Multiple sequence alignment - TraesCS7B01G315100

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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 TraesCS7B01G315100 chr7B 100.000 1622 0 0 896 2517 562743836 562745457 0.000000e+00 2996
1 TraesCS7B01G315100 chr7B 100.000 447 0 0 1 447 562742941 562743387 0.000000e+00 826
2 TraesCS7B01G315100 chr7D 88.169 1589 89 52 981 2517 526239904 526241445 0.000000e+00 1801
3 TraesCS7B01G315100 chr7D 90.850 459 14 9 1 444 526189078 526189523 7.750000e-165 590
4 TraesCS7B01G315100 chr7A 86.075 991 81 34 896 1837 606559648 606560630 0.000000e+00 1013
5 TraesCS7B01G315100 chr7A 88.514 444 25 10 10 445 606558720 606559145 4.800000e-142 514
6 TraesCS7B01G315100 chr7A 82.789 459 30 17 2099 2517 606561535 606561984 5.120000e-97 364
7 TraesCS7B01G315100 chr7A 93.651 126 7 1 1903 2027 606560653 606560778 1.190000e-43 187
8 TraesCS7B01G315100 chr5D 84.938 644 51 26 1856 2456 388345351 388344711 5.950000e-171 610


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 TraesCS7B01G315100 chr7B 562742941 562745457 2516 False 1911.0 2996 100.00000 1 2517 2 chr7B.!!$F1 2516
1 TraesCS7B01G315100 chr7D 526239904 526241445 1541 False 1801.0 1801 88.16900 981 2517 1 chr7D.!!$F2 1536
2 TraesCS7B01G315100 chr7A 606558720 606561984 3264 False 519.5 1013 87.75725 10 2517 4 chr7A.!!$F1 2507
3 TraesCS7B01G315100 chr5D 388344711 388345351 640 True 610.0 610 84.93800 1856 2456 1 chr5D.!!$R1 600

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
72 74 0.106519 CCCCATTAAGGTGGAGGCAG 60.107 60.0 0.00 0.00 42.02 4.85 F
1198 1293 0.103208 ATGGAGGTGATCGAACGAGC 59.897 55.0 5.52 5.52 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 1482 0.028637 GTACTAGTACGCGAGGTGCC 59.971 60.0 15.93 0.00 42.08 5.01 R
2326 3184 0.888619 CAAGTGCTCGACCAGGTCTA 59.111 55.0 17.95 5.79 0.00 2.59 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
48 50 9.939802 TGATGAAATATCATACAGAGGAAGATG 57.060 33.333 0.00 0.00 46.30 2.90
65 67 4.510167 AGATGTCTTCCCCATTAAGGTG 57.490 45.455 0.00 0.00 34.66 4.00
66 68 3.203040 AGATGTCTTCCCCATTAAGGTGG 59.797 47.826 0.00 0.00 39.05 4.61
68 70 2.576191 TGTCTTCCCCATTAAGGTGGAG 59.424 50.000 0.00 0.00 42.02 3.86
69 71 2.092375 GTCTTCCCCATTAAGGTGGAGG 60.092 54.545 0.00 0.00 42.02 4.30
