Multiple sequence alignment - TraesCS4D01G051200

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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 TraesCS4D01G051200 chr4D 100.000 2351 0 0 1 2351 27114016 27116366 0.000000e+00 4342.0
1 TraesCS4D01G051200 chr4D 94.421 717 33 4 1635 2350 231982987 231982277 0.000000e+00 1096.0
2 TraesCS4D01G051200 chr4B 88.274 1373 65 38 318 1635 39734952 39736283 0.000000e+00 1555.0
3 TraesCS4D01G051200 chr4A 86.275 1377 70 34 318 1635 575807897 575809213 0.000000e+00 1386.0
4 TraesCS4D01G051200 chr4A 86.517 89 11 1 1 88 575806890 575806978 1.920000e-16 97.1
5 TraesCS4D01G051200 chr4A 91.549 71 5 1 123 192 575807057 575807127 1.920000e-16 97.1
6 TraesCS4D01G051200 chr4A 94.340 53 2 1 270 321 575807220 575807272 1.940000e-11 80.5
7 TraesCS4D01G051200 chr7D 88.112 715 76 7 1637 2348 610713991 610713283 0.000000e+00 841.0
8 TraesCS4D01G051200 chr3A 88.022 718 75 9 1635 2348 684764232 684764942 0.000000e+00 839.0
9 TraesCS4D01G051200 chr6A 87.727 717 82 4 1635 2350 23217915 23217204 0.000000e+00 832.0
10 TraesCS4D01G051200 chr6A 87.744 718 77 10 1635 2348 21705080 21704370 0.000000e+00 828.0
11 TraesCS4D01G051200 chr7B 87.587 717 79 8 1635 2348 630559262 630558553 0.000000e+00 822.0
12 TraesCS4D01G051200 chr6D 87.623 711 81 5 1640 2348 201582907 201582202 0.000000e+00 819.0
13 TraesCS4D01G051200 chr5D 87.552 715 79 8 1637 2348 70886576 70885869 0.000000e+00 819.0
14 TraesCS4D01G051200 chrUn 87.413 715 81 7 1637 2348 245739042 245739750 0.000000e+00 813.0


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 TraesCS4D01G051200 chr4D 27114016 27116366 2350 False 4342.000 4342 100.00000 1 2351 1 chr4D.!!$F1 2350
1 TraesCS4D01G051200 chr4D 231982277 231982987 710 True 1096.000 1096 94.42100 1635 2350 1 chr4D.!!$R1 715
2 TraesCS4D01G051200 chr4B 39734952 39736283 1331 False 1555.000 1555 88.27400 318 1635 1 chr4B.!!$F1 1317
3 TraesCS4D01G051200 chr4A 575806890 575809213 2323 False 415.175 1386 89.67025 1 1635 4 chr4A.!!$F1 1634
4 TraesCS4D01G051200 chr7D 610713283 610713991 708 True 841.000 841 88.11200 1637 2348 1 chr7D.!!$R1 711
5 TraesCS4D01G051200 chr3A 684764232 684764942 710 False 839.000 839 88.02200 1635 2348 1 chr3A.!!$F1 713
6 TraesCS4D01G051200 chr6A 23217204 23217915 711 True 832.000 832 87.72700 1635 2350 1 chr6A.!!$R2 715
7 TraesCS4D01G051200 chr6A 21704370 21705080 710 True 828.000 828 87.74400 1635 2348 1 chr6A.!!$R1 713
8 TraesCS4D01G051200 chr7B 630558553 630559262 709 True 822.000 822 87.58700 1635 2348 1 chr7B.!!$R1 713
