Multiple sequence alignment - TraesCS7B01G170500

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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 TraesCS7B01G170500 chr7B 100.000 4484 0 0 1 4484 242679604 242675121 0.000000e+00 8281.0
1 TraesCS7B01G170500 chr7A 93.782 3281 114 36 723 3952 284758912 284762153 0.000000e+00 4846.0
2 TraesCS7B01G170500 chr7A 93.750 288 9 2 3974 4252 284776884 284777171 1.490000e-114 424.0
3 TraesCS7B01G170500 chr7A 84.434 424 39 12 3 401 284757984 284758405 4.200000e-105 392.0
4 TraesCS7B01G170500 chr7A 91.667 276 15 7 412 680 284758641 284758915 4.230000e-100 375.0
5 TraesCS7B01G170500 chr7A 89.113 248 26 1 4237 4484 284778355 284778601 1.570000e-79 307.0
6 TraesCS7B01G170500 chr7D 94.805 2310 68 13 1903 4190 261866097 261868376 0.000000e+00 3554.0
7 TraesCS7B01G170500 chr7D 94.192 1429 46 12 435 1840 261864683 261866097 0.000000e+00 2145.0
8 TraesCS7B01G170500 chr7D 91.749 303 23 1 4182 4484 261868542 261868842 1.930000e-113 420.0
9 TraesCS7B01G170500 chr1A 80.741 135 23 3 164 297 576137327 576137195 7.940000e-18 102.0
10 TraesCS7B01G170500 chr5D 85.393 89 13 0 1116 1204 422697179 422697267 4.780000e-15 93.5
11 TraesCS7B01G170500 chr1B 78.523 149 26 6 161 305 667932991 667933137 4.780000e-15 93.5
12 TraesCS7B01G170500 chr5A 89.041 73 8 0 1116 1188 536119416 536119488 1.720000e-14 91.6


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 TraesCS7B01G170500 chr7B 242675121 242679604 4483 True 8281.000000 8281 100.0000 1 4484 1 chr7B.!!$R1 4483
1 TraesCS7B01G170500 chr7A 284757984 284762153 4169 False 1871.000000 4846 89.9610 3 3952 3 chr7A.!!$F1 3949
2 TraesCS7B01G170500 chr7A 284776884 284778601 1717 False 365.500000 424 91.4315 3974 4484 2 chr7A.!!$F2 510
3 TraesCS7B01G170500 chr7D 261864683 261868842 4159 False 2039.666667 3554 93.5820 435 4484 3 chr7D.!!$F1 4049

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
318 320 0.108207 GGGAGACGACTATCGGAGGA 59.892 60.0 2.97 0.0 45.59 3.71 F
402 428 0.108709 TGGTGCGTACGGTTGGATAC 60.109 55.0 18.39 0.0 0.00 2.24 F
403 429 0.174162 GGTGCGTACGGTTGGATACT 59.826 55.0 18.39 0.0 37.61 2.12 F
1234 1515 0.884704 ACGCTGATGCTTCGTGGTTT 60.885 50.0 8.83 0.0 34.92 3.27 F
1417 1698 0.955752 AGGAGGAGGGGAATGAGGAT 59.044 55.0 0.00 0.0 0.00 3.24 F
1611 1892 1.117142 TCACGTTTTCTCCCGGTCCT 61.117 55.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 2140 0.031585 GGTTGAAAAACTGGGCCGAC 59.968 55.000 0.0 0.0 0.00 4.79 R
