Multiple sequence alignment - TraesCS2B01G393200

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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 TraesCS2B01G393200 chr2B 100.000 3209 0 0 1 3209 557366709 557363501 0.000000e+00 5927.0
1 TraesCS2B01G393200 chr2A 94.145 1093 45 2 1267 2359 618435299 618434226 0.000000e+00 1646.0
2 TraesCS2B01G393200 chr2A 81.213 1006 130 35 1 984 618436690 618435722 0.000000e+00 756.0
3 TraesCS2B01G393200 chr2A 79.851 536 97 9 2681 3209 468341012 468341543 6.500000e-102 381.0
4 TraesCS2B01G393200 chr2A 90.876 274 16 1 944 1208 618435711 618435438 3.040000e-95 359.0
5 TraesCS2B01G393200 chr2A 91.860 86 1 3 2358 2437 618434144 618434059 7.270000e-22 115.0
6 TraesCS2B01G393200 chr2D 91.758 1007 66 5 1553 2543 476365232 476364227 0.000000e+00 1384.0
7 TraesCS2B01G393200 chr2D 81.939 1207 143 39 30 1208 476389746 476388587 0.000000e+00 952.0
8 TraesCS2B01G393200 chr2D 94.046 571 29 3 1553 2121 476386374 476385807 0.000000e+00 861.0
9 TraesCS2B01G393200 chr2D 95.184 353 16 1 1207 1559 476388471 476388120 1.010000e-154 556.0
10 TraesCS2B01G393200 chr2D 74.933 742 168 14 1336 2071 593137886 593138615 1.110000e-84 324.0
11 TraesCS2B01G393200 chr2D 85.446 213 30 1 2018 2230 476432917 476432706 1.500000e-53 220.0
12 TraesCS2B01G393200 chr2D 98.039 51 1 0 2098 2148 476385813 476385763 4.410000e-14 89.8
13 TraesCS2B01G393200 chr1B 94.461 668 34 1 2545 3209 557528902 557528235 0.000000e+00 1026.0
14 TraesCS2B01G393200 chr1B 79.658 644 113 12 2570 3209 328877265 328876636 6.310000e-122 448.0
15 TraesCS2B01G393200 chr7A 94.286 665 34 2 2545 3209 108881530 108880870 0.000000e+00 1014.0
16 TraesCS2B01G393200 chr5D 93.016 673 30 4 2549 3209 389493257 389492590 0.000000e+00 966.0
17 TraesCS2B01G393200 chr5D 84.069 634 87 8 2581 3204 91847319 91846690 1.650000e-167 599.0
18 TraesCS2B01G393200 chr7B 91.970 660 32 9 2545 3204 147733556 147734194 0.000000e+00 905.0
19 TraesCS2B01G393200 chr1D 88.009 442 53 0 2768 3209 9406070 9406511 1.020000e-144 523.0
20 TraesCS2B01G393200 chr6B 79.661 649 108 13 2570 3209 93719160 93719793 2.270000e-121 446.0
21 TraesCS2B01G393200 chr3D 80.935 556 94 9 2663 3209 569928016 569927464 2.290000e-116 429.0


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 TraesCS2B01G393200 chr2B 557363501 557366709 3208 True 5927.0 5927 100.0000 1 3209 1 chr2B.!!$R1 3208
1 TraesCS2B01G393200 chr2A 618434059 618436690 2631 True 719.0 1646 89.5235 1 2437 4 chr2A.!!$R1 2436
