Multiple sequence alignment - TraesCS3A01G072900

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 TraesCS3A01G072900 chr3A 100.000 4490 0 0 1 4490 45082623 45087112 0.000000e+00 8292.0
1 TraesCS3A01G072900 chr3D 93.027 4044 192 47 510 4486 32592424 32596444 0.000000e+00 5823.0
2 TraesCS3A01G072900 chr3D 86.367 2934 296 50 677 3591 32584196 32587044 0.000000e+00 3107.0
3 TraesCS3A01G072900 chr3D 87.188 320 25 8 301 612 32583881 32584192 2.570000e-92 350.0
4 TraesCS3A01G072900 chr3D 91.589 214 8 8 1 208 339869692 339869901 2.040000e-73 287.0
5 TraesCS3A01G072900 chr3D 88.182 220 9 4 233 443 32592210 32592421 3.470000e-61 246.0
6 TraesCS3A01G072900 chr3D 89.130 92 7 3 216 305 32545026 32545116 1.320000e-20 111.0
7 TraesCS3A01G072900 chr3B 93.937 2903 144 12 922 3810 55126407 55129291 0.000000e+00 4357.0
8 TraesCS3A01G072900 chr3B 92.271 634 19 9 213 831 55125579 55126197 0.000000e+00 872.0
9 TraesCS3A01G072900 chr3B 81.549 710 68 31 3800 4486 55130357 55131026 1.110000e-145 527.0
10 TraesCS3A01G072900 chr2B 77.987 2494 455 54 1037 3462 729766626 729769093 0.000000e+00 1478.0
11 TraesCS3A01G072900 chr2B 77.334 2506 463 56 1034 3491 4754266 4751818 0.000000e+00 1384.0
12 TraesCS3A01G072900 chr2B 76.995 2556 459 78 1005 3466 548623989 548626509 0.000000e+00 1343.0
13 TraesCS3A01G072900 chr2A 77.823 2444 456 48 1080 3462 733628985 733631403 0.000000e+00 1432.0
14 TraesCS3A01G072900 chr2A 91.509 212 13 5 3 210 719334445 719334235 2.040000e-73 287.0
15 TraesCS3A01G072900 chr2A 73.346 544 108 23 1118 1635 611302949 611303481 2.780000e-37 167.0
16 TraesCS3A01G072900 chr4B 78.966 2030 356 40 1485 3462 36635359 36633349 0.000000e+00 1317.0
17 TraesCS3A01G072900 chr1A 78.727 2026 368 36 1485 3462 8144001 8141991 0.000000e+00 1295.0
18 TraesCS3A01G072900 chr1A 75.137 1826 369 53 1036 2805 9375621 9373825 0.000000e+00 778.0
19 TraesCS3A01G072900 chr1D 78.689 2013 369 32 1500 3466 6714094 6712096 0.000000e+00 1286.0
20 TraesCS3A01G072900 chr1B 76.371 2552 476 69 1005 3466 10007486 10004972 0.000000e+00 1254.0
21 TraesCS3A01G072900 chr1B 78.671 1730 319 31 1776 3462 8855128 8853406 0.000000e+00 1105.0
22 TraesCS3A01G072900 chr2D 76.308 2562 475 87 1005 3466 469990586 469993115 0.000000e+00 1247.0
23 TraesCS3A01G072900 chr5A 75.049 2541 517 77 1012 3462 565499124 565496611 0.000000e+00 1072.0
