Multiple sequence alignment - TraesCS3B01G371900

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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 TraesCS3B01G371900 chr3B 100.000 4886 0 0 1 4886 584699017 584694132 0.000000e+00 9023
1 TraesCS3B01G371900 chr3B 90.464 1573 115 19 1368 2914 588439840 588441403 0.000000e+00 2041
2 TraesCS3B01G371900 chr3B 92.753 1435 68 20 2923 4350 588441451 588442856 0.000000e+00 2041
3 TraesCS3B01G371900 chr3B 97.584 538 12 1 4349 4886 620821796 620821260 0.000000e+00 920
4 TraesCS3B01G371900 chr3B 79.437 355 36 23 2733 3065 588441590 588441929 2.960000e-52 217
5 TraesCS3B01G371900 chr3B 78.736 348 35 21 2748 3065 584695941 584695603 3.860000e-46 196
6 TraesCS3B01G371900 chr3B 78.736 348 35 21 3077 3415 584696270 584695953 3.860000e-46 196
7 TraesCS3B01G371900 chr3A 93.888 3027 122 32 1012 3985 587564629 587561613 0.000000e+00 4506
8 TraesCS3B01G371900 chr3A 85.522 967 63 26 1 939 587565820 587564903 0.000000e+00 939
9 TraesCS3B01G371900 chr3A 93.473 383 16 5 3977 4350 587559074 587558692 1.190000e-155 560
10 TraesCS3B01G371900 chr3A 81.098 492 69 19 4 480 587571474 587570992 5.970000e-99 372
11 TraesCS3B01G371900 chr3A 83.846 390 43 16 4 390 587568928 587568556 2.160000e-93 353
12 TraesCS3B01G371900 chr3A 79.472 492 73 23 1 473 587574162 587573680 1.700000e-84 324
13 TraesCS3B01G371900 chr3A 78.337 517 60 33 1 479 587567429 587566927 2.230000e-73 287
14 TraesCS3B01G371900 chr3A 78.571 322 35 17 2768 3065 587562494 587562183 1.080000e-41 182
15 TraesCS3B01G371900 chr3D 91.925 2514 111 45 527 2970 445811325 445808834 0.000000e+00 3434
16 TraesCS3B01G371900 chr3D 96.739 1196 30 4 3160 4350 445808482 445807291 0.000000e+00 1984
17 TraesCS3B01G371900 chr3D 83.398 512 37 23 1 480 445814019 445813524 9.720000e-117 431
18 TraesCS3B01G371900 chr3D 83.200 500 51 14 1 480 445814800 445814314 1.260000e-115 427
19 TraesCS3B01G371900 chr3D 82.635 501 58 17 1 480 445815597 445815105 2.720000e-112 416
20 TraesCS3B01G371900 chr3D 93.214 280 18 1 3 282 445812352 445812074 1.270000e-110 411
21 TraesCS3B01G371900 chr3D 85.979 378 41 9 16 390 445817219 445816851 1.270000e-105 394
22 TraesCS3B01G371900 chr3D 97.423 194 5 0 2966 3159 445808755 445808562 1.010000e-86 331
23 TraesCS3B01G371900 chr3D 80.144 277 28 17 221 480 445812934 445812668 1.080000e-41 182
24 TraesCS3B01G371900 chr3D 91.057 123 9 2 405 525 445811612 445811490 1.090000e-36 165
25 TraesCS3B01G371900 chr3D 87.500 144 15 2 2925 3065 445808373 445808230 3.910000e-36 163
26 TraesCS3B01G371900 chr3D 91.000 100 9 0 3316 3415 445808755 445808656 8.530000e-28 135
27 TraesCS3B01G371900 chr2B 97.207 537 14 1 4349 4885 627322009 627321474 0.000000e+00 907
