Multiple sequence alignment - TraesCS2A01G320200

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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 TraesCS2A01G320200 chr2A 100.000 4454 0 0 1 4454 549676724 549681177 0.000000e+00 8226
1 TraesCS2A01G320200 chr2A 95.307 277 13 0 1636 1912 549678266 549678542 1.470000e-119 440
2 TraesCS2A01G320200 chr2A 95.307 277 13 0 1543 1819 549678359 549678635 1.470000e-119 440
3 TraesCS2A01G320200 chr2A 93.182 176 12 0 1729 1904 549678266 549678441 4.420000e-65 259
4 TraesCS2A01G320200 chr2A 93.182 176 12 0 1543 1718 549678452 549678627 4.420000e-65 259
5 TraesCS2A01G320200 chr2A 91.304 92 6 2 1543 1633 549678545 549678635 1.680000e-24 124
6 TraesCS2A01G320200 chr2D 95.933 3787 94 25 523 4273 439443607 439439845 0.000000e+00 6085
7 TraesCS2A01G320200 chr2D 92.118 406 8 9 1 401 439444272 439443886 6.510000e-153 551
8 TraesCS2A01G320200 chr2D 96.283 269 10 0 1636 1904 439442593 439442325 4.090000e-120 442
9 TraesCS2A01G320200 chr2D 93.863 277 17 0 1543 1819 439442500 439442224 6.890000e-113 418
10 TraesCS2A01G320200 chr2D 96.216 185 7 0 4268 4452 439439759 439439575 2.010000e-78 303
11 TraesCS2A01G320200 chr2D 94.022 184 11 0 1729 1912 439442593 439442410 3.390000e-71 279
12 TraesCS2A01G320200 chr2D 90.710 183 15 2 1543 1724 439442407 439442226 4.450000e-60 243
13 TraesCS2A01G320200 chr2D 92.771 83 6 0 1822 1904 439442593 439442511 2.180000e-23 121
14 TraesCS2A01G320200 chr2B 93.032 2569 124 25 1727 4267 517383871 517381330 0.000000e+00 3701
15 TraesCS2A01G320200 chr2B 91.357 1238 60 20 526 1724 517384917 517383688 0.000000e+00 1650
16 TraesCS2A01G320200 chr2B 85.319 470 26 23 1 437 517385692 517385233 3.160000e-121 446
17 TraesCS2A01G320200 chr2B 97.222 180 3 1 4273 4452 517381235 517381058 2.010000e-78 303
18 TraesCS2A01G320200 chr2B 93.011 186 13 0 1634 1819 517383871 517383686 5.680000e-69 272
19 TraesCS2A01G320200 chr2B 93.548 93 6 0 1820 1912 517383871 517383779 6.010000e-29 139


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 TraesCS2A01G320200 chr2A 549676724 549681177 4453 False 1624.666667 8226 94.713667 1 4454 6 chr2A.!!$F1 4453
1 TraesCS2A01G320200 chr2D 439439575 439444272 4697 True 1055.250000 6085 93.989500 1 4452 8 chr2D.!!$R1 4451
2 TraesCS2A01G320200 chr2B 517381058 517385692 4634 True 1085.166667 3701 92.248167 1 4452 6 chr2B.!!$R1 4451

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
