Multiple sequence alignment - TraesCS5A01G344600

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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 TraesCS5A01G344600 chr5A 100.000 2426 0 0 1 2426 549152835 549155260 0.000000e+00 4481
1 TraesCS5A01G344600 chr5A 87.500 536 52 6 971 1494 548240340 548239808 2.670000e-169 604
2 TraesCS5A01G344600 chr5B 86.155 2174 178 53 41 2165 527061725 527059626 0.000000e+00 2233
3 TraesCS5A01G344600 chr5B 90.932 1202 81 8 567 1742 528524299 528525498 0.000000e+00 1591
4 TraesCS5A01G344600 chr5B 92.915 621 28 7 1814 2421 528538493 528539110 0.000000e+00 889
5 TraesCS5A01G344600 chr5B 81.982 888 125 15 564 1436 527050160 527049293 0.000000e+00 721
6 TraesCS5A01G344600 chr5B 90.613 522 27 10 1 510 528523773 528524284 0.000000e+00 673
7 TraesCS5A01G344600 chr5B 86.678 593 65 3 980 1558 527058956 527058364 0.000000e+00 645
8 TraesCS5A01G344600 chr5B 93.035 402 27 1 980 1380 528537545 528537946 9.660000e-164 586
9 TraesCS5A01G344600 chr5B 85.269 353 38 8 1727 2067 527058155 527057805 3.840000e-93 351
10 TraesCS5A01G344600 chr5D 83.510 1601 139 61 7 1558 435236694 435238218 0.000000e+00 1378
11 TraesCS5A01G344600 chr5D 81.509 1087 132 27 654 1702 434322824 434323879 0.000000e+00 830
12 TraesCS5A01G344600 chr5D 91.326 611 38 6 1826 2423 435246016 435246624 0.000000e+00 821
13 TraesCS5A01G344600 chr5D 81.417 974 132 20 564 1510 434394103 434393152 0.000000e+00 750


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 TraesCS5A01G344600 chr5A 549152835 549155260 2425 False 4481.000000 4481 100.0000 1 2426 1 chr5A.!!$F1 2425
1 TraesCS5A01G344600 chr5A 548239808 548240340 532 True 604.000000 604 87.5000 971 1494 1 chr5A.!!$R1 523
2 TraesCS5A01G344600 chr5B 528523773 528525498 1725 False 1132.000000 1591 90.7725 1 1742 2 chr5B.!!$F1 1741
3 TraesCS5A01G344600 chr5B 527057805 527061725 3920 True 1076.333333 2233 86.0340 41 2165 3 chr5B.!!$R2 2124
4 TraesCS5A01G344600 chr5B 528537545 528539110 1565 False 737.500000 889 92.9750 980 2421 2 chr5B.!!$F2 1441
5 TraesCS5A01G344600 chr5B 527049293 527050160 867 True 721.000000 721 81.9820 564 1436 1 chr5B.!!$R1 872
6 TraesCS5A01G344600 chr5D 435236694 435238218 1524 False 1378.000000 1378 83.5100 7 1558 1 chr5D.!!$F2 1551
7 TraesCS5A01G344600 chr5D 434322824 434323879 1055 False 830.000000 830 81.5090 654 1702 1 chr5D.!!$F1 1048
