Multiple sequence alignment - TraesCS3D01G091300

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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 TraesCS3D01G091300 chr3D 100.000 4785 0 0 1 4785 46250116 46245332 0.000000e+00 8837.0
1 TraesCS3D01G091300 chr3B 91.975 3078 140 44 1 3056 72318271 72315279 0.000000e+00 4217.0
2 TraesCS3D01G091300 chr3B 90.226 972 48 21 3061 3990 72315209 72314243 0.000000e+00 1225.0
3 TraesCS3D01G091300 chr3B 92.529 522 14 4 3796 4313 72232941 72232441 0.000000e+00 725.0
4 TraesCS3D01G091300 chr3B 93.525 417 25 1 3379 3795 72237836 72237422 1.890000e-173 619.0
5 TraesCS3D01G091300 chr3B 92.920 339 17 1 4398 4729 72228607 72228269 2.000000e-133 486.0
6 TraesCS3D01G091300 chr3B 97.727 88 2 0 4313 4400 72231682 72231595 8.290000e-33 152.0
7 TraesCS3D01G091300 chr3A 96.574 2131 59 5 932 3061 57858860 57856743 0.000000e+00 3518.0
8 TraesCS3D01G091300 chr3A 90.673 1040 50 24 3061 4084 57856663 57855655 0.000000e+00 1339.0
9 TraesCS3D01G091300 chr3A 81.701 776 82 29 175 926 57859785 57859046 4.120000e-165 592.0
10 TraesCS3D01G091300 chr3A 81.553 103 9 7 47 146 57859887 57859792 5.140000e-10 76.8
11 TraesCS3D01G091300 chr7B 92.308 52 2 2 4706 4755 105036219 105036270 6.640000e-09 73.1


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 TraesCS3D01G091300 chr3D 46245332 46250116 4784 True 8837.000000 8837 100.00000 1 4785 1 chr3D.!!$R1 4784
1 TraesCS3D01G091300 chr3B 72314243 72318271 4028 True 2721.000000 4217 91.10050 1 3990 2 chr3B.!!$R3 3989
2 TraesCS3D01G091300 chr3B 72228269 72232941 4672 True 454.333333 725 94.39200 3796 4729 3 chr3B.!!$R2 933
3 TraesCS3D01G091300 chr3A 57855655 57859887 4232 True 1381.450000 3518 87.62525 47 4084 4 chr3A.!!$R1 4037

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
284 304 0.179150 CTGTTCCTCCTCTCGCTTCG 60.179 60.0 0.00 0.0 0.00 3.79 F
586 609 0.391661 CTGTATCAGCTGCGGTGGTT 60.392 55.0 9.47 0.0 0.00 3.67 F
905 934 0.471591 TGCAACCTTGGCCCATTTCT 60.472 50.0 0.00 0.0 0.00 2.52 F
1425 1659 0.620556 TCTCATTCTTGGGGTCAGGC 59.379 55.0 0.00 0.0 0.00 4.85 F
3066 3383 0.179215 CTTGCGTTTCGATGGCACTC 60.179 55.0 5.21 0.0 36.23 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 2377 1.504912 CAGAGGGTGGAGACCATGAT 58.495 55.000 0.00 0.00 45.25 2.45 R
2237 2471 3.159213 AGATGTTGGCCACATGAAAGA 57.841 42.857 20.93 0.00 46.96 2.52 R
2809 3045 1.589716 GCATTCGGCTGCTGAAGGTT 61.590 55.000 29.48 12.74 39.12 3.50 R
3249 3578 0.238289 ATTTGGCTCTGTGCGTTTCG 59.762 50.000 0.00 0.00 44.05 3.46 R
4256 4621 0.251165 CACACCAATTCCCGGTTCCT 60.251 55.000 0.00 0.00 33.25 3.36 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
137 141 2.214914 GCGTAACACGTAAGCTAATCCG 59.785 50.000 0.26 0.00 44.73 4.18
