Multiple sequence alignment - TraesCS6A01G031700

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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 TraesCS6A01G031700 chr6A 100.000 2864 0 0 1 2864 15895363 15892500 0.000000e+00 5289
1 TraesCS6A01G031700 chr6A 93.467 1148 63 10 1722 2864 15912909 15911769 0.000000e+00 1694
2 TraesCS6A01G031700 chr6A 86.376 1079 136 9 791 1863 15914044 15912971 0.000000e+00 1168
3 TraesCS6A01G031700 chr6A 83.745 1255 170 27 628 1856 15694529 15695775 0.000000e+00 1157
4 TraesCS6A01G031700 chr6B 87.547 1333 124 26 522 1835 27059040 27057731 0.000000e+00 1504
5 TraesCS6A01G031700 chr6B 83.624 1203 176 17 663 1856 27065987 27064797 0.000000e+00 1110
6 TraesCS6A01G031700 chr6B 83.036 1232 178 15 657 1863 26488568 26489793 0.000000e+00 1088
7 TraesCS6A01G031700 chr6B 81.900 1221 188 15 660 1856 26688261 26687050 0.000000e+00 1000
8 TraesCS6A01G031700 chr6B 90.560 625 40 9 2256 2864 27057311 27056690 0.000000e+00 809
9 TraesCS6A01G031700 chr6B 93.962 265 15 1 1 264 27059470 27059206 1.600000e-107 399
10 TraesCS6A01G031700 chr6B 88.571 175 6 5 305 479 27059214 27059054 1.740000e-47 200
11 TraesCS6A01G031700 chr5D 83.835 1330 189 18 550 1863 27985627 27984308 0.000000e+00 1242
12 TraesCS6A01G031700 chr5D 83.333 156 7 7 382 523 27983348 27983198 3.000000e-25 126
13 TraesCS6A01G031700 chr6D 84.739 1245 161 13 621 1850 14503295 14504525 0.000000e+00 1219
14 TraesCS6A01G031700 chr6D 83.527 1202 175 12 673 1856 14727348 14726152 0.000000e+00 1101
15 TraesCS6A01G031700 chr6D 93.077 390 24 3 1 388 14733435 14733047 4.140000e-158 568
16 TraesCS6A01G031700 chr1B 84.788 1203 159 17 671 1856 48062372 48061177 0.000000e+00 1186
17 TraesCS6A01G031700 chr1B 88.271 665 58 13 1902 2555 640174128 640174783 0.000000e+00 778
18 TraesCS6A01G031700 chr1B 88.271 665 57 13 1902 2555 651208023 651207369 0.000000e+00 776
19 TraesCS6A01G031700 chr1B 83.398 777 68 31 1 765 48106033 48105306 0.000000e+00 664
20 TraesCS6A01G031700 chr7A 88.088 680 62 12 1902 2570 333987912 333988583 0.000000e+00 789
21 TraesCS6A01G031700 chr7A 93.171 205 14 0 2660 2864 333988582 333988786 4.640000e-78 302
22 TraesCS6A01G031700 chrUn 88.271 665 58 13 1902 2555 62725000 62724345 0.000000e+00 778
23 TraesCS6A01G031700 chrUn 89.714 175 17 1 1662 1835 23843020 23843194 3.710000e-54 222
24 TraesCS6A01G031700 chrUn 93.182 132 9 0 2733 2864 62724346 62724215 8.100000e-46 195
25 TraesCS6A01G031700 chrUn 93.182 132 9 0 2733 2864 286691077 286691208 8.100000e-46 195