8 TraesCS5A01G344600 chr5D 435246016 435246624 608 False 821.000000 821 91.3260 1826 2423 1 chr5D.!!$F3 597
9 TraesCS5A01G344600 chr5D 434393152 434394103 951 True 750.000000 750 81.4170 564 1510 1 chr5D.!!$R1 946

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
636 698 0.531657 TGCACATTGCCAATAGCCAC 59.468 50.0 10.4 0.0 44.23 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 3905 0.474184 ACTTGTGGAGTGAACCCTGG 59.526 55.0 0.0 0.0 37.17 4.45 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
23 24 1.352352 TCCAGGAAAGAGAGCCCAAAG 59.648 52.381 0.00 0.00 0.00 2.77
133 158 7.558444 AGTGTCCTAATTAGAGAACTGGAGTAG 59.442 40.741 14.28 0.00 0.00 2.57
181 209 5.527214 TGAACTGAGTCCAAATACTTGTGTG 59.473 40.000 0.00 0.00 0.00 3.82
223 259 3.737266 GGGCATTCAAATCGTTATGCATG 59.263 43.478 10.16 0.00 43.89 4.06
238 278 6.086241 CGTTATGCATGCATTTTATACGGAAC 59.914 38.462 36.23 26.60 37.82 3.62
244 284 4.079970 TGCATTTTATACGGAACCCAACA 58.920 39.130 0.00 0.00 0.00 3.33
300 340 7.560991 TGGAAATGTGATATATCTGCCACTTTT 59.439 33.333 13.79 12.87 38.62 2.27
382 430 1.683943 CCCAAGAGGTACCATGCATG 58.316 55.000 20.19 20.19 0.00 4.06
383 431 1.064463 CCCAAGAGGTACCATGCATGT 60.064 52.381 24.58 15.01 0.00 3.21
384 432 2.019249 CCAAGAGGTACCATGCATGTG 58.981 52.381 24.58 17.76 0.00 3.21
385 433 2.356022 CCAAGAGGTACCATGCATGTGA 60.356 50.000 24.58 9.68 0.00 3.58
392 440 2.502142 ACCATGCATGTGATGTGAGT 57.498 45.000 24.58 10.21 0.00 3.41
444 497 1.199327 CGACCACGAGCTTTCTGACTA 59.801 52.381 0.00 0.00 42.66 2.59
466 519 8.147642 ACTAAATCTTCACAAAGAACAGACTG 57.852 34.615 0.00 0.00 44.49 3.51
467 520 7.987458 ACTAAATCTTCACAAAGAACAGACTGA 59.013 33.333 10.08 0.00 44.49 3.41
468 521 7.814264 AAATCTTCACAAAGAACAGACTGAT 57.186 32.000 10.08 0.00 44.49 2.90
469 522 7.432350 AATCTTCACAAAGAACAGACTGATC 57.568 36.000 10.08 7.08 44.49 2.92
500 555 2.093310 GCATGAACGACTCACATCACAG 59.907 50.000 0.00 0.00 36.69 3.66
501 556 1.783284 TGAACGACTCACATCACAGC 58.217 50.000 0.00 0.00 0.00 4.40
510 565 3.324846 ACTCACATCACAGCTTCAGGTAA 59.675 43.478 0.00 0.00 0.00 2.85
511 566 4.019860 ACTCACATCACAGCTTCAGGTAAT 60.020 41.667 0.00 0.00 0.00 1.89
512 567 4.910195 TCACATCACAGCTTCAGGTAATT 58.090 39.130 0.00 0.00 0.00 1.40
513 568 6.048732 TCACATCACAGCTTCAGGTAATTA 57.951 37.500 0.00 0.00 0.00 1.40
