Multiple sequence alignment - TraesCS2D01G351800

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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 TraesCS2D01G351800 chr2D 100.000 5702 0 0 1 5702 450201722 450207423 0.000000e+00 10530.0
1 TraesCS2D01G351800 chr2D 95.293 871 31 6 1 866 450060709 450061574 0.000000e+00 1373.0
2 TraesCS2D01G351800 chr2D 92.417 422 23 5 1 414 450162054 450162474 1.370000e-165 593.0
3 TraesCS2D01G351800 chr2D 91.469 422 27 8 1 414 450016199 450015779 6.410000e-159 571.0
4 TraesCS2D01G351800 chr2A 95.677 3817 105 20 840 4618 594435232 594439026 0.000000e+00 6080.0
5 TraesCS2D01G351800 chr2A 86.036 444 23 13 4648 5090 594439027 594439432 1.890000e-119 440.0
6 TraesCS2D01G351800 chr2A 84.330 351 29 14 414 741 306100590 306100937 2.560000e-83 320.0
7 TraesCS2D01G351800 chr2B 96.979 2880 80 3 840 3714 530271192 530274069 0.000000e+00 4830.0
8 TraesCS2D01G351800 chr2B 89.140 1593 69 41 3626 5151 530274080 530275635 0.000000e+00 1888.0
9 TraesCS2D01G351800 chr2B 84.821 560 73 10 5151 5699 381925158 381925716 2.320000e-153 553.0
10 TraesCS2D01G351800 chr2B 79.673 428 61 13 420 823 718957432 718957007 9.350000e-73 285.0
11 TraesCS2D01G351800 chrUn 87.546 546 67 1 5155 5699 8093118 8093663 1.040000e-176 630.0
12 TraesCS2D01G351800 chr1D 86.429 560 73 3 5141 5699 460746080 460746637 1.360000e-170 610.0
13 TraesCS2D01G351800 chr1D 91.686 421 26 6 1 413 258231376 258231795 4.950000e-160 575.0
14 TraesCS2D01G351800 chr1D 84.865 555 79 5 5149 5699 402432397 402432950 6.450000e-154 555.0
15 TraesCS2D01G351800 chr1D 83.333 90 10 3 651 735 222927518 222927429 1.700000e-10 78.7
16 TraesCS2D01G351800 chr1D 97.297 37 0 1 4738 4774 119287640 119287675 1.720000e-05 62.1
17 TraesCS2D01G351800 chr1D 91.111 45 3 1 4731 4774 461380071 461380115 6.170000e-05 60.2
18 TraesCS2D01G351800 chr5A 86.607 560 64 5 5151 5699 592201974 592202533 4.890000e-170 608.0
19 TraesCS2D01G351800 chr5A 97.222 36 0 1 4739 4774 11996543 11996509 6.170000e-05 60.2
20 TraesCS2D01G351800 chr3D 92.326 417 28 4 1 414 335493523 335493108 1.770000e-164 590.0
21 TraesCS2D01G351800 chr3D 91.469 422 28 8 1 414 410574553 410574132 1.780000e-159 573.0
22 TraesCS2D01G351800 chr3D 83.793 290 33 10 414 690 31960561 31960849 4.380000e-66 263.0
23 TraesCS2D01G351800 chr3D 97.297 37 1 0 4738 4774 125504558 125504522 4.770000e-06 63.9
24 TraesCS2D01G351800 chr6D 92.180 422 24 5 1 413 441694991 441694570 6.360000e-164 588.0
