Multiple sequence alignment - TraesCS5D01G350100

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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 TraesCS5D01G350100 chr5D 100.000 2453 0 0 1 2453 434567973 434565521 0.000000e+00 4530.0
1 TraesCS5D01G350100 chr5D 87.773 1832 158 29 646 2453 434688358 434690147 0.000000e+00 2082.0
2 TraesCS5D01G350100 chr5D 85.095 946 116 11 637 1572 434600567 434599637 0.000000e+00 942.0
3 TraesCS5D01G350100 chr5D 83.567 712 68 25 713 1399 434548939 434548252 2.680000e-174 621.0
4 TraesCS5D01G350100 chr5D 84.643 560 62 17 741 1292 434666557 434667100 9.980000e-149 536.0
5 TraesCS5D01G350100 chr5D 87.353 340 40 3 1013 1351 434675699 434676036 1.060000e-103 387.0
6 TraesCS5D01G350100 chr5D 93.023 172 11 1 10 181 434680831 434681001 1.460000e-62 250.0
7 TraesCS5D01G350100 chr5D 80.364 275 36 13 1839 2110 434599619 434599360 2.490000e-45 193.0
8 TraesCS5D01G350100 chr5D 87.059 85 9 2 2364 2446 332920328 332920412 7.220000e-16 95.3
9 TraesCS5D01G350100 chr5B 93.089 1939 87 9 523 2453 527601779 527599880 0.000000e+00 2795.0
10 TraesCS5D01G350100 chr5B 90.142 1552 125 17 631 2172 527769666 527768133 0.000000e+00 1993.0
11 TraesCS5D01G350100 chr5B 84.382 890 101 16 738 1603 527492249 527491374 0.000000e+00 839.0
12 TraesCS5D01G350100 chr5B 98.160 326 6 0 10 335 527604247 527603922 9.840000e-159 569.0
13 TraesCS5D01G350100 chr5B 85.202 223 23 5 542 762 527604061 527603847 1.140000e-53 220.0
14 TraesCS5D01G350100 chr5B 79.079 239 50 0 1148 1386 528566857 528566619 5.430000e-37 165.0
15 TraesCS5D01G350100 chr5B 91.549 71 3 2 450 517 527603888 527603818 7.220000e-16 95.3
16 TraesCS5D01G350100 chr5A 88.841 923 90 7 726 1641 548658120 548657204 0.000000e+00 1122.0
17 TraesCS5D01G350100 chr5A 80.181 994 127 41 639 1604 548503565 548504516 0.000000e+00 680.0
18 TraesCS5D01G350100 chr5A 91.954 174 12 2 8 181 548664208 548664037 2.440000e-60 243.0
19 TraesCS5D01G350100 chr5A 93.590 156 10 0 535 690 548658268 548658113 1.470000e-57 233.0
20 TraesCS5D01G350100 chr5A 94.079 152 9 0 184 335 548658508 548658357 5.280000e-57 231.0
21 TraesCS5D01G350100 chr5A 97.391 115 3 0 335 449 577784068 577784182 1.920000e-46 196.0
22 TraesCS5D01G350100 chr5A 97.368 114 3 0 336 449 387438630 387438517 6.920000e-46 195.0
23 TraesCS5D01G350100 chr5A 91.837 49 4 0 450 498 548658318 548658270 4.380000e-08 69.4
24 TraesCS5D01G350100 chr7A 98.246 114 2 0 336 449 466311266 466311153 1.490000e-47 200.0
25 TraesCS5D01G350100 chr6D 98.246 114 2 0 336 449 142326668 142326781 1.490000e-47 200.0
26 TraesCS5D01G350100 chr6D 98.246 114 2 0 336 449 345490425 345490312 1.490000e-47 200.0
27 TraesCS5D01G350100 chr3D 98.246 114 2 0 336 449 359257718 359257831 1.490000e-47 200.0
