Multiple sequence alignment - TraesCS6A01G176900

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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 TraesCS6A01G176900 chr6A 100.000 8614 0 0 1 8614 196185964 196194577 0.000000e+00 15908.0
1 TraesCS6A01G176900 chr6B 96.050 5493 153 26 2522 7987 274211508 274206053 0.000000e+00 8883.0
2 TraesCS6A01G176900 chr6B 96.801 1344 30 7 1205 2536 274213560 274212218 0.000000e+00 2231.0
3 TraesCS6A01G176900 chr6B 96.603 1148 31 5 3 1149 274214721 274213581 0.000000e+00 1897.0
4 TraesCS6A01G176900 chr6B 95.000 120 6 0 8495 8614 274205837 274205718 1.140000e-43 189.0
5 TraesCS6A01G176900 chr6B 97.436 78 2 0 8023 8100 274205960 274205883 5.420000e-27 134.0
6 TraesCS6A01G176900 chr6B 100.000 33 0 0 7985 8017 274206040 274206008 2.600000e-05 62.1
7 TraesCS6A01G176900 chr6B 94.595 37 2 0 6846 6882 274207163 274207127 3.360000e-04 58.4
8 TraesCS6A01G176900 chr6D 96.655 4693 130 11 3315 7987 149731231 149726546 0.000000e+00 7771.0
9 TraesCS6A01G176900 chr6D 96.621 3285 78 14 14 3277 149734503 149731231 0.000000e+00 5421.0
10 TraesCS6A01G176900 chr6D 91.456 316 24 3 8023 8337 149726462 149726149 1.720000e-116 431.0
11 TraesCS6A01G176900 chr6D 94.565 276 13 1 8339 8614 149726098 149725825 7.990000e-115 425.0
12 TraesCS6A01G176900 chr6D 97.297 37 1 0 6846 6882 149727661 149727625 7.220000e-06 63.9
13 TraesCS6A01G176900 chr2D 86.567 268 30 5 1884 2150 535222759 535222497 3.040000e-74 291.0
14 TraesCS6A01G176900 chr2D 83.704 270 38 5 1884 2152 635873095 635873359 5.160000e-62 250.0
15 TraesCS6A01G176900 chr2D 85.106 94 13 1 8100 8192 429468245 429468338 2.560000e-15 95.3
16 TraesCS6A01G176900 chr3B 86.590 261 29 4 1884 2143 351995111 351995366 5.090000e-72 283.0
17 TraesCS6A01G176900 chr3B 84.470 264 35 5 1884 2146 344948750 344949008 1.110000e-63 255.0
18 TraesCS6A01G176900 chr3B 85.714 91 12 1 8100 8189 327059380 327059290 2.560000e-15 95.3
19 TraesCS6A01G176900 chr1A 85.827 254 31 4 1884 2136 531220943 531221192 1.840000e-66 265.0
20 TraesCS6A01G176900 chr1A 86.139 101 12 2 8091 8189 447120746 447120646 3.290000e-19 108.0
21 TraesCS6A01G176900 chr1A 80.734 109 17 4 8086 8190 584510968 584511076 1.990000e-11 82.4
22 TraesCS6A01G176900 chr1B 84.906 265 34 5 1883 2146 629066074 629065815 6.630000e-66 263.0
23 TraesCS6A01G176900 chr4D 84.470 264 35 5 1884 2146 506872335 506872077 1.110000e-63 255.0
24 TraesCS6A01G176900 chr5D 86.316 95 12 1 8100 8193 256747562 256747468 1.530000e-17 102.0
25 TraesCS6A01G176900 chr5D 86.022 93 8 5 8100 8189 490024190 490024100 2.560000e-15 95.3
26 TraesCS6A01G176900 chr2B 86.813 91 11 1 8100 8189 113599116 113599206 5.500000e-17 100.0
27 TraesCS6A01G176900 chr7D 84.783 92 13 1 8103 8193 621305192 621305101 3.310000e-14 91.6