207 212 1.203237 TGCTCTGTCTCTTCTTCCCCT 60.203 52.381 0.00 0.00 0.00 4.79
274 287 2.743928 CGTGCCTGCTGTTCCTCC 60.744 66.667 0.00 0.00 0.00 4.30
275 288 2.753029 GTGCCTGCTGTTCCTCCT 59.247 61.111 0.00 0.00 0.00 3.69
276 289 1.376553 GTGCCTGCTGTTCCTCCTC 60.377 63.158 0.00 0.00 0.00 3.71
277 290 1.537397 TGCCTGCTGTTCCTCCTCT 60.537 57.895 0.00 0.00 0.00 3.69
278 291 1.220477 GCCTGCTGTTCCTCCTCTC 59.780 63.158 0.00 0.00 0.00 3.20
279 292 1.515020 CCTGCTGTTCCTCCTCTCG 59.485 63.158 0.00 0.00 0.00 4.04
281 294 1.603236 CTGCTGTTCCTCCTCTCGCT 61.603 60.000 0.00 0.00 0.00 4.93
284 304 0.179150 CTGTTCCTCCTCTCGCTTCG 60.179 60.000 0.00 0.00 0.00 3.79
329 349 3.757248 ATCCACGATGCCTTCCGCC 62.757 63.158 0.00 0.00 36.24 6.13
351 371 2.119611 TGCGTTCCCTCCCTCTCA 59.880 61.111 0.00 0.00 0.00 3.27
368 388 4.767255 AGTAGCTGCCGTGCCTGC 62.767 66.667 0.00 0.00 0.00 4.85
434 454 4.836125 TCGGTAAATTACGGTAGCCTAG 57.164 45.455 9.91 0.00 0.00 3.02
440 460 7.327032 CGGTAAATTACGGTAGCCTAGATAAAC 59.673 40.741 2.97 0.00 0.00 2.01
469 489 3.436496 CTGGTACGAATCGAGTTCCTTC 58.564 50.000 10.55 0.00 33.04 3.46
473 493 1.272490 ACGAATCGAGTTCCTTCTGCA 59.728 47.619 10.55 0.00 33.04 4.41
509 532 2.159382 TGCCTGTTTTGCCTTAGTAGC 58.841 47.619 0.00 0.00 0.00 3.58
511 534 2.820197 GCCTGTTTTGCCTTAGTAGCTT 59.180 45.455 0.00 0.00 0.00 3.74
517 540 0.457853 TGCCTTAGTAGCTTGCGACG 60.458 55.000 0.00 0.00 0.00 5.12
529 552 2.735857 GCGACGGCCGTACAAACT 60.736 61.111 34.36 6.25 41.15 2.66
530 553 1.444212 GCGACGGCCGTACAAACTA 60.444 57.895 34.36 0.00 41.15 2.24
576 599 7.212976 TGTCTTTAATCATCCTCTGTATCAGC 58.787 38.462 0.00 0.00 0.00 4.26
577 600 7.070447 TGTCTTTAATCATCCTCTGTATCAGCT 59.930 37.037 0.00 0.00 0.00 4.24
578 601 7.384660 GTCTTTAATCATCCTCTGTATCAGCTG 59.615 40.741 7.63 7.63 0.00 4.24
579 602 3.681593 ATCATCCTCTGTATCAGCTGC 57.318 47.619 9.47 0.00 0.00 5.25
580 603 1.339291 TCATCCTCTGTATCAGCTGCG 59.661 52.381 9.47 0.00 0.00 5.18
583 606 0.529337 CCTCTGTATCAGCTGCGGTG 60.529 60.000 9.47 1.35 0.00 4.94
584 607 0.529337 CTCTGTATCAGCTGCGGTGG 60.529 60.000 9.47 0.00 0.00 4.61
585 608 1.219124 CTGTATCAGCTGCGGTGGT 59.781 57.895 9.47 3.85 0.00 4.16
586 609 0.391661 CTGTATCAGCTGCGGTGGTT 60.392 55.000 9.47 0.00 0.00 3.67
587 610 0.673333 TGTATCAGCTGCGGTGGTTG 60.673 55.000 9.47 0.00 0.00 3.77
588 611 1.078497 TATCAGCTGCGGTGGTTGG 60.078 57.895 9.47 0.00 0.00 3.77
589 612 2.535485 TATCAGCTGCGGTGGTTGGG 62.535 60.000 9.47 0.00 0.00 4.12
590 613 4.954970 CAGCTGCGGTGGTTGGGT 62.955 66.667 0.00 0.00 0.00 4.51
606 629 1.641123 GGGTTTGGGTACATGCGTCG 61.641 60.000 0.00 0.00 0.00 5.12
641 664 2.511600 GCGATGGTCGTTGGAGGG 60.512 66.667 1.11 0.00 42.81 4.30
670 693 9.772973 TTGTTTTGTCTCTAGAGTTATGCTTTA 57.227 29.630 19.21 0.00 0.00 1.85