28 TraesCS3B01G371900 chr6B 97.026 538 15 1 4349 4886 602490441 602490977 0.000000e+00 904
29 TraesCS3B01G371900 chr4A 97.026 538 15 1 4349 4886 661308656 661308120 0.000000e+00 904
30 TraesCS3B01G371900 chr1B 97.026 538 15 1 4349 4886 161398729 161398193 0.000000e+00 904
31 TraesCS3B01G371900 chr1B 96.840 538 16 1 4349 4886 638818676 638818140 0.000000e+00 898
32 TraesCS3B01G371900 chr7B 96.654 538 17 1 4349 4886 110319299 110318763 0.000000e+00 893
33 TraesCS3B01G371900 chr5B 96.468 538 18 1 4349 4886 78311271 78311807 0.000000e+00 887
34 TraesCS3B01G371900 chr5B 96.468 538 18 1 4349 4886 495529520 495528984 0.000000e+00 887


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 TraesCS3B01G371900 chr3B 584694132 584699017 4885 True 3138.333333 9023 85.824000 1 4886 3 chr3B.!!$R2 4885
1 TraesCS3B01G371900 chr3B 588439840 588442856 3016 False 1433.000000 2041 87.551333 1368 4350 3 chr3B.!!$F1 2982
2 TraesCS3B01G371900 chr3B 620821260 620821796 536 True 920.000000 920 97.584000 4349 4886 1 chr3B.!!$R1 537
3 TraesCS3B01G371900 chr3A 587558692 587574162 15470 True 940.375000 4506 84.275875 1 4350 8 chr3A.!!$R1 4349
4 TraesCS3B01G371900 chr3D 445807291 445817219 9928 True 706.083333 3434 88.684500 1 4350 12 chr3D.!!$R1 4349
5 TraesCS3B01G371900 chr2B 627321474 627322009 535 True 907.000000 907 97.207000 4349 4885 1 chr2B.!!$R1 536
6 TraesCS3B01G371900 chr6B 602490441 602490977 536 False 904.000000 904 97.026000 4349 4886 1 chr6B.!!$F1 537
7 TraesCS3B01G371900 chr4A 661308120 661308656 536 True 904.000000 904 97.026000 4349 4886 1 chr4A.!!$R1 537
8 TraesCS3B01G371900 chr1B 161398193 161398729 536 True 904.000000 904 97.026000 4349 4886 1 chr1B.!!$R1 537
9 TraesCS3B01G371900 chr1B 638818140 638818676 536 True 898.000000 898 96.840000 4349 4886 1 chr1B.!!$R2 537
10 TraesCS3B01G371900 chr7B 110318763 110319299 536 True 893.000000 893 96.654000 4349 4886 1 chr7B.!!$R1 537
11 TraesCS3B01G371900 chr5B 78311271 78311807 536 False 887.000000 887 96.468000 4349 4886 1 chr5B.!!$F1 537
12 TraesCS3B01G371900 chr5B 495528984 495529520 536 True 887.000000 887 96.468000 4349 4886 1 chr5B.!!$R1 537

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
832 10047 0.047176 TCTCTCTCTCCCTCCCTCCT 59.953 60.0 0.00 0.0 0.0 3.69 F
837 10052 0.105709 CTCTCCCTCCCTCCTCCTTC 60.106 65.0 0.00 0.0 0.0 3.46 F
2352 11811 0.173708 CAGTCTAGACGGGTGGCTTC 59.826 60.0 17.07 0.0 36.2 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 11276 1.074727 TGGACATTGGACCACCGATTT 59.925 47.619 0.0 0.0 38.15 2.17 R
2441 11923 1.341852 TGTCACCGACAAAAGGATCGA 59.658 47.619 0.0 0.0 39.78 3.59 R
4241 16485 1.461127 CACAAACGTCAGAGCTTAGGC 59.539 52.381 0.0 0.0 39.06 3.93 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