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 TraesCS6A01G176900 chr6A 196185964 196194577 8613 False 15908.000 15908 100.0000 1 8614 1 chr6A.!!$F1 8613
1 TraesCS6A01G176900 chr6B 274205718 274211508 5790 True 2317.025 8883 97.1215 2522 8614 4 chr6B.!!$R2 6092
2 TraesCS6A01G176900 chr6B 274212218 274214721 2503 True 2064.000 2231 96.7020 3 2536 2 chr6B.!!$R3 2533
3 TraesCS6A01G176900 chr6D 149725825 149734503 8678 True 2822.380 7771 95.3188 14 8614 5 chr6D.!!$R1 8600

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
521 524 1.146774 TGATTGGTTCCCAGGCAAAGA 59.853 47.619 0.00 0.0 33.81 2.52 F
2257 2280 0.033920 CTTGCTTTTTCCAGGGTGGC 59.966 55.000 0.00 0.0 37.47 5.01 F
3522 3545 0.969917 TGCTTGTTGGGTGCACTTGT 60.970 50.000 17.98 0.0 0.00 3.16 F
4383 4412 0.917333 TGGTAAAGGCCGGGGATCTT 60.917 55.000 2.18 0.0 0.00 2.40 F
5723 5754 1.209504 CTGAAAGGAAGGCCGGTATCA 59.790 52.381 1.90 0.0 39.96 2.15 F
6811 6842 1.207089 CCAAGACGATACAGAAGCCCA 59.793 52.381 0.00 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2412 2435 0.386476 AGTACCGACGCAGAAACACA 59.614 50.000 0.0 0.0 0.00 3.72 R
4174 4203 2.162208 CGAAAATATGGGGATCATGCCG 59.838 50.000 0.0 0.0 37.30 5.69 R
5521 5552 1.620819 AGGCAGTGAGTAGTTGACAGG 59.379 52.381 0.0 0.0 0.00 4.00 R
6285 6316 0.250989 TCCGGCTAAAACCCTTGTGG 60.251 55.000 0.0 0.0 41.37 4.17 R
7261 7305 0.739561 GTACCTGCTAGACCTCCACG 59.260 60.000 0.0 0.0 0.00 4.94 R
8532 8690 0.178967 TGTTGCAAGCCCCATCTTCA 60.179 50.000 0.0 0.0 0.00 3.02 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
63 64 2.592308 GGCAGCCCGAATCTCCTT 59.408 61.111 0.00 0.00 0.00 3.36
282 285 1.904378 GGCGGGTTTTAGGGTTGCA 60.904 57.895 0.00 0.00 0.00 4.08
319 322 2.367512 ATCTGGGTGAGGGGGAGC 60.368 66.667 0.00 0.00 0.00 4.70
521 524 1.146774 TGATTGGTTCCCAGGCAAAGA 59.853 47.619 0.00 0.00 33.81 2.52
528 531 3.291611 CCAGGCAAAGACATGGGC 58.708 61.111 0.00 0.00 37.85 5.36
557 561 4.558496 GCGTTTCTTGATGGTTGATTTGGA 60.558 41.667 0.00 0.00 0.00 3.53
627 631 4.764823 TGAACGGTAAAATCTGGCTTTCAT 59.235 37.500 0.00 0.00 0.00 2.57
705 709 6.725369 TGCTATGGAACCAATGCCATTTATAT 59.275 34.615 14.87 0.00 42.03 0.86
856 860 4.096682 GGTTTACTTACTTGGTTGTGTGCA 59.903 41.667 0.00 0.00 0.00 4.57
877 881 2.353323 TCTGCATGACTGATTGACTGC 58.647 47.619 0.00 0.00 0.00 4.40
946 950 9.295825 CCCTATTTTTGTCTGCACCATTATATA 57.704 33.333 0.00 0.00 0.00 0.86
1183 1192 4.521146 CTGTGCCCTCAGATTTATCAAGT 58.479 43.478 0.00 0.00 37.61 3.16
1186 1195 4.574013 GTGCCCTCAGATTTATCAAGTCTG 59.426 45.833 5.36 5.36 40.48 3.51
1332 1341 4.757149 GGTGAATAGATACAAGTGCCATCC 59.243 45.833 0.00 0.00 0.00 3.51
1344 1353 1.377987 GCCATCCGTGCCCAAGTTA 60.378 57.895 0.00 0.00 0.00 2.24
1345 1354 1.654023 GCCATCCGTGCCCAAGTTAC 61.654 60.000 0.00 0.00 0.00 2.50
1346 1355 0.035439 CCATCCGTGCCCAAGTTACT 60.035 55.000 0.00 0.00 0.00 2.24
1347 1356 1.613255 CCATCCGTGCCCAAGTTACTT 60.613 52.381 0.00 0.00 0.00 2.24
