Multiple sequence alignment - TraesCS1A01G134900

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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 TraesCS1A01G134900 chr1A 100.000 2573 0 0 1 2573 205225771 205223199 0.000000e+00 4752
1 TraesCS1A01G134900 chr1A 83.259 896 114 25 1691 2573 101274438 101275310 0.000000e+00 791
2 TraesCS1A01G134900 chr1A 91.667 384 30 2 2191 2573 71545579 71545197 4.870000e-147 531
3 TraesCS1A01G134900 chrUn 90.543 1068 82 9 636 1694 6050811 6051868 0.000000e+00 1395
4 TraesCS1A01G134900 chr7D 85.823 790 90 11 1 785 376832204 376831432 0.000000e+00 819
5 TraesCS1A01G134900 chr7D 88.867 512 48 7 1690 2192 199600361 199600872 2.810000e-174 621
6 TraesCS1A01G134900 chr7D 83.463 514 68 12 1692 2192 360484368 360483859 1.800000e-126 462
7 TraesCS1A01G134900 chr7D 82.946 516 64 19 1690 2192 528783820 528784324 6.530000e-121 444
8 TraesCS1A01G134900 chr1D 90.123 648 39 8 524 1167 155328176 155328802 0.000000e+00 819
9 TraesCS1A01G134900 chr1D 93.375 483 30 2 1 482 155327343 155327824 0.000000e+00 713
10 TraesCS1A01G134900 chr1D 87.755 539 39 7 1162 1694 155340310 155340827 2.830000e-169 604
11 TraesCS1A01G134900 chr4B 83.291 790 117 15 1 784 198444237 198445017 0.000000e+00 713
12 TraesCS1A01G134900 chr4B 80.175 802 125 22 1 785 311223313 311224097 1.030000e-158 569
13 TraesCS1A01G134900 chr2B 84.043 752 93 11 1 746 275186134 275186864 0.000000e+00 699
14 TraesCS1A01G134900 chr2B 77.903 801 131 26 1 785 277326229 277326999 8.390000e-125 457
15 TraesCS1A01G134900 chr4D 82.256 789 111 17 1 784 152795870 152796634 0.000000e+00 654
16 TraesCS1A01G134900 chr4D 84.808 520 59 14 1689 2192 179880353 179879838 2.950000e-139 505
17 TraesCS1A01G134900 chr1B 81.445 803 118 23 1 784 488493620 488492830 1.680000e-176 628
18 TraesCS1A01G134900 chr3D 81.916 741 114 16 1 735 338213262 338213988 2.190000e-170 608
19 TraesCS1A01G134900 chr6D 89.827 462 38 5 1689 2141 224668957 224669418 3.690000e-163 584
20 TraesCS1A01G134900 chr7A 80.150 801 128 23 1 784 487473869 487473083 1.030000e-158 569
21 TraesCS1A01G134900 chr4A 85.798 514 61 10 1691 2192 609300180 609299667 3.770000e-148 534
22 TraesCS1A01G134900 chr6A 91.192 386 33 1 2189 2573 446470842 446471227 8.160000e-145 523
23 TraesCS1A01G134900 chr6A 91.169 385 32 2 2191 2573 141302276 141302660 2.930000e-144 521
24 TraesCS1A01G134900 chr6A 90.674 386 36 0 2188 2573 35087675 35088060 4.910000e-142 514
