Multiple sequence alignment - TraesCS1D01G311000

Loading Multiple Alignment...

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 TraesCS1D01G311000 chr1D 100.000 3643 0 0 1 3643 407162685 407159043 0.000000e+00 6728.0
1 TraesCS1D01G311000 chr1D 76.884 199 30 6 2989 3174 290704491 290704686 8.330000e-17 99.0
2 TraesCS1D01G311000 chr1D 94.595 37 2 0 2301 2337 448788663 448788699 1.410000e-04 58.4
3 TraesCS1D01G311000 chr1B 92.133 3432 168 41 1 3370 547525728 547522337 0.000000e+00 4748.0
4 TraesCS1D01G311000 chr1B 87.879 264 26 3 3384 3643 547522357 547522096 4.570000e-79 305.0
5 TraesCS1D01G311000 chr1B 75.912 274 42 16 2918 3174 311741566 311741300 6.390000e-23 119.0
6 TraesCS1D01G311000 chr1B 94.595 37 2 0 2301 2337 614506740 614506776 1.410000e-04 58.4
7 TraesCS1D01G311000 chr1A 90.145 3450 178 63 1 3370 502807513 502804146 0.000000e+00 4338.0
8 TraesCS1D01G311000 chr1A 88.760 258 28 1 3384 3641 502804166 502803910 7.590000e-82 315.0
9 TraesCS1D01G311000 chr1A 76.812 276 40 12 2917 3174 554783414 554783145 2.280000e-27 134.0
10 TraesCS1D01G311000 chr1A 94.595 37 2 0 2301 2337 544391486 544391522 1.410000e-04 58.4
11 TraesCS1D01G311000 chr2B 81.900 221 30 10 2923 3136 688430043 688429826 1.040000e-40 178.0
12 TraesCS1D01G311000 chr2D 80.995 221 34 8 2922 3136 473433517 473433299 6.260000e-38 169.0
13 TraesCS1D01G311000 chr7D 84.756 164 25 0 1760 1923 417357560 417357397 8.090000e-37 165.0
14 TraesCS1D01G311000 chr7D 77.239 268 40 12 2923 3174 497321258 497321520 1.760000e-28 137.0
15 TraesCS1D01G311000 chr6D 80.822 219 32 10 2925 3136 382344194 382343979 2.910000e-36 163.0
16 TraesCS1D01G311000 chr6D 78.544 261 37 11 2925 3169 304688521 304688778 1.750000e-33 154.0
17 TraesCS1D01G311000 chr6D 75.185 270 41 20 2924 3174 144144179 144144441 1.790000e-18 104.0
18 TraesCS1D01G311000 chr5B 79.026 267 35 14 2925 3175 464316238 464315977 2.910000e-36 163.0
19 TraesCS1D01G311000 chr7B 83.929 168 27 0 1760 1927 433064154 433063987 1.050000e-35 161.0
20 TraesCS1D01G311000 chr7B 79.911 224 28 15 2923 3136 72605128 72604912 8.150000e-32 148.0
21 TraesCS1D01G311000 chr7A 83.537 164 27 0 1760 1923 482217921 482217758 1.750000e-33 154.0
22 TraesCS1D01G311000 chr6B 79.630 216 36 8 2924 3133 299623804 299624017 8.150000e-32 148.0
23 TraesCS1D01G311000 chr6B 97.436 39 1 0 367 405 571738436 571738398 2.350000e-07 67.6
24 TraesCS1D01G311000 chr3D 79.821 223 28 14 2924 3137 610424081 610423867 2.930000e-31 147.0
25 TraesCS1D01G311000 chr3D 90.741 54 5 0 308 361 570399443 570399496 5.050000e-09 73.1