25 TraesCS2D01G351800 chr6D 91.803 427 22 10 1 414 441703075 441702649 2.960000e-162 582.0
26 TraesCS2D01G351800 chr6D 80.711 394 48 15 414 780 126623303 126622911 1.210000e-71 281.0
27 TraesCS2D01G351800 chr7D 85.613 563 68 7 5149 5699 92215677 92216238 3.830000e-161 579.0
28 TraesCS2D01G351800 chr7D 77.576 825 105 35 3685 4464 17266981 17267770 5.280000e-115 425.0
29 TraesCS2D01G351800 chr6A 91.408 419 29 6 1 414 377968416 377968832 8.290000e-158 568.0
30 TraesCS2D01G351800 chr7B 84.794 559 78 3 5150 5702 666539582 666539025 6.450000e-154 555.0
31 TraesCS2D01G351800 chr7B 80.222 450 57 16 414 836 63075036 63074592 5.550000e-80 309.0
32 TraesCS2D01G351800 chr7B 80.000 450 58 16 414 836 63037043 63036599 2.580000e-78 303.0
33 TraesCS2D01G351800 chr7B 86.170 282 27 8 436 706 670083467 670083187 1.550000e-75 294.0
34 TraesCS2D01G351800 chr7B 79.204 452 61 16 410 834 162953930 162954375 3.360000e-72 283.0
35 TraesCS2D01G351800 chr7B 84.806 283 33 8 434 706 670041296 670041014 5.630000e-70 276.0
36 TraesCS2D01G351800 chr7B 97.297 37 0 1 4738 4774 27274702 27274737 1.720000e-05 62.1
37 TraesCS2D01G351800 chr7A 84.875 562 72 7 5149 5699 94311979 94312538 6.450000e-154 555.0
38 TraesCS2D01G351800 chr7A 84.740 557 76 6 5154 5702 134009722 134009167 3.000000e-152 549.0
39 TraesCS2D01G351800 chr7A 78.182 385 54 18 414 774 27272113 27271735 9.620000e-53 219.0
40 TraesCS2D01G351800 chr7A 82.105 95 17 0 680 774 27259431 27259337 1.320000e-11 82.4
41 TraesCS2D01G351800 chr7A 80.822 73 11 3 710 781 246576 246506 3.000000e-03 54.7
42 TraesCS2D01G351800 chr5D 83.077 455 47 14 411 836 391292717 391293170 2.490000e-103 387.0
43 TraesCS2D01G351800 chr5D 97.222 36 0 1 4739 4774 541575919 541575885 6.170000e-05 60.2
44 TraesCS2D01G351800 chr1A 79.310 377 46 19 416 767 403376683 403376314 9.550000e-58 235.0
45 TraesCS2D01G351800 chr3A 93.750 48 1 1 693 738 430870353 430870400 2.850000e-08 71.3
46 TraesCS2D01G351800 chr4B 97.297 37 0 1 4737 4773 69425734 69425699 1.720000e-05 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 TraesCS2D01G351800 chr2D 450201722 450207423 5701 False 10530 10530 100.0000 1 5702 1 chr2D.!!$F3 5701
1 TraesCS2D01G351800 chr2D 450060709 450061574 865 False 1373 1373 95.2930 1 866 1 chr2D.!!$F1 865
2 TraesCS2D01G351800 chr2A 594435232 594439432 4200 False 3260 6080 90.8565 840 5090 2 chr2A.!!$F2 4250
3 TraesCS2D01G351800 chr2B 530271192 530275635 4443 False 3359 4830 93.0595 840 5151 2 chr2B.!!$F2 4311
4 TraesCS2D01G351800 chr2B 381925158 381925716 558 False 553 553 84.8210 5151 5699 1 chr2B.!!$F1 548
