Multiple sequence alignment - TraesCS3D01G280300

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 TraesCS3D01G280300 chr3D 100.000 6484 0 0 1 6484 388443377 388449860 0.000000e+00 11974.0
1 TraesCS3D01G280300 chr3D 79.638 938 146 26 3349 4252 43008347 43009273 3.300000e-177 632.0
2 TraesCS3D01G280300 chr3D 85.375 547 73 4 4951 5497 43009927 43010466 1.580000e-155 560.0
3 TraesCS3D01G280300 chr3D 80.315 127 22 3 499 623 26183895 26184020 6.920000e-15 93.5
4 TraesCS3D01G280300 chr3D 79.381 97 13 4 383 477 391238338 391238429 1.950000e-05 62.1
5 TraesCS3D01G280300 chr3A 95.441 3290 124 17 2758 6040 509541022 509544292 0.000000e+00 5221.0
6 TraesCS3D01G280300 chr3A 95.661 1936 61 8 811 2740 509539048 509540966 0.000000e+00 3088.0
7 TraesCS3D01G280300 chr3A 77.549 1314 219 59 3085 4364 55033024 55034295 0.000000e+00 723.0
8 TraesCS3D01G280300 chr3A 84.601 539 76 3 4959 5497 55034909 55035440 4.450000e-146 529.0
9 TraesCS3D01G280300 chr3A 79.778 722 120 20 2028 2728 55032073 55032789 9.710000e-138 501.0
10 TraesCS3D01G280300 chr3A 92.898 352 14 3 6144 6484 509547771 509548122 9.710000e-138 501.0
11 TraesCS3D01G280300 chr3A 82.780 482 55 17 4341 4816 55034342 55034801 7.830000e-109 405.0
12 TraesCS3D01G280300 chr3A 85.804 317 36 7 417 727 509538675 509538988 1.740000e-85 327.0
13 TraesCS3D01G280300 chr3A 82.289 367 55 5 3341 3701 54938001 54938363 6.310000e-80 309.0
14 TraesCS3D01G280300 chr3A 97.170 106 3 0 6043 6148 509544642 509544747 5.170000e-41 180.0
15 TraesCS3D01G280300 chr3A 84.971 173 20 5 1017 1186 55031276 55031445 3.110000e-38 171.0
16 TraesCS3D01G280300 chr3B 95.379 2597 84 15 3322 5895 505266318 505268901 0.000000e+00 4098.0
17 TraesCS3D01G280300 chr3B 96.931 945 28 1 1797 2740 505264682 505265626 0.000000e+00 1583.0
18 TraesCS3D01G280300 chr3B 88.291 1264 69 28 528 1781 505263381 505264575 0.000000e+00 1441.0
19 TraesCS3D01G280300 chr3B 90.909 594 32 10 2740 3323 505265656 505266237 0.000000e+00 778.0
20 TraesCS3D01G280300 chr3B 84.291 522 73 5 4959 5480 66876992 66877504 9.710000e-138 501.0
21 TraesCS3D01G280300 chr3B 81.669 611 91 16 2134 2728 66874201 66874806 7.560000e-134 488.0
22 TraesCS3D01G280300 chr3B 81.290 465 74 12 3906 4364 66875938 66876395 1.330000e-96 364.0
23 TraesCS3D01G280300 chr3B 94.492 236 8 3 6254 6484 505286828 505287063 6.180000e-95 359.0
24 TraesCS3D01G280300 chr3B 77.043 575 91 26 1010 1549 66873293 66873861 6.360000e-75 292.0
25 TraesCS3D01G280300 chr3B 81.073 354 50 9 3349 3687 66875302 66875653 3.850000e-67 267.0
26 TraesCS3D01G280300 chr3B 83.333 168 20 8 1 162 505262144 505262309 1.460000e-31 148.0