26 TraesCS1D01G311000 chr3A 81.564 179 21 4 3007 3174 486930676 486930499 1.760000e-28 137.0
27 TraesCS1D01G311000 chr3A 90.741 54 5 0 308 361 703302721 703302774 5.050000e-09 73.1
28 TraesCS1D01G311000 chr3A 93.478 46 3 0 3179 3224 668988441 668988486 6.530000e-08 69.4
29 TraesCS1D01G311000 chr3A 100.000 29 0 0 358 386 530911745 530911773 2.000000e-03 54.7
30 TraesCS1D01G311000 chr6A 93.478 46 3 0 360 405 579135568 579135523 6.530000e-08 69.4
31 TraesCS1D01G311000 chr6A 100.000 28 0 0 360 387 596351848 596351821 7.000000e-03 52.8
32 TraesCS1D01G311000 chr2A 76.613 124 28 1 1861 1984 661082847 661082969 2.350000e-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 TraesCS1D01G311000 chr1D 407159043 407162685 3642 True 6728.0 6728 100.0000 1 3643 1 chr1D.!!$R1 3642
1 TraesCS1D01G311000 chr1B 547522096 547525728 3632 True 2526.5 4748 90.0060 1 3643 2 chr1B.!!$R2 3642
2 TraesCS1D01G311000 chr1A 502803910 502807513 3603 True 2326.5 4338 89.4525 1 3641 2 chr1A.!!$R2 3640

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
636 658 0.108585 AGCACAAGTCCAACCACGAT 59.891 50.000 0.00 0.00 0.0 3.73 F
873 908 0.390860 CTAGATTCCCGGGACAGCAG 59.609 60.000 26.87 14.76 0.0 4.24 F
1673 1729 1.135721 CCTAACCCAGCCACGTACTAC 59.864 57.143 0.00 0.00 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 1764 1.279496 TCTAGCACTCACTGGCCATT 58.721 50.000 5.51 0.0 0.0 3.16 R
2552 2618 1.374885 CACAATGGGCGTCGTGGTA 60.375 57.895 0.00 0.0 0.0 3.25 R
3615 3720 0.320771 GTTGACACAGGTGCGAGGAT 60.321 55.000 0.00 0.0 0.0 3.24 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
159 170 2.359975 GGGTTGGTTCGGCTGGAG 60.360 66.667 0.00 0.00 0.00 3.86
330 342 2.778187 GAGGATCCTCTAACGTTCGG 57.222 55.000 31.11 4.33 39.80 4.30
347 359 4.751431 GCACCCTGCCATTCTTCT 57.249 55.556 0.00 0.00 37.42 2.85
368 380 1.133699 ACTGACATGTGGGCCCATATG 60.134 52.381 43.61 43.61 46.43 1.78
417 434 0.534412 CAGAGGAATCCAGCACGACT 59.466 55.000 0.61 0.00 0.00 4.18
423 440 2.197577 GAATCCAGCACGACTAAGAGC 58.802 52.381 0.00 0.00 0.00 4.09
458 475 9.195411 CACATATAGTTGCACTCAAAATTTTGT 57.805 29.630 25.98 9.17 39.18 2.83
490 511 2.977808 TGGAAGATAGGGTGATCCTCC 58.022 52.381 0.00 0.00 44.06 4.30
517 538 9.657419 ATTTCCATTAATAGAAACCAAAAGCTG 57.343 29.630 10.64 0.00 34.97 4.24
558 580 2.231964 ACCACCGAAAGCATAGTCGTTA 59.768 45.455 0.00 0.00 35.48 3.18
574 596 1.976728 CGTTACACTCAGCAGTACACG 59.023 52.381 0.00 0.00 0.00 4.49
611 633 3.231965 GCAGATCATTTATCGTGCATGC 58.768 45.455 11.82 11.82 39.79 4.06
612 634 3.304190 GCAGATCATTTATCGTGCATGCA 60.304 43.478 18.46 18.46 39.79 3.96
636 658 0.108585 AGCACAAGTCCAACCACGAT 59.891 50.000 0.00 0.00 0.00 3.73
