Multiple sequence alignment - TraesCS3B01G014600

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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 TraesCS3B01G014600 chr3B 100.000 2314 0 0 1 2314 6180350 6182663 0.000000e+00 4274.0
1 TraesCS3B01G014600 chr3B 96.774 31 1 0 1263 1293 6172259 6172289 4.000000e-03 52.8
2 TraesCS3B01G014600 chr3A 94.943 969 39 8 1351 2314 9293658 9294621 0.000000e+00 1509.0
3 TraesCS3B01G014600 chr3A 86.486 740 70 11 632 1353 9285421 9286148 0.000000e+00 785.0
4 TraesCS3B01G014600 chr3A 95.853 434 16 2 1883 2314 9248336 9248769 0.000000e+00 701.0
5 TraesCS3B01G014600 chr3A 96.774 31 1 0 1263 1293 9233272 9233302 4.000000e-03 52.8
6 TraesCS3B01G014600 chr3D 85.271 774 62 18 630 1357 326343 325576 0.000000e+00 750.0
7 TraesCS3B01G014600 chr3D 85.348 273 26 9 2048 2314 324836 324572 1.050000e-68 270.0
8 TraesCS3B01G014600 chr5A 88.774 579 44 3 1 579 589032141 589032698 0.000000e+00 689.0
9 TraesCS3B01G014600 chr5A 82.684 462 76 3 142 603 311969541 311969084 7.700000e-110 407.0
10 TraesCS3B01G014600 chr2D 90.456 461 39 3 1 461 618567785 618567330 9.150000e-169 603.0
11 TraesCS3B01G014600 chr4D 85.132 491 68 4 112 602 452559494 452559979 4.440000e-137 497.0
12 TraesCS3B01G014600 chr1D 84.959 492 67 7 112 602 413584893 413585378 2.070000e-135 492.0
13 TraesCS3B01G014600 chr6B 85.470 468 66 1 137 604 39304906 39304441 9.610000e-134 486.0
14 TraesCS3B01G014600 chr7D 83.603 494 74 6 112 604 614651050 614650563 7.540000e-125 457.0
15 TraesCS3B01G014600 chr7B 83.766 462 72 3 137 598 6086170 6086628 3.530000e-118 435.0
16 TraesCS3B01G014600 chr1B 82.150 493 79 8 112 602 338017520 338017035 4.600000e-112 414.0
17 TraesCS3B01G014600 chrUn 96.774 31 1 0 1263 1293 35911200 35911230 4.000000e-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 TraesCS3B01G014600 chr3B 6180350 6182663 2313 False 4274 4274 100.0000 1 2314 1 chr3B.!!$F2 2313
1 TraesCS3B01G014600 chr3A 9293658 9294621 963 False 1509 1509 94.9430 1351 2314 1 chr3A.!!$F4 963
2 TraesCS3B01G014600 chr3A 9285421 9286148 727 False 785 785 86.4860 632 1353 1 chr3A.!!$F3 721
3 TraesCS3B01G014600 chr3D 324572 326343 1771 True 510 750 85.3095 630 2314 2 chr3D.!!$R1 1684
4 TraesCS3B01G014600 chr5A 589032141 589032698 557 False 689 689 88.7740 1 579 1 chr5A.!!$F1 578

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
648 649 0.460311 CTACTAGGGGGAGCACGTTG 59.54 60.0 0.0 0.0 0.0 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 1859 2.145905 GCGCGTGCGAATTTCCTTG 61.146 57.895 19.66 0.0 42.83 3.61 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
65 66 1.064060 GTGTTTGTGCTGACTTTCGCT 59.936 47.619 0.00 0.00 0.00 4.93
74 75 2.854805 GCTGACTTTCGCTGGTTTTGAC 60.855 50.000 0.00 0.00 0.00 3.18
