Multiple sequence alignment - TraesCS5D01G300500

Loading Multiple Alignment...

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 TraesCS5D01G300500 chr5D 100.000 2636 0 0 1 2636 397937281 397934646 0.000000e+00 4868.0
1 TraesCS5D01G300500 chr5A 87.159 2017 191 33 1 1972 503057414 503055421 0.000000e+00 2228.0
2 TraesCS5D01G300500 chr5A 88.424 622 34 7 2018 2636 503055424 503054838 0.000000e+00 715.0
3 TraesCS5D01G300500 chr5B 89.303 1692 134 28 1 1673 477980656 477978993 0.000000e+00 2078.0
4 TraesCS5D01G300500 chr5B 90.509 727 37 17 1927 2636 477977948 477977237 0.000000e+00 931.0
5 TraesCS5D01G300500 chr3D 78.378 111 16 6 15 121 596666862 596666756 6.090000e-07 65.8
6 TraesCS5D01G300500 chr3D 75.510 147 28 6 168 310 597480984 597481126 6.090000e-07 65.8
7 TraesCS5D01G300500 chr3B 78.378 111 16 6 15 121 802601262 802601368 6.090000e-07 65.8
8 TraesCS5D01G300500 chr3B 90.909 44 4 0 168 211 804171367 804171410 2.830000e-05 60.2


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 TraesCS5D01G300500 chr5D 397934646 397937281 2635 True 4868.0 4868 100.0000 1 2636 1 chr5D.!!$R1 2635
1 TraesCS5D01G300500 chr5A 503054838 503057414 2576 True 1471.5 2228 87.7915 1 2636 2 chr5A.!!$R1 2635
2 TraesCS5D01G300500 chr5B 477977237 477980656 3419 True 1504.5 2078 89.9060 1 2636 2 chr5B.!!$R1 2635

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
893 906 0.687354 ACAGACACTTGCTACCCTGG 59.313 55.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2840 2.163412 TGCAAGGGCGTCAATTAATCAC 59.837 45.455 0.0 0.0 45.35 3.06 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
69 70 7.962995 TCATCTTGGTATATATCCAGAGGAC 57.037 40.000 7.22 0.00 36.28 3.85
73 74 3.594685 TGGTATATATCCAGAGGACCGGA 59.405 47.826 9.46 0.00 32.98 5.14
75 76 4.645588 GGTATATATCCAGAGGACCGGAAG 59.354 50.000 9.46 0.00 32.98 3.46
84 85 1.757118 GAGGACCGGAAGATCATGACA 59.243 52.381 9.46 0.00 0.00 3.58
130 131 2.288640 GCTGAAGATTTTGTGCCTTGCT 60.289 45.455 0.00 0.00 0.00 3.91
167 168 0.745845 CGAGAGGATGTTGCAAGGGG 60.746 60.000 0.00 0.00 0.00 4.79
181 182 2.223900 GCAAGGGGCTATTTCAATGAGC 60.224 50.000 0.00 0.00 40.25 4.26
183 184 3.677156 AGGGGCTATTTCAATGAGCTT 57.323 42.857 0.00 0.00 36.43 3.74
364 365 1.264826 GTAAGATCCGTCGGCTCTCTC 59.735 57.143 17.53 10.14 27.07 3.20
410 411 2.429610 TCTCGGTACCAGGAGCAATTAC 59.570 50.000 13.54 0.00 0.00 1.89
445 446 2.676076 GATCGCTTGCAACATTTGGTT 58.324 42.857 0.00 0.00 41.47 3.67
446 447 3.669290 CGATCGCTTGCAACATTTGGTTA 60.669 43.478 0.26 0.00 37.72 2.85
