Multiple sequence alignment - TraesCS7B01G056100

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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 TraesCS7B01G056100 chr7B 100.000 3617 0 0 1 3617 59093983 59097599 0.000000e+00 6680
1 TraesCS7B01G056100 chr7D 93.098 1985 97 20 391 2360 101762374 101760415 0.000000e+00 2870
2 TraesCS7B01G056100 chr7D 97.576 330 7 1 2370 2699 101759630 101759302 6.780000e-157 564
3 TraesCS7B01G056100 chr7D 89.691 388 23 8 1 375 101772204 101771821 2.530000e-131 479
4 TraesCS7B01G056100 chr7A 86.375 1644 156 40 2 1585 105624889 105626524 0.000000e+00 1733
5 TraesCS7B01G056100 chr7A 88.571 245 23 3 2694 2934 39140751 39140994 3.530000e-75 292
6 TraesCS7B01G056100 chr5A 91.292 689 48 2 2941 3617 3238350 3239038 0.000000e+00 929
7 TraesCS7B01G056100 chr5A 88.389 689 67 9 2941 3617 311537239 311536552 0.000000e+00 817
8 TraesCS7B01G056100 chr5A 92.116 241 18 1 2696 2936 3238073 3238312 4.470000e-89 339
9 TraesCS7B01G056100 chr4B 91.292 689 48 2 2941 3617 441667746 441668434 0.000000e+00 929
10 TraesCS7B01G056100 chr4B 93.776 241 13 2 2697 2936 441667469 441667708 9.550000e-96 361
11 TraesCS7B01G056100 chr5B 90.407 688 54 2 2942 3617 325806067 325806754 0.000000e+00 894
12 TraesCS7B01G056100 chr5B 89.099 688 63 2 2942 3617 325744667 325745354 0.000000e+00 845
13 TraesCS7B01G056100 chr5B 93.421 228 14 1 2710 2936 325805801 325806028 1.610000e-88 337
14 TraesCS7B01G056100 chr5B 79.467 375 60 12 3140 3503 546865381 546865013 2.160000e-62 250
15 TraesCS7B01G056100 chr3A 87.988 691 69 3 2941 3617 705315672 705314982 0.000000e+00 804
16 TraesCS7B01G056100 chr2B 84.682 692 91 6 2941 3617 649976651 649977342 0.000000e+00 676
17 TraesCS7B01G056100 chr1B 84.746 413 48 3 2942 3342 83626935 83626526 2.020000e-107 399
18 TraesCS7B01G056100 chr1B 88.333 240 24 4 2697 2933 657422774 657422536 5.910000e-73 285
19 TraesCS7B01G056100 chr3D 89.627 241 21 3 2697 2934 84673549 84673788 1.630000e-78 303
20 TraesCS7B01G056100 chr2D 89.787 235 20 3 2703 2934 140911222 140911455 7.590000e-77 298
21 TraesCS7B01G056100 chr3B 88.571 245 23 4 2694 2934 651531955 651531712 3.530000e-75 292
22 TraesCS7B01G056100 chr3B 82.258 248 39 5 3147 3393 23901122 23900879 3.660000e-50 209
23 TraesCS7B01G056100 chrUn 88.477 243 22 4 2696 2934 76049084 76048844 4.570000e-74 289
24 TraesCS7B01G056100 chr6B 80.447 179 17 9 2941 3104 142171196 142171371 1.760000e-23 121


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 TraesCS7B01G056100 chr7B 59093983 59097599 3616 False 6680.0 6680 100.000 1 3617 1 chr7B.!!$F1 3616