76 77 0.661020 ACTTTCGCTGGTTTTGACCG 59.339 50.000 0.00 0.00 0.00 4.79
88 89 3.855379 GGTTTTGACCGTGTTTTGACTTC 59.145 43.478 0.00 0.00 0.00 3.01
92 93 2.933906 TGACCGTGTTTTGACTTCTGAC 59.066 45.455 0.00 0.00 0.00 3.51
103 104 7.094420 TGTTTTGACTTCTGACTCAAATTCACA 60.094 33.333 9.40 8.60 36.51 3.58
126 127 9.146984 CACATACTTTCTTCAAGTCCGTTTATA 57.853 33.333 0.00 0.00 42.62 0.98
135 136 6.431198 TCAAGTCCGTTTATATTTTCAGGC 57.569 37.500 0.00 0.00 0.00 4.85
163 164 7.689812 CGCATACTTTCTACAAAAGTTCATGAG 59.310 37.037 8.32 5.86 40.58 2.90
164 165 8.507249 GCATACTTTCTACAAAAGTTCATGAGT 58.493 33.333 8.32 0.00 40.58 3.41
168 169 8.956426 ACTTTCTACAAAAGTTCATGAGTTTGA 58.044 29.630 24.15 13.20 37.18 2.69
169 170 9.787532 CTTTCTACAAAAGTTCATGAGTTTGAA 57.212 29.630 24.15 13.18 31.32 2.69
175 176 9.520204 ACAAAAGTTCATGAGTTTGAATAAGTG 57.480 29.630 24.15 12.52 37.88 3.16
176 177 8.482429 CAAAAGTTCATGAGTTTGAATAAGTGC 58.518 33.333 17.31 0.00 37.88 4.40
177 178 6.882610 AGTTCATGAGTTTGAATAAGTGCA 57.117 33.333 0.00 0.00 37.88 4.57
178 179 6.672147 AGTTCATGAGTTTGAATAAGTGCAC 58.328 36.000 9.40 9.40 37.88 4.57
179 180 5.281693 TCATGAGTTTGAATAAGTGCACG 57.718 39.130 12.01 0.00 0.00 5.34
180 181 4.154015 TCATGAGTTTGAATAAGTGCACGG 59.846 41.667 12.01 0.00 0.00 4.94
208 209 1.331756 AGCAGTGCACGAACTTGAAAG 59.668 47.619 19.20 0.00 0.00 2.62
211 212 3.548818 GCAGTGCACGAACTTGAAAGAAT 60.549 43.478 11.09 0.00 0.00 2.40
218 219 5.137403 CACGAACTTGAAAGAATTACACGG 58.863 41.667 0.00 0.00 0.00 4.94
289 290 6.795098 ATTGCGTGAACTTGATAAAGTACA 57.205 33.333 0.00 0.00 31.72 2.90
345 346 9.900264 GGATATGTGAATTTGAAATTTTTACGC 57.100 29.630 4.46 0.00 0.00 4.42
363 364 3.868835 ACGCGAACATGAAAAAGTACAC 58.131 40.909 15.93 0.00 0.00 2.90
364 365 2.894000 CGCGAACATGAAAAAGTACACG 59.106 45.455 0.00 0.00 0.00 4.49
365 366 2.650297 GCGAACATGAAAAAGTACACGC 59.350 45.455 0.00 0.00 36.06 5.34
367 368 3.900116 CGAACATGAAAAAGTACACGCAG 59.100 43.478 0.00 0.00 0.00 5.18
368 369 4.318475 CGAACATGAAAAAGTACACGCAGA 60.318 41.667 0.00 0.00 0.00 4.26
370 371 5.034554 ACATGAAAAAGTACACGCAGATG 57.965 39.130 0.00 0.00 0.00 2.90
371 372 4.754618 ACATGAAAAAGTACACGCAGATGA 59.245 37.500 0.00 0.00 0.00 2.92
409 410 8.692110 TGAATTTCAAAAGATTCATGGATTCG 57.308 30.769 0.00 0.00 37.35 3.34
421 422 9.273016 AGATTCATGGATTCGAAAAATATACGT 57.727 29.630 0.00 0.00 0.00 3.57
442 443 3.124636 GTGTATTTAAGTCAGCACCGGTG 59.875 47.826 30.66 30.66 0.00 4.94
446 447 2.623878 TAAGTCAGCACCGGTGAAAA 57.376 45.000 38.30 18.37 41.75 2.29
447 448 1.981256 AAGTCAGCACCGGTGAAAAT 58.019 45.000 38.30 17.81 41.75 1.82
448 449 1.523758 AGTCAGCACCGGTGAAAATC 58.476 50.000 38.30 19.53 41.75 2.17
449 450 1.202758 AGTCAGCACCGGTGAAAATCA 60.203 47.619 38.30 11.66 41.75 2.57
471 472 2.681152 GTGAGTTAGCACCAAAACCG 57.319 50.000 0.00 0.00 32.68 4.44
