Multiple sequence alignment - TraesCS2A01G460800

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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 TraesCS2A01G460800 chr2A 100.000 2228 0 0 1 2228 707063311 707065538 0.000000e+00 4115.0
1 TraesCS2A01G460800 chr2A 77.034 553 86 26 894 1411 707235716 707236262 1.680000e-71 279.0
2 TraesCS2A01G460800 chr2A 77.326 516 66 32 894 1367 707222012 707222518 7.890000e-65 257.0
3 TraesCS2A01G460800 chr2A 76.654 514 65 33 962 1437 707168682 707169178 1.330000e-57 233.0
4 TraesCS2A01G460800 chr2B 92.343 1737 80 22 531 2228 680237075 680238797 0.000000e+00 2422.0
5 TraesCS2A01G460800 chr2B 86.009 436 36 9 6 440 680236671 680237082 5.650000e-121 444.0
6 TraesCS2A01G460800 chr2B 76.087 736 90 44 868 1537 680408829 680409544 2.780000e-79 305.0
7 TraesCS2A01G460800 chr2B 76.686 519 67 33 894 1367 680445982 680446491 2.860000e-59 239.0
8 TraesCS2A01G460800 chr2B 75.882 510 63 33 850 1326 680308573 680309055 2.900000e-49 206.0
9 TraesCS2A01G460800 chr2B 87.059 85 7 3 868 951 680322376 680322457 2.360000e-15 93.5
10 TraesCS2A01G460800 chr2D 90.660 1167 59 20 501 1635 567584180 567585328 0.000000e+00 1506.0
11 TraesCS2A01G460800 chr2D 95.358 517 20 1 1712 2228 567585784 567586296 0.000000e+00 819.0
12 TraesCS2A01G460800 chr2D 86.944 337 23 8 203 534 567575504 567575824 2.100000e-95 359.0
13 TraesCS2A01G460800 chr2D 78.364 550 74 25 894 1411 567677801 567678337 4.620000e-82 315.0
14 TraesCS2A01G460800 chr2D 75.073 686 97 44 806 1437 567641833 567642498 3.670000e-63 252.0
15 TraesCS2A01G460800 chr2D 72.444 1125 167 82 669 1695 567051247 567052326 6.190000e-56 228.0
16 TraesCS2A01G460800 chr2D 90.604 149 8 2 3 145 567575345 567575493 2.260000e-45 193.0
17 TraesCS2A01G460800 chr2D 89.623 106 9 2 973 1078 567589844 567589947 1.390000e-27 134.0
18 TraesCS2A01G460800 chr2D 76.109 293 44 20 681 967 567594523 567594795 1.800000e-26 130.0
19 TraesCS2A01G460800 chr5D 92.718 206 15 0 1713 1918 526418673 526418468 4.650000e-77 298.0
20 TraesCS2A01G460800 chr1A 91.584 202 17 0 1713 1914 403605599 403605800 1.680000e-71 279.0
21 TraesCS2A01G460800 chrUn 91.111 45 4 0 1856 1900 336021194 336021238 6.640000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G460800 chr2A 707063311 707065538 2227 False 4115.000000 4115 100.000000 1 2228 1 chr2A.!!$F1 2227
1 TraesCS2A01G460800 chr2A 707235716 707236262 546 False 279.000000 279 77.034000 894 1411 1 chr2A.!!$F4 517
2 TraesCS2A01G460800 chr2A 707222012 707222518 506 False 257.000000 257 77.326000 894 1367 1 chr2A.!!$F3 473
3 TraesCS2A01G460800 chr2B 680236671 680238797 2126 False 1433.000000 2422 89.176000 6 2228 2 chr2B.!!$F5 2222
4 TraesCS2A01G460800 chr2B 680408829 680409544 715 False 305.000000 305 76.087000 868 1537 1 chr2B.!!$F3 669
5 TraesCS2A01G460800 chr2B 680445982 680446491 509 False 239.000000 239 76.686000 894 1367 1 chr2B.!!$F4 473
6 TraesCS2A01G460800 chr2D 567584180 567589947 5767 False 819.666667 1506 91.880333 501 2228 3 chr2D.!!$F6 1727
