Multiple sequence alignment - TraesCS7A01G405500

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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 TraesCS7A01G405500 chr7A 100.000 5160 0 0 1 5160 589141212 589136053 0.000000e+00 9529
1 TraesCS7A01G405500 chr7A 98.049 615 10 2 4439 5051 48024281 48023667 0.000000e+00 1068
2 TraesCS7A01G405500 chr7A 97.720 614 12 2 4439 5050 116130759 116131372 0.000000e+00 1055
3 TraesCS7A01G405500 chr7A 97.557 614 13 2 4439 5050 716396805 716397418 0.000000e+00 1050
4 TraesCS7A01G405500 chr7D 95.622 4454 163 21 1 4442 515475558 515471125 0.000000e+00 7116
5 TraesCS7A01G405500 chr7D 92.982 114 7 1 5047 5160 515471114 515471002 1.150000e-36 165
6 TraesCS7A01G405500 chr7B 94.674 2272 99 11 2182 4441 546020630 546018369 0.000000e+00 3506
7 TraesCS7A01G405500 chr7B 94.428 2064 87 12 1 2062 546023090 546021053 0.000000e+00 3149
8 TraesCS7A01G405500 chr7B 94.495 109 5 1 5051 5159 546018362 546018255 3.200000e-37 167
9 TraesCS7A01G405500 chr5A 98.691 611 6 2 4439 5047 648788323 648788933 0.000000e+00 1083
10 TraesCS7A01G405500 chr1A 98.363 611 8 2 4439 5047 558173436 558172826 0.000000e+00 1072
11 TraesCS7A01G405500 chr1B 98.355 608 8 2 4439 5044 258836857 258837464 0.000000e+00 1066
12 TraesCS7A01G405500 chr2A 95.050 606 27 3 4439 5042 591177553 591176949 0.000000e+00 950
13 TraesCS7A01G405500 chr2D 94.092 457 21 4 4439 4890 28923799 28923344 0.000000e+00 689
14 TraesCS7A01G405500 chr3B 86.495 622 68 7 4440 5050 346618705 346618089 0.000000e+00 669


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 TraesCS7A01G405500 chr7A 589136053 589141212 5159 True 9529.0 9529 100.000000 1 5160 1 chr7A.!!$R2 5159
1 TraesCS7A01G405500 chr7A 48023667 48024281 614 True 1068.0 1068 98.049000 4439 5051 1 chr7A.!!$R1 612
2 TraesCS7A01G405500 chr7A 116130759 116131372 613 False 1055.0 1055 97.720000 4439 5050 1 chr7A.!!$F1 611
3 TraesCS7A01G405500 chr7A 716396805 716397418 613 False 1050.0 1050 97.557000 4439 5050 1 chr7A.!!$F2 611
4 TraesCS7A01G405500 chr7D 515471002 515475558 4556 True 3640.5 7116 94.302000 1 5160 2 chr7D.!!$R1 5159
5 TraesCS7A01G405500 chr7B 546018255 546023090 4835 True 2274.0 3506 94.532333 1 5159 3 chr7B.!!$R1 5158
6 TraesCS7A01G405500 chr5A 648788323 648788933 610 False 1083.0 1083 98.691000 4439 5047 1 chr5A.!!$F1 608
7 TraesCS7A01G405500 chr1A 558172826 558173436 610 True 1072.0 1072 98.363000 4439 5047 1 chr1A.!!$R1 608