1 TraesCS7B01G056100 chr7D 101759302 101762374 3072 True 1717.0 2870 95.337 391 2699 2 chr7D.!!$R2 2308
2 TraesCS7B01G056100 chr7A 105624889 105626524 1635 False 1733.0 1733 86.375 2 1585 1 chr7A.!!$F2 1583
3 TraesCS7B01G056100 chr5A 311536552 311537239 687 True 817.0 817 88.389 2941 3617 1 chr5A.!!$R1 676
4 TraesCS7B01G056100 chr5A 3238073 3239038 965 False 634.0 929 91.704 2696 3617 2 chr5A.!!$F1 921
5 TraesCS7B01G056100 chr4B 441667469 441668434 965 False 645.0 929 92.534 2697 3617 2 chr4B.!!$F1 920
6 TraesCS7B01G056100 chr5B 325744667 325745354 687 False 845.0 845 89.099 2942 3617 1 chr5B.!!$F1 675
7 TraesCS7B01G056100 chr5B 325805801 325806754 953 False 615.5 894 91.914 2710 3617 2 chr5B.!!$F2 907
8 TraesCS7B01G056100 chr3A 705314982 705315672 690 True 804.0 804 87.988 2941 3617 1 chr3A.!!$R1 676
9 TraesCS7B01G056100 chr2B 649976651 649977342 691 False 676.0 676 84.682 2941 3617 1 chr2B.!!$F1 676

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
362 369 0.253327 CCTACCTCAGCCAAAGGGTC 59.747 60.000 2.10 0.0 38.29 4.46 F
363 370 0.984230 CTACCTCAGCCAAAGGGTCA 59.016 55.000 2.10 0.0 38.29 4.02 F
1023 1065 1.131883 GCAACACAGAAGCTAGCCATG 59.868 52.381 12.13 10.4 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 2157 1.239347 GGAGCTTCTGGAAAAACGCT 58.761 50.0 0.0 0.0 0.00 5.07 R
2312 2379 2.417243 GCCTAAACACATGGATTGGTGC 60.417 50.0 0.0 0.0 38.57 5.01 R
2813 3654 0.466543 TGTGGCTAGGTTGTTCGTGT 59.533 50.0 0.0 0.0 0.00 4.49 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
246 252 5.849357 AACGGAAAAGAAACAAAACCAAC 57.151 34.783 0.00 0.00 0.00 3.77
353 360 0.960861 GTGCCAAACCCTACCTCAGC 60.961 60.000 0.00 0.00 0.00 4.26
362 369 0.253327 CCTACCTCAGCCAAAGGGTC 59.747 60.000 2.10 0.00 38.29 4.46
363 370 0.984230 CTACCTCAGCCAAAGGGTCA 59.016 55.000 2.10 0.00 38.29 4.02
364 371 1.561542 CTACCTCAGCCAAAGGGTCAT 59.438 52.381 2.10 0.00 38.29 3.06
365 372 1.668826 ACCTCAGCCAAAGGGTCATA 58.331 50.000 2.10 0.00 38.29 2.15
366 373 2.208872 ACCTCAGCCAAAGGGTCATAT 58.791 47.619 2.10 0.00 38.29 1.78
368 375 2.441001 CCTCAGCCAAAGGGTCATATCT 59.559 50.000 0.00 0.00 36.17 1.98
461 469 4.025145 GTCTAGTCGTTTCAAACCTTGGTG 60.025 45.833 0.00 0.00 0.00 4.17
541 549 3.427161 GCCACTAGCATTTTGGATGTC 57.573 47.619 0.60 0.00 42.97 3.06
568 576 9.615295 TCTGCTTATTTTACGGTAACAAATTTC 57.385 29.630 0.00 0.00 0.00 2.17
581 589 7.410728 CGGTAACAAATTTCATCTTTGCATCAC 60.411 37.037 0.00 0.00 37.15 3.06
