Multiple sequence alignment - TraesCS1A01G302100

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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 TraesCS1A01G302100 chr1A 100.000 3053 0 0 1 3053 496091131 496088079 0.000000e+00 5638.0
1 TraesCS1A01G302100 chr1A 89.726 146 13 2 30 174 72758085 72757941 5.200000e-43 185.0
2 TraesCS1A01G302100 chr1A 91.304 46 4 0 434 479 488625674 488625719 2.540000e-06 63.9
3 TraesCS1A01G302100 chr1D 90.502 2569 145 26 554 3053 399264365 399261827 0.000000e+00 3301.0
4 TraesCS1A01G302100 chr1D 78.552 1091 208 17 991 2065 464030119 464029039 0.000000e+00 695.0
5 TraesCS1A01G302100 chr1D 83.673 441 59 6 2560 2997 119408138 119407708 1.320000e-108 403.0
6 TraesCS1A01G302100 chr1D 90.244 82 8 0 478 559 399264788 399264707 1.160000e-19 108.0
7 TraesCS1A01G302100 chr6D 87.075 1470 153 16 810 2250 14509826 14511287 0.000000e+00 1628.0
8 TraesCS1A01G302100 chr6D 87.808 1378 139 14 886 2238 14722176 14720803 0.000000e+00 1587.0
9 TraesCS1A01G302100 chr6D 92.157 51 4 0 2937 2987 452397868 452397918 4.220000e-09 73.1
10 TraesCS1A01G302100 chr6A 86.538 676 75 7 962 1626 15875902 15875232 0.000000e+00 730.0
11 TraesCS1A01G302100 chr6A 85.554 623 67 9 1654 2253 15875236 15874614 5.560000e-177 630.0
12 TraesCS1A01G302100 chr7A 93.427 426 25 3 1 423 213837108 213837533 2.000000e-176 628.0
13 TraesCS1A01G302100 chr6B 89.278 485 46 5 1144 1625 26728763 26728282 1.210000e-168 603.0
14 TraesCS1A01G302100 chr6B 83.333 66 10 1 2396 2461 508781866 508781930 3.290000e-05 60.2
15 TraesCS1A01G302100 chr6B 89.130 46 5 0 2396 2441 619424841 619424796 1.180000e-04 58.4
16 TraesCS1A01G302100 chr3A 90.337 445 21 11 1 438 187290843 187290414 5.710000e-157 564.0
17 TraesCS1A01G302100 chr3A 90.071 282 17 8 164 438 328884297 328884574 3.740000e-94 355.0
18 TraesCS1A01G302100 chr5D 81.532 666 86 20 2396 3031 254632795 254632137 5.840000e-142 514.0
19 TraesCS1A01G302100 chr5B 81.325 664 90 21 2396 3031 287811281 287811938 2.720000e-140 508.0
20 TraesCS1A01G302100 chr5B 85.106 282 21 9 174 438 473656426 473656703 5.020000e-68 268.0
21 TraesCS1A01G302100 chr5B 94.286 175 9 1 1 174 473655986 473656160 1.800000e-67 267.0
22 TraesCS1A01G302100 chr5B 80.503 159 27 4 2705 2860 465826186 465826343 5.350000e-23 119.0
