Multiple sequence alignment - TraesCS4D01G012200

Loading Multiple Alignment...

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 TraesCS4D01G012200 chr4D 100.000 2699 0 0 1 2699 5683962 5686660 0.000000e+00 4985.0
1 TraesCS4D01G012200 chr4D 85.366 1107 67 37 340 1376 25695126 25694045 0.000000e+00 1059.0
2 TraesCS4D01G012200 chr4D 90.807 805 29 6 1376 2169 25693415 25692645 0.000000e+00 1035.0
3 TraesCS4D01G012200 chr4D 94.484 417 15 3 2184 2597 25692484 25692073 1.050000e-178 636.0
4 TraesCS4D01G012200 chr4D 95.057 263 8 2 283 541 182470963 182470702 2.500000e-110 409.0
5 TraesCS4D01G012200 chr4D 81.851 281 25 17 3 272 25695511 25695246 2.100000e-51 213.0
6 TraesCS4D01G012200 chr4D 100.000 28 0 0 386 413 5684404 5684431 5.000000e-03 52.8
7 TraesCS4D01G012200 chr6B 86.987 1437 100 35 1 1373 626213423 626214836 0.000000e+00 1537.0
8 TraesCS4D01G012200 chr6B 87.293 724 66 20 1376 2087 626216680 626217389 0.000000e+00 804.0
9 TraesCS4D01G012200 chr6B 100.000 29 0 0 2118 2146 626217807 626217835 1.000000e-03 54.7
10 TraesCS4D01G012200 chr4A 86.170 1034 63 31 413 1376 692385202 692384179 0.000000e+00 1044.0
11 TraesCS4D01G012200 chr4A 87.771 646 61 10 1376 2015 692383549 692382916 0.000000e+00 739.0
12 TraesCS4D01G012200 chr4A 89.011 273 19 5 2428 2697 597837065 597836801 7.210000e-86 327.0
13 TraesCS4D01G012200 chr4A 83.577 274 28 14 3 272 692385630 692385370 9.660000e-60 241.0
14 TraesCS4D01G012200 chr4A 88.312 154 17 1 2204 2357 597837210 597837058 1.650000e-42 183.0
15 TraesCS4D01G012200 chr4A 100.000 29 0 0 2118 2146 692382507 692382479 1.000000e-03 54.7
16 TraesCS4D01G012200 chr7A 85.962 1040 67 30 410 1376 32632275 32631242 0.000000e+00 1038.0
17 TraesCS4D01G012200 chr7A 89.060 649 46 11 1376 2015 32630612 32629980 0.000000e+00 782.0
18 TraesCS4D01G012200 chr7A 83.977 518 32 19 2184 2699 32629066 32628598 1.470000e-122 449.0
19 TraesCS4D01G012200 chr7A 83.636 275 26 16 3 272 32632706 32632446 9.660000e-60 241.0
20 TraesCS4D01G012200 chr7A 94.444 36 2 0 2111 2146 32629586 32629551 3.750000e-04 56.5
21 TraesCS4D01G012200 chr4B 92.391 736 34 6 1376 2100 38026000 38025276 0.000000e+00 1029.0
22 TraesCS4D01G012200 chr4B 84.491 1109 73 38 340 1376 38027711 38026630 0.000000e+00 1003.0
23 TraesCS4D01G012200 chr4B 93.370 543 25 8 1396 1928 9948276 9948817 0.000000e+00 793.0
24 TraesCS4D01G012200 chr4B 80.539 519 32 22 2184 2699 9949762 9950214 4.310000e-88 335.0
25 TraesCS4D01G012200 chr4B 84.791 263 23 12 3 264 38028094 38027848 5.770000e-62 248.0
26 TraesCS4D01G012200 chr4B 94.340 106 3 1 984 1089 9948089 9947987 2.780000e-35 159.0
