Multiple sequence alignment - TraesCS2B01G315000

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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 TraesCS2B01G315000 chr2B 100.000 2267 0 0 1 2267 450259229 450256963 0.000000e+00 4187
1 TraesCS2B01G315000 chr2B 94.393 107 6 0 346 452 496541739 496541633 5.010000e-37 165
2 TraesCS2B01G315000 chr2A 87.904 1827 91 46 528 2267 513854242 513852459 0.000000e+00 2030
3 TraesCS2B01G315000 chr2A 88.136 236 14 7 1 231 513854540 513854314 3.710000e-68 268
4 TraesCS2B01G315000 chr2D 89.336 1341 72 25 966 2267 378909826 378908518 0.000000e+00 1618
5 TraesCS2B01G315000 chr2D 91.875 320 6 6 531 840 378910203 378909894 1.610000e-116 429
6 TraesCS2B01G315000 chr2D 91.810 232 9 4 1 230 378910606 378910383 4.700000e-82 315
7 TraesCS2B01G315000 chr7B 94.595 111 5 1 342 452 497896299 497896190 1.080000e-38 171
8 TraesCS2B01G315000 chr7B 94.393 107 6 0 346 452 540062093 540061987 5.010000e-37 165
9 TraesCS2B01G315000 chr3A 95.283 106 5 0 347 452 9945013 9945118 3.870000e-38 169
10 TraesCS2B01G315000 chr5D 92.857 112 8 0 342 453 512449400 512449289 1.800000e-36 163
11 TraesCS2B01G315000 chr6B 94.286 105 6 0 348 452 117072345 117072241 6.480000e-36 161
12 TraesCS2B01G315000 chr6B 93.519 108 7 0 345 452 119833378 119833485 6.480000e-36 161
13 TraesCS2B01G315000 chr6B 98.889 90 1 0 882 971 592983721 592983810 6.480000e-36 161
14 TraesCS2B01G315000 chr5A 93.458 107 7 0 346 452 552517833 552517939 2.330000e-35 159
15 TraesCS2B01G315000 chr5A 93.458 107 7 0 346 452 574487227 574487121 2.330000e-35 159


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 TraesCS2B01G315000 chr2B 450256963 450259229 2266 True 4187.000000 4187 100.000 1 2267 1 chr2B.!!$R1 2266
1 TraesCS2B01G315000 chr2A 513852459 513854540 2081 True 1149.000000 2030 88.020 1 2267 2 chr2A.!!$R1 2266
2 TraesCS2B01G315000 chr2D 378908518 378910606 2088 True 787.333333 1618 91.007 1 2267 3 chr2D.!!$R1 2266

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
455 466 0.029834 GGCATGCCAATTACTCAGCG 59.97 55.0 32.08 0.0 35.81 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 1576 0.030101 CGCGTTTGCAAAGGAAGGAA 59.97 50.0 30.43 0.0 42.97 3.36 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
50 53 3.826754 CCGCGCTCTCTGCCTGTA 61.827 66.667 5.56 0.00 38.78 2.74
51 54 2.580867 CGCGCTCTCTGCCTGTAC 60.581 66.667 5.56 0.00 38.78 2.90
53 56 1.216710 GCGCTCTCTGCCTGTACTT 59.783 57.895 0.00 0.00 38.78 2.24
54 57 0.390472 GCGCTCTCTGCCTGTACTTT 60.390 55.000 0.00 0.00 38.78 2.66
55 58 1.634702 CGCTCTCTGCCTGTACTTTC 58.365 55.000 0.00 0.00 38.78 2.62
56 59 1.203523 CGCTCTCTGCCTGTACTTTCT 59.796 52.381 0.00 0.00 38.78 2.52
57 60 2.353208 CGCTCTCTGCCTGTACTTTCTT 60.353 50.000 0.00 0.00 38.78 2.52
58 61 2.999355 GCTCTCTGCCTGTACTTTCTTG 59.001 50.000 0.00 0.00 35.15 3.02
59 62 3.306364 GCTCTCTGCCTGTACTTTCTTGA 60.306 47.826 0.00 0.00 35.15 3.02
