Multiple sequence alignment - TraesCS2A01G559600

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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 TraesCS2A01G559600 chr2A 100.000 4442 0 0 1 4442 762314733 762319174 0.000000e+00 8203
1 TraesCS2A01G559600 chr2A 78.392 597 53 46 1275 1858 753815347 753815880 7.170000e-83 318
2 TraesCS2A01G559600 chr2A 93.878 49 3 0 1238 1286 753815287 753815335 1.710000e-09 75
3 TraesCS2A01G559600 chr2B 90.093 4512 261 83 1 4442 795049415 795045020 0.000000e+00 5685
4 TraesCS2A01G559600 chr2B 78.903 711 101 28 1275 1965 545170426 545169745 1.900000e-118 436
5 TraesCS2A01G559600 chr2B 77.518 814 105 43 1194 1965 98258156 98258933 6.870000e-113 418
6 TraesCS2A01G559600 chr2B 86.563 387 40 5 149 535 523781589 523781963 2.470000e-112 416
7 TraesCS2A01G559600 chr2D 89.911 4381 266 73 22 4290 637635192 637630876 0.000000e+00 5480
8 TraesCS2A01G559600 chr2D 83.826 643 69 11 2811 3440 637606936 637606316 2.980000e-161 579
9 TraesCS2A01G559600 chr2D 93.909 197 8 1 2460 2656 637607282 637607090 1.210000e-75 294
10 TraesCS2A01G559600 chr2D 95.312 64 2 1 2718 2781 637607069 637607007 2.830000e-17 100
11 TraesCS2A01G559600 chr1A 87.020 547 52 10 149 688 168548632 168548098 2.290000e-167 599
12 TraesCS2A01G559600 chr1A 77.952 703 102 30 1281 1965 96732036 96732703 1.500000e-104 390
13 TraesCS2A01G559600 chr3A 79.667 841 104 28 1077 1882 610535670 610536478 1.090000e-150 544
14 TraesCS2A01G559600 chr3A 79.543 831 106 26 1077 1875 610533236 610534034 6.540000e-148 534
15 TraesCS2A01G559600 chr3A 79.543 831 106 35 1077 1875 610534453 610535251 6.540000e-148 534
16 TraesCS2A01G559600 chr3A 79.095 641 90 25 1344 1965 572536597 572537212 6.920000e-108 401
17 TraesCS2A01G559600 chr7A 79.619 839 106 33 1077 1882 580495947 580496753 3.910000e-150 542
18 TraesCS2A01G559600 chr7A 78.520 838 115 33 1077 1882 724002079 724002883 1.440000e-134 490
19 TraesCS2A01G559600 chr6A 79.570 837 106 33 1078 1882 196013638 196014441 5.060000e-149 538
20 TraesCS2A01G559600 chr5D 78.781 853 98 42 1077 1882 19106002 19106818 3.090000e-136 496
21 TraesCS2A01G559600 chr4A 78.136 837 125 30 1077 1882 174391276 174390467 3.110000e-131 479
22 TraesCS2A01G559600 chr5B 79.483 580 66 26 1090 1640 24678244 24678799 3.270000e-96 363


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 TraesCS2A01G559600 chr2A 762314733 762319174 4441 False 8203.000000 8203 100.000000 1 4442 1 chr2A.!!$F1 4441
1 TraesCS2A01G559600 chr2B 795045020 795049415 4395 True 5685.000000 5685 90.093000 1 4442 1 chr2B.!!$R2 4441
2 TraesCS2A01G559600 chr2B 545169745 545170426 681 True 436.000000 436 78.903000 1275 1965 1 chr2B.!!$R1 690
3 TraesCS2A01G559600 chr2B 98258156 98258933 777 False 418.000000 418 77.518000 1194 1965 1 chr2B.!!$F1 771
4 TraesCS2A01G559600 chr2D 637630876 637635192 4316 True 5480.000000 5480 89.911000 22 4290 1 chr2D.!!$R1 4268
