Multiple sequence alignment - TraesCS3A01G403000

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 TraesCS3A01G403000 chr3A 100.000 2336 0 0 1 2336 648242738 648240403 0.000000e+00 4314
1 TraesCS3A01G403000 chr3D 85.554 1779 129 47 1 1705 512667825 512666101 0.000000e+00 1744
2 TraesCS3A01G403000 chr7B 98.873 621 7 0 1716 2336 695448281 695448901 0.000000e+00 1109
3 TraesCS3A01G403000 chr7B 98.421 570 9 0 1767 2336 654250306 654249737 0.000000e+00 1003
4 TraesCS3A01G403000 chr7A 98.546 619 9 0 1718 2336 291802624 291802006 0.000000e+00 1094
5 TraesCS3A01G403000 chr6B 98.384 619 10 0 1718 2336 696347300 696346682 0.000000e+00 1088
6 TraesCS3A01G403000 chr4B 97.920 625 11 2 1714 2336 662784079 662784703 0.000000e+00 1081
7 TraesCS3A01G403000 chr4A 98.068 621 12 0 1716 2336 629116759 629117379 0.000000e+00 1081
8 TraesCS3A01G403000 chr6A 98.211 615 10 1 1723 2336 9487311 9487925 0.000000e+00 1074
9 TraesCS3A01G403000 chr5B 97.581 620 14 1 1718 2336 30697031 30697650 0.000000e+00 1061
10 TraesCS3A01G403000 chr6D 96.607 619 14 5 1718 2336 12345726 12346337 0.000000e+00 1020
11 TraesCS3A01G403000 chr2D 92.980 641 21 8 1720 2336 642960745 642960105 0.000000e+00 913
12 TraesCS3A01G403000 chr1D 92.188 640 27 9 1719 2336 324721695 324721057 0.000000e+00 883
13 TraesCS3A01G403000 chr3B 85.591 812 50 19 940 1702 675151757 675152550 0.000000e+00 789
14 TraesCS3A01G403000 chr3B 88.981 363 27 9 1 353 675148378 675148737 9.910000e-119 436
15 TraesCS3A01G403000 chr3B 87.919 298 17 10 545 840 675151393 675151673 1.340000e-87 333


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 TraesCS3A01G403000 chr3A 648240403 648242738 2335 True 4314.000000 4314 100.000 1 2336 1 chr3A.!!$R1 2335
1 TraesCS3A01G403000 chr3D 512666101 512667825 1724 True 1744.000000 1744 85.554 1 1705 1 chr3D.!!$R1 1704
2 TraesCS3A01G403000 chr7B 695448281 695448901 620 False 1109.000000 1109 98.873 1716 2336 1 chr7B.!!$F1 620
3 TraesCS3A01G403000 chr7B 654249737 654250306 569 True 1003.000000 1003 98.421 1767 2336 1 chr7B.!!$R1 569
4 TraesCS3A01G403000 chr7A 291802006 291802624 618 True 1094.000000 1094 98.546 1718 2336 1 chr7A.!!$R1 618
5 TraesCS3A01G403000 chr6B 696346682 696347300 618 True 1088.000000 1088 98.384 1718 2336 1 chr6B.!!$R1 618
6 TraesCS3A01G403000 chr4B 662784079 662784703 624 False 1081.000000 1081 97.920 1714 2336 1 chr4B.!!$F1 622
7 TraesCS3A01G403000 chr4A 629116759 629117379 620 False 1081.000000 1081 98.068 1716 2336 1 chr4A.!!$F1 620
8 TraesCS3A01G403000 chr6A 9487311 9487925 614 False 1074.000000 1074 98.211 1723 2336 1 chr6A.!!$F1 613
9 TraesCS3A01G403000 chr5B 30697031 30697650 619 False 1061.000000 1061 97.581 1718 2336 1 chr5B.!!$F1 618
