Multiple sequence alignment - TraesCS7A01G226700

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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 TraesCS7A01G226700 chr7A 100.000 2776 0 0 1 2776 196141753 196144528 0.000000e+00 5127.0
1 TraesCS7A01G226700 chr7A 83.871 62 8 2 2610 2671 347377881 347377822 1.070000e-04 58.4
2 TraesCS7A01G226700 chr7D 90.798 2695 202 25 91 2776 187916378 187913721 0.000000e+00 3561.0
3 TraesCS7A01G226700 chr7B 89.446 2691 243 21 91 2776 331659060 331656406 0.000000e+00 3358.0
4 TraesCS7A01G226700 chr4D 95.455 88 4 0 1 88 10098956 10099043 1.040000e-29 141.0
5 TraesCS7A01G226700 chr4D 95.455 88 4 0 1 88 278595907 278595994 1.040000e-29 141.0
6 TraesCS7A01G226700 chr4D 94.444 90 5 0 1 90 134413294 134413383 3.730000e-29 139.0
7 TraesCS7A01G226700 chr6A 95.455 88 3 1 1 88 591023107 591023193 3.730000e-29 139.0
8 TraesCS7A01G226700 chr6D 94.382 89 5 0 1 89 143749911 143749999 1.340000e-28 137.0
9 TraesCS7A01G226700 chr6D 94.382 89 5 0 1 89 186755491 186755579 1.340000e-28 137.0
10 TraesCS7A01G226700 chr6D 94.382 89 5 0 1 89 235622372 235622284 1.340000e-28 137.0
11 TraesCS7A01G226700 chr6D 93.548 93 5 1 1 93 381619801 381619892 1.340000e-28 137.0
12 TraesCS7A01G226700 chr6D 86.275 51 7 0 2587 2637 297320085 297320135 3.860000e-04 56.5
13 TraesCS7A01G226700 chr5A 86.726 113 12 3 1 113 333634567 333634458 3.750000e-24 122.0
14 TraesCS7A01G226700 chr4B 100.000 28 0 0 2254 2281 340787533 340787560 5.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G226700 chr7A 196141753 196144528 2775 False 5127 5127 100.000 1 2776 1 chr7A.!!$F1 2775
1 TraesCS7A01G226700 chr7D 187913721 187916378 2657 True 3561 3561 90.798 91 2776 1 chr7D.!!$R1 2685
2 TraesCS7A01G226700 chr7B 331656406 331659060 2654 True 3358 3358 89.446 91 2776 1 chr7B.!!$R1 2685

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
408 409 0.116143 ACTGTTGGGAGGCTCTCTCT 59.884 55.000 16.74 0.0 42.1 3.10 F
411 412 1.229304 TTGGGAGGCTCTCTCTGCA 60.229 57.895 16.74 0.0 42.1 4.41 F
716 717 1.271856 TGAACCTTATGCCACTCCGA 58.728 50.000 0.00 0.0 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1288 1293 0.537188 TCCATCGAGAAGTCCTTGGC 59.463 55.000 0.0 0.0 0.0 4.52 R
1308 1313 1.463444 GTCGTGTTTGGTGATAGTGGC 59.537 52.381 0.0 0.0 0.0 5.01 R
1916 1922 2.159014 CCCATCCGTTTAGTCGATTCCA 60.159 50.000 0.0 0.0 0.0 3.53 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
23 24 6.726258 GCCAAGACATAAAATTGGGAAAAG 57.274 37.500 5.43 0.00 43.06 2.27
24 25 5.643348 GCCAAGACATAAAATTGGGAAAAGG 59.357 40.000 5.43 0.00 43.06 3.11
25 26 5.643348 CCAAGACATAAAATTGGGAAAAGGC 59.357 40.000 0.00 0.00 39.87 4.35
26 27 6.466812 CAAGACATAAAATTGGGAAAAGGCT 58.533 36.000 0.00 0.00 0.00 4.58
27 28 7.310361 CCAAGACATAAAATTGGGAAAAGGCTA 60.310 37.037 0.00 0.00 39.87 3.93
28 29 7.410120 AGACATAAAATTGGGAAAAGGCTAG 57.590 36.000 0.00 0.00 0.00 3.42
29 30 7.182060 AGACATAAAATTGGGAAAAGGCTAGA 58.818 34.615 0.00 0.00 0.00 2.43
