Multiple sequence alignment - TraesCS3B01G538800

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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 TraesCS3B01G538800 chr3B 100.000 3024 0 0 1 3024 778441504 778444527 0.000000e+00 5585.0
1 TraesCS3B01G538800 chr3B 92.312 1652 86 10 1387 3021 778392816 778394443 0.000000e+00 2309.0
2 TraesCS3B01G538800 chr3B 89.937 1421 84 24 6 1386 778402888 778404289 0.000000e+00 1777.0
3 TraesCS3B01G538800 chr3B 88.738 959 68 12 1503 2440 778432593 778433532 0.000000e+00 1136.0
4 TraesCS3B01G538800 chr3B 94.775 689 32 3 1387 2074 778404371 778405056 0.000000e+00 1070.0
5 TraesCS3B01G538800 chr3B 95.907 562 18 4 2460 3021 778433527 778434083 0.000000e+00 905.0
6 TraesCS3B01G538800 chr3B 91.905 630 46 3 724 1350 778392045 778392672 0.000000e+00 876.0
7 TraesCS3B01G538800 chr3B 92.727 495 32 2 914 1406 778432029 778432521 0.000000e+00 712.0
8 TraesCS3B01G538800 chr3B 79.218 409 83 2 1633 2040 776120960 776120553 1.770000e-72 283.0
9 TraesCS3B01G538800 chr3B 79.899 199 36 3 1037 1233 779525028 779525224 3.140000e-30 143.0
10 TraesCS3B01G538800 chr3B 80.282 142 25 3 208 348 16082982 16083121 1.480000e-18 104.0
11 TraesCS3B01G538800 chr3B 92.188 64 5 0 1887 1950 776178971 776178908 1.150000e-14 91.6
12 TraesCS3B01G538800 chr3B 77.622 143 26 4 209 347 157368361 157368221 6.950000e-12 82.4
13 TraesCS3B01G538800 chr3B 97.143 35 1 0 1352 1386 778392700 778392734 3.260000e-05 60.2
14 TraesCS3B01G538800 chr4A 89.049 347 32 5 1 347 628691976 628692316 2.790000e-115 425.0
15 TraesCS3B01G538800 chr6A 89.219 269 28 1 1 269 146782710 146782443 4.830000e-88 335.0
16 TraesCS3B01G538800 chr6A 86.508 126 11 3 222 347 146782460 146782341 1.890000e-27 134.0
17 TraesCS3B01G538800 chr6A 79.167 144 27 2 207 347 610213961 610214104 2.480000e-16 97.1
18 TraesCS3B01G538800 chr6A 91.045 67 6 0 57 123 568143495 568143561 1.150000e-14 91.6
19 TraesCS3B01G538800 chr3D 80.964 394 71 3 1633 2024 580587230 580586839 2.930000e-80 309.0
20 TraesCS3B01G538800 chr5A 88.106 227 26 1 1 227 513888646 513888871 4.970000e-68 268.0
21 TraesCS3B01G538800 chr5A 82.787 122 14 6 226 344 543959067 543959184 5.330000e-18 102.0
22 TraesCS3B01G538800 chr3A 78.032 437 79 16 1633 2060 716097777 716097349 2.990000e-65 259.0
23 TraesCS3B01G538800 chr6B 85.714 105 7 5 251 348 654823485 654823588 1.480000e-18 104.0
24 TraesCS3B01G538800 chr5B 79.433 141 29 0 208 348 37769473 37769333 1.920000e-17 100.0
