Multiple sequence alignment - TraesCS3D01G300500

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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 TraesCS3D01G300500 chr3D 100.000 4944 0 0 1 4944 415164844 415169787 0.000000e+00 9130.0
1 TraesCS3D01G300500 chr3D 85.742 519 51 12 166 669 375210727 375211237 1.220000e-145 527.0
2 TraesCS3D01G300500 chr3D 86.250 80 11 0 90 169 375210627 375210706 2.450000e-13 87.9
3 TraesCS3D01G300500 chr3A 94.068 2849 119 26 81 2888 535190526 535187687 0.000000e+00 4279.0
4 TraesCS3D01G300500 chr3A 95.257 1286 35 9 2883 4159 535185077 535183809 0.000000e+00 2013.0
5 TraesCS3D01G300500 chr3A 93.963 762 24 6 3406 4159 535178078 535177331 0.000000e+00 1133.0
6 TraesCS3D01G300500 chr3A 85.493 517 55 13 157 663 498246555 498247061 5.670000e-144 521.0
7 TraesCS3D01G300500 chr3A 95.000 200 7 2 4416 4615 535177195 535176999 1.340000e-80 311.0
8 TraesCS3D01G300500 chr3A 95.000 200 7 2 4416 4615 535183673 535183477 1.340000e-80 311.0
9 TraesCS3D01G300500 chr3A 81.661 289 33 14 4661 4943 535176698 535176424 6.440000e-54 222.0
10 TraesCS3D01G300500 chr3A 91.453 117 5 3 4286 4401 535177288 535177176 6.630000e-34 156.0
11 TraesCS3D01G300500 chr3A 91.453 117 5 3 4286 4401 535183766 535183654 6.630000e-34 156.0
12 TraesCS3D01G300500 chr3A 98.113 53 1 0 4201 4253 535177335 535177283 5.270000e-15 93.5
13 TraesCS3D01G300500 chr3A 98.113 53 1 0 4201 4253 535183813 535183761 5.270000e-15 93.5
14 TraesCS3D01G300500 chr3B 94.809 1310 49 6 2851 4142 541210527 541211835 0.000000e+00 2025.0
15 TraesCS3D01G300500 chr3B 95.005 1041 32 15 1821 2852 541209336 541210365 0.000000e+00 1616.0
16 TraesCS3D01G300500 chr3B 94.229 953 42 5 332 1273 541207764 541208714 0.000000e+00 1443.0
17 TraesCS3D01G300500 chr3B 85.749 821 43 19 4142 4943 541211875 541212640 0.000000e+00 800.0
18 TraesCS3D01G300500 chr3B 94.095 525 27 3 1309 1829 541208717 541209241 0.000000e+00 795.0
19 TraesCS3D01G300500 chr3B 82.927 533 59 11 157 663 489361281 489361807 7.550000e-123 451.0
20 TraesCS3D01G300500 chr4B 84.569 661 62 17 13 648 513101124 513100479 1.950000e-173 619.0
21 TraesCS3D01G300500 chr7D 85.185 513 56 11 163 665 175918915 175919417 4.420000e-140 508.0
22 TraesCS3D01G300500 chr4A 83.503 588 45 23 1 545 47626924 47627502 7.390000e-138 501.0
23 TraesCS3D01G300500 chr4A 80.606 165 26 5 1 162 593353753 593353592 6.720000e-24 122.0
24 TraesCS3D01G300500 chr7B 84.854 515 55 13 163 665 141798502 141799005 9.560000e-137 497.0
25 TraesCS3D01G300500 chr1B 84.971 519 47 19 157 665 429583710 429584207 9.560000e-137 497.0
26 TraesCS3D01G300500 chr4D 83.362 583 43 22 1 548 416451427 416450864 1.600000e-134 490.0
