Multiple sequence alignment - TraesCS6A01G365400

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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 TraesCS6A01G365400 chr6A 100.000 2547 0 0 1 2547 593573208 593575754 0.000000e+00 4704.0
1 TraesCS6A01G365400 chr6A 94.286 525 29 1 1 525 605393854 605393331 0.000000e+00 802.0
2 TraesCS6A01G365400 chr6A 81.244 965 122 33 594 1532 593695649 593696580 0.000000e+00 725.0
3 TraesCS6A01G365400 chr6A 94.614 427 20 3 1722 2146 2695089 2695514 0.000000e+00 658.0
4 TraesCS6A01G365400 chr6A 85.619 452 55 5 1088 1532 593613580 593614028 1.380000e-127 466.0
5 TraesCS6A01G365400 chr6A 82.772 505 66 12 1088 1571 593732858 593733362 5.030000e-117 431.0
6 TraesCS6A01G365400 chr6A 82.917 480 56 16 1108 1574 593562283 593561817 2.360000e-110 409.0
7 TraesCS6A01G365400 chr6A 86.095 338 34 11 618 947 593681942 593682274 4.030000e-93 351.0
8 TraesCS6A01G365400 chr6A 83.012 259 29 10 1088 1343 593792309 593792555 1.190000e-53 220.0
9 TraesCS6A01G365400 chr6A 94.366 71 3 1 504 573 593573657 593573727 9.640000e-20 108.0
10 TraesCS6A01G365400 chr6A 90.196 51 1 1 844 894 593692186 593692232 2.120000e-06 63.9
11 TraesCS6A01G365400 chr3A 96.472 822 26 3 1729 2547 713142903 713143724 0.000000e+00 1354.0
12 TraesCS6A01G365400 chr3A 93.524 525 34 0 1 525 699514653 699515177 0.000000e+00 782.0
13 TraesCS6A01G365400 chr7A 96.024 830 29 4 1721 2547 160577822 160578650 0.000000e+00 1347.0
14 TraesCS6A01G365400 chr4A 94.512 820 39 2 1729 2547 551719627 551720441 0.000000e+00 1260.0
15 TraesCS6A01G365400 chr4A 94.990 519 26 0 1 519 83763708 83764226 0.000000e+00 815.0
16 TraesCS6A01G365400 chr4A 94.667 525 28 0 1 525 640919616 640920140 0.000000e+00 815.0
17 TraesCS6A01G365400 chr1A 94.476 525 28 1 1 525 99877728 99877205 0.000000e+00 808.0
18 TraesCS6A01G365400 chr1A 93.714 525 33 0 1 525 23314742 23314218 0.000000e+00 787.0
19 TraesCS6A01G365400 chr1A 93.524 525 34 0 1 525 511249389 511249913 0.000000e+00 782.0
20 TraesCS6A01G365400 chr2A 94.095 525 31 0 1 525 125843080 125842556 0.000000e+00 798.0
21 TraesCS6A01G365400 chr5A 93.905 525 32 0 1 525 620163754 620164278 0.000000e+00 793.0
22 TraesCS6A01G365400 chr6B 81.828 963 103 33 616 1531 675792255 675793192 0.000000e+00 743.0
23 TraesCS6A01G365400 chr6B 87.556 450 50 3 1089 1532 675796992 675797441 1.350000e-142 516.0
24 TraesCS6A01G365400 chr6B 81.875 480 72 6 1108 1575 676036469 676036945 8.540000e-105 390.0
25 TraesCS6A01G365400 chr6B 83.113 302 42 5 1088 1383 676136384 676136682 1.500000e-67 267.0
26 TraesCS6A01G365400 chr6B 93.478 46 2 1 793 837 676035538 676035583 1.640000e-07 67.6
