Multiple sequence alignment - TraesCS6D01G348400

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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 TraesCS6D01G348400 chr6D 100.000 2273 0 0 1 2273 446488285 446490557 0.000000e+00 4198.0
1 TraesCS6D01G348400 chr6D 91.171 521 45 1 1733 2253 204943045 204942526 0.000000e+00 706.0
2 TraesCS6D01G348400 chr6D 91.525 118 9 1 330 446 14982387 14982504 6.500000e-36 161.0
3 TraesCS6D01G348400 chr6B 89.444 1620 88 27 168 1734 674934666 674936255 0.000000e+00 1967.0
4 TraesCS6D01G348400 chr6B 85.556 90 9 3 76 162 624134136 624134224 8.650000e-15 91.6
5 TraesCS6D01G348400 chr6A 86.829 1640 94 54 145 1734 593352962 593354529 0.000000e+00 1720.0
6 TraesCS6D01G348400 chr4B 88.707 673 54 6 609 1279 658585604 658584952 0.000000e+00 802.0
7 TraesCS6D01G348400 chr4B 92.308 117 9 0 330 446 122852201 122852085 1.400000e-37 167.0
8 TraesCS6D01G348400 chr7D 91.522 519 42 1 1735 2253 416154639 416155155 0.000000e+00 713.0
9 TraesCS6D01G348400 chr7D 91.363 521 44 1 1734 2253 65433311 65433831 0.000000e+00 712.0
10 TraesCS6D01G348400 chr7D 90.909 121 10 1 330 450 489153149 489153030 6.500000e-36 161.0
11 TraesCS6D01G348400 chr4D 91.013 523 45 2 1735 2257 72586768 72586248 0.000000e+00 704.0
12 TraesCS6D01G348400 chr4D 90.559 519 46 1 1735 2253 62841129 62841644 0.000000e+00 684.0
13 TraesCS6D01G348400 chr4D 79.516 703 80 34 805 1460 479962552 479961867 2.070000e-120 442.0
14 TraesCS6D01G348400 chr4D 90.647 139 13 0 462 600 77371334 77371196 3.860000e-43 185.0
15 TraesCS6D01G348400 chr4D 89.928 139 14 0 462 600 105123028 105122890 1.790000e-41 180.0
16 TraesCS6D01G348400 chr4D 91.525 118 9 1 330 446 105123130 105123013 6.500000e-36 161.0
17 TraesCS6D01G348400 chr4D 90.909 55 3 1 1591 1643 479961759 479961705 3.130000e-09 73.1
18 TraesCS6D01G348400 chr4D 87.931 58 6 1 1658 1715 479961707 479961651 1.460000e-07 67.6
19 TraesCS6D01G348400 chr5D 90.944 519 45 2 1735 2253 37304363 37303847 0.000000e+00 697.0
20 TraesCS6D01G348400 chr5D 90.944 519 45 1 1735 2253 496320531 496320015 0.000000e+00 697.0
21 TraesCS6D01G348400 chr5D 86.122 490 48 11 828 1304 371441016 371440534 5.600000e-141 510.0
22 TraesCS6D01G348400 chr5D 79.646 113 14 8 197 303 371440036 371439927 3.130000e-09 73.1
23 TraesCS6D01G348400 chr1B 90.944 519 45 1 1735 2253 567474059 567473543 0.000000e+00 697.0
24 TraesCS6D01G348400 chr1D 90.751 519 47 1 1735 2253 346670619 346671136 0.000000e+00 691.0