25 TraesCS3B01G538800 chr5B 94.872 39 2 0 7 45 637957913 637957875 9.050000e-06 62.1
26 TraesCS3B01G538800 chr1B 93.478 46 3 0 1 46 39976818 39976863 5.410000e-08 69.4
27 TraesCS3B01G538800 chr7A 92.500 40 3 0 6 45 71109582 71109621 1.170000e-04 58.4


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 TraesCS3B01G538800 chr3B 778441504 778444527 3023 False 5585.000000 5585 100.000000 1 3024 1 chr3B.!!$F2 3023
1 TraesCS3B01G538800 chr3B 778402888 778405056 2168 False 1423.500000 1777 92.356000 6 2074 2 chr3B.!!$F5 2068
2 TraesCS3B01G538800 chr3B 778392045 778394443 2398 False 1081.733333 2309 93.786667 724 3021 3 chr3B.!!$F4 2297
3 TraesCS3B01G538800 chr3B 778432029 778434083 2054 False 917.666667 1136 92.457333 914 3021 3 chr3B.!!$F6 2107

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
504 540 0.109153 TGCTCTGCTTTGCTCCTTGA 59.891 50.000 0.0 0.0 0.0 3.02 F
1164 1205 1.003718 CGTCCACAAGAAGGTCCCC 60.004 63.158 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 2145 1.334384 TAGCATGGACTTGGCCGCTA 61.334 55.0 0.0 0.0 0.0 4.26 R
2611 2793 2.009681 AACCAATCAAACCCCCACTC 57.990 50.0 0.0 0.0 0.0 3.51 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
64 65 7.994334 TCTAATTAGAGACCAGGAGAGTTAGAC 59.006 40.741 11.24 0.00 0.00 2.59
70 71 2.225066 ACCAGGAGAGTTAGACGGTTCT 60.225 50.000 0.00 0.00 35.66 3.01
88 89 5.925969 CGGTTCTTCTAATTGCCAAACATTT 59.074 36.000 0.00 0.00 0.00 2.32
90 91 7.061789 CGGTTCTTCTAATTGCCAAACATTTAC 59.938 37.037 0.00 0.00 0.00 2.01
106 107 4.456566 ACATTTACGCGTAACCTCCAATTT 59.543 37.500 30.01 11.02 0.00 1.82
135 136 9.630098 ATCTGCTGTGTTATCAGTTTAATTTTG 57.370 29.630 0.00 0.00 37.70 2.44
160 161 8.407064 TGTTTTATCCGTGTTTTGTATCTTGTT 58.593 29.630 0.00 0.00 0.00 2.83
318 325 5.458015 GCCTAAGTTTTTAGTTTCGCACAT 58.542 37.500 0.00 0.00 35.51 3.21
319 326 6.348704 GGCCTAAGTTTTTAGTTTCGCACATA 60.349 38.462 0.00 0.00 35.51 2.29
322 329 5.043189 AGTTTTTAGTTTCGCACATAGCC 57.957 39.130 0.00 0.00 41.38 3.93
323 330 4.082949 AGTTTTTAGTTTCGCACATAGCCC 60.083 41.667 0.00 0.00 41.38 5.19
334 341 2.101783 CACATAGCCCCAGATTTTGCA 58.898 47.619 0.00 0.00 0.00 4.08
356 363 2.822637 CCAGCCCTGGTCGCCATAT 61.823 63.158 6.15 0.00 45.53 1.78
357 364 1.598962 CAGCCCTGGTCGCCATATG 60.599 63.158 0.00 0.00 30.82 1.78
358 365 2.072487 AGCCCTGGTCGCCATATGT 61.072 57.895 1.24 0.00 30.82 2.29
