Multiple sequence alignment - TraesCS4D01G067600

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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 TraesCS4D01G067600 chr4D 100.000 3810 0 0 1488 5297 43068183 43064374 0.000000e+00 7036.0
1 TraesCS4D01G067600 chr4D 100.000 1103 0 0 1 1103 43069670 43068568 0.000000e+00 2037.0
2 TraesCS4D01G067600 chr4A 93.963 2021 100 16 1488 3492 556826387 556828401 0.000000e+00 3037.0
3 TraesCS4D01G067600 chr4A 94.611 1336 57 11 3493 4821 556828442 556829769 0.000000e+00 2054.0
4 TraesCS4D01G067600 chr4A 91.192 1158 39 16 1 1103 556825169 556826318 0.000000e+00 1515.0
5 TraesCS4D01G067600 chr4A 90.792 467 35 5 4838 5297 556829758 556830223 7.540000e-173 617.0
6 TraesCS4D01G067600 chr4B 89.482 1968 134 40 1488 3427 61309869 61307947 0.000000e+00 2420.0
7 TraesCS4D01G067600 chr4B 94.643 1232 47 11 3452 4672 61307951 61306728 0.000000e+00 1892.0
8 TraesCS4D01G067600 chr4B 92.683 1107 43 12 1 1103 61311012 61309940 0.000000e+00 1561.0
9 TraesCS4D01G067600 chr4B 86.384 683 49 11 4628 5297 61306726 61306075 0.000000e+00 706.0
10 TraesCS4D01G067600 chr7D 100.000 29 0 0 4985 5013 43276566 43276538 3.000000e-03 54.7
11 TraesCS4D01G067600 chr1D 100.000 29 0 0 4985 5013 450147853 450147825 3.000000e-03 54.7
12 TraesCS4D01G067600 chr6D 100.000 28 0 0 4986 5013 58433752 58433779 1.000000e-02 52.8
13 TraesCS4D01G067600 chr6D 100.000 28 0 0 4986 5013 471540001 471540028 1.000000e-02 52.8
14 TraesCS4D01G067600 chr5D 100.000 28 0 0 4986 5013 494809012 494808985 1.000000e-02 52.8
15 TraesCS4D01G067600 chr3D 100.000 28 0 0 4986 5013 362864501 362864528 1.000000e-02 52.8
16 TraesCS4D01G067600 chr1A 100.000 28 0 0 4986 5013 457957378 457957405 1.000000e-02 52.8


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 TraesCS4D01G067600 chr4D 43064374 43069670 5296 True 4536.50 7036 100.0000 1 5297 2 chr4D.!!$R1 5296
1 TraesCS4D01G067600 chr4A 556825169 556830223 5054 False 1805.75 3037 92.6395 1 5297 4 chr4A.!!$F1 5296
2 TraesCS4D01G067600 chr4B 61306075 61311012 4937 True 1644.75 2420 90.7980 1 5297 4 chr4B.!!$R1 5296

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
493 513 0.981943 CCCTTGAGGAAGTTACCGGT 59.018 55.000 13.98 13.98 38.24 5.28 F
1529 1587 1.003116 GTTCTGATGATGTGATGCGGC 60.003 52.381 0.00 0.00 0.00 6.53 F
2557 2645 0.243095 CTTCTGCTTCAAGCCTTGCC 59.757 55.000 7.01 0.00 41.51 4.52 F