27 TraesCS3D01G300500 chr5A 82.651 513 60 15 166 665 577964077 577963581 1.270000e-115 427.0
28 TraesCS3D01G300500 chr2D 86.585 82 9 1 83 162 566987003 566987084 6.820000e-14 89.8
29 TraesCS3D01G300500 chr2B 96.970 33 1 0 633 665 437091749 437091717 6.910000e-04 56.5


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 TraesCS3D01G300500 chr3D 415164844 415169787 4943 False 9130.00 9130 100.0000 1 4944 1 chr3D.!!$F1 4943
1 TraesCS3D01G300500 chr3D 375210627 375211237 610 False 307.45 527 85.9960 90 669 2 chr3D.!!$F2 579
2 TraesCS3D01G300500 chr3A 535183477 535190526 7049 True 1370.50 4279 94.7782 81 4615 5 chr3A.!!$R2 4534
3 TraesCS3D01G300500 chr3A 498246555 498247061 506 False 521.00 521 85.4930 157 663 1 chr3A.!!$F1 506
4 TraesCS3D01G300500 chr3A 535176424 535178078 1654 True 383.10 1133 92.0380 3406 4943 5 chr3A.!!$R1 1537
5 TraesCS3D01G300500 chr3B 541207764 541212640 4876 False 1335.80 2025 92.7774 332 4943 5 chr3B.!!$F2 4611
6 TraesCS3D01G300500 chr3B 489361281 489361807 526 False 451.00 451 82.9270 157 663 1 chr3B.!!$F1 506
7 TraesCS3D01G300500 chr4B 513100479 513101124 645 True 619.00 619 84.5690 13 648 1 chr4B.!!$R1 635
8 TraesCS3D01G300500 chr7D 175918915 175919417 502 False 508.00 508 85.1850 163 665 1 chr7D.!!$F1 502
9 TraesCS3D01G300500 chr4A 47626924 47627502 578 False 501.00 501 83.5030 1 545 1 chr4A.!!$F1 544
10 TraesCS3D01G300500 chr7B 141798502 141799005 503 False 497.00 497 84.8540 163 665 1 chr7B.!!$F1 502
11 TraesCS3D01G300500 chr4D 416450864 416451427 563 True 490.00 490 83.3620 1 548 1 chr4D.!!$R1 547

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
867 989 1.075050 ACCTCGTCCCTTCAGTGTAGA 59.925 52.381 0.00 0.00 0.00 2.59 F
1420 1553 0.250295 TGTGGGCTTACTCTGTGCAC 60.250 55.000 10.75 10.75 0.00 4.57 F
1691 1828 1.607509 CCAGAGTGGCTTGACTCAGTG 60.608 57.143 11.84 0.00 44.25 3.66 F
2526 2776 0.036010 GGCCTCATGGATGGGTATCG 60.036 60.000 0.00 0.00 33.98 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2330 0.178975 AAAAATGGTGGTGGGAGCGA 60.179 50.000 0.00 0.0 0.00 4.93 R
2411 2659 1.832366 CCAATGGTCATTTGCCCATCA 59.168 47.619 0.00 0.0 40.57 3.07 R
2786 3041 1.892474 TGGTGCAGTATTGAAAAGGCC 59.108 47.619 0.00 0.0 0.00 5.19 R
4265 7360 0.179161 CTCCAGCGGACAAGTACGAG 60.179 60.000 9.36 0.0 39.85 4.18 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
65 78 1.448922 GCCTCCTCATCGCTAGACGT 61.449 60.000 0.00 0.00 44.19 4.34
109 139 2.281761 CCACTGCGCTTCCTTGGT 60.282 61.111 9.73 0.00 0.00 3.67
276 351 4.202441 GTCTATTGCATCAATCAGGTGGT 58.798 43.478 0.00 0.00 35.54 4.16
330 410 3.181475 CGGACTTGCTATCCAGTACATGT 60.181 47.826 2.69 2.69 35.83 3.21
