Multiple sequence alignment - TraesCS2D01G270100

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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 TraesCS2D01G270100 chr2D 100.000 2912 0 0 1 2912 333645671 333648582 0.000000e+00 5378
1 TraesCS2D01G270100 chr2D 82.979 141 21 3 2297 2434 509744441 509744301 1.100000e-24 124
2 TraesCS2D01G270100 chr2A 95.439 1798 31 19 523 2304 443644528 443646290 0.000000e+00 2819
3 TraesCS2D01G270100 chr2A 89.720 428 40 2 2486 2912 443646511 443646935 7.100000e-151 544
4 TraesCS2D01G270100 chr2A 85.650 223 24 5 1 217 443644177 443644397 8.120000e-56 228
5 TraesCS2D01G270100 chr2A 93.694 111 6 1 404 513 11549926 11549816 6.460000e-37 165
6 TraesCS2D01G270100 chr2B 96.715 1583 23 11 524 2095 401814997 401816561 0.000000e+00 2608
7 TraesCS2D01G270100 chr2B 83.333 864 75 26 2099 2912 401818170 401819014 0.000000e+00 734
8 TraesCS2D01G270100 chr2B 81.481 351 57 6 2565 2912 506051621 506051966 6.140000e-72 281
9 TraesCS2D01G270100 chr2B 88.235 119 14 0 404 522 346655609 346655491 3.020000e-30 143
10 TraesCS2D01G270100 chr2B 87.179 117 15 0 403 519 448923705 448923589 1.820000e-27 134
11 TraesCS2D01G270100 chr3D 84.527 349 49 4 1000 1347 46471865 46471521 9.990000e-90 340
12 TraesCS2D01G270100 chr3B 84.241 349 50 4 1000 1347 72478138 72477794 4.650000e-88 335
13 TraesCS2D01G270100 chr3B 82.069 145 24 2 2297 2439 732437886 732438030 3.940000e-24 122
14 TraesCS2D01G270100 chr3A 83.095 349 54 5 1000 1347 57886850 57886506 2.180000e-81 313
15 TraesCS2D01G270100 chr4D 81.579 380 55 13 993 1364 504178235 504177863 1.700000e-77 300
16 TraesCS2D01G270100 chr4D 84.191 272 36 6 983 1252 504115855 504115589 1.040000e-64 257
17 TraesCS2D01G270100 chr4B 81.481 378 58 12 993 1364 650706892 650706521 1.700000e-77 300
18 TraesCS2D01G270100 chr4B 81.707 328 54 4 2565 2890 29620046 29619723 4.780000e-68 268
19 TraesCS2D01G270100 chr4B 80.734 327 59 2 2565 2890 29632195 29631872 4.820000e-63 252
20 TraesCS2D01G270100 chr7D 80.791 354 56 8 2565 2912 384041534 384041187 1.720000e-67 267
21 TraesCS2D01G270100 chr7D 84.127 126 18 1 2297 2420 478591338 478591463 1.420000e-23 121
22 TraesCS2D01G270100 chr5A 79.943 349 62 8 987 1330 688832031 688831686 1.730000e-62 250
23 TraesCS2D01G270100 chr5A 80.137 292 43 7 2487 2777 37498933 37498656 1.370000e-48 204
24 TraesCS2D01G270100 chr5A 88.793 116 10 3 407 520 562111228 562111114 3.910000e-29 139
25 TraesCS2D01G270100 chr4A 81.073 317 56 4 2597 2912 495328551 495328238 1.730000e-62 250
26 TraesCS2D01G270100 chr4A 82.069 145 21 4 2293 2434 687579897 687580039 5.100000e-23 119
27 TraesCS2D01G270100 chr5D 80.685 321 54 6 2571 2888 457400079 457399764 2.900000e-60 243
28 TraesCS2D01G270100 chr5D 85.156 128 12 5 2293 2416 558845761 558845885 1.100000e-24 124
29 TraesCS2D01G270100 chrUn 80.374 321 59 2 2565 2884 434742807 434743124 1.040000e-59 241
30 TraesCS2D01G270100 chr1A 88.235 119 14 0 401 519 584805232 584805114 3.020000e-30 143