449 450 4.233789 TCGCTTGCAACATTTGGTTATTC 58.766 39.130 0.00 0.00 37.72 1.75
452 453 4.389687 GCTTGCAACATTTGGTTATTCTGG 59.610 41.667 0.00 0.00 37.72 3.86
453 454 5.540911 CTTGCAACATTTGGTTATTCTGGT 58.459 37.500 0.00 0.00 37.72 4.00
454 455 4.880759 TGCAACATTTGGTTATTCTGGTG 58.119 39.130 0.00 0.00 37.72 4.17
455 456 4.586421 TGCAACATTTGGTTATTCTGGTGA 59.414 37.500 0.00 0.00 37.72 4.02
456 457 5.245751 TGCAACATTTGGTTATTCTGGTGAT 59.754 36.000 0.00 0.00 37.72 3.06
457 458 6.165577 GCAACATTTGGTTATTCTGGTGATT 58.834 36.000 0.00 0.00 37.72 2.57
458 459 6.311200 GCAACATTTGGTTATTCTGGTGATTC 59.689 38.462 0.00 0.00 37.72 2.52
459 460 7.605449 CAACATTTGGTTATTCTGGTGATTCT 58.395 34.615 0.00 0.00 37.72 2.40
460 461 7.161773 ACATTTGGTTATTCTGGTGATTCTG 57.838 36.000 0.00 0.00 0.00 3.02
466 467 5.705441 GGTTATTCTGGTGATTCTGTTGACA 59.295 40.000 0.00 0.00 0.00 3.58
468 469 3.407424 TCTGGTGATTCTGTTGACAGG 57.593 47.619 10.97 0.00 43.91 4.00
473 474 3.941483 GGTGATTCTGTTGACAGGGTATG 59.059 47.826 10.97 0.00 43.91 2.39
477 478 2.256306 TCTGTTGACAGGGTATGCTCA 58.744 47.619 10.97 0.00 43.91 4.26
490 491 4.142381 GGGTATGCTCAAGGCTAAAGTTTG 60.142 45.833 0.00 0.00 42.39 2.93
510 511 2.960384 TGTTCGAGTCCTAGTGGTTGAA 59.040 45.455 0.00 0.00 34.23 2.69
511 512 3.005472 TGTTCGAGTCCTAGTGGTTGAAG 59.995 47.826 0.00 0.00 34.23 3.02
517 518 1.616865 TCCTAGTGGTTGAAGGACGTG 59.383 52.381 0.00 0.00 34.46 4.49
522 523 2.028385 AGTGGTTGAAGGACGTGGTATC 60.028 50.000 0.00 0.00 0.00 2.24
561 562 1.584380 GAGTTTGCCTGCTGCTCCAG 61.584 60.000 0.00 0.00 42.00 3.86
613 617 5.798132 TGGATTATGAGGATGATGCAGTAC 58.202 41.667 0.00 0.00 0.00 2.73
614 618 5.545335 TGGATTATGAGGATGATGCAGTACT 59.455 40.000 0.00 0.00 0.00 2.73
615 619 6.725834 TGGATTATGAGGATGATGCAGTACTA 59.274 38.462 0.00 0.00 0.00 1.82
616 620 7.038659 GGATTATGAGGATGATGCAGTACTAC 58.961 42.308 0.00 0.00 0.00 2.73
644 648 6.049955 TCCTGAAATTCTGAATCTACGGTT 57.950 37.500 2.92 0.00 0.00 4.44
664 668 5.659048 GTTTCTGGAAACGCTGGATATAG 57.341 43.478 9.91 0.00 40.85 1.31
672 676 3.309961 ACGCTGGATATAGCAGATGTG 57.690 47.619 0.00 0.00 43.87 3.21
673 677 2.630098 ACGCTGGATATAGCAGATGTGT 59.370 45.455 0.00 0.00 43.87 3.72
859 872 3.492309 CGGGACCAATCTCAGAGATCTTG 60.492 52.174 13.63 9.75 32.89 3.02
865 878 5.721000 ACCAATCTCAGAGATCTTGAACTCT 59.279 40.000 13.63 4.85 43.13 3.24
875 888 8.770438 AGAGATCTTGAACTCTGTTTTGATAC 57.230 34.615 9.18 0.00 41.19 2.24
876 889 8.370940 AGAGATCTTGAACTCTGTTTTGATACA 58.629 33.333 9.18 0.00 41.19 2.29