748 774 4.023963 GCTCCAGTACAACCTTGTTCTTTC 60.024 45.833 0.00 0.00 42.35 2.62
750 776 3.875134 CCAGTACAACCTTGTTCTTTCGT 59.125 43.478 0.00 0.00 42.35 3.85
758 784 8.891671 ACAACCTTGTTCTTTCGTAATAACTA 57.108 30.769 5.01 0.00 38.47 2.24
762 788 9.852091 ACCTTGTTCTTTCGTAATAACTAGTAG 57.148 33.333 0.00 0.00 28.45 2.57
763 789 9.852091 CCTTGTTCTTTCGTAATAACTAGTAGT 57.148 33.333 0.00 0.00 28.45 2.73
814 843 9.482627 AAATCAGGTGATATTAATCGAGTCTTC 57.517 33.333 0.00 0.00 34.60 2.87
835 864 1.589716 GCTCATGCCCTGTGTGGAAC 61.590 60.000 0.00 0.00 38.35 3.62
905 934 0.471591 TGCAACCTTGGCCCATTTCT 60.472 50.000 0.00 0.00 0.00 2.52
906 935 1.203112 TGCAACCTTGGCCCATTTCTA 60.203 47.619 0.00 0.00 0.00 2.10
907 936 2.110578 GCAACCTTGGCCCATTTCTAT 58.889 47.619 0.00 0.00 0.00 1.98
908 937 2.501316 GCAACCTTGGCCCATTTCTATT 59.499 45.455 0.00 0.00 0.00 1.73
909 938 3.704061 GCAACCTTGGCCCATTTCTATTA 59.296 43.478 0.00 0.00 0.00 0.98
910 939 4.161377 GCAACCTTGGCCCATTTCTATTAA 59.839 41.667 0.00 0.00 0.00 1.40
911 940 5.660460 CAACCTTGGCCCATTTCTATTAAC 58.340 41.667 0.00 0.00 0.00 2.01
912 941 5.206905 ACCTTGGCCCATTTCTATTAACT 57.793 39.130 0.00 0.00 0.00 2.24
913 942 4.956075 ACCTTGGCCCATTTCTATTAACTG 59.044 41.667 0.00 0.00 0.00 3.16
914 943 4.202151 CCTTGGCCCATTTCTATTAACTGC 60.202 45.833 0.00 0.00 0.00 4.40
915 944 3.974719 TGGCCCATTTCTATTAACTGCA 58.025 40.909 0.00 0.00 0.00 4.41
916 945 3.953612 TGGCCCATTTCTATTAACTGCAG 59.046 43.478 13.48 13.48 0.00 4.41
1011 1245 3.392616 AGTCAGTGACCATGAAAACCTCT 59.607 43.478 19.71 0.00 32.18 3.69
1012 1246 3.499918 GTCAGTGACCATGAAAACCTCTG 59.500 47.826 12.54 0.00 0.00 3.35
1044 1278 1.434555 TTTATCACTCGTTGCCCGTG 58.565 50.000 0.00 0.00 37.94 4.94
1191 1425 3.933332 CTGGAAATGTCGTTAACTCCCTC 59.067 47.826 3.71 0.00 0.00 4.30
1216 1450 1.172812 AAAACTGTCCGGGCAGAAGC 61.173 55.000 41.30 4.77 39.62 3.86
1257 1491 6.638468 GCGGAAATGATTTTCTTGATGGATAC 59.362 38.462 0.00 0.00 40.91 2.24
1281 1515 5.410746 CGAATGTCCTGATGATTATTGGGAG 59.589 44.000 0.00 0.00 0.00 4.30
1425 1659 0.620556 TCTCATTCTTGGGGTCAGGC 59.379 55.000 0.00 0.00 0.00 4.85
1438 1672 1.474677 GGTCAGGCAGTGATGGAGATG 60.475 57.143 0.00 0.00 37.56 2.90
1710 1944 1.300620 TCGTGAGCGAAACCCACAG 60.301 57.895 0.00 0.00 44.92 3.66
1866 2100 6.610830 TGCCTATTGGATTAACATTGGAACAT 59.389 34.615 0.00 0.00 34.08 2.71
2143 2377 3.291584 AGTTGCTCGTAGATCAGATGGA 58.708 45.455 0.00 0.00 32.89 3.41
2234 2468 6.036953 GGTTGCAGAATTCTTCTCTGTATCTG 59.963 42.308 4.86 0.00 42.01 2.90
2235 2469 6.291648 TGCAGAATTCTTCTCTGTATCTGT 57.708 37.500 4.86 0.00 42.01 3.41
2236 2470 7.410120 TGCAGAATTCTTCTCTGTATCTGTA 57.590 36.000 4.86 0.00 42.01 2.74
2237 2471 8.016301 TGCAGAATTCTTCTCTGTATCTGTAT 57.984 34.615 4.86 0.00 42.01 2.29
