Multiple sequence alignment - TraesCS6A01G231500

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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 TraesCS6A01G231500 chr6A 100.000 3350 0 0 1 3350 437020204 437023553 0.000000e+00 6187.0
1 TraesCS6A01G231500 chr6D 95.983 1892 45 6 522 2393 288542319 288540439 0.000000e+00 3044.0
2 TraesCS6A01G231500 chr6D 84.554 505 44 13 2392 2872 288540145 288539651 1.410000e-128 470.0
3 TraesCS6A01G231500 chr6D 86.199 442 48 9 3 437 288542899 288542464 1.820000e-127 466.0
4 TraesCS6A01G231500 chr6D 85.833 120 14 1 3234 3350 288539378 288539259 1.260000e-24 124.0
5 TraesCS6A01G231500 chr6D 100.000 44 0 0 498 541 288542375 288542332 7.700000e-12 82.4
6 TraesCS6A01G231500 chr6B 94.577 1973 67 14 498 2449 448668796 448666843 0.000000e+00 3014.0
7 TraesCS6A01G231500 chr6B 87.514 873 82 13 2503 3349 448666599 448665728 0.000000e+00 983.0
8 TraesCS6A01G231500 chr6B 84.328 268 37 3 2 265 448669530 448669264 1.190000e-64 257.0
9 TraesCS6A01G231500 chr6B 86.620 142 18 1 3050 3191 703681420 703681560 4.480000e-34 156.0
10 TraesCS6A01G231500 chr2A 83.308 1336 200 18 1032 2351 600529951 600528623 0.000000e+00 1210.0
11 TraesCS6A01G231500 chr2D 82.689 1346 197 23 1034 2351 457255779 457254442 0.000000e+00 1162.0
12 TraesCS6A01G231500 chr2D 85.906 149 21 0 3050 3198 252144576 252144724 3.460000e-35 159.0
13 TraesCS6A01G231500 chr2D 85.714 147 21 0 3050 3196 612651114 612651260 4.480000e-34 156.0
14 TraesCS6A01G231500 chr2B 82.638 1342 204 21 1032 2351 538012152 538010818 0.000000e+00 1160.0
15 TraesCS6A01G231500 chr2B 86.577 149 20 0 3050 3198 636775465 636775613 7.440000e-37 165.0
16 TraesCS6A01G231500 chrUn 88.740 373 38 4 1166 1536 479365935 479365565 1.420000e-123 453.0
17 TraesCS6A01G231500 chrUn 84.810 158 23 1 3050 3207 45262139 45261983 1.240000e-34 158.0
18 TraesCS6A01G231500 chr1B 77.691 511 96 15 1047 1545 632634803 632634299 2.530000e-76 296.0
19 TraesCS6A01G231500 chr7B 76.981 530 87 23 1047 1545 74299826 74300351 1.530000e-68 270.0
20 TraesCS6A01G231500 chr1A 76.758 512 98 17 1047 1545 551680504 551680001 1.980000e-67 267.0
21 TraesCS6A01G231500 chr7D 76.723 537 81 31 1047 1545 114818050 114818580 3.320000e-65 259.0
22 TraesCS6A01G231500 chr3B 87.075 147 17 2 3050 3196 519399171 519399315 7.440000e-37 165.0
23 TraesCS6A01G231500 chr3B 88.312 77 7 2 46 121 488880759 488880684 1.280000e-14 91.6
24 TraesCS6A01G231500 chr3D 85.443 158 22 1 3050 3207 554769073 554769229 2.670000e-36 163.0
25 TraesCS6A01G231500 chr3D 79.500 200 30 8 29 220 134822164 134822360 7.540000e-27 132.0
26 TraesCS6A01G231500 chr4A 84.615 156 24 0 3050 3205 674523544 674523389 4.480000e-34 156.0
27 TraesCS6A01G231500 chr5D 85.271 129 16 3 12 139 75356359 75356233 2.710000e-26 130.0


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 TraesCS6A01G231500 chr6A 437020204 437023553 3349 False 6187.00 6187 100.000000 1 3350 1 chr6A.!!$F1 3349
1 TraesCS6A01G231500 chr6D 288539259 288542899 3640 True 837.28 3044 90.513800 3 3350 5 chr6D.!!$R1 3347
