Multiple sequence alignment - TraesCS1D01G175100

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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 TraesCS1D01G175100 chr1D 100.000 3669 0 0 1 3669 249318310 249321978 0.000000e+00 6776.0
1 TraesCS1D01G175100 chr1D 100.000 94 0 0 3974 4067 249322283 249322376 1.500000e-39 174.0
2 TraesCS1D01G175100 chr1A 95.114 3213 116 16 1 3187 298155667 298152470 0.000000e+00 5025.0
3 TraesCS1D01G175100 chr1B 94.872 2730 103 14 479 3187 329298192 329295479 0.000000e+00 4231.0
4 TraesCS1D01G175100 chr1B 91.942 484 24 7 1 481 329298851 329298380 0.000000e+00 664.0
5 TraesCS1D01G175100 chr1B 80.739 514 57 21 3192 3667 49019685 49019176 2.990000e-96 363.0
6 TraesCS1D01G175100 chr7B 89.876 484 18 8 3192 3645 616417235 616417717 9.730000e-166 593.0
7 TraesCS1D01G175100 chr7B 100.000 31 0 0 2566 2596 72280012 72280042 1.580000e-04 58.4
8 TraesCS1D01G175100 chr5D 93.015 272 14 4 3401 3669 367504125 367504394 3.810000e-105 392.0
9 TraesCS1D01G175100 chr5D 91.753 194 13 3 3477 3669 367504117 367503926 2.410000e-67 267.0
10 TraesCS1D01G175100 chr5D 88.660 97 8 2 3974 4067 367504475 367504571 9.240000e-22 115.0
11 TraesCS1D01G175100 chr4D 97.222 72 2 0 3192 3263 317549508 317549579 5.520000e-24 122.0
12 TraesCS1D01G175100 chr4B 98.039 51 1 0 10 60 106959423 106959373 5.600000e-14 89.8
13 TraesCS1D01G175100 chr7A 100.000 31 0 0 2566 2596 118106117 118106147 1.580000e-04 58.4


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 TraesCS1D01G175100 chr1D 249318310 249322376 4066 False 3475.0 6776 100.000 1 4067 2 chr1D.!!$F1 4066
1 TraesCS1D01G175100 chr1A 298152470 298155667 3197 True 5025.0 5025 95.114 1 3187 1 chr1A.!!$R1 3186
2 TraesCS1D01G175100 chr1B 329295479 329298851 3372 True 2447.5 4231 93.407 1 3187 2 chr1B.!!$R2 3186
3 TraesCS1D01G175100 chr1B 49019176 49019685 509 True 363.0 363 80.739 3192 3667 1 chr1B.!!$R1 475

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
461 465 0.370273 CGCGAATTCAAGAACTCGGG 59.630 55.0 14.39 14.39 43.91 5.14 F
896 1100 0.700564 TTCCCTTGCCTTGCATCTCT 59.299 50.0 0.00 0.00 38.76 3.10 F
2463 2701 0.735632 GTGCAGAGAACAGAGGCGAG 60.736 60.0 0.00 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2389 2627 0.394216 TCTCACCAAATCGCCATGGG 60.394 55.000 15.13 3.69 41.17 4.00 R
2540 2778 1.153127 TGGAAAAACGGCACCGACT 60.153 52.632 17.40 0.00 42.83 4.18 R
3264 3502 0.323633 CCCTTGCATCATCACACCCA 60.324 55.000 0.00 0.00 0.00 4.51 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