9 TraesCS4D01G051200 chr6D 201582202 201582907 705 True 819.000 819 87.62300 1640 2348 1 chr6D.!!$R1 708
10 TraesCS4D01G051200 chr5D 70885869 70886576 707 True 819.000 819 87.55200 1637 2348 1 chr5D.!!$R1 711
11 TraesCS4D01G051200 chrUn 245739042 245739750 708 False 813.000 813 87.41300 1637 2348 1 chrUn.!!$F1 711

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
430 1178 0.039437 TCTCTTGAACGAGTGGCGAC 60.039 55.0 0.0 0.0 44.57 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2856 0.321564 CCCGACCTTTCATGTGCTGA 60.322 55.0 0.0 0.0 0.0 4.26 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
42 43 1.418637 ACCAAGAAACTGGGTCGCTAA 59.581 47.619 0.00 0.00 30.77 3.09
47 48 2.093447 AGAAACTGGGTCGCTAAGATGG 60.093 50.000 0.00 0.00 0.00 3.51
62 63 2.756907 AGATGGACCAGATGCTACAGT 58.243 47.619 0.00 0.00 0.00 3.55
73 74 2.383527 GCTACAGTGCACCGACTGC 61.384 63.158 14.63 8.41 46.28 4.40
76 77 0.526211 TACAGTGCACCGACTGCTAG 59.474 55.000 14.63 0.00 46.28 3.42
78 79 2.501390 ACAGTGCACCGACTGCTAGAT 61.501 52.381 14.63 0.00 46.28 1.98
88 90 3.865745 CCGACTGCTAGATTAACTGGTTG 59.134 47.826 0.00 0.00 0.00 3.77
89 91 3.865745 CGACTGCTAGATTAACTGGTTGG 59.134 47.826 0.00 0.00 0.00 3.77
137 183 2.530958 TTACTGCTTACTGGGCCGGC 62.531 60.000 21.18 21.18 0.00 6.13
154 200 1.523154 GGCCCATTGTGCTCGTTTCA 61.523 55.000 0.00 0.00 0.00 2.69
155 201 0.109597 GCCCATTGTGCTCGTTTCAG 60.110 55.000 0.00 0.00 0.00 3.02
180 227 2.551270 GCTCACTGTTTGACGGCG 59.449 61.111 4.80 4.80 0.00 6.46
181 228 2.244651 GCTCACTGTTTGACGGCGT 61.245 57.895 14.65 14.65 0.00 5.68
217 281 4.696479 GGTGACCACTTATGATGGATCT 57.304 45.455 0.00 0.00 39.87 2.75
218 282 5.041191 GGTGACCACTTATGATGGATCTT 57.959 43.478 0.00 0.00 39.87 2.40
219 283 5.440610 GGTGACCACTTATGATGGATCTTT 58.559 41.667 0.00 0.00 39.87 2.52
220 284 5.297776 GGTGACCACTTATGATGGATCTTTG 59.702 44.000 0.00 0.00 39.87 2.77
221 285 5.882557 GTGACCACTTATGATGGATCTTTGT 59.117 40.000 0.00 0.00 39.87 2.83
222 286 6.037610 GTGACCACTTATGATGGATCTTTGTC 59.962 42.308 0.00 0.00 39.87 3.18
223 287 6.070021 TGACCACTTATGATGGATCTTTGTCT 60.070 38.462 0.00 0.00 39.87 3.41
224 288 6.352516 ACCACTTATGATGGATCTTTGTCTC 58.647 40.000 0.00 0.00 39.87 3.36
225 289 6.070021 ACCACTTATGATGGATCTTTGTCTCA 60.070 38.462 0.00 0.00 39.87 3.27
226 290 6.825213 CCACTTATGATGGATCTTTGTCTCAA 59.175 38.462 0.00 0.00 39.87 3.02
227 291 7.337689 CCACTTATGATGGATCTTTGTCTCAAA 59.662 37.037 0.00 0.00 39.87 2.69
228 292 8.733458 CACTTATGATGGATCTTTGTCTCAAAA 58.267 33.333 0.00 0.00 0.00 2.44
229 293 9.300681 ACTTATGATGGATCTTTGTCTCAAAAA 57.699 29.630 0.00 0.00 0.00 1.94
307 402 6.923508 AGCAAAACTGCTATAACTGGTTTTTC 59.076 34.615 0.00 0.00 44.28 2.29
