Multiple sequence alignment - TraesCS2A01G063500

Loading Multiple Alignment...

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 TraesCS2A01G063500 chr2A 100.000 3695 0 0 1561 5255 27969937 27966243 0.000000e+00 6824.0
1 TraesCS2A01G063500 chr2A 84.563 2481 360 10 1563 4039 745267060 745264599 0.000000e+00 2438.0
2 TraesCS2A01G063500 chr2A 100.000 1122 0 0 1 1122 27971497 27970376 0.000000e+00 2073.0
3 TraesCS2A01G063500 chr2A 87.745 408 50 0 3608 4015 27967860 27967453 1.320000e-130 477.0
4 TraesCS2A01G063500 chr2A 87.745 408 50 0 3638 4045 27967890 27967483 1.320000e-130 477.0
5 TraesCS2A01G063500 chr2A 76.582 158 11 8 5094 5232 27955554 27955404 4.390000e-06 63.9
6 TraesCS2A01G063500 chr2D 96.372 3528 124 3 1561 5085 25354579 25351053 0.000000e+00 5803.0
7 TraesCS2A01G063500 chr2D 83.945 2317 346 12 1733 4045 615063362 615061068 0.000000e+00 2194.0
8 TraesCS2A01G063500 chr2D 92.512 828 34 11 1 812 25358037 25357222 0.000000e+00 1160.0
9 TraesCS2A01G063500 chr2D 83.881 670 85 13 154 815 25364319 25363665 7.480000e-173 617.0
10 TraesCS2A01G063500 chr2D 92.157 408 32 0 3638 4045 25352532 25352125 1.270000e-160 577.0
11 TraesCS2A01G063500 chr2D 87.500 416 52 0 3608 4023 25352502 25352087 1.020000e-131 481.0
12 TraesCS2A01G063500 chr2D 90.769 325 12 6 813 1119 25354937 25354613 8.140000e-113 418.0
13 TraesCS2A01G063500 chr2D 90.683 161 15 0 1563 1723 615063828 615063668 1.150000e-51 215.0
14 TraesCS2A01G063500 chr2D 95.455 66 3 0 5190 5255 25351052 25350987 7.200000e-19 106.0
15 TraesCS2A01G063500 chr2D 85.075 67 3 2 5168 5234 25342250 25342191 1.580000e-05 62.1
16 TraesCS2A01G063500 chr2B 95.499 2466 111 0 1575 4040 41147452 41144987 0.000000e+00 3940.0
17 TraesCS2A01G063500 chr2B 84.522 2481 364 10 1563 4039 749421505 749419041 0.000000e+00 2436.0
18 TraesCS2A01G063500 chr2B 94.801 1481 63 8 3608 5085 41145329 41143860 0.000000e+00 2296.0
19 TraesCS2A01G063500 chr2B 90.046 432 43 0 3614 4045 41145353 41144922 1.280000e-155 560.0
20 TraesCS2A01G063500 chr2B 87.224 407 52 0 3617 4023 41145290 41144884 1.030000e-126 464.0
21 TraesCS2A01G063500 chr2B 89.767 215 10 6 911 1119 41148085 41147877 1.120000e-66 265.0
22 TraesCS2A01G063500 chr2B 95.455 66 3 0 5190 5255 41143859 41143794 7.200000e-19 106.0
23 TraesCS2A01G063500 chr2B 100.000 30 0 0 5168 5197 41135674 41135645 7.350000e-04 56.5
24 TraesCS2A01G063500 chr1D 90.244 82 8 0 4649 4730 378099498 378099579 2.000000e-19 108.0


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 TraesCS2A01G063500 chr2A 27966243 27971497 5254 True 2462.750000 6824 93.872500 1 5255 4 chr2A.!!$R3 5254
1 TraesCS2A01G063500 chr2A 745264599 745267060 2461 True 2438.000000 2438 84.563000 1563 4039 1 chr2A.!!$R2 2476
2 TraesCS2A01G063500 chr2D 25350987 25358037 7050 True 1424.166667 5803 92.460833 1 5255 6 chr2D.!!$R3 5254
3 TraesCS2A01G063500 chr2D 615061068 615063828 2760 True 1204.500000 2194 87.314000 1563 4045 2 chr2D.!!$R4 2482