451 488 0.030092 CCCCTACCTCCTCCCATCAA 60.030 60.0 0.0 0.0 0.00 2.57 F
1614 1942 0.030504 CTGCATTGTTGTGCCGTGAA 59.969 50.0 0.0 0.0 44.43 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2423 2758 0.264657 TACTGGCCCTAGCTCCATCA 59.735 55.0 0.0 0.0 39.73 3.07 R
3555 3894 0.036294 TGTCAAACGACCACACACCA 60.036 50.0 0.0 0.0 32.01 4.17 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
223 245 3.845625 GGAACGCAACAAACCAGAG 57.154 52.632 0.00 0.00 0.00 3.35
354 391 2.962138 AACCCCTCTCCTCCTCCCC 61.962 68.421 0.00 0.00 0.00 4.81
419 456 2.816777 AGGAGCCTTGGAGATTTTCC 57.183 50.000 0.00 0.00 46.98 3.13
437 474 4.745013 CGGAACCCCCACCCCCTA 62.745 72.222 0.00 0.00 34.14 3.53
438 475 3.019418 GGAACCCCCACCCCCTAC 61.019 72.222 0.00 0.00 34.14 3.18
439 476 3.019418 GAACCCCCACCCCCTACC 61.019 72.222 0.00 0.00 0.00 3.18
440 477 3.559172 AACCCCCACCCCCTACCT 61.559 66.667 0.00 0.00 0.00 3.08
441 478 3.591331 AACCCCCACCCCCTACCTC 62.591 68.421 0.00 0.00 0.00 3.85
442 479 4.837421 CCCCCACCCCCTACCTCC 62.837 77.778 0.00 0.00 0.00 4.30
443 480 3.707189 CCCCACCCCCTACCTCCT 61.707 72.222 0.00 0.00 0.00 3.69
444 481 2.040779 CCCACCCCCTACCTCCTC 60.041 72.222 0.00 0.00 0.00 3.71
445 482 2.040779 CCACCCCCTACCTCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
446 483 2.040779 CACCCCCTACCTCCTCCC 60.041 72.222 0.00 0.00 0.00 4.30
447 484 2.542541 ACCCCCTACCTCCTCCCA 60.543 66.667 0.00 0.00 0.00 4.37
448 485 1.952766 ACCCCCTACCTCCTCCCAT 60.953 63.158 0.00 0.00 0.00 4.00
449 486 1.152008 CCCCCTACCTCCTCCCATC 60.152 68.421 0.00 0.00 0.00 3.51
450 487 1.632164 CCCCTACCTCCTCCCATCA 59.368 63.158 0.00 0.00 0.00 3.07
451 488 0.030092 CCCCTACCTCCTCCCATCAA 60.030 60.000 0.00 0.00 0.00 2.57
452 489 1.428869 CCCTACCTCCTCCCATCAAG 58.571 60.000 0.00 0.00 0.00 3.02
453 490 1.428869 CCTACCTCCTCCCATCAAGG 58.571 60.000 0.00 0.00 35.05 3.61
454 491 1.344496 CCTACCTCCTCCCATCAAGGT 60.344 57.143 0.00 0.00 44.24 3.50
455 492 2.482494 CTACCTCCTCCCATCAAGGTT 58.518 52.381 0.00 0.00 42.13 3.50
456 493 1.760405 ACCTCCTCCCATCAAGGTTT 58.240 50.000 0.00 0.00 39.05 3.27
457 494 1.636003 ACCTCCTCCCATCAAGGTTTC 59.364 52.381 0.00 0.00 39.05 2.78
458 495 1.635487 CCTCCTCCCATCAAGGTTTCA 59.365 52.381 0.00 0.00 35.29 2.69
459 496 2.619074 CCTCCTCCCATCAAGGTTTCAC 60.619 54.545 0.00 0.00 35.29 3.18
460 497 1.354368 TCCTCCCATCAAGGTTTCACC 59.646 52.381 0.00 0.00 38.99 4.02
461 498 1.075374 CCTCCCATCAAGGTTTCACCA 59.925 52.381 0.00 0.00 41.95 4.17