386 482 3.055385 TGCTATCCAGTACTTGAACACCC 60.055 47.826 0.07 0.00 0.00 4.61
399 496 3.073678 TGAACACCCGATCAATGACAAG 58.926 45.455 0.00 0.00 0.00 3.16
406 509 4.766891 ACCCGATCAATGACAAGATTTGTT 59.233 37.500 0.00 0.00 45.52 2.83
453 569 2.430465 ACTCTAACGACGCCACTCTTA 58.570 47.619 0.00 0.00 0.00 2.10
463 579 5.107220 ACGACGCCACTCTTAAACAAATTAG 60.107 40.000 0.00 0.00 0.00 1.73
688 810 1.472376 CGCTCCAAGGTCTCTCCAATC 60.472 57.143 0.00 0.00 39.02 2.67
692 814 3.710677 CTCCAAGGTCTCTCCAATCAGAT 59.289 47.826 0.00 0.00 39.02 2.90
712 834 1.451567 CCGTCGACTGGCTCCTAGA 60.452 63.158 14.70 0.00 0.00 2.43
779 901 3.003173 CCAACGCCTCCCCTCAGA 61.003 66.667 0.00 0.00 0.00 3.27
782 904 1.306141 AACGCCTCCCCTCAGATCA 60.306 57.895 0.00 0.00 0.00 2.92
796 918 1.118838 AGATCACAGTCTGCTAGCCC 58.881 55.000 13.29 0.00 0.00 5.19
805 927 1.144093 GTCTGCTAGCCCCTCTCTCTA 59.856 57.143 13.29 0.00 0.00 2.43
814 936 1.413662 CCCCTCTCTCTAGCATCCCAA 60.414 57.143 0.00 0.00 0.00 4.12
847 969 4.662961 CGGCTCACCACGCACTCA 62.663 66.667 0.00 0.00 34.57 3.41
867 989 1.075050 ACCTCGTCCCTTCAGTGTAGA 59.925 52.381 0.00 0.00 0.00 2.59
1180 1302 2.363306 AGCAATTGGTGTTGAGGACA 57.637 45.000 9.83 0.00 35.42 4.02
1217 1339 6.489675 CAAATGTAAGTGGTCATGTATGCTC 58.510 40.000 0.00 0.00 0.00 4.26
1218 1340 4.137116 TGTAAGTGGTCATGTATGCTCC 57.863 45.455 0.00 0.00 0.00 4.70
1296 1420 6.640518 TGGAGTATTTACAGTCCATTCACTC 58.359 40.000 0.00 0.00 42.04 3.51
1299 1423 7.064728 GGAGTATTTACAGTCCATTCACTCAAC 59.935 40.741 0.00 0.00 37.87 3.18
1307 1432 4.638421 AGTCCATTCACTCAACGTTTGAAA 59.362 37.500 15.65 0.29 39.58 2.69
1378 1511 2.233431 TCCAACTGCAAACAAAGCACTT 59.767 40.909 0.00 0.00 37.02 3.16
1415 1548 5.647658 TGAATTTGTATGTGGGCTTACTCTG 59.352 40.000 0.00 0.00 0.00 3.35
1420 1553 0.250295 TGTGGGCTTACTCTGTGCAC 60.250 55.000 10.75 10.75 0.00 4.57
1449 1582 2.428544 AGGACTAGAGCGATGTCTGT 57.571 50.000 0.00 0.00 0.00 3.41
1512 1645 6.715264 ACTGTAGACCTTCAATTTTGTTAGGG 59.285 38.462 14.32 0.00 36.26 3.53
1534 1667 6.320418 AGGGAAAAACTAGTGTTGTGGTTTAG 59.680 38.462 0.00 0.00 36.39 1.85
1562 1695 8.862325 AATCCTGTGACACACATTTCTATTTA 57.138 30.769 3.56 0.00 43.71 1.40
1657 1791 5.694231 TCATGACTTTCCTGTGTTTGATG 57.306 39.130 0.00 0.00 0.00 3.07
1691 1828 1.607509 CCAGAGTGGCTTGACTCAGTG 60.608 57.143 11.84 0.00 44.25 3.66
1706 1843 4.738124 ACTCAGTGTAGTCATGATTGTCG 58.262 43.478 0.00 0.00 0.00 4.35
1717 1854 6.054941 AGTCATGATTGTCGTTGCCATTATA 58.945 36.000 0.00 0.00 0.00 0.98
1718 1855 6.017934 AGTCATGATTGTCGTTGCCATTATAC 60.018 38.462 0.00 0.00 0.00 1.47
1761 1898 5.758296 GGGATGTCGTCTTAATTCTGCAATA 59.242 40.000 0.00 0.00 0.00 1.90
1995 2241 8.084073 AGATGATTTCAAAACACTGGTATGTTG 58.916 33.333 0.00 0.00 42.01 3.33