8 TraesCS7A01G405500 chr1B 258836857 258837464 607 False 1066.0 1066 98.355000 4439 5044 1 chr1B.!!$F1 605
9 TraesCS7A01G405500 chr2A 591176949 591177553 604 True 950.0 950 95.050000 4439 5042 1 chr2A.!!$R1 603
10 TraesCS7A01G405500 chr3B 346618089 346618705 616 True 669.0 669 86.495000 4440 5050 1 chr3B.!!$R1 610

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
262 263 0.170339 CTCGCCGGAAATTTTGGACC 59.830 55.0 5.05 0.00 0.00 4.46 F
1017 1018 0.991920 AAATGGGAGTGGTCGGTCAT 59.008 50.0 0.00 0.00 0.00 3.06 F
1020 1021 1.874129 TGGGAGTGGTCGGTCATAAT 58.126 50.0 0.00 0.00 0.00 1.28 F
1515 1517 2.044492 ACTCCCATCTCAACCTAGGTCA 59.956 50.0 16.64 3.94 0.00 4.02 F
2689 2997 0.396435 ATGCCACTGTTGAGGAACGA 59.604 50.0 0.00 0.00 34.49 3.85 F
3705 4019 0.874607 GACGGTGTCGCACTTCTTGT 60.875 55.0 9.31 2.58 40.63 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2229 2533 2.107950 TCCAGACCAAAGGCATTACG 57.892 50.000 0.00 0.0 0.00 3.18 R
2680 2988 4.878971 TGATCAAAAAGTTGTCGTTCCTCA 59.121 37.500 0.00 0.0 36.07 3.86 R
2689 2997 5.693104 GCATGTGACATGATCAAAAAGTTGT 59.307 36.000 28.21 0.0 39.72 3.32 R
3051 3365 1.257743 TCTCCATATCGGCCAGTAGC 58.742 55.000 2.24 0.0 42.60 3.58 R
4140 4455 0.249280 TCAGTTCGAAGACGCTTGCA 60.249 50.000 0.00 0.0 39.58 4.08 R
5115 5448 2.875317 TGATTGCTGTGTTCGCTTTGTA 59.125 40.909 0.00 0.0 0.00 2.41 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
97 98 1.303806 CCGGATTCCGTGGGGTTTT 60.304 57.895 22.83 0.00 46.80 2.43
123 124 2.626266 GGGTTTTGTCGGGTTTCTTGAT 59.374 45.455 0.00 0.00 0.00 2.57
124 125 3.069016 GGGTTTTGTCGGGTTTCTTGATT 59.931 43.478 0.00 0.00 0.00 2.57
125 126 4.442332 GGGTTTTGTCGGGTTTCTTGATTT 60.442 41.667 0.00 0.00 0.00 2.17
189 190 3.335534 GTTGTGGTCTCGCGCGTT 61.336 61.111 30.98 0.00 0.00 4.84
204 205 0.248296 GCGTTCGTTTGCCTGTTTGA 60.248 50.000 0.00 0.00 0.00 2.69
205 206 1.462791 CGTTCGTTTGCCTGTTTGAC 58.537 50.000 0.00 0.00 0.00 3.18
262 263 0.170339 CTCGCCGGAAATTTTGGACC 59.830 55.000 5.05 0.00 0.00 4.46
292 293 6.249035 TGTTGGAATTTAGGAGCTTTAACG 57.751 37.500 0.00 0.00 0.00 3.18
350 351 4.946478 AGCTCGTATGCCTAGAAATTCT 57.054 40.909 0.00 0.00 0.00 2.40
351 352 4.626042 AGCTCGTATGCCTAGAAATTCTG 58.374 43.478 5.64 0.00 0.00 3.02
447 448 6.623767 GCCAGATGGAATTTACTGTTCAGAAC 60.624 42.308 6.32 6.32 37.39 3.01
473 474 7.362315 CCTGAATGCTTCAACATTATCTGAACA 60.362 37.037 0.00 0.00 40.31 3.18