25 TraesCS1A01G134900 chr5D 85.521 518 56 13 1690 2192 293363856 293363343 8.160000e-145 523
26 TraesCS1A01G134900 chr5A 91.384 383 32 1 2191 2573 524876618 524876999 8.160000e-145 523
27 TraesCS1A01G134900 chr5A 91.557 379 31 1 2196 2573 376012416 376012794 2.930000e-144 521
28 TraesCS1A01G134900 chr5A 90.956 387 34 1 2188 2573 540065715 540066101 1.060000e-143 520
29 TraesCS1A01G134900 chr3A 91.534 378 30 2 2196 2573 556966583 556966208 1.060000e-143 520
30 TraesCS1A01G134900 chr6B 83.689 515 66 12 1690 2189 454740459 454740970 1.080000e-128 470


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 TraesCS1A01G134900 chr1A 205223199 205225771 2572 True 4752 4752 100.000 1 2573 1 chr1A.!!$R2 2572
1 TraesCS1A01G134900 chr1A 101274438 101275310 872 False 791 791 83.259 1691 2573 1 chr1A.!!$F1 882
2 TraesCS1A01G134900 chrUn 6050811 6051868 1057 False 1395 1395 90.543 636 1694 1 chrUn.!!$F1 1058
3 TraesCS1A01G134900 chr7D 376831432 376832204 772 True 819 819 85.823 1 785 1 chr7D.!!$R2 784
4 TraesCS1A01G134900 chr7D 199600361 199600872 511 False 621 621 88.867 1690 2192 1 chr7D.!!$F1 502
5 TraesCS1A01G134900 chr7D 360483859 360484368 509 True 462 462 83.463 1692 2192 1 chr7D.!!$R1 500
6 TraesCS1A01G134900 chr7D 528783820 528784324 504 False 444 444 82.946 1690 2192 1 chr7D.!!$F2 502
7 TraesCS1A01G134900 chr1D 155327343 155328802 1459 False 766 819 91.749 1 1167 2 chr1D.!!$F2 1166
8 TraesCS1A01G134900 chr1D 155340310 155340827 517 False 604 604 87.755 1162 1694 1 chr1D.!!$F1 532
9 TraesCS1A01G134900 chr4B 198444237 198445017 780 False 713 713 83.291 1 784 1 chr4B.!!$F1 783
10 TraesCS1A01G134900 chr4B 311223313 311224097 784 False 569 569 80.175 1 785 1 chr4B.!!$F2 784
11 TraesCS1A01G134900 chr2B 275186134 275186864 730 False 699 699 84.043 1 746 1 chr2B.!!$F1 745
12 TraesCS1A01G134900 chr2B 277326229 277326999 770 False 457 457 77.903 1 785 1 chr2B.!!$F2 784
13 TraesCS1A01G134900 chr4D 152795870 152796634 764 False 654 654 82.256 1 784 1 chr4D.!!$F1 783
14 TraesCS1A01G134900 chr4D 179879838 179880353 515 True 505 505 84.808 1689 2192 1 chr4D.!!$R1 503
15 TraesCS1A01G134900 chr1B 488492830 488493620 790 True 628 628 81.445 1 784 1 chr1B.!!$R1 783
16 TraesCS1A01G134900 chr3D 338213262 338213988 726 False 608 608 81.916 1 735 1 chr3D.!!$F1 734
17 TraesCS1A01G134900 chr7A 487473083 487473869 786 True 569 569 80.150 1 784 1 chr7A.!!$R1 783
18 TraesCS1A01G134900 chr4A 609299667 609300180 513 True 534 534 85.798 1691 2192 1 chr4A.!!$R1 501
