Multiple sequence alignment - TraesCS1B01G066600

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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 TraesCS1B01G066600 chr1B 100.000 3536 0 0 1 3536 50949572 50953107 0.000000e+00 6530.0
1 TraesCS1B01G066600 chr1B 98.316 2375 26 7 609 2971 50900270 50902642 0.000000e+00 4152.0
2 TraesCS1B01G066600 chr1B 95.088 570 26 2 2966 3535 50923746 50924313 0.000000e+00 896.0
3 TraesCS1B01G066600 chr1A 93.608 2331 117 9 609 2920 32110764 32113081 0.000000e+00 3450.0
4 TraesCS1B01G066600 chr1A 92.333 300 23 0 3237 3536 32169984 32170283 9.070000e-116 427.0
5 TraesCS1B01G066600 chr1A 90.909 264 19 2 1 261 32110354 32110615 2.020000e-92 350.0
6 TraesCS1B01G066600 chr1A 89.963 269 16 4 2976 3242 32113085 32113344 1.570000e-88 337.0
7 TraesCS1B01G066600 chr1A 93.750 64 3 1 518 580 9654703 9654766 1.040000e-15 95.3
8 TraesCS1B01G066600 chr1A 81.609 87 13 3 431 517 287739476 287739559 6.330000e-08 69.4
9 TraesCS1B01G066600 chr1D 92.994 2298 123 13 609 2877 33595349 33597637 0.000000e+00 3317.0
10 TraesCS1B01G066600 chr1D 88.909 550 46 8 2898 3445 33597626 33598162 0.000000e+00 664.0
11 TraesCS1B01G066600 chr1D 83.036 112 15 4 429 538 48456650 48456541 8.080000e-17 99.0
12 TraesCS1B01G066600 chr1D 97.917 48 1 0 386 433 33595308 33595355 2.260000e-12 84.2
13 TraesCS1B01G066600 chr7D 86.088 2063 228 36 733 2752 497321003 497318957 0.000000e+00 2165.0
14 TraesCS1B01G066600 chr7D 89.806 1550 154 2 991 2539 28578580 28577034 0.000000e+00 1984.0
15 TraesCS1B01G066600 chr7A 85.201 2142 235 59 707 2777 563293695 563291565 0.000000e+00 2124.0
16 TraesCS1B01G066600 chr7A 85.618 2079 231 40 733 2752 563247107 563245038 0.000000e+00 2121.0
17 TraesCS1B01G066600 chr7A 87.097 93 10 2 425 517 39207470 39207560 1.740000e-18 104.0
18 TraesCS1B01G066600 chr2D 87.857 1787 196 15 1000 2769 608559379 608557597 0.000000e+00 2078.0
19 TraesCS1B01G066600 chr2D 95.122 41 2 0 259 299 634075065 634075025 8.190000e-07 65.8
20 TraesCS1B01G066600 chr4A 87.493 1799 193 16 991 2766 702327814 702326025 0.000000e+00 2047.0
21 TraesCS1B01G066600 chr2A 76.512 281 50 11 696 970 740079348 740079078 4.760000e-29 139.0
22 TraesCS1B01G066600 chr2A 76.512 281 50 11 696 970 740119192 740118922 4.760000e-29 139.0
23 TraesCS1B01G066600 chr2A 76.512 281 50 11 696 970 740143380 740143110 4.760000e-29 139.0
24 TraesCS1B01G066600 chr2A 88.158 76 9 0 432 507 189419916 189419991 1.350000e-14 91.6
25 TraesCS1B01G066600 chr2A 89.655 58 5 1 428 484 221750374 221750317 4.900000e-09 73.1
26 TraesCS1B01G066600 chr4B 83.929 112 15 3 429 538 395663601 395663491 1.740000e-18 104.0
