Multiple sequence alignment - TraesCS3A01G114800

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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 TraesCS3A01G114800 chr3A 100.000 2702 0 0 1 2702 82397443 82394742 0.000000e+00 4990.0
1 TraesCS3A01G114800 chr3A 90.678 118 11 0 238 355 147557830 147557947 1.000000e-34 158.0
2 TraesCS3A01G114800 chr3D 90.863 1981 91 41 801 2702 70716650 70714681 0.000000e+00 2573.0
3 TraesCS3A01G114800 chr3D 88.068 352 34 3 361 704 70717157 70716806 6.960000e-111 411.0
4 TraesCS3A01G114800 chr3D 84.259 216 17 8 12 222 70718507 70718304 7.630000e-46 195.0
5 TraesCS3A01G114800 chr3D 93.243 74 5 0 733 806 70716757 70716684 2.840000e-20 110.0
6 TraesCS3A01G114800 chr3D 100.000 29 0 0 724 752 70716801 70716773 1.000000e-03 54.7
7 TraesCS3A01G114800 chr3B 90.328 1158 44 18 813 1922 116151740 116150603 0.000000e+00 1456.0
8 TraesCS3A01G114800 chr3B 82.278 790 113 17 1922 2702 116149971 116149200 0.000000e+00 658.0
9 TraesCS3A01G114800 chr3B 83.032 442 28 11 1922 2345 116150562 116150150 9.200000e-95 357.0
10 TraesCS3A01G114800 chr3B 88.142 253 20 7 361 605 116153744 116153494 2.630000e-75 292.0
11 TraesCS3A01G114800 chr3B 91.818 110 3 1 13 122 116153945 116153842 6.030000e-32 148.0
12 TraesCS3A01G114800 chr6A 93.458 107 7 0 247 353 101997962 101997856 2.780000e-35 159.0
13 TraesCS3A01G114800 chr5A 92.593 108 8 0 243 350 119066897 119067004 3.600000e-34 156.0
14 TraesCS3A01G114800 chr5A 90.517 116 10 1 241 355 382766644 382766759 4.660000e-33 152.0
15 TraesCS3A01G114800 chr5A 87.500 128 15 1 240 367 113851838 113851964 2.170000e-31 147.0
16 TraesCS3A01G114800 chr1B 91.150 113 10 0 238 350 492329849 492329961 1.300000e-33 154.0
17 TraesCS3A01G114800 chr7D 89.256 121 13 0 239 359 598012946 598013066 4.660000e-33 152.0
18 TraesCS3A01G114800 chr7B 90.351 114 11 0 244 357 667088652 667088765 1.680000e-32 150.0
19 TraesCS3A01G114800 chr1A 89.744 117 12 0 238 354 502769345 502769461 1.680000e-32 150.0


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 TraesCS3A01G114800 chr3A 82394742 82397443 2701 True 4990.00 4990 100.0000 1 2702 1 chr3A.!!$R1 2701
1 TraesCS3A01G114800 chr3D 70714681 70718507 3826 True 668.74 2573 91.2866 12 2702 5 chr3D.!!$R1 2690
2 TraesCS3A01G114800 chr3B 116149200 116153945 4745 True 582.20 1456 87.1196 13 2702 5 chr3B.!!$R1 2689

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
136 142 0.033601 AGACAAACCTTGGGTGTGCA 60.034 50.0 6.78 0.0 44.36 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 4447 1.069296 GCAGCAGTTCATAAACGCACA 60.069 47.619 0.0 0.0 40.48 4.57 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
53 54 2.315925 CCGCAGATCAATGTGGTACT 57.684 50.000 6.42 0.00 44.30 2.73
54 55 1.935873 CCGCAGATCAATGTGGTACTG 59.064 52.381 6.42 0.00 44.30 2.74
55 56 1.935873 CGCAGATCAATGTGGTACTGG 59.064 52.381 0.00 0.00 0.00 4.00
56 57 2.677902 CGCAGATCAATGTGGTACTGGT 60.678 50.000 0.00 0.00 0.00 4.00
57 58 3.430236 CGCAGATCAATGTGGTACTGGTA 60.430 47.826 0.00 0.00 0.00 3.25
74 75 3.211865 TGGTAGTAGTAGATGACCAGCG 58.788 50.000 0.00 0.00 35.26 5.18
81 82 4.819761 GATGACCAGCGCTCGCCA 62.820 66.667 7.13 0.00 43.17 5.69
