Multiple sequence alignment - TraesCS1D01G074700

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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 TraesCS1D01G074700 chr1D 100.000 4150 0 0 1 4150 56431029 56426880 0.000000e+00 7664.0
1 TraesCS1D01G074700 chr1D 93.342 1517 80 12 1848 3357 56874417 56872915 0.000000e+00 2222.0
2 TraesCS1D01G074700 chr1D 92.527 1365 70 15 399 1735 56610981 56609621 0.000000e+00 1927.0
3 TraesCS1D01G074700 chr1D 92.819 1323 56 12 2396 3681 56529582 56528262 0.000000e+00 1881.0
4 TraesCS1D01G074700 chr1D 88.882 1556 104 33 223 1735 56531619 56530090 0.000000e+00 1851.0
5 TraesCS1D01G074700 chr1D 91.561 1339 64 11 1995 3323 56609460 56608161 0.000000e+00 1801.0
6 TraesCS1D01G074700 chr1D 88.735 1447 80 33 329 1735 56875897 56874494 0.000000e+00 1692.0
7 TraesCS1D01G074700 chr1D 94.647 411 20 2 3604 4013 56869027 56868618 1.630000e-178 636.0
8 TraesCS1D01G074700 chr1D 93.023 387 21 4 1 383 56618832 56618448 1.010000e-155 560.0
9 TraesCS1D01G074700 chr1D 86.157 484 47 10 135 602 56612821 56612342 4.790000e-139 505.0
10 TraesCS1D01G074700 chr1D 86.758 438 27 8 367 793 56618435 56618018 3.780000e-125 459.0
11 TraesCS1D01G074700 chr1D 94.636 261 14 0 3382 3642 56608151 56607891 5.000000e-109 405.0
12 TraesCS1D01G074700 chr1D 80.268 522 44 21 1905 2396 57073748 57073256 5.140000e-89 339.0
13 TraesCS1D01G074700 chr1D 83.554 377 41 11 1439 1811 57200749 57200390 2.390000e-87 333.0
14 TraesCS1D01G074700 chr1D 90.323 248 24 0 985 1232 57219350 57219103 4.000000e-85 326.0
15 TraesCS1D01G074700 chr1D 88.382 241 13 6 2090 2323 56529807 56529575 4.090000e-70 276.0
16 TraesCS1D01G074700 chr1D 96.835 158 5 0 3358 3515 56869542 56869385 8.850000e-67 265.0
17 TraesCS1D01G074700 chr1D 90.355 197 19 0 1245 1441 57212907 57212711 4.120000e-65 259.0
18 TraesCS1D01G074700 chr1D 88.406 138 11 3 206 338 56876310 56876173 1.190000e-35 161.0
19 TraesCS1D01G074700 chr1D 96.203 79 2 1 113 191 56612930 56612853 1.210000e-25 128.0
20 TraesCS1D01G074700 chr1D 92.045 88 7 0 1848 1935 56609544 56609457 1.570000e-24 124.0
21 TraesCS1D01G074700 chr1D 100.000 29 0 0 1758 1786 56530050 56530022 2.000000e-03 54.7
22 TraesCS1D01G074700 chr1A 96.047 2049 68 5 2091 4134 54459970 54462010 0.000000e+00 3323.0
23 TraesCS1D01G074700 chr1A 91.653 2432 128 26 1250 3642 56369549 56371944 0.000000e+00 3297.0
24 TraesCS1D01G074700 chr1A 88.146 1780 119 45 329 2044 56336704 56338455 0.000000e+00 2034.0
25 TraesCS1D01G074700 chr1A 87.698 1707 133 39 135 1785 54458050 54459735 0.000000e+00 1917.0
