Multiple sequence alignment - TraesCS5D01G439300

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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 TraesCS5D01G439300 chr5D 100.000 3131 0 0 1 3131 492744310 492747440 0.000000e+00 5782.0
1 TraesCS5D01G439300 chr5D 85.143 976 109 25 1243 2205 492183315 492182363 0.000000e+00 966.0
2 TraesCS5D01G439300 chr5D 79.911 1344 162 45 875 2205 492293071 492291823 0.000000e+00 887.0
3 TraesCS5D01G439300 chr5D 85.565 672 79 11 1531 2198 492155319 492154662 0.000000e+00 688.0
4 TraesCS5D01G439300 chr5D 84.949 691 85 12 1517 2203 492146313 492145638 0.000000e+00 682.0
5 TraesCS5D01G439300 chr5D 84.660 691 88 12 1517 2203 492149066 492148390 0.000000e+00 673.0
6 TraesCS5D01G439300 chr5D 84.660 691 88 11 1517 2203 492172765 492172089 0.000000e+00 673.0
7 TraesCS5D01G439300 chr5D 84.343 677 91 10 1243 1911 492235212 492234543 0.000000e+00 649.0
8 TraesCS5D01G439300 chr5D 81.453 523 63 27 2628 3131 492225996 492225489 6.290000e-107 398.0
9 TraesCS5D01G439300 chr5D 85.185 324 33 10 2817 3131 491809320 491809003 5.040000e-83 318.0
10 TraesCS5D01G439300 chr5D 87.195 164 17 3 971 1134 492236814 492236655 1.920000e-42 183.0
11 TraesCS5D01G439300 chr5D 86.585 164 18 3 971 1134 492237646 492237487 8.920000e-41 178.0
12 TraesCS5D01G439300 chr5A 90.026 2286 139 40 232 2478 615158425 615156190 0.000000e+00 2876.0
13 TraesCS5D01G439300 chr5A 89.043 575 47 11 2562 3131 615156190 615155627 0.000000e+00 699.0
14 TraesCS5D01G439300 chr5A 77.994 618 75 33 457 1049 614767887 614767306 6.470000e-87 331.0
15 TraesCS5D01G439300 chr5A 78.065 620 70 36 457 1049 614957715 614957135 6.470000e-87 331.0
16 TraesCS5D01G439300 chr5A 77.832 618 76 33 457 1049 614829792 614829211 3.010000e-85 326.0
17 TraesCS5D01G439300 chr5A 77.670 618 75 33 457 1049 614738828 614738249 5.040000e-83 318.0
18 TraesCS5D01G439300 chr5A 77.581 620 73 36 457 1049 614923839 614923259 6.520000e-82 315.0
19 TraesCS5D01G439300 chr5A 89.583 240 24 1 1 239 615163199 615162960 1.410000e-78 303.0
20 TraesCS5D01G439300 chr5A 82.105 190 21 5 457 633 614802938 614802749 1.950000e-32 150.0
21 TraesCS5D01G439300 chr5A 93.878 49 3 0 675 723 614939534 614939486 1.200000e-09 75.0
22 TraesCS5D01G439300 chr5B 95.821 1029 28 2 1232 2259 607468292 607467278 0.000000e+00 1648.0
23 TraesCS5D01G439300 chr5B 90.279 895 58 16 2243 3131 607467262 607466391 0.000000e+00 1144.0