19 TraesCS1A01G134900 chr5D 293363343 293363856 513 True 523 523 85.521 1690 2192 1 chr5D.!!$R1 502
20 TraesCS1A01G134900 chr6B 454740459 454740970 511 False 470 470 83.689 1690 2189 1 chr6B.!!$F1 499

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
459 474 1.032114 GTCACTGTGGGCCCATAAGC 61.032 60.0 31.45 16.27 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 2535 0.030638 CACCTGTTTGCCAAACTCCG 59.969 55.0 20.11 10.24 41.9 4.63 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
175 177 9.712305 ACATCGAGGAGAACATTATATTAAAGG 57.288 33.333 3.06 0.00 0.00 3.11
179 181 8.979574 CGAGGAGAACATTATATTAAAGGTCAC 58.020 37.037 0.00 0.00 0.00 3.67
201 213 5.302568 CACAGAGAGAGAAGAAGCCATCTAT 59.697 44.000 0.00 0.00 37.42 1.98
217 229 5.008217 GCCATCTATCTACTAGCTATGGACG 59.992 48.000 9.97 0.00 35.33 4.79
241 253 4.768968 TGTAGGTCTGTGGTAAACTACTCC 59.231 45.833 0.00 0.00 33.73 3.85
258 271 1.149174 CCCACATCATCGGAAGGGG 59.851 63.158 0.00 0.00 35.02 4.79
445 460 5.014123 TGGAATTAGGTCAAATGGAGTCACT 59.986 40.000 0.00 0.00 0.00 3.41
459 474 1.032114 GTCACTGTGGGCCCATAAGC 61.032 60.000 31.45 16.27 0.00 3.09
560 894 3.309296 CTCCCAAAGCATCTAGGGTCTA 58.691 50.000 0.00 0.00 42.12 2.59
603 938 5.296531 GTCAAAAAGTTTCATGGCATTTGGT 59.703 36.000 0.00 0.00 0.00 3.67
606 941 6.418057 AAAAGTTTCATGGCATTTGGTCTA 57.582 33.333 0.00 0.00 0.00 2.59
624 959 6.693466 TGGTCTACGTTTGATACTGATTTCA 58.307 36.000 0.00 0.00 0.00 2.69
672 1007 2.784356 GCAACTGGCACTTGGCACA 61.784 57.895 0.49 0.00 46.12 4.57
819 1173 1.846007 TTCAACTTGTGTGCCAGGTT 58.154 45.000 0.00 0.00 43.50 3.50
848 1202 4.213564 ACTTAGCATTCTCTTGACCTGG 57.786 45.455 0.00 0.00 0.00 4.45
852 1206 2.027377 AGCATTCTCTTGACCTGGACAG 60.027 50.000 0.00 0.00 0.00 3.51
920 1274 4.331968 AGATTCCTCGGTTTTGTGCATTA 58.668 39.130 0.00 0.00 0.00 1.90
943 1297 2.965147 TGCATAGGGTTGATCGAGATGA 59.035 45.455 0.00 0.00 0.00 2.92
948 1302 2.774234 AGGGTTGATCGAGATGACCATT 59.226 45.455 13.71 3.33 32.00 3.16
949 1303 3.967326 AGGGTTGATCGAGATGACCATTA 59.033 43.478 13.71 0.00 32.00 1.90
950 1304 4.408921 AGGGTTGATCGAGATGACCATTAA 59.591 41.667 13.71 0.00 32.00 1.40
981 1335 2.385013 TGATCGGTGGTGATGACTTG 57.615 50.000 0.00 0.00 0.00 3.16
1034 1388 0.597072 GTCGACTTCCTCTTCGGTGT 59.403 55.000 8.70 0.00 35.89 4.16
1073 1427 6.069088 AGGAAACTTATGGGTGATGGTCATTA 60.069 38.462 0.00 0.00 37.44 1.90
1098 1452 5.983333 ATCCTCCCATTGTCAAACTAGAT 57.017 39.130 0.00 0.00 0.00 1.98
1133 1488 9.904647 CTGATCAAATACTTGTTTGTGTTTTTG 57.095 29.630 0.00 0.00 39.50 2.44