2 TraesCS6A01G231500 chr6B 448665728 448669530 3802 True 1418.00 3014 88.806333 2 3349 3 chr6B.!!$R1 3347
3 TraesCS6A01G231500 chr2A 600528623 600529951 1328 True 1210.00 1210 83.308000 1032 2351 1 chr2A.!!$R1 1319
4 TraesCS6A01G231500 chr2D 457254442 457255779 1337 True 1162.00 1162 82.689000 1034 2351 1 chr2D.!!$R1 1317
5 TraesCS6A01G231500 chr2B 538010818 538012152 1334 True 1160.00 1160 82.638000 1032 2351 1 chr2B.!!$R1 1319
6 TraesCS6A01G231500 chr1B 632634299 632634803 504 True 296.00 296 77.691000 1047 1545 1 chr1B.!!$R1 498
7 TraesCS6A01G231500 chr7B 74299826 74300351 525 False 270.00 270 76.981000 1047 1545 1 chr7B.!!$F1 498
8 TraesCS6A01G231500 chr1A 551680001 551680504 503 True 267.00 267 76.758000 1047 1545 1 chr1A.!!$R1 498
9 TraesCS6A01G231500 chr7D 114818050 114818580 530 False 259.00 259 76.723000 1047 1545 1 chr7D.!!$F1 498

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
462 777 0.027716 CGACCTGACGATACAGACCG 59.972 60.0 9.63 8.57 39.94 4.79 F
469 784 0.245539 ACGATACAGACCGTTGTGGG 59.754 55.0 0.00 0.00 44.64 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 2311 1.379044 CCGGAAATCCAGCAGGCTT 60.379 57.895 0.0 0.0 35.14 4.35 R
2351 2775 1.618343 TCCTCGCACAAGATGACAAGA 59.382 47.619 0.0 0.0 0.00 3.02 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
63 64 2.038557 ACAGAGAGGTGTTTAATGCCGT 59.961 45.455 0.00 0.00 0.00 5.68
67 69 0.322322 AGGTGTTTAATGCCGTCGGA 59.678 50.000 17.49 0.00 0.00 4.55
115 117 0.809385 CACCGGAGTAGCTTTCTCGA 59.191 55.000 9.46 0.00 33.26 4.04
121 123 2.030185 GGAGTAGCTTTCTCGACACACA 60.030 50.000 0.00 0.00 33.26 3.72
123 125 2.059541 GTAGCTTTCTCGACACACACC 58.940 52.381 0.00 0.00 0.00 4.16
125 127 1.557443 GCTTTCTCGACACACACCCG 61.557 60.000 0.00 0.00 0.00 5.28
139 141 1.035385 CACCCGGGTTTAATGGAGGC 61.035 60.000 27.83 0.00 0.00 4.70
165 167 3.013921 GGGTAGACGGATGCAATTTCAA 58.986 45.455 0.00 0.00 0.00 2.69
169 171 5.295787 GGTAGACGGATGCAATTTCAATGTA 59.704 40.000 0.00 0.00 0.00 2.29
184 186 3.506067 TCAATGTAGAGAGAAGACGTGCA 59.494 43.478 0.00 0.00 0.00 4.57
239 245 2.202479 CGCGAGCGAGATGTCACA 60.202 61.111 12.58 0.00 42.83 3.58
241 247 0.317020 CGCGAGCGAGATGTCACATA 60.317 55.000 12.58 0.00 42.83 2.29
242 248 1.664302 CGCGAGCGAGATGTCACATAT 60.664 52.381 12.58 0.00 42.83 1.78
248 254 5.560953 CGAGCGAGATGTCACATATGTTCTA 60.561 44.000 5.37 0.00 0.00 2.10
255 261 3.641436 TGTCACATATGTTCTAGGCCGAT 59.359 43.478 5.37 0.00 0.00 4.18
281 319 3.795638 GGAACGGCCGCTTTAGAG 58.204 61.111 28.58 0.00 0.00 2.43
282 320 1.079336 GGAACGGCCGCTTTAGAGT 60.079 57.895 28.58 0.00 0.00 3.24
283 321 1.359459 GGAACGGCCGCTTTAGAGTG 61.359 60.000 28.58 0.00 0.00 3.51
284 322 1.967597 GAACGGCCGCTTTAGAGTGC 61.968 60.000 28.58 0.00 31.93 4.40
285 323 3.195698 CGGCCGCTTTAGAGTGCC 61.196 66.667 14.67 6.05 38.67 5.01
286 324 2.046314 GGCCGCTTTAGAGTGCCA 60.046 61.111 9.98 0.00 40.50 4.92
287 325 1.452108 GGCCGCTTTAGAGTGCCAT 60.452 57.895 9.98 0.00 40.50 4.40
288 326 1.718757 GGCCGCTTTAGAGTGCCATG 61.719 60.000 9.98 0.00 40.50 3.66