7 TraesCS2A01G460800 chr2D 567677801 567678337 536 False 315.000000 315 78.364000 894 1411 1 chr2D.!!$F4 517
8 TraesCS2A01G460800 chr2D 567641833 567642498 665 False 252.000000 252 75.073000 806 1437 1 chr2D.!!$F3 631
9 TraesCS2A01G460800 chr2D 567051247 567052326 1079 False 228.000000 228 72.444000 669 1695 1 chr2D.!!$F1 1026

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
498 499 0.178301 GTAGTACTTGAGCCTGGGCC 59.822 60.0 0.0 0.0 43.17 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 2424 0.251297 TGTTCTTGGGCAGATGGGTG 60.251 55.0 0.0 0.0 0.0 4.61 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
38 39 2.549754 GGCTAACACAATGATCGATGGG 59.450 50.000 0.54 0.00 0.00 4.00
52 53 1.743772 CGATGGGGAGGTACAAAGCTG 60.744 57.143 0.00 0.00 32.30 4.24
63 64 2.393271 ACAAAGCTGGGAGAATCGAG 57.607 50.000 0.00 0.00 34.37 4.04
69 70 2.093764 AGCTGGGAGAATCGAGAGTTTG 60.094 50.000 0.00 0.00 34.37 2.93
159 160 9.681062 TGAAAATAAACTTATTCCTCCGATTCT 57.319 29.630 0.00 0.00 32.46 2.40
160 161 9.937175 GAAAATAAACTTATTCCTCCGATTCTG 57.063 33.333 0.00 0.00 32.46 3.02
162 163 8.664211 AATAAACTTATTCCTCCGATTCTGAC 57.336 34.615 0.00 0.00 0.00 3.51
163 164 5.677319 AACTTATTCCTCCGATTCTGACA 57.323 39.130 0.00 0.00 0.00 3.58
164 165 5.012328 ACTTATTCCTCCGATTCTGACAC 57.988 43.478 0.00 0.00 0.00 3.67
165 166 2.990066 ATTCCTCCGATTCTGACACC 57.010 50.000 0.00 0.00 0.00 4.16
166 167 0.530744 TTCCTCCGATTCTGACACCG 59.469 55.000 0.00 0.00 0.00 4.94
169 170 0.243907 CTCCGATTCTGACACCGTGT 59.756 55.000 3.13 3.13 0.00 4.49
170 171 0.677288 TCCGATTCTGACACCGTGTT 59.323 50.000 5.45 0.00 0.00 3.32
171 172 1.887854 TCCGATTCTGACACCGTGTTA 59.112 47.619 5.45 0.15 0.00 2.41
172 173 2.094906 TCCGATTCTGACACCGTGTTAG 60.095 50.000 15.58 15.58 35.56 2.34
175 176 3.850273 CGATTCTGACACCGTGTTAGTAC 59.150 47.826 19.66 12.48 35.70 2.73
176 177 4.614306 CGATTCTGACACCGTGTTAGTACA 60.614 45.833 19.66 6.59 35.70 2.90
178 179 4.859304 TCTGACACCGTGTTAGTACAAT 57.141 40.909 19.66 0.00 35.70 2.71
179 180 5.204409 TCTGACACCGTGTTAGTACAATT 57.796 39.130 19.66 0.00 35.70 2.32
180 181 5.603596 TCTGACACCGTGTTAGTACAATTT 58.396 37.500 19.66 0.00 35.70 1.82
181 182 6.050432 TCTGACACCGTGTTAGTACAATTTT 58.950 36.000 19.66 0.00 35.70 1.82
182 183 6.018588 TCTGACACCGTGTTAGTACAATTTTG 60.019 38.462 19.66 0.00 35.70 2.44
183 184 5.585445 TGACACCGTGTTAGTACAATTTTGT 59.415 36.000 5.45 1.08 44.86 2.83
184 185 6.760298 TGACACCGTGTTAGTACAATTTTGTA 59.240 34.615 5.45 0.00 42.35 2.41
185 186 7.441760 TGACACCGTGTTAGTACAATTTTGTAT 59.558 33.333 5.45 0.24 44.59 2.29
186 187 8.156994 ACACCGTGTTAGTACAATTTTGTATT 57.843 30.769 6.45 5.28 44.59 1.89
187 188 9.270640 ACACCGTGTTAGTACAATTTTGTATTA 57.729 29.630 6.45 4.38 44.59 0.98
245 246 2.035442 GGAGTTCCTGCTTGGTCGC 61.035 63.158 0.00 0.00 37.07 5.19
249 250 1.301716 TTCCTGCTTGGTCGCTCAC 60.302 57.895 0.00 0.00 37.07 3.51
294 295 0.666274 TCGGTGTGACGATGCTTGTC 60.666 55.000 0.00 0.00 38.06 3.18
297 298 0.944311 GTGTGACGATGCTTGTCCGT 60.944 55.000 0.00 0.00 39.41 4.69
298 299 0.249699 TGTGACGATGCTTGTCCGTT 60.250 50.000 0.00 0.00 36.60 4.44
