Multiple sequence alignment - TraesCS7B01G277800

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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 TraesCS7B01G277800 chr7B 100.000 3501 0 0 1 3501 508196901 508193401 0.000000e+00 6466.0
1 TraesCS7B01G277800 chr7D 92.010 3592 155 61 1 3501 482135626 482132076 0.000000e+00 4922.0
2 TraesCS7B01G277800 chr7D 90.323 62 6 0 1282 1343 93949361 93949300 8.050000e-12 82.4
3 TraesCS7B01G277800 chr7D 90.323 62 6 0 1282 1343 94005574 94005635 8.050000e-12 82.4
4 TraesCS7B01G277800 chr7A 90.534 3148 128 65 117 3171 549359266 549356196 0.000000e+00 4006.0
5 TraesCS7B01G277800 chr7A 94.099 322 13 3 3179 3495 549356109 549355789 5.250000e-133 484.0
6 TraesCS7B01G277800 chr6D 81.316 380 52 14 1558 1936 153865439 153865078 1.230000e-74 291.0
7 TraesCS7B01G277800 chr6D 88.000 100 11 1 1248 1347 153865661 153865563 2.210000e-22 117.0
8 TraesCS7B01G277800 chr6D 87.356 87 10 1 2026 2111 153865014 153864928 8.000000e-17 99.0
9 TraesCS7B01G277800 chr6B 81.316 380 52 14 1558 1936 277624375 277624014 1.230000e-74 291.0
10 TraesCS7B01G277800 chr6B 88.298 94 10 1 1254 1347 277624590 277624498 1.030000e-20 111.0
11 TraesCS7B01G277800 chr6B 91.803 61 5 0 1282 1342 668029995 668029935 6.230000e-13 86.1
12 TraesCS7B01G277800 chr6A 80.637 377 54 14 1561 1936 206352287 206351929 1.240000e-69 274.0
13 TraesCS7B01G277800 chr6A 88.000 100 11 1 1248 1347 206352511 206352413 2.210000e-22 117.0
14 TraesCS7B01G277800 chr6A 87.356 87 10 1 2026 2111 206351865 206351779 8.000000e-17 99.0
15 TraesCS7B01G277800 chr6A 91.803 61 5 0 1282 1342 591381175 591381115 6.230000e-13 86.1


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 TraesCS7B01G277800 chr7B 508193401 508196901 3500 True 6466 6466 100.0000 1 3501 1 chr7B.!!$R1 3500
1 TraesCS7B01G277800 chr7D 482132076 482135626 3550 True 4922 4922 92.0100 1 3501 1 chr7D.!!$R2 3500
2 TraesCS7B01G277800 chr7A 549355789 549359266 3477 True 2245 4006 92.3165 117 3495 2 chr7A.!!$R1 3378
3 TraesCS7B01G277800 chr6B 277624014 277624590 576 True 201 291 84.8070 1254 1936 2 chr6B.!!$R2 682

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
483 494 0.106967 GCTCCAACCTCCCTCCAATC 60.107 60.0 0.0 0.0 0.0 2.67 F
1402 1502 0.106335 TCTACTCCTACTCTCCGGCG 59.894 60.0 0.0 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1683 0.179032 TTCCTGCGAACCACACACAT 60.179 50.000 0.0 0.0 0.0 3.21 R
3050 3233 1.002773 GGGTTACACACGGGAACATCT 59.997 52.381 0.0 0.0 0.0 2.90 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
26 27 8.674607 CACACAAGGAATTTATAAGAGTAACCC 58.325 37.037 0.00 0.00 0.00 4.11
60 61 3.580895 TGACAACCAGCTGGAGTATGTAA 59.419 43.478 39.19 24.52 38.94 2.41
94 95 2.355108 GCAGGGAGCAACAAGAGTGATA 60.355 50.000 0.00 0.00 44.79 2.15