26 TraesCS1D01G074700 chr1A 94.278 1136 50 7 2090 3218 56338470 56339597 0.000000e+00 1724.0
27 TraesCS1D01G074700 chr1A 93.266 787 53 0 3217 4003 56340308 56341094 0.000000e+00 1160.0
28 TraesCS1D01G074700 chr1A 89.841 502 27 8 451 938 56368136 56368627 1.270000e-174 623.0
29 TraesCS1D01G074700 chr1A 89.097 321 29 3 135 449 56367776 56368096 1.080000e-105 394.0
30 TraesCS1D01G074700 chr1A 93.833 227 14 0 1010 1236 56369276 56369502 3.970000e-90 342.0
31 TraesCS1D01G074700 chr1A 85.517 290 25 11 64 338 56365270 56365557 1.890000e-73 287.0
32 TraesCS1D01G074700 chr1A 90.863 197 11 3 1 191 54457820 54458015 1.480000e-64 257.0
33 TraesCS1D01G074700 chr1A 92.727 165 10 2 27 191 56367581 56367743 1.930000e-58 237.0
34 TraesCS1D01G074700 chr1A 100.000 29 0 0 4122 4150 54462045 54462073 2.000000e-03 54.7
35 TraesCS1D01G074700 chr1B 93.443 2120 91 12 1902 4003 91881289 91879200 0.000000e+00 3101.0
36 TraesCS1D01G074700 chr1B 90.498 863 58 9 972 1824 91882368 91881520 0.000000e+00 1118.0
37 TraesCS1D01G074700 chr1B 84.906 583 37 17 325 892 91882938 91882392 3.650000e-150 542.0
38 TraesCS1D01G074700 chr1B 84.615 286 26 12 69 338 91883498 91883215 6.840000e-68 268.0
39 TraesCS1D01G074700 chr1B 87.379 103 11 2 1295 1396 608950044 608950145 2.620000e-22 117.0
40 TraesCS1D01G074700 chr7B 76.075 372 72 14 1295 1659 409712036 409711675 1.190000e-40 178.0
41 TraesCS1D01G074700 chr5D 85.135 74 9 2 1109 1181 315485471 315485399 1.600000e-09 75.0


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 TraesCS1D01G074700 chr1D 56426880 56431029 4149 True 7664.000000 7664 100.000000 1 4150 1 chr1D.!!$R1 4149
1 TraesCS1D01G074700 chr1D 56528262 56531619 3357 True 1015.675000 1881 92.520750 223 3681 4 chr1D.!!$R6 3458
2 TraesCS1D01G074700 chr1D 56868618 56876310 7692 True 995.200000 2222 92.393000 206 4013 5 chr1D.!!$R9 3807
3 TraesCS1D01G074700 chr1D 56607891 56612930 5039 True 815.000000 1927 92.188167 113 3642 6 chr1D.!!$R7 3529
4 TraesCS1D01G074700 chr1D 56618018 56618832 814 True 509.500000 560 89.890500 1 793 2 chr1D.!!$R8 792
5 TraesCS1D01G074700 chr1A 56336704 56341094 4390 False 1639.333333 2034 91.896667 329 4003 3 chr1A.!!$F2 3674
6 TraesCS1D01G074700 chr1A 54457820 54462073 4253 False 1387.925000 3323 93.652000 1 4150 4 chr1A.!!$F1 4149
7 TraesCS1D01G074700 chr1A 56365270 56371944 6674 False 863.333333 3297 90.444667 27 3642 6 chr1A.!!$F3 3615
8 TraesCS1D01G074700 chr1B 91879200 91883498 4298 True 1257.250000 3101 88.365500 69 4003 4 chr1B.!!$R1 3934


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
