Multiple sequence alignment - TraesCS4D01G277500

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 TraesCS4D01G277500 chr4D 100.000 4373 0 0 1 4373 449730749 449735121 0.000000e+00 8076.0
1 TraesCS4D01G277500 chr4A 95.862 2803 84 6 924 3703 17261844 17259051 0.000000e+00 4505.0
2 TraesCS4D01G277500 chr4A 91.139 474 28 7 3700 4167 17259025 17258560 7.980000e-177 630.0
3 TraesCS4D01G277500 chr4A 88.841 233 6 11 20 245 17262617 17262398 7.210000e-68 268.0
4 TraesCS4D01G277500 chr4A 76.638 458 64 24 422 862 17262293 17261862 3.430000e-51 213.0
5 TraesCS4D01G277500 chr4A 91.603 131 5 5 4166 4293 17258502 17258375 4.490000e-40 176.0
6 TraesCS4D01G277500 chr4A 92.500 40 3 0 4330 4369 16985753 16985792 1.700000e-04 58.4
7 TraesCS4D01G277500 chr4B 95.277 2795 97 8 907 3681 562355779 562358558 0.000000e+00 4397.0
8 TraesCS4D01G277500 chr4B 93.383 665 28 12 3715 4373 562358698 562359352 0.000000e+00 970.0
9 TraesCS4D01G277500 chr4B 89.873 474 28 9 439 904 562355194 562355655 3.770000e-165 592.0
10 TraesCS4D01G277500 chr4B 81.859 441 29 18 1 414 562354791 562355207 1.520000e-84 324.0
11 TraesCS4D01G277500 chr3A 78.698 169 19 10 3874 4028 30397291 30397456 3.600000e-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 TraesCS4D01G277500 chr4D 449730749 449735121 4372 False 8076.00 8076 100.0000 1 4373 1 chr4D.!!$F1 4372
1 TraesCS4D01G277500 chr4A 17258375 17262617 4242 True 1158.40 4505 88.8166 20 4293 5 chr4A.!!$R1 4273
2 TraesCS4D01G277500 chr4B 562354791 562359352 4561 False 1570.75 4397 90.0980 1 4373 4 chr4B.!!$F1 4372

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
292 330 0.249073 CCGCCTCAGTGAGTATTCCG 60.249 60.0 18.74 11.94 0.00 4.30 F
304 342 0.320508 GTATTCCGCCCCGATTCCTC 60.321 60.0 0.00 0.00 0.00 3.71 F
1692 1876 0.179004 TGGCTCGCCAAAAAGAGGAA 60.179 50.0 8.43 0.00 44.12 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 1813 0.749454 GCCCGATCTGCTTGGACATT 60.749 55.000 0.00 0.00 0.0 2.71 R
2208 2392 1.153745 CTTGTCCCGGCTTCTCGAG 60.154 63.158 5.93 5.93 0.0 4.04 R
3403 3587 0.321122 CAGAAGGTGGACACTGAGCC 60.321 60.000 2.13 0.00 32.9 4.70 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
40 41 2.109126 GCCGGCATGGTTCTCACTC 61.109 63.158 24.80 0.00 41.21 3.51
50 58 1.474879 GGTTCTCACTCCTCTCCTTCG 59.525 57.143 0.00 0.00 0.00 3.79
54 62 1.742831 CTCACTCCTCTCCTTCGACAG 59.257 57.143 0.00 0.00 0.00 3.51
75 83 0.250989 GGATCCAACCCAACCGAACA 60.251 55.000 6.95 0.00 0.00 3.18
91 104 2.288458 CGAACAAAACCAAACGGAGCTA 59.712 45.455 0.00 0.00 0.00 3.32
92 105 3.606153 CGAACAAAACCAAACGGAGCTAG 60.606 47.826 0.00 0.00 0.00 3.42
93 106 1.607148 ACAAAACCAAACGGAGCTAGC 59.393 47.619 6.62 6.62 0.00 3.42
94 107 1.880027 CAAAACCAAACGGAGCTAGCT 59.120 47.619 19.45 19.45 0.00 3.32
115 133 1.640917 TAGACGGATGGCCCTATTCC 58.359 55.000 0.00 0.11 0.00 3.01
259 289 4.951963 CCGCCGCCGATCTTCTCC 62.952 72.222 0.00 0.00 36.29 3.71
