Multiple sequence alignment - TraesCS3D01G109800

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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 TraesCS3D01G109800 chr3D 100.000 3006 0 0 1 3006 63461954 63458949 0.000000e+00 5552.0
1 TraesCS3D01G109800 chr3D 91.146 192 11 3 996 1187 63467815 63467630 3.850000e-64 255.0
2 TraesCS3D01G109800 chr3D 83.824 136 20 2 1216 1350 395065176 395065042 8.750000e-26 128.0
3 TraesCS3D01G109800 chr3A 91.692 1312 45 16 817 2093 72898122 72896840 0.000000e+00 1760.0
4 TraesCS3D01G109800 chr3A 86.885 610 41 20 2433 3006 72896441 72895835 0.000000e+00 647.0
5 TraesCS3D01G109800 chr3A 89.760 459 33 4 19 463 72899076 72898618 2.600000e-160 575.0
6 TraesCS3D01G109800 chr3A 87.421 318 13 10 532 825 72898610 72898296 1.030000e-89 340.0
7 TraesCS3D01G109800 chr3A 95.187 187 9 0 2196 2382 72896636 72896450 2.270000e-76 296.0
8 TraesCS3D01G109800 chr3A 91.346 104 9 0 1711 1814 72897170 72897067 3.120000e-30 143.0
9 TraesCS3D01G109800 chr3A 85.542 83 10 2 1466 1547 514611935 514611854 5.340000e-13 86.1
10 TraesCS3D01G109800 chr3B 92.148 866 32 14 1216 2072 103722464 103721626 0.000000e+00 1190.0
11 TraesCS3D01G109800 chr3B 85.542 913 64 27 2094 2957 103721544 103720651 0.000000e+00 893.0
12 TraesCS3D01G109800 chr3B 89.213 686 24 12 530 1183 103723202 103722535 0.000000e+00 811.0
13 TraesCS3D01G109800 chr3B 84.440 482 28 11 19 464 103723675 103723205 5.950000e-117 431.0
14 TraesCS3D01G109800 chr3B 90.826 218 14 4 2740 2957 103239674 103239463 1.360000e-73 287.0
15 TraesCS3D01G109800 chr3B 80.124 161 24 8 1000 1157 478323394 478323239 2.450000e-21 113.0
16 TraesCS3D01G109800 chr3B 81.618 136 23 2 1216 1350 519777995 519777861 8.810000e-21 111.0
17 TraesCS3D01G109800 chr3B 82.927 82 10 4 1231 1310 416514083 416514004 1.500000e-08 71.3
18 TraesCS3D01G109800 chr3B 100.000 33 0 0 2694 2726 103239740 103239708 9.000000e-06 62.1
19 TraesCS3D01G109800 chr5A 87.407 135 15 2 1213 1346 436089393 436089526 1.440000e-33 154.0
20 TraesCS3D01G109800 chr5A 83.212 137 19 4 1216 1350 691677519 691677385 4.070000e-24 122.0
21 TraesCS3D01G109800 chr5A 85.542 83 10 2 1466 1547 451389468 451389549 5.340000e-13 86.1
22 TraesCS3D01G109800 chr5B 86.667 135 16 2 1213 1346 391144955 391145088 6.710000e-32 148.0
23 TraesCS3D01G109800 chr5D 92.784 97 7 0 1213 1309 334255462 334255558 1.120000e-29 141.0
24 TraesCS3D01G109800 chr5D 85.542 83 10 2 1466 1547 350953950 350954031 5.340000e-13 86.1
25 TraesCS3D01G109800 chr2D 90.361 83 8 0 1465 1547 424015076 424014994 3.170000e-20 110.0
