Multiple sequence alignment - TraesCS4A01G237300

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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 TraesCS4A01G237300 chr4A 100.000 3875 0 0 1 3875 546209168 546213042 0.000000e+00 7156.0
1 TraesCS4A01G237300 chr4D 91.055 3667 161 75 310 3874 50772600 50768999 0.000000e+00 4800.0
2 TraesCS4A01G237300 chr4D 94.400 125 4 2 111 235 50775469 50775348 5.110000e-44 189.0
3 TraesCS4A01G237300 chr4D 100.000 29 0 0 29 57 50775502 50775474 2.000000e-03 54.7
4 TraesCS4A01G237300 chr4B 90.135 3710 187 77 257 3875 74683894 74680273 0.000000e+00 4658.0
5 TraesCS4A01G237300 chr4B 91.275 149 4 6 94 235 74684131 74683985 1.100000e-45 195.0
6 TraesCS4A01G237300 chr4B 94.231 52 1 2 29 78 74684167 74684116 1.150000e-10 78.7
7 TraesCS4A01G237300 chr5D 84.122 592 86 4 2253 2840 89381395 89381982 2.020000e-157 566.0
8 TraesCS4A01G237300 chr5D 83.708 356 54 4 1793 2146 89380935 89381288 2.230000e-87 333.0
9 TraesCS4A01G237300 chr5D 79.638 442 59 23 993 1414 89379990 89380420 4.900000e-74 289.0
10 TraesCS4A01G237300 chr5B 84.122 592 86 4 2253 2840 94676973 94676386 2.020000e-157 566.0
11 TraesCS4A01G237300 chr5B 83.008 359 57 4 1793 2149 94677444 94677088 4.830000e-84 322.0
12 TraesCS4A01G237300 chr5A 83.752 597 89 5 2248 2840 83277860 83278452 3.380000e-155 558.0
13 TraesCS4A01G237300 chr5A 83.427 356 55 4 1793 2146 83277404 83277757 1.040000e-85 327.0
14 TraesCS4A01G237300 chr5A 79.545 440 63 18 993 1414 83276469 83276899 4.900000e-74 289.0
15 TraesCS4A01G237300 chr2A 81.420 479 83 6 2253 2728 164704373 164703898 1.690000e-103 387.0
16 TraesCS4A01G237300 chr2A 77.657 367 66 9 1793 2145 164704823 164704459 3.920000e-50 209.0
17 TraesCS4A01G237300 chr2A 73.226 310 61 17 1120 1408 164705227 164704919 4.120000e-15 93.5
18 TraesCS4A01G237300 chr2D 82.353 442 74 4 2294 2733 136832834 136833273 7.860000e-102 381.0
19 TraesCS4A01G237300 chr2D 74.267 307 60 16 1120 1408 136831944 136832249 1.140000e-20 111.0
20 TraesCS4A01G237300 chr2B 82.243 107 17 2 1303 1408 195529767 195529872 1.480000e-14 91.6


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 TraesCS4A01G237300 chr4A 546209168 546213042 3874 False 7156.000000 7156 100.000000 1 3875 1 chr4A.!!$F1 3874
1 TraesCS4A01G237300 chr4D 50768999 50775502 6503 True 1681.233333 4800 95.151667 29 3874 3 chr4D.!!$R1 3845
2 TraesCS4A01G237300 chr4B 74680273 74684167 3894 True 1643.900000 4658 91.880333 29 3875 3 chr4B.!!$R1 3846
3 TraesCS4A01G237300 chr5D 89379990 89381982 1992 False 396.000000 566 82.489333 993 2840 3 chr5D.!!$F1 1847
4 TraesCS4A01G237300 chr5B 94676386 94677444 1058 True 444.000000 566 83.565000 1793 2840 2 chr5B.!!$R1 1047
5 TraesCS4A01G237300 chr5A 83276469 83278452 1983 False 391.333333 558 82.241333 993 2840 3 chr5A.!!$F1 1847
6 TraesCS4A01G237300 chr2A 164703898 164705227 1329 True 229.833333 387 77.434333 1120 2728 3 chr2A.!!$R1 1608
7 TraesCS4A01G237300 chr2D 136831944 136833273 1329 False 246.000000 381 78.310000 1120 2733 2 chr2D.!!$F1 1613

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