758 777 9.617975 CTTCTTCTTAATTTGAATGACCAGTTC 57.382 33.333 0.00 0.00 0.00 3.01
760 779 6.834168 TCTTAATTTGAATGACCAGTTCCC 57.166 37.500 0.00 0.00 0.00 3.97
782 801 4.322801 CCAAACCGAGGTCAAGTCTTCTAT 60.323 45.833 0.00 0.00 0.00 1.98
825 844 1.478471 TTTGAGCAAGCAGCCCAAGTA 60.478 47.619 0.00 0.00 42.18 2.24
846 865 9.827411 CAAGTAGAGGCTTATAAAAAGTGTTTC 57.173 33.333 0.00 0.00 0.00 2.78
918 937 3.365465 CGATCGATATCAAAGCTCGAGGT 60.365 47.826 12.24 12.24 43.78 3.85
919 938 3.627732 TCGATATCAAAGCTCGAGGTC 57.372 47.619 18.90 2.24 36.57 3.85
920 939 2.293677 TCGATATCAAAGCTCGAGGTCC 59.706 50.000 18.90 0.00 36.57 4.46
921 940 2.294791 CGATATCAAAGCTCGAGGTCCT 59.705 50.000 18.90 5.43 34.41 3.85
956 975 7.041098 ACCTTAAGTAAATCTGCAAAGACACAG 60.041 37.037 0.97 0.00 35.15 3.66
960 979 4.825546 AAATCTGCAAAGACACAGTCAG 57.174 40.909 0.00 0.00 34.60 3.51
961 980 2.988010 TCTGCAAAGACACAGTCAGT 57.012 45.000 0.00 0.00 34.60 3.41
965 984 2.093500 TGCAAAGACACAGTCAGTCAGT 60.093 45.455 0.00 0.00 38.46 3.41
972 991 2.233676 ACACAGTCAGTCAGTCACACAA 59.766 45.455 0.00 0.00 0.00 3.33
977 996 3.195610 AGTCAGTCAGTCACACAAGTCAA 59.804 43.478 0.00 0.00 0.00 3.18
979 998 4.572389 GTCAGTCAGTCACACAAGTCAATT 59.428 41.667 0.00 0.00 0.00 2.32
981 1000 5.753438 TCAGTCAGTCACACAAGTCAATTAC 59.247 40.000 0.00 0.00 0.00 1.89
982 1001 4.745125 AGTCAGTCACACAAGTCAATTACG 59.255 41.667 0.00 0.00 0.00 3.18
983 1002 4.743151 GTCAGTCACACAAGTCAATTACGA 59.257 41.667 0.00 0.00 0.00 3.43
984 1003 5.405571 GTCAGTCACACAAGTCAATTACGAT 59.594 40.000 0.00 0.00 0.00 3.73
994 1015 8.869897 CACAAGTCAATTACGATATAGTGTGTT 58.130 33.333 0.00 0.00 0.00 3.32
1023 1065 1.131883 GCAACACAGAAGCTAGCCATG 59.868 52.381 12.13 10.40 0.00 3.66
1200 1242 4.162690 GGCTGTGGGCTCCGTAGG 62.163 72.222 0.00 0.00 44.29 3.18
1236 1278 4.446413 GACGACGAACCCCGCCAT 62.446 66.667 0.00 0.00 43.32 4.40
1239 1281 2.189521 GACGAACCCCGCCATCAT 59.810 61.111 0.00 0.00 43.32 2.45
1359 1407 4.736896 GTCGTGTGGCCGGACTCC 62.737 72.222 9.82 0.00 0.00 3.85
1374 1422 1.194781 ACTCCACCAAGATCGGCTGT 61.195 55.000 0.00 0.00 0.00 4.40
1596 1661 4.816385 AGACATATGCTTCCATGTAAACCG 59.184 41.667 1.58 0.00 35.55 4.44
1675 1740 7.359595 TGTACTAAAGCTGCAACAAAGTAATG 58.640 34.615 1.02 0.00 0.00 1.90
1692 1757 1.705873 ATGTGGATCGGGGAGAGTAC 58.294 55.000 0.00 0.00 0.00 2.73
1698 1763 3.521937 TGGATCGGGGAGAGTACAAAAAT 59.478 43.478 0.00 0.00 0.00 1.82
1704 1769 5.941647 TCGGGGAGAGTACAAAAATTAAAGG 59.058 40.000 0.00 0.00 0.00 3.11
1705 1770 5.941647 CGGGGAGAGTACAAAAATTAAAGGA 59.058 40.000 0.00 0.00 0.00 3.36