1136 1491 8.818141 TCAAATACTTGTTTGTGTTTTTGTCA 57.182 26.923 0.00 0.00 39.50 3.58
1137 1492 9.429359 TCAAATACTTGTTTGTGTTTTTGTCAT 57.571 25.926 0.00 0.00 39.50 3.06
1145 1500 2.292016 TGTGTTTTTGTCATAGCCCACG 59.708 45.455 0.00 0.00 0.00 4.94
1168 1523 2.744823 CGATTGCCAGCTATAACCACCA 60.745 50.000 0.00 0.00 0.00 4.17
1190 1545 1.196808 GGCAACAACGACGACATGAAT 59.803 47.619 0.00 0.00 0.00 2.57
1196 1551 3.057526 ACAACGACGACATGAATCTCTCA 60.058 43.478 0.00 0.00 38.81 3.27
1199 1554 2.468831 GACGACATGAATCTCTCAGCC 58.531 52.381 0.00 0.00 37.52 4.85
1206 1561 0.174389 GAATCTCTCAGCCACGCAGA 59.826 55.000 0.00 0.00 0.00 4.26
1213 1568 3.198068 TCTCAGCCACGCAGATATTTTC 58.802 45.455 0.00 0.00 0.00 2.29
1232 1587 4.617253 TTCGTCCAAAGAGATCTCCAAA 57.383 40.909 19.30 0.00 0.00 3.28
1245 1600 2.432972 CCAAAAGCGGCATGGTGC 60.433 61.111 1.45 0.00 44.08 5.01
1285 1640 2.037511 ACGACATCTTTTACAACCCCGA 59.962 45.455 0.00 0.00 0.00 5.14
1343 1700 2.391616 TACAGAGTCCTTGCATGCAG 57.608 50.000 21.50 14.51 0.00 4.41
1472 1834 1.407299 CGAGATCTTCATGGGTGGCAA 60.407 52.381 0.00 0.00 0.00 4.52
1539 1901 1.490490 GCACCCATCATCCTTGACCTA 59.510 52.381 0.00 0.00 33.85 3.08
1546 1908 3.107402 TCATCCTTGACCTAGTGCTCT 57.893 47.619 0.00 0.00 0.00 4.09
1548 1910 3.196469 TCATCCTTGACCTAGTGCTCTTG 59.804 47.826 0.00 0.00 0.00 3.02
1570 1932 1.476085 CTGAGCTCGACACAAGGATCT 59.524 52.381 9.64 0.00 0.00 2.75
1611 1973 5.011586 CAGGCAAAATTTTCCCCAAATGAT 58.988 37.500 7.29 0.00 35.09 2.45
1743 2105 1.692411 AAGAAAACCACCACAGAGCC 58.308 50.000 0.00 0.00 0.00 4.70
1746 2108 1.943730 AAAACCACCACAGAGCCCCA 61.944 55.000 0.00 0.00 0.00 4.96
1747 2109 1.729267 AAACCACCACAGAGCCCCAT 61.729 55.000 0.00 0.00 0.00 4.00
1749 2111 1.224592 CCACCACAGAGCCCCATAC 59.775 63.158 0.00 0.00 0.00 2.39
1750 2112 1.561769 CCACCACAGAGCCCCATACA 61.562 60.000 0.00 0.00 0.00 2.29
1751 2113 0.548031 CACCACAGAGCCCCATACAT 59.452 55.000 0.00 0.00 0.00 2.29
1765 2131 5.794894 CCCCATACATATAGAGGTTCACAC 58.205 45.833 0.00 0.00 0.00 3.82
1832 2201 1.069049 GCACAACTCAACAAGCCCAAT 59.931 47.619 0.00 0.00 0.00 3.16
1872 2255 0.687354 GGAAGGCCAGAGACAAGTCA 59.313 55.000 5.01 0.00 0.00 3.41
1892 2279 1.227973 GCTCCTAATCCGGCTTGGG 60.228 63.158 13.88 13.88 38.76 4.12
1942 2329 3.604629 CATCGAGTGGAGGTCGGT 58.395 61.111 0.00 0.00 38.02 4.69
2008 2395 0.593128 CGCCAAAGCTGCAAGTAACT 59.407 50.000 1.02 0.00 36.60 2.24
2020 2407 6.148480 AGCTGCAAGTAACTAGACAATTTGAG 59.852 38.462 1.02 0.00 35.30 3.02
