Multiple sequence alignment - TraesCS3D01G523400

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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 TraesCS3D01G523400 chr3D 100.000 3738 0 0 1 3738 604126001 604122264 0.000000e+00 6903
1 TraesCS3D01G523400 chr3D 90.220 2638 203 20 870 3454 602800014 602797379 0.000000e+00 3391
2 TraesCS3D01G523400 chr3D 89.765 1573 134 18 1848 3398 604014855 604013288 0.000000e+00 1988
3 TraesCS3D01G523400 chr3D 81.978 1931 290 33 1373 3277 604137795 604135897 0.000000e+00 1585
4 TraesCS3D01G523400 chr3D 82.540 1701 252 17 1622 3292 603962728 603964413 0.000000e+00 1454
5 TraesCS3D01G523400 chr3D 81.413 1727 257 34 1602 3291 602803914 602802215 0.000000e+00 1352
6 TraesCS3D01G523400 chr3D 80.267 1723 273 33 1602 3291 603943578 603945266 0.000000e+00 1236
7 TraesCS3D01G523400 chr3D 100.000 526 0 0 3978 4503 604122024 604121499 0.000000e+00 972
8 TraesCS3D01G523400 chr3D 82.596 1040 140 30 873 1874 604024453 604023417 0.000000e+00 880
9 TraesCS3D01G523400 chr3D 82.683 999 139 11 870 1836 604026869 604025873 0.000000e+00 856
10 TraesCS3D01G523400 chr3D 95.817 526 22 0 3978 4503 593370887 593370362 0.000000e+00 850
11 TraesCS3D01G523400 chr3D 81.870 1048 142 29 870 1878 604021564 604020526 0.000000e+00 839
12 TraesCS3D01G523400 chr3D 95.057 526 25 1 3978 4503 300831594 300832118 0.000000e+00 826
13 TraesCS3D01G523400 chr3D 95.122 82 4 0 3394 3475 604009755 604009674 3.660000e-26 130
14 TraesCS3D01G523400 chr3B 94.024 3514 148 17 1 3475 811114599 811111109 0.000000e+00 5269
15 TraesCS3D01G523400 chr3B 90.261 2639 198 22 870 3454 810951737 810954370 0.000000e+00 3395
16 TraesCS3D01G523400 chr3B 82.449 1715 253 20 1622 3302 811079416 811081116 0.000000e+00 1456
17 TraesCS3D01G523400 chr3B 80.140 1712 266 46 1602 3291 811040798 811042457 0.000000e+00 1210
18 TraesCS3D01G523400 chr3A 93.011 3491 164 37 1 3475 733625326 733621900 0.000000e+00 5022
19 TraesCS3D01G523400 chr3A 90.571 2153 166 13 870 2986 733042967 733045118 0.000000e+00 2817
20 TraesCS3D01G523400 chr3A 88.498 1252 103 18 2255 3475 733532477 733531236 0.000000e+00 1476
21 TraesCS3D01G523400 chr3A 80.916 1724 269 31 1602 3291 733039285 733040982 0.000000e+00 1306
22 TraesCS3D01G523400 chr3A 80.606 1748 263 41 1602 3296 733860281 733858557 0.000000e+00 1280
23 TraesCS3D01G523400 chr3A 80.256 1722 287 30 1602 3291 733411474 733413174 0.000000e+00 1247
24 TraesCS3D01G523400 chr3A 79.977 1738 281 31 1602 3291 733333155 733334873 0.000000e+00 1219
25 TraesCS3D01G523400 chr3A 79.838 1726 289 34 1602 3291 733436269 733437971 0.000000e+00 1205