4 TraesCS2A01G063500 chr2D 25363665 25364319 654 True 617.000000 617 83.881000 154 815 1 chr2D.!!$R2 661
5 TraesCS2A01G063500 chr2B 749419041 749421505 2464 True 2436.000000 2436 84.522000 1563 4039 1 chr2B.!!$R2 2476
6 TraesCS2A01G063500 chr2B 41143794 41148085 4291 True 1271.833333 3940 92.132000 911 5255 6 chr2B.!!$R3 4344

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
250 251 2.025699 ACAACATGTATTAACGGGCCCT 60.026 45.455 22.43 4.01 0.0 5.19 F
1921 4948 1.887198 TCTTCGACTTCTTCTTCCGCT 59.113 47.619 0.00 0.00 0.0 5.52 F
2922 5949 2.143122 GAGATCAAGCCGAACACAACA 58.857 47.619 0.00 0.00 0.0 3.33 F
3962 7142 0.111253 GGGTATGGGGCTCATCAAGG 59.889 60.000 1.35 0.00 37.3 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 5033 1.768077 AGCATCTCCTGGTAGGCCC 60.768 63.158 0.00 0.0 34.61 5.80 R
3004 6031 0.814010 GGAGTTGCGACAACACCACT 60.814 55.000 23.47 7.3 32.24 4.00 R
4045 7285 0.179702 GATGGCTGTGATGGCTGAGA 59.820 55.000 0.00 0.0 0.00 3.27 R
5107 8350 0.180642 ATGGCAGAGCTGGACATGAG 59.819 55.000 0.00 0.0 0.00 2.90 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
29 30 7.631933 TCCCAAATGCATGGAATTTTTAAGAT 58.368 30.769 7.97 0.00 43.54 2.40
250 251 2.025699 ACAACATGTATTAACGGGCCCT 60.026 45.455 22.43 4.01 0.00 5.19
375 389 4.341235 TGCCTCTAATAGCGTGTGATAAGT 59.659 41.667 0.00 0.00 0.00 2.24
383 397 7.520451 AATAGCGTGTGATAAGTAGGACATA 57.480 36.000 0.00 0.00 0.00 2.29
446 460 7.393234 CCCGTATGATGTCCACCATTTTTATAT 59.607 37.037 0.00 0.00 32.56 0.86
535 554 5.286082 CACTAGTTGTGTGTGAAGCAAAAAC 59.714 40.000 0.00 0.00 41.53 2.43
550 569 7.915923 TGAAGCAAAAACGTGTTCATGTATTTA 59.084 29.630 0.00 0.00 0.00 1.40
856 3164 2.270923 GAAATGAAAGCGAAATGGCCC 58.729 47.619 0.00 0.00 0.00 5.80
1921 4948 1.887198 TCTTCGACTTCTTCTTCCGCT 59.113 47.619 0.00 0.00 0.00 5.52
2031 5058 2.503061 CAGGAGATGCTGGACGGG 59.497 66.667 0.00 0.00 0.00 5.28
2163 5190 4.473520 CAGGGCGCCGACTCCATT 62.474 66.667 22.54 0.00 0.00 3.16
2769 5796 4.929808 GTGGATGACACGATTCAGTACTTT 59.070 41.667 0.00 0.00 40.85 2.66
2893 5920 2.253610 TGAAGGTGTACGGAAGGATGT 58.746 47.619 0.00 0.00 0.00 3.06
2922 5949 2.143122 GAGATCAAGCCGAACACAACA 58.857 47.619 0.00 0.00 0.00 3.33
3004 6031 1.685224 GTGAGGGACATGGCAAGGA 59.315 57.895 0.00 0.00 0.00 3.36
3254 6281 2.165030 CTCCACAACCATTTCATCCTGC 59.835 50.000 0.00 0.00 0.00 4.85
3312 6339 1.279271 TCTCCTAAACTTCAGCAGCCC 59.721 52.381 0.00 0.00 0.00 5.19
3368 6395 5.016173 TGTTGGTGCTTCTAATAAATGGCT 58.984 37.500 0.00 0.00 0.00 4.75
3401 6428 7.461182 TTTCTTCTCCTCAAGAAAAACAACA 57.539 32.000 6.01 0.00 45.32 3.33
3427 6454 1.304282 GCCCTGCCTCAAGATGGAA 59.696 57.895 0.00 0.00 0.00 3.53
3486 6513 1.212935 ACAGTTGGTGCTCCTCAAGTT 59.787 47.619 6.34 0.00 34.23 2.66
3516 6543 2.584835 ATTTTGGCTCAGCTACACCA 57.415 45.000 0.00 0.00 0.00 4.17
3517 6544 1.604604 TTTTGGCTCAGCTACACCAC 58.395 50.000 0.00 0.00 0.00 4.16
3621 6651 0.548031 CATGGCAGACAGGGTATGGT 59.452 55.000 0.00 0.00 0.00 3.55