76 77 0.472352 TAACCCAACCCGAGTGGAGT 60.472 55.0 1.03 0.0 37.49 3.85 F
1422 4289 0.172803 TCGTAAGCGCTTCCTCTTCC 59.827 55.0 28.82 6.0 38.14 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 5291 0.693430 TCTCAGGAGCCATCTGCCAT 60.693 55.0 0.0 0.0 42.71 4.40 R
2992 6337 0.255318 CCTCATGCTGCTTCCTTCCT 59.745 55.0 0.0 0.0 0.00 3.36 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.519377 ATGTGAACAACCGAGACGAA 57.481 45.000 0.00 0.00 0.00 3.85
20 21 2.296831 TGTGAACAACCGAGACGAAA 57.703 45.000 0.00 0.00 0.00 3.46
21 22 2.198406 TGTGAACAACCGAGACGAAAG 58.802 47.619 0.00 0.00 0.00 2.62
22 23 2.159212 TGTGAACAACCGAGACGAAAGA 60.159 45.455 0.00 0.00 0.00 2.52
23 24 2.471743 GTGAACAACCGAGACGAAAGAG 59.528 50.000 0.00 0.00 0.00 2.85
24 25 2.359848 TGAACAACCGAGACGAAAGAGA 59.640 45.455 0.00 0.00 0.00 3.10
25 26 3.181484 TGAACAACCGAGACGAAAGAGAA 60.181 43.478 0.00 0.00 0.00 2.87
26 27 3.014604 ACAACCGAGACGAAAGAGAAG 57.985 47.619 0.00 0.00 0.00 2.85
27 28 2.621998 ACAACCGAGACGAAAGAGAAGA 59.378 45.455 0.00 0.00 0.00 2.87
63 64 4.042174 CTCCCACCTAACCTAATAACCCA 58.958 47.826 0.00 0.00 0.00 4.51
65 66 4.227982 TCCCACCTAACCTAATAACCCAAC 59.772 45.833 0.00 0.00 0.00 3.77
68 69 3.200605 ACCTAACCTAATAACCCAACCCG 59.799 47.826 0.00 0.00 0.00 5.28
69 70 3.455543 CCTAACCTAATAACCCAACCCGA 59.544 47.826 0.00 0.00 0.00 5.14
70 71 3.639672 AACCTAATAACCCAACCCGAG 57.360 47.619 0.00 0.00 0.00 4.63
71 72 2.554563 ACCTAATAACCCAACCCGAGT 58.445 47.619 0.00 0.00 0.00 4.18
72 73 2.237893 ACCTAATAACCCAACCCGAGTG 59.762 50.000 0.00 0.00 0.00 3.51
73 74 2.420967 CCTAATAACCCAACCCGAGTGG 60.421 54.545 0.00 0.00 41.37 4.00
74 75 1.364269 AATAACCCAACCCGAGTGGA 58.636 50.000 1.03 0.00 37.49 4.02
75 76 0.909623 ATAACCCAACCCGAGTGGAG 59.090 55.000 1.03 0.00 37.49 3.86
76 77 0.472352 TAACCCAACCCGAGTGGAGT 60.472 55.000 1.03 0.00 37.49 3.85
77 78 0.472352 AACCCAACCCGAGTGGAGTA 60.472 55.000 1.03 0.00 37.49 2.59
78 79 1.190178 ACCCAACCCGAGTGGAGTAC 61.190 60.000 1.03 0.00 37.49 2.73
79 80 1.595357 CCAACCCGAGTGGAGTACC 59.405 63.158 0.00 0.00 37.49 3.34
80 81 1.595357 CAACCCGAGTGGAGTACCC 59.405 63.158 0.00 0.00 37.49 3.69
81 82 1.980772 AACCCGAGTGGAGTACCCG 60.981 63.158 0.00 0.00 37.49 5.28
82 83 3.834799 CCCGAGTGGAGTACCCGC 61.835 72.222 5.97 5.97 45.81 6.13
192 199 0.988832 TTACCATCCACCCTCACCAC 59.011 55.000 0.00 0.00 0.00 4.16
198 205 2.113139 CACCCTCACCACCACCAC 59.887 66.667 0.00 0.00 0.00 4.16
201 208 2.113139 CCTCACCACCACCACCAC 59.887 66.667 0.00 0.00 0.00 4.16
235 243 9.124807 AGCGACTAATTTAAACAGCAAAATAAC 57.875 29.630 0.00 0.00 0.00 1.89
261 338 8.594687 CAAAAATCAACACTTTCAGTTAACCAG 58.405 33.333 0.88 0.00 0.00 4.00
268 345 4.520492 CACTTTCAGTTAACCAGGAGCAAT 59.480 41.667 0.88 0.00 0.00 3.56
289 366 0.513717 CGCTTGCTTACGAACGAACG 60.514 55.000 0.14 0.00 39.31 3.95
291 368 1.201672 GCTTGCTTACGAACGAACGAG 60.202 52.381 11.97 2.73 37.03 4.18
293 370 2.624316 TGCTTACGAACGAACGAGAT 57.376 45.000 11.97 0.00 37.03 2.75
299 376 5.276584 GCTTACGAACGAACGAGATACTCTA 60.277 44.000 11.97 0.00 37.03 2.43