70 72 0.629058 TTCCCCATTAAGGTGGAGGC 59.371 55.000 0.00 0.00 42.02 4.70
71 73 0.551377 TCCCCATTAAGGTGGAGGCA 60.551 55.000 0.00 0.00 42.02 4.75
72 74 0.106519 CCCCATTAAGGTGGAGGCAG 60.107 60.000 0.00 0.00 42.02 4.85
73 75 0.918983 CCCATTAAGGTGGAGGCAGA 59.081 55.000 0.00 0.00 42.02 4.26
74 76 1.408822 CCCATTAAGGTGGAGGCAGAC 60.409 57.143 0.00 0.00 42.02 3.51
75 77 1.656652 CATTAAGGTGGAGGCAGACG 58.343 55.000 0.00 0.00 0.00 4.18
82 84 0.951040 GTGGAGGCAGACGAACCTTG 60.951 60.000 0.00 0.00 36.05 3.61
85 87 2.032681 GGCAGACGAACCTTGGCT 59.967 61.111 0.00 0.00 0.00 4.75
157 159 1.377725 CGGATTGGGCTTCTGCTGT 60.378 57.895 0.00 0.00 39.59 4.40
166 168 1.512996 GCTTCTGCTGTTGCTGCTGA 61.513 55.000 0.00 4.15 40.48 4.26
167 169 0.949397 CTTCTGCTGTTGCTGCTGAA 59.051 50.000 15.20 15.20 41.14 3.02
168 170 1.335810 CTTCTGCTGTTGCTGCTGAAA 59.664 47.619 16.18 0.00 42.07 2.69
172 174 0.383231 GCTGTTGCTGCTGAAACTGT 59.617 50.000 18.45 0.00 34.36 3.55
280 285 1.737816 CTGCTGCTGCTGTTGGTTT 59.262 52.632 17.00 0.00 40.48 3.27
288 293 0.459489 TGCTGTTGGTTTGAGTTGGC 59.541 50.000 0.00 0.00 0.00 4.52
368 373 2.676632 TACATACAAATCCACGGCGT 57.323 45.000 6.77 6.77 0.00 5.68
949 1011 0.602106 AGAGACCACGAACGAGACGA 60.602 55.000 0.14 0.00 34.70 4.20
978 1040 4.803426 GCGCTGGTGTCCTCCTCG 62.803 72.222 0.00 0.00 0.00 4.63
979 1041 3.374402 CGCTGGTGTCCTCCTCGT 61.374 66.667 0.00 0.00 0.00 4.18
985 1048 2.031616 TGTCCTCCTCGTCGTCGT 59.968 61.111 1.33 0.00 38.33 4.34
1130 1193 0.386838 GGTACGTACCCCCTTCATCG 59.613 60.000 30.84 0.00 40.53 3.84
1133 1196 2.108362 GTACCCCCTTCATCGGCG 59.892 66.667 0.00 0.00 0.00 6.46
1134 1197 3.857038 TACCCCCTTCATCGGCGC 61.857 66.667 0.00 0.00 0.00 6.53
1141 1204 1.941734 CTTCATCGGCGCGAGAGAC 60.942 63.158 12.10 0.00 39.91 3.36
1144 1207 4.194720 ATCGGCGCGAGAGACCAC 62.195 66.667 12.10 0.00 39.91 4.16
1148 1211 4.194720 GCGCGAGAGACCACCGAT 62.195 66.667 12.10 0.00 0.00 4.18
1168 1258 3.574354 TGGCACATCACAGGCATATAA 57.426 42.857 0.00 0.00 35.21 0.98
1170 1260 4.074259 TGGCACATCACAGGCATATAATC 58.926 43.478 0.00 0.00 35.21 1.75
1193 1288 3.452264 AGTTGATGATGGAGGTGATCGAA 59.548 43.478 0.00 0.00 0.00 3.71
1195 1290 2.223805 TGATGATGGAGGTGATCGAACG 60.224 50.000 0.00 0.00 0.00 3.95