514 569 6.472016 TCACATCACAGCTTCAGGTAATTAA 58.528 36.000 0.00 0.00 0.00 1.40
521 580 5.701290 ACAGCTTCAGGTAATTAACTGTCAC 59.299 40.000 25.97 17.15 31.85 3.67
522 581 5.122396 CAGCTTCAGGTAATTAACTGTCACC 59.878 44.000 25.97 14.72 36.17 4.02
524 583 5.106673 GCTTCAGGTAATTAACTGTCACCAC 60.107 44.000 25.97 10.43 36.17 4.16
587 646 4.218417 CCGAAATTGTTCAATCCCTCAAGT 59.782 41.667 0.00 0.00 32.89 3.16
595 654 1.812571 CAATCCCTCAAGTTGGAACCG 59.187 52.381 2.34 0.00 33.54 4.44
608 668 3.735037 GAACCGATCGCTGTCCCCC 62.735 68.421 10.32 0.00 0.00 5.40
636 698 0.531657 TGCACATTGCCAATAGCCAC 59.468 50.000 10.40 0.00 44.23 5.01
711 777 3.813596 GCAGACCAATGCCTACCG 58.186 61.111 0.00 0.00 40.43 4.02
815 892 1.389609 GCTGATCCCATGGCCTTGTG 61.390 60.000 16.81 6.33 0.00 3.33
826 903 2.736531 CCTTGTGCCTTGCCAACC 59.263 61.111 0.00 0.00 0.00 3.77
838 915 3.512724 CCTTGCCAACCTTTCTCAATGAT 59.487 43.478 0.00 0.00 0.00 2.45
858 942 1.059098 AGCTCCACTTCACCATCACA 58.941 50.000 0.00 0.00 0.00 3.58
903 989 4.821805 TGCCTATAAATTCAGTAAGCTGCC 59.178 41.667 0.00 0.00 42.29 4.85
941 1035 3.106827 TCATCAGCTCATCCACCAACTA 58.893 45.455 0.00 0.00 0.00 2.24
948 1042 5.416952 CAGCTCATCCACCAACTAAGAATTT 59.583 40.000 0.00 0.00 0.00 1.82
1098 1195 3.557595 CGGTATCAGCCAAAGAAGATCAC 59.442 47.826 0.00 0.00 0.00 3.06
1116 1213 0.877649 ACGACTGCTGCAGTTCTGTG 60.878 55.000 33.33 22.16 45.44 3.66
1152 1249 1.214325 TGTCATGTACACGGCCGAG 59.786 57.895 35.90 28.39 31.43 4.63
1254 1351 1.782044 GCTTTGCAAGCGATGGAAAA 58.218 45.000 11.90 0.00 46.84 2.29
1269 1366 2.224018 TGGAAAAATCACACTGCCTTGC 60.224 45.455 0.00 0.00 0.00 4.01
1275 1372 3.425713 ACACTGCCTTGCGATGCG 61.426 61.111 0.00 0.00 0.00 4.73
1338 1435 4.838486 GCCGAGGTCGAGAGTGCG 62.838 72.222 0.00 0.00 43.02 5.34
1347 1444 1.081175 CGAGAGTGCGTTGCTGAGA 60.081 57.895 0.00 0.00 0.00 3.27
1476 1642 2.846193 TCTTGTGTAGTTTGCCTGGAC 58.154 47.619 0.00 0.00 0.00 4.02
1490 1656 4.606210 TGCCTGGACAGTGTAAGATAGTA 58.394 43.478 0.00 0.00 0.00 1.82
1500 1666 9.953697 GACAGTGTAAGATAGTAAGATAACAGG 57.046 37.037 0.00 0.00 0.00 4.00
1566 3590 3.744660 AGAAACAAAGCAGTACTCTGGG 58.255 45.455 0.00 0.00 41.57 4.45
1609 3654 5.964958 AGTTTCATACAACTCCACAATGG 57.035 39.130 0.00 0.00 39.43 3.16
1674 3719 0.740868 TGCTGCACAGAGAATACGCC 60.741 55.000 0.00 0.00 0.00 5.68