26 TraesCS6A01G031700 chrUn 93.182 132 9 0 2733 2864 289112065 289111934 8.100000e-46 195
27 TraesCS6A01G031700 chrUn 93.182 132 9 0 2733 2864 310288598 310288729 8.100000e-46 195
28 TraesCS6A01G031700 chrUn 93.182 132 9 0 2733 2864 335692012 335691881 8.100000e-46 195
29 TraesCS6A01G031700 chrUn 93.182 132 9 0 2733 2864 449629511 449629642 8.100000e-46 195
30 TraesCS6A01G031700 chr7B 88.271 665 59 12 1902 2555 513476566 513475910 0.000000e+00 778
31 TraesCS6A01G031700 chr3B 88.271 665 58 14 1902 2555 54680741 54680086 0.000000e+00 778
32 TraesCS6A01G031700 chr2A 88.271 665 59 12 1902 2555 149678019 149677363 0.000000e+00 778
33 TraesCS6A01G031700 chr3A 87.970 665 60 13 1902 2555 84998685 84998030 0.000000e+00 767


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 TraesCS6A01G031700 chr6A 15892500 15895363 2863 True 5289.0 5289 100.0000 1 2864 1 chr6A.!!$R1 2863
1 TraesCS6A01G031700 chr6A 15911769 15914044 2275 True 1431.0 1694 89.9215 791 2864 2 chr6A.!!$R2 2073
2 TraesCS6A01G031700 chr6A 15694529 15695775 1246 False 1157.0 1157 83.7450 628 1856 1 chr6A.!!$F1 1228
3 TraesCS6A01G031700 chr6B 27064797 27065987 1190 True 1110.0 1110 83.6240 663 1856 1 chr6B.!!$R2 1193
4 TraesCS6A01G031700 chr6B 26488568 26489793 1225 False 1088.0 1088 83.0360 657 1863 1 chr6B.!!$F1 1206
5 TraesCS6A01G031700 chr6B 26687050 26688261 1211 True 1000.0 1000 81.9000 660 1856 1 chr6B.!!$R1 1196
6 TraesCS6A01G031700 chr6B 27056690 27059470 2780 True 728.0 1504 90.1600 1 2864 4 chr6B.!!$R3 2863
7 TraesCS6A01G031700 chr5D 27983198 27985627 2429 True 684.0 1242 83.5840 382 1863 2 chr5D.!!$R1 1481
8 TraesCS6A01G031700 chr6D 14503295 14504525 1230 False 1219.0 1219 84.7390 621 1850 1 chr6D.!!$F1 1229
9 TraesCS6A01G031700 chr6D 14726152 14727348 1196 True 1101.0 1101 83.5270 673 1856 1 chr6D.!!$R1 1183
10 TraesCS6A01G031700 chr1B 48061177 48062372 1195 True 1186.0 1186 84.7880 671 1856 1 chr1B.!!$R1 1185
11 TraesCS6A01G031700 chr1B 640174128 640174783 655 False 778.0 778 88.2710 1902 2555 1 chr1B.!!$F1 653
12 TraesCS6A01G031700 chr1B 651207369 651208023 654 True 776.0 776 88.2710 1902 2555 1 chr1B.!!$R3 653
13 TraesCS6A01G031700 chr1B 48105306 48106033 727 True 664.0 664 83.3980 1 765 1 chr1B.!!$R2 764
14 TraesCS6A01G031700 chr7A 333987912 333988786 874 False 545.5 789 90.6295 1902 2864 2 chr7A.!!$F1 962
15 TraesCS6A01G031700 chrUn 62724215 62725000 785 True 486.5 778 90.7265 1902 2864 2 chrUn.!!$R3 962
16 TraesCS6A01G031700 chr7B 513475910 513476566 656 True 778.0 778 88.2710 1902 2555 1 chr7B.!!$R1 653
