Multiple sequence alignment - TraesCS7B01G038500

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 TraesCS7B01G038500 chr7B 100.000 3632 0 0 1 3632 37424181 37420550 0.000000e+00 6708.0
1 TraesCS7B01G038500 chr7B 94.611 1670 59 18 949 2611 67106228 67104583 0.000000e+00 2556.0
2 TraesCS7B01G038500 chr7B 93.918 1677 67 18 946 2611 37607116 37605464 0.000000e+00 2499.0
3 TraesCS7B01G038500 chr7B 95.785 949 37 2 1 948 67107225 67106279 0.000000e+00 1528.0
4 TraesCS7B01G038500 chr7B 92.055 944 69 6 8 948 37608096 37607156 0.000000e+00 1323.0
5 TraesCS7B01G038500 chr7B 95.448 703 26 2 2935 3631 37601121 37600419 0.000000e+00 1116.0
6 TraesCS7B01G038500 chr7B 95.448 703 26 2 2935 3631 67354142 67353440 0.000000e+00 1116.0
7 TraesCS7B01G038500 chr7B 81.077 687 106 17 1108 1779 38660360 38659683 8.930000e-146 527.0
8 TraesCS7B01G038500 chr7B 80.820 683 115 13 1108 1779 38783120 38783797 4.160000e-144 521.0
9 TraesCS7B01G038500 chr7B 80.936 299 40 11 2226 2523 38784210 38784492 1.700000e-53 220.0
10 TraesCS7B01G038500 chr7B 82.128 235 36 5 518 749 643041452 643041683 2.860000e-46 196.0
11 TraesCS7B01G038500 chr7D 88.322 1961 124 46 949 2866 88133204 88135102 0.000000e+00 2255.0
12 TraesCS7B01G038500 chr7D 89.690 1775 117 30 862 2611 88180462 88178729 0.000000e+00 2204.0
13 TraesCS7B01G038500 chr7D 95.565 699 31 0 2934 3632 88142436 88143134 0.000000e+00 1120.0
14 TraesCS7B01G038500 chr7D 81.845 683 108 11 1108 1779 88370793 88370116 8.810000e-156 560.0
15 TraesCS7B01G038500 chr7D 79.239 289 53 4 2230 2518 88899496 88899777 1.030000e-45 195.0
16 TraesCS7B01G038500 chr7D 84.568 162 23 2 2356 2517 413240962 413240803 3.750000e-35 159.0
17 TraesCS7B01G038500 chr7A 94.176 704 36 3 2933 3631 89809045 89809748 0.000000e+00 1068.0
18 TraesCS7B01G038500 chr7A 89.130 874 60 15 946 1810 89758449 89759296 0.000000e+00 1055.0
19 TraesCS7B01G038500 chr7A 85.808 761 69 16 1806 2557 89781333 89782063 0.000000e+00 771.0
20 TraesCS7B01G038500 chr7A 82.059 680 109 9 1108 1776 89974461 89975138 5.260000e-158 568.0
21 TraesCS7B01G038500 chr7A 82.394 568 91 7 1123 1684 89948037 89947473 1.520000e-133 486.0
22 TraesCS7B01G038500 chr7A 86.464 362 49 0 1108 1469 89965786 89965425 7.310000e-107 398.0
23 TraesCS7B01G038500 chr7A 81.271 299 39 13 2226 2523 89975521 89975803 3.650000e-55 226.0
24 TraesCS7B01G038500 chr7A 78.231 294 55 6 2226 2518 90336838 90337123 2.880000e-41 180.0
25 TraesCS7B01G038500 chr7A 81.991 211 25 11 647 851 579067987 579068190 2.240000e-37 167.0
26 TraesCS7B01G038500 chr4B 84.096 874 100 25 9 855 149072040 149072901 0.000000e+00 808.0
27 TraesCS7B01G038500 chr4B 84.586 266 39 2 497 762 149066139 149065876 2.780000e-66 263.0
28 TraesCS7B01G038500 chr2B 80.638 878 121 37 5 851 206367215 206368074 5.120000e-178 634.0
29 TraesCS7B01G038500 chr2B 78.299 341 60 12 516 851 70819942 70820273 1.320000e-49 207.0
