Multiple sequence alignment - TraesCS1B01G013600

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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 TraesCS1B01G013600 chr1B 100.000 3324 0 0 1 3324 6445969 6442646 0.000000e+00 6139.0
1 TraesCS1B01G013600 chr1B 78.090 890 128 30 986 1863 7143627 7144461 4.950000e-138 501.0
2 TraesCS1B01G013600 chr1B 81.439 528 49 20 609 1095 6502355 6502874 1.450000e-103 387.0
3 TraesCS1B01G013600 chr1B 82.251 231 34 3 1614 1843 6503390 6503614 3.380000e-45 193.0
4 TraesCS1B01G013600 chr1D 91.884 2267 128 23 625 2845 4249285 4251541 0.000000e+00 3116.0
5 TraesCS1B01G013600 chr1D 90.032 2468 152 24 609 3000 3738555 3736106 0.000000e+00 3109.0
6 TraesCS1B01G013600 chr1D 95.493 821 34 3 1592 2410 7179561 7178742 0.000000e+00 1308.0
7 TraesCS1B01G013600 chr1D 95.371 821 35 3 1592 2410 4309172 4309991 0.000000e+00 1303.0
8 TraesCS1B01G013600 chr1D 88.749 1031 81 11 609 1608 3860451 3859425 0.000000e+00 1229.0
9 TraesCS1B01G013600 chr1D 84.884 860 94 16 2201 3040 3847479 3846636 0.000000e+00 835.0
10 TraesCS1B01G013600 chr1D 88.800 625 40 15 1598 2201 3857620 3857005 0.000000e+00 739.0
11 TraesCS1B01G013600 chr1D 91.498 494 41 1 1098 1590 7180181 7179688 0.000000e+00 678.0
12 TraesCS1B01G013600 chr1D 91.296 494 42 1 1098 1590 4308552 4309045 0.000000e+00 673.0
13 TraesCS1B01G013600 chr1D 78.167 884 130 31 997 1870 3582641 3581811 3.830000e-139 505.0
14 TraesCS1B01G013600 chr1D 85.714 511 36 16 622 1100 4300275 4300780 3.830000e-139 505.0
15 TraesCS1B01G013600 chr1D 79.779 544 75 21 988 1526 4525071 4525584 2.440000e-96 363.0
16 TraesCS1B01G013600 chr1D 81.870 353 35 13 764 1095 4577301 4577645 1.520000e-68 270.0
17 TraesCS1B01G013600 chr1D 88.112 143 17 0 3182 3324 3734607 3734465 1.590000e-38 171.0
18 TraesCS1B01G013600 chr1A 88.272 1296 113 20 1105 2369 6510757 6512044 0.000000e+00 1515.0
19 TraesCS1B01G013600 chr1A 89.194 546 49 7 1 539 101774644 101775186 0.000000e+00 673.0
20 TraesCS1B01G013600 chr1A 81.772 790 108 17 1063 1840 5153252 5152487 2.180000e-176 628.0
21 TraesCS1B01G013600 chr1A 81.107 524 52 16 612 1095 5096547 5096031 3.130000e-100 375.0
22 TraesCS1B01G013600 chr1A 86.585 246 24 4 859 1099 6506002 6506243 2.540000e-66 263.0
23 TraesCS1B01G013600 chr1A 78.070 342 40 13 707 1018 5153587 5153251 2.040000e-42 183.0
24 TraesCS1B01G013600 chr1A 95.745 47 2 0 799 845 6504239 6504285 3.560000e-10 76.8
25 TraesCS1B01G013600 chr5A 92.751 538 38 1 1 537 548718902 548718365 0.000000e+00 776.0
