Multiple sequence alignment - TraesCS6B01G027800

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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 TraesCS6B01G027800 chr6B 100.000 5599 0 0 1 5599 16439498 16445096 0.000000e+00 10340.0
1 TraesCS6B01G027800 chr6B 95.972 4196 140 16 1 4184 15211226 15207048 0.000000e+00 6785.0
2 TraesCS6B01G027800 chr6D 93.834 4022 186 27 543 4539 8545351 8541367 0.000000e+00 5997.0
3 TraesCS6B01G027800 chr6D 86.854 3849 318 74 440 4204 34080926 34084670 0.000000e+00 4132.0
4 TraesCS6B01G027800 chr6D 94.118 2244 85 18 433 2643 8807150 8809379 0.000000e+00 3369.0
5 TraesCS6B01G027800 chr6D 93.374 1977 85 14 2581 4539 8809377 8811325 0.000000e+00 2883.0
6 TraesCS6B01G027800 chr6D 96.477 1192 41 1 1203 2394 8561403 8560213 0.000000e+00 1967.0
7 TraesCS6B01G027800 chr6D 88.569 1216 72 29 3728 4904 8559338 8558151 0.000000e+00 1413.0
8 TraesCS6B01G027800 chr6D 95.270 592 27 1 3140 3730 8560053 8559462 0.000000e+00 937.0
9 TraesCS6B01G027800 chr6D 91.692 662 28 5 543 1202 8562383 8561747 0.000000e+00 893.0
10 TraesCS6B01G027800 chr6D 94.689 546 26 3 1 545 8546025 8545482 0.000000e+00 845.0
11 TraesCS6B01G027800 chr6D 82.771 859 94 37 4418 5257 34084819 34085642 0.000000e+00 717.0
12 TraesCS6B01G027800 chr6D 89.144 479 31 11 4567 5025 8811324 8811801 1.350000e-160 577.0
13 TraesCS6B01G027800 chr6D 88.309 479 35 11 4567 5025 8541368 8540891 6.340000e-154 555.0
14 TraesCS6B01G027800 chr6D 93.884 327 19 1 219 545 8562839 8562514 5.040000e-135 492.0
15 TraesCS6B01G027800 chr6D 90.379 343 28 3 5258 5599 8554803 8554465 3.980000e-121 446.0
16 TraesCS6B01G027800 chr6D 95.181 166 7 1 2935 3100 8560216 8560052 1.550000e-65 261.0
17 TraesCS6B01G027800 chr6D 94.375 160 8 1 68 226 8563340 8563181 1.560000e-60 244.0
18 TraesCS6B01G027800 chr6A 91.653 3786 229 38 1 3730 9481393 9485147 0.000000e+00 5160.0
19 TraesCS6B01G027800 chr6A 89.225 1420 109 20 3728 5109 9485271 9486684 0.000000e+00 1735.0
20 TraesCS6B01G027800 chr5B 85.167 3290 314 77 507 3730 556786580 556783399 0.000000e+00 3212.0
21 TraesCS6B01G027800 chr5B 84.563 583 69 9 4324 4906 17672766 17673327 4.900000e-155 558.0
22 TraesCS6B01G027800 chr5B 85.060 502 48 10 3728 4204 556783276 556782777 2.340000e-133 486.0
23 TraesCS6B01G027800 chr5B 86.571 417 35 9 4457 4873 556782368 556781973 1.850000e-119 440.0