30 31 7.841222 AGACATAAAATTGGGAAAAGGCTAGAT 59.159 33.333 0.00 0.00 0.00 1.98
31 32 8.379428 ACATAAAATTGGGAAAAGGCTAGATT 57.621 30.769 0.00 0.00 0.00 2.40
32 33 8.825774 ACATAAAATTGGGAAAAGGCTAGATTT 58.174 29.630 0.00 0.00 0.00 2.17
33 34 9.671279 CATAAAATTGGGAAAAGGCTAGATTTT 57.329 29.630 0.00 0.00 32.68 1.82
39 40 9.671279 ATTGGGAAAAGGCTAGATTTTTATTTG 57.329 29.630 0.00 0.00 30.22 2.32
40 41 7.619965 TGGGAAAAGGCTAGATTTTTATTTGG 58.380 34.615 0.00 0.00 30.22 3.28
41 42 7.236640 TGGGAAAAGGCTAGATTTTTATTTGGT 59.763 33.333 0.00 0.00 30.22 3.67
42 43 7.764443 GGGAAAAGGCTAGATTTTTATTTGGTC 59.236 37.037 0.00 0.00 30.22 4.02
43 44 8.311109 GGAAAAGGCTAGATTTTTATTTGGTCA 58.689 33.333 0.00 0.00 30.22 4.02
44 45 9.705290 GAAAAGGCTAGATTTTTATTTGGTCAA 57.295 29.630 0.00 0.00 30.22 3.18
45 46 9.710900 AAAAGGCTAGATTTTTATTTGGTCAAG 57.289 29.630 0.00 0.00 0.00 3.02
46 47 8.422577 AAGGCTAGATTTTTATTTGGTCAAGT 57.577 30.769 0.00 0.00 0.00 3.16
47 48 9.528489 AAGGCTAGATTTTTATTTGGTCAAGTA 57.472 29.630 0.00 0.00 0.00 2.24
48 49 9.178758 AGGCTAGATTTTTATTTGGTCAAGTAG 57.821 33.333 0.00 0.00 0.00 2.57
49 50 8.957466 GGCTAGATTTTTATTTGGTCAAGTAGT 58.043 33.333 0.00 0.00 0.00 2.73
58 59 8.611654 TTATTTGGTCAAGTAGTTTAGTCACC 57.388 34.615 0.00 0.00 0.00 4.02
59 60 4.612264 TGGTCAAGTAGTTTAGTCACCC 57.388 45.455 0.00 0.00 0.00 4.61
60 61 3.325716 TGGTCAAGTAGTTTAGTCACCCC 59.674 47.826 0.00 0.00 0.00 4.95
61 62 3.307269 GGTCAAGTAGTTTAGTCACCCCC 60.307 52.174 0.00 0.00 0.00 5.40
77 78 3.301746 CCCCCTCTCGACCTACTTT 57.698 57.895 0.00 0.00 0.00 2.66
78 79 1.112950 CCCCCTCTCGACCTACTTTC 58.887 60.000 0.00 0.00 0.00 2.62
79 80 0.739561 CCCCTCTCGACCTACTTTCG 59.260 60.000 0.00 0.00 37.85 3.46
80 81 1.681166 CCCCTCTCGACCTACTTTCGA 60.681 57.143 0.00 0.00 43.07 3.71
81 82 2.299521 CCCTCTCGACCTACTTTCGAT 58.700 52.381 0.00 0.00 44.18 3.59
82 83 2.688958 CCCTCTCGACCTACTTTCGATT 59.311 50.000 0.00 0.00 44.18 3.34
83 84 3.243134 CCCTCTCGACCTACTTTCGATTC 60.243 52.174 0.00 0.00 44.18 2.52
84 85 3.628487 CCTCTCGACCTACTTTCGATTCT 59.372 47.826 0.00 0.00 44.18 2.40
85 86 4.815308 CCTCTCGACCTACTTTCGATTCTA 59.185 45.833 0.00 0.00 44.18 2.10
86 87 5.277442 CCTCTCGACCTACTTTCGATTCTAC 60.277 48.000 0.00 0.00 44.18 2.59
87 88 5.181009 TCTCGACCTACTTTCGATTCTACA 58.819 41.667 0.00 0.00 44.18 2.74
88 89 5.645067 TCTCGACCTACTTTCGATTCTACAA 59.355 40.000 0.00 0.00 44.18 2.41
89 90 5.634896 TCGACCTACTTTCGATTCTACAAC 58.365 41.667 0.00 0.00 40.51 3.32
93 94 5.126707 ACCTACTTTCGATTCTACAACCGAT 59.873 40.000 0.00 0.00 0.00 4.18
118 119 2.120940 TCGGGTTGCCTAGGTCCA 59.879 61.111 11.31 0.00 0.00 4.02
125 126 1.847798 TTGCCTAGGTCCATGCCGTT 61.848 55.000 11.31 0.00 0.00 4.44
162 163 2.268920 GCATCACCCCGAGAAGCA 59.731 61.111 0.00 0.00 0.00 3.91
179 180 3.819652 ACCCACAGCAAGCCACCA 61.820 61.111 0.00 0.00 0.00 4.17
217 218 1.075525 ATGGGCGTACTGGCTAGGA 60.076 57.895 0.85 0.00 44.11 2.94
303 304 0.834261 TCCACCGGTCATGGAGTTGA 60.834 55.000 2.59 0.00 41.47 3.18
310 311 0.320374 GTCATGGAGTTGACGGGTCA 59.680 55.000 0.00 0.00 36.93 4.02