128 134 0.232303 GACGCACGAGACAAACCTTG 59.768 55.000 0.00 0.00 0.00 3.61
136 142 0.033601 AGACAAACCTTGGGTGTGCA 60.034 50.000 6.78 0.00 44.36 4.57
150 160 2.164624 GGTGTGCACTAGACTAGACCAG 59.835 54.545 19.41 4.45 0.00 4.00
151 161 2.164624 GTGTGCACTAGACTAGACCAGG 59.835 54.545 19.41 1.86 0.00 4.45
152 162 1.135333 GTGCACTAGACTAGACCAGGC 59.865 57.143 16.55 10.96 0.00 4.85
153 163 0.747852 GCACTAGACTAGACCAGGCC 59.252 60.000 16.55 0.00 29.16 5.19
154 164 1.025812 CACTAGACTAGACCAGGCCG 58.974 60.000 16.55 0.00 29.16 6.13
155 165 0.752376 ACTAGACTAGACCAGGCCGC 60.752 60.000 16.55 0.00 29.16 6.53
156 166 0.466555 CTAGACTAGACCAGGCCGCT 60.467 60.000 3.13 0.00 29.16 5.52
157 167 0.752009 TAGACTAGACCAGGCCGCTG 60.752 60.000 0.00 0.00 29.16 5.18
164 174 4.778143 CCAGGCCGCTGGTGGTAC 62.778 72.222 2.74 0.00 39.56 3.34
165 175 4.778143 CAGGCCGCTGGTGGTACC 62.778 72.222 4.43 4.43 39.22 3.34
183 193 5.148651 GTACCATACCAGTGTGTTTCTCT 57.851 43.478 0.00 0.00 0.00 3.10
195 205 2.031944 GTGTTTCTCTTGCGGTTTCCTC 60.032 50.000 0.00 0.00 0.00 3.71
222 1324 7.610305 TGACCACCCTAGTCTTTTGATATTTTC 59.390 37.037 0.00 0.00 35.21 2.29
243 1345 7.921786 TTTCGGTTCATTTGATTGATCTAGT 57.078 32.000 0.00 0.00 0.00 2.57
244 1346 9.443323 TTTTCGGTTCATTTGATTGATCTAGTA 57.557 29.630 0.00 0.00 0.00 1.82
245 1347 9.613428 TTTCGGTTCATTTGATTGATCTAGTAT 57.387 29.630 0.00 0.00 0.00 2.12
247 1349 9.261180 TCGGTTCATTTGATTGATCTAGTATTC 57.739 33.333 0.00 0.00 0.00 1.75
248 1350 8.499162 CGGTTCATTTGATTGATCTAGTATTCC 58.501 37.037 0.00 0.00 0.00 3.01
249 1351 8.787852 GGTTCATTTGATTGATCTAGTATTCCC 58.212 37.037 0.00 0.00 0.00 3.97
252 1354 9.784531 TCATTTGATTGATCTAGTATTCCCTTC 57.215 33.333 0.00 0.00 0.00 3.46
253 1355 8.715998 CATTTGATTGATCTAGTATTCCCTTCG 58.284 37.037 0.00 0.00 0.00 3.79
254 1356 6.978674 TGATTGATCTAGTATTCCCTTCGT 57.021 37.500 0.00 0.00 0.00 3.85
255 1357 7.361457 TGATTGATCTAGTATTCCCTTCGTT 57.639 36.000 0.00 0.00 0.00 3.85
256 1358 7.434492 TGATTGATCTAGTATTCCCTTCGTTC 58.566 38.462 0.00 0.00 0.00 3.95
257 1359 5.786264 TGATCTAGTATTCCCTTCGTTCC 57.214 43.478 0.00 0.00 0.00 3.62
258 1360 4.277672 TGATCTAGTATTCCCTTCGTTCCG 59.722 45.833 0.00 0.00 0.00 4.30
259 1361 3.889815 TCTAGTATTCCCTTCGTTCCGA 58.110 45.455 0.00 0.00 0.00 4.55
260 1362 4.272489 TCTAGTATTCCCTTCGTTCCGAA 58.728 43.478 0.00 0.00 43.75 4.30
262 1364 4.482952 AGTATTCCCTTCGTTCCGAATT 57.517 40.909 0.00 0.00 44.85 2.17
263 1365 5.603170 AGTATTCCCTTCGTTCCGAATTA 57.397 39.130 0.00 0.00 44.85 1.40
264 1366 5.354767 AGTATTCCCTTCGTTCCGAATTAC 58.645 41.667 0.00 0.00 44.85 1.89
267 1369 3.592059 TCCCTTCGTTCCGAATTACTTG 58.408 45.455 0.00 0.00 44.85 3.16
270 1372 2.459060 TCGTTCCGAATTACTTGGCA 57.541 45.000 0.00 0.00 31.06 4.92
272 1374 1.801771 CGTTCCGAATTACTTGGCACA 59.198 47.619 0.00 0.00 0.00 4.57
273 1375 4.050828 TCGTTCCGAATTACTTGGCACAA 61.051 43.478 0.00 0.00 36.67 3.33
274 1376 5.852665 TCGTTCCGAATTACTTGGCACAAG 61.853 45.833 11.87 11.87 36.67 3.16
276 1378 8.889795 TCGTTCCGAATTACTTGGCACAAGTA 62.890 42.308 18.27 18.27 36.67 2.24
289 1391 6.101650 TGGCACAAGTATGGATGTATCTAG 57.898 41.667 0.00 0.00 31.92 2.43