27 TraesCS6A01G365400 chr2D 95.024 422 19 2 1729 2149 524527493 524527073 0.000000e+00 662.0
28 TraesCS6A01G365400 chr2D 95.607 387 17 0 2161 2547 147425453 147425067 2.780000e-174 621.0
29 TraesCS6A01G365400 chr3D 95.012 421 19 2 1730 2149 573041461 573041042 0.000000e+00 660.0
30 TraesCS6A01G365400 chr1D 94.787 422 20 2 1729 2149 451283920 451283500 0.000000e+00 656.0
31 TraesCS6A01G365400 chr7D 94.988 419 18 3 1729 2146 391210222 391210638 0.000000e+00 654.0
32 TraesCS6A01G365400 chr7D 95.866 387 16 0 2161 2547 242012863 242012477 5.980000e-176 627.0
33 TraesCS6A01G365400 chr7D 95.607 387 17 0 2161 2547 262347298 262346912 2.780000e-174 621.0
34 TraesCS6A01G365400 chr5D 94.550 422 21 2 1726 2146 450111882 450112302 0.000000e+00 651.0
35 TraesCS6A01G365400 chr5D 95.607 387 17 0 2161 2547 450112425 450112811 2.780000e-174 621.0
36 TraesCS6A01G365400 chr5D 95.349 387 18 0 2161 2547 549580350 549580736 1.290000e-172 616.0
37 TraesCS6A01G365400 chr6D 95.607 387 17 0 2161 2547 449270559 449270173 2.780000e-174 621.0
38 TraesCS6A01G365400 chr6D 85.593 590 56 14 959 1532 446814670 446815246 2.180000e-165 592.0
39 TraesCS6A01G365400 chr6D 82.818 582 77 16 959 1532 446845662 446846228 1.360000e-137 499.0
40 TraesCS6A01G365400 chr6D 81.693 508 72 11 1088 1574 446728041 446727534 1.100000e-108 403.0
41 TraesCS6A01G365400 chr6D 86.575 365 34 10 594 950 446745142 446745499 3.070000e-104 388.0
42 TraesCS6A01G365400 chr6D 87.097 279 20 10 633 900 446814383 446814656 4.120000e-78 302.0
43 TraesCS6A01G365400 chr6D 95.139 144 6 1 1586 1728 446745660 446745803 2.550000e-55 226.0
44 TraesCS6A01G365400 chr6D 90.566 53 1 1 844 896 446845520 446845568 1.640000e-07 67.6
45 TraesCS6A01G365400 chrUn 85.144 451 58 4 1088 1532 81268099 81268546 1.070000e-123 453.0


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 TraesCS6A01G365400 chr6A 593573208 593575754 2546 False 2406.00 4704 97.1830 1 2547 2 chr6A.!!$F6 2546
1 TraesCS6A01G365400 chr6A 605393331 605393854 523 True 802.00 802 94.2860 1 525 1 chr6A.!!$R2 524
2 TraesCS6A01G365400 chr6A 593732858 593733362 504 False 431.00 431 82.7720 1088 1571 1 chr6A.!!$F4 483
3 TraesCS6A01G365400 chr6A 593692186 593696580 4394 False 394.45 725 85.7200 594 1532 2 chr6A.!!$F7 938
4 TraesCS6A01G365400 chr3A 713142903 713143724 821 False 1354.00 1354 96.4720 1729 2547 1 chr3A.!!$F2 818
5 TraesCS6A01G365400 chr3A 699514653 699515177 524 False 782.00 782 93.5240 1 525 1 chr3A.!!$F1 524
6 TraesCS6A01G365400 chr7A 160577822 160578650 828 False 1347.00 1347 96.0240 1721 2547 1 chr7A.!!$F1 826
