Multiple sequence alignment - TraesCS2B01G264000

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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 TraesCS2B01G264000 chr2B 100.000 3536 0 0 1 3536 356581230 356584765 0.000000e+00 6530.0
1 TraesCS2B01G264000 chr2A 90.991 1110 54 14 1605 2677 378848787 378849887 0.000000e+00 1454.0
2 TraesCS2B01G264000 chr2A 89.722 720 45 12 310 1017 378846226 378846928 0.000000e+00 893.0
3 TraesCS2B01G264000 chr2A 76.960 829 151 19 2713 3536 183332040 183331247 1.510000e-118 436.0
4 TraesCS2B01G264000 chr2A 88.779 303 21 3 9 311 378839121 378839410 3.360000e-95 359.0
5 TraesCS2B01G264000 chr2A 93.421 228 12 1 1095 1319 378846950 378847177 5.660000e-88 335.0
6 TraesCS2B01G264000 chr2A 85.577 312 11 8 1310 1613 378848270 378848555 2.670000e-76 296.0
7 TraesCS2B01G264000 chr2D 90.527 1119 52 23 508 1599 301760992 301762083 0.000000e+00 1430.0
8 TraesCS2B01G264000 chr2D 95.163 827 31 3 2711 3536 446264925 446265743 0.000000e+00 1297.0
9 TraesCS2B01G264000 chr2D 89.600 1000 47 24 1605 2563 301762427 301763410 0.000000e+00 1218.0
10 TraesCS2B01G264000 chr2D 82.139 823 126 10 2713 3531 378733599 378732794 0.000000e+00 686.0
11 TraesCS2B01G264000 chr2D 90.272 514 38 6 7 515 301755804 301756310 0.000000e+00 662.0
12 TraesCS2B01G264000 chr2D 95.798 119 5 0 2559 2677 301816829 301816947 3.600000e-45 193.0
13 TraesCS2B01G264000 chr3D 94.075 827 40 3 2711 3536 19797436 19796618 0.000000e+00 1247.0
14 TraesCS2B01G264000 chr3A 94.987 758 38 0 2779 3536 621830170 621830927 0.000000e+00 1190.0
15 TraesCS2B01G264000 chr7A 92.319 677 52 0 2860 3536 732740963 732741639 0.000000e+00 963.0
16 TraesCS2B01G264000 chr4D 94.701 585 31 0 2952 3536 110808930 110809514 0.000000e+00 909.0
17 TraesCS2B01G264000 chr4D 83.262 699 105 7 2836 3531 464519345 464520034 1.790000e-177 632.0
18 TraesCS2B01G264000 chr4D 91.364 220 8 3 2705 2923 110808728 110808937 1.240000e-74 291.0
19 TraesCS2B01G264000 chr5D 81.283 764 129 13 2776 3536 179648046 179647294 1.090000e-169 606.0
20 TraesCS2B01G264000 chr1D 77.548 775 146 19 2770 3535 299280394 299279639 3.240000e-120 442.0
21 TraesCS2B01G264000 chr5A 75.000 320 59 17 165 469 608271365 608271678 1.030000e-25 128.0
22 TraesCS2B01G264000 chr1B 96.970 33 1 0 403 435 314574046 314574078 4.930000e-04 56.5


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 TraesCS2B01G264000 chr2B 356581230 356584765 3535 False 6530.0 6530 100.00000 1 3536 1 chr2B.!!$F1 3535
1 TraesCS2B01G264000 chr2A 378846226 378849887 3661 False 744.5 1454 89.92775 310 2677 4 chr2A.!!$F2 2367
2 TraesCS2B01G264000 chr2A 183331247 183332040 793 True 436.0 436 76.96000 2713 3536 1 chr2A.!!$R1 823
3 TraesCS2B01G264000 chr2D 301760992 301763410 2418 False 1324.0 1430 90.06350 508 2563 2 chr2D.!!$F4 2055
4 TraesCS2B01G264000 chr2D 446264925 446265743 818 False 1297.0 1297 95.16300 2711 3536 1 chr2D.!!$F3 825
