Multiple sequence alignment - TraesCS1B01G123800

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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 TraesCS1B01G123800 chr1B 100.000 2725 0 0 1 2725 150524623 150521899 0.000000e+00 5033
1 TraesCS1B01G123800 chr1A 92.240 1920 77 35 1 1875 104223885 104221993 0.000000e+00 2654
2 TraesCS1B01G123800 chr1A 76.413 407 81 14 1891 2290 552262627 552262229 3.560000e-49 206
3 TraesCS1B01G123800 chr1A 85.057 174 14 3 2554 2715 104221969 104221796 1.680000e-37 167
4 TraesCS1B01G123800 chr1D 91.399 1930 65 41 1 1875 101277477 101279360 0.000000e+00 2551
5 TraesCS1B01G123800 chr1D 84.868 152 10 5 2543 2682 101279370 101279520 1.020000e-29 141
6 TraesCS1B01G123800 chr7D 84.308 650 95 7 1881 2527 14585865 14585220 1.780000e-176 628
7 TraesCS1B01G123800 chr7D 85.082 429 62 2 2112 2540 585436605 585437031 1.160000e-118 436
8 TraesCS1B01G123800 chr3B 82.655 663 100 10 1890 2543 4388775 4388119 8.460000e-160 573
9 TraesCS1B01G123800 chr7A 82.154 650 108 8 1881 2527 13827612 13826968 3.970000e-153 551
10 TraesCS1B01G123800 chr7A 81.173 324 54 6 1877 2197 696202662 696202343 1.250000e-63 254
11 TraesCS1B01G123800 chr5B 78.000 600 116 14 1893 2489 375795849 375796435 1.990000e-96 363
12 TraesCS1B01G123800 chr4B 77.913 575 111 13 1893 2463 10789396 10789958 7.220000e-91 344
13 TraesCS1B01G123800 chr4D 77.604 576 111 14 1893 2463 6180641 6181203 1.560000e-87 333
14 TraesCS1B01G123800 chr6A 77.102 559 113 14 1892 2443 2206529 2205979 2.640000e-80 309
15 TraesCS1B01G123800 chr7B 81.395 301 52 4 1880 2178 339619564 339619266 2.710000e-60 243
16 TraesCS1B01G123800 chr7B 75.576 434 87 17 2074 2500 590193705 590193284 2.140000e-46 196


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 TraesCS1B01G123800 chr1B 150521899 150524623 2724 True 5033.0 5033 100.0000 1 2725 1 chr1B.!!$R1 2724
1 TraesCS1B01G123800 chr1A 104221796 104223885 2089 True 1410.5 2654 88.6485 1 2715 2 chr1A.!!$R2 2714
2 TraesCS1B01G123800 chr1D 101277477 101279520 2043 False 1346.0 2551 88.1335 1 2682 2 chr1D.!!$F1 2681
3 TraesCS1B01G123800 chr7D 14585220 14585865 645 True 628.0 628 84.3080 1881 2527 1 chr7D.!!$R1 646
4 TraesCS1B01G123800 chr3B 4388119 4388775 656 True 573.0 573 82.6550 1890 2543 1 chr3B.!!$R1 653
