Multiple sequence alignment - TraesCS1A01G074900

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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 TraesCS1A01G074900 chr1A 100.000 3416 0 0 1 3416 58166966 58170381 0.000000e+00 6309.0
1 TraesCS1A01G074900 chr1A 100.000 199 0 0 3716 3914 58170681 58170879 6.180000e-98 368.0
2 TraesCS1A01G074900 chr1D 96.777 2358 65 5 922 3269 59519994 59522350 0.000000e+00 3923.0
3 TraesCS1A01G074900 chr1D 85.697 832 68 16 4 797 59518353 59519171 0.000000e+00 830.0
4 TraesCS1A01G074900 chr1D 96.154 182 2 2 3735 3914 59522811 59522989 3.830000e-75 292.0
5 TraesCS1A01G074900 chr1D 97.701 87 2 0 3326 3412 59522352 59522438 2.440000e-32 150.0
6 TraesCS1A01G074900 chr1D 93.548 62 3 1 866 927 59519910 59519970 1.500000e-14 91.6
7 TraesCS1A01G074900 chr1B 95.919 2181 78 5 922 3096 94973813 94975988 0.000000e+00 3524.0
8 TraesCS1A01G074900 chr1B 91.798 317 16 7 3099 3412 94976434 94976743 2.160000e-117 433.0
9 TraesCS1A01G074900 chr1B 94.500 200 5 3 3717 3914 94976802 94976997 1.770000e-78 303.0
10 TraesCS1A01G074900 chr1B 78.409 264 26 11 685 927 94973535 94973788 4.080000e-30 143.0
11 TraesCS1A01G074900 chr2B 89.030 237 22 2 456 692 137209478 137209710 1.380000e-74 291.0
12 TraesCS1A01G074900 chr2B 88.066 243 24 5 454 694 44120213 44119974 2.300000e-72 283.0


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 TraesCS1A01G074900 chr1A 58166966 58170879 3913 False 3338.50 6309 100.0000 1 3914 2 chr1A.!!$F1 3913
1 TraesCS1A01G074900 chr1D 59518353 59522989 4636 False 1057.32 3923 93.9754 4 3914 5 chr1D.!!$F1 3910
2 TraesCS1A01G074900 chr1B 94973535 94976997 3462 False 1100.75 3524 90.1565 685 3914 4 chr1B.!!$F1 3229

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
106 108 0.179084 CGCCTACCCGACATTCACAT 60.179 55.0 0.0 0.0 0.0 3.21 F
125 127 0.251073 TAGTGAACCCGCCCTTAAGC 59.749 55.0 0.0 0.0 0.0 3.09 F
918 1665 0.467804 GCTTCAAAACCAGGCCCAAA 59.532 50.0 0.0 0.0 0.0 3.28 F
1683 2463 0.739813 GCTCCTCGTACAATGCCGTT 60.740 55.0 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 2633 0.598065 ATTTGGAGCACAACCTTCGC 59.402 50.0 0.00 0.0 39.19 4.70 R
1902 2682 1.668419 CCTTTCCGGCATCGAAGAAT 58.332 50.0 0.00 0.0 43.58 2.40 R
2329 3109 0.671781 CTTCCCACTCTTCCGCAGTG 60.672 60.0 0.00 0.0 40.96 3.66 R
3323 4555 0.392461 ATTAATGTCGTGTGCGCCCT 60.392 50.0 4.18 0.0 38.14 5.19 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