1860 2142 2.425562 AGGTTGAAAAACTGGGCCG 58.574 52.632 0.0 0.0 46.40 6.13 R
2185 2473 3.054065 AGGATGCTTTCCCTTCCTTACTG 60.054 47.826 3.0 0.0 46.81 2.74 R
3011 3312 1.003718 GAAGAACAGGGGGTGGACG 60.004 63.158 0.0 0.0 0.00 4.79 R
3362 3681 8.926710 ACAGTTTTCTAGTATTCAGTTTCATCG 58.073 33.333 0.0 0.0 0.00 3.84 R
3526 3845 3.243002 GCTTAAATCTCACCAGCATCAGC 60.243 47.826 0.0 0.0 42.56 4.26 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
46 48 2.449464 TGATGTTGAGAGGGCATTTGG 58.551 47.619 0.00 0.00 0.00 3.28
65 67 0.255890 GAGTGCCTCCAAGCCCATTA 59.744 55.000 0.00 0.00 0.00 1.90
71 73 3.117169 TGCCTCCAAGCCCATTATGTAAT 60.117 43.478 0.00 0.00 0.00 1.89
103 105 6.183360 GGGACCTGCTAAACTATGAGATGTAA 60.183 42.308 0.00 0.00 0.00 2.41
106 108 7.620880 ACCTGCTAAACTATGAGATGTAAACA 58.379 34.615 0.00 0.00 0.00 2.83
107 109 7.549488 ACCTGCTAAACTATGAGATGTAAACAC 59.451 37.037 0.00 0.00 0.00 3.32
117 119 5.003160 TGAGATGTAAACACATTGTGGGAG 58.997 41.667 20.33 0.00 37.94 4.30
157 159 3.425758 GGTCGCCAAGGTCTAAAATTTCG 60.426 47.826 0.00 0.00 0.00 3.46
166 168 5.675538 AGGTCTAAAATTTCGAGAGATGGG 58.324 41.667 3.58 0.00 41.60 4.00
183 185 5.096521 AGATGGGTGATCATATCCAGCTTA 58.903 41.667 20.41 1.70 42.54 3.09
186 188 3.589988 GGTGATCATATCCAGCTTACGG 58.410 50.000 0.00 0.00 0.00 4.02
189 191 5.482908 GTGATCATATCCAGCTTACGGAAT 58.517 41.667 0.00 0.00 35.77 3.01
196 198 4.602340 TCCAGCTTACGGAATAGAATCC 57.398 45.455 0.00 0.00 36.05 3.01
198 200 4.058817 CCAGCTTACGGAATAGAATCCAC 58.941 47.826 0.00 0.00 39.61 4.02
199 201 3.736252 CAGCTTACGGAATAGAATCCACG 59.264 47.826 0.00 0.00 39.61 4.94
200 202 3.383825 AGCTTACGGAATAGAATCCACGT 59.616 43.478 0.00 0.00 39.61 4.49
217 219 3.120649 CCACGTCGTTTGAGGATTTTCTC 60.121 47.826 0.00 0.00 34.17 2.87
233 235 8.361592 GGATTTTCTCCAAATGCATCATTAAG 57.638 34.615 0.00 0.00 44.26 1.85
240 242 4.266029 CCAAATGCATCATTAAGTTCGCAC 59.734 41.667 0.00 0.00 32.43 5.34
246 248 2.876091 TCATTAAGTTCGCACTCGAGG 58.124 47.619 18.41 6.97 46.34 4.63
267 269 6.049955 AGGAACTCAATGATTAGTTTCGGA 57.950 37.500 0.00 0.00 36.50 4.55
273 275 8.147642 ACTCAATGATTAGTTTCGGAATGATC 57.852 34.615 0.00 0.00 0.00 2.92
274 276 7.227512 ACTCAATGATTAGTTTCGGAATGATCC 59.772 37.037 0.00 0.00 42.80 3.36
292 294 3.202829 TCCGGTTTAACATCTATGGGC 57.797 47.619 0.00 0.00 0.00 5.36