10 TraesCS3A01G403000 chr6D 12345726 12346337 611 False 1020.000000 1020 96.607 1718 2336 1 chr6D.!!$F1 618
11 TraesCS3A01G403000 chr2D 642960105 642960745 640 True 913.000000 913 92.980 1720 2336 1 chr2D.!!$R1 616
12 TraesCS3A01G403000 chr1D 324721057 324721695 638 True 883.000000 883 92.188 1719 2336 1 chr1D.!!$R1 617
13 TraesCS3A01G403000 chr3B 675148378 675152550 4172 False 519.333333 789 87.497 1 1702 3 chr3B.!!$F1 1701

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
899 3474 0.107643 GCTGAAGCCTCATACCTCCC 59.892 60.0 0.0 0.0 34.31 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 4365 0.03467 CAGAGGAGGGCCCAAGAAAG 60.035 60.0 27.56 5.62 37.41 2.62 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
35 39 2.793790 CAGACGATAACAGCTCAGCATC 59.206 50.000 0.00 0.00 0.00 3.91
104 108 2.290122 ATCTTCAGCCGAGTCGCCTG 62.290 60.000 16.98 16.98 0.00 4.85
130 134 0.249868 TCAGCACGTGTTCTTCCCAG 60.250 55.000 18.38 0.00 0.00 4.45
200 204 4.155310 ACAAACTAAATTAGCACGCCAC 57.845 40.909 0.00 0.00 0.00 5.01
201 205 3.057806 ACAAACTAAATTAGCACGCCACC 60.058 43.478 0.00 0.00 0.00 4.61
202 206 2.483014 ACTAAATTAGCACGCCACCA 57.517 45.000 0.00 0.00 0.00 4.17
203 207 2.999331 ACTAAATTAGCACGCCACCAT 58.001 42.857 0.00 0.00 0.00 3.55
204 208 3.352648 ACTAAATTAGCACGCCACCATT 58.647 40.909 0.00 0.00 0.00 3.16
254 274 1.449601 GCACGATGGTGTCCCGAAT 60.450 57.895 9.74 0.00 46.13 3.34
286 306 2.034221 GACAGGGAAGGCACACCC 59.966 66.667 0.00 0.00 44.94 4.61
327 347 2.738521 CGGGACACTGAACCTGCG 60.739 66.667 0.00 0.00 0.00 5.18
428 453 3.327404 GTCGCCCCCTTCCCTCAA 61.327 66.667 0.00 0.00 0.00 3.02
429 454 3.327404 TCGCCCCCTTCCCTCAAC 61.327 66.667 0.00 0.00 0.00 3.18
434 459 1.725169 CCCCCTTCCCTCAACCAACA 61.725 60.000 0.00 0.00 0.00 3.33
443 468 1.064952 CCTCAACCAACAAACACGTCC 59.935 52.381 0.00 0.00 0.00 4.79
448 501 4.641094 TCAACCAACAAACACGTCCTAATT 59.359 37.500 0.00 0.00 0.00 1.40
449 502 4.561735 ACCAACAAACACGTCCTAATTG 57.438 40.909 0.00 0.00 0.00 2.32
451 504 3.305064 CCAACAAACACGTCCTAATTGGG 60.305 47.826 0.35 0.35 33.25 4.12
453 506 2.159382 CAAACACGTCCTAATTGGGCT 58.841 47.619 2.26 0.00 38.58 5.19
454 507 3.244630 ACAAACACGTCCTAATTGGGCTA 60.245 43.478 2.26 0.00 38.58 3.93
455 508 3.706600 AACACGTCCTAATTGGGCTAA 57.293 42.857 2.26 0.00 38.58 3.09
456 509 3.926058 ACACGTCCTAATTGGGCTAAT 57.074 42.857 2.26 0.00 38.58 1.73
458 511 4.700700 ACACGTCCTAATTGGGCTAATAC 58.299 43.478 2.26 0.00 38.58 1.89
459 512 3.739300 CACGTCCTAATTGGGCTAATACG 59.261 47.826 14.74 14.74 38.58 3.06
460 513 3.638160 ACGTCCTAATTGGGCTAATACGA 59.362 43.478 20.79 3.99 38.58 3.43
461 514 3.985925 CGTCCTAATTGGGCTAATACGAC 59.014 47.826 11.98 8.50 38.58 4.34