889 902 5.468746 TGTTTTGATACAGACACTTGCTACC 59.531 40.000 0.00 0.00 0.00 3.18
893 906 0.687354 ACAGACACTTGCTACCCTGG 59.313 55.000 0.00 0.00 0.00 4.45
898 911 2.187946 CTTGCTACCCTGGCGAGG 59.812 66.667 7.99 7.99 37.50 4.63
976 995 6.430308 ACATCTAGCTATCGTTTCGGAAGATA 59.570 38.462 0.00 0.00 41.60 1.98
980 999 6.570672 AGCTATCGTTTCGGAAGATATGTA 57.429 37.500 0.00 0.00 41.60 2.29
981 1000 6.978338 AGCTATCGTTTCGGAAGATATGTAA 58.022 36.000 0.00 0.00 41.60 2.41
1004 1023 3.181469 GGCGACCAATCTCTACCAATGTA 60.181 47.826 0.00 0.00 0.00 2.29
1006 1025 5.279306 GGCGACCAATCTCTACCAATGTATA 60.279 44.000 0.00 0.00 0.00 1.47
1017 1036 8.363390 TCTCTACCAATGTATAATCAGCTGAAG 58.637 37.037 22.50 8.67 0.00 3.02
1018 1037 6.931281 TCTACCAATGTATAATCAGCTGAAGC 59.069 38.462 22.50 9.64 42.49 3.86
1060 1079 9.126151 CAGGAAATCTAGAGACACTACATCTAA 57.874 37.037 0.00 0.00 0.00 2.10
1203 1230 4.202172 GCCCTTCTCTACCTCAAGATGTAC 60.202 50.000 0.00 0.00 0.00 2.90
1207 1234 6.239176 CCTTCTCTACCTCAAGATGTACATCC 60.239 46.154 28.26 13.32 38.58 3.51
1213 1240 4.281182 ACCTCAAGATGTACATCCCGATAC 59.719 45.833 28.26 6.31 38.58 2.24
1230 1257 3.535860 GATACGCATCGCTGAAACAATC 58.464 45.455 0.00 0.00 0.00 2.67
1240 1267 2.159627 GCTGAAACAATCGTCATCCGTT 59.840 45.455 0.00 0.00 37.94 4.44
1259 1286 2.122729 TGGGAGTGGGAGTGGGAG 59.877 66.667 0.00 0.00 0.00 4.30
1261 1288 1.390926 GGGAGTGGGAGTGGGAGTA 59.609 63.158 0.00 0.00 0.00 2.59
1262 1289 0.688087 GGGAGTGGGAGTGGGAGTAG 60.688 65.000 0.00 0.00 0.00 2.57
1263 1290 0.688087 GGAGTGGGAGTGGGAGTAGG 60.688 65.000 0.00 0.00 0.00 3.18
1266 1293 2.040606 GGGAGTGGGAGTAGGGCA 59.959 66.667 0.00 0.00 0.00 5.36
1291 1318 1.202915 TCCCAGCACTCAAGCATTTCA 60.203 47.619 0.00 0.00 36.85 2.69
1333 1360 1.115326 GGTGGCTTTTGAGCAAGGGT 61.115 55.000 0.47 0.00 36.33 4.34
1401 1428 1.671742 GGAGGAACGTGGAAGAGCA 59.328 57.895 0.00 0.00 0.00 4.26
1413 1440 0.964358 GAAGAGCACCTGCAGGCATT 60.964 55.000 33.06 18.96 45.16 3.56
1427 1454 0.539438 GGCATTCACAACCTGGGTGA 60.539 55.000 20.68 10.28 43.12 4.02
1438 1465 0.400213 CCTGGGTGAGTTGCAGGTAA 59.600 55.000 0.00 0.00 0.00 2.85
1505 1532 1.349627 CTAAATCTGCGCTGCGTGG 59.650 57.895 24.04 15.85 0.00 4.94
1525 1552 1.893808 GCAATCGACGGCCATCCAT 60.894 57.895 2.24 0.00 0.00 3.41
1557 1584 2.229792 GTTGACATCAGCCAAGGAACA 58.770 47.619 0.00 0.00 0.00 3.18
1558 1585 2.189594 TGACATCAGCCAAGGAACAG 57.810 50.000 0.00 0.00 0.00 3.16
1560 1587 2.106338 TGACATCAGCCAAGGAACAGAA 59.894 45.455 0.00 0.00 0.00 3.02