3705 6825 2.753009 ATCAAGCGCAACAGCCTGGA 62.753 55.000 11.47 0.00 38.01 3.86
3744 6894 2.256591 GCAGCCTGGATATGGTGCG 61.257 63.158 0.00 0.00 0.00 5.34
3820 7000 3.818787 CCCATCAGGCGCAACAGC 61.819 66.667 10.83 0.00 0.00 4.40
3839 7019 1.375908 CCGGATATGGCACCCATCG 60.376 63.158 0.00 0.00 40.74 3.84
3962 7142 0.111253 GGGTATGGGGCTCATCAAGG 59.889 60.000 1.35 0.00 37.30 3.61
3992 7172 1.143813 AGGTATGGGGCTCATCAAGG 58.856 55.000 1.35 0.00 37.30 3.61
3993 7173 0.846693 GGTATGGGGCTCATCAAGGT 59.153 55.000 1.35 0.00 37.30 3.50
3996 7236 1.229131 ATGGGGCTCATCAAGGTCAT 58.771 50.000 0.00 0.00 0.00 3.06
4045 7285 1.304282 CAGCCTGGGTATGGTGCTT 59.696 57.895 0.00 0.00 0.00 3.91
4058 7298 0.321919 GGTGCTTCTCAGCCATCACA 60.322 55.000 0.00 0.00 46.74 3.58
4180 7420 0.679505 TTCTCGTCAAGGTGGACCAG 59.320 55.000 0.00 0.00 38.89 4.00
4222 7462 3.324930 CTGCTGAGGCCCCAGACA 61.325 66.667 20.04 14.15 36.29 3.41
4230 7470 2.036256 GCCCCAGACAACATGGCT 59.964 61.111 0.00 0.00 34.86 4.75
4231 7471 1.302949 GCCCCAGACAACATGGCTA 59.697 57.895 0.00 0.00 29.42 3.93
4247 7487 3.457234 TGGCTATCAAATACAGTCAGCG 58.543 45.455 0.00 0.00 0.00 5.18
4292 7532 3.373767 GGGCTCCAAACCAAATATACCCT 60.374 47.826 0.00 0.00 0.00 4.34
4341 7581 7.040755 TGTGTCCCTAATTAAACAGTGTTCATG 60.041 37.037 9.40 0.00 0.00 3.07
4376 7616 6.397831 CACATTTTATTCCATGTGTGCAAG 57.602 37.500 4.44 0.00 43.60 4.01
4400 7640 7.918076 AGTGTTTGATCTTATTTCTAGACCCA 58.082 34.615 0.00 0.00 0.00 4.51
4554 7794 5.105432 GGTCGGGTTCTAGTAACTTTCAGAT 60.105 44.000 0.00 0.00 0.00 2.90
4656 7896 3.534554 TCACAATGAGTTGGATCATCGG 58.465 45.455 0.00 0.00 39.00 4.18
4766 8006 9.857656 ATATTGTTTTATCACAGAGATGTCCAT 57.142 29.630 0.00 0.00 37.57 3.41
5001 8241 7.093596 TGGATACATGGCTGATGATCTTACTAG 60.094 40.741 0.00 0.00 46.17 2.57
5005 8245 6.552725 ACATGGCTGATGATCTTACTAGAAGA 59.447 38.462 0.00 1.84 35.80 2.87
5034 8274 1.610522 GCACTCTGCACAAGGTTCAAT 59.389 47.619 0.00 0.00 44.26 2.57
5039 8279 5.005971 CACTCTGCACAAGGTTCAATTTTTG 59.994 40.000 0.00 0.00 0.00 2.44
5040 8280 4.440880 TCTGCACAAGGTTCAATTTTTGG 58.559 39.130 0.00 0.00 0.00 3.28
5041 8281 4.161189 TCTGCACAAGGTTCAATTTTTGGA 59.839 37.500 0.00 0.00 0.00 3.53
5043 8283 5.248640 TGCACAAGGTTCAATTTTTGGAAA 58.751 33.333 0.00 0.00 0.00 3.13
5044 8284 5.884792 TGCACAAGGTTCAATTTTTGGAAAT 59.115 32.000 0.00 0.00 37.06 2.17
5108 8351 9.486123 AATGATCTATATGATGTAGTAGTGGCT 57.514 33.333 0.00 0.00 35.14 4.75
5109 8352 8.512966 TGATCTATATGATGTAGTAGTGGCTC 57.487 38.462 0.00 0.00 35.14 4.70
5110 8353 8.109634 TGATCTATATGATGTAGTAGTGGCTCA 58.890 37.037 0.00 0.00 35.14 4.26
5111 8354 9.130661 GATCTATATGATGTAGTAGTGGCTCAT 57.869 37.037 0.00 0.00 35.14 2.90
5112 8355 8.286191 TCTATATGATGTAGTAGTGGCTCATG 57.714 38.462 0.00 0.00 0.00 3.07
5113 8356 6.924913 ATATGATGTAGTAGTGGCTCATGT 57.075 37.500 0.00 0.00 0.00 3.21
5114 8357 4.655762 TGATGTAGTAGTGGCTCATGTC 57.344 45.455 0.00 0.00 0.00 3.06