26 TraesCS3D01G109800 chr2B 90.361 83 8 0 1465 1547 498310556 498310474 3.170000e-20 110.0
27 TraesCS3D01G109800 chr2A 90.361 83 8 0 1465 1547 564218838 564218920 3.170000e-20 110.0
28 TraesCS3D01G109800 chr6B 92.958 71 5 0 997 1067 652631348 652631278 1.470000e-18 104.0
29 TraesCS3D01G109800 chr6B 79.661 118 17 6 999 1114 477689272 477689384 8.930000e-11 78.7
30 TraesCS3D01G109800 chr6A 92.958 71 5 0 997 1067 578887723 578887653 1.470000e-18 104.0
31 TraesCS3D01G109800 chr6A 79.661 118 17 6 999 1114 446520785 446520897 8.930000e-11 78.7
32 TraesCS3D01G109800 chrUn 84.091 88 13 1 1460 1547 232286094 232286008 1.920000e-12 84.2
33 TraesCS3D01G109800 chr6D 79.661 118 17 6 999 1114 309718608 309718720 8.930000e-11 78.7


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 TraesCS3D01G109800 chr3D 63458949 63461954 3005 True 5552.000000 5552 100.000000 1 3006 1 chr3D.!!$R1 3005
1 TraesCS3D01G109800 chr3A 72895835 72899076 3241 True 626.833333 1760 90.381833 19 3006 6 chr3A.!!$R2 2987
2 TraesCS3D01G109800 chr3B 103720651 103723675 3024 True 831.250000 1190 87.835750 19 2957 4 chr3B.!!$R5 2938

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
493 538 0.250295 TCAACCCGAGTCTTGCAAGG 60.25 55.0 25.73 12.37 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2401 2853 0.039256 TTTTTGGTGCTGCTCATCGC 60.039 50.0 0.0 0.0 39.77 4.58 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
100 101 4.359706 CCTTTTGGAACGAACTTTTCTGG 58.640 43.478 0.00 0.00 44.07 3.86
124 125 5.363979 CAGAAGTGCTACTTTTTCCCTTC 57.636 43.478 3.56 0.00 38.80 3.46
210 229 3.873952 GCCTTAATCATGGTGAGAGTGTC 59.126 47.826 0.00 0.00 0.00 3.67
265 300 1.878953 TTCGTCAAAGCCAAGGAGAC 58.121 50.000 0.00 0.00 0.00 3.36
267 302 0.868406 CGTCAAAGCCAAGGAGACAC 59.132 55.000 0.00 0.00 0.00 3.67
272 307 2.047179 GCCAAGGAGACACCGGTC 60.047 66.667 2.59 0.00 44.74 4.79
407 442 6.328672 AGAGGGATCTTCAGTGCAGTAATAAT 59.671 38.462 0.00 0.00 0.00 1.28
434 479 2.631267 ACAAAAGCAAAAGCAAGGTGG 58.369 42.857 0.00 0.00 0.00 4.61
438 483 0.461135 AGCAAAAGCAAGGTGGTGTG 59.539 50.000 0.00 0.00 0.00 3.82
444 489 1.103398 AGCAAGGTGGTGTGTGAAGC 61.103 55.000 0.00 0.00 0.00 3.86
464 509 1.067516 CTTTCACCAAAGGCACACCAG 59.932 52.381 0.00 0.00 39.06 4.00
466 511 0.465460 TCACCAAAGGCACACCAGAC 60.465 55.000 0.00 0.00 39.06 3.51
467 512 1.525995 ACCAAAGGCACACCAGACG 60.526 57.895 0.00 0.00 39.06 4.18
468 513 2.260869 CCAAAGGCACACCAGACGG 61.261 63.158 0.00 0.00 39.06 4.79
469 514 1.227823 CAAAGGCACACCAGACGGA 60.228 57.895 0.00 0.00 39.06 4.69