7 TraesCS6A01G365400 chr4A 551719627 551720441 814 False 1260.00 1260 94.5120 1729 2547 1 chr4A.!!$F2 818
8 TraesCS6A01G365400 chr4A 83763708 83764226 518 False 815.00 815 94.9900 1 519 1 chr4A.!!$F1 518
9 TraesCS6A01G365400 chr4A 640919616 640920140 524 False 815.00 815 94.6670 1 525 1 chr4A.!!$F3 524
10 TraesCS6A01G365400 chr1A 99877205 99877728 523 True 808.00 808 94.4760 1 525 1 chr1A.!!$R2 524
11 TraesCS6A01G365400 chr1A 23314218 23314742 524 True 787.00 787 93.7140 1 525 1 chr1A.!!$R1 524
12 TraesCS6A01G365400 chr1A 511249389 511249913 524 False 782.00 782 93.5240 1 525 1 chr1A.!!$F1 524
13 TraesCS6A01G365400 chr2A 125842556 125843080 524 True 798.00 798 94.0950 1 525 1 chr2A.!!$R1 524
14 TraesCS6A01G365400 chr5A 620163754 620164278 524 False 793.00 793 93.9050 1 525 1 chr5A.!!$F1 524
15 TraesCS6A01G365400 chr6B 675792255 675797441 5186 False 629.50 743 84.6920 616 1532 2 chr6B.!!$F2 916
16 TraesCS6A01G365400 chr6B 676035538 676036945 1407 False 228.80 390 87.6765 793 1575 2 chr6B.!!$F3 782
17 TraesCS6A01G365400 chr5D 450111882 450112811 929 False 636.00 651 95.0785 1726 2547 2 chr5D.!!$F2 821
18 TraesCS6A01G365400 chr6D 446814383 446815246 863 False 447.00 592 86.3450 633 1532 2 chr6D.!!$F2 899
19 TraesCS6A01G365400 chr6D 446727534 446728041 507 True 403.00 403 81.6930 1088 1574 1 chr6D.!!$R1 486
20 TraesCS6A01G365400 chr6D 446745142 446745803 661 False 307.00 388 90.8570 594 1728 2 chr6D.!!$F1 1134
21 TraesCS6A01G365400 chr6D 446845520 446846228 708 False 283.30 499 86.6920 844 1532 2 chr6D.!!$F3 688

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
565 566 0.106149 CCGTTCTATTTAGGCGCCCT 59.894 55.0 26.15 13.52 37.71 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2454 10419 0.608308 GCGGGGTTAGTTTTCTGCCT 60.608 55.0 0.0 0.0 0.0 4.75 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
158 159 4.988598 CACACGGACGCCAAGCCT 62.989 66.667 0.00 0.00 0.00 4.58
176 177 1.674441 CCTGAACGACGCCTCTACATA 59.326 52.381 0.00 0.00 0.00 2.29
312 313 1.131623 CATTGCGCACGCGAACTTA 59.868 52.632 15.93 0.00 45.51 2.24
355 356 0.523072 GTAACGCCAGACTACGTCCA 59.477 55.000 0.00 0.00 42.68 4.02
514 515 1.202486 CGTTCTATTTAGGCGCCCTGA 60.202 52.381 26.15 9.59 34.61 3.86
529 530 3.298958 TGAGGGGCAGAACTAGCG 58.701 61.111 0.00 0.00 0.00 4.26
530 531 2.202946 GAGGGGCAGAACTAGCGC 60.203 66.667 0.00 0.00 43.37 5.92
559 560 2.288273 CCTCGAGGCCGTTCTATTTAGG 60.288 54.545 20.67 0.00 37.05 2.69
563 564 1.939597 GCCGTTCTATTTAGGCGCC 59.060 57.895 21.89 21.89 40.17 6.53
565 566 0.106149 CCGTTCTATTTAGGCGCCCT 59.894 55.000 26.15 13.52 37.71 5.19