48 8737 0.764890 CCTCAAATCCCGGAGCCATA 59.235 55.000 0.73 0.00 0.00 2.74
135 8825 3.568430 CGTTGCTAAAAGAGAACCCCTTT 59.432 43.478 0.00 0.00 35.55 3.11
141 8831 0.400594 AAGAGAACCCCTTTCCCACG 59.599 55.000 0.00 0.00 34.32 4.94
152 8842 2.992607 TTTCCCACGCGCTACCGTTT 62.993 55.000 5.73 0.00 39.83 3.60
157 8847 1.062258 CACGCGCTACCGTTTAGAAA 58.938 50.000 5.73 0.00 39.83 2.52
160 8850 1.319669 CGCGCTACCGTTTAGAAAGTC 59.680 52.381 5.56 0.00 36.67 3.01
161 8851 2.331194 GCGCTACCGTTTAGAAAGTCA 58.669 47.619 0.00 0.00 36.67 3.41
210 8900 1.083489 TAAGGTTGAATCCTTGCGCG 58.917 50.000 0.00 0.00 45.96 6.86
212 8902 2.560861 GTTGAATCCTTGCGCGCA 59.439 55.556 33.09 33.09 0.00 6.09
228 8918 0.826715 CGCAGATTGGGGAAGAGAGA 59.173 55.000 0.00 0.00 0.00 3.10
263 8953 5.079643 AGGCTATGGTTCAAAAGTGAATGT 58.920 37.500 0.00 0.00 45.38 2.71
282 8972 7.903431 GTGAATGTGTATTGGTCGAAATCTTAC 59.097 37.037 0.00 0.00 0.00 2.34
286 9279 6.128391 TGTGTATTGGTCGAAATCTTACTTGC 60.128 38.462 0.00 0.00 0.00 4.01
316 9309 8.964150 CGACGGAAGAAAATAAAGTTCAAATTT 58.036 29.630 0.00 0.00 0.00 1.82
352 9346 5.642063 TCTCCTCGAAATGTGTGGTATTTTC 59.358 40.000 0.00 0.00 0.00 2.29
353 9347 5.556915 TCCTCGAAATGTGTGGTATTTTCT 58.443 37.500 0.00 0.00 0.00 2.52
354 9348 6.001460 TCCTCGAAATGTGTGGTATTTTCTT 58.999 36.000 0.00 0.00 0.00 2.52
355 9349 6.148811 TCCTCGAAATGTGTGGTATTTTCTTC 59.851 38.462 0.00 0.00 0.00 2.87
373 9367 3.648067 TCTTCTTCTTCTTCTTGCAGGGA 59.352 43.478 0.00 0.00 0.00 4.20
560 9763 3.934457 AATGGAAAGGTGGTAAAAGCG 57.066 42.857 0.00 0.00 0.00 4.68
602 9805 4.904466 GCGTTTTCCTCCGCTCTA 57.096 55.556 0.00 0.00 46.08 2.43
603 9806 3.364277 GCGTTTTCCTCCGCTCTAT 57.636 52.632 0.00 0.00 46.08 1.98
616 9819 1.268692 CGCTCTATACCACCGCGTAAA 60.269 52.381 4.92 0.00 39.07 2.01
726 9935 1.901654 GCCTGCCATCCATTGCCAAA 61.902 55.000 0.00 0.00 0.00 3.28
758 9967 3.425659 GAGAAAAAGGAATCCCACTGCT 58.574 45.455 0.00 0.00 33.88 4.24
774 9983 1.008538 GCTGCAGAAAACACACCGG 60.009 57.895 20.43 0.00 0.00 5.28
819 10034 2.361865 AGCCCGAACGCTCTCTCT 60.362 61.111 0.00 0.00 32.06 3.10
824 10039 1.720694 CCGAACGCTCTCTCTCTCCC 61.721 65.000 0.00 0.00 0.00 4.30
827 10042 0.395173 AACGCTCTCTCTCTCCCTCC 60.395 60.000 0.00 0.00 0.00 4.30
829 10044 1.930520 GCTCTCTCTCTCCCTCCCT 59.069 63.158 0.00 0.00 0.00 4.20
830 10045 0.178990 GCTCTCTCTCTCCCTCCCTC 60.179 65.000 0.00 0.00 0.00 4.30
831 10046 0.478507 CTCTCTCTCTCCCTCCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
832 10047 0.047176 TCTCTCTCTCCCTCCCTCCT 59.953 60.000 0.00 0.00 0.00 3.69
833 10048 0.478507 CTCTCTCTCCCTCCCTCCTC 59.521 65.000 0.00 0.00 0.00 3.71
834 10049 0.996762 TCTCTCTCCCTCCCTCCTCC 60.997 65.000 0.00 0.00 0.00 4.30
835 10050 0.998945 CTCTCTCCCTCCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
