Multiple sequence alignment - TraesCS4A01G095200

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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 TraesCS4A01G095200 chr4A 100.000 4682 0 0 1 4682 103491547 103496228 0.000000e+00 8647
1 TraesCS4A01G095200 chr4A 88.404 664 71 6 1 661 12152151 12152811 0.000000e+00 795
2 TraesCS4A01G095200 chr4D 94.508 2021 73 18 673 2674 361363668 361361667 0.000000e+00 3083
3 TraesCS4A01G095200 chr4D 95.531 1007 38 6 2719 3723 361361455 361360454 0.000000e+00 1604
4 TraesCS4A01G095200 chr4B 93.398 1333 45 18 771 2073 446736581 446735262 0.000000e+00 1934
5 TraesCS4A01G095200 chr4B 94.148 957 43 3 2768 3723 446734149 446733205 0.000000e+00 1445
6 TraesCS4A01G095200 chr4B 94.382 623 25 6 2064 2678 446735004 446734384 0.000000e+00 948
7 TraesCS4A01G095200 chr4B 92.763 152 10 1 805 956 446767317 446767167 7.890000e-53 219
8 TraesCS4A01G095200 chr1A 94.606 964 40 4 3720 4682 404446167 404447119 0.000000e+00 1482
9 TraesCS4A01G095200 chr1A 84.418 661 98 5 1 659 557045452 557046109 0.000000e+00 645
10 TraesCS4A01G095200 chr5A 94.312 967 43 4 3717 4682 403953654 403954609 0.000000e+00 1471
11 TraesCS4A01G095200 chr5A 93.776 964 48 5 3720 4682 426770981 426770029 0.000000e+00 1437
12 TraesCS4A01G095200 chr3A 94.295 964 43 3 3720 4682 401066980 401067932 0.000000e+00 1465
13 TraesCS4A01G095200 chr2A 94.295 964 43 6 3720 4682 270423148 270422196 0.000000e+00 1465
14 TraesCS4A01G095200 chr7A 94.087 964 44 5 3720 4682 412509903 412508952 0.000000e+00 1452
15 TraesCS4A01G095200 chr7A 94.167 960 42 6 3724 4682 669937726 669936780 0.000000e+00 1450
16 TraesCS4A01G095200 chr7A 93.880 964 47 6 3720 4682 207514389 207513437 0.000000e+00 1443
17 TraesCS4A01G095200 chr7A 84.242 660 102 2 1 659 695889619 695890277 3.950000e-180 641
18 TraesCS4A01G095200 chr7A 84.027 601 94 2 60 659 681707800 681708399 1.130000e-160 577
19 TraesCS4A01G095200 chr6A 94.075 962 45 4 3720 4680 182680585 182679635 0.000000e+00 1450
20 TraesCS4A01G095200 chr6A 83.333 660 108 2 1 659 566604173 566604831 4.010000e-170 608
21 TraesCS4A01G095200 chr7B 88.084 663 76 3 1 662 458632206 458631546 0.000000e+00 784
22 TraesCS4A01G095200 chr3B 84.394 660 99 4 1 659 702840476 702841132 0.000000e+00 645
23 TraesCS4A01G095200 chr1B 83.939 660 99 7 3 659 532663726 532664381 3.980000e-175 625
24 TraesCS4A01G095200 chr1B 83.030 660 110 2 1 659 659070921 659071579 8.670000e-167 597


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 TraesCS4A01G095200 chr4A 103491547 103496228 4681 False 8647.000000 8647 100.0000 1 4682 1 chr4A.!!$F2 4681