2569 2657 0.109132 GCCTTGCCGAAACCATTCAG 60.109 55.000 0.00 0.00 35.15 3.02 F
2762 2850 0.314935 AAATGCTTGAGCGTGTTGGG 59.685 50.000 0.00 0.00 45.83 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 1678 0.914417 TCCGGCCCATTCTCCTTCTT 60.914 55.0 0.00 0.0 0.00 2.52 R
2569 2657 0.324943 TGGCAGGTAGTTCTCCTTGC 59.675 55.0 0.00 0.0 32.37 4.01 R
3617 3749 0.537143 TGCGAACCTGCAAAGGTGAT 60.537 50.0 0.00 0.0 43.02 3.06 R
4266 4404 0.950555 GCATCGAGGTGCAGACAACA 60.951 55.0 6.13 0.0 44.43 3.33 R
4729 4920 0.756442 TGCTTCCCTTGCAAACTGCT 60.756 50.0 0.00 0.0 45.31 4.24 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
32 33 3.646611 TGACACATTTGCATTCACCAG 57.353 42.857 0.00 0.00 0.00 4.00
43 44 2.354103 GCATTCACCAGAGCTGTACAGA 60.354 50.000 27.08 2.12 0.00 3.41
63 64 4.697592 GCAATGCAATGCAACCCA 57.302 50.000 21.74 0.00 43.62 4.51
255 275 1.852067 AAGCTGTAAAACAGGCGGCG 61.852 55.000 0.51 0.51 46.01 6.46
256 276 2.175811 CTGTAAAACAGGCGGCGC 59.824 61.111 26.17 26.17 42.35 6.53
347 367 2.070028 GAGAAAGGAACAAGGAGCGTC 58.930 52.381 0.00 0.00 0.00 5.19
493 513 0.981943 CCCTTGAGGAAGTTACCGGT 59.018 55.000 13.98 13.98 38.24 5.28
506 529 2.856039 TACCGGTGGAGGAGGAGCAG 62.856 65.000 19.93 0.00 34.73 4.24
668 694 3.074369 TTCTCCGCCGCATCCTCA 61.074 61.111 0.00 0.00 0.00 3.86
670 696 2.578163 TTCTCCGCCGCATCCTCAAG 62.578 60.000 0.00 0.00 0.00 3.02
719 745 2.125147 TCGGCCGCTTCTTCCATG 60.125 61.111 23.51 0.00 0.00 3.66
760 810 2.653702 GCAGAGCGACCAGACTGT 59.346 61.111 0.93 0.00 33.57 3.55
969 1021 3.992317 GGTAGATCCGGCGAGGCC 61.992 72.222 9.30 0.00 46.75 5.19
1529 1587 1.003116 GTTCTGATGATGTGATGCGGC 60.003 52.381 0.00 0.00 0.00 6.53
1633 1694 2.443958 GGGGGAAAGAAGGAGAATGG 57.556 55.000 0.00 0.00 0.00 3.16
1729 1790 4.182433 GGGCCAGGCTAGCACCTC 62.182 72.222 18.24 0.00 38.26 3.85
1848 1911 2.427453 GCTCAAGGTCTTCGATACCTCA 59.573 50.000 17.65 8.85 46.85 3.86
1986 2049 3.402628 TCCCTGAGTTGCTTAGTGTTC 57.597 47.619 0.00 0.00 0.00 3.18
2033 2096 4.067896 ACTGAATTGCTGAACCTACAGTG 58.932 43.478 0.00 0.00 39.73 3.66
2038 2101 1.347378 TGCTGAACCTACAGTGCATGA 59.653 47.619 0.00 0.00 39.73 3.07
2045 2108 3.403038 ACCTACAGTGCATGAAACAGTC 58.597 45.455 0.00 0.00 0.00 3.51
2046 2109 3.181455 ACCTACAGTGCATGAAACAGTCA 60.181 43.478 0.00 0.00 41.67 3.41
2070 2141 3.718434 AGCACCTATGATCAAATCCTCCA 59.282 43.478 0.00 0.00 0.00 3.86
2073 2144 6.044754 AGCACCTATGATCAAATCCTCCAATA 59.955 38.462 0.00 0.00 0.00 1.90
