Multiple sequence alignment - TraesCS1D01G294700

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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 TraesCS1D01G294700 chr1D 100.000 5849 0 0 1 5849 393769720 393775568 0.000000e+00 10802.0
1 TraesCS1D01G294700 chr1D 92.653 490 33 3 5362 5849 115072785 115072297 0.000000e+00 702.0
2 TraesCS1D01G294700 chr1D 98.182 55 1 0 504 558 393770174 393770228 4.820000e-16 97.1
3 TraesCS1D01G294700 chr1D 98.182 55 1 0 455 509 393770223 393770277 4.820000e-16 97.1
4 TraesCS1D01G294700 chr1B 98.579 3729 47 4 1644 5372 529211348 529207626 0.000000e+00 6588.0
5 TraesCS1D01G294700 chr1B 95.333 857 30 3 790 1643 529212321 529211472 0.000000e+00 1352.0
6 TraesCS1D01G294700 chr1B 94.908 491 21 4 5362 5849 529206739 529206250 0.000000e+00 765.0
7 TraesCS1D01G294700 chr1B 90.730 507 30 11 13 509 529213086 529212587 0.000000e+00 660.0
8 TraesCS1D01G294700 chr1B 91.329 346 11 8 504 839 529212641 529212305 6.910000e-124 455.0
9 TraesCS1D01G294700 chr1B 100.000 28 0 0 90 117 506175777 506175750 1.100000e-02 52.8
10 TraesCS1D01G294700 chr1A 89.905 2932 188 50 2108 4983 491649779 491646900 0.000000e+00 3675.0
11 TraesCS1D01G294700 chr1A 97.742 1993 42 3 3374 5364 491987511 491985520 0.000000e+00 3428.0
12 TraesCS1D01G294700 chr1A 97.065 1397 26 7 1644 3036 491990045 491988660 0.000000e+00 2338.0
13 TraesCS1D01G294700 chr1A 94.038 738 35 5 911 1643 491990902 491990169 0.000000e+00 1110.0
14 TraesCS1D01G294700 chr1A 93.204 618 34 2 1034 1643 491651547 491650930 0.000000e+00 902.0
15 TraesCS1D01G294700 chr1A 93.519 432 25 2 1644 2075 491650782 491650354 1.780000e-179 640.0
16 TraesCS1D01G294700 chr1A 97.554 368 9 0 3021 3388 491988645 491988278 1.070000e-176 630.0
17 TraesCS1D01G294700 chr1A 91.542 201 12 2 5024 5219 491646815 491646615 7.470000e-69 272.0
18 TraesCS1D01G294700 chr1A 88.144 194 18 5 504 693 491991354 491991162 5.900000e-55 226.0
19 TraesCS1D01G294700 chr1A 80.556 144 19 8 294 435 541981830 541981694 1.040000e-17 102.0
20 TraesCS1D01G294700 chr1A 79.032 124 17 7 3415 3533 29994267 29994386 6.290000e-10 76.8
21 TraesCS1D01G294700 chr1A 84.416 77 4 1 680 756 491991147 491991079 1.050000e-07 69.4
22 TraesCS1D01G294700 chr3B 89.778 1399 113 12 2618 4000 785505904 785504520 0.000000e+00 1764.0
23 TraesCS1D01G294700 chr3B 94.822 309 14 2 4095 4401 785504494 785504186 1.140000e-131 481.0
24 TraesCS1D01G294700 chr3B 95.113 266 11 2 4137 4401 785505900 785506164 9.070000e-113 418.0
25 TraesCS1D01G294700 chr3B 77.642 246 40 11 152 389 753873166 753873404 1.020000e-27 135.0