5115 8358 3.384789 TGATGTAGTAGTGGCTCATGTCC 59.615 47.826 0.00 0.00 0.00 4.02
5116 8359 2.815158 TGTAGTAGTGGCTCATGTCCA 58.185 47.619 5.54 5.54 0.00 4.02
5117 8360 2.760650 TGTAGTAGTGGCTCATGTCCAG 59.239 50.000 9.20 0.00 33.63 3.86
5118 8361 0.539051 AGTAGTGGCTCATGTCCAGC 59.461 55.000 9.20 3.31 33.63 4.85
5119 8362 0.539051 GTAGTGGCTCATGTCCAGCT 59.461 55.000 9.20 11.10 37.05 4.24
5120 8363 0.826715 TAGTGGCTCATGTCCAGCTC 59.173 55.000 9.20 2.39 37.05 4.09
5121 8364 0.908656 AGTGGCTCATGTCCAGCTCT 60.909 55.000 9.20 4.26 37.05 4.09
5122 8365 0.743701 GTGGCTCATGTCCAGCTCTG 60.744 60.000 9.20 0.00 37.05 3.35
5123 8366 1.818785 GGCTCATGTCCAGCTCTGC 60.819 63.158 5.02 0.00 37.05 4.26
5124 8367 1.818785 GCTCATGTCCAGCTCTGCC 60.819 63.158 0.00 0.00 33.75 4.85
5125 8368 1.600638 CTCATGTCCAGCTCTGCCA 59.399 57.895 0.00 0.00 0.00 4.92
5126 8369 0.180642 CTCATGTCCAGCTCTGCCAT 59.819 55.000 0.00 0.00 0.00 4.40
5127 8370 0.622136 TCATGTCCAGCTCTGCCATT 59.378 50.000 0.00 0.00 0.00 3.16
5128 8371 1.022735 CATGTCCAGCTCTGCCATTC 58.977 55.000 0.00 0.00 0.00 2.67
5129 8372 0.622136 ATGTCCAGCTCTGCCATTCA 59.378 50.000 0.00 0.00 0.00 2.57
5130 8373 0.401356 TGTCCAGCTCTGCCATTCAA 59.599 50.000 0.00 0.00 0.00 2.69
5131 8374 1.202915 TGTCCAGCTCTGCCATTCAAA 60.203 47.619 0.00 0.00 0.00 2.69
5132 8375 2.097825 GTCCAGCTCTGCCATTCAAAT 58.902 47.619 0.00 0.00 0.00 2.32
5133 8376 2.097036 TCCAGCTCTGCCATTCAAATG 58.903 47.619 0.00 0.00 36.17 2.32
5134 8377 1.822990 CCAGCTCTGCCATTCAAATGT 59.177 47.619 2.31 0.00 34.60 2.71
5135 8378 3.018856 CCAGCTCTGCCATTCAAATGTA 58.981 45.455 2.31 0.00 34.60 2.29
5136 8379 3.181493 CCAGCTCTGCCATTCAAATGTAC 60.181 47.826 2.31 0.00 34.60 2.90
5137 8380 3.441222 CAGCTCTGCCATTCAAATGTACA 59.559 43.478 0.00 0.00 34.60 2.90
5138 8381 4.081406 AGCTCTGCCATTCAAATGTACAA 58.919 39.130 0.00 0.00 34.60 2.41
5139 8382 4.523943 AGCTCTGCCATTCAAATGTACAAA 59.476 37.500 0.00 0.00 34.60 2.83
5140 8383 4.860907 GCTCTGCCATTCAAATGTACAAAG 59.139 41.667 0.00 0.00 34.60 2.77
5141 8384 5.565439 GCTCTGCCATTCAAATGTACAAAGT 60.565 40.000 0.00 0.00 34.60 2.66
5142 8385 6.349280 GCTCTGCCATTCAAATGTACAAAGTA 60.349 38.462 0.00 0.00 34.60 2.24
5143 8386 7.629222 GCTCTGCCATTCAAATGTACAAAGTAT 60.629 37.037 0.00 0.00 34.60 2.12
5144 8387 7.537715 TCTGCCATTCAAATGTACAAAGTATG 58.462 34.615 0.00 2.79 34.60 2.39
5145 8388 6.098679 TGCCATTCAAATGTACAAAGTATGC 58.901 36.000 0.00 0.00 34.60 3.14
5146 8389 6.098679 GCCATTCAAATGTACAAAGTATGCA 58.901 36.000 0.00 0.00 34.60 3.96
5147 8390 6.034898 GCCATTCAAATGTACAAAGTATGCAC 59.965 38.462 0.00 0.00 34.60 4.57
5148 8391 7.089538 CCATTCAAATGTACAAAGTATGCACA 58.910 34.615 0.00 0.00 39.58 4.57
5149 8392 7.062138 CCATTCAAATGTACAAAGTATGCACAC 59.938 37.037 0.00 0.00 38.11 3.82
5150 8393 6.625873 TCAAATGTACAAAGTATGCACACA 57.374 33.333 0.00 0.00 38.11 3.72
5151 8394 7.213216 TCAAATGTACAAAGTATGCACACAT 57.787 32.000 0.00 0.00 38.11 3.21