60 63 4.800914 GCTCTCTGCCTGTACTTTCTTGAA 60.801 45.833 0.00 0.00 35.15 2.69
61 64 5.486526 CTCTCTGCCTGTACTTTCTTGAAT 58.513 41.667 0.00 0.00 0.00 2.57
157 160 0.716108 CTGCACCAACTCGAACGATC 59.284 55.000 0.00 0.00 0.00 3.69
213 221 5.501252 CGCACCAAATTATCCTAACGTGTAC 60.501 44.000 0.00 0.00 0.00 2.90
230 238 4.677250 CGTGTACATAACCCTGAGTTCCTC 60.677 50.000 0.00 0.00 40.05 3.71
231 239 4.466726 GTGTACATAACCCTGAGTTCCTCT 59.533 45.833 0.00 0.00 40.05 3.69
232 240 5.046520 GTGTACATAACCCTGAGTTCCTCTT 60.047 44.000 0.00 0.00 40.05 2.85
233 241 4.828072 ACATAACCCTGAGTTCCTCTTC 57.172 45.455 0.00 0.00 40.05 2.87
234 242 3.519913 ACATAACCCTGAGTTCCTCTTCC 59.480 47.826 0.00 0.00 40.05 3.46
235 243 1.363246 AACCCTGAGTTCCTCTTCCC 58.637 55.000 0.00 0.00 30.99 3.97
236 244 0.547954 ACCCTGAGTTCCTCTTCCCC 60.548 60.000 0.00 0.00 0.00 4.81
237 245 1.617947 CCCTGAGTTCCTCTTCCCCG 61.618 65.000 0.00 0.00 0.00 5.73
238 246 1.219393 CTGAGTTCCTCTTCCCCGC 59.781 63.158 0.00 0.00 0.00 6.13
239 247 1.535444 TGAGTTCCTCTTCCCCGCA 60.535 57.895 0.00 0.00 0.00 5.69
240 248 1.125093 TGAGTTCCTCTTCCCCGCAA 61.125 55.000 0.00 0.00 0.00 4.85
241 249 0.036306 GAGTTCCTCTTCCCCGCAAA 59.964 55.000 0.00 0.00 0.00 3.68
242 250 0.476771 AGTTCCTCTTCCCCGCAAAA 59.523 50.000 0.00 0.00 0.00 2.44
243 251 1.133606 AGTTCCTCTTCCCCGCAAAAA 60.134 47.619 0.00 0.00 0.00 1.94
295 306 3.185246 ACTGTGAATTAGCTGATCCGG 57.815 47.619 0.00 0.00 0.00 5.14
300 311 4.202357 TGTGAATTAGCTGATCCGGCTATT 60.202 41.667 15.19 10.62 46.03 1.73
310 321 5.121454 GCTGATCCGGCTATTCAGAAAATAG 59.879 44.000 20.63 1.32 39.36 1.73
311 322 6.174720 TGATCCGGCTATTCAGAAAATAGT 57.825 37.500 0.00 0.00 33.79 2.12
338 349 2.662006 TTTCCTCTCATGACTCAGCG 57.338 50.000 0.00 0.00 0.00 5.18
346 357 3.696548 TCTCATGACTCAGCGTGATAGTT 59.303 43.478 0.00 0.00 33.65 2.24
347 358 4.158579 TCTCATGACTCAGCGTGATAGTTT 59.841 41.667 0.00 0.00 33.65 2.66
348 359 4.820897 TCATGACTCAGCGTGATAGTTTT 58.179 39.130 0.00 0.00 0.00 2.43
349 360 5.237815 TCATGACTCAGCGTGATAGTTTTT 58.762 37.500 0.00 0.00 0.00 1.94
372 383 6.773976 TTTTTCGAAATGGAGGCATAAGAT 57.226 33.333 12.12 0.00 0.00 2.40
373 384 6.773976 TTTTCGAAATGGAGGCATAAGATT 57.226 33.333 12.12 0.00 0.00 2.40
374 385 6.773976 TTTCGAAATGGAGGCATAAGATTT 57.226 33.333 6.47 0.00 0.00 2.17
375 386 5.756195 TCGAAATGGAGGCATAAGATTTG 57.244 39.130 0.00 0.00 0.00 2.32
376 387 4.036734 TCGAAATGGAGGCATAAGATTTGC 59.963 41.667 0.00 0.00 39.41 3.68
427 438 7.506328 AAGTTTAGAGAATTACAACACACCC 57.494 36.000 0.00 0.00 0.00 4.61
428 439 6.597562 AGTTTAGAGAATTACAACACACCCA 58.402 36.000 0.00 0.00 0.00 4.51
429 440 6.485648 AGTTTAGAGAATTACAACACACCCAC 59.514 38.462 0.00 0.00 0.00 4.61
430 441 4.431416 AGAGAATTACAACACACCCACA 57.569 40.909 0.00 0.00 0.00 4.17
431 442 4.134563 AGAGAATTACAACACACCCACAC 58.865 43.478 0.00 0.00 0.00 3.82
432 443 3.880490 GAGAATTACAACACACCCACACA 59.120 43.478 0.00 0.00 0.00 3.72