2 TraesCS2B01G393200 chr2A 468341012 468341543 531 False 381.0 381 79.8510 2681 3209 1 chr2A.!!$F1 528
3 TraesCS2B01G393200 chr2D 476364227 476365232 1005 True 1384.0 1384 91.7580 1553 2543 1 chr2D.!!$R1 990
4 TraesCS2B01G393200 chr2D 476385763 476389746 3983 True 614.7 952 92.3020 30 2148 4 chr2D.!!$R3 2118
5 TraesCS2B01G393200 chr2D 593137886 593138615 729 False 324.0 324 74.9330 1336 2071 1 chr2D.!!$F1 735
6 TraesCS2B01G393200 chr1B 557528235 557528902 667 True 1026.0 1026 94.4610 2545 3209 1 chr1B.!!$R2 664
7 TraesCS2B01G393200 chr1B 328876636 328877265 629 True 448.0 448 79.6580 2570 3209 1 chr1B.!!$R1 639
8 TraesCS2B01G393200 chr7A 108880870 108881530 660 True 1014.0 1014 94.2860 2545 3209 1 chr7A.!!$R1 664
9 TraesCS2B01G393200 chr5D 389492590 389493257 667 True 966.0 966 93.0160 2549 3209 1 chr5D.!!$R2 660
10 TraesCS2B01G393200 chr5D 91846690 91847319 629 True 599.0 599 84.0690 2581 3204 1 chr5D.!!$R1 623
11 TraesCS2B01G393200 chr7B 147733556 147734194 638 False 905.0 905 91.9700 2545 3204 1 chr7B.!!$F1 659
12 TraesCS2B01G393200 chr6B 93719160 93719793 633 False 446.0 446 79.6610 2570 3209 1 chr6B.!!$F1 639
13 TraesCS2B01G393200 chr3D 569927464 569928016 552 True 429.0 429 80.9350 2663 3209 1 chr3D.!!$R1 546

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
889 937 0.032952 CACCCCACGTTTCTTCTCGA 59.967 55.0 0.0 0.0 0.00 4.04 F
1304 1551 0.106569 TATGAATGGCAGCACCCCTG 60.107 55.0 0.0 0.0 44.67 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 3983 0.179111 CCGCCTGAATCGTTAGCTCA 60.179 55.0 0.0 0.0 0.0 4.26 R
2897 5052 0.971447 GAGAGGAGCCGTTACCACCT 60.971 60.0 0.0 0.0 0.0 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
23 24 6.729391 TGTTAGTTTTTGCTTTTTGTTCCC 57.271 33.333 0.00 0.00 0.00 3.97
26 27 5.878332 AGTTTTTGCTTTTTGTTCCCTTG 57.122 34.783 0.00 0.00 0.00 3.61
27 28 5.555966 AGTTTTTGCTTTTTGTTCCCTTGA 58.444 33.333 0.00 0.00 0.00 3.02
55 59 8.485976 AAAAGTTTGTGCAAAGCTATTAACAA 57.514 26.923 0.00 0.00 0.00 2.83
59 63 5.720371 TGTGCAAAGCTATTAACAATGGT 57.280 34.783 0.00 0.00 0.00 3.55
80 84 8.927675 ATGGTACTAGTTTTAGAGATCTCGAT 57.072 34.615 16.97 3.37 34.09 3.59
97 101 1.658596 CGATGCGAGAAATTCAACGGA 59.341 47.619 12.47 10.64 0.00 4.69
103 107 4.215399 TGCGAGAAATTCAACGGAGAAAAT 59.785 37.500 12.47 0.00 0.00 1.82
104 108 4.554973 GCGAGAAATTCAACGGAGAAAATG 59.445 41.667 12.47 0.00 0.00 2.32