25 TraesCS6D01G348400 chr1D 91.453 117 10 0 330 446 489115555 489115671 6.500000e-36 161.0
26 TraesCS6D01G348400 chr4A 83.546 626 42 27 838 1432 686385707 686385112 1.550000e-146 529.0
27 TraesCS6D01G348400 chr4A 81.425 463 51 19 843 1287 641610544 641610989 1.670000e-91 346.0
28 TraesCS6D01G348400 chr4A 90.683 161 10 3 598 756 641610276 641610433 2.290000e-50 209.0
29 TraesCS6D01G348400 chr4A 95.000 40 1 1 1431 1469 686384880 686384841 6.780000e-06 62.1
30 TraesCS6D01G348400 chr2D 80.932 708 77 21 604 1282 582495248 582494570 7.240000e-140 507.0
31 TraesCS6D01G348400 chr2D 82.112 464 33 18 852 1288 488229081 488229521 3.590000e-93 351.0
32 TraesCS6D01G348400 chr2D 93.103 116 7 1 332 446 458504332 458504217 3.880000e-38 169.0
33 TraesCS6D01G348400 chr2D 91.566 83 2 4 674 756 488228894 488228971 2.390000e-20 110.0
34 TraesCS6D01G348400 chr5B 84.787 493 50 12 828 1302 441446517 441446032 2.640000e-129 472.0
35 TraesCS6D01G348400 chr5B 86.364 88 7 3 623 709 441446676 441446593 8.650000e-15 91.6
36 TraesCS6D01G348400 chr5B 78.947 114 14 8 198 303 448797542 448797431 4.050000e-08 69.4
37 TraesCS6D01G348400 chr2B 82.936 545 46 17 786 1304 572586332 572586855 4.450000e-122 448.0
38 TraesCS6D01G348400 chr2B 83.191 470 56 10 824 1279 701491116 701490656 2.100000e-110 409.0
39 TraesCS6D01G348400 chr2B 85.625 160 17 5 602 759 701492429 701492274 1.810000e-36 163.0
40 TraesCS6D01G348400 chr2B 85.625 160 17 5 602 759 701492801 701492646 1.810000e-36 163.0
41 TraesCS6D01G348400 chr2B 92.222 90 1 5 668 756 572586159 572586243 3.070000e-24 122.0
42 TraesCS6D01G348400 chr5A 83.669 496 35 22 828 1304 474537708 474537240 2.090000e-115 425.0
43 TraesCS6D01G348400 chr5A 82.301 113 8 4 598 709 474537886 474537785 1.120000e-13 87.9
44 TraesCS6D01G348400 chr5A 80.357 112 14 7 197 303 474536235 474536127 6.730000e-11 78.7
45 TraesCS6D01G348400 chr5A 78.947 114 15 8 197 303 456484747 456484636 4.050000e-08 69.4
46 TraesCS6D01G348400 chrUn 93.571 140 6 2 1 137 79346753 79346892 2.960000e-49 206.0
47 TraesCS6D01G348400 chrUn 91.852 135 11 0 465 599 100239865 100239731 2.980000e-44 189.0
48 TraesCS6D01G348400 chr7B 91.304 138 11 1 462 599 537460484 537460348 1.070000e-43 187.0
49 TraesCS6D01G348400 chr7B 89.510 143 15 0 462 604 668921553 668921411 4.990000e-42 182.0
50 TraesCS6D01G348400 chr3A 90.647 139 13 0 462 600 10402743 10402605 3.860000e-43 185.0
51 TraesCS6D01G348400 chr7A 90.071 141 14 0 462 602 149170743 149170603 1.390000e-42 183.0
52 TraesCS6D01G348400 chr7A 92.308 117 9 0 330 446 579804852 579804736 1.400000e-37 167.0
