Multiple sequence alignment - TraesCS1B01G157700

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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 TraesCS1B01G157700 chr1B 100.000 4262 0 0 1 4262 267971940 267967679 0 7871
1 TraesCS1B01G157700 chr1A 93.398 4317 151 56 4 4262 239106252 239102012 0 6270
2 TraesCS1B01G157700 chr1D 91.923 3479 152 36 2 3431 193364215 193360817 0 4748
3 TraesCS1B01G157700 chr1D 97.689 779 17 1 3484 4262 193360819 193360042 0 1338


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 TraesCS1B01G157700 chr1B 267967679 267971940 4261 True 7871 7871 100.000 1 4262 1 chr1B.!!$R1 4261
1 TraesCS1B01G157700 chr1A 239102012 239106252 4240 True 6270 6270 93.398 4 4262 1 chr1A.!!$R1 4258
2 TraesCS1B01G157700 chr1D 193360042 193364215 4173 True 3043 4748 94.806 2 4262 2 chr1D.!!$R1 4260


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
250 264 0.029567 CACCATACTCGTCTCGCCTC 59.970 60.0 0.0 0.0 0.0 4.70 F
1293 1334 0.036388 TCCGCATCTTCACCTTCCAC 60.036 55.0 0.0 0.0 0.0 4.02 F
2161 2212 0.179121 CGGTATGTAACGAGCAGCCA 60.179 55.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 1570 0.034059 GGTTGATGATCGGATCGCCT 59.966 55.000 12.99 0.84 0.00 5.52 R
2202 2260 0.748450 ATTGCGCCATGGAATTGAGG 59.252 50.000 18.40 0.00 34.61 3.86 R
4038 4127 3.334583 TCCGGAGCATGCTATATTTCC 57.665 47.619 22.74 15.62 0.00 3.13 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
128 140 9.716507 TTTCTTCTTTTGAACTTTGATTACTCG 57.283 29.630 0.00 0.00 34.31 4.18
234 248 1.228552 AACACCTGCACCCATCACC 60.229 57.895 0.00 0.00 0.00 4.02
235 249 2.005606 AACACCTGCACCCATCACCA 62.006 55.000 0.00 0.00 0.00 4.17
236 250 1.000521 CACCTGCACCCATCACCAT 60.001 57.895 0.00 0.00 0.00 3.55
237 251 0.255604 CACCTGCACCCATCACCATA 59.744 55.000 0.00 0.00 0.00 2.74
238 252 0.255890 ACCTGCACCCATCACCATAC 59.744 55.000 0.00 0.00 0.00 2.39
239 253 0.548031 CCTGCACCCATCACCATACT 59.452 55.000 0.00 0.00 0.00 2.12
240 254 1.475751 CCTGCACCCATCACCATACTC 60.476 57.143 0.00 0.00 0.00 2.59
241 255 0.177836 TGCACCCATCACCATACTCG 59.822 55.000 0.00 0.00 0.00 4.18
242 256 0.178068 GCACCCATCACCATACTCGT 59.822 55.000 0.00 0.00 0.00 4.18
243 257 1.806623 GCACCCATCACCATACTCGTC 60.807 57.143 0.00 0.00 0.00 4.20
244 258 1.757118 CACCCATCACCATACTCGTCT 59.243 52.381 0.00 0.00 0.00 4.18
245 259 2.032620 ACCCATCACCATACTCGTCTC 58.967 52.381 0.00 0.00 0.00 3.36
246 260 1.001268 CCCATCACCATACTCGTCTCG 60.001 57.143 0.00 0.00 0.00 4.04
247 261 1.600663 CCATCACCATACTCGTCTCGC 60.601 57.143 0.00 0.00 0.00 5.03