1679 3724 2.009774 GCACAGAGAATACGCCACAAT 58.990 47.619 0.00 0.00 0.00 2.71
1687 3732 3.879295 AGAATACGCCACAATTCTCCATG 59.121 43.478 0.00 0.00 37.83 3.66
1703 3748 7.550597 TTCTCCATGCAATCTATCATCTAGT 57.449 36.000 0.00 0.00 0.00 2.57
1706 3751 5.781818 TCCATGCAATCTATCATCTAGTCCA 59.218 40.000 0.00 0.00 0.00 4.02
1707 3752 6.070938 TCCATGCAATCTATCATCTAGTCCAG 60.071 42.308 0.00 0.00 0.00 3.86
1733 3857 8.921670 GTGGAAAATAAATACAACACCATCAAC 58.078 33.333 0.00 0.00 0.00 3.18
1742 3866 8.532977 AATACAACACCATCAACAAAATAAGC 57.467 30.769 0.00 0.00 0.00 3.09
1752 3876 9.079833 CCATCAACAAAATAAGCAATGAAGTAG 57.920 33.333 0.00 0.00 0.00 2.57
1754 3878 8.177119 TCAACAAAATAAGCAATGAAGTAGGT 57.823 30.769 0.00 0.00 0.00 3.08
1755 3879 9.290988 TCAACAAAATAAGCAATGAAGTAGGTA 57.709 29.630 0.00 0.00 0.00 3.08
1773 3899 9.758651 AAGTAGGTAAAAATCACAAAATGGAAC 57.241 29.630 0.00 0.00 0.00 3.62
1774 3900 8.079809 AGTAGGTAAAAATCACAAAATGGAACG 58.920 33.333 0.00 0.00 0.00 3.95
1776 3902 5.407084 GGTAAAAATCACAAAATGGAACGGG 59.593 40.000 0.00 0.00 0.00 5.28
1779 3905 3.934457 ATCACAAAATGGAACGGGAAC 57.066 42.857 0.00 0.00 0.00 3.62
1796 3922 0.923358 AACCAGGGTTCACTCCACAA 59.077 50.000 0.00 0.00 32.09 3.33
1798 3924 0.474184 CCAGGGTTCACTCCACAAGT 59.526 55.000 0.00 0.00 39.44 3.16
1799 3925 1.697432 CCAGGGTTCACTCCACAAGTA 59.303 52.381 0.00 0.00 36.07 2.24
1804 3930 5.643777 CAGGGTTCACTCCACAAGTATTTAG 59.356 44.000 0.00 0.00 36.07 1.85
1805 3931 4.941873 GGGTTCACTCCACAAGTATTTAGG 59.058 45.833 0.00 0.00 36.07 2.69
1809 3935 2.241430 ACTCCACAAGTATTTAGGGGGC 59.759 50.000 0.00 0.00 36.07 5.80
1811 3937 2.241176 TCCACAAGTATTTAGGGGGCAG 59.759 50.000 0.00 0.00 0.00 4.85
1813 3939 3.117512 CCACAAGTATTTAGGGGGCAGAT 60.118 47.826 0.00 0.00 0.00 2.90
1814 3940 4.536765 CACAAGTATTTAGGGGGCAGATT 58.463 43.478 0.00 0.00 0.00 2.40
1815 3941 4.580580 CACAAGTATTTAGGGGGCAGATTC 59.419 45.833 0.00 0.00 0.00 2.52
1816 3942 4.229582 ACAAGTATTTAGGGGGCAGATTCA 59.770 41.667 0.00 0.00 0.00 2.57
1817 3943 5.103515 ACAAGTATTTAGGGGGCAGATTCAT 60.104 40.000 0.00 0.00 0.00 2.57
1818 3944 5.669798 AGTATTTAGGGGGCAGATTCATT 57.330 39.130 0.00 0.00 0.00 2.57
1819 3945 6.030727 AGTATTTAGGGGGCAGATTCATTT 57.969 37.500 0.00 0.00 0.00 2.32
1822 3948 5.419239 TTTAGGGGGCAGATTCATTTTTG 57.581 39.130 0.00 0.00 0.00 2.44