21 22 3.251479 TGTCTGCGTCTTATTCATGCT 57.749 42.857 0.00 0.00 0.00 3.79
39 40 1.970917 CTGATGAAGCGAACGTGGCC 61.971 60.000 8.11 0.00 0.00 5.36
40 41 2.746277 ATGAAGCGAACGTGGCCC 60.746 61.111 0.00 2.41 0.00 5.80
56 57 3.374402 CCGACAGGGCAGACGACT 61.374 66.667 0.00 0.00 0.00 4.18
57 58 2.044555 CCGACAGGGCAGACGACTA 61.045 63.158 0.00 0.00 0.00 2.59
58 59 1.136984 CGACAGGGCAGACGACTAC 59.863 63.158 0.00 0.00 0.00 2.73
62 63 4.509737 GGGCAGACGACTACCCGC 62.510 72.222 7.46 0.00 39.61 6.13
63 64 4.849329 GGCAGACGACTACCCGCG 62.849 72.222 0.00 0.00 0.00 6.46
74 76 2.345880 CTACCCGCGCTAATGTCGGT 62.346 60.000 5.56 2.02 41.46 4.69
106 108 0.179084 CGCCTACCCGACATTCACAT 60.179 55.000 0.00 0.00 0.00 3.21
125 127 0.251073 TAGTGAACCCGCCCTTAAGC 59.749 55.000 0.00 0.00 0.00 3.09
141 143 6.040247 CCCTTAAGCTTTTTGAAGTCGTTTT 58.960 36.000 3.20 0.00 0.00 2.43
194 196 7.444183 TCATTGTTGTCGTTAGGAAAGAAGAAT 59.556 33.333 0.00 0.00 0.00 2.40
228 239 2.924290 GCAGAGGAACATGTAAGACGAC 59.076 50.000 0.00 0.00 0.00 4.34
289 301 1.937899 GACGGTAAACAACACAGTGCT 59.062 47.619 0.00 0.00 0.00 4.40
290 302 3.125316 GACGGTAAACAACACAGTGCTA 58.875 45.455 0.00 0.00 0.00 3.49
362 374 7.510685 TGCCATATCAACTCCTTACTCTAATCT 59.489 37.037 0.00 0.00 0.00 2.40
376 388 4.471386 ACTCTAATCTTTGCCTCTTAGCCA 59.529 41.667 0.00 0.00 0.00 4.75
389 401 0.895530 TTAGCCACTTCTCTCACCCG 59.104 55.000 0.00 0.00 0.00 5.28
393 405 1.797025 CCACTTCTCTCACCCGAAAC 58.203 55.000 0.00 0.00 0.00 2.78
414 426 6.072008 GAAACGAGTTTCTCTTAGGTACTCCT 60.072 42.308 18.35 0.00 44.03 3.69
464 502 4.701765 ACAATGATTGAGGAGAAGGATCG 58.298 43.478 12.80 0.00 0.00 3.69
471 509 0.970937 AGGAGAAGGATCGTTCGCCA 60.971 55.000 36.25 0.00 45.98 5.69
488 526 3.185203 AGGGGCAGCCTTGGTTGA 61.185 61.111 12.43 0.00 0.00 3.18
510 548 6.100004 TGAGGAGATCAAACGTCTATTGAAC 58.900 40.000 5.33 3.38 39.98 3.18
511 549 6.037786 AGGAGATCAAACGTCTATTGAACA 57.962 37.500 5.33 0.00 39.98 3.18
512 550 6.644347 AGGAGATCAAACGTCTATTGAACAT 58.356 36.000 5.33 0.00 39.98 2.71
513 551 6.536582 AGGAGATCAAACGTCTATTGAACATG 59.463 38.462 5.33 0.00 39.98 3.21
514 552 6.238211 GGAGATCAAACGTCTATTGAACATGG 60.238 42.308 5.33 0.00 39.98 3.66
515 553 5.586243 AGATCAAACGTCTATTGAACATGGG 59.414 40.000 5.33 0.00 39.98 4.00
516 554 3.438781 TCAAACGTCTATTGAACATGGGC 59.561 43.478 0.00 0.00 34.04 5.36
517 555 2.779755 ACGTCTATTGAACATGGGCA 57.220 45.000 0.00 0.00 0.00 5.36