362 369 2.426522 CCCTGGTCGCCATATGTTATG 58.573 52.381 1.24 0.00 30.82 1.90
383 390 3.731547 TCCACCTGCAGGGAGATG 58.268 61.111 35.42 23.70 40.27 2.90
385 392 0.842030 TCCACCTGCAGGGAGATGTT 60.842 55.000 35.42 11.03 40.27 2.71
387 394 1.457346 CACCTGCAGGGAGATGTTTC 58.543 55.000 35.42 0.00 40.27 2.78
415 451 1.082679 TCTCGAGTCGTCGGTGCTAG 61.083 60.000 13.13 0.00 46.80 3.42
432 468 5.358160 GGTGCTAGAAAAATGGTTATGAGCT 59.642 40.000 0.00 0.00 0.00 4.09
433 469 6.261118 GTGCTAGAAAAATGGTTATGAGCTG 58.739 40.000 0.00 0.00 0.00 4.24
441 477 1.339055 TGGTTATGAGCTGTGGACTGC 60.339 52.381 0.00 0.65 40.53 4.40
504 540 0.109153 TGCTCTGCTTTGCTCCTTGA 59.891 50.000 0.00 0.00 0.00 3.02
516 552 4.558226 TGCTCCTTGATCTGCTTTCTAA 57.442 40.909 0.00 0.00 0.00 2.10
519 555 4.210955 GCTCCTTGATCTGCTTTCTAATCG 59.789 45.833 0.00 0.00 0.00 3.34
532 568 5.605534 CTTTCTAATCGAGGATGGTGTCAT 58.394 41.667 0.00 0.00 36.09 3.06
550 586 3.817647 GTCATTGTTTCTCCTTGCTCTGT 59.182 43.478 0.00 0.00 0.00 3.41
580 616 3.758755 ATCAGCTTCGCCATCAAGATA 57.241 42.857 0.00 0.00 0.00 1.98
639 677 4.688879 TGGAAACATACAGAACACATCGAC 59.311 41.667 0.00 0.00 33.40 4.20
678 716 9.743057 CAAAGTCACTGTCCTTCTAGATTATAG 57.257 37.037 0.00 0.00 0.00 1.31
680 718 8.685838 AGTCACTGTCCTTCTAGATTATAGTC 57.314 38.462 0.00 0.00 0.00 2.59
681 719 8.499406 AGTCACTGTCCTTCTAGATTATAGTCT 58.501 37.037 3.03 3.03 0.00 3.24
682 720 9.781633 GTCACTGTCCTTCTAGATTATAGTCTA 57.218 37.037 5.02 5.02 0.00 2.59
790 828 2.762887 TGAGCATCCTCTACCTGTCAAG 59.237 50.000 0.00 0.00 38.93 3.02
843 881 4.156739 CCAAGCTTCTCCTTTTGACCATAC 59.843 45.833 0.00 0.00 0.00 2.39
856 894 8.190784 CCTTTTGACCATACCAATTGATAAGAC 58.809 37.037 7.12 0.00 0.00 3.01
871 909 9.911788 AATTGATAAGACCAAATGACACTAGAT 57.088 29.630 0.00 0.00 0.00 1.98
894 933 7.673926 AGATAAACAAGAATAAGAAAAGGGCCA 59.326 33.333 6.18 0.00 0.00 5.36
1008 1049 7.484140 TGATATATCAGTCGATAATGGCAGAC 58.516 38.462 11.49 0.00 37.65 3.51
1023 1064 1.735386 CAGACCCAGTGAAGCTCATG 58.265 55.000 0.00 0.00 0.00 3.07
1053 1094 3.319198 AGCCCATTCGTCCACCGT 61.319 61.111 0.00 0.00 37.94 4.83
1164 1205 1.003718 CGTCCACAAGAAGGTCCCC 60.004 63.158 0.00 0.00 0.00 4.81
1167 1208 1.003718 CCACAAGAAGGTCCCCGTC 60.004 63.158 0.00 0.00 32.29 4.79
1173 1214 1.612739 GAAGGTCCCCGTCCTCCTT 60.613 63.158 0.00 0.00 42.10 3.36
1236 1277 1.372499 CGTCGACGAGGCCTTTGAA 60.372 57.895 33.35 0.00 43.02 2.69
1255 1296 4.740822 GGCCACCCATCTTGCCGT 62.741 66.667 0.00 0.00 33.59 5.68