110 114 7.809806 AGAAATTCAACGGAGAAAATGATTCAC 59.190 33.333 0.00 0.00 0.00 3.18
115 119 5.880054 ACGGAGAAAATGATTCACGATTT 57.120 34.783 10.67 0.00 0.00 2.17
118 122 6.037172 ACGGAGAAAATGATTCACGATTTAGG 59.963 38.462 10.67 0.00 0.00 2.69
119 123 6.202226 GGAGAAAATGATTCACGATTTAGGC 58.798 40.000 0.00 0.00 0.00 3.93
121 125 5.354234 AGAAAATGATTCACGATTTAGGCGT 59.646 36.000 0.00 0.00 43.67 5.68
238 249 5.885465 AGGAGTTGGAGTGATCTTTTCAAT 58.115 37.500 0.00 0.00 35.70 2.57
264 275 7.123383 AGGTATCCCTTAATTAGTGGTTTTGG 58.877 38.462 6.04 0.00 38.13 3.28
271 282 8.154203 CCCTTAATTAGTGGTTTTGGACAAATT 58.846 33.333 0.00 0.00 0.00 1.82
275 286 6.531503 TTAGTGGTTTTGGACAAATTGACA 57.468 33.333 0.00 0.00 0.00 3.58
279 290 4.020218 TGGTTTTGGACAAATTGACACCAA 60.020 37.500 13.14 15.13 34.86 3.67
323 334 4.520179 AGTTTCGCGGTTATCCCTATTTT 58.480 39.130 6.13 0.00 0.00 1.82
329 340 3.568007 GCGGTTATCCCTATTTTGATGCA 59.432 43.478 0.00 0.00 0.00 3.96
331 342 4.578516 CGGTTATCCCTATTTTGATGCACA 59.421 41.667 0.00 0.00 0.00 4.57
349 360 2.916716 CACATTGCATTAACTTGTCGGC 59.083 45.455 0.00 0.00 0.00 5.54
350 361 2.819608 ACATTGCATTAACTTGTCGGCT 59.180 40.909 0.00 0.00 0.00 5.52
359 370 2.902705 ACTTGTCGGCTTAACTCACA 57.097 45.000 0.00 0.00 0.00 3.58
360 371 2.480845 ACTTGTCGGCTTAACTCACAC 58.519 47.619 0.00 0.00 0.00 3.82
364 375 0.666274 TCGGCTTAACTCACACGCAG 60.666 55.000 0.00 0.00 0.00 5.18
365 376 0.666274 CGGCTTAACTCACACGCAGA 60.666 55.000 0.00 0.00 0.00 4.26
367 378 1.661112 GGCTTAACTCACACGCAGATC 59.339 52.381 0.00 0.00 0.00 2.75
368 379 1.661112 GCTTAACTCACACGCAGATCC 59.339 52.381 0.00 0.00 0.00 3.36
382 393 3.304391 CGCAGATCCTGACTAAGTAGAGC 60.304 52.174 0.00 0.00 32.44 4.09
383 394 3.634448 GCAGATCCTGACTAAGTAGAGCA 59.366 47.826 0.00 0.00 32.44 4.26
388 399 2.103373 CTGACTAAGTAGAGCAGGCCA 58.897 52.381 5.01 0.00 0.00 5.36
389 400 1.825474 TGACTAAGTAGAGCAGGCCAC 59.175 52.381 5.01 0.00 0.00 5.01
401 412 0.610785 CAGGCCACCCCATTTAACGT 60.611 55.000 5.01 0.00 35.39 3.99
470 486 3.682696 AGAAGGTTCCAATCCGGTTAAC 58.317 45.455 0.00 0.00 35.57 2.01
537 555 5.518847 CCTTTCGTTTTTCCTTCAGTTTTCC 59.481 40.000 0.00 0.00 0.00 3.13
710 731 3.980646 ACTTGTTAGCAAATGTTCGCA 57.019 38.095 0.00 0.00 33.73 5.10
781 829 1.749638 CTCGGCTCGGTACAGTCCT 60.750 63.158 0.00 0.00 0.00 3.85
788 836 0.038892 TCGGTACAGTCCTTCGCAAC 60.039 55.000 0.00 0.00 0.00 4.17
804 852 2.203394 ACTGTGCTGGCCCAGTTG 60.203 61.111 13.35 2.96 38.76 3.16
882 930 3.887335 TAGGCGCACCCCACGTTTC 62.887 63.158 10.83 0.00 36.11 2.78