17 TraesCS6A01G031700 chr3B 54680086 54680741 655 True 778.0 778 88.2710 1902 2555 1 chr3B.!!$R1 653
18 TraesCS6A01G031700 chr2A 149677363 149678019 656 True 778.0 778 88.2710 1902 2555 1 chr2A.!!$R1 653
19 TraesCS6A01G031700 chr3A 84998030 84998685 655 True 767.0 767 87.9700 1902 2555 1 chr3A.!!$R1 653

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
811 950 0.182775 CCATTTCCCCGAACCCTAGG 59.817 60.0 0.06 0.06 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2558 2959 0.107508 GCAACAGCAGCCCAGATCTA 60.108 55.0 0.0 0.0 0.0 1.98 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
281 334 9.979578 ACTATTTCACTGAAATTTGTTTATGCA 57.020 25.926 19.72 0.00 41.64 3.96
286 339 9.585099 TTCACTGAAATTTGTTTATGCATATCC 57.415 29.630 7.36 1.79 0.00 2.59
287 340 8.747471 TCACTGAAATTTGTTTATGCATATCCA 58.253 29.630 7.36 4.54 0.00 3.41
288 341 9.368674 CACTGAAATTTGTTTATGCATATCCAA 57.631 29.630 7.36 10.39 0.00 3.53
303 356 6.979817 TGCATATCCAATAAAATGTTCACAGC 59.020 34.615 0.00 0.00 0.00 4.40
304 357 6.979817 GCATATCCAATAAAATGTTCACAGCA 59.020 34.615 0.00 0.00 0.00 4.41
305 358 7.043192 GCATATCCAATAAAATGTTCACAGCAC 60.043 37.037 0.00 0.00 0.00 4.40
306 359 6.594788 ATCCAATAAAATGTTCACAGCACT 57.405 33.333 0.00 0.00 0.00 4.40
307 360 7.701539 ATCCAATAAAATGTTCACAGCACTA 57.298 32.000 0.00 0.00 0.00 2.74
308 361 7.701539 TCCAATAAAATGTTCACAGCACTAT 57.298 32.000 0.00 0.00 0.00 2.12
309 362 8.121305 TCCAATAAAATGTTCACAGCACTATT 57.879 30.769 0.00 0.00 0.00 1.73
310 363 8.584157 TCCAATAAAATGTTCACAGCACTATTT 58.416 29.630 0.00 0.00 0.00 1.40
311 364 8.863049 CCAATAAAATGTTCACAGCACTATTTC 58.137 33.333 0.00 0.00 0.00 2.17
312 365 9.409312 CAATAAAATGTTCACAGCACTATTTCA 57.591 29.630 0.00 0.00 0.00 2.69
415 468 5.189736 TGGAAGGTCACTTTATGCAGATAGT 59.810 40.000 0.00 0.00 36.97 2.12
422 475 7.928706 GGTCACTTTATGCAGATAGTGAGTATT 59.071 37.037 27.69 0.00 45.34 1.89
423 476 8.973378 GTCACTTTATGCAGATAGTGAGTATTC 58.027 37.037 27.69 15.81 45.34 1.75
424 477 8.144478 TCACTTTATGCAGATAGTGAGTATTCC 58.856 37.037 24.69 0.00 41.34 3.01
425 478 8.147058 CACTTTATGCAGATAGTGAGTATTCCT 58.853 37.037 22.56 0.00 40.24 3.36
426 479 8.147058 ACTTTATGCAGATAGTGAGTATTCCTG 58.853 37.037 3.52 0.00 0.00 3.86
449 502 8.085296 CCTGTCCTGACTCTATTTACACATATC 58.915 40.741 0.00 0.00 0.00 1.63
487 545 0.823356 TTTGCAGGGCCAGTTCTGTC 60.823 55.000 6.18 0.00 33.81 3.51
497 555 0.389166 CAGTTCTGTCTGGTCGAGCC 60.389 60.000 12.85 4.60 37.90 4.70
511 569 4.051922 GGTCGAGCCTGTTAATGTATCAG 58.948 47.826 2.39 0.00 0.00 2.90