1348 1357 1.468520 CATCCGTGCCCAAGTTACTTG 59.531 52.381 17.37 17.37 40.75 3.16
1351 1360 1.588674 CGTGCCCAAGTTACTTGTGA 58.411 50.000 21.63 4.43 39.58 3.58
1352 1361 1.263217 CGTGCCCAAGTTACTTGTGAC 59.737 52.381 21.63 13.94 39.58 3.67
1374 1387 5.906073 ACTGTGAAAAATTAGCTGCAGTTT 58.094 33.333 16.64 6.51 32.84 2.66
1401 1414 8.626526 TGGTTTAGAAGGTTTATTGTGAACTTC 58.373 33.333 0.00 0.00 0.00 3.01
1515 1528 0.844661 TGTTGTCCTAGGGCCCACAT 60.845 55.000 27.56 5.74 0.00 3.21
1997 2014 9.295825 TGGATTGAACATGTATAAATGGTATCC 57.704 33.333 13.07 13.07 31.63 2.59
2004 2021 9.871238 AACATGTATAAATGGTATCCTCGTATC 57.129 33.333 7.81 0.00 31.46 2.24
2257 2280 0.033920 CTTGCTTTTTCCAGGGTGGC 59.966 55.000 0.00 0.00 37.47 5.01
2369 2392 1.915489 TGCACAAGACCCTACCATCAT 59.085 47.619 0.00 0.00 0.00 2.45
2374 2397 5.300752 CACAAGACCCTACCATCATATGAC 58.699 45.833 7.78 0.00 0.00 3.06
2377 2400 4.832492 AGACCCTACCATCATATGACCTT 58.168 43.478 7.78 0.00 0.00 3.50
2473 2496 4.978186 CAAGTATGCACAAGATGGTTGAG 58.022 43.478 0.00 0.00 0.00 3.02
2592 2615 6.486993 AGGGAAAGAGTTTCATAACAGTTCAC 59.513 38.462 0.00 0.00 41.43 3.18
2875 2898 6.765403 TGCTAGTTGTAGACACACCTAAAAT 58.235 36.000 0.00 0.00 30.22 1.82
3158 3181 2.722094 AGGTTTCAGACTTGCACAACA 58.278 42.857 0.00 0.00 0.00 3.33
3161 3184 4.275936 AGGTTTCAGACTTGCACAACATAC 59.724 41.667 0.00 0.00 0.00 2.39
3164 3187 3.925379 TCAGACTTGCACAACATACGAT 58.075 40.909 0.00 0.00 0.00 3.73
3206 3229 2.093869 GTGCCTGAGGTACCGTTATCAA 60.094 50.000 8.68 0.00 32.14 2.57
3398 3421 8.926374 TGTCCAATTGCATATAAAATCAGGAAT 58.074 29.630 0.00 0.00 0.00 3.01
3522 3545 0.969917 TGCTTGTTGGGTGCACTTGT 60.970 50.000 17.98 0.00 0.00 3.16
3533 3556 6.563222 TGGGTGCACTTGTATTTAAGTTAC 57.437 37.500 17.98 0.00 38.78 2.50
3631 3654 6.259638 TGTGTAATCGTTTTCTGTTTCCAAC 58.740 36.000 0.00 0.00 0.00 3.77
3660 3683 2.205074 GTTCTGATGCCATCCGTACTG 58.795 52.381 1.49 0.00 0.00 2.74
3739 3763 8.991243 AATCATGGATGTGACTACAAAAATTG 57.009 30.769 0.00 0.00 40.84 2.32
3741 3765 7.369607 TCATGGATGTGACTACAAAAATTGTG 58.630 34.615 6.01 0.00 45.03 3.33
3775 3801 5.739752 TGAATGTGTGACACTCAGAAAAG 57.260 39.130 17.47 0.00 35.11 2.27
3779 3805 5.282055 TGTGTGACACTCAGAAAAGAGAT 57.718 39.130 17.47 0.00 38.98 2.75
3780 3806 5.292765 TGTGTGACACTCAGAAAAGAGATC 58.707 41.667 17.47 0.00 38.98 2.75
3781 3807 5.163416 TGTGTGACACTCAGAAAAGAGATCA 60.163 40.000 17.47 0.00 38.98 2.92
3782 3808 5.755375 GTGTGACACTCAGAAAAGAGATCAA 59.245 40.000 8.76 0.00 38.98 2.57
3783 3809 5.987953 TGTGACACTCAGAAAAGAGATCAAG 59.012 40.000 7.20 0.00 38.98 3.02
3784 3810 4.993584 TGACACTCAGAAAAGAGATCAAGC 59.006 41.667 0.00 0.00 38.98 4.01
3785 3811 5.221601 TGACACTCAGAAAAGAGATCAAGCT 60.222 40.000 0.00 0.00 38.98 3.74
3990 4019 8.175716 GTGGAATGAATGTAGTTGCTTAGTTAC 58.824 37.037 0.00 0.00 0.00 2.50