566 567 1.217882 CGTTCTATTTAGGCGCCCTG 58.782 55.000 26.15 7.22 34.61 4.45
567 568 1.202486 CGTTCTATTTAGGCGCCCTGA 60.202 52.381 26.15 9.59 34.61 3.86
569 570 1.048601 TCTATTTAGGCGCCCTGAGG 58.951 55.000 26.15 9.75 34.61 3.86
643 3514 1.113788 AGTAAATTGCGCCCATGCAT 58.886 45.000 4.18 0.00 45.78 3.96
653 3524 1.202177 CGCCCATGCATACAAAGACAC 60.202 52.381 0.00 0.00 37.32 3.67
654 3525 1.818060 GCCCATGCATACAAAGACACA 59.182 47.619 0.00 0.00 37.47 3.72
657 3528 3.376234 CCCATGCATACAAAGACACAGAG 59.624 47.826 0.00 0.00 0.00 3.35
670 3541 4.054671 AGACACAGAGAAAAGAAAGCGAG 58.945 43.478 0.00 0.00 0.00 5.03
673 3544 3.431572 CACAGAGAAAAGAAAGCGAGAGG 59.568 47.826 0.00 0.00 0.00 3.69
701 3584 2.383527 GGCAGTGAAAGAGACGGCG 61.384 63.158 4.80 4.80 35.61 6.46
742 3625 1.472376 CCAGAATCGAAGGAGAGCCAC 60.472 57.143 0.00 0.00 36.29 5.01
744 3629 2.114616 AGAATCGAAGGAGAGCCACAT 58.885 47.619 0.00 0.00 36.29 3.21
862 3846 1.660560 GCTCCCGTGCATGCATTTCT 61.661 55.000 25.64 0.00 0.00 2.52
950 4434 1.711206 GTTGTTCAGGTCCTAGTCGC 58.289 55.000 0.00 0.00 0.00 5.19
951 4435 0.242825 TTGTTCAGGTCCTAGTCGCG 59.757 55.000 0.00 0.00 0.00 5.87
954 4438 1.320344 TTCAGGTCCTAGTCGCGCAT 61.320 55.000 8.75 0.00 0.00 4.73
956 4440 2.353607 GGTCCTAGTCGCGCATCG 60.354 66.667 8.75 0.00 40.15 3.84
975 4509 1.268899 CGCCGTCTCTATAAATCCCGT 59.731 52.381 0.00 0.00 0.00 5.28
992 4526 2.203938 TCCAACCCGCTTCCCTCT 60.204 61.111 0.00 0.00 0.00 3.69
1005 4539 3.676093 CTTCCCTCTGGTTTACAACTCC 58.324 50.000 0.00 0.00 0.00 3.85
1016 4550 3.887621 TTACAACTCCCAGAATCTCCG 57.112 47.619 0.00 0.00 0.00 4.63
1025 4559 2.092968 CCCAGAATCTCCGAAACCATCA 60.093 50.000 0.00 0.00 0.00 3.07
1026 4560 3.434167 CCCAGAATCTCCGAAACCATCAT 60.434 47.826 0.00 0.00 0.00 2.45
1027 4561 3.812053 CCAGAATCTCCGAAACCATCATC 59.188 47.826 0.00 0.00 0.00 2.92
1058 4593 3.312736 AGTGACACCAAAACCTCCATT 57.687 42.857 0.84 0.00 0.00 3.16
1067 4602 0.704664 AAACCTCCATTCCCTCCACC 59.295 55.000 0.00 0.00 0.00 4.61
1069 4604 2.386935 CCTCCATTCCCTCCACCCC 61.387 68.421 0.00 0.00 0.00 4.95
1071 4606 2.287194 CCATTCCCTCCACCCCCT 60.287 66.667 0.00 0.00 0.00 4.79
1073 4608 1.619363 CATTCCCTCCACCCCCTCA 60.619 63.158 0.00 0.00 0.00 3.86
1074 4609 1.308216 ATTCCCTCCACCCCCTCAG 60.308 63.158 0.00 0.00 0.00 3.35
1075 4610 1.837533 ATTCCCTCCACCCCCTCAGA 61.838 60.000 0.00 0.00 0.00 3.27
1076 4611 2.366167 CCCTCCACCCCCTCAGAG 60.366 72.222 0.00 0.00 0.00 3.35
1081 4640 1.687493 CCACCCCCTCAGAGTCTCC 60.687 68.421 0.00 0.00 0.00 3.71
1082 4641 1.390125 CACCCCCTCAGAGTCTCCT 59.610 63.158 0.00 0.00 0.00 3.69