26 TraesCS3D01G523400 chr3A 80.861 1045 151 24 870 1874 733563754 733562719 0.000000e+00 776
27 TraesCS3D01G523400 chr3A 89.072 485 38 4 3006 3475 733045351 733045835 5.020000e-164 588
28 TraesCS3D01G523400 chr3A 86.826 501 64 2 1400 1898 733576216 733575716 3.930000e-155 558
29 TraesCS3D01G523400 chr3A 79.649 570 83 18 870 1410 733538330 733537765 3.290000e-101 379
30 TraesCS3D01G523400 chr3A 79.108 493 79 11 2809 3291 733715331 733714853 7.270000e-83 318
31 TraesCS3D01G523400 chrUn 81.243 1738 250 39 1602 3304 42260130 42261826 0.000000e+00 1334
32 TraesCS3D01G523400 chr5A 95.817 526 22 0 3978 4503 655094901 655095426 0.000000e+00 850
33 TraesCS3D01G523400 chr5A 95.247 526 23 2 3978 4503 709726027 709726550 0.000000e+00 832
34 TraesCS3D01G523400 chr1D 95.817 526 21 1 3978 4503 404677923 404678447 0.000000e+00 848
35 TraesCS3D01G523400 chr1D 92.218 257 18 2 3475 3731 404677637 404677891 3.310000e-96 363
36 TraesCS3D01G523400 chr1D 84.026 313 41 6 2 307 339318087 339318397 4.410000e-75 292
37 TraesCS3D01G523400 chr1D 79.100 311 37 11 2 307 454520217 454519930 5.950000e-44 189
38 TraesCS3D01G523400 chr2D 95.627 526 21 2 3978 4503 21146836 21147359 0.000000e+00 843
39 TraesCS3D01G523400 chr2D 91.011 267 18 5 3475 3738 95687999 95688262 5.540000e-94 355
40 TraesCS3D01G523400 chr2D 90.909 264 21 3 3476 3738 32141932 32141671 7.170000e-93 351
41 TraesCS3D01G523400 chr2D 90.805 261 22 2 3472 3732 10559513 10559771 9.270000e-92 348
42 TraesCS3D01G523400 chr7D 95.247 526 25 0 3978 4503 59560442 59560967 0.000000e+00 833
43 TraesCS3D01G523400 chr7D 83.706 313 42 6 2 307 555540589 555540899 2.050000e-73 287
44 TraesCS3D01G523400 chr7D 81.620 321 42 9 2 307 627617359 627617041 2.690000e-62 250
45 TraesCS3D01G523400 chr5D 95.048 525 25 1 3978 4502 119590619 119590096 0.000000e+00 824
46 TraesCS3D01G523400 chr5D 92.395 263 17 3 3476 3738 493677464 493677205 5.500000e-99 372
47 TraesCS3D01G523400 chr5D 91.667 264 20 2 3475 3738 534389331 534389070 9.210000e-97 364
48 TraesCS3D01G523400 chr5D 91.635 263 20 2 3476 3738 288903628 288903888 3.310000e-96 363
49 TraesCS3D01G523400 chr5D 91.255 263 20 2 3476 3738 493624160 493623901 5.540000e-94 355
50 TraesCS3D01G523400 chr1A 94.867 526 25 1 3978 4503 291559434 291558911 0.000000e+00 821
51 TraesCS3D01G523400 chr4A 90.262 267 23 3 3473 3738 687659215 687658951 3.330000e-91 346
52 TraesCS3D01G523400 chr2A 88.971 136 12 3 738 871 578117505 578117639 1.000000e-36 165
53 TraesCS3D01G523400 chr1B 82.114 123 21 1 743 865 68949642 68949763 2.220000e-18 104


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 TraesCS3D01G523400 chr3D 604121499 604126001 4502 True 3937.500000 6903 100.0000 1 4503 2 chr3D.!!$R6 4502
