Multiple sequence alignment - TraesCS1B01G463000

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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 TraesCS1B01G463000 chr1B 100.000 4592 0 0 1 4592 675315799 675311208 0.000000e+00 8480.0
1 TraesCS1B01G463000 chr1B 82.063 223 13 11 4048 4261 646687345 646687141 1.020000e-36 165.0
2 TraesCS1B01G463000 chr1B 82.273 220 12 11 4051 4261 646776596 646776395 1.020000e-36 165.0
3 TraesCS1B01G463000 chr1B 88.889 108 5 2 4161 4268 675227265 675227365 4.820000e-25 126.0
4 TraesCS1B01G463000 chr1B 87.037 108 7 1 4161 4268 674934697 674934597 1.040000e-21 115.0
5 TraesCS1B01G463000 chr1B 96.364 55 2 0 4159 4213 675227214 675227268 1.760000e-14 91.6
6 TraesCS1B01G463000 chr1A 93.064 2624 111 20 1295 3904 582221615 582219049 0.000000e+00 3771.0
7 TraesCS1B01G463000 chr1A 94.943 1305 32 5 1 1304 582222925 582221654 0.000000e+00 2013.0
8 TraesCS1B01G463000 chr1A 82.270 564 41 15 3905 4455 582218982 582218465 2.540000e-117 433.0
9 TraesCS1B01G463000 chr1D 93.293 1491 61 16 1295 2774 485023401 485021939 0.000000e+00 2163.0
10 TraesCS1B01G463000 chr1D 96.489 1310 34 6 3 1306 485024741 485023438 0.000000e+00 2154.0
11 TraesCS1B01G463000 chr1D 93.696 1047 31 12 2874 3901 485021795 485020765 0.000000e+00 1535.0
12 TraesCS1B01G463000 chr1D 88.714 700 36 8 3900 4592 485020685 485020022 0.000000e+00 815.0
13 TraesCS1B01G463000 chr1D 84.615 221 13 10 4051 4268 484871407 484871205 2.800000e-47 200.0
14 TraesCS1B01G463000 chr1D 83.710 221 15 10 4051 4268 466605540 466605338 6.060000e-44 189.0


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 TraesCS1B01G463000 chr1B 675311208 675315799 4591 True 8480.000000 8480 100.000000 1 4592 1 chr1B.!!$R4 4591
1 TraesCS1B01G463000 chr1A 582218465 582222925 4460 True 2072.333333 3771 90.092333 1 4455 3 chr1A.!!$R1 4454
2 TraesCS1B01G463000 chr1D 485020022 485024741 4719 True 1666.750000 2163 93.048000 3 4592 4 chr1D.!!$R3 4589

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
625 655 0.890542 TCAACCTGTGTGCCAGATGC 60.891 55.0 0.00 0.0 44.49 3.91 F
1473 1553 0.108662 TCGCAGTGTCGATGCAGAAT 60.109 50.0 9.92 0.0 44.05 2.40 F
3231 3381 0.035152 CAGCCATGGCAGAGGTAACA 60.035 55.0 37.18 0.0 44.88 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2072 0.403750 TATTATCCCCCACCCCCACC 60.404 60.0 0.00 0.0 0.00 4.61 R
3298 3448 0.168348 CGAGTAGAGGTCACCACACG 59.832 60.0 0.00 0.0 0.00 4.49 R
4327 4599 0.321298 GAGGTAAGTTTGCGCCTCCA 60.321 55.0 4.18 0.0 41.08 3.86 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
126 131 7.439655 GTCTCAGGAATATGTACCTTCATGAAC 59.560 40.741 3.38 0.00 40.42 3.18
231 236 4.780815 TGATAGGTACTCCTGGCAAAATG 58.219 43.478 0.00 0.00 44.81 2.32
449 455 8.320295 CCATTTTATTTAACTTTGTAGCATGCG 58.680 33.333 13.01 0.00 0.00 4.73
453 459 5.682943 TTTAACTTTGTAGCATGCGAGTT 57.317 34.783 13.01 18.42 34.97 3.01
477 483 1.470098 CCAATTCGTGGGCAGAAGAAG 59.530 52.381 0.00 0.00 44.64 2.85
497 503 3.203040 AAGGCAGTGGGCATTAATACTCT 59.797 43.478 0.00 0.00 46.14 3.24
531 537 1.276138 GGGAAATTCTTGGTTGGCTGG 59.724 52.381 0.00 0.00 0.00 4.85
609 639 4.951715 ACTGCCAAAGATGCATCTTATCAA 59.048 37.500 35.78 22.55 45.83 2.57
610 640 5.163581 ACTGCCAAAGATGCATCTTATCAAC 60.164 40.000 35.78 24.24 45.83 3.18