890 5211 0.035881 CGATGGGTGGAGCATAGCAT 59.964 55.000 0.00 0.0 0.00 3.79 F
914 5235 0.376152 GCTGATCACTCCATTGCACG 59.624 55.000 0.00 0.0 0.00 5.34 F
1752 6751 0.872021 GCTTACATGCGAGAGACCGG 60.872 60.000 0.00 0.0 0.00 5.28 F
2163 7419 1.682684 ACCGTGGCCTCTACCAGAG 60.683 63.158 3.32 0.0 41.46 3.35 F
2365 7626 2.119495 CACCAGGAGTACAAGGCCTAT 58.881 52.381 5.16 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 7311 0.389025 TCGTCTGTCTGTGTGCACAT 59.611 50.000 24.69 0.0 41.01 3.21 R
2717 7979 1.007336 GCGTGACGAGGACGAACATT 61.007 55.000 10.10 0.0 42.66 2.71 R
2819 8081 1.080025 GTAGTCCACCTGTGACCGC 60.080 63.158 0.00 0.0 0.00 5.68 R
2976 8245 1.670087 CGCAGACCTGTGGAAGTACTG 60.670 57.143 0.00 0.0 37.43 2.74 R
3759 13408 2.689983 GGTTGCTGCAGCCATAAACTAT 59.310 45.455 34.64 0.0 41.18 2.12 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
91 92 1.621992 AGAGAAGAGTGAGCACCGAA 58.378 50.000 0.00 0.00 0.00 4.30
174 185 1.436336 GCCCTCACATTGCTCATGC 59.564 57.895 0.00 0.00 36.14 4.06
188 378 4.384056 TGCTCATGCTCTAAATAGGCTTC 58.616 43.478 0.00 0.00 40.48 3.86
226 416 4.978580 GTGTTTCTTGTTTGATGGAAGCTC 59.021 41.667 0.00 0.00 0.00 4.09
232 422 2.087646 GTTTGATGGAAGCTCAGGGTC 58.912 52.381 0.00 0.00 0.00 4.46
235 425 1.280133 TGATGGAAGCTCAGGGTCTTG 59.720 52.381 0.00 0.00 0.00 3.02
322 512 2.789409 ATGAGGCCCAACAACTACTC 57.211 50.000 0.00 0.00 0.00 2.59
324 514 0.690762 GAGGCCCAACAACTACTCCA 59.309 55.000 0.00 0.00 0.00 3.86
326 516 1.710809 AGGCCCAACAACTACTCCAAT 59.289 47.619 0.00 0.00 0.00 3.16
327 517 2.092323 GGCCCAACAACTACTCCAATC 58.908 52.381 0.00 0.00 0.00 2.67
348 2971 7.920738 CAATCTGGCTATTGGAGTAGTAAAAC 58.079 38.462 5.54 0.00 33.95 2.43
466 3161 5.690409 CAGTGCATTTCATTATCCATCTTGC 59.310 40.000 0.00 0.00 0.00 4.01
545 4814 7.946381 AGTCCTTTTATTCCCAAAAGAGATC 57.054 36.000 9.34 0.00 44.68 2.75
546 4815 6.892456 AGTCCTTTTATTCCCAAAAGAGATCC 59.108 38.462 9.34 0.00 44.68 3.36
547 4816 6.663523 GTCCTTTTATTCCCAAAAGAGATCCA 59.336 38.462 9.34 0.00 44.68 3.41
548 4817 7.343057 GTCCTTTTATTCCCAAAAGAGATCCAT 59.657 37.037 9.34 0.00 44.68 3.41
549 4818 7.342799 TCCTTTTATTCCCAAAAGAGATCCATG 59.657 37.037 9.34 0.00 44.68 3.66
550 4819 7.124750 CCTTTTATTCCCAAAAGAGATCCATGT 59.875 37.037 9.34 0.00 44.68 3.21
551 4820 7.408756 TTTATTCCCAAAAGAGATCCATGTG 57.591 36.000 0.00 0.00 0.00 3.21
552 4821 2.726821 TCCCAAAAGAGATCCATGTGC 58.273 47.619 0.00 0.00 0.00 4.57
553 4822 2.041485 TCCCAAAAGAGATCCATGTGCA 59.959 45.455 0.00 0.00 0.00 4.57
584 4875 1.332686 CATGATCTGCAACATGTCCGG 59.667 52.381 15.48 0.00 38.98 5.14
681 4975 4.884744 CGGGGTGGATATGTTTACATTTGA 59.115 41.667 0.02 0.00 37.76 2.69