1706 1771 6.431852 CGGGGAGAGTACAAAAATTAAAGGAA 59.568 38.462 0.00 0.00 0.00 3.36
1781 1846 4.354155 TGAGAAAACCTCACCGCG 57.646 55.556 0.00 0.00 46.38 6.46
1847 1912 6.563222 TGGTTCAGTTTATAAGGAAAACCG 57.437 37.500 13.03 0.00 38.16 4.44
1882 1947 6.663523 ACCCTAACATTTTCAGTTAATCAGGG 59.336 38.462 9.12 9.12 38.34 4.45
1884 1949 7.561356 CCCTAACATTTTCAGTTAATCAGGGAT 59.439 37.037 5.97 0.00 36.24 3.85
1889 1954 6.995511 TTTTCAGTTAATCAGGGATAACCG 57.004 37.500 0.00 0.00 46.96 4.44
1900 1965 3.064820 CAGGGATAACCGAATGAAAACCG 59.935 47.826 0.00 0.00 46.96 4.44
1936 2001 9.919348 TGTCTAACTTTAACAATACACGTTTTC 57.081 29.630 0.00 0.00 0.00 2.29
2179 2246 4.705110 TGCCATGGAAGCTAGCTTTATA 57.295 40.909 29.84 19.01 36.26 0.98
2226 2293 8.253113 ACATCCAAAATAAGGCTATTGTCAAAG 58.747 33.333 0.00 0.00 0.00 2.77
2312 2379 8.848474 ATAACCCCATTGTATAGAAGAAATCG 57.152 34.615 0.00 0.00 0.00 3.34
2335 2402 4.269183 CACCAATCCATGTGTTTAGGCTA 58.731 43.478 0.00 0.00 0.00 3.93
2372 3037 5.970317 AACATATGTATCACATGCCCATG 57.030 39.130 9.21 6.71 39.53 3.66
2421 3262 8.633075 TTTTCAAGTTCAAGAAGCACATAAAG 57.367 30.769 0.00 0.00 0.00 1.85
2480 3321 0.597118 TGTGCGTTTTCTTGGCATGC 60.597 50.000 9.90 9.90 39.14 4.06
2521 3362 4.798387 GTGCTAACAAATTCCCTTATTGCG 59.202 41.667 0.00 0.00 0.00 4.85
2540 3381 2.848302 GCGCTTTTGATACAGTGAATGC 59.152 45.455 0.00 0.00 0.00 3.56
2821 3662 4.164087 ACGGGGCACACACGAACA 62.164 61.111 0.00 0.00 0.00 3.18
2826 3667 0.533308 GGGCACACACGAACAACCTA 60.533 55.000 0.00 0.00 0.00 3.08
2837 3678 1.944709 GAACAACCTAGCCACAAACGT 59.055 47.619 0.00 0.00 0.00 3.99
2851 3692 2.678836 ACAAACGTCAAACAATCGACCA 59.321 40.909 0.00 0.00 0.00 4.02
2858 3700 2.356382 TCAAACAATCGACCAAAGCGTT 59.644 40.909 0.00 0.00 0.00 4.84
2936 3778 0.320697 GCACCGACCTAGTCCAAAGT 59.679 55.000 0.00 0.00 0.00 2.66
2937 3779 1.270678 GCACCGACCTAGTCCAAAGTT 60.271 52.381 0.00 0.00 0.00 2.66
2938 3780 2.685100 CACCGACCTAGTCCAAAGTTC 58.315 52.381 0.00 0.00 0.00 3.01
2939 3781 2.036733 CACCGACCTAGTCCAAAGTTCA 59.963 50.000 0.00 0.00 0.00 3.18
2993 3868 1.377366 CCGCAGCTCCGACTTCTCTA 61.377 60.000 0.00 0.00 0.00 2.43
3010 3885 5.164620 TCTCTATCACAGCATGAAACCAA 57.835 39.130 0.00 0.00 41.93 3.67
3126 4013 4.873129 CCACATCGCCGGACGGAG 62.873 72.222 15.99 11.97 43.89 4.63
3160 4047 4.996434 GCTGTGCACGTCCAGCCT 62.996 66.667 13.13 0.00 46.55 4.58
3207 4094 4.675976 TCTTCAAGACGACACCCTAAAA 57.324 40.909 0.00 0.00 0.00 1.52
3238 4125 4.717629 CTGAAGACGACGCCGCCA 62.718 66.667 0.00 0.00 39.95 5.69