306 308 2.434359 GGGCGTTTCAGGGAGACG 60.434 66.667 5.10 5.10 41.90 4.18
307 309 2.654877 GGCGTTTCAGGGAGACGA 59.345 61.111 12.64 0.00 41.60 4.20
310 312 0.524862 GCGTTTCAGGGAGACGACTA 59.475 55.000 12.64 0.00 41.60 2.59
311 313 1.134560 GCGTTTCAGGGAGACGACTAT 59.865 52.381 12.64 0.00 41.60 2.12
312 314 2.795331 GCGTTTCAGGGAGACGACTATC 60.795 54.545 12.64 0.00 41.60 2.08
313 315 2.539142 CGTTTCAGGGAGACGACTATCG 60.539 54.545 3.53 0.00 41.60 2.92
314 316 1.676746 TTCAGGGAGACGACTATCGG 58.323 55.000 2.97 0.00 45.59 4.18
316 318 1.202663 TCAGGGAGACGACTATCGGAG 60.203 57.143 2.97 0.00 45.59 4.63
318 320 0.108207 GGGAGACGACTATCGGAGGA 59.892 60.000 2.97 0.00 45.59 3.71
328 354 7.119553 AGACGACTATCGGAGGAAGTATTTATC 59.880 40.741 2.97 0.00 45.59 1.75
332 358 9.413048 GACTATCGGAGGAAGTATTTATCTTTG 57.587 37.037 0.00 0.00 0.00 2.77
366 392 6.421202 CAGTACTCTCGGCATAGGAATAAAAC 59.579 42.308 0.00 0.00 0.00 2.43
370 396 6.985059 ACTCTCGGCATAGGAATAAAACTTAC 59.015 38.462 0.00 0.00 0.00 2.34
372 398 5.991861 TCGGCATAGGAATAAAACTTACCA 58.008 37.500 0.00 0.00 0.00 3.25
375 401 5.009710 GGCATAGGAATAAAACTTACCAGGC 59.990 44.000 0.00 0.00 0.00 4.85
389 415 0.875474 CCAGGCAAACTTTTGGTGCG 60.875 55.000 3.95 0.00 39.22 5.34
401 427 0.607112 TTGGTGCGTACGGTTGGATA 59.393 50.000 18.39 0.00 0.00 2.59
402 428 0.108709 TGGTGCGTACGGTTGGATAC 60.109 55.000 18.39 0.00 0.00 2.24
403 429 0.174162 GGTGCGTACGGTTGGATACT 59.826 55.000 18.39 0.00 37.61 2.12
407 658 1.836383 CGTACGGTTGGATACTCAGC 58.164 55.000 7.57 0.00 37.61 4.26
409 660 2.223735 CGTACGGTTGGATACTCAGCAT 60.224 50.000 7.57 0.00 37.61 3.79
410 661 2.315925 ACGGTTGGATACTCAGCATG 57.684 50.000 0.00 0.00 37.61 4.06
426 677 3.242944 CAGCATGTTAGTCGGTGATTACG 59.757 47.826 0.00 0.00 0.00 3.18
430 681 3.825308 TGTTAGTCGGTGATTACGTGTC 58.175 45.455 0.00 0.00 0.00 3.67
431 682 3.252944 TGTTAGTCGGTGATTACGTGTCA 59.747 43.478 0.00 0.00 0.00 3.58
433 684 2.156917 AGTCGGTGATTACGTGTCAGA 58.843 47.619 0.00 0.00 0.00 3.27
439 690 5.803461 TCGGTGATTACGTGTCAGAATTAAG 59.197 40.000 0.00 0.00 0.00 1.85
442 693 7.037438 GGTGATTACGTGTCAGAATTAAGGTA 58.963 38.462 0.00 0.00 0.00 3.08
443 694 7.709613 GGTGATTACGTGTCAGAATTAAGGTAT 59.290 37.037 0.00 0.00 0.00 2.73
445 696 9.093970 TGATTACGTGTCAGAATTAAGGTATTG 57.906 33.333 0.00 0.00 0.00 1.90
446 697 9.095065 GATTACGTGTCAGAATTAAGGTATTGT 57.905 33.333 0.00 0.00 0.00 2.71