248 262 0.669077 ATCACCATACTCGTCTCGCC 59.331 55.000 0.00 0.00 0.00 5.54
249 263 0.393944 TCACCATACTCGTCTCGCCT 60.394 55.000 0.00 0.00 0.00 5.52
250 264 0.029567 CACCATACTCGTCTCGCCTC 59.970 60.000 0.00 0.00 0.00 4.70
251 265 0.107116 ACCATACTCGTCTCGCCTCT 60.107 55.000 0.00 0.00 0.00 3.69
252 266 0.589223 CCATACTCGTCTCGCCTCTC 59.411 60.000 0.00 0.00 0.00 3.20
253 267 0.233590 CATACTCGTCTCGCCTCTCG 59.766 60.000 0.00 0.00 40.15 4.04
254 268 1.500512 ATACTCGTCTCGCCTCTCGC 61.501 60.000 0.00 0.00 38.27 5.03
255 269 4.244802 CTCGTCTCGCCTCTCGCC 62.245 72.222 0.00 0.00 38.27 5.54
376 399 1.825191 CCGGCCATCCATTGACCTG 60.825 63.158 2.24 0.00 0.00 4.00
384 407 4.384056 CCATCCATTGACCTGCTAACTAG 58.616 47.826 0.00 0.00 0.00 2.57
477 503 0.322906 GGCTCAGCTAGGTGGCTTTT 60.323 55.000 24.72 0.00 41.00 2.27
503 529 3.119096 GAGCAGGAAACGACCCGC 61.119 66.667 0.00 0.00 0.00 6.13
520 546 1.743252 GCCCCGTGAAGAGAGCTTG 60.743 63.158 0.00 0.00 33.61 4.01
537 568 5.036117 AGCTTGGTGTCTTTCAACTTCTA 57.964 39.130 0.00 0.00 34.34 2.10
547 578 5.048013 GTCTTTCAACTTCTATTGGGTTGGG 60.048 44.000 0.00 0.00 40.20 4.12
559 590 0.756294 GGGTTGGGTTTGGACTTTGG 59.244 55.000 0.00 0.00 0.00 3.28
564 595 2.661718 TGGGTTTGGACTTTGGAGAAC 58.338 47.619 0.00 0.00 0.00 3.01
565 596 2.024846 TGGGTTTGGACTTTGGAGAACA 60.025 45.455 0.00 0.00 0.00 3.18
566 597 3.028130 GGGTTTGGACTTTGGAGAACAA 58.972 45.455 0.00 0.00 37.28 2.83
575 606 1.593196 TTGGAGAACAAGGTTGAGCG 58.407 50.000 0.00 0.00 33.18 5.03
754 787 7.613022 AGGATCTCATCTTATTTGAAAAGTGCA 59.387 33.333 0.00 0.00 0.00 4.57
755 788 8.411683 GGATCTCATCTTATTTGAAAAGTGCAT 58.588 33.333 0.00 0.00 0.00 3.96
759 792 9.674824 CTCATCTTATTTGAAAAGTGCATATCC 57.325 33.333 0.00 0.00 0.00 2.59
772 805 3.448660 GTGCATATCCCTTTTGCCTCTTT 59.551 43.478 0.00 0.00 35.51 2.52
801 834 7.914427 ACCCCTTTAGTTTTCTTCTTTTGAT 57.086 32.000 0.00 0.00 0.00 2.57
814 847 5.363580 TCTTCTTTTGATGCCTTCAAGGTTT 59.636 36.000 5.03 0.00 44.90 3.27
815 848 5.200368 TCTTTTGATGCCTTCAAGGTTTC 57.800 39.130 5.03 3.10 44.90 2.78
816 849 3.641437 TTTGATGCCTTCAAGGTTTCG 57.359 42.857 5.03 0.00 44.90 3.46
817 850 0.881118 TGATGCCTTCAAGGTTTCGC 59.119 50.000 5.03 0.00 37.80 4.70
818 851 1.168714 GATGCCTTCAAGGTTTCGCT 58.831 50.000 5.03 0.00 37.80 4.93
819 852 1.131315 GATGCCTTCAAGGTTTCGCTC 59.869 52.381 5.03 0.00 37.80 5.03
820 853 0.108585 TGCCTTCAAGGTTTCGCTCT 59.891 50.000 5.03 0.00 37.80 4.09
821 854 0.799393 GCCTTCAAGGTTTCGCTCTC 59.201 55.000 5.03 0.00 37.80 3.20