27 TraesCS4D01G012200 chr7D 85.605 1042 65 37 410 1376 32608964 32607933 0.000000e+00 1014.0
28 TraesCS4D01G012200 chr7D 89.392 641 45 9 1376 2015 32607303 32606685 0.000000e+00 785.0
29 TraesCS4D01G012200 chr7D 82.885 520 33 19 2184 2699 32606049 32605582 1.490000e-112 416.0
30 TraesCS4D01G012200 chr7D 83.942 274 27 15 3 272 32609411 32609151 2.080000e-61 246.0
31 TraesCS4D01G012200 chr1D 93.094 362 17 3 184 541 145884659 145885016 8.560000e-145 523.0
32 TraesCS4D01G012200 chr1D 94.297 263 9 2 283 541 82976556 82976296 5.410000e-107 398.0
33 TraesCS4D01G012200 chr3D 95.437 263 7 2 283 541 494379405 494379144 5.380000e-112 414.0
34 TraesCS4D01G012200 chr3D 95.057 263 8 2 283 541 495015819 495015558 2.500000e-110 409.0
35 TraesCS4D01G012200 chr3D 100.000 28 0 0 386 413 495015660 495015633 5.000000e-03 52.8
36 TraesCS4D01G012200 chr5D 95.057 263 8 2 283 541 485215672 485215411 2.500000e-110 409.0
37 TraesCS4D01G012200 chr3B 81.182 457 63 12 792 1243 680749901 680750339 1.990000e-91 346.0
38 TraesCS4D01G012200 chr3B 73.876 356 55 21 427 746 680749535 680749888 1.020000e-19 108.0


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 TraesCS4D01G012200 chr4D 5683962 5686660 2698 False 2518.900000 4985 100.000000 1 2699 2 chr4D.!!$F1 2698
1 TraesCS4D01G012200 chr4D 25692073 25695511 3438 True 735.750000 1059 88.127000 3 2597 4 chr4D.!!$R2 2594
2 TraesCS4D01G012200 chr6B 626213423 626217835 4412 False 798.566667 1537 91.426667 1 2146 3 chr6B.!!$F1 2145
3 TraesCS4D01G012200 chr4A 692382479 692385630 3151 True 519.675000 1044 89.379500 3 2146 4 chr4A.!!$R2 2143
4 TraesCS4D01G012200 chr7A 32628598 32632706 4108 True 513.300000 1038 87.415800 3 2699 5 chr7A.!!$R1 2696
5 TraesCS4D01G012200 chr4B 38025276 38028094 2818 True 760.000000 1029 87.224333 3 2100 3 chr4B.!!$R2 2097
6 TraesCS4D01G012200 chr4B 9948276 9950214 1938 False 564.000000 793 86.954500 1396 2699 2 chr4B.!!$F1 1303
7 TraesCS4D01G012200 chr7D 32605582 32609411 3829 True 615.250000 1014 85.456000 3 2699 4 chr7D.!!$R1 2696
8 TraesCS4D01G012200 chr3B 680749535 680750339 804 False 227.000000 346 77.529000 427 1243 2 chr3B.!!$F1 816

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
800 939 0.030638 GTTGTTGCCATGCGTGAACT 59.969 50.0 7.72 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 4042 0.036388 AAGATGTTGTGGCCGTCGAT 60.036 50.0 0.0 0.0 0.0 3.59 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
139 140 0.179073 AGCAAATCGCCGTCTAGCAT 60.179 50.000 0.00 0.00 44.04 3.79
