Multiple sequence alignment - TraesCS5A01G173200

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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 TraesCS5A01G173200 chr5A 100.000 5403 0 0 1 5403 366628933 366634335 0.000000e+00 9978.0
1 TraesCS5A01G173200 chr5A 75.000 304 48 18 21 321 574711911 574712189 1.230000e-21 115.0
2 TraesCS5A01G173200 chr5D 96.145 3632 110 18 1788 5403 277556843 277560460 0.000000e+00 5904.0
3 TraesCS5A01G173200 chr5D 87.070 1454 111 34 359 1746 277555316 277556758 0.000000e+00 1572.0
4 TraesCS5A01G173200 chr5D 87.166 374 41 4 1 369 277554923 277555294 8.370000e-113 418.0
5 TraesCS5A01G173200 chr5D 91.837 49 3 1 1327 1374 490603523 490603571 3.490000e-07 67.6
6 TraesCS5A01G173200 chr5B 94.606 3634 127 15 1788 5403 315611003 315614585 0.000000e+00 5561.0
7 TraesCS5A01G173200 chr5B 85.248 1471 120 41 360 1748 315609465 315610920 0.000000e+00 1424.0
8 TraesCS5A01G173200 chr5B 87.576 330 27 9 42 369 315609125 315609442 2.380000e-98 370.0
9 TraesCS5A01G173200 chr5B 81.944 288 45 5 1464 1748 358537479 358537762 2.520000e-58 237.0
10 TraesCS5A01G173200 chr1A 81.849 292 46 5 1462 1751 309691858 309691572 6.990000e-59 239.0
11 TraesCS5A01G173200 chr3B 81.882 287 46 4 1464 1748 11551819 11552101 2.520000e-58 237.0
12 TraesCS5A01G173200 chrUn 81.724 290 45 6 1464 1751 301838177 301837894 9.050000e-58 235.0
13 TraesCS5A01G173200 chr7A 81.570 293 47 5 1461 1751 671404915 671404628 9.050000e-58 235.0
14 TraesCS5A01G173200 chr4B 81.724 290 46 5 1464 1751 385922979 385922695 9.050000e-58 235.0
15 TraesCS5A01G173200 chr2A 81.724 290 46 5 1461 1748 32504936 32505220 9.050000e-58 235.0
16 TraesCS5A01G173200 chr7B 81.293 294 48 6 1460 1751 51911332 51911044 1.170000e-56 231.0


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 TraesCS5A01G173200 chr5A 366628933 366634335 5402 False 9978.000000 9978 100.000000 1 5403 1 chr5A.!!$F1 5402
1 TraesCS5A01G173200 chr5D 277554923 277560460 5537 False 2631.333333 5904 90.127000 1 5403 3 chr5D.!!$F2 5402
2 TraesCS5A01G173200 chr5B 315609125 315614585 5460 False 2451.666667 5561 89.143333 42 5403 3 chr5B.!!$F2 5361

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
37 41 0.030101 GAGACGATCTCCTCCTTGCG 59.970 60.0 0.00 0.00 37.55 4.85 F
101 106 0.099436 GCAACGGCATCAAGATCCAC 59.901 55.0 0.00 0.00 40.72 4.02 F
756 812 0.322456 TTTTCTGGATGGCTCACCCG 60.322 55.0 0.00 0.00 35.87 5.28 F
1921 2095 0.255890 TAAGGATGGTGCTCCCTTGC 59.744 55.0 1.59 0.00 40.26 4.01 F
2086 2260 0.110192 CTCGCTCGCTTTGGTTTTCC 60.110 55.0 0.00 0.00 41.14 3.13 F
2570 2744 0.179067 TGGGAACACGTGACAAGTCC 60.179 55.0 25.01 18.17 33.40 3.85 F
2781 2966 0.323451 CCTGGTAGGGGTTCCAAAGC 60.323 60.0 0.00 0.00 33.06 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1238 1308 0.037605 AAGTTCGCCAGTTACGAGGG 60.038 55.0 0.00 0.0 41.18 4.30 R