300 377 4.775440 ACGAACGAACGAGATACTCTAG 57.225 45.455 11.97 0.00 37.03 2.43
301 378 3.555139 ACGAACGAACGAGATACTCTAGG 59.445 47.826 11.97 0.00 37.03 3.02
302 379 3.604314 CGAACGAACGAGATACTCTAGGC 60.604 52.174 0.14 0.00 35.09 3.93
303 380 2.915349 ACGAACGAGATACTCTAGGCA 58.085 47.619 0.14 0.00 0.00 4.75
305 382 3.312973 ACGAACGAGATACTCTAGGCAAG 59.687 47.826 0.14 0.00 0.00 4.01
306 383 3.312973 CGAACGAGATACTCTAGGCAAGT 59.687 47.826 0.00 0.00 0.00 3.16
337 3095 3.853355 ATCTCCCAAGATGTCATGGAC 57.147 47.619 5.88 0.00 40.84 4.02
338 3096 1.839994 TCTCCCAAGATGTCATGGACC 59.160 52.381 5.88 0.00 36.89 4.46
339 3097 0.541392 TCCCAAGATGTCATGGACCG 59.459 55.000 5.88 0.00 36.89 4.79
440 3198 1.069204 CACTGCACGGCATAGATAGGT 59.931 52.381 0.00 0.00 38.13 3.08
441 3199 2.296190 CACTGCACGGCATAGATAGGTA 59.704 50.000 0.00 0.00 38.13 3.08
442 3200 2.296471 ACTGCACGGCATAGATAGGTAC 59.704 50.000 0.00 0.00 38.13 3.34
484 3249 3.406361 GCTGTGGCTCACGTGTCG 61.406 66.667 16.51 9.25 37.14 4.35
485 3250 3.406361 CTGTGGCTCACGTGTCGC 61.406 66.667 16.51 18.25 37.14 5.19
516 3291 3.060602 CTCCGAAACTGAAACTGACTCC 58.939 50.000 0.00 0.00 0.00 3.85
520 3295 2.240493 AACTGAAACTGACTCCACCG 57.760 50.000 0.00 0.00 0.00 4.94
533 3308 4.025401 CACCGGCAAGCGTCCAAC 62.025 66.667 0.00 0.00 0.00 3.77
544 3319 3.112709 GTCCAACGCGAGCCACTC 61.113 66.667 15.93 0.00 0.00 3.51
615 3390 4.148825 ATGCAGCTCCGGACGGAC 62.149 66.667 9.76 7.23 39.76 4.79
687 3462 1.372997 TCAGAAACTGACGCCGCTC 60.373 57.895 0.00 0.00 35.39 5.03
771 3574 1.003851 GCGCCGCTAGTAAATGTGAA 58.996 50.000 0.00 0.00 0.00 3.18
972 3781 3.580193 GCAGCAGCGGCATACCAG 61.580 66.667 13.20 0.00 44.61 4.00
973 3782 2.898840 CAGCAGCGGCATACCAGG 60.899 66.667 12.44 0.00 44.61 4.45
974 3783 4.181010 AGCAGCGGCATACCAGGG 62.181 66.667 12.44 0.00 44.61 4.45
1422 4289 0.172803 TCGTAAGCGCTTCCTCTTCC 59.827 55.000 28.82 6.00 38.14 3.46
1453 4327 1.364626 CTCATGCCGCTGTCTTGGTC 61.365 60.000 0.00 0.00 0.00 4.02
1533 4434 6.128063 CCAGTCAAATCTCTTCTCAAATGTCC 60.128 42.308 0.00 0.00 0.00 4.02
1541 4442 3.320826 TCTTCTCAAATGTCCGTGTCTGA 59.679 43.478 0.00 0.00 0.00 3.27
1559 4460 5.104374 GTCTGAGCTCTCTTGATTCTTCAG 58.896 45.833 16.19 0.00 32.27 3.02
1587 4488 3.425758 GGTCCTGCATACTGTAAAAACGC 60.426 47.826 0.00 0.00 0.00 4.84
1592 4496 5.272167 TGCATACTGTAAAAACGCAGTAC 57.728 39.130 6.56 0.00 45.00 2.73
1604 4508 3.152261 ACGCAGTACTTACTCATGCTC 57.848 47.619 0.00 0.00 41.94 4.26
1607 4511 3.190874 GCAGTACTTACTCATGCTCACC 58.809 50.000 0.00 0.00 33.46 4.02
1667 4571 3.499918 GTCTGCTGCATTTGTTGTCTAGT 59.500 43.478 1.31 0.00 0.00 2.57
1734 4638 1.831580 AGCTGTTTGATTCAGGGAGC 58.168 50.000 0.00 5.26 33.98 4.70
1786 4694 3.602390 TTACTGTCACGAGCTTTTTGC 57.398 42.857 0.00 0.00 43.29 3.68
1787 4695 0.663153 ACTGTCACGAGCTTTTTGCC 59.337 50.000 0.00 0.00 44.23 4.52
1986 5291 4.451150 CCAGGCCGCTTCGTGCTA 62.451 66.667 0.00 0.00 40.11 3.49
2079 5384 2.598394 AAGCTTGTGTGGCGCCAT 60.598 55.556 35.23 12.34 34.52 4.40
2184 5491 2.732658 GCCTAGCATGCCATTGCC 59.267 61.111 15.66 0.00 43.83 4.52
2234 5541 6.756074 TCTTGGCACTTTTACTCAAATGTTTG 59.244 34.615 0.00 0.00 39.48 2.93