611 641 4.098349 TGCCAAAGATGCATCTTATCAACC 59.902 41.667 35.78 22.11 45.83 3.77
612 642 4.340381 GCCAAAGATGCATCTTATCAACCT 59.660 41.667 35.78 19.54 45.83 3.50
613 643 5.735354 GCCAAAGATGCATCTTATCAACCTG 60.735 44.000 35.78 27.40 45.83 4.00
614 644 5.359009 CCAAAGATGCATCTTATCAACCTGT 59.641 40.000 35.78 18.20 45.83 4.00
615 645 6.263344 CAAAGATGCATCTTATCAACCTGTG 58.737 40.000 35.78 24.21 45.83 3.66
616 646 5.108187 AGATGCATCTTATCAACCTGTGT 57.892 39.130 23.75 0.00 31.97 3.72
617 647 4.880120 AGATGCATCTTATCAACCTGTGTG 59.120 41.667 23.75 0.00 31.97 3.82
618 648 2.749076 TGCATCTTATCAACCTGTGTGC 59.251 45.455 0.00 0.00 0.00 4.57
619 649 2.098117 GCATCTTATCAACCTGTGTGCC 59.902 50.000 0.00 0.00 0.00 5.01
620 650 3.346315 CATCTTATCAACCTGTGTGCCA 58.654 45.455 0.00 0.00 0.00 4.92
621 651 3.057969 TCTTATCAACCTGTGTGCCAG 57.942 47.619 0.00 0.00 41.15 4.85
622 652 2.637382 TCTTATCAACCTGTGTGCCAGA 59.363 45.455 0.00 0.00 44.49 3.86
623 653 3.264193 TCTTATCAACCTGTGTGCCAGAT 59.736 43.478 0.00 0.00 44.49 2.90
624 654 1.830279 ATCAACCTGTGTGCCAGATG 58.170 50.000 0.00 0.00 44.49 2.90
625 655 0.890542 TCAACCTGTGTGCCAGATGC 60.891 55.000 0.00 0.00 44.49 3.91
712 742 3.370840 TGTGCCAGATGCTTCCTTATT 57.629 42.857 0.00 0.00 42.00 1.40
737 767 7.665690 TGAGCAATATAGCCTTCAAAAACAAA 58.334 30.769 0.00 0.00 34.23 2.83
903 934 6.569127 TTCAGGCCTCCACTATAAATACAA 57.431 37.500 0.00 0.00 0.00 2.41
958 989 8.188799 TCCTTACGTCTAAGATCATACAAACTG 58.811 37.037 0.00 0.00 32.29 3.16
974 1005 4.202357 ACAAACTGAAGCATCACCTAGTGA 60.202 41.667 0.00 0.00 46.90 3.41
1026 1057 2.947127 ATTATGGAGGCAGCTCTTCC 57.053 50.000 7.19 7.19 0.00 3.46
1049 1080 5.233689 CCGGTAATTTTCATCTTCTCCGTAC 59.766 44.000 0.00 0.00 34.70 3.67
1050 1081 5.051907 CGGTAATTTTCATCTTCTCCGTACG 60.052 44.000 8.69 8.69 0.00 3.67
1051 1082 5.809051 GGTAATTTTCATCTTCTCCGTACGT 59.191 40.000 15.21 0.00 0.00 3.57
1052 1083 6.974622 GGTAATTTTCATCTTCTCCGTACGTA 59.025 38.462 15.21 0.00 0.00 3.57
1290 1322 2.373707 GCTCAGGTGATGCCCCTCT 61.374 63.158 0.00 0.00 38.26 3.69
1415 1495 5.009010 GTGTGAATGTAATAGGGATGCAAGG 59.991 44.000 0.00 0.00 0.00 3.61
1446 1526 5.695851 ATGTCAACCAGAAAAGACATGAC 57.304 39.130 0.00 0.00 46.59 3.06
1473 1553 0.108662 TCGCAGTGTCGATGCAGAAT 60.109 50.000 9.92 0.00 44.05 2.40
1516 1597 2.877168 AGCCTGAAATGATCGATGAAGC 59.123 45.455 0.54 0.00 0.00 3.86
1621 1702 8.674263 ACAATCTTCTCAAGGACATCAATATC 57.326 34.615 0.00 0.00 0.00 1.63
1626 1707 4.594920 TCTCAAGGACATCAATATCCCTCC 59.405 45.833 0.00 0.00 35.38 4.30
1746 1831 3.599348 ACCTAATTCCTATCCCCTGTCC 58.401 50.000 0.00 0.00 0.00 4.02
1893 1993 6.429385 AGCCTCAAGAGAAAAGACAATAACAG 59.571 38.462 0.00 0.00 0.00 3.16
1990 2090 1.703597 GGTGGGGGTGGGGGATAAT 60.704 63.158 0.00 0.00 0.00 1.28
2057 2157 6.735145 GCAGGAAGCTGGAATGAAATATCTTG 60.735 42.308 0.00 0.00 41.15 3.02
2278 2378 4.469657 AGATTAGTCCTGTTGCAACCAAA 58.530 39.130 26.14 7.52 31.68 3.28
2408 2508 3.312421 TGAGTTTCTTCTTGCTTGGAACG 59.688 43.478 0.00 0.00 0.00 3.95
2447 2547 4.018609 CTGCTTCGTATGCGGGAG 57.981 61.111 2.62 3.35 38.89 4.30
2461 2561 2.199291 CGGGAGCTTTTCATGAATGC 57.801 50.000 19.88 19.88 38.36 3.56
2466 2566 4.296690 GGAGCTTTTCATGAATGCTATGC 58.703 43.478 26.13 17.30 45.59 3.14