4000 4029 3.695830 TGCTTAGTTACCTCCCTGTTG 57.304 47.619 0.00 0.00 0.00 3.33
4047 4076 6.040504 AGTTTCTGGGTTACAAAGTTGAATCC 59.959 38.462 0.00 0.00 0.00 3.01
4122 4151 7.903145 AGTCACAGTGTACATATACTTTCCAA 58.097 34.615 0.00 0.00 32.00 3.53
4174 4203 6.281405 ACAGCATATGTAGCAGGTTAACTAC 58.719 40.000 5.42 0.88 41.60 2.73
4325 4354 8.035984 GTGGATGGTTCTACTAATAAGCCTATC 58.964 40.741 0.00 0.00 31.08 2.08
4383 4412 0.917333 TGGTAAAGGCCGGGGATCTT 60.917 55.000 2.18 0.00 0.00 2.40
4415 4444 7.039504 ACTGAAAATGGTACTGCTCAAATCAAT 60.040 33.333 0.00 0.00 0.00 2.57
4516 4545 8.930760 GCGTGATCTAAGCATCTAATAATTCTT 58.069 33.333 0.00 0.00 33.68 2.52
4544 4573 8.635765 TCTTTTTACCATCTTTTCTGTGCTAT 57.364 30.769 0.00 0.00 0.00 2.97
4918 4948 7.545615 AGAAGTCAAAAAGGTTTGTTCACATTC 59.454 33.333 0.00 0.00 43.90 2.67
4937 4967 6.707161 CACATTCCCAAATTGAACATTTCAGT 59.293 34.615 0.00 0.00 41.38 3.41
5014 5044 3.189080 TGAAACTGGAAATGCGAGTGATG 59.811 43.478 0.00 0.00 35.58 3.07
5110 5140 3.967332 ATTTCCTTTTGTGGCTGATGG 57.033 42.857 0.00 0.00 0.00 3.51
5284 5315 7.630242 TCTCAAATCCCTAAGCATACAAAAG 57.370 36.000 0.00 0.00 0.00 2.27
5367 5398 6.610020 TGTTAGGTAGTGGTATTCAGCTACAT 59.390 38.462 0.00 0.00 34.57 2.29
5404 5435 2.026542 TCTCTGCACTCAGGCATCATTT 60.027 45.455 0.00 0.00 43.97 2.32
5655 5686 3.149196 TGGCACAAGAAGACAAATCTCC 58.851 45.455 0.00 0.00 29.64 3.71
5723 5754 1.209504 CTGAAAGGAAGGCCGGTATCA 59.790 52.381 1.90 0.00 39.96 2.15
6016 6047 4.351054 AAAGCAGGAGCCCACCCG 62.351 66.667 0.00 0.00 43.56 5.28
6088 6119 3.993535 CTGGAAGGGCAAGCAGAC 58.006 61.111 0.00 0.00 0.00 3.51
6090 6121 2.032681 GGAAGGGCAAGCAGACGT 59.967 61.111 0.00 0.00 0.00 4.34
6285 6316 3.608316 ACTTCTGCAAGATCTCCACTC 57.392 47.619 0.00 0.00 46.36 3.51
6321 6352 1.682257 GAGCCCTGATATGCCTCCC 59.318 63.158 0.00 0.00 0.00 4.30
6576 6607 5.600908 TTACTCAACGTTACTCATTTGCC 57.399 39.130 0.00 0.00 0.00 4.52
6717 6748 9.821240 ATCTCTGTAGATATCAGTTACCAAGAT 57.179 33.333 5.32 7.10 40.82 2.40
6811 6842 1.207089 CCAAGACGATACAGAAGCCCA 59.793 52.381 0.00 0.00 0.00 5.36
6837 6868 5.283457 AGAAGAGCATCACCAAGGTATAC 57.717 43.478 0.00 0.00 37.82 1.47
6838 6869 4.965532 AGAAGAGCATCACCAAGGTATACT 59.034 41.667 2.25 0.00 37.82 2.12
6839 6870 4.679373 AGAGCATCACCAAGGTATACTG 57.321 45.455 2.25 0.00 37.82 2.74
6840 6871 4.033709 AGAGCATCACCAAGGTATACTGT 58.966 43.478 2.25 0.00 37.82 3.55
6841 6872 5.208890 AGAGCATCACCAAGGTATACTGTA 58.791 41.667 2.25 0.00 37.82 2.74
6889 6923 6.238103 CGTACAACAATTGGACATATGACTCC 60.238 42.308 10.38 7.57 45.00 3.85
6902 6936 2.470983 TGACTCCGAATGATTGCACA 57.529 45.000 0.00 0.00 0.00 4.57
6925 6959 8.436970 CACATACAACAATTGGACATGATTTTG 58.563 33.333 10.83 4.41 34.12 2.44
7179 7223 5.009010 GTGTGGTGATGAACATCTTTCAACT 59.991 40.000 14.50 0.00 38.60 3.16
7226 7270 7.415765 GCACATATGTATAGCCTAGTCTAGTGG 60.416 44.444 8.32 0.00 0.00 4.00
