Multiple sequence alignment - TraesCS1B01G169800

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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 TraesCS1B01G169800 chr1B 100.000 3741 0 0 1 3741 301251322 301255062 0.000000e+00 6909.0
1 TraesCS1B01G169800 chr1B 100.000 2844 0 0 4087 6930 301255408 301258251 0.000000e+00 5252.0
2 TraesCS1B01G169800 chr1B 100.000 30 0 0 4576 4605 32987829 32987858 1.000000e-03 56.5
3 TraesCS1B01G169800 chr1D 96.415 2817 94 3 1 2814 205477379 205480191 0.000000e+00 4636.0
4 TraesCS1B01G169800 chr1D 91.958 1517 73 18 4400 5897 205480183 205481669 0.000000e+00 2080.0
5 TraesCS1B01G169800 chr1D 94.823 1043 49 4 5892 6930 205481700 205482741 0.000000e+00 1622.0
6 TraesCS1B01G169800 chr1A 96.265 2811 101 2 1 2811 262011109 262013915 0.000000e+00 4606.0
7 TraesCS1B01G169800 chr1A 94.869 1072 46 4 4400 5470 262013910 262014973 0.000000e+00 1666.0
8 TraesCS1B01G169800 chr1A 95.288 1040 44 5 5892 6930 262841771 262840736 0.000000e+00 1644.0
9 TraesCS1B01G169800 chr1A 93.301 418 15 3 5493 5897 262842219 262841802 7.690000e-169 604.0
10 TraesCS1B01G169800 chr5B 98.162 925 16 1 2818 3741 26946486 26947410 0.000000e+00 1613.0
11 TraesCS1B01G169800 chr5B 98.058 927 16 2 2817 3741 10171058 10171984 0.000000e+00 1611.0
12 TraesCS1B01G169800 chr5B 96.617 266 9 0 4089 4354 10172110 10172375 6.380000e-120 442.0
13 TraesCS1B01G169800 chr5B 92.691 301 13 1 4087 4378 26947534 26947834 6.420000e-115 425.0
14 TraesCS1B01G169800 chr3B 97.727 924 19 2 2819 3741 335830066 335830988 0.000000e+00 1589.0
15 TraesCS1B01G169800 chr3B 96.875 928 28 1 2815 3741 783420359 783421286 0.000000e+00 1552.0
16 TraesCS1B01G169800 chr3B 96.269 268 10 0 4087 4354 783421410 783421677 2.290000e-119 440.0
17 TraesCS1B01G169800 chr3B 93.380 287 10 1 4103 4380 335831361 335831647 3.870000e-112 416.0
18 TraesCS1B01G169800 chr5A 96.544 926 31 1 2815 3739 355371557 355372482 0.000000e+00 1531.0
19 TraesCS1B01G169800 chr5A 94.776 268 13 1 4087 4354 355372584 355372850 3.870000e-112 416.0
20 TraesCS1B01G169800 chr5A 100.000 29 0 0 4342 4370 355372847 355372875 3.000000e-03 54.7
21 TraesCS1B01G169800 chr3A 96.425 923 30 3 2818 3739 734149668 734150588 0.000000e+00 1519.0
22 TraesCS1B01G169800 chr3A 93.284 268 17 1 4087 4354 734150714 734150980 1.810000e-105 394.0
23 TraesCS1B01G169800 chr2A 95.883 923 35 3 2818 3739 59565594 59564674 0.000000e+00 1491.0
24 TraesCS1B01G169800 chr2A 95.445 922 41 1 2819 3739 20867233 20866312 0.000000e+00 1469.0
25 TraesCS1B01G169800 chr2A 95.522 268 12 0 4087 4354 20866186 20865919 4.970000e-116 429.0
26 TraesCS1B01G169800 chr2A 94.224 277 13 1 4100 4373 59564043 59563767 2.990000e-113 420.0
27 TraesCS1B01G169800 chr2A 96.875 32 1 0 4342 4373 20865922 20865891 3.000000e-03 54.7
28 TraesCS1B01G169800 chr7D 93.548 930 53 4 2817 3740 73132254 73131326 0.000000e+00 1378.0
29 TraesCS1B01G169800 chr7D 85.075 268 36 2 4090 4353 611861944 611861677 3.190000e-68 270.0
