Multiple sequence alignment - TraesCS5D01G313100

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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 TraesCS5D01G313100 chr5D 100.000 3020 0 0 1 3020 408545593 408548612 0.000000e+00 5578.0
1 TraesCS5D01G313100 chr5D 86.193 507 64 6 2517 3018 545540347 545539842 7.360000e-151 544.0
2 TraesCS5D01G313100 chr5B 90.763 2490 147 28 1 2444 490100575 490103027 0.000000e+00 3247.0
3 TraesCS5D01G313100 chr5B 80.242 248 49 0 138 385 535148295 535148542 1.430000e-43 187.0
4 TraesCS5D01G313100 chr5B 92.647 68 5 0 1573 1640 10514064 10514131 6.890000e-17 99.0
5 TraesCS5D01G313100 chr5B 97.436 39 1 0 2473 2511 490103074 490103112 1.940000e-07 67.6
6 TraesCS5D01G313100 chr5A 90.123 2278 111 43 231 2444 514451172 514453399 0.000000e+00 2856.0
7 TraesCS5D01G313100 chr5A 88.889 504 51 4 2517 3019 574011486 574011985 1.540000e-172 616.0
8 TraesCS5D01G313100 chr5A 86.444 509 59 10 2517 3018 680763200 680762695 1.580000e-152 549.0
9 TraesCS5D01G313100 chr5A 100.000 33 0 0 2473 2505 514453446 514453478 9.040000e-06 62.1
10 TraesCS5D01G313100 chr7D 95.842 505 17 3 2517 3020 631811408 631811909 0.000000e+00 813.0
11 TraesCS5D01G313100 chr7D 92.050 239 15 2 1844 2082 73561262 73561496 1.740000e-87 333.0
12 TraesCS5D01G313100 chr7D 81.087 423 48 13 984 1401 185357493 185357888 2.920000e-80 309.0
13 TraesCS5D01G313100 chr7D 78.693 352 71 4 1 349 25513141 25513491 6.510000e-57 231.0
14 TraesCS5D01G313100 chr4D 94.653 505 20 5 2517 3020 375074949 375074451 0.000000e+00 776.0
15 TraesCS5D01G313100 chr7A 89.307 505 49 4 2517 3020 15541135 15541635 1.980000e-176 628.0
16 TraesCS5D01G313100 chr7A 82.143 420 43 8 984 1392 193120782 193121180 6.240000e-87 331.0
17 TraesCS5D01G313100 chr7A 90.594 202 19 0 1433 1634 193121189 193121390 4.960000e-68 268.0
18 TraesCS5D01G313100 chr7A 95.588 68 3 0 1573 1640 623459539 623459606 3.180000e-20 110.0
19 TraesCS5D01G313100 chr7A 94.118 68 4 0 1573 1640 717180659 717180726 1.480000e-18 104.0
20 TraesCS5D01G313100 chr1D 88.911 505 46 5 2517 3020 335419320 335418825 5.530000e-172 614.0
21 TraesCS5D01G313100 chr4A 88.048 502 55 5 2516 3016 708328169 708328666 9.330000e-165 590.0
22 TraesCS5D01G313100 chr4A 87.674 503 55 4 2517 3018 702241040 702241536 2.020000e-161 579.0
23 TraesCS5D01G313100 chr4A 79.098 244 47 4 142 385 641301373 641301612 6.700000e-37 165.0
24 TraesCS5D01G313100 chrUn 90.617 373 21 6 1881 2251 421058938 421059298 1.630000e-132 483.0
25 TraesCS5D01G313100 chrUn 89.121 239 22 2 1844 2082 47704255 47704021 8.190000e-76 294.0
26 TraesCS5D01G313100 chr3B 90.959 365 21 4 1881 2245 778546415 778546063 5.860000e-132 481.0