885 933 2.943653 CGCACCCCACGTTTCTTC 59.056 61.111 0.00 0.00 0.00 2.87
887 935 1.566018 CGCACCCCACGTTTCTTCTC 61.566 60.000 0.00 0.00 0.00 2.87
888 936 1.566018 GCACCCCACGTTTCTTCTCG 61.566 60.000 0.00 0.00 0.00 4.04
889 937 0.032952 CACCCCACGTTTCTTCTCGA 59.967 55.000 0.00 0.00 0.00 4.04
926 978 2.224784 CACGTTAGCAACCAAACCCTAC 59.775 50.000 0.00 0.00 0.00 3.18
928 980 3.324556 ACGTTAGCAACCAAACCCTACTA 59.675 43.478 0.00 0.00 0.00 1.82
1080 1210 0.324738 ACAGGATCGAGGCTGAGGAA 60.325 55.000 0.00 0.00 0.00 3.36
1188 1318 2.704424 GGATGTGGCCTTGGGGGAT 61.704 63.158 3.32 0.00 37.23 3.85
1193 1323 4.759205 GGCCTTGGGGGATGCGTT 62.759 66.667 0.00 0.00 37.23 4.84
1233 1480 5.471797 CGAAGGAGAGATACATGCTCTTCTA 59.528 44.000 9.36 0.00 45.46 2.10
1262 1509 1.530293 GCTGCTCGCCTCATTTGATAG 59.470 52.381 0.00 0.00 0.00 2.08
1304 1551 0.106569 TATGAATGGCAGCACCCCTG 60.107 55.000 0.00 0.00 44.67 4.45
1410 1657 2.025981 AGTATCATGGTGGCAGAAGCAA 60.026 45.455 0.00 0.00 44.61 3.91
1447 1712 2.443390 AGCGGGCAGGGTACGTAT 60.443 61.111 0.00 0.00 0.00 3.06
1448 1713 1.152694 AGCGGGCAGGGTACGTATA 60.153 57.895 0.00 0.00 0.00 1.47
1449 1714 1.006922 GCGGGCAGGGTACGTATAC 60.007 63.158 0.00 0.00 0.00 1.47
1450 1715 1.283793 CGGGCAGGGTACGTATACG 59.716 63.158 23.24 23.24 46.33 3.06
1451 1716 1.006922 GGGCAGGGTACGTATACGC 60.007 63.158 24.64 9.63 44.43 4.42
1485 1750 0.179081 GCCTGATTACCGGACCAGAC 60.179 60.000 9.46 0.00 0.00 3.51
1564 3582 1.151777 CGACGACACATACATGGGGC 61.152 60.000 0.00 0.00 35.28 5.80
1630 3648 1.359459 GCTAAGGGAAGTCGCCGTTG 61.359 60.000 0.00 0.00 36.74 4.10
1641 3659 0.675083 TCGCCGTTGTCAAGAGGTTA 59.325 50.000 8.36 0.00 0.00 2.85
1886 3904 4.878397 ACTTTACCAGATGTATGAGCAAGC 59.122 41.667 0.00 0.00 0.00 4.01
1896 3914 0.743701 ATGAGCAAGCCGAGCAAGAG 60.744 55.000 0.00 0.00 0.00 2.85
1902 3920 2.654987 CAAGCCGAGCAAGAGAAAAAC 58.345 47.619 0.00 0.00 0.00 2.43
1975 3993 1.468520 GGCAGCAAAATGAGCTAACGA 59.531 47.619 0.00 0.00 41.14 3.85
2025 4043 0.115152 TGGAAGACCTGCAGAGGAGA 59.885 55.000 17.39 0.00 42.93 3.71
2087 4108 0.466124 AAGGAGGCAGCTAATCGGAC 59.534 55.000 0.00 0.00 0.00 4.79
2088 4109 1.069935 GGAGGCAGCTAATCGGACC 59.930 63.158 0.00 0.00 0.00 4.46
2140 4179 4.338879 AGATGATGCTTACTTTTGCACCT 58.661 39.130 0.00 0.00 42.26 4.00
2177 4216 2.511218 TGGAAGAATCTGATTGGGGGAG 59.489 50.000 7.78 0.00 0.00 4.30
2214 4253 0.107831 TGTGCCAAAGCTAGGAACGT 59.892 50.000 9.21 0.00 37.52 3.99
