Multiple sequence alignment - TraesCS7A01G515900

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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 TraesCS7A01G515900 chr7A 100.000 3470 0 0 1 3470 701267454 701270923 0.000000e+00 6408.0
1 TraesCS7A01G515900 chr7A 85.735 2068 246 29 398 2437 701185759 701187805 0.000000e+00 2139.0
2 TraesCS7A01G515900 chr7A 81.666 1849 284 37 128 1932 701250877 701252714 0.000000e+00 1485.0
3 TraesCS7A01G515900 chr7A 90.390 1103 74 12 843 1916 701194364 701195463 0.000000e+00 1421.0
4 TraesCS7A01G515900 chr7A 81.515 660 96 17 127 773 701193704 701194350 1.430000e-143 520.0
5 TraesCS7A01G515900 chr7A 87.599 379 41 3 2065 2437 701252802 701253180 5.320000e-118 435.0
6 TraesCS7A01G515900 chr7A 84.337 249 33 4 126 372 701185460 701185704 4.480000e-59 239.0
7 TraesCS7A01G515900 chr7D 93.893 2489 112 14 1 2455 611218255 611220737 0.000000e+00 3718.0
8 TraesCS7A01G515900 chr7D 85.221 2375 298 25 126 2455 611147814 611150180 0.000000e+00 2392.0
9 TraesCS7A01G515900 chr7D 88.633 651 58 8 2746 3396 611223115 611223749 0.000000e+00 778.0
10 TraesCS7A01G515900 chr7D 85.817 416 33 5 3041 3455 611231157 611231547 5.360000e-113 418.0
11 TraesCS7A01G515900 chr7D 90.116 172 12 3 2484 2654 611222902 611223069 5.830000e-53 219.0
12 TraesCS7A01G515900 chr7D 94.643 56 3 0 3415 3470 612440270 612440215 1.720000e-13 87.9
13 TraesCS7A01G515900 chr7B 92.351 2484 151 17 1 2455 700386848 700389321 0.000000e+00 3498.0
14 TraesCS7A01G515900 chr7B 86.356 579 59 11 2823 3398 700391564 700392125 6.370000e-172 614.0
15 TraesCS7A01G515900 chr7B 82.564 585 62 17 2886 3460 700381801 700382355 2.420000e-131 479.0
16 TraesCS7A01G515900 chr7B 82.292 384 38 15 3094 3470 701873193 701872833 4.350000e-79 305.0
17 TraesCS7A01G515900 chr6B 75.529 1937 393 51 552 2445 75520202 75518304 0.000000e+00 876.0
18 TraesCS7A01G515900 chr6B 77.653 1244 226 25 130 1355 5586251 5585042 0.000000e+00 710.0
19 TraesCS7A01G515900 chr5A 74.348 2031 422 58 454 2437 18675449 18673471 0.000000e+00 773.0
20 TraesCS7A01G515900 chr4A 73.206 2355 516 84 131 2418 47654833 47657139 0.000000e+00 747.0
21 TraesCS7A01G515900 chr4A 74.317 1978 407 78 553 2455 621130532 621132483 0.000000e+00 745.0
22 TraesCS7A01G515900 chr5D 77.928 1255 236 28 130 1360 549584260 549585497 0.000000e+00 745.0
23 TraesCS7A01G515900 chr5D 75.773 194 42 4 2248 2437 27012847 27012655 3.690000e-15 93.5
24 TraesCS7A01G515900 chr2A 79.638 1051 186 19 132 1163 15878678 15879719 0.000000e+00 730.0
25 TraesCS7A01G515900 chr2B 79.750 1042 179 24 135 1155 24917580 24916550 0.000000e+00 726.0