27 TraesCS5D01G313100 chr3D 91.102 236 16 3 1847 2082 443423645 443423415 6.280000e-82 315.0
28 TraesCS5D01G313100 chr3D 78.906 256 45 9 137 388 529882289 529882039 6.700000e-37 165.0
29 TraesCS5D01G313100 chr7B 77.494 391 72 11 6 383 418045763 418045376 1.410000e-53 220.0
30 TraesCS5D01G313100 chr7B 89.552 67 4 1 1574 1640 727672438 727672501 6.940000e-12 82.4
31 TraesCS5D01G313100 chr2A 77.078 397 74 13 1 384 70042660 70042268 2.360000e-51 213.0
32 TraesCS5D01G313100 chr2A 81.933 238 40 3 147 384 646626744 646626978 6.600000e-47 198.0
33 TraesCS5D01G313100 chr2D 76.590 346 71 7 1 339 436001659 436001317 6.650000e-42 182.0
34 TraesCS5D01G313100 chr2B 78.800 250 51 2 137 385 771812215 771811967 1.860000e-37 167.0
35 TraesCS5D01G313100 chr6D 96.552 58 2 0 1583 1640 27404348 27404405 2.480000e-16 97.1


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 TraesCS5D01G313100 chr5D 408545593 408548612 3019 False 5578.00 5578 100.0000 1 3020 1 chr5D.!!$F1 3019
1 TraesCS5D01G313100 chr5D 545539842 545540347 505 True 544.00 544 86.1930 2517 3018 1 chr5D.!!$R1 501
2 TraesCS5D01G313100 chr5B 490100575 490103112 2537 False 1657.30 3247 94.0995 1 2511 2 chr5B.!!$F3 2510
3 TraesCS5D01G313100 chr5A 514451172 514453478 2306 False 1459.05 2856 95.0615 231 2505 2 chr5A.!!$F2 2274
4 TraesCS5D01G313100 chr5A 680762695 680763200 505 True 549.00 549 86.4440 2517 3018 1 chr5A.!!$R1 501
5 TraesCS5D01G313100 chr7D 631811408 631811909 501 False 813.00 813 95.8420 2517 3020 1 chr7D.!!$F4 503
6 TraesCS5D01G313100 chr7A 15541135 15541635 500 False 628.00 628 89.3070 2517 3020 1 chr7A.!!$F1 503
7 TraesCS5D01G313100 chr7A 193120782 193121390 608 False 299.50 331 86.3685 984 1634 2 chr7A.!!$F4 650

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
75 76 0.034337 GAAGGGCGTGTGGAGTTGTA 59.966 55.0 0.00 0.0 0.00 2.41 F
91 92 0.099968 TGTATCTTCGGCGGAACTCG 59.900 55.0 7.21 0.0 42.76 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1095 1158 1.654743 GACGATGCCGAGCGAGTAC 60.655 63.158 0.0 0.0 39.50 2.73 R
2115 2178 0.036199 TATGGTGGGTTTCCGTTCCG 60.036 55.000 0.0 0.0 35.24 4.30 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
20 21 3.041508 GATGGAATAAGGTCCTACCGC 57.958 52.381 0.00 0.00 44.90 5.68
24 25 2.901839 GGAATAAGGTCCTACCGCCATA 59.098 50.000 0.00 0.00 44.90 2.74
27 28 1.408453 AAGGTCCTACCGCCATAGCC 61.408 60.000 0.00 0.00 44.90 3.93
30 31 4.003788 CCTACCGCCATAGCCCCG 62.004 72.222 0.00 0.00 34.57 5.73
31 32 3.231736 CTACCGCCATAGCCCCGT 61.232 66.667 0.00 0.00 34.57 5.28
32 33 3.222354 CTACCGCCATAGCCCCGTC 62.222 68.421 0.00 0.00 34.57 4.79
48 49 1.065928 GTCCCGACGGTGCATCTAG 59.934 63.158 13.94 0.00 0.00 2.43
