Multiple sequence alignment - TraesCS7D01G379400

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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 TraesCS7D01G379400 chr7D 100.000 4457 0 0 1 4457 491791940 491787484 0.000000e+00 8231.0
1 TraesCS7D01G379400 chr7D 93.196 3248 183 22 924 4148 491801069 491797837 0.000000e+00 4739.0
2 TraesCS7D01G379400 chr7D 88.287 2715 271 28 935 3624 491864565 491861873 0.000000e+00 3208.0
3 TraesCS7D01G379400 chr7D 80.198 303 45 5 3623 3911 491861999 491861698 3.490000e-51 213.0
4 TraesCS7D01G379400 chr7D 83.688 141 15 5 3614 3747 491798499 491798360 4.680000e-25 126.0
5 TraesCS7D01G379400 chr7D 82.645 121 10 7 3514 3623 491798356 491798236 3.670000e-16 97.1
6 TraesCS7D01G379400 chr7A 96.575 4087 95 18 406 4457 558083162 558079086 0.000000e+00 6730.0
7 TraesCS7D01G379400 chr7A 94.967 2404 102 11 1372 3760 558093050 558090651 0.000000e+00 3751.0
8 TraesCS7D01G379400 chr7A 87.741 2692 271 41 934 3590 558102227 558099560 0.000000e+00 3088.0
9 TraesCS7D01G379400 chr7A 90.329 517 38 8 926 1430 558093535 558093019 0.000000e+00 667.0
10 TraesCS7D01G379400 chr7A 92.347 392 24 4 3759 4148 558090365 558089978 1.810000e-153 553.0
11 TraesCS7D01G379400 chr7A 91.707 205 10 5 173 370 558083362 558083158 1.220000e-70 278.0
12 TraesCS7D01G379400 chr7A 77.258 299 49 6 3626 3911 558099636 558099344 1.660000e-34 158.0
13 TraesCS7D01G379400 chr7A 83.206 131 15 4 3623 3747 558090917 558090788 3.640000e-21 113.0
14 TraesCS7D01G379400 chr7B 96.027 3146 104 9 540 3672 521124207 521121070 0.000000e+00 5097.0
15 TraesCS7D01G379400 chr7B 93.454 3254 180 15 924 4148 521133804 521130555 0.000000e+00 4798.0
16 TraesCS7D01G379400 chr7B 88.693 2441 230 27 935 3355 521142914 521140500 0.000000e+00 2937.0
17 TraesCS7D01G379400 chr7B 97.089 790 19 4 3670 4457 521120874 521120087 0.000000e+00 1328.0
18 TraesCS7D01G379400 chr7B 89.170 277 23 4 1 270 521124628 521124352 5.520000e-89 339.0
19 TraesCS7D01G379400 chr7B 86.245 269 28 6 3 267 491146876 491146613 2.620000e-72 283.0
20 TraesCS7D01G379400 chr7B 95.714 70 3 0 292 361 521124289 521124220 3.640000e-21 113.0
21 TraesCS7D01G379400 chr7B 83.471 121 9 7 3514 3623 521131074 521130954 7.890000e-18 102.0
22 TraesCS7D01G379400 chr7B 84.286 70 7 3 4387 4454 617555094 617555027 1.030000e-06 65.8