474 475 0.951558 AGTTAGCACCAAAACCGCTG 59.048 50.000 0.00 0.00 37.20 5.18
499 500 1.484240 CTGAGACCAGGGATGAACCTC 59.516 57.143 0.00 0.00 39.34 3.85
519 520 2.559668 TCGTCCCGTTTCAGTAGTTGAT 59.440 45.455 0.00 0.00 35.27 2.57
521 522 3.000727 GTCCCGTTTCAGTAGTTGATGG 58.999 50.000 0.00 0.00 35.27 3.51
534 535 0.950836 TTGATGGTGCAAGTTGTCCG 59.049 50.000 4.48 0.00 0.00 4.79
536 537 0.605319 GATGGTGCAAGTTGTCCGGA 60.605 55.000 0.00 0.00 0.00 5.14
540 541 1.234821 GTGCAAGTTGTCCGGATTCA 58.765 50.000 7.81 0.00 0.00 2.57
546 547 4.290155 CAAGTTGTCCGGATTCAAAGTTG 58.710 43.478 7.81 14.85 0.00 3.16
563 564 7.865820 TCAAAGTTGAGGGATCAAATCTAGAT 58.134 34.615 0.00 0.00 32.50 1.98
565 566 8.964772 CAAAGTTGAGGGATCAAATCTAGATTT 58.035 33.333 22.43 22.43 41.33 2.17
569 570 5.070981 TGAGGGATCAAATCTAGATTTCGCT 59.929 40.000 24.72 24.51 38.84 4.93
574 575 7.330700 GGGATCAAATCTAGATTTCGCTAAGAG 59.669 40.741 24.72 12.98 38.84 2.85
579 580 8.538856 CAAATCTAGATTTCGCTAAGAGTTGAG 58.461 37.037 24.72 7.64 38.84 3.02
580 581 6.137794 TCTAGATTTCGCTAAGAGTTGAGG 57.862 41.667 0.00 0.00 0.00 3.86
581 582 4.130286 AGATTTCGCTAAGAGTTGAGGG 57.870 45.455 0.00 0.00 0.00 4.30
582 583 3.769844 AGATTTCGCTAAGAGTTGAGGGA 59.230 43.478 0.00 0.00 33.26 4.20
583 584 3.314541 TTTCGCTAAGAGTTGAGGGAC 57.685 47.619 0.00 0.00 34.69 4.46
584 585 0.809385 TCGCTAAGAGTTGAGGGACG 59.191 55.000 0.00 0.00 30.41 4.79
585 586 0.809385 CGCTAAGAGTTGAGGGACGA 59.191 55.000 0.00 0.00 0.00 4.20
586 587 1.202200 CGCTAAGAGTTGAGGGACGAG 60.202 57.143 0.00 0.00 0.00 4.18
587 588 2.093106 GCTAAGAGTTGAGGGACGAGA 58.907 52.381 0.00 0.00 0.00 4.04
588 589 2.492484 GCTAAGAGTTGAGGGACGAGAA 59.508 50.000 0.00 0.00 0.00 2.87
589 590 3.056749 GCTAAGAGTTGAGGGACGAGAAA 60.057 47.826 0.00 0.00 0.00 2.52
590 591 4.382147 GCTAAGAGTTGAGGGACGAGAAAT 60.382 45.833 0.00 0.00 0.00 2.17
591 592 5.163540 GCTAAGAGTTGAGGGACGAGAAATA 60.164 44.000 0.00 0.00 0.00 1.40
592 593 5.941555 AAGAGTTGAGGGACGAGAAATAT 57.058 39.130 0.00 0.00 0.00 1.28
593 594 7.255520 GCTAAGAGTTGAGGGACGAGAAATATA 60.256 40.741 0.00 0.00 0.00 0.86
594 595 6.394025 AGAGTTGAGGGACGAGAAATATAC 57.606 41.667 0.00 0.00 0.00 1.47
595 596 6.130569 AGAGTTGAGGGACGAGAAATATACT 58.869 40.000 0.00 0.00 0.00 2.12
596 597 6.608002 AGAGTTGAGGGACGAGAAATATACTT 59.392 38.462 0.00 0.00 0.00 2.24
597 598 7.124448 AGAGTTGAGGGACGAGAAATATACTTT 59.876 37.037 0.00 0.00 0.00 2.66
598 599 7.621796 AGTTGAGGGACGAGAAATATACTTTT 58.378 34.615 0.00 0.00 0.00 2.27
599 600 7.764901 AGTTGAGGGACGAGAAATATACTTTTC 59.235 37.037 0.00 0.00 36.13 2.29
600 601 7.419711 TGAGGGACGAGAAATATACTTTTCT 57.580 36.000 1.72 1.72 46.08 2.52
616 617 8.976986 ATACTTTTCTCAAAGCACAATCATTC 57.023 30.769 0.00 0.00 43.03 2.67
617 618 7.047460 ACTTTTCTCAAAGCACAATCATTCT 57.953 32.000 0.00 0.00 43.03 2.40