26 TraesCS1D01G294700 chr3B 90.385 52 5 0 74 125 187439942 187439993 1.050000e-07 69.4
27 TraesCS1D01G294700 chr5A 91.633 490 38 3 5362 5849 162382796 162382308 0.000000e+00 675.0
28 TraesCS1D01G294700 chr5A 90.612 490 42 4 5362 5849 162417418 162416931 0.000000e+00 647.0
29 TraesCS1D01G294700 chr5A 90.426 94 9 0 270 363 578048659 578048752 2.210000e-24 124.0
30 TraesCS1D01G294700 chr7D 91.020 490 40 4 5362 5849 289710955 289711442 0.000000e+00 658.0
31 TraesCS1D01G294700 chr7D 90.428 491 43 4 5362 5849 323861818 323862307 1.370000e-180 643.0
32 TraesCS1D01G294700 chr7D 78.235 170 22 11 74 234 160627258 160627421 1.740000e-15 95.3
33 TraesCS1D01G294700 chr6D 90.612 490 43 3 5362 5849 307677003 307676515 0.000000e+00 647.0
34 TraesCS1D01G294700 chr6D 90.184 489 44 4 5364 5849 392027188 392026701 8.270000e-178 634.0
35 TraesCS1D01G294700 chr3D 90.224 491 44 4 5362 5849 100237487 100237976 6.390000e-179 638.0
36 TraesCS1D01G294700 chr3D 75.000 236 49 6 155 387 699537 699765 3.730000e-17 100.0
37 TraesCS1D01G294700 chr3D 92.308 52 4 0 74 125 130942068 130942119 2.260000e-09 75.0
38 TraesCS1D01G294700 chr5B 83.893 149 19 5 293 438 563123503 563123649 2.840000e-28 137.0
39 TraesCS1D01G294700 chr5D 90.722 97 8 1 270 366 459067729 459067824 1.710000e-25 128.0
40 TraesCS1D01G294700 chr4D 83.108 148 15 6 274 416 499388303 499388161 6.150000e-25 126.0
41 TraesCS1D01G294700 chr2D 82.759 145 16 5 280 417 2766524 2766382 2.860000e-23 121.0
42 TraesCS1D01G294700 chr7B 79.070 172 23 10 74 238 121873576 121873741 8.020000e-19 106.0
43 TraesCS1D01G294700 chr6A 97.368 38 1 0 73 110 475097707 475097670 1.360000e-06 65.8


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 TraesCS1D01G294700 chr1D 393769720 393775568 5848 False 10802.000000 10802 100.000000 1 5849 1 chr1D.!!$F1 5848
1 TraesCS1D01G294700 chr1B 529206250 529213086 6836 True 1964.000000 6588 94.175800 13 5849 5 chr1B.!!$R2 5836
2 TraesCS1D01G294700 chr1A 491646615 491651547 4932 True 1372.250000 3675 92.042500 1034 5219 4 chr1A.!!$R2 4185
3 TraesCS1D01G294700 chr1A 491985520 491991354 5834 True 1300.233333 3428 93.159833 504 5364 6 chr1A.!!$R3 4860
4 TraesCS1D01G294700 chr3B 785504186 785505904 1718 True 1122.500000 1764 92.300000 2618 4401 2 chr3B.!!$R1 1783

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
75 76 0.173708 TGTATGTGCGTACATGCCGA 59.826 50.000 26.72 9.69 46.63 5.54 F
97 98 0.801836 GTGCTCTTCTCAGCTCGAGC 60.802 60.000 30.01 30.01 46.74 5.03 F
929 1089 1.006832 CTCCCAAATGCCGAACGTAG 58.993 55.000 0.00 0.00 0.00 3.51 F
1284 1450 1.732259 GTGTTGATTGGTCAGGCGTAG 59.268 52.381 0.00 0.00 35.39 3.51 F