147 148 2.100087 TCGCCGTCTAGCATGTTGAATA 59.900 45.455 0.00 0.00 0.00 1.75
218 222 7.201821 GGTTACCGTGTTACTACTATGGTGTAT 60.202 40.741 0.00 0.00 0.00 2.29
281 292 6.834168 ATTTTGGGTTCTGTACATAGGTTG 57.166 37.500 0.00 0.00 0.00 3.77
329 382 4.336993 TGTTGGTCTGTGTTTGGTTGATAC 59.663 41.667 0.00 0.00 0.00 2.24
344 418 2.616960 TGATACGTGATGTTGGTCTGC 58.383 47.619 0.00 0.00 0.00 4.26
350 424 0.804364 TGATGTTGGTCTGCGATTGC 59.196 50.000 0.00 0.00 43.20 3.56
383 459 5.178061 TGATTGTTGTTGCGATATGACTCT 58.822 37.500 0.00 0.00 0.00 3.24
384 460 4.926860 TTGTTGTTGCGATATGACTCTG 57.073 40.909 0.00 0.00 0.00 3.35
386 462 4.314961 TGTTGTTGCGATATGACTCTGTT 58.685 39.130 0.00 0.00 0.00 3.16
387 463 4.388773 TGTTGTTGCGATATGACTCTGTTC 59.611 41.667 0.00 0.00 0.00 3.18
388 464 4.186856 TGTTGCGATATGACTCTGTTCA 57.813 40.909 0.00 0.00 0.00 3.18
391 467 4.391405 TGCGATATGACTCTGTTCATGT 57.609 40.909 0.00 0.00 36.84 3.21
392 468 4.114794 TGCGATATGACTCTGTTCATGTG 58.885 43.478 0.00 0.00 36.84 3.21
393 469 4.115516 GCGATATGACTCTGTTCATGTGT 58.884 43.478 0.00 0.00 36.84 3.72
394 470 4.026228 GCGATATGACTCTGTTCATGTGTG 60.026 45.833 0.00 0.00 36.84 3.82
395 471 4.505556 CGATATGACTCTGTTCATGTGTGG 59.494 45.833 0.00 0.00 36.84 4.17
396 472 3.777106 ATGACTCTGTTCATGTGTGGT 57.223 42.857 0.00 0.00 34.79 4.16
397 473 3.111853 TGACTCTGTTCATGTGTGGTC 57.888 47.619 0.00 0.00 0.00 4.02
398 474 2.700371 TGACTCTGTTCATGTGTGGTCT 59.300 45.455 0.00 0.00 0.00 3.85
399 475 3.134623 TGACTCTGTTCATGTGTGGTCTT 59.865 43.478 0.00 0.00 0.00 3.01
400 476 4.130118 GACTCTGTTCATGTGTGGTCTTT 58.870 43.478 0.00 0.00 0.00 2.52
401 477 4.130118 ACTCTGTTCATGTGTGGTCTTTC 58.870 43.478 0.00 0.00 0.00 2.62
402 478 4.141620 ACTCTGTTCATGTGTGGTCTTTCT 60.142 41.667 0.00 0.00 0.00 2.52
403 479 4.129380 TCTGTTCATGTGTGGTCTTTCTG 58.871 43.478 0.00 0.00 0.00 3.02
404 480 3.879295 CTGTTCATGTGTGGTCTTTCTGT 59.121 43.478 0.00 0.00 0.00 3.41
405 481 5.029807 TGTTCATGTGTGGTCTTTCTGTA 57.970 39.130 0.00 0.00 0.00 2.74
406 482 5.432645 TGTTCATGTGTGGTCTTTCTGTAA 58.567 37.500 0.00 0.00 0.00 2.41
407 483 5.883115 TGTTCATGTGTGGTCTTTCTGTAAA 59.117 36.000 0.00 0.00 0.00 2.01
408 484 6.375736 TGTTCATGTGTGGTCTTTCTGTAAAA 59.624 34.615 0.00 0.00 0.00 1.52
424 500 8.964420 TTCTGTAAAAGTTGAACTGAAACTTG 57.036 30.769 0.00 0.00 44.93 3.16
433 509 8.570068 AGTTGAACTGAAACTTGGTTTAGTTA 57.430 30.769 8.25 0.00 37.37 2.24
464 541 7.424803 CAATTCATGTGTGGTCTTTCTGTAAA 58.575 34.615 0.00 0.00 0.00 2.01
495 575 3.926527 TGTTTAGTTGCTCGATGTAGCTG 59.073 43.478 0.00 0.00 43.19 4.24
553 639 4.947645 ACACTGATTTGTTTTGGTCATGG 58.052 39.130 0.00 0.00 0.00 3.66