1 TraesCS3D01G523400 chr3D 602797379 602803914 6535 True 2371.500000 3391 85.8165 870 3454 2 chr3D.!!$R3 2584
2 TraesCS3D01G523400 chr3D 604135897 604137795 1898 True 1585.000000 1585 81.9780 1373 3277 1 chr3D.!!$R2 1904
3 TraesCS3D01G523400 chr3D 603962728 603964413 1685 False 1454.000000 1454 82.5400 1622 3292 1 chr3D.!!$F3 1670
4 TraesCS3D01G523400 chr3D 603943578 603945266 1688 False 1236.000000 1236 80.2670 1602 3291 1 chr3D.!!$F2 1689
5 TraesCS3D01G523400 chr3D 604009674 604014855 5181 True 1059.000000 1988 92.4435 1848 3475 2 chr3D.!!$R4 1627
6 TraesCS3D01G523400 chr3D 604020526 604026869 6343 True 858.333333 880 82.3830 870 1878 3 chr3D.!!$R5 1008
7 TraesCS3D01G523400 chr3D 593370362 593370887 525 True 850.000000 850 95.8170 3978 4503 1 chr3D.!!$R1 525
8 TraesCS3D01G523400 chr3D 300831594 300832118 524 False 826.000000 826 95.0570 3978 4503 1 chr3D.!!$F1 525
9 TraesCS3D01G523400 chr3B 811111109 811114599 3490 True 5269.000000 5269 94.0240 1 3475 1 chr3B.!!$R1 3474
10 TraesCS3D01G523400 chr3B 810951737 810954370 2633 False 3395.000000 3395 90.2610 870 3454 1 chr3B.!!$F1 2584
11 TraesCS3D01G523400 chr3B 811079416 811081116 1700 False 1456.000000 1456 82.4490 1622 3302 1 chr3B.!!$F3 1680
12 TraesCS3D01G523400 chr3B 811040798 811042457 1659 False 1210.000000 1210 80.1400 1602 3291 1 chr3B.!!$F2 1689
13 TraesCS3D01G523400 chr3A 733621900 733625326 3426 True 5022.000000 5022 93.0110 1 3475 1 chr3A.!!$R5 3474
14 TraesCS3D01G523400 chr3A 733039285 733045835 6550 False 1570.333333 2817 86.8530 870 3475 3 chr3A.!!$F4 2605
15 TraesCS3D01G523400 chr3A 733531236 733532477 1241 True 1476.000000 1476 88.4980 2255 3475 1 chr3A.!!$R1 1220
16 TraesCS3D01G523400 chr3A 733858557 733860281 1724 True 1280.000000 1280 80.6060 1602 3296 1 chr3A.!!$R7 1694
17 TraesCS3D01G523400 chr3A 733411474 733413174 1700 False 1247.000000 1247 80.2560 1602 3291 1 chr3A.!!$F2 1689
18 TraesCS3D01G523400 chr3A 733333155 733334873 1718 False 1219.000000 1219 79.9770 1602 3291 1 chr3A.!!$F1 1689
19 TraesCS3D01G523400 chr3A 733436269 733437971 1702 False 1205.000000 1205 79.8380 1602 3291 1 chr3A.!!$F3 1689
20 TraesCS3D01G523400 chr3A 733562719 733563754 1035 True 776.000000 776 80.8610 870 1874 1 chr3A.!!$R3 1004
21 TraesCS3D01G523400 chr3A 733575716 733576216 500 True 558.000000 558 86.8260 1400 1898 1 chr3A.!!$R4 498
22 TraesCS3D01G523400 chr3A 733537765 733538330 565 True 379.000000 379 79.6490 870 1410 1 chr3A.!!$R2 540
23 TraesCS3D01G523400 chrUn 42260130 42261826 1696 False 1334.000000 1334 81.2430 1602 3304 1 chrUn.!!$F1 1702