5 TraesCS2B01G264000 chr2D 378732794 378733599 805 True 686.0 686 82.13900 2713 3531 1 chr2D.!!$R1 818
6 TraesCS2B01G264000 chr2D 301755804 301756310 506 False 662.0 662 90.27200 7 515 1 chr2D.!!$F1 508
7 TraesCS2B01G264000 chr3D 19796618 19797436 818 True 1247.0 1247 94.07500 2711 3536 1 chr3D.!!$R1 825
8 TraesCS2B01G264000 chr3A 621830170 621830927 757 False 1190.0 1190 94.98700 2779 3536 1 chr3A.!!$F1 757
9 TraesCS2B01G264000 chr7A 732740963 732741639 676 False 963.0 963 92.31900 2860 3536 1 chr7A.!!$F1 676
10 TraesCS2B01G264000 chr4D 464519345 464520034 689 False 632.0 632 83.26200 2836 3531 1 chr4D.!!$F1 695
11 TraesCS2B01G264000 chr4D 110808728 110809514 786 False 600.0 909 93.03250 2705 3536 2 chr4D.!!$F2 831
12 TraesCS2B01G264000 chr5D 179647294 179648046 752 True 606.0 606 81.28300 2776 3536 1 chr5D.!!$R1 760
13 TraesCS2B01G264000 chr1D 299279639 299280394 755 True 442.0 442 77.54800 2770 3535 1 chr1D.!!$R1 765

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
120 121 0.034896 GATGTTGGTGGTCGGAGTGT 59.965 55.0 0.0 0.0 0.0 3.55 F
1003 1035 0.523966 AGAGAGAGCTGCGTGTGTAC 59.476 55.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1025 1057 0.242286 CGAGACCAGATATCAGCCGG 59.758 60.0 5.32 0.0 0.0 6.13 R
2687 4239 0.030603 AGAGGAGGGAGATGGGGAAC 60.031 60.0 0.00 0.0 0.0 3.62 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
27 28 3.195661 GGTGGATCACCGATGAAAGTAC 58.804 50.000 1.01 0.00 44.95 2.73
58 59 1.063806 CCGAGAGTTTGAGCAGTTCG 58.936 55.000 0.00 0.00 0.00 3.95
77 78 1.603172 CGAGTGTGTTGACCTCCTGAC 60.603 57.143 0.00 0.00 0.00 3.51
78 79 1.412710 GAGTGTGTTGACCTCCTGACA 59.587 52.381 0.00 0.00 0.00 3.58
87 88 1.367471 CCTCCTGACACGTGAGCAA 59.633 57.895 25.01 5.09 0.00 3.91
91 92 1.073964 CCTGACACGTGAGCAATGAG 58.926 55.000 25.01 2.20 0.00 2.90
92 93 1.073964 CTGACACGTGAGCAATGAGG 58.926 55.000 25.01 4.00 0.00 3.86
93 94 0.392706 TGACACGTGAGCAATGAGGT 59.607 50.000 25.01 0.00 0.00 3.85
120 121 0.034896 GATGTTGGTGGTCGGAGTGT 59.965 55.000 0.00 0.00 0.00 3.55
138 139 1.070914 TGTCGTGAGTTGCATTGGGTA 59.929 47.619 0.00 0.00 0.00 3.69
175 176 2.082231 GAGTGCATGCATCTTCACAGT 58.918 47.619 25.64 0.00 32.25 3.55
205 206 1.404748 GTTCCGGGTCTGCTACTCTAC 59.595 57.143 0.00 0.00 0.00 2.59
217 218 3.196463 GCTACTCTACTAGCAGTCACGA 58.804 50.000 0.00 0.00 39.26 4.35
259 260 2.224066 GGTGGGATGATGACTAACTCGG 60.224 54.545 0.00 0.00 0.00 4.63
272 273 3.836562 ACTAACTCGGTGGAACAGGTTAT 59.163 43.478 0.00 0.00 41.80 1.89
292 293 8.141268 AGGTTATCGTTGATTTGTGTGAATTTT 58.859 29.630 0.00 0.00 0.00 1.82
294 295 6.768029 ATCGTTGATTTGTGTGAATTTTGG 57.232 33.333 0.00 0.00 0.00 3.28
375 381 4.329462 TGTTTTGGTGGGCTTTGTATTC 57.671 40.909 0.00 0.00 0.00 1.75
381 387 2.297880 GGTGGGCTTTGTATTCGGTTTT 59.702 45.455 0.00 0.00 0.00 2.43