576 665 7.340256 TGGTTTTACTTTAGGAGTTTCAGTCA 58.660 34.615 0.00 0.00 39.86 3.41
607 700 7.634671 TGCAGCCATATGAATTTATAGATGG 57.365 36.000 3.65 7.38 0.00 3.51
636 742 4.537751 TGTGGTTCTATCCTAGGACTGAG 58.462 47.826 15.42 12.00 34.59 3.35
637 743 4.017407 TGTGGTTCTATCCTAGGACTGAGT 60.017 45.833 15.42 0.00 34.59 3.41
639 745 4.229812 TGGTTCTATCCTAGGACTGAGTCA 59.770 45.833 15.42 13.10 34.59 3.41
640 746 5.103473 TGGTTCTATCCTAGGACTGAGTCAT 60.103 44.000 15.42 10.27 34.59 3.06
642 748 5.913946 TCTATCCTAGGACTGAGTCATGA 57.086 43.478 15.42 2.22 33.68 3.07
643 749 6.267492 TCTATCCTAGGACTGAGTCATGAA 57.733 41.667 15.42 0.00 33.68 2.57
655 786 7.714377 GGACTGAGTCATGAAGATAATGTGAAT 59.286 37.037 15.33 0.00 33.68 2.57
659 790 9.676861 TGAGTCATGAAGATAATGTGAATTCTT 57.323 29.630 7.05 0.00 0.00 2.52
662 793 8.133627 GTCATGAAGATAATGTGAATTCTTGGG 58.866 37.037 7.05 0.00 0.00 4.12
664 795 8.857098 CATGAAGATAATGTGAATTCTTGGGAT 58.143 33.333 7.05 0.00 0.00 3.85
666 797 9.565090 TGAAGATAATGTGAATTCTTGGGATAG 57.435 33.333 7.05 0.00 0.00 2.08
667 798 7.992754 AGATAATGTGAATTCTTGGGATAGC 57.007 36.000 7.05 0.00 0.00 2.97
702 835 1.085091 CTTGACCTCTGATGCTGCAC 58.915 55.000 3.57 0.00 0.00 4.57
746 881 9.551734 TGATAAGATTTGGTCATTCAGATAGTG 57.448 33.333 0.00 0.00 0.00 2.74
754 889 9.952030 TTTGGTCATTCAGATAGTGTTATGTTA 57.048 29.630 0.00 0.00 0.00 2.41
756 891 9.546428 TGGTCATTCAGATAGTGTTATGTTATG 57.454 33.333 0.00 0.00 0.00 1.90
757 892 9.764363 GGTCATTCAGATAGTGTTATGTTATGA 57.236 33.333 0.00 0.00 0.00 2.15
793 932 4.684877 TCATTCATATGTTGTTGCCATGC 58.315 39.130 1.90 0.00 33.34 4.06
794 933 2.847959 TCATATGTTGTTGCCATGCG 57.152 45.000 1.90 0.00 0.00 4.73
800 939 0.030638 GTTGTTGCCATGCGTGAACT 59.969 50.000 7.72 0.00 0.00 3.01
801 940 1.265635 GTTGTTGCCATGCGTGAACTA 59.734 47.619 7.72 0.00 0.00 2.24
809 954 3.261580 CCATGCGTGAACTATTCTGTCA 58.738 45.455 7.72 0.00 0.00 3.58
814 959 4.994217 TGCGTGAACTATTCTGTCAATTGA 59.006 37.500 3.38 3.38 0.00 2.57
816 961 5.120830 GCGTGAACTATTCTGTCAATTGACT 59.879 40.000 32.57 18.77 44.99 3.41
832 979 3.627395 TGACTTAACCTATGCCCTGTG 57.373 47.619 0.00 0.00 0.00 3.66
835 982 3.939592 GACTTAACCTATGCCCTGTGTTC 59.060 47.826 0.00 0.00 0.00 3.18
837 984 2.496899 AACCTATGCCCTGTGTTCTG 57.503 50.000 0.00 0.00 0.00 3.02
848 1000 2.229784 CCTGTGTTCTGGAGGAAAATGC 59.770 50.000 0.00 0.00 35.51 3.56
871 1023 5.756347 GCGTGTCTATATTGTTATGGTCCAA 59.244 40.000 0.00 0.00 0.00 3.53
873 1025 6.759356 CGTGTCTATATTGTTATGGTCCAACA 59.241 38.462 0.00 0.00 34.18 3.33
1109 1268 4.952262 TTTCTCTGTCTATGCATTGTGC 57.048 40.909 3.54 1.59 45.29 4.57