62 63 0.461961 ATCTAGCGTCACTGAAGGGC 59.538 55.000 0.00 0.00 0.00 5.19
63 64 1.517257 CTAGCGTCACTGAAGGGCG 60.517 63.158 0.00 0.00 0.00 6.13
70 71 1.669115 CACTGAAGGGCGTGTGGAG 60.669 63.158 0.00 0.00 0.00 3.86
71 72 2.140792 ACTGAAGGGCGTGTGGAGT 61.141 57.895 0.00 0.00 0.00 3.85
75 76 0.034337 GAAGGGCGTGTGGAGTTGTA 59.966 55.000 0.00 0.00 0.00 2.41
79 80 1.338769 GGGCGTGTGGAGTTGTATCTT 60.339 52.381 0.00 0.00 0.00 2.40
91 92 0.099968 TGTATCTTCGGCGGAACTCG 59.900 55.000 7.21 0.00 42.76 4.18
95 96 4.367023 TTCGGCGGAACTCGTGGG 62.367 66.667 7.21 0.00 41.72 4.61
100 101 3.382832 CGGAACTCGTGGGGCTCT 61.383 66.667 0.00 0.00 0.00 4.09
102 103 2.435059 GAACTCGTGGGGCTCTGC 60.435 66.667 0.00 0.00 0.00 4.26
119 120 1.826487 GCCGGTGTTGGTCTTTGGT 60.826 57.895 1.90 0.00 0.00 3.67
126 128 2.758423 GTGTTGGTCTTTGGTGGACTTT 59.242 45.455 0.00 0.00 34.47 2.66
140 142 4.654262 GGTGGACTTTATGGATCCAGTCTA 59.346 45.833 23.69 18.35 43.18 2.59
142 144 6.459923 GTGGACTTTATGGATCCAGTCTATC 58.540 44.000 23.69 16.60 43.18 2.08
148 150 7.724506 ACTTTATGGATCCAGTCTATCTTCGTA 59.275 37.037 21.33 0.00 29.93 3.43
156 158 6.589135 TCCAGTCTATCTTCGTATGTCTACA 58.411 40.000 0.00 0.00 0.00 2.74
171 173 4.503910 TGTCTACATGTTGGATCCTTTCG 58.496 43.478 14.23 0.26 0.00 3.46
191 193 5.040715 TCGATCTATGCTTCTCTTCATCG 57.959 43.478 0.00 0.00 34.55 3.84
194 196 2.057316 CTATGCTTCTCTTCATCGGCG 58.943 52.381 0.00 0.00 0.00 6.46
213 215 1.727857 CGACGGTTGCTATTTTGGTGC 60.728 52.381 0.00 0.00 0.00 5.01
224 226 0.107831 TTTTGGTGCGCTAGTCCTGT 59.892 50.000 9.73 0.00 0.00 4.00
226 228 1.468506 TTGGTGCGCTAGTCCTGTCA 61.469 55.000 9.73 0.00 0.00 3.58
229 231 2.202810 GCGCTAGTCCTGTCAGGC 60.203 66.667 14.64 9.42 34.61 4.85
238 240 0.835971 TCCTGTCAGGCCTTAGCACA 60.836 55.000 14.64 2.66 42.56 4.57
257 259 0.879765 AACGACTACCCGACTGTCTG 59.120 55.000 6.21 0.00 0.00 3.51
273 275 3.876914 CTGTCTGCTACAACAAGGTTTGA 59.123 43.478 0.00 0.00 37.74 2.69
307 309 4.171103 AGGGGTGATAACGGCGGC 62.171 66.667 13.24 0.00 0.00 6.53
308 310 4.476752 GGGGTGATAACGGCGGCA 62.477 66.667 13.24 0.28 0.00 5.69
324 326 3.423154 CACGTCTTTGGCCCGCTC 61.423 66.667 0.00 0.00 0.00 5.03
325 327 4.699522 ACGTCTTTGGCCCGCTCC 62.700 66.667 0.00 0.00 0.00 4.70
341 345 4.262635 CCCGCTCCAGTGATTATAGTCATT 60.263 45.833 0.83 0.00 0.00 2.57
349 353 7.728532 TCCAGTGATTATAGTCATTGCTAGGTA 59.271 37.037 13.30 0.00 35.30 3.08
402 408 7.678947 ACTTCTGATGAATAGTTTGGAAGTG 57.321 36.000 0.00 0.00 40.01 3.16
406 412 8.463930 TCTGATGAATAGTTTGGAAGTGTTTT 57.536 30.769 0.00 0.00 0.00 2.43
407 413 8.352201 TCTGATGAATAGTTTGGAAGTGTTTTG 58.648 33.333 0.00 0.00 0.00 2.44
408 414 6.922957 TGATGAATAGTTTGGAAGTGTTTTGC 59.077 34.615 0.00 0.00 0.00 3.68
