Multiple sequence alignment - TraesCS7D01G191900

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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 TraesCS7D01G191900 chr7D 100.000 1619 0 0 2218 3836 147577052 147575434 0.000000e+00 2990.0
1 TraesCS7D01G191900 chr7D 100.000 1549 0 0 1 1549 147579269 147577721 0.000000e+00 2861.0
2 TraesCS7D01G191900 chr7D 95.780 545 23 0 3292 3836 240875020 240874476 0.000000e+00 880.0
3 TraesCS7D01G191900 chr7D 95.596 545 23 1 3292 3836 406996283 406995740 0.000000e+00 872.0
4 TraesCS7D01G191900 chr7D 93.548 62 4 0 671 732 182813670 182813731 4.080000e-15 93.5
5 TraesCS7D01G191900 chr7B 91.135 1286 62 16 1 1265 110352703 110351449 0.000000e+00 1696.0
6 TraesCS7D01G191900 chr7B 95.833 192 8 0 3100 3291 110351447 110351256 1.030000e-80 311.0
7 TraesCS7D01G191900 chr3D 95.404 892 35 3 2218 3103 526482034 526481143 0.000000e+00 1415.0
8 TraesCS7D01G191900 chr3D 95.421 546 24 1 3292 3836 105355329 105355874 0.000000e+00 869.0
9 TraesCS7D01G191900 chr3D 95.255 548 24 1 3289 3836 420601763 420602308 0.000000e+00 867.0
10 TraesCS7D01G191900 chr3D 90.459 283 23 1 1267 1549 486147829 486147551 1.680000e-98 370.0
11 TraesCS7D01G191900 chr5D 95.480 885 36 2 2219 3100 326744041 326744924 0.000000e+00 1410.0
12 TraesCS7D01G191900 chr5D 93.505 893 46 5 2222 3104 357076870 357075980 0.000000e+00 1317.0
13 TraesCS7D01G191900 chr5D 96.330 545 19 1 3292 3836 117651635 117651092 0.000000e+00 894.0
14 TraesCS7D01G191900 chr5D 95.413 545 24 1 3292 3836 300034526 300033983 0.000000e+00 867.0
15 TraesCS7D01G191900 chr5D 91.727 278 18 2 1272 1549 326743004 326743276 7.780000e-102 381.0
16 TraesCS7D01G191900 chr5D 91.912 272 22 0 1267 1538 444747590 444747319 7.780000e-102 381.0
17 TraesCS7D01G191900 chrUn 94.607 890 40 3 2222 3103 108949060 108948171 0.000000e+00 1371.0
18 TraesCS7D01G191900 chrUn 94.231 884 46 3 2222 3102 79926018 79925137 0.000000e+00 1345.0
19 TraesCS7D01G191900 chrUn 90.391 281 27 0 1267 1547 427412142 427412422 1.680000e-98 370.0
20 TraesCS7D01G191900 chr1D 94.476 887 42 3 2222 3102 479343126 479342241 0.000000e+00 1360.0
21 TraesCS7D01G191900 chr1D 92.537 268 19 1 1267 1533 13229700 13229433 2.160000e-102 383.0
22 TraesCS7D01G191900 chr1D 89.691 291 27 3 1262 1549 441580052 441580342 6.050000e-98 368.0
23 TraesCS7D01G191900 chr2D 94.558 882 38 4 2222 3100 489651460 489652334 0.000000e+00 1354.0
24 TraesCS7D01G191900 chr2D 93.878 882 47 4 2222 3100 54890003 54889126 0.000000e+00 1323.0
25 TraesCS7D01G191900 chr2D 95.963 545 22 0 3292 3836 153160606 153160062 0.000000e+00 885.0
26 TraesCS7D01G191900 chr2D 87.912 273 22 4 704 971 140491208 140491474 1.030000e-80 311.0