109 110 5.186198 AGAGTGATATCGAAAACCAAAGGG 58.814 41.667 0.00 0.00 41.29 3.95
296 303 1.525077 GGCCACAGTTCACCGACAA 60.525 57.895 0.00 0.00 0.00 3.18
316 323 3.118454 CACCCCAGCAGCGTAACG 61.118 66.667 0.00 0.00 0.00 3.18
342 350 1.230314 CCCTCTTCCCTTCCCCCTT 60.230 63.158 0.00 0.00 0.00 3.95
343 351 0.851332 CCCTCTTCCCTTCCCCCTTT 60.851 60.000 0.00 0.00 0.00 3.11
368 378 2.163815 CTCGCCGGAGAGACTTTTCTTA 59.836 50.000 29.23 0.00 43.27 2.10
369 379 2.094854 TCGCCGGAGAGACTTTTCTTAC 60.095 50.000 5.05 0.00 29.47 2.34
370 380 2.094649 CGCCGGAGAGACTTTTCTTACT 60.095 50.000 5.05 0.00 29.47 2.24
371 381 3.513662 GCCGGAGAGACTTTTCTTACTC 58.486 50.000 5.05 0.00 29.47 2.59
372 382 3.193903 GCCGGAGAGACTTTTCTTACTCT 59.806 47.826 5.05 0.00 41.52 3.24
481 492 2.231380 GGCTCCAACCTCCCTCCAA 61.231 63.158 0.00 0.00 0.00 3.53
482 493 1.575447 GGCTCCAACCTCCCTCCAAT 61.575 60.000 0.00 0.00 0.00 3.16
483 494 0.106967 GCTCCAACCTCCCTCCAATC 60.107 60.000 0.00 0.00 0.00 2.67
484 495 1.589414 CTCCAACCTCCCTCCAATCT 58.411 55.000 0.00 0.00 0.00 2.40
485 496 1.488393 CTCCAACCTCCCTCCAATCTC 59.512 57.143 0.00 0.00 0.00 2.75
488 499 3.115390 CCAACCTCCCTCCAATCTCTAA 58.885 50.000 0.00 0.00 0.00 2.10
490 501 4.018415 CCAACCTCCCTCCAATCTCTAAAA 60.018 45.833 0.00 0.00 0.00 1.52
492 503 5.379706 ACCTCCCTCCAATCTCTAAAATG 57.620 43.478 0.00 0.00 0.00 2.32
495 506 5.131809 CCTCCCTCCAATCTCTAAAATGACT 59.868 44.000 0.00 0.00 0.00 3.41
496 507 6.353429 CCTCCCTCCAATCTCTAAAATGACTT 60.353 42.308 0.00 0.00 0.00 3.01
497 508 7.147479 CCTCCCTCCAATCTCTAAAATGACTTA 60.147 40.741 0.00 0.00 0.00 2.24
498 509 7.565680 TCCCTCCAATCTCTAAAATGACTTAC 58.434 38.462 0.00 0.00 0.00 2.34
499 510 7.182026 TCCCTCCAATCTCTAAAATGACTTACA 59.818 37.037 0.00 0.00 0.00 2.41
500 511 7.497249 CCCTCCAATCTCTAAAATGACTTACAG 59.503 40.741 0.00 0.00 0.00 2.74
501 512 8.043710 CCTCCAATCTCTAAAATGACTTACAGT 58.956 37.037 0.00 0.00 0.00 3.55
504 515 9.877178 CCAATCTCTAAAATGACTTACAGTAGT 57.123 33.333 0.00 0.00 0.00 2.73
508 519 8.684520 TCTCTAAAATGACTTACAGTAGTAGGC 58.315 37.037 0.00 0.00 30.96 3.93
554 565 5.071250 CCCTTTAGGCACCACTACATATGTA 59.929 44.000 14.75 14.75 0.00 2.29
555 566 6.239887 CCCTTTAGGCACCACTACATATGTAT 60.240 42.308 15.81 4.33 0.00 2.29
557 568 7.387948 CCTTTAGGCACCACTACATATGTATTC 59.612 40.741 15.81 0.00 0.00 1.75
558 569 5.887214 AGGCACCACTACATATGTATTCA 57.113 39.130 15.81 0.00 0.00 2.57
559 570 5.858381 AGGCACCACTACATATGTATTCAG 58.142 41.667 15.81 8.74 0.00 3.02
560 571 5.602561 AGGCACCACTACATATGTATTCAGA 59.397 40.000 15.81 0.00 0.00 3.27
562 573 7.454694 AGGCACCACTACATATGTATTCAGATA 59.545 37.037 15.81 0.00 0.00 1.98
563 574 7.545965 GGCACCACTACATATGTATTCAGATAC 59.454 40.741 15.81 2.98 38.88 2.24
603 631 2.472029 ACTTCCATAGGGAGTGGTGAG 58.528 52.381 0.00 0.00 46.01 3.51
612 640 1.143073 GGGAGTGGTGAGTTTCAACCT 59.857 52.381 0.00 0.00 31.76 3.50
