Multiple sequence alignment - TraesCS4B01G254500

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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 TraesCS4B01G254500 chr4B 100.000 4107 0 0 1 4107 519801270 519797164 0.000000e+00 7585.0
1 TraesCS4B01G254500 chr4A 92.395 2919 152 35 520 3382 40871318 40874222 0.000000e+00 4096.0
2 TraesCS4B01G254500 chr4A 93.443 427 20 4 3381 3806 40874326 40874745 9.690000e-176 627.0
3 TraesCS4B01G254500 chr4A 91.584 202 14 2 3907 4107 40874767 40874966 4.040000e-70 276.0
4 TraesCS4B01G254500 chr4A 95.238 63 3 0 3805 3867 6936614 6936552 2.610000e-17 100.0
5 TraesCS4B01G254500 chr4A 94.828 58 3 0 3821 3878 556767994 556768051 1.570000e-14 91.6
6 TraesCS4B01G254500 chr4A 88.732 71 5 3 3823 3892 462830480 462830548 2.630000e-12 84.2
7 TraesCS4B01G254500 chr4D 91.684 2826 154 33 1007 3808 423387734 423384966 0.000000e+00 3842.0
8 TraesCS4B01G254500 chr4D 93.801 371 18 4 520 886 423388577 423388208 1.670000e-153 553.0
9 TraesCS4B01G254500 chr4D 91.667 240 20 0 3868 4107 423384966 423384727 2.370000e-87 333.0
10 TraesCS4B01G254500 chr4D 95.122 41 1 1 968 1007 423387798 423387758 3.430000e-06 63.9
11 TraesCS4B01G254500 chr7A 98.228 508 7 2 1 508 690858555 690858050 0.000000e+00 887.0
12 TraesCS4B01G254500 chr7A 97.490 518 13 0 2 519 686924429 686923912 0.000000e+00 885.0
13 TraesCS4B01G254500 chr7A 92.857 70 4 1 3805 3874 486086984 486086916 2.610000e-17 100.0
14 TraesCS4B01G254500 chr6A 98.980 490 5 0 1 490 188252735 188252246 0.000000e+00 878.0
15 TraesCS4B01G254500 chr1A 92.673 505 31 3 3 507 4658989 4659487 0.000000e+00 723.0
16 TraesCS4B01G254500 chr5B 90.392 510 35 13 16 520 613159249 613158749 0.000000e+00 658.0
17 TraesCS4B01G254500 chr6B 90.038 522 30 17 1 514 276519969 276520476 0.000000e+00 656.0
18 TraesCS4B01G254500 chr6B 89.847 522 31 17 1 514 276517065 276517572 0.000000e+00 651.0
19 TraesCS4B01G254500 chr6B 89.847 522 31 17 1 514 276518788 276519295 0.000000e+00 651.0
20 TraesCS4B01G254500 chr1B 89.615 520 33 16 2 514 494067326 494066821 3.460000e-180 641.0
21 TraesCS4B01G254500 chr1D 90.909 66 6 0 3805 3870 48193877 48193812 5.650000e-14 89.8
22 TraesCS4B01G254500 chr2A 86.585 82 5 1 3793 3868 17251803 17251884 7.310000e-13 86.1
23 TraesCS4B01G254500 chr3D 89.231 65 7 0 3805 3869 157440638 157440574 9.460000e-12 82.4
24 TraesCS4B01G254500 chr3D 89.231 65 7 0 3805 3869 499895716 499895652 9.460000e-12 82.4
25 TraesCS4B01G254500 chr2B 85.366 82 6 1 3793 3868 27088376 27088457 3.400000e-11 80.5


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 TraesCS4B01G254500 chr4B 519797164 519801270 4106 True 7585.000000 7585 100.000000 1 4107 1 chr4B.!!$R1 4106