2023 2410 7.168219 TGCAAGTAACTAGACAATTTGAGGAT 58.832 34.615 2.79 0.00 0.00 3.24
2037 2424 0.390860 GAGGATGGCGTCAGTAGCAT 59.609 55.000 9.27 0.00 36.08 3.79
2042 2429 1.878522 GGCGTCAGTAGCATGTCGG 60.879 63.158 0.00 0.00 33.29 4.79
2089 2476 2.833582 GCGGATCGTCCAGAGGGA 60.834 66.667 5.15 0.00 42.29 4.20
2147 2535 0.106967 GAGAATGCAGGGGGAGTTCC 60.107 60.000 0.00 0.00 0.00 3.62
2154 2542 1.151877 AGGGGGAGTTCCGGAGTTT 60.152 57.895 3.34 0.00 36.71 2.66
2166 2554 0.030638 CGGAGTTTGGCAAACAGGTG 59.969 55.000 36.37 22.38 43.79 4.00
2181 2569 0.565674 AGGTGGGGGAAATTGGTGTT 59.434 50.000 0.00 0.00 0.00 3.32
2200 2588 1.626686 TGCACCAATTGTTCGGGAAT 58.373 45.000 4.43 0.00 0.00 3.01
2215 2603 5.913137 TCGGGAATGCAGTATTTCAAAAT 57.087 34.783 0.00 0.00 0.00 1.82
2216 2604 6.279513 TCGGGAATGCAGTATTTCAAAATT 57.720 33.333 0.00 0.00 0.00 1.82
2217 2605 6.696411 TCGGGAATGCAGTATTTCAAAATTT 58.304 32.000 0.00 0.00 0.00 1.82
2273 2662 0.331954 AGCAACGAGAGGGGAGAGTA 59.668 55.000 0.00 0.00 0.00 2.59
2302 2691 2.295253 ACCCTCGTAGATTGAAAGCG 57.705 50.000 0.00 0.00 33.89 4.68
2333 2722 2.229543 AGTAACGCGGTTGATGTAGTCA 59.770 45.455 12.47 0.00 34.25 3.41
2346 2735 5.838529 TGATGTAGTCAAACGTCTTCTTGA 58.161 37.500 0.00 0.00 36.53 3.02
2389 2778 1.067212 GTACATCACCTCCGCGATCTT 59.933 52.381 8.23 0.00 0.00 2.40
2390 2779 0.103208 ACATCACCTCCGCGATCTTC 59.897 55.000 8.23 0.00 0.00 2.87
2404 2793 1.651138 GATCTTCACACGTTCAGCTCG 59.349 52.381 0.00 0.00 0.00 5.03
2407 2796 0.874175 TTCACACGTTCAGCTCGGTG 60.874 55.000 0.00 4.03 33.93 4.94
2409 2798 1.299926 ACACGTTCAGCTCGGTGAC 60.300 57.895 9.25 0.00 0.00 3.67
2410 2799 1.299850 CACGTTCAGCTCGGTGACA 60.300 57.895 0.00 0.00 0.00 3.58
2423 2812 1.765230 GGTGACATCCCTCGTACTCT 58.235 55.000 0.00 0.00 0.00 3.24
2474 2863 1.134946 TCAGCACGATGACATGTCGAT 59.865 47.619 20.54 14.53 41.40 3.59
2496 2885 3.259625 TGGTGATGATGAAGTTACCGACA 59.740 43.478 0.00 0.00 0.00 4.35
2507 2896 1.180456 TTACCGACACAGGGCTTCGA 61.180 55.000 0.00 0.00 34.62 3.71
2537 2926 3.695830 ACAACAATATGACCGAGGTGT 57.304 42.857 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.648725 AGTCTTCTCTGAACTCTTTTATGCAC 59.351 38.462 0.00 0.00 0.00 4.57
175 177 2.560542 TGGCTTCTTCTCTCTCTGTGAC 59.439 50.000 0.00 0.00 0.00 3.67
179 181 5.771666 AGATAGATGGCTTCTTCTCTCTCTG 59.228 44.000 8.31 0.00 35.79 3.35
201 213 4.102210 ACCTACACGTCCATAGCTAGTAGA 59.898 45.833 13.03 1.84 31.56 2.59
217 229 5.336293 GGAGTAGTTTACCACAGACCTACAC 60.336 48.000 0.00 0.00 0.00 2.90
