Multiple sequence alignment - TraesCS7B01G256600

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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 TraesCS7B01G256600 chr7B 100.000 3569 0 0 1 3569 475666288 475662720 0.000000e+00 6591
1 TraesCS7B01G256600 chr7D 94.233 2705 104 14 1 2672 452712962 452710277 0.000000e+00 4084
2 TraesCS7B01G256600 chr7D 87.634 372 39 5 2833 3202 452705732 452705366 3.290000e-115 425
3 TraesCS7B01G256600 chr7D 88.835 206 21 2 3366 3569 452705178 452704973 5.910000e-63 252
4 TraesCS7B01G256600 chr7D 95.556 90 4 0 2728 2817 452705958 452705869 1.030000e-30 145
5 TraesCS7B01G256600 chr7A 91.999 2837 161 23 2 2813 545070173 545067378 0.000000e+00 3921
6 TraesCS7B01G256600 chr7A 83.333 354 38 12 3232 3569 545066883 545066535 1.240000e-79 307


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 TraesCS7B01G256600 chr7B 475662720 475666288 3568 True 6591 6591 100.000 1 3569 1 chr7B.!!$R1 3568
1 TraesCS7B01G256600 chr7D 452710277 452712962 2685 True 4084 4084 94.233 1 2672 1 chr7D.!!$R1 2671
2 TraesCS7B01G256600 chr7D 452704973 452705958 985 True 274 425 90.675 2728 3569 3 chr7D.!!$R2 841
3 TraesCS7B01G256600 chr7A 545066535 545070173 3638 True 2114 3921 87.666 2 3569 2 chr7A.!!$R1 3567

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
158 162 0.323302 TTGTCTGGCCATAAGCGTCA 59.677 50.0 5.51 0.00 45.17 4.35 F
283 287 0.586802 GTTTCACCGGTTCTGAGCAC 59.413 55.0 2.97 0.00 0.00 4.40 F
1611 1639 0.179018 AAGAGGCGGTGAAGCTGTTT 60.179 50.0 0.00 0.00 37.29 2.83 F
2363 2406 0.250640 CTCCTCACTGCTTGCAAGGT 60.251 55.0 27.10 14.92 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1399 0.600255 CTTCTCTGTTTCGGCCACGT 60.600 55.000 2.24 0.0 41.85 4.49 R
1978 2021 0.868406 CGTTCAAAGACCTCCACTGC 59.132 55.000 0.00 0.0 0.00 4.40 R
2564 2607 1.340889 GTGCCAACTGCCATTTTCAGA 59.659 47.619 0.00 0.0 40.16 3.27 R
3332 3547 1.680338 ACCTGCTGAACAACCTGAAC 58.320 50.000 0.00 0.0 0.00 3.18 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
24 25 2.126228 CTGCACATTGGCCGCAAG 60.126 61.111 0.00 0.00 34.75 4.01
34 35 1.327303 TGGCCGCAAGAACAAGAAAT 58.673 45.000 0.00 0.00 43.02 2.17
67 71 6.816640 TCCGTGATGAACTAATGTCCTAAAAG 59.183 38.462 0.00 0.00 0.00 2.27
90 94 4.331168 GCGAGCTGATCAACTACTGAAAAT 59.669 41.667 0.00 0.00 37.67 1.82
91 95 5.520288 GCGAGCTGATCAACTACTGAAAATA 59.480 40.000 0.00 0.00 37.67 1.40
92 96 6.201806 GCGAGCTGATCAACTACTGAAAATAT 59.798 38.462 0.00 0.00 37.67 1.28