2106 2177 3.393089 AACTGTCGACTCAGAATGCTT 57.607 42.857 17.92 0.00 38.63 3.91
2309 2383 6.433404 AGCATAGATGGGATTCTAAAAGCATG 59.567 38.462 0.00 0.00 32.20 4.06
2389 2465 4.847757 CGTTTTGCAGTGTCAATATGTCAG 59.152 41.667 0.00 0.00 0.00 3.51
2392 2468 3.599343 TGCAGTGTCAATATGTCAGGTC 58.401 45.455 0.00 0.00 0.00 3.85
2394 2470 3.372206 GCAGTGTCAATATGTCAGGTCAC 59.628 47.826 0.00 0.00 0.00 3.67
2395 2471 4.825422 CAGTGTCAATATGTCAGGTCACT 58.175 43.478 0.00 0.00 35.69 3.41
2399 2475 7.387673 CAGTGTCAATATGTCAGGTCACTTTTA 59.612 37.037 0.00 0.00 33.54 1.52
2400 2476 8.103305 AGTGTCAATATGTCAGGTCACTTTTAT 58.897 33.333 0.00 0.00 32.15 1.40
2401 2477 8.177663 GTGTCAATATGTCAGGTCACTTTTATG 58.822 37.037 0.00 0.00 0.00 1.90
2402 2478 7.882791 TGTCAATATGTCAGGTCACTTTTATGT 59.117 33.333 0.00 0.00 0.00 2.29
2443 2529 2.095692 GTGCCAACAAACCTGCAAAAAG 59.904 45.455 0.00 0.00 35.16 2.27
2487 2575 5.948992 AGGAACTCTTCAATTTAGTGTGC 57.051 39.130 0.00 0.00 0.00 4.57
2489 2577 5.703130 AGGAACTCTTCAATTTAGTGTGCTC 59.297 40.000 0.00 0.00 0.00 4.26
2493 2581 6.398918 ACTCTTCAATTTAGTGTGCTCGTAT 58.601 36.000 0.00 0.00 0.00 3.06
2494 2582 7.544622 ACTCTTCAATTTAGTGTGCTCGTATA 58.455 34.615 0.00 0.00 0.00 1.47
2557 2645 0.243095 CTTCTGCTTCAAGCCTTGCC 59.757 55.000 7.01 0.00 41.51 4.52
2569 2657 0.109132 GCCTTGCCGAAACCATTCAG 60.109 55.000 0.00 0.00 35.15 3.02
2762 2850 0.314935 AAATGCTTGAGCGTGTTGGG 59.685 50.000 0.00 0.00 45.83 4.12
2852 2940 2.224378 TGACCAGCAAACAGAAGAGGAG 60.224 50.000 0.00 0.00 0.00 3.69
2927 3015 1.347707 CAGTTGGAGGTGTGGCTTCTA 59.652 52.381 0.00 0.00 0.00 2.10
2939 3027 5.863935 GGTGTGGCTTCTATTTTCACATTTC 59.136 40.000 0.00 0.00 39.93 2.17
2953 3041 0.523072 CATTTCCTTCGTGTGCTGGG 59.477 55.000 0.00 0.00 0.00 4.45
3027 3117 2.565841 GAACTGGAAGCACTGTCAAGT 58.434 47.619 0.00 0.00 37.60 3.16
3148 3238 7.554959 ACTCTTAGTACCAAGATTGAGGAAA 57.445 36.000 4.14 0.00 34.14 3.13
3155 3245 2.833338 CCAAGATTGAGGAAAATGGGCA 59.167 45.455 0.00 0.00 0.00 5.36
3280 3370 1.134610 CGGGGTAGGCATAACTCGTTT 60.135 52.381 7.71 0.00 37.82 3.60
3286 3376 4.342092 GGTAGGCATAACTCGTTTACCCTA 59.658 45.833 0.00 0.00 30.78 3.53
3433 3524 4.142337 TGAACATGATTGCACATCATCCAC 60.142 41.667 16.56 12.36 36.69 4.02
3616 3748 9.569122 AAACATCTTACATGGTTACACTTACTT 57.431 29.630 0.00 0.00 0.00 2.24
4008 4142 4.143179 GCTACAAGTTTTGCTACAGGTACG 60.143 45.833 0.00 0.00 0.00 3.67