315 316 1.448497 GAGTTGACGGGTCACCCAA 59.552 57.895 15.17 0.00 45.83 4.12
317 318 1.052124 AGTTGACGGGTCACCCAAGA 61.052 55.000 15.17 0.00 45.83 3.02
321 322 1.458777 ACGGGTCACCCAAGAGTGA 60.459 57.895 15.17 0.00 45.83 3.41
341 342 7.015974 AGAGTGATATCCAAGCAGTTCATATGA 59.984 37.037 0.00 0.00 0.00 2.15
350 351 2.548707 GCAGTTCATATGATCCGGAGCA 60.549 50.000 26.87 26.87 0.00 4.26
358 359 1.198094 TGATCCGGAGCACTCCCAAA 61.198 55.000 20.59 0.00 46.96 3.28
374 375 1.532794 AAATGGCTCCCGTGGCAAA 60.533 52.632 0.00 0.00 45.43 3.68
380 381 1.003839 CTCCCGTGGCAAAGCACTA 60.004 57.895 0.00 0.00 0.00 2.74
386 387 1.535028 CGTGGCAAAGCACTACATGAA 59.465 47.619 0.00 0.00 0.00 2.57
391 392 3.503748 GGCAAAGCACTACATGAAAGACT 59.496 43.478 0.00 0.00 0.00 3.24
393 394 4.023707 GCAAAGCACTACATGAAAGACTGT 60.024 41.667 0.00 0.00 0.00 3.55
395 396 5.679734 AAGCACTACATGAAAGACTGTTG 57.320 39.130 0.00 0.00 0.00 3.33
408 409 0.116143 ACTGTTGGGAGGCTCTCTCT 59.884 55.000 16.74 0.00 42.10 3.10
411 412 1.229304 TTGGGAGGCTCTCTCTGCA 60.229 57.895 16.74 0.00 42.10 4.41
454 455 4.560919 CGGCTACTCCACCTTCCATTATAC 60.561 50.000 0.00 0.00 34.01 1.47
458 459 4.543689 ACTCCACCTTCCATTATACGAGA 58.456 43.478 0.00 0.00 0.00 4.04
466 467 6.154706 ACCTTCCATTATACGAGAAGTGACTT 59.845 38.462 0.00 0.00 35.10 3.01
509 510 2.130272 AGGTGAGAGTCATAGCACGA 57.870 50.000 0.00 0.00 32.24 4.35
518 519 5.164954 AGAGTCATAGCACGAGAAGTTTTC 58.835 41.667 0.00 0.00 0.00 2.29
555 556 5.041191 AGATTCTTCACAGGACACAAAGT 57.959 39.130 0.00 0.00 0.00 2.66
580 581 9.028185 GTCATGAAATTTTAAGGAATGATGAGC 57.972 33.333 0.00 0.00 0.00 4.26
581 582 7.916977 TCATGAAATTTTAAGGAATGATGAGCG 59.083 33.333 0.00 0.00 0.00 5.03
595 596 4.787280 AGCGGAGGAGGGAGGTGG 62.787 72.222 0.00 0.00 0.00 4.61
613 614 1.555075 TGGTCAAAGGGAGATTCCTCG 59.445 52.381 0.00 0.00 40.33 4.63
659 660 6.375174 TCCATGAAACCATCTGATACAAACAG 59.625 38.462 0.00 0.00 36.80 3.16
692 693 4.005650 TCAGAGTCATGCCACTTTGAATC 58.994 43.478 5.58 0.00 35.23 2.52
693 694 4.008330 CAGAGTCATGCCACTTTGAATCT 58.992 43.478 0.17 0.00 45.27 2.40
694 695 4.458295 CAGAGTCATGCCACTTTGAATCTT 59.542 41.667 0.61 0.00 42.73 2.40
695 696 5.048224 CAGAGTCATGCCACTTTGAATCTTT 60.048 40.000 0.61 0.00 42.73 2.52
696 697 5.537674 AGAGTCATGCCACTTTGAATCTTTT 59.462 36.000 0.00 0.00 42.73 2.27
697 698 6.041296 AGAGTCATGCCACTTTGAATCTTTTT 59.959 34.615 0.00 0.00 42.73 1.94
698 699 5.987347 AGTCATGCCACTTTGAATCTTTTTG 59.013 36.000 0.00 0.00 0.00 2.44
699 700 5.984926 GTCATGCCACTTTGAATCTTTTTGA 59.015 36.000 0.00 0.00 0.00 2.69
700 701 6.479660 GTCATGCCACTTTGAATCTTTTTGAA 59.520 34.615 0.00 0.00 0.00 2.69
701 702 6.479660 TCATGCCACTTTGAATCTTTTTGAAC 59.520 34.615 0.00 0.00 0.00 3.18
702 703 5.115480 TGCCACTTTGAATCTTTTTGAACC 58.885 37.500 0.00 0.00 0.00 3.62
703 704 5.104982 TGCCACTTTGAATCTTTTTGAACCT 60.105 36.000 0.00 0.00 0.00 3.50
704 705 5.817296 GCCACTTTGAATCTTTTTGAACCTT 59.183 36.000 0.00 0.00 0.00 3.50