5152 8395 7.656412 TCAAATGTACAAAGTATGCACACATT 58.344 30.769 0.00 0.00 38.11 2.71
5153 8396 8.140628 TCAAATGTACAAAGTATGCACACATTT 58.859 29.630 0.00 0.00 43.13 2.32
5154 8397 8.763356 CAAATGTACAAAGTATGCACACATTTT 58.237 29.630 0.00 0.00 41.90 1.82
5155 8398 7.872163 ATGTACAAAGTATGCACACATTTTG 57.128 32.000 7.96 7.96 38.11 2.44
5156 8399 5.689514 TGTACAAAGTATGCACACATTTTGC 59.310 36.000 9.13 0.00 37.45 3.68
5157 8400 4.057432 ACAAAGTATGCACACATTTTGCC 58.943 39.130 9.13 0.00 37.45 4.52
5158 8401 4.202243 ACAAAGTATGCACACATTTTGCCT 60.202 37.500 9.13 0.00 37.45 4.75
5159 8402 3.581024 AGTATGCACACATTTTGCCTG 57.419 42.857 0.00 0.00 39.39 4.85
5160 8403 2.892852 AGTATGCACACATTTTGCCTGT 59.107 40.909 0.00 0.00 39.39 4.00
5161 8404 4.078537 AGTATGCACACATTTTGCCTGTA 58.921 39.130 0.00 0.00 39.39 2.74
5162 8405 2.791383 TGCACACATTTTGCCTGTAC 57.209 45.000 0.00 0.00 39.39 2.90
5163 8406 2.027385 TGCACACATTTTGCCTGTACA 58.973 42.857 0.00 0.00 39.39 2.90
5164 8407 2.034432 TGCACACATTTTGCCTGTACAG 59.966 45.455 16.34 16.34 39.39 2.74
5165 8408 2.034558 GCACACATTTTGCCTGTACAGT 59.965 45.455 21.18 0.00 33.58 3.55
5166 8409 3.853307 GCACACATTTTGCCTGTACAGTC 60.853 47.826 21.18 9.74 33.58 3.51
5167 8410 3.314913 CACACATTTTGCCTGTACAGTCA 59.685 43.478 21.18 12.62 0.00 3.41
5168 8411 3.951037 ACACATTTTGCCTGTACAGTCAA 59.049 39.130 21.18 18.16 0.00 3.18
5169 8412 4.584325 ACACATTTTGCCTGTACAGTCAAT 59.416 37.500 19.15 3.66 0.00 2.57
5170 8413 5.767665 ACACATTTTGCCTGTACAGTCAATA 59.232 36.000 19.15 15.02 0.00 1.90
5171 8414 6.264292 ACACATTTTGCCTGTACAGTCAATAA 59.736 34.615 19.15 15.48 0.00 1.40
5172 8415 7.039784 ACACATTTTGCCTGTACAGTCAATAAT 60.040 33.333 19.15 16.74 0.00 1.28
5173 8416 8.458052 CACATTTTGCCTGTACAGTCAATAATA 58.542 33.333 19.15 2.58 0.00 0.98
5174 8417 9.189156 ACATTTTGCCTGTACAGTCAATAATAT 57.811 29.630 19.15 9.10 0.00 1.28
5177 8420 9.853555 TTTTGCCTGTACAGTCAATAATATTTG 57.146 29.630 19.15 1.79 0.00 2.32
5178 8421 8.574251 TTGCCTGTACAGTCAATAATATTTGT 57.426 30.769 21.18 0.00 0.00 2.83
5179 8422 8.574251 TGCCTGTACAGTCAATAATATTTGTT 57.426 30.769 21.18 0.00 0.00 2.83
5180 8423 8.673711 TGCCTGTACAGTCAATAATATTTGTTC 58.326 33.333 21.18 0.00 0.00 3.18
5181 8424 8.673711 GCCTGTACAGTCAATAATATTTGTTCA 58.326 33.333 21.18 0.00 0.00 3.18
5197 8440 9.725019 ATATTTGTTCATGAGTTGACTAGTCAA 57.275 29.630 30.07 30.07 46.27 3.18
5242 8485 5.927281 TCTACAACTACTCATTACCCACC 57.073 43.478 0.00 0.00 0.00 4.61
5247 8490 4.996788 ACTACTCATTACCCACCGTTAG 57.003 45.455 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 8.407832 TCATATTGAAAAATCGTTCTCATGCAT 58.592 29.630 0.00 0.00 0.00 3.96
75 76 9.382275 TCATCTCATATTGAAAAATCGTTCTCA 57.618 29.630 0.00 0.00 0.00 3.27
147 148 9.892130 AAAAATACAACTGGAATACTAGAGAGG 57.108 33.333 0.00 0.00 0.00 3.69
250 251 5.152623 AGAGTAATGTGCTAGCACTCAAA 57.847 39.130 39.44 25.02 46.30 2.69
330 332 0.764890 TAGGAGCCCCACATATGTGC 59.235 55.000 27.27 17.67 44.34 4.57