23 TraesCS1A01G302100 chr5B 83.333 66 10 1 2396 2461 136230256 136230192 3.290000e-05 60.2
24 TraesCS1A01G302100 chr5B 94.118 34 2 0 2396 2429 449107251 449107284 6.000000e-03 52.8
25 TraesCS1A01G302100 chr5A 84.355 473 65 8 2564 3031 338178537 338178069 3.590000e-124 455.0
26 TraesCS1A01G302100 chr5A 77.809 356 42 20 2499 2843 689431229 689430900 5.200000e-43 185.0
27 TraesCS1A01G302100 chr5A 81.275 251 26 12 166 416 489103052 489102823 1.870000e-42 183.0
28 TraesCS1A01G302100 chr7B 89.123 285 16 8 164 438 63070917 63071196 1.050000e-89 340.0
29 TraesCS1A01G302100 chr7B 88.421 285 18 8 164 438 63032608 63032887 2.270000e-86 329.0
30 TraesCS1A01G302100 chr7B 81.673 251 25 12 166 416 542880021 542879792 4.020000e-44 189.0
31 TraesCS1A01G302100 chr1B 89.076 238 23 3 2557 2792 182201981 182201745 2.980000e-75 292.0
32 TraesCS1A01G302100 chr4B 98.701 154 2 0 1 154 207109759 207109912 1.080000e-69 274.0
33 TraesCS1A01G302100 chr4B 88.426 216 16 2 210 416 207110583 207110798 5.050000e-63 252.0
34 TraesCS1A01G302100 chr4B 97.143 35 0 1 2778 2811 664752035 664752069 1.180000e-04 58.4
35 TraesCS1A01G302100 chr2B 94.969 159 8 0 1 159 242823228 242823070 1.820000e-62 250.0
36 TraesCS1A01G302100 chr2B 88.050 159 16 3 260 416 242822767 242822610 5.200000e-43 185.0
37 TraesCS1A01G302100 chr2B 92.157 51 4 0 2937 2987 542839829 542839779 4.220000e-09 73.1
38 TraesCS1A01G302100 chr2A 92.571 175 11 2 1 174 449288823 449288996 1.820000e-62 250.0
39 TraesCS1A01G302100 chr2A 84.118 170 9 5 164 333 449289282 449289433 6.820000e-32 148.0
40 TraesCS1A01G302100 chr2A 92.157 51 4 0 2937 2987 533534518 533534568 4.220000e-09 73.1
41 TraesCS1A01G302100 chr7D 78.747 367 53 10 2569 2933 590814111 590813768 3.960000e-54 222.0
42 TraesCS1A01G302100 chr7D 73.356 289 66 9 2749 3030 204883830 204883546 2.510000e-16 97.1
43 TraesCS1A01G302100 chr7D 90.196 51 5 0 2937 2987 528549281 528549231 1.960000e-07 67.6
44 TraesCS1A01G302100 chr4A 89.855 138 13 1 30 167 625160931 625161067 3.130000e-40 176.0
45 TraesCS1A01G302100 chr4D 87.879 132 12 3 2570 2699 490416794 490416665 5.270000e-33 152.0
46 TraesCS1A01G302100 chr2D 87.692 130 13 2 38 167 33316256 33316130 6.820000e-32 148.0


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 TraesCS1A01G302100 chr1A 496088079 496091131 3052 True 5638.0 5638 100.0000 1 3053 1 chr1A.!!$R2 3052