1 TraesCS4A01G095200 chr4A 12152151 12152811 660 False 795.000000 795 88.4040 1 661 1 chr4A.!!$F1 660
2 TraesCS4A01G095200 chr4D 361360454 361363668 3214 True 2343.500000 3083 95.0195 673 3723 2 chr4D.!!$R1 3050
3 TraesCS4A01G095200 chr4B 446733205 446736581 3376 True 1442.333333 1934 93.9760 771 3723 3 chr4B.!!$R2 2952
4 TraesCS4A01G095200 chr1A 404446167 404447119 952 False 1482.000000 1482 94.6060 3720 4682 1 chr1A.!!$F1 962
5 TraesCS4A01G095200 chr1A 557045452 557046109 657 False 645.000000 645 84.4180 1 659 1 chr1A.!!$F2 658
6 TraesCS4A01G095200 chr5A 403953654 403954609 955 False 1471.000000 1471 94.3120 3717 4682 1 chr5A.!!$F1 965
7 TraesCS4A01G095200 chr5A 426770029 426770981 952 True 1437.000000 1437 93.7760 3720 4682 1 chr5A.!!$R1 962
8 TraesCS4A01G095200 chr3A 401066980 401067932 952 False 1465.000000 1465 94.2950 3720 4682 1 chr3A.!!$F1 962
9 TraesCS4A01G095200 chr2A 270422196 270423148 952 True 1465.000000 1465 94.2950 3720 4682 1 chr2A.!!$R1 962
10 TraesCS4A01G095200 chr7A 412508952 412509903 951 True 1452.000000 1452 94.0870 3720 4682 1 chr7A.!!$R2 962
11 TraesCS4A01G095200 chr7A 669936780 669937726 946 True 1450.000000 1450 94.1670 3724 4682 1 chr7A.!!$R3 958
12 TraesCS4A01G095200 chr7A 207513437 207514389 952 True 1443.000000 1443 93.8800 3720 4682 1 chr7A.!!$R1 962
13 TraesCS4A01G095200 chr7A 695889619 695890277 658 False 641.000000 641 84.2420 1 659 1 chr7A.!!$F2 658
14 TraesCS4A01G095200 chr7A 681707800 681708399 599 False 577.000000 577 84.0270 60 659 1 chr7A.!!$F1 599
15 TraesCS4A01G095200 chr6A 182679635 182680585 950 True 1450.000000 1450 94.0750 3720 4680 1 chr6A.!!$R1 960
16 TraesCS4A01G095200 chr6A 566604173 566604831 658 False 608.000000 608 83.3330 1 659 1 chr6A.!!$F1 658
17 TraesCS4A01G095200 chr7B 458631546 458632206 660 True 784.000000 784 88.0840 1 662 1 chr7B.!!$R1 661
18 TraesCS4A01G095200 chr3B 702840476 702841132 656 False 645.000000 645 84.3940 1 659 1 chr3B.!!$F1 658
19 TraesCS4A01G095200 chr1B 532663726 532664381 655 False 625.000000 625 83.9390 3 659 1 chr1B.!!$F1 656
20 TraesCS4A01G095200 chr1B 659070921 659071579 658 False 597.000000 597 83.0300 1 659 1 chr1B.!!$F2 658

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
706 709 0.318614 AAAGAAAACATGGCGTGGCG 60.319 50.0 12.05 0.0 0.0 5.69 F
1046 1065 0.994247 AGCATCACCTCCATCCACAA 59.006 50.0 0.00 0.0 0.0 3.33 F
2440 2752 0.976641 TCGCACTTCATTCCCTGTCT 59.023 50.0 0.00 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 1981 1.548081 TCCGTCCGGACATCTTGTAA 58.452 50.0 32.80 6.75 39.76 2.41 R
2933 3476 0.601311 GTAGCCTATTCAGCTGCCGG 60.601 60.0 9.47 7.41 41.71 6.13 R
