Multiple sequence alignment - TraesCS3D01G371700

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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 TraesCS3D01G371700 chr3D 100.000 2744 0 0 1 2744 484827093 484829836 0.000000e+00 5068
1 TraesCS3D01G371700 chr3A 91.479 1291 67 22 428 1683 627929160 627930442 0.000000e+00 1735
2 TraesCS3D01G371700 chr3A 86.427 361 46 3 2385 2744 627949081 627949439 2.560000e-105 392
3 TraesCS3D01G371700 chr3A 86.691 278 21 6 1930 2193 627948167 627948442 7.430000e-76 294
4 TraesCS3D01G371700 chr3A 93.750 192 11 1 1745 1936 627930658 627930848 1.240000e-73 287
5 TraesCS3D01G371700 chr3A 90.244 164 12 2 2194 2353 627948594 627948757 7.700000e-51 211
6 TraesCS3D01G371700 chr3B 92.619 1138 56 14 506 1622 647698193 647699323 0.000000e+00 1611
7 TraesCS3D01G371700 chr3B 88.732 568 46 8 1651 2201 647699320 647699886 0.000000e+00 678
8 TraesCS3D01G371700 chr3B 88.288 555 60 3 2194 2744 647700030 647700583 0.000000e+00 660
9 TraesCS3D01G371700 chr3B 91.841 429 33 2 2 428 647697600 647698028 5.060000e-167 597
10 TraesCS3D01G371700 chr3B 87.147 389 46 4 35 421 112391554 112391168 3.240000e-119 438
11 TraesCS3D01G371700 chr1B 88.889 387 41 2 37 421 678205615 678205229 2.470000e-130 475
12 TraesCS3D01G371700 chr1D 88.083 386 45 1 37 421 106293107 106292722 8.960000e-125 457
13 TraesCS3D01G371700 chr1D 80.198 202 35 4 428 625 493761262 493761062 2.200000e-31 147
14 TraesCS3D01G371700 chr5D 87.565 386 47 1 37 421 260680664 260681049 1.940000e-121 446
15 TraesCS3D01G371700 chr5D 82.412 199 31 4 428 623 46308536 46308733 1.310000e-38 171
16 TraesCS3D01G371700 chr5D 81.026 195 34 3 435 626 441401537 441401343 4.730000e-33 152
17 TraesCS3D01G371700 chr2A 87.728 383 44 3 37 418 699838635 699839015 6.970000e-121 444
18 TraesCS3D01G371700 chr2A 82.673 202 32 3 428 626 722110581 722110782 2.810000e-40 176
19 TraesCS3D01G371700 chr4D 86.979 384 46 3 38 421 16139772 16140151 1.950000e-116 429
20 TraesCS3D01G371700 chr4D 86.753 385 50 1 37 420 18398137 18398521 7.020000e-116 427
21 TraesCS3D01G371700 chr4D 86.753 385 46 3 38 421 447334188 447333808 9.080000e-115 424
22 TraesCS3D01G371700 chr4D 79.012 243 50 1 2328 2570 189114844 189115085 6.080000e-37 165
23 TraesCS3D01G371700 chr4D 81.592 201 30 7 428 624 63250586 63250783 2.830000e-35 159