5 TraesCS1B01G123800 chr7A 13826968 13827612 644 True 551.0 551 82.1540 1881 2527 1 chr7A.!!$R1 646
6 TraesCS1B01G123800 chr5B 375795849 375796435 586 False 363.0 363 78.0000 1893 2489 1 chr5B.!!$F1 596
7 TraesCS1B01G123800 chr4B 10789396 10789958 562 False 344.0 344 77.9130 1893 2463 1 chr4B.!!$F1 570
8 TraesCS1B01G123800 chr4D 6180641 6181203 562 False 333.0 333 77.6040 1893 2463 1 chr4D.!!$F1 570
9 TraesCS1B01G123800 chr6A 2205979 2206529 550 True 309.0 309 77.1020 1892 2443 1 chr6A.!!$R1 551

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
713 738 0.040058 ATCATGTGGTGGCATGTGGT 59.96 50.0 0.0 0.0 44.68 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2493 2577 1.065636 GTGGCTAGGGTTTGTCCTACC 60.066 57.143 0.0 0.0 38.3 3.18 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
24 25 0.249280 CGATACATGTGCCGGCAGTA 60.249 55.000 33.73 27.95 0.00 2.74
38 39 1.338579 GGCAGTAGCACAAGAAGCTCT 60.339 52.381 0.00 0.00 42.32 4.09
39 40 2.093973 GGCAGTAGCACAAGAAGCTCTA 60.094 50.000 0.00 0.00 42.32 2.43
40 41 2.926838 GCAGTAGCACAAGAAGCTCTAC 59.073 50.000 0.00 0.00 42.32 2.59
41 42 3.367910 GCAGTAGCACAAGAAGCTCTACT 60.368 47.826 3.77 3.77 42.32 2.57
42 43 4.142359 GCAGTAGCACAAGAAGCTCTACTA 60.142 45.833 8.27 0.00 42.32 1.82
43 44 5.451242 GCAGTAGCACAAGAAGCTCTACTAT 60.451 44.000 8.27 0.00 42.32 2.12
44 45 6.238786 GCAGTAGCACAAGAAGCTCTACTATA 60.239 42.308 8.27 0.00 42.32 1.31
146 147 4.015578 GTGTCGTGCACGTTACCA 57.984 55.556 35.74 24.42 38.45 3.25
149 150 1.652124 GTGTCGTGCACGTTACCATAG 59.348 52.381 35.74 7.69 38.45 2.23
151 152 0.799152 TCGTGCACGTTACCATAGCG 60.799 55.000 35.74 8.87 40.80 4.26
170 171 8.446273 CCATAGCGAAGAATATATGTCAAAAGG 58.554 37.037 0.00 0.00 0.00 3.11
172 173 6.591935 AGCGAAGAATATATGTCAAAAGGGA 58.408 36.000 0.00 0.00 0.00 4.20
238 239 3.981210 GCATGTGCAACGAATTTGATTG 58.019 40.909 0.00 2.14 42.39 2.67
316 328 3.939740 ACATGGTGGCACATTATCTCT 57.060 42.857 20.82 0.00 44.52 3.10
369 381 6.071278 GGAGGAGGGAGATGTATTACATGTAC 60.071 46.154 13.93 10.51 39.27 2.90
372 384 8.232412 AGGAGGGAGATGTATTACATGTACTAA 58.768 37.037 13.93 0.00 39.27 2.24
423 435 4.061949 TGTGTGCACATGACGCAT 57.938 50.000 24.69 0.00 42.32 4.73
484 498 0.769247 GGGGTTAGAGTGGTGTGGTT 59.231 55.000 0.00 0.00 0.00 3.67