2238 2472 8.140628 TGCAGAATTCTTCTCTGTATCTGTATC 58.859 37.037 4.86 0.00 42.01 2.24
2239 2473 8.359642 GCAGAATTCTTCTCTGTATCTGTATCT 58.640 37.037 4.86 0.00 42.01 1.98
2249 2483 6.283694 TCTGTATCTGTATCTTTCATGTGGC 58.716 40.000 0.00 0.00 0.00 5.01
2384 2618 8.905702 GCGAATGGTGTATGATAAAAATGATTC 58.094 33.333 0.00 0.00 0.00 2.52
2463 2697 6.427853 CACACTTGTTTCATGTCTTAGGATGA 59.572 38.462 0.00 0.00 0.00 2.92
2632 2868 3.044986 CTGAGCAAAAACATGTTGGACG 58.955 45.455 12.82 2.63 0.00 4.79
2758 2994 8.630054 TGTTTTATCTTAACATACAGCTTGGT 57.370 30.769 0.00 0.00 30.96 3.67
2794 3030 4.906065 TTTCATCATAGTGCTTCATGGC 57.094 40.909 0.00 0.00 0.00 4.40
2796 3032 2.440627 TCATCATAGTGCTTCATGGCCT 59.559 45.455 3.32 0.00 0.00 5.19
2809 3045 1.614903 CATGGCCTTGAAGCTGTGAAA 59.385 47.619 13.33 0.00 0.00 2.69
2914 3150 5.189736 TGATGTGAGAGCTGGTAATAAAGGT 59.810 40.000 0.00 0.00 0.00 3.50
3034 3271 8.878333 GTTTGTATTGCGTTTTTATTTTTGAGC 58.122 29.630 0.00 0.00 0.00 4.26
3052 3289 0.301388 GCAAACACAAAAGCCTTGCG 59.699 50.000 0.00 0.00 33.74 4.85
3066 3383 0.179215 CTTGCGTTTCGATGGCACTC 60.179 55.000 5.21 0.00 36.23 3.51
3149 3467 1.072806 TGCTCAGCACCAGATCTGTTT 59.927 47.619 21.11 5.13 31.71 2.83
3158 3483 5.769662 AGCACCAGATCTGTTTGTTTATTGA 59.230 36.000 21.11 0.00 0.00 2.57
3249 3578 8.283291 CCGTGGTCTGCTTAATTTTATATTCTC 58.717 37.037 0.00 0.00 0.00 2.87
3316 3645 8.567285 AGTAAGAAATGGTATTCTTGTTCCTG 57.433 34.615 11.46 0.00 46.35 3.86
3389 3718 5.310451 TGGTGTTCTTGGTGGATAACTTAC 58.690 41.667 0.00 0.00 0.00 2.34
3393 3722 5.414454 TGTTCTTGGTGGATAACTTACATGC 59.586 40.000 0.00 0.00 0.00 4.06
3409 3738 0.464373 ATGCAATACCCGCAGTCTGG 60.464 55.000 1.14 0.00 43.88 3.86
3445 3776 8.893727 GTCCAGCAATGAACTTAGTATACAAAT 58.106 33.333 5.50 0.00 0.00 2.32
3484 3815 5.048846 AGTAAACAAGCTTGGGAGAAAGA 57.951 39.130 29.18 3.97 0.00 2.52
3485 3816 5.635120 AGTAAACAAGCTTGGGAGAAAGAT 58.365 37.500 29.18 2.92 0.00 2.40
3488 3820 7.890655 AGTAAACAAGCTTGGGAGAAAGATATT 59.109 33.333 29.18 7.95 0.00 1.28
3619 3951 1.021968 GCGCATTTATCGGGGTTTCT 58.978 50.000 0.30 0.00 0.00 2.52
3769 4101 2.293677 AGCGTTGGATGACCTATACTCG 59.706 50.000 0.00 0.00 37.04 4.18
3914 4273 3.423539 TCAGATAAACAGCTGCAACCT 57.576 42.857 15.27 1.84 32.27 3.50
3915 4274 3.076621 TCAGATAAACAGCTGCAACCTG 58.923 45.455 15.27 14.43 36.41 4.00
3959 4320 7.877612 TCTGTAAAGTCAATGTCTTGCTATGAA 59.122 33.333 0.00 0.00 32.11 2.57
4157 4518 4.183865 CGAGATGGTCTTGCTGTATCAAA 58.816 43.478 0.00 0.00 0.00 2.69
4160 4521 6.510799 CGAGATGGTCTTGCTGTATCAAATTC 60.511 42.308 0.00 0.00 0.00 2.17
4206 4567 2.614983 GAGATGGTCTCCGTACTGTCTC 59.385 54.545 0.00 0.00 37.55 3.36
4266 4631 4.165372 AGCAATAAATTCTAGGAACCGGGA 59.835 41.667 6.32 0.00 0.00 5.14