534 572 1.302033 CAGGGAGCACGCCATATCC 60.302 63.158 0.00 0.00 0.00 2.59
535 573 1.766059 AGGGAGCACGCCATATCCA 60.766 57.895 0.00 0.00 33.24 3.41
541 579 3.432749 GGAGCACGCCATATCCATGATAT 60.433 47.826 0.00 0.00 35.86 1.63
544 582 3.691118 GCACGCCATATCCATGATATGTT 59.309 43.478 18.06 4.64 45.99 2.71
545 583 4.437794 GCACGCCATATCCATGATATGTTG 60.438 45.833 18.06 13.52 45.99 3.33
552 590 4.613925 ATCCATGATATGTTGCTCTCGT 57.386 40.909 0.00 0.00 0.00 4.18
563 601 0.524816 TGCTCTCGTAATTCGGTCGC 60.525 55.000 0.00 0.00 40.32 5.19
569 607 3.313249 TCTCGTAATTCGGTCGCTCATAA 59.687 43.478 0.00 0.00 40.32 1.90
578 616 2.386249 GGTCGCTCATAACTTAGCTCG 58.614 52.381 0.00 0.00 36.56 5.03
583 621 4.045104 CGCTCATAACTTAGCTCGAATGT 58.955 43.478 0.00 0.00 36.56 2.71
585 623 4.210120 GCTCATAACTTAGCTCGAATGTGG 59.790 45.833 0.00 0.00 35.80 4.17
594 632 3.813443 AGCTCGAATGTGGCATAATTCT 58.187 40.909 18.13 3.28 31.83 2.40
600 638 4.376413 CGAATGTGGCATAATTCTACTCGC 60.376 45.833 18.13 0.00 31.83 5.03
605 643 2.221981 GGCATAATTCTACTCGCACTGC 59.778 50.000 0.00 0.00 0.00 4.40
620 658 1.334869 CACTGCTGTTTGGTTGAGGTC 59.665 52.381 0.00 0.00 0.00 3.85
621 659 0.954452 CTGCTGTTTGGTTGAGGTCC 59.046 55.000 0.00 0.00 0.00 4.46
625 663 2.021457 CTGTTTGGTTGAGGTCCGTTT 58.979 47.619 0.00 0.00 0.00 3.60
638 676 4.974399 AGGTCCGTTTCTCAAGAAATTCT 58.026 39.130 8.34 0.00 44.69 2.40
654 692 4.853924 AATTCTTGTGCCGACTCAAAAT 57.146 36.364 0.00 0.00 0.00 1.82
656 694 2.844946 TCTTGTGCCGACTCAAAATGA 58.155 42.857 0.00 0.00 0.00 2.57
665 703 6.251376 GTGCCGACTCAAAATGATTTGTAATC 59.749 38.462 0.00 0.00 45.02 1.75
696 734 8.805175 TGATTAAGCAATGAATTTCTTTCTCCA 58.195 29.630 0.00 0.00 35.23 3.86
761 799 0.827368 AAGGCTTCTCGGATGTCTCC 59.173 55.000 0.00 0.00 38.29 3.71
763 801 1.330655 GGCTTCTCGGATGTCTCCCA 61.331 60.000 0.00 0.00 38.45 4.37
782 820 3.157087 CCACTGCCCATACTTTGAGTTT 58.843 45.455 0.00 0.00 0.00 2.66
918 1665 0.467804 GCTTCAAAACCAGGCCCAAA 59.532 50.000 0.00 0.00 0.00 3.28
919 1666 1.810031 GCTTCAAAACCAGGCCCAAAC 60.810 52.381 0.00 0.00 0.00 2.93
920 1667 1.484240 CTTCAAAACCAGGCCCAAACA 59.516 47.619 0.00 0.00 0.00 2.83
973 1753 1.125711 ACGGGGCCACTACTCTGTTT 61.126 55.000 1.96 0.00 0.00 2.83
978 1758 1.429463 GCCACTACTCTGTTTGACCG 58.571 55.000 0.00 0.00 0.00 4.79
989 1769 4.431809 TCTGTTTGACCGTCGAAGTTTTA 58.568 39.130 1.08 0.00 0.00 1.52
