Multiple sequence alignment - TraesCS1B01G147200

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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 TraesCS1B01G147200 chr1B 100.000 3714 0 0 1 3714 210212243 210208530 0.000000e+00 6859.0
1 TraesCS1B01G147200 chr1B 100.000 143 0 0 4040 4182 210208204 210208062 8.910000e-67 265.0
2 TraesCS1B01G147200 chr1B 92.241 116 8 1 321 435 332136160 332136275 3.350000e-36 163.0
3 TraesCS1B01G147200 chr1D 95.638 3278 101 26 445 3714 136953362 136950119 0.000000e+00 5223.0
4 TraesCS1B01G147200 chr1D 97.046 237 7 0 87 323 136953613 136953377 2.340000e-107 399.0
5 TraesCS1B01G147200 chr1D 93.909 197 10 2 3369 3565 23947883 23947689 3.160000e-76 296.0
6 TraesCS1B01G147200 chr1D 97.203 143 4 0 4040 4182 136949887 136949745 4.180000e-60 243.0
7 TraesCS1B01G147200 chr1D 100.000 44 0 0 4040 4083 136950069 136950026 9.640000e-12 82.4
8 TraesCS1B01G147200 chr1A 95.224 3287 98 18 435 3698 167149843 167153093 0.000000e+00 5145.0
9 TraesCS1B01G147200 chr1A 93.189 323 14 2 1 323 167149522 167149836 6.330000e-128 468.0
10 TraesCS1B01G147200 chr1A 96.552 116 3 1 321 435 562161046 562161161 1.530000e-44 191.0
11 TraesCS1B01G147200 chr1A 94.565 92 5 0 4091 4182 167153418 167153509 4.360000e-30 143.0
12 TraesCS1B01G147200 chr3D 94.416 197 9 2 3369 3565 402476149 402476343 6.790000e-78 302.0
13 TraesCS1B01G147200 chr5D 93.909 197 10 2 3369 3565 55336716 55336910 3.160000e-76 296.0
14 TraesCS1B01G147200 chr5D 91.057 123 10 1 321 442 320886288 320886166 9.300000e-37 165.0
15 TraesCS1B01G147200 chr7D 93.401 197 11 2 3369 3565 476878965 476879159 1.470000e-74 291.0
16 TraesCS1B01G147200 chr7D 90.833 120 9 2 317 435 4241699 4241817 4.330000e-35 159.0
17 TraesCS1B01G147200 chr6D 93.401 197 11 2 3369 3565 117040913 117040719 1.470000e-74 291.0
18 TraesCS1B01G147200 chr6D 91.597 119 9 1 318 435 9359194 9359076 3.350000e-36 163.0
19 TraesCS1B01G147200 chr4D 93.401 197 11 2 3369 3565 200997560 200997754 1.470000e-74 291.0
20 TraesCS1B01G147200 chr2D 93.401 197 11 2 3369 3565 8648027 8648221 1.470000e-74 291.0
21 TraesCS1B01G147200 chr3A 92.308 117 7 2 320 435 291825333 291825448 9.300000e-37 165.0
22 TraesCS1B01G147200 chr3A 91.453 117 9 1 320 435 49978665 49978781 4.330000e-35 159.0
23 TraesCS1B01G147200 chr5B 91.453 117 9 1 320 435 38365241 38365125 4.330000e-35 159.0
24 TraesCS1B01G147200 chr6A 90.756 119 10 1 318 435 11163573 11163691 1.560000e-34 158.0


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 TraesCS1B01G147200 chr1B 210208062 210212243 4181 True 3562.000000 6859 100.00000 1 4182 2 chr1B.!!$R1 4181
1 TraesCS1B01G147200 chr1D 136949745 136953613 3868 True 1486.850000 5223 97.47175 87 4182 4 chr1D.!!$R2 4095
2 TraesCS1B01G147200 chr1A 167149522 167153509 3987 False 1918.666667 5145 94.32600 1 4182 3 chr1A.!!$F2 4181

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
339 340 0.032813 TACTCCCTCCGTCCCGAATT 60.033 55.0 0.0 0.0 0.0 2.17 F
342 343 0.032813 TCCCTCCGTCCCGAATTACT 60.033 55.0 0.0 0.0 0.0 2.24 F