27 TraesCS3D01G280300 chr3B 76.018 221 40 9 443 659 786864525 786864736 1.150000e-17 102.0
28 TraesCS3D01G280300 chr3B 84.906 106 8 6 1 98 308469603 308469708 4.140000e-17 100.0
29 TraesCS3D01G280300 chr6A 86.161 448 57 5 4954 5397 148529794 148529348 4.550000e-131 479.0
30 TraesCS3D01G280300 chr6A 79.859 427 69 14 3289 3703 148531457 148531036 4.920000e-76 296.0
31 TraesCS3D01G280300 chr6A 84.758 269 39 1 4546 4814 148530217 148529951 1.070000e-67 268.0
32 TraesCS3D01G280300 chr1D 78.202 367 73 5 3343 3703 316008871 316009236 1.820000e-55 228.0
33 TraesCS3D01G280300 chr1D 76.316 304 49 19 30 316 93095933 93095636 2.440000e-29 141.0
34 TraesCS3D01G280300 chr5D 75.599 459 78 30 421 863 5327900 5327460 5.130000e-46 196.0
35 TraesCS3D01G280300 chr5D 97.619 42 0 1 618 659 286170290 286170330 3.240000e-08 71.3
36 TraesCS3D01G280300 chr7D 77.966 295 47 13 1 278 473646469 473646762 1.120000e-37 169.0
37 TraesCS3D01G280300 chr7B 76.897 290 51 14 138 414 222551141 222550855 4.050000e-32 150.0
38 TraesCS3D01G280300 chr7B 89.041 73 6 2 421 493 599883190 599883260 8.950000e-14 89.8
39 TraesCS3D01G280300 chr7B 83.721 86 8 3 404 489 623720777 623720698 6.970000e-10 76.8
40 TraesCS3D01G280300 chr7A 82.659 173 24 6 441 610 528340444 528340275 1.460000e-31 148.0
41 TraesCS3D01G280300 chr7A 83.333 120 13 5 618 734 97601880 97601765 3.200000e-18 104.0
42 TraesCS3D01G280300 chr4B 75.281 356 50 22 443 768 147142437 147142784 1.130000e-27 135.0
43 TraesCS3D01G280300 chr4B 79.144 187 26 7 441 623 534402526 534402349 4.110000e-22 117.0
44 TraesCS3D01G280300 chr1A 81.132 159 29 1 3343 3500 396442134 396442292 6.830000e-25 126.0
45 TraesCS3D01G280300 chr4D 73.913 345 71 14 521 848 509043852 509044194 3.180000e-23 121.0
46 TraesCS3D01G280300 chr4D 85.393 89 6 5 421 506 14834729 14834645 1.160000e-12 86.1
47 TraesCS3D01G280300 chr4D 75.000 208 30 13 617 822 47344381 47344568 6.970000e-10 76.8
48 TraesCS3D01G280300 chr4D 94.118 51 2 1 622 672 130542546 130542497 6.970000e-10 76.8
49 TraesCS3D01G280300 chr2D 77.941 204 30 13 402 599 162497099 162497293 5.310000e-21 113.0
50 TraesCS3D01G280300 chr2D 80.612 98 16 3 518 614 22212983 22212888 9.020000e-09 73.1
51 TraesCS3D01G280300 chr5A 72.289 498 89 36 22 497 276639350 276639820 6.870000e-20 110.0
52 TraesCS3D01G280300 chr5A 88.235 68 6 2 237 303 575169992 575169926 5.390000e-11 80.5
53 TraesCS3D01G280300 chr4A 83.333 114 14 5 240 349 165062275 165062387 4.140000e-17 100.0
54 TraesCS3D01G280300 chr6B 88.235 51 2 2 219 266 602483414 602483365 2.530000e-04 58.4


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 TraesCS3D01G280300 chr3D 388443377 388449860 6483 False 11974.000000 11974 100.000000 1 6484 1 chr3D.!!$F2 6483