290 1392 5.838521 TGGCACAAGTATGGATGTATCTAGA 59.161 40.000 0.00 0.00 31.92 2.43
291 1393 6.498303 TGGCACAAGTATGGATGTATCTAGAT 59.502 38.462 10.73 10.73 31.92 1.98
292 1394 6.815641 GGCACAAGTATGGATGTATCTAGATG 59.184 42.308 15.79 0.00 0.00 2.90
293 1395 7.382110 GCACAAGTATGGATGTATCTAGATGT 58.618 38.462 15.79 1.25 0.00 3.06
294 1396 8.523658 GCACAAGTATGGATGTATCTAGATGTA 58.476 37.037 15.79 4.44 0.00 2.29
333 1435 9.778741 ATACATCCATTTGTATGACGAGTAATT 57.221 29.630 0.00 0.00 40.44 1.40
334 1436 8.506168 ACATCCATTTGTATGACGAGTAATTT 57.494 30.769 0.00 0.00 33.37 1.82
335 1437 8.397906 ACATCCATTTGTATGACGAGTAATTTG 58.602 33.333 0.00 0.00 33.37 2.32
336 1438 8.611757 CATCCATTTGTATGACGAGTAATTTGA 58.388 33.333 0.00 0.00 33.37 2.69
337 1439 8.554835 TCCATTTGTATGACGAGTAATTTGAA 57.445 30.769 0.00 0.00 33.37 2.69
338 1440 9.004717 TCCATTTGTATGACGAGTAATTTGAAA 57.995 29.630 0.00 0.00 33.37 2.69
339 1441 9.061610 CCATTTGTATGACGAGTAATTTGAAAC 57.938 33.333 0.00 0.00 33.37 2.78
340 1442 8.775884 CATTTGTATGACGAGTAATTTGAAACG 58.224 33.333 0.00 0.00 33.37 3.60
341 1443 6.397831 TGTATGACGAGTAATTTGAAACGG 57.602 37.500 0.00 0.00 0.00 4.44
342 1444 6.157904 TGTATGACGAGTAATTTGAAACGGA 58.842 36.000 0.00 0.00 0.00 4.69
343 1445 6.645827 TGTATGACGAGTAATTTGAAACGGAA 59.354 34.615 0.00 0.00 0.00 4.30
344 1446 5.585500 TGACGAGTAATTTGAAACGGAAG 57.415 39.130 0.00 0.00 0.00 3.46
345 1447 4.449743 TGACGAGTAATTTGAAACGGAAGG 59.550 41.667 0.00 0.00 0.00 3.46
346 1448 4.634199 ACGAGTAATTTGAAACGGAAGGA 58.366 39.130 0.00 0.00 0.00 3.36
347 1449 4.689345 ACGAGTAATTTGAAACGGAAGGAG 59.311 41.667 0.00 0.00 0.00 3.69
348 1450 4.689345 CGAGTAATTTGAAACGGAAGGAGT 59.311 41.667 0.00 0.00 0.00 3.85
349 1451 5.865552 CGAGTAATTTGAAACGGAAGGAGTA 59.134 40.000 0.00 0.00 0.00 2.59
350 1452 6.034683 CGAGTAATTTGAAACGGAAGGAGTAG 59.965 42.308 0.00 0.00 0.00 2.57
351 1453 7.001099 AGTAATTTGAAACGGAAGGAGTAGA 57.999 36.000 0.00 0.00 0.00 2.59
352 1454 7.621796 AGTAATTTGAAACGGAAGGAGTAGAT 58.378 34.615 0.00 0.00 0.00 1.98
353 1455 6.743575 AATTTGAAACGGAAGGAGTAGATG 57.256 37.500 0.00 0.00 0.00 2.90
354 1456 3.247006 TGAAACGGAAGGAGTAGATGC 57.753 47.619 0.00 0.00 0.00 3.91
355 1457 2.093658 TGAAACGGAAGGAGTAGATGCC 60.094 50.000 0.00 0.00 0.00 4.40
356 1458 1.568504 AACGGAAGGAGTAGATGCCA 58.431 50.000 0.00 0.00 0.00 4.92
357 1459 1.568504 ACGGAAGGAGTAGATGCCAA 58.431 50.000 0.00 0.00 0.00 4.52
358 1460 1.207329 ACGGAAGGAGTAGATGCCAAC 59.793 52.381 0.00 0.00 0.00 3.77
359 1461 1.802880 CGGAAGGAGTAGATGCCAACG 60.803 57.143 0.00 0.00 0.00 4.10
412 1519 5.517411 CCTAAGCATTGCACATTACAACATG 59.483 40.000 11.91 0.00 0.00 3.21
413 1520 3.255725 AGCATTGCACATTACAACATGC 58.744 40.909 11.91 6.17 34.66 4.06
494 1606 2.014128 AGGGTTCACGTCAAAACACAG 58.986 47.619 9.24 0.00 31.03 3.66
496 1608 2.937799 GGGTTCACGTCAAAACACAGTA 59.062 45.455 7.16 0.00 0.00 2.74
500 1612 3.967401 TCACGTCAAAACACAGTATCGA 58.033 40.909 0.00 0.00 0.00 3.59
506 1618 7.794810 CACGTCAAAACACAGTATCGAAAAATA 59.205 33.333 0.00 0.00 0.00 1.40
528 1645 1.144716 TGGCGCTCATCATCTGGTC 59.855 57.895 7.64 0.00 0.00 4.02
532 1649 2.548707 GGCGCTCATCATCTGGTCAATA 60.549 50.000 7.64 0.00 0.00 1.90