31 TraesCS2D01G270100 chr1A 86.667 120 14 2 402 520 583674716 583674834 6.550000e-27 132
32 TraesCS2D01G270100 chr6A 88.034 117 14 0 403 519 17740006 17739890 3.910000e-29 139
33 TraesCS2D01G270100 chr6A 85.938 128 13 3 2306 2430 16532696 16532571 6.550000e-27 132
34 TraesCS2D01G270100 chr6A 82.857 140 19 4 2293 2430 39136462 39136326 1.420000e-23 121
35 TraesCS2D01G270100 chr6D 87.288 118 15 0 402 519 307327612 307327729 5.060000e-28 135
36 TraesCS2D01G270100 chr5B 84.559 136 17 3 2297 2430 34915406 34915539 6.550000e-27 132
37 TraesCS2D01G270100 chr6B 86.441 118 16 0 403 520 626592830 626592713 2.360000e-26 130
38 TraesCS2D01G270100 chr7B 82.609 138 18 5 2297 2430 364351020 364351155 1.830000e-22 117


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 TraesCS2D01G270100 chr2D 333645671 333648582 2911 False 5378 5378 100.000000 1 2912 1 chr2D.!!$F1 2911
1 TraesCS2D01G270100 chr2A 443644177 443646935 2758 False 1197 2819 90.269667 1 2912 3 chr2A.!!$F1 2911
2 TraesCS2D01G270100 chr2B 401814997 401819014 4017 False 1671 2608 90.024000 524 2912 2 chr2B.!!$F2 2388

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
416 422 0.107459 ACGTAGTACTCCCTCCGTCC 60.107 60.0 0.0 0.0 41.94 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 3795 0.455005 GAAGCCGTAGAACCGTAGCT 59.545 55.0 0.0 0.0 0.0 3.32 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
85 88 1.420138 GTTTCTTCCTCACCTCCACCA 59.580 52.381 0.00 0.00 0.00 4.17
118 121 1.743321 CTGCCTCGGTCATCCCTCTC 61.743 65.000 0.00 0.00 0.00 3.20
119 122 2.503382 GCCTCGGTCATCCCTCTCC 61.503 68.421 0.00 0.00 0.00 3.71
136 139 3.863606 CCCCCTCTCGATCTGGAC 58.136 66.667 0.00 0.00 0.00 4.02
148 151 4.430765 CTGGACGAACCCCGACGG 62.431 72.222 6.99 6.99 41.76 4.79
187 193 3.435026 CCCCAAGTTTCTTTCTCACCTCA 60.435 47.826 0.00 0.00 0.00 3.86
253 259 4.148825 CGGAAGGTCCTGGCTCGG 62.149 72.222 0.00 0.00 33.30 4.63
254 260 4.475135 GGAAGGTCCTGGCTCGGC 62.475 72.222 0.00 0.00 32.53 5.54
290 296 1.953231 CTCATCGCTGCCACTCCTCA 61.953 60.000 0.00 0.00 0.00 3.86
291 297 1.812922 CATCGCTGCCACTCCTCAC 60.813 63.158 0.00 0.00 0.00 3.51
310 316 3.727258 CCATCCCCACCTTCGGCA 61.727 66.667 0.00 0.00 0.00 5.69
337 343 5.981174 TGCATAATAGAAATAAACCGACGC 58.019 37.500 0.00 0.00 0.00 5.19
374 380 5.415701 TCAGGCACCTAAGATTTAGCAAAAG 59.584 40.000 0.00 0.00 0.00 2.27
377 383 4.678044 GCACCTAAGATTTAGCAAAAGCCC 60.678 45.833 0.00 0.00 31.17 5.19
393 399 6.093909 GCAAAAGCCCAAATAATTTATGCAGT 59.906 34.615 0.00 0.00 0.00 4.40
402 408 9.811655 CCAAATAATTTATGCAGTGATACGTAG 57.188 33.333 0.08 0.00 0.00 3.51
415 421 2.604046 TACGTAGTACTCCCTCCGTC 57.396 55.000 0.00 0.00 45.11 4.79
416 422 0.107459 ACGTAGTACTCCCTCCGTCC 60.107 60.000 0.00 0.00 41.94 4.79
417 423 0.107508 CGTAGTACTCCCTCCGTCCA 60.108 60.000 0.00 0.00 0.00 4.02
418 424 1.677942 GTAGTACTCCCTCCGTCCAG 58.322 60.000 0.00 0.00 0.00 3.86
419 425 1.211457 GTAGTACTCCCTCCGTCCAGA 59.789 57.143 0.00 0.00 0.00 3.86
420 426 0.702902 AGTACTCCCTCCGTCCAGAA 59.297 55.000 0.00 0.00 0.00 3.02