606 681 0.889306 AGACGGACCAGAGCAACTAC 59.111 55.000 0.00 0.00 0.00 2.73
608 683 0.603569 ACGGACCAGAGCAACTACTG 59.396 55.000 0.00 0.00 0.00 2.74
609 684 0.888619 CGGACCAGAGCAACTACTGA 59.111 55.000 0.00 0.00 36.38 3.41
610 685 1.135257 CGGACCAGAGCAACTACTGAG 60.135 57.143 0.00 0.00 36.38 3.35
611 686 2.171840 GGACCAGAGCAACTACTGAGA 58.828 52.381 0.00 0.00 36.38 3.27
612 687 2.763448 GGACCAGAGCAACTACTGAGAT 59.237 50.000 0.00 0.00 36.38 2.75
613 688 3.430098 GGACCAGAGCAACTACTGAGATG 60.430 52.174 0.00 0.00 36.38 2.90
614 689 3.435275 ACCAGAGCAACTACTGAGATGA 58.565 45.455 0.00 0.00 36.38 2.92
615 690 3.446873 ACCAGAGCAACTACTGAGATGAG 59.553 47.826 0.00 0.00 36.38 2.90
616 691 3.698539 CCAGAGCAACTACTGAGATGAGA 59.301 47.826 0.00 0.00 36.38 3.27
617 692 4.439974 CCAGAGCAACTACTGAGATGAGAC 60.440 50.000 0.00 0.00 36.38 3.36
618 693 3.699038 AGAGCAACTACTGAGATGAGACC 59.301 47.826 0.00 0.00 0.00 3.85
619 694 2.425312 AGCAACTACTGAGATGAGACCG 59.575 50.000 0.00 0.00 0.00 4.79
620 695 2.803451 CAACTACTGAGATGAGACCGC 58.197 52.381 0.00 0.00 0.00 5.68
621 696 2.130272 ACTACTGAGATGAGACCGCA 57.870 50.000 0.00 0.00 0.00 5.69
622 697 2.020720 ACTACTGAGATGAGACCGCAG 58.979 52.381 0.00 0.00 0.00 5.18
623 698 2.020720 CTACTGAGATGAGACCGCAGT 58.979 52.381 0.00 0.00 42.04 4.40
624 699 2.130272 ACTGAGATGAGACCGCAGTA 57.870 50.000 0.00 0.00 37.98 2.74
625 700 2.020720 ACTGAGATGAGACCGCAGTAG 58.979 52.381 0.00 0.00 37.98 2.57
636 711 1.133025 ACCGCAGTAGCAATTGCAATC 59.867 47.619 30.89 19.45 45.16 2.67
811 950 0.182775 CCATTTCCCCGAACCCTAGG 59.817 60.000 0.06 0.06 0.00 3.02
1021 1160 0.179124 GCGCCAAAGTGGACAAAACA 60.179 50.000 0.00 0.00 40.96 2.83
1081 1221 4.451150 GTCCTGACATCGCCCGCA 62.451 66.667 0.00 0.00 0.00 5.69
1190 1330 2.188994 GCTCCGGATGCTCAAGCT 59.811 61.111 3.57 0.00 42.66 3.74
1293 1433 1.473677 TGTGATATTGCCAAGCTGTGC 59.526 47.619 0.88 0.88 0.00 4.57
1298 1438 1.263356 ATTGCCAAGCTGTGCATCTT 58.737 45.000 10.85 0.00 37.33 2.40
1529 1669 1.606668 GTATCCGAGTCTGCTGAGGAG 59.393 57.143 0.00 0.00 33.54 3.69
1533 1673 1.806568 GAGTCTGCTGAGGAGGTCG 59.193 63.158 0.00 0.00 0.00 4.79
1572 1712 2.815158 AGGTCTGAGTTCCTCTTCTCC 58.185 52.381 0.00 0.00 0.00 3.71
1574 1714 2.164338 GTCTGAGTTCCTCTTCTCCGT 58.836 52.381 0.00 0.00 0.00 4.69
1582 1722 1.913762 CTCTTCTCCGTGGTGGGGT 60.914 63.158 0.00 0.00 40.23 4.95
1608 1748 1.821241 CGGCGTACATTGCTCATCGG 61.821 60.000 0.00 0.00 0.00 4.18
1647 1787 2.681778 CTGGAGGGCCGACTCAGT 60.682 66.667 10.72 0.00 39.27 3.41