26 TraesCS1B01G013600 chr2B 92.265 543 34 4 1 542 560176680 560177215 0.000000e+00 763.0
27 TraesCS1B01G013600 chr6D 91.667 540 40 5 1 539 64598419 64597884 0.000000e+00 743.0
28 TraesCS1B01G013600 chr3B 91.513 542 41 5 1 541 30295782 30296319 0.000000e+00 741.0
29 TraesCS1B01G013600 chr7D 90.993 544 45 4 1 543 579195479 579194939 0.000000e+00 730.0
30 TraesCS1B01G013600 chr6A 90.257 544 43 4 1 543 614159772 614159238 0.000000e+00 702.0
31 TraesCS1B01G013600 chr3A 90.293 546 40 11 3 543 45941809 45942346 0.000000e+00 702.0
32 TraesCS1B01G013600 chr4A 90.221 542 43 7 1 538 577983992 577984527 0.000000e+00 699.0
33 TraesCS1B01G013600 chrUn 77.667 900 129 31 986 1870 293593400 293592558 1.790000e-132 483.0


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 TraesCS1B01G013600 chr1B 6442646 6445969 3323 True 6139.0 6139 100.0000 1 3324 1 chr1B.!!$R1 3323
1 TraesCS1B01G013600 chr1B 7143627 7144461 834 False 501.0 501 78.0900 986 1863 1 chr1B.!!$F1 877
2 TraesCS1B01G013600 chr1B 6502355 6503614 1259 False 290.0 387 81.8450 609 1843 2 chr1B.!!$F2 1234
3 TraesCS1B01G013600 chr1D 4249285 4251541 2256 False 3116.0 3116 91.8840 625 2845 1 chr1D.!!$F1 2220
4 TraesCS1B01G013600 chr1D 3734465 3738555 4090 True 1640.0 3109 89.0720 609 3324 2 chr1D.!!$R3 2715
5 TraesCS1B01G013600 chr1D 7178742 7180181 1439 True 993.0 1308 93.4955 1098 2410 2 chr1D.!!$R5 1312
6 TraesCS1B01G013600 chr1D 4308552 4309991 1439 False 988.0 1303 93.3335 1098 2410 2 chr1D.!!$F5 1312
7 TraesCS1B01G013600 chr1D 3857005 3860451 3446 True 984.0 1229 88.7745 609 2201 2 chr1D.!!$R4 1592
8 TraesCS1B01G013600 chr1D 3846636 3847479 843 True 835.0 835 84.8840 2201 3040 1 chr1D.!!$R2 839
9 TraesCS1B01G013600 chr1D 3581811 3582641 830 True 505.0 505 78.1670 997 1870 1 chr1D.!!$R1 873
10 TraesCS1B01G013600 chr1D 4300275 4300780 505 False 505.0 505 85.7140 622 1100 1 chr1D.!!$F2 478
11 TraesCS1B01G013600 chr1D 4525071 4525584 513 False 363.0 363 79.7790 988 1526 1 chr1D.!!$F3 538
12 TraesCS1B01G013600 chr1A 6510757 6512044 1287 False 1515.0 1515 88.2720 1105 2369 1 chr1A.!!$F1 1264
13 TraesCS1B01G013600 chr1A 101774644 101775186 542 False 673.0 673 89.1940 1 539 1 chr1A.!!$F2 538
14 TraesCS1B01G013600 chr1A 5152487 5153587 1100 True 405.5 628 79.9210 707 1840 2 chr1A.!!$R2 1133
15 TraesCS1B01G013600 chr1A 5096031 5096547 516 True 375.0 375 81.1070 612 1095 1 chr1A.!!$R1 483
16 TraesCS1B01G013600 chr5A 548718365 548718902 537 True 776.0 776 92.7510 1 537 1 chr5A.!!$R1 536
