Multiple sequence alignment - TraesCS3D01G420500

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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 TraesCS3D01G420500 chr3D 100.000 3884 0 0 1 3884 532854353 532858236 0.000000e+00 7173.0
1 TraesCS3D01G420500 chr3D 72.265 786 173 28 772 1534 537563626 537564389 6.580000e-48 202.0
2 TraesCS3D01G420500 chr3A 92.185 1446 82 11 2394 3814 668212803 668214242 0.000000e+00 2015.0
3 TraesCS3D01G420500 chr3A 90.301 1031 70 18 251 1278 668550437 668551440 0.000000e+00 1323.0
4 TraesCS3D01G420500 chr3A 88.716 1090 80 15 2394 3459 668553685 668554755 0.000000e+00 1291.0
5 TraesCS3D01G420500 chr3A 93.238 769 17 11 1563 2304 668211939 668212699 0.000000e+00 1099.0
6 TraesCS3D01G420500 chr3A 92.691 602 35 6 927 1521 668211337 668211936 0.000000e+00 859.0
7 TraesCS3D01G420500 chr3A 86.364 396 33 9 370 761 668210794 668211172 2.790000e-111 412.0
8 TraesCS3D01G420500 chr3A 83.439 471 48 10 269 733 668067621 668068067 1.000000e-110 411.0
9 TraesCS3D01G420500 chr3A 87.888 322 37 1 1264 1585 668551461 668551780 1.020000e-100 377.0
10 TraesCS3D01G420500 chr3A 80.605 397 42 15 370 761 668090148 668090514 1.370000e-69 274.0
11 TraesCS3D01G420500 chr3A 100.000 75 0 0 3810 3884 668214350 668214424 5.230000e-29 139.0
12 TraesCS3D01G420500 chr3B 91.248 1154 80 8 2392 3526 705139650 705140801 0.000000e+00 1552.0
13 TraesCS3D01G420500 chr3B 91.610 1037 65 12 251 1278 705135180 705136203 0.000000e+00 1413.0
14 TraesCS3D01G420500 chr3B 86.707 331 32 10 1264 1585 705136220 705136547 1.330000e-94 357.0
15 TraesCS3D01G420500 chr3B 91.045 201 15 2 36 235 705134998 705135196 6.400000e-68 268.0
16 TraesCS3D01G420500 chr3B 89.706 204 19 2 250 452 705033647 705033849 3.850000e-65 259.0
17 TraesCS3D01G420500 chr3B 88.750 160 17 1 75 234 705033505 705033663 1.100000e-45 195.0
18 TraesCS3D01G420500 chr3B 85.542 83 9 2 2223 2302 705139510 705139592 2.490000e-12 84.2
19 TraesCS3D01G420500 chrUn 75.743 202 33 5 3619 3814 47630282 47630091 1.920000e-13 87.9


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 TraesCS3D01G420500 chr3D 532854353 532858236 3883 False 7173.00 7173 100.000000 1 3884 1 chr3D.!!$F1 3883
1 TraesCS3D01G420500 chr3D 537563626 537564389 763 False 202.00 202 72.265000 772 1534 1 chr3D.!!$F2 762
2 TraesCS3D01G420500 chr3A 668550437 668554755 4318 False 997.00 1323 88.968333 251 3459 3 chr3A.!!$F4 3208
3 TraesCS3D01G420500 chr3A 668210794 668214424 3630 False 904.80 2015 92.895600 370 3884 5 chr3A.!!$F3 3514
4 TraesCS3D01G420500 chr3B 705134998 705140801 5803 False 734.84 1552 89.230400 36 3526 5 chr3B.!!$F2 3490

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
362 364 0.316841 TTCCGGCAACTGCATTTTCC 59.683 50.0 0.00 0.0 44.36 3.13 F
2057 5744 0.035458 ATGCTATTGTCCGCTAGCCC 59.965 55.0 9.66 0.0 39.68 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 6040 0.318955 ATTGCCAAACGCTGTGAAGC 60.319 50.0 0.0 0.0 38.78 3.86 R