618 619 7.495055 ACTTTTCTCAAAGCACAATCATTCTT 58.505 30.769 0.00 0.00 43.03 2.52
619 620 7.437267 ACTTTTCTCAAAGCACAATCATTCTTG 59.563 33.333 0.00 0.00 43.03 3.02
620 621 4.801891 TCTCAAAGCACAATCATTCTTGC 58.198 39.130 0.00 0.00 35.08 4.01
621 622 3.916761 TCAAAGCACAATCATTCTTGCC 58.083 40.909 0.00 0.00 35.47 4.52
622 623 3.321396 TCAAAGCACAATCATTCTTGCCA 59.679 39.130 0.00 0.00 35.47 4.92
623 624 4.020928 TCAAAGCACAATCATTCTTGCCAT 60.021 37.500 0.00 0.00 35.47 4.40
624 625 5.185442 TCAAAGCACAATCATTCTTGCCATA 59.815 36.000 0.00 0.00 35.47 2.74
625 626 4.913335 AGCACAATCATTCTTGCCATAG 57.087 40.909 0.00 0.00 35.47 2.23
626 627 4.529897 AGCACAATCATTCTTGCCATAGA 58.470 39.130 0.00 0.00 35.47 1.98
627 628 5.138276 AGCACAATCATTCTTGCCATAGAT 58.862 37.500 0.00 0.00 35.47 1.98
628 629 6.301486 AGCACAATCATTCTTGCCATAGATA 58.699 36.000 0.00 0.00 35.47 1.98
629 630 6.206243 AGCACAATCATTCTTGCCATAGATAC 59.794 38.462 0.00 0.00 35.47 2.24
630 631 6.206243 GCACAATCATTCTTGCCATAGATACT 59.794 38.462 0.00 0.00 0.00 2.12
631 632 7.388776 GCACAATCATTCTTGCCATAGATACTA 59.611 37.037 0.00 0.00 0.00 1.82
632 633 8.715998 CACAATCATTCTTGCCATAGATACTAC 58.284 37.037 0.00 0.00 0.00 2.73
633 634 8.654997 ACAATCATTCTTGCCATAGATACTACT 58.345 33.333 0.00 0.00 0.00 2.57
636 637 8.354711 TCATTCTTGCCATAGATACTACTAGG 57.645 38.462 0.00 0.00 0.00 3.02
648 649 0.460311 CTACTAGGGGGAGCACGTTG 59.540 60.000 0.00 0.00 0.00 4.10
656 657 1.374758 GGAGCACGTTGTCTCCCAG 60.375 63.158 14.31 0.00 42.30 4.45
660 661 1.000955 AGCACGTTGTCTCCCAGTTAG 59.999 52.381 0.00 0.00 0.00 2.34
664 665 2.296471 ACGTTGTCTCCCAGTTAGAGTG 59.704 50.000 0.00 0.00 32.93 3.51
676 677 5.532779 CCCAGTTAGAGTGCTTTCTTTTTCT 59.467 40.000 0.00 0.00 0.00 2.52
681 682 5.665381 AGAGTGCTTTCTTTTTCTCTTCG 57.335 39.130 0.00 0.00 0.00 3.79
799 814 7.841282 TGACTTCCCAGGTCTATAGATAAAG 57.159 40.000 5.57 6.49 35.04 1.85
818 833 4.729227 AAGGACGAAAGAGGAAGATCTC 57.271 45.455 0.00 0.00 0.00 2.75
848 863 3.357079 GGGCCACTGACGCTGTTG 61.357 66.667 4.39 0.00 0.00 3.33
858 873 0.880278 GACGCTGTTGTCAAGCCAGA 60.880 55.000 7.25 0.00 38.75 3.86
860 875 1.845809 CGCTGTTGTCAAGCCAGACC 61.846 60.000 7.25 0.00 37.73 3.85
882 897 4.442192 CCAATTTTTCCAAGGTTGACGGAA 60.442 41.667 0.00 0.00 37.03 4.30
899 914 2.087646 GGAAGGCAGACTTTGACCATC 58.912 52.381 0.00 0.00 40.21 3.51
903 918 2.158623 AGGCAGACTTTGACCATCAACA 60.159 45.455 0.00 0.00 35.89 3.33
946 972 9.710818 TCCCCTATAATACAAGGCTAGTAATAG 57.289 37.037 0.00 0.00 0.00 1.73
967 999 5.303747 AGCGTTATACTATGCAGCTAGAG 57.696 43.478 1.33 0.00 32.39 2.43
968 1000 5.004448 AGCGTTATACTATGCAGCTAGAGA 58.996 41.667 1.33 0.00 32.39 3.10
969 1001 5.123186 AGCGTTATACTATGCAGCTAGAGAG 59.877 44.000 1.33 0.00 32.39 3.20
1103 1156 1.023513 ATTCGCAGCTCAGTTGCCTC 61.024 55.000 8.06 0.00 36.44 4.70