5 TraesCS2A01G559600 chr2D 637606316 637607282 966 True 324.333333 579 91.015667 2460 3440 3 chr2D.!!$R2 980
6 TraesCS2A01G559600 chr1A 168548098 168548632 534 True 599.000000 599 87.020000 149 688 1 chr1A.!!$R1 539
7 TraesCS2A01G559600 chr1A 96732036 96732703 667 False 390.000000 390 77.952000 1281 1965 1 chr1A.!!$F1 684
8 TraesCS2A01G559600 chr3A 610533236 610536478 3242 False 537.333333 544 79.584333 1077 1882 3 chr3A.!!$F2 805
9 TraesCS2A01G559600 chr3A 572536597 572537212 615 False 401.000000 401 79.095000 1344 1965 1 chr3A.!!$F1 621
10 TraesCS2A01G559600 chr7A 580495947 580496753 806 False 542.000000 542 79.619000 1077 1882 1 chr7A.!!$F1 805
11 TraesCS2A01G559600 chr7A 724002079 724002883 804 False 490.000000 490 78.520000 1077 1882 1 chr7A.!!$F2 805
12 TraesCS2A01G559600 chr6A 196013638 196014441 803 False 538.000000 538 79.570000 1078 1882 1 chr6A.!!$F1 804
13 TraesCS2A01G559600 chr5D 19106002 19106818 816 False 496.000000 496 78.781000 1077 1882 1 chr5D.!!$F1 805
14 TraesCS2A01G559600 chr4A 174390467 174391276 809 True 479.000000 479 78.136000 1077 1882 1 chr4A.!!$R1 805
15 TraesCS2A01G559600 chr5B 24678244 24678799 555 False 363.000000 363 79.483000 1090 1640 1 chr5B.!!$F1 550

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
757 795 0.390340 TGCAGCTTCGACATGTCTCC 60.390 55.000 22.95 8.69 0.00 3.71 F
759 797 0.803768 CAGCTTCGACATGTCTCCGG 60.804 60.000 22.95 8.12 0.00 5.14 F
1737 4292 0.671163 TGCCCGGTCGACATGTAAAC 60.671 55.000 18.91 0.00 0.00 2.01 F
1889 4479 2.034812 GCCGTATGTCTCTAGTTCCCTG 59.965 54.545 0.00 0.00 0.00 4.45 F
2915 5554 1.190323 GATCCGCTTCTATTTGTCGCG 59.810 52.381 0.00 0.00 43.08 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 4272 0.250793 TTTACATGTCGACCGGGCAT 59.749 50.000 8.76 2.38 0.00 4.40 R
1813 4401 0.322816 GCACAGGCCTGAAAGATGGA 60.323 55.000 39.19 0.00 34.07 3.41 R
2909 5548 0.108992 GACATACCTTGACCGCGACA 60.109 55.000 8.23 4.48 0.00 4.35 R
3215 5855 1.756538 TCTTCATCTATGGCGCTCACA 59.243 47.619 7.64 0.00 0.00 3.58 R
3737 6397 7.595502 CCGACAATACTACTAAATCCACTCATC 59.404 40.741 0.00 0.00 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
43 44 5.230726 GCCGATTGCAAATGATAAACTGAAG 59.769 40.000 1.71 0.00 40.77 3.02
63 65 7.722285 ACTGAAGTATATTCAGACTCCTCTACC 59.278 40.741 21.08 0.00 46.57 3.18
83 85 3.957497 ACCAGAGTCTAGAGGTATGCAAG 59.043 47.826 0.00 0.00 31.32 4.01
84 86 3.243704 CCAGAGTCTAGAGGTATGCAAGC 60.244 52.174 0.00 0.00 0.00 4.01
86 88 4.099266 CAGAGTCTAGAGGTATGCAAGCTT 59.901 45.833 0.00 0.00 35.60 3.74
87 89 4.714308 AGAGTCTAGAGGTATGCAAGCTTT 59.286 41.667 0.00 0.00 35.60 3.51
150 154 8.611051 AGAATTCTACAAGAGGTATACAAGGT 57.389 34.615 6.06 0.00 0.00 3.50
227 234 2.780643 TCGTACGCTTCGTCCGAG 59.219 61.111 11.24 0.00 42.50 4.63
321 328 1.369091 GATGTGCAGCCGGTACCTTG 61.369 60.000 10.90 6.93 0.00 3.61
362 369 2.481952 CCAACAGCAGCAGTAGAAAGAC 59.518 50.000 0.00 0.00 0.00 3.01