27 TraesCS1B01G066600 chr6D 97.561 41 1 0 259 299 131624674 131624634 1.760000e-08 71.3
28 TraesCS1B01G066600 chr5A 97.500 40 1 0 257 296 643295490 643295529 6.330000e-08 69.4
29 TraesCS1B01G066600 chrUn 95.122 41 2 0 259 299 23901248 23901208 8.190000e-07 65.8
30 TraesCS1B01G066600 chr2B 95.122 41 2 0 259 299 755146289 755146249 8.190000e-07 65.8
31 TraesCS1B01G066600 chr2B 95.122 41 2 0 259 299 799161450 799161410 8.190000e-07 65.8
32 TraesCS1B01G066600 chr2B 95.122 41 2 0 259 299 799214606 799214566 8.190000e-07 65.8
33 TraesCS1B01G066600 chr2B 92.683 41 3 0 256 296 34141099 34141139 3.810000e-05 60.2
34 TraesCS1B01G066600 chr2B 92.683 41 3 0 259 299 793966493 793966453 3.810000e-05 60.2


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 TraesCS1B01G066600 chr1B 50949572 50953107 3535 False 6530.000000 6530 100.000000 1 3536 1 chr1B.!!$F3 3535
1 TraesCS1B01G066600 chr1B 50900270 50902642 2372 False 4152.000000 4152 98.316000 609 2971 1 chr1B.!!$F1 2362
2 TraesCS1B01G066600 chr1B 50923746 50924313 567 False 896.000000 896 95.088000 2966 3535 1 chr1B.!!$F2 569
3 TraesCS1B01G066600 chr1A 32110354 32113344 2990 False 1379.000000 3450 91.493333 1 3242 3 chr1A.!!$F4 3241
4 TraesCS1B01G066600 chr1D 33595308 33598162 2854 False 1355.066667 3317 93.273333 386 3445 3 chr1D.!!$F1 3059
5 TraesCS1B01G066600 chr7D 497318957 497321003 2046 True 2165.000000 2165 86.088000 733 2752 1 chr7D.!!$R2 2019
6 TraesCS1B01G066600 chr7D 28577034 28578580 1546 True 1984.000000 1984 89.806000 991 2539 1 chr7D.!!$R1 1548
7 TraesCS1B01G066600 chr7A 563291565 563293695 2130 True 2124.000000 2124 85.201000 707 2777 1 chr7A.!!$R2 2070
8 TraesCS1B01G066600 chr7A 563245038 563247107 2069 True 2121.000000 2121 85.618000 733 2752 1 chr7A.!!$R1 2019
9 TraesCS1B01G066600 chr2D 608557597 608559379 1782 True 2078.000000 2078 87.857000 1000 2769 1 chr2D.!!$R1 1769
10 TraesCS1B01G066600 chr4A 702326025 702327814 1789 True 2047.000000 2047 87.493000 991 2766 1 chr4A.!!$R1 1775

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
457 491 0.034863 TCCGTCCTGGTTTATTGGCC 60.035 55.0 0.0 0.0 39.52 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2829 2967 4.44472 CGGTCTAACAAGAAAGTGAGTGAC 59.555 45.833 0.0 0.0 0.0 3.67 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
30 31 6.578023 AGACTGGCTGAATCTGATAGTAAAC 58.422 40.000 0.00 0.00 0.00 2.01
33 34 6.820656 ACTGGCTGAATCTGATAGTAAACTTG 59.179 38.462 0.00 0.00 0.00 3.16
39 40 8.703604 TGAATCTGATAGTAAACTTGTACTGC 57.296 34.615 0.00 0.00 35.85 4.40
42 43 7.462571 TCTGATAGTAAACTTGTACTGCAGA 57.537 36.000 23.35 0.48 40.58 4.26