24 TraesCS3A01G072900 chr7B 74.554 841 192 17 2555 3387 586967349 586966523 9.240000e-92 348.0
25 TraesCS3A01G072900 chr5D 91.549 213 12 5 1 208 490946683 490946472 5.680000e-74 289.0
26 TraesCS3A01G072900 chr5B 90.094 212 16 5 1 209 694305156 694305365 2.060000e-68 270.0
27 TraesCS3A01G072900 chr7D 89.855 69 7 0 140 208 31998294 31998226 6.190000e-14 89.8


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 TraesCS3A01G072900 chr3A 45082623 45087112 4489 False 8292.000000 8292 100.000000 1 4490 1 chr3A.!!$F1 4489
1 TraesCS3A01G072900 chr3D 32592210 32596444 4234 False 3034.500000 5823 90.604500 233 4486 2 chr3D.!!$F4 4253
2 TraesCS3A01G072900 chr3D 32583881 32587044 3163 False 1728.500000 3107 86.777500 301 3591 2 chr3D.!!$F3 3290
3 TraesCS3A01G072900 chr3B 55125579 55131026 5447 False 1918.666667 4357 89.252333 213 4486 3 chr3B.!!$F1 4273
4 TraesCS3A01G072900 chr2B 729766626 729769093 2467 False 1478.000000 1478 77.987000 1037 3462 1 chr2B.!!$F2 2425
5 TraesCS3A01G072900 chr2B 4751818 4754266 2448 True 1384.000000 1384 77.334000 1034 3491 1 chr2B.!!$R1 2457
6 TraesCS3A01G072900 chr2B 548623989 548626509 2520 False 1343.000000 1343 76.995000 1005 3466 1 chr2B.!!$F1 2461
7 TraesCS3A01G072900 chr2A 733628985 733631403 2418 False 1432.000000 1432 77.823000 1080 3462 1 chr2A.!!$F2 2382
8 TraesCS3A01G072900 chr4B 36633349 36635359 2010 True 1317.000000 1317 78.966000 1485 3462 1 chr4B.!!$R1 1977
9 TraesCS3A01G072900 chr1A 8141991 8144001 2010 True 1295.000000 1295 78.727000 1485 3462 1 chr1A.!!$R1 1977
10 TraesCS3A01G072900 chr1A 9373825 9375621 1796 True 778.000000 778 75.137000 1036 2805 1 chr1A.!!$R2 1769
11 TraesCS3A01G072900 chr1D 6712096 6714094 1998 True 1286.000000 1286 78.689000 1500 3466 1 chr1D.!!$R1 1966
12 TraesCS3A01G072900 chr1B 10004972 10007486 2514 True 1254.000000 1254 76.371000 1005 3466 1 chr1B.!!$R2 2461
13 TraesCS3A01G072900 chr1B 8853406 8855128 1722 True 1105.000000 1105 78.671000 1776 3462 1 chr1B.!!$R1 1686
14 TraesCS3A01G072900 chr2D 469990586 469993115 2529 False 1247.000000 1247 76.308000 1005 3466 1 chr2D.!!$F1 2461
15 TraesCS3A01G072900 chr5A 565496611 565499124 2513 True 1072.000000 1072 75.049000 1012 3462 1 chr5A.!!$R1 2450
16 TraesCS3A01G072900 chr7B 586966523 586967349 826 True 348.000000 348 74.554000 2555 3387 1 chr7B.!!$R1 832

