Multiple sequence alignment - TraesCS6D01G054400

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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 TraesCS6D01G054400 chr6D 100.000 3202 0 0 1 3202 25806088 25802887 0.000000e+00 5914.0
1 TraesCS6D01G054400 chr6D 80.715 1343 186 48 895 2211 25852752 25851457 0.000000e+00 977.0
2 TraesCS6D01G054400 chr6D 85.440 886 102 19 1339 2204 25879821 25878943 0.000000e+00 896.0
3 TraesCS6D01G054400 chr6D 80.693 1155 147 53 448 1568 25914426 25915538 0.000000e+00 828.0
4 TraesCS6D01G054400 chr6D 83.836 730 86 21 1626 2338 25915637 25916351 0.000000e+00 665.0
5 TraesCS6D01G054400 chr6D 81.950 482 67 11 778 1250 25880325 25879855 1.080000e-104 390.0
6 TraesCS6D01G054400 chr6D 81.856 485 60 11 785 1250 25827831 25827356 1.800000e-102 383.0
7 TraesCS6D01G054400 chr6D 86.029 272 13 4 2955 3202 448541357 448541627 5.270000e-68 268.0
8 TraesCS6D01G054400 chr6D 75.741 371 70 18 1797 2157 90924110 90924470 5.490000e-38 169.0
9 TraesCS6D01G054400 chr6D 88.679 53 6 0 1497 1549 89308603 89308551 7.410000e-07 65.8
10 TraesCS6D01G054400 chr6B 91.827 2447 119 30 4 2402 42006755 42004342 0.000000e+00 3336.0
11 TraesCS6D01G054400 chr6B 84.321 861 113 14 1359 2211 42393374 42394220 0.000000e+00 822.0
12 TraesCS6D01G054400 chr6B 79.553 851 123 33 425 1250 42392470 42393294 7.760000e-156 560.0
13 TraesCS6D01G054400 chr6B 81.560 564 82 15 2400 2954 52509702 52510252 2.270000e-121 446.0
14 TraesCS6D01G054400 chr6B 81.383 564 83 15 2400 2954 52541290 52541840 1.050000e-119 440.0
15 TraesCS6D01G054400 chr6B 80.515 544 66 18 730 1250 42212263 42211737 6.480000e-102 381.0
16 TraesCS6D01G054400 chr6B 87.451 255 23 5 2949 3199 1436623 1436872 5.230000e-73 285.0
17 TraesCS6D01G054400 chr6B 80.519 385 51 14 873 1250 42318991 42318624 1.130000e-69 274.0
18 TraesCS6D01G054400 chr6A 92.804 1084 48 13 1261 2326 23896483 23895412 0.000000e+00 1543.0
19 TraesCS6D01G054400 chr6A 80.040 1994 244 102 425 2338 24048069 24049988 0.000000e+00 1336.0
20 TraesCS6D01G054400 chr6A 94.025 887 38 9 388 1263 23897404 23896522 0.000000e+00 1330.0
21 TraesCS6D01G054400 chr6A 83.616 1001 122 33 1332 2305 24031142 24030157 0.000000e+00 902.0
22 TraesCS6D01G054400 chr6A 88.889 558 47 6 2400 2954 595940549 595941094 0.000000e+00 673.0
23 TraesCS6D01G054400 chr6A 79.289 647 85 30 619 1250 24031807 24031195 1.070000e-109 407.0
24 TraesCS6D01G054400 chr6A 75.405 370 73 17 1797 2157 109137111 109137471 2.560000e-36 163.0
25 TraesCS6D01G054400 chr1D 93.322 569 20 9 2402 2954 439356296 439356862 0.000000e+00 824.0
26 TraesCS6D01G054400 chr1D 92.820 571 23 8 2402 2954 12361635 12362205 0.000000e+00 811.0
27 TraesCS6D01G054400 chr1D 92.091 569 29 8 2402 2954 473432877 473432309 0.000000e+00 787.0