375 389 2.313317 CGGTTAGTGGGCTATGTCCTA 58.687 52.381 0.00 0.00 0.00 2.94
446 460 2.692024 GGGGTTTAACCAGGGGAAAAA 58.308 47.619 16.58 0.00 41.02 1.94
856 3164 3.200522 GCTTGGGCCATTTCTCCG 58.799 61.111 7.26 0.00 0.00 4.63
949 3265 0.402861 AGGGAAGGGTTCTGGTGGAA 60.403 55.000 0.00 0.00 0.00 3.53
2006 5033 1.768077 AGCATCTCCTGGTAGGCCC 60.768 63.158 0.00 0.00 34.61 5.80
2031 5058 3.412408 GGGGAGAAGGAGGTGGCC 61.412 72.222 0.00 0.00 0.00 5.36
2094 5121 2.514824 GCCTCCTGGATGCGTTCC 60.515 66.667 8.22 0.00 45.69 3.62
2096 5123 4.115199 GGGCCTCCTGGATGCGTT 62.115 66.667 16.23 0.00 34.57 4.84
2163 5190 3.119955 CGTCGATGAGGTTCTTGTAGACA 60.120 47.826 0.00 0.00 0.00 3.41
2769 5796 2.432444 CTCCCGTCTGCCATTTTGTAA 58.568 47.619 0.00 0.00 0.00 2.41
2893 5920 1.205655 CGGCTTGATCTCCTTGTCAGA 59.794 52.381 0.00 0.00 0.00 3.27
2922 5949 6.650390 GTGCATTAACCAGGATTTCAAATGTT 59.350 34.615 0.00 0.00 0.00 2.71
3004 6031 0.814010 GGAGTTGCGACAACACCACT 60.814 55.000 23.47 7.30 32.24 4.00
3254 6281 1.469251 GCACTTGAGATGCAGCATTGG 60.469 52.381 9.90 1.36 42.88 3.16
3312 6339 2.014128 ACTTGTTGGTTTCCAGACACG 58.986 47.619 0.00 0.00 33.81 4.49
3368 6395 4.842531 TGAGGAGAAGAAATACCATGCA 57.157 40.909 0.00 0.00 0.00 3.96
3486 6513 3.495331 TGAGCCAAAATTAGGTTGCTGA 58.505 40.909 0.00 0.00 0.00 4.26
3516 6543 1.715019 TACCAAACCCAGGCTGCAGT 61.715 55.000 16.64 5.73 0.00 4.40
3517 6544 0.962356 CTACCAAACCCAGGCTGCAG 60.962 60.000 10.11 10.11 0.00 4.41
3744 6894 4.849329 GGCTGCTGCGCTTGATGC 62.849 66.667 9.73 6.69 40.82 3.91
3820 7000 1.002134 GATGGGTGCCATATCCGGG 60.002 63.158 0.00 0.00 45.26 5.73
3992 7172 0.839946 ACCATACCCAGGCTGATGAC 59.160 55.000 17.94 0.00 0.00 3.06
3993 7173 2.047061 GTACCATACCCAGGCTGATGA 58.953 52.381 17.94 0.00 0.00 2.92
3996 7236 1.007842 TGAGTACCATACCCAGGCTGA 59.992 52.381 17.94 0.00 0.00 4.26
4045 7285 0.179702 GATGGCTGTGATGGCTGAGA 59.820 55.000 0.00 0.00 0.00 3.27
4130 7370 4.760715 GCTGATCATGCTCATTTCCTATGT 59.239 41.667 0.00 0.00 0.00 2.29
4180 7420 0.453390 GGTGGCTGAGTGCTAAATGC 59.547 55.000 0.00 0.00 42.39 3.56
4200 7440 4.792804 GGGGCCTCAGCAGTCTGC 62.793 72.222 17.48 17.48 45.46 4.26
4222 7462 5.297776 GCTGACTGTATTTGATAGCCATGTT 59.702 40.000 0.00 0.00 0.00 2.71
4230 7470 7.993101 ACTAGTAACGCTGACTGTATTTGATA 58.007 34.615 0.00 0.00 0.00 2.15
4231 7471 6.864342 ACTAGTAACGCTGACTGTATTTGAT 58.136 36.000 0.00 0.00 0.00 2.57
4262 7502 2.203625 TTTGGAGCCCAGGGTTGC 60.204 61.111 6.93 6.93 33.81 4.17
4263 7503 1.908299 GGTTTGGAGCCCAGGGTTG 60.908 63.158 7.55 0.00 33.81 3.77
4264 7504 1.955458 TTGGTTTGGAGCCCAGGGTT 61.955 55.000 7.55 0.00 33.81 4.11
4265 7505 1.955458 TTTGGTTTGGAGCCCAGGGT 61.955 55.000 7.55 0.00 33.81 4.34
4267 7507 2.230130 TATTTGGTTTGGAGCCCAGG 57.770 50.000 0.00 0.00 33.81 4.45
4268 7508 3.636764 GGTATATTTGGTTTGGAGCCCAG 59.363 47.826 0.00 0.00 33.81 4.45
4292 7532 7.979537 CACATGCAGTACCTACTCATTAACTTA 59.020 37.037 0.00 0.00 33.46 2.24
4341 7581 8.266392 TGGAATAAAATGTGAAATCAAATGGC 57.734 30.769 0.00 0.00 0.00 4.40