614 642 2.158813 GGAGTGGTGAGTTTCAACCTGA 60.159 50.000 0.00 0.00 31.76 3.86
615 643 3.541632 GAGTGGTGAGTTTCAACCTGAA 58.458 45.455 0.00 0.00 31.76 3.02
616 644 3.945285 GAGTGGTGAGTTTCAACCTGAAA 59.055 43.478 0.00 0.00 43.37 2.69
649 696 5.152934 ACTCCTGGAAGTAACTTTGTCCTA 58.847 41.667 0.00 0.00 0.00 2.94
651 698 4.020485 TCCTGGAAGTAACTTTGTCCTAGC 60.020 45.833 0.00 0.00 0.00 3.42
656 703 5.408909 GGAAGTAACTTTGTCCTAGCAAGAC 59.591 44.000 0.00 0.00 34.72 3.01
659 706 3.305398 ACTTTGTCCTAGCAAGACGAG 57.695 47.619 0.00 0.00 37.04 4.18
757 809 1.409427 AGTACTCCAATGTCCTAGCGC 59.591 52.381 0.00 0.00 0.00 5.92
784 836 2.800544 CAGTACAAGTGAACAAGGACGG 59.199 50.000 0.00 0.00 0.00 4.79
823 876 2.093152 CCAACCGTTAACAGATACGTGC 59.907 50.000 6.39 0.00 36.09 5.34
838 891 3.136791 TGCAACGCAAGGCACACA 61.137 55.556 0.00 0.00 46.39 3.72
858 911 4.034048 CACACACTCACACTTGAAGTTACC 59.966 45.833 0.00 0.00 0.00 2.85
896 949 5.339530 CCCAAATCCATTCTTCACTACTCCT 60.340 44.000 0.00 0.00 0.00 3.69
923 976 0.182537 CCCCCTCTTTCACACACACA 59.817 55.000 0.00 0.00 0.00 3.72
925 978 0.937304 CCCTCTTTCACACACACACG 59.063 55.000 0.00 0.00 0.00 4.49
927 980 0.304705 CTCTTTCACACACACACGCC 59.695 55.000 0.00 0.00 0.00 5.68
928 981 1.092921 TCTTTCACACACACACGCCC 61.093 55.000 0.00 0.00 0.00 6.13
929 982 1.372838 CTTTCACACACACACGCCCA 61.373 55.000 0.00 0.00 0.00 5.36
930 983 1.649390 TTTCACACACACACGCCCAC 61.649 55.000 0.00 0.00 0.00 4.61
931 984 3.582120 CACACACACACGCCCACC 61.582 66.667 0.00 0.00 0.00 4.61
932 985 4.868116 ACACACACACGCCCACCC 62.868 66.667 0.00 0.00 0.00 4.61
939 992 2.515991 CACGCCCACCCGCAATAT 60.516 61.111 0.00 0.00 0.00 1.28
949 1002 1.608590 ACCCGCAATATGCAATGTAGC 59.391 47.619 2.99 0.00 45.36 3.58
954 1007 3.120199 CGCAATATGCAATGTAGCCCTAC 60.120 47.826 2.99 0.00 45.36 3.18
959 1012 3.380479 TGCAATGTAGCCCTACGTATC 57.620 47.619 0.00 0.00 38.85 2.24
960 1013 2.696187 TGCAATGTAGCCCTACGTATCA 59.304 45.455 0.00 0.69 38.85 2.15
961 1014 3.323691 TGCAATGTAGCCCTACGTATCAT 59.676 43.478 0.00 0.00 38.85 2.45
962 1015 3.679980 GCAATGTAGCCCTACGTATCATG 59.320 47.826 0.00 0.00 38.85 3.07
963 1016 4.799586 GCAATGTAGCCCTACGTATCATGT 60.800 45.833 0.00 0.00 38.85 3.21
964 1017 5.566032 GCAATGTAGCCCTACGTATCATGTA 60.566 44.000 0.00 0.00 38.85 2.29
965 1018 6.631016 CAATGTAGCCCTACGTATCATGTAT 58.369 40.000 0.00 0.00 38.85 2.29
966 1019 5.638596 TGTAGCCCTACGTATCATGTATG 57.361 43.478 0.00 0.00 38.85 2.39
967 1020 5.074804 TGTAGCCCTACGTATCATGTATGT 58.925 41.667 0.00 0.00 38.85 2.29
968 1021 6.240145 TGTAGCCCTACGTATCATGTATGTA 58.760 40.000 0.00 0.60 38.85 2.29
969 1022 6.888088 TGTAGCCCTACGTATCATGTATGTAT 59.112 38.462 0.00 0.00 38.85 2.29
970 1023 8.048514 TGTAGCCCTACGTATCATGTATGTATA 58.951 37.037 0.00 0.00 38.85 1.47