1278 1319 1.486726 GACCCTCATGAAAGGTCCGAT 59.513 52.381 24.77 3.11 43.60 4.18
1413 1567 6.344572 TCATACATATTGTGTTGAGCGTTC 57.655 37.500 0.00 0.00 42.29 3.95
1426 1580 3.411446 TGAGCGTTCAATTGGTCTCAAT 58.589 40.909 5.42 0.00 44.77 2.57
1527 1688 9.745880 TCTAAAGATAGTATTTTCAGCTTACCG 57.254 33.333 0.00 0.00 0.00 4.02
1536 1697 8.993121 AGTATTTTCAGCTTACCGATATGAATG 58.007 33.333 0.00 0.00 30.56 2.67
1741 1906 2.107204 AGTGGAGGCACAACTCAAAGAT 59.893 45.455 0.00 0.00 39.27 2.40
1807 1972 1.304134 TGCCAGCCTACTGTCTCGA 60.304 57.895 0.00 0.00 42.81 4.04
1834 1999 2.456119 CGTGATGCAAGAGGTCGCC 61.456 63.158 0.00 0.00 0.00 5.54
1852 2017 2.125106 GGGGTGAGCGTGATGACC 60.125 66.667 0.00 0.00 0.00 4.02
1928 2093 1.301716 GTCAAGGAGTGCTTGCCGA 60.302 57.895 18.79 0.00 0.00 5.54
1980 2145 0.693049 ATCAGGGGAAAGTGCGTCTT 59.307 50.000 0.00 0.00 38.10 3.01
1981 2146 1.344065 TCAGGGGAAAGTGCGTCTTA 58.656 50.000 0.00 0.00 35.02 2.10
2096 2276 2.633509 GGGAGCTGCTGGCAAGTTG 61.634 63.158 7.01 0.00 44.79 3.16
2186 2366 3.186047 CGACTAGCAAACGGGCCG 61.186 66.667 27.06 27.06 0.00 6.13
2303 2483 1.038280 AACTCGTCCAACTTCGTCCT 58.962 50.000 0.00 0.00 0.00 3.85
2336 2516 1.334160 TGTCCCAGTCGTAGCTCAAA 58.666 50.000 0.00 0.00 0.00 2.69
2349 2529 0.759060 GCTCAAAAAGGGGTGTGGGT 60.759 55.000 0.00 0.00 0.00 4.51
2446 2628 4.480115 TCACTAAACAGAAGGTGGAGAGA 58.520 43.478 0.00 0.00 0.00 3.10
2447 2629 4.524714 TCACTAAACAGAAGGTGGAGAGAG 59.475 45.833 0.00 0.00 0.00 3.20
2448 2630 2.849294 AAACAGAAGGTGGAGAGAGC 57.151 50.000 0.00 0.00 0.00 4.09
2449 2631 0.605589 AACAGAAGGTGGAGAGAGCG 59.394 55.000 0.00 0.00 0.00 5.03
2453 2635 0.603569 GAAGGTGGAGAGAGCGTTCA 59.396 55.000 1.01 0.00 0.00 3.18
2466 2648 5.419471 AGAGAGCGTTCAGTTATAGAGGTTT 59.581 40.000 1.01 0.00 0.00 3.27
2499 2681 4.938832 TCCCTATGTTATGGTTTTGACACG 59.061 41.667 0.00 0.00 0.00 4.49
2557 2739 6.122850 ACTTTTTAGCGTTTCCGTAACTTT 57.877 33.333 0.00 0.00 34.46 2.66
2611 2793 2.413796 TGTTTTTACCGCAGTAGCATCG 59.586 45.455 0.00 0.00 42.27 3.84
2660 2842 3.262405 TGTACTATGGTGGTCTGTTTCCC 59.738 47.826 0.00 0.00 0.00 3.97
2661 2843 2.632537 ACTATGGTGGTCTGTTTCCCT 58.367 47.619 0.00 0.00 0.00 4.20
2821 3003 5.691305 GCATGTCTTGTGCTGTTTTCATTTA 59.309 36.000 0.00 0.00 39.45 1.40
2958 3140 4.453819 GTCAACAGGGATATCAAGCATAGC 59.546 45.833 4.83 0.00 0.00 2.97
2970 3152 8.815141 ATATCAAGCATAGCGAATCAGATATC 57.185 34.615 0.00 0.00 0.00 1.63