4302 4667 5.227569 TGTAGAGTTTTTGAGCTCCATCA 57.772 39.130 12.15 0.00 32.47 3.07
4303 4668 5.240891 TGTAGAGTTTTTGAGCTCCATCAG 58.759 41.667 12.15 0.00 32.47 2.90
4305 4670 4.322567 AGAGTTTTTGAGCTCCATCAGTC 58.677 43.478 12.15 5.61 32.47 3.51
4306 4671 4.041444 AGAGTTTTTGAGCTCCATCAGTCT 59.959 41.667 12.15 7.81 32.47 3.24
4307 4672 4.723309 AGTTTTTGAGCTCCATCAGTCTT 58.277 39.130 12.15 0.00 0.00 3.01
4308 4673 4.759183 AGTTTTTGAGCTCCATCAGTCTTC 59.241 41.667 12.15 0.00 0.00 2.87
4310 4675 4.564782 TTTGAGCTCCATCAGTCTTCAT 57.435 40.909 12.15 0.00 0.00 2.57
4311 4676 5.682234 TTTGAGCTCCATCAGTCTTCATA 57.318 39.130 12.15 0.00 0.00 2.15
4390 5512 8.879759 CATGTACAGAACGTAACCAATATTTCT 58.120 33.333 0.33 0.00 0.00 2.52
4395 5517 9.314321 ACAGAACGTAACCAATATTTCTATCTG 57.686 33.333 0.00 0.00 35.42 2.90
4418 8530 2.317530 GTGATAAGCACTGGACCTCC 57.682 55.000 0.00 0.00 44.27 4.30
4443 8555 2.433664 GTTGCCCCAGTACGTCGG 60.434 66.667 0.00 0.00 0.00 4.79
4451 8563 0.815734 CCAGTACGTCGGGATGTTCT 59.184 55.000 0.00 0.00 33.18 3.01
4511 8630 5.391523 CGAGCTTCCGAAATCCATGTTAAAA 60.392 40.000 0.00 0.00 0.00 1.52
4521 8640 8.293867 CGAAATCCATGTTAAAAGGTGAGTTAA 58.706 33.333 0.00 0.00 0.00 2.01
4550 8669 7.308770 CCTCTTAAAATTGTGACTTCTCATGCA 60.309 37.037 0.00 0.00 0.00 3.96
4602 8721 9.043548 ACCACTAACTACTGTTGACCTTATATT 57.956 33.333 0.00 0.00 37.59 1.28
4623 8742 2.519377 TCAACCAGACGACGTGATTT 57.481 45.000 4.58 0.00 0.00 2.17
4688 8807 3.134458 GTCTGGAGTGAACCAAGTGAAG 58.866 50.000 0.00 0.00 39.59 3.02
4698 8817 1.208614 CAAGTGAAGCAGCTTCCGC 59.791 57.895 28.73 21.48 39.51 5.54
4710 8829 2.004733 AGCTTCCGCCGTAATTGTAAC 58.995 47.619 0.00 0.00 36.60 2.50
4714 8833 3.598019 TCCGCCGTAATTGTAACTTCT 57.402 42.857 0.00 0.00 0.00 2.85
4721 8840 6.799925 CGCCGTAATTGTAACTTCTGATTTTT 59.200 34.615 0.00 0.00 0.00 1.94
4744 8863 9.997482 TTTTGAGTAATACAAGAATTATTCGCC 57.003 29.630 0.00 0.00 33.21 5.54
4745 8864 8.725405 TTGAGTAATACAAGAATTATTCGCCA 57.275 30.769 0.00 0.00 33.21 5.69
4746 8865 8.725405 TGAGTAATACAAGAATTATTCGCCAA 57.275 30.769 0.00 0.00 33.21 4.52
4747 8866 8.609176 TGAGTAATACAAGAATTATTCGCCAAC 58.391 33.333 0.00 0.00 33.21 3.77
4748 8867 8.500753 AGTAATACAAGAATTATTCGCCAACA 57.499 30.769 0.00 0.00 34.02 3.33
4749 8868 8.952278 AGTAATACAAGAATTATTCGCCAACAA 58.048 29.630 0.00 0.00 34.02 2.83
4750 8869 9.562583 GTAATACAAGAATTATTCGCCAACAAA 57.437 29.630 0.00 0.00 34.02 2.83
4752 8871 9.482627 AATACAAGAATTATTCGCCAACAAAAA 57.517 25.926 0.00 0.00 34.02 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.749865 CCGGGTTACTGTGCATGCG 61.750 63.158 14.09 0.76 0.00 4.73
171 175 1.305297 GCAAAGGGGGAAAGGGAGG 60.305 63.158 0.00 0.00 0.00 4.30
267 280 1.139947 CCGAAGCGAGAGGAGGAAC 59.860 63.158 0.00 0.00 0.00 3.62