2253 4292 4.886489 GGGACTACGAAACCTACAGAGTAT 59.114 45.833 0.00 0.00 0.00 2.12
2256 4295 7.255070 GGGACTACGAAACCTACAGAGTATAAG 60.255 44.444 0.00 0.00 0.00 1.73
2294 4341 9.109393 GACTGCTAACATTTGATAGAACCATAA 57.891 33.333 0.00 0.00 0.00 1.90
2310 4357 7.425606 AGAACCATAATTTTCACACACTTGTC 58.574 34.615 0.00 0.00 31.66 3.18
2433 4570 5.285401 TCCCTCCATAAGACAACATTAGGA 58.715 41.667 0.00 0.00 0.00 2.94
2436 4573 7.062957 CCCTCCATAAGACAACATTAGGAAAT 58.937 38.462 0.00 0.00 0.00 2.17
2469 4606 5.227152 ACAAATGAGGCGGTAAAAACAATC 58.773 37.500 0.00 0.00 0.00 2.67
2470 4607 4.450082 AATGAGGCGGTAAAAACAATCC 57.550 40.909 0.00 0.00 0.00 3.01
2482 4619 7.269724 CGGTAAAAACAATCCGAATTACTGAAC 59.730 37.037 0.00 0.00 44.86 3.18
2489 4626 6.932400 ACAATCCGAATTACTGAACTGTGTTA 59.068 34.615 0.00 0.00 0.00 2.41
2506 4643 3.985279 GTGTTACTCGTCTGCATTGTGTA 59.015 43.478 0.00 0.00 0.00 2.90
2507 4644 4.090066 GTGTTACTCGTCTGCATTGTGTAG 59.910 45.833 0.00 0.00 0.00 2.74
2513 4650 5.405571 ACTCGTCTGCATTGTGTAGTTTTAG 59.594 40.000 0.00 0.00 31.74 1.85
2517 4654 6.910433 CGTCTGCATTGTGTAGTTTTAGTTTT 59.090 34.615 0.00 0.00 31.74 2.43
2521 4658 8.942669 TGCATTGTGTAGTTTTAGTTTTATCG 57.057 30.769 0.00 0.00 0.00 2.92
2543 4680 5.243730 TCGACTGCAGATTGTGATATATGGA 59.756 40.000 23.35 0.00 0.00 3.41
2897 5052 1.829222 GTCCTCGGTCATGAACCCTTA 59.171 52.381 4.85 0.00 46.27 2.69
3097 5262 3.744940 TGGATGATTTGGGCTTCTTCT 57.255 42.857 0.00 0.00 0.00 2.85
3199 5364 2.158784 GCCATCATCTCTGAGGAGCTTT 60.159 50.000 4.59 0.00 39.31 3.51
3204 5369 1.283347 TCTCTGAGGAGCTTTGCCAT 58.717 50.000 4.59 0.00 39.31 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 59 8.788806 CATCGAGATCTCTAAAACTAGTACCAT 58.211 37.037 20.26 0.00 0.00 3.55
59 63 6.704937 TCGCATCGAGATCTCTAAAACTAGTA 59.295 38.462 20.26 0.00 0.00 1.82
80 84 2.448926 TCTCCGTTGAATTTCTCGCA 57.551 45.000 0.00 0.00 0.00 5.10
86 90 6.582295 CGTGAATCATTTTCTCCGTTGAATTT 59.418 34.615 0.00 0.00 0.00 1.82
90 94 4.311606 TCGTGAATCATTTTCTCCGTTGA 58.688 39.130 0.00 0.00 0.00 3.18
97 101 5.354234 ACGCCTAAATCGTGAATCATTTTCT 59.646 36.000 0.00 0.00 38.88 2.52
103 107 4.109766 CACTACGCCTAAATCGTGAATCA 58.890 43.478 0.00 0.00 40.69 2.57
104 108 4.110482 ACACTACGCCTAAATCGTGAATC 58.890 43.478 0.00 0.00 40.69 2.52
110 114 3.800506 CCCTTAACACTACGCCTAAATCG 59.199 47.826 0.00 0.00 0.00 3.34
115 119 6.543430 TTTTATCCCTTAACACTACGCCTA 57.457 37.500 0.00 0.00 0.00 3.93