2974 6705 0.037232 GGCTCAGTAACACGCCTTCT 60.037 55.0 0.0 0.0 39.42 2.85 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
26 27 9.307121 CCATAACTCTGAGTGATGTTTACTAAG 57.693 37.037 26.21 10.48 35.66 2.18
27 28 9.307121 CATAACTCTGAGTGATGTTTACTAAGG 57.693 37.037 22.15 0.00 33.28 2.69
28 29 6.919775 ACTCTGAGTGATGTTTACTAAGGT 57.080 37.500 10.00 0.00 29.17 3.50
29 30 7.304497 ACTCTGAGTGATGTTTACTAAGGTT 57.696 36.000 10.00 0.00 29.17 3.50
30 31 8.418597 ACTCTGAGTGATGTTTACTAAGGTTA 57.581 34.615 10.00 0.00 29.17 2.85
31 32 9.036980 ACTCTGAGTGATGTTTACTAAGGTTAT 57.963 33.333 10.00 0.00 29.17 1.89
32 33 9.877178 CTCTGAGTGATGTTTACTAAGGTTATT 57.123 33.333 0.00 0.00 29.17 1.40
33 34 9.871238 TCTGAGTGATGTTTACTAAGGTTATTC 57.129 33.333 0.00 0.00 29.17 1.75
34 35 9.877178 CTGAGTGATGTTTACTAAGGTTATTCT 57.123 33.333 0.00 0.00 0.00 2.40
64 65 5.854157 ACAGCGTGTTGTCTTATTTTATCG 58.146 37.500 0.00 0.00 0.00 2.92
70 71 9.564041 GCGTGTTGTCTTATTTTATCGTTATAG 57.436 33.333 0.00 0.00 0.00 1.31
80 81 4.813750 TTATCGTTATAGCTTAGGGGGC 57.186 45.455 0.00 0.00 0.00 5.80
106 107 4.261280 CCGACCAACTTTATGTTCCGTTTT 60.261 41.667 0.00 0.00 36.63 2.43
108 109 5.504337 CGACCAACTTTATGTTCCGTTTTCA 60.504 40.000 0.00 0.00 36.63 2.69
121 122 8.275015 TGTTCCGTTTTCAATGATGTGTATAT 57.725 30.769 0.00 0.00 0.00 0.86
150 151 4.207019 GCACACACTCAAAACATAGTTTGC 59.793 41.667 0.00 0.00 38.20 3.68
199 201 5.106157 CCAAAATCTTCATTAGAGGCGTGTT 60.106 40.000 0.00 0.00 36.02 3.32
218 220 5.334802 CGTGTTTCCTTTCAAGCACATATCA 60.335 40.000 1.89 0.00 37.34 2.15
219 221 6.446318 GTGTTTCCTTTCAAGCACATATCAA 58.554 36.000 0.00 0.00 37.42 2.57
220 222 6.583806 GTGTTTCCTTTCAAGCACATATCAAG 59.416 38.462 0.00 0.00 37.42 3.02
221 223 6.489700 TGTTTCCTTTCAAGCACATATCAAGA 59.510 34.615 0.00 0.00 0.00 3.02
222 224 7.177216 TGTTTCCTTTCAAGCACATATCAAGAT 59.823 33.333 0.00 0.00 0.00 2.40
223 225 8.677300 GTTTCCTTTCAAGCACATATCAAGATA 58.323 33.333 0.00 0.00 0.00 1.98
224 226 8.806429 TTCCTTTCAAGCACATATCAAGATAA 57.194 30.769 0.00 0.00 0.00 1.75
225 227 8.806429 TCCTTTCAAGCACATATCAAGATAAA 57.194 30.769 0.00 0.00 0.00 1.40
226 228 8.896744 TCCTTTCAAGCACATATCAAGATAAAG 58.103 33.333 0.00 0.00 0.00 1.85
227 229 8.896744 CCTTTCAAGCACATATCAAGATAAAGA 58.103 33.333 0.00 0.00 0.00 2.52
228 230 9.713740 CTTTCAAGCACATATCAAGATAAAGAC 57.286 33.333 0.00 0.00 0.00 3.01
229 231 7.792374 TCAAGCACATATCAAGATAAAGACC 57.208 36.000 0.00 0.00 0.00 3.85
230 232 7.337938 TCAAGCACATATCAAGATAAAGACCA 58.662 34.615 0.00 0.00 0.00 4.02
231 233 7.994911 TCAAGCACATATCAAGATAAAGACCAT 59.005 33.333 0.00 0.00 0.00 3.55
232 234 9.276590 CAAGCACATATCAAGATAAAGACCATA 57.723 33.333 0.00 0.00 0.00 2.74
233 235 9.499479 AAGCACATATCAAGATAAAGACCATAG 57.501 33.333 0.00 0.00 0.00 2.23
234 236 8.099537 AGCACATATCAAGATAAAGACCATAGG 58.900 37.037 0.00 0.00 0.00 2.57