53 TraesCS6D01G348400 chr7A 79.082 196 29 9 4 196 19260107 19259921 8.520000e-25 124.0
54 TraesCS6D01G348400 chr2A 86.325 117 8 5 194 302 632613014 632613130 1.100000e-23 121.0
55 TraesCS6D01G348400 chr2A 85.600 125 4 8 632 756 632613449 632613559 3.970000e-23 119.0


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 TraesCS6D01G348400 chr6D 446488285 446490557 2272 False 4198.00 4198 100.000000 1 2273 1 chr6D.!!$F2 2272
1 TraesCS6D01G348400 chr6D 204942526 204943045 519 True 706.00 706 91.171000 1733 2253 1 chr6D.!!$R1 520
2 TraesCS6D01G348400 chr6B 674934666 674936255 1589 False 1967.00 1967 89.444000 168 1734 1 chr6B.!!$F2 1566
3 TraesCS6D01G348400 chr6A 593352962 593354529 1567 False 1720.00 1720 86.829000 145 1734 1 chr6A.!!$F1 1589
4 TraesCS6D01G348400 chr4B 658584952 658585604 652 True 802.00 802 88.707000 609 1279 1 chr4B.!!$R2 670
5 TraesCS6D01G348400 chr7D 416154639 416155155 516 False 713.00 713 91.522000 1735 2253 1 chr7D.!!$F2 518
6 TraesCS6D01G348400 chr7D 65433311 65433831 520 False 712.00 712 91.363000 1734 2253 1 chr7D.!!$F1 519
7 TraesCS6D01G348400 chr4D 72586248 72586768 520 True 704.00 704 91.013000 1735 2257 1 chr4D.!!$R1 522
8 TraesCS6D01G348400 chr4D 62841129 62841644 515 False 684.00 684 90.559000 1735 2253 1 chr4D.!!$F1 518
9 TraesCS6D01G348400 chr5D 37303847 37304363 516 True 697.00 697 90.944000 1735 2253 1 chr5D.!!$R1 518
10 TraesCS6D01G348400 chr5D 496320015 496320531 516 True 697.00 697 90.944000 1735 2253 1 chr5D.!!$R2 518
11 TraesCS6D01G348400 chr5D 371439927 371441016 1089 True 291.55 510 82.884000 197 1304 2 chr5D.!!$R3 1107
12 TraesCS6D01G348400 chr1B 567473543 567474059 516 True 697.00 697 90.944000 1735 2253 1 chr1B.!!$R1 518
13 TraesCS6D01G348400 chr1D 346670619 346671136 517 False 691.00 691 90.751000 1735 2253 1 chr1D.!!$F1 518
14 TraesCS6D01G348400 chr4A 686384841 686385707 866 True 295.55 529 89.273000 838 1469 2 chr4A.!!$R1 631
15 TraesCS6D01G348400 chr4A 641610276 641610989 713 False 277.50 346 86.054000 598 1287 2 chr4A.!!$F1 689
16 TraesCS6D01G348400 chr2D 582494570 582495248 678 True 507.00 507 80.932000 604 1282 1 chr2D.!!$R2 678
17 TraesCS6D01G348400 chr2D 488228894 488229521 627 False 230.50 351 86.839000 674 1288 2 chr2D.!!$F1 614
18 TraesCS6D01G348400 chr5B 441446032 441446676 644 True 281.80 472 85.575500 623 1302 2 chr5B.!!$R2 679
19 TraesCS6D01G348400 chr2B 572586159 572586855 696 False 285.00 448 87.579000 668 1304 2 chr2B.!!$F1 636