2044 2290 7.542477 ACTGATAAACACAAGATCAAGTACTCG 59.458 37.037 0.00 0.00 0.00 4.18
2081 2329 8.924691 TCATTTTGTTCTGTAATTAATGCTTGC 58.075 29.630 0.00 0.00 0.00 4.01
2082 2330 8.928733 CATTTTGTTCTGTAATTAATGCTTGCT 58.071 29.630 0.00 0.00 0.00 3.91
2185 2433 3.744238 ATGTGGAAAACCGAAAAAGGG 57.256 42.857 0.00 0.00 35.02 3.95
2243 2491 6.825721 CAGGTCTATCTGTATTGGCTTCTTTT 59.174 38.462 0.00 0.00 0.00 2.27
2244 2492 7.337942 CAGGTCTATCTGTATTGGCTTCTTTTT 59.662 37.037 0.00 0.00 0.00 1.94
2333 2581 9.926158 ACAAACAAATCAAAACAGCATCATATA 57.074 25.926 0.00 0.00 0.00 0.86
2341 2589 9.743581 ATCAAAACAGCATCATATATATGTGGA 57.256 29.630 19.78 4.16 35.26 4.02
2342 2590 9.571816 TCAAAACAGCATCATATATATGTGGAA 57.428 29.630 19.78 3.83 35.26 3.53
2349 2597 8.435187 AGCATCATATATATGTGGAATGGGTAG 58.565 37.037 19.78 0.00 35.26 3.18
2383 2631 7.976175 TGTGTATCTAGCTGTACAGAAAAGATG 59.024 37.037 27.93 13.62 31.95 2.90
2423 2672 6.183360 GCTTTTAATCTGTTGATGGGCAAATG 60.183 38.462 0.00 0.00 38.44 2.32
2426 2675 2.170166 TCTGTTGATGGGCAAATGACC 58.830 47.619 0.00 0.00 45.93 4.02
2513 2763 0.325933 CTTGGAGTGTCATGGCCTCA 59.674 55.000 14.97 0.00 0.00 3.86
2521 2771 4.513777 CATGGCCTCATGGATGGG 57.486 61.111 3.32 0.00 45.19 4.00
2526 2776 0.036010 GGCCTCATGGATGGGTATCG 60.036 60.000 0.00 0.00 33.98 2.92
2578 2828 1.676635 GCTGATGCAGGCTTGGTCA 60.677 57.895 0.00 0.00 39.41 4.02
2582 2832 1.251251 GATGCAGGCTTGGTCAAAGT 58.749 50.000 0.00 0.00 38.25 2.66
2597 2847 9.612620 CTTGGTCAAAGTTAATTTACAGATGTC 57.387 33.333 0.00 0.00 0.00 3.06
2627 2877 2.671070 GCCAGCAAACACTAAAATCGGG 60.671 50.000 0.00 0.00 0.00 5.14
2786 3041 9.677567 CGAAGGAAATATTACCCAAATATGTTG 57.322 33.333 8.87 0.00 39.41 3.33
3023 6059 0.030504 CAAATCACAGTGCGGCACAA 59.969 50.000 32.29 16.24 36.74 3.33
3024 6060 0.311790 AAATCACAGTGCGGCACAAG 59.688 50.000 32.29 25.42 36.74 3.16
3175 6212 6.426980 TGCATATCGAAGATAATGCCATTC 57.573 37.500 13.76 0.00 45.12 2.67
3270 6307 4.098044 GGTCAATCTTCTCCAGATGTACGA 59.902 45.833 0.00 0.00 41.93 3.43
3372 6409 5.415221 CAAGTAAGCCTTCTTGTAGGAGAG 58.585 45.833 7.88 0.00 37.50 3.20
3454 6491 4.089361 CTCAAAGGTGATAGCCCCTTTTT 58.911 43.478 4.61 0.00 46.38 1.94
3464 6501 1.215423 AGCCCCTTTTTCTCTGTGTGT 59.785 47.619 0.00 0.00 0.00 3.72
3558 6595 5.316987 AGACTGCTATTAGGCTGTTTTGTT 58.683 37.500 0.00 0.00 42.73 2.83
3582 6619 4.633565 GGGAAATGACTGTCATGTCTCTTC 59.366 45.833 30.18 23.75 38.34 2.87
3747 6784 1.470098 GCAGTTTGCATACTCCAGGTG 59.530 52.381 6.86 0.00 44.26 4.00
3781 6818 3.899980 TCCAGGATGACATCATACTCCAG 59.100 47.826 17.08 0.00 43.90 3.86
3806 6843 3.945285 ACTCGGTTCATGTTTTCAGTTGT 59.055 39.130 0.00 0.00 0.00 3.32