2470 2570 4.980434 GCTTTTCATGAATGCTATGCGAAT 59.020 37.500 20.08 0.00 35.97 3.34
2473 2573 4.492791 TCATGAATGCTATGCGAATTGG 57.507 40.909 0.00 0.00 0.00 3.16
2477 2577 3.187022 TGAATGCTATGCGAATTGGATCG 59.813 43.478 0.00 0.00 45.41 3.69
2485 2585 2.159430 TGCGAATTGGATCGTGTTTCTG 59.841 45.455 0.00 0.00 44.49 3.02
2486 2586 2.774007 CGAATTGGATCGTGTTTCTGC 58.226 47.619 0.00 0.00 38.01 4.26
2511 2611 4.970662 ATTCATGTGAAATTCGGTCAGG 57.029 40.909 0.00 0.00 37.61 3.86
2513 2613 2.039746 TCATGTGAAATTCGGTCAGGGT 59.960 45.455 0.00 0.00 0.00 4.34
2568 2668 7.979537 AGTTTTTAATGAACTGAAACAGGGTTC 59.020 33.333 0.00 0.00 36.08 3.62
2583 2683 0.788391 GGTTCGACGTTGATGACACC 59.212 55.000 6.27 7.47 0.00 4.16
2655 2755 1.376543 TAGCGAACCTACTGTCCTCG 58.623 55.000 0.00 0.00 0.00 4.63
2675 2775 2.693591 CGGAGCCTTCTGATGGTACTAA 59.306 50.000 10.85 0.00 0.00 2.24
2766 2866 2.755952 AGGCCCAGTGTTCTTTTTCT 57.244 45.000 0.00 0.00 0.00 2.52
2802 2902 3.002791 CGCACAAGAATCTCAAAGCCTA 58.997 45.455 0.00 0.00 0.00 3.93
2803 2903 3.181516 CGCACAAGAATCTCAAAGCCTAC 60.182 47.826 0.00 0.00 0.00 3.18
2827 2940 2.305928 TGTGGTCCTGTTGGTTCATTG 58.694 47.619 0.00 0.00 34.23 2.82
2842 2955 3.213206 TCATTGGACTGCAACTGAACT 57.787 42.857 0.00 0.00 0.00 3.01
2851 2964 2.874086 CTGCAACTGAACTCATGTGTCA 59.126 45.455 0.03 1.18 0.00 3.58
3006 3155 3.094498 GGCACCCCCTACCCGATT 61.094 66.667 0.00 0.00 0.00 3.34
3018 3167 1.300233 CCCGATTACTCTCAGCGCC 60.300 63.158 2.29 0.00 0.00 6.53
3125 3274 4.459337 CCTAATTCCAGAACAAACCCTGAC 59.541 45.833 0.00 0.00 32.37 3.51
3146 3296 2.604914 CGATCTTGGTGAATTCAGGACG 59.395 50.000 8.80 4.80 0.00 4.79
3228 3378 2.215191 CTCAGCCATGGCAGAGGTA 58.785 57.895 38.48 17.42 46.50 3.08
3229 3379 0.543277 CTCAGCCATGGCAGAGGTAA 59.457 55.000 38.48 17.08 46.50 2.85
3230 3380 0.253044 TCAGCCATGGCAGAGGTAAC 59.747 55.000 37.18 5.77 44.88 2.50
3231 3381 0.035152 CAGCCATGGCAGAGGTAACA 60.035 55.000 37.18 0.00 44.88 2.41
3266 3416 1.270199 CCTACAGGCTAGCTGCTGATG 60.270 57.143 22.92 15.24 42.39 3.07
3298 3448 4.278170 TGTTTCATGGTGTCACTGAATTCC 59.722 41.667 2.27 2.46 0.00 3.01
3327 3477 1.729470 CCTCTACTCGTGCAGCGGAT 61.729 60.000 8.46 1.43 41.72 4.18
3419 3569 2.536761 TTCAAGTCCTACAACGGGTG 57.463 50.000 0.00 0.00 0.00 4.61
3452 3602 1.140312 ACCCCTGACAAAGCTCTTCA 58.860 50.000 0.00 0.00 0.00 3.02
3469 3619 5.157940 TCTTCATCTGTTCTTCCTTCCTG 57.842 43.478 0.00 0.00 0.00 3.86
3590 3740 2.215604 GCGTCGACCGATCTCGTTG 61.216 63.158 10.58 0.00 39.56 4.10
3622 3772 0.439985 CTTCTGTCATTCCGCGTGTG 59.560 55.000 4.92 0.24 0.00 3.82
3623 3773 0.249699 TTCTGTCATTCCGCGTGTGT 60.250 50.000 4.92 0.00 0.00 3.72
3856 4027 3.131933 ACCAGTGCTTGTTTTGTAATGCA 59.868 39.130 0.00 0.00 0.00 3.96
3901 4072 7.895962 AGACCATATACTATTCATGCTACCAGA 59.104 37.037 0.00 0.00 0.00 3.86
3960 4212 5.022335 CGGCAACTATTATGCTGTATGTG 57.978 43.478 0.00 0.00 43.60 3.21
3976 4228 6.109156 TGTATGTGTGTTCTCAGGTGTATT 57.891 37.500 0.00 0.00 0.00 1.89
3987 4239 4.652881 TCTCAGGTGTATTGCTCTGATCAT 59.347 41.667 0.00 0.00 35.95 2.45
4046 4298 4.271816 CGAGGATGTCCGGAGCCG 62.272 72.222 3.06 1.06 42.08 5.52
4085 4337 0.438830 CCGTGCTTGCTTCGAGTAAC 59.561 55.000 10.75 0.00 0.00 2.50
4088 4340 1.871039 GTGCTTGCTTCGAGTAACCAA 59.129 47.619 0.00 0.00 0.00 3.67