462 515 4.313282 GTCCTAATTGGGCTAATACGACC 58.687 47.826 2.26 0.00 37.49 4.79
463 516 4.040095 GTCCTAATTGGGCTAATACGACCT 59.960 45.833 2.26 0.00 37.49 3.85
464 517 4.039973 TCCTAATTGGGCTAATACGACCTG 59.960 45.833 2.26 0.00 36.20 4.00
465 518 2.930826 ATTGGGCTAATACGACCTGG 57.069 50.000 0.00 0.00 31.45 4.45
467 520 1.868713 TGGGCTAATACGACCTGGAA 58.131 50.000 0.00 0.00 31.45 3.53
468 521 2.404559 TGGGCTAATACGACCTGGAAT 58.595 47.619 0.00 0.00 31.45 3.01
469 522 2.775384 TGGGCTAATACGACCTGGAATT 59.225 45.455 0.00 0.00 31.45 2.17
485 3027 1.068127 GAATTCATGCTCCCCACATGC 59.932 52.381 0.00 0.00 43.71 4.06
486 3028 1.105167 ATTCATGCTCCCCACATGCG 61.105 55.000 0.00 0.00 43.71 4.73
487 3029 2.438975 CATGCTCCCCACATGCGT 60.439 61.111 0.00 0.00 38.58 5.24
488 3030 2.124570 ATGCTCCCCACATGCGTC 60.125 61.111 0.00 0.00 0.00 5.19
514 3056 2.109181 GGCTCCTCCACATACGCC 59.891 66.667 0.00 0.00 34.01 5.68
553 3095 2.634777 CCGAGACGCCGAGATCTC 59.365 66.667 13.05 13.05 38.40 2.75
554 3096 2.634777 CGAGACGCCGAGATCTCC 59.365 66.667 17.13 3.07 38.53 3.71
560 3102 2.024871 GCCGAGATCTCCACGTCG 59.975 66.667 17.13 5.01 0.00 5.12
561 3103 2.024871 CCGAGATCTCCACGTCGC 59.975 66.667 17.13 0.00 0.00 5.19
563 3105 2.024871 GAGATCTCCACGTCGCCG 59.975 66.667 12.00 0.00 40.83 6.46
640 3184 1.971167 GTGCTTGCATGGGAACGGA 60.971 57.895 0.00 0.00 0.00 4.69
644 3188 1.019673 CTTGCATGGGAACGGAGATG 58.980 55.000 0.00 0.00 0.00 2.90
659 3231 2.553172 GGAGATGCGACTATACGAGGTT 59.447 50.000 0.00 0.00 35.09 3.50
661 3233 2.293677 AGATGCGACTATACGAGGTTGG 59.706 50.000 0.00 0.00 35.09 3.77
662 3234 0.742505 TGCGACTATACGAGGTTGGG 59.257 55.000 0.00 0.00 35.09 4.12
663 3235 0.596859 GCGACTATACGAGGTTGGGC 60.597 60.000 0.00 0.00 35.09 5.36
664 3236 0.317603 CGACTATACGAGGTTGGGCG 60.318 60.000 0.00 0.00 35.09 6.13
665 3237 0.743097 GACTATACGAGGTTGGGCGT 59.257 55.000 0.00 0.00 43.86 5.68
666 3238 0.458669 ACTATACGAGGTTGGGCGTG 59.541 55.000 0.00 0.00 41.35 5.34
667 3239 0.249322 CTATACGAGGTTGGGCGTGG 60.249 60.000 0.00 0.00 41.35 4.94
668 3240 2.300850 TATACGAGGTTGGGCGTGGC 62.301 60.000 0.00 0.00 41.35 5.01
700 3272 2.030371 TCCAGTCAAAACATGCAGCAA 58.970 42.857 0.00 0.00 0.00 3.91
760 3335 1.750399 CCGCCCCACTTTGATCCTG 60.750 63.158 0.00 0.00 0.00 3.86
769 3344 3.431486 CCACTTTGATCCTGCTCCTACTC 60.431 52.174 0.00 0.00 0.00 2.59
770 3345 2.769095 ACTTTGATCCTGCTCCTACTCC 59.231 50.000 0.00 0.00 0.00 3.85
771 3346 2.856760 TTGATCCTGCTCCTACTCCT 57.143 50.000 0.00 0.00 0.00 3.69
772 3347 3.973472 TTGATCCTGCTCCTACTCCTA 57.027 47.619 0.00 0.00 0.00 2.94
773 3348 3.231207 TGATCCTGCTCCTACTCCTAC 57.769 52.381 0.00 0.00 0.00 3.18
794 3369 6.478016 CCTACTACTAATAAAGCCGTTGAACC 59.522 42.308 0.00 0.00 0.00 3.62