1 TraesCS4B01G254500 chr4A 40871318 40874966 3648 False 1666.333333 4096 92.474000 520 4107 3 chr4A.!!$F3 3587
2 TraesCS4B01G254500 chr4D 423384727 423388577 3850 True 1197.975000 3842 93.068500 520 4107 4 chr4D.!!$R1 3587
3 TraesCS4B01G254500 chr7A 690858050 690858555 505 True 887.000000 887 98.228000 1 508 1 chr7A.!!$R3 507
4 TraesCS4B01G254500 chr7A 686923912 686924429 517 True 885.000000 885 97.490000 2 519 1 chr7A.!!$R2 517
5 TraesCS4B01G254500 chr5B 613158749 613159249 500 True 658.000000 658 90.392000 16 520 1 chr5B.!!$R1 504
6 TraesCS4B01G254500 chr6B 276517065 276520476 3411 False 652.666667 656 89.910667 1 514 3 chr6B.!!$F1 513
7 TraesCS4B01G254500 chr1B 494066821 494067326 505 True 641.000000 641 89.615000 2 514 1 chr1B.!!$R1 512

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
944 2687 0.790993 AACCCTACTCACTCCCTCCA 59.209 55.0 0.00 0.00 0.0 3.86 F
2161 4245 0.592247 AACAAACGCGCTGCTTCTTG 60.592 50.0 5.73 1.16 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2559 4643 0.108804 CCTTCATGTCGTACGCCTGT 60.109 55.0 11.24 0.0 0.0 4.00 R
3963 6441 0.250770 ACCGCTTTTTGTCCCTCTCC 60.251 55.0 0.00 0.0 0.0 3.71 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
263 1981 3.507924 GTTGATGATGGCGCGGCA 61.508 61.111 37.91 37.91 0.00 5.69
452 2173 6.663093 AGCCTCTACTCCTCATGTATTCTATG 59.337 42.308 0.00 0.00 0.00 2.23
460 2181 8.402683 ACTCCTCATGTATTCTATGTATACCCT 58.597 37.037 0.00 0.00 0.00 4.34
631 2353 2.816087 CCTTGCTGCTGTTAACATCTGT 59.184 45.455 9.13 0.00 0.00 3.41
651 2376 3.251571 GTCACTAACCTTTACCTGCTCG 58.748 50.000 0.00 0.00 0.00 5.03
659 2384 2.932614 CCTTTACCTGCTCGACATTCAG 59.067 50.000 0.00 0.00 0.00 3.02
776 2501 2.271944 AACCAGGAACAGCAGTAACC 57.728 50.000 0.00 0.00 0.00 2.85
778 2506 1.298859 CCAGGAACAGCAGTAACCGC 61.299 60.000 0.00 0.00 32.13 5.68
887 2615 4.441495 CCACTGCTAATTGACTGACCGATA 60.441 45.833 0.00 0.00 0.00 2.92
888 2616 5.292765 CACTGCTAATTGACTGACCGATAT 58.707 41.667 0.00 0.00 0.00 1.63
889 2617 5.176406 CACTGCTAATTGACTGACCGATATG 59.824 44.000 0.00 0.00 0.00 1.78
890 2618 4.058124 TGCTAATTGACTGACCGATATGC 58.942 43.478 0.00 0.00 0.00 3.14
891 2619 4.058124 GCTAATTGACTGACCGATATGCA 58.942 43.478 0.00 0.00 0.00 3.96
892 2620 4.084328 GCTAATTGACTGACCGATATGCAC 60.084 45.833 0.00 0.00 0.00 4.57
893 2621 3.827008 ATTGACTGACCGATATGCACT 57.173 42.857 0.00 0.00 0.00 4.40
894 2622 4.937201 ATTGACTGACCGATATGCACTA 57.063 40.909 0.00 0.00 0.00 2.74
935 2663 4.041198 CCCACTTCTACAAAACCCTACTCA 59.959 45.833 0.00 0.00 0.00 3.41
939 2667 5.011840 ACTTCTACAAAACCCTACTCACTCC 59.988 44.000 0.00 0.00 0.00 3.85
942 2685 2.638363 ACAAAACCCTACTCACTCCCTC 59.362 50.000 0.00 0.00 0.00 4.30
944 2687 0.790993 AACCCTACTCACTCCCTCCA 59.209 55.000 0.00 0.00 0.00 3.86