503 504 4.032960 TGTATGGTTGAAGTGAGGCAAT 57.967 40.909 0.00 0.00 0.00 3.56
526 527 1.812922 GCGTGGGTCAGCAGATGAG 60.813 63.158 0.00 0.00 39.07 2.90
583 584 3.071602 TCTTGAAAGTCTGGGAAGGTCTG 59.928 47.826 0.00 0.00 0.00 3.51
650 651 5.163405 TGTGTAGTCTTGCCCATCTATCTTC 60.163 44.000 0.00 0.00 0.00 2.87
658 659 5.329191 TGCCCATCTATCTTCATGGATTT 57.671 39.130 0.00 0.00 42.11 2.17
662 663 5.415077 CCCATCTATCTTCATGGATTTGAGC 59.585 44.000 0.00 0.00 42.11 4.26
724 725 7.331934 TCTGCTTTCAGAGTATCACAACAATAC 59.668 37.037 0.00 0.00 43.95 1.89
750 751 9.109533 CATTTCGTGGTATTTAGTTTGTACAAC 57.890 33.333 8.07 4.01 0.00 3.32
783 784 5.709631 TGCTAATGGTCTAAAGTTGCATCAA 59.290 36.000 0.00 0.00 0.00 2.57
784 785 6.377996 TGCTAATGGTCTAAAGTTGCATCAAT 59.622 34.615 0.00 0.00 0.00 2.57
785 786 6.694411 GCTAATGGTCTAAAGTTGCATCAATG 59.306 38.462 0.00 0.00 0.00 2.82
841 842 2.620251 TCTGTTTGGGTGTGAGACAG 57.380 50.000 0.00 0.00 39.16 3.51
842 843 2.115427 TCTGTTTGGGTGTGAGACAGA 58.885 47.619 0.74 0.74 43.02 3.41
915 916 2.548057 TCGAAGTGAACATGCCTTGAAC 59.452 45.455 0.00 0.00 0.00 3.18
1010 1011 4.463050 TTTGACCTAAAATGGGAGTGGT 57.537 40.909 0.00 0.00 0.00 4.16
1017 1018 0.991920 AAATGGGAGTGGTCGGTCAT 59.008 50.000 0.00 0.00 0.00 3.06
1020 1021 1.874129 TGGGAGTGGTCGGTCATAAT 58.126 50.000 0.00 0.00 0.00 1.28
1114 1115 9.426534 CCCTCCCTCTTAAGAATTATCATTTTT 57.573 33.333 6.63 0.00 0.00 1.94
1141 1142 4.773510 CTCGCACTTTTTGAGAGGTAAAC 58.226 43.478 0.00 0.00 45.75 2.01
1150 1151 8.244113 ACTTTTTGAGAGGTAAACTGAAAACAG 58.756 33.333 0.00 0.00 32.34 3.16
1419 1420 3.343617 CCAACTCCAAATCCGAGCTTAA 58.656 45.455 0.00 0.00 0.00 1.85
1426 1427 5.601662 TCCAAATCCGAGCTTAATAGACTG 58.398 41.667 0.00 0.00 0.00 3.51
1435 1436 5.807520 CGAGCTTAATAGACTGCTTTCTTCA 59.192 40.000 0.00 0.00 35.76 3.02
1515 1517 2.044492 ACTCCCATCTCAACCTAGGTCA 59.956 50.000 16.64 3.94 0.00 4.02
1618 1620 6.644775 GCATTTCTGCTAGAGTTTATCTTCG 58.355 40.000 0.00 0.00 45.32 3.79
1626 1628 9.601971 CTGCTAGAGTTTATCTTCGAGTATAAC 57.398 37.037 0.00 0.00 39.64 1.89
1889 1892 7.148340 ACGAGGATGATCTTTCAATGAAGAAAC 60.148 37.037 0.00 0.00 38.98 2.78
2046 2049 4.022068 CCTGAAGGCATTGTATGTTTGTGT 60.022 41.667 0.00 0.00 0.00 3.72
2163 2410 6.544197 TGTTGAAGTCTAAACTGTGGCATTAA 59.456 34.615 0.00 0.00 35.36 1.40
2311 2618 8.846943 TTTCTTTTGTATTGCAGAGTGATAGA 57.153 30.769 0.00 0.00 0.00 1.98
