Multiple sequence alignment - TraesCS6A01G070300

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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 TraesCS6A01G070300 chr6A 100.000 2321 0 0 1 2321 38455175 38452855 0.000000e+00 4287.0
1 TraesCS6A01G070300 chr6A 99.353 309 2 0 1241 1549 38447516 38447208 5.600000e-156 560.0
2 TraesCS6A01G070300 chr6A 81.685 273 42 6 923 1188 38403441 38403170 1.080000e-53 220.0
3 TraesCS6A01G070300 chr6A 82.692 208 32 4 1035 1240 38105041 38104836 5.090000e-42 182.0
4 TraesCS6A01G070300 chr7D 96.866 1085 29 4 1241 2321 278337596 278336513 0.000000e+00 1810.0
5 TraesCS6A01G070300 chr1D 95.985 1046 38 3 1241 2282 95761468 95762513 0.000000e+00 1696.0
6 TraesCS6A01G070300 chr1D 95.527 313 11 2 1238 1547 95778828 95779140 4.450000e-137 497.0
7 TraesCS6A01G070300 chr3A 98.616 867 11 1 1456 2321 47546322 47547188 0.000000e+00 1533.0
8 TraesCS6A01G070300 chr3A 97.749 311 7 0 1238 1548 47551196 47551506 9.440000e-149 536.0
9 TraesCS6A01G070300 chr7B 83.380 1065 155 19 1241 2299 275691907 275692955 0.000000e+00 966.0
10 TraesCS6A01G070300 chr7B 94.888 313 13 3 1238 1547 275696984 275697296 9.640000e-134 486.0
11 TraesCS6A01G070300 chr7B 81.481 135 23 1 512 644 194609688 194609822 2.440000e-20 110.0
12 TraesCS6A01G070300 chr2A 95.267 486 20 3 1235 1719 165340976 165340493 0.000000e+00 767.0
13 TraesCS6A01G070300 chr6D 91.111 450 34 3 794 1240 34306172 34305726 2.550000e-169 604.0
14 TraesCS6A01G070300 chr6D 90.275 473 26 13 779 1240 34297809 34297346 3.300000e-168 601.0
15 TraesCS6A01G070300 chr6D 81.176 680 87 19 1 644 34308217 34307543 2.060000e-140 508.0
16 TraesCS6A01G070300 chr6D 81.340 209 33 6 1035 1240 33305567 33305362 5.130000e-37 165.0
17 TraesCS6A01G070300 chr6D 94.286 70 4 0 693 762 34307307 34307238 8.770000e-20 108.0
18 TraesCS6A01G070300 chr4D 95.238 315 12 2 1241 1552 163953593 163953279 1.600000e-136 496.0
19 TraesCS6A01G070300 chr4D 81.879 149 18 7 554 697 488687596 488687452 1.460000e-22 117.0
20 TraesCS6A01G070300 chr6B 84.672 411 35 10 643 1050 70756982 70756597 3.620000e-103 385.0
21 TraesCS6A01G070300 chr6B 85.455 165 22 2 1030 1193 70564584 70564421 1.100000e-38 171.0
22 TraesCS6A01G070300 chr6B 81.283 187 27 4 1061 1240 70053466 70053281 6.680000e-31 145.0
23 TraesCS6A01G070300 chr6B 77.181 149 24 8 554 697 14546028 14545885 6.880000e-11 78.7
24 TraesCS6A01G070300 chr7A 81.081 148 22 6 554 697 157394 157249 1.880000e-21 113.0