1384 1484 0.179225 CGAAAATGTTCCGTGGCGAG 60.179 55.0 0.00 0.0 0.00 5.03 R
1941 2115 0.249953 TGCAGCAATGCAAGGTTTGG 60.250 50.0 8.35 0.0 42.40 3.28 R
3295 3481 0.037139 GTCATGCTGCCCAATTTGCA 60.037 50.0 0.00 0.0 39.83 4.08 R
3410 3597 0.790814 GTCTTCCTACACACTTGCGC 59.209 55.0 0.00 0.0 0.00 6.09 R
3411 3598 1.060713 CGTCTTCCTACACACTTGCG 58.939 55.0 0.00 0.0 0.00 4.85 R
4717 4916 1.632422 CGTAGGTACGTTCGCCAATT 58.368 50.0 0.00 0.0 44.13 2.32 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
37 41 0.030101 GAGACGATCTCCTCCTTGCG 59.970 60.000 0.00 0.00 37.55 4.85
41 45 0.249238 CGATCTCCTCCTTGCGGAAG 60.249 60.000 10.08 10.08 39.29 3.46
49 53 3.494336 CTTGCGGAAGGAGCTGCG 61.494 66.667 9.08 0.00 43.09 5.18
50 54 3.939837 CTTGCGGAAGGAGCTGCGA 62.940 63.158 9.08 0.00 43.09 5.10
55 60 2.202676 GAAGGAGCTGCGACCGAG 60.203 66.667 0.00 0.00 0.00 4.63
84 89 3.473647 CCCTGGAGAGCGATGGCA 61.474 66.667 1.50 0.00 43.41 4.92
101 106 0.099436 GCAACGGCATCAAGATCCAC 59.901 55.000 0.00 0.00 40.72 4.02
118 123 2.279784 CGGAAGATCCAGAGCCGC 60.280 66.667 0.00 0.00 35.91 6.53
120 125 1.456196 CGGAAGATCCAGAGCCGCTA 61.456 60.000 0.00 0.00 35.91 4.26
200 206 1.281899 GAGTTCGAAGAAGCGGATGG 58.718 55.000 0.00 0.00 45.90 3.51
206 212 4.845580 AGAAGCGGATGGGCGCAG 62.846 66.667 10.83 0.00 38.18 5.18
254 260 3.132629 ACAGATTATATAGACGCGGCG 57.867 47.619 22.36 22.36 0.00 6.46
257 263 3.063588 CAGATTATATAGACGCGGCGAGA 59.936 47.826 30.94 13.55 0.00 4.04
267 273 2.579201 CGGCGAGACCAGGTGAAT 59.421 61.111 0.00 0.00 39.03 2.57
271 277 1.983224 CGAGACCAGGTGAATGGGT 59.017 57.895 0.00 0.00 45.25 4.51
291 297 2.042831 GTCAGCCCGCTTCAATGCT 61.043 57.895 0.00 0.00 33.52 3.79
409 448 2.785357 ACATGGGAAAGGGTTTTGGA 57.215 45.000 0.00 0.00 0.00 3.53
434 474 3.490759 GATGTGTCAGGCGCCACG 61.491 66.667 31.54 19.89 34.28 4.94
451 501 0.838987 ACGAAGCCCCCTCTGGTTTA 60.839 55.000 0.00 0.00 0.00 2.01
454 504 0.838987 AAGCCCCCTCTGGTTTACGA 60.839 55.000 0.00 0.00 0.00 3.43
456 506 1.905512 CCCCCTCTGGTTTACGAGG 59.094 63.158 0.00 0.00 45.10 4.63
463 513 3.991367 CTCTGGTTTACGAGGAAACAGT 58.009 45.455 12.40 0.00 40.43 3.55
493 543 3.375239 TTCACGGACGGATGCGGA 61.375 61.111 12.44 0.00 45.25 5.54
502 557 1.143838 CGGATGCGGAGTTGGATGA 59.856 57.895 0.00 0.00 0.00 2.92
539 594 4.854784 TGCGCTCGAGACGGATGC 62.855 66.667 18.75 9.68 0.00 3.91
540 595 4.854784 GCGCTCGAGACGGATGCA 62.855 66.667 18.75 0.00 0.00 3.96
597 652 8.935614 AAAGTATTTTAACTGCCTCCTAAGTT 57.064 30.769 0.00 0.00 31.62 2.66
604 659 1.073923 CTGCCTCCTAAGTTGGTGGTT 59.926 52.381 11.58 0.00 41.45 3.67
665 721 5.305585 TGATTCTCAGGTGACCAAAGTTAC 58.694 41.667 3.63 0.00 0.00 2.50
729 785 2.125512 GCGTGCCAGTAGGTCCAG 60.126 66.667 0.00 0.00 37.19 3.86
