Multiple sequence alignment - TraesCS7B01G444700

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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 TraesCS7B01G444700 chr7B 100.000 3265 0 0 787 4051 709001207 709004471 0.000000e+00 6030.0
1 TraesCS7B01G444700 chr7B 100.000 438 0 0 1 438 709000421 709000858 0.000000e+00 809.0
2 TraesCS7B01G444700 chr7B 88.889 117 10 1 324 437 715948579 715948695 1.520000e-29 141.0
3 TraesCS7B01G444700 chr7B 88.889 117 10 1 324 437 715986939 715987055 1.520000e-29 141.0
4 TraesCS7B01G444700 chr7D 96.041 2753 105 4 787 3538 615932865 615935614 0.000000e+00 4477.0
5 TraesCS7B01G444700 chr7D 93.474 521 27 4 3535 4051 615935895 615936412 0.000000e+00 767.0
6 TraesCS7B01G444700 chr7D 93.563 435 27 1 3 437 615932049 615932482 0.000000e+00 647.0
7 TraesCS7B01G444700 chrUn 88.889 117 10 1 324 437 176268845 176268729 1.520000e-29 141.0
8 TraesCS7B01G444700 chrUn 88.889 117 10 1 324 437 176301519 176301403 1.520000e-29 141.0
9 TraesCS7B01G444700 chrUn 88.889 117 10 1 324 437 176325711 176325595 1.520000e-29 141.0
10 TraesCS7B01G444700 chrUn 88.889 117 10 1 324 437 256305864 256305748 1.520000e-29 141.0
11 TraesCS7B01G444700 chrUn 88.889 117 10 1 324 437 415532104 415532220 1.520000e-29 141.0
12 TraesCS7B01G444700 chr5A 81.818 88 12 4 241 326 569300061 569299976 2.020000e-08 71.3
13 TraesCS7B01G444700 chr5A 87.097 62 6 2 265 326 27508306 27508365 7.270000e-08 69.4
14 TraesCS7B01G444700 chr5A 80.723 83 13 3 247 328 476762196 476762116 1.220000e-05 62.1
15 TraesCS7B01G444700 chr2B 90.741 54 3 2 273 326 281881316 281881265 2.020000e-08 71.3
16 TraesCS7B01G444700 chr7A 88.889 54 6 0 273 326 379034613 379034666 2.610000e-07 67.6
17 TraesCS7B01G444700 chr6D 88.889 54 6 0 273 326 453503465 453503412 2.610000e-07 67.6
18 TraesCS7B01G444700 chr4B 87.719 57 5 2 270 326 142915550 142915604 9.400000e-07 65.8
19 TraesCS7B01G444700 chr2D 84.615 65 8 2 265 329 625022472 625022410 3.380000e-06 63.9


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 TraesCS7B01G444700 chr7B 709000421 709004471 4050 False 3419.500000 6030 100.000000 1 4051 2 chr7B.!!$F3 4050
1 TraesCS7B01G444700 chr7D 615932049 615936412 4363 False 1963.666667 4477 94.359333 3 4051 3 chr7D.!!$F1 4048

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
274 275 0.321919 TTGTGAGGCCATGAGTCTGC 60.322 55.000 5.01 0.0 0.00 4.26 F
1252 1287 0.108233 GCTCTCTCTCCTTGTGGCTG 60.108 60.000 0.00 0.0 0.00 4.85 F