289 327 0.744414 GCCGCTTTAGAGTGCCATGA 60.744 55.000 0.00 0.00 31.93 3.07
290 328 1.737838 CCGCTTTAGAGTGCCATGAA 58.262 50.000 0.00 0.00 31.93 2.57
291 329 2.292267 CCGCTTTAGAGTGCCATGAAT 58.708 47.619 0.00 0.00 31.93 2.57
292 330 3.466836 CCGCTTTAGAGTGCCATGAATA 58.533 45.455 0.00 0.00 31.93 1.75
293 331 4.067896 CCGCTTTAGAGTGCCATGAATAT 58.932 43.478 0.00 0.00 31.93 1.28
294 332 4.083643 CCGCTTTAGAGTGCCATGAATATG 60.084 45.833 0.00 0.00 31.93 1.78
311 349 3.459063 GGGTAGCTCGCTTCGGGT 61.459 66.667 0.00 0.00 0.00 5.28
318 356 1.078426 CTCGCTTCGGGTGGGAAAT 60.078 57.895 0.00 0.00 0.00 2.17
328 366 4.794648 TGGGAAATGGCGCGGGAG 62.795 66.667 8.83 0.00 0.00 4.30
332 370 3.385749 GAAATGGCGCGGGAGAGGA 62.386 63.158 8.83 0.00 0.00 3.71
355 393 3.863606 TTTTTGGGCGGGACAAGG 58.136 55.556 0.00 0.00 0.00 3.61
356 394 2.503382 TTTTTGGGCGGGACAAGGC 61.503 57.895 0.00 0.00 0.00 4.35
357 395 3.740495 TTTTGGGCGGGACAAGGCA 62.740 57.895 0.00 0.00 35.71 4.75
366 404 1.673665 GGACAAGGCAGGCAGTCAG 60.674 63.158 17.60 0.00 32.79 3.51
391 429 1.221840 GTGTGGCAGTGATCCGGAT 59.778 57.895 19.21 19.21 0.00 4.18
394 432 0.249911 GTGGCAGTGATCCGGATACC 60.250 60.000 19.15 14.15 0.00 2.73
395 433 1.371558 GGCAGTGATCCGGATACCC 59.628 63.158 19.15 9.56 0.00 3.69
415 453 2.159379 CCGCAAAGCCCTCTAATTTGTC 60.159 50.000 0.00 0.00 36.52 3.18
417 455 3.426695 CGCAAAGCCCTCTAATTTGTCTG 60.427 47.826 0.00 0.00 36.52 3.51
418 456 3.119352 GCAAAGCCCTCTAATTTGTCTGG 60.119 47.826 0.00 0.00 36.52 3.86
419 457 4.082125 CAAAGCCCTCTAATTTGTCTGGT 58.918 43.478 0.00 0.00 0.00 4.00
420 458 4.388577 AAGCCCTCTAATTTGTCTGGTT 57.611 40.909 0.00 0.00 0.00 3.67
422 460 4.082125 AGCCCTCTAATTTGTCTGGTTTG 58.918 43.478 0.00 0.00 0.00 2.93
423 461 3.367395 GCCCTCTAATTTGTCTGGTTTGC 60.367 47.826 0.00 0.00 0.00 3.68
445 487 3.062585 AAAAACACGTCGGAACCGA 57.937 47.368 12.04 12.04 46.87 4.69
453 768 2.281692 TCGGAACCGACCTGACGA 60.282 61.111 12.04 0.00 44.01 4.20
455 770 0.392863 TCGGAACCGACCTGACGATA 60.393 55.000 12.04 0.00 44.01 2.92
458 773 1.202268 GGAACCGACCTGACGATACAG 60.202 57.143 0.00 0.00 37.61 2.74
461 776 0.381089 CCGACCTGACGATACAGACC 59.619 60.000 9.63 2.50 39.94 3.85
462 777 0.027716 CGACCTGACGATACAGACCG 59.972 60.000 9.63 8.57 39.94 4.79
466 781 1.201647 CCTGACGATACAGACCGTTGT 59.798 52.381 9.63 0.00 39.30 3.32
469 784 0.245539 ACGATACAGACCGTTGTGGG 59.754 55.000 0.00 0.00 44.64 4.61
480 795 1.362355 GTTGTGGGCGGTTTGAAGG 59.638 57.895 0.00 0.00 0.00 3.46
483 798 1.362355 GTGGGCGGTTTGAAGGTTG 59.638 57.895 0.00 0.00 0.00 3.77
491 806 2.661718 GGTTTGAAGGTTGGTTGGAGA 58.338 47.619 0.00 0.00 0.00 3.71
492 807 3.230976 GGTTTGAAGGTTGGTTGGAGAT 58.769 45.455 0.00 0.00 0.00 2.75
493 808 3.005791 GGTTTGAAGGTTGGTTGGAGATG 59.994 47.826 0.00 0.00 0.00 2.90
494 809 2.584835 TGAAGGTTGGTTGGAGATGG 57.415 50.000 0.00 0.00 0.00 3.51
495 810 1.177401 GAAGGTTGGTTGGAGATGGC 58.823 55.000 0.00 0.00 0.00 4.40
496 811 0.251787 AAGGTTGGTTGGAGATGGCC 60.252 55.000 0.00 0.00 0.00 5.36