737 793 1.538135 AGTAGGTCCAGCGGGGTTT 60.538 57.895 2.05 0.00 38.11 3.27
756 812 0.322456 TTTTCTGGATGGCTCACCCG 60.322 55.000 0.00 0.00 35.87 5.28
770 826 3.365265 CCCGCAGCAGTCCAAACC 61.365 66.667 0.00 0.00 0.00 3.27
801 857 9.342308 TCTCAGATGACCATTTCAAATTATACC 57.658 33.333 0.00 0.00 37.92 2.73
956 1012 2.254350 TCGCAAGACCGAGTCACG 59.746 61.111 6.78 7.11 45.01 4.35
1005 1064 2.281345 GGATCCTCTGCCATGGCG 60.281 66.667 30.87 24.20 45.51 5.69
1050 1109 0.891373 TCTTCTTCCTCCTGCTGTCG 59.109 55.000 0.00 0.00 0.00 4.35
1053 1112 0.539669 TCTTCCTCCTGCTGTCGTCA 60.540 55.000 0.00 0.00 0.00 4.35
1082 1141 2.592308 GGCCGCCCAGAAGAATCT 59.408 61.111 0.00 0.00 35.88 2.40
1134 1193 4.403752 TGGATCTGTCACCTCTGTATTCTG 59.596 45.833 0.00 0.00 0.00 3.02
1146 1205 5.866633 CCTCTGTATTCTGTTCAGTCAGTTC 59.133 44.000 0.00 0.00 36.85 3.01
1149 1208 4.991056 TGTATTCTGTTCAGTCAGTTCTGC 59.009 41.667 0.00 0.00 36.85 4.26
1194 1264 6.183360 GCTGCGTCCTTTTTATGATCTTTTTG 60.183 38.462 0.00 0.00 0.00 2.44
1231 1301 7.308348 CCGTGTGGTTAAGTACTGATTTGATTT 60.308 37.037 0.00 0.00 0.00 2.17
1233 1303 8.564574 GTGTGGTTAAGTACTGATTTGATTTGA 58.435 33.333 0.00 0.00 0.00 2.69
1234 1304 8.564574 TGTGGTTAAGTACTGATTTGATTTGAC 58.435 33.333 0.00 0.00 0.00 3.18
1235 1305 8.784043 GTGGTTAAGTACTGATTTGATTTGACT 58.216 33.333 0.00 0.00 0.00 3.41
1240 1310 7.923414 AGTACTGATTTGATTTGACTAACCC 57.077 36.000 0.00 0.00 0.00 4.11
1241 1311 7.690256 AGTACTGATTTGATTTGACTAACCCT 58.310 34.615 0.00 0.00 0.00 4.34
1242 1312 7.824779 AGTACTGATTTGATTTGACTAACCCTC 59.175 37.037 0.00 0.00 0.00 4.30
1243 1313 5.643777 ACTGATTTGATTTGACTAACCCTCG 59.356 40.000 0.00 0.00 0.00 4.63
1256 1326 1.183676 ACCCTCGTAACTGGCGAACT 61.184 55.000 0.00 0.00 37.93 3.01
1258 1328 1.347320 CCTCGTAACTGGCGAACTTC 58.653 55.000 0.00 0.00 37.93 3.01
1259 1329 1.067776 CCTCGTAACTGGCGAACTTCT 60.068 52.381 0.00 0.00 37.93 2.85
1260 1330 2.609737 CCTCGTAACTGGCGAACTTCTT 60.610 50.000 0.00 0.00 37.93 2.52
1261 1331 3.366679 CCTCGTAACTGGCGAACTTCTTA 60.367 47.826 0.00 0.00 37.93 2.10
1262 1332 4.232221 CTCGTAACTGGCGAACTTCTTAA 58.768 43.478 0.00 0.00 37.93 1.85
1265 1335 4.682860 CGTAACTGGCGAACTTCTTAAAGA 59.317 41.667 0.00 0.00 36.30 2.52
1266 1336 5.347907 CGTAACTGGCGAACTTCTTAAAGAT 59.652 40.000 0.00 0.00 36.30 2.40
1289 1387 5.782047 TGTGGCATTTTTAGTTGATGAAGG 58.218 37.500 0.00 0.00 0.00 3.46
1292 1390 4.466015 GGCATTTTTAGTTGATGAAGGGGA 59.534 41.667 0.00 0.00 0.00 4.81
1308 1406 3.250617 AGGGGAAAGATGTGGCATTTTT 58.749 40.909 0.00 0.00 0.00 1.94
1384 1484 0.879090 CACCCCCTTAAAGCGAACAC 59.121 55.000 0.00 0.00 0.00 3.32
1410 1511 3.911964 CCACGGAACATTTTCGTTTGATC 59.088 43.478 0.00 0.00 31.78 2.92
1421 1522 7.227512 ACATTTTCGTTTGATCAAGTCTCTTCT 59.772 33.333 8.41 0.00 0.00 2.85
1424 1525 5.601662 TCGTTTGATCAAGTCTCTTCTTGT 58.398 37.500 8.41 0.00 43.44 3.16
