Multiple sequence alignment - TraesCS7A01G519500

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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 TraesCS7A01G519500 chr7A 100.000 2795 0 0 1 2795 704256292 704259086 0.000000e+00 5162.0
1 TraesCS7A01G519500 chr7A 98.387 248 4 0 1 248 704234988 704235235 1.190000e-118 436.0
2 TraesCS7A01G519500 chr7A 77.333 600 108 18 1 586 703602169 703602754 2.080000e-86 329.0
3 TraesCS7A01G519500 chr7A 77.167 600 109 18 1 586 703650969 703651554 9.660000e-85 324.0
4 TraesCS7A01G519500 chr7A 77.709 323 61 6 1 313 703699902 703700223 1.320000e-43 187.0
5 TraesCS7A01G519500 chr1A 97.920 2163 44 1 634 2795 376489597 376491759 0.000000e+00 3744.0
6 TraesCS7A01G519500 chr1A 95.597 2112 72 8 632 2740 549429751 549431844 0.000000e+00 3365.0
7 TraesCS7A01G519500 chr5A 97.689 2164 48 2 634 2795 509128607 509130770 0.000000e+00 3718.0
8 TraesCS7A01G519500 chr4A 97.687 2162 30 5 634 2795 37984867 37982726 0.000000e+00 3698.0
9 TraesCS7A01G519500 chr6A 97.412 2164 44 4 634 2795 558828814 558830967 0.000000e+00 3675.0
10 TraesCS7A01G519500 chr6A 96.771 2168 64 6 632 2795 532336338 532334173 0.000000e+00 3611.0
11 TraesCS7A01G519500 chr3A 97.180 2163 59 2 634 2795 741177982 741175821 0.000000e+00 3655.0
12 TraesCS7A01G519500 chr3D 95.591 1905 81 3 633 2535 374010879 374008976 0.000000e+00 3049.0
13 TraesCS7A01G519500 chr3D 84.815 270 19 14 2529 2795 374009031 374008781 4.620000e-63 252.0
14 TraesCS7A01G519500 chr2D 94.473 1972 97 7 634 2596 633747075 633749043 0.000000e+00 3027.0
15 TraesCS7A01G519500 chr2D 84.815 270 19 14 2529 2795 207004388 207004138 4.620000e-63 252.0
16 TraesCS7A01G519500 chr2D 85.778 225 21 8 2578 2795 633748921 633749141 7.790000e-56 228.0
17 TraesCS7A01G519500 chr2D 76.134 419 74 19 1 397 557920350 557920764 2.200000e-46 196.0
18 TraesCS7A01G519500 chr7D 76.884 398 66 14 7 382 611857278 611856885 4.720000e-48 202.0
19 TraesCS7A01G519500 chr7D 75.802 405 72 18 198 586 612428232 612428626 6.150000e-42 182.0
20 TraesCS7A01G519500 chr7D 81.410 156 26 3 192 344 612881956 612882111 1.050000e-24 124.0
21 TraesCS7A01G519500 chr7D 80.000 115 20 3 478 589 579325204 579325318 6.420000e-12 82.4
22 TraesCS7A01G519500 chrUn 91.228 57 5 0 124 180 46099122 46099066 8.300000e-11 78.7
23 TraesCS7A01G519500 chrUn 100.000 30 0 0 209 238 127013163 127013192 3.890000e-04 56.5
24 TraesCS7A01G519500 chrUn 100.000 28 0 0 545 572 126738870 126738897 5.000000e-03 52.8
25 TraesCS7A01G519500 chr6D 96.774 31 1 0 545 575 456002739 456002709 5.000000e-03 52.8
26 TraesCS7A01G519500 chr6B 96.774 31 1 0 545 575 693333080 693333050 5.000000e-03 52.8


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 TraesCS7A01G519500 chr7A 704256292 704259086 2794 False 5162.0 5162 100.0000 1 2795 1 chr7A.!!$F5 2794
1 TraesCS7A01G519500 chr7A 703602169 703602754 585 False 329.0 329 77.3330 1 586 1 chr7A.!!$F1 585