25 TraesCS6A01G070300 chr7A 78.125 96 18 3 119 212 91400452 91400546 8.960000e-05 58.4
26 TraesCS6A01G070300 chr2B 81.884 138 16 7 565 697 98393940 98393807 8.770000e-20 108.0
27 TraesCS6A01G070300 chr4B 80.556 144 19 7 559 697 150420846 150420985 4.080000e-18 102.0
28 TraesCS6A01G070300 chr4B 79.866 149 21 7 554 697 529837305 529837161 1.470000e-17 100.0
29 TraesCS6A01G070300 chr3B 80.142 141 25 2 512 649 809608491 809608631 4.080000e-18 102.0
30 TraesCS6A01G070300 chr3B 81.731 104 17 1 543 644 732316173 732316276 4.110000e-13 86.1
31 TraesCS6A01G070300 chr2D 80.000 150 19 8 554 697 632465672 632465528 1.470000e-17 100.0
32 TraesCS6A01G070300 chr3D 80.435 138 18 7 565 697 420484255 420484388 1.900000e-16 97.1
33 TraesCS6A01G070300 chr1B 77.869 122 18 7 569 685 39659716 39659833 1.490000e-07 67.6


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 TraesCS6A01G070300 chr6A 38452855 38455175 2320 True 4287.000000 4287 100.000000 1 2321 1 chr6A.!!$R4 2320
1 TraesCS6A01G070300 chr7D 278336513 278337596 1083 True 1810.000000 1810 96.866000 1241 2321 1 chr7D.!!$R1 1080
2 TraesCS6A01G070300 chr1D 95761468 95762513 1045 False 1696.000000 1696 95.985000 1241 2282 1 chr1D.!!$F1 1041
3 TraesCS6A01G070300 chr3A 47546322 47547188 866 False 1533.000000 1533 98.616000 1456 2321 1 chr3A.!!$F1 865
4 TraesCS6A01G070300 chr7B 275691907 275692955 1048 False 966.000000 966 83.380000 1241 2299 1 chr7B.!!$F2 1058
5 TraesCS6A01G070300 chr6D 34305726 34308217 2491 True 406.666667 604 88.857667 1 1240 3 chr6D.!!$R3 1239

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
160 161 0.030908 GATGTCCCAGTCGACGGATC 59.969 60.0 22.53 15.29 35.4 3.36 F
361 372 0.108804 TCGAACCTCTTCATGTCGCC 60.109 55.0 0.00 0.00 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 2500 0.036388 GGAGGAAGGCGTGACAATGA 60.036 55.0 0.0 0.0 0.0 2.57 R
1697 2967 0.317160 TTCGTGATCTTGGACAGCGT 59.683 50.0 0.0 0.0 0.0 5.07 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
30 31 0.882042 CGAATCCGAGAGCCCATTGG 60.882 60.000 0.00 0.00 38.22 3.16
56 57 3.134623 ACACAATGGATTCCGCTAGATCA 59.865 43.478 0.00 0.00 0.00 2.92
87 88 3.611674 TCGGGCGCACTTCTCACA 61.612 61.111 8.62 0.00 0.00 3.58
88 89 3.414700 CGGGCGCACTTCTCACAC 61.415 66.667 8.62 0.00 0.00 3.82
95 96 1.895280 GCACTTCTCACACGAGCAGC 61.895 60.000 0.00 0.00 36.11 5.25
99 100 1.515521 TTCTCACACGAGCAGCGAGA 61.516 55.000 5.99 0.00 44.57 4.04
112 113 4.116328 CGAGAGCCTTGCGGTCGA 62.116 66.667 7.15 0.00 44.07 4.20