822 855 1.609320 GCCTTCAAGGTTTCGCTCTCT 60.609 52.381 5.03 0.00 37.80 3.10
823 856 2.342179 CCTTCAAGGTTTCGCTCTCTC 58.658 52.381 0.00 0.00 0.00 3.20
824 857 2.028567 CCTTCAAGGTTTCGCTCTCTCT 60.029 50.000 0.00 0.00 0.00 3.10
825 858 3.249917 CTTCAAGGTTTCGCTCTCTCTC 58.750 50.000 0.00 0.00 0.00 3.20
826 859 2.520069 TCAAGGTTTCGCTCTCTCTCT 58.480 47.619 0.00 0.00 0.00 3.10
827 860 2.490115 TCAAGGTTTCGCTCTCTCTCTC 59.510 50.000 0.00 0.00 0.00 3.20
828 861 2.491693 CAAGGTTTCGCTCTCTCTCTCT 59.508 50.000 0.00 0.00 0.00 3.10
829 862 2.365582 AGGTTTCGCTCTCTCTCTCTC 58.634 52.381 0.00 0.00 0.00 3.20
830 863 2.026262 AGGTTTCGCTCTCTCTCTCTCT 60.026 50.000 0.00 0.00 0.00 3.10
831 864 2.354821 GGTTTCGCTCTCTCTCTCTCTC 59.645 54.545 0.00 0.00 0.00 3.20
832 865 3.270877 GTTTCGCTCTCTCTCTCTCTCT 58.729 50.000 0.00 0.00 0.00 3.10
833 866 2.890808 TCGCTCTCTCTCTCTCTCTC 57.109 55.000 0.00 0.00 0.00 3.20
834 867 2.388735 TCGCTCTCTCTCTCTCTCTCT 58.611 52.381 0.00 0.00 0.00 3.10
835 868 2.362397 TCGCTCTCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
836 869 2.363680 CGCTCTCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
837 870 3.551863 CGCTCTCTCTCTCTCTCTCTCTC 60.552 56.522 0.00 0.00 0.00 3.20
848 881 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
874 910 5.191722 TCCTTCTGGTTGTAGAATAATGGCT 59.808 40.000 0.00 0.00 36.21 4.75
875 911 5.529060 CCTTCTGGTTGTAGAATAATGGCTC 59.471 44.000 0.00 0.00 36.21 4.70
876 912 5.957771 TCTGGTTGTAGAATAATGGCTCT 57.042 39.130 0.00 0.00 0.00 4.09
877 913 6.313519 TCTGGTTGTAGAATAATGGCTCTT 57.686 37.500 0.00 0.00 0.00 2.85
878 914 6.721318 TCTGGTTGTAGAATAATGGCTCTTT 58.279 36.000 0.00 0.00 0.00 2.52
879 915 7.175104 TCTGGTTGTAGAATAATGGCTCTTTT 58.825 34.615 0.00 0.00 0.00 2.27
880 916 7.336931 TCTGGTTGTAGAATAATGGCTCTTTTC 59.663 37.037 0.00 0.00 0.00 2.29
881 917 6.377146 TGGTTGTAGAATAATGGCTCTTTTCC 59.623 38.462 0.00 0.00 0.00 3.13
956 992 0.673644 GAGAGCTTGCCTTTACCGCA 60.674 55.000 0.00 0.00 0.00 5.69
1030 1068 0.548031 TTATTGCAGAGCAGGAGGGG 59.452 55.000 0.00 0.00 40.61 4.79
1031 1069 1.348008 TATTGCAGAGCAGGAGGGGG 61.348 60.000 0.00 0.00 40.61 5.40
1106 1147 3.478274 GGAGGAGGAGCTGCAGGG 61.478 72.222 17.12 0.00 0.00 4.45
1157 1198 2.202797 CAGCATCTCCACGGACCG 60.203 66.667 13.61 13.61 0.00 4.79
1237 1278 2.283388 AGTCCTTCGGCCGGTACA 60.283 61.111 27.83 1.61 0.00 2.90
1293 1334 0.036388 TCCGCATCTTCACCTTCCAC 60.036 55.000 0.00 0.00 0.00 4.02
1332 1373 1.963338 GAGCTTCAGCCGTGCACTT 60.963 57.895 16.19 0.00 43.38 3.16