24 TraesCS5D01G439300 chr5B 80.911 1252 167 36 960 2205 607059323 607058138 0.000000e+00 922.0
25 TraesCS5D01G439300 chr5B 80.911 1252 167 36 960 2205 607114528 607113343 0.000000e+00 922.0
26 TraesCS5D01G439300 chr5B 80.671 1252 166 38 960 2205 607136098 607134917 0.000000e+00 902.0
27 TraesCS5D01G439300 chr5B 95.390 564 23 2 679 1239 607470863 607470300 0.000000e+00 894.0
28 TraesCS5D01G439300 chr5B 89.671 668 42 6 1 667 607471575 607470934 0.000000e+00 826.0
29 TraesCS5D01G439300 chr5B 79.207 1236 185 29 875 2107 606986393 606985227 0.000000e+00 793.0
30 TraesCS5D01G439300 chr5B 80.897 513 69 20 2628 3121 606860451 606859949 8.200000e-101 377.0
31 TraesCS5D01G439300 chr5B 78.896 616 72 33 457 1051 607139095 607138517 6.380000e-97 364.0
32 TraesCS5D01G439300 chr5B 80.122 493 56 28 1854 2335 607021452 607020991 2.330000e-86 329.0
33 TraesCS5D01G439300 chr5B 80.122 493 56 28 1854 2335 607079706 607079245 2.330000e-86 329.0
34 TraesCS5D01G439300 chr5B 77.435 616 81 33 457 1051 607062319 607061741 6.520000e-82 315.0
35 TraesCS5D01G439300 chr5B 79.433 282 45 10 1507 1783 607205553 607205280 1.480000e-43 187.0
36 TraesCS5D01G439300 chr5B 79.237 236 43 5 9 243 609684055 609684285 3.230000e-35 159.0
37 TraesCS5D01G439300 chr5B 85.294 136 10 6 2263 2397 607024857 607024731 7.050000e-27 132.0
38 TraesCS5D01G439300 chr5B 85.294 136 10 6 2263 2397 607081533 607081407 7.050000e-27 132.0
39 TraesCS5D01G439300 chr5B 84.559 136 11 6 2263 2397 606983914 606983788 3.280000e-25 126.0
40 TraesCS5D01G439300 chr5B 84.559 136 11 6 2263 2397 607034591 607034465 3.280000e-25 126.0
41 TraesCS5D01G439300 chr5B 84.559 136 11 6 2263 2397 607091272 607091146 3.280000e-25 126.0
42 TraesCS5D01G439300 chr5B 76.652 227 40 13 19 238 419253731 419253511 2.550000e-21 113.0
43 TraesCS5D01G439300 chr5B 90.000 70 7 0 1328 1397 607468292 607468223 1.200000e-14 91.6
44 TraesCS5D01G439300 chr5B 75.610 205 30 9 1410 1604 607073869 607073675 2.000000e-12 84.2
45 TraesCS5D01G439300 chr7B 83.898 236 29 9 6 239 51052048 51052276 1.890000e-52 217.0
46 TraesCS5D01G439300 chr7D 84.422 199 25 4 42 236 571265381 571265577 1.150000e-44 191.0
47 TraesCS5D01G439300 chr4A 79.668 241 23 15 10 245 710173110 710173329 1.950000e-32 150.0
48 TraesCS5D01G439300 chr6D 78.205 234 40 9 10 239 135115007 135114781 4.210000e-29 139.0
49 TraesCS5D01G439300 chr6B 76.382 199 36 10 19 211 145545529 145545336 2.570000e-16 97.1