396 405 1.997874 GAGGAGATGCAGGTGGGGT 60.998 63.158 0.00 0.00 0.00 4.95
397 406 2.262774 GAGGAGATGCAGGTGGGGTG 62.263 65.000 0.00 0.00 0.00 4.61
400 409 4.447342 GATGCAGGTGGGGTGGGG 62.447 72.222 0.00 0.00 0.00 4.96
616 654 4.262981 GCCATTAGAGATGAGATCCAAGCT 60.263 45.833 0.00 0.00 0.00 3.74
617 655 5.239351 CCATTAGAGATGAGATCCAAGCTG 58.761 45.833 0.00 0.00 0.00 4.24
629 667 2.045524 TCCAAGCTGGAGATGAGATCC 58.954 52.381 0.00 0.00 42.67 3.36
665 703 2.496817 CCTACCTGCTGCGAGACC 59.503 66.667 0.00 0.00 0.00 3.85
688 726 3.069318 GTCGGAGGCGAAGGAGGT 61.069 66.667 0.00 0.00 0.00 3.85
756 794 0.997932 CTGCAGCTTCGACATGTCTC 59.002 55.000 22.95 9.67 0.00 3.36
757 795 0.390340 TGCAGCTTCGACATGTCTCC 60.390 55.000 22.95 8.69 0.00 3.71
758 796 1.416813 GCAGCTTCGACATGTCTCCG 61.417 60.000 22.95 11.44 0.00 4.63
759 797 0.803768 CAGCTTCGACATGTCTCCGG 60.804 60.000 22.95 8.12 0.00 5.14
760 798 1.215647 GCTTCGACATGTCTCCGGT 59.784 57.895 22.95 0.00 0.00 5.28
922 965 1.078143 AAATGAGGCCCGTGAGAGC 60.078 57.895 0.00 0.00 0.00 4.09
970 1020 1.914108 TCTCCTCGTCTTCTACCTCCA 59.086 52.381 0.00 0.00 0.00 3.86
978 1028 2.005960 CTTCTACCTCCAGACCCGCG 62.006 65.000 0.00 0.00 0.00 6.46
1403 3933 1.379642 GGGTACAGGGACTACGACGG 61.380 65.000 0.00 0.00 36.02 4.79
1548 4095 2.997869 CGCATCGTCACCATCGTG 59.002 61.111 0.00 0.00 41.72 4.35
1576 4125 6.822667 ACATCACATTCAGCTTTGTCATAA 57.177 33.333 0.00 0.00 0.00 1.90
1622 4177 4.142945 GCATTATCCTAAGCTCATCTTGCG 60.143 45.833 0.00 0.00 36.25 4.85
1629 4184 4.333649 CCTAAGCTCATCTTGCGAATTTGA 59.666 41.667 0.00 0.00 36.25 2.69
1717 4272 2.417379 GGATCACGAGTGCTTGCTTCTA 60.417 50.000 0.00 0.00 0.00 2.10
1737 4292 0.671163 TGCCCGGTCGACATGTAAAC 60.671 55.000 18.91 0.00 0.00 2.01
1747 4308 4.746115 GTCGACATGTAAACAACCACACTA 59.254 41.667 11.55 0.00 0.00 2.74
1776 4347 9.702494 CATATCTTAGTAGCAATGTTCATGAGA 57.298 33.333 0.00 0.00 0.00 3.27
1781 4352 9.755804 CTTAGTAGCAATGTTCATGAGAGATTA 57.244 33.333 0.00 0.00 0.00 1.75
1793 4381 7.118496 TCATGAGAGATTACCCTCTTCTTTC 57.882 40.000 0.00 0.00 43.11 2.62
1795 4383 6.287589 TGAGAGATTACCCTCTTCTTTCAC 57.712 41.667 0.00 0.00 43.11 3.18
1797 4385 6.498651 TGAGAGATTACCCTCTTCTTTCACTT 59.501 38.462 0.00 0.00 43.11 3.16
1798 4386 7.674348 TGAGAGATTACCCTCTTCTTTCACTTA 59.326 37.037 0.00 0.00 43.11 2.24
1799 4387 8.073467 AGAGATTACCCTCTTCTTTCACTTAG 57.927 38.462 0.00 0.00 40.40 2.18
1800 4388 6.645306 AGATTACCCTCTTCTTTCACTTAGC 58.355 40.000 0.00 0.00 0.00 3.09
1801 4389 5.818678 TTACCCTCTTCTTTCACTTAGCA 57.181 39.130 0.00 0.00 0.00 3.49
1802 4390 4.706842 ACCCTCTTCTTTCACTTAGCAA 57.293 40.909 0.00 0.00 0.00 3.91
1803 4391 4.646572 ACCCTCTTCTTTCACTTAGCAAG 58.353 43.478 0.00 0.00 0.00 4.01
1804 4392 4.348168 ACCCTCTTCTTTCACTTAGCAAGA 59.652 41.667 3.37 0.00 0.00 3.02
1805 4393 4.934602 CCCTCTTCTTTCACTTAGCAAGAG 59.065 45.833 0.00 0.00 37.62 2.85
1806 4394 5.512232 CCCTCTTCTTTCACTTAGCAAGAGT 60.512 44.000 0.00 0.00 36.61 3.24