241 253 0.107456 CTCCCCTTCCGATGATGTGG 59.893 60.000 0.00 0.00 0.00 4.17
258 271 2.284190 GCCTCTACATCAACCTTGCTC 58.716 52.381 0.00 0.00 0.00 4.26
445 460 0.623324 AGGTAGCTTATGGGCCCACA 60.623 55.000 31.51 15.29 0.00 4.17
459 474 4.587189 GTAGGCGCGCCCAGGTAG 62.587 72.222 44.47 0.00 36.58 3.18
518 539 3.071479 GGAGACCATACGTGCAAAAAGA 58.929 45.455 0.00 0.00 0.00 2.52
522 855 1.066430 GGAGGAGACCATACGTGCAAA 60.066 52.381 0.00 0.00 0.00 3.68
603 938 7.165460 TCCTGAAATCAGTATCAAACGTAGA 57.835 36.000 9.43 0.00 42.27 2.59
606 941 7.504924 TTTTCCTGAAATCAGTATCAAACGT 57.495 32.000 9.43 0.00 42.27 3.99
624 959 3.990959 TGCCTGTTTTTGGTTTTTCCT 57.009 38.095 0.00 0.00 37.07 3.36
625 960 5.378292 TTTTGCCTGTTTTTGGTTTTTCC 57.622 34.783 0.00 0.00 0.00 3.13
819 1173 6.813649 GTCAAGAGAATGCTAAGTATGTGTGA 59.186 38.462 0.00 0.00 0.00 3.58
920 1274 4.040829 TCATCTCGATCAACCCTATGCATT 59.959 41.667 3.54 0.00 0.00 3.56
943 1297 6.540189 CCGATCAATGAGTTCTTCTTAATGGT 59.460 38.462 0.00 0.00 0.00 3.55
948 1302 5.046591 ACCACCGATCAATGAGTTCTTCTTA 60.047 40.000 0.00 0.00 0.00 2.10
949 1303 4.256920 CCACCGATCAATGAGTTCTTCTT 58.743 43.478 0.00 0.00 0.00 2.52
950 1304 3.261897 ACCACCGATCAATGAGTTCTTCT 59.738 43.478 0.00 0.00 0.00 2.85
981 1335 0.889186 TCTTGGTTTGCCCGCTCTTC 60.889 55.000 0.00 0.00 35.15 2.87
1034 1388 7.396055 CCATAAGTTTCCTTACCTTGATTCCAA 59.604 37.037 0.00 0.00 36.03 3.53
1073 1427 6.552008 TCTAGTTTGACAATGGGAGGATTTT 58.448 36.000 0.00 0.00 0.00 1.82
1133 1488 1.209128 CAATCGACGTGGGCTATGAC 58.791 55.000 0.00 0.00 0.00 3.06
1136 1491 1.227556 GGCAATCGACGTGGGCTAT 60.228 57.895 0.00 0.00 0.00 2.97
1137 1492 2.185867 GGCAATCGACGTGGGCTA 59.814 61.111 0.00 0.00 0.00 3.93
1145 1500 2.544267 GTGGTTATAGCTGGCAATCGAC 59.456 50.000 0.00 0.00 0.00 4.20
1168 1523 0.586319 CATGTCGTCGTTGTTGCCTT 59.414 50.000 0.00 0.00 0.00 4.35
1190 1545 1.697284 ATATCTGCGTGGCTGAGAGA 58.303 50.000 3.68 0.00 39.64 3.10
1196 1551 1.933853 GACGAAAATATCTGCGTGGCT 59.066 47.619 0.00 0.00 37.07 4.75
1199 1554 4.092821 TCTTTGGACGAAAATATCTGCGTG 59.907 41.667 0.00 0.00 37.07 5.34
1206 1561 6.889198 TGGAGATCTCTTTGGACGAAAATAT 58.111 36.000 21.81 0.00 0.00 1.28
1213 1568 3.126000 GCTTTTGGAGATCTCTTTGGACG 59.874 47.826 21.81 6.64 0.00 4.79
1232 1587 2.361483 TCATGCACCATGCCGCTT 60.361 55.556 0.00 0.00 44.23 4.68
1245 1600 1.129251 GTTGCTGACGACCATGTCATG 59.871 52.381 5.79 5.79 46.98 3.07
1267 1622 2.640826 TCCTCGGGGTTGTAAAAGATGT 59.359 45.455 0.00 0.00 0.00 3.06