130 131 2.193248 CCAAATCCTCCTCGCCCC 59.807 66.667 0.00 0.00 0.00 5.80
155 156 1.139095 GGACGATGTCCCAGTCGAC 59.861 63.158 7.70 7.70 46.19 4.20
160 161 0.030908 GATGTCCCAGTCGACGGATC 59.969 60.000 22.53 15.29 35.40 3.36
178 179 2.786495 CGGGAGTGTCTGGATCGGG 61.786 68.421 0.00 0.00 0.00 5.14
225 236 1.000771 GGAAGAGAGTTTGGGGGCC 60.001 63.158 0.00 0.00 0.00 5.80
229 240 3.330720 AGAGTTTGGGGGCCGGAG 61.331 66.667 5.05 0.00 0.00 4.63
231 242 3.920093 GAGTTTGGGGGCCGGAGTG 62.920 68.421 5.05 0.00 0.00 3.51
238 249 4.410400 GGGCCGGAGTGGAGTTGG 62.410 72.222 5.05 0.00 42.00 3.77
239 250 3.319198 GGCCGGAGTGGAGTTGGA 61.319 66.667 5.05 0.00 42.00 3.53
240 251 2.047179 GCCGGAGTGGAGTTGGAC 60.047 66.667 5.05 0.00 42.00 4.02
242 253 2.261671 CGGAGTGGAGTTGGACGG 59.738 66.667 0.00 0.00 0.00 4.79
243 254 2.571216 CGGAGTGGAGTTGGACGGT 61.571 63.158 0.00 0.00 0.00 4.83
244 255 1.752833 GGAGTGGAGTTGGACGGTT 59.247 57.895 0.00 0.00 0.00 4.44
255 266 3.118149 AGTTGGACGGTTAGAGTTTGGTT 60.118 43.478 0.00 0.00 0.00 3.67
256 267 3.564053 TGGACGGTTAGAGTTTGGTTT 57.436 42.857 0.00 0.00 0.00 3.27
290 301 6.086011 TGAGGACAAATATATGTGGGGTTT 57.914 37.500 7.81 0.00 32.57 3.27
291 302 7.214460 TGAGGACAAATATATGTGGGGTTTA 57.786 36.000 7.81 0.00 32.57 2.01
292 303 7.287061 TGAGGACAAATATATGTGGGGTTTAG 58.713 38.462 7.81 0.00 32.57 1.85
293 304 6.610830 AGGACAAATATATGTGGGGTTTAGG 58.389 40.000 7.81 0.00 32.57 2.69
294 305 6.161526 AGGACAAATATATGTGGGGTTTAGGT 59.838 38.462 7.81 0.00 32.57 3.08
295 306 7.351454 AGGACAAATATATGTGGGGTTTAGGTA 59.649 37.037 7.81 0.00 32.57 3.08
296 307 7.664318 GGACAAATATATGTGGGGTTTAGGTAG 59.336 40.741 7.81 0.00 32.57 3.18
334 345 3.469863 GACTTGCCGGACACACCCA 62.470 63.158 5.05 0.00 34.64 4.51
335 346 2.034066 CTTGCCGGACACACCCAT 59.966 61.111 5.05 0.00 34.64 4.00
345 356 4.673298 ACACCCATGCGCGTTCGA 62.673 61.111 8.43 0.00 38.10 3.71
350 361 2.395690 CATGCGCGTTCGAACCTC 59.604 61.111 22.07 13.03 38.10 3.85
358 369 1.390463 GCGTTCGAACCTCTTCATGTC 59.610 52.381 22.07 0.00 0.00 3.06
361 372 0.108804 TCGAACCTCTTCATGTCGCC 60.109 55.000 0.00 0.00 0.00 5.54
367 378 3.034635 ACCTCTTCATGTCGCCTTAGAT 58.965 45.455 0.00 0.00 0.00 1.98
386 397 3.199946 AGATTTTGGGCTGGATACGAAGA 59.800 43.478 0.00 0.00 42.51 2.87
396 407 1.741706 GGATACGAAGAGTGTCGGTCA 59.258 52.381 0.00 0.00 45.40 4.02
415 426 1.145531 CAATCCAGGCATATGGGACCA 59.854 52.381 4.56 0.00 41.01 4.02
454 465 7.962964 TTATCGATTAGTGAACAATCCATCC 57.037 36.000 1.71 0.00 0.00 3.51
456 467 4.119862 CGATTAGTGAACAATCCATCCGT 58.880 43.478 0.00 0.00 0.00 4.69