28 TraesCS6D01G054400 chr1D 87.726 277 10 2 2949 3202 12362395 12362670 5.190000e-78 302.0
29 TraesCS6D01G054400 chr1D 87.004 277 12 3 2949 3202 13521099 13521374 1.120000e-74 291.0
30 TraesCS6D01G054400 chr1D 86.282 277 14 3 2949 3202 475468541 475468816 2.430000e-71 279.0
31 TraesCS6D01G054400 chr1D 86.282 277 13 3 2949 3202 473432117 473431843 8.750000e-71 278.0
32 TraesCS6D01G054400 chr1D 85.971 278 14 4 2949 3202 427856991 427856715 1.130000e-69 274.0
33 TraesCS6D01G054400 chr1D 92.857 42 3 0 1497 1538 81726354 81726395 9.590000e-06 62.1
34 TraesCS6D01G054400 chr1D 81.333 75 14 0 1453 1527 302879256 302879182 9.590000e-06 62.1
35 TraesCS6D01G054400 chr1D 91.111 45 4 0 1497 1541 467611680 467611636 9.590000e-06 62.1
36 TraesCS6D01G054400 chr3D 92.970 569 24 8 2402 2954 37521892 37521324 0.000000e+00 815.0
37 TraesCS6D01G054400 chr3D 92.430 568 27 8 2403 2954 437469345 437468778 0.000000e+00 797.0
38 TraesCS6D01G054400 chr3D 92.267 569 27 8 2402 2954 506159158 506158591 0.000000e+00 791.0
39 TraesCS6D01G054400 chr3D 90.244 574 30 11 2398 2954 25209167 25208603 0.000000e+00 726.0
40 TraesCS6D01G054400 chr3D 90.196 255 22 3 2949 3202 590207806 590208058 2.380000e-86 329.0
41 TraesCS6D01G054400 chr3D 88.448 277 8 2 2949 3202 8326058 8325783 2.400000e-81 313.0
42 TraesCS6D01G054400 chr3D 88.087 277 9 2 2949 3202 437468590 437468315 1.120000e-79 307.0
43 TraesCS6D01G054400 chr3D 85.971 278 14 4 2949 3202 61909089 61909365 1.130000e-69 274.0
44 TraesCS6D01G054400 chr2D 92.945 567 24 7 2401 2951 605423846 605424412 0.000000e+00 811.0
45 TraesCS6D01G054400 chr2D 92.055 579 25 12 2393 2954 641989982 641990556 0.000000e+00 795.0
46 TraesCS6D01G054400 chr7A 81.954 1003 131 29 1341 2305 670946942 670945952 0.000000e+00 804.0
47 TraesCS6D01G054400 chr7D 92.469 571 26 9 2400 2954 27036664 27036095 0.000000e+00 800.0
48 TraesCS6D01G054400 chr7D 83.314 863 110 18 1364 2200 579100024 579099170 0.000000e+00 765.0
49 TraesCS6D01G054400 chr7D 90.361 581 36 11 2390 2954 56958976 56959552 0.000000e+00 745.0
50 TraesCS6D01G054400 chr7D 82.783 575 84 14 1632 2199 75948184 75948750 1.720000e-137 499.0
51 TraesCS6D01G054400 chr7D 90.347 259 19 3 2949 3202 637038245 637037988 5.120000e-88 335.0
52 TraesCS6D01G054400 chr7D 88.809 277 7 3 2949 3202 41081958 41081683 5.150000e-83 318.0
53 TraesCS6D01G054400 chr7D 76.562 512 99 17 1632 2135 478328201 478328699 8.810000e-66 261.0
54 TraesCS6D01G054400 chr7D 76.078 510 90 25 1639 2135 478571983 478571493 1.480000e-58 237.0
55 TraesCS6D01G054400 chr7D 76.978 417 82 11 1795 2209 478891827 478891423 3.210000e-55 226.0
56 TraesCS6D01G054400 chr7D 88.000 175 13 4 2399 2570 580502389 580502558 1.950000e-47 200.0
