A01G364200 chr5B 674491006 674496518 5512 False 3908.500000 6913 88.827000 1 5482 2 chr5B.!!$F2 5481
5 TraesCS4A01G364200 chr5B 674337367 674339259 1892 False 1511.000000 1511 81.234000 975 2890 1 chr5B.!!$F1 1915

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
343 380 0.048117 TCTCCTCCTCCTACTCCCCT 59.952 60.0 0.0 0.0 0.00 4.79 F
344 381 0.481128 CTCCTCCTCCTACTCCCCTC 59.519 65.0 0.0 0.0 0.00 4.30 F
2191 2588 0.954452 GGTCCAGTCAACAAAGGCAG 59.046 55.0 0.0 0.0 0.00 4.85 F
2834 3234 1.056660 GACTTCTGGGGTGAGGTCAA 58.943 55.0 0.0 0.0 41.05 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1276 1662 0.865769 GAACACGCACCGAGTTTGAT 59.134 50.000 2.33 0.0 40.27 2.57 R
2197 2594 1.123077 CCATGCCCACTCTGCTACTA 58.877 55.000 0.00 0.0 0.00 1.82 R
3470 3930 2.698274 AGTTCCCAATTTCCGCAGTTTT 59.302 40.909 0.00 0.0 0.00 2.43 R
4537 5021 0.819582 CATCAAATGGTGGGCAGGTC 59.180 55.000 0.00 0.0 0.00 3.85 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
71 76 6.099269 TCCTAATCACCATAGTTACCCTCAAC 59.901 42.308 0.00 0.00 0.00 3.18
82 87 2.361085 ACCCTCAACAATCCCCTACT 57.639 50.000 0.00 0.00 0.00 2.57
83 88 2.644151 ACCCTCAACAATCCCCTACTT 58.356 47.619 0.00 0.00 0.00 2.24
84 89 3.810623 ACCCTCAACAATCCCCTACTTA 58.189 45.455 0.00 0.00 0.00 2.24
85 90 4.380791 ACCCTCAACAATCCCCTACTTAT 58.619 43.478 0.00 0.00 0.00 1.73
86 91 4.794067 ACCCTCAACAATCCCCTACTTATT 59.206 41.667 0.00 0.00 0.00 1.40
87 92 5.255443 ACCCTCAACAATCCCCTACTTATTT 59.745 40.000 0.00 0.00 0.00 1.40
206 238 1.598685 ACGGGCCGTGGTAAAACAG 60.599 57.895 33.71 0.00 39.18 3.16
211 243 1.000394 GGCCGTGGTAAAACAGCAAAT 60.000 47.619 0.00 0.00 36.14 2.32
213 245 3.305471 GGCCGTGGTAAAACAGCAAATAA 60.305 43.478 0.00 0.00 36.14 1.40
314 351 1.907222 ATTTCCTTCCCCGTCCGTCC 61.907 60.000 0.00 0.00 0.00 4.79
333 370 1.541672 CCCCCTCTCTCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
336 373 1.700907 CCCCTCTCTCTCCTCCTCCTA 60.701 61.905 0.00 0.00 0.00 2.94
337 374 1.423921 CCCTCTCTCTCCTCCTCCTAC 59.576 61.905 0.00 0.00 0.00 3.18
338 375 2.418669 CCTCTCTCTCCTCCTCCTACT 58.581 57.143 0.00 0.00 0.00 2.57
339 376 2.372172 CCTCTCTCTCCTCCTCCTACTC 59.628 59.091 0.00 0.00 0.00 2.59
340 377 2.372172 CTCTCTCTCCTCCTCCTACTCC 59.628 59.091 0.00 0.00 0.00 3.85
341 378 1.423921 CTCTCTCCTCCTCCTACTCCC 59.576 61.905 0.00 0.00 0.00 4.30
342 379 0.481128 CTCTCCTCCTCCTACTCCCC 59.519 65.000 0.00 0.00 0.00 4.81
343 380 0.048117 TCTCCTCCTCCTACTCCCCT 59.952 60.000 0.00 0.00 0.00 4.79
