Multiple sequence alignment - TraesCS1D01G302900

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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 TraesCS1D01G302900 chr1D 100.000 3403 0 0 1 3403 400791449 400794851 0.000000e+00 6285.0
1 TraesCS1D01G302900 chr1D 89.829 934 95 0 1491 2424 40597990 40598923 0.000000e+00 1199.0
2 TraesCS1D01G302900 chr1D 86.824 425 41 12 1007 1429 40597375 40597786 8.600000e-126 460.0
3 TraesCS1D01G302900 chr1B 93.755 3427 161 20 1 3403 537770508 537773905 0.000000e+00 5094.0
4 TraesCS1D01G302900 chr1B 86.746 1426 155 25 1029 2429 60109090 60107674 0.000000e+00 1555.0
5 TraesCS1D01G302900 chr1B 88.974 916 99 2 1510 2424 60473811 60474725 0.000000e+00 1131.0
6 TraesCS1D01G302900 chr1B 90.110 273 26 1 2543 2814 563706004 563706276 1.500000e-93 353.0
7 TraesCS1D01G302900 chr1B 93.000 200 14 0 1230 1429 60473294 60473493 3.320000e-75 292.0
8 TraesCS1D01G302900 chr1B 89.865 148 9 6 1000 1144 60456804 60456948 5.800000e-43 185.0
9 TraesCS1D01G302900 chr1B 74.919 307 65 9 348 648 558086629 558086929 2.760000e-26 130.0
10 TraesCS1D01G302900 chr1B 91.111 45 4 0 886 930 60456661 60456705 1.020000e-05 62.1
11 TraesCS1D01G302900 chr1A 96.550 1884 62 2 663 2543 497082964 497084847 0.000000e+00 3116.0
12 TraesCS1D01G302900 chr1A 85.049 1632 183 40 838 2429 39872318 39870708 0.000000e+00 1605.0
13 TraesCS1D01G302900 chr1A 78.857 175 35 2 476 649 9816667 9816494 2.150000e-22 117.0
14 TraesCS1D01G302900 chr7A 86.493 1688 152 37 797 2432 130400947 130399284 0.000000e+00 1784.0
15 TraesCS1D01G302900 chr7A 89.662 532 55 0 2811 3342 39235970 39235439 0.000000e+00 678.0
16 TraesCS1D01G302900 chr7A 90.511 274 25 1 2543 2815 39236814 39236541 8.980000e-96 361.0
17 TraesCS1D01G302900 chr7A 77.305 141 29 3 475 612 511032546 511032406 2.810000e-11 80.5
18 TraesCS1D01G302900 chr7D 87.483 1510 144 28 955 2432 131652336 131650840 0.000000e+00 1700.0
19 TraesCS1D01G302900 chr7D 87.941 539 61 3 2806 3342 163220931 163221467 1.720000e-177 632.0
20 TraesCS1D01G302900 chr7D 90.441 272 24 2 2544 2814 163220097 163220367 1.160000e-94 357.0
21 TraesCS1D01G302900 chr7B 87.500 1504 146 22 955 2432 93068028 93066541 0.000000e+00 1698.0
22 TraesCS1D01G302900 chr7B 90.842 273 24 1 2543 2814 641787930 641788202 6.940000e-97 364.0
23 TraesCS1D01G302900 chr6A 89.662 532 55 0 2811 3342 53087635 53087104 0.000000e+00 678.0
24 TraesCS1D01G302900 chr6A 89.744 273 24 2 2543 2814 53088475 53088206 2.510000e-91 346.0
25 TraesCS1D01G302900 chr6A 89.091 55 4 2 433 487 404460615 404460667 2.190000e-07 67.6