410 416 7.575414 TGAATAGTTTGGAAGTGTTTTGCTA 57.425 32.000 0.00 0.00 0.00 3.49
413 419 8.871686 AATAGTTTGGAAGTGTTTTGCTAAAG 57.128 30.769 0.00 0.00 0.00 1.85
414 420 6.524101 AGTTTGGAAGTGTTTTGCTAAAGA 57.476 33.333 0.00 0.00 0.00 2.52
415 421 6.564328 AGTTTGGAAGTGTTTTGCTAAAGAG 58.436 36.000 0.00 0.00 0.00 2.85
420 426 7.607250 TGGAAGTGTTTTGCTAAAGAGAAAAA 58.393 30.769 0.00 0.00 37.79 1.94
452 458 2.283604 TCGCTGGGCAGTGAGGTA 60.284 61.111 0.00 0.00 42.43 3.08
453 459 2.125512 CGCTGGGCAGTGAGGTAC 60.126 66.667 0.00 0.00 41.24 3.34
483 489 8.616076 GGTTAATGAAGAAGTACATTCAGATGG 58.384 37.037 12.01 0.00 40.67 3.51
565 572 0.669932 CAGGCAGAGTCAGTGAGTGC 60.670 60.000 4.86 9.20 0.00 4.40
581 588 3.024547 GAGTGCCAGAGTATCCACACTA 58.975 50.000 0.00 0.00 41.30 2.74
582 589 3.639094 GAGTGCCAGAGTATCCACACTAT 59.361 47.826 0.00 0.00 41.30 2.12
694 726 2.026915 TGATCAGATTCACCACCCACAG 60.027 50.000 0.00 0.00 0.00 3.66
719 751 3.883744 AACCCGTCCAAGCAGAGCG 62.884 63.158 0.00 0.00 0.00 5.03
751 785 0.819259 CACCCCTCACCAACACACAG 60.819 60.000 0.00 0.00 0.00 3.66
776 810 6.596309 AAAGATCAAAACTTTCTCCCCATC 57.404 37.500 0.00 0.00 33.08 3.51
777 811 5.527026 AGATCAAAACTTTCTCCCCATCT 57.473 39.130 0.00 0.00 0.00 2.90
778 812 5.896963 AGATCAAAACTTTCTCCCCATCTT 58.103 37.500 0.00 0.00 0.00 2.40
779 813 5.948758 AGATCAAAACTTTCTCCCCATCTTC 59.051 40.000 0.00 0.00 0.00 2.87
780 814 5.324832 TCAAAACTTTCTCCCCATCTTCT 57.675 39.130 0.00 0.00 0.00 2.85
781 815 5.316987 TCAAAACTTTCTCCCCATCTTCTC 58.683 41.667 0.00 0.00 0.00 2.87
897 936 6.072175 GCTCCCGCTATCTATCCATCTATAAG 60.072 46.154 0.00 0.00 0.00 1.73
904 943 7.201741 GCTATCTATCCATCTATAAGTGCGACA 60.202 40.741 0.00 0.00 0.00 4.35
1010 1061 0.306840 GGTGCGTGCATGATCATGAG 59.693 55.000 34.65 24.69 41.20 2.90
1095 1158 1.064296 CATCGTCTTCTCCGTCGGG 59.936 63.158 12.29 2.17 0.00 5.14
1845 1908 3.499737 GCGGACATCAACCTGGCG 61.500 66.667 0.00 0.00 0.00 5.69
1953 2016 4.344865 TTCGCCAGGGTGAAGGGC 62.345 66.667 10.13 0.00 44.27 5.19
1962 2025 2.358737 GTGAAGGGCCTCACCGTG 60.359 66.667 19.36 0.00 39.93 4.94
2115 2178 4.212913 TCTCGCGAGGCATCCAGC 62.213 66.667 33.98 0.00 44.65 4.85
2197 2265 4.452733 CGCCTTGTCCCCGGTCTC 62.453 72.222 0.00 0.00 0.00 3.36
2198 2266 3.003763 GCCTTGTCCCCGGTCTCT 61.004 66.667 0.00 0.00 0.00 3.10
2259 2328 5.237127 GCCATTTTTCTTTTCTCCACCAAAG 59.763 40.000 0.00 0.00 0.00 2.77
2284 2355 1.927174 CATTCTTCTTACACGGCGAGG 59.073 52.381 16.62 7.98 0.00 4.63
2302 2373 4.783242 CGAGGAATCAACAAACACGATTT 58.217 39.130 0.00 0.00 29.67 2.17
2393 2470 7.440556 ACTTATCGACCAAGATGAGATTGATTG 59.559 37.037 13.94 0.00 37.58 2.67
2416 2493 9.914131 ATTGTTTATCTTCTGGTAAAGAAAAGC 57.086 29.630 0.00 0.00 44.38 3.51