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 TraesCS5D01G439300 chr5D 492744310 492747440 3130 False 5782.000000 5782 100.0000 1 3131 1 chr5D.!!$F1 3130
1 TraesCS5D01G439300 chr5D 492182363 492183315 952 True 966.000000 966 85.1430 1243 2205 1 chr5D.!!$R4 962
2 TraesCS5D01G439300 chr5D 492291823 492293071 1248 True 887.000000 887 79.9110 875 2205 1 chr5D.!!$R6 1330
3 TraesCS5D01G439300 chr5D 492154662 492155319 657 True 688.000000 688 85.5650 1531 2198 1 chr5D.!!$R2 667
4 TraesCS5D01G439300 chr5D 492145638 492149066 3428 True 677.500000 682 84.8045 1517 2203 2 chr5D.!!$R7 686
5 TraesCS5D01G439300 chr5D 492172089 492172765 676 True 673.000000 673 84.6600 1517 2203 1 chr5D.!!$R3 686
6 TraesCS5D01G439300 chr5D 492225489 492225996 507 True 398.000000 398 81.4530 2628 3131 1 chr5D.!!$R5 503
7 TraesCS5D01G439300 chr5D 492234543 492237646 3103 True 336.666667 649 86.0410 971 1911 3 chr5D.!!$R8 940
8 TraesCS5D01G439300 chr5A 615155627 615158425 2798 True 1787.500000 2876 89.5345 232 3131 2 chr5A.!!$R9 2899
9 TraesCS5D01G439300 chr5A 614767306 614767887 581 True 331.000000 331 77.9940 457 1049 1 chr5A.!!$R2 592
10 TraesCS5D01G439300 chr5A 614957135 614957715 580 True 331.000000 331 78.0650 457 1049 1 chr5A.!!$R7 592
11 TraesCS5D01G439300 chr5A 614829211 614829792 581 True 326.000000 326 77.8320 457 1049 1 chr5A.!!$R4 592
12 TraesCS5D01G439300 chr5A 614738249 614738828 579 True 318.000000 318 77.6700 457 1049 1 chr5A.!!$R1 592
13 TraesCS5D01G439300 chr5A 614923259 614923839 580 True 315.000000 315 77.5810 457 1049 1 chr5A.!!$R5 592
14 TraesCS5D01G439300 chr5B 607113343 607114528 1185 True 922.000000 922 80.9110 960 2205 1 chr5B.!!$R6 1245
15 TraesCS5D01G439300 chr5B 607466391 607471575 5184 True 920.720000 1648 92.2322 1 3131 5 chr5B.!!$R13 3130
16 TraesCS5D01G439300 chr5B 607134917 607139095 4178 True 633.000000 902 79.7835 457 2205 2 chr5B.!!$R12 1748
17 TraesCS5D01G439300 chr5B 607058138 607062319 4181 True 618.500000 922 79.1730 457 2205 2 chr5B.!!$R10 1748
18 TraesCS5D01G439300 chr5B 606983788 606986393 2605 True 459.500000 793 81.8830 875 2397 2 chr5B.!!$R8 1522
19 TraesCS5D01G439300 chr5B 606859949 606860451 502 True 377.000000 377 80.8970 2628 3121 1 chr5B.!!$R2 493
20 TraesCS5D01G439300 chr5B 607020991 607024857 3866 True 230.500000 329 82.7080 1854 2397 2 chr5B.!!$R9 543