1063 1843 2.361104 GCCATTTCTCCACCGCCA 60.361 61.111 0.00 0.00 0.00 5.69
1124 1904 4.467084 GTGGCCGGAGCGATCCAA 62.467 66.667 21.44 0.00 41.24 3.53
1416 2196 3.771160 CGGGAGAACCTGGTCGGG 61.771 72.222 0.00 0.00 38.80 5.14
1447 2227 2.295253 GGTGTACGAGAACATGAGGG 57.705 55.000 0.00 0.00 0.00 4.30
1482 2262 1.234821 CCAACGTGCACACCTACAAT 58.765 50.000 18.64 0.00 0.00 2.71
1605 2385 1.674611 CGACGATCGTTTCTGCGCTT 61.675 55.000 23.63 0.00 34.72 4.68
1617 2397 2.727544 GCGCTTTGCAAGTTGGGA 59.272 55.556 0.00 0.00 45.45 4.37
1653 2433 2.203640 AGGGTCGTGGCAGAGACA 60.204 61.111 20.17 0.00 39.01 3.41
1683 2463 0.739813 GCTCCTCGTACAATGCCGTT 60.740 55.000 0.00 0.00 0.00 4.44
1773 2553 2.403132 GACTGCACCCAGAACCTGCT 62.403 60.000 0.00 0.00 41.77 4.24
1816 2596 2.203983 TCTGCAAGGCTGGGGAGA 60.204 61.111 6.56 6.56 0.00 3.71
1820 2600 1.304282 GCAAGGCTGGGGAGATGAA 59.696 57.895 0.00 0.00 0.00 2.57
1902 2682 3.358111 TTCACTGTGTTGGTCAAAGGA 57.642 42.857 7.79 0.00 35.78 3.36
1914 2694 2.356069 GGTCAAAGGATTCTTCGATGCC 59.644 50.000 0.00 0.00 31.82 4.40
2329 3109 1.728971 CGTTGATCAGAAGCCTGTGTC 59.271 52.381 0.00 0.00 41.16 3.67
2473 3253 0.857935 CGCTCTTCGAATGCTGATCC 59.142 55.000 17.24 0.00 41.67 3.36
2504 3284 1.457346 CATGGGCTTGAGTTGACTCC 58.543 55.000 8.56 0.00 42.20 3.85
2684 3464 1.350684 TGCTGCTTGGATGTTAGGTCA 59.649 47.619 0.00 0.00 0.00 4.02
2690 3470 3.763897 GCTTGGATGTTAGGTCAAATGGT 59.236 43.478 0.00 0.00 0.00 3.55
2745 3525 1.701847 ACAAGTCTGATGTCAGGGCTT 59.298 47.619 9.94 11.10 43.91 4.35
3020 3806 2.815158 TGACAGTCCAGTGGTGCTATA 58.185 47.619 9.54 0.00 0.00 1.31
3055 3841 6.128063 GCAGCAAGTTCTCTTTGATAGTTCAT 60.128 38.462 0.00 0.00 0.00 2.57
3286 4518 6.199342 GCGTAGTCATTAGAAGGACTTCATTC 59.801 42.308 14.12 0.00 46.73 2.67
3323 4555 4.537751 TGTACCATCCCTTTGTTTCAACA 58.462 39.130 0.00 0.00 37.08 3.33
3412 4644 5.574891 TTTAATTGTTATCTGTGCGCCAT 57.425 34.783 4.18 0.00 0.00 4.40
3415 4647 4.754372 ATTGTTATCTGTGCGCCATATG 57.246 40.909 4.18 0.00 0.00 1.78
3778 5062 7.903431 GCTTTTATGTAGTCTTGATTACCAACG 59.097 37.037 1.78 0.00 0.00 4.10
3779 5063 8.836268 TTTTATGTAGTCTTGATTACCAACGT 57.164 30.769 1.78 0.00 0.00 3.99
3780 5064 8.470040 TTTATGTAGTCTTGATTACCAACGTC 57.530 34.615 0.00 0.00 0.00 4.34
3885 5169 5.045213 TCTGACCCTCCAATGCTTTGTATAA 60.045 40.000 11.03 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.371898 CAGCATGAATAAGACGCAGACAA 59.628 43.478 0.00 0.00 39.69 3.18