30 TraesCS7B01G038500 chr5D 79.065 898 112 46 5 853 236180989 236180119 6.860000e-152 547.0
31 TraesCS7B01G038500 chrUn 76.056 781 124 44 117 854 280092863 280092103 7.460000e-92 348.0
32 TraesCS7B01G038500 chrUn 84.746 354 45 5 117 462 339031298 339031650 2.680000e-91 346.0
33 TraesCS7B01G038500 chr3B 84.507 355 46 5 117 463 740133188 740133541 3.470000e-90 342.0
34 TraesCS7B01G038500 chr3B 75.833 360 68 17 500 853 410733563 410733909 8.070000e-37 165.0
35 TraesCS7B01G038500 chr3B 80.838 167 27 4 688 853 756683607 756683769 3.810000e-25 126.0
36 TraesCS7B01G038500 chr5B 84.463 354 46 5 117 462 584711627 584711979 1.250000e-89 340.0
37 TraesCS7B01G038500 chr5B 80.000 115 23 0 587 701 420920830 420920944 6.460000e-13 86.1
38 TraesCS7B01G038500 chr6B 78.212 358 70 8 499 853 693902851 693903203 4.720000e-54 222.0
39 TraesCS7B01G038500 chr4A 78.655 342 56 17 518 853 688797623 688797953 1.020000e-50 211.0
40 TraesCS7B01G038500 chr4A 76.720 378 71 17 484 853 448643170 448642802 1.030000e-45 195.0
41 TraesCS7B01G038500 chr1B 76.755 413 72 22 453 855 3200998 3200600 3.670000e-50 209.0
42 TraesCS7B01G038500 chr2D 74.170 542 102 26 2963 3470 30335565 30335028 1.330000e-44 191.0


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 TraesCS7B01G038500 chr7B 37420550 37424181 3631 True 6708.0 6708 100.0000 1 3632 1 chr7B.!!$R1 3631
1 TraesCS7B01G038500 chr7B 67104583 67107225 2642 True 2042.0 2556 95.1980 1 2611 2 chr7B.!!$R6 2610
2 TraesCS7B01G038500 chr7B 37605464 37608096 2632 True 1911.0 2499 92.9865 8 2611 2 chr7B.!!$R5 2603
3 TraesCS7B01G038500 chr7B 37600419 37601121 702 True 1116.0 1116 95.4480 2935 3631 1 chr7B.!!$R2 696
4 TraesCS7B01G038500 chr7B 67353440 67354142 702 True 1116.0 1116 95.4480 2935 3631 1 chr7B.!!$R4 696
5 TraesCS7B01G038500 chr7B 38659683 38660360 677 True 527.0 527 81.0770 1108 1779 1 chr7B.!!$R3 671
6 TraesCS7B01G038500 chr7B 38783120 38784492 1372 False 370.5 521 80.8780 1108 2523 2 chr7B.!!$F2 1415
7 TraesCS7B01G038500 chr7D 88133204 88135102 1898 False 2255.0 2255 88.3220 949 2866 1 chr7D.!!$F1 1917
8 TraesCS7B01G038500 chr7D 88178729 88180462 1733 True 2204.0 2204 89.6900 862 2611 1 chr7D.!!$R1 1749
9 TraesCS7B01G038500 chr7D 88142436 88143134 698 False 1120.0 1120 95.5650 2934 3632 1 chr7D.!!$F2 698
10 TraesCS7B01G038500 chr7D 88370116 88370793 677 True 560.0 560 81.8450 1108 1779 1 chr7D.!!$R2 671
11 TraesCS7B01G038500 chr7A 89809045 89809748 703 False 1068.0 1068 94.1760 2933 3631 1 chr7A.!!$F3 698
12 TraesCS7B01G038500 chr7A 89758449 89759296 847 False 1055.0 1055 89.1300 946 1810 1 chr7A.!!$F1 864
13 TraesCS7B01G038500 chr7A 89781333 89782063 730 False 771.0 771 85.8080 1806 2557 1 chr7A.!!$F2 751
14 TraesCS7B01G038500 chr7A 89947473 89948037 564 True 486.0 486 82.3940 1123 1684 1 chr7A.!!$R1 561