2417 2494 8.458573 TGTTTATCTTCTGGTAAAGAAAAGCA 57.541 30.769 0.00 0.00 44.38 3.91
2418 2495 8.567948 TGTTTATCTTCTGGTAAAGAAAAGCAG 58.432 33.333 0.00 0.00 44.38 4.24
2419 2496 5.635417 ATCTTCTGGTAAAGAAAAGCAGC 57.365 39.130 0.00 0.00 44.38 5.25
2423 2502 0.526211 GGTAAAGAAAAGCAGCGGGG 59.474 55.000 0.00 0.00 0.00 5.73
2425 2504 1.611977 GTAAAGAAAAGCAGCGGGGTT 59.388 47.619 0.00 0.00 39.32 4.11
2451 2530 2.595238 GGTACGGAGATGGTGATAGGT 58.405 52.381 0.00 0.00 0.00 3.08
2452 2531 2.296471 GGTACGGAGATGGTGATAGGTG 59.704 54.545 0.00 0.00 0.00 4.00
2453 2532 2.454336 ACGGAGATGGTGATAGGTGA 57.546 50.000 0.00 0.00 0.00 4.02
2456 2535 2.028658 CGGAGATGGTGATAGGTGATGG 60.029 54.545 0.00 0.00 0.00 3.51
2458 2537 3.843027 GGAGATGGTGATAGGTGATGGAT 59.157 47.826 0.00 0.00 0.00 3.41
2460 2539 3.586174 AGATGGTGATAGGTGATGGATGG 59.414 47.826 0.00 0.00 0.00 3.51
2461 2540 3.059051 TGGTGATAGGTGATGGATGGA 57.941 47.619 0.00 0.00 0.00 3.41
2462 2541 2.705658 TGGTGATAGGTGATGGATGGAC 59.294 50.000 0.00 0.00 0.00 4.02
2464 2543 3.392616 GGTGATAGGTGATGGATGGACTT 59.607 47.826 0.00 0.00 0.00 3.01
2465 2544 4.384056 GTGATAGGTGATGGATGGACTTG 58.616 47.826 0.00 0.00 0.00 3.16
2468 2547 1.098050 GGTGATGGATGGACTTGTGC 58.902 55.000 0.00 0.00 0.00 4.57
2469 2548 1.614051 GGTGATGGATGGACTTGTGCA 60.614 52.381 0.00 0.00 0.00 4.57
2470 2549 1.470098 GTGATGGATGGACTTGTGCAC 59.530 52.381 10.75 10.75 0.00 4.57
2527 2624 0.529773 CGGCTGCGGAGTAAATAGCA 60.530 55.000 5.62 0.00 36.15 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.065928 CTAGATGCACCGTCGGGAC 59.934 63.158 17.28 7.57 36.97 4.46
31 32 2.782222 GCTAGATGCACCGTCGGGA 61.782 63.158 17.28 0.00 42.31 5.14
32 33 2.279517 GCTAGATGCACCGTCGGG 60.280 66.667 17.28 5.79 42.31 5.14
35 36 3.999051 GACGCTAGATGCACCGTC 58.001 61.111 0.00 9.00 42.39 4.79
36 37 1.153823 GTGACGCTAGATGCACCGT 60.154 57.895 0.00 0.00 43.06 4.83
38 39 0.173481 TCAGTGACGCTAGATGCACC 59.827 55.000 0.00 0.00 43.06 5.01
39 40 1.923204 CTTCAGTGACGCTAGATGCAC 59.077 52.381 0.00 0.00 43.06 4.57
43 44 0.461961 GCCCTTCAGTGACGCTAGAT 59.538 55.000 0.00 0.00 0.00 1.98
46 47 2.273179 ACGCCCTTCAGTGACGCTA 61.273 57.895 0.00 0.00 0.00 4.26
48 49 3.414700 CACGCCCTTCAGTGACGC 61.415 66.667 0.00 0.00 40.56 5.19
53 54 1.696097 AACTCCACACGCCCTTCAGT 61.696 55.000 0.00 0.00 0.00 3.41
54 55 1.071471 AACTCCACACGCCCTTCAG 59.929 57.895 0.00 0.00 0.00 3.02
55 56 1.227823 CAACTCCACACGCCCTTCA 60.228 57.895 0.00 0.00 0.00 3.02
62 63 2.259618 CCGAAGATACAACTCCACACG 58.740 52.381 0.00 0.00 0.00 4.49
63 64 2.000447 GCCGAAGATACAACTCCACAC 59.000 52.381 0.00 0.00 0.00 3.82
70 71 1.925185 GAGTTCCGCCGAAGATACAAC 59.075 52.381 0.00 0.00 0.00 3.32