57 TraesCS6D01G054400 chr7D 77.124 153 33 2 1415 1566 478576073 478576224 1.580000e-13 87.9
58 TraesCS6D01G054400 chr7B 81.478 1015 129 42 1336 2305 643462539 643463539 0.000000e+00 778.0
59 TraesCS6D01G054400 chr7B 86.690 571 73 3 1639 2208 643292159 643291591 5.830000e-177 630.0
60 TraesCS6D01G054400 chr7B 83.216 709 98 14 1614 2305 643295755 643295051 5.830000e-177 630.0
61 TraesCS6D01G054400 chr7B 81.185 287 43 9 969 1251 643462183 643462462 1.500000e-53 220.0
62 TraesCS6D01G054400 chr5A 81.475 556 84 13 2402 2952 644563565 644563024 3.790000e-119 438.0
63 TraesCS6D01G054400 chr3A 81.475 556 82 16 2402 2952 18236057 18236596 1.360000e-118 436.0
64 TraesCS6D01G054400 chr4A 80.576 556 88 14 2402 2952 577809594 577810134 8.270000e-111 411.0
65 TraesCS6D01G054400 chr1A 87.365 277 10 4 2949 3202 526649187 526649461 8.690000e-76 294.0
66 TraesCS6D01G054400 chr5D 89.655 58 6 0 1495 1552 124857534 124857477 1.230000e-09 75.0
67 TraesCS6D01G054400 chr5D 90.566 53 5 0 1497 1549 393801777 393801725 1.590000e-08 71.3
68 TraesCS6D01G054400 chr4D 93.182 44 3 0 1498 1541 394378970 394378927 7.410000e-07 65.8
69 TraesCS6D01G054400 chr4D 79.545 88 16 2 1441 1527 394361964 394362050 9.590000e-06 62.1


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 TraesCS6D01G054400 chr6D 25802887 25806088 3201 True 5914.0 5914 100.0000 1 3202 1 chr6D.!!$R1 3201
1 TraesCS6D01G054400 chr6D 25851457 25852752 1295 True 977.0 977 80.7150 895 2211 1 chr6D.!!$R3 1316
2 TraesCS6D01G054400 chr6D 25914426 25916351 1925 False 746.5 828 82.2645 448 2338 2 chr6D.!!$F3 1890
3 TraesCS6D01G054400 chr6D 25878943 25880325 1382 True 643.0 896 83.6950 778 2204 2 chr6D.!!$R5 1426
4 TraesCS6D01G054400 chr6B 42004342 42006755 2413 True 3336.0 3336 91.8270 4 2402 1 chr6B.!!$R1 2398
5 TraesCS6D01G054400 chr6B 42392470 42394220 1750 False 691.0 822 81.9370 425 2211 2 chr6B.!!$F4 1786
6 TraesCS6D01G054400 chr6B 52509702 52510252 550 False 446.0 446 81.5600 2400 2954 1 chr6B.!!$F2 554
7 TraesCS6D01G054400 chr6B 52541290 52541840 550 False 440.0 440 81.3830 2400 2954 1 chr6B.!!$F3 554
8 TraesCS6D01G054400 chr6B 42211737 42212263 526 True 381.0 381 80.5150 730 1250 1 chr6B.!!$R2 520
9 TraesCS6D01G054400 chr6A 23895412 23897404 1992 True 1436.5 1543 93.4145 388 2326 2 chr6A.!!$R1 1938
10 TraesCS6D01G054400 chr6A 24048069 24049988 1919 False 1336.0 1336 80.0400 425 2338 1 chr6A.!!$F1 1913
11 TraesCS6D01G054400 chr6A 595940549 595941094 545 False 673.0 673 88.8890 2400 2954 1 chr6A.!!$F3 554
12 TraesCS6D01G054400 chr6A 24030157 24031807 1650 True 654.5 902 81.4525 619 2305 2 chr6A.!!$R2 1686
13 TraesCS6D01G054400 chr1D 439356296 439356862 566 False 824.0 824 93.3220 2402 2954 1 chr1D.!!$F3 552