3812 6849 6.359617 CGGTTCATGTTTTCAGTTGTCATAAC 59.640 38.462 0.00 0.00 0.00 1.89
3835 6872 6.994221 ACCATTATAGTAGATCTTTGGGTCG 58.006 40.000 0.00 0.00 0.00 4.79
4010 7047 6.368791 GCCTCTTTGTTTGTTTCTTTCTTGTT 59.631 34.615 0.00 0.00 0.00 2.83
4018 7071 7.655328 TGTTTGTTTCTTTCTTGTTTGTGTGAT 59.345 29.630 0.00 0.00 0.00 3.06
4063 7116 6.392354 ACAATTTGCATAGGTCAATGAACAG 58.608 36.000 0.00 0.00 0.00 3.16
4161 7256 3.744238 TTCAGTTGGTCGAGATGTGAA 57.256 42.857 0.00 0.00 0.00 3.18
4174 7269 3.093057 AGATGTGAACTTAGCTCCGAGT 58.907 45.455 0.00 0.00 0.00 4.18
4175 7270 3.129638 AGATGTGAACTTAGCTCCGAGTC 59.870 47.826 0.00 0.00 0.00 3.36
4198 7293 0.595310 GCGTCGTTAGGCCTCTGATC 60.595 60.000 9.68 0.00 0.00 2.92
4200 7295 1.268794 CGTCGTTAGGCCTCTGATCTG 60.269 57.143 9.68 0.00 0.00 2.90
4201 7296 2.025155 GTCGTTAGGCCTCTGATCTGA 58.975 52.381 9.68 2.03 0.00 3.27
4202 7297 2.625790 GTCGTTAGGCCTCTGATCTGAT 59.374 50.000 9.68 0.00 0.00 2.90
4203 7298 2.625314 TCGTTAGGCCTCTGATCTGATG 59.375 50.000 9.68 1.79 0.00 3.07
4204 7299 2.363680 CGTTAGGCCTCTGATCTGATGT 59.636 50.000 9.68 0.00 0.00 3.06
4277 7372 0.243907 TGCAGCTCTCGTACTTGTCC 59.756 55.000 0.00 0.00 0.00 4.02
4278 7373 0.798771 GCAGCTCTCGTACTTGTCCG 60.799 60.000 0.00 0.00 0.00 4.79
4279 7374 0.798771 CAGCTCTCGTACTTGTCCGC 60.799 60.000 0.00 0.00 0.00 5.54
4297 7392 0.378610 GCTGGAGGCAAATTAGTCGC 59.621 55.000 0.00 0.00 41.35 5.19
4354 7449 3.160269 CCTTCTTTCCTTGCAACCTCAT 58.840 45.455 0.00 0.00 0.00 2.90
4355 7450 3.192212 CCTTCTTTCCTTGCAACCTCATC 59.808 47.826 0.00 0.00 0.00 2.92
4395 7490 2.159558 GCATAAGCTGATGATGATGCCG 60.160 50.000 15.87 0.00 34.88 5.69
4432 7527 0.543277 GTCTGATGATGGAGGTGGCA 59.457 55.000 0.00 0.00 0.00 4.92
4499 7594 5.328691 TCTAATTTCCACAAATTAAGCGCG 58.671 37.500 0.00 0.00 41.75 6.86
4508 7603 0.305922 AATTAAGCGCGCAGATGCTC 59.694 50.000 35.10 0.00 39.76 4.26
4617 7712 3.775654 GGAGTGGAGTGAGCCCCG 61.776 72.222 0.00 0.00 0.00 5.73
4741 8137 1.645034 CGGGCAGGCATATATTCTCG 58.355 55.000 0.00 0.00 0.00 4.04
4775 8188 5.721480 TGTCTGATCAAAGGATAGACAAGGA 59.279 40.000 8.72 0.00 39.03 3.36
4810 8223 6.147656 AGGAATTTTGCGACAAAATCAAATCC 59.852 34.615 22.09 22.30 32.85 3.01
4818 8231 4.380867 CGACAAAATCAAATCCCCTTGAGG 60.381 45.833 0.00 0.00 38.66 3.86
4819 8232 3.261643 ACAAAATCAAATCCCCTTGAGGC 59.738 43.478 0.00 0.00 38.66 4.70
4820 8233 3.479866 AAATCAAATCCCCTTGAGGCT 57.520 42.857 0.00 0.00 38.66 4.58
4821 8234 2.744352 ATCAAATCCCCTTGAGGCTC 57.256 50.000 7.79 7.79 38.66 4.70
4822 8235 1.673767 TCAAATCCCCTTGAGGCTCT 58.326 50.000 16.72 0.00 31.67 4.09
4823 8236 1.283029 TCAAATCCCCTTGAGGCTCTG 59.717 52.381 16.72 8.47 31.67 3.35