26 TraesCS7A01G515900 chr2B 82.775 209 20 5 3261 3469 300401827 300401635 4.600000e-39 172.0
27 TraesCS7A01G515900 chr5B 77.448 1246 240 28 130 1351 701161223 701162451 0.000000e+00 706.0
28 TraesCS7A01G515900 chr5B 82.775 209 20 6 3261 3469 427518057 427518249 4.600000e-39 172.0
29 TraesCS7A01G515900 chr5B 81.429 210 22 7 3261 3469 695581968 695582161 4.640000e-34 156.0
30 TraesCS7A01G515900 chr5B 81.043 211 19 10 3261 3469 317800253 317800062 7.760000e-32 148.0
31 TraesCS7A01G515900 chr3B 82.775 209 20 5 3261 3469 772285413 772285221 4.600000e-39 172.0
32 TraesCS7A01G515900 chr4D 75.493 355 81 5 2076 2424 416402427 416402073 5.960000e-38 169.0
33 TraesCS7A01G515900 chr1B 81.991 211 18 9 3261 3469 71447328 71447520 9.970000e-36 161.0
34 TraesCS7A01G515900 chr1B 81.818 209 22 6 3261 3469 662955800 662955992 9.970000e-36 161.0
35 TraesCS7A01G515900 chr2D 85.714 77 9 1 2894 2968 244752843 244752767 2.870000e-11 80.5
36 TraesCS7A01G515900 chr2D 85.714 77 9 1 2894 2968 287295187 287295111 2.870000e-11 80.5


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 TraesCS7A01G515900 chr7A 701267454 701270923 3469 False 6408.000000 6408 100.000000 1 3470 1 chr7A.!!$F1 3469
1 TraesCS7A01G515900 chr7A 701185460 701187805 2345 False 1189.000000 2139 85.036000 126 2437 2 chr7A.!!$F2 2311
2 TraesCS7A01G515900 chr7A 701193704 701195463 1759 False 970.500000 1421 85.952500 127 1916 2 chr7A.!!$F3 1789
3 TraesCS7A01G515900 chr7A 701250877 701253180 2303 False 960.000000 1485 84.632500 128 2437 2 chr7A.!!$F4 2309
4 TraesCS7A01G515900 chr7D 611147814 611150180 2366 False 2392.000000 2392 85.221000 126 2455 1 chr7D.!!$F1 2329
5 TraesCS7A01G515900 chr7D 611218255 611223749 5494 False 1571.666667 3718 90.880667 1 3396 3 chr7D.!!$F3 3395
6 TraesCS7A01G515900 chr7B 700386848 700392125 5277 False 2056.000000 3498 89.353500 1 3398 2 chr7B.!!$F2 3397
7 TraesCS7A01G515900 chr7B 700381801 700382355 554 False 479.000000 479 82.564000 2886 3460 1 chr7B.!!$F1 574
8 TraesCS7A01G515900 chr6B 75518304 75520202 1898 True 876.000000 876 75.529000 552 2445 1 chr6B.!!$R2 1893
9 TraesCS7A01G515900 chr6B 5585042 5586251 1209 True 710.000000 710 77.653000 130 1355 1 chr6B.!!$R1 1225
10 TraesCS7A01G515900 chr5A 18673471 18675449 1978 True 773.000000 773 74.348000 454 2437 1 chr5A.!!$R1 1983
11 TraesCS7A01G515900 chr4A 47654833 47657139 2306 False 747.000000 747 73.206000 131 2418 1 chr4A.!!$F1 2287
12 TraesCS7A01G515900 chr4A 621130532 621132483 1951 False 745.000000 745 74.317000 553 2455 1 chr4A.!!$F2 1902
13 TraesCS7A01G515900 chr5D 549584260 549585497 1237 False 745.000000 745 77.928000 130 1360 1 chr5D.!!$F1 1230