1807 4395 5.994668 CCTCTTCTTTCACTTAGCAAGAGTT 59.005 40.000 0.00 0.00 36.61 3.01
1808 4396 6.147000 CCTCTTCTTTCACTTAGCAAGAGTTC 59.853 42.308 0.00 0.00 36.61 3.01
1809 4397 5.992217 TCTTCTTTCACTTAGCAAGAGTTCC 59.008 40.000 3.37 0.00 0.00 3.62
1810 4398 5.290493 TCTTTCACTTAGCAAGAGTTCCA 57.710 39.130 3.37 0.00 0.00 3.53
1811 4399 5.680619 TCTTTCACTTAGCAAGAGTTCCAA 58.319 37.500 3.37 0.00 0.00 3.53
1812 4400 6.299141 TCTTTCACTTAGCAAGAGTTCCAAT 58.701 36.000 3.37 0.00 0.00 3.16
1813 4401 6.772716 TCTTTCACTTAGCAAGAGTTCCAATT 59.227 34.615 3.37 0.00 0.00 2.32
1814 4402 6.560253 TTCACTTAGCAAGAGTTCCAATTC 57.440 37.500 3.37 0.00 0.00 2.17
1815 4403 5.003804 TCACTTAGCAAGAGTTCCAATTCC 58.996 41.667 3.37 0.00 0.00 3.01
1816 4404 4.761739 CACTTAGCAAGAGTTCCAATTCCA 59.238 41.667 3.37 0.00 0.00 3.53
1861 4451 2.945008 CAAGAGCACAAACTTCAGTGGA 59.055 45.455 0.00 0.00 36.29 4.02
1889 4479 2.034812 GCCGTATGTCTCTAGTTCCCTG 59.965 54.545 0.00 0.00 0.00 4.45
2005 4597 7.383843 GGTTTTTAATGAGGTAAATGGTGTGTG 59.616 37.037 0.00 0.00 0.00 3.82
2008 4600 5.705609 AATGAGGTAAATGGTGTGTGTTC 57.294 39.130 0.00 0.00 0.00 3.18
2016 4608 4.853924 AATGGTGTGTGTTCTTCCATTC 57.146 40.909 0.00 0.00 42.79 2.67
2017 4609 3.576078 TGGTGTGTGTTCTTCCATTCT 57.424 42.857 0.00 0.00 0.00 2.40
2018 4610 3.213506 TGGTGTGTGTTCTTCCATTCTG 58.786 45.455 0.00 0.00 0.00 3.02
2126 4718 3.670625 CGGGTAAGGATCACACAGAAAA 58.329 45.455 0.00 0.00 0.00 2.29
2134 4726 5.003804 AGGATCACACAGAAAACACCATAC 58.996 41.667 0.00 0.00 0.00 2.39
2141 4733 4.382457 CACAGAAAACACCATACAAATGCG 59.618 41.667 0.00 0.00 0.00 4.73
2145 4737 4.576216 AAACACCATACAAATGCGAACA 57.424 36.364 0.00 0.00 0.00 3.18
2241 4833 6.036083 GCTTATGTAACACACTGACACTATGG 59.964 42.308 0.00 0.00 0.00 2.74
2337 4934 4.685575 GCCCTCTGTTTCAGATTCTGCTAT 60.686 45.833 8.89 0.00 39.92 2.97
2396 4993 2.640826 TCCAAGAATTCCACGGTAACCT 59.359 45.455 0.65 0.00 0.00 3.50
2407 5004 3.395639 CACGGTAACCTGAAGCACTAAA 58.604 45.455 0.00 0.00 0.00 1.85
2408 5005 3.810941 CACGGTAACCTGAAGCACTAAAA 59.189 43.478 0.00 0.00 0.00 1.52
2641 5238 6.218746 AGAGATTTGCAACTTCAATTTGGTC 58.781 36.000 0.00 0.00 0.00 4.02
2717 5314 5.769484 TCATATTCCGACCAAGTAGAGAC 57.231 43.478 0.00 0.00 0.00 3.36
2767 5365 9.771534 GCCTTCTCAGAATAGTTAACATATTCT 57.228 33.333 21.85 21.85 46.17 2.40
2864 5503 3.679917 CGTGGATACTCTGTTTGCAGGAT 60.680 47.826 0.00 0.00 42.78 3.24
2909 5548 2.431057 ACCAGTCGATCCGCTTCTATTT 59.569 45.455 0.00 0.00 0.00 1.40
2915 5554 1.190323 GATCCGCTTCTATTTGTCGCG 59.810 52.381 0.00 0.00 43.08 5.87
2935 5574 2.612972 CGGTCAAGGTATGTCAGTTGCT 60.613 50.000 0.00 0.00 0.00 3.91
2959 5598 1.349026 TCAGCCTGCTTAGCAACTCTT 59.651 47.619 8.68 0.00 38.41 2.85
2991 5630 5.675684 ATGCTTTTATAAACCCCCACAAG 57.324 39.130 0.00 0.00 0.00 3.16
3097 5736 8.834004 AGTCCAGTTACCACTATTCTTATACA 57.166 34.615 0.00 0.00 0.00 2.29
3100 5739 9.925545 TCCAGTTACCACTATTCTTATACACTA 57.074 33.333 0.00 0.00 0.00 2.74