462 499 2.162681 CTCCCATCAAGGTTTCACCAC 58.837 52.381 0.00 0.00 41.95 4.16
463 500 1.203001 TCCCATCAAGGTTTCACCACC 60.203 52.381 0.00 0.00 41.95 4.61
464 501 1.480312 CCCATCAAGGTTTCACCACCA 60.480 52.381 0.00 0.00 41.95 4.17
465 502 1.613437 CCATCAAGGTTTCACCACCAC 59.387 52.381 0.00 0.00 41.95 4.16
466 503 1.613437 CATCAAGGTTTCACCACCACC 59.387 52.381 0.00 0.00 41.95 4.61
467 504 0.464735 TCAAGGTTTCACCACCACCG 60.465 55.000 0.00 0.00 41.95 4.94
468 505 1.826487 AAGGTTTCACCACCACCGC 60.826 57.895 0.00 0.00 41.95 5.68
469 506 3.292159 GGTTTCACCACCACCGCC 61.292 66.667 0.00 0.00 38.42 6.13
470 507 3.292159 GTTTCACCACCACCGCCC 61.292 66.667 0.00 0.00 0.00 6.13
471 508 4.939368 TTTCACCACCACCGCCCG 62.939 66.667 0.00 0.00 0.00 6.13
513 550 3.140141 CATCGCCGCCCCAACAAT 61.140 61.111 0.00 0.00 0.00 2.71
514 551 2.828549 ATCGCCGCCCCAACAATC 60.829 61.111 0.00 0.00 0.00 2.67
518 555 2.755469 CCGCCCCAACAATCCCAG 60.755 66.667 0.00 0.00 0.00 4.45
519 556 2.035626 CGCCCCAACAATCCCAGT 59.964 61.111 0.00 0.00 0.00 4.00
520 557 2.046285 CGCCCCAACAATCCCAGTC 61.046 63.158 0.00 0.00 0.00 3.51
521 558 2.046285 GCCCCAACAATCCCAGTCG 61.046 63.158 0.00 0.00 0.00 4.18
635 920 4.570663 CCCGTCGGCTCGTGGATC 62.571 72.222 5.50 0.00 0.00 3.36
636 921 3.518998 CCGTCGGCTCGTGGATCT 61.519 66.667 0.00 0.00 0.00 2.75
637 922 2.024871 CGTCGGCTCGTGGATCTC 59.975 66.667 0.00 0.00 0.00 2.75
638 923 2.024871 GTCGGCTCGTGGATCTCG 59.975 66.667 0.00 0.00 0.00 4.04
639 924 3.209812 TCGGCTCGTGGATCTCGG 61.210 66.667 9.93 4.07 0.00 4.63
640 925 4.933064 CGGCTCGTGGATCTCGGC 62.933 72.222 9.93 11.06 0.00 5.54
641 926 3.532155 GGCTCGTGGATCTCGGCT 61.532 66.667 16.15 0.00 0.00 5.52
642 927 2.279120 GCTCGTGGATCTCGGCTG 60.279 66.667 9.93 0.00 0.00 4.85
668 953 3.717294 GACGGTGCTGGTGGGGAT 61.717 66.667 0.00 0.00 0.00 3.85
672 957 2.046285 GGTGCTGGTGGGGATTTCG 61.046 63.158 0.00 0.00 0.00 3.46
692 977 1.092348 GGTCCCGTGTTTATTGCTCC 58.908 55.000 0.00 0.00 0.00 4.70
1167 1474 3.393106 TGCTCTGCCCTGATGCGA 61.393 61.111 0.00 0.00 0.00 5.10
1251 1558 0.035458 GGGATGATTTCGAGCCCGAT 59.965 55.000 0.00 0.00 45.10 4.18
1271 1578 1.069765 CTGCGGATCTATTGCCCGT 59.930 57.895 0.00 0.00 44.63 5.28
1439 1764 4.195334 CTCCCGGGGGCCATCTTG 62.195 72.222 23.50 0.00 34.68 3.02
1552 1880 1.002868 CCCCTTGTGTCCTGCTCAG 60.003 63.158 0.00 0.00 0.00 3.35
1614 1942 0.030504 CTGCATTGTTGTGCCGTGAA 59.969 50.000 0.00 0.00 44.43 3.18
1626 1954 0.674895 GCCGTGAAGGAGTTGATGCT 60.675 55.000 0.00 0.00 45.00 3.79