14 TraesCS7A01G515900 chr2A 15878678 15879719 1041 False 730.000000 730 79.638000 132 1163 1 chr2A.!!$F1 1031
15 TraesCS7A01G515900 chr2B 24916550 24917580 1030 True 726.000000 726 79.750000 135 1155 1 chr2B.!!$R1 1020
16 TraesCS7A01G515900 chr5B 701161223 701162451 1228 False 706.000000 706 77.448000 130 1351 1 chr5B.!!$F3 1221

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
827 898 0.332972 AAAGGGGGTCTCATGGAAGC 59.667 55.0 0.0 0.0 0.00 3.86 F
1870 2001 0.035881 CATCACTGCTATCCGCCCAT 59.964 55.0 0.0 0.0 38.05 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 2048 0.036732 CAGAGTGTAGCTTGGGGCAA 59.963 55.000 0.0 0.0 44.79 4.52 R
3358 5894 1.270305 GGGGAAAACTTGCTCTTTGCC 60.270 52.381 0.0 0.0 41.05 4.52 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
66 67 6.449635 AGAATTCAAGTTGTTGCACACTTA 57.550 33.333 8.44 0.00 33.23 2.24
96 100 8.911918 ATTTATATTTATCCGGCGGCATATTA 57.088 30.769 23.83 10.50 0.00 0.98
98 102 8.911918 TTATATTTATCCGGCGGCATATTATT 57.088 30.769 23.83 4.95 0.00 1.40
99 103 9.999660 TTATATTTATCCGGCGGCATATTATTA 57.000 29.630 23.83 0.00 0.00 0.98
102 106 7.718272 TTTATCCGGCGGCATATTATTATAC 57.282 36.000 23.83 0.00 0.00 1.47
103 107 4.739587 TCCGGCGGCATATTATTATACA 57.260 40.909 23.83 0.00 0.00 2.29
105 109 5.489249 TCCGGCGGCATATTATTATACAAA 58.511 37.500 23.83 0.00 0.00 2.83
107 111 7.273712 TCCGGCGGCATATTATTATACAAATA 58.726 34.615 23.83 0.00 0.00 1.40
108 112 7.934665 TCCGGCGGCATATTATTATACAAATAT 59.065 33.333 23.83 0.00 0.00 1.28
184 188 1.425066 ACCGGTATGGATGGCATCAAT 59.575 47.619 27.39 24.01 42.00 2.57
334 341 2.109834 TGGTGAGGACAAAACATGGGAT 59.890 45.455 0.00 0.00 0.00 3.85
615 664 1.462670 GCTCTACAACTGCAGCTTCAC 59.537 52.381 15.27 0.00 0.00 3.18
827 898 0.332972 AAAGGGGGTCTCATGGAAGC 59.667 55.000 0.00 0.00 0.00 3.86
910 985 2.665185 GTGGTCACGGTGGACAGC 60.665 66.667 8.50 0.00 39.59 4.40
1226 1323 4.561105 TGCGGTCGATTGCATAACATATA 58.439 39.130 10.09 0.00 35.90 0.86
1242 1339 2.812358 TATACCTGCATGCACTACCG 57.188 50.000 18.46 6.59 0.00 4.02
1303 1406 6.549433 AAATAATTGACCTCCATGCAATGT 57.451 33.333 0.00 0.00 44.81 2.71
1433 1542 3.258372 ACGAAAAGATCAGTGGTCTGCTA 59.742 43.478 6.69 0.00 41.10 3.49
1534 1649 4.285292 GCTCAATAGCCGATCACAAAATG 58.715 43.478 0.00 0.00 43.40 2.32
1865 1996 0.390492 TGCTCCATCACTGCTATCCG 59.610 55.000 0.00 0.00 0.00 4.18
1870 2001 0.035881 CATCACTGCTATCCGCCCAT 59.964 55.000 0.00 0.00 38.05 4.00
1905 2048 6.299141 ACTAAAATGGTGTCATGTTGAGAGT 58.701 36.000 0.00 0.00 33.22 3.24
1966 2109 5.462398 GGAACATACAGCTTTCCGTGTATAG 59.538 44.000 0.00 0.00 37.70 1.31
2007 2150 0.630673 TCCTGGTGGCCTATTGCATT 59.369 50.000 3.32 0.00 43.89 3.56
2043 2192 6.903419 CAAGAGAACTTGGAATGACCTTTAC 58.097 40.000 0.00 0.00 46.67 2.01