948 2691 2.104170 CCTACTCACTCCCTCCACTTC 58.896 57.143 0.00 0.00 0.00 3.01
949 2692 2.291930 CCTACTCACTCCCTCCACTTCT 60.292 54.545 0.00 0.00 0.00 2.85
954 2697 3.578716 CTCACTCCCTCCACTTCTACAAA 59.421 47.826 0.00 0.00 0.00 2.83
956 2699 3.325135 CACTCCCTCCACTTCTACAAACT 59.675 47.826 0.00 0.00 0.00 2.66
965 2708 6.650120 TCCACTTCTACAAACTCAAGAAACT 58.350 36.000 0.00 0.00 0.00 2.66
966 2709 6.538742 TCCACTTCTACAAACTCAAGAAACTG 59.461 38.462 0.00 0.00 0.00 3.16
972 3029 5.567138 ACAAACTCAAGAAACTGACCAAG 57.433 39.130 0.00 0.00 0.00 3.61
1028 3109 1.377725 CCCGCAAGAGCAAGTCCAT 60.378 57.895 0.00 0.00 42.27 3.41
1029 3110 1.651240 CCCGCAAGAGCAAGTCCATG 61.651 60.000 0.00 0.00 42.27 3.66
1182 3266 2.047179 GCGTTCTTCCGGGAGCTT 60.047 61.111 4.24 0.00 0.00 3.74
1193 3277 1.153349 GGGAGCTTCCTTACAGCGG 60.153 63.158 2.76 0.00 42.55 5.52
1302 3386 1.222936 GTGCATGTCCCTCCTCCTG 59.777 63.158 0.00 0.00 0.00 3.86
1779 3863 2.660572 CTCTACTTCCTGAGCTGCCTA 58.339 52.381 0.00 0.00 0.00 3.93
2031 4115 2.654079 CGACTGCCTGCTCCTCCTT 61.654 63.158 0.00 0.00 0.00 3.36
2042 4126 1.707239 CTCCTCCTTCTCGACGACCG 61.707 65.000 0.00 0.00 40.25 4.79
2067 4151 3.943479 TTGGCACGCCGTCGCTAAT 62.943 57.895 3.13 0.00 39.84 1.73
2070 4154 3.925238 CACGCCGTCGCTAATGCC 61.925 66.667 0.00 0.00 39.84 4.40
2161 4245 0.592247 AACAAACGCGCTGCTTCTTG 60.592 50.000 5.73 1.16 0.00 3.02
2193 4277 3.192922 GGCCATGTACGTGTCCGC 61.193 66.667 13.91 9.82 37.70 5.54
2355 4439 2.031919 ATGTTCTGGCACGGCGAA 59.968 55.556 16.62 0.00 32.53 4.70
2363 4447 2.970324 GCACGGCGAAGTGGACAA 60.970 61.111 16.62 0.00 42.09 3.18
2376 4460 1.522580 GGACAAGGCCATCGAGCTC 60.523 63.158 5.01 2.73 0.00 4.09
2709 4793 2.277756 CTACCGTACTGCGTCGCC 60.278 66.667 15.88 0.00 39.32 5.54
2735 4819 2.996168 ATCGGTAAGCAGATGGGCGC 62.996 60.000 0.00 0.00 39.27 6.53
2799 5143 1.625818 GGAAGGGATGATCGCATAGGT 59.374 52.381 12.18 0.00 34.11 3.08
2857 5205 0.172578 TGATTGCGACGACGAGGAAT 59.827 50.000 12.29 8.17 42.66 3.01
2950 5302 1.993370 GATCAGGTTAGTGTGTCACGC 59.007 52.381 8.54 8.54 39.64 5.34
2954 5309 1.068748 AGGTTAGTGTGTCACGCTACG 60.069 52.381 22.84 0.00 40.51 3.51
2966 5321 1.000233 ACGCTACGTTACGTGTGCAG 61.000 55.000 26.48 22.01 41.76 4.41
2979 5334 4.741342 ACGTGTGCAGTACCTATCTTTAC 58.259 43.478 0.00 0.00 0.00 2.01
2981 5336 4.798907 CGTGTGCAGTACCTATCTTTACTG 59.201 45.833 4.69 4.69 45.45 2.74
2989 5344 6.588756 CAGTACCTATCTTTACTGTTGCGAAA 59.411 38.462 0.00 0.00 40.19 3.46
2992 5347 7.073342 ACCTATCTTTACTGTTGCGAAATTC 57.927 36.000 0.00 0.00 0.00 2.17
2998 5353 5.697473 TTACTGTTGCGAAATTCATTGGA 57.303 34.783 0.00 0.00 0.00 3.53
3000 5355 4.298332 ACTGTTGCGAAATTCATTGGAAC 58.702 39.130 0.00 0.00 35.46 3.62
3002 5357 4.880759 TGTTGCGAAATTCATTGGAACAT 58.119 34.783 1.47 0.00 39.30 2.71