118 122 6.673154 ACATTTTATCCCTTAACACTACGC 57.327 37.500 0.00 0.00 0.00 4.42
119 123 9.337091 CAAAACATTTTATCCCTTAACACTACG 57.663 33.333 0.00 0.00 0.00 3.51
158 162 9.927668 CCTGTGAGTTTTGTTTATTTTCCATAT 57.072 29.630 0.00 0.00 0.00 1.78
163 167 6.756542 ACAGCCTGTGAGTTTTGTTTATTTTC 59.243 34.615 0.00 0.00 0.00 2.29
217 227 6.881602 ACCTATTGAAAAGATCACTCCAACTC 59.118 38.462 0.00 0.00 37.92 3.01
220 230 7.993183 GGATACCTATTGAAAAGATCACTCCAA 59.007 37.037 0.00 0.00 37.92 3.53
271 282 0.403655 TGGCTAGCCAATTGGTGTCA 59.596 50.000 34.27 19.07 44.12 3.58
292 303 3.994204 AACCGCGAAACTATTGGTTTT 57.006 38.095 8.23 0.00 46.77 2.43
297 308 3.463944 AGGGATAACCGCGAAACTATTG 58.536 45.455 8.23 0.00 46.96 1.90
306 317 3.364964 GCATCAAAATAGGGATAACCGCG 60.365 47.826 0.00 0.00 46.96 6.46
329 340 2.819608 AGCCGACAAGTTAATGCAATGT 59.180 40.909 0.00 0.00 0.00 2.71
331 342 5.183140 AGTTAAGCCGACAAGTTAATGCAAT 59.817 36.000 0.00 0.00 0.00 3.56
336 347 5.178809 GTGTGAGTTAAGCCGACAAGTTAAT 59.821 40.000 0.00 0.00 0.00 1.40
345 356 0.666274 CTGCGTGTGAGTTAAGCCGA 60.666 55.000 0.00 0.00 0.00 5.54
349 360 2.926200 CAGGATCTGCGTGTGAGTTAAG 59.074 50.000 0.00 0.00 0.00 1.85
350 361 2.560981 TCAGGATCTGCGTGTGAGTTAA 59.439 45.455 0.00 0.00 34.14 2.01
359 370 3.880490 CTCTACTTAGTCAGGATCTGCGT 59.120 47.826 0.00 0.00 0.00 5.24
360 371 3.304391 GCTCTACTTAGTCAGGATCTGCG 60.304 52.174 0.00 0.00 0.00 5.18
364 375 3.005367 GCCTGCTCTACTTAGTCAGGATC 59.995 52.174 18.34 2.12 42.25 3.36
365 376 2.962421 GCCTGCTCTACTTAGTCAGGAT 59.038 50.000 18.34 0.00 42.25 3.24
367 378 1.410882 GGCCTGCTCTACTTAGTCAGG 59.589 57.143 11.96 11.96 42.39 3.86
368 379 2.103373 TGGCCTGCTCTACTTAGTCAG 58.897 52.381 3.32 0.00 0.00 3.51
382 393 0.610785 ACGTTAAATGGGGTGGCCTG 60.611 55.000 3.32 0.00 0.00 4.85
383 394 0.113580 AACGTTAAATGGGGTGGCCT 59.886 50.000 3.32 0.00 0.00 5.19
388 399 8.488668 ACTACTATATCAAACGTTAAATGGGGT 58.511 33.333 0.00 0.00 0.00 4.95
389 400 8.897872 ACTACTATATCAAACGTTAAATGGGG 57.102 34.615 0.00 0.00 0.00 4.96
431 447 7.709149 ACCTTCTAGAAGATTCCCAAAATTG 57.291 36.000 30.17 13.04 40.79 2.32
470 486 4.561735 TTTTGTAGAGAACCAAAAGCGG 57.438 40.909 0.00 0.00 36.06 5.52
525 543 6.267699 AGGAAAACCATAAGGAAAACTGAAGG 59.732 38.462 0.00 0.00 38.69 3.46
590 610 7.433719 CAGGAACATATTTTCAAACGTGAACAA 59.566 33.333 4.11 0.00 43.52 2.83
647 668 8.334632 CCAACGCAAATAGTTTTTGATTTTTCT 58.665 29.630 9.88 0.00 0.00 2.52
648 669 8.119845 ACCAACGCAAATAGTTTTTGATTTTTC 58.880 29.630 9.88 0.00 0.00 2.29