17 TraesCS1B01G013600 chr2B 560176680 560177215 535 False 763.0 763 92.2650 1 542 1 chr2B.!!$F1 541
18 TraesCS1B01G013600 chr6D 64597884 64598419 535 True 743.0 743 91.6670 1 539 1 chr6D.!!$R1 538
19 TraesCS1B01G013600 chr3B 30295782 30296319 537 False 741.0 741 91.5130 1 541 1 chr3B.!!$F1 540
20 TraesCS1B01G013600 chr7D 579194939 579195479 540 True 730.0 730 90.9930 1 543 1 chr7D.!!$R1 542
21 TraesCS1B01G013600 chr6A 614159238 614159772 534 True 702.0 702 90.2570 1 543 1 chr6A.!!$R1 542
22 TraesCS1B01G013600 chr3A 45941809 45942346 537 False 702.0 702 90.2930 3 543 1 chr3A.!!$F1 540
23 TraesCS1B01G013600 chr4A 577983992 577984527 535 False 699.0 699 90.2210 1 538 1 chr4A.!!$F1 537
24 TraesCS1B01G013600 chrUn 293592558 293593400 842 True 483.0 483 77.6670 986 1870 1 chrUn.!!$R1 884

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
561 580 0.033894 GCCTTTTACCCGATTCCCCA 60.034 55.0 0.00 0.0 0.0 4.96 F
564 583 0.393267 TTTTACCCGATTCCCCAGCG 60.393 55.0 0.00 0.0 0.0 5.18 F
599 618 0.940126 GGCGCATCGATTCACAGATT 59.060 50.0 10.83 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 3871 2.745037 GGGGTTGGTGAGTGCGTA 59.255 61.111 0.0 0.0 0.00 4.42 R
2030 4233 4.374689 TGGCTACATACCAAGAAACCAA 57.625 40.909 0.0 0.0 33.12 3.67 R
2539 4779 5.964758 ACTGTTTTGAGAGAACATTTTGCA 58.035 33.333 0.0 0.0 36.51 4.08 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
177 181 3.552384 AACAAGGACGCCGGACCA 61.552 61.111 5.05 0.00 0.00 4.02
549 568 4.104183 CGGGGGAGCGGCCTTTTA 62.104 66.667 0.00 0.00 36.66 1.52
550 569 2.439701 GGGGGAGCGGCCTTTTAC 60.440 66.667 0.00 0.00 36.66 2.01
551 570 2.439701 GGGGAGCGGCCTTTTACC 60.440 66.667 0.00 0.00 36.66 2.85
552 571 2.439701 GGGAGCGGCCTTTTACCC 60.440 66.667 0.00 2.74 36.66 3.69
553 572 2.822701 GGAGCGGCCTTTTACCCG 60.823 66.667 0.00 0.00 46.94 5.28
556 575 0.746923 GAGCGGCCTTTTACCCGATT 60.747 55.000 0.00 0.00 44.08 3.34
557 576 2.670761 GAGCGGCCTTTTACCCGATTC 61.671 57.143 0.00 0.00 44.08 2.52
559 578 2.803203 GGCCTTTTACCCGATTCCC 58.197 57.895 0.00 0.00 0.00 3.97
560 579 0.754217 GGCCTTTTACCCGATTCCCC 60.754 60.000 0.00 0.00 0.00 4.81
561 580 0.033894 GCCTTTTACCCGATTCCCCA 60.034 55.000 0.00 0.00 0.00 4.96
562 581 2.022238 GCCTTTTACCCGATTCCCCAG 61.022 57.143 0.00 0.00 0.00 4.45
563 582 1.389555 CTTTTACCCGATTCCCCAGC 58.610 55.000 0.00 0.00 0.00 4.85
564 583 0.393267 TTTTACCCGATTCCCCAGCG 60.393 55.000 0.00 0.00 0.00 5.18
565 584 2.260088 TTTACCCGATTCCCCAGCGG 62.260 60.000 0.00 0.00 44.42 5.52