260 290 3.905678 CGCCGCCGATCTTCTCCT 61.906 66.667 0.00 0.00 36.29 3.69
262 292 2.786495 GCCGCCGATCTTCTCCTCA 61.786 63.158 0.00 0.00 0.00 3.86
286 324 3.023949 GCATCCCGCCTCAGTGAGT 62.024 63.158 18.74 0.00 32.94 3.41
292 330 0.249073 CCGCCTCAGTGAGTATTCCG 60.249 60.000 18.74 11.94 0.00 4.30
293 331 0.872021 CGCCTCAGTGAGTATTCCGC 60.872 60.000 18.74 12.21 0.00 5.54
299 337 0.759436 AGTGAGTATTCCGCCCCGAT 60.759 55.000 0.00 0.00 0.00 4.18
304 342 0.320508 GTATTCCGCCCCGATTCCTC 60.321 60.000 0.00 0.00 0.00 3.71
328 366 4.183101 CCTTCTCTTCTACGTACGTCTCT 58.817 47.826 26.53 2.16 0.00 3.10
331 369 2.534298 TCTTCTACGTACGTCTCTCCG 58.466 52.381 26.53 9.82 0.00 4.63
332 370 1.002366 TTCTACGTACGTCTCTCCGC 58.998 55.000 26.53 0.00 0.00 5.54
334 372 1.079197 TACGTACGTCTCTCCGCCA 60.079 57.895 26.53 0.00 0.00 5.69
335 373 0.462581 TACGTACGTCTCTCCGCCAT 60.463 55.000 26.53 0.00 0.00 4.40
336 374 1.298413 CGTACGTCTCTCCGCCATG 60.298 63.158 7.22 0.00 0.00 3.66
338 376 2.049767 TACGTCTCTCCGCCATGCA 61.050 57.895 0.00 0.00 0.00 3.96
352 390 0.729116 CATGCATGGACCAACTCGAC 59.271 55.000 19.40 0.00 0.00 4.20
355 393 1.234821 GCATGGACCAACTCGACAAA 58.765 50.000 0.00 0.00 0.00 2.83
370 408 0.394352 ACAAATGCCCCATCGGTCTC 60.394 55.000 0.00 0.00 0.00 3.36
376 414 2.415010 CCCATCGGTCTCTGCTCG 59.585 66.667 0.00 0.00 0.00 5.03
379 417 2.441164 ATCGGTCTCTGCTCGCCT 60.441 61.111 0.00 0.00 0.00 5.52
382 420 4.863925 GGTCTCTGCTCGCCTCGC 62.864 72.222 0.00 0.00 0.00 5.03
394 432 2.202932 CCTCGCCGTGGATTGAGG 60.203 66.667 0.00 7.57 41.82 3.86
418 456 4.104183 CCGGCCCGCTTTCCCTTA 62.104 66.667 0.00 0.00 0.00 2.69
419 457 2.192175 CGGCCCGCTTTCCCTTAT 59.808 61.111 0.00 0.00 0.00 1.73
420 458 1.453197 CGGCCCGCTTTCCCTTATT 60.453 57.895 0.00 0.00 0.00 1.40
421 459 1.444917 CGGCCCGCTTTCCCTTATTC 61.445 60.000 0.00 0.00 0.00 1.75
422 460 1.107538 GGCCCGCTTTCCCTTATTCC 61.108 60.000 0.00 0.00 0.00 3.01
423 461 1.107538 GCCCGCTTTCCCTTATTCCC 61.108 60.000 0.00 0.00 0.00 3.97
424 462 0.551396 CCCGCTTTCCCTTATTCCCT 59.449 55.000 0.00 0.00 0.00 4.20
425 463 1.477014 CCCGCTTTCCCTTATTCCCTC 60.477 57.143 0.00 0.00 0.00 4.30
426 464 1.490910 CCGCTTTCCCTTATTCCCTCT 59.509 52.381 0.00 0.00 0.00 3.69
427 465 2.485657 CCGCTTTCCCTTATTCCCTCTC 60.486 54.545 0.00 0.00 0.00 3.20
428 466 2.485657 CGCTTTCCCTTATTCCCTCTCC 60.486 54.545 0.00 0.00 0.00 3.71
429 467 2.158593 GCTTTCCCTTATTCCCTCTCCC 60.159 54.545 0.00 0.00 0.00 4.30
430 468 3.398490 CTTTCCCTTATTCCCTCTCCCT 58.602 50.000 0.00 0.00 0.00 4.20
431 469 2.496679 TCCCTTATTCCCTCTCCCTG 57.503 55.000 0.00 0.00 0.00 4.45
432 470 1.657162 TCCCTTATTCCCTCTCCCTGT 59.343 52.381 0.00 0.00 0.00 4.00
433 471 2.050918 CCCTTATTCCCTCTCCCTGTC 58.949 57.143 0.00 0.00 0.00 3.51
434 472 2.360854 CCCTTATTCCCTCTCCCTGTCT 60.361 54.545 0.00 0.00 0.00 3.41
435 473 3.388913 CCTTATTCCCTCTCCCTGTCTT 58.611 50.000 0.00 0.00 0.00 3.01