731 5025 5.049474 TCTCCTCACATCGTCAAAACAAATG 60.049 40.000 0.00 0.00 0.00 2.32
793 5092 1.753930 ATGCGTGCATTTCTGATGGA 58.246 45.000 0.51 0.00 31.82 3.41
794 5093 0.804364 TGCGTGCATTTCTGATGGAC 59.196 50.000 0.00 1.20 37.07 4.02
795 5094 0.099436 GCGTGCATTTCTGATGGACC 59.901 55.000 5.31 0.00 37.11 4.46
796 5095 0.374758 CGTGCATTTCTGATGGACCG 59.625 55.000 5.31 0.00 37.11 4.79
797 5096 0.734889 GTGCATTTCTGATGGACCGG 59.265 55.000 0.00 0.00 34.83 5.28
840 5143 3.888930 GTGGATTGAAACCTTGTTCCTCA 59.111 43.478 0.00 0.00 0.00 3.86
844 5150 1.133606 TGAAACCTTGTTCCTCACCCC 60.134 52.381 0.00 0.00 0.00 4.95
845 5151 0.930726 AAACCTTGTTCCTCACCCCA 59.069 50.000 0.00 0.00 0.00 4.96
848 5164 0.995024 CCTTGTTCCTCACCCCATCT 59.005 55.000 0.00 0.00 0.00 2.90
874 5190 1.386533 AATACACTCGTCCCGTCGAT 58.613 50.000 0.00 0.00 39.12 3.59
887 5208 0.319040 CGTCGATGGGTGGAGCATAG 60.319 60.000 0.00 0.00 0.00 2.23
888 5209 0.601311 GTCGATGGGTGGAGCATAGC 60.601 60.000 0.00 0.00 0.00 2.97
889 5210 1.048160 TCGATGGGTGGAGCATAGCA 61.048 55.000 0.00 0.00 0.00 3.49
890 5211 0.035881 CGATGGGTGGAGCATAGCAT 59.964 55.000 0.00 0.00 0.00 3.79
891 5212 1.276138 CGATGGGTGGAGCATAGCATA 59.724 52.381 0.00 0.00 0.00 3.14
908 5229 2.288702 GCATACTCGCTGATCACTCCAT 60.289 50.000 0.00 0.00 0.00 3.41
914 5235 0.376152 GCTGATCACTCCATTGCACG 59.624 55.000 0.00 0.00 0.00 5.34
931 5252 4.248402 GCACAACGCGGTAGTACA 57.752 55.556 12.47 0.00 0.00 2.90
932 5253 2.519826 GCACAACGCGGTAGTACAA 58.480 52.632 12.47 0.00 0.00 2.41
959 5309 3.622166 ACAACGGTAGGACCTAATTGG 57.378 47.619 18.75 6.95 42.93 3.16
961 5311 3.583966 ACAACGGTAGGACCTAATTGGAA 59.416 43.478 18.75 0.00 39.71 3.53
975 5325 6.824196 ACCTAATTGGAAAGAAACTAGCTAGC 59.176 38.462 20.91 6.62 39.71 3.42
1007 5360 1.153628 GGACGACGAAGATGGTGGG 60.154 63.158 0.00 0.00 0.00 4.61
1056 5972 2.036387 GTGGTAGGGTTTTTGGCAACT 58.964 47.619 0.00 0.00 37.61 3.16
1263 6222 1.261885 TGTACATGTTTGGTTCGTGCG 59.738 47.619 2.30 0.00 0.00 5.34
1536 6506 4.008933 GGCCACTCAGACCACGCT 62.009 66.667 0.00 0.00 0.00 5.07
1589 6559 1.527370 GGAGGGCCTACATGGTGAC 59.473 63.158 12.07 0.00 38.35 3.67
1741 6726 6.250527 GGTGCGTATTTTTACTTGCTTACATG 59.749 38.462 0.00 0.00 0.00 3.21
1750 6736 1.929836 CTTGCTTACATGCGAGAGACC 59.070 52.381 0.00 0.00 44.94 3.85
1752 6751 0.872021 GCTTACATGCGAGAGACCGG 60.872 60.000 0.00 0.00 0.00 5.28
1931 7174 5.049060 CACATCACAAATTGGACGGTTTCTA 60.049 40.000 0.00 0.00 0.00 2.10
1936 7179 2.799126 ATTGGACGGTTTCTATGGCA 57.201 45.000 0.00 0.00 0.00 4.92
2005 7249 8.253810 CCATTTCATAGAGTCGTGGTCATATAT 58.746 37.037 0.00 0.00 0.00 0.86