1832 3966 5.411361 GCAGATTCATTTTTGGGGGTAAAAC 59.589 40.000 0.00 0.00 29.89 2.43
1833 3967 6.529220 CAGATTCATTTTTGGGGGTAAAACA 58.471 36.000 0.00 0.00 29.89 2.83
1836 3970 8.224025 AGATTCATTTTTGGGGGTAAAACAAAT 58.776 29.630 0.00 0.00 34.47 2.32
1841 3975 9.289782 CATTTTTGGGGGTAAAACAAATTGATA 57.710 29.630 0.00 0.00 34.47 2.15
1845 3979 7.619512 TGGGGGTAAAACAAATTGATAGTTT 57.380 32.000 0.00 0.00 37.08 2.66
1979 4123 2.494059 CAAAGGAAAGTGCGGAGAAGA 58.506 47.619 0.00 0.00 0.00 2.87
2047 4191 5.678583 CCATCAACAGGACTGAGTTATGAT 58.321 41.667 6.29 5.26 0.00 2.45
2049 4193 6.927936 CCATCAACAGGACTGAGTTATGATAG 59.072 42.308 6.29 0.00 0.00 2.08
2061 4207 7.613801 ACTGAGTTATGATAGTGTTCAGAGAGT 59.386 37.037 5.68 0.00 35.68 3.24
2067 4213 5.532557 TGATAGTGTTCAGAGAGTTGTGTG 58.467 41.667 0.00 0.00 0.00 3.82
2068 4214 3.895232 AGTGTTCAGAGAGTTGTGTGT 57.105 42.857 0.00 0.00 0.00 3.72
2083 4229 5.813672 AGTTGTGTGTGTTACGTCAACTAAT 59.186 36.000 11.84 0.00 45.75 1.73
2087 4233 7.647228 TGTGTGTGTTACGTCAACTAATACTA 58.353 34.615 0.00 0.00 38.05 1.82
2105 4251 6.936968 ATACTATCCCTTCCACACCTAATC 57.063 41.667 0.00 0.00 0.00 1.75
2145 4291 8.062448 CACGCTAAATTACTAATCCAACTAAGC 58.938 37.037 0.00 0.00 0.00 3.09
2211 4361 0.109342 ATGCTGGCTAGATTTCCCCG 59.891 55.000 0.00 0.00 0.00 5.73
2423 4586 1.224722 TGCTTGCGACATTGCACGTA 61.225 50.000 0.00 0.00 46.25 3.57
2424 4587 0.789383 GCTTGCGACATTGCACGTAC 60.789 55.000 0.00 0.00 46.25 3.67
2425 4588 0.179225 CTTGCGACATTGCACGTACC 60.179 55.000 0.00 0.00 46.25 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 158 7.605691 TCAGAATGATCCAGAAGAGAAAAACTC 59.394 37.037 0.00 0.00 42.56 3.01
181 209 2.546789 CCGTTGTAGTTGGGTTTCTCAC 59.453 50.000 0.00 0.00 0.00 3.51
223 259 4.417506 GTGTTGGGTTCCGTATAAAATGC 58.582 43.478 0.00 0.00 0.00 3.56
238 278 4.212004 CAGATGTATCTTATGCGTGTTGGG 59.788 45.833 0.00 0.00 34.22 4.12
244 284 3.657634 CAGGCAGATGTATCTTATGCGT 58.342 45.455 0.00 0.00 34.22 5.24
300 340 0.108585 GCCACCTTTGTGTCCTCTGA 59.891 55.000 0.00 0.00 41.09 3.27
381 429 0.320683 CTCCGGCAACTCACATCACA 60.321 55.000 0.00 0.00 0.00 3.58
382 430 0.037326 TCTCCGGCAACTCACATCAC 60.037 55.000 0.00 0.00 0.00 3.06
383 431 0.904649 ATCTCCGGCAACTCACATCA 59.095 50.000 0.00 0.00 0.00 3.07
384 432 1.134699 TGATCTCCGGCAACTCACATC 60.135 52.381 0.00 0.00 0.00 3.06
385 433 0.904649 TGATCTCCGGCAACTCACAT 59.095 50.000 0.00 0.00 0.00 3.21