28 TraesCS5D01G350100 chr1D 98.230 113 2 0 337 449 270900882 270900994 5.350000e-47 198.0
29 TraesCS5D01G350100 chr1D 78.049 123 11 12 1640 1759 462155556 462155665 2.040000e-06 63.9
30 TraesCS5D01G350100 chr2B 97.391 115 3 0 335 449 396725536 396725422 1.920000e-46 196.0
31 TraesCS5D01G350100 chr2B 85.714 70 10 0 94 163 515262220 515262289 9.410000e-10 75.0
32 TraesCS5D01G350100 chr2B 100.000 29 0 0 498 526 201368859 201368831 1.000000e-03 54.7
33 TraesCS5D01G350100 chr3B 92.424 132 6 3 336 465 223213687 223213558 4.170000e-43 185.0
34 TraesCS5D01G350100 chr4D 76.453 344 67 10 2108 2446 485381782 485382116 9.020000e-40 174.0
35 TraesCS5D01G350100 chr4D 96.970 33 1 0 494 526 507687430 507687398 3.410000e-04 56.5
36 TraesCS5D01G350100 chr7B 82.443 131 16 7 2311 2438 610269171 610269297 9.280000e-20 108.0
37 TraesCS5D01G350100 chr7B 89.286 56 6 0 1700 1755 739478864 739478809 1.220000e-08 71.3
38 TraesCS5D01G350100 chr7B 97.059 34 1 0 1640 1673 568424892 568424859 9.470000e-05 58.4
39 TraesCS5D01G350100 chr1B 83.721 86 10 4 2363 2446 454359133 454359050 7.270000e-11 78.7
40 TraesCS5D01G350100 chr1B 95.122 41 2 0 94 134 51361203 51361163 5.660000e-07 65.8
41 TraesCS5D01G350100 chr3A 82.278 79 14 0 94 172 212735961 212735883 4.380000e-08 69.4
42 TraesCS5D01G350100 chr3A 81.013 79 15 0 94 172 287372422 287372344 2.040000e-06 63.9
43 TraesCS5D01G350100 chr6B 100.000 32 0 0 495 526 137378941 137378910 2.630000e-05 60.2
44 TraesCS5D01G350100 chr6B 90.698 43 1 3 486 525 462642961 462642919 1.000000e-03 54.7
45 TraesCS5D01G350100 chr6B 100.000 29 0 0 498 526 577456838 577456810 1.000000e-03 54.7
46 TraesCS5D01G350100 chr4A 100.000 31 0 0 1640 1670 624921908 624921938 9.470000e-05 58.4
47 TraesCS5D01G350100 chr7D 94.595 37 1 1 490 525 156200246 156200210 3.410000e-04 56.5
48 TraesCS5D01G350100 chr7D 97.059 34 0 1 493 526 570645315 570645283 3.410000e-04 56.5
49 TraesCS5D01G350100 chr7D 100.000 29 0 0 498 526 629902187 629902215 1.000000e-03 54.7


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 TraesCS5D01G350100 chr5D 434565521 434567973 2452 True 4530.000 4530 100.00000 1 2453 1 chr5D.!!$R2 2452
1 TraesCS5D01G350100 chr5D 434688358 434690147 1789 False 2082.000 2082 87.77300 646 2453 1 chr5D.!!$F5 1807
2 TraesCS5D01G350100 chr5D 434548252 434548939 687 True 621.000 621 83.56700 713 1399 1 chr5D.!!$R1 686
3 TraesCS5D01G350100 chr5D 434599360 434600567 1207 True 567.500 942 82.72950 637 2110 2 chr5D.!!$R3 1473
4 TraesCS5D01G350100 chr5D 434666557 434667100 543 False 536.000 536 84.64300 741 1292 1 chr5D.!!$F2 551
5 TraesCS5D01G350100 chr5B 527768133 527769666 1533 True 1993.000 1993 90.14200 631 2172 1 chr5B.!!$R2 1541
6 TraesCS5D01G350100 chr5B 527599880 527604247 4367 True 919.825 2795 92.00000 10 2453 4 chr5B.!!$R4 2443