1 TraesCS1A01G302100 chr1D 399261827 399264788 2961 True 1704.5 3301 90.3730 478 3053 2 chr1D.!!$R3 2575
2 TraesCS1A01G302100 chr1D 464029039 464030119 1080 True 695.0 695 78.5520 991 2065 1 chr1D.!!$R2 1074
3 TraesCS1A01G302100 chr6D 14509826 14511287 1461 False 1628.0 1628 87.0750 810 2250 1 chr6D.!!$F1 1440
4 TraesCS1A01G302100 chr6D 14720803 14722176 1373 True 1587.0 1587 87.8080 886 2238 1 chr6D.!!$R1 1352
5 TraesCS1A01G302100 chr6A 15874614 15875902 1288 True 680.0 730 86.0460 962 2253 2 chr6A.!!$R1 1291
6 TraesCS1A01G302100 chr5D 254632137 254632795 658 True 514.0 514 81.5320 2396 3031 1 chr5D.!!$R1 635
7 TraesCS1A01G302100 chr5B 287811281 287811938 657 False 508.0 508 81.3250 2396 3031 1 chr5B.!!$F1 635
8 TraesCS1A01G302100 chr5B 473655986 473656703 717 False 267.5 268 89.6960 1 438 2 chr5B.!!$F4 437
9 TraesCS1A01G302100 chr4B 207109759 207110798 1039 False 263.0 274 93.5635 1 416 2 chr4B.!!$F2 415
10 TraesCS1A01G302100 chr2B 242822610 242823228 618 True 217.5 250 91.5095 1 416 2 chr2B.!!$R2 415

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
906 1954 1.134521 TGAAAGTGACTCCGCAACTGT 60.135 47.619 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 3189 0.03601 ATGCCTTCACAGTTCCCTCG 60.036 55.0 0.0 0.0 0.0 4.63 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
90 91 2.418746 CGGAGAAATCCATCTTCGTGGT 60.419 50.000 0.00 0.00 42.32 4.16
233 881 3.157217 GATGCGCGATGGGAGGAGT 62.157 63.158 12.10 0.00 0.00 3.85
358 1015 4.212425 CGTGGCTTGTAGTGTTAAACATGA 59.788 41.667 0.00 0.00 0.00 3.07
361 1018 6.975772 GTGGCTTGTAGTGTTAAACATGAAAA 59.024 34.615 0.00 0.00 0.00 2.29
418 1082 7.178983 TGAATTAGATTGTTTGGATCTGCCTTT 59.821 33.333 0.00 0.00 35.56 3.11
457 1121 9.988350 AGTAGATACATTTATTTTTGCAACGAG 57.012 29.630 0.00 0.00 0.00 4.18
458 1122 9.769093 GTAGATACATTTATTTTTGCAACGAGT 57.231 29.630 0.00 0.00 0.00 4.18
470 1134 9.906660 ATTTTTGCAACGAGTAATTTAGAATGA 57.093 25.926 0.00 0.00 0.00 2.57
471 1135 9.737427 TTTTTGCAACGAGTAATTTAGAATGAA 57.263 25.926 0.00 0.00 0.00 2.57
472 1136 8.948853 TTTGCAACGAGTAATTTAGAATGAAG 57.051 30.769 0.00 0.00 0.00 3.02
473 1137 7.072177 TGCAACGAGTAATTTAGAATGAAGG 57.928 36.000 0.00 0.00 0.00 3.46
474 1138 6.093495 TGCAACGAGTAATTTAGAATGAAGGG 59.907 38.462 0.00 0.00 0.00 3.95
475 1139 6.315393 GCAACGAGTAATTTAGAATGAAGGGA 59.685 38.462 0.00 0.00 0.00 4.20