1 TraesCS3D01G280300 chr3D 43008347 43010466 2119 False 596.000000 632 82.506500 3349 5497 2 chr3D.!!$F4 2148
2 TraesCS3D01G280300 chr3A 509538675 509548122 9447 False 1863.400000 5221 93.394800 417 6484 5 chr3A.!!$F3 6067
3 TraesCS3D01G280300 chr3A 55031276 55035440 4164 False 465.800000 723 81.935800 1017 5497 5 chr3A.!!$F2 4480
4 TraesCS3D01G280300 chr3B 505262144 505268901 6757 False 1609.600000 4098 90.968600 1 5895 5 chr3B.!!$F5 5894
5 TraesCS3D01G280300 chr3B 66873293 66877504 4211 False 382.400000 501 81.073200 1010 5480 5 chr3B.!!$F4 4470
6 TraesCS3D01G280300 chr6A 148529348 148531457 2109 True 347.666667 479 83.592667 3289 5397 3 chr6A.!!$R1 2108

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
823 1595 0.802607 CTGACGCGAGGCTTTCCTAC 60.803 60.000 15.93 0.00 44.46 3.18 F
943 1715 3.695606 TGGTCCGTGGAGCAGAGC 61.696 66.667 16.37 0.00 46.01 4.09 F
1758 2611 2.073117 CATTTGCTGCATGCTCAACA 57.927 45.000 20.33 8.74 43.37 3.33 F
2959 4121 1.412710 GTGGACACTGGACAAGAGTCA 59.587 52.381 9.33 0.00 45.40 3.41 F
3314 4485 0.390998 GCTCCTCCTGTTCTGTGAGC 60.391 60.000 0.00 0.00 38.51 4.26 F
3498 4753 3.364366 CCATCTTCTGTGCGTTCTTTGTC 60.364 47.826 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1702 2555 3.402628 AGCCGTCATGTACAGTTTTCT 57.597 42.857 0.33 0.00 0.00 2.52 R
2889 4051 0.827507 ATGGTGAACACTTGCCCACC 60.828 55.000 11.63 11.63 46.82 4.61 R
3065 4228 0.167470 CGCAGCAGAATGGACAGTTG 59.833 55.000 0.00 0.00 35.86 3.16 R
3789 5100 1.024271 ACAAACAATGCGCAGACAGT 58.976 45.000 18.32 8.67 0.00 3.55 R
4141 5521 1.479730 AGAAATACCGACGAGGGGAAC 59.520 52.381 0.00 0.00 46.96 3.62 R
5492 7001 0.254462 TGCCCTGTTTGACAGTGACA 59.746 50.000 0.00 0.00 44.50 3.58 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
101 106 9.906660 TTTGAATACATGGTCACATTTTTCTAC 57.093 29.630 0.00 0.00 34.35 2.59
105 110 6.072112 ACATGGTCACATTTTTCTACACAC 57.928 37.500 0.00 0.00 34.35 3.82
108 113 7.446931 ACATGGTCACATTTTTCTACACACATA 59.553 33.333 0.00 0.00 34.35 2.29
111 116 8.855110 TGGTCACATTTTTCTACACACATATTT 58.145 29.630 0.00 0.00 0.00 1.40
290 436 7.821595 TCCTATACACATGTAACACTTTTCG 57.178 36.000 0.00 0.00 33.76 3.46
303 449 7.801315 TGTAACACTTTTCGAATGCTTGATTAC 59.199 33.333 0.00 3.91 0.00 1.89
304 450 5.382303 ACACTTTTCGAATGCTTGATTACG 58.618 37.500 0.00 0.00 0.00 3.18
320 466 8.170553 GCTTGATTACGATTTTTGAAATGCAAT 58.829 29.630 0.00 0.00 36.15 3.56
546 1284 8.094798 ACGTTCTTCAACTGCTTGATTAATTA 57.905 30.769 0.00 0.00 36.26 1.40
818 1590 4.394712 CCCCTGACGCGAGGCTTT 62.395 66.667 15.93 0.00 42.42 3.51
823 1595 0.802607 CTGACGCGAGGCTTTCCTAC 60.803 60.000 15.93 0.00 44.46 3.18