2361 5690 1.227943 GAAGCTGTGCACTGACCCA 60.228 57.895 25.94 0.00 0.00 4.51
2472 5801 2.092323 CACATCGAGGACTCACACCTA 58.908 52.381 3.06 0.00 37.93 3.08
2780 6109 1.209019 CCCTCATGGTGGTGAGAAGAG 59.791 57.143 5.53 0.00 46.77 2.85
2863 6192 1.814772 CGAGCTAGCATGGAGGGGAG 61.815 65.000 18.83 0.00 0.00 4.30
2880 6209 2.091885 GGGAGCCCATACCTGAAAATCA 60.092 50.000 0.00 0.00 35.81 2.57
2884 6213 4.415596 AGCCCATACCTGAAAATCACAAA 58.584 39.130 0.00 0.00 0.00 2.83
2886 6215 5.127682 AGCCCATACCTGAAAATCACAAATC 59.872 40.000 0.00 0.00 0.00 2.17
2946 6291 3.252701 GTGTAGAGAGAAACAGGTCGACA 59.747 47.826 18.91 0.00 0.00 4.35
2948 6293 2.865079 AGAGAGAAACAGGTCGACAGA 58.135 47.619 18.91 0.00 0.00 3.41
2989 6334 4.271696 TCCAAATGACCTCTGTGTACAG 57.728 45.455 5.67 5.67 45.08 2.74
2990 6335 3.007940 TCCAAATGACCTCTGTGTACAGG 59.992 47.826 11.76 0.00 43.91 4.00
2991 6336 3.007940 CCAAATGACCTCTGTGTACAGGA 59.992 47.826 11.76 2.57 43.91 3.86
2992 6337 4.504864 CCAAATGACCTCTGTGTACAGGAA 60.505 45.833 11.76 0.00 43.91 3.36
3025 6370 1.108776 ATGAGGCATTCACATGGTGC 58.891 50.000 0.00 1.85 38.99 5.01
3061 6406 3.689002 CTCTTCAAGGGGGAGCGGC 62.689 68.421 0.00 0.00 0.00 6.53
3073 6418 1.143401 GAGCGGCAGTAGGTAACCC 59.857 63.158 1.45 0.00 37.17 4.11
3139 6484 1.151679 TGCGTTCCCCATTCCAACA 59.848 52.632 0.00 0.00 0.00 3.33
3156 6501 3.748568 CCAACAACTCTACCTGAGAAAGC 59.251 47.826 0.00 0.00 45.39 3.51
3209 6554 8.856153 TTTAGCAAATACTAATTGGTCAGTGA 57.144 30.769 0.00 0.00 39.12 3.41
3212 6557 6.149474 AGCAAATACTAATTGGTCAGTGACAC 59.851 38.462 24.20 13.99 33.53 3.67
3240 6591 2.205022 ATTGGCTGCTCAGTTTGCTA 57.795 45.000 0.00 0.00 0.00 3.49
3241 6592 1.979855 TTGGCTGCTCAGTTTGCTAA 58.020 45.000 0.00 0.00 0.00 3.09
3242 6593 2.205022 TGGCTGCTCAGTTTGCTAAT 57.795 45.000 0.00 0.00 0.00 1.73
3243 6594 2.517959 TGGCTGCTCAGTTTGCTAATT 58.482 42.857 0.00 0.00 0.00 1.40
3244 6595 2.229543 TGGCTGCTCAGTTTGCTAATTG 59.770 45.455 0.00 0.00 0.00 2.32
3245 6596 2.257034 GCTGCTCAGTTTGCTAATTGC 58.743 47.619 0.00 0.00 43.25 3.56
3246 6597 2.094854 GCTGCTCAGTTTGCTAATTGCT 60.095 45.455 0.00 0.00 43.37 3.91
3247 6598 3.127548 GCTGCTCAGTTTGCTAATTGCTA 59.872 43.478 0.00 0.00 43.37 3.49
3288 6639 3.265791 GTGAAGCTAACCATGTCAGAGG 58.734 50.000 0.00 0.00 0.00 3.69
3293 6644 0.175760 TAACCATGTCAGAGGAGCGC 59.824 55.000 0.00 0.00 0.00 5.92
3323 6702 7.985589 TCTTAGGTTTTCCATAGTTCTTCCTT 58.014 34.615 0.00 0.00 43.73 3.36
3324 6703 8.101419 TCTTAGGTTTTCCATAGTTCTTCCTTC 58.899 37.037 0.00 0.00 43.73 3.46
3325 6704 5.571285 AGGTTTTCCATAGTTCTTCCTTCC 58.429 41.667 0.00 0.00 43.73 3.46
3326 6705 5.313506 AGGTTTTCCATAGTTCTTCCTTCCT 59.686 40.000 0.00 0.00 43.73 3.36
3376 6755 6.427853 TGAGATGAAGGTTGTTGTACTCATTG 59.572 38.462 0.00 0.00 0.00 2.82
3389 6768 3.911661 ACTCATTGACAGAAGCTTTGC 57.088 42.857 0.00 0.00 0.00 3.68
3447 6828 3.117888 AGTGTCTTGTGATGTCCCTGTTT 60.118 43.478 0.00 0.00 0.00 2.83
3464 6845 0.109086 TTTTTGCACACCACACCACG 60.109 50.000 0.00 0.00 0.00 4.94
3497 6878 5.046807 AGGGAATGATTTCAGCTTTTTCCTG 60.047 40.000 8.86 0.00 33.05 3.86