543 890 2.303022 AGTGGTTCATGATCTTCACCGT 59.697 45.455 8.60 0.00 0.00 4.83
566 913 1.933181 CGAACAGTGAAGTTGCTGTCA 59.067 47.619 9.34 0.00 44.21 3.58
574 921 0.888285 AAGTTGCTGTCAGCCTGCTC 60.888 55.000 21.99 7.82 41.51 4.26
695 1042 3.792047 CGCACCGCACTCACCATG 61.792 66.667 0.00 0.00 0.00 3.66
705 1052 2.417924 GCACTCACCATGACGAGAAGAT 60.418 50.000 15.70 0.00 33.33 2.40
754 1107 1.084289 GTAAACAAATCCCTCGCGCT 58.916 50.000 5.56 0.00 0.00 5.92
810 1163 4.440127 GAACGCCGCCGACCCTTA 62.440 66.667 0.00 0.00 38.29 2.69
828 1181 2.851263 TATTGCGTCCAAGGAACAGT 57.149 45.000 0.00 0.00 33.80 3.55
1014 1384 1.741401 GACTATGTGCACGCCAGCA 60.741 57.895 13.13 0.00 43.35 4.41
1890 2311 2.833794 CGGGCGGATTCTTCTTTCATA 58.166 47.619 0.00 0.00 0.00 2.15
2348 2772 2.734591 GCCACCGCCGATCATCTA 59.265 61.111 0.00 0.00 0.00 1.98
2351 2775 0.389391 CCACCGCCGATCATCTAACT 59.611 55.000 0.00 0.00 0.00 2.24
2352 2776 1.603172 CCACCGCCGATCATCTAACTC 60.603 57.143 0.00 0.00 0.00 3.01
2353 2777 1.338337 CACCGCCGATCATCTAACTCT 59.662 52.381 0.00 0.00 0.00 3.24
2354 2778 2.032620 ACCGCCGATCATCTAACTCTT 58.967 47.619 0.00 0.00 0.00 2.85
2355 2779 2.223829 ACCGCCGATCATCTAACTCTTG 60.224 50.000 0.00 0.00 0.00 3.02
2356 2780 2.223829 CCGCCGATCATCTAACTCTTGT 60.224 50.000 0.00 0.00 0.00 3.16
2357 2781 3.046390 CGCCGATCATCTAACTCTTGTC 58.954 50.000 0.00 0.00 0.00 3.18
2358 2782 3.489229 CGCCGATCATCTAACTCTTGTCA 60.489 47.826 0.00 0.00 0.00 3.58
2501 3242 9.492973 ACTTGTATTTCCAATTCCAAAAATGAG 57.507 29.630 0.00 0.00 0.00 2.90
2534 3444 5.105351 TGAGTGGAGTGTTGTCATTATCGAT 60.105 40.000 2.16 2.16 0.00 3.59
2568 3478 6.939551 ATTGTCAATTCTTTGCGATTTCAG 57.060 33.333 0.00 0.00 32.61 3.02
2607 3517 7.404671 AAATTGACCCTCCATACAATACAAC 57.595 36.000 0.00 0.00 33.50 3.32
2673 3606 6.994221 TGAATTTATTTTAGGGTTTTCGGCA 58.006 32.000 0.00 0.00 0.00 5.69
2711 3644 7.060864 GTGAAAGTAGATGTTCTCGTTGACTAC 59.939 40.741 0.00 0.00 0.00 2.73
2738 3671 7.646922 GGAACGTCTATAATGACTACGTCAATT 59.353 37.037 0.00 0.00 45.96 2.32
2740 3673 8.922058 ACGTCTATAATGACTACGTCAATTTT 57.078 30.769 0.00 0.00 45.96 1.82
2768 3701 7.856145 ATATTATGCCAGCTCAGTATTTAGC 57.144 36.000 0.00 0.00 39.08 3.09
2781 3715 5.303589 TCAGTATTTAGCGGTGCTTATAGGT 59.696 40.000 0.00 0.00 40.44 3.08
2786 3720 9.080915 GTATTTAGCGGTGCTTATAGGTATAAC 57.919 37.037 0.00 0.00 40.44 1.89
2815 3749 2.487934 ACATGCGCTCATAAGGATGAC 58.512 47.619 9.73 0.00 37.15 3.06
2817 3751 3.321968 ACATGCGCTCATAAGGATGACTA 59.678 43.478 9.73 0.00 37.15 2.59
2844 3778 2.935849 CAGCATCTGCAATTGTACCGTA 59.064 45.455 7.40 0.00 45.16 4.02
2852 3786 7.618502 TCTGCAATTGTACCGTATTAACATT 57.381 32.000 7.40 0.00 0.00 2.71
2936 3906 8.707796 TTCCTATGTTTGTGGGTTAATGTTTA 57.292 30.769 0.00 0.00 0.00 2.01
2966 3936 4.115516 GTGAGCGCAAGATATCTCTTCAA 58.884 43.478 11.47 0.00 39.78 2.69
2967 3937 4.026145 GTGAGCGCAAGATATCTCTTCAAC 60.026 45.833 11.47 0.00 39.78 3.18
2983 3953 6.369890 TCTCTTCAACACTGATGAATAAGTGC 59.630 38.462 7.60 0.00 46.28 4.40
3021 3991 7.233553 CAGGAGGTCATACTAAATCATGGACTA 59.766 40.741 0.00 0.00 0.00 2.59