3152 5792 9.248291 CAACTTAAAAGCACTTTGTGTATGAAT 57.752 29.630 0.00 0.00 35.75 2.57
3160 5800 6.878923 AGCACTTTGTGTATGAATAGCAACTA 59.121 34.615 0.00 0.00 35.75 2.24
3215 5855 1.224592 GATGGACGACCCCAGCATT 59.775 57.895 0.34 0.00 41.93 3.56
3331 5975 6.767902 TCCTAGCTACTTTTTGCTATTGATGG 59.232 38.462 0.00 0.00 40.43 3.51
3332 5976 5.254339 AGCTACTTTTTGCTATTGATGGC 57.746 39.130 0.00 0.00 37.81 4.40
3440 6099 2.417339 GGCGACGATGATGTTAGCTA 57.583 50.000 0.00 0.00 0.00 3.32
3473 6132 6.123045 TGCATGATGAGAATGTGAGGATAT 57.877 37.500 0.00 0.00 0.00 1.63
3474 6133 7.248743 TGCATGATGAGAATGTGAGGATATA 57.751 36.000 0.00 0.00 0.00 0.86
3535 6194 4.634184 ATGTTGTTAGATCTCGCGTAGT 57.366 40.909 5.77 0.00 0.00 2.73
3561 6220 4.230745 ACGTATTTTGCAGGTAGGGATT 57.769 40.909 0.00 0.00 0.00 3.01
3628 6288 1.470494 GGTTAAGAAGAAGCTGCAGGC 59.530 52.381 17.12 7.98 42.19 4.85
3737 6397 6.825213 TGTCTATGAGTTGGAGAAATTGATGG 59.175 38.462 0.00 0.00 0.00 3.51
3763 6423 6.802608 TGAGTGGATTTAGTAGTATTGTCGG 58.197 40.000 0.00 0.00 0.00 4.79
3811 6471 9.856162 AAGTTTAGAGGGATACACAAGTTTTTA 57.144 29.630 0.00 0.00 39.74 1.52
3876 6536 8.790718 ACCACAAATGCATTTTAATAATTTGCA 58.209 25.926 21.95 11.14 40.32 4.08
4089 6775 0.179171 ACTTGTGATACTCGACGCCG 60.179 55.000 0.00 0.00 37.07 6.46
4099 6785 2.527100 ACTCGACGCCGAAATTAAGAG 58.473 47.619 0.00 0.00 45.04 2.85
4160 6846 8.067784 TGTAAAGATAGAGCAACTTTTTCAACG 58.932 33.333 0.00 0.00 35.79 4.10
4333 7020 9.632807 TGTGTTATTTGTTAATGAATAGGCAAC 57.367 29.630 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.324819 ACTTCAGTTTATCATTTGCAATCGG 58.675 36.000 0.00 0.00 0.00 4.18
43 44 7.228590 ACTCTGGTAGAGGAGTCTGAATATAC 58.771 42.308 10.31 0.00 46.45 1.47
63 65 3.636300 AGCTTGCATACCTCTAGACTCTG 59.364 47.826 0.00 0.00 0.00 3.35
92 94 9.989869 GAAACATACTTCAGCTTATTCCTTAAC 57.010 33.333 0.00 0.00 0.00 2.01
110 112 8.988064 TGTAGAATTCTCAGTCTGAAACATAC 57.012 34.615 12.24 0.00 0.00 2.39
124 126 8.697292 ACCTTGTATACCTCTTGTAGAATTCTC 58.303 37.037 12.24 4.68 31.61 2.87
125 127 8.478877 CACCTTGTATACCTCTTGTAGAATTCT 58.521 37.037 13.56 13.56 31.61 2.40
150 154 9.527157 TTCCAGTTTATAAGATGAATTTGGACA 57.473 29.630 0.00 0.00 30.11 4.02
227 234 2.791849 GCTCGTCGAGAAGTACACCATC 60.792 54.545 26.11 0.00 0.00 3.51
321 328 2.224018 GGACTGATGATGGTCTGCTCTC 60.224 54.545 0.00 0.00 33.46 3.20
362 369 5.723672 TCTCCTCTTGTTAACTACTGGTG 57.276 43.478 7.22 5.78 0.00 4.17
616 654 2.121948 CAACCCAGGATCTCATCTCCA 58.878 52.381 0.00 0.00 35.08 3.86
617 655 1.419387 CCAACCCAGGATCTCATCTCC 59.581 57.143 0.00 0.00 0.00 3.71
620 658 1.216990 ACCCAACCCAGGATCTCATC 58.783 55.000 0.00 0.00 0.00 2.92
621 659 1.285962 CAACCCAACCCAGGATCTCAT 59.714 52.381 0.00 0.00 0.00 2.90
622 660 0.698238 CAACCCAACCCAGGATCTCA 59.302 55.000 0.00 0.00 0.00 3.27
623 661 0.034089 CCAACCCAACCCAGGATCTC 60.034 60.000 0.00 0.00 0.00 2.75
624 662 0.776080 ACCAACCCAACCCAGGATCT 60.776 55.000 0.00 0.00 0.00 2.75