638 660 0.790207 CACAAGTCCAACCACGATCG 59.210 55.000 14.88 14.88 0.00 3.69
639 661 0.677288 ACAAGTCCAACCACGATCGA 59.323 50.000 24.34 0.00 0.00 3.59
640 662 1.069513 ACAAGTCCAACCACGATCGAA 59.930 47.619 24.34 0.00 0.00 3.71
641 663 1.459592 CAAGTCCAACCACGATCGAAC 59.540 52.381 24.34 7.70 0.00 3.95
642 664 0.677288 AGTCCAACCACGATCGAACA 59.323 50.000 24.34 0.00 0.00 3.18
725 747 0.583438 CCACGCTTCTTGACACTGTG 59.417 55.000 6.19 6.19 0.00 3.66
755 778 0.622665 GCTCCCATGCCAGCCTATAT 59.377 55.000 3.28 0.00 0.00 0.86
766 789 4.408921 TGCCAGCCTATATATCCATGTACC 59.591 45.833 0.00 0.00 0.00 3.34
872 907 1.686325 GCTAGATTCCCGGGACAGCA 61.686 60.000 26.87 9.42 0.00 4.41
873 908 0.390860 CTAGATTCCCGGGACAGCAG 59.609 60.000 26.87 14.76 0.00 4.24
874 909 1.686325 TAGATTCCCGGGACAGCAGC 61.686 60.000 26.87 12.13 0.00 5.25
875 910 4.473520 ATTCCCGGGACAGCAGCG 62.474 66.667 26.87 0.00 0.00 5.18
951 992 3.505480 ATCCATCCTTGAGCTGAATCC 57.495 47.619 0.00 0.00 0.00 3.01
954 995 3.203710 TCCATCCTTGAGCTGAATCCAAT 59.796 43.478 0.00 0.00 0.00 3.16
956 997 3.287867 TCCTTGAGCTGAATCCAATCC 57.712 47.619 0.00 0.00 0.00 3.01
965 1006 2.426024 CTGAATCCAATCCAGCCAACAG 59.574 50.000 0.00 0.00 0.00 3.16
987 1028 3.232213 AGCAAATTCATCAGCTTGCAG 57.768 42.857 8.21 0.00 45.22 4.41
989 1030 2.929161 GCAAATTCATCAGCTTGCAGCA 60.929 45.455 10.16 0.00 45.56 4.41
1013 1054 1.696097 GCTCTAATGGAGGCCCGGAA 61.696 60.000 0.73 0.00 42.08 4.30
1095 1136 3.422303 CGCCACCACCATCACACG 61.422 66.667 0.00 0.00 0.00 4.49
1107 1148 3.767230 CACACGAAGCGCCACTCG 61.767 66.667 19.03 19.03 42.12 4.18
1166 1207 2.583593 GCGTGCTCCTTCGCCTAG 60.584 66.667 0.00 0.00 45.54 3.02
1170 1211 2.202946 GCTCCTTCGCCTAGGCAC 60.203 66.667 32.47 5.38 42.06 5.01
1171 1212 2.726351 GCTCCTTCGCCTAGGCACT 61.726 63.158 32.47 0.00 46.37 4.40
1172 1213 1.439644 CTCCTTCGCCTAGGCACTC 59.560 63.158 32.47 4.19 41.75 3.51
1260 1316 1.798725 CGGCGACAACGTGTACGAT 60.799 57.895 11.79 0.00 43.02 3.73
1455 1511 2.182791 CTGCAGATCGACGGCACT 59.817 61.111 8.42 0.00 43.90 4.40
1641 1697 2.836154 GGACCTTGTGACAGCCCA 59.164 61.111 0.00 0.00 0.00 5.36
1671 1727 1.896122 GCCTAACCCAGCCACGTACT 61.896 60.000 0.00 0.00 0.00 2.73
1672 1728 1.477553 CCTAACCCAGCCACGTACTA 58.522 55.000 0.00 0.00 0.00 1.82
1673 1729 1.135721 CCTAACCCAGCCACGTACTAC 59.864 57.143 0.00 0.00 0.00 2.73
2054 2110 1.442526 GGCATCAGGTTCGCATCCAG 61.443 60.000 0.00 0.00 0.00 3.86
2062 2118 2.026822 AGGTTCGCATCCAGTTCATTCT 60.027 45.455 0.00 0.00 0.00 2.40
2065 2121 2.632377 TCGCATCCAGTTCATTCTTCC 58.368 47.619 0.00 0.00 0.00 3.46
2067 2123 3.450817 TCGCATCCAGTTCATTCTTCCTA 59.549 43.478 0.00 0.00 0.00 2.94