433 444 4.469657 AGAATTACAACACACCCACACAT 58.530 39.130 0.00 0.00 0.00 3.21
434 445 4.892934 AGAATTACAACACACCCACACATT 59.107 37.500 0.00 0.00 0.00 2.71
435 446 6.065374 AGAATTACAACACACCCACACATTA 58.935 36.000 0.00 0.00 0.00 1.90
436 447 5.957842 ATTACAACACACCCACACATTAG 57.042 39.130 0.00 0.00 0.00 1.73
437 448 2.582052 ACAACACACCCACACATTAGG 58.418 47.619 0.00 0.00 0.00 2.69
438 449 1.269448 CAACACACCCACACATTAGGC 59.731 52.381 0.00 0.00 0.00 3.93
439 450 0.476338 ACACACCCACACATTAGGCA 59.524 50.000 0.00 0.00 0.00 4.75
440 451 1.075374 ACACACCCACACATTAGGCAT 59.925 47.619 0.00 0.00 0.00 4.40
441 452 1.473677 CACACCCACACATTAGGCATG 59.526 52.381 0.00 0.00 39.07 4.06
442 453 0.457035 CACCCACACATTAGGCATGC 59.543 55.000 9.90 9.90 36.14 4.06
443 454 0.684153 ACCCACACATTAGGCATGCC 60.684 55.000 30.12 30.12 36.14 4.40
444 455 0.683828 CCCACACATTAGGCATGCCA 60.684 55.000 37.18 19.62 36.14 4.92
445 456 1.184431 CCACACATTAGGCATGCCAA 58.816 50.000 37.18 27.29 36.14 4.52
446 457 1.758280 CCACACATTAGGCATGCCAAT 59.242 47.619 37.18 28.14 36.14 3.16
447 458 2.168936 CCACACATTAGGCATGCCAATT 59.831 45.455 37.18 20.37 36.14 2.32
448 459 3.384146 CCACACATTAGGCATGCCAATTA 59.616 43.478 37.18 19.24 36.14 1.40
449 460 4.362279 CACACATTAGGCATGCCAATTAC 58.638 43.478 37.18 10.50 36.14 1.89
450 461 4.098349 CACACATTAGGCATGCCAATTACT 59.902 41.667 37.18 18.83 36.14 2.24
451 462 4.339247 ACACATTAGGCATGCCAATTACTC 59.661 41.667 37.18 8.91 36.14 2.59
452 463 4.338964 CACATTAGGCATGCCAATTACTCA 59.661 41.667 37.18 8.65 36.14 3.41
453 464 4.581824 ACATTAGGCATGCCAATTACTCAG 59.418 41.667 37.18 20.71 36.14 3.35
454 465 1.396653 AGGCATGCCAATTACTCAGC 58.603 50.000 37.18 6.78 38.92 4.26
455 466 0.029834 GGCATGCCAATTACTCAGCG 59.970 55.000 32.08 0.00 35.81 5.18
456 467 0.734889 GCATGCCAATTACTCAGCGT 59.265 50.000 6.36 0.00 0.00 5.07
457 468 1.532505 GCATGCCAATTACTCAGCGTG 60.533 52.381 6.36 0.00 43.52 5.34
458 469 2.009051 CATGCCAATTACTCAGCGTGA 58.991 47.619 0.00 0.00 43.39 4.35
459 470 2.401583 TGCCAATTACTCAGCGTGAT 57.598 45.000 0.00 0.00 0.00 3.06
460 471 3.535280 TGCCAATTACTCAGCGTGATA 57.465 42.857 0.00 0.00 0.00 2.15
461 472 3.457234 TGCCAATTACTCAGCGTGATAG 58.543 45.455 0.00 0.00 0.00 2.08
462 473 3.118775 TGCCAATTACTCAGCGTGATAGT 60.119 43.478 0.00 0.00 0.00 2.12
473 484 4.573607 TCAGCGTGATAGTCAGTATACGTT 59.426 41.667 0.00 0.00 34.37 3.99
512 524 7.230913 ACAGACTCACAGTAGTGTACATAGTTT 59.769 37.037 2.08 0.00 46.01 2.66
526 567 9.158233 GTGTACATAGTTTGAGGCACTATTAAA 57.842 33.333 0.00 0.00 41.55 1.52
548 589 2.282820 GCTTTTCGCCTCTCATTACTCG 59.717 50.000 0.00 0.00 0.00 4.18
551 592 1.300233 CGCCTCTCATTACTCGGCC 60.300 63.158 0.00 0.00 37.47 6.13
683 730 5.975344 CCAGAAAATGACATCATGCATGTAC 59.025 40.000 25.43 15.08 46.53 2.90
684 731 6.183360 CCAGAAAATGACATCATGCATGTACT 60.183 38.462 25.43 9.28 46.53 2.73
685 732 7.012610 CCAGAAAATGACATCATGCATGTACTA 59.987 37.037 25.43 7.44 46.53 1.82