1196 1291 1.470051 TGATGGAGGTGATCGAACGA 58.530 50.000 0.00 0.00 0.00 3.85
1197 1292 1.405463 TGATGGAGGTGATCGAACGAG 59.595 52.381 2.94 0.00 0.00 4.18
1198 1293 0.103208 ATGGAGGTGATCGAACGAGC 59.897 55.000 5.52 5.52 0.00 5.03
1376 1471 1.041437 AGCCGCCTCTACTGGTAATC 58.959 55.000 0.00 0.00 0.00 1.75
1378 1473 1.138266 GCCGCCTCTACTGGTAATCAA 59.862 52.381 0.00 0.00 0.00 2.57
1381 1476 3.069586 CCGCCTCTACTGGTAATCAATCA 59.930 47.826 0.00 0.00 0.00 2.57
1382 1477 4.302455 CGCCTCTACTGGTAATCAATCAG 58.698 47.826 0.00 0.00 34.91 2.90
1384 1479 4.443457 GCCTCTACTGGTAATCAATCAGCA 60.443 45.833 0.00 0.00 32.19 4.41
1386 1481 5.525378 CCTCTACTGGTAATCAATCAGCAAC 59.475 44.000 0.00 0.00 32.19 4.17
1387 1482 5.109210 TCTACTGGTAATCAATCAGCAACG 58.891 41.667 0.00 0.00 32.19 4.10
1388 1483 3.009723 ACTGGTAATCAATCAGCAACGG 58.990 45.455 0.00 0.00 32.19 4.44
1389 1484 1.742831 TGGTAATCAATCAGCAACGGC 59.257 47.619 0.00 0.00 41.61 5.68
1390 1485 1.742831 GGTAATCAATCAGCAACGGCA 59.257 47.619 0.00 0.00 44.61 5.69
1393 1488 0.322816 ATCAATCAGCAACGGCACCT 60.323 50.000 0.00 0.00 44.61 4.00
1400 1502 3.475774 CAACGGCACCTCGCGTAC 61.476 66.667 5.77 0.00 43.84 3.67
1407 1509 0.729116 GCACCTCGCGTACTAGTACA 59.271 55.000 28.03 11.64 35.87 2.90
1408 1510 1.131126 GCACCTCGCGTACTAGTACAA 59.869 52.381 28.03 14.44 35.87 2.41
1410 1512 1.740025 ACCTCGCGTACTAGTACAACC 59.260 52.381 28.03 16.33 35.87 3.77
1413 1515 0.726827 CGCGTACTAGTACAACCGGA 59.273 55.000 28.03 0.00 35.87 5.14
1415 1517 1.064654 GCGTACTAGTACAACCGGAGG 59.935 57.143 28.03 13.15 45.10 4.30
1417 1519 1.064654 GTACTAGTACAACCGGAGGCG 59.935 57.143 25.02 0.00 43.53 5.52
1418 1520 3.258380 GTACTAGTACAACCGGAGGCGA 61.258 54.545 25.02 0.00 43.53 5.54
1419 1521 5.320212 GTACTAGTACAACCGGAGGCGAC 62.320 56.522 25.02 1.49 43.53 5.19
1433 1535 3.182967 GAGGCGACTAACTGATGAGTTG 58.817 50.000 7.92 0.85 42.66 3.16
1437 1539 4.511457 CGACTAACTGATGAGTTGCATG 57.489 45.455 7.92 0.00 42.66 4.06
1440 1542 5.750547 CGACTAACTGATGAGTTGCATGTAT 59.249 40.000 7.92 0.00 42.66 2.29
1542 1652 1.892819 CGAAGCTCTTGCCCAGGAGA 61.893 60.000 11.09 0.00 40.80 3.71
1545 1655 0.998145 AGCTCTTGCCCAGGAGAAAT 59.002 50.000 11.09 0.00 40.80 2.17
1560 1670 2.744202 GAGAAATGACAGGCACGTTCAT 59.256 45.455 4.65 0.00 36.49 2.57