50 51 8.345565 AGTAAACTTGTACTGCAGAATTTTCAG 58.654 33.333 23.35 8.85 32.97 3.02
103 107 6.317391 TGATATGATTACAAACATCGTTGGCA 59.683 34.615 0.00 0.00 32.50 4.92
142 146 7.512058 ACACTATGATCTCATCCATAAGTCCTT 59.488 37.037 0.00 0.00 37.76 3.36
156 160 8.573035 TCCATAAGTCCTTGTTGTATTTTGAAC 58.427 33.333 0.00 0.00 0.00 3.18
158 162 6.783708 AAGTCCTTGTTGTATTTTGAACCA 57.216 33.333 0.00 0.00 0.00 3.67
272 276 9.847224 TGTTATTTCTAATACTTCCTCCATTCC 57.153 33.333 0.00 0.00 0.00 3.01
273 277 9.286170 GTTATTTCTAATACTTCCTCCATTCCC 57.714 37.037 0.00 0.00 0.00 3.97
274 278 7.713704 ATTTCTAATACTTCCTCCATTCCCT 57.286 36.000 0.00 0.00 0.00 4.20
275 279 7.525158 TTTCTAATACTTCCTCCATTCCCTT 57.475 36.000 0.00 0.00 0.00 3.95
276 280 8.632731 TTTCTAATACTTCCTCCATTCCCTTA 57.367 34.615 0.00 0.00 0.00 2.69
277 281 8.814448 TTCTAATACTTCCTCCATTCCCTTAT 57.186 34.615 0.00 0.00 0.00 1.73
278 282 9.907819 TTCTAATACTTCCTCCATTCCCTTATA 57.092 33.333 0.00 0.00 0.00 0.98
279 283 9.322769 TCTAATACTTCCTCCATTCCCTTATAC 57.677 37.037 0.00 0.00 0.00 1.47
280 284 7.947782 AATACTTCCTCCATTCCCTTATACA 57.052 36.000 0.00 0.00 0.00 2.29
281 285 7.947782 ATACTTCCTCCATTCCCTTATACAA 57.052 36.000 0.00 0.00 0.00 2.41
282 286 6.652205 ACTTCCTCCATTCCCTTATACAAA 57.348 37.500 0.00 0.00 0.00 2.83
283 287 6.663734 ACTTCCTCCATTCCCTTATACAAAG 58.336 40.000 0.00 0.00 0.00 2.77
284 288 5.048846 TCCTCCATTCCCTTATACAAAGC 57.951 43.478 0.00 0.00 0.00 3.51
285 289 4.141251 TCCTCCATTCCCTTATACAAAGCC 60.141 45.833 0.00 0.00 0.00 4.35
286 290 4.386312 CCTCCATTCCCTTATACAAAGCCA 60.386 45.833 0.00 0.00 0.00 4.75
287 291 4.532834 TCCATTCCCTTATACAAAGCCAC 58.467 43.478 0.00 0.00 0.00 5.01
288 292 4.229582 TCCATTCCCTTATACAAAGCCACT 59.770 41.667 0.00 0.00 0.00 4.00
289 293 5.430417 TCCATTCCCTTATACAAAGCCACTA 59.570 40.000 0.00 0.00 0.00 2.74
290 294 6.102615 TCCATTCCCTTATACAAAGCCACTAT 59.897 38.462 0.00 0.00 0.00 2.12
291 295 6.207417 CCATTCCCTTATACAAAGCCACTATG 59.793 42.308 0.00 0.00 0.00 2.23
292 296 6.569127 TTCCCTTATACAAAGCCACTATGA 57.431 37.500 0.00 0.00 0.00 2.15
293 297 6.569127 TCCCTTATACAAAGCCACTATGAA 57.431 37.500 0.00 0.00 0.00 2.57
294 298 6.964464 TCCCTTATACAAAGCCACTATGAAA 58.036 36.000 0.00 0.00 0.00 2.69
295 299 7.406916 TCCCTTATACAAAGCCACTATGAAAA 58.593 34.615 0.00 0.00 0.00 2.29
296 300 7.556275 TCCCTTATACAAAGCCACTATGAAAAG 59.444 37.037 0.00 0.00 0.00 2.27
307 311 8.943909 AGCCACTATGAAAAGTAGTACATAAC 57.056 34.615 2.52 0.00 31.46 1.89
383 417 6.598064 AGGGACTAATAAATCGTGACAAAAGG 59.402 38.462 0.00 0.00 36.02 3.11
432 466 5.583061 GTGACGAAAATGGTCCATGTATGTA 59.417 40.000 4.74 0.00 33.46 2.29
433 467 5.583061 TGACGAAAATGGTCCATGTATGTAC 59.417 40.000 4.74 0.00 33.46 2.90