943 1715 3.695606 TGGTCCGTGGAGCAGAGC 61.696 66.667 16.37 0.00 46.01 4.09
944 1716 3.695606 GGTCCGTGGAGCAGAGCA 61.696 66.667 13.01 0.00 41.72 4.26
1238 2022 4.102838 CCTTCCATCTGAGGTCATCTGAAT 59.897 45.833 0.00 0.00 39.10 2.57
1245 2030 6.617782 TCTGAGGTCATCTGAATCTTCTTT 57.382 37.500 0.00 0.00 33.37 2.52
1247 2032 7.102346 TCTGAGGTCATCTGAATCTTCTTTTC 58.898 38.462 0.00 0.00 33.37 2.29
1363 2171 9.611284 GCAAGGGAAATTGAAAATACATTTTTC 57.389 29.630 1.69 4.31 39.86 2.29
1549 2372 6.465084 ACCAGAAGTACAATGTTAGTCTTCC 58.535 40.000 0.00 0.00 33.94 3.46
1570 2397 4.588951 TCCGATGACAAGGATATTGTAGCT 59.411 41.667 0.00 0.00 31.96 3.32
1588 2415 5.920273 TGTAGCTTTGCTATTGTGCTTTTTC 59.080 36.000 0.00 0.00 43.30 2.29
1702 2555 3.556775 GCGCCATGTAAGAAACGGTTATA 59.443 43.478 0.00 0.00 0.00 0.98
1703 2556 4.318546 GCGCCATGTAAGAAACGGTTATAG 60.319 45.833 0.00 0.00 0.00 1.31
1758 2611 2.073117 CATTTGCTGCATGCTCAACA 57.927 45.000 20.33 8.74 43.37 3.33
1814 2758 5.619757 GCTGTATGCTGCATGTTCTAAACAA 60.620 40.000 24.59 0.00 41.00 2.83
2004 2951 3.839490 AGATAGGCTTGGGAGATGATCAG 59.161 47.826 0.09 0.00 0.00 2.90
2060 3039 4.825085 TGTTTTGGGGAAGTCTAATGTCAC 59.175 41.667 0.00 0.00 0.00 3.67
2215 3211 5.450412 GGAATCGCTGAATAAAGCAAATCCA 60.450 40.000 0.00 0.00 43.73 3.41
2380 3378 9.826574 TTCTAATGTTAGCGATAACCTGTAAAT 57.173 29.630 19.99 3.77 0.00 1.40
2830 3992 8.486210 TGTATGCATAAGACTGGAGTAGATTTT 58.514 33.333 8.28 0.00 0.00 1.82
2923 4085 5.470098 TGTTCACCATAGACAAGCTCTTTTC 59.530 40.000 0.00 0.00 0.00 2.29
2959 4121 1.412710 GTGGACACTGGACAAGAGTCA 59.587 52.381 9.33 0.00 45.40 3.41
3065 4228 6.278363 TGTTACTTGTTCTGTAGACACTTCC 58.722 40.000 0.00 0.00 0.00 3.46
3109 4272 2.083774 GCTTGCCACTAACTGTGCATA 58.916 47.619 0.00 0.00 44.92 3.14
3279 4450 6.388619 AACAACAGACTGGGGATAGTTATT 57.611 37.500 7.51 0.00 0.00 1.40
3314 4485 0.390998 GCTCCTCCTGTTCTGTGAGC 60.391 60.000 0.00 0.00 38.51 4.26
3334 4587 8.210265 TGTGAGCATATAATAGGTTGTTGATGA 58.790 33.333 0.00 0.00 0.00 2.92
3336 4589 9.056005 TGAGCATATAATAGGTTGTTGATGAAC 57.944 33.333 0.00 0.00 0.00 3.18
3498 4753 3.364366 CCATCTTCTGTGCGTTCTTTGTC 60.364 47.826 0.00 0.00 0.00 3.18
3556 4826 5.049680 TGCGAAGAGGTTGTAAGATTGTTTC 60.050 40.000 0.00 0.00 0.00 2.78
3673 4948 3.557595 CGCTGTAACTTGGATCCAGATTC 59.442 47.826 15.53 6.79 0.00 2.52
3822 5138 7.322222 GCGCATTGTTTGTTGCAAAATTAAATA 59.678 29.630 0.30 0.00 38.80 1.40
4074 5453 3.759618 TGAAGTTTCCAACGGTTCACTTT 59.240 39.130 0.00 0.00 36.23 2.66
4141 5521 2.756207 TGACAATGGATGTTGCATCAGG 59.244 45.455 10.71 0.88 44.12 3.86
4857 6359 1.228988 TCACTGCTCCTGCTCCTGA 60.229 57.895 0.00 0.00 40.48 3.86