5 TraesCS2D01G351800 chrUn 8093118 8093663 545 False 630 630 87.5460 5155 5699 1 chrUn.!!$F1 544
6 TraesCS2D01G351800 chr1D 460746080 460746637 557 False 610 610 86.4290 5141 5699 1 chr1D.!!$F4 558
7 TraesCS2D01G351800 chr1D 402432397 402432950 553 False 555 555 84.8650 5149 5699 1 chr1D.!!$F3 550
8 TraesCS2D01G351800 chr5A 592201974 592202533 559 False 608 608 86.6070 5151 5699 1 chr5A.!!$F1 548
9 TraesCS2D01G351800 chr7D 92215677 92216238 561 False 579 579 85.6130 5149 5699 1 chr7D.!!$F2 550
10 TraesCS2D01G351800 chr7D 17266981 17267770 789 False 425 425 77.5760 3685 4464 1 chr7D.!!$F1 779
11 TraesCS2D01G351800 chr7B 666539025 666539582 557 True 555 555 84.7940 5150 5702 1 chr7B.!!$R3 552
12 TraesCS2D01G351800 chr7A 94311979 94312538 559 False 555 555 84.8750 5149 5699 1 chr7A.!!$F1 550
13 TraesCS2D01G351800 chr7A 134009167 134009722 555 True 549 549 84.7400 5154 5702 1 chr7A.!!$R4 548

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
213 216 0.108138 CGGTGGTTCTTGGCTCTAGG 60.108 60.000 0.0 0.0 0.00 3.02 F
926 936 0.179051 CTTCTCTGAGCCTCCATGCC 60.179 60.000 0.0 0.0 0.00 4.40 F
978 988 0.267054 AGCTCCCATCCCATCTCAGA 59.733 55.000 0.0 0.0 0.00 3.27 F
1090 1105 1.152922 ATCGAGGGAGGACGGAGAC 60.153 63.158 0.0 0.0 0.00 3.36 F
1741 1759 3.134127 GGCAATGTCGACCAGGCC 61.134 66.667 20.8 20.8 39.42 5.19 F
3639 3657 0.677731 TCTGTTGCATAGCCCAGCAC 60.678 55.000 0.0 0.0 41.05 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1759 0.108520 AATTGCCAAATGCTCGCAGG 60.109 50.000 0.00 0.00 42.00 4.85 R
2464 2482 3.119884 TGCATGACTTTTGTTGCCGATAG 60.120 43.478 0.00 0.00 35.82 2.08 R
2612 2630 3.181458 GGAACAACAAGTCCAGACTGGTA 60.181 47.826 21.06 5.51 44.48 3.25 R
2684 2702 3.754965 TCTTTGCTTTCACACAGCCTAT 58.245 40.909 0.00 0.00 36.33 2.57 R
3717 3834 1.079057 GACTTCTCCCTCCAACGGC 60.079 63.158 0.00 0.00 0.00 5.68 R
5570 5819 0.461339 ACAACGCCTTCAACGTGACT 60.461 50.000 0.00 0.00 44.30 3.41 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
20 21 1.776667 TGGCCTCCCATGAAGAATAGG 59.223 52.381 3.32 0.00 35.79 2.57
30 31 1.480954 TGAAGAATAGGAGGTGACGGC 59.519 52.381 0.00 0.00 0.00 5.68
48 49 2.087009 CGGCTCCGTCTCGTGAAAC 61.087 63.158 0.00 0.00 34.35 2.78
70 71 3.377172 CGCGATAATTCTTTTCCCCTGTT 59.623 43.478 0.00 0.00 0.00 3.16
105 106 7.417496 AAATAGGATTTTATAGCGTCGGTTC 57.583 36.000 0.65 0.00 0.00 3.62
106 107 4.395959 AGGATTTTATAGCGTCGGTTCA 57.604 40.909 0.65 0.00 0.00 3.18
