Multiple sequence alignment - TraesCS3A01G157600

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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 TraesCS3A01G157600 chr3A 100.000 3218 0 0 1 3218 154743329 154740112 0.000000e+00 5943.0
1 TraesCS3A01G157600 chr3B 93.260 2626 105 26 626 3217 199928818 199926231 0.000000e+00 3803.0
2 TraesCS3A01G157600 chr3B 94.442 2339 93 20 888 3217 200365772 200368082 0.000000e+00 3565.0
3 TraesCS3A01G157600 chr3B 94.487 1451 52 11 626 2066 199704432 199703000 0.000000e+00 2211.0
4 TraesCS3A01G157600 chr3B 92.960 1179 44 12 2059 3217 199702520 199701361 0.000000e+00 1681.0
5 TraesCS3A01G157600 chr3B 91.589 214 14 2 693 902 200365544 200365757 3.140000e-75 292.0
6 TraesCS3A01G157600 chr3B 93.333 195 12 1 17 210 199704623 199704429 1.460000e-73 287.0
7 TraesCS3A01G157600 chr3B 91.795 195 15 1 17 210 199929009 199928815 1.470000e-68 270.0
8 TraesCS3A01G157600 chr3B 90.640 203 16 2 11 210 200365296 200365498 1.900000e-67 267.0
9 TraesCS3A01G157600 chr3B 85.043 234 26 3 201 433 167963879 167964104 2.500000e-56 230.0
10 TraesCS3A01G157600 chr3B 82.479 234 30 7 203 434 97732953 97732729 9.110000e-46 195.0
11 TraesCS3A01G157600 chr3D 95.985 1594 61 2 671 2261 136776381 136774788 0.000000e+00 2586.0
12 TraesCS3A01G157600 chr3D 94.650 972 25 11 2257 3217 136774621 136773666 0.000000e+00 1482.0
13 TraesCS3A01G157600 chr3D 86.063 696 67 11 12 685 136777082 136776395 0.000000e+00 721.0
14 TraesCS3A01G157600 chr1B 89.634 1640 122 13 840 2462 131789936 131788328 0.000000e+00 2043.0
15 TraesCS3A01G157600 chr1B 89.281 1642 127 17 838 2462 131505323 131503714 0.000000e+00 2012.0
16 TraesCS3A01G157600 chr1B 84.406 917 90 21 806 1711 131179862 131178988 0.000000e+00 852.0
17 TraesCS3A01G157600 chr1B 88.274 452 53 0 1811 2262 131670674 131670223 2.820000e-150 542.0
18 TraesCS3A01G157600 chr1B 89.919 248 14 7 2981 3217 130859579 130859332 3.120000e-80 309.0
19 TraesCS3A01G157600 chr1B 89.919 248 14 7 2981 3217 131380108 131379861 3.120000e-80 309.0
20 TraesCS3A01G157600 chr1B 89.558 249 14 8 2981 3217 130794038 130793790 4.030000e-79 305.0
21 TraesCS3A01G157600 chr1B 89.558 249 14 8 2981 3217 131583412 131583164 4.030000e-79 305.0
22 TraesCS3A01G157600 chr1B 78.618 304 47 12 803 1099 130742829 130742537 5.480000e-43 185.0
23 TraesCS3A01G157600 chr1B 93.069 101 7 0 2735 2835 131787364 131787264 7.190000e-32 148.0
24 TraesCS3A01G157600 chr1B 88.073 109 5 4 2735 2835 131129883 131129775 4.360000e-24 122.0
25 TraesCS3A01G157600 chr1B 97.059 68 1 1 2394 2461 130795270 130795204 2.620000e-21 113.0
26 TraesCS3A01G157600 chr1B 97.015 67 1 1 2394 2460 131602258 131602193 9.440000e-21 111.0