344 381 0.481128 CTCCTCCTCCTACTCCCCTC 59.519 65.000 0.00 0.00 0.00 4.30
384 421 4.994471 CAGCACGGCAGCAGGACA 62.994 66.667 0.00 0.00 36.85 4.02
385 422 4.694233 AGCACGGCAGCAGGACAG 62.694 66.667 0.00 0.00 36.85 3.51
400 702 1.386533 GACAGGACAGCATTGATGGG 58.613 55.000 6.88 0.00 0.00 4.00
483 785 1.906333 GCGGATCCTCCTCCTCCTC 60.906 68.421 10.75 0.00 33.30 3.71
493 795 4.779733 TCCTCCTCCACCTCCGCC 62.780 72.222 0.00 0.00 0.00 6.13
682 1002 1.227292 GGAAGGACGGATCTTCGCC 60.227 63.158 0.00 0.00 40.95 5.54
689 1009 3.262686 GGATCTTCGCCGGCGTTC 61.263 66.667 44.16 32.83 40.74 3.95
690 1010 2.202756 GATCTTCGCCGGCGTTCT 60.203 61.111 44.16 28.23 40.74 3.01
691 1011 2.202756 ATCTTCGCCGGCGTTCTC 60.203 61.111 44.16 6.58 40.74 2.87
692 1012 3.718210 ATCTTCGCCGGCGTTCTCC 62.718 63.158 44.16 5.73 40.74 3.71
767 1093 1.338674 TGGGTGTTACCTGCATTCTCG 60.339 52.381 0.00 0.00 38.64 4.04
770 1096 2.093869 GGTGTTACCTGCATTCTCGGTA 60.094 50.000 0.00 0.00 34.73 4.02
778 1104 3.257393 CTGCATTCTCGGTATATCTGCC 58.743 50.000 0.00 0.00 0.00 4.85
848 1196 9.807649 CAAATTCCAGATAAAGATCGGATTTTT 57.192 29.630 10.80 10.80 36.91 1.94
868 1216 2.515901 GGGGGATGATTGGTCCGG 59.484 66.667 0.00 0.00 36.58 5.14
909 1260 4.744136 ACCTACTTTTAGCTGCGTTTTC 57.256 40.909 0.00 0.00 0.00 2.29
963 1318 3.132111 TGTGCTTGAGTAGTTGAGTGTGA 59.868 43.478 0.00 0.00 0.00 3.58
967 1322 4.151335 GCTTGAGTAGTTGAGTGTGACATG 59.849 45.833 0.00 0.00 0.00 3.21
1057 1418 1.628340 TCTTCGGCCTCTTTGATTGGA 59.372 47.619 0.00 0.00 0.00 3.53
1136 1497 3.323403 TCCCAGGGTAAGCAAATGTTTTG 59.677 43.478 5.01 0.00 0.00 2.44
1139 1500 5.227152 CCAGGGTAAGCAAATGTTTTGTAC 58.773 41.667 2.32 0.00 0.00 2.90
1162 1537 3.508845 ATCAAGTGGTTGCTGTAAGGT 57.491 42.857 0.00 0.00 33.23 3.50
1171 1546 6.322712 AGTGGTTGCTGTAAGGTTTGATAAAA 59.677 34.615 0.00 0.00 0.00 1.52
1174 1549 7.870445 TGGTTGCTGTAAGGTTTGATAAAATTC 59.130 33.333 0.00 0.00 0.00 2.17
1276 1662 3.770040 AGCATGCCGAGTACGCCA 61.770 61.111 15.66 0.00 38.29 5.69
1299 1685 4.657824 CTCGGTGCGTGTTCGGGT 62.658 66.667 0.00 0.00 37.56 5.28
1333 1729 2.847327 TCTAGCTGCTCTGTTTGCTT 57.153 45.000 4.91 0.00 37.02 3.91
1335 1731 2.149578 CTAGCTGCTCTGTTTGCTTGT 58.850 47.619 4.91 0.00 37.02 3.16
1353 1749 5.764686 TGCTTGTTTACTGTCATTCTGATGT 59.235 36.000 0.00 0.00 34.77 3.06
1354 1750 6.073058 TGCTTGTTTACTGTCATTCTGATGTC 60.073 38.462 0.00 0.00 34.77 3.06