7261 7305 5.949735 TCATATTTCTCTTGTTTTTCCGCC 58.050 37.500 0.00 0.00 0.00 6.13
7331 7375 0.456221 CACCAGCTTATCGAGACCGT 59.544 55.000 0.00 0.00 37.05 4.83
7384 7428 1.516603 GTAGTCGTTCGCCTCCTGC 60.517 63.158 0.00 0.00 0.00 4.85
7513 7557 0.039618 GCCTCCCCATCTCCAAAACA 59.960 55.000 0.00 0.00 0.00 2.83
7731 7775 7.595819 TTGGTTGAATTATCTTTGGACAACT 57.404 32.000 0.00 0.00 37.09 3.16
7845 7895 6.049149 TCAAAGCTGCTACATGTAATCCTAC 58.951 40.000 7.06 0.00 0.00 3.18
7886 7936 1.001406 CCGAGTCCCTTATGATCCAGC 59.999 57.143 0.00 0.00 0.00 4.85
7901 7951 1.209504 TCCAGCCCGAGTTATCTTTGG 59.790 52.381 0.00 0.00 0.00 3.28
7907 7957 3.432326 GCCCGAGTTATCTTTGGTCTCAT 60.432 47.826 0.00 0.00 0.00 2.90
7908 7958 4.770795 CCCGAGTTATCTTTGGTCTCATT 58.229 43.478 0.00 0.00 0.00 2.57
7930 7980 9.529325 TCATTAACGATCTTGAGGTTTAGTATG 57.471 33.333 0.00 0.00 0.00 2.39
7956 8006 4.970611 GCACGTCCGTATGCTATATATGAG 59.029 45.833 0.00 0.00 38.84 2.90
8020 8085 1.531739 GGCTGCGTTCCCATTTTGGA 61.532 55.000 0.00 0.00 40.96 3.53
8035 8143 0.878416 TTGGAGTACATGTTTGGCGC 59.122 50.000 2.30 0.00 0.00 6.53
8053 8161 2.386249 CGCTAGTTATCAGCTTCCGAC 58.614 52.381 0.00 0.00 36.86 4.79
8110 8219 9.802039 TTTGGTATAATATTACTCCATCCCAAC 57.198 33.333 16.31 0.00 0.00 3.77
8182 8291 5.470368 TGAGACACTTATTTTGAGACGGAG 58.530 41.667 0.00 0.00 0.00 4.63
8254 8363 3.608796 TCTCATCGTTGCCATTGAATGA 58.391 40.909 6.76 0.00 0.00 2.57
8258 8367 5.722263 TCATCGTTGCCATTGAATGATTTT 58.278 33.333 6.76 0.00 28.45 1.82
8275 8384 9.696917 GAATGATTTTAAAAGGTTCAGTGTCAT 57.303 29.630 6.79 4.73 0.00 3.06
8312 8421 3.311322 CGCAATTGTCGTGGTATATTGGT 59.689 43.478 7.40 0.00 0.00 3.67
8321 8430 5.694910 GTCGTGGTATATTGGTATCCAGTTG 59.305 44.000 0.00 0.00 33.81 3.16
8326 8435 5.106157 GGTATATTGGTATCCAGTTGCATGC 60.106 44.000 11.82 11.82 33.81 4.06
8337 8446 0.171903 GTTGCATGCATCTGGTCCAC 59.828 55.000 23.37 10.29 0.00 4.02
8348 8506 5.128919 GCATCTGGTCCACTATTTCTTGAT 58.871 41.667 0.00 0.00 0.00 2.57
8419 8577 8.455903 TTGACATTTGATCCCTCTATTCATTC 57.544 34.615 0.00 0.00 0.00 2.67
8452 8610 3.407698 AGCATCGTTTACAACCATGTGA 58.592 40.909 0.00 0.00 40.84 3.58
8453 8611 4.009675 AGCATCGTTTACAACCATGTGAT 58.990 39.130 0.00 0.00 40.84 3.06
8473 8631 3.334583 TCACATCCTTTGGTACAGAGC 57.665 47.619 0.00 0.00 39.45 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.384532 GGAGGGGCACGAACCGTA 61.385 66.667 0.00 0.00 38.32 4.02
319 322 4.393062 ACAGCTCATTACACGAATCCAAAG 59.607 41.667 0.00 0.00 0.00 2.77
361 364 2.707902 GGGATCTAAGCGCCCTTTG 58.292 57.895 2.29 0.00 38.85 2.77
705 709 0.606096 TGCCTACTACTTGCGCAAGA 59.394 50.000 46.69 31.08 40.79 3.02
816 820 4.725790 AAACCATAATTTGAGAGCAGGC 57.274 40.909 0.00 0.00 0.00 4.85
856 860 2.943690 GCAGTCAATCAGTCATGCAGAT 59.056 45.455 0.00 0.00 33.92 2.90
877 881 5.001874 CCCATCACCATCTGATTCTACATG 58.998 45.833 0.00 0.00 37.53 3.21