42 43 5.783111 TCTCACAATCATGAAAAGACTCGA 58.217 37.500 0.00 0.00 0.00 4.04
89 90 2.271800 CCAGACAGTGATTTACGCTCC 58.728 52.381 0.00 0.00 37.22 4.70
103 104 1.084370 CGCTCCAATCACCCGTCTTC 61.084 60.000 0.00 0.00 0.00 2.87
156 157 2.691522 CGCGCAATCACAGAGACG 59.308 61.111 8.75 0.00 0.00 4.18
244 248 2.401351 GGCGTACGATTCCTTATCCAC 58.599 52.381 21.65 0.00 0.00 4.02
246 250 2.035576 GCGTACGATTCCTTATCCACCT 59.964 50.000 21.65 0.00 0.00 4.00
274 278 2.098117 CCAAAGGTCGAATGATGGCTTC 59.902 50.000 0.00 0.00 0.00 3.86
381 385 1.153168 CCCACCATCCATCGGTCAC 60.153 63.158 0.00 0.00 33.25 3.67
426 430 2.820973 GCAGCCAGCACCCAAAAA 59.179 55.556 0.00 0.00 44.79 1.94
428 432 1.069596 CAGCCAGCACCCAAAAACC 59.930 57.895 0.00 0.00 0.00 3.27
461 465 0.370273 CGCGAATTCAAGAACTCGGG 59.630 55.000 14.39 14.39 43.91 5.14
462 466 0.727398 GCGAATTCAAGAACTCGGGG 59.273 55.000 14.30 0.00 39.99 5.73
818 1022 5.137429 ACCACTACTACCATTCCCCTACTAT 59.863 44.000 0.00 0.00 0.00 2.12
892 1096 1.986210 GCCTTCCCTTGCCTTGCAT 60.986 57.895 0.00 0.00 38.76 3.96
893 1097 1.953231 GCCTTCCCTTGCCTTGCATC 61.953 60.000 0.00 0.00 38.76 3.91
896 1100 0.700564 TTCCCTTGCCTTGCATCTCT 59.299 50.000 0.00 0.00 38.76 3.10
1011 1215 1.934463 CGACGCCATGGATAAGCAC 59.066 57.895 18.40 0.00 0.00 4.40
1054 1258 1.561769 ATCGCTGGTGGTTCCATGGA 61.562 55.000 11.44 11.44 46.12 3.41
1695 1899 4.851179 GGGTCGGGTTCGCCATCC 62.851 72.222 0.00 0.00 39.65 3.51
1709 1913 2.518587 ATCCGCCGACGATGGAGA 60.519 61.111 12.51 0.00 43.93 3.71
1712 1916 4.907034 CGCCGACGATGGAGACCG 62.907 72.222 0.00 0.00 43.93 4.79
1716 1920 1.444917 CCGACGATGGAGACCGATCA 61.445 60.000 0.00 0.00 0.00 2.92
1720 1924 1.738346 CGATGGAGACCGATCAGCCA 61.738 60.000 0.00 0.00 36.39 4.75
1724 1928 1.227205 GAGACCGATCAGCCAGCAG 60.227 63.158 0.00 0.00 0.00 4.24
1891 2095 2.259917 TCCTGCATCAGACCAAGAAGA 58.740 47.619 0.00 0.00 32.44 2.87
1892 2096 2.235650 TCCTGCATCAGACCAAGAAGAG 59.764 50.000 0.00 0.00 32.44 2.85
1895 2099 1.339438 GCATCAGACCAAGAAGAGCCA 60.339 52.381 0.00 0.00 0.00 4.75
2280 2484 1.666553 CGCGTGCTACCACTCCAAA 60.667 57.895 0.00 0.00 39.86 3.28
2361 2569 3.208623 TACGTCCCCCTCGTGGTCA 62.209 63.158 2.33 0.00 41.62 4.02
2389 2627 6.040166 ACATGCATCTCCATTTTCCATTAGTC 59.960 38.462 0.00 0.00 0.00 2.59
2418 2656 3.488678 CGATTTGGTGAGATCGACTGATG 59.511 47.826 0.00 0.00 45.90 3.07
2463 2701 0.735632 GTGCAGAGAACAGAGGCGAG 60.736 60.000 0.00 0.00 0.00 5.03
2469 2707 2.604686 AACAGAGGCGAGGGCAGA 60.605 61.111 0.00 0.00 42.47 4.26