1461 1858 1.618640 GACGAAGCTTGTGCGAGGAC 61.619 60.000 2.10 0.00 45.42 3.85
1873 2270 3.726517 CGTGCCTTCAGCCCAACG 61.727 66.667 0.00 0.00 42.71 4.10
1944 2341 2.679059 GCTCTGCATCTTCTAAGCCACA 60.679 50.000 0.00 0.00 0.00 4.17
2071 2468 1.199327 GTCAGTCGACCATCGTCAGAA 59.801 52.381 13.01 0.00 41.35 3.02
2191 2588 0.954452 GGTCCAGTCAACAAAGGCAG 59.046 55.000 0.00 0.00 0.00 4.85
2197 2594 3.571401 CCAGTCAACAAAGGCAGAAGATT 59.429 43.478 0.00 0.00 0.00 2.40
2369 2766 3.850098 AAGGCTGGGGTCACAAGCG 62.850 63.158 0.00 0.00 0.00 4.68
2494 2891 3.553922 CGAGAAGATTACCAGATGAGGGC 60.554 52.174 0.00 0.00 0.00 5.19
2500 2897 1.337384 TACCAGATGAGGGCATGCGT 61.337 55.000 12.44 0.26 34.11 5.24
2599 2996 2.096496 GGAGCAATCATCTTTCACCACG 59.904 50.000 0.00 0.00 0.00 4.94
2713 3113 6.149474 CAGTGGAAAAACGGTCAATAGAGAAT 59.851 38.462 0.00 0.00 0.00 2.40
2740 3140 3.375299 ACTCAGTGTCAACTTCAAGCAAC 59.625 43.478 0.00 0.00 32.98 4.17
2834 3234 1.056660 GACTTCTGGGGTGAGGTCAA 58.943 55.000 0.00 0.00 41.05 3.18
3124 3572 3.187022 GCATTGGCTGGAAAACAAATGAC 59.813 43.478 0.00 0.00 36.96 3.06
3191 3640 6.656632 TGGTACATTCTAGAGCAGGATTAG 57.343 41.667 0.00 0.00 0.00 1.73
3194 3643 6.265649 GGTACATTCTAGAGCAGGATTAGTGA 59.734 42.308 0.00 0.00 0.00 3.41
3196 3645 6.578023 ACATTCTAGAGCAGGATTAGTGAAC 58.422 40.000 0.00 0.00 0.00 3.18
3219 3668 6.237901 ACATGGTTAGTTTATCTTGCACTCA 58.762 36.000 0.00 0.00 0.00 3.41
3224 3673 7.230510 TGGTTAGTTTATCTTGCACTCATGTTT 59.769 33.333 0.00 0.00 0.00 2.83
3225 3674 7.538678 GGTTAGTTTATCTTGCACTCATGTTTG 59.461 37.037 0.00 0.00 0.00 2.93
3280 3729 8.936864 GTTGATAGTACAACATAAAGAGCAACT 58.063 33.333 0.00 0.00 46.19 3.16
3302 3751 6.166982 ACTATCTGTGTTGTCCTTTAGAAGC 58.833 40.000 0.00 0.00 0.00 3.86
3305 3754 4.574828 TCTGTGTTGTCCTTTAGAAGCAAC 59.425 41.667 0.00 0.00 39.62 4.17
3310 3759 3.141398 TGTCCTTTAGAAGCAACAGCAG 58.859 45.455 0.00 0.00 0.00 4.24
3313 3762 4.755123 GTCCTTTAGAAGCAACAGCAGTAA 59.245 41.667 0.00 0.00 0.00 2.24
3426 3886 4.878397 AGCTTTGGTATACTGCATTGAGAC 59.122 41.667 2.25 0.00 0.00 3.36
3434 3894 7.069950 TGGTATACTGCATTGAGACTTGATAGT 59.930 37.037 2.25 0.00 37.31 2.12
3435 3895 7.928706 GGTATACTGCATTGAGACTTGATAGTT 59.071 37.037 2.25 0.00 33.84 2.24
3436 3896 9.319143 GTATACTGCATTGAGACTTGATAGTTT 57.681 33.333 0.00 0.00 33.84 2.66
3437 3897 6.492007 ACTGCATTGAGACTTGATAGTTTG 57.508 37.500 0.00 0.00 33.84 2.93
3438 3898 6.233434 ACTGCATTGAGACTTGATAGTTTGA 58.767 36.000 0.00 0.00 33.84 2.69