24 TraesCS3D01G523400 chr5A 655094901 655095426 525 False 850.000000 850 95.8170 3978 4503 1 chr5A.!!$F1 525
25 TraesCS3D01G523400 chr5A 709726027 709726550 523 False 832.000000 832 95.2470 3978 4503 1 chr5A.!!$F2 525
26 TraesCS3D01G523400 chr1D 404677637 404678447 810 False 605.500000 848 94.0175 3475 4503 2 chr1D.!!$F2 1028
27 TraesCS3D01G523400 chr2D 21146836 21147359 523 False 843.000000 843 95.6270 3978 4503 1 chr2D.!!$F2 525
28 TraesCS3D01G523400 chr7D 59560442 59560967 525 False 833.000000 833 95.2470 3978 4503 1 chr7D.!!$F1 525
29 TraesCS3D01G523400 chr5D 119590096 119590619 523 True 824.000000 824 95.0480 3978 4502 1 chr5D.!!$R1 524
30 TraesCS3D01G523400 chr1A 291558911 291559434 523 True 821.000000 821 94.8670 3978 4503 1 chr1A.!!$R1 525

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
669 671 0.250166 ACAAGCGAGTTACCCCACAC 60.25 55.0 0.0 0.0 0.0 3.82 F
1197 4262 0.040425 GCCACATCGAACACCAACAC 60.04 55.0 0.0 0.0 0.0 3.32 F
2409 8030 0.320073 CGTTCTGCCCCGTACTGAAA 60.32 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2526 8150 2.781667 AGATAGAGGATGGCCACCTTT 58.218 47.619 22.78 20.02 37.93 3.11 R
2790 8481 1.241165 TCGAGCCGAGTAAACACAGA 58.759 50.000 0.00 0.00 0.00 3.41 R
3676 13236 0.388520 GCGTGGATGCTTTTTGGTCC 60.389 55.000 0.00 0.00 0.00 4.46 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
106 107 9.638239 GAGCAATTGGTATATTCTAAGAGAGAG 57.362 37.037 10.70 0.00 34.93 3.20
136 137 1.814394 GCCCAAAGGGTACTAAAACGG 59.186 52.381 3.68 0.00 46.51 4.44
158 159 4.000988 GCAAGGAAGTCGGAAGATACAAA 58.999 43.478 0.00 0.00 45.19 2.83
223 224 0.597568 CATGAAAGGCGCAGTTGGAA 59.402 50.000 10.83 0.00 0.00 3.53
307 309 3.006323 AGCGACCTGGAGATCATTACATC 59.994 47.826 0.00 0.00 0.00 3.06
324 326 7.607607 TCATTACATCCTTGCGCAAGATATATT 59.392 33.333 43.49 27.21 40.79 1.28
414 416 2.497675 CAAATCGAGGAGGAGAGGAACA 59.502 50.000 0.00 0.00 0.00 3.18
416 418 2.534042 TCGAGGAGGAGAGGAACAAT 57.466 50.000 0.00 0.00 0.00 2.71
527 529 4.190772 CACATGGCAAAACAGGAAAAACT 58.809 39.130 0.00 0.00 0.00 2.66
620 622 2.237643 ACGGGCCACATAGAACACATTA 59.762 45.455 4.39 0.00 0.00 1.90
669 671 0.250166 ACAAGCGAGTTACCCCACAC 60.250 55.000 0.00 0.00 0.00 3.82
675 677 0.677842 GAGTTACCCCACACGTCAGT 59.322 55.000 0.00 0.00 0.00 3.41
769 771 3.060615 CGAAGGTCGTCCGGGAGT 61.061 66.667 0.00 0.00 39.05 3.85
832 834 1.374190 CACCAGTGCCTGAGCTCTT 59.626 57.895 16.19 0.00 40.79 2.85
920 3980 3.446442 AGCCCAATTCTGAAGTCACAT 57.554 42.857 0.00 0.00 0.00 3.21
993 4054 1.078497 CCACGGCATGGCAGAAGTA 60.078 57.895 20.37 0.00 43.24 2.24
996 4061 1.221840 CGGCATGGCAGAAGTACCT 59.778 57.895 20.37 0.00 0.00 3.08
1138 4203 4.065281 CGCCGTCTCCTCCCGTTT 62.065 66.667 0.00 0.00 0.00 3.60