3023 3205 7.389803 TTTTGTTCAAGATGTTTGAGTCTGA 57.610 32.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.935808 GCCGAAGTTAATCAGAAAGAAGGA 59.064 41.667 0.00 0.00 0.00 3.36
1 2 4.938226 AGCCGAAGTTAATCAGAAAGAAGG 59.062 41.667 0.00 0.00 0.00 3.46
2 3 5.064071 GGAGCCGAAGTTAATCAGAAAGAAG 59.936 44.000 0.00 0.00 0.00 2.85
3 4 4.935808 GGAGCCGAAGTTAATCAGAAAGAA 59.064 41.667 0.00 0.00 0.00 2.52
4 5 4.223032 AGGAGCCGAAGTTAATCAGAAAGA 59.777 41.667 0.00 0.00 0.00 2.52
50 51 2.448453 AGAACCGTCTAACTCTCCTGG 58.552 52.381 0.00 0.00 29.93 4.45
64 65 4.497473 TGTTTGGCAATTAGAAGAACCG 57.503 40.909 0.00 0.00 0.00 4.44
70 71 4.854291 CGCGTAAATGTTTGGCAATTAGAA 59.146 37.500 0.00 0.00 0.00 2.10
88 89 6.864685 CAGATATAAATTGGAGGTTACGCGTA 59.135 38.462 16.41 16.41 0.00 4.42
90 91 5.389516 GCAGATATAAATTGGAGGTTACGCG 60.390 44.000 3.53 3.53 0.00 6.01
130 131 9.974980 AGATACAAAACACGGATAAAACAAAAT 57.025 25.926 0.00 0.00 0.00 1.82
135 136 8.791355 AACAAGATACAAAACACGGATAAAAC 57.209 30.769 0.00 0.00 0.00 2.43
188 189 8.134202 TGTCTTACTAGAATGATGTTTCCTGA 57.866 34.615 0.00 0.00 30.65 3.86
189 190 8.954950 ATGTCTTACTAGAATGATGTTTCCTG 57.045 34.615 0.00 0.00 30.65 3.86
281 283 8.818622 AAAAACTTAGGCCCTATTTTACTAGG 57.181 34.615 0.00 0.00 38.43 3.02
284 287 9.818270 AACTAAAAACTTAGGCCCTATTTTACT 57.182 29.630 0.00 0.00 0.00 2.24
299 302 5.458015 GGCTATGTGCGAAACTAAAAACTT 58.542 37.500 0.00 0.00 44.05 2.66
301 304 4.163552 GGGCTATGTGCGAAACTAAAAAC 58.836 43.478 0.00 0.00 44.05 2.43
318 325 0.684153 GCCTGCAAAATCTGGGGCTA 60.684 55.000 2.30 0.00 36.96 3.93
319 326 1.986210 GCCTGCAAAATCTGGGGCT 60.986 57.895 2.30 0.00 36.96 5.19
322 329 1.610086 TGGGCCTGCAAAATCTGGG 60.610 57.895 4.53 0.00 0.00 4.45
323 330 1.895238 CTGGGCCTGCAAAATCTGG 59.105 57.895 4.53 0.00 0.00 3.86
356 363 2.290260 CCTGCAGGTGGAGAACATAACA 60.290 50.000 25.53 0.00 35.31 2.41
357 364 2.359900 CCTGCAGGTGGAGAACATAAC 58.640 52.381 25.53 0.00 35.31 1.89
358 365 1.281867 CCCTGCAGGTGGAGAACATAA 59.718 52.381 30.63 0.00 35.31 1.90
362 369 3.483587 TCCCTGCAGGTGGAGAAC 58.516 61.111 30.63 0.00 35.31 3.01
382 389 1.535896 CTCGAGAGTGAGACCGAAACA 59.464 52.381 6.58 0.00 38.28 2.83
383 390 1.536331 ACTCGAGAGTGAGACCGAAAC 59.464 52.381 21.68 0.00 40.75 2.78
385 392 1.440708 GACTCGAGAGTGAGACCGAA 58.559 55.000 21.68 0.00 42.66 4.30
387 394 1.015085 ACGACTCGAGAGTGAGACCG 61.015 60.000 21.68 9.69 42.66 4.79
415 451 5.183904 AGTCCACAGCTCATAACCATTTTTC 59.816 40.000 0.00 0.00 0.00 2.29