2044 2193 5.561679 AGAGAACTTGGAATGACCTTTACC 58.438 41.667 0.00 0.00 39.86 2.85
2045 2194 4.663334 AGAACTTGGAATGACCTTTACCC 58.337 43.478 0.00 0.00 39.86 3.69
2062 2211 0.252012 CCCCAGACACCAGAGTCTCT 60.252 60.000 0.00 0.00 45.35 3.10
2117 2266 2.584391 GGCTGGTGTTCGTCCTCCT 61.584 63.158 0.00 0.00 0.00 3.69
2377 2544 1.523711 CCGGCCGTAGCACATCAAT 60.524 57.895 26.12 0.00 42.56 2.57
2378 2545 1.095228 CCGGCCGTAGCACATCAATT 61.095 55.000 26.12 0.00 42.56 2.32
2455 2622 2.488771 CTTGAGGGCTGGGCATCACA 62.489 60.000 10.78 3.14 0.00 3.58
2456 2623 1.866483 TTGAGGGCTGGGCATCACAT 61.866 55.000 10.78 0.00 0.00 3.21
2460 2627 0.403271 GGGCTGGGCATCACATATCT 59.597 55.000 0.00 0.00 0.00 1.98
2461 2628 1.630369 GGGCTGGGCATCACATATCTA 59.370 52.381 0.00 0.00 0.00 1.98
2462 2629 2.616510 GGGCTGGGCATCACATATCTAC 60.617 54.545 0.00 0.00 0.00 2.59
2464 2631 2.038952 GCTGGGCATCACATATCTACCA 59.961 50.000 0.00 0.00 0.00 3.25
2481 4768 3.784511 ACCATATAATGCAGAGCAGCT 57.215 42.857 0.00 0.00 43.65 4.24
2482 4769 3.672808 ACCATATAATGCAGAGCAGCTC 58.327 45.455 15.25 15.25 43.65 4.09
2550 4999 6.370186 AAAGATTTAACGGGTCCTCTAGTT 57.630 37.500 0.00 0.00 0.00 2.24
2560 5009 2.418884 GGTCCTCTAGTTAGGTTGCAGC 60.419 54.545 0.00 0.00 37.91 5.25
2572 5021 4.884668 AGGTTGCAGCTTACAAGTAGTA 57.115 40.909 0.00 0.00 0.00 1.82
2583 5032 5.567025 GCTTACAAGTAGTAACCTCAGCTGT 60.567 44.000 14.67 0.00 37.77 4.40
2588 5037 4.097418 AGTAGTAACCTCAGCTGTGGAAT 58.903 43.478 35.28 25.43 33.21 3.01
2616 5066 3.753272 CCGTATGGATAAAATGCTCCTGG 59.247 47.826 0.00 0.00 37.49 4.45
2617 5067 3.189287 CGTATGGATAAAATGCTCCTGGC 59.811 47.826 0.00 0.00 42.22 4.85
2634 5084 4.402155 TCCTGGCATGCATTTAGGTAAAAG 59.598 41.667 21.36 0.00 0.00 2.27
2636 5086 5.069516 CCTGGCATGCATTTAGGTAAAAGAT 59.930 40.000 21.36 0.00 0.00 2.40
2647 5097 6.887626 TTAGGTAAAAGATGGTGTGGTTTC 57.112 37.500 0.00 0.00 0.00 2.78
2656 5106 1.269174 TGGTGTGGTTTCAATGATGCG 59.731 47.619 0.00 0.00 0.00 4.73
2657 5107 1.402720 GGTGTGGTTTCAATGATGCGG 60.403 52.381 0.00 0.00 0.00 5.69
2659 5109 0.173255 GTGGTTTCAATGATGCGGGG 59.827 55.000 0.00 0.00 0.00 5.73
2660 5110 0.038890 TGGTTTCAATGATGCGGGGA 59.961 50.000 0.00 0.00 0.00 4.81
2661 5111 1.341877 TGGTTTCAATGATGCGGGGAT 60.342 47.619 0.00 0.00 0.00 3.85
2676 5136 3.343617 CGGGGATCAGAAGCAAACTAAA 58.656 45.455 0.00 0.00 0.00 1.85
2771 5233 6.605471 TGTTTAATCTTCTGTAGAGCAGGA 57.395 37.500 0.00 0.00 45.08 3.86
2773 5235 7.624549 TGTTTAATCTTCTGTAGAGCAGGAAT 58.375 34.615 0.00 0.00 45.08 3.01
2786 5248 4.043059 AGAGCAGGAATAATCATCATGGCT 59.957 41.667 0.00 0.00 0.00 4.75
2836 5362 4.489810 AGTTTGTGAGAAGATAGCACTCG 58.510 43.478 0.00 0.00 33.93 4.18