1714 1720 0.322456 TGCTTCCCTGGACGAAATGG 60.322 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1552 1558 2.309528 TTGACAGACACTGCGAAGTT 57.690 45.0 0.0 0.0 34.37 2.66 R
2173 2191 2.421424 CCTTACATGGTTCAGCAAGAGC 59.579 50.0 0.0 0.0 42.56 4.09 R
3428 3454 0.106318 ATTCCTCTTGGATGCCCTGC 60.106 55.0 0.0 0.0 42.81 4.85 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
37 38 7.373617 TCTATACTGGCCACAAGAATCATTA 57.626 36.000 0.00 0.00 0.00 1.90
48 49 6.183360 CCACAAGAATCATTACATGAGTGACC 60.183 42.308 0.00 0.00 43.53 4.02
71 72 1.159713 CGCACTGCAAGAGAACCACA 61.160 55.000 1.11 0.00 37.43 4.17
72 73 0.308993 GCACTGCAAGAGAACCACAC 59.691 55.000 0.00 0.00 37.43 3.82
113 114 9.463443 GCAAGAAACACACAAATTAATAAGAGT 57.537 29.630 0.00 0.00 0.00 3.24
252 253 1.786928 GCAGTTGCTCGTTACGAATGC 60.787 52.381 9.23 10.38 34.74 3.56
326 327 6.647229 TCAGATAATGATGCATGATACTCCC 58.353 40.000 2.46 0.00 31.12 4.30
327 328 6.442885 TCAGATAATGATGCATGATACTCCCT 59.557 38.462 2.46 0.00 31.12 4.20
328 329 6.762187 CAGATAATGATGCATGATACTCCCTC 59.238 42.308 2.46 0.00 0.00 4.30
329 330 3.996921 ATGATGCATGATACTCCCTCC 57.003 47.619 2.46 0.00 0.00 4.30
332 333 1.040646 TGCATGATACTCCCTCCGTC 58.959 55.000 0.00 0.00 0.00 4.79
333 334 0.318762 GCATGATACTCCCTCCGTCC 59.681 60.000 0.00 0.00 0.00 4.79
334 335 0.969894 CATGATACTCCCTCCGTCCC 59.030 60.000 0.00 0.00 0.00 4.46
337 338 0.466922 GATACTCCCTCCGTCCCGAA 60.467 60.000 0.00 0.00 0.00 4.30
338 339 0.187851 ATACTCCCTCCGTCCCGAAT 59.812 55.000 0.00 0.00 0.00 3.34
339 340 0.032813 TACTCCCTCCGTCCCGAATT 60.033 55.000 0.00 0.00 0.00 2.17
340 341 0.032813 ACTCCCTCCGTCCCGAATTA 60.033 55.000 0.00 0.00 0.00 1.40
341 342 0.388294 CTCCCTCCGTCCCGAATTAC 59.612 60.000 0.00 0.00 0.00 1.89
342 343 0.032813 TCCCTCCGTCCCGAATTACT 60.033 55.000 0.00 0.00 0.00 2.24
343 344 0.388294 CCCTCCGTCCCGAATTACTC 59.612 60.000 0.00 0.00 0.00 2.59
345 346 0.737219 CTCCGTCCCGAATTACTCGT 59.263 55.000 0.00 0.00 46.65 4.18
346 347 0.734889 TCCGTCCCGAATTACTCGTC 59.265 55.000 0.00 0.00 46.65 4.20
347 348 0.590732 CCGTCCCGAATTACTCGTCG 60.591 60.000 0.00 0.00 46.65 5.12
348 349 1.198608 CGTCCCGAATTACTCGTCGC 61.199 60.000 0.00 0.00 46.65 5.19
349 350 1.063006 TCCCGAATTACTCGTCGCG 59.937 57.895 0.00 0.00 46.65 5.87
350 351 1.942712 CCCGAATTACTCGTCGCGG 60.943 63.158 6.13 0.00 46.65 6.46
351 352 1.063006 CCGAATTACTCGTCGCGGA 59.937 57.895 6.13 0.00 46.65 5.54
352 353 0.523968 CCGAATTACTCGTCGCGGAA 60.524 55.000 6.13 0.00 46.65 4.30
353 354 1.261989 CGAATTACTCGTCGCGGAAA 58.738 50.000 6.13 0.00 42.89 3.13
354 355 1.850441 CGAATTACTCGTCGCGGAAAT 59.150 47.619 6.13 0.00 42.89 2.17
355 356 2.346376 CGAATTACTCGTCGCGGAAATG 60.346 50.000 6.13 0.00 42.89 2.32
356 357 1.567504 ATTACTCGTCGCGGAAATGG 58.432 50.000 6.13 0.00 0.00 3.16
357 358 0.527113 TTACTCGTCGCGGAAATGGA 59.473 50.000 6.13 0.00 0.00 3.41
358 359 0.742505 TACTCGTCGCGGAAATGGAT 59.257 50.000 6.13 0.00 0.00 3.41
359 360 0.742505 ACTCGTCGCGGAAATGGATA 59.257 50.000 6.13 0.00 0.00 2.59
360 361 1.135527 ACTCGTCGCGGAAATGGATAA 59.864 47.619 6.13 0.00 0.00 1.75
361 362 2.198406 CTCGTCGCGGAAATGGATAAA 58.802 47.619 6.13 0.00 0.00 1.40