649 670 7.980062 ACCAACGCAAATAGTTTTTGATTTTT 58.020 26.923 9.88 0.00 0.00 1.94
650 671 7.546778 ACCAACGCAAATAGTTTTTGATTTT 57.453 28.000 9.88 0.00 0.00 1.82
651 672 8.649973 TTACCAACGCAAATAGTTTTTGATTT 57.350 26.923 9.88 0.00 0.00 2.17
652 673 8.649973 TTTACCAACGCAAATAGTTTTTGATT 57.350 26.923 9.88 1.33 0.00 2.57
653 674 8.649973 TTTTACCAACGCAAATAGTTTTTGAT 57.350 26.923 9.88 0.00 0.00 2.57
654 675 8.475331 TTTTTACCAACGCAAATAGTTTTTGA 57.525 26.923 9.88 0.00 0.00 2.69
686 707 4.606012 GCGAACATTTGCTAACAAGTTTGC 60.606 41.667 11.49 11.49 40.87 3.68
906 958 2.105306 AGTAGGGTTTGGTTGCTAACGT 59.895 45.455 0.00 0.00 0.00 3.99
926 978 0.759346 CCGAGGGGAAGTTGGGATAG 59.241 60.000 0.00 0.00 34.06 2.08
928 980 2.680370 GCCGAGGGGAAGTTGGGAT 61.680 63.158 0.00 0.00 34.06 3.85
1060 1190 0.324738 TCCTCAGCCTCGATCCTGTT 60.325 55.000 10.96 0.00 0.00 3.16
1080 1210 3.013682 GGAGTGGACATCCTTCCCT 57.986 57.895 9.63 0.00 35.68 4.20
1172 1302 2.691732 CATCCCCCAAGGCCACAT 59.308 61.111 5.01 0.00 34.51 3.21
1178 1308 2.440247 GGAACGCATCCCCCAAGG 60.440 66.667 0.00 0.00 43.00 3.61
1255 1502 0.248012 TCCTTGCGTCGCCTATCAAA 59.752 50.000 15.88 0.00 0.00 2.69
1304 1551 4.929808 TCTTCCTTTCGCTGACTGAATAAC 59.070 41.667 0.00 0.00 0.00 1.89
1379 1626 2.689983 CACCATGATACTTGGGCTTTCC 59.310 50.000 0.00 0.00 38.64 3.13
1410 1657 2.432300 CGGAGGGAAGCGGGTGTAT 61.432 63.158 0.00 0.00 0.00 2.29
1458 1723 2.514013 GGTAATCAGGCGTGCGACG 61.514 63.158 0.35 4.61 45.88 5.12
1459 1724 2.514013 CGGTAATCAGGCGTGCGAC 61.514 63.158 0.35 0.00 0.00 5.19
1460 1725 2.202690 CGGTAATCAGGCGTGCGA 60.203 61.111 0.35 0.00 0.00 5.10
1461 1726 3.261951 CCGGTAATCAGGCGTGCG 61.262 66.667 0.35 0.00 0.00 5.34
1462 1727 2.171725 GTCCGGTAATCAGGCGTGC 61.172 63.158 0.00 0.00 0.00 5.34
1463 1728 1.520787 GGTCCGGTAATCAGGCGTG 60.521 63.158 0.00 0.00 0.00 5.34
1464 1729 1.956629 CTGGTCCGGTAATCAGGCGT 61.957 60.000 0.00 0.00 0.00 5.68
1485 1750 0.179089 CCTGCTCCAGATGAAGTCCG 60.179 60.000 0.00 0.00 32.44 4.79
1564 3582 1.063006 CATCTTTGCGCCATGGTCG 59.937 57.895 19.99 19.99 0.00 4.79
1610 3628 2.202892 CGGCGACTTCCCTTAGCC 60.203 66.667 0.00 0.00 44.00 3.93
1770 3788 1.000607 TCCGTGAACTTGGAAGAGACG 60.001 52.381 0.00 0.00 0.00 4.18
1886 3904 1.946768 TGGTGTTTTTCTCTTGCTCGG 59.053 47.619 0.00 0.00 0.00 4.63
1896 3914 5.049167 TGTTTCTCATGCATGGTGTTTTTC 58.951 37.500 25.97 10.07 0.00 2.29
1902 3920 4.157105 TGATCTTGTTTCTCATGCATGGTG 59.843 41.667 25.97 18.36 0.00 4.17