3439 3899 6.712095 ACTGCATTGAGACTTGATAGTTTGAA 59.288 34.615 0.00 0.00 33.84 2.69
3440 3900 6.902341 TGCATTGAGACTTGATAGTTTGAAC 58.098 36.000 0.00 0.00 33.84 3.18
3463 3923 5.888161 ACTTTGAACACTTGACCTTCTCATT 59.112 36.000 0.00 0.00 0.00 2.57
3466 3926 5.300752 TGAACACTTGACCTTCTCATTCTC 58.699 41.667 0.00 0.00 0.00 2.87
3470 3930 3.326006 ACTTGACCTTCTCATTCTCTGCA 59.674 43.478 0.00 0.00 0.00 4.41
3479 3939 1.536766 TCATTCTCTGCAAAACTGCGG 59.463 47.619 0.00 0.00 42.25 5.69
3753 4226 6.149474 GCAAATGGTGAGTGAGTATACAGTTT 59.851 38.462 5.50 0.00 0.00 2.66
3790 4265 2.836981 AGCACTAGCCACAGATCTTTCT 59.163 45.455 0.00 0.00 43.56 2.52
4058 4542 5.751028 AGATAATGCTTGCTCTTACTTCGAC 59.249 40.000 0.00 0.00 0.00 4.20
4447 4931 3.620821 GCAGAGTTGCTAGAATCCTTGAC 59.379 47.826 0.00 0.00 46.95 3.18
4630 5115 5.163723 CGGTTGTCATGATGCAGAAAATAGT 60.164 40.000 0.00 0.00 0.00 2.12
4677 5163 5.442391 TCCTTACTATGGCCCATTGTTAAC 58.558 41.667 15.89 0.00 32.74 2.01
4710 5196 6.148811 GCTGGTACTGTATGTTGTACAATGTT 59.851 38.462 12.26 2.57 40.34 2.71
4756 5242 6.204882 GTGGTCTGTTCTTTGCAAACTATACT 59.795 38.462 8.05 0.00 0.00 2.12
4836 5322 5.176774 CAGCTGTGTTTATCTCGTGTTGTTA 59.823 40.000 5.25 0.00 0.00 2.41
4924 5412 5.844004 TGTTCTTACAAACCAGTCTCTCTC 58.156 41.667 0.00 0.00 0.00 3.20
5164 5922 3.008813 AGTTCCAGCATCAGAGTCAACAT 59.991 43.478 0.00 0.00 0.00 2.71
5203 5961 3.976490 CTCTACCGGAGCCACCCCA 62.976 68.421 9.46 0.00 35.08 4.96
5360 6118 3.190849 CTGATGCCTCACACGCCG 61.191 66.667 0.00 0.00 0.00 6.46
5463 6239 4.597075 TGGTTCTCTTATAGGCATGCCATA 59.403 41.667 37.18 26.71 38.92 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 8.548880 AACTATGGTGATTAGGAGCTTAAGTA 57.451 34.615 4.02 0.00 0.00 2.24
172 203 7.919724 ACGGCCCGTGTTCAAAATTTGAATT 62.920 40.000 21.97 0.00 41.26 2.17
211 243 8.588789 CGTCACGATTATTGTATGTCTTGTTTA 58.411 33.333 0.00 0.00 0.00 2.01
213 245 6.455113 GCGTCACGATTATTGTATGTCTTGTT 60.455 38.462 0.00 0.00 0.00 2.83
320 357 2.414612 GGAGTAGGAGGAGGAGAGAGA 58.585 57.143 0.00 0.00 0.00 3.10
324 361 0.048117 AGGGGAGTAGGAGGAGGAGA 59.952 60.000 0.00 0.00 0.00 3.71
325 362 0.481128 GAGGGGAGTAGGAGGAGGAG 59.519 65.000 0.00 0.00 0.00 3.69
326 363 1.000041 GGAGGGGAGTAGGAGGAGGA 61.000 65.000 0.00 0.00 0.00 3.71
327 364 1.544703 GGAGGGGAGTAGGAGGAGG 59.455 68.421 0.00 0.00 0.00 4.30
328 365 1.544703 GGGAGGGGAGTAGGAGGAG 59.455 68.421 0.00 0.00 0.00 3.69
333 370 2.615773 GAGGGGGAGGGGAGTAGG 59.384 72.222 0.00 0.00 0.00 3.18