7 TraesCS5D01G350100 chr5B 527491374 527492249 875 True 839.000 839 84.38200 738 1603 1 chr5B.!!$R1 865
8 TraesCS5D01G350100 chr5A 548503565 548504516 951 False 680.000 680 80.18100 639 1604 1 chr5A.!!$F1 965
9 TraesCS5D01G350100 chr5A 548657204 548658508 1304 True 413.850 1122 92.08675 184 1641 4 chr5A.!!$R3 1457

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
423 424 0.110295 CCCACATGTCAGTGACCCAA 59.89 55.0 20.43 2.34 42.05 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 4323 0.107361 CATCGACACCCCTAAACCCC 60.107 60.0 0.0 0.0 0.0 4.95 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
54 55 6.910536 ATACTCTCTCTTTGCCAAATTACG 57.089 37.500 0.00 0.00 0.00 3.18
83 84 8.647226 GCATATAAAATTTGGTCACAGTCAAAC 58.353 33.333 0.00 0.00 35.97 2.93
91 92 6.576662 TTGGTCACAGTCAAACTTTGTAAA 57.423 33.333 1.44 0.00 28.64 2.01
335 336 2.520039 CGAGTATGGCAGCACGCTG 61.520 63.158 14.73 14.73 46.15 5.18
336 337 2.124983 AGTATGGCAGCACGCTGG 60.125 61.111 20.00 2.98 43.77 4.85
337 338 2.125147 GTATGGCAGCACGCTGGA 60.125 61.111 20.00 0.00 43.77 3.86
338 339 2.125147 TATGGCAGCACGCTGGAC 60.125 61.111 20.00 4.76 43.77 4.02
344 345 4.074526 AGCACGCTGGACGATGCT 62.075 61.111 8.58 8.58 46.78 3.79
357 358 0.652592 CGATGCTTCGGTGCCTTAAG 59.347 55.000 13.82 0.00 41.74 1.85
358 359 1.017387 GATGCTTCGGTGCCTTAAGG 58.983 55.000 17.81 17.81 38.53 2.69
375 376 1.435256 AGGCACCTACCTTTGTGTCT 58.565 50.000 0.00 0.00 42.30 3.41
376 377 2.616524 AGGCACCTACCTTTGTGTCTA 58.383 47.619 0.00 0.00 45.05 2.59
377 378 3.182152 AGGCACCTACCTTTGTGTCTAT 58.818 45.455 0.00 0.00 45.05 1.98
378 379 3.055094 AGGCACCTACCTTTGTGTCTATG 60.055 47.826 0.00 0.00 45.05 2.23
379 380 3.055385 GGCACCTACCTTTGTGTCTATGA 60.055 47.826 0.00 0.00 34.34 2.15
380 381 3.933332 GCACCTACCTTTGTGTCTATGAC 59.067 47.826 0.00 0.00 34.94 3.06
381 382 4.562757 GCACCTACCTTTGTGTCTATGACA 60.563 45.833 0.00 0.00 40.50 3.58
382 383 5.734720 CACCTACCTTTGTGTCTATGACAT 58.265 41.667 3.65 0.00 44.63 3.06
383 384 5.582269 CACCTACCTTTGTGTCTATGACATG 59.418 44.000 3.65 0.00 44.63 3.21
384 385 5.248477 ACCTACCTTTGTGTCTATGACATGT 59.752 40.000 0.00 0.00 44.63 3.21
385 386 5.582269 CCTACCTTTGTGTCTATGACATGTG 59.418 44.000 1.15 0.00 44.63 3.21
386 387 4.326826 ACCTTTGTGTCTATGACATGTGG 58.673 43.478 1.15 0.00 44.63 4.17
387 388 3.691118 CCTTTGTGTCTATGACATGTGGG 59.309 47.826 1.15 2.15 44.63 4.61
388 389 2.401583 TGTGTCTATGACATGTGGGC 57.598 50.000 1.15 0.00 44.63 5.36
389 390 1.065491 TGTGTCTATGACATGTGGGCC 60.065 52.381 1.15 0.00 44.63 5.80
390 391 0.546122 TGTCTATGACATGTGGGCCC 59.454 55.000 17.59 17.59 37.67 5.80
391 392 0.546122 GTCTATGACATGTGGGCCCA 59.454 55.000 24.45 24.45 32.09 5.36
392 393 1.064758 GTCTATGACATGTGGGCCCAA 60.065 52.381 30.64 17.87 32.09 4.12