476 487 2.523657 GGCGTAGGGAGGGGGTAG 60.524 72.222 0.00 0.00 0.00 3.18
481 492 1.201424 GTAGGGAGGGGGTAGTGTTG 58.799 60.000 0.00 0.00 0.00 3.33
499 533 0.395586 TGTGTTGGGCAAAGCTCAGT 60.396 50.000 0.00 0.00 41.35 3.41
500 534 0.312102 GTGTTGGGCAAAGCTCAGTC 59.688 55.000 0.00 0.00 41.35 3.51
505 539 1.301716 GGCAAAGCTCAGTCCGACA 60.302 57.895 0.40 0.00 0.00 4.35
515 549 3.525537 CTCAGTCCGACACATGCTAATT 58.474 45.455 0.40 0.00 0.00 1.40
519 553 2.095853 GTCCGACACATGCTAATTGTGG 59.904 50.000 8.50 0.00 46.89 4.17
525 559 0.818938 CATGCTAATTGTGGCAGGCA 59.181 50.000 0.00 0.00 45.32 4.75
527 561 1.137404 GCTAATTGTGGCAGGCACG 59.863 57.895 21.33 8.43 0.00 5.34
528 562 1.305219 GCTAATTGTGGCAGGCACGA 61.305 55.000 19.03 19.03 0.00 4.35
531 565 1.795170 AATTGTGGCAGGCACGACAC 61.795 55.000 19.12 6.00 0.00 3.67
563 597 2.352388 GCATGTTTAGTAAGCGGGTCA 58.648 47.619 0.00 0.00 0.00 4.02
567 601 1.326548 GTTTAGTAAGCGGGTCATGCG 59.673 52.381 0.00 0.00 37.44 4.73
568 602 0.179094 TTAGTAAGCGGGTCATGCGG 60.179 55.000 0.00 0.00 37.44 5.69
606 640 4.421515 CTCCAGGCCCAGGCACAG 62.422 72.222 11.50 0.00 44.11 3.66
622 658 0.535797 ACAGCCTAGTTTAGACGGGC 59.464 55.000 12.97 12.97 44.22 6.13
626 662 1.227176 CTAGTTTAGACGGGCCGGC 60.227 63.158 31.78 30.09 33.59 6.13
649 876 4.397832 GGCCCGTTTAGCCGGTGA 62.398 66.667 1.90 0.00 46.66 4.02
655 882 1.019278 CGTTTAGCCGGTGATGTGCT 61.019 55.000 1.90 0.00 39.10 4.40
657 884 1.135689 GTTTAGCCGGTGATGTGCTTG 60.136 52.381 1.90 0.00 36.57 4.01
754 981 0.536006 GCTTTGACAGCCACTCACCT 60.536 55.000 0.00 0.00 43.65 4.00
762 989 1.194781 AGCCACTCACCTCCAACGAT 61.195 55.000 0.00 0.00 0.00 3.73
764 991 1.442769 CCACTCACCTCCAACGATTG 58.557 55.000 0.00 0.00 0.00 2.67
767 994 1.971357 ACTCACCTCCAACGATTGTCT 59.029 47.619 0.00 0.00 0.00 3.41
768 995 2.028930 ACTCACCTCCAACGATTGTCTC 60.029 50.000 0.00 0.00 0.00 3.36
769 996 1.967779 TCACCTCCAACGATTGTCTCA 59.032 47.619 0.00 0.00 0.00 3.27
771 998 3.138304 CACCTCCAACGATTGTCTCAAA 58.862 45.455 0.00 0.00 0.00 2.69
772 999 3.563808 CACCTCCAACGATTGTCTCAAAA 59.436 43.478 0.00 0.00 0.00 2.44
773 1000 4.036262 CACCTCCAACGATTGTCTCAAAAA 59.964 41.667 0.00 0.00 0.00 1.94
797 1039 4.904253 AAACCTCCGACGAATTTGAAAA 57.096 36.364 0.00 0.00 0.00 2.29
803 1045 5.502153 TCCGACGAATTTGAAAAGGAAAA 57.498 34.783 0.00 0.00 0.00 2.29
804 1046 5.516090 TCCGACGAATTTGAAAAGGAAAAG 58.484 37.500 0.00 0.00 0.00 2.27
806 1048 4.148174 CGACGAATTTGAAAAGGAAAAGCC 59.852 41.667 0.00 0.00 0.00 4.35