946 950 6.261826 GCTGTGAGTAAAATGAAGAGCCATAT 59.738 38.462 0.00 0.00 0.00 1.78
947 951 5.586243 GCTGTGAGTAAAATGAAGAGCCATA 59.414 40.000 0.00 0.00 0.00 2.74
948 952 4.397417 GCTGTGAGTAAAATGAAGAGCCAT 59.603 41.667 0.00 0.00 0.00 4.40
949 953 3.753272 GCTGTGAGTAAAATGAAGAGCCA 59.247 43.478 0.00 0.00 0.00 4.75
950 954 4.006319 AGCTGTGAGTAAAATGAAGAGCC 58.994 43.478 0.00 0.00 0.00 4.70
1332 1341 1.263217 GTCACAAGTAACTTGGGCACG 59.737 52.381 0.00 0.00 43.80 5.34
1344 1353 6.498304 CAGCTAATTTTTCACAGTCACAAGT 58.502 36.000 0.00 0.00 0.00 3.16
1345 1354 5.400485 GCAGCTAATTTTTCACAGTCACAAG 59.600 40.000 0.00 0.00 0.00 3.16
1346 1355 5.163571 TGCAGCTAATTTTTCACAGTCACAA 60.164 36.000 0.00 0.00 0.00 3.33
1347 1356 4.337836 TGCAGCTAATTTTTCACAGTCACA 59.662 37.500 0.00 0.00 0.00 3.58
1348 1357 4.858935 TGCAGCTAATTTTTCACAGTCAC 58.141 39.130 0.00 0.00 0.00 3.67
1351 1360 5.520376 AACTGCAGCTAATTTTTCACAGT 57.480 34.783 15.27 0.00 38.70 3.55
1352 1361 6.292488 CCAAAACTGCAGCTAATTTTTCACAG 60.292 38.462 15.27 1.23 0.00 3.66
1374 1387 8.528044 AGTTCACAATAAACCTTCTAAACCAA 57.472 30.769 0.00 0.00 0.00 3.67
1401 1414 7.381678 GGCATTCTATTTACCTACTAGTGTTCG 59.618 40.741 5.39 0.00 0.00 3.95
1473 1486 2.936202 AGGCATGCCTTAACCACTATG 58.064 47.619 34.07 0.00 45.70 2.23
1997 2014 6.727824 ATTGTTTTGGAAGACAGATACGAG 57.272 37.500 0.00 0.00 0.00 4.18
2303 2326 9.744468 ACAAATAGGTCAAACAAAATGTAAGAC 57.256 29.630 6.67 6.67 35.12 3.01
2369 2392 8.380742 AGATACAGGAGAAGAAAAAGGTCATA 57.619 34.615 0.00 0.00 0.00 2.15
2374 2397 6.476378 TGGAAGATACAGGAGAAGAAAAAGG 58.524 40.000 0.00 0.00 0.00 3.11
2377 2400 7.689299 TCAATGGAAGATACAGGAGAAGAAAA 58.311 34.615 0.00 0.00 0.00 2.29
2412 2435 0.386476 AGTACCGACGCAGAAACACA 59.614 50.000 0.00 0.00 0.00 3.72
2466 2489 5.227569 TCAAAACTAGCATCTCTCAACCA 57.772 39.130 0.00 0.00 0.00 3.67
2560 2583 3.831323 TGAAACTCTTTCCCTGCATCAA 58.169 40.909 0.00 0.00 38.90 2.57
2561 2584 3.507162 TGAAACTCTTTCCCTGCATCA 57.493 42.857 0.00 0.00 38.90 3.07
2622 2645 4.021368 GCAGGGGTACTACTATGTGTATGG 60.021 50.000 0.00 0.00 0.00 2.74
2875 2898 5.470777 CGGGAGAAAATGTGTTGGTAAGTTA 59.529 40.000 0.00 0.00 0.00 2.24
3158 3181 5.473504 GGTTGCCCAAATCTTATGATCGTAT 59.526 40.000 0.00 0.00 31.51 3.06
3161 3184 3.004734 GGGTTGCCCAAATCTTATGATCG 59.995 47.826 0.00 0.00 44.65 3.69
3191 3214 5.320549 TCTCTTGTTGATAACGGTACCTC 57.679 43.478 10.90 0.70 0.00 3.85
3206 3229 7.370383 ACAACATTTATTTTCGCATCTCTTGT 58.630 30.769 0.00 0.00 0.00 3.16
3282 3305 9.725019 CTATAGTAAGGCACATCAAAATATGGA 57.275 33.333 0.00 0.00 0.00 3.41
3330 3353 8.816144 TGTTTAGCATTGAAAACAAAATCTGTC 58.184 29.630 12.59 0.00 41.34 3.51
3398 3421 6.040278 TCACATGAAAGACTGCAATGGTTTTA 59.960 34.615 0.00 0.00 0.00 1.52
3533 3556 4.461781 ACTGGAAAGATTTGAATCAGGCAG 59.538 41.667 6.50 0.00 37.89 4.85
3631 3654 3.003394 TGGCATCAGAACACCCATAAG 57.997 47.619 0.00 0.00 0.00 1.73