26 TraesCS1D01G302900 chr3D 90.211 521 50 1 2822 3342 110308013 110307494 0.000000e+00 678.0
27 TraesCS1D01G302900 chr3D 90.566 53 5 0 593 645 388782454 388782402 1.690000e-08 71.3
28 TraesCS1D01G302900 chr5D 89.239 539 56 1 2806 3342 550507618 550507080 0.000000e+00 673.0
29 TraesCS1D01G302900 chr5D 90.110 273 26 1 2543 2814 550508456 550508184 1.500000e-93 353.0
30 TraesCS1D01G302900 chr5D 78.261 161 34 1 500 659 520966214 520966374 6.010000e-18 102.0
31 TraesCS1D01G302900 chr4D 89.474 532 56 0 2811 3342 35598964 35598433 0.000000e+00 673.0
32 TraesCS1D01G302900 chr4D 91.241 274 22 2 2543 2814 35599809 35599536 4.150000e-99 372.0
33 TraesCS1D01G302900 chr5B 89.054 539 56 3 2806 3342 275024529 275025066 0.000000e+00 665.0
34 TraesCS1D01G302900 chr5B 82.051 78 9 2 437 514 14192389 14192317 1.020000e-05 62.1
35 TraesCS1D01G302900 chr6D 87.782 532 64 1 2811 3342 456686806 456686276 3.730000e-174 621.0
36 TraesCS1D01G302900 chr6D 89.744 273 25 2 2543 2814 34534688 34534418 2.510000e-91 346.0
37 TraesCS1D01G302900 chr6B 84.483 116 16 2 548 661 712493545 712493660 2.780000e-21 113.0
38 TraesCS1D01G302900 chr4A 75.909 220 42 9 439 654 733672606 733672394 6.010000e-18 102.0
39 TraesCS1D01G302900 chr3B 91.525 59 3 2 597 654 671417529 671417472 2.810000e-11 80.5
40 TraesCS1D01G302900 chr3B 76.515 132 29 1 365 494 537836297 537836428 1.690000e-08 71.3
41 TraesCS1D01G302900 chr3B 78.378 111 17 5 556 662 712757370 712757477 7.880000e-07 65.8
42 TraesCS1D01G302900 chr5A 80.412 97 17 2 535 630 611118489 611118584 4.710000e-09 73.1


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 TraesCS1D01G302900 chr1D 400791449 400794851 3402 False 6285.0 6285 100.0000 1 3403 1 chr1D.!!$F1 3402
1 TraesCS1D01G302900 chr1D 40597375 40598923 1548 False 829.5 1199 88.3265 1007 2424 2 chr1D.!!$F2 1417
2 TraesCS1D01G302900 chr1B 537770508 537773905 3397 False 5094.0 5094 93.7550 1 3403 1 chr1B.!!$F1 3402
3 TraesCS1D01G302900 chr1B 60107674 60109090 1416 True 1555.0 1555 86.7460 1029 2429 1 chr1B.!!$R1 1400
4 TraesCS1D01G302900 chr1B 60473294 60474725 1431 False 711.5 1131 90.9870 1230 2424 2 chr1B.!!$F5 1194
5 TraesCS1D01G302900 chr1A 497082964 497084847 1883 False 3116.0 3116 96.5500 663 2543 1 chr1A.!!$F1 1880
6 TraesCS1D01G302900 chr1A 39870708 39872318 1610 True 1605.0 1605 85.0490 838 2429 1 chr1A.!!$R2 1591
7 TraesCS1D01G302900 chr7A 130399284 130400947 1663 True 1784.0 1784 86.4930 797 2432 1 chr7A.!!$R1 1635