476 1140 7.466050 GCAACGAGTAATTTAGAATGAAGGGAG 60.466 40.741 0.00 0.00 0.00 4.30
492 1156 8.789767 ATGAAGGGAGTATTTCATAGAAGAGA 57.210 34.615 0.00 0.00 41.04 3.10
497 1161 8.428063 AGGGAGTATTTCATAGAAGAGAATGTG 58.572 37.037 0.00 0.00 0.00 3.21
505 1169 6.567959 TCATAGAAGAGAATGTGTACTGCAG 58.432 40.000 13.48 13.48 0.00 4.41
510 1174 4.564041 AGAGAATGTGTACTGCAGAAGTG 58.436 43.478 23.35 0.00 40.26 3.16
513 1177 4.993584 AGAATGTGTACTGCAGAAGTGAAG 59.006 41.667 23.35 0.00 40.26 3.02
546 1210 3.278574 TCCGGATTAGTTGGATTTGCAG 58.721 45.455 0.00 0.00 0.00 4.41
552 1216 5.448632 GGATTAGTTGGATTTGCAGGTTACG 60.449 44.000 0.00 0.00 0.00 3.18
744 1781 4.100084 CGTGGCCAGATCCCAGCA 62.100 66.667 5.11 0.00 31.89 4.41
871 1919 4.893424 TGCCTTCACTTTGTAGTTTGTC 57.107 40.909 0.00 0.00 30.26 3.18
873 1921 3.004419 GCCTTCACTTTGTAGTTTGTCCC 59.996 47.826 0.00 0.00 30.26 4.46
879 1927 5.099575 CACTTTGTAGTTTGTCCCAACAAC 58.900 41.667 0.00 0.00 44.90 3.32
906 1954 1.134521 TGAAAGTGACTCCGCAACTGT 60.135 47.619 0.00 0.00 0.00 3.55
907 1955 1.527311 GAAAGTGACTCCGCAACTGTC 59.473 52.381 0.00 0.00 0.00 3.51
1014 2081 2.279517 GAGATGGCCCGTGTAGCG 60.280 66.667 0.00 0.00 40.95 4.26
1081 2148 0.669318 GAACGATGCCGACAACCTCA 60.669 55.000 0.00 0.00 39.50 3.86
1242 2310 0.250513 AGCCAACGGACATCTTCCTC 59.749 55.000 0.00 0.00 43.25 3.71
1269 2337 2.515398 CCCAAGTCTGGCACCACA 59.485 61.111 0.00 0.00 41.99 4.17
1412 2488 1.227704 AACCGGTCGATGTTGTGCA 60.228 52.632 8.04 0.00 0.00 4.57
1420 2496 1.307355 CGATGTTGTGCAGGGCATCA 61.307 55.000 18.38 6.95 41.91 3.07
1474 2550 1.203050 CCCACTTCCCATTGTCCTTGT 60.203 52.381 0.00 0.00 0.00 3.16
1493 2569 2.896854 GCCGGAGCGCATCAATGA 60.897 61.111 11.47 0.00 0.00 2.57
1725 2801 3.139077 CAAGGTGTTGTTCCTCAGGTAC 58.861 50.000 0.00 0.00 33.76 3.34
1749 2825 1.141019 GATGCTACGAGACCCGCAA 59.859 57.895 0.00 0.00 43.32 4.85
1824 2900 3.140225 GAAGGCCGGCGTCCTAGAG 62.140 68.421 23.85 0.00 32.65 2.43
1848 2924 0.183492 TCTTGGAGTTGTGCAGCCTT 59.817 50.000 0.00 0.00 0.00 4.35
1888 2964 2.281484 TGAACCAGAGCGGCAACC 60.281 61.111 1.45 0.00 39.03 3.77
1968 3044 0.676466 GGATCAACCACATGACGCCA 60.676 55.000 0.00 0.00 38.79 5.69
2031 3118 1.200020 CAAGGCACCGGATTTGACTTC 59.800 52.381 9.46 0.00 40.56 3.01
2090 3189 1.625818 CACATATCTCCTGGTAGCCCC 59.374 57.143 0.00 0.00 0.00 5.80