592 611 3.706668 GGAGCGGCGCATCGATTC 61.707 66.667 35.02 20.77 0.00 2.52
593 612 2.961721 GAGCGGCGCATCGATTCA 60.962 61.111 35.02 0.00 0.00 2.57
594 613 3.215606 GAGCGGCGCATCGATTCAC 62.216 63.158 35.02 9.17 0.00 3.18
595 614 3.563088 GCGGCGCATCGATTCACA 61.563 61.111 29.21 0.00 0.00 3.58
596 615 2.622629 CGGCGCATCGATTCACAG 59.377 61.111 10.83 0.00 0.00 3.66
597 616 1.878069 CGGCGCATCGATTCACAGA 60.878 57.895 10.83 0.00 0.00 3.41
598 617 1.217585 CGGCGCATCGATTCACAGAT 61.218 55.000 10.83 0.00 0.00 2.90
599 618 0.940126 GGCGCATCGATTCACAGATT 59.060 50.000 10.83 0.00 0.00 2.40
600 619 1.070309 GGCGCATCGATTCACAGATTC 60.070 52.381 10.83 0.00 0.00 2.52
601 620 1.594397 GCGCATCGATTCACAGATTCA 59.406 47.619 0.30 0.00 0.00 2.57
602 621 2.030823 GCGCATCGATTCACAGATTCAA 59.969 45.455 0.30 0.00 0.00 2.69
603 622 3.601356 CGCATCGATTCACAGATTCAAC 58.399 45.455 0.00 0.00 0.00 3.18
604 623 3.601356 GCATCGATTCACAGATTCAACG 58.399 45.455 0.00 0.00 0.00 4.10
605 624 3.544834 GCATCGATTCACAGATTCAACGG 60.545 47.826 0.00 0.00 0.00 4.44
606 625 1.999735 TCGATTCACAGATTCAACGGC 59.000 47.619 0.00 0.00 0.00 5.68
607 626 1.267038 CGATTCACAGATTCAACGGCG 60.267 52.381 4.80 4.80 0.00 6.46
619 638 1.086696 CAACGGCGATGAATCCTTGT 58.913 50.000 16.62 0.00 0.00 3.16
691 713 2.636830 GAAAATCTAGGCTGCTGCTCA 58.363 47.619 15.64 2.75 39.59 4.26
736 758 7.990886 TGTAAAGATAAGAATGGGCGTCTAATT 59.009 33.333 0.00 0.00 0.00 1.40
845 905 2.959030 TGTGATCTCCGAGGGTTGATAG 59.041 50.000 0.00 0.00 0.00 2.08
862 926 7.275920 GGTTGATAGATGTACAAGGAATCAGT 58.724 38.462 0.00 0.00 0.00 3.41
897 961 9.031537 TGTAGTTGTCTATCCTAACTGAAATGA 57.968 33.333 0.00 0.00 36.22 2.57
991 1055 5.531122 TGGAACGAATATGCTAGCTAGTT 57.469 39.130 21.62 12.23 0.00 2.24
1048 1115 2.959030 TCTCTCACACAGCTAACACACT 59.041 45.455 0.00 0.00 0.00 3.55
1102 1192 4.219115 CCTCCTAGCTACCATCTTCTTCA 58.781 47.826 0.00 0.00 0.00 3.02
1124 1217 2.158755 GCCAGCCAAAATCCTAGCTAGA 60.159 50.000 22.70 8.71 33.33 2.43
1131 1224 5.136105 CCAAAATCCTAGCTAGAAATGGCT 58.864 41.667 22.70 0.00 41.92 4.75
1332 1425 4.318332 CATCAGAGTTTGGTCTAACTGCA 58.682 43.478 2.82 0.00 38.43 4.41
1733 3871 3.206150 GCACGTGGGATCATCAAGTATT 58.794 45.455 18.88 0.00 0.00 1.89
1742 3880 5.289595 GGATCATCAAGTATTACGCACTCA 58.710 41.667 0.00 0.00 0.00 3.41
1802 3941 6.791887 ATATCCATGCATTCTACGTCAAAG 57.208 37.500 0.00 0.00 0.00 2.77
2030 4233 9.479549 ACAAATTTCCATCAGTACCTTAATGAT 57.520 29.630 0.00 0.00 43.48 2.45
2050 4253 4.947388 TGATTGGTTTCTTGGTATGTAGCC 59.053 41.667 0.00 0.00 0.00 3.93