2891 5417 7.250569 CCATATCACAAATGTGGAGTTGTTAC 58.749 38.462 13.22 0.00 45.65 2.50
2925 5451 7.444299 AGATTGTTGTCACTGGCAAATAAAAT 58.556 30.769 0.00 0.00 0.00 1.82
2957 5483 4.022603 TGAGAGCAGAGAGAAATAGCACT 58.977 43.478 0.00 0.00 0.00 4.40
2963 5489 4.803088 GCAGAGAGAAATAGCACTGTACAG 59.197 45.833 21.44 21.44 0.00 2.74
2975 5501 2.935849 CACTGTACAGAGTGCACAAACA 59.064 45.455 29.30 13.48 37.16 2.83
2989 5515 2.531103 CACAAACACAATGTGCTGAACG 59.469 45.455 19.00 4.26 41.42 3.95
3019 5545 8.154856 TCTAACTGGAACTAAATAACTTGTGCT 58.845 33.333 0.00 0.00 0.00 4.40
3020 5546 6.560253 ACTGGAACTAAATAACTTGTGCTG 57.440 37.500 0.00 0.00 0.00 4.41
3021 5547 6.296026 ACTGGAACTAAATAACTTGTGCTGA 58.704 36.000 0.00 0.00 0.00 4.26
3026 5552 3.915437 AAATAACTTGTGCTGAACCCG 57.085 42.857 0.00 0.00 0.00 5.28
3043 5569 2.747446 ACCCGAAGTCCAATGAAATTCG 59.253 45.455 0.00 0.00 39.68 3.34
3044 5570 2.747446 CCCGAAGTCCAATGAAATTCGT 59.253 45.455 1.12 0.00 38.95 3.85
3133 5666 9.727627 TCATTGGCAAACAAAATGAAATAAAAC 57.272 25.926 3.01 0.00 43.46 2.43
3152 5685 8.706492 ATAAAACACATGCTTCACCAATATTG 57.294 30.769 8.58 8.58 0.00 1.90
3158 5691 3.700538 TGCTTCACCAATATTGCCTCTT 58.299 40.909 10.11 0.00 0.00 2.85
3159 5692 3.696051 TGCTTCACCAATATTGCCTCTTC 59.304 43.478 10.11 0.00 0.00 2.87
3161 5694 4.158394 GCTTCACCAATATTGCCTCTTCAA 59.842 41.667 10.11 0.00 0.00 2.69
3162 5695 5.336690 GCTTCACCAATATTGCCTCTTCAAA 60.337 40.000 10.11 0.00 0.00 2.69
3164 5697 6.855763 TCACCAATATTGCCTCTTCAAATT 57.144 33.333 10.11 0.00 0.00 1.82
3165 5698 7.953005 TCACCAATATTGCCTCTTCAAATTA 57.047 32.000 10.11 0.00 0.00 1.40
3167 5700 8.980596 TCACCAATATTGCCTCTTCAAATTATT 58.019 29.630 10.11 0.00 0.00 1.40
3199 5732 5.297527 TCATCACAGTTGTCATCCATTATGC 59.702 40.000 0.00 0.00 35.38 3.14
3204 5737 3.134623 AGTTGTCATCCATTATGCGGAGA 59.865 43.478 0.00 0.00 35.56 3.71
3232 5765 9.208022 CATACGGTTGATTCAGTTGATGTATAT 57.792 33.333 0.00 0.00 0.00 0.86
3261 5796 4.829492 AGCTGACCTTTTTAGTTTGCAGAT 59.171 37.500 0.00 0.00 0.00 2.90
3276 5812 1.271597 GCAGATAGTTAGGGGCCATGG 60.272 57.143 7.63 7.63 0.00 3.66
3302 5838 6.155827 GGCACAAGCATTTAAACAACTGATA 58.844 36.000 0.00 0.00 44.61 2.15
3303 5839 6.089417 GGCACAAGCATTTAAACAACTGATAC 59.911 38.462 0.00 0.00 44.61 2.24
3304 5840 6.640499 GCACAAGCATTTAAACAACTGATACA 59.360 34.615 0.00 0.00 41.58 2.29
3305 5841 7.148918 GCACAAGCATTTAAACAACTGATACAG 60.149 37.037 0.00 0.00 41.58 2.74
3307 5843 9.062524 ACAAGCATTTAAACAACTGATACAGTA 57.937 29.630 4.84 0.00 44.62 2.74
3358 5894 7.806690 TGCACAAGAATTTTGCTAGTAGTTAG 58.193 34.615 0.00 0.00 37.16 2.34
3370 5906 8.696302 TTTGCTAGTAGTTAGGCAAAGAGCAAG 61.696 40.741 7.68 0.00 45.58 4.01