15 TraesCS7B01G038500 chr7A 89974461 89975803 1342 False 397.0 568 81.6650 1108 2523 2 chr7A.!!$F6 1415
16 TraesCS7B01G038500 chr4B 149072040 149072901 861 False 808.0 808 84.0960 9 855 1 chr4B.!!$F1 846
17 TraesCS7B01G038500 chr2B 206367215 206368074 859 False 634.0 634 80.6380 5 851 1 chr2B.!!$F2 846
18 TraesCS7B01G038500 chr5D 236180119 236180989 870 True 547.0 547 79.0650 5 853 1 chr5D.!!$R1 848
19 TraesCS7B01G038500 chrUn 280092103 280092863 760 True 348.0 348 76.0560 117 854 1 chrUn.!!$R1 737

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
489 580 1.211818 CTAATCTCGGCTCGCAGCAC 61.212 60.0 9.78 0.36 44.75 4.40 F
2185 2454 0.107993 GAGCTGCTGCAGGTATGACA 60.108 55.0 31.60 2.34 42.53 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 2659 0.109319 CCGCCTGCACACAAATTACC 60.109 55.000 0.0 0.0 0.00 2.85 R
3453 3794 1.956170 CCTGCACGCTGTTCGAAGT 60.956 57.895 0.0 0.0 41.67 3.01 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
25 26 4.038522 TCCAGCCAAAATCACGAATGAAAA 59.961 37.500 0.00 0.00 38.69 2.29
35 36 3.689161 TCACGAATGAAAATGGCTACCAG 59.311 43.478 0.00 0.00 36.75 4.00
60 61 8.190784 AGGTTTTTCTTTCTGTGTATTCTTGTG 58.809 33.333 0.00 0.00 0.00 3.33
343 397 5.720202 CGGGAATACGATTCCAGATTATCA 58.280 41.667 20.84 0.00 40.32 2.15
411 475 1.891919 GTTGTCACCTCCGCTGCAA 60.892 57.895 0.00 0.00 0.00 4.08
489 580 1.211818 CTAATCTCGGCTCGCAGCAC 61.212 60.000 9.78 0.36 44.75 4.40
557 648 4.063967 CACGACCTGCACGGCCTA 62.064 66.667 0.00 0.00 35.61 3.93
902 1005 2.700773 GGGCGTTTGCAGGATGGAC 61.701 63.158 0.00 0.00 45.35 4.02
917 1020 5.532406 CAGGATGGACGGTCAAATGATTTAT 59.468 40.000 10.76 0.00 0.00 1.40
978 1137 2.064581 GGCTAGGCTCCTCGGGAAA 61.065 63.158 9.46 0.00 0.00 3.13
1510 1709 3.636231 CCAGGGACAACTCCGGCA 61.636 66.667 0.00 0.00 37.46 5.69
1953 2163 3.647824 GCATATGCTGGCGGAGAC 58.352 61.111 20.64 0.00 38.21 3.36
2000 2210 1.537202 CAAAGAAGGTGAAAGCCGAGG 59.463 52.381 0.00 0.00 32.25 4.63
2061 2271 4.073425 AGAAGAGGAATCTGGAGGAAGT 57.927 45.455 0.00 0.00 0.00 3.01
2181 2450 2.914289 GGGAGCTGCTGCAGGTAT 59.086 61.111 31.60 6.51 42.53 2.73
2182 2451 1.525535 GGGAGCTGCTGCAGGTATG 60.526 63.158 31.60 7.91 42.53 2.39
2183 2452 1.524002 GGAGCTGCTGCAGGTATGA 59.476 57.895 31.60 0.00 42.53 2.15
2185 2454 0.107993 GAGCTGCTGCAGGTATGACA 60.108 55.000 31.60 2.34 42.53 3.58
2187 2456 0.661552 GCTGCTGCAGGTATGACATG 59.338 55.000 29.05 2.86 39.41 3.21
2188 2457 1.306148 CTGCTGCAGGTATGACATGG 58.694 55.000 21.71 0.00 29.37 3.66
2190 2459 1.836802 TGCTGCAGGTATGACATGGTA 59.163 47.619 17.12 0.00 29.37 3.25
2191 2460 2.158914 TGCTGCAGGTATGACATGGTAG 60.159 50.000 17.12 0.00 29.37 3.18
2209 2478 3.994729 GCAAATGCGCAGTATGACA 57.005 47.368 18.32 0.00 39.69 3.58
2210 2479 2.480224 GCAAATGCGCAGTATGACAT 57.520 45.000 18.32 0.00 39.69 3.06
2211 2480 2.114056 GCAAATGCGCAGTATGACATG 58.886 47.619 18.32 8.54 39.69 3.21
2212 2481 2.723209 CAAATGCGCAGTATGACATGG 58.277 47.619 18.32 0.00 39.69 3.66