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
205 206 0.179062 CTCGGCCTCTGCTATGCTTT 60.179 55.0 0.00 0.0 37.74 3.51 F
206 207 0.253044 TCGGCCTCTGCTATGCTTTT 59.747 50.0 0.00 0.0 37.74 2.27 F
944 1109 0.319555 GCAGACAACGTGCACTAGGA 60.320 55.0 16.19 0.0 40.86 2.94 F
1722 2005 0.392998 ATGCGCCCGAAACTTCAGAT 60.393 50.0 4.18 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 1519 0.034574 TGGGGTCAATGATTGGGTCG 60.035 55.000 5.20 0.00 0.00 4.79 R
2070 2380 1.018752 TGCACCCATGTGTTCGATCG 61.019 55.000 9.36 9.36 44.65 3.69 R
2090 2400 4.754618 TGCAATATAGCGGTGTATTTCTGG 59.245 41.667 13.12 4.74 37.31 3.86 R
3705 4115 0.169009 GCGCCAACAACTTCATCCTC 59.831 55.000 0.00 0.00 0.00 3.71 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
31 32 7.100458 GATAAAGCCCATTTTATCTGTGTGT 57.900 36.000 9.93 0.00 42.60 3.72
32 33 5.806654 AAAGCCCATTTTATCTGTGTGTT 57.193 34.783 0.00 0.00 0.00 3.32
33 34 5.806654 AAGCCCATTTTATCTGTGTGTTT 57.193 34.783 0.00 0.00 0.00 2.83
34 35 6.909550 AAGCCCATTTTATCTGTGTGTTTA 57.090 33.333 0.00 0.00 0.00 2.01
35 36 7.480760 AAGCCCATTTTATCTGTGTGTTTAT 57.519 32.000 0.00 0.00 0.00 1.40
36 37 7.100458 AGCCCATTTTATCTGTGTGTTTATC 57.900 36.000 0.00 0.00 0.00 1.75
37 38 6.891908 AGCCCATTTTATCTGTGTGTTTATCT 59.108 34.615 0.00 0.00 0.00 1.98
38 39 7.397192 AGCCCATTTTATCTGTGTGTTTATCTT 59.603 33.333 0.00 0.00 0.00 2.40
39 40 8.034804 GCCCATTTTATCTGTGTGTTTATCTTT 58.965 33.333 0.00 0.00 0.00 2.52
40 41 9.927668 CCCATTTTATCTGTGTGTTTATCTTTT 57.072 29.630 0.00 0.00 0.00 2.27
193 194 3.073735 CTCTGTGGAGCTCGGCCT 61.074 66.667 7.83 0.00 32.43 5.19
194 195 3.071206 TCTGTGGAGCTCGGCCTC 61.071 66.667 7.83 0.00 0.00 4.70
195 196 3.073735 CTGTGGAGCTCGGCCTCT 61.074 66.667 7.83 0.00 32.43 3.69
196 197 3.368190 CTGTGGAGCTCGGCCTCTG 62.368 68.421 7.83 0.00 32.43 3.35
197 198 4.828925 GTGGAGCTCGGCCTCTGC 62.829 72.222 7.83 1.79 32.43 4.26
199 200 2.835431 GGAGCTCGGCCTCTGCTA 60.835 66.667 7.83 0.00 37.16 3.49
200 201 2.206536 GGAGCTCGGCCTCTGCTAT 61.207 63.158 7.83 0.00 37.16 2.97
201 202 1.006337 GAGCTCGGCCTCTGCTATG 60.006 63.158 12.80 0.00 37.16 2.23
202 203 2.664518 GCTCGGCCTCTGCTATGC 60.665 66.667 0.00 0.00 37.74 3.14
203 204 3.136750 CTCGGCCTCTGCTATGCT 58.863 61.111 0.00 0.00 37.74 3.79
204 205 1.445095 CTCGGCCTCTGCTATGCTT 59.555 57.895 0.00 0.00 37.74 3.91