1131 1291 4.727734 GCAGGCTGTCATTTAATACGTGTG 60.728 45.833 17.16 0.00 0.00 3.82
1134 1294 6.091577 CAGGCTGTCATTTAATACGTGTGTTA 59.908 38.462 6.28 0.00 0.00 2.41
1175 1335 1.691434 TCCATTGGGTTTTCAGTTGGC 59.309 47.619 2.09 0.00 34.93 4.52
1177 1337 2.548493 CCATTGGGTTTTCAGTTGGCAG 60.548 50.000 0.00 0.00 0.00 4.85
1194 1359 6.096846 AGTTGGCAGAGTCAAAACAAATAAGT 59.903 34.615 0.00 0.00 0.00 2.24
1195 1360 7.284489 AGTTGGCAGAGTCAAAACAAATAAGTA 59.716 33.333 0.00 0.00 0.00 2.24
1477 3513 1.825090 TCGCAGAGGTAAGTTCCGTA 58.175 50.000 0.00 0.00 0.00 4.02
1583 3622 2.261671 CGAGTGGGACGTCAAGGG 59.738 66.667 18.91 0.00 0.00 3.95
1757 3801 3.370840 TTCCCATGAAGAGGTGGATTG 57.629 47.619 0.00 0.00 37.72 2.67
1775 3824 0.539438 TGTTGGATTGCCCTGTGACC 60.539 55.000 0.00 0.00 35.38 4.02
2022 4097 3.257933 CTCGCGCAGAGCCTTTTT 58.742 55.556 8.75 0.00 44.76 1.94
2071 4158 5.295292 CCAGTTTAGTGGCAGAAGTCATATG 59.705 44.000 0.00 0.00 0.00 1.78
2077 4164 6.259550 AGTGGCAGAAGTCATATGAAAAAC 57.740 37.500 7.07 0.00 0.00 2.43
2170 5133 7.829725 TGCAATATATTGACAGGGAATTATGC 58.170 34.615 26.22 9.05 40.14 3.14
2171 5134 7.093814 TGCAATATATTGACAGGGAATTATGCC 60.094 37.037 26.22 5.81 40.14 4.40
2173 5136 8.805175 CAATATATTGACAGGGAATTATGCCAA 58.195 33.333 18.92 0.00 38.61 4.52
2224 5375 9.561069 AATCTAATGGAGTACATGGTATTCAAC 57.439 33.333 0.00 0.00 40.44 3.18
2240 5391 6.879458 GGTATTCAACAAGACAGGTTACAGAT 59.121 38.462 0.00 0.00 0.00 2.90
2264 5415 7.985634 TTTCTGAAAGCACAATAAGAAACAC 57.014 32.000 0.00 0.00 30.79 3.32
2298 5451 2.195922 AGAAAACTGCAAAAGCGCAAG 58.804 42.857 11.47 0.00 42.45 4.01
2343 5496 5.239306 GGTCATAAACAGCAGCATTAGCATA 59.761 40.000 0.00 0.00 45.49 3.14
2344 5497 6.072286 GGTCATAAACAGCAGCATTAGCATAT 60.072 38.462 0.00 0.00 45.49 1.78
2345 5498 7.365741 GTCATAAACAGCAGCATTAGCATATT 58.634 34.615 0.00 0.00 45.49 1.28
2346 5499 7.864379 GTCATAAACAGCAGCATTAGCATATTT 59.136 33.333 0.00 0.00 45.49 1.40
2347 5500 8.415553 TCATAAACAGCAGCATTAGCATATTTT 58.584 29.630 0.00 0.00 45.49 1.82
2348 5501 9.037737 CATAAACAGCAGCATTAGCATATTTTT 57.962 29.630 0.00 0.00 45.49 1.94
2385 5549 1.443702 GCCCACGACCGCATTTTTC 60.444 57.895 0.00 0.00 0.00 2.29
2457 5622 7.715657 ACAGAAGAATACATCTGATCTGAGAC 58.284 38.462 9.56 0.00 42.16 3.36
2532 5701 9.751542 AATACAAAGAAGATAGATCAGTAACCG 57.248 33.333 0.00 0.00 0.00 4.44
2533 5702 6.574350 ACAAAGAAGATAGATCAGTAACCGG 58.426 40.000 0.00 0.00 0.00 5.28
2534 5703 5.793030 AAGAAGATAGATCAGTAACCGGG 57.207 43.478 6.32 0.00 0.00 5.73
2574 5743 0.398318 ACACAAGGAAGGACCAGAGC 59.602 55.000 0.00 0.00 42.04 4.09