2213 2482 2.042686 AATGCGCAGTATGACATGGT 57.957 45.000 18.32 0.00 39.69 3.55
2214 2483 2.908688 ATGCGCAGTATGACATGGTA 57.091 45.000 18.32 0.00 39.69 3.25
2215 2484 2.908688 TGCGCAGTATGACATGGTAT 57.091 45.000 5.66 0.00 39.69 2.73
2216 2485 2.482864 TGCGCAGTATGACATGGTATG 58.517 47.619 5.66 0.00 39.69 2.39
2217 2486 2.102252 TGCGCAGTATGACATGGTATGA 59.898 45.455 5.66 0.00 39.69 2.15
2218 2487 2.476619 GCGCAGTATGACATGGTATGAC 59.523 50.000 0.30 0.00 39.69 3.06
2219 2488 2.726241 CGCAGTATGACATGGTATGACG 59.274 50.000 0.00 0.00 39.69 4.35
2220 2489 3.059884 GCAGTATGACATGGTATGACGG 58.940 50.000 0.00 0.00 39.69 4.79
2221 2490 3.243737 GCAGTATGACATGGTATGACGGA 60.244 47.826 0.00 0.00 39.69 4.69
2222 2491 4.550422 CAGTATGACATGGTATGACGGAG 58.450 47.826 0.00 0.00 39.69 4.63
2223 2492 4.278419 CAGTATGACATGGTATGACGGAGA 59.722 45.833 0.00 0.00 39.69 3.71
2224 2493 5.047731 CAGTATGACATGGTATGACGGAGAT 60.048 44.000 0.00 0.00 39.69 2.75
2275 2544 2.438975 ACCGAGCCGTCCGATGTA 60.439 61.111 0.00 0.00 0.00 2.29
2311 2580 2.499693 TGTTGCGATTCTCCAGGTATGA 59.500 45.455 0.00 0.00 0.00 2.15
2315 2584 3.062763 GCGATTCTCCAGGTATGACATG 58.937 50.000 0.00 0.00 0.00 3.21
2380 2662 2.160205 GGAGTCCGATCGATCATGGTA 58.840 52.381 24.40 6.77 0.00 3.25
2629 2962 4.321899 GGCACAAAGAAAATGGACTATGCA 60.322 41.667 0.00 0.00 0.00 3.96
2630 2963 4.622740 GCACAAAGAAAATGGACTATGCAC 59.377 41.667 0.00 0.00 0.00 4.57
2645 2978 1.953559 TGCACTTGTCAGTTCCTCAC 58.046 50.000 0.00 0.00 0.00 3.51
2662 2995 5.368145 TCCTCACCATATGCTACATTGAAC 58.632 41.667 0.00 0.00 0.00 3.18
2704 3037 7.201617 CCAAGTTTCTTAGTTTCGTCAAGTCTT 60.202 37.037 0.00 0.00 0.00 3.01
2733 3066 5.395682 TGAATTTCAGCCTTGAGAAATGG 57.604 39.130 0.00 0.00 42.02 3.16
2737 3070 2.783135 TCAGCCTTGAGAAATGGTCAC 58.217 47.619 0.00 0.00 0.00 3.67
2775 3108 6.489361 ACTTTCTTCAGATCAAAGTCTTGCAT 59.511 34.615 0.00 0.00 35.86 3.96
2800 3133 3.628008 TGAACGAGGGAGTAGAAGCATA 58.372 45.455 0.00 0.00 0.00 3.14
2805 3138 5.138276 ACGAGGGAGTAGAAGCATACATAA 58.862 41.667 0.00 0.00 0.00 1.90
2829 3162 5.123227 TCTCTGAAACGTGAAACCTGAATT 58.877 37.500 0.00 0.00 0.00 2.17
2832 3165 5.007626 TCTGAAACGTGAAACCTGAATTCTG 59.992 40.000 7.05 6.17 0.00 3.02
2834 3167 1.880027 ACGTGAAACCTGAATTCTGCC 59.120 47.619 7.05 0.00 0.00 4.85
2846 3182 3.446873 TGAATTCTGCCCAAATATTGCGT 59.553 39.130 7.05 0.00 0.00 5.24
2866 3202 3.211288 CGAGAGCCATTCCTCGGT 58.789 61.111 0.00 0.00 45.93 4.69
2867 3203 1.227089 CGAGAGCCATTCCTCGGTG 60.227 63.158 0.00 0.00 45.93 4.94
2868 3204 1.901085 GAGAGCCATTCCTCGGTGT 59.099 57.895 0.00 0.00 36.95 4.16
2869 3205 0.250513 GAGAGCCATTCCTCGGTGTT 59.749 55.000 0.00 0.00 36.95 3.32
2870 3206 0.036010 AGAGCCATTCCTCGGTGTTG 60.036 55.000 0.00 0.00 36.95 3.33
2871 3207 1.648467 GAGCCATTCCTCGGTGTTGC 61.648 60.000 0.00 0.00 0.00 4.17
2872 3208 2.700773 GCCATTCCTCGGTGTTGCC 61.701 63.158 0.00 0.00 0.00 4.52