116 117 2.027625 GTCGGTTCAAGGGTCTGCG 61.028 63.158 0.00 0.00 0.00 5.18
184 187 4.218686 GGTTGTGCCCACCCAGGT 62.219 66.667 0.00 0.00 34.66 4.00
213 216 0.108138 CGGTGGTTCTTGGCTCTAGG 60.108 60.000 0.00 0.00 0.00 3.02
266 269 5.048782 CACAAAGTTTCATTCCATTCCGAGA 60.049 40.000 0.00 0.00 0.00 4.04
293 296 8.945057 ACTTTTATTTCTGCACAAAAACAACAT 58.055 25.926 0.00 0.00 0.00 2.71
306 309 7.167968 CACAAAAACAACATCATGGTAGTTCTG 59.832 37.037 0.00 0.00 0.00 3.02
309 312 4.005650 ACAACATCATGGTAGTTCTGCTG 58.994 43.478 0.00 0.00 0.00 4.41
373 376 8.099364 TGCAAATTAGAGTCTAAAACAAGAGG 57.901 34.615 16.37 2.92 0.00 3.69
572 575 1.946283 GCGGGAAATGGCCTATCTAGC 60.946 57.143 3.32 5.98 0.00 3.42
655 661 3.242804 TGGCCGTTTGTCTTAACTTTTCG 60.243 43.478 0.00 0.00 0.00 3.46
690 696 1.599797 CGTGGTTTTCCCTTCCGCT 60.600 57.895 0.00 0.00 39.73 5.52
692 698 0.536460 GTGGTTTTCCCTTCCGCTGA 60.536 55.000 0.00 0.00 39.73 4.26
734 740 3.260888 TGGGATCACCGGGCCAAA 61.261 61.111 6.32 0.00 44.64 3.28
753 759 2.933495 AAAACGGATCGAGTCGATGA 57.067 45.000 31.55 3.47 47.00 2.92
859 865 3.003478 CCATCGTTAGCGCGGAAC 58.997 61.111 8.83 15.70 38.14 3.62
926 936 0.179051 CTTCTCTGAGCCTCCATGCC 60.179 60.000 0.00 0.00 0.00 4.40
978 988 0.267054 AGCTCCCATCCCATCTCAGA 59.733 55.000 0.00 0.00 0.00 3.27
1090 1105 1.152922 ATCGAGGGAGGACGGAGAC 60.153 63.158 0.00 0.00 0.00 3.36
1319 1337 3.947834 CCACCACTTCATATTTCCTGGAC 59.052 47.826 0.00 0.00 0.00 4.02
1328 1346 5.491070 TCATATTTCCTGGACTGTTCTGTG 58.509 41.667 0.00 0.00 0.00 3.66
1690 1708 3.810896 GCGCCATCCCGTGAAACC 61.811 66.667 0.00 0.00 0.00 3.27
1741 1759 3.134127 GGCAATGTCGACCAGGCC 61.134 66.667 20.80 20.80 39.42 5.19
1889 1907 6.704493 GGTTCTGTCAGTTTATCAGTGTAACA 59.296 38.462 0.00 0.00 41.43 2.41
2059 2077 4.214119 CACATGTTGAAGTCACAAGTAGGG 59.786 45.833 0.00 0.00 0.00 3.53
2120 2138 7.086376 CGAGTGTTTCTTGGATCAAATTTCAT 58.914 34.615 0.00 0.00 0.00 2.57
2464 2482 6.328714 TGCTGCAGATCTTATAATCGATCTC 58.671 40.000 20.43 9.18 43.24 2.75
2672 2690 4.532834 TGTTCCTAGTGAAAAGGCTGTTT 58.467 39.130 0.00 0.00 33.94 2.83
2684 2702 8.349983 GTGAAAAGGCTGTTTCTAAACTTATCA 58.650 33.333 17.13 0.88 39.59 2.15
2834 2852 2.355513 GCCGCTCATGATATCCTGGATT 60.356 50.000 15.55 2.80 0.00 3.01
2967 2985 6.252599 ACAGAAAATAGCATCTACCATGGA 57.747 37.500 21.47 0.67 0.00 3.41
3097 3115 5.281314 ACTGAACACTATAACCCTGGAGAT 58.719 41.667 0.00 0.00 0.00 2.75
3106 3124 6.901300 ACTATAACCCTGGAGATCACTTAACA 59.099 38.462 0.00 0.00 0.00 2.41
3253 3271 6.640518 ACTGTGTGGATATTCGTCATTAAGT 58.359 36.000 0.00 0.00 0.00 2.24