3269 4156 2.165167 CAGCAGGATCTTGGCTTTCAA 58.835 47.619 6.99 0.00 35.27 2.69
3313 4200 2.515071 GGATGCGCAGATCTCCCCT 61.515 63.158 18.32 0.00 0.00 4.79
3314 4201 1.005156 GATGCGCAGATCTCCCCTC 60.005 63.158 18.32 0.29 0.00 4.30
3414 4301 0.107831 GTAGCACAACCACCACTCCA 59.892 55.000 0.00 0.00 0.00 3.86
3421 4308 1.978455 AACCACCACTCCAACGCAGA 61.978 55.000 0.00 0.00 0.00 4.26
3528 4416 2.034558 ACAAGCCAGAACAAACCAATCG 59.965 45.455 0.00 0.00 0.00 3.34
3560 4448 3.550431 ACCCACACTCGCTGCACT 61.550 61.111 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 6.349243 TCATTGTTTGCATTTCATTCTCCT 57.651 33.333 0.00 0.00 0.00 3.69
66 67 5.467902 TTCTTGTGCTTTTCATTGTTTGC 57.532 34.783 0.00 0.00 0.00 3.68
69 70 7.614124 ACATTTTCTTGTGCTTTTCATTGTT 57.386 28.000 0.00 0.00 0.00 2.83
219 225 6.073167 TGGTTTTGTTTCTTTTCCGTTTTTCC 60.073 34.615 0.00 0.00 0.00 3.13
221 227 6.862711 TGGTTTTGTTTCTTTTCCGTTTTT 57.137 29.167 0.00 0.00 0.00 1.94
226 232 5.847670 TTGTTGGTTTTGTTTCTTTTCCG 57.152 34.783 0.00 0.00 0.00 4.30
228 234 9.198837 TCTACTTTGTTGGTTTTGTTTCTTTTC 57.801 29.630 0.00 0.00 0.00 2.29
237 243 9.203421 ACTTTTTCTTCTACTTTGTTGGTTTTG 57.797 29.630 0.00 0.00 0.00 2.44
269 276 0.468585 GGGAAGGGTTTGTTCGGGTT 60.469 55.000 0.00 0.00 0.00 4.11
270 277 1.152138 GGGAAGGGTTTGTTCGGGT 59.848 57.895 0.00 0.00 0.00 5.28
274 281 1.817357 CGGTAGGGAAGGGTTTGTTC 58.183 55.000 0.00 0.00 0.00 3.18
320 327 1.698506 TGGCACCGTTTTCTCCATTT 58.301 45.000 0.00 0.00 0.00 2.32
325 332 3.562639 GGTTTGGCACCGTTTTCTC 57.437 52.632 0.00 0.00 35.12 2.87
333 340 0.322546 CTGAGGTAGGGTTTGGCACC 60.323 60.000 0.00 0.00 46.46 5.01
347 354 2.441001 AGATATGACCCTTTGGCTGAGG 59.559 50.000 0.42 0.42 33.59 3.86
353 360 5.278463 CGCCAAATAAGATATGACCCTTTGG 60.278 44.000 6.76 6.76 42.44 3.28
362 369 7.182761 GCTGTATAAGCGCCAAATAAGATATG 58.817 38.462 2.29 0.00 43.45 1.78
363 370 7.308782 GCTGTATAAGCGCCAAATAAGATAT 57.691 36.000 2.29 0.00 43.45 1.63
364 371 6.721571 GCTGTATAAGCGCCAAATAAGATA 57.278 37.500 2.29 0.00 43.45 1.98
365 372 5.613358 GCTGTATAAGCGCCAAATAAGAT 57.387 39.130 2.29 0.00 43.45 2.40
430 437 2.485426 TGAAACGACTAGACTACCCACG 59.515 50.000 0.00 0.00 0.00 4.94
461 469 3.730715 GCAATACTTTGTCTTGCACACAC 59.269 43.478 13.39 0.00 42.50 3.82
541 549 9.620660 AAATTTGTTACCGTAAAATAAGCAGAG 57.379 29.630 0.00 0.00 0.00 3.35
568 576 1.004610 CGCTACCGTGATGCAAAGATG 60.005 52.381 0.00 0.00 0.00 2.90
581 589 1.065928 CTAGGGTCAAGCGCTACCG 59.934 63.158 20.39 8.92 40.99 4.02
669 685 2.041596 GGGTACACTAGGCCCCCA 59.958 66.667 0.00 0.00 36.46 4.96