308 328 1.526917 GGAAGGCATCGTGGATGGG 60.527 63.158 7.63 0.00 40.10 4.00
368 388 1.670059 ACCCTAGAAAGAACCCCTGG 58.330 55.000 0.00 0.00 0.00 4.45
434 454 7.792508 CGATTCGTACCAGCTAATTTGTTTATC 59.207 37.037 0.00 0.00 0.00 1.75
440 460 4.804139 ACTCGATTCGTACCAGCTAATTTG 59.196 41.667 5.89 0.00 0.00 2.32
469 489 3.242518 CATGAGCACAAACAAGATGCAG 58.757 45.455 0.00 0.00 41.97 4.41
473 493 2.230508 CAGGCATGAGCACAAACAAGAT 59.769 45.455 0.00 0.00 44.61 2.40
509 532 2.311701 TTTGTACGGCCGTCGCAAG 61.312 57.895 38.01 0.83 43.89 4.01
511 534 2.139888 TAGTTTGTACGGCCGTCGCA 62.140 55.000 38.01 30.41 43.89 5.10
517 540 3.433274 GGTTTGTACTAGTTTGTACGGCC 59.567 47.826 0.00 0.00 44.01 6.13
576 599 2.727544 CAAACCCAACCACCGCAG 59.272 61.111 0.00 0.00 0.00 5.18
577 600 2.835431 CCAAACCCAACCACCGCA 60.835 61.111 0.00 0.00 0.00 5.69
578 601 2.980105 TACCCAAACCCAACCACCGC 62.980 60.000 0.00 0.00 0.00 5.68
579 602 1.150992 TACCCAAACCCAACCACCG 59.849 57.895 0.00 0.00 0.00 4.94
580 603 0.106116 TGTACCCAAACCCAACCACC 60.106 55.000 0.00 0.00 0.00 4.61
583 606 0.606096 GCATGTACCCAAACCCAACC 59.394 55.000 0.00 0.00 0.00 3.77
584 607 0.242555 CGCATGTACCCAAACCCAAC 59.757 55.000 0.00 0.00 0.00 3.77
585 608 0.178987 ACGCATGTACCCAAACCCAA 60.179 50.000 0.00 0.00 0.00 4.12
586 609 0.606944 GACGCATGTACCCAAACCCA 60.607 55.000 0.00 0.00 0.00 4.51
587 610 1.641123 CGACGCATGTACCCAAACCC 61.641 60.000 0.00 0.00 0.00 4.11
588 611 1.791662 CGACGCATGTACCCAAACC 59.208 57.895 0.00 0.00 0.00 3.27
589 612 1.133869 GCGACGCATGTACCCAAAC 59.866 57.895 16.42 0.00 0.00 2.93
590 613 1.301795 TGCGACGCATGTACCCAAA 60.302 52.632 20.50 0.00 31.71 3.28
606 629 1.420641 GCCGCCGGAAATTTCAATGC 61.421 55.000 19.49 15.78 0.00 3.56
632 655 0.593773 CAAAACAACGCCCTCCAACG 60.594 55.000 0.00 0.00 0.00 4.10
641 664 6.526222 CATAACTCTAGAGACAAAACAACGC 58.474 40.000 26.57 0.00 0.00 4.84
716 742 0.327924 TGTACTGGAGCCACCCAATG 59.672 55.000 0.00 0.00 35.47 2.82
771 797 9.626045 CACCTGATTTTCCATTAGTAAAAGAAC 57.374 33.333 0.00 0.00 0.00 3.01
772 798 9.581289 TCACCTGATTTTCCATTAGTAAAAGAA 57.419 29.630 0.00 0.00 0.00 2.52
792 821 5.859114 CGGAAGACTCGATTAATATCACCTG 59.141 44.000 0.00 0.00 0.00 4.00
806 835 1.880340 GGCATGAGCGGAAGACTCG 60.880 63.158 0.00 0.00 43.41 4.18
814 843 3.129502 CACACAGGGCATGAGCGG 61.130 66.667 5.99 0.00 43.41 5.52
835 864 2.667969 GCAAAGCCAGCTTTAAATTCCG 59.332 45.455 16.75 4.90 43.56 4.30
863 892 3.181466 TGGCTGCGCTCATCTAAAATCTA 60.181 43.478 9.73 0.00 0.00 1.98
895 924 3.954258 ACTGCAGTTAATAGAAATGGGCC 59.046 43.478 15.25 0.00 0.00 5.80
914 943 5.877012 ACAATGACAATAGCAGGTTCTACTG 59.123 40.000 0.00 0.00 41.41 2.74
915 944 6.054860 ACAATGACAATAGCAGGTTCTACT 57.945 37.500 0.00 0.00 0.00 2.57