470 515 1.227853 AAAGGCACACCAGACGGAC 60.228 57.895 0.00 0.00 39.06 4.79
471 516 2.989055 AAAGGCACACCAGACGGACG 62.989 60.000 0.00 0.00 39.06 4.79
473 518 4.664677 GCACACCAGACGGACGCT 62.665 66.667 0.00 0.00 35.59 5.07
474 519 2.029073 CACACCAGACGGACGCTT 59.971 61.111 0.00 0.00 35.59 4.68
475 520 2.022129 CACACCAGACGGACGCTTC 61.022 63.158 0.00 0.00 35.59 3.86
476 521 2.338620 CACCAGACGGACGCTTCA 59.661 61.111 0.00 0.00 35.59 3.02
477 522 1.300620 CACCAGACGGACGCTTCAA 60.301 57.895 0.00 0.00 35.59 2.69
478 523 1.300697 ACCAGACGGACGCTTCAAC 60.301 57.895 0.00 0.00 35.59 3.18
479 524 2.027625 CCAGACGGACGCTTCAACC 61.028 63.158 0.00 0.00 0.00 3.77
480 525 2.027625 CAGACGGACGCTTCAACCC 61.028 63.158 0.00 0.00 0.00 4.11
481 526 3.110178 GACGGACGCTTCAACCCG 61.110 66.667 0.00 0.00 46.65 5.28
482 527 3.562779 GACGGACGCTTCAACCCGA 62.563 63.158 6.66 0.00 44.29 5.14
483 528 2.809601 CGGACGCTTCAACCCGAG 60.810 66.667 0.00 0.00 44.29 4.63
484 529 2.342648 GGACGCTTCAACCCGAGT 59.657 61.111 0.00 0.00 0.00 4.18
485 530 1.737008 GGACGCTTCAACCCGAGTC 60.737 63.158 0.00 0.00 0.00 3.36
486 531 1.289380 GACGCTTCAACCCGAGTCT 59.711 57.895 0.00 0.00 0.00 3.24
487 532 0.319641 GACGCTTCAACCCGAGTCTT 60.320 55.000 0.00 0.00 0.00 3.01
488 533 0.600255 ACGCTTCAACCCGAGTCTTG 60.600 55.000 0.00 0.00 0.00 3.02
489 534 1.869690 GCTTCAACCCGAGTCTTGC 59.130 57.895 0.00 0.00 0.00 4.01
490 535 0.884704 GCTTCAACCCGAGTCTTGCA 60.885 55.000 0.00 0.00 0.00 4.08
491 536 1.593196 CTTCAACCCGAGTCTTGCAA 58.407 50.000 0.00 0.00 0.00 4.08
492 537 1.532868 CTTCAACCCGAGTCTTGCAAG 59.467 52.381 20.81 20.81 0.00 4.01
493 538 0.250295 TCAACCCGAGTCTTGCAAGG 60.250 55.000 25.73 12.37 0.00 3.61
494 539 1.600916 AACCCGAGTCTTGCAAGGC 60.601 57.895 23.53 23.53 0.00 4.35
495 540 2.747855 CCCGAGTCTTGCAAGGCC 60.748 66.667 26.87 16.94 0.00 5.19
496 541 3.121030 CCGAGTCTTGCAAGGCCG 61.121 66.667 26.87 26.01 0.00 6.13
497 542 2.048222 CGAGTCTTGCAAGGCCGA 60.048 61.111 26.87 4.60 0.00 5.54
498 543 2.097038 CGAGTCTTGCAAGGCCGAG 61.097 63.158 26.87 14.67 0.00 4.63
499 544 2.359230 AGTCTTGCAAGGCCGAGC 60.359 61.111 26.87 14.61 0.00 5.03
500 545 3.793144 GTCTTGCAAGGCCGAGCG 61.793 66.667 25.73 0.00 0.00 5.03
501 546 4.002506 TCTTGCAAGGCCGAGCGA 62.003 61.111 25.73 13.69 0.00 4.93
502 547 3.049674 CTTGCAAGGCCGAGCGAA 61.050 61.111 19.14 10.94 0.00 4.70
503 548 3.031964 CTTGCAAGGCCGAGCGAAG 62.032 63.158 19.14 15.29 0.00 3.79
516 561 3.668386 CGAAGCTTTCACCCCCAC 58.332 61.111 0.00 0.00 0.00 4.61
517 562 1.228124 CGAAGCTTTCACCCCCACA 60.228 57.895 0.00 0.00 0.00 4.17