4376 7616 8.451748 GTTGGGTCTAGAAATAAGATCAAACAC 58.548 37.037 0.00 0.00 37.76 3.32
4400 7640 7.573843 GCAAGTAGCAGAACATAAACATCAGTT 60.574 37.037 0.00 0.00 44.79 3.16
4554 7794 3.181468 TGCAAATGATGACAGCCAACAAA 60.181 39.130 0.00 0.00 31.17 2.83
4656 7896 4.499183 CTCACTAACTGTTCAGGTGGATC 58.501 47.826 8.14 0.00 0.00 3.36
4766 8006 5.129634 TGAAAGAAACACCAGTCTATGCAA 58.870 37.500 0.00 0.00 0.00 4.08
5085 8328 8.512966 TGAGCCACTACTACATCATATAGATC 57.487 38.462 0.00 0.00 33.72 2.75
5086 8329 8.911965 CATGAGCCACTACTACATCATATAGAT 58.088 37.037 0.00 0.00 37.48 1.98
5087 8330 7.890655 ACATGAGCCACTACTACATCATATAGA 59.109 37.037 0.00 0.00 0.00 1.98
5088 8331 8.060931 ACATGAGCCACTACTACATCATATAG 57.939 38.462 0.00 0.00 0.00 1.31
5089 8332 7.122799 GGACATGAGCCACTACTACATCATATA 59.877 40.741 0.00 0.00 0.00 0.86
5090 8333 6.071108 GGACATGAGCCACTACTACATCATAT 60.071 42.308 0.00 0.00 0.00 1.78
5091 8334 5.243954 GGACATGAGCCACTACTACATCATA 59.756 44.000 0.00 0.00 0.00 2.15
5092 8335 4.039730 GGACATGAGCCACTACTACATCAT 59.960 45.833 0.00 0.00 0.00 2.45
5093 8336 3.384789 GGACATGAGCCACTACTACATCA 59.615 47.826 0.00 0.00 0.00 3.07
5094 8337 3.384789 TGGACATGAGCCACTACTACATC 59.615 47.826 0.00 0.00 0.00 3.06
5095 8338 3.374764 TGGACATGAGCCACTACTACAT 58.625 45.455 0.00 0.00 0.00 2.29
5096 8339 2.760650 CTGGACATGAGCCACTACTACA 59.239 50.000 0.00 0.00 0.00 2.74
5097 8340 2.482142 GCTGGACATGAGCCACTACTAC 60.482 54.545 0.00 0.00 0.00 2.73
5098 8341 1.757118 GCTGGACATGAGCCACTACTA 59.243 52.381 0.00 0.00 0.00 1.82
5099 8342 0.539051 GCTGGACATGAGCCACTACT 59.461 55.000 0.00 0.00 0.00 2.57
5100 8343 0.539051 AGCTGGACATGAGCCACTAC 59.461 55.000 0.00 0.00 37.12 2.73
5101 8344 0.826715 GAGCTGGACATGAGCCACTA 59.173 55.000 0.00 0.00 37.12 2.74
5102 8345 0.908656 AGAGCTGGACATGAGCCACT 60.909 55.000 0.00 6.90 37.12 4.00
5103 8346 0.743701 CAGAGCTGGACATGAGCCAC 60.744 60.000 0.00 2.32 37.12 5.01
5104 8347 1.600638 CAGAGCTGGACATGAGCCA 59.399 57.895 0.00 5.77 37.12 4.75
5105 8348 1.818785 GCAGAGCTGGACATGAGCC 60.819 63.158 0.00 0.40 37.12 4.70
5106 8349 1.818785 GGCAGAGCTGGACATGAGC 60.819 63.158 0.00 0.00 36.65 4.26
5107 8350 0.180642 ATGGCAGAGCTGGACATGAG 59.819 55.000 0.00 0.00 0.00 2.90
5108 8351 0.622136 AATGGCAGAGCTGGACATGA 59.378 50.000 0.00 0.00 0.00 3.07
5109 8352 1.022735 GAATGGCAGAGCTGGACATG 58.977 55.000 4.15 0.00 0.00 3.21
5110 8353 0.622136 TGAATGGCAGAGCTGGACAT 59.378 50.000 0.00 0.00 0.00 3.06
5111 8354 0.401356 TTGAATGGCAGAGCTGGACA 59.599 50.000 0.00 0.00 0.00 4.02
5112 8355 1.538047 TTTGAATGGCAGAGCTGGAC 58.462 50.000 0.00 0.00 0.00 4.02
5113 8356 2.097036 CATTTGAATGGCAGAGCTGGA 58.903 47.619 0.00 0.00 32.78 3.86
5114 8357 1.822990 ACATTTGAATGGCAGAGCTGG 59.177 47.619 8.44 0.00 40.70 4.85
5115 8358 3.441222 TGTACATTTGAATGGCAGAGCTG 59.559 43.478 8.44 0.00 40.70 4.24
5116 8359 3.689347 TGTACATTTGAATGGCAGAGCT 58.311 40.909 8.44 0.00 40.70 4.09