758 777 0.396811 AGACTTGACCTCGGTTTGGG 59.603 55.000 0.00 0.00 0.00 4.12
760 779 3.113260 AGAAGACTTGACCTCGGTTTG 57.887 47.619 0.00 0.00 0.00 2.93
825 844 7.333672 CGTAGGAAACACTTTTTATAAGCCTCT 59.666 37.037 0.00 0.00 0.00 3.69
834 853 6.808212 CCTATCGACGTAGGAAACACTTTTTA 59.192 38.462 14.61 0.00 43.27 1.52
835 854 5.636543 CCTATCGACGTAGGAAACACTTTTT 59.363 40.000 14.61 0.00 43.27 1.94
846 865 0.037303 TAGGCCCCTATCGACGTAGG 59.963 60.000 0.00 13.43 40.81 3.18
918 937 3.453059 ACTTAAGGTCTTCCTCGAGGA 57.547 47.619 30.49 30.49 44.35 3.71
919 938 5.656213 TTTACTTAAGGTCTTCCTCGAGG 57.344 43.478 26.32 26.32 44.35 4.63
920 939 6.975772 CAGATTTACTTAAGGTCTTCCTCGAG 59.024 42.308 5.13 5.13 44.35 4.04
921 940 6.627508 GCAGATTTACTTAAGGTCTTCCTCGA 60.628 42.308 7.53 0.00 44.35 4.04
923 942 6.407202 TGCAGATTTACTTAAGGTCTTCCTC 58.593 40.000 7.53 0.00 44.35 3.71
925 944 7.390718 TCTTTGCAGATTTACTTAAGGTCTTCC 59.609 37.037 7.53 0.37 0.00 3.46
926 945 8.231161 GTCTTTGCAGATTTACTTAAGGTCTTC 58.769 37.037 7.53 0.67 0.00 2.87
927 946 7.719633 TGTCTTTGCAGATTTACTTAAGGTCTT 59.280 33.333 7.53 0.00 0.00 3.01
928 947 7.173390 GTGTCTTTGCAGATTTACTTAAGGTCT 59.827 37.037 7.53 2.16 0.00 3.85
929 948 7.041372 TGTGTCTTTGCAGATTTACTTAAGGTC 60.041 37.037 7.53 0.00 0.00 3.85
930 949 6.770785 TGTGTCTTTGCAGATTTACTTAAGGT 59.229 34.615 7.53 0.00 0.00 3.50
931 950 7.041098 ACTGTGTCTTTGCAGATTTACTTAAGG 60.041 37.037 7.53 0.00 36.62 2.69
932 951 7.865707 ACTGTGTCTTTGCAGATTTACTTAAG 58.134 34.615 0.00 0.00 36.62 1.85
933 952 7.497579 TGACTGTGTCTTTGCAGATTTACTTAA 59.502 33.333 0.00 0.00 36.62 1.85
934 953 6.989759 TGACTGTGTCTTTGCAGATTTACTTA 59.010 34.615 0.00 0.00 36.62 2.24
935 954 5.822519 TGACTGTGTCTTTGCAGATTTACTT 59.177 36.000 0.00 0.00 36.62 2.24
939 958 4.202441 ACTGACTGTGTCTTTGCAGATTT 58.798 39.130 0.00 0.00 36.62 2.17
956 975 3.165058 TGACTTGTGTGACTGACTGAC 57.835 47.619 0.00 0.00 0.00 3.51
960 979 4.743151 TCGTAATTGACTTGTGTGACTGAC 59.257 41.667 0.00 0.00 0.00 3.51
961 980 4.939271 TCGTAATTGACTTGTGTGACTGA 58.061 39.130 0.00 0.00 0.00 3.41
965 984 8.248253 ACACTATATCGTAATTGACTTGTGTGA 58.752 33.333 0.00 0.00 33.39 3.58
972 991 6.916387 CCGAACACACTATATCGTAATTGACT 59.084 38.462 0.00 0.00 33.65 3.41
977 996 6.381481 TGACCGAACACACTATATCGTAAT 57.619 37.500 0.00 0.00 33.65 1.89
979 998 5.278120 CCATGACCGAACACACTATATCGTA 60.278 44.000 0.00 0.00 33.65 3.43
981 1000 3.981416 CCATGACCGAACACACTATATCG 59.019 47.826 0.00 0.00 35.19 2.92
982 1001 3.741344 GCCATGACCGAACACACTATATC 59.259 47.826 0.00 0.00 0.00 1.63