421 427 1.076677 AGTACTCCCTCCGTCCAGAAA 59.923 52.381 0.00 0.00 0.00 2.52
422 428 2.108970 GTACTCCCTCCGTCCAGAAAT 58.891 52.381 0.00 0.00 0.00 2.17
423 429 2.544844 ACTCCCTCCGTCCAGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
424 430 2.108970 ACTCCCTCCGTCCAGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
425 431 2.292323 ACTCCCTCCGTCCAGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
426 432 2.766828 CTCCCTCCGTCCAGAAATACTT 59.233 50.000 0.00 0.00 0.00 2.24
427 433 2.500098 TCCCTCCGTCCAGAAATACTTG 59.500 50.000 0.00 0.00 0.00 3.16
428 434 2.236395 CCCTCCGTCCAGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
429 435 3.522553 CCTCCGTCCAGAAATACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
430 436 3.195825 CCTCCGTCCAGAAATACTTGTCT 59.804 47.826 0.00 0.00 0.00 3.41
431 437 4.322801 CCTCCGTCCAGAAATACTTGTCTT 60.323 45.833 0.00 0.00 0.00 3.01
432 438 5.105473 CCTCCGTCCAGAAATACTTGTCTTA 60.105 44.000 0.00 0.00 0.00 2.10
433 439 6.407074 CCTCCGTCCAGAAATACTTGTCTTAT 60.407 42.308 0.00 0.00 0.00 1.73
434 440 7.201884 CCTCCGTCCAGAAATACTTGTCTTATA 60.202 40.741 0.00 0.00 0.00 0.98
435 441 8.070034 TCCGTCCAGAAATACTTGTCTTATAA 57.930 34.615 0.00 0.00 0.00 0.98
436 442 8.533657 TCCGTCCAGAAATACTTGTCTTATAAA 58.466 33.333 0.00 0.00 0.00 1.40
437 443 9.326413 CCGTCCAGAAATACTTGTCTTATAAAT 57.674 33.333 0.00 0.00 0.00 1.40
485 491 9.886132 AATTAAAATAAGTCTAGACACACCGAT 57.114 29.630 24.44 7.74 0.00 4.18
486 492 9.886132 ATTAAAATAAGTCTAGACACACCGATT 57.114 29.630 24.44 10.56 0.00 3.34
487 493 9.715121 TTAAAATAAGTCTAGACACACCGATTT 57.285 29.630 24.44 15.99 0.00 2.17
488 494 8.617290 AAAATAAGTCTAGACACACCGATTTT 57.383 30.769 24.44 18.97 0.00 1.82
489 495 8.617290 AAATAAGTCTAGACACACCGATTTTT 57.383 30.769 24.44 8.52 0.00 1.94
490 496 9.715121 AAATAAGTCTAGACACACCGATTTTTA 57.285 29.630 24.44 10.33 0.00 1.52
491 497 8.928270 ATAAGTCTAGACACACCGATTTTTAG 57.072 34.615 24.44 0.00 0.00 1.85
492 498 5.721232 AGTCTAGACACACCGATTTTTAGG 58.279 41.667 24.44 0.00 0.00 2.69
493 499 5.479375 AGTCTAGACACACCGATTTTTAGGA 59.521 40.000 24.44 0.00 0.00 2.94
494 500 5.575995 GTCTAGACACACCGATTTTTAGGAC 59.424 44.000 18.20 0.00 0.00 3.85
495 501 4.345859 AGACACACCGATTTTTAGGACA 57.654 40.909 0.00 0.00 0.00 4.02
496 502 4.710324 AGACACACCGATTTTTAGGACAA 58.290 39.130 0.00 0.00 0.00 3.18
497 503 5.127491 AGACACACCGATTTTTAGGACAAA 58.873 37.500 0.00 0.00 0.00 2.83
498 504 5.768164 AGACACACCGATTTTTAGGACAAAT 59.232 36.000 0.00 0.00 0.00 2.32
499 505 6.938030 AGACACACCGATTTTTAGGACAAATA 59.062 34.615 0.00 0.00 0.00 1.40
500 506 7.610305 AGACACACCGATTTTTAGGACAAATAT 59.390 33.333 0.00 0.00 0.00 1.28
501 507 8.117813 ACACACCGATTTTTAGGACAAATATT 57.882 30.769 0.00 0.00 0.00 1.28
502 508 8.581578 ACACACCGATTTTTAGGACAAATATTT 58.418 29.630 0.00 0.00 0.00 1.40
503 509 9.418045 CACACCGATTTTTAGGACAAATATTTT 57.582 29.630 0.00 0.00 0.00 1.82
504 510 9.634163 ACACCGATTTTTAGGACAAATATTTTC 57.366 29.630 0.00 0.54 0.00 2.29
505 511 8.794406 CACCGATTTTTAGGACAAATATTTTCG 58.206 33.333 0.00 1.70 0.00 3.46