4074 4212 6.680758 CGCGCAAACTTAATTTTGTTCTTTTT 59.319 30.769 16.75 0.00 38.51 1.94
4154 4292 2.437359 AGACAAGCAGGGCGATGC 60.437 61.111 5.27 5.27 46.88 3.91
4266 4404 1.404391 CTCCAGTACCTCGCATACGTT 59.596 52.381 0.00 0.00 41.18 3.99
4287 4425 2.512515 GTCTGCACCTCGATGCCC 60.513 66.667 8.46 0.00 45.50 5.36
4297 4435 1.009829 CTCGATGCCCAGTGTTTAGC 58.990 55.000 0.00 0.00 0.00 3.09
4405 4546 8.975663 TCTAGCTAGTTATGAAAGCTACACTA 57.024 34.615 20.10 0.00 44.55 2.74
4531 4672 7.099764 TCCTGAGAACAATGAGAATTACTGAC 58.900 38.462 0.00 0.00 0.00 3.51
4539 4680 8.151141 ACAATGAGAATTACTGACATATGCAG 57.849 34.615 19.31 19.31 39.26 4.41
4566 4707 4.650131 AGATAGAAGTTTACCTAAGCGCCT 59.350 41.667 2.29 0.00 0.00 5.52
4573 4714 4.156008 AGTTTACCTAAGCGCCTTCATTTG 59.844 41.667 2.29 0.00 0.00 2.32
4575 4716 1.004277 ACCTAAGCGCCTTCATTTGGA 59.996 47.619 2.29 0.00 0.00 3.53
4653 4796 7.384660 CACATGAGATACTATTGAGAAAGGAGC 59.615 40.741 0.00 0.00 0.00 4.70
4676 4866 5.173673 GCACATATTATTGCGATTTGTGTGG 59.826 40.000 19.25 8.58 38.15 4.17
4686 4876 3.189287 GCGATTTGTGTGGTCTTTGATCT 59.811 43.478 0.00 0.00 0.00 2.75
4687 4877 4.320494 GCGATTTGTGTGGTCTTTGATCTT 60.320 41.667 0.00 0.00 0.00 2.40
4693 4883 5.924356 TGTGTGGTCTTTGATCTTAACTCA 58.076 37.500 0.00 0.00 0.00 3.41
4729 4920 6.376299 CCTGGAATGATGATTTCTTGAAGTGA 59.624 38.462 0.00 0.00 0.00 3.41
4767 4958 7.012421 GGGAAGCAACTATGTGTTATTAAGAGG 59.988 40.741 0.00 0.00 37.07 3.69
4774 4965 7.749666 ACTATGTGTTATTAAGAGGCCATGAT 58.250 34.615 5.01 0.00 0.00 2.45
4789 4980 6.189859 AGGCCATGATCAAAATAAGTTGAGA 58.810 36.000 5.01 0.00 40.72 3.27
4809 5029 7.664082 TGAGAAGAAACAGTCAAATCATCTC 57.336 36.000 0.00 0.00 37.24 2.75
4810 5030 7.448420 TGAGAAGAAACAGTCAAATCATCTCT 58.552 34.615 7.94 0.00 37.47 3.10
4811 5031 7.935755 TGAGAAGAAACAGTCAAATCATCTCTT 59.064 33.333 7.94 0.00 37.47 2.85
4812 5032 8.688747 AGAAGAAACAGTCAAATCATCTCTTT 57.311 30.769 0.00 0.00 0.00 2.52
4813 5033 9.129532 AGAAGAAACAGTCAAATCATCTCTTTT 57.870 29.630 0.00 0.00 0.00 2.27
4814 5034 9.741647 GAAGAAACAGTCAAATCATCTCTTTTT 57.258 29.630 0.00 0.00 0.00 1.94
4815 5035 9.741647 AAGAAACAGTCAAATCATCTCTTTTTC 57.258 29.630 0.00 0.00 0.00 2.29
4816 5036 8.355913 AGAAACAGTCAAATCATCTCTTTTTCC 58.644 33.333 0.00 0.00 30.20 3.13
4817 5037 7.587037 AACAGTCAAATCATCTCTTTTTCCA 57.413 32.000 0.00 0.00 0.00 3.53
4818 5038 7.587037 ACAGTCAAATCATCTCTTTTTCCAA 57.413 32.000 0.00 0.00 0.00 3.53