393 394 1.064758 TCTATGACATGTGGGCCCAAC 60.065 52.381 30.64 21.29 0.00 3.77
394 395 0.701147 TATGACATGTGGGCCCAACA 59.299 50.000 30.64 26.33 0.00 3.33
395 396 0.612732 ATGACATGTGGGCCCAACAG 60.613 55.000 30.64 21.28 0.00 3.16
396 397 1.074775 GACATGTGGGCCCAACAGA 59.925 57.895 30.64 11.67 0.00 3.41
397 398 0.323725 GACATGTGGGCCCAACAGAT 60.324 55.000 30.64 17.86 0.00 2.90
398 399 0.612732 ACATGTGGGCCCAACAGATG 60.613 55.000 30.64 25.94 43.08 2.90
406 407 2.757099 CCAACAGATGGCTGGCCC 60.757 66.667 9.28 0.00 46.60 5.80
414 415 3.578286 TGGCTGGCCCACATGTCA 61.578 61.111 9.28 0.00 39.18 3.58
415 416 2.753043 GGCTGGCCCACATGTCAG 60.753 66.667 0.00 7.70 0.00 3.51
416 417 2.034687 GCTGGCCCACATGTCAGT 59.965 61.111 12.37 0.00 0.00 3.41
417 418 2.338015 GCTGGCCCACATGTCAGTG 61.338 63.158 12.37 0.00 39.21 3.66
418 419 1.376086 CTGGCCCACATGTCAGTGA 59.624 57.895 0.00 0.00 42.05 3.41
419 420 0.957395 CTGGCCCACATGTCAGTGAC 60.957 60.000 16.68 16.68 42.05 3.67
420 421 1.675641 GGCCCACATGTCAGTGACC 60.676 63.158 20.43 2.99 42.05 4.02
421 422 1.675641 GCCCACATGTCAGTGACCC 60.676 63.158 20.43 0.00 42.05 4.46
422 423 1.760527 CCCACATGTCAGTGACCCA 59.239 57.895 20.43 3.20 42.05 4.51
423 424 0.110295 CCCACATGTCAGTGACCCAA 59.890 55.000 20.43 2.34 42.05 4.12
424 425 1.478471 CCCACATGTCAGTGACCCAAA 60.478 52.381 20.43 1.95 42.05 3.28
425 426 1.881973 CCACATGTCAGTGACCCAAAG 59.118 52.381 20.43 8.14 42.05 2.77
426 427 1.881973 CACATGTCAGTGACCCAAAGG 59.118 52.381 20.43 6.15 42.05 3.11
427 428 0.883833 CATGTCAGTGACCCAAAGGC 59.116 55.000 20.43 0.00 36.11 4.35
428 429 0.478072 ATGTCAGTGACCCAAAGGCA 59.522 50.000 20.43 0.00 36.11 4.75
429 430 0.179020 TGTCAGTGACCCAAAGGCAG 60.179 55.000 20.43 0.00 36.11 4.85
430 431 0.890996 GTCAGTGACCCAAAGGCAGG 60.891 60.000 12.54 0.00 36.11 4.85
431 432 1.151450 CAGTGACCCAAAGGCAGGT 59.849 57.895 0.00 0.00 39.75 4.00
432 433 1.151450 AGTGACCCAAAGGCAGGTG 59.849 57.895 0.00 0.00 36.17 4.00
433 434 2.203480 TGACCCAAAGGCAGGTGC 60.203 61.111 0.00 0.00 36.17 5.01
491 492 3.538634 AACCGATAGCCCTAGACAAAC 57.461 47.619 0.00 0.00 0.00 2.93
492 493 2.748388 ACCGATAGCCCTAGACAAACT 58.252 47.619 0.00 0.00 0.00 2.66
517 521 7.698163 AAATCTACTCCCTCTGTTCCATAAT 57.302 36.000 0.00 0.00 0.00 1.28
518 522 6.678568 ATCTACTCCCTCTGTTCCATAATG 57.321 41.667 0.00 0.00 0.00 1.90
519 523 5.529289 TCTACTCCCTCTGTTCCATAATGT 58.471 41.667 0.00 0.00 0.00 2.71
520 524 6.679542 TCTACTCCCTCTGTTCCATAATGTA 58.320 40.000 0.00 0.00 0.00 2.29
521 525 7.130099 TCTACTCCCTCTGTTCCATAATGTAA 58.870 38.462 0.00 0.00 0.00 2.41
561 2598 6.923012 TCACATTTCATTTGGTAAGACATGG 58.077 36.000 0.00 0.00 0.00 3.66
648 2685 6.543831 GGTCTCCATGTGCTTCTTATATTTGT 59.456 38.462 0.00 0.00 0.00 2.83
682 2719 0.250038 AGTATGGCAGCACGCTATGG 60.250 55.000 7.17 0.00 42.62 2.74