3499 6880 5.047092 GGAATGATTTCAGCTTTTTCCTGGA 60.047 40.000 0.00 0.00 30.98 3.86
3500 6881 5.656213 ATGATTTCAGCTTTTTCCTGGAG 57.344 39.130 0.00 0.00 0.00 3.86
3501 6882 4.728772 TGATTTCAGCTTTTTCCTGGAGA 58.271 39.130 0.00 0.00 0.00 3.71
3502 6883 5.327732 TGATTTCAGCTTTTTCCTGGAGAT 58.672 37.500 0.00 0.00 0.00 2.75
3503 6884 5.184479 TGATTTCAGCTTTTTCCTGGAGATG 59.816 40.000 0.00 0.00 0.00 2.90
3504 6885 3.795688 TCAGCTTTTTCCTGGAGATGT 57.204 42.857 0.00 0.00 0.00 3.06
3837 7238 4.406649 CCTTTCCCTTGGCATTAATGACAT 59.593 41.667 24.42 0.00 46.90 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.519377 TTCGTCTCGGTTGTTCACAT 57.481 45.000 0.00 0.00 0.00 3.21
1 2 2.159212 TCTTTCGTCTCGGTTGTTCACA 60.159 45.455 0.00 0.00 0.00 3.58
2 3 2.466846 TCTTTCGTCTCGGTTGTTCAC 58.533 47.619 0.00 0.00 0.00 3.18
3 4 2.359848 TCTCTTTCGTCTCGGTTGTTCA 59.640 45.455 0.00 0.00 0.00 3.18
4 5 3.009301 TCTCTTTCGTCTCGGTTGTTC 57.991 47.619 0.00 0.00 0.00 3.18
5 6 3.067742 TCTTCTCTTTCGTCTCGGTTGTT 59.932 43.478 0.00 0.00 0.00 2.83
6 7 2.621998 TCTTCTCTTTCGTCTCGGTTGT 59.378 45.455 0.00 0.00 0.00 3.32
7 8 3.238441 CTCTTCTCTTTCGTCTCGGTTG 58.762 50.000 0.00 0.00 0.00 3.77
8 9 2.885894 ACTCTTCTCTTTCGTCTCGGTT 59.114 45.455 0.00 0.00 0.00 4.44
9 10 2.485038 GACTCTTCTCTTTCGTCTCGGT 59.515 50.000 0.00 0.00 0.00 4.69
10 11 2.745281 AGACTCTTCTCTTTCGTCTCGG 59.255 50.000 0.00 0.00 29.55 4.63
11 12 3.998522 GAGACTCTTCTCTTTCGTCTCG 58.001 50.000 0.00 0.00 44.54 4.04
12 13 4.007659 AGGAGACTCTTCTCTTTCGTCTC 58.992 47.826 1.74 8.73 46.80 3.36
13 14 4.028993 AGGAGACTCTTCTCTTTCGTCT 57.971 45.455 1.74 0.00 46.80 4.18
14 15 4.022676 ACAAGGAGACTCTTCTCTTTCGTC 60.023 45.833 1.74 0.00 42.96 4.20
15 16 3.892588 ACAAGGAGACTCTTCTCTTTCGT 59.107 43.478 1.74 0.49 42.96 3.85
16 17 4.481463 GACAAGGAGACTCTTCTCTTTCG 58.519 47.826 1.74 0.00 42.96 3.46
17 18 4.282195 TGGACAAGGAGACTCTTCTCTTTC 59.718 45.833 1.74 0.00 42.96 2.62
18 19 4.039852 GTGGACAAGGAGACTCTTCTCTTT 59.960 45.833 1.74 0.00 46.39 2.52
19 20 3.576550 GTGGACAAGGAGACTCTTCTCTT 59.423 47.826 1.74 0.00 46.80 2.85
20 21 3.161866 GTGGACAAGGAGACTCTTCTCT 58.838 50.000 1.74 0.00 46.80 3.10
21 22 3.161866 AGTGGACAAGGAGACTCTTCTC 58.838 50.000 1.74 0.00 46.90 2.87
22 23 3.161866 GAGTGGACAAGGAGACTCTTCT 58.838 50.000 1.74 0.00 42.68 2.85
23 24 2.232696 GGAGTGGACAAGGAGACTCTTC 59.767 54.545 1.74 0.00 42.68 2.87
24 25 2.252714 GGAGTGGACAAGGAGACTCTT 58.747 52.381 1.74 0.00 42.68 2.85
25 26 1.551329 GGGAGTGGACAAGGAGACTCT 60.551 57.143 1.74 0.00 42.68 3.24
26 27 0.899019 GGGAGTGGACAAGGAGACTC 59.101 60.000 0.00 0.00 42.68 3.36
63 64 4.125239 GGGTACTCCACTCGGGTT 57.875 61.111 0.00 0.00 38.11 4.11
68 69 1.886886 TTTTTGCGGGTACTCCACTC 58.113 50.000 0.00 0.00 34.36 3.51
90 91 3.899980 ACTACTACTCCACTCGGGTTTTT 59.100 43.478 0.00 0.00 38.11 1.94
91 92 3.504375 ACTACTACTCCACTCGGGTTTT 58.496 45.455 0.00 0.00 38.11 2.43
92 93 3.166560 ACTACTACTCCACTCGGGTTT 57.833 47.619 0.00 0.00 38.11 3.27
93 94 2.895242 ACTACTACTCCACTCGGGTT 57.105 50.000 0.00 0.00 38.11 4.11
94 95 3.110705 TCTACTACTACTCCACTCGGGT 58.889 50.000 0.00 0.00 38.11 5.28