205 206 0.179062 CTCGGCCTCTGCTATGCTTT 60.179 55.000 0.00 0.00 37.74 3.51
206 207 0.253044 TCGGCCTCTGCTATGCTTTT 59.747 50.000 0.00 0.00 37.74 2.27
207 208 1.098050 CGGCCTCTGCTATGCTTTTT 58.902 50.000 0.00 0.00 37.74 1.94
208 209 1.064654 CGGCCTCTGCTATGCTTTTTC 59.935 52.381 0.00 0.00 37.74 2.29
209 210 1.064654 GGCCTCTGCTATGCTTTTTCG 59.935 52.381 0.00 0.00 37.74 3.46
210 211 1.740025 GCCTCTGCTATGCTTTTTCGT 59.260 47.619 0.00 0.00 33.53 3.85
211 212 2.936498 GCCTCTGCTATGCTTTTTCGTA 59.064 45.455 0.00 0.00 33.53 3.43
534 545 9.088512 GTTGTCCTTATCAGTGACAGTTAATAG 57.911 37.037 0.00 0.00 39.89 1.73
535 546 8.362464 TGTCCTTATCAGTGACAGTTAATAGT 57.638 34.615 0.00 0.00 34.28 2.12
536 547 9.470399 TGTCCTTATCAGTGACAGTTAATAGTA 57.530 33.333 0.00 0.00 34.28 1.82
551 562 9.256477 CAGTTAATAGTACAAACAGTGAACAGA 57.744 33.333 0.00 0.00 0.00 3.41
618 632 2.118404 AGTTTGGCGTGTGGTGTGG 61.118 57.895 0.00 0.00 0.00 4.17
620 634 4.885270 TTGGCGTGTGGTGTGGGG 62.885 66.667 0.00 0.00 0.00 4.96
652 679 2.878580 TGTTGGCATCAATCAAATCGC 58.121 42.857 0.00 0.00 35.10 4.58
831 870 2.283676 TCTCCTCCCGGTCACCAC 60.284 66.667 0.00 0.00 0.00 4.16
868 918 0.982673 CTGCGTACTACGTGTTCAGC 59.017 55.000 10.23 0.00 44.73 4.26
870 920 1.257539 GCGTACTACGTGTTCAGCTC 58.742 55.000 10.23 0.00 44.73 4.09
871 921 1.400629 GCGTACTACGTGTTCAGCTCA 60.401 52.381 10.23 0.00 44.73 4.26
872 922 2.919387 GCGTACTACGTGTTCAGCTCAA 60.919 50.000 10.23 0.00 44.73 3.02
873 923 2.655474 CGTACTACGTGTTCAGCTCAAC 59.345 50.000 0.00 0.00 36.74 3.18
874 924 2.882927 ACTACGTGTTCAGCTCAACA 57.117 45.000 0.00 0.00 33.75 3.33
875 925 3.173668 ACTACGTGTTCAGCTCAACAA 57.826 42.857 4.16 0.00 38.01 2.83
876 926 2.864343 ACTACGTGTTCAGCTCAACAAC 59.136 45.455 4.16 0.00 38.01 3.32
917 967 2.561069 GGGTCCTCTTCCTCCTTTCTCT 60.561 54.545 0.00 0.00 0.00 3.10
918 968 2.764010 GGTCCTCTTCCTCCTTTCTCTC 59.236 54.545 0.00 0.00 0.00 3.20
944 1109 0.319555 GCAGACAACGTGCACTAGGA 60.320 55.000 16.19 0.00 40.86 2.94
983 1148 7.344134 TCTCTCCAACTCATTCAATCATTCAT 58.656 34.615 0.00 0.00 0.00 2.57
997 1169 6.765036 TCAATCATTCATAGCACTCTTCTTCC 59.235 38.462 0.00 0.00 0.00 3.46
1187 1398 2.308570 TCCATCCACCAAGCAACACTAT 59.691 45.455 0.00 0.00 0.00 2.12
1189 1400 3.129287 CCATCCACCAAGCAACACTATTC 59.871 47.826 0.00 0.00 0.00 1.75
1204 1427 4.929808 ACACTATTCTTAGCAAGTCCAACG 59.070 41.667 0.00 0.00 0.00 4.10