848 3423 1.203364 AGCCTCCTTCCTCTTCCAGAA 60.203 52.381 0.00 0.00 0.00 3.02
870 3445 1.895707 CAATCCATCGCAGCCTCCC 60.896 63.158 0.00 0.00 0.00 4.30
889 3464 3.080121 CCTCCTCCGCTGAAGCCT 61.080 66.667 0.00 0.00 37.91 4.58
890 3465 2.498726 CTCCTCCGCTGAAGCCTC 59.501 66.667 0.00 0.00 37.91 4.70
891 3466 2.283894 TCCTCCGCTGAAGCCTCA 60.284 61.111 0.00 0.00 37.91 3.86
892 3467 1.684386 CTCCTCCGCTGAAGCCTCAT 61.684 60.000 0.00 0.00 37.91 2.90
893 3468 0.397114 TCCTCCGCTGAAGCCTCATA 60.397 55.000 0.00 0.00 37.91 2.15
894 3469 0.249657 CCTCCGCTGAAGCCTCATAC 60.250 60.000 0.00 0.00 37.91 2.39
896 3471 0.687757 TCCGCTGAAGCCTCATACCT 60.688 55.000 0.00 0.00 37.91 3.08
897 3472 0.249657 CCGCTGAAGCCTCATACCTC 60.250 60.000 0.00 0.00 37.91 3.85
899 3474 0.107643 GCTGAAGCCTCATACCTCCC 59.892 60.000 0.00 0.00 34.31 4.30
900 3475 0.761802 CTGAAGCCTCATACCTCCCC 59.238 60.000 0.00 0.00 0.00 4.81
953 3554 0.387367 CTCTCGTGGTCCGTCAGTTG 60.387 60.000 0.00 0.00 37.94 3.16
954 3555 2.022129 CTCGTGGTCCGTCAGTTGC 61.022 63.158 0.00 0.00 37.94 4.17
955 3556 3.041940 CGTGGTCCGTCAGTTGCC 61.042 66.667 0.00 0.00 0.00 4.52
956 3557 2.426023 GTGGTCCGTCAGTTGCCT 59.574 61.111 0.00 0.00 0.00 4.75
957 3558 1.227853 GTGGTCCGTCAGTTGCCTT 60.228 57.895 0.00 0.00 0.00 4.35
958 3559 1.070786 TGGTCCGTCAGTTGCCTTC 59.929 57.895 0.00 0.00 0.00 3.46
959 3560 2.027625 GGTCCGTCAGTTGCCTTCG 61.028 63.158 0.00 0.00 0.00 3.79
960 3561 2.357034 TCCGTCAGTTGCCTTCGC 60.357 61.111 0.00 0.00 0.00 4.70
961 3562 3.777925 CCGTCAGTTGCCTTCGCG 61.778 66.667 0.00 0.00 38.08 5.87
962 3563 3.777925 CGTCAGTTGCCTTCGCGG 61.778 66.667 6.13 0.00 38.08 6.46
975 3585 1.750341 TTCGCGGGGTCTGAACTTCA 61.750 55.000 6.13 0.00 0.00 3.02
989 3599 0.172803 ACTTCACGTACGATCCCTGC 59.827 55.000 24.41 0.00 0.00 4.85
1039 3655 1.153549 GGCACCTCTGATCACCGTC 60.154 63.158 0.00 0.00 0.00 4.79
1561 4218 9.603921 GTGGAATCCATAAATCATTTGTTGAAT 57.396 29.630 4.81 0.00 35.05 2.57
1581 4238 7.360575 TGAATAAAGAAAGAAACTACTCCGC 57.639 36.000 0.00 0.00 0.00 5.54
1588 4245 0.735287 GAAACTACTCCGCGTGTCCC 60.735 60.000 4.92 0.00 0.00 4.46
1595 4252 1.758280 ACTCCGCGTGTCCCATAATAA 59.242 47.619 4.92 0.00 0.00 1.40
1630 4287 4.641954 CAAGCTATGTTAGACTGCAAACG 58.358 43.478 0.00 0.00 0.00 3.60
1632 4289 3.056107 AGCTATGTTAGACTGCAAACGGA 60.056 43.478 0.00 0.00 0.00 4.69
1653 4310 1.374252 ACCGCATCCGTTGACAGAC 60.374 57.895 0.00 0.00 0.00 3.51
1658 4315 0.608130 CATCCGTTGACAGACAGGGA 59.392 55.000 0.00 0.00 37.35 4.20
1659 4316 0.608640 ATCCGTTGACAGACAGGGAC 59.391 55.000 0.00 0.00 36.35 4.46
1660 4317 0.757561 TCCGTTGACAGACAGGGACA 60.758 55.000 0.00 0.00 31.28 4.02
1661 4318 0.319900 CCGTTGACAGACAGGGACAG 60.320 60.000 0.00 0.00 0.00 3.51