686 733 8.068380 CAGAAAATGACATCATGCATGTACTAG 58.932 37.037 25.43 14.00 46.53 2.57
687 734 7.772292 AGAAAATGACATCATGCATGTACTAGT 59.228 33.333 25.43 16.75 46.53 2.57
688 735 8.962884 AAAATGACATCATGCATGTACTAGTA 57.037 30.769 25.43 5.50 46.53 1.82
689 736 8.599055 AAATGACATCATGCATGTACTAGTAG 57.401 34.615 25.43 10.28 46.53 2.57
690 737 6.715347 TGACATCATGCATGTACTAGTAGT 57.285 37.500 25.43 8.14 46.53 2.73
691 738 7.817418 TGACATCATGCATGTACTAGTAGTA 57.183 36.000 25.43 5.90 46.53 1.82
878 934 2.025321 ACTCACCAAAACCTTCACCAGT 60.025 45.455 0.00 0.00 0.00 4.00
927 983 2.293318 CCTCCACACCTGGCTGCTA 61.293 63.158 0.00 0.00 37.49 3.49
1087 1147 2.041265 TCCTCCTCCTCCTTGCCC 59.959 66.667 0.00 0.00 0.00 5.36
1183 1243 2.514803 CCAACCATTTCTTCGGGTTCT 58.485 47.619 0.00 0.00 42.78 3.01
1349 1411 5.928264 ACGTGTATGATGATGACATATGGTG 59.072 40.000 7.80 0.00 36.82 4.17
1350 1412 5.928264 CGTGTATGATGATGACATATGGTGT 59.072 40.000 7.80 0.00 45.83 4.16
1351 1413 7.090173 CGTGTATGATGATGACATATGGTGTA 58.910 38.462 7.80 0.00 42.36 2.90
1370 1444 9.880157 ATGGTGTAGATTAATGTTTACGTAGTT 57.120 29.630 0.00 0.00 37.78 2.24
1456 1545 2.435059 GGAGCCGGCAGAGTTGTC 60.435 66.667 31.54 15.47 0.00 3.18
1476 1565 2.162681 CGATGCTTCCCAACTTTCCTT 58.837 47.619 0.00 0.00 0.00 3.36
1477 1566 2.162408 CGATGCTTCCCAACTTTCCTTC 59.838 50.000 0.00 0.00 0.00 3.46
1478 1567 1.995376 TGCTTCCCAACTTTCCTTCC 58.005 50.000 0.00 0.00 0.00 3.46
1479 1568 1.499007 TGCTTCCCAACTTTCCTTCCT 59.501 47.619 0.00 0.00 0.00 3.36
1480 1569 2.091333 TGCTTCCCAACTTTCCTTCCTT 60.091 45.455 0.00 0.00 0.00 3.36
1481 1570 2.558795 GCTTCCCAACTTTCCTTCCTTC 59.441 50.000 0.00 0.00 0.00 3.46
1482 1571 2.971901 TCCCAACTTTCCTTCCTTCC 57.028 50.000 0.00 0.00 0.00 3.46
1483 1572 2.428901 TCCCAACTTTCCTTCCTTCCT 58.571 47.619 0.00 0.00 0.00 3.36
1484 1573 2.789399 TCCCAACTTTCCTTCCTTCCTT 59.211 45.455 0.00 0.00 0.00 3.36
1485 1574 3.157881 CCCAACTTTCCTTCCTTCCTTC 58.842 50.000 0.00 0.00 0.00 3.46
1486 1575 3.157881 CCAACTTTCCTTCCTTCCTTCC 58.842 50.000 0.00 0.00 0.00 3.46
1487 1576 3.181428 CCAACTTTCCTTCCTTCCTTCCT 60.181 47.826 0.00 0.00 0.00 3.36
1488 1577 4.474394 CAACTTTCCTTCCTTCCTTCCTT 58.526 43.478 0.00 0.00 0.00 3.36
1489 1578 4.374689 ACTTTCCTTCCTTCCTTCCTTC 57.625 45.455 0.00 0.00 0.00 3.46
1490 1579 3.074687 ACTTTCCTTCCTTCCTTCCTTCC 59.925 47.826 0.00 0.00 0.00 3.46
1491 1580 2.743131 TCCTTCCTTCCTTCCTTCCT 57.257 50.000 0.00 0.00 0.00 3.36
1506 1595 0.030101 TTCCTTCCTTTGCAAACGCG 59.970 50.000 8.05 3.53 0.00 6.01
1574 1664 7.327214 TGTGATATGATATATACCGCTGCAAA 58.673 34.615 0.00 0.00 0.00 3.68
1575 1665 7.277760 TGTGATATGATATATACCGCTGCAAAC 59.722 37.037 0.00 0.00 0.00 2.93
1669 1765 0.673437 CCCTGCGTTGACAAAATGGT 59.327 50.000 0.00 0.00 0.00 3.55
1709 1805 5.220662 CGTTGCACCTTCCTTTGACTATATG 60.221 44.000 0.00 0.00 0.00 1.78
1711 1807 5.815581 TGCACCTTCCTTTGACTATATGTT 58.184 37.500 0.00 0.00 0.00 2.71
1737 1838 6.852853 CGTATAGCTATTTCAAGCCAACATTG 59.147 38.462 12.39 0.00 43.86 2.82