2165 3266 7.623630 CATCATCTTGGGGTTTTTATTTTCCT 58.376 34.615 0.00 0.00 0.00 3.36
2177 3283 8.894731 GGTTTTTATTTTCCTTTTTGTAAGCCA 58.105 29.630 0.00 0.00 0.00 4.75
2195 3301 3.720949 CCAATTCATCGGCATCAATGT 57.279 42.857 0.00 0.00 0.00 2.71
2258 3369 0.595567 GTGTGTGCATGCTGTTGGTG 60.596 55.000 20.33 0.00 0.00 4.17
2299 3410 8.474006 AAAAAGTAAAACATCTGTGGTTTGTC 57.526 30.769 1.94 0.00 44.64 3.18
2308 3419 2.680841 TCTGTGGTTTGTCGTGGAAAAG 59.319 45.455 0.00 0.00 0.00 2.27
2313 3424 3.506455 TGGTTTGTCGTGGAAAAGAAACA 59.494 39.130 0.00 0.00 0.00 2.83
2320 3431 4.441087 GTCGTGGAAAAGAAACATTTGCTC 59.559 41.667 0.00 0.00 0.00 4.26
2322 3433 4.676924 CGTGGAAAAGAAACATTTGCTCTC 59.323 41.667 0.00 0.00 0.00 3.20
2336 3447 1.066645 TGCTCTCTGTATGTGTGCCTG 60.067 52.381 0.00 0.00 0.00 4.85
2360 3471 6.209192 TGTGTTGTTTCATCTCCAGCAAATAT 59.791 34.615 0.00 0.00 0.00 1.28
2364 3475 7.514784 TGTTTCATCTCCAGCAAATATATGG 57.485 36.000 0.00 0.00 35.30 2.74
2431 3543 9.554395 TCCAATACATCACGTAAAATACATCAT 57.446 29.630 0.00 0.00 32.59 2.45
2469 3582 9.202273 TCAAGTAAATTTACATCACCAAAATGC 57.798 29.630 26.06 0.00 36.12 3.56
2470 3583 9.206870 CAAGTAAATTTACATCACCAAAATGCT 57.793 29.630 26.06 1.87 36.12 3.79
2552 3684 2.877097 TGATGTAGAAAAGGCCAGCA 57.123 45.000 5.01 0.00 0.00 4.41
2574 3720 4.088923 CAGCGCAACAACTTCAAACATATG 59.911 41.667 11.47 0.00 0.00 1.78
2715 3861 4.281688 ACAACAAGGCTCAGCAAACAATAT 59.718 37.500 0.00 0.00 0.00 1.28
2743 3889 3.980775 AGTTCATGCGCAATACAACAAAC 59.019 39.130 17.11 9.96 0.00 2.93
2756 3902 8.928733 GCAATACAACAAACATTGAGATGAAAT 58.071 29.630 0.00 0.00 36.73 2.17
2775 3921 0.844661 TTAGGAGGCTTGCTCCCCAA 60.845 55.000 0.00 0.00 41.76 4.12
2776 3922 0.844661 TAGGAGGCTTGCTCCCCAAA 60.845 55.000 0.00 0.00 41.76 3.28
2785 3932 2.649129 GCTCCCCAAACCATGCCAC 61.649 63.158 0.00 0.00 0.00 5.01
2888 4035 6.874278 TGATTTGATCTTCCCTTCTACTCA 57.126 37.500 0.00 0.00 0.00 3.41
2895 4042 1.475403 TCCCTTCTACTCAGCCGAAG 58.525 55.000 0.00 0.00 35.19 3.79
2933 4080 7.182026 TGAGGTCATAGAAGGTCTAATCCAAAA 59.818 37.037 0.00 0.00 31.96 2.44
2934 4081 7.928873 AGGTCATAGAAGGTCTAATCCAAAAA 58.071 34.615 0.00 0.00 31.96 1.94
3031 4182 3.260380 CCCAATATCTAGCCAGTCCTCAG 59.740 52.174 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.257676 GTTCCTCGACCTCGCGTT 59.742 61.111 5.77 0.00 39.60 4.84