1435 1536 6.811253 AGTCTCTTCTTGTAGTAGTCACAG 57.189 41.667 0.00 0.00 0.00 3.66
1483 1611 3.680777 AGGACTCCTTTGGTTTGGAAA 57.319 42.857 0.00 0.00 31.23 3.13
1594 1723 4.960469 TCTACGGAGGAATTGTTACCATCT 59.040 41.667 0.00 0.00 0.00 2.90
1604 1733 6.350445 GGAATTGTTACCATCTTGCACATCTT 60.350 38.462 0.00 0.00 0.00 2.40
1612 1741 5.183904 ACCATCTTGCACATCTTAGGAAAAC 59.816 40.000 0.00 0.00 0.00 2.43
1635 1764 5.882557 ACAAACATTAGCCTAGACTCAATGG 59.117 40.000 0.00 0.00 32.20 3.16
1807 1981 7.545265 ACCGAACATGAAATATTTCCAACAATG 59.455 33.333 22.42 19.62 36.36 2.82
1878 2052 2.484417 CCACTTCGGCTGCAAGATAGAT 60.484 50.000 0.50 0.00 34.07 1.98
1921 2095 0.255890 TAAGGATGGTGCTCCCTTGC 59.744 55.000 1.59 0.00 40.26 4.01
1941 2115 3.266636 GCTCTCTCTTAGCCAGGAAAAC 58.733 50.000 0.00 0.00 33.73 2.43
2030 2204 0.250295 CTGGTCTTGCGAAACTGGGA 60.250 55.000 0.00 0.00 0.00 4.37
2040 2214 6.266786 TCTTGCGAAACTGGGATATGAGTATA 59.733 38.462 0.00 0.00 0.00 1.47
2086 2260 0.110192 CTCGCTCGCTTTGGTTTTCC 60.110 55.000 0.00 0.00 41.14 3.13
2142 2316 5.939883 GCCTGCAATATTCACAGTGGATATA 59.060 40.000 13.97 4.53 0.00 0.86
2199 2373 0.542938 TGACAGAGACTCCCAGGTGG 60.543 60.000 0.00 0.00 0.00 4.61
2333 2507 4.707030 TTCAGCTGCAATGTTAGAATGG 57.293 40.909 9.47 0.00 0.00 3.16
2341 2515 5.577835 TGCAATGTTAGAATGGCGTATTTC 58.422 37.500 0.00 0.00 0.00 2.17
2412 2586 4.968287 GCAATCTAGCTGCAAATGGAACAG 60.968 45.833 1.02 0.00 40.25 3.16
2471 2645 0.185175 ACGGGAAAGGGCTCAAACTT 59.815 50.000 0.00 0.00 0.00 2.66
2475 2649 1.613925 GGAAAGGGCTCAAACTTGGAC 59.386 52.381 0.00 0.00 0.00 4.02
2512 2686 3.995048 GGGTATGCGCTTTATAGAGAACC 59.005 47.826 9.73 3.94 0.00 3.62
2517 2691 2.128035 CGCTTTATAGAGAACCCGCAG 58.872 52.381 0.00 0.00 0.00 5.18
2543 2717 9.691362 GAAAATTAGCCAGTCAAAATGTTTCTA 57.309 29.630 0.00 0.00 0.00 2.10
2564 2738 2.736144 TATGACTGGGAACACGTGAC 57.264 50.000 25.01 15.20 35.60 3.67
2566 2740 0.537653 TGACTGGGAACACGTGACAA 59.462 50.000 25.01 4.54 35.60 3.18
2569 2743 1.217882 CTGGGAACACGTGACAAGTC 58.782 55.000 25.01 10.53 35.60 3.01
2570 2744 0.179067 TGGGAACACGTGACAAGTCC 60.179 55.000 25.01 18.17 33.40 3.85
2750 2930 8.412608 AGATCATCTAAAACTTACACATGTCG 57.587 34.615 0.00 0.00 0.00 4.35
2752 2932 7.812309 TCATCTAAAACTTACACATGTCGAG 57.188 36.000 0.00 0.00 0.00 4.04
2781 2966 0.323451 CCTGGTAGGGGTTCCAAAGC 60.323 60.000 0.00 0.00 33.06 3.51
2798 2983 5.010012 TCCAAAGCAGGAGAAAAACTGATTC 59.990 40.000 0.00 0.00 41.90 2.52
2833 3018 4.259356 GTGTTACAAGGGGATTGACTACC 58.741 47.826 0.00 0.00 41.83 3.18
2893 3078 6.016860 CCCACTAACAAGGTAACCTTTACAAC 60.017 42.308 0.00 0.00 41.69 3.32
2898 3083 9.498176 CTAACAAGGTAACCTTTACAACTACAT 57.502 33.333 0.00 0.00 41.69 2.29
2916 3101 8.988934 CAACTACATAACTTAGAAGCTTGTCAA 58.011 33.333 2.10 0.00 0.00 3.18