1311 1477 2.203070 ATGGCGGCGGAAGACATC 60.203 61.111 9.78 0.00 41.50 3.06 F
1594 1770 5.721876 TCAAGCAAAAACAGCTGAAATTG 57.278 34.783 23.35 20.46 42.53 2.32 F
3079 3989 5.685841 TGTCGAAATTCGTTTGATCTTTCC 58.314 37.500 15.34 0.00 41.35 3.13 F
3525 5221 5.066593 GTCAAACTCTCAATGAGGAGGTTT 58.933 41.667 10.71 14.78 46.72 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 1477 0.318441 TCTCCAACTCCAGTCTTGCG 59.682 55.000 0.0 0.0 0.00 4.85 R
1594 1770 6.508777 TGCAATACTTGGTTAAACCTGTTTC 58.491 36.000 0.0 0.0 39.58 2.78 R
2366 3242 3.060272 GTGATGCAATAATCGGACTCGTG 60.060 47.826 0.0 0.0 37.69 4.35 R
2975 3855 5.425217 TGAGACTATCAGAAATGTAAGCCCA 59.575 40.000 0.0 0.0 32.77 5.36 R
3079 3989 6.234177 ACTGTTTAGTCCCTGATGAAAGAAG 58.766 40.000 0.0 0.0 28.79 2.85 R
3183 4096 7.713518 ACCTCTATCTATCCAGATCAATGGTA 58.286 38.462 0.0 0.0 40.81 3.25 R
4477 6209 0.322098 CAGGACCCGCCAACAATACA 60.322 55.000 0.0 0.0 40.02 2.29 R
5380 8090 0.250081 GTGATCGAGGCCCCTTCATC 60.250 60.000 0.0 0.0 0.00 2.92 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
56 57 8.095169 ACGAGGTAAAACTCTTCAAGATACATT 58.905 33.333 0.00 0.00 35.33 2.71
72 73 3.673746 ACATTGTATGTGCGTACATGC 57.326 42.857 26.72 25.18 46.63 4.06
75 76 0.173708 TGTATGTGCGTACATGCCGA 59.826 50.000 26.72 9.69 46.63 5.54
90 91 1.074752 GCCGAAAGTGCTCTTCTCAG 58.925 55.000 0.74 0.00 32.90 3.35
97 98 0.801836 GTGCTCTTCTCAGCTCGAGC 60.802 60.000 30.01 30.01 46.74 5.03
125 126 4.755411 TGAGCTCGGGTGAATAGTAAAAG 58.245 43.478 9.64 0.00 0.00 2.27
206 208 2.079170 TGCAAAGTTTCACCATGGGA 57.921 45.000 18.09 7.80 0.00 4.37
215 217 5.065914 AGTTTCACCATGGGATGATATTCG 58.934 41.667 18.09 0.00 0.00 3.34
238 240 6.872670 GTGGAATACGTGACAAAAACAAAA 57.127 33.333 0.00 0.00 0.00 2.44
239 241 7.279470 GTGGAATACGTGACAAAAACAAAAA 57.721 32.000 0.00 0.00 0.00 1.94
240 242 7.387945 GTGGAATACGTGACAAAAACAAAAAG 58.612 34.615 0.00 0.00 0.00 2.27
258 260 6.207810 ACAAAAAGCAAAATGGATGCATCAAT 59.792 30.769 27.25 19.74 46.22 2.57
287 289 5.643379 TGAAATAACATTGTTGGAGCCTC 57.357 39.130 12.30 1.73 0.00 4.70
291 293 3.627395 AACATTGTTGGAGCCTCGATA 57.373 42.857 0.15 0.00 0.00 2.92
317 321 1.203038 TGCCATGTCTCCCACAAATGT 60.203 47.619 0.00 0.00 38.97 2.71
322 326 4.267536 CATGTCTCCCACAAATGTCATCT 58.732 43.478 0.00 0.00 38.97 2.90
363 367 8.231837 GCAAGCAATCAAAACATTTGTCAATAT 58.768 29.630 3.06 0.00 0.00 1.28
375 379 9.500864 AACATTTGTCAATATTTGCAACAAAAC 57.499 25.926 12.99 2.74 39.34 2.43
422 432 2.835701 TTCACCCGAGCTCGCATGAC 62.836 60.000 29.34 0.00 38.18 3.06
483 494 6.438425 ACTGAAAAATGGAAATACATCTGCCT 59.562 34.615 0.00 0.00 0.00 4.75
484 495 6.632909 TGAAAAATGGAAATACATCTGCCTG 58.367 36.000 0.00 0.00 0.00 4.85