30 TraesCS1B01G169800 chr7A 88.028 142 8 1 4238 4370 690702882 690703023 7.190000e-35 159.0


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 TraesCS1B01G169800 chr1B 301251322 301258251 6929 False 6080.500000 6909 100.000000 1 6930 2 chr1B.!!$F2 6929
1 TraesCS1B01G169800 chr1D 205477379 205482741 5362 False 2779.333333 4636 94.398667 1 6930 3 chr1D.!!$F1 6929
2 TraesCS1B01G169800 chr1A 262011109 262014973 3864 False 3136.000000 4606 95.567000 1 5470 2 chr1A.!!$F1 5469
3 TraesCS1B01G169800 chr1A 262840736 262842219 1483 True 1124.000000 1644 94.294500 5493 6930 2 chr1A.!!$R1 1437
4 TraesCS1B01G169800 chr5B 10171058 10172375 1317 False 1026.500000 1611 97.337500 2817 4354 2 chr5B.!!$F1 1537
5 TraesCS1B01G169800 chr5B 26946486 26947834 1348 False 1019.000000 1613 95.426500 2818 4378 2 chr5B.!!$F2 1560
6 TraesCS1B01G169800 chr3B 335830066 335831647 1581 False 1002.500000 1589 95.553500 2819 4380 2 chr3B.!!$F1 1561
7 TraesCS1B01G169800 chr3B 783420359 783421677 1318 False 996.000000 1552 96.572000 2815 4354 2 chr3B.!!$F2 1539
8 TraesCS1B01G169800 chr5A 355371557 355372875 1318 False 667.233333 1531 97.106667 2815 4370 3 chr5A.!!$F1 1555
9 TraesCS1B01G169800 chr3A 734149668 734150980 1312 False 956.500000 1519 94.854500 2818 4354 2 chr3A.!!$F1 1536
10 TraesCS1B01G169800 chr2A 59563767 59565594 1827 True 955.500000 1491 95.053500 2818 4373 2 chr2A.!!$R2 1555
11 TraesCS1B01G169800 chr2A 20865891 20867233 1342 True 650.900000 1469 95.947333 2819 4373 3 chr2A.!!$R1 1554
12 TraesCS1B01G169800 chr7D 73131326 73132254 928 True 1378.000000 1378 93.548000 2817 3740 1 chr7D.!!$R1 923

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
534 535 0.322277 AGGACATTGCTGCACTGAGG 60.322 55.0 24.23 4.99 0.00 3.86 F
1575 1576 0.238289 CTGCAAGTAAGGTGCCAACG 59.762 55.0 0.00 0.00 41.49 4.10 F
2681 2682 0.109132 CGTTCCTGCCAAGAAATGCC 60.109 55.0 0.00 0.00 0.00 4.40 F
3187 3192 0.517755 CTAGCTATCGTCGACGCCAT 59.482 55.0 32.19 23.00 39.60 4.40 F
4382 4662 0.108041 GCGGGGGATGTTTTCTCGTA 60.108 55.0 0.00 0.00 0.00 3.43 F
5456 5745 0.107703 CGCCCTCCATTTGCAGAGTA 60.108 55.0 0.61 0.00 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2273 2274 0.178995 TGCCATGGTTGCTTCAGTCA 60.179 50.000 14.67 0.0 0.00 3.41 R
3460 3466 0.541998 TGCCGTCTCTCTCTTGGGAA 60.542 55.000 0.00 0.0 0.00 3.97 R
4363 4643 0.108041 TACGAGAAAACATCCCCCGC 60.108 55.000 0.00 0.0 0.00 6.13 R
4982 5270 0.107017 ATTCAGTTCCCCATCGGCAG 60.107 55.000 0.00 0.0 0.00 4.85 R
5685 5992 0.326927 CCCCACCGTTTACTCCACAT 59.673 55.000 0.00 0.0 0.00 3.21 R
6562 6914 2.125912 ACGCTGAAGCTAGGCACG 60.126 61.111 0.10 0.0 39.32 5.34 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
263 264 4.462508 TTGTCGATTCTTCAGCTCTCAT 57.537 40.909 0.00 0.00 0.00 2.90
460 461 4.007644 CTGGCGGCCTCAGACACA 62.008 66.667 21.46 0.00 34.36 3.72
523 524 0.742281 CGAGGCTGTGGAGGACATTG 60.742 60.000 0.00 0.00 32.74 2.82
524 525 1.001641 AGGCTGTGGAGGACATTGC 60.002 57.895 0.00 0.00 32.74 3.56
534 535 0.322277 AGGACATTGCTGCACTGAGG 60.322 55.000 24.23 4.99 0.00 3.86
