Multiple sequence alignment - TraesCS7D01G280400

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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 TraesCS7D01G280400 chr7D 100.000 4859 0 0 1 4859 273830684 273835542 0.000000e+00 8973.0
1 TraesCS7D01G280400 chr7A 94.110 4024 88 38 534 4468 307235654 307239617 0.000000e+00 5980.0
2 TraesCS7D01G280400 chr7A 90.547 402 33 5 1 402 307078284 307078680 1.200000e-145 527.0
3 TraesCS7D01G280400 chr7A 91.321 265 11 2 4607 4859 307239765 307240029 7.740000e-93 351.0
4 TraesCS7D01G280400 chr7A 97.087 103 3 0 4504 4606 307239617 307239719 1.800000e-39 174.0
5 TraesCS7D01G280400 chr7B 94.786 3778 99 35 539 4259 264066461 264062725 0.000000e+00 5795.0
6 TraesCS7D01G280400 chr7B 91.713 543 38 4 1 542 264067031 264066495 0.000000e+00 747.0
7 TraesCS7D01G280400 chr7B 90.189 265 10 5 4607 4859 264058407 264058147 1.010000e-86 331.0
8 TraesCS7D01G280400 chr7B 90.500 200 4 5 4339 4531 264062527 264062336 2.900000e-62 250.0
9 TraesCS7D01G280400 chr2A 87.755 196 18 6 322 517 733529249 733529438 1.760000e-54 224.0
10 TraesCS7D01G280400 chr3A 92.000 75 6 0 437 511 714735947 714735873 6.650000e-19 106.0
11 TraesCS7D01G280400 chr5A 93.333 60 2 2 4122 4179 659257207 659257266 2.410000e-13 87.9
12 TraesCS7D01G280400 chr6B 86.667 60 6 2 4122 4179 690477588 690477647 1.130000e-06 65.8


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 TraesCS7D01G280400 chr7D 273830684 273835542 4858 False 8973.000000 8973 100.000000 1 4859 1 chr7D.!!$F1 4858
1 TraesCS7D01G280400 chr7A 307235654 307240029 4375 False 2168.333333 5980 94.172667 534 4859 3 chr7A.!!$F2 4325
2 TraesCS7D01G280400 chr7B 264058147 264067031 8884 True 1780.750000 5795 91.797000 1 4859 4 chr7B.!!$R1 4858

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
817 877 1.002274 ACGCCAATCCCTCTCCTCT 59.998 57.895 0.00 0.0 0.00 3.69 F
1066 1136 0.193574 TCTCTGTCTCCCCCAAACCT 59.806 55.000 0.00 0.0 0.00 3.50 F
2628 2731 0.313043 GAATGGAATGGCGATGGCAG 59.687 55.000 1.01 0.0 42.43 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 2479 1.537202 GAAGCAGCAACGAAACAGGAT 59.463 47.619 0.00 0.0 0.0 3.24 R
2890 2999 1.003839 TGCCACCGATGAAGTCACC 60.004 57.895 0.00 0.0 0.0 4.02 R
4606 4927 0.105811 CCTTACCTACCGGGCTACCT 60.106 60.000 6.32 0.0 39.1 3.08 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
68 69 4.150098 CACGAGTTAGTACAGTTTTGGAGC 59.850 45.833 0.00 0.00 0.00 4.70
73 74 6.062095 AGTTAGTACAGTTTTGGAGCACAAT 58.938 36.000 0.00 0.00 39.21 2.71