3829 4373 0.393944 AGCCGGAGTATGTGTCGAGA 60.394 55.0 5.05 0.00 0.00 4.04 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
71 72 1.960689 CGGTCCAAACCATCACCTTTT 59.039 47.619 0.00 0.00 46.86 2.27
82 83 3.834231 CCATCACCTTTTGTGGATTCCTT 59.166 43.478 3.95 0.00 45.48 3.36
95 96 7.252612 TGTGGATTCCTTCTTACATGAGTTA 57.747 36.000 0.00 0.00 0.00 2.24
133 134 2.333938 CATGCCGCCATTAGCAGC 59.666 61.111 0.00 0.00 45.68 5.25
136 137 2.825836 GCCGCCATTAGCAGCTGT 60.826 61.111 16.64 4.79 41.96 4.40
172 173 2.489073 CCACTAAGGAAAGGTGGCTTGT 60.489 50.000 0.00 0.00 42.91 3.16
173 174 3.222603 CACTAAGGAAAGGTGGCTTGTT 58.777 45.455 0.00 0.00 0.00 2.83
187 188 1.337823 GCTTGTTCCGCCTCAAGACTA 60.338 52.381 13.15 0.00 42.22 2.59
202 203 8.663911 GCCTCAAGACTATATGAAGATTAATGC 58.336 37.037 0.00 0.00 0.00 3.56
232 233 0.727970 GTCGCTCGCTACAGAAGAGA 59.272 55.000 6.41 0.00 34.13 3.10
243 244 1.543802 ACAGAAGAGAAGGAGCAGTCG 59.456 52.381 0.00 0.00 0.00 4.18
251 252 1.961180 AAGGAGCAGTCGCGGCTATT 61.961 55.000 15.40 3.86 42.78 1.73
262 263 4.277672 AGTCGCGGCTATTTATAGAGACAA 59.722 41.667 13.78 0.00 32.05 3.18
288 289 3.381335 GGTCTATACCTTGGGTCCTCAA 58.619 50.000 0.00 0.00 43.08 3.02
318 319 2.121963 AGGGAGTGACTGGCCCAA 60.122 61.111 11.51 0.00 44.55 4.12
324 325 0.700564 AGTGACTGGCCCAATGATGT 59.299 50.000 0.00 0.00 0.00 3.06
330 331 1.479323 CTGGCCCAATGATGTTTGAGG 59.521 52.381 0.00 0.00 0.00 3.86
335 336 3.620472 GCCCAATGATGTTTGAGGCATTT 60.620 43.478 10.06 0.00 40.11 2.32
338 339 4.250464 CAATGATGTTTGAGGCATTTGCT 58.750 39.130 2.12 0.00 41.70 3.91
349 350 0.319405 GCATTTGCTTGCAGGGAAGT 59.681 50.000 2.48 0.00 42.31 3.01
382 384 9.745880 CTTGCAGAAGATCTTAATTTGCATAAT 57.254 29.630 24.68 0.00 39.49 1.28
404 406 3.969287 TCACAGTTGCTTCTGATAGCT 57.031 42.857 13.78 0.00 41.76 3.32
437 439 1.677552 GACATCAACAGGGGGACGT 59.322 57.895 0.00 0.00 0.00 4.34
556 558 7.168219 ATGAGACTCATAAACTTGCCAAGTTA 58.832 34.615 22.25 11.53 41.57 2.24
615 618 2.134789 AATCCTCATGACCCAACAGC 57.865 50.000 0.00 0.00 0.00 4.40
634 637 3.940852 CAGCTGTACCTATGAATGTTGCA 59.059 43.478 5.25 0.00 0.00 4.08
706 709 0.318614 AAAGAAAACATGGCGTGGCG 60.319 50.000 12.05 0.00 0.00 5.69
739 745 2.346545 GCGTTCGCTATTTTTACTCCGT 59.653 45.455 9.99 0.00 0.00 4.69
740 746 3.547468 GCGTTCGCTATTTTTACTCCGTA 59.453 43.478 9.99 0.00 0.00 4.02
741 747 4.207841 GCGTTCGCTATTTTTACTCCGTAT 59.792 41.667 9.99 0.00 0.00 3.06
796 802 4.254492 GGACCAGAAATAATATCCCGAGC 58.746 47.826 0.00 0.00 0.00 5.03
797 803 4.020128 GGACCAGAAATAATATCCCGAGCT 60.020 45.833 0.00 0.00 0.00 4.09
798 804 5.513267 GGACCAGAAATAATATCCCGAGCTT 60.513 44.000 0.00 0.00 0.00 3.74