518 563 0.821711 CGAAGCTTTCACCCCCACAA 60.822 55.000 0.00 0.00 0.00 3.33
519 564 1.408969 GAAGCTTTCACCCCCACAAA 58.591 50.000 0.00 0.00 0.00 2.83
520 565 1.970640 GAAGCTTTCACCCCCACAAAT 59.029 47.619 0.00 0.00 0.00 2.32
521 566 1.632589 AGCTTTCACCCCCACAAATC 58.367 50.000 0.00 0.00 0.00 2.17
522 567 0.608130 GCTTTCACCCCCACAAATCC 59.392 55.000 0.00 0.00 0.00 3.01
523 568 1.827245 GCTTTCACCCCCACAAATCCT 60.827 52.381 0.00 0.00 0.00 3.24
524 569 2.171003 CTTTCACCCCCACAAATCCTC 58.829 52.381 0.00 0.00 0.00 3.71
525 570 1.455822 TTCACCCCCACAAATCCTCT 58.544 50.000 0.00 0.00 0.00 3.69
526 571 2.352561 TCACCCCCACAAATCCTCTA 57.647 50.000 0.00 0.00 0.00 2.43
527 572 1.913419 TCACCCCCACAAATCCTCTAC 59.087 52.381 0.00 0.00 0.00 2.59
528 573 0.909623 ACCCCCACAAATCCTCTACG 59.090 55.000 0.00 0.00 0.00 3.51
529 574 1.200519 CCCCCACAAATCCTCTACGA 58.799 55.000 0.00 0.00 0.00 3.43
530 575 1.557832 CCCCCACAAATCCTCTACGAA 59.442 52.381 0.00 0.00 0.00 3.85
550 595 4.970003 CGAAACAGGCAGTAAAAAGAAGTG 59.030 41.667 0.00 0.00 0.00 3.16
551 596 5.448632 CGAAACAGGCAGTAAAAAGAAGTGT 60.449 40.000 0.00 0.00 0.00 3.55
565 610 3.679389 AGAAGTGTAACATGCCAGGAAG 58.321 45.455 0.00 0.00 41.43 3.46
577 622 3.222603 TGCCAGGAAGAAAAAGGAAGTC 58.777 45.455 0.00 0.00 0.00 3.01
578 623 3.117512 TGCCAGGAAGAAAAAGGAAGTCT 60.118 43.478 0.00 0.00 0.00 3.24
581 626 5.746361 GCCAGGAAGAAAAAGGAAGTCTAGT 60.746 44.000 0.00 0.00 0.00 2.57
621 671 3.256383 TGCCAGGAGAATCAACAATGTTG 59.744 43.478 19.23 19.23 36.25 3.33
730 805 3.817647 GAGAATCAAGGATCGAAATGGGG 59.182 47.826 0.00 0.00 33.17 4.96
789 864 0.393267 ACCCCTCTCTCTTCTCGACG 60.393 60.000 0.00 0.00 0.00 5.12
793 869 1.651987 CTCTCTCTTCTCGACGCTCT 58.348 55.000 0.00 0.00 0.00 4.09
851 1107 2.667418 CAGAGGACCCTGCAGTGG 59.333 66.667 13.81 15.65 0.00 4.00
1272 1602 2.494918 CTCAACTACCTCCGCCCG 59.505 66.667 0.00 0.00 0.00 6.13
1353 1683 2.034879 GCTCGGCAGCAAGTAAGCA 61.035 57.895 0.00 0.00 46.06 3.91
1354 1684 1.372087 GCTCGGCAGCAAGTAAGCAT 61.372 55.000 0.00 0.00 46.06 3.79
1355 1685 0.654683 CTCGGCAGCAAGTAAGCATC 59.345 55.000 0.00 0.00 36.85 3.91
1356 1686 1.083806 TCGGCAGCAAGTAAGCATCG 61.084 55.000 0.00 0.00 36.85 3.84
1380 1714 4.082463 ACTCTTCTCTTTCTCGATCACCAC 60.082 45.833 0.00 0.00 0.00 4.16
1432 1766 1.437573 GGCATGACCGATCGAGACA 59.562 57.895 18.66 13.31 0.00 3.41
1440 1774 3.013990 GATCGAGACAGACGCGCG 61.014 66.667 30.96 30.96 41.27 6.86
1468 1802 1.501337 GGCATTCATCGCATCGCAGA 61.501 55.000 0.00 0.00 45.75 4.26
2072 2415 1.990563 ACCGATCGATCAAACGTGTTC 59.009 47.619 24.40 0.00 34.70 3.18
2127 2534 4.761739 TGTGGTTCTTGAATCTTGATCACC 59.238 41.667 0.00 0.00 0.00 4.02