4089 4341 2.484264 GTGCTTGCTTCGAGTAACCAAT 59.516 45.455 0.00 0.00 0.00 3.16
4090 4342 2.742053 TGCTTGCTTCGAGTAACCAATC 59.258 45.455 0.00 0.00 0.00 2.67
4091 4343 2.222819 GCTTGCTTCGAGTAACCAATCG 60.223 50.000 0.00 0.00 40.26 3.34
4143 4395 5.291128 GTGTTTACAGTGGGATATCTGAACG 59.709 44.000 2.05 0.00 35.84 3.95
4180 4437 5.395768 GCACTGTCTTGAGGATGGTAAGTAT 60.396 44.000 0.00 0.00 0.00 2.12
4205 4462 1.669779 GGTGACTTGCATCATGCTCTC 59.330 52.381 11.84 3.15 45.31 3.20
4212 4469 2.747436 TGCATCATGCTCTCGTATGTC 58.253 47.619 11.84 0.00 45.31 3.06
4213 4470 1.718178 GCATCATGCTCTCGTATGTCG 59.282 52.381 1.02 0.00 40.96 4.35
4214 4471 2.323059 CATCATGCTCTCGTATGTCGG 58.677 52.381 0.00 0.00 40.32 4.79
4215 4472 1.675552 TCATGCTCTCGTATGTCGGA 58.324 50.000 0.00 0.00 40.32 4.55
4216 4473 2.021457 TCATGCTCTCGTATGTCGGAA 58.979 47.619 0.00 0.00 40.32 4.30
4217 4474 2.120232 CATGCTCTCGTATGTCGGAAC 58.880 52.381 0.00 0.00 40.32 3.62
4218 4475 1.460504 TGCTCTCGTATGTCGGAACT 58.539 50.000 0.00 0.00 40.32 3.01
4281 4553 3.771577 AGGGTTACCAACTCTGAACAG 57.228 47.619 2.98 0.00 41.71 3.16
4282 4554 3.314693 AGGGTTACCAACTCTGAACAGA 58.685 45.455 2.98 4.45 41.71 3.41
4283 4555 3.071167 AGGGTTACCAACTCTGAACAGAC 59.929 47.826 2.98 0.00 41.71 3.51
4284 4556 3.181458 GGGTTACCAACTCTGAACAGACA 60.181 47.826 2.98 0.00 36.50 3.41
4285 4557 4.505039 GGGTTACCAACTCTGAACAGACAT 60.505 45.833 2.98 0.00 36.50 3.06
4286 4558 5.279809 GGGTTACCAACTCTGAACAGACATA 60.280 44.000 2.98 0.00 36.50 2.29
4287 4559 5.638234 GGTTACCAACTCTGAACAGACATAC 59.362 44.000 0.00 0.00 33.22 2.39
4288 4560 3.914312 ACCAACTCTGAACAGACATACG 58.086 45.455 0.00 0.00 33.22 3.06
4289 4561 2.668457 CCAACTCTGAACAGACATACGC 59.332 50.000 0.00 0.00 33.22 4.42
4290 4562 3.579709 CAACTCTGAACAGACATACGCT 58.420 45.455 0.00 0.00 33.22 5.07
4291 4563 3.223423 ACTCTGAACAGACATACGCTG 57.777 47.619 0.00 0.00 39.26 5.18
4292 4564 2.820197 ACTCTGAACAGACATACGCTGA 59.180 45.455 0.00 0.00 36.86 4.26
4293 4565 3.255888 ACTCTGAACAGACATACGCTGAA 59.744 43.478 0.00 0.00 36.86 3.02
4294 4566 3.575630 TCTGAACAGACATACGCTGAAC 58.424 45.455 0.00 0.00 36.86 3.18
4308 4580 4.380531 ACGCTGAACTTTGATTTCTCTCA 58.619 39.130 0.00 0.00 0.00 3.27
4331 4603 1.929836 GAACTGCGCAGATAAGTGGAG 59.070 52.381 42.03 14.48 42.31 3.86
4341 4613 2.084546 GATAAGTGGAGGCGCAAACTT 58.915 47.619 10.83 14.78 36.80 2.66
4352 4624 1.266891 GCGCAAACTTACCTCGAATCG 60.267 52.381 0.30 0.00 0.00 3.34
4361 4645 0.035439 ACCTCGAATCGTGGCCATTT 60.035 50.000 21.75 3.01 43.18 2.32
4364 4648 0.676466 TCGAATCGTGGCCATTTGCT 60.676 50.000 9.72 0.00 40.92 3.91
4365 4649 0.248215 CGAATCGTGGCCATTTGCTC 60.248 55.000 9.72 1.44 40.92 4.26
4366 4650 0.248215 GAATCGTGGCCATTTGCTCG 60.248 55.000 9.72 6.81 40.92 5.03
4367 4651 1.656818 AATCGTGGCCATTTGCTCGG 61.657 55.000 9.72 0.00 40.92 4.63
4368 4652 2.819984 ATCGTGGCCATTTGCTCGGT 62.820 55.000 9.72 0.00 40.92 4.69
4369 4653 2.625823 CGTGGCCATTTGCTCGGTT 61.626 57.895 9.72 0.00 40.92 4.44
4370 4654 1.212751 GTGGCCATTTGCTCGGTTC 59.787 57.895 9.72 0.00 40.92 3.62
4371 4655 1.228398 TGGCCATTTGCTCGGTTCA 60.228 52.632 0.00 0.00 40.92 3.18
4372 4656 1.243342 TGGCCATTTGCTCGGTTCAG 61.243 55.000 0.00 0.00 40.92 3.02
4373 4657 0.960364 GGCCATTTGCTCGGTTCAGA 60.960 55.000 0.00 0.00 40.92 3.27