2383 2690 2.625087 CCTTGGGATGGATTTCTTGGCT 60.625 50.000 0.00 0.00 0.00 4.75
2604 2912 7.679659 TTCGTATGTGATCTTATTTCTGACG 57.320 36.000 0.00 0.00 0.00 4.35
2605 2913 6.792326 TCGTATGTGATCTTATTTCTGACGT 58.208 36.000 0.00 0.00 0.00 4.34
2680 2988 3.763897 GGAACTTAATGGATGCCACTGTT 59.236 43.478 0.00 0.00 35.80 3.16
2689 2997 0.396435 ATGCCACTGTTGAGGAACGA 59.604 50.000 0.00 0.00 34.49 3.85
2814 3122 3.393089 TCTTCTCTCAGTGAGTTTGGC 57.607 47.619 19.53 0.00 43.13 4.52
3051 3365 3.724508 AGTATGTTCGAGCCATCAGAG 57.275 47.619 0.00 0.00 0.00 3.35
3256 3570 3.567478 AAGGGAGGATATCAAGTGTGC 57.433 47.619 4.83 0.00 0.00 4.57
3299 3613 0.892755 CACCAGCATTGTTCTGCCAT 59.107 50.000 0.00 0.00 43.33 4.40
3346 3660 1.002430 CTTGCTTGGCTGTGGACTCTA 59.998 52.381 0.00 0.00 0.00 2.43
3490 3804 4.965532 TGAAAATGGTTTCTTCCTGGGAAA 59.034 37.500 3.55 0.00 43.13 3.13
3500 3814 1.838112 TCCTGGGAAATGCATCACAC 58.162 50.000 0.00 0.00 0.00 3.82
3559 3873 5.175127 ACACATACTTGCATGATACGTGAA 58.825 37.500 6.60 0.00 0.00 3.18
3610 3924 8.213518 TGACCTAACTTTTCATGCATATCTTC 57.786 34.615 0.00 0.00 0.00 2.87
3705 4019 0.874607 GACGGTGTCGCACTTCTTGT 60.875 55.000 9.31 2.58 40.63 3.16
3769 4083 2.167487 AGAGAAGCGAAGAATGAGGGTC 59.833 50.000 0.00 0.00 0.00 4.46
3834 4148 1.117994 TCCAGCGAATCATCTCTGCT 58.882 50.000 0.00 0.00 37.13 4.24
3836 4150 2.093288 TCCAGCGAATCATCTCTGCTTT 60.093 45.455 0.00 0.00 37.13 3.51
3845 4160 6.600882 AATCATCTCTGCTTTCCATGTTTT 57.399 33.333 0.00 0.00 0.00 2.43
3846 4161 5.381174 TCATCTCTGCTTTCCATGTTTTG 57.619 39.130 0.00 0.00 0.00 2.44
3847 4162 3.648339 TCTCTGCTTTCCATGTTTTGC 57.352 42.857 0.00 0.00 0.00 3.68
3873 4188 3.786635 ACTGTTCTATCTGCCGTTCATC 58.213 45.455 0.00 0.00 0.00 2.92
3946 4261 4.035102 GGGTCAAAGCCGAGCCCT 62.035 66.667 5.52 0.00 45.93 5.19
4140 4455 3.041940 CAAGGACGACGCGGCTTT 61.042 61.111 11.76 0.00 33.59 3.51
4155 4470 0.041312 GCTTTGCAAGCGTCTTCGAA 60.041 50.000 0.00 0.00 45.74 3.71
4173 4488 1.555075 GAACTGACACCTGGCCTATCA 59.445 52.381 3.32 0.00 0.00 2.15
4182 4497 2.590092 GGCCTATCAGTGCCGGTT 59.410 61.111 1.90 0.00 38.00 4.44
4264 4585 4.184629 GTGGAGCGAGAGTTTAATGTGAT 58.815 43.478 0.00 0.00 0.00 3.06
4304 4625 2.158900 CGCCTCTGTAACTGGATGGATT 60.159 50.000 0.00 0.00 0.00 3.01
4305 4626 3.209410 GCCTCTGTAACTGGATGGATTG 58.791 50.000 0.00 0.00 0.00 2.67
4315 4636 4.212716 ACTGGATGGATTGATGGATGTTG 58.787 43.478 0.00 0.00 0.00 3.33