2542 2780 3.238497 TGGCGTACCTGCACCAGT 61.238 61.111 0.00 0.00 36.63 4.00
2545 2783 2.126071 CGTACCTGCACCAGTCGG 60.126 66.667 0.00 0.00 38.77 4.79
2615 2853 1.613317 ATCATCCTGTCGACGCCCAA 61.613 55.000 11.62 0.00 0.00 4.12
2727 2965 4.078516 AAGTGCCCGGAGTACGCC 62.079 66.667 0.73 5.41 42.52 5.68
3101 3339 1.813513 AGGAGACCATTTGTGCTTCG 58.186 50.000 0.00 0.00 0.00 3.79
3106 3344 1.169661 ACCATTTGTGCTTCGGCGAA 61.170 50.000 22.33 22.33 45.37 4.70
3126 3364 4.494764 CGAAACACGATCTCTTAGTTACCG 59.505 45.833 0.00 0.00 45.77 4.02
3187 3425 8.319146 TGTTTCTCTTTATTCTCGGAAGGTATT 58.681 33.333 0.00 0.00 0.00 1.89
3188 3426 8.604890 GTTTCTCTTTATTCTCGGAAGGTATTG 58.395 37.037 0.00 0.00 0.00 1.90
3189 3427 7.419711 TCTCTTTATTCTCGGAAGGTATTGT 57.580 36.000 0.00 0.00 0.00 2.71
3190 3428 7.848128 TCTCTTTATTCTCGGAAGGTATTGTT 58.152 34.615 0.00 0.00 0.00 2.83
3203 3441 4.631234 AGGTATTGTTAGGATGGAGGTGA 58.369 43.478 0.00 0.00 0.00 4.02
3224 3462 7.260603 GGTGATGCCTTATGAAATATAATGCC 58.739 38.462 0.00 0.00 0.00 4.40
3237 3475 6.417191 AATATAATGCCGCATACTTTACCG 57.583 37.500 6.22 0.00 0.00 4.02
3238 3476 0.661020 AATGCCGCATACTTTACCGC 59.339 50.000 6.22 0.00 0.00 5.68
3242 3480 1.365699 CCGCATACTTTACCGCTTGT 58.634 50.000 0.00 0.00 0.00 3.16
3244 3482 1.730064 CGCATACTTTACCGCTTGTGT 59.270 47.619 0.00 0.00 0.00 3.72
3250 3488 6.468000 GCATACTTTACCGCTTGTGTTATTTC 59.532 38.462 0.00 0.00 0.00 2.17
3253 3491 5.761234 ACTTTACCGCTTGTGTTATTTCTGA 59.239 36.000 0.00 0.00 0.00 3.27
3254 3492 5.856126 TTACCGCTTGTGTTATTTCTGAG 57.144 39.130 0.00 0.00 0.00 3.35
3263 3501 6.024552 TGTGTTATTTCTGAGGCATTTTCC 57.975 37.500 0.00 0.00 0.00 3.13
3264 3502 5.774690 TGTGTTATTTCTGAGGCATTTTCCT 59.225 36.000 0.00 0.00 39.67 3.36
3272 3511 0.482446 AGGCATTTTCCTGGGTGTGA 59.518 50.000 0.00 0.00 34.56 3.58
3273 3512 1.077663 AGGCATTTTCCTGGGTGTGAT 59.922 47.619 0.00 0.00 34.56 3.06
3274 3513 1.205417 GGCATTTTCCTGGGTGTGATG 59.795 52.381 0.00 0.00 0.00 3.07
3294 3534 1.595093 ATGCAAGGGCCAAGTTACGC 61.595 55.000 6.18 0.00 40.13 4.42
3299 3539 2.033602 GGCCAAGTTACGCCCAGT 59.966 61.111 0.00 0.00 39.39 4.00
3300 3540 2.038837 GGCCAAGTTACGCCCAGTC 61.039 63.158 0.00 0.00 39.39 3.51
3303 3543 1.600023 CCAAGTTACGCCCAGTCAAA 58.400 50.000 0.00 0.00 0.00 2.69
3304 3544 2.159382 CCAAGTTACGCCCAGTCAAAT 58.841 47.619 0.00 0.00 0.00 2.32
3305 3545 2.556622 CCAAGTTACGCCCAGTCAAATT 59.443 45.455 0.00 0.00 0.00 1.82
3309 3549 5.813080 AGTTACGCCCAGTCAAATTTATC 57.187 39.130 0.00 0.00 0.00 1.75
3315 3555 6.119536 ACGCCCAGTCAAATTTATCTTCATA 58.880 36.000 0.00 0.00 0.00 2.15