2 TraesCS7A01G519500 chr7A 703650969 703651554 585 False 324.0 324 77.1670 1 586 1 chr7A.!!$F2 585
3 TraesCS7A01G519500 chr1A 376489597 376491759 2162 False 3744.0 3744 97.9200 634 2795 1 chr1A.!!$F1 2161
4 TraesCS7A01G519500 chr1A 549429751 549431844 2093 False 3365.0 3365 95.5970 632 2740 1 chr1A.!!$F2 2108
5 TraesCS7A01G519500 chr5A 509128607 509130770 2163 False 3718.0 3718 97.6890 634 2795 1 chr5A.!!$F1 2161
6 TraesCS7A01G519500 chr4A 37982726 37984867 2141 True 3698.0 3698 97.6870 634 2795 1 chr4A.!!$R1 2161
7 TraesCS7A01G519500 chr6A 558828814 558830967 2153 False 3675.0 3675 97.4120 634 2795 1 chr6A.!!$F1 2161
8 TraesCS7A01G519500 chr6A 532334173 532336338 2165 True 3611.0 3611 96.7710 632 2795 1 chr6A.!!$R1 2163
9 TraesCS7A01G519500 chr3A 741175821 741177982 2161 True 3655.0 3655 97.1800 634 2795 1 chr3A.!!$R1 2161
10 TraesCS7A01G519500 chr3D 374008781 374010879 2098 True 1650.5 3049 90.2030 633 2795 2 chr3D.!!$R1 2162
11 TraesCS7A01G519500 chr2D 633747075 633749141 2066 False 1627.5 3027 90.1255 634 2795 2 chr2D.!!$F2 2161

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
622 638 0.170339 GTGCTTGGTATTTGGCGACC 59.83 55.0 0.0 0.0 36.17 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2152 2.0947 CAGCTCAGCAATGCAACAATCT 60.095 45.455 8.35 0.0 0.0 2.4 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
53 54 3.167414 CCCACGGTTTCCCTCCTT 58.833 61.111 0.00 0.00 0.00 3.36
55 56 1.758592 CCACGGTTTCCCTCCTTGA 59.241 57.895 0.00 0.00 0.00 3.02
63 64 2.202932 CCCTCCTTGACATCCGCG 60.203 66.667 0.00 0.00 0.00 6.46
65 66 1.811266 CCTCCTTGACATCCGCGTG 60.811 63.158 4.92 0.00 0.00 5.34
70 71 4.758251 TGACATCCGCGTGCCCAG 62.758 66.667 4.92 0.00 0.00 4.45
97 101 2.743538 GCATGTCACCGAGCAGCA 60.744 61.111 0.00 0.00 0.00 4.41
99 103 1.668793 CATGTCACCGAGCAGCACA 60.669 57.895 0.00 0.00 0.00 4.57
100 104 1.375140 ATGTCACCGAGCAGCACAG 60.375 57.895 0.00 0.00 0.00 3.66
180 184 1.964223 AGGAGTTCGTCTTTGAGCTCA 59.036 47.619 13.74 13.74 45.00 4.26
181 185 2.365617 AGGAGTTCGTCTTTGAGCTCAA 59.634 45.455 25.16 25.16 45.00 3.02
182 186 3.131396 GGAGTTCGTCTTTGAGCTCAAA 58.869 45.455 33.65 33.65 45.00 2.69
195 208 0.318441 GCTCAAAGGCTTTGGTTCCC 59.682 55.000 33.00 16.64 40.98 3.97
196 209 1.703411 CTCAAAGGCTTTGGTTCCCA 58.297 50.000 33.00 16.22 40.98 4.37
206 219 1.808531 TTGGTTCCCACGTCGTCGAT 61.809 55.000 9.47 0.00 40.62 3.59
213 226 1.583967 CACGTCGTCGATCTGCCTC 60.584 63.158 9.47 0.00 40.62 4.70
243 256 2.124983 CCACCTCCATCGTGCTGG 60.125 66.667 0.00 0.00 37.66 4.85
244 257 2.659063 CCACCTCCATCGTGCTGGA 61.659 63.158 4.51 4.51 43.09 3.86
252 265 1.026718 CATCGTGCTGGACCTTTCCC 61.027 60.000 0.00 0.00 42.01 3.97
261 274 2.938798 ACCTTTCCCCCGCCATCA 60.939 61.111 0.00 0.00 0.00 3.07
265 278 3.643595 TTTCCCCCGCCATCAGCTG 62.644 63.158 7.63 7.63 40.39 4.24
308 321 2.563942 GCACTCGAGACGCTGTCT 59.436 61.111 21.68 10.33 46.42 3.41
327 340 1.515088 CTCTCGTACTGCACTGCCG 60.515 63.158 0.00 0.00 0.00 5.69