571 572 1.066573 ACGCACCTGATCTGAAGAAGG 60.067 52.381 0.38 0.00 35.82 3.46
580 581 3.068732 TGATCTGAAGAAGGTATCAGGCG 59.931 47.826 3.23 0.00 42.62 5.52
615 616 2.972713 GGACCTTAGCATATCCCACTGA 59.027 50.000 0.00 0.00 0.00 3.41
678 679 4.731483 GCAGTGCGCTTATTTGATCATCAA 60.731 41.667 9.73 0.00 37.77 2.57
690 691 9.577222 TTATTTGATCATCAATTGCAGGAGATA 57.423 29.630 0.00 0.00 36.11 1.98
929 930 3.692257 AACTGCTGCTTCTGATAGTGT 57.308 42.857 0.00 0.00 0.00 3.55
961 962 1.701704 GGCAGAAAACAGAAATGCCG 58.298 50.000 0.00 0.00 46.19 5.69
977 978 1.728490 GCCGATCAAGATGTTGGGGC 61.728 60.000 14.18 14.18 37.58 5.80
1167 1168 1.865970 GCTGAGGAAGATGCAGATTCG 59.134 52.381 7.39 0.00 0.00 3.34
1190 1191 1.202794 TGTGCTGTTTCCTGCTCATCA 60.203 47.619 0.00 0.00 35.15 3.07
1316 1317 0.464554 GGTCCTGATGCAACTAGGCC 60.465 60.000 0.00 0.00 0.00 5.19
1429 1430 0.320771 CTTGGTCCGTGAAGGGTCTG 60.321 60.000 0.00 0.00 41.52 3.51
1452 1453 6.228258 TGGAGTAATCAACAGTACTGAAACC 58.772 40.000 29.30 16.39 33.50 3.27
1575 1576 0.238289 CTGCAAGTAAGGTGCCAACG 59.762 55.000 0.00 0.00 41.49 4.10
1605 1606 5.351740 GGTTGGCAGTGACTCTAAAGTATTC 59.648 44.000 0.00 0.00 35.28 1.75
1681 1682 7.750903 GGCAAGTAACATTCAACATAAGAGAAC 59.249 37.037 0.00 0.00 0.00 3.01
1713 1714 1.739929 CGCCGCTGTACATTCACCA 60.740 57.895 0.00 0.00 0.00 4.17
1761 1762 4.109766 GCAAGGTAAAAGTGACAACAACC 58.890 43.478 0.00 0.00 0.00 3.77
1810 1811 2.633967 ACAATGCCAGAAATTCCAGCAA 59.366 40.909 10.84 0.00 36.95 3.91
1821 1822 6.205464 CAGAAATTCCAGCAAACAGAGAAGTA 59.795 38.462 0.00 0.00 0.00 2.24
1854 1855 1.795286 GTTGGCACTATCGATAGCAGC 59.205 52.381 28.76 28.76 35.34 5.25
1859 1860 3.675698 GGCACTATCGATAGCAGCTTAAC 59.324 47.826 32.07 20.45 35.96 2.01
1917 1918 4.494350 TTCTACTCGTACTGGTGTTGAC 57.506 45.455 0.00 0.00 0.00 3.18
1947 1948 2.023015 TGGTCATATGGAGGACAGGAGT 60.023 50.000 2.13 0.00 38.14 3.85
2177 2178 5.993441 CCTCGGAGAAAGTTACCTACAAAAA 59.007 40.000 6.58 0.00 34.09 1.94
2274 2275 2.739292 CCGTCTTGTACCATCGGTATG 58.261 52.381 0.00 0.00 40.54 2.39
2358 2359 0.465705 TCTCCATCGACATCAAGGCC 59.534 55.000 0.00 0.00 0.00 5.19
2359 2360 0.877649 CTCCATCGACATCAAGGCCG 60.878 60.000 0.00 0.00 0.00 6.13
2360 2361 1.143838 CCATCGACATCAAGGCCGA 59.856 57.895 0.00 0.00 35.43 5.54
2656 2657 2.846193 TGTTAACTCCAGTTCTGCACC 58.154 47.619 7.22 0.00 39.31 5.01
2663 2664 1.148310 CCAGTTCTGCACCTGTAACG 58.852 55.000 0.00 0.00 0.00 3.18
2681 2682 0.109132 CGTTCCTGCCAAGAAATGCC 60.109 55.000 0.00 0.00 0.00 4.40
2684 2685 1.259609 TCCTGCCAAGAAATGCCAAG 58.740 50.000 0.00 0.00 0.00 3.61
2687 2688 2.562298 CCTGCCAAGAAATGCCAAGTAA 59.438 45.455 0.00 0.00 0.00 2.24
2702 2703 5.951747 TGCCAAGTAATTTGCTCCTTTCTAT 59.048 36.000 0.55 0.00 35.37 1.98
2719 2720 7.012327 TCCTTTCTATTGTCTCACTTGTTGTTG 59.988 37.037 0.00 0.00 0.00 3.33
3102 3107 2.755876 TCCGGCGTGCTCTCAGAT 60.756 61.111 6.01 0.00 0.00 2.90
3145 3150 3.181471 CCGCTCCATCTTCAGAACTGTAT 60.181 47.826 1.73 0.00 0.00 2.29
3187 3192 0.517755 CTAGCTATCGTCGACGCCAT 59.482 55.000 32.19 23.00 39.60 4.40