3342 3588 6.014242 CCATGGCTAGATAGTTACTTCCATCA 60.014 42.308 0.00 0.00 31.93 3.07
3344 3590 6.817184 TGGCTAGATAGTTACTTCCATCAAC 58.183 40.000 0.00 0.00 0.00 3.18
3348 3594 7.982354 GCTAGATAGTTACTTCCATCAACTTGT 59.018 37.037 0.00 0.00 34.48 3.16
3356 3624 8.969267 GTTACTTCCATCAACTTGTAGATATCG 58.031 37.037 0.00 0.00 0.00 2.92
3358 3626 4.883083 TCCATCAACTTGTAGATATCGGC 58.117 43.478 0.00 0.00 0.00 5.54
3362 3630 5.290493 TCAACTTGTAGATATCGGCCATT 57.710 39.130 2.24 0.00 0.00 3.16
3376 3644 2.101249 CGGCCATTTTTCCTGCATGTAT 59.899 45.455 2.24 0.00 0.00 2.29
3517 3786 8.713971 TGATATATTTGGAAGAGCACTTAAGGA 58.286 33.333 7.53 0.00 36.39 3.36
3519 3788 3.703001 TTGGAAGAGCACTTAAGGAGG 57.297 47.619 7.53 0.00 36.39 4.30
3520 3789 2.621070 TGGAAGAGCACTTAAGGAGGT 58.379 47.619 7.53 4.51 36.39 3.85
3521 3790 3.786553 TGGAAGAGCACTTAAGGAGGTA 58.213 45.455 7.53 0.00 36.39 3.08
3522 3791 4.362677 TGGAAGAGCACTTAAGGAGGTAT 58.637 43.478 7.53 0.00 36.39 2.73
3524 3793 6.143915 TGGAAGAGCACTTAAGGAGGTATAT 58.856 40.000 7.53 0.00 36.39 0.86
3526 3795 7.956315 TGGAAGAGCACTTAAGGAGGTATATAT 59.044 37.037 7.53 0.00 36.39 0.86
3542 3811 8.410673 AGGTATATATATGCCTCGGAGTAATG 57.589 38.462 22.72 0.00 44.09 1.90
3544 3813 7.450634 GGTATATATATGCCTCGGAGTAATGGA 59.549 40.741 19.52 0.00 35.81 3.41
3554 3823 5.395324 CCTCGGAGTAATGGACAAACTGTAT 60.395 44.000 4.02 0.00 0.00 2.29
3555 3824 6.183360 CCTCGGAGTAATGGACAAACTGTATA 60.183 42.308 4.02 0.00 0.00 1.47
3556 3825 7.356089 TCGGAGTAATGGACAAACTGTATAT 57.644 36.000 0.00 0.00 0.00 0.86
3557 3826 8.467963 TCGGAGTAATGGACAAACTGTATATA 57.532 34.615 0.00 0.00 0.00 0.86
3558 3827 9.085645 TCGGAGTAATGGACAAACTGTATATAT 57.914 33.333 0.00 0.00 0.00 0.86
3575 3847 9.988815 CTGTATATATAGTAGATGCCATTTCCC 57.011 37.037 0.00 0.00 0.00 3.97
3576 3848 9.729550 TGTATATATAGTAGATGCCATTTCCCT 57.270 33.333 0.00 0.00 0.00 4.20
3632 3905 9.639563 TCACATATTTTATCTGGCCTTTTATCA 57.360 29.630 3.32 0.00 0.00 2.15
4045 4318 2.783135 CCACACATGGTTAAGCTGACT 58.217 47.619 6.19 0.00 41.64 3.41
4046 4319 3.937814 CCACACATGGTTAAGCTGACTA 58.062 45.455 6.19 0.00 41.64 2.59
4047 4320 4.323417 CCACACATGGTTAAGCTGACTAA 58.677 43.478 6.19 0.00 41.64 2.24
4048 4321 4.759693 CCACACATGGTTAAGCTGACTAAA 59.240 41.667 6.19 0.00 41.64 1.85
4049 4322 5.415701 CCACACATGGTTAAGCTGACTAAAT 59.584 40.000 6.19 0.00 41.64 1.40
4050 4323 6.317088 CACACATGGTTAAGCTGACTAAATG 58.683 40.000 6.19 2.18 0.00 2.32
4051 4324 6.149308 CACACATGGTTAAGCTGACTAAATGA 59.851 38.462 6.19 0.00 0.00 2.57