21 TraesCS5D01G439300 chr5B 607079245 607081533 2288 True 230.500000 329 82.7080 1854 2397 2 chr5B.!!$R11 543

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
158 160 0.023732 CGTGCTATGCTCGTTGTTCG 59.976 55.0 5.95 0.0 40.03 3.95 F
899 971 0.039180 GACCCCGAAACAATTCCCCT 59.961 55.0 0.00 0.0 31.52 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1104 4649 0.592148 AGAGTGACAGGTCGACGTTC 59.408 55.0 8.27 10.12 0.0 3.95 R
2279 9118 0.395311 AGACCAAGCGATCGACCCTA 60.395 55.0 21.57 0.00 0.0 3.53 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
158 160 0.023732 CGTGCTATGCTCGTTGTTCG 59.976 55.000 5.95 0.00 40.03 3.95
172 174 0.942410 TGTTCGCAGCGAGTGGTAAC 60.942 55.000 18.62 12.64 37.14 2.50
264 266 8.700051 AGACATATTGAGTATCTAGTTGCAGTT 58.300 33.333 0.00 0.00 34.92 3.16
313 315 6.724441 TCAGAACTACAGAGGGAGTAATTCAA 59.276 38.462 0.00 0.00 31.98 2.69
341 343 3.868754 GCAAAGTACCCTTCCGAAGACAT 60.869 47.826 9.87 0.00 0.00 3.06
342 344 4.324267 CAAAGTACCCTTCCGAAGACATT 58.676 43.478 9.87 0.00 0.00 2.71
344 346 4.635699 AGTACCCTTCCGAAGACATTTT 57.364 40.909 9.87 0.00 0.00 1.82
345 347 5.750352 AGTACCCTTCCGAAGACATTTTA 57.250 39.130 9.87 0.00 0.00 1.52
348 350 3.009143 ACCCTTCCGAAGACATTTTAGCT 59.991 43.478 9.87 0.00 0.00 3.32
351 353 5.048013 CCCTTCCGAAGACATTTTAGCTTTT 60.048 40.000 9.87 0.00 0.00 2.27
667 679 2.537560 GGGCGATGTGATTGGCTCG 61.538 63.158 0.00 0.00 39.11 5.03
825 897 1.226603 CTCCGTCGCGAAACCCTAG 60.227 63.158 12.06 0.00 0.00 3.02
827 899 2.884207 CGTCGCGAAACCCTAGCC 60.884 66.667 12.06 0.00 0.00 3.93
828 900 2.263540 GTCGCGAAACCCTAGCCA 59.736 61.111 12.06 0.00 0.00 4.75
829 901 2.098831 GTCGCGAAACCCTAGCCAC 61.099 63.158 12.06 0.00 0.00 5.01
830 902 2.818274 CGCGAAACCCTAGCCACC 60.818 66.667 0.00 0.00 0.00 4.61
831 903 2.818274 GCGAAACCCTAGCCACCG 60.818 66.667 0.00 0.00 0.00 4.94
832 904 2.660802 CGAAACCCTAGCCACCGT 59.339 61.111 0.00 0.00 0.00 4.83
834 906 1.078637 GAAACCCTAGCCACCGTCC 60.079 63.158 0.00 0.00 0.00 4.79
835 907 2.847435 GAAACCCTAGCCACCGTCCG 62.847 65.000 0.00 0.00 0.00 4.79
836 908 4.691359 ACCCTAGCCACCGTCCGT 62.691 66.667 0.00 0.00 0.00 4.69
837 909 3.834799 CCCTAGCCACCGTCCGTC 61.835 72.222 0.00 0.00 0.00 4.79
839 911 2.754658 CTAGCCACCGTCCGTCCT 60.755 66.667 0.00 0.00 0.00 3.85
840 912 3.064987 CTAGCCACCGTCCGTCCTG 62.065 68.421 0.00 0.00 0.00 3.86
850 922 4.508128 CCGTCCTGCGCCGTATGT 62.508 66.667 4.18 0.00 39.71 2.29
855 927 1.001048 GTCCTGCGCCGTATGTATACA 60.001 52.381 8.27 8.27 32.87 2.29