1702 1842 5.185454 CAAATGGATTGCTAGGTCAGTACA 58.815 41.667 0.00 0.00 31.00 2.90
1739 1879 2.125350 CACCCTGAGCGAGAAGGC 60.125 66.667 0.00 0.00 31.71 4.35
1744 1884 1.012841 CCTGAGCGAGAAGGCATTTC 58.987 55.000 0.00 0.00 35.97 2.17
1805 1945 2.028112 ACCTCGCTGAAGACTATGCAAA 60.028 45.455 0.00 0.00 0.00 3.68
1838 1979 2.614057 GGTCATGCCGACTAATTTCAGG 59.386 50.000 3.66 0.00 44.70 3.86
1915 2263 4.811557 GTGTTCTATGCCTAACTGGATGTC 59.188 45.833 0.00 0.00 38.35 3.06
1974 2324 5.874810 TGGTCATTGCTAACTCTTGATGTAC 59.125 40.000 0.00 0.00 0.00 2.90
1975 2325 6.109359 GGTCATTGCTAACTCTTGATGTACT 58.891 40.000 0.00 0.00 0.00 2.73
2009 2360 0.886490 CTGAACCCCCGATATGCTGC 60.886 60.000 0.00 0.00 0.00 5.25
2020 2371 3.547413 CCGATATGCTGCTGTTGTCATTG 60.547 47.826 0.00 0.00 0.00 2.82
2028 2379 2.485426 TGCTGTTGTCATTGCTTAGAGC 59.515 45.455 0.00 0.00 42.82 4.09
2036 2387 6.187125 TGTCATTGCTTAGAGCTGATTTTC 57.813 37.500 0.00 0.00 42.97 2.29
2055 2406 8.830580 TGATTTTCGATAATGAGAAGTCCAATC 58.169 33.333 5.79 0.00 0.00 2.67
2136 2487 5.048713 GTCAATGGACCAACTTTCCAGTAAG 60.049 44.000 0.00 0.00 46.46 2.34
2204 2556 8.525316 TCATCTGCTTTCATGACAATGTTTATT 58.475 29.630 0.00 0.00 35.15 1.40
2215 2567 9.356433 CATGACAATGTTTATTTAGCATGTTCA 57.644 29.630 0.00 0.00 30.14 3.18
2221 2573 7.636259 TGTTTATTTAGCATGTTCAGTTTGC 57.364 32.000 0.00 0.00 36.63 3.68
2223 2575 8.572185 TGTTTATTTAGCATGTTCAGTTTGCTA 58.428 29.630 0.00 0.00 44.51 3.49
2241 2593 9.860898 AGTTTGCTAGATTTCATTGTATTTTCC 57.139 29.630 0.00 0.00 0.00 3.13
2329 2722 6.192234 ACCGTTCGATGTCTATCATATACC 57.808 41.667 0.00 0.00 36.83 2.73
2340 2733 8.040002 TGTCTATCATATACCACCATTTTCCA 57.960 34.615 0.00 0.00 0.00 3.53
2374 2767 5.882557 AGACATGAAAGACCACAACCATATC 59.117 40.000 0.00 0.00 0.00 1.63
2390 2783 7.554118 ACAACCATATCGATCTGAAAAGAACAT 59.446 33.333 12.05 0.00 0.00 2.71
2485 2879 1.303561 GATGAAGTGCCCACCAGCA 60.304 57.895 0.00 0.00 41.46 4.41
2558 2959 3.972227 GCGTCTGCAGTGGTCAAT 58.028 55.556 14.67 0.00 42.15 2.57
2580 2981 0.329261 ATCTGGGCTGCTGTTGCTAA 59.671 50.000 0.00 0.00 40.48 3.09
2672 3073 8.850007 AATAGAGAAGAACTTAAGGGACAAAC 57.150 34.615 7.53 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
277 330 7.654520 GCTGTGAACATTTTATTGGATATGCAT 59.345 33.333 3.79 3.79 0.00 3.96
278 331 6.979817 GCTGTGAACATTTTATTGGATATGCA 59.020 34.615 0.00 0.00 0.00 3.96
279 332 6.979817 TGCTGTGAACATTTTATTGGATATGC 59.020 34.615 0.00 0.00 0.00 3.14
280 333 8.192774 AGTGCTGTGAACATTTTATTGGATATG 58.807 33.333 0.00 0.00 0.00 1.78