392 440 2.632377 GATCTGTTTGATCTCCGGCAA 58.368 47.619 0.00 0.00 46.05 4.52
444 497 7.307632 CGATCAGTCTGTTCTTTGTGAAGATTT 60.308 37.037 8.85 0.00 41.35 2.17
466 519 2.413112 CGTTCATGCACCCATATCGATC 59.587 50.000 0.00 0.00 0.00 3.69
467 520 2.037121 TCGTTCATGCACCCATATCGAT 59.963 45.455 2.16 2.16 0.00 3.59
468 521 1.410882 TCGTTCATGCACCCATATCGA 59.589 47.619 0.00 0.00 0.00 3.59
469 522 1.526887 GTCGTTCATGCACCCATATCG 59.473 52.381 0.00 0.00 0.00 2.92
500 555 5.001232 TGGTGACAGTTAATTACCTGAAGC 58.999 41.667 16.12 12.75 35.01 3.86
501 556 5.995282 TGTGGTGACAGTTAATTACCTGAAG 59.005 40.000 16.12 0.00 44.46 3.02
510 565 1.535462 GCGCTTGTGGTGACAGTTAAT 59.465 47.619 0.00 0.00 44.46 1.40
511 566 0.941542 GCGCTTGTGGTGACAGTTAA 59.058 50.000 0.00 0.00 44.46 2.01
512 567 0.882927 GGCGCTTGTGGTGACAGTTA 60.883 55.000 7.64 0.00 44.46 2.24
513 568 2.186826 GGCGCTTGTGGTGACAGTT 61.187 57.895 7.64 0.00 44.46 3.16
514 569 1.754380 TAGGCGCTTGTGGTGACAGT 61.754 55.000 7.64 0.00 44.46 3.55
535 594 3.243569 CCGATTGGTTCCACTCTAGCTAG 60.244 52.174 15.01 15.01 0.00 3.42
536 595 2.693591 CCGATTGGTTCCACTCTAGCTA 59.306 50.000 7.42 0.00 0.00 3.32
537 596 1.482593 CCGATTGGTTCCACTCTAGCT 59.517 52.381 7.42 0.00 0.00 3.32
538 597 1.941325 CCGATTGGTTCCACTCTAGC 58.059 55.000 7.42 0.00 0.00 3.42
587 646 1.079405 GGACAGCGATCGGTTCCAA 60.079 57.895 28.06 0.00 0.00 3.53
608 668 1.503542 GCAATGTGCAAGGAGTCGG 59.496 57.895 0.00 0.00 44.26 4.79
636 698 1.081376 AAGAGGCGTGTCGAGAACG 60.081 57.895 14.56 14.56 43.81 3.95
679 741 4.183865 TGGTCTGCTTTCTTATCATCGTG 58.816 43.478 0.00 0.00 0.00 4.35
680 742 4.471904 TGGTCTGCTTTCTTATCATCGT 57.528 40.909 0.00 0.00 0.00 3.73
682 744 5.506982 GGCATTGGTCTGCTTTCTTATCATC 60.507 44.000 0.00 0.00 41.95 2.92
711 777 2.767505 CCGGAGCCTATTGTCATAACC 58.232 52.381 0.00 0.00 0.00 2.85
815 892 1.039856 TTGAGAAAGGTTGGCAAGGC 58.960 50.000 0.00 0.00 0.00 4.35
826 903 6.036953 GTGAAGTGGAGCTATCATTGAGAAAG 59.963 42.308 0.00 0.00 0.00 2.62
838 915 2.256306 TGTGATGGTGAAGTGGAGCTA 58.744 47.619 0.00 0.00 0.00 3.32
858 942 1.923395 TGGCGAGGGGAAGGACATT 60.923 57.895 0.00 0.00 0.00 2.71
903 989 2.654749 TGAAGTGTGATACTGAGCCG 57.345 50.000 0.00 0.00 40.26 5.52
941 1035 6.888632 AGTGAGCTATGGATGTTGAAATTCTT 59.111 34.615 0.00 0.00 0.00 2.52