71 72 1.468565 CGAGTTCCGCCGAAGATACAA 60.469 52.381 0.00 0.00 0.00 2.41
75 76 1.153823 CACGAGTTCCGCCGAAGAT 60.154 57.895 0.00 0.00 43.32 2.40
95 96 4.643387 ACCAACACCGGCAGAGCC 62.643 66.667 0.00 0.00 46.75 4.70
96 97 3.050275 GACCAACACCGGCAGAGC 61.050 66.667 0.00 0.00 0.00 4.09
97 98 0.535102 AAAGACCAACACCGGCAGAG 60.535 55.000 0.00 0.00 0.00 3.35
99 100 1.654220 CAAAGACCAACACCGGCAG 59.346 57.895 0.00 0.00 0.00 4.85
100 101 1.826054 CCAAAGACCAACACCGGCA 60.826 57.895 0.00 0.00 0.00 5.69
102 103 1.452145 CCACCAAAGACCAACACCGG 61.452 60.000 0.00 0.00 0.00 5.28
107 108 4.022329 CCATAAAGTCCACCAAAGACCAAC 60.022 45.833 0.00 0.00 34.67 3.77
119 120 6.385443 AGATAGACTGGATCCATAAAGTCCA 58.615 40.000 22.02 13.31 39.92 4.02
126 128 7.175797 ACATACGAAGATAGACTGGATCCATA 58.824 38.462 16.63 5.35 0.00 2.74
140 142 6.465439 TCCAACATGTAGACATACGAAGAT 57.535 37.500 0.00 0.00 34.26 2.40
142 144 5.692204 GGATCCAACATGTAGACATACGAAG 59.308 44.000 6.95 0.00 34.26 3.79
148 150 5.104941 TCGAAAGGATCCAACATGTAGACAT 60.105 40.000 15.82 0.00 36.96 3.06
171 173 3.925913 GCCGATGAAGAGAAGCATAGATC 59.074 47.826 0.00 0.00 0.00 2.75
191 193 0.179174 CCAAAATAGCAACCGTCGCC 60.179 55.000 0.00 0.00 0.00 5.54
194 196 1.727857 CGCACCAAAATAGCAACCGTC 60.728 52.381 0.00 0.00 0.00 4.79
213 215 2.496817 GGCCTGACAGGACTAGCG 59.503 66.667 26.25 0.00 41.45 4.26
224 226 0.320421 GTCGTTGTGCTAAGGCCTGA 60.320 55.000 5.69 0.00 37.74 3.86
226 228 1.067071 GTAGTCGTTGTGCTAAGGCCT 60.067 52.381 0.00 0.00 37.74 5.19
229 231 1.734707 CGGGTAGTCGTTGTGCTAAGG 60.735 57.143 0.00 0.00 0.00 2.69
238 240 0.879765 CAGACAGTCGGGTAGTCGTT 59.120 55.000 0.00 0.00 37.36 3.85
257 259 2.287608 GCTGGTCAAACCTTGTTGTAGC 60.288 50.000 0.00 0.00 39.58 3.58
273 275 1.686110 CTCCCTTACCGGAGCTGGT 60.686 63.158 9.46 6.22 43.01 4.00
307 309 3.423154 GAGCGGGCCAAAGACGTG 61.423 66.667 4.39 0.00 0.00 4.49
308 310 4.699522 GGAGCGGGCCAAAGACGT 62.700 66.667 4.39 0.00 0.00 4.34
315 317 1.344953 ATAATCACTGGAGCGGGCCA 61.345 55.000 4.39 0.00 36.30 5.36
322 324 7.095910 CCTAGCAATGACTATAATCACTGGAG 58.904 42.308 0.00 0.00 0.00 3.86
323 325 6.554982 ACCTAGCAATGACTATAATCACTGGA 59.445 38.462 0.00 0.00 0.00 3.86
324 326 6.763355 ACCTAGCAATGACTATAATCACTGG 58.237 40.000 0.00 0.00 0.00 4.00
325 327 8.580720 ACTACCTAGCAATGACTATAATCACTG 58.419 37.037 0.00 0.00 0.00 3.66
371 377 8.877779 CCAAACTATTCATCAGAAGTAACAGAG 58.122 37.037 0.00 0.00 37.14 3.35
375 381 9.220767 ACTTCCAAACTATTCATCAGAAGTAAC 57.779 33.333 0.00 0.00 40.51 2.50
437 443 3.393360 AGTACCTCACTGCCCAGC 58.607 61.111 0.00 0.00 35.62 4.85
452 458 8.375506 TGAATGTACTTCTTCATTAACCTCAGT 58.624 33.333 0.00 0.00 34.92 3.41
453 459 8.777865 TGAATGTACTTCTTCATTAACCTCAG 57.222 34.615 0.00 0.00 34.92 3.35