1561 1588 2.485814 GACATCAGCCAAGGAACAGAAC 59.514 50.000 0.00 0.00 0.00 3.01
1562 1589 1.466167 CATCAGCCAAGGAACAGAACG 59.534 52.381 0.00 0.00 0.00 3.95
1563 1590 0.468226 TCAGCCAAGGAACAGAACGT 59.532 50.000 0.00 0.00 0.00 3.99
1564 1591 0.868406 CAGCCAAGGAACAGAACGTC 59.132 55.000 0.00 0.00 0.00 4.34
1565 1592 0.250338 AGCCAAGGAACAGAACGTCC 60.250 55.000 0.00 0.00 0.00 4.79
1570 1597 3.262420 CAAGGAACAGAACGTCCCTATG 58.738 50.000 0.00 0.00 0.00 2.23
1571 1598 1.831736 AGGAACAGAACGTCCCTATGG 59.168 52.381 0.00 0.00 0.00 2.74
1595 1625 8.692710 TGGTATTTATACGGAGGAGCAATATAG 58.307 37.037 0.00 0.00 34.11 1.31
1596 1626 8.142551 GGTATTTATACGGAGGAGCAATATAGG 58.857 40.741 0.00 0.00 34.11 2.57
1597 1627 5.593679 TTATACGGAGGAGCAATATAGGC 57.406 43.478 0.00 0.00 0.00 3.93
1598 1628 1.717032 ACGGAGGAGCAATATAGGCA 58.283 50.000 2.55 0.00 0.00 4.75
1599 1629 2.260822 ACGGAGGAGCAATATAGGCAT 58.739 47.619 2.55 0.00 0.00 4.40
1600 1630 2.234908 ACGGAGGAGCAATATAGGCATC 59.765 50.000 2.55 0.00 0.00 3.91
1602 1632 3.430098 CGGAGGAGCAATATAGGCATCTC 60.430 52.174 2.55 7.39 34.25 2.75
1603 1633 3.517100 GGAGGAGCAATATAGGCATCTCA 59.483 47.826 16.21 0.00 35.63 3.27
1604 1634 4.019860 GGAGGAGCAATATAGGCATCTCAA 60.020 45.833 16.21 0.00 35.63 3.02
1605 1635 5.339035 GGAGGAGCAATATAGGCATCTCAAT 60.339 44.000 16.21 0.00 35.63 2.57
1606 1636 6.137104 AGGAGCAATATAGGCATCTCAATT 57.863 37.500 2.55 0.00 0.00 2.32
1687 1738 3.445008 TCCCAGTCAGCTGTAAATCTCT 58.555 45.455 14.67 0.00 41.02 3.10
1752 2046 9.525409 GTATTAGTACAACGGATTGATTACACT 57.475 33.333 0.00 0.00 39.30 3.55
1758 2052 4.882671 ACGGATTGATTACACTCATTGC 57.117 40.909 0.00 0.00 0.00 3.56
1763 2057 5.528690 GGATTGATTACACTCATTGCTAGCA 59.471 40.000 14.93 14.93 0.00 3.49
1813 2123 8.668510 AAATCTCTAGTGCCACATATTACAAG 57.331 34.615 0.00 0.00 0.00 3.16
1852 2162 5.015515 TGGCCATCAAAACACTGATAATCA 58.984 37.500 0.00 0.00 34.20 2.57
1881 2191 9.039870 CATATTGCAGTGTTTTTAAAACCTCAA 57.960 29.630 16.62 16.13 0.00 3.02
1890 2200 6.805760 TGTTTTTAAAACCTCAACGTGTTACC 59.194 34.615 16.62 0.00 0.00 2.85
1892 2202 5.738118 TTAAAACCTCAACGTGTTACCAG 57.262 39.130 0.00 0.00 0.00 4.00
1910 2220 8.590204 TGTTACCAGATTTCACTATGTACTTCA 58.410 33.333 0.00 0.00 0.00 3.02
1925 2755 6.303021 TGTACTTCATGTTTCCGGTTTAAC 57.697 37.500 0.00 5.64 0.00 2.01
1938 2768 3.128068 CCGGTTTAACCTTTAGTGCATCC 59.872 47.826 12.66 0.00 35.66 3.51
1953 2783 4.081642 AGTGCATCCGTAGTTATCACAGTT 60.082 41.667 0.00 0.00 0.00 3.16
1966 2800 4.974645 ATCACAGTTGTTACCTTCCTGA 57.025 40.909 0.00 0.00 0.00 3.86