780 2824 9.073368 CAGACAAATCAAATCAAGATCACATTC 57.927 33.333 0.00 0.00 0.00 2.67
786 2838 8.674263 ATCAAATCAAGATCACATTCTACTCC 57.326 34.615 0.00 0.00 0.00 3.85
943 3009 3.126514 GCACCACATCAGTTCATTCAGAG 59.873 47.826 0.00 0.00 0.00 3.35
955 3028 1.129998 CATTCAGAGACCAAAGCAGCG 59.870 52.381 0.00 0.00 0.00 5.18
1140 3230 3.343421 GCAACTTCGCCGTCGGTT 61.343 61.111 13.94 0.00 36.13 4.44
1239 3332 3.306595 CTTCTGCGAGCTCCTGGCA 62.307 63.158 8.47 11.28 42.48 4.92
1248 3341 1.304381 GCTCCTGGCAATGTCCCAA 60.304 57.895 0.00 0.00 41.35 4.12
1273 3366 3.790416 TTCGGCTTTGCAGGTGGCT 62.790 57.895 7.41 0.00 45.15 4.75
1432 3536 1.297364 GTGGGCGTAGGGCTTAACA 59.703 57.895 8.99 0.00 42.94 2.41
1454 3563 2.814336 AGCAAGCAGTAGTTTGTTAGCC 59.186 45.455 0.00 0.00 38.13 3.93
1464 3573 6.706270 CAGTAGTTTGTTAGCCTCTGAAGAAA 59.294 38.462 0.00 0.00 0.00 2.52
1511 3620 6.190587 AGATTTAGCCCTGCTCTGTTAATTT 58.809 36.000 0.00 0.00 40.44 1.82
1540 3653 9.208022 TGATATGAATATACTGTAGCAAGTTGC 57.792 33.333 20.44 20.44 45.46 4.17
1577 3690 7.012421 AGGAAATTTATGAAGATTACCTCGCAC 59.988 37.037 0.00 0.00 0.00 5.34
1629 3750 8.584063 TCCAATAAAGAAAACCTTGGGTATAC 57.416 34.615 0.00 0.00 37.53 1.47
1687 3809 2.598394 GCTTTGAGCAGGGTGCCA 60.598 61.111 0.00 0.00 46.52 4.92
1693 3815 0.698238 TGAGCAGGGTGCCACTAAAT 59.302 50.000 0.00 0.00 46.52 1.40
1705 3827 5.770162 GGTGCCACTAAATGAAAGGCTATAT 59.230 40.000 0.00 0.00 45.42 0.86
1710 3832 8.579863 GCCACTAAATGAAAGGCTATATGATTT 58.420 33.333 0.00 0.00 42.01 2.17
1744 3866 5.008613 TGTGCGAAAAAGTTCTGAAATAGCT 59.991 36.000 0.00 0.00 0.00 3.32
1791 3913 2.513897 GGAGCGCCGCTATTTGGT 60.514 61.111 13.54 0.00 39.88 3.67
1792 3914 2.112815 GGAGCGCCGCTATTTGGTT 61.113 57.895 13.54 0.00 39.88 3.67
1825 3947 8.076178 GCTATTTAAAACAATGATAGTGGCGAT 58.924 33.333 0.00 0.00 0.00 4.58
1903 4025 8.531146 TGTGTATCATTTCTTCTGTCTGATGTA 58.469 33.333 0.00 0.00 0.00 2.29
2015 4137 9.297037 ACAAGCTACACTAGTTATTGGAAAAAT 57.703 29.630 0.00 0.00 0.00 1.82
2196 4323 1.772182 AGTCAGAGTCGTTTTGCTCG 58.228 50.000 0.00 0.00 36.88 5.03
2227 4354 1.763968 TGTCGATGACACCTCTAGGG 58.236 55.000 0.20 0.00 37.67 3.53
2241 4368 5.063017 CCTCTAGGGTAGGAGTGATAACA 57.937 47.826 0.00 0.00 36.08 2.41
2391 4519 4.978083 TCGCTCGGTTTCTTCTAAGTAT 57.022 40.909 0.00 0.00 0.00 2.12
2395 4523 4.608951 CTCGGTTTCTTCTAAGTATCCGG 58.391 47.826 14.79 0.00 35.74 5.14
2438 4566 5.991861 TGAATGCAATAATCCTGCCATTTT 58.008 33.333 0.00 0.00 39.13 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.584839 GTACTTGTTTGGTGTACTAATTAAACG 57.415 33.333 0.00 0.00 35.16 3.60
1 2 9.584839 CGTACTTGTTTGGTGTACTAATTAAAC 57.415 33.333 0.00 0.00 35.67 2.01
2 3 9.323985 ACGTACTTGTTTGGTGTACTAATTAAA 57.676 29.630 0.00 0.00 35.67 1.52
3 4 8.885494 ACGTACTTGTTTGGTGTACTAATTAA 57.115 30.769 0.00 0.00 35.67 1.40