24 TraesCS6B01G027800 chr4A 73.472 1440 262 74 796 2185 737063916 737062547 3.100000e-117 433.0
25 TraesCS6B01G027800 chr4A 84.127 126 17 3 3975 4097 737067112 737066987 9.850000e-23 119.0
26 TraesCS6B01G027800 chr4A 80.357 112 21 1 500 610 737065050 737064939 3.590000e-12 84.2
27 TraesCS6B01G027800 chr5D 87.838 296 27 5 3895 4183 42078790 42079083 6.950000e-89 339.0
28 TraesCS6B01G027800 chr5A 80.000 120 20 4 5456 5573 520466632 520466515 9.990000e-13 86.1
29 TraesCS6B01G027800 chr2D 92.857 56 3 1 3027 3081 549126189 549126134 4.650000e-11 80.5


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 TraesCS6B01G027800 chr6B 16439498 16445096 5598 False 10340.000000 10340 100.000000 1 5599 1 chr6B.!!$F1 5598
1 TraesCS6B01G027800 chr6B 15207048 15211226 4178 True 6785.000000 6785 95.972000 1 4184 1 chr6B.!!$R1 4183
2 TraesCS6B01G027800 chr6D 8540891 8546025 5134 True 2465.666667 5997 92.277333 1 5025 3 chr6D.!!$R1 5024
3 TraesCS6B01G027800 chr6D 34080926 34085642 4716 False 2424.500000 4132 84.812500 440 5257 2 chr6D.!!$F2 4817
4 TraesCS6B01G027800 chr6D 8807150 8811801 4651 False 2276.333333 3369 92.212000 433 5025 3 chr6D.!!$F1 4592
5 TraesCS6B01G027800 chr6D 8554465 8563340 8875 True 831.625000 1967 93.228375 68 5599 8 chr6D.!!$R2 5531
6 TraesCS6B01G027800 chr6A 9481393 9486684 5291 False 3447.500000 5160 90.439000 1 5109 2 chr6A.!!$F1 5108
7 TraesCS6B01G027800 chr5B 556781973 556786580 4607 True 1379.333333 3212 85.599333 507 4873 3 chr5B.!!$R1 4366
8 TraesCS6B01G027800 chr5B 17672766 17673327 561 False 558.000000 558 84.563000 4324 4906 1 chr5B.!!$F1 582
9 TraesCS6B01G027800 chr4A 737062547 737067112 4565 True 212.066667 433 79.318667 500 4097 3 chr4A.!!$R1 3597

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
298 649 1.279496 TGCTCTTGTATGCTCCCACT 58.721 50.0 0.00 0.0 0.00 4.00 F
1991 5037 1.375551 AACCGATTGGCCGTTGTATC 58.624 50.0 0.00 0.0 39.70 2.24 F
3675 7453 0.179076 GGCAATGCCCCAATTAGCAC 60.179 55.0 14.47 0.0 44.06 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 5135 0.109919 GCCAAACGGTTTGTCGGATC 60.110 55.0 26.67 9.19 38.98 3.36 R
3695 7473 0.596082 GCGGCAAAACTTAGCTTCCA 59.404 50.0 0.00 0.00 0.00 3.53 R
5560 12747 0.034756 TGTGTGTGATGAACTCCGGG 59.965 55.0 0.00 0.00 0.00 5.73 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
266 617 6.291377 AGATTGCACCATCGATGTAGTTTAT 58.709 36.000 23.27 9.68 0.00 1.40