2006 2840 2.182537 GGCATTGCGCTTCAAGGG 59.817 61.111 9.73 0.00 41.91 3.95
2063 2906 5.183228 TCTCTCCGTGATGGGAATAAAAAC 58.817 41.667 0.00 0.00 38.76 2.43
2100 2943 0.531753 GCTAGGCCACTTAGCTCAGC 60.532 60.000 13.81 0.00 34.21 4.26
2118 2961 4.026744 TCAGCTTAGCCAGATGAGTAAGT 58.973 43.478 0.00 0.00 43.25 2.24
2120 2963 3.386402 AGCTTAGCCAGATGAGTAAGTCC 59.614 47.826 0.00 0.00 0.00 3.85
2133 2976 3.256704 AGTAAGTCCCTCCAATTCACCA 58.743 45.455 0.00 0.00 0.00 4.17
2142 2985 6.210584 GTCCCTCCAATTCACCAGAAAAATTA 59.789 38.462 0.00 0.00 37.29 1.40
2145 2988 7.765819 CCCTCCAATTCACCAGAAAAATTATTC 59.234 37.037 0.00 0.00 37.29 1.75
2356 3200 9.612620 CTAATTTTTACTTTGTAGGTCAGCAAG 57.387 33.333 0.00 0.00 0.00 4.01
2415 3259 8.909423 ATTTGTTTCCCATCCTTAAATCCTAA 57.091 30.769 0.00 0.00 0.00 2.69
2487 3332 8.677148 AAGTAGAAAAAGATGTGTATGTGTGT 57.323 30.769 0.00 0.00 0.00 3.72
2488 3333 8.087982 AGTAGAAAAAGATGTGTATGTGTGTG 57.912 34.615 0.00 0.00 0.00 3.82
2633 3482 3.369546 AAGGTGAAAATGGCGTCAAAG 57.630 42.857 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 3.740631 TCATCTGTCATGATCTTCCGG 57.259 47.619 0.00 0.00 0.00 5.14
73 74 6.420638 TCACCAAATCATCTGTCATGATCTT 58.579 36.000 0.00 0.00 37.75 2.40
75 76 6.688637 TTCACCAAATCATCTGTCATGATC 57.311 37.500 0.00 0.00 37.75 2.92
84 85 3.449737 CCCATTGCTTCACCAAATCATCT 59.550 43.478 0.00 0.00 0.00 2.90
167 168 5.702865 TGTTGACAAGCTCATTGAAATAGC 58.297 37.500 0.00 0.00 41.83 2.97
364 365 4.259356 TGATTCTCTTGGTCAGATTGCAG 58.741 43.478 0.00 0.00 0.00 4.41
410 411 1.651138 GCGATCGAACTTGTGTCAGAG 59.349 52.381 21.57 0.00 0.00 3.35
445 446 5.491070 CCTGTCAACAGAATCACCAGAATA 58.509 41.667 11.70 0.00 46.59 1.75
446 447 4.330250 CCTGTCAACAGAATCACCAGAAT 58.670 43.478 11.70 0.00 46.59 2.40
449 450 2.224621 ACCCTGTCAACAGAATCACCAG 60.225 50.000 11.70 0.00 46.59 4.00
452 453 3.375299 GCATACCCTGTCAACAGAATCAC 59.625 47.826 11.70 0.00 46.59 3.06
453 454 3.264193 AGCATACCCTGTCAACAGAATCA 59.736 43.478 11.70 0.00 46.59 2.57
454 455 3.873952 GAGCATACCCTGTCAACAGAATC 59.126 47.826 11.70 0.00 46.59 2.52
455 456 3.264193 TGAGCATACCCTGTCAACAGAAT 59.736 43.478 11.70 2.07 46.59 2.40
456 457 2.637382 TGAGCATACCCTGTCAACAGAA 59.363 45.455 11.70 0.00 46.59 3.02
457 458 2.256306 TGAGCATACCCTGTCAACAGA 58.744 47.619 11.70 0.00 46.59 3.41
458 459 2.768253 TGAGCATACCCTGTCAACAG 57.232 50.000 3.08 3.08 43.40 3.16
459 460 2.290260 CCTTGAGCATACCCTGTCAACA 60.290 50.000 0.00 0.00 0.00 3.33
460 461 2.359900 CCTTGAGCATACCCTGTCAAC 58.640 52.381 0.00 0.00 0.00 3.18