27 TraesCS7D01G191900 chr4D 94.299 877 45 2 2229 3102 145625252 145624378 0.000000e+00 1338.0
28 TraesCS7D01G191900 chr7A 91.000 1000 55 21 1 971 148832129 148831136 0.000000e+00 1315.0
29 TraesCS7D01G191900 chr7A 91.327 196 13 2 3100 3291 148830924 148830729 8.170000e-67 265.0
30 TraesCS7D01G191900 chr7A 93.701 127 8 0 1016 1142 148831129 148831003 1.410000e-44 191.0
31 TraesCS7D01G191900 chr6D 96.147 545 21 0 3292 3836 312348065 312347521 0.000000e+00 891.0
32 TraesCS7D01G191900 chr6D 95.780 545 22 1 3292 3836 33859534 33860077 0.000000e+00 878.0
33 TraesCS7D01G191900 chr6D 91.667 96 2 6 707 797 157316787 157316693 1.120000e-25 128.0
34 TraesCS7D01G191900 chr3A 92.391 276 21 0 1267 1542 9515441 9515716 9.990000e-106 394.0
35 TraesCS7D01G191900 chr3B 90.813 283 26 0 1267 1549 207205128 207204846 2.800000e-101 379.0
36 TraesCS7D01G191900 chr5B 90.845 284 22 2 1266 1549 517573189 517572910 1.010000e-100 377.0
37 TraesCS7D01G191900 chr4B 100.000 34 0 0 685 718 14508671 14508704 3.200000e-06 63.9
38 TraesCS7D01G191900 chr4B 100.000 34 0 0 685 718 14509542 14509575 3.200000e-06 63.9
39 TraesCS7D01G191900 chr4B 100.000 34 0 0 685 718 14512394 14512427 3.200000e-06 63.9
40 TraesCS7D01G191900 chr4B 100.000 34 0 0 685 718 14512622 14512655 3.200000e-06 63.9
41 TraesCS7D01G191900 chr4B 100.000 34 0 0 685 718 14513503 14513536 3.200000e-06 63.9
42 TraesCS7D01G191900 chr4B 100.000 34 0 0 685 718 14513731 14513764 3.200000e-06 63.9


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 TraesCS7D01G191900 chr7D 147575434 147579269 3835 True 2925.500000 2990 100.000000 1 3836 2 chr7D.!!$R3 3835
1 TraesCS7D01G191900 chr7D 240874476 240875020 544 True 880.000000 880 95.780000 3292 3836 1 chr7D.!!$R1 544
2 TraesCS7D01G191900 chr7D 406995740 406996283 543 True 872.000000 872 95.596000 3292 3836 1 chr7D.!!$R2 544
3 TraesCS7D01G191900 chr7B 110351256 110352703 1447 True 1003.500000 1696 93.484000 1 3291 2 chr7B.!!$R1 3290
4 TraesCS7D01G191900 chr3D 526481143 526482034 891 True 1415.000000 1415 95.404000 2218 3103 1 chr3D.!!$R2 885
5 TraesCS7D01G191900 chr3D 105355329 105355874 545 False 869.000000 869 95.421000 3292 3836 1 chr3D.!!$F1 544
6 TraesCS7D01G191900 chr3D 420601763 420602308 545 False 867.000000 867 95.255000 3289 3836 1 chr3D.!!$F2 547
7 TraesCS7D01G191900 chr5D 357075980 357076870 890 True 1317.000000 1317 93.505000 2222 3104 1 chr5D.!!$R3 882
8 TraesCS7D01G191900 chr5D 326743004 326744924 1920 False 895.500000 1410 93.603500 1272 3100 2 chr5D.!!$F1 1828
9 TraesCS7D01G191900 chr5D 117651092 117651635 543 True 894.000000 894 96.330000 3292 3836 1 chr5D.!!$R1 544