24 TraesCS3D01G371700 chr4D 79.208 202 39 3 428 626 28471617 28471416 1.330000e-28 137
25 TraesCS3D01G371700 chr4A 80.100 201 36 4 428 624 534542510 534542710 2.200000e-31 147


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 TraesCS3D01G371700 chr3D 484827093 484829836 2743 False 5068.0 5068 100.000000 1 2744 1 chr3D.!!$F1 2743
1 TraesCS3D01G371700 chr3A 627929160 627930848 1688 False 1011.0 1735 92.614500 428 1936 2 chr3A.!!$F1 1508
2 TraesCS3D01G371700 chr3A 627948167 627949439 1272 False 299.0 392 87.787333 1930 2744 3 chr3A.!!$F2 814
3 TraesCS3D01G371700 chr3B 647697600 647700583 2983 False 886.5 1611 90.370000 2 2744 4 chr3B.!!$F1 2742

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
162 164 0.099436 CATAAGCACCGAAGCAAGCC 59.901 55.0 2.02 0.0 36.85 4.35 F
769 864 0.692419 CCTCCTACCAGCACCCATCT 60.692 60.0 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1054 1166 0.107654 GTAGGGCTGCGATGGAAACT 60.108 55.0 0.0 0.0 0.0 2.66 R
2395 2896 0.173708 CTGGAGTCCGTGTTAGAGCC 59.826 60.0 4.3 0.0 0.0 4.70 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
62 64 7.519032 TTTTTGTGGGAAACTTTCGATCTAT 57.481 32.000 0.00 0.00 0.00 1.98
67 69 6.884295 TGTGGGAAACTTTCGATCTATTCATT 59.116 34.615 0.00 0.00 0.00 2.57
69 71 8.244113 GTGGGAAACTTTCGATCTATTCATTTT 58.756 33.333 0.00 0.00 0.00 1.82
70 72 8.458843 TGGGAAACTTTCGATCTATTCATTTTC 58.541 33.333 0.00 0.00 0.00 2.29
96 98 1.937223 TGGCAGTACAACGAACACAAG 59.063 47.619 0.00 0.00 0.00 3.16
142 144 1.002684 CATAGACCACCTAGCGACGAC 60.003 57.143 0.00 0.00 0.00 4.34
143 145 0.745845 TAGACCACCTAGCGACGACC 60.746 60.000 0.00 0.00 0.00 4.79
152 154 0.101759 TAGCGACGACCATAAGCACC 59.898 55.000 0.00 0.00 0.00 5.01
158 160 0.739462 CGACCATAAGCACCGAAGCA 60.739 55.000 2.02 0.00 36.85 3.91
162 164 0.099436 CATAAGCACCGAAGCAAGCC 59.901 55.000 2.02 0.00 36.85 4.35
216 219 0.955905 GAGCCGGGCACAACTTTTTA 59.044 50.000 23.09 0.00 0.00 1.52
234 237 7.545489 ACTTTTTATAGTAGACAGTCGGGAAG 58.455 38.462 0.00 0.00 0.00 3.46
267 270 0.696501 ACCCCATAGGACCAACACAC 59.303 55.000 0.00 0.00 39.89 3.82
281 284 1.808411 ACACACCAGAATAGCAACCG 58.192 50.000 0.00 0.00 0.00 4.44
306 309 5.352284 TGCCGATGAAGAGAAGTTTAGATC 58.648 41.667 0.00 0.00 0.00 2.75
373 376 2.031157 CGGATCCACAAAAGACAACCAC 60.031 50.000 13.41 0.00 0.00 4.16