235 237 7.148340 GCACATATCAAGATAAAGACCATAGGC 60.148 40.741 0.00 0.00 0.00 3.93
236 238 7.335422 CACATATCAAGATAAAGACCATAGGCC 59.665 40.741 0.00 0.00 0.00 5.19
237 239 4.706842 TCAAGATAAAGACCATAGGCCC 57.293 45.455 0.00 0.00 0.00 5.80
238 240 3.394606 TCAAGATAAAGACCATAGGCCCC 59.605 47.826 0.00 0.00 0.00 5.80
239 241 3.074857 AGATAAAGACCATAGGCCCCA 57.925 47.619 0.00 0.00 0.00 4.96
240 242 2.711547 AGATAAAGACCATAGGCCCCAC 59.288 50.000 0.00 0.00 0.00 4.61
241 243 1.974028 TAAAGACCATAGGCCCCACA 58.026 50.000 0.00 0.00 0.00 4.17
242 244 1.080638 AAAGACCATAGGCCCCACAA 58.919 50.000 0.00 0.00 0.00 3.33
243 245 1.080638 AAGACCATAGGCCCCACAAA 58.919 50.000 0.00 0.00 0.00 2.83
244 246 1.080638 AGACCATAGGCCCCACAAAA 58.919 50.000 0.00 0.00 0.00 2.44
245 247 1.431243 AGACCATAGGCCCCACAAAAA 59.569 47.619 0.00 0.00 0.00 1.94
323 325 8.888419 AGGATTGTCATGACATAGGAAGATAAT 58.112 33.333 28.32 14.73 41.52 1.28
362 364 0.316841 TTCCGGCAACTGCATTTTCC 59.683 50.000 0.00 0.00 44.36 3.13
477 483 1.499007 AGTTTGTGGGACATGAGGGTT 59.501 47.619 0.00 0.00 44.52 4.11
521 527 3.004210 GCATGTGTGTGTGTGTTATTGGA 59.996 43.478 0.00 0.00 0.00 3.53
573 580 0.652592 GAGGCGATGATGTTTGTCGG 59.347 55.000 0.00 0.00 36.00 4.79
575 582 1.024579 GGCGATGATGTTTGTCGGGT 61.025 55.000 0.00 0.00 36.00 5.28
580 587 2.577606 TGATGTTTGTCGGGTTCCAT 57.422 45.000 0.00 0.00 0.00 3.41
603 611 3.279434 GTCAACCTATCCATTGGTGTCC 58.721 50.000 1.86 0.00 36.07 4.02
853 911 1.486211 TCTCTCCCCGAATTCTCCAC 58.514 55.000 3.52 0.00 0.00 4.02
1409 1527 0.610232 AGCATGCAGAAAGGGTGGTC 60.610 55.000 21.98 0.00 0.00 4.02
1427 1545 4.267928 GTGGTCACTGCGAGATTACATAAC 59.732 45.833 0.00 0.00 0.00 1.89
1524 1646 3.948702 ACCCAAACAAGGTGCACC 58.051 55.556 29.22 29.22 35.85 5.01
1543 1665 6.640907 GTGCACCCTGTTTACTTATTCTTTTG 59.359 38.462 5.22 0.00 0.00 2.44
1545 1667 7.502895 TGCACCCTGTTTACTTATTCTTTTGTA 59.497 33.333 0.00 0.00 0.00 2.41
1547 1669 9.840427 CACCCTGTTTACTTATTCTTTTGTATG 57.160 33.333 0.00 0.00 0.00 2.39
1559 1687 9.613428 TTATTCTTTTGTATGTATCCTGGTCTG 57.387 33.333 0.00 0.00 0.00 3.51
1577 1705 2.023984 TCTGGTCCATCTCTTGGCTAGA 60.024 50.000 0.00 0.00 46.01 2.43
1627 5230 6.070951 TCCTGATGATGAAATCTCCTGTTT 57.929 37.500 0.00 0.00 45.81 2.83
1831 5514 2.040178 GTCCTGGTTCTCCATCCGTAT 58.960 52.381 0.00 0.00 43.43 3.06
1933 5620 2.943690 TCTGTAGCCATCGTGTAGTCTC 59.056 50.000 0.00 0.00 0.00 3.36
1984 5671 6.315393 GCTTCGTCCCTTGAAACTATCAATTA 59.685 38.462 0.00 0.00 46.62 1.40
1985 5672 7.466050 GCTTCGTCCCTTGAAACTATCAATTAG 60.466 40.741 0.00 0.00 46.62 1.73
1986 5673 5.815740 TCGTCCCTTGAAACTATCAATTAGC 59.184 40.000 0.00 0.00 46.62 3.09
1987 5674 5.817816 CGTCCCTTGAAACTATCAATTAGCT 59.182 40.000 0.00 0.00 46.62 3.32
2028 5715 7.335924 TCATCACCTGCCTAAAATTAACACTAC 59.664 37.037 0.00 0.00 0.00 2.73
2033 5720 8.520351 ACCTGCCTAAAATTAACACTACATTTC 58.480 33.333 0.00 0.00 0.00 2.17