362 363 2.605818 CTCGTCGCGGAAATGGATAAAA 59.394 45.455 6.13 0.00 0.00 1.52
363 364 3.001414 TCGTCGCGGAAATGGATAAAAA 58.999 40.909 6.13 0.00 0.00 1.94
364 365 3.623960 TCGTCGCGGAAATGGATAAAAAT 59.376 39.130 6.13 0.00 0.00 1.82
365 366 3.723764 CGTCGCGGAAATGGATAAAAATG 59.276 43.478 6.13 0.00 0.00 2.32
366 367 4.041723 GTCGCGGAAATGGATAAAAATGG 58.958 43.478 6.13 0.00 0.00 3.16
367 368 3.948473 TCGCGGAAATGGATAAAAATGGA 59.052 39.130 6.13 0.00 0.00 3.41
368 369 4.582656 TCGCGGAAATGGATAAAAATGGAT 59.417 37.500 6.13 0.00 0.00 3.41
369 370 4.681025 CGCGGAAATGGATAAAAATGGATG 59.319 41.667 0.00 0.00 0.00 3.51
370 371 5.600696 GCGGAAATGGATAAAAATGGATGT 58.399 37.500 0.00 0.00 0.00 3.06
371 372 6.514212 CGCGGAAATGGATAAAAATGGATGTA 60.514 38.462 0.00 0.00 0.00 2.29
372 373 7.378181 GCGGAAATGGATAAAAATGGATGTAT 58.622 34.615 0.00 0.00 0.00 2.29
373 374 7.542130 GCGGAAATGGATAAAAATGGATGTATC 59.458 37.037 0.00 0.00 0.00 2.24
374 375 8.796475 CGGAAATGGATAAAAATGGATGTATCT 58.204 33.333 0.00 0.00 0.00 1.98
389 390 8.687292 TGGATGTATCTAGAACTACAATACGT 57.313 34.615 9.65 0.00 32.02 3.57
390 391 8.781196 TGGATGTATCTAGAACTACAATACGTC 58.219 37.037 9.65 9.64 37.78 4.34
391 392 9.001542 GGATGTATCTAGAACTACAATACGTCT 57.998 37.037 9.65 0.00 38.23 4.18
401 402 9.001542 AGAACTACAATACGTCTAGATACATCC 57.998 37.037 0.00 0.00 0.00 3.51
402 403 8.687292 AACTACAATACGTCTAGATACATCCA 57.313 34.615 0.00 0.00 0.00 3.41
403 404 8.865420 ACTACAATACGTCTAGATACATCCAT 57.135 34.615 0.00 0.00 0.00 3.41
404 405 9.298250 ACTACAATACGTCTAGATACATCCATT 57.702 33.333 0.00 0.00 0.00 3.16
407 408 7.808381 ACAATACGTCTAGATACATCCATTTCG 59.192 37.037 0.00 0.00 0.00 3.46
408 409 5.122512 ACGTCTAGATACATCCATTTCGG 57.877 43.478 0.00 0.00 0.00 4.30
409 410 4.583489 ACGTCTAGATACATCCATTTCGGT 59.417 41.667 0.00 0.00 35.57 4.69
410 411 4.917998 CGTCTAGATACATCCATTTCGGTG 59.082 45.833 0.00 0.00 35.57 4.94
411 412 5.278315 CGTCTAGATACATCCATTTCGGTGA 60.278 44.000 0.00 0.00 35.57 4.02
412 413 5.921408 GTCTAGATACATCCATTTCGGTGAC 59.079 44.000 0.00 0.00 35.57 3.67
413 414 4.753516 AGATACATCCATTTCGGTGACA 57.246 40.909 0.00 0.00 35.57 3.58
414 415 5.097742 AGATACATCCATTTCGGTGACAA 57.902 39.130 0.00 0.00 35.57 3.18
415 416 5.118990 AGATACATCCATTTCGGTGACAAG 58.881 41.667 0.00 0.00 35.57 3.16
416 417 3.140325 ACATCCATTTCGGTGACAAGT 57.860 42.857 0.00 0.00 35.57 3.16
417 418 4.280436 ACATCCATTTCGGTGACAAGTA 57.720 40.909 0.00 0.00 35.57 2.24
418 419 4.647611 ACATCCATTTCGGTGACAAGTAA 58.352 39.130 0.00 0.00 35.57 2.24
419 420 5.253330 ACATCCATTTCGGTGACAAGTAAT 58.747 37.500 0.00 0.00 35.57 1.89
420 421 5.354234 ACATCCATTTCGGTGACAAGTAATC 59.646 40.000 0.00 0.00 35.57 1.75
421 422 4.258543 TCCATTTCGGTGACAAGTAATCC 58.741 43.478 0.00 0.00 35.57 3.01
422 423 3.063452 CCATTTCGGTGACAAGTAATCCG 59.937 47.826 0.00 0.00 42.12 4.18
423 424 2.373540 TTCGGTGACAAGTAATCCGG 57.626 50.000 0.00 0.00 41.27 5.14
424 425 1.548081 TCGGTGACAAGTAATCCGGA 58.452 50.000 6.61 6.61 41.27 5.14
425 426 1.203052 TCGGTGACAAGTAATCCGGAC 59.797 52.381 6.12 0.00 41.27 4.79
426 427 1.636988 GGTGACAAGTAATCCGGACG 58.363 55.000 6.12 0.00 0.00 4.79