342 379 4.416601 AAGACGGGGGAGGGGGAG 62.417 72.222 0.00 0.00 0.00 4.30
343 380 4.410033 GAAGACGGGGGAGGGGGA 62.410 72.222 0.00 0.00 0.00 4.81
354 391 2.049156 TGCTGCACGAGGAAGACG 60.049 61.111 0.00 0.00 0.00 4.18
382 419 0.682209 GCCCATCAATGCTGTCCTGT 60.682 55.000 0.00 0.00 0.00 4.00
383 420 1.721664 CGCCCATCAATGCTGTCCTG 61.722 60.000 0.00 0.00 0.00 3.86
384 421 1.452651 CGCCCATCAATGCTGTCCT 60.453 57.895 0.00 0.00 0.00 3.85
385 422 3.113745 CGCCCATCAATGCTGTCC 58.886 61.111 0.00 0.00 0.00 4.02
386 423 2.410469 GCGCCCATCAATGCTGTC 59.590 61.111 0.00 0.00 0.00 3.51
476 778 4.779733 GGCGGAGGTGGAGGAGGA 62.780 72.222 0.00 0.00 0.00 3.71
506 808 3.735514 CGATCTTTCTCCTCGTCCCTTTC 60.736 52.174 0.00 0.00 0.00 2.62
507 809 2.166664 CGATCTTTCTCCTCGTCCCTTT 59.833 50.000 0.00 0.00 0.00 3.11
509 811 1.394618 CGATCTTTCTCCTCGTCCCT 58.605 55.000 0.00 0.00 0.00 4.20
510 812 0.249114 GCGATCTTTCTCCTCGTCCC 60.249 60.000 0.00 0.00 34.96 4.46
511 813 0.741915 AGCGATCTTTCTCCTCGTCC 59.258 55.000 0.00 0.00 34.96 4.79
512 814 1.833860 CAGCGATCTTTCTCCTCGTC 58.166 55.000 0.00 0.00 34.96 4.20
513 815 0.179124 GCAGCGATCTTTCTCCTCGT 60.179 55.000 0.00 0.00 34.96 4.18
514 816 0.102120 AGCAGCGATCTTTCTCCTCG 59.898 55.000 0.00 0.00 35.57 4.63
515 817 2.200899 GAAGCAGCGATCTTTCTCCTC 58.799 52.381 0.00 0.00 0.00 3.71
716 1039 3.607370 GAGCGCCGGAAGAAACCCT 62.607 63.158 5.05 0.00 0.00 4.34
767 1093 2.230660 GCAACCCAAGGCAGATATACC 58.769 52.381 0.00 0.00 0.00 2.73
770 1096 0.929244 AGGCAACCCAAGGCAGATAT 59.071 50.000 0.00 0.00 37.17 1.63
909 1260 6.522855 TCGAATAAAAGCAATCACATTTCACG 59.477 34.615 0.00 0.00 0.00 4.35
963 1318 4.575645 CCAAAACCTGCAAATCAAACATGT 59.424 37.500 0.00 0.00 0.00 3.21
967 1322 4.187694 TGTCCAAAACCTGCAAATCAAAC 58.812 39.130 0.00 0.00 0.00 2.93
1057 1418 2.502295 CTTGGACTTCTTGCTCTTGCT 58.498 47.619 0.00 0.00 40.48 3.91
1091 1452 1.375326 GAATATCCCCCGCCTCCAC 59.625 63.158 0.00 0.00 0.00 4.02
1092 1453 2.214216 CGAATATCCCCCGCCTCCA 61.214 63.158 0.00 0.00 0.00 3.86
1116 1477 4.335400 ACAAAACATTTGCTTACCCTGG 57.665 40.909 2.88 0.00 0.00 4.45
1136 1497 2.806244 ACAGCAACCACTTGATTCGTAC 59.194 45.455 0.00 0.00 0.00 3.67
1139 1500 3.120199 CCTTACAGCAACCACTTGATTCG 60.120 47.826 0.00 0.00 0.00 3.34
1171 1546 3.774766 GCCCCTGTTTTTATTCCTGGAAT 59.225 43.478 24.25 24.25 36.20 3.01
1174 1549 2.497273 CAGCCCCTGTTTTTATTCCTGG 59.503 50.000 0.00 0.00 0.00 4.45