4824 8237 0.033699 AAATCCCCTTGAGGCTCTGC 60.034 55.000 16.72 0.00 0.00 4.26
4900 8313 2.054799 ACCAGGAAAGTTAGGCTCACA 58.945 47.619 1.11 0.00 0.00 3.58
4901 8314 2.224548 ACCAGGAAAGTTAGGCTCACAC 60.225 50.000 1.11 0.00 0.00 3.82
4943 8356 1.038280 AACTTCGTCCGTCCAAGTCT 58.962 50.000 0.00 0.00 29.85 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 242 2.257207 ACCTCAAGTCCTCAAATCGGA 58.743 47.619 0.00 0.00 0.00 4.55
276 351 5.357314 AGCTAACGCAATAGACTTGACTCTA 59.643 40.000 0.00 0.00 39.10 2.43
347 427 7.424803 TGGATAGCAAAATTATGTGTATGTGC 58.575 34.615 0.00 0.00 0.00 4.57
386 482 8.370321 CAATCAAACAAATCTTGTCATTGATCG 58.630 33.333 14.95 5.66 44.28 3.69
399 496 5.754890 AGAGTGGCAAACAATCAAACAAATC 59.245 36.000 0.00 0.00 46.19 2.17
406 509 5.843673 TGTTAAGAGTGGCAAACAATCAA 57.156 34.783 0.00 0.00 46.19 2.57
453 569 4.751098 CAGTGTGGCATTGCTAATTTGTTT 59.249 37.500 8.82 0.00 0.00 2.83
463 579 2.514205 AAAAGACAGTGTGGCATTGC 57.486 45.000 0.00 0.00 0.00 3.56
608 727 6.841119 TCTTTCGACAACAAATATGACATGG 58.159 36.000 0.00 0.00 0.00 3.66
712 834 4.444081 AGAGCCGGCGACCTAGGT 62.444 66.667 23.20 16.26 0.00 3.08
779 901 0.326048 AGGGGCTAGCAGACTGTGAT 60.326 55.000 18.24 0.00 0.00 3.06
782 904 0.686112 GAGAGGGGCTAGCAGACTGT 60.686 60.000 18.24 9.40 0.00 3.55
796 918 1.969923 CCTTGGGATGCTAGAGAGAGG 59.030 57.143 0.00 0.00 0.00 3.69
847 969 1.075050 TCTACACTGAAGGGACGAGGT 59.925 52.381 0.00 0.00 0.00 3.85
1180 1302 6.869913 CCACTTACATTTGCATCAAGAAACAT 59.130 34.615 0.00 0.00 0.00 2.71
1217 1339 6.515272 AACCATTCTTGTGCATTACTTAGG 57.485 37.500 0.00 0.00 0.00 2.69
1264 1388 6.049790 GGACTGTAAATACTCCACTCCATTC 58.950 44.000 0.00 0.00 0.00 2.67
1288 1412 8.594687 AGAAAAATTTCAAACGTTGAGTGAATG 58.405 29.630 13.15 1.64 41.38 2.67
1333 1466 3.591527 AGTCCAATTCCAACAGGGTGATA 59.408 43.478 0.00 0.00 38.11 2.15
1363 1496 6.633500 ATTACTAGAAGTGCTTTGTTTGCA 57.367 33.333 0.00 0.00 38.19 4.08
1403 1536 1.005037 CGTGCACAGAGTAAGCCCA 60.005 57.895 18.64 0.00 0.00 5.36
1420 1553 3.064958 TCGCTCTAGTCCTAACACAATCG 59.935 47.826 0.00 0.00 0.00 3.34
1449 1582 7.643569 ATGAAGTTATGCCAACATCAACATA 57.356 32.000 9.40 0.00 37.74 2.29
1512 1645 9.628746 TTTTCTAAACCACAACACTAGTTTTTC 57.371 29.630 0.00 0.00 35.28 2.29
1562 1695 1.002087 GTGTGATCGAAACAGGTCCCT 59.998 52.381 4.66 0.00 0.00 4.20
1657 1791 1.141053 ACTCTGGTCTGGGTGAAACAC 59.859 52.381 0.00 0.00 44.11 3.32
1691 1828 3.000041 TGGCAACGACAATCATGACTAC 59.000 45.455 0.00 0.00 42.51 2.73
1706 1843 5.193679 AGAAACTGGGAGTATAATGGCAAC 58.806 41.667 0.00 0.00 0.00 4.17
1717 1854 2.224867 CCATGTCCAAGAAACTGGGAGT 60.225 50.000 0.00 0.00 33.66 3.85
1718 1855 2.440409 CCATGTCCAAGAAACTGGGAG 58.560 52.381 0.00 0.00 33.66 4.30