441 479 0.614979 CCTCTCCCTGTCTTTCCCGA 60.615 60.000 0.00 0.00 0.00 5.14
486 524 4.467107 AGGGAGGGGACGGAGCTC 62.467 72.222 4.71 4.71 0.00 4.09
542 581 1.414866 GGGGAAGGGAGGAGAGATGC 61.415 65.000 0.00 0.00 0.00 3.91
554 593 1.830477 GAGAGATGCAGACAAGGGAGT 59.170 52.381 0.00 0.00 0.00 3.85
596 639 2.566913 TGTGCAGTGTAAATTCACCGT 58.433 42.857 0.00 0.00 38.91 4.83
612 655 1.202842 ACCGTCGGTTTCCTTTTCCAT 60.203 47.619 12.23 0.00 27.29 3.41
630 673 3.068732 TCCATTGGAGATTACTCTCTGCG 59.931 47.826 9.69 0.00 46.11 5.18
632 675 4.442052 CCATTGGAGATTACTCTCTGCGAA 60.442 45.833 9.69 0.18 46.11 4.70
654 697 1.589716 AATTTCCCTGCTGCAGCGAC 61.590 55.000 32.11 8.59 45.83 5.19
662 705 0.953727 TGCTGCAGCGACTTGAATTT 59.046 45.000 32.11 0.00 45.83 1.82
713 759 5.342259 GTGATCGTTTAGCAATTTGGTTGAC 59.658 40.000 6.39 5.40 40.37 3.18
722 768 3.674753 GCAATTTGGTTGACCGATTCTTG 59.325 43.478 0.00 0.91 40.37 3.02
723 769 4.236935 CAATTTGGTTGACCGATTCTTGG 58.763 43.478 0.00 0.00 40.37 3.61
726 772 2.938838 TGGTTGACCGATTCTTGGTTT 58.061 42.857 0.00 0.00 40.63 3.27
727 773 2.882137 TGGTTGACCGATTCTTGGTTTC 59.118 45.455 0.00 0.00 40.63 2.78
728 774 2.228103 GGTTGACCGATTCTTGGTTTCC 59.772 50.000 0.00 0.00 40.63 3.13
730 776 2.778299 TGACCGATTCTTGGTTTCCTG 58.222 47.619 0.00 0.00 40.63 3.86
733 779 2.304761 ACCGATTCTTGGTTTCCTGCTA 59.695 45.455 0.00 0.00 35.82 3.49
734 780 2.939103 CCGATTCTTGGTTTCCTGCTAG 59.061 50.000 0.00 0.00 0.00 3.42
735 781 2.352960 CGATTCTTGGTTTCCTGCTAGC 59.647 50.000 8.10 8.10 0.00 3.42
858 913 0.662970 GCCGCGTCAATTTGCTTTGA 60.663 50.000 4.92 0.00 33.32 2.69
866 921 4.150451 CGTCAATTTGCTTTGATTTGACCC 59.850 41.667 8.12 0.00 37.88 4.46
895 950 1.681264 ACTGCCTTACAAACTGCCAAC 59.319 47.619 0.00 0.00 0.00 3.77
897 952 2.297033 CTGCCTTACAAACTGCCAACAT 59.703 45.455 0.00 0.00 0.00 2.71
904 959 7.255590 GCCTTACAAACTGCCAACATCATATAT 60.256 37.037 0.00 0.00 0.00 0.86
905 960 9.283768 CCTTACAAACTGCCAACATCATATATA 57.716 33.333 0.00 0.00 0.00 0.86
951 1132 5.190528 TCCCAAACTTCTAGAGATGCATCTT 59.809 40.000 29.26 20.17 37.25 2.40
952 1133 5.884792 CCCAAACTTCTAGAGATGCATCTTT 59.115 40.000 29.26 25.44 37.25 2.52
953 1134 6.376581 CCCAAACTTCTAGAGATGCATCTTTT 59.623 38.462 29.26 21.74 37.25 2.27
954 1135 7.414984 CCCAAACTTCTAGAGATGCATCTTTTC 60.415 40.741 29.26 17.29 37.25 2.29
955 1136 7.120285 CCAAACTTCTAGAGATGCATCTTTTCA 59.880 37.037 29.26 13.93 37.25 2.69
956 1137 7.608308 AACTTCTAGAGATGCATCTTTTCAC 57.392 36.000 29.26 16.37 37.25 3.18
957 1138 5.809562 ACTTCTAGAGATGCATCTTTTCACG 59.190 40.000 29.26 18.25 37.25 4.35
958 1139 4.686972 TCTAGAGATGCATCTTTTCACGG 58.313 43.478 29.26 15.00 37.25 4.94
962 1143 1.470098 GATGCATCTTTTCACGGCTGT 59.530 47.619 19.70 0.00 0.00 4.40
1009 1193 5.794687 TTACAGTTAAATCATGGCTGACG 57.205 39.130 0.00 0.00 33.22 4.35
1024 1208 2.868044 GCTGACGAGCCAAAGAAGAGAA 60.868 50.000 0.00 0.00 39.57 2.87