8 TraesCS1D01G302900 chr7A 39235439 39236814 1375 True 519.5 678 90.0865 2543 3342 2 chr7A.!!$R3 799
9 TraesCS1D01G302900 chr7D 131650840 131652336 1496 True 1700.0 1700 87.4830 955 2432 1 chr7D.!!$R1 1477
10 TraesCS1D01G302900 chr7D 163220097 163221467 1370 False 494.5 632 89.1910 2544 3342 2 chr7D.!!$F1 798
11 TraesCS1D01G302900 chr7B 93066541 93068028 1487 True 1698.0 1698 87.5000 955 2432 1 chr7B.!!$R1 1477
12 TraesCS1D01G302900 chr6A 53087104 53088475 1371 True 512.0 678 89.7030 2543 3342 2 chr6A.!!$R1 799
13 TraesCS1D01G302900 chr3D 110307494 110308013 519 True 678.0 678 90.2110 2822 3342 1 chr3D.!!$R1 520
14 TraesCS1D01G302900 chr5D 550507080 550508456 1376 True 513.0 673 89.6745 2543 3342 2 chr5D.!!$R1 799
15 TraesCS1D01G302900 chr4D 35598433 35599809 1376 True 522.5 673 90.3575 2543 3342 2 chr4D.!!$R1 799
16 TraesCS1D01G302900 chr5B 275024529 275025066 537 False 665.0 665 89.0540 2806 3342 1 chr5B.!!$F1 536
17 TraesCS1D01G302900 chr6D 456686276 456686806 530 True 621.0 621 87.7820 2811 3342 1 chr6D.!!$R2 531

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
290 294 0.106116 GGGACGAGGTGGAGGTCTAT 60.106 60.0 0.00 0.0 0.00 1.98 F
1179 1252 0.177604 GCTCCACTGTCTAGCTGCAT 59.822 55.0 1.02 0.0 33.40 3.96 F
2237 2644 0.679002 AGAACATGCAGGCGCTCATT 60.679 50.0 7.64 0.0 39.64 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 2344 0.459759 GGTAGTTGCTGTACTCGGCC 60.460 60.0 0.00 0.0 44.62 6.13 R
2378 2785 0.395173 AGTTGAGGTTGGTTTGGCGT 60.395 50.0 0.00 0.0 0.00 5.68 R
3249 4251 2.554344 GGAGGGCCAAAACATCACTACA 60.554 50.0 6.18 0.0 0.00 2.74 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
21 22 4.086706 CCTCAACTTGTCCCAGTTAAGT 57.913 45.455 0.00 0.00 35.10 2.24
33 34 3.937706 CCCAGTTAAGTCAGAGATGCAAG 59.062 47.826 0.00 0.00 0.00 4.01
35 36 4.323028 CCAGTTAAGTCAGAGATGCAAGGA 60.323 45.833 0.00 0.00 0.00 3.36
36 37 5.426504 CAGTTAAGTCAGAGATGCAAGGAT 58.573 41.667 0.00 0.00 0.00 3.24
37 38 5.293814 CAGTTAAGTCAGAGATGCAAGGATG 59.706 44.000 0.00 0.00 0.00 3.51
65 68 1.271379 CATGCAGAGCACCAAACACAT 59.729 47.619 0.00 0.00 43.04 3.21
72 75 5.185454 CAGAGCACCAAACACATCCTTATA 58.815 41.667 0.00 0.00 0.00 0.98
100 103 5.415701 TGAGGCCTTCAACATAGAATTTCAC 59.584 40.000 6.77 0.00 31.34 3.18
145 148 1.269448 ACCATTGTTCCATGCAACGTC 59.731 47.619 0.00 0.00 0.00 4.34
147 150 0.109781 ATTGTTCCATGCAACGTCGC 60.110 50.000 0.00 0.00 0.00 5.19
211 214 3.066380 CCAAAACATGCAAAACTAGGGC 58.934 45.455 0.00 0.00 0.00 5.19
289 293 1.305623 GGGACGAGGTGGAGGTCTA 59.694 63.158 0.00 0.00 0.00 2.59
290 294 0.106116 GGGACGAGGTGGAGGTCTAT 60.106 60.000 0.00 0.00 0.00 1.98