1249 1475 2.218603 GGTACCTTGGCATATGGTTCG 58.781 52.381 4.06 0.00 37.87 3.95
1434 1684 1.603802 ACACGAACCAGCAACATGAAG 59.396 47.619 0.00 0.00 0.00 3.02
1483 1763 5.128499 AGTGGAAATCTAGTCCTCACATCAG 59.872 44.000 0.07 0.00 36.03 2.90
1665 1945 3.099141 CACCAATGGCAAAGGGATAGTT 58.901 45.455 12.44 0.00 0.00 2.24
1722 2005 0.392998 ATGCGCCCGAAACTTCAGAT 60.393 50.000 4.18 0.00 0.00 2.90
2070 2380 1.068921 ACAACATTGGGCGTTTGGC 59.931 52.632 0.00 0.00 42.51 4.52
3411 3787 2.421399 GGTACGGGTTCTCGAGGGG 61.421 68.421 13.56 0.23 0.00 4.79
3533 3916 9.973450 TGCAAACAATGTTGTACTAATATTTGT 57.027 25.926 0.00 7.67 41.31 2.83
3576 3960 8.075574 TGAAGTTGCATTGTGTACTGAATTAAG 58.924 33.333 0.00 0.00 0.00 1.85
3667 4077 6.499106 TGGATCCATCAAACTAGCAGAATA 57.501 37.500 11.44 0.00 0.00 1.75
3700 4110 2.591571 TGAGTGGATCAATCAGAGCG 57.408 50.000 0.00 0.00 33.50 5.03
3705 4115 1.958205 GATCAATCAGAGCGCCCGG 60.958 63.158 2.29 0.00 0.00 5.73
3722 4132 0.804989 CGGAGGATGAAGTTGTTGGC 59.195 55.000 0.00 0.00 0.00 4.52
3734 4144 2.736995 GTTGGCGCAGTCGTAGCA 60.737 61.111 10.83 0.00 38.14 3.49
3751 4161 3.973516 ACGCCGACTCGTGCTTCA 61.974 61.111 0.00 0.00 41.62 3.02
3792 4204 0.250166 TCGCCGTGATCTATCTCCGA 60.250 55.000 0.00 0.00 0.00 4.55
3939 5437 4.838152 CGACCCCTCCACCATGCG 62.838 72.222 0.00 0.00 0.00 4.73
3990 5491 6.586868 TTGCTTGTTCAACAAAACATGATC 57.413 33.333 4.13 0.00 37.69 2.92
3995 5496 8.177013 GCTTGTTCAACAAAACATGATCTTTTT 58.823 29.630 4.13 0.00 37.69 1.94
4024 5525 6.767524 AAATGTGTGAACACTTCTAAACCA 57.232 33.333 14.28 0.00 46.55 3.67
4336 5850 7.275779 TCGAGCACTTTCTTTAGTTATGATCAC 59.724 37.037 0.00 0.00 0.00 3.06
4486 6002 8.125978 ACACACATTGAACATTTCTGGAATAT 57.874 30.769 0.00 0.00 0.00 1.28
4487 6003 8.030692 ACACACATTGAACATTTCTGGAATATG 58.969 33.333 0.00 0.00 0.00 1.78
4488 6004 7.009815 CACACATTGAACATTTCTGGAATATGC 59.990 37.037 0.00 0.00 0.00 3.14
4489 6005 7.036829 CACATTGAACATTTCTGGAATATGCA 58.963 34.615 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.100458 ACACACAGATAAAATGGGCTTTATC 57.900 36.000 8.79 8.79 43.86 1.75
8 9 7.480760 AACACACAGATAAAATGGGCTTTAT 57.519 32.000 0.00 0.00 34.81 1.40
9 10 6.909550 AACACACAGATAAAATGGGCTTTA 57.090 33.333 0.00 0.00 0.00 1.85
10 11 5.806654 AACACACAGATAAAATGGGCTTT 57.193 34.783 0.00 0.00 0.00 3.51
11 12 5.806654 AAACACACAGATAAAATGGGCTT 57.193 34.783 0.00 0.00 0.00 4.35