134 135 6.856426 GGGAAATAATTTTAAAGATCTCGGCG 59.144 38.462 0.00 0.00 0.00 6.46
142 143 7.605410 TTTTAAAGATCTCGGCGTAAGAAAT 57.395 32.000 6.85 0.00 43.02 2.17
151 152 7.830940 TCTCGGCGTAAGAAATTAAACAATA 57.169 32.000 6.85 0.00 43.02 1.90
243 244 1.003696 AGAACAAACAGCTAGCCTCCC 59.996 52.381 12.13 0.00 0.00 4.30
248 249 2.827921 CAAACAGCTAGCCTCCCAAAAT 59.172 45.455 12.13 0.00 0.00 1.82
262 263 6.736794 GCCTCCCAAAATTTAGCACATATGAG 60.737 42.308 10.38 2.11 0.00 2.90
309 310 3.033184 CAACACATAGGCCCCAAATGAT 58.967 45.455 0.00 0.00 0.00 2.45
316 317 5.044846 ACATAGGCCCCAAATGATCCTATAC 60.045 44.000 0.00 0.00 37.87 1.47
317 318 2.649816 AGGCCCCAAATGATCCTATACC 59.350 50.000 0.00 0.00 0.00 2.73
319 320 3.181423 GGCCCCAAATGATCCTATACCAA 60.181 47.826 0.00 0.00 0.00 3.67
325 326 7.125659 CCCCAAATGATCCTATACCAACTTTTT 59.874 37.037 0.00 0.00 0.00 1.94
363 365 9.489084 CCTATACTTTATTGATCGAATTCCACA 57.511 33.333 0.00 0.00 0.00 4.17
413 415 1.358759 GGCCAAACCACACAAGACG 59.641 57.895 0.00 0.00 38.86 4.18
414 416 1.299089 GCCAAACCACACAAGACGC 60.299 57.895 0.00 0.00 0.00 5.19
421 423 1.667830 CACACAAGACGCCGTGGAT 60.668 57.895 0.00 0.00 37.45 3.41
433 435 3.827302 ACGCCGTGGATCTAGATTAAGAT 59.173 43.478 6.70 0.00 38.95 2.40
475 477 8.879342 ATGAGCTTGTATGTTACTATCTTGAC 57.121 34.615 0.00 0.00 0.00 3.18
479 481 9.372369 AGCTTGTATGTTACTATCTTGACTTTC 57.628 33.333 0.00 0.00 0.00 2.62
512 514 7.563888 AACTACAAGAAAAAGTGGTAGAACC 57.436 36.000 0.00 0.00 39.22 3.62
536 538 3.503748 GCTGCAAATGACCCTATACCATC 59.496 47.826 0.00 0.00 0.00 3.51
613 655 5.588246 ACCATGGGCTAAGTTTTTGTTTTTG 59.412 36.000 18.09 0.00 0.00 2.44
614 656 5.588246 CCATGGGCTAAGTTTTTGTTTTTGT 59.412 36.000 2.85 0.00 0.00 2.83
815 875 2.427245 CGACGCCAATCCCTCTCCT 61.427 63.158 0.00 0.00 0.00 3.69
816 876 1.443828 GACGCCAATCCCTCTCCTC 59.556 63.158 0.00 0.00 0.00 3.71
817 877 1.002274 ACGCCAATCCCTCTCCTCT 59.998 57.895 0.00 0.00 0.00 3.69
818 878 1.045911 ACGCCAATCCCTCTCCTCTC 61.046 60.000 0.00 0.00 0.00 3.20
819 879 1.753368 CGCCAATCCCTCTCCTCTCC 61.753 65.000 0.00 0.00 0.00 3.71
949 1019 5.202004 AGACGCTCTCCCTTTTAGATCTTA 58.798 41.667 0.00 0.00 0.00 2.10
1066 1136 0.193574 TCTCTGTCTCCCCCAAACCT 59.806 55.000 0.00 0.00 0.00 3.50
1067 1137 1.068121 CTCTGTCTCCCCCAAACCTT 58.932 55.000 0.00 0.00 0.00 3.50
1289 1359 5.907207 TGGTTGCTATCTCTCACAATCTAC 58.093 41.667 0.00 0.00 0.00 2.59
1376 1453 2.698274 TGGACTGTCAGTGCTTTGACTA 59.302 45.455 23.06 0.52 46.00 2.59
1475 1552 3.932710 TGTCGCATCATTAGTTTGTCCTC 59.067 43.478 0.00 0.00 0.00 3.71
1531 1608 5.224888 ACTTATTAGTCGTTTTGTCTGCGA 58.775 37.500 0.00 0.00 0.00 5.10