2384 2450 2.799371 GCCGTCTTCGTCTCCGAT 59.201 61.111 0.00 0.00 43.80 4.18
2552 2618 0.739813 GCTGGAACGTCTACGGCAAT 60.740 55.000 7.50 0.00 44.95 3.56
2621 2687 1.202651 CCCAGGAACGTGGATGATACC 60.203 57.143 14.02 0.00 40.44 2.73
2701 2770 8.049721 AGATAAGGAAGTAATTGAAACCAGAGG 58.950 37.037 0.00 0.00 0.00 3.69
2834 2911 7.279981 GTGACAGTTACCAGAATATACATGCAA 59.720 37.037 0.00 0.00 0.00 4.08
2848 2925 9.801873 AATATACATGCAAAATGTTCTGTAACC 57.198 29.630 0.00 0.00 34.49 2.85
2968 3064 2.093890 TCATCATTCGCAATGGCAGTT 58.906 42.857 0.00 0.00 41.24 3.16
2978 3074 1.270550 CAATGGCAGTTCAAGGACACC 59.729 52.381 0.00 0.00 0.00 4.16
2979 3075 0.251341 ATGGCAGTTCAAGGACACCC 60.251 55.000 0.00 0.00 0.00 4.61
2989 3085 4.088056 TCAAGGACACCCGAAATAACAA 57.912 40.909 0.00 0.00 37.58 2.83
3024 3120 0.036105 TCGTAGACCACCTAGCGACA 60.036 55.000 0.00 0.00 31.20 4.35
3029 3125 1.817447 AGACCACCTAGCGACAACTAC 59.183 52.381 0.00 0.00 0.00 2.73
3037 3133 1.502231 AGCGACAACTACAAGCACTG 58.498 50.000 0.00 0.00 0.00 3.66
3040 3136 1.270094 CGACAACTACAAGCACTGGGA 60.270 52.381 0.00 0.00 0.00 4.37
3076 3172 2.590092 CCGTCATTGTCCCCCTCC 59.410 66.667 0.00 0.00 0.00 4.30
3101 3197 2.473816 GAAGCCAGGAAAACTTGTTGC 58.526 47.619 0.00 0.00 0.00 4.17
3103 3199 1.136891 AGCCAGGAAAACTTGTTGCAC 59.863 47.619 0.00 0.00 0.00 4.57
3124 3220 0.791422 AGACACTCGAGAAGTCGTCG 59.209 55.000 21.68 0.00 46.85 5.12
3139 3235 1.805945 GTCGTGCTAAGGACCAGCG 60.806 63.158 0.00 0.00 42.13 5.18
3153 3249 2.033141 AGCGCACCAGAACAGCAT 59.967 55.556 11.47 0.00 0.00 3.79
3169 3265 2.318224 CATCCGCTGCAGATGAAGG 58.682 57.895 20.43 11.75 43.15 3.46
3181 3277 1.648467 GATGAAGGGAAGTGGCGTGC 61.648 60.000 0.00 0.00 0.00 5.34
3182 3278 2.281484 GAAGGGAAGTGGCGTGCA 60.281 61.111 0.00 0.00 0.00 4.57
3199 3295 2.033801 GTGCATGTGTTCATAGGGATGC 59.966 50.000 0.00 0.00 32.62 3.91
3217 3313 4.094294 GGATGCGTGTATGTATGTGTTTGT 59.906 41.667 0.00 0.00 0.00 2.83
3224 3320 6.035542 CGTGTATGTATGTGTTTGTGAGCATA 59.964 38.462 0.00 0.00 0.00 3.14
3225 3321 7.254421 CGTGTATGTATGTGTTTGTGAGCATAT 60.254 37.037 0.00 0.00 0.00 1.78
3325 3426 9.151471 CGGAATTTCATCTAGACTTTTCTAACA 57.849 33.333 0.00 0.00 33.73 2.41
3367 3468 4.100963 TCTGTGAACAAGTACACTCATGGT 59.899 41.667 0.00 0.00 37.81 3.55
3368 3469 4.776349 TGTGAACAAGTACACTCATGGTT 58.224 39.130 0.00 0.00 37.81 3.67
3369 3470 5.189928 TGTGAACAAGTACACTCATGGTTT 58.810 37.500 0.00 0.00 37.81 3.27
3370 3471 5.295787 TGTGAACAAGTACACTCATGGTTTC 59.704 40.000 0.00 0.00 37.81 2.78
3371 3472 4.819630 TGAACAAGTACACTCATGGTTTCC 59.180 41.667 0.00 0.00 0.00 3.13