23 TraesCS7D01G379400 chr2D 76.016 1697 329 47 1814 3450 599927245 599928923 0.000000e+00 808.0
24 TraesCS7D01G379400 chr2B 75.722 1697 334 46 1814 3450 729767415 729769093 0.000000e+00 780.0
25 TraesCS7D01G379400 chr2B 80.000 150 24 5 586 731 381239266 381239119 6.100000e-19 106.0
26 TraesCS7D01G379400 chr2B 87.356 87 5 6 789 870 770265484 770265399 1.320000e-15 95.3
27 TraesCS7D01G379400 chr3B 88.603 272 21 8 3 267 141802813 141803081 5.560000e-84 322.0
28 TraesCS7D01G379400 chr3B 79.487 195 36 4 538 730 41185501 41185309 7.780000e-28 135.0
29 TraesCS7D01G379400 chr3B 81.818 154 21 4 581 730 10196321 10196171 6.050000e-24 122.0
30 TraesCS7D01G379400 chr3A 89.147 258 22 5 3 255 144444014 144444270 2.590000e-82 316.0
31 TraesCS7D01G379400 chr3A 75.258 291 63 7 1076 1360 678314240 678314527 3.620000e-26 130.0
32 TraesCS7D01G379400 chr3A 80.800 125 22 2 603 726 15557660 15557537 3.670000e-16 97.1
33 TraesCS7D01G379400 chr6D 85.556 270 33 5 3 267 471476917 471477185 1.220000e-70 278.0
34 TraesCS7D01G379400 chr2A 85.662 272 30 8 3 267 536694783 536694514 1.220000e-70 278.0
35 TraesCS7D01G379400 chr2A 85.448 268 31 8 3 264 38313283 38313018 5.680000e-69 272.0
36 TraesCS7D01G379400 chr4B 85.448 268 31 8 3 264 171214111 171213846 5.680000e-69 272.0
37 TraesCS7D01G379400 chr4B 78.226 124 26 1 603 725 438602618 438602741 1.330000e-10 78.7
38 TraesCS7D01G379400 chr5B 84.926 272 34 5 3 269 288391994 288391725 7.350000e-68 268.0
39 TraesCS7D01G379400 chr4A 75.170 294 61 9 1076 1360 738514088 738514378 1.300000e-25 128.0
40 TraesCS7D01G379400 chr4A 83.594 128 21 0 603 730 644207499 644207372 2.180000e-23 121.0
41 TraesCS7D01G379400 chr5A 80.769 130 22 3 603 730 519850700 519850572 1.020000e-16 99.0
42 TraesCS7D01G379400 chr5D 76.974 152 29 5 581 727 379580269 379580419 1.030000e-11 82.4
43 TraesCS7D01G379400 chr6B 95.349 43 2 0 828 870 668918618 668918576 8.000000e-08 69.4


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 TraesCS7D01G379400 chr7D 491787484 491791940 4456 True 8231.000000 8231 100.000000 1 4457 1 chr7D.!!$R1 4456
1 TraesCS7D01G379400 chr7D 491861698 491864565 2867 True 1710.500000 3208 84.242500 935 3911 2 chr7D.!!$R3 2976
2 TraesCS7D01G379400 chr7D 491797837 491801069 3232 True 1654.033333 4739 86.509667 924 4148 3 chr7D.!!$R2 3224