3120 5478 4.357918 AGATGTGAAGTGTAAACAGCCT 57.642 40.909 0.00 0.00 30.64 4.58
3211 5569 0.901124 AGAGCTAGAGTGGTTGCTGG 59.099 55.000 0.00 0.00 35.76 4.85
3220 5578 2.277591 TGGTTGCTGGATTGGCTGC 61.278 57.895 0.00 0.00 0.00 5.25
3224 5582 1.477700 GTTGCTGGATTGGCTGCATAA 59.522 47.619 0.50 0.00 35.27 1.90
3265 5623 5.473504 ACTTGTAACCTTTGCATTCTAGGTG 59.526 40.000 10.07 2.45 41.33 4.00
3269 5627 1.398390 CCTTTGCATTCTAGGTGCGTC 59.602 52.381 13.78 0.00 45.37 5.19
3274 5632 1.863454 GCATTCTAGGTGCGTCATCAG 59.137 52.381 5.48 0.00 32.29 2.90
3303 5661 5.426504 ACATGACTTAGCAAGAGAATGAGG 58.573 41.667 0.00 0.00 0.00 3.86
3305 5663 5.078411 TGACTTAGCAAGAGAATGAGGTC 57.922 43.478 3.37 0.00 0.00 3.85
3348 5706 4.084223 CCGCACGGGTAATATATGTTCAAC 60.084 45.833 0.00 0.00 0.00 3.18
3461 5924 9.181805 GCCTTACAACTCTTCATTTTCTTTTAC 57.818 33.333 0.00 0.00 0.00 2.01
3502 5967 6.312426 TGCTATTTATTGCCAAAAATGGTTCG 59.688 34.615 7.43 0.00 0.00 3.95
3602 6070 9.057089 GGTATTTGGTCAGAAGGTATTTCTATG 57.943 37.037 0.00 0.00 44.34 2.23
3681 6149 5.673337 TTTATTTGCATCATACTCGCTCC 57.327 39.130 0.00 0.00 0.00 4.70
3696 6164 1.463674 GCTCCCATGTGATTTTCGGT 58.536 50.000 0.00 0.00 0.00 4.69
3813 6291 7.354751 ACATAAGGTTTGATCTACTCTCTCC 57.645 40.000 0.00 0.00 0.00 3.71
3814 6292 4.993029 AAGGTTTGATCTACTCTCTCCG 57.007 45.455 0.00 0.00 0.00 4.63
3815 6293 3.970842 AGGTTTGATCTACTCTCTCCGT 58.029 45.455 0.00 0.00 0.00 4.69
3816 6294 3.949113 AGGTTTGATCTACTCTCTCCGTC 59.051 47.826 0.00 0.00 0.00 4.79
3817 6295 3.067040 GGTTTGATCTACTCTCTCCGTCC 59.933 52.174 0.00 0.00 0.00 4.79
3818 6296 2.642154 TGATCTACTCTCTCCGTCCC 57.358 55.000 0.00 0.00 0.00 4.46
3819 6297 1.844497 TGATCTACTCTCTCCGTCCCA 59.156 52.381 0.00 0.00 0.00 4.37
3820 6298 2.443632 TGATCTACTCTCTCCGTCCCAT 59.556 50.000 0.00 0.00 0.00 4.00
3821 6299 3.651423 TGATCTACTCTCTCCGTCCCATA 59.349 47.826 0.00 0.00 0.00 2.74
3822 6300 3.773418 TCTACTCTCTCCGTCCCATAG 57.227 52.381 0.00 0.00 0.00 2.23
3823 6301 3.047115 TCTACTCTCTCCGTCCCATAGT 58.953 50.000 0.00 0.00 0.00 2.12
3824 6302 2.060050 ACTCTCTCCGTCCCATAGTG 57.940 55.000 0.00 0.00 0.00 2.74
3825 6303 1.285373 ACTCTCTCCGTCCCATAGTGT 59.715 52.381 0.00 0.00 0.00 3.55
3826 6304 2.508716 ACTCTCTCCGTCCCATAGTGTA 59.491 50.000 0.00 0.00 0.00 2.90
3827 6305 3.142951 CTCTCTCCGTCCCATAGTGTAG 58.857 54.545 0.00 0.00 0.00 2.74
3828 6306 2.508716 TCTCTCCGTCCCATAGTGTAGT 59.491 50.000 0.00 0.00 0.00 2.73
3829 6307 2.619177 CTCTCCGTCCCATAGTGTAGTG 59.381 54.545 0.00 0.00 0.00 2.74
3830 6308 2.025605 TCTCCGTCCCATAGTGTAGTGT 60.026 50.000 0.00 0.00 0.00 3.55
3831 6309 2.358267 CTCCGTCCCATAGTGTAGTGTC 59.642 54.545 0.00 0.00 0.00 3.67
3832 6310 2.097036 CCGTCCCATAGTGTAGTGTCA 58.903 52.381 0.00 0.00 0.00 3.58