2134 2541 6.409704 TCTTGAATCTTGATCACCTCGATTT 58.590 36.000 0.00 0.00 33.17 2.17
2200 2652 5.518848 TGAGCAGAAATTTTGTGACACAT 57.481 34.783 9.55 0.00 0.00 3.21
2267 2719 1.971167 TCCATGTGAAAGGCCGTGC 60.971 57.895 0.00 0.00 0.00 5.34
2343 2795 2.537625 GACCGATCTGAAGATTCGCTTG 59.462 50.000 0.00 0.00 36.83 4.01
2422 2874 1.267806 CGATGAGCAGCACCAAAAAGT 59.732 47.619 0.00 0.00 0.00 2.66
2532 2984 0.247301 GCTAATGACGACGCTTGTGC 60.247 55.000 0.00 0.00 0.00 4.57
2551 3003 2.029560 TGCGATGATAGAGGCACATCTC 60.030 50.000 0.00 0.00 38.43 2.75
2651 3106 6.706295 AGGCTATATTATCCTTGCTTGACTC 58.294 40.000 0.00 0.00 0.00 3.36
2676 3132 5.558888 GCAGAAACAAGACAATTTACGTACG 59.441 40.000 15.01 15.01 0.00 3.67
2677 3133 6.562640 GCAGAAACAAGACAATTTACGTACGA 60.563 38.462 24.41 0.00 0.00 3.43
2678 3134 7.507304 CAGAAACAAGACAATTTACGTACGAT 58.493 34.615 24.41 8.93 0.00 3.73
2692 3166 5.311016 ACGTACGATCATTTTTATCTGCG 57.689 39.130 24.41 0.00 0.00 5.18
2729 3215 5.492895 GCTGAGAGATGATGATGATGGATT 58.507 41.667 0.00 0.00 0.00 3.01
2894 3380 2.291741 AGCAGAACAGAAAAAGGAAGCG 59.708 45.455 0.00 0.00 0.00 4.68
2998 3493 3.966543 CCCCGACCCACCAAAGCT 61.967 66.667 0.00 0.00 0.00 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.339151 ACGTGAAGATGGGCTTTCCTC 60.339 52.381 0.00 0.00 36.83 3.71
1 2 0.693049 ACGTGAAGATGGGCTTTCCT 59.307 50.000 0.00 0.00 36.83 3.36
2 3 1.468914 GAACGTGAAGATGGGCTTTCC 59.531 52.381 0.00 0.00 36.83 3.13
3 4 1.468914 GGAACGTGAAGATGGGCTTTC 59.531 52.381 0.00 0.00 36.83 2.62
4 5 1.202879 TGGAACGTGAAGATGGGCTTT 60.203 47.619 0.00 0.00 36.83 3.51
5 6 0.400213 TGGAACGTGAAGATGGGCTT 59.600 50.000 0.00 0.00 40.25 4.35
6 7 0.321653 GTGGAACGTGAAGATGGGCT 60.322 55.000 0.00 0.00 0.00 5.19
7 8 2.171635 GTGGAACGTGAAGATGGGC 58.828 57.895 0.00 0.00 0.00 5.36
46 47 3.121030 CGCAGGAAAGGGCACGAG 61.121 66.667 0.00 0.00 0.00 4.18
96 97 1.352083 AAGTAGCACTTCTGCCCAGA 58.648 50.000 0.00 0.00 45.53 3.86
98 99 2.656947 AAAAGTAGCACTTCTGCCCA 57.343 45.000 2.65 0.00 45.53 5.36
100 101 2.229062 GGGAAAAAGTAGCACTTCTGCC 59.771 50.000 2.65 4.71 45.53 4.85
121 122 0.745845 CCCGTGCTTCATCCCAGAAG 60.746 60.000 0.00 0.00 46.06 2.85
124 125 2.825836 GCCCGTGCTTCATCCCAG 60.826 66.667 0.00 0.00 33.53 4.45
210 229 4.039357 ACACGACGTCGCCCTCAG 62.039 66.667 35.92 20.55 44.43 3.35
265 300 3.252215 TCTTGCTTATTTTGTGACCGGTG 59.748 43.478 14.63 0.00 0.00 4.94
267 302 4.226761 GTTCTTGCTTATTTTGTGACCGG 58.773 43.478 0.00 0.00 0.00 5.28
272 307 6.418819 CCTCTGTTGTTCTTGCTTATTTTGTG 59.581 38.462 0.00 0.00 0.00 3.33