328 1051 4.307432 TCGGAAGAGACAATCAACTCAAC 58.693 43.478 0.00 0.00 35.83 3.18
333 1056 5.201713 AGAGACAATCAACTCAACGAAGA 57.798 39.130 0.00 0.00 35.83 2.87
356 1079 1.736586 GCATCTCGTCCTGGTCGAT 59.263 57.895 15.93 0.18 36.73 3.59
361 1084 1.337071 TCTCGTCCTGGTCGATAATGC 59.663 52.381 15.93 0.00 36.73 3.56
382 1105 1.373497 CACACCGACTGAGTGGAGC 60.373 63.158 7.84 0.00 39.63 4.70
387 1110 4.803426 GACTGAGTGGAGCGGCGG 62.803 72.222 9.78 0.00 0.00 6.13
429 1177 0.888619 ATCTCTTGAACGAGTGGCGA 59.111 50.000 0.00 0.00 44.57 5.54
430 1178 0.039437 TCTCTTGAACGAGTGGCGAC 60.039 55.000 0.00 0.00 44.57 5.19
431 1179 1.337817 CTCTTGAACGAGTGGCGACG 61.338 60.000 0.00 0.00 44.57 5.12
432 1180 1.371267 CTTGAACGAGTGGCGACGA 60.371 57.895 0.00 0.00 44.57 4.20
433 1181 1.606350 CTTGAACGAGTGGCGACGAC 61.606 60.000 0.00 0.00 44.57 4.34
434 1182 3.164011 GAACGAGTGGCGACGACG 61.164 66.667 16.22 16.22 44.57 5.12
474 1222 2.677971 CGGATGTCGGCTAAGTTGG 58.322 57.895 0.00 0.00 34.75 3.77
476 1224 1.674817 CGGATGTCGGCTAAGTTGGTT 60.675 52.381 0.00 0.00 34.75 3.67
503 1254 1.269448 GAACCATCGTGTTTGTGCCAT 59.731 47.619 0.00 0.00 0.00 4.40
504 1255 0.881118 ACCATCGTGTTTGTGCCATC 59.119 50.000 0.00 0.00 0.00 3.51
505 1256 0.880441 CCATCGTGTTTGTGCCATCA 59.120 50.000 0.00 0.00 0.00 3.07
508 1267 1.646540 CGTGTTTGTGCCATCACGT 59.353 52.632 16.74 0.00 46.01 4.49
524 1283 2.099427 TCACGTGGCAGCGTATATGTAA 59.901 45.455 17.00 0.00 43.83 2.41
525 1284 2.471370 CACGTGGCAGCGTATATGTAAG 59.529 50.000 7.95 0.00 43.83 2.34
579 1342 2.342648 GACGTTCCGGCCTGTCTT 59.657 61.111 0.00 0.00 0.00 3.01
580 1343 2.027625 GACGTTCCGGCCTGTCTTG 61.028 63.158 0.00 0.00 0.00 3.02
671 1455 1.479709 ACTCAAGGATCAGCTAGCGT 58.520 50.000 9.55 0.00 0.00 5.07
688 1472 3.926616 AGCGTTACATGTATATGGAGGC 58.073 45.455 6.36 8.56 38.66 4.70
694 1478 3.424703 ACATGTATATGGAGGCAATGGC 58.575 45.455 0.00 0.00 38.66 4.40
701 1485 4.481112 GAGGCAATGGCGCGTTGG 62.481 66.667 20.92 5.07 42.47 3.77
712 1496 2.390599 CGCGTTGGGTGGATGTCAG 61.391 63.158 0.00 0.00 0.00 3.51
718 1502 2.693074 GTTGGGTGGATGTCAGTGTTTT 59.307 45.455 0.00 0.00 0.00 2.43
770 1558 1.007734 ACACACACGCCACTACGAG 60.008 57.895 0.00 0.00 36.70 4.18
771 1559 2.049433 ACACACGCCACTACGAGC 60.049 61.111 0.00 0.00 36.70 5.03
772 1560 2.258591 CACACGCCACTACGAGCT 59.741 61.111 0.00 0.00 36.70 4.09
773 1561 2.088763 CACACGCCACTACGAGCTG 61.089 63.158 0.00 0.00 36.70 4.24
774 1562 3.181967 CACGCCACTACGAGCTGC 61.182 66.667 0.00 0.00 36.70 5.25
775 1563 4.436998 ACGCCACTACGAGCTGCC 62.437 66.667 0.00 0.00 36.70 4.85