434 468 5.741011 ACGAAAATGGTCCATGTATGTACT 58.259 37.500 4.74 0.00 0.00 2.73
435 469 6.880484 ACGAAAATGGTCCATGTATGTACTA 58.120 36.000 4.74 0.00 0.00 1.82
436 470 7.506114 ACGAAAATGGTCCATGTATGTACTAT 58.494 34.615 4.74 0.00 0.00 2.12
437 471 7.656137 ACGAAAATGGTCCATGTATGTACTATC 59.344 37.037 4.74 0.00 0.00 2.08
438 472 7.872993 CGAAAATGGTCCATGTATGTACTATCT 59.127 37.037 4.74 0.00 0.00 1.98
439 473 9.209175 GAAAATGGTCCATGTATGTACTATCTC 57.791 37.037 4.74 0.00 0.00 2.75
440 474 6.859112 ATGGTCCATGTATGTACTATCTCC 57.141 41.667 2.68 0.00 0.00 3.71
441 475 4.765339 TGGTCCATGTATGTACTATCTCCG 59.235 45.833 0.00 0.00 0.00 4.63
442 476 4.765856 GGTCCATGTATGTACTATCTCCGT 59.234 45.833 0.00 0.00 0.00 4.69
443 477 5.106237 GGTCCATGTATGTACTATCTCCGTC 60.106 48.000 0.00 0.00 0.00 4.79
444 478 5.008331 TCCATGTATGTACTATCTCCGTCC 58.992 45.833 0.00 0.00 0.00 4.79
445 479 5.010933 CCATGTATGTACTATCTCCGTCCT 58.989 45.833 0.00 0.00 0.00 3.85
446 480 5.106118 CCATGTATGTACTATCTCCGTCCTG 60.106 48.000 0.00 0.00 0.00 3.86
447 481 4.395625 TGTATGTACTATCTCCGTCCTGG 58.604 47.826 0.00 0.00 40.09 4.45
448 482 3.596940 ATGTACTATCTCCGTCCTGGT 57.403 47.619 0.00 0.00 39.52 4.00
449 483 3.377253 TGTACTATCTCCGTCCTGGTT 57.623 47.619 0.00 0.00 39.52 3.67
450 484 3.705051 TGTACTATCTCCGTCCTGGTTT 58.295 45.455 0.00 0.00 39.52 3.27
451 485 4.858850 TGTACTATCTCCGTCCTGGTTTA 58.141 43.478 0.00 0.00 39.52 2.01
452 486 5.452255 TGTACTATCTCCGTCCTGGTTTAT 58.548 41.667 0.00 0.00 39.52 1.40
453 487 5.895534 TGTACTATCTCCGTCCTGGTTTATT 59.104 40.000 0.00 0.00 39.52 1.40
454 488 5.277857 ACTATCTCCGTCCTGGTTTATTG 57.722 43.478 0.00 0.00 39.52 1.90
455 489 3.560636 ATCTCCGTCCTGGTTTATTGG 57.439 47.619 0.00 0.00 39.52 3.16
456 490 1.065709 TCTCCGTCCTGGTTTATTGGC 60.066 52.381 0.00 0.00 39.52 4.52
457 491 0.034863 TCCGTCCTGGTTTATTGGCC 60.035 55.000 0.00 0.00 39.52 5.36
458 492 1.035385 CCGTCCTGGTTTATTGGCCC 61.035 60.000 0.00 0.00 0.00 5.80
459 493 1.035385 CGTCCTGGTTTATTGGCCCC 61.035 60.000 0.00 0.00 0.00 5.80
460 494 0.686441 GTCCTGGTTTATTGGCCCCC 60.686 60.000 0.00 0.00 0.00 5.40
598 632 9.549078 TGGTCAAAAATTAAGAACCAATAAACC 57.451 29.630 0.00 0.00 0.00 3.27
599 633 9.549078 GGTCAAAAATTAAGAACCAATAAACCA 57.451 29.630 0.00 0.00 0.00 3.67
605 639 8.596271 AATTAAGAACCAATAAACCAAAACGG 57.404 30.769 0.00 0.00 42.50 4.44
606 640 5.855740 AAGAACCAATAAACCAAAACGGA 57.144 34.783 0.00 0.00 38.63 4.69
607 641 5.447624 AGAACCAATAAACCAAAACGGAG 57.552 39.130 0.00 0.00 38.63 4.63
608 642 4.279922 AGAACCAATAAACCAAAACGGAGG 59.720 41.667 0.00 0.00 38.63 4.30
609 643 3.568443 ACCAATAAACCAAAACGGAGGT 58.432 40.909 0.00 0.00 40.61 3.85