4819 5039 7.655490 ACAGTCAAATCATCTCTTTTTCCAAG 58.345 34.615 0.00 0.00 0.00 3.61
4820 5040 7.503566 ACAGTCAAATCATCTCTTTTTCCAAGA 59.496 33.333 0.00 0.00 0.00 3.02
4821 5041 8.521176 CAGTCAAATCATCTCTTTTTCCAAGAT 58.479 33.333 0.00 0.00 0.00 2.40
4822 5042 9.086758 AGTCAAATCATCTCTTTTTCCAAGATT 57.913 29.630 0.00 0.00 0.00 2.40
4823 5043 9.351570 GTCAAATCATCTCTTTTTCCAAGATTC 57.648 33.333 0.00 0.00 0.00 2.52
4824 5044 9.305555 TCAAATCATCTCTTTTTCCAAGATTCT 57.694 29.630 0.00 0.00 0.00 2.40
4825 5045 9.570488 CAAATCATCTCTTTTTCCAAGATTCTC 57.430 33.333 0.00 0.00 0.00 2.87
4826 5046 8.874744 AATCATCTCTTTTTCCAAGATTCTCA 57.125 30.769 0.00 0.00 0.00 3.27
4827 5047 8.874744 ATCATCTCTTTTTCCAAGATTCTCAA 57.125 30.769 0.00 0.00 0.00 3.02
4828 5048 8.696043 TCATCTCTTTTTCCAAGATTCTCAAA 57.304 30.769 0.00 0.00 0.00 2.69
4829 5049 9.135189 TCATCTCTTTTTCCAAGATTCTCAAAA 57.865 29.630 0.00 0.00 0.00 2.44
4830 5050 9.754382 CATCTCTTTTTCCAAGATTCTCAAAAA 57.246 29.630 9.07 9.07 0.00 1.94
4859 5079 5.857268 ACTTTTTCCAAGACATTCATTGGG 58.143 37.500 4.26 0.00 45.03 4.12
4860 5080 5.366477 ACTTTTTCCAAGACATTCATTGGGT 59.634 36.000 4.26 0.00 45.03 4.51
4861 5081 5.467035 TTTTCCAAGACATTCATTGGGTC 57.533 39.130 4.26 0.00 45.03 4.46
4888 5111 6.993786 TCGAATGTTGATGCCTTATTTACA 57.006 33.333 0.00 0.00 0.00 2.41
4904 5127 7.440255 CCTTATTTACACTTATACTTCCCCACG 59.560 40.741 0.00 0.00 0.00 4.94
4935 5158 6.516527 GCATCTCAAAACCAACAATTACTCCA 60.517 38.462 0.00 0.00 0.00 3.86
4947 5170 7.201732 CCAACAATTACTCCAGTTGTATCATCC 60.202 40.741 0.00 0.00 39.63 3.51
5104 5329 6.089016 GTGAAAATCACAATCAAGACATGCAG 59.911 38.462 5.65 0.00 46.22 4.41
5109 5334 7.634671 ATCACAATCAAGACATGCAGAATTA 57.365 32.000 0.00 0.00 0.00 1.40
5172 5397 0.526211 TGTCGAGTGGATGGACTTCG 59.474 55.000 0.00 0.00 37.52 3.79
5273 5504 2.446435 GCATGGGATACAGTTTGTGGT 58.554 47.619 0.00 0.00 39.74 4.16
5277 5508 5.238650 GCATGGGATACAGTTTGTGGTATAC 59.761 44.000 0.00 0.00 39.74 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.220940 TCTGGTGAATGCAAATGTGTCA 58.779 40.909 0.00 0.00 0.00 3.58
32 33 2.421073 TGCATTGCAATCTGTACAGCTC 59.579 45.455 18.45 7.19 34.76 4.09
55 56 1.896183 CATGTCACGGTGGGTTGCA 60.896 57.895 8.50 1.13 0.00 4.08
56 57 1.599518 TCATGTCACGGTGGGTTGC 60.600 57.895 8.50 0.00 0.00 4.17
58 59 0.181587 TTGTCATGTCACGGTGGGTT 59.818 50.000 8.50 0.00 0.00 4.11
59 60 0.181587 TTTGTCATGTCACGGTGGGT 59.818 50.000 8.50 0.00 0.00 4.51