374 377 2.296190 GGATCCACAAAAGACAACCACC 59.704 50.000 6.95 0.00 0.00 4.61
375 378 1.384525 TCCACAAAAGACAACCACCG 58.615 50.000 0.00 0.00 0.00 4.94
378 381 1.064952 CACAAAAGACAACCACCGACC 59.935 52.381 0.00 0.00 0.00 4.79
379 382 1.340211 ACAAAAGACAACCACCGACCA 60.340 47.619 0.00 0.00 0.00 4.02
394 397 3.325135 ACCGACCAAATCCTATGAGATCC 59.675 47.826 0.00 0.00 0.00 3.36
449 480 6.349280 CGCAACCTTATTCCATCTTCAAGAAA 60.349 38.462 0.00 0.00 0.00 2.52
459 490 2.458006 CTTCAAGAAACCGCCACCGC 62.458 60.000 0.00 0.00 0.00 5.68
470 501 4.452733 CCACCGCCTCGTCTTCCC 62.453 72.222 0.00 0.00 0.00 3.97
529 561 6.071728 GCACATAAAAATAGATCCCTCCCATG 60.072 42.308 0.00 0.00 0.00 3.66
541 632 2.257409 CTCCCATGACAAGGACCGGG 62.257 65.000 6.32 0.00 34.81 5.73
640 735 1.004277 AGCCGCAGATTACAAAAGGGA 59.996 47.619 0.00 0.00 0.00 4.20
665 760 2.048222 TCTGTGGCTTCTTCCGCG 60.048 61.111 0.00 0.00 39.42 6.46
666 761 3.793144 CTGTGGCTTCTTCCGCGC 61.793 66.667 0.00 0.00 39.42 6.86
728 823 3.772025 CCAGATCGGATTTATCCCTAGCT 59.228 47.826 3.23 0.00 44.24 3.32
769 864 0.692419 CCTCCTACCAGCACCCATCT 60.692 60.000 0.00 0.00 0.00 2.90
973 1085 1.079750 GACGACCTGGCACTTCTCC 60.080 63.158 0.00 0.00 0.00 3.71
974 1086 1.534235 ACGACCTGGCACTTCTCCT 60.534 57.895 0.00 0.00 0.00 3.69
975 1087 1.216710 CGACCTGGCACTTCTCCTC 59.783 63.158 0.00 0.00 0.00 3.71
1051 1163 1.294780 CCAAGCGAGAGACCAAGCT 59.705 57.895 0.00 0.00 42.35 3.74
1054 1166 2.047844 GCGAGAGACCAAGCTGCA 60.048 61.111 1.02 0.00 0.00 4.41
1075 1187 1.271840 TTTCCATCGCAGCCCTACCT 61.272 55.000 0.00 0.00 0.00 3.08
1222 1334 3.764466 CAGCGGAAGGAGAGCGGT 61.764 66.667 0.00 0.00 35.78 5.68
1330 1454 2.751837 GCCGGGAAGCTCAAAGGG 60.752 66.667 2.18 0.00 0.00 3.95
1522 1652 1.950909 CCACCGTGAAAGCTTTGGTAA 59.049 47.619 18.30 0.00 0.00 2.85
1564 1694 2.586635 TCGGTTGCGTGTGACCAC 60.587 61.111 0.00 0.00 35.63 4.16
1608 1738 7.954539 TCCTTTCTTCCTCCCATCTTATAAT 57.045 36.000 0.00 0.00 0.00 1.28
1610 1740 9.635284 TCCTTTCTTCCTCCCATCTTATAATAT 57.365 33.333 0.00 0.00 0.00 1.28
1683 2001 7.596749 TCGGTTGAGTAAGATTCTTTGATTC 57.403 36.000 3.86 0.00 0.00 2.52
1696 2014 5.180367 TCTTTGATTCAATTGTTCGTGCA 57.820 34.783 5.13 0.00 0.00 4.57
1701 2019 5.868257 TGATTCAATTGTTCGTGCATAGAC 58.132 37.500 5.13 0.00 0.00 2.59