610 644 4.727677 ACCAATAAACCAAAACGGAGGTA 58.272 39.130 0.00 0.00 37.07 3.08
611 645 4.763279 ACCAATAAACCAAAACGGAGGTAG 59.237 41.667 0.00 0.00 37.07 3.18
612 646 4.763279 CCAATAAACCAAAACGGAGGTAGT 59.237 41.667 0.00 0.00 37.07 2.73
2562 2677 2.622942 TCATTCCAGAAGCCACACAAAC 59.377 45.455 0.00 0.00 0.00 2.93
2829 2967 2.032117 GCGCCTGAATTTTTGTTTTGGG 60.032 45.455 0.00 0.00 0.00 4.12
2877 3015 7.059945 CGTGAGATTAATGCAACAAGTTCTTTC 59.940 37.037 0.00 0.00 0.00 2.62
2933 3072 6.917533 AGACAAACTCATGAAGCCTTTATTG 58.082 36.000 0.00 0.00 0.00 1.90
3149 3289 4.634004 CACTCCGCTGGTTATGTCATTTAA 59.366 41.667 0.00 0.00 0.00 1.52
3167 3307 5.534207 TTTAAGACCACCTTACAAGTCGA 57.466 39.130 0.00 0.00 37.10 4.20
3168 3308 5.534207 TTAAGACCACCTTACAAGTCGAA 57.466 39.130 0.00 0.00 37.10 3.71
3169 3309 3.662247 AGACCACCTTACAAGTCGAAG 57.338 47.619 0.00 0.00 34.41 3.79
3170 3310 2.299297 AGACCACCTTACAAGTCGAAGG 59.701 50.000 0.00 0.00 46.56 3.46
3171 3311 1.270678 ACCACCTTACAAGTCGAAGGC 60.271 52.381 0.00 0.00 45.28 4.35
3173 3313 2.338500 CACCTTACAAGTCGAAGGCTC 58.662 52.381 0.00 0.00 40.46 4.70
3174 3314 1.067776 ACCTTACAAGTCGAAGGCTCG 60.068 52.381 0.00 0.00 40.46 5.03
3195 3343 0.252881 AGCCACCTGAATCCTCTGGA 60.253 55.000 5.19 0.00 41.99 3.86
3245 3394 0.804989 CCTTACCGCCAAAGCTTCAG 59.195 55.000 0.00 0.00 36.60 3.02
3251 3400 0.608035 CGCCAAAGCTTCAGGGGTTA 60.608 55.000 20.37 0.00 36.60 2.85
3276 3425 3.922171 GTCAGAGATCTTTGACCCCAT 57.078 47.619 27.94 0.00 38.16 4.00
3315 3464 1.463674 AACATCCAAAGGTCATCGCC 58.536 50.000 0.00 0.00 0.00 5.54
3326 3475 3.254654 CATCGCCGCACACTACCG 61.255 66.667 0.00 0.00 0.00 4.02
3338 3487 2.348888 ACTACCGGAACTGCTCCCG 61.349 63.158 9.46 0.00 41.87 5.14
3371 3520 4.220382 TCCTTGTCAAAGCCACATAAATGG 59.780 41.667 0.00 0.00 43.26 3.16
3493 3642 1.633945 ACATAGGAAACTGACACCCCC 59.366 52.381 0.00 0.00 43.88 5.40
3535 3684 5.374071 TCCTTTTCCACTTTTCTACCACTC 58.626 41.667 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 7.462571 TCTGCAGTACAAGTTTACTATCAGA 57.537 36.000 14.67 15.47 37.90 3.27
28 29 6.942532 TCTGAAAATTCTGCAGTACAAGTT 57.057 33.333 14.67 3.46 0.00 2.66
30 31 8.725148 AGTAATCTGAAAATTCTGCAGTACAAG 58.275 33.333 14.67 4.13 0.00 3.16
33 34 8.507249 ACAAGTAATCTGAAAATTCTGCAGTAC 58.493 33.333 14.67 4.19 0.00 2.73
73 74 8.357796 ACGATGTTTGTAATCATATCAGTCTG 57.642 34.615 0.00 0.00 0.00 3.51
82 83 4.217334 TGTGCCAACGATGTTTGTAATCAT 59.783 37.500 0.00 0.00 0.00 2.45
83 84 3.565902 TGTGCCAACGATGTTTGTAATCA 59.434 39.130 0.00 0.00 0.00 2.57
139 143 6.391227 AGACTGGTTCAAAATACAACAAGG 57.609 37.500 0.00 0.00 28.89 3.61