1747 1848 5.540911 TCAAGCCAACATTGATTCCTTTTC 58.459 37.500 0.00 0.00 31.86 2.29
1756 1857 3.559238 TGATTCCTTTTCAAAGCGAGC 57.441 42.857 0.00 0.00 34.69 5.03
1774 1875 3.326747 GAGCACGTACATCTTGTTCCTT 58.673 45.455 0.00 0.00 0.00 3.36
1778 1879 4.307432 CACGTACATCTTGTTCCTTGACT 58.693 43.478 0.00 0.00 0.00 3.41
1781 1882 6.422701 CACGTACATCTTGTTCCTTGACTTAA 59.577 38.462 0.00 0.00 0.00 1.85
1817 1923 3.140325 AGACAAACCATCCACGATGTT 57.860 42.857 0.00 0.00 38.28 2.71
1828 1934 2.746904 TCCACGATGTTATTGGTGCAAG 59.253 45.455 0.00 0.00 0.00 4.01
1829 1935 2.487762 CCACGATGTTATTGGTGCAAGT 59.512 45.455 0.00 0.00 0.00 3.16
1830 1936 3.687212 CCACGATGTTATTGGTGCAAGTA 59.313 43.478 0.00 0.00 0.00 2.24
1831 1937 4.335315 CCACGATGTTATTGGTGCAAGTAT 59.665 41.667 0.00 0.00 0.00 2.12
1832 1938 5.501715 CACGATGTTATTGGTGCAAGTATC 58.498 41.667 0.00 0.00 0.00 2.24
1833 1939 4.270084 ACGATGTTATTGGTGCAAGTATCG 59.730 41.667 0.00 0.00 40.27 2.92
1834 1940 4.527564 GATGTTATTGGTGCAAGTATCGC 58.472 43.478 0.00 0.00 0.00 4.58
1835 1941 2.680841 TGTTATTGGTGCAAGTATCGCC 59.319 45.455 0.00 0.00 34.79 5.54
1836 1942 2.680841 GTTATTGGTGCAAGTATCGCCA 59.319 45.455 0.00 0.00 41.85 5.69
1837 1943 1.382522 ATTGGTGCAAGTATCGCCAG 58.617 50.000 0.00 0.00 43.98 4.85
1838 1944 0.036164 TTGGTGCAAGTATCGCCAGT 59.964 50.000 0.00 0.00 43.98 4.00
1855 1961 5.352016 TCGCCAGTTAGTTAAATATTTGCGT 59.648 36.000 17.62 4.29 38.37 5.24
1875 1996 3.731216 CGTTAGGATGATGTCATGTCGTC 59.269 47.826 0.00 5.34 36.57 4.20
1893 2014 0.939577 TCGATCGCGGATTAAGCAGC 60.940 55.000 11.09 5.73 38.28 5.25
1902 2023 1.210478 GGATTAAGCAGCCTCCTGTGA 59.790 52.381 0.00 0.00 41.26 3.58
1978 2102 2.819608 CCCGTGACATTTGGTGAAAGAT 59.180 45.455 0.00 0.00 0.00 2.40
1979 2103 3.255642 CCCGTGACATTTGGTGAAAGATT 59.744 43.478 0.00 0.00 0.00 2.40
2045 2177 0.729478 AGTCGTGACATGACGCTTCG 60.729 55.000 19.58 0.00 39.07 3.79
2080 2217 1.853963 TGGCCTCCAGAGTAGACTTC 58.146 55.000 3.32 0.00 0.00 3.01
2085 2222 3.317993 GCCTCCAGAGTAGACTTCTCATC 59.682 52.174 11.23 0.00 34.73 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 64 9.753674 AGGATAGGATACATTTTTGAAACTTGA 57.246 29.630 0.00 0.00 41.41 3.02
157 160 2.662249 CGCGCCTATAGTCTACGAACAG 60.662 54.545 0.00 0.00 0.00 3.16
256 264 2.814336 AGTTTGGAAGATTGCGAGGAAC 59.186 45.455 0.00 0.00 0.00 3.62
257 265 2.813754 CAGTTTGGAAGATTGCGAGGAA 59.186 45.455 0.00 0.00 0.00 3.36
258 266 2.224523 ACAGTTTGGAAGATTGCGAGGA 60.225 45.455 0.00 0.00 0.00 3.71
259 267 2.095567 CACAGTTTGGAAGATTGCGAGG 60.096 50.000 0.00 0.00 0.00 4.63
260 268 2.807967 TCACAGTTTGGAAGATTGCGAG 59.192 45.455 0.00 0.00 0.00 5.03
261 269 2.844946 TCACAGTTTGGAAGATTGCGA 58.155 42.857 0.00 0.00 0.00 5.10
262 270 3.624326 TTCACAGTTTGGAAGATTGCG 57.376 42.857 0.00 0.00 0.00 4.85
349 360 6.773976 ATCTTATGCCTCCATTTCGAAAAA 57.226 33.333 15.66 2.87 32.85 1.94
350 361 6.773976 AATCTTATGCCTCCATTTCGAAAA 57.226 33.333 15.66 0.00 32.85 2.29