3833 6311 2.494471 CCGTCCCATAGTGTAGTGTCAA 59.506 50.000 0.00 0.00 0.00 3.18
3834 6312 3.056393 CCGTCCCATAGTGTAGTGTCAAA 60.056 47.826 0.00 0.00 0.00 2.69
3835 6313 4.561938 CCGTCCCATAGTGTAGTGTCAAAA 60.562 45.833 0.00 0.00 0.00 2.44
3836 6314 4.992319 CGTCCCATAGTGTAGTGTCAAAAA 59.008 41.667 0.00 0.00 0.00 1.94
3858 6336 7.383156 AAAAGGTCTTATATTATGGGACGGA 57.617 36.000 0.00 0.00 0.00 4.69
3859 6337 6.607004 AAGGTCTTATATTATGGGACGGAG 57.393 41.667 0.00 0.00 0.00 4.63
3860 6338 5.024118 AGGTCTTATATTATGGGACGGAGG 58.976 45.833 0.00 0.00 0.00 4.30
3861 6339 4.161754 GGTCTTATATTATGGGACGGAGGG 59.838 50.000 0.00 0.00 0.00 4.30
3862 6340 5.021458 GTCTTATATTATGGGACGGAGGGA 58.979 45.833 0.00 0.00 0.00 4.20
3863 6341 5.127356 GTCTTATATTATGGGACGGAGGGAG 59.873 48.000 0.00 0.00 0.00 4.30
3920 6398 6.899393 ACATGTCACAATAAATCAACAGGT 57.101 33.333 0.00 0.00 0.00 4.00
3921 6399 6.913170 ACATGTCACAATAAATCAACAGGTC 58.087 36.000 0.00 0.00 26.52 3.85
3963 6441 5.486526 ACAATGCAAACTAGAGAAGAGGAG 58.513 41.667 0.00 0.00 0.00 3.69
3970 6448 2.783510 ACTAGAGAAGAGGAGGAGAGGG 59.216 54.545 0.00 0.00 0.00 4.30
3985 6463 1.452145 GAGGGACAAAAAGCGGTGCA 61.452 55.000 0.00 0.00 0.00 4.57
3987 6465 1.733526 GGACAAAAAGCGGTGCAGT 59.266 52.632 0.00 0.00 0.00 4.40
4027 6505 4.601084 TGGGAACTACTTGTGGTTGAAAA 58.399 39.130 7.22 0.00 0.00 2.29
4064 6542 7.492352 AACAACTAATTACATATTCGCCTCC 57.508 36.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 1981 1.337071 TGTGCTTTCGTCGTCTTCTCT 59.663 47.619 0.00 0.00 0.00 3.10
436 2156 8.398743 TGAGGGTATACATAGAATACATGAGGA 58.601 37.037 5.01 0.00 32.49 3.71
460 2181 1.262417 TTGCTCTCACCCGTGTATGA 58.738 50.000 0.00 0.00 0.00 2.15
518 2239 3.765511 TGGACCGTAGCAGTACAATAACT 59.234 43.478 0.00 0.00 0.00 2.24
631 2353 3.057033 GTCGAGCAGGTAAAGGTTAGTGA 60.057 47.826 0.00 0.00 0.00 3.41
651 2376 8.499403 AGGTAGCTAATCTTTTTCTGAATGTC 57.501 34.615 0.00 0.00 0.00 3.06
659 2384 8.404765 AGTAGTACGAGGTAGCTAATCTTTTTC 58.595 37.037 0.00 0.00 0.00 2.29
755 2480 3.072211 GGTTACTGCTGTTCCTGGTTAC 58.928 50.000 0.09 0.00 0.00 2.50
776 2501 2.223112 CGGGATGAACTTTTCAGATGCG 60.223 50.000 0.00 0.00 43.98 4.73
778 2506 2.098117 GCCGGGATGAACTTTTCAGATG 59.902 50.000 2.18 0.00 43.98 2.90
889 2617 2.547211 GGACATGATGCAGATGTAGTGC 59.453 50.000 12.83 2.87 41.59 4.40
890 2618 3.136763 GGGACATGATGCAGATGTAGTG 58.863 50.000 12.83 0.00 34.10 2.74
891 2619 2.105477 GGGGACATGATGCAGATGTAGT 59.895 50.000 12.83 0.00 34.10 2.73
892 2620 2.551721 GGGGGACATGATGCAGATGTAG 60.552 54.545 12.83 0.00 34.10 2.74
893 2621 1.421268 GGGGGACATGATGCAGATGTA 59.579 52.381 12.83 0.00 34.10 2.29
894 2622 0.184451 GGGGGACATGATGCAGATGT 59.816 55.000 12.73 12.73 36.73 3.06