447 698 6.721571 ACGTGTCAGAATTAAGGTATTGTG 57.278 37.500 0.00 0.00 31.89 3.33
448 699 6.228258 ACGTGTCAGAATTAAGGTATTGTGT 58.772 36.000 0.00 0.00 32.36 3.72
495 748 6.483405 ACCCGTGATTTACCAACCTAAATAA 58.517 36.000 0.00 0.00 0.00 1.40
698 957 6.053005 AGGAGTACTAGAGACAGAGATTTCG 58.947 44.000 0.00 0.00 0.00 3.46
699 958 6.050432 GGAGTACTAGAGACAGAGATTTCGA 58.950 44.000 0.00 0.00 0.00 3.71
708 967 1.923204 CAGAGATTTCGAAGCGTGAGG 59.077 52.381 0.00 0.00 0.00 3.86
767 1031 3.287867 ACCAGATACCTCCTGCATTTG 57.712 47.619 0.00 0.00 0.00 2.32
803 1069 8.451908 ACAGATACCTCATGTTTTAATAAGGC 57.548 34.615 0.00 0.00 0.00 4.35
804 1070 8.275040 ACAGATACCTCATGTTTTAATAAGGCT 58.725 33.333 0.00 0.00 0.00 4.58
805 1071 9.778741 CAGATACCTCATGTTTTAATAAGGCTA 57.221 33.333 0.00 0.00 0.00 3.93
877 1145 1.810755 TCCTCATATAGCTACCGCGTG 59.189 52.381 4.92 0.00 42.32 5.34
881 1149 1.863662 ATATAGCTACCGCGTGCGCT 61.864 55.000 9.73 15.70 42.32 5.92
938 1206 4.142622 TGCCACTATTGAATTTCTGCTTCG 60.143 41.667 0.00 0.00 0.00 3.79
966 1234 1.272769 CGTTCCCTTCTCCTTCTCGTT 59.727 52.381 0.00 0.00 0.00 3.85
1189 1469 1.267574 CCTCCAGGAGCAGGTAAGCA 61.268 60.000 11.57 0.00 37.39 3.91
1234 1515 0.884704 ACGCTGATGCTTCGTGGTTT 60.885 50.000 8.83 0.00 34.92 3.27
1236 1517 1.463056 CGCTGATGCTTCGTGGTTTAA 59.537 47.619 0.00 0.00 36.97 1.52
1238 1519 3.426159 CGCTGATGCTTCGTGGTTTAATT 60.426 43.478 0.00 0.00 36.97 1.40
1243 1524 7.624360 TGATGCTTCGTGGTTTAATTATCTT 57.376 32.000 0.00 0.00 0.00 2.40
1250 1531 5.416326 TCGTGGTTTAATTATCTTGGGTTGG 59.584 40.000 0.00 0.00 0.00 3.77
1345 1626 2.409651 GACGCTGGGAGCTACGAG 59.590 66.667 3.05 3.05 39.60 4.18
1409 1690 1.921294 GACTACGAGGAGGAGGGGA 59.079 63.158 0.00 0.00 34.15 4.81
1417 1698 0.955752 AGGAGGAGGGGAATGAGGAT 59.044 55.000 0.00 0.00 0.00 3.24
1578 1859 2.042464 TGAGTGCAGGAGACAAGACTT 58.958 47.619 0.00 0.00 0.00 3.01
1611 1892 1.117142 TCACGTTTTCTCCCGGTCCT 61.117 55.000 0.00 0.00 0.00 3.85
1932 2215 2.584835 TGCTCATGTTAGGGTTTGCT 57.415 45.000 0.00 0.00 0.00 3.91
1958 2241 9.905713 TTTGTATCTTCATTATTGCCTTCTAGT 57.094 29.630 0.00 0.00 0.00 2.57
2049 2337 5.308759 AGTTGGTGGCTAAAACCTAGAACTA 59.691 40.000 0.00 0.00 38.60 2.24
2080 2368 9.474313 ACATGTAGTAAAATAATGTGGATTGGT 57.526 29.630 0.00 0.00 30.53 3.67
2093 2381 2.564947 TGGATTGGTTTAACATGGTGGC 59.435 45.455 0.00 0.00 0.00 5.01
2118 2406 3.951775 TTGCGCCTTAATTCCATTGTT 57.048 38.095 4.18 0.00 0.00 2.83