485 496 4.660789 AAATGGAAATACATCTGCCTGC 57.339 40.909 0.00 0.00 0.00 4.85
486 497 1.667236 TGGAAATACATCTGCCTGCG 58.333 50.000 0.00 0.00 0.00 5.18
487 498 1.209261 TGGAAATACATCTGCCTGCGA 59.791 47.619 0.00 0.00 0.00 5.10
488 499 1.599542 GGAAATACATCTGCCTGCGAC 59.400 52.381 0.00 0.00 0.00 5.19
489 500 2.555199 GAAATACATCTGCCTGCGACT 58.445 47.619 0.00 0.00 0.00 4.18
490 501 3.492656 GGAAATACATCTGCCTGCGACTA 60.493 47.826 0.00 0.00 0.00 2.59
491 502 3.377346 AATACATCTGCCTGCGACTAG 57.623 47.619 0.00 0.00 0.00 2.57
530 541 9.638239 TTAACTGAAAAATGGAAATACATCTGC 57.362 29.630 0.00 0.00 0.00 4.26
531 542 6.633856 ACTGAAAAATGGAAATACATCTGCC 58.366 36.000 0.00 0.00 0.00 4.85
533 544 4.654091 AAAATGGAAATACATCTGCCCG 57.346 40.909 0.00 0.00 0.00 6.13
543 554 2.427245 ATCTGCCCGCGACTAGCTT 61.427 57.895 8.23 0.00 45.59 3.74
723 768 2.158900 AGCAGGATCCACGATTTACTGG 60.159 50.000 15.82 0.00 0.00 4.00
724 769 2.213499 CAGGATCCACGATTTACTGGC 58.787 52.381 15.82 0.00 0.00 4.85
725 770 1.837439 AGGATCCACGATTTACTGGCA 59.163 47.619 15.82 0.00 0.00 4.92
726 771 2.158900 AGGATCCACGATTTACTGGCAG 60.159 50.000 15.82 14.16 0.00 4.85
727 772 2.420129 GGATCCACGATTTACTGGCAGT 60.420 50.000 25.34 25.34 0.00 4.40
728 773 2.380084 TCCACGATTTACTGGCAGTC 57.620 50.000 25.80 8.81 0.00 3.51
729 774 1.899814 TCCACGATTTACTGGCAGTCT 59.100 47.619 25.80 10.30 0.00 3.24
730 775 2.002586 CCACGATTTACTGGCAGTCTG 58.997 52.381 25.80 12.60 0.00 3.51
813 950 1.947456 GTCAGCCCGTTTCAAAGACTT 59.053 47.619 0.00 0.00 0.00 3.01
875 1012 7.622713 CCTCTCATCAGGCTAAATAATCATCT 58.377 38.462 0.00 0.00 0.00 2.90
890 1027 1.948834 TCATCTGTTTGCGCCATATGG 59.051 47.619 18.07 18.07 38.53 2.74
891 1028 1.677576 CATCTGTTTGCGCCATATGGT 59.322 47.619 22.79 0.00 37.57 3.55
929 1089 1.006832 CTCCCAAATGCCGAACGTAG 58.993 55.000 0.00 0.00 0.00 3.51
1146 1312 4.809193 TGAATCAGGTACTAGAGGAGCAT 58.191 43.478 0.00 0.00 36.02 3.79
1150 1316 4.082845 TCAGGTACTAGAGGAGCATATGC 58.917 47.826 20.36 20.36 36.02 3.14
1284 1450 1.732259 GTGTTGATTGGTCAGGCGTAG 59.268 52.381 0.00 0.00 35.39 3.51
1311 1477 2.203070 ATGGCGGCGGAAGACATC 60.203 61.111 9.78 0.00 41.50 3.06
1594 1770 5.721876 TCAAGCAAAAACAGCTGAAATTG 57.278 34.783 23.35 20.46 42.53 2.32
3079 3989 5.685841 TGTCGAAATTCGTTTGATCTTTCC 58.314 37.500 15.34 0.00 41.35 3.13
3525 5221 5.066593 GTCAAACTCTCAATGAGGAGGTTT 58.933 41.667 10.71 14.78 46.72 3.27
3670 5367 8.758829 TCACAACCTCTAGTATGTGTTTGATAT 58.241 33.333 14.70 0.00 42.80 1.63
4201 5933 5.776208 TGTTGCATGCAGGATCCATATTTAT 59.224 36.000 21.50 0.00 0.00 1.40
4704 6436 1.078918 CAGCCAGCAGATTGACCGA 60.079 57.895 0.00 0.00 0.00 4.69