1272 1627 0.766131 TGCTCCTCGGGGTTGTAAAA 59.234 50.000 0.00 0.00 0.00 1.52
1285 1640 3.518998 CGTCGTCGGGATGCTCCT 61.519 66.667 0.00 0.00 36.57 3.69
1325 1682 0.399454 ACTGCATGCAAGGACTCTGT 59.601 50.000 22.88 10.48 0.00 3.41
1343 1700 1.886886 TTTCCCTAAACTCCGCACAC 58.113 50.000 0.00 0.00 0.00 3.82
1355 1712 9.871175 ATTTAGGTTTCTAACAAGTTTTCCCTA 57.129 29.630 0.00 0.00 35.40 3.53
1515 1877 1.097547 CAAGGATGATGGGTGCGACC 61.098 60.000 0.00 0.00 37.60 4.79
1517 1879 0.107703 GTCAAGGATGATGGGTGCGA 60.108 55.000 0.00 0.00 38.01 5.10
1546 1908 0.601046 CTTGTGTCGAGCTCAGCCAA 60.601 55.000 15.40 9.37 0.00 4.52
1548 1910 1.739562 CCTTGTGTCGAGCTCAGCC 60.740 63.158 15.40 0.69 0.00 4.85
1558 1920 3.620821 GCTTTCAGCTAGATCCTTGTGTC 59.379 47.826 0.00 0.00 38.45 3.67
1570 1932 1.003580 CTGGTCTTGGGCTTTCAGCTA 59.996 52.381 0.00 0.00 41.99 3.32
1586 1948 1.813102 TGGGGAAAATTTTGCCTGGT 58.187 45.000 32.39 0.00 46.56 4.00
1598 1960 8.820831 ACAACATAAACATATCATTTGGGGAAA 58.179 29.630 0.00 0.00 0.00 3.13
1611 1973 8.510243 AGAGCATCATCAACAACATAAACATA 57.490 30.769 0.00 0.00 37.82 2.29
1727 2089 1.152546 GGGGCTCTGTGGTGGTTTT 60.153 57.895 0.00 0.00 0.00 2.43
1743 2105 5.566826 CGGTGTGAACCTCTATATGTATGGG 60.567 48.000 0.00 0.00 0.00 4.00
1746 2108 4.587262 TGCGGTGTGAACCTCTATATGTAT 59.413 41.667 0.00 0.00 0.00 2.29
1747 2109 3.955551 TGCGGTGTGAACCTCTATATGTA 59.044 43.478 0.00 0.00 0.00 2.29
1749 2111 3.123804 GTGCGGTGTGAACCTCTATATG 58.876 50.000 0.00 0.00 0.00 1.78
1750 2112 2.764010 TGTGCGGTGTGAACCTCTATAT 59.236 45.455 0.00 0.00 0.00 0.86
1751 2113 2.094390 GTGTGCGGTGTGAACCTCTATA 60.094 50.000 0.00 0.00 0.00 1.31
1765 2131 1.961277 GAGACTTGGGTGTGTGCGG 60.961 63.158 0.00 0.00 0.00 5.69
1849 2226 1.544825 TTGTCTCTGGCCTTCCTCGG 61.545 60.000 3.32 0.00 0.00 4.63
1850 2227 0.108424 CTTGTCTCTGGCCTTCCTCG 60.108 60.000 3.32 0.00 0.00 4.63
1872 2255 1.700042 CCAAGCCGGATTAGGAGCCT 61.700 60.000 3.74 0.00 36.56 4.58
1942 2329 1.146930 GCCATCTCCGCCTTCATCA 59.853 57.895 0.00 0.00 0.00 3.07
1967 2354 2.812619 GCTTAGCCGCCCTCAGGAT 61.813 63.158 0.00 0.00 33.47 3.24
2008 2395 3.055458 TGACGCCATCCTCAAATTGTCTA 60.055 43.478 0.00 0.00 0.00 2.59
2020 2407 0.179073 ACATGCTACTGACGCCATCC 60.179 55.000 0.00 0.00 0.00 3.51
2023 2410 1.153842 CGACATGCTACTGACGCCA 60.154 57.895 0.00 0.00 0.00 5.69
2089 2476 0.749454 GATTGGGGCACTCGCTTGAT 60.749 55.000 0.00 0.00 38.60 2.57
2147 2535 0.030638 CACCTGTTTGCCAAACTCCG 59.969 55.000 20.11 10.24 41.90 4.63