2228 2516 2.463752 AGCCATTGCATCCTCAAATGT 58.536 42.857 0.00 0.00 41.13 2.71
2367 2663 9.282905 TGAATCTATCAATATCCATCCCATACA 57.717 33.333 0.00 0.00 34.30 2.29
2617 2915 9.905171 GCATATGAGGATTTAAGATTCTTTTCC 57.095 33.333 6.97 8.95 0.00 3.13
2647 2945 7.296628 ACTAGACTGAACTTCAAGATTCACT 57.703 36.000 0.00 0.00 31.62 3.41
3011 3312 1.303317 CAAGGTACAGCCACCACCC 60.303 63.158 0.00 0.00 41.40 4.61
3362 3681 4.506288 GGGAATTTGTTATTAATGGCGCAC 59.494 41.667 10.83 0.00 0.00 5.34
3479 3798 2.352030 GGCATGACATTCTGTTGTGGTG 60.352 50.000 0.00 0.00 0.00 4.17
3526 3845 8.734386 GGAAGAAATAGGGACAGCATATATTTG 58.266 37.037 0.00 0.00 0.00 2.32
3569 3888 3.149196 CACCAGGAGCTGTTGTATTGTT 58.851 45.455 0.00 0.00 0.00 2.83
3767 4087 1.137404 CGCTAGTTGCCCATTGTGC 59.863 57.895 0.00 0.00 38.78 4.57
3768 4088 1.308069 CGCTAGTTGCCCATTGTGCT 61.308 55.000 0.00 0.00 38.78 4.40
3825 4146 4.394920 TCATTCTTTTACACTTGATCGCCC 59.605 41.667 0.00 0.00 0.00 6.13
3827 4148 2.028839 TCTTTTACACTTGATCGCCCGA 60.029 45.455 0.00 0.00 0.00 5.14
3881 4202 2.053627 CGTTGCTGAAAAATGCTGGAC 58.946 47.619 0.00 0.00 0.00 4.02
3894 4215 3.220999 CTGGACGGAGCGTTGGTGA 62.221 63.158 0.00 0.00 41.37 4.02
3909 4230 1.318158 GGTGATTGCCCAAGCTCTGG 61.318 60.000 7.69 7.69 45.97 3.86
3955 4276 2.034939 TGCAACATGCCACTCTGAAAAG 59.965 45.455 0.00 0.00 44.23 2.27
3961 4282 4.162131 ACATGCCACTCTGAAAAGGTTTTT 59.838 37.500 0.00 0.00 0.00 1.94
4004 4337 2.238521 TCACTGTGAAAAAGGGATGCC 58.761 47.619 8.27 0.00 18.74 4.40
4314 6028 2.084546 CCGAAATCCCTCAAACTGGTC 58.915 52.381 0.00 0.00 0.00 4.02
4354 6070 4.038080 GCGGCACCAAAACGAGGG 62.038 66.667 0.00 0.00 0.00 4.30
4355 6071 3.361977 CGGCACCAAAACGAGGGG 61.362 66.667 0.00 0.00 0.00 4.79
4368 6084 0.109723 CGAGGGGAGGTTTGTGGAAA 59.890 55.000 0.00 0.00 0.00 3.13
4373 6089 1.271707 GGGAGGTTTGTGGAAATCCGA 60.272 52.381 0.00 0.00 39.43 4.55
4400 6116 2.547211 CGTCACGTAGGACTCCGATAAT 59.453 50.000 4.72 0.00 35.63 1.28
4459 6175 0.658829 TTCGCCATTGTTTTCGCACG 60.659 50.000 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 26 4.079844 TCCAAATGCCCTCTCAACATCATA 60.080 41.667 0.00 0.00 0.00 2.15
52 54 6.469782 AACAATTACATAATGGGCTTGGAG 57.530 37.500 0.00 0.00 0.00 3.86
55 57 5.816777 CCCAAACAATTACATAATGGGCTTG 59.183 40.000 0.00 0.00 0.00 4.01
57 59 4.408596 CCCCAAACAATTACATAATGGGCT 59.591 41.667 2.36 0.00 32.99 5.19
58 60 4.407296 TCCCCAAACAATTACATAATGGGC 59.593 41.667 2.36 0.00 32.99 5.36