705 706 6.983890 GCCACTTTGAATCTTTTTGAACCTTA 59.016 34.615 0.00 0.00 0.00 2.69
706 707 7.657354 GCCACTTTGAATCTTTTTGAACCTTAT 59.343 33.333 0.00 0.00 0.00 1.73
707 708 8.981647 CCACTTTGAATCTTTTTGAACCTTATG 58.018 33.333 0.00 0.00 0.00 1.90
708 709 8.490355 CACTTTGAATCTTTTTGAACCTTATGC 58.510 33.333 0.00 0.00 0.00 3.14
709 710 7.657354 ACTTTGAATCTTTTTGAACCTTATGCC 59.343 33.333 0.00 0.00 0.00 4.40
710 711 6.662865 TGAATCTTTTTGAACCTTATGCCA 57.337 33.333 0.00 0.00 0.00 4.92
711 712 6.454795 TGAATCTTTTTGAACCTTATGCCAC 58.545 36.000 0.00 0.00 0.00 5.01
712 713 6.267471 TGAATCTTTTTGAACCTTATGCCACT 59.733 34.615 0.00 0.00 0.00 4.00
713 714 5.705609 TCTTTTTGAACCTTATGCCACTC 57.294 39.130 0.00 0.00 0.00 3.51
714 715 4.522789 TCTTTTTGAACCTTATGCCACTCC 59.477 41.667 0.00 0.00 0.00 3.85
715 716 2.107950 TTGAACCTTATGCCACTCCG 57.892 50.000 0.00 0.00 0.00 4.63
716 717 1.271856 TGAACCTTATGCCACTCCGA 58.728 50.000 0.00 0.00 0.00 4.55
717 718 1.626321 TGAACCTTATGCCACTCCGAA 59.374 47.619 0.00 0.00 0.00 4.30
718 719 2.238646 TGAACCTTATGCCACTCCGAAT 59.761 45.455 0.00 0.00 0.00 3.34
743 744 3.338249 TCTGCTACATTGCAAACTCTCC 58.662 45.455 1.71 0.00 42.83 3.71
751 752 2.727123 TGCAAACTCTCCCAAGTTGA 57.273 45.000 3.87 0.00 39.40 3.18
971 972 7.506296 AATGAAAATTTATTTCGTTCCTCGC 57.494 32.000 0.00 0.00 33.72 5.03
1046 1047 6.745159 ATACGTAGCACATAGATCTCGAAT 57.255 37.500 0.00 0.00 0.00 3.34
1095 1100 2.666508 GTCTTTCGTTGAAGCTCGCATA 59.333 45.455 0.00 0.00 0.00 3.14
1098 1103 4.212425 TCTTTCGTTGAAGCTCGCATAAAA 59.788 37.500 0.00 0.00 0.00 1.52
1162 1167 2.026641 CACCAATGATACCAAGCCCAG 58.973 52.381 0.00 0.00 0.00 4.45
1269 1274 5.541868 CCTAGAGAATAGGAGGAAGCATGAA 59.458 44.000 0.00 0.00 36.85 2.57
1288 1293 6.532657 GCATGAAGAATACATGACCAAAAAGG 59.467 38.462 0.00 0.00 45.22 3.11
1296 1301 1.408969 TGACCAAAAAGGCCAAGGAC 58.591 50.000 5.01 0.00 43.14 3.85
1308 1313 1.472376 GCCAAGGACTTCTCGATGGAG 60.472 57.143 0.00 0.00 41.89 3.86
1327 1332 1.346395 AGCCACTATCACCAAACACGA 59.654 47.619 0.00 0.00 0.00 4.35
1494 1499 2.455674 TGATGTTGACCGTGGAAGAG 57.544 50.000 0.00 0.00 0.00 2.85
1502 1507 2.104170 GACCGTGGAAGAGAAGGAGAT 58.896 52.381 0.00 0.00 0.00 2.75
1578 1583 5.587443 TGATTCATCACTATGAGTTTGCTGG 59.413 40.000 0.00 0.00 42.97 4.85
1583 1588 4.682787 TCACTATGAGTTTGCTGGTATCG 58.317 43.478 0.00 0.00 0.00 2.92
1634 1639 8.125978 TCTTTGCTGGAAGAATTTGATGTATT 57.874 30.769 0.00 0.00 34.07 1.89
1760 1765 8.641155 CGTTGTACGAAATACTTCTTATCAACA 58.359 33.333 11.99 0.00 46.05 3.33
1784 1789 7.601886 ACATTCATTGTTTGGCGAATAAATTCA 59.398 29.630 0.48 0.00 33.74 2.57
1787 1792 9.814899 TTCATTGTTTGGCGAATAAATTCATAT 57.185 25.926 0.48 0.00 36.61 1.78
1807 1812 2.254546 AATGGTGAGTCTGTTCGCAA 57.745 45.000 0.00 0.00 0.00 4.85
1810 1815 1.202639 TGGTGAGTCTGTTCGCAACAT 60.203 47.619 2.83 0.00 41.26 2.71
1855 1860 7.966246 TGCATAGCATTTCAGATTTTTGTTT 57.034 28.000 0.00 0.00 31.71 2.83
1936 1942 3.173668 TGGAATCGACTAAACGGATGG 57.826 47.619 0.00 0.00 0.00 3.51
2276 2283 9.263538 CTAAACAAGGCGTGTAATATACCATTA 57.736 33.333 6.48 0.00 40.60 1.90