4734 6466 6.071952 TGTTCTTTCAACCATTAGAATCTGGC 60.072 38.462 0.00 0.00 35.88 4.85
4800 6532 1.524008 CCGTTGGCTGGTCCCTTTTC 61.524 60.000 0.00 0.00 0.00 2.29
5279 7093 9.762381 AGGGTATACAAATGAACCATTCTTTTA 57.238 29.630 5.01 0.00 35.89 1.52
5412 8122 1.070376 TCGATCACGATAACTACGCGG 60.070 52.381 12.47 0.00 43.81 6.46
5445 8156 0.613260 ACAAGCGGAACTCCATAGCA 59.387 50.000 0.00 0.00 35.14 3.49
5506 8218 0.038744 TCCGTCCGGTAAGACTTCCT 59.961 55.000 0.00 0.00 34.46 3.36
5525 8237 3.689161 TCCTTGAAATCTGGCATAACACG 59.311 43.478 0.00 0.00 0.00 4.49
5572 8284 3.067883 TGCAAGCTCACAACAAGCATAAA 59.932 39.130 0.00 0.00 42.35 1.40
5578 8290 6.980593 AGCTCACAACAAGCATAAACATAAA 58.019 32.000 0.00 0.00 42.35 1.40
5579 8291 7.605449 AGCTCACAACAAGCATAAACATAAAT 58.395 30.769 0.00 0.00 42.35 1.40
5581 8293 7.201461 GCTCACAACAAGCATAAACATAAATGG 60.201 37.037 0.00 0.00 39.61 3.16
5582 8294 6.589523 TCACAACAAGCATAAACATAAATGGC 59.410 34.615 0.00 0.00 0.00 4.40
5586 8298 8.452534 CAACAAGCATAAACATAAATGGCAAAT 58.547 29.630 0.00 0.00 0.00 2.32
5635 8347 3.330267 TGCAATGCGATAACACACTACA 58.670 40.909 0.00 0.00 0.00 2.74
5636 8348 3.370672 TGCAATGCGATAACACACTACAG 59.629 43.478 0.00 0.00 0.00 2.74
5673 8385 0.684535 TTGTGCATTGAGTCCCTCGA 59.315 50.000 0.00 0.00 32.35 4.04
5715 8427 2.224354 ACCTCGTAACCAAACGGTGATT 60.224 45.455 0.00 0.00 43.05 2.57
5799 8511 7.280876 TCTCACAAATATCATCACTTAACCAGC 59.719 37.037 0.00 0.00 0.00 4.85
5802 8514 2.698855 ATCATCACTTAACCAGCGCT 57.301 45.000 2.64 2.64 0.00 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.448990 CACATGACAGGAATGCCGTG 59.551 55.000 0.00 0.00 39.96 4.94
1 2 0.677731 CCACATGACAGGAATGCCGT 60.678 55.000 0.00 0.00 39.96 5.68
2 3 0.677731 ACCACATGACAGGAATGCCG 60.678 55.000 0.00 0.00 39.96 5.69
3 4 1.474077 GAACCACATGACAGGAATGCC 59.526 52.381 0.00 0.00 0.00 4.40
4 5 1.131126 CGAACCACATGACAGGAATGC 59.869 52.381 0.00 0.00 0.00 3.56
5 6 2.674852 CTCGAACCACATGACAGGAATG 59.325 50.000 0.00 0.00 0.00 2.67
6 7 2.567169 TCTCGAACCACATGACAGGAAT 59.433 45.455 0.00 0.00 0.00 3.01
7 8 1.967779 TCTCGAACCACATGACAGGAA 59.032 47.619 0.00 0.00 0.00 3.36
8 9 1.627864 TCTCGAACCACATGACAGGA 58.372 50.000 0.00 0.00 0.00 3.86
9 10 2.029020 TCTTCTCGAACCACATGACAGG 60.029 50.000 0.00 0.35 0.00 4.00
10 11 2.989840 GTCTTCTCGAACCACATGACAG 59.010 50.000 0.00 0.00 0.00 3.51
11 12 2.607038 CGTCTTCTCGAACCACATGACA 60.607 50.000 0.00 0.00 0.00 3.58
56 57 0.173708 TCGGCATGTACGCACATACA 59.826 50.000 0.00 0.00 43.73 2.29
60 61 0.601576 ACTTTCGGCATGTACGCACA 60.602 50.000 7.01 0.00 39.52 4.57
72 73 1.074752 GCTGAGAAGAGCACTTTCGG 58.925 55.000 0.00 4.58 38.95 4.30