142 146 7.254852 GTCAAAGACTGGTTCAAAATACAACA 58.745 34.615 0.00 0.00 0.00 3.33
158 162 9.515226 TGCTAGTTAAATTTATGGTCAAAGACT 57.485 29.630 0.00 0.00 32.47 3.24
250 254 7.713704 AGGGAATGGAGGAAGTATTAGAAAT 57.286 36.000 0.00 0.00 0.00 2.17
254 258 9.101325 TGTATAAGGGAATGGAGGAAGTATTAG 57.899 37.037 0.00 0.00 0.00 1.73
255 259 9.455144 TTGTATAAGGGAATGGAGGAAGTATTA 57.545 33.333 0.00 0.00 0.00 0.98
256 260 7.947782 TGTATAAGGGAATGGAGGAAGTATT 57.052 36.000 0.00 0.00 0.00 1.89
257 261 7.947782 TTGTATAAGGGAATGGAGGAAGTAT 57.052 36.000 0.00 0.00 0.00 2.12
258 262 7.637301 GCTTTGTATAAGGGAATGGAGGAAGTA 60.637 40.741 0.00 0.00 0.00 2.24
259 263 6.652205 TTTGTATAAGGGAATGGAGGAAGT 57.348 37.500 0.00 0.00 0.00 3.01
260 264 5.532779 GCTTTGTATAAGGGAATGGAGGAAG 59.467 44.000 0.00 0.00 0.00 3.46
261 265 5.445964 GCTTTGTATAAGGGAATGGAGGAA 58.554 41.667 0.00 0.00 0.00 3.36
262 266 4.141251 GGCTTTGTATAAGGGAATGGAGGA 60.141 45.833 0.00 0.00 0.00 3.71
263 267 4.145052 GGCTTTGTATAAGGGAATGGAGG 58.855 47.826 0.00 0.00 0.00 4.30
264 268 4.580580 GTGGCTTTGTATAAGGGAATGGAG 59.419 45.833 0.00 0.00 0.00 3.86
265 269 4.229582 AGTGGCTTTGTATAAGGGAATGGA 59.770 41.667 0.00 0.00 0.00 3.41
266 270 4.536765 AGTGGCTTTGTATAAGGGAATGG 58.463 43.478 0.00 0.00 0.00 3.16
267 271 6.998074 TCATAGTGGCTTTGTATAAGGGAATG 59.002 38.462 0.00 0.00 0.00 2.67
268 272 7.149202 TCATAGTGGCTTTGTATAAGGGAAT 57.851 36.000 0.00 0.00 0.00 3.01
269 273 6.569127 TCATAGTGGCTTTGTATAAGGGAA 57.431 37.500 0.00 0.00 0.00 3.97
270 274 6.569127 TTCATAGTGGCTTTGTATAAGGGA 57.431 37.500 0.00 0.00 0.00 4.20
271 275 7.339466 ACTTTTCATAGTGGCTTTGTATAAGGG 59.661 37.037 0.00 0.00 0.00 3.95
272 276 8.281212 ACTTTTCATAGTGGCTTTGTATAAGG 57.719 34.615 0.00 0.00 0.00 2.69
274 278 9.953565 ACTACTTTTCATAGTGGCTTTGTATAA 57.046 29.630 0.00 0.00 31.54 0.98
276 280 9.379791 GTACTACTTTTCATAGTGGCTTTGTAT 57.620 33.333 0.00 0.00 34.66 2.29
277 281 8.369424 TGTACTACTTTTCATAGTGGCTTTGTA 58.631 33.333 0.00 0.00 34.66 2.41
278 282 7.221450 TGTACTACTTTTCATAGTGGCTTTGT 58.779 34.615 0.00 0.00 34.66 2.83
279 283 7.667043 TGTACTACTTTTCATAGTGGCTTTG 57.333 36.000 0.00 0.00 34.66 2.77
280 284 9.953565 TTATGTACTACTTTTCATAGTGGCTTT 57.046 29.630 0.00 0.00 34.66 3.51
281 285 9.379791 GTTATGTACTACTTTTCATAGTGGCTT 57.620 33.333 0.00 0.00 34.66 4.35
282 286 8.537016 TGTTATGTACTACTTTTCATAGTGGCT 58.463 33.333 0.00 0.00 34.66 4.75
283 287 8.712285 TGTTATGTACTACTTTTCATAGTGGC 57.288 34.615 0.00 0.00 34.66 5.01
333 337 8.262715 TGCTATTTTGTATCGAACTTTGATCA 57.737 30.769 0.00 0.00 0.00 2.92
344 348 8.827177 TTATTAGTCCCTGCTATTTTGTATCG 57.173 34.615 0.00 0.00 0.00 2.92
347 351 9.268268 CGATTTATTAGTCCCTGCTATTTTGTA 57.732 33.333 0.00 0.00 0.00 2.41