444 489 1.067516 CTGGTGTGCCTTTGGTGAAAG 59.932 52.381 0.00 0.00 38.71 2.62
456 501 4.664677 AGCGTCCGTCTGGTGTGC 62.665 66.667 0.00 0.00 36.30 4.57
464 509 3.110178 CGGGTTGAAGCGTCCGTC 61.110 66.667 0.00 0.00 37.92 4.79
466 511 2.809601 CTCGGGTTGAAGCGTCCG 60.810 66.667 0.00 0.00 43.42 4.79
467 512 1.737008 GACTCGGGTTGAAGCGTCC 60.737 63.158 0.00 0.00 0.00 4.79
468 513 0.319641 AAGACTCGGGTTGAAGCGTC 60.320 55.000 0.00 0.00 0.00 5.19
469 514 0.600255 CAAGACTCGGGTTGAAGCGT 60.600 55.000 0.00 0.00 0.00 5.07
470 515 1.901650 GCAAGACTCGGGTTGAAGCG 61.902 60.000 0.00 0.00 0.00 4.68
471 516 0.884704 TGCAAGACTCGGGTTGAAGC 60.885 55.000 0.00 0.00 0.00 3.86
472 517 1.532868 CTTGCAAGACTCGGGTTGAAG 59.467 52.381 22.31 0.00 0.00 3.02
473 518 1.593196 CTTGCAAGACTCGGGTTGAA 58.407 50.000 22.31 0.00 0.00 2.69
474 519 0.250295 CCTTGCAAGACTCGGGTTGA 60.250 55.000 28.05 0.00 0.00 3.18
475 520 1.856265 GCCTTGCAAGACTCGGGTTG 61.856 60.000 28.05 8.52 0.00 3.77
476 521 1.600916 GCCTTGCAAGACTCGGGTT 60.601 57.895 28.05 0.00 0.00 4.11
477 522 2.032681 GCCTTGCAAGACTCGGGT 59.967 61.111 28.05 0.00 0.00 5.28
478 523 2.747855 GGCCTTGCAAGACTCGGG 60.748 66.667 28.05 11.88 0.00 5.14
479 524 3.121030 CGGCCTTGCAAGACTCGG 61.121 66.667 28.05 12.65 0.00 4.63
480 525 2.048222 TCGGCCTTGCAAGACTCG 60.048 61.111 28.05 23.99 0.00 4.18
481 526 2.394563 GCTCGGCCTTGCAAGACTC 61.395 63.158 28.05 15.12 0.00 3.36
482 527 2.359230 GCTCGGCCTTGCAAGACT 60.359 61.111 28.05 0.00 0.00 3.24
483 528 3.793144 CGCTCGGCCTTGCAAGAC 61.793 66.667 28.05 16.79 0.00 3.01
484 529 3.529341 TTCGCTCGGCCTTGCAAGA 62.529 57.895 28.05 6.99 0.00 3.02
485 530 3.031964 CTTCGCTCGGCCTTGCAAG 62.032 63.158 19.93 19.93 0.00 4.01
486 531 3.049674 CTTCGCTCGGCCTTGCAA 61.050 61.111 15.45 0.00 0.00 4.08
489 534 2.245714 GAAAGCTTCGCTCGGCCTTG 62.246 60.000 0.00 0.00 38.25 3.61
490 535 2.032681 AAAGCTTCGCTCGGCCTT 59.967 55.556 0.00 0.00 38.25 4.35
491 536 2.435059 GAAAGCTTCGCTCGGCCT 60.435 61.111 0.00 0.00 38.25 5.19
492 537 2.742372 TGAAAGCTTCGCTCGGCC 60.742 61.111 0.00 0.00 38.25 6.13
493 538 2.476499 GTGAAAGCTTCGCTCGGC 59.524 61.111 0.00 0.00 38.25 5.54
494 539 2.391389 GGGTGAAAGCTTCGCTCGG 61.391 63.158 0.00 0.00 38.25 4.63
495 540 2.391389 GGGGTGAAAGCTTCGCTCG 61.391 63.158 0.00 0.00 41.56 5.03
496 541 2.041115 GGGGGTGAAAGCTTCGCTC 61.041 63.158 0.00 0.00 38.25 5.03
497 542 2.034221 GGGGGTGAAAGCTTCGCT 59.966 61.111 0.00 0.00 42.56 4.93
498 543 2.282180 TGGGGGTGAAAGCTTCGC 60.282 61.111 0.00 0.00 39.40 4.70
499 544 0.821711 TTGTGGGGGTGAAAGCTTCG 60.822 55.000 0.00 0.00 0.00 3.79