54 55 6.630071 ACTGTGACCAAATTTTATATGCACC 58.370 36.000 0.00 0.00 0.00 5.01
156 157 6.157820 TGACACCTGGTTCATCAAGGAATATA 59.842 38.462 0.00 0.00 0.00 0.86
339 340 1.017387 CCTTAAGGCACCGAAGCATC 58.983 55.000 9.00 0.00 35.83 3.91
357 358 3.055385 TCATAGACACAAAGGTAGGTGCC 60.055 47.826 0.00 0.00 38.57 5.01
358 359 3.933332 GTCATAGACACAAAGGTAGGTGC 59.067 47.826 0.00 0.00 38.57 5.01
361 362 5.582269 CACATGTCATAGACACAAAGGTAGG 59.418 44.000 0.00 0.00 45.65 3.18
364 365 4.326826 CCACATGTCATAGACACAAAGGT 58.673 43.478 0.00 0.00 45.65 3.50
365 366 3.691118 CCCACATGTCATAGACACAAAGG 59.309 47.826 0.00 3.02 45.65 3.11
366 367 3.127548 GCCCACATGTCATAGACACAAAG 59.872 47.826 0.00 0.00 45.65 2.77
367 368 3.081061 GCCCACATGTCATAGACACAAA 58.919 45.455 0.00 0.00 45.65 2.83
368 369 2.617788 GGCCCACATGTCATAGACACAA 60.618 50.000 0.00 0.00 45.65 3.33
369 370 1.065491 GGCCCACATGTCATAGACACA 60.065 52.381 0.00 0.00 45.65 3.72
370 371 1.668419 GGCCCACATGTCATAGACAC 58.332 55.000 0.00 0.00 45.65 3.67
371 372 0.546122 GGGCCCACATGTCATAGACA 59.454 55.000 19.95 1.95 46.90 3.41
372 373 0.546122 TGGGCCCACATGTCATAGAC 59.454 55.000 24.45 0.00 0.00 2.59
373 374 1.064758 GTTGGGCCCACATGTCATAGA 60.065 52.381 28.70 1.58 0.00 1.98
374 375 1.340893 TGTTGGGCCCACATGTCATAG 60.341 52.381 28.70 0.00 0.00 2.23
375 376 0.701147 TGTTGGGCCCACATGTCATA 59.299 50.000 28.70 3.51 0.00 2.15
376 377 0.612732 CTGTTGGGCCCACATGTCAT 60.613 55.000 28.70 0.00 0.00 3.06
377 378 1.228521 CTGTTGGGCCCACATGTCA 60.229 57.895 28.70 17.15 0.00 3.58
378 379 0.323725 ATCTGTTGGGCCCACATGTC 60.324 55.000 28.70 13.28 0.00 3.06
379 380 0.612732 CATCTGTTGGGCCCACATGT 60.613 55.000 28.70 13.82 0.00 3.21
380 381 1.324740 CCATCTGTTGGGCCCACATG 61.325 60.000 28.70 22.50 42.33 3.21
381 382 1.000739 CCATCTGTTGGGCCCACAT 59.999 57.895 28.70 11.68 42.33 3.21
382 383 2.440147 CCATCTGTTGGGCCCACA 59.560 61.111 28.70 23.95 42.33 4.17
383 384 3.070576 GCCATCTGTTGGGCCCAC 61.071 66.667 28.70 20.43 46.55 4.61
388 389 2.757099 GGCCAGCCATCTGTTGGG 60.757 66.667 3.12 0.00 46.55 4.12
390 391 2.036098 TGGGCCAGCCATCTGTTG 59.964 61.111 11.50 0.00 38.66 3.33
391 392 2.036256 GTGGGCCAGCCATCTGTT 59.964 61.111 6.40 0.00 38.66 3.16
392 393 2.619446 ATGTGGGCCAGCCATCTGT 61.619 57.895 6.40 0.00 38.66 3.41
393 394 2.125326 CATGTGGGCCAGCCATCTG 61.125 63.158 6.40 0.00 40.02 2.90
394 395 2.277737 CATGTGGGCCAGCCATCT 59.722 61.111 6.40 0.00 37.98 2.90
395 396 2.043652 ACATGTGGGCCAGCCATC 60.044 61.111 6.40 0.00 37.98 3.51
396 397 2.043652 GACATGTGGGCCAGCCAT 60.044 61.111 6.40 4.86 37.98 4.40
397 398 3.572447 CTGACATGTGGGCCAGCCA 62.572 63.158 6.40 1.84 37.98 4.75
398 399 2.753043 CTGACATGTGGGCCAGCC 60.753 66.667 6.40 0.00 0.00 4.85
399 400 2.034687 ACTGACATGTGGGCCAGC 59.965 61.111 6.40 2.28 0.00 4.85
400 401 0.957395 GTCACTGACATGTGGGCCAG 60.957 60.000 6.40 6.93 38.40 4.85
