Multiple sequence alignment - TraesCS1D01G408500

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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 TraesCS1D01G408500 chr1D 100.000 2714 0 0 1 2714 470735307 470732594 0.000000e+00 5012.0
1 TraesCS1D01G408500 chr1A 92.174 1840 87 20 890 2714 564397750 564395953 0.000000e+00 2547.0
2 TraesCS1D01G408500 chr1A 87.097 341 22 8 10 342 564398356 564398030 1.540000e-97 366.0
3 TraesCS1D01G408500 chr1A 88.636 176 10 5 680 850 564397920 564397750 3.540000e-49 206.0
4 TraesCS1D01G408500 chr1B 86.068 2426 202 66 348 2714 654032719 654030371 0.000000e+00 2483.0
5 TraesCS1D01G408500 chr1B 91.391 302 13 5 1 292 654033649 654033351 4.210000e-108 401.0
6 TraesCS1D01G408500 chr1B 96.774 31 1 0 296 326 654033321 654033291 5.000000e-03 52.8


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 TraesCS1D01G408500 chr1D 470732594 470735307 2713 True 5012.000000 5012 100.000000 1 2714 1 chr1D.!!$R1 2713
1 TraesCS1D01G408500 chr1A 564395953 564398356 2403 True 1039.666667 2547 89.302333 10 2714 3 chr1A.!!$R1 2704
2 TraesCS1D01G408500 chr1B 654030371 654033649 3278 True 978.933333 2483 91.411000 1 2714 3 chr1B.!!$R1 2713

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
426 1019 0.105964 CGTGTGGTTGGGTCTCTTCA 59.894 55.0 0.0 0.0 0.0 3.02 F
431 1024 0.107654 GGTTGGGTCTCTTCATCCGG 60.108 60.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 2423 0.313987 CAACTCCCGGCTCCAAAAAC 59.686 55.000 0.00 0.00 0.0 2.43 R
1805 2544 2.022195 CATGGCCATGACCTCTTCTTG 58.978 52.381 37.84 10.15 41.2 3.02 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
48 49 1.264557 CATAGCACGACTACGCTAGCT 59.735 52.381 13.93 2.46 43.58 3.32
57 58 1.309950 CTACGCTAGCTAGCTCACCA 58.690 55.000 36.02 18.72 46.85 4.17
124 135 5.066968 ACGTGAGGAAAAAGAGAGAGATC 57.933 43.478 0.00 0.00 0.00 2.75
133 144 0.250124 AGAGAGAGATCGCGATCGGT 60.250 55.000 35.89 28.62 42.48 4.69
158 169 2.356278 GTCAAGGGCTGGCCATCA 59.644 61.111 23.25 0.00 37.98 3.07
260 275 9.490663 CACTATTTTGAAGATACGGTGAAAATC 57.509 33.333 0.00 0.00 0.00 2.17
267 282 5.779806 AGATACGGTGAAAATCGACTTTG 57.220 39.130 0.00 0.00 0.00 2.77
279 294 4.935885 ATCGACTTTGACTTGAAGATGC 57.064 40.909 0.00 0.00 0.00 3.91
342 413 3.784701 TGCTTCTCAAGACTACGATCC 57.215 47.619 0.00 0.00 0.00 3.36
343 414 3.089284 TGCTTCTCAAGACTACGATCCA 58.911 45.455 0.00 0.00 0.00 3.41