776 1564 4.435436 CGCCACTACGAGCTGCCA 62.435 66.667 0.00 0.00 34.06 4.92
777 1565 2.815647 GCCACTACGAGCTGCCAC 60.816 66.667 0.00 0.00 0.00 5.01
778 1566 2.125512 CCACTACGAGCTGCCACC 60.126 66.667 0.00 0.00 0.00 4.61
779 1567 2.656646 CACTACGAGCTGCCACCA 59.343 61.111 0.00 0.00 0.00 4.17
780 1568 1.005037 CACTACGAGCTGCCACCAA 60.005 57.895 0.00 0.00 0.00 3.67
781 1569 0.602638 CACTACGAGCTGCCACCAAA 60.603 55.000 0.00 0.00 0.00 3.28
782 1570 0.107831 ACTACGAGCTGCCACCAAAA 59.892 50.000 0.00 0.00 0.00 2.44
783 1571 1.271379 ACTACGAGCTGCCACCAAAAT 60.271 47.619 0.00 0.00 0.00 1.82
784 1572 2.027561 ACTACGAGCTGCCACCAAAATA 60.028 45.455 0.00 0.00 0.00 1.40
785 1573 1.165270 ACGAGCTGCCACCAAAATAC 58.835 50.000 0.00 0.00 0.00 1.89
786 1574 0.451783 CGAGCTGCCACCAAAATACC 59.548 55.000 0.00 0.00 0.00 2.73
787 1575 1.839424 GAGCTGCCACCAAAATACCT 58.161 50.000 0.00 0.00 0.00 3.08
788 1576 1.745653 GAGCTGCCACCAAAATACCTC 59.254 52.381 0.00 0.00 0.00 3.85
789 1577 0.817654 GCTGCCACCAAAATACCTCC 59.182 55.000 0.00 0.00 0.00 4.30
790 1578 1.890573 GCTGCCACCAAAATACCTCCA 60.891 52.381 0.00 0.00 0.00 3.86
791 1579 1.818674 CTGCCACCAAAATACCTCCAC 59.181 52.381 0.00 0.00 0.00 4.02
792 1580 1.427368 TGCCACCAAAATACCTCCACT 59.573 47.619 0.00 0.00 0.00 4.00
793 1581 2.645297 TGCCACCAAAATACCTCCACTA 59.355 45.455 0.00 0.00 0.00 2.74
841 1632 2.304761 GACACCTCTTATTCCACCACCA 59.695 50.000 0.00 0.00 0.00 4.17
842 1633 2.039879 ACACCTCTTATTCCACCACCAC 59.960 50.000 0.00 0.00 0.00 4.16
844 1635 1.406887 CCTCTTATTCCACCACCACCG 60.407 57.143 0.00 0.00 0.00 4.94
845 1636 0.616371 TCTTATTCCACCACCACCGG 59.384 55.000 0.00 0.00 0.00 5.28
851 1642 4.343323 CACCACCACCGGCCATCA 62.343 66.667 0.00 0.00 0.00 3.07
856 1647 1.077501 ACCACCGGCCATCAATCAG 60.078 57.895 0.00 0.00 0.00 2.90
858 1649 1.097547 CCACCGGCCATCAATCAGAC 61.098 60.000 0.00 0.00 0.00 3.51
872 1663 2.509166 TCAGACCCACTCACGTAGAT 57.491 50.000 0.00 0.00 0.00 1.98
873 1664 3.639672 TCAGACCCACTCACGTAGATA 57.360 47.619 0.00 0.00 0.00 1.98
907 1706 3.129502 CTCCACACAGCCATGCCG 61.130 66.667 0.00 0.00 0.00 5.69
944 1750 1.641577 CCTGCGACCTAAGCTACAAC 58.358 55.000 0.00 0.00 35.28 3.32
945 1751 1.641577 CTGCGACCTAAGCTACAACC 58.358 55.000 0.00 0.00 35.28 3.77
946 1752 0.248289 TGCGACCTAAGCTACAACCC 59.752 55.000 0.00 0.00 35.28 4.11
947 1753 0.248289 GCGACCTAAGCTACAACCCA 59.752 55.000 0.00 0.00 0.00 4.51
957 1763 0.687354 CTACAACCCAGAGCACCACT 59.313 55.000 0.00 0.00 0.00 4.00
958 1764 1.899814 CTACAACCCAGAGCACCACTA 59.100 52.381 0.00 0.00 0.00 2.74
959 1765 0.396811 ACAACCCAGAGCACCACTAC 59.603 55.000 0.00 0.00 0.00 2.73
960 1766 0.670546 CAACCCAGAGCACCACTACG 60.671 60.000 0.00 0.00 0.00 3.51