2166 4376 3.118738 ACGGGTAGCTATGAAAGGAACTG 60.119 47.826 0.00 0.00 40.86 3.16
2174 4384 4.938226 GCTATGAAAGGAACTGTACAAGCT 59.062 41.667 0.00 0.00 40.86 3.74
2183 4393 5.594317 AGGAACTGTACAAGCTTTGTCAATT 59.406 36.000 0.00 0.00 39.97 2.32
2455 4695 5.009110 TGTTCGAAATTGGTGCAATTACTCA 59.991 36.000 0.00 0.00 42.32 3.41
2481 4721 9.349713 ACTTAAACACAAGAGAACAAATGGATA 57.650 29.630 0.00 0.00 0.00 2.59
2523 4763 9.678260 AAGAACATTTCTATTCTGATTGTAGCT 57.322 29.630 0.00 0.00 39.61 3.32
2681 4943 1.309499 ACCACCACCAACACAACACG 61.309 55.000 0.00 0.00 0.00 4.49
2715 4981 4.404185 AGTTTTTAAGGCATCCCTCCTT 57.596 40.909 0.00 0.00 41.90 3.36
2773 5040 4.339429 CAACACAACGAAGACACGAAAAT 58.661 39.130 0.00 0.00 37.03 1.82
2793 5060 9.227490 CGAAAATACACAGTGTTTTACAATGAA 57.773 29.630 12.53 0.00 46.01 2.57
2861 5129 8.061304 ACTAATGGAATAGACACAATCCCAAAT 58.939 33.333 0.00 0.00 0.00 2.32
2899 5169 2.689175 GGGGAATCCATGGCACCA 59.311 61.111 6.96 0.00 35.00 4.17
2930 5200 6.524101 TCTGGCTTGAAAAACTTTAGTTGT 57.476 33.333 0.00 0.00 38.44 3.32
2948 5219 3.685139 TGTGACTCATTCCAGAAGTCC 57.315 47.619 0.00 0.00 0.00 3.85
2968 5239 4.883300 CGTCCCGTCGTAGCGCTC 62.883 72.222 16.34 4.78 0.00 5.03
2983 5254 1.959226 GCTCGTTTTGCGTCCTCCA 60.959 57.895 0.00 0.00 42.13 3.86
3003 5325 2.409064 TCACCTACAGGGAACTCCAA 57.591 50.000 0.00 0.00 40.21 3.53
3010 5332 5.672194 ACCTACAGGGAACTCCAATCATTAT 59.328 40.000 0.00 0.00 40.21 1.28
3012 5334 6.712547 CCTACAGGGAACTCCAATCATTATTC 59.287 42.308 0.00 0.00 40.21 1.75
3041 5363 6.808321 AGCTACCCTAAACATGATAACAGA 57.192 37.500 0.00 0.00 0.00 3.41
3073 5395 5.138125 AGGCCACTTGTGATTAAAACATG 57.862 39.130 5.01 0.00 0.00 3.21
3082 5404 9.979578 ACTTGTGATTAAAACATGCTAAATTCA 57.020 25.926 0.00 0.00 0.00 2.57
3085 5407 8.910666 TGTGATTAAAACATGCTAAATTCAACG 58.089 29.630 0.00 0.00 0.00 4.10
3096 5418 4.742659 GCTAAATTCAACGCTTTCCAAACA 59.257 37.500 0.00 0.00 0.00 2.83
3105 5427 6.640499 TCAACGCTTTCCAAACAATTATCAAG 59.360 34.615 0.00 0.00 0.00 3.02
3107 5429 5.242838 ACGCTTTCCAAACAATTATCAAGGA 59.757 36.000 0.00 0.00 0.00 3.36
3128 5450 6.194235 AGGAAAACCAGCAACATATTATGGA 58.806 36.000 8.48 0.00 34.99 3.41
3132 5454 8.776376 AAAACCAGCAACATATTATGGAAAAG 57.224 30.769 8.48 0.00 34.99 2.27
3182 5504 6.544928 AATTCATTGGGTATTGAAACCTCC 57.455 37.500 0.00 0.00 39.65 4.30
3185 5507 5.261216 TCATTGGGTATTGAAACCTCCTTC 58.739 41.667 0.00 0.00 39.65 3.46
3223 6811 8.141268 TCATTGAAACCAACTTTGTTATTCCTC 58.859 33.333 0.00 0.00 0.00 3.71
3227 6815 3.181437 ACCAACTTTGTTATTCCTCGGGT 60.181 43.478 0.00 0.00 0.00 5.28