12 13 6.891908 AGATAAACACACAGATAAAATGGGCT 59.108 34.615 0.00 0.00 0.00 5.19
13 14 7.100458 AGATAAACACACAGATAAAATGGGC 57.900 36.000 0.00 0.00 0.00 5.36
14 15 9.927668 AAAAGATAAACACACAGATAAAATGGG 57.072 29.630 0.00 0.00 0.00 4.00
176 177 3.073735 AGGCCGAGCTCCACAGAG 61.074 66.667 8.47 0.00 43.57 3.35
177 178 3.071206 GAGGCCGAGCTCCACAGA 61.071 66.667 8.47 0.00 0.00 3.41
178 179 3.073735 AGAGGCCGAGCTCCACAG 61.074 66.667 8.47 0.00 0.00 3.66
179 180 3.385384 CAGAGGCCGAGCTCCACA 61.385 66.667 8.47 0.00 0.00 4.17
180 181 4.828925 GCAGAGGCCGAGCTCCAC 62.829 72.222 8.47 0.00 0.00 4.02
181 182 2.936160 ATAGCAGAGGCCGAGCTCCA 62.936 60.000 20.37 7.34 42.56 3.86
182 183 2.206536 ATAGCAGAGGCCGAGCTCC 61.207 63.158 20.37 0.00 42.56 4.70
183 184 1.006337 CATAGCAGAGGCCGAGCTC 60.006 63.158 20.37 2.73 42.56 4.09
184 185 3.136750 CATAGCAGAGGCCGAGCT 58.863 61.111 20.54 20.54 42.56 4.09
185 186 2.657102 AAGCATAGCAGAGGCCGAGC 62.657 60.000 8.78 8.78 42.56 5.03
186 187 0.179062 AAAGCATAGCAGAGGCCGAG 60.179 55.000 0.00 0.00 42.56 4.63
187 188 0.253044 AAAAGCATAGCAGAGGCCGA 59.747 50.000 0.00 0.00 42.56 5.54
188 189 1.064654 GAAAAAGCATAGCAGAGGCCG 59.935 52.381 0.00 0.00 42.56 6.13
189 190 1.064654 CGAAAAAGCATAGCAGAGGCC 59.935 52.381 0.00 0.00 42.56 5.19
190 191 1.740025 ACGAAAAAGCATAGCAGAGGC 59.260 47.619 0.00 0.00 41.61 4.70
191 192 5.065218 ACATTACGAAAAAGCATAGCAGAGG 59.935 40.000 0.00 0.00 0.00 3.69
192 193 6.111768 ACATTACGAAAAAGCATAGCAGAG 57.888 37.500 0.00 0.00 0.00 3.35
193 194 6.036735 GGTACATTACGAAAAAGCATAGCAGA 59.963 38.462 0.00 0.00 0.00 4.26
194 195 6.192360 GGTACATTACGAAAAAGCATAGCAG 58.808 40.000 0.00 0.00 0.00 4.24
195 196 5.065474 GGGTACATTACGAAAAAGCATAGCA 59.935 40.000 0.00 0.00 0.00 3.49
196 197 5.296035 AGGGTACATTACGAAAAAGCATAGC 59.704 40.000 0.00 0.00 0.00 2.97
197 198 6.018180 GGAGGGTACATTACGAAAAAGCATAG 60.018 42.308 0.00 0.00 0.00 2.23
198 199 5.818857 GGAGGGTACATTACGAAAAAGCATA 59.181 40.000 0.00 0.00 0.00 3.14
199 200 4.638865 GGAGGGTACATTACGAAAAAGCAT 59.361 41.667 0.00 0.00 0.00 3.79
200 201 4.004982 GGAGGGTACATTACGAAAAAGCA 58.995 43.478 0.00 0.00 0.00 3.91
201 202 3.376234 GGGAGGGTACATTACGAAAAAGC 59.624 47.826 0.00 0.00 0.00 3.51
202 203 4.840271 AGGGAGGGTACATTACGAAAAAG 58.160 43.478 0.00 0.00 0.00 2.27
203 204 4.914177 AGGGAGGGTACATTACGAAAAA 57.086 40.909 0.00 0.00 0.00 1.94