3411 5947 9.003658 ACAAAGAGAATTAGTAGTTTCCACATG 57.996 33.333 0.00 0.00 0.00 3.21
3413 5949 6.951971 AGAGAATTAGTAGTTTCCACATGCT 58.048 36.000 0.00 0.00 0.00 3.79
3414 5950 6.820656 AGAGAATTAGTAGTTTCCACATGCTG 59.179 38.462 0.00 0.00 0.00 4.41
3415 5951 6.476378 AGAATTAGTAGTTTCCACATGCTGT 58.524 36.000 0.00 0.00 0.00 4.40
3428 5965 7.172868 TCCACATGCTGTTGATAAATGAAAT 57.827 32.000 0.00 0.00 0.00 2.17
3460 5997 4.960938 AGTGATCACTGCAGTTTCTAACA 58.039 39.130 27.37 9.01 40.75 2.41
3461 5998 5.555017 AGTGATCACTGCAGTTTCTAACAT 58.445 37.500 27.37 0.39 40.75 2.71
3462 5999 6.701340 AGTGATCACTGCAGTTTCTAACATA 58.299 36.000 27.37 0.00 40.75 2.29
3463 6000 7.334090 AGTGATCACTGCAGTTTCTAACATAT 58.666 34.615 27.37 0.00 40.75 1.78
3464 6001 8.478066 AGTGATCACTGCAGTTTCTAACATATA 58.522 33.333 27.37 0.00 40.75 0.86
3465 6002 9.265901 GTGATCACTGCAGTTTCTAACATATAT 57.734 33.333 18.94 0.00 0.00 0.86
3469 6006 9.710900 TCACTGCAGTTTCTAACATATATATGG 57.289 33.333 18.94 8.89 38.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 6.995686 TGCCGCCGGATAAATATAAATATCAT 59.004 34.615 7.68 0.00 31.51 2.45
84 88 9.381027 CAATATTTGTATAATAATATGCCGCCG 57.619 33.333 0.00 0.00 29.73 6.46
107 111 9.537192 CAATACATTTTCAATATGAGGTGCAAT 57.463 29.630 0.00 0.00 0.00 3.56
108 112 7.492020 GCAATACATTTTCAATATGAGGTGCAA 59.508 33.333 0.00 0.00 32.24 4.08
184 188 6.321181 AGAAGCAATCCAAAACTGTTTCTGTA 59.679 34.615 6.20 0.00 38.64 2.74
334 341 8.688747 TCACATGATACAATGTATTGCCAATA 57.311 30.769 7.39 0.00 38.75 1.90
615 664 4.522022 ACTGAAAAGGAGGAGATGCAAAAG 59.478 41.667 0.00 0.00 0.00 2.27
692 750 0.829182 CTTGGCCCTCCACTTTGCTT 60.829 55.000 0.00 0.00 43.33 3.91
910 985 5.635417 TCATCATATCTACGGAAGAGCAG 57.365 43.478 0.00 0.00 37.74 4.24
1226 1323 0.253044 ATTCGGTAGTGCATGCAGGT 59.747 50.000 23.41 14.34 0.00 4.00
1242 1339 2.169561 GAGGTCCAGTTCCTCCAGATTC 59.830 54.545 0.98 0.00 43.90 2.52
1303 1406 3.260884 AGCTTCTTGAGTTTCGGGACATA 59.739 43.478 0.00 0.00 0.00 2.29
1433 1542 2.243221 CCAAAGGATCCCTGTTCTCCAT 59.757 50.000 8.55 0.00 32.13 3.41
1534 1649 0.977395 AGGTACACCTTGGAGACAGC 59.023 55.000 0.00 0.00 46.09 4.40
1870 2001 4.597507 ACACCATTTTAGTCTCTCCCAGAA 59.402 41.667 0.00 0.00 30.72 3.02
1905 2048 0.036732 CAGAGTGTAGCTTGGGGCAA 59.963 55.000 0.00 0.00 44.79 4.52
1966 2109 7.385752 CAGGAGATCAGAAGCTGAAAATATCTC 59.614 40.741 12.95 12.95 44.04 2.75
2007 2150 1.004745 GTTCTCTTGATGCCTCCCCAA 59.995 52.381 0.00 0.00 0.00 4.12
2039 2188 1.975680 GACTCTGGTGTCTGGGGTAAA 59.024 52.381 0.00 0.00 34.39 2.01
2040 2189 1.149288 AGACTCTGGTGTCTGGGGTAA 59.851 52.381 4.78 0.00 44.64 2.85