1108 1161 2.295885 GCAGCTCAGTTGCCTCATTAT 58.704 47.619 1.14 0.00 33.76 1.28
1109 1162 3.470709 GCAGCTCAGTTGCCTCATTATA 58.529 45.455 1.14 0.00 33.76 0.98
1124 1177 7.773690 TGCCTCATTATAGGATGATGATTGATG 59.226 37.037 0.00 0.00 39.15 3.07
1125 1178 7.991460 GCCTCATTATAGGATGATGATTGATGA 59.009 37.037 0.00 0.00 39.15 2.92
1247 1300 2.189521 CCACCACCGCCTATGGAC 59.810 66.667 2.67 0.00 39.87 4.02
1253 1306 1.024579 CACCGCCTATGGACACAACC 61.025 60.000 0.00 0.00 0.00 3.77
1303 1356 1.069090 AGGCTGTTTCGAGCGTTCA 59.931 52.632 0.00 0.00 40.13 3.18
1308 1361 2.785681 GCTGTTTCGAGCGTTCATCATG 60.786 50.000 0.00 0.00 0.00 3.07
1397 1508 0.307760 CTGTGTTGGCGACTGAAACC 59.692 55.000 6.41 0.00 0.00 3.27
1460 1693 3.211045 GTGAGGCAGTCCAACTTGTAAA 58.789 45.455 0.00 0.00 33.74 2.01
1466 1699 6.280643 AGGCAGTCCAACTTGTAAAATTTTC 58.719 36.000 6.72 0.37 33.74 2.29
1693 1929 3.818180 AGAAGCTGGATCATAGCCAAAG 58.182 45.455 15.21 0.00 42.07 2.77
1714 1950 5.215252 AGTACAGTAACTCATGTGCTTGT 57.785 39.130 0.00 0.00 38.97 3.16
1771 2007 6.265577 GTGTGCCACATAGGATAAACAAATC 58.734 40.000 0.00 0.00 41.22 2.17
1804 2046 4.503370 GTGAAGATAGTAAACTAGCACGGC 59.497 45.833 8.02 0.00 37.32 5.68
1831 2073 8.087750 TCTTGATGCAAAGTCGGAAAATTAATT 58.912 29.630 0.00 0.00 0.00 1.40
1968 2233 4.796265 AGAGGGACAGGGGAGAAAAATAAT 59.204 41.667 0.00 0.00 0.00 1.28
2010 2276 5.345741 CCATTGCAGTAACATGCTTACAAAC 59.654 40.000 15.75 8.40 46.63 2.93
2249 2519 1.964373 CCGCAACCGCTTACCAAGT 60.964 57.895 0.00 0.00 35.30 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.597937 CCAGCGAAAGTCAGCACAAAC 60.598 52.381 0.00 0.00 35.48 2.93
65 66 2.820787 AGTCAAAACACGGTCAAAACCA 59.179 40.909 0.00 0.00 46.86 3.67
74 75 3.194861 TGAGTCAGAAGTCAAAACACGG 58.805 45.455 0.00 0.00 31.79 4.94
88 89 8.777413 TGAAGAAAGTATGTGAATTTGAGTCAG 58.223 33.333 0.00 0.00 0.00 3.51
126 127 2.143876 AAGTATGCGGGCCTGAAAAT 57.856 45.000 18.31 7.94 0.00 1.82
135 136 5.180492 TGAACTTTTGTAGAAAGTATGCGGG 59.820 40.000 4.75 0.00 39.36 6.13
163 164 5.457140 TCAAATCCGTGCACTTATTCAAAC 58.543 37.500 16.19 0.00 0.00 2.93
164 165 5.697473 TCAAATCCGTGCACTTATTCAAA 57.303 34.783 16.19 1.54 0.00 2.69
165 166 5.697473 TTCAAATCCGTGCACTTATTCAA 57.303 34.783 16.19 7.93 0.00 2.69
166 167 5.697473 TTTCAAATCCGTGCACTTATTCA 57.303 34.783 16.19 2.54 0.00 2.57
167 168 4.558860 GCTTTCAAATCCGTGCACTTATTC 59.441 41.667 16.19 0.00 0.00 1.75
168 169 4.022416 TGCTTTCAAATCCGTGCACTTATT 60.022 37.500 16.19 11.17 0.00 1.40
169 170 3.505680 TGCTTTCAAATCCGTGCACTTAT 59.494 39.130 16.19 5.08 0.00 1.73
170 171 2.881513 TGCTTTCAAATCCGTGCACTTA 59.118 40.909 16.19 2.53 0.00 2.24
171 172 1.680735 TGCTTTCAAATCCGTGCACTT 59.319 42.857 16.19 0.00 0.00 3.16
172 173 1.267806 CTGCTTTCAAATCCGTGCACT 59.732 47.619 16.19 0.00 0.00 4.40
173 174 1.001378 ACTGCTTTCAAATCCGTGCAC 60.001 47.619 6.82 6.82 0.00 4.57