799 805 5.308825 ACCAGAAATAATATCCCGAGCTTG 58.691 41.667 0.00 0.00 0.00 4.01
800 806 5.163195 ACCAGAAATAATATCCCGAGCTTGT 60.163 40.000 0.00 0.00 0.00 3.16
801 807 5.409826 CCAGAAATAATATCCCGAGCTTGTC 59.590 44.000 0.00 0.00 0.00 3.18
816 822 1.812686 TTGTCTCCTTGACCGGACCG 61.813 60.000 9.46 6.99 44.75 4.79
934 941 1.368203 TCTTATCCCCTTCACCCTCCA 59.632 52.381 0.00 0.00 0.00 3.86
1042 1061 1.527844 GGCAGCATCACCTCCATCC 60.528 63.158 0.00 0.00 0.00 3.51
1043 1062 1.225426 GCAGCATCACCTCCATCCA 59.775 57.895 0.00 0.00 0.00 3.41
1046 1065 0.994247 AGCATCACCTCCATCCACAA 59.006 50.000 0.00 0.00 0.00 3.33
1058 1081 2.355513 CCATCCACAACAAGAGCTAGCT 60.356 50.000 19.45 19.45 0.00 3.32
1074 1097 2.568127 GCTAGCTAGCGAACACGAC 58.432 57.895 28.89 1.73 39.82 4.34
1440 1474 1.952296 GGAGTGGGCTATGCTGAAATG 59.048 52.381 0.00 0.00 0.00 2.32
1454 1488 3.849645 GCTGAAATGTGTTTGTCCTCGTG 60.850 47.826 0.00 0.00 0.00 4.35
1560 1595 3.115892 CCGTGGCTTTAGCGCGAA 61.116 61.111 12.10 0.00 43.26 4.70
1946 1981 1.844687 GGAATTCTCTGGGCTGCTTT 58.155 50.000 5.23 0.00 0.00 3.51
2003 2038 6.183360 CGAAGCAAGAAGTTGAGTTATCAGAG 60.183 42.308 0.00 0.00 36.61 3.35
2016 2051 4.721776 AGTTATCAGAGGGCATTCAGGTAA 59.278 41.667 0.00 0.00 0.00 2.85
2034 2069 5.924254 CAGGTAACGAAGACTAACACAATGA 59.076 40.000 0.00 0.00 46.39 2.57
2108 2413 5.865085 TGCTGGTGTCTGACTAAGTTTATT 58.135 37.500 9.51 0.00 0.00 1.40
2173 2478 1.164041 AGGTTGCACACTACAACGGC 61.164 55.000 0.00 0.00 46.65 5.68
2246 2551 2.103263 ACTTTGAGGAAACGTCTCAGCT 59.897 45.455 5.68 0.00 41.57 4.24
2435 2747 1.808411 TTGACTCGCACTTCATTCCC 58.192 50.000 0.00 0.00 0.00 3.97
2440 2752 0.976641 TCGCACTTCATTCCCTGTCT 59.023 50.000 0.00 0.00 0.00 3.41
2441 2753 2.166459 CTCGCACTTCATTCCCTGTCTA 59.834 50.000 0.00 0.00 0.00 2.59
2649 2961 8.490355 GCAACAATTTCACTCTTAATTTCTTGG 58.510 33.333 0.00 0.00 0.00 3.61
2678 2990 8.341892 TGATGTAAGCACATTTGGTAATTACA 57.658 30.769 17.16 1.24 45.58 2.41
2679 2991 8.965819 TGATGTAAGCACATTTGGTAATTACAT 58.034 29.630 17.16 6.59 45.58 2.29
2680 2992 9.450807 GATGTAAGCACATTTGGTAATTACATC 57.549 33.333 17.16 14.08 46.32 3.06
2681 2993 8.341892 TGTAAGCACATTTGGTAATTACATCA 57.658 30.769 17.16 4.36 35.94 3.07
2682 2994 8.240682 TGTAAGCACATTTGGTAATTACATCAC 58.759 33.333 17.16 0.67 35.94 3.06
2683 2995 7.466746 AAGCACATTTGGTAATTACATCACT 57.533 32.000 17.16 1.16 31.49 3.41
2684 2996 7.466746 AGCACATTTGGTAATTACATCACTT 57.533 32.000 17.16 0.00 0.00 3.16
2710 3251 9.802039 TTGTATATTGGGTAGATTTTATGGGAC 57.198 33.333 0.00 0.00 0.00 4.46
2711 3252 9.177927 TGTATATTGGGTAGATTTTATGGGACT 57.822 33.333 0.00 0.00 0.00 3.85