2873 3209 1.002134 CCATTCCTCGGTGTTGCCT 60.002 57.895 0.00 0.00 34.25 4.75
2874 3210 1.026718 CCATTCCTCGGTGTTGCCTC 61.027 60.000 0.00 0.00 34.25 4.70
2875 3211 1.079127 ATTCCTCGGTGTTGCCTCG 60.079 57.895 0.00 0.00 34.25 4.63
2876 3212 3.876589 TTCCTCGGTGTTGCCTCGC 62.877 63.158 0.00 0.00 34.25 5.03
2887 3223 4.789075 GCCTCGCGCACGGTAGAA 62.789 66.667 8.75 0.00 40.63 2.10
2888 3224 2.126228 CCTCGCGCACGGTAGAAA 60.126 61.111 8.75 0.00 40.63 2.52
2889 3225 1.735198 CCTCGCGCACGGTAGAAAA 60.735 57.895 8.75 0.00 40.63 2.29
2890 3226 1.082117 CCTCGCGCACGGTAGAAAAT 61.082 55.000 8.75 0.00 40.63 1.82
2891 3227 0.297820 CTCGCGCACGGTAGAAAATC 59.702 55.000 8.75 0.00 40.63 2.17
2892 3228 0.108992 TCGCGCACGGTAGAAAATCT 60.109 50.000 8.75 0.00 40.63 2.40
2893 3229 0.025001 CGCGCACGGTAGAAAATCTG 59.975 55.000 8.75 0.00 34.97 2.90
2894 3230 0.373716 GCGCACGGTAGAAAATCTGG 59.626 55.000 0.30 0.00 0.00 3.86
2895 3231 1.722011 CGCACGGTAGAAAATCTGGT 58.278 50.000 0.00 0.00 0.00 4.00
2896 3232 2.073816 CGCACGGTAGAAAATCTGGTT 58.926 47.619 0.00 0.00 0.00 3.67
2897 3233 2.482721 CGCACGGTAGAAAATCTGGTTT 59.517 45.455 0.00 0.00 0.00 3.27
2898 3234 3.424433 CGCACGGTAGAAAATCTGGTTTC 60.424 47.826 0.00 0.00 37.70 2.78
2899 3235 3.751698 GCACGGTAGAAAATCTGGTTTCT 59.248 43.478 5.58 5.58 46.88 2.52
2900 3236 4.142881 GCACGGTAGAAAATCTGGTTTCTC 60.143 45.833 3.57 0.77 42.88 2.87
2901 3237 4.392138 CACGGTAGAAAATCTGGTTTCTCC 59.608 45.833 3.57 5.23 42.88 3.71
2902 3238 3.939592 CGGTAGAAAATCTGGTTTCTCCC 59.060 47.826 3.57 1.93 42.88 4.30
2903 3239 4.270834 GGTAGAAAATCTGGTTTCTCCCC 58.729 47.826 3.57 2.90 42.88 4.81
2904 3240 4.018324 GGTAGAAAATCTGGTTTCTCCCCT 60.018 45.833 3.57 0.00 42.88 4.79
2905 3241 4.039603 AGAAAATCTGGTTTCTCCCCTG 57.960 45.455 0.00 0.00 42.88 4.45
2906 3242 3.657727 AGAAAATCTGGTTTCTCCCCTGA 59.342 43.478 0.00 0.00 42.88 3.86
2907 3243 3.728385 AAATCTGGTTTCTCCCCTGAG 57.272 47.619 0.00 0.00 40.17 3.35
2908 3244 2.649742 ATCTGGTTTCTCCCCTGAGA 57.350 50.000 0.00 0.00 45.90 3.27
2929 3265 4.267349 ACGAAAGTGCTGGTACATTACT 57.733 40.909 0.00 0.00 46.97 2.24
2930 3266 4.638304 ACGAAAGTGCTGGTACATTACTT 58.362 39.130 0.00 0.00 46.97 2.24
2931 3267 4.689345 ACGAAAGTGCTGGTACATTACTTC 59.311 41.667 0.00 0.00 46.97 3.01
2974 3312 1.175654 TCACATCACATTGCCGCAAT 58.824 45.000 13.00 13.00 34.04 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.524328 CAGAAAGAAAAACCTGGTAGCCAT 59.476 41.667 0.00 0.00 30.82 4.40
35 36 7.435192 CCACAAGAATACACAGAAAGAAAAACC 59.565 37.037 0.00 0.00 0.00 3.27
60 61 3.767131 ACCTCTCTGCTCTCTTTAAGTCC 59.233 47.826 0.00 0.00 0.00 3.85
314 368 0.249911 GAATCGTATTCCCGCCTGCT 60.250 55.000 0.00 0.00 0.00 4.24
343 397 2.057137 TGCTTTCTGCCACAAGTTCT 57.943 45.000 0.00 0.00 42.00 3.01
411 475 0.239347 GATGCTGCGAAACTTGCTGT 59.761 50.000 0.00 0.00 34.23 4.40
449 513 2.095213 GCAAACAACGCTGATTCCGATA 59.905 45.455 0.00 0.00 0.00 2.92