3022 3992 7.789831 AGGAGGTCATACTAAATCATGGACTAA 59.210 37.037 0.00 0.00 0.00 2.24
3023 3993 8.598041 GGAGGTCATACTAAATCATGGACTAAT 58.402 37.037 0.00 0.00 0.00 1.73
3037 4007 6.609616 TCATGGACTAATTTAAAATGTCCCCC 59.390 38.462 23.09 9.06 44.60 5.40
3038 4008 6.160483 TGGACTAATTTAAAATGTCCCCCT 57.840 37.500 23.09 0.00 44.60 4.79
3043 4036 7.013834 ACTAATTTAAAATGTCCCCCTGAACA 58.986 34.615 0.00 0.00 0.00 3.18
3079 4072 5.392286 TGTTAAAACACGACAACTTTGTCC 58.608 37.500 14.96 0.71 43.02 4.02
3082 4075 9.336850 TGTTAAAACACGACAACTTTGTCCCAA 62.337 37.037 14.96 0.00 43.02 4.12
3151 4144 6.470877 TGAACTAAAGTTGTCATGAAAAACGC 59.529 34.615 13.91 0.00 38.56 4.84
3152 4145 5.278604 ACTAAAGTTGTCATGAAAAACGCC 58.721 37.500 13.91 0.00 0.00 5.68
3156 4149 0.535328 TGTCATGAAAAACGCCCGGA 60.535 50.000 0.73 0.00 0.00 5.14
3161 4154 1.445410 GAAAAACGCCCGGATTGCC 60.445 57.895 0.73 0.00 0.00 4.52
3173 4166 3.432046 CCCGGATTGCCATGCTTAAAATT 60.432 43.478 0.73 0.00 0.00 1.82
3175 4168 3.486841 CGGATTGCCATGCTTAAAATTCG 59.513 43.478 0.00 0.00 0.00 3.34
3176 4169 4.432712 GGATTGCCATGCTTAAAATTCGT 58.567 39.130 0.00 0.00 0.00 3.85
3179 4172 6.144402 GGATTGCCATGCTTAAAATTCGTATG 59.856 38.462 0.00 0.00 0.00 2.39
3183 4176 5.231991 GCCATGCTTAAAATTCGTATGTTGG 59.768 40.000 0.00 0.00 0.00 3.77
3189 4182 7.039270 GCTTAAAATTCGTATGTTGGGGATTT 58.961 34.615 0.00 0.00 0.00 2.17
3198 4191 9.635404 TTCGTATGTTGGGGATTTATTATTTCT 57.365 29.630 0.00 0.00 0.00 2.52
3228 4221 7.166691 TCATACTAACTAGAAGGGTTGTCAC 57.833 40.000 0.00 0.00 0.00 3.67
3229 4222 4.516365 ACTAACTAGAAGGGTTGTCACG 57.484 45.455 0.00 0.00 0.00 4.35
3340 4407 0.394488 TTGGCGGTTTGGTTCTGTGA 60.394 50.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.806434 TCCGCCCGCTATATAAACCTA 58.194 47.619 0.00 0.00 0.00 3.08
63 64 0.742505 ACGTCTGTTCTTGTGTCCGA 59.257 50.000 0.00 0.00 0.00 4.55
67 69 1.651987 CCACACGTCTGTTCTTGTGT 58.348 50.000 0.00 0.00 45.79 3.72
96 98 0.809385 TCGAGAAAGCTACTCCGGTG 59.191 55.000 0.00 0.00 0.00 4.94
97 99 0.810016 GTCGAGAAAGCTACTCCGGT 59.190 55.000 0.00 0.00 0.00 5.28
115 117 1.611519 CATTAAACCCGGGTGTGTGT 58.388 50.000 31.05 8.26 0.00 3.72
121 123 1.305287 GCCTCCATTAAACCCGGGT 59.695 57.895 24.16 24.16 0.00 5.28
123 125 0.751643 CCTGCCTCCATTAAACCCGG 60.752 60.000 0.00 0.00 0.00 5.73
125 127 1.384222 CGCCTGCCTCCATTAAACCC 61.384 60.000 0.00 0.00 0.00 4.11
139 141 2.417516 CATCCGTCTACCCGCCTG 59.582 66.667 0.00 0.00 0.00 4.85
165 167 2.820197 TGTGCACGTCTTCTCTCTACAT 59.180 45.455 13.13 0.00 0.00 2.29
169 171 1.268352 GACTGTGCACGTCTTCTCTCT 59.732 52.381 24.79 0.29 0.00 3.10
225 231 4.615949 AGAACATATGTGACATCTCGCTC 58.384 43.478 9.63 0.00 0.00 5.03
239 245 4.955811 TTGACATCGGCCTAGAACATAT 57.044 40.909 0.00 0.00 0.00 1.78
241 247 3.470709 CATTGACATCGGCCTAGAACAT 58.529 45.455 0.00 0.00 0.00 2.71
242 248 2.905075 CATTGACATCGGCCTAGAACA 58.095 47.619 0.00 0.00 0.00 3.18
248 254 2.514592 CCGCATTGACATCGGCCT 60.515 61.111 0.00 0.00 36.53 5.19
255 261 3.053291 GGCCGTTCCGCATTGACA 61.053 61.111 0.00 0.00 0.00 3.58