2714 3255 7.707467 ATTGGGTAGATTTTATGGGACTAGT 57.293 36.000 0.00 0.00 0.00 2.57
2793 3334 4.829064 TTAGAACAGACCAATGTTGCAC 57.171 40.909 0.00 0.00 43.32 4.57
2811 3352 2.418976 GCACCCGGATCTTTCTTTGTAC 59.581 50.000 0.73 0.00 0.00 2.90
2823 3364 7.202016 TCTTTCTTTGTACACCAATGTGATC 57.798 36.000 0.00 0.00 45.76 2.92
2827 3368 1.065782 TGTACACCAATGTGATCCCGG 60.066 52.381 0.00 0.00 45.76 5.73
2828 3369 1.065709 GTACACCAATGTGATCCCGGT 60.066 52.381 0.00 0.00 45.76 5.28
2829 3370 2.481212 CACCAATGTGATCCCGGTG 58.519 57.895 0.00 0.00 45.76 4.94
2858 3401 5.860579 TGGTATGAGCCCCTATATAATCCA 58.139 41.667 0.00 0.00 0.00 3.41
3100 3643 0.667487 TGCTCACTACGCTCTGCAAC 60.667 55.000 0.00 0.00 0.00 4.17
3158 3701 0.391661 ATCGCACTTGTGGCTACTGG 60.392 55.000 0.64 0.00 0.00 4.00
3187 3730 1.238439 CCTGCACTTTACCTGGTGTG 58.762 55.000 10.23 10.41 36.03 3.82
3418 3961 0.884514 GATCCGGCAGATCGAGATGA 59.115 55.000 0.00 0.00 42.06 2.92
3474 4017 0.170561 CGTCGCTACAGCACTACCTT 59.829 55.000 1.61 0.00 42.21 3.50
3480 4023 1.550524 CTACAGCACTACCTTGAGCCA 59.449 52.381 0.00 0.00 0.00 4.75
3596 4139 1.090052 GTACTGGATTGCCTGCCGTC 61.090 60.000 0.00 0.00 36.65 4.79
3597 4140 1.549243 TACTGGATTGCCTGCCGTCA 61.549 55.000 0.00 0.00 36.65 4.35
3616 4159 5.013236 CGTCATTTTGAAGGATTAACGACG 58.987 41.667 0.00 0.00 36.91 5.12
3788 4332 1.635817 CCCTCCCCACCACATCGATT 61.636 60.000 0.00 0.00 0.00 3.34
3810 4354 2.800881 ATCATCGACGCTAATGCAGA 57.199 45.000 0.00 0.00 39.64 4.26
3836 4380 4.509970 ACGATTCATTGTGTTTTCTCGACA 59.490 37.500 0.00 0.00 0.00 4.35
3978 4522 3.476181 CAACATATCAGCGCATGATTCG 58.524 45.455 21.71 16.51 46.97 3.34
3979 4523 2.759191 ACATATCAGCGCATGATTCGT 58.241 42.857 21.71 16.98 46.97 3.85
4163 4707 0.472471 AACAGCCGGAAAACTCCTGA 59.528 50.000 5.05 0.00 0.00 3.86
4255 4800 4.019174 CCCAACAGACCTCAAGCAAATAT 58.981 43.478 0.00 0.00 0.00 1.28
4278 4823 0.251121 AATTGACCGGATGTGTGGCA 60.251 50.000 9.46 0.00 0.00 4.92
4426 4971 0.467290 GGCAACAAACCCAGTCCTGA 60.467 55.000 0.00 0.00 0.00 3.86
4427 4972 1.620822 GCAACAAACCCAGTCCTGAT 58.379 50.000 0.00 0.00 0.00 2.90
4529 5074 2.737252 GAGAAGTGGACGGACACAAATC 59.263 50.000 13.14 8.57 43.72 2.17
4559 5104 4.214545 TCAAAAGCCGGTTTACTATGTGTG 59.785 41.667 3.14 0.00 0.00 3.82
4573 5118 4.770531 ACTATGTGTGCACTGTCCTTACTA 59.229 41.667 19.41 0.00 0.00 1.82
4671 5216 7.381408 CACTACTTTCAAGAGTGTTCGATAACA 59.619 37.037 0.00 0.00 43.32 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.347221 GCTTTTCGCCGGACATACG 59.653 57.895 5.05 0.00 0.00 3.06
13 14 1.154035 GTGGATTGCTTTTCGCCGG 60.154 57.895 0.00 0.00 38.05 6.13