335 348 2.125952 TGCACTGCCGACATCGAG 60.126 61.111 2.09 0.00 43.02 4.04
353 366 2.263852 CGCTTGCTCTCCTGCTGA 59.736 61.111 0.00 0.00 0.00 4.26
354 367 1.153409 CGCTTGCTCTCCTGCTGAT 60.153 57.895 0.00 0.00 0.00 2.90
360 373 4.212913 TCTCCTGCTGATCGCGCC 62.213 66.667 0.00 0.00 43.27 6.53
381 394 4.819761 GCACGCTCCGCCTCATCA 62.820 66.667 0.00 0.00 0.00 3.07
382 395 2.125552 CACGCTCCGCCTCATCAA 60.126 61.111 0.00 0.00 0.00 2.57
383 396 1.522355 CACGCTCCGCCTCATCAAT 60.522 57.895 0.00 0.00 0.00 2.57
388 401 2.288666 GCTCCGCCTCATCAATGTTTA 58.711 47.619 0.00 0.00 0.00 2.01
395 408 4.963953 CGCCTCATCAATGTTTATTTCGAC 59.036 41.667 0.00 0.00 0.00 4.20
399 412 7.530010 CCTCATCAATGTTTATTTCGACAAGT 58.470 34.615 0.00 0.00 0.00 3.16
400 413 7.482743 CCTCATCAATGTTTATTTCGACAAGTG 59.517 37.037 0.00 0.00 0.00 3.16
402 415 6.066054 TCAATGTTTATTTCGACAAGTGCA 57.934 33.333 0.00 0.00 0.00 4.57
403 416 6.499172 TCAATGTTTATTTCGACAAGTGCAA 58.501 32.000 0.00 0.00 0.00 4.08
409 422 1.581934 TTCGACAAGTGCAACCTGAG 58.418 50.000 0.00 0.00 37.80 3.35
422 435 2.125912 CTGAGGGTCAACTCGGCG 60.126 66.667 0.00 0.00 40.39 6.46
423 436 2.599281 TGAGGGTCAACTCGGCGA 60.599 61.111 10.14 10.14 40.39 5.54
424 437 1.949847 CTGAGGGTCAACTCGGCGAT 61.950 60.000 11.27 0.00 40.39 4.58
428 441 2.456119 GGTCAACTCGGCGATGCTG 61.456 63.158 11.27 8.38 36.06 4.41
445 458 2.343758 GCAGGAGCTTGTCGTGGA 59.656 61.111 0.00 0.00 40.76 4.02
446 459 1.078848 GCAGGAGCTTGTCGTGGAT 60.079 57.895 0.00 0.00 40.76 3.41
447 460 1.086634 GCAGGAGCTTGTCGTGGATC 61.087 60.000 0.00 0.00 40.76 3.36
448 461 0.247460 CAGGAGCTTGTCGTGGATCA 59.753 55.000 0.00 0.00 37.40 2.92
461 474 0.546122 TGGATCACGGGAAATGGAGG 59.454 55.000 0.00 0.00 0.00 4.30
462 475 0.819666 GGATCACGGGAAATGGAGGC 60.820 60.000 0.00 0.00 0.00 4.70
464 477 0.331278 ATCACGGGAAATGGAGGCAA 59.669 50.000 0.00 0.00 0.00 4.52
465 478 0.608035 TCACGGGAAATGGAGGCAAC 60.608 55.000 0.00 0.00 0.00 4.17
466 479 1.674322 ACGGGAAATGGAGGCAACG 60.674 57.895 0.00 0.00 46.39 4.10
467 480 1.674322 CGGGAAATGGAGGCAACGT 60.674 57.895 0.00 0.00 46.39 3.99
468 481 1.883021 GGGAAATGGAGGCAACGTG 59.117 57.895 0.00 0.00 46.39 4.49
469 482 0.893727 GGGAAATGGAGGCAACGTGT 60.894 55.000 0.00 0.00 46.39 4.49
470 483 0.521735 GGAAATGGAGGCAACGTGTC 59.478 55.000 0.00 0.00 46.39 3.67
471 484 1.234821 GAAATGGAGGCAACGTGTCA 58.765 50.000 0.00 0.00 46.39 3.58
472 485 1.606668 GAAATGGAGGCAACGTGTCAA 59.393 47.619 0.00 0.00 46.39 3.18
473 486 1.909700 AATGGAGGCAACGTGTCAAT 58.090 45.000 0.00 0.00 46.39 2.57
474 487 1.167851 ATGGAGGCAACGTGTCAATG 58.832 50.000 0.00 0.00 46.39 2.82
475 488 0.888736 TGGAGGCAACGTGTCAATGG 60.889 55.000 0.00 0.00 46.39 3.16
476 489 0.889186 GGAGGCAACGTGTCAATGGT 60.889 55.000 0.00 0.00 46.39 3.55
477 490 0.238289 GAGGCAACGTGTCAATGGTG 59.762 55.000 0.00 0.00 46.39 4.17
478 491 0.465460 AGGCAACGTGTCAATGGTGT 60.465 50.000 0.00 0.00 46.39 4.16
479 492 0.317770 GGCAACGTGTCAATGGTGTG 60.318 55.000 0.00 0.00 32.14 3.82