625 663 0.611896 CACCAACCCAACCCAGGATC 60.612 60.000 0.00 0.00 0.00 3.36
626 664 1.464722 CACCAACCCAACCCAGGAT 59.535 57.895 0.00 0.00 0.00 3.24
627 665 2.773527 CCACCAACCCAACCCAGGA 61.774 63.158 0.00 0.00 0.00 3.86
628 666 2.203625 CCACCAACCCAACCCAGG 60.204 66.667 0.00 0.00 0.00 4.45
629 667 2.917227 GCCACCAACCCAACCCAG 60.917 66.667 0.00 0.00 0.00 4.45
649 687 2.496817 GGGTCTCGCAGCAGGTAG 59.503 66.667 0.00 0.00 0.00 3.18
688 726 1.069090 GTCACGCACTCCAACCTCA 59.931 57.895 0.00 0.00 0.00 3.86
773 811 2.098680 CCAGAGAGTCGTCGTCGC 59.901 66.667 0.00 0.00 36.96 5.19
774 812 1.015085 AGACCAGAGAGTCGTCGTCG 61.015 60.000 0.00 0.00 41.83 5.12
775 813 0.444651 CAGACCAGAGAGTCGTCGTC 59.555 60.000 0.00 0.00 41.83 4.20
897 940 2.830370 GGGCCTCATTTGAGCCCG 60.830 66.667 18.19 2.40 43.41 6.13
898 941 2.830370 CGGGCCTCATTTGAGCCC 60.830 66.667 20.96 20.96 46.14 5.19
899 942 2.044946 ACGGGCCTCATTTGAGCC 60.045 61.111 0.84 7.16 40.75 4.70
901 944 0.250234 TCTCACGGGCCTCATTTGAG 59.750 55.000 0.84 7.90 41.71 3.02
903 946 1.372087 GCTCTCACGGGCCTCATTTG 61.372 60.000 0.84 0.00 0.00 2.32
905 948 2.586792 GCTCTCACGGGCCTCATT 59.413 61.111 0.84 0.00 0.00 2.57
922 965 4.047822 GAGTGGAGACAGATATTTGCTCG 58.952 47.826 9.79 0.00 44.46 5.03
978 1028 6.183360 CCATCTTTCACTTTCACTATCCGTTC 60.183 42.308 0.00 0.00 0.00 3.95
1403 3933 1.152652 TCCTCCTCATCCTCCTCGC 60.153 63.158 0.00 0.00 0.00 5.03
1548 4095 6.073058 TGACAAAGCTGAATGTGATGTAACTC 60.073 38.462 4.93 0.00 0.00 3.01
1553 4100 6.432162 AGTTATGACAAAGCTGAATGTGATGT 59.568 34.615 4.93 0.00 0.00 3.06
1555 4102 8.565896 TTAGTTATGACAAAGCTGAATGTGAT 57.434 30.769 4.93 5.08 0.00 3.06
1622 4177 4.033684 GCGTCATCAATCTGCTCAAATTC 58.966 43.478 0.00 0.00 0.00 2.17
1629 4184 1.002366 GTTCGCGTCATCAATCTGCT 58.998 50.000 5.77 0.00 0.00 4.24
1717 4272 0.250793 TTTACATGTCGACCGGGCAT 59.749 50.000 8.76 2.38 0.00 4.40
1737 4292 9.627395 GCTACTAAGATATGTATAGTGTGGTTG 57.373 37.037 0.00 0.00 32.44 3.77
1755 4320 8.659925 AATCTCTCATGAACATTGCTACTAAG 57.340 34.615 0.00 0.00 0.00 2.18
1758 4323 6.989169 GGTAATCTCTCATGAACATTGCTACT 59.011 38.462 0.00 0.00 0.00 2.57
1759 4324 6.203723 GGGTAATCTCTCATGAACATTGCTAC 59.796 42.308 0.00 0.00 0.00 3.58
1761 4332 5.104193 AGGGTAATCTCTCATGAACATTGCT 60.104 40.000 0.00 0.00 0.00 3.91
1773 4344 6.538945 AGTGAAAGAAGAGGGTAATCTCTC 57.461 41.667 0.00 0.00 42.75 3.20
1776 4347 6.213600 TGCTAAGTGAAAGAAGAGGGTAATCT 59.786 38.462 0.00 0.00 0.00 2.40
1781 4352 4.348168 TCTTGCTAAGTGAAAGAAGAGGGT 59.652 41.667 0.00 0.00 0.00 4.34
1793 4381 4.761739 TGGAATTGGAACTCTTGCTAAGTG 59.238 41.667 0.00 0.00 0.00 3.16
1795 4383 5.884792 AGATGGAATTGGAACTCTTGCTAAG 59.115 40.000 0.00 0.00 0.00 2.18
1797 4385 5.441718 AGATGGAATTGGAACTCTTGCTA 57.558 39.130 0.00 0.00 0.00 3.49
1798 4386 4.313020 AGATGGAATTGGAACTCTTGCT 57.687 40.909 0.00 0.00 0.00 3.91
1799 4387 5.047802 TGAAAGATGGAATTGGAACTCTTGC 60.048 40.000 0.00 0.00 0.00 4.01
1800 4388 6.349944 CCTGAAAGATGGAATTGGAACTCTTG 60.350 42.308 0.00 0.00 34.07 3.02