500 545 1.408969 TTTGTGGGGGTGAAAGCTTC 58.591 50.000 0.00 0.00 0.00 3.86
501 546 1.970640 GATTTGTGGGGGTGAAAGCTT 59.029 47.619 0.00 0.00 0.00 3.74
502 547 1.632589 GATTTGTGGGGGTGAAAGCT 58.367 50.000 0.00 0.00 0.00 3.74
503 548 0.608130 GGATTTGTGGGGGTGAAAGC 59.392 55.000 0.00 0.00 0.00 3.51
504 549 2.171003 GAGGATTTGTGGGGGTGAAAG 58.829 52.381 0.00 0.00 0.00 2.62
505 550 1.786441 AGAGGATTTGTGGGGGTGAAA 59.214 47.619 0.00 0.00 0.00 2.69
506 551 1.455822 AGAGGATTTGTGGGGGTGAA 58.544 50.000 0.00 0.00 0.00 3.18
507 552 1.913419 GTAGAGGATTTGTGGGGGTGA 59.087 52.381 0.00 0.00 0.00 4.02
508 553 1.406887 CGTAGAGGATTTGTGGGGGTG 60.407 57.143 0.00 0.00 0.00 4.61
509 554 0.909623 CGTAGAGGATTTGTGGGGGT 59.090 55.000 0.00 0.00 0.00 4.95
510 555 1.200519 TCGTAGAGGATTTGTGGGGG 58.799 55.000 0.00 0.00 0.00 5.40
511 556 3.007635 GTTTCGTAGAGGATTTGTGGGG 58.992 50.000 0.00 0.00 38.43 4.96
512 557 3.670625 TGTTTCGTAGAGGATTTGTGGG 58.329 45.455 0.00 0.00 38.43 4.61
513 558 3.684788 CCTGTTTCGTAGAGGATTTGTGG 59.315 47.826 0.00 0.00 39.71 4.17
514 559 3.125316 GCCTGTTTCGTAGAGGATTTGTG 59.875 47.826 7.48 0.00 39.71 3.33
515 560 3.244422 TGCCTGTTTCGTAGAGGATTTGT 60.244 43.478 7.48 0.00 39.71 2.83
516 561 3.334691 TGCCTGTTTCGTAGAGGATTTG 58.665 45.455 7.48 0.00 39.71 2.32
517 562 3.008049 ACTGCCTGTTTCGTAGAGGATTT 59.992 43.478 7.48 0.00 39.71 2.17
518 563 2.567615 ACTGCCTGTTTCGTAGAGGATT 59.432 45.455 7.48 0.00 39.71 3.01
519 564 2.180276 ACTGCCTGTTTCGTAGAGGAT 58.820 47.619 7.48 0.00 39.71 3.24
520 565 1.629043 ACTGCCTGTTTCGTAGAGGA 58.371 50.000 7.48 0.00 39.71 3.71
521 566 3.587797 TTACTGCCTGTTTCGTAGAGG 57.412 47.619 0.00 0.00 40.30 3.69
522 567 5.694910 TCTTTTTACTGCCTGTTTCGTAGAG 59.305 40.000 0.00 0.00 38.43 2.43
523 568 5.603596 TCTTTTTACTGCCTGTTTCGTAGA 58.396 37.500 0.00 0.00 0.00 2.59
524 569 5.917541 TCTTTTTACTGCCTGTTTCGTAG 57.082 39.130 0.00 0.00 0.00 3.51
525 570 5.818857 ACTTCTTTTTACTGCCTGTTTCGTA 59.181 36.000 0.00 0.00 0.00 3.43
526 571 4.638865 ACTTCTTTTTACTGCCTGTTTCGT 59.361 37.500 0.00 0.00 0.00 3.85
527 572 4.970003 CACTTCTTTTTACTGCCTGTTTCG 59.030 41.667 0.00 0.00 0.00 3.46
528 573 5.891451 ACACTTCTTTTTACTGCCTGTTTC 58.109 37.500 0.00 0.00 0.00 2.78
529 574 5.914898 ACACTTCTTTTTACTGCCTGTTT 57.085 34.783 0.00 0.00 0.00 2.83
530 575 6.376018 TGTTACACTTCTTTTTACTGCCTGTT 59.624 34.615 0.00 0.00 0.00 3.16
550 595 4.522789 TCCTTTTTCTTCCTGGCATGTTAC 59.477 41.667 0.00 0.00 0.00 2.50
551 596 4.735369 TCCTTTTTCTTCCTGGCATGTTA 58.265 39.130 0.00 0.00 0.00 2.41
621 671 1.010419 ACATTGTACGCGACCGAACC 61.010 55.000 15.93 0.00 38.29 3.62