856 928 1.890489 TCCTGCGCCGTATGTATACAT 59.110 47.619 21.57 21.57 40.22 2.29
869 941 4.540359 TGTATACATACGGGGTATTGCC 57.460 45.455 0.08 0.00 36.06 4.52
871 943 3.695830 ATACATACGGGGTATTGCCAG 57.304 47.619 0.00 0.00 39.65 4.85
872 944 0.472471 ACATACGGGGTATTGCCAGG 59.528 55.000 0.00 0.00 39.65 4.45
873 945 0.472471 CATACGGGGTATTGCCAGGT 59.528 55.000 0.00 0.00 39.65 4.00
874 946 0.763035 ATACGGGGTATTGCCAGGTC 59.237 55.000 0.00 0.00 39.65 3.85
875 947 0.618107 TACGGGGTATTGCCAGGTCA 60.618 55.000 0.00 0.00 39.65 4.02
880 952 1.676006 GGGTATTGCCAGGTCATTTCG 59.324 52.381 0.00 0.00 39.65 3.46
881 953 2.639065 GGTATTGCCAGGTCATTTCGA 58.361 47.619 0.00 0.00 37.17 3.71
882 954 2.354821 GGTATTGCCAGGTCATTTCGAC 59.645 50.000 0.00 0.00 39.58 4.20
899 971 0.039180 GACCCCGAAACAATTCCCCT 59.961 55.000 0.00 0.00 31.52 4.79
900 972 0.039180 ACCCCGAAACAATTCCCCTC 59.961 55.000 0.00 0.00 31.52 4.30
901 973 0.683179 CCCCGAAACAATTCCCCTCC 60.683 60.000 0.00 0.00 31.52 4.30
933 1005 1.757699 CTCAGCACCTACCTACCTTCC 59.242 57.143 0.00 0.00 0.00 3.46
939 1011 1.008084 ACCTACCTACCTTCCACCTCC 59.992 57.143 0.00 0.00 0.00 4.30
943 1015 1.132495 ACCTACCTTCCACCTCCAGTT 60.132 52.381 0.00 0.00 0.00 3.16
952 1024 0.953960 CACCTCCAGTTGTAACGGCC 60.954 60.000 0.00 0.00 0.00 6.13
954 1026 1.740296 CTCCAGTTGTAACGGCCGG 60.740 63.158 31.76 11.88 0.00 6.13
955 1027 3.428282 CCAGTTGTAACGGCCGGC 61.428 66.667 31.76 21.18 0.00 6.13
960 1032 3.993376 TTGTAACGGCCGGCGCTAG 62.993 63.158 31.76 14.17 34.44 3.42
972 1044 4.740235 CGCTAGCTAGGGCAGTTC 57.260 61.111 23.11 3.76 41.70 3.01
1119 4664 1.105167 ACCTGAACGTCGACCTGTCA 61.105 55.000 10.58 9.85 0.00 3.58
2088 7665 3.197790 CGCCCGTGCCTTCTGATG 61.198 66.667 0.00 0.00 0.00 3.07
2170 8970 3.380004 CGCTGGGATCCTAGTATCTCATC 59.620 52.174 24.55 6.08 35.81 2.92
2279 9118 3.552875 TGTATCGTAGTGAGCTAGCCTT 58.447 45.455 12.13 0.00 0.00 4.35
2287 9126 0.257905 TGAGCTAGCCTTAGGGTCGA 59.742 55.000 12.13 0.00 34.28 4.20
2288 9127 1.133450 TGAGCTAGCCTTAGGGTCGAT 60.133 52.381 12.13 0.00 34.28 3.59
2289 9128 1.542472 GAGCTAGCCTTAGGGTCGATC 59.458 57.143 12.13 5.23 34.28 3.69
2290 9129 0.241481 GCTAGCCTTAGGGTCGATCG 59.759 60.000 6.12 9.36 34.28 3.69
2337 9176 6.775142 TGTATCTTAGTGATCAGCTAGCTCTT 59.225 38.462 16.15 4.75 36.65 2.85
2450 9290 1.036707 GGGCAGTTGCAAGGTACAAA 58.963 50.000 0.00 0.00 44.36 2.83