1590 1700 2.106338 TGGGACTGCATTTCTCACAAGA 59.894 45.455 0.00 0.00 0.00 3.02
1591 1701 2.746362 GGGACTGCATTTCTCACAAGAG 59.254 50.000 0.00 0.00 43.48 2.85
1592 1702 3.406764 GGACTGCATTTCTCACAAGAGT 58.593 45.455 0.00 0.00 42.66 3.24
1777 1898 4.118410 GACCATGAGCAACAGAGATACAG 58.882 47.826 0.00 0.00 0.00 2.74
1809 1934 5.841957 ATGAATGCCTTCAACTGATAACC 57.158 39.130 8.55 0.00 44.29 2.85
1852 1977 8.192774 TCAAATACAGCATCTTTCAATGGATTC 58.807 33.333 0.00 0.00 0.00 2.52
1899 2026 1.979855 TTCTAGCCAAGCTGTTGCAA 58.020 45.000 0.00 0.00 40.10 4.08
2031 2170 9.104965 TGCTTATAAATTGTACCACTACATGAC 57.895 33.333 0.00 0.00 32.70 3.06
2047 2816 3.118629 ACATGACAAGTACCGCAGATCAT 60.119 43.478 0.00 0.00 0.00 2.45
2085 2913 7.972832 CACAATACATTTTGCCACATACATGTA 59.027 33.333 8.27 8.27 39.39 2.29
2091 2919 4.551702 TTGCCACATACATGTAGTCAGT 57.448 40.909 11.91 4.69 39.39 3.41
2092 2920 5.669164 TTGCCACATACATGTAGTCAGTA 57.331 39.130 11.91 0.00 39.39 2.74
2093 2921 5.262588 TGCCACATACATGTAGTCAGTAG 57.737 43.478 11.91 2.39 39.39 2.57
2094 2922 4.953579 TGCCACATACATGTAGTCAGTAGA 59.046 41.667 11.91 0.00 39.39 2.59
2095 2923 5.598417 TGCCACATACATGTAGTCAGTAGAT 59.402 40.000 11.91 0.00 39.39 1.98
2096 2924 6.775629 TGCCACATACATGTAGTCAGTAGATA 59.224 38.462 11.91 0.00 39.39 1.98
2097 2925 7.085116 GCCACATACATGTAGTCAGTAGATAC 58.915 42.308 11.91 0.00 39.39 2.24
2125 2953 4.637276 ACACAACACCTTCATAACGATCA 58.363 39.130 0.00 0.00 0.00 2.92
2213 3042 0.250338 ACAAGAGGTCGAGGCAAACC 60.250 55.000 0.00 0.00 35.69 3.27
2231 3060 3.105959 ACCAGCCAATTAATCCAGCTT 57.894 42.857 4.55 0.00 0.00 3.74
2326 3184 1.352017 TGGATGTGCACTTGTGATCCT 59.648 47.619 25.28 0.56 34.74 3.24
2406 3266 0.036022 GCTTCCTTGCACCTCTGACT 59.964 55.000 0.00 0.00 0.00 3.41
2428 3289 6.166279 ACTTGATGATCGACTGTTACAACAT 58.834 36.000 0.00 0.00 38.41 2.71
2477 3346 3.469008 TGCTGTTGCACAAGTACTAGT 57.531 42.857 0.00 0.00 45.31 2.57
2478 3347 3.390135 TGCTGTTGCACAAGTACTAGTC 58.610 45.455 0.00 0.00 45.31 2.59
2480 3349 3.430218 GCTGTTGCACAAGTACTAGTCAG 59.570 47.826 0.00 0.00 39.41 3.51
2481 3350 4.796290 GCTGTTGCACAAGTACTAGTCAGA 60.796 45.833 0.00 0.00 39.41 3.27
2482 3351 5.270893 TGTTGCACAAGTACTAGTCAGAA 57.729 39.130 0.00 0.00 0.00 3.02
2483 3352 5.853936 TGTTGCACAAGTACTAGTCAGAAT 58.146 37.500 0.00 0.00 0.00 2.40