298 649 1.279496 TGCTCTTGTATGCTCCCACT 58.721 50.000 0.00 0.00 0.00 4.00
299 650 1.630369 TGCTCTTGTATGCTCCCACTT 59.370 47.619 0.00 0.00 0.00 3.16
1240 4241 1.407437 GCCCCAGACTTCATCGACAAT 60.407 52.381 0.00 0.00 0.00 2.71
1272 4273 4.519437 CTGCGAGGATGGCGAGCA 62.519 66.667 0.00 0.00 45.68 4.26
1356 4357 4.009370 TGTTGTGTGATCCGACCATTAA 57.991 40.909 0.00 0.00 0.00 1.40
1551 4573 7.495606 TGCAATAGTATAGGAACTGTGATTGTG 59.504 37.037 0.00 0.00 41.52 3.33
1608 4630 4.498513 CGCTGTTCGATACATGGTAAGGTA 60.499 45.833 0.00 0.00 41.67 3.08
1888 4931 3.981212 CCATTTATTTGGGGAGAGGTGT 58.019 45.455 0.00 0.00 32.80 4.16
1898 4941 2.777692 GGGGAGAGGTGTCATCCATTTA 59.222 50.000 0.00 0.00 34.62 1.40
1950 4994 3.551082 ACGAACAATTTTGTCGTCGTACA 59.449 39.130 17.06 0.00 46.56 2.90
1991 5037 1.375551 AACCGATTGGCCGTTGTATC 58.624 50.000 0.00 0.00 39.70 2.24
1994 5040 1.536496 CCGATTGGCCGTTGTATCGTA 60.536 52.381 17.06 0.00 38.48 3.43
2089 5135 5.449041 GCCATTGTACTGTTGTGTGATATGG 60.449 44.000 0.00 0.00 33.62 2.74
2335 5440 7.123098 ACATCATATGTTCCACACACATCAAAT 59.877 33.333 1.90 0.00 41.63 2.32
2354 5461 5.477984 TCAAATGGCTCAAAGATAGCACTTT 59.522 36.000 0.00 0.00 41.93 2.66
2362 5469 6.760770 GCTCAAAGATAGCACTTTACATCTCT 59.239 38.462 0.00 0.00 39.83 3.10
2448 5563 5.351189 CACAACGTTCCATGACATAGATCAA 59.649 40.000 0.00 0.00 30.82 2.57
2621 5736 4.271049 CACAACATTCCGTGACATAGATCC 59.729 45.833 0.00 0.00 35.02 3.36
2869 5990 5.585047 GGTCTATACATGTGGTTCTTGGAAC 59.415 44.000 9.11 2.19 0.00 3.62
2882 6003 4.826274 TCTTGGAACCAGAGGATGTAAG 57.174 45.455 0.00 0.00 0.00 2.34
3043 6770 1.616159 ATTGCTTTGCTTACACCGGT 58.384 45.000 0.00 0.00 0.00 5.28
3051 6778 3.134574 TGCTTACACCGGTCTTTCATT 57.865 42.857 2.59 0.00 0.00 2.57
3503 7278 1.906574 AGATTTTGGGCGACTCCACTA 59.093 47.619 0.00 0.00 36.38 2.74
3538 7313 8.291191 GGTTAGGAATATAACCGCTCTAGTAT 57.709 38.462 0.22 0.00 43.86 2.12
3640 7416 2.370349 TGAAACGAAAAGCTGGGTTCA 58.630 42.857 4.31 4.31 0.00 3.18
3675 7453 0.179076 GGCAATGCCCCAATTAGCAC 60.179 55.000 14.47 0.00 44.06 4.40
3695 7473 5.817816 AGCACAGCGTTTAGAGCTATAAAAT 59.182 36.000 14.80 2.40 44.06 1.82
3711 7489 7.976175 AGCTATAAAATGGAAGCTAAGTTTTGC 59.024 33.333 0.00 0.00 43.29 3.68
3713 7491 3.575965 AATGGAAGCTAAGTTTTGCCG 57.424 42.857 0.00 0.00 0.00 5.69
3714 7492 0.596082 TGGAAGCTAAGTTTTGCCGC 59.404 50.000 0.00 0.00 0.00 6.53