2023 7267 9.630098 GTCATATATTGGCTAAAAATGGATGTG 57.370 33.333 0.00 0.00 0.00 3.21
2063 7311 7.074653 AGAAAACTGAAGGTGGACTTGTATA 57.925 36.000 0.00 0.00 40.21 1.47
2163 7419 1.682684 ACCGTGGCCTCTACCAGAG 60.683 63.158 3.32 0.00 41.46 3.35
2255 7515 9.624697 TGTCACAATAATGAACAGAAAAATAGC 57.375 29.630 0.00 0.00 0.00 2.97
2256 7516 9.624697 GTCACAATAATGAACAGAAAAATAGCA 57.375 29.630 0.00 0.00 0.00 3.49
2292 7553 6.584563 TGTAAAGCAAACACTGAAACTTGTTC 59.415 34.615 0.00 0.00 34.82 3.18
2365 7626 2.119495 CACCAGGAGTACAAGGCCTAT 58.881 52.381 5.16 0.00 0.00 2.57
2492 7754 7.069344 TGATCCTAGTATTGGTCTGATGAAGA 58.931 38.462 0.00 0.00 0.00 2.87
2497 7759 6.805016 AGTATTGGTCTGATGAAGAGACAT 57.195 37.500 0.00 0.00 41.50 3.06
2819 8081 3.234041 CAGCTCGTCTCGTTCGCG 61.234 66.667 0.00 0.00 42.98 5.87
2999 8268 3.241530 TTCCACAGGTCTGCGCCT 61.242 61.111 4.18 0.00 39.99 5.52
3167 8443 3.809832 ACTGATGTTCCTGTTTTCAGTCG 59.190 43.478 0.00 0.00 42.40 4.18
3182 8458 1.931841 CAGTCGAGAGATGTGCAATGG 59.068 52.381 0.00 0.00 45.19 3.16
3294 9283 6.747280 ACTTTGAAAAGAACTTCAACATCACG 59.253 34.615 9.71 0.00 43.29 4.35
3759 13408 0.776810 ATGTGGTTCCATGGTCACCA 59.223 50.000 25.96 25.96 38.30 4.17
3819 13468 2.299975 GCCAATGGGAAGGCCATTT 58.700 52.632 5.01 0.00 45.18 2.32
4093 13743 4.728772 ACAATGATCAGAAAGTTGTCCCA 58.271 39.130 0.09 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 140 8.671028 GGCCGTCTAAGAAGAAAATATTTACAA 58.329 33.333 0.01 0.00 32.16 2.41
188 378 8.801715 ACAAGAAACACTGCAATACAATTAAG 57.198 30.769 0.00 0.00 0.00 1.85
226 416 8.915057 ATATAAATCAATGAGACAAGACCCTG 57.085 34.615 0.00 0.00 0.00 4.45
261 451 6.330278 ACTGGCAACTTTTCTGTTAGTTTTC 58.670 36.000 0.00 0.00 32.50 2.29
324 514 7.054751 GGTTTTACTACTCCAATAGCCAGATT 58.945 38.462 0.00 0.00 0.00 2.40
326 516 5.104652 GGGTTTTACTACTCCAATAGCCAGA 60.105 44.000 0.00 0.00 0.00 3.86
327 517 5.123936 GGGTTTTACTACTCCAATAGCCAG 58.876 45.833 0.00 0.00 0.00 4.85
348 2971 3.824133 TCTTGCACAATATGAGATGGGG 58.176 45.455 0.00 0.00 0.00 4.96
466 3161 6.813649 TCTTTGGAGATCGAAGAGTTAACATG 59.186 38.462 8.61 0.00 43.63 3.21
534 4803 2.165030 GGTGCACATGGATCTCTTTTGG 59.835 50.000 20.43 0.00 0.00 3.28
535 4804 2.159476 CGGTGCACATGGATCTCTTTTG 60.159 50.000 20.43 0.00 0.00 2.44
536 4805 2.086869 CGGTGCACATGGATCTCTTTT 58.913 47.619 20.43 0.00 0.00 2.27
537 4806 1.278985 TCGGTGCACATGGATCTCTTT 59.721 47.619 20.43 0.00 0.00 2.52
538 4807 0.904649 TCGGTGCACATGGATCTCTT 59.095 50.000 20.43 0.00 0.00 2.85
539 4808 1.126488 ATCGGTGCACATGGATCTCT 58.874 50.000 20.43 0.00 0.00 3.10