302 303 1.263217 GACGATGCTTGTCCGTTTGTT 59.737 47.619 0.00 0.00 36.60 2.83
325 326 2.094130 CCTTCCCTTCTCAACGGTAGAC 60.094 54.545 0.00 0.00 0.00 2.59
343 344 1.286260 CGATCTAGTAGTGGCCGGC 59.714 63.158 21.18 21.18 0.00 6.13
362 363 0.389948 CGGCAGCGAGTAGGTTTTCT 60.390 55.000 0.00 0.00 0.00 2.52
432 433 0.670162 ACACAACTACCGTGTACGCT 59.330 50.000 4.67 0.00 45.55 5.07
433 434 1.067516 ACACAACTACCGTGTACGCTT 59.932 47.619 4.67 0.00 45.55 4.68
434 435 2.129607 CACAACTACCGTGTACGCTTT 58.870 47.619 4.67 0.00 38.18 3.51
435 436 2.540931 CACAACTACCGTGTACGCTTTT 59.459 45.455 4.67 0.00 38.18 2.27
436 437 3.001533 CACAACTACCGTGTACGCTTTTT 59.998 43.478 4.67 0.00 38.18 1.94
460 461 8.883789 TTTTTACTTTGAGACAAACAACTACG 57.116 30.769 0.00 0.00 0.00 3.51
461 462 6.592798 TTACTTTGAGACAAACAACTACGG 57.407 37.500 0.00 0.00 0.00 4.02
462 463 4.510571 ACTTTGAGACAAACAACTACGGT 58.489 39.130 0.00 0.00 0.00 4.83
463 464 4.331717 ACTTTGAGACAAACAACTACGGTG 59.668 41.667 0.00 0.00 0.00 4.94
464 465 3.530265 TGAGACAAACAACTACGGTGT 57.470 42.857 0.00 0.00 0.00 4.16
465 466 4.652421 TGAGACAAACAACTACGGTGTA 57.348 40.909 0.00 0.00 0.00 2.90
466 467 4.362279 TGAGACAAACAACTACGGTGTAC 58.638 43.478 0.00 0.00 0.00 2.90
467 468 4.098349 TGAGACAAACAACTACGGTGTACT 59.902 41.667 0.00 0.00 0.00 2.73
468 469 4.614946 AGACAAACAACTACGGTGTACTC 58.385 43.478 0.00 0.00 0.00 2.59
469 470 3.721035 ACAAACAACTACGGTGTACTCC 58.279 45.455 3.76 3.76 0.00 3.85
470 471 3.385755 ACAAACAACTACGGTGTACTCCT 59.614 43.478 11.98 2.47 0.00 3.69
471 472 4.584325 ACAAACAACTACGGTGTACTCCTA 59.416 41.667 11.98 3.42 0.00 2.94
472 473 4.773323 AACAACTACGGTGTACTCCTAC 57.227 45.455 11.98 0.00 0.00 3.18
473 474 2.744202 ACAACTACGGTGTACTCCTACG 59.256 50.000 11.98 1.99 0.00 3.51
474 475 2.744202 CAACTACGGTGTACTCCTACGT 59.256 50.000 11.98 7.50 41.10 3.57
475 476 2.350522 ACTACGGTGTACTCCTACGTG 58.649 52.381 11.98 0.00 38.34 4.49
476 477 2.028112 ACTACGGTGTACTCCTACGTGA 60.028 50.000 11.98 0.00 38.34 4.35
477 478 1.446907 ACGGTGTACTCCTACGTGAG 58.553 55.000 11.98 0.00 36.32 3.51
478 479 1.002430 ACGGTGTACTCCTACGTGAGA 59.998 52.381 11.98 0.00 36.32 3.27
479 480 1.664659 CGGTGTACTCCTACGTGAGAG 59.335 57.143 11.98 11.68 36.22 3.20
480 481 2.709213 GGTGTACTCCTACGTGAGAGT 58.291 52.381 21.37 21.37 45.20 3.24
481 482 3.677148 CGGTGTACTCCTACGTGAGAGTA 60.677 52.174 19.72 19.72 43.09 2.59
482 483 3.870419 GGTGTACTCCTACGTGAGAGTAG 59.130 52.174 22.55 2.90 44.18 2.57
483 484 4.502962 GTGTACTCCTACGTGAGAGTAGT 58.497 47.826 22.55 8.16 44.18 2.73
484 485 5.394663 GGTGTACTCCTACGTGAGAGTAGTA 60.395 48.000 22.55 15.06 44.18 1.82
485 486 5.518487 GTGTACTCCTACGTGAGAGTAGTAC 59.482 48.000 22.55 20.03 44.18 2.73
486 487 5.420421 TGTACTCCTACGTGAGAGTAGTACT 59.580 44.000 22.55 1.37 44.18 2.73
487 488 5.419239 ACTCCTACGTGAGAGTAGTACTT 57.581 43.478 17.69 0.00 41.51 2.24
488 489 5.177326 ACTCCTACGTGAGAGTAGTACTTG 58.823 45.833 17.69 0.00 41.51 3.16
489 490 5.046735 ACTCCTACGTGAGAGTAGTACTTGA 60.047 44.000 17.69 0.00 41.51 3.02