265 303 1.967597 GCACTCTAAAGCGGCCGTTC 61.968 60.000 28.70 11.34 0.00 3.95
266 304 2.033194 GCACTCTAAAGCGGCCGTT 61.033 57.895 28.70 20.13 0.00 4.44
267 305 2.434359 GCACTCTAAAGCGGCCGT 60.434 61.111 28.70 9.89 0.00 5.68
268 306 3.195698 GGCACTCTAAAGCGGCCG 61.196 66.667 24.05 24.05 36.78 6.13
269 307 1.452108 ATGGCACTCTAAAGCGGCC 60.452 57.895 0.00 0.00 43.29 6.13
270 308 0.744414 TCATGGCACTCTAAAGCGGC 60.744 55.000 0.00 0.00 0.00 6.53
271 309 1.737838 TTCATGGCACTCTAAAGCGG 58.262 50.000 0.00 0.00 0.00 5.52
272 310 4.083643 CCATATTCATGGCACTCTAAAGCG 60.084 45.833 0.00 0.00 45.29 4.68
273 311 5.368256 CCATATTCATGGCACTCTAAAGC 57.632 43.478 0.00 0.00 45.29 3.51
285 323 3.325293 AGCGAGCTACCCATATTCATG 57.675 47.619 0.00 0.00 0.00 3.07
286 324 3.615110 CGAAGCGAGCTACCCATATTCAT 60.615 47.826 0.00 0.00 0.00 2.57
287 325 2.288213 CGAAGCGAGCTACCCATATTCA 60.288 50.000 0.00 0.00 0.00 2.57
288 326 2.329379 CGAAGCGAGCTACCCATATTC 58.671 52.381 0.00 0.00 0.00 1.75
289 327 1.000955 CCGAAGCGAGCTACCCATATT 59.999 52.381 0.00 0.00 0.00 1.28
290 328 0.603569 CCGAAGCGAGCTACCCATAT 59.396 55.000 0.00 0.00 0.00 1.78
291 329 1.461091 CCCGAAGCGAGCTACCCATA 61.461 60.000 0.00 0.00 0.00 2.74
292 330 2.797278 CCCGAAGCGAGCTACCCAT 61.797 63.158 0.00 0.00 0.00 4.00
293 331 3.458163 CCCGAAGCGAGCTACCCA 61.458 66.667 0.00 0.00 0.00 4.51
294 332 3.459063 ACCCGAAGCGAGCTACCC 61.459 66.667 0.00 0.00 0.00 3.69
295 333 2.202756 CACCCGAAGCGAGCTACC 60.203 66.667 0.00 0.00 0.00 3.18
296 334 2.202756 CCACCCGAAGCGAGCTAC 60.203 66.667 0.00 0.00 0.00 3.58
302 340 2.406616 CCATTTCCCACCCGAAGCG 61.407 63.158 0.00 0.00 0.00 4.68
303 341 2.710902 GCCATTTCCCACCCGAAGC 61.711 63.158 0.00 0.00 0.00 3.86
311 349 4.794648 CTCCCGCGCCATTTCCCA 62.795 66.667 0.00 0.00 0.00 4.37
353 391 2.350514 GCTTCTGACTGCCTGCCT 59.649 61.111 0.00 0.00 0.00 4.75
354 392 3.123620 CGCTTCTGACTGCCTGCC 61.124 66.667 0.00 0.00 0.00 4.85
355 393 3.123620 CCGCTTCTGACTGCCTGC 61.124 66.667 0.00 0.00 0.00 4.85
356 394 2.435586 CCCGCTTCTGACTGCCTG 60.436 66.667 0.00 0.00 0.00 4.85
357 395 2.925170 ACCCGCTTCTGACTGCCT 60.925 61.111 0.00 0.00 0.00 4.75
366 404 3.357079 CACTGCCACACCCGCTTC 61.357 66.667 0.00 0.00 0.00 3.86
391 429 1.209621 ATTAGAGGGCTTTGCGGGTA 58.790 50.000 0.00 0.00 0.00 3.69
394 432 1.818674 ACAAATTAGAGGGCTTTGCGG 59.181 47.619 0.00 0.00 34.08 5.69
395 433 2.749621 AGACAAATTAGAGGGCTTTGCG 59.250 45.455 0.00 0.00 34.08 4.85
438 480 0.813184 TGTATCGTCAGGTCGGTTCC 59.187 55.000 0.00 0.00 0.00 3.62
443 485 0.027716 CGGTCTGTATCGTCAGGTCG 59.972 60.000 0.00 0.00 36.25 4.79
445 487 1.201647 CAACGGTCTGTATCGTCAGGT 59.798 52.381 0.00 0.00 43.04 4.00
447 489 2.251040 CACAACGGTCTGTATCGTCAG 58.749 52.381 0.00 0.00 43.04 3.51
449 491 1.625616 CCACAACGGTCTGTATCGTC 58.374 55.000 0.00 0.00 43.04 4.20
453 768 1.079405 CGCCCACAACGGTCTGTAT 60.079 57.895 0.00 0.00 0.00 2.29
455 770 4.619227 CCGCCCACAACGGTCTGT 62.619 66.667 0.00 0.00 45.70 3.41
461 776 1.008995 CTTCAAACCGCCCACAACG 60.009 57.895 0.00 0.00 0.00 4.10