2652 5821 2.237143 TGCCCACCTCTAGAGAACATTG 59.763 50.000 21.76 5.63 0.00 2.82
2653 5822 2.501723 GCCCACCTCTAGAGAACATTGA 59.498 50.000 21.76 0.00 0.00 2.57
2654 5823 3.055094 GCCCACCTCTAGAGAACATTGAA 60.055 47.826 21.76 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 140 6.262944 ACACAGACAGAAAGCATTATTCAACA 59.737 34.615 0.00 0.00 0.00 3.33
147 148 2.551459 GCTCACACAGACAGAAAGCATT 59.449 45.455 0.00 0.00 0.00 3.56
218 222 4.011698 TCTTCGCATACACCTACAGTACA 58.988 43.478 0.00 0.00 0.00 2.90
281 292 9.669353 CAGGACACAAAGCATAATGATAATAAC 57.331 33.333 0.00 0.00 0.00 1.89
329 382 1.078709 AATCGCAGACCAACATCACG 58.921 50.000 0.00 0.00 42.51 4.35
350 424 3.240401 GCAACAACAATCAAACACGACTG 59.760 43.478 0.00 0.00 0.00 3.51
383 459 3.884895 ACAGAAAGACCACACATGAACA 58.115 40.909 0.00 0.00 0.00 3.18
384 460 6.371809 TTTACAGAAAGACCACACATGAAC 57.628 37.500 0.00 0.00 0.00 3.18
386 462 6.119536 ACTTTTACAGAAAGACCACACATGA 58.880 36.000 0.00 0.00 0.00 3.07
387 463 6.377327 ACTTTTACAGAAAGACCACACATG 57.623 37.500 5.60 0.00 0.00 3.21
388 464 6.601613 TCAACTTTTACAGAAAGACCACACAT 59.398 34.615 5.60 0.00 0.00 3.21
391 467 6.657541 AGTTCAACTTTTACAGAAAGACCACA 59.342 34.615 5.60 0.00 0.00 4.17
392 468 6.967199 CAGTTCAACTTTTACAGAAAGACCAC 59.033 38.462 5.60 0.00 0.00 4.16
393 469 6.882140 TCAGTTCAACTTTTACAGAAAGACCA 59.118 34.615 5.60 0.00 0.00 4.02
394 470 7.316544 TCAGTTCAACTTTTACAGAAAGACC 57.683 36.000 5.60 0.00 0.00 3.85
395 471 9.062674 GTTTCAGTTCAACTTTTACAGAAAGAC 57.937 33.333 5.60 0.00 31.05 3.01
396 472 9.010029 AGTTTCAGTTCAACTTTTACAGAAAGA 57.990 29.630 5.60 0.00 31.05 2.52
397 473 9.626045 AAGTTTCAGTTCAACTTTTACAGAAAG 57.374 29.630 0.00 0.00 40.83 2.62
398 474 9.405587 CAAGTTTCAGTTCAACTTTTACAGAAA 57.594 29.630 0.00 0.00 41.58 2.52
399 475 8.026607 CCAAGTTTCAGTTCAACTTTTACAGAA 58.973 33.333 0.00 0.00 41.58 3.02
400 476 7.175990 ACCAAGTTTCAGTTCAACTTTTACAGA 59.824 33.333 0.00 0.00 41.58 3.41
401 477 7.312899 ACCAAGTTTCAGTTCAACTTTTACAG 58.687 34.615 0.00 0.00 41.58 2.74
402 478 7.222000 ACCAAGTTTCAGTTCAACTTTTACA 57.778 32.000 0.00 0.00 41.58 2.41
403 479 8.528917 AAACCAAGTTTCAGTTCAACTTTTAC 57.471 30.769 0.00 0.00 41.58 2.01
404 480 9.849166 CTAAACCAAGTTTCAGTTCAACTTTTA 57.151 29.630 0.00 0.00 41.58 1.52
405 481 8.364894 ACTAAACCAAGTTTCAGTTCAACTTTT 58.635 29.630 0.00 0.00 41.58 2.27
406 482 7.892609 ACTAAACCAAGTTTCAGTTCAACTTT 58.107 30.769 0.00 0.00 41.58 2.66
407 483 7.462571 ACTAAACCAAGTTTCAGTTCAACTT 57.537 32.000 0.00 0.00 43.80 2.66
408 484 7.462571 AACTAAACCAAGTTTCAGTTCAACT 57.537 32.000 0.00 0.00 36.26 3.16
433 509 0.602562 CCACACATGAATTGCCGGTT 59.397 50.000 1.90 0.00 0.00 4.44