490 491 5.417811 TCCTACGTGAGAGTAGTACTTGAG 58.582 45.833 0.00 0.00 41.76 3.02
491 492 4.034279 CCTACGTGAGAGTAGTACTTGAGC 59.966 50.000 0.00 0.00 41.76 4.26
492 493 2.748532 ACGTGAGAGTAGTACTTGAGCC 59.251 50.000 0.00 0.00 0.00 4.70
493 494 3.011119 CGTGAGAGTAGTACTTGAGCCT 58.989 50.000 0.00 0.00 0.00 4.58
494 495 3.181505 CGTGAGAGTAGTACTTGAGCCTG 60.182 52.174 0.00 0.00 0.00 4.85
495 496 3.129638 GTGAGAGTAGTACTTGAGCCTGG 59.870 52.174 0.00 0.00 0.00 4.45
496 497 2.691011 GAGAGTAGTACTTGAGCCTGGG 59.309 54.545 0.00 0.00 0.00 4.45
497 498 1.137282 GAGTAGTACTTGAGCCTGGGC 59.863 57.143 0.00 3.00 42.33 5.36
498 499 0.178301 GTAGTACTTGAGCCTGGGCC 59.822 60.000 0.00 0.00 43.17 5.80
499 500 0.981277 TAGTACTTGAGCCTGGGCCC 60.981 60.000 17.59 17.59 43.17 5.80
500 501 2.124996 TACTTGAGCCTGGGCCCT 59.875 61.111 25.70 0.66 43.17 5.19
501 502 1.541368 TACTTGAGCCTGGGCCCTT 60.541 57.895 25.70 5.78 43.17 3.95
502 503 1.140134 TACTTGAGCCTGGGCCCTTT 61.140 55.000 25.70 5.36 43.17 3.11
503 504 1.680314 CTTGAGCCTGGGCCCTTTC 60.680 63.158 25.70 15.14 43.17 2.62
504 505 3.224007 TTGAGCCTGGGCCCTTTCC 62.224 63.158 25.70 8.80 43.17 3.13
505 506 3.342477 GAGCCTGGGCCCTTTCCT 61.342 66.667 25.70 13.86 43.17 3.36
506 507 2.866015 AGCCTGGGCCCTTTCCTT 60.866 61.111 25.70 0.24 43.17 3.36
507 508 2.363018 GCCTGGGCCCTTTCCTTC 60.363 66.667 25.70 0.99 34.56 3.46
508 509 2.923910 GCCTGGGCCCTTTCCTTCT 61.924 63.158 25.70 0.00 34.56 2.85
517 518 0.981943 CCTTTCCTTCTACGGTGGGT 59.018 55.000 0.00 0.00 0.00 4.51
591 593 5.878116 CAGCAATCACATTTCCATTTTCCAT 59.122 36.000 0.00 0.00 0.00 3.41
592 594 6.373216 CAGCAATCACATTTCCATTTTCCATT 59.627 34.615 0.00 0.00 0.00 3.16
593 595 6.943718 AGCAATCACATTTCCATTTTCCATTT 59.056 30.769 0.00 0.00 0.00 2.32
594 596 7.449086 AGCAATCACATTTCCATTTTCCATTTT 59.551 29.630 0.00 0.00 0.00 1.82
595 597 7.751793 GCAATCACATTTCCATTTTCCATTTTC 59.248 33.333 0.00 0.00 0.00 2.29
597 599 6.835174 TCACATTTCCATTTTCCATTTTCCA 58.165 32.000 0.00 0.00 0.00 3.53
598 600 7.460071 TCACATTTCCATTTTCCATTTTCCAT 58.540 30.769 0.00 0.00 0.00 3.41
599 601 7.943447 TCACATTTCCATTTTCCATTTTCCATT 59.057 29.630 0.00 0.00 0.00 3.16
600 602 8.578151 CACATTTCCATTTTCCATTTTCCATTT 58.422 29.630 0.00 0.00 0.00 2.32
601 603 8.795513 ACATTTCCATTTTCCATTTTCCATTTC 58.204 29.630 0.00 0.00 0.00 2.17
602 604 7.757941 TTTCCATTTTCCATTTTCCATTTCC 57.242 32.000 0.00 0.00 0.00 3.13
603 605 6.445451 TCCATTTTCCATTTTCCATTTCCA 57.555 33.333 0.00 0.00 0.00 3.53
604 606 7.030234 TCCATTTTCCATTTTCCATTTCCAT 57.970 32.000 0.00 0.00 0.00 3.41
645 666 2.289072 CCAATTGACTCACCTCGACTGT 60.289 50.000 7.12 0.00 0.00 3.55
717 739 4.170468 AGGACAATAATTCCATCCGCTT 57.830 40.909 0.00 0.00 35.33 4.68
951 994 2.233271 CCCAAGCTCACTCAAACACAT 58.767 47.619 0.00 0.00 0.00 3.21
955 998 3.213206 AGCTCACTCAAACACATCCAA 57.787 42.857 0.00 0.00 0.00 3.53
990 1089 0.387202 CAGTACATCAGAGCCTCCCG 59.613 60.000 0.00 0.00 0.00 5.14
1249 1384 0.464013 ATCTCTGGCTCATGTGCTGC 60.464 55.000 18.44 4.59 0.00 5.25
1252 1387 1.222661 CTGGCTCATGTGCTGCCTA 59.777 57.895 18.44 6.70 46.23 3.93