491 504 1.896220 ATGGTGTGAACATCGTTGCT 58.104 45.000 0.00 0.00 0.00 3.91
494 507 0.517316 GTGTGAACATCGTTGCTCCC 59.483 55.000 0.00 0.00 0.00 4.30
500 513 2.434884 ATCGTTGCTCCCGTGCTG 60.435 61.111 0.00 0.00 0.00 4.41
503 516 2.671177 CGTTGCTCCCGTGCTGAAG 61.671 63.158 0.00 0.00 0.00 3.02
504 517 1.301716 GTTGCTCCCGTGCTGAAGA 60.302 57.895 0.00 0.00 0.00 2.87
511 524 3.012518 CTCCCGTGCTGAAGAAATTGAT 58.987 45.455 0.00 0.00 0.00 2.57
516 529 4.348656 CGTGCTGAAGAAATTGATCATGG 58.651 43.478 0.00 0.00 0.00 3.66
519 532 3.383825 GCTGAAGAAATTGATCATGGCCT 59.616 43.478 3.32 0.00 0.00 5.19
522 535 6.363167 TGAAGAAATTGATCATGGCCTTTT 57.637 33.333 3.32 0.00 0.00 2.27
523 536 6.771573 TGAAGAAATTGATCATGGCCTTTTT 58.228 32.000 3.32 0.00 0.00 1.94
530 543 1.923356 TCATGGCCTTTTTCACCTCC 58.077 50.000 3.32 0.00 0.00 4.30
531 544 1.146774 TCATGGCCTTTTTCACCTCCA 59.853 47.619 3.32 0.00 0.00 3.86
540 556 2.727123 TTTCACCTCCAAAGTCAGCA 57.273 45.000 0.00 0.00 0.00 4.41
546 562 2.158475 ACCTCCAAAGTCAGCATTTCCA 60.158 45.455 0.00 0.00 0.00 3.53
547 563 3.094572 CCTCCAAAGTCAGCATTTCCAT 58.905 45.455 0.00 0.00 0.00 3.41
557 573 0.896923 GCATTTCCATCTTGGCACCA 59.103 50.000 0.00 0.00 37.47 4.17
581 597 0.534203 TGGAGAAGGTTTCGTGGCAC 60.534 55.000 7.79 7.79 34.02 5.01
586 602 0.751643 AAGGTTTCGTGGCACTGCTT 60.752 50.000 16.72 5.40 0.00 3.91
587 603 1.166531 AGGTTTCGTGGCACTGCTTC 61.167 55.000 16.72 2.73 0.00 3.86
588 604 1.166531 GGTTTCGTGGCACTGCTTCT 61.167 55.000 16.72 0.00 0.00 2.85
589 605 0.663153 GTTTCGTGGCACTGCTTCTT 59.337 50.000 16.72 0.00 0.00 2.52
590 606 1.065551 GTTTCGTGGCACTGCTTCTTT 59.934 47.619 16.72 0.00 0.00 2.52
591 607 0.662619 TTCGTGGCACTGCTTCTTTG 59.337 50.000 16.72 0.00 0.00 2.77
592 608 1.165907 TCGTGGCACTGCTTCTTTGG 61.166 55.000 16.72 0.00 0.00 3.28
593 609 1.662044 GTGGCACTGCTTCTTTGGG 59.338 57.895 11.13 0.00 0.00 4.12
594 610 1.531365 TGGCACTGCTTCTTTGGGG 60.531 57.895 0.00 0.00 0.00 4.96
595 611 1.531602 GGCACTGCTTCTTTGGGGT 60.532 57.895 0.00 0.00 0.00 4.95
596 612 1.662044 GCACTGCTTCTTTGGGGTG 59.338 57.895 0.00 0.00 0.00 4.61
597 613 1.109323 GCACTGCTTCTTTGGGGTGT 61.109 55.000 0.00 0.00 0.00 4.16
598 614 0.954452 CACTGCTTCTTTGGGGTGTC 59.046 55.000 0.00 0.00 0.00 3.67
599 615 0.846693 ACTGCTTCTTTGGGGTGTCT 59.153 50.000 0.00 0.00 0.00 3.41
600 616 2.054799 ACTGCTTCTTTGGGGTGTCTA 58.945 47.619 0.00 0.00 0.00 2.59
601 617 2.644798 ACTGCTTCTTTGGGGTGTCTAT 59.355 45.455 0.00 0.00 0.00 1.98
602 618 3.074538 ACTGCTTCTTTGGGGTGTCTATT 59.925 43.478 0.00 0.00 0.00 1.73
603 619 3.420893 TGCTTCTTTGGGGTGTCTATTG 58.579 45.455 0.00 0.00 0.00 1.90
604 620 3.181434 TGCTTCTTTGGGGTGTCTATTGT 60.181 43.478 0.00 0.00 0.00 2.71
605 621 3.191371 GCTTCTTTGGGGTGTCTATTGTG 59.809 47.826 0.00 0.00 0.00 3.33
606 622 2.790433 TCTTTGGGGTGTCTATTGTGC 58.210 47.619 0.00 0.00 0.00 4.57
607 623 2.375174 TCTTTGGGGTGTCTATTGTGCT 59.625 45.455 0.00 0.00 0.00 4.40
608 624 2.969821 TTGGGGTGTCTATTGTGCTT 57.030 45.000 0.00 0.00 0.00 3.91