59 61 5.163353 GGTCCCCAAACAATTACATAATGGG 60.163 44.000 0.00 0.00 0.00 4.00
65 67 2.831526 GCAGGTCCCCAAACAATTACAT 59.168 45.455 0.00 0.00 0.00 2.29
71 73 2.091555 AGTTTAGCAGGTCCCCAAACAA 60.092 45.455 0.00 0.00 32.75 2.83
103 105 2.644299 TCATCCTCTCCCACAATGTGTT 59.356 45.455 12.79 0.00 0.00 3.32
106 108 2.269023 TGTCATCCTCTCCCACAATGT 58.731 47.619 0.00 0.00 0.00 2.71
107 109 3.012518 GTTGTCATCCTCTCCCACAATG 58.987 50.000 0.00 0.00 30.06 2.82
117 119 2.808543 GACCACACAAGTTGTCATCCTC 59.191 50.000 5.27 0.00 39.51 3.71
157 159 4.382901 GCTGGATATGATCACCCATCTCTC 60.383 50.000 12.14 0.08 31.92 3.20
166 168 4.521130 TCCGTAAGCTGGATATGATCAC 57.479 45.455 0.00 0.00 0.00 3.06
183 185 1.747355 ACGACGTGGATTCTATTCCGT 59.253 47.619 3.97 0.00 38.74 4.69
186 188 4.267928 CCTCAAACGACGTGGATTCTATTC 59.732 45.833 3.97 0.00 0.00 1.75
189 191 2.821378 TCCTCAAACGACGTGGATTCTA 59.179 45.455 3.97 0.00 0.00 2.10
196 198 3.120649 GGAGAAAATCCTCAAACGACGTG 60.121 47.826 0.00 0.00 45.64 4.49
198 200 3.724295 GGAGAAAATCCTCAAACGACG 57.276 47.619 0.00 0.00 45.64 5.12
217 219 4.266029 GTGCGAACTTAATGATGCATTTGG 59.734 41.667 0.00 0.00 35.54 3.28
240 242 6.020281 CGAAACTAATCATTGAGTTCCTCGAG 60.020 42.308 5.13 5.13 37.79 4.04
246 248 7.974675 TCATTCCGAAACTAATCATTGAGTTC 58.025 34.615 0.00 0.00 34.81 3.01
267 269 6.003950 CCCATAGATGTTAAACCGGATCATT 58.996 40.000 9.46 0.00 0.00 2.57
273 275 1.871039 CGCCCATAGATGTTAAACCGG 59.129 52.381 0.00 0.00 0.00 5.28
274 276 2.557317 ACGCCCATAGATGTTAAACCG 58.443 47.619 0.00 0.00 0.00 4.44
279 281 3.433031 CCCTGAAACGCCCATAGATGTTA 60.433 47.826 0.00 0.00 0.00 2.41
292 294 2.539142 CGATAGTCGTCTCCCTGAAACG 60.539 54.545 0.00 0.00 34.72 3.60
306 308 9.413048 CAAAGATAAATACTTCCTCCGATAGTC 57.587 37.037 0.00 0.00 0.00 2.59
307 309 9.144298 TCAAAGATAAATACTTCCTCCGATAGT 57.856 33.333 0.00 0.00 0.00 2.12
328 354 7.064609 TGCCGAGAGTACTGAAAATAATCAAAG 59.935 37.037 0.00 0.00 0.00 2.77
332 358 7.329717 CCTATGCCGAGAGTACTGAAAATAATC 59.670 40.741 0.00 0.00 0.00 1.75
341 367 5.707242 TTATTCCTATGCCGAGAGTACTG 57.293 43.478 0.00 0.00 0.00 2.74
349 375 5.991861 TGGTAAGTTTTATTCCTATGCCGA 58.008 37.500 0.00 0.00 0.00 5.54
350 376 5.238650 CCTGGTAAGTTTTATTCCTATGCCG 59.761 44.000 0.00 0.00 0.00 5.69
366 392 3.716601 CACCAAAAGTTTGCCTGGTAAG 58.283 45.455 9.60 0.00 40.23 2.34
370 396 0.875474 CGCACCAAAAGTTTGCCTGG 60.875 55.000 3.67 3.67 36.86 4.45