2478 9318 5.637006 TTGTGGGGAATTTCGATAACTTG 57.363 39.130 0.00 0.00 0.00 3.16
2495 9336 2.036733 ACTTGTATGGTACGTGCACTGT 59.963 45.455 16.19 16.29 0.00 3.55
2506 9347 6.072008 TGGTACGTGCACTGTAGAAATTACTA 60.072 38.462 16.19 3.47 0.00 1.82
2507 9348 6.252228 GGTACGTGCACTGTAGAAATTACTAC 59.748 42.308 16.19 5.60 41.90 2.73
2508 9349 6.022163 ACGTGCACTGTAGAAATTACTACT 57.978 37.500 16.19 0.00 42.01 2.57
2513 9354 5.642063 GCACTGTAGAAATTACTACTTGGCA 59.358 40.000 0.00 0.00 42.01 4.92
2515 9356 6.649141 CACTGTAGAAATTACTACTTGGCACA 59.351 38.462 0.00 0.00 42.01 4.57
2525 9366 1.370778 CTTGGCACACACGCACATG 60.371 57.895 0.00 0.00 39.29 3.21
2532 9373 2.672996 ACACGCACATGGGAAGGC 60.673 61.111 0.00 0.00 0.00 4.35
2573 9414 0.804544 CTAGAAATCGGTTGGCGCGA 60.805 55.000 12.10 0.00 0.00 5.87
2574 9415 0.179094 TAGAAATCGGTTGGCGCGAT 60.179 50.000 12.10 0.00 32.31 4.58
2585 9426 1.913778 TGGCGCGATATTACCCTAGA 58.086 50.000 12.10 0.00 0.00 2.43
2646 9487 9.974980 TTTGTCATATGCGAAACTATCTATACA 57.025 29.630 0.00 0.00 0.00 2.29
2692 9533 9.538508 AACCACTTACCGAATATATGTTAGTTC 57.461 33.333 0.00 0.00 0.00 3.01
2693 9534 7.864379 ACCACTTACCGAATATATGTTAGTTCG 59.136 37.037 0.00 0.00 42.08 3.95
2771 9618 4.838423 TCCCTCATAAGTCAGAACAGAACA 59.162 41.667 0.00 0.00 0.00 3.18
2820 9676 9.141400 GATAAATATGTTAGATCACGGTTCCTC 57.859 37.037 0.00 0.00 0.00 3.71
2832 9688 4.828939 TCACGGTTCCTCAGAAGTTTAGTA 59.171 41.667 0.00 0.00 30.91 1.82
2833 9689 5.479375 TCACGGTTCCTCAGAAGTTTAGTAT 59.521 40.000 0.00 0.00 30.91 2.12
2937 9794 8.547967 TTATGACCTTGTGATAACTTTCACTC 57.452 34.615 6.20 0.00 45.07 3.51
2939 9796 5.991606 TGACCTTGTGATAACTTTCACTCTG 59.008 40.000 6.20 0.00 45.07 3.35
2999 9857 7.231317 TGCCCTCCTTGAAATCATTACATATTC 59.769 37.037 0.00 0.00 0.00 1.75
3085 9946 9.033481 CGAATGCATGTTCATTTGGTTATTATT 57.967 29.630 0.00 0.00 36.85 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 160 1.797025 AGAAAGTTACCACTCGCTGC 58.203 50.000 0.00 0.00 30.45 5.25
238 240 8.243961 ACTGCAACTAGATACTCAATATGTCT 57.756 34.615 0.00 0.00 0.00 3.41
243 245 9.314321 GCTTTAACTGCAACTAGATACTCAATA 57.686 33.333 0.00 0.00 0.00 1.90
264 266 8.046708 TGAACCAATTATCTGAAGCTAGCTTTA 58.953 33.333 29.84 24.55 36.26 1.85
313 315 5.881923 TCGGAAGGGTACTTTGCTATATT 57.118 39.130 0.00 0.00 36.97 1.28
319 321 2.074576 GTCTTCGGAAGGGTACTTTGC 58.925 52.381 17.19 0.00 36.97 3.68
388 390 9.844790 ACATACATACAAAAATGAGTGAACATG 57.155 29.630 0.00 0.00 0.00 3.21