4052 4325 6.149474 ACACATGGTTAAGCTGACTAAATGAC 59.851 38.462 6.19 0.00 0.00 3.06
4053 4326 6.149308 CACATGGTTAAGCTGACTAAATGACA 59.851 38.462 6.19 0.00 0.00 3.58
4054 4327 6.714810 ACATGGTTAAGCTGACTAAATGACAA 59.285 34.615 6.19 0.00 0.00 3.18
4055 4328 7.230510 ACATGGTTAAGCTGACTAAATGACAAA 59.769 33.333 6.19 0.00 0.00 2.83
4056 4329 7.202016 TGGTTAAGCTGACTAAATGACAAAG 57.798 36.000 6.19 0.00 0.00 2.77
4057 4330 6.770785 TGGTTAAGCTGACTAAATGACAAAGT 59.229 34.615 6.19 0.00 0.00 2.66
4058 4331 7.078228 GGTTAAGCTGACTAAATGACAAAGTG 58.922 38.462 0.00 0.00 0.00 3.16
4059 4332 7.041372 GGTTAAGCTGACTAAATGACAAAGTGA 60.041 37.037 0.00 0.00 0.00 3.41
4060 4333 6.551385 AAGCTGACTAAATGACAAAGTGAG 57.449 37.500 0.00 0.17 0.00 3.51
4061 4334 4.999950 AGCTGACTAAATGACAAAGTGAGG 59.000 41.667 0.00 0.00 0.00 3.86
4062 4335 4.154918 GCTGACTAAATGACAAAGTGAGGG 59.845 45.833 5.17 0.00 0.00 4.30
4063 4336 5.304686 TGACTAAATGACAAAGTGAGGGT 57.695 39.130 0.00 0.00 0.00 4.34
4064 4337 5.305585 TGACTAAATGACAAAGTGAGGGTC 58.694 41.667 0.00 0.00 0.00 4.46
4065 4338 4.652822 ACTAAATGACAAAGTGAGGGTCC 58.347 43.478 0.00 0.00 0.00 4.46
4066 4339 3.884037 AAATGACAAAGTGAGGGTCCT 57.116 42.857 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 0.413434 AAAATGGGGGTGCTAAGCCT 59.587 50.000 0.00 0.00 43.94 4.58
89 90 2.493675 TCTCTCTGAAGACGGGTGATTG 59.506 50.000 0.00 0.00 0.00 2.67
103 104 1.517242 AAAGGCGTTGCTTCTCTCTG 58.483 50.000 0.00 0.00 0.00 3.35
208 211 0.377203 CGCCGGCTTTACCTTTGATC 59.623 55.000 26.68 0.00 35.61 2.92
217 220 0.528249 GGAATCGTACGCCGGCTTTA 60.528 55.000 26.68 12.94 37.11 1.85
222 225 1.668047 GGATAAGGAATCGTACGCCGG 60.668 57.143 11.24 0.00 35.21 6.13
244 248 0.322456 TCGACCTTTGGCAATGGAGG 60.322 55.000 31.86 23.14 35.39 4.30
246 250 1.818060 CATTCGACCTTTGGCAATGGA 59.182 47.619 31.86 14.67 0.00 3.41
381 385 1.376812 GGGAGGCTACAACAACCGG 60.377 63.158 0.00 0.00 0.00 5.28
415 419 1.142262 ACTACGAGGTTTTTGGGTGCT 59.858 47.619 0.00 0.00 0.00 4.40
426 430 0.668401 CGCGGGAAAAACTACGAGGT 60.668 55.000 0.00 0.00 0.00 3.85
428 432 1.421382 TTCGCGGGAAAAACTACGAG 58.579 50.000 13.07 0.00 0.00 4.18
462 466 2.093658 TCTTATGGACGCAAAGGAGGTC 60.094 50.000 0.00 0.00 0.00 3.85
468 472 5.174035 CGACTCTTATCTTATGGACGCAAAG 59.826 44.000 0.00 0.00 0.00 2.77
621 822 2.426522 CTGAATCGGTTGAGGCTTTCA 58.573 47.619 0.00 0.00 0.00 2.69
1054 1258 0.322456 CCCACCATGACCACGACAAT 60.322 55.000 0.00 0.00 0.00 2.71
1084 1288 4.717629 CGCCAACTCAGCCGTCGA 62.718 66.667 0.00 0.00 0.00 4.20
1167 1371 4.329545 TGCAGGTCCTTGGCCGAC 62.330 66.667 0.00 0.00 29.39 4.79