1720 2038 7.116948 GCATAGACACCAGATATGTACATGTTC 59.883 40.741 18.81 14.23 31.04 3.18
1774 2092 6.704050 TGCTTCAATTGCAGCGTAACTATATA 59.296 34.615 22.26 1.09 37.11 0.86
1791 2109 6.473758 ACTATATACATACGGAGCAGTCTCA 58.526 40.000 0.00 0.00 41.13 3.27
1863 2181 1.616865 CTACCACCTTTCACCGTGAGA 59.383 52.381 0.64 0.00 31.36 3.27
1945 2263 7.067496 TCTATGATAAGAACTCCCCAATGTC 57.933 40.000 0.00 0.00 0.00 3.06
1946 2264 4.137116 TGATAAGAACTCCCCAATGTCG 57.863 45.455 0.00 0.00 0.00 4.35
1962 2280 8.746530 CCCCAATGTCGTAGTATATACACTATT 58.253 37.037 15.18 8.63 33.71 1.73
2103 2434 8.741101 TTTCACATTATTAATTGCAGTGTCAC 57.259 30.769 0.00 0.00 0.00 3.67
2145 2476 4.309933 TGCCAATGCTTATGATACTCTCG 58.690 43.478 0.00 0.00 38.71 4.04
2164 2495 4.342092 TCTCGTTGATGCTCTATCCATTCA 59.658 41.667 0.00 0.00 34.77 2.57
2166 2497 5.233225 TCGTTGATGCTCTATCCATTCATC 58.767 41.667 0.00 0.00 34.77 2.92
2170 2503 7.386025 CGTTGATGCTCTATCCATTCATCTTTA 59.614 37.037 0.00 0.00 35.74 1.85
2179 2512 8.267183 TCTATCCATTCATCTTTACTTTGCTCA 58.733 33.333 0.00 0.00 0.00 4.26
2212 2697 1.408127 CGCATACCATCTCCAAACCCA 60.408 52.381 0.00 0.00 0.00 4.51
2264 2749 1.714899 CGTGGCCAACCGAATCATCC 61.715 60.000 7.24 0.00 39.70 3.51
2277 2766 4.446371 CGAATCATCCTACTGCTTTCCTT 58.554 43.478 0.00 0.00 0.00 3.36
2318 2807 6.284459 AGTGATGTAAGCAAGCTATAAGGAC 58.716 40.000 0.00 0.00 28.10 3.85
2326 2815 6.944234 AGCAAGCTATAAGGACCAAAATAC 57.056 37.500 0.00 0.00 0.00 1.89
2354 2855 6.609237 TTTTCACTGAGTTGAATGAGAGTG 57.391 37.500 0.00 0.00 35.42 3.51
2355 2856 5.535753 TTCACTGAGTTGAATGAGAGTGA 57.464 39.130 0.00 0.00 38.39 3.41
2356 2857 5.131594 TCACTGAGTTGAATGAGAGTGAG 57.868 43.478 0.00 0.00 35.94 3.51
2357 2858 4.021632 TCACTGAGTTGAATGAGAGTGAGG 60.022 45.833 0.00 0.00 35.94 3.86
2358 2859 4.021632 CACTGAGTTGAATGAGAGTGAGGA 60.022 45.833 0.00 0.00 34.06 3.71
2359 2860 4.776837 ACTGAGTTGAATGAGAGTGAGGAT 59.223 41.667 0.00 0.00 0.00 3.24
2360 2861 5.082251 TGAGTTGAATGAGAGTGAGGATG 57.918 43.478 0.00 0.00 0.00 3.51
2361 2862 4.774200 TGAGTTGAATGAGAGTGAGGATGA 59.226 41.667 0.00 0.00 0.00 2.92
2362 2863 5.424573 TGAGTTGAATGAGAGTGAGGATGAT 59.575 40.000 0.00 0.00 0.00 2.45
2365 2866 6.041865 AGTTGAATGAGAGTGAGGATGATAGG 59.958 42.308 0.00 0.00 0.00 2.57
2376 2877 4.413189 TGAGGATGATAGGGAATGAAAGCA 59.587 41.667 0.00 0.00 0.00 3.91