971 1024 9.064706 GTAGCCCTACGTATCATGTATGTATAT 57.935 37.037 0.00 0.00 0.00 0.86
973 1026 9.809395 AGCCCTACGTATCATGTATGTATATAT 57.191 33.333 0.00 0.00 0.00 0.86
974 1027 9.841880 GCCCTACGTATCATGTATGTATATATG 57.158 37.037 0.00 3.13 34.40 1.78
975 1028 9.841880 CCCTACGTATCATGTATGTATATATGC 57.158 37.037 0.00 0.00 33.50 3.14
1198 1266 0.627451 TGCCTGCTGATCATTCCCTT 59.373 50.000 0.00 0.00 0.00 3.95
1246 1333 1.761784 AGAATCTCCGCTCTGCATTCT 59.238 47.619 0.00 0.00 0.00 2.40
1325 1415 1.045911 GCTCCTGGGTCTCCGAGATT 61.046 60.000 0.33 0.00 35.24 2.40
1350 1440 1.118838 CCCTCTCCTGTAAGCCTCAG 58.881 60.000 0.00 0.00 0.00 3.35
1352 1442 1.480137 CCTCTCCTGTAAGCCTCAGTG 59.520 57.143 0.00 0.00 0.00 3.66
1354 1444 0.107945 CTCCTGTAAGCCTCAGTGCC 60.108 60.000 0.00 0.00 0.00 5.01
1355 1445 0.545309 TCCTGTAAGCCTCAGTGCCT 60.545 55.000 0.00 0.00 0.00 4.75
1357 1447 0.610174 CTGTAAGCCTCAGTGCCTCA 59.390 55.000 0.00 0.00 0.00 3.86
1375 1475 1.214175 TCACCCCTAGCTCTCTCTCAG 59.786 57.143 0.00 0.00 0.00 3.35
1396 1496 4.081322 GTAGCTGCTCTACTCCTACTCT 57.919 50.000 4.91 0.00 43.37 3.24
1397 1497 3.208747 AGCTGCTCTACTCCTACTCTC 57.791 52.381 0.00 0.00 0.00 3.20
1398 1498 2.158667 AGCTGCTCTACTCCTACTCTCC 60.159 54.545 0.00 0.00 0.00 3.71
1399 1499 2.489971 CTGCTCTACTCCTACTCTCCG 58.510 57.143 0.00 0.00 0.00 4.63
1400 1500 1.141254 TGCTCTACTCCTACTCTCCGG 59.859 57.143 0.00 0.00 0.00 5.14
1401 1501 1.886886 CTCTACTCCTACTCTCCGGC 58.113 60.000 0.00 0.00 0.00 6.13
1402 1502 0.106335 TCTACTCCTACTCTCCGGCG 59.894 60.000 0.00 0.00 0.00 6.46
1403 1503 0.885596 CTACTCCTACTCTCCGGCGG 60.886 65.000 22.51 22.51 0.00 6.13
1431 1531 2.139323 ACTCGTGTAGCTATCCCACA 57.861 50.000 12.05 0.00 0.00 4.17
1461 1561 9.022884 TCCTGAGAGATAGATACATTGATTCTG 57.977 37.037 0.00 0.00 0.00 3.02
1513 1660 5.389935 GCTTTCGTCGATTTTCTCTTGATGT 60.390 40.000 0.00 0.00 0.00 3.06
1514 1661 5.515548 TTCGTCGATTTTCTCTTGATGTG 57.484 39.130 0.00 0.00 0.00 3.21
1534 1681 2.830321 TGGTTCCAAATGCATGCATGTA 59.170 40.909 32.79 23.60 36.68 2.29
1536 1683 4.648307 TGGTTCCAAATGCATGCATGTATA 59.352 37.500 32.79 16.09 36.68 1.47
1548 1696 5.513376 CATGCATGTATATGTGTGTGGTTC 58.487 41.667 18.91 0.00 36.65 3.62
1619 1767 3.900892 CGGGCGTATGACGAGGCT 61.901 66.667 2.65 0.00 46.05 4.58
1661 1809 1.228124 CGCCAAGACCAACTTCCCA 60.228 57.895 0.00 0.00 36.61 4.37
1802 1953 2.111878 AAGCTCCGCAAGTGCTGT 59.888 55.556 1.21 0.00 42.83 4.40
1811 1962 1.593196 GCAAGTGCTGTAAGACACCA 58.407 50.000 0.00 0.00 40.34 4.17
1838 1989 2.759973 CTCACCTGCCTCCGCCTA 60.760 66.667 0.00 0.00 0.00 3.93
2227 2385 3.121406 TAGGGTGGTTGGCGCACAA 62.121 57.895 10.83 8.61 36.54 3.33
2241 2399 2.726066 GCGCACAAGCAGTTAAGATCAC 60.726 50.000 0.30 0.00 42.27 3.06
2275 2437 0.105778 GGTACCAGCTGAGCATCTCC 59.894 60.000 17.39 3.94 34.92 3.71
2331 2494 7.487829 GGAAACGATTAATTACTACCGTGTGTA 59.512 37.037 0.00 0.00 0.00 2.90