316 320 2.254023 AGGAGGGATCTGGGAGGTAATT 59.746 50.000 0.00 0.00 0.00 1.40
325 329 3.596046 TCTGGGAGGTAATTGGGTGAAAT 59.404 43.478 0.00 0.00 0.00 2.17
405 410 4.611310 ACGCATACGCTCATATATACGT 57.389 40.909 11.05 11.05 45.53 3.57
408 413 4.352039 GCATACGCTCATATATACGTGCT 58.648 43.478 14.46 0.00 39.43 4.40
420 425 8.464404 TCATATATACGTGCTTACACTTATCCC 58.536 37.037 0.00 0.00 45.10 3.85
421 426 2.685850 ACGTGCTTACACTTATCCCC 57.314 50.000 0.00 0.00 45.10 4.81
430 435 2.845659 ACACTTATCCCCATGGACTCA 58.154 47.619 15.22 0.00 45.58 3.41
445 450 1.899814 GACTCACACACATCCTACCCA 59.100 52.381 0.00 0.00 0.00 4.51
489 494 5.861251 CCGAGCAGACATATTATCTTGAGAC 59.139 44.000 0.00 0.00 0.00 3.36
504 509 0.247736 GAGACTGACGAAGGCACCAT 59.752 55.000 0.00 0.00 35.71 3.55
506 511 1.478510 AGACTGACGAAGGCACCATAG 59.521 52.381 0.00 0.00 35.71 2.23
507 512 1.476891 GACTGACGAAGGCACCATAGA 59.523 52.381 0.00 0.00 32.10 1.98
514 519 0.537188 AAGGCACCATAGACACCTCG 59.463 55.000 0.00 0.00 0.00 4.63
522 527 5.601662 CACCATAGACACCTCGTAATTGAT 58.398 41.667 0.00 0.00 0.00 2.57
524 529 5.362717 ACCATAGACACCTCGTAATTGATGA 59.637 40.000 0.00 0.00 0.00 2.92
529 534 5.995282 AGACACCTCGTAATTGATGAAAACA 59.005 36.000 0.00 0.00 0.00 2.83
534 539 7.273381 CACCTCGTAATTGATGAAAACATTTCC 59.727 37.037 0.77 0.00 0.00 3.13
537 542 8.964420 TCGTAATTGATGAAAACATTTCCTTC 57.036 30.769 0.77 0.00 0.00 3.46
540 545 9.657419 GTAATTGATGAAAACATTTCCTTCCAT 57.343 29.630 0.77 0.00 0.00 3.41
552 557 5.890424 TTTCCTTCCATTAAACACGGATC 57.110 39.130 0.00 0.00 0.00 3.36
553 558 4.561500 TCCTTCCATTAAACACGGATCA 57.438 40.909 0.00 0.00 0.00 2.92
554 559 5.110814 TCCTTCCATTAAACACGGATCAT 57.889 39.130 0.00 0.00 0.00 2.45
589 594 8.547967 TGAAATAAATCCAGGATAATACGAGC 57.452 34.615 1.02 0.00 0.00 5.03
590 595 8.154203 TGAAATAAATCCAGGATAATACGAGCA 58.846 33.333 1.02 0.00 0.00 4.26
591 596 9.167311 GAAATAAATCCAGGATAATACGAGCAT 57.833 33.333 1.02 0.00 0.00 3.79
592 597 9.520515 AAATAAATCCAGGATAATACGAGCATT 57.479 29.630 1.02 0.00 0.00 3.56
605 610 4.992381 ACGAGCATTAGAACTTGAACAC 57.008 40.909 0.00 0.00 0.00 3.32
612 617 4.764050 TTAGAACTTGAACACTGGTGGA 57.236 40.909 5.70 0.00 34.19 4.02
618 623 0.692756 TGAACACTGGTGGACTGGGA 60.693 55.000 5.70 0.00 34.19 4.37
621 626 2.038863 ACACTGGTGGACTGGGAATA 57.961 50.000 5.70 0.00 34.19 1.75
627 632 1.065418 GGTGGACTGGGAATACCACTG 60.065 57.143 13.50 0.00 46.80 3.66
651 656 3.379372 CCTTCTAACCATCCAAGCACATG 59.621 47.826 0.00 0.00 0.00 3.21
654 659 5.172687 TCTAACCATCCAAGCACATGTTA 57.827 39.130 0.00 0.00 0.00 2.41