351 362 6.563422 CAAATCTTATGCCTCCATTTCGAAA 58.437 36.000 13.91 13.91 32.85 3.46
352 363 5.450412 GCAAATCTTATGCCTCCATTTCGAA 60.450 40.000 0.00 0.00 37.85 3.71
353 364 4.036734 GCAAATCTTATGCCTCCATTTCGA 59.963 41.667 0.00 0.00 37.85 3.71
354 365 4.293415 GCAAATCTTATGCCTCCATTTCG 58.707 43.478 0.00 0.00 37.85 3.46
401 412 9.059260 GGGTGTGTTGTAATTCTCTAAACTTTA 57.941 33.333 0.00 0.00 0.00 1.85
402 413 7.558444 TGGGTGTGTTGTAATTCTCTAAACTTT 59.442 33.333 0.00 0.00 0.00 2.66
403 414 7.012989 GTGGGTGTGTTGTAATTCTCTAAACTT 59.987 37.037 0.00 0.00 0.00 2.66
404 415 6.485648 GTGGGTGTGTTGTAATTCTCTAAACT 59.514 38.462 0.00 0.00 0.00 2.66
405 416 6.261381 TGTGGGTGTGTTGTAATTCTCTAAAC 59.739 38.462 0.00 0.00 0.00 2.01
406 417 6.261381 GTGTGGGTGTGTTGTAATTCTCTAAA 59.739 38.462 0.00 0.00 0.00 1.85
407 418 5.761234 GTGTGGGTGTGTTGTAATTCTCTAA 59.239 40.000 0.00 0.00 0.00 2.10
408 419 5.163290 TGTGTGGGTGTGTTGTAATTCTCTA 60.163 40.000 0.00 0.00 0.00 2.43
409 420 4.134563 GTGTGGGTGTGTTGTAATTCTCT 58.865 43.478 0.00 0.00 0.00 3.10
410 421 3.880490 TGTGTGGGTGTGTTGTAATTCTC 59.120 43.478 0.00 0.00 0.00 2.87
411 422 3.892284 TGTGTGGGTGTGTTGTAATTCT 58.108 40.909 0.00 0.00 0.00 2.40
412 423 4.846779 ATGTGTGGGTGTGTTGTAATTC 57.153 40.909 0.00 0.00 0.00 2.17
413 424 5.242838 CCTAATGTGTGGGTGTGTTGTAATT 59.757 40.000 0.00 0.00 0.00 1.40
414 425 4.764823 CCTAATGTGTGGGTGTGTTGTAAT 59.235 41.667 0.00 0.00 0.00 1.89
415 426 4.138290 CCTAATGTGTGGGTGTGTTGTAA 58.862 43.478 0.00 0.00 0.00 2.41
416 427 3.745799 CCTAATGTGTGGGTGTGTTGTA 58.254 45.455 0.00 0.00 0.00 2.41
417 428 2.582052 CCTAATGTGTGGGTGTGTTGT 58.418 47.619 0.00 0.00 0.00 3.32
418 429 1.269448 GCCTAATGTGTGGGTGTGTTG 59.731 52.381 0.00 0.00 0.00 3.33
419 430 1.133637 TGCCTAATGTGTGGGTGTGTT 60.134 47.619 0.00 0.00 0.00 3.32
420 431 0.476338 TGCCTAATGTGTGGGTGTGT 59.524 50.000 0.00 0.00 0.00 3.72
421 432 1.473677 CATGCCTAATGTGTGGGTGTG 59.526 52.381 0.00 0.00 0.00 3.82
422 433 1.838112 CATGCCTAATGTGTGGGTGT 58.162 50.000 0.00 0.00 0.00 4.16
423 434 0.457035 GCATGCCTAATGTGTGGGTG 59.543 55.000 6.36 0.00 38.65 4.61
424 435 0.684153 GGCATGCCTAATGTGTGGGT 60.684 55.000 29.98 0.00 38.65 4.51
425 436 0.683828 TGGCATGCCTAATGTGTGGG 60.684 55.000 35.53 0.00 38.65 4.61
426 437 1.184431 TTGGCATGCCTAATGTGTGG 58.816 50.000 35.53 0.00 38.65 4.17
427 438 3.530265 AATTGGCATGCCTAATGTGTG 57.470 42.857 35.53 0.00 38.65 3.82
428 439 4.280819 AGTAATTGGCATGCCTAATGTGT 58.719 39.130 35.53 19.47 38.65 3.72
429 440 4.338964 TGAGTAATTGGCATGCCTAATGTG 59.661 41.667 35.53 0.00 38.65 3.21
430 441 4.535781 TGAGTAATTGGCATGCCTAATGT 58.464 39.130 35.53 20.04 38.65 2.71
431 442 4.558095 GCTGAGTAATTGGCATGCCTAATG 60.558 45.833 35.53 19.29 39.49 1.90
432 443 3.571401 GCTGAGTAATTGGCATGCCTAAT 59.429 43.478 35.53 27.50 36.94 1.73
433 444 2.951642 GCTGAGTAATTGGCATGCCTAA 59.048 45.455 35.53 26.63 36.94 2.69
434 445 2.575532 GCTGAGTAATTGGCATGCCTA 58.424 47.619 35.53 29.60 36.94 3.93