1662 4319 0.319900 CGTTGACAGACAGGGACAGG 60.320 60.000 0.00 0.00 0.00 4.00
1663 4320 0.759346 GTTGACAGACAGGGACAGGT 59.241 55.000 0.00 0.00 0.00 4.00
1666 4323 1.140852 TGACAGACAGGGACAGGTTTG 59.859 52.381 0.00 0.00 0.00 2.93
1670 4328 2.672996 CAGGGACAGGTTTGCGGG 60.673 66.667 0.00 0.00 0.00 6.13
1680 4338 2.036006 GTTTGCGGGCACGGATGTA 61.036 57.895 11.92 0.00 41.08 2.29
1697 4355 2.443394 TAGGAGCCGGCCATCCAAG 61.443 63.158 30.35 0.00 38.12 3.61
1702 4360 1.223487 GCCGGCCATCCAAGACTAA 59.777 57.895 18.11 0.00 0.00 2.24
1705 4363 0.251916 CGGCCATCCAAGACTAACCA 59.748 55.000 2.24 0.00 0.00 3.67
1706 4364 1.751437 GGCCATCCAAGACTAACCAC 58.249 55.000 0.00 0.00 0.00 4.16
1707 4365 1.682087 GGCCATCCAAGACTAACCACC 60.682 57.143 0.00 0.00 0.00 4.61
1708 4366 1.282157 GCCATCCAAGACTAACCACCT 59.718 52.381 0.00 0.00 0.00 4.00
1709 4367 2.290960 GCCATCCAAGACTAACCACCTT 60.291 50.000 0.00 0.00 0.00 3.50
1710 4368 3.814316 GCCATCCAAGACTAACCACCTTT 60.814 47.826 0.00 0.00 0.00 3.11
1711 4369 4.010349 CCATCCAAGACTAACCACCTTTC 58.990 47.826 0.00 0.00 0.00 2.62
1712 4370 4.263506 CCATCCAAGACTAACCACCTTTCT 60.264 45.833 0.00 0.00 0.00 2.52
1713 4371 5.316987 CATCCAAGACTAACCACCTTTCTT 58.683 41.667 0.00 0.00 0.00 2.52
1714 4372 4.714632 TCCAAGACTAACCACCTTTCTTG 58.285 43.478 0.00 0.00 41.84 3.02
2275 4958 1.601419 GATGTTCGTCCTCGACCCCA 61.601 60.000 0.00 0.00 46.03 4.96
2295 4978 4.158764 CCCAATCTACTCCGATCTGTATCC 59.841 50.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 39 0.454957 GCTTAAGCGTGTGTGCATGG 60.455 55.000 12.53 0.00 37.31 3.66
42 46 2.860293 CACGGGCTTAAGCGTGTG 59.140 61.111 26.22 26.22 43.26 3.82
130 134 4.660105 CTCGTACTGTACTAGTTCTTGGC 58.340 47.826 15.35 0.00 40.89 4.52
192 196 2.081425 TTGTTGGAATGGTGGCGTGC 62.081 55.000 0.00 0.00 0.00 5.34
200 204 2.095263 GTCATCACGGTTGTTGGAATGG 60.095 50.000 0.00 0.00 0.00 3.16
201 205 2.412716 CGTCATCACGGTTGTTGGAATG 60.413 50.000 0.00 0.00 42.73 2.67
202 206 1.804151 CGTCATCACGGTTGTTGGAAT 59.196 47.619 0.00 0.00 42.73 3.01
203 207 1.202545 TCGTCATCACGGTTGTTGGAA 60.203 47.619 0.00 0.00 46.70 3.53
204 208 0.389757 TCGTCATCACGGTTGTTGGA 59.610 50.000 0.00 0.00 46.70 3.53
238 256 2.104967 TCTAATTCGGGACACCATCGT 58.895 47.619 0.00 0.00 36.13 3.73
240 258 3.312697 GCTTTCTAATTCGGGACACCATC 59.687 47.826 0.00 0.00 36.13 3.51
241 259 3.279434 GCTTTCTAATTCGGGACACCAT 58.721 45.455 0.00 0.00 36.13 3.55
242 260 2.706890 GCTTTCTAATTCGGGACACCA 58.293 47.619 0.00 0.00 36.13 4.17
243 261 1.664151 CGCTTTCTAATTCGGGACACC 59.336 52.381 0.00 0.00 0.00 4.16
244 262 1.664151 CCGCTTTCTAATTCGGGACAC 59.336 52.381 0.00 0.00 38.35 3.67
254 274 2.812178 GTCGCCGCCGCTTTCTAA 60.812 61.111 0.00 0.00 0.00 2.10