609 625 2.198827 TGGGGTGTCTATTGTGCTTG 57.801 50.000 0.00 0.00 0.00 4.01
610 626 1.271871 TGGGGTGTCTATTGTGCTTGG 60.272 52.381 0.00 0.00 0.00 3.61
611 627 1.271926 GGGGTGTCTATTGTGCTTGGT 60.272 52.381 0.00 0.00 0.00 3.67
612 628 2.026636 GGGGTGTCTATTGTGCTTGGTA 60.027 50.000 0.00 0.00 0.00 3.25
613 629 3.371595 GGGGTGTCTATTGTGCTTGGTAT 60.372 47.826 0.00 0.00 0.00 2.73
614 630 4.270008 GGGTGTCTATTGTGCTTGGTATT 58.730 43.478 0.00 0.00 0.00 1.89
615 631 4.705023 GGGTGTCTATTGTGCTTGGTATTT 59.295 41.667 0.00 0.00 0.00 1.40
616 632 5.393027 GGGTGTCTATTGTGCTTGGTATTTG 60.393 44.000 0.00 0.00 0.00 2.32
617 633 5.393027 GGTGTCTATTGTGCTTGGTATTTGG 60.393 44.000 0.00 0.00 0.00 3.28
618 634 4.157656 TGTCTATTGTGCTTGGTATTTGGC 59.842 41.667 0.00 0.00 0.00 4.52
619 635 2.652941 ATTGTGCTTGGTATTTGGCG 57.347 45.000 0.00 0.00 0.00 5.69
620 636 1.610363 TTGTGCTTGGTATTTGGCGA 58.390 45.000 0.00 0.00 0.00 5.54
621 637 0.878416 TGTGCTTGGTATTTGGCGAC 59.122 50.000 0.00 0.00 0.00 5.19
622 638 0.170339 GTGCTTGGTATTTGGCGACC 59.830 55.000 0.00 0.00 36.17 4.79
623 639 0.963355 TGCTTGGTATTTGGCGACCC 60.963 55.000 0.00 0.00 34.58 4.46
624 640 0.963355 GCTTGGTATTTGGCGACCCA 60.963 55.000 0.00 0.00 40.06 4.51
676 692 3.055963 CACATTTGGGGCTTATCTTGCAA 60.056 43.478 0.00 0.00 0.00 4.08
922 959 1.252175 TTTCTCTGCTCTCACGCTCT 58.748 50.000 0.00 0.00 0.00 4.09
946 983 2.164865 CTCTGCTCCCACACTCGCTT 62.165 60.000 0.00 0.00 0.00 4.68
985 1023 4.361971 TCCTCTCCGGTCACCGCT 62.362 66.667 12.05 0.00 46.86 5.52
1147 1185 4.566545 ACATTTGCTCGATTTGAACACA 57.433 36.364 0.00 0.00 0.00 3.72
1167 1205 6.282930 ACACATTTTTGTTGGATTTCTCAGG 58.717 36.000 0.00 0.00 0.00 3.86
1405 1444 7.231467 AGGGTTCATAGTTACTGTTCATGTTT 58.769 34.615 0.00 0.00 0.00 2.83
1718 1758 3.067601 TGAGCATAGCCAGCATGAAAATG 59.932 43.478 0.00 0.00 39.69 2.32
2110 2152 7.690256 ACCTGAAGAAAAAGAAGGATAAGCTA 58.310 34.615 0.00 0.00 0.00 3.32
2673 2719 6.471233 AGTAGCTGCATAGATACAACTGAA 57.529 37.500 4.12 0.00 45.83 3.02
2775 2821 3.584406 TCCTCCTTCTTCAGCATCTTCAA 59.416 43.478 0.00 0.00 0.00 2.69
2787 2833 2.747467 GCATCTTCAAGCATAGGGAGCA 60.747 50.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 3.499737 GGGCACGCGGATGTCAAG 61.500 66.667 12.47 0.00 0.00 3.02
53 54 4.758251 CTGGGCACGCGGATGTCA 62.758 66.667 12.47 3.11 0.00 3.58
78 79 2.821366 CTGCTCGGTGACATGCCC 60.821 66.667 0.00 0.00 0.00 5.36
79 80 3.503363 GCTGCTCGGTGACATGCC 61.503 66.667 0.00 0.00 0.00 4.40
80 81 2.743538 TGCTGCTCGGTGACATGC 60.744 61.111 0.00 0.00 0.00 4.06
82 83 1.375140 CTGTGCTGCTCGGTGACAT 60.375 57.895 0.00 0.00 0.00 3.06
83 84 2.029518 CTGTGCTGCTCGGTGACA 59.970 61.111 0.00 0.00 0.00 3.58
117 121 1.375268 GGAGCAGCGAGTTCAAGCT 60.375 57.895 0.00 0.00 45.74 3.74
118 122 2.734673 CGGAGCAGCGAGTTCAAGC 61.735 63.158 0.00 0.00 0.00 4.01
154 158 0.541296 AAAGACGAACTCCTCCGGGA 60.541 55.000 0.00 0.00 39.70 5.14
155 159 0.389948 CAAAGACGAACTCCTCCGGG 60.390 60.000 0.00 0.00 0.00 5.73