346 417 4.732355 GCTTCTCAAGACTACGATCCACTC 60.732 50.000 0.00 0.00 0.00 3.51
368 961 2.203001 CACATGCCGCCGATGGTA 60.203 61.111 0.00 0.00 0.00 3.25
381 974 4.690748 CGCCGATGGTATCTTCAATAACAT 59.309 41.667 0.00 0.00 34.85 2.71
382 975 5.179368 CGCCGATGGTATCTTCAATAACATT 59.821 40.000 0.00 0.00 32.52 2.71
388 981 8.915057 ATGGTATCTTCAATAACATTCCTCAG 57.085 34.615 0.00 0.00 28.16 3.35
390 983 8.328758 TGGTATCTTCAATAACATTCCTCAGTT 58.671 33.333 0.00 0.00 0.00 3.16
406 999 1.226128 GTTGCGCTTTCGGCATCTC 60.226 57.895 9.73 0.00 40.62 2.75
407 1000 2.398554 TTGCGCTTTCGGCATCTCC 61.399 57.895 9.73 0.00 40.62 3.71
423 1016 1.458777 TCCGTGTGGTTGGGTCTCT 60.459 57.895 0.00 0.00 36.30 3.10
426 1019 0.105964 CGTGTGGTTGGGTCTCTTCA 59.894 55.000 0.00 0.00 0.00 3.02
427 1020 1.270839 CGTGTGGTTGGGTCTCTTCAT 60.271 52.381 0.00 0.00 0.00 2.57
431 1024 0.107654 GGTTGGGTCTCTTCATCCGG 60.108 60.000 0.00 0.00 0.00 5.14
432 1025 0.613777 GTTGGGTCTCTTCATCCGGT 59.386 55.000 0.00 0.00 0.00 5.28
434 1027 1.320344 TGGGTCTCTTCATCCGGTCG 61.320 60.000 0.00 0.00 0.00 4.79
438 1031 0.809385 TCTCTTCATCCGGTCGTCAC 59.191 55.000 0.00 0.00 0.00 3.67
440 1033 0.809385 TCTTCATCCGGTCGTCACTC 59.191 55.000 0.00 0.00 0.00 3.51
448 1041 1.269998 CCGGTCGTCACTCTTCTTCTT 59.730 52.381 0.00 0.00 0.00 2.52
453 1047 2.225963 TCGTCACTCTTCTTCTTCGGAC 59.774 50.000 0.00 0.00 0.00 4.79
461 1055 5.184340 TCTTCTTCTTCGGACCGATAATC 57.816 43.478 19.12 0.00 35.23 1.75
479 1073 2.378445 TCCGTGCTTCGAATCATCAA 57.622 45.000 4.82 0.00 42.86 2.57
480 1074 1.999735 TCCGTGCTTCGAATCATCAAC 59.000 47.619 4.82 0.00 42.86 3.18
482 1076 1.802839 GTGCTTCGAATCATCAACGC 58.197 50.000 4.82 0.00 0.00 4.84
483 1077 1.394917 GTGCTTCGAATCATCAACGCT 59.605 47.619 4.82 0.00 0.00 5.07
485 1079 1.267732 GCTTCGAATCATCAACGCTGG 60.268 52.381 0.00 0.00 0.00 4.85
486 1080 0.726827 TTCGAATCATCAACGCTGGC 59.273 50.000 0.00 0.00 0.00 4.85
490 1084 3.974835 ATCATCAACGCTGGCGCCA 62.975 57.895 30.59 30.59 44.19 5.69
503 1097 1.068921 GCGCCACCCAACAACATTT 59.931 52.632 0.00 0.00 0.00 2.32
508 1102 2.036992 GCCACCCAACAACATTTGATGA 59.963 45.455 0.00 0.00 35.70 2.92
512 1106 4.746115 CACCCAACAACATTTGATGACTTG 59.254 41.667 0.00 0.00 35.70 3.16
514 1108 5.104982 ACCCAACAACATTTGATGACTTGTT 60.105 36.000 0.00 4.69 38.93 2.83
527 1121 2.742774 GACTTGTTGTCAATGTTGGCC 58.257 47.619 0.00 0.00 44.73 5.36
531 1125 1.152652 TTGTCAATGTTGGCCCCGT 60.153 52.632 0.00 0.00 30.03 5.28