3660 3683 7.933577 TCAATGTGTATATCAACAAGATCTCCC 59.066 37.037 0.00 0.00 38.19 4.30
3748 3772 6.284891 TCTGAGTGTCACACATTCATCATA 57.715 37.500 11.40 0.00 42.61 2.15
3749 3773 5.156608 TCTGAGTGTCACACATTCATCAT 57.843 39.130 11.40 0.00 42.61 2.45
3750 3774 4.605640 TCTGAGTGTCACACATTCATCA 57.394 40.909 11.40 3.62 42.61 3.07
3751 3775 5.929697 TTTCTGAGTGTCACACATTCATC 57.070 39.130 11.40 0.00 42.61 2.92
3752 3776 6.057533 TCTTTTCTGAGTGTCACACATTCAT 58.942 36.000 11.40 0.00 42.61 2.57
3775 3801 8.131731 ACAAAAACAAGACTTAAGCTTGATCTC 58.868 33.333 29.85 11.18 44.16 2.75
3779 3805 8.276252 AGTACAAAAACAAGACTTAAGCTTGA 57.724 30.769 29.85 14.06 44.16 3.02
3900 3929 7.828223 TGCGGTCTTAACCCATTAATACTTAAA 59.172 33.333 0.00 0.00 43.21 1.52
3990 4019 2.751259 CACATTCACATCAACAGGGAGG 59.249 50.000 0.00 0.00 0.00 4.30
4000 4029 3.806380 AGAGAGCATCCACATTCACATC 58.194 45.455 0.00 0.00 33.66 3.06
4047 4076 3.228453 AGTACCATACGTCCATACCTGG 58.772 50.000 0.00 0.00 44.64 4.45
4122 4151 8.220559 ACTTGTAATCCTGCCATATTTGATACT 58.779 33.333 0.00 0.00 0.00 2.12
4133 4162 3.244735 TGCTGTAACTTGTAATCCTGCCA 60.245 43.478 0.00 0.00 0.00 4.92
4174 4203 2.162208 CGAAAATATGGGGATCATGCCG 59.838 50.000 0.00 0.00 37.30 5.69
4325 4354 6.036083 CACAATCCACTATTCTTACTGGAACG 59.964 42.308 0.00 0.00 36.39 3.95
4383 4412 5.376625 AGCAGTACCATTTTCAGTTGAGAA 58.623 37.500 0.00 0.00 0.00 2.87
4415 4444 6.436847 TCCAGTCCATTTGAAAATTGCTATCA 59.563 34.615 0.00 0.00 0.00 2.15
4434 4463 5.163774 GCAGTTGATTTGAGAATCTCCAGTC 60.164 44.000 7.91 3.95 41.80 3.51
4516 4545 7.231317 AGCACAGAAAAGATGGTAAAAAGATCA 59.769 33.333 0.00 0.00 0.00 2.92
4918 4948 5.846203 ACAGACTGAAATGTTCAATTTGGG 58.154 37.500 10.08 0.00 39.58 4.12
4937 4967 9.448438 AACTTATGTTATATGTCAGCAAACAGA 57.552 29.630 0.00 0.00 33.90 3.41
5014 5044 2.203181 GGCATCCTCAGAGCTGCC 60.203 66.667 20.59 20.59 46.54 4.85
5049 5079 3.225940 GGCCTTAGATTTCCTTCCATGG 58.774 50.000 4.97 4.97 0.00 3.66
5110 5140 8.883954 ATATGCATAGATATGTACAGCACATC 57.116 34.615 12.79 1.90 44.99 3.06
5220 5251 8.303876 GTTTTCAGTATTTTGATGTACATGGGT 58.696 33.333 14.43 0.00 0.00 4.51
5404 5435 7.276438 GCATATTCGATGATGCAGACAGTAATA 59.724 37.037 21.12 2.43 46.29 0.98
5521 5552 1.620819 AGGCAGTGAGTAGTTGACAGG 59.379 52.381 0.00 0.00 0.00 4.00
5655 5686 1.579698 CATCTCGCCATTCTCCAGTG 58.420 55.000 0.00 0.00 0.00 3.66
5692 5723 4.655963 CCTTCCTTTCAGATTTGGAGTCA 58.344 43.478 0.00 0.00 0.00 3.41
6016 6047 4.040217 ACTCATGCTCATATTCCTCTGTCC 59.960 45.833 0.00 0.00 0.00 4.02
6285 6316 0.250989 TCCGGCTAAAACCCTTGTGG 60.251 55.000 0.00 0.00 41.37 4.17
6321 6352 3.434984 GGCTTCTGCTTGTAGTCTTTCTG 59.565 47.826 0.00 0.00 39.59 3.02
6576 6607 4.169508 CAGAAGGTGAACGATACTGTCTG 58.830 47.826 0.00 0.00 0.00 3.51
6811 6842 2.553904 CCTTGGTGATGCTCTTCTTGGT 60.554 50.000 0.00 0.00 0.00 3.67