401 402 1.073025 GTCACTGACATGTGGGCCA 59.927 57.895 1.15 0.00 38.40 5.36
402 403 1.675641 GGTCACTGACATGTGGGCC 60.676 63.158 1.15 0.00 38.40 5.80
403 404 1.675641 GGGTCACTGACATGTGGGC 60.676 63.158 1.15 0.00 38.40 5.36
404 405 0.110295 TTGGGTCACTGACATGTGGG 59.890 55.000 1.15 0.00 38.40 4.61
405 406 1.881973 CTTTGGGTCACTGACATGTGG 59.118 52.381 1.15 0.00 38.40 4.17
406 407 1.881973 CCTTTGGGTCACTGACATGTG 59.118 52.381 1.15 0.00 39.15 3.21
407 408 1.819305 GCCTTTGGGTCACTGACATGT 60.819 52.381 11.34 0.00 33.68 3.21
408 409 0.883833 GCCTTTGGGTCACTGACATG 59.116 55.000 11.34 0.00 33.68 3.21
409 410 0.478072 TGCCTTTGGGTCACTGACAT 59.522 50.000 11.34 0.00 33.68 3.06
410 411 0.179020 CTGCCTTTGGGTCACTGACA 60.179 55.000 11.34 0.00 33.68 3.58
411 412 0.890996 CCTGCCTTTGGGTCACTGAC 60.891 60.000 0.00 0.00 34.45 3.51
412 413 1.352622 ACCTGCCTTTGGGTCACTGA 61.353 55.000 0.00 0.00 34.45 3.41
413 414 1.151450 ACCTGCCTTTGGGTCACTG 59.849 57.895 0.00 0.00 34.45 3.66
414 415 1.151450 CACCTGCCTTTGGGTCACT 59.849 57.895 0.00 0.00 32.95 3.41
415 416 2.564721 GCACCTGCCTTTGGGTCAC 61.565 63.158 0.00 0.00 32.95 3.67
416 417 2.203480 GCACCTGCCTTTGGGTCA 60.203 61.111 0.00 0.00 32.95 4.02
426 427 0.888619 GGTTCCTTAAAGGCACCTGC 59.111 55.000 0.00 0.00 46.46 4.85
429 430 1.900245 TTCGGTTCCTTAAAGGCACC 58.100 50.000 0.00 0.00 46.50 5.01
430 431 4.259356 ACTATTCGGTTCCTTAAAGGCAC 58.741 43.478 0.00 0.00 34.61 5.01
431 432 4.563140 ACTATTCGGTTCCTTAAAGGCA 57.437 40.909 0.00 0.00 34.61 4.75
432 433 6.512903 GCATAACTATTCGGTTCCTTAAAGGC 60.513 42.308 0.00 0.00 34.61 4.35
433 434 6.017357 GGCATAACTATTCGGTTCCTTAAAGG 60.017 42.308 0.00 0.00 36.46 3.11
434 435 6.017357 GGGCATAACTATTCGGTTCCTTAAAG 60.017 42.308 0.00 0.00 0.00 1.85
435 436 5.824097 GGGCATAACTATTCGGTTCCTTAAA 59.176 40.000 0.00 0.00 0.00 1.52
436 437 5.104444 TGGGCATAACTATTCGGTTCCTTAA 60.104 40.000 0.00 0.00 0.00 1.85
437 438 4.409574 TGGGCATAACTATTCGGTTCCTTA 59.590 41.667 0.00 0.00 0.00 2.69
438 439 3.201266 TGGGCATAACTATTCGGTTCCTT 59.799 43.478 0.00 0.00 0.00 3.36
439 440 2.775384 TGGGCATAACTATTCGGTTCCT 59.225 45.455 0.00 0.00 0.00 3.36
440 441 3.202829 TGGGCATAACTATTCGGTTCC 57.797 47.619 0.00 0.00 0.00 3.62
441 442 3.942748 TGTTGGGCATAACTATTCGGTTC 59.057 43.478 5.64 0.00 0.00 3.62
442 443 3.958018 TGTTGGGCATAACTATTCGGTT 58.042 40.909 5.64 0.00 0.00 4.44
443 444 3.637911 TGTTGGGCATAACTATTCGGT 57.362 42.857 5.64 0.00 0.00 4.69
444 445 3.945285 ACTTGTTGGGCATAACTATTCGG 59.055 43.478 5.64 0.00 0.00 4.30
445 446 4.201910 CCACTTGTTGGGCATAACTATTCG 60.202 45.833 5.64 0.00 42.54 3.34
446 447 5.248870 CCACTTGTTGGGCATAACTATTC 57.751 43.478 5.64 0.00 42.54 1.75
483 484 7.894364 ACAGAGGGAGTAGATTTAGTTTGTCTA 59.106 37.037 0.00 0.00 0.00 2.59