3 TraesCS7D01G379400 chr7A 558079086 558083362 4276 True 3504.000000 6730 94.141000 173 4457 2 chr7A.!!$R1 4284
4 TraesCS7D01G379400 chr7A 558099344 558102227 2883 True 1623.000000 3088 82.499500 934 3911 2 chr7A.!!$R3 2977
5 TraesCS7D01G379400 chr7A 558089978 558093535 3557 True 1271.000000 3751 90.212250 926 4148 4 chr7A.!!$R2 3222
6 TraesCS7D01G379400 chr7B 521140500 521142914 2414 True 2937.000000 2937 88.693000 935 3355 1 chr7B.!!$R2 2420
7 TraesCS7D01G379400 chr7B 521130555 521133804 3249 True 2450.000000 4798 88.462500 924 4148 2 chr7B.!!$R5 3224
8 TraesCS7D01G379400 chr7B 521120087 521124628 4541 True 1719.250000 5097 94.500000 1 4457 4 chr7B.!!$R4 4456
9 TraesCS7D01G379400 chr2D 599927245 599928923 1678 False 808.000000 808 76.016000 1814 3450 1 chr2D.!!$F1 1636
10 TraesCS7D01G379400 chr2B 729767415 729769093 1678 False 780.000000 780 75.722000 1814 3450 1 chr2B.!!$F1 1636

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
522 574 0.034089 GCTATGGGTGGCTCTTTGGT 60.034 55.000 0.00 0.0 0.0 3.67 F
528 580 0.322546 GGTGGCTCTTTGGTGGTAGG 60.323 60.000 0.00 0.0 0.0 3.18 F
1302 1410 0.526524 GACCCGATCTGAGAGCAACG 60.527 60.000 0.00 0.0 0.0 4.10 F
1338 1446 1.880027 GAAGATGGCAACCTTGTCGTT 59.120 47.619 9.74 0.0 35.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1338 1446 2.036089 GGATTGGGTGGCGTTGTTTAAA 59.964 45.455 0.00 0.0 0.00 1.52 R
1389 1500 3.222603 GGAGATGTTGGTGTTGGTTCTT 58.777 45.455 0.00 0.0 0.00 2.52 R
2389 2569 3.552890 CCAGCTGCTGGTTTTCTTTTACC 60.553 47.826 35.03 0.0 45.82 2.85 R
3592 3818 9.241919 TCAAATGAACTATAAGATGCAGGAAAA 57.758 29.630 0.00 0.0 0.00 2.29 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
26 27 8.236586 GCTCAAAATTCAACATACACATACAGA 58.763 33.333 0.00 0.00 0.00 3.41
135 138 6.844696 TTTCTCTATGCGTATGTTGGATTC 57.155 37.500 0.00 0.00 0.00 2.52
136 139 5.791336 TCTCTATGCGTATGTTGGATTCT 57.209 39.130 0.00 0.00 0.00 2.40
313 365 0.107312 CCCTGCTTCATGGTCAGAGG 60.107 60.000 10.10 6.95 0.00 3.69
361 413 2.768833 ATAATGCATGTGCGCAGAAG 57.231 45.000 12.22 8.22 46.99 2.85
362 414 1.452110 TAATGCATGTGCGCAGAAGT 58.548 45.000 12.22 0.00 46.99 3.01
363 415 1.452110 AATGCATGTGCGCAGAAGTA 58.548 45.000 12.22 6.70 46.99 2.24
364 416 1.012086 ATGCATGTGCGCAGAAGTAG 58.988 50.000 12.22 2.49 46.99 2.57
365 417 0.320683 TGCATGTGCGCAGAAGTAGT 60.321 50.000 12.22 0.00 45.83 2.73