594 612 1.209019 CAGGGTGTTCTGATGAGGAGG 59.791 57.143 0.00 0.00 36.93 4.30
662 685 1.355381 TCTGCCTGTGTTTGGATGGAT 59.645 47.619 0.00 0.00 0.00 3.41
713 738 0.040058 ATCATGTGGTGGCATGTGGT 59.960 50.000 0.00 0.00 44.68 4.16
772 801 0.178953 AATACCTCCCATGCATGCCC 60.179 55.000 21.69 0.00 0.00 5.36
773 802 2.085343 ATACCTCCCATGCATGCCCC 62.085 60.000 21.69 0.00 0.00 5.80
774 803 3.829226 CCTCCCATGCATGCCCCT 61.829 66.667 21.69 0.00 0.00 4.79
775 804 2.203451 CTCCCATGCATGCCCCTC 60.203 66.667 21.69 0.00 0.00 4.30
777 806 2.203451 CCCATGCATGCCCCTCTC 60.203 66.667 21.69 0.00 0.00 3.20
778 807 2.764737 CCCATGCATGCCCCTCTCT 61.765 63.158 21.69 0.00 0.00 3.10
786 826 1.133388 CATGCCCCTCTCTCTCTCTCT 60.133 57.143 0.00 0.00 0.00 3.10
1040 1088 0.475906 ACCAGCTGCATTATCTCCCC 59.524 55.000 8.66 0.00 0.00 4.81
1067 1115 3.560239 CGATCCATCTCCTCTAGCCACTA 60.560 52.174 0.00 0.00 0.00 2.74
1068 1116 3.231207 TCCATCTCCTCTAGCCACTAC 57.769 52.381 0.00 0.00 0.00 2.73
1069 1117 2.786445 TCCATCTCCTCTAGCCACTACT 59.214 50.000 0.00 0.00 0.00 2.57
1071 1119 3.181434 CCATCTCCTCTAGCCACTACTCT 60.181 52.174 0.00 0.00 0.00 3.24
1072 1120 4.042311 CCATCTCCTCTAGCCACTACTCTA 59.958 50.000 0.00 0.00 0.00 2.43
1073 1121 4.693042 TCTCCTCTAGCCACTACTCTAC 57.307 50.000 0.00 0.00 0.00 2.59
1074 1122 3.069872 TCTCCTCTAGCCACTACTCTACG 59.930 52.174 0.00 0.00 0.00 3.51
1075 1123 2.770802 TCCTCTAGCCACTACTCTACGT 59.229 50.000 0.00 0.00 0.00 3.57
1076 1124 3.963374 TCCTCTAGCCACTACTCTACGTA 59.037 47.826 0.00 0.00 0.00 3.57
1088 1138 0.109458 TCTACGTACGCACTTGCCTG 60.109 55.000 16.72 0.00 37.91 4.85
1089 1139 1.683790 CTACGTACGCACTTGCCTGC 61.684 60.000 16.72 0.00 37.91 4.85
1092 1142 2.047274 TACGCACTTGCCTGCCTC 60.047 61.111 0.00 0.00 37.91 4.70
1096 1146 2.039405 GCACTTGCCTGCCTCTCTG 61.039 63.158 0.00 0.00 34.31 3.35
1097 1147 1.374190 CACTTGCCTGCCTCTCTGT 59.626 57.895 0.00 0.00 0.00 3.41
1116 1166 6.545666 TCTCTGTCTCTATCTCTCATTCCAAC 59.454 42.308 0.00 0.00 0.00 3.77
1117 1167 6.430864 TCTGTCTCTATCTCTCATTCCAACT 58.569 40.000 0.00 0.00 0.00 3.16
1118 1168 6.545666 TCTGTCTCTATCTCTCATTCCAACTC 59.454 42.308 0.00 0.00 0.00 3.01
1119 1169 5.596361 TGTCTCTATCTCTCATTCCAACTCC 59.404 44.000 0.00 0.00 0.00 3.85