20 TraesCS6D01G348400 chr2B 701490656 701492801 2145 True 245.00 409 84.813667 602 1279 3 chr2B.!!$R1 677

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
138 139 0.037605 ATCGAACGGGTGAACCAGAC 60.038 55.0 6.63 0.14 40.22 3.51 F
942 2572 0.322636 TCAACACAACCACAACCGGT 60.323 50.0 0.00 0.00 42.71 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1181 2861 0.807496 GAACATGGAGCTGACCTTGC 59.193 55.0 0.0 0.0 38.23 4.01 R
2215 4256 0.400093 GGGTATGGGCAGGGTAGAGT 60.400 60.0 0.0 0.0 0.00 3.24 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
121 122 9.949174 ATTTTATTGCTTGAAAAACCAACAATC 57.051 25.926 0.00 0.00 33.81 2.67
122 123 5.655893 ATTGCTTGAAAAACCAACAATCG 57.344 34.783 0.00 0.00 30.01 3.34
123 124 4.377839 TGCTTGAAAAACCAACAATCGA 57.622 36.364 0.00 0.00 0.00 3.59
124 125 4.748892 TGCTTGAAAAACCAACAATCGAA 58.251 34.783 0.00 0.00 0.00 3.71
125 126 4.564769 TGCTTGAAAAACCAACAATCGAAC 59.435 37.500 0.00 0.00 0.00 3.95
126 127 4.317069 GCTTGAAAAACCAACAATCGAACG 60.317 41.667 0.00 0.00 0.00 3.95
127 128 3.696898 TGAAAAACCAACAATCGAACGG 58.303 40.909 0.00 0.00 0.00 4.44
128 129 2.785713 AAAACCAACAATCGAACGGG 57.214 45.000 0.00 0.00 0.00 5.28
129 130 1.682740 AAACCAACAATCGAACGGGT 58.317 45.000 0.00 0.00 0.00 5.28
130 131 0.948678 AACCAACAATCGAACGGGTG 59.051 50.000 0.00 0.00 0.00 4.61
131 132 0.107081 ACCAACAATCGAACGGGTGA 59.893 50.000 0.00 0.00 0.00 4.02
132 133 1.231221 CCAACAATCGAACGGGTGAA 58.769 50.000 0.00 0.00 0.00 3.18
133 134 1.069500 CCAACAATCGAACGGGTGAAC 60.069 52.381 0.00 0.00 0.00 3.18
134 135 1.069500 CAACAATCGAACGGGTGAACC 60.069 52.381 0.00 0.00 0.00 3.62
135 136 0.107081 ACAATCGAACGGGTGAACCA 59.893 50.000 1.16 0.00 40.22 3.67
136 137 0.796312 CAATCGAACGGGTGAACCAG 59.204 55.000 1.16 0.00 40.22 4.00
137 138 0.682852 AATCGAACGGGTGAACCAGA 59.317 50.000 6.63 0.00 40.22 3.86
138 139 0.037605 ATCGAACGGGTGAACCAGAC 60.038 55.000 6.63 0.14 40.22 3.51
139 140 1.068417 CGAACGGGTGAACCAGACA 59.932 57.895 6.63 0.00 40.22 3.41
140 141 1.219522 CGAACGGGTGAACCAGACAC 61.220 60.000 6.63 0.00 40.22 3.67
148 149 3.584868 GAACCAGACACCCGACCGG 62.585 68.421 0.00 0.00 37.81 5.28
272 274 7.763985 TCAACGTCATTACATACATCACTGAAT 59.236 33.333 0.00 0.00 0.00 2.57
295 297 3.502211 TGACGGAGAAAAAGAATGAAGGC 59.498 43.478 0.00 0.00 0.00 4.35
315 317 1.410224 CCCATCTGGACTTTTAGCCCC 60.410 57.143 0.00 0.00 37.39 5.80
318 320 1.681229 TCTGGACTTTTAGCCCCCAT 58.319 50.000 0.00 0.00 0.00 4.00
341 358 8.932610 CCATATCTACTCCCTCTGCATATAAAT 58.067 37.037 0.00 0.00 0.00 1.40