916 945 6.109359 AGACAATGACAATAGCAGGTTCTAC 58.891 40.000 0.00 0.00 0.00 2.59
952 1179 8.770828 TCCTGAAAGAAGAAAAACAGTATTACG 58.229 33.333 0.00 0.00 34.07 3.18
994 1228 1.541588 GCCAGAGGTTTTCATGGTCAC 59.458 52.381 0.00 0.00 35.17 3.67
1044 1278 1.744741 GCTGTCTTGAGCTCCTGGC 60.745 63.158 12.15 5.97 42.19 4.85
1191 1425 1.566018 GCCCGGACAGTTTTGACTCG 61.566 60.000 0.73 0.00 0.00 4.18
1257 1491 5.308014 TCCCAATAATCATCAGGACATTCG 58.692 41.667 0.00 0.00 0.00 3.34
1281 1515 1.879380 TGTGCCTTGTGCTGTTCATAC 59.121 47.619 0.00 0.00 42.00 2.39
1335 1569 3.244387 TGCGGCCAATGATAGCAACTATA 60.244 43.478 2.24 0.00 34.66 1.31
1425 1659 2.879026 CAAGGATGCATCTCCATCACTG 59.121 50.000 25.28 7.04 42.63 3.66
1710 1944 2.541120 GCATGCATCGCAGACCCTC 61.541 63.158 14.21 0.00 43.65 4.30
1866 2100 5.047021 GGATACTGCTGCCTTGTATATCTCA 60.047 44.000 0.00 0.00 0.00 3.27
2143 2377 1.504912 CAGAGGGTGGAGACCATGAT 58.495 55.000 0.00 0.00 45.25 2.45
2234 2468 4.641989 AGATGTTGGCCACATGAAAGATAC 59.358 41.667 20.93 7.59 46.96 2.24
2235 2469 4.858850 AGATGTTGGCCACATGAAAGATA 58.141 39.130 20.93 0.00 46.96 1.98
2236 2470 3.705051 AGATGTTGGCCACATGAAAGAT 58.295 40.909 20.93 4.07 46.96 2.40
2237 2471 3.159213 AGATGTTGGCCACATGAAAGA 57.841 42.857 20.93 0.00 46.96 2.52
2238 2472 5.047802 AGTTTAGATGTTGGCCACATGAAAG 60.048 40.000 20.93 0.00 46.96 2.62
2239 2473 4.832266 AGTTTAGATGTTGGCCACATGAAA 59.168 37.500 20.93 17.14 46.96 2.69
2319 2553 7.518188 AGTAGTAGGTTATGGCTGCAATTATT 58.482 34.615 0.50 0.00 0.00 1.40
2384 2618 6.360618 AGATAGGAGAAATGCAGGGTTAAAG 58.639 40.000 0.00 0.00 0.00 1.85
2582 2817 6.173339 AGACCATGTTCTACACAAACATAGG 58.827 40.000 0.00 8.00 43.62 2.57
2632 2868 4.846779 TCAATTTTAGGCAACAGTCACC 57.153 40.909 0.00 0.00 41.41 4.02
2794 3030 3.969899 GAAGGTTTTCACAGCTTCAAGG 58.030 45.455 7.58 0.00 46.33 3.61
2809 3045 1.589716 GCATTCGGCTGCTGAAGGTT 61.590 55.000 29.48 12.74 39.12 3.50
2914 3150 9.143155 TGACTATATGTATAGCAAACTCCAGAA 57.857 33.333 6.91 0.00 39.36 3.02
3034 3271 1.639280 ACGCAAGGCTTTTGTGTTTG 58.361 45.000 12.71 0.00 39.83 2.93
3052 3289 2.750888 GCCGGAGTGCCATCGAAAC 61.751 63.158 5.05 0.00 0.00 2.78
3074 3391 5.791303 ATGTAAAACTTAAGTAGCCCCCT 57.209 39.130 8.92 0.00 0.00 4.79
3149 3467 8.301002 GGGCAGTAAATTTGTACTCAATAAACA 58.699 33.333 0.00 0.00 31.78 2.83
3158 3483 3.761897 TGCAGGGCAGTAAATTTGTACT 58.238 40.909 0.00 0.00 34.56 2.73
3199 3525 7.548075 CGGAATATAATTAAACCTCCGCTACAT 59.452 37.037 12.72 0.00 38.07 2.29
3249 3578 0.238289 ATTTGGCTCTGTGCGTTTCG 59.762 50.000 0.00 0.00 44.05 3.46
3254 3583 0.734889 CCCTTATTTGGCTCTGTGCG 59.265 55.000 0.00 0.00 44.05 5.34
3289 3618 9.014297 AGGAACAAGAATACCATTTCTTACTTG 57.986 33.333 0.00 0.00 42.58 3.16
3316 3645 4.442192 CCCTTATCTGGCTCTGTACAAGTC 60.442 50.000 0.00 0.00 0.00 3.01