95 96 3.134442 ACTCTACTACTACTCCACTCGGG 59.866 52.174 0.00 0.00 38.37 5.14
96 97 4.405116 ACTCTACTACTACTCCACTCGG 57.595 50.000 0.00 0.00 0.00 4.63
97 98 6.389830 TCTACTCTACTACTACTCCACTCG 57.610 45.833 0.00 0.00 0.00 4.18
98 99 7.015487 TGGATCTACTCTACTACTACTCCACTC 59.985 44.444 0.00 0.00 0.00 3.51
99 100 6.845446 TGGATCTACTCTACTACTACTCCACT 59.155 42.308 0.00 0.00 0.00 4.00
100 101 7.065120 TGGATCTACTCTACTACTACTCCAC 57.935 44.000 0.00 0.00 0.00 4.02
101 102 7.567994 TCTTGGATCTACTCTACTACTACTCCA 59.432 40.741 0.00 0.00 0.00 3.86
102 103 7.965718 TCTTGGATCTACTCTACTACTACTCC 58.034 42.308 0.00 0.00 0.00 3.85
192 199 0.179086 GCTTTTGTTGGTGGTGGTGG 60.179 55.000 0.00 0.00 0.00 4.61
198 205 3.915437 ATTAGTCGCTTTTGTTGGTGG 57.085 42.857 0.00 0.00 0.00 4.61
201 208 7.566868 GCTGTTTAAATTAGTCGCTTTTGTTGG 60.567 37.037 0.00 0.00 0.00 3.77
268 345 1.190763 GTTCGTTCGTAAGCAAGCGAA 59.809 47.619 5.40 5.40 43.55 4.70
291 368 5.233988 CAATGCCTACTTGCCTAGAGTATC 58.766 45.833 0.00 0.00 0.00 2.24
293 370 3.388024 CCAATGCCTACTTGCCTAGAGTA 59.612 47.826 0.00 0.00 0.00 2.59
299 376 0.032813 ATGCCAATGCCTACTTGCCT 60.033 50.000 0.00 0.00 36.33 4.75
300 377 0.386838 GATGCCAATGCCTACTTGCC 59.613 55.000 0.00 0.00 36.33 4.52
301 378 1.336125 GAGATGCCAATGCCTACTTGC 59.664 52.381 0.00 0.00 36.33 4.01
302 379 1.952296 GGAGATGCCAATGCCTACTTG 59.048 52.381 0.00 0.00 36.33 3.16
303 380 1.133668 GGGAGATGCCAATGCCTACTT 60.134 52.381 0.00 0.00 38.95 2.24
305 382 0.183492 TGGGAGATGCCAATGCCTAC 59.817 55.000 0.00 0.00 38.95 3.18
306 383 0.925558 TTGGGAGATGCCAATGCCTA 59.074 50.000 1.14 0.00 38.95 3.93
329 3087 2.388232 GCACGAACCGGTCCATGAC 61.388 63.158 8.04 0.00 0.00 3.06
331 3089 1.745115 ATGCACGAACCGGTCCATG 60.745 57.895 8.04 7.63 0.00 3.66
337 3095 0.165944 GAGAAACATGCACGAACCGG 59.834 55.000 0.00 0.00 0.00 5.28
338 3096 0.165944 GGAGAAACATGCACGAACCG 59.834 55.000 0.00 0.00 0.00 4.44
339 3097 0.521735 GGGAGAAACATGCACGAACC 59.478 55.000 0.00 0.00 0.00 3.62
419 3177 1.143305 CTATCTATGCCGTGCAGTGC 58.857 55.000 8.58 8.58 43.65 4.40
422 3180 2.668556 CGTACCTATCTATGCCGTGCAG 60.669 54.545 4.90 0.00 43.65 4.41
440 3198 1.402968 GACGTTGGAGGCATCTACGTA 59.597 52.381 24.07 0.00 42.46 3.57
441 3199 0.172803 GACGTTGGAGGCATCTACGT 59.827 55.000 24.20 24.20 43.88 3.57
442 3200 0.527817 GGACGTTGGAGGCATCTACG 60.528 60.000 19.46 19.46 38.51 3.51
486 3251 2.509561 GTTTCGGAGGAGCTCGCC 60.510 66.667 7.83 10.80 0.00 5.54
487 3252 1.807573 CAGTTTCGGAGGAGCTCGC 60.808 63.158 7.83 1.84 0.00 5.03
488 3253 0.243907 TTCAGTTTCGGAGGAGCTCG 59.756 55.000 7.83 0.00 0.00 5.03
489 3254 2.070028 GTTTCAGTTTCGGAGGAGCTC 58.930 52.381 4.71 4.71 0.00 4.09
516 3291 4.025401 GTTGGACGCTTGCCGGTG 62.025 66.667 1.90 0.00 42.52 4.94
560 3335 3.188786 GACGGCGTCCATGTCAGC 61.189 66.667 28.72 0.73 32.91 4.26
561 3336 2.880879 CGACGGCGTCCATGTCAG 60.881 66.667 31.86 13.91 32.91 3.51
641 3416 2.734673 CGTTTGCTGCCGCTCTCTC 61.735 63.158 0.70 0.00 36.97 3.20
649 3424 0.660300 CTTTCCGTTCGTTTGCTGCC 60.660 55.000 0.00 0.00 0.00 4.85
747 3550 4.541482 TTACTAGCGGCGCGACGG 62.541 66.667 37.85 22.54 0.00 4.79