1267 1302 0.379669 GGCTGCATCACCAATCTTCG 59.620 55.000 0.50 0.0 0.00 3.79 F
1618 1653 1.406069 CGGTGTCTTCTCAAGATGGGG 60.406 57.143 0.00 0.0 40.18 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 1877 1.815003 GTTGGGAGAGGCTCATTGTTG 59.185 52.381 18.26 0.0 31.08 3.33 R
2749 2784 0.976641 TCGCTTCCAGATGGACTTGT 59.023 50.000 0.00 0.0 45.39 3.16 R
2987 3022 3.019564 CTCCAATGAAGCCAAACTAGGG 58.980 50.000 0.00 0.0 0.00 3.53 R
3397 3432 2.280186 GGATCATGTCGCGTCCCC 60.280 66.667 5.77 0.0 0.00 4.81 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
34 35 1.759445 GAGAGCTGAGGAGGCAATGTA 59.241 52.381 0.00 0.00 0.00 2.29
42 43 1.285962 AGGAGGCAATGTATTGGTGCT 59.714 47.619 6.72 0.00 38.36 4.40
87 88 3.000041 GTCGTGTATGCCTTGAATGTGA 59.000 45.455 0.00 0.00 0.00 3.58
91 92 4.083324 CGTGTATGCCTTGAATGTGAAAGT 60.083 41.667 0.00 0.00 0.00 2.66
97 98 5.291178 TGCCTTGAATGTGAAAGTCAATTG 58.709 37.500 0.00 0.00 41.70 2.32
98 99 5.163426 TGCCTTGAATGTGAAAGTCAATTGT 60.163 36.000 5.13 0.00 41.70 2.71
152 153 2.698855 AGGCTTGACAATGAGCGTAT 57.301 45.000 0.00 0.00 39.78 3.06
157 158 4.319046 GGCTTGACAATGAGCGTATACATG 60.319 45.833 3.32 0.00 39.78 3.21
192 193 3.129638 CAGTGAGCCTAGTAAGAGTGACC 59.870 52.174 0.00 0.00 0.00 4.02
211 212 2.290260 ACCTGAATGAAGGATCACGCAA 60.290 45.455 0.00 0.00 40.02 4.85
221 222 5.240623 TGAAGGATCACGCAACAAAAATAGT 59.759 36.000 0.00 0.00 0.00 2.12
225 226 6.653320 AGGATCACGCAACAAAAATAGTTAGA 59.347 34.615 0.00 0.00 0.00 2.10
250 251 3.013921 AGTTTTCTTTTGCTGACGTGGA 58.986 40.909 0.00 0.00 0.00 4.02
263 264 3.006940 TGACGTGGAATATTTGTGAGGC 58.993 45.455 0.00 0.00 0.00 4.70
266 267 2.951642 CGTGGAATATTTGTGAGGCCAT 59.048 45.455 5.01 0.00 0.00 4.40
274 275 0.321919 TTGTGAGGCCATGAGTCTGC 60.322 55.000 5.01 0.00 0.00 4.26
287 288 6.206243 GCCATGAGTCTGCATGTTAAGATAAT 59.794 38.462 0.00 0.00 43.16 1.28
302 303 9.220906 TGTTAAGATAATTAAAGCTAGAGGGGA 57.779 33.333 0.00 0.00 0.00 4.81
305 306 8.511748 AAGATAATTAAAGCTAGAGGGGATCA 57.488 34.615 0.00 0.00 0.00 2.92
351 352 5.181245 ACGGTTTCTAGTACTTGCTACGTTA 59.819 40.000 0.00 0.00 0.00 3.18
378 379 8.169268 GTCGATCACTTAAACTCCAAAACTATG 58.831 37.037 0.00 0.00 0.00 2.23
415 416 0.978667 GTCCAGACCCTTCTCTCCCC 60.979 65.000 0.00 0.00 0.00 4.81
427 428 3.675348 TCTCTCCCCTATTTGTCGGTA 57.325 47.619 0.00 0.00 0.00 4.02
437 438 5.529800 CCCTATTTGTCGGTAACCTTTATGG 59.470 44.000 0.00 0.00 42.93 2.74
833 867 6.126623 GGGAATTTAATTGGAAAAGGCCCATA 60.127 38.462 0.00 0.00 35.11 2.74
835 869 7.365563 GGAATTTAATTGGAAAAGGCCCATACT 60.366 37.037 0.00 0.00 33.04 2.12