3460 3466 1.568612 CGCTGCTCCACAAACGATGT 61.569 55.000 0.00 0.00 45.34 3.06
3556 3562 0.532862 AGCACGAGTGGGTTGACAAG 60.533 55.000 5.32 0.00 0.00 3.16
3560 3566 1.068741 ACGAGTGGGTTGACAAGAGTC 59.931 52.381 0.00 0.00 45.19 3.36
4251 4531 3.458163 GATGTCCTCCGCCACCGA 61.458 66.667 0.00 0.00 36.29 4.69
4374 4654 4.446413 GACGACGCGGGGGATGTT 62.446 66.667 12.47 0.00 0.00 2.71
4375 4655 3.945304 GACGACGCGGGGGATGTTT 62.945 63.158 12.47 0.00 0.00 2.83
4376 4656 2.744709 CGACGCGGGGGATGTTTT 60.745 61.111 12.47 0.00 0.00 2.43
4377 4657 2.746803 CGACGCGGGGGATGTTTTC 61.747 63.158 12.47 0.00 0.00 2.29
4378 4658 1.376812 GACGCGGGGGATGTTTTCT 60.377 57.895 12.47 0.00 0.00 2.52
4379 4659 1.366854 GACGCGGGGGATGTTTTCTC 61.367 60.000 12.47 0.00 0.00 2.87
4380 4660 2.461110 CGCGGGGGATGTTTTCTCG 61.461 63.158 0.00 0.00 0.00 4.04
4381 4661 1.376812 GCGGGGGATGTTTTCTCGT 60.377 57.895 0.00 0.00 0.00 4.18
4382 4662 0.108041 GCGGGGGATGTTTTCTCGTA 60.108 55.000 0.00 0.00 0.00 3.43
4383 4663 1.935933 CGGGGGATGTTTTCTCGTAG 58.064 55.000 0.00 0.00 0.00 3.51
4384 4664 1.479323 CGGGGGATGTTTTCTCGTAGA 59.521 52.381 0.00 0.00 0.00 2.59
4399 4679 3.713288 TCGTAGAGCAATTGGTTATCCG 58.287 45.455 12.13 11.61 36.30 4.18
4400 4680 2.221055 CGTAGAGCAATTGGTTATCCGC 59.779 50.000 12.13 0.00 36.30 5.54
4401 4681 2.717639 AGAGCAATTGGTTATCCGCT 57.282 45.000 12.13 0.00 36.30 5.52
4402 4682 2.292267 AGAGCAATTGGTTATCCGCTG 58.708 47.619 12.13 0.00 36.30 5.18
4403 4683 0.740737 AGCAATTGGTTATCCGCTGC 59.259 50.000 3.82 0.00 36.25 5.25
4404 4684 0.592247 GCAATTGGTTATCCGCTGCG 60.592 55.000 16.34 16.34 36.30 5.18
4405 4685 0.732571 CAATTGGTTATCCGCTGCGT 59.267 50.000 21.59 5.80 36.30 5.24
4406 4686 1.014352 AATTGGTTATCCGCTGCGTC 58.986 50.000 21.59 5.69 36.30 5.19
4485 4768 1.403249 GCTCTTGCGGTTTTGCATCAT 60.403 47.619 0.00 0.00 45.78 2.45
4752 5040 4.687018 CAGCACTCGTACTCTATCTACGAT 59.313 45.833 1.46 0.00 43.69 3.73
4801 5089 2.375173 CAAAATCTTGGGAAGGCAGC 57.625 50.000 0.00 0.00 0.00 5.25
4835 5123 0.729116 TAAGAAGACGTACCCGAGCG 59.271 55.000 0.00 0.00 37.88 5.03
4837 5125 2.360350 AAGACGTACCCGAGCGGA 60.360 61.111 11.05 0.00 37.50 5.54
4955 5243 5.697067 TGGATCTCTAGTTCTCTAACCCTC 58.303 45.833 0.00 0.00 36.15 4.30
4961 5249 2.258109 AGTTCTCTAACCCTCGCCTTT 58.742 47.619 0.00 0.00 36.15 3.11
4997 5285 3.011517 AGCTGCCGATGGGGAACT 61.012 61.111 0.00 0.00 38.47 3.01
4998 5286 2.825836 GCTGCCGATGGGGAACTG 60.826 66.667 0.00 0.00 38.47 3.16
5011 5299 0.179054 GGAACTGAATCCCTACCCGC 60.179 60.000 0.00 0.00 33.05 6.13
5012 5300 0.179054 GAACTGAATCCCTACCCGCC 60.179 60.000 0.00 0.00 0.00 6.13
5013 5301 1.968050 AACTGAATCCCTACCCGCCG 61.968 60.000 0.00 0.00 0.00 6.46
5049 5337 2.099263 GGACGATGAGATTCCGAACTCA 59.901 50.000 12.73 12.73 45.19 3.41
5050 5338 3.428999 GGACGATGAGATTCCGAACTCAA 60.429 47.826 13.76 3.31 44.47 3.02
5120 5408 2.029918 TCAGGGTATCAATCGATCTGCG 60.030 50.000 0.00 0.00 42.69 5.18
5121 5409 1.071605 GGGTATCAATCGATCTGCGC 58.928 55.000 0.00 0.00 40.61 6.09