1120 1170 5.596361 GTCTCTATCTCTCATTCCAACTCCA 59.404 44.000 0.00 0.00 0.00 3.86
1121 1171 5.596361 TCTCTATCTCTCATTCCAACTCCAC 59.404 44.000 0.00 0.00 0.00 4.02
1140 1190 1.645455 GTAGTAGCCGTCGCGATCA 59.355 57.895 14.06 0.00 41.18 2.92
1258 1312 0.099968 TAAGTCGTCGCCGAGGAATG 59.900 55.000 11.45 0.00 45.26 2.67
1277 1331 1.003355 CCAAGAGAAGGAGCGGCAA 60.003 57.895 1.45 0.00 0.00 4.52
1295 1349 0.391597 AAGAAGGCGACGAGGACAAA 59.608 50.000 0.00 0.00 0.00 2.83
1301 1355 2.654877 GACGAGGACAAAGGCCGA 59.345 61.111 0.00 0.00 0.00 5.54
1305 1359 3.296709 GAGGACAAAGGCCGAGCGA 62.297 63.158 0.00 0.00 0.00 4.93
1516 1570 2.805099 GAGCACACCAAAGACTCTTGAG 59.195 50.000 0.00 0.00 0.00 3.02
1524 1578 9.653287 CACACCAAAGACTCTTGAGTATTTATA 57.347 33.333 18.86 0.00 32.32 0.98
1609 1670 4.201608 CCGCGTACGTATACAAATTGTGTT 60.202 41.667 17.90 0.00 38.57 3.32
1610 1671 5.004251 CCGCGTACGTATACAAATTGTGTTA 59.996 40.000 17.90 0.00 38.57 2.41
1662 1723 6.033966 TCTTTCTTTCTCTTTTGGCGTTTTC 58.966 36.000 0.00 0.00 0.00 2.29
1866 1939 9.483916 AATTTTGGTTGCTAGTATTTGTTTACC 57.516 29.630 0.00 0.00 0.00 2.85
1875 1948 9.727859 TGCTAGTATTTGTTTACCAATCACTAA 57.272 29.630 0.00 0.00 33.12 2.24
1939 2012 5.129320 TCTGTCATGGCAGTACATAGAACAT 59.871 40.000 25.84 0.00 37.70 2.71
1983 2059 1.061812 AGATCCATGGACCACCTAGCT 60.062 52.381 18.99 0.00 37.04 3.32
1985 2061 2.561209 TCCATGGACCACCTAGCTAA 57.439 50.000 11.44 0.00 37.04 3.09
1986 2062 2.840511 TCCATGGACCACCTAGCTAAA 58.159 47.619 11.44 0.00 37.04 1.85
2012 2088 1.153823 GCACTAGAGCGAGCCGAAA 60.154 57.895 0.00 0.00 0.00 3.46
2013 2089 0.736325 GCACTAGAGCGAGCCGAAAA 60.736 55.000 0.00 0.00 0.00 2.29
2061 2140 2.483877 CAGAAGCCGAGCAAACATGTTA 59.516 45.455 12.39 0.00 0.00 2.41
2109 2189 4.572571 GGCCACACGGGACCAACA 62.573 66.667 0.00 0.00 39.68 3.33
2151 2231 4.049186 GCCGATGAAGAGAAGCGTAAATA 58.951 43.478 0.00 0.00 0.00 1.40
2164 2244 7.283329 AGAAGCGTAAATAGGAAGGATCAAAT 58.717 34.615 0.00 0.00 0.00 2.32
2167 2247 7.283329 AGCGTAAATAGGAAGGATCAAATCTT 58.717 34.615 0.00 0.00 0.00 2.40
2178 2258 7.337942 GGAAGGATCAAATCTTTAGACACACAT 59.662 37.037 0.00 0.00 0.00 3.21
2183 2263 8.585471 ATCAAATCTTTAGACACACATCCAAT 57.415 30.769 0.00 0.00 0.00 3.16
2226 2306 4.443978 AATAGATCCACCAATGACCAGG 57.556 45.455 0.00 0.00 0.00 4.45