1627 1955 1.081892 CCGTGAAGGAGTTGATGCTG 58.918 55.000 0.00 0.00 45.00 4.41
1702 2030 0.942410 CAGTGCTGCATTGTTGTGCC 60.942 55.000 16.02 0.00 44.43 5.01
1724 2052 1.648467 GAAGGAGTTGATGCCGTGGC 61.648 60.000 3.30 3.30 42.35 5.01
1795 2123 1.529948 AGTGCTGCATTGGTGTGCT 60.530 52.632 5.27 0.00 45.27 4.40
1904 2232 2.038820 TGTGCTGTGATGGAGTTGATGA 59.961 45.455 0.00 0.00 0.00 2.92
2111 2442 2.079925 GACACAGAAGATTCCAGGTGC 58.920 52.381 8.62 0.00 31.48 5.01
2423 2758 1.254954 GTACGGACACAACTCCCTCT 58.745 55.000 0.00 0.00 0.00 3.69
2484 2819 7.974501 GGTAGTCGAATGTAGATGTTATATGGG 59.025 40.741 0.00 0.00 0.00 4.00
2650 2985 5.782893 TTACATTTAGCACCAACAAAGCT 57.217 34.783 0.00 0.00 42.14 3.74
3396 3733 1.139853 GATCCGGCTTCACCATCTCTT 59.860 52.381 0.00 0.00 39.03 2.85
3420 3757 3.008485 GTGTGGAAAAGGATCTGGTCTCT 59.992 47.826 0.00 0.00 0.00 3.10
3472 3809 1.555075 GACCATGGAGGAGCAACAGTA 59.445 52.381 21.47 0.00 41.22 2.74
3518 3855 7.050377 TCTTTCTTAGCATTACTGATGAAGGG 58.950 38.462 0.00 0.00 38.03 3.95
3642 3981 3.902218 TCCAGCAGAAATAAAGGGATGG 58.098 45.455 0.00 0.00 36.41 3.51
3671 4010 2.167398 TTACAGCCTCACCAGCGACC 62.167 60.000 0.00 0.00 34.64 4.79
3673 4012 3.005539 AGCCTCACCAGCGACCAT 61.006 61.111 0.00 0.00 34.64 3.55
3930 4269 4.717991 TGCGTCACATTGTAATAGTTTGC 58.282 39.130 0.00 0.00 0.00 3.68
3935 4274 5.183140 GTCACATTGTAATAGTTTGCCCTGT 59.817 40.000 0.00 0.00 0.00 4.00
4057 4398 4.184079 AGCATCCTTTTTCATCTGTTGC 57.816 40.909 0.00 0.00 0.00 4.17
4089 4430 6.166279 TGGAGTTTACTGTGAATCTGTGATC 58.834 40.000 0.00 0.00 0.00 2.92
4096 4437 6.744175 ACTGTGAATCTGTGATCATATCCT 57.256 37.500 0.00 0.00 0.00 3.24
4103 4444 8.098912 TGAATCTGTGATCATATCCTGTTATGG 58.901 37.037 0.00 0.00 31.71 2.74
4106 4447 7.896811 TCTGTGATCATATCCTGTTATGGTAC 58.103 38.462 0.00 0.00 31.71 3.34
4122 4463 1.065126 GGTACAATCTGCTCCTTGGCT 60.065 52.381 0.00 0.00 0.00 4.75
4126 4467 0.392193 AATCTGCTCCTTGGCTGTCG 60.392 55.000 0.00 0.00 33.78 4.35
4160 4501 4.911514 TTTGGTAAAACCTGAGCAGTTC 57.088 40.909 0.00 0.00 39.58 3.01
4161 4502 2.489971 TGGTAAAACCTGAGCAGTTCG 58.510 47.619 0.00 0.00 39.58 3.95
4180 4538 7.544217 GCAGTTCGTTATGAAATTTTGGGTATT 59.456 33.333 0.00 0.00 38.60 1.89
4188 4548 6.710499 TGAAATTTTGGGTATTTGGGGAAT 57.290 33.333 0.00 0.00 0.00 3.01
4205 4565 4.281657 GGGAATCCCTTGTTAAGATTGCT 58.718 43.478 11.95 0.00 41.34 3.91
4211 4571 8.773033 AATCCCTTGTTAAGATTGCTTGATAT 57.227 30.769 0.00 0.00 35.56 1.63