1306 1464 2.677524 TGTAGGTAGCACCGCCGT 60.678 61.111 0.00 0.00 44.90 5.68
1411 1605 7.165154 CAGTTCATGTTGTCGTATTTTTCGTTT 59.835 33.333 0.00 0.00 0.00 3.60
1499 1706 2.424601 GCAAATCTCAACTGGCTGCATA 59.575 45.455 0.50 0.00 0.00 3.14
1539 1747 4.080863 GTCACTCTAATCACCAAGTCCCAT 60.081 45.833 0.00 0.00 0.00 4.00
1614 1826 3.297472 GCTTTGAAAGCGTTAAGGTGAC 58.703 45.455 14.70 0.00 45.74 3.67
1620 1832 2.674796 AGCGTTAAGGTGACTGGATC 57.325 50.000 0.00 0.00 42.68 3.36
1697 1909 4.320935 GGAGTTTTCTTTGTGTGTGTGTGT 60.321 41.667 0.00 0.00 0.00 3.72
1700 1912 3.550950 TTCTTTGTGTGTGTGTGTGTG 57.449 42.857 0.00 0.00 0.00 3.82
1701 1913 2.499197 TCTTTGTGTGTGTGTGTGTGT 58.501 42.857 0.00 0.00 0.00 3.72
1702 1914 2.225255 TCTTTGTGTGTGTGTGTGTGTG 59.775 45.455 0.00 0.00 0.00 3.82
1705 1917 0.958382 GTGTGTGTGTGTGTGTGGGT 60.958 55.000 0.00 0.00 0.00 4.51
1706 1918 0.675208 TGTGTGTGTGTGTGTGGGTC 60.675 55.000 0.00 0.00 0.00 4.46
1707 1919 1.448717 TGTGTGTGTGTGTGGGTCG 60.449 57.895 0.00 0.00 0.00 4.79
1708 1920 1.448893 GTGTGTGTGTGTGGGTCGT 60.449 57.895 0.00 0.00 0.00 4.34
1709 1921 1.448717 TGTGTGTGTGTGGGTCGTG 60.449 57.895 0.00 0.00 0.00 4.35
1710 1922 1.153529 GTGTGTGTGTGGGTCGTGA 60.154 57.895 0.00 0.00 0.00 4.35
1785 2376 0.320421 TTTGCCACGAGTCCAGCTAC 60.320 55.000 0.00 0.00 0.00 3.58
1798 2389 2.760385 GCTACCTCGTCAGGCCCT 60.760 66.667 0.00 0.00 45.05 5.19
1868 2459 6.038356 CCAAGAACATGGCTGACATTATTTC 58.962 40.000 0.00 0.00 37.84 2.17
1870 2461 5.185454 AGAACATGGCTGACATTATTTCGA 58.815 37.500 0.00 0.00 37.84 3.71
1916 2507 0.631753 CTCTCTACCTCCCTCCACCA 59.368 60.000 0.00 0.00 0.00 4.17
1951 2542 5.803461 CAGTGTACTGGCATCATGAAAAATG 59.197 40.000 0.00 0.00 40.20 2.32
1960 2551 5.413499 GCATCATGAAAAATGTAGCCACTT 58.587 37.500 0.00 0.00 0.00 3.16
2057 2648 7.178983 ACATGTCAAATTGGAAGGTGATTGTAT 59.821 33.333 0.00 0.00 0.00 2.29
2218 2809 5.893897 TGAGAGAGATACATCATCGATGG 57.106 43.478 24.61 12.41 43.60 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.092301 GTTAGCCAGCAAAAGGAGGATT 58.908 45.455 0.00 0.00 0.00 3.01
3 4 2.041620 TGTTAGCCAGCAAAAGGAGGAT 59.958 45.455 0.00 0.00 0.00 3.24
4 5 1.423541 TGTTAGCCAGCAAAAGGAGGA 59.576 47.619 0.00 0.00 0.00 3.71
5 6 1.541588 GTGTTAGCCAGCAAAAGGAGG 59.458 52.381 0.00 0.00 0.00 4.30
7 8 2.356665 TGTGTTAGCCAGCAAAAGGA 57.643 45.000 0.00 0.00 0.00 3.36
38 39 1.276622 TCTCCCAGCTTTGTACCTCC 58.723 55.000 0.00 0.00 0.00 4.30
52 53 2.682155 AGCAAACTCTCGATTCTCCC 57.318 50.000 0.00 0.00 0.00 4.30
63 64 9.899226 AGACATTGAAAACTAATTAGCAAACTC 57.101 29.630 12.54 7.30 0.00 3.01
69 70 7.308435 ACTGCAGACATTGAAAACTAATTAGC 58.692 34.615 23.35 0.00 0.00 3.09
113 114 6.854496 TTCAGTGTTAGATTAGTTTGCGTT 57.146 33.333 0.00 0.00 0.00 4.84
132 133 9.937175 GAATCGGAGGAATAAGTTTATTTTCAG 57.063 33.333 0.00 2.78 33.72 3.02
145 146 2.361119 CGGTGTCAGAATCGGAGGAATA 59.639 50.000 0.00 0.00 0.00 1.75
159 160 5.585445 ACAAAATTGTACTAACACGGTGTCA 59.415 36.000 15.09 4.85 40.16 3.58
160 161 6.051646 ACAAAATTGTACTAACACGGTGTC 57.948 37.500 15.09 1.99 40.16 3.67