415 434 6.866010 ATTCAGCATTCGCACTATGAAATA 57.134 33.333 0.00 0.00 42.27 1.40
446 465 9.571816 TTATCAGATGCACCATGAAATGTATTA 57.428 29.630 0.00 0.00 44.81 0.98
469 488 0.958091 TTTTGCGGGAACACCATGAG 59.042 50.000 0.00 0.00 40.22 2.90
593 615 5.431179 AGCGGAGTAAAAAGAAAGGGATA 57.569 39.130 0.00 0.00 0.00 2.59
652 689 7.451501 TTGTTAACGAAGGGGGTTATTAAAG 57.548 36.000 0.26 0.00 30.59 1.85
662 699 3.704566 GGGGTTATTAAAGCAAGGAAGGG 59.295 47.826 0.00 0.00 34.70 3.95
665 706 4.095932 GGTTATTAAAGCAAGGAAGGGACG 59.904 45.833 0.00 0.00 33.20 4.79
778 2307 7.815840 TCAAGAATCCATGTTTACTTGTGAA 57.184 32.000 14.69 0.00 36.91 3.18
779 2319 7.874940 TCAAGAATCCATGTTTACTTGTGAAG 58.125 34.615 14.69 0.00 36.91 3.02
781 2321 7.823745 AGAATCCATGTTTACTTGTGAAGTT 57.176 32.000 0.00 0.00 42.81 2.66
790 2330 8.669946 TGTTTACTTGTGAAGTTGTGATCATA 57.330 30.769 0.00 0.00 42.81 2.15
791 2331 9.283768 TGTTTACTTGTGAAGTTGTGATCATAT 57.716 29.630 0.00 0.00 42.81 1.78
942 2572 0.322636 TCAACACAACCACAACCGGT 60.323 50.000 0.00 0.00 42.71 5.28
1181 2861 1.735386 CACTGGGAGTGCATCAAGAG 58.265 55.000 0.00 0.00 39.62 2.85
1532 3562 6.528072 CAGCTCAAAGAAAATTACCGGATTTC 59.472 38.462 9.46 12.99 34.14 2.17
1541 3571 7.556635 AGAAAATTACCGGATTTCTTTAGAGGG 59.443 37.037 9.46 0.00 39.67 4.30
1542 3572 6.570654 AATTACCGGATTTCTTTAGAGGGA 57.429 37.500 9.46 0.00 0.00 4.20
1543 3573 5.609533 TTACCGGATTTCTTTAGAGGGAG 57.390 43.478 9.46 0.00 0.00 4.30
1544 3574 2.772515 ACCGGATTTCTTTAGAGGGAGG 59.227 50.000 9.46 0.00 0.00 4.30
1603 3639 3.942829 TCTGTCAATTAGTCCAAGGCAG 58.057 45.455 0.00 0.00 0.00 4.85
1725 3761 4.998051 AGGTCTACAATTCCCAACAATGT 58.002 39.130 0.00 0.00 0.00 2.71
1747 3783 1.265365 GCTTCGCTAAGGATGGCAATC 59.735 52.381 0.00 0.00 32.98 2.67
1753 3789 3.495100 CGCTAAGGATGGCAATCTTACCT 60.495 47.826 0.00 0.00 31.43 3.08
1761 3797 3.311091 TGGCAATCTTACCTACGGGTAT 58.689 45.455 0.00 0.00 46.25 2.73
1802 3838 2.926250 GCATGGGCAGGGTATGGA 59.074 61.111 0.00 0.00 40.72 3.41
1822 3858 4.043561 TGGACACACTTTTATACCCATGGT 59.956 41.667 11.73 1.30 40.16 3.55
1825 3861 6.094464 GGACACACTTTTATACCCATGGTTAC 59.906 42.308 11.73 0.00 37.09 2.50
1829 3865 8.044908 CACACTTTTATACCCATGGTTACTACT 58.955 37.037 11.73 0.00 37.09 2.57
1978 4014 7.015292 TGTGACTTGTCTACTCCTATTGACTTT 59.985 37.037 2.35 0.00 0.00 2.66
1980 4016 8.088981 TGACTTGTCTACTCCTATTGACTTTTC 58.911 37.037 2.35 0.00 0.00 2.29
1997 4033 8.310406 TGACTTTTCAGTATGTTGTACTCATG 57.690 34.615 12.13 0.00 37.40 3.07
2095 4136 5.713025 TGTGTACTATTTGTTCTACCCGTC 58.287 41.667 0.00 0.00 0.00 4.79