2236 2316 2.036475 CCAATGACCAGGACCGATAGAG 59.964 54.545 0.00 0.00 39.76 2.43
2276 2356 3.751518 AGATAAAACTTCACACGCCCTT 58.248 40.909 0.00 0.00 0.00 3.95
2292 2372 3.191581 CGCCCTTCGATGACACTAGATAT 59.808 47.826 0.00 0.00 41.67 1.63
2311 2391 3.911698 CCATCGCGACGGGGATCA 61.912 66.667 14.67 0.00 43.27 2.92
2345 2425 8.568617 AGACATTATTTCTACTAGGGGACATT 57.431 34.615 0.00 0.00 0.00 2.71
2540 2624 4.166144 AGAGTTTCTTGTGGAGGAGGAAAA 59.834 41.667 0.00 0.00 0.00 2.29
2606 2690 0.377203 GGCGGGTTTGCTATTTCTCG 59.623 55.000 0.00 0.00 34.52 4.04
2612 2696 4.569162 CGGGTTTGCTATTTCTCGATTACA 59.431 41.667 0.00 0.00 0.00 2.41
2640 2736 7.837863 AGAATAGAAATCGAACCAACTAGTGA 58.162 34.615 0.00 0.00 0.00 3.41
2649 2745 4.935205 CGAACCAACTAGTGATTTGATGGA 59.065 41.667 13.25 0.00 0.00 3.41
2666 2762 2.759355 TGGATAAGAGGGTGGTGGTAG 58.241 52.381 0.00 0.00 0.00 3.18
2677 2773 2.559252 GGTGGTGGTAGTCCTAACCTCT 60.559 54.545 0.00 0.00 37.91 3.69
2683 2779 3.271225 TGGTAGTCCTAACCTCTCATGGA 59.729 47.826 0.00 0.00 37.91 3.41
2690 2786 3.639094 CCTAACCTCTCATGGATCGAACT 59.361 47.826 0.00 0.00 0.00 3.01
2702 2798 2.168521 GGATCGAACTCCATGGTTGAGA 59.831 50.000 12.58 6.87 35.24 3.27
2707 2803 5.070001 TCGAACTCCATGGTTGAGATTTTT 58.930 37.500 12.58 0.00 33.95 1.94
2715 2811 5.009911 CCATGGTTGAGATTTTTGTGTCTCA 59.990 40.000 2.57 1.23 46.60 3.27
2722 2818 7.496529 TGAGATTTTTGTGTCTCAAAGTAGG 57.503 36.000 2.82 0.00 45.64 3.18
2723 2819 7.279615 TGAGATTTTTGTGTCTCAAAGTAGGA 58.720 34.615 2.82 0.00 45.64 2.94
2724 2820 7.442364 TGAGATTTTTGTGTCTCAAAGTAGGAG 59.558 37.037 2.82 0.00 45.64 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.415950 ACATATATAGTAGAGCTTCTTGTGCT 57.584 34.615 0.00 0.00 44.24 4.40
104 105 3.607987 CTTGATCCGCGCGACGTC 61.608 66.667 34.63 24.43 41.42 4.34
105 106 3.411418 ATCTTGATCCGCGCGACGT 62.411 57.895 34.63 16.81 41.42 4.34
146 147 8.375506 TCCCTTTTGACATATATTCTTCGCTAT 58.624 33.333 0.00 0.00 0.00 2.97
149 150 6.861065 TCCCTTTTGACATATATTCTTCGC 57.139 37.500 0.00 0.00 0.00 4.70
170 171 4.397417 CCTGATTTCCTGACATGTTCTTCC 59.603 45.833 0.00 0.00 0.00 3.46
172 173 3.760684 GCCTGATTTCCTGACATGTTCTT 59.239 43.478 0.00 0.00 0.00 2.52
238 239 4.396790 TGTGCCGATTTAACTAATTGGACC 59.603 41.667 7.76 0.00 46.92 4.46