216 217 3.091545 GCAGGAACTCCATCCAATTCAA 58.908 45.455 0.00 0.00 42.27 2.69
222 223 0.329261 CCAAGCAGGAACTCCATCCA 59.671 55.000 0.00 0.00 42.27 3.41
226 227 1.371183 CGACCAAGCAGGAACTCCA 59.629 57.895 1.83 0.00 41.22 3.86
262 263 0.391661 ACACCGATCCACAGTGCATC 60.392 55.000 0.00 0.00 34.83 3.91
265 266 1.005037 TCACACCGATCCACAGTGC 60.005 57.895 0.00 0.00 34.83 4.40
267 268 1.176619 TCGTCACACCGATCCACAGT 61.177 55.000 0.00 0.00 30.63 3.55
287 288 0.106918 AGGGAACAAACGGACAAGCA 60.107 50.000 0.00 0.00 0.00 3.91
294 295 1.202891 AGAAGGGAAGGGAACAAACGG 60.203 52.381 0.00 0.00 0.00 4.44
297 298 3.562182 GTTGAGAAGGGAAGGGAACAAA 58.438 45.455 0.00 0.00 0.00 2.83
298 299 2.486548 CGTTGAGAAGGGAAGGGAACAA 60.487 50.000 0.00 0.00 0.00 2.83
302 303 0.473117 ACCGTTGAGAAGGGAAGGGA 60.473 55.000 2.17 0.00 39.67 4.20
325 326 1.286260 GCCGGCCACTACTAGATCG 59.714 63.158 18.11 0.00 0.00 3.69
343 344 0.389948 AGAAAACCTACTCGCTGCCG 60.390 55.000 0.00 0.00 0.00 5.69
362 363 1.945354 GACCCCAGTCTTGCGATCGA 61.945 60.000 21.57 0.59 40.10 3.59
376 377 0.035439 TTTCCAATCTGCTCGACCCC 60.035 55.000 0.00 0.00 0.00 4.95
435 436 7.964011 CCGTAGTTGTTTGTCTCAAAGTAAAAA 59.036 33.333 0.00 0.00 0.00 1.94
436 437 7.119553 ACCGTAGTTGTTTGTCTCAAAGTAAAA 59.880 33.333 0.00 0.00 0.00 1.52
437 438 6.594937 ACCGTAGTTGTTTGTCTCAAAGTAAA 59.405 34.615 0.00 0.00 0.00 2.01
438 439 6.036300 CACCGTAGTTGTTTGTCTCAAAGTAA 59.964 38.462 0.00 0.00 0.00 2.24
439 440 5.521010 CACCGTAGTTGTTTGTCTCAAAGTA 59.479 40.000 0.00 0.00 0.00 2.24
440 441 4.331717 CACCGTAGTTGTTTGTCTCAAAGT 59.668 41.667 0.00 0.00 0.00 2.66
441 442 4.331717 ACACCGTAGTTGTTTGTCTCAAAG 59.668 41.667 0.00 0.00 0.00 2.77
442 443 4.255301 ACACCGTAGTTGTTTGTCTCAAA 58.745 39.130 0.00 0.00 0.00 2.69
443 444 3.864243 ACACCGTAGTTGTTTGTCTCAA 58.136 40.909 0.00 0.00 0.00 3.02
444 445 3.530265 ACACCGTAGTTGTTTGTCTCA 57.470 42.857 0.00 0.00 0.00 3.27
445 446 4.614946 AGTACACCGTAGTTGTTTGTCTC 58.385 43.478 0.00 0.00 0.00 3.36
446 447 4.500375 GGAGTACACCGTAGTTGTTTGTCT 60.500 45.833 0.00 0.00 0.00 3.41
447 448 3.737774 GGAGTACACCGTAGTTGTTTGTC 59.262 47.826 0.00 0.00 0.00 3.18
448 449 3.385755 AGGAGTACACCGTAGTTGTTTGT 59.614 43.478 3.50 0.00 34.73 2.83
449 450 3.986277 AGGAGTACACCGTAGTTGTTTG 58.014 45.455 3.50 0.00 34.73 2.93
450 451 4.320494 CGTAGGAGTACACCGTAGTTGTTT 60.320 45.833 3.50 0.00 34.73 2.83
451 452 3.189287 CGTAGGAGTACACCGTAGTTGTT 59.811 47.826 3.50 0.00 34.73 2.83
452 453 2.744202 CGTAGGAGTACACCGTAGTTGT 59.256 50.000 3.50 0.00 34.73 3.32
453 454 2.744202 ACGTAGGAGTACACCGTAGTTG 59.256 50.000 3.50 0.00 34.73 3.16
454 455 2.744202 CACGTAGGAGTACACCGTAGTT 59.256 50.000 3.50 0.00 34.73 2.24
455 456 2.028112 TCACGTAGGAGTACACCGTAGT 60.028 50.000 3.50 2.69 34.73 2.73
456 457 2.606725 CTCACGTAGGAGTACACCGTAG 59.393 54.545 3.50 2.09 34.73 3.51
457 458 2.233676 TCTCACGTAGGAGTACACCGTA 59.766 50.000 3.50 0.00 36.30 4.02
458 459 1.002430 TCTCACGTAGGAGTACACCGT 59.998 52.381 3.50 0.00 36.30 4.83
459 460 1.664659 CTCTCACGTAGGAGTACACCG 59.335 57.143 3.50 0.00 36.30 4.94