4376 4698 9.944663 TGAATAACTGACACTTTTACAATGTTC 57.055 29.630 0.00 0.00 0.00 3.18
5102 5435 5.529060 ACCAAGCAACTGAAAAGTAAGAGAG 59.471 40.000 0.00 0.00 0.00 3.20
5115 5448 5.543507 AGTAAGAGAGAAATCATGGCGAT 57.456 39.130 0.00 0.00 35.12 4.58
5123 5456 3.002656 AGAAATCATGGCGATACAAAGCG 59.997 43.478 0.00 0.00 37.63 4.68
5149 5482 4.698780 CACAGCAATCAGGATCTGAAGAAA 59.301 41.667 1.53 0.00 44.04 2.52
5151 5484 4.096081 CAGCAATCAGGATCTGAAGAAACC 59.904 45.833 1.53 0.00 44.04 3.27
5152 5485 4.018597 AGCAATCAGGATCTGAAGAAACCT 60.019 41.667 1.53 4.32 44.04 3.50
5153 5486 5.190528 AGCAATCAGGATCTGAAGAAACCTA 59.809 40.000 1.53 1.48 44.04 3.08
5154 5487 6.060788 GCAATCAGGATCTGAAGAAACCTAT 58.939 40.000 1.53 3.10 44.04 2.57
5155 5488 6.017275 GCAATCAGGATCTGAAGAAACCTATG 60.017 42.308 1.53 9.06 44.04 2.23
5156 5489 6.821616 ATCAGGATCTGAAGAAACCTATGT 57.178 37.500 1.53 0.00 44.04 2.29
5157 5490 7.921041 ATCAGGATCTGAAGAAACCTATGTA 57.079 36.000 1.53 0.00 44.04 2.29
5158 5491 7.113658 TCAGGATCTGAAGAAACCTATGTAC 57.886 40.000 8.44 0.00 37.57 2.90
5159 5492 6.667848 TCAGGATCTGAAGAAACCTATGTACA 59.332 38.462 0.00 0.00 37.57 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 1.647334 AACCCGACAAAACCCTCCCA 61.647 55.000 0.00 0.00 0.00 4.37
158 159 2.286772 ACCACAACGAAATCGCTGAAAC 60.287 45.455 12.62 0.00 44.43 2.78
178 179 2.201885 CAAACGAACGCGCGAGAC 60.202 61.111 39.36 23.85 42.48 3.36
189 190 1.668751 GAGTGTCAAACAGGCAAACGA 59.331 47.619 0.00 0.00 30.62 3.85
192 193 2.997980 TCAGAGTGTCAAACAGGCAAA 58.002 42.857 0.00 0.00 30.62 3.68
270 271 5.413523 TCCGTTAAAGCTCCTAAATTCCAAC 59.586 40.000 0.00 0.00 0.00 3.77
272 273 5.168647 TCCGTTAAAGCTCCTAAATTCCA 57.831 39.130 0.00 0.00 0.00 3.53
292 293 1.535226 GCGCCAAAATTACCCGATTCC 60.535 52.381 0.00 0.00 0.00 3.01
350 351 5.223449 AGAAAACCATAACGACCTTCTCA 57.777 39.130 0.00 0.00 0.00 3.27
351 352 4.326548 CGAGAAAACCATAACGACCTTCTC 59.673 45.833 0.00 0.00 35.87 2.87
503 504 4.639906 TGCTGACCCACGCATGCA 62.640 61.111 19.57 0.00 0.00 3.96
526 527 2.549754 CGAATGGGCCATTCTGATACAC 59.450 50.000 41.12 23.21 45.48 2.90
546 547 4.963276 TTCAAGAAATGGTGATAAGCCG 57.037 40.909 0.00 0.00 0.00 5.52
550 551 6.434028 CCCAGACTTTCAAGAAATGGTGATAA 59.566 38.462 10.91 0.00 0.00 1.75
650 651 4.913335 ACATAAGCTGCTCAAATCCATG 57.087 40.909 1.00 1.41 0.00 3.66
724 725 9.109533 GTTGTACAAACTAAATACCACGAAATG 57.890 33.333 10.51 0.00 0.00 2.32