432 468 1.005037 GTCGACCATGCAGTCCACA 60.005 57.895 3.51 0.00 32.91 4.17
433 469 0.391661 ATGTCGACCATGCAGTCCAC 60.392 55.000 14.12 0.00 32.91 4.02
504 540 4.346418 ACCATCCTCGATTAGAAAGCAGAT 59.654 41.667 0.00 0.00 0.00 2.90
516 552 3.634397 AACAATGACACCATCCTCGAT 57.366 42.857 0.00 0.00 31.40 3.59
519 555 3.691609 GGAGAAACAATGACACCATCCTC 59.308 47.826 0.00 0.00 31.40 3.71
532 568 5.659440 AAAAACAGAGCAAGGAGAAACAA 57.341 34.783 0.00 0.00 0.00 2.83
626 664 2.866156 ACTTGTGTGTCGATGTGTTCTG 59.134 45.455 0.00 0.00 0.00 3.02
633 671 3.942539 TGTTTGACTTGTGTGTCGATG 57.057 42.857 0.00 0.00 39.64 3.84
639 677 4.853196 CAGTGACTTTGTTTGACTTGTGTG 59.147 41.667 0.00 0.00 0.00 3.82
678 716 9.463443 AACACAGTGAGCAAATTAAAAATAGAC 57.537 29.630 7.81 0.00 0.00 2.59
680 718 9.683069 AGAACACAGTGAGCAAATTAAAAATAG 57.317 29.630 7.81 0.00 0.00 1.73
685 723 9.502091 AGTATAGAACACAGTGAGCAAATTAAA 57.498 29.630 7.81 0.00 0.00 1.52
765 803 3.561143 ACAGGTAGAGGATGCTCACTAG 58.439 50.000 17.24 10.74 0.00 2.57
790 828 7.334844 AGGGAAGCTGTAATTAAAATGCTAC 57.665 36.000 0.00 0.00 0.00 3.58
843 881 7.161773 AGTGTCATTTGGTCTTATCAATTGG 57.838 36.000 5.42 0.00 0.00 3.16
871 909 7.007723 TCTGGCCCTTTTCTTATTCTTGTTTA 58.992 34.615 0.00 0.00 0.00 2.01
875 913 4.158579 GGTCTGGCCCTTTTCTTATTCTTG 59.841 45.833 0.00 0.00 0.00 3.02
876 914 4.202673 TGGTCTGGCCCTTTTCTTATTCTT 60.203 41.667 0.00 0.00 36.04 2.52
882 920 2.110721 AGAATGGTCTGGCCCTTTTCTT 59.889 45.455 0.00 0.00 36.04 2.52
884 922 2.222227 AGAATGGTCTGGCCCTTTTC 57.778 50.000 0.00 0.00 36.04 2.29
894 933 3.328931 TGCTTCTTCTCCAAGAATGGTCT 59.671 43.478 0.00 0.00 45.70 3.85
917 956 0.039527 GTTGGTCCAAATGGTGTCGC 60.040 55.000 5.69 0.00 36.34 5.19
994 1035 1.138859 CACTGGGTCTGCCATTATCGA 59.861 52.381 0.00 0.00 36.17 3.59
996 1037 3.209410 CTTCACTGGGTCTGCCATTATC 58.791 50.000 0.00 0.00 36.17 1.75
1004 1045 1.678123 CCATGAGCTTCACTGGGTCTG 60.678 57.143 0.00 0.00 33.06 3.51
1005 1046 0.617413 CCATGAGCTTCACTGGGTCT 59.383 55.000 0.00 0.00 33.06 3.85
1008 1049 0.107312 CTCCCATGAGCTTCACTGGG 60.107 60.000 14.48 14.48 41.98 4.45
1112 1153 1.220529 CAACAGCTCGCTCTTGTTGA 58.779 50.000 13.88 0.00 41.42 3.18
1113 1154 0.385223 GCAACAGCTCGCTCTTGTTG 60.385 55.000 14.47 14.47 41.70 3.33
1164 1205 2.678934 TCCCCGTGAAGGAGGACG 60.679 66.667 0.00 0.00 45.00 4.79
1167 1208 1.296715 CTTGTCCCCGTGAAGGAGG 59.703 63.158 0.00 0.00 45.00 4.30
1173 1214 2.847234 ACAGCCTTGTCCCCGTGA 60.847 61.111 0.00 0.00 29.46 4.35