1341 1382 0.810031 GCCGTGCACTTATGATCGGT 60.810 55.000 16.19 0.00 42.01 4.69
1460 1501 2.290577 GCCTCCAGGTGACATTCTCTTT 60.291 50.000 0.00 0.00 37.57 2.52
1497 1538 2.046892 CCAGCTCCACCCAACTCG 60.047 66.667 0.00 0.00 0.00 4.18
1523 1564 3.430042 AACATGGTGTCAGAGCTCATT 57.570 42.857 17.77 0.00 0.00 2.57
1529 1570 2.093288 GGTGTCAGAGCTCATTCATGGA 60.093 50.000 17.77 0.00 0.00 3.41
1532 1573 1.140452 TCAGAGCTCATTCATGGAGGC 59.860 52.381 17.77 0.00 32.96 4.70
1545 1586 1.967535 GGAGGCGATCCGATCATCA 59.032 57.895 9.07 0.00 38.67 3.07
1561 1602 1.130373 CATCAACCCGAACAACCATCG 59.870 52.381 0.00 0.00 39.92 3.84
1577 1618 2.420642 CATCGGTAATCTGGATGGCTG 58.579 52.381 0.00 0.00 35.15 4.85
1581 1622 2.613977 CGGTAATCTGGATGGCTGGATC 60.614 54.545 0.00 0.00 0.00 3.36
1620 1661 2.292267 CTTTGATTCGTCATCCAGGGG 58.708 52.381 0.00 0.00 0.00 4.79
1869 1910 2.673368 CAAGTACCTGCACGAAGATTCC 59.327 50.000 0.00 0.00 0.00 3.01
1885 1926 5.104259 AGATTCCGAATTCAAGGTAAGCT 57.896 39.130 6.22 2.37 0.00 3.74
1994 2044 4.229582 TGCCTTTTACCCAGTCCTGATATT 59.770 41.667 0.00 0.00 0.00 1.28
1995 2045 4.580580 GCCTTTTACCCAGTCCTGATATTG 59.419 45.833 0.00 0.00 0.00 1.90
2000 2050 2.171448 ACCCAGTCCTGATATTGTCTGC 59.829 50.000 0.00 0.00 0.00 4.26
2012 2063 7.065923 CCTGATATTGTCTGCCATCTATGAATG 59.934 40.741 0.00 0.00 0.00 2.67
2014 2065 8.596293 TGATATTGTCTGCCATCTATGAATGTA 58.404 33.333 0.00 0.00 0.00 2.29
2080 2131 2.426183 CGACGAGAACTGGAACGCG 61.426 63.158 3.53 3.53 35.67 6.01
2161 2212 0.179121 CGGTATGTAACGAGCAGCCA 60.179 55.000 0.00 0.00 0.00 4.75
2162 2213 1.737696 CGGTATGTAACGAGCAGCCAA 60.738 52.381 0.00 0.00 0.00 4.52
2163 2214 2.352388 GGTATGTAACGAGCAGCCAAA 58.648 47.619 0.00 0.00 0.00 3.28
2202 2260 1.590932 CAGCACCTGATGGCACTATC 58.409 55.000 0.00 0.00 36.63 2.08
2247 2305 8.367156 TGCTGACATATTGAATAGCATACTGTA 58.633 33.333 0.00 0.00 36.37 2.74
2257 2315 9.719355 TTGAATAGCATACTGTAACTTTCAGAA 57.281 29.630 2.65 0.00 36.81 3.02
2288 2348 4.009675 GCAAGTTCACCCAAGTATGATCA 58.990 43.478 0.00 0.00 0.00 2.92
2303 2363 9.121658 CAAGTATGATCAGTTCAGTAGGTACTA 57.878 37.037 0.09 0.00 37.62 1.82
2367 2427 4.086457 ACTTGTCAGACAAACCCAAAACT 58.914 39.130 16.85 0.00 37.69 2.66
2482 2555 4.371855 TCCTAGATACACAAGCAGAACG 57.628 45.455 0.00 0.00 0.00 3.95
2487 2560 2.163818 TACACAAGCAGAACGAAGGG 57.836 50.000 0.00 0.00 0.00 3.95
2539 2612 0.898326 TGCTAGTGCAGGAAGACCGA 60.898 55.000 0.00 0.00 45.31 4.69
2556 2629 2.103263 ACCGATTAGGAAAGCCAGCTAG 59.897 50.000 0.00 0.00 45.00 3.42
2572 2645 0.962356 CTAGCCCTGCTGGTTGGTTG 60.962 60.000 9.00 0.00 40.10 3.77