1035 1219 5.665459 CCAAAGAAGAGAACTATCGTGGAT 58.335 41.667 0.00 0.00 0.00 3.41
1041 1225 2.553172 GAGAACTATCGTGGATAGCGGT 59.447 50.000 11.53 0.00 44.00 5.68
1113 1297 4.290622 GGCCCCATGATCCGGCAT 62.291 66.667 0.00 0.00 44.90 4.40
1212 1396 2.102252 AGAGCTATGCAGGCTTCACTAC 59.898 50.000 16.35 4.89 40.40 2.73
1242 1426 1.210931 CCTTGCCGTCGACGAGTTA 59.789 57.895 37.65 17.89 43.02 2.24
1473 1657 2.573462 AGAAGCTAAGTTCCATCCTGCA 59.427 45.455 0.00 0.00 0.00 4.41
1524 1708 4.947388 GGATACCTGCAAAACATTCCTGTA 59.053 41.667 0.00 0.00 33.36 2.74
1530 1714 5.865552 CCTGCAAAACATTCCTGTAAAGATG 59.134 40.000 0.00 0.00 33.36 2.90
1629 1813 6.417258 TGATTGGCTTGTTCATATCAGAAGA 58.583 36.000 0.00 0.00 0.00 2.87
1692 1876 0.179004 TGGCTCGCCAAAAAGAGGAA 60.179 50.000 8.43 0.00 44.12 3.36
2083 2267 4.105486 CGTTGCGAAGATGACATCTCTAA 58.895 43.478 18.21 8.53 39.08 2.10
2109 2293 1.298859 GCCAGTTTTCTCGCATCGGT 61.299 55.000 0.00 0.00 34.27 4.69
2208 2392 6.949352 ACCACACCATTGATCAATATTCTC 57.051 37.500 20.32 0.00 0.00 2.87
2256 2440 0.392706 TGCTTCTTTCTGAGTGCCGA 59.607 50.000 0.00 0.00 0.00 5.54
2487 2671 2.978156 ATGGTGGTGACATGAACCTT 57.022 45.000 18.78 6.44 46.14 3.50
2550 2734 4.810790 AGGTATTGAACGACTGTCTTCTG 58.189 43.478 6.21 0.00 0.00 3.02
2805 2989 5.066375 CGATGATTTTATGGTGCTCTTGGAA 59.934 40.000 0.00 0.00 0.00 3.53
3069 3253 0.323269 TGGAGGCATTTGCGGATGAA 60.323 50.000 3.53 0.00 43.26 2.57
3123 3307 3.247886 GGAAGGAAACAACGTTCAGAGAC 59.752 47.826 0.00 0.00 36.70 3.36
3340 3524 1.726853 CACGAGGTCCTTGGATGTTC 58.273 55.000 11.08 0.00 0.00 3.18
3342 3526 1.550976 ACGAGGTCCTTGGATGTTCTC 59.449 52.381 11.08 0.00 0.00 2.87
3402 3586 5.189180 GCTGGTATTCTTCTCCAACAATCT 58.811 41.667 0.00 0.00 0.00 2.40
3403 3587 5.065731 GCTGGTATTCTTCTCCAACAATCTG 59.934 44.000 0.00 0.00 0.00 2.90
3440 3624 8.905702 CACCTTCTGAATTTTATTTCTGTTTCG 58.094 33.333 0.00 0.00 0.00 3.46
3441 3625 8.846211 ACCTTCTGAATTTTATTTCTGTTTCGA 58.154 29.630 0.00 0.00 0.00 3.71
3457 3642 2.703798 CGACCCCCTCGCGTTCTAA 61.704 63.158 5.77 0.00 35.06 2.10
3483 3668 3.299340 ACAAGACGCGTCTATTTGTCT 57.701 42.857 39.33 21.06 43.18 3.41
3485 3670 1.630148 AGACGCGTCTATTTGTCTGC 58.370 50.000 38.67 9.13 40.03 4.26
3491 3676 2.159085 GCGTCTATTTGTCTGCCTAGGT 60.159 50.000 11.31 0.00 0.00 3.08
3492 3677 3.679083 GCGTCTATTTGTCTGCCTAGGTT 60.679 47.826 11.31 0.00 0.00 3.50
3528 3713 8.812147 TGTTTATCAGTTACAGTGAAGTAGTG 57.188 34.615 0.00 0.00 30.32 2.74
3675 3879 4.257267 AGTTTGAAGCCTGTTAAATGCC 57.743 40.909 0.00 0.00 0.00 4.40
3693 3961 0.750249 CCCCCTGTTCCACAAACAAC 59.250 55.000 0.00 0.00 46.95 3.32
3811 4123 9.573133 ACTCTTAATTCAAATCTTAAAATGGCG 57.427 29.630 0.00 0.00 0.00 5.69
3828 4144 2.333926 GGCGATTGGCAAGGTAAAAAC 58.666 47.619 5.96 0.00 46.16 2.43
3837 4153 2.288213 GCAAGGTAAAAACTCCTGTGCC 60.288 50.000 0.00 0.00 34.76 5.01
4052 4368 7.361371 GCGTAATATACAGCTCTGTCTGTCTAT 60.361 40.741 5.72 6.71 45.32 1.98