1537 1614 2.546778 TCGTTTTGTCTGCGACTTTCT 58.453 42.857 9.49 0.00 33.15 2.52
1539 1616 3.000925 TCGTTTTGTCTGCGACTTTCTTC 59.999 43.478 9.49 0.00 33.15 2.87
1540 1617 3.242284 CGTTTTGTCTGCGACTTTCTTCA 60.242 43.478 9.49 0.00 33.15 3.02
1632 1712 3.830178 ACACCTGTTGCCCCTAAATAAAC 59.170 43.478 0.00 0.00 0.00 2.01
1719 1809 3.862877 TGTTGCCTGCAGGATATACAT 57.137 42.857 37.21 0.00 37.39 2.29
1722 1812 4.136796 GTTGCCTGCAGGATATACATTCA 58.863 43.478 37.21 17.88 37.39 2.57
2335 2425 2.038952 ACCAGCTGAGCACTGATTGTTA 59.961 45.455 17.39 0.00 37.32 2.41
2376 2479 6.550938 AGTGTCTCCTGATAATGTTCATGA 57.449 37.500 0.00 0.00 0.00 3.07
2514 2617 5.766670 TCTGAAGAAAATGATGCTGTTGACT 59.233 36.000 0.00 0.00 0.00 3.41
2628 2731 0.313043 GAATGGAATGGCGATGGCAG 59.687 55.000 1.01 0.00 42.43 4.85
2730 2833 5.629133 GCTTCTATTGTATGTGGGACCTTCA 60.629 44.000 0.00 0.00 0.00 3.02
2820 2929 1.228675 CTGCAAAAGCCCCACCTCT 60.229 57.895 0.00 0.00 0.00 3.69
2981 3090 5.991606 GGTTTTTCTTTCTTTATGCTTGCCT 59.008 36.000 0.00 0.00 0.00 4.75
2982 3091 7.015195 AGGTTTTTCTTTCTTTATGCTTGCCTA 59.985 33.333 0.00 0.00 0.00 3.93
3217 3326 9.149225 GATTCTGATTCACCACTTGCTATATAG 57.851 37.037 5.30 5.30 0.00 1.31
3293 3402 5.957842 ACTATGCTTTTGTGGAATTCGAA 57.042 34.783 0.00 0.00 0.00 3.71
3409 3518 8.760980 TTATATTGCTTAGGTTTGGCTTGTAT 57.239 30.769 0.00 0.00 0.00 2.29
3509 3631 3.439857 AATGGGCGGCAGATATATGTT 57.560 42.857 12.47 0.00 0.00 2.71
3636 3759 2.493675 CTGCTAGTAGAAGTGTGAGCCA 59.506 50.000 0.81 0.00 0.00 4.75
3945 4072 2.436417 GCTCCATTCTGTTAGGTTGCA 58.564 47.619 0.00 0.00 0.00 4.08
3970 4097 1.202475 CGGTTTTGGGGTTTGTCTTGG 60.202 52.381 0.00 0.00 0.00 3.61
3998 4125 2.265739 GCAGCTCGTCCATGGACA 59.734 61.111 37.42 25.18 44.77 4.02
4003 4130 1.524002 CTCGTCCATGGACATGCCT 59.476 57.895 37.42 0.00 44.77 4.75
4200 4346 2.187239 TCCCCATCTGCATCTCTTCT 57.813 50.000 0.00 0.00 0.00 2.85
4217 4363 3.070878 TCTTCTGCCATATATGTTCGCCA 59.929 43.478 11.73 0.81 0.00 5.69
4218 4364 3.483808 TCTGCCATATATGTTCGCCAA 57.516 42.857 11.73 0.00 0.00 4.52
4219 4365 3.402110 TCTGCCATATATGTTCGCCAAG 58.598 45.455 11.73 3.47 0.00 3.61
4220 4366 2.485426 CTGCCATATATGTTCGCCAAGG 59.515 50.000 11.73 0.00 0.00 3.61
4240 4386 1.203994 GCTGCAGTGATGCCTCAAAAT 59.796 47.619 16.64 0.00 31.85 1.82
4245 4391 4.020928 TGCAGTGATGCCTCAAAATTGATT 60.021 37.500 0.00 0.00 36.46 2.57
4270 4416 5.934781 AGGCCTCCTTTTGTTCATAGATAG 58.065 41.667 0.00 0.00 0.00 2.08
4271 4417 5.066593 GGCCTCCTTTTGTTCATAGATAGG 58.933 45.833 0.00 0.00 0.00 2.57