2332 2495 7.740519 AACGATTAATTACTACCGTGTGTAC 57.259 36.000 0.00 0.00 0.00 2.90
2528 2700 7.094549 GGAATAAACACCTTGTAATGCAGTACA 60.095 37.037 22.18 22.18 32.11 2.90
2587 2759 2.413310 AGTGTTGTTTTCAGTCGGGT 57.587 45.000 0.00 0.00 0.00 5.28
2601 2773 1.395954 GTCGGGTGAATTTAAGCGTCC 59.604 52.381 0.00 0.00 0.00 4.79
2623 2795 6.484977 GTCCCTCTTCATCAAAAGGATATCAC 59.515 42.308 4.83 0.00 33.95 3.06
2636 2808 6.918067 AAGGATATCACGAATATGGTGAGA 57.082 37.500 13.40 10.25 46.55 3.27
2741 2916 6.983474 AAGAACAAGGTTCCAAAAATTGTG 57.017 33.333 5.54 0.00 34.50 3.33
2742 2917 6.048732 AGAACAAGGTTCCAAAAATTGTGT 57.951 33.333 5.54 0.00 34.50 3.72
2746 2921 7.118496 ACAAGGTTCCAAAAATTGTGTATGA 57.882 32.000 0.00 0.00 33.09 2.15
2836 3019 5.530712 GGAAGGAGTAATCACCGAAGATAC 58.469 45.833 0.00 0.00 0.00 2.24
2852 3035 1.339610 GATACGAGAGAGCATGCACCT 59.660 52.381 21.98 16.27 0.00 4.00
2884 3067 5.069648 TCCTGTACATCATCTCAACTCCATC 59.930 44.000 0.00 0.00 0.00 3.51
3050 3233 4.033009 TGAGACTCTCCATGCAATTCCTA 58.967 43.478 3.68 0.00 0.00 2.94
3179 3371 2.729360 CGAACTCAAATACGTCAGTGCA 59.271 45.455 0.00 0.00 0.00 4.57
3189 3461 8.172484 TCAAATACGTCAGTGCATTAACATTAC 58.828 33.333 0.00 0.00 0.00 1.89
3227 3499 9.327529 GCATCGAATTTGAAAGAATATCAGATC 57.672 33.333 0.00 0.00 0.00 2.75
3238 3510 7.959689 AAGAATATCAGATCCACATTTCTCG 57.040 36.000 0.00 0.00 0.00 4.04
3306 3578 8.998277 ACCATGTTAGACTATGACTAGTACAT 57.002 34.615 0.00 4.29 38.33 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 7.514721 TGTCATTTGTTTCTAAGGGTTACTCT 58.485 34.615 0.00 0.00 0.00 3.24
25 26 5.010012 AGCTGGTTGTCATTTGTTTCTAAGG 59.990 40.000 0.00 0.00 0.00 2.69
26 27 5.916883 CAGCTGGTTGTCATTTGTTTCTAAG 59.083 40.000 5.57 0.00 0.00 2.18
60 61 2.591072 CCCTGCTCAGTGCCACTCT 61.591 63.158 0.00 0.00 42.00 3.24
94 95 4.021229 GGTAATCCCCTTTGGTTTTCGAT 58.979 43.478 0.00 0.00 34.77 3.59
109 110 3.498661 CCCCCAGCTCTTATTGGTAATCC 60.499 52.174 0.00 0.00 32.40 3.01
368 378 5.779771 AGACAAAGATCAAAGGAGAGAGAGT 59.220 40.000 0.00 0.00 0.00 3.24
369 379 6.284891 AGACAAAGATCAAAGGAGAGAGAG 57.715 41.667 0.00 0.00 0.00 3.20
370 380 6.678568 AAGACAAAGATCAAAGGAGAGAGA 57.321 37.500 0.00 0.00 0.00 3.10
371 381 6.371271 GGAAAGACAAAGATCAAAGGAGAGAG 59.629 42.308 0.00 0.00 0.00 3.20
372 382 6.234177 GGAAAGACAAAGATCAAAGGAGAGA 58.766 40.000 0.00 0.00 0.00 3.10
415 426 4.506838 CGTGTAGCAAGTGATAAAGCTC 57.493 45.455 0.00 0.00 38.47 4.09
488 499 7.148239 GCAATTGCCTACTACTGTAAGTCATTT 60.148 37.037 20.06 0.00 40.55 2.32
490 501 5.817816 GCAATTGCCTACTACTGTAAGTCAT 59.182 40.000 20.06 0.00 40.55 3.06
492 503 5.420409 AGCAATTGCCTACTACTGTAAGTC 58.580 41.667 26.45 0.00 43.90 3.01
495 506 5.128827 AGCTAGCAATTGCCTACTACTGTAA 59.871 40.000 26.45 0.00 43.38 2.41
496 507 4.649674 AGCTAGCAATTGCCTACTACTGTA 59.350 41.667 26.45 8.29 43.38 2.74