93 97 7.254590 GCGAGCTGATCAACTACTGAAAATATT 60.255 37.037 0.00 0.00 37.67 1.28
94 98 8.272176 CGAGCTGATCAACTACTGAAAATATTC 58.728 37.037 0.00 0.00 37.67 1.75
95 99 8.136057 AGCTGATCAACTACTGAAAATATTCG 57.864 34.615 0.00 0.00 37.67 3.34
96 100 7.981789 AGCTGATCAACTACTGAAAATATTCGA 59.018 33.333 0.00 0.00 37.67 3.71
119 123 9.934190 TCGATGTAATGTTCATATGTGAAATTG 57.066 29.630 6.45 0.63 45.38 2.32
139 143 5.606348 TTGTTTGTTGCCTCCTAAATTGT 57.394 34.783 0.00 0.00 0.00 2.71
144 148 4.469657 TGTTGCCTCCTAAATTGTTGTCT 58.530 39.130 0.00 0.00 0.00 3.41
146 150 3.420893 TGCCTCCTAAATTGTTGTCTGG 58.579 45.455 0.00 0.00 0.00 3.86
147 151 2.164422 GCCTCCTAAATTGTTGTCTGGC 59.836 50.000 0.00 0.00 0.00 4.85
154 158 3.874392 AATTGTTGTCTGGCCATAAGC 57.126 42.857 5.51 0.00 42.60 3.09
158 162 0.323302 TTGTCTGGCCATAAGCGTCA 59.677 50.000 5.51 0.00 45.17 4.35
161 165 1.130561 GTCTGGCCATAAGCGTCAAAC 59.869 52.381 5.51 0.00 45.17 2.93
168 172 4.095782 GGCCATAAGCGTCAAACAGATTTA 59.904 41.667 0.00 0.00 45.17 1.40
283 287 0.586802 GTTTCACCGGTTCTGAGCAC 59.413 55.000 2.97 0.00 0.00 4.40
550 559 3.056607 CCTATGCCCACAAGGAAAACAAG 60.057 47.826 0.00 0.00 38.24 3.16
914 940 2.505628 ATCGCTCACTGCTATCTGTG 57.494 50.000 0.00 0.00 41.68 3.66
938 966 2.357075 GGCACCTGGCTACTAAAAGTC 58.643 52.381 0.00 0.00 44.01 3.01
1050 1078 2.099062 CGCGAATGCAACCTGCTC 59.901 61.111 0.00 0.00 45.31 4.26
1277 1305 2.799562 CGCTCATGGACATGTACACGAT 60.800 50.000 14.44 0.00 39.72 3.73
1371 1399 3.962718 TGATGATCAGGTGCTATGTCAGA 59.037 43.478 0.09 0.00 0.00 3.27
1385 1413 1.300620 TCAGACGTGGCCGAAACAG 60.301 57.895 0.00 0.00 37.88 3.16
1416 1444 1.746516 GCTTTGGCTGAGGAGATGGAG 60.747 57.143 0.00 0.00 35.22 3.86
1418 1446 1.956869 TTGGCTGAGGAGATGGAGAA 58.043 50.000 0.00 0.00 0.00 2.87
1551 1579 2.032528 TTCAGCCTCCCAGTTGCG 59.967 61.111 0.00 0.00 0.00 4.85
1611 1639 0.179018 AAGAGGCGGTGAAGCTGTTT 60.179 50.000 0.00 0.00 37.29 2.83
1641 1669 1.588404 CCGTCGAGGAACATCATTTCG 59.412 52.381 6.70 0.00 45.00 3.46
1680 1708 1.388547 GATATGCCTTTGCCGGACAA 58.611 50.000 5.05 6.40 36.33 3.18
1686 1714 1.237285 CCTTTGCCGGACAAGTGGAG 61.237 60.000 5.05 3.46 40.06 3.86
1696 1724 0.605589 ACAAGTGGAGAAGGCGAGAG 59.394 55.000 0.00 0.00 0.00 3.20
1741 1769 8.428063 CAGAGAAGGATCTAATTATGTGGACTT 58.572 37.037 0.00 0.00 35.54 3.01
1808 1836 1.525197 GTCGTTGTTTCGAGACATGCA 59.475 47.619 9.87 0.00 40.52 3.96
1897 1940 3.650647 TGGATCCACCAGTTTGCTC 57.349 52.632 11.44 0.00 44.64 4.26
1916 1959 3.625313 GCTCAAGGTAAGAAGATGAAGCC 59.375 47.826 0.00 0.00 0.00 4.35