383 389 2.959707 TGGGCTTTGTATTCGGTTTTGT 59.040 40.909 0.00 0.00 0.00 2.83
386 392 4.210328 GGGCTTTGTATTCGGTTTTGTTTG 59.790 41.667 0.00 0.00 0.00 2.93
435 442 8.557029 ACAACCTTCTTCTTAGTTAATGAAACG 58.443 33.333 0.00 0.00 43.29 3.60
436 443 7.130303 ACCTTCTTCTTAGTTAATGAAACGC 57.870 36.000 0.00 0.00 43.29 4.84
464 471 3.063861 GCTTTTGCCTTGTGTTTTGGAAG 59.936 43.478 0.00 0.00 40.15 3.46
611 619 0.668706 CACTGAACTCCTGGACGCAG 60.669 60.000 11.89 11.89 0.00 5.18
650 659 3.304726 GCCGAAAAGAGGTGGAAAAGAAG 60.305 47.826 0.00 0.00 0.00 2.85
660 669 2.616842 GTGGAAAAGAAGCGGAACAGAA 59.383 45.455 0.00 0.00 0.00 3.02
675 684 4.687483 GGAACAGAAATGTCAAAGCAATGG 59.313 41.667 0.00 0.00 0.00 3.16
729 742 2.097299 CACAAATCATGCGCACACAAAC 60.097 45.455 14.90 0.00 0.00 2.93
745 758 3.619038 CACAAACTAAGCCAGCTAGCTAC 59.381 47.826 18.86 12.91 44.11 3.58
799 821 2.585153 GAGCGGAGAAGGTTCCCC 59.415 66.667 0.00 0.00 33.46 4.81
844 869 2.003937 TACAGGAGTACACAGCCACA 57.996 50.000 0.00 0.00 0.00 4.17
845 870 0.681733 ACAGGAGTACACAGCCACAG 59.318 55.000 0.00 0.00 0.00 3.66
983 1013 2.057408 AAGCGGGGCAGAGAGAGAG 61.057 63.158 0.00 0.00 0.00 3.20
984 1014 2.441164 GCGGGGCAGAGAGAGAGA 60.441 66.667 0.00 0.00 0.00 3.10
990 1020 1.490490 GGGCAGAGAGAGAGAGAGAGA 59.510 57.143 0.00 0.00 0.00 3.10
991 1021 2.486191 GGGCAGAGAGAGAGAGAGAGAG 60.486 59.091 0.00 0.00 0.00 3.20
992 1022 2.216898 GCAGAGAGAGAGAGAGAGAGC 58.783 57.143 0.00 0.00 0.00 4.09
995 1025 2.158842 AGAGAGAGAGAGAGAGAGCTGC 60.159 54.545 0.00 0.00 0.00 5.25
1003 1035 0.523966 AGAGAGAGCTGCGTGTGTAC 59.476 55.000 0.00 0.00 0.00 2.90
1030 1062 4.043100 GGCCAAACCCTACCGGCT 62.043 66.667 0.00 0.00 44.27 5.52
1070 1102 2.625790 ACTCTCACGCATATCCTTCCTC 59.374 50.000 0.00 0.00 0.00 3.71
1203 1235 3.797353 GGCGAGATGGGGGAAGCA 61.797 66.667 0.00 0.00 0.00 3.91
1235 1267 1.604023 AGCGGAGGTCGAACTGAGT 60.604 57.895 8.28 0.00 42.43 3.41
1385 2522 6.224665 TCATTTTAATTTGCTCCATCCCTG 57.775 37.500 0.00 0.00 0.00 4.45
1394 2531 1.072806 GCTCCATCCCTGCATGTATCA 59.927 52.381 0.00 0.00 0.00 2.15
1428 2574 6.808321 ACCCTAAGTAGTTAATCATGCTCA 57.192 37.500 0.00 0.00 0.00 4.26
1429 2575 6.583562 ACCCTAAGTAGTTAATCATGCTCAC 58.416 40.000 0.00 0.00 0.00 3.51
1433 2579 7.868415 CCTAAGTAGTTAATCATGCTCACCTAC 59.132 40.741 0.00 0.00 0.00 3.18
1465 2611 4.301628 GTCATCACTGACGATCATGCATA 58.698 43.478 0.00 0.00 42.24 3.14
1467 2613 6.095377 GTCATCACTGACGATCATGCATATA 58.905 40.000 0.00 0.00 42.24 0.86
1468 2614 6.034363 GTCATCACTGACGATCATGCATATAC 59.966 42.308 0.00 0.00 42.24 1.47
1469 2615 5.712152 TCACTGACGATCATGCATATACT 57.288 39.130 0.00 0.00 0.00 2.12
1470 2616 6.089249 TCACTGACGATCATGCATATACTT 57.911 37.500 0.00 0.00 0.00 2.24
1471 2617 7.214467 TCACTGACGATCATGCATATACTTA 57.786 36.000 0.00 0.00 0.00 2.24
1472 2618 7.830739 TCACTGACGATCATGCATATACTTAT 58.169 34.615 0.00 0.00 0.00 1.73
1473 2619 8.956426 TCACTGACGATCATGCATATACTTATA 58.044 33.333 0.00 0.00 0.00 0.98