303 323 1.613928 TTCAGTGTCCCGGGGCATA 60.614 57.895 34.24 17.67 0.00 3.14
311 331 3.050275 GCGCAGGTTCAGTGTCCC 61.050 66.667 0.30 0.00 0.00 4.46
421 446 1.340211 ACGTGTTTGTTGGTTGAGGGA 60.340 47.619 0.00 0.00 0.00 4.20
422 447 1.064952 GACGTGTTTGTTGGTTGAGGG 59.935 52.381 0.00 0.00 0.00 4.30
423 448 1.064952 GGACGTGTTTGTTGGTTGAGG 59.935 52.381 0.00 0.00 0.00 3.86
424 449 2.014128 AGGACGTGTTTGTTGGTTGAG 58.986 47.619 0.00 0.00 0.00 3.02
425 450 2.116827 AGGACGTGTTTGTTGGTTGA 57.883 45.000 0.00 0.00 0.00 3.18
426 451 4.561735 ATTAGGACGTGTTTGTTGGTTG 57.438 40.909 0.00 0.00 0.00 3.77
427 452 4.202070 CCAATTAGGACGTGTTTGTTGGTT 60.202 41.667 0.00 0.00 41.22 3.67
428 453 3.316868 CCAATTAGGACGTGTTTGTTGGT 59.683 43.478 0.00 0.00 41.22 3.67
429 454 3.305064 CCCAATTAGGACGTGTTTGTTGG 60.305 47.826 0.00 1.94 41.22 3.77
434 459 2.579410 AGCCCAATTAGGACGTGTTT 57.421 45.000 0.00 0.00 41.22 2.83
443 468 4.039973 TCCAGGTCGTATTAGCCCAATTAG 59.960 45.833 0.00 0.00 0.00 1.73
448 501 1.868713 TTCCAGGTCGTATTAGCCCA 58.131 50.000 0.00 0.00 0.00 5.36
449 502 3.181458 TGAATTCCAGGTCGTATTAGCCC 60.181 47.826 2.27 0.00 0.00 5.19
451 504 4.083802 GCATGAATTCCAGGTCGTATTAGC 60.084 45.833 2.27 0.00 0.00 3.09
453 506 5.290493 AGCATGAATTCCAGGTCGTATTA 57.710 39.130 2.27 0.00 0.00 0.98
454 507 4.130118 GAGCATGAATTCCAGGTCGTATT 58.870 43.478 2.27 0.00 0.00 1.89
455 508 3.495100 GGAGCATGAATTCCAGGTCGTAT 60.495 47.826 15.70 0.00 33.55 3.06
456 509 2.158957 GGAGCATGAATTCCAGGTCGTA 60.159 50.000 15.70 0.00 33.55 3.43
458 511 1.303309 GGAGCATGAATTCCAGGTCG 58.697 55.000 15.70 0.00 33.55 4.79
459 512 1.685148 GGGAGCATGAATTCCAGGTC 58.315 55.000 14.53 14.53 35.09 3.85
460 513 0.259938 GGGGAGCATGAATTCCAGGT 59.740 55.000 2.27 0.59 35.09 4.00
461 514 0.259647 TGGGGAGCATGAATTCCAGG 59.740 55.000 2.27 0.00 35.09 4.45
462 515 1.341285 TGTGGGGAGCATGAATTCCAG 60.341 52.381 2.27 0.00 35.09 3.86
463 516 0.703488 TGTGGGGAGCATGAATTCCA 59.297 50.000 2.27 0.00 35.09 3.53
464 517 1.684983 CATGTGGGGAGCATGAATTCC 59.315 52.381 2.27 0.00 44.60 3.01
465 518 1.068127 GCATGTGGGGAGCATGAATTC 59.932 52.381 9.17 0.00 44.60 2.17
467 520 1.105167 CGCATGTGGGGAGCATGAAT 61.105 55.000 9.17 0.00 44.60 2.57
468 521 1.750018 CGCATGTGGGGAGCATGAA 60.750 57.895 9.17 0.00 44.60 2.57
469 522 2.124612 CGCATGTGGGGAGCATGA 60.125 61.111 9.17 0.00 44.60 3.07
485 3027 4.436998 GGAGCCAGTGGACGGACG 62.437 72.222 15.20 0.00 0.00 4.79
486 3028 2.997897 AGGAGCCAGTGGACGGAC 60.998 66.667 15.20 0.00 0.00 4.79
487 3029 2.680352 GAGGAGCCAGTGGACGGA 60.680 66.667 15.20 0.00 0.00 4.69
488 3030 3.775654 GGAGGAGCCAGTGGACGG 61.776 72.222 15.20 0.00 36.34 4.79
534 3076 4.632458 GATCTCGGCGTCTCGGGC 62.632 72.222 6.85 0.00 0.00 6.13