535 1129 0.916086 TCAATGTTGGCCCCGTCTAT 59.084 50.000 0.00 0.00 0.00 1.98
539 1133 1.377987 GTTGGCCCCGTCTATGCAA 60.378 57.895 0.00 0.00 0.00 4.08
560 1155 1.075374 ACCAGGTGCAAAATGGAGCTA 59.925 47.619 17.47 0.00 44.63 3.32
564 1159 1.134995 GGTGCAAAATGGAGCTAAGCC 60.135 52.381 0.00 0.00 33.31 4.35
573 1168 4.796231 AGCTAAGCCCACGTCGCG 62.796 66.667 0.00 0.00 0.00 5.87
600 1195 2.453638 GCGTGCGGGTAAGAGAAGC 61.454 63.158 0.00 0.00 0.00 3.86
610 1205 3.449632 GGTAAGAGAAGCCGTTCATCTC 58.550 50.000 0.00 0.00 39.24 2.75
612 1207 4.338682 GGTAAGAGAAGCCGTTCATCTCTA 59.661 45.833 9.19 0.00 45.97 2.43
613 1208 4.647424 AAGAGAAGCCGTTCATCTCTAG 57.353 45.455 9.19 0.00 45.97 2.43
619 1214 1.476891 GCCGTTCATCTCTAGTGGACA 59.523 52.381 0.00 0.00 0.00 4.02
622 1217 3.119291 CGTTCATCTCTAGTGGACATGC 58.881 50.000 0.00 0.00 0.00 4.06
624 1219 2.042464 TCATCTCTAGTGGACATGCCC 58.958 52.381 0.00 0.00 34.97 5.36
633 1228 3.161866 AGTGGACATGCCCGTAATTTTT 58.838 40.909 0.00 0.00 34.97 1.94
637 1232 6.071051 AGTGGACATGCCCGTAATTTTTAATT 60.071 34.615 0.00 0.00 34.97 1.40
642 1237 9.361315 GACATGCCCGTAATTTTTAATTTTACT 57.639 29.630 0.00 0.00 0.00 2.24
643 1238 9.145865 ACATGCCCGTAATTTTTAATTTTACTG 57.854 29.630 0.00 0.00 0.00 2.74
646 1241 8.800332 TGCCCGTAATTTTTAATTTTACTGGTA 58.200 29.630 8.38 3.19 34.53 3.25
647 1242 9.292846 GCCCGTAATTTTTAATTTTACTGGTAG 57.707 33.333 8.38 0.00 34.53 3.18
666 1313 5.163405 TGGTAGTGATTTCATAGGTCTCAGC 60.163 44.000 0.00 0.00 0.00 4.26
670 1317 5.045286 AGTGATTTCATAGGTCTCAGCCTTT 60.045 40.000 0.00 0.00 39.94 3.11
734 1383 9.459640 GGAATTTTCCTTCAAACTTTACACTAC 57.540 33.333 1.97 0.00 44.11 2.73
850 1516 1.663702 CACCGCTCGAAAACGACCT 60.664 57.895 3.94 0.00 0.00 3.85
851 1517 1.663702 ACCGCTCGAAAACGACCTG 60.664 57.895 3.94 0.00 0.00 4.00
852 1518 2.470286 CGCTCGAAAACGACCTGC 59.530 61.111 0.00 0.00 0.00 4.85
854 1520 2.470286 CTCGAAAACGACCTGCGC 59.530 61.111 0.00 0.00 46.04 6.09
855 1521 3.335259 CTCGAAAACGACCTGCGCG 62.335 63.158 0.00 0.00 46.04 6.86
869 1535 4.186172 CGCGCGCGTGTTATCGTT 62.186 61.111 42.49 0.00 34.35 3.85
870 1536 2.640457 GCGCGCGTGTTATCGTTG 60.640 61.111 32.35 0.00 0.00 4.10
871 1537 2.640457 CGCGCGTGTTATCGTTGC 60.640 61.111 24.19 0.00 0.00 4.17
872 1538 2.276430 GCGCGTGTTATCGTTGCC 60.276 61.111 8.43 0.00 0.00 4.52
873 1539 2.398036 CGCGTGTTATCGTTGCCC 59.602 61.111 0.00 0.00 0.00 5.36
874 1540 2.098233 CGCGTGTTATCGTTGCCCT 61.098 57.895 0.00 0.00 0.00 5.19