4233 4593 9.160496 GATATTAGATCGATTCATCCAAAGCTT 57.840 33.333 0.00 0.00 0.00 3.74
4236 4596 2.715046 TCGATTCATCCAAAGCTTGCT 58.285 42.857 0.00 0.00 0.00 3.91
4268 4628 1.880027 GCTCCCAATAATGTAAGCGGG 59.120 52.381 0.00 0.00 34.81 6.13
4349 4799 2.955660 AGGGATTCGTTAGAGCTGAGAG 59.044 50.000 0.00 0.00 0.00 3.20
4410 4860 0.178767 TCCACATTCTCATCCGGCAG 59.821 55.000 0.00 0.00 0.00 4.85
4452 4902 2.736995 GCACCTGTCGCGTTGCTA 60.737 61.111 5.77 0.00 0.00 3.49
4453 4903 2.100631 GCACCTGTCGCGTTGCTAT 61.101 57.895 5.77 0.00 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 57 0.390472 GCCGGTTGGACTCTCTCTTG 60.390 60.000 1.90 0.00 37.49 3.02
54 59 2.344203 CGCCGGTTGGACTCTCTCT 61.344 63.158 1.90 0.00 37.49 3.10
55 60 2.182030 CGCCGGTTGGACTCTCTC 59.818 66.667 1.90 0.00 37.49 3.20
56 61 4.070552 GCGCCGGTTGGACTCTCT 62.071 66.667 1.90 0.00 37.49 3.10
112 117 0.613777 TCTTCCCGGGCTTTCTCTTC 59.386 55.000 18.49 0.00 0.00 2.87
113 118 1.064825 TTCTTCCCGGGCTTTCTCTT 58.935 50.000 18.49 0.00 0.00 2.85
114 119 1.064825 TTTCTTCCCGGGCTTTCTCT 58.935 50.000 18.49 0.00 0.00 3.10
115 120 1.905637 TTTTCTTCCCGGGCTTTCTC 58.094 50.000 18.49 0.00 0.00 2.87
116 121 2.604912 ATTTTCTTCCCGGGCTTTCT 57.395 45.000 18.49 0.00 0.00 2.52
177 182 2.035961 GGTTTTCCTTTCTCTTGGGTGC 59.964 50.000 0.00 0.00 36.94 5.01
186 208 0.178973 CGGTGGGGGTTTTCCTTTCT 60.179 55.000 0.00 0.00 40.46 2.52
219 241 2.837291 CTCCCCGCTCTCCCTCTG 60.837 72.222 0.00 0.00 0.00 3.35
354 391 4.416601 AGGGAGGGGGAGGGAACG 62.417 72.222 0.00 0.00 0.00 3.95
437 474 1.636003 GAAACCTTGATGGGAGGAGGT 59.364 52.381 0.00 0.00 44.11 3.85
438 475 1.635487 TGAAACCTTGATGGGAGGAGG 59.365 52.381 0.00 0.00 41.11 4.30
439 476 2.716217 GTGAAACCTTGATGGGAGGAG 58.284 52.381 0.00 0.00 41.11 3.69
440 477 2.879103 GTGAAACCTTGATGGGAGGA 57.121 50.000 0.00 0.00 41.11 3.71
453 490 3.292159 GGGCGGTGGTGGTGAAAC 61.292 66.667 0.00 0.00 0.00 2.78
454 491 4.939368 CGGGCGGTGGTGGTGAAA 62.939 66.667 0.00 0.00 0.00 2.69
496 533 3.124798 GATTGTTGGGGCGGCGATG 62.125 63.158 12.98 0.00 0.00 3.84
497 534 2.828549 GATTGTTGGGGCGGCGAT 60.829 61.111 12.98 0.00 0.00 4.58
501 538 2.755469 CTGGGATTGTTGGGGCGG 60.755 66.667 0.00 0.00 0.00 6.13
502 539 2.035626 ACTGGGATTGTTGGGGCG 59.964 61.111 0.00 0.00 0.00 6.13
503 540 2.046285 CGACTGGGATTGTTGGGGC 61.046 63.158 0.00 0.00 0.00 5.80
504 541 0.392998 CTCGACTGGGATTGTTGGGG 60.393 60.000 0.00 0.00 0.00 4.96
505 542 0.324943 ACTCGACTGGGATTGTTGGG 59.675 55.000 0.00 0.00 0.00 4.12