506 512 7.971722 ACCGATTTTTAGGACAAATATTTTCGG 59.028 33.333 20.73 20.73 34.53 4.30
507 513 8.185505 CCGATTTTTAGGACAAATATTTTCGGA 58.814 33.333 18.89 3.35 32.04 4.55
508 514 9.006215 CGATTTTTAGGACAAATATTTTCGGAC 57.994 33.333 0.00 0.00 0.00 4.79
509 515 9.849166 GATTTTTAGGACAAATATTTTCGGACA 57.151 29.630 0.00 0.00 0.00 4.02
512 518 9.685828 TTTTAGGACAAATATTTTCGGACAAAG 57.314 29.630 0.00 0.00 0.00 2.77
513 519 6.267496 AGGACAAATATTTTCGGACAAAGG 57.733 37.500 0.00 0.00 0.00 3.11
514 520 6.007703 AGGACAAATATTTTCGGACAAAGGA 58.992 36.000 0.00 0.00 0.00 3.36
515 521 6.492087 AGGACAAATATTTTCGGACAAAGGAA 59.508 34.615 0.00 0.00 0.00 3.36
516 522 6.806739 GGACAAATATTTTCGGACAAAGGAAG 59.193 38.462 0.00 0.00 0.00 3.46
517 523 7.284919 ACAAATATTTTCGGACAAAGGAAGT 57.715 32.000 0.00 0.00 0.00 3.01
518 524 8.398878 ACAAATATTTTCGGACAAAGGAAGTA 57.601 30.769 0.00 0.00 0.00 2.24
519 525 8.294577 ACAAATATTTTCGGACAAAGGAAGTAC 58.705 33.333 0.00 0.00 0.00 2.73
520 526 7.989416 AATATTTTCGGACAAAGGAAGTACA 57.011 32.000 0.00 0.00 0.00 2.90
521 527 8.575649 AATATTTTCGGACAAAGGAAGTACAT 57.424 30.769 0.00 0.00 0.00 2.29
769 777 4.134563 CAATACCCTAATACCAGCACCAC 58.865 47.826 0.00 0.00 0.00 4.16
930 942 2.356330 CCTCTCTCCTCGTAGACACCTT 60.356 54.545 0.00 0.00 0.00 3.50
931 943 2.940410 CTCTCTCCTCGTAGACACCTTC 59.060 54.545 0.00 0.00 0.00 3.46
932 944 2.572556 TCTCTCCTCGTAGACACCTTCT 59.427 50.000 0.00 0.00 38.51 2.85
973 985 4.996434 GTGCAGGCTCCAGCACGT 62.996 66.667 18.33 0.00 46.26 4.49
974 986 3.310307 TGCAGGCTCCAGCACGTA 61.310 61.111 1.63 0.00 44.36 3.57
975 987 2.815647 GCAGGCTCCAGCACGTAC 60.816 66.667 0.03 0.00 44.36 3.67
1239 1254 4.155733 TGCGGCCGGATCGTCAAT 62.156 61.111 29.38 0.00 0.00 2.57
1254 1269 1.689273 GTCAATCCCATCTACGGCTCT 59.311 52.381 0.00 0.00 0.00 4.09
1910 1937 4.148825 CGGGCTCCGGTTCCTCTG 62.149 72.222 0.00 0.00 44.15 3.35
1979 2007 8.713036 AGAGAGCTATTTGATGGACTCTTTTAT 58.287 33.333 0.00 0.00 34.75 1.40
1990 2018 9.973661 TGATGGACTCTTTTATCTTTAATTGGA 57.026 29.630 0.00 0.00 0.00 3.53
2108 3742 4.875544 TGTGTTTTGCAGTCTGTTCTAC 57.124 40.909 0.93 0.00 0.00 2.59
2142 3776 4.202151 TGTCAGTCCAGTATGATTGGATCG 60.202 45.833 0.00 0.00 45.85 3.69
2161 3795 5.747197 GGATCGTGAAATCTAAGCGTTCTAA 59.253 40.000 0.00 0.00 0.00 2.10
2249 3884 0.387622 CTTTTACGTCCGCTCGGTGA 60.388 55.000 8.28 0.00 36.47 4.02
2270 3906 6.418819 GGTGATTTCGGATGCTAAAAATGATG 59.581 38.462 0.00 0.00 0.00 3.07
2271 3907 6.418819 GTGATTTCGGATGCTAAAAATGATGG 59.581 38.462 0.00 0.00 0.00 3.51
2294 3930 1.761784 CTCTGCAATGCTACTCCCTCT 59.238 52.381 6.82 0.00 0.00 3.69
2309 4012 7.279090 GCTACTCCCTCTGTTTCTAAAGATTTC 59.721 40.741 0.00 0.00 0.00 2.17
2373 4076 7.976135 AATATAGATTCGCTCATTTTGCTCT 57.024 32.000 0.00 0.00 0.00 4.09
2381 4084 4.815846 TCGCTCATTTTGCTCTATATGCAA 59.184 37.500 8.61 8.61 46.90 4.08
2455 4159 1.095228 AATGCTACAATGGCGTCCCG 61.095 55.000 0.00 0.00 0.00 5.14
2478 4182 4.968259 TCCATCTTGAAGAAGGACGAAAA 58.032 39.130 14.61 0.00 37.20 2.29
2479 4183 5.560724 TCCATCTTGAAGAAGGACGAAAAT 58.439 37.500 14.61 0.00 37.20 1.82