3295 3313 4.360951 ACTGTGGGGAGAAATAAAACGA 57.639 40.909 0.00 0.00 0.00 3.85
3639 3657 0.677731 TCTGTTGCATAGCCCAGCAC 60.678 55.000 0.00 0.00 41.05 4.40
3697 3715 5.205056 AGTCTGGTAATTCTAGAGAGTGGG 58.795 45.833 0.00 0.00 34.40 4.61
3717 3834 3.328505 GGTCACATTTGAATTGGGCAAG 58.671 45.455 0.00 0.00 31.90 4.01
3769 3901 1.100510 CTGTGGCACTATGCTGCAAT 58.899 50.000 19.83 0.00 44.28 3.56
3845 3984 3.623703 TGATGCATGGTTATCACTGCTT 58.376 40.909 2.46 0.00 33.84 3.91
3966 4122 1.165270 GTTGGCACTGCTCGGTTATT 58.835 50.000 0.00 0.00 0.00 1.40
4037 4202 0.449388 GCTCGGTCATTTCAAGCCAG 59.551 55.000 0.00 0.00 0.00 4.85
4189 4362 5.625721 CGAGTGTTTGACTACTTACTGACAG 59.374 44.000 0.00 0.00 33.83 3.51
4190 4363 6.512903 CGAGTGTTTGACTACTTACTGACAGA 60.513 42.308 10.08 0.00 33.83 3.41
4206 4379 6.164876 ACTGACAGAAGATGTTCAGATCTTG 58.835 40.000 10.08 0.00 44.17 3.02
4216 4389 8.774546 AGATGTTCAGATCTTGGTAAGAGATA 57.225 34.615 0.00 0.00 41.61 1.98
4219 4392 7.212976 TGTTCAGATCTTGGTAAGAGATATGC 58.787 38.462 0.00 0.00 40.75 3.14
4251 4428 4.571580 CCAGTTCGGTGTGTTGTTTAACTA 59.428 41.667 0.00 0.00 37.68 2.24
4312 4498 3.833304 GCCTTAGGCTGCATGGTC 58.167 61.111 17.16 0.00 46.69 4.02
4313 4499 1.825622 GCCTTAGGCTGCATGGTCC 60.826 63.158 17.16 0.00 46.69 4.46
4314 4500 1.524621 CCTTAGGCTGCATGGTCCG 60.525 63.158 0.50 0.00 0.00 4.79
4380 4570 2.114616 TCAGGTGCATGGTTTGGTTTT 58.885 42.857 0.00 0.00 0.00 2.43
4381 4571 3.300388 TCAGGTGCATGGTTTGGTTTTA 58.700 40.909 0.00 0.00 0.00 1.52
4382 4572 3.900601 TCAGGTGCATGGTTTGGTTTTAT 59.099 39.130 0.00 0.00 0.00 1.40
4591 4795 2.768527 TCATTTGCAAAAGTTCACCCCA 59.231 40.909 17.19 0.00 0.00 4.96
4624 4829 7.730364 AGAATACCACGGATGTCATTTATTC 57.270 36.000 0.00 0.00 0.00 1.75
4626 4831 2.612212 ACCACGGATGTCATTTATTCGC 59.388 45.455 0.00 0.00 29.61 4.70
4649 4854 4.680110 CGAAAATTCACGTGTGAGTAGACT 59.320 41.667 16.51 0.00 41.13 3.24
4707 4913 7.064016 AGCGAAGAAAATGAACTCAGATCTTAC 59.936 37.037 0.00 2.70 30.96 2.34
4708 4914 7.064016 GCGAAGAAAATGAACTCAGATCTTACT 59.936 37.037 0.00 0.00 30.96 2.24
4709 4915 9.574458 CGAAGAAAATGAACTCAGATCTTACTA 57.426 33.333 0.00 0.00 30.96 1.82
4921 5155 5.036117 TCCTAGAATACCAAAGATGCCAC 57.964 43.478 0.00 0.00 0.00 5.01
4971 5205 2.171027 AGTCGACCAAGTTTAACACCCA 59.829 45.455 13.01 0.00 0.00 4.51
5110 5344 2.484065 CGAGTGAGTGGGTTTGGTTACA 60.484 50.000 0.00 0.00 0.00 2.41
5117 5351 4.394729 AGTGGGTTTGGTTACATGTGTAG 58.605 43.478 9.11 0.00 0.00 2.74
5220 5455 1.002430 CAGTTAGGTCTGGCTGAGCAA 59.998 52.381 22.71 13.16 44.98 3.91