1083 4642 0.631753 CACCCCCTCAGAGTCTCCTA 59.368 60.000 0.00 0.00 0.00 2.94
1085 4649 0.466555 CCCCCTCAGAGTCTCCTACG 60.467 65.000 0.00 0.00 0.00 3.51
1086 4650 0.256464 CCCCTCAGAGTCTCCTACGT 59.744 60.000 0.00 0.00 0.00 3.57
1152 4716 4.335647 CACCCAACTGCCGCTCCT 62.336 66.667 0.00 0.00 0.00 3.69
1153 4717 2.606519 ACCCAACTGCCGCTCCTA 60.607 61.111 0.00 0.00 0.00 2.94
1158 4722 0.176680 CAACTGCCGCTCCTACTCAT 59.823 55.000 0.00 0.00 0.00 2.90
1201 4777 4.988598 CGACGCCACCCACTTGCT 62.989 66.667 0.00 0.00 0.00 3.91
1252 4837 2.293318 CCACCAGGAGCCAGCACTA 61.293 63.158 0.00 0.00 36.89 2.74
1266 4851 2.088763 CACTACTGCACGTGCTCCG 61.089 63.158 37.59 27.19 42.66 4.63
1299 4890 3.918220 GCTCGTTCCGATGCAGCG 61.918 66.667 19.16 19.16 34.61 5.18
1373 9224 4.570663 CCGTCCATCCGCGGTCTC 62.571 72.222 27.15 11.29 42.73 3.36
1390 9241 1.205485 CTCGGCTCGAAGCGAATGAG 61.205 60.000 0.00 0.00 43.62 2.90
1508 9362 4.436998 CTCTCCGCCGTGTCCACC 62.437 72.222 0.00 0.00 0.00 4.61
1535 9389 2.202570 CGTCCCCGCGACAACTAG 60.203 66.667 8.23 0.00 42.07 2.57
1536 9390 2.693762 CGTCCCCGCGACAACTAGA 61.694 63.158 8.23 0.00 42.07 2.43
1537 9391 1.153881 GTCCCCGCGACAACTAGAC 60.154 63.158 8.23 0.00 41.54 2.59
1552 9406 6.951643 ACAACTAGACGTAAACAAATCAACC 58.048 36.000 0.00 0.00 0.00 3.77
1580 9434 3.386768 GCCATAGCAAGGTAGAATCGA 57.613 47.619 0.00 0.00 39.53 3.59
1581 9435 3.931578 GCCATAGCAAGGTAGAATCGAT 58.068 45.455 0.00 0.00 39.53 3.59
1582 9436 4.319177 GCCATAGCAAGGTAGAATCGATT 58.681 43.478 11.20 11.20 39.53 3.34
1583 9437 4.390297 GCCATAGCAAGGTAGAATCGATTC 59.610 45.833 27.16 27.16 39.53 2.52
1584 9438 4.932200 CCATAGCAAGGTAGAATCGATTCC 59.068 45.833 29.82 18.31 37.51 3.01
1608 9462 3.810386 GCCTAGTCAATTAGCTAAGCCAC 59.190 47.826 12.54 7.69 0.00 5.01
1689 9544 6.263168 CCCTGGTTTTGGATATAGATGAACAC 59.737 42.308 0.00 0.00 0.00 3.32
1697 9552 5.592688 TGGATATAGATGAACACGAGTGACA 59.407 40.000 10.50 9.71 0.00 3.58
1714 9569 2.557924 TGACAAATTGGAGACACATGGC 59.442 45.455 0.00 0.00 42.67 4.40
1814 9671 0.395724 GGGCATCTTTTCATCCCCGT 60.396 55.000 0.00 0.00 0.00 5.28
1927 9784 6.561945 TCCGCGAAATTACATTATTTTTGC 57.438 33.333 8.23 0.00 36.11 3.68
2011 9868 9.884465 GGATAAGAAACAAATATATGAGTGTGC 57.116 33.333 0.00 0.00 0.00 4.57
2123 9980 6.647334 TGCTGACAATGAATAAGGACAAAA 57.353 33.333 0.00 0.00 0.00 2.44
2175 10140 7.124599 ACATTCTCATAGATTTGGCATTGGAAA 59.875 33.333 0.00 0.00 0.00 3.13
2383 10348 8.500753 AAATGTTATTCTTTGTCGCCACTATA 57.499 30.769 0.00 0.00 0.00 1.31
2420 10385 6.406692 TTTGATTTTATCGTGGGTTTTCCA 57.593 33.333 0.00 0.00 44.79 3.53
2454 10419 1.276140 CCCGATGGGTTTAGGGGACA 61.276 60.000 0.00 0.00 40.51 4.02