174 175 1.001487 CACTGCTTTCAAATCCGTGCA 60.001 47.619 0.00 0.00 0.00 4.57
175 176 1.689959 CACTGCTTTCAAATCCGTGC 58.310 50.000 0.00 0.00 0.00 5.34
176 177 1.001487 TGCACTGCTTTCAAATCCGTG 60.001 47.619 1.98 0.00 0.00 4.94
177 178 1.001378 GTGCACTGCTTTCAAATCCGT 60.001 47.619 10.32 0.00 0.00 4.69
178 179 1.689959 GTGCACTGCTTTCAAATCCG 58.310 50.000 10.32 0.00 0.00 4.18
179 180 1.266718 TCGTGCACTGCTTTCAAATCC 59.733 47.619 16.19 0.00 0.00 3.01
180 181 2.686558 TCGTGCACTGCTTTCAAATC 57.313 45.000 16.19 0.00 0.00 2.17
211 212 9.058174 TCAAGTATTTTTCTCAAATCCGTGTAA 57.942 29.630 0.00 0.00 0.00 2.41
345 346 3.867665 TGCGTGTACTTTTTCATGTTCG 58.132 40.909 0.00 0.00 0.00 3.95
421 422 3.007074 TCACCGGTGCTGACTTAAATACA 59.993 43.478 30.25 4.05 0.00 2.29
442 443 4.686839 GTGCTAACTCACCCTGATTTTC 57.313 45.455 0.00 0.00 0.00 2.29
471 472 0.676151 CCCTGGTCTCAGCTTTCAGC 60.676 60.000 0.00 0.00 42.84 4.26
474 475 1.556911 TCATCCCTGGTCTCAGCTTTC 59.443 52.381 0.00 0.00 39.61 2.62
504 505 2.805671 TGCACCATCAACTACTGAAACG 59.194 45.455 0.00 0.00 37.67 3.60
519 520 0.179004 AATCCGGACAACTTGCACCA 60.179 50.000 6.12 0.00 0.00 4.17
521 522 1.234821 TGAATCCGGACAACTTGCAC 58.765 50.000 6.12 0.00 0.00 4.57
534 535 5.982890 TTTGATCCCTCAACTTTGAATCC 57.017 39.130 0.00 0.00 41.05 3.01
536 537 8.331740 TCTAGATTTGATCCCTCAACTTTGAAT 58.668 33.333 0.00 0.00 41.05 2.57
540 541 9.183368 GAAATCTAGATTTGATCCCTCAACTTT 57.817 33.333 30.65 6.04 41.05 2.66
546 547 5.546526 AGCGAAATCTAGATTTGATCCCTC 58.453 41.667 30.65 15.88 40.77 4.30
563 564 2.352421 CGTCCCTCAACTCTTAGCGAAA 60.352 50.000 0.00 0.00 0.00 3.46
565 566 0.809385 CGTCCCTCAACTCTTAGCGA 59.191 55.000 0.00 0.00 0.00 4.93
569 570 7.778853 AGTATATTTCTCGTCCCTCAACTCTTA 59.221 37.037 0.00 0.00 0.00 2.10
574 575 7.764901 AGAAAAGTATATTTCTCGTCCCTCAAC 59.235 37.037 0.00 0.00 44.28 3.18
591 592 8.800332 AGAATGATTGTGCTTTGAGAAAAGTAT 58.200 29.630 0.64 0.00 32.52 2.12
592 593 8.169977 AGAATGATTGTGCTTTGAGAAAAGTA 57.830 30.769 0.64 0.00 32.52 2.24
593 594 7.047460 AGAATGATTGTGCTTTGAGAAAAGT 57.953 32.000 0.64 0.00 32.52 2.66
594 595 7.568861 GCAAGAATGATTGTGCTTTGAGAAAAG 60.569 37.037 3.80 0.00 34.13 2.27
595 596 6.201425 GCAAGAATGATTGTGCTTTGAGAAAA 59.799 34.615 3.80 0.00 34.13 2.29
596 597 5.693104 GCAAGAATGATTGTGCTTTGAGAAA 59.307 36.000 3.80 0.00 34.13 2.52
597 598 5.224888 GCAAGAATGATTGTGCTTTGAGAA 58.775 37.500 3.80 0.00 34.13 2.87
598 599 4.321452 GGCAAGAATGATTGTGCTTTGAGA 60.321 41.667 9.49 0.00 37.17 3.27
599 600 3.924686 GGCAAGAATGATTGTGCTTTGAG 59.075 43.478 9.49 0.00 37.17 3.02
600 601 3.321396 TGGCAAGAATGATTGTGCTTTGA 59.679 39.130 9.49 0.00 37.17 2.69
601 602 3.655486 TGGCAAGAATGATTGTGCTTTG 58.345 40.909 9.49 0.00 37.17 2.77
602 603 4.546829 ATGGCAAGAATGATTGTGCTTT 57.453 36.364 9.49 0.00 37.17 3.51