1474 2620 9.741647 CACTGACGATCATGCATATACTTATAT 57.258 33.333 0.00 0.00 0.00 0.86
1475 2621 9.958234 ACTGACGATCATGCATATACTTATATC 57.042 33.333 0.00 0.00 0.00 1.63
1568 2718 2.851824 CCACGAGTTGTTTTTGCAGTTC 59.148 45.455 0.00 0.00 0.00 3.01
1602 2752 2.286418 GCCAAGAAATAGAATCGGCGTG 60.286 50.000 6.85 0.00 0.00 5.34
1603 2753 2.936498 CCAAGAAATAGAATCGGCGTGT 59.064 45.455 6.85 0.00 0.00 4.49
1604 2754 3.374058 CCAAGAAATAGAATCGGCGTGTT 59.626 43.478 6.85 3.06 0.00 3.32
1605 2755 4.569162 CCAAGAAATAGAATCGGCGTGTTA 59.431 41.667 6.85 0.00 0.00 2.41
1607 2757 5.258456 AGAAATAGAATCGGCGTGTTAGA 57.742 39.130 6.85 0.00 0.00 2.10
1608 2758 5.282510 AGAAATAGAATCGGCGTGTTAGAG 58.717 41.667 6.85 0.00 0.00 2.43
1629 3131 1.620822 CAAAGTCCTTTGTGAGGGGG 58.379 55.000 10.86 0.00 46.31 5.40
1684 3189 4.212425 TGTGTTTATTTCAGCACGTCGATT 59.788 37.500 0.00 0.00 34.86 3.34
1694 3199 1.778334 CACGTCGATTGAGTTGGACA 58.222 50.000 0.00 0.00 0.00 4.02
1724 3234 5.823570 TCCAGTACGGTTGAAATTTCAGAAA 59.176 36.000 19.64 4.05 38.61 2.52
1726 3236 6.416750 CCAGTACGGTTGAAATTTCAGAAAAC 59.583 38.462 19.64 14.88 38.61 2.43
1729 3239 8.557029 AGTACGGTTGAAATTTCAGAAAACTAG 58.443 33.333 19.64 14.65 38.61 2.57
1730 3240 6.735130 ACGGTTGAAATTTCAGAAAACTAGG 58.265 36.000 19.64 11.28 38.61 3.02
1852 3362 6.931838 CACATTTAGTCTTGGTGGAGTAGTA 58.068 40.000 0.00 0.00 0.00 1.82
1853 3363 7.036220 CACATTTAGTCTTGGTGGAGTAGTAG 58.964 42.308 0.00 0.00 0.00 2.57
1854 3364 6.154706 ACATTTAGTCTTGGTGGAGTAGTAGG 59.845 42.308 0.00 0.00 0.00 3.18
1915 3428 5.587289 GCGATCATCTCTTAGTCAGACTTT 58.413 41.667 8.80 0.00 0.00 2.66
1975 3492 6.494835 AGCAATTAGTCAGAAAAAGGGACAAT 59.505 34.615 0.00 0.00 34.04 2.71
1986 3503 4.510167 AAAGGGACAATCCTCCATACAG 57.490 45.455 0.00 0.00 36.57 2.74
2040 3557 6.506827 CGATCGCACCAAAAATCAAAATGATC 60.507 38.462 0.26 0.00 35.76 2.92
2112 3631 2.661537 CGCAGACGTGGCTGTGAA 60.662 61.111 10.78 0.00 46.56 3.18
2167 3686 3.686227 AGGGAAATCATAACCATGGCA 57.314 42.857 13.04 0.00 32.61 4.92
2255 3780 2.683152 GCTCATCAGAATCCAAGCCAGT 60.683 50.000 0.00 0.00 0.00 4.00
2455 4007 0.696501 AGGCCGGTGGTTAAAGACAT 59.303 50.000 1.90 0.00 0.00 3.06
2464 4016 5.634859 CGGTGGTTAAAGACATTTACGTACT 59.365 40.000 0.00 0.00 30.58 2.73
2465 4017 6.146021 CGGTGGTTAAAGACATTTACGTACTT 59.854 38.462 0.00 0.00 30.58 2.24
2469 4021 9.195411 TGGTTAAAGACATTTACGTACTTGTAG 57.805 33.333 9.02 0.00 30.58 2.74
2538 4090 5.125097 AGCATGAGATTGGAGTGTTCAAATC 59.875 40.000 0.00 0.00 42.02 2.17
2589 4141 8.196378 ACTAGTTAGTTTCTTGGAGATCAACT 57.804 34.615 0.00 0.00 32.06 3.16
2602 4154 4.999939 CAACTTGTTGGCGGCCGC 63.000 66.667 41.63 41.63 41.06 6.53
2614 4166 0.383231 GCGGCCGCTAGAGTAACTTA 59.617 55.000 41.71 0.00 38.26 2.24
2623 4175 4.738740 CGCTAGAGTAACTTATTCGTTGGG 59.261 45.833 0.00 0.00 0.00 4.12