875 1541 1.423845 GCGTGTTATCGTTGCCCTG 59.576 57.895 0.00 0.00 0.00 4.45
876 1542 1.296056 GCGTGTTATCGTTGCCCTGT 61.296 55.000 0.00 0.00 0.00 4.00
877 1543 0.719465 CGTGTTATCGTTGCCCTGTC 59.281 55.000 0.00 0.00 0.00 3.51
878 1544 1.671850 CGTGTTATCGTTGCCCTGTCT 60.672 52.381 0.00 0.00 0.00 3.41
879 1545 2.423577 GTGTTATCGTTGCCCTGTCTT 58.576 47.619 0.00 0.00 0.00 3.01
880 1546 2.415512 GTGTTATCGTTGCCCTGTCTTC 59.584 50.000 0.00 0.00 0.00 2.87
881 1547 2.007608 GTTATCGTTGCCCTGTCTTCC 58.992 52.381 0.00 0.00 0.00 3.46
882 1548 1.568504 TATCGTTGCCCTGTCTTCCT 58.431 50.000 0.00 0.00 0.00 3.36
883 1549 0.693049 ATCGTTGCCCTGTCTTCCTT 59.307 50.000 0.00 0.00 0.00 3.36
884 1550 0.250295 TCGTTGCCCTGTCTTCCTTG 60.250 55.000 0.00 0.00 0.00 3.61
885 1551 0.535102 CGTTGCCCTGTCTTCCTTGT 60.535 55.000 0.00 0.00 0.00 3.16
886 1552 1.270625 CGTTGCCCTGTCTTCCTTGTA 60.271 52.381 0.00 0.00 0.00 2.41
887 1553 2.152016 GTTGCCCTGTCTTCCTTGTAC 58.848 52.381 0.00 0.00 0.00 2.90
888 1554 1.429930 TGCCCTGTCTTCCTTGTACA 58.570 50.000 0.00 0.00 0.00 2.90
889 1555 1.071699 TGCCCTGTCTTCCTTGTACAC 59.928 52.381 0.00 0.00 0.00 2.90
890 1556 1.939838 GCCCTGTCTTCCTTGTACACG 60.940 57.143 0.00 0.00 0.00 4.49
891 1557 1.616865 CCCTGTCTTCCTTGTACACGA 59.383 52.381 0.00 0.00 0.00 4.35
892 1558 2.609737 CCCTGTCTTCCTTGTACACGAC 60.610 54.545 0.00 1.89 0.00 4.34
985 1679 2.631428 CATAAATCACGCCGCCCG 59.369 61.111 0.00 0.00 44.21 6.13
1008 1703 2.748465 CGAAGACCCACCCAAAAGACTT 60.748 50.000 0.00 0.00 0.00 3.01
1009 1704 2.658807 AGACCCACCCAAAAGACTTC 57.341 50.000 0.00 0.00 0.00 3.01
1010 1705 1.145119 AGACCCACCCAAAAGACTTCC 59.855 52.381 0.00 0.00 0.00 3.46
1012 1707 0.187361 CCCACCCAAAAGACTTCCCA 59.813 55.000 0.00 0.00 0.00 4.37
1016 1711 1.063266 ACCCAAAAGACTTCCCAAGCA 60.063 47.619 0.00 0.00 0.00 3.91
1018 1713 2.031120 CCAAAAGACTTCCCAAGCACA 58.969 47.619 0.00 0.00 0.00 4.57
1019 1714 2.035066 CCAAAAGACTTCCCAAGCACAG 59.965 50.000 0.00 0.00 0.00 3.66
1020 1715 1.322442 AAAGACTTCCCAAGCACAGC 58.678 50.000 0.00 0.00 0.00 4.40
1021 1716 0.538287 AAGACTTCCCAAGCACAGCC 60.538 55.000 0.00 0.00 0.00 4.85
1022 1717 2.281761 ACTTCCCAAGCACAGCCG 60.282 61.111 0.00 0.00 0.00 5.52
1456 2160 0.248843 CGCTCTCCTGCTTCTTCCTT 59.751 55.000 0.00 0.00 0.00 3.36
1565 2283 5.585500 TTTTTCGTTTTCATCGATCGTCT 57.415 34.783 15.94 0.69 37.18 4.18
1566 2284 6.693761 TTTTTCGTTTTCATCGATCGTCTA 57.306 33.333 15.94 0.00 37.18 2.59