2215 4256 7.651607 ACTATACGGGTATGGGTATGGTATTA 58.348 38.462 7.05 0.00 38.53 0.98
2237 4278 1.799575 TCTACCCTGCCCATACCCTAT 59.200 52.381 0.00 0.00 0.00 2.57
2238 4279 2.183661 TCTACCCTGCCCATACCCTATT 59.816 50.000 0.00 0.00 0.00 1.73
2253 4294 5.605540 ACCCTATTCATTGCCATCCTTAT 57.394 39.130 0.00 0.00 0.00 1.73
2254 4295 5.327732 ACCCTATTCATTGCCATCCTTATG 58.672 41.667 0.00 0.00 0.00 1.90
2255 4296 4.159135 CCCTATTCATTGCCATCCTTATGC 59.841 45.833 0.00 0.00 0.00 3.14
2256 4297 5.014858 CCTATTCATTGCCATCCTTATGCT 58.985 41.667 0.00 0.00 0.00 3.79
2259 4300 2.880268 TCATTGCCATCCTTATGCTTCG 59.120 45.455 0.00 0.00 0.00 3.79
2261 4302 0.819259 TGCCATCCTTATGCTTCGCC 60.819 55.000 0.00 0.00 0.00 5.54
2263 4304 1.270839 GCCATCCTTATGCTTCGCCTA 60.271 52.381 0.00 0.00 0.00 3.93
2264 4305 2.417719 CCATCCTTATGCTTCGCCTAC 58.582 52.381 0.00 0.00 0.00 3.18
2267 4308 1.138266 TCCTTATGCTTCGCCTACCAC 59.862 52.381 0.00 0.00 0.00 4.16
2269 4310 2.627945 CTTATGCTTCGCCTACCACAA 58.372 47.619 0.00 0.00 0.00 3.33
2270 4311 2.772077 TATGCTTCGCCTACCACAAA 57.228 45.000 0.00 0.00 0.00 2.83
2272 4313 0.948678 TGCTTCGCCTACCACAAAAC 59.051 50.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 4.748892 TCGATTGTTGGTTTTTCAAGCAA 58.251 34.783 0.00 0.00 45.92 3.91
102 103 4.377839 TCGATTGTTGGTTTTTCAAGCA 57.622 36.364 0.00 0.00 38.66 3.91
103 104 4.317069 CGTTCGATTGTTGGTTTTTCAAGC 60.317 41.667 0.00 0.00 0.00 4.01
104 105 4.206200 CCGTTCGATTGTTGGTTTTTCAAG 59.794 41.667 0.00 0.00 0.00 3.02
105 106 4.106197 CCGTTCGATTGTTGGTTTTTCAA 58.894 39.130 0.00 0.00 0.00 2.69
106 107 3.489398 CCCGTTCGATTGTTGGTTTTTCA 60.489 43.478 0.00 0.00 0.00 2.69
107 108 3.047093 CCCGTTCGATTGTTGGTTTTTC 58.953 45.455 0.00 0.00 0.00 2.29
108 109 2.427812 ACCCGTTCGATTGTTGGTTTTT 59.572 40.909 0.00 0.00 0.00 1.94
109 110 2.025898 ACCCGTTCGATTGTTGGTTTT 58.974 42.857 0.00 0.00 0.00 2.43
110 111 1.335496 CACCCGTTCGATTGTTGGTTT 59.665 47.619 0.00 0.00 0.00 3.27
111 112 0.948678 CACCCGTTCGATTGTTGGTT 59.051 50.000 0.00 0.00 0.00 3.67
112 113 0.107081 TCACCCGTTCGATTGTTGGT 59.893 50.000 0.00 0.00 0.00 3.67
113 114 1.069500 GTTCACCCGTTCGATTGTTGG 60.069 52.381 0.00 0.00 0.00 3.77
114 115 1.069500 GGTTCACCCGTTCGATTGTTG 60.069 52.381 0.00 0.00 0.00 3.33
115 116 1.232119 GGTTCACCCGTTCGATTGTT 58.768 50.000 0.00 0.00 0.00 2.83
116 117 0.107081 TGGTTCACCCGTTCGATTGT 59.893 50.000 0.00 0.00 35.15 2.71
117 118 0.796312 CTGGTTCACCCGTTCGATTG 59.204 55.000 0.00 0.00 35.15 2.67