5131 5419 1.424493 CGATCTGCGCCCTTGTTCTC 61.424 60.000 4.18 0.00 0.00 2.87
5456 5745 0.107703 CGCCCTCCATTTGCAGAGTA 60.108 55.000 0.61 0.00 0.00 2.59
5519 5808 1.075896 ACTCGCCTCTTCCCTAGGG 60.076 63.158 23.22 23.22 34.46 3.53
5680 5987 2.126914 AAGATCTCTCGCCGAATTCG 57.873 50.000 20.92 20.92 39.44 3.34
5685 5992 2.011947 TCTCTCGCCGAATTCGTTCTA 58.988 47.619 25.10 8.83 37.74 2.10
5689 5996 2.190161 TCGCCGAATTCGTTCTATGTG 58.810 47.619 25.10 15.20 37.74 3.21
5888 6200 2.093973 GGCACTAGCTAGCTTCAACAGA 60.094 50.000 24.88 1.10 41.70 3.41
5906 6254 2.130073 GACGCCCCAGTTTGCAAGTC 62.130 60.000 0.00 0.00 0.00 3.01
5942 6290 7.595819 TGTAAAATTCCATGAAACCAGTCTT 57.404 32.000 0.00 0.00 0.00 3.01
5954 6302 8.755018 CATGAAACCAGTCTTGTTTATTCAAAC 58.245 33.333 2.19 0.00 43.67 2.93
5959 6307 6.605594 ACCAGTCTTGTTTATTCAAACTCCAA 59.394 34.615 2.33 0.00 43.73 3.53
5972 6320 2.375173 ACTCCAAACGACGTTATCCC 57.625 50.000 14.59 0.00 0.00 3.85
5982 6330 2.532778 CGACGTTATCCCGCGTTAAAAC 60.533 50.000 4.92 3.47 41.70 2.43
6009 6357 9.248291 GTTCGTGCAATTCATTATGGAAATAAT 57.752 29.630 0.00 0.00 0.00 1.28
6031 6379 1.332552 CGGAACACGGAGTTGAAAACG 60.333 52.381 0.00 0.00 45.86 3.60
6059 6407 2.747446 GCTTTGGAGAATGGCTCGTAAA 59.253 45.455 0.00 0.00 44.91 2.01
6196 6546 8.830580 TGTTACAATGCTTTCTTGCTATAGATC 58.169 33.333 3.21 0.00 0.00 2.75
6287 6637 1.152963 ACGCAGTCAATATGCCCCC 60.153 57.895 0.00 0.00 29.74 5.40
6319 6670 1.065709 TGGCCCGTCTAGAATTGGTTC 60.066 52.381 0.00 0.00 34.46 3.62
6538 6890 2.562635 CTCTGCAATCTCCTCCACATG 58.437 52.381 0.00 0.00 0.00 3.21
6562 6914 4.505217 CAAGATGCGCGCGGTGAC 62.505 66.667 33.06 15.46 0.00 3.67
6700 7052 3.448301 GGGAACAGATCATGGCAAATCAA 59.552 43.478 13.65 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 264 3.317603 TGAACTCTGCATCGATTGACA 57.682 42.857 0.00 0.00 0.00 3.58
346 347 5.220662 CCATCCATGTTTCAAGCTTACGTAG 60.221 44.000 0.00 0.00 0.00 3.51
523 524 1.093159 CTCAATTCCCTCAGTGCAGC 58.907 55.000 0.00 0.00 0.00 5.25
524 525 1.093159 GCTCAATTCCCTCAGTGCAG 58.907 55.000 0.00 0.00 0.00 4.41
578 579 2.747855 CCTCAAGGGAAGGCACGC 60.748 66.667 0.00 0.00 37.23 5.34
615 616 1.227764 CACAGTCTGCAGCACTGGT 60.228 57.895 31.62 21.60 44.86 4.00
664 665 7.885009 TCTCCTGCAATTGATGATCAAATAA 57.115 32.000 12.36 0.00 40.12 1.40
678 679 3.718434 TCCATCTTGGTATCTCCTGCAAT 59.282 43.478 0.00 0.00 39.03 3.56
690 691 0.749454 GCGCCTTGATCCATCTTGGT 60.749 55.000 0.00 0.00 39.03 3.67
725 726 0.671781 GCTTGTGACATCCAGCGAGT 60.672 55.000 0.00 0.00 0.00 4.18
929 930 2.125552 CTGCCGACGCCTCATCAA 60.126 61.111 0.00 0.00 0.00 2.57
961 962 0.743097 GCAGCCCCAACATCTTGATC 59.257 55.000 0.00 0.00 0.00 2.92
977 978 0.322975 ACCAGTACCTGAAGCTGCAG 59.677 55.000 15.56 15.56 32.44 4.41
999 1000 1.460504 AGAAGCCACTGATGTGCATG 58.539 50.000 0.00 0.00 42.54 4.06
1045 1046 1.371467 TTTCCTTCAGCCATGGGAGA 58.629 50.000 15.13 0.00 0.00 3.71
1167 1168 0.312102 GAGCAGGAAACAGCACAACC 59.688 55.000 0.00 0.00 46.80 3.77
1190 1191 3.941483 CACTCGTGAATGGGATTTAGCTT 59.059 43.478 0.00 0.00 0.00 3.74