2610 2686 4.922206 TCTGGCTGATTTCCAATTGTAGT 58.078 39.130 4.43 0.00 32.41 2.73
2639 2715 9.949174 TTTATCACATGTGATGATAAATTTCCG 57.051 29.630 39.40 6.93 46.58 4.30
2658 2734 3.442977 TCCGAGTAAAAGTAGCCTCTGTC 59.557 47.826 0.00 0.00 0.00 3.51
2661 2737 4.082679 CGAGTAAAAGTAGCCTCTGTCTGT 60.083 45.833 0.00 0.00 0.00 3.41
2663 2739 6.270156 AGTAAAAGTAGCCTCTGTCTGTAC 57.730 41.667 0.00 0.00 0.00 2.90
2664 2740 5.773680 AGTAAAAGTAGCCTCTGTCTGTACA 59.226 40.000 0.00 0.00 0.00 2.90
2781 2862 4.439426 GCAGCTCCTGAGTATATCCATACG 60.439 50.000 0.00 0.00 36.12 3.06
2823 2904 6.956435 AGAATGACATATGGAGCTATGGAGTA 59.044 38.462 7.80 0.00 34.11 2.59
2972 3053 1.640917 AGGCTCGAAGGGAACTACAA 58.359 50.000 0.00 0.00 42.68 2.41
3123 3204 2.053244 CCAGAGCATCCCCTGATAAGT 58.947 52.381 0.00 0.00 33.66 2.24
3318 3399 6.182627 ACTTTGACATCCAGAGATATTTGCA 58.817 36.000 0.00 0.00 31.89 4.08
3400 3481 9.994432 GAACATGATAACTAAAAACAGGAGATG 57.006 33.333 0.00 0.00 0.00 2.90
3411 3499 1.030488 CAGGAGATGTGGCAAGCCTG 61.030 60.000 12.96 0.00 37.21 4.85
3477 3565 4.368391 CACAGGCAGTGTCCACTC 57.632 61.111 1.31 0.00 43.40 3.51
3538 3626 5.360714 TGGAAAATCAAAACTGAAGCAGTCT 59.639 36.000 0.00 0.00 44.62 3.24
3582 3670 6.773200 TGGTGTACAGTTTAACATGGAATTCA 59.227 34.615 7.93 0.00 0.00 2.57
3803 3891 9.592196 AGAATTTGCCTGTGTATATCCATAAAT 57.408 29.630 0.00 0.00 0.00 1.40
3951 4040 4.703897 TGCTAACTGCTCTTTGTGTACTT 58.296 39.130 0.00 0.00 43.37 2.24
4038 4127 7.116805 TCACTATTCATAGCACAAATCGCATAG 59.883 37.037 0.00 0.00 33.68 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.888326 ACAGATCTCTCAGAAAGCAACT 57.112 40.909 0.00 0.00 0.00 3.16
63 64 0.934496 CGTATGGTTGCCGTACATGG 59.066 55.000 15.32 0.00 43.93 3.66
128 140 5.241506 GGGTTGTGGGGTAGTAAAACTTAAC 59.758 44.000 0.00 0.00 0.00 2.01
131 143 3.464456 AGGGTTGTGGGGTAGTAAAACTT 59.536 43.478 0.00 0.00 0.00 2.66
234 248 0.233590 CGAGAGGCGAGACGAGTATG 59.766 60.000 0.00 0.00 44.57 2.39
235 249 1.500512 GCGAGAGGCGAGACGAGTAT 61.501 60.000 0.00 0.00 44.57 2.12
236 250 2.172372 GCGAGAGGCGAGACGAGTA 61.172 63.158 0.00 0.00 44.57 2.59
237 251 3.501548 GCGAGAGGCGAGACGAGT 61.502 66.667 0.00 0.00 44.57 4.18
247 261 1.452108 GGGTTTGGATGGCGAGAGG 60.452 63.158 0.00 0.00 0.00 3.69
248 262 0.462759 GAGGGTTTGGATGGCGAGAG 60.463 60.000 0.00 0.00 0.00 3.20
249 263 1.198094 TGAGGGTTTGGATGGCGAGA 61.198 55.000 0.00 0.00 0.00 4.04
250 264 1.026718 GTGAGGGTTTGGATGGCGAG 61.027 60.000 0.00 0.00 0.00 5.03
251 265 1.002624 GTGAGGGTTTGGATGGCGA 60.003 57.895 0.00 0.00 0.00 5.54