372 384 8.521170 TTGCTAAGCACGATATAGGAGTATAT 57.479 34.615 0.00 0.00 38.71 0.86
376 388 5.069251 AGTTTGCTAAGCACGATATAGGAGT 59.931 40.000 0.00 0.00 38.71 3.85
377 389 5.533482 AGTTTGCTAAGCACGATATAGGAG 58.467 41.667 0.00 0.00 38.71 3.69
378 390 5.531122 AGTTTGCTAAGCACGATATAGGA 57.469 39.130 0.00 0.00 38.71 2.94
379 391 6.868864 ACATAGTTTGCTAAGCACGATATAGG 59.131 38.462 0.00 0.00 38.71 2.57
380 392 7.875316 ACATAGTTTGCTAAGCACGATATAG 57.125 36.000 0.00 0.00 38.71 1.31
381 393 9.353999 CATACATAGTTTGCTAAGCACGATATA 57.646 33.333 0.00 0.00 38.71 0.86
423 435 2.330440 TGCAGCACAGAAAAGTCTCA 57.670 45.000 0.00 0.00 28.78 3.27
484 498 1.074775 GTGTCAAGGGCCCACATGA 59.925 57.895 27.56 21.94 0.00 3.07
552 570 2.304056 CCCTCCCTCCACTGCATGT 61.304 63.158 0.00 0.00 0.00 3.21
594 612 4.357142 CATGCATGCACTCCTTTTATGAC 58.643 43.478 25.37 0.00 0.00 3.06
662 685 7.572523 ACAACAAACATTTCTGATCTTCTCA 57.427 32.000 0.00 0.00 0.00 3.27
713 738 3.582647 TGCATGTTCCTCCTAACTCAAGA 59.417 43.478 0.00 0.00 0.00 3.02
772 801 4.040829 TGATGCTAGAGAGAGAGAGAGAGG 59.959 50.000 0.00 0.00 0.00 3.69
773 802 4.993584 GTGATGCTAGAGAGAGAGAGAGAG 59.006 50.000 0.00 0.00 0.00 3.20
774 803 4.408596 TGTGATGCTAGAGAGAGAGAGAGA 59.591 45.833 0.00 0.00 0.00 3.10
775 804 4.707105 TGTGATGCTAGAGAGAGAGAGAG 58.293 47.826 0.00 0.00 0.00 3.20
777 806 7.509141 TTTATGTGATGCTAGAGAGAGAGAG 57.491 40.000 0.00 0.00 0.00 3.20
778 807 9.579932 TTATTTATGTGATGCTAGAGAGAGAGA 57.420 33.333 0.00 0.00 0.00 3.10
1040 1088 3.378112 GCTAGAGGAGATGGATCGATGAG 59.622 52.174 0.54 0.00 0.00 2.90
1067 1115 0.109412 GGCAAGTGCGTACGTAGAGT 60.109 55.000 17.90 1.42 43.26 3.24
1068 1116 0.170561 AGGCAAGTGCGTACGTAGAG 59.829 55.000 17.90 6.21 43.26 2.43
1069 1117 0.109458 CAGGCAAGTGCGTACGTAGA 60.109 55.000 17.90 0.00 43.26 2.59
1071 1119 1.735198 GCAGGCAAGTGCGTACGTA 60.735 57.895 17.90 10.06 43.26 3.57
1072 1120 3.041940 GCAGGCAAGTGCGTACGT 61.042 61.111 17.90 0.00 43.26 3.57
1073 1121 3.788766 GGCAGGCAAGTGCGTACG 61.789 66.667 11.84 11.84 45.00 3.67
1074 1122 2.358737 AGGCAGGCAAGTGCGTAC 60.359 61.111 0.00 0.00 45.00 3.67
1075 1123 2.047274 GAGGCAGGCAAGTGCGTA 60.047 61.111 0.00 0.00 45.00 4.42
1076 1124 3.890936 GAGAGGCAGGCAAGTGCGT 62.891 63.158 0.00 0.37 45.00 5.24
1088 1138 4.085357 TGAGAGATAGAGACAGAGAGGC 57.915 50.000 0.00 0.00 0.00 4.70