2057 5744 0.035458 ATGCTATTGTCCGCTAGCCC 59.965 55.000 9.66 0.00 39.68 5.19
2088 5775 1.341531 CATCCCTACCTGTTCTAGCCG 59.658 57.143 0.00 0.00 0.00 5.52
2211 5901 8.262715 TGAATTGCTGTTAATACGATGAAAGA 57.737 30.769 0.00 0.00 0.00 2.52
2262 5953 6.769822 AGATCCACTACCAGAAATTAGCATTG 59.230 38.462 0.00 0.00 0.00 2.82
2267 5958 7.189512 CACTACCAGAAATTAGCATTGCTTAC 58.810 38.462 17.71 4.57 40.44 2.34
2312 6006 8.934023 TTCCCTTTTGTTTAGTATGATGAACT 57.066 30.769 0.00 0.00 0.00 3.01
2320 6023 7.262772 TGTTTAGTATGATGAACTAGAACCGG 58.737 38.462 0.00 0.00 31.37 5.28
2337 6040 5.590259 AGAACCGGGATATCAAAATGTTCAG 59.410 40.000 6.32 0.00 34.73 3.02
2338 6041 3.632145 ACCGGGATATCAAAATGTTCAGC 59.368 43.478 6.32 0.00 0.00 4.26
2339 6042 3.885297 CCGGGATATCAAAATGTTCAGCT 59.115 43.478 4.83 0.00 0.00 4.24
2364 6067 0.038343 GCGTTTGGCAATGTCCATGT 60.038 50.000 0.00 0.00 42.87 3.21
2365 6068 1.201181 GCGTTTGGCAATGTCCATGTA 59.799 47.619 0.00 0.00 42.87 2.29
2366 6069 2.159254 GCGTTTGGCAATGTCCATGTAT 60.159 45.455 0.00 0.00 42.87 2.29
2367 6070 3.066064 GCGTTTGGCAATGTCCATGTATA 59.934 43.478 0.00 0.00 42.87 1.47
2368 6071 4.597079 CGTTTGGCAATGTCCATGTATAC 58.403 43.478 0.00 0.00 35.77 1.47
2369 6072 4.095632 CGTTTGGCAATGTCCATGTATACA 59.904 41.667 8.27 8.27 35.77 2.29
2372 6075 5.771153 TGGCAATGTCCATGTATACAATG 57.229 39.130 10.14 8.68 31.16 2.82
2375 6078 6.183360 TGGCAATGTCCATGTATACAATGTTC 60.183 38.462 10.14 1.16 30.75 3.18
2376 6079 6.208644 GCAATGTCCATGTATACAATGTTCC 58.791 40.000 10.14 0.00 30.75 3.62
2377 6080 6.183360 GCAATGTCCATGTATACAATGTTCCA 60.183 38.462 10.14 3.07 30.75 3.53
2378 6081 7.470424 GCAATGTCCATGTATACAATGTTCCAT 60.470 37.037 10.14 5.19 30.75 3.41
2379 6082 6.940831 TGTCCATGTATACAATGTTCCATG 57.059 37.500 10.14 10.61 0.00 3.66
2380 6083 5.299028 TGTCCATGTATACAATGTTCCATGC 59.701 40.000 10.14 0.00 0.00 4.06
2381 6084 5.532406 GTCCATGTATACAATGTTCCATGCT 59.468 40.000 10.14 0.00 0.00 3.79
2416 6127 8.183104 TGTATATGCTATTCAGTCTTACAGCT 57.817 34.615 0.00 0.00 0.00 4.24
2469 6180 6.207691 TGCTTCCAATTTATTAGCTTGGTC 57.792 37.500 0.00 0.00 40.28 4.02
2531 6242 4.082190 TGTGAACACAGTACTATCTCTGGC 60.082 45.833 3.39 0.00 36.21 4.85
2618 6332 5.204409 ACTTCACCAGTATCGTGTTACAA 57.796 39.130 0.00 0.00 31.97 2.41
2621 6335 7.380536 ACTTCACCAGTATCGTGTTACAATAA 58.619 34.615 0.00 0.00 31.97 1.40
2666 6388 3.372730 GGCAACGCAGGCAATCCA 61.373 61.111 0.00 0.00 33.74 3.41
2727 6449 1.002430 AGCTGTCCATTCTGCTTCGAA 59.998 47.619 0.00 0.00 39.00 3.71
2743 6473 1.880340 GAAGAGCTGGTCGATGCGG 60.880 63.158 0.00 0.00 0.00 5.69
2785 6515 0.167470 CTTCTGCCACAAGTGCATCG 59.833 55.000 0.00 0.00 38.22 3.84
2807 6537 1.138661 GTTCTCCATCCAGGCTCAGAG 59.861 57.143 0.00 0.00 37.29 3.35
2819 6549 1.821936 CTCAGAGCAGGTGCCCTAG 59.178 63.158 0.00 0.00 43.38 3.02
2913 6643 1.880340 CCTTCTCGTCGCTGCCATC 60.880 63.158 0.00 0.00 0.00 3.51