281 334 8.297470 AGTGCTGTGAACATTTTATTGGATAT 57.703 30.769 0.00 0.00 0.00 1.63
282 335 7.701539 AGTGCTGTGAACATTTTATTGGATA 57.298 32.000 0.00 0.00 0.00 2.59
283 336 6.594788 AGTGCTGTGAACATTTTATTGGAT 57.405 33.333 0.00 0.00 0.00 3.41
284 337 7.701539 ATAGTGCTGTGAACATTTTATTGGA 57.298 32.000 0.00 0.00 0.00 3.53
285 338 8.761575 AAATAGTGCTGTGAACATTTTATTGG 57.238 30.769 0.00 0.00 0.00 3.16
286 339 9.409312 TGAAATAGTGCTGTGAACATTTTATTG 57.591 29.630 0.00 0.00 0.00 1.90
288 341 9.793252 GATGAAATAGTGCTGTGAACATTTTAT 57.207 29.630 0.00 0.00 0.00 1.40
289 342 8.791675 TGATGAAATAGTGCTGTGAACATTTTA 58.208 29.630 0.00 0.00 0.00 1.52
290 343 7.660112 TGATGAAATAGTGCTGTGAACATTTT 58.340 30.769 0.00 0.00 0.00 1.82
291 344 7.175467 TCTGATGAAATAGTGCTGTGAACATTT 59.825 33.333 0.00 0.00 0.00 2.32
292 345 6.656270 TCTGATGAAATAGTGCTGTGAACATT 59.344 34.615 0.00 0.00 0.00 2.71
293 346 6.175471 TCTGATGAAATAGTGCTGTGAACAT 58.825 36.000 0.00 0.00 0.00 2.71
294 347 5.550290 TCTGATGAAATAGTGCTGTGAACA 58.450 37.500 0.00 0.00 0.00 3.18
295 348 6.674694 ATCTGATGAAATAGTGCTGTGAAC 57.325 37.500 0.00 0.00 0.00 3.18
296 349 8.791327 TTTATCTGATGAAATAGTGCTGTGAA 57.209 30.769 0.00 0.00 0.00 3.18
297 350 8.260114 TCTTTATCTGATGAAATAGTGCTGTGA 58.740 33.333 0.00 0.00 0.00 3.58
298 351 8.429493 TCTTTATCTGATGAAATAGTGCTGTG 57.571 34.615 0.00 0.00 0.00 3.66
299 352 9.453572 TTTCTTTATCTGATGAAATAGTGCTGT 57.546 29.630 0.00 0.00 0.00 4.40
380 433 3.134804 AGTGACCTTCCAGGCATACATAC 59.865 47.826 0.00 0.00 39.63 2.39
390 443 3.942829 TCTGCATAAAGTGACCTTCCAG 58.057 45.455 0.00 0.00 0.00 3.86
404 457 6.209589 GGACAGGAATACTCACTATCTGCATA 59.790 42.308 0.00 0.00 0.00 3.14
415 468 4.323569 AGAGTCAGGACAGGAATACTCA 57.676 45.455 1.84 0.00 36.63 3.41
422 475 5.330233 TGTGTAAATAGAGTCAGGACAGGA 58.670 41.667 1.84 0.00 0.00 3.86
423 476 5.661056 TGTGTAAATAGAGTCAGGACAGG 57.339 43.478 1.84 0.00 0.00 4.00
424 477 8.855110 AGATATGTGTAAATAGAGTCAGGACAG 58.145 37.037 1.84 0.00 0.00 3.51
425 478 8.768501 AGATATGTGTAAATAGAGTCAGGACA 57.231 34.615 1.84 0.00 0.00 4.02
449 502 4.386652 GCAAACATGCACAAGGAATGTAAG 59.613 41.667 0.00 0.00 41.46 2.34
453 506 2.734606 CTGCAAACATGCACAAGGAATG 59.265 45.455 0.00 0.00 40.23 2.67
461 514 2.047939 GGCCCTGCAAACATGCAC 60.048 61.111 0.00 0.00 40.23 4.57
487 545 2.386661 ACATTAACAGGCTCGACCAG 57.613 50.000 6.78 1.78 43.14 4.00
497 555 6.051717 CAGTCTTCCCCTGATACATTAACAG 58.948 44.000 0.00 0.00 31.38 3.16
606 681 1.268999 GCTACTGCGGTCTCATCTCAG 60.269 57.143 0.00 0.00 0.00 3.35
608 683 0.741326 TGCTACTGCGGTCTCATCTC 59.259 55.000 0.00 0.00 43.34 2.75