10 TraesCS7D01G191900 chr5D 300033983 300034526 543 True 867.000000 867 95.413000 3292 3836 1 chr5D.!!$R2 544
11 TraesCS7D01G191900 chrUn 108948171 108949060 889 True 1371.000000 1371 94.607000 2222 3103 1 chrUn.!!$R2 881
12 TraesCS7D01G191900 chrUn 79925137 79926018 881 True 1345.000000 1345 94.231000 2222 3102 1 chrUn.!!$R1 880
13 TraesCS7D01G191900 chr1D 479342241 479343126 885 True 1360.000000 1360 94.476000 2222 3102 1 chr1D.!!$R2 880
14 TraesCS7D01G191900 chr2D 489651460 489652334 874 False 1354.000000 1354 94.558000 2222 3100 1 chr2D.!!$F2 878
15 TraesCS7D01G191900 chr2D 54889126 54890003 877 True 1323.000000 1323 93.878000 2222 3100 1 chr2D.!!$R1 878
16 TraesCS7D01G191900 chr2D 153160062 153160606 544 True 885.000000 885 95.963000 3292 3836 1 chr2D.!!$R2 544
17 TraesCS7D01G191900 chr4D 145624378 145625252 874 True 1338.000000 1338 94.299000 2229 3102 1 chr4D.!!$R1 873
18 TraesCS7D01G191900 chr7A 148830729 148832129 1400 True 590.333333 1315 92.009333 1 3291 3 chr7A.!!$R1 3290
19 TraesCS7D01G191900 chr6D 312347521 312348065 544 True 891.000000 891 96.147000 3292 3836 1 chr6D.!!$R2 544
20 TraesCS7D01G191900 chr6D 33859534 33860077 543 False 878.000000 878 95.780000 3292 3836 1 chr6D.!!$F1 544

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
610 645 0.252742 AAGATTCGGGGGAGGTCACT 60.253 55.000 0.0 0.0 0.00 3.41 F
1192 1238 0.307453 TTGAGCGACAACATGCACAC 59.693 50.000 0.0 0.0 31.47 3.82 F
1494 1541 1.135689 CACTTCATTTCCTTTCCCGCG 60.136 52.381 0.0 0.0 0.00 6.46 F
2582 2723 1.745489 GAGGCGATGGCGAGGTTTT 60.745 57.895 0.0 0.0 41.24 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2582 2723 0.032515 TACTCCGGATGCTCCCAAGA 60.033 55.000 3.57 0.0 31.13 3.02 R
2780 2936 0.954449 CTGCAGAACTGTGCCCAGAG 60.954 60.000 8.42 0.0 43.28 3.35 R
2788 2944 1.005630 GTCGGAGCTGCAGAACTGT 60.006 57.895 20.43 0.0 0.00 3.55 R
3781 3942 0.531200 GCGAGGCTACAGTAACCAGT 59.469 55.000 2.77 0.0 0.00 4.00 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
33 34 2.747446 GCCAACCGATTCTTTTCTGCTA 59.253 45.455 0.00 0.00 0.00 3.49
120 127 1.224592 GGTGTCCATAGGCTGGTGG 59.775 63.158 12.95 12.95 46.08 4.61
121 128 1.562672 GGTGTCCATAGGCTGGTGGT 61.563 60.000 17.06 0.00 46.08 4.16
122 129 0.392998 GTGTCCATAGGCTGGTGGTG 60.393 60.000 17.06 1.00 46.08 4.17
123 130 1.224592 GTCCATAGGCTGGTGGTGG 59.775 63.158 17.06 8.81 46.08 4.61
124 131 1.229820 TCCATAGGCTGGTGGTGGT 60.230 57.895 17.06 0.00 46.08 4.16
125 132 1.077501 CCATAGGCTGGTGGTGGTG 60.078 63.158 11.40 0.00 40.49 4.17
206 216 6.699575 ACAGCAGTAGAACTCAATTTTGTT 57.300 33.333 0.00 0.00 0.00 2.83
279 293 5.578157 TCATCATCTCCCATCATCATGTT 57.422 39.130 0.00 0.00 0.00 2.71