2281 2288 9.959749 CAAGGCGTGTAATATACCATTAAAAAT 57.040 29.630 0.00 0.00 0.00 1.82
2328 2335 8.337532 TCTCATATACGTCATTCTTGCAAATTG 58.662 33.333 0.00 0.00 0.00 2.32
2338 2345 7.062605 GTCATTCTTGCAAATTGGTCATAGTTG 59.937 37.037 0.00 0.00 0.00 3.16
2347 2354 6.655078 AATTGGTCATAGTTGAAAAGCAGT 57.345 33.333 0.00 0.00 32.48 4.40
2350 2357 6.109156 TGGTCATAGTTGAAAAGCAGTCTA 57.891 37.500 0.00 0.00 32.48 2.59
2355 2362 9.387123 GTCATAGTTGAAAAGCAGTCTAAAAAG 57.613 33.333 0.00 0.00 32.48 2.27
2356 2363 9.337396 TCATAGTTGAAAAGCAGTCTAAAAAGA 57.663 29.630 0.00 0.00 0.00 2.52
2357 2364 9.387123 CATAGTTGAAAAGCAGTCTAAAAAGAC 57.613 33.333 0.00 0.00 39.00 3.01
2358 2365 6.487103 AGTTGAAAAGCAGTCTAAAAAGACG 58.513 36.000 0.18 0.00 43.15 4.18
2359 2366 6.315393 AGTTGAAAAGCAGTCTAAAAAGACGA 59.685 34.615 0.00 0.00 43.15 4.20
2360 2367 6.861065 TGAAAAGCAGTCTAAAAAGACGAT 57.139 33.333 0.00 0.00 43.15 3.73
2461 2470 4.081406 TGCTGGAAATCTGCTACAAACAT 58.919 39.130 0.00 0.00 40.43 2.71
2483 2492 4.086457 TGCCCCTTTAGAAACATTTCTCC 58.914 43.478 10.11 0.00 43.72 3.71
2485 2494 4.158579 GCCCCTTTAGAAACATTTCTCCAG 59.841 45.833 10.11 7.68 43.72 3.86
2489 2498 6.348540 CCCTTTAGAAACATTTCTCCAGTTCG 60.349 42.308 10.11 0.00 43.72 3.95
2494 2503 6.464222 AGAAACATTTCTCCAGTTCGATACA 58.536 36.000 0.87 0.00 43.72 2.29
2504 2513 7.837863 TCTCCAGTTCGATACAGTTTAAAGAT 58.162 34.615 0.00 0.00 0.00 2.40
2734 2745 2.222227 AAAGGTTTCTCAGATGGGGC 57.778 50.000 0.00 0.00 0.00 5.80
2746 2757 5.549228 TCTCAGATGGGGCAAATGATATACT 59.451 40.000 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.643348 CCTTTTCCCAATTTTATGTCTTGGC 59.357 40.000 0.00 0.00 38.47 4.52
1 2 5.643348 GCCTTTTCCCAATTTTATGTCTTGG 59.357 40.000 0.00 0.00 39.31 3.61
2 3 6.466812 AGCCTTTTCCCAATTTTATGTCTTG 58.533 36.000 0.00 0.00 0.00 3.02
3 4 6.686484 AGCCTTTTCCCAATTTTATGTCTT 57.314 33.333 0.00 0.00 0.00 3.01
4 5 7.182060 TCTAGCCTTTTCCCAATTTTATGTCT 58.818 34.615 0.00 0.00 0.00 3.41
5 6 7.404671 TCTAGCCTTTTCCCAATTTTATGTC 57.595 36.000 0.00 0.00 0.00 3.06
6 7 7.978099 ATCTAGCCTTTTCCCAATTTTATGT 57.022 32.000 0.00 0.00 0.00 2.29
7 8 9.671279 AAAATCTAGCCTTTTCCCAATTTTATG 57.329 29.630 0.00 0.00 0.00 1.90
13 14 9.671279 CAAATAAAAATCTAGCCTTTTCCCAAT 57.329 29.630 5.25 0.00 0.00 3.16
14 15 8.100164 CCAAATAAAAATCTAGCCTTTTCCCAA 58.900 33.333 5.25 0.00 0.00 4.12
15 16 7.236640 ACCAAATAAAAATCTAGCCTTTTCCCA 59.763 33.333 5.25 0.00 0.00 4.37
16 17 7.620880 ACCAAATAAAAATCTAGCCTTTTCCC 58.379 34.615 5.25 0.00 0.00 3.97
17 18 8.311109 TGACCAAATAAAAATCTAGCCTTTTCC 58.689 33.333 5.25 0.00 0.00 3.13
18 19 9.705290 TTGACCAAATAAAAATCTAGCCTTTTC 57.295 29.630 5.25 0.00 0.00 2.29
19 20 9.710900 CTTGACCAAATAAAAATCTAGCCTTTT 57.289 29.630 6.78 6.78 0.00 2.27
20 21 8.870116 ACTTGACCAAATAAAAATCTAGCCTTT 58.130 29.630 0.00 0.00 0.00 3.11
21 22 8.422577 ACTTGACCAAATAAAAATCTAGCCTT 57.577 30.769 0.00 0.00 0.00 4.35
22 23 9.178758 CTACTTGACCAAATAAAAATCTAGCCT 57.821 33.333 0.00 0.00 0.00 4.58