4374 4658 0.449388 GCCATTTGCTCGGTTCAGAG 59.551 55.000 0.00 0.00 41.03 3.35
4381 4665 3.649277 CTCGGTTCAGAGCACCCCG 62.649 68.421 0.00 0.00 39.98 5.73
4475 4769 3.007506 TCAGTAATTGATGGTGTGGTCGT 59.992 43.478 0.00 0.00 0.00 4.34
4476 4770 3.370978 CAGTAATTGATGGTGTGGTCGTC 59.629 47.826 0.00 0.00 0.00 4.20
4477 4771 1.438651 AATTGATGGTGTGGTCGTCG 58.561 50.000 0.00 0.00 0.00 5.12
4521 4815 2.203070 CCTACGCCATCAGCACCC 60.203 66.667 0.00 0.00 44.04 4.61
4546 4840 2.317609 CCGGTGTTTGACTCGCCTG 61.318 63.158 0.00 0.00 33.79 4.85
4552 4846 0.661483 GTTTGACTCGCCTGCTTTGC 60.661 55.000 0.00 0.00 0.00 3.68
4566 4860 1.199852 CTTTGCACACGCGGAACAAC 61.200 55.000 12.47 0.00 42.97 3.32
4583 4877 0.517316 AACGGAAATCACAAGAGCGC 59.483 50.000 0.00 0.00 0.00 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.255304 GACATCATATGGTTCTCTTCTTACTTC 57.745 37.037 2.13 0.00 33.60 3.01
78 79 5.967088 ACCTAAGTACTCTGTAGCAACATG 58.033 41.667 0.00 0.00 34.37 3.21
126 131 0.874390 AGCATAAACGTGGTGCACTG 59.126 50.000 17.98 9.66 41.19 3.66
231 236 0.980423 AGAGCCAAGGAAGAGTGACC 59.020 55.000 0.00 0.00 0.00 4.02
477 483 3.214696 AGAGTATTAATGCCCACTGCC 57.785 47.619 0.00 0.00 40.16 4.85
531 537 5.749462 TCCTCTCCCTTTGATCTCATTTTC 58.251 41.667 0.00 0.00 0.00 2.29
617 647 2.409948 AGGTAAAGAGTGCATCTGGC 57.590 50.000 0.00 0.00 38.67 4.85
618 648 3.119708 GCAAAGGTAAAGAGTGCATCTGG 60.120 47.826 0.00 0.00 38.67 3.86
619 649 3.503363 TGCAAAGGTAAAGAGTGCATCTG 59.497 43.478 0.00 0.00 40.14 2.90
620 650 3.754965 TGCAAAGGTAAAGAGTGCATCT 58.245 40.909 0.00 0.00 40.14 2.90
624 654 4.503741 TTCATGCAAAGGTAAAGAGTGC 57.496 40.909 0.00 0.00 35.75 4.40
625 655 5.865552 CCATTTCATGCAAAGGTAAAGAGTG 59.134 40.000 0.00 0.00 0.00 3.51
626 656 5.539955 ACCATTTCATGCAAAGGTAAAGAGT 59.460 36.000 3.06 0.00 0.00 3.24
627 657 6.029346 ACCATTTCATGCAAAGGTAAAGAG 57.971 37.500 3.06 0.00 0.00 2.85
628 658 6.152661 CCTACCATTTCATGCAAAGGTAAAGA 59.847 38.462 12.23 0.00 32.16 2.52
629 659 6.071391 ACCTACCATTTCATGCAAAGGTAAAG 60.071 38.462 12.23 9.53 35.04 1.85
630 660 5.777732 ACCTACCATTTCATGCAAAGGTAAA 59.222 36.000 12.23 0.00 35.04 2.01
631 661 5.329399 ACCTACCATTTCATGCAAAGGTAA 58.671 37.500 12.23 0.00 35.04 2.85
632 662 4.929479 ACCTACCATTTCATGCAAAGGTA 58.071 39.130 10.97 10.97 35.04 3.08
665 695 0.514691 CAGCCTTGAGACAGAAACGC 59.485 55.000 0.00 0.00 0.00 4.84
712 742 6.832520 TGTTTTTGAAGGCTATATTGCTCA 57.167 33.333 9.02 3.38 0.00 4.26
737 767 5.212472 AGCTCTGGGGATTAGGAATTTTT 57.788 39.130 0.00 0.00 0.00 1.94
833 864 2.941480 ACAATCCCTGGAATCTGCATC 58.059 47.619 0.00 0.00 0.00 3.91
903 934 1.084018 AGTCCACATCCCCATTTGGT 58.916 50.000 0.00 0.00 32.30 3.67
1015 1046 1.751437 AAATTACCGGAAGAGCTGCC 58.249 50.000 9.46 0.00 0.00 4.85
1026 1057 5.051907 CGTACGGAGAAGATGAAAATTACCG 60.052 44.000 7.57 0.00 42.78 4.02
1049 1080 8.370493 AGGTTTTGAACATGATCATATCTACG 57.630 34.615 8.15 0.00 0.00 3.51
1050 1081 9.330063 TGAGGTTTTGAACATGATCATATCTAC 57.670 33.333 8.15 9.30 0.00 2.59
1051 1082 9.904198 TTGAGGTTTTGAACATGATCATATCTA 57.096 29.630 8.15 4.48 0.00 1.98
1052 1083 8.812513 TTGAGGTTTTGAACATGATCATATCT 57.187 30.769 8.15 4.07 0.00 1.98
1072 1103 1.340248 GCATCCATGGAGCATTTGAGG 59.660 52.381 21.33 0.00 0.00 3.86