603 604 4.951715 TCTATGGCAAGAATGATTGTGCTT 59.048 37.500 9.49 2.67 37.17 3.91
604 605 4.529897 TCTATGGCAAGAATGATTGTGCT 58.470 39.130 9.49 0.00 37.17 4.40
605 606 4.906065 TCTATGGCAAGAATGATTGTGC 57.094 40.909 0.00 2.62 36.24 4.57
606 607 7.741027 AGTATCTATGGCAAGAATGATTGTG 57.259 36.000 0.00 0.00 32.56 3.33
607 608 8.654997 AGTAGTATCTATGGCAAGAATGATTGT 58.345 33.333 0.00 0.00 32.56 2.71
610 611 8.976353 CCTAGTAGTATCTATGGCAAGAATGAT 58.024 37.037 0.00 0.00 0.00 2.45
611 612 7.397476 CCCTAGTAGTATCTATGGCAAGAATGA 59.603 40.741 0.00 0.00 0.00 2.57
612 613 7.364232 CCCCTAGTAGTATCTATGGCAAGAATG 60.364 44.444 0.00 0.00 0.00 2.67
613 614 6.670027 CCCCTAGTAGTATCTATGGCAAGAAT 59.330 42.308 0.00 0.00 0.00 2.40
614 615 6.017192 CCCCTAGTAGTATCTATGGCAAGAA 58.983 44.000 0.00 0.00 0.00 2.52
615 616 5.518546 CCCCCTAGTAGTATCTATGGCAAGA 60.519 48.000 0.00 0.00 0.00 3.02
616 617 4.712337 CCCCCTAGTAGTATCTATGGCAAG 59.288 50.000 0.00 0.00 0.00 4.01
617 618 4.358918 TCCCCCTAGTAGTATCTATGGCAA 59.641 45.833 0.00 0.00 0.00 4.52
618 619 3.927322 TCCCCCTAGTAGTATCTATGGCA 59.073 47.826 0.00 0.00 0.00 4.92
619 620 4.538738 CTCCCCCTAGTAGTATCTATGGC 58.461 52.174 0.00 0.00 0.00 4.40
620 621 4.017407 TGCTCCCCCTAGTAGTATCTATGG 60.017 50.000 0.00 0.00 0.00 2.74
621 622 4.951094 GTGCTCCCCCTAGTAGTATCTATG 59.049 50.000 0.00 0.00 0.00 2.23
622 623 4.324408 CGTGCTCCCCCTAGTAGTATCTAT 60.324 50.000 0.00 0.00 0.00 1.98
623 624 3.008813 CGTGCTCCCCCTAGTAGTATCTA 59.991 52.174 0.00 0.00 0.00 1.98
624 625 2.224818 CGTGCTCCCCCTAGTAGTATCT 60.225 54.545 0.00 0.00 0.00 1.98
625 626 2.161030 CGTGCTCCCCCTAGTAGTATC 58.839 57.143 0.00 0.00 0.00 2.24
626 627 1.498145 ACGTGCTCCCCCTAGTAGTAT 59.502 52.381 0.00 0.00 0.00 2.12
627 628 0.921896 ACGTGCTCCCCCTAGTAGTA 59.078 55.000 0.00 0.00 0.00 1.82
628 629 0.040794 AACGTGCTCCCCCTAGTAGT 59.959 55.000 0.00 0.00 0.00 2.73
629 630 0.460311 CAACGTGCTCCCCCTAGTAG 59.540 60.000 0.00 0.00 0.00 2.57
630 631 0.251922 ACAACGTGCTCCCCCTAGTA 60.252 55.000 0.00 0.00 0.00 1.82
631 632 1.535687 ACAACGTGCTCCCCCTAGT 60.536 57.895 0.00 0.00 0.00 2.57
632 633 1.218316 GACAACGTGCTCCCCCTAG 59.782 63.158 0.00 0.00 0.00 3.02
633 634 1.229082 AGACAACGTGCTCCCCCTA 60.229 57.895 0.00 0.00 0.00 3.53
634 635 2.526873 AGACAACGTGCTCCCCCT 60.527 61.111 0.00 0.00 0.00 4.79
635 636 2.047179 GAGACAACGTGCTCCCCC 60.047 66.667 0.00 0.00 0.00 5.40
636 637 2.047179 GGAGACAACGTGCTCCCC 60.047 66.667 17.20 0.20 43.91 4.81
648 649 3.259625 AGAAAGCACTCTAACTGGGAGAC 59.740 47.826 0.00 0.00 35.10 3.36
656 657 7.066505 CGAAGAGAAAAAGAAAGCACTCTAAC 58.933 38.462 0.00 0.00 34.33 2.34
660 661 4.777823 CCGAAGAGAAAAAGAAAGCACTC 58.222 43.478 0.00 0.00 0.00 3.51
664 665 3.500299 AGAGCCGAAGAGAAAAAGAAAGC 59.500 43.478 0.00 0.00 0.00 3.51