27 TraesCS3A01G157600 chr1B 94.521 73 2 2 2853 2924 345311161 345311232 9.440000e-21 111.0
28 TraesCS3A01G157600 chr1B 92.308 78 1 4 2854 2926 453344420 453344497 4.390000e-19 106.0
29 TraesCS3A01G157600 chr1D 88.856 1669 116 10 806 2461 80006138 80004527 0.000000e+00 1988.0
30 TraesCS3A01G157600 chr1D 88.646 1647 126 19 822 2462 79950146 79948555 0.000000e+00 1949.0
31 TraesCS3A01G157600 chr1D 90.400 375 24 6 2464 2835 79948222 79947857 1.740000e-132 483.0
32 TraesCS3A01G157600 chr1D 89.641 251 12 8 2981 3217 80001933 80001683 1.120000e-79 307.0
33 TraesCS3A01G157600 chr1D 95.050 101 5 0 2735 2835 79947000 79946900 3.320000e-35 159.0
34 TraesCS3A01G157600 chr1D 89.908 109 3 4 2735 2835 80002122 80002014 2.010000e-27 134.0
35 TraesCS3A01G157600 chr1A 87.856 1614 112 12 871 2462 98604580 98603029 0.000000e+00 1818.0
36 TraesCS3A01G157600 chr6B 86.087 230 25 1 206 435 8131965 8131743 1.150000e-59 241.0
37 TraesCS3A01G157600 chr2B 85.837 233 26 1 206 438 719971011 719970786 1.150000e-59 241.0
38 TraesCS3A01G157600 chr2B 94.118 85 5 0 2843 2927 173468231 173468315 2.610000e-26 130.0
39 TraesCS3A01G157600 chr2B 90.244 82 4 1 2843 2924 551551548 551551625 1.580000e-18 104.0
40 TraesCS3A01G157600 chr5A 85.169 236 28 1 207 442 129619224 129619452 5.370000e-58 235.0
41 TraesCS3A01G157600 chr2D 85.841 226 25 1 208 433 291400 291618 1.930000e-57 233.0
42 TraesCS3A01G157600 chr2A 85.841 226 24 2 208 433 217691 217474 1.930000e-57 233.0
43 TraesCS3A01G157600 chr7B 84.416 231 26 5 207 435 464555666 464555888 5.410000e-53 219.0
44 TraesCS3A01G157600 chr5B 82.143 224 32 4 210 433 317076657 317076872 5.480000e-43 185.0
45 TraesCS3A01G157600 chr4A 94.521 73 2 2 2853 2924 498697545 498697474 9.440000e-21 111.0
46 TraesCS3A01G157600 chr4A 94.521 73 2 2 2853 2924 498697492 498697563 9.440000e-21 111.0
47 TraesCS3A01G157600 chr4A 78.102 137 18 7 474 600 545619771 545619905 3.440000e-10 76.8
48 TraesCS3A01G157600 chr5D 81.600 125 14 5 455 571 532664520 532664397 9.500000e-16 95.3
49 TraesCS3A01G157600 chr4B 88.679 53 6 0 548 600 75189493 75189441 7.450000e-07 65.8
50 TraesCS3A01G157600 chr4B 97.297 37 1 0 452 488 115063001 115062965 2.680000e-06 63.9


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 TraesCS3A01G157600 chr3A 154740112 154743329 3217 True 5943.000000 5943 100.000000 1 3218 1 chr3A.!!$R1 3217
1 TraesCS3A01G157600 chr3B 199926231 199929009 2778 True 2036.500000 3803 92.527500 17 3217 2 chr3B.!!$R3 3200
2 TraesCS3A01G157600 chr3B 199701361 199704623 3262 True 1393.000000 2211 93.593333 17 3217 3 chr3B.!!$R2 3200