2391 2892 8.730680 GGAATGAAAGCAAGTTGTAGAATAAGA 58.269 33.333 4.48 0.00 0.00 2.10
2395 2896 4.184629 AGCAAGTTGTAGAATAAGAGCCG 58.815 43.478 4.48 0.00 0.00 5.52
2414 3219 0.173708 GGCTCTAACACGGACTCCAG 59.826 60.000 0.00 0.00 0.00 3.86
2439 3244 6.128172 GGAAACATTGTGAGAGTGTAAGATGG 60.128 42.308 0.00 0.00 0.00 3.51
2445 3250 4.532126 TGTGAGAGTGTAAGATGGGTCATT 59.468 41.667 0.00 0.00 0.00 2.57
2505 3310 8.444783 ACCATACATATTGGCTATTAGGTTGAA 58.555 33.333 0.00 0.00 37.81 2.69
2534 3339 7.390027 AGATGATATGTCAACAAGGTATAGCC 58.610 38.462 0.00 0.00 38.01 3.93
2537 3342 7.517320 TGATATGTCAACAAGGTATAGCCATT 58.483 34.615 0.00 0.00 40.61 3.16
2583 3388 4.020751 TGCTCTAAGCTCATGACACTTCTT 60.021 41.667 9.05 3.14 42.97 2.52
2604 3409 5.598417 TCTTCCTTTGGATCATATCGAGACA 59.402 40.000 0.00 0.00 0.00 3.41
2633 3439 0.178987 TCTCCTAGCTCCGTCCCATC 60.179 60.000 0.00 0.00 0.00 3.51
2642 3448 0.826256 TCCGTCCCATCCAGTATCGG 60.826 60.000 0.00 0.00 38.16 4.18
2644 3450 1.464376 CGTCCCATCCAGTATCGGCT 61.464 60.000 0.00 0.00 0.00 5.52
2665 3471 0.032017 AGGAAGGCCACGACCTATCT 60.032 55.000 5.01 0.00 39.93 1.98
2669 3475 1.049289 AGGCCACGACCTATCTTCCC 61.049 60.000 5.01 0.00 38.67 3.97
2673 3479 1.762957 CCACGACCTATCTTCCCACAT 59.237 52.381 0.00 0.00 0.00 3.21
2681 3487 4.728860 ACCTATCTTCCCACATGAAAGGAT 59.271 41.667 0.00 0.00 0.00 3.24
2682 3488 5.163152 ACCTATCTTCCCACATGAAAGGATC 60.163 44.000 0.00 0.00 0.00 3.36
2700 3506 1.145598 CGATGCATCTGGCTGAGGT 59.854 57.895 23.73 0.00 45.15 3.85
2706 3512 0.322277 CATCTGGCTGAGGTGCAGTT 60.322 55.000 0.00 0.00 46.62 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.840890 AAGCGGCGATTTCAATAACAA 57.159 38.095 12.98 0.00 0.00 2.83
43 44 6.927294 ATGAATAGATCGAAAGTTTCCCAC 57.073 37.500 10.01 1.93 0.00 4.61
45 46 8.458843 TGAAAATGAATAGATCGAAAGTTTCCC 58.541 33.333 10.01 0.29 0.00 3.97
46 47 9.840427 TTGAAAATGAATAGATCGAAAGTTTCC 57.160 29.630 10.01 0.00 0.00 3.13
62 64 6.587206 TGTACTGCCATGATTGAAAATGAA 57.413 33.333 0.00 0.00 0.00 2.57
67 69 4.068599 TCGTTGTACTGCCATGATTGAAA 58.931 39.130 0.00 0.00 0.00 2.69
69 71 3.326836 TCGTTGTACTGCCATGATTGA 57.673 42.857 0.00 0.00 0.00 2.57
70 72 3.188254 TGTTCGTTGTACTGCCATGATTG 59.812 43.478 0.00 0.00 0.00 2.67
118 120 3.609644 CGTCGCTAGGTGGTCTATGAATC 60.610 52.174 0.00 0.00 0.00 2.52