2467 10432 2.062636 AGGGGACAGGCAGAAAACTAA 58.937 47.619 0.00 0.00 0.00 2.24
2485 10450 2.178876 AACCCCGCACACGATGATGA 62.179 55.000 0.00 0.00 43.93 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 159 1.065102 GCTATGTAGAGGCGTCGTTCA 59.935 52.381 0.00 2.61 0.00 3.18
219 220 2.383527 CGTTGTCGGAGCTGCTTCC 61.384 63.158 2.53 5.85 0.00 3.46
284 285 0.721154 GTGCGCAATGAATCACTCGA 59.279 50.000 14.00 0.00 0.00 4.04
355 356 3.196648 GCCACAAATCCGGCGATT 58.803 55.556 9.30 3.38 40.58 3.34
435 436 0.966370 GACCTAGCTCCCAGTCACGT 60.966 60.000 0.00 0.00 0.00 4.49
487 488 1.068127 GCCTAAATAGAACGGCCTCGA 59.932 52.381 0.00 0.00 40.11 4.04
489 490 1.499049 CGCCTAAATAGAACGGCCTC 58.501 55.000 0.00 0.00 39.34 4.70
514 515 3.787001 GGCGCTAGTTCTGCCCCT 61.787 66.667 7.64 0.00 43.06 4.79
520 521 4.796231 CGTGCCGGCGCTAGTTCT 62.796 66.667 35.04 0.00 35.36 3.01
538 539 2.288273 CCTAAATAGAACGGCCTCGAGG 60.288 54.545 27.83 27.83 40.11 4.63
539 540 2.862921 GCCTAAATAGAACGGCCTCGAG 60.863 54.545 5.13 5.13 40.11 4.04
541 542 1.499049 GCCTAAATAGAACGGCCTCG 58.501 55.000 0.00 0.00 43.02 4.63
542 543 1.499049 CGCCTAAATAGAACGGCCTC 58.501 55.000 0.00 0.00 39.34 4.70
544 545 1.504647 GGCGCCTAAATAGAACGGCC 61.505 60.000 22.15 0.00 40.03 6.13
545 546 1.504647 GGGCGCCTAAATAGAACGGC 61.505 60.000 28.56 15.82 42.77 5.68
547 548 1.202486 TCAGGGCGCCTAAATAGAACG 60.202 52.381 28.56 2.98 29.64 3.95
549 550 1.416401 CCTCAGGGCGCCTAAATAGAA 59.584 52.381 28.56 2.58 29.64 2.10
550 551 1.048601 CCTCAGGGCGCCTAAATAGA 58.951 55.000 28.56 13.74 29.64 1.98
551 552 0.035458 CCCTCAGGGCGCCTAAATAG 59.965 60.000 28.56 16.00 35.35 1.73
552 553 2.142220 CCCTCAGGGCGCCTAAATA 58.858 57.895 28.56 6.86 35.35 1.40
573 574 4.899239 GGCATCTCCAGCCGTCCG 62.899 72.222 0.00 0.00 43.15 4.79
611 3482 1.734163 ATTTACTGTGTACTGCCGGC 58.266 50.000 22.73 22.73 0.00 6.13
620 3491 1.202114 CATGGGCGCAATTTACTGTGT 59.798 47.619 10.83 0.00 0.00 3.72
643 3514 6.238103 CGCTTTCTTTTCTCTGTGTCTTTGTA 60.238 38.462 0.00 0.00 0.00 2.41
653 3524 2.999355 CCCTCTCGCTTTCTTTTCTCTG 59.001 50.000 0.00 0.00 0.00 3.35
654 3525 2.900546 TCCCTCTCGCTTTCTTTTCTCT 59.099 45.455 0.00 0.00 0.00 3.10
657 3528 3.364068 CGTTTCCCTCTCGCTTTCTTTTC 60.364 47.826 0.00 0.00 0.00 2.29
670 3541 1.026718 CACTGCCATCCGTTTCCCTC 61.027 60.000 0.00 0.00 0.00 4.30
673 3544 1.200020 CTTTCACTGCCATCCGTTTCC 59.800 52.381 0.00 0.00 0.00 3.13
701 3584 0.856490 CGACCGAACGATCAGACGTC 60.856 60.000 7.70 7.70 45.83 4.34
744 3629 0.533978 TTTGTTGCTACCGCTCAGCA 60.534 50.000 0.00 0.18 46.96 4.41
747 3632 0.591170 GCTTTTGTTGCTACCGCTCA 59.409 50.000 0.00 0.00 36.97 4.26