827 842 1.078497 CAGCGTCAGTGGCCCATAA 60.078 57.895 0.00 0.00 0.00 1.90
848 863 3.069443 TGGAAAAATTGGTCTGGCTTGAC 59.931 43.478 3.28 3.28 36.31 3.18
858 873 3.181470 CCGTCAACCTTGGAAAAATTGGT 60.181 43.478 0.00 0.00 0.00 3.67
860 875 4.314740 TCCGTCAACCTTGGAAAAATTG 57.685 40.909 0.00 0.00 0.00 2.32
882 897 2.158623 TGTTGATGGTCAAAGTCTGCCT 60.159 45.455 0.00 0.00 38.22 4.75
899 914 2.224066 ACGGTCTTGGAGACTCTTGTTG 60.224 50.000 1.74 0.00 44.46 3.33
903 918 1.258676 GGACGGTCTTGGAGACTCTT 58.741 55.000 8.23 0.00 44.46 2.85
946 972 5.298197 TCTCTAGCTGCATAGTATAACGC 57.702 43.478 1.02 0.00 0.00 4.84
967 999 1.005156 GCTCCATGATCCTCCGCTC 60.005 63.158 0.00 0.00 0.00 5.03
968 1000 2.865598 CGCTCCATGATCCTCCGCT 61.866 63.158 0.00 0.00 0.00 5.52
969 1001 2.356793 CGCTCCATGATCCTCCGC 60.357 66.667 0.00 0.00 0.00 5.54
970 1002 2.356793 GCGCTCCATGATCCTCCG 60.357 66.667 0.00 0.00 0.00 4.63
971 1003 1.005156 GAGCGCTCCATGATCCTCC 60.005 63.158 27.22 0.00 0.00 4.30
1007 1060 3.953775 CCAGGAGGGCAACACCGT 61.954 66.667 0.00 0.00 40.62 4.83
1026 1079 1.399791 GCTAACCAACAGCAGATGAGC 59.600 52.381 0.00 0.00 38.93 4.26
1081 1134 1.645034 GCAACTGAGCTGCGAATAGA 58.355 50.000 0.00 0.00 0.00 1.98
1108 1161 9.832445 CATGTATCATCATCAATCATCATCCTA 57.168 33.333 0.00 0.00 0.00 2.94
1109 1162 7.283354 GCATGTATCATCATCAATCATCATCCT 59.717 37.037 0.00 0.00 0.00 3.24
1124 1177 3.002656 CCGGAACAACTGCATGTATCATC 59.997 47.826 0.00 0.00 32.02 2.92
1125 1178 2.945008 CCGGAACAACTGCATGTATCAT 59.055 45.455 0.00 0.00 32.02 2.45
1126 1179 2.027653 TCCGGAACAACTGCATGTATCA 60.028 45.455 0.00 0.00 32.02 2.15
1187 1240 2.448931 ACCGGGTTCTGGTTCCCA 60.449 61.111 6.32 0.00 43.57 4.37
1217 1270 2.434185 GGTGGCGACGCAATCTCA 60.434 61.111 23.09 6.92 44.70 3.27
1303 1356 2.868583 GCGACAGTGCTTCATACATGAT 59.131 45.455 0.00 0.00 36.56 2.45
1466 1699 8.946085 TCCTTTAGCTATTCAATGTGTACAAAG 58.054 33.333 0.00 0.00 0.00 2.77
1625 1859 2.145905 GCGCGTGCGAATTTCCTTG 61.146 57.895 19.66 0.00 42.83 3.61
1693 1929 5.924475 AACAAGCACATGAGTTACTGTAC 57.076 39.130 0.00 0.00 0.00 2.90
1792 2034 2.350522 CATCAAGAGCCGTGCTAGTTT 58.649 47.619 0.00 0.00 39.88 2.66
1804 2046 4.488126 TTTTCCGACTTTGCATCAAGAG 57.512 40.909 5.15 0.00 0.00 2.85
1831 2073 5.046159 CCATGTAGGTGTACCCTCTAACAAA 60.046 44.000 6.21 0.00 44.81 2.83
1887 2151 5.398603 TGTGCCTGTTACCAAAAATATGG 57.601 39.130 0.00 0.00 46.38 2.74
1934 2198 6.669631 TCCCCTGTCCCTCTTTTATATTTTC 58.330 40.000 0.00 0.00 0.00 2.29
1968 2233 3.339253 TGGTCACGCAGTACTAGTAGA 57.661 47.619 1.87 0.00 41.61 2.59
2046 2312 9.265901 GCATATTGAGTATGACTTGTTATGAGT 57.734 33.333 0.00 0.00 42.34 3.41
2093 2361 6.653320 TGTTTTGCTGTATTTATCTCTCGGTT 59.347 34.615 0.00 0.00 0.00 4.44
2202 2470 5.696724 CCCGTGGTAGAGTTGATTGAATATC 59.303 44.000 0.00 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.