427 428 1.636988 GTGACAAGTAATCCGGACGG 58.363 55.000 6.12 3.96 0.00 4.79
436 437 4.753662 TCCGGACGGAGGGAGTGG 62.754 72.222 9.76 0.00 39.76 4.00
437 438 4.753662 CCGGACGGAGGGAGTGGA 62.754 72.222 4.40 0.00 37.50 4.02
438 439 2.442272 CGGACGGAGGGAGTGGAT 60.442 66.667 0.00 0.00 0.00 3.41
439 440 2.786495 CGGACGGAGGGAGTGGATG 61.786 68.421 0.00 0.00 0.00 3.51
440 441 2.435693 GGACGGAGGGAGTGGATGG 61.436 68.421 0.00 0.00 0.00 3.51
441 442 1.381327 GACGGAGGGAGTGGATGGA 60.381 63.158 0.00 0.00 0.00 3.41
442 443 0.760945 GACGGAGGGAGTGGATGGAT 60.761 60.000 0.00 0.00 0.00 3.41
443 444 1.050988 ACGGAGGGAGTGGATGGATG 61.051 60.000 0.00 0.00 0.00 3.51
479 483 7.710475 ACATGTATGGAAAAAGTGAACAAAAGG 59.290 33.333 0.00 0.00 0.00 3.11
749 754 7.500227 TGGAATAATTAACTGGATTCTGAGCAG 59.500 37.037 0.00 0.00 0.00 4.24
782 787 3.245586 TGGCCATTTCACCCTTACTTGAT 60.246 43.478 0.00 0.00 0.00 2.57
943 948 1.813786 GCGTGCCCCTTGTTATAAACA 59.186 47.619 0.00 0.00 40.21 2.83
1137 1142 4.646945 TGTAGTCTGCTTTCTCCTCTATGG 59.353 45.833 0.00 0.00 37.10 2.74
1509 1515 6.371548 TGTTCCATTAGCATGTCAGTAACTTC 59.628 38.462 0.00 0.00 0.00 3.01
1531 1537 2.287608 GCGGTAAGAAAATATGGCTGCC 60.288 50.000 12.87 12.87 0.00 4.85
1532 1538 2.948979 CGGTAAGAAAATATGGCTGCCA 59.051 45.455 25.65 25.65 38.19 4.92
1533 1539 3.003689 CGGTAAGAAAATATGGCTGCCAG 59.996 47.826 27.20 4.41 36.75 4.85
1534 1540 3.954258 GGTAAGAAAATATGGCTGCCAGT 59.046 43.478 27.20 15.16 36.75 4.00
1535 1541 4.402474 GGTAAGAAAATATGGCTGCCAGTT 59.598 41.667 27.20 20.02 36.75 3.16
1536 1542 4.460948 AAGAAAATATGGCTGCCAGTTG 57.539 40.909 27.20 0.00 36.75 3.16
1537 1543 3.700538 AGAAAATATGGCTGCCAGTTGA 58.299 40.909 27.20 12.25 36.75 3.18
1538 1544 4.284178 AGAAAATATGGCTGCCAGTTGAT 58.716 39.130 27.20 12.23 36.75 2.57
1539 1545 5.448654 AGAAAATATGGCTGCCAGTTGATA 58.551 37.500 27.20 14.14 36.75 2.15
1540 1546 6.073314 AGAAAATATGGCTGCCAGTTGATAT 58.927 36.000 27.20 15.80 36.75 1.63
1541 1547 7.233632 AGAAAATATGGCTGCCAGTTGATATA 58.766 34.615 27.20 12.65 36.75 0.86
1542 1548 7.892241 AGAAAATATGGCTGCCAGTTGATATAT 59.108 33.333 27.20 14.38 36.75 0.86
1543 1549 7.636150 AAATATGGCTGCCAGTTGATATATC 57.364 36.000 27.20 5.73 36.75 1.63
1544 1550 4.645863 ATGGCTGCCAGTTGATATATCA 57.354 40.909 27.20 11.49 36.75 2.15
1545 1551 4.436113 TGGCTGCCAGTTGATATATCAA 57.564 40.909 21.67 21.67 43.94 2.57
1714 1720 0.322456 TGCTTCCCTGGACGAAATGG 60.322 55.000 0.00 0.00 0.00 3.16
1767 1777 9.880157 ATTTTTATCACATTCAGAGAAATTGGG 57.120 29.630 0.00 0.00 0.00 4.12
1770 1780 5.964958 TCACATTCAGAGAAATTGGGAAC 57.035 39.130 0.00 0.00 0.00 3.62
1784 1794 9.512588 AGAAATTGGGAACTCATAAGCTATATG 57.487 33.333 8.69 8.69 0.00 1.78
1879 1894 8.892723 CCTAACTCTTGCATATTAATGTGACAA 58.107 33.333 15.64 15.62 35.38 3.18
2007 2022 8.934023 ACAGTTATTGTTTAGGGAAATGAAGA 57.066 30.769 0.00 0.00 36.31 2.87
2037 2052 9.962809 AGAATCTAGTTACTAGTGACTTAGTGT 57.037 33.333 23.64 9.24 35.72 3.55
2426 2444 5.512749 GCTTGTCATGATGATGGTATCTCCT 60.513 44.000 0.00 0.00 37.07 3.69
2507 2525 5.866335 AAATGCGTAAAGTATTTGTCGGA 57.134 34.783 0.00 0.00 42.28 4.55
2664 2682 4.134563 ACAACGTTCTAAGCCTGACAAAT 58.865 39.130 0.00 0.00 0.00 2.32