985 1791 3.050275 GTGCACTTCCACTCCCGC 61.050 66.667 10.32 0.00 33.02 6.13
989 1795 1.669115 CACTTCCACTCCCGCACTG 60.669 63.158 0.00 0.00 0.00 3.66
990 1796 2.743928 CTTCCACTCCCGCACTGC 60.744 66.667 0.00 0.00 0.00 4.40
991 1797 3.535629 CTTCCACTCCCGCACTGCA 62.536 63.158 1.11 0.00 0.00 4.41
993 1799 2.594303 CCACTCCCGCACTGCAAA 60.594 61.111 1.11 0.00 0.00 3.68
1258 2077 1.742880 GCCATCAAGCTCAGCGTCA 60.743 57.895 0.00 0.00 0.00 4.35
1363 2182 2.271800 GCTCGTGAAGTCCCAACATAG 58.728 52.381 0.00 0.00 0.00 2.23
1364 2183 2.271800 CTCGTGAAGTCCCAACATAGC 58.728 52.381 0.00 0.00 0.00 2.97
1365 2184 1.899814 TCGTGAAGTCCCAACATAGCT 59.100 47.619 0.00 0.00 0.00 3.32
1366 2185 2.002586 CGTGAAGTCCCAACATAGCTG 58.997 52.381 0.00 0.00 0.00 4.24
1367 2186 2.353704 CGTGAAGTCCCAACATAGCTGA 60.354 50.000 0.00 0.00 0.00 4.26
1368 2187 3.679917 CGTGAAGTCCCAACATAGCTGAT 60.680 47.826 0.00 0.00 0.00 2.90
1451 2277 2.840038 ACCTTCTCATGTGTGCCATAGA 59.160 45.455 0.00 0.00 30.71 1.98
1453 2279 4.080129 ACCTTCTCATGTGTGCCATAGATT 60.080 41.667 0.00 0.00 30.71 2.40
1454 2280 4.885907 CCTTCTCATGTGTGCCATAGATTT 59.114 41.667 0.00 0.00 30.71 2.17
1455 2281 5.220989 CCTTCTCATGTGTGCCATAGATTTG 60.221 44.000 0.00 0.00 30.71 2.32
1469 2295 6.486248 CCATAGATTTGTTGTTGTATCCGTG 58.514 40.000 0.00 0.00 0.00 4.94
1614 2441 5.060506 CCCGTGTATGTCCAAGCATAAATA 58.939 41.667 0.00 0.00 33.67 1.40
1677 2504 4.345257 ACATATGTTGGTCCGCTTATCTCT 59.655 41.667 1.41 0.00 0.00 3.10
1739 2567 0.893727 AGACCGGGTCCATGTTTTGC 60.894 55.000 23.21 0.00 32.18 3.68
1782 2610 6.641314 GCGTAAATCTAAATCTCATTCCTCGA 59.359 38.462 0.00 0.00 0.00 4.04
1783 2611 7.148885 GCGTAAATCTAAATCTCATTCCTCGAG 60.149 40.741 5.13 5.13 0.00 4.04
1784 2612 8.076781 CGTAAATCTAAATCTCATTCCTCGAGA 58.923 37.037 15.71 0.00 43.41 4.04
1785 2613 9.751542 GTAAATCTAAATCTCATTCCTCGAGAA 57.248 33.333 15.71 6.89 42.57 2.87
1805 2633 5.720202 AGAAAGAAAGAAACAAAAACCGCT 58.280 33.333 0.00 0.00 0.00 5.52
1929 2757 4.009675 TGATTGTGTAAGAGAACATGGGC 58.990 43.478 0.00 0.00 0.00 5.36
2028 2856 3.244215 CGACTACACATGGCATTCCCTAT 60.244 47.826 0.00 0.00 0.00 2.57
2038 2866 2.487805 GGCATTCCCTATCAGCACATGA 60.488 50.000 0.00 0.00 43.70 3.07
2058 2887 2.797285 AAGGTCGGGAGGAATCCTAT 57.203 50.000 0.00 0.00 31.76 2.57
2350 3179 4.241590 TCCTGTTCAATGTTGTGATTGC 57.758 40.909 0.00 0.00 33.95 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.578583 CAGTTTCTTGGTCGGTTCGT 58.421 50.000 0.00 0.00 0.00 3.85
15 16 0.865769 CCAGTTTCTTGGTCGGTTCG 59.134 55.000 0.00 0.00 33.38 3.95
16 17 1.235724 CCCAGTTTCTTGGTCGGTTC 58.764 55.000 0.00 0.00 36.45 3.62