2927 3112 3.855689 AGCTTGTCAAATTTCATCCGG 57.144 42.857 0.00 0.00 0.00 5.14
3054 3240 6.096141 TGGTAACTGATTCTTGCTTTTCAACA 59.904 34.615 0.00 0.00 37.61 3.33
3078 3264 2.492088 CCAAAAGGGAGGGTTCGAATTC 59.508 50.000 0.00 0.00 40.01 2.17
3206 3392 3.222603 AGAACACATGGGAAAGGTGAAC 58.777 45.455 0.00 0.00 43.35 3.18
3287 3473 8.748179 ATGGAGATTCTAATTCCTATCCTGAA 57.252 34.615 0.00 0.00 32.12 3.02
3400 3587 8.808092 GTTAGTCTCTGTAGGCCTATGATAAAT 58.192 37.037 17.38 10.12 0.00 1.40
3411 3598 7.609056 AGGCCTATGATAAATTTTGATCATGC 58.391 34.615 19.89 16.31 41.72 4.06
3450 3637 2.172717 CGGATGTAGGATCTGGGGTTTT 59.827 50.000 0.00 0.00 0.00 2.43
3451 3638 3.371595 CGGATGTAGGATCTGGGGTTTTT 60.372 47.826 0.00 0.00 0.00 1.94
3743 3932 2.297315 CCTCTGATACTTGGCTGCGATA 59.703 50.000 0.00 0.00 0.00 2.92
3772 3961 0.179032 TGAGCGCTGAAACCAAGGAA 60.179 50.000 18.48 0.00 0.00 3.36
3780 3969 4.488879 GCTGAAACCAAGGAAATCATCAC 58.511 43.478 0.00 0.00 0.00 3.06
3925 4114 4.393062 CGTAAAGTGCAACAAGATGGAGAT 59.607 41.667 0.00 0.00 41.43 2.75
4228 4417 6.988580 CACTTTGTCTAATCATATGAGCCTCA 59.011 38.462 11.78 0.00 0.00 3.86
4289 4478 3.296854 ACTGTTCTTCAACCCCCTTTTC 58.703 45.455 0.00 0.00 0.00 2.29
4296 4485 1.530655 AACCCCCTTTTCCTGCGTG 60.531 57.895 0.00 0.00 0.00 5.34
4354 4543 2.270352 TGCAAGGAAACCTGACGAAT 57.730 45.000 0.00 0.00 32.13 3.34
4551 4750 5.065602 CCATGTCACATGTGTCCAGATTTAG 59.934 44.000 24.63 9.78 0.00 1.85
4777 4976 0.114954 TGGGCTCATTTTGCTCCCTT 59.885 50.000 0.00 0.00 37.83 3.95
5065 5264 2.617274 GGACGGCACCAGAGTTTGC 61.617 63.158 0.00 0.00 38.06 3.68
5089 5288 1.935327 GACTGACTAAGCGAGCCGGT 61.935 60.000 1.90 0.00 40.00 5.28
5148 5347 1.867919 CGGGCGGGCACATTTTACAA 61.868 55.000 3.27 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.803117 CGTCTCCTCTAGCGACAACA 59.197 55.000 0.00 0.00 0.00 3.33
37 41 3.708220 CTCGGTCGCAGCTCCTTCC 62.708 68.421 0.00 0.00 0.00 3.46
41 45 4.200283 CTCCTCGGTCGCAGCTCC 62.200 72.222 0.00 0.00 0.00 4.70
70 75 2.125552 CGTTGCCATCGCTCTCCA 60.126 61.111 0.00 0.00 35.36 3.86
84 89 0.744414 CCGTGGATCTTGATGCCGTT 60.744 55.000 0.00 0.00 0.00 4.44
101 106 1.456196 TAGCGGCTCTGGATCTTCCG 61.456 60.000 5.39 0.00 40.17 4.30
134 139 2.815589 GCCCAAGTTGTGTTCTCCTCAT 60.816 50.000 1.45 0.00 0.00 2.90
135 140 1.476833 GCCCAAGTTGTGTTCTCCTCA 60.477 52.381 1.45 0.00 0.00 3.86
136 141 1.239347 GCCCAAGTTGTGTTCTCCTC 58.761 55.000 1.45 0.00 0.00 3.71
200 206 3.200593 CATCCACAGCTCTGCGCC 61.201 66.667 4.18 0.00 40.39 6.53
206 212 0.737715 GACGTCCACATCCACAGCTC 60.738 60.000 3.51 0.00 0.00 4.09
254 260 0.035056 CCACCCATTCACCTGGTCTC 60.035 60.000 0.00 0.00 34.23 3.36
257 263 1.065410 TGACCACCCATTCACCTGGT 61.065 55.000 0.00 0.00 39.84 4.00
271 277 1.675310 CATTGAAGCGGGCTGACCA 60.675 57.895 0.00 0.00 40.22 4.02