2676 2694 4.529377 AGCCTGACAAATTGATCCACAAAT 59.471 37.500 0.00 0.00 42.03 2.32
2678 2696 5.786311 CCTGACAAATTGATCCACAAATGT 58.214 37.500 0.00 0.00 41.68 2.71
2736 2754 9.316730 CCACAATATCTAAAAATGGTTCAATGG 57.683 33.333 0.00 0.00 0.00 3.16
3263 3281 3.374058 GTGTCTTGTAACCGCATAATGCT 59.626 43.478 0.00 0.00 42.25 3.79
3330 3348 8.198109 TCCTAGTCAACTATTGCAGATCTAAAC 58.802 37.037 0.00 0.00 0.00 2.01
3349 3367 6.945435 TCTAAACAATTTGCTAATGAGGTGGA 59.055 34.615 0.00 0.00 0.00 4.02
3420 3446 3.321497 CTTGACTTGACTAGCAGTGGAC 58.679 50.000 0.00 0.00 0.00 4.02
3421 3447 2.598565 TGACTTGACTAGCAGTGGACT 58.401 47.619 0.00 0.00 0.00 3.85
3424 3450 2.965831 ACTTGACTAGCAGTGGACTTGA 59.034 45.455 0.00 0.00 0.00 3.02
3425 3451 3.243907 ACTTGACTAGCAGTGGACTTGAC 60.244 47.826 0.00 0.00 0.00 3.18
3426 3452 2.598565 TGACTAGCAGTGGACTTGACT 58.401 47.619 0.00 0.00 0.00 3.41
3428 3454 3.759086 TGACTAGCAGTGGACTTGACTAG 59.241 47.826 0.00 0.00 34.61 2.57
3569 3595 1.945387 CCACATACTGCTAGCCACTG 58.055 55.000 13.29 7.17 0.00 3.66
4088 4115 8.562892 CATATTAGATCGTTCAAAAGCCAGAAT 58.437 33.333 0.00 0.00 0.00 2.40
4099 4126 6.666678 TCAAAAGCCAGAATCTTAGGATCAT 58.333 36.000 0.00 0.00 0.00 2.45
4116 4143 9.837681 TTAGGATCATGAACCTACCATTAGATA 57.162 33.333 26.59 9.96 38.31 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.002430 AGTGCGAATGGTCACTCATGT 59.998 47.619 0.00 0.00 39.11 3.21
48 49 1.135859 GGTTCTCTTGCAGTGCGAATG 60.136 52.381 11.20 4.35 0.00 2.67
71 72 2.026542 TCTTGCCTCATGAGCATTCTGT 60.027 45.455 17.76 0.00 40.59 3.41
72 73 2.640184 TCTTGCCTCATGAGCATTCTG 58.360 47.619 17.76 3.64 40.59 3.02
113 114 7.490962 ACTTACTGATTCATGTTTCGTTTCA 57.509 32.000 0.00 0.00 0.00 2.69
145 146 9.685276 AATGTAATGATCCTGAGTAAATGTTCA 57.315 29.630 0.00 0.00 0.00 3.18
252 253 6.436843 AAAAGGACCGATACATTTGCTTAG 57.563 37.500 0.00 0.00 0.00 2.18
337 338 1.135527 TCCATTTCCGCGACGAGTAAT 59.864 47.619 8.23 0.00 0.00 1.89
338 339 0.527113 TCCATTTCCGCGACGAGTAA 59.473 50.000 8.23 0.00 0.00 2.24
339 340 0.742505 ATCCATTTCCGCGACGAGTA 59.257 50.000 8.23 0.00 0.00 2.59
340 341 0.742505 TATCCATTTCCGCGACGAGT 59.257 50.000 8.23 0.00 0.00 4.18
341 342 1.847818 TTATCCATTTCCGCGACGAG 58.152 50.000 8.23 0.00 0.00 4.18
342 343 2.296831 TTTATCCATTTCCGCGACGA 57.703 45.000 8.23 0.00 0.00 4.20
343 344 3.392769 TTTTTATCCATTTCCGCGACG 57.607 42.857 8.23 0.00 0.00 5.12
344 345 4.041723 CCATTTTTATCCATTTCCGCGAC 58.958 43.478 8.23 0.00 0.00 5.19
345 346 3.948473 TCCATTTTTATCCATTTCCGCGA 59.052 39.130 8.23 0.00 0.00 5.87
346 347 4.300189 TCCATTTTTATCCATTTCCGCG 57.700 40.909 0.00 0.00 0.00 6.46
347 348 5.600696 ACATCCATTTTTATCCATTTCCGC 58.399 37.500 0.00 0.00 0.00 5.54
348 349 8.796475 AGATACATCCATTTTTATCCATTTCCG 58.204 33.333 0.00 0.00 0.00 4.30
363 364 9.298250 ACGTATTGTAGTTCTAGATACATCCAT 57.702 33.333 6.96 2.16 32.24 3.41
364 365 8.687292 ACGTATTGTAGTTCTAGATACATCCA 57.313 34.615 6.96 0.00 32.24 3.41
365 366 9.001542 AGACGTATTGTAGTTCTAGATACATCC 57.998 37.037 6.96 0.00 32.24 3.51
375 376 9.001542 GGATGTATCTAGACGTATTGTAGTTCT 57.998 37.037 0.00 0.00 0.00 3.01