864 898 7.938140 TTCCAAGGGTGTTATATCTTGAAAG 57.062 36.000 0.00 0.00 38.96 2.62
923 957 8.727910 CAGACTAAAATTAGGAAAGTAACCACC 58.272 37.037 5.27 0.00 35.08 4.61
975 1010 7.238710 AGGTTGGAGTAAAAACTTGATGGTAT 58.761 34.615 0.00 0.00 0.00 2.73
991 1026 9.961265 CTTGATGGTATTATAACTCGTTCTGTA 57.039 33.333 0.00 0.00 0.00 2.74
1141 1176 2.939103 GAGGCATACACATTGGAGACAC 59.061 50.000 0.00 0.00 42.67 3.67
1152 1187 2.418368 TGGAGACACTGCAAACTGTT 57.582 45.000 0.00 0.00 33.40 3.16
1177 1212 1.876156 GATTCATTCGGTGCCATCCTC 59.124 52.381 0.00 0.00 0.00 3.71
1251 1286 1.264045 GGCTCTCTCTCCTTGTGGCT 61.264 60.000 0.00 0.00 0.00 4.75
1252 1287 0.108233 GCTCTCTCTCCTTGTGGCTG 60.108 60.000 0.00 0.00 0.00 4.85
1267 1302 0.379669 GGCTGCATCACCAATCTTCG 59.620 55.000 0.50 0.00 0.00 3.79
1294 1329 2.719705 ACTGGTTTATTCCTTGGGGTCA 59.280 45.455 0.00 0.00 0.00 4.02
1363 1398 5.495640 ACAAAAAGATAGAGAAGGCTCCTG 58.504 41.667 0.00 0.00 42.30 3.86
1409 1444 6.319658 ACTGCTAAACCAATTGAGGATGTATG 59.680 38.462 7.12 0.00 0.00 2.39
1457 1492 7.307751 CGAAGAAAGAATAGCTAACCACAACAA 60.308 37.037 0.00 0.00 0.00 2.83
1507 1542 2.903357 GCCGAGGCTCTTCATCCA 59.097 61.111 13.50 0.00 38.26 3.41
1554 1589 3.866449 GCTCAGAAATCGATACCCATCCC 60.866 52.174 0.00 0.00 0.00 3.85
1592 1627 4.770874 GCTTAGGTCGGCCGCCAA 62.771 66.667 31.19 22.91 40.50 4.52
1618 1653 1.406069 CGGTGTCTTCTCAAGATGGGG 60.406 57.143 0.00 0.00 40.18 4.96
1637 1672 2.762327 GGGATTCCATTGACAGCAACAT 59.238 45.455 4.80 0.00 36.72 2.71
1663 1698 3.378427 GGATGAAACCGGAAATCAAGAGG 59.622 47.826 9.46 0.00 0.00 3.69
1683 1718 5.482878 AGAGGGCAATGATGAAAATGAACTT 59.517 36.000 0.00 0.00 0.00 2.66
1694 1729 6.639632 TGAAAATGAACTTGAGGAGAAAGG 57.360 37.500 0.00 0.00 0.00 3.11
1700 1735 3.133141 ACTTGAGGAGAAAGGAAGTGC 57.867 47.619 0.00 0.00 0.00 4.40
1842 1877 3.133141 AGGAACTTGAGAGAGTTTGGC 57.867 47.619 0.00 0.00 39.84 4.52
1888 1923 7.637631 AAGGAGGAGCTCTCAAAATTTAATC 57.362 36.000 14.64 0.00 44.19 1.75
1919 1954 5.826643 TCCAACTATTTTTGCACCTAGGAT 58.173 37.500 17.98 0.00 0.00 3.24
1968 2003 2.769095 AGATAACTTCCCAGAGTCTGCC 59.231 50.000 15.10 0.00 0.00 4.85
1982 2017 2.283101 TGCCCCATCTGCACCAAC 60.283 61.111 0.00 0.00 32.85 3.77
1991 2026 4.142315 CCCATCTGCACCAACTAAAATGAG 60.142 45.833 0.00 0.00 0.00 2.90
2097 2132 5.747565 TGTGTTGCGTCTCAAATAAGAAAG 58.252 37.500 0.00 0.00 36.26 2.62
2140 2175 1.907936 AGAGCTTCACAGAAGGAGCAT 59.092 47.619 8.66 0.00 0.00 3.79
2145 2180 3.442977 GCTTCACAGAAGGAGCATCATTT 59.557 43.478 8.66 0.00 40.37 2.32