838 2099 2.802667 CGATTCTTGTGGCGGCGAG 61.803 63.158 12.98 0.00 0.00 5.03
920 2181 5.490139 AACTTTATTCCGTCTCATGCATG 57.510 39.130 21.07 21.07 0.00 4.06
934 2195 1.451028 GCATGCCCACTCTCTCCAC 60.451 63.158 6.36 0.00 0.00 4.02
939 2200 1.390125 CCCACTCTCTCCACCCTCT 59.610 63.158 0.00 0.00 0.00 3.69
1025 2286 1.440938 CCTGGTAGCGAGGACGAGAG 61.441 65.000 4.89 0.00 42.66 3.20
1074 2338 0.180406 GTGCACTCCCCGACCATATT 59.820 55.000 10.32 0.00 0.00 1.28
1094 2358 1.077169 TCTCCACCACCTGCTCTCTTA 59.923 52.381 0.00 0.00 0.00 2.10
1182 2446 3.716539 TACAGGCCTGCGCATCGTC 62.717 63.158 33.06 5.70 36.38 4.20
1191 2455 3.554692 CGCATCGTCGGCCTTGAC 61.555 66.667 0.00 0.02 35.49 3.18
1199 2463 1.680989 TCGGCCTTGACGATGAGGA 60.681 57.895 0.00 0.00 38.55 3.71
1201 2465 1.667154 CGGCCTTGACGATGAGGAGA 61.667 60.000 0.00 0.00 35.20 3.71
1223 2487 1.070134 TGTCCAAGTTCAAGACCTCCG 59.930 52.381 0.00 0.00 0.00 4.63
1227 2491 2.417719 CAAGTTCAAGACCTCCGGAAG 58.582 52.381 5.23 0.57 0.00 3.46
1231 2495 1.712056 TCAAGACCTCCGGAAGTTCA 58.288 50.000 7.25 0.00 0.00 3.18
1236 2500 1.486726 GACCTCCGGAAGTTCATGGAT 59.513 52.381 7.25 3.58 0.00 3.41
1297 2561 1.610673 GGCTCCAGACTCCCTGACA 60.611 63.158 0.00 0.00 45.78 3.58
1299 2563 0.687354 GCTCCAGACTCCCTGACAAA 59.313 55.000 0.00 0.00 45.78 2.83
1446 2711 6.817765 TGTAATTGAATCCTGTGAACCTTC 57.182 37.500 0.00 0.00 0.00 3.46
1447 2712 6.542821 TGTAATTGAATCCTGTGAACCTTCT 58.457 36.000 0.00 0.00 0.00 2.85
1448 2713 6.655003 TGTAATTGAATCCTGTGAACCTTCTC 59.345 38.462 0.00 0.00 0.00 2.87
1449 2714 4.705110 TTGAATCCTGTGAACCTTCTCA 57.295 40.909 0.00 0.00 0.00 3.27
1450 2715 4.916041 TGAATCCTGTGAACCTTCTCAT 57.084 40.909 0.00 0.00 31.23 2.90
1616 2886 6.700081 CGAGATCAATCCGTAAAATTCCACTA 59.300 38.462 0.00 0.00 0.00 2.74
1879 3150 0.389948 GGAGTTTGGCGACGAGATGT 60.390 55.000 0.00 0.00 0.00 3.06
2299 3587 4.816385 CGATGTGGTTTCAGGCATATAAGT 59.184 41.667 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.671251 GCTCTCGGATTCGGTCTGAT 59.329 55.000 0.00 0.00 41.33 2.90
30 31 0.099436 GCGGAATCCATTGTGTCAGC 59.901 55.000 0.00 0.00 0.00 4.26
32 33 2.499693 TCTAGCGGAATCCATTGTGTCA 59.500 45.455 0.00 0.00 0.00 3.58
46 47 3.742433 AGGTCAGATTTGATCTAGCGG 57.258 47.619 0.00 0.00 43.00 5.52
56 57 1.134788 CGCCCGACTAAGGTCAGATTT 60.135 52.381 0.00 0.00 42.21 2.17
87 88 3.377759 AAGGCTCTCGCTGCTCGT 61.378 61.111 0.00 0.00 39.67 4.18
88 89 2.884685 CAAGGCTCTCGCTGCTCG 60.885 66.667 0.00 0.00 40.15 5.03