473 474 3.250040 TCGAACAAACTTTAGCCTTGAGC 59.750 43.478 0.00 0.00 44.25 4.26
477 478 3.813724 GGACTCGAACAAACTTTAGCCTT 59.186 43.478 0.00 0.00 0.00 4.35
490 491 3.576648 CTTCAACCACTAGGACTCGAAC 58.423 50.000 0.00 0.00 38.69 3.95
517 518 2.223829 CCATGTCGTCCAGAGTGATACC 60.224 54.545 0.00 0.00 0.00 2.73
522 523 0.738762 CAGCCATGTCGTCCAGAGTG 60.739 60.000 0.00 0.00 0.00 3.51
586 587 7.054751 ACTGCATCATCCTCATAATCCATATG 58.945 38.462 0.00 0.00 42.40 1.78
595 599 6.659668 GGTAGTAGTACTGCATCATCCTCATA 59.340 42.308 18.55 0.00 32.12 2.15
601 605 5.048364 CAGGAGGTAGTAGTACTGCATCATC 60.048 48.000 26.87 15.02 42.10 2.92
602 606 4.830046 CAGGAGGTAGTAGTACTGCATCAT 59.170 45.833 26.87 20.70 42.10 2.45
607 611 5.855740 ATTTCAGGAGGTAGTAGTACTGC 57.144 43.478 13.29 11.44 0.00 4.40
608 612 7.339721 TCAGAATTTCAGGAGGTAGTAGTACTG 59.660 40.741 13.29 0.00 0.00 2.74
613 617 8.017418 AGATTCAGAATTTCAGGAGGTAGTAG 57.983 38.462 0.00 0.00 0.00 2.57
614 618 7.979786 AGATTCAGAATTTCAGGAGGTAGTA 57.020 36.000 0.00 0.00 0.00 1.82
615 619 6.882768 AGATTCAGAATTTCAGGAGGTAGT 57.117 37.500 0.00 0.00 0.00 2.73
616 620 6.920758 CGTAGATTCAGAATTTCAGGAGGTAG 59.079 42.308 0.00 0.00 0.00 3.18
644 648 3.133901 TGCTATATCCAGCGTTTCCAGAA 59.866 43.478 0.00 0.00 44.88 3.02
664 668 3.070018 GGGTAGCATCATACACATCTGC 58.930 50.000 0.00 0.00 0.00 4.26
672 676 4.345257 TCTTCTGGAAGGGTAGCATCATAC 59.655 45.833 10.01 0.00 38.88 2.39
673 677 4.556697 TCTTCTGGAAGGGTAGCATCATA 58.443 43.478 10.01 0.00 38.88 2.15
808 815 5.175126 CGTTTATACAGGCTACGGAATTCTG 59.825 44.000 12.91 12.91 0.00 3.02
865 878 5.468746 GGTAGCAAGTGTCTGTATCAAAACA 59.531 40.000 0.00 0.00 0.00 2.83
874 887 0.687354 CCAGGGTAGCAAGTGTCTGT 59.313 55.000 0.00 0.00 0.00 3.41
875 888 0.674895 GCCAGGGTAGCAAGTGTCTG 60.675 60.000 0.00 0.00 0.00 3.51
876 889 1.679898 GCCAGGGTAGCAAGTGTCT 59.320 57.895 0.00 0.00 0.00 3.41
889 902 1.524621 CTACATTGCCCTCGCCAGG 60.525 63.158 0.00 0.00 39.98 4.45
893 906 0.389391 TAGAGCTACATTGCCCTCGC 59.611 55.000 0.00 0.00 0.00 5.03
976 995 3.069729 GGTAGAGATTGGTCGCCTTACAT 59.930 47.826 0.00 0.00 0.00 2.29
980 999 1.568504 TGGTAGAGATTGGTCGCCTT 58.431 50.000 0.00 0.00 0.00 4.35
981 1000 1.568504 TTGGTAGAGATTGGTCGCCT 58.431 50.000 0.00 0.00 0.00 5.52
1004 1023 2.208431 GCAGACGCTTCAGCTGATTAT 58.792 47.619 19.04 3.46 39.32 1.28
1006 1025 0.321034 TGCAGACGCTTCAGCTGATT 60.321 50.000 19.04 2.02 39.64 2.57
1017 1036 1.009829 CTGGTAAGGAATGCAGACGC 58.990 55.000 0.00 0.00 39.24 5.19
1060 1079 4.202357 TGGAATAGTAGGCATGCGATCTTT 60.202 41.667 12.44 0.77 0.00 2.52