347 367 9.586150 CTGCAGTCGATGATATTACAAATTAAC 57.414 33.333 5.25 0.00 0.00 2.01
348 368 8.272866 TGCAGTCGATGATATTACAAATTAACG 58.727 33.333 0.00 0.00 0.00 3.18
350 370 9.567917 CAGTCGATGATATTACAAATTAACGTG 57.432 33.333 0.00 0.00 0.00 4.49
351 371 8.761497 AGTCGATGATATTACAAATTAACGTGG 58.239 33.333 0.00 0.00 0.00 4.94
353 373 9.747293 TCGATGATATTACAAATTAACGTGGTA 57.253 29.630 0.00 0.00 0.00 3.25
470 494 9.988815 CACTAATATAGATAGTCCAGCAACTTT 57.011 33.333 0.00 0.00 31.33 2.66
489 513 3.775654 GGTGGCGCCTCTGCTAGT 61.776 66.667 29.70 0.00 34.43 2.57
538 573 7.559590 AGCAAGAAATGGCAAGTACTAATAG 57.440 36.000 0.00 0.00 0.00 1.73
569 604 5.515270 GCAACTTAATTAAGACCGCAAATCC 59.485 40.000 27.92 4.37 37.08 3.01
575 610 2.435938 GACCGCAAATCCGCCAGA 60.436 61.111 0.00 0.00 0.00 3.86
607 642 1.830836 GGAAGATTCGGGGGAGGTC 59.169 63.158 0.00 0.00 0.00 3.85
608 643 0.981277 GGAAGATTCGGGGGAGGTCA 60.981 60.000 0.00 0.00 0.00 4.02
610 645 0.252742 AAGATTCGGGGGAGGTCACT 60.253 55.000 0.00 0.00 0.00 3.41
679 714 5.634439 CCGTGAGATGATGAGATCAGATTTC 59.366 44.000 0.00 0.00 43.53 2.17
680 715 5.342791 CGTGAGATGATGAGATCAGATTTCG 59.657 44.000 0.00 0.00 43.53 3.46
761 797 7.137426 GCACCTCATCATCAAGAATCAAATAC 58.863 38.462 0.00 0.00 0.00 1.89
762 798 7.350467 CACCTCATCATCAAGAATCAAATACG 58.650 38.462 0.00 0.00 0.00 3.06
763 799 7.225341 CACCTCATCATCAAGAATCAAATACGA 59.775 37.037 0.00 0.00 0.00 3.43
764 800 7.440556 ACCTCATCATCAAGAATCAAATACGAG 59.559 37.037 0.00 0.00 0.00 4.18
765 801 7.440556 CCTCATCATCAAGAATCAAATACGAGT 59.559 37.037 0.00 0.00 0.00 4.18
766 802 9.468532 CTCATCATCAAGAATCAAATACGAGTA 57.531 33.333 0.00 0.00 0.00 2.59
778 818 2.071844 TACGAGTATGCCGCTGCTCC 62.072 60.000 0.70 0.00 38.71 4.70
817 863 2.284625 ATGCTGGGTCTGGACGGA 60.285 61.111 0.00 0.00 0.00 4.69
833 879 2.637383 GGAGACCTCCGCTTGTCGT 61.637 63.158 0.00 0.00 40.36 4.34
844 890 1.917273 GCTTGTCGTACTGGCGATTA 58.083 50.000 0.00 0.00 43.07 1.75
935 981 2.290260 TGGGTTTACTCCTCGTCGTAGA 60.290 50.000 0.00 0.00 0.00 2.59
943 989 3.695060 ACTCCTCGTCGTAGATCAACAAT 59.305 43.478 0.00 0.00 40.67 2.71
949 995 4.619760 TCGTCGTAGATCAACAATTGACAC 59.380 41.667 13.59 0.00 43.48 3.67
953 999 5.408299 TCGTAGATCAACAATTGACACAAGG 59.592 40.000 13.59 0.00 43.48 3.61
954 1000 5.390885 CGTAGATCAACAATTGACACAAGGG 60.391 44.000 13.59 0.00 43.48 3.95
971 1017 3.452755 AGGGTTCGCCAAAAAGAAAAG 57.547 42.857 0.00 0.00 39.65 2.27
973 1019 3.449377 AGGGTTCGCCAAAAAGAAAAGAA 59.551 39.130 0.00 0.00 39.65 2.52
976 1022 5.122554 GGGTTCGCCAAAAAGAAAAGAAAAA 59.877 36.000 0.00 0.00 39.65 1.94
977 1023 6.183360 GGGTTCGCCAAAAAGAAAAGAAAAAT 60.183 34.615 0.00 0.00 39.65 1.82