752 3555 1.003851 TTCACATTTACTAGCGGCGC 58.996 50.000 26.86 26.86 0.00 6.53
757 3560 2.096980 GCCCGGTTTCACATTTACTAGC 59.903 50.000 0.00 0.00 0.00 3.42
761 3564 0.169451 CGGCCCGGTTTCACATTTAC 59.831 55.000 0.00 0.00 0.00 2.01
963 3772 1.271840 TGTGGTCTCCCTGGTATGCC 61.272 60.000 0.00 0.00 0.00 4.40
964 3773 0.179000 CTGTGGTCTCCCTGGTATGC 59.821 60.000 0.00 0.00 0.00 3.14
965 3774 0.179000 GCTGTGGTCTCCCTGGTATG 59.821 60.000 0.00 0.00 0.00 2.39
966 3775 0.983378 GGCTGTGGTCTCCCTGGTAT 60.983 60.000 0.00 0.00 0.00 2.73
967 3776 1.612442 GGCTGTGGTCTCCCTGGTA 60.612 63.158 0.00 0.00 0.00 3.25
968 3777 2.930562 GGCTGTGGTCTCCCTGGT 60.931 66.667 0.00 0.00 0.00 4.00
969 3778 3.721706 GGGCTGTGGTCTCCCTGG 61.722 72.222 0.00 0.00 37.08 4.45
970 3779 2.930019 TGGGCTGTGGTCTCCCTG 60.930 66.667 0.00 0.00 40.69 4.45
971 3780 2.930562 GTGGGCTGTGGTCTCCCT 60.931 66.667 0.00 0.00 40.69 4.20
972 3781 4.394712 CGTGGGCTGTGGTCTCCC 62.395 72.222 0.00 0.00 40.47 4.30
1422 4289 0.758123 GGCATGAGGAGGAAGGAGAG 59.242 60.000 0.00 0.00 0.00 3.20
1453 4327 5.365314 ACCAAATCTAGAGCTAGGGAAAGAG 59.635 44.000 0.00 0.00 34.06 2.85
1533 4434 2.937469 ATCAAGAGAGCTCAGACACG 57.063 50.000 17.77 0.00 0.00 4.49
1541 4442 5.480642 TGAACTGAAGAATCAAGAGAGCT 57.519 39.130 0.00 0.00 34.49 4.09
1559 4460 2.991250 ACAGTATGCAGGACCATGAAC 58.009 47.619 0.00 0.00 42.53 3.18
1587 4488 3.119459 ACGGTGAGCATGAGTAAGTACTG 60.119 47.826 0.00 0.00 36.50 2.74
1592 4496 1.002366 GCACGGTGAGCATGAGTAAG 58.998 55.000 13.29 0.00 0.00 2.34
1625 4529 4.054671 GACATCAGCGAAGAAGATAAGGG 58.945 47.826 0.00 0.00 0.00 3.95
1667 4571 3.734463 TCGTAAGGAACAAACAGCATCA 58.266 40.909 0.00 0.00 38.47 3.07
1734 4638 6.030849 TGTTTACTGGACGTTTGTGATTTTG 58.969 36.000 0.00 0.00 0.00 2.44
1773 4681 1.601903 TGTGTAGGCAAAAAGCTCGTG 59.398 47.619 0.00 0.00 44.79 4.35
1786 4694 1.096416 GACGAGGTCTCCTGTGTAGG 58.904 60.000 0.00 0.00 46.06 3.18
1787 4695 0.727970 CGACGAGGTCTCCTGTGTAG 59.272 60.000 0.00 0.00 31.76 2.74
1986 5291 0.693430 TCTCAGGAGCCATCTGCCAT 60.693 55.000 0.00 0.00 42.71 4.40
2184 5491 3.476185 TCCATGGCTGTATGGGCACAG 62.476 57.143 6.96 0.00 46.16 3.66
2207 5514 7.759489 ACATTTGAGTAAAAGTGCCAAGATA 57.241 32.000 0.00 0.00 0.00 1.98
2234 5541 5.013599 AGGCCCTATAGAAAGACATTGATCC 59.986 44.000 0.00 0.00 0.00 3.36
2361 5690 2.286523 CCGTGCCTTGAGGGTCTCT 61.287 63.158 0.00 0.00 37.43 3.10
2394 5723 2.521105 TGACATGCCTGATGATCTCG 57.479 50.000 0.00 0.00 35.80 4.04
2472 5801 1.263217 GTTGTTGACTGAATCCGCGTT 59.737 47.619 4.92 0.00 0.00 4.84
2780 6109 2.046217 GGGGAGGACCGAACTTGC 60.046 66.667 0.00 0.00 41.60 4.01
2863 6192 4.799564 TTTGTGATTTTCAGGTATGGGC 57.200 40.909 0.00 0.00 0.00 5.36
2880 6209 9.199982 CAATGAAAAGAAGCAAGTATGATTTGT 57.800 29.630 0.00 0.00 34.77 2.83
2884 6213 6.927416 TGCAATGAAAAGAAGCAAGTATGAT 58.073 32.000 0.00 0.00 31.42 2.45
2886 6215 6.643770 AGTTGCAATGAAAAGAAGCAAGTATG 59.356 34.615 0.59 0.00 44.39 2.39
2946 6291 6.437162 TGGAATTTCCAAAATCGAAATCCTCT 59.563 34.615 15.83 0.00 45.00 3.69
2948 6293 6.603940 TGGAATTTCCAAAATCGAAATCCT 57.396 33.333 15.83 0.00 45.00 3.24