3 TraesCS3A01G157600 chr3B 200365296 200368082 2786 False 1374.666667 3565 92.223667 11 3217 3 chr3B.!!$F2 3206
4 TraesCS3A01G157600 chr3D 136773666 136777082 3416 True 1596.333333 2586 92.232667 12 3217 3 chr3D.!!$R1 3205
5 TraesCS3A01G157600 chr1B 131503714 131505323 1609 True 2012.000000 2012 89.281000 838 2462 1 chr1B.!!$R6 1624
6 TraesCS3A01G157600 chr1B 131787264 131789936 2672 True 1095.500000 2043 91.351500 840 2835 2 chr1B.!!$R11 1995
7 TraesCS3A01G157600 chr1B 131178988 131179862 874 True 852.000000 852 84.406000 806 1711 1 chr1B.!!$R4 905
8 TraesCS3A01G157600 chr1B 130793790 130795270 1480 True 209.000000 305 93.308500 2394 3217 2 chr1B.!!$R10 823
9 TraesCS3A01G157600 chr1D 79946900 79950146 3246 True 863.666667 1949 91.365333 822 2835 3 chr1D.!!$R1 2013
10 TraesCS3A01G157600 chr1D 80001683 80006138 4455 True 809.666667 1988 89.468333 806 3217 3 chr1D.!!$R2 2411
11 TraesCS3A01G157600 chr1A 98603029 98604580 1551 True 1818.000000 1818 87.856000 871 2462 1 chr1A.!!$R1 1591


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
270 272 0.037734 CGACCCCTACCCAGCTTTTT 59.962 55.0 0.00 0.00 0.00 1.94 F
448 450 0.181350 GGCCTAGACCTTGTCCATGG 59.819 60.0 4.97 4.97 32.18 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 2826 0.318529 ATCGCTGATAGCTCGCTGTG 60.319 55.0 0.85 0.0 39.60 3.66 R
2417 3250 0.246635 GGATCCACAGCTACGTGTGT 59.753 55.0 6.95 0.0 45.47 3.72 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
36 37 2.504920 CGGGAGCCACTCTGATACA 58.495 57.895 0.00 0.00 0.00 2.29
127 128 2.283388 CCTGTGCCACCATTGCCT 60.283 61.111 0.00 0.00 0.00 4.75
130 131 1.457267 TGTGCCACCATTGCCTTGT 60.457 52.632 0.00 0.00 0.00 3.16
215 217 1.439543 GGTGAGAGGATAAGGCCCAT 58.560 55.000 0.00 0.00 0.00 4.00
228 230 0.975887 GGCCCATTTCTTTTGCCAGA 59.024 50.000 0.00 0.00 41.76 3.86
256 258 3.203716 GGATTGTAACAGAATCCGACCC 58.796 50.000 0.00 0.00 39.58 4.46
260 262 2.762327 TGTAACAGAATCCGACCCCTAC 59.238 50.000 0.00 0.00 0.00 3.18
268 270 2.298661 CCGACCCCTACCCAGCTTT 61.299 63.158 0.00 0.00 0.00 3.51
270 272 0.037734 CGACCCCTACCCAGCTTTTT 59.962 55.000 0.00 0.00 0.00 1.94
272 274 0.408309 ACCCCTACCCAGCTTTTTCC 59.592 55.000 0.00 0.00 0.00 3.13
273 275 0.679960 CCCCTACCCAGCTTTTTCCG 60.680 60.000 0.00 0.00 0.00 4.30
279 281 1.075536 ACCCAGCTTTTTCCGGAATCT 59.924 47.619 19.62 10.09 0.00 2.40
280 282 2.171003 CCCAGCTTTTTCCGGAATCTT 58.829 47.619 19.62 0.00 0.00 2.40
281 283 2.562738 CCCAGCTTTTTCCGGAATCTTT 59.437 45.455 19.62 0.08 0.00 2.52
282 284 3.578688 CCAGCTTTTTCCGGAATCTTTG 58.421 45.455 19.62 12.61 0.00 2.77
283 285 3.255642 CCAGCTTTTTCCGGAATCTTTGA 59.744 43.478 19.62 0.00 0.00 2.69
284 286 4.479619 CAGCTTTTTCCGGAATCTTTGAG 58.520 43.478 19.62 10.54 0.00 3.02