4943 6446 7.790782 AAAAAGCATTGACCCCTCTTAATTA 57.209 32.000 0.00 0.00 0.00 1.40
5028 6534 2.615912 CCAAAGCCATCGATTCCTCTTC 59.384 50.000 0.00 0.00 0.00 2.87
5336 6845 0.179009 TATGCTCTGGGGCTGCAATC 60.179 55.000 0.50 0.00 40.24 2.67
5484 6993 8.791355 ATTTAACATTGAAACTTGGTCGTAAC 57.209 30.769 0.00 0.00 0.00 2.50
5485 6994 4.823790 ACATTGAAACTTGGTCGTAACC 57.176 40.909 0.00 0.00 46.66 2.85
5496 7005 2.406130 GGTCGTAACCGTGATTTGTCA 58.594 47.619 0.00 0.00 35.36 3.58
5497 7006 2.156310 GGTCGTAACCGTGATTTGTCAC 59.844 50.000 0.00 0.00 35.36 3.67
5498 7007 3.054878 GTCGTAACCGTGATTTGTCACT 58.945 45.455 6.95 0.00 38.40 3.41
5589 7098 6.653273 TTCAGCGTAGATCAAAGATTTCAG 57.347 37.500 0.00 0.00 0.00 3.02
5646 7155 7.858382 AGATACAGAGTCATTTATTCTTCGACG 59.142 37.037 0.00 0.00 0.00 5.12
5752 7264 0.519961 GTGGCGGCTTGATTTTACGT 59.480 50.000 11.43 0.00 0.00 3.57
5773 7285 5.467735 ACGTAGTGGGATAAAAACAAGTGAC 59.532 40.000 0.00 0.00 42.51 3.67
5776 7288 6.331369 AGTGGGATAAAAACAAGTGACATG 57.669 37.500 0.00 0.00 0.00 3.21
5777 7289 5.833131 AGTGGGATAAAAACAAGTGACATGT 59.167 36.000 0.00 0.00 0.00 3.21
5789 7301 0.321034 TGACATGTGGTGAGAGCAGC 60.321 55.000 1.15 0.00 42.72 5.25
5820 7332 7.009540 GCTGTATTTGATGTGGTTTTAATCTGC 59.990 37.037 0.00 0.00 0.00 4.26
5824 7336 5.233957 TGATGTGGTTTTAATCTGCGATG 57.766 39.130 0.00 0.00 0.00 3.84
5832 7344 5.064707 GGTTTTAATCTGCGATGCTCTGTTA 59.935 40.000 0.00 0.00 0.00 2.41
5923 7446 3.111853 TGACGCCCTATGATCATTCAC 57.888 47.619 14.65 0.78 33.85 3.18
5947 7470 5.397240 CGATTTCCGTTTGAACAGTTAAACC 59.603 40.000 10.36 0.00 34.21 3.27
5954 7477 4.630894 TTGAACAGTTAAACCTGCAGTG 57.369 40.909 13.81 6.81 35.83 3.66
6018 7541 8.960591 CATATATGTTTGTCCTTGGTTCTTCTT 58.039 33.333 4.43 0.00 0.00 2.52
6022 7545 6.419791 TGTTTGTCCTTGGTTCTTCTTTCTA 58.580 36.000 0.00 0.00 0.00 2.10
6137 8008 5.278266 GCGAGATCTATTTCAGCTCTACAGT 60.278 44.000 0.00 0.00 29.75 3.55
6157 11056 0.802607 CGAGTCTTAGTTGGCGCCTC 60.803 60.000 29.70 20.25 0.00 4.70
6170 11069 1.541588 GGCGCCTCCCATATTTGAATC 59.458 52.381 22.15 0.00 0.00 2.52
6181 11080 4.836736 CCATATTTGAATCCCCATGCTCTT 59.163 41.667 0.00 0.00 0.00 2.85
6186 11085 1.680207 GAATCCCCATGCTCTTTCTGC 59.320 52.381 0.00 0.00 0.00 4.26
6190 11089 2.511218 TCCCCATGCTCTTTCTGCTTAT 59.489 45.455 0.00 0.00 0.00 1.73
6257 11157 9.631257 TTTTGAATGGAGAAATAGCATAGATCA 57.369 29.630 0.00 0.00 0.00 2.92
6266 11166 9.794685 GAGAAATAGCATAGATCAACGATGATA 57.205 33.333 8.29 0.00 46.30 2.15
6347 11249 1.375523 CCCACACTCCGTACAAGCC 60.376 63.158 0.00 0.00 0.00 4.35
6404 11306 4.545610 CAACAACAACGGAAATGTATGCT 58.454 39.130 0.00 0.00 0.00 3.79