204 205 4.914177 AAGGGAGGGTACATTACGAAAA 57.086 40.909 0.00 0.00 0.00 2.29
205 206 4.914177 AAAGGGAGGGTACATTACGAAA 57.086 40.909 0.00 0.00 0.00 3.46
206 207 4.041938 ACAAAAGGGAGGGTACATTACGAA 59.958 41.667 0.00 0.00 0.00 3.85
207 208 3.583966 ACAAAAGGGAGGGTACATTACGA 59.416 43.478 0.00 0.00 0.00 3.43
208 209 3.937079 GACAAAAGGGAGGGTACATTACG 59.063 47.826 0.00 0.00 0.00 3.18
209 210 5.045797 AGAGACAAAAGGGAGGGTACATTAC 60.046 44.000 0.00 0.00 0.00 1.89
210 211 5.098663 AGAGACAAAAGGGAGGGTACATTA 58.901 41.667 0.00 0.00 0.00 1.90
211 212 3.916989 AGAGACAAAAGGGAGGGTACATT 59.083 43.478 0.00 0.00 0.00 2.71
499 509 5.866633 CACTGATAAGGACAACTCTCTTGAC 59.133 44.000 0.00 0.00 0.00 3.18
534 545 6.781138 TGTTCAATCTGTTCACTGTTTGTAC 58.219 36.000 8.91 8.91 31.76 2.90
535 546 6.993786 TGTTCAATCTGTTCACTGTTTGTA 57.006 33.333 7.23 0.00 0.00 2.41
536 547 5.895636 TGTTCAATCTGTTCACTGTTTGT 57.104 34.783 7.23 0.00 0.00 2.83
628 653 4.678287 CGATTTGATTGATGCCAACATAGC 59.322 41.667 0.00 0.00 36.35 2.97
652 679 8.309656 TGTCAGCTGATCCTATATATGTCAAAG 58.690 37.037 21.47 0.00 0.00 2.77
669 696 1.486310 AGACCAAACTGTGTCAGCTGA 59.514 47.619 13.74 13.74 34.37 4.26
720 747 4.457496 CCAGAGCGCGGTCACCAT 62.457 66.667 36.38 16.20 0.00 3.55
831 870 2.931320 GCAGGAAACAGTAGGAACTCGG 60.931 54.545 0.00 0.00 41.75 4.63
868 918 8.275015 TGTATATATGGTTGTTGGTTGTTGAG 57.725 34.615 0.00 0.00 0.00 3.02
870 920 7.920151 CCATGTATATATGGTTGTTGGTTGTTG 59.080 37.037 18.01 0.00 42.16 3.33
871 921 7.069331 CCCATGTATATATGGTTGTTGGTTGTT 59.931 37.037 22.73 0.00 44.98 2.83
872 922 6.549364 CCCATGTATATATGGTTGTTGGTTGT 59.451 38.462 22.73 0.00 44.98 3.32
873 923 6.015519 CCCCATGTATATATGGTTGTTGGTTG 60.016 42.308 22.73 7.81 44.98 3.77
874 924 6.074648 CCCCATGTATATATGGTTGTTGGTT 58.925 40.000 22.73 0.00 44.98 3.67
875 925 5.135362 ACCCCATGTATATATGGTTGTTGGT 59.865 40.000 22.73 19.09 44.98 3.67
876 926 5.640147 ACCCCATGTATATATGGTTGTTGG 58.360 41.667 22.73 18.57 44.98 3.77
898 948 3.436243 TGAGAGAAAGGAGGAAGAGGAC 58.564 50.000 0.00 0.00 0.00 3.85
917 967 0.249447 CACGTTGTCTGCCACTCTGA 60.249 55.000 0.00 0.00 0.00 3.27
918 968 1.835483 GCACGTTGTCTGCCACTCTG 61.835 60.000 0.00 0.00 0.00 3.35
944 1109 4.329638 TGGAGAGAAGAGGAAGAGATGT 57.670 45.455 0.00 0.00 0.00 3.06
983 1148 1.839994 CCATGGGGAAGAAGAGTGCTA 59.160 52.381 2.85 0.00 35.59 3.49