285 287 3.507622 AGCTTTTTCCGGAATCTTTGAGG 59.492 43.478 19.62 4.16 0.00 3.86
295 297 3.425659 GAATCTTTGAGGTTTGAGCCCT 58.574 45.455 0.00 0.00 34.11 5.19
308 310 5.924254 GGTTTGAGCCCTATTTGTTTTACAC 59.076 40.000 0.00 0.00 0.00 2.90
326 328 8.412456 GTTTTACACTCCTATCTAGTTAGGGTC 58.588 40.741 21.70 6.83 39.45 4.46
399 401 1.551452 GATAGGGATCGGACTCTGGG 58.449 60.000 0.00 0.00 0.00 4.45
429 431 5.215160 CCGAGATTTTGACAAAAGAACTGG 58.785 41.667 17.73 15.61 33.22 4.00
433 435 2.452600 TTGACAAAAGAACTGGGCCT 57.547 45.000 4.53 0.00 0.00 5.19
446 448 0.253160 TGGGCCTAGACCTTGTCCAT 60.253 55.000 4.53 0.00 32.18 3.41
448 450 0.181350 GGCCTAGACCTTGTCCATGG 59.819 60.000 4.97 4.97 32.18 3.66
452 454 0.548926 TAGACCTTGTCCATGGGCCA 60.549 55.000 15.27 9.61 34.34 5.36
496 512 1.227263 CCTGGGCCTGTCGTATTCG 60.227 63.158 4.53 0.00 38.55 3.34
498 514 2.960129 GGGCCTGTCGTATTCGCG 60.960 66.667 0.84 0.00 36.96 5.87
499 515 2.202703 GGCCTGTCGTATTCGCGT 60.203 61.111 5.77 0.00 36.96 6.01
540 563 2.360225 GGTCCGGCGGGCTTTTAA 60.360 61.111 31.34 3.28 0.00 1.52
552 575 0.885196 GCTTTTAACGTGATGGGCCA 59.115 50.000 9.61 9.61 0.00 5.36
594 617 1.632965 ATCAGGTTTCGGTAGGCCCC 61.633 60.000 0.00 0.00 0.00 5.80
606 629 4.493049 GGCCCCGCCCGACAAATA 62.493 66.667 0.00 0.00 44.06 1.40
607 630 2.438795 GCCCCGCCCGACAAATAA 60.439 61.111 0.00 0.00 0.00 1.40
608 631 2.478033 GCCCCGCCCGACAAATAAG 61.478 63.158 0.00 0.00 0.00 1.73
612 635 0.742990 CCGCCCGACAAATAAGCAGA 60.743 55.000 0.00 0.00 0.00 4.26
673 696 1.071605 GGTAGAAAGCACACAGAGCG 58.928 55.000 0.00 0.00 37.01 5.03
680 731 0.734253 AGCACACAGAGCGAACGATC 60.734 55.000 4.29 4.29 37.01 3.69
706 757 1.986378 CGGCTGAAGTGTCGAGTAAAG 59.014 52.381 0.00 0.00 0.00 1.85
729 780 4.387862 GTGCTTCAAGATTCATGCAAAAGG 59.612 41.667 0.00 0.00 32.10 3.11
732 783 5.291128 GCTTCAAGATTCATGCAAAAGGATG 59.709 40.000 0.00 0.00 0.00 3.51
736 787 6.155565 TCAAGATTCATGCAAAAGGATGGAAT 59.844 34.615 0.00 0.00 0.00 3.01
752 804 3.505790 AATGGTGGCTGGGCGTTCA 62.506 57.895 0.00 0.00 0.00 3.18
764 816 1.070786 GCGTTCACTGGGACTTCCA 59.929 57.895 0.00 0.00 44.79 3.53
779 831 2.306805 ACTTCCATGAGAATGTCAGCCA 59.693 45.455 0.00 0.00 39.07 4.75
852 910 1.749638 CCTACGTCACCGCTCTCCT 60.750 63.158 0.00 0.00 37.70 3.69
979 1083 0.741221 CGTCAAACCCTAGCTGGCTC 60.741 60.000 0.00 0.00 0.00 4.70
1047 1151 2.125552 CGTGGCCTCATCTTCGCA 60.126 61.111 3.32 0.00 0.00 5.10
1091 1195 2.249413 ATCCACCTCCAGCGCAAGAG 62.249 60.000 11.47 15.08 43.02 2.85
1612 1734 3.869272 GGCGATGCCTGCAGTTCG 61.869 66.667 20.34 20.34 46.69 3.95
1616 1738 1.078848 GATGCCTGCAGTTCGGTCT 60.079 57.895 13.81 0.00 0.00 3.85