4092 4408 7.228706 ACCAAGTCAATTCTGAAAGTACGATTT 59.771 33.333 0.00 0.00 31.88 2.17
4112 4428 2.355197 TCTTTTGCGCAATGCTAGCTA 58.645 42.857 25.64 2.70 46.63 3.32
4113 4429 2.095853 TCTTTTGCGCAATGCTAGCTAC 59.904 45.455 25.64 1.59 46.63 3.58
4114 4430 1.447945 TTTGCGCAATGCTAGCTACA 58.552 45.000 25.64 0.97 46.63 2.74
4115 4431 1.009078 TTGCGCAATGCTAGCTACAG 58.991 50.000 21.02 4.54 46.63 2.74
4116 4432 0.108186 TGCGCAATGCTAGCTACAGT 60.108 50.000 17.23 0.00 46.63 3.55
4117 4433 1.136110 TGCGCAATGCTAGCTACAGTA 59.864 47.619 17.23 0.57 46.63 2.74
4118 4434 1.789464 GCGCAATGCTAGCTACAGTAG 59.211 52.381 17.23 2.85 41.73 2.57
4119 4435 3.986015 GCGCAATGCTAGCTACAGTAGC 61.986 54.545 23.17 23.17 46.08 3.58
4223 4600 1.978617 CGGCATGTGGAGGGCTTTT 60.979 57.895 0.00 0.00 0.00 2.27
4238 4615 2.989166 GGCTTTTGCTTCCATTTTCTCG 59.011 45.455 0.00 0.00 46.54 4.04
4245 4622 3.244770 TGCTTCCATTTTCTCGGTTAGGT 60.245 43.478 0.00 0.00 0.00 3.08
4265 4642 0.605319 GTGCGGTTGATCAGGTCCAA 60.605 55.000 12.04 0.00 0.00 3.53
4322 4699 7.021790 GTGCTTGCTGAAAAATAAGTACTACC 58.978 38.462 0.00 0.00 34.37 3.18
4328 4705 6.074463 GCTGAAAAATAAGTACTACCCGATCG 60.074 42.308 8.51 8.51 0.00 3.69
4331 4708 8.632679 TGAAAAATAAGTACTACCCGATCGTAT 58.367 33.333 15.09 3.87 0.00 3.06
4333 4710 8.807667 AAAATAAGTACTACCCGATCGTATTG 57.192 34.615 15.09 5.14 0.00 1.90
4362 4742 4.109050 GTCATCTCTTTGACATCTCGTCC 58.891 47.826 0.00 0.00 44.71 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.388065 ATCCGCTGTCGAAGGAGAGG 61.388 60.000 4.35 4.35 37.49 3.69
50 58 1.002624 TTGGGTTGGATCCGCTGTC 60.003 57.895 7.39 0.00 0.00 3.51
54 62 3.131478 CGGTTGGGTTGGATCCGC 61.131 66.667 7.39 2.16 35.01 5.54
75 83 2.271944 AGCTAGCTCCGTTTGGTTTT 57.728 45.000 12.68 0.00 36.30 2.43
91 104 0.115349 AGGGCCATCCGTCTATAGCT 59.885 55.000 6.18 0.00 41.52 3.32
92 105 1.848652 TAGGGCCATCCGTCTATAGC 58.151 55.000 6.18 0.00 41.52 2.97
93 106 3.385111 GGAATAGGGCCATCCGTCTATAG 59.615 52.174 6.18 0.00 41.52 1.31
94 107 3.371965 GGAATAGGGCCATCCGTCTATA 58.628 50.000 6.18 0.00 41.52 1.31
198 228 1.557269 AATGGAACCTCTGGCGAGCT 61.557 55.000 0.00 0.00 35.90 4.09
199 229 0.678048 AAATGGAACCTCTGGCGAGC 60.678 55.000 0.00 0.00 35.90 5.03
248 278 2.697431 GATCGTGAGGAGAAGATCGG 57.303 55.000 0.00 0.00 31.61 4.18
250 280 1.335182 TGCGATCGTGAGGAGAAGATC 59.665 52.381 17.81 0.00 36.92 2.75
251 281 1.393603 TGCGATCGTGAGGAGAAGAT 58.606 50.000 17.81 0.00 0.00 2.40
252 282 1.335182 GATGCGATCGTGAGGAGAAGA 59.665 52.381 17.81 0.00 0.00 2.87
255 285 1.456196 GGGATGCGATCGTGAGGAGA 61.456 60.000 17.81 0.00 0.00 3.71
257 287 2.845550 CGGGATGCGATCGTGAGGA 61.846 63.158 17.81 0.00 0.00 3.71
258 288 2.355126 CGGGATGCGATCGTGAGG 60.355 66.667 17.81 0.00 0.00 3.86
259 289 3.032609 GCGGGATGCGATCGTGAG 61.033 66.667 17.81 4.10 0.00 3.51
286 324 1.477685 GGAGGAATCGGGGCGGAATA 61.478 60.000 0.00 0.00 0.00 1.75
292 330 3.097162 AAGGGGAGGAATCGGGGC 61.097 66.667 0.00 0.00 0.00 5.80