540 4809 2.820059 TATCGGTGCACATGGATCTC 57.180 50.000 20.43 0.00 0.00 2.75
541 4810 3.558931 TTTATCGGTGCACATGGATCT 57.441 42.857 20.43 1.51 0.00 2.75
542 4811 3.610114 GCATTTATCGGTGCACATGGATC 60.610 47.826 20.43 0.00 40.94 3.36
543 4812 2.294233 GCATTTATCGGTGCACATGGAT 59.706 45.455 20.43 18.72 40.94 3.41
544 4813 1.675483 GCATTTATCGGTGCACATGGA 59.325 47.619 20.43 12.85 40.94 3.41
545 4814 1.404748 TGCATTTATCGGTGCACATGG 59.595 47.619 20.43 7.33 45.60 3.66
546 4815 2.847959 TGCATTTATCGGTGCACATG 57.152 45.000 20.43 13.29 45.60 3.21
551 4820 3.818387 CAGATCATGCATTTATCGGTGC 58.182 45.455 0.00 0.00 41.61 5.01
577 4868 5.473504 GCCAGTTCATATATTTTCCGGACAT 59.526 40.000 1.83 1.30 0.00 3.06
584 4875 8.677148 TTCCTACAGCCAGTTCATATATTTTC 57.323 34.615 0.00 0.00 0.00 2.29
681 4975 0.108019 GACCTTCAGAAACCGGGTGT 59.892 55.000 6.32 0.00 0.00 4.16
731 5025 2.348872 CGCCATGCATGAACGAGTATTC 60.349 50.000 28.31 3.05 31.67 1.75
793 5092 3.639094 TGAATTGGTGAAACAAATCCGGT 59.361 39.130 0.00 0.00 40.31 5.28
794 5093 4.250116 TGAATTGGTGAAACAAATCCGG 57.750 40.909 0.00 0.00 40.31 5.14
795 5094 6.527722 CACTATGAATTGGTGAAACAAATCCG 59.472 38.462 0.00 0.00 40.31 4.18
796 5095 6.813152 CCACTATGAATTGGTGAAACAAATCC 59.187 38.462 0.00 0.00 40.31 3.01
797 5096 7.601856 TCCACTATGAATTGGTGAAACAAATC 58.398 34.615 0.00 0.00 40.31 2.17
840 5143 5.480772 CGAGTGTATTTATAGGAGATGGGGT 59.519 44.000 0.00 0.00 0.00 4.95
844 5150 6.622549 GGGACGAGTGTATTTATAGGAGATG 58.377 44.000 0.00 0.00 0.00 2.90
845 5151 6.837471 GGGACGAGTGTATTTATAGGAGAT 57.163 41.667 0.00 0.00 0.00 2.75
874 5190 1.694150 GAGTATGCTATGCTCCACCCA 59.306 52.381 0.00 0.00 36.20 4.51
878 5194 1.000171 CAGCGAGTATGCTATGCTCCA 60.000 52.381 7.00 0.00 45.23 3.86
887 5208 1.067669 TGGAGTGATCAGCGAGTATGC 59.932 52.381 0.00 0.00 0.00 3.14
888 5209 3.657015 ATGGAGTGATCAGCGAGTATG 57.343 47.619 0.00 0.00 0.00 2.39
889 5210 3.801638 GCAATGGAGTGATCAGCGAGTAT 60.802 47.826 0.00 0.00 0.00 2.12
890 5211 2.481969 GCAATGGAGTGATCAGCGAGTA 60.482 50.000 0.00 0.00 0.00 2.59
891 5212 1.741732 GCAATGGAGTGATCAGCGAGT 60.742 52.381 0.00 0.00 0.00 4.18
914 5235 1.073177 ATTGTACTACCGCGTTGTGC 58.927 50.000 4.92 4.96 41.47 4.57
926 5247 7.260603 GTCCTACCGTTGTATTGTATTGTACT 58.739 38.462 0.00 0.00 0.00 2.73
928 5249 6.380846 AGGTCCTACCGTTGTATTGTATTGTA 59.619 38.462 0.00 0.00 44.90 2.41
929 5250 5.188359 AGGTCCTACCGTTGTATTGTATTGT 59.812 40.000 0.00 0.00 44.90 2.71
930 5251 5.667466 AGGTCCTACCGTTGTATTGTATTG 58.333 41.667 0.00 0.00 44.90 1.90
931 5252 5.945144 AGGTCCTACCGTTGTATTGTATT 57.055 39.130 0.00 0.00 44.90 1.89
932 5253 7.607615 ATTAGGTCCTACCGTTGTATTGTAT 57.392 36.000 0.00 0.00 44.90 2.29