2950 6681 5.895534 TGAACTATACTTCACCGGGTTATCT 59.104 40.000 6.32 0.00 0.00 1.98
2974 6705 4.974645 ACCATTGAACTTCTGGTACTCA 57.025 40.909 1.65 0.00 41.43 3.41
3176 6911 3.105937 GTCTTGCGTTGTCACCTTTTTC 58.894 45.455 0.00 0.00 0.00 2.29
3195 6933 6.609237 TTTTCTGAATCTCACAAGTCACAG 57.391 37.500 0.00 0.00 0.00 3.66
3310 7050 0.817654 GAACTTGCATAAGGCCACCC 59.182 55.000 5.01 0.00 43.89 4.61
3313 7053 2.837031 CTTGCATAAGGCCACCCCGT 62.837 60.000 5.01 0.00 43.89 5.28
3332 7072 5.394883 CCCCGTAGAACTCACTTAGCATAAA 60.395 44.000 0.00 0.00 0.00 1.40
3446 7196 1.447838 CCACGATCCCTTGTCACCG 60.448 63.158 0.00 0.00 0.00 4.94
3597 7347 0.103208 ATCTTCGATGGACTGGCGAC 59.897 55.000 0.00 0.00 33.33 5.19
3701 7451 0.042731 CCTTCTCCCCTGACCTGGTA 59.957 60.000 0.00 0.00 0.00 3.25
3743 7493 7.740519 AGCATGCAAATAAAAATTAGTCGTC 57.259 32.000 21.98 0.00 0.00 4.20
3746 7496 6.243811 TGCAAATAAAAATTAGTCGTCGGT 57.756 33.333 0.00 0.00 0.00 4.69
3747 7497 7.361889 TGCAAATAAAAATTAGTCGTCGGTA 57.638 32.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.307121 CTTAGTAAACATCACTCAGAGTTATGG 57.693 37.037 23.11 9.85 34.89 2.74
1 2 9.307121 CCTTAGTAAACATCACTCAGAGTTATG 57.693 37.037 19.33 19.33 36.25 1.90
3 4 8.418597 ACCTTAGTAAACATCACTCAGAGTTA 57.581 34.615 0.00 0.00 0.00 2.24
6 7 9.877178 AATAACCTTAGTAAACATCACTCAGAG 57.123 33.333 0.00 0.00 0.00 3.35
8 9 9.877178 AGAATAACCTTAGTAAACATCACTCAG 57.123 33.333 0.00 0.00 0.00 3.35
37 38 8.865590 ATAAAATAAGACAACACGCTGTTTTT 57.134 26.923 1.37 1.32 38.77 1.94
38 39 7.322699 CGATAAAATAAGACAACACGCTGTTTT 59.677 33.333 1.37 0.00 38.77 2.43
39 40 6.795114 CGATAAAATAAGACAACACGCTGTTT 59.205 34.615 1.37 0.00 38.77 2.83
40 41 6.073440 ACGATAAAATAAGACAACACGCTGTT 60.073 34.615 0.00 0.00 42.08 3.16
41 42 5.407387 ACGATAAAATAAGACAACACGCTGT 59.593 36.000 0.00 0.00 0.00 4.40
42 43 5.854157 ACGATAAAATAAGACAACACGCTG 58.146 37.500 0.00 0.00 0.00 5.18
43 44 6.476243 AACGATAAAATAAGACAACACGCT 57.524 33.333 0.00 0.00 0.00 5.07
44 45 9.564041 CTATAACGATAAAATAAGACAACACGC 57.436 33.333 0.00 0.00 0.00 5.34
45 46 9.564041 GCTATAACGATAAAATAAGACAACACG 57.436 33.333 0.00 0.00 0.00 4.49
64 65 0.321387 GCGGCCCCCTAAGCTATAAC 60.321 60.000 0.00 0.00 0.00 1.89
80 81 1.129811 GAACATAAAGTTGGTCGGCGG 59.870 52.381 7.21 0.00 41.51 6.13
85 86 5.823353 TGAAAACGGAACATAAAGTTGGTC 58.177 37.500 0.00 0.00 41.51 4.02
106 107 8.183536 GTGTGCTTTCAATATACACATCATTGA 58.816 33.333 0.00 0.00 42.63 2.57
108 109 8.054152 TGTGTGCTTTCAATATACACATCATT 57.946 30.769 0.00 0.00 44.52 2.57
121 122 4.511617 TGTTTTGAGTGTGTGCTTTCAA 57.488 36.364 0.00 0.00 0.00 2.69
128 129 4.739716 GGCAAACTATGTTTTGAGTGTGTG 59.260 41.667 5.31 0.00 38.54 3.82
129 130 4.400884 TGGCAAACTATGTTTTGAGTGTGT 59.599 37.500 5.31 0.00 38.54 3.72
135 136 8.347004 TGATTAGATGGCAAACTATGTTTTGA 57.653 30.769 0.00 0.00 38.54 2.69
150 151 9.988350 GGCGTTAAATACATTATGATTAGATGG 57.012 33.333 0.00 0.00 0.00 3.51