71 72 5.762179 ACTCATGTAAGAAGGAATCCACA 57.238 39.130 0.61 0.00 0.00 4.17
82 83 8.635328 TCTGTAACTGTTGTAACTCATGTAAGA 58.365 33.333 2.69 0.00 0.00 2.10
95 96 2.480845 GTCGGCTTCTGTAACTGTTGT 58.519 47.619 2.69 0.00 0.00 3.32
125 126 1.134670 GGAGGTCGAACAGCTGCTAAT 60.135 52.381 15.27 0.00 37.93 1.73
127 128 1.890894 GGAGGTCGAACAGCTGCTA 59.109 57.895 15.27 0.00 37.93 3.49
156 157 1.704641 GGAACAAGCCACCTTTCCTT 58.295 50.000 0.00 0.00 29.18 3.36
172 173 4.893524 TCTTCATATAGTCTTGAGGCGGAA 59.106 41.667 0.00 0.00 0.00 4.30
173 174 4.470602 TCTTCATATAGTCTTGAGGCGGA 58.529 43.478 0.00 0.00 0.00 5.54
187 188 4.389992 CGCCGTCAGCATTAATCTTCATAT 59.610 41.667 0.00 0.00 44.04 1.78
222 223 2.750166 CGACTGCTCCTTCTCTTCTGTA 59.250 50.000 0.00 0.00 0.00 2.74
232 233 1.961180 AATAGCCGCGACTGCTCCTT 61.961 55.000 8.23 2.74 40.23 3.36
243 244 6.091441 CCTTGATTGTCTCTATAAATAGCCGC 59.909 42.308 0.00 0.00 0.00 6.53
288 289 0.252103 ACTCCCTGGTACACCATCGT 60.252 55.000 0.60 0.00 46.46 3.73
301 302 1.542375 ATTGGGCCAGTCACTCCCT 60.542 57.895 6.23 0.00 40.69 4.20
318 319 4.250464 CAAGCAAATGCCTCAAACATCAT 58.750 39.130 0.94 0.00 43.38 2.45
324 325 1.270412 CCTGCAAGCAAATGCCTCAAA 60.270 47.619 0.94 0.00 45.83 2.69
330 331 0.319405 ACTTCCCTGCAAGCAAATGC 59.681 50.000 0.00 0.00 46.58 3.56
335 336 3.009473 AGAGATAAACTTCCCTGCAAGCA 59.991 43.478 0.00 0.00 0.00 3.91
338 339 3.758554 GCAAGAGATAAACTTCCCTGCAA 59.241 43.478 0.00 0.00 0.00 4.08
382 384 5.604758 AGCTATCAGAAGCAACTGTGATA 57.395 39.130 9.36 5.47 45.30 2.15
404 406 2.894765 TGATGTCGTCAACCACTCCTTA 59.105 45.455 0.00 0.00 32.78 2.69
442 444 2.970987 TGTACTATAGCAGCATGGGGA 58.029 47.619 0.00 0.00 35.86 4.81
473 475 8.355169 ACATAACTGAAAACTACTCTTACGACA 58.645 33.333 0.00 0.00 0.00 4.35
615 618 5.589855 TCCAATGCAACATTCATAGGTACAG 59.410 40.000 0.00 0.00 0.00 2.74
634 637 4.220602 ACTCGCCAAGCTTTTTATTCCAAT 59.779 37.500 0.00 0.00 0.00 3.16
675 678 7.148918 CGCCATGTTTTCTTTTATCAGTTCAAG 60.149 37.037 0.00 0.00 0.00 3.02
681 684 4.858692 CCACGCCATGTTTTCTTTTATCAG 59.141 41.667 0.00 0.00 0.00 2.90
690 693 2.126502 CCGCCACGCCATGTTTTC 60.127 61.111 0.00 0.00 0.00 2.29
718 724 2.346545 ACGGAGTAAAAATAGCGAACGC 59.653 45.455 11.31 11.31 41.94 4.84
739 745 3.568007 GGCCCGTGCAAGAAATTGATATA 59.432 43.478 0.00 0.00 40.13 0.86
740 746 2.362077 GGCCCGTGCAAGAAATTGATAT 59.638 45.455 0.00 0.00 40.13 1.63
741 747 1.748493 GGCCCGTGCAAGAAATTGATA 59.252 47.619 0.00 0.00 40.13 2.15
765 771 7.039923 GGATATTATTTCTGGTCCGACTACAGA 60.040 40.741 4.00 4.00 39.31 3.41
799 805 2.572284 CGGTCCGGTCAAGGAGAC 59.428 66.667 2.34 0.00 46.83 3.36
800 806 2.678934 CCGGTCCGGTCAAGGAGA 60.679 66.667 23.02 0.00 42.73 3.71