371 375 3.830744 TCCTTTCTCCTTTTGTCACGA 57.169 42.857 0.00 0.00 0.00 4.35
372 376 5.438761 AAATCCTTTCTCCTTTTGTCACG 57.561 39.130 0.00 0.00 0.00 4.35
432 466 4.101119 CCAATAAACCAGGACGGAGATAGT 59.899 45.833 0.00 0.00 38.63 2.12
433 467 4.632153 CCAATAAACCAGGACGGAGATAG 58.368 47.826 0.00 0.00 38.63 2.08
434 468 3.181458 GCCAATAAACCAGGACGGAGATA 60.181 47.826 0.00 0.00 38.63 1.98
435 469 2.421529 GCCAATAAACCAGGACGGAGAT 60.422 50.000 0.00 0.00 38.63 2.75
436 470 1.065709 GCCAATAAACCAGGACGGAGA 60.066 52.381 0.00 0.00 38.63 3.71
437 471 1.379527 GCCAATAAACCAGGACGGAG 58.620 55.000 0.00 0.00 38.63 4.63
438 472 0.034863 GGCCAATAAACCAGGACGGA 60.035 55.000 0.00 0.00 38.63 4.69
439 473 1.035385 GGGCCAATAAACCAGGACGG 61.035 60.000 4.39 0.00 42.50 4.79
440 474 1.035385 GGGGCCAATAAACCAGGACG 61.035 60.000 4.39 0.00 0.00 4.79
441 475 0.686441 GGGGGCCAATAAACCAGGAC 60.686 60.000 4.39 0.00 0.00 3.85
442 476 1.700985 GGGGGCCAATAAACCAGGA 59.299 57.895 4.39 0.00 0.00 3.86
443 477 4.373551 GGGGGCCAATAAACCAGG 57.626 61.111 4.39 0.00 0.00 4.45
572 606 9.549078 GGTTTATTGGTTCTTAATTTTTGACCA 57.451 29.630 0.00 0.00 0.00 4.02
573 607 9.549078 TGGTTTATTGGTTCTTAATTTTTGACC 57.451 29.630 0.00 0.00 0.00 4.02
579 613 9.047371 CCGTTTTGGTTTATTGGTTCTTAATTT 57.953 29.630 0.00 0.00 0.00 1.82
580 614 8.422566 TCCGTTTTGGTTTATTGGTTCTTAATT 58.577 29.630 0.00 0.00 39.52 1.40
581 615 7.953752 TCCGTTTTGGTTTATTGGTTCTTAAT 58.046 30.769 0.00 0.00 39.52 1.40
582 616 7.344095 TCCGTTTTGGTTTATTGGTTCTTAA 57.656 32.000 0.00 0.00 39.52 1.85
583 617 6.016108 CCTCCGTTTTGGTTTATTGGTTCTTA 60.016 38.462 0.00 0.00 39.52 2.10
584 618 5.221362 CCTCCGTTTTGGTTTATTGGTTCTT 60.221 40.000 0.00 0.00 39.52 2.52
585 619 4.279922 CCTCCGTTTTGGTTTATTGGTTCT 59.720 41.667 0.00 0.00 39.52 3.01
586 620 4.038282 ACCTCCGTTTTGGTTTATTGGTTC 59.962 41.667 0.00 0.00 39.52 3.62
587 621 3.962063 ACCTCCGTTTTGGTTTATTGGTT 59.038 39.130 0.00 0.00 39.52 3.67
588 622 3.568443 ACCTCCGTTTTGGTTTATTGGT 58.432 40.909 0.00 0.00 39.52 3.67
589 623 4.763279 ACTACCTCCGTTTTGGTTTATTGG 59.237 41.667 0.00 0.00 39.52 3.16
590 624 5.952526 ACTACCTCCGTTTTGGTTTATTG 57.047 39.130 0.00 0.00 39.52 1.90
591 625 5.645067 GCTACTACCTCCGTTTTGGTTTATT 59.355 40.000 0.00 0.00 39.52 1.40
592 626 5.181009 GCTACTACCTCCGTTTTGGTTTAT 58.819 41.667 0.00 0.00 39.52 1.40
593 627 4.040217 TGCTACTACCTCCGTTTTGGTTTA 59.960 41.667 0.00 0.00 39.52 2.01
594 628 3.181452 TGCTACTACCTCCGTTTTGGTTT 60.181 43.478 0.00 0.00 39.52 3.27
595 629 2.369532 TGCTACTACCTCCGTTTTGGTT 59.630 45.455 0.00 0.00 39.52 3.67
596 630 1.972795 TGCTACTACCTCCGTTTTGGT 59.027 47.619 0.00 0.00 39.52 3.67