1276 1662 0.865769 GAACACGCACCGAGTTTGAT 59.134 50.000 2.33 0.00 40.27 2.57
1314 1704 2.224378 ACAAGCAAACAGAGCAGCTAGA 60.224 45.455 0.00 0.00 36.07 2.43
1315 1705 2.149578 ACAAGCAAACAGAGCAGCTAG 58.850 47.619 0.00 0.00 36.07 3.42
1320 1710 3.694072 ACAGTAAACAAGCAAACAGAGCA 59.306 39.130 0.00 0.00 0.00 4.26
1353 1749 3.419943 TGCCAATATGCACAGTTTGAGA 58.580 40.909 0.00 0.00 36.04 3.27
1354 1750 3.441222 TCTGCCAATATGCACAGTTTGAG 59.559 43.478 0.00 0.00 36.04 3.02
1873 2270 3.895232 TGCTGGACTCTTACAATCTCC 57.105 47.619 0.00 0.00 0.00 3.71
1944 2341 2.169352 CCATCCAACGATCTTCCACTCT 59.831 50.000 0.00 0.00 0.00 3.24
2071 2468 4.646492 CCTTGGCCATTTGTAGCTCTAAAT 59.354 41.667 6.09 0.00 0.00 1.40
2191 2588 3.133003 TGCCCACTCTGCTACTAATCTTC 59.867 47.826 0.00 0.00 0.00 2.87
2197 2594 1.123077 CCATGCCCACTCTGCTACTA 58.877 55.000 0.00 0.00 0.00 1.82
2369 2766 2.736721 TCATAGTGTTTTCAGAGCGTGC 59.263 45.455 0.00 0.00 0.00 5.34
2494 2891 3.060339 GCTGGTTTTTCTTTGAACGCATG 60.060 43.478 0.00 0.00 0.00 4.06
2500 2897 4.221703 TCACTTGGCTGGTTTTTCTTTGAA 59.778 37.500 0.00 0.00 0.00 2.69
2599 2996 6.974622 TCTCAGTGCTGATTTTCTTTTTGTTC 59.025 34.615 2.06 0.00 39.13 3.18
2713 3113 4.214986 TGAAGTTGACACTGAGTTCCAA 57.785 40.909 0.00 0.00 31.60 3.53
2740 3140 6.372381 TGGTATCTGATTCAGTGTTTGATGTG 59.628 38.462 13.23 0.00 35.27 3.21
2834 3234 3.435601 CCATTGGCTGGCTTAGAATAGGT 60.436 47.826 2.00 0.00 38.47 3.08
3022 3422 4.775236 AGGAAGAGTGGTATCTCAAATGC 58.225 43.478 0.00 0.00 36.97 3.56
3124 3572 6.420913 ACTATGCCTAACTAGGTAACATGG 57.579 41.667 11.52 11.02 45.42 3.66
3191 3640 6.801862 GTGCAAGATAAACTAACCATGTTCAC 59.198 38.462 0.00 0.00 0.00 3.18
3194 3643 6.714810 TGAGTGCAAGATAAACTAACCATGTT 59.285 34.615 0.00 0.00 0.00 2.71
3196 3645 6.741992 TGAGTGCAAGATAAACTAACCATG 57.258 37.500 0.00 0.00 0.00 3.66
3219 3668 7.111247 TCAGGTTTTCACAATCTTCAAACAT 57.889 32.000 0.00 0.00 0.00 2.71
3224 3673 6.713762 ACATTCAGGTTTTCACAATCTTCA 57.286 33.333 0.00 0.00 0.00 3.02
3225 3674 7.202526 TGAACATTCAGGTTTTCACAATCTTC 58.797 34.615 0.00 0.00 32.50 2.87
3260 3709 8.314751 ACAGATAGTTGCTCTTTATGTTGTACT 58.685 33.333 0.00 0.00 28.28 2.73
3277 3726 6.651225 GCTTCTAAAGGACAACACAGATAGTT 59.349 38.462 0.00 0.00 0.00 2.24
3280 3729 6.109156 TGCTTCTAAAGGACAACACAGATA 57.891 37.500 0.00 0.00 0.00 1.98
3302 3751 5.163622 CCCCAATATCAGTTTACTGCTGTTG 60.164 44.000 13.10 13.10 43.46 3.33
3305 3754 4.526970 ACCCCAATATCAGTTTACTGCTG 58.473 43.478 5.00 0.00 43.46 4.41