801 807 3.771160 CCCGGTCCGGTCAAGGAG 61.771 72.222 28.39 7.83 46.80 3.69
934 941 4.021925 GGTGGGCGCTCTTGGTCT 62.022 66.667 9.62 0.00 0.00 3.85
1005 1013 1.343142 CCGGCTAGTGTGGTATGCATA 59.657 52.381 1.16 1.16 0.00 3.14
1090 1113 1.065928 CACGACGACATCCCTAGCC 59.934 63.158 0.00 0.00 0.00 3.93
1260 1283 2.682494 TCCGGCGGCTAAGGACTT 60.682 61.111 23.83 0.00 0.00 3.01
1326 1349 0.687757 AGGCTGGTGCTATCCGAAGA 60.688 55.000 0.00 0.00 39.59 2.87
1389 1412 6.216801 TCTTATAATACAGTTCAGCACGGT 57.783 37.500 0.00 0.00 37.58 4.83
1440 1474 3.195661 AGAAAGACACGAGGACAAACAC 58.804 45.455 0.00 0.00 0.00 3.32
1454 1488 6.455360 TCCAATATCCAATGCAAGAAAGAC 57.545 37.500 0.00 0.00 0.00 3.01
1859 1894 2.749076 CCGATCACTGAAAGATTTGGCA 59.251 45.455 0.00 0.00 37.43 4.92
1862 1897 3.064545 GCCTCCGATCACTGAAAGATTTG 59.935 47.826 0.00 0.00 37.43 2.32
1946 1981 1.548081 TCCGTCCGGACATCTTGTAA 58.452 50.000 32.80 6.75 39.76 2.41
2003 2038 2.007608 GTCTTCGTTACCTGAATGCCC 58.992 52.381 0.00 0.00 0.00 5.36
2016 2051 4.750098 CCTTGTCATTGTGTTAGTCTTCGT 59.250 41.667 0.00 0.00 0.00 3.85
2034 2069 7.523293 TGATAAAAATCACACATGTCCTTGT 57.477 32.000 0.00 0.00 0.00 3.16
2108 2413 2.362397 GGAGATCCTGCGTCAGTTCATA 59.638 50.000 6.19 0.00 0.00 2.15
2246 2551 7.936496 TCATGTTCTTGCAGTAAATTCCATA 57.064 32.000 0.00 0.00 0.00 2.74
2440 2752 3.394606 GCCCTGAATCCCTTCCTGTATTA 59.605 47.826 0.00 0.00 0.00 0.98
2441 2753 2.175715 GCCCTGAATCCCTTCCTGTATT 59.824 50.000 0.00 0.00 0.00 1.89
2649 2961 4.870363 ACCAAATGTGCTTACATCAACAC 58.130 39.130 0.00 0.00 0.00 3.32
2684 2996 9.802039 GTCCCATAAAATCTACCCAATATACAA 57.198 33.333 0.00 0.00 0.00 2.41
2693 3234 8.260099 ACTTACTAGTCCCATAAAATCTACCC 57.740 38.462 0.00 0.00 0.00 3.69
2700 3241 8.686334 CGGTTACTACTTACTAGTCCCATAAAA 58.314 37.037 0.00 0.00 36.95 1.52
2701 3242 7.285401 CCGGTTACTACTTACTAGTCCCATAAA 59.715 40.741 0.00 0.00 36.95 1.40
2707 3248 4.781934 TCCCGGTTACTACTTACTAGTCC 58.218 47.826 0.00 0.00 36.95 3.85
2708 3249 5.066634 GGTTCCCGGTTACTACTTACTAGTC 59.933 48.000 0.00 0.00 36.95 2.59
2709 3250 4.950475 GGTTCCCGGTTACTACTTACTAGT 59.050 45.833 0.00 0.00 39.24 2.57
2710 3251 4.949856 TGGTTCCCGGTTACTACTTACTAG 59.050 45.833 0.00 0.00 0.00 2.57
2711 3252 4.929479 TGGTTCCCGGTTACTACTTACTA 58.071 43.478 0.00 0.00 0.00 1.82
2712 3253 3.778265 TGGTTCCCGGTTACTACTTACT 58.222 45.455 0.00 0.00 0.00 2.24
2713 3254 4.535526 TTGGTTCCCGGTTACTACTTAC 57.464 45.455 0.00 0.00 0.00 2.34
2714 3255 4.560513 CGTTTGGTTCCCGGTTACTACTTA 60.561 45.833 0.00 0.00 0.00 2.24
2783 3324 1.176527 AAGATCCGGGTGCAACATTG 58.823 50.000 3.06 0.00 39.98 2.82