460 461 2.709213 ACTCTCACGTAGGAGTACACC 58.291 52.381 17.33 0.27 40.49 4.16
461 462 4.502962 ACTACTCTCACGTAGGAGTACAC 58.497 47.826 19.31 0.00 42.06 2.90
462 463 4.815533 ACTACTCTCACGTAGGAGTACA 57.184 45.455 19.31 8.29 42.06 2.90
463 464 5.901552 AGTACTACTCTCACGTAGGAGTAC 58.098 45.833 23.42 23.42 42.06 2.73
464 465 6.153510 TCAAGTACTACTCTCACGTAGGAGTA 59.846 42.308 20.88 20.88 42.06 2.59
465 466 5.046735 TCAAGTACTACTCTCACGTAGGAGT 60.047 44.000 20.88 20.88 43.93 3.85
466 467 5.417811 TCAAGTACTACTCTCACGTAGGAG 58.582 45.833 13.25 13.25 40.87 3.69
467 468 5.411831 TCAAGTACTACTCTCACGTAGGA 57.588 43.478 0.00 0.00 40.87 2.94
468 469 4.034279 GCTCAAGTACTACTCTCACGTAGG 59.966 50.000 0.00 0.00 40.87 3.18
469 470 4.034279 GGCTCAAGTACTACTCTCACGTAG 59.966 50.000 0.00 0.00 41.98 3.51
470 471 3.937706 GGCTCAAGTACTACTCTCACGTA 59.062 47.826 0.00 0.00 0.00 3.57
471 472 2.748532 GGCTCAAGTACTACTCTCACGT 59.251 50.000 0.00 0.00 0.00 4.49
472 473 3.011119 AGGCTCAAGTACTACTCTCACG 58.989 50.000 0.00 0.00 0.00 4.35
473 474 3.129638 CCAGGCTCAAGTACTACTCTCAC 59.870 52.174 0.00 0.00 0.00 3.51
474 475 3.357203 CCAGGCTCAAGTACTACTCTCA 58.643 50.000 0.00 0.00 0.00 3.27
475 476 2.691011 CCCAGGCTCAAGTACTACTCTC 59.309 54.545 0.00 0.00 0.00 3.20
476 477 2.741145 CCCAGGCTCAAGTACTACTCT 58.259 52.381 0.00 0.00 0.00 3.24
477 478 1.137282 GCCCAGGCTCAAGTACTACTC 59.863 57.143 0.08 0.00 38.26 2.59
478 479 1.196012 GCCCAGGCTCAAGTACTACT 58.804 55.000 0.08 0.00 38.26 2.57
479 480 0.178301 GGCCCAGGCTCAAGTACTAC 59.822 60.000 8.89 0.00 41.60 2.73
480 481 0.981277 GGGCCCAGGCTCAAGTACTA 60.981 60.000 19.95 0.00 42.14 1.82
481 482 2.301738 GGGCCCAGGCTCAAGTACT 61.302 63.158 19.95 0.00 42.14 2.73
482 483 1.853250 AAGGGCCCAGGCTCAAGTAC 61.853 60.000 27.56 0.00 45.68 2.73
483 484 1.140134 AAAGGGCCCAGGCTCAAGTA 61.140 55.000 27.56 0.00 45.68 2.24
484 485 2.432174 GAAAGGGCCCAGGCTCAAGT 62.432 60.000 27.56 0.00 45.68 3.16
485 486 1.680314 GAAAGGGCCCAGGCTCAAG 60.680 63.158 27.56 0.00 45.68 3.02
486 487 2.440599 GAAAGGGCCCAGGCTCAA 59.559 61.111 27.56 0.00 45.68 3.02
487 488 3.661648 GGAAAGGGCCCAGGCTCA 61.662 66.667 27.56 0.00 45.68 4.26
488 489 2.845638 GAAGGAAAGGGCCCAGGCTC 62.846 65.000 27.56 14.06 43.08 4.70
489 490 2.866015 AAGGAAAGGGCCCAGGCT 60.866 61.111 27.56 4.26 41.60 4.58
490 491 1.571773 TAGAAGGAAAGGGCCCAGGC 61.572 60.000 27.56 12.20 41.06 4.85
491 492 0.256177 GTAGAAGGAAAGGGCCCAGG 59.744 60.000 27.56 0.00 0.00 4.45
492 493 0.107654 CGTAGAAGGAAAGGGCCCAG 60.108 60.000 27.56 0.00 0.00 4.45
493 494 1.559065 CCGTAGAAGGAAAGGGCCCA 61.559 60.000 27.56 0.00 0.00 5.36
494 495 1.223763 CCGTAGAAGGAAAGGGCCC 59.776 63.158 16.46 16.46 0.00 5.80
495 496 0.392595 CACCGTAGAAGGAAAGGGCC 60.393 60.000 0.00 0.00 34.73 5.80
496 497 0.392595 CCACCGTAGAAGGAAAGGGC 60.393 60.000 0.00 0.00 34.73 5.19
497 498 0.252197 CCCACCGTAGAAGGAAAGGG 59.748 60.000 0.00 0.00 36.01 3.95
498 499 0.981943 ACCCACCGTAGAAGGAAAGG 59.018 55.000 0.00 0.00 34.73 3.11
499 500 2.224450 ACAACCCACCGTAGAAGGAAAG 60.224 50.000 0.00 0.00 34.73 2.62