1647 1769 3.061848 CCAAATCCGCCCGCACTT 61.062 61.111 0.00 0.00 0.00 3.16
1676 1798 5.282055 ACATCGGAGATTCAAGAAGCATA 57.718 39.130 0.63 0.00 45.12 3.14
1725 1856 2.948720 GCACGAACCAGAGGAGCCT 61.949 63.158 0.00 0.00 0.00 4.58
1734 1865 0.979665 CAGAGGAGCCTCAAGAACCA 59.020 55.000 18.16 0.00 44.99 3.67
1809 1940 2.358737 GACCACGCCCTGACCTTG 60.359 66.667 0.00 0.00 0.00 3.61
1896 2045 0.740868 CGTCGACGGTACTACTGGGA 60.741 60.000 29.70 0.00 35.37 4.37
2185 2826 1.452145 TTGTTGGTCTTTCCCGCAGC 61.452 55.000 0.00 0.00 34.77 5.25
2411 3244 1.498865 CGGCGATGTAACTGGGATGC 61.499 60.000 0.00 0.00 0.00 3.91
2412 3245 0.463654 GGCGATGTAACTGGGATGCA 60.464 55.000 0.00 0.00 0.00 3.96
2413 3246 0.657840 GCGATGTAACTGGGATGCAC 59.342 55.000 0.00 0.00 0.00 4.57
2414 3247 2.011548 GCGATGTAACTGGGATGCACA 61.012 52.381 0.00 0.00 0.00 4.57
2415 3248 1.665679 CGATGTAACTGGGATGCACAC 59.334 52.381 0.00 0.00 0.00 3.82
2416 3249 2.710377 GATGTAACTGGGATGCACACA 58.290 47.619 0.00 0.00 0.00 3.72
2417 3250 2.647683 TGTAACTGGGATGCACACAA 57.352 45.000 0.00 0.00 0.00 3.33
2487 5093 9.377383 CGTGGTTTAGTACAAGAGTTTATTTTG 57.623 33.333 0.00 0.00 0.00 2.44
2592 5198 0.847373 TCTTGTTTACCTGGCCCACA 59.153 50.000 0.00 0.00 0.00 4.17
2659 5266 9.057089 GTAGTCTCCTATTCATATGTTTTTGGG 57.943 37.037 1.90 0.08 0.00 4.12
2786 6362 4.219944 GGGTAGAACAATGGTTTTCCTTCC 59.780 45.833 0.00 0.00 41.38 3.46
2805 6389 4.857871 TCCGCGTATCTGAAAATGAAAG 57.142 40.909 4.92 0.00 0.00 2.62
2932 6543 5.882557 TCGGACGGAGGGAGTATATAATTAC 59.117 44.000 0.00 0.00 0.00 1.89
2999 6636 7.978099 TGAGCAGAGCCTGGATATAATTATA 57.022 36.000 7.62 7.62 31.21 0.98
3138 6783 5.889853 ACAAAGTCATGCCATCAATAGTCAT 59.110 36.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.904178 TATCAGAGTGGCTCCCGCGA 62.904 60.000 8.23 0.00 39.30 5.87
36 37 4.796231 GTGGCGCGACACCTCGAT 62.796 66.667 34.88 0.00 43.06 3.59
149 150 2.961536 TTCACCCATCCCTTCTCCTA 57.038 50.000 0.00 0.00 0.00 2.94
215 217 3.713764 TCCCCAAATTCTGGCAAAAGAAA 59.286 39.130 0.00 0.00 44.90 2.52
228 230 5.127031 CGGATTCTGTTACAATCCCCAAATT 59.873 40.000 9.68 0.00 44.64 1.82
240 242 2.102084 GGTAGGGGTCGGATTCTGTTAC 59.898 54.545 0.00 0.00 0.00 2.50
242 244 1.201424 GGTAGGGGTCGGATTCTGTT 58.799 55.000 0.00 0.00 0.00 3.16
243 245 0.690077 GGGTAGGGGTCGGATTCTGT 60.690 60.000 0.00 0.00 0.00 3.41
256 258 0.326927 TCCGGAAAAAGCTGGGTAGG 59.673 55.000 0.00 0.00 34.94 3.18
260 262 1.839424 AGATTCCGGAAAAAGCTGGG 58.161 50.000 23.08 0.00 34.94 4.45
268 270 4.465886 TCAAACCTCAAAGATTCCGGAAA 58.534 39.130 23.08 4.74 0.00 3.13
270 272 3.674997 CTCAAACCTCAAAGATTCCGGA 58.325 45.455 0.00 0.00 0.00 5.14
272 274 2.162408 GGCTCAAACCTCAAAGATTCCG 59.838 50.000 0.00 0.00 0.00 4.30