3229 6817 4.069304 CAACTTTGTTATTCCTCGGGTCA 58.931 43.478 0.00 0.00 0.00 4.02
3230 6818 4.569719 ACTTTGTTATTCCTCGGGTCAT 57.430 40.909 0.00 0.00 0.00 3.06
3242 6830 3.016736 CTCGGGTCATTATTTTGTGCCT 58.983 45.455 0.00 0.00 0.00 4.75
3243 6831 2.752354 TCGGGTCATTATTTTGTGCCTG 59.248 45.455 0.00 0.00 0.00 4.85
3253 6841 1.981256 TTTGTGCCTGAAGGAGGTTC 58.019 50.000 0.00 0.00 44.97 3.62
3264 6852 3.181440 TGAAGGAGGTTCTGCAGTGAAAT 60.181 43.478 14.67 0.00 35.99 2.17
3265 6853 3.515602 AGGAGGTTCTGCAGTGAAATT 57.484 42.857 14.67 0.00 0.00 1.82
3266 6854 3.837355 AGGAGGTTCTGCAGTGAAATTT 58.163 40.909 14.67 0.00 0.00 1.82
3267 6855 4.218312 AGGAGGTTCTGCAGTGAAATTTT 58.782 39.130 14.67 0.00 0.00 1.82
3269 6857 4.984785 GGAGGTTCTGCAGTGAAATTTTTC 59.015 41.667 14.67 0.00 37.69 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
543 562 2.022238 GCTGGGGAATCGGGTAAAAGG 61.022 57.143 0.00 0.00 0.00 3.11
544 563 1.389555 GCTGGGGAATCGGGTAAAAG 58.610 55.000 0.00 0.00 0.00 2.27
545 564 0.393267 CGCTGGGGAATCGGGTAAAA 60.393 55.000 0.00 0.00 0.00 1.52
546 565 1.222387 CGCTGGGGAATCGGGTAAA 59.778 57.895 0.00 0.00 0.00 2.01
547 566 2.737881 CCGCTGGGGAATCGGGTAA 61.738 63.158 4.46 0.00 39.52 2.85
548 567 3.158648 CCGCTGGGGAATCGGGTA 61.159 66.667 4.46 0.00 39.52 3.69
575 594 3.706668 GAATCGATGCGCCGCTCC 61.707 66.667 11.67 0.35 0.00 4.70
576 595 2.961721 TGAATCGATGCGCCGCTC 60.962 61.111 11.67 4.49 0.00 5.03
577 596 3.264897 GTGAATCGATGCGCCGCT 61.265 61.111 11.67 0.00 0.00 5.52
578 597 3.497407 CTGTGAATCGATGCGCCGC 62.497 63.158 14.42 0.00 0.00 6.53
579 598 1.217585 ATCTGTGAATCGATGCGCCG 61.218 55.000 14.42 8.23 0.00 6.46
580 599 0.940126 AATCTGTGAATCGATGCGCC 59.060 50.000 14.42 0.16 0.00 6.53
581 600 1.594397 TGAATCTGTGAATCGATGCGC 59.406 47.619 10.19 10.19 0.00 6.09
582 601 3.601356 GTTGAATCTGTGAATCGATGCG 58.399 45.455 0.00 0.00 0.00 4.73
583 602 3.544834 CCGTTGAATCTGTGAATCGATGC 60.545 47.826 0.00 0.00 0.00 3.91
584 603 3.544834 GCCGTTGAATCTGTGAATCGATG 60.545 47.826 0.00 0.00 0.00 3.84
585 604 2.609459 GCCGTTGAATCTGTGAATCGAT 59.391 45.455 0.00 0.00 0.00 3.59
586 605 1.999735 GCCGTTGAATCTGTGAATCGA 59.000 47.619 0.00 0.00 0.00 3.59
587 606 1.267038 CGCCGTTGAATCTGTGAATCG 60.267 52.381 0.00 0.00 0.00 3.34
588 607 1.999735 TCGCCGTTGAATCTGTGAATC 59.000 47.619 0.00 0.00 0.00 2.52
589 608 2.093306 TCGCCGTTGAATCTGTGAAT 57.907 45.000 0.00 0.00 0.00 2.57
590 609 1.731709 CATCGCCGTTGAATCTGTGAA 59.268 47.619 0.00 0.00 0.00 3.18