2154 2542 2.243774 TTTCCCCCACCTGTTTGCCA 62.244 55.000 0.00 0.00 0.00 4.92
2166 2554 0.034756 GTGCAACACCAATTTCCCCC 59.965 55.000 0.00 0.00 36.32 5.40
2181 2569 1.271934 CATTCCCGAACAATTGGTGCA 59.728 47.619 10.83 0.00 0.00 4.57
2194 2582 6.966435 AAATTTTGAAATACTGCATTCCCG 57.034 33.333 0.00 0.00 0.00 5.14
2200 2588 7.877003 TCGTAGGAAAATTTTGAAATACTGCA 58.123 30.769 8.47 0.00 0.00 4.41
2215 2603 5.674525 AGATCTTGCATGATCGTAGGAAAA 58.325 37.500 27.51 0.00 45.35 2.29
2216 2604 5.282055 AGATCTTGCATGATCGTAGGAAA 57.718 39.130 27.51 0.00 45.35 3.13
2217 2605 4.944619 AGATCTTGCATGATCGTAGGAA 57.055 40.909 27.51 0.00 45.35 3.36
2229 2618 5.082425 TGCATCTCCTAGATAGATCTTGCA 58.918 41.667 0.00 3.73 39.47 4.08
2294 2683 2.215196 ACTAAACGCTTCCGCTTTCAA 58.785 42.857 0.00 0.00 38.22 2.69
2295 2684 1.873698 ACTAAACGCTTCCGCTTTCA 58.126 45.000 0.00 0.00 38.22 2.69
2333 2722 2.806244 CGGTTGGATCAAGAAGACGTTT 59.194 45.455 0.00 0.00 0.00 3.60
2363 2752 0.448990 CGGAGGTGATGTACGTTCGA 59.551 55.000 0.00 0.00 46.43 3.71
2369 2758 0.669077 AGATCGCGGAGGTGATGTAC 59.331 55.000 6.13 0.00 43.23 2.90
2370 2759 1.337071 GAAGATCGCGGAGGTGATGTA 59.663 52.381 6.13 0.00 43.23 2.29
2373 2762 0.103208 GTGAAGATCGCGGAGGTGAT 59.897 55.000 6.13 0.00 45.75 3.06
2374 2763 1.248101 TGTGAAGATCGCGGAGGTGA 61.248 55.000 6.13 0.00 37.04 4.02
2389 2778 1.299850 CACCGAGCTGAACGTGTGA 60.300 57.895 0.00 0.00 35.60 3.58
2390 2779 1.299850 TCACCGAGCTGAACGTGTG 60.300 57.895 0.00 0.00 35.24 3.82
2404 2793 1.765230 AGAGTACGAGGGATGTCACC 58.235 55.000 0.00 0.00 0.00 4.02
2407 2796 3.004944 GGATCAAGAGTACGAGGGATGTC 59.995 52.174 0.00 0.00 0.00 3.06
2409 2798 2.959030 TGGATCAAGAGTACGAGGGATG 59.041 50.000 0.00 0.00 0.00 3.51
2410 2799 3.226777 CTGGATCAAGAGTACGAGGGAT 58.773 50.000 0.00 0.00 0.00 3.85
2423 2812 1.964608 CTCGGCCTCAGCTGGATCAA 61.965 60.000 15.13 0.00 46.14 2.57
2463 2852 3.132646 TCATCATCACCATCGACATGTCA 59.867 43.478 24.93 12.75 0.00 3.58
2465 2854 3.825143 TCATCATCACCATCGACATGT 57.175 42.857 0.00 0.00 0.00 3.21
2467 2856 4.412796 ACTTCATCATCACCATCGACAT 57.587 40.909 0.00 0.00 0.00 3.06
2470 2859 4.693283 GGTAACTTCATCATCACCATCGA 58.307 43.478 0.00 0.00 0.00 3.59
2471 2860 3.490896 CGGTAACTTCATCATCACCATCG 59.509 47.826 0.00 0.00 0.00 3.84
2474 2863 3.259625 TGTCGGTAACTTCATCATCACCA 59.740 43.478 0.00 0.00 0.00 4.17
2507 2896 5.810587 CGGTCATATTGTTGTAGTGCTTAGT 59.189 40.000 0.00 0.00 0.00 2.24
2519 2908 6.148811 CAGTTTTACACCTCGGTCATATTGTT 59.851 38.462 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.