3736 7640 4.511082 GCCTTCTCTGAATATTGTCTCTGC 59.489 45.833 0.00 0.00 0.00 4.26
3820 7725 9.799106 CCAGGGTGATATTCATAAAACTTCTAT 57.201 33.333 0.00 0.00 0.00 1.98
3968 7903 3.988379 TTCTTTCGTGAGCTGCAAATT 57.012 38.095 1.02 0.00 0.00 1.82
4096 8031 7.336931 CCACATGCTTCAGGTACTACTTTTTAT 59.663 37.037 0.00 0.00 36.02 1.40
4129 8064 9.127277 ACCTTAAAACTCTTTGTAGCATTACAA 57.873 29.630 0.00 0.00 45.54 2.41
4130 8065 9.394477 CCTTAAAACTCTTTGTAGCATTACAAC 57.606 33.333 0.00 0.00 46.53 3.32
4268 8331 2.464157 AAAGTGTACTCAGAGCCAGC 57.536 50.000 0.00 0.00 0.00 4.85
4392 8483 7.023575 GGTCACTATAGTTTTGCATCAACTTG 58.976 38.462 15.06 8.90 35.95 3.16
4454 8575 5.357878 TGATGGACATCTTTGCAAATACTCC 59.642 40.000 13.23 13.85 38.60 3.85
4494 8619 6.368243 GGGCTGTAGTTCTTAGTAAAACTCAC 59.632 42.308 11.36 9.68 37.02 3.51
4553 8678 5.392595 GCAACTAACCTGTTGTTCTGTTTCA 60.393 40.000 8.78 0.00 46.33 2.69
4805 8936 9.699410 TGGAATTCTCAGTGGTCAAATAATAAT 57.301 29.630 5.23 0.00 0.00 1.28
4859 8990 6.882140 TGGTGGTTAATATGGTGTCTTAGTTG 59.118 38.462 0.00 0.00 0.00 3.16
4907 9045 5.240713 GCAGCTGCAATGTAATCTTTAGT 57.759 39.130 33.36 0.00 41.59 2.24
4908 9046 5.644644 GCAGCTGCAATGTAATCTTTAGTT 58.355 37.500 33.36 0.00 41.59 2.24
4910 9048 6.587608 GCAGCTGCAATGTAATCTTTAGTTTT 59.412 34.615 33.36 0.00 41.59 2.43
4913 9051 7.809806 AGCTGCAATGTAATCTTTAGTTTTGAC 59.190 33.333 1.02 0.00 0.00 3.18
4931 9903 5.708736 TTGACTGGTGGTATATTGTGGAT 57.291 39.130 0.00 0.00 0.00 3.41
4994 9966 0.730265 TGCAAACAAGTCACCACGTC 59.270 50.000 0.00 0.00 0.00 4.34
4997 9969 2.159435 GCAAACAAGTCACCACGTCTTT 60.159 45.455 0.00 0.00 0.00 2.52
5039 10011 7.334844 TCTGCTGATTATACGGTATATCCAG 57.665 40.000 20.99 20.99 35.57 3.86
5114 12153 8.506437 CATGAGTGTTTGTGTTAGAATACATGT 58.494 33.333 2.69 2.69 30.00 3.21
5117 12156 6.995686 AGTGTTTGTGTTAGAATACATGTCCA 59.004 34.615 0.00 0.00 30.00 4.02
5119 12158 7.962918 GTGTTTGTGTTAGAATACATGTCCATC 59.037 37.037 0.00 0.00 30.00 3.51
5124 12163 9.764363 TGTGTTAGAATACATGTCCATCTATTC 57.236 33.333 0.00 5.10 32.38 1.75
5139 12178 5.048921 CCATCTATTCGCTTGCATCAGAATT 60.049 40.000 13.66 0.00 35.30 2.17
5141 12180 2.925578 TTCGCTTGCATCAGAATTGG 57.074 45.000 0.00 0.00 0.00 3.16
5143 12182 2.011947 TCGCTTGCATCAGAATTGGAG 58.988 47.619 0.00 0.00 0.00 3.86
5155 12194 5.569355 TCAGAATTGGAGCAATGGAAGTTA 58.431 37.500 0.00 0.00 34.04 2.24