1935 1978 1.531423 CTGATGCAGTTCTTGGCACT 58.469 50.000 0.00 0.00 43.75 4.40
1944 1987 1.001378 GTTCTTGGCACTGCGTTGATT 60.001 47.619 0.00 0.00 0.00 2.57
1978 2021 1.556911 AGTGTGGGCATGTAGAGAAGG 59.443 52.381 0.00 0.00 0.00 3.46
2213 2256 3.620488 GTGCCATGAAGGAGGTTTATCA 58.380 45.455 0.00 0.00 41.22 2.15
2298 2341 6.002704 ACTTGATGAAGCTGAGAAGTTGATT 58.997 36.000 0.00 0.00 31.68 2.57
2301 2344 7.369803 TGATGAAGCTGAGAAGTTGATTAAC 57.630 36.000 0.00 0.00 37.06 2.01
2302 2345 6.936335 TGATGAAGCTGAGAAGTTGATTAACA 59.064 34.615 2.93 0.00 39.30 2.41
2363 2406 0.250640 CTCCTCACTGCTTGCAAGGT 60.251 55.000 27.10 14.92 0.00 3.50
2385 2428 2.234661 TCAAGGCAATGTCGAGATGAGT 59.765 45.455 0.00 0.00 0.00 3.41
2484 2527 0.460987 CTGCAAGTCGATGGGAGGAC 60.461 60.000 0.00 0.00 0.00 3.85
2486 2529 1.519455 CAAGTCGATGGGAGGACGC 60.519 63.158 0.00 0.00 38.20 5.19
2564 2607 2.420687 GCTTGATCGAGGTGAAGGGATT 60.421 50.000 12.06 0.00 0.00 3.01
2614 2657 8.023021 ACATCTAGTGCTTCAACATAGGAATA 57.977 34.615 0.00 0.00 0.00 1.75
2657 2700 6.371548 TCTGAGTAATTTTTCCTTGTGATCCG 59.628 38.462 0.00 0.00 0.00 4.18
2661 2704 4.519540 ATTTTTCCTTGTGATCCGTTGG 57.480 40.909 0.00 0.00 0.00 3.77
2673 2716 2.743636 TCCGTTGGTCTGAGTTCATC 57.256 50.000 0.00 0.00 0.00 2.92
2684 2727 5.468072 GGTCTGAGTTCATCGCATTGATATT 59.532 40.000 0.00 0.00 34.83 1.28
2689 2732 6.424812 TGAGTTCATCGCATTGATATTACCAG 59.575 38.462 0.00 0.00 34.83 4.00
2722 2765 2.698274 TCAGTTTAGCTGTGGTGACTCA 59.302 45.455 0.00 0.00 45.23 3.41
2768 2811 4.273235 GCTCAAAATTCCACCTGGTTTTTG 59.727 41.667 20.65 20.65 43.00 2.44
2776 2819 2.593026 CACCTGGTTTTTGCCTCCTAA 58.407 47.619 0.00 0.00 0.00 2.69
2817 2860 6.459923 ACTTTCAGAACAGAGGTATTCAGAC 58.540 40.000 0.00 0.00 0.00 3.51
2818 2861 5.407407 TTCAGAACAGAGGTATTCAGACC 57.593 43.478 0.00 0.00 40.08 3.85
2840 3004 5.105837 ACCTCTGGAAACGATCACTACTTAC 60.106 44.000 0.00 0.00 0.00 2.34
2903 3068 3.587061 TGGAGCTGGTTTCTTCCTATTGA 59.413 43.478 0.00 0.00 0.00 2.57
2933 3098 2.428890 CGAGCCACCTCTTCTATCTGTT 59.571 50.000 0.00 0.00 35.90 3.16
2934 3099 3.632604 CGAGCCACCTCTTCTATCTGTTA 59.367 47.826 0.00 0.00 35.90 2.41
2935 3100 4.261405 CGAGCCACCTCTTCTATCTGTTAG 60.261 50.000 0.00 0.00 35.90 2.34
3007 3173 9.620660 GTTTATTAACTCCAACAATGAAACGAT 57.379 29.630 0.00 0.00 0.00 3.73
3072 3238 9.700831 AAGCCATTAGTATCTTTCACCTATTTT 57.299 29.630 0.00 0.00 0.00 1.82
3082 3248 5.241506 TCTTTCACCTATTTTCTGTTGCAGG 59.758 40.000 0.00 0.00 31.51 4.85