2041 2190 0.784495 AGACTCTGGTGTCTGGGGTA 59.216 55.000 4.78 0.00 44.64 3.69
2042 2191 0.543174 GAGACTCTGGTGTCTGGGGT 60.543 60.000 9.58 0.00 46.11 4.95
2043 2192 0.252012 AGAGACTCTGGTGTCTGGGG 60.252 60.000 3.56 0.00 46.11 4.96
2044 2193 1.638529 AAGAGACTCTGGTGTCTGGG 58.361 55.000 5.55 0.00 46.11 4.45
2045 2194 3.157881 TGTAAGAGACTCTGGTGTCTGG 58.842 50.000 5.55 0.00 46.11 3.86
2062 2211 3.134623 AGGTATATGTGCTGCAGCTGTAA 59.865 43.478 36.61 21.10 42.66 2.41
2117 2266 1.146774 TGGGCAAGGTGAAGGAAATGA 59.853 47.619 0.00 0.00 0.00 2.57
2372 2539 2.025321 ACCACCGGCTTAGGAAATTGAT 60.025 45.455 0.00 0.00 34.73 2.57
2377 2544 1.128809 TCCACCACCGGCTTAGGAAA 61.129 55.000 0.00 0.00 34.73 3.13
2378 2545 1.536907 TCCACCACCGGCTTAGGAA 60.537 57.895 0.00 0.00 34.73 3.36
2455 2622 7.070946 AGCTGCTCTGCATTATATGGTAGATAT 59.929 37.037 0.00 0.00 38.13 1.63
2456 2623 6.382282 AGCTGCTCTGCATTATATGGTAGATA 59.618 38.462 0.00 0.00 38.13 1.98
2460 2627 4.529769 AGAGCTGCTCTGCATTATATGGTA 59.470 41.667 29.99 0.00 39.62 3.25
2461 2628 3.327172 AGAGCTGCTCTGCATTATATGGT 59.673 43.478 29.99 2.32 39.62 3.55
2462 2629 3.940319 AGAGCTGCTCTGCATTATATGG 58.060 45.455 29.99 0.00 39.62 2.74
2464 2631 4.529769 TGGTAGAGCTGCTCTGCATTATAT 59.470 41.667 36.72 16.29 43.33 0.86
2529 4978 5.597594 CCTAACTAGAGGACCCGTTAAATCT 59.402 44.000 0.00 0.00 39.15 2.40
2550 4999 4.884668 ACTACTTGTAAGCTGCAACCTA 57.115 40.909 1.02 0.00 0.00 3.08
2560 5009 5.864474 CACAGCTGAGGTTACTACTTGTAAG 59.136 44.000 23.35 0.00 41.29 2.34
2572 5021 4.706962 GGATTTAATTCCACAGCTGAGGTT 59.293 41.667 26.72 18.04 35.72 3.50
2616 5066 5.750067 CACCATCTTTTACCTAAATGCATGC 59.250 40.000 11.82 11.82 0.00 4.06
2617 5067 6.753279 CACACCATCTTTTACCTAAATGCATG 59.247 38.462 0.00 0.00 0.00 4.06
2618 5068 6.127366 CCACACCATCTTTTACCTAAATGCAT 60.127 38.462 0.00 0.00 0.00 3.96
2619 5069 5.184864 CCACACCATCTTTTACCTAAATGCA 59.815 40.000 0.00 0.00 0.00 3.96
2620 5070 5.185056 ACCACACCATCTTTTACCTAAATGC 59.815 40.000 0.00 0.00 0.00 3.56
2634 5084 3.514645 GCATCATTGAAACCACACCATC 58.485 45.455 0.00 0.00 0.00 3.51
2636 5086 1.269174 CGCATCATTGAAACCACACCA 59.731 47.619 0.00 0.00 0.00 4.17
2647 5097 1.878088 CTTCTGATCCCCGCATCATTG 59.122 52.381 0.00 0.00 32.21 2.82
2656 5106 5.722021 TTTTTAGTTTGCTTCTGATCCCC 57.278 39.130 0.00 0.00 0.00 4.81
2739 5201 8.762645 TCTACAGAAGATTAAACATCTCCATGT 58.237 33.333 0.00 0.00 45.89 3.21
2743 5205 7.268586 TGCTCTACAGAAGATTAAACATCTCC 58.731 38.462 0.00 0.00 32.41 3.71
2771 5233 5.452255 AGTGTGGAAGCCATGATGATTATT 58.548 37.500 0.00 0.00 35.28 1.40
2773 5235 4.508551 AGTGTGGAAGCCATGATGATTA 57.491 40.909 0.00 0.00 35.28 1.75
2786 5248 2.107378 TGGTGATTGCCTAAGTGTGGAA 59.893 45.455 0.00 0.00 0.00 3.53