1 2 2.931969 CAGCATGAATAAGACGCAGACA 59.068 45.455 0.00 0.00 39.69 3.41
2 3 3.190079 TCAGCATGAATAAGACGCAGAC 58.810 45.455 0.00 0.00 45.97 3.51
21 22 2.032634 GGCCACGTTCGCTTCATCA 61.033 57.895 0.00 0.00 0.00 3.07
39 40 2.044555 TAGTCGTCTGCCCTGTCGG 61.045 63.158 0.00 0.00 0.00 4.79
40 41 1.136984 GTAGTCGTCTGCCCTGTCG 59.863 63.158 0.00 0.00 0.00 4.35
49 50 1.099879 ATTAGCGCGGGTAGTCGTCT 61.100 55.000 8.83 0.00 0.00 4.18
51 52 1.065273 CATTAGCGCGGGTAGTCGT 59.935 57.895 8.83 0.00 0.00 4.34
52 53 0.933509 GACATTAGCGCGGGTAGTCG 60.934 60.000 8.83 0.00 0.00 4.18
53 54 0.933509 CGACATTAGCGCGGGTAGTC 60.934 60.000 8.83 7.35 0.00 2.59
54 55 1.065273 CGACATTAGCGCGGGTAGT 59.935 57.895 8.83 0.00 0.00 2.73
55 56 1.660575 CCGACATTAGCGCGGGTAG 60.661 63.158 8.83 0.00 41.29 3.18
56 57 1.947597 AACCGACATTAGCGCGGGTA 61.948 55.000 8.83 0.00 44.44 3.69
60 61 1.136992 CGATTAACCGACATTAGCGCG 60.137 52.381 0.00 0.00 0.00 6.86
61 62 1.191647 CCGATTAACCGACATTAGCGC 59.808 52.381 0.00 0.00 0.00 5.92
62 63 1.191647 GCCGATTAACCGACATTAGCG 59.808 52.381 0.00 0.00 0.00 4.26
63 64 1.529865 GGCCGATTAACCGACATTAGC 59.470 52.381 0.00 0.00 0.00 3.09
87 89 0.179084 ATGTGAATGTCGGGTAGGCG 60.179 55.000 0.00 0.00 0.00 5.52
106 108 0.251073 GCTTAAGGGCGGGTTCACTA 59.749 55.000 4.29 0.00 0.00 2.74
125 127 3.420904 GCGGCTAAAACGACTTCAAAAAG 59.579 43.478 0.00 0.00 38.54 2.27
194 196 4.041567 TGTTCCTCTGCAAGGTGAAGAATA 59.958 41.667 12.71 0.00 46.32 1.75
200 202 1.421268 ACATGTTCCTCTGCAAGGTGA 59.579 47.619 12.71 0.00 46.32 4.02
222 224 1.611977 TCACCAGTTGAATCGTCGTCT 59.388 47.619 0.00 0.00 0.00 4.18
228 239 2.076863 GGGTCTTCACCAGTTGAATCG 58.923 52.381 0.00 0.00 45.94 3.34
289 301 2.038863 TCTGGGCTTTGTCCCTTCTA 57.961 50.000 0.12 0.00 46.67 2.10
290 302 1.376649 ATCTGGGCTTTGTCCCTTCT 58.623 50.000 0.12 0.00 46.67 2.85
376 388 1.269998 CTCGTTTCGGGTGAGAGAAGT 59.730 52.381 0.00 0.00 31.31 3.01
389 401 6.072008 AGGAGTACCTAAGAGAAACTCGTTTC 60.072 42.308 13.23 13.23 45.83 2.78
488 526 6.037786 TGTTCAATAGACGTTTGATCTCCT 57.962 37.500 2.19 0.00 33.37 3.69
501 539 2.173356 CTCCCTGCCCATGTTCAATAGA 59.827 50.000 0.00 0.00 0.00 1.98
505 543 1.304381 GCTCCCTGCCCATGTTCAA 60.304 57.895 0.00 0.00 35.15 2.69
515 553 1.963338 GATATGGCGTGCTCCCTGC 60.963 63.158 0.00 0.00 43.25 4.85
516 554 1.302033 GGATATGGCGTGCTCCCTG 60.302 63.158 0.00 0.00 0.00 4.45
517 555 1.130054 ATGGATATGGCGTGCTCCCT 61.130 55.000 7.45 0.00 0.00 4.20