1801 4389 5.713861 CCTGAAAGATGGAATTGGAACTCTT 59.286 40.000 0.00 0.00 34.07 2.85
1802 4390 5.259632 CCTGAAAGATGGAATTGGAACTCT 58.740 41.667 0.00 0.00 34.07 3.24
1803 4391 4.142293 GCCTGAAAGATGGAATTGGAACTC 60.142 45.833 0.00 0.00 34.07 3.01
1804 4392 3.766051 GCCTGAAAGATGGAATTGGAACT 59.234 43.478 0.00 0.00 34.07 3.01
1805 4393 3.118992 GGCCTGAAAGATGGAATTGGAAC 60.119 47.826 0.00 0.00 34.07 3.62
1806 4394 3.099141 GGCCTGAAAGATGGAATTGGAA 58.901 45.455 0.00 0.00 34.07 3.53
1807 4395 2.312741 AGGCCTGAAAGATGGAATTGGA 59.687 45.455 3.11 0.00 34.07 3.53
1808 4396 2.429610 CAGGCCTGAAAGATGGAATTGG 59.570 50.000 29.88 0.00 34.07 3.16
1809 4397 3.094572 ACAGGCCTGAAAGATGGAATTG 58.905 45.455 39.19 8.65 34.07 2.32
1810 4398 3.094572 CACAGGCCTGAAAGATGGAATT 58.905 45.455 39.19 9.18 34.07 2.17
1811 4399 2.731572 CACAGGCCTGAAAGATGGAAT 58.268 47.619 39.19 9.77 34.07 3.01
1812 4400 1.887956 GCACAGGCCTGAAAGATGGAA 60.888 52.381 39.19 0.00 34.07 3.53
1813 4401 0.322816 GCACAGGCCTGAAAGATGGA 60.323 55.000 39.19 0.00 34.07 3.41
1814 4402 0.609957 TGCACAGGCCTGAAAGATGG 60.610 55.000 39.19 17.98 40.13 3.51
1815 4403 0.809385 CTGCACAGGCCTGAAAGATG 59.191 55.000 39.19 25.82 40.13 2.90
1816 4404 0.323178 CCTGCACAGGCCTGAAAGAT 60.323 55.000 39.19 13.98 42.44 2.40
1861 4451 3.898123 ACTAGAGACATACGGCAATCCAT 59.102 43.478 0.00 0.00 0.00 3.41
1889 4479 4.025015 AGCACTCAATCGATGAAAATGC 57.975 40.909 0.00 6.25 39.79 3.56
1982 4574 7.589958 ACACACACCATTTACCTCATTAAAA 57.410 32.000 0.00 0.00 0.00 1.52
1991 4583 3.886505 TGGAAGAACACACACCATTTACC 59.113 43.478 0.00 0.00 0.00 2.85
1997 4589 3.213506 CAGAATGGAAGAACACACACCA 58.786 45.455 0.00 0.00 35.09 4.17
1998 4590 3.214328 ACAGAATGGAAGAACACACACC 58.786 45.455 0.00 0.00 43.62 4.16
1999 4591 4.096382 ACAACAGAATGGAAGAACACACAC 59.904 41.667 0.00 0.00 43.62 3.82
2005 4597 5.763204 TCAACCTACAACAGAATGGAAGAAC 59.237 40.000 0.00 0.00 43.62 3.01
2008 4600 4.152402 CGTCAACCTACAACAGAATGGAAG 59.848 45.833 0.00 0.00 43.62 3.46
2016 4608 2.993899 GGTCATCGTCAACCTACAACAG 59.006 50.000 0.00 0.00 32.54 3.16
2017 4609 2.365941 TGGTCATCGTCAACCTACAACA 59.634 45.455 4.88 0.00 36.47 3.33
2018 4610 2.993899 CTGGTCATCGTCAACCTACAAC 59.006 50.000 4.88 0.00 36.47 3.32
2126 4718 4.009675 AGATGTTCGCATTTGTATGGTGT 58.990 39.130 0.00 0.00 38.08 4.16
2134 4726 8.424731 GTTAAAAAGGTTAGATGTTCGCATTTG 58.575 33.333 0.00 0.00 38.08 2.32
2141 4733 9.665264 CAGTTCAGTTAAAAAGGTTAGATGTTC 57.335 33.333 0.00 0.00 0.00 3.18
2145 4737 9.274206 GTCTCAGTTCAGTTAAAAAGGTTAGAT 57.726 33.333 0.00 0.00 0.00 1.98
2299 4891 8.773033 AAACAGAGGGCAAGAATTATTATCAT 57.227 30.769 0.00 0.00 0.00 2.45
2300 4892 7.833682 TGAAACAGAGGGCAAGAATTATTATCA 59.166 33.333 0.00 0.00 0.00 2.15
2301 4893 8.225603 TGAAACAGAGGGCAAGAATTATTATC 57.774 34.615 0.00 0.00 0.00 1.75
2302 4894 8.055181 TCTGAAACAGAGGGCAAGAATTATTAT 58.945 33.333 0.00 0.00 35.39 1.28