751 851 2.829914 TTGATCATGGCGGCAGGC 60.830 61.111 19.73 6.52 44.11 4.85
752 852 2.191513 CCTTGATCATGGCGGCAGG 61.192 63.158 18.43 18.43 0.00 4.85
902 1005 3.725740 GCTTGCGATAAATCATTTGACCG 59.274 43.478 0.00 0.00 0.00 4.79
917 1020 4.681025 GTCAAAATGAATCAAAGCTTGCGA 59.319 37.500 0.00 0.00 0.00 5.10
978 1137 0.178932 TAGCAGTGGAGTGGAGTGGT 60.179 55.000 0.00 0.00 0.00 4.16
1510 1709 2.123428 GCATCCCCTTGAAGCGCAT 61.123 57.895 11.47 0.00 0.00 4.73
2037 2247 6.026186 ACTTCCTCCAGATTCCTCTTCTTTA 58.974 40.000 0.00 0.00 0.00 1.85
2061 2271 3.706373 GGCCCTCCTCGCTGTTGA 61.706 66.667 0.00 0.00 0.00 3.18
2089 2299 2.094659 CAGCGGCGTGTTCAGTAGG 61.095 63.158 9.37 0.00 0.00 3.18
2092 2302 2.661866 GACAGCGGCGTGTTCAGT 60.662 61.111 9.37 0.00 0.00 3.41
2181 2450 0.451383 GCGCATTTGCTACCATGTCA 59.549 50.000 0.30 0.00 39.32 3.58
2182 2451 0.451383 TGCGCATTTGCTACCATGTC 59.549 50.000 5.66 0.00 39.32 3.06
2183 2452 0.452987 CTGCGCATTTGCTACCATGT 59.547 50.000 12.24 0.00 39.32 3.21
2185 2454 2.036958 TACTGCGCATTTGCTACCAT 57.963 45.000 12.24 0.00 39.32 3.55
2187 2456 1.939934 TCATACTGCGCATTTGCTACC 59.060 47.619 12.24 0.00 39.32 3.18
2188 2457 2.351418 TGTCATACTGCGCATTTGCTAC 59.649 45.455 12.24 6.26 39.32 3.58
2190 2459 1.452110 TGTCATACTGCGCATTTGCT 58.548 45.000 12.24 0.00 39.32 3.91
2191 2460 2.114056 CATGTCATACTGCGCATTTGC 58.886 47.619 12.24 6.25 37.78 3.68
2200 2469 4.278419 TCTCCGTCATACCATGTCATACTG 59.722 45.833 0.00 0.00 0.00 2.74
2201 2470 4.470602 TCTCCGTCATACCATGTCATACT 58.529 43.478 0.00 0.00 0.00 2.12
2202 2471 4.848562 TCTCCGTCATACCATGTCATAC 57.151 45.455 0.00 0.00 0.00 2.39
2203 2472 4.832823 ACATCTCCGTCATACCATGTCATA 59.167 41.667 0.00 0.00 0.00 2.15
2204 2473 3.643320 ACATCTCCGTCATACCATGTCAT 59.357 43.478 0.00 0.00 0.00 3.06
2205 2474 3.031013 ACATCTCCGTCATACCATGTCA 58.969 45.455 0.00 0.00 0.00 3.58
2206 2475 3.643763 GACATCTCCGTCATACCATGTC 58.356 50.000 0.00 0.00 35.88 3.06
2207 2476 2.034685 CGACATCTCCGTCATACCATGT 59.965 50.000 0.00 0.00 35.54 3.21
2208 2477 2.666026 CGACATCTCCGTCATACCATG 58.334 52.381 0.00 0.00 35.54 3.66
2209 2478 1.000163 GCGACATCTCCGTCATACCAT 60.000 52.381 0.00 0.00 35.54 3.55
2210 2479 0.384309 GCGACATCTCCGTCATACCA 59.616 55.000 0.00 0.00 35.54 3.25
2211 2480 0.660595 CGCGACATCTCCGTCATACC 60.661 60.000 0.00 0.00 35.54 2.73
2212 2481 1.269444 GCGCGACATCTCCGTCATAC 61.269 60.000 12.10 0.00 35.54 2.39
2213 2482 1.008881 GCGCGACATCTCCGTCATA 60.009 57.895 12.10 0.00 35.54 2.15
2214 2483 2.278857 GCGCGACATCTCCGTCAT 60.279 61.111 12.10 0.00 35.54 3.06
2215 2484 4.492160 GGCGCGACATCTCCGTCA 62.492 66.667 12.10 0.00 35.54 4.35
2216 2485 4.492160 TGGCGCGACATCTCCGTC 62.492 66.667 12.71 0.00 0.00 4.79
2217 2486 4.796231 GTGGCGCGACATCTCCGT 62.796 66.667 22.20 0.00 0.00 4.69
2275 2544 3.064987 AACATAGCTCGCCGCGACT 62.065 57.895 12.39 15.82 45.59 4.18