5265 12451 8.296713 GCTGTGAGTCAAATTGGATTTTTACTA 58.703 33.333 0.00 0.00 30.31 1.82
5382 12568 1.740043 GCTGCCGGCAAAATAAGCATT 60.740 47.619 32.09 0.00 41.35 3.56
5387 12573 3.447742 CCGGCAAAATAAGCATTCTTCC 58.552 45.455 0.00 0.00 33.85 3.46
5402 12588 3.325293 TCTTCCTGCAGCTTGACTTAG 57.675 47.619 8.66 0.00 0.00 2.18
5405 12591 2.529632 TCCTGCAGCTTGACTTAGAGA 58.470 47.619 8.66 0.00 0.00 3.10
5407 12593 2.999355 CCTGCAGCTTGACTTAGAGAAC 59.001 50.000 8.66 0.00 0.00 3.01
5420 12606 6.768861 TGACTTAGAGAACCTCTAGTAGATGC 59.231 42.308 0.00 0.00 42.92 3.91
5421 12607 6.066032 ACTTAGAGAACCTCTAGTAGATGCC 58.934 44.000 0.00 0.00 42.92 4.40
5431 12617 5.782845 CCTCTAGTAGATGCCCTAAATTCCT 59.217 44.000 0.00 0.00 0.00 3.36
5436 12622 4.455070 AGATGCCCTAAATTCCTTACCC 57.545 45.455 0.00 0.00 0.00 3.69
5452 12638 4.490743 CTTACCCGCAAAACCTAAAATGG 58.509 43.478 0.00 0.00 0.00 3.16
5499 12685 4.201628 CGCAGAAGATATACCGCAAATAGC 60.202 45.833 0.00 0.00 40.87 2.97
5508 12694 0.179140 CCGCAAATAGCACCGCAAAT 60.179 50.000 0.00 0.00 46.13 2.32
5536 12722 8.692110 AAAAACTTAAACTTAAACAGGTTCCG 57.308 30.769 0.00 0.00 33.04 4.30
5537 12723 7.395190 AAACTTAAACTTAAACAGGTTCCGT 57.605 32.000 0.00 0.00 33.04 4.69
5538 12724 7.395190 AACTTAAACTTAAACAGGTTCCGTT 57.605 32.000 0.00 0.00 33.04 4.44
5539 12725 6.788243 ACTTAAACTTAAACAGGTTCCGTTG 58.212 36.000 0.00 0.00 33.04 4.10
5558 12745 2.388735 TGCATAGATCAGTCCGGAACT 58.611 47.619 5.23 2.71 39.44 3.01
5560 12747 2.288518 GCATAGATCAGTCCGGAACTCC 60.289 54.545 5.23 0.00 35.45 3.85
5578 12765 0.673644 CCCCGGAGTTCATCACACAC 60.674 60.000 0.73 0.00 0.00 3.82
5579 12766 0.034756 CCCGGAGTTCATCACACACA 59.965 55.000 0.73 0.00 0.00 3.72
5580 12767 1.148310 CCGGAGTTCATCACACACAC 58.852 55.000 0.00 0.00 0.00 3.82
5586 12773 4.060900 GAGTTCATCACACACACACAGAT 58.939 43.478 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
266 617 4.339872 ACAAGAGCAATGGCAAAATTCA 57.660 36.364 0.00 0.00 44.61 2.57
298 649 3.511699 CTGTTATGTCTCGCTACAGCAA 58.488 45.455 1.61 0.00 42.21 3.91
299 650 2.159240 CCTGTTATGTCTCGCTACAGCA 60.159 50.000 1.61 0.00 42.21 4.41
1147 3805 1.786937 AGCCCACCAAATGAACACAA 58.213 45.000 0.00 0.00 0.00 3.33
1240 4241 2.605094 GCAGAAGAGCGTGACAACA 58.395 52.632 0.00 0.00 0.00 3.33
1356 4357 6.976934 AAAATCAAACCAACCACTCTACAT 57.023 33.333 0.00 0.00 0.00 2.29