23 24 2.076863 CTTAGCGACCCAGTTTCTTGG 58.923 52.381 0.00 0.00 38.00 3.61
42 43 2.433604 CACTGTAGCATCTGGTCCATCT 59.566 50.000 0.00 0.00 0.00 2.90
47 48 3.840831 TGCACTGTAGCATCTGGTC 57.159 52.632 1.65 0.00 40.11 4.02
73 74 5.812642 CACTGTAGCCAACCAGTTAATCTAG 59.187 44.000 0.00 0.00 39.83 2.43
76 77 3.127030 GCACTGTAGCCAACCAGTTAATC 59.873 47.826 0.00 0.00 39.83 1.75
78 79 2.500229 GCACTGTAGCCAACCAGTTAA 58.500 47.619 0.00 0.00 39.83 2.01
88 90 0.815734 TAGGAGAACGCACTGTAGCC 59.184 55.000 0.00 0.00 0.00 3.93
89 91 1.201647 TGTAGGAGAACGCACTGTAGC 59.798 52.381 0.00 0.00 0.00 3.58
137 183 0.523072 CCTGAAACGAGCACAATGGG 59.477 55.000 0.00 0.00 0.00 4.00
203 267 8.868522 TTTTGAGACAAAGATCCATCATAAGT 57.131 30.769 0.00 0.00 0.00 2.24
231 295 8.954350 CAAGTCTCAGATCCATCATAAGTTTTT 58.046 33.333 0.00 0.00 0.00 1.94
232 296 8.324306 TCAAGTCTCAGATCCATCATAAGTTTT 58.676 33.333 0.00 0.00 0.00 2.43
233 297 7.855375 TCAAGTCTCAGATCCATCATAAGTTT 58.145 34.615 0.00 0.00 0.00 2.66
234 298 7.429374 TCAAGTCTCAGATCCATCATAAGTT 57.571 36.000 0.00 0.00 0.00 2.66
301 395 6.061231 AGTTGATTGTCTCTTCCGAAAAAC 57.939 37.500 0.00 0.00 0.00 2.43
307 402 3.121944 CGTTGAGTTGATTGTCTCTTCCG 59.878 47.826 0.00 0.00 0.00 4.30
328 1051 0.526524 GACGAGATGCCACCTCTTCG 60.527 60.000 0.00 0.00 0.00 3.79
333 1056 2.362369 CCAGGACGAGATGCCACCT 61.362 63.158 0.00 0.00 0.00 4.00
356 1079 2.233676 ACTCAGTCGGTGTGATGCATTA 59.766 45.455 0.00 0.00 0.00 1.90
361 1084 0.603065 TCCACTCAGTCGGTGTGATG 59.397 55.000 6.73 0.00 42.24 3.07
382 1105 2.516930 AATCCATTGCTCCCGCCG 60.517 61.111 0.00 0.00 34.43 6.46
387 1110 5.587388 TCAAAAGATGAATCCATTGCTCC 57.413 39.130 0.00 0.00 34.30 4.70
508 1267 9.350951 AGATATATACTTACATATACGCTGCCA 57.649 33.333 0.00 0.00 0.00 4.92
524 1283 9.240734 CCTTTCGGTTGTAGGTAGATATATACT 57.759 37.037 7.41 0.00 0.00 2.12
525 1284 9.018582 ACCTTTCGGTTGTAGGTAGATATATAC 57.981 37.037 0.00 0.00 42.13 1.47
574 1337 0.394938 ACCATGTACGTGCCAAGACA 59.605 50.000 9.72 0.00 0.00 3.41
576 1339 3.225272 CACCATGTACGTGCCAAGA 57.775 52.632 9.72 0.00 0.00 3.02
671 1455 5.009631 GCCATTGCCTCCATATACATGTAA 58.990 41.667 10.14 0.00 0.00 2.41
688 1472 4.418401 CCACCCAACGCGCCATTG 62.418 66.667 5.73 6.97 0.00 2.82
694 1478 2.358125 TGACATCCACCCAACGCG 60.358 61.111 3.53 3.53 0.00 6.01
701 1485 1.680735 TGCAAAACACTGACATCCACC 59.319 47.619 0.00 0.00 0.00 4.61
712 1496 1.012780 GGCGCGTTTTGCAAAACAC 60.013 52.632 39.47 33.02 46.52 3.32
745 1533 1.141234 TGGCGTGTGTGTGAACGTA 59.859 52.632 0.00 0.00 41.76 3.57
770 1558 0.817654 GGAGGTATTTTGGTGGCAGC 59.182 55.000 10.30 10.30 0.00 5.25