23 24 8.957466 ACTACTTGACCAAATAAAAATCTAGCC 58.043 33.333 0.00 0.00 0.00 3.93
32 33 9.059260 GGTGACTAAACTACTTGACCAAATAAA 57.941 33.333 0.00 0.00 0.00 1.40
33 34 7.662669 GGGTGACTAAACTACTTGACCAAATAA 59.337 37.037 0.00 0.00 0.00 1.40
34 35 7.163441 GGGTGACTAAACTACTTGACCAAATA 58.837 38.462 0.00 0.00 0.00 1.40
35 36 6.002082 GGGTGACTAAACTACTTGACCAAAT 58.998 40.000 0.00 0.00 0.00 2.32
36 37 5.370679 GGGTGACTAAACTACTTGACCAAA 58.629 41.667 0.00 0.00 0.00 3.28
37 38 4.202388 GGGGTGACTAAACTACTTGACCAA 60.202 45.833 0.00 0.00 0.00 3.67
38 39 3.325716 GGGGTGACTAAACTACTTGACCA 59.674 47.826 0.00 0.00 0.00 4.02
39 40 3.307269 GGGGGTGACTAAACTACTTGACC 60.307 52.174 0.00 0.00 0.00 4.02
40 41 3.935315 GGGGGTGACTAAACTACTTGAC 58.065 50.000 0.00 0.00 0.00 3.18
59 60 1.112950 GAAAGTAGGTCGAGAGGGGG 58.887 60.000 0.00 0.00 0.00 5.40
60 61 0.739561 CGAAAGTAGGTCGAGAGGGG 59.260 60.000 0.00 0.00 41.02 4.79
61 62 1.747709 TCGAAAGTAGGTCGAGAGGG 58.252 55.000 0.00 0.00 42.31 4.30
67 68 4.797349 GGTTGTAGAATCGAAAGTAGGTCG 59.203 45.833 0.00 0.00 39.88 4.79
68 69 4.797349 CGGTTGTAGAATCGAAAGTAGGTC 59.203 45.833 0.00 0.00 37.97 3.85
69 70 4.460382 TCGGTTGTAGAATCGAAAGTAGGT 59.540 41.667 5.36 0.00 41.75 3.08
70 71 4.990257 TCGGTTGTAGAATCGAAAGTAGG 58.010 43.478 5.36 0.00 41.75 3.18
78 79 2.361119 TGGGAGATCGGTTGTAGAATCG 59.639 50.000 0.00 0.00 37.01 3.34
79 80 3.385111 ACTGGGAGATCGGTTGTAGAATC 59.615 47.826 0.00 0.00 0.00 2.52
80 81 3.375699 ACTGGGAGATCGGTTGTAGAAT 58.624 45.455 0.00 0.00 0.00 2.40
81 82 2.758979 GACTGGGAGATCGGTTGTAGAA 59.241 50.000 0.00 0.00 0.00 2.10
82 83 2.376109 GACTGGGAGATCGGTTGTAGA 58.624 52.381 0.00 0.00 0.00 2.59
83 84 1.065701 CGACTGGGAGATCGGTTGTAG 59.934 57.143 0.00 0.00 34.67 2.74
84 85 1.100510 CGACTGGGAGATCGGTTGTA 58.899 55.000 0.00 0.00 34.67 2.41
85 86 1.890894 CGACTGGGAGATCGGTTGT 59.109 57.895 0.00 0.00 34.67 3.32
86 87 4.814900 CGACTGGGAGATCGGTTG 57.185 61.111 0.00 0.00 34.67 3.77
107 108 2.252072 GAACGGCATGGACCTAGGCA 62.252 60.000 9.30 0.00 0.00 4.75
111 112 2.727392 CCCGAACGGCATGGACCTA 61.727 63.158 7.80 0.00 0.00 3.08
162 163 3.797507 CTGGTGGCTTGCTGTGGGT 62.798 63.158 0.00 0.00 0.00 4.51
196 197 0.032678 CTAGCCAGTACGCCCATGAG 59.967 60.000 0.00 0.00 0.00 2.90
217 218 4.547367 GCCCTTATGCTCGGCCGT 62.547 66.667 27.15 8.36 36.63 5.68
249 250 1.767759 GTCATTGGGCAGCATTAGGT 58.232 50.000 0.00 0.00 0.00 3.08
277 278 0.035534 CATGACCGGTGGATTGTCCA 60.036 55.000 14.63 0.00 45.98 4.02
310 311 2.846206 TGCTTGGATATCACTCTTGGGT 59.154 45.455 4.83 0.00 0.00 4.51
315 316 5.627182 ATGAACTGCTTGGATATCACTCT 57.373 39.130 4.83 0.00 0.00 3.24
317 318 7.071069 TCATATGAACTGCTTGGATATCACT 57.929 36.000 1.98 0.00 0.00 3.41
321 322 6.111382 CGGATCATATGAACTGCTTGGATAT 58.889 40.000 9.99 0.00 0.00 1.63
328 329 2.289320 GCTCCGGATCATATGAACTGCT 60.289 50.000 9.99 0.00 0.00 4.24
350 351 2.231380 ACGGGAGCCATTTGGGAGT 61.231 57.895 0.00 0.00 40.01 3.85
358 359 2.361610 CTTTGCCACGGGAGCCAT 60.362 61.111 0.00 0.00 0.00 4.40