4273 4419 6.357367 GCCTCCTTTTGTTCATAGATAGGAA 58.643 40.000 0.00 0.00 30.51 3.36
4405 4676 4.394729 GAACCAGTCCTACAAACCAATGA 58.605 43.478 0.00 0.00 0.00 2.57
4496 4767 6.721208 TGCAAAGGGAAAAGAAGTGATTATCT 59.279 34.615 0.00 0.00 0.00 1.98
4497 4768 7.233348 TGCAAAGGGAAAAGAAGTGATTATCTT 59.767 33.333 0.00 0.00 37.49 2.40
4498 4769 7.543520 GCAAAGGGAAAAGAAGTGATTATCTTG 59.456 37.037 0.00 0.00 36.09 3.02
4499 4770 8.796475 CAAAGGGAAAAGAAGTGATTATCTTGA 58.204 33.333 0.00 0.00 36.09 3.02
4500 4771 9.539194 AAAGGGAAAAGAAGTGATTATCTTGAT 57.461 29.630 0.00 0.00 36.09 2.57
4572 4893 9.830186 ACAGGTCTACCTAATTATATCTGTCAT 57.170 33.333 0.25 0.00 46.65 3.06
4574 4895 9.261035 AGGTCTACCTAATTATATCTGTCATGG 57.739 37.037 0.00 0.00 46.48 3.66
4575 4896 9.256228 GGTCTACCTAATTATATCTGTCATGGA 57.744 37.037 0.00 0.00 0.00 3.41
4577 4898 9.480861 TCTACCTAATTATATCTGTCATGGAGG 57.519 37.037 0.00 0.00 0.00 4.30
4578 4899 9.480861 CTACCTAATTATATCTGTCATGGAGGA 57.519 37.037 0.00 0.00 0.00 3.71
4579 4900 8.140112 ACCTAATTATATCTGTCATGGAGGAC 57.860 38.462 0.00 0.00 38.29 3.85
4580 4901 7.093727 ACCTAATTATATCTGTCATGGAGGACG 60.094 40.741 0.00 0.00 40.72 4.79
4597 4918 2.824041 GGTGCCATGCTGTACCCG 60.824 66.667 0.00 0.00 0.00 5.28
4606 4927 2.041301 CTGTACCCGGGGGATGGA 60.041 66.667 27.92 0.68 38.96 3.41
4607 4928 2.041301 TGTACCCGGGGGATGGAG 60.041 66.667 27.92 0.00 38.96 3.86
4608 4929 2.847715 GTACCCGGGGGATGGAGG 60.848 72.222 27.92 0.00 38.96 4.30
4609 4930 3.370277 TACCCGGGGGATGGAGGT 61.370 66.667 27.92 1.85 38.96 3.85
4616 8840 3.242291 GGGATGGAGGTAGCCCGG 61.242 72.222 0.00 0.00 36.40 5.73
4621 8845 1.957822 ATGGAGGTAGCCCGGTAGGT 61.958 60.000 0.00 0.00 38.26 3.08
4675 8906 5.708544 TCAGTATATAAAGGAGGAACCGGA 58.291 41.667 9.46 0.00 44.74 5.14
4777 9008 1.372087 CTCGGTGGCTTGAATCTGGC 61.372 60.000 0.00 0.00 0.00 4.85
4782 9013 3.026694 GGTGGCTTGAATCTGGCTAAAT 58.973 45.455 0.00 0.00 0.00 1.40
4853 9089 1.382695 GGGGGTCCCTTCGATCTCA 60.383 63.158 8.15 0.00 41.34 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 4.496175 GGCAAAAATTGTGCTCCAAAACTG 60.496 41.667 8.17 0.00 41.88 3.16
117 118 7.605410 TTTCTTACGCCGAGATCTTTAAAAT 57.395 32.000 0.00 0.00 0.00 1.82
176 177 3.861276 AACGACATATCTCGTGAACCA 57.139 42.857 6.80 0.00 46.13 3.67
177 178 6.636666 TTTAAACGACATATCTCGTGAACC 57.363 37.500 6.80 0.00 46.13 3.62
220 221 3.189495 GGAGGCTAGCTGTTTGTTCTTTC 59.811 47.826 15.72 0.00 0.00 2.62
222 223 2.553247 GGGAGGCTAGCTGTTTGTTCTT 60.553 50.000 15.72 0.00 0.00 2.52
223 224 1.003696 GGGAGGCTAGCTGTTTGTTCT 59.996 52.381 15.72 0.00 0.00 3.01