752 3637 1.080772 GGCCGCTTTTGTTGCTACC 60.081 57.895 0.00 0.00 0.00 3.18
793 3678 0.914417 GGAAGGGATGGTGGAGTGGA 60.914 60.000 0.00 0.00 0.00 4.02
794 3679 0.916358 AGGAAGGGATGGTGGAGTGG 60.916 60.000 0.00 0.00 0.00 4.00
795 3680 0.995024 AAGGAAGGGATGGTGGAGTG 59.005 55.000 0.00 0.00 0.00 3.51
796 3681 1.290134 GAAGGAAGGGATGGTGGAGT 58.710 55.000 0.00 0.00 0.00 3.85
862 3846 2.031465 GAAAACCGGCCGACCTCA 59.969 61.111 30.73 0.00 0.00 3.86
933 3934 1.880894 CGCGACTAGGACCTGAACA 59.119 57.895 0.00 0.00 0.00 3.18
950 4434 2.046283 TTTATAGAGACGGCGATGCG 57.954 50.000 16.62 0.00 0.00 4.73
951 4435 2.924290 GGATTTATAGAGACGGCGATGC 59.076 50.000 16.62 1.94 0.00 3.91
954 4438 1.538512 CGGGATTTATAGAGACGGCGA 59.461 52.381 16.62 0.00 0.00 5.54
956 4440 2.352519 GGACGGGATTTATAGAGACGGC 60.353 54.545 0.00 0.00 0.00 5.68
957 4441 2.889045 TGGACGGGATTTATAGAGACGG 59.111 50.000 0.00 0.00 0.00 4.79
975 4509 2.203938 AGAGGGAAGCGGGTTGGA 60.204 61.111 0.00 0.00 0.00 3.53
1005 4539 3.266510 TGATGGTTTCGGAGATTCTGG 57.733 47.619 0.00 0.00 35.04 3.86
1016 4550 1.529826 GCGAGTTGCGATGATGGTTTC 60.530 52.381 0.00 0.00 44.57 2.78
1058 4593 2.874245 TCTGAGGGGGTGGAGGGA 60.874 66.667 0.00 0.00 0.00 4.20
1067 4602 0.256464 ACGTAGGAGACTCTGAGGGG 59.744 60.000 9.85 0.00 43.67 4.79
1069 4604 2.712709 TGAACGTAGGAGACTCTGAGG 58.287 52.381 9.85 0.00 43.67 3.86
1071 4606 3.017442 CCATGAACGTAGGAGACTCTGA 58.983 50.000 1.74 0.00 43.67 3.27
1073 4608 1.751924 GCCATGAACGTAGGAGACTCT 59.248 52.381 1.74 0.00 43.67 3.24
1074 4609 1.534175 CGCCATGAACGTAGGAGACTC 60.534 57.143 0.00 0.00 43.67 3.36
1075 4610 4.089314 GTCGCCATGAACGTAGGAGACT 62.089 54.545 18.73 0.00 45.20 3.24
1076 4611 0.454600 TCGCCATGAACGTAGGAGAC 59.545 55.000 0.00 0.00 0.00 3.36
1081 4640 2.514013 GCCGTCGCCATGAACGTAG 61.514 63.158 12.20 6.56 0.00 3.51
1082 4641 2.507547 GCCGTCGCCATGAACGTA 60.508 61.111 12.20 0.00 0.00 3.57
1152 4716 0.252330 TTGACGGGGGTGGATGAGTA 60.252 55.000 0.00 0.00 0.00 2.59
1153 4717 1.537889 TTGACGGGGGTGGATGAGT 60.538 57.895 0.00 0.00 0.00 3.41
1158 4722 3.319198 GAGCTTGACGGGGGTGGA 61.319 66.667 0.00 0.00 0.00 4.02
1198 4774 3.535629 CTGACGGACTTGCCCAGCA 62.536 63.158 0.00 0.00 36.47 4.41
1201 4777 4.680237 CGCTGACGGACTTGCCCA 62.680 66.667 0.00 0.00 34.97 5.36
1233 4815 4.729918 GTGCTGGCTCCTGGTGGG 62.730 72.222 0.00 0.00 0.00 4.61
1292 4883 1.376424 CTCCTTGTGGACGCTGCAT 60.376 57.895 0.00 0.00 37.46 3.96
1299 4890 2.970974 GCTTGCGCTCCTTGTGGAC 61.971 63.158 9.73 0.00 37.46 4.02
1347 4941 4.626081 GATGGACGGCGGGGATGG 62.626 72.222 13.24 0.00 0.00 3.51
1373 9224 2.864931 GCTCATTCGCTTCGAGCCG 61.865 63.158 0.00 0.94 45.14 5.52