366 418 1.067213 TGCATGTGCGCAGAAGTAGTA 60.067 47.619 12.22 0.00 45.83 1.82
367 419 1.324736 GCATGTGCGCAGAAGTAGTAC 59.675 52.381 12.22 0.00 0.00 2.73
368 420 1.927174 CATGTGCGCAGAAGTAGTACC 59.073 52.381 12.22 0.00 0.00 3.34
369 421 0.963225 TGTGCGCAGAAGTAGTACCA 59.037 50.000 12.22 0.00 0.00 3.25
370 422 1.336517 TGTGCGCAGAAGTAGTACCAC 60.337 52.381 12.22 0.00 0.00 4.16
371 423 1.067776 GTGCGCAGAAGTAGTACCACT 60.068 52.381 12.22 0.00 0.00 4.00
372 424 1.067846 TGCGCAGAAGTAGTACCACTG 60.068 52.381 5.66 15.59 0.00 3.66
373 425 1.630148 CGCAGAAGTAGTACCACTGC 58.370 55.000 26.01 26.01 46.69 4.40
376 428 3.771798 GCAGAAGTAGTACCACTGCTAC 58.228 50.000 27.36 0.00 46.66 3.58
377 429 3.444388 GCAGAAGTAGTACCACTGCTACT 59.556 47.826 27.36 6.40 46.79 2.57
378 430 4.639310 GCAGAAGTAGTACCACTGCTACTA 59.361 45.833 27.36 0.00 44.84 1.82
379 431 5.220892 GCAGAAGTAGTACCACTGCTACTAG 60.221 48.000 27.36 0.00 44.84 2.57
380 432 4.883006 AGAAGTAGTACCACTGCTACTAGC 59.117 45.833 0.00 0.61 44.84 3.42
381 433 3.553904 AGTAGTACCACTGCTACTAGCC 58.446 50.000 5.58 0.00 44.08 3.93
382 434 2.830651 AGTACCACTGCTACTAGCCT 57.169 50.000 5.58 0.00 41.51 4.58
383 435 3.947612 AGTACCACTGCTACTAGCCTA 57.052 47.619 5.58 0.00 41.51 3.93
384 436 3.822940 AGTACCACTGCTACTAGCCTAG 58.177 50.000 5.58 0.00 41.51 3.02
385 437 3.458857 AGTACCACTGCTACTAGCCTAGA 59.541 47.826 5.58 0.00 41.51 2.43
386 438 2.938838 ACCACTGCTACTAGCCTAGAG 58.061 52.381 5.58 0.12 41.51 2.43
387 439 1.611491 CCACTGCTACTAGCCTAGAGC 59.389 57.143 5.58 10.41 41.51 4.09
396 448 3.640761 GCCTAGAGCTTGGAGCCT 58.359 61.111 2.09 0.00 43.77 4.58
397 449 2.827715 GCCTAGAGCTTGGAGCCTA 58.172 57.895 2.09 0.00 43.77 3.93
398 450 0.678950 GCCTAGAGCTTGGAGCCTAG 59.321 60.000 13.75 13.75 43.77 3.02
399 451 2.032151 GCCTAGAGCTTGGAGCCTAGT 61.032 57.143 16.81 0.00 43.77 2.57
400 452 2.753507 GCCTAGAGCTTGGAGCCTAGTA 60.754 54.545 16.81 0.00 43.77 1.82
401 453 3.153919 CCTAGAGCTTGGAGCCTAGTAG 58.846 54.545 16.81 0.00 43.77 2.57
402 454 2.838637 AGAGCTTGGAGCCTAGTAGT 57.161 50.000 0.00 0.00 43.77 2.73
403 455 3.108847 AGAGCTTGGAGCCTAGTAGTT 57.891 47.619 0.00 0.00 43.77 2.24
404 456 3.445987 AGAGCTTGGAGCCTAGTAGTTT 58.554 45.455 0.00 0.00 43.77 2.66
412 464 4.407945 TGGAGCCTAGTAGTTTTACCATCC 59.592 45.833 0.00 0.00 0.00 3.51
422 474 7.124052 AGTAGTTTTACCATCCACTCTAGCTA 58.876 38.462 0.00 0.00 0.00 3.32