914 2642 5.855045 AGTGAGTAGGGTTTTGTAGAAGTG 58.145 41.667 0.00 0.00 0.00 3.16
935 2663 3.579151 GAGTTTGTAGAAGTGGAGGGAGT 59.421 47.826 0.00 0.00 0.00 3.85
939 2667 5.215252 TCTTGAGTTTGTAGAAGTGGAGG 57.785 43.478 0.00 0.00 0.00 4.30
942 2685 6.538742 TCAGTTTCTTGAGTTTGTAGAAGTGG 59.461 38.462 0.00 0.00 30.32 4.00
944 2687 6.539103 GGTCAGTTTCTTGAGTTTGTAGAAGT 59.461 38.462 0.00 0.00 30.32 3.01
948 2691 6.677781 TTGGTCAGTTTCTTGAGTTTGTAG 57.322 37.500 0.00 0.00 0.00 2.74
949 2692 5.065988 GCTTGGTCAGTTTCTTGAGTTTGTA 59.934 40.000 0.00 0.00 0.00 2.41
954 2697 3.567478 AGCTTGGTCAGTTTCTTGAGT 57.433 42.857 0.00 0.00 0.00 3.41
956 2699 3.135712 TGGTAGCTTGGTCAGTTTCTTGA 59.864 43.478 0.00 0.00 0.00 3.02
965 2708 0.476338 TTGCCTTGGTAGCTTGGTCA 59.524 50.000 0.00 0.00 0.00 4.02
966 2709 1.168714 CTTGCCTTGGTAGCTTGGTC 58.831 55.000 0.00 0.00 0.00 4.02
972 3029 1.340017 TGGTGATCTTGCCTTGGTAGC 60.340 52.381 0.00 0.00 0.00 3.58
1012 3093 1.798735 CCATGGACTTGCTCTTGCG 59.201 57.895 5.56 0.00 43.34 4.85
1028 3109 1.001020 ACGATCTTTGCCATGGCCA 60.001 52.632 33.44 21.36 41.09 5.36
1029 3110 1.434696 CACGATCTTTGCCATGGCC 59.565 57.895 33.44 15.91 41.09 5.36
1038 3119 1.007238 TCCTCCTCCTCCACGATCTTT 59.993 52.381 0.00 0.00 0.00 2.52
1182 3266 2.992689 TCGTGCCCGCTGTAAGGA 60.993 61.111 0.00 0.00 0.00 3.36
1779 3863 0.553819 ATGACGGGTCTCTAGAGGCT 59.446 55.000 23.11 4.20 32.63 4.58
2031 4115 2.121564 AAGTTTCGCGGTCGTCGAGA 62.122 55.000 6.13 4.51 45.41 4.04
2064 4148 3.124270 CACGGCGCTGTGGCATTA 61.124 61.111 36.44 0.00 45.16 1.90
2147 4231 3.406361 CGTCAAGAAGCAGCGCGT 61.406 61.111 8.43 0.00 0.00 6.01
2161 4245 2.943034 GCCGTCGTCGTCATCGTC 60.943 66.667 0.71 0.00 38.33 4.20
2289 4373 1.067213 GCCAGAAGCTTTCTCTCGAGT 60.067 52.381 13.13 0.00 38.11 4.18
2355 4439 1.599047 CTCGATGGCCTTGTCCACT 59.401 57.895 3.32 0.00 39.25 4.00
2363 4447 1.729470 CGTGTAGAGCTCGATGGCCT 61.729 60.000 8.37 0.00 36.31 5.19
2376 4460 3.417275 CTCCAGCGCCTCCGTGTAG 62.417 68.421 2.29 0.00 36.67 2.74
2559 4643 0.108804 CCTTCATGTCGTACGCCTGT 60.109 55.000 11.24 0.00 0.00 4.00
2842 5190 1.018910 TCATATTCCTCGTCGTCGCA 58.981 50.000 0.00 0.00 36.96 5.10
2857 5205 1.066454 ACAATCGTCGCCATCGTCATA 59.934 47.619 0.00 0.00 36.96 2.15
2950 5302 2.095567 AGGTACTGCACACGTAACGTAG 60.096 50.000 0.00 0.00 35.39 3.51
2954 5309 4.367386 AGATAGGTACTGCACACGTAAC 57.633 45.455 0.00 0.00 41.52 2.50
2966 5321 6.956299 TTTCGCAACAGTAAAGATAGGTAC 57.044 37.500 0.00 0.00 0.00 3.34
2979 5334 4.297510 TGTTCCAATGAATTTCGCAACAG 58.702 39.130 0.00 0.00 31.98 3.16
2981 5336 4.922692 TGATGTTCCAATGAATTTCGCAAC 59.077 37.500 0.00 0.00 31.98 4.17
2998 5353 8.498054 ACAAGAAGATTACGATCATTGATGTT 57.502 30.769 3.32 0.00 34.60 2.71