2485 3354 6.866770 TGTTGCACAAGTACTAGTCAGAATAC 59.133 38.462 0.00 0.00 0.00 1.89
2486 3355 6.584185 TGCACAAGTACTAGTCAGAATACA 57.416 37.500 0.00 0.00 0.00 2.29
2487 3356 6.621613 TGCACAAGTACTAGTCAGAATACAG 58.378 40.000 0.00 0.00 0.00 2.74
2503 3373 9.295825 TCAGAATACAGTTTAAATGTTGGACAT 57.704 29.630 2.78 0.00 41.31 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.608617 CTCTGTATGATATTTCATCAATTGCAC 57.391 33.333 1.58 0.00 41.73 4.57
48 50 2.092375 CCTCCACCTTAATGGGGAAGAC 60.092 54.545 3.14 0.00 43.79 3.01
61 63 2.584391 GGTTCGTCTGCCTCCACCT 61.584 63.158 0.00 0.00 0.00 4.00
62 64 2.047179 GGTTCGTCTGCCTCCACC 60.047 66.667 0.00 0.00 0.00 4.61
65 67 1.376037 CCAAGGTTCGTCTGCCTCC 60.376 63.158 0.00 0.00 33.24 4.30
66 68 2.035442 GCCAAGGTTCGTCTGCCTC 61.035 63.158 0.00 0.00 33.24 4.70
68 70 2.032681 AGCCAAGGTTCGTCTGCC 59.967 61.111 0.00 0.00 0.00 4.85
69 71 2.328099 CCAGCCAAGGTTCGTCTGC 61.328 63.158 0.00 0.00 0.00 4.26
70 72 1.672356 CCCAGCCAAGGTTCGTCTG 60.672 63.158 0.00 0.00 0.00 3.51
71 73 2.750350 CCCAGCCAAGGTTCGTCT 59.250 61.111 0.00 0.00 0.00 4.18
72 74 3.056328 GCCCAGCCAAGGTTCGTC 61.056 66.667 0.00 0.00 0.00 4.20
127 129 1.211709 CAATCCGTTTGGGTTCGGC 59.788 57.895 0.00 0.00 45.44 5.54
136 138 0.251341 AGCAGAAGCCCAATCCGTTT 60.251 50.000 0.00 0.00 43.56 3.60
142 144 0.541296 AGCAACAGCAGAAGCCCAAT 60.541 50.000 0.00 0.00 43.56 3.16
157 159 0.746063 CCCAACAGTTTCAGCAGCAA 59.254 50.000 0.00 0.00 0.00 3.91
166 168 1.453015 TGCGCAGTCCCAACAGTTT 60.453 52.632 5.66 0.00 0.00 2.66
167 169 2.186826 GTGCGCAGTCCCAACAGTT 61.187 57.895 12.22 0.00 0.00 3.16
168 170 2.591715 GTGCGCAGTCCCAACAGT 60.592 61.111 12.22 0.00 0.00 3.55
172 174 4.243008 TTCGGTGCGCAGTCCCAA 62.243 61.111 12.22 0.56 0.00 4.12
261 266 2.359570 AAACCAACAGCAGCAGCAGC 62.360 55.000 3.17 0.46 45.49 5.25
262 267 0.596600 CAAACCAACAGCAGCAGCAG 60.597 55.000 3.17 0.00 45.49 4.24
263 268 1.036481 TCAAACCAACAGCAGCAGCA 61.036 50.000 3.17 0.00 45.49 4.41
264 269 0.318445 CTCAAACCAACAGCAGCAGC 60.318 55.000 0.00 0.00 42.56 5.25
265 270 1.027357 ACTCAAACCAACAGCAGCAG 58.973 50.000 0.00 0.00 0.00 4.24
266 271 1.134753 CAACTCAAACCAACAGCAGCA 59.865 47.619 0.00 0.00 0.00 4.41
267 272 1.536709 CCAACTCAAACCAACAGCAGC 60.537 52.381 0.00 0.00 0.00 5.25