506 543 1.001974 TGACTCGACTGGGATTGTTGG 59.998 52.381 0.00 0.00 0.00 3.77
507 544 2.455674 TGACTCGACTGGGATTGTTG 57.544 50.000 0.00 0.00 0.00 3.33
508 545 2.093447 GGATGACTCGACTGGGATTGTT 60.093 50.000 0.00 0.00 0.00 2.83
509 546 1.482593 GGATGACTCGACTGGGATTGT 59.517 52.381 0.00 0.00 0.00 2.71
510 547 1.536922 CGGATGACTCGACTGGGATTG 60.537 57.143 0.00 0.00 0.00 2.67
511 548 0.747255 CGGATGACTCGACTGGGATT 59.253 55.000 0.00 0.00 0.00 3.01
512 549 1.739338 GCGGATGACTCGACTGGGAT 61.739 60.000 0.00 0.00 0.00 3.85
513 550 2.415608 GCGGATGACTCGACTGGGA 61.416 63.158 0.00 0.00 0.00 4.37
514 551 2.105128 GCGGATGACTCGACTGGG 59.895 66.667 0.00 0.00 0.00 4.45
515 552 2.105128 GGCGGATGACTCGACTGG 59.895 66.667 0.00 0.00 32.06 4.00
516 553 2.105128 GGGCGGATGACTCGACTG 59.895 66.667 0.00 0.00 35.69 3.51
517 554 2.362503 TGGGCGGATGACTCGACT 60.363 61.111 0.00 0.00 35.69 4.18
518 555 2.202756 GTGGGCGGATGACTCGAC 60.203 66.667 0.00 0.00 34.40 4.20
519 556 3.458163 GGTGGGCGGATGACTCGA 61.458 66.667 0.00 0.00 0.00 4.04
520 557 4.530857 GGGTGGGCGGATGACTCG 62.531 72.222 0.00 0.00 0.00 4.18
521 558 4.176752 GGGGTGGGCGGATGACTC 62.177 72.222 0.00 0.00 0.00 3.36
595 866 2.920384 GGCTCTCGGGAGGGGATC 60.920 72.222 15.59 0.00 39.80 3.36
652 937 2.764637 GAAATCCCCACCAGCACCGT 62.765 60.000 0.00 0.00 0.00 4.83
658 943 1.077716 GACCCGAAATCCCCACCAG 60.078 63.158 0.00 0.00 0.00 4.00
659 944 2.608550 GGACCCGAAATCCCCACCA 61.609 63.158 0.00 0.00 0.00 4.17
660 945 2.274432 GGACCCGAAATCCCCACC 59.726 66.667 0.00 0.00 0.00 4.61
672 957 1.092348 GAGCAATAAACACGGGACCC 58.908 55.000 0.00 0.00 0.00 4.46
692 977 0.601311 GAGAATCAGGGCCCGAATCG 60.601 60.000 18.44 3.82 33.17 3.34
764 1052 3.249559 GCCCGAATCAGAATCAGAATCAC 59.750 47.826 0.00 0.00 0.00 3.06
829 1127 2.436109 GGCAGAGAAACCAGGGCA 59.564 61.111 0.00 0.00 0.00 5.36
830 1128 2.747855 CGGCAGAGAAACCAGGGC 60.748 66.667 0.00 0.00 0.00 5.19
831 1129 1.899437 TAGCGGCAGAGAAACCAGGG 61.899 60.000 1.45 0.00 0.00 4.45
832 1130 0.179000 ATAGCGGCAGAGAAACCAGG 59.821 55.000 1.45 0.00 0.00 4.45
1035 1333 2.041405 CTCCTCCTCACCCCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
1167 1474 2.959484 CGACCAGCATCCACACCCT 61.959 63.158 0.00 0.00 0.00 4.34
1552 1880 2.420687 CCTCTCCAGGTACAATTGAGCC 60.421 54.545 13.59 13.09 34.60 4.70
1614 1942 0.617413 CTCCCACAGCATCAACTCCT 59.383 55.000 0.00 0.00 0.00 3.69
1702 2030 0.670546 ACGGCATCAACTCCTTCACG 60.671 55.000 0.00 0.00 0.00 4.35