774 775 5.122554 TGAATTTTCATGGCATTGATGCAAC 59.877 36.000 16.92 2.29 43.06 4.17
783 784 3.371965 AGAGCCTGAATTTTCATGGCAT 58.628 40.909 23.49 14.88 45.57 4.40
784 785 2.811410 AGAGCCTGAATTTTCATGGCA 58.189 42.857 23.49 0.00 45.57 4.92
785 786 3.950395 ACTAGAGCCTGAATTTTCATGGC 59.050 43.478 18.27 18.27 44.54 4.40
841 842 8.023128 ACATTACACAAACAATGAAGCTACATC 58.977 33.333 1.58 0.00 36.00 3.06
842 843 7.809331 CACATTACACAAACAATGAAGCTACAT 59.191 33.333 1.58 0.00 36.00 2.29
915 916 9.294030 GCAAATTTAACTCTGAAACTATCATGG 57.706 33.333 0.00 0.00 37.44 3.66
1114 1115 4.552166 CTCTCAAAAAGTGCGAGGAAAA 57.448 40.909 0.00 0.00 35.74 2.29
1150 1151 2.307934 AATGGTGTTTGTGTTGCCAC 57.692 45.000 0.00 0.00 42.19 5.01
1223 1224 8.842280 CACAAACCAGTTACTAATAAAACCTGA 58.158 33.333 0.00 0.00 0.00 3.86
1419 1420 3.840666 TCCCAGTGAAGAAAGCAGTCTAT 59.159 43.478 0.00 0.00 0.00 1.98
1426 1427 2.810852 CAGTTCTCCCAGTGAAGAAAGC 59.189 50.000 8.86 0.70 0.00 3.51
1435 1436 4.223923 CCAGAAATAGACAGTTCTCCCAGT 59.776 45.833 0.00 0.00 36.99 4.00
1663 1666 2.787473 TGTCAGGCTGTAAATCAGGG 57.213 50.000 15.27 0.00 43.78 4.45
2064 2067 9.829507 TGGATTTGAGAAACACATAAAACATTT 57.170 25.926 0.00 0.00 0.00 2.32
2117 2120 6.341408 ACATCAAGGGGGTAATGATTACTT 57.659 37.500 14.34 0.00 36.39 2.24
2229 2533 2.107950 TCCAGACCAAAGGCATTACG 57.892 50.000 0.00 0.00 0.00 3.18
2311 2618 5.981315 CACAAAGTCAAGAATCTTGTGCAAT 59.019 36.000 20.91 0.38 0.00 3.56
2383 2690 6.127423 GGCTAGGATGAACTTCAGTAACAGTA 60.127 42.308 0.00 0.00 0.00 2.74
2510 2817 6.418057 TCACTGCAAATTTACCTTTCCAAT 57.582 33.333 0.00 0.00 0.00 3.16
2604 2912 6.976088 TGAATCTAAGAGAGCATAGCACTAC 58.024 40.000 0.00 0.00 28.14 2.73
2605 2913 7.588497 TTGAATCTAAGAGAGCATAGCACTA 57.412 36.000 0.00 0.00 28.14 2.74
2680 2988 4.878971 TGATCAAAAAGTTGTCGTTCCTCA 59.121 37.500 0.00 0.00 36.07 3.86
2689 2997 5.693104 GCATGTGACATGATCAAAAAGTTGT 59.307 36.000 28.21 0.00 39.72 3.32
2771 3079 8.103948 AGAAAACACATCTTAACCTGATCAAG 57.896 34.615 0.00 0.00 0.00 3.02
2814 3122 8.592998 GTGAACAAGGACTACTTTATCAATACG 58.407 37.037 0.00 0.00 37.29 3.06
3051 3365 1.257743 TCTCCATATCGGCCAGTAGC 58.742 55.000 2.24 0.00 42.60 3.58
3102 3416 5.441718 TCTCCAATATGTCCTTTCTGCTT 57.558 39.130 0.00 0.00 0.00 3.91
3182 3496 7.096551 GGTAACATGACAAATTTTGCATACCT 58.903 34.615 18.02 10.70 30.01 3.08
3295 3609 3.703052 ACTTCATGGAGAATGGAAATGGC 59.297 43.478 8.39 0.00 36.86 4.40