2793 3334 3.007635 GGTGTACAAAGAAAGATCCGGG 58.992 50.000 0.00 0.00 0.00 5.73
2811 3352 2.481212 CACCGGGATCACATTGGTG 58.519 57.895 6.32 6.17 46.66 4.17
2827 3368 1.452108 GGCTCATACCAGCACCCAC 60.452 63.158 0.00 0.00 41.65 4.61
2828 3369 2.679342 GGGCTCATACCAGCACCCA 61.679 63.158 0.00 0.00 41.65 4.51
2829 3370 2.193248 GGGCTCATACCAGCACCC 59.807 66.667 0.00 0.00 41.65 4.61
2858 3401 5.450412 CGCCTATAAATCAAACAGCACCATT 60.450 40.000 0.00 0.00 0.00 3.16
2933 3476 0.601311 GTAGCCTATTCAGCTGCCGG 60.601 60.000 9.47 7.41 41.71 6.13
3100 3643 5.523552 TGTGTTATTCAGATAGACATTGGCG 59.476 40.000 0.00 0.00 0.00 5.69
3158 3701 3.945921 GGTAAAGTGCAGGGATTTAGGTC 59.054 47.826 0.00 0.00 0.00 3.85
3187 3730 0.254178 ATCTCCTGTGGTGGTGATGC 59.746 55.000 0.00 0.00 38.45 3.91
3501 4044 0.534203 ATAACACGGCCGGCAATAGG 60.534 55.000 31.76 14.79 0.00 2.57
3506 4049 1.605971 TACTCATAACACGGCCGGCA 61.606 55.000 31.76 11.59 0.00 5.69
3596 4139 5.922546 TGTCGTCGTTAATCCTTCAAAATG 58.077 37.500 0.00 0.00 0.00 2.32
3597 4140 6.737254 ATGTCGTCGTTAATCCTTCAAAAT 57.263 33.333 0.00 0.00 0.00 1.82
3616 4159 5.083389 GCTCGAGAGTGAATCGTATATGTC 58.917 45.833 18.75 0.00 40.95 3.06
3767 4311 3.420482 GATGTGGTGGGGAGGGGG 61.420 72.222 0.00 0.00 0.00 5.40
3768 4312 3.797353 CGATGTGGTGGGGAGGGG 61.797 72.222 0.00 0.00 0.00 4.79
3769 4313 1.635817 AATCGATGTGGTGGGGAGGG 61.636 60.000 0.00 0.00 0.00 4.30
3770 4314 1.128200 TAATCGATGTGGTGGGGAGG 58.872 55.000 0.00 0.00 0.00 4.30
3771 4315 3.275617 TTTAATCGATGTGGTGGGGAG 57.724 47.619 0.00 0.00 0.00 4.30
3772 4316 3.201045 TGATTTAATCGATGTGGTGGGGA 59.799 43.478 0.00 0.00 0.00 4.81
3773 4317 3.550820 TGATTTAATCGATGTGGTGGGG 58.449 45.455 0.00 0.00 0.00 4.96
3774 4318 5.362556 GATGATTTAATCGATGTGGTGGG 57.637 43.478 0.00 0.00 0.00 4.61
3788 4332 4.616953 TCTGCATTAGCGTCGATGATTTA 58.383 39.130 9.31 0.00 46.23 1.40
3804 4348 3.503363 ACACAATGAATCGTGTTCTGCAT 59.497 39.130 0.00 0.00 43.71 3.96
3829 4373 0.393944 AGCCGGAGTATGTGTCGAGA 60.394 55.000 5.05 0.00 0.00 4.04
3836 4380 2.082140 TGATGGTAGCCGGAGTATGT 57.918 50.000 5.05 0.00 0.00 2.29
4163 4707 5.276440 ACCTCTACTGGAGACAATGAATCT 58.724 41.667 0.00 0.00 44.45 2.40
4255 4800 3.057174 GCCACACATCCGGTCAATTTTTA 60.057 43.478 0.00 0.00 0.00 1.52
4278 4823 2.036604 GGAGATAAAGCGGCTTAGAGCT 59.963 50.000 16.73 14.70 46.97 4.09
4315 4860 2.105993 GGAGGCGATAAAGGGGTAATGT 59.894 50.000 0.00 0.00 0.00 2.71
4559 5104 2.972625 TGCATGTAGTAAGGACAGTGC 58.027 47.619 0.00 0.00 34.60 4.40
4573 5118 1.459450 GGGTACCGTGATTTGCATGT 58.541 50.000 5.65 0.00 40.86 3.21


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

AutoCloner maintained by Alex Coulton.