2311 2580 0.810648 CACCGCATTTGCTACCATGT 59.189 50.000 0.51 0.00 39.32 3.21
2315 2584 0.878416 TTGACACCGCATTTGCTACC 59.122 50.000 0.51 0.00 39.32 3.18
2317 2586 1.890876 ACTTGACACCGCATTTGCTA 58.109 45.000 0.51 0.00 39.32 3.49
2366 2648 5.434706 CACACAAATTACCATGATCGATCG 58.565 41.667 20.03 9.36 0.00 3.69
2377 2659 0.109319 CCGCCTGCACACAAATTACC 60.109 55.000 0.00 0.00 0.00 2.85
2380 2662 2.339712 GCCGCCTGCACACAAATT 59.660 55.556 0.00 0.00 40.77 1.82
2590 2893 2.716017 GCCGCTCTGCTACCACTCT 61.716 63.158 0.00 0.00 0.00 3.24
2629 2962 4.836825 CATATGGTGAGGAACTGACAAGT 58.163 43.478 0.00 0.00 46.77 3.16
2630 2963 3.624861 GCATATGGTGAGGAACTGACAAG 59.375 47.826 4.56 0.00 46.77 3.16
2662 2995 2.482721 ACTTGGGTCGCGATTTTAACAG 59.517 45.455 14.06 5.09 0.00 3.16
2704 3037 6.009589 TCTCAAGGCTGAAATTCAACCAATA 58.990 36.000 16.69 1.77 35.13 1.90
2733 3066 2.510768 AGTTCGTCAAGGTGAGTGAC 57.489 50.000 0.00 0.00 41.66 3.67
2737 3070 4.119862 TGAAGAAAGTTCGTCAAGGTGAG 58.880 43.478 7.14 0.00 41.50 3.51
2775 3108 3.618351 CTTCTACTCCCTCGTTCAGGTA 58.382 50.000 0.00 0.00 41.51 3.08
2791 3124 8.414003 ACGTTTCAGAGATTATGTATGCTTCTA 58.586 33.333 0.00 0.00 0.00 2.10
2800 3133 6.147821 CAGGTTTCACGTTTCAGAGATTATGT 59.852 38.462 0.00 0.00 0.00 2.29
2805 3138 4.336889 TCAGGTTTCACGTTTCAGAGAT 57.663 40.909 0.00 0.00 0.00 2.75
2829 3162 2.353269 CGTAACGCAATATTTGGGCAGA 59.647 45.455 4.43 0.00 46.40 4.26
2832 3165 2.610374 TCTCGTAACGCAATATTTGGGC 59.390 45.455 4.43 0.00 46.40 5.36
2834 3167 3.303132 GGCTCTCGTAACGCAATATTTGG 60.303 47.826 0.00 0.00 0.00 3.28
2870 3206 4.789075 TTCTACCGTGCGCGAGGC 62.789 66.667 23.45 0.00 41.33 4.70
2871 3207 1.082117 ATTTTCTACCGTGCGCGAGG 61.082 55.000 23.45 17.86 41.33 4.63
2872 3208 0.297820 GATTTTCTACCGTGCGCGAG 59.702 55.000 23.45 11.90 41.33 5.03
2873 3209 0.108992 AGATTTTCTACCGTGCGCGA 60.109 50.000 23.45 0.00 41.33 5.87
2874 3210 0.025001 CAGATTTTCTACCGTGCGCG 59.975 55.000 13.88 13.88 37.95 6.86
2875 3211 0.373716 CCAGATTTTCTACCGTGCGC 59.626 55.000 0.00 0.00 0.00 6.09
2876 3212 1.722011 ACCAGATTTTCTACCGTGCG 58.278 50.000 0.00 0.00 0.00 5.34
2877 3213 3.751698 AGAAACCAGATTTTCTACCGTGC 59.248 43.478 0.00 0.00 42.79 5.34
2878 3214 4.392138 GGAGAAACCAGATTTTCTACCGTG 59.608 45.833 0.00 0.00 44.27 4.94
2879 3215 4.576879 GGAGAAACCAGATTTTCTACCGT 58.423 43.478 0.00 0.00 44.27 4.83
2882 3218 4.944317 CAGGGGAGAAACCAGATTTTCTAC 59.056 45.833 0.00 0.00 44.27 2.59
2883 3219 4.849810 TCAGGGGAGAAACCAGATTTTCTA 59.150 41.667 0.00 0.00 44.27 2.10
2884 3220 3.657727 TCAGGGGAGAAACCAGATTTTCT 59.342 43.478 0.00 0.00 46.41 2.52
2885 3221 4.013050 CTCAGGGGAGAAACCAGATTTTC 58.987 47.826 0.00 0.00 44.26 2.29
2886 3222 3.657727 TCTCAGGGGAGAAACCAGATTTT 59.342 43.478 0.00 0.00 46.94 1.82
2887 3223 3.260205 TCTCAGGGGAGAAACCAGATTT 58.740 45.455 0.00 0.00 46.94 2.17
2888 3224 2.921221 TCTCAGGGGAGAAACCAGATT 58.079 47.619 0.00 0.00 46.94 2.40