533 1650 2.735663 GCGCTCATCATCTGGTCAATAG 59.264 50.000 0.00 0.00 0.00 1.73
549 1666 0.040646 ATAGTCCACCTCGGGTCACA 59.959 55.000 0.00 0.00 31.02 3.58
664 1889 9.672086 TCATTTTACTCGATTGTTACCTTTTTG 57.328 29.630 0.00 0.00 0.00 2.44
672 1897 6.483974 TCGATTGTTACCTTTTTGTAAGCTCA 59.516 34.615 0.00 0.00 31.66 4.26
690 1921 6.006275 AGCTCACAATGGGTTATCATTAGT 57.994 37.500 0.00 0.00 35.78 2.24
712 1943 3.025924 TCGTAAGACGGTGGAGTGT 57.974 52.632 0.00 0.00 45.01 3.55
713 1944 1.321474 TCGTAAGACGGTGGAGTGTT 58.679 50.000 0.00 0.00 45.01 3.32
714 1945 2.503331 TCGTAAGACGGTGGAGTGTTA 58.497 47.619 0.00 0.00 45.01 2.41
715 1946 2.485426 TCGTAAGACGGTGGAGTGTTAG 59.515 50.000 0.00 0.00 45.01 2.34
716 1947 2.603953 GTAAGACGGTGGAGTGTTAGC 58.396 52.381 0.00 0.00 31.79 3.09
717 1948 0.320697 AAGACGGTGGAGTGTTAGCC 59.679 55.000 0.00 0.00 0.00 3.93
718 1949 1.445582 GACGGTGGAGTGTTAGCCG 60.446 63.158 0.00 0.00 46.83 5.52
719 1950 2.125673 CGGTGGAGTGTTAGCCGG 60.126 66.667 0.00 0.00 38.86 6.13
720 1951 2.939261 CGGTGGAGTGTTAGCCGGT 61.939 63.158 1.90 0.00 38.86 5.28
721 1952 1.079336 GGTGGAGTGTTAGCCGGTC 60.079 63.158 1.90 0.00 0.00 4.79
722 1953 1.669440 GTGGAGTGTTAGCCGGTCA 59.331 57.895 1.90 0.00 0.00 4.02
799 3441 3.204827 CGCTCAATGGGCCCGAAG 61.205 66.667 19.37 12.58 0.00 3.79
851 3532 4.415150 CCGGCCCACTGCATCAGT 62.415 66.667 0.00 0.00 46.51 3.41
967 3657 0.684153 AAATCCAAGCACCATCCCCG 60.684 55.000 0.00 0.00 0.00 5.73
988 3678 3.379372 CGACAAGATCTGCCAAATCCAAT 59.621 43.478 0.00 0.00 0.00 3.16
1067 3758 0.695347 CAAGTTGAAGGGGAGGAGCT 59.305 55.000 0.00 0.00 0.00 4.09
1218 3948 3.474570 GAGGAGGCGGATGCTGGT 61.475 66.667 0.00 0.00 42.25 4.00
1227 3957 4.479993 GATGCTGGTGCCGAGGCT 62.480 66.667 15.75 0.00 42.51 4.58
1265 3995 1.079987 AGGCTGAAGAGGAGGAGCA 59.920 57.895 0.00 0.00 32.83 4.26
1572 4302 2.749441 GACTGCCTTCCAGCTGCC 60.749 66.667 8.66 0.00 45.78 4.85
1641 4371 3.782244 GTCGCCGAAGCAGCAGTG 61.782 66.667 0.00 0.00 39.83 3.66
1717 4447 2.306512 ACTTAGAGGTGTCTCTCTCCGT 59.693 50.000 0.00 0.00 46.79 4.69
1721 4451 1.080434 GGTGTCTCTCTCCGTGTGC 60.080 63.158 0.00 0.00 0.00 4.57
1739 4469 1.197492 TGCGTTTATGAACTGCTGCTG 59.803 47.619 14.58 4.89 36.74 4.41
1773 4503 1.142870 TGTATTCCTACCCTGCCATGC 59.857 52.381 0.00 0.00 0.00 4.06
1799 4529 8.338259 CGATGGAAGTAGAACCTATGAATTTTG 58.662 37.037 0.00 0.00 0.00 2.44
1910 4646 1.321743 GTAGTGCGAATTCAGCAGTCG 59.678 52.381 25.36 6.19 44.09 4.18
2038 4815 8.642020 CAAAATTAAGACTGCTGCTAAATTCAC 58.358 33.333 0.00 0.00 0.00 3.18
2044 4821 3.240069 CTGCTGCTAAATTCACACTTGC 58.760 45.455 0.00 0.00 0.00 4.01
2132 4915 4.636249 ACCTGCTAACAAGAGAAACTGAG 58.364 43.478 0.00 0.00 0.00 3.35
2175 4975 4.746535 TGGTCCGCAAGAGTTATGATTA 57.253 40.909 0.00 0.00 43.02 1.75
2205 5007 7.969536 ATATGTAGCGATTCAGCAGTTATTT 57.030 32.000 0.00 0.00 40.15 1.40
2323 5720 1.075659 GCTGGTTTCCCTCTTGCCT 59.924 57.895 0.00 0.00 0.00 4.75
2346 5743 2.684881 GGGACATACTGGCATCACAAAG 59.315 50.000 0.00 0.00 0.00 2.77
2402 5799 5.047731 TGTTTGCATGGGAAACGAATCAATA 60.048 36.000 8.46 0.00 36.30 1.90
2487 5885 3.523972 AGTTGGGGGTCTAAAGAGGATTC 59.476 47.826 0.00 0.00 0.00 2.52