771 1559 1.818674 GTGGAGGTATTTTGGTGGCAG 59.181 52.381 0.00 0.00 0.00 4.85
772 1560 1.427368 AGTGGAGGTATTTTGGTGGCA 59.573 47.619 0.00 0.00 0.00 4.92
773 1561 2.215942 AGTGGAGGTATTTTGGTGGC 57.784 50.000 0.00 0.00 0.00 5.01
774 1562 3.055675 TCGTAGTGGAGGTATTTTGGTGG 60.056 47.826 0.00 0.00 0.00 4.61
775 1563 4.181578 CTCGTAGTGGAGGTATTTTGGTG 58.818 47.826 0.00 0.00 0.00 4.17
776 1564 3.369157 GCTCGTAGTGGAGGTATTTTGGT 60.369 47.826 0.00 0.00 34.56 3.67
777 1565 3.118738 AGCTCGTAGTGGAGGTATTTTGG 60.119 47.826 0.00 0.00 42.57 3.28
778 1566 3.865745 CAGCTCGTAGTGGAGGTATTTTG 59.134 47.826 0.00 0.00 42.50 2.44
779 1567 3.679083 GCAGCTCGTAGTGGAGGTATTTT 60.679 47.826 0.00 0.00 42.50 1.82
780 1568 2.159085 GCAGCTCGTAGTGGAGGTATTT 60.159 50.000 0.00 0.00 42.50 1.40
781 1569 1.409427 GCAGCTCGTAGTGGAGGTATT 59.591 52.381 0.00 0.00 42.50 1.89
782 1570 1.033574 GCAGCTCGTAGTGGAGGTAT 58.966 55.000 0.00 0.00 42.50 2.73
783 1571 1.035932 GGCAGCTCGTAGTGGAGGTA 61.036 60.000 0.00 0.00 42.50 3.08
784 1572 2.352032 GGCAGCTCGTAGTGGAGGT 61.352 63.158 0.00 0.00 45.06 3.85
785 1573 2.290122 CTGGCAGCTCGTAGTGGAGG 62.290 65.000 0.00 0.00 34.56 4.30
786 1574 1.140589 CTGGCAGCTCGTAGTGGAG 59.859 63.158 0.00 0.00 37.11 3.86
787 1575 3.006756 GCTGGCAGCTCGTAGTGGA 62.007 63.158 31.37 0.00 38.45 4.02
788 1576 2.510238 GCTGGCAGCTCGTAGTGG 60.510 66.667 31.37 0.00 38.45 4.00
789 1577 2.819117 TTCGCTGGCAGCTCGTAGTG 62.819 60.000 34.17 18.49 39.60 2.74
790 1578 2.154798 TTTCGCTGGCAGCTCGTAGT 62.155 55.000 34.17 0.00 39.60 2.73
791 1579 0.807667 ATTTCGCTGGCAGCTCGTAG 60.808 55.000 34.17 19.91 39.60 3.51
792 1580 0.458260 TATTTCGCTGGCAGCTCGTA 59.542 50.000 34.17 19.25 39.60 3.43
793 1581 0.179073 ATATTTCGCTGGCAGCTCGT 60.179 50.000 34.17 20.19 39.60 4.18
806 1594 3.970640 AGAGGTGTCCCAGGAGATATTTC 59.029 47.826 0.00 0.00 0.00 2.17
841 1632 1.224592 GGTCTGATTGATGGCCGGT 59.775 57.895 1.90 0.00 0.00 5.28
842 1633 1.526917 GGGTCTGATTGATGGCCGG 60.527 63.158 0.00 0.00 0.00 6.13
844 1635 0.257039 AGTGGGTCTGATTGATGGCC 59.743 55.000 0.00 0.00 0.00 5.36
845 1636 1.065199 TGAGTGGGTCTGATTGATGGC 60.065 52.381 0.00 0.00 0.00 4.40
848 1639 1.902508 ACGTGAGTGGGTCTGATTGAT 59.097 47.619 0.00 0.00 46.97 2.57
849 1640 1.338107 ACGTGAGTGGGTCTGATTGA 58.662 50.000 0.00 0.00 46.97 2.57
850 1641 3.914984 ACGTGAGTGGGTCTGATTG 57.085 52.632 0.00 0.00 46.97 2.67
872 1663 9.237187 TGTGTGGAGCATTTATAGTCAAATTTA 57.763 29.630 0.00 0.00 0.00 1.40
873 1664 8.121305 TGTGTGGAGCATTTATAGTCAAATTT 57.879 30.769 0.00 0.00 0.00 1.82
907 1706 2.514824 GCGTGGGATGGCTCTTCC 60.515 66.667 0.00 0.00 0.00 3.46