462 777 1.362355 CCTTCAAACCGCCCACAAC 59.638 57.895 0.00 0.00 0.00 3.32
466 781 1.830408 CCAACCTTCAAACCGCCCA 60.830 57.895 0.00 0.00 0.00 5.36
469 784 0.249280 CCAACCAACCTTCAAACCGC 60.249 55.000 0.00 0.00 0.00 5.68
475 790 1.547675 GCCATCTCCAACCAACCTTCA 60.548 52.381 0.00 0.00 0.00 3.02
480 795 2.369394 CTTAGGCCATCTCCAACCAAC 58.631 52.381 5.01 0.00 0.00 3.77
483 798 0.255890 TGCTTAGGCCATCTCCAACC 59.744 55.000 5.01 0.00 37.74 3.77
491 806 1.768870 ACTACCGATTGCTTAGGCCAT 59.231 47.619 5.01 0.00 37.74 4.40
492 807 1.134521 CACTACCGATTGCTTAGGCCA 60.135 52.381 5.01 0.00 37.74 5.36
493 808 1.583054 CACTACCGATTGCTTAGGCC 58.417 55.000 0.00 0.00 37.74 5.19
494 809 0.938008 GCACTACCGATTGCTTAGGC 59.062 55.000 0.00 0.00 35.74 3.93
543 890 3.527533 ACAGCAACTTCACTGTTCGTTA 58.472 40.909 0.00 0.00 44.59 3.18
566 913 0.833834 ACTGGTACACTGAGCAGGCT 60.834 55.000 7.45 0.00 46.89 4.58
574 921 3.556423 GGGTGGACTTAACTGGTACACTG 60.556 52.174 8.21 0.00 45.10 3.66
608 955 5.348997 GTGCTGACTGTAGTGGATTAGAAAC 59.651 44.000 0.00 0.00 0.00 2.78
681 1028 2.048222 CGTCATGGTGAGTGCGGT 60.048 61.111 0.00 0.00 0.00 5.68
692 1039 3.551863 GGTGGCTCTATCTTCTCGTCATG 60.552 52.174 0.00 0.00 0.00 3.07
695 1042 2.025155 TGGTGGCTCTATCTTCTCGTC 58.975 52.381 0.00 0.00 0.00 4.20
705 1052 3.702048 GGGTGCGTGGTGGCTCTA 61.702 66.667 0.00 0.00 0.00 2.43
754 1107 3.099841 TGGTCTTGTGGTGGGGCA 61.100 61.111 0.00 0.00 0.00 5.36
805 1158 1.743394 GTTCCTTGGACGCAATAAGGG 59.257 52.381 0.00 0.00 41.01 3.95
810 1163 1.523758 GACTGTTCCTTGGACGCAAT 58.476 50.000 0.00 0.00 0.00 3.56
856 1209 4.814294 GGTGGCGACGGAAGCGAT 62.814 66.667 0.00 0.00 35.00 4.58
920 1284 0.107897 TTGGAATGACCGGGTCGATG 60.108 55.000 21.52 0.00 42.61 3.84
984 1353 3.891400 ATAGTCGGCCGCGCGTAA 61.891 61.111 29.95 7.86 0.00 3.18
1036 1406 2.248431 GACGTTCAAGCACACGCC 59.752 61.111 0.00 0.00 40.16 5.68
1042 1412 4.287781 TCCGCCGACGTTCAAGCA 62.288 61.111 0.00 0.00 37.70 3.91
1203 1603 3.293901 GAGCAGGTCGAGCAGCACT 62.294 63.158 29.64 13.42 0.00 4.40
1648 2069 2.660064 CGGGGGTGAAGGACCTGAG 61.660 68.421 0.00 0.00 45.33 3.35
1764 2185 1.542915 TCGTAGAAGAAACCCGTCTGG 59.457 52.381 0.00 0.00 35.29 3.86
1890 2311 1.379044 CCGGAAATCCAGCAGGCTT 60.379 57.895 0.00 0.00 35.14 4.35
2348 2772 3.062763 CTCGCACAAGATGACAAGAGTT 58.937 45.455 0.00 0.00 0.00 3.01
2351 2775 1.618343 TCCTCGCACAAGATGACAAGA 59.382 47.619 0.00 0.00 0.00 3.02
2352 2776 2.084610 TCCTCGCACAAGATGACAAG 57.915 50.000 0.00 0.00 0.00 3.16
2353 2777 2.768253 ATCCTCGCACAAGATGACAA 57.232 45.000 0.00 0.00 0.00 3.18
2354 2778 2.768253 AATCCTCGCACAAGATGACA 57.232 45.000 0.00 0.00 0.00 3.58
2355 2779 3.786635 ACTAATCCTCGCACAAGATGAC 58.213 45.455 0.00 0.00 0.00 3.06
2356 2780 3.447229 TGACTAATCCTCGCACAAGATGA 59.553 43.478 0.00 0.00 0.00 2.92
2357 2781 3.553511 GTGACTAATCCTCGCACAAGATG 59.446 47.826 0.00 0.00 0.00 2.90
2358 2782 3.195610 TGTGACTAATCCTCGCACAAGAT 59.804 43.478 0.00 0.00 36.63 2.40
2498 3239 9.588096 ACAACACTCCACTCATATATATACTCA 57.412 33.333 0.00 0.00 0.00 3.41
2534 3444 8.296713 GCAAAGAATTGACAATAAAGGTGTCTA 58.703 33.333 0.00 0.00 44.70 2.59