1567 2285 5.675778 TTTCGTTTTCATCGATCGTCTAC 57.324 39.130 15.94 5.43 37.18 2.59
1568 2286 4.611310 TCGTTTTCATCGATCGTCTACT 57.389 40.909 15.94 0.00 32.30 2.57
1638 2361 4.885907 TCCCAATCTGCTCAAGATGATTTC 59.114 41.667 0.00 0.00 45.37 2.17
1685 2423 5.327616 TGGATGGTGTGATGCAATTTTAG 57.672 39.130 0.00 0.00 0.00 1.85
1743 2482 1.959747 CTGTCTCGTGCAAATGCTTG 58.040 50.000 6.97 0.00 42.66 4.01
1752 2491 2.699910 CAAATGCTTGCACGACGAC 58.300 52.632 0.00 0.00 0.00 4.34
1753 2492 1.054348 CAAATGCTTGCACGACGACG 61.054 55.000 5.58 5.58 45.75 5.12
1805 2544 1.194781 TGGGAGTGAAGGAGGACTGC 61.195 60.000 0.00 0.00 0.00 4.40
2638 3386 2.444895 GACGGCCAGGAGGAGGAT 60.445 66.667 2.24 0.00 36.89 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 144 2.070039 CAGCCCTTGACCCCGGATA 61.070 63.158 0.73 0.00 0.00 2.59
145 156 2.277737 CATGTGATGGCCAGCCCT 59.722 61.111 20.33 0.00 34.56 5.19
260 275 3.742882 TCTGCATCTTCAAGTCAAAGTCG 59.257 43.478 0.00 0.00 0.00 4.18
279 294 0.324091 AAGCCTTGGGGAGCAATCTG 60.324 55.000 0.00 0.00 33.58 2.90
342 413 3.027170 GCGGCATGTGGAACGAGTG 62.027 63.158 0.00 0.00 42.39 3.51
343 414 2.742372 GCGGCATGTGGAACGAGT 60.742 61.111 0.00 0.00 42.39 4.18
347 418 2.824041 ATCGGCGGCATGTGGAAC 60.824 61.111 10.53 0.00 37.35 3.62
349 420 4.854924 CCATCGGCGGCATGTGGA 62.855 66.667 16.25 2.39 31.59 4.02
350 421 3.748660 TACCATCGGCGGCATGTGG 62.749 63.158 18.65 18.65 36.06 4.17
353 946 0.603707 AAGATACCATCGGCGGCATG 60.604 55.000 10.53 11.68 0.00 4.06
363 956 8.497745 ACTGAGGAATGTTATTGAAGATACCAT 58.502 33.333 0.00 0.00 0.00 3.55
368 961 6.183360 CGCAACTGAGGAATGTTATTGAAGAT 60.183 38.462 0.00 0.00 0.00 2.40
381 974 1.227999 CCGAAAGCGCAACTGAGGAA 61.228 55.000 11.47 0.00 35.83 3.36
382 975 1.667830 CCGAAAGCGCAACTGAGGA 60.668 57.895 11.47 0.00 35.83 3.71
406 999 0.602905 GAAGAGACCCAACCACACGG 60.603 60.000 0.00 0.00 38.77 4.94
407 1000 0.105964 TGAAGAGACCCAACCACACG 59.894 55.000 0.00 0.00 0.00 4.49
423 1016 1.201647 GAAGAGTGACGACCGGATGAA 59.798 52.381 9.46 0.00 0.00 2.57
426 1019 1.473278 GAAGAAGAGTGACGACCGGAT 59.527 52.381 9.46 0.00 0.00 4.18
427 1020 0.879765 GAAGAAGAGTGACGACCGGA 59.120 55.000 9.46 0.00 0.00 5.14
431 1024 2.225963 TCCGAAGAAGAAGAGTGACGAC 59.774 50.000 0.00 0.00 0.00 4.34
432 1025 2.225963 GTCCGAAGAAGAAGAGTGACGA 59.774 50.000 0.00 0.00 0.00 4.20
434 1027 2.668834 CGGTCCGAAGAAGAAGAGTGAC 60.669 54.545 4.91 0.00 0.00 3.67