1089 1139 5.707298 GGAATGAGAGATAGAGACAGAGAGG 59.293 48.000 0.00 0.00 0.00 3.69
1092 1142 6.547141 AGTTGGAATGAGAGATAGAGACAGAG 59.453 42.308 0.00 0.00 0.00 3.35
1096 1146 5.596361 TGGAGTTGGAATGAGAGATAGAGAC 59.404 44.000 0.00 0.00 0.00 3.36
1097 1147 5.596361 GTGGAGTTGGAATGAGAGATAGAGA 59.404 44.000 0.00 0.00 0.00 3.10
1116 1166 1.351012 CGACGGCTACTACGTGGAG 59.649 63.158 5.70 0.00 45.68 3.86
1117 1167 2.753966 GCGACGGCTACTACGTGGA 61.754 63.158 5.70 0.00 45.68 4.02
1118 1168 2.277756 GCGACGGCTACTACGTGG 60.278 66.667 0.00 0.00 45.68 4.94
1119 1169 2.370824 ATCGCGACGGCTACTACGTG 62.371 60.000 12.93 0.00 45.68 4.49
1121 1171 1.438384 GATCGCGACGGCTACTACG 60.438 63.158 12.93 0.00 36.88 3.51
1140 1190 1.001020 TGCAACCATGGCGGATCTT 60.001 52.632 13.04 0.00 38.63 2.40
1258 1312 2.821810 GCCGCTCCTTCTCTTGGC 60.822 66.667 0.00 0.00 35.04 4.52
1277 1331 0.038159 CTTTGTCCTCGTCGCCTTCT 60.038 55.000 0.00 0.00 0.00 2.85
1315 1369 0.399091 TTCCTCCTGATCGCCTCCAT 60.399 55.000 0.00 0.00 0.00 3.41
1524 1578 5.049543 GCTCGACACGACCTAGTAGAAATAT 60.050 44.000 0.00 0.00 0.00 1.28
1525 1579 4.272018 GCTCGACACGACCTAGTAGAAATA 59.728 45.833 0.00 0.00 0.00 1.40
1552 1613 3.428870 GGTATGCGTGTACATGTATCTGC 59.571 47.826 20.21 13.00 0.00 4.26
1653 1714 3.306917 TCATACTTCTCGAAAACGCCA 57.693 42.857 0.00 0.00 0.00 5.69
1662 1723 6.398918 CCCCCTATGTATTTCATACTTCTCG 58.601 44.000 0.00 0.00 37.91 4.04
1684 1745 2.224843 CCCACCCGTATAATTAACCCCC 60.225 54.545 0.00 0.00 0.00 5.40
1830 1901 7.731054 ACTAGCAACCAAAATTTCCATTGTAA 58.269 30.769 0.00 0.00 0.00 2.41
1881 1954 3.199677 TGGAAGTTTCTCTCGCGAAAAA 58.800 40.909 11.33 8.54 34.93 1.94
1882 1955 2.828877 TGGAAGTTTCTCTCGCGAAAA 58.171 42.857 11.33 5.16 34.93 2.29
1883 1956 2.519377 TGGAAGTTTCTCTCGCGAAA 57.481 45.000 11.33 0.00 0.00 3.46
1884 1957 2.519377 TTGGAAGTTTCTCTCGCGAA 57.481 45.000 11.33 0.02 0.00 4.70
1885 1958 2.231478 AGATTGGAAGTTTCTCTCGCGA 59.769 45.455 9.26 9.26 0.00 5.87
1886 1959 2.611518 AGATTGGAAGTTTCTCTCGCG 58.388 47.619 0.00 0.00 0.00 5.87
1952 2028 5.192722 TGGTCCATGGATCTGGTTGTAATTA 59.807 40.000 25.35 0.00 37.57 1.40
1983 2059 5.381174 TCGCTCTAGTGCTTGTAGTTTTA 57.619 39.130 14.40 0.00 0.00 1.52
1985 2061 3.839293 CTCGCTCTAGTGCTTGTAGTTT 58.161 45.455 14.40 0.00 0.00 2.66