1551 4573 2.054140 TTTGCACGCCAAGAACCGAC 62.054 55.000 0.00 0.00 34.34 4.79
1608 4630 2.793017 TCTCCCCCAAGATGATTGGAT 58.207 47.619 8.20 0.00 42.06 3.41
1802 4833 4.900635 ATTTTTGTCGGATCTACATGGC 57.099 40.909 0.00 0.00 0.00 4.40
1888 4931 6.413783 TGAGTATAACGGCTAAATGGATGA 57.586 37.500 0.00 0.00 0.00 2.92
1898 4941 8.958119 TCAAAATCTAAATGAGTATAACGGCT 57.042 30.769 0.00 0.00 0.00 5.52
1991 5037 6.452244 TTGTCGAATGCAGATCATATTACG 57.548 37.500 0.00 0.00 34.33 3.18
2089 5135 0.109919 GCCAAACGGTTTGTCGGATC 60.110 55.000 26.67 9.19 38.98 3.36
2244 5345 8.253113 ACAATGGCTGAATCGATTTTCTTAATT 58.747 29.630 12.81 6.17 0.00 1.40
2257 5359 9.754382 ATTATTAAACATGACAATGGCTGAATC 57.246 29.630 0.00 0.00 38.19 2.52
2335 5440 4.905429 TGTAAAGTGCTATCTTTGAGCCA 58.095 39.130 10.61 0.00 39.30 4.75
2499 5614 2.476185 GCTTGATGTGTGCGGAACATAC 60.476 50.000 0.00 0.00 41.97 2.39
2621 5736 1.872952 TGCAGTGGAACATGTTTCTCG 59.127 47.619 17.76 11.17 44.52 4.04
2798 5913 2.452600 AGGCAAGGGAACAGTTTGAA 57.547 45.000 0.00 0.00 0.00 2.69
2799 5914 3.586470 TTAGGCAAGGGAACAGTTTGA 57.414 42.857 0.00 0.00 0.00 2.69
2869 5990 3.118112 ACTCATTGGCTTACATCCTCTGG 60.118 47.826 0.00 0.00 0.00 3.86
2882 6003 2.094762 AGTGGTAACGACTCATTGGC 57.905 50.000 0.00 0.00 42.51 4.52
2943 6665 7.743104 AGTTTCTGTAATGAAAGTGCTAATCG 58.257 34.615 0.00 0.00 37.95 3.34
3095 6822 5.984695 TCCTAAGCGAATAGATGTAGCAT 57.015 39.130 0.00 0.00 0.00 3.79
3503 7278 6.605995 GGTTATATTCCTAACCCAACAAGCTT 59.394 38.462 0.00 0.00 43.23 3.74
3640 7416 1.890876 TGCCGTCAATGCTGTAAAGT 58.109 45.000 0.00 0.00 0.00 2.66
3672 7450 5.464965 TTTTATAGCTCTAAACGCTGTGC 57.535 39.130 3.93 0.00 38.38 4.57
3675 7453 6.844696 TCCATTTTATAGCTCTAAACGCTG 57.155 37.500 3.93 3.42 38.38 5.18
3695 7473 0.596082 GCGGCAAAACTTAGCTTCCA 59.404 50.000 0.00 0.00 0.00 3.53
3711 7489 4.054671 GAGACAATATTCAGAGAAGGCGG 58.945 47.826 0.00 0.00 0.00 6.13
3713 7491 4.511082 GCAGAGACAATATTCAGAGAAGGC 59.489 45.833 0.00 0.00 0.00 4.35
3714 7492 5.916318 AGCAGAGACAATATTCAGAGAAGG 58.084 41.667 0.00 0.00 0.00 3.46
3736 7640 8.491152 CACTTGCGTCCATAGAAAATAATCTAG 58.509 37.037 0.00 0.00 35.48 2.43
3858 7764 4.403432 CCATTACAATTTGCCTCCACAGAT 59.597 41.667 0.00 0.00 0.00 2.90
3911 7844 2.653890 CAGCTCGTGGAAAACATGTTG 58.346 47.619 12.82 0.00 37.38 3.33
3922 7855 5.984233 TGTTAATAATTAGCAGCTCGTGG 57.016 39.130 0.00 0.00 0.00 4.94