2530 5928 8.635765 ACAAGATTAGAATTAGGAACTGCAAA 57.364 30.769 0.00 0.00 41.52 3.68
2571 5969 6.370442 TGTGTCTAAGCGCATAAAGTTGTAAT 59.630 34.615 11.47 0.00 0.00 1.89
2637 6035 6.741992 TCTAATAACAAGTCAACATGGCTG 57.258 37.500 0.00 0.00 29.54 4.85
2647 6045 3.808726 GTCAACATGGCTGATCTGATCTC 59.191 47.826 17.82 9.84 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.756950 CCTCCCGAAGTCCCGATCA 60.757 63.158 0.00 0.00 0.00 2.92
1 2 2.499827 CCCTCCCGAAGTCCCGATC 61.500 68.421 0.00 0.00 0.00 3.69
2 3 2.313749 ATCCCTCCCGAAGTCCCGAT 62.314 60.000 0.00 0.00 0.00 4.18
3 4 1.648302 TATCCCTCCCGAAGTCCCGA 61.648 60.000 0.00 0.00 0.00 5.14
4 5 0.542232 ATATCCCTCCCGAAGTCCCG 60.542 60.000 0.00 0.00 0.00 5.14
5 6 1.268066 GATATCCCTCCCGAAGTCCC 58.732 60.000 0.00 0.00 0.00 4.46
6 7 1.268066 GGATATCCCTCCCGAAGTCC 58.732 60.000 11.02 0.00 0.00 3.85
7 8 2.011122 TGGATATCCCTCCCGAAGTC 57.989 55.000 19.34 0.00 34.12 3.01
8 9 2.489528 TTGGATATCCCTCCCGAAGT 57.510 50.000 19.34 0.00 34.12 3.01
9 10 3.477530 GTTTTGGATATCCCTCCCGAAG 58.522 50.000 19.34 0.00 34.12 3.79
10 11 2.173996 GGTTTTGGATATCCCTCCCGAA 59.826 50.000 19.34 2.56 34.12 4.30
53 54 3.211865 CGCTGGTCATCTACTACTACCA 58.788 50.000 0.00 0.00 37.88 3.25
54 55 2.030981 GCGCTGGTCATCTACTACTACC 60.031 54.545 0.00 0.00 0.00 3.18
55 56 2.879646 AGCGCTGGTCATCTACTACTAC 59.120 50.000 10.39 0.00 0.00 2.73
56 57 3.139850 GAGCGCTGGTCATCTACTACTA 58.860 50.000 18.48 0.00 0.00 1.82
57 58 1.950909 GAGCGCTGGTCATCTACTACT 59.049 52.381 18.48 0.00 0.00 2.57
81 82 2.716424 TGATCTTCCCAAGACCAACCTT 59.284 45.455 0.00 0.00 41.01 3.50
128 134 1.477295 GGTCTAGTCTAGTGCACACCC 59.523 57.143 21.04 3.60 0.00 4.61
136 142 0.752376 GCGGCCTGGTCTAGTCTAGT 60.752 60.000 0.00 0.00 0.00 2.57
161 171 5.148651 AGAGAAACACACTGGTATGGTAC 57.851 43.478 0.00 0.00 0.00 3.34
162 172 5.547465 CAAGAGAAACACACTGGTATGGTA 58.453 41.667 0.00 0.00 0.00 3.25
163 173 4.389374 CAAGAGAAACACACTGGTATGGT 58.611 43.478 0.00 0.00 0.00 3.55
164 174 3.189287 GCAAGAGAAACACACTGGTATGG 59.811 47.826 0.00 0.00 0.00 2.74
165 175 3.120546 CGCAAGAGAAACACACTGGTATG 60.121 47.826 0.00 0.00 43.02 2.39
166 176 3.067106 CGCAAGAGAAACACACTGGTAT 58.933 45.455 0.00 0.00 43.02 2.73
172 182 2.540973 GGAAACCGCAAGAGAAACACAC 60.541 50.000 0.00 0.00 43.02 3.82
175 185 2.158813 AGAGGAAACCGCAAGAGAAACA 60.159 45.455 0.00 0.00 43.02 2.83
183 193 0.534203 GTGGTCAGAGGAAACCGCAA 60.534 55.000 0.43 0.00 43.91 4.85
195 205 4.559862 ATCAAAAGACTAGGGTGGTCAG 57.440 45.455 0.00 0.00 36.29 3.51
222 1324 8.499162 GGAATACTAGATCAATCAAATGAACCG 58.501 37.037 0.00 0.00 32.06 4.44
251 1353 8.889795 TACTTGTGCCAAGTAATTCGGAACGA 62.890 42.308 19.30 0.00 43.82 3.85
252 1354 6.809171 TACTTGTGCCAAGTAATTCGGAACG 61.809 44.000 19.30 0.00 40.66 3.95
253 1355 3.252458 ACTTGTGCCAAGTAATTCGGAAC 59.748 43.478 16.08 0.00 0.00 3.62
254 1356 3.482436 ACTTGTGCCAAGTAATTCGGAA 58.518 40.909 16.08 0.00 0.00 4.30
255 1357 3.134574 ACTTGTGCCAAGTAATTCGGA 57.865 42.857 16.08 0.00 0.00 4.55
256 1358 4.201910 CCATACTTGTGCCAAGTAATTCGG 60.202 45.833 23.03 18.20 36.45 4.30
257 1359 4.634004 TCCATACTTGTGCCAAGTAATTCG 59.366 41.667 23.03 15.04 36.45 3.34