552 560 1.477553 CTCCATCCCCACCACATTTG 58.522 55.000 0.00 0.00 0.00 2.32
821 893 3.834799 GGACGGACGGTGGCTAGG 61.835 72.222 0.00 0.00 0.00 3.02
822 894 2.754658 AGGACGGACGGTGGCTAG 60.755 66.667 0.00 0.00 0.00 3.42
834 906 6.433099 TATGTATACATACGGCGCAGGACG 62.433 50.000 19.51 7.42 43.37 4.79
835 907 1.001048 TGTATACATACGGCGCAGGAC 60.001 52.381 13.26 0.00 36.06 3.85
836 908 1.320507 TGTATACATACGGCGCAGGA 58.679 50.000 13.26 2.76 36.06 3.86
837 909 2.363788 ATGTATACATACGGCGCAGG 57.636 50.000 16.85 0.00 36.06 4.85
845 917 6.351202 TGGCAATACCCCGTATGTATACATAC 60.351 42.308 32.71 32.71 45.05 2.39
847 919 4.532916 TGGCAATACCCCGTATGTATACAT 59.467 41.667 21.57 21.57 37.79 2.29
850 922 3.516300 CCTGGCAATACCCCGTATGTATA 59.484 47.826 0.00 0.00 37.83 1.47
855 927 0.763035 GACCTGGCAATACCCCGTAT 59.237 55.000 0.00 0.00 37.83 3.06
856 928 0.618107 TGACCTGGCAATACCCCGTA 60.618 55.000 0.00 0.00 37.83 4.02
859 931 2.031870 GAAATGACCTGGCAATACCCC 58.968 52.381 0.00 0.00 37.83 4.95
861 933 2.354821 GTCGAAATGACCTGGCAATACC 59.645 50.000 0.00 0.00 42.04 2.73
862 934 3.675467 GTCGAAATGACCTGGCAATAC 57.325 47.619 0.00 0.00 42.04 1.89
880 952 0.039180 AGGGGAATTGTTTCGGGGTC 59.961 55.000 0.00 0.00 32.28 4.46
881 953 0.039180 GAGGGGAATTGTTTCGGGGT 59.961 55.000 0.00 0.00 32.28 4.95
882 954 0.683179 GGAGGGGAATTGTTTCGGGG 60.683 60.000 0.00 0.00 32.28 5.73
909 981 2.771639 TAGGTAGGTGCTGAGCGCG 61.772 63.158 12.28 0.00 43.27 6.86
924 996 1.279271 CAACTGGAGGTGGAAGGTAGG 59.721 57.143 0.00 0.00 0.00 3.18
928 1000 2.779506 GTTACAACTGGAGGTGGAAGG 58.220 52.381 0.00 0.00 0.00 3.46
933 1005 0.953960 GGCCGTTACAACTGGAGGTG 60.954 60.000 0.00 0.00 0.00 4.00
939 1011 3.784412 CGCCGGCCGTTACAACTG 61.784 66.667 26.12 6.93 0.00 3.16
943 1015 4.501714 CTAGCGCCGGCCGTTACA 62.502 66.667 26.12 3.85 41.24 2.41
952 1024 4.654412 CTGCCCTAGCTAGCGCCG 62.654 72.222 24.09 16.01 40.80 6.46
954 1026 1.592939 GAACTGCCCTAGCTAGCGC 60.593 63.158 21.16 21.16 40.80 5.92
955 1027 1.299468 CGAACTGCCCTAGCTAGCG 60.299 63.158 15.74 8.23 40.80 4.26
968 1040 1.909141 ATCGACGACACGAGCGAACT 61.909 55.000 0.00 1.84 45.22 3.01
969 1041 1.454370 GATCGACGACACGAGCGAAC 61.454 60.000 0.00 10.03 45.22 3.95
1104 4649 0.592148 AGAGTGACAGGTCGACGTTC 59.408 55.000 8.27 10.12 0.00 3.95
2088 7665 4.699522 ACGCCGTCCTTCTTGGCC 62.700 66.667 0.00 0.00 46.12 5.36
2170 8970 0.892358 AGGCACAGTTGACATGCAGG 60.892 55.000 0.00 0.00 41.27 4.85