109 110 1.515954 GCGAGGAGGATTTGGTCGA 59.484 57.895 0.00 0.00 32.32 4.20
110 111 1.521681 GGCGAGGAGGATTTGGTCG 60.522 63.158 0.00 0.00 0.00 4.79
112 113 2.680370 GGGGCGAGGAGGATTTGGT 61.680 63.158 0.00 0.00 0.00 3.67
130 131 2.588877 GGACATCGTCCCATGCGG 60.589 66.667 1.47 0.00 46.19 5.69
155 156 1.109920 ATCCAGACACTCCCGATCCG 61.110 60.000 0.00 0.00 0.00 4.18
160 161 2.786495 CCCGATCCAGACACTCCCG 61.786 68.421 0.00 0.00 0.00 5.14
178 179 3.127533 GCATGGCGGACAGTGGAC 61.128 66.667 0.00 0.00 0.00 4.02
198 209 0.827368 AACTCTCTTCCGGCCATCTC 59.173 55.000 2.24 0.00 0.00 2.75
203 214 1.377333 CCCAAACTCTCTTCCGGCC 60.377 63.158 0.00 0.00 0.00 6.13
205 216 1.299976 CCCCCAAACTCTCTTCCGG 59.700 63.158 0.00 0.00 0.00 5.14
225 236 2.095978 AACCGTCCAACTCCACTCCG 62.096 60.000 0.00 0.00 0.00 4.63
229 240 1.617357 ACTCTAACCGTCCAACTCCAC 59.383 52.381 0.00 0.00 0.00 4.02
231 242 3.064931 CAAACTCTAACCGTCCAACTCC 58.935 50.000 0.00 0.00 0.00 3.85
236 247 3.207778 CAAACCAAACTCTAACCGTCCA 58.792 45.455 0.00 0.00 0.00 4.02
238 249 2.551032 CCCAAACCAAACTCTAACCGTC 59.449 50.000 0.00 0.00 0.00 4.79
239 250 2.173143 TCCCAAACCAAACTCTAACCGT 59.827 45.455 0.00 0.00 0.00 4.83
240 251 2.853705 TCCCAAACCAAACTCTAACCG 58.146 47.619 0.00 0.00 0.00 4.44
242 253 3.365969 CGCATCCCAAACCAAACTCTAAC 60.366 47.826 0.00 0.00 0.00 2.34
243 254 2.817258 CGCATCCCAAACCAAACTCTAA 59.183 45.455 0.00 0.00 0.00 2.10
244 255 2.432444 CGCATCCCAAACCAAACTCTA 58.568 47.619 0.00 0.00 0.00 2.43
255 266 1.271127 TGTCCTCATCCGCATCCCAA 61.271 55.000 0.00 0.00 0.00 4.12
256 267 1.271127 TTGTCCTCATCCGCATCCCA 61.271 55.000 0.00 0.00 0.00 4.37
290 301 1.544093 CGATCCACGGTAGCCTACCTA 60.544 57.143 18.49 2.40 46.81 3.08
291 302 0.822532 CGATCCACGGTAGCCTACCT 60.823 60.000 18.49 3.44 46.81 3.08
292 303 1.658673 CGATCCACGGTAGCCTACC 59.341 63.158 11.09 11.09 45.52 3.18
319 330 2.282110 CATGGGTGTGTCCGGCAA 60.282 61.111 0.00 0.00 37.00 4.52
328 339 4.673298 TCGAACGCGCATGGGTGT 62.673 61.111 21.92 21.92 41.67 4.16
330 341 3.419759 GTTCGAACGCGCATGGGT 61.420 61.111 13.36 0.00 44.11 4.51
334 345 1.352156 GAAGAGGTTCGAACGCGCAT 61.352 55.000 21.34 9.59 37.46 4.73
335 346 2.019951 GAAGAGGTTCGAACGCGCA 61.020 57.895 21.34 0.00 37.46 6.09
337 348 0.366871 CATGAAGAGGTTCGAACGCG 59.633 55.000 21.34 3.53 35.17 6.01
345 356 2.832129 TCTAAGGCGACATGAAGAGGTT 59.168 45.455 0.00 0.00 0.00 3.50
350 361 4.201950 CCCAAAATCTAAGGCGACATGAAG 60.202 45.833 0.00 0.00 0.00 3.02
361 372 4.703897 TCGTATCCAGCCCAAAATCTAAG 58.296 43.478 0.00 0.00 0.00 2.18