674 749 3.246226 CGGTTGTTCTCTCTTTCACAGTG 59.754 47.826 0.00 0.00 0.00 3.66
765 840 1.081277 GAAGAGAGAGGGGTGGGGT 59.919 63.158 0.00 0.00 0.00 4.95
770 845 0.393267 CGTCGAGAAGAGAGAGGGGT 60.393 60.000 0.00 0.00 0.00 4.95
851 1107 1.004277 CGTCGGTGAACAGAGCAGAC 61.004 60.000 0.00 0.00 0.00 3.51
940 1196 1.820481 GAGAGAGACCGGACGAGGG 60.820 68.421 9.46 0.00 35.02 4.30
1353 1683 4.878971 TGATCGAGAAAGAGAAGAGTCGAT 59.121 41.667 4.82 4.82 46.72 3.59
1354 1684 4.093703 GTGATCGAGAAAGAGAAGAGTCGA 59.906 45.833 0.00 0.00 40.40 4.20
1355 1685 4.339429 GTGATCGAGAAAGAGAAGAGTCG 58.661 47.826 0.00 0.00 0.00 4.18
1356 1686 4.156922 TGGTGATCGAGAAAGAGAAGAGTC 59.843 45.833 0.00 0.00 0.00 3.36
1386 1720 0.179189 CACGAAAAGGATGCCGCTTC 60.179 55.000 0.00 0.00 0.00 3.86
1440 1774 3.480225 GATGAATGCCAGCGCCAGC 62.480 63.158 12.07 12.07 45.58 4.85
1441 1775 2.719979 GATGAATGCCAGCGCCAG 59.280 61.111 2.29 0.00 0.00 4.85
1738 2081 4.516195 GCCGAAGACGAGCCCTCC 62.516 72.222 0.00 0.00 42.66 4.30
2018 2361 3.466260 CGCGCGTGACACATCGAA 61.466 61.111 24.19 0.00 0.00 3.71
2072 2415 2.675844 TGATCGGGTGCTTTTGATAACG 59.324 45.455 0.00 0.00 0.00 3.18
2127 2534 2.098607 ACATGGAAGCATGCAAATCGAG 59.901 45.455 21.98 6.44 36.08 4.04
2134 2541 1.307355 CGTGGACATGGAAGCATGCA 61.307 55.000 21.98 0.00 36.08 3.96
2200 2652 2.070028 GTGTGTGTGTGTGTGTGTGTA 58.930 47.619 0.00 0.00 0.00 2.90
2401 2853 0.039256 TTTTTGGTGCTGCTCATCGC 60.039 50.000 0.00 0.00 39.77 4.58
2406 2858 2.226674 GGACTACTTTTTGGTGCTGCTC 59.773 50.000 0.00 0.00 0.00 4.26
2409 2861 3.057315 CCATGGACTACTTTTTGGTGCTG 60.057 47.826 5.56 0.00 0.00 4.41
2411 2863 2.231235 CCCATGGACTACTTTTTGGTGC 59.769 50.000 15.22 0.00 0.00 5.01
2438 2890 1.482593 CTGTCTCTCCGGCTTTACCAT 59.517 52.381 0.00 0.00 39.03 3.55
2471 2923 2.145536 CCCAGCCAATTTTGTTCTTGC 58.854 47.619 0.00 0.00 0.00 4.01
2532 2984 4.517952 AAGAGATGTGCCTCTATCATCG 57.482 45.455 0.00 0.00 42.31 3.84
2561 3014 0.320374 AATCGGAGTCTGCGAACCAA 59.680 50.000 20.70 0.00 44.81 3.67
2651 3106 4.523813 ACGTAAATTGTCTTGTTTCTGCG 58.476 39.130 0.00 0.00 0.00 5.18
2678 3134 9.219603 CCTCTAATTATCCGCAGATAAAAATGA 57.780 33.333 6.47 3.24 45.71 2.57
2692 3166 4.421131 TCTCTCAGCCCCTCTAATTATCC 58.579 47.826 0.00 0.00 0.00 2.59
2703 3180 1.976404 TCATCATCATCTCTCAGCCCC 59.024 52.381 0.00 0.00 0.00 5.80
2729 3215 3.411446 CTGTTCATGCCAGGTCACTTTA 58.589 45.455 4.74 0.00 0.00 1.85
2817 3303 4.547859 GGGATGAGCATCGCACTT 57.452 55.556 18.93 0.00 46.31 3.16
2877 3363 2.349532 CGTCCGCTTCCTTTTTCTGTTC 60.350 50.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.