2303 4895 7.402054 TCTGAAACAGAGGGCAAGAATTATTA 58.598 34.615 0.00 0.00 35.39 0.98
2304 4896 6.248433 TCTGAAACAGAGGGCAAGAATTATT 58.752 36.000 0.00 0.00 35.39 1.40
2305 4897 5.819991 TCTGAAACAGAGGGCAAGAATTAT 58.180 37.500 0.00 0.00 35.39 1.28
2306 4898 5.241403 TCTGAAACAGAGGGCAAGAATTA 57.759 39.130 0.00 0.00 35.39 1.40
2307 4899 4.104383 TCTGAAACAGAGGGCAAGAATT 57.896 40.909 0.00 0.00 35.39 2.17
2309 4901 3.795688 ATCTGAAACAGAGGGCAAGAA 57.204 42.857 7.50 0.00 44.08 2.52
2337 4934 3.246112 AAGCCACCCCGTGCTGTA 61.246 61.111 0.00 0.00 31.34 2.74
2447 5044 3.255888 CCTTTTCTTACAAGCAGGAACCC 59.744 47.826 0.00 0.00 0.00 4.11
2679 5276 5.767168 GGAATATGATTCTTTGGCTACAGCT 59.233 40.000 0.54 0.00 41.70 4.24
2717 5314 6.237542 GCAAATAAATTACAGTTCACCGCATG 60.238 38.462 0.00 0.00 0.00 4.06
2767 5365 7.331026 AGATATTTACAGTAGCAGCAAGACAA 58.669 34.615 0.00 0.00 0.00 3.18
2820 5459 4.319046 CGCTAAGTGCCAGCAATAACATAG 60.319 45.833 0.00 0.00 39.04 2.23
2864 5503 7.309805 GGTGTATAGATCATATAGTGTGCACCA 60.310 40.741 15.69 0.00 39.65 4.17
2909 5548 0.108992 GACATACCTTGACCGCGACA 60.109 55.000 8.23 4.48 0.00 4.35
2915 5554 3.003480 GAGCAACTGACATACCTTGACC 58.997 50.000 0.00 0.00 0.00 4.02
2935 5574 2.154462 GTTGCTAAGCAGGCTGAAAGA 58.846 47.619 20.86 0.00 40.61 2.52
2985 5624 5.649782 ATGCATAACTTCTTTCCTTGTGG 57.350 39.130 0.00 0.00 0.00 4.17
3013 5652 2.299297 TGCACAATGACATGCCAATCAA 59.701 40.909 0.00 0.00 41.33 2.57
3097 5736 5.645497 GCCAATCATCAAAACACTCTCTAGT 59.355 40.000 0.00 0.00 35.91 2.57
3100 5739 4.401022 TGCCAATCATCAAAACACTCTCT 58.599 39.130 0.00 0.00 0.00 3.10
3106 5745 2.364647 TGCACTGCCAATCATCAAAACA 59.635 40.909 0.00 0.00 0.00 2.83
3152 5792 7.864108 TCACCGTAAGTAAGTATAGTTGCTA 57.136 36.000 10.85 0.00 0.00 3.49
3160 5800 8.742777 TGTTTACAGATCACCGTAAGTAAGTAT 58.257 33.333 0.00 0.00 0.00 2.12
3171 5811 2.352651 CCTGCATGTTTACAGATCACCG 59.647 50.000 0.00 0.00 35.90 4.94
3215 5855 1.756538 TCTTCATCTATGGCGCTCACA 59.243 47.619 7.64 0.00 0.00 3.58
3331 5975 5.183140 ACACCAGTCAGTACAAAAATATGGC 59.817 40.000 0.00 0.00 0.00 4.40
3332 5976 6.817765 ACACCAGTCAGTACAAAAATATGG 57.182 37.500 0.00 0.00 0.00 2.74
3449 6108 4.432980 TCCTCACATTCTCATCATGCAT 57.567 40.909 0.00 0.00 0.00 3.96
3514 6173 4.095932 TCACTACGCGAGATCTAACAACAT 59.904 41.667 15.93 0.00 0.00 2.71
3535 6194 4.382254 CCCTACCTGCAAAATACGTACTCA 60.382 45.833 0.00 0.00 0.00 3.41
3561 6220 4.459390 ACAGCACCAACGTATGTGTATA 57.541 40.909 16.04 0.00 34.94 1.47
3628 6288 5.658190 ACCATTACATCCTCCAAATTCAAGG 59.342 40.000 0.00 0.00 0.00 3.61
3729 6389 8.497745 ACTACTAAATCCACTCATCCATCAATT 58.502 33.333 0.00 0.00 0.00 2.32
3737 6397 7.595502 CCGACAATACTACTAAATCCACTCATC 59.404 40.741 0.00 0.00 0.00 2.92
4040 6724 9.571810 TTTTGCAATGAACATAGTGATGAATAC 57.428 29.630 0.00 0.00 36.48 1.89
4160 6846 8.976986 ATCACATTGAGCTTTCAATTAAGTTC 57.023 30.769 0.00 0.00 38.16 3.01


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

AutoCloner maintained by Alex Coulton.