1187 1398 3.128349 GTGTCGTTGGACTTGCTAAGAA 58.872 45.455 3.37 0.00 43.79 2.52
1189 1400 1.798813 GGTGTCGTTGGACTTGCTAAG 59.201 52.381 0.00 0.00 43.79 2.18
1204 1427 2.032681 GCTGTGGGAGGTGGTGTC 59.967 66.667 0.00 0.00 0.00 3.67
1249 1475 4.992951 AGTTGTACAAACCGGTATCTTGTC 59.007 41.667 22.97 15.83 35.09 3.18
1293 1519 0.034574 TGGGGTCAATGATTGGGTCG 60.035 55.000 5.20 0.00 0.00 4.79
1434 1684 1.192146 TGAGGACTACACTGGTGGCC 61.192 60.000 0.00 0.00 34.19 5.36
1483 1763 2.268076 ACAACGGTTGGCCAGATGC 61.268 57.895 23.51 0.00 40.16 3.91
1665 1945 3.353836 GGTTTGCGGCGCTTGAGA 61.354 61.111 33.26 9.45 0.00 3.27
1756 2045 3.210232 TGTTCGTGGGTCCAATTGTAA 57.790 42.857 4.43 0.00 0.00 2.41
2070 2380 1.018752 TGCACCCATGTGTTCGATCG 61.019 55.000 9.36 9.36 44.65 3.69
2090 2400 4.754618 TGCAATATAGCGGTGTATTTCTGG 59.245 41.667 13.12 4.74 37.31 3.86
3210 3583 3.311322 GGAAATATTCAACACGATCGCCA 59.689 43.478 16.60 0.00 0.00 5.69
3411 3787 0.599728 GCATGTCGATCTCCTGGAGC 60.600 60.000 19.08 5.07 0.00 4.70
3532 3915 7.635973 GCAACTTCAAGATTTGCTAAAACAAAC 59.364 33.333 5.65 0.00 42.01 2.93
3533 3916 7.332926 TGCAACTTCAAGATTTGCTAAAACAAA 59.667 29.630 12.55 0.00 44.87 2.83
3534 3917 6.815641 TGCAACTTCAAGATTTGCTAAAACAA 59.184 30.769 12.55 0.00 44.87 2.83
3535 3918 6.336566 TGCAACTTCAAGATTTGCTAAAACA 58.663 32.000 12.55 0.00 44.87 2.83
3576 3960 0.964700 AGCTTGCTTGCCTTCCTTTC 59.035 50.000 0.00 0.00 0.00 2.62
3629 4039 7.795047 TGATGGATCCATGGACATATATGTAC 58.205 38.462 32.05 19.64 42.08 2.90
3691 4101 3.854669 CCTCCGGGCGCTCTGATT 61.855 66.667 5.36 0.00 0.00 2.57
3700 4110 0.322546 AACAACTTCATCCTCCGGGC 60.323 55.000 0.00 0.00 0.00 6.13
3705 4115 0.169009 GCGCCAACAACTTCATCCTC 59.831 55.000 0.00 0.00 0.00 3.71
3716 4126 2.736995 GCTACGACTGCGCCAACA 60.737 61.111 4.18 0.00 42.48 3.33
3734 4144 3.973516 TGAAGCACGAGTCGGCGT 61.974 61.111 18.30 14.95 46.88 5.68
3771 4183 0.241481 GGAGATAGATCACGGCGACC 59.759 60.000 16.62 0.00 0.00 4.79
3914 5412 4.452733 GGAGGGGTCGAAGCACCG 62.453 72.222 0.00 0.00 37.30 4.94
3916 5414 2.047179 GTGGAGGGGTCGAAGCAC 60.047 66.667 0.00 0.00 0.00 4.40
3917 5415 3.319198 GGTGGAGGGGTCGAAGCA 61.319 66.667 0.00 0.00 0.00 3.91
4445 5961 5.804692 TGTGTGTTTAAACAACGTCAGAT 57.195 34.783 22.14 0.00 41.21 2.90


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

AutoCloner maintained by Alex Coulton.