944 1750 0.172803 GTACGTAGTGGTGCTCTGGG 59.827 60.000 0.00 0.00 45.73 4.45
945 1751 0.179171 CGTACGTAGTGGTGCTCTGG 60.179 60.000 7.22 0.00 45.73 3.86
946 1752 0.520404 ACGTACGTAGTGGTGCTCTG 59.480 55.000 21.41 0.00 45.73 3.35
947 1753 1.734465 GTACGTACGTAGTGGTGCTCT 59.266 52.381 27.48 0.00 45.73 4.09
960 1766 1.055338 GTGGAAGTGCACGTACGTAC 58.945 55.000 22.34 16.78 0.00 3.67
985 1791 1.425412 GCCATTGCTTCTTTGCAGTG 58.575 50.000 5.25 5.25 45.96 3.66
989 1795 0.733909 GGACGCCATTGCTTCTTTGC 60.734 55.000 0.00 0.00 36.12 3.68
990 1796 0.597568 TGGACGCCATTGCTTCTTTG 59.402 50.000 0.00 0.00 36.12 2.77
991 1797 1.270550 CTTGGACGCCATTGCTTCTTT 59.729 47.619 0.00 0.00 36.12 2.52
993 1799 0.250901 ACTTGGACGCCATTGCTTCT 60.251 50.000 0.00 0.00 36.12 2.85
1047 1854 2.266055 GCGACCAGGAGGAGGTTG 59.734 66.667 0.00 0.00 40.09 3.77
1258 2077 1.151450 GGTTGATGGGGATGCCGAT 59.849 57.895 0.00 0.00 0.00 4.18
1451 2277 4.764823 ACATCCACGGATACAACAACAAAT 59.235 37.500 0.00 0.00 32.93 2.32
1453 2279 3.745799 ACATCCACGGATACAACAACAA 58.254 40.909 0.00 0.00 32.93 2.83
1454 2280 3.410631 ACATCCACGGATACAACAACA 57.589 42.857 0.00 0.00 32.93 3.33
1455 2281 4.668177 CGAAACATCCACGGATACAACAAC 60.668 45.833 0.00 0.00 32.93 3.32
1469 2295 3.181397 CATGCCAATCAACGAAACATCC 58.819 45.455 0.00 0.00 0.00 3.51
1574 2401 2.567615 ACGGGAGAAATTAGCAGTCACT 59.432 45.455 0.00 0.00 0.00 3.41
1614 2441 8.622870 TCCTCCTATGAATAGAGAGAAGATCAT 58.377 37.037 13.24 0.00 33.37 2.45
1677 2504 1.134220 GTGACCTCACCAACCAAGTGA 60.134 52.381 0.00 0.00 41.84 3.41
1702 2529 3.640029 GGTCTTGCATCATCCAATCCAAT 59.360 43.478 0.00 0.00 0.00 3.16
1739 2567 1.487231 CAAAGACGCCGTGAAGTCG 59.513 57.895 0.00 0.00 41.86 4.18
1782 2610 5.720202 AGCGGTTTTTGTTTCTTTCTTTCT 58.280 33.333 0.00 0.00 0.00 2.52
1783 2611 5.575218 TGAGCGGTTTTTGTTTCTTTCTTTC 59.425 36.000 0.00 0.00 0.00 2.62
1784 2612 5.474825 TGAGCGGTTTTTGTTTCTTTCTTT 58.525 33.333 0.00 0.00 0.00 2.52
1785 2613 5.066968 TGAGCGGTTTTTGTTTCTTTCTT 57.933 34.783 0.00 0.00 0.00 2.52
1805 2633 3.074412 GTGGAAATCTTCGCCTTCTTGA 58.926 45.455 0.00 0.00 0.00 3.02
1929 2757 2.995258 CGGAAATTGCCACAAAATCCAG 59.005 45.455 2.58 4.89 0.00 3.86
2028 2856 0.321564 CCCGACCTTTCATGTGCTGA 60.322 55.000 0.00 0.00 0.00 4.26
2038 2866 2.563039 TAGGATTCCTCCCGACCTTT 57.437 50.000 8.94 0.00 43.21 3.11
2074 2903 3.182887 AGGCCAACAAATCCATGGTTA 57.817 42.857 12.58 0.00 36.57 2.85
2219 3048 3.195661 GTTATCCTTAGCCAGGTTCACG 58.804 50.000 0.00 0.00 44.37 4.35
2247 3076 1.683385 GTCCCCTCCAATAAGCATTGC 59.317 52.381 0.00 0.00 40.28 3.56


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

AutoCloner maintained by Alex Coulton.