252 266 2.398554 CGTGAGGGTTTGGATGGCG 61.399 63.158 0.00 0.00 0.00 5.69
253 267 0.893727 AACGTGAGGGTTTGGATGGC 60.894 55.000 0.00 0.00 0.00 4.40
254 268 1.539827 GAAACGTGAGGGTTTGGATGG 59.460 52.381 0.00 0.00 40.05 3.51
255 269 2.484264 GAGAAACGTGAGGGTTTGGATG 59.516 50.000 0.00 0.00 40.05 3.51
318 341 1.781025 TTTCTGCTTGGTTGGTCGCG 61.781 55.000 0.00 0.00 0.00 5.87
376 399 3.820557 TGGATTGGATTGCCTAGTTAGC 58.179 45.455 0.00 0.00 34.31 3.09
384 407 1.069049 CGGGATTTGGATTGGATTGCC 59.931 52.381 0.00 0.00 0.00 4.52
477 503 2.459969 TTTCCTGCTCACCTGGGCA 61.460 57.895 0.00 0.00 36.94 5.36
503 529 1.078848 CCAAGCTCTCTTCACGGGG 60.079 63.158 0.00 0.00 0.00 5.73
520 546 5.070685 ACCCAATAGAAGTTGAAAGACACC 58.929 41.667 0.00 0.00 0.00 4.16
537 568 2.437651 CAAAGTCCAAACCCAACCCAAT 59.562 45.455 0.00 0.00 0.00 3.16
547 578 3.699538 ACCTTGTTCTCCAAAGTCCAAAC 59.300 43.478 0.00 0.00 31.20 2.93
559 590 1.264288 CAACCGCTCAACCTTGTTCTC 59.736 52.381 0.00 0.00 0.00 2.87
564 595 0.030638 CAACCAACCGCTCAACCTTG 59.969 55.000 0.00 0.00 0.00 3.61
565 596 1.106944 CCAACCAACCGCTCAACCTT 61.107 55.000 0.00 0.00 0.00 3.50
566 597 1.528309 CCAACCAACCGCTCAACCT 60.528 57.895 0.00 0.00 0.00 3.50
575 606 0.101579 CAACAACCGACCAACCAACC 59.898 55.000 0.00 0.00 0.00 3.77
754 787 6.295859 GGTTTCAAAAGAGGCAAAAGGGATAT 60.296 38.462 0.00 0.00 0.00 1.63
755 788 5.011635 GGTTTCAAAAGAGGCAAAAGGGATA 59.988 40.000 0.00 0.00 0.00 2.59
759 792 3.466836 GGGTTTCAAAAGAGGCAAAAGG 58.533 45.455 0.00 0.00 0.00 3.11
772 805 7.727578 AAGAAGAAAACTAAAGGGGTTTCAA 57.272 32.000 7.56 0.00 36.09 2.69
801 834 0.108585 AGAGCGAAACCTTGAAGGCA 59.891 50.000 11.96 0.00 39.63 4.75
814 847 2.362397 GAGAGAGAGAGAGAGAGAGCGA 59.638 54.545 0.00 0.00 0.00 4.93
815 848 2.363680 AGAGAGAGAGAGAGAGAGAGCG 59.636 54.545 0.00 0.00 0.00 5.03
816 849 3.640967 AGAGAGAGAGAGAGAGAGAGAGC 59.359 52.174 0.00 0.00 0.00 4.09
817 850 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
818 851 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
819 852 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
820 853 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
821 854 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
822 855 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
823 856 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
824 857 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
825 858 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
826 859 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