1236 1277 4.066139 GGCAAGATGGGTGGCCCT 62.066 66.667 0.00 0.00 45.70 5.19
1249 1290 1.191489 TCATGAGGGTCAGACGGCAA 61.191 55.000 0.00 0.00 0.00 4.52
1275 1316 2.892425 GACCAGAAGCGGGCATCG 60.892 66.667 0.00 0.00 42.76 3.84
1278 1319 2.424842 ATTTGGACCAGAAGCGGGCA 62.425 55.000 0.00 0.00 34.73 5.36
1339 1380 7.500227 TCCTACCTAGCAGAATTGATTTGAATG 59.500 37.037 0.00 0.00 0.00 2.67
1408 1562 3.829886 TGATTGAGACCAATTGAACGC 57.170 42.857 7.12 3.02 42.66 4.84
1494 1655 5.881923 AAATACTATCTTTAGACCCCGCA 57.118 39.130 0.00 0.00 0.00 5.69
1495 1656 6.285990 TGAAAATACTATCTTTAGACCCCGC 58.714 40.000 0.00 0.00 0.00 6.13
1597 1759 9.545105 AAAATTGTCAGCAAGTATTTCAATTGA 57.455 25.926 3.38 3.38 38.10 2.57
1741 1906 1.338769 GCGCCTCCAAAGAACCTCTTA 60.339 52.381 0.00 0.00 35.27 2.10
1807 1972 1.940883 CTTGCATCACGCTTGCCCAT 61.941 55.000 0.00 0.00 43.06 4.00
1834 1999 2.509336 GTCATCACGCTCACCCCG 60.509 66.667 0.00 0.00 0.00 5.73
1928 2093 5.723887 AGTAGGAGATGAGATGGTTTCTGTT 59.276 40.000 0.00 0.00 33.74 3.16
1980 2145 1.334384 TAGCATGGACTTGGCCGCTA 61.334 55.000 0.00 0.00 0.00 4.26
1981 2146 2.669133 TAGCATGGACTTGGCCGCT 61.669 57.895 0.00 0.00 0.00 5.52
2186 2366 7.429636 TTGCAACTAGGACAACTACAATTAC 57.570 36.000 0.00 0.00 0.00 1.89
2217 2397 4.452455 CCTAGTTGCGAGTTGAAGTTGAAT 59.548 41.667 0.00 0.00 0.00 2.57
2303 2483 5.392165 CGACTGGGACAACAAAAACAAACTA 60.392 40.000 0.00 0.00 38.70 2.24
2336 2516 2.969262 CAACATTAACCCACACCCCTTT 59.031 45.455 0.00 0.00 0.00 3.11
2384 2566 8.816640 ACATGTTATCTTCATTTTGACAAACC 57.183 30.769 0.00 0.00 0.00 3.27
2446 2628 5.790593 TCAAAACCTCTATAACTGAACGCT 58.209 37.500 0.00 0.00 0.00 5.07
2447 2629 6.476243 TTCAAAACCTCTATAACTGAACGC 57.524 37.500 0.00 0.00 0.00 4.84
2448 2630 7.857569 TGTTTCAAAACCTCTATAACTGAACG 58.142 34.615 3.33 0.00 38.11 3.95
2449 2631 8.290325 CCTGTTTCAAAACCTCTATAACTGAAC 58.710 37.037 3.33 0.00 38.11 3.18
2453 2635 6.940867 GGACCTGTTTCAAAACCTCTATAACT 59.059 38.462 3.33 0.00 38.11 2.24
2466 2648 5.014755 ACCATAACATAGGGACCTGTTTCAA 59.985 40.000 0.00 0.00 36.38 2.69
2510 2692 5.693769 ACTGCATAAAAACTAGCTCCCTA 57.306 39.130 0.00 0.00 0.00 3.53
2611 2793 2.009681 AACCAATCAAACCCCCACTC 57.990 50.000 0.00 0.00 0.00 3.51
2958 3140 9.774742 TCATCAATACTAACGATATCTGATTCG 57.225 33.333 15.61 15.61 41.04 3.34
2970 3152 5.592054 TCTCTGCCTTCATCAATACTAACG 58.408 41.667 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.