168 169 7.535139 CCTCTAATGAAGATTTTGGCGTTAAA 58.465 34.615 0.00 0.00 32.41 1.52
174 175 3.378427 ACGCCTCTAATGAAGATTTTGGC 59.622 43.478 0.00 0.00 32.41 4.52
185 186 3.751175 TGAAAGGAAACACGCCTCTAATG 59.249 43.478 0.00 0.00 33.76 1.90
199 201 8.806429 TTATCTTGATATGTGCTTGAAAGGAA 57.194 30.769 0.00 0.00 0.00 3.36
218 220 3.138468 GTGGGGCCTATGGTCTTTATCTT 59.862 47.826 0.84 0.00 0.00 2.40
219 221 2.711547 GTGGGGCCTATGGTCTTTATCT 59.288 50.000 0.84 0.00 0.00 1.98
220 222 2.441750 TGTGGGGCCTATGGTCTTTATC 59.558 50.000 0.84 0.00 0.00 1.75
221 223 2.498441 TGTGGGGCCTATGGTCTTTAT 58.502 47.619 0.84 0.00 0.00 1.40
222 224 1.974028 TGTGGGGCCTATGGTCTTTA 58.026 50.000 0.84 0.00 0.00 1.85
223 225 1.080638 TTGTGGGGCCTATGGTCTTT 58.919 50.000 0.84 0.00 0.00 2.52
224 226 1.080638 TTTGTGGGGCCTATGGTCTT 58.919 50.000 0.84 0.00 0.00 3.01
225 227 1.080638 TTTTGTGGGGCCTATGGTCT 58.919 50.000 0.84 0.00 0.00 3.85
226 228 1.931635 TTTTTGTGGGGCCTATGGTC 58.068 50.000 0.84 0.00 0.00 4.02
245 247 9.674068 GTCTTCCTATGGTCTTTATCTTTCTTT 57.326 33.333 0.00 0.00 0.00 2.52
246 248 7.982354 CGTCTTCCTATGGTCTTTATCTTTCTT 59.018 37.037 0.00 0.00 0.00 2.52
247 249 7.493367 CGTCTTCCTATGGTCTTTATCTTTCT 58.507 38.462 0.00 0.00 0.00 2.52
248 250 6.201234 GCGTCTTCCTATGGTCTTTATCTTTC 59.799 42.308 0.00 0.00 0.00 2.62
249 251 6.049790 GCGTCTTCCTATGGTCTTTATCTTT 58.950 40.000 0.00 0.00 0.00 2.52
323 325 0.528017 AGCGACGCTTGAGAAGATCA 59.472 50.000 18.46 0.00 33.89 2.92
443 445 5.900123 TCCCACAAACTTTCCCATTTCTTTA 59.100 36.000 0.00 0.00 0.00 1.85
444 446 4.719273 TCCCACAAACTTTCCCATTTCTTT 59.281 37.500 0.00 0.00 0.00 2.52
446 448 3.641436 GTCCCACAAACTTTCCCATTTCT 59.359 43.478 0.00 0.00 0.00 2.52
447 449 3.386402 TGTCCCACAAACTTTCCCATTTC 59.614 43.478 0.00 0.00 0.00 2.17
496 502 2.425610 CACACACACACATGCGCG 60.426 61.111 0.00 0.00 0.00 6.86
501 507 3.568007 GGTCCAATAACACACACACACAT 59.432 43.478 0.00 0.00 0.00 3.21
502 508 2.946329 GGTCCAATAACACACACACACA 59.054 45.455 0.00 0.00 0.00 3.72
503 509 2.292292 GGGTCCAATAACACACACACAC 59.708 50.000 0.00 0.00 0.00 3.82
504 510 2.092375 TGGGTCCAATAACACACACACA 60.092 45.455 0.00 0.00 0.00 3.72
505 511 2.577700 TGGGTCCAATAACACACACAC 58.422 47.619 0.00 0.00 0.00 3.82
521 527 3.161450 ATGCGGCGATAGGTGGGT 61.161 61.111 12.98 0.00 0.00 4.51
573 580 3.963129 TGGATAGGTTGACAATGGAACC 58.037 45.455 8.01 8.01 41.81 3.62
575 582 4.955450 CCAATGGATAGGTTGACAATGGAA 59.045 41.667 0.00 0.00 36.27 3.53
580 587 4.331968 GACACCAATGGATAGGTTGACAA 58.668 43.478 6.16 0.00 35.52 3.18
853 911 1.672881 GCGTTGATTTGGATCAGGGAG 59.327 52.381 0.00 0.00 42.90 4.30
996 1065 0.525761 CGCCCAACCGATTCATTTGT 59.474 50.000 0.00 0.00 0.00 2.83
999 1068 2.414785 GCCGCCCAACCGATTCATT 61.415 57.895 0.00 0.00 0.00 2.57
1285 1397 4.846779 TTATGTCAAACAAGACCTTGCC 57.153 40.909 9.48 0.00 44.03 4.52