836 10051 0.556380 TCTCTCCCTCCCTCCTCCTT 60.556 60.000 0.00 0.00 0.00 3.36
837 10052 0.105709 CTCTCCCTCCCTCCTCCTTC 60.106 65.000 0.00 0.00 0.00 3.46
838 10053 1.456705 CTCCCTCCCTCCTCCTTCG 60.457 68.421 0.00 0.00 0.00 3.79
839 10054 3.157949 CCCTCCCTCCTCCTTCGC 61.158 72.222 0.00 0.00 0.00 4.70
840 10055 2.042435 CCTCCCTCCTCCTTCGCT 60.042 66.667 0.00 0.00 0.00 4.93
841 10056 2.131067 CCTCCCTCCTCCTTCGCTC 61.131 68.421 0.00 0.00 0.00 5.03
842 10057 2.440430 TCCCTCCTCCTTCGCTCG 60.440 66.667 0.00 0.00 0.00 5.03
843 10058 2.440430 CCCTCCTCCTTCGCTCGA 60.440 66.667 0.00 0.00 0.00 4.04
844 10059 2.485795 CCCTCCTCCTTCGCTCGAG 61.486 68.421 8.45 8.45 0.00 4.04
894 10109 3.160047 CTCTGCCCTCTCCGCCAT 61.160 66.667 0.00 0.00 0.00 4.40
904 10119 2.762459 TCCGCCATACTTCCCGCT 60.762 61.111 0.00 0.00 0.00 5.52
905 10120 2.189521 CCGCCATACTTCCCGCTT 59.810 61.111 0.00 0.00 0.00 4.68
942 10157 1.229336 CCCATATCTCCCTCCGCCT 60.229 63.158 0.00 0.00 0.00 5.52
945 10160 1.304547 ATATCTCCCTCCGCCTCCG 60.305 63.158 0.00 0.00 0.00 4.63
946 10161 2.082836 ATATCTCCCTCCGCCTCCGT 62.083 60.000 0.00 0.00 0.00 4.69
948 10163 4.824515 CTCCCTCCGCCTCCGTCT 62.825 72.222 0.00 0.00 0.00 4.18
949 10164 4.816984 TCCCTCCGCCTCCGTCTC 62.817 72.222 0.00 0.00 0.00 3.36
950 10165 4.824515 CCCTCCGCCTCCGTCTCT 62.825 72.222 0.00 0.00 0.00 3.10
956 10171 2.043852 GCCTCCGTCTCTCCTCCA 60.044 66.667 0.00 0.00 0.00 3.86
960 10175 0.825840 CTCCGTCTCTCCTCCATCCC 60.826 65.000 0.00 0.00 0.00 3.85
1497 10925 2.133553 CTCTGCATCATCCATCACGTC 58.866 52.381 0.00 0.00 0.00 4.34
1514 10942 7.010183 CCATCACGTCTCACGAAAAATTACTAT 59.990 37.037 2.48 0.00 46.05 2.12
1515 10943 9.016623 CATCACGTCTCACGAAAAATTACTATA 57.983 33.333 2.48 0.00 46.05 1.31
1516 10944 8.610855 TCACGTCTCACGAAAAATTACTATAG 57.389 34.615 2.48 0.00 46.05 1.31
1517 10945 8.239314 TCACGTCTCACGAAAAATTACTATAGT 58.761 33.333 10.87 10.87 46.05 2.12
1518 10946 9.494479 CACGTCTCACGAAAAATTACTATAGTA 57.506 33.333 8.59 8.59 46.05 1.82
1519 10947 9.713740 ACGTCTCACGAAAAATTACTATAGTAG 57.286 33.333 12.28 2.67 46.05 2.57
1520 10948 9.713740 CGTCTCACGAAAAATTACTATAGTAGT 57.286 33.333 12.28 7.36 46.05 2.73
1546 10981 2.519963 GCTTTGCTATTTCTGTTCGCC 58.480 47.619 0.00 0.00 0.00 5.54
1588 11028 4.577677 TTGGCCCGTGCTCTGCAA 62.578 61.111 0.00 0.00 41.47 4.08
1599 11039 1.134189 TGCTCTGCAATCATCCTCTGG 60.134 52.381 0.00 0.00 34.76 3.86
1606 11046 2.478539 GCAATCATCCTCTGGCGTTTTC 60.479 50.000 0.00 0.00 0.00 2.29
1640 11080 1.541588 CATCTACGATGCATCCGAGGA 59.458 52.381 20.87 13.52 0.00 3.71
1661 11101 7.272299 CGAGGAAGATACATTCACGAATATCAG 59.728 40.741 0.00 0.00 34.70 2.90
1752 11201 3.139850 CCTAGTACTGATCGATCGGTGT 58.860 50.000 38.36 29.29 45.49 4.16
1776 11225 0.457851 CTCTCTCCGATGGTGACCAC 59.542 60.000 6.40 0.00 35.80 4.16