438 1031 4.634184 TTATCGGTCCGAAGAAGAAGAG 57.366 45.455 19.76 0.00 39.99 2.85
440 1033 4.299978 GGATTATCGGTCCGAAGAAGAAG 58.700 47.826 19.76 0.00 39.99 2.85
453 1047 1.847818 TTCGAAGCACGGATTATCGG 58.152 50.000 0.00 0.00 42.82 4.18
461 1055 1.267038 CGTTGATGATTCGAAGCACGG 60.267 52.381 19.71 2.57 42.82 4.94
482 1076 3.977244 GTTGTTGGGTGGCGCCAG 61.977 66.667 33.73 0.00 39.65 4.85
483 1077 4.822628 TGTTGTTGGGTGGCGCCA 62.823 61.111 29.03 29.03 39.65 5.69
485 1079 1.068921 AAATGTTGTTGGGTGGCGC 59.931 52.632 0.00 0.00 0.00 6.53
486 1080 0.387202 TCAAATGTTGTTGGGTGGCG 59.613 50.000 0.00 0.00 0.00 5.69
490 1084 4.405358 ACAAGTCATCAAATGTTGTTGGGT 59.595 37.500 0.55 0.00 28.65 4.51
508 1102 1.412343 GGGCCAACATTGACAACAAGT 59.588 47.619 4.39 0.00 39.46 3.16
512 1106 1.288752 CGGGGCCAACATTGACAAC 59.711 57.895 4.39 0.00 0.00 3.32
514 1108 1.602323 GACGGGGCCAACATTGACA 60.602 57.895 4.39 0.00 0.00 3.58
518 1112 0.751643 GCATAGACGGGGCCAACATT 60.752 55.000 4.39 0.00 0.00 2.71
527 1121 0.035439 ACCTGGTTTGCATAGACGGG 60.035 55.000 0.00 0.00 0.00 5.28
539 1133 0.681175 GCTCCATTTTGCACCTGGTT 59.319 50.000 0.00 0.00 0.00 3.67
553 1147 2.978824 GACGTGGGCTTAGCTCCA 59.021 61.111 0.00 5.96 0.00 3.86
554 1148 2.202756 CGACGTGGGCTTAGCTCC 60.203 66.667 0.00 3.06 0.00 4.70
582 1177 2.453638 GCTTCTCTTACCCGCACGC 61.454 63.158 0.00 0.00 0.00 5.34
583 1178 1.810030 GGCTTCTCTTACCCGCACG 60.810 63.158 0.00 0.00 0.00 5.34
585 1180 1.823169 AACGGCTTCTCTTACCCGCA 61.823 55.000 0.00 0.00 44.29 5.69
589 1184 3.449632 GAGATGAACGGCTTCTCTTACC 58.550 50.000 12.93 0.00 41.91 2.85
600 1195 3.711086 CATGTCCACTAGAGATGAACGG 58.289 50.000 0.00 0.00 46.76 4.44
602 1197 3.462021 GGCATGTCCACTAGAGATGAAC 58.538 50.000 0.00 0.00 46.76 3.18
603 1198 2.435805 GGGCATGTCCACTAGAGATGAA 59.564 50.000 12.68 0.00 46.76 2.57
604 1199 2.042464 GGGCATGTCCACTAGAGATGA 58.958 52.381 12.68 0.00 46.76 2.92
610 1205 2.910688 ATTACGGGCATGTCCACTAG 57.089 50.000 18.31 1.81 36.21 2.57
611 1206 3.637911 AAATTACGGGCATGTCCACTA 57.362 42.857 18.31 1.50 36.21 2.74
612 1207 2.507407 AAATTACGGGCATGTCCACT 57.493 45.000 18.31 2.61 36.21 4.00
613 1208 3.586100 AAAAATTACGGGCATGTCCAC 57.414 42.857 18.31 1.50 36.21 4.02
619 1214 8.315482 ACCAGTAAAATTAAAAATTACGGGCAT 58.685 29.630 18.53 6.36 43.95 4.40
637 1232 8.375493 AGACCTATGAAATCACTACCAGTAAA 57.625 34.615 0.00 0.00 0.00 2.01
642 1237 5.163405 GCTGAGACCTATGAAATCACTACCA 60.163 44.000 0.00 0.00 0.00 3.25