268 273 1.536709 GCCAACTCAAACCAACAGCAG 60.537 52.381 0.00 0.00 0.00 4.24
269 274 0.459489 GCCAACTCAAACCAACAGCA 59.541 50.000 0.00 0.00 0.00 4.41
270 275 0.594796 CGCCAACTCAAACCAACAGC 60.595 55.000 0.00 0.00 0.00 4.40
271 276 0.738389 ACGCCAACTCAAACCAACAG 59.262 50.000 0.00 0.00 0.00 3.16
272 277 0.453793 CACGCCAACTCAAACCAACA 59.546 50.000 0.00 0.00 0.00 3.33
280 285 2.202946 TTCGTGCACGCCAACTCA 60.203 55.556 33.63 12.62 39.60 3.41
327 332 1.376424 CTGGTTCTGGATGCTGCGT 60.376 57.895 0.00 0.00 0.00 5.24
975 1037 3.458579 CGGCACAACGACGACGAG 61.459 66.667 15.32 8.51 42.66 4.18
1075 1138 2.289444 GGATGTTGGAGAAGTTGTCCGA 60.289 50.000 13.96 9.65 36.82 4.55
1076 1139 2.076863 GGATGTTGGAGAAGTTGTCCG 58.923 52.381 13.96 0.00 36.82 4.79
1077 1140 2.437413 GGGATGTTGGAGAAGTTGTCC 58.563 52.381 12.13 12.13 34.31 4.02
1133 1196 2.105128 CCATCGGTGGTCTCTCGC 59.895 66.667 6.53 0.00 40.83 5.03
1144 1207 2.475466 GCCTGTGATGTGCCATCGG 61.475 63.158 9.65 6.85 0.00 4.18
1147 1210 2.670019 ATATGCCTGTGATGTGCCAT 57.330 45.000 0.00 0.00 0.00 4.40
1148 1211 3.574354 TTATATGCCTGTGATGTGCCA 57.426 42.857 0.00 0.00 0.00 4.92
1162 1252 8.098912 TCACCTCCATCATCAACTGATTATATG 58.901 37.037 0.00 0.00 42.07 1.78
1165 1255 6.505048 TCACCTCCATCATCAACTGATTAT 57.495 37.500 0.00 0.00 42.07 1.28
1166 1256 5.955961 TCACCTCCATCATCAACTGATTA 57.044 39.130 0.00 0.00 42.07 1.75
1167 1257 4.849813 TCACCTCCATCATCAACTGATT 57.150 40.909 0.00 0.00 42.07 2.57
1168 1258 4.502777 CGATCACCTCCATCATCAACTGAT 60.503 45.833 0.00 0.00 45.78 2.90
1170 1260 3.129109 CGATCACCTCCATCATCAACTG 58.871 50.000 0.00 0.00 0.00 3.16
1193 1288 1.303888 TCGTCCCCTACAAGCTCGT 60.304 57.895 0.00 0.00 0.00 4.18
1195 1290 0.606604 TTGTCGTCCCCTACAAGCTC 59.393 55.000 0.00 0.00 32.11 4.09
1196 1291 0.608640 CTTGTCGTCCCCTACAAGCT 59.391 55.000 2.60 0.00 44.23 3.74
1197 1292 3.139029 CTTGTCGTCCCCTACAAGC 57.861 57.895 2.60 0.00 44.23 4.01
1309 1404 2.190578 GGGCCTCCGGACATTGAG 59.809 66.667 0.00 0.00 27.52 3.02
1376 1471 1.503542 GAGGTGCCGTTGCTGATTG 59.496 57.895 0.00 0.00 38.71 2.67
1378 1473 2.434884 CGAGGTGCCGTTGCTGAT 60.435 61.111 0.00 0.00 38.71 2.90
1384 1479 2.262471 CTAGTACGCGAGGTGCCGTT 62.262 60.000 15.93 0.00 42.08 4.44
1386 1481 1.431488 TACTAGTACGCGAGGTGCCG 61.431 60.000 15.93 0.00 42.08 5.69