273 275 2.493675 GGGCTCAAACCTCAAAGATTCC 59.506 50.000 0.00 0.00 0.00 3.01
279 281 4.479158 ACAAATAGGGCTCAAACCTCAAA 58.521 39.130 0.00 0.00 39.54 2.69
280 282 4.112634 ACAAATAGGGCTCAAACCTCAA 57.887 40.909 0.00 0.00 39.54 3.02
281 283 3.806949 ACAAATAGGGCTCAAACCTCA 57.193 42.857 0.00 0.00 39.54 3.86
282 284 5.468540 AAAACAAATAGGGCTCAAACCTC 57.531 39.130 0.00 0.00 39.54 3.85
283 285 5.836358 TGTAAAACAAATAGGGCTCAAACCT 59.164 36.000 0.00 0.00 42.15 3.50
284 286 5.924254 GTGTAAAACAAATAGGGCTCAAACC 59.076 40.000 0.00 0.00 0.00 3.27
285 287 6.745116 AGTGTAAAACAAATAGGGCTCAAAC 58.255 36.000 0.00 0.00 0.00 2.93
363 365 5.136048 TCCCTATCCAGCTTTTCCCATAATT 59.864 40.000 0.00 0.00 0.00 1.40
367 369 2.502745 TCCCTATCCAGCTTTTCCCAT 58.497 47.619 0.00 0.00 0.00 4.00
369 371 2.551071 CGATCCCTATCCAGCTTTTCCC 60.551 54.545 0.00 0.00 0.00 3.97
399 401 5.880054 TTTGTCAAAATCTCGGGATTCTC 57.120 39.130 11.77 3.20 40.86 2.87
417 419 2.224793 GGTCTAGGCCCAGTTCTTTTGT 60.225 50.000 0.30 0.00 0.00 2.83
429 431 0.181350 CCATGGACAAGGTCTAGGCC 59.819 60.000 5.56 4.79 32.47 5.19
433 435 0.548926 TGGCCCATGGACAAGGTCTA 60.549 55.000 15.22 0.00 38.06 2.59
480 496 2.185867 GCGAATACGACAGGCCCA 59.814 61.111 0.00 0.00 42.66 5.36
486 502 1.643326 CGTTAACACGCGAATACGACA 59.357 47.619 15.93 0.00 40.18 4.35
496 512 0.386352 GGGCCTTTTCGTTAACACGC 60.386 55.000 0.84 0.00 46.70 5.34
498 514 0.239082 CCGGGCCTTTTCGTTAACAC 59.761 55.000 0.84 0.00 0.00 3.32
499 515 1.517210 GCCGGGCCTTTTCGTTAACA 61.517 55.000 8.12 0.00 0.00 2.41
521 537 2.414658 TTAAAAGCCCGCCGGACCTT 62.415 55.000 5.05 3.65 0.00 3.50
529 552 0.179174 CCATCACGTTAAAAGCCCGC 60.179 55.000 0.00 0.00 0.00 6.13
540 563 3.650950 AAGCCTGGCCCATCACGT 61.651 61.111 16.57 0.00 0.00 4.49
575 598 1.632965 GGGGCCTACCGAAACCTGAT 61.633 60.000 0.84 0.00 41.60 2.90
594 617 1.299541 ATCTGCTTATTTGTCGGGCG 58.700 50.000 0.00 0.00 0.00 6.13
603 626 8.097662 GCTTAGGACCAGTTATATCTGCTTATT 58.902 37.037 5.42 0.00 34.47 1.40
606 629 5.221742 GGCTTAGGACCAGTTATATCTGCTT 60.222 44.000 5.42 0.00 34.47 3.91
607 630 4.284746 GGCTTAGGACCAGTTATATCTGCT 59.715 45.833 5.42 1.30 34.47 4.24
608 631 4.284746 AGGCTTAGGACCAGTTATATCTGC 59.715 45.833 5.42 0.00 34.47 4.26
612 635 4.841246 CAGGAGGCTTAGGACCAGTTATAT 59.159 45.833 0.00 0.00 0.00 0.86
622 645 0.178903 ACACCACAGGAGGCTTAGGA 60.179 55.000 0.00 0.00 0.00 2.94
706 757 4.387862 CCTTTTGCATGAATCTTGAAGCAC 59.612 41.667 0.00 0.00 0.00 4.40
729 780 2.129785 GCCCAGCCACCATTCCATC 61.130 63.158 0.00 0.00 0.00 3.51
732 783 4.740822 ACGCCCAGCCACCATTCC 62.741 66.667 0.00 0.00 0.00 3.01
736 787 4.947147 GTGAACGCCCAGCCACCA 62.947 66.667 0.00 0.00 0.00 4.17