6431 11333 9.444668 AGGATGCAAGATACCATATACTCATAT 57.555 33.333 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 81 8.511321 TGTGTAGAAAAATGTGACCATGTATTC 58.489 33.333 0.00 0.00 0.00 1.75
264 272 8.714179 CGAAAAGTGTTACATGTGTATAGGAAA 58.286 33.333 9.11 0.00 0.00 3.13
265 273 8.089597 TCGAAAAGTGTTACATGTGTATAGGAA 58.910 33.333 9.11 0.00 0.00 3.36
266 274 7.604549 TCGAAAAGTGTTACATGTGTATAGGA 58.395 34.615 9.11 0.00 0.00 2.94
267 275 7.821595 TCGAAAAGTGTTACATGTGTATAGG 57.178 36.000 9.11 0.00 0.00 2.57
268 276 9.689075 CATTCGAAAAGTGTTACATGTGTATAG 57.311 33.333 9.11 0.00 0.00 1.31
278 424 7.006210 CGTAATCAAGCATTCGAAAAGTGTTAC 59.994 37.037 0.00 5.71 0.00 2.50
284 430 7.725610 AAATCGTAATCAAGCATTCGAAAAG 57.274 32.000 0.00 0.00 31.89 2.27
290 436 9.679596 CATTTCAAAAATCGTAATCAAGCATTC 57.320 29.630 0.00 0.00 0.00 2.67
434 605 7.559590 AATGCTGACCATGTATTAAGAGAAC 57.440 36.000 0.00 0.00 33.49 3.01
512 684 6.560711 AGCAGTTGAAGAACGTTAAAACAAT 58.439 32.000 0.00 0.00 37.15 2.71
515 687 6.025280 TCAAGCAGTTGAAGAACGTTAAAAC 58.975 36.000 0.00 3.85 39.85 2.43
737 1509 7.221838 CGGCCACATTTATTCGTTAATTTTCAT 59.778 33.333 2.24 0.00 0.00 2.57
749 1521 3.641031 GCCACGGCCACATTTATTC 57.359 52.632 2.24 0.00 34.56 1.75
790 1562 3.473647 TCAGGGGAGCGCCTGATG 61.474 66.667 26.54 8.27 38.03 3.07
801 1573 4.394712 AAAGCCTCGCGTCAGGGG 62.395 66.667 15.00 7.94 33.58 4.79
802 1574 2.815647 GAAAGCCTCGCGTCAGGG 60.816 66.667 15.00 10.17 33.58 4.45
803 1575 1.945354 TAGGAAAGCCTCGCGTCAGG 61.945 60.000 5.77 7.91 45.54 3.86
804 1576 0.802607 GTAGGAAAGCCTCGCGTCAG 60.803 60.000 5.77 0.00 45.54 3.51
805 1577 1.214589 GTAGGAAAGCCTCGCGTCA 59.785 57.895 5.77 0.00 45.54 4.35
806 1578 1.872679 CGTAGGAAAGCCTCGCGTC 60.873 63.158 5.77 0.00 45.54 5.19
807 1579 2.181021 CGTAGGAAAGCCTCGCGT 59.819 61.111 5.77 0.00 45.54 6.01
808 1580 1.872679 GACGTAGGAAAGCCTCGCG 60.873 63.158 0.00 0.00 45.54 5.87
809 1581 0.525882 GAGACGTAGGAAAGCCTCGC 60.526 60.000 0.00 0.00 45.54 5.03
818 1590 1.709147 GCTTACCGCGAGACGTAGGA 61.709 60.000 8.23 0.00 41.42 2.94
967 1739 2.095415 GGTTATGCGTGGAGTTTGGTTC 60.095 50.000 0.00 0.00 0.00 3.62
1238 2022 5.431765 ACTCTGCACAAAGAGAAAAGAAGA 58.568 37.500 7.62 0.00 45.59 2.87
1363 2171 3.490526 CCAAAATCGACAAACTTGCAAGG 59.509 43.478 29.18 14.74 0.00 3.61
1514 2334 1.568504 ACTTCTGGTAGCCCGAATCA 58.431 50.000 0.00 0.00 0.00 2.57
1549 2372 6.653183 CAAAGCTACAATATCCTTGTCATCG 58.347 40.000 0.00 0.00 34.11 3.84
1570 2397 9.142515 CATTATCTGAAAAAGCACAATAGCAAA 57.857 29.630 0.00 0.00 36.85 3.68
1588 2415 1.501169 TCACGGCGCATCATTATCTG 58.499 50.000 10.83 0.00 0.00 2.90
1702 2555 3.402628 AGCCGTCATGTACAGTTTTCT 57.597 42.857 0.33 0.00 0.00 2.52