90 91 3.749064 GAGACACAGCGGGCTCGA 61.749 66.667 12.03 0.00 39.00 4.04
216 864 3.157252 ACTCCTCCCATCGCGCAT 61.157 61.111 8.75 0.00 0.00 4.73
217 865 4.147449 CACTCCTCCCATCGCGCA 62.147 66.667 8.75 0.00 0.00 6.09
293 942 4.891727 ATCGCTAAGCCCGCCGTG 62.892 66.667 0.00 0.00 0.00 4.94
394 1051 7.486407 AAAGGCAGATCCAAACAATCTAATT 57.514 32.000 0.00 0.00 37.29 1.40
395 1052 7.486407 AAAAGGCAGATCCAAACAATCTAAT 57.514 32.000 0.00 0.00 37.29 1.73
444 1108 9.906660 TCATTCTAAATTACTCGTTGCAAAAAT 57.093 25.926 0.00 0.00 0.00 1.82
445 1109 9.737427 TTCATTCTAAATTACTCGTTGCAAAAA 57.263 25.926 0.00 0.00 0.00 1.94
446 1110 9.393249 CTTCATTCTAAATTACTCGTTGCAAAA 57.607 29.630 0.00 0.00 0.00 2.44
447 1111 8.020819 CCTTCATTCTAAATTACTCGTTGCAAA 58.979 33.333 0.00 0.00 0.00 3.68
448 1112 7.361713 CCCTTCATTCTAAATTACTCGTTGCAA 60.362 37.037 0.00 0.00 0.00 4.08
449 1113 6.093495 CCCTTCATTCTAAATTACTCGTTGCA 59.907 38.462 0.00 0.00 0.00 4.08
450 1114 6.315393 TCCCTTCATTCTAAATTACTCGTTGC 59.685 38.462 0.00 0.00 0.00 4.17
451 1115 7.549488 ACTCCCTTCATTCTAAATTACTCGTTG 59.451 37.037 0.00 0.00 0.00 4.10
452 1116 7.621796 ACTCCCTTCATTCTAAATTACTCGTT 58.378 34.615 0.00 0.00 0.00 3.85
453 1117 7.184067 ACTCCCTTCATTCTAAATTACTCGT 57.816 36.000 0.00 0.00 0.00 4.18
454 1118 9.765795 AATACTCCCTTCATTCTAAATTACTCG 57.234 33.333 0.00 0.00 0.00 4.18
464 1128 9.218525 TCTTCTATGAAATACTCCCTTCATTCT 57.781 33.333 2.90 0.00 41.41 2.40
465 1129 9.487790 CTCTTCTATGAAATACTCCCTTCATTC 57.512 37.037 2.90 0.00 41.41 2.67
466 1130 9.218525 TCTCTTCTATGAAATACTCCCTTCATT 57.781 33.333 2.90 0.00 41.41 2.57
467 1131 8.789767 TCTCTTCTATGAAATACTCCCTTCAT 57.210 34.615 3.11 3.11 43.15 2.57
468 1132 8.609617 TTCTCTTCTATGAAATACTCCCTTCA 57.390 34.615 0.00 0.00 36.08 3.02
469 1133 9.487790 CATTCTCTTCTATGAAATACTCCCTTC 57.512 37.037 0.00 0.00 0.00 3.46
470 1134 8.997734 ACATTCTCTTCTATGAAATACTCCCTT 58.002 33.333 0.00 0.00 0.00 3.95
471 1135 8.428063 CACATTCTCTTCTATGAAATACTCCCT 58.572 37.037 0.00 0.00 0.00 4.20
472 1136 8.207545 ACACATTCTCTTCTATGAAATACTCCC 58.792 37.037 0.00 0.00 0.00 4.30
483 1147 6.782082 TCTGCAGTACACATTCTCTTCTAT 57.218 37.500 14.67 0.00 0.00 1.98
492 1156 3.499918 GCTTCACTTCTGCAGTACACATT 59.500 43.478 14.67 0.00 32.76 2.71
497 1161 3.032017 TGAGCTTCACTTCTGCAGTAC 57.968 47.619 14.67 0.00 32.76 2.73