1290 1322 7.834881 TTCAGTTAAGAGAAGTGAAGTCCTA 57.165 36.000 3.93 0.00 35.38 2.94
1379 1459 4.488126 ACATTCACACAGCATACAACAC 57.512 40.909 0.00 0.00 0.00 3.32
1382 1462 6.542005 CCCTATTACATTCACACAGCATACAA 59.458 38.462 0.00 0.00 0.00 2.41
1415 1495 2.571212 TCTGGTTGACATGTGTGGTTC 58.429 47.619 1.15 0.00 0.00 3.62
1473 1553 5.221362 GCTAAAAGGTGTAAGGGAAAAAGCA 60.221 40.000 0.00 0.00 0.00 3.91
1486 1567 4.396166 CGATCATTTCAGGCTAAAAGGTGT 59.604 41.667 0.00 0.00 0.00 4.16
1516 1597 1.446618 GCATGCAAAAAGGAGGCCG 60.447 57.895 14.21 0.00 39.62 6.13
1621 1702 1.957113 GCATGAAGGAAAGTGGGAGGG 60.957 57.143 0.00 0.00 0.00 4.30
1626 1707 4.074970 ACTTACTGCATGAAGGAAAGTGG 58.925 43.478 18.29 2.67 30.66 4.00
1707 1791 2.370189 AGGTATCTTGCATGAGCTACCC 59.630 50.000 20.66 11.00 38.13 3.69
1893 1993 9.523168 TTAGAAAGATACCTAGATCCTTCTAGC 57.477 37.037 10.27 0.00 46.90 3.42
1971 2071 3.854990 TATTATCCCCCACCCCCACCC 62.855 61.905 0.00 0.00 0.00 4.61
1972 2072 0.403750 TATTATCCCCCACCCCCACC 60.404 60.000 0.00 0.00 0.00 4.61
1973 2073 1.073098 CTATTATCCCCCACCCCCAC 58.927 60.000 0.00 0.00 0.00 4.61
1974 2074 0.656829 ACTATTATCCCCCACCCCCA 59.343 55.000 0.00 0.00 0.00 4.96
1975 2075 1.073098 CACTATTATCCCCCACCCCC 58.927 60.000 0.00 0.00 0.00 5.40
1976 2076 1.829138 ACACTATTATCCCCCACCCC 58.171 55.000 0.00 0.00 0.00 4.95
1977 2077 5.594199 AATTACACTATTATCCCCCACCC 57.406 43.478 0.00 0.00 0.00 4.61
1978 2078 7.668469 CCTAAAATTACACTATTATCCCCCACC 59.332 40.741 0.00 0.00 0.00 4.61
1979 2079 7.176165 GCCTAAAATTACACTATTATCCCCCAC 59.824 40.741 0.00 0.00 0.00 4.61
1980 2080 7.147105 TGCCTAAAATTACACTATTATCCCCCA 60.147 37.037 0.00 0.00 0.00 4.96
1981 2081 7.176165 GTGCCTAAAATTACACTATTATCCCCC 59.824 40.741 0.00 0.00 0.00 5.40
1990 2090 6.150307 CACACATGGTGCCTAAAATTACACTA 59.850 38.462 0.00 0.00 41.36 2.74
2023 2123 1.407851 CCAGCTTCCTGCAGCAGATTA 60.408 52.381 24.90 5.97 45.94 1.75
2057 2157 1.881973 TCAGGAACAGAATTGCAGCAC 59.118 47.619 0.00 0.00 0.00 4.40
2408 2508 1.787012 CCTCAAAACCATGCAGCAAC 58.213 50.000 0.00 0.00 0.00 4.17
2447 2547 3.956233 TCGCATAGCATTCATGAAAAGC 58.044 40.909 21.91 21.91 0.00 3.51
2461 2561 4.271049 AGAAACACGATCCAATTCGCATAG 59.729 41.667 0.00 0.00 42.82 2.23
2466 2566 2.774007 GCAGAAACACGATCCAATTCG 58.226 47.619 0.00 0.00 44.56 3.34
2470 2570 1.872388 TTCGCAGAAACACGATCCAA 58.128 45.000 0.00 0.00 45.90 3.53
2473 2573 4.065423 TGAATTTCGCAGAAACACGATC 57.935 40.909 5.99 0.00 45.90 3.69
2477 2577 4.536065 TCACATGAATTTCGCAGAAACAC 58.464 39.130 0.00 4.84 45.90 3.32
2505 2605 2.593026 TCAAAATTCACCACCCTGACC 58.407 47.619 0.00 0.00 0.00 4.02
2511 2611 9.589111 TTTAGTAAGTTTTCAAAATTCACCACC 57.411 29.630 0.00 0.00 0.00 4.61
2550 2650 3.139077 GTCGAACCCTGTTTCAGTTCAT 58.861 45.455 0.00 0.00 39.89 2.57
2568 2668 1.071019 CCGAGGTGTCATCAACGTCG 61.071 60.000 10.66 10.66 36.22 5.12
2583 2683 3.872728 TCGCGACCATCGACCGAG 61.873 66.667 3.71 0.00 43.74 4.63
2655 2755 4.965200 ATTAGTACCATCAGAAGGCTCC 57.035 45.455 0.00 0.00 0.00 4.70
2766 2866 6.020971 TCTTGTGCGTGTTCTTAGAGATAA 57.979 37.500 0.00 0.00 0.00 1.75
2782 2882 3.127721 GGTAGGCTTTGAGATTCTTGTGC 59.872 47.826 0.00 0.00 0.00 4.57
2803 2903 1.613437 GAACCAACAGGACCACAATGG 59.387 52.381 0.00 0.00 45.02 3.16
2827 2940 2.225019 CACATGAGTTCAGTTGCAGTCC 59.775 50.000 0.00 0.00 0.00 3.85