2148 2183 4.511527 TCACAGAAGGAGCATCATTTCTC 58.488 43.478 0.00 0.00 40.37 2.87
2164 2199 2.102070 TCTCGCTAATTTCCGGCAAA 57.898 45.000 0.00 0.00 0.00 3.68
2166 2201 3.013921 TCTCGCTAATTTCCGGCAAAAT 58.986 40.909 0.00 0.00 0.00 1.82
2172 2207 5.646606 GCTAATTTCCGGCAAAATCTACAA 58.353 37.500 0.00 0.00 0.00 2.41
2229 2264 3.080641 TCCGACGAGGGGACTACA 58.919 61.111 0.00 0.00 44.43 2.74
2274 2309 2.760374 AGTGAAAAGAGCTCGGTTCAG 58.240 47.619 26.06 0.00 30.94 3.02
2295 2330 7.123355 TCAGGATTTGGACAATTTTTCAGTT 57.877 32.000 0.00 0.00 0.00 3.16
2326 2361 9.880157 ATCAAGAAATCCAAAATGTTCTATTGG 57.120 29.630 0.00 0.00 43.97 3.16
2336 2371 3.232213 TGTTCTATTGGCTCTCGACAC 57.768 47.619 0.00 0.00 0.00 3.67
2347 2382 3.359523 TCGACACCGAGACACCCG 61.360 66.667 0.00 0.00 40.30 5.28
2393 2428 5.208121 TGATGACATGTATCTACCAGGTGA 58.792 41.667 0.76 0.00 0.00 4.02
2460 2495 6.964807 AATTTATGTCATGCTGCTCCATTA 57.035 33.333 0.00 0.00 0.00 1.90
2466 2501 2.773661 TCATGCTGCTCCATTAGAAGGA 59.226 45.455 0.00 0.00 35.29 3.36
2504 2539 2.305927 ACCCACAAGAAATGGAGACGAT 59.694 45.455 0.00 0.00 39.87 3.73
2505 2540 2.679837 CCCACAAGAAATGGAGACGATG 59.320 50.000 0.00 0.00 39.87 3.84
2511 2546 4.148128 AGAAATGGAGACGATGAGCAAT 57.852 40.909 0.00 0.00 0.00 3.56
2513 2548 1.590932 ATGGAGACGATGAGCAATGC 58.409 50.000 0.00 0.00 0.00 3.56
2539 2574 5.369409 ACATCAGATGTCTCCACATTCAT 57.631 39.130 10.53 0.00 43.79 2.57
2540 2575 5.123936 ACATCAGATGTCTCCACATTCATG 58.876 41.667 10.53 0.00 43.79 3.07
2590 2625 3.315191 TGAAGCTACAGAACCTTTTGCAC 59.685 43.478 0.00 0.00 0.00 4.57
2597 2632 5.607119 ACAGAACCTTTTGCACGTAATAG 57.393 39.130 0.00 0.00 0.00 1.73
2621 2656 1.611977 TGAAGTACCAGGTGACGTCTG 59.388 52.381 17.92 6.71 0.00 3.51
2709 2744 6.830838 CCTTATTTCTAGGCAAGGAAGTTGAT 59.169 38.462 6.70 0.00 40.02 2.57
2798 2833 6.933521 CCTACATCTATGAGTTCTCCAATTGG 59.066 42.308 19.08 19.08 0.00 3.16
2801 2836 5.762179 TCTATGAGTTCTCCAATTGGTGT 57.238 39.130 23.76 6.13 36.34 4.16
2803 2838 6.640518 TCTATGAGTTCTCCAATTGGTGTAC 58.359 40.000 23.76 22.68 36.34 2.90
2809 2844 5.891551 AGTTCTCCAATTGGTGTACTTTTGT 59.108 36.000 24.77 9.86 36.39 2.83
2826 2861 9.685828 GTACTTTTGTTGCATGAAGGTAATTAA 57.314 29.630 0.00 0.00 0.00 1.40
2831 2866 5.417580 TGTTGCATGAAGGTAATTAAGGACC 59.582 40.000 0.00 1.08 35.83 4.46
2836 2871 6.039382 GCATGAAGGTAATTAAGGACCGAAAT 59.961 38.462 0.00 0.00 40.91 2.17
2845 2880 7.703058 AATTAAGGACCGAAATGACTTGATT 57.297 32.000 0.00 0.00 0.00 2.57