1524 9378 2.309693 TGTTTACGTCTAGTTGTCGCG 58.690 47.619 0.00 0.00 0.00 5.87
1535 9389 4.209703 TGTCGAGGTTGATTTGTTTACGTC 59.790 41.667 0.00 0.00 0.00 4.34
1536 9390 4.121317 TGTCGAGGTTGATTTGTTTACGT 58.879 39.130 0.00 0.00 0.00 3.57
1537 9391 4.718858 TGTCGAGGTTGATTTGTTTACG 57.281 40.909 0.00 0.00 0.00 3.18
1571 9425 2.557490 ACTAGGCCGGAATCGATTCTAC 59.443 50.000 31.32 21.78 39.00 2.59
1575 9429 1.410004 TGACTAGGCCGGAATCGATT 58.590 50.000 11.20 11.20 39.00 3.34
1576 9430 1.410004 TTGACTAGGCCGGAATCGAT 58.590 50.000 5.05 0.00 39.00 3.59
1577 9431 1.410004 ATTGACTAGGCCGGAATCGA 58.590 50.000 5.05 0.00 39.00 3.59
1578 9432 2.240493 AATTGACTAGGCCGGAATCG 57.760 50.000 5.05 0.00 0.00 3.34
1579 9433 3.067833 GCTAATTGACTAGGCCGGAATC 58.932 50.000 5.05 0.00 0.00 2.52
1580 9434 2.706190 AGCTAATTGACTAGGCCGGAAT 59.294 45.455 5.05 0.00 0.00 3.01
1581 9435 2.116238 AGCTAATTGACTAGGCCGGAA 58.884 47.619 5.05 0.00 0.00 4.30
1582 9436 1.789523 AGCTAATTGACTAGGCCGGA 58.210 50.000 5.05 0.00 0.00 5.14
1583 9437 3.654414 CTTAGCTAATTGACTAGGCCGG 58.346 50.000 6.64 0.00 0.00 6.13
1584 9438 3.060602 GCTTAGCTAATTGACTAGGCCG 58.939 50.000 6.64 0.00 35.94 6.13
1608 9462 4.582656 AGGCTCACTCTATGTACAGCTAAG 59.417 45.833 0.33 0.00 35.33 2.18
1660 9515 0.923358 ATATCCAAAACCAGGGGCGA 59.077 50.000 0.00 0.00 0.00 5.54
1689 9544 3.130633 TGTGTCTCCAATTTGTCACTCG 58.869 45.455 0.00 0.00 0.00 4.18
1697 9552 2.596346 TGTGCCATGTGTCTCCAATTT 58.404 42.857 0.00 0.00 0.00 1.82
1714 9569 2.884827 TCTTGAGATCAGACGCATGTG 58.115 47.619 4.30 4.30 0.00 3.21
1784 9641 3.171388 GATGCCCATCCCCGTCCT 61.171 66.667 0.00 0.00 31.76 3.85
1814 9671 4.149019 TGCCCAACAACAGCCCCA 62.149 61.111 0.00 0.00 0.00 4.96
1904 9761 6.034044 GTGCAAAAATAATGTAATTTCGCGGA 59.966 34.615 6.13 0.00 37.87 5.54
1927 9784 2.159142 GGGTAAGATGACTACGGTGGTG 60.159 54.545 0.49 0.00 0.00 4.17
2005 9862 7.112122 TGATGATATGTAAAGAAAGGCACACT 58.888 34.615 0.00 0.00 0.00 3.55
2123 9980 5.819825 GTCTTGAAGACAACTCCAAAAGT 57.180 39.130 19.73 0.00 44.45 2.66
2175 10140 4.218417 CCTCCAAACGACCATCTTCAAATT 59.782 41.667 0.00 0.00 0.00 1.82
2267 10232 9.982651 GATGGTTCAACAGCTATATAAGTTCTA 57.017 33.333 0.00 0.00 0.00 2.10
2416 10381 0.676736 GTTTCGGCAAACCCATGGAA 59.323 50.000 15.22 0.00 36.62 3.53
2417 10382 2.346597 GTTTCGGCAAACCCATGGA 58.653 52.632 15.22 0.00 36.62 3.41
2454 10419 0.608308 GCGGGGTTAGTTTTCTGCCT 60.608 55.000 0.00 0.00 0.00 4.75
2467 10432 2.125147 CATCATCGTGTGCGGGGT 60.125 61.111 0.00 0.00 38.89 4.95
2485 10450 2.120274 TAAACCCGTCCCCGTCCT 59.880 61.111 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.