2627 4179 7.761249 GCTAGAGTAACTTATTCGTTGGGTAAA 59.239 37.037 0.00 0.00 0.00 2.01
2677 4229 9.791838 GTACTTAATTCAATTTTTCTTTTGCGG 57.208 29.630 0.00 0.00 0.00 5.69
2678 4230 7.351981 ACTTAATTCAATTTTTCTTTTGCGGC 58.648 30.769 0.00 0.00 0.00 6.53
2679 4231 4.747540 ATTCAATTTTTCTTTTGCGGCC 57.252 36.364 0.00 0.00 0.00 6.13
2680 4232 2.131183 TCAATTTTTCTTTTGCGGCCG 58.869 42.857 24.05 24.05 0.00 6.13
2681 4233 1.194322 CAATTTTTCTTTTGCGGCCGG 59.806 47.619 29.38 10.00 0.00 6.13
2682 4234 0.320334 ATTTTTCTTTTGCGGCCGGG 60.320 50.000 29.38 0.00 0.00 5.73
2683 4235 2.980213 TTTTTCTTTTGCGGCCGGGC 62.980 55.000 29.38 20.04 0.00 6.13
2686 4238 4.067913 CTTTTGCGGCCGGGCATT 62.068 61.111 29.38 0.00 43.52 3.56
2687 4239 4.370066 TTTTGCGGCCGGGCATTG 62.370 61.111 29.38 13.13 43.52 2.82
2695 4247 2.043046 CCGGGCATTGTTCCCCAT 60.043 61.111 0.00 0.00 41.57 4.00
2696 4248 2.127232 CCGGGCATTGTTCCCCATC 61.127 63.158 0.00 0.00 41.57 3.51
2697 4249 1.076777 CGGGCATTGTTCCCCATCT 60.077 57.895 0.00 0.00 41.57 2.90
2698 4250 1.103398 CGGGCATTGTTCCCCATCTC 61.103 60.000 0.00 0.00 41.57 2.75
2699 4251 0.756815 GGGCATTGTTCCCCATCTCC 60.757 60.000 0.00 0.00 41.13 3.71
2700 4252 0.756815 GGCATTGTTCCCCATCTCCC 60.757 60.000 0.00 0.00 0.00 4.30
2701 4253 0.259938 GCATTGTTCCCCATCTCCCT 59.740 55.000 0.00 0.00 0.00 4.20
2702 4254 1.752084 GCATTGTTCCCCATCTCCCTC 60.752 57.143 0.00 0.00 0.00 4.30
2703 4255 1.133668 CATTGTTCCCCATCTCCCTCC 60.134 57.143 0.00 0.00 0.00 4.30
2704 4256 0.121197 TTGTTCCCCATCTCCCTCCT 59.879 55.000 0.00 0.00 0.00 3.69
2705 4257 0.326618 TGTTCCCCATCTCCCTCCTC 60.327 60.000 0.00 0.00 0.00 3.71
2706 4258 0.030603 GTTCCCCATCTCCCTCCTCT 60.031 60.000 0.00 0.00 0.00 3.69
2707 4259 0.266152 TTCCCCATCTCCCTCCTCTC 59.734 60.000 0.00 0.00 0.00 3.20
2708 4260 0.631998 TCCCCATCTCCCTCCTCTCT 60.632 60.000 0.00 0.00 0.00 3.10
2709 4261 0.178935 CCCCATCTCCCTCCTCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
2939 4531 2.358737 GCTTAGTGGCGTGGTGCT 60.359 61.111 0.00 0.00 45.43 4.40
2940 4532 2.680913 GCTTAGTGGCGTGGTGCTG 61.681 63.158 0.00 0.00 45.43 4.41
2941 4533 2.668212 TTAGTGGCGTGGTGCTGC 60.668 61.111 0.00 0.00 45.43 5.25
2946 4538 4.166011 GGCGTGGTGCTGCGATTC 62.166 66.667 0.00 0.00 45.43 2.52
2947 4539 4.505217 GCGTGGTGCTGCGATTCG 62.505 66.667 0.62 0.62 41.73 3.34
2993 4585 3.966543 CGGGGGTGGTTTGAGCCT 61.967 66.667 0.00 0.00 33.70 4.58
2999 4591 0.034337 GGTGGTTTGAGCCTCGTACA 59.966 55.000 0.00 0.00 0.00 2.90
3064 4657 2.173569 CCCCGATCCTCTTCTTTGGATT 59.826 50.000 0.00 0.00 42.56 3.01
3298 4892 2.267006 CGTGCTGGAGATGGCAGT 59.733 61.111 0.00 0.00 39.22 4.40
3406 5000 1.891919 GGCTTGTGTGGTGAGCGAA 60.892 57.895 0.00 0.00 37.29 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.870307 CTCCGCCCGTACTTTCATCG 60.870 60.000 0.00 0.00 0.00 3.84
48 49 1.136110 TCAACACACTCGAACTGCTCA 59.864 47.619 0.00 0.00 0.00 4.26