14 TraesCS6D01G054400 chr1D 12361635 12362670 1035 False 556.5 811 90.2730 2402 3202 2 chr1D.!!$F5 800
15 TraesCS6D01G054400 chr1D 473431843 473432877 1034 True 532.5 787 89.1865 2402 3202 2 chr1D.!!$R4 800
16 TraesCS6D01G054400 chr3D 37521324 37521892 568 True 815.0 815 92.9700 2402 2954 1 chr3D.!!$R3 552
17 TraesCS6D01G054400 chr3D 506158591 506159158 567 True 791.0 791 92.2670 2402 2954 1 chr3D.!!$R4 552
18 TraesCS6D01G054400 chr3D 25208603 25209167 564 True 726.0 726 90.2440 2398 2954 1 chr3D.!!$R2 556
19 TraesCS6D01G054400 chr3D 437468315 437469345 1030 True 552.0 797 90.2585 2403 3202 2 chr3D.!!$R5 799
20 TraesCS6D01G054400 chr2D 605423846 605424412 566 False 811.0 811 92.9450 2401 2951 1 chr2D.!!$F1 550
21 TraesCS6D01G054400 chr2D 641989982 641990556 574 False 795.0 795 92.0550 2393 2954 1 chr2D.!!$F2 561
22 TraesCS6D01G054400 chr7A 670945952 670946942 990 True 804.0 804 81.9540 1341 2305 1 chr7A.!!$R1 964
23 TraesCS6D01G054400 chr7D 27036095 27036664 569 True 800.0 800 92.4690 2400 2954 1 chr7D.!!$R1 554
24 TraesCS6D01G054400 chr7D 579099170 579100024 854 True 765.0 765 83.3140 1364 2200 1 chr7D.!!$R5 836
25 TraesCS6D01G054400 chr7D 56958976 56959552 576 False 745.0 745 90.3610 2390 2954 1 chr7D.!!$F1 564
26 TraesCS6D01G054400 chr7D 75948184 75948750 566 False 499.0 499 82.7830 1632 2199 1 chr7D.!!$F2 567
27 TraesCS6D01G054400 chr7B 643291591 643295755 4164 True 630.0 630 84.9530 1614 2305 2 chr7B.!!$R1 691
28 TraesCS6D01G054400 chr7B 643462183 643463539 1356 False 499.0 778 81.3315 969 2305 2 chr7B.!!$F1 1336
29 TraesCS6D01G054400 chr5A 644563024 644563565 541 True 438.0 438 81.4750 2402 2952 1 chr5A.!!$R1 550
30 TraesCS6D01G054400 chr3A 18236057 18236596 539 False 436.0 436 81.4750 2402 2952 1 chr3A.!!$F1 550
31 TraesCS6D01G054400 chr4A 577809594 577810134 540 False 411.0 411 80.5760 2402 2952 1 chr4A.!!$F1 550

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
275 295 1.710244 TGGAACCATGTGGGAGATTGT 59.290 47.619 3.77 0.0 41.15 2.71 F
1022 1112 0.964358 GCTTCCAGTTCCAGCTGCAT 60.964 55.000 8.66 0.0 35.28 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 4075 0.458669 CGACCAGGTTGCGGTAGTAT 59.541 55.0 0.00 0.0 36.69 2.12 R
2605 4778 0.109458 CGGTTCCTGTCACGAATCGA 60.109 55.0 10.55 0.0 44.69 3.59 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
43 44 9.453572 GCATCCCTATATGTCTCATCAATTAAA 57.546 33.333 0.00 0.00 0.00 1.52
71 72 9.610705 TTCATGGTTCAAATTTGATTTCAGAAA 57.389 25.926 21.10 13.45 37.00 2.52
98 99 7.424227 TGGAACAAATTTTGCTGATTTCATC 57.576 32.000 9.04 0.00 31.92 2.92
113 114 9.875675 GCTGATTTCATCTTTATATGTCTCAAC 57.124 33.333 0.00 0.00 0.00 3.18
118 119 7.770801 TCATCTTTATATGTCTCAACCAACG 57.229 36.000 0.00 0.00 0.00 4.10