1366 1484 5.299279 TCCAATCTGGAAACTCAAGAACAAC 59.701 40.000 0.00 0.00 45.00 3.32
1409 1527 3.702330 TCCGTTATGTAATCTCGCAGTG 58.298 45.455 0.00 0.00 0.00 3.66
1427 1545 2.039418 TCATCAGGTACCCTCAATCCG 58.961 52.381 8.74 0.00 0.00 4.18
1522 1644 9.582648 ACATACAAAAGAATAAGTAAACAGGGT 57.417 29.630 0.00 0.00 0.00 4.34
1543 1665 3.305720 TGGACCAGACCAGGATACATAC 58.694 50.000 0.00 0.00 41.41 2.39
1545 1667 2.568546 TGGACCAGACCAGGATACAT 57.431 50.000 0.00 0.00 41.41 2.29
1547 1669 2.630580 GAGATGGACCAGACCAGGATAC 59.369 54.545 0.00 0.00 43.49 2.24
1549 1671 1.293458 AGAGATGGACCAGACCAGGAT 59.707 52.381 0.00 0.00 43.49 3.24
1551 1673 1.209019 CAAGAGATGGACCAGACCAGG 59.791 57.143 0.00 0.00 43.49 4.45
1572 1700 4.434520 AGACAGCGATTTACCTTTCTAGC 58.565 43.478 0.00 0.00 0.00 3.42
1577 1705 3.865745 CGATGAGACAGCGATTTACCTTT 59.134 43.478 3.34 0.00 46.56 3.11
1627 5230 1.640917 AGTACTCCCTCTGCCGAAAA 58.359 50.000 0.00 0.00 0.00 2.29
1933 5620 1.518572 CGCTTGCACCCGTACCTAG 60.519 63.158 0.00 0.00 0.00 3.02
1984 5671 4.703575 TGATGAGCAAATTTGAAGCTAGCT 59.296 37.500 22.31 12.68 39.02 3.32
1985 5672 4.797349 GTGATGAGCAAATTTGAAGCTAGC 59.203 41.667 22.31 6.62 39.02 3.42
1986 5673 5.125097 AGGTGATGAGCAAATTTGAAGCTAG 59.875 40.000 22.31 0.00 39.02 3.42
1987 5674 5.012239 AGGTGATGAGCAAATTTGAAGCTA 58.988 37.500 22.31 3.27 39.02 3.32
2028 5715 5.928839 AGCGGACAATAGCATAGTAGAAATG 59.071 40.000 0.00 0.00 35.48 2.32
2033 5720 4.416620 GCTAGCGGACAATAGCATAGTAG 58.583 47.826 0.00 0.00 43.17 2.57
2057 5744 1.077787 TAGGGATGCAAACTGGGCG 60.078 57.895 0.00 0.00 0.00 6.13
2062 5749 2.644798 AGAACAGGTAGGGATGCAAACT 59.355 45.455 0.00 0.00 0.00 2.66
2132 5819 7.928908 TGTGTTCTTTTCAGCACATAAATTC 57.071 32.000 0.00 0.00 37.00 2.17
2133 5820 7.095523 GCATGTGTTCTTTTCAGCACATAAATT 60.096 33.333 8.41 0.00 46.76 1.82
2134 5821 6.366877 GCATGTGTTCTTTTCAGCACATAAAT 59.633 34.615 8.41 0.00 46.76 1.40
2135 5822 5.691305 GCATGTGTTCTTTTCAGCACATAAA 59.309 36.000 8.41 0.00 46.76 1.40
2262 5953 4.545208 AAGAGTCTGAAGGAAGGTAAGC 57.455 45.455 0.00 0.00 0.00 3.09
2267 5958 5.883115 GGGAAATTAAGAGTCTGAAGGAAGG 59.117 44.000 0.00 0.00 0.00 3.46
2305 5999 5.723672 TGATATCCCGGTTCTAGTTCATC 57.276 43.478 0.00 0.00 0.00 2.92
2307 6001 5.943349 TTTGATATCCCGGTTCTAGTTCA 57.057 39.130 0.00 0.00 0.00 3.18
2309 6003 6.659824 ACATTTTGATATCCCGGTTCTAGTT 58.340 36.000 0.00 0.00 0.00 2.24
2312 6006 6.654959 TGAACATTTTGATATCCCGGTTCTA 58.345 36.000 0.00 0.00 35.61 2.10
2316 6019 3.632145 GCTGAACATTTTGATATCCCGGT 59.368 43.478 0.00 0.00 0.00 5.28
2318 6021 5.066375 TGAAGCTGAACATTTTGATATCCCG 59.934 40.000 0.00 0.00 0.00 5.14
2320 6023 6.855836 TGTGAAGCTGAACATTTTGATATCC 58.144 36.000 0.00 0.00 0.00 2.59
2337 6040 0.318955 ATTGCCAAACGCTGTGAAGC 60.319 50.000 0.00 0.00 38.78 3.86
2338 6041 1.269206 ACATTGCCAAACGCTGTGAAG 60.269 47.619 0.00 0.00 38.78 3.02
2339 6042 0.743688 ACATTGCCAAACGCTGTGAA 59.256 45.000 0.00 0.00 38.78 3.18