983 1002 3.133901 TGCCATGACCGAACACACTATAT 59.866 43.478 0.00 0.00 0.00 0.86
984 1003 2.498078 TGCCATGACCGAACACACTATA 59.502 45.455 0.00 0.00 0.00 1.31
994 1015 0.107643 TTCTGTGTTGCCATGACCGA 59.892 50.000 0.00 0.00 0.00 4.69
1055 1097 1.599576 GAGTTCAGGGAGAGGGCAC 59.400 63.158 0.00 0.00 0.00 5.01
1056 1098 1.613630 GGAGTTCAGGGAGAGGGCA 60.614 63.158 0.00 0.00 0.00 5.36
1059 1101 2.060980 CGGGGAGTTCAGGGAGAGG 61.061 68.421 0.00 0.00 0.00 3.69
1063 1105 2.038975 CTCCGGGGAGTTCAGGGA 59.961 66.667 0.00 0.00 37.47 4.20
1067 1109 0.324091 GTAGTCCTCCGGGGAGTTCA 60.324 60.000 20.36 5.25 44.94 3.18
1127 1169 4.715523 CGTCCCATGCCACCGGTT 62.716 66.667 2.97 0.00 0.00 4.44
1137 1179 3.771160 GCCACCTCGTCGTCCCAT 61.771 66.667 0.00 0.00 0.00 4.00
1226 1268 1.351017 CATACCTATGATGGCGGGGTT 59.649 52.381 0.00 0.00 35.75 4.11
1236 1278 4.152647 ACAGATTCTCGCCATACCTATGA 58.847 43.478 0.00 0.00 35.75 2.15
1239 1281 3.321111 GGAACAGATTCTCGCCATACCTA 59.679 47.826 0.00 0.00 34.98 3.08
1359 1407 2.401766 GGCACAGCCGATCTTGGTG 61.402 63.158 9.06 9.06 39.62 4.17
1596 1661 9.838975 ACATGAAATTTTCACAAAAGAAAAACC 57.161 25.926 13.80 0.84 46.81 3.27
1635 1700 6.571150 GCTTTAGTACAACTTTAGTCCGAGGA 60.571 42.308 0.00 0.00 0.00 3.71
1675 1740 1.481871 TTGTACTCTCCCCGATCCAC 58.518 55.000 0.00 0.00 0.00 4.02
1721 1786 7.662897 ACGTTAATTTCCTTTATCCAAAAGCA 58.337 30.769 0.00 0.00 0.00 3.91
1798 1863 7.963981 TCTGCGTTCTTCTTATTAATGAACTG 58.036 34.615 11.59 7.82 36.03 3.16
1857 1922 6.663523 CCCTGATTAACTGAAAATGTTAGGGT 59.336 38.462 0.00 0.00 32.00 4.34
1868 1933 5.943349 TCGGTTATCCCTGATTAACTGAA 57.057 39.130 2.68 0.00 35.59 3.02
1870 1935 6.288294 TCATTCGGTTATCCCTGATTAACTG 58.712 40.000 0.00 0.00 0.00 3.16
1872 1937 7.562454 TTTCATTCGGTTATCCCTGATTAAC 57.438 36.000 0.00 0.00 0.00 2.01
1882 1947 6.168164 TGTTACGGTTTTCATTCGGTTATC 57.832 37.500 0.00 0.00 0.00 1.75
1884 1949 6.557291 AATGTTACGGTTTTCATTCGGTTA 57.443 33.333 0.00 0.00 0.00 2.85
1916 1981 8.816144 TCTTACGAAAACGTGTATTGTTAAAGT 58.184 29.630 5.54 0.00 0.00 2.66
1955 2020 9.449719 CTAACAGAATTACTATCCAAAACTGGT 57.550 33.333 0.00 0.00 0.00 4.00
1992 2057 6.070824 TCCTCATCTAAACAAGAGTATGTGCA 60.071 38.462 0.00 0.00 37.74 4.57
2080 2145 8.330466 TCTGGAAAAACGCTGATTAGATTTAA 57.670 30.769 0.00 0.00 0.00 1.52
2081 2146 7.915293 TCTGGAAAAACGCTGATTAGATTTA 57.085 32.000 0.00 0.00 0.00 1.40
2092 2157 1.239347 GGAGCTTCTGGAAAAACGCT 58.761 50.000 0.00 0.00 0.00 5.07
2154 2221 3.582998 AGCTAGCTTCCATGGCAATTA 57.417 42.857 12.68 0.00 0.00 1.40