1745 1882 7.221452 CCAAGCACATTATTGCAGAATTAAGAC 59.779 37.037 0.00 0.00 45.62 3.01
1761 1898 3.436704 CACGACAATAGACCAAGCACATT 59.563 43.478 0.00 0.00 0.00 2.71
1995 2241 9.202545 CAGTAAGTTTTAAACGTGAACAAGTAC 57.797 33.333 6.53 0.00 36.23 2.73
2081 2329 0.609131 AAAATGGTGGTGGGAGCGAG 60.609 55.000 0.00 0.00 0.00 5.03
2082 2330 0.178975 AAAAATGGTGGTGGGAGCGA 60.179 50.000 0.00 0.00 0.00 4.93
2185 2433 6.799512 ACTTAATGCCAATAAGAGCACATTC 58.200 36.000 6.54 0.00 42.84 2.67
2243 2491 9.016438 GGTAAATGAAATGGGTAACTTGAGTAA 57.984 33.333 0.00 0.00 0.00 2.24
2244 2492 8.387813 AGGTAAATGAAATGGGTAACTTGAGTA 58.612 33.333 0.00 0.00 0.00 2.59
2285 2533 4.704540 GTGGTCAATTATCAATGTCACCCA 59.295 41.667 0.00 0.00 0.00 4.51
2333 2581 7.619302 ACACAAAAATCTACCCATTCCACATAT 59.381 33.333 0.00 0.00 0.00 1.78
2336 2584 5.010516 CACACAAAAATCTACCCATTCCACA 59.989 40.000 0.00 0.00 0.00 4.17
2338 2586 5.144100 ACACACAAAAATCTACCCATTCCA 58.856 37.500 0.00 0.00 0.00 3.53
2339 2587 5.722021 ACACACAAAAATCTACCCATTCC 57.278 39.130 0.00 0.00 0.00 3.01
2341 2589 9.396022 CTAGATACACACAAAAATCTACCCATT 57.604 33.333 0.00 0.00 31.38 3.16
2342 2590 7.499232 GCTAGATACACACAAAAATCTACCCAT 59.501 37.037 0.00 0.00 31.38 4.00
2349 2597 8.251750 TGTACAGCTAGATACACACAAAAATC 57.748 34.615 0.00 0.00 0.00 2.17
2411 2659 1.832366 CCAATGGTCATTTGCCCATCA 59.168 47.619 0.00 0.00 40.57 3.07
2426 2675 2.906691 TTTGCAAAGTGGGACCAATG 57.093 45.000 8.05 0.00 0.00 2.82
2462 2712 3.495193 CATTGCGATATAACATGCCTGC 58.505 45.455 0.00 0.00 0.00 4.85
2513 2763 2.050144 AGAGTTGCGATACCCATCCAT 58.950 47.619 0.00 0.00 0.00 3.41
2578 2828 6.128007 CCAGCGGACATCTGTAAATTAACTTT 60.128 38.462 0.00 0.00 0.00 2.66
2582 2832 4.080807 TCCCAGCGGACATCTGTAAATTAA 60.081 41.667 0.00 0.00 31.13 1.40
2627 2877 5.465390 TGCGCCATAAGATTGACAATACTAC 59.535 40.000 4.18 0.00 0.00 2.73
2752 3007 7.566569 TGGGTAATATTTCCTTCGTGTTATCA 58.433 34.615 10.57 0.00 0.00 2.15
2760 3015 9.677567 CAACATATTTGGGTAATATTTCCTTCG 57.322 33.333 10.57 0.00 37.33 3.79
2786 3041 1.892474 TGGTGCAGTATTGAAAAGGCC 59.108 47.619 0.00 0.00 0.00 5.19
3023 6059 5.784177 CACTACTACCAGTGTTTGATGTCT 58.216 41.667 0.00 0.00 40.89 3.41
3159 6196 7.816945 AAACAAAAGAATGGCATTATCTTCG 57.183 32.000 13.65 10.38 32.45 3.79
3270 6307 6.120220 GTGAACTATACTACCAAAAGGGCAT 58.880 40.000 0.00 0.00 42.05 4.40
3372 6409 5.656480 TCAAGTTTCCCAGTTTTACAAAGC 58.344 37.500 0.00 0.00 0.00 3.51
3454 6491 9.645059 CTATTTGAATAAGAAGACACACAGAGA 57.355 33.333 0.00 0.00 0.00 3.10
3558 6595 3.584406 AGAGACATGACAGTCATTTCCCA 59.416 43.478 21.35 0.00 40.98 4.37
3582 6619 9.233232 GAAAACTTCACAACCAAATACTTGTAG 57.767 33.333 0.00 0.00 0.00 2.74
3747 6784 3.451894 CCTGGATTTGGTGGGCGC 61.452 66.667 0.00 0.00 0.00 6.53