3006 3155 2.745100 ACGACGGCGCTGAGAGTA 60.745 61.111 25.98 0.00 42.48 2.59
3018 3167 3.175240 CCGCTCAAGCTGACGACG 61.175 66.667 0.00 0.00 39.32 5.12
3111 3260 3.403038 CAAGATCGTCAGGGTTTGTTCT 58.597 45.455 0.00 0.00 0.00 3.01
3112 3261 2.484264 CCAAGATCGTCAGGGTTTGTTC 59.516 50.000 0.00 0.00 0.00 3.18
3125 3274 2.604914 CGTCCTGAATTCACCAAGATCG 59.395 50.000 3.38 0.41 0.00 3.69
3146 3296 1.153005 CTCCATCTTGCCCCTCAGC 60.153 63.158 0.00 0.00 0.00 4.26
3228 3378 6.425417 CCTGTAGGTTTGTTTGTTTGTTTGTT 59.575 34.615 0.00 0.00 0.00 2.83
3229 3379 5.929415 CCTGTAGGTTTGTTTGTTTGTTTGT 59.071 36.000 0.00 0.00 0.00 2.83
3230 3380 5.163903 GCCTGTAGGTTTGTTTGTTTGTTTG 60.164 40.000 0.00 0.00 37.57 2.93
3231 3381 4.932799 GCCTGTAGGTTTGTTTGTTTGTTT 59.067 37.500 0.00 0.00 37.57 2.83
3266 3416 3.981211 ACACCATGAAACACATCTTTGC 58.019 40.909 0.00 0.00 37.07 3.68
3272 3422 3.819368 TCAGTGACACCATGAAACACAT 58.181 40.909 0.84 0.00 40.17 3.21
3276 3426 4.613622 CGGAATTCAGTGACACCATGAAAC 60.614 45.833 12.64 10.18 36.59 2.78
3298 3448 0.168348 CGAGTAGAGGTCACCACACG 59.832 60.000 0.00 0.00 0.00 4.49
3327 3477 0.490017 TCCTGTAGGGGACAACCTCA 59.510 55.000 0.00 0.00 42.09 3.86
3419 3569 0.328258 AGGGGTGGTGTAAGATGTGC 59.672 55.000 0.00 0.00 0.00 4.57
3452 3602 5.419239 CTTCTCAGGAAGGAAGAACAGAT 57.581 43.478 0.00 0.00 43.68 2.90
3469 3619 7.440523 ACCATGTTTAATGTTCTGACTTCTC 57.559 36.000 0.00 0.00 0.00 2.87
3501 3651 4.715523 TAGTGGCCCAACCTGCGC 62.716 66.667 0.00 0.00 40.22 6.09
3590 3740 2.371902 CAGAAGCGCTGCTCTCTTC 58.628 57.895 17.30 4.66 38.25 2.87
3666 3818 9.750783 TTCACCTCTCTATAGTAAGTTTACACT 57.249 33.333 0.00 0.00 36.12 3.55
3759 3930 0.109412 GCACTCATGGTTGCTTGCTC 60.109 55.000 11.07 0.00 31.30 4.26
3901 4072 2.032681 GGGGTGCTTCAGTTCGCT 59.967 61.111 0.00 0.00 0.00 4.93
3960 4212 3.681897 CAGAGCAATACACCTGAGAACAC 59.318 47.826 0.00 0.00 0.00 3.32
3976 4228 6.015603 CAGTTGACCTAGATATGATCAGAGCA 60.016 42.308 8.49 0.00 0.00 4.26
3987 4239 5.893824 TCAGATGCTTCAGTTGACCTAGATA 59.106 40.000 2.07 0.00 0.00 1.98
4044 4296 0.831288 AGAGCTCCATGATCCTCCGG 60.831 60.000 10.93 0.00 0.00 5.14
4045 4297 0.602562 GAGAGCTCCATGATCCTCCG 59.397 60.000 10.93 0.00 0.00 4.63
4046 4298 0.602562 CGAGAGCTCCATGATCCTCC 59.397 60.000 10.93 0.00 0.00 4.30
4085 4337 5.064707 CCTGTATGTTCCTTGTAACGATTGG 59.935 44.000 0.00 0.00 31.76 3.16
4088 4340 5.670792 TCCTGTATGTTCCTTGTAACGAT 57.329 39.130 0.00 0.00 31.76 3.73
4089 4341 5.471556 TTCCTGTATGTTCCTTGTAACGA 57.528 39.130 0.00 0.00 31.76 3.85
4090 4342 6.036083 CAGATTCCTGTATGTTCCTTGTAACG 59.964 42.308 0.00 0.00 35.70 3.18
4091 4343 6.316390 CCAGATTCCTGTATGTTCCTTGTAAC 59.684 42.308 0.00 0.00 38.74 2.50
4143 4395 2.284995 AGTGCCCACTCTCCTCCC 60.285 66.667 0.00 0.00 36.92 4.30
4180 4437 2.749076 GCATGATGCAAGTCACCTTACA 59.251 45.455 13.36 0.00 44.26 2.41
4205 4462 2.186076 GCTTCAGAGTTCCGACATACG 58.814 52.381 0.00 0.00 42.18 3.06
4212 4469 1.546476 ACAGTAGGCTTCAGAGTTCCG 59.454 52.381 0.00 0.00 0.00 4.30
4213 4470 2.563179 TGACAGTAGGCTTCAGAGTTCC 59.437 50.000 0.00 0.00 0.00 3.62
4214 4471 3.944055 TGACAGTAGGCTTCAGAGTTC 57.056 47.619 0.00 0.00 0.00 3.01
4215 4472 3.834813 TGATGACAGTAGGCTTCAGAGTT 59.165 43.478 0.00 0.00 0.00 3.01