372 398 1.066454 GTACGCACCAAAAGTTTGCCT 59.934 47.619 0.00 0.00 36.86 4.75
375 401 1.064357 ACCGTACGCACCAAAAGTTTG 59.936 47.619 10.49 0.00 37.90 2.93
389 415 2.953466 TGCTGAGTATCCAACCGTAC 57.047 50.000 0.00 0.00 0.00 3.67
401 427 1.893137 TCACCGACTAACATGCTGAGT 59.107 47.619 0.00 0.00 0.00 3.41
402 428 2.654749 TCACCGACTAACATGCTGAG 57.345 50.000 0.00 0.00 0.00 3.35
403 429 3.610040 AATCACCGACTAACATGCTGA 57.390 42.857 0.00 0.00 0.00 4.26
407 658 4.171005 ACACGTAATCACCGACTAACATG 58.829 43.478 0.00 0.00 0.00 3.21
409 660 3.252944 TGACACGTAATCACCGACTAACA 59.747 43.478 0.00 0.00 0.00 2.41
410 661 3.825308 TGACACGTAATCACCGACTAAC 58.175 45.455 0.00 0.00 0.00 2.34
468 721 3.175594 AGGTTGGTAAATCACGGGTAGA 58.824 45.455 0.00 0.00 0.00 2.59
555 810 5.934935 TTTGAAATCCGTCTTAACTGTCC 57.065 39.130 0.00 0.00 0.00 4.02
698 957 4.246458 AGATAGAAACAACCTCACGCTTC 58.754 43.478 0.00 0.00 0.00 3.86
699 958 4.246458 GAGATAGAAACAACCTCACGCTT 58.754 43.478 0.00 0.00 0.00 4.68
708 967 5.124138 TCAGGAGACTCGAGATAGAAACAAC 59.876 44.000 21.68 0.00 40.21 3.32
822 1090 1.792118 GCCGTGGGTTTGAACAGGAC 61.792 60.000 0.00 0.00 0.00 3.85
938 1206 0.389556 GAGAAGGGAACGACGGGAAC 60.390 60.000 0.00 0.00 0.00 3.62
966 1234 1.120530 GGAGCAGTTAGGGATCGGAA 58.879 55.000 0.00 0.00 0.00 4.30
1189 1469 0.539901 CGACCCCGGTAGATCTGGAT 60.540 60.000 5.18 0.00 45.09 3.41
1219 1499 7.415095 CCAAGATAATTAAACCACGAAGCATCA 60.415 37.037 0.00 0.00 0.00 3.07
1234 1515 1.944024 CGCGCCAACCCAAGATAATTA 59.056 47.619 0.00 0.00 0.00 1.40
1236 1517 1.724582 GCGCGCCAACCCAAGATAAT 61.725 55.000 23.24 0.00 0.00 1.28
1238 1519 2.822255 GCGCGCCAACCCAAGATA 60.822 61.111 23.24 0.00 0.00 1.98
1308 1589 1.433879 GAGGCATCGTACTCGCTGT 59.566 57.895 0.00 0.00 35.90 4.40
1345 1626 2.898705 TCCTCTTCCTCGTCGTAGTAC 58.101 52.381 0.00 0.00 0.00 2.73
1409 1690 1.516110 CCCACCTCCTCATCCTCATT 58.484 55.000 0.00 0.00 0.00 2.57
1578 1859 6.548171 AGAAAACGTGACTGAATTTCGAAAA 58.452 32.000 15.66 0.00 35.66 2.29
1611 1892 5.073144 AGAGACTAATCAACACCCCAAAAGA 59.927 40.000 0.00 0.00 0.00 2.52
1806 2087 7.119846 ACACAAACTTGAAGCTATCCTGAATAC 59.880 37.037 0.00 0.00 0.00 1.89
1858 2140 0.031585 GGTTGAAAAACTGGGCCGAC 59.968 55.000 0.00 0.00 0.00 4.79
1860 2142 2.425562 AGGTTGAAAAACTGGGCCG 58.574 52.632 0.00 0.00 46.40 6.13
1932 2215 9.905713 ACTAGAAGGCAATAATGAAGATACAAA 57.094 29.630 0.00 0.00 0.00 2.83