948 1042 3.378512 AGGAGTGAGCTATGGATGTTGA 58.621 45.455 0.00 0.00 0.00 3.18
1005 1102 0.250467 GAGCAAGTCTCTTGGCACCA 60.250 55.000 10.76 0.00 38.78 4.17
1098 1195 1.858041 CACAGAACTGCAGCAGTCG 59.142 57.895 28.38 20.58 44.62 4.18
1152 1249 2.353610 TACCTCGAAACGCCTCCCC 61.354 63.158 0.00 0.00 0.00 4.81
1251 1348 1.680735 TCGCAAGGCAGTGTGATTTTT 59.319 42.857 0.85 0.00 33.17 1.94
1254 1351 0.806868 CATCGCAAGGCAGTGTGATT 59.193 50.000 12.81 0.00 44.40 2.57
1269 1366 2.202919 TCCATCACTGCCGCATCG 60.203 61.111 0.00 0.00 0.00 3.84
1275 1372 2.988010 TGACATACTCCATCACTGCC 57.012 50.000 0.00 0.00 0.00 4.85
1338 1435 2.012673 GTCACCATGGATCTCAGCAAC 58.987 52.381 21.47 0.00 0.00 4.17
1347 1444 1.750399 GCAAGGCGTCACCATGGAT 60.750 57.895 21.47 0.00 43.14 3.41
1383 1535 0.698238 TGGCTCCAACAGTAGGCATT 59.302 50.000 0.00 0.00 42.67 3.56
1476 1642 8.414003 TGCCTGTTATCTTACTATCTTACACTG 58.586 37.037 0.00 0.00 0.00 3.66
1490 1656 4.445448 CCTGCTCCTATTGCCTGTTATCTT 60.445 45.833 0.00 0.00 0.00 2.40
1500 1666 4.725790 ACAATTTTCCTGCTCCTATTGC 57.274 40.909 0.00 0.00 0.00 3.56
1547 3571 2.863809 CCCCAGAGTACTGCTTTGTTT 58.136 47.619 0.00 0.00 42.25 2.83
1650 3695 2.803030 ATTCTCTGTGCAGCAGGATT 57.197 45.000 13.87 6.48 45.08 3.01
1674 3719 6.628919 TGATAGATTGCATGGAGAATTGTG 57.371 37.500 0.00 0.00 0.00 3.33
1679 3724 7.310299 GGACTAGATGATAGATTGCATGGAGAA 60.310 40.741 0.00 0.00 0.00 2.87
1687 3732 5.244851 TCCACTGGACTAGATGATAGATTGC 59.755 44.000 0.00 0.00 0.00 3.56
1703 3748 6.778069 TGGTGTTGTATTTATTTTCCACTGGA 59.222 34.615 0.00 0.00 0.00 3.86
1706 3751 8.415950 TGATGGTGTTGTATTTATTTTCCACT 57.584 30.769 0.00 0.00 0.00 4.00
1707 3752 8.921670 GTTGATGGTGTTGTATTTATTTTCCAC 58.078 33.333 0.00 0.00 0.00 4.02
1752 3876 5.407084 CCCGTTCCATTTTGTGATTTTTACC 59.593 40.000 0.00 0.00 0.00 2.85
1754 3878 6.406692 TCCCGTTCCATTTTGTGATTTTTA 57.593 33.333 0.00 0.00 0.00 1.52
1755 3879 5.283457 TCCCGTTCCATTTTGTGATTTTT 57.717 34.783 0.00 0.00 0.00 1.94
1758 3882 3.006430 GGTTCCCGTTCCATTTTGTGATT 59.994 43.478 0.00 0.00 0.00 2.57
1760 3884 1.957877 GGTTCCCGTTCCATTTTGTGA 59.042 47.619 0.00 0.00 0.00 3.58
1761 3885 1.683917 TGGTTCCCGTTCCATTTTGTG 59.316 47.619 0.00 0.00 0.00 3.33
1762 3886 1.960689 CTGGTTCCCGTTCCATTTTGT 59.039 47.619 0.00 0.00 33.01 2.83
1763 3887 1.272212 CCTGGTTCCCGTTCCATTTTG 59.728 52.381 0.00 0.00 33.01 2.44