2483 4187 4.755123 TCTTGAAGAAGGACGAAAATGGAC 59.245 41.667 0.00 0.00 0.00 4.02
2517 4245 2.875087 TTGTGGATGCTTGCATATGC 57.125 45.000 21.09 21.09 42.50 3.14
2553 4281 1.829222 GTGGGACAAGTATCTCCGGAA 59.171 52.381 5.23 0.00 44.16 4.30
2560 4288 4.597004 ACAAGTATCTCCGGAAGTCTACA 58.403 43.478 5.23 0.00 0.00 2.74
2562 4290 5.299782 ACAAGTATCTCCGGAAGTCTACATC 59.700 44.000 5.23 0.00 0.00 3.06
2605 4333 6.543465 TGCGGAGATGTTATGATCAGATTTTT 59.457 34.615 0.09 0.00 0.00 1.94
2634 4362 2.128535 TGGTCAAGGTGTTTGGACCTA 58.871 47.619 10.62 0.00 46.29 3.08
2636 4364 2.882761 GGTCAAGGTGTTTGGACCTAAC 59.117 50.000 11.40 11.40 46.29 2.34
2656 4384 3.996480 ACTACTTGAGAGAACCAACTGC 58.004 45.455 0.00 0.00 0.00 4.40
2735 4467 2.034305 GGATCTCTTGATTGCATGCACC 59.966 50.000 22.58 15.85 32.19 5.01
2736 4468 2.203470 TCTCTTGATTGCATGCACCA 57.797 45.000 22.58 18.41 0.00 4.17
2777 4509 5.450965 CCAAAAGCTCTACAAGGGCAATATG 60.451 44.000 0.99 0.00 0.00 1.78
2807 4539 6.869913 CCATGTTAAGAAGCACAACATCATTT 59.130 34.615 0.00 0.00 40.09 2.32
2819 4551 6.457257 GCACAACATCATTTTTGAAGCAGTTT 60.457 34.615 0.00 0.00 31.90 2.66
2821 4553 6.817641 ACAACATCATTTTTGAAGCAGTTTCA 59.182 30.769 0.00 0.00 43.92 2.69
2823 4555 8.980610 CAACATCATTTTTGAAGCAGTTTCATA 58.019 29.630 0.00 0.00 44.90 2.15
2834 4566 6.430616 TGAAGCAGTTTCATAATCACATGACA 59.569 34.615 0.00 0.00 40.82 3.58
2890 4622 6.572519 TCGATCTCACAATGACATCAATGTA 58.427 36.000 2.33 0.00 41.95 2.29
2896 4628 7.761249 TCTCACAATGACATCAATGTACTACAG 59.239 37.037 2.33 0.00 41.95 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.271840 TTGGGGTTCCTCCAGATCGG 61.272 60.000 0.00 0.00 38.11 4.18
15 16 1.152204 TCGTTGGGGTTCCTCCAGA 60.152 57.895 0.00 0.00 38.11 3.86
45 46 1.601419 TTAACTGGGAGGCGGTCGAG 61.601 60.000 0.00 0.00 0.00 4.04
46 47 1.601419 CTTAACTGGGAGGCGGTCGA 61.601 60.000 0.00 0.00 0.00 4.20
47 48 1.153628 CTTAACTGGGAGGCGGTCG 60.154 63.158 0.00 0.00 0.00 4.79
48 49 0.323957 AACTTAACTGGGAGGCGGTC 59.676 55.000 0.00 0.00 0.00 4.79
53 56 4.041691 TGAGGAAGAAACTTAACTGGGAGG 59.958 45.833 0.00 0.00 0.00 4.30
105 108 2.844839 GGGGGAGAGGGATGACCG 60.845 72.222 0.00 0.00 46.96 4.79
119 122 2.196925 CGTCCAGATCGAGAGGGGG 61.197 68.421 0.00 0.00 0.00 5.40
123 126 0.382515 GGGTTCGTCCAGATCGAGAG 59.617 60.000 0.00 0.00 38.52 3.20
126 129 2.412323 CGGGGTTCGTCCAGATCGA 61.412 63.158 0.00 0.00 38.11 3.59
127 130 2.104331 CGGGGTTCGTCCAGATCG 59.896 66.667 2.42 0.00 38.11 3.69
148 151 2.920384 GGGAGGAGATCGGGGAGC 60.920 72.222 0.00 0.00 0.00 4.70
150 153 3.846254 GGGGGAGGAGATCGGGGA 61.846 72.222 0.00 0.00 0.00 4.81
168 174 5.334414 CGGATTGAGGTGAGAAAGAAACTTG 60.334 44.000 0.00 0.00 0.00 3.16
178 184 0.252057 TGTCCCGGATTGAGGTGAGA 60.252 55.000 0.73 0.00 0.00 3.27
179 185 0.108138 GTGTCCCGGATTGAGGTGAG 60.108 60.000 0.73 0.00 0.00 3.51
183 189 1.153628 GTCGTGTCCCGGATTGAGG 60.154 63.158 0.73 0.00 37.11 3.86
187 193 2.227089 GAGCTGTCGTGTCCCGGATT 62.227 60.000 0.73 0.00 37.11 3.01
233 239 2.685380 AGCCAGGACCTTCCGGAG 60.685 66.667 3.34 0.00 42.75 4.63