195 208 1.583967 GAGGCAGATCGACGACGTG 60.584 63.158 4.58 1.36 40.69 4.49
196 209 2.792599 GAGGCAGATCGACGACGT 59.207 61.111 0.00 0.00 40.69 4.34
243 256 2.124278 GATGGCGGGGGAAAGGTC 60.124 66.667 0.00 0.00 0.00 3.85
244 257 2.938798 TGATGGCGGGGGAAAGGT 60.939 61.111 0.00 0.00 0.00 3.50
256 269 3.587095 CTGGCACACAGCTGATGG 58.413 61.111 23.35 11.87 44.79 3.51
305 318 1.466697 GCAGTGCAGTACGAGAGAGAC 60.467 57.143 11.09 0.00 0.00 3.36
308 321 1.883732 GGCAGTGCAGTACGAGAGA 59.116 57.895 18.61 0.00 0.00 3.10
335 348 3.497932 CAGCAGGAGAGCAAGCGC 61.498 66.667 0.00 0.00 36.85 5.92
372 385 4.963953 GTCGAAATAAACATTGATGAGGCG 59.036 41.667 0.00 0.00 0.00 5.52
373 386 5.879237 TGTCGAAATAAACATTGATGAGGC 58.121 37.500 0.00 0.00 0.00 4.70
379 392 6.066054 TGCACTTGTCGAAATAAACATTGA 57.934 33.333 0.00 0.00 0.00 2.57
381 394 5.689961 GGTTGCACTTGTCGAAATAAACATT 59.310 36.000 0.00 0.00 0.00 2.71
382 395 5.009610 AGGTTGCACTTGTCGAAATAAACAT 59.990 36.000 0.00 0.00 0.00 2.71
383 396 4.336993 AGGTTGCACTTGTCGAAATAAACA 59.663 37.500 0.00 0.00 0.00 2.83
388 401 2.549754 CTCAGGTTGCACTTGTCGAAAT 59.450 45.455 0.00 0.00 0.00 2.17
409 422 3.195698 GCATCGCCGAGTTGACCC 61.196 66.667 0.00 0.00 0.00 4.46
428 441 1.078848 ATCCACGACAAGCTCCTGC 60.079 57.895 0.00 0.00 40.05 4.85
445 458 0.331278 TTGCCTCCATTTCCCGTGAT 59.669 50.000 0.00 0.00 0.00 3.06
446 459 0.608035 GTTGCCTCCATTTCCCGTGA 60.608 55.000 0.00 0.00 0.00 4.35
447 460 1.883021 GTTGCCTCCATTTCCCGTG 59.117 57.895 0.00 0.00 0.00 4.94
448 461 1.674322 CGTTGCCTCCATTTCCCGT 60.674 57.895 0.00 0.00 0.00 5.28
450 463 0.893727 ACACGTTGCCTCCATTTCCC 60.894 55.000 0.00 0.00 0.00 3.97
452 465 1.234821 TGACACGTTGCCTCCATTTC 58.765 50.000 0.00 0.00 0.00 2.17
454 467 1.541147 CATTGACACGTTGCCTCCATT 59.459 47.619 0.00 0.00 0.00 3.16
455 468 1.167851 CATTGACACGTTGCCTCCAT 58.832 50.000 0.00 0.00 0.00 3.41
456 469 0.888736 CCATTGACACGTTGCCTCCA 60.889 55.000 0.00 0.00 0.00 3.86
457 470 0.889186 ACCATTGACACGTTGCCTCC 60.889 55.000 0.00 0.00 0.00 4.30
458 471 0.238289 CACCATTGACACGTTGCCTC 59.762 55.000 0.00 0.00 0.00 4.70
461 474 0.660488 TCACACCATTGACACGTTGC 59.340 50.000 0.00 0.00 0.00 4.17
462 475 2.096657 TGTTCACACCATTGACACGTTG 59.903 45.455 0.00 0.00 0.00 4.10
464 477 2.031258 TGTTCACACCATTGACACGT 57.969 45.000 0.00 0.00 0.00 4.49
465 478 2.411418 CGATGTTCACACCATTGACACG 60.411 50.000 0.00 0.00 0.00 4.49
466 479 2.548057 ACGATGTTCACACCATTGACAC 59.452 45.455 0.00 0.00 0.00 3.67
467 480 2.844946 ACGATGTTCACACCATTGACA 58.155 42.857 0.00 0.00 0.00 3.58
468 481 3.554524 CAACGATGTTCACACCATTGAC 58.445 45.455 0.00 0.00 0.00 3.18
469 482 2.031245 GCAACGATGTTCACACCATTGA 60.031 45.455 0.00 0.00 0.00 2.57
470 483 2.030893 AGCAACGATGTTCACACCATTG 60.031 45.455 0.00 0.00 0.00 2.82
471 484 2.226437 GAGCAACGATGTTCACACCATT 59.774 45.455 4.66 0.00 36.83 3.16
472 485 1.806542 GAGCAACGATGTTCACACCAT 59.193 47.619 4.66 0.00 36.83 3.55
473 486 1.225855 GAGCAACGATGTTCACACCA 58.774 50.000 4.66 0.00 36.83 4.17