534 572 6.400409 CCGAATTACGAGAGCAACATATCATG 60.400 42.308 0.00 0.00 45.77 3.07
535 573 5.635280 CCGAATTACGAGAGCAACATATCAT 59.365 40.000 0.00 0.00 45.77 2.45
541 579 2.602878 GACCGAATTACGAGAGCAACA 58.397 47.619 0.00 0.00 45.77 3.33
544 582 0.524816 GCGACCGAATTACGAGAGCA 60.525 55.000 0.00 0.00 45.77 4.26
545 583 0.248539 AGCGACCGAATTACGAGAGC 60.249 55.000 0.00 0.00 45.77 4.09
552 590 4.980434 GCTAAGTTATGAGCGACCGAATTA 59.020 41.667 0.00 0.00 0.00 1.40
563 601 4.210120 GCCACATTCGAGCTAAGTTATGAG 59.790 45.833 0.00 0.00 0.00 2.90
569 607 2.698855 ATGCCACATTCGAGCTAAGT 57.301 45.000 0.00 0.00 0.00 2.24
578 616 4.511454 TGCGAGTAGAATTATGCCACATTC 59.489 41.667 0.00 0.00 0.00 2.67
583 621 3.457234 CAGTGCGAGTAGAATTATGCCA 58.543 45.455 0.00 0.00 0.00 4.92
585 623 3.060003 CAGCAGTGCGAGTAGAATTATGC 60.060 47.826 10.00 0.00 0.00 3.14
594 632 0.105964 ACCAAACAGCAGTGCGAGTA 59.894 50.000 15.11 0.00 0.00 2.59
600 638 1.334869 GACCTCAACCAAACAGCAGTG 59.665 52.381 0.00 0.00 0.00 3.66
605 643 1.675552 AACGGACCTCAACCAAACAG 58.324 50.000 0.00 0.00 0.00 3.16
638 676 4.202101 ACAAATCATTTTGAGTCGGCACAA 60.202 37.500 0.00 0.00 44.11 3.33
643 681 8.183536 TGATGATTACAAATCATTTTGAGTCGG 58.816 33.333 14.52 0.00 44.11 4.79
644 682 9.726232 ATGATGATTACAAATCATTTTGAGTCG 57.274 29.630 14.52 0.00 44.11 4.18
681 719 8.744652 TGTGTTTTTACTGGAGAAAGAAATTCA 58.255 29.630 0.00 0.00 40.72 2.57
682 720 9.581099 TTGTGTTTTTACTGGAGAAAGAAATTC 57.419 29.630 0.00 0.00 38.39 2.17
724 762 5.206587 AGCCTTCCGTCCTACTTTCTTATA 58.793 41.667 0.00 0.00 0.00 0.98
725 763 4.031611 AGCCTTCCGTCCTACTTTCTTAT 58.968 43.478 0.00 0.00 0.00 1.73
726 764 3.438183 AGCCTTCCGTCCTACTTTCTTA 58.562 45.455 0.00 0.00 0.00 2.10
730 768 2.234168 GAGAAGCCTTCCGTCCTACTTT 59.766 50.000 0.00 0.00 0.00 2.66
761 799 2.496899 ACTCAAAGTATGGGCAGTGG 57.503 50.000 0.00 0.00 30.00 4.00
763 801 3.832527 ACAAACTCAAAGTATGGGCAGT 58.167 40.909 0.00 0.00 30.00 4.40
852 934 6.905076 CGAACTCGTTCTCATCAAAAGAAAAA 59.095 34.615 8.04 0.00 37.44 1.94
918 1665 1.134491 GTACTTCAGGCCGCCTAATGT 60.134 52.381 12.83 9.07 29.64 2.71
919 1666 1.583054 GTACTTCAGGCCGCCTAATG 58.417 55.000 12.83 2.23 29.64 1.90
920 1667 0.468648 GGTACTTCAGGCCGCCTAAT 59.531 55.000 12.83 0.21 29.64 1.73
973 1753 2.400399 CAGCTAAAACTTCGACGGTCA 58.600 47.619 9.10 0.00 0.00 4.02
1063 1843 4.011517 CCGGTGGTTAGGTGGCGT 62.012 66.667 0.00 0.00 0.00 5.68