258 1360 6.095440 ACATCCATACTTGTGCCAAGTAATTC 59.905 38.462 23.03 0.00 36.45 2.17
259 1361 5.951747 ACATCCATACTTGTGCCAAGTAATT 59.048 36.000 23.03 11.33 36.45 1.40
260 1362 5.509498 ACATCCATACTTGTGCCAAGTAAT 58.491 37.500 23.03 14.09 36.45 1.89
262 1364 4.568072 ACATCCATACTTGTGCCAAGTA 57.432 40.909 22.06 22.06 37.18 2.24
263 1365 3.439857 ACATCCATACTTGTGCCAAGT 57.560 42.857 19.86 19.86 0.00 3.16
264 1366 5.371526 AGATACATCCATACTTGTGCCAAG 58.628 41.667 11.87 11.87 0.00 3.61
267 1369 6.346477 TCTAGATACATCCATACTTGTGCC 57.654 41.667 0.00 0.00 0.00 5.01
307 1409 9.778741 AATTACTCGTCATACAAATGGATGTAT 57.221 29.630 5.56 0.00 45.12 2.29
308 1410 9.607988 AAATTACTCGTCATACAAATGGATGTA 57.392 29.630 5.56 0.00 39.91 2.29
309 1411 8.397906 CAAATTACTCGTCATACAAATGGATGT 58.602 33.333 5.56 0.00 37.32 3.06
310 1412 8.611757 TCAAATTACTCGTCATACAAATGGATG 58.388 33.333 0.00 0.00 33.61 3.51
311 1413 8.731275 TCAAATTACTCGTCATACAAATGGAT 57.269 30.769 0.00 0.00 33.61 3.41
312 1414 8.554835 TTCAAATTACTCGTCATACAAATGGA 57.445 30.769 0.00 0.00 33.61 3.41
313 1415 9.061610 GTTTCAAATTACTCGTCATACAAATGG 57.938 33.333 0.00 0.00 33.61 3.16
314 1416 8.775884 CGTTTCAAATTACTCGTCATACAAATG 58.224 33.333 0.00 0.00 0.00 2.32
315 1417 7.960738 CCGTTTCAAATTACTCGTCATACAAAT 59.039 33.333 0.00 0.00 0.00 2.32
316 1418 7.171167 TCCGTTTCAAATTACTCGTCATACAAA 59.829 33.333 0.00 0.00 0.00 2.83
317 1419 6.645827 TCCGTTTCAAATTACTCGTCATACAA 59.354 34.615 0.00 0.00 0.00 2.41
318 1420 6.157904 TCCGTTTCAAATTACTCGTCATACA 58.842 36.000 0.00 0.00 0.00 2.29
319 1421 6.636666 TCCGTTTCAAATTACTCGTCATAC 57.363 37.500 0.00 0.00 0.00 2.39
320 1422 6.311935 CCTTCCGTTTCAAATTACTCGTCATA 59.688 38.462 0.00 0.00 0.00 2.15
321 1423 5.121768 CCTTCCGTTTCAAATTACTCGTCAT 59.878 40.000 0.00 0.00 0.00 3.06
322 1424 4.449743 CCTTCCGTTTCAAATTACTCGTCA 59.550 41.667 0.00 0.00 0.00 4.35
323 1425 4.687483 TCCTTCCGTTTCAAATTACTCGTC 59.313 41.667 0.00 0.00 0.00 4.20
324 1426 4.634199 TCCTTCCGTTTCAAATTACTCGT 58.366 39.130 0.00 0.00 0.00 4.18
325 1427 4.689345 ACTCCTTCCGTTTCAAATTACTCG 59.311 41.667 0.00 0.00 0.00 4.18
326 1428 7.095270 TCTACTCCTTCCGTTTCAAATTACTC 58.905 38.462 0.00 0.00 0.00 2.59
327 1429 7.001099 TCTACTCCTTCCGTTTCAAATTACT 57.999 36.000 0.00 0.00 0.00 2.24
328 1430 7.676572 GCATCTACTCCTTCCGTTTCAAATTAC 60.677 40.741 0.00 0.00 0.00 1.89
329 1431 6.315393 GCATCTACTCCTTCCGTTTCAAATTA 59.685 38.462 0.00 0.00 0.00 1.40
330 1432 5.123979 GCATCTACTCCTTCCGTTTCAAATT 59.876 40.000 0.00 0.00 0.00 1.82
331 1433 4.636206 GCATCTACTCCTTCCGTTTCAAAT 59.364 41.667 0.00 0.00 0.00 2.32
332 1434 4.000988 GCATCTACTCCTTCCGTTTCAAA 58.999 43.478 0.00 0.00 0.00 2.69
333 1435 3.596214 GCATCTACTCCTTCCGTTTCAA 58.404 45.455 0.00 0.00 0.00 2.69
334 1436 2.093658 GGCATCTACTCCTTCCGTTTCA 60.094 50.000 0.00 0.00 0.00 2.69
335 1437 2.093658 TGGCATCTACTCCTTCCGTTTC 60.094 50.000 0.00 0.00 0.00 2.78
336 1438 1.906574 TGGCATCTACTCCTTCCGTTT 59.093 47.619 0.00 0.00 0.00 3.60
337 1439 1.568504 TGGCATCTACTCCTTCCGTT 58.431 50.000 0.00 0.00 0.00 4.44
338 1440 1.207329 GTTGGCATCTACTCCTTCCGT 59.793 52.381 0.00 0.00 0.00 4.69
339 1441 1.802880 CGTTGGCATCTACTCCTTCCG 60.803 57.143 0.00 0.00 0.00 4.30