2851 2886 7.391620 AGGACCGAAATGACTTGATTTAACTA 58.608 34.615 0.00 0.00 0.00 2.24
2987 3022 4.107127 TCCTTCTAGTGAGATAGCCTCC 57.893 50.000 0.00 0.00 41.25 4.30
3098 3133 4.275689 CGCATATTCTTTCAGCCATACCAA 59.724 41.667 0.00 0.00 0.00 3.67
3099 3134 5.048504 CGCATATTCTTTCAGCCATACCAAT 60.049 40.000 0.00 0.00 0.00 3.16
3162 3197 8.752005 ATCAGCACATAACATAGTGGTAAATT 57.248 30.769 0.00 0.00 43.83 1.82
3252 3287 4.236527 AGTAATGTTGACCCTTGGGATC 57.763 45.455 13.39 6.97 0.00 3.36
3273 3308 7.037438 GGATCTTTGAAAGCTGCAAATATCAA 58.963 34.615 25.25 11.91 39.04 2.57
3283 3318 6.923012 AGCTGCAAATATCAAACACACATAA 58.077 32.000 1.02 0.00 0.00 1.90
3294 3329 7.643569 TCAAACACACATAATGGCATAGATT 57.356 32.000 0.00 0.00 0.00 2.40
3319 3354 1.236616 TGAACCGTGCAATGCTCCAG 61.237 55.000 6.82 0.00 0.00 3.86
3414 3449 2.280186 GGGGACGCGACATGATCC 60.280 66.667 15.93 8.08 0.00 3.36
3483 3518 2.640184 GAGAAGAAACAATACCCGGGG 58.360 52.381 27.92 12.73 0.00 5.73
3595 3914 8.737168 AGTTGTCATGCATATACATGTAAAGT 57.263 30.769 10.14 10.31 46.15 2.66
3670 3989 2.101783 TGCCTACTTTGCATTGATGGG 58.898 47.619 0.00 0.00 32.85 4.00
3671 3990 2.291475 TGCCTACTTTGCATTGATGGGA 60.291 45.455 0.00 0.00 32.85 4.37
3688 4007 0.327259 GGAGTAAGGGGTTGGTGTCC 59.673 60.000 0.00 0.00 0.00 4.02
3705 4027 5.221945 TGGTGTCCAAATGTAGTAATGGTCA 60.222 40.000 0.00 0.00 34.50 4.02
3733 4055 8.844441 TGAAAAATAACTTTGTTACCACTTCG 57.156 30.769 0.00 0.00 0.00 3.79
3765 4087 2.993937 AGGACGGAAAGTGTCAAACAA 58.006 42.857 0.00 0.00 38.10 2.83
3925 4247 9.613428 TTACATAAAAGTGGATGGTAGAATCTG 57.387 33.333 0.00 0.00 0.00 2.90
3946 4268 1.053424 TGCTCCCTTTGGTAGACGTT 58.947 50.000 0.00 0.00 0.00 3.99
3995 4317 2.053627 CACTTGAAATTGCCTTCGTGC 58.946 47.619 0.00 0.00 0.00 5.34
4006 4328 3.263261 TGCCTTCGTGCGATTACATTTA 58.737 40.909 0.00 0.00 0.00 1.40
4011 4333 5.521010 CCTTCGTGCGATTACATTTACCTAA 59.479 40.000 0.00 0.00 0.00 2.69
4014 4336 5.291614 TCGTGCGATTACATTTACCTAAACC 59.708 40.000 0.00 0.00 0.00 3.27
4033 4355 2.186076 CCTCTCACTAATTGTCGACGC 58.814 52.381 11.62 0.00 0.00 5.19
4034 4356 1.840741 CTCTCACTAATTGTCGACGCG 59.159 52.381 11.62 3.53 0.00 6.01
4036 4358 1.840741 CTCACTAATTGTCGACGCGAG 59.159 52.381 15.93 6.55 36.23 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.067413 CCTCAGCTCTCACATGCAAATTAAT 59.933 40.000 0.00 0.00 0.00 1.40
1 2 4.397103 CCTCAGCTCTCACATGCAAATTAA 59.603 41.667 0.00 0.00 0.00 1.40
34 35 2.173519 CTCCCATTGTGAAGCACCAAT 58.826 47.619 0.00 0.00 32.73 3.16
42 43 3.573538 CACCATTTGTCTCCCATTGTGAA 59.426 43.478 0.00 0.00 0.00 3.18