3107 3273 8.714906 GGTGAATATACCTATGGGCTAATATGT 58.285 37.037 0.00 0.00 37.74 2.29
3108 3274 9.547753 GTGAATATACCTATGGGCTAATATGTG 57.452 37.037 0.00 0.00 35.63 3.21
3118 3284 2.287915 GGCTAATATGTGCCTTGACACG 59.712 50.000 10.88 0.00 45.26 4.49
3120 3286 3.246226 GCTAATATGTGCCTTGACACGAG 59.754 47.826 0.00 0.00 43.74 4.18
3171 3337 7.041848 CGCCATTTGTAATCTTATGATGAGACA 60.042 37.037 0.00 0.00 32.44 3.41
3208 3392 5.008316 TCGTTTAATCGACTAGCTGCTGATA 59.992 40.000 13.43 0.00 34.85 2.15
3230 3414 2.260844 TTTCAGCCTGAACTGACCAG 57.739 50.000 6.65 0.00 46.13 4.00
3243 3458 3.539604 ACTGACCAGCATTATCTTCAGC 58.460 45.455 0.00 0.00 34.98 4.26
3271 3486 4.937620 TGTTCAGGAGATCACATAAGTTGC 59.062 41.667 0.00 0.00 0.00 4.17
3289 3504 0.255890 GCCTGCCTCCCAACATCTTA 59.744 55.000 0.00 0.00 0.00 2.10
3293 3508 3.193479 CCTGCCTCCCAACATCTTAAAAC 59.807 47.826 0.00 0.00 0.00 2.43
3316 3531 2.876091 TCTCTTGTAAGTTCATCCGCG 58.124 47.619 0.00 0.00 0.00 6.46
3328 3543 2.809446 TCATCCGCGAGTTACAGAATG 58.191 47.619 8.23 0.00 46.00 2.67
3329 3544 1.258982 CATCCGCGAGTTACAGAATGC 59.741 52.381 8.23 0.00 42.53 3.56
3330 3545 0.530744 TCCGCGAGTTACAGAATGCT 59.469 50.000 8.23 0.00 42.53 3.79
3332 3547 2.120232 CCGCGAGTTACAGAATGCTAG 58.880 52.381 8.23 0.00 42.53 3.42
3337 3552 4.266502 GCGAGTTACAGAATGCTAGTTCAG 59.733 45.833 0.00 0.00 42.53 3.02
3339 3554 5.622460 CGAGTTACAGAATGCTAGTTCAGGT 60.622 44.000 0.00 0.00 42.53 4.00
3340 3555 6.115448 AGTTACAGAATGCTAGTTCAGGTT 57.885 37.500 0.00 0.00 42.53 3.50
3341 3556 5.934625 AGTTACAGAATGCTAGTTCAGGTTG 59.065 40.000 0.00 0.00 42.53 3.77
3342 3557 4.357918 ACAGAATGCTAGTTCAGGTTGT 57.642 40.909 0.00 0.00 42.53 3.32
3344 3559 4.757149 ACAGAATGCTAGTTCAGGTTGTTC 59.243 41.667 0.00 0.00 42.53 3.18
3345 3560 4.756642 CAGAATGCTAGTTCAGGTTGTTCA 59.243 41.667 0.00 0.00 0.00 3.18
3346 3561 4.999950 AGAATGCTAGTTCAGGTTGTTCAG 59.000 41.667 0.00 0.00 0.00 3.02
3347 3562 2.494059 TGCTAGTTCAGGTTGTTCAGC 58.506 47.619 0.00 0.00 0.00 4.26
3348 3563 2.158827 TGCTAGTTCAGGTTGTTCAGCA 60.159 45.455 0.00 0.00 35.55 4.41
3353 3568 3.118038 AGTTCAGGTTGTTCAGCAGGTTA 60.118 43.478 0.00 0.00 0.00 2.85
3354 3569 3.788227 TCAGGTTGTTCAGCAGGTTAT 57.212 42.857 0.00 0.00 0.00 1.89
3355 3570 4.098914 TCAGGTTGTTCAGCAGGTTATT 57.901 40.909 0.00 0.00 0.00 1.40
3356 3571 5.235850 TCAGGTTGTTCAGCAGGTTATTA 57.764 39.130 0.00 0.00 0.00 0.98
3357 3572 5.626142 TCAGGTTGTTCAGCAGGTTATTAA 58.374 37.500 0.00 0.00 0.00 1.40
3358 3573 5.705441 TCAGGTTGTTCAGCAGGTTATTAAG 59.295 40.000 0.00 0.00 0.00 1.85