1740 2068 2.196595 TCCTCTCCAGGTACAATTGGG 58.803 52.381 10.83 0.63 41.28 4.12
1795 2123 0.324614 ACGGCATCAACTCCATCACA 59.675 50.000 0.00 0.00 0.00 3.58
2254 2585 2.816087 CAAATATGATCCCAGGCCTTCG 59.184 50.000 0.00 0.00 0.00 3.79
2423 2758 0.264657 TACTGGCCCTAGCTCCATCA 59.735 55.000 0.00 0.00 39.73 3.07
2484 2819 4.082026 AGAGCAAGAAAAACATGGTATGCC 60.082 41.667 0.00 0.00 33.19 4.40
2634 2969 5.472137 CCTAACTTAGCTTTGTTGGTGCTAA 59.528 40.000 12.42 0.00 44.02 3.09
3396 3733 1.780309 ACCAGATCCTTTTCCACACCA 59.220 47.619 0.00 0.00 0.00 4.17
3420 3757 9.561069 GAAGCTATTCTTCCACTGGATAAAATA 57.439 33.333 0.00 3.51 44.22 1.40
3472 3809 0.682209 GGCTGAATGGCTGGACATGT 60.682 55.000 0.00 0.00 38.32 3.21
3555 3894 0.036294 TGTCAAACGACCACACACCA 60.036 50.000 0.00 0.00 32.01 4.17
3642 3981 3.532542 GTGAGGCTGTAATAGTGGGAAC 58.467 50.000 0.00 0.00 0.00 3.62
3671 4010 4.720902 TGCGCCACCCACCTCATG 62.721 66.667 4.18 0.00 0.00 3.07
3673 4012 2.597818 TAATGCGCCACCCACCTCA 61.598 57.895 4.18 0.00 0.00 3.86
3913 4252 5.643379 ACAGGGCAAACTATTACAATGTG 57.357 39.130 0.00 0.00 0.00 3.21
3930 4269 0.729116 ACGACACGACGTATACAGGG 59.271 55.000 0.00 0.00 44.72 4.45
4057 4398 6.592798 TTCACAGTAAACTCCAACTAAACG 57.407 37.500 0.00 0.00 0.00 3.60
4089 4430 7.164122 AGCAGATTGTACCATAACAGGATATG 58.836 38.462 0.00 0.00 33.85 1.78
4096 4437 5.185454 CAAGGAGCAGATTGTACCATAACA 58.815 41.667 0.00 0.00 0.00 2.41
4103 4444 2.012673 CAGCCAAGGAGCAGATTGTAC 58.987 52.381 0.00 0.00 34.23 2.90
4106 4447 1.093159 GACAGCCAAGGAGCAGATTG 58.907 55.000 0.00 0.00 34.23 2.67
4160 4501 6.536941 CCCCAAATACCCAAAATTTCATAACG 59.463 38.462 0.00 0.00 0.00 3.18
4161 4502 7.625469 TCCCCAAATACCCAAAATTTCATAAC 58.375 34.615 0.00 0.00 0.00 1.89
4188 4548 9.342308 CTAATATCAAGCAATCTTAACAAGGGA 57.658 33.333 0.00 0.00 0.00 4.20
4205 4565 8.939929 GCTTTGGATGAATCGATCTAATATCAA 58.060 33.333 0.00 0.00 0.00 2.57
4211 4571 5.008019 GCAAGCTTTGGATGAATCGATCTAA 59.992 40.000 0.00 0.00 0.00 2.10
4233 4593 0.604780 GGAGCAGAACAAGCAGAGCA 60.605 55.000 0.00 0.00 0.00 4.26
4236 4596 0.473755 TTGGGAGCAGAACAAGCAGA 59.526 50.000 0.00 0.00 0.00 4.26
4268 4628 1.464997 GAGTCGACATGCTTCCCAAAC 59.535 52.381 19.50 0.00 0.00 2.93
4349 4799 4.410400 AACCTACTGCTGGCCGCC 62.410 66.667 15.40 1.04 38.05 6.13
4410 4860 0.819666 GCTTCCGGGACATGGATTCC 60.820 60.000 0.00 0.00 34.91 3.01


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

AutoCloner maintained by Alex Coulton.