60 61 0.874390 CTTTGTCATGTCACGGTGGG 59.126 55.000 8.50 0.00 0.00 4.61
61 62 0.874390 CCTTTGTCATGTCACGGTGG 59.126 55.000 8.50 0.00 0.00 4.61
62 63 1.877637 TCCTTTGTCATGTCACGGTG 58.122 50.000 0.56 0.56 0.00 4.94
63 64 2.494059 CTTCCTTTGTCATGTCACGGT 58.506 47.619 0.00 0.00 0.00 4.83
223 227 2.352422 AGCTTGAATGGCTGCCGA 59.648 55.556 14.98 3.61 38.73 5.54
241 254 2.127003 GTGCGCCGCCTGTTTTAC 60.127 61.111 6.63 0.00 0.00 2.01
256 276 4.760047 CCGTCGGAGGCCAAGGTG 62.760 72.222 4.91 0.00 0.00 4.00
275 295 4.385405 GAGCACACCGCAGAGGCT 62.385 66.667 0.00 0.00 46.52 4.58
347 367 1.482593 ACCTTCTTATGCCCTCGACTG 59.517 52.381 0.00 0.00 0.00 3.51
398 418 2.223829 CCTCCGCATGTTCTACCTGTAG 60.224 54.545 0.00 0.00 34.56 2.74
493 513 4.421554 CCCCCTGCTCCTCCTCCA 62.422 72.222 0.00 0.00 0.00 3.86
506 529 4.097361 GACCAGTTCCGCTCCCCC 62.097 72.222 0.00 0.00 0.00 5.40
593 616 4.756458 GAGGACGCTGCTGCTGCT 62.756 66.667 25.43 14.57 40.48 4.24
704 730 3.521796 GCCATGGAAGAAGCGGCC 61.522 66.667 18.40 0.00 36.73 6.13
719 745 1.111277 GAGGAGAGAGAGTTCCAGCC 58.889 60.000 0.00 0.00 35.88 4.85
969 1021 3.060615 GGGGTTGCTGCTGCTCTG 61.061 66.667 17.00 0.00 40.48 3.35
1045 1103 3.123620 CTGCTCGTCTTGCTGGGC 61.124 66.667 0.00 0.00 0.00 5.36
1498 1556 2.816411 TCATCAGAACCCTAACCGTCT 58.184 47.619 0.00 0.00 0.00 4.18
1620 1678 0.914417 TCCGGCCCATTCTCCTTCTT 60.914 55.000 0.00 0.00 0.00 2.52
1622 1680 1.147153 CTCCGGCCCATTCTCCTTC 59.853 63.158 0.00 0.00 0.00 3.46
1766 1829 2.754552 CACCAATCCATCGACCACATTT 59.245 45.455 0.00 0.00 0.00 2.32
1848 1911 1.893786 GGTCGTGATGCTCTCCACT 59.106 57.895 0.00 0.00 0.00 4.00
2033 2096 2.035066 AGGTGCTTTGACTGTTTCATGC 59.965 45.455 0.00 0.00 35.67 4.06
2038 2101 5.316167 TGATCATAGGTGCTTTGACTGTTT 58.684 37.500 0.00 0.00 0.00 2.83
2045 2108 5.009410 GGAGGATTTGATCATAGGTGCTTTG 59.991 44.000 0.00 0.00 0.00 2.77
2046 2109 5.136105 GGAGGATTTGATCATAGGTGCTTT 58.864 41.667 0.00 0.00 0.00 3.51
2078 2149 8.391106 GCATTCTGAGTCGACAGTTAATTATTT 58.609 33.333 19.50 0.00 38.79 1.40
2087 2158 2.297315 TCAAGCATTCTGAGTCGACAGT 59.703 45.455 19.50 0.00 38.79 3.55
2093 2164 6.690194 AACCATAATCAAGCATTCTGAGTC 57.310 37.500 0.00 0.00 0.00 3.36
2165 2238 7.610580 ATTCTTGAACCAACAAAGGGAAATA 57.389 32.000 0.00 0.00 0.00 1.40
2191 2264 4.642429 ACGGGCAAGAAATCCATATACTC 58.358 43.478 0.00 0.00 0.00 2.59
2309 2383 1.453148 GCAGCGTTTTGATGAAAGTGC 59.547 47.619 0.00 0.00 35.47 4.40