591 610 1.067213 TCATCGCCGTTGAATCTGTGA 60.067 47.619 0.00 0.00 0.00 3.58
592 611 1.358877 TCATCGCCGTTGAATCTGTG 58.641 50.000 0.00 0.00 0.00 3.66
593 612 2.093306 TTCATCGCCGTTGAATCTGT 57.907 45.000 6.51 0.00 0.00 3.41
597 616 2.332063 AGGATTCATCGCCGTTGAAT 57.668 45.000 20.04 20.04 44.40 2.57
598 617 1.737236 CAAGGATTCATCGCCGTTGAA 59.263 47.619 12.47 12.47 37.49 2.69
599 618 1.338674 ACAAGGATTCATCGCCGTTGA 60.339 47.619 0.00 0.00 0.00 3.18
600 619 1.086696 ACAAGGATTCATCGCCGTTG 58.913 50.000 0.00 0.00 0.00 4.10
601 620 2.684001 TACAAGGATTCATCGCCGTT 57.316 45.000 0.00 0.00 0.00 4.44
602 621 2.910688 ATACAAGGATTCATCGCCGT 57.089 45.000 0.00 0.00 0.00 5.68
603 622 3.559655 TCAAATACAAGGATTCATCGCCG 59.440 43.478 0.00 0.00 0.00 6.46
604 623 5.066505 AGTTCAAATACAAGGATTCATCGCC 59.933 40.000 0.00 0.00 0.00 5.54
605 624 6.124088 AGTTCAAATACAAGGATTCATCGC 57.876 37.500 0.00 0.00 0.00 4.58
606 625 8.023128 ACAAAGTTCAAATACAAGGATTCATCG 58.977 33.333 0.00 0.00 0.00 3.84
645 664 0.577269 GACAACGAGCACACTGTCAC 59.423 55.000 7.45 0.00 38.43 3.67
691 713 9.090103 TCTTTACATCTAATTGTATCTCCGGAT 57.910 33.333 3.57 0.00 32.39 4.18
736 758 6.151691 GCAGCATTGACAAAGACTAAAATGA 58.848 36.000 0.00 0.00 0.00 2.57
845 905 5.237815 TGTGTGACTGATTCCTTGTACATC 58.762 41.667 0.00 0.00 0.00 3.06
991 1055 4.404715 GGGTACTATTTGTAGTGCTCCAGA 59.595 45.833 0.00 0.00 33.92 3.86
1048 1115 4.402056 AACTGACTCTTTCCTTTGTCGA 57.598 40.909 0.00 0.00 32.64 4.20
1102 1192 0.627986 AGCTAGGATTTTGGCTGGCT 59.372 50.000 2.00 0.00 33.50 4.75
1131 1224 3.039011 CAGGACTAAAAGGCTAGGGCTA 58.961 50.000 0.00 0.00 37.50 3.93
1332 1425 1.991121 TCACAGTCCAGTCGGTAACT 58.009 50.000 0.00 0.00 39.44 2.24
1733 3871 2.745037 GGGGTTGGTGAGTGCGTA 59.255 61.111 0.00 0.00 0.00 4.42
1802 3941 8.480643 AGTTGAATGTATGTACTTACAGAAGC 57.519 34.615 21.79 13.61 39.92 3.86
1853 4007 7.710907 TGGACAAGATATACATGCTAGAAACAC 59.289 37.037 0.00 0.00 0.00 3.32
2030 4233 4.374689 TGGCTACATACCAAGAAACCAA 57.625 40.909 0.00 0.00 33.12 3.67
2235 4445 7.052873 ACAAACAAATGGACATGGATTTTTGA 58.947 30.769 15.74 0.00 0.00 2.69
2455 4695 7.639113 TCCATTTGTTCTCTTGTGTTTAAGT 57.361 32.000 0.00 0.00 0.00 2.24
2539 4779 5.964758 ACTGTTTTGAGAGAACATTTTGCA 58.035 33.333 0.00 0.00 36.51 4.08
2641 4903 4.435784 GGTTGCGTTTTGGTTGTAAAAACC 60.436 41.667 0.15 0.15 42.09 3.27
2681 4943 5.860182 GCCTTAAAAACTTAATTCCGTGTCC 59.140 40.000 0.00 0.00 0.00 4.02
2715 4981 0.606401 GTTGCTCAGCTAGGGTTGCA 60.606 55.000 0.00 0.00 0.00 4.08
2738 5004 2.351706 TGTGTTGGTTGTTCCCCTAC 57.648 50.000 0.00 0.00 34.77 3.18