233 234 3.023832 TGCTAAATTTTGGGAGGCTAGC 58.976 45.455 6.04 6.04 0.00 3.42
235 236 4.040936 TGTGCTAAATTTTGGGAGGCTA 57.959 40.909 0.00 0.00 0.00 3.93
237 238 3.893326 ATGTGCTAAATTTTGGGAGGC 57.107 42.857 0.00 0.00 0.00 4.70
248 249 8.750515 TGATGGATTTTCTCATATGTGCTAAA 57.249 30.769 1.90 5.25 0.00 1.85
325 326 8.783903 TCAATAAAGTATAGGCTTTCCCCTAAA 58.216 33.333 0.00 0.00 40.67 1.85
328 329 6.841781 TCAATAAAGTATAGGCTTTCCCCT 57.158 37.500 0.00 0.00 39.22 4.79
329 330 6.371825 CGATCAATAAAGTATAGGCTTTCCCC 59.628 42.308 0.00 0.00 39.22 4.81
334 335 9.220767 GGAATTCGATCAATAAAGTATAGGCTT 57.779 33.333 0.00 0.00 0.00 4.35
345 347 6.758416 CACTCTCTGTGGAATTCGATCAATAA 59.242 38.462 0.00 0.00 42.68 1.40
363 365 6.506538 AATGTAAGCATTATCCCACTCTCT 57.493 37.500 0.00 0.00 42.96 3.10
413 415 5.392767 TGATCTTAATCTAGATCCACGGC 57.607 43.478 5.51 0.00 46.50 5.68
414 416 9.130661 AGATATGATCTTAATCTAGATCCACGG 57.869 37.037 5.51 0.00 46.50 4.94
499 501 1.142870 TGCAGCTGGTTCTACCACTTT 59.857 47.619 17.12 0.00 44.79 2.66
512 514 2.880890 GGTATAGGGTCATTTGCAGCTG 59.119 50.000 10.11 10.11 0.00 4.24
613 655 1.271840 TGGCCCATGGTCTCCACTAC 61.272 60.000 11.73 0.00 35.80 2.73
614 656 0.548926 TTGGCCCATGGTCTCCACTA 60.549 55.000 11.73 0.00 35.80 2.74
809 869 1.421646 GGAGAGGAGAGGAGAGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
815 875 1.498576 CAGGATGGAGAGGAGAGGAGA 59.501 57.143 0.00 0.00 0.00 3.71
816 876 1.999648 CAGGATGGAGAGGAGAGGAG 58.000 60.000 0.00 0.00 0.00 3.69
817 877 0.105760 GCAGGATGGAGAGGAGAGGA 60.106 60.000 0.00 0.00 35.86 3.71
818 878 1.462731 CGCAGGATGGAGAGGAGAGG 61.463 65.000 0.00 0.00 35.86 3.69
819 879 0.467106 TCGCAGGATGGAGAGGAGAG 60.467 60.000 0.00 0.00 35.86 3.20
949 1019 2.650813 GATCTGCTGATTCCGCGGGT 62.651 60.000 27.83 15.14 34.56 5.28
1018 1088 1.152383 GGGATTACTTGAGTCGCCGC 61.152 60.000 0.00 0.00 0.00 6.53
1019 1089 0.529992 GGGGATTACTTGAGTCGCCG 60.530 60.000 0.00 0.00 35.64 6.46
1020 1090 0.179054 GGGGGATTACTTGAGTCGCC 60.179 60.000 0.00 0.00 42.40 5.54
1067 1137 1.472480 GAGCATAAGAGGGCGCAAAAA 59.528 47.619 10.83 0.00 34.54 1.94
1475 1552 3.127548 GCAGATGGACAAACACCACATAG 59.872 47.826 0.00 0.00 40.36 2.23
1536 1613 8.261492 ACAGCATCAATAAGTAAACTCTGAAG 57.739 34.615 0.00 0.00 0.00 3.02
1537 1614 8.621532 AACAGCATCAATAAGTAAACTCTGAA 57.378 30.769 0.00 0.00 0.00 3.02
1539 1616 8.173775 CAGAACAGCATCAATAAGTAAACTCTG 58.826 37.037 0.00 0.00 0.00 3.35
1540 1617 7.880195 ACAGAACAGCATCAATAAGTAAACTCT 59.120 33.333 0.00 0.00 0.00 3.24