1957 2240 9.265901 ACTGCAAAATACATAGATGATGAGTAC 57.734 33.333 0.00 0.00 39.06 2.73
1958 2241 9.264719 CACTGCAAAATACATAGATGATGAGTA 57.735 33.333 0.00 0.00 39.06 2.59
1959 2242 7.989170 TCACTGCAAAATACATAGATGATGAGT 59.011 33.333 0.00 0.00 39.06 3.41
2093 2381 5.984926 ACAATGGAATTAAGGCGCAAATATG 59.015 36.000 10.83 4.20 32.46 1.78
2107 2395 8.655651 ATTTACAAACGACAAACAATGGAATT 57.344 26.923 0.00 0.00 36.63 2.17
2118 2406 8.928733 GGTCTTCTGTATATTTACAAACGACAA 58.071 33.333 8.01 0.00 37.86 3.18
2183 2471 4.567747 GGATGCTTTCCCTTCCTTACTGAA 60.568 45.833 0.00 0.00 38.75 3.02
2185 2473 3.054065 AGGATGCTTTCCCTTCCTTACTG 60.054 47.826 3.00 0.00 46.81 2.74
2186 2474 3.193782 AGGATGCTTTCCCTTCCTTACT 58.806 45.455 3.00 0.00 46.81 2.24
2187 2475 3.653835 AGGATGCTTTCCCTTCCTTAC 57.346 47.619 3.00 0.00 46.81 2.34
2212 2500 4.142315 GCTGTGTACATTTGAGGATGCAAT 60.142 41.667 0.00 0.00 0.00 3.56
2228 2516 6.993786 TTCAAAATTCGATATGGCTGTGTA 57.006 33.333 0.00 0.00 0.00 2.90
2432 2730 5.324409 ACCAACTTCATGCTTGGAAGATTA 58.676 37.500 18.37 0.00 43.46 1.75
2617 2915 7.925703 TCTTGAAGTTCAGTCTAGTTTAACG 57.074 36.000 5.56 0.00 0.00 3.18
2625 2923 7.055667 ACAGTGAATCTTGAAGTTCAGTCTA 57.944 36.000 5.56 0.00 36.21 2.59
3011 3312 1.003718 GAAGAACAGGGGGTGGACG 60.004 63.158 0.00 0.00 0.00 4.79
3362 3681 8.926710 ACAGTTTTCTAGTATTCAGTTTCATCG 58.073 33.333 0.00 0.00 0.00 3.84
3479 3798 3.443681 CCCATTATTCGCCCATCATTACC 59.556 47.826 0.00 0.00 0.00 2.85
3526 3845 3.243002 GCTTAAATCTCACCAGCATCAGC 60.243 47.826 0.00 0.00 42.56 4.26
3569 3888 4.644685 AGGCTTGTTTGCTAGTTTCTTTGA 59.355 37.500 0.00 0.00 0.00 2.69
3825 4146 3.053455 GCATGTAGCTAGGCTAAAGTCG 58.947 50.000 0.00 0.00 43.07 4.18
3881 4202 2.480555 GCAATCACCAACGCTCCG 59.519 61.111 0.00 0.00 0.00 4.63
3909 4230 5.588648 TCTGGAAAACCGATACCATCATTTC 59.411 40.000 0.00 0.00 0.00 2.17
4004 4337 2.355513 CCCAAATCACTCTGAGGTCTGG 60.356 54.545 9.85 7.85 0.00 3.86
4010 4343 2.089980 CAAGCCCCAAATCACTCTGAG 58.910 52.381 2.45 2.45 0.00 3.35
4273 5987 2.232941 GACATCCTGACCGGTTCTTACA 59.767 50.000 9.42 0.00 0.00 2.41
4354 6070 2.194201 TCGGATTTCCACAAACCTCC 57.806 50.000 0.00 0.00 35.14 4.30
4355 6071 2.095919 CGTTCGGATTTCCACAAACCTC 60.096 50.000 0.00 0.00 35.14 3.85
4400 6116 2.374184 CTCATTTTTGATGGGCCCGTA 58.626 47.619 19.13 0.00 0.00 4.02
4465 6181 1.763770 AGGCAGTGGGAAAGGACAG 59.236 57.895 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.