376 377 8.781196 TGGATGTATCTAGACGTATTGTAGTTC 58.219 37.037 0.00 0.00 0.00 3.01
377 378 8.687292 TGGATGTATCTAGACGTATTGTAGTT 57.313 34.615 0.00 0.00 0.00 2.24
378 379 8.865420 ATGGATGTATCTAGACGTATTGTAGT 57.135 34.615 0.00 0.00 0.00 2.73
381 382 7.808381 CGAAATGGATGTATCTAGACGTATTGT 59.192 37.037 0.00 0.00 0.00 2.71
382 383 7.273598 CCGAAATGGATGTATCTAGACGTATTG 59.726 40.741 0.00 0.00 42.00 1.90
383 384 7.039923 ACCGAAATGGATGTATCTAGACGTATT 60.040 37.037 0.00 0.00 42.00 1.89
384 385 6.433404 ACCGAAATGGATGTATCTAGACGTAT 59.567 38.462 0.00 0.00 42.00 3.06
385 386 5.766670 ACCGAAATGGATGTATCTAGACGTA 59.233 40.000 0.00 0.00 42.00 3.57
386 387 4.583489 ACCGAAATGGATGTATCTAGACGT 59.417 41.667 0.00 0.00 42.00 4.34
387 388 4.917998 CACCGAAATGGATGTATCTAGACG 59.082 45.833 0.00 0.00 42.00 4.18
388 389 5.921408 GTCACCGAAATGGATGTATCTAGAC 59.079 44.000 0.00 0.00 42.00 2.59
389 390 5.596772 TGTCACCGAAATGGATGTATCTAGA 59.403 40.000 0.00 0.00 42.00 2.43
390 391 5.842907 TGTCACCGAAATGGATGTATCTAG 58.157 41.667 0.00 0.00 42.00 2.43
391 392 5.862678 TGTCACCGAAATGGATGTATCTA 57.137 39.130 0.00 0.00 42.00 1.98
392 393 4.753516 TGTCACCGAAATGGATGTATCT 57.246 40.909 0.00 0.00 42.00 1.98
393 394 4.876107 ACTTGTCACCGAAATGGATGTATC 59.124 41.667 0.00 0.00 42.00 2.24
394 395 4.843728 ACTTGTCACCGAAATGGATGTAT 58.156 39.130 0.00 0.00 42.00 2.29
395 396 4.280436 ACTTGTCACCGAAATGGATGTA 57.720 40.909 0.00 0.00 42.00 2.29
396 397 3.140325 ACTTGTCACCGAAATGGATGT 57.860 42.857 0.00 0.00 42.00 3.06
397 398 5.220854 GGATTACTTGTCACCGAAATGGATG 60.221 44.000 0.00 0.00 42.00 3.51
398 399 4.881850 GGATTACTTGTCACCGAAATGGAT 59.118 41.667 0.00 0.00 42.00 3.41
399 400 4.258543 GGATTACTTGTCACCGAAATGGA 58.741 43.478 0.00 0.00 42.00 3.41
400 401 3.063452 CGGATTACTTGTCACCGAAATGG 59.937 47.826 0.00 0.00 45.31 3.16
401 402 3.063452 CCGGATTACTTGTCACCGAAATG 59.937 47.826 0.00 0.00 45.31 2.32
402 403 3.055675 TCCGGATTACTTGTCACCGAAAT 60.056 43.478 0.00 0.00 45.31 2.17
403 404 2.299582 TCCGGATTACTTGTCACCGAAA 59.700 45.455 0.00 0.00 45.31 3.46
404 405 1.894466 TCCGGATTACTTGTCACCGAA 59.106 47.619 0.00 0.00 45.31 4.30
405 406 1.203052 GTCCGGATTACTTGTCACCGA 59.797 52.381 7.81 0.00 45.31 4.69
406 407 1.636988 GTCCGGATTACTTGTCACCG 58.363 55.000 7.81 0.00 42.67 4.94
407 408 1.636988 CGTCCGGATTACTTGTCACC 58.363 55.000 7.81 0.00 0.00 4.02
408 409 1.203052 TCCGTCCGGATTACTTGTCAC 59.797 52.381 7.81 0.00 39.76 3.67
409 410 1.475280 CTCCGTCCGGATTACTTGTCA 59.525 52.381 7.81 0.00 44.24 3.58
410 411 1.202382 CCTCCGTCCGGATTACTTGTC 60.202 57.143 7.81 0.00 44.24 3.18
411 412 0.822164 CCTCCGTCCGGATTACTTGT 59.178 55.000 7.81 0.00 44.24 3.16
412 413 0.104304 CCCTCCGTCCGGATTACTTG 59.896 60.000 7.81 0.00 44.24 3.16
413 414 0.032813 TCCCTCCGTCCGGATTACTT 60.033 55.000 7.81 0.00 44.24 2.24
414 415 0.467659 CTCCCTCCGTCCGGATTACT 60.468 60.000 7.81 0.00 44.24 2.24
415 416 0.754587 ACTCCCTCCGTCCGGATTAC 60.755 60.000 7.81 0.00 44.24 1.89
416 417 0.754217 CACTCCCTCCGTCCGGATTA 60.754 60.000 7.81 0.00 44.24 1.75
417 418 2.058595 CACTCCCTCCGTCCGGATT 61.059 63.158 7.81 0.00 44.24 3.01
418 419 2.442272 CACTCCCTCCGTCCGGAT 60.442 66.667 7.81 0.00 44.24 4.18