1813 11262 7.741554 AGATTTCCTCAAAGTACAGGTCTAT 57.258 36.000 0.00 0.00 0.00 1.98
1827 11276 3.195610 CAGGTCTATAGGTGCACTTGTCA 59.804 47.826 17.98 0.00 0.00 3.58
1908 11357 0.596577 TCCCTCAGTTTCACTCGTCG 59.403 55.000 0.00 0.00 0.00 5.12
1925 11374 2.706123 CGAAATTGCGCGCAACACC 61.706 57.895 44.93 32.23 38.88 4.16
1952 11401 7.604545 TGAATTCATCGTCCACTTTGTTATACA 59.395 33.333 3.38 0.00 0.00 2.29
2106 11556 1.301716 GCCGTCTGGTTGCTTCAGA 60.302 57.895 0.00 0.00 38.75 3.27
2238 11693 4.437390 CGATTCAGTGGGTGATAAAGCAAC 60.437 45.833 0.00 0.00 34.17 4.17
2319 11774 0.820074 TGCCGTGTGGAATCCGTTTT 60.820 50.000 0.00 0.00 37.49 2.43
2352 11811 0.173708 CAGTCTAGACGGGTGGCTTC 59.826 60.000 17.07 0.00 36.20 3.86
2412 11894 2.421424 AGCGTACTAAACTACCAGTCCG 59.579 50.000 0.00 0.00 0.00 4.79
2441 11923 6.072728 TGCATAAAGTTTGTCGTTTGATAGCT 60.073 34.615 0.00 0.00 0.00 3.32
2684 12166 0.038618 GGGTTGGTTTGATGGCGTTC 60.039 55.000 0.00 0.00 0.00 3.95
2750 12235 6.038714 ACACAAAAAGAGAGTGATGTCTTTCC 59.961 38.462 0.00 0.00 41.21 3.13
3251 12940 4.624913 AGATATCTTGGGGTCTGACTTGA 58.375 43.478 7.85 0.37 0.00 3.02
3441 13131 2.282462 CCCCTTGCACTGACACCC 60.282 66.667 0.00 0.00 0.00 4.61
3456 13146 0.107456 CACCCGAGGATGATCCAAGG 59.893 60.000 14.90 15.28 39.61 3.61
3507 13197 6.480981 CACATTTGGAAGAAATCAACAAGCTT 59.519 34.615 0.00 0.00 0.00 3.74
3648 13338 1.594293 CTTCACAACTGCGACGGGT 60.594 57.895 0.00 0.00 0.00 5.28
3868 13558 0.527169 CATCGCTCATCTGCACGAGT 60.527 55.000 1.36 0.00 38.04 4.18
3888 13578 4.517285 AGTTGTCTGTTCACAAGTGACAT 58.483 39.130 1.73 0.00 38.31 3.06
3910 13600 1.227002 GCCCTTCCGTCGCTCTAAG 60.227 63.158 0.00 0.00 0.00 2.18
4079 16317 0.546598 GGCCAGCAACCCAGTATAGT 59.453 55.000 0.00 0.00 0.00 2.12
4227 16471 8.311836 TGGGATTCAGTAGTTCTTACTTAAGTG 58.688 37.037 18.56 2.38 40.68 3.16
4239 16483 8.403236 GTTCTTACTTAAGTGTTGGTTGATTGT 58.597 33.333 18.56 0.00 34.93 2.71
4241 16485 8.402472 TCTTACTTAAGTGTTGGTTGATTGTTG 58.598 33.333 18.56 0.00 34.93 3.33
4340 16593 4.189231 GGTACTTCGTAATGTGCCTTCAT 58.811 43.478 0.00 0.00 36.30 2.57
4407 16660 5.146298 TCTGGATGCACTCTCTGAAGATAT 58.854 41.667 0.00 0.00 0.00 1.63
4426 16679 8.978874 AAGATATTATTGTGTGGAAGCATACA 57.021 30.769 0.00 0.00 0.00 2.29
4432 16685 3.814625 TGTGTGGAAGCATACAACAAGA 58.185 40.909 0.00 0.00 0.00 3.02
4443 16696 4.517285 CATACAACAAGAGGGCACTACAT 58.483 43.478 0.00 0.00 0.00 2.29
4453 16706 1.450312 GCACTACATTGCGGCCTCT 60.450 57.895 0.00 0.00 31.51 3.69
4496 16749 1.556911 GCTTGGTTCTCTCTCCCATGA 59.443 52.381 0.00 0.00 0.00 3.07
4819 17072 1.304713 CAACAGGAAGGCCATGGCT 60.305 57.895 34.70 17.99 41.24 4.75
4851 17104 1.812571 GCTCGTGTCATGGACCATTTT 59.187 47.619 3.52 0.00 0.00 1.82