3360 3575 6.206634 CAGGTTGTTCAGCAGGTTATTAAGAA 59.793 38.462 0.00 0.00 0.00 2.52
3362 3577 7.451566 AGGTTGTTCAGCAGGTTATTAAGAATT 59.548 33.333 0.00 0.00 0.00 2.17
3406 3635 1.630369 TCAAGGCTTGTAGCTGGTGAT 59.370 47.619 25.39 0.00 41.99 3.06
3407 3636 1.741706 CAAGGCTTGTAGCTGGTGATG 59.258 52.381 19.07 0.00 41.99 3.07
3413 3642 5.486775 AGGCTTGTAGCTGGTGATGATATAT 59.513 40.000 0.00 0.00 41.99 0.86
3417 3646 5.970592 TGTAGCTGGTGATGATATATCAGC 58.029 41.667 21.45 21.45 45.37 4.26
3424 3654 5.545335 TGGTGATGATATATCAGCTTCTGGT 59.455 40.000 26.54 6.70 43.23 4.00
3439 3669 5.697633 AGCTTCTGGTTGTATTTGCATTTTG 59.302 36.000 0.00 0.00 0.00 2.44
3460 3691 8.498054 TTTTGGTTGCTTTGTTCATTTCATAA 57.502 26.923 0.00 0.00 0.00 1.90
3468 3699 9.770097 TGCTTTGTTCATTTCATAATTTTGGTA 57.230 25.926 0.00 0.00 0.00 3.25
3544 3775 6.430000 TCTTTTTCATGAAGGTAACCTGCTAC 59.570 38.462 8.41 0.00 32.13 3.58
3551 3782 3.103080 AGGTAACCTGCTACTACTGCT 57.897 47.619 0.00 0.00 29.57 4.24
3557 3788 7.343833 AGGTAACCTGCTACTACTGCTTATTAA 59.656 37.037 0.00 0.00 29.57 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.096417 CGGACGACACCATTTCTTGTTC 60.096 50.000 0.00 0.00 0.00 3.18
34 35 0.319211 GTTCATCACGGACGACACCA 60.319 55.000 0.00 0.00 0.00 4.17
67 71 2.568696 TCAGTAGTTGATCAGCTCGC 57.431 50.000 16.01 10.20 0.00 5.03
93 97 9.934190 CAATTTCACATATGAACATTACATCGA 57.066 29.630 10.38 0.00 44.66 3.59
94 98 9.720667 ACAATTTCACATATGAACATTACATCG 57.279 29.630 10.38 0.00 44.66 3.84
101 105 8.497554 GCAACAAACAATTTCACATATGAACAT 58.502 29.630 10.38 0.00 44.66 2.71
102 106 7.042187 GGCAACAAACAATTTCACATATGAACA 60.042 33.333 10.38 0.00 44.66 3.18
103 107 7.171337 AGGCAACAAACAATTTCACATATGAAC 59.829 33.333 10.38 0.00 41.83 3.18
104 108 7.215789 AGGCAACAAACAATTTCACATATGAA 58.784 30.769 10.38 0.00 40.82 2.57
105 109 6.757237 AGGCAACAAACAATTTCACATATGA 58.243 32.000 10.38 0.00 41.41 2.15
106 110 6.091169 GGAGGCAACAAACAATTTCACATATG 59.909 38.462 0.00 0.00 41.41 1.78
107 111 6.014327 AGGAGGCAACAAACAATTTCACATAT 60.014 34.615 0.00 0.00 41.41 1.78
108 112 5.304101 AGGAGGCAACAAACAATTTCACATA 59.696 36.000 0.00 0.00 41.41 2.29
109 113 4.101430 AGGAGGCAACAAACAATTTCACAT 59.899 37.500 0.00 0.00 41.41 3.21
110 114 3.450457 AGGAGGCAACAAACAATTTCACA 59.550 39.130 0.00 0.00 41.41 3.58
115 119 6.591001 ACAATTTAGGAGGCAACAAACAATT 58.409 32.000 0.00 0.00 41.41 2.32
119 123 5.356426 ACAACAATTTAGGAGGCAACAAAC 58.644 37.500 0.00 0.00 41.41 2.93
139 143 0.323302 TGACGCTTATGGCCAGACAA 59.677 50.000 13.05 4.19 37.74 3.18