505 1169 3.465871 GAGATGGGATGAGCTTCACTTC 58.534 50.000 0.00 0.00 0.00 3.01
510 1174 0.034616 CCGGAGATGGGATGAGCTTC 59.965 60.000 0.00 0.00 0.00 3.86
513 1177 0.689623 AATCCGGAGATGGGATGAGC 59.310 55.000 11.34 0.00 43.43 4.26
552 1216 1.291132 CTAGCTTGTTCCGCCTTAGC 58.709 55.000 0.00 0.00 0.00 3.09
656 1667 4.827087 AGGGCGCTGCTGATCACG 62.827 66.667 7.64 0.00 0.00 4.35
657 1668 3.200593 CAGGGCGCTGCTGATCAC 61.201 66.667 18.62 0.00 0.00 3.06
871 1919 4.039004 TCACTTTCATTCATGGTTGTTGGG 59.961 41.667 0.00 0.00 0.00 4.12
873 1921 5.835257 AGTCACTTTCATTCATGGTTGTTG 58.165 37.500 0.00 0.00 0.00 3.33
879 1927 2.096496 GCGGAGTCACTTTCATTCATGG 59.904 50.000 0.00 0.00 0.00 3.66
906 1954 3.695830 AAATACTCAGTTGAAGGCGGA 57.304 42.857 0.00 0.00 0.00 5.54
907 1955 4.876107 ACATAAATACTCAGTTGAAGGCGG 59.124 41.667 0.00 0.00 0.00 6.13
1007 2074 1.197036 GGAGTTTTTGCTCCGCTACAC 59.803 52.381 0.00 0.00 44.64 2.90
1242 2310 2.743928 GACTTGGGGCAGCTCACG 60.744 66.667 0.00 0.00 0.00 4.35
1404 2480 1.307355 CGATGATGCCCTGCACAACA 61.307 55.000 0.00 0.00 43.04 3.33
1412 2488 1.832608 TACGCCTCGATGATGCCCT 60.833 57.895 0.00 0.00 0.00 5.19
1420 2496 2.132352 GGGAAGGGTACGCCTCGAT 61.132 63.158 6.27 0.00 34.45 3.59
1493 2569 2.188829 CGGCACCCGCAATCATCAT 61.189 57.895 0.00 0.00 41.17 2.45
1518 2594 2.398754 TGGGATCCCGACAGATGTAT 57.601 50.000 26.03 0.00 39.42 2.29
1725 2801 0.589223 GGTCTCGTAGCATCTCCTCG 59.411 60.000 0.00 0.00 0.00 4.63
1749 2825 1.478288 GCCAGCCTCCTAAGATTGCAT 60.478 52.381 0.00 0.00 0.00 3.96
1824 2900 0.895100 TGCACAACTCCAAGATGGCC 60.895 55.000 0.00 0.00 37.47 5.36
1888 2964 3.462982 TCATGGGTTCGTCATTAATCCG 58.537 45.455 0.00 0.00 28.95 4.18
1889 2965 5.063204 TCATCATGGGTTCGTCATTAATCC 58.937 41.667 0.00 0.00 0.00 3.01
1896 2972 1.273886 TCGTTCATCATGGGTTCGTCA 59.726 47.619 0.00 0.00 0.00 4.35
1968 3044 3.397613 GAGCCTTGCCGCCATCTCT 62.398 63.158 0.00 0.00 0.00 3.10
2090 3189 0.036010 ATGCCTTCACAGTTCCCTCG 60.036 55.000 0.00 0.00 0.00 4.63
2141 3242 7.813087 AGGAAAATAAAAACCCCAAGATGAT 57.187 32.000 0.00 0.00 0.00 2.45
2145 3246 8.110271 ACAAAAAGGAAAATAAAAACCCCAAGA 58.890 29.630 0.00 0.00 0.00 3.02
2177 3283 4.435425 CCAAACATTGATGCCGATGAATT 58.565 39.130 0.00 0.00 37.56 2.17
2195 3301 0.469070 ACAATGCCAAGCAAGCCAAA 59.531 45.000 0.00 0.00 43.62 3.28
2233 3340 2.079158 ACAGCATGCACACACTCATAC 58.921 47.619 21.98 0.00 42.53 2.39