2545 3455 6.364165 CACTGAAATCGCAAAGAATTGACAAT 59.636 34.615 0.00 0.00 38.94 2.71
2568 3478 5.408299 GGGTCAATTTTTGCTTGGTAATCAC 59.592 40.000 0.00 0.00 0.00 3.06
2607 3517 5.127845 AGTGTACATCTGACCTACATTCAGG 59.872 44.000 0.00 0.00 40.87 3.86
2648 3581 7.093992 TGCCGAAAACCCTAAAATAAATTCAG 58.906 34.615 0.00 0.00 0.00 3.02
2651 3584 7.880713 ACATTGCCGAAAACCCTAAAATAAATT 59.119 29.630 0.00 0.00 0.00 1.82
2673 3606 6.706270 ACATCTACTTTCACTGAACGAACATT 59.294 34.615 2.42 0.00 0.00 2.71
2711 3644 5.088141 ACGTAGTCATTATAGACGTTCCG 57.912 43.478 0.00 0.00 43.72 4.30
2766 3699 3.571401 ACGTTATACCTATAAGCACCGCT 59.429 43.478 0.00 0.00 42.56 5.52
2767 3700 3.671928 CACGTTATACCTATAAGCACCGC 59.328 47.826 0.00 0.00 0.00 5.68
2768 3701 4.678287 CACACGTTATACCTATAAGCACCG 59.322 45.833 0.00 0.00 0.00 4.94
2795 3729 2.103771 AGTCATCCTTATGAGCGCATGT 59.896 45.455 13.71 0.00 42.80 3.21
2797 3731 4.815533 ATAGTCATCCTTATGAGCGCAT 57.184 40.909 11.47 8.35 42.80 4.73
2815 3749 6.555812 ACAATTGCAGATGCTGACATATAG 57.444 37.500 5.05 0.00 42.66 1.31
2817 3751 5.240183 GGTACAATTGCAGATGCTGACATAT 59.760 40.000 5.05 0.00 42.66 1.78
2936 3906 2.391616 TCTTGCGCTCACATCTTCAT 57.608 45.000 9.73 0.00 0.00 2.57
2966 3936 6.155221 TCTCCTAAGCACTTATTCATCAGTGT 59.845 38.462 3.64 0.00 42.19 3.55
2967 3937 6.577103 TCTCCTAAGCACTTATTCATCAGTG 58.423 40.000 0.00 0.00 42.94 3.66
2983 3953 2.091055 TGACCTCCTGGGATCTCCTAAG 60.091 54.545 0.00 0.00 38.76 2.18
3021 3991 6.950860 ATGTTCAGGGGGACATTTTAAATT 57.049 33.333 0.00 0.00 0.00 1.82
3022 3992 6.950860 AATGTTCAGGGGGACATTTTAAAT 57.049 33.333 0.00 0.00 29.59 1.40
3023 3993 6.755542 AAATGTTCAGGGGGACATTTTAAA 57.244 33.333 8.00 0.00 39.01 1.52
3024 3994 6.755542 AAAATGTTCAGGGGGACATTTTAA 57.244 33.333 19.86 0.00 45.29 1.52
3029 3999 4.132122 AGAAAAATGTTCAGGGGGACAT 57.868 40.909 0.00 0.00 0.00 3.06
3031 4001 4.955811 AAAGAAAAATGTTCAGGGGGAC 57.044 40.909 0.00 0.00 0.00 4.46
3032 4002 5.711698 ACTAAAGAAAAATGTTCAGGGGGA 58.288 37.500 0.00 0.00 0.00 4.81
3033 4003 6.183360 ACAACTAAAGAAAAATGTTCAGGGGG 60.183 38.462 0.00 0.00 0.00 5.40
3034 4004 6.816136 ACAACTAAAGAAAAATGTTCAGGGG 58.184 36.000 0.00 0.00 0.00 4.79
3035 4005 9.810545 TTAACAACTAAAGAAAAATGTTCAGGG 57.189 29.630 0.00 0.00 33.48 4.45
3098 4091 4.815846 AGGTTGGCAAACATGACAATTTTC 59.184 37.500 18.93 0.00 39.24 2.29
3106 4099 0.950836 CGTGAGGTTGGCAAACATGA 59.049 50.000 18.93 0.00 38.10 3.07
3151 4144 1.110442 TTTAAGCATGGCAATCCGGG 58.890 50.000 0.00 0.00 34.14 5.73
3152 4145 2.957491 TTTTAAGCATGGCAATCCGG 57.043 45.000 0.00 0.00 34.14 5.14
3156 4149 6.572519 ACATACGAATTTTAAGCATGGCAAT 58.427 32.000 0.00 0.00 0.00 3.56
3161 4154 5.748152 CCCCAACATACGAATTTTAAGCATG 59.252 40.000 0.00 0.00 0.00 4.06
3173 4166 9.062524 CAGAAATAATAAATCCCCAACATACGA 57.937 33.333 0.00 0.00 0.00 3.43
3228 4221 3.446161 TGAGATCCTAACAACACCTACCG 59.554 47.826 0.00 0.00 0.00 4.02
3229 4222 5.615925 ATGAGATCCTAACAACACCTACC 57.384 43.478 0.00 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.