2312 2379 2.417243 GCCTAAACACATGGATTGGTGC 60.417 50.000 0.00 0.00 38.57 5.01
2351 2418 3.760151 GCATGGGCATGTGATACATATGT 59.240 43.478 13.93 13.93 36.53 2.29
2352 2419 4.365899 GCATGGGCATGTGATACATATG 57.634 45.455 0.00 0.00 36.53 1.78
2372 3037 1.264020 TGAGAAATGTCTGCAACGTGC 59.736 47.619 0.00 0.00 45.29 5.34
2480 3321 1.801771 CACAATTTGCCACATTGCCAG 59.198 47.619 3.53 0.00 35.36 4.85
2495 3336 6.818142 GCAATAAGGGAATTTGTTAGCACAAT 59.182 34.615 0.00 0.00 42.66 2.71
2506 3347 5.146010 TCAAAAGCGCAATAAGGGAATTT 57.854 34.783 11.47 0.00 0.00 1.82
2521 3362 4.340894 TCGCATTCACTGTATCAAAAGC 57.659 40.909 0.00 0.00 0.00 3.51
2540 3381 1.004918 ACCGCCCTTCTCAAGTTCG 60.005 57.895 0.00 0.00 0.00 3.95
2719 3560 8.338072 TGCTTAATCAATGAAAATGGCAAATT 57.662 26.923 0.00 0.00 0.00 1.82
2780 3621 4.566278 GGGGGTTGTAATCTAGGTTTTCGT 60.566 45.833 0.00 0.00 0.00 3.85
2813 3654 0.466543 TGTGGCTAGGTTGTTCGTGT 59.533 50.000 0.00 0.00 0.00 4.49
2821 3662 2.335316 TTGACGTTTGTGGCTAGGTT 57.665 45.000 0.00 0.00 0.00 3.50
2826 3667 2.540769 CGATTGTTTGACGTTTGTGGCT 60.541 45.455 0.00 0.00 0.00 4.75
2837 3678 1.944024 ACGCTTTGGTCGATTGTTTGA 59.056 42.857 0.00 0.00 0.00 2.69
2851 3692 0.537143 TGCCATGTCCTCAACGCTTT 60.537 50.000 0.00 0.00 0.00 3.51
2858 3700 2.993008 GGAGCTGCCATGTCCTCA 59.007 61.111 0.00 0.00 36.34 3.86
2936 3778 2.076100 GCAACGATGACTCCATGTGAA 58.924 47.619 0.00 0.00 32.09 3.18
2937 3779 1.675714 GGCAACGATGACTCCATGTGA 60.676 52.381 0.00 0.00 32.09 3.58
2938 3780 0.729116 GGCAACGATGACTCCATGTG 59.271 55.000 0.00 0.00 32.09 3.21
2939 3781 3.159298 GGCAACGATGACTCCATGT 57.841 52.632 0.00 0.00 32.09 3.21
2993 3868 4.561938 CCAATGTTGGTTTCATGCTGTGAT 60.562 41.667 3.58 0.00 43.43 3.06
3010 3885 2.672996 GGTCCAGTGCGCCAATGT 60.673 61.111 4.18 0.00 0.00 2.71
3031 3918 1.808945 GTGGCTTGTCCTTCTGATGTG 59.191 52.381 0.00 0.00 35.26 3.21
3126 4013 3.499737 CATTGCGGTCGGCTGGTC 61.500 66.667 0.00 0.00 44.05 4.02
3207 4094 1.202604 TCTTCAGCGTCGTTTTCCCTT 60.203 47.619 0.00 0.00 0.00 3.95
3269 4156 4.290942 ACTCCCGGATCAAGATCTTTAGT 58.709 43.478 4.86 6.19 37.92 2.24
3313 4200 1.609501 CCTCCTTGGAGGTGTCGGA 60.610 63.158 23.92 0.00 36.53 4.55
3314 4201 1.609501 TCCTCCTTGGAGGTGTCGG 60.610 63.158 28.88 9.34 42.79 4.79
3421 4308 4.003788 CGTGGACCAGCGGAGGTT 62.004 66.667 0.00 0.00 43.38 3.50
3528 4416 1.451028 GGGTGCCAGATCTGACTGC 60.451 63.158 24.62 18.45 36.67 4.40
3586 4476 3.775654 CCCTCCGGCTCAGGTGAC 61.776 72.222 6.91 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.