58 59 1.412710 TGTCAGGAGGTCAACACACTC 59.587 52.381 0.00 0.00 0.00 3.51
87 88 3.087031 CCAACATCAAGAGCAACCTCAT 58.913 45.455 0.00 0.00 40.68 2.90
91 92 1.270550 CCACCAACATCAAGAGCAACC 59.729 52.381 0.00 0.00 0.00 3.77
92 93 1.956477 ACCACCAACATCAAGAGCAAC 59.044 47.619 0.00 0.00 0.00 4.17
93 94 2.229792 GACCACCAACATCAAGAGCAA 58.770 47.619 0.00 0.00 0.00 3.91
120 121 1.338674 CCTACCCAATGCAACTCACGA 60.339 52.381 0.00 0.00 0.00 4.35
138 139 1.135094 CTCCATAGGACATGTGCCCT 58.865 55.000 14.38 12.33 36.60 5.19
185 186 1.404748 GTAGAGTAGCAGACCCGGAAC 59.595 57.143 0.73 0.00 0.00 3.62
205 206 3.438781 AGAGAAGAAGTCGTGACTGCTAG 59.561 47.826 10.90 0.00 46.47 3.42
217 218 3.070018 CACATTGCCGAAGAGAAGAAGT 58.930 45.455 0.00 0.00 0.00 3.01
259 260 5.048991 ACAAATCAACGATAACCTGTTCCAC 60.049 40.000 0.00 0.00 0.00 4.02
272 273 5.655488 ACCAAAATTCACACAAATCAACGA 58.345 33.333 0.00 0.00 0.00 3.85
292 293 2.505635 ATCACATCAGCACGCGACCA 62.506 55.000 15.93 0.00 0.00 4.02
294 295 1.346197 CATCACATCAGCACGCGAC 59.654 57.895 15.93 4.00 0.00 5.19
334 340 2.837291 GCCACAAGCCACACCCAA 60.837 61.111 0.00 0.00 34.35 4.12
359 365 0.402504 ACCGAATACAAAGCCCACCA 59.597 50.000 0.00 0.00 0.00 4.17
375 381 5.758570 TTACGAAAAACCAAACAAAACCG 57.241 34.783 0.00 0.00 0.00 4.44
381 387 9.934190 GTCTAGTTAATTACGAAAAACCAAACA 57.066 29.630 0.00 0.00 0.00 2.83
386 392 9.934190 TTGTTGTCTAGTTAATTACGAAAAACC 57.066 29.630 0.00 0.00 0.00 3.27
406 413 8.974060 TCATTAACTAAGAAGAAGGTTGTTGT 57.026 30.769 0.00 0.00 0.00 3.32
435 442 1.153597 ACAAGGCAAAAGCTTTGCGC 61.154 50.000 20.36 20.36 45.78 6.09
436 443 0.578211 CACAAGGCAAAAGCTTTGCG 59.422 50.000 13.54 8.47 45.78 4.85
472 479 3.253188 GCTTAAAATCACAGCACCAGACA 59.747 43.478 0.00 0.00 33.45 3.41
473 480 3.253188 TGCTTAAAATCACAGCACCAGAC 59.747 43.478 0.00 0.00 38.65 3.51
474 481 3.485394 TGCTTAAAATCACAGCACCAGA 58.515 40.909 0.00 0.00 38.65 3.86
475 482 3.921119 TGCTTAAAATCACAGCACCAG 57.079 42.857 0.00 0.00 38.65 4.00
544 552 6.426328 CACTCTTCTATTCAGCAGTTTGACTT 59.574 38.462 0.00 0.00 0.00 3.01
611 619 0.238553 GGCACGTGCTCTTTTCCTTC 59.761 55.000 36.84 14.82 41.70 3.46
650 659 2.287547 TGCTTTGACATTTCTGTTCCGC 60.288 45.455 0.00 0.00 35.14 5.54
660 669 3.149196 ACGAGACCATTGCTTTGACATT 58.851 40.909 0.00 0.00 0.00 2.71
675 684 8.171840 ACGTACTACTACTAATGAAAACGAGAC 58.828 37.037 0.00 0.00 0.00 3.36
729 742 0.319125 GCCGTAGCTAGCTGGCTTAG 60.319 60.000 30.52 22.05 44.16 2.18
745 758 2.211353 TTTTCCCTTTTCGTTTGCCG 57.789 45.000 0.00 0.00 38.13 5.69
983 1013 0.805614 TACACACGCAGCTCTCTCTC 59.194 55.000 0.00 0.00 0.00 3.20
984 1014 0.523966 GTACACACGCAGCTCTCTCT 59.476 55.000 0.00 0.00 0.00 3.10
990 1020 2.930040 GTCAATATGTACACACGCAGCT 59.070 45.455 0.00 0.00 0.00 4.24
991 1021 2.285026 CGTCAATATGTACACACGCAGC 60.285 50.000 0.00 0.00 0.00 5.25
992 1022 2.281498 CCGTCAATATGTACACACGCAG 59.719 50.000 0.00 0.00 0.00 5.18