454 460 8.593679 TCTGAATGTACTTCTTCATTAACCTCA 58.406 33.333 0.00 0.00 34.92 3.86
455 461 9.606631 ATCTGAATGTACTTCTTCATTAACCTC 57.393 33.333 0.00 0.00 34.92 3.85
456 462 9.388506 CATCTGAATGTACTTCTTCATTAACCT 57.611 33.333 0.00 0.00 34.92 3.50
457 463 8.616076 CCATCTGAATGTACTTCTTCATTAACC 58.384 37.037 0.00 0.00 34.92 2.85
458 464 8.616076 CCCATCTGAATGTACTTCTTCATTAAC 58.384 37.037 0.00 0.00 34.92 2.01
459 465 7.283127 GCCCATCTGAATGTACTTCTTCATTAA 59.717 37.037 0.00 0.00 34.92 1.40
460 466 6.767902 GCCCATCTGAATGTACTTCTTCATTA 59.232 38.462 0.00 0.00 34.92 1.90
483 489 1.160137 CAGTGAAGGTGCAACTAGCC 58.840 55.000 3.69 0.00 44.83 3.93
521 527 2.307098 CCTGGAGAATCTGGTTCACCTT 59.693 50.000 16.41 0.00 44.91 3.50
565 572 6.493115 AGAGAATGATAGTGTGGATACTCTGG 59.507 42.308 0.00 0.00 33.14 3.86
581 588 4.015084 CTGTGGCAGGAAAAGAGAATGAT 58.985 43.478 0.00 0.00 0.00 2.45
582 589 3.072915 TCTGTGGCAGGAAAAGAGAATGA 59.927 43.478 0.00 0.00 31.51 2.57
643 651 1.786937 AGGAGCATCAGGTAGTGGAG 58.213 55.000 0.00 0.00 36.25 3.86
694 726 1.966451 CTTGGACGGGTTGGTGAGC 60.966 63.158 0.00 0.00 0.00 4.26
719 751 2.267324 GGGTGACTGCTCTGCTCC 59.733 66.667 0.00 0.00 0.00 4.70
726 758 1.770110 TTGGTGAGGGGTGACTGCT 60.770 57.895 0.00 0.00 0.00 4.24
727 759 1.600916 GTTGGTGAGGGGTGACTGC 60.601 63.158 0.00 0.00 0.00 4.40
728 760 0.535102 GTGTTGGTGAGGGGTGACTG 60.535 60.000 0.00 0.00 0.00 3.51
729 761 0.986019 TGTGTTGGTGAGGGGTGACT 60.986 55.000 0.00 0.00 0.00 3.41
730 762 0.818040 GTGTGTTGGTGAGGGGTGAC 60.818 60.000 0.00 0.00 0.00 3.67
751 785 6.405278 TGGGGAGAAAGTTTTGATCTTTTC 57.595 37.500 0.00 0.00 35.62 2.29
776 810 2.243407 CGAACGAAACGAGAGGAGAAG 58.757 52.381 0.00 0.00 0.00 2.85
777 811 1.605710 ACGAACGAAACGAGAGGAGAA 59.394 47.619 0.14 0.00 34.70 2.87
778 812 1.069432 CACGAACGAAACGAGAGGAGA 60.069 52.381 0.14 0.00 34.70 3.71
779 813 1.328439 CACGAACGAAACGAGAGGAG 58.672 55.000 0.14 0.00 34.70 3.69
780 814 0.662374 GCACGAACGAAACGAGAGGA 60.662 55.000 0.14 0.00 34.70 3.71
781 815 0.937699 TGCACGAACGAAACGAGAGG 60.938 55.000 0.14 0.00 34.70 3.69
897 936 1.669760 TTGGTTCGGGATGTCGCAC 60.670 57.895 0.00 0.00 0.00 5.34
904 943 1.562672 CCTGGAGGTTGGTTCGGGAT 61.563 60.000 0.00 0.00 0.00 3.85
1000 1039 1.596203 CACGCGGCCTCATGATCAT 60.596 57.895 12.47 1.18 0.00 2.45
1095 1158 1.654743 GACGATGCCGAGCGAGTAC 60.655 63.158 0.00 0.00 39.50 2.73
2115 2178 0.036199 TATGGTGGGTTTCCGTTCCG 60.036 55.000 0.00 0.00 35.24 4.30
2116 2179 1.456296 GTATGGTGGGTTTCCGTTCC 58.544 55.000 0.00 0.00 35.24 3.62
2117 2180 1.081094 CGTATGGTGGGTTTCCGTTC 58.919 55.000 0.00 0.00 35.24 3.95
2118 2181 0.397564 ACGTATGGTGGGTTTCCGTT 59.602 50.000 0.00 0.00 35.24 4.44