643 1238 5.293560 GCTGAGACCTATGAAATCACTACC 58.706 45.833 0.00 0.00 0.00 3.18
646 1241 4.036518 AGGCTGAGACCTATGAAATCACT 58.963 43.478 0.00 0.00 38.67 3.41
647 1242 4.414337 AGGCTGAGACCTATGAAATCAC 57.586 45.455 0.00 0.00 38.67 3.06
734 1383 8.509690 GGTGATCCATGTTAATTATCACTGATG 58.490 37.037 12.60 2.90 43.72 3.07
749 1399 6.070656 TCTTTTCAGAAAAGGTGATCCATGT 58.929 36.000 28.05 0.00 46.11 3.21
853 1519 2.640457 CAACGATAACACGCGCGC 60.640 61.111 32.58 23.91 36.70 6.86
854 1520 2.640457 GCAACGATAACACGCGCG 60.640 61.111 30.96 30.96 36.70 6.86
855 1521 2.276430 GGCAACGATAACACGCGC 60.276 61.111 5.73 0.00 36.70 6.86
856 1522 2.098233 AGGGCAACGATAACACGCG 61.098 57.895 3.53 3.53 36.70 6.01
857 1523 1.296056 ACAGGGCAACGATAACACGC 61.296 55.000 0.00 0.00 36.70 5.34
858 1524 0.719465 GACAGGGCAACGATAACACG 59.281 55.000 0.00 0.00 39.31 4.49
859 1525 2.094762 AGACAGGGCAACGATAACAC 57.905 50.000 0.00 0.00 37.60 3.32
860 1526 2.614481 GGAAGACAGGGCAACGATAACA 60.614 50.000 0.00 0.00 37.60 2.41
861 1527 2.007608 GGAAGACAGGGCAACGATAAC 58.992 52.381 0.00 0.00 37.60 1.89
862 1528 1.906574 AGGAAGACAGGGCAACGATAA 59.093 47.619 0.00 0.00 37.60 1.75
863 1529 1.568504 AGGAAGACAGGGCAACGATA 58.431 50.000 0.00 0.00 37.60 2.92
864 1530 0.693049 AAGGAAGACAGGGCAACGAT 59.307 50.000 0.00 0.00 37.60 3.73
865 1531 0.250295 CAAGGAAGACAGGGCAACGA 60.250 55.000 0.00 0.00 37.60 3.85
866 1532 0.535102 ACAAGGAAGACAGGGCAACG 60.535 55.000 0.00 0.00 37.60 4.10
867 1533 2.152016 GTACAAGGAAGACAGGGCAAC 58.848 52.381 0.00 0.00 0.00 4.17
868 1534 1.771854 TGTACAAGGAAGACAGGGCAA 59.228 47.619 0.00 0.00 0.00 4.52
869 1535 1.071699 GTGTACAAGGAAGACAGGGCA 59.928 52.381 0.00 0.00 0.00 5.36
870 1536 1.809684 GTGTACAAGGAAGACAGGGC 58.190 55.000 0.00 0.00 0.00 5.19
871 1537 1.616865 TCGTGTACAAGGAAGACAGGG 59.383 52.381 8.98 0.00 31.53 4.45
872 1538 2.673833 GTCGTGTACAAGGAAGACAGG 58.326 52.381 8.98 0.00 0.00 4.00
873 1539 2.316792 CGTCGTGTACAAGGAAGACAG 58.683 52.381 8.98 2.88 0.00 3.51
874 1540 1.601162 GCGTCGTGTACAAGGAAGACA 60.601 52.381 8.98 0.00 0.00 3.41
875 1541 1.058404 GCGTCGTGTACAAGGAAGAC 58.942 55.000 8.98 7.56 0.00 3.01
876 1542 0.038892 GGCGTCGTGTACAAGGAAGA 60.039 55.000 8.98 0.00 0.00 2.87
877 1543 0.319211 TGGCGTCGTGTACAAGGAAG 60.319 55.000 8.98 7.68 0.00 3.46
878 1544 0.104487 TTGGCGTCGTGTACAAGGAA 59.896 50.000 8.98 0.00 0.00 3.36
879 1545 0.319211 CTTGGCGTCGTGTACAAGGA 60.319 55.000 8.98 1.38 37.31 3.36