144 148 1.164411 CTGTTTGACGCTTATGGCCA 58.836 50.000 8.56 8.56 37.74 5.36
146 150 3.764885 AATCTGTTTGACGCTTATGGC 57.235 42.857 0.00 0.00 37.64 4.40
147 151 8.612619 AGTTATAAATCTGTTTGACGCTTATGG 58.387 33.333 0.00 0.00 0.00 2.74
154 158 7.330946 TCAGGTGAGTTATAAATCTGTTTGACG 59.669 37.037 13.58 0.00 0.00 4.35
158 162 7.398024 AGCTCAGGTGAGTTATAAATCTGTTT 58.602 34.615 13.58 0.00 43.85 2.83
161 165 7.044181 TCAAGCTCAGGTGAGTTATAAATCTG 58.956 38.462 13.58 4.71 43.85 2.90
168 172 3.177228 ACCTCAAGCTCAGGTGAGTTAT 58.823 45.455 15.12 0.00 43.10 1.89
251 255 2.342648 GAAACGGTGGAGGTCGCT 59.657 61.111 0.00 0.00 0.00 4.93
550 559 1.028868 ATCGCAGCTTGGCTTCTTCC 61.029 55.000 0.00 0.00 36.40 3.46
815 841 2.682494 GTGGTGGGAGGGAGCGTA 60.682 66.667 0.00 0.00 0.00 4.42
846 872 0.326904 ATGGCTCCTGAGATGGGTGA 60.327 55.000 0.00 0.00 0.00 4.02
914 940 2.515996 TTAGTAGCCAGGTGCCGTGC 62.516 60.000 0.00 0.00 42.71 5.34
938 966 2.830370 GGCCGGCCAAGATGGAAG 60.830 66.667 40.73 0.00 40.96 3.46
1050 1078 2.415010 CTCGCGAGGGTCCTGATG 59.585 66.667 28.40 0.00 0.00 3.07
1131 1159 1.153823 CGGGTAGGTGAAGCTGTCG 60.154 63.158 0.00 0.00 0.00 4.35
1277 1305 3.636231 CTTCAGGGCGGTCCACCA 61.636 66.667 0.00 0.00 38.24 4.17
1290 1318 3.986006 ACCTTCCGCGCGACTTCA 61.986 61.111 34.63 8.82 0.00 3.02
1371 1399 0.600255 CTTCTCTGTTTCGGCCACGT 60.600 55.000 2.24 0.00 41.85 4.49
1416 1444 2.047179 GGTGTGAGACCGCCCTTC 60.047 66.667 0.00 0.00 34.02 3.46
1551 1579 1.171308 ACATGTCCAGCAGTGCATTC 58.829 50.000 19.20 5.33 0.00 2.67
1641 1669 2.756760 TCCCGACACAAGTATAGTCCAC 59.243 50.000 0.00 0.00 0.00 4.02
1680 1708 1.004979 AGTACTCTCGCCTTCTCCACT 59.995 52.381 0.00 0.00 0.00 4.00
1686 1714 2.093106 TGGAAGAGTACTCTCGCCTTC 58.907 52.381 29.96 22.01 44.65 3.46
1696 1724 1.070134 TGTGCACTGGTGGAAGAGTAC 59.930 52.381 19.41 0.00 31.21 2.73
1741 1769 3.049912 GTGCATACGCGTTGATCATAGA 58.950 45.455 20.78 0.00 42.97 1.98
1808 1836 1.816835 CTGGCACAACTTGATGCATCT 59.183 47.619 26.32 4.61 43.93 2.90
1891 1934 5.182001 GCTTCATCTTCTTACCTTGAGCAAA 59.818 40.000 0.00 0.00 0.00 3.68
1897 1940 4.836825 TCAGGCTTCATCTTCTTACCTTG 58.163 43.478 0.00 0.00 0.00 3.61
1916 1959 1.199327 CAGTGCCAAGAACTGCATCAG 59.801 52.381 0.00 0.00 38.72 2.90
1935 1978 2.097304 GGCATACATGTCAATCAACGCA 59.903 45.455 0.00 0.00 31.41 5.24
1944 1987 2.435422 CCACACTTGGCATACATGTCA 58.565 47.619 0.00 0.00 41.25 3.58
1978 2021 0.868406 CGTTCAAAGACCTCCACTGC 59.132 55.000 0.00 0.00 0.00 4.40