4860 17113 2.649531 TGGACCATTTTGGAACGAGT 57.350 45.000 0.00 0.00 40.96 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 8737 1.129998 CGACGATACCGACAACTGACT 59.870 52.381 0.00 0.00 39.50 3.41
135 8825 2.546645 CTAAACGGTAGCGCGTGGGA 62.547 60.000 15.35 0.00 0.00 4.37
141 8831 2.331194 TGACTTTCTAAACGGTAGCGC 58.669 47.619 15.35 0.00 0.00 5.92
152 8842 4.871933 TGTCTGAGCACATGACTTTCTA 57.128 40.909 0.00 0.00 0.00 2.10
157 8847 2.354503 GGTGATGTCTGAGCACATGACT 60.355 50.000 0.00 0.00 43.20 3.41
160 8850 1.004595 CGGTGATGTCTGAGCACATG 58.995 55.000 2.97 0.00 43.20 3.21
161 8851 0.897621 TCGGTGATGTCTGAGCACAT 59.102 50.000 0.00 0.00 43.20 3.21
210 8900 3.356529 TTTCTCTCTTCCCCAATCTGC 57.643 47.619 0.00 0.00 0.00 4.26
212 8902 5.252630 AGAACATTTCTCTCTTCCCCAATCT 59.747 40.000 0.00 0.00 34.07 2.40
228 8918 6.662755 TGAACCATAGCCTATCAGAACATTT 58.337 36.000 0.00 0.00 0.00 2.32
263 8953 5.353123 GGCAAGTAAGATTTCGACCAATACA 59.647 40.000 0.00 0.00 0.00 2.29
282 8972 1.508632 TTTCTTCCGTCGAAGGCAAG 58.491 50.000 13.06 15.67 44.88 4.01
286 9279 5.857822 ACTTTATTTTCTTCCGTCGAAGG 57.142 39.130 11.59 11.59 44.88 3.46
316 9309 4.579454 TTCGAGGAGAGTTTTCGAAAGA 57.421 40.909 10.98 0.00 46.53 2.52
352 9346 4.013267 TCCCTGCAAGAAGAAGAAGAAG 57.987 45.455 0.00 0.00 34.07 2.85
353 9347 4.437682 TTCCCTGCAAGAAGAAGAAGAA 57.562 40.909 0.00 0.00 34.07 2.52
354 9348 4.437682 TTTCCCTGCAAGAAGAAGAAGA 57.562 40.909 0.00 0.00 34.07 2.87
355 9349 5.010415 ACATTTTCCCTGCAAGAAGAAGAAG 59.990 40.000 0.00 0.00 34.07 2.85
373 9367 4.736473 AGCCTTAAGTACCCACACATTTT 58.264 39.130 0.97 0.00 0.00 1.82
425 9459 8.292448 CGCGAAAAGGTATAAGTAGATAGGTTA 58.708 37.037 0.00 0.00 0.00 2.85
429 9463 8.851416 CATTCGCGAAAAGGTATAAGTAGATAG 58.149 37.037 27.23 0.00 0.00 2.08
434 9468 9.531942 TTATTCATTCGCGAAAAGGTATAAGTA 57.468 29.630 27.23 0.00 0.00 2.24
474 9511 1.786937 AACACACATTTCCCTTGCCA 58.213 45.000 0.00 0.00 0.00 4.92
475 9512 4.535526 AATAACACACATTTCCCTTGCC 57.464 40.909 0.00 0.00 0.00 4.52
476 9513 5.988561 TCAAAATAACACACATTTCCCTTGC 59.011 36.000 0.00 0.00 0.00 4.01
477 9514 6.646240 CCTCAAAATAACACACATTTCCCTTG 59.354 38.462 0.00 0.00 0.00 3.61
478 9515 6.741240 GCCTCAAAATAACACACATTTCCCTT 60.741 38.462 0.00 0.00 0.00 3.95
479 9516 5.279456 GCCTCAAAATAACACACATTTCCCT 60.279 40.000 0.00 0.00 0.00 4.20
599 9802 3.119029 AGCTTTTTACGCGGTGGTATAGA 60.119 43.478 12.47 0.00 0.00 1.98
600 9803 3.000925 CAGCTTTTTACGCGGTGGTATAG 59.999 47.826 12.47 0.00 0.00 1.31
602 9805 1.735571 CAGCTTTTTACGCGGTGGTAT 59.264 47.619 12.47 0.00 0.00 2.73
603 9806 1.149987 CAGCTTTTTACGCGGTGGTA 58.850 50.000 12.47 0.00 0.00 3.25
616 9819 6.916360 TGATATTTGGAAGGAAACAGCTTT 57.084 33.333 0.00 0.00 0.00 3.51
726 9935 4.729227 TCCTTTTTCTCGCTTGGTTTTT 57.271 36.364 0.00 0.00 0.00 1.94