827 860 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
828 861 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
829 862 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
830 863 4.078922 AGGAGAGAGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
831 864 4.222336 AGGAGAGAGAGAGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
832 865 4.271807 AGGAGAGAGAGAGAGAGAGAGA 57.728 50.000 0.00 0.00 0.00 3.10
833 866 4.653341 AGAAGGAGAGAGAGAGAGAGAGAG 59.347 50.000 0.00 0.00 0.00 3.20
834 867 4.406972 CAGAAGGAGAGAGAGAGAGAGAGA 59.593 50.000 0.00 0.00 0.00 3.10
835 868 4.444022 CCAGAAGGAGAGAGAGAGAGAGAG 60.444 54.167 0.00 0.00 36.89 3.20
836 869 3.455910 CCAGAAGGAGAGAGAGAGAGAGA 59.544 52.174 0.00 0.00 36.89 3.10
837 870 3.200825 ACCAGAAGGAGAGAGAGAGAGAG 59.799 52.174 0.00 0.00 38.69 3.20
848 881 6.632672 GCCATTATTCTACAACCAGAAGGAGA 60.633 42.308 0.00 0.00 37.93 3.71
874 910 0.593128 GCAGAAAGCAGCGGAAAAGA 59.407 50.000 0.00 0.00 44.79 2.52
875 911 3.098032 GCAGAAAGCAGCGGAAAAG 57.902 52.632 0.00 0.00 44.79 2.27
918 954 3.055819 TCTCGGATCTTGGAAGTTGGAAG 60.056 47.826 0.00 0.00 0.00 3.46
919 955 2.903784 TCTCGGATCTTGGAAGTTGGAA 59.096 45.455 0.00 0.00 0.00 3.53
920 956 2.497675 CTCTCGGATCTTGGAAGTTGGA 59.502 50.000 0.00 0.00 0.00 3.53
921 957 2.898705 CTCTCGGATCTTGGAAGTTGG 58.101 52.381 0.00 0.00 0.00 3.77
922 958 2.093764 AGCTCTCGGATCTTGGAAGTTG 60.094 50.000 0.00 0.00 0.00 3.16
923 959 2.183679 AGCTCTCGGATCTTGGAAGTT 58.816 47.619 0.00 0.00 0.00 2.66
924 960 1.859302 AGCTCTCGGATCTTGGAAGT 58.141 50.000 0.00 0.00 0.00 3.01
956 992 9.635404 AGCTACTATAGTAATCAGTTTCAGACT 57.365 33.333 13.51 0.30 39.89 3.24
989 1025 1.171549 TGACAGCATCAAAGGCGCAA 61.172 50.000 10.83 0.00 33.02 4.85
1030 1068 0.110010 GCGCTTCTTCTGCTTTGACC 60.110 55.000 0.00 0.00 0.00 4.02
1031 1069 0.451792 CGCGCTTCTTCTGCTTTGAC 60.452 55.000 5.56 0.00 0.00 3.18
1106 1147 3.941657 GACTGAGACCGTGCAGGCC 62.942 68.421 0.00 0.00 46.52 5.19
1293 1334 3.184683 GTGGCGCTCTTGAGCTCG 61.185 66.667 18.75 7.03 39.02 5.03
1332 1373 1.046472 AACCGCCCTCACCGATCATA 61.046 55.000 0.00 0.00 0.00 2.15
1341 1382 2.597217 CAGCCAAAACCGCCCTCA 60.597 61.111 0.00 0.00 0.00 3.86
1460 1501 3.324268 TGGAAGCAATGCATGAGGAAAAA 59.676 39.130 8.35 0.00 0.00 1.94
1497 1538 2.098117 GCTCTGACACCATGTTTATGCC 59.902 50.000 0.00 0.00 32.79 4.40
1523 1564 0.827507 TGATCGGATCGCCTCCATGA 60.828 55.000 12.99 0.00 45.24 3.07
1529 1570 0.034059 GGTTGATGATCGGATCGCCT 59.966 55.000 12.99 0.84 0.00 5.52