1779 3905 0.474184 ACTTGTGGAGTGAACCCTGG 59.526 55.000 0.00 0.00 37.17 4.45
1787 3913 3.886123 CCCCCTAAATACTTGTGGAGTG 58.114 50.000 0.00 0.00 39.48 3.51
1796 3922 5.669798 AATGAATCTGCCCCCTAAATACT 57.330 39.130 0.00 0.00 0.00 2.12
1798 3924 6.099557 CCAAAAATGAATCTGCCCCCTAAATA 59.900 38.462 0.00 0.00 0.00 1.40
1799 3925 5.104402 CCAAAAATGAATCTGCCCCCTAAAT 60.104 40.000 0.00 0.00 0.00 1.40
1804 3930 1.210234 CCCAAAAATGAATCTGCCCCC 59.790 52.381 0.00 0.00 0.00 5.40
1805 3931 1.210234 CCCCAAAAATGAATCTGCCCC 59.790 52.381 0.00 0.00 0.00 5.80
1809 3935 6.529220 TGTTTTACCCCCAAAAATGAATCTG 58.471 36.000 0.00 0.00 0.00 2.90
1811 3937 7.809546 TTTGTTTTACCCCCAAAAATGAATC 57.190 32.000 0.00 0.00 0.00 2.52
1813 3939 7.834181 TCAATTTGTTTTACCCCCAAAAATGAA 59.166 29.630 0.00 0.00 32.39 2.57
1814 3940 7.346471 TCAATTTGTTTTACCCCCAAAAATGA 58.654 30.769 0.00 0.00 32.39 2.57
1815 3941 7.573968 TCAATTTGTTTTACCCCCAAAAATG 57.426 32.000 0.00 0.00 32.39 2.32
1816 3942 9.513906 CTATCAATTTGTTTTACCCCCAAAAAT 57.486 29.630 0.00 0.00 32.39 1.82
1817 3943 8.495260 ACTATCAATTTGTTTTACCCCCAAAAA 58.505 29.630 0.00 0.00 32.39 1.94
1818 3944 8.035448 ACTATCAATTTGTTTTACCCCCAAAA 57.965 30.769 0.00 0.00 32.39 2.44
1819 3945 7.619512 ACTATCAATTTGTTTTACCCCCAAA 57.380 32.000 0.00 0.00 33.09 3.28
1822 3948 8.809066 AGTAAACTATCAATTTGTTTTACCCCC 58.191 33.333 14.70 0.00 35.77 5.40
1845 3979 9.349713 AGGACATTCAATTTTTCAGTAACAGTA 57.650 29.630 0.00 0.00 0.00 2.74
2047 4191 4.159693 ACACACACAACTCTCTGAACACTA 59.840 41.667 0.00 0.00 0.00 2.74
2049 4193 3.262420 ACACACACAACTCTCTGAACAC 58.738 45.455 0.00 0.00 0.00 3.32
2061 4207 6.979817 AGTATTAGTTGACGTAACACACACAA 59.020 34.615 0.00 0.00 41.88 3.33
2067 4213 7.710896 AGGGATAGTATTAGTTGACGTAACAC 58.289 38.462 0.00 0.00 41.88 3.32
2068 4214 7.886629 AGGGATAGTATTAGTTGACGTAACA 57.113 36.000 0.00 0.00 41.88 2.41
2083 4229 5.784023 TGATTAGGTGTGGAAGGGATAGTA 58.216 41.667 0.00 0.00 0.00 1.82
2087 4233 4.946160 TTTGATTAGGTGTGGAAGGGAT 57.054 40.909 0.00 0.00 0.00 3.85
2145 4291 7.148340 CCTTTAGTTTAGCAGATGAGAAACTGG 60.148 40.741 16.58 9.65 41.13 4.00
2211 4361 1.527311 GACAAGACTTCTGGTTGCGAC 59.473 52.381 0.00 0.00 28.24 5.19
2358 4521 8.000709 AGATTGGATATTGATTTGAGCCAACTA 58.999 33.333 0.00 0.00 36.83 2.24


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

AutoCloner maintained by Alex Coulton.