1387 1482 0.028637 GTACTAGTACGCGAGGTGCC 59.971 60.000 15.93 0.00 42.08 5.01
1388 1483 0.729116 TGTACTAGTACGCGAGGTGC 59.271 55.000 24.36 7.87 38.85 5.01
1389 1484 2.476854 GGTTGTACTAGTACGCGAGGTG 60.477 54.545 24.36 0.77 38.85 4.00
1390 1485 1.740025 GGTTGTACTAGTACGCGAGGT 59.260 52.381 24.36 6.27 38.85 3.85
1393 1488 0.726827 CCGGTTGTACTAGTACGCGA 59.273 55.000 24.36 12.56 38.85 5.87
1397 1499 1.064654 CGCCTCCGGTTGTACTAGTAC 59.935 57.143 23.58 23.58 36.63 2.73
1399 1501 0.322816 TCGCCTCCGGTTGTACTAGT 60.323 55.000 0.00 0.00 34.56 2.57
1400 1502 0.100146 GTCGCCTCCGGTTGTACTAG 59.900 60.000 0.00 0.00 34.56 2.57
1407 1509 0.896940 TCAGTTAGTCGCCTCCGGTT 60.897 55.000 0.00 0.00 34.56 4.44
1408 1510 0.683504 ATCAGTTAGTCGCCTCCGGT 60.684 55.000 0.00 0.00 34.56 5.28
1410 1512 0.738975 TCATCAGTTAGTCGCCTCCG 59.261 55.000 0.00 0.00 0.00 4.63
1413 1515 2.675317 GCAACTCATCAGTTAGTCGCCT 60.675 50.000 0.00 0.00 41.24 5.52
1415 1517 2.337583 TGCAACTCATCAGTTAGTCGC 58.662 47.619 0.00 0.00 41.24 5.19
1417 1519 6.941802 CATACATGCAACTCATCAGTTAGTC 58.058 40.000 0.00 0.00 41.24 2.59
1418 1520 6.915544 CATACATGCAACTCATCAGTTAGT 57.084 37.500 0.00 0.00 41.24 2.24
1434 1536 5.750650 TGCACAGAATTAATCGCATACATG 58.249 37.500 0.00 0.00 0.00 3.21
1435 1537 5.561532 GCTGCACAGAATTAATCGCATACAT 60.562 40.000 0.81 0.00 0.00 2.29
1437 1539 4.214437 GCTGCACAGAATTAATCGCATAC 58.786 43.478 0.81 0.00 0.00 2.39
1440 1542 1.401552 GGCTGCACAGAATTAATCGCA 59.598 47.619 0.50 0.00 0.00 5.10
1442 1544 2.938451 TCAGGCTGCACAGAATTAATCG 59.062 45.455 10.34 0.00 0.00 3.34
1444 1546 3.689347 TGTCAGGCTGCACAGAATTAAT 58.311 40.909 10.34 0.00 0.00 1.40
1542 1652 1.541147 CCATGAACGTGCCTGTCATTT 59.459 47.619 0.00 0.00 0.00 2.32
1545 1655 1.965930 GCCATGAACGTGCCTGTCA 60.966 57.895 0.00 0.00 0.00 3.58
1560 1670 2.203480 GCAGTCCCAGTTTGGCCA 60.203 61.111 0.00 0.00 35.79 5.36
1566 1676 2.158623 TGTGAGAAATGCAGTCCCAGTT 60.159 45.455 0.00 0.00 0.00 3.16
1590 1700 1.024579 AATTTCCGCCGCGATTCACT 61.025 50.000 15.93 0.00 0.00 3.41
1591 1701 0.588980 GAATTTCCGCCGCGATTCAC 60.589 55.000 15.93 0.00 0.00 3.18
1592 1702 1.711060 GGAATTTCCGCCGCGATTCA 61.711 55.000 15.93 0.00 31.72 2.57
1725 1842 3.258872 TGCCAAAAATGTATTGCTCTGCT 59.741 39.130 0.00 0.00 0.00 4.24