464 541 5.302360 TCGAGCAACTAAACATACCAACTT 58.698 37.500 0.00 0.00 0.00 2.66
495 575 2.187946 CCACCACATCCTCGAGCC 59.812 66.667 6.99 0.00 0.00 4.70
594 683 7.945134 ACCACATTCAAGCCATCTATAAATTC 58.055 34.615 0.00 0.00 0.00 2.17
607 700 5.059833 CCTAGGATAGAACCACATTCAAGC 58.940 45.833 1.05 0.00 42.77 4.01
608 701 6.098982 AGTCCTAGGATAGAACCACATTCAAG 59.901 42.308 16.27 0.00 42.77 3.02
615 708 4.538738 ACTCAGTCCTAGGATAGAACCAC 58.461 47.826 16.27 0.00 42.77 4.16
636 742 8.133627 CCCAAGAATTCACATTATCTTCATGAC 58.866 37.037 8.44 0.00 30.01 3.06
637 743 8.054572 TCCCAAGAATTCACATTATCTTCATGA 58.945 33.333 8.44 0.00 30.01 3.07
640 746 9.565090 CTATCCCAAGAATTCACATTATCTTCA 57.435 33.333 8.44 0.00 30.01 3.02
642 748 8.000709 TGCTATCCCAAGAATTCACATTATCTT 58.999 33.333 8.44 0.00 32.55 2.40
643 749 7.520798 TGCTATCCCAAGAATTCACATTATCT 58.479 34.615 8.44 0.00 0.00 1.98
655 786 3.939740 AGAGCAATGCTATCCCAAGAA 57.060 42.857 8.12 0.00 39.88 2.52
659 790 3.378112 CGAAAAAGAGCAATGCTATCCCA 59.622 43.478 8.12 0.00 39.88 4.37
662 793 5.476752 AGTCGAAAAAGAGCAATGCTATC 57.523 39.130 8.12 0.00 39.88 2.08
664 795 4.754618 TCAAGTCGAAAAAGAGCAATGCTA 59.245 37.500 8.12 0.00 39.88 3.49
666 797 3.665871 GTCAAGTCGAAAAAGAGCAATGC 59.334 43.478 0.00 0.00 0.00 3.56
667 798 4.023707 AGGTCAAGTCGAAAAAGAGCAATG 60.024 41.667 9.31 0.00 0.00 2.82
786 921 2.009051 CAGAATAGTTCACGCATGGCA 58.991 47.619 0.00 0.00 0.00 4.92
809 954 4.949856 CACAGGGCATAGGTTAAGTCAATT 59.050 41.667 0.00 0.00 0.00 2.32
814 959 3.587506 AGAACACAGGGCATAGGTTAAGT 59.412 43.478 0.00 0.00 0.00 2.24
816 961 3.308117 CCAGAACACAGGGCATAGGTTAA 60.308 47.826 0.00 0.00 0.00 2.01
832 979 1.880027 ACACGCATTTTCCTCCAGAAC 59.120 47.619 0.00 0.00 32.95 3.01
835 982 1.813513 AGACACGCATTTTCCTCCAG 58.186 50.000 0.00 0.00 0.00 3.86
837 984 5.527582 ACAATATAGACACGCATTTTCCTCC 59.472 40.000 0.00 0.00 0.00 4.30
848 1000 6.759356 TGTTGGACCATAACAATATAGACACG 59.241 38.462 0.00 0.00 35.29 4.49
896 1048 7.550906 GCTGCTCTATTAAGGATAAATCGGAAT 59.449 37.037 0.00 0.00 0.00 3.01
1070 1229 5.417580 AGAGAAAACAACTGCAAAGTGGTAA 59.582 36.000 0.00 0.00 0.00 2.85
1071 1230 4.947388 AGAGAAAACAACTGCAAAGTGGTA 59.053 37.500 0.00 0.00 0.00 3.25
1109 1268 4.391830 ACACACGTATTAAATGACAGCCTG 59.608 41.667 0.00 0.00 0.00 4.85
1131 1291 5.745227 TGATGAAGGAGAACAGGGAATAAC 58.255 41.667 0.00 0.00 0.00 1.89
1134 1294 4.141298 GGATGATGAAGGAGAACAGGGAAT 60.141 45.833 0.00 0.00 0.00 3.01
1373 1566 4.037684 CAGGTAATCGTATCCCTTCTCGTT 59.962 45.833 0.00 0.00 0.00 3.85
1717 3758 5.105595 GGGAAATTCAGTCCAAAGATGAAGG 60.106 44.000 0.00 0.00 36.47 3.46