3000 5355 8.134905 TGACAAGAAGATTACGATCATTGATG 57.865 34.615 3.32 0.00 34.60 3.07
3002 5357 7.819415 AGTTGACAAGAAGATTACGATCATTGA 59.181 33.333 0.00 0.00 34.60 2.57
3011 5369 7.173390 ACCTGCTTTAGTTGACAAGAAGATTAC 59.827 37.037 9.07 0.00 27.77 1.89
3015 5373 5.036117 ACCTGCTTTAGTTGACAAGAAGA 57.964 39.130 9.07 0.00 27.77 2.87
3016 5374 5.106908 GCTACCTGCTTTAGTTGACAAGAAG 60.107 44.000 0.00 0.00 38.95 2.85
3017 5375 4.755123 GCTACCTGCTTTAGTTGACAAGAA 59.245 41.667 0.00 0.00 38.95 2.52
3120 5478 5.920840 GGATCGACGATCATGAGATAACAAA 59.079 40.000 32.48 0.00 40.50 2.83
3168 5526 2.489938 AGCCAGCTAATGACCGAAAA 57.510 45.000 0.00 0.00 0.00 2.29
3211 5569 5.593968 TCACATCAAATTATGCAGCCAATC 58.406 37.500 0.00 0.00 0.00 2.67
3265 5623 2.537625 GTCATGTAGAAGCTGATGACGC 59.462 50.000 0.00 0.00 36.42 5.19
3269 5627 5.354767 TGCTAAGTCATGTAGAAGCTGATG 58.645 41.667 11.91 0.00 30.60 3.07
3274 5632 5.655488 TCTCTTGCTAAGTCATGTAGAAGC 58.345 41.667 0.00 0.00 0.00 3.86
3334 5692 9.316730 GTGGAAGTAACCGTTGAACATATATTA 57.683 33.333 0.00 0.00 0.00 0.98
3398 5861 2.686915 GCATGCTTAGGATGACAAAGCT 59.313 45.455 17.76 0.00 44.66 3.74
3399 5862 2.540361 CGCATGCTTAGGATGACAAAGC 60.540 50.000 17.76 0.13 44.63 3.51
3502 5967 6.025749 TCTCATGGTCGATGGTATTATGTC 57.974 41.667 0.00 0.00 32.26 3.06
3581 6049 6.636454 ACCATAGAAATACCTTCTGACCAA 57.364 37.500 0.00 0.00 44.47 3.67
3681 6149 2.926159 GCCAACACCGAAAATCACATGG 60.926 50.000 0.00 0.00 0.00 3.66
3696 6164 1.246649 ACAATGAAGCGATGCCAACA 58.753 45.000 0.00 0.00 0.00 3.33
3771 6249 6.238621 CCTTATGTTTGCGTTCTTGGCATATA 60.239 38.462 0.00 0.00 40.62 0.86
3800 6278 2.642154 TGGGACGGAGAGAGTAGATC 57.358 55.000 0.00 0.00 0.00 2.75
3801 6279 3.653836 ACTATGGGACGGAGAGAGTAGAT 59.346 47.826 0.00 0.00 0.00 1.98
3802 6280 3.047115 ACTATGGGACGGAGAGAGTAGA 58.953 50.000 0.00 0.00 0.00 2.59
3803 6281 3.142951 CACTATGGGACGGAGAGAGTAG 58.857 54.545 0.00 0.00 0.00 2.57
3804 6282 2.508716 ACACTATGGGACGGAGAGAGTA 59.491 50.000 0.00 0.00 0.00 2.59
3805 6283 1.285373 ACACTATGGGACGGAGAGAGT 59.715 52.381 0.00 0.00 0.00 3.24
3806 6284 2.060050 ACACTATGGGACGGAGAGAG 57.940 55.000 0.00 0.00 0.00 3.20
3807 6285 2.508716 ACTACACTATGGGACGGAGAGA 59.491 50.000 0.00 0.00 0.00 3.10
3808 6286 2.619177 CACTACACTATGGGACGGAGAG 59.381 54.545 0.00 0.00 0.00 3.20
3809 6287 2.025605 ACACTACACTATGGGACGGAGA 60.026 50.000 0.00 0.00 0.00 3.71
3810 6288 2.358267 GACACTACACTATGGGACGGAG 59.642 54.545 0.00 0.00 0.00 4.63
3811 6289 2.291089 TGACACTACACTATGGGACGGA 60.291 50.000 0.00 0.00 0.00 4.69
3812 6290 2.097036 TGACACTACACTATGGGACGG 58.903 52.381 0.00 0.00 0.00 4.79
3813 6291 3.861276 TTGACACTACACTATGGGACG 57.139 47.619 0.00 0.00 0.00 4.79
3833 6311 7.808218 TCCGTCCCATAATATAAGACCTTTTT 58.192 34.615 0.00 0.00 0.00 1.94