91 92 6.772233 TCTTCTCTCCATTTTGTCACAATTGA 59.228 34.615 13.59 0.00 0.00 2.57
97 98 7.856145 ATACATCTTCTCTCCATTTTGTCAC 57.144 36.000 0.00 0.00 0.00 3.67
98 99 7.337689 CCAATACATCTTCTCTCCATTTTGTCA 59.662 37.037 0.00 0.00 0.00 3.58
138 139 5.004922 TCACATGTATACGCTCATTGTCA 57.995 39.130 0.00 0.00 0.00 3.58
176 177 4.402793 TCATTCAGGTCACTCTTACTAGGC 59.597 45.833 0.00 0.00 0.00 3.93
192 193 2.743664 TGTTGCGTGATCCTTCATTCAG 59.256 45.455 0.00 0.00 33.56 3.02
221 222 6.201044 CGTCAGCAAAAGAAAACTCTCTCTAA 59.799 38.462 0.00 0.00 0.00 2.10
225 226 4.034510 CACGTCAGCAAAAGAAAACTCTCT 59.965 41.667 0.00 0.00 0.00 3.10
235 236 5.343058 CACAAATATTCCACGTCAGCAAAAG 59.657 40.000 0.00 0.00 0.00 2.27
250 251 4.885907 CAGACTCATGGCCTCACAAATATT 59.114 41.667 3.32 0.00 0.00 1.28
263 264 7.741027 ATTATCTTAACATGCAGACTCATGG 57.259 36.000 15.07 0.00 46.02 3.66
287 288 7.691993 AATAGTTGATCCCCTCTAGCTTTAA 57.308 36.000 0.00 0.00 0.00 1.52
290 291 6.271159 CCTAAATAGTTGATCCCCTCTAGCTT 59.729 42.308 0.00 0.00 0.00 3.74
351 352 6.289064 AGTTTTGGAGTTTAAGTGATCGACT 58.711 36.000 0.00 0.00 35.94 4.18
404 405 2.103263 CCGACAAATAGGGGAGAGAAGG 59.897 54.545 0.00 0.00 0.00 3.46
806 840 5.339944 GGGCCTTTTCCAATTAAATTCCCAT 60.340 40.000 0.84 0.00 31.53 4.00
813 847 6.943899 AAGTATGGGCCTTTTCCAATTAAA 57.056 33.333 4.53 0.00 37.87 1.52
923 957 5.873179 TTTTCACTAGGCTTTACATTCCG 57.127 39.130 0.00 0.00 0.00 4.30
1010 1045 8.695456 ACAACCTTCTTATCTCAACAAAACAAT 58.305 29.630 0.00 0.00 0.00 2.71
1251 1286 4.332543 GTGAATACGAAGATTGGTGATGCA 59.667 41.667 0.00 0.00 0.00 3.96
1252 1287 4.572389 AGTGAATACGAAGATTGGTGATGC 59.428 41.667 0.00 0.00 0.00 3.91
1267 1302 5.359860 CCCCAAGGAATAAACCAGTGAATAC 59.640 44.000 0.00 0.00 33.47 1.89
1363 1398 6.363357 GCAGTGTTGTGAATATTCCAAGTTTC 59.637 38.462 12.90 5.80 0.00 2.78
1431 1466 6.147164 TGTTGTGGTTAGCTATTCTTTCTTCG 59.853 38.462 0.00 0.00 0.00 3.79
1457 1492 7.902087 TCCCTTCCGAAATTTATTTTCATTGT 58.098 30.769 0.00 0.00 43.32 2.71
1573 1608 4.893601 GGCGGCCGACCTAAGCTC 62.894 72.222 33.48 7.28 0.00 4.09
1592 1627 4.808414 TCTTGAGAAGACACCGATGAAT 57.192 40.909 0.00 0.00 31.20 2.57
1618 1653 5.063180 TCAATGTTGCTGTCAATGGAATC 57.937 39.130 0.00 0.00 34.29 2.52
1637 1672 4.027674 TGATTTCCGGTTTCATCCTCAA 57.972 40.909 0.00 0.00 0.00 3.02
1663 1698 5.579511 CCTCAAGTTCATTTTCATCATTGCC 59.420 40.000 0.00 0.00 0.00 4.52
1683 1718 4.348168 ACTTTAGCACTTCCTTTCTCCTCA 59.652 41.667 0.00 0.00 0.00 3.86