293 331 1.384643 AGAAGGGGAGGAATCGGGG 60.385 63.158 0.00 0.00 0.00 5.73
299 337 2.042706 ACGTAGAAGAGAAGGGGAGGAA 59.957 50.000 0.00 0.00 0.00 3.36
304 342 2.354199 GACGTACGTAGAAGAGAAGGGG 59.646 54.545 22.87 0.00 0.00 4.79
334 372 0.324614 TGTCGAGTTGGTCCATGCAT 59.675 50.000 0.00 0.00 0.00 3.96
335 373 0.107643 TTGTCGAGTTGGTCCATGCA 59.892 50.000 0.00 0.00 0.00 3.96
336 374 1.234821 TTTGTCGAGTTGGTCCATGC 58.765 50.000 0.00 0.00 0.00 4.06
338 376 1.812571 GCATTTGTCGAGTTGGTCCAT 59.187 47.619 0.00 0.00 0.00 3.41
376 414 2.892425 CTCAATCCACGGCGAGGC 60.892 66.667 18.95 0.00 0.00 4.70
379 417 4.467084 GGCCTCAATCCACGGCGA 62.467 66.667 16.62 0.00 44.68 5.54
382 420 4.506255 GGGGGCCTCAATCCACGG 62.506 72.222 4.16 0.00 0.00 4.94
406 444 1.490910 AGAGGGAATAAGGGAAAGCGG 59.509 52.381 0.00 0.00 0.00 5.52
407 445 2.485657 GGAGAGGGAATAAGGGAAAGCG 60.486 54.545 0.00 0.00 0.00 4.68
408 446 2.158593 GGGAGAGGGAATAAGGGAAAGC 60.159 54.545 0.00 0.00 0.00 3.51
409 447 3.137360 CAGGGAGAGGGAATAAGGGAAAG 59.863 52.174 0.00 0.00 0.00 2.62
410 448 3.123273 CAGGGAGAGGGAATAAGGGAAA 58.877 50.000 0.00 0.00 0.00 3.13
411 449 2.047296 ACAGGGAGAGGGAATAAGGGAA 59.953 50.000 0.00 0.00 0.00 3.97
412 450 1.657162 ACAGGGAGAGGGAATAAGGGA 59.343 52.381 0.00 0.00 0.00 4.20
413 451 2.050918 GACAGGGAGAGGGAATAAGGG 58.949 57.143 0.00 0.00 0.00 3.95
414 452 3.053359 AGACAGGGAGAGGGAATAAGG 57.947 52.381 0.00 0.00 0.00 2.69
415 453 4.141597 GGAAAGACAGGGAGAGGGAATAAG 60.142 50.000 0.00 0.00 0.00 1.73
416 454 3.780850 GGAAAGACAGGGAGAGGGAATAA 59.219 47.826 0.00 0.00 0.00 1.40
417 455 3.385115 GGAAAGACAGGGAGAGGGAATA 58.615 50.000 0.00 0.00 0.00 1.75
418 456 2.200955 GGAAAGACAGGGAGAGGGAAT 58.799 52.381 0.00 0.00 0.00 3.01
419 457 1.657804 GGAAAGACAGGGAGAGGGAA 58.342 55.000 0.00 0.00 0.00 3.97
420 458 0.252742 GGGAAAGACAGGGAGAGGGA 60.253 60.000 0.00 0.00 0.00 4.20
421 459 1.617947 CGGGAAAGACAGGGAGAGGG 61.618 65.000 0.00 0.00 0.00 4.30
422 460 0.614979 TCGGGAAAGACAGGGAGAGG 60.615 60.000 0.00 0.00 0.00 3.69
423 461 0.533032 GTCGGGAAAGACAGGGAGAG 59.467 60.000 0.00 0.00 40.65 3.20
424 462 1.248785 CGTCGGGAAAGACAGGGAGA 61.249 60.000 0.00 0.00 40.98 3.71
425 463 1.215647 CGTCGGGAAAGACAGGGAG 59.784 63.158 0.00 0.00 40.98 4.30
426 464 2.939261 GCGTCGGGAAAGACAGGGA 61.939 63.158 0.00 0.00 40.98 4.20
427 465 2.434359 GCGTCGGGAAAGACAGGG 60.434 66.667 0.00 0.00 40.98 4.45
428 466 2.434359 GGCGTCGGGAAAGACAGG 60.434 66.667 0.00 0.00 40.98 4.00
429 467 2.809601 CGGCGTCGGGAAAGACAG 60.810 66.667 0.00 0.00 40.98 3.51
459 497 4.835891 CCCTCCCTCGCCGGTAGT 62.836 72.222 1.90 0.00 0.00 2.73
468 506 4.467107 AGCTCCGTCCCCTCCCTC 62.467 72.222 0.00 0.00 0.00 4.30
542 581 1.302832 GTGGCCACTCCCTTGTCTG 60.303 63.158 29.12 0.00 0.00 3.51
596 639 3.153919 CTCCAATGGAAAAGGAAACCGA 58.846 45.455 2.61 0.00 0.00 4.69
612 655 3.429547 GCTTCGCAGAGAGTAATCTCCAA 60.430 47.826 16.25 4.35 41.26 3.53