517 521 3.201487 TGATCTACTCCCTCCGTCTTACA 59.799 47.826 0.00 0.00 0.00 2.41
518 522 3.565063 GTGATCTACTCCCTCCGTCTTAC 59.435 52.174 0.00 0.00 0.00 2.34
519 523 3.201487 TGTGATCTACTCCCTCCGTCTTA 59.799 47.826 0.00 0.00 0.00 2.10
520 524 2.025226 TGTGATCTACTCCCTCCGTCTT 60.025 50.000 0.00 0.00 0.00 3.01
521 525 1.564818 TGTGATCTACTCCCTCCGTCT 59.435 52.381 0.00 0.00 0.00 4.18
561 2598 3.940209 TCATTTGGGTGCTTGATGAAC 57.060 42.857 0.00 0.00 0.00 3.18
648 2685 6.048732 TGCCATACTCATCTGTTTTAGTGA 57.951 37.500 0.00 0.00 0.00 3.41
682 2719 0.820871 TTTTGGGTGTGCTTGGACAC 59.179 50.000 15.42 15.42 44.72 3.67
780 2824 3.965292 CATGCAATGCTGAAGGAGTAG 57.035 47.619 6.82 0.00 37.62 2.57
943 3009 2.157085 GTGTAGTAACGCTGCTTTGGTC 59.843 50.000 1.19 0.00 33.16 4.02
955 3028 6.034161 TCTTTCTTGGCTAGGTGTAGTAAC 57.966 41.667 0.00 0.00 0.00 2.50
1054 3135 1.762460 GCCTCTTCCTCCCGATGGA 60.762 63.158 0.00 0.00 38.75 3.41
1140 3230 1.153524 ACAGTGGCCCTTCATTGCA 59.846 52.632 0.00 0.00 0.00 4.08
1239 3332 1.279271 CCGAACTCCTCTTGGGACATT 59.721 52.381 0.00 0.00 39.58 2.71
1248 3341 0.321122 CTGCAAAGCCGAACTCCTCT 60.321 55.000 0.00 0.00 0.00 3.69
1273 3366 2.026542 GCAGCATGATCCTCCCATCATA 60.027 50.000 0.00 0.00 40.86 2.15
1432 3536 3.253432 GGCTAACAAACTACTGCTTGCTT 59.747 43.478 0.00 0.00 0.00 3.91
1439 3543 5.784177 TCTTCAGAGGCTAACAAACTACTG 58.216 41.667 0.00 0.00 0.00 2.74
1442 3546 6.231211 CCTTTCTTCAGAGGCTAACAAACTA 58.769 40.000 0.00 0.00 0.00 2.24
1454 3563 1.132643 GCTGCATGCCTTTCTTCAGAG 59.867 52.381 16.68 2.40 35.15 3.35
1464 3573 0.979709 TCCTCTACAGCTGCATGCCT 60.980 55.000 16.68 2.40 44.23 4.75
1540 3653 8.742777 TCTTCATAAATTTCCTTGTCCAATCTG 58.257 33.333 0.00 0.00 0.00 2.90
1573 3686 0.388520 TCACCATGTCGAGAAGTGCG 60.389 55.000 10.24 0.00 0.00 5.34
1577 3690 4.273480 ACAAAAGTTCACCATGTCGAGAAG 59.727 41.667 0.00 0.00 0.00 2.85
1705 3827 8.803201 TTTTTCGCACAATTGTACATAAATCA 57.197 26.923 11.53 0.00 0.00 2.57
1710 3832 7.589587 CAGAACTTTTTCGCACAATTGTACATA 59.410 33.333 11.53 0.00 36.78 2.29
1757 3879 3.006323 CGCTCCTCCAAATCAGCTATAGT 59.994 47.826 0.84 0.00 0.00 2.12
2196 4323 0.107361 CATCGACACCCCTAAACCCC 60.107 60.000 0.00 0.00 0.00 4.95
2227 4354 3.802685 GGCGTCATTGTTATCACTCCTAC 59.197 47.826 0.00 0.00 0.00 3.18
2228 4355 3.449377 TGGCGTCATTGTTATCACTCCTA 59.551 43.478 0.00 0.00 0.00 2.94
2229 4356 2.236146 TGGCGTCATTGTTATCACTCCT 59.764 45.455 0.00 0.00 0.00 3.69
2327 4454 3.562182 AGAGAAAACCCGGTGACAAAAT 58.438 40.909 0.00 0.00 0.00 1.82
2328 4455 3.007473 AGAGAAAACCCGGTGACAAAA 57.993 42.857 0.00 0.00 0.00 2.44
2391 4519 1.420138 AGAAGAAAAGAGTTGCCCGGA 59.580 47.619 0.73 0.00 0.00 5.14
2395 4523 7.062722 GCATTCATTAAGAAGAAAAGAGTTGCC 59.937 37.037 0.00 0.00 40.15 4.52


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

AutoCloner maintained by Alex Coulton.