291 297 4.431416 AACCAACTCTGACCATTGTGTA 57.569 40.909 0.00 0.00 0.00 2.90
396 435 0.613260 GGCCCATCCAAAACCCTTTC 59.387 55.000 0.00 0.00 34.01 2.62
397 436 0.104725 TGGCCCATCCAAAACCCTTT 60.105 50.000 0.00 0.00 43.21 3.11
398 437 0.545071 CTGGCCCATCCAAAACCCTT 60.545 55.000 0.00 0.00 46.01 3.95
409 448 1.611419 CCTGACACATCTGGCCCAT 59.389 57.895 0.00 0.00 37.16 4.00
429 468 4.785453 CAGAGGGGGCTTCGTGGC 62.785 72.222 0.00 0.00 40.96 5.01
434 474 0.392595 CGTAAACCAGAGGGGGCTTC 60.393 60.000 0.00 0.00 42.91 3.86
451 501 1.285023 CGGACGACTGTTTCCTCGT 59.715 57.895 7.54 0.00 45.62 4.18
454 504 1.664306 GTCCGGACGACTGTTTCCT 59.336 57.895 20.85 0.00 38.57 3.36
456 506 0.666577 CAGGTCCGGACGACTGTTTC 60.667 60.000 27.68 11.57 41.64 2.78
463 513 2.911484 CGTGAACAGGTCCGGACGA 61.911 63.158 27.68 4.83 0.00 4.20
475 525 3.186047 CCGCATCCGTCCGTGAAC 61.186 66.667 0.00 0.00 0.00 3.18
539 594 5.336690 CCAACATTGACCCTTAAACCATCTG 60.337 44.000 0.00 0.00 0.00 2.90
540 595 4.772100 CCAACATTGACCCTTAAACCATCT 59.228 41.667 0.00 0.00 0.00 2.90
571 626 8.935614 ACTTAGGAGGCAGTTAAAATACTTTT 57.064 30.769 0.00 0.00 36.67 2.27
574 629 6.884836 CCAACTTAGGAGGCAGTTAAAATACT 59.115 38.462 0.00 0.00 31.78 2.12
585 640 1.145571 AACCACCAACTTAGGAGGCA 58.854 50.000 0.00 0.00 42.50 4.75
586 641 3.428413 TTAACCACCAACTTAGGAGGC 57.572 47.619 0.00 0.00 42.50 4.70
587 642 4.981812 AGTTTAACCACCAACTTAGGAGG 58.018 43.478 0.00 0.00 44.11 4.30
592 647 4.101430 ACGAGGAGTTTAACCACCAACTTA 59.899 41.667 10.45 0.00 33.22 2.24
597 652 2.322658 AGACGAGGAGTTTAACCACCA 58.677 47.619 10.45 0.00 0.00 4.17
678 734 1.535015 CGAGAGAAATGCGGAGAGACC 60.535 57.143 0.00 0.00 0.00 3.85
737 793 0.322456 CGGGTGAGCCATCCAGAAAA 60.322 55.000 0.08 0.00 33.50 2.29
756 812 0.746659 AAACAGGTTTGGACTGCTGC 59.253 50.000 0.00 0.00 39.55 5.25
770 826 6.564709 TTGAAATGGTCATCTGAGAAACAG 57.435 37.500 0.00 0.00 46.97 3.16
801 857 1.281960 GCAGCTGTGTGCAGAACTG 59.718 57.895 16.64 5.67 45.28 3.16
898 954 3.112205 ATCTCCACGCATCCTGGGC 62.112 63.158 0.00 0.00 33.10 5.36
973 1032 0.107459 GATCCCTTCACTGTCCCTGC 60.107 60.000 0.00 0.00 0.00 4.85
1017 1076 1.379176 GAAGAAGGGGAGCAAGGGC 60.379 63.158 0.00 0.00 41.61 5.19
1068 1127 1.661341 CAAGGAGATTCTTCTGGGCG 58.339 55.000 0.00 0.00 30.30 6.13
1134 1193 4.811557 AGTTACAAGCAGAACTGACTGAAC 59.188 41.667 5.97 7.84 39.94 3.18
1146 1205 5.801947 GCATTTGTATGGAAGTTACAAGCAG 59.198 40.000 0.00 0.00 39.84 4.24
1149 1208 5.801947 GCAGCATTTGTATGGAAGTTACAAG 59.198 40.000 0.00 0.00 39.84 3.16
1194 1264 1.078426 CCACACGGACCAGATTCCC 60.078 63.158 0.00 0.00 31.03 3.97
1231 1301 1.547372 GCCAGTTACGAGGGTTAGTCA 59.453 52.381 0.00 0.00 0.00 3.41
1233 1303 0.529378 CGCCAGTTACGAGGGTTAGT 59.471 55.000 0.00 0.00 0.00 2.24
1234 1304 0.813184 TCGCCAGTTACGAGGGTTAG 59.187 55.000 0.00 0.00 33.96 2.34