234 240 2.683933 GAGCCAGGACCTTCCGGA 60.684 66.667 0.00 0.00 42.75 5.14
235 241 4.148825 CGAGCCAGGACCTTCCGG 62.149 72.222 0.00 0.00 42.75 5.14
236 242 4.148825 CCGAGCCAGGACCTTCCG 62.149 72.222 0.00 0.00 42.75 4.30
237 243 4.475135 GCCGAGCCAGGACCTTCC 62.475 72.222 0.00 0.00 36.58 3.46
255 261 4.827087 AGCGTCGGCCATGCTGAG 62.827 66.667 17.69 0.00 46.43 3.35
259 265 3.643978 GATGAGCGTCGGCCATGC 61.644 66.667 2.24 7.44 41.24 4.06
260 266 3.333189 CGATGAGCGTCGGCCATG 61.333 66.667 2.24 0.00 41.24 3.66
283 289 3.083997 GGGGATGGCGTGAGGAGT 61.084 66.667 0.00 0.00 0.00 3.85
290 296 4.096003 CGAAGGTGGGGATGGCGT 62.096 66.667 0.00 0.00 0.00 5.68
310 316 7.117812 CGTCGGTTTATTTCTATTATGCAGGAT 59.882 37.037 0.00 0.00 0.00 3.24
321 327 2.423185 TCCTCGCGTCGGTTTATTTCTA 59.577 45.455 5.77 0.00 0.00 2.10
328 334 2.692817 TTTTTCCTCGCGTCGGTTT 58.307 47.368 5.77 0.00 0.00 3.27
351 357 5.643379 TTTTGCTAAATCTTAGGTGCCTG 57.357 39.130 0.12 0.00 0.00 4.85
367 373 6.179040 TGCATAAATTATTTGGGCTTTTGCT 58.821 32.000 13.55 0.00 46.54 3.91
374 380 6.582295 CGTATCACTGCATAAATTATTTGGGC 59.418 38.462 0.00 4.70 0.00 5.36
393 399 3.117491 CGGAGGGAGTACTACGTATCA 57.883 52.381 0.00 0.00 39.92 2.15
402 408 1.553706 TTTCTGGACGGAGGGAGTAC 58.446 55.000 0.00 0.00 0.00 2.73
403 409 2.544844 ATTTCTGGACGGAGGGAGTA 57.455 50.000 0.00 0.00 0.00 2.59
404 410 2.108970 GTATTTCTGGACGGAGGGAGT 58.891 52.381 0.00 0.00 0.00 3.85
405 411 2.389715 AGTATTTCTGGACGGAGGGAG 58.610 52.381 0.00 0.00 0.00 4.30
406 412 2.500098 CAAGTATTTCTGGACGGAGGGA 59.500 50.000 0.00 0.00 0.00 4.20
407 413 2.236395 ACAAGTATTTCTGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
408 414 3.195825 AGACAAGTATTTCTGGACGGAGG 59.804 47.826 0.00 0.00 0.00 4.30
409 415 4.457834 AGACAAGTATTTCTGGACGGAG 57.542 45.455 0.00 0.00 0.00 4.63
410 416 4.884668 AAGACAAGTATTTCTGGACGGA 57.115 40.909 0.00 0.00 0.00 4.69
411 417 8.712285 TTTATAAGACAAGTATTTCTGGACGG 57.288 34.615 0.00 0.00 0.00 4.79
459 465 9.886132 ATCGGTGTGTCTAGACTTATTTTAATT 57.114 29.630 23.01 0.00 0.00 1.40
460 466 9.886132 AATCGGTGTGTCTAGACTTATTTTAAT 57.114 29.630 23.01 5.62 0.00 1.40
461 467 9.715121 AAATCGGTGTGTCTAGACTTATTTTAA 57.285 29.630 23.01 0.00 0.00 1.52
462 468 9.715121 AAAATCGGTGTGTCTAGACTTATTTTA 57.285 29.630 23.01 4.85 30.50 1.52
463 469 8.617290 AAAATCGGTGTGTCTAGACTTATTTT 57.383 30.769 23.01 18.55 0.00 1.82
464 470 8.617290 AAAAATCGGTGTGTCTAGACTTATTT 57.383 30.769 23.01 14.83 0.00 1.40
465 471 9.367444 CTAAAAATCGGTGTGTCTAGACTTATT 57.633 33.333 23.01 10.56 0.00 1.40
466 472 7.980099 CCTAAAAATCGGTGTGTCTAGACTTAT 59.020 37.037 23.01 5.61 0.00 1.73
467 473 7.177216 TCCTAAAAATCGGTGTGTCTAGACTTA 59.823 37.037 23.01 9.67 0.00 2.24
468 474 6.014840 TCCTAAAAATCGGTGTGTCTAGACTT 60.015 38.462 23.01 7.97 0.00 3.01
469 475 5.479375 TCCTAAAAATCGGTGTGTCTAGACT 59.521 40.000 23.01 0.00 0.00 3.24
470 476 5.575995 GTCCTAAAAATCGGTGTGTCTAGAC 59.424 44.000 16.32 16.32 0.00 2.59
471 477 5.244402 TGTCCTAAAAATCGGTGTGTCTAGA 59.756 40.000 0.00 0.00 0.00 2.43