2989 6334 1.101331 CATGCTGCTTCCTTCCTTCC 58.899 55.000 0.00 0.00 0.00 3.46
2990 6335 2.015587 CTCATGCTGCTTCCTTCCTTC 58.984 52.381 0.00 0.00 0.00 3.46
2991 6336 1.340795 CCTCATGCTGCTTCCTTCCTT 60.341 52.381 0.00 0.00 0.00 3.36
2992 6337 0.255318 CCTCATGCTGCTTCCTTCCT 59.745 55.000 0.00 0.00 0.00 3.36
3240 6591 3.368248 ACCATCACCAAGCATAGCAATT 58.632 40.909 0.00 0.00 0.00 2.32
3241 6592 3.022557 ACCATCACCAAGCATAGCAAT 57.977 42.857 0.00 0.00 0.00 3.56
3242 6593 2.512692 ACCATCACCAAGCATAGCAA 57.487 45.000 0.00 0.00 0.00 3.91
3243 6594 2.368439 GAACCATCACCAAGCATAGCA 58.632 47.619 0.00 0.00 0.00 3.49
3244 6595 1.678101 GGAACCATCACCAAGCATAGC 59.322 52.381 0.00 0.00 0.00 2.97
3245 6596 2.947652 CAGGAACCATCACCAAGCATAG 59.052 50.000 0.00 0.00 0.00 2.23
3246 6597 2.357050 CCAGGAACCATCACCAAGCATA 60.357 50.000 0.00 0.00 0.00 3.14
3247 6598 1.617804 CCAGGAACCATCACCAAGCAT 60.618 52.381 0.00 0.00 0.00 3.79
3302 6653 5.313506 AGGAAGGAAGAACTATGGAAAACCT 59.686 40.000 0.00 0.00 0.00 3.50
3303 6654 5.571285 AGGAAGGAAGAACTATGGAAAACC 58.429 41.667 0.00 0.00 0.00 3.27
3323 6702 5.798125 AATAAGAGATGAGATGCGAAGGA 57.202 39.130 0.00 0.00 0.00 3.36
3324 6703 6.857777 AAAATAAGAGATGAGATGCGAAGG 57.142 37.500 0.00 0.00 0.00 3.46
3325 6704 7.226325 AGGAAAAATAAGAGATGAGATGCGAAG 59.774 37.037 0.00 0.00 0.00 3.79
3326 6705 7.011763 CAGGAAAAATAAGAGATGAGATGCGAA 59.988 37.037 0.00 0.00 0.00 4.70
3376 6755 3.067320 AGGAAACAAGCAAAGCTTCTGTC 59.933 43.478 0.00 0.00 46.77 3.51
3389 6768 8.143835 AGATGTTTTGGATTACAAGGAAACAAG 58.856 33.333 2.35 0.00 39.43 3.16
3447 6828 3.057547 GCGTGGTGTGGTGTGCAAA 62.058 57.895 0.00 0.00 0.00 3.68
3470 6851 2.744352 AGCTGAAATCATTCCCTCCC 57.256 50.000 0.00 0.00 34.49 4.30
3471 6852 5.411831 AAAAAGCTGAAATCATTCCCTCC 57.588 39.130 0.00 0.00 34.49 4.30
3472 6853 5.186603 AGGAAAAAGCTGAAATCATTCCCTC 59.813 40.000 8.43 0.00 36.38 4.30
3473 6854 5.046807 CAGGAAAAAGCTGAAATCATTCCCT 60.047 40.000 8.43 0.00 36.38 4.20
3497 6878 2.083774 TGATGCCGTTCAAACATCTCC 58.916 47.619 0.00 0.00 40.66 3.71
3499 6880 3.507233 ACATTGATGCCGTTCAAACATCT 59.493 39.130 0.00 0.00 40.66 2.90
3500 6881 3.609373 CACATTGATGCCGTTCAAACATC 59.391 43.478 0.00 0.00 38.98 3.06
3501 6882 3.577667 CACATTGATGCCGTTCAAACAT 58.422 40.909 0.00 0.00 38.98 2.71
3502 6883 2.861750 GCACATTGATGCCGTTCAAACA 60.862 45.455 0.00 0.00 38.98 2.83
3503 6884 1.720852 GCACATTGATGCCGTTCAAAC 59.279 47.619 0.00 0.00 38.98 2.93
3504 6885 2.063156 GCACATTGATGCCGTTCAAA 57.937 45.000 0.00 0.00 38.98 2.69
3565 6961 1.043816 ATCATCACTACTCCCGCCAG 58.956 55.000 0.00 0.00 0.00 4.85
3569 6965 6.422100 CAGTAAATGAATCATCACTACTCCCG 59.578 42.308 9.28 0.00 38.69 5.14
3690 7087 8.069356 TCAGGAGTACAGATTATAAAAGGGGTA 58.931 37.037 0.00 0.00 0.00 3.69
3746 7143 3.643159 GGAGCACACCGAAAGAAAAAT 57.357 42.857 0.00 0.00 0.00 1.82
3767 7164 2.231478 TCGGTCTTCACTCTTCATGGAC 59.769 50.000 0.00 0.00 0.00 4.02
3771 7168 1.205893 GCCTCGGTCTTCACTCTTCAT 59.794 52.381 0.00 0.00 0.00 2.57
3837 7238 4.887071 ACAACAAGAAAGGAGTGCAATACA 59.113 37.500 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.