4216 4473 3.194542 GTGATGACAGTAGGCTTCAGAGT 59.805 47.826 0.00 0.00 0.00 3.24
4217 4474 3.446873 AGTGATGACAGTAGGCTTCAGAG 59.553 47.826 0.00 0.00 0.00 3.35
4218 4475 3.194329 CAGTGATGACAGTAGGCTTCAGA 59.806 47.826 0.00 0.00 0.00 3.27
4280 4552 5.934625 AGAAATCAAAGTTCAGCGTATGTCT 59.065 36.000 0.00 0.00 0.00 3.41
4281 4553 6.091441 AGAGAAATCAAAGTTCAGCGTATGTC 59.909 38.462 0.00 0.00 0.00 3.06
4282 4554 5.934625 AGAGAAATCAAAGTTCAGCGTATGT 59.065 36.000 0.00 0.00 0.00 2.29
4283 4555 6.091305 TGAGAGAAATCAAAGTTCAGCGTATG 59.909 38.462 0.00 0.00 0.00 2.39
4284 4556 6.166279 TGAGAGAAATCAAAGTTCAGCGTAT 58.834 36.000 0.00 0.00 0.00 3.06
4285 4557 5.538118 TGAGAGAAATCAAAGTTCAGCGTA 58.462 37.500 0.00 0.00 0.00 4.42
4286 4558 4.380531 TGAGAGAAATCAAAGTTCAGCGT 58.619 39.130 0.00 0.00 0.00 5.07
4287 4559 4.668686 GCTGAGAGAAATCAAAGTTCAGCG 60.669 45.833 7.68 0.00 44.21 5.18
4288 4560 4.721142 GCTGAGAGAAATCAAAGTTCAGC 58.279 43.478 7.68 7.68 46.01 4.26
4289 4561 4.687948 TCGCTGAGAGAAATCAAAGTTCAG 59.312 41.667 0.00 0.00 35.03 3.02
4290 4562 4.631131 TCGCTGAGAGAAATCAAAGTTCA 58.369 39.130 0.00 0.00 0.00 3.18
4291 4563 5.178438 AGTTCGCTGAGAGAAATCAAAGTTC 59.822 40.000 0.00 0.00 0.00 3.01
4292 4564 5.059833 AGTTCGCTGAGAGAAATCAAAGTT 58.940 37.500 0.00 0.00 0.00 2.66
4293 4565 4.636249 AGTTCGCTGAGAGAAATCAAAGT 58.364 39.130 0.00 0.00 0.00 2.66
4318 4590 0.744414 TTGCGCCTCCACTTATCTGC 60.744 55.000 4.18 0.00 0.00 4.26
4327 4599 0.321298 GAGGTAAGTTTGCGCCTCCA 60.321 55.000 4.18 0.00 41.08 3.86
4331 4603 1.062148 GATTCGAGGTAAGTTTGCGCC 59.938 52.381 4.18 0.00 0.00 6.53
4341 4613 0.828022 AATGGCCACGATTCGAGGTA 59.172 50.000 21.08 12.57 39.64 3.08
4352 4624 1.212751 GAACCGAGCAAATGGCCAC 59.787 57.895 8.16 0.00 46.50 5.01
4365 4649 4.760047 CCGGGGTGCTCTGAACCG 62.760 72.222 0.00 0.00 43.89 4.44
4366 4650 3.607370 GACCGGGGTGCTCTGAACC 62.607 68.421 6.32 0.00 36.94 3.62
4367 4651 2.047179 GACCGGGGTGCTCTGAAC 60.047 66.667 6.32 0.00 0.00 3.18
4368 4652 3.691342 CGACCGGGGTGCTCTGAA 61.691 66.667 6.32 0.00 0.00 3.02
4369 4653 4.988716 ACGACCGGGGTGCTCTGA 62.989 66.667 6.32 0.00 0.00 3.27
4370 4654 4.436998 GACGACCGGGGTGCTCTG 62.437 72.222 6.32 0.00 0.00 3.35
4375 4659 4.373116 CTGTGGACGACCGGGGTG 62.373 72.222 6.32 0.00 39.42 4.61
4376 4660 3.899545 ATCTGTGGACGACCGGGGT 62.900 63.158 6.32 2.45 39.42 4.95
4377 4661 2.656069 AATCTGTGGACGACCGGGG 61.656 63.158 6.32 0.00 39.42 5.73
4378 4662 1.447838 CAATCTGTGGACGACCGGG 60.448 63.158 6.32 0.00 39.42 5.73
4475 4769 1.371758 GACGAAGCAGTGCAGACGA 60.372 57.895 26.08 0.00 0.00 4.20
4476 4770 1.612469 CTGACGAAGCAGTGCAGACG 61.612 60.000 19.20 20.10 0.00 4.18
4477 4771 1.287730 CCTGACGAAGCAGTGCAGAC 61.288 60.000 19.20 9.09 34.06 3.51
4524 4818 1.683790 GCGAGTCAAACACCGGATCG 61.684 60.000 9.46 5.64 0.00 3.69
4534 4828 1.100463 TGCAAAGCAGGCGAGTCAAA 61.100 50.000 0.00 0.00 33.32 2.69
4536 4830 2.110835 TGCAAAGCAGGCGAGTCA 59.889 55.556 0.00 0.00 33.32 3.41
4546 4840 2.725815 GTTCCGCGTGTGCAAAGC 60.726 61.111 4.92 0.00 42.97 3.51
4552 4846 2.037913 TTTCCGTTGTTCCGCGTGTG 62.038 55.000 4.92 0.00 0.00 3.82
4559 4853 3.609409 GCTCTTGTGATTTCCGTTGTTCC 60.609 47.826 0.00 0.00 0.00 3.62
4566 4860 1.059369 CGCGCTCTTGTGATTTCCG 59.941 57.895 5.56 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.