497 508 3.452627 AGCTAGCAATTGCCTACTACTGT 59.547 43.478 26.45 7.51 43.38 3.55
498 509 3.806521 CAGCTAGCAATTGCCTACTACTG 59.193 47.826 26.45 19.45 43.38 2.74
499 510 3.706594 TCAGCTAGCAATTGCCTACTACT 59.293 43.478 26.45 12.62 43.38 2.57
500 511 4.060038 TCAGCTAGCAATTGCCTACTAC 57.940 45.455 26.45 10.59 43.38 2.73
501 512 4.753516 TTCAGCTAGCAATTGCCTACTA 57.246 40.909 26.45 11.49 43.38 1.82
503 514 4.604976 CAATTCAGCTAGCAATTGCCTAC 58.395 43.478 26.45 15.50 43.38 3.18
504 515 4.906065 CAATTCAGCTAGCAATTGCCTA 57.094 40.909 26.45 16.12 43.38 3.93
505 516 3.795623 CAATTCAGCTAGCAATTGCCT 57.204 42.857 26.45 13.95 43.38 4.75
508 519 3.444916 CAGGCAATTCAGCTAGCAATTG 58.555 45.455 25.36 25.36 41.20 2.32
554 565 9.190317 TGACATTAGTGACTACTGTATCTGAAT 57.810 33.333 14.45 0.00 37.78 2.57
555 566 8.459635 GTGACATTAGTGACTACTGTATCTGAA 58.540 37.037 14.45 0.00 37.78 3.02
557 568 7.762382 TGTGACATTAGTGACTACTGTATCTG 58.238 38.462 14.45 0.00 37.78 2.90
558 569 7.939784 TGTGACATTAGTGACTACTGTATCT 57.060 36.000 14.45 0.00 37.78 1.98
559 570 8.244802 AGTTGTGACATTAGTGACTACTGTATC 58.755 37.037 14.45 11.13 43.45 2.24
560 571 8.123639 AGTTGTGACATTAGTGACTACTGTAT 57.876 34.615 14.45 0.00 43.45 2.29
562 573 6.406692 AGTTGTGACATTAGTGACTACTGT 57.593 37.500 14.38 14.38 43.45 3.55
563 574 6.366332 GGAAGTTGTGACATTAGTGACTACTG 59.634 42.308 8.24 8.24 44.04 2.74
612 640 6.099269 ACTTCCAGGAGTACAACTTAGTTTCA 59.901 38.462 0.00 0.00 0.00 2.69
614 642 6.496144 ACTTCCAGGAGTACAACTTAGTTT 57.504 37.500 0.00 0.00 0.00 2.66
615 643 7.289549 AGTTACTTCCAGGAGTACAACTTAGTT 59.710 37.037 0.00 0.00 28.78 2.24
616 644 6.781507 AGTTACTTCCAGGAGTACAACTTAGT 59.218 38.462 0.00 0.00 28.78 2.24
617 645 7.229581 AGTTACTTCCAGGAGTACAACTTAG 57.770 40.000 0.00 0.00 28.78 2.18
618 646 7.607615 AAGTTACTTCCAGGAGTACAACTTA 57.392 36.000 14.39 0.00 36.99 2.24
620 648 6.126854 ACAAAGTTACTTCCAGGAGTACAACT 60.127 38.462 0.00 0.00 32.53 3.16
621 649 6.053650 ACAAAGTTACTTCCAGGAGTACAAC 58.946 40.000 0.00 0.00 32.12 3.32
622 650 6.243216 ACAAAGTTACTTCCAGGAGTACAA 57.757 37.500 0.00 0.00 32.12 2.41
623 651 5.221581 GGACAAAGTTACTTCCAGGAGTACA 60.222 44.000 0.00 0.00 32.12 2.90
624 652 5.011840 AGGACAAAGTTACTTCCAGGAGTAC 59.988 44.000 0.00 0.00 32.12 2.73
625 653 5.152934 AGGACAAAGTTACTTCCAGGAGTA 58.847 41.667 0.00 0.00 0.00 2.59
626 654 3.974642 AGGACAAAGTTACTTCCAGGAGT 59.025 43.478 0.00 0.00 0.00 3.85
649 696 0.039911 AGTCTACCCCTCGTCTTGCT 59.960 55.000 0.00 0.00 0.00 3.91
651 698 0.733729 CGAGTCTACCCCTCGTCTTG 59.266 60.000 1.87 0.00 45.09 3.02
659 706 3.066814 ACGCACCGAGTCTACCCC 61.067 66.667 0.00 0.00 0.00 4.95
757 809 4.449068 CCTTGTTCACTTGTACTGCTACTG 59.551 45.833 0.00 0.00 0.00 2.74
784 836 2.106332 GCTGCTTCCATGCATGCC 59.894 61.111 21.69 9.21 42.48 4.40