3834 6312 7.383156 TCCGTCCCATAATATAAGACCTTTT 57.617 36.000 0.00 0.00 0.00 2.27
3835 6313 6.013639 CCTCCGTCCCATAATATAAGACCTTT 60.014 42.308 0.00 0.00 0.00 3.11
3836 6314 5.484290 CCTCCGTCCCATAATATAAGACCTT 59.516 44.000 0.00 0.00 0.00 3.50
3837 6315 5.024118 CCTCCGTCCCATAATATAAGACCT 58.976 45.833 0.00 0.00 0.00 3.85
3838 6316 4.161754 CCCTCCGTCCCATAATATAAGACC 59.838 50.000 0.00 0.00 0.00 3.85
3839 6317 5.021458 TCCCTCCGTCCCATAATATAAGAC 58.979 45.833 0.00 0.00 0.00 3.01
3840 6318 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3841 6319 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3842 6320 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3843 6321 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3844 6322 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3845 6323 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
3846 6324 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3847 6325 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3848 6326 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3849 6327 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
3850 6328 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3851 6329 1.064091 AGTTACTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
3852 6330 2.433662 AGTTACTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
3853 6331 5.904362 TTTTAGTTACTACTCCCTCCGTC 57.096 43.478 0.00 0.00 35.78 4.79
3854 6332 7.397192 TGTTATTTTAGTTACTACTCCCTCCGT 59.603 37.037 0.00 0.00 35.78 4.69
3855 6333 7.775120 TGTTATTTTAGTTACTACTCCCTCCG 58.225 38.462 0.00 0.00 35.78 4.63
3856 6334 9.543783 CATGTTATTTTAGTTACTACTCCCTCC 57.456 37.037 0.00 0.00 35.78 4.30
3857 6335 9.543783 CCATGTTATTTTAGTTACTACTCCCTC 57.456 37.037 0.00 0.00 35.78 4.30
3858 6336 7.991460 GCCATGTTATTTTAGTTACTACTCCCT 59.009 37.037 0.00 0.00 35.78 4.20
3859 6337 7.991460 AGCCATGTTATTTTAGTTACTACTCCC 59.009 37.037 0.00 0.00 35.78 4.30
3860 6338 8.959705 AGCCATGTTATTTTAGTTACTACTCC 57.040 34.615 0.00 0.00 35.78 3.85
3920 6398 2.949177 AGCACACAATGGGTAAGTGA 57.051 45.000 0.00 0.00 37.05 3.41
3921 6399 3.407698 TGTAGCACACAATGGGTAAGTG 58.592 45.455 0.00 0.00 39.12 3.16
3963 6441 0.250770 ACCGCTTTTTGTCCCTCTCC 60.251 55.000 0.00 0.00 0.00 3.71
3970 6448 2.225491 TCATACTGCACCGCTTTTTGTC 59.775 45.455 0.00 0.00 0.00 3.18
3985 6463 3.134081 CCATGAAACCGTACCCTCATACT 59.866 47.826 0.00 0.00 0.00 2.12
3987 6465 2.436542 CCCATGAAACCGTACCCTCATA 59.563 50.000 0.00 0.00 0.00 2.15
4059 6537 4.965119 ACAATAATGTCGAAAAGGAGGC 57.035 40.909 0.00 0.00 33.41 4.70
4064 6542 6.494893 TCTCCCAACAATAATGTCGAAAAG 57.505 37.500 0.00 0.00 39.40 2.27


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

AutoCloner maintained by Alex Coulton.