975 5325 0.729116 TCGTCCTCGGCGTTAACTAG 59.271 55.000 6.85 0.00 37.69 2.57
1007 5360 2.586357 GCAGCACCCTAGCGCTAC 60.586 66.667 14.45 3.14 36.50 3.58
1263 6222 2.286242 CGATCAAGCATGTCAGCATCAC 60.286 50.000 0.00 0.00 36.85 3.06
1741 6726 2.887568 CATGCACCGGTCTCTCGC 60.888 66.667 2.59 5.28 0.00 5.03
1750 6736 2.539274 CCAAAACTCAAAACATGCACCG 59.461 45.455 0.00 0.00 0.00 4.94
1752 6751 2.935201 TGCCAAAACTCAAAACATGCAC 59.065 40.909 0.00 0.00 0.00 4.57
1911 7091 4.457603 CCATAGAAACCGTCCAATTTGTGA 59.542 41.667 0.00 0.00 0.00 3.58
1970 7214 6.313905 ACGACTCTATGAAATGGTTTGCTAAG 59.686 38.462 0.00 0.00 0.00 2.18
2005 7249 9.956640 ATTAATTTCACATCCATTTTTAGCCAA 57.043 25.926 0.00 0.00 0.00 4.52
2063 7311 0.389025 TCGTCTGTCTGTGTGCACAT 59.611 50.000 24.69 0.00 41.01 3.21
2163 7419 2.829914 TGGCCGATGGAATGCTGC 60.830 61.111 0.00 0.00 0.00 5.25
2253 7513 9.703892 TGTTTGCTTTACAATAACAATAATGCT 57.296 25.926 0.00 0.00 38.31 3.79
2254 7514 9.739786 GTGTTTGCTTTACAATAACAATAATGC 57.260 29.630 0.00 0.00 38.31 3.56
2259 7519 9.593134 TTTCAGTGTTTGCTTTACAATAACAAT 57.407 25.926 0.00 0.00 38.31 2.71
2260 7520 8.865001 GTTTCAGTGTTTGCTTTACAATAACAA 58.135 29.630 0.00 0.00 38.31 2.83
2261 7521 8.247562 AGTTTCAGTGTTTGCTTTACAATAACA 58.752 29.630 0.00 0.00 38.31 2.41
2262 7522 8.628882 AGTTTCAGTGTTTGCTTTACAATAAC 57.371 30.769 0.00 0.00 38.31 1.89
2263 7523 9.081997 CAAGTTTCAGTGTTTGCTTTACAATAA 57.918 29.630 0.00 0.00 38.31 1.40
2278 7539 3.242739 CCTGTTCCGAACAAGTTTCAGTG 60.243 47.826 14.74 0.70 41.61 3.66
2292 7553 2.811317 GCAGCTCGTCCTGTTCCG 60.811 66.667 6.87 0.00 35.28 4.30
2492 7754 8.160106 AGTTCCTGAAGATAAAAGTTGATGTCT 58.840 33.333 0.00 0.00 0.00 3.41
2497 7759 8.156820 TCATCAGTTCCTGAAGATAAAAGTTGA 58.843 33.333 0.00 0.00 44.04 3.18
2507 7769 5.299531 CGGTATAGTCATCAGTTCCTGAAGA 59.700 44.000 0.00 0.00 44.04 2.87
2717 7979 1.007336 GCGTGACGAGGACGAACATT 61.007 55.000 10.10 0.00 42.66 2.71
2819 8081 1.080025 GTAGTCCACCTGTGACCGC 60.080 63.158 0.00 0.00 0.00 5.68
2976 8245 1.670087 CGCAGACCTGTGGAAGTACTG 60.670 57.143 0.00 0.00 37.43 2.74
2999 8268 2.927477 GCCGTCGATCACATTCAAGTTA 59.073 45.455 0.00 0.00 0.00 2.24
3182 8458 2.939460 AATTACAAGGACGGCATTGC 57.061 45.000 16.97 0.00 39.28 3.56
3294 9283 8.352942 GGGAATAAAATGTCATGTTGGACTATC 58.647 37.037 0.00 0.00 38.61 2.08
3759 13408 2.689983 GGTTGCTGCAGCCATAAACTAT 59.310 45.455 34.64 0.00 41.18 2.12
4093 13743 3.454858 TGCTTCCTAATTCTGGGAGACT 58.545 45.455 9.28 0.00 33.01 3.24



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

AutoCloner maintained by Alex Coulton.