535 3077 2.899044 GAGATCTCGGCGTCTCGGG 61.899 68.421 7.04 0.00 32.40 5.14
536 3078 2.634777 GAGATCTCGGCGTCTCGG 59.365 66.667 7.04 0.00 32.40 4.63
537 3079 2.180862 TGGAGATCTCGGCGTCTCG 61.181 63.158 16.46 1.84 41.36 4.04
538 3080 1.357334 GTGGAGATCTCGGCGTCTC 59.643 63.158 16.46 15.32 40.06 3.36
539 3081 2.473760 CGTGGAGATCTCGGCGTCT 61.474 63.158 21.74 1.68 0.00 4.18
540 3082 2.024871 CGTGGAGATCTCGGCGTC 59.975 66.667 21.74 8.63 0.00 5.19
541 3083 2.750637 ACGTGGAGATCTCGGCGT 60.751 61.111 26.70 26.70 36.41 5.68
542 3084 2.024871 GACGTGGAGATCTCGGCG 59.975 66.667 25.71 25.71 34.98 6.46
543 3085 2.024871 CGACGTGGAGATCTCGGC 59.975 66.667 16.46 7.35 0.00 5.54
544 3086 2.024871 GCGACGTGGAGATCTCGG 59.975 66.667 16.46 10.53 0.00 4.63
545 3087 2.024871 GGCGACGTGGAGATCTCG 59.975 66.667 16.46 8.62 0.00 4.04
640 3184 2.293677 CCAACCTCGTATAGTCGCATCT 59.706 50.000 0.00 0.00 0.00 2.90
644 3188 0.596859 GCCCAACCTCGTATAGTCGC 60.597 60.000 0.00 0.00 0.00 5.19
667 3239 4.154347 CTGGACTCGGGCTCCAGC 62.154 72.222 17.37 0.00 46.53 4.85
669 3241 2.680352 GACTGGACTCGGGCTCCA 60.680 66.667 6.46 6.46 36.34 3.86
700 3272 2.774439 GTTGAACAACGTGATGGCTT 57.226 45.000 1.96 0.00 0.00 4.35
760 3335 7.094248 GGCTTTATTAGTAGTAGGAGTAGGAGC 60.094 44.444 0.00 0.00 0.00 4.70
769 3344 6.478016 GGTTCAACGGCTTTATTAGTAGTAGG 59.522 42.308 0.00 0.00 0.00 3.18
770 3345 7.009907 GTGGTTCAACGGCTTTATTAGTAGTAG 59.990 40.741 0.00 0.00 0.00 2.57
771 3346 6.813152 GTGGTTCAACGGCTTTATTAGTAGTA 59.187 38.462 0.00 0.00 0.00 1.82
772 3347 5.640783 GTGGTTCAACGGCTTTATTAGTAGT 59.359 40.000 0.00 0.00 0.00 2.73
773 3348 5.064325 GGTGGTTCAACGGCTTTATTAGTAG 59.936 44.000 0.00 0.00 0.00 2.57
794 3369 2.187946 GGGATCGAGCTGGTGGTG 59.812 66.667 0.00 0.00 0.00 4.17
824 3399 0.392327 GAAGAGGAAGGAGGCTGCAC 60.392 60.000 9.23 1.51 0.00 4.57
848 3423 2.117156 GGCTGCGATGGATTGTGCT 61.117 57.895 0.00 0.00 0.00 4.40
870 3445 4.168291 GCTTCAGCGGAGGAGGGG 62.168 72.222 0.00 0.00 0.00 4.79
889 3464 1.152819 CTCGTCGGGGGAGGTATGA 60.153 63.158 0.00 0.00 0.00 2.15
890 3465 2.857744 GCTCGTCGGGGGAGGTATG 61.858 68.421 0.00 0.00 32.10 2.39
891 3466 2.521224 GCTCGTCGGGGGAGGTAT 60.521 66.667 0.00 0.00 32.10 2.73
892 3467 3.711059 GAGCTCGTCGGGGGAGGTA 62.711 68.421 0.00 0.00 41.91 3.08
953 3554 4.388499 TTCAGACCCCGCGAAGGC 62.388 66.667 8.23 0.00 39.21 4.35
954 3555 2.434359 GTTCAGACCCCGCGAAGG 60.434 66.667 8.23 11.17 40.63 3.46
955 3556 1.004918 AAGTTCAGACCCCGCGAAG 60.005 57.895 8.23 0.00 0.00 3.79
956 3557 1.005394 GAAGTTCAGACCCCGCGAA 60.005 57.895 8.23 0.00 0.00 4.70
957 3558 2.204461 TGAAGTTCAGACCCCGCGA 61.204 57.895 8.23 0.00 0.00 5.87
958 3559 2.027625 GTGAAGTTCAGACCCCGCG 61.028 63.158 5.62 0.00 0.00 6.46