142 144 0.099436 GCTTGCTTCGGTGCTTATGG 59.901 55.000 2.64 0.00 0.00 2.74
143 145 0.099436 GGCTTGCTTCGGTGCTTATG 59.901 55.000 2.64 0.00 0.00 1.90
216 219 3.204526 CGACTTCCCGACTGTCTACTAT 58.795 50.000 6.21 0.00 0.00 2.12
234 237 1.153881 GGGGTCTTAGCACGACGAC 60.154 63.158 0.00 0.00 32.24 4.34
281 284 1.731720 AACTTCTCTTCATCGGCAGC 58.268 50.000 0.00 0.00 0.00 5.25
290 293 8.871686 GATCCTTCTGATCTAAACTTCTCTTC 57.128 38.462 0.00 0.00 45.46 2.87
306 309 4.453819 GTGTCTTCAAGTTGGATCCTTCTG 59.546 45.833 14.23 5.41 0.00 3.02
315 318 4.898829 TGTTCATGTGTCTTCAAGTTGG 57.101 40.909 2.34 0.00 0.00 3.77
316 319 5.230726 GCTTTGTTCATGTGTCTTCAAGTTG 59.769 40.000 0.00 0.00 0.00 3.16
320 323 3.068024 GGGCTTTGTTCATGTGTCTTCAA 59.932 43.478 0.00 0.00 0.00 2.69
361 364 2.131776 TTGGTCGGTGGTTGTCTTTT 57.868 45.000 0.00 0.00 0.00 2.27
373 376 3.615110 CGGATCTCATAGGATTTGGTCGG 60.615 52.174 0.00 0.00 0.00 4.79
374 377 3.579709 CGGATCTCATAGGATTTGGTCG 58.420 50.000 0.00 0.00 0.00 4.79
375 378 3.866449 GCCGGATCTCATAGGATTTGGTC 60.866 52.174 5.05 0.00 0.00 4.02
378 381 2.029020 TCGCCGGATCTCATAGGATTTG 60.029 50.000 5.05 0.00 0.00 2.32
379 382 2.248248 TCGCCGGATCTCATAGGATTT 58.752 47.619 5.05 0.00 0.00 2.17
394 397 2.432628 GGAGGTGTGTCTTCGCCG 60.433 66.667 0.00 0.00 42.18 6.46
468 499 2.219325 GAGTCTGTGTCCTGCTCGGG 62.219 65.000 0.00 0.00 0.00 5.14
470 501 1.214062 GGAGTCTGTGTCCTGCTCG 59.786 63.158 0.00 0.00 0.00 5.03
519 551 0.914417 GGTCCTTGTCATGGGAGGGA 60.914 60.000 4.99 1.92 31.66 4.20
521 553 1.221840 CGGTCCTTGTCATGGGAGG 59.778 63.158 4.99 0.00 31.66 4.30
529 561 0.739813 CGTGAATCCCGGTCCTTGTC 60.740 60.000 0.00 0.00 0.00 3.18
541 632 1.009829 GTCATGGGTGAGCGTGAATC 58.990 55.000 0.00 0.00 34.36 2.52
602 694 0.679960 CTAGGGTTTTTGCCTCCCGG 60.680 60.000 0.00 0.00 45.27 5.73
612 707 2.026636 TGTAATCTGCGGCTAGGGTTTT 60.027 45.455 0.00 0.00 0.00 2.43
640 735 3.890936 GAAGCCACAGAGCAGCGGT 62.891 63.158 0.00 0.00 34.23 5.68
666 761 2.403252 ACAATGAACTCGCCCTAAGG 57.597 50.000 0.00 0.00 0.00 2.69
667 762 2.348666 CGAACAATGAACTCGCCCTAAG 59.651 50.000 0.00 0.00 0.00 2.18
728 823 2.356135 GATTTTAACCTGCTGCGAGGA 58.644 47.619 20.14 3.09 36.51 3.71
990 1102 4.713824 ATATATGTATGTGGTAGCGCGT 57.286 40.909 8.43 5.41 0.00 6.01
991 1103 4.974275 GGTATATATGTATGTGGTAGCGCG 59.026 45.833 0.00 0.00 0.00 6.86