3372 3473 3.751518 ACAAGTACACTCATGGTTTCCC 58.248 45.455 0.00 0.00 0.00 3.97
3373 3474 3.081804 CAAGTACACTCATGGTTTCCCC 58.918 50.000 0.00 0.00 0.00 4.81
3374 3475 1.278127 AGTACACTCATGGTTTCCCCG 59.722 52.381 0.00 0.00 35.15 5.73
3375 3476 0.035820 TACACTCATGGTTTCCCCGC 60.036 55.000 0.00 0.00 35.15 6.13
3376 3477 1.303236 CACTCATGGTTTCCCCGCA 60.303 57.895 0.00 0.00 35.15 5.69
3377 3478 0.893270 CACTCATGGTTTCCCCGCAA 60.893 55.000 0.00 0.00 35.15 4.85
3378 3479 0.178975 ACTCATGGTTTCCCCGCAAA 60.179 50.000 0.00 0.00 35.15 3.68
3379 3480 0.965439 CTCATGGTTTCCCCGCAAAA 59.035 50.000 0.00 0.00 35.15 2.44
3380 3481 1.342819 CTCATGGTTTCCCCGCAAAAA 59.657 47.619 0.00 0.00 35.15 1.94
3441 3542 6.823286 TCCATATTGTGACCCTGAAAGATA 57.177 37.500 0.00 0.00 34.07 1.98
3513 3618 5.657474 GCCATGGCATAATGAATAGATTGG 58.343 41.667 32.08 0.00 41.49 3.16
3584 3689 4.163649 TCATCAGAACCATGATCAAGCTCT 59.836 41.667 0.00 0.00 37.84 4.09
3597 3702 2.034939 TCAAGCTCTGTGGCACATTTTG 59.965 45.455 22.35 20.20 44.52 2.44
3627 3732 0.678395 AGCATAGATCCTCGCACCTG 59.322 55.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 213 1.153188 TGCACACTGACACCCACAG 60.153 57.895 0.00 0.00 40.68 3.66
330 342 1.065126 AGTAGAAGAATGGCAGGGTGC 60.065 52.381 0.00 0.00 44.08 5.01
340 352 3.370953 GGCCCACATGTCAGTAGAAGAAT 60.371 47.826 0.00 0.00 0.00 2.40
347 359 1.886422 TATGGGCCCACATGTCAGTA 58.114 50.000 31.51 10.47 32.39 2.74
417 434 4.096003 GTGGCCGGGCAGCTCTTA 62.096 66.667 33.64 3.90 0.00 2.10
423 440 0.108585 AACTATATGTGGCCGGGCAG 59.891 55.000 33.64 20.84 0.00 4.85
458 475 8.611257 TCACCCTATCTTCCAATAGAAAAGAAA 58.389 33.333 0.00 0.00 33.10 2.52
490 511 9.657419 AGCTTTTGGTTTCTATTAATGGAAATG 57.343 29.630 24.36 13.91 39.05 2.32
517 538 5.046529 TGGTGTTGTGTGTTGAATAATTGC 58.953 37.500 0.00 0.00 0.00 3.56
558 580 2.610479 CCAATCGTGTACTGCTGAGTGT 60.610 50.000 0.00 0.00 33.21 3.55
574 596 3.848272 TCTGCAAACCGATTTCCAATC 57.152 42.857 0.00 0.00 0.00 2.67
611 633 0.040958 GTTGGACTTGTGCTCGCTTG 60.041 55.000 0.00 0.00 0.00 4.01
612 634 1.166531 GGTTGGACTTGTGCTCGCTT 61.167 55.000 0.00 0.00 0.00 4.68
725 747 1.607467 ATGGGAGCCAAAGTGCACC 60.607 57.895 14.63 0.00 40.78 5.01
728 750 2.575461 GCATGGGAGCCAAAGTGC 59.425 61.111 0.00 0.00 36.95 4.40
755 778 1.663739 GAGCGCGGGTACATGGATA 59.336 57.895 8.83 0.00 0.00 2.59
766 789 3.119709 GAGAGAGTGAGGAGCGCGG 62.120 68.421 8.83 0.00 0.00 6.46
872 907 2.443016 AGGAAGGCCGAGATCGCT 60.443 61.111 0.00 0.00 39.96 4.93
873 908 2.028337 GAGGAAGGCCGAGATCGC 59.972 66.667 0.00 0.00 39.96 4.58
874 909 1.361993 CAGAGGAAGGCCGAGATCG 59.638 63.158 0.00 0.00 39.96 3.69
875 910 1.745264 CCAGAGGAAGGCCGAGATC 59.255 63.158 0.00 0.00 39.96 2.75