758 9967 0.179234 TCTCCGGTGTGTTTTCTGCA 59.821 50.000 0.00 0.00 0.00 4.41
774 9983 1.956802 CGTGGGGTTTTTGCCTCTC 59.043 57.895 0.00 0.00 0.00 3.20
807 10022 1.021968 GAGGGAGAGAGAGAGCGTTC 58.978 60.000 0.00 0.00 0.00 3.95
808 10023 0.395173 GGAGGGAGAGAGAGAGCGTT 60.395 60.000 0.00 0.00 0.00 4.84
810 10025 1.528309 GGGAGGGAGAGAGAGAGCG 60.528 68.421 0.00 0.00 0.00 5.03
819 10034 1.939082 CGAAGGAGGAGGGAGGGAGA 61.939 65.000 0.00 0.00 0.00 3.71
824 10039 2.485795 CGAGCGAAGGAGGAGGGAG 61.486 68.421 0.00 0.00 0.00 4.30
827 10042 3.115556 CTCGAGCGAAGGAGGAGG 58.884 66.667 0.00 0.00 0.00 4.30
839 10054 2.202810 GGGAAAGGCTCGCTCGAG 60.203 66.667 8.45 8.45 44.56 4.04
840 10055 4.129737 CGGGAAAGGCTCGCTCGA 62.130 66.667 3.03 0.00 34.85 4.04
904 10119 2.358247 GAGGCGGTCAAAGCGGAA 60.358 61.111 0.49 0.00 39.82 4.30
905 10120 4.388499 GGAGGCGGTCAAAGCGGA 62.388 66.667 0.49 0.00 39.82 5.54
942 10157 1.230497 GGGATGGAGGAGAGACGGA 59.770 63.158 0.00 0.00 0.00 4.69
945 10160 1.051556 GGGTGGGATGGAGGAGAGAC 61.052 65.000 0.00 0.00 0.00 3.36
946 10161 1.314867 GGGTGGGATGGAGGAGAGA 59.685 63.158 0.00 0.00 0.00 3.10
948 10163 2.041922 CGGGTGGGATGGAGGAGA 60.042 66.667 0.00 0.00 0.00 3.71
949 10164 3.866582 GCGGGTGGGATGGAGGAG 61.867 72.222 0.00 0.00 0.00 3.69
986 10201 4.143333 ACATCGGTCTTCGCGGGG 62.143 66.667 6.13 0.00 39.05 5.73
1092 10508 2.359230 GGCAGCCTGAAAGCGACT 60.359 61.111 3.29 0.00 38.01 4.18
1094 10510 4.722700 GGGGCAGCCTGAAAGCGA 62.723 66.667 12.43 0.00 38.01 4.93
1514 10942 7.652105 CAGAAATAGCAAAGCCGAATACTACTA 59.348 37.037 0.00 0.00 0.00 1.82
1515 10943 6.480320 CAGAAATAGCAAAGCCGAATACTACT 59.520 38.462 0.00 0.00 0.00 2.57
1516 10944 6.258068 ACAGAAATAGCAAAGCCGAATACTAC 59.742 38.462 0.00 0.00 0.00 2.73
1517 10945 6.346096 ACAGAAATAGCAAAGCCGAATACTA 58.654 36.000 0.00 0.00 0.00 1.82
1518 10946 5.186198 ACAGAAATAGCAAAGCCGAATACT 58.814 37.500 0.00 0.00 0.00 2.12
1519 10947 5.485662 ACAGAAATAGCAAAGCCGAATAC 57.514 39.130 0.00 0.00 0.00 1.89
1520 10948 5.220586 CGAACAGAAATAGCAAAGCCGAATA 60.221 40.000 0.00 0.00 0.00 1.75
1521 10949 4.437390 CGAACAGAAATAGCAAAGCCGAAT 60.437 41.667 0.00 0.00 0.00 3.34
1546 10981 4.917415 CGCAAACTTAAGAGGAACCAAATG 59.083 41.667 10.09 0.00 0.00 2.32
1588 11028 1.207089 TCGAAAACGCCAGAGGATGAT 59.793 47.619 0.00 0.00 0.00 2.45
1599 11039 2.656897 GCCTCAGAAATTTCGAAAACGC 59.343 45.455 15.66 6.89 0.00 4.84
1606 11046 4.112634 TCGTAGATGCCTCAGAAATTTCG 58.887 43.478 12.42 7.92 0.00 3.46
1640 11080 5.119279 GCGCTGATATTCGTGAATGTATCTT 59.881 40.000 0.00 0.00 32.50 2.40
1752 11201 1.186200 CACCATCGGAGAGAGGAACA 58.814 55.000 0.00 0.00 43.63 3.18
1776 11225 2.093447 AGGAAATCTACCGAACAGCTGG 60.093 50.000 19.93 1.81 0.00 4.85
1813 11262 2.224426 ACCGATTTGACAAGTGCACCTA 60.224 45.455 14.63 0.00 0.00 3.08