1694 1729 3.568538 CATGCCACAACTTTAGCACTTC 58.431 45.455 0.00 0.00 38.21 3.01
1700 1735 3.837213 CAGTCCATGCCACAACTTTAG 57.163 47.619 0.00 0.00 0.00 1.85
1725 1760 5.791367 TTTTCAAGATGCTCTTCTGATCG 57.209 39.130 0.00 0.00 33.78 3.69
1842 1877 1.815003 GTTGGGAGAGGCTCATTGTTG 59.185 52.381 18.26 0.00 31.08 3.33
1888 1923 7.442062 AGGTGCAAAAATAGTTGGAATTTGAAG 59.558 33.333 0.00 0.00 33.86 3.02
1919 1954 6.801718 TGTAGGGAAGATCGAAAGGATTTA 57.198 37.500 0.00 0.00 39.27 1.40
1968 2003 3.763360 TCATTTTAGTTGGTGCAGATGGG 59.237 43.478 0.00 0.00 0.00 4.00
2115 2150 2.235650 TCCTTCTGTGAAGCTCTCATGG 59.764 50.000 0.00 0.00 36.14 3.66
2140 2175 2.612212 GCCGGAAATTAGCGAGAAATGA 59.388 45.455 5.05 0.00 0.00 2.57
2145 2180 2.102070 TTTGCCGGAAATTAGCGAGA 57.898 45.000 5.05 0.00 0.00 4.04
2148 2183 3.420839 AGATTTTGCCGGAAATTAGCG 57.579 42.857 5.05 0.00 29.75 4.26
2274 2309 7.650104 TCGTTAACTGAAAAATTGTCCAAATCC 59.350 33.333 3.71 0.00 0.00 3.01
2295 2330 8.792633 AGAACATTTTGGATTTCTTGATCGTTA 58.207 29.630 0.00 0.00 0.00 3.18
2336 2371 3.629398 ACTAATTAGTACGGGTGTCTCGG 59.371 47.826 16.60 0.00 34.13 4.63
2393 2428 6.840705 AGCTTCCACCCAATCATTTATATGTT 59.159 34.615 0.00 0.00 33.34 2.71
2444 2479 2.877168 CCTTCTAATGGAGCAGCATGAC 59.123 50.000 0.00 0.00 39.69 3.06
2452 2487 5.346181 ACACTAAGTCCTTCTAATGGAGC 57.654 43.478 0.00 0.00 33.78 4.70
2460 2495 5.746990 ATTGCACTACACTAAGTCCTTCT 57.253 39.130 0.00 0.00 0.00 2.85
2466 2501 4.285003 TGTGGGTATTGCACTACACTAAGT 59.715 41.667 16.44 0.00 36.55 2.24
2504 2539 4.945543 ACATCTGATGTAAAGCATTGCTCA 59.054 37.500 21.10 6.30 42.78 4.26
2505 2540 5.296283 AGACATCTGATGTAAAGCATTGCTC 59.704 40.000 22.31 6.46 45.03 4.26
2511 2546 4.020307 TGTGGAGACATCTGATGTAAAGCA 60.020 41.667 22.31 14.48 45.03 3.91
2513 2548 6.820152 TGAATGTGGAGACATCTGATGTAAAG 59.180 38.462 22.31 0.00 45.03 1.85
2539 2574 3.421919 TGGCATCAAGTCAAGATCACA 57.578 42.857 0.00 0.00 0.00 3.58
2540 2575 3.943381 TGATGGCATCAAGTCAAGATCAC 59.057 43.478 27.03 0.00 34.09 3.06
2590 2625 5.234329 CACCTGGTACTTCATTGCTATTACG 59.766 44.000 0.00 0.00 0.00 3.18
2597 2632 1.732259 CGTCACCTGGTACTTCATTGC 59.268 52.381 0.00 0.00 0.00 3.56
2621 2656 4.557205 CCTACACCGCTAAGTGATATTCC 58.443 47.826 5.52 0.00 40.34 3.01
2709 2744 2.335681 TCTGGGTGTCATCAAGGGTA 57.664 50.000 0.00 0.00 0.00 3.69
2739 2774 4.382040 CCAGATGGACTTGTATCGTCAACT 60.382 45.833 0.00 0.00 37.39 3.16
2743 2778 4.363999 CTTCCAGATGGACTTGTATCGTC 58.636 47.826 0.00 0.00 45.39 4.20
2749 2784 0.976641 TCGCTTCCAGATGGACTTGT 59.023 50.000 0.00 0.00 45.39 3.16