443 495 6.258947 AGCTAAGTTGACTTCAGAAGTTCAAC 59.741 38.462 29.04 29.04 43.03 3.18
444 496 6.037172 GCTAAGTTGACTTCAGAAGTTCAACA 59.963 38.462 32.73 23.08 43.71 3.33
445 497 5.803020 AGTTGACTTCAGAAGTTCAACAC 57.197 39.130 32.73 21.67 43.71 3.32
450 502 6.582636 TGACTTCAGAAGTTCAACACAGTAT 58.417 36.000 17.19 0.00 43.03 2.12
452 504 5.760253 ACTTCAGAAGTTCAACACAGTATGG 59.240 40.000 10.27 0.00 38.73 2.74
493 545 0.321919 AGATCGCACTTGTGGCATGT 60.322 50.000 2.81 0.00 0.00 3.21
497 549 1.007038 GCACTTGTGGCATGTGTGG 60.007 57.895 15.74 0.00 40.25 4.17
509 561 0.810648 ATGTGTGGCAAACGCTATGG 59.189 50.000 2.85 0.00 40.15 2.74
510 562 1.240641 TGTGTGGCAAACGCTATGGG 61.241 55.000 2.85 0.00 40.15 4.00
516 568 1.993369 GCAAACGCTATGGGTGGCTC 61.993 60.000 0.00 0.00 30.92 4.70
521 573 1.097547 CGCTATGGGTGGCTCTTTGG 61.098 60.000 0.00 0.00 0.00 3.28
522 574 0.034089 GCTATGGGTGGCTCTTTGGT 60.034 55.000 0.00 0.00 0.00 3.67
528 580 0.322546 GGTGGCTCTTTGGTGGTAGG 60.323 60.000 0.00 0.00 0.00 3.18
529 581 0.690762 GTGGCTCTTTGGTGGTAGGA 59.309 55.000 0.00 0.00 0.00 2.94
531 583 1.559682 TGGCTCTTTGGTGGTAGGATC 59.440 52.381 0.00 0.00 0.00 3.36
532 584 1.840635 GGCTCTTTGGTGGTAGGATCT 59.159 52.381 0.00 0.00 0.00 2.75
533 585 2.239907 GGCTCTTTGGTGGTAGGATCTT 59.760 50.000 0.00 0.00 0.00 2.40
535 587 4.080526 GGCTCTTTGGTGGTAGGATCTTAA 60.081 45.833 0.00 0.00 0.00 1.85
536 588 4.876679 GCTCTTTGGTGGTAGGATCTTAAC 59.123 45.833 0.00 0.00 0.00 2.01
538 590 3.899052 TTGGTGGTAGGATCTTAACGG 57.101 47.619 0.00 0.00 0.00 4.44
553 627 7.011763 GGATCTTAACGGTAGGGTATTTTTCAC 59.988 40.741 0.00 0.00 0.00 3.18
650 724 1.595357 ACCTCGGCGGTAGGAAAAG 59.405 57.895 20.12 1.33 46.73 2.27
655 729 1.449070 GGCGGTAGGAAAAGGGTCG 60.449 63.158 0.00 0.00 0.00 4.79
808 885 2.880770 CCATGTGGCCACGGTATTT 58.119 52.632 30.07 8.29 0.00 1.40
857 939 4.282957 TCATTCCCAGCACTTTTTAATGCA 59.717 37.500 1.90 0.00 44.59 3.96
860 942 2.327568 CCAGCACTTTTTAATGCACGG 58.672 47.619 0.00 0.00 44.59 4.94
910 992 3.643978 GATGCCGCTGCGTCCATC 61.644 66.667 25.83 25.83 45.92 3.51
962 1049 3.343617 CCTCCTTCGTTAAATGGCAGAA 58.656 45.455 0.00 0.00 0.00 3.02
988 1075 1.340017 GGAGGGCAAGCAGACATACAA 60.340 52.381 0.00 0.00 0.00 2.41
1050 1155 1.222936 CCTCCTCTCCATGCACACC 59.777 63.158 0.00 0.00 0.00 4.16
1251 1359 1.275666 TCCATGTCATCACTCCCGTT 58.724 50.000 0.00 0.00 0.00 4.44