978 1024 6.686679 GGTTCGCCAAAAAGAAAAGAAAAATG 59.313 34.615 0.00 0.00 37.19 2.32
988 1034 7.486802 AAGAAAAGAAAAATGGCAGTTGATG 57.513 32.000 0.00 0.00 0.00 3.07
992 1038 6.403866 AAGAAAAATGGCAGTTGATGTACA 57.596 33.333 0.00 0.00 0.00 2.90
995 1041 7.444299 AGAAAAATGGCAGTTGATGTACAATT 58.556 30.769 0.00 0.00 40.76 2.32
1066 1112 6.292596 GGATCTGAAGAATCGAATTACAGCAC 60.293 42.308 0.00 0.00 0.00 4.40
1160 1206 2.425143 TCAGCATCTGAAATGGGGAC 57.575 50.000 0.00 0.00 37.57 4.46
1161 1207 1.019673 CAGCATCTGAAATGGGGACG 58.980 55.000 0.00 0.00 32.44 4.79
1165 1211 1.605710 CATCTGAAATGGGGACGATGC 59.394 52.381 0.00 0.00 0.00 3.91
1192 1238 0.307453 TTGAGCGACAACATGCACAC 59.693 50.000 0.00 0.00 31.47 3.82
1205 1251 5.424121 ACATGCACACTACACTTTTCTTC 57.576 39.130 0.00 0.00 0.00 2.87
1209 1255 3.303132 GCACACTACACTTTTCTTCCACG 60.303 47.826 0.00 0.00 0.00 4.94
1265 1312 7.218228 ACATTGTCATTTCAAGTTGAGCATA 57.782 32.000 5.56 0.00 0.00 3.14
1266 1313 7.660112 ACATTGTCATTTCAAGTTGAGCATAA 58.340 30.769 5.56 0.00 0.00 1.90
1267 1314 7.811236 ACATTGTCATTTCAAGTTGAGCATAAG 59.189 33.333 5.56 0.00 0.00 1.73
1268 1315 5.702865 TGTCATTTCAAGTTGAGCATAAGC 58.297 37.500 5.56 0.00 42.56 3.09
1269 1316 5.241285 TGTCATTTCAAGTTGAGCATAAGCA 59.759 36.000 5.56 0.00 45.49 3.91
1270 1317 6.071784 TGTCATTTCAAGTTGAGCATAAGCAT 60.072 34.615 5.56 0.00 45.49 3.79
1271 1318 6.471519 GTCATTTCAAGTTGAGCATAAGCATC 59.528 38.462 5.56 0.00 45.49 3.91
1272 1319 6.376299 TCATTTCAAGTTGAGCATAAGCATCT 59.624 34.615 5.56 0.00 45.49 2.90
1273 1320 6.579666 TTTCAAGTTGAGCATAAGCATCTT 57.420 33.333 5.56 0.00 45.49 2.40
1274 1321 5.808042 TCAAGTTGAGCATAAGCATCTTC 57.192 39.130 0.08 0.00 45.49 2.87
1275 1322 5.247862 TCAAGTTGAGCATAAGCATCTTCA 58.752 37.500 0.08 0.00 45.49 3.02
1276 1323 5.706833 TCAAGTTGAGCATAAGCATCTTCAA 59.293 36.000 0.08 0.00 45.49 2.69
1323 1370 9.486857 GTAACTAATTTTTGAATCGTCTAAGGC 57.513 33.333 0.00 0.00 0.00 4.35
1399 1446 5.527582 GCCTCCTCGTGATGTAAAATACAAT 59.472 40.000 0.00 0.00 42.76 2.71
1405 1452 7.096189 CCTCGTGATGTAAAATACAATACCTCG 60.096 40.741 0.00 0.00 42.76 4.63
1428 1475 3.124466 CGGTGCAAATTTACATCACGAGA 59.876 43.478 2.67 0.00 0.00 4.04
1494 1541 1.135689 CACTTCATTTCCTTTCCCGCG 60.136 52.381 0.00 0.00 0.00 6.46
2451 2592 2.025793 ACTTCCCAGAGATCGAGAGTCA 60.026 50.000 0.00 0.00 0.00 3.41
2497 2638 2.449464 CAGGGCATCAACATGAAGGAA 58.551 47.619 0.00 0.00 30.57 3.36
2543 2684 2.744307 GAAGCCGTCGGTTGTCGTCT 62.744 60.000 13.94 0.00 40.32 4.18
2582 2723 1.745489 GAGGCGATGGCGAGGTTTT 60.745 57.895 0.00 0.00 41.24 2.43
2755 2909 2.015726 GGAGGAGGAGGAGGAGGGA 61.016 68.421 0.00 0.00 0.00 4.20
2778 2934 2.362632 CGACCCGGAGAAGGAGGT 60.363 66.667 0.73 0.00 34.57 3.85