1126 1145 3.134081 GGGTTCAACCTCTCGATTCCATA 59.866 47.826 6.51 0.00 38.64 2.74
1179 1206 2.930109 TCTTGAGGTAGAGAAGGGCT 57.070 50.000 0.00 0.00 0.00 5.19
1213 1240 0.095245 ACGATTGTTTCAGCGATGCG 59.905 50.000 0.00 0.00 0.00 4.73
1240 1267 2.529136 CCCACTCCCACTCCCACA 60.529 66.667 0.00 0.00 0.00 4.17
1259 1286 4.645809 CTGGGAAAGCTGCCCTAC 57.354 61.111 21.84 1.15 46.19 3.18
1285 1312 3.674753 GGCGAACAAATGAGGTTGAAATG 59.325 43.478 0.00 0.00 32.59 2.32
1291 1318 1.579429 GCGGCGAACAAATGAGGTT 59.421 52.632 12.98 0.00 0.00 3.50
1333 1360 0.034767 CTCTGGAGCTTGGGCATTGA 60.035 55.000 0.00 0.00 41.70 2.57
1401 1428 1.181098 GGTTGTGAATGCCTGCAGGT 61.181 55.000 32.81 14.76 37.57 4.00
1413 1440 0.465460 GCAACTCACCCAGGTTGTGA 60.465 55.000 0.00 0.00 43.07 3.58
1427 1454 2.829720 TGTACCGAGATTACCTGCAACT 59.170 45.455 0.00 0.00 0.00 3.16
1505 1532 2.709475 GATGGCCGTCGATTGCAC 59.291 61.111 9.75 2.24 0.00 4.57
1525 1552 0.756294 ATGTCAACACGAGGGTCACA 59.244 50.000 0.00 0.00 0.00 3.58
1557 1584 6.071728 CCGTATAAATACCATAGGGACGTTCT 60.072 42.308 0.00 0.00 36.45 3.01
1558 1585 6.071952 TCCGTATAAATACCATAGGGACGTTC 60.072 42.308 0.00 0.00 37.77 3.95
1560 1587 5.324409 TCCGTATAAATACCATAGGGACGT 58.676 41.667 0.00 0.00 37.77 4.34
1561 1588 5.163581 CCTCCGTATAAATACCATAGGGACG 60.164 48.000 0.00 0.00 37.77 4.79
1562 1589 5.954150 TCCTCCGTATAAATACCATAGGGAC 59.046 44.000 0.00 0.00 37.77 4.46
1563 1590 6.156554 TCCTCCGTATAAATACCATAGGGA 57.843 41.667 0.00 4.31 39.44 4.20
1564 1591 5.163437 GCTCCTCCGTATAAATACCATAGGG 60.163 48.000 0.00 0.00 41.29 3.53
1565 1592 5.421056 TGCTCCTCCGTATAAATACCATAGG 59.579 44.000 0.00 0.00 0.00 2.57
1570 1597 8.142551 CCTATATTGCTCCTCCGTATAAATACC 58.857 40.741 0.00 0.00 0.00 2.73
1571 1598 7.652507 GCCTATATTGCTCCTCCGTATAAATAC 59.347 40.741 0.00 0.00 0.00 1.89
1595 1625 2.945008 TCATCGTCCAAATTGAGATGCC 59.055 45.455 15.66 0.00 38.71 4.40
1596 1626 4.825546 ATCATCGTCCAAATTGAGATGC 57.174 40.909 15.66 0.00 38.71 3.91
1597 1627 6.652062 TCCATATCATCGTCCAAATTGAGATG 59.348 38.462 14.86 14.86 37.49 2.90
1598 1628 6.652481 GTCCATATCATCGTCCAAATTGAGAT 59.348 38.462 0.00 0.00 0.00 2.75
1599 1629 5.991606 GTCCATATCATCGTCCAAATTGAGA 59.008 40.000 0.00 0.00 0.00 3.27
1600 1630 5.759763 TGTCCATATCATCGTCCAAATTGAG 59.240 40.000 0.00 0.00 0.00 3.02
1602 1632 6.429078 AGATGTCCATATCATCGTCCAAATTG 59.571 38.462 0.00 0.00 44.20 2.32
1603 1633 6.537355 AGATGTCCATATCATCGTCCAAATT 58.463 36.000 0.00 0.00 44.20 1.82