713 759 1.826385 AGCAGGAAACCAAGAATCGG 58.174 50.000 0.00 0.00 0.00 4.18
722 768 0.608308 AAACCGGCTAGCAGGAAACC 60.608 55.000 36.29 7.84 35.27 3.27
723 769 1.244816 AAAACCGGCTAGCAGGAAAC 58.755 50.000 36.29 8.60 35.27 2.78
816 871 5.291614 GCGATTCACGGGTTTATTTGTACTA 59.708 40.000 0.00 0.00 42.83 1.82
817 872 4.093850 GCGATTCACGGGTTTATTTGTACT 59.906 41.667 0.00 0.00 42.83 2.73
818 873 4.336932 GCGATTCACGGGTTTATTTGTAC 58.663 43.478 0.00 0.00 42.83 2.90
904 959 7.656137 GGGAATTAGATGCGACAAAGAAGTATA 59.344 37.037 0.00 0.00 0.00 1.47
905 960 6.483640 GGGAATTAGATGCGACAAAGAAGTAT 59.516 38.462 0.00 0.00 0.00 2.12
917 1093 6.049149 TCTAGAAGTTTGGGAATTAGATGCG 58.951 40.000 0.00 0.00 0.00 4.73
920 1096 7.936301 GCATCTCTAGAAGTTTGGGAATTAGAT 59.064 37.037 0.00 0.00 0.00 1.98
951 1132 1.317613 ATTTCAGCACAGCCGTGAAA 58.682 45.000 3.69 8.28 46.80 2.69
952 1133 1.001487 CAATTTCAGCACAGCCGTGAA 60.001 47.619 3.69 0.00 46.80 3.18
953 1134 0.592637 CAATTTCAGCACAGCCGTGA 59.407 50.000 3.69 0.00 46.80 4.35
954 1135 0.311790 ACAATTTCAGCACAGCCGTG 59.688 50.000 0.00 0.00 46.56 4.94
955 1136 1.535462 GTACAATTTCAGCACAGCCGT 59.465 47.619 0.00 0.00 0.00 5.68
956 1137 1.535028 TGTACAATTTCAGCACAGCCG 59.465 47.619 0.00 0.00 0.00 5.52
957 1138 3.441572 AGATGTACAATTTCAGCACAGCC 59.558 43.478 0.00 0.00 0.00 4.85
958 1139 4.409570 CAGATGTACAATTTCAGCACAGC 58.590 43.478 0.00 0.00 0.00 4.40
962 1143 4.582869 AGAGCAGATGTACAATTTCAGCA 58.417 39.130 12.93 0.00 0.00 4.41
1035 1219 1.101635 CGAGACCTCCATCACCGCTA 61.102 60.000 0.00 0.00 0.00 4.26
1041 1225 1.689243 CCATGCCGAGACCTCCATCA 61.689 60.000 0.00 0.00 0.00 3.07
1113 1297 0.817013 GCTTGCCGGAATCAAATCCA 59.183 50.000 5.05 0.00 39.61 3.41
1116 1300 1.666209 CGGGCTTGCCGGAATCAAAT 61.666 55.000 5.05 0.00 0.00 2.32
1227 1411 2.174107 CGTAACTCGTCGACGGCA 59.826 61.111 35.05 18.04 40.29 5.69
1242 1426 3.001902 ATCGACCATCACACCGCGT 62.002 57.895 4.92 0.00 0.00 6.01
1359 1543 1.263217 CCCACGTTTTTCTTGACCGAG 59.737 52.381 0.00 0.00 0.00 4.63
1473 1657 6.119240 TCAATCAAATCCAGAGTCTTGAGT 57.881 37.500 0.00 0.00 31.70 3.41
1524 1708 6.556874 TCCCAACCACCTTTTTAATCATCTTT 59.443 34.615 0.00 0.00 0.00 2.52
1530 1714 4.830600 TGTCTCCCAACCACCTTTTTAATC 59.169 41.667 0.00 0.00 0.00 1.75
1629 1813 0.749454 GCCCGATCTGCTTGGACATT 60.749 55.000 0.00 0.00 0.00 2.71
2083 2267 1.677217 GCGAGAAAACTGGCTCTCCAT 60.677 52.381 0.00 0.00 42.51 3.41
2109 2293 4.715130 AGGAGGTGGCTGGCCGTA 62.715 66.667 7.14 0.00 39.42 4.02
2158 2342 6.727231 TGGTAACCATACTTCCTTAGAACTGA 59.273 38.462 0.00 0.00 32.36 3.41
2208 2392 1.153745 CTTGTCCCGGCTTCTCGAG 60.154 63.158 5.93 5.93 0.00 4.04
2256 2440 4.263243 GCAAGGATATCATCTACCTGCCTT 60.263 45.833 4.83 0.00 35.03 4.35
2487 2671 5.876357 AGGTAAGCTTTCACCACTTCATAA 58.124 37.500 18.52 0.00 37.28 1.90
2520 2704 5.408604 ACAGTCGTTCAATACCTCAATCAAC 59.591 40.000 0.00 0.00 0.00 3.18