1051 1163 2.334946 GGCTGCGATGGAAACTGCA 61.335 57.895 0.00 0.00 35.75 4.41
1054 1166 0.107654 GTAGGGCTGCGATGGAAACT 60.108 55.000 0.00 0.00 0.00 2.66
1075 1187 2.348362 CGACGCTGCTGAATTATCAACA 59.652 45.455 0.00 0.00 34.49 3.33
1148 1260 1.218316 CTACTTCTTCGGCGGCCTT 59.782 57.895 18.34 0.00 0.00 4.35
1155 1267 2.092321 TCTCCTCCCTCTACTTCTTCGG 60.092 54.545 0.00 0.00 0.00 4.30
1157 1269 3.970842 TGTCTCCTCCCTCTACTTCTTC 58.029 50.000 0.00 0.00 0.00 2.87
1330 1454 1.452833 GGCCCACTTCCTGATCTGC 60.453 63.158 0.00 0.00 0.00 4.26
1522 1652 4.217983 CGGTCAAGGAGTACTCTTGTAAGT 59.782 45.833 21.88 0.00 41.52 2.24
1564 1694 5.897050 AGGAAGAAGCTGAATAACTCTACG 58.103 41.667 0.00 0.00 0.00 3.51
1575 1705 3.008485 GGAGGAAGAAAGGAAGAAGCTGA 59.992 47.826 0.00 0.00 0.00 4.26
1683 2001 3.188254 TGGTGTCTATGCACGAACAATTG 59.812 43.478 3.24 3.24 40.08 2.32
1696 2014 8.250143 TGAACATGTACATATCTGGTGTCTAT 57.750 34.615 8.32 0.00 0.00 1.98
1736 2054 5.180868 GCAATTGAAGCATCCATAGTAGGAG 59.819 44.000 10.34 0.00 41.90 3.69
1743 2061 3.720949 GCTGCAATTGAAGCATCCATA 57.279 42.857 30.12 0.00 46.14 2.74
1774 2092 2.223595 CGATTGAGACTGCTCCGTATGT 60.224 50.000 0.00 0.00 40.55 2.29
2092 2423 5.008118 TGAAAAATATGACGTGACACTGCAA 59.992 36.000 3.68 0.00 0.00 4.08
2103 2434 7.015226 TGGCATCTAAGTGAAAAATATGACG 57.985 36.000 0.00 0.00 0.00 4.35
2145 2476 7.507733 AAAGATGAATGGATAGAGCATCAAC 57.492 36.000 0.00 0.00 38.19 3.18
2170 2503 6.072728 TGCGTGATTAAAGTTATGAGCAAAGT 60.073 34.615 0.00 0.00 0.00 2.66
2179 2512 7.387948 GGAGATGGTATGCGTGATTAAAGTTAT 59.612 37.037 0.00 0.00 0.00 1.89
2212 2697 0.249868 CATCGGGTATGCACGGATGT 60.250 55.000 5.38 0.00 42.74 3.06
2249 2734 2.213499 CAGTAGGATGATTCGGTTGGC 58.787 52.381 0.00 0.00 0.00 4.52
2251 2736 3.185246 AGCAGTAGGATGATTCGGTTG 57.815 47.619 0.00 0.00 0.00 3.77
2254 2739 3.134458 GGAAAGCAGTAGGATGATTCGG 58.866 50.000 0.00 0.00 0.00 4.30
2255 2740 4.065321 AGGAAAGCAGTAGGATGATTCG 57.935 45.455 0.00 0.00 0.00 3.34
2351 2852 5.455899 GCTTTCATTCCCTATCATCCTCACT 60.456 44.000 0.00 0.00 0.00 3.41
2352 2853 4.759183 GCTTTCATTCCCTATCATCCTCAC 59.241 45.833 0.00 0.00 0.00 3.51
2353 2854 4.413189 TGCTTTCATTCCCTATCATCCTCA 59.587 41.667 0.00 0.00 0.00 3.86
2354 2855 4.978099 TGCTTTCATTCCCTATCATCCTC 58.022 43.478 0.00 0.00 0.00 3.71