2400 2476 9.685828 GGCACTCAAAACATTATTAAACTAACA 57.314 29.630 0.00 0.00 0.00 2.41
2401 2477 9.685828 TGGCACTCAAAACATTATTAAACTAAC 57.314 29.630 0.00 0.00 0.00 2.34
2557 2645 2.426522 TCTCCTTGCTGAATGGTTTCG 58.573 47.619 0.00 0.00 34.39 3.46
2569 2657 0.324943 TGGCAGGTAGTTCTCCTTGC 59.675 55.000 0.00 0.00 32.37 4.01
2602 2690 3.237268 ACCTCTAAAATGGTTGGTGCA 57.763 42.857 0.00 0.00 31.62 4.57
2700 2788 2.233922 ACTTCCCTGTCTGTGGTAATCG 59.766 50.000 0.00 0.00 0.00 3.34
2762 2850 4.748892 TGATCAACTCCATCGTCTCTTTC 58.251 43.478 0.00 0.00 0.00 2.62
2852 2940 5.231147 GTCGAATGATACTTCTTCAGACTGC 59.769 44.000 0.00 0.00 0.00 4.40
2927 3015 4.037923 AGCACACGAAGGAAATGTGAAAAT 59.962 37.500 7.74 0.00 45.34 1.82
2939 3027 1.338674 TGATAACCCAGCACACGAAGG 60.339 52.381 0.00 0.00 0.00 3.46
2953 3041 4.277423 GGTAGAGAGCCAGAGACTGATAAC 59.723 50.000 0.00 0.00 32.44 1.89
3027 3117 5.869344 CCTATTAAATAGCAGCGCATAGTGA 59.131 40.000 11.47 0.00 0.00 3.41
3148 3238 2.957402 TTGTCAGAGTCTTGCCCATT 57.043 45.000 0.00 0.00 0.00 3.16
3155 3245 4.656112 TCTTCTTCCCTTTGTCAGAGTCTT 59.344 41.667 0.00 0.00 0.00 3.01
3327 3417 5.771666 CCCACTAATTGCATCATAACCTGAT 59.228 40.000 0.00 0.00 45.78 2.90
3433 3524 3.930336 TGTGAGTTTCTGCAGTGGATAG 58.070 45.455 14.67 0.00 0.00 2.08
3612 3744 4.250464 CGAACCTGCAAAGGTGATAAGTA 58.750 43.478 0.00 0.00 42.20 2.24
3614 3746 2.159517 GCGAACCTGCAAAGGTGATAAG 60.160 50.000 0.00 0.00 42.20 1.73
3615 3747 1.810151 GCGAACCTGCAAAGGTGATAA 59.190 47.619 0.00 0.00 42.20 1.75
3616 3748 1.271108 TGCGAACCTGCAAAGGTGATA 60.271 47.619 0.00 0.00 43.02 2.15
3617 3749 0.537143 TGCGAACCTGCAAAGGTGAT 60.537 50.000 0.00 0.00 43.02 3.06
3618 3750 1.153066 TGCGAACCTGCAAAGGTGA 60.153 52.632 0.00 0.00 43.02 4.02
3619 3751 3.431055 TGCGAACCTGCAAAGGTG 58.569 55.556 0.00 0.00 43.02 4.00
3781 3913 1.203287 TGACAATCTCTGCAGGACGAG 59.797 52.381 15.13 3.90 0.00 4.18
4008 4142 6.801862 CACGAGGGAAAATAGATTGTTTTCAC 59.198 38.462 11.88 8.95 45.06 3.18
4074 4212 6.692849 ACATCTGAGATGCCTATGGATTTA 57.307 37.500 21.62 0.00 0.00 1.40
4154 4292 2.821366 GCACCGACTGATGCAGGG 60.821 66.667 0.00 0.00 41.65 4.45
4266 4404 0.950555 GCATCGAGGTGCAGACAACA 60.951 55.000 6.13 0.00 44.43 3.33
4287 4425 1.813513 CACTCCAGGGCTAAACACTG 58.186 55.000 0.00 0.00 0.00 3.66
4405 4546 3.153919 ACAAACACACCACAAGACAACT 58.846 40.909 0.00 0.00 0.00 3.16
4531 4672 8.768955 GGTAAACTTCTATCTCAACTGCATATG 58.231 37.037 0.00 0.00 0.00 1.78