2550 2734 2.131183 GAGCGAGCATACATCCTGTTC 58.869 52.381 0.00 0.00 0.00 3.18
2754 2938 7.911651 TCTTGGAATTGGCCATGTTTATTAAA 58.088 30.769 6.09 0.68 37.86 1.52
2805 2989 1.065636 TCCACTATCCAGTCGACGTCT 60.066 52.381 14.70 0.00 30.46 4.18
2991 3175 1.950828 TCGTTAACCTTTTCACGCCA 58.049 45.000 0.00 0.00 32.59 5.69
3063 3247 4.423732 CGGTGATGTGGAATTTTTCATCC 58.576 43.478 12.00 0.00 36.75 3.51
3069 3253 0.894835 GCCCGGTGATGTGGAATTTT 59.105 50.000 0.00 0.00 0.00 1.82
3123 3307 2.681848 CTGCCTTATCTCAACCAAGCAG 59.318 50.000 0.00 0.00 0.00 4.24
3340 3524 1.566211 TCCTTGAGCCTCCTCTTGAG 58.434 55.000 0.00 0.00 38.93 3.02
3342 3526 3.362870 AAATCCTTGAGCCTCCTCTTG 57.637 47.619 0.00 0.00 38.93 3.02
3402 3586 0.764369 AGAAGGTGGACACTGAGCCA 60.764 55.000 2.13 0.00 0.00 4.75
3403 3587 0.321122 CAGAAGGTGGACACTGAGCC 60.321 60.000 2.13 0.00 32.90 4.70
3440 3624 0.529992 CATTAGAACGCGAGGGGGTC 60.530 60.000 15.93 0.00 38.54 4.46
3441 3625 1.520666 CATTAGAACGCGAGGGGGT 59.479 57.895 15.93 0.00 41.70 4.95
3457 3642 3.795623 ATAGACGCGTCTTGTAACCAT 57.204 42.857 42.90 26.66 40.93 3.55
3483 3668 4.980573 ACAGTCAAAACATAACCTAGGCA 58.019 39.130 9.30 0.00 0.00 4.75
3485 3670 9.226606 TGATAAACAGTCAAAACATAACCTAGG 57.773 33.333 7.41 7.41 0.00 3.02
3521 3706 7.775053 TGAAAATTATTTGAGGGCACTACTT 57.225 32.000 0.00 0.00 0.00 2.24
3528 3713 9.440773 AGAGAAAATTGAAAATTATTTGAGGGC 57.559 29.630 0.00 0.00 0.00 5.19
3693 3961 9.025020 CCGTATGCTAGTATGCTATATTTTCTG 57.975 37.037 3.24 0.00 0.00 3.02
3811 4123 4.280929 ACAGGAGTTTTTACCTTGCCAATC 59.719 41.667 0.00 0.00 33.91 2.67
3828 4144 2.365617 ACGAATGGTATAGGCACAGGAG 59.634 50.000 0.00 0.00 0.00 3.69
3837 4153 0.036306 GGGCCCCACGAATGGTATAG 59.964 60.000 12.23 0.00 45.66 1.31
3861 4177 5.474532 TGTTCCATGTCTTCATCTCCAAAAG 59.525 40.000 0.00 0.00 31.15 2.27
4092 4408 1.167851 AGCTAGCATTGCGCAAAAGA 58.832 45.000 28.81 11.78 46.13 2.52
4114 4430 3.130693 GGTTTCCGATCTACAGTGCTACT 59.869 47.826 0.00 0.00 0.00 2.57
4115 4431 3.119245 TGGTTTCCGATCTACAGTGCTAC 60.119 47.826 0.00 0.00 0.00 3.58
4116 4432 3.093814 TGGTTTCCGATCTACAGTGCTA 58.906 45.455 0.00 0.00 0.00 3.49
4117 4433 1.899814 TGGTTTCCGATCTACAGTGCT 59.100 47.619 0.00 0.00 0.00 4.40
4118 4434 2.094182 TCTGGTTTCCGATCTACAGTGC 60.094 50.000 0.00 0.00 0.00 4.40
4119 4435 3.868757 TCTGGTTTCCGATCTACAGTG 57.131 47.619 0.00 0.00 0.00 3.66
4218 4595 2.989166 CCGAGAAAATGGAAGCAAAAGC 59.011 45.455 0.00 0.00 0.00 3.51
4223 4600 3.244770 ACCTAACCGAGAAAATGGAAGCA 60.245 43.478 0.00 0.00 0.00 3.91
4238 4615 1.084289 GATCAACCGCACACCTAACC 58.916 55.000 0.00 0.00 0.00 2.85
4245 4622 1.003839 GGACCTGATCAACCGCACA 60.004 57.895 0.00 0.00 0.00 4.57
4265 4642 1.465689 CGATCGAGGCGCAACAATTTT 60.466 47.619 10.26 0.00 0.00 1.82
4322 4699 3.186909 TGACTTTGAGCAATACGATCGG 58.813 45.455 20.98 2.04 30.45 4.18


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

AutoCloner maintained by Alex Coulton.