5227 5462 0.037160 TCTGGCTGAGCAAATGCAGA 59.963 50.000 6.82 6.51 45.16 4.26
5267 5502 4.698304 GCACTTAGTTTGGTTGCCTACATA 59.302 41.667 0.00 0.00 0.00 2.29
5268 5503 5.182380 GCACTTAGTTTGGTTGCCTACATAA 59.818 40.000 0.00 0.00 0.00 1.90
5275 5510 5.765576 TTGGTTGCCTACATAACCTCTAA 57.234 39.130 7.56 0.00 45.16 2.10
5330 5566 0.181587 TTGCGGACTTGTTTGAGGGA 59.818 50.000 0.00 0.00 0.00 4.20
5336 5572 3.317993 CGGACTTGTTTGAGGGAAAACAT 59.682 43.478 3.57 0.00 46.44 2.71
5344 5580 4.627284 TTGAGGGAAAACATAAGTCCGA 57.373 40.909 0.00 0.00 31.73 4.55
5347 5583 6.302535 TGAGGGAAAACATAAGTCCGATTA 57.697 37.500 0.00 0.00 31.73 1.75
5468 5716 8.732746 ACTTAGACACAAACACAAGTCTTAAT 57.267 30.769 0.00 0.00 41.27 1.40
5478 5726 4.937620 ACACAAGTCTTAATCACGCATCAT 59.062 37.500 0.00 0.00 0.00 2.45
5559 5808 0.248866 CAACAAGGAACGGGCAACAC 60.249 55.000 0.00 0.00 39.74 3.32
5570 5819 2.327343 GGCAACACGAGCTCATGCA 61.327 57.895 23.61 0.00 42.74 3.96
5577 5826 1.445066 CGAGCTCATGCAGTCACGT 60.445 57.895 15.40 0.00 42.74 4.49
5578 5827 1.010935 CGAGCTCATGCAGTCACGTT 61.011 55.000 15.40 0.00 42.74 3.99
5668 5918 1.497309 ATGGTGTCGGGGGTCAACAT 61.497 55.000 0.00 0.00 37.19 2.71
5699 5949 5.922544 CGTCAGCATGTACTTGATCATGATA 59.077 40.000 8.54 0.00 42.52 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.753662 AGCCGCCGTCACCTCCTA 62.754 66.667 0.00 0.00 0.00 2.94
30 31 2.087009 GTTTCACGAGACGGAGCCG 61.087 63.158 7.48 7.48 46.03 5.52
48 49 2.943033 ACAGGGGAAAAGAATTATCGCG 59.057 45.455 0.00 0.00 0.00 5.87
79 80 7.797038 ACCGACGCTATAAAATCCTATTTTT 57.203 32.000 3.19 0.00 33.56 1.94
266 269 8.778358 TGTTGTTTTTGTGCAGAAATAAAAGTT 58.222 25.926 10.13 0.00 0.00 2.66
293 296 4.713553 TGTTTTCAGCAGAACTACCATGA 58.286 39.130 0.00 0.00 32.39 3.07
309 312 2.556287 CGGGCTGACGCTGTTTTC 59.444 61.111 0.00 0.00 36.09 2.29
362 365 6.056884 TCCTAACGCTTTTCCTCTTGTTTTA 58.943 36.000 0.00 0.00 0.00 1.52
373 376 8.880750 ACATATCTACTTTTCCTAACGCTTTTC 58.119 33.333 0.00 0.00 0.00 2.29
572 575 3.326578 TCCCATCACCCACCACCG 61.327 66.667 0.00 0.00 0.00 4.94
655 661 0.882474 ACGTCTAGACACTGTCAGGC 59.118 55.000 22.37 7.38 34.60 4.85
690 696 4.020617 CAGCACTCGGGGGCTTCA 62.021 66.667 10.92 0.00 38.56 3.02
734 740 2.933495 TCATCGACTCGATCCGTTTT 57.067 45.000 11.09 0.00 45.19 2.43
738 744 3.060272 CCAAAATTCATCGACTCGATCCG 60.060 47.826 11.09 1.95 45.19 4.18
742 748 1.658596 CGCCAAAATTCATCGACTCGA 59.341 47.619 3.06 3.06 41.13 4.04
783 789 1.589022 CGCGTCGACGATGAAAAATCC 60.589 52.381 39.74 17.32 43.02 3.01