1235 1305 1.067635 GTTCGCCAGTTACGAGGGTTA 60.068 52.381 0.00 0.00 41.18 2.85
1236 1306 0.320160 GTTCGCCAGTTACGAGGGTT 60.320 55.000 0.00 0.00 41.18 4.11
1237 1307 1.183676 AGTTCGCCAGTTACGAGGGT 61.184 55.000 0.00 0.00 41.18 4.34
1238 1308 0.037605 AAGTTCGCCAGTTACGAGGG 60.038 55.000 0.00 0.00 41.18 4.30
1240 1310 2.349297 AGAAGTTCGCCAGTTACGAG 57.651 50.000 0.00 0.00 41.18 4.18
1241 1311 2.806608 AAGAAGTTCGCCAGTTACGA 57.193 45.000 0.00 0.00 37.86 3.43
1242 1312 4.682860 TCTTTAAGAAGTTCGCCAGTTACG 59.317 41.667 0.00 0.00 34.41 3.18
1243 1313 6.147328 ACATCTTTAAGAAGTTCGCCAGTTAC 59.853 38.462 0.00 0.00 34.41 2.50
1256 1326 9.474920 CAACTAAAAATGCCACATCTTTAAGAA 57.525 29.630 0.00 0.00 0.00 2.52
1258 1328 9.643693 ATCAACTAAAAATGCCACATCTTTAAG 57.356 29.630 0.00 0.00 0.00 1.85
1259 1329 9.421806 CATCAACTAAAAATGCCACATCTTTAA 57.578 29.630 0.00 0.00 0.00 1.52
1260 1330 8.801299 TCATCAACTAAAAATGCCACATCTTTA 58.199 29.630 0.00 0.00 0.00 1.85
1261 1331 7.669427 TCATCAACTAAAAATGCCACATCTTT 58.331 30.769 0.00 0.00 0.00 2.52
1262 1332 7.230849 TCATCAACTAAAAATGCCACATCTT 57.769 32.000 0.00 0.00 0.00 2.40
1265 1335 6.400568 CCTTCATCAACTAAAAATGCCACAT 58.599 36.000 0.00 0.00 0.00 3.21
1266 1336 5.279406 CCCTTCATCAACTAAAAATGCCACA 60.279 40.000 0.00 0.00 0.00 4.17
1308 1406 9.872757 GTTGTAAAACGAGAATATCTTGTGAAA 57.127 29.630 1.13 0.00 40.12 2.69
1384 1484 0.179225 CGAAAATGTTCCGTGGCGAG 60.179 55.000 0.00 0.00 0.00 5.03
1391 1491 5.212194 ACTTGATCAAACGAAAATGTTCCG 58.788 37.500 9.88 0.00 0.00 4.30
1421 1522 7.331934 GCAGATCATTTTCTGTGACTACTACAA 59.668 37.037 0.00 0.00 44.10 2.41
1424 1525 7.123397 AGAGCAGATCATTTTCTGTGACTACTA 59.877 37.037 0.00 0.00 44.10 1.82
1435 1536 4.035441 GCAAGAGGAGAGCAGATCATTTTC 59.965 45.833 0.00 0.00 0.00 2.29
1451 1552 2.192263 AGGAGTCCTAAAGGCAAGAGG 58.808 52.381 10.94 0.00 34.44 3.69
1594 1723 6.214191 TGTTTGTTTTCCTAAGATGTGCAA 57.786 33.333 0.00 0.00 0.00 4.08
1604 1733 7.686434 AGTCTAGGCTAATGTTTGTTTTCCTA 58.314 34.615 0.00 0.00 0.00 2.94
1612 1741 6.115446 TCCATTGAGTCTAGGCTAATGTTTG 58.885 40.000 17.62 8.79 0.00 2.93
1652 1781 8.641498 AGAAAAATAGATGTCTGTTGGTTCAT 57.359 30.769 13.59 0.00 30.91 2.57
1715 1846 9.832445 TCATAGGAATATGAAACTTGTAGGAAC 57.168 33.333 0.00 0.00 33.89 3.62
1878 2052 6.895782 ACCTATTTTTCGGATTATCACCTCA 58.104 36.000 0.00 0.00 0.00 3.86
1921 2095 3.261897 TGGTTTTCCTGGCTAAGAGAGAG 59.738 47.826 0.00 0.00 41.38 3.20
1941 2115 0.249953 TGCAGCAATGCAAGGTTTGG 60.250 50.000 8.35 0.00 42.40 3.28
2074 2248 2.171659 TGAAAAGGGGGAAAACCAAAGC 59.828 45.455 0.00 0.00 42.91 3.51
2086 2260 5.535753 AAACATGAAGAGTTGAAAAGGGG 57.464 39.130 0.00 0.00 0.00 4.79
2142 2316 4.798387 GTCGTCTGCAGTTTCAAAACAAAT 59.202 37.500 14.67 0.00 41.30 2.32
2288 2462 3.762779 GCTTATGCTGGTTTCACATGAC 58.237 45.455 0.00 0.00 36.03 3.06