1757 3801 1.250840 GGGTCACAGGGCAATCCAAC 61.251 60.000 0.00 0.00 38.24 3.77
1775 3824 6.183360 ACGATTTAACAAAATAGTACAGCCGG 60.183 38.462 0.00 0.00 0.00 6.13
1843 3894 2.028567 TCCTTTTGCCATTTTAAGCCGG 60.029 45.455 0.00 0.00 0.00 6.13
1967 4039 2.126228 GTTGTGGCCGTCGATCGA 60.126 61.111 15.15 15.15 42.86 3.59
1968 4040 1.752501 GATGTTGTGGCCGTCGATCG 61.753 60.000 9.36 9.36 39.52 3.69
1969 4041 0.460284 AGATGTTGTGGCCGTCGATC 60.460 55.000 0.00 0.00 0.00 3.69
1970 4042 0.036388 AAGATGTTGTGGCCGTCGAT 60.036 50.000 0.00 0.00 0.00 3.59
2020 4095 6.660094 TGATCATCTGACCATTGTGAATGAAA 59.340 34.615 0.00 0.00 41.46 2.69
2021 4096 6.181908 TGATCATCTGACCATTGTGAATGAA 58.818 36.000 0.00 0.00 41.46 2.57
2022 4097 5.747342 TGATCATCTGACCATTGTGAATGA 58.253 37.500 0.00 0.00 41.46 2.57
2071 4158 7.826260 TGTTGTTCCTTTCAAGATGTTTTTC 57.174 32.000 0.00 0.00 0.00 2.29
2224 5375 7.496529 TTTCAGAAATCTGTAACCTGTCTTG 57.503 36.000 10.06 0.00 44.12 3.02
2240 5391 6.978080 GGTGTTTCTTATTGTGCTTTCAGAAA 59.022 34.615 0.00 0.00 0.00 2.52
2264 5415 4.025145 GCAGTTTTCTATCGGATAAACGGG 60.025 45.833 13.23 9.40 36.03 5.28
2298 5451 5.249420 ACCTCTCTTTCATCCTGTTTTAGC 58.751 41.667 0.00 0.00 0.00 3.09
2345 5498 2.985809 GTGCGCATCTTGTATGCAAAAA 59.014 40.909 15.91 0.00 44.75 1.94
2346 5499 2.594321 GTGCGCATCTTGTATGCAAAA 58.406 42.857 15.91 0.00 44.75 2.44
2347 5500 1.465521 CGTGCGCATCTTGTATGCAAA 60.466 47.619 15.91 0.00 44.75 3.68
2348 5501 0.096802 CGTGCGCATCTTGTATGCAA 59.903 50.000 15.91 0.00 44.75 4.08
2349 5502 1.715000 CGTGCGCATCTTGTATGCA 59.285 52.632 15.91 0.00 44.75 3.96
2350 5503 1.652329 GCGTGCGCATCTTGTATGC 60.652 57.895 15.91 0.76 41.49 3.14
2351 5504 1.010797 GGCGTGCGCATCTTGTATG 60.011 57.895 15.91 0.00 44.11 2.39
2352 5505 2.180204 GGGCGTGCGCATCTTGTAT 61.180 57.895 15.91 0.00 44.11 2.29
2353 5506 2.817834 GGGCGTGCGCATCTTGTA 60.818 61.111 15.91 0.00 44.11 2.41
2376 5540 5.231779 TGACATTTCTGTTGTGAAAAATGCG 59.768 36.000 6.59 0.00 39.08 4.73
2385 5549 6.070897 TGTTACCATGACATTTCTGTTGTG 57.929 37.500 0.00 0.00 35.14 3.33
2414 5579 1.346068 TGTATGCACAGTACAGTGGCA 59.654 47.619 18.72 16.30 39.87 4.92
2457 5622 5.967674 GCGATTATGGAAAGATGTTGACAAG 59.032 40.000 0.00 0.00 0.00 3.16
2574 5743 8.583765 GTTGTTGTTCAGTTTAAAGTTTGCTAG 58.416 33.333 0.00 0.00 0.00 3.42
2652 5821 3.120304 GGCGATGGACACACTAGTTTTTC 60.120 47.826 0.00 0.00 0.00 2.29
2653 5822 2.812011 GGCGATGGACACACTAGTTTTT 59.188 45.455 0.00 0.00 0.00 1.94
2654 5823 2.224426 TGGCGATGGACACACTAGTTTT 60.224 45.455 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.