859 865 1.649390 CCTCACTCGTCGTCCTCCTG 61.649 65.000 0.00 0.00 0.00 3.86
926 936 1.978580 ACTAGATGGGCTTTATCGGGG 59.021 52.381 0.00 0.00 0.00 5.73
1319 1337 1.905215 AGAGGGGATCACACAGAACAG 59.095 52.381 0.00 0.00 0.00 3.16
1328 1346 0.688087 AACCGGAGAGAGGGGATCAC 60.688 60.000 9.46 0.00 0.00 3.06
1562 1580 0.476338 TTGGCCTAGGACAAGTGCAA 59.524 50.000 27.00 2.50 38.36 4.08
1690 1708 4.115516 CAACATCAATCGTCCTCAGTAGG 58.884 47.826 0.00 0.00 45.21 3.18
1741 1759 0.108520 AATTGCCAAATGCTCGCAGG 60.109 50.000 0.00 0.00 42.00 4.85
1889 1907 4.439974 CGAGCTAGAGTTGAGAAGATTGCT 60.440 45.833 0.00 0.00 0.00 3.91
2059 2077 3.191078 ACATCAGCTGCAAGATAGGAC 57.809 47.619 9.47 0.00 34.07 3.85
2464 2482 3.119884 TGCATGACTTTTGTTGCCGATAG 60.120 43.478 0.00 0.00 35.82 2.08
2612 2630 3.181458 GGAACAACAAGTCCAGACTGGTA 60.181 47.826 21.06 5.51 44.48 3.25
2672 2690 7.418337 TCACACAGCCTATGATAAGTTTAGA 57.582 36.000 0.00 0.00 0.00 2.10
2684 2702 3.754965 TCTTTGCTTTCACACAGCCTAT 58.245 40.909 0.00 0.00 36.33 2.57
2834 2852 5.126869 CAGGAATCTCAGCTGACTCTAAAGA 59.873 44.000 13.74 7.20 0.00 2.52
2928 2946 7.678947 ATTTTCTGTATCTGTTGGAGAAGTG 57.321 36.000 0.00 0.00 33.12 3.16
2929 2947 7.550906 GCTATTTTCTGTATCTGTTGGAGAAGT 59.449 37.037 0.00 0.00 33.12 3.01
3253 3271 9.475620 CACAGTATGGTAATCTCCCTATACATA 57.524 37.037 0.00 0.00 43.62 2.29
3295 3313 7.925993 CAGATATTTCTCTGTACTCGAGTCTT 58.074 38.462 23.89 0.00 38.27 3.01
3639 3657 2.753452 ACATTGGAGAAGAATGCTGCAG 59.247 45.455 10.11 10.11 45.66 4.41
3697 3715 2.738314 GCTTGCCCAATTCAAATGTGAC 59.262 45.455 0.00 0.00 31.90 3.67
3717 3834 1.079057 GACTTCTCCCTCCAACGGC 60.079 63.158 0.00 0.00 0.00 5.68
3966 4122 4.196193 CACGGCATCCTTATACTCCAAAA 58.804 43.478 0.00 0.00 0.00 2.44
4037 4202 3.904339 TCCTGAGAATAATCTGGTAGGGC 59.096 47.826 0.00 0.00 35.54 5.19
4165 4330 5.516996 TGTCAGTAAGTAGTCAAACACTCG 58.483 41.667 0.00 0.00 36.43 4.18
4182 4355 5.999205 AGATCTGAACATCTTCTGTCAGT 57.001 39.130 0.00 0.00 36.98 3.41
4189 4362 7.551585 TCTCTTACCAAGATCTGAACATCTTC 58.448 38.462 0.00 0.00 40.52 2.87
4190 4363 7.487822 TCTCTTACCAAGATCTGAACATCTT 57.512 36.000 0.00 0.00 42.80 2.40
4206 4379 3.760580 AGCAGTGGCATATCTCTTACC 57.239 47.619 0.00 0.00 44.61 2.85
4216 4389 0.391661 CGAACTGGTAGCAGTGGCAT 60.392 55.000 27.15 12.35 44.61 4.40
4219 4392 4.598257 CCGAACTGGTAGCAGTGG 57.402 61.111 27.15 20.44 35.30 4.00
4243 4420 7.041372 TCCAGCAACAGAATCAACTAGTTAAAC 60.041 37.037 8.04 0.89 0.00 2.01
4244 4421 6.995686 TCCAGCAACAGAATCAACTAGTTAAA 59.004 34.615 8.04 0.00 0.00 1.52