2889 3225 2.649742 TCTCAGGGGAGAAACCAGAT 57.350 50.000 0.00 0.00 46.94 2.90
2898 3234 0.390472 GCACTTTCGTCTCAGGGGAG 60.390 60.000 0.00 0.00 42.80 4.30
2899 3235 0.832135 AGCACTTTCGTCTCAGGGGA 60.832 55.000 0.00 0.00 0.00 4.81
2900 3236 0.671781 CAGCACTTTCGTCTCAGGGG 60.672 60.000 0.00 0.00 0.00 4.79
2901 3237 0.671781 CCAGCACTTTCGTCTCAGGG 60.672 60.000 0.00 0.00 0.00 4.45
2902 3238 0.034059 ACCAGCACTTTCGTCTCAGG 59.966 55.000 0.00 0.00 0.00 3.86
2903 3239 2.288213 TGTACCAGCACTTTCGTCTCAG 60.288 50.000 0.00 0.00 0.00 3.35
2904 3240 1.684450 TGTACCAGCACTTTCGTCTCA 59.316 47.619 0.00 0.00 0.00 3.27
2905 3241 2.433868 TGTACCAGCACTTTCGTCTC 57.566 50.000 0.00 0.00 0.00 3.36
2906 3242 3.402628 AATGTACCAGCACTTTCGTCT 57.597 42.857 0.00 0.00 0.00 4.18
2907 3243 4.243270 AGTAATGTACCAGCACTTTCGTC 58.757 43.478 0.00 0.00 0.00 4.20
2908 3244 4.267349 AGTAATGTACCAGCACTTTCGT 57.733 40.909 0.00 0.00 0.00 3.85
2909 3245 4.092968 GGAAGTAATGTACCAGCACTTTCG 59.907 45.833 0.00 0.00 29.89 3.46
2910 3246 5.001232 TGGAAGTAATGTACCAGCACTTTC 58.999 41.667 0.00 0.00 29.89 2.62
2911 3247 4.980573 TGGAAGTAATGTACCAGCACTTT 58.019 39.130 0.00 0.00 29.89 2.66
2912 3248 4.565652 CCTGGAAGTAATGTACCAGCACTT 60.566 45.833 0.00 0.00 45.72 3.16
2913 3249 3.055094 CCTGGAAGTAATGTACCAGCACT 60.055 47.826 0.00 0.00 45.72 4.40
2914 3250 3.270877 CCTGGAAGTAATGTACCAGCAC 58.729 50.000 0.00 0.00 45.72 4.40
2915 3251 2.238646 CCCTGGAAGTAATGTACCAGCA 59.761 50.000 0.00 0.00 45.72 4.41
2916 3252 2.238898 ACCCTGGAAGTAATGTACCAGC 59.761 50.000 0.00 0.00 45.72 4.85
2917 3253 3.517901 TCACCCTGGAAGTAATGTACCAG 59.482 47.826 0.00 0.00 46.37 4.00
2918 3254 3.522759 TCACCCTGGAAGTAATGTACCA 58.477 45.455 0.00 0.00 0.00 3.25
2919 3255 4.224370 TCTTCACCCTGGAAGTAATGTACC 59.776 45.833 0.00 0.00 43.72 3.34
2920 3256 5.416271 TCTTCACCCTGGAAGTAATGTAC 57.584 43.478 0.00 0.00 43.72 2.90
2921 3257 5.568023 CGTTCTTCACCCTGGAAGTAATGTA 60.568 44.000 0.00 0.00 43.72 2.29
2922 3258 4.652822 GTTCTTCACCCTGGAAGTAATGT 58.347 43.478 0.00 0.00 43.72 2.71
2923 3259 3.684788 CGTTCTTCACCCTGGAAGTAATG 59.315 47.826 0.00 0.00 43.72 1.90
2924 3260 3.581332 TCGTTCTTCACCCTGGAAGTAAT 59.419 43.478 0.00 0.00 43.72 1.89
2925 3261 2.967201 TCGTTCTTCACCCTGGAAGTAA 59.033 45.455 0.00 0.00 43.72 2.24
2926 3262 2.561419 CTCGTTCTTCACCCTGGAAGTA 59.439 50.000 0.00 0.00 43.72 2.24
2927 3263 1.344763 CTCGTTCTTCACCCTGGAAGT 59.655 52.381 0.00 0.00 43.72 3.01
2928 3264 1.941668 GCTCGTTCTTCACCCTGGAAG 60.942 57.143 0.00 0.00 44.46 3.46
2929 3265 0.034896 GCTCGTTCTTCACCCTGGAA 59.965 55.000 0.00 0.00 0.00 3.53
2930 3266 1.118965 TGCTCGTTCTTCACCCTGGA 61.119 55.000 0.00 0.00 0.00 3.86
2931 3267 0.671781 CTGCTCGTTCTTCACCCTGG 60.672 60.000 0.00 0.00 0.00 4.45
3453 3794 1.956170 CCTGCACGCTGTTCGAAGT 60.956 57.895 0.00 0.00 41.67 3.01


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

AutoCloner maintained by Alex Coulton.