664 669 3.476295 AGCACATGTTAATTCGCACTG 57.524 42.857 0.00 0.00 0.00 3.66
669 674 3.193267 ACATGTTAATTCGCACTGCCAAT 59.807 39.130 0.00 0.00 0.00 3.16
1125 1194 1.599047 CACCATCCTCGCCTGTCTT 59.401 57.895 0.00 0.00 0.00 3.01
1143 1212 1.072965 CTTGAGTCCAAGCTCCAGGTT 59.927 52.381 0.00 0.00 42.72 3.50
1179 1252 0.177604 GCTCCACTGTCTAGCTGCAT 59.822 55.000 1.02 0.00 33.40 3.96
1205 1301 5.063880 TCTTCGTCATCCTAGATCGATTGA 58.936 41.667 0.00 0.00 0.00 2.57
1206 1302 5.707764 TCTTCGTCATCCTAGATCGATTGAT 59.292 40.000 0.00 0.00 37.60 2.57
1207 1303 5.966742 TCGTCATCCTAGATCGATTGATT 57.033 39.130 0.00 0.00 34.09 2.57
1208 1304 5.703876 TCGTCATCCTAGATCGATTGATTG 58.296 41.667 0.00 0.00 34.09 2.67
1209 1305 5.473504 TCGTCATCCTAGATCGATTGATTGA 59.526 40.000 0.00 0.00 34.09 2.57
1210 1306 6.151817 TCGTCATCCTAGATCGATTGATTGAT 59.848 38.462 0.00 0.00 34.09 2.57
1211 1307 6.810676 CGTCATCCTAGATCGATTGATTGATT 59.189 38.462 0.00 0.00 34.09 2.57
1212 1308 7.201418 CGTCATCCTAGATCGATTGATTGATTG 60.201 40.741 0.00 0.00 34.09 2.67
1227 1323 0.795735 GATTGTGACATGCGCTGTGC 60.796 55.000 15.61 6.19 46.70 4.57
1243 1345 1.614525 TGCCTGACAGGAGCTGGAT 60.615 57.895 26.25 0.00 37.67 3.41
1429 1561 3.984200 GAGGAGGTACGCACGCACC 62.984 68.421 4.22 4.22 34.86 5.01
1446 1585 2.360980 CTCTCCTCCCGGTGGACT 59.639 66.667 9.11 0.00 35.03 3.85
1607 2014 4.990526 ACAAGATCAAGAACCTCACCAAT 58.009 39.130 0.00 0.00 0.00 3.16
2141 2548 1.037493 TGCTGTTCCAGTCACTACGT 58.963 50.000 0.00 0.00 33.43 3.57
2237 2644 0.679002 AGAACATGCAGGCGCTCATT 60.679 50.000 7.64 0.00 39.64 2.57
2239 2646 0.961857 AACATGCAGGCGCTCATTGA 60.962 50.000 7.64 0.00 39.64 2.57
2400 2813 1.754201 GCCAAACCAACCTCAACTCCT 60.754 52.381 0.00 0.00 0.00 3.69
2636 3057 2.406616 GCCCACAAGTACGGCATGG 61.407 63.158 4.07 3.25 42.52 3.66
2652 3073 3.098555 GGCAATTACTCGCCCACG 58.901 61.111 0.00 0.00 42.82 4.94
2780 3202 5.387342 CCGTGCGTTTCTTTCATTTCAAATC 60.387 40.000 0.00 0.00 0.00 2.17
2791 3213 6.816134 TTCATTTCAAATCATCCACGAGAA 57.184 33.333 0.00 0.00 0.00 2.87
2801 3223 3.624410 TCATCCACGAGAAAAGCATGATG 59.376 43.478 0.00 0.00 0.00 3.07
2802 3224 3.333029 TCCACGAGAAAAGCATGATGA 57.667 42.857 0.00 0.00 0.00 2.92
2814 3816 2.025605 AGCATGATGAGAGAGGCCAAAA 60.026 45.455 5.01 0.00 0.00 2.44
2819 3821 4.665451 TGATGAGAGAGGCCAAAAATGAA 58.335 39.130 5.01 0.00 0.00 2.57
2841 3843 3.283751 CGGTGCAATATCCTTGGGTTTA 58.716 45.455 0.00 0.00 0.00 2.01
2860 3862 2.747686 GACCAAGAAGCCACGGGA 59.252 61.111 0.00 0.00 0.00 5.14
2863 3865 2.335712 CCAAGAAGCCACGGGAAGC 61.336 63.158 0.00 0.00 0.00 3.86