4245 4422 6.530120 TCCAGCAACAGAATCAACTAGTTAA 58.470 36.000 8.04 0.00 0.00 2.01
4247 4424 4.973168 TCCAGCAACAGAATCAACTAGTT 58.027 39.130 1.12 1.12 0.00 2.24
4251 4428 3.567164 CAGTTCCAGCAACAGAATCAACT 59.433 43.478 0.00 0.00 37.48 3.16
4313 4499 2.141122 AAATTCCACAAGGCCGCACG 62.141 55.000 0.00 0.00 33.74 5.34
4314 4500 0.885196 TAAATTCCACAAGGCCGCAC 59.115 50.000 0.00 0.00 33.74 5.34
4380 4570 4.637977 TCATTTCAACGCATGCAACCTATA 59.362 37.500 19.57 0.00 0.00 1.31
4381 4571 3.443329 TCATTTCAACGCATGCAACCTAT 59.557 39.130 19.57 0.41 0.00 2.57
4382 4572 2.816672 TCATTTCAACGCATGCAACCTA 59.183 40.909 19.57 0.00 0.00 3.08
4567 4771 4.442753 GGGGTGAACTTTTGCAAATGAGAA 60.443 41.667 26.53 11.48 0.00 2.87
4568 4772 3.069443 GGGGTGAACTTTTGCAAATGAGA 59.931 43.478 26.53 6.59 0.00 3.27
4591 4795 1.971357 CCGTGGTATTCTAGGCATCCT 59.029 52.381 0.00 0.00 37.71 3.24
4626 4831 4.680110 AGTCTACTCACACGTGAATTTTCG 59.320 41.667 25.01 4.88 39.39 3.46
4649 4854 5.423704 TGGGTATCAAACTTGGTCGATTA 57.576 39.130 0.00 0.00 0.00 1.75
5069 5303 5.296780 ACTCGCTTGTTGGAATATATGTTGG 59.703 40.000 0.00 0.00 0.00 3.77
5110 5344 3.457380 ACAGATTCTGGGCATCTACACAT 59.543 43.478 17.66 0.00 35.51 3.21
5117 5351 2.093288 TGAGACACAGATTCTGGGCATC 60.093 50.000 15.92 13.66 38.67 3.91
5220 5455 6.449698 CAGATGTTGGTTTTTAGTCTGCATT 58.550 36.000 0.00 0.00 0.00 3.56
5227 5462 5.852282 AAGTGCAGATGTTGGTTTTTAGT 57.148 34.783 0.00 0.00 0.00 2.24
5267 5502 1.352352 AGCACATGCAGGTTAGAGGTT 59.648 47.619 0.00 0.00 45.16 3.50
5268 5503 0.987294 AGCACATGCAGGTTAGAGGT 59.013 50.000 0.00 0.00 45.16 3.85
5275 5510 1.181098 GGGTTTCAGCACATGCAGGT 61.181 55.000 0.00 0.00 45.16 4.00
5336 5572 9.104965 CTGAATGTAACCAAATAATCGGACTTA 57.895 33.333 0.00 0.00 0.00 2.24
5344 5580 8.522830 CAACTGTCCTGAATGTAACCAAATAAT 58.477 33.333 0.00 0.00 0.00 1.28
5347 5583 5.833131 ACAACTGTCCTGAATGTAACCAAAT 59.167 36.000 0.00 0.00 0.00 2.32
5468 5716 6.469139 TCGTTTAAAACTTATGATGCGTGA 57.531 33.333 0.00 0.00 0.00 4.35
5501 5750 8.689061 AGACTTGGGTTTCGTTTAAAACTTATT 58.311 29.630 0.00 0.00 38.81 1.40
5559 5808 1.010935 AACGTGACTGCATGAGCTCG 61.011 55.000 9.64 0.00 42.74 5.03
5570 5819 0.461339 ACAACGCCTTCAACGTGACT 60.461 50.000 0.00 0.00 44.30 3.41
5577 5826 1.495584 GAGCACGACAACGCCTTCAA 61.496 55.000 0.00 0.00 43.96 2.69
5578 5827 1.954146 GAGCACGACAACGCCTTCA 60.954 57.895 0.00 0.00 43.96 3.02
5668 5918 3.660501 AGTACATGCTGACGTTCAAGA 57.339 42.857 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.