1692 1896 2.518587 TCTCCATCGTCGGCGGAT 60.519 61.111 10.62 0.00 38.89 4.18
1695 1899 4.907034 CGGTCTCCATCGTCGGCG 62.907 72.222 1.15 1.15 39.92 6.46
1709 1913 4.479993 GGCTGCTGGCTGATCGGT 62.480 66.667 10.05 0.00 41.46 4.69
1895 2099 2.752238 CACCGAGACGAGCCTCCT 60.752 66.667 0.00 0.00 0.00 3.69
2025 2229 3.134879 TCCGCACGGAAGAACTGT 58.865 55.556 9.81 0.00 42.05 3.55
2253 2457 3.807538 TAGCACGCGACGACCTCC 61.808 66.667 15.93 0.00 0.00 4.30
2280 2484 2.361865 ACGGCGAGCTTCTCCTCT 60.362 61.111 16.62 0.00 0.00 3.69
2361 2569 3.833650 TGGAAAATGGAGATGCATGTTGT 59.166 39.130 2.46 0.00 0.00 3.32
2389 2627 0.394216 TCTCACCAAATCGCCATGGG 60.394 55.000 15.13 3.69 41.17 4.00
2418 2656 2.286654 GCAACAGACAGAACAGAGCAAC 60.287 50.000 0.00 0.00 0.00 4.17
2540 2778 1.153127 TGGAAAAACGGCACCGACT 60.153 52.632 17.40 0.00 42.83 4.18
2542 2780 2.188161 GGTGGAAAAACGGCACCGA 61.188 57.895 17.40 0.00 42.83 4.69
2545 2783 2.333581 CCGGTGGAAAAACGGCAC 59.666 61.111 0.00 0.00 41.23 5.01
2615 2853 3.058160 GATGCTGGTGCTTGCCGT 61.058 61.111 0.00 0.00 40.48 5.68
3029 3267 1.215647 CACCTCCCTTTCTCGTCCG 59.784 63.158 0.00 0.00 0.00 4.79
3033 3271 1.901085 CTCCCACCTCCCTTTCTCG 59.099 63.158 0.00 0.00 0.00 4.04
3101 3339 2.877335 ACTAAGAGATCGTGTTTCGCC 58.123 47.619 0.00 0.00 39.67 5.54
3106 3344 3.428589 GGCGGTAACTAAGAGATCGTGTT 60.429 47.826 0.00 0.00 0.00 3.32
3126 3364 6.973229 TTACTTAGATACAAAAAGACGGGC 57.027 37.500 0.00 0.00 0.00 6.13
3155 3393 6.990349 TCCGAGAATAAAGAGAAACACAAAGT 59.010 34.615 0.00 0.00 0.00 2.66
3156 3394 7.421530 TCCGAGAATAAAGAGAAACACAAAG 57.578 36.000 0.00 0.00 0.00 2.77
3172 3410 6.464465 CCATCCTAACAATACCTTCCGAGAAT 60.464 42.308 0.00 0.00 0.00 2.40
3187 3425 1.490490 GGCATCACCTCCATCCTAACA 59.510 52.381 0.00 0.00 34.51 2.41
3188 3426 2.262423 GGCATCACCTCCATCCTAAC 57.738 55.000 0.00 0.00 34.51 2.34
3203 3441 5.418524 TGCGGCATTATATTTCATAAGGCAT 59.581 36.000 13.58 0.00 41.41 4.40
3213 3451 6.622028 GCGGTAAAGTATGCGGCATTATATTT 60.622 38.462 21.99 17.12 39.30 1.40
3215 3453 4.331717 GCGGTAAAGTATGCGGCATTATAT 59.668 41.667 21.99 8.34 39.30 0.86
3217 3455 2.482721 GCGGTAAAGTATGCGGCATTAT 59.517 45.455 21.99 7.29 39.30 1.28
3218 3456 1.868498 GCGGTAAAGTATGCGGCATTA 59.132 47.619 21.99 5.18 39.30 1.90
3224 3462 1.730064 ACACAAGCGGTAAAGTATGCG 59.270 47.619 0.00 0.00 0.00 4.73
3237 3475 4.708726 ATGCCTCAGAAATAACACAAGC 57.291 40.909 0.00 0.00 0.00 4.01
3238 3476 6.587608 GGAAAATGCCTCAGAAATAACACAAG 59.412 38.462 0.00 0.00 0.00 3.16