2925 3927 5.185249 AGTCGTAGAGGCATAGAAAAACTCA 59.815 40.000 0.00 0.00 36.95 3.41
2965 3967 0.251787 GCTTCCCAGTCCAACCCATT 60.252 55.000 0.00 0.00 0.00 3.16
3001 4003 1.142060 TCCATTCGAACCACAACCACT 59.858 47.619 0.00 0.00 0.00 4.00
3059 4061 2.750141 ACTCGAAGGCCTCCATACTA 57.250 50.000 5.23 0.00 0.00 1.82
3119 4121 3.622826 ACCCGTGGTCTTGTCCGG 61.623 66.667 0.00 0.00 40.12 5.14
3138 4140 1.700186 GGACTGGACCAAAGGAAGACT 59.300 52.381 0.00 0.00 0.00 3.24
3153 4155 6.036577 AGGAAGACTCTCTCAATCTTGTTC 57.963 41.667 0.00 0.00 32.83 3.18
3161 4163 6.070309 ACTCTCTCAATCTTGTTCAGGCTATT 60.070 38.462 0.00 0.00 0.00 1.73
3164 4166 5.877012 TCTCAATCTTGTTCAGGCTATTGAC 59.123 40.000 3.17 0.00 31.87 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 47 0.670162 GTGTTTGGTGCTCTGCATGT 59.330 50.000 0.00 0.00 41.91 3.21
45 48 0.669619 TGTGTTTGGTGCTCTGCATG 59.330 50.000 0.00 0.00 41.91 4.06
65 68 5.428457 TGTTGAAGGCCTCAATCTATAAGGA 59.572 40.000 5.23 0.00 45.74 3.36
72 75 5.441718 TTCTATGTTGAAGGCCTCAATCT 57.558 39.130 5.23 6.59 45.74 2.40
100 103 5.130145 ACCCTGGTCTCAATCTAGATGAAAG 59.870 44.000 5.86 4.62 0.00 2.62
145 148 2.514592 ATTCAGATGGCGGTGGCG 60.515 61.111 0.00 0.00 41.24 5.69
147 150 3.831883 CCATTCAGATGGCGGTGG 58.168 61.111 0.00 0.00 45.96 4.61
166 169 1.226746 GTCTTGGTTTCGAGGTGGTG 58.773 55.000 0.00 0.00 0.00 4.17
167 170 0.108019 GGTCTTGGTTTCGAGGTGGT 59.892 55.000 0.00 0.00 0.00 4.16
172 175 3.396260 TGGTTAGGTCTTGGTTTCGAG 57.604 47.619 0.00 0.00 0.00 4.04
275 279 4.225492 TCCTCTATATAGACCTCCACCTCG 59.775 50.000 8.44 0.00 0.00 4.63
289 293 3.535590 CCTCCCAGATCCCTCCTCTATAT 59.464 52.174 0.00 0.00 0.00 0.86
290 294 2.929724 CCTCCCAGATCCCTCCTCTATA 59.070 54.545 0.00 0.00 0.00 1.31
316 320 5.042463 TCAGAAGTTACACATTTCACCCA 57.958 39.130 0.00 0.00 0.00 4.51
383 388 4.791676 CACGTATATATGAGCGTATGCGTT 59.208 41.667 8.98 0.00 43.64 4.84
384 389 4.340263 CACGTATATATGAGCGTATGCGT 58.660 43.478 8.98 3.34 45.80 5.24
386 391 4.352039 AGCACGTATATATGAGCGTATGC 58.648 43.478 15.79 10.50 43.24 3.14
387 392 6.964934 TGTAAGCACGTATATATGAGCGTATG 59.035 38.462 17.80 4.24 35.71 2.39
388 393 6.965500 GTGTAAGCACGTATATATGAGCGTAT 59.035 38.462 17.80 11.72 35.75 3.06
405 410 3.119319 TCCATGGGGATAAGTGTAAGCA 58.881 45.455 13.02 0.00 38.64 3.91
420 425 1.280133 AGGATGTGTGTGAGTCCATGG 59.720 52.381 4.97 4.97 33.12 3.66
421 426 2.775911 AGGATGTGTGTGAGTCCATG 57.224 50.000 0.00 0.00 33.12 3.66
430 435 3.071602 GCTCATATGGGTAGGATGTGTGT 59.928 47.826 4.11 0.00 0.00 3.72