419 420 4.753662 CCACTCCCTCCGTCCGGA 62.754 72.222 0.00 0.00 42.90 5.14
420 421 4.753662 TCCACTCCCTCCGTCCGG 62.754 72.222 0.00 0.00 0.00 5.14
421 422 2.442272 ATCCACTCCCTCCGTCCG 60.442 66.667 0.00 0.00 0.00 4.79
422 423 2.435693 CCATCCACTCCCTCCGTCC 61.436 68.421 0.00 0.00 0.00 4.79
423 424 0.760945 ATCCATCCACTCCCTCCGTC 60.761 60.000 0.00 0.00 0.00 4.79
424 425 1.050988 CATCCATCCACTCCCTCCGT 61.051 60.000 0.00 0.00 0.00 4.69
425 426 1.050988 ACATCCATCCACTCCCTCCG 61.051 60.000 0.00 0.00 0.00 4.63
426 427 0.471617 CACATCCATCCACTCCCTCC 59.528 60.000 0.00 0.00 0.00 4.30
427 428 0.179034 GCACATCCATCCACTCCCTC 60.179 60.000 0.00 0.00 0.00 4.30
428 429 0.622738 AGCACATCCATCCACTCCCT 60.623 55.000 0.00 0.00 0.00 4.20
429 430 0.257039 AAGCACATCCATCCACTCCC 59.743 55.000 0.00 0.00 0.00 4.30
430 431 1.211457 AGAAGCACATCCATCCACTCC 59.789 52.381 0.00 0.00 0.00 3.85
431 432 2.706339 AGAAGCACATCCATCCACTC 57.294 50.000 0.00 0.00 0.00 3.51
432 433 4.263462 TGTTAAGAAGCACATCCATCCACT 60.263 41.667 0.00 0.00 0.00 4.00
433 434 4.009675 TGTTAAGAAGCACATCCATCCAC 58.990 43.478 0.00 0.00 0.00 4.02
434 435 4.299586 TGTTAAGAAGCACATCCATCCA 57.700 40.909 0.00 0.00 0.00 3.41
435 436 4.641989 ACATGTTAAGAAGCACATCCATCC 59.358 41.667 0.00 0.00 30.90 3.51
436 437 5.824904 ACATGTTAAGAAGCACATCCATC 57.175 39.130 0.00 0.00 30.90 3.51
437 438 6.263842 CCATACATGTTAAGAAGCACATCCAT 59.736 38.462 2.30 0.00 30.90 3.41
438 439 5.589855 CCATACATGTTAAGAAGCACATCCA 59.410 40.000 2.30 0.00 30.90 3.41
439 440 5.822519 TCCATACATGTTAAGAAGCACATCC 59.177 40.000 2.30 0.00 30.90 3.51
440 441 6.925610 TCCATACATGTTAAGAAGCACATC 57.074 37.500 2.30 0.00 30.90 3.06
441 442 7.701539 TTTCCATACATGTTAAGAAGCACAT 57.298 32.000 2.30 0.00 33.72 3.21
442 443 7.517614 TTTTCCATACATGTTAAGAAGCACA 57.482 32.000 2.30 0.00 0.00 4.57
443 444 8.082242 ACTTTTTCCATACATGTTAAGAAGCAC 58.918 33.333 2.30 0.00 0.00 4.40
479 483 0.321653 AGGGTGAGAATCGTTGGTGC 60.322 55.000 0.00 0.00 38.61 5.01
637 642 7.559335 TGGAGAATCTGGTATGTTATAGCAT 57.441 36.000 7.28 7.28 33.73 3.79
749 754 3.125658 GTGAAATGGCCATGCATGTTTTC 59.874 43.478 21.63 23.00 0.00 2.29
758 763 2.738743 AGTAAGGGTGAAATGGCCATG 58.261 47.619 21.63 0.00 0.00 3.66
782 787 1.098869 TTTCAGCAAGACCGCAAACA 58.901 45.000 0.00 0.00 0.00 2.83
943 948 2.629017 AGATTTGCCCAGGGTTCATT 57.371 45.000 7.55 0.00 0.00 2.57
1137 1142 1.755179 AGGCATGTACATTGGTGCTC 58.245 50.000 16.47 8.64 37.70 4.26
1509 1515 2.602217 GCAGCCATATTTTCTTACCGCG 60.602 50.000 0.00 0.00 0.00 6.46
1539 1545 9.627395 GACACTGCGAAGTTATATAGTTGATAT 57.373 33.333 0.00 0.00 34.89 1.63
1540 1546 8.847196 AGACACTGCGAAGTTATATAGTTGATA 58.153 33.333 0.00 0.00 0.00 2.15
1541 1547 7.649705 CAGACACTGCGAAGTTATATAGTTGAT 59.350 37.037 0.00 0.00 0.00 2.57
1542 1548 6.972901 CAGACACTGCGAAGTTATATAGTTGA 59.027 38.462 0.00 0.00 0.00 3.18
1543 1549 6.752351 ACAGACACTGCGAAGTTATATAGTTG 59.248 38.462 0.00 0.00 34.37 3.16
1544 1550 6.864342 ACAGACACTGCGAAGTTATATAGTT 58.136 36.000 0.00 0.00 34.37 2.24
1545 1551 6.095021 TGACAGACACTGCGAAGTTATATAGT 59.905 38.462 0.00 0.00 34.37 2.12