823 876 1.586042 GTGTGTGTGCCTTGCGTTG 60.586 57.895 0.00 0.00 0.00 4.10
838 891 3.454375 CGGTAACTTCAAGTGTGAGTGT 58.546 45.455 0.00 0.00 34.49 3.55
896 949 1.098589 TGAAAGAGGGGGAGAGGGTA 58.901 55.000 0.00 0.00 0.00 3.69
923 976 2.515991 CATATTGCGGGTGGGCGT 60.516 61.111 0.00 0.00 35.06 5.68
931 984 6.151287 GTAGGGCTACATTGCATATTGCGG 62.151 50.000 0.00 0.00 39.95 5.69
932 985 3.120199 GTAGGGCTACATTGCATATTGCG 60.120 47.826 0.00 0.00 39.95 4.85
933 986 3.120199 CGTAGGGCTACATTGCATATTGC 60.120 47.826 0.00 0.00 38.74 3.56
934 987 4.065088 ACGTAGGGCTACATTGCATATTG 58.935 43.478 0.00 0.00 35.87 1.90
935 988 4.351874 ACGTAGGGCTACATTGCATATT 57.648 40.909 0.00 0.00 35.87 1.28
939 992 2.696187 TGATACGTAGGGCTACATTGCA 59.304 45.455 0.08 0.00 35.87 4.08
949 1002 9.841880 GCATATATACATACATGATACGTAGGG 57.158 37.037 0.00 0.00 0.00 3.53
954 1007 8.420189 CGCTTGCATATATACATACATGATACG 58.580 37.037 0.00 0.00 0.00 3.06
959 1012 7.547119 CGTACGCTTGCATATATACATACATG 58.453 38.462 0.52 0.00 0.00 3.21
960 1013 6.198403 GCGTACGCTTGCATATATACATACAT 59.802 38.462 31.95 0.00 38.26 2.29
961 1014 5.513849 GCGTACGCTTGCATATATACATACA 59.486 40.000 31.95 0.00 38.26 2.29
962 1015 5.330571 CGCGTACGCTTGCATATATACATAC 60.331 44.000 34.69 2.89 39.32 2.39
963 1016 4.731480 CGCGTACGCTTGCATATATACATA 59.269 41.667 34.69 0.00 39.32 2.29
964 1017 3.546271 CGCGTACGCTTGCATATATACAT 59.454 43.478 34.69 0.00 39.32 2.29
965 1018 2.912345 CGCGTACGCTTGCATATATACA 59.088 45.455 34.69 0.00 39.32 2.29
966 1019 2.912967 ACGCGTACGCTTGCATATATAC 59.087 45.455 34.69 4.72 45.53 1.47
967 1020 3.206034 ACGCGTACGCTTGCATATATA 57.794 42.857 34.69 0.00 45.53 0.86
968 1021 2.060326 ACGCGTACGCTTGCATATAT 57.940 45.000 34.69 8.54 45.53 0.86
969 1022 2.684754 TACGCGTACGCTTGCATATA 57.315 45.000 34.69 9.56 45.53 0.86
970 1023 2.060326 ATACGCGTACGCTTGCATAT 57.940 45.000 34.69 20.79 45.53 1.78
971 1024 2.309693 GTATACGCGTACGCTTGCATA 58.690 47.619 34.69 22.24 45.53 3.14
972 1025 1.126079 GTATACGCGTACGCTTGCAT 58.874 50.000 34.69 23.14 45.53 3.96
973 1026 1.195513 CGTATACGCGTACGCTTGCA 61.196 55.000 34.69 18.50 45.53 4.08
974 1027 1.475810 CGTATACGCGTACGCTTGC 59.524 57.895 34.69 21.61 45.53 4.01
1198 1266 3.239627 AAGAGGACGGGCAGAGGGA 62.240 63.158 0.00 0.00 0.00 4.20
1246 1333 3.557054 GGACTGTACCATGTTTCTCTGCA 60.557 47.826 0.00 0.00 0.00 4.41
1325 1415 1.965318 GCTTACAGGAGAGGGTGCCTA 60.965 57.143 0.00 0.00 31.76 3.93
1350 1440 1.681486 GAGAGCTAGGGGTGAGGCAC 61.681 65.000 0.00 0.00 0.00 5.01
1352 1442 1.075600 AGAGAGCTAGGGGTGAGGC 60.076 63.158 0.00 0.00 0.00 4.70
1354 1444 1.214175 TGAGAGAGAGCTAGGGGTGAG 59.786 57.143 0.00 0.00 0.00 3.51
1355 1445 1.214175 CTGAGAGAGAGCTAGGGGTGA 59.786 57.143 0.00 0.00 0.00 4.02
1357 1447 1.304891 ACTGAGAGAGAGCTAGGGGT 58.695 55.000 0.00 0.00 0.00 4.95
1401 1501 4.189188 CACGAGTAGGCCGGACCG 62.189 72.222 1.76 6.99 46.52 4.79