1302 1410 0.526524 GACCCGATCTGAGAGCAACG 60.527 60.000 0.00 0.00 0.00 4.10
1338 1446 1.880027 GAAGATGGCAACCTTGTCGTT 59.120 47.619 9.74 0.00 35.00 3.85
1389 1500 3.417101 GTCCACCAACATCACCAATACA 58.583 45.455 0.00 0.00 0.00 2.29
2389 2569 4.058124 TGTTCCGAGTTCAACAAGAGATG 58.942 43.478 0.00 0.00 29.43 2.90
2849 3050 4.403432 CCATCTGTTCCAAAGCAATGGTAT 59.597 41.667 7.57 0.00 41.46 2.73
3577 3788 8.916654 CGTGTAATAGCTCAAAGGTCATATAAG 58.083 37.037 0.00 0.00 0.00 1.73
4309 5038 1.480789 ACCCCCAAGAACAACACAAC 58.519 50.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 6.892310 AGAAGACAAAAGCAAAAATGACAC 57.108 33.333 0.00 0.00 0.00 3.67
146 149 3.278668 TGTGTCGACAACCCCTAAAAA 57.721 42.857 21.95 0.00 0.00 1.94
232 240 8.162085 CCAGCCCTTATATGCTATCATGATATT 58.838 37.037 15.71 6.97 35.69 1.28
353 405 1.630148 CAGTGGTACTACTTCTGCGC 58.370 55.000 9.48 0.00 0.00 6.09
361 413 3.553904 AGGCTAGTAGCAGTGGTACTAC 58.446 50.000 29.58 24.89 43.69 2.73
362 414 3.947612 AGGCTAGTAGCAGTGGTACTA 57.052 47.619 30.53 30.53 43.69 1.82
363 415 2.830651 AGGCTAGTAGCAGTGGTACT 57.169 50.000 31.43 31.43 46.50 2.73
364 416 3.816523 CTCTAGGCTAGTAGCAGTGGTAC 59.183 52.174 23.24 22.13 44.75 3.34
365 417 3.748027 GCTCTAGGCTAGTAGCAGTGGTA 60.748 52.174 26.83 0.00 44.75 3.25
366 418 2.938838 CTCTAGGCTAGTAGCAGTGGT 58.061 52.381 23.24 0.00 44.75 4.16
367 419 1.611491 GCTCTAGGCTAGTAGCAGTGG 59.389 57.143 26.83 11.85 44.75 4.00
379 431 0.678950 CTAGGCTCCAAGCTCTAGGC 59.321 60.000 12.73 8.02 41.99 3.93
380 432 2.080654 ACTAGGCTCCAAGCTCTAGG 57.919 55.000 19.48 2.31 41.86 3.02
381 433 3.827722 ACTACTAGGCTCCAAGCTCTAG 58.172 50.000 16.33 16.33 42.55 2.43
382 434 3.955524 ACTACTAGGCTCCAAGCTCTA 57.044 47.619 0.00 0.00 41.99 2.43
383 435 2.838637 ACTACTAGGCTCCAAGCTCT 57.161 50.000 0.00 0.00 41.99 4.09
384 436 3.897141 AAACTACTAGGCTCCAAGCTC 57.103 47.619 0.00 0.00 41.99 4.09
385 437 4.081031 GGTAAAACTACTAGGCTCCAAGCT 60.081 45.833 0.00 0.00 41.99 3.74
386 438 4.190001 GGTAAAACTACTAGGCTCCAAGC 58.810 47.826 0.00 0.00 41.46 4.01
387 439 5.416271 TGGTAAAACTACTAGGCTCCAAG 57.584 43.478 0.00 0.00 0.00 3.61
388 440 5.104652 GGATGGTAAAACTACTAGGCTCCAA 60.105 44.000 0.00 0.00 0.00 3.53
389 441 4.407945 GGATGGTAAAACTACTAGGCTCCA 59.592 45.833 0.00 0.00 0.00 3.86
390 442 4.407945 TGGATGGTAAAACTACTAGGCTCC 59.592 45.833 0.00 0.00 0.00 4.70