1546 1552 6.495706 TGACAGACACTGCGAAGTTATATAG 58.504 40.000 0.00 0.00 34.37 1.31
1547 1553 6.445357 TGACAGACACTGCGAAGTTATATA 57.555 37.500 0.00 0.00 34.37 0.86
1548 1554 5.324784 TGACAGACACTGCGAAGTTATAT 57.675 39.130 0.00 0.00 34.37 0.86
1549 1555 4.776795 TGACAGACACTGCGAAGTTATA 57.223 40.909 0.00 0.00 34.37 0.98
1550 1556 3.660501 TGACAGACACTGCGAAGTTAT 57.339 42.857 0.00 0.00 34.37 1.89
1551 1557 3.446310 TTGACAGACACTGCGAAGTTA 57.554 42.857 0.00 0.00 34.37 2.24
1552 1558 2.309528 TTGACAGACACTGCGAAGTT 57.690 45.000 0.00 0.00 34.37 2.66
1553 1559 2.309528 TTTGACAGACACTGCGAAGT 57.690 45.000 0.00 0.00 34.37 3.01
1554 1560 3.885484 ATTTTGACAGACACTGCGAAG 57.115 42.857 0.00 0.00 34.37 3.79
1555 1561 4.597079 GAAATTTTGACAGACACTGCGAA 58.403 39.130 0.00 0.00 34.37 4.70
1556 1562 3.303066 CGAAATTTTGACAGACACTGCGA 60.303 43.478 0.00 0.00 34.37 5.10
1557 1563 2.966708 CGAAATTTTGACAGACACTGCG 59.033 45.455 0.00 0.00 34.37 5.18
1558 1564 3.725740 CACGAAATTTTGACAGACACTGC 59.274 43.478 12.54 0.00 34.37 4.40
1634 1640 6.610075 ATTTATCATGTCCAAGCAAGGTTT 57.390 33.333 0.00 0.00 0.00 3.27
1714 1720 8.608844 AGGAGTAAATATGTGCTTATTGCTAC 57.391 34.615 0.00 0.00 43.37 3.58
1745 1755 7.890127 AGTTCCCAATTTCTCTGAATGTGATAA 59.110 33.333 0.00 0.00 0.00 1.75
1746 1756 7.405292 AGTTCCCAATTTCTCTGAATGTGATA 58.595 34.615 0.00 0.00 0.00 2.15
1759 1769 9.507329 TCATATAGCTTATGAGTTCCCAATTTC 57.493 33.333 11.99 0.00 31.09 2.17
1879 1894 6.362248 ACCTACACATGTTTACAACCTCTTT 58.638 36.000 0.00 0.00 0.00 2.52
1891 1906 7.938140 ACTTAATTGCATACCTACACATGTT 57.062 32.000 0.00 0.00 0.00 2.71
2173 2191 2.421424 CCTTACATGGTTCAGCAAGAGC 59.579 50.000 0.00 0.00 42.56 4.09
2252 2270 9.610104 TGAAATAGTACCTATAAAGCCTATGGA 57.390 33.333 0.00 0.00 0.00 3.41
2426 2444 6.208007 CAGCCATGCCAAAGATGATTAGAATA 59.792 38.462 0.00 0.00 0.00 1.75
2459 2477 4.898265 TGGGTGTGGAATGAGAAAATTGAA 59.102 37.500 0.00 0.00 0.00 2.69
2507 2525 1.070601 GAAGCCACCAAACCAATGCTT 59.929 47.619 0.00 0.00 41.38 3.91
2664 2682 8.806429 ACTTATCACATACATTTGTGGATCAA 57.194 30.769 4.89 0.00 45.63 2.57
2825 2843 4.566004 TCGTCCTGATAACTTGTTTCTGG 58.434 43.478 11.42 11.42 0.00 3.86
3012 3030 2.875296 TGAAGCTTGGTGCCTTTACAT 58.125 42.857 2.10 0.00 44.23 2.29
3330 3348 4.142116 TGCATCCACCTCATTAGCAAATTG 60.142 41.667 0.00 0.00 0.00 2.32
3420 3446 0.543277 TGGATGCCCTGCTAGTCAAG 59.457 55.000 0.00 0.00 0.00 3.02
3421 3447 0.991146 TTGGATGCCCTGCTAGTCAA 59.009 50.000 0.00 0.00 0.00 3.18
3424 3450 0.835941 CTCTTGGATGCCCTGCTAGT 59.164 55.000 0.00 0.00 0.00 2.57
3425 3451 0.108207 CCTCTTGGATGCCCTGCTAG 59.892 60.000 0.00 0.00 34.57 3.42
3426 3452 0.326522 TCCTCTTGGATGCCCTGCTA 60.327 55.000 0.00 0.00 37.46 3.49
3428 3454 0.106318 ATTCCTCTTGGATGCCCTGC 60.106 55.000 0.00 0.00 42.81 4.85
3588 3614 3.120792 GTTGCCGCTTATCTACGAATCA 58.879 45.455 0.00 0.00 0.00 2.57
3649 3675 3.017442 TGTCACCGTGTTTTTCCATGAA 58.983 40.909 0.00 0.00 0.00 2.57
4088 4115 8.010697 TCTAATGGTAGGTTCATGATCCTAAGA 58.989 37.037 26.99 22.51 37.94 2.10
4116 4143 9.366216 GCCGTTCCTTCAAAATTTTCTTATAAT 57.634 29.630 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.