374 375 4.067896 CCAACAGTCTTTCATGTAGTGCT 58.932 43.478 0.00 0.00 0.00 4.40
380 381 2.815589 GCCTCCCAACAGTCTTTCATGT 60.816 50.000 0.00 0.00 0.00 3.21
386 387 0.980423 GAGAGCCTCCCAACAGTCTT 59.020 55.000 0.00 0.00 0.00 3.01
391 392 1.548357 GCAGAGAGAGCCTCCCAACA 61.548 60.000 0.00 0.00 42.97 3.33
393 394 0.619832 ATGCAGAGAGAGCCTCCCAA 60.620 55.000 0.00 0.00 42.97 4.12
395 396 1.336632 ACATGCAGAGAGAGCCTCCC 61.337 60.000 0.00 0.00 42.97 4.30
480 481 5.878406 ATGACTCTCACCTTAGGGTATTG 57.122 43.478 2.32 0.00 45.41 1.90
504 505 5.652744 TTCACTTAGAAAACTTCTCGTGC 57.347 39.130 11.16 0.00 41.14 5.34
533 534 5.041191 ACTTTGTGTCCTGTGAAGAATCT 57.959 39.130 0.00 0.00 0.00 2.40
555 556 7.916977 CGCTCATCATTCCTTAAAATTTCATGA 59.083 33.333 0.00 0.00 0.00 3.07
562 563 4.823989 CCTCCGCTCATCATTCCTTAAAAT 59.176 41.667 0.00 0.00 0.00 1.82
566 567 2.630098 CTCCTCCGCTCATCATTCCTTA 59.370 50.000 0.00 0.00 0.00 2.69
580 581 2.760385 GACCACCTCCCTCCTCCG 60.760 72.222 0.00 0.00 0.00 4.63
581 582 0.840722 TTTGACCACCTCCCTCCTCC 60.841 60.000 0.00 0.00 0.00 4.30
595 596 2.233922 TGACGAGGAATCTCCCTTTGAC 59.766 50.000 0.00 0.00 37.19 3.18
613 614 6.690530 TGGACATTTGAAGGATTTTGATGAC 58.309 36.000 0.00 0.00 0.00 3.06
659 660 3.427233 GCATGACTCTGAACATTGCTTCC 60.427 47.826 0.00 0.00 0.00 3.46
692 693 4.615912 CGGAGTGGCATAAGGTTCAAAAAG 60.616 45.833 0.00 0.00 0.00 2.27
693 694 3.254657 CGGAGTGGCATAAGGTTCAAAAA 59.745 43.478 0.00 0.00 0.00 1.94
694 695 2.817258 CGGAGTGGCATAAGGTTCAAAA 59.183 45.455 0.00 0.00 0.00 2.44
695 696 2.039216 TCGGAGTGGCATAAGGTTCAAA 59.961 45.455 0.00 0.00 0.00 2.69
696 697 1.626321 TCGGAGTGGCATAAGGTTCAA 59.374 47.619 0.00 0.00 0.00 2.69
697 698 1.271856 TCGGAGTGGCATAAGGTTCA 58.728 50.000 0.00 0.00 0.00 3.18
698 699 2.396590 TTCGGAGTGGCATAAGGTTC 57.603 50.000 0.00 0.00 0.00 3.62
699 700 2.026262 ACATTCGGAGTGGCATAAGGTT 60.026 45.455 5.46 0.00 0.00 3.50
700 701 1.559682 ACATTCGGAGTGGCATAAGGT 59.440 47.619 5.46 0.00 0.00 3.50
701 702 2.332063 ACATTCGGAGTGGCATAAGG 57.668 50.000 5.46 0.00 0.00 2.69
702 703 3.941483 AGAAACATTCGGAGTGGCATAAG 59.059 43.478 5.46 0.00 34.02 1.73
703 704 3.689161 CAGAAACATTCGGAGTGGCATAA 59.311 43.478 5.46 0.00 34.02 1.90
704 705 3.270027 CAGAAACATTCGGAGTGGCATA 58.730 45.455 5.46 0.00 34.02 3.14
705 706 2.086869 CAGAAACATTCGGAGTGGCAT 58.913 47.619 5.46 0.00 34.02 4.40
706 707 1.522668 CAGAAACATTCGGAGTGGCA 58.477 50.000 5.46 0.00 34.02 4.92
707 708 0.169009 GCAGAAACATTCGGAGTGGC 59.831 55.000 5.46 0.00 34.02 5.01
708 709 1.813513 AGCAGAAACATTCGGAGTGG 58.186 50.000 5.46 0.00 34.02 4.00
709 710 3.325870 TGTAGCAGAAACATTCGGAGTG 58.674 45.455 0.00 0.00 34.02 3.51
710 711 3.678056 TGTAGCAGAAACATTCGGAGT 57.322 42.857 0.00 0.00 34.02 3.85
711 712 4.728882 GCAATGTAGCAGAAACATTCGGAG 60.729 45.833 0.00 0.00 43.84 4.63
712 713 3.126858 GCAATGTAGCAGAAACATTCGGA 59.873 43.478 0.00 0.00 43.84 4.55
713 714 3.119884 TGCAATGTAGCAGAAACATTCGG 60.120 43.478 0.00 0.00 43.84 4.30
714 715 4.082274 TGCAATGTAGCAGAAACATTCG 57.918 40.909 0.00 0.00 43.84 3.34