391 443 5.128991 AGTGGATGGTAAAACTACTAGGCTC 59.871 44.000 0.00 0.00 0.00 4.70
392 444 5.030820 AGTGGATGGTAAAACTACTAGGCT 58.969 41.667 0.00 0.00 0.00 4.58
393 445 5.128991 AGAGTGGATGGTAAAACTACTAGGC 59.871 44.000 0.00 0.00 0.00 3.93
394 446 6.793505 AGAGTGGATGGTAAAACTACTAGG 57.206 41.667 0.00 0.00 0.00 3.02
395 447 7.285858 AGCTAGAGTGGATGGTAAAACTACTAG 59.714 40.741 0.00 0.00 0.00 2.57
396 448 7.124052 AGCTAGAGTGGATGGTAAAACTACTA 58.876 38.462 0.00 0.00 0.00 1.82
397 449 5.958987 AGCTAGAGTGGATGGTAAAACTACT 59.041 40.000 0.00 0.00 0.00 2.57
398 450 6.223351 AGCTAGAGTGGATGGTAAAACTAC 57.777 41.667 0.00 0.00 0.00 2.73
399 451 7.618512 ACTTAGCTAGAGTGGATGGTAAAACTA 59.381 37.037 0.00 0.00 0.00 2.24
400 452 6.440965 ACTTAGCTAGAGTGGATGGTAAAACT 59.559 38.462 0.00 0.00 0.00 2.66
401 453 6.641474 ACTTAGCTAGAGTGGATGGTAAAAC 58.359 40.000 0.00 0.00 0.00 2.43
402 454 6.869206 ACTTAGCTAGAGTGGATGGTAAAA 57.131 37.500 0.00 0.00 0.00 1.52
403 455 6.439375 TCAACTTAGCTAGAGTGGATGGTAAA 59.561 38.462 8.67 0.00 0.00 2.01
404 456 5.955959 TCAACTTAGCTAGAGTGGATGGTAA 59.044 40.000 8.67 0.00 0.00 2.85
412 464 6.260870 TCTGAAGTCAACTTAGCTAGAGTG 57.739 41.667 8.67 2.38 36.11 3.51
422 474 5.705441 TGTGTTGAACTTCTGAAGTCAACTT 59.295 36.000 34.07 20.73 42.85 2.66
443 495 5.253330 AGTATTGGGTTTCACCATACTGTG 58.747 41.667 5.52 0.00 41.02 3.66
444 496 5.250774 AGAGTATTGGGTTTCACCATACTGT 59.749 40.000 9.55 4.69 41.02 3.55
445 497 5.745227 AGAGTATTGGGTTTCACCATACTG 58.255 41.667 9.55 0.00 41.02 2.74
450 502 7.567250 TCTGATATAGAGTATTGGGTTTCACCA 59.433 37.037 0.00 0.00 41.02 4.17
452 504 9.646427 GATCTGATATAGAGTATTGGGTTTCAC 57.354 37.037 0.00 0.00 39.20 3.18
464 516 5.278709 CCACAAGTGCGATCTGATATAGAGT 60.279 44.000 0.00 0.00 39.20 3.24
465 517 5.159925 CCACAAGTGCGATCTGATATAGAG 58.840 45.833 0.00 0.00 39.20 2.43
466 518 4.559502 GCCACAAGTGCGATCTGATATAGA 60.560 45.833 0.00 0.00 40.37 1.98
467 519 3.677121 GCCACAAGTGCGATCTGATATAG 59.323 47.826 0.00 0.00 0.00 1.31
468 520 3.069443 TGCCACAAGTGCGATCTGATATA 59.931 43.478 0.00 0.00 0.00 0.86
475 527 0.179181 CACATGCCACAAGTGCGATC 60.179 55.000 0.00 0.00 0.00 3.69
493 545 1.074072 ACCCATAGCGTTTGCCACA 59.926 52.632 0.00 0.00 44.31 4.17
497 549 1.993369 GAGCCACCCATAGCGTTTGC 61.993 60.000 0.00 0.00 43.24 3.68
500 552 0.328258 AAAGAGCCACCCATAGCGTT 59.672 50.000 0.00 0.00 0.00 4.84