6851 6882 6.735678 ATTGTTGTACGTGCAATCATTCTA 57.264 33.333 21.92 6.46 0.00 2.10
6889 6923 6.237622 CCAATTGTTGTATGTGCAATCATTCG 60.238 38.462 4.43 0.00 32.38 3.34
6902 6936 8.761575 GACAAAATCATGTCCAATTGTTGTAT 57.238 30.769 4.43 0.00 43.11 2.29
6998 7032 1.533625 ACATCATTTGTGTGGGGTCG 58.466 50.000 0.00 0.00 37.11 4.79
7046 7080 7.284489 ACTGCAACAAATTTCCTTACAAGTCTA 59.716 33.333 0.00 0.00 0.00 2.59
7048 7082 6.198966 CACTGCAACAAATTTCCTTACAAGTC 59.801 38.462 0.00 0.00 0.00 3.01
7067 7101 7.010091 CGATAACACAATAGTTGATACACTGCA 59.990 37.037 0.00 0.00 33.07 4.41
7069 7103 7.704899 TCCGATAACACAATAGTTGATACACTG 59.295 37.037 0.00 0.00 33.07 3.66
7261 7305 0.739561 GTACCTGCTAGACCTCCACG 59.260 60.000 0.00 0.00 0.00 4.94
7331 7375 2.204074 TAGCCACCTCCCCTTGCA 60.204 61.111 0.00 0.00 0.00 4.08
7403 7447 2.261671 GACCGTGCACGATCACCT 59.738 61.111 39.10 14.20 43.02 4.00
7513 7557 1.338769 GGGACCTGTCGTTACTTGCAT 60.339 52.381 0.00 0.00 0.00 3.96
7722 7766 8.375493 ACTAACCTCAGATTATAGTTGTCCAA 57.625 34.615 0.00 0.00 0.00 3.53
7845 7895 5.049060 TCGGTGTCCATATTTGTCAAAAGTG 60.049 40.000 1.31 4.47 0.00 3.16
7873 7923 1.051812 ACTCGGGCTGGATCATAAGG 58.948 55.000 0.00 0.00 0.00 2.69
7886 7936 3.887621 TGAGACCAAAGATAACTCGGG 57.112 47.619 0.00 0.00 0.00 5.14
7901 7951 6.969828 AAACCTCAAGATCGTTAATGAGAC 57.030 37.500 3.36 0.66 41.38 3.36
7908 7958 8.133627 GCTACATACTAAACCTCAAGATCGTTA 58.866 37.037 0.00 0.00 0.00 3.18
7956 8006 6.816640 TGTAGTATGTGACAAATAGGAACAGC 59.183 38.462 0.00 0.00 0.00 4.40
8020 8085 2.762535 ACTAGCGCCAAACATGTACT 57.237 45.000 2.29 0.00 0.00 2.73
8035 8143 4.902443 TCTGTCGGAAGCTGATAACTAG 57.098 45.455 0.00 0.00 0.00 2.57
8157 8266 6.285224 TCCGTCTCAAAATAAGTGTCTCAAA 58.715 36.000 0.00 0.00 0.00 2.69
8166 8275 6.395629 TGTACTTCCTCCGTCTCAAAATAAG 58.604 40.000 0.00 0.00 0.00 1.73
8167 8276 6.349243 TGTACTTCCTCCGTCTCAAAATAA 57.651 37.500 0.00 0.00 0.00 1.40
8175 8284 5.997384 ATTAACTTGTACTTCCTCCGTCT 57.003 39.130 0.00 0.00 0.00 4.18
8205 8314 9.587772 GCTCAGTTTAAGATATCTGAACTACAA 57.412 33.333 23.74 15.71 36.67 2.41
8254 8363 7.147567 ACCCAATGACACTGAACCTTTTAAAAT 60.148 33.333 0.09 0.00 0.00 1.82
8258 8367 4.798882 ACCCAATGACACTGAACCTTTTA 58.201 39.130 0.00 0.00 0.00 1.52
8321 8430 2.267174 ATAGTGGACCAGATGCATGC 57.733 50.000 11.82 11.82 0.00 4.06
8326 8435 6.600822 ACAATCAAGAAATAGTGGACCAGATG 59.399 38.462 0.00 0.00 0.00 2.90
8402 8560 7.597288 TTCTTACGAATGAATAGAGGGATCA 57.403 36.000 0.00 0.00 0.00 2.92
8419 8577 7.389603 TGTAAACGATGCTATGATTCTTACG 57.610 36.000 0.00 0.00 0.00 3.18
8452 8610 3.370953 GGCTCTGTACCAAAGGATGTGAT 60.371 47.826 0.00 0.00 0.00 3.06
8453 8611 2.027192 GGCTCTGTACCAAAGGATGTGA 60.027 50.000 0.00 0.00 0.00 3.58
8473 8631 5.573380 TCTCCTCATAATTTCTGGATGGG 57.427 43.478 0.00 0.00 0.00 4.00
8532 8690 0.178967 TGTTGCAAGCCCCATCTTCA 60.179 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.