597 631 2.232941 TCTGCTACTACCTCCGTTTTGG 59.767 50.000 0.00 0.00 40.09 3.28
598 632 3.056749 AGTCTGCTACTACCTCCGTTTTG 60.057 47.826 0.00 0.00 36.36 2.44
599 633 3.163467 AGTCTGCTACTACCTCCGTTTT 58.837 45.455 0.00 0.00 36.36 2.43
600 634 2.805194 AGTCTGCTACTACCTCCGTTT 58.195 47.619 0.00 0.00 36.36 3.60
601 635 2.510928 AGTCTGCTACTACCTCCGTT 57.489 50.000 0.00 0.00 36.36 4.44
602 636 2.745812 GCTAGTCTGCTACTACCTCCGT 60.746 54.545 0.00 0.00 39.80 4.69
603 637 1.874872 GCTAGTCTGCTACTACCTCCG 59.125 57.143 0.00 0.00 39.80 4.63
604 638 2.882137 CTGCTAGTCTGCTACTACCTCC 59.118 54.545 0.00 0.00 39.80 4.30
605 639 3.562557 GTCTGCTAGTCTGCTACTACCTC 59.437 52.174 0.00 0.00 39.80 3.85
606 640 3.547746 GTCTGCTAGTCTGCTACTACCT 58.452 50.000 0.00 0.00 39.80 3.08
607 641 2.288458 CGTCTGCTAGTCTGCTACTACC 59.712 54.545 0.00 0.00 39.80 3.18
608 642 3.001533 GTCGTCTGCTAGTCTGCTACTAC 59.998 52.174 0.00 0.00 39.80 2.73
609 643 3.118702 AGTCGTCTGCTAGTCTGCTACTA 60.119 47.826 0.00 0.53 39.80 1.82
610 644 2.011222 GTCGTCTGCTAGTCTGCTACT 58.989 52.381 0.00 0.00 42.62 2.57
611 645 2.011222 AGTCGTCTGCTAGTCTGCTAC 58.989 52.381 0.00 0.00 0.00 3.58
612 646 2.010497 CAGTCGTCTGCTAGTCTGCTA 58.990 52.381 0.00 0.00 34.79 3.49
626 660 3.190535 GTCATAAATTGCCAACCAGTCGT 59.809 43.478 0.00 0.00 0.00 4.34
2829 2967 4.444720 CGGTCTAACAAGAAAGTGAGTGAC 59.555 45.833 0.00 0.00 0.00 3.67
3034 3173 3.506810 GACCTCAAATGTCGAGACTCAG 58.493 50.000 2.82 0.00 31.84 3.35
3100 3239 4.809426 GCAAGTTACGGTGCTATCATTAGT 59.191 41.667 6.79 0.00 37.78 2.24
3149 3289 2.299297 CCTTCGACTTGTAAGGTGGTCT 59.701 50.000 0.00 0.00 37.96 3.85
3170 3310 1.092345 GGATTCAGGTGGCTTCGAGC 61.092 60.000 0.00 0.00 41.46 5.03
3171 3311 0.539051 AGGATTCAGGTGGCTTCGAG 59.461 55.000 0.00 0.00 0.00 4.04
3172 3312 0.537188 GAGGATTCAGGTGGCTTCGA 59.463 55.000 0.00 0.00 0.00 3.71
3173 3313 0.539051 AGAGGATTCAGGTGGCTTCG 59.461 55.000 0.00 0.00 0.00 3.79
3174 3314 1.407989 CCAGAGGATTCAGGTGGCTTC 60.408 57.143 0.00 0.00 0.00 3.86
3195 3343 4.334203 GTCTCTCGCCGATGATCTATACAT 59.666 45.833 0.00 0.00 0.00 2.29
3245 3394 3.049344 AGATCTCTGACCCAATAACCCC 58.951 50.000 0.00 0.00 0.00 4.95
3276 3425 2.082140 TCTAGGAGCTTCGGCCATAA 57.918 50.000 2.24 0.00 43.01 1.90
3315 3464 2.380410 GCAGTTCCGGTAGTGTGCG 61.380 63.158 16.29 0.00 0.00 5.34
3338 3487 1.234821 TTGACAAGGAATGGTGTCGC 58.765 50.000 0.00 0.00 34.32 5.19
3371 3520 7.284716 CCCTCCAGAAAATATTACCAAGGTTAC 59.715 40.741 0.00 0.00 0.00 2.50
3391 3540 0.856982 AACATTGGTTGGTCCCTCCA 59.143 50.000 0.00 0.00 45.60 3.86
3493 3642 1.069358 GAGGAGGATTTGAGTAGGCCG 59.931 57.143 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.