2780 2936 3.003763 ACCCGGAGAAGGAGGTGC 61.004 66.667 0.73 0.00 0.00 5.01
2818 2974 2.759783 CTCCGACGACGAGGAGTAA 58.240 57.895 25.13 5.10 46.68 2.24
2819 2975 1.081892 CTCCGACGACGAGGAGTAAA 58.918 55.000 25.13 4.82 46.68 2.01
3127 3283 0.526662 CCCTGTCCTGTACGAGACAC 59.473 60.000 12.38 2.16 38.07 3.67
3158 3314 1.945394 GGCACCAATATCACAGCAGAG 59.055 52.381 0.00 0.00 0.00 3.35
3323 3483 1.087202 GTGCGACATATGCCAACGGA 61.087 55.000 1.58 2.69 0.00 4.69
3398 3558 2.809174 CGAAGACATGCACGCCGA 60.809 61.111 0.00 0.00 0.00 5.54
3427 3587 2.685380 CAGGTTCGGGGCTCTCCT 60.685 66.667 0.00 0.00 35.33 3.69
3684 3845 2.184579 GGTCCTAGCCGTCAGTGC 59.815 66.667 0.00 0.00 0.00 4.40
3781 3942 2.122769 TGGGGGTCTTGTCGGTGA 60.123 61.111 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
206 216 7.676004 TCTGGACAAATTCTGTGACTATTACA 58.324 34.615 0.00 0.00 38.84 2.41
315 335 2.967599 ATCATCGACTGCAGCACTAA 57.032 45.000 15.27 0.00 0.00 2.24
360 381 3.788227 AAGGTAGGAAGTGTCATGCAA 57.212 42.857 0.00 0.00 0.00 4.08
510 534 5.070001 AGTACTTGCCATTTCTTGCTTGTA 58.930 37.500 0.00 0.00 0.00 2.41
515 539 7.281100 ACTCTATTAGTACTTGCCATTTCTTGC 59.719 37.037 0.00 0.00 36.36 4.01
538 573 5.063564 CGGTCTTAATTAAGTTGCTGGACTC 59.936 44.000 21.69 7.23 34.93 3.36
607 642 2.502510 GCGGTTGCAATGCGAGTG 60.503 61.111 0.59 0.00 42.15 3.51
761 797 2.659897 GGAGCAGCGGCATACTCG 60.660 66.667 12.44 0.00 44.61 4.18
762 798 2.659897 CGGAGCAGCGGCATACTC 60.660 66.667 12.44 5.57 44.61 2.59
763 799 2.521958 AAACGGAGCAGCGGCATACT 62.522 55.000 12.44 0.00 44.61 2.12
764 800 1.644786 AAAACGGAGCAGCGGCATAC 61.645 55.000 12.44 1.84 44.61 2.39
765 801 0.958382 AAAAACGGAGCAGCGGCATA 60.958 50.000 12.44 0.00 44.61 3.14
766 802 2.268076 AAAAACGGAGCAGCGGCAT 61.268 52.632 12.44 0.00 44.61 4.40
791 831 0.322277 AGACCCAGCATGCAGTTCAG 60.322 55.000 21.98 4.57 31.97 3.02
817 863 0.608582 AGTACGACAAGCGGAGGTCT 60.609 55.000 0.00 0.00 46.49 3.85
833 879 1.134521 CAGGCTTGGTAATCGCCAGTA 60.135 52.381 2.12 0.00 46.14 2.74
844 890 1.597027 CCGAACGAACAGGCTTGGT 60.597 57.895 0.00 0.00 0.00 3.67
935 981 4.261572 CGAACCCTTGTGTCAATTGTTGAT 60.262 41.667 5.13 0.00 42.47 2.57
943 989 0.394488 TTGGCGAACCCTTGTGTCAA 60.394 50.000 0.00 0.00 33.59 3.18
949 995 2.880963 TTCTTTTTGGCGAACCCTTG 57.119 45.000 0.00 0.00 33.59 3.61
953 999 5.788055 TTTTCTTTTCTTTTTGGCGAACC 57.212 34.783 0.00 0.00 0.00 3.62
954 1000 6.686679 CCATTTTTCTTTTCTTTTTGGCGAAC 59.313 34.615 0.00 0.00 0.00 3.95
971 1017 7.599998 AGAATTGTACATCAACTGCCATTTTTC 59.400 33.333 0.00 0.00 38.97 2.29
973 1019 6.996509 AGAATTGTACATCAACTGCCATTTT 58.003 32.000 0.00 0.00 38.97 1.82
976 1022 6.435277 AGAAAGAATTGTACATCAACTGCCAT 59.565 34.615 0.00 0.00 38.97 4.40