1169 4234 2.024319 GCAGAAACTGAGCGCGAGT 61.024 57.895 12.10 9.09 32.44 4.18
1197 4262 0.040425 GCCACATCGAACACCAACAC 60.040 55.000 0.00 0.00 0.00 3.32
1249 4315 7.364522 TCCTATTTCAGAGTCGAACAATTTG 57.635 36.000 0.00 0.00 0.00 2.32
1326 4447 2.300433 ACTGCTTGTTCACATGCTTGA 58.700 42.857 16.27 0.00 44.41 3.02
1339 4460 6.623486 TCACATGCTTGATTAGATTTGTTGG 58.377 36.000 6.60 0.00 0.00 3.77
1628 7167 1.953686 GCTTTTCAGCCTACCAACACA 59.046 47.619 0.00 0.00 40.61 3.72
1718 7258 3.670055 CGGCTGTTGCTTATTCTTTGTTG 59.330 43.478 0.00 0.00 39.59 3.33
2334 7955 2.820197 CCAAGGTTTCAAGAGCCTAACC 59.180 50.000 0.00 0.00 40.22 2.85
2371 7992 4.042062 ACAATTTCTCATCCACAGACAGGA 59.958 41.667 0.00 0.00 39.97 3.86
2409 8030 0.320073 CGTTCTGCCCCGTACTGAAA 60.320 55.000 0.00 0.00 0.00 2.69
2526 8150 6.104094 ACATTAATTTGGAGGCCCCTAATCTA 59.896 38.462 16.18 10.15 39.02 1.98
2623 8247 5.688807 ACCATATCAAGAAGTCATTGGGAG 58.311 41.667 0.00 0.00 0.00 4.30
2749 8440 0.608130 GTTGCCATTTCCCCCTTGTC 59.392 55.000 0.00 0.00 0.00 3.18
2790 8481 4.439968 GCGTATACTTACAAAGCTCCCTT 58.560 43.478 0.56 0.00 0.00 3.95
2804 8504 2.931320 GCTCCCTTCTGTGTTTACTCGG 60.931 54.545 0.00 0.00 0.00 4.63
2919 8623 1.519898 GCGGTGTGGGTACGTATGG 60.520 63.158 0.00 0.00 0.00 2.74
2989 8708 2.226330 TGCAACGCCTAATGAGTTGTT 58.774 42.857 9.83 0.00 44.88 2.83
2996 8715 7.619161 GCAACGCCTAATGAGTTGTTATTTTTG 60.619 37.037 9.83 0.00 44.88 2.44
2997 8716 5.861787 ACGCCTAATGAGTTGTTATTTTTGC 59.138 36.000 0.00 0.00 0.00 3.68
3219 9170 1.696063 AACAGACTGCAGCATGGTTT 58.304 45.000 15.27 1.34 35.86 3.27
3237 9188 9.709693 GCATGGTTTTTGCCAAGCTATTAGCTA 62.710 40.741 18.25 0.16 44.66 3.32
3304 9269 2.125326 CATGCTGCCCCATCACCTG 61.125 63.158 0.00 0.00 0.00 4.00
3305 9270 4.746309 TGCTGCCCCATCACCTGC 62.746 66.667 0.00 0.00 0.00 4.85
3428 12945 8.415950 ACATTTTGTGGGAGTATTTAATGTGA 57.584 30.769 0.00 0.00 34.67 3.58
3499 13016 3.961480 AGTAGAAAAAGGCCCATTTGC 57.039 42.857 8.01 4.92 0.00 3.68
3508 13025 2.283532 CCCATTTGCCCCGGTTCA 60.284 61.111 0.00 0.00 0.00 3.18
3549 13066 0.252197 CTGGAACCGGGACTAAAGGG 59.748 60.000 6.32 0.00 0.00 3.95
3550 13067 1.077930 GGAACCGGGACTAAAGGGC 60.078 63.158 6.32 0.00 0.00 5.19
3551 13068 1.077930 GAACCGGGACTAAAGGGCC 60.078 63.158 6.32 0.00 44.23 5.80
3552 13069 2.864378 GAACCGGGACTAAAGGGCCG 62.864 65.000 6.32 0.00 46.52 6.13
3555 13072 2.689771 GGGACTAAAGGGCCGGGA 60.690 66.667 2.18 0.00 46.52 5.14
3556 13073 2.303282 GGGACTAAAGGGCCGGGAA 61.303 63.158 2.18 0.00 46.52 3.97
3567 13126 0.973496 GGCCGGGAATAAAGCCCAAA 60.973 55.000 2.18 0.00 46.36 3.28
3570 13129 1.896465 CCGGGAATAAAGCCCAAAACA 59.104 47.619 0.00 0.00 46.36 2.83