132 133 1.885560 CCAACGTTGATGGTGGTGTA 58.114 50.000 29.35 0.00 33.08 2.90
146 147 7.450014 TGATGGTGGTGTACTATGAATGTTTTT 59.550 33.333 0.00 0.00 29.68 1.94
225 245 5.926542 CCTTGAAGACTTCGACAGATGTTTA 59.073 40.000 10.56 0.00 35.27 2.01
267 287 8.292444 TCTATTAAGATTTTGGAACCATGTGG 57.708 34.615 0.00 0.00 42.17 4.17
275 295 1.710244 TGGAACCATGTGGGAGATTGT 59.290 47.619 3.77 0.00 41.15 2.71
296 316 9.295825 GATTGTAAAATGTGTCATATATCCCCA 57.704 33.333 0.00 0.00 0.00 4.96
297 317 9.827198 ATTGTAAAATGTGTCATATATCCCCAT 57.173 29.630 0.00 0.00 0.00 4.00
304 325 7.822161 TGTGTCATATATCCCCATTTTTCAG 57.178 36.000 0.00 0.00 0.00 3.02
319 340 5.576447 TTTTTCAGTGAAGTTTCCAGGAC 57.424 39.130 5.56 0.00 0.00 3.85
336 357 7.278461 TCCAGGACGTTTCAAATATTTCAAA 57.722 32.000 0.00 0.00 0.00 2.69
402 423 8.345565 CAGCAACATTAATACATAACTCTTCCC 58.654 37.037 0.00 0.00 0.00 3.97
403 424 8.052748 AGCAACATTAATACATAACTCTTCCCA 58.947 33.333 0.00 0.00 0.00 4.37
412 433 9.975218 AATACATAACTCTTCCCACAAAAGTAT 57.025 29.630 0.00 0.00 0.00 2.12
478 499 6.948309 ACTGCTCTTATGGTTCCTTAATTGTT 59.052 34.615 0.00 0.00 0.00 2.83
534 557 6.127925 TGGAATTGTTGCTATCACATGACTTC 60.128 38.462 0.00 0.00 0.00 3.01
950 1013 4.020543 AGCAAACTACTACTGAGCTAGCT 58.979 43.478 19.45 19.45 0.00 3.32
954 1018 6.674066 CAAACTACTACTGAGCTAGCTATCC 58.326 44.000 19.38 6.05 0.00 2.59
1022 1112 0.964358 GCTTCCAGTTCCAGCTGCAT 60.964 55.000 8.66 0.00 35.28 3.96
1276 1409 3.964909 TCTCCGTACATTCATGTCGATG 58.035 45.455 11.13 0.00 41.97 3.84
1575 1752 7.255569 CACTTCTCTGGTACGTACAATCAATA 58.744 38.462 26.02 6.54 0.00 1.90
1580 1757 7.284716 TCTCTGGTACGTACAATCAATAGACAT 59.715 37.037 26.02 0.00 0.00 3.06
1584 1761 7.147966 TGGTACGTACAATCAATAGACATCTGT 60.148 37.037 26.02 0.00 0.00 3.41
1694 3784 3.733960 CAGGACTCGACGACGGCA 61.734 66.667 7.55 0.00 40.21 5.69
1727 3817 3.241530 AACAGCGACCTCCCAGCA 61.242 61.111 0.00 0.00 0.00 4.41
1985 4075 2.014554 GCTCGTCTTCGACAACGCA 61.015 57.895 12.61 3.38 41.35 5.24
2189 4279 4.586235 AGGCGCAACTGCAGGGTT 62.586 61.111 19.93 1.43 42.21 4.11
2232 4354 0.032540 TCATCCATCGGCTCACATCG 59.967 55.000 0.00 0.00 0.00 3.84
2359 4515 2.232452 GCTGGCTAGTTCAGAAGTGAGA 59.768 50.000 16.03 0.00 32.98 3.27
2374 4531 3.185455 AGTGAGATTAGCAACCCTCCTT 58.815 45.455 0.00 0.00 0.00 3.36
2389 4546 0.914417 TCCTTCTCGGCTGGGGATTT 60.914 55.000 0.00 0.00 0.00 2.17
2416 4573 4.617253 TGCCTGCACTAGTAGAAAAAGA 57.383 40.909 3.59 0.00 0.00 2.52
2471 4630 4.308458 CTGCCACGAACCGGGACA 62.308 66.667 6.32 0.00 28.17 4.02
2556 4729 1.546773 CCCATTTGTCCCGGTTCTTGA 60.547 52.381 0.00 0.00 0.00 3.02
2575 4748 1.004320 CACGAACCGGGACCAATGA 60.004 57.895 6.32 0.00 28.17 2.57
2605 4778 1.004745 CTGGCCCACAACTATTGGTCT 59.995 52.381 0.00 0.00 31.46 3.85
2615 4788 4.082408 ACAACTATTGGTCTCGATTCGTGA 60.082 41.667 5.89 6.34 34.12 4.35