2355 2856 5.103771 ACTTGCTTTCATTCCCTATCATCCT 60.104 40.000 0.00 0.00 0.00 3.24
2356 2857 5.136105 ACTTGCTTTCATTCCCTATCATCC 58.864 41.667 0.00 0.00 0.00 3.51
2357 2858 6.096001 ACAACTTGCTTTCATTCCCTATCATC 59.904 38.462 0.00 0.00 0.00 2.92
2358 2859 5.954150 ACAACTTGCTTTCATTCCCTATCAT 59.046 36.000 0.00 0.00 0.00 2.45
2359 2860 5.324409 ACAACTTGCTTTCATTCCCTATCA 58.676 37.500 0.00 0.00 0.00 2.15
2360 2861 5.904362 ACAACTTGCTTTCATTCCCTATC 57.096 39.130 0.00 0.00 0.00 2.08
2361 2862 6.721318 TCTACAACTTGCTTTCATTCCCTAT 58.279 36.000 0.00 0.00 0.00 2.57
2362 2863 6.121776 TCTACAACTTGCTTTCATTCCCTA 57.878 37.500 0.00 0.00 0.00 3.53
2365 2866 8.730680 TCTTATTCTACAACTTGCTTTCATTCC 58.269 33.333 0.00 0.00 0.00 3.01
2376 2877 3.197983 AGCCGGCTCTTATTCTACAACTT 59.802 43.478 27.08 0.00 0.00 2.66
2391 2892 2.678934 TCCGTGTTAGAGCCGGCT 60.679 61.111 33.48 33.48 41.46 5.52
2395 2896 0.173708 CTGGAGTCCGTGTTAGAGCC 59.826 60.000 4.30 0.00 0.00 4.70
2400 2901 2.040939 TGTTTCCTGGAGTCCGTGTTA 58.959 47.619 4.30 0.00 0.00 2.41
2402 2903 1.056660 ATGTTTCCTGGAGTCCGTGT 58.943 50.000 4.30 0.00 0.00 4.49
2414 3219 6.128172 CCATCTTACACTCTCACAATGTTTCC 60.128 42.308 0.00 0.00 0.00 3.13
2515 3320 8.029782 AGTAATGGCTATACCTTGTTGACATA 57.970 34.615 0.00 0.00 40.22 2.29
2519 3324 6.119536 CCAAGTAATGGCTATACCTTGTTGA 58.880 40.000 15.72 0.00 43.80 3.18
2534 3339 8.958119 TTGGTTAATAGTAGAGCCAAGTAATG 57.042 34.615 0.00 0.00 32.88 1.90
2537 3342 6.990349 GCATTGGTTAATAGTAGAGCCAAGTA 59.010 38.462 8.51 0.00 39.04 2.24
2583 3388 4.895889 AGTGTCTCGATATGATCCAAAGGA 59.104 41.667 0.00 0.00 35.55 3.36
2633 3439 1.270358 GCCTTCCTAAGCCGATACTGG 60.270 57.143 0.00 0.00 0.00 4.00
2642 3448 1.449778 GGTCGTGGCCTTCCTAAGC 60.450 63.158 3.32 0.00 0.00 3.09
2644 3450 2.037144 GATAGGTCGTGGCCTTCCTAA 58.963 52.381 3.32 0.00 39.94 2.69
2665 3471 3.544684 CATCGATCCTTTCATGTGGGAA 58.455 45.455 0.00 0.00 32.53 3.97
2669 3475 3.813724 AGATGCATCGATCCTTTCATGTG 59.186 43.478 20.67 0.00 0.00 3.21
2673 3479 2.842457 CCAGATGCATCGATCCTTTCA 58.158 47.619 20.67 0.00 0.00 2.69
2681 3487 1.332889 ACCTCAGCCAGATGCATCGA 61.333 55.000 20.67 10.61 44.83 3.59
2682 3488 1.145598 ACCTCAGCCAGATGCATCG 59.854 57.895 20.67 14.92 44.83 3.84
2706 3512 1.963855 CGGCCATGGTTGTCGTTCA 60.964 57.895 14.67 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.