367 378 2.304761 ACTCTTCGTATCCAGCCCAAAA 59.695 45.455 0.00 0.00 0.00 2.44
386 397 1.296715 GCCTGGATTGACCGACACT 59.703 57.895 0.00 0.00 42.61 3.55
396 407 1.533187 TGGTCCCATATGCCTGGATT 58.467 50.000 0.00 0.00 38.69 3.01
430 441 6.645003 CGGATGGATTGTTCACTAATCGATAA 59.355 38.462 0.00 0.00 34.50 1.75
431 442 6.156519 CGGATGGATTGTTCACTAATCGATA 58.843 40.000 0.00 0.00 34.50 2.92
438 449 2.159156 CCGACGGATGGATTGTTCACTA 60.159 50.000 8.64 0.00 0.00 2.74
444 455 2.189521 GCCCGACGGATGGATTGT 59.810 61.111 17.49 0.00 0.00 2.71
476 487 0.175531 AGCTTTGCCCAACACAACAC 59.824 50.000 0.00 0.00 0.00 3.32
481 492 0.312102 GACTGAGCTTTGCCCAACAC 59.688 55.000 0.00 0.00 0.00 3.32
499 533 2.355197 CCACAATTAGCATGTGTCGGA 58.645 47.619 5.99 0.00 45.23 4.55
500 534 1.202177 GCCACAATTAGCATGTGTCGG 60.202 52.381 5.99 0.00 45.23 4.79
505 539 0.819582 GCCTGCCACAATTAGCATGT 59.180 50.000 0.00 0.00 38.56 3.21
532 566 2.487274 TAAACATGCCCCCGTGGACC 62.487 60.000 0.00 0.00 35.39 4.46
539 573 1.021968 CGCTTACTAAACATGCCCCC 58.978 55.000 0.00 0.00 0.00 5.40
546 580 2.352388 GCATGACCCGCTTACTAAACA 58.648 47.619 0.00 0.00 0.00 2.83
574 608 3.660111 GAGGTGCAACACGTGGGC 61.660 66.667 21.57 22.25 39.98 5.36
579 613 3.357079 GCCTGGAGGTGCAACACG 61.357 66.667 3.64 0.00 39.98 4.49
605 639 1.673808 CGGCCCGTCTAAACTAGGCT 61.674 60.000 0.00 0.00 40.51 4.58
606 640 1.227176 CGGCCCGTCTAAACTAGGC 60.227 63.158 0.00 0.00 40.16 3.93
644 680 3.443045 GGGCCAAGCACATCACCG 61.443 66.667 4.39 0.00 0.00 4.94
645 681 2.283101 TGGGCCAAGCACATCACC 60.283 61.111 2.13 0.00 36.87 4.02
700 927 4.637387 AGATCATCTAGCCTCAAATGGG 57.363 45.455 0.00 0.00 0.00 4.00
703 930 8.719645 ACTAGTAAGATCATCTAGCCTCAAAT 57.280 34.615 14.44 0.00 35.83 2.32
774 1001 4.904253 TTCAAATTCGTCGGAGGTTTTT 57.096 36.364 0.00 0.00 0.00 1.94
775 1002 4.904253 TTTCAAATTCGTCGGAGGTTTT 57.096 36.364 0.00 0.00 0.00 2.43
776 1003 4.261447 CCTTTTCAAATTCGTCGGAGGTTT 60.261 41.667 0.00 0.00 0.00 3.27
781 1023 5.502153 TTTTCCTTTTCAAATTCGTCGGA 57.498 34.783 0.00 0.00 0.00 4.55
783 1025 4.148174 GGCTTTTCCTTTTCAAATTCGTCG 59.852 41.667 0.00 0.00 0.00 5.12
797 1039 2.663196 CGGACTCCGGCTTTTCCT 59.337 61.111 9.85 0.00 44.15 3.36
838 2099 1.134946 CCGGCAAATCCAGATTTCCAC 59.865 52.381 2.62 0.00 38.84 4.02
866 2127 2.813908 CCGCCTCACGTACCTTGC 60.814 66.667 0.00 0.00 41.42 4.01
889 2150 0.989164 GGAATAAAGTTTTGCGGCGC 59.011 50.000 27.44 27.44 0.00 6.53
890 2151 1.255767 CGGAATAAAGTTTTGCGGCG 58.744 50.000 0.51 0.51 34.75 6.46