3925 7860 8.338259 AGAAACATGTTAATAATTAGCAGCTCG 58.662 33.333 12.39 0.00 29.82 5.03
3968 7903 5.123227 CAGTAACTTGTGAAACTCCTTCCA 58.877 41.667 0.00 0.00 38.04 3.53
4096 8031 8.833493 GCTACAAAGAGTTTTAAGGTGAGTTTA 58.167 33.333 0.00 0.00 0.00 2.01
4103 8038 8.685838 TGTAATGCTACAAAGAGTTTTAAGGT 57.314 30.769 0.00 0.00 35.03 3.50
4104 8039 9.394477 GTTGTAATGCTACAAAGAGTTTTAAGG 57.606 33.333 0.50 0.00 46.91 2.69
4108 8043 7.996385 ACTGTTGTAATGCTACAAAGAGTTTT 58.004 30.769 0.50 0.00 46.91 2.43
4129 8064 3.502211 CCTTCGCATTCCAGTTTTACTGT 59.498 43.478 6.13 0.00 44.50 3.55
4130 8065 3.751175 TCCTTCGCATTCCAGTTTTACTG 59.249 43.478 0.00 0.00 45.53 2.74
4208 8188 7.874016 TGCATTCATCTCATTAACAAGCTTTTT 59.126 29.630 0.00 0.00 0.00 1.94
4268 8331 6.105333 ACACTACTCTAGACAACTAGTACCG 58.895 44.000 0.00 0.00 44.45 4.02
4351 8441 3.449018 AGTGACCTTTCGAGCTACATGAT 59.551 43.478 0.00 0.00 0.00 2.45
4454 8575 2.098443 ACAGCCCAAACAGTTAAACACG 59.902 45.455 0.00 0.00 0.00 4.49
4494 8619 5.825507 AGAAAAGCTTGCACTGTAAGAAAG 58.174 37.500 10.77 0.00 37.43 2.62
4571 8696 5.586643 CAGTTTAGGATTAAGGCTTGGACTC 59.413 44.000 10.69 1.08 0.00 3.36
4572 8697 5.014228 ACAGTTTAGGATTAAGGCTTGGACT 59.986 40.000 10.69 5.49 0.00 3.85
4616 8741 2.558378 ACCATCAGAACATGCAGATCG 58.442 47.619 0.00 0.00 0.00 3.69
4619 8744 3.979101 TGTACCATCAGAACATGCAGA 57.021 42.857 0.00 0.00 0.00 4.26
4805 8936 3.549827 CGCAAAACAACCACAGCTGAATA 60.550 43.478 23.35 0.00 0.00 1.75
4859 8990 1.494824 ACGAGCAACAAACCGACTAC 58.505 50.000 0.00 0.00 0.00 2.73
4906 9044 5.708230 TCCACAATATACCACCAGTCAAAAC 59.292 40.000 0.00 0.00 0.00 2.43
4907 9045 5.882040 TCCACAATATACCACCAGTCAAAA 58.118 37.500 0.00 0.00 0.00 2.44
4908 9046 5.506730 TCCACAATATACCACCAGTCAAA 57.493 39.130 0.00 0.00 0.00 2.69
4910 9048 6.157123 TGTTATCCACAATATACCACCAGTCA 59.843 38.462 0.00 0.00 29.87 3.41
4913 9051 9.739276 AATATGTTATCCACAATATACCACCAG 57.261 33.333 0.00 0.00 39.50 4.00
4972 9944 1.333308 CGTGGTGACTTGTTTGCATCA 59.667 47.619 0.00 0.00 0.00 3.07
4975 9947 0.730265 GACGTGGTGACTTGTTTGCA 59.270 50.000 0.00 0.00 0.00 4.08
5039 10011 7.968405 ACGGTTTTGAAAATCATCTGCTATAAC 59.032 33.333 1.52 0.00 0.00 1.89
5047 10019 9.594478 AGTTTTTAACGGTTTTGAAAATCATCT 57.406 25.926 0.00 0.00 36.23 2.90
5114 12153 3.070015 TCTGATGCAAGCGAATAGATGGA 59.930 43.478 0.00 0.00 0.00 3.41
5117 12156 5.048921 CCAATTCTGATGCAAGCGAATAGAT 60.049 40.000 0.00 0.00 28.68 1.98