876 911 1.764054 CCCAGAGGAAGGCCGAGAT 60.764 63.158 0.00 0.00 39.96 2.75
877 912 2.364317 CCCAGAGGAAGGCCGAGA 60.364 66.667 0.00 0.00 39.96 4.04
951 992 1.250328 TGCTTCTGTTGGCTGGATTG 58.750 50.000 0.00 0.00 0.00 2.67
954 995 1.999648 ATTTGCTTCTGTTGGCTGGA 58.000 45.000 0.00 0.00 0.00 3.86
956 997 3.374220 TGAATTTGCTTCTGTTGGCTG 57.626 42.857 0.00 0.00 34.75 4.85
965 1006 3.581755 TGCAAGCTGATGAATTTGCTTC 58.418 40.909 9.14 0.00 44.59 3.86
987 1028 1.403323 GCCTCCATTAGAGCAAAGTGC 59.597 52.381 0.00 0.00 45.46 4.40
989 1030 1.064389 GGGCCTCCATTAGAGCAAAGT 60.064 52.381 0.84 0.00 41.74 2.66
1089 1130 2.355837 GAGTGGCGCTTCGTGTGA 60.356 61.111 7.64 0.00 0.00 3.58
1152 1193 2.683572 TGCCTAGGCGAAGGAGCA 60.684 61.111 28.28 5.61 45.51 4.26
1161 1202 2.809010 GGAGACGAGTGCCTAGGC 59.191 66.667 27.71 27.71 42.35 3.93
1236 1292 4.988486 ACGTTGTCGCCGTCGTCC 62.988 66.667 0.00 0.00 41.18 4.79
1260 1316 0.389817 CGCCGAAGTCCTTGATGACA 60.390 55.000 0.00 0.00 37.73 3.58
1641 1697 1.489560 GGGTTAGGCCACTCACCACT 61.490 60.000 5.01 0.00 41.79 4.00
1671 1727 3.396260 AAAGGCTTGAAGCAGTACGTA 57.604 42.857 19.89 0.00 44.75 3.57
1672 1728 2.256117 AAAGGCTTGAAGCAGTACGT 57.744 45.000 19.89 0.00 44.75 3.57
1673 1729 3.496884 TGTTAAAGGCTTGAAGCAGTACG 59.503 43.478 19.89 0.00 44.75 3.67
1674 1730 4.515567 ACTGTTAAAGGCTTGAAGCAGTAC 59.484 41.667 22.34 9.39 44.75 2.73
1705 1761 2.584835 AGCACTCACTGGCCATTTAA 57.415 45.000 5.51 0.00 0.00 1.52
1706 1762 2.837591 TCTAGCACTCACTGGCCATTTA 59.162 45.455 5.51 0.00 0.00 1.40
1707 1763 1.630369 TCTAGCACTCACTGGCCATTT 59.370 47.619 5.51 0.00 0.00 2.32
1708 1764 1.279496 TCTAGCACTCACTGGCCATT 58.721 50.000 5.51 0.00 0.00 3.16
1718 1774 4.982999 TCAACGTCAGTTATCTAGCACTC 58.017 43.478 0.00 0.00 38.79 3.51
2054 2110 8.554835 AAGAAAAGCTACTAGGAAGAATGAAC 57.445 34.615 0.00 0.00 0.00 3.18
2062 2118 7.246171 ACATCTGAAGAAAAGCTACTAGGAA 57.754 36.000 0.00 0.00 0.00 3.36
2095 2154 2.028112 GTCAGTCAATGCCACTGGAGTA 60.028 50.000 0.00 0.00 41.51 2.59
2122 2184 2.976356 TGCTGCGATGAGAGCACT 59.024 55.556 0.00 0.00 40.30 4.40
2384 2450 1.663739 GATGCCGGCGTAGGTGATA 59.336 57.895 23.94 0.00 0.00 2.15
2552 2618 1.374885 CACAATGGGCGTCGTGGTA 60.375 57.895 0.00 0.00 0.00 3.25
2621 2687 3.133691 TCAGTAACACTTCAAGCTGCTG 58.866 45.455 1.35 0.00 0.00 4.41
2691 2757 7.231467 TGGCCTAATATATTTCCTCTGGTTTC 58.769 38.462 3.32 0.00 0.00 2.78
2942 3038 5.845103 TGCCATTGCGAATGATGAATAATT 58.155 33.333 9.56 0.00 41.46 1.40
2968 3064 3.773418 TGTTATTTCGGGTGTCCTTGA 57.227 42.857 0.00 0.00 0.00 3.02
2989 3085 9.106070 GTGGTCTACGAACCTGAATATAATTTT 57.894 33.333 0.00 0.00 40.20 1.82