118 119 0.682852 TCTGGTTCACCCGTTCGATT 59.317 50.000 0.00 0.00 35.15 3.34
119 120 0.037605 GTCTGGTTCACCCGTTCGAT 60.038 55.000 0.00 0.00 35.15 3.59
120 121 1.364901 GTCTGGTTCACCCGTTCGA 59.635 57.895 0.00 0.00 35.15 3.71
121 122 1.068417 TGTCTGGTTCACCCGTTCG 59.932 57.895 0.00 0.00 35.15 3.95
122 123 0.883370 GGTGTCTGGTTCACCCGTTC 60.883 60.000 4.00 0.00 46.63 3.95
123 124 1.147600 GGTGTCTGGTTCACCCGTT 59.852 57.895 4.00 0.00 46.63 4.44
124 125 2.826702 GGTGTCTGGTTCACCCGT 59.173 61.111 4.00 0.00 46.63 5.28
128 129 1.301479 GGTCGGGTGTCTGGTTCAC 60.301 63.158 0.00 0.00 35.36 3.18
129 130 2.863346 CGGTCGGGTGTCTGGTTCA 61.863 63.158 0.00 0.00 0.00 3.18
130 131 2.048503 CGGTCGGGTGTCTGGTTC 60.049 66.667 0.00 0.00 0.00 3.62
131 132 3.622826 CCGGTCGGGTGTCTGGTT 61.623 66.667 0.74 0.00 0.00 3.67
163 164 1.519455 CCGAACCGATGAGGCTGTC 60.519 63.158 0.00 0.00 46.52 3.51
272 274 4.023193 GCCTTCATTCTTTTTCTCCGTCAA 60.023 41.667 0.00 0.00 0.00 3.18
295 297 1.410224 GGGGCTAAAAGTCCAGATGGG 60.410 57.143 0.00 0.00 43.30 4.00
311 313 1.079658 AGAGGGAGTAGATATGGGGGC 59.920 57.143 0.00 0.00 0.00 5.80
315 317 7.904558 TTATATGCAGAGGGAGTAGATATGG 57.095 40.000 0.00 0.00 0.00 2.74
392 410 5.762825 ATTTCATAGTGCGAATGCTGAAT 57.237 34.783 0.00 0.00 43.34 2.57
393 411 6.676237 TTATTTCATAGTGCGAATGCTGAA 57.324 33.333 0.00 0.00 43.34 3.02
415 434 9.923143 CATTTCATGGTGCATCTGATAATATTT 57.077 29.630 0.00 0.00 0.00 1.40
588 610 8.262933 GTCTAGGAAGTAGAGATACTCTATCCC 58.737 44.444 17.57 14.68 43.69 3.85
593 615 8.373220 GCTTAGTCTAGGAAGTAGAGATACTCT 58.627 40.741 6.53 6.53 43.83 3.24
617 639 2.226330 TCGTTAACAATGTGCCAAGCT 58.774 42.857 6.39 0.00 0.00 3.74
652 689 2.420466 TTTCCCCGTCCCTTCCTTGC 62.420 60.000 0.00 0.00 0.00 4.01
662 699 2.354503 GGAACTACTCCTTTTCCCCGTC 60.355 54.545 0.00 0.00 41.61 4.79
764 1208 7.566760 TGATCACAACTTCACAAGTAAACAT 57.433 32.000 0.00 0.00 41.91 2.71
778 2307 9.458727 AAACAAAGAGATGATATGATCACAACT 57.541 29.630 0.00 0.00 43.01 3.16
779 2319 9.713740 GAAACAAAGAGATGATATGATCACAAC 57.286 33.333 0.00 0.00 43.01 3.32
781 2321 9.676861 AAGAAACAAAGAGATGATATGATCACA 57.323 29.630 0.00 0.00 43.01 3.58
790 2330 8.363390 GGGAAAAGAAAGAAACAAAGAGATGAT 58.637 33.333 0.00 0.00 0.00 2.45
791 2331 7.201911 GGGGAAAAGAAAGAAACAAAGAGATGA 60.202 37.037 0.00 0.00 0.00 2.92
916 2528 1.827344 TGTGGTTGTGTTGATTTGGCA 59.173 42.857 0.00 0.00 0.00 4.92
917 2529 2.593346 TGTGGTTGTGTTGATTTGGC 57.407 45.000 0.00 0.00 0.00 4.52
923 2541 0.322636 ACCGGTTGTGGTTGTGTTGA 60.323 50.000 0.00 0.00 39.99 3.18