1703 2556 4.630069 ACATAGCCGTCATGTACAGTTTTC 59.370 41.667 0.33 0.00 34.88 2.29
1758 2611 6.770746 AAGTAGCAATGAGAAATGAGCATT 57.229 33.333 0.00 0.00 32.83 3.56
1814 2758 6.135819 ACAAAGGGCAAAACCTACTACTAT 57.864 37.500 0.00 0.00 40.87 2.12
2830 3992 2.598394 GCCTTGCCAGCCAACAGA 60.598 61.111 0.00 0.00 0.00 3.41
2849 4011 8.462016 GTCAAATAAGCTAAATCCAACATGAGT 58.538 33.333 0.00 0.00 0.00 3.41
2852 4014 7.546358 TGGTCAAATAAGCTAAATCCAACATG 58.454 34.615 0.00 0.00 0.00 3.21
2888 4050 1.454847 GGTGAACACTTGCCCACCA 60.455 57.895 13.00 0.00 46.13 4.17
2889 4051 0.827507 ATGGTGAACACTTGCCCACC 60.828 55.000 11.63 11.63 46.82 4.61
3065 4228 0.167470 CGCAGCAGAATGGACAGTTG 59.833 55.000 0.00 0.00 35.86 3.16
3109 4272 1.678101 GAACTGCAACTTGAGCTTGGT 59.322 47.619 0.00 0.00 0.00 3.67
3279 4450 1.838112 GAGCATCCCCACAATGAACA 58.162 50.000 0.00 0.00 0.00 3.18
3334 4587 8.788806 TGGATCGACTAAATTACAACAATTGTT 58.211 29.630 18.13 18.13 42.22 2.83
3336 4589 9.438291 GATGGATCGACTAAATTACAACAATTG 57.562 33.333 3.24 3.24 0.00 2.32
3498 4753 2.998670 CTGCGAGCTAACATCATATGGG 59.001 50.000 2.13 0.00 33.60 4.00
3570 4845 2.522836 ACTTGATAGCTGATCGCCTG 57.477 50.000 0.00 0.00 40.39 4.85
3673 4948 6.570692 ACAGATCAACCTACCGTTATGTAAG 58.429 40.000 0.00 0.00 31.77 2.34
3789 5100 1.024271 ACAAACAATGCGCAGACAGT 58.976 45.000 18.32 8.67 0.00 3.55
3822 5138 3.626930 TGACCCAGTTAAAGCAGTTGTT 58.373 40.909 0.00 0.00 0.00 2.83
4074 5453 3.476740 GACCCATCGAGCCATTCAA 57.523 52.632 0.00 0.00 0.00 2.69
4141 5521 1.479730 AGAAATACCGACGAGGGGAAC 59.520 52.381 0.00 0.00 46.96 3.62
4272 5657 8.721019 AAATTGAAGTTGTGTGAACATCAAAT 57.279 26.923 8.70 0.00 39.99 2.32
4943 6446 8.362639 AGATTTTCTGCACATAAACAAAGTGAT 58.637 29.630 0.00 0.00 35.33 3.06
5028 6534 4.469945 TCCTGTTCCTGGTCCAATAAGTAG 59.530 45.833 0.00 0.00 0.00 2.57
5336 6845 2.416972 GGTAGAAGACCCTGCAACGTAG 60.417 54.545 0.00 0.00 43.25 3.51
5492 7001 0.254462 TGCCCTGTTTGACAGTGACA 59.746 50.000 0.00 0.00 44.50 3.58
5493 7002 1.334869 CTTGCCCTGTTTGACAGTGAC 59.665 52.381 0.00 0.00 44.50 3.67
5494 7003 1.211703 TCTTGCCCTGTTTGACAGTGA 59.788 47.619 0.00 0.00 44.50 3.41
5495 7004 1.679139 TCTTGCCCTGTTTGACAGTG 58.321 50.000 7.26 0.00 44.50 3.66
5496 7005 2.435372 TTCTTGCCCTGTTTGACAGT 57.565 45.000 7.26 0.00 44.50 3.55
5497 7006 2.689983 ACTTTCTTGCCCTGTTTGACAG 59.310 45.455 1.14 1.14 45.53 3.51
5498 7007 2.733956 ACTTTCTTGCCCTGTTTGACA 58.266 42.857 0.00 0.00 0.00 3.58
5589 7098 9.929180 TTATGTGCAGATATACATCTACTTTCC 57.071 33.333 4.14 0.00 39.62 3.13
5625 7134 5.340803 TCCGTCGAAGAATAAATGACTCTG 58.659 41.667 0.00 0.00 39.69 3.35
5627 7136 6.642683 TTTCCGTCGAAGAATAAATGACTC 57.357 37.500 0.00 0.00 39.69 3.36