472 478 5.475719 TGTCCTAAAAATCGGTGTGTCTAG 58.524 41.667 0.00 0.00 0.00 2.43
473 479 5.471556 TGTCCTAAAAATCGGTGTGTCTA 57.528 39.130 0.00 0.00 0.00 2.59
474 480 4.345859 TGTCCTAAAAATCGGTGTGTCT 57.654 40.909 0.00 0.00 0.00 3.41
475 481 5.427036 TTTGTCCTAAAAATCGGTGTGTC 57.573 39.130 0.00 0.00 0.00 3.67
476 482 7.696992 ATATTTGTCCTAAAAATCGGTGTGT 57.303 32.000 0.00 0.00 0.00 3.72
477 483 8.980143 AAATATTTGTCCTAAAAATCGGTGTG 57.020 30.769 0.00 0.00 0.00 3.82
478 484 9.634163 GAAAATATTTGTCCTAAAAATCGGTGT 57.366 29.630 0.39 0.00 0.00 4.16
479 485 8.794406 CGAAAATATTTGTCCTAAAAATCGGTG 58.206 33.333 0.39 0.00 0.00 4.94
480 486 7.971722 CCGAAAATATTTGTCCTAAAAATCGGT 59.028 33.333 16.79 0.00 30.65 4.69
481 487 8.185505 TCCGAAAATATTTGTCCTAAAAATCGG 58.814 33.333 18.10 18.10 33.80 4.18
482 488 9.006215 GTCCGAAAATATTTGTCCTAAAAATCG 57.994 33.333 0.39 3.37 0.00 3.34
483 489 9.849166 TGTCCGAAAATATTTGTCCTAAAAATC 57.151 29.630 0.39 0.00 0.00 2.17
486 492 9.685828 CTTTGTCCGAAAATATTTGTCCTAAAA 57.314 29.630 0.39 0.00 0.00 1.52
487 493 8.301002 CCTTTGTCCGAAAATATTTGTCCTAAA 58.699 33.333 0.39 0.27 0.00 1.85
488 494 7.666388 TCCTTTGTCCGAAAATATTTGTCCTAA 59.334 33.333 0.39 0.00 0.00 2.69
489 495 7.169591 TCCTTTGTCCGAAAATATTTGTCCTA 58.830 34.615 0.39 0.00 0.00 2.94
490 496 6.007703 TCCTTTGTCCGAAAATATTTGTCCT 58.992 36.000 0.39 0.00 0.00 3.85
491 497 6.262193 TCCTTTGTCCGAAAATATTTGTCC 57.738 37.500 0.39 0.00 0.00 4.02
492 498 7.368059 ACTTCCTTTGTCCGAAAATATTTGTC 58.632 34.615 0.39 1.54 0.00 3.18
493 499 7.284919 ACTTCCTTTGTCCGAAAATATTTGT 57.715 32.000 0.39 0.00 0.00 2.83
494 500 8.293867 TGTACTTCCTTTGTCCGAAAATATTTG 58.706 33.333 0.39 0.00 0.00 2.32
495 501 8.398878 TGTACTTCCTTTGTCCGAAAATATTT 57.601 30.769 0.00 0.00 0.00 1.40
496 502 7.989416 TGTACTTCCTTTGTCCGAAAATATT 57.011 32.000 0.00 0.00 0.00 1.28
497 503 9.847224 ATATGTACTTCCTTTGTCCGAAAATAT 57.153 29.630 0.00 0.00 0.00 1.28
499 505 9.326413 CTATATGTACTTCCTTTGTCCGAAAAT 57.674 33.333 0.00 0.00 0.00 1.82
500 506 8.533657 TCTATATGTACTTCCTTTGTCCGAAAA 58.466 33.333 0.00 0.00 0.00 2.29
501 507 8.070034 TCTATATGTACTTCCTTTGTCCGAAA 57.930 34.615 0.00 0.00 0.00 3.46
502 508 7.649533 TCTATATGTACTTCCTTTGTCCGAA 57.350 36.000 0.00 0.00 0.00 4.30
503 509 7.834881 ATCTATATGTACTTCCTTTGTCCGA 57.165 36.000 0.00 0.00 0.00 4.55
504 510 9.976511 TTTATCTATATGTACTTCCTTTGTCCG 57.023 33.333 0.00 0.00 0.00 4.79
514 520 9.436957 CGCCCTTTGATTTATCTATATGTACTT 57.563 33.333 0.00 0.00 0.00 2.24
515 521 7.549488 GCGCCCTTTGATTTATCTATATGTACT 59.451 37.037 0.00 0.00 0.00 2.73
516 522 7.549488 AGCGCCCTTTGATTTATCTATATGTAC 59.451 37.037 2.29 0.00 0.00 2.90
517 523 7.620880 AGCGCCCTTTGATTTATCTATATGTA 58.379 34.615 2.29 0.00 0.00 2.29
518 524 6.476378 AGCGCCCTTTGATTTATCTATATGT 58.524 36.000 2.29 0.00 0.00 2.29
519 525 6.992063 AGCGCCCTTTGATTTATCTATATG 57.008 37.500 2.29 0.00 0.00 1.78
520 526 7.168219 TCAAGCGCCCTTTGATTTATCTATAT 58.832 34.615 2.29 0.00 0.00 0.86
521 527 6.530120 TCAAGCGCCCTTTGATTTATCTATA 58.470 36.000 2.29 0.00 0.00 1.31