340 1442 1.480954 TCGTTGGCATCTACTCCTTCC 59.519 52.381 0.00 0.00 0.00 3.46
341 1443 2.961526 TCGTTGGCATCTACTCCTTC 57.038 50.000 0.00 0.00 0.00 3.46
342 1444 2.743183 GCATCGTTGGCATCTACTCCTT 60.743 50.000 0.00 0.00 0.00 3.36
343 1445 1.202580 GCATCGTTGGCATCTACTCCT 60.203 52.381 0.00 0.00 0.00 3.69
344 1446 1.221414 GCATCGTTGGCATCTACTCC 58.779 55.000 0.00 0.00 0.00 3.85
345 1447 0.855349 CGCATCGTTGGCATCTACTC 59.145 55.000 0.00 0.00 0.00 2.59
346 1448 0.530650 CCGCATCGTTGGCATCTACT 60.531 55.000 0.00 0.00 0.00 2.57
347 1449 1.934463 CCGCATCGTTGGCATCTAC 59.066 57.895 0.00 0.00 0.00 2.59
348 1450 4.436515 CCGCATCGTTGGCATCTA 57.563 55.556 0.00 0.00 0.00 1.98
354 1456 1.353103 GAGATTGCCGCATCGTTGG 59.647 57.895 0.00 0.00 0.00 3.77
355 1457 0.659427 ATGAGATTGCCGCATCGTTG 59.341 50.000 0.00 0.00 28.77 4.10
356 1458 1.867233 GTATGAGATTGCCGCATCGTT 59.133 47.619 0.00 0.00 36.65 3.85
357 1459 1.502231 GTATGAGATTGCCGCATCGT 58.498 50.000 0.00 0.00 36.65 3.73
358 1460 0.436150 CGTATGAGATTGCCGCATCG 59.564 55.000 0.00 0.00 36.65 3.84
359 1461 0.792640 CCGTATGAGATTGCCGCATC 59.207 55.000 0.00 0.00 36.65 3.91
366 1468 4.681942 GGTCTTTCGATCCGTATGAGATTG 59.318 45.833 0.00 0.00 0.00 2.67
367 1469 4.585162 AGGTCTTTCGATCCGTATGAGATT 59.415 41.667 0.00 0.00 0.00 2.40
412 1519 0.718343 GCATCAAGACTGACTGACGC 59.282 55.000 0.00 0.00 33.30 5.19
413 1520 0.987715 CGCATCAAGACTGACTGACG 59.012 55.000 0.00 0.00 33.30 4.35
494 1606 3.250040 AGCGCCACCATATTTTTCGATAC 59.750 43.478 2.29 0.00 0.00 2.24
496 1608 2.290641 GAGCGCCACCATATTTTTCGAT 59.709 45.455 2.29 0.00 0.00 3.59
500 1612 3.023119 TGATGAGCGCCACCATATTTTT 58.977 40.909 2.29 0.00 0.00 1.94
506 1618 0.534427 CAGATGATGAGCGCCACCAT 60.534 55.000 2.29 4.31 0.00 3.55
528 1645 1.134788 GTGACCCGAGGTGGACTATTG 60.135 57.143 0.00 0.00 42.00 1.90
532 1649 1.908793 CTGTGACCCGAGGTGGACT 60.909 63.158 0.00 0.00 42.00 3.85
533 1650 2.156051 GACTGTGACCCGAGGTGGAC 62.156 65.000 0.00 0.00 42.00 4.02
608 1725 8.930846 AAATAGCAAATCCATCTAGCTAATGT 57.069 30.769 12.12 0.00 40.70 2.71
609 1834 8.457261 GGAAATAGCAAATCCATCTAGCTAATG 58.543 37.037 0.00 2.25 40.70 1.90
613 1838 5.320277 GGGAAATAGCAAATCCATCTAGCT 58.680 41.667 0.00 0.00 39.22 3.32
614 1839 4.460731 GGGGAAATAGCAAATCCATCTAGC 59.539 45.833 0.00 0.00 34.82 3.42
664 1889 6.699575 AATGATAACCCATTGTGAGCTTAC 57.300 37.500 0.78 0.78 35.60 2.34
672 1897 5.365619 GACCGACTAATGATAACCCATTGT 58.634 41.667 0.00 0.00 37.34 2.71
690 1921 1.300971 CTCCACCGTCTTACGACCGA 61.301 60.000 0.15 0.00 46.05 4.69
704 1935 0.389948 CTGACCGGCTAACACTCCAC 60.390 60.000 0.00 0.00 0.00 4.02
705 1936 1.972198 CTGACCGGCTAACACTCCA 59.028 57.895 0.00 0.00 0.00 3.86
708 1939 1.004918 GTGCTGACCGGCTAACACT 60.005 57.895 0.00 0.00 0.00 3.55
709 1940 0.882927 TTGTGCTGACCGGCTAACAC 60.883 55.000 0.00 6.32 0.00 3.32
710 1941 0.602638 CTTGTGCTGACCGGCTAACA 60.603 55.000 0.00 0.00 0.00 2.41
711 1942 1.298859 CCTTGTGCTGACCGGCTAAC 61.299 60.000 0.00 0.00 0.00 2.34
712 1943 1.003839 CCTTGTGCTGACCGGCTAA 60.004 57.895 0.00 0.00 0.00 3.09
713 1944 2.662596 CCTTGTGCTGACCGGCTA 59.337 61.111 0.00 0.00 0.00 3.93