435 446 1.396653 GCTGAGTAATTGGCATGCCT 58.603 50.000 35.53 19.66 36.94 4.75
436 447 0.029834 CGCTGAGTAATTGGCATGCC 59.970 55.000 30.54 30.54 0.00 4.40
437 448 0.734889 ACGCTGAGTAATTGGCATGC 59.265 50.000 9.90 9.90 0.00 4.06
438 449 2.009051 TCACGCTGAGTAATTGGCATG 58.991 47.619 0.00 0.00 0.00 4.06
439 450 2.401583 TCACGCTGAGTAATTGGCAT 57.598 45.000 0.00 0.00 0.00 4.40
440 451 2.401583 ATCACGCTGAGTAATTGGCA 57.598 45.000 0.00 0.00 0.00 4.92
441 452 3.458189 ACTATCACGCTGAGTAATTGGC 58.542 45.455 0.00 0.00 0.00 4.52
442 453 4.682787 TGACTATCACGCTGAGTAATTGG 58.317 43.478 0.00 0.00 0.00 3.16
443 454 5.344066 ACTGACTATCACGCTGAGTAATTG 58.656 41.667 0.00 0.00 0.00 2.32
444 455 5.584253 ACTGACTATCACGCTGAGTAATT 57.416 39.130 0.00 0.00 0.00 1.40
445 456 6.885952 ATACTGACTATCACGCTGAGTAAT 57.114 37.500 0.00 0.00 0.00 1.89
446 457 6.073927 CGTATACTGACTATCACGCTGAGTAA 60.074 42.308 0.56 0.00 0.00 2.24
447 458 5.404667 CGTATACTGACTATCACGCTGAGTA 59.595 44.000 0.56 0.00 0.00 2.59
448 459 4.211584 CGTATACTGACTATCACGCTGAGT 59.788 45.833 0.56 0.00 0.00 3.41
449 460 4.211584 ACGTATACTGACTATCACGCTGAG 59.788 45.833 0.56 0.00 32.90 3.35
450 461 4.124970 ACGTATACTGACTATCACGCTGA 58.875 43.478 0.56 0.00 32.90 4.26
451 462 4.469625 ACGTATACTGACTATCACGCTG 57.530 45.455 0.56 0.00 32.90 5.18
452 463 6.609237 TTAACGTATACTGACTATCACGCT 57.391 37.500 0.56 0.00 32.90 5.07
453 464 7.848716 AATTAACGTATACTGACTATCACGC 57.151 36.000 0.56 0.00 32.90 5.34
483 494 5.070685 TGTACACTACTGTGAGTCTGTGAT 58.929 41.667 13.35 4.68 46.55 3.06
489 500 7.591165 TCAAACTATGTACACTACTGTGAGTC 58.409 38.462 0.00 0.00 46.55 3.36
512 524 4.142687 GCGAAAAGCTTTAATAGTGCCTCA 60.143 41.667 13.10 0.00 44.04 3.86
548 589 2.543238 CGTAACCGACTAGAATCAGGCC 60.543 54.545 0.00 0.00 35.63 5.19
551 592 4.094590 ACTCACGTAACCGACTAGAATCAG 59.905 45.833 0.00 0.00 37.88 2.90
605 649 7.040823 GCTGCTTTAATAGTGCCTCAGATTATT 60.041 37.037 0.00 0.00 0.00 1.40
712 759 2.412421 CTTGTTCACAAGCAAGAGGC 57.588 50.000 6.75 0.00 45.59 4.70
878 934 6.147164 GGTTTGAGAAAGATGTACGTGATGAA 59.853 38.462 0.00 0.00 0.00 2.57
927 983 4.021925 GGGAGAGTTGGTGGCGCT 62.022 66.667 7.64 0.00 0.00 5.92
995 1052 1.883084 CTCGTTCGCCCCATGTAGC 60.883 63.158 0.00 0.00 0.00 3.58
1051 1111 4.459089 GAGCAGGGGCAGGACGTC 62.459 72.222 7.13 7.13 44.61 4.34
1075 1135 4.479993 CGCCAGGGCAAGGAGGAG 62.480 72.222 11.42 0.00 42.06 3.69
1370 1444 0.626916 GCCAACCTACCCCCATACAA 59.373 55.000 0.00 0.00 0.00 2.41
1456 1545 1.826385 AGGAAAGTTGGGAAGCATCG 58.174 50.000 0.00 0.00 0.00 3.84
1476 1565 2.743131 AGGAAGGAAGGAAGGAAGGA 57.257 50.000 0.00 0.00 0.00 3.36
1477 1566 3.425659 CAAAGGAAGGAAGGAAGGAAGG 58.574 50.000 0.00 0.00 0.00 3.46
1478 1567 2.822561 GCAAAGGAAGGAAGGAAGGAAG 59.177 50.000 0.00 0.00 0.00 3.46
1479 1568 2.176798 TGCAAAGGAAGGAAGGAAGGAA 59.823 45.455 0.00 0.00 0.00 3.36
1480 1569 1.780309 TGCAAAGGAAGGAAGGAAGGA 59.220 47.619 0.00 0.00 0.00 3.36