1632 1712 9.350357 GCAGACTCAAATTGCATATATAATTGG 57.650 33.333 0.00 0.00 37.75 3.16
1719 1809 7.121168 GTGAAATTGAGGGACATGATAAGTGAA 59.879 37.037 0.00 0.00 0.00 3.18
1722 1812 5.888161 GGTGAAATTGAGGGACATGATAAGT 59.112 40.000 0.00 0.00 0.00 2.24
2335 2425 7.200434 AGACACTAATATTTCTCCATGGTGT 57.800 36.000 12.58 3.63 37.96 4.16
2376 2479 1.537202 GAAGCAGCAACGAAACAGGAT 59.463 47.619 0.00 0.00 0.00 3.24
2514 2617 3.006537 GGTGGCTCAGAGTAAGTGTAACA 59.993 47.826 0.00 0.00 41.43 2.41
2628 2731 2.033141 TTGTGCTGGCTCCTCTGC 59.967 61.111 0.00 0.00 0.00 4.26
2730 2833 6.814644 CACAACACAATGCATATGAAGGAAAT 59.185 34.615 15.82 0.00 0.00 2.17
2820 2929 4.264253 CACTGATTGAGCAATAGGGAACA 58.736 43.478 0.00 0.00 0.00 3.18
2890 2999 1.003839 TGCCACCGATGAAGTCACC 60.004 57.895 0.00 0.00 0.00 4.02
3173 3282 8.352137 TCAGAATCAGAAAGCCAATTCAATTA 57.648 30.769 0.00 0.00 31.90 1.40
3230 3339 6.540914 GCAAATTCCACCATCAATCAAATGAT 59.459 34.615 0.00 0.00 40.64 2.45
3293 3402 0.464036 TGTGAACGCCACTCAGTTCT 59.536 50.000 9.49 0.00 45.86 3.01
3509 3631 0.902984 TGTTAGGCTTCCGCTCCTCA 60.903 55.000 0.00 0.00 36.09 3.86
3622 3745 2.038952 ACAAGCATGGCTCACACTTCTA 59.961 45.455 0.00 0.00 38.25 2.10
3636 3759 3.683847 GCTCAGGGTATCTTCACAAGCAT 60.684 47.826 0.00 0.00 0.00 3.79
3859 3982 5.654209 GGATCAAAACCTCTTATGCTTCCTT 59.346 40.000 0.00 0.00 0.00 3.36
3945 4072 3.452990 AGACAAACCCCAAAACCGAAAAT 59.547 39.130 0.00 0.00 0.00 1.82
3998 4125 0.981183 TGGTAAGAACGGACAGGCAT 59.019 50.000 0.00 0.00 0.00 4.40
4003 4130 4.525487 AGTATCTGTTGGTAAGAACGGACA 59.475 41.667 0.00 0.00 42.63 4.02
4200 4346 2.503331 CCTTGGCGAACATATATGGCA 58.497 47.619 16.96 5.39 34.88 4.92
4220 4366 6.637795 TCAATTTTGAGGCATCACTGCAGC 62.638 45.833 15.27 0.00 40.27 5.25
4240 4386 5.144100 TGAACAAAAGGAGGCCTAAATCAA 58.856 37.500 4.42 0.00 31.13 2.57
4245 4391 5.772393 TCTATGAACAAAAGGAGGCCTAA 57.228 39.130 4.42 0.00 31.13 2.69
4270 4416 9.778741 TTCACTACAGGAATTGTATGATATTCC 57.221 33.333 0.00 0.00 46.63 3.01
4549 4870 9.256228 TCCATGACAGATATAATTAGGTAGACC 57.744 37.037 0.00 0.00 0.00 3.85
4551 4872 9.480861 CCTCCATGACAGATATAATTAGGTAGA 57.519 37.037 0.00 0.00 0.00 2.59
4552 4873 9.480861 TCCTCCATGACAGATATAATTAGGTAG 57.519 37.037 0.00 0.00 0.00 3.18
4553 4874 9.256228 GTCCTCCATGACAGATATAATTAGGTA 57.744 37.037 0.00 0.00 35.29 3.08
4554 4875 7.093727 CGTCCTCCATGACAGATATAATTAGGT 60.094 40.741 0.00 0.00 34.88 3.08
4555 4876 7.261325 CGTCCTCCATGACAGATATAATTAGG 58.739 42.308 0.00 0.00 34.88 2.69
4556 4877 7.093727 ACCGTCCTCCATGACAGATATAATTAG 60.094 40.741 0.00 0.00 34.88 1.73