445 450 3.304996 CGGTCTCTCGAATGTGCTCATAT 60.305 47.826 0.93 0.00 33.49 1.78
489 494 1.204704 TGTCTATGGTGCCTTCGTCAG 59.795 52.381 0.00 0.00 0.00 3.51
504 509 7.156000 TGTTTTCATCAATTACGAGGTGTCTA 58.844 34.615 0.00 0.00 0.00 2.59
506 511 6.236017 TGTTTTCATCAATTACGAGGTGTC 57.764 37.500 0.00 0.00 0.00 3.67
507 512 6.817765 ATGTTTTCATCAATTACGAGGTGT 57.182 33.333 0.00 0.00 35.32 4.16
514 519 9.657419 ATGGAAGGAAATGTTTTCATCAATTAC 57.343 29.630 2.74 0.00 39.94 1.89
522 527 7.436673 CGTGTTTAATGGAAGGAAATGTTTTCA 59.563 33.333 2.74 0.00 0.00 2.69
524 529 6.704050 CCGTGTTTAATGGAAGGAAATGTTTT 59.296 34.615 0.00 0.00 37.06 2.43
537 542 7.222611 GGATTTTTGATGATCCGTGTTTAATGG 59.777 37.037 0.00 0.00 33.12 3.16
540 545 7.175816 TCAGGATTTTTGATGATCCGTGTTTAA 59.824 33.333 0.00 0.00 45.21 1.52
542 547 5.476599 TCAGGATTTTTGATGATCCGTGTTT 59.523 36.000 0.00 0.00 45.21 2.83
583 588 5.633601 CAGTGTTCAAGTTCTAATGCTCGTA 59.366 40.000 0.00 0.00 0.00 3.43
584 589 4.449068 CAGTGTTCAAGTTCTAATGCTCGT 59.551 41.667 0.00 0.00 0.00 4.18
585 590 4.143030 CCAGTGTTCAAGTTCTAATGCTCG 60.143 45.833 0.00 0.00 0.00 5.03
586 591 4.757149 ACCAGTGTTCAAGTTCTAATGCTC 59.243 41.667 0.00 0.00 0.00 4.26
587 592 4.516698 CACCAGTGTTCAAGTTCTAATGCT 59.483 41.667 0.00 0.00 0.00 3.79
588 593 4.320494 CCACCAGTGTTCAAGTTCTAATGC 60.320 45.833 0.00 0.00 0.00 3.56
589 594 5.049405 GTCCACCAGTGTTCAAGTTCTAATG 60.049 44.000 0.00 0.00 0.00 1.90
590 595 5.063880 GTCCACCAGTGTTCAAGTTCTAAT 58.936 41.667 0.00 0.00 0.00 1.73
591 596 4.163458 AGTCCACCAGTGTTCAAGTTCTAA 59.837 41.667 0.00 0.00 0.00 2.10
592 597 3.709653 AGTCCACCAGTGTTCAAGTTCTA 59.290 43.478 0.00 0.00 0.00 2.10
605 610 1.065418 GTGGTATTCCCAGTCCACCAG 60.065 57.143 0.00 0.00 46.45 4.00
618 623 5.104485 GGATGGTTAGAAGGACAGTGGTATT 60.104 44.000 0.00 0.00 0.00 1.89
621 626 2.572104 GGATGGTTAGAAGGACAGTGGT 59.428 50.000 0.00 0.00 0.00 4.16
627 632 3.010420 GTGCTTGGATGGTTAGAAGGAC 58.990 50.000 0.00 0.00 30.98 3.85
651 656 3.485947 TCATTGGCAGTGCGAATTAAC 57.514 42.857 21.17 0.46 34.94 2.01
654 659 1.064505 CGATCATTGGCAGTGCGAATT 59.935 47.619 21.17 9.44 34.94 2.17
664 669 1.137404 GTGCACCACGATCATTGGC 59.863 57.895 5.22 0.00 37.69 4.52
669 674 0.249699 AACGAAGTGCACCACGATCA 60.250 50.000 30.05 0.00 45.00 2.92
1125 1194 0.687354 GAACCTGGAGCTTGGACTCA 59.313 55.000 0.00 0.00 38.50 3.41
1143 1212 2.885113 CTGCAGACGGATGGACGA 59.115 61.111 8.42 0.00 37.61 4.20
1179 1252 4.642429 TCGATCTAGGATGACGAAGATGA 58.358 43.478 0.00 0.00 30.09 2.92
1205 1301 1.814394 ACAGCGCATGTCACAATCAAT 59.186 42.857 11.47 0.00 37.75 2.57