891 2152 2.095415 AGACGGAATAAAGTTTTGCGGC 60.095 45.455 6.23 2.97 45.10 6.53
892 2153 3.187637 TGAGACGGAATAAAGTTTTGCGG 59.812 43.478 6.23 0.00 41.46 5.69
893 2154 4.398549 TGAGACGGAATAAAGTTTTGCG 57.601 40.909 0.00 0.00 42.62 4.85
903 2164 1.543208 GGGCATGCATGAGACGGAATA 60.543 52.381 30.64 0.00 0.00 1.75
920 2181 2.284995 AGGGTGGAGAGAGTGGGC 60.285 66.667 0.00 0.00 0.00 5.36
934 2195 0.170561 ACGATCAAACGACGAGAGGG 59.829 55.000 0.00 0.00 37.03 4.30
939 2200 2.977829 CAGAGAAACGATCAAACGACGA 59.022 45.455 0.00 0.00 37.03 4.20
1056 2320 0.468226 GAATATGGTCGGGGAGTGCA 59.532 55.000 0.00 0.00 0.00 4.57
1065 2329 1.762957 AGGTGGTGGAGAATATGGTCG 59.237 52.381 0.00 0.00 0.00 4.79
1074 2338 0.178921 AAGAGAGCAGGTGGTGGAGA 60.179 55.000 0.00 0.00 0.00 3.71
1160 2424 3.687321 ATGCGCAGGCCTGTAGTGG 62.687 63.158 32.81 17.82 38.85 4.00
1182 2446 1.227089 CTCCTCATCGTCAAGGCCG 60.227 63.158 0.00 0.00 32.37 6.13
1190 2454 1.821753 CTTGGACAGTCTCCTCATCGT 59.178 52.381 0.00 0.00 40.26 3.73
1191 2455 1.821753 ACTTGGACAGTCTCCTCATCG 59.178 52.381 0.00 0.00 40.26 3.84
1199 2463 3.041946 AGGTCTTGAACTTGGACAGTCT 58.958 45.455 0.00 0.00 32.94 3.24
1201 2465 2.104963 GGAGGTCTTGAACTTGGACAGT 59.895 50.000 0.00 0.00 37.30 3.55
1223 2487 4.201851 CGTGACAATGATCCATGAACTTCC 60.202 45.833 0.00 0.00 0.00 3.46
1227 2491 2.223340 GGCGTGACAATGATCCATGAAC 60.223 50.000 0.00 0.47 0.00 3.18
1231 2495 2.292267 GAAGGCGTGACAATGATCCAT 58.708 47.619 0.00 0.00 0.00 3.41
1236 2500 0.036388 GGAGGAAGGCGTGACAATGA 60.036 55.000 0.00 0.00 0.00 2.57
1297 2561 2.030958 GTCGTTCGCCGGTCCATTT 61.031 57.895 1.90 0.00 37.11 2.32
1299 2563 4.789075 CGTCGTTCGCCGGTCCAT 62.789 66.667 1.90 0.00 37.11 3.41
1446 2711 8.610248 ATGAGATTATCAGCTGAAAAGATGAG 57.390 34.615 22.50 0.00 42.53 2.90
1447 2712 7.660617 GGATGAGATTATCAGCTGAAAAGATGA 59.339 37.037 22.50 0.15 44.04 2.92
1448 2713 7.094720 GGGATGAGATTATCAGCTGAAAAGATG 60.095 40.741 22.50 0.00 44.04 2.90
1449 2714 6.941436 GGGATGAGATTATCAGCTGAAAAGAT 59.059 38.462 22.50 11.93 44.04 2.40
1450 2715 6.294473 GGGATGAGATTATCAGCTGAAAAGA 58.706 40.000 22.50 7.32 44.04 2.52
1616 2886 1.000274 GCAAATCAAGGCACCTTTCGT 60.000 47.619 0.00 0.00 33.42 3.85
1697 2967 0.317160 TTCGTGATCTTGGACAGCGT 59.683 50.000 0.00 0.00 0.00 5.07
1879 3150 2.817834 GCGGCGCTTGATGTGGTA 60.818 61.111 26.86 0.00 0.00 3.25
2299 3587 3.660501 AGTGAGACGTCTATGCAAACA 57.339 42.857 20.09 7.45 0.00 2.83


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

AutoCloner maintained by Alex Coulton.