1316 1317 4.260170 CTCTCCCATCTTTGACCTTCTTG 58.740 47.826 0.00 0.00 0.00 3.02
1429 1430 5.347907 CGGTTTCAGTACTGTTGATTACTCC 59.652 44.000 21.99 11.22 0.00 3.85
1452 1453 7.006476 CGTACACTGATGTTTGAATTTTGATCG 59.994 37.037 0.00 0.00 40.48 3.69
1575 1576 1.103398 AGTCACTGCCAACCACTTGC 61.103 55.000 0.00 0.00 0.00 4.01
1581 1582 3.127425 ACTTTAGAGTCACTGCCAACC 57.873 47.619 0.00 0.00 0.00 3.77
1713 1714 8.023128 CCGACATTCTTCTGATTAATTGTGTTT 58.977 33.333 0.00 0.00 0.00 2.83
1776 1777 2.134346 GGCATTGTTGTCGCATTTGTT 58.866 42.857 0.00 0.00 0.00 2.83
1810 1811 5.471456 CAGATTTTGGTGCTACTTCTCTGTT 59.529 40.000 0.00 0.00 0.00 3.16
1821 1822 1.069049 GTGCCAACAGATTTTGGTGCT 59.931 47.619 3.92 0.00 46.89 4.40
1845 1846 3.179443 TCAAGGGTTAAGCTGCTATCG 57.821 47.619 0.90 0.00 0.00 2.92
1854 1855 5.530915 TGTGTGATGAACTTCAAGGGTTAAG 59.469 40.000 0.00 0.00 0.00 1.85
1859 1860 3.480470 ACTGTGTGATGAACTTCAAGGG 58.520 45.455 0.00 0.00 0.00 3.95
1903 1904 3.303725 CCAATGTTGTCAACACCAGTACG 60.304 47.826 20.41 4.60 45.50 3.67
1917 1918 3.633525 CCTCCATATGACCACCAATGTTG 59.366 47.826 3.65 0.00 0.00 3.33
1947 1948 2.291475 TGGATTGGCTGGCAAACTGATA 60.291 45.455 20.82 4.27 0.00 2.15
2273 2274 0.178995 TGCCATGGTTGCTTCAGTCA 60.179 50.000 14.67 0.00 0.00 3.41
2274 2275 1.180029 ATGCCATGGTTGCTTCAGTC 58.820 50.000 14.67 0.00 0.00 3.51
2495 2496 3.447025 GAGCCGTGCTTCGCCCTAT 62.447 63.158 0.00 0.00 39.88 2.57
2656 2657 2.163818 TCTTGGCAGGAACGTTACAG 57.836 50.000 14.18 5.81 0.00 2.74
2681 2682 8.734386 AGACAATAGAAAGGAGCAAATTACTTG 58.266 33.333 0.00 0.00 38.15 3.16
2684 2685 8.178313 GTGAGACAATAGAAAGGAGCAAATTAC 58.822 37.037 0.00 0.00 0.00 1.89
2687 2688 6.479884 AGTGAGACAATAGAAAGGAGCAAAT 58.520 36.000 0.00 0.00 0.00 2.32
2702 2703 5.957842 AAAGACAACAACAAGTGAGACAA 57.042 34.783 0.00 0.00 0.00 3.18
2764 2765 5.138800 TCAATTAAGCGAATTAGCGTGAC 57.861 39.130 9.09 0.00 43.00 3.67
3145 3150 1.469703 CGAGCAAGGTTGATGCATCAA 59.530 47.619 33.08 33.08 46.22 2.57
3460 3466 0.541998 TGCCGTCTCTCTCTTGGGAA 60.542 55.000 0.00 0.00 0.00 3.97
3556 3562 1.929836 GAAGGCATCATCGTGTGACTC 59.070 52.381 0.00 0.00 40.28 3.36
4357 4637 3.945304 AAACATCCCCCGCGTCGTC 62.945 63.158 4.92 0.00 0.00 4.20
4358 4638 3.540367 AAAACATCCCCCGCGTCGT 62.540 57.895 4.92 0.00 0.00 4.34
4359 4639 2.744709 AAAACATCCCCCGCGTCG 60.745 61.111 4.92 0.00 0.00 5.12
4360 4640 1.366854 GAGAAAACATCCCCCGCGTC 61.367 60.000 4.92 0.00 0.00 5.19
4361 4641 1.376812 GAGAAAACATCCCCCGCGT 60.377 57.895 4.92 0.00 0.00 6.01
4362 4642 2.461110 CGAGAAAACATCCCCCGCG 61.461 63.158 0.00 0.00 0.00 6.46
4363 4643 0.108041 TACGAGAAAACATCCCCCGC 60.108 55.000 0.00 0.00 0.00 6.13
4364 4644 1.479323 TCTACGAGAAAACATCCCCCG 59.521 52.381 0.00 0.00 0.00 5.73
4365 4645 2.742204 GCTCTACGAGAAAACATCCCCC 60.742 54.545 0.00 0.00 0.00 5.40
4366 4646 2.093658 TGCTCTACGAGAAAACATCCCC 60.094 50.000 0.00 0.00 0.00 4.81
4367 4647 3.247006 TGCTCTACGAGAAAACATCCC 57.753 47.619 0.00 0.00 0.00 3.85
4368 4648 5.447818 CCAATTGCTCTACGAGAAAACATCC 60.448 44.000 0.00 0.00 30.20 3.51