509 561 0.322546 CCTACCACCAAAGAGCCACC 60.323 60.000 0.00 0.00 0.00 4.61
510 562 0.690762 TCCTACCACCAAAGAGCCAC 59.309 55.000 0.00 0.00 0.00 5.01
516 568 4.189231 CCGTTAAGATCCTACCACCAAAG 58.811 47.826 0.00 0.00 0.00 2.77
521 573 3.320256 CCCTACCGTTAAGATCCTACCAC 59.680 52.174 0.00 0.00 0.00 4.16
522 574 3.052642 ACCCTACCGTTAAGATCCTACCA 60.053 47.826 0.00 0.00 0.00 3.25
528 580 7.254218 CGTGAAAAATACCCTACCGTTAAGATC 60.254 40.741 0.00 0.00 0.00 2.75
529 581 6.536224 CGTGAAAAATACCCTACCGTTAAGAT 59.464 38.462 0.00 0.00 0.00 2.40
531 583 5.639082 ACGTGAAAAATACCCTACCGTTAAG 59.361 40.000 0.00 0.00 0.00 1.85
532 584 5.546526 ACGTGAAAAATACCCTACCGTTAA 58.453 37.500 0.00 0.00 0.00 2.01
533 585 5.146010 ACGTGAAAAATACCCTACCGTTA 57.854 39.130 0.00 0.00 0.00 3.18
535 587 3.006752 TGACGTGAAAAATACCCTACCGT 59.993 43.478 0.00 0.00 0.00 4.83
536 588 3.587923 TGACGTGAAAAATACCCTACCG 58.412 45.455 0.00 0.00 0.00 4.02
538 590 5.376537 CGTTTGACGTGAAAAATACCCTAC 58.623 41.667 0.56 0.00 36.74 3.18
601 675 0.319297 GGGTATAACTGCCTACCGCG 60.319 60.000 0.00 0.00 42.08 6.46
641 715 1.835531 TGGATCCGACCCTTTTCCTAC 59.164 52.381 7.39 0.00 0.00 3.18
668 745 6.022958 AGCCAAATTTAACCCTGGTCTAAAT 58.977 36.000 0.00 0.00 0.00 1.40
671 748 4.668138 AGCCAAATTTAACCCTGGTCTA 57.332 40.909 0.00 0.00 0.00 2.59
688 765 3.131400 ACCTTTTTGCGAAACTTAAGCCA 59.869 39.130 1.29 0.00 0.00 4.75
730 807 0.751452 TGTGCCTTGCTGCATTCAAA 59.249 45.000 1.84 0.00 44.30 2.69
909 991 2.795556 AGAGGAGATAGGGAGAGTGGA 58.204 52.381 0.00 0.00 0.00 4.02
910 992 3.655777 AGTAGAGGAGATAGGGAGAGTGG 59.344 52.174 0.00 0.00 0.00 4.00
911 993 4.597507 AGAGTAGAGGAGATAGGGAGAGTG 59.402 50.000 0.00 0.00 0.00 3.51
912 994 4.839589 AGAGTAGAGGAGATAGGGAGAGT 58.160 47.826 0.00 0.00 0.00 3.24
1050 1155 2.369860 TGTGGCTATGCTAGGAGGAATG 59.630 50.000 0.00 0.00 0.00 2.67
1302 1410 3.037431 TCTTCTGAGACTTGAAGCTGC 57.963 47.619 11.87 0.00 39.41 5.25
1338 1446 2.036089 GGATTGGGTGGCGTTGTTTAAA 59.964 45.455 0.00 0.00 0.00 1.52
1389 1500 3.222603 GGAGATGTTGGTGTTGGTTCTT 58.777 45.455 0.00 0.00 0.00 2.52
2389 2569 3.552890 CCAGCTGCTGGTTTTCTTTTACC 60.553 47.826 35.03 0.00 45.82 2.85
3592 3818 9.241919 TCAAATGAACTATAAGATGCAGGAAAA 57.758 29.630 0.00 0.00 0.00 2.29
4309 5038 6.990939 TCAGATCTTTCTTTATGATGGAGCAG 59.009 38.462 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.