1437 2217 2.190578 CCGGCCTCCCTCATGTTC 59.809 66.667 0.00 0.00 0.00 3.18
1471 2251 3.865446 TCATGAGCAGATTGTAGGTGTG 58.135 45.455 0.00 0.00 0.00 3.82
1482 2262 1.449070 CAGCGCCTTCATGAGCAGA 60.449 57.895 2.29 0.00 0.00 4.26
1574 2354 2.486636 GATCGTCGTGTGGCTCACCA 62.487 60.000 13.55 0.00 46.51 4.17
1605 2385 0.758685 CCACCCTTCCCAACTTGCAA 60.759 55.000 0.00 0.00 0.00 4.08
1612 2392 2.221299 CCTCGTCCACCCTTCCCAA 61.221 63.158 0.00 0.00 0.00 4.12
1617 2397 3.322466 CTGGCCTCGTCCACCCTT 61.322 66.667 3.32 0.00 31.74 3.95
1653 2433 2.746359 GAGGAGCACACAGGCACT 59.254 61.111 0.00 0.00 43.88 4.40
1695 2475 1.930908 GCATCCTGAACTGCCTGCAC 61.931 60.000 0.00 0.00 32.15 4.57
1773 2553 5.183014 CATCGACTATGCTTGTGTAGGTA 57.817 43.478 0.00 0.00 0.00 3.08
1797 2577 2.530151 TCCCCAGCCTTGCAGAGT 60.530 61.111 0.00 0.00 0.00 3.24
1809 2589 1.213678 CAAGCCATCTTCATCTCCCCA 59.786 52.381 0.00 0.00 0.00 4.96
1853 2633 0.598065 ATTTGGAGCACAACCTTCGC 59.402 50.000 0.00 0.00 39.19 4.70
1902 2682 1.668419 CCTTTCCGGCATCGAAGAAT 58.332 50.000 0.00 0.00 43.58 2.40
2028 2808 3.007506 TGAAAACAGACGATGCCCTCTTA 59.992 43.478 0.00 0.00 0.00 2.10
2161 2941 2.796593 GCTTGAAACCAGCATTTGTCAC 59.203 45.455 0.00 0.00 0.00 3.67
2270 3050 5.710099 GTGTTAGGAGGACAATTTTCCATCA 59.290 40.000 13.08 0.72 38.25 3.07
2329 3109 0.671781 CTTCCCACTCTTCCGCAGTG 60.672 60.000 0.00 0.00 40.96 3.66
2473 3253 2.062971 AGCCCATGGTTTAGCATCTG 57.937 50.000 11.73 0.00 0.00 2.90
2684 3464 5.296748 GTGGACAATTAACTGCAACCATTT 58.703 37.500 0.00 0.00 0.00 2.32
2690 3470 1.950216 TGCGTGGACAATTAACTGCAA 59.050 42.857 0.00 0.00 0.00 4.08
2805 3585 6.154877 TCCATGTTGCTTCATTTGGACATATT 59.845 34.615 0.00 0.00 0.00 1.28
3000 3785 1.644509 ATAGCACCACTGGACTGTCA 58.355 50.000 10.38 0.00 0.00 3.58
3020 3806 1.537202 GAACTTGCTGCTTGTCCGATT 59.463 47.619 0.00 0.00 0.00 3.34
3210 4439 5.050126 TCGACTCAGTCCCAGACTATATT 57.950 43.478 0.00 0.00 41.37 1.28
3305 4537 2.299867 CCCTGTTGAAACAAAGGGATGG 59.700 50.000 12.93 2.49 43.54 3.51
3323 4555 0.392461 ATTAATGTCGTGTGCGCCCT 60.392 50.000 4.18 0.00 38.14 5.19
3344 4576 5.688176 CGTATTTTGACCAACGGACAATTTT 59.312 36.000 0.00 0.00 37.24 1.82
3715 4947 6.118852 TGTGTGGTGCATTGTGTATGTATAT 58.881 36.000 0.00 0.00 36.57 0.86
3803 5087 3.135712 TGTTAGGTCACATGCCGGAATAT 59.864 43.478 5.05 0.00 0.00 1.28
3885 5169 2.490903 GTGCAGCCTGAGATTGACAAAT 59.509 45.455 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.