1986 2062 2.416162 GCTCGCTCTAGTGCTTGTAGTT 60.416 50.000 14.40 0.00 0.00 2.24
2061 2140 5.048643 CGATGACTTCCCGATTGTCTACTAT 60.049 44.000 0.00 0.00 0.00 2.12
2109 2189 1.603802 CGGCAGATGTTGTTCTTGTGT 59.396 47.619 0.00 0.00 0.00 3.72
2151 2231 6.881602 GTGTGTCTAAAGATTTGATCCTTCCT 59.118 38.462 0.00 0.00 0.00 3.36
2164 2244 4.929211 CGTCATTGGATGTGTGTCTAAAGA 59.071 41.667 0.00 0.00 0.00 2.52
2167 2247 4.529109 TCGTCATTGGATGTGTGTCTAA 57.471 40.909 0.00 0.00 0.00 2.10
2178 2258 2.609491 CCAGTCTTCGTTCGTCATTGGA 60.609 50.000 0.00 0.00 0.00 3.53
2183 2263 1.201647 GGATCCAGTCTTCGTTCGTCA 59.798 52.381 6.95 0.00 0.00 4.35
2226 2306 1.404391 TCTTGCGGAACTCTATCGGTC 59.596 52.381 0.00 0.00 0.00 4.79
2236 2316 2.165301 CCGTCGGATCTTGCGGAAC 61.165 63.158 4.91 0.00 46.33 3.62
2292 2372 2.520020 ATCCCCGTCGCGATGGTA 60.520 61.111 37.85 28.21 35.70 3.25
2311 2391 7.682787 AGTAGAAATAATGTCTCCCACATCT 57.317 36.000 0.00 0.00 45.77 2.90
2392 2476 1.494960 GCAGGAGGGATCTCACTCTT 58.505 55.000 9.23 0.00 45.52 2.85
2489 2573 2.751688 GGGTTTGTCCTACCCGCA 59.248 61.111 0.00 0.00 45.42 5.69
2493 2577 1.065636 GTGGCTAGGGTTTGTCCTACC 60.066 57.143 0.00 0.00 38.30 3.18
2500 2584 2.572104 ACTCTTAGGTGGCTAGGGTTTG 59.428 50.000 0.00 0.00 0.00 2.93
2540 2624 9.651913 AACAAACTTCACATGAGTAAACATTTT 57.348 25.926 0.00 0.00 0.00 1.82
2543 2627 7.643764 CGAAACAAACTTCACATGAGTAAACAT 59.356 33.333 0.00 0.00 0.00 2.71
2544 2628 6.964370 CGAAACAAACTTCACATGAGTAAACA 59.036 34.615 0.00 0.00 0.00 2.83
2545 2629 6.413818 CCGAAACAAACTTCACATGAGTAAAC 59.586 38.462 0.00 0.00 0.00 2.01
2552 2636 7.922505 TTTATTCCGAAACAAACTTCACATG 57.077 32.000 0.00 0.00 0.00 3.21
2606 2690 9.261180 TGGTTCGATTTCTATTCTCATGTAATC 57.739 33.333 0.00 0.00 0.00 1.75
2612 2696 8.478877 ACTAGTTGGTTCGATTTCTATTCTCAT 58.521 33.333 0.00 0.00 0.00 2.90
2640 2736 4.386761 CCACCACCCTCTTATCCATCAAAT 60.387 45.833 0.00 0.00 0.00 2.32
2649 2745 2.318207 AGGACTACCACCACCCTCTTAT 59.682 50.000 0.00 0.00 38.94 1.73
2666 2762 3.223435 TCGATCCATGAGAGGTTAGGAC 58.777 50.000 0.00 0.00 0.00 3.85
2683 2779 4.494091 AATCTCAACCATGGAGTTCGAT 57.506 40.909 21.47 10.26 34.04 3.59
2690 2786 5.139727 AGACACAAAAATCTCAACCATGGA 58.860 37.500 21.47 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.