1965 3983 0.179111 CCGCCTGAATCGTTAGCTCA 60.179 55.000 0.00 0.00 0.00 4.26
1975 3993 1.147824 CATGCTCCTCCGCCTGAAT 59.852 57.895 0.00 0.00 0.00 2.57
2025 4043 1.143684 TGTTTCTTGCTCTCAGCCCTT 59.856 47.619 0.00 0.00 41.51 3.95
2087 4108 0.404040 TGTTCTTGCTACCCCCTTGG 59.596 55.000 0.00 0.00 41.37 3.61
2088 4109 1.351017 TCTGTTCTTGCTACCCCCTTG 59.649 52.381 0.00 0.00 0.00 3.61
2140 4179 1.651737 TCCAGAAGGGGAAATGTCGA 58.348 50.000 0.00 0.00 37.22 4.20
2177 4216 2.110006 GCTCCTCTTCCGATGGCC 59.890 66.667 0.00 0.00 0.00 5.36
2231 4270 7.281999 ACTTATACTCTGTAGGTTTCGTAGTCC 59.718 40.741 0.00 0.00 0.00 3.85
2253 4292 6.540551 TGTTAGCAGTCAAAATCACACACTTA 59.459 34.615 0.00 0.00 0.00 2.24
2256 4295 5.168526 TGTTAGCAGTCAAAATCACACAC 57.831 39.130 0.00 0.00 0.00 3.82
2294 4341 5.895636 TGACAAGACAAGTGTGTGAAAAT 57.104 34.783 0.00 0.00 38.41 1.82
2310 4357 6.483307 TGAGTTCACAGGAATTACTTGACAAG 59.517 38.462 13.77 13.77 35.05 3.16
2433 4570 6.866248 CCGCCTCATTTGTAAAGTTGTAATTT 59.134 34.615 0.00 0.00 0.00 1.82
2436 4573 4.822896 ACCGCCTCATTTGTAAAGTTGTAA 59.177 37.500 0.00 0.00 0.00 2.41
2439 4576 3.915437 ACCGCCTCATTTGTAAAGTTG 57.085 42.857 0.00 0.00 0.00 3.16
2445 4582 5.769484 TTGTTTTTACCGCCTCATTTGTA 57.231 34.783 0.00 0.00 0.00 2.41
2448 4585 4.617298 CGGATTGTTTTTACCGCCTCATTT 60.617 41.667 0.00 0.00 38.98 2.32
2469 4606 5.060569 CGAGTAACACAGTTCAGTAATTCGG 59.939 44.000 0.00 0.00 0.00 4.30
2470 4607 5.628193 ACGAGTAACACAGTTCAGTAATTCG 59.372 40.000 0.00 0.00 0.00 3.34
2482 4619 3.059884 ACAATGCAGACGAGTAACACAG 58.940 45.455 0.00 0.00 0.00 3.66
2489 4626 3.386768 AACTACACAATGCAGACGAGT 57.613 42.857 0.00 0.00 0.00 4.18
2506 4643 7.907214 ATCTGCAGTCGATAAAACTAAAACT 57.093 32.000 14.67 0.00 0.00 2.66
2507 4644 8.015658 ACAATCTGCAGTCGATAAAACTAAAAC 58.984 33.333 14.67 0.00 0.00 2.43
2513 4650 5.530519 TCACAATCTGCAGTCGATAAAAC 57.469 39.130 14.67 0.00 0.00 2.43
2517 4654 7.122650 TCCATATATCACAATCTGCAGTCGATA 59.877 37.037 14.67 13.12 0.00 2.92
2521 4658 5.350914 GCTCCATATATCACAATCTGCAGTC 59.649 44.000 14.67 0.00 0.00 3.51
2543 4680 2.344203 CGGAGAAGGTCCTCACGCT 61.344 63.158 0.00 0.00 44.35 5.07
2888 5043 1.624813 CCGTTACCACCTAAGGGTTCA 59.375 52.381 0.00 0.00 44.73 3.18
2897 5052 0.971447 GAGAGGAGCCGTTACCACCT 60.971 60.000 0.00 0.00 0.00 4.00
2904 5059 3.069318 GACGGGAGAGGAGCCGTT 61.069 66.667 0.00 0.00 39.03 4.44


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

AutoCloner maintained by Alex Coulton.