880 1546 0.599204 ACTTGGCGTCGTGTACAAGG 60.599 55.000 8.98 0.00 43.36 3.61
881 1547 0.782384 GACTTGGCGTCGTGTACAAG 59.218 55.000 0.00 0.00 44.32 3.16
882 1548 0.102663 TGACTTGGCGTCGTGTACAA 59.897 50.000 0.00 0.00 45.87 2.41
883 1549 0.102663 TTGACTTGGCGTCGTGTACA 59.897 50.000 0.00 0.00 45.87 2.90
884 1550 0.782384 CTTGACTTGGCGTCGTGTAC 59.218 55.000 0.00 0.00 45.87 2.90
885 1551 0.942410 GCTTGACTTGGCGTCGTGTA 60.942 55.000 0.00 0.00 45.87 2.90
886 1552 2.244651 GCTTGACTTGGCGTCGTGT 61.245 57.895 0.00 0.00 45.87 4.49
887 1553 2.551270 GCTTGACTTGGCGTCGTG 59.449 61.111 0.00 0.00 45.87 4.35
888 1554 2.665185 GGCTTGACTTGGCGTCGT 60.665 61.111 0.00 0.00 45.87 4.34
889 1555 3.777925 CGGCTTGACTTGGCGTCG 61.778 66.667 0.00 0.00 45.87 5.12
956 1650 2.023673 TGATTTATGGGGCGAGCAAAG 58.976 47.619 0.00 0.00 0.00 2.77
957 1651 1.748493 GTGATTTATGGGGCGAGCAAA 59.252 47.619 0.00 0.00 0.00 3.68
958 1652 1.388547 GTGATTTATGGGGCGAGCAA 58.611 50.000 0.00 0.00 0.00 3.91
985 1679 1.524008 CTTTTGGGTGGGTCTTCGCC 61.524 60.000 0.00 0.00 36.62 5.54
988 1682 2.658807 AGTCTTTTGGGTGGGTCTTC 57.341 50.000 0.00 0.00 0.00 2.87
1012 1707 4.087892 ATCTCGGCGGCTGTGCTT 62.088 61.111 7.21 0.00 34.52 3.91
1195 1899 3.766691 GTCTTCCACCGGCGGCTA 61.767 66.667 28.71 8.86 0.00 3.93
1554 2272 4.212425 AGCAGAGTAAGTAGACGATCGATG 59.788 45.833 24.34 0.00 0.00 3.84
1563 2281 8.372459 TGGAAAATTTACAGCAGAGTAAGTAGA 58.628 33.333 0.00 0.00 35.57 2.59
1565 2283 7.389607 GGTGGAAAATTTACAGCAGAGTAAGTA 59.610 37.037 14.59 0.00 35.57 2.24
1566 2284 6.206829 GGTGGAAAATTTACAGCAGAGTAAGT 59.793 38.462 14.59 0.00 35.57 2.24
1567 2285 6.612306 GGTGGAAAATTTACAGCAGAGTAAG 58.388 40.000 14.59 0.00 35.57 2.34
1568 2286 5.180492 CGGTGGAAAATTTACAGCAGAGTAA 59.820 40.000 18.71 0.00 33.18 2.24
1638 2361 2.168054 GTTCATCCCCAAACGACGG 58.832 57.895 0.00 0.00 0.00 4.79
1685 2423 0.313987 CAACTCCCGGCTCCAAAAAC 59.686 55.000 0.00 0.00 0.00 2.43
1762 2501 3.850173 TCCCCAACTAACCAAAGCTAGAT 59.150 43.478 0.00 0.00 0.00 1.98
1774 2513 2.638325 TCACTCCCAATCCCCAACTAA 58.362 47.619 0.00 0.00 0.00 2.24
1805 2544 2.022195 CATGGCCATGACCTCTTCTTG 58.978 52.381 37.84 10.15 41.20 3.02
2377 3122 2.523507 CGCGATCTTGCTGCTCTGG 61.524 63.158 0.00 0.00 0.00 3.86
2467 3212 3.991536 GAGGAACAGCCGCTCGTCC 62.992 68.421 9.95 9.95 43.43 4.79
2638 3386 2.280797 GGCAGCACGTTGACCTCA 60.281 61.111 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.