995 1025 1.591158 GCCCGTCAATATGTACACACG 59.409 52.381 0.00 2.03 0.00 4.49
1023 1055 2.515854 GAGACCAGATATCAGCCGGTA 58.484 52.381 1.90 0.00 0.00 4.02
1025 1057 0.242286 CGAGACCAGATATCAGCCGG 59.758 60.000 5.32 0.00 0.00 6.13
1026 1058 0.955178 ACGAGACCAGATATCAGCCG 59.045 55.000 5.32 2.49 0.00 5.52
1027 1059 2.235016 AGACGAGACCAGATATCAGCC 58.765 52.381 5.32 0.00 0.00 4.85
1028 1060 4.517453 AGTTAGACGAGACCAGATATCAGC 59.483 45.833 5.32 0.00 0.00 4.26
1029 1061 5.995282 AGAGTTAGACGAGACCAGATATCAG 59.005 44.000 5.32 0.00 0.00 2.90
1030 1062 5.931294 AGAGTTAGACGAGACCAGATATCA 58.069 41.667 5.32 0.00 0.00 2.15
1070 1102 2.271173 GGCCCGGTACTTGGAAGG 59.729 66.667 0.00 0.00 0.00 3.46
1203 1235 3.574445 CGCTCCCTCGTCGTCGAT 61.574 66.667 5.00 0.00 45.21 3.59
1213 1245 3.069318 GTTCGACCTCCGCTCCCT 61.069 66.667 0.00 0.00 38.37 4.20
1385 2522 5.590259 AGGGTTGAAACATACTGATACATGC 59.410 40.000 0.00 0.00 0.00 4.06
1429 2575 8.509715 GTCAGTGATGACCAACCTAGTGTAGG 62.510 50.000 0.00 0.00 40.98 3.18
1433 2579 3.589988 GTCAGTGATGACCAACCTAGTG 58.410 50.000 0.00 0.00 32.97 2.74
1467 2613 8.497910 TCCAAGATTGAGCTAAGGATATAAGT 57.502 34.615 0.00 0.00 0.00 2.24
1468 2614 9.434420 CTTCCAAGATTGAGCTAAGGATATAAG 57.566 37.037 0.00 0.00 0.00 1.73
1469 2615 8.938883 ACTTCCAAGATTGAGCTAAGGATATAA 58.061 33.333 0.00 0.00 0.00 0.98
1470 2616 8.370940 CACTTCCAAGATTGAGCTAAGGATATA 58.629 37.037 0.00 0.00 0.00 0.86
1471 2617 7.071698 TCACTTCCAAGATTGAGCTAAGGATAT 59.928 37.037 0.00 0.00 0.00 1.63
1472 2618 6.384015 TCACTTCCAAGATTGAGCTAAGGATA 59.616 38.462 0.00 0.00 0.00 2.59
1473 2619 5.190528 TCACTTCCAAGATTGAGCTAAGGAT 59.809 40.000 0.00 0.00 0.00 3.24
1474 2620 4.532126 TCACTTCCAAGATTGAGCTAAGGA 59.468 41.667 0.00 0.00 0.00 3.36
1475 2621 4.836825 TCACTTCCAAGATTGAGCTAAGG 58.163 43.478 0.00 0.00 0.00 2.69
1568 2718 7.471721 TCTATTTCTTGGCATCGTTTACATTG 58.528 34.615 0.00 0.00 0.00 2.82
1627 3129 6.312672 GCATACATTGTTACCATGTTTTTCCC 59.687 38.462 7.37 0.00 0.00 3.97
1628 3130 6.870965 TGCATACATTGTTACCATGTTTTTCC 59.129 34.615 7.37 0.00 0.00 3.13
1629 3131 7.881643 TGCATACATTGTTACCATGTTTTTC 57.118 32.000 7.37 0.00 0.00 2.29
1661 3166 3.124560 TCGACGTGCTGAAATAAACACA 58.875 40.909 0.00 0.00 33.23 3.72
1703 3213 7.329588 AGTTTTCTGAAATTTCAACCGTACT 57.670 32.000 20.82 16.10 36.64 2.73
1750 3260 3.245048 GCACAAGAATTTTGACCCAAACG 59.755 43.478 7.18 0.00 32.79 3.60
1852 3362 2.490903 GCTTGTCAATTGCACATCTCCT 59.509 45.455 0.00 0.00 0.00 3.69
1853 3363 2.229543 TGCTTGTCAATTGCACATCTCC 59.770 45.455 0.00 0.00 0.00 3.71
1854 3364 3.564235 TGCTTGTCAATTGCACATCTC 57.436 42.857 0.00 0.73 0.00 2.75
1963 3480 5.015178 TCTGTATGGAGGATTGTCCCTTTTT 59.985 40.000 0.00 0.00 37.19 1.94
1975 3492 5.277250 TGGTTGTCTATTCTGTATGGAGGA 58.723 41.667 0.00 0.00 0.00 3.71
1986 3503 7.744715 CACGTGTTTAATTCTGGTTGTCTATTC 59.255 37.037 7.58 0.00 0.00 1.75
2077 3595 2.346847 TGCGCACACATTTCAAACAAAC 59.653 40.909 5.66 0.00 0.00 2.93