3344 3673 6.485313 ACCATTTCTTACTCATTTCGTGTCAA 59.515 34.615 0.00 0.00 0.00 3.18
3353 3682 6.777580 ACCAAGAACACCATTTCTTACTCATT 59.222 34.615 0.00 0.00 42.74 2.57
3389 3718 0.659427 CAGACTGCGGGTATTGCATG 59.341 55.000 0.00 0.00 42.32 4.06
3393 3722 2.107950 TTTCCAGACTGCGGGTATTG 57.892 50.000 0.00 0.00 0.00 1.90
3409 3738 3.009723 TCATTGCTGGACTCCGATTTTC 58.990 45.455 0.00 0.00 0.00 2.29
3596 3928 2.639286 CCCGATAAATGCGCCTGC 59.361 61.111 4.18 0.00 43.20 4.85
3769 4101 1.066430 TCGTGCTAACAATCCAGACCC 60.066 52.381 0.00 0.00 0.00 4.46
3914 4273 1.559682 GACTTCCATCCTAGGGCAACA 59.440 52.381 9.46 0.00 39.74 3.33
3915 4274 1.840635 AGACTTCCATCCTAGGGCAAC 59.159 52.381 9.46 0.00 0.00 4.17
3917 4276 1.273838 ACAGACTTCCATCCTAGGGCA 60.274 52.381 9.46 0.00 0.00 5.36
3918 4277 1.501582 ACAGACTTCCATCCTAGGGC 58.498 55.000 9.46 0.00 0.00 5.19
3919 4278 4.717280 ACTTTACAGACTTCCATCCTAGGG 59.283 45.833 9.46 0.00 0.00 3.53
3959 4320 8.289939 AGTGTATTTCATTCTGCTGATCAAAT 57.710 30.769 0.00 2.83 0.00 2.32
4024 4385 4.771577 TGGTCATTCATTTGGCAGTGTATT 59.228 37.500 0.00 0.00 0.00 1.89
4157 4518 1.825090 TGCAATCAGAAGTGCCGAAT 58.175 45.000 6.93 0.00 45.69 3.34
4160 4521 2.420628 TTTTGCAATCAGAAGTGCCG 57.579 45.000 0.00 0.00 45.69 5.69
4206 4567 7.849804 ACTTAGTACTTCCAAATGCACATAG 57.150 36.000 0.00 0.00 0.00 2.23
4253 4618 1.557832 CACCAATTCCCGGTTCCTAGA 59.442 52.381 0.00 0.00 33.25 2.43
4256 4621 0.251165 CACACCAATTCCCGGTTCCT 60.251 55.000 0.00 0.00 33.25 3.36
4261 4626 1.677576 CATCATCACACCAATTCCCGG 59.322 52.381 0.00 0.00 0.00 5.73
4266 4631 7.765695 AAAACTCTACATCATCACACCAATT 57.234 32.000 0.00 0.00 0.00 2.32
4306 4671 9.411801 GCGATTCTACTTGAACATATCTATGAA 57.588 33.333 4.26 0.00 37.52 2.57
4307 4672 8.797438 AGCGATTCTACTTGAACATATCTATGA 58.203 33.333 4.26 0.00 37.52 2.15
4308 4673 8.978564 AGCGATTCTACTTGAACATATCTATG 57.021 34.615 0.00 0.00 37.52 2.23
4411 8523 0.606673 GCAACAAGGTCAGGAGGTCC 60.607 60.000 0.00 0.00 0.00 4.46
4418 8530 0.400213 TACTGGGGCAACAAGGTCAG 59.600 55.000 0.00 0.00 39.74 3.51
4492 8611 5.770663 TCACCTTTTAACATGGATTTCGGAA 59.229 36.000 0.00 0.00 0.00 4.30
4511 8630 7.451566 ACAATTTTAAGAGGCATTAACTCACCT 59.548 33.333 0.00 0.00 37.43 4.00
4521 8640 6.716628 TGAGAAGTCACAATTTTAAGAGGCAT 59.283 34.615 0.00 0.00 0.00 4.40
4602 8721 2.519377 ATCACGTCGTCTGGTTGAAA 57.481 45.000 0.00 0.00 0.00 2.69
4623 8742 7.833285 AAGGCTCTTCAAAAGTATTAACCAA 57.167 32.000 0.00 0.00 0.00 3.67
4659 8778 2.609737 GGTTCACTCCAGACACCTTACG 60.610 54.545 0.00 0.00 0.00 3.18
4698 8817 9.329913 CTCAAAAATCAGAAGTTACAATTACGG 57.670 33.333 0.00 0.00 0.00 4.02
4721 8840 8.609176 GTTGGCGAATAATTCTTGTATTACTCA 58.391 33.333 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.