75 76 1.615883 TCGAGCTGAGAAGAGCACTTT 59.384 47.619 0.00 0.00 41.83 2.66
97 98 0.247460 TTCACCCGAGCTCATGTGAG 59.753 55.000 25.48 5.66 44.75 3.51
199 201 3.701205 TCCACGAATATCATCCCATGG 57.299 47.619 4.14 4.14 0.00 3.66
215 217 6.872670 TTTTGTTTTTGTCACGTATTCCAC 57.127 33.333 0.00 0.00 0.00 4.02
234 236 5.614923 TGATGCATCCATTTTGCTTTTTG 57.385 34.783 23.67 0.00 40.77 2.44
236 238 7.925993 CATATTGATGCATCCATTTTGCTTTT 58.074 30.769 23.67 0.00 40.77 2.27
237 239 7.490962 CATATTGATGCATCCATTTTGCTTT 57.509 32.000 23.67 0.00 40.77 3.51
258 260 7.545265 GCTCCAACAATGTTATTTCAAAGCATA 59.455 33.333 0.00 0.00 0.00 3.14
265 267 4.155826 CGAGGCTCCAACAATGTTATTTCA 59.844 41.667 9.32 0.00 0.00 2.69
392 402 2.350772 GCTCGGGTGAACAGTGAAATTG 60.351 50.000 0.00 0.00 0.00 2.32
398 408 1.734477 CGAGCTCGGGTGAACAGTG 60.734 63.158 28.40 0.00 35.37 3.66
422 432 5.007136 GGTTATGAAAAATCTGAGCTCGAGG 59.993 44.000 15.58 1.97 0.00 4.63
508 519 6.044682 GGGCAGATGTATTTCCATTTTTCAG 58.955 40.000 0.00 0.00 0.00 3.02
530 541 2.583593 GCTCAAGCTAGTCGCGGG 60.584 66.667 6.13 0.00 45.59 6.13
543 554 0.530744 ACGCGGTTAATCTGAGCTCA 59.469 50.000 17.19 17.19 0.00 4.26
551 562 1.616620 TGTACGTGACGCGGTTAATC 58.383 50.000 12.47 0.00 46.52 1.75
610 622 6.384258 TTGTGCATGAGTAGCTAACAAAAA 57.616 33.333 0.00 0.00 28.79 1.94
682 727 7.942341 TCCTGCTCTAAAAAGGAAAAGTAATCA 59.058 33.333 0.00 0.00 37.16 2.57
694 739 3.861840 TCGTGGATCCTGCTCTAAAAAG 58.138 45.455 14.23 0.00 0.00 2.27
723 768 0.674895 ATTTCCTCGTGCCAGACTGC 60.675 55.000 0.00 0.00 0.00 4.40
724 769 1.338105 TGATTTCCTCGTGCCAGACTG 60.338 52.381 0.00 0.00 0.00 3.51
725 770 0.976641 TGATTTCCTCGTGCCAGACT 59.023 50.000 0.00 0.00 0.00 3.24
726 771 1.734465 CTTGATTTCCTCGTGCCAGAC 59.266 52.381 0.00 0.00 0.00 3.51
727 772 1.623311 TCTTGATTTCCTCGTGCCAGA 59.377 47.619 0.00 0.00 0.00 3.86
728 773 2.005451 CTCTTGATTTCCTCGTGCCAG 58.995 52.381 0.00 0.00 0.00 4.85
729 774 1.623311 TCTCTTGATTTCCTCGTGCCA 59.377 47.619 0.00 0.00 0.00 4.92
730 775 2.093973 TCTCTCTTGATTTCCTCGTGCC 60.094 50.000 0.00 0.00 0.00 5.01
813 950 1.065709 GGGCCGACATGAGGTTTCTTA 60.066 52.381 0.00 0.00 0.00 2.10
872 1009 1.677576 CACCATATGGCGCAAACAGAT 59.322 47.619 22.18 0.00 39.32 2.90
875 1012 1.761449 ATCACCATATGGCGCAAACA 58.239 45.000 22.18 0.00 39.32 2.83
890 1027 0.391661 TTGAGAGGCTCGCCAATCAC 60.392 55.000 15.82 0.00 38.92 3.06
891 1028 0.391661 GTTGAGAGGCTCGCCAATCA 60.392 55.000 21.77 12.47 38.92 2.57
892 1029 0.107945 AGTTGAGAGGCTCGCCAATC 60.108 55.000 21.77 16.56 38.92 2.67
893 1030 0.107945 GAGTTGAGAGGCTCGCCAAT 60.108 55.000 21.77 9.83 38.92 3.16
894 1031 1.293498 GAGTTGAGAGGCTCGCCAA 59.707 57.895 15.82 16.67 38.92 4.52