1604 1634 6.119240 AGATGTCCATATCATCGTCCAAAT 57.881 37.500 0.00 0.00 44.20 2.32
1605 1635 5.511373 GGAGATGTCCATATCATCGTCCAAA 60.511 44.000 3.49 0.00 44.20 3.28
1606 1636 4.021104 GGAGATGTCCATATCATCGTCCAA 60.021 45.833 3.49 0.00 44.20 3.53
1707 1764 2.457598 ACCTAGCTTCCAGATCGTTCA 58.542 47.619 0.00 0.00 0.00 3.18
1712 1769 7.762588 TGTACTAATACCTAGCTTCCAGATC 57.237 40.000 0.00 0.00 0.00 2.75
1778 2076 8.349983 TGTGGCACTAGAGATTTTCTTTTAAAC 58.650 33.333 19.83 0.00 37.36 2.01
1784 2082 9.331282 GTAATATGTGGCACTAGAGATTTTCTT 57.669 33.333 19.83 0.47 37.36 2.52
1792 2090 9.197694 GATTACTTGTAATATGTGGCACTAGAG 57.802 37.037 19.83 7.75 0.00 2.43
1881 2191 5.790593 ACATAGTGAAATCTGGTAACACGT 58.209 37.500 0.00 0.00 46.17 4.49
1890 2200 9.979270 GAAACATGAAGTACATAGTGAAATCTG 57.021 33.333 0.00 0.00 37.46 2.90
1892 2202 8.116753 CGGAAACATGAAGTACATAGTGAAATC 58.883 37.037 0.00 0.00 37.46 2.17
1910 2220 5.278610 GCACTAAAGGTTAAACCGGAAACAT 60.279 40.000 9.46 4.28 44.90 2.71
1925 2755 5.462398 GTGATAACTACGGATGCACTAAAGG 59.538 44.000 0.00 0.00 0.00 3.11
1938 2768 6.309737 GGAAGGTAACAACTGTGATAACTACG 59.690 42.308 0.00 0.00 29.26 3.51
1953 2783 3.346315 CATGCATGTCAGGAAGGTAACA 58.654 45.455 18.91 0.00 41.41 2.41
2006 2840 2.163412 TGCAAGGGCGTCAATTAATCAC 59.837 45.455 0.00 0.00 45.35 3.06
2100 2943 3.964031 AGGGACTTACTCATCTGGCTAAG 59.036 47.826 0.00 0.00 27.25 2.18
2118 2961 3.893753 TTTTCTGGTGAATTGGAGGGA 57.106 42.857 0.00 0.00 31.56 4.20
2120 2963 8.313292 TGAATAATTTTTCTGGTGAATTGGAGG 58.687 33.333 9.59 0.00 31.56 4.30
2142 2985 6.725364 ACAACATTGTCTCTAAGGGATGAAT 58.275 36.000 0.00 0.00 36.50 2.57
2145 2988 9.613428 TTATAACAACATTGTCTCTAAGGGATG 57.387 33.333 0.00 0.00 41.31 3.51
2212 3056 8.861086 CCTTTTGCTACTAATCTGATCCTAGTA 58.139 37.037 8.29 8.29 0.00 1.82
2217 3061 9.160496 CATATCCTTTTGCTACTAATCTGATCC 57.840 37.037 0.00 0.00 0.00 3.36
2385 3229 9.533253 GATTTAAGGATGGGAAACAAATACATG 57.467 33.333 0.00 0.00 0.00 3.21
2386 3230 8.704668 GGATTTAAGGATGGGAAACAAATACAT 58.295 33.333 0.00 0.00 0.00 2.29
2464 3308 7.798516 CACACACACATACACATCTTTTTCTAC 59.201 37.037 0.00 0.00 0.00 2.59
2487 3332 8.744568 TGAAGGAACAACATATATAATGCACA 57.255 30.769 0.00 0.00 0.00 4.57
2488 3333 9.669353 CTTGAAGGAACAACATATATAATGCAC 57.331 33.333 0.00 0.00 0.00 4.57
2562 3411 9.283768 CACATATATGCACATACCCTTTTTCTA 57.716 33.333 12.79 0.00 0.00 2.10
2565 3414 6.748132 GCACATATATGCACATACCCTTTTT 58.252 36.000 12.79 0.00 45.39 1.94


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

AutoCloner maintained by Alex Coulton.