474 487 0.517316 GGAGCAACGATGTTCACACC 59.483 55.000 11.40 0.00 38.43 4.16
475 488 0.517316 GGGAGCAACGATGTTCACAC 59.483 55.000 11.40 0.00 39.74 3.82
476 489 0.948623 CGGGAGCAACGATGTTCACA 60.949 55.000 12.03 0.00 39.94 3.58
477 490 0.949105 ACGGGAGCAACGATGTTCAC 60.949 55.000 11.40 6.78 38.43 3.18
478 491 0.948623 CACGGGAGCAACGATGTTCA 60.949 55.000 11.40 0.00 38.43 3.18
479 492 1.787847 CACGGGAGCAACGATGTTC 59.212 57.895 0.72 0.72 36.17 3.18
491 504 2.559698 TCAATTTCTTCAGCACGGGA 57.440 45.000 0.00 0.00 0.00 5.14
494 507 4.348656 CCATGATCAATTTCTTCAGCACG 58.651 43.478 0.00 0.00 0.00 5.34
500 513 6.875195 TGAAAAAGGCCATGATCAATTTCTTC 59.125 34.615 5.01 2.47 0.00 2.87
503 516 5.352293 GGTGAAAAAGGCCATGATCAATTTC 59.648 40.000 5.01 0.00 0.00 2.17
504 517 5.013391 AGGTGAAAAAGGCCATGATCAATTT 59.987 36.000 5.01 0.00 0.00 1.82
511 524 1.146774 TGGAGGTGAAAAAGGCCATGA 59.853 47.619 5.01 0.00 0.00 3.07
516 529 2.693074 TGACTTTGGAGGTGAAAAAGGC 59.307 45.455 0.00 0.00 39.04 4.35
519 532 3.360867 TGCTGACTTTGGAGGTGAAAAA 58.639 40.909 0.00 0.00 0.00 1.94
522 535 2.957402 ATGCTGACTTTGGAGGTGAA 57.043 45.000 0.00 0.00 0.00 3.18
523 536 2.957402 AATGCTGACTTTGGAGGTGA 57.043 45.000 0.00 0.00 0.00 4.02
530 543 4.491676 CCAAGATGGAAATGCTGACTTTG 58.508 43.478 0.00 0.00 40.96 2.77
531 544 3.056322 GCCAAGATGGAAATGCTGACTTT 60.056 43.478 0.00 0.00 40.96 2.66
540 556 2.502538 CCATTGGTGCCAAGATGGAAAT 59.497 45.455 15.15 0.00 40.96 2.17
557 573 2.504367 CACGAAACCTTCTCCACCATT 58.496 47.619 0.00 0.00 0.00 3.16
563 579 0.250338 AGTGCCACGAAACCTTCTCC 60.250 55.000 0.00 0.00 0.00 3.71
569 585 1.166531 AGAAGCAGTGCCACGAAACC 61.167 55.000 12.58 0.00 0.00 3.27
581 597 2.859165 TAGACACCCCAAAGAAGCAG 57.141 50.000 0.00 0.00 0.00 4.24
586 602 2.375174 AGCACAATAGACACCCCAAAGA 59.625 45.455 0.00 0.00 0.00 2.52
587 603 2.795329 AGCACAATAGACACCCCAAAG 58.205 47.619 0.00 0.00 0.00 2.77
588 604 2.890311 CAAGCACAATAGACACCCCAAA 59.110 45.455 0.00 0.00 0.00 3.28
589 605 2.513753 CAAGCACAATAGACACCCCAA 58.486 47.619 0.00 0.00 0.00 4.12
590 606 1.271871 CCAAGCACAATAGACACCCCA 60.272 52.381 0.00 0.00 0.00 4.96
591 607 1.271926 ACCAAGCACAATAGACACCCC 60.272 52.381 0.00 0.00 0.00 4.95
592 608 2.200373 ACCAAGCACAATAGACACCC 57.800 50.000 0.00 0.00 0.00 4.61
593 609 5.393027 CCAAATACCAAGCACAATAGACACC 60.393 44.000 0.00 0.00 0.00 4.16
594 610 5.640732 CCAAATACCAAGCACAATAGACAC 58.359 41.667 0.00 0.00 0.00 3.67
595 611 4.157656 GCCAAATACCAAGCACAATAGACA 59.842 41.667 0.00 0.00 0.00 3.41
596 612 4.672409 GCCAAATACCAAGCACAATAGAC 58.328 43.478 0.00 0.00 0.00 2.59
597 613 3.376859 CGCCAAATACCAAGCACAATAGA 59.623 43.478 0.00 0.00 0.00 1.98
598 614 3.376859 TCGCCAAATACCAAGCACAATAG 59.623 43.478 0.00 0.00 0.00 1.73
599 615 3.127895 GTCGCCAAATACCAAGCACAATA 59.872 43.478 0.00 0.00 0.00 1.90
600 616 2.094752 GTCGCCAAATACCAAGCACAAT 60.095 45.455 0.00 0.00 0.00 2.71
601 617 1.268352 GTCGCCAAATACCAAGCACAA 59.732 47.619 0.00 0.00 0.00 3.33