3578 13137 6.816640 GGAATAAAGCCCAAAACATTTAGTCC 59.183 38.462 7.12 7.12 41.96 3.85
3584 13143 3.322541 CCCAAAACATTTAGTCCCGGTTT 59.677 43.478 0.00 0.00 33.45 3.27
3602 13161 0.322322 TTGCTTACGAACCGGGACAT 59.678 50.000 6.32 0.00 0.00 3.06
3685 13245 0.324460 ACACCAACCGGGACCAAAAA 60.324 50.000 6.32 0.00 41.15 1.94
3699 13297 0.040514 CAAAAAGCATCCACGCGTCA 60.041 50.000 9.86 0.00 36.85 4.35
3706 13304 0.867753 CATCCACGCGTCAGTAGCTC 60.868 60.000 9.86 0.00 0.00 4.09
3709 13307 1.515088 CACGCGTCAGTAGCTCAGG 60.515 63.158 9.86 0.00 0.00 3.86
3722 13320 3.633361 CTCAGGAGCCGGAGTTTTT 57.367 52.632 5.05 0.00 34.39 1.94
3723 13321 1.160137 CTCAGGAGCCGGAGTTTTTG 58.840 55.000 5.05 0.00 34.39 2.44
3724 13322 0.472471 TCAGGAGCCGGAGTTTTTGT 59.528 50.000 5.05 0.00 0.00 2.83
3725 13323 1.133915 TCAGGAGCCGGAGTTTTTGTT 60.134 47.619 5.05 0.00 0.00 2.83
4204 13804 6.438259 TGGTCGAACAACAAGTTTTCATAA 57.562 33.333 0.00 0.00 41.51 1.90
4311 14872 0.104120 CCGGCTGGATTGATGACGTA 59.896 55.000 5.28 0.00 37.49 3.57
4427 14988 5.296151 AGAGGGTCAATACATGTGTATGG 57.704 43.478 9.11 4.05 40.78 2.74
4448 15009 6.462552 TGGATGAAACTCAACACAAATGAA 57.537 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 3.247006 TGTATCTTCCGACTTCCTTGC 57.753 47.619 0.00 0.00 0.00 4.01
223 224 3.391665 CTCCCGCCAATCGCCTTCT 62.392 63.158 0.00 0.00 36.73 2.85
307 309 6.902341 ACAACATAATATATCTTGCGCAAGG 58.098 36.000 41.00 26.79 38.88 3.61
414 416 1.421646 CCATTCGCCCCCTTCTCTATT 59.578 52.381 0.00 0.00 0.00 1.73
416 418 1.054406 CCCATTCGCCCCCTTCTCTA 61.054 60.000 0.00 0.00 0.00 2.43
460 462 0.521735 CGTCGATGAGGTGTGAGACA 59.478 55.000 0.00 0.00 0.00 3.41
461 463 0.798771 GCGTCGATGAGGTGTGAGAC 60.799 60.000 9.31 0.00 0.00 3.36
495 497 2.751436 GCCATGTGCGTGGTGGAT 60.751 61.111 11.59 0.00 41.47 3.41
540 542 1.732259 GATAATTAGCATGACCCGCCG 59.268 52.381 0.00 0.00 0.00 6.46
574 576 2.940410 CGCGGTCCAACAGGTAAATATT 59.060 45.455 0.00 0.00 0.00 1.28
669 671 1.132844 CGACCGAGACTCACTGACG 59.867 63.158 2.82 0.00 0.00 4.35
675 677 0.596577 CTGGTTTCGACCGAGACTCA 59.403 55.000 11.83 8.02 31.01 3.41
754 756 1.977544 CTCACTCCCGGACGACCTT 60.978 63.158 0.73 0.00 0.00 3.50
769 771 0.750546 ATTCCGTCCGTCCGATCTCA 60.751 55.000 0.00 0.00 0.00 3.27
832 834 0.970937 AGCACCCTACAAGCGCTCTA 60.971 55.000 12.06 1.99 0.00 2.43
920 3980 6.395780 TTGTAGGATAGGGTTCCAATTTCA 57.604 37.500 0.00 0.00 38.32 2.69
1169 4234 1.858372 TTCGATGTGGCTCGACGACA 61.858 55.000 0.00 5.60 46.53 4.35
1197 4262 3.416119 TCAACTTACTCCTATGTCGCG 57.584 47.619 0.00 0.00 0.00 5.87
1396 4518 8.462143 TCTACGAAATTGTCACTTTAGATGTC 57.538 34.615 3.37 0.00 0.00 3.06
1628 7167 5.517322 AACAGAACTGAACTCGACTACTT 57.483 39.130 8.87 0.00 0.00 2.24