1402 1502 1.722636 CTACACGAGTAGGCCGGACC 61.723 65.000 1.76 4.96 43.24 4.46
1403 1503 1.726265 CTACACGAGTAGGCCGGAC 59.274 63.158 5.05 0.00 43.24 4.79
1431 1531 7.293828 TCAATGTATCTATCTCTCAGGACACT 58.706 38.462 0.00 0.00 0.00 3.55
1461 1561 7.019418 CCTTAAAGTACGTAGCAATTCAAACC 58.981 38.462 0.00 0.00 0.00 3.27
1513 1660 1.624312 ACATGCATGCATTTGGAACCA 59.376 42.857 30.32 0.00 33.90 3.67
1514 1661 2.389962 ACATGCATGCATTTGGAACC 57.610 45.000 30.32 0.00 33.90 3.62
1534 1681 1.277842 TCCTGCGAACCACACACATAT 59.722 47.619 0.00 0.00 0.00 1.78
1536 1683 0.179032 TTCCTGCGAACCACACACAT 60.179 50.000 0.00 0.00 0.00 3.21
1548 1696 2.286523 ACACCCTCCTCTTCCTGCG 61.287 63.158 0.00 0.00 0.00 5.18
1610 1758 2.685017 AGGATGGCAGCCTCGTCA 60.685 61.111 20.65 0.00 0.00 4.35
1619 1767 2.507452 CCGCTCATCAGGATGGCA 59.493 61.111 17.08 0.00 39.24 4.92
1661 1809 4.269523 TTGGCGCTCCTTGGCACT 62.270 61.111 7.64 0.00 42.04 4.40
1802 1953 0.979187 GGGACGGGGATGGTGTCTTA 60.979 60.000 0.00 0.00 33.21 2.10
1811 1962 2.365635 CAGGTGAGGGACGGGGAT 60.366 66.667 0.00 0.00 0.00 3.85
1838 1989 0.469331 TGTGGGACTTCTCGGTGTCT 60.469 55.000 0.00 0.00 34.01 3.41
2241 2399 1.067212 GGTACCTACGATGTGGAGCAG 59.933 57.143 4.06 0.00 0.00 4.24
2331 2494 1.300388 GGGCTTCACACACGTACGT 60.300 57.895 16.72 16.72 0.00 3.57
2332 2495 2.025418 GGGGCTTCACACACGTACG 61.025 63.158 15.01 15.01 0.00 3.67
2528 2700 9.260002 CTAACAAAGGAAATTAAATGCACAAGT 57.740 29.630 0.00 0.00 0.00 3.16
2601 2773 6.283694 TCGTGATATCCTTTTGATGAAGAGG 58.716 40.000 0.00 0.00 34.76 3.69
2623 2795 7.095102 TGTGCAAATATCATCTCACCATATTCG 60.095 37.037 0.00 0.00 0.00 3.34
2636 2808 7.546667 GTCAAACCAAGAATGTGCAAATATCAT 59.453 33.333 0.00 0.00 0.00 2.45
2671 2843 4.960938 AGAATGAACAGTGCTTACAGACA 58.039 39.130 0.00 0.00 0.00 3.41
2741 2916 6.805271 GCTTGCATTCATATGATGGTTCATAC 59.195 38.462 6.17 0.00 45.29 2.39
2742 2917 6.490721 TGCTTGCATTCATATGATGGTTCATA 59.509 34.615 6.17 0.00 46.25 2.15
2746 2921 4.403113 TGTGCTTGCATTCATATGATGGTT 59.597 37.500 6.17 0.00 33.37 3.67
2836 3019 1.588403 CGAGGTGCATGCTCTCTCG 60.588 63.158 28.82 28.82 40.68 4.04
2852 3035 5.185056 TGAGATGATGTACAGGAAAACTCGA 59.815 40.000 0.33 0.00 0.00 4.04
2884 3067 3.978687 ACTACGTTCTTTGAGGTCACTG 58.021 45.455 0.00 0.00 0.00 3.66
3050 3233 1.002773 GGGTTACACACGGGAACATCT 59.997 52.381 0.00 0.00 0.00 2.90
3179 3371 7.695480 TGCACTAACACATGGTAATGTTAAT 57.305 32.000 7.72 0.00 44.94 1.40
3189 3461 4.621068 AATTCGATGCACTAACACATGG 57.379 40.909 0.00 0.00 0.00 3.66
3227 3499 8.446599 ACCTATTTTAATACCGAGAAATGTGG 57.553 34.615 0.00 0.00 0.00 4.17
3238 3510 6.665695 TCCCAACTGGACCTATTTTAATACC 58.334 40.000 0.00 0.00 38.61 2.73
3306 3578 3.446161 GGTGCAGTAGTGTGTATGGTCTA 59.554 47.826 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.