763 3402 0.874607 GTCGACGGTGATGGTATGCC 60.875 60.000 0.00 0.00 0.00 4.40
799 3441 3.262915 AGCCCAACATATATCTGCTCTCC 59.737 47.826 0.00 0.00 0.00 3.71
830 3511 2.676471 ATGCAGTGGGCCGGTTTC 60.676 61.111 1.90 0.00 43.89 2.78
851 3532 0.685097 CCGGAAGAAACCTCCTGTGA 59.315 55.000 0.00 0.00 0.00 3.58
967 3657 4.202090 GGATTGGATTTGGCAGATCTTGTC 60.202 45.833 16.52 11.48 0.00 3.18
1177 3880 2.203126 GCCTTCCTCCATCGGCTG 60.203 66.667 0.00 0.00 39.42 4.85
1189 3892 2.736826 CCTCCTCCCCTTCGCCTTC 61.737 68.421 0.00 0.00 0.00 3.46
1218 3948 3.002583 TCCATGTGAGCCTCGGCA 61.003 61.111 11.02 0.00 44.88 5.69
1227 3957 1.825341 CTCCGATGCCTCCATGTGA 59.175 57.895 0.00 0.00 0.00 3.58
1293 4023 1.076339 CTCCGCTTCCTCCTCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
1294 4024 2.131067 CCTCCGCTTCCTCCTCCTC 61.131 68.421 0.00 0.00 0.00 3.71
1295 4025 2.042435 CCTCCGCTTCCTCCTCCT 60.042 66.667 0.00 0.00 0.00 3.69
1629 4359 2.974489 CTTGGGCACTGCTGCTTCG 61.974 63.158 0.00 0.00 43.66 3.79
1717 4447 1.069296 GCAGCAGTTCATAAACGCACA 60.069 47.619 0.00 0.00 40.48 4.57
1721 4451 1.887320 GCAGCAGCAGTTCATAAACG 58.113 50.000 0.00 0.00 40.48 3.60
1739 4469 5.391312 AGGAATACATTTCAACCACTTGC 57.609 39.130 0.00 0.00 0.00 4.01
1749 4479 4.164843 TGGCAGGGTAGGAATACATTTC 57.835 45.455 0.00 0.00 0.00 2.17
1773 4503 8.338259 CAAAATTCATAGGTTCTACTTCCATCG 58.662 37.037 0.00 0.00 0.00 3.84
1799 4529 7.602517 AAGACAACTGCATACTTAGATTGAC 57.397 36.000 0.00 0.00 0.00 3.18
1884 4614 2.480419 GCTGAATTCGCACTACACAAGT 59.520 45.455 14.59 0.00 39.81 3.16
1910 4646 8.925700 CCCTAAAACATAATGCTCAAGAAAAAC 58.074 33.333 0.00 0.00 0.00 2.43
2010 4787 9.840427 GAATTTAGCAGCAGTCTTAATTTTGTA 57.160 29.630 0.00 0.00 0.00 2.41
2011 4788 8.359642 TGAATTTAGCAGCAGTCTTAATTTTGT 58.640 29.630 0.00 0.00 0.00 2.83
2028 4805 2.558359 ACCCAGCAAGTGTGAATTTAGC 59.442 45.455 0.00 0.00 0.00 3.09
2038 4815 4.207891 ACTCTGTAATACCCAGCAAGTG 57.792 45.455 0.00 0.00 0.00 3.16
2044 4821 4.464951 TGGTGTGTACTCTGTAATACCCAG 59.535 45.833 0.00 0.00 0.00 4.45
2175 4975 5.853936 TGCTGAATCGCTACATATAAACCT 58.146 37.500 0.00 0.00 0.00 3.50
2205 5007 2.865119 ATGACAGTGTTCATCAGCCA 57.135 45.000 0.00 0.00 29.74 4.75
2258 5655 4.201970 CGTCTTAGCTTCCTAACCAGAGAG 60.202 50.000 0.00 0.00 30.63 3.20
2323 5720 0.464036 GTGATGCCAGTATGTCCCGA 59.536 55.000 0.00 0.00 0.00 5.14
2412 5809 4.934797 TCCTTGAAACTGATCCCAATCT 57.065 40.909 0.00 0.00 32.75 2.40
2551 5949 5.065988 ACCCATTACAACTTTATGCGCTTAG 59.934 40.000 9.73 0.00 0.00 2.18
2571 5969 1.746220 CAACTTTGACGGTTTGACCCA 59.254 47.619 0.00 0.00 33.75 4.51
2616 6014 7.066163 CAGATCAGCCATGTTGACTTGTTATTA 59.934 37.037 0.00 0.00 0.00 0.98
2617 6015 5.948162 AGATCAGCCATGTTGACTTGTTATT 59.052 36.000 0.00 0.00 0.00 1.40
2618 6016 5.356190 CAGATCAGCCATGTTGACTTGTTAT 59.644 40.000 0.00 0.00 0.00 1.89
2624 6022 3.455177 AGATCAGATCAGCCATGTTGACT 59.545 43.478 13.14 0.00 0.00 3.41
2637 6035 9.699703 GTACCCACTTAATTAAGAGATCAGATC 57.300 37.037 27.92 1.64 37.08 2.75
2647 6045 6.708285 ACCTGTCAGTACCCACTTAATTAAG 58.292 40.000 21.21 21.21 39.18 1.85


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

AutoCloner maintained by Alex Coulton.