1532 1573 0.313987 TCGGGTTGATGATCGGATCG 59.686 55.000 12.99 0.00 0.00 3.69
1561 1602 2.290577 GGATCCAGCCATCCAGATTACC 60.291 54.545 6.95 0.00 42.02 2.85
1577 1618 4.217118 GCATTGGTGTTATCATCTGGATCC 59.783 45.833 4.20 4.20 37.44 3.36
1581 1622 5.125900 TCAAAGCATTGGTGTTATCATCTGG 59.874 40.000 1.24 0.00 37.15 3.86
1620 1661 1.134220 TCGGTCACCCATTCCTTATGC 60.134 52.381 0.00 0.00 32.60 3.14
1836 1877 0.889306 GGTACTTGAGACCACGAGCT 59.111 55.000 0.00 0.00 36.91 4.09
1869 1910 3.678072 TGACGAAGCTTACCTTGAATTCG 59.322 43.478 0.00 0.00 43.67 3.34
1885 1926 1.887242 GCCGCATGCCTATGACGAA 60.887 57.895 13.15 0.00 36.56 3.85
1994 2044 7.071069 AGAATACATTCATAGATGGCAGACA 57.929 36.000 4.85 0.00 39.23 3.41
1995 2045 7.118971 GGAAGAATACATTCATAGATGGCAGAC 59.881 40.741 4.85 0.00 39.23 3.51
2080 2131 0.319641 AGCCGAAGTCCGACAGTTTC 60.320 55.000 0.40 0.00 41.76 2.78
2162 2213 3.966665 TGGACAAAGAAGATGGGCTTTTT 59.033 39.130 0.00 0.00 36.83 1.94
2163 2214 3.575687 CTGGACAAAGAAGATGGGCTTTT 59.424 43.478 0.00 0.00 36.83 2.27
2202 2260 0.748450 ATTGCGCCATGGAATTGAGG 59.252 50.000 18.40 0.00 34.61 3.86
2247 2305 3.089573 GCAAAGCTGCTTCTGAAAGTT 57.910 42.857 16.28 0.00 45.74 2.66
2288 2348 6.215227 ACTGACTACCTAGTACCTACTGAACT 59.785 42.308 0.00 0.00 36.50 3.01
2303 2363 6.663953 TGAACTATTCTTGCTACTGACTACCT 59.336 38.462 0.00 0.00 0.00 3.08
2390 2451 2.283298 CTGCTAAGCATCCATTCACGT 58.717 47.619 0.00 0.00 38.13 4.49
2482 2555 0.909623 TGCCTAACTGCCTACCCTTC 59.090 55.000 0.00 0.00 0.00 3.46
2539 2612 1.143889 GGGCTAGCTGGCTTTCCTAAT 59.856 52.381 22.23 0.00 41.48 1.73
2556 2629 1.398958 TTTCAACCAACCAGCAGGGC 61.399 55.000 0.00 0.00 42.05 5.19
2572 2645 5.635417 AGCCAGAAAAGTTAGCTGATTTC 57.365 39.130 0.00 1.95 31.23 2.17
2639 2715 5.394224 ACAGACAGAGGCTACTTTTACTC 57.606 43.478 0.00 0.00 0.00 2.59
2658 2734 9.121658 TGTCAGGTATCTAGAGTTAATGTACAG 57.878 37.037 0.33 0.00 0.00 2.74
2781 2862 1.153549 CTTACTGCTGAGGCGTCCC 60.154 63.158 3.56 0.00 42.25 4.46
2972 3053 3.540211 CTGACTGCCGATTTCAGGT 57.460 52.632 0.00 0.00 35.94 4.00
3269 3350 7.172875 GTCATAAAGAGGAACATCTCATCCATG 59.827 40.741 0.00 0.00 35.35 3.66
3582 3670 7.043565 ACTCAAAATTCAGTCAGCAAAAATGT 58.956 30.769 0.00 0.00 0.00 2.71
3898 3987 3.888930 TGACCTGTGAATCCACCTTTTTC 59.111 43.478 0.00 0.00 42.53 2.29
3977 4066 8.258007 TCCTGAAAGTCATATGGTACTTTACTG 58.742 37.037 17.81 14.70 43.97 2.74
4038 4127 3.334583 TCCGGAGCATGCTATATTTCC 57.665 47.619 22.74 15.62 0.00 3.13



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

AutoCloner maintained by Alex Coulton.