4369 4649 5.122396 ACCAATTGCTCTACGAGAAAACATC 59.878 40.000 0.00 0.00 30.20 3.06
4370 4650 5.003804 ACCAATTGCTCTACGAGAAAACAT 58.996 37.500 0.00 0.00 30.20 2.71
4371 4651 4.385825 ACCAATTGCTCTACGAGAAAACA 58.614 39.130 0.00 0.00 30.20 2.83
4372 4652 5.358298 AACCAATTGCTCTACGAGAAAAC 57.642 39.130 0.00 0.00 30.20 2.43
4373 4653 6.315393 GGATAACCAATTGCTCTACGAGAAAA 59.685 38.462 0.00 0.00 31.62 2.29
4374 4654 5.815740 GGATAACCAATTGCTCTACGAGAAA 59.184 40.000 0.00 0.00 32.07 2.52
4375 4655 5.357257 GGATAACCAATTGCTCTACGAGAA 58.643 41.667 0.00 0.00 35.97 2.87
4376 4656 4.499188 CGGATAACCAATTGCTCTACGAGA 60.499 45.833 0.00 0.00 35.59 4.04
4377 4657 3.736252 CGGATAACCAATTGCTCTACGAG 59.264 47.826 0.00 0.00 35.59 4.18
4378 4658 3.713288 CGGATAACCAATTGCTCTACGA 58.287 45.455 0.00 0.00 35.59 3.43
4379 4659 2.221055 GCGGATAACCAATTGCTCTACG 59.779 50.000 0.00 1.42 35.59 3.51
4380 4660 3.248602 CAGCGGATAACCAATTGCTCTAC 59.751 47.826 0.00 0.00 35.59 2.59
4381 4661 3.466836 CAGCGGATAACCAATTGCTCTA 58.533 45.455 0.00 0.00 35.59 2.43
4382 4662 2.292267 CAGCGGATAACCAATTGCTCT 58.708 47.619 0.00 0.00 35.59 4.09
4383 4663 1.268743 GCAGCGGATAACCAATTGCTC 60.269 52.381 0.00 0.00 35.22 4.26
4384 4664 0.740737 GCAGCGGATAACCAATTGCT 59.259 50.000 0.00 0.00 35.22 3.91
4385 4665 0.592247 CGCAGCGGATAACCAATTGC 60.592 55.000 7.00 0.00 34.95 3.56
4386 4666 0.732571 ACGCAGCGGATAACCAATTG 59.267 50.000 21.15 0.00 35.59 2.32
4387 4667 1.014352 GACGCAGCGGATAACCAATT 58.986 50.000 21.15 0.00 35.59 2.32
4388 4668 0.178068 AGACGCAGCGGATAACCAAT 59.822 50.000 21.15 0.00 35.59 3.16
4389 4669 0.739462 CAGACGCAGCGGATAACCAA 60.739 55.000 21.15 0.00 35.59 3.67
4390 4670 1.153647 CAGACGCAGCGGATAACCA 60.154 57.895 21.15 0.00 35.59 3.67
4391 4671 1.146358 GACAGACGCAGCGGATAACC 61.146 60.000 21.15 0.00 0.00 2.85
4392 4672 1.146358 GGACAGACGCAGCGGATAAC 61.146 60.000 21.15 7.35 0.00 1.89
4393 4673 1.141019 GGACAGACGCAGCGGATAA 59.859 57.895 21.15 0.00 0.00 1.75
4394 4674 2.004808 CTGGACAGACGCAGCGGATA 62.005 60.000 21.15 0.00 0.00 2.59
4395 4675 3.362399 CTGGACAGACGCAGCGGAT 62.362 63.158 21.15 3.62 0.00 4.18
4396 4676 4.056125 CTGGACAGACGCAGCGGA 62.056 66.667 21.15 0.00 0.00 5.54
4397 4677 2.842394 ATTCTGGACAGACGCAGCGG 62.842 60.000 21.15 3.58 37.14 5.52
4398 4678 0.179137 TATTCTGGACAGACGCAGCG 60.179 55.000 14.82 14.82 37.14 5.18
4399 4679 2.010145 TTATTCTGGACAGACGCAGC 57.990 50.000 0.67 0.00 37.14 5.25
4400 4680 6.851222 ATATTTTATTCTGGACAGACGCAG 57.149 37.500 0.67 0.00 37.14 5.18
4401 4681 8.609176 GTTTATATTTTATTCTGGACAGACGCA 58.391 33.333 0.67 0.00 37.14 5.24
4402 4682 8.609176 TGTTTATATTTTATTCTGGACAGACGC 58.391 33.333 0.67 0.00 37.14 5.19
4567 4850 7.745594 GCTCTTACGAGTTAAGACTAATATCCG 59.254 40.741 0.00 0.00 41.19 4.18
4752 5040 5.893500 TGTCTCTCTCCTTTCTCCTTTCTA 58.106 41.667 0.00 0.00 0.00 2.10
4794 5082 0.680280 CTGCTTCCTCATGCTGCCTT 60.680 55.000 0.00 0.00 0.00 4.35
4799 5087 4.767578 TCTTATTCTGCTTCCTCATGCT 57.232 40.909 0.00 0.00 0.00 3.79
4801 5089 5.233902 CGTCTTCTTATTCTGCTTCCTCATG 59.766 44.000 0.00 0.00 0.00 3.07