3242 3480 5.185635 CCAGGAAAATGCCTCAGAAATAACA 59.814 40.000 0.00 0.00 35.66 2.41
3244 3482 4.711355 CCCAGGAAAATGCCTCAGAAATAA 59.289 41.667 0.00 0.00 35.66 1.40
3250 3488 1.180029 CACCCAGGAAAATGCCTCAG 58.820 55.000 0.00 0.00 35.66 3.35
3253 3491 0.482446 TCACACCCAGGAAAATGCCT 59.518 50.000 0.00 0.00 39.37 4.75
3254 3492 1.205417 CATCACACCCAGGAAAATGCC 59.795 52.381 0.00 0.00 0.00 4.40
3263 3501 1.100510 CCTTGCATCATCACACCCAG 58.899 55.000 0.00 0.00 0.00 4.45
3264 3502 0.323633 CCCTTGCATCATCACACCCA 60.324 55.000 0.00 0.00 0.00 4.51
3272 3511 2.102578 GTAACTTGGCCCTTGCATCAT 58.897 47.619 0.00 0.00 40.13 2.45
3273 3512 1.544724 GTAACTTGGCCCTTGCATCA 58.455 50.000 0.00 0.00 40.13 3.07
3274 3513 0.451783 CGTAACTTGGCCCTTGCATC 59.548 55.000 0.00 0.00 40.13 3.91
3294 3534 8.696043 TGGATATGAAGATAAATTTGACTGGG 57.304 34.615 0.00 0.00 0.00 4.45
3298 3538 8.800332 AGCCATGGATATGAAGATAAATTTGAC 58.200 33.333 18.40 0.00 36.36 3.18
3299 3539 8.945195 AGCCATGGATATGAAGATAAATTTGA 57.055 30.769 18.40 0.00 36.36 2.69
3305 3545 9.720874 ACTATCTAGCCATGGATATGAAGATAA 57.279 33.333 18.40 3.28 36.36 1.75
3309 3549 8.976353 AGTAACTATCTAGCCATGGATATGAAG 58.024 37.037 18.40 12.86 36.36 3.02
3315 3555 6.084738 TGGAAGTAACTATCTAGCCATGGAT 58.915 40.000 18.40 13.25 0.00 3.41
3342 3588 6.039382 GGAAAAATGGCCGATATCTACAAGTT 59.961 38.462 0.00 0.00 0.00 2.66
3344 3590 5.765182 AGGAAAAATGGCCGATATCTACAAG 59.235 40.000 0.00 0.00 0.00 3.16
3348 3594 4.072131 GCAGGAAAAATGGCCGATATCTA 58.928 43.478 0.00 0.00 0.00 1.98
3353 3621 1.137479 CATGCAGGAAAAATGGCCGAT 59.863 47.619 0.00 0.00 0.00 4.18
3356 3624 3.132646 TCATACATGCAGGAAAAATGGCC 59.867 43.478 4.84 0.00 0.00 5.36
3358 3626 6.151663 TGATCATACATGCAGGAAAAATGG 57.848 37.500 4.84 0.00 0.00 3.16
3512 3781 7.147177 ACTCCGAGGCATATATATACCTCCTTA 60.147 40.741 26.50 15.82 41.31 2.69
3513 3782 6.027025 TCCGAGGCATATATATACCTCCTT 57.973 41.667 26.50 4.31 41.31 3.36
3514 3783 5.134679 ACTCCGAGGCATATATATACCTCCT 59.865 44.000 26.50 16.14 41.31 3.69
3517 3786 7.451877 CCATTACTCCGAGGCATATATATACCT 59.548 40.741 13.54 13.54 32.11 3.08
3519 3788 8.298140 GTCCATTACTCCGAGGCATATATATAC 58.702 40.741 0.00 0.00 0.00 1.47
3520 3789 8.002459 TGTCCATTACTCCGAGGCATATATATA 58.998 37.037 0.00 0.00 0.00 0.86
3521 3790 6.839134 TGTCCATTACTCCGAGGCATATATAT 59.161 38.462 0.00 0.00 0.00 0.86
3522 3791 6.192044 TGTCCATTACTCCGAGGCATATATA 58.808 40.000 0.00 0.00 0.00 0.86
3524 3793 4.412843 TGTCCATTACTCCGAGGCATATA 58.587 43.478 0.00 0.00 0.00 0.86
3526 3795 2.673258 TGTCCATTACTCCGAGGCATA 58.327 47.619 0.00 0.00 0.00 3.14