1827 11276 1.074727 TGGACATTGGACCACCGATTT 59.925 47.619 0.00 0.00 38.15 2.17
1908 11357 1.371635 AGGTGTTGCGCGCAATTTC 60.372 52.632 44.33 33.54 38.28 2.17
1925 11374 5.362556 AACAAAGTGGACGATGAATTCAG 57.637 39.130 14.54 3.71 0.00 3.02
1952 11401 4.623932 TCTGCTATTCAGGTTGAACAGT 57.376 40.909 0.00 0.00 39.45 3.55
2006 11455 3.060614 ATGGTTGCCATCCTCCCGG 62.061 63.158 0.00 0.00 40.74 5.73
2008 11457 1.456331 CCATGGTTGCCATCCTCCC 60.456 63.158 2.57 0.00 43.15 4.30
2031 11480 1.940613 CTGTTCCATAGGCTAAACGGC 59.059 52.381 0.00 0.00 38.75 5.68
2106 11556 4.250305 ACCACTTGGAGCCGCGTT 62.250 61.111 4.92 0.00 38.94 4.84
2238 11693 3.149005 AGCTAGAGGAGAAGGTATCGG 57.851 52.381 0.00 0.00 0.00 4.18
2342 11801 2.594303 TGCACAAGAAGCCACCCG 60.594 61.111 0.00 0.00 0.00 5.28
2412 11894 3.216147 ACGACAAACTTTATGCATGGC 57.784 42.857 10.16 0.00 0.00 4.40
2441 11923 1.341852 TGTCACCGACAAAAGGATCGA 59.658 47.619 0.00 0.00 39.78 3.59
2750 12235 8.720562 GGAACCAAATCAATTAAAAATGTCTGG 58.279 33.333 0.00 0.00 0.00 3.86
2971 12578 5.088730 TGTTCCACTACTACTACCCATGTT 58.911 41.667 0.00 0.00 0.00 2.71
3130 12737 2.756760 CACATGAGCTGCCCAAGTAAAT 59.243 45.455 0.00 0.00 0.00 1.40
3251 12940 6.118170 TGTCACGCTACTACTATAGACCTTT 58.882 40.000 6.78 0.00 0.00 3.11
3441 13131 2.042464 TCCTTCCTTGGATCATCCTCG 58.958 52.381 4.96 0.00 37.46 4.63
3456 13146 2.741517 GAGTTGCTTGAGCTCTTCCTTC 59.258 50.000 16.19 2.10 42.66 3.46
3507 13197 2.186160 CCGGACTTGCTTGTGTGCA 61.186 57.895 0.00 0.00 41.65 4.57
3648 13338 2.652530 GCGTACCCGACAACCAGA 59.347 61.111 0.00 0.00 35.63 3.86
3868 13558 5.423886 TGTATGTCACTTGTGAACAGACAA 58.576 37.500 20.15 11.21 41.86 3.18
3888 13578 2.678934 AGCGACGGAAGGGCTGTA 60.679 61.111 0.00 0.00 42.22 2.74
4079 16317 8.314021 TCAGCAATGTACAAAAGAGAGAGATAA 58.686 33.333 0.00 0.00 0.00 1.75
4117 16359 4.190001 AGCAGTACAAGCATCAAGATCAG 58.810 43.478 12.08 0.00 0.00 2.90
4227 16471 3.005791 AGCTTAGGCAACAATCAACCAAC 59.994 43.478 0.00 0.00 41.70 3.77
4239 16483 2.143122 CAAACGTCAGAGCTTAGGCAA 58.857 47.619 0.00 0.00 41.70 4.52
4241 16485 1.461127 CACAAACGTCAGAGCTTAGGC 59.539 52.381 0.00 0.00 39.06 3.93
4407 16660 6.488344 TCTTGTTGTATGCTTCCACACAATAA 59.512 34.615 0.00 0.00 40.18 1.40
4426 16679 2.162681 GCAATGTAGTGCCCTCTTGTT 58.837 47.619 0.00 0.00 38.66 2.83
4432 16685 2.438434 GCCGCAATGTAGTGCCCT 60.438 61.111 0.00 0.00 41.73 5.19
4510 16763 3.615709 GGTGGCGCCCAAGCTTTT 61.616 61.111 26.77 0.00 34.18 2.27
4819 17072 2.560981 TGACACGAGCATGGTTAGAGAA 59.439 45.455 0.00 0.00 0.00 2.87
4851 17104 1.866237 GCGCATTTCACTCGTTCCA 59.134 52.632 0.30 0.00 0.00 3.53
4860 17113 0.658829 CGGAAAACACGCGCATTTCA 60.659 50.000 24.04 0.00 35.32 2.69


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

AutoCloner maintained by Alex Coulton.