500 501 1.770061 ACAACCCACCGTAGAAGGAAA 59.230 47.619 0.00 0.00 34.73 3.13
501 502 1.426751 ACAACCCACCGTAGAAGGAA 58.573 50.000 0.00 0.00 34.73 3.36
502 503 1.345415 GAACAACCCACCGTAGAAGGA 59.655 52.381 0.00 0.00 34.73 3.36
503 504 1.346722 AGAACAACCCACCGTAGAAGG 59.653 52.381 0.00 0.00 37.30 3.46
504 505 2.833631 AGAACAACCCACCGTAGAAG 57.166 50.000 0.00 0.00 0.00 2.85
505 506 3.564053 AAAGAACAACCCACCGTAGAA 57.436 42.857 0.00 0.00 0.00 2.10
506 507 3.564053 AAAAGAACAACCCACCGTAGA 57.436 42.857 0.00 0.00 0.00 2.59
528 529 9.653516 TGCCCAAATATCAGGAGAAAATAAATA 57.346 29.630 0.00 0.00 0.00 1.40
591 593 6.902771 TCGGTAGAAAATGGAAATGGAAAA 57.097 33.333 0.00 0.00 0.00 2.29
592 594 6.717540 TCTTCGGTAGAAAATGGAAATGGAAA 59.282 34.615 0.00 0.00 35.71 3.13
593 595 6.242396 TCTTCGGTAGAAAATGGAAATGGAA 58.758 36.000 0.00 0.00 35.71 3.53
594 596 5.811190 TCTTCGGTAGAAAATGGAAATGGA 58.189 37.500 0.00 0.00 35.71 3.41
595 597 6.509418 TTCTTCGGTAGAAAATGGAAATGG 57.491 37.500 0.00 0.00 39.90 3.16
645 666 0.895530 AGTCGATCGAGAAGGCCAAA 59.104 50.000 20.09 0.00 0.00 3.28
717 739 2.798145 CGACGTCGATGGATTGGAATGA 60.798 50.000 33.35 0.00 43.02 2.57
745 767 2.853290 GCATGCTGCAGGTATGGCC 61.853 63.158 17.12 0.00 44.26 5.36
951 994 4.593206 ACTGAGGAGATAGTGTTGTTTGGA 59.407 41.667 0.00 0.00 0.00 3.53
955 998 6.437477 TGATGTACTGAGGAGATAGTGTTGTT 59.563 38.462 0.00 0.00 0.00 2.83
990 1089 4.399303 AGACACTTTGCCATATTGCTAACC 59.601 41.667 0.00 0.00 0.00 2.85
1110 1227 4.170062 TTAGACTCGCCGACGCCG 62.170 66.667 0.00 0.00 39.84 6.46
1198 1333 1.439543 ATAGCAGGGATCCCAGGAAC 58.560 55.000 32.69 15.90 38.92 3.62
1411 1605 6.819284 TGATGATACATGTAGCACATCAAGA 58.181 36.000 29.50 18.14 40.25 3.02
1457 1659 1.627864 TCCCAGAAGACGATCACACA 58.372 50.000 0.00 0.00 0.00 3.72
1499 1706 5.067936 AGAGTGACGAAATAGGACATCGATT 59.932 40.000 0.00 0.00 39.73 3.34
1539 1747 3.390135 GGAACATGAACGACTCTGAACA 58.610 45.455 0.00 0.00 0.00 3.18
1614 1826 5.104235 TCCATGCATATCCCTATTGATCCAG 60.104 44.000 0.00 0.00 0.00 3.86
1731 2322 8.125978 TGCTCCTAGTTGATTGAATGAAAAAT 57.874 30.769 0.00 0.00 0.00 1.82
1798 2389 0.393402 CTGCTGTATGGCTGAGGCAA 60.393 55.000 14.16 0.00 42.43 4.52
1833 2424 0.251297 TGTTCTTGGGCAGATGGGTG 60.251 55.000 0.00 0.00 0.00 4.61
1868 2459 6.901887 GTGTTATTGCATGTGAGTAGAAATCG 59.098 38.462 0.00 0.00 0.00 3.34
1870 2461 7.686438 TGTGTTATTGCATGTGAGTAGAAAT 57.314 32.000 0.00 0.00 0.00 2.17
1916 2507 2.305927 CCAGTACACTGATTGGTCCCTT 59.694 50.000 10.96 0.00 46.59 3.95
1951 2542 4.981806 TCCATAATGCAAAAGTGGCTAC 57.018 40.909 0.00 0.00 0.00 3.58
1960 2551 7.046652 CACCCACAAATAATCCATAATGCAAA 58.953 34.615 0.00 0.00 0.00 3.68
2080 2671 7.541916 TGGGGTTTACATGTATCGTCATATA 57.458 36.000 6.36 0.00 0.00 0.86
2081 2672 6.428083 TGGGGTTTACATGTATCGTCATAT 57.572 37.500 6.36 0.00 0.00 1.78
2082 2673 5.873146 TGGGGTTTACATGTATCGTCATA 57.127 39.130 6.36 0.00 0.00 2.15
2083 2674 4.764050 TGGGGTTTACATGTATCGTCAT 57.236 40.909 6.36 0.00 0.00 3.06
2124 2715 2.308866 AGTTGAGGATTCCAAACCCGAT 59.691 45.455 14.41 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.