3542 3811 9.804758 GGCATCTACTATATATACAGTTTGTCC 57.195 37.037 0.00 0.00 0.00 4.02
3554 3823 8.321353 CACAAGGGAAATGGCATCTACTATATA 58.679 37.037 0.00 0.00 0.00 0.86
3555 3824 7.017551 TCACAAGGGAAATGGCATCTACTATAT 59.982 37.037 0.00 0.00 0.00 0.86
3556 3825 6.328934 TCACAAGGGAAATGGCATCTACTATA 59.671 38.462 0.00 0.00 0.00 1.31
3557 3826 5.132648 TCACAAGGGAAATGGCATCTACTAT 59.867 40.000 0.00 0.00 0.00 2.12
3558 3827 4.473196 TCACAAGGGAAATGGCATCTACTA 59.527 41.667 0.00 0.00 0.00 1.82
3559 3828 3.266772 TCACAAGGGAAATGGCATCTACT 59.733 43.478 0.00 0.00 0.00 2.57
3560 3829 3.620488 TCACAAGGGAAATGGCATCTAC 58.380 45.455 0.00 0.00 0.00 2.59
3561 3830 4.524802 ATCACAAGGGAAATGGCATCTA 57.475 40.909 0.00 0.00 0.00 1.98
3605 3877 9.899226 GATAAAAGGCCAGATAAAATATGTGAC 57.101 33.333 5.01 0.00 0.00 3.67
4026 4299 5.940192 TTTAGTCAGCTTAACCATGTGTG 57.060 39.130 0.00 0.00 0.00 3.82
4027 4300 6.149474 GTCATTTAGTCAGCTTAACCATGTGT 59.851 38.462 0.00 0.00 0.00 3.72
4028 4301 6.149308 TGTCATTTAGTCAGCTTAACCATGTG 59.851 38.462 0.00 0.00 0.00 3.21
4029 4302 6.237901 TGTCATTTAGTCAGCTTAACCATGT 58.762 36.000 0.00 0.00 0.00 3.21
4030 4303 6.741992 TGTCATTTAGTCAGCTTAACCATG 57.258 37.500 0.00 0.00 0.00 3.66
4031 4304 7.448469 ACTTTGTCATTTAGTCAGCTTAACCAT 59.552 33.333 0.00 0.00 0.00 3.55
4032 4305 6.770785 ACTTTGTCATTTAGTCAGCTTAACCA 59.229 34.615 0.00 0.00 0.00 3.67
4033 4306 7.041372 TCACTTTGTCATTTAGTCAGCTTAACC 60.041 37.037 0.00 0.00 0.00 2.85
4034 4307 7.861630 TCACTTTGTCATTTAGTCAGCTTAAC 58.138 34.615 0.00 0.00 0.00 2.01
4035 4308 7.173218 CCTCACTTTGTCATTTAGTCAGCTTAA 59.827 37.037 0.00 0.00 0.00 1.85
4036 4309 6.650807 CCTCACTTTGTCATTTAGTCAGCTTA 59.349 38.462 0.00 0.00 0.00 3.09
4037 4310 5.471456 CCTCACTTTGTCATTTAGTCAGCTT 59.529 40.000 0.00 0.00 0.00 3.74
4038 4311 4.999950 CCTCACTTTGTCATTTAGTCAGCT 59.000 41.667 0.00 0.00 0.00 4.24
4039 4312 4.154918 CCCTCACTTTGTCATTTAGTCAGC 59.845 45.833 0.00 0.00 0.00 4.26
4040 4313 5.308825 ACCCTCACTTTGTCATTTAGTCAG 58.691 41.667 0.00 0.00 0.00 3.51
4041 4314 5.304686 ACCCTCACTTTGTCATTTAGTCA 57.695 39.130 0.00 0.00 0.00 3.41
4042 4315 4.695928 GGACCCTCACTTTGTCATTTAGTC 59.304 45.833 0.00 0.00 0.00 2.59
4043 4316 4.351111 AGGACCCTCACTTTGTCATTTAGT 59.649 41.667 0.00 0.00 0.00 2.24
4044 4317 4.911390 AGGACCCTCACTTTGTCATTTAG 58.089 43.478 0.00 0.00 0.00 1.85
4045 4318 4.993705 AGGACCCTCACTTTGTCATTTA 57.006 40.909 0.00 0.00 0.00 1.40
4046 4319 3.884037 AGGACCCTCACTTTGTCATTT 57.116 42.857 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.