977 1023 5.769662 AGAAAGAATTGTACATCAACTGCCA 59.230 36.000 0.00 0.00 38.97 4.92
978 1024 6.259550 AGAAAGAATTGTACATCAACTGCC 57.740 37.500 0.00 0.00 38.97 4.85
1066 1112 3.691049 ACATCGGGAATATTGCGTTTG 57.309 42.857 0.46 1.26 0.00 2.93
1160 1206 0.027194 CGCTCAAATCACCAGCATCG 59.973 55.000 0.00 0.00 32.27 3.84
1161 1207 1.063174 GTCGCTCAAATCACCAGCATC 59.937 52.381 0.00 0.00 32.27 3.91
1165 1211 1.872952 TGTTGTCGCTCAAATCACCAG 59.127 47.619 0.00 0.00 37.81 4.00
1192 1238 1.804748 GCCCGTGGAAGAAAAGTGTAG 59.195 52.381 0.00 0.00 0.00 2.74
1205 1251 2.325583 ATTGTACATGTAGCCCGTGG 57.674 50.000 5.62 0.00 34.14 4.94
1209 1255 6.264744 TCACTAGAGTATTGTACATGTAGCCC 59.735 42.308 5.62 0.00 0.00 5.19
1253 1300 5.556355 TGAAGATGCTTATGCTCAACTTG 57.444 39.130 1.96 0.00 40.48 3.16
1303 1350 8.655651 TTTTTGCCTTAGACGATTCAAAAATT 57.344 26.923 0.00 0.00 38.01 1.82
1405 1452 1.910819 CGTGATGTAAATTTGCACCGC 59.089 47.619 11.35 7.61 0.00 5.68
1466 1513 0.388520 GGAAATGAAGTGGCGGTTGC 60.389 55.000 0.00 0.00 41.71 4.17
1476 1523 0.179163 GCGCGGGAAAGGAAATGAAG 60.179 55.000 8.83 0.00 0.00 3.02
1480 1527 3.810896 GCGCGCGGGAAAGGAAAT 61.811 61.111 33.06 0.00 0.00 2.17
2220 2267 1.826054 ATCGGAGAGCGGTGAGAGG 60.826 63.158 0.00 0.00 43.63 3.69
2275 2416 2.357034 TTCTGCCTCACGCCGAAC 60.357 61.111 0.00 0.00 35.97 3.95
2299 2440 1.264295 ACTCCACTCCGAAGTTACCC 58.736 55.000 0.00 0.00 31.71 3.69
2451 2592 4.537433 GCATCTCCGCTTCCGCCT 62.537 66.667 0.00 0.00 0.00 5.52
2497 2638 2.415625 CGTCTTCTTCTTCGTCGGGATT 60.416 50.000 0.00 0.00 0.00 3.01
2543 2684 4.357947 GTCGGTCTCGCCAGCACA 62.358 66.667 0.00 0.00 36.97 4.57
2582 2723 0.032515 TACTCCGGATGCTCCCAAGA 60.033 55.000 3.57 0.00 31.13 3.02
2755 2909 3.064987 CTTCTCCGGGTCGTCGCAT 62.065 63.158 0.00 0.00 0.00 4.73
2780 2936 0.954449 CTGCAGAACTGTGCCCAGAG 60.954 60.000 8.42 0.00 43.28 3.35
2788 2944 1.005630 GTCGGAGCTGCAGAACTGT 60.006 57.895 20.43 0.00 0.00 3.55
3040 3196 7.309316 GGTCCAAAACCGGAGATGTAAAATTTA 60.309 37.037 9.46 0.00 38.58 1.40
3127 3283 1.602323 TTGGTGCCCAAGCCGTTAG 60.602 57.895 2.84 0.00 38.75 2.34
3169 3325 9.490379 AGAGTTTCGTCAACAAAGAAATATAGT 57.510 29.630 3.61 0.00 37.61 2.12
3226 3386 4.993705 TCCCACAGACTTCACCTAATTT 57.006 40.909 0.00 0.00 0.00 1.82
3323 3483 2.590821 GCTCCCACAATGATAAGCCAT 58.409 47.619 0.00 0.00 0.00 4.40
3398 3558 1.206371 CCGAACCTGGGTAAGATTCGT 59.794 52.381 12.08 0.00 40.32 3.85
3427 3587 3.013648 AGGACTAGGGGTGTTATCTCCAA 59.986 47.826 0.00 0.00 0.00 3.53
3684 3845 0.876342 GAGAAGCCGGCGAATACAGG 60.876 60.000 23.20 0.00 0.00 4.00
3781 3942 0.531200 GCGAGGCTACAGTAACCAGT 59.469 55.000 2.77 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.