602 618 0.878416 GTCGCCAAATACCAAGCACA 59.122 50.000 0.00 0.00 0.00 4.57
603 619 0.170339 GGTCGCCAAATACCAAGCAC 59.830 55.000 0.00 0.00 35.73 4.40
604 620 0.963355 GGGTCGCCAAATACCAAGCA 60.963 55.000 0.00 0.00 37.51 3.91
605 621 0.963355 TGGGTCGCCAAATACCAAGC 60.963 55.000 0.00 0.00 37.51 4.01
606 622 1.540267 TTGGGTCGCCAAATACCAAG 58.460 50.000 0.00 0.00 36.37 3.61
607 623 1.540267 CTTGGGTCGCCAAATACCAA 58.460 50.000 0.00 0.00 38.76 3.67
608 624 0.963355 GCTTGGGTCGCCAAATACCA 60.963 55.000 0.00 0.00 37.51 3.25
609 625 0.963355 TGCTTGGGTCGCCAAATACC 60.963 55.000 0.00 0.00 34.85 2.73
610 626 0.451783 CTGCTTGGGTCGCCAAATAC 59.548 55.000 0.00 0.00 0.00 1.89
611 627 0.679640 CCTGCTTGGGTCGCCAAATA 60.680 55.000 0.00 0.00 0.00 1.40
612 628 1.978617 CCTGCTTGGGTCGCCAAAT 60.979 57.895 0.00 0.00 0.00 2.32
613 629 2.597217 CCTGCTTGGGTCGCCAAA 60.597 61.111 0.00 0.00 0.00 3.28
614 630 3.884774 ACCTGCTTGGGTCGCCAA 61.885 61.111 0.00 0.00 41.11 4.52
615 631 4.641645 CACCTGCTTGGGTCGCCA 62.642 66.667 1.69 0.00 41.11 5.69
617 633 4.329545 TCCACCTGCTTGGGTCGC 62.330 66.667 1.69 0.00 41.11 5.19
618 634 2.046892 CTCCACCTGCTTGGGTCG 60.047 66.667 1.69 0.00 41.11 4.79
619 635 1.302832 CACTCCACCTGCTTGGGTC 60.303 63.158 1.69 0.00 41.11 4.46
620 636 1.352622 TTCACTCCACCTGCTTGGGT 61.353 55.000 1.69 0.00 41.11 4.51
621 637 0.038744 ATTCACTCCACCTGCTTGGG 59.961 55.000 1.69 0.00 41.11 4.12
622 638 1.542915 CAATTCACTCCACCTGCTTGG 59.457 52.381 0.00 0.00 42.93 3.61
623 639 1.068055 GCAATTCACTCCACCTGCTTG 60.068 52.381 0.00 0.00 0.00 4.01
624 640 1.251251 GCAATTCACTCCACCTGCTT 58.749 50.000 0.00 0.00 0.00 3.91
625 641 0.111061 TGCAATTCACTCCACCTGCT 59.889 50.000 0.00 0.00 0.00 4.24
626 642 0.961019 TTGCAATTCACTCCACCTGC 59.039 50.000 0.00 0.00 0.00 4.85
627 643 2.507484 TCTTGCAATTCACTCCACCTG 58.493 47.619 0.00 0.00 0.00 4.00
628 644 2.957402 TCTTGCAATTCACTCCACCT 57.043 45.000 0.00 0.00 0.00 4.00
629 645 3.552890 GGTTTCTTGCAATTCACTCCACC 60.553 47.826 0.00 0.00 0.00 4.61
630 646 3.068024 TGGTTTCTTGCAATTCACTCCAC 59.932 43.478 0.00 0.00 0.00 4.02
676 692 3.312973 TGATTAGCGACCACGTTGTTTTT 59.687 39.130 0.00 0.00 41.98 1.94
922 959 0.407528 AGTGTGGGAGCAGAGAGAGA 59.592 55.000 0.00 0.00 0.00 3.10
946 983 1.304282 GAGCAAATGGGAGGGAGCA 59.696 57.895 0.00 0.00 0.00 4.26
993 1031 2.591753 CAGGACACCATGGCGGAT 59.408 61.111 13.04 0.00 38.63 4.18
1147 1185 5.012046 GGGACCTGAGAAATCCAACAAAAAT 59.988 40.000 0.00 0.00 33.87 1.82
1167 1205 2.615912 GCTCATCAATTGTAGCTGGGAC 59.384 50.000 17.25 0.00 32.18 4.46
1405 1444 6.156256 ACATGAGCAGTAACTATGAACCCTAA 59.844 38.462 0.00 0.00 0.00 2.69
1718 1758 2.203451 CTCCAGGCATGCCATCCC 60.203 66.667 37.18 11.30 38.92 3.85
2096 2138 6.418101 TGCAACAATCTAGCTTATCCTTCTT 58.582 36.000 0.00 0.00 0.00 2.52
2110 2152 2.094700 CAGCTCAGCAATGCAACAATCT 60.095 45.455 8.35 0.00 0.00 2.40
2775 2821 3.083349 TGCGGTGCTCCCTATGCT 61.083 61.111 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.