2118 3637 9.467258 CCTGCGATTAATCAATCAACAAATTAT 57.533 29.630 15.57 0.00 40.61 1.28
2119 3638 7.434897 GCCTGCGATTAATCAATCAACAAATTA 59.565 33.333 15.57 0.00 40.61 1.40
2120 3639 6.256321 GCCTGCGATTAATCAATCAACAAATT 59.744 34.615 15.57 0.00 40.61 1.82
2167 3686 3.057526 GCTCGGTTAGAATTTGTTGGCTT 60.058 43.478 0.00 0.00 0.00 4.35
2455 4007 6.741992 TGCTAGCTACTACAAGTACGTAAA 57.258 37.500 17.23 0.00 0.00 2.01
2464 4016 6.978674 ATAACCAGATGCTAGCTACTACAA 57.021 37.500 17.23 0.00 0.00 2.41
2465 4017 6.978674 AATAACCAGATGCTAGCTACTACA 57.021 37.500 17.23 0.00 0.00 2.74
2469 4021 7.321745 ACAAAAATAACCAGATGCTAGCTAC 57.678 36.000 17.23 9.79 0.00 3.58
2538 4090 4.399978 ACACTCGAACAAACGAAAACTTG 58.600 39.130 0.00 0.00 41.67 3.16
2589 4141 3.950794 CTCTAGCGGCCGCCAACAA 62.951 63.158 44.47 24.81 43.17 2.83
2602 4154 9.813446 ATTTACCCAACGAATAAGTTACTCTAG 57.187 33.333 0.00 0.00 32.35 2.43
2614 4166 4.279671 TGAGTTTGCATTTACCCAACGAAT 59.720 37.500 0.00 0.00 0.00 3.34
2681 4233 0.756815 GGGAGATGGGGAACAATGCC 60.757 60.000 0.00 0.00 36.03 4.40
2682 4234 0.259938 AGGGAGATGGGGAACAATGC 59.740 55.000 0.00 0.00 0.00 3.56
2683 4235 1.133668 GGAGGGAGATGGGGAACAATG 60.134 57.143 0.00 0.00 0.00 2.82
2684 4236 1.226311 GGAGGGAGATGGGGAACAAT 58.774 55.000 0.00 0.00 0.00 2.71
2685 4237 0.121197 AGGAGGGAGATGGGGAACAA 59.879 55.000 0.00 0.00 0.00 2.83
2686 4238 0.326618 GAGGAGGGAGATGGGGAACA 60.327 60.000 0.00 0.00 0.00 3.18
2687 4239 0.030603 AGAGGAGGGAGATGGGGAAC 60.031 60.000 0.00 0.00 0.00 3.62
2688 4240 0.266152 GAGAGGAGGGAGATGGGGAA 59.734 60.000 0.00 0.00 0.00 3.97
2689 4241 0.631998 AGAGAGGAGGGAGATGGGGA 60.632 60.000 0.00 0.00 0.00 4.81
2690 4242 0.178935 GAGAGAGGAGGGAGATGGGG 60.179 65.000 0.00 0.00 0.00 4.96
2691 4243 0.178935 GGAGAGAGGAGGGAGATGGG 60.179 65.000 0.00 0.00 0.00 4.00
2692 4244 0.178935 GGGAGAGAGGAGGGAGATGG 60.179 65.000 0.00 0.00 0.00 3.51
2693 4245 0.178935 GGGGAGAGAGGAGGGAGATG 60.179 65.000 0.00 0.00 0.00 2.90
2694 4246 1.376249 GGGGGAGAGAGGAGGGAGAT 61.376 65.000 0.00 0.00 0.00 2.75
2695 4247 2.015726 GGGGGAGAGAGGAGGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
2696 4248 2.612251 GGGGGAGAGAGGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
2923 4515 2.680913 GCAGCACCACGCCACTAAG 61.681 63.158 0.00 0.00 44.04 2.18
2924 4516 2.668212 GCAGCACCACGCCACTAA 60.668 61.111 0.00 0.00 44.04 2.24
2929 4521 4.166011 GAATCGCAGCACCACGCC 62.166 66.667 0.00 0.00 44.04 5.68
2930 4522 4.505217 CGAATCGCAGCACCACGC 62.505 66.667 0.00 0.00 42.91 5.34
3296 4890 3.515316 CTGGACGGTGGTTCGCACT 62.515 63.158 0.00 0.00 0.00 4.40
3298 4892 2.107041 AATCTGGACGGTGGTTCGCA 62.107 55.000 0.00 0.00 0.00 5.10
3406 5000 4.640690 ACCACCGGGAGAGCACCT 62.641 66.667 6.32 0.00 38.05 4.00
3446 5040 2.398554 CGGCGATCCAACACCAAGG 61.399 63.158 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.