752 760 0.182775 GGGTGGTGCTGGTATTAGGG 59.817 60.000 0.00 0.00 0.00 3.53
769 777 2.622962 GCGAAAACTGGGAACGGGG 61.623 63.158 0.00 0.00 42.76 5.73
930 942 4.020128 GCAAGGAAACCTAGAAGGAGAAGA 60.020 45.833 0.00 0.00 37.67 2.87
931 943 4.257731 GCAAGGAAACCTAGAAGGAGAAG 58.742 47.826 0.00 0.00 37.67 2.85
932 944 3.009143 GGCAAGGAAACCTAGAAGGAGAA 59.991 47.826 0.00 0.00 37.67 2.87
973 985 2.079158 CGTCGGTCCTTGAGTGTAGTA 58.921 52.381 0.00 0.00 0.00 1.82
974 986 0.879765 CGTCGGTCCTTGAGTGTAGT 59.120 55.000 0.00 0.00 0.00 2.73
975 987 1.135746 GTCGTCGGTCCTTGAGTGTAG 60.136 57.143 0.00 0.00 0.00 2.74
1239 1254 1.101635 CGACAGAGCCGTAGATGGGA 61.102 60.000 0.00 0.00 0.00 4.37
1254 1269 3.695606 GACCAGAGCAGGCCGACA 61.696 66.667 0.00 0.00 0.00 4.35
1910 1937 6.941857 TGTGCTTAAAATTTCCCCCTATTTC 58.058 36.000 0.00 0.00 0.00 2.17
2086 2117 5.008019 CAGTAGAACAGACTGCAAAACACAT 59.992 40.000 1.25 0.00 38.06 3.21
2108 3742 1.955778 TGGACTGACAAAATGCACCAG 59.044 47.619 0.00 0.00 0.00 4.00
2142 3776 6.291164 CGTAGCTTAGAACGCTTAGATTTCAC 60.291 42.308 0.00 0.00 38.86 3.18
2161 3795 0.455005 GAAGCCGTAGAACCGTAGCT 59.545 55.000 0.00 0.00 0.00 3.32
2249 3884 5.363580 ACCCATCATTTTTAGCATCCGAAAT 59.636 36.000 0.00 0.00 0.00 2.17
2270 3906 1.474143 GGAGTAGCATTGCAGAGACCC 60.474 57.143 11.91 0.61 0.00 4.46
2271 3907 1.474143 GGGAGTAGCATTGCAGAGACC 60.474 57.143 11.91 7.29 0.00 3.85
2352 4055 9.096160 CATATAGAGCAAAATGAGCGAATCTAT 57.904 33.333 0.00 0.00 33.92 1.98
2415 4119 6.516718 CATTGTATTGTACTCCCTCGATTCT 58.483 40.000 0.00 0.00 0.00 2.40
2420 4124 4.060038 AGCATTGTATTGTACTCCCTCG 57.940 45.455 0.00 0.00 0.00 4.63
2421 4125 5.914033 TGTAGCATTGTATTGTACTCCCTC 58.086 41.667 0.00 0.00 0.00 4.30
2430 4134 4.282068 GACGCCATTGTAGCATTGTATTG 58.718 43.478 0.00 0.00 0.00 1.90
2473 4177 2.352651 AGTCATGCATCGTCCATTTTCG 59.647 45.455 0.00 0.00 0.00 3.46
2475 4179 3.770263 CAGTCATGCATCGTCCATTTT 57.230 42.857 0.00 0.00 0.00 1.82
2517 4245 1.497278 CACAAATCTGCGGTCGTGG 59.503 57.895 0.00 0.00 0.00 4.94
2536 4264 3.025262 AGACTTCCGGAGATACTTGTCC 58.975 50.000 3.34 0.00 31.87 4.02
2553 4281 4.580167 GCTCTCAGACATCAGATGTAGACT 59.420 45.833 16.40 6.72 45.03 3.24
2560 4288 2.098614 ACGTGCTCTCAGACATCAGAT 58.901 47.619 0.00 0.00 0.00 2.90
2562 4290 1.626747 CACGTGCTCTCAGACATCAG 58.373 55.000 0.82 0.00 0.00 2.90
2605 4333 0.250124 CACCTTGACCACCGCAGTAA 60.250 55.000 0.00 0.00 0.00 2.24
2634 4362 4.381411 GCAGTTGGTTCTCTCAAGTAGTT 58.619 43.478 0.00 0.00 0.00 2.24
2636 4364 3.244215 TGGCAGTTGGTTCTCTCAAGTAG 60.244 47.826 0.00 0.00 0.00 2.57
2735 4467 6.639632 TTTTGGGAAGTTCTTTCATCTCTG 57.360 37.500 2.25 0.00 37.54 3.35
2736 4468 5.242615 GCTTTTGGGAAGTTCTTTCATCTCT 59.757 40.000 2.25 0.00 37.54 3.10
2777 4509 1.745653 GTGCTTCTTAACATGGCCCTC 59.254 52.381 0.00 0.00 0.00 4.30
2786 4518 8.351495 TCAAAAATGATGTTGTGCTTCTTAAC 57.649 30.769 0.00 0.00 0.00 2.01
2867 4599 5.729974 ACATTGATGTCATTGTGAGATCG 57.270 39.130 11.07 2.31 46.54 3.69


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

AutoCloner maintained by Alex Coulton.