2279 9118 0.395311 AGACCAAGCGATCGACCCTA 60.395 55.000 21.57 0.00 0.00 3.53
2287 9126 4.820894 ACTTAACCTAAGACCAAGCGAT 57.179 40.909 0.52 0.00 39.09 4.58
2288 9127 4.202284 ACAACTTAACCTAAGACCAAGCGA 60.202 41.667 0.52 0.00 39.09 4.93
2289 9128 4.062991 ACAACTTAACCTAAGACCAAGCG 58.937 43.478 0.52 0.00 39.09 4.68
2290 9129 5.298527 ACAACAACTTAACCTAAGACCAAGC 59.701 40.000 0.52 0.00 39.09 4.01
2394 9233 9.014297 ACCCATAAGAAGAACAAATTAGAAGTG 57.986 33.333 0.00 0.00 0.00 3.16
2422 9262 0.403655 TGCAACTGCCCCATAACTCA 59.596 50.000 0.00 0.00 41.18 3.41
2472 9312 4.239304 CAGTGCACGTACCATACAAGTTA 58.761 43.478 12.01 0.00 0.00 2.24
2478 9318 3.770263 TCTACAGTGCACGTACCATAC 57.230 47.619 12.01 0.00 0.00 2.39
2495 9336 5.636121 CGTGTGTGCCAAGTAGTAATTTCTA 59.364 40.000 0.00 0.00 0.00 2.10
2506 9347 1.823470 ATGTGCGTGTGTGCCAAGT 60.823 52.632 0.00 0.00 0.00 3.16
2507 9348 1.370778 CATGTGCGTGTGTGCCAAG 60.371 57.895 0.00 0.00 0.00 3.61
2508 9349 2.720605 CATGTGCGTGTGTGCCAA 59.279 55.556 0.00 0.00 0.00 4.52
2513 9354 1.600636 CCTTCCCATGTGCGTGTGT 60.601 57.895 0.00 0.00 0.00 3.72
2515 9356 2.672996 GCCTTCCCATGTGCGTGT 60.673 61.111 0.00 0.00 0.00 4.49
2549 9390 2.223735 CGCCAACCGATTTCTAGCTAGA 60.224 50.000 19.72 19.72 40.02 2.43
2554 9395 0.804544 TCGCGCCAACCGATTTCTAG 60.805 55.000 0.00 0.00 40.02 2.43
2573 9414 6.653740 GCGCCAAGTTATTTCTAGGGTAATAT 59.346 38.462 0.00 0.00 0.00 1.28
2574 9415 5.993441 GCGCCAAGTTATTTCTAGGGTAATA 59.007 40.000 0.00 0.00 0.00 0.98
2585 9426 0.948678 ACGTGTGCGCCAAGTTATTT 59.051 45.000 4.18 0.00 42.83 1.40
2626 9467 6.095021 TCCGCTGTATAGATAGTTTCGCATAT 59.905 38.462 0.00 0.00 0.00 1.78
2646 9487 5.071250 TGGTTACCAAGATAATACATCCGCT 59.929 40.000 0.00 0.00 0.00 5.52
2701 9542 9.621629 CATGGGAAATACTGGTTACAAATAGTA 57.378 33.333 0.00 0.00 0.00 1.82
2702 9543 8.333235 TCATGGGAAATACTGGTTACAAATAGT 58.667 33.333 0.00 0.00 0.00 2.12
2703 9544 8.621286 GTCATGGGAAATACTGGTTACAAATAG 58.379 37.037 0.00 0.00 0.00 1.73
2810 9660 3.991367 ACTAAACTTCTGAGGAACCGTG 58.009 45.455 0.00 0.00 0.00 4.94
2937 9794 4.796038 ATGAGGCAAGATTTCCAAACAG 57.204 40.909 0.00 0.00 0.00 3.16
2939 9796 8.552083 AAATAAATGAGGCAAGATTTCCAAAC 57.448 30.769 0.00 0.00 0.00 2.93
2999 9857 4.883026 GCATGTTGCCTGCTTGAG 57.117 55.556 0.00 0.00 37.42 3.02
3050 9911 1.063006 CATGCATTCGAGTTGCCCG 59.937 57.895 16.81 6.81 39.39 6.13


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

AutoCloner maintained by Alex Coulton.