5117 8360 4.439305 TTGTACATTTGAATGGCAGAGC 57.561 40.909 0.00 0.00 40.70 4.09
5118 8361 6.017400 ACTTTGTACATTTGAATGGCAGAG 57.983 37.500 0.00 11.76 40.70 3.35
5119 8362 7.537715 CATACTTTGTACATTTGAATGGCAGA 58.462 34.615 0.00 2.45 40.70 4.26
5120 8363 6.254157 GCATACTTTGTACATTTGAATGGCAG 59.746 38.462 0.00 0.36 40.70 4.85
5121 8364 6.098679 GCATACTTTGTACATTTGAATGGCA 58.901 36.000 0.00 0.00 40.70 4.92
5122 8365 6.034898 GTGCATACTTTGTACATTTGAATGGC 59.965 38.462 0.00 0.00 40.35 4.40
5123 8366 7.089538 TGTGCATACTTTGTACATTTGAATGG 58.910 34.615 0.00 0.00 44.69 3.16
5132 8375 5.689514 GCAAAATGTGTGCATACTTTGTACA 59.310 36.000 21.26 0.00 46.94 2.90
5133 8376 5.118510 GGCAAAATGTGTGCATACTTTGTAC 59.881 40.000 21.26 14.54 44.07 2.90
5134 8377 5.010516 AGGCAAAATGTGTGCATACTTTGTA 59.989 36.000 21.26 2.47 44.07 2.41
5135 8378 4.057432 GGCAAAATGTGTGCATACTTTGT 58.943 39.130 21.26 12.54 44.07 2.83
5136 8379 4.150980 CAGGCAAAATGTGTGCATACTTTG 59.849 41.667 18.18 18.18 44.07 2.77
5137 8380 4.202243 ACAGGCAAAATGTGTGCATACTTT 60.202 37.500 15.05 11.66 44.07 2.66
5138 8381 3.321682 ACAGGCAAAATGTGTGCATACTT 59.678 39.130 15.05 5.63 44.07 2.24
5139 8382 2.892852 ACAGGCAAAATGTGTGCATACT 59.107 40.909 15.05 0.00 44.07 2.12
5140 8383 3.302365 ACAGGCAAAATGTGTGCATAC 57.698 42.857 6.65 6.65 44.07 2.39
5141 8384 3.823304 TGTACAGGCAAAATGTGTGCATA 59.177 39.130 0.00 0.00 44.07 3.14
5142 8385 2.627221 TGTACAGGCAAAATGTGTGCAT 59.373 40.909 0.00 0.00 44.07 3.96
5143 8386 2.027385 TGTACAGGCAAAATGTGTGCA 58.973 42.857 0.00 0.00 44.07 4.57
5144 8387 2.034558 ACTGTACAGGCAAAATGTGTGC 59.965 45.455 26.12 0.00 41.45 4.57
5145 8388 3.314913 TGACTGTACAGGCAAAATGTGTG 59.685 43.478 29.33 0.00 44.93 3.82
5146 8389 3.550820 TGACTGTACAGGCAAAATGTGT 58.449 40.909 29.33 2.58 44.93 3.72
5154 8397 8.574251 AACAAATATTATTGACTGTACAGGCA 57.426 30.769 27.87 27.87 46.54 4.75
5155 8398 8.673711 TGAACAAATATTATTGACTGTACAGGC 58.326 33.333 26.12 24.45 36.85 4.85
5170 8413 9.725019 TGACTAGTCAACTCATGAACAAATATT 57.275 29.630 23.24 0.00 40.50 1.28
5171 8414 9.725019 TTGACTAGTCAACTCATGAACAAATAT 57.275 29.630 30.07 0.00 43.90 1.28
5172 8415 9.208022 CTTGACTAGTCAACTCATGAACAAATA 57.792 33.333 30.07 8.17 43.90 1.40
5173 8416 7.716998 ACTTGACTAGTCAACTCATGAACAAAT 59.283 33.333 30.07 4.77 43.90 2.32
5174 8417 7.047891 ACTTGACTAGTCAACTCATGAACAAA 58.952 34.615 30.07 9.18 43.90 2.83
5175 8418 6.582636 ACTTGACTAGTCAACTCATGAACAA 58.417 36.000 30.07 9.37 43.90 2.83
5176 8419 6.161855 ACTTGACTAGTCAACTCATGAACA 57.838 37.500 30.07 9.86 43.90 3.18
5177 8420 6.146347 GGAACTTGACTAGTCAACTCATGAAC 59.854 42.308 30.07 18.32 43.90 3.18
5178 8421 6.042093 AGGAACTTGACTAGTCAACTCATGAA 59.958 38.462 30.07 11.22 43.90 2.57
5179 8422 5.540337 AGGAACTTGACTAGTCAACTCATGA 59.460 40.000 30.07 11.92 43.90 3.07
5180 8423 5.788450 AGGAACTTGACTAGTCAACTCATG 58.212 41.667 30.07 22.51 43.90 3.07


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

AutoCloner maintained by Alex Coulton.