2642 4815 1.604915 GGGACAGAAGGAAGGCCTC 59.395 63.158 5.23 0.00 46.28 4.70
2816 4995 1.338674 TGTTCGATGAAATGCCCGAGT 60.339 47.619 0.00 0.00 32.41 4.18
2829 5008 2.629137 TGCCCGAGTCACACTAGTTAAA 59.371 45.455 0.00 0.00 0.00 1.52
2845 5024 7.866393 CACTAGTTAAACTTTCTCCTCTCGAAA 59.134 37.037 0.00 0.00 0.00 3.46
2907 5087 4.362279 GTTTATATTAGCGGTCCGTCACA 58.638 43.478 13.94 0.00 0.00 3.58
2973 5349 1.484038 AAGTGGCTGAGGCAAACAAA 58.516 45.000 11.29 0.00 40.46 2.83
2999 5375 7.178983 ACAGAATGGTTTTATGTGATGTCCATT 59.821 33.333 6.28 6.28 43.75 3.16
3045 5421 5.182760 GTCTTACTCTGACTCGAAAACCCTA 59.817 44.000 0.00 0.00 0.00 3.53
3085 5461 2.726821 AGGGTTTCATGCCACACTATG 58.273 47.619 0.00 0.00 0.00 2.23
3104 5503 7.294720 ACACTATGATAGGGGTTATGATGGAAA 59.705 37.037 6.67 0.00 32.03 3.13
3119 5518 6.443934 TGATGGAAAACAACGAAGAAGAAA 57.556 33.333 0.00 0.00 0.00 2.52
3130 5529 4.628074 ACGAAGAAGAAAAGGACGATGAA 58.372 39.130 0.00 0.00 0.00 2.57
3168 5567 3.803082 CGGTGATGCTGCAACGGG 61.803 66.667 6.36 0.00 44.76 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.454858 AGGGATGCTCCTTAGTGAGAAA 58.545 45.455 2.65 0.00 36.57 2.52
5 6 2.856760 AGGGATGCTCCTTAGTGAGA 57.143 50.000 2.65 0.00 36.57 3.27
8 9 5.719085 AGACATATAGGGATGCTCCTTAGTG 59.281 44.000 0.00 4.46 38.30 2.74
43 44 8.423349 TCTGAAATCAAATTTGAACCATGAACT 58.577 29.630 23.91 2.25 41.13 3.01
71 72 8.223177 TGAAATCAGCAAAATTTGTTCCATTT 57.777 26.923 7.60 7.85 0.00 2.32
113 114 1.533731 GTACACCACCATCAACGTTGG 59.466 52.381 27.02 15.60 40.26 3.77
114 115 2.489971 AGTACACCACCATCAACGTTG 58.510 47.619 22.35 22.35 0.00 4.10
118 119 5.880332 ACATTCATAGTACACCACCATCAAC 59.120 40.000 0.00 0.00 0.00 3.18
121 122 7.391148 AAAACATTCATAGTACACCACCATC 57.609 36.000 0.00 0.00 0.00 3.51
146 147 7.211573 TCTGGAACGAACTAGTATTGTGAAAA 58.788 34.615 0.00 0.00 0.00 2.29
151 152 8.064336 ACTTATCTGGAACGAACTAGTATTGT 57.936 34.615 0.00 0.00 0.00 2.71
155 156 6.810182 GCAAACTTATCTGGAACGAACTAGTA 59.190 38.462 0.00 0.00 0.00 1.82
157 158 5.637810 TGCAAACTTATCTGGAACGAACTAG 59.362 40.000 0.00 0.00 0.00 2.57
158 159 5.543714 TGCAAACTTATCTGGAACGAACTA 58.456 37.500 0.00 0.00 0.00 2.24
296 316 5.221048 CGTCCTGGAAACTTCACTGAAAAAT 60.221 40.000 0.00 0.00 0.00 1.82
297 317 4.095782 CGTCCTGGAAACTTCACTGAAAAA 59.904 41.667 0.00 0.00 0.00 1.94
302 323 2.240493 ACGTCCTGGAAACTTCACTG 57.760 50.000 0.00 0.00 0.00 3.66
304 325 2.940410 TGAAACGTCCTGGAAACTTCAC 59.060 45.455 0.00 0.00 0.00 3.18
377 398 8.052748 TGGGAAGAGTTATGTATTAATGTTGCT 58.947 33.333 0.00 0.00 0.00 3.91
402 423 8.531530 GGCAAGCGAATTAAATATACTTTTGTG 58.468 33.333 0.00 0.00 0.00 3.33
403 424 8.466798 AGGCAAGCGAATTAAATATACTTTTGT 58.533 29.630 0.00 0.00 0.00 2.83