942 2572 4.321304 GGTGAAGAGAAGAAGACGATGTCA 60.321 45.833 0.00 0.00 34.60 3.58
1028 2684 3.080121 CCTGCGCCTCCTTCTCCT 61.080 66.667 4.18 0.00 0.00 3.69
1062 2742 0.933509 ACTTGAAGCACGTCGACGAC 60.934 55.000 41.52 30.78 43.02 4.34
1181 2861 0.807496 GAACATGGAGCTGACCTTGC 59.193 55.000 0.00 0.00 38.23 4.01
1232 2933 1.282817 CGTTGTGTTGGTCGTTGAGA 58.717 50.000 0.00 0.00 0.00 3.27
1315 3036 8.265108 TGATCCTCATAGAGTAGTACAGTAGT 57.735 38.462 2.52 0.00 0.00 2.73
1469 3441 5.851047 AGTAAACAACGTACAAGCATACC 57.149 39.130 0.00 0.00 0.00 2.73
1470 3442 7.111041 CACAAAGTAAACAACGTACAAGCATAC 59.889 37.037 0.00 0.00 0.00 2.39
1471 3443 7.127042 CACAAAGTAAACAACGTACAAGCATA 58.873 34.615 0.00 0.00 0.00 3.14
1477 3449 5.163774 GGGAACACAAAGTAAACAACGTACA 60.164 40.000 0.00 0.00 0.00 2.90
1478 3450 5.065090 AGGGAACACAAAGTAAACAACGTAC 59.935 40.000 0.00 0.00 0.00 3.67
1479 3451 5.184711 AGGGAACACAAAGTAAACAACGTA 58.815 37.500 0.00 0.00 0.00 3.57
1480 3452 4.011698 AGGGAACACAAAGTAAACAACGT 58.988 39.130 0.00 0.00 0.00 3.99
1481 3453 4.625972 AGGGAACACAAAGTAAACAACG 57.374 40.909 0.00 0.00 0.00 4.10
1532 3562 2.552093 TCCAGGTCCTCCCTCTAAAG 57.448 55.000 0.00 0.00 43.86 1.85
1543 3573 4.352298 AGGAATTCATAAGGATCCAGGTCC 59.648 45.833 15.82 8.56 38.62 4.46
1544 3574 5.574970 AGGAATTCATAAGGATCCAGGTC 57.425 43.478 15.82 0.00 32.47 3.85
1603 3639 1.730446 GCGTTGGATTCTTTGCTGCTC 60.730 52.381 0.00 0.00 0.00 4.26
1709 3745 4.379652 GAAGCAACATTGTTGGGAATTGT 58.620 39.130 26.33 0.00 0.00 2.71
1802 3838 6.786122 AGTAACCATGGGTATAAAAGTGTGT 58.214 36.000 13.92 0.00 33.12 3.72
1822 3858 4.796110 ACGGGTAGGGTATGAGTAGTAA 57.204 45.455 0.00 0.00 0.00 2.24
1825 3861 5.136105 ACTTAACGGGTAGGGTATGAGTAG 58.864 45.833 0.00 0.00 0.00 2.57
1829 3865 3.979911 TGACTTAACGGGTAGGGTATGA 58.020 45.455 0.00 0.00 0.00 2.15
1896 3932 2.121291 TATTTCACAAGCGGGCATGA 57.879 45.000 2.59 0.00 0.00 3.07
1898 3934 2.760092 ACATTATTTCACAAGCGGGCAT 59.240 40.909 0.00 0.00 0.00 4.40
1997 4033 8.768955 CAATTATCTCAGCTCAATAACAGGTAC 58.231 37.037 0.00 0.00 0.00 3.34
2095 4136 2.166254 ACCCGTACACATTTAGTACCCG 59.834 50.000 0.00 0.00 38.85 5.28
2158 4199 8.098912 GGTACAAAATTCTATCCATACCCGTAT 58.901 37.037 0.00 0.00 0.00 3.06
2215 4256 0.400093 GGGTATGGGCAGGGTAGAGT 60.400 60.000 0.00 0.00 0.00 3.24
2237 4278 3.316029 CGAAGCATAAGGATGGCAATGAA 59.684 43.478 0.00 0.00 33.26 2.57
2238 4279 2.880268 CGAAGCATAAGGATGGCAATGA 59.120 45.455 0.00 0.00 33.26 2.57


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

AutoCloner maintained by Alex Coulton.