715 716 5.922544 AGTTTGCAATGTAGCAGAAACATTC 59.077 36.000 0.00 0.00 43.84 2.67
716 717 5.846203 AGTTTGCAATGTAGCAGAAACATT 58.154 33.333 0.00 0.00 45.97 2.71
717 718 5.242393 AGAGTTTGCAATGTAGCAGAAACAT 59.758 36.000 0.00 0.00 46.54 2.71
718 719 4.580167 AGAGTTTGCAATGTAGCAGAAACA 59.420 37.500 0.00 0.00 46.54 2.83
743 744 3.256631 CCAATTCAGGGAGTTCAACTTGG 59.743 47.826 0.00 0.00 0.00 3.61
751 752 6.160459 AGGTGATATTACCAATTCAGGGAGTT 59.840 38.462 18.19 0.00 43.37 3.01
786 787 6.402981 AGATTTGGGAGTAGTAAATGGGTT 57.597 37.500 0.00 0.00 0.00 4.11
1057 1058 7.384477 ACGAAAGACCTTTGCTAGTTTACTAT 58.616 34.615 0.00 0.00 32.11 2.12
1095 1100 0.975887 AGCCGGTTGCCATGAATTTT 59.024 45.000 1.90 0.00 42.71 1.82
1098 1103 1.754234 GGAGCCGGTTGCCATGAAT 60.754 57.895 1.90 0.00 42.71 2.57
1162 1167 3.198872 GGCAGAAGGAGCAAGTGTATAC 58.801 50.000 0.00 0.00 0.00 1.47
1288 1293 0.537188 TCCATCGAGAAGTCCTTGGC 59.463 55.000 0.00 0.00 0.00 4.52
1296 1301 2.625314 TGATAGTGGCTCCATCGAGAAG 59.375 50.000 0.00 0.00 38.52 2.85
1308 1313 1.463444 GTCGTGTTTGGTGATAGTGGC 59.537 52.381 0.00 0.00 0.00 5.01
1327 1332 5.353394 TTGCGATACCTTCTCCAATAAGT 57.647 39.130 0.00 0.00 0.00 2.24
1494 1499 5.640147 TCCTCTTCATCTCCTATCTCCTTC 58.360 45.833 0.00 0.00 0.00 3.46
1502 1507 4.230733 TCAGGTTCTCCTCTTCATCTCCTA 59.769 45.833 0.00 0.00 43.07 2.94
1526 1531 6.998074 TCACAACTTCAAGGTAAGATCAATGT 59.002 34.615 0.00 0.00 0.00 2.71
1760 1765 8.721019 ATGAATTTATTCGCCAAACAATGAAT 57.279 26.923 0.00 0.00 39.62 2.57
1766 1771 9.689976 CCATTATATGAATTTATTCGCCAAACA 57.310 29.630 0.00 0.00 39.62 2.83
1784 1789 5.276461 TGCGAACAGACTCACCATTATAT 57.724 39.130 0.00 0.00 0.00 0.86
1787 1792 3.064207 GTTGCGAACAGACTCACCATTA 58.936 45.455 0.00 0.00 0.00 1.90
1843 1848 9.695526 TGGTTCAAGATATCAAACAAAAATCTG 57.304 29.630 5.32 0.00 0.00 2.90
1916 1922 2.159014 CCCATCCGTTTAGTCGATTCCA 60.159 50.000 0.00 0.00 0.00 3.53
1927 1933 5.047590 GGTTTGATTAGTTTCCCATCCGTTT 60.048 40.000 0.00 0.00 0.00 3.60
1936 1942 6.024552 TGATGCAAGGTTTGATTAGTTTCC 57.975 37.500 0.00 0.00 0.00 3.13
2208 2214 5.539582 GACATTTGGTCGTATGCAGTTTA 57.460 39.130 0.00 0.00 36.65 2.01
2251 2258 9.610705 TTAATGGTATATTACACGCCTTGTTTA 57.389 29.630 0.00 0.00 39.91 2.01
2281 2288 8.394971 TGAGAATTTATCTTCTTGTGCTCAAA 57.605 30.769 2.44 0.00 38.96 2.69
2312 2319 6.624423 ACTATGACCAATTTGCAAGAATGAC 58.376 36.000 0.00 0.10 0.00 3.06
2328 2335 7.435068 TTTAGACTGCTTTTCAACTATGACC 57.565 36.000 0.00 0.00 34.61 4.02
2338 2345 8.561932 AAAATCGTCTTTTTAGACTGCTTTTC 57.438 30.769 4.05 0.00 36.71 2.29
2461 2470 4.086457 GGAGAAATGTTTCTAAAGGGGCA 58.914 43.478 7.91 0.00 46.84 5.36
2494 2503 9.981114 CCACCACTTTTCAAATATCTTTAAACT 57.019 29.630 0.00 0.00 0.00 2.66
2541 2550 9.897744 TTCAAAGTTAGAGCAAAATATGTCTTG 57.102 29.630 0.00 0.00 0.00 3.02
2561 2571 5.717038 AATTTTGACAAGCCGTTTCAAAG 57.283 34.783 0.00 0.00 39.68 2.77


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

AutoCloner maintained by Alex Coulton.