2773 5040 6.915300 GCATGTTCATTGTAAAACACTGTGTA 59.085 34.615 14.69 0.00 38.14 2.90
2793 5060 2.342650 GGTGTTGGCATCGGCATGT 61.343 57.895 0.00 0.00 43.71 3.21
2845 5112 5.710099 GGACTTGAATTTGGGATTGTGTCTA 59.290 40.000 0.00 0.00 0.00 2.59
2861 5129 1.004745 GGCTGGAAGATGGGACTTGAA 59.995 52.381 0.00 0.00 34.07 2.69
2930 5200 2.027745 GCAGGACTTCTGGAATGAGTCA 60.028 50.000 0.00 0.00 43.54 3.41
2983 5254 2.642171 TGGAGTTCCCTGTAGGTGAT 57.358 50.000 0.00 0.00 36.75 3.06
3003 5325 8.506196 TTAGGGTAGCTTACTGGAATAATGAT 57.494 34.615 0.00 0.00 0.00 2.45
3010 5332 5.486063 TCATGTTTAGGGTAGCTTACTGGAA 59.514 40.000 0.00 0.00 0.00 3.53
3012 5334 5.353394 TCATGTTTAGGGTAGCTTACTGG 57.647 43.478 0.00 0.00 0.00 4.00
3041 5363 0.036010 CAAGTGGCCTTCTGATCCGT 60.036 55.000 3.32 0.00 0.00 4.69
3069 5391 4.022416 TGGAAAGCGTTGAATTTAGCATGT 60.022 37.500 0.00 0.00 0.00 3.21
3073 5395 4.742659 TGTTTGGAAAGCGTTGAATTTAGC 59.257 37.500 0.00 0.00 0.00 3.09
3082 5404 5.925969 CCTTGATAATTGTTTGGAAAGCGTT 59.074 36.000 0.00 0.00 0.00 4.84
3083 5405 5.242838 TCCTTGATAATTGTTTGGAAAGCGT 59.757 36.000 0.00 0.00 0.00 5.07
3085 5407 7.961325 TTTCCTTGATAATTGTTTGGAAAGC 57.039 32.000 10.70 0.00 37.24 3.51
3096 5418 6.418057 TGTTGCTGGTTTTCCTTGATAATT 57.582 33.333 0.00 0.00 41.38 1.40
3105 5427 6.463995 TCCATAATATGTTGCTGGTTTTCC 57.536 37.500 0.00 0.00 41.14 3.13
3107 5429 7.823799 CCTTTTCCATAATATGTTGCTGGTTTT 59.176 33.333 0.00 0.00 0.00 2.43
3128 5450 7.027874 TGATTGACTAATGGTCCTACCTTTT 57.972 36.000 2.94 0.00 43.89 2.27
3132 5454 7.062749 TGTATGATTGACTAATGGTCCTACC 57.937 40.000 0.00 0.00 43.89 3.18
3144 5466 9.425248 ACCCAATGAATTTATGTATGATTGACT 57.575 29.630 0.00 0.00 0.00 3.41
3169 5491 9.543783 AGTAATTATCGAAGGAGGTTTCAATAC 57.456 33.333 0.00 0.00 0.00 1.89
3185 5507 9.840427 AGTTGGTTTCAATGAAAGTAATTATCG 57.160 29.630 8.88 0.00 35.10 2.92
3213 6801 6.887545 ACAAAATAATGACCCGAGGAATAACA 59.112 34.615 0.00 0.00 0.00 2.41
3223 6811 2.752354 TCAGGCACAAAATAATGACCCG 59.248 45.455 0.00 0.00 0.00 5.28
3227 6815 4.706476 CCTCCTTCAGGCACAAAATAATGA 59.294 41.667 0.00 0.00 34.56 2.57
3242 6830 1.423584 TCACTGCAGAACCTCCTTCA 58.576 50.000 23.35 0.00 0.00 3.02
3243 6831 2.550830 TTCACTGCAGAACCTCCTTC 57.449 50.000 23.35 0.00 0.00 3.46
3281 6869 7.388224 TCAGTATTTACTTGTATGACGGCAAAA 59.612 33.333 0.00 0.00 33.46 2.44
3283 6871 6.399743 TCAGTATTTACTTGTATGACGGCAA 58.600 36.000 0.00 0.00 33.46 4.52


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

AutoCloner maintained by Alex Coulton.