609 684 1.186200 TTGCTACTGCGGTCTCATCT 58.814 50.000 0.00 0.00 43.34 2.90
610 685 2.231215 ATTGCTACTGCGGTCTCATC 57.769 50.000 0.00 0.00 43.34 2.92
611 686 2.283298 CAATTGCTACTGCGGTCTCAT 58.717 47.619 0.00 0.00 43.34 2.90
612 687 1.725641 CAATTGCTACTGCGGTCTCA 58.274 50.000 0.00 0.00 43.34 3.27
613 688 0.375106 GCAATTGCTACTGCGGTCTC 59.625 55.000 23.21 0.00 43.34 3.36
614 689 0.321564 TGCAATTGCTACTGCGGTCT 60.322 50.000 29.37 0.00 41.63 3.85
615 690 0.521291 TTGCAATTGCTACTGCGGTC 59.479 50.000 29.37 0.00 41.63 4.79
616 691 1.133025 GATTGCAATTGCTACTGCGGT 59.867 47.619 29.37 2.42 41.63 5.68
617 692 1.534595 GGATTGCAATTGCTACTGCGG 60.535 52.381 29.37 0.00 41.63 5.69
618 693 1.534595 GGGATTGCAATTGCTACTGCG 60.535 52.381 29.37 0.00 41.63 5.18
619 694 1.477700 TGGGATTGCAATTGCTACTGC 59.522 47.619 29.37 18.25 42.66 4.40
620 695 2.159198 GGTGGGATTGCAATTGCTACTG 60.159 50.000 29.37 0.00 42.66 2.74
621 696 2.102578 GGTGGGATTGCAATTGCTACT 58.897 47.619 29.37 14.77 42.66 2.57
622 697 1.202290 CGGTGGGATTGCAATTGCTAC 60.202 52.381 29.37 19.35 42.66 3.58
623 698 1.102154 CGGTGGGATTGCAATTGCTA 58.898 50.000 29.37 23.31 42.66 3.49
624 699 1.606885 CCGGTGGGATTGCAATTGCT 61.607 55.000 29.37 12.03 37.46 3.91
625 700 1.153588 CCGGTGGGATTGCAATTGC 60.154 57.895 23.69 23.69 37.19 3.56
636 711 2.545952 CGACAGAGATATTTCCGGTGGG 60.546 54.545 0.00 0.00 0.00 4.61
881 1020 0.979665 TTGAGGTGGGAGAGCTTCAG 59.020 55.000 0.00 0.00 30.42 3.02
882 1021 1.434188 TTTGAGGTGGGAGAGCTTCA 58.566 50.000 0.00 0.00 30.42 3.02
1021 1160 2.348888 CGACGACCTTAGGGCCAGT 61.349 63.158 6.18 0.00 35.63 4.00
1081 1221 2.041819 GGGGGTGAGGGAGACGAT 60.042 66.667 0.00 0.00 0.00 3.73
1190 1330 0.904865 AGACAACAGGCGGGATGAGA 60.905 55.000 0.27 0.00 0.00 3.27
1244 1384 2.581354 CGCACTCCCTCAGGAAGG 59.419 66.667 0.00 0.00 43.40 3.46
1245 1385 2.581354 CCGCACTCCCTCAGGAAG 59.419 66.667 0.00 0.00 43.40 3.46
1293 1433 0.379669 GCATCCTCGGCACAAAGATG 59.620 55.000 0.00 0.00 0.00 2.90
1298 1438 1.375908 GTGAGCATCCTCGGCACAA 60.376 57.895 0.00 0.00 41.13 3.33
1503 1643 3.628032 TCAGCAGACTCGGATACTTACAG 59.372 47.826 0.00 0.00 0.00 2.74
1529 1669 2.545731 GCTTCAGAGATTCCTTCGACC 58.454 52.381 0.00 0.00 0.00 4.79
1533 1673 3.131400 ACCTACGCTTCAGAGATTCCTTC 59.869 47.826 0.00 0.00 0.00 3.46
1572 1712 2.596338 GGTTCCAACCCCACCACG 60.596 66.667 0.00 0.00 43.43 4.94
1574 1714 3.892162 CCGGTTCCAACCCCACCA 61.892 66.667 2.78 0.00 46.53 4.17
1582 1722 1.579084 GCAATGTACGCCGGTTCCAA 61.579 55.000 1.90 0.00 0.00 3.53