412 433 4.947388 AGTGGAAGGCAAGCGAATTAAATA 59.053 37.500 0.00 0.00 0.00 1.40
505 528 3.245229 TGTGATAGCAACAATTCCAGGGT 60.245 43.478 0.00 0.00 0.00 4.34
534 557 7.832503 TGCCGTGATGAATATATGTAATCAG 57.167 36.000 5.79 0.00 0.00 2.90
925 988 5.744819 GCTAGCTCAGTAGTAGTTTGCTTAC 59.255 44.000 7.70 0.00 0.00 2.34
973 1040 7.012799 GGCTCACAAATTTATCTAGCTAAGCTT 59.987 37.037 3.48 3.48 40.44 3.74
1011 1101 2.055633 CCATGCCATGCAGCTGGAA 61.056 57.895 13.45 0.00 43.65 3.53
1427 1604 1.301423 CCGAGTTCACGTTGGGAAAA 58.699 50.000 0.00 0.00 0.00 2.29
1575 1752 6.824553 ACTATTCATGCACATACAGATGTCT 58.175 36.000 0.00 0.00 44.82 3.41
1580 1757 9.264719 CATAAGAACTATTCATGCACATACAGA 57.735 33.333 0.00 0.00 0.00 3.41
1584 1761 7.933033 TCAGCATAAGAACTATTCATGCACATA 59.067 33.333 13.29 0.00 43.46 2.29
1694 3784 2.173519 CTGTTGGCCTCCATCATGTTT 58.826 47.619 3.32 0.00 33.46 2.83
1763 3853 1.970114 GCTCAGCTGCTTCTTGGCA 60.970 57.895 9.47 0.00 40.15 4.92
1985 4075 0.458669 CGACCAGGTTGCGGTAGTAT 59.541 55.000 0.00 0.00 36.69 2.12
2189 4279 2.568509 TGGATGAGATCAGCTGTTGACA 59.431 45.455 14.67 10.74 38.99 3.58
2232 4354 6.019398 GCCAACCAAACTTTACACATTTACAC 60.019 38.462 0.00 0.00 0.00 2.90
2294 4450 2.348666 CGAACCAGATTAACGGCTCTTG 59.651 50.000 0.00 0.00 0.00 3.02
2339 4495 4.734398 ATCTCACTTCTGAACTAGCCAG 57.266 45.455 6.44 6.44 0.00 4.85
2359 4515 1.486726 CCGAGAAGGAGGGTTGCTAAT 59.513 52.381 0.00 0.00 45.00 1.73
2374 4531 1.676678 CTCGAAATCCCCAGCCGAGA 61.677 60.000 0.00 0.00 46.62 4.04
2389 4546 1.950216 CTACTAGTGCAGGCATCTCGA 59.050 52.381 5.39 0.00 0.00 4.04
2416 4573 2.358737 CCAGGCCGAACGAAAGCT 60.359 61.111 0.00 0.00 0.00 3.74
2437 4596 1.200519 CAGAACCGGGACTAATGGGA 58.799 55.000 6.32 0.00 0.00 4.37
2471 4630 1.065854 CCTGGGCTCTCGAAGACATTT 60.066 52.381 3.41 0.00 32.94 2.32
2556 4729 1.302192 CATTGGTCCCGGTTCGTGT 60.302 57.895 0.00 0.00 0.00 4.49
2605 4778 0.109458 CGGTTCCTGTCACGAATCGA 60.109 55.000 10.55 0.00 44.69 3.59
2615 4788 1.481056 CCTTCTGTCCCGGTTCCTGT 61.481 60.000 0.00 0.00 0.00 4.00
2816 4995 7.521748 CGAGAGGAGAAAGTTTAACTAGTGTGA 60.522 40.741 0.00 0.00 0.00 3.58
2829 5008 3.147629 TCGAGTTTCGAGAGGAGAAAGT 58.852 45.455 0.00 0.00 44.82 2.66
2973 5349 6.009589 TGGACATCACATAAAACCATTCTGT 58.990 36.000 0.00 0.00 0.00 3.41
3045 5421 3.561313 CCTTATAAAGCAGGTGGGTGTGT 60.561 47.826 0.00 0.00 0.00 3.72
3085 5461 6.238648 CGTTGTTTTCCATCATAACCCCTATC 60.239 42.308 0.00 0.00 0.00 2.08
3104 5503 4.186159 TCGTCCTTTTCTTCTTCGTTGTT 58.814 39.130 0.00 0.00 0.00 2.83
3119 5518 3.689649 GGCACATAGTTTTCATCGTCCTT 59.310 43.478 0.00 0.00 0.00 3.36
3130 5529 3.684413 CGTATTCAGGGGGCACATAGTTT 60.684 47.826 0.00 0.00 0.00 2.66
3168 5567 2.015587 CTTGATCTTCAGCAGCTTCCC 58.984 52.381 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.