4539 4680 6.019720 GCGCTTAGGTAAACTTCTATCTCAAC 60.020 42.308 0.00 0.00 0.00 3.18
4626 4769 8.311395 TCCTTTCTCAATAGTATCTCATGTGT 57.689 34.615 0.00 0.00 0.00 3.72
4630 4773 7.070447 TGTGCTCCTTTCTCAATAGTATCTCAT 59.930 37.037 0.00 0.00 0.00 2.90
4653 4796 6.264832 ACCACACAAATCGCAATAATATGTG 58.735 36.000 0.00 0.00 41.69 3.21
4676 4866 9.907576 CGATGTAAATGAGTTAAGATCAAAGAC 57.092 33.333 0.00 0.00 0.00 3.01
4686 4876 6.288941 TCCAGGTCGATGTAAATGAGTTAA 57.711 37.500 0.00 0.00 0.00 2.01
4687 4877 5.925506 TCCAGGTCGATGTAAATGAGTTA 57.074 39.130 0.00 0.00 0.00 2.24
4693 4883 5.928976 TCATCATTCCAGGTCGATGTAAAT 58.071 37.500 12.41 0.00 37.21 1.40
4701 4891 4.877823 TCAAGAAATCATCATTCCAGGTCG 59.122 41.667 0.00 0.00 0.00 4.79
4729 4920 0.756442 TGCTTCCCTTGCAAACTGCT 60.756 50.000 0.00 0.00 45.31 4.24
4742 4933 7.467403 GCCTCTTAATAACACATAGTTGCTTCC 60.467 40.741 0.00 0.00 41.50 3.46
4767 4958 7.765307 TCTTCTCAACTTATTTTGATCATGGC 58.235 34.615 0.00 0.00 34.96 4.40
4774 4965 9.173021 TGACTGTTTCTTCTCAACTTATTTTGA 57.827 29.630 0.00 0.00 34.30 2.69
4789 4980 9.741647 GAAAAAGAGATGATTTGACTGTTTCTT 57.258 29.630 0.00 0.00 34.17 2.52
4794 4985 7.503566 TCTTGGAAAAAGAGATGATTTGACTGT 59.496 33.333 0.00 0.00 0.00 3.55
4832 5052 8.676401 CCAATGAATGTCTTGGAAAAAGTTTTT 58.324 29.630 13.35 13.35 43.83 1.94
4833 5053 7.282901 CCCAATGAATGTCTTGGAAAAAGTTTT 59.717 33.333 2.95 0.00 43.83 2.43
4834 5054 6.767423 CCCAATGAATGTCTTGGAAAAAGTTT 59.233 34.615 2.95 0.00 43.83 2.66
4835 5055 6.126796 ACCCAATGAATGTCTTGGAAAAAGTT 60.127 34.615 2.95 0.00 43.83 2.66
4836 5056 5.366477 ACCCAATGAATGTCTTGGAAAAAGT 59.634 36.000 2.95 0.00 43.83 2.66
4853 5073 1.016627 ACATTCGATGCGACCCAATG 58.983 50.000 0.00 0.00 34.89 2.82
4854 5074 1.401552 CAACATTCGATGCGACCCAAT 59.598 47.619 0.00 0.00 34.89 3.16
4857 5077 1.003545 CATCAACATTCGATGCGACCC 60.004 52.381 0.00 0.00 34.89 4.46
4888 5111 4.382362 GCAGTAACGTGGGGAAGTATAAGT 60.382 45.833 0.00 0.00 0.00 2.24
4904 5127 5.181690 TGTTGGTTTTGAGATGCAGTAAC 57.818 39.130 0.00 0.00 0.00 2.50
4935 5158 3.136641 ACCCAGGAGGATGATACAACT 57.863 47.619 0.00 0.00 39.89 3.16
4947 5170 8.696374 CCTACAATATGTATATGTACCCAGGAG 58.304 40.741 0.00 0.00 31.66 3.69
5080 5305 6.016108 TCTGCATGTCTTGATTGTGATTTTCA 60.016 34.615 0.00 0.00 0.00 2.69
5172 5397 4.938226 GGCAGCCTGATTACTATGATTACC 59.062 45.833 3.29 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.