1206 1302 1.069091 CACAGCGCATGTCACAATCAA 60.069 47.619 11.47 0.00 41.41 2.57
1207 1303 0.518195 CACAGCGCATGTCACAATCA 59.482 50.000 11.47 0.00 41.41 2.57
1208 1304 0.795735 GCACAGCGCATGTCACAATC 60.796 55.000 11.47 0.00 41.41 2.67
1209 1305 1.210931 GCACAGCGCATGTCACAAT 59.789 52.632 11.47 0.00 41.41 2.71
1210 1306 2.638719 GCACAGCGCATGTCACAA 59.361 55.556 11.47 0.00 41.41 3.33
1211 1307 3.356267 GGCACAGCGCATGTCACA 61.356 61.111 11.47 0.00 41.41 3.58
1212 1308 3.052082 AGGCACAGCGCATGTCAC 61.052 61.111 17.19 9.67 41.41 3.67
1227 1323 1.525923 CCATCCAGCTCCTGTCAGG 59.474 63.158 13.21 13.21 36.46 3.86
1441 1573 2.294791 CCAAATTTTGGTGCGTAGTCCA 59.705 45.455 18.34 0.00 45.93 4.02
1937 2344 0.459759 GGTAGTTGCTGTACTCGGCC 60.460 60.000 0.00 0.00 44.62 6.13
2141 2548 2.417933 GCGTAGGTAGTTCTTCTCGACA 59.582 50.000 0.00 0.00 0.00 4.35
2213 2620 0.744414 GCGCCTGCATGTTCTCCTTA 60.744 55.000 0.00 0.00 42.15 2.69
2237 2644 1.300971 GCAGCTTGTTGCCGATCTCA 61.301 55.000 0.00 0.00 44.23 3.27
2239 2646 1.002868 AGCAGCTTGTTGCCGATCT 60.003 52.632 5.86 0.00 45.18 2.75
2378 2785 0.395173 AGTTGAGGTTGGTTTGGCGT 60.395 50.000 0.00 0.00 0.00 5.68
2381 2788 2.364972 AGGAGTTGAGGTTGGTTTGG 57.635 50.000 0.00 0.00 0.00 3.28
2400 2813 8.433599 TCTCTCGAATCTTCCTCTTCTCTATTA 58.566 37.037 0.00 0.00 0.00 0.98
2600 3021 3.810941 TGGGCGTGTTGTAAAACTCTAAG 59.189 43.478 0.00 0.00 0.00 2.18
2636 3057 4.195308 TCGTGGGCGAGTAATTGC 57.805 55.556 0.00 0.00 42.81 3.56
2652 3073 6.420903 GCGCAAAGAAATTAGGGGATATTTTC 59.579 38.462 0.30 0.00 35.42 2.29
2660 3081 0.459899 GGGCGCAAAGAAATTAGGGG 59.540 55.000 10.83 0.00 0.00 4.79
2780 3202 3.624410 TCATCATGCTTTTCTCGTGGATG 59.376 43.478 0.00 0.00 0.00 3.51
2791 3213 1.562942 TGGCCTCTCTCATCATGCTTT 59.437 47.619 3.32 0.00 0.00 3.51
2801 3223 2.162408 CCGTTCATTTTTGGCCTCTCTC 59.838 50.000 3.32 0.00 0.00 3.20
2802 3224 2.162681 CCGTTCATTTTTGGCCTCTCT 58.837 47.619 3.32 0.00 0.00 3.10
2814 3816 3.381272 CCAAGGATATTGCACCGTTCATT 59.619 43.478 0.00 0.00 0.00 2.57
2819 3821 0.623723 ACCCAAGGATATTGCACCGT 59.376 50.000 0.00 0.00 0.00 4.83
2841 3843 2.030562 CCGTGGCTTCTTGGTCGT 59.969 61.111 0.00 0.00 0.00 4.34
2947 3949 3.669939 ATAATGGGTTGGACTGGGAAG 57.330 47.619 0.00 0.00 0.00 3.46
2965 3967 0.542333 TGGAACGATCCCCGCAAATA 59.458 50.000 9.50 0.00 45.95 1.40
3119 4121 2.635427 AGAGTCTTCCTTTGGTCCAGTC 59.365 50.000 0.00 0.00 0.00 3.51
3138 4140 5.946942 ATAGCCTGAACAAGATTGAGAGA 57.053 39.130 0.00 0.00 0.00 3.10
3249 4251 2.554344 GGAGGGCCAAAACATCACTACA 60.554 50.000 6.18 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.