2213 2256 4.866508 TGTTCAACTCTTGGTCGTATCT 57.133 40.909 0.00 0.00 0.00 1.98
2298 2341 8.614346 GCGTCCTTGTTAATTGGTATATTGTTA 58.386 33.333 0.00 0.00 0.00 2.41
2301 2344 7.259290 AGCGTCCTTGTTAATTGGTATATTG 57.741 36.000 0.00 0.00 0.00 1.90
2302 2345 8.999431 CATAGCGTCCTTGTTAATTGGTATATT 58.001 33.333 0.00 0.00 0.00 1.28
2314 2357 0.324943 AGTGGCATAGCGTCCTTGTT 59.675 50.000 0.00 0.00 0.00 2.83
2363 2406 3.264947 CTCATCTCGACATTGCCTTGAA 58.735 45.455 0.00 0.00 0.00 2.69
2385 2428 2.045561 TTCGTTTGGTCAGCCTTTCA 57.954 45.000 0.00 0.00 35.27 2.69
2484 2527 2.941453 TGCTCCTTACTCTTACTGCG 57.059 50.000 0.00 0.00 0.00 5.18
2486 2529 5.355596 CCATCTTGCTCCTTACTCTTACTG 58.644 45.833 0.00 0.00 0.00 2.74
2564 2607 1.340889 GTGCCAACTGCCATTTTCAGA 59.659 47.619 0.00 0.00 40.16 3.27
2588 2631 5.907207 TCCTATGTTGAAGCACTAGATGTC 58.093 41.667 0.00 0.00 0.00 3.06
2614 2657 6.951971 ACTCAGACTAATGGATGTTTTAGCT 58.048 36.000 0.00 0.00 0.00 3.32
2657 2700 1.795768 TGCGATGAACTCAGACCAAC 58.204 50.000 0.00 0.00 0.00 3.77
2661 2704 6.536731 AATATCAATGCGATGAACTCAGAC 57.463 37.500 0.00 0.00 35.39 3.51
2704 2747 3.113260 ACTGAGTCACCACAGCTAAAC 57.887 47.619 0.00 0.00 37.61 2.01
2713 2756 3.804786 TGTTAACGAACTGAGTCACCA 57.195 42.857 0.26 0.00 36.45 4.17
2722 2765 7.485810 AGCACCTTTTTAATTGTTAACGAACT 58.514 30.769 0.00 0.00 36.45 3.01
2768 2811 1.483004 GTCCAGAGGTCTTTAGGAGGC 59.517 57.143 0.00 0.00 0.00 4.70
2776 2819 6.099845 TCTGAAAGTTTTAGTCCAGAGGTCTT 59.900 38.462 7.22 0.00 33.76 3.01
2817 2860 4.457834 AAGTAGTGATCGTTTCCAGAGG 57.542 45.455 0.00 0.00 0.00 3.69
2818 2861 6.197364 AGTAAGTAGTGATCGTTTCCAGAG 57.803 41.667 0.00 0.00 0.00 3.35
2820 2863 6.866770 TGAAAGTAAGTAGTGATCGTTTCCAG 59.133 38.462 0.00 0.00 0.00 3.86
2822 2865 6.310711 CCTGAAAGTAAGTAGTGATCGTTTCC 59.689 42.308 0.00 0.00 0.00 3.13
2840 3004 3.199880 ACCTGTGTCAGTTCCTGAAAG 57.800 47.619 0.00 0.00 42.46 2.62
2954 3119 9.906660 AATAATTTGACAAGTATCGCTGAAAAA 57.093 25.926 0.00 0.00 0.00 1.94
2979 3144 9.239002 CGTTTCATTGTTGGAGTTAATAAACAA 57.761 29.630 2.66 2.66 44.15 2.83
3082 3248 9.547753 CACATATTAGCCCATAGGTATATTCAC 57.452 37.037 0.00 0.00 34.57 3.18
3107 3273 3.261580 CATTATCACTCGTGTCAAGGCA 58.738 45.455 0.00 0.00 0.00 4.75
3108 3274 3.262420 ACATTATCACTCGTGTCAAGGC 58.738 45.455 0.00 0.00 0.00 4.35
3145 3311 7.041848 TGTCTCATCATAAGATTACAAATGGCG 60.042 37.037 0.00 0.00 30.20 5.69
3146 3312 8.158169 TGTCTCATCATAAGATTACAAATGGC 57.842 34.615 0.00 0.00 30.20 4.40
3171 3337 6.334989 TCGATTAAACGACCAATGTCATACT 58.665 36.000 3.45 0.00 41.85 2.12