4557 4878 6.724441 ACCGTCCTCCATGACAGATATAATTA 59.276 38.462 0.00 0.00 34.88 1.40
4558 4879 5.544176 ACCGTCCTCCATGACAGATATAATT 59.456 40.000 0.00 0.00 34.88 1.40
4559 4880 5.047021 CACCGTCCTCCATGACAGATATAAT 60.047 44.000 0.00 0.00 34.88 1.28
4560 4881 4.280929 CACCGTCCTCCATGACAGATATAA 59.719 45.833 0.00 0.00 34.88 0.98
4561 4882 3.826729 CACCGTCCTCCATGACAGATATA 59.173 47.826 0.00 0.00 34.88 0.86
4562 4883 2.630098 CACCGTCCTCCATGACAGATAT 59.370 50.000 0.00 0.00 34.88 1.63
4563 4884 2.031870 CACCGTCCTCCATGACAGATA 58.968 52.381 0.00 0.00 34.88 1.98
4564 4885 0.826715 CACCGTCCTCCATGACAGAT 59.173 55.000 0.00 0.00 34.88 2.90
4565 4886 1.888436 GCACCGTCCTCCATGACAGA 61.888 60.000 0.00 0.00 34.88 3.41
4566 4887 1.448540 GCACCGTCCTCCATGACAG 60.449 63.158 0.00 0.00 34.88 3.51
4567 4888 2.662596 GCACCGTCCTCCATGACA 59.337 61.111 0.00 0.00 34.88 3.58
4568 4889 2.125106 GGCACCGTCCTCCATGAC 60.125 66.667 0.00 0.00 0.00 3.06
4569 4890 1.995066 ATGGCACCGTCCTCCATGA 60.995 57.895 0.00 0.00 39.01 3.07
4570 4891 2.591753 ATGGCACCGTCCTCCATG 59.408 61.111 0.00 0.00 39.01 3.66
4571 4892 2.591753 CATGGCACCGTCCTCCAT 59.408 61.111 0.00 0.00 40.98 3.41
4572 4893 4.408821 GCATGGCACCGTCCTCCA 62.409 66.667 0.00 0.00 0.00 3.86
4573 4894 4.101448 AGCATGGCACCGTCCTCC 62.101 66.667 0.00 0.00 0.00 4.30
4574 4895 2.238847 TACAGCATGGCACCGTCCTC 62.239 60.000 0.00 0.00 43.62 3.71
4575 4896 2.290287 TACAGCATGGCACCGTCCT 61.290 57.895 0.00 0.00 43.62 3.85
4576 4897 2.106683 GTACAGCATGGCACCGTCC 61.107 63.158 0.00 0.00 43.62 4.79
4577 4898 2.106683 GGTACAGCATGGCACCGTC 61.107 63.158 0.00 0.00 43.62 4.79
4578 4899 2.046314 GGTACAGCATGGCACCGT 60.046 61.111 0.00 0.00 43.62 4.83
4579 4900 2.824041 GGGTACAGCATGGCACCG 60.824 66.667 0.00 0.00 43.78 4.94
4580 4901 2.824041 CGGGTACAGCATGGCACC 60.824 66.667 0.00 0.00 43.62 5.01
4597 4918 2.854523 GGGCTACCTCCATCCCCC 60.855 72.222 0.00 0.00 32.60 5.40
4606 4927 0.105811 CCTTACCTACCGGGCTACCT 60.106 60.000 6.32 0.00 39.10 3.08
4607 4928 1.117749 CCCTTACCTACCGGGCTACC 61.118 65.000 6.32 0.00 39.10 3.18
4608 4929 0.106015 TCCCTTACCTACCGGGCTAC 60.106 60.000 6.32 0.00 37.89 3.58
4609 4930 0.636101 TTCCCTTACCTACCGGGCTA 59.364 55.000 6.32 0.00 37.89 3.93
4616 8840 5.361571 CCTCTTTCTCTCTTCCCTTACCTAC 59.638 48.000 0.00 0.00 0.00 3.18
4621 8845 3.772025 CAGCCTCTTTCTCTCTTCCCTTA 59.228 47.826 0.00 0.00 0.00 2.69
4675 8906 2.470057 TTGTTCCCCTTTTTCTGGCT 57.530 45.000 0.00 0.00 0.00 4.75
4703 8934 5.764686 TCTTGCTGAGTTATGTGTGAATGTT 59.235 36.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.