2836 5362 8.297426 ACCACTTTGAGTTAGCTAAATTTAAGC 58.703 33.333 19.89 5.61 40.40 3.09
2891 5417 6.144854 CCAGTGACAACAATCTTTACACATG 58.855 40.000 0.00 0.00 0.00 3.21
2957 5483 2.979240 TGTGTTTGTGCACTCTGTACA 58.021 42.857 19.41 13.35 41.12 2.90
2969 5495 2.479389 CCGTTCAGCACATTGTGTTTGT 60.479 45.455 17.64 0.00 35.75 2.83
2975 5501 2.783135 AGATTCCGTTCAGCACATTGT 58.217 42.857 0.00 0.00 0.00 2.71
3019 5545 2.940994 TTCATTGGACTTCGGGTTCA 57.059 45.000 0.00 0.00 0.00 3.18
3020 5546 4.671766 CGAATTTCATTGGACTTCGGGTTC 60.672 45.833 9.04 0.00 35.97 3.62
3021 5547 3.190535 CGAATTTCATTGGACTTCGGGTT 59.809 43.478 9.04 0.00 35.97 4.11
3026 5552 7.402640 GTCTCATACGAATTTCATTGGACTTC 58.597 38.462 0.00 0.00 0.00 3.01
3043 5569 3.056749 ACCTGAAGTTGGTCGTCTCATAC 60.057 47.826 0.00 0.00 31.03 2.39
3044 5570 3.162666 ACCTGAAGTTGGTCGTCTCATA 58.837 45.455 0.00 0.00 31.03 2.15
3055 5581 4.137543 AGCAGAAAGGTTACCTGAAGTTG 58.862 43.478 3.99 1.18 32.13 3.16
3123 5656 6.154203 TGGTGAAGCATGTGTTTTATTTCA 57.846 33.333 0.00 0.00 0.00 2.69
3133 5666 3.131577 AGGCAATATTGGTGAAGCATGTG 59.868 43.478 17.02 0.00 0.00 3.21
3165 5698 9.630098 GATGACAACTGTGATGACATTTTTAAT 57.370 29.630 0.00 0.00 34.24 1.40
3167 5700 7.230309 TGGATGACAACTGTGATGACATTTTTA 59.770 33.333 0.00 0.00 34.24 1.52
3168 5701 6.040729 TGGATGACAACTGTGATGACATTTTT 59.959 34.615 0.00 0.00 34.24 1.94
3173 5706 3.767902 TGGATGACAACTGTGATGACA 57.232 42.857 0.00 0.00 0.00 3.58
3174 5707 6.722301 CATAATGGATGACAACTGTGATGAC 58.278 40.000 0.00 0.00 37.82 3.06
3199 5732 3.517602 TGAATCAACCGTATGTTCTCCG 58.482 45.455 0.00 0.00 34.00 4.63
3204 5737 5.705441 ACATCAACTGAATCAACCGTATGTT 59.295 36.000 0.00 0.00 37.80 2.71
3232 5765 6.312672 GCAAACTAAAAAGGTCAGCTCAAAAA 59.687 34.615 0.00 0.00 0.00 1.94
3240 5775 7.440523 ACTATCTGCAAACTAAAAAGGTCAG 57.559 36.000 0.00 0.00 0.00 3.51
3261 5796 2.627771 CCACCATGGCCCCTAACTA 58.372 57.895 13.04 0.00 0.00 2.24
3276 5812 4.025813 CAGTTGTTTAAATGCTTGTGCCAC 60.026 41.667 0.00 0.00 38.71 5.01
3333 5869 6.633500 AACTACTAGCAAAATTCTTGTGCA 57.367 33.333 4.94 0.00 40.83 4.57
3341 5877 7.362142 GCTCTTTGCCTAACTACTAGCAAAATT 60.362 37.037 9.90 0.00 35.30 1.82
3358 5894 1.270305 GGGGAAAACTTGCTCTTTGCC 60.270 52.381 0.00 0.00 41.05 4.52
3387 5923 7.885399 AGCATGTGGAAACTACTAATTCTCTTT 59.115 33.333 0.00 0.00 0.00 2.52
3408 5944 9.016623 CAGTGTATTTCATTTATCAACAGCATG 57.983 33.333 0.00 0.00 46.00 4.06
3411 5947 9.443283 GATCAGTGTATTTCATTTATCAACAGC 57.557 33.333 0.00 0.00 0.00 4.40
3439 5976 5.869753 ATGTTAGAAACTGCAGTGATCAC 57.130 39.130 22.49 18.47 0.00 3.06


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

AutoCloner maintained by Alex Coulton.