5654 7163 6.935167 GGAATGTGTTTGATTTCCCTTGTAT 58.065 36.000 0.00 0.00 33.08 2.29
5655 7164 6.339587 GGAATGTGTTTGATTTCCCTTGTA 57.660 37.500 0.00 0.00 33.08 2.41
5719 7228 0.512952 CGCCACTCTTCTTTGAACCG 59.487 55.000 0.00 0.00 0.00 4.44
5752 7264 7.001674 ACATGTCACTTGTTTTTATCCCACTA 58.998 34.615 0.00 0.00 0.00 2.74
5773 7285 0.321387 ACTGCTGCTCTCACCACATG 60.321 55.000 0.00 0.00 0.00 3.21
5776 7288 2.242113 CAACTGCTGCTCTCACCAC 58.758 57.895 0.00 0.00 0.00 4.16
5777 7289 4.785767 CAACTGCTGCTCTCACCA 57.214 55.556 0.00 0.00 0.00 4.17
5789 7301 4.771590 ACCACATCAAATACAGCAACTG 57.228 40.909 0.00 0.00 37.52 3.16
5820 7332 5.569059 GGTCAACAAATTTAACAGAGCATCG 59.431 40.000 0.00 0.00 42.67 3.84
5824 7336 8.296713 TCATAAGGTCAACAAATTTAACAGAGC 58.703 33.333 0.00 0.00 0.00 4.09
5832 7344 8.877864 TCCTACATCATAAGGTCAACAAATTT 57.122 30.769 0.00 0.00 34.30 1.82
5923 7446 5.397240 GGTTTAACTGTTCAAACGGAAATCG 59.603 40.000 8.65 0.00 45.88 3.34
5938 7461 4.611355 CGAATGACACTGCAGGTTTAACTG 60.611 45.833 19.93 7.70 41.41 3.16
5947 7470 1.991264 CTGTCTCGAATGACACTGCAG 59.009 52.381 13.48 13.48 41.43 4.41
5954 7477 2.370281 TTCAGCCTGTCTCGAATGAC 57.630 50.000 0.00 0.00 37.47 3.06
5982 7505 5.939883 GGACAAACATATATGCAGATGGCTA 59.060 40.000 12.79 0.00 45.15 3.93
6018 7541 9.292195 CCAAGTTAATACCAAGGAAAACTAGAA 57.708 33.333 0.00 0.00 0.00 2.10
6022 7545 6.015434 CAGCCAAGTTAATACCAAGGAAAACT 60.015 38.462 0.00 0.00 0.00 2.66
6060 7931 5.299531 GGTTTATTCAAGGTTATCTCAGCCC 59.700 44.000 0.00 0.00 0.00 5.19
6063 7934 6.037172 CACCGGTTTATTCAAGGTTATCTCAG 59.963 42.308 2.97 0.00 32.04 3.35
6137 8008 1.214589 GGCGCCAACTAAGACTCGA 59.785 57.895 24.80 0.00 0.00 4.04
6157 11056 3.512724 GAGCATGGGGATTCAAATATGGG 59.487 47.826 0.00 0.00 0.00 4.00
6170 11069 2.425143 TAAGCAGAAAGAGCATGGGG 57.575 50.000 0.00 0.00 0.00 4.96
6181 11080 5.478407 TCTTGATCGTCAACATAAGCAGAA 58.522 37.500 0.00 0.00 32.21 3.02
6186 11085 7.588143 AACTTCTCTTGATCGTCAACATAAG 57.412 36.000 0.00 0.00 32.21 1.73
6190 11089 6.538742 AGAAAAACTTCTCTTGATCGTCAACA 59.461 34.615 0.00 0.00 32.21 3.33
6266 11166 8.657712 ACAGACTGGTACTTATTTACCTCTTTT 58.342 33.333 7.51 0.00 42.03 2.27
6347 11249 3.925238 GCGTTGCCAGTATCGCCG 61.925 66.667 0.44 0.00 42.33 6.46
6404 11306 8.844865 ATGAGTATATGGTATCTTGCATCCTA 57.155 34.615 0.00 0.00 0.00 2.94
6431 11333 0.809385 GACGCTGCTGTGTCCTACTA 59.191 55.000 22.55 0.00 45.19 1.82
6454 11364 3.568538 GTTCGTTTACGTTCTAGCCTCA 58.431 45.455 0.00 0.00 40.80 3.86
6457 11367 1.058270 GCGTTCGTTTACGTTCTAGCC 59.942 52.381 0.00 0.00 43.22 3.93


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

AutoCloner maintained by Alex Coulton.