3310 3759 7.554835 TCATGTACAACCCCAATATCAGTTTAC 59.445 37.037 0.00 0.00 0.00 2.01
3313 3762 6.073447 TCATGTACAACCCCAATATCAGTT 57.927 37.500 0.00 0.00 0.00 3.16
3426 3886 9.013490 CAAGTGTTCAAAGTTCAAACTATCAAG 57.987 33.333 0.00 0.00 38.57 3.02
3434 3894 5.975693 AGGTCAAGTGTTCAAAGTTCAAA 57.024 34.783 0.00 0.00 0.00 2.69
3435 3895 5.710099 AGAAGGTCAAGTGTTCAAAGTTCAA 59.290 36.000 0.00 0.00 0.00 2.69
3436 3896 5.253330 AGAAGGTCAAGTGTTCAAAGTTCA 58.747 37.500 0.00 0.00 0.00 3.18
3437 3897 5.354234 TGAGAAGGTCAAGTGTTCAAAGTTC 59.646 40.000 0.00 0.00 29.64 3.01
3438 3898 5.253330 TGAGAAGGTCAAGTGTTCAAAGTT 58.747 37.500 0.00 0.00 29.64 2.66
3439 3899 4.843728 TGAGAAGGTCAAGTGTTCAAAGT 58.156 39.130 0.00 0.00 29.64 2.66
3440 3900 6.261826 AGAATGAGAAGGTCAAGTGTTCAAAG 59.738 38.462 0.00 0.00 39.19 2.77
3470 3930 2.698274 AGTTCCCAATTTCCGCAGTTTT 59.302 40.909 0.00 0.00 0.00 2.43
3479 3939 3.572255 TGGCACAGTTAGTTCCCAATTTC 59.428 43.478 0.00 0.00 31.87 2.17
3575 4040 2.991250 TGACTGGCCATAAAGAGAAGC 58.009 47.619 5.51 0.00 0.00 3.86
3576 4041 5.033589 AGATGACTGGCCATAAAGAGAAG 57.966 43.478 5.51 0.00 0.00 2.85
3790 4265 8.491045 AAAGGGAGAAATATTGAAGGTTTTGA 57.509 30.769 0.00 0.00 0.00 2.69
4029 4513 7.065120 AGTAAGAGCAAGCATTATCTCTGAT 57.935 36.000 0.00 0.00 37.31 2.90
4447 4931 2.549633 GTCAGCAACCATTTCATCGG 57.450 50.000 0.00 0.00 0.00 4.18
4537 5021 0.819582 CATCAAATGGTGGGCAGGTC 59.180 55.000 0.00 0.00 0.00 3.85
4602 5086 3.346315 TCTGCATCATGACAACCGAAAT 58.654 40.909 0.00 0.00 0.00 2.17
4677 5163 6.312918 ACAACATACAGTACCAGCTATTTTCG 59.687 38.462 0.00 0.00 0.00 3.46
4710 5196 5.163530 CCACCATTCATACAGCTAAAATGCA 60.164 40.000 0.00 0.00 34.99 3.96
4756 5242 5.483811 TCAGACGACAAATAATTACCAGCA 58.516 37.500 0.00 0.00 0.00 4.41
4836 5322 2.910319 TGCAGTACCAGTTACCTCCATT 59.090 45.455 0.00 0.00 0.00 3.16
4867 5353 7.176515 TCCATACAGCTACAAAATGTCACATTT 59.823 33.333 10.14 10.14 0.00 2.32
4924 5412 6.421801 TCAGATCATGATAAATACAGCACACG 59.578 38.462 8.54 0.00 31.12 4.49
5143 5901 2.771089 TGTTGACTCTGATGCTGGAAC 58.229 47.619 0.00 0.00 0.00 3.62
5164 5922 4.604156 AGGATATAGGAGATGATGCGTCA 58.396 43.478 11.83 11.83 39.04 4.35
5360 6118 4.366586 TGCGAGAGATCAAGATCAACATC 58.633 43.478 12.21 1.65 40.22 3.06
5463 6239 2.046285 GGCCTTGCAGCCGTAACAT 61.046 57.895 0.59 0.00 44.57 2.71


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

AutoCloner maintained by Alex Coulton.