895 1032 2.650116 GGAGTTGAGAGGCTCGCCA 61.650 63.158 15.82 11.71 38.92 5.69
929 1089 1.398692 CTGACCTAGACTCCTCTGGC 58.601 60.000 0.00 0.00 0.00 4.85
997 1160 2.584608 CGAACCCGCCTCCATCTT 59.415 61.111 0.00 0.00 0.00 2.40
1055 1218 3.733883 TCTTCCTCGAGGTTCTCCTAA 57.266 47.619 30.17 14.58 45.24 2.69
1146 1312 4.127744 GCCACCAGCCCCTGCATA 62.128 66.667 0.00 0.00 41.13 3.14
1284 1450 1.961277 CGCCGCCATCTTATCCACC 60.961 63.158 0.00 0.00 0.00 4.61
1311 1477 0.318441 TCTCCAACTCCAGTCTTGCG 59.682 55.000 0.00 0.00 0.00 4.85
1594 1770 6.508777 TGCAATACTTGGTTAAACCTGTTTC 58.491 36.000 0.00 0.00 39.58 2.78
2121 2986 7.802720 AGCGATTTAATTGAAAAATGCAAAACC 59.197 29.630 0.00 0.00 0.00 3.27
2265 3131 9.814899 CATATGTGGCCAAAAATATGAAACTAA 57.185 29.630 26.09 1.16 35.80 2.24
2366 3242 3.060272 GTGATGCAATAATCGGACTCGTG 60.060 47.826 0.00 0.00 37.69 4.35
2975 3855 5.425217 TGAGACTATCAGAAATGTAAGCCCA 59.575 40.000 0.00 0.00 32.77 5.36
3079 3989 6.234177 ACTGTTTAGTCCCTGATGAAAGAAG 58.766 40.000 0.00 0.00 28.79 2.85
3183 4096 7.713518 ACCTCTATCTATCCAGATCAATGGTA 58.286 38.462 0.00 0.00 40.81 3.25
4477 6209 0.322098 CAGGACCCGCCAACAATACA 60.322 55.000 0.00 0.00 40.02 2.29
4704 6436 6.187727 TCTAATGGTTGAAAGAACACCTCT 57.812 37.500 0.00 0.00 35.13 3.69
4734 6466 4.878774 AGCGAACGAGAGCTTCTG 57.121 55.556 0.00 0.00 41.52 3.02
4800 6532 3.463944 GTCAGTGGGATAACATAACGGG 58.536 50.000 0.00 0.00 0.00 5.28
4845 6577 0.605589 GCAGCTACTATCCGCCTCAT 59.394 55.000 0.00 0.00 0.00 2.90
5279 7093 3.073062 ACATAAGGAAGTGCAAGACCAGT 59.927 43.478 0.00 0.00 0.00 4.00
5380 8090 0.250081 GTGATCGAGGCCCCTTCATC 60.250 60.000 0.00 0.00 0.00 2.92
5419 8129 1.606350 GAGTTCCGCTTGTCGTCGTG 61.606 60.000 0.00 0.00 36.19 4.35
5445 8156 1.535444 TCCACATCGGTGTCCCTGT 60.535 57.895 0.00 0.00 43.71 4.00
5506 8218 3.485947 GCGTGTTATGCCAGATTTCAA 57.514 42.857 0.00 0.00 0.00 2.69
5549 8261 0.382873 TGCTTGTTGTGAGCTTGCAG 59.617 50.000 0.00 0.00 40.75 4.41
5609 8321 5.572211 AGTGTGTTATCGCATTGCATTTAG 58.428 37.500 9.69 0.00 36.45 1.85
5635 8347 5.526115 CACAAGTTTGATTTCACTGCATCT 58.474 37.500 0.00 0.00 0.00 2.90
5636 8348 4.149396 GCACAAGTTTGATTTCACTGCATC 59.851 41.667 0.00 0.00 0.00 3.91
5715 8427 0.537653 TCGTTTGTGATCCGGGCATA 59.462 50.000 0.00 0.00 0.00 3.14
5751 8463 4.470334 TCATGAAGATGATCGTTGTGGA 57.530 40.909 0.00 0.00 33.40 4.02
5782 8494 3.819564 AGCGCTGGTTAAGTGATGATA 57.180 42.857 10.39 0.00 38.83 2.15
5802 8514 9.743057 ATTTTGCACGCTAAATTTATATGCTTA 57.257 25.926 20.36 11.45 29.78 3.09


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

AutoCloner maintained by Alex Coulton.