5119 12158 4.274214 TCCAATTCTGATGCAAGCGAATAG 59.726 41.667 0.00 0.00 28.68 1.73
5124 12163 1.533338 GCTCCAATTCTGATGCAAGCG 60.533 52.381 0.00 0.00 0.00 4.68
5139 12178 4.314522 TGGATTAACTTCCATTGCTCCA 57.685 40.909 0.00 0.00 40.90 3.86
5141 12180 6.272822 AGTTTGGATTAACTTCCATTGCTC 57.727 37.500 0.00 0.00 45.08 4.26
5143 12182 8.250332 TGATTAGTTTGGATTAACTTCCATTGC 58.750 33.333 0.00 0.00 45.08 3.56
5155 12194 8.695456 GGTAACAATGGATGATTAGTTTGGATT 58.305 33.333 0.00 0.00 0.00 3.01
5176 12215 5.544650 TGCTTGAGTTAGTAGGTTGGTAAC 58.455 41.667 0.00 0.00 0.00 2.50
5265 12451 7.867921 TCACTTATAACATGGAGTGGGTATTT 58.132 34.615 0.00 0.00 39.85 1.40
5371 12557 4.465305 AGCTGCAGGAAGAATGCTTATTTT 59.535 37.500 17.12 0.00 44.17 1.82
5372 12558 4.021916 AGCTGCAGGAAGAATGCTTATTT 58.978 39.130 17.12 0.00 44.17 1.40
5373 12559 3.629087 AGCTGCAGGAAGAATGCTTATT 58.371 40.909 17.12 0.00 44.17 1.40
5382 12568 2.899900 TCTAAGTCAAGCTGCAGGAAGA 59.100 45.455 17.12 1.83 0.00 2.87
5387 12573 2.999355 GGTTCTCTAAGTCAAGCTGCAG 59.001 50.000 10.11 10.11 0.00 4.41
5402 12588 3.839778 AGGGCATCTACTAGAGGTTCTC 58.160 50.000 0.00 0.00 0.00 2.87
5405 12591 6.043358 GGAATTTAGGGCATCTACTAGAGGTT 59.957 42.308 0.00 0.00 0.00 3.50
5407 12593 5.782845 AGGAATTTAGGGCATCTACTAGAGG 59.217 44.000 0.00 0.00 0.00 3.69
5420 12606 2.721425 TGCGGGTAAGGAATTTAGGG 57.279 50.000 0.00 0.00 0.00 3.53
5421 12607 4.381185 GGTTTTGCGGGTAAGGAATTTAGG 60.381 45.833 0.00 0.00 0.00 2.69
5431 12617 3.896272 ACCATTTTAGGTTTTGCGGGTAA 59.104 39.130 0.00 0.00 39.34 2.85
5452 12638 1.732683 CATGAACCGCCCGCAAAAC 60.733 57.895 0.00 0.00 0.00 2.43
5483 12669 2.093783 GCGGTGCTATTTGCGGTATATC 59.906 50.000 0.00 0.00 46.63 1.63
5485 12671 1.202545 TGCGGTGCTATTTGCGGTATA 60.203 47.619 0.00 0.00 46.63 1.47
5528 12714 2.868583 CTGATCTATGCAACGGAACCTG 59.131 50.000 0.00 0.00 0.00 4.00
5536 12722 2.866762 GTTCCGGACTGATCTATGCAAC 59.133 50.000 1.83 0.00 0.00 4.17
5537 12723 2.766263 AGTTCCGGACTGATCTATGCAA 59.234 45.455 1.83 0.00 37.17 4.08
5538 12724 2.362397 GAGTTCCGGACTGATCTATGCA 59.638 50.000 1.83 0.00 39.19 3.96
5539 12725 2.288518 GGAGTTCCGGACTGATCTATGC 60.289 54.545 1.83 0.00 39.19 3.14
5558 12745 0.834261 TGTGTGATGAACTCCGGGGA 60.834 55.000 9.33 0.00 0.00 4.81
5560 12747 0.034756 TGTGTGTGATGAACTCCGGG 59.965 55.000 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.