2999 3095 2.719739 CTAGGTGGTCTACGAACCTGA 58.280 52.381 13.57 1.88 44.13 3.86
3024 3120 2.438021 TCTTGTCCCAGTGCTTGTAGTT 59.562 45.455 0.00 0.00 0.00 2.24
3029 3125 2.260844 TCTTCTTGTCCCAGTGCTTG 57.739 50.000 0.00 0.00 0.00 4.01
3037 3133 1.302511 TGCGCCTTCTTCTTGTCCC 60.303 57.895 4.18 0.00 0.00 4.46
3040 3136 1.961277 CGGTGCGCCTTCTTCTTGT 60.961 57.895 15.69 0.00 0.00 3.16
3076 3172 0.537371 AGTTTTCCTGGCTTCGGTGG 60.537 55.000 0.00 0.00 0.00 4.61
3101 3197 2.737783 ACGACTTCTCGAGTGTCTAGTG 59.262 50.000 25.96 17.94 43.06 2.74
3103 3199 2.028284 CGACGACTTCTCGAGTGTCTAG 59.972 54.545 25.96 18.63 43.06 2.43
3124 3220 2.047274 TGCGCTGGTCCTTAGCAC 60.047 61.111 9.73 0.00 41.18 4.40
3139 3235 3.044059 GCGGATGCTGTTCTGGTGC 62.044 63.158 0.00 0.00 38.39 5.01
3153 3249 1.552799 TTCCCTTCATCTGCAGCGGA 61.553 55.000 9.47 6.33 0.00 5.54
3158 3254 0.322816 GCCACTTCCCTTCATCTGCA 60.323 55.000 0.00 0.00 0.00 4.41
3159 3255 1.372087 CGCCACTTCCCTTCATCTGC 61.372 60.000 0.00 0.00 0.00 4.26
3169 3265 1.795170 AACACATGCACGCCACTTCC 61.795 55.000 0.00 0.00 0.00 3.46
3181 3277 2.288729 CACGCATCCCTATGAACACATG 59.711 50.000 0.00 0.00 34.84 3.21
3182 3278 2.092968 ACACGCATCCCTATGAACACAT 60.093 45.455 0.00 0.00 34.84 3.21
3199 3295 4.151512 TGCTCACAAACACATACATACACG 59.848 41.667 0.00 0.00 0.00 4.49
3217 3313 4.875536 ACAAATTACAGACGCATATGCTCA 59.124 37.500 24.56 6.72 39.32 4.26
3224 3320 9.691362 AAATTAAGAAACAAATTACAGACGCAT 57.309 25.926 0.00 0.00 0.00 4.73
3225 3321 9.522804 AAAATTAAGAAACAAATTACAGACGCA 57.477 25.926 0.00 0.00 0.00 5.24
3325 3426 8.322906 TCACAGACTTCATGACGATAATTTTT 57.677 30.769 6.16 0.00 0.00 1.94
3330 3431 5.778862 TGTTCACAGACTTCATGACGATAA 58.221 37.500 6.16 0.00 0.00 1.75
3335 3436 5.753438 TGTACTTGTTCACAGACTTCATGAC 59.247 40.000 0.00 0.00 0.00 3.06
3338 3439 5.918608 AGTGTACTTGTTCACAGACTTCAT 58.081 37.500 11.85 0.00 37.07 2.57
3429 3530 3.952967 GTCCGTAGACTATCTTTCAGGGT 59.047 47.826 0.00 0.00 40.10 4.34
3467 3568 8.609176 TGGCAATACGAAGAACATAGAAATAAC 58.391 33.333 0.00 0.00 0.00 1.89
3476 3577 2.358898 GCCATGGCAATACGAAGAACAT 59.641 45.455 32.08 0.00 41.49 2.71
3534 3639 5.339200 CCAGAGCTTAAAGAAGGGTCCAATA 60.339 44.000 0.00 0.00 32.84 1.90
3538 3643 2.572104 TCCAGAGCTTAAAGAAGGGTCC 59.428 50.000 0.00 0.00 32.84 4.46
3597 3702 2.957491 ATCTATGCTAGATCCTGCGC 57.043 50.000 0.00 0.00 41.55 6.09
3615 3720 0.320771 GTTGACACAGGTGCGAGGAT 60.321 55.000 0.00 0.00 0.00 3.24
3619 3724 0.943673 CATTGTTGACACAGGTGCGA 59.056 50.000 0.00 0.00 33.22 5.10


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

AutoCloner maintained by Alex Coulton.