4941 5229 1.939980 AAGGCGAGGGTTAGAGAACT 58.060 50.000 0.00 0.00 35.74 3.01
4942 5230 2.289506 ACAAAGGCGAGGGTTAGAGAAC 60.290 50.000 0.00 0.00 34.56 3.01
4955 5243 2.162408 GAGGATCCAAGAAACAAAGGCG 59.838 50.000 15.82 0.00 0.00 5.52
4982 5270 0.107017 ATTCAGTTCCCCATCGGCAG 60.107 55.000 0.00 0.00 0.00 4.85
4983 5271 0.107214 GATTCAGTTCCCCATCGGCA 60.107 55.000 0.00 0.00 0.00 5.69
4997 5285 3.857038 GCGGCGGGTAGGGATTCA 61.857 66.667 9.78 0.00 0.00 2.57
4998 5286 4.620937 GGCGGCGGGTAGGGATTC 62.621 72.222 9.78 0.00 0.00 2.52
5023 5311 0.598680 GGAATCTCATCGTCCTGCGG 60.599 60.000 0.00 0.00 41.72 5.69
5026 5314 2.099921 AGTTCGGAATCTCATCGTCCTG 59.900 50.000 0.00 0.00 0.00 3.86
5120 5408 1.607801 GCAATGGGGAGAACAAGGGC 61.608 60.000 0.00 0.00 0.00 5.19
5121 5409 1.315257 CGCAATGGGGAGAACAAGGG 61.315 60.000 0.00 0.00 0.00 3.95
5456 5745 7.815068 CACAAACTAGTAGTAGCATGAAGAGTT 59.185 37.037 2.50 0.00 0.00 3.01
5519 5808 3.286751 TTGCTGCTCGTGTTGCCC 61.287 61.111 0.00 0.00 0.00 5.36
5594 5892 4.862823 CCCCTCCCCCTCGTCCTC 62.863 77.778 0.00 0.00 0.00 3.71
5596 5894 4.410033 TTCCCCTCCCCCTCGTCC 62.410 72.222 0.00 0.00 0.00 4.79
5597 5895 2.764547 CTTCCCCTCCCCCTCGTC 60.765 72.222 0.00 0.00 0.00 4.20
5598 5896 4.416601 CCTTCCCCTCCCCCTCGT 62.417 72.222 0.00 0.00 0.00 4.18
5680 5987 3.930848 CCACCGTTTACTCCACATAGAAC 59.069 47.826 0.00 0.00 0.00 3.01
5685 5992 0.326927 CCCCACCGTTTACTCCACAT 59.673 55.000 0.00 0.00 0.00 3.21
5689 5996 1.078637 GCTCCCCACCGTTTACTCC 60.079 63.158 0.00 0.00 0.00 3.85
5721 6032 2.917172 GCCAAAAGCACCACCAATG 58.083 52.632 0.00 0.00 42.97 2.82
5888 6200 2.123897 ACTTGCAAACTGGGGCGT 60.124 55.556 0.00 0.00 0.00 5.68
5942 6290 5.064962 ACGTCGTTTGGAGTTTGAATAAACA 59.935 36.000 0.00 0.00 46.76 2.83
5954 6302 1.274596 CGGGATAACGTCGTTTGGAG 58.725 55.000 16.98 1.26 0.00 3.86
5959 6307 1.080569 AACGCGGGATAACGTCGTT 60.081 52.632 15.97 15.97 44.74 3.85
5982 6330 4.271590 TCCATAATGAATTGCACGAACG 57.728 40.909 0.00 0.00 0.00 3.95
5987 6335 9.128107 CCGTATTATTTCCATAATGAATTGCAC 57.872 33.333 0.00 0.00 36.43 4.57
6009 6357 2.865551 GTTTTCAACTCCGTGTTCCGTA 59.134 45.455 0.00 0.00 36.63 4.02
6017 6365 2.248835 CGGCCGTTTTCAACTCCGT 61.249 57.895 19.50 0.00 39.05 4.69
6019 6367 1.281656 CACGGCCGTTTTCAACTCC 59.718 57.895 32.11 0.00 0.00 3.85
6031 6379 1.678970 ATTCTCCAAAGCCACGGCC 60.679 57.895 3.95 0.00 43.17 6.13
6034 6382 0.962356 AGCCATTCTCCAAAGCCACG 60.962 55.000 0.00 0.00 0.00 4.94
6059 6407 9.563748 ACTTGGAAATTTTTGACATGATTGATT 57.436 25.926 0.00 0.00 0.00 2.57
6110 6460 1.336056 GGCGCCGTAAACCATTTTTGA 60.336 47.619 12.58 0.00 0.00 2.69
6118 6468 2.469516 CCATGAGGCGCCGTAAACC 61.470 63.158 23.20 7.87 0.00 3.27
6196 6546 0.858369 TAGGGCTAGGGGGTCTAGTG 59.142 60.000 0.00 0.00 45.55 2.74
6562 6914 2.125912 ACGCTGAAGCTAGGCACG 60.126 61.111 0.10 0.00 39.32 5.34
6700 7052 6.099701 AGGAACCAAAGCTTCAGGTAAAATTT 59.900 34.615 20.21 7.05 34.63 1.82


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

AutoCloner maintained by Alex Coulton.