1481 1570 2.292828 TGCAAAGGAAGGAAGGAAGG 57.707 50.000 0.00 0.00 0.00 3.46
1482 1571 3.550842 CGTTTGCAAAGGAAGGAAGGAAG 60.551 47.826 23.99 0.00 0.00 3.46
1483 1572 2.360801 CGTTTGCAAAGGAAGGAAGGAA 59.639 45.455 23.99 0.00 0.00 3.36
1484 1573 1.953686 CGTTTGCAAAGGAAGGAAGGA 59.046 47.619 23.99 0.00 0.00 3.36
1485 1574 1.602920 GCGTTTGCAAAGGAAGGAAGG 60.603 52.381 30.43 7.35 42.15 3.46
1486 1575 1.770957 GCGTTTGCAAAGGAAGGAAG 58.229 50.000 30.43 4.96 42.15 3.46
1487 1576 0.030101 CGCGTTTGCAAAGGAAGGAA 59.970 50.000 30.43 0.00 42.97 3.36
1488 1577 1.652012 CGCGTTTGCAAAGGAAGGA 59.348 52.632 30.43 0.00 42.97 3.36
1489 1578 1.371635 CCGCGTTTGCAAAGGAAGG 60.372 57.895 30.43 26.19 42.97 3.46
1490 1579 2.016165 GCCGCGTTTGCAAAGGAAG 61.016 57.895 30.43 22.45 42.97 3.46
1491 1580 2.026879 GCCGCGTTTGCAAAGGAA 59.973 55.556 30.43 0.00 42.97 3.36
1602 1697 1.726791 ACGACGCAGCAAAGTCATTAG 59.273 47.619 0.00 0.00 37.23 1.73
1709 1805 6.036735 TGTTGGCTTGAAATAGCTATACGAAC 59.963 38.462 6.68 7.07 40.99 3.95
1711 1807 5.666462 TGTTGGCTTGAAATAGCTATACGA 58.334 37.500 6.68 3.91 40.99 3.43
1737 1838 3.237628 GTGCTCGCTTTGAAAAGGAATC 58.762 45.455 5.02 0.00 36.53 2.52
1747 1848 1.350193 AGATGTACGTGCTCGCTTTG 58.650 50.000 8.29 0.00 41.18 2.77
1756 1857 4.307432 AGTCAAGGAACAAGATGTACGTG 58.693 43.478 0.00 0.00 0.00 4.49
1800 1901 4.157656 ACCAATAACATCGTGGATGGTTTG 59.842 41.667 10.10 9.77 43.60 2.93
1811 1914 4.761745 CGATACTTGCACCAATAACATCG 58.238 43.478 0.00 0.00 0.00 3.84
1817 1923 2.093181 ACTGGCGATACTTGCACCAATA 60.093 45.455 0.00 0.00 0.00 1.90
1828 1934 7.529519 CGCAAATATTTAACTAACTGGCGATAC 59.470 37.037 14.82 0.00 41.84 2.24
1829 1935 7.225145 ACGCAAATATTTAACTAACTGGCGATA 59.775 33.333 22.48 0.00 41.84 2.92
1830 1936 6.037830 ACGCAAATATTTAACTAACTGGCGAT 59.962 34.615 22.48 10.00 41.84 4.58
1831 1937 5.352016 ACGCAAATATTTAACTAACTGGCGA 59.648 36.000 22.48 0.00 41.84 5.54
1832 1938 5.565695 ACGCAAATATTTAACTAACTGGCG 58.434 37.500 17.09 17.09 44.46 5.69
1833 1939 7.642586 CCTAACGCAAATATTTAACTAACTGGC 59.357 37.037 0.00 0.00 0.00 4.85
1834 1940 8.885722 TCCTAACGCAAATATTTAACTAACTGG 58.114 33.333 0.00 0.00 0.00 4.00
1855 1961 3.630312 TCGACGACATGACATCATCCTAA 59.370 43.478 0.00 0.00 33.61 2.69
1875 1996 1.488957 GCTGCTTAATCCGCGATCG 59.511 57.895 11.69 11.69 0.00 3.69
1893 2014 3.640967 CCCTCTCTTATCTTCACAGGAGG 59.359 52.174 0.00 0.00 38.87 4.30
1902 2023 1.135960 GCAGCCCCCTCTCTTATCTT 58.864 55.000 0.00 0.00 0.00 2.40
1978 2102 1.681780 GCCCGTCTTTCCATCCATCAA 60.682 52.381 0.00 0.00 0.00 2.57
1979 2103 0.107214 GCCCGTCTTTCCATCCATCA 60.107 55.000 0.00 0.00 0.00 3.07
2080 2217 3.064545 GTCAAAGATTTGGAGGCGATGAG 59.935 47.826 5.52 0.00 38.66 2.90
2085 2222 1.135972 CACGTCAAAGATTTGGAGGCG 60.136 52.381 5.52 7.79 38.66 5.52
2133 2270 4.832608 CCCTTGTCCTACCCGCGC 62.833 72.222 0.00 0.00 0.00 6.86


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

AutoCloner maintained by Alex Coulton.