2285 3396 1.877637 TCCACGACAAACCACAGATG 58.122 50.000 0.00 0.00 0.00 2.90
2288 3399 2.680841 TCTTTTCCACGACAAACCACAG 59.319 45.455 0.00 0.00 0.00 3.66
2299 3410 4.610945 AGAGCAAATGTTTCTTTTCCACG 58.389 39.130 0.00 0.00 0.00 4.94
2308 3419 6.082338 CACACATACAGAGAGCAAATGTTTC 58.918 40.000 0.00 0.00 0.00 2.78
2313 3424 3.012518 GGCACACATACAGAGAGCAAAT 58.987 45.455 0.00 0.00 0.00 2.32
2320 3431 2.462456 ACACAGGCACACATACAGAG 57.538 50.000 0.00 0.00 0.00 3.35
2322 3433 2.221169 ACAACACAGGCACACATACAG 58.779 47.619 0.00 0.00 0.00 2.74
2336 3447 3.988379 TTGCTGGAGATGAAACAACAC 57.012 42.857 0.00 0.00 0.00 3.32
2378 3489 6.991938 TGCTCTTAAAGGCAACATTTATTGT 58.008 32.000 0.31 0.00 41.53 2.71
2379 3490 7.977853 AGATGCTCTTAAAGGCAACATTTATTG 59.022 33.333 6.18 0.00 41.90 1.90
2380 3491 8.071177 AGATGCTCTTAAAGGCAACATTTATT 57.929 30.769 6.18 0.00 41.90 1.40
2382 3493 6.095440 GGAGATGCTCTTAAAGGCAACATTTA 59.905 38.462 6.18 0.00 41.90 1.40
2445 3557 9.423061 GAGCATTTTGGTGATGTAAATTTACTT 57.577 29.630 24.81 19.85 34.77 2.24
2509 3625 4.532834 TCATTGGAGGCCCTATTTTACAC 58.467 43.478 0.00 0.00 0.00 2.90
2552 3684 2.869233 ATGTTTGAAGTTGTTGCGCT 57.131 40.000 9.73 0.00 0.00 5.92
2715 3861 6.092807 TGTTGTATTGCGCATGAACTATGTTA 59.907 34.615 12.75 0.00 39.08 2.41
2743 3889 6.735145 GCAAGCCTCCTAATTTCATCTCAATG 60.735 42.308 0.00 0.00 0.00 2.82
2775 3921 1.380302 GAGGAGTGGTGGCATGGTT 59.620 57.895 0.00 0.00 0.00 3.67
2776 3922 2.606587 GGAGGAGTGGTGGCATGGT 61.607 63.158 0.00 0.00 0.00 3.55
2785 3932 6.359804 TCAAAAAGATATCATGGAGGAGTGG 58.640 40.000 5.32 0.00 0.00 4.00
2852 3999 6.630444 AGATCAAATCAAGCGCTTCATTAT 57.370 33.333 19.96 10.58 0.00 1.28
2853 4000 6.441093 AAGATCAAATCAAGCGCTTCATTA 57.559 33.333 19.96 5.66 0.00 1.90
2854 4001 4.978083 AGATCAAATCAAGCGCTTCATT 57.022 36.364 22.21 17.89 0.00 2.57
2888 4035 0.693049 ATGGAAAGACACCTTCGGCT 59.307 50.000 0.00 0.00 0.00 5.52
2895 4042 2.859165 TGACCTCATGGAAAGACACC 57.141 50.000 0.00 0.00 37.04 4.16
2933 4080 4.062293 TCGTTGAGAATGACCGTGATTTT 58.938 39.130 0.00 0.00 0.00 1.82
2934 4081 3.659786 TCGTTGAGAATGACCGTGATTT 58.340 40.909 0.00 0.00 0.00 2.17
2935 4082 3.313012 TCGTTGAGAATGACCGTGATT 57.687 42.857 0.00 0.00 0.00 2.57
2936 4083 3.119137 TGATCGTTGAGAATGACCGTGAT 60.119 43.478 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.