2333 2507 4.330620 TGAACGAAACCTATGGAAATACGC 59.669 41.667 0.00 0.00 0.00 4.42
2341 2515 2.955614 ACGACTGAACGAAACCTATGG 58.044 47.619 0.00 0.00 37.03 2.74
2471 2645 2.004808 CTGCATCGCCGTAGAGTCCA 62.005 60.000 0.00 0.00 0.00 4.02
2475 2649 1.452953 TACCCTGCATCGCCGTAGAG 61.453 60.000 0.00 0.00 0.00 2.43
2512 2686 2.083774 TGACTGGCTAATTTTCTGCGG 58.916 47.619 0.00 0.00 0.00 5.69
2517 2691 8.593492 AGAAACATTTTGACTGGCTAATTTTC 57.407 30.769 0.00 0.00 0.00 2.29
2543 2717 3.007506 TGTCACGTGTTCCCAGTCATATT 59.992 43.478 16.51 0.00 0.00 1.28
2750 2930 3.621558 CCCTACCAGGAAAACCATTCTC 58.378 50.000 0.00 0.00 37.67 2.87
2752 2932 2.042569 ACCCCTACCAGGAAAACCATTC 59.957 50.000 0.00 0.00 37.67 2.67
2798 2983 7.013846 TCCCCTTGTAACACAACAATTTAGAAG 59.986 37.037 0.00 0.00 38.61 2.85
2833 3018 5.207768 GTTGTTGCAGTTGTCATACTTCAG 58.792 41.667 0.00 0.00 0.00 3.02
3054 3240 0.400594 CGAACCCTCCCTTTTGGTCT 59.599 55.000 0.00 0.00 38.10 3.85
3206 3392 6.884280 AAAGTTCTCCAGGATGTAAACTTG 57.116 37.500 15.12 0.00 38.94 3.16
3295 3481 0.037139 GTCATGCTGCCCAATTTGCA 60.037 50.000 0.00 0.00 39.83 4.08
3400 3587 2.034432 ACACACTTGCGCATGATCAAAA 59.966 40.909 27.85 1.81 0.00 2.44
3410 3597 0.790814 GTCTTCCTACACACTTGCGC 59.209 55.000 0.00 0.00 0.00 6.09
3411 3598 1.060713 CGTCTTCCTACACACTTGCG 58.939 55.000 0.00 0.00 0.00 4.85
3758 3947 4.488879 GTGATGATTTCCTTGGTTTCAGC 58.511 43.478 0.00 0.00 0.00 4.26
3772 3961 7.489160 CAATGACATTCTGATTGGTGATGATT 58.511 34.615 0.00 0.00 0.00 2.57
3780 3969 4.713824 ACTGCAATGACATTCTGATTGG 57.286 40.909 0.00 0.00 0.00 3.16
3866 4055 5.741388 AGTTTGTCTAATGATGAATCGGC 57.259 39.130 0.00 0.00 0.00 5.54
3904 4093 5.809001 AGATCTCCATCTTGTTGCACTTTA 58.191 37.500 0.00 0.00 35.67 1.85
3980 4169 7.346471 ACATGGTACTATGATTTTTGCCTACT 58.654 34.615 24.30 0.00 0.00 2.57
4044 4233 2.009681 CCCAAACCTAAGCCCAAGTT 57.990 50.000 0.00 0.00 0.00 2.66
4279 4468 2.115266 CACGCAGGAAAAGGGGGT 59.885 61.111 0.00 0.00 0.00 4.95
4334 4523 2.270352 TTCGTCAGGTTTCCTTGCAT 57.730 45.000 0.00 0.00 0.00 3.96
4354 4543 4.784177 TGCAAGCATGAGAATCCATCTTA 58.216 39.130 0.00 0.00 38.96 2.10
4633 4832 6.190954 GTTTCACTGAAACCTGTAAGTTGT 57.809 37.500 19.98 0.00 44.04 3.32
4716 4915 2.796304 CGTAGGTACGTTCGCCAATTA 58.204 47.619 0.00 0.00 44.13 1.40
4717 4916 1.632422 CGTAGGTACGTTCGCCAATT 58.368 50.000 0.00 0.00 44.13 2.32
5049 5248 0.751643 AAAGCAAACTCTGGTGCCGT 60.752 50.000 0.00 0.00 41.88 5.68
5065 5264 2.413453 GGCTCGCTTAGTCAGTCAAAAG 59.587 50.000 0.00 0.00 0.00 2.27
5089 5288 2.170187 AGGGCATCACAAAGCAACAAAA 59.830 40.909 0.00 0.00 0.00 2.44
5140 5339 5.215160 CGAAAGCTCAAGCAGTTGTAAAAT 58.785 37.500 4.59 0.00 45.16 1.82
5148 5347 3.660621 GCCGAAAGCTCAAGCAGT 58.339 55.556 4.59 0.00 45.16 4.40


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

AutoCloner maintained by Alex Coulton.