1777 1898 4.689071 TGAAGGCATTCATTCATTCATGC 58.311 39.130 10.22 0.00 40.54 4.06
1829 1954 6.543465 TCGAATCCATTGAAAGATGCTGTATT 59.457 34.615 0.00 0.00 0.00 1.89
1852 1977 3.610242 CAGGAATCTTCAACTTCTCGTCG 59.390 47.826 0.00 0.00 0.00 5.12
1866 1993 3.840666 TGGCTAGAAACAGACAGGAATCT 59.159 43.478 0.00 0.00 0.00 2.40
1899 2026 3.509575 TCAGCAGGTTTGTTTCAACAGTT 59.490 39.130 0.00 0.00 40.50 3.16
2021 2157 2.923655 CTGCGGTACTTGTCATGTAGTG 59.076 50.000 0.00 0.00 0.00 2.74
2031 2170 3.055591 CAGCTATGATCTGCGGTACTTG 58.944 50.000 0.00 0.00 0.00 3.16
2047 2816 1.003003 TGTATTGTGTGCCTGCAGCTA 59.997 47.619 8.66 0.00 44.23 3.32
2085 2913 9.111613 GTGTTGTGTATCTAGTATCTACTGACT 57.888 37.037 0.06 0.00 37.10 3.41
2091 2919 9.642343 ATGAAGGTGTTGTGTATCTAGTATCTA 57.358 33.333 0.00 0.00 0.00 1.98
2092 2920 7.956328 TGAAGGTGTTGTGTATCTAGTATCT 57.044 36.000 0.00 0.00 0.00 1.98
2095 2923 8.186163 CGTTATGAAGGTGTTGTGTATCTAGTA 58.814 37.037 0.00 0.00 0.00 1.82
2096 2924 7.033791 CGTTATGAAGGTGTTGTGTATCTAGT 58.966 38.462 0.00 0.00 0.00 2.57
2097 2925 7.255569 TCGTTATGAAGGTGTTGTGTATCTAG 58.744 38.462 0.00 0.00 0.00 2.43
2102 2930 5.636121 GTGATCGTTATGAAGGTGTTGTGTA 59.364 40.000 0.00 0.00 0.00 2.90
2125 2953 8.581253 AACTAGCTAGCAAATAAAATGAAGGT 57.419 30.769 20.91 0.00 0.00 3.50
2213 3042 3.627577 ACGTAAGCTGGATTAATTGGCTG 59.372 43.478 10.13 3.52 45.62 4.85
2231 3060 5.961272 TGTCAGATAAATCTTGAGCACGTA 58.039 37.500 0.00 0.00 34.22 3.57
2326 3184 0.888619 CAAGTGCTCGACCAGGTCTA 59.111 55.000 17.95 5.79 0.00 2.59
2349 3207 0.944386 GAACTGAGCTGTTTCGGCAA 59.056 50.000 0.00 0.00 38.37 4.52
2350 3208 1.221466 CGAACTGAGCTGTTTCGGCA 61.221 55.000 11.40 0.00 38.37 5.69
2351 3209 0.944311 TCGAACTGAGCTGTTTCGGC 60.944 55.000 16.69 0.00 35.73 5.54
2406 3266 7.093992 TGTATGTTGTAACAGTCGATCATCAA 58.906 34.615 3.66 0.00 43.04 2.57
2475 3344 8.784043 GTCCAACATTTAAACTGTATTCTGACT 58.216 33.333 0.00 0.00 0.00 3.41
2476 3345 8.564574 TGTCCAACATTTAAACTGTATTCTGAC 58.435 33.333 0.00 0.00 0.00 3.51
2477 3346 8.684386 TGTCCAACATTTAAACTGTATTCTGA 57.316 30.769 0.00 0.00 0.00 3.27
2478 3347 9.912634 AATGTCCAACATTTAAACTGTATTCTG 57.087 29.630 0.00 0.00 45.80 3.02


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

AutoCloner maintained by Alex Coulton.