1718 7258 4.293415 GCATAGTTGCTTATTCATGGCAC 58.707 43.478 0.00 0.00 45.77 5.01
2334 7955 6.173339 TGAGAAATTGTTTAGGCTCAGGTAG 58.827 40.000 0.00 0.00 0.00 3.18
2371 7992 7.041508 GCAGAACGAGATCAGATTTTGGATATT 60.042 37.037 0.00 0.00 0.00 1.28
2526 8150 2.781667 AGATAGAGGATGGCCACCTTT 58.218 47.619 22.78 20.02 37.93 3.11
2623 8247 6.038714 CCAAGTATTTTGATCTCACTTAGGCC 59.961 42.308 0.00 0.00 0.00 5.19
2749 8440 2.476619 CGCCCTTTTGATAGATACTGCG 59.523 50.000 0.00 0.00 0.00 5.18
2790 8481 1.241165 TCGAGCCGAGTAAACACAGA 58.759 50.000 0.00 0.00 0.00 3.41
2919 8623 4.154176 GAGGGAGGGAGAGGATTTACTAC 58.846 52.174 0.00 0.00 0.00 2.73
3142 9093 2.552743 GGTGCCCAACTCAGTAACTTTC 59.447 50.000 0.00 0.00 0.00 2.62
3237 9188 4.101448 GGCAGACACCCTCGGCAT 62.101 66.667 0.00 0.00 41.57 4.40
3304 9269 2.005451 ACATTCGCATGAACTCAGAGC 58.995 47.619 0.94 0.00 36.81 4.09
3305 9270 3.553511 GGTACATTCGCATGAACTCAGAG 59.446 47.826 0.94 0.00 36.81 3.35
3428 12945 7.686371 TTTCATATGAAAAACACATGCTGGTGT 60.686 33.333 25.11 7.95 44.54 4.16
3499 13016 4.426313 GGGCCTCTTGAACCGGGG 62.426 72.222 6.32 0.00 0.00 5.73
3508 13025 1.000896 CGGGACAAATGGGCCTCTT 60.001 57.895 4.53 0.00 0.00 2.85
3549 13066 0.899019 TTTTGGGCTTTATTCCCGGC 59.101 50.000 0.00 0.00 46.92 6.13
3550 13067 1.896465 TGTTTTGGGCTTTATTCCCGG 59.104 47.619 0.00 0.00 46.92 5.73
3551 13068 3.885724 ATGTTTTGGGCTTTATTCCCG 57.114 42.857 0.00 0.00 46.92 5.14
3552 13069 6.707290 ACTAAATGTTTTGGGCTTTATTCCC 58.293 36.000 0.00 0.00 44.17 3.97
3555 13072 6.573485 CGGGACTAAATGTTTTGGGCTTTATT 60.573 38.462 0.00 0.00 0.00 1.40
3556 13073 5.105513 CGGGACTAAATGTTTTGGGCTTTAT 60.106 40.000 0.00 0.00 0.00 1.40
3567 13126 2.871453 AGCAAACCGGGACTAAATGTT 58.129 42.857 6.32 0.00 0.00 2.71
3570 13129 3.004862 CGTAAGCAAACCGGGACTAAAT 58.995 45.455 6.32 0.00 0.00 1.40
3584 13143 0.390603 CATGTCCCGGTTCGTAAGCA 60.391 55.000 0.00 0.00 37.18 3.91
3643 13203 2.609534 AACCGGGACTAAAGGCCCC 61.610 63.158 15.63 7.40 41.50 5.80
3676 13236 0.388520 GCGTGGATGCTTTTTGGTCC 60.389 55.000 0.00 0.00 0.00 4.46
3685 13245 1.139734 CTACTGACGCGTGGATGCT 59.860 57.895 20.70 0.00 0.00 3.79
3706 13304 1.318576 AACAAAAACTCCGGCTCCTG 58.681 50.000 0.00 0.00 0.00 3.86
4002 13600 8.900802 AGAGATCACTTCCCTCTATTAGATAGT 58.099 37.037 0.00 0.00 35.68 2.12
4016 13614 4.825085 ACGGAGATAAGAGAGATCACTTCC 59.175 45.833 0.00 0.00 0.00 3.46
4024 13622 2.690497 CCAAGCACGGAGATAAGAGAGA 59.310 50.000 0.00 0.00 0.00 3.10
4311 14872 1.351017 TGGCGGGATTCTTTCTTGACT 59.649 47.619 0.00 0.00 0.00 3.41
4427 14988 6.507023 ACCTTCATTTGTGTTGAGTTTCATC 58.493 36.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.