959 3560 2.027625 CGTGAAGTTCAGACCCCGC 61.028 63.158 5.62 0.00 0.00 6.13
960 3561 0.599558 TACGTGAAGTTCAGACCCCG 59.400 55.000 5.62 8.48 0.00 5.73
961 3562 1.668047 CGTACGTGAAGTTCAGACCCC 60.668 57.143 5.62 0.00 0.00 4.95
962 3563 1.267806 TCGTACGTGAAGTTCAGACCC 59.732 52.381 16.05 0.00 0.00 4.46
975 3585 4.203076 GGCGCAGGGATCGTACGT 62.203 66.667 16.05 2.33 0.00 3.57
989 3599 0.390860 CCTCTCCATCCTTGTAGGCG 59.609 60.000 0.00 0.00 34.61 5.52
1064 3680 4.400961 GCGGCTTCTGCTCCACCT 62.401 66.667 0.00 0.00 39.59 4.00
1290 3924 2.888998 GACGTTGTTGTGGGCGTCC 61.889 63.158 0.00 0.00 45.24 4.79
1449 4086 6.655425 AGCCAAAAAGTAGTCCTCTGTTAATC 59.345 38.462 0.00 0.00 0.00 1.75
1554 4211 8.770828 CGGAGTAGTTTCTTTCTTTATTCAACA 58.229 33.333 0.00 0.00 0.00 3.33
1561 4218 4.682860 CACGCGGAGTAGTTTCTTTCTTTA 59.317 41.667 12.47 0.00 0.00 1.85
1562 4219 3.493503 CACGCGGAGTAGTTTCTTTCTTT 59.506 43.478 12.47 0.00 0.00 2.52
1588 4245 8.483307 AGCTTGCAAAATGGTCTTTTATTATG 57.517 30.769 0.00 0.00 0.00 1.90
1595 4252 5.473066 ACATAGCTTGCAAAATGGTCTTT 57.527 34.783 16.24 0.00 0.00 2.52
1630 4287 1.669760 TCAACGGATGCGGTGTTCC 60.670 57.895 24.35 0.00 0.00 3.62
1632 4289 1.227704 TGTCAACGGATGCGGTGTT 60.228 52.632 24.35 0.00 0.00 3.32
1653 4310 2.672996 CCCGCAAACCTGTCCCTG 60.673 66.667 0.00 0.00 0.00 4.45
1660 4317 4.344865 ATCCGTGCCCGCAAACCT 62.345 61.111 0.00 0.00 0.00 3.50
1661 4318 4.114997 CATCCGTGCCCGCAAACC 62.115 66.667 0.00 0.00 0.00 3.27
1662 4319 1.977594 CTACATCCGTGCCCGCAAAC 61.978 60.000 0.00 0.00 0.00 2.93
1663 4320 1.743623 CTACATCCGTGCCCGCAAA 60.744 57.895 0.00 0.00 0.00 3.68
1666 4323 3.792053 CTCCTACATCCGTGCCCGC 62.792 68.421 0.00 0.00 0.00 6.13
1670 4328 2.279517 CGGCTCCTACATCCGTGC 60.280 66.667 0.00 0.00 38.47 5.34
1680 4338 3.801997 CTTGGATGGCCGGCTCCT 61.802 66.667 29.08 14.77 36.79 3.69
1697 4355 2.160205 GCCCAAGAAAGGTGGTTAGTC 58.840 52.381 0.00 0.00 34.01 2.59
1702 4360 2.081585 GAGGGCCCAAGAAAGGTGGT 62.082 60.000 27.56 0.00 34.01 4.16
1705 4363 1.466186 AGGAGGGCCCAAGAAAGGT 60.466 57.895 27.56 0.00 37.41 3.50
1706 4364 1.210885 AGAGGAGGGCCCAAGAAAGG 61.211 60.000 27.56 0.00 37.41 3.11
1707 4365 0.034670 CAGAGGAGGGCCCAAGAAAG 60.035 60.000 27.56 5.62 37.41 2.62
1708 4366 1.500783 CCAGAGGAGGGCCCAAGAAA 61.501 60.000 27.56 0.00 37.41 2.52
1709 4367 1.925455 CCAGAGGAGGGCCCAAGAA 60.925 63.158 27.56 0.00 37.41 2.52
1710 4368 2.285668 CCAGAGGAGGGCCCAAGA 60.286 66.667 27.56 0.00 37.41 3.02
1711 4369 4.120755 GCCAGAGGAGGGCCCAAG 62.121 72.222 27.56 6.35 45.87 3.61
2275 4958 4.907809 TCGGATACAGATCGGAGTAGATT 58.092 43.478 0.00 0.00 36.72 2.40
2295 4978 4.856801 CCACCAAGGGCCGGATCG 62.857 72.222 5.05 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.