3299 3613 6.239289 GGTTTCAACTTCATGGAGAATGGAAA 60.239 38.462 8.39 8.68 36.86 3.13
3365 3679 4.240888 CTGTATCTGTTATCATCCTGCCG 58.759 47.826 0.00 0.00 0.00 5.69
3490 3804 3.480470 GCCATAAGGTAGTGTGATGCAT 58.520 45.455 0.00 0.00 37.19 3.96
3500 3814 1.598130 GCCAGCGGCCATAAGGTAG 60.598 63.158 2.24 0.00 44.06 3.18
3554 3868 1.557443 GCACTCACGTTCCCTTCACG 61.557 60.000 0.00 0.00 43.52 4.35
3559 3873 0.889306 GACTAGCACTCACGTTCCCT 59.111 55.000 0.00 0.00 0.00 4.20
3579 3893 7.575414 TGCATGAAAAGTTAGGTCAGTTTAA 57.425 32.000 0.00 0.00 0.00 1.52
3583 3897 7.341805 AGATATGCATGAAAAGTTAGGTCAGT 58.658 34.615 10.16 0.00 0.00 3.41
3610 3924 0.669619 TGTCAACAATGGCTGCAGTG 59.330 50.000 16.64 8.09 30.51 3.66
3705 4019 3.885724 TTCTGTATTCGTCCAGCATCA 57.114 42.857 0.00 0.00 0.00 3.07
3769 4083 2.223377 GGAACGGCACAAAAGAGTACTG 59.777 50.000 0.00 0.00 0.00 2.74
3834 4148 3.450457 ACAGTTGAGGCAAAACATGGAAA 59.550 39.130 0.00 0.00 0.00 3.13
3836 4150 2.665165 ACAGTTGAGGCAAAACATGGA 58.335 42.857 0.00 0.00 0.00 3.41
3845 4160 2.355108 GGCAGATAGAACAGTTGAGGCA 60.355 50.000 0.00 0.00 0.00 4.75
3846 4161 2.284190 GGCAGATAGAACAGTTGAGGC 58.716 52.381 0.00 0.00 0.00 4.70
3847 4162 2.093973 ACGGCAGATAGAACAGTTGAGG 60.094 50.000 0.00 0.00 0.00 3.86
3873 4188 4.518249 GTTTATCTTCTTCTGGTCCTGGG 58.482 47.826 0.00 0.00 0.00 4.45
4027 4342 2.357881 TTCTGCTGCTGCACCGAG 60.358 61.111 14.93 5.19 45.31 4.63
4140 4455 0.249280 TCAGTTCGAAGACGCTTGCA 60.249 50.000 0.00 0.00 39.58 4.08
4155 4470 1.198713 CTGATAGGCCAGGTGTCAGT 58.801 55.000 5.01 0.00 33.42 3.41
4173 4488 1.276622 ATACTTCTCCAACCGGCACT 58.723 50.000 0.00 0.00 0.00 4.40
4182 4497 3.099905 ACTGCACAGCTATACTTCTCCA 58.900 45.455 0.00 0.00 0.00 3.86
4264 4585 1.000843 CGATTCCCGCCATGACTATCA 59.999 52.381 0.00 0.00 0.00 2.15
4304 4625 1.623311 ACACGAGACCAACATCCATCA 59.377 47.619 0.00 0.00 0.00 3.07
4305 4626 2.386661 ACACGAGACCAACATCCATC 57.613 50.000 0.00 0.00 0.00 3.51
4315 4636 3.482722 TTCGATCTACAACACGAGACC 57.517 47.619 0.00 0.00 36.22 3.85
4960 5292 2.933906 GTGTTTGTTTGAGTCAGACCGA 59.066 45.455 11.03 0.00 0.00 4.69
5102 5435 3.002246 TCGCTTTGTATCGCCATGATTTC 59.998 43.478 0.00 0.00 38.57 2.17
5115 5448 2.875317 TGATTGCTGTGTTCGCTTTGTA 59.125 40.909 0.00 0.00 0.00 2.41
5123 5456 3.603532 TCAGATCCTGATTGCTGTGTTC 58.396 45.455 0.00 0.00 35.39 3.18


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

AutoCloner maintained by Alex Coulton.