2119 2182 0.320946 CACGTATGGTGGGTTTCCGT 60.321 55.000 0.00 0.00 43.16 4.69
2197 2265 1.135257 ACCTCGATCGCAAGTTCAGAG 60.135 52.381 11.09 0.00 36.93 3.35
2198 2266 0.888619 ACCTCGATCGCAAGTTCAGA 59.111 50.000 11.09 0.00 35.82 3.27
2259 2328 3.423123 CGCCGTGTAAGAAGAATGTGTTC 60.423 47.826 0.00 0.00 34.46 3.18
2279 2350 1.529438 TCGTGTTTGTTGATTCCTCGC 59.471 47.619 0.00 0.00 0.00 5.03
2284 2355 5.422878 GTGCAAAATCGTGTTTGTTGATTC 58.577 37.500 12.77 0.25 40.06 2.52
2393 2470 7.539022 GCTGCTTTTCTTTACCAGAAGATAAAC 59.461 37.037 0.00 0.00 42.76 2.01
2415 2492 4.050934 CCGGAAAAACCCCGCTGC 62.051 66.667 0.00 0.00 45.24 5.25
2416 2493 1.302671 TACCGGAAAAACCCCGCTG 60.303 57.895 9.46 0.00 45.24 5.18
2417 2494 1.302752 GTACCGGAAAAACCCCGCT 60.303 57.895 9.46 0.00 45.24 5.52
2418 2495 2.679934 CGTACCGGAAAAACCCCGC 61.680 63.158 9.46 0.00 45.24 6.13
2419 2496 3.565050 CGTACCGGAAAAACCCCG 58.435 61.111 9.46 0.00 46.10 5.73
2444 2523 4.040047 ACAAGTCCATCCATCACCTATCA 58.960 43.478 0.00 0.00 0.00 2.15
2446 2525 3.434167 GCACAAGTCCATCCATCACCTAT 60.434 47.826 0.00 0.00 0.00 2.57
2447 2526 2.092968 GCACAAGTCCATCCATCACCTA 60.093 50.000 0.00 0.00 0.00 3.08
2449 2528 1.098050 GCACAAGTCCATCCATCACC 58.902 55.000 0.00 0.00 0.00 4.02
2450 2529 1.470098 GTGCACAAGTCCATCCATCAC 59.530 52.381 13.17 0.00 0.00 3.06
2451 2530 1.073603 TGTGCACAAGTCCATCCATCA 59.926 47.619 19.28 0.00 0.00 3.07
2452 2531 1.741706 CTGTGCACAAGTCCATCCATC 59.258 52.381 21.98 0.00 0.00 3.51
2453 2532 1.074405 ACTGTGCACAAGTCCATCCAT 59.926 47.619 21.98 0.00 0.00 3.41
2456 2535 1.726791 CGTACTGTGCACAAGTCCATC 59.273 52.381 21.98 10.77 0.00 3.51
2458 2537 0.462375 ACGTACTGTGCACAAGTCCA 59.538 50.000 21.98 4.61 0.00 4.02
2460 2539 2.724690 CACTACGTACTGTGCACAAGTC 59.275 50.000 21.98 12.17 0.00 3.01
2461 2540 2.545113 CCACTACGTACTGTGCACAAGT 60.545 50.000 21.98 21.11 33.26 3.16
2462 2541 2.058798 CCACTACGTACTGTGCACAAG 58.941 52.381 21.98 16.12 33.26 3.16
2464 2543 1.268625 CTCCACTACGTACTGTGCACA 59.731 52.381 20.37 20.37 33.26 4.57
2465 2544 1.402456 CCTCCACTACGTACTGTGCAC 60.402 57.143 10.75 10.75 33.26 4.57
2468 2547 3.014623 TCATCCTCCACTACGTACTGTG 58.985 50.000 7.75 7.75 0.00 3.66
2469 2548 3.361281 TCATCCTCCACTACGTACTGT 57.639 47.619 0.00 0.00 0.00 3.55
2470 2549 3.632604 ACATCATCCTCCACTACGTACTG 59.367 47.826 0.00 0.00 0.00 2.74
2537 2634 5.633655 TGAAACCCTAACCTGTAAACTGA 57.366 39.130 0.00 0.00 0.00 3.41
2734 2832 2.755064 TTCCGACCGGACCGCATA 60.755 61.111 9.46 0.00 45.11 3.14
2808 2910 0.830444 TCGCCAACCTAGGTCAGTGT 60.830 55.000 16.64 0.00 0.00 3.55
2973 3075 1.607801 CTCGATCCACCTGAGCCACA 61.608 60.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.