1647 1787 6.099269 GGAACTTGATAACATAGTACCTGGGA 59.901 42.308 0.00 0.00 0.00 4.37
1702 1842 7.896496 CAGGGTGACTATATTATAGAAGTCCCT 59.104 40.741 15.99 18.96 38.04 4.20
1724 1864 0.393537 AAATGCCTTCTCGCTCAGGG 60.394 55.000 0.00 0.00 0.00 4.45
1739 1879 5.009410 GGGCATATGAACTTCTCCAGAAATG 59.991 44.000 6.97 0.00 33.07 2.32
1744 1884 3.135348 TGAGGGCATATGAACTTCTCCAG 59.865 47.826 6.97 0.00 0.00 3.86
1805 1945 0.248289 GCATGACCCTTTGCAAGCAT 59.752 50.000 0.00 0.00 38.72 3.79
1819 1959 3.627395 ACCTGAAATTAGTCGGCATGA 57.373 42.857 0.00 0.00 0.00 3.07
1820 1960 4.701956 AAACCTGAAATTAGTCGGCATG 57.298 40.909 0.00 0.00 0.00 4.06
1838 1979 6.759497 AGGCTATTCTTGGTTCATGTAAAC 57.241 37.500 0.00 0.00 0.00 2.01
1915 2263 8.029522 TGTAACAGAGACACTAAAAGATAGCAG 58.970 37.037 0.00 0.00 0.00 4.24
1974 2324 6.183360 GGGGGTTCAGGAATCAAATTATCAAG 60.183 42.308 0.00 0.00 0.00 3.02
1975 2325 5.660864 GGGGGTTCAGGAATCAAATTATCAA 59.339 40.000 0.00 0.00 0.00 2.57
2009 2360 3.999001 TCAGCTCTAAGCAATGACAACAG 59.001 43.478 1.29 0.00 45.56 3.16
2020 2371 7.383572 TCTCATTATCGAAAATCAGCTCTAAGC 59.616 37.037 0.00 0.00 42.84 3.09
2028 2379 7.776933 TGGACTTCTCATTATCGAAAATCAG 57.223 36.000 0.00 0.00 0.00 2.90
2036 2387 7.757173 ACATATCGATTGGACTTCTCATTATCG 59.243 37.037 1.71 0.00 35.88 2.92
2055 2406 8.430063 ACGTTAGTTAGAAACACAAACATATCG 58.570 33.333 0.00 0.00 0.00 2.92
2129 2480 7.176589 AGGACTCTTCTGTTATTCTTACTGG 57.823 40.000 0.00 0.00 0.00 4.00
2136 2487 6.091034 GGAAACGAAGGACTCTTCTGTTATTC 59.909 42.308 12.66 9.52 45.36 1.75
2215 2567 9.860898 GGAAAATACAATGAAATCTAGCAAACT 57.139 29.630 0.00 0.00 0.00 2.66
2221 2573 8.673711 TGGAACGGAAAATACAATGAAATCTAG 58.326 33.333 0.00 0.00 0.00 2.43
2222 2574 8.568676 TGGAACGGAAAATACAATGAAATCTA 57.431 30.769 0.00 0.00 0.00 1.98
2223 2575 7.461182 TGGAACGGAAAATACAATGAAATCT 57.539 32.000 0.00 0.00 0.00 2.40
2241 2593 8.873215 AGTACTAACTGAAATATGATGGAACG 57.127 34.615 0.00 0.00 33.57 3.95
2329 2722 9.874205 ATGTCTTTTATAACATGGAAAATGGTG 57.126 29.630 0.00 0.00 34.88 4.17
2340 2733 9.295825 TGTGGTCTTTCATGTCTTTTATAACAT 57.704 29.630 0.00 0.00 36.56 2.71
2362 2755 5.817296 TCTTTTCAGATCGATATGGTTGTGG 59.183 40.000 19.28 6.32 0.00 4.17
2485 2879 6.240894 TGAGAAAGCAACTTAGAATCACCAT 58.759 36.000 0.00 0.00 0.00 3.55
2557 2958 1.476471 GCAACAGCAGCCCAGATCTAT 60.476 52.381 0.00 0.00 0.00 1.98
2558 2959 0.107508 GCAACAGCAGCCCAGATCTA 60.108 55.000 0.00 0.00 0.00 1.98
2706 3222 8.976471 CAAATATAAAGCACACATCAACACAAA 58.024 29.630 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.