3781 6818 3.560068 ACTGAAAACATGAACCGAGTGAC 59.440 43.478 0.00 0.00 0.00 3.67
3812 6849 6.994221 ACGACCCAAAGATCTACTATAATGG 58.006 40.000 0.00 0.00 0.00 3.16
3858 6895 4.984161 CACAAAGGAAAATTCTCAATGCGT 59.016 37.500 0.00 0.00 0.00 5.24
4010 7047 7.066887 ACAACAAAGATGTCAGTTATCACACAA 59.933 33.333 0.00 0.00 39.40 3.33
4174 7269 4.424566 GGCCTAACGACGCACCGA 62.425 66.667 0.00 0.00 0.00 4.69
4175 7270 4.430765 AGGCCTAACGACGCACCG 62.431 66.667 1.29 0.00 0.00 4.94
4180 7275 1.025812 AGATCAGAGGCCTAACGACG 58.974 55.000 4.42 0.00 0.00 5.12
4198 7293 1.479730 TCAGCTCTGCACCTACATCAG 59.520 52.381 0.00 0.00 0.00 2.90
4200 7295 1.205655 TGTCAGCTCTGCACCTACATC 59.794 52.381 0.00 0.00 0.00 3.06
4201 7296 1.269958 TGTCAGCTCTGCACCTACAT 58.730 50.000 0.00 0.00 0.00 2.29
4202 7297 1.269958 ATGTCAGCTCTGCACCTACA 58.730 50.000 0.00 0.00 0.00 2.74
4203 7298 3.742433 ATATGTCAGCTCTGCACCTAC 57.258 47.619 0.00 0.00 0.00 3.18
4204 7299 3.070159 GGAATATGTCAGCTCTGCACCTA 59.930 47.826 0.00 0.00 0.00 3.08
4258 7353 0.243907 GGACAAGTACGAGAGCTGCA 59.756 55.000 1.02 0.00 0.00 4.41
4265 7360 0.179161 CTCCAGCGGACAAGTACGAG 60.179 60.000 9.36 0.00 39.85 4.18
4278 7373 0.378610 GCGACTAATTTGCCTCCAGC 59.621 55.000 0.00 0.00 44.14 4.85
4279 7374 1.737838 TGCGACTAATTTGCCTCCAG 58.262 50.000 0.00 0.00 32.85 3.86
4297 7392 6.994496 TCTTCCCAATAGATTAGCATCAGTTG 59.006 38.462 0.00 0.00 0.00 3.16
4354 7449 2.036475 GCCGAGAATCTCATAAGCAGGA 59.964 50.000 11.18 0.00 0.00 3.86
4355 7450 2.224137 TGCCGAGAATCTCATAAGCAGG 60.224 50.000 11.18 2.63 0.00 4.85
4413 7508 0.543277 TGCCACCTCCATCATCAGAC 59.457 55.000 0.00 0.00 0.00 3.51
4415 7510 0.253894 TGTGCCACCTCCATCATCAG 59.746 55.000 0.00 0.00 0.00 2.90
4617 7712 2.035321 TGGTTTGCCATTTCCGAGAAAC 59.965 45.455 1.85 0.00 40.46 2.78
4718 8107 0.962356 AATATATGCCTGCCCGCAGC 60.962 55.000 11.29 7.54 43.26 5.25
4719 8108 1.089920 GAATATATGCCTGCCCGCAG 58.910 55.000 9.80 9.80 43.26 5.18
4741 8137 6.748132 TCCTTTGATCAGACAATCCAAAAAC 58.252 36.000 0.00 0.00 0.00 2.43
4775 8188 3.248125 TCGCAAAATTCCTTACGACGTTT 59.752 39.130 5.50 0.00 0.00 3.60
4798 8211 3.516700 AGCCTCAAGGGGATTTGATTTTG 59.483 43.478 0.00 0.00 36.55 2.44
4800 8213 3.012161 AGAGCCTCAAGGGGATTTGATTT 59.988 43.478 0.00 0.00 36.55 2.17
4825 8238 2.961721 CGATGTCATCCGGCACCG 60.962 66.667 7.25 1.02 39.44 4.94
4826 8239 1.883084 GACGATGTCATCCGGCACC 60.883 63.158 7.25 0.00 33.27 5.01
4827 8240 2.230940 CGACGATGTCATCCGGCAC 61.231 63.158 7.25 0.00 32.40 5.01
4900 8313 1.862201 TGTCGTCGCAAAATTCTTCGT 59.138 42.857 0.00 0.00 0.00 3.85
4901 8314 2.486128 CTGTCGTCGCAAAATTCTTCG 58.514 47.619 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.