2780 2815 6.644347 AGTACACCAATTGGAGAACTCATAG 58.356 40.000 31.22 9.01 38.94 2.23
2798 2833 4.932146 ACCTTCATGCAACAAAAGTACAC 58.068 39.130 0.00 0.00 0.00 2.90
2801 2836 9.906660 CTTAATTACCTTCATGCAACAAAAGTA 57.093 29.630 0.00 0.00 0.00 2.24
2803 2838 8.087750 TCCTTAATTACCTTCATGCAACAAAAG 58.912 33.333 0.00 0.00 0.00 2.27
2809 2844 4.638421 CGGTCCTTAATTACCTTCATGCAA 59.362 41.667 0.00 0.00 33.34 4.08
2826 2861 6.238648 AGTTAAATCAAGTCATTTCGGTCCT 58.761 36.000 0.00 0.00 0.00 3.85
2959 2994 5.221165 GCTATCTCACTAGAAGGAACCTCAC 60.221 48.000 0.00 0.00 34.73 3.51
2987 3022 3.019564 CTCCAATGAAGCCAAACTAGGG 58.980 50.000 0.00 0.00 0.00 3.53
3224 3259 6.070424 CCCAAGGGTCAACATTACTACTAAGA 60.070 42.308 0.00 0.00 0.00 2.10
3252 3287 7.042590 TGTGTTTGATATTTGCAGCTTTCAAAG 60.043 33.333 14.09 0.00 36.93 2.77
3283 3318 7.202526 CACGGTTCAAAATTAATCTATGCCAT 58.797 34.615 0.00 0.00 0.00 4.40
3294 3329 4.233789 GAGCATTGCACGGTTCAAAATTA 58.766 39.130 11.91 0.00 0.00 1.40
3303 3338 2.360350 CCTGGAGCATTGCACGGT 60.360 61.111 11.91 0.00 0.00 4.83
3305 3340 3.494378 CTCCTGGAGCATTGCACG 58.506 61.111 11.42 0.78 0.00 5.34
3319 3354 3.119029 TGAAAAATTGGCATGCTAGCTCC 60.119 43.478 18.92 14.34 34.17 4.70
3397 3432 2.280186 GGATCATGTCGCGTCCCC 60.280 66.667 5.77 0.00 0.00 4.81
3443 3478 2.577112 CTGGACGTCGCTAGCGTG 60.577 66.667 34.10 28.27 43.04 5.34
3555 3874 8.629158 TGCATGACAACTTTTAAACTAATGACT 58.371 29.630 0.00 0.00 0.00 3.41
3571 3890 9.225201 CAACTTTACATGTATATGCATGACAAC 57.775 33.333 32.39 7.68 46.65 3.32
3595 3914 3.755112 TCTCATTGTGTAACCCGACAA 57.245 42.857 0.00 0.00 36.54 3.18
3670 3989 1.061546 TGGACACCAACCCCTTACTC 58.938 55.000 0.00 0.00 0.00 2.59
3671 3990 1.525175 TTGGACACCAACCCCTTACT 58.475 50.000 0.00 0.00 38.75 2.24
3777 4099 5.006153 TGGATATACGAGACTTTGTGGTG 57.994 43.478 0.00 0.00 0.00 4.17
3903 4225 7.067494 GCAACAGATTCTACCATCCACTTTTAT 59.933 37.037 0.00 0.00 0.00 1.40
3912 4234 3.135530 AGGGAGCAACAGATTCTACCATC 59.864 47.826 0.00 0.00 33.17 3.51
3925 4247 1.270678 ACGTCTACCAAAGGGAGCAAC 60.271 52.381 0.00 0.00 38.05 4.17
3946 4268 2.224090 TGTTGTAGTTCTAGCGGCAACA 60.224 45.455 1.45 0.00 42.23 3.33
3995 4317 7.980099 AGTGAGAGGTTTAGGTAAATGTAATCG 59.020 37.037 0.00 0.00 0.00 3.34
4006 4328 5.479375 TCGACAATTAGTGAGAGGTTTAGGT 59.521 40.000 0.00 0.00 0.00 3.08
4011 4333 3.834610 CGTCGACAATTAGTGAGAGGTT 58.165 45.455 17.16 0.00 0.00 3.50
4014 4336 1.840741 CGCGTCGACAATTAGTGAGAG 59.159 52.381 17.16 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.