2346 6049 3.781079 ATACATGGACATTGCCAAACG 57.219 42.857 0.00 0.00 42.16 3.60
2350 6053 5.199723 ACATTGTATACATGGACATTGCCA 58.800 37.500 6.36 2.90 43.23 4.92
2351 6054 5.772825 ACATTGTATACATGGACATTGCC 57.227 39.130 6.36 0.00 32.65 4.52
2352 6055 6.183360 TGGAACATTGTATACATGGACATTGC 60.183 38.462 6.36 2.60 32.65 3.56
2389 6097 8.085296 GCTGTAAGACTGAATAGCATATACAGT 58.915 37.037 0.00 0.00 43.10 3.55
2390 6098 8.303156 AGCTGTAAGACTGAATAGCATATACAG 58.697 37.037 8.80 0.00 34.07 2.74
2416 6127 1.407258 GGGCGCACCATTTAGCATAAA 59.593 47.619 10.83 0.00 39.85 1.40
2425 6136 1.102978 GATTTACAGGGCGCACCATT 58.897 50.000 5.73 0.00 43.89 3.16
2426 6137 0.034574 TGATTTACAGGGCGCACCAT 60.035 50.000 5.73 0.00 43.89 3.55
2428 6139 0.381801 CATGATTTACAGGGCGCACC 59.618 55.000 5.73 6.39 40.67 5.01
2432 6143 1.334869 GGAAGCATGATTTACAGGGCG 59.665 52.381 0.00 0.00 37.66 6.13
2469 6180 2.035066 CCCTGGAAAGAAAGCAACACAG 59.965 50.000 0.00 0.00 0.00 3.66
2618 6332 8.997323 GTAGCAGTGATGAGCTGATAAAATTAT 58.003 33.333 0.00 0.00 41.97 1.28
2621 6335 5.762218 GGTAGCAGTGATGAGCTGATAAAAT 59.238 40.000 0.00 0.00 41.97 1.82
2666 6388 1.561542 CCTCCTCCTTAACAGGTGCAT 59.438 52.381 0.00 0.00 41.69 3.96
2680 6402 1.272760 TGGTTCCTCTGAGACCTCCTC 60.273 57.143 14.49 0.00 42.30 3.71
2727 6449 4.521062 GCCGCATCGACCAGCTCT 62.521 66.667 0.00 0.00 0.00 4.09
2743 6473 2.024319 GGCCGCAGATAGTCGATGC 61.024 63.158 0.00 0.00 36.60 3.91
2785 6515 1.138661 CTGAGCCTGGATGGAGAACTC 59.861 57.143 0.00 0.00 38.35 3.01
2819 6549 3.005539 TGAGTCCCCTCCAGCAGC 61.006 66.667 0.00 0.00 36.86 5.25
2913 6643 9.072375 TGAAGTATAGTTCAGATAGGATGACAG 57.928 37.037 17.33 0.00 32.54 3.51
2974 6705 0.037232 GGCTCAGTAACACGCCTTCT 60.037 55.000 0.00 0.00 39.42 2.85
3095 6827 4.102649 GCGCAAACAACCAAATATACCTC 58.897 43.478 0.30 0.00 0.00 3.85
3147 6879 3.496884 GTGACAACGCAAGACCAAATCTA 59.503 43.478 0.00 0.00 36.27 1.98
3176 6911 3.993081 GGTCTGTGACTTGTGAGATTCAG 59.007 47.826 0.00 0.00 32.47 3.02
3195 6933 8.352942 CCAGAACTATTGCCAATTAATAAGGTC 58.647 37.037 0.00 0.00 0.00 3.85
3310 7050 5.519206 GGTTTATGCTAAGTGAGTTCTACGG 59.481 44.000 0.00 0.00 0.00 4.02
3313 7053 8.202137 GGTATGGTTTATGCTAAGTGAGTTCTA 58.798 37.037 0.00 0.00 0.00 2.10
3446 7196 0.621082 AACTTAGAAGGGAGGCAGCC 59.379 55.000 1.84 1.84 0.00 4.85
3597 7347 1.102154 ACAGCCAGATCTGTCTCTCG 58.898 55.000 21.11 5.09 43.28 4.04
3656 7406 0.037697 GGAACAAATGGCGGGGTTTC 60.038 55.000 0.00 0.00 0.00 2.78
3660 7410 2.350458 CCTGGAACAAATGGCGGGG 61.350 63.158 0.00 0.00 38.70 5.73
3701 7451 1.308998 CTTGCTTCGGTGTTTCCAGT 58.691 50.000 0.00 0.00 35.57 4.00
3743 7493 5.875910 TCATGTGTAAAAGGTGGTAATACCG 59.124 40.000 4.83 0.00 45.56 4.02
3746 7496 8.693120 TTGTTCATGTGTAAAAGGTGGTAATA 57.307 30.769 0.00 0.00 0.00 0.98
3747 7497 7.589958 TTGTTCATGTGTAAAAGGTGGTAAT 57.410 32.000 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.