764 816 7.971201 TCTTATTATCTGGCTGACATTCTCAT 58.029 34.615 0.00 0.00 0.00 2.90
808 860 5.716094 AGCTCGGTTTGTTTTGTAAGTTTT 58.284 33.333 0.00 0.00 0.00 2.43
814 869 2.614983 GGTGAGCTCGGTTTGTTTTGTA 59.385 45.455 9.64 0.00 0.00 2.41
852 910 0.315544 GCGTGCGAAAGTGAAAACGA 60.316 50.000 0.00 0.00 33.03 3.85
979 1083 4.824515 AGGAGGAGGGACGGAGCG 62.825 72.222 0.00 0.00 0.00 5.03
1558 1662 4.462417 CTCGACGGAGCGCTCGTT 62.462 66.667 29.81 19.54 41.22 3.85
1647 1769 3.885724 TGAATCTCCGATGTAGCAACA 57.114 42.857 0.00 0.00 40.69 3.33
1725 1856 1.005867 GCGTACCGGTGGTTCTTGA 60.006 57.895 19.93 0.00 37.09 3.02
1734 1865 1.153706 GTGTGCTATGCGTACCGGT 60.154 57.895 13.98 13.98 0.00 5.28
1856 2005 0.806492 GTCGCTCAGGTCCGAATTCC 60.806 60.000 0.00 0.00 35.00 3.01
1886 2035 5.129815 ACGAAGCCATAATTTCCCAGTAGTA 59.870 40.000 0.00 0.00 0.00 1.82
1896 2045 3.941483 CTGGTGAGACGAAGCCATAATTT 59.059 43.478 0.00 0.00 0.00 1.82
2185 2826 0.318529 ATCGCTGATAGCTCGCTGTG 60.319 55.000 0.85 0.00 39.60 3.66
2202 2843 4.032104 GCATTCAATCAGGCGTCAAAAATC 59.968 41.667 0.00 0.00 0.00 2.17
2210 2851 2.161855 TCAAAGCATTCAATCAGGCGT 58.838 42.857 0.00 0.00 0.00 5.68
2411 3244 1.005032 CACAGCTACGTGTGTTGTGTG 60.005 52.381 22.32 13.28 42.52 3.82
2412 3245 1.286501 CACAGCTACGTGTGTTGTGT 58.713 50.000 22.32 6.97 42.52 3.72
2413 3246 0.581529 CCACAGCTACGTGTGTTGTG 59.418 55.000 23.09 23.09 45.47 3.33
2414 3247 0.462375 TCCACAGCTACGTGTGTTGT 59.538 50.000 0.00 2.47 45.47 3.32
2415 3248 1.726791 GATCCACAGCTACGTGTGTTG 59.273 52.381 0.00 1.76 45.47 3.33
2416 3249 1.337823 GGATCCACAGCTACGTGTGTT 60.338 52.381 6.95 0.00 45.47 3.32
2417 3250 0.246635 GGATCCACAGCTACGTGTGT 59.753 55.000 6.95 0.00 45.47 3.72
2487 5093 3.365472 ACTAAATCAATTGGAGGCCCAC 58.635 45.455 5.42 0.00 43.41 4.61
2489 5095 5.420725 AAAACTAAATCAATTGGAGGCCC 57.579 39.130 5.42 0.00 0.00 5.80
2592 5198 5.148651 AGTTCTTCACCTTATAACGCTGT 57.851 39.130 0.00 0.00 0.00 4.40
2659 5266 9.956720 CACATTAAGATTTAAGAATCATCACCC 57.043 33.333 2.41 0.00 43.35 4.61
2786 6362 5.456192 ACTCTTTCATTTTCAGATACGCG 57.544 39.130 3.53 3.53 0.00 6.01
2805 6389 6.202516 AGTATCACTTAGAGCACTGAACTC 57.797 41.667 0.00 0.00 0.00 3.01
2961 6572 5.598005 GGCTCTGCTCATATCATATACCTCT 59.402 44.000 0.00 0.00 0.00 3.69
2971 6582 6.477053 TTATATCCAGGCTCTGCTCATATC 57.523 41.667 0.00 0.00 0.00 1.63
3031 6669 8.374743 ACAGGTATTGCTAATTCAAACCAAAAT 58.625 29.630 10.77 0.00 33.53 1.82
3034 6672 6.909550 ACAGGTATTGCTAATTCAAACCAA 57.090 33.333 10.77 0.00 33.53 3.67
3138 6783 7.765360 ACATTGTTTCTGAATCTGCAAAAAGAA 59.235 29.630 0.00 0.00 0.00 2.52



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

AutoCloner maintained by Alex Coulton.