3203 3369 5.523188 GTCAGTTCAGGCTGAAATCTATCAG 59.477 44.000 30.06 16.25 45.75 2.90
3208 3392 2.373169 TGGTCAGTTCAGGCTGAAATCT 59.627 45.455 30.06 20.91 45.75 2.40
3230 3414 4.156556 TGAACAACCTGCTGAAGATAATGC 59.843 41.667 0.00 0.00 0.00 3.56
3243 3458 3.407424 TGTGATCTCCTGAACAACCTG 57.593 47.619 0.00 0.00 0.00 4.00
3271 3486 2.806945 TTAAGATGTTGGGAGGCAGG 57.193 50.000 0.00 0.00 0.00 4.85
3289 3504 7.064728 GCGGATGAACTTACAAGAGATAGTTTT 59.935 37.037 0.00 0.00 31.41 2.43
3293 3508 4.677378 CGCGGATGAACTTACAAGAGATAG 59.323 45.833 0.00 0.00 0.00 2.08
3316 3531 5.725362 ACCTGAACTAGCATTCTGTAACTC 58.275 41.667 0.00 0.00 0.00 3.01
3328 3543 2.481952 CTGCTGAACAACCTGAACTAGC 59.518 50.000 0.00 0.00 0.00 3.42
3329 3544 3.070018 CCTGCTGAACAACCTGAACTAG 58.930 50.000 0.00 0.00 0.00 2.57
3330 3545 2.438021 ACCTGCTGAACAACCTGAACTA 59.562 45.455 0.00 0.00 0.00 2.24
3332 3547 1.680338 ACCTGCTGAACAACCTGAAC 58.320 50.000 0.00 0.00 0.00 3.18
3337 3552 6.569179 TTCTTAATAACCTGCTGAACAACC 57.431 37.500 0.00 0.00 0.00 3.77
3340 3555 9.461312 ACATAATTCTTAATAACCTGCTGAACA 57.539 29.630 0.00 0.00 0.00 3.18
3354 3569 9.048446 GCCTCGTATGGTAAACATAATTCTTAA 57.952 33.333 0.00 0.00 43.36 1.85
3355 3570 8.205512 TGCCTCGTATGGTAAACATAATTCTTA 58.794 33.333 0.00 0.00 43.36 2.10
3356 3571 7.051623 TGCCTCGTATGGTAAACATAATTCTT 58.948 34.615 0.00 0.00 43.36 2.52
3357 3572 6.588204 TGCCTCGTATGGTAAACATAATTCT 58.412 36.000 0.00 0.00 43.36 2.40
3358 3573 6.854496 TGCCTCGTATGGTAAACATAATTC 57.146 37.500 0.00 0.00 43.36 2.17
3360 3575 7.633193 TTTTGCCTCGTATGGTAAACATAAT 57.367 32.000 7.34 0.00 43.36 1.28
3362 3577 7.337184 TGAATTTTGCCTCGTATGGTAAACATA 59.663 33.333 7.34 0.00 40.44 2.29
3364 3579 5.473846 TGAATTTTGCCTCGTATGGTAAACA 59.526 36.000 7.34 2.42 40.44 2.83
3406 3635 9.276590 CAAATACAACCAGAAGCTGATATATCA 57.723 33.333 14.64 14.64 32.44 2.15
3407 3636 8.233190 GCAAATACAACCAGAAGCTGATATATC 58.767 37.037 5.73 5.73 32.44 1.63
3413 3642 3.485394 TGCAAATACAACCAGAAGCTGA 58.515 40.909 0.00 0.00 32.44 4.26
3417 3646 5.990996 ACCAAAATGCAAATACAACCAGAAG 59.009 36.000 0.00 0.00 0.00 2.85
3424 3654 6.094603 ACAAAGCAACCAAAATGCAAATACAA 59.905 30.769 0.00 0.00 46.22 2.41
3439 3669 9.384682 CAAAATTATGAAATGAACAAAGCAACC 57.615 29.630 0.00 0.00 0.00 3.77
3460 3691 9.802039 TTTCTTCCACATAAGTACTACCAAAAT 57.198 29.630 0.00 0.00 0.00 1.82
3468 3699 9.965902 ATTCTGATTTTCTTCCACATAAGTACT 57.034 29.630 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.