Multiple sequence alignment - TraesCS3B01G027600

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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 TraesCS3B01G027600 chr3B 100.000 3138 0 0 1 3138 11945197 11942060 0.000000e+00 5795
1 TraesCS3B01G027600 chr3B 97.423 970 22 2 2171 3138 4503336 4504304 0.000000e+00 1650
2 TraesCS3B01G027600 chr2B 90.103 970 80 7 2171 3138 25741472 25742427 0.000000e+00 1245
3 TraesCS3B01G027600 chr2B 93.148 613 39 3 123 733 90448273 90447662 0.000000e+00 896
4 TraesCS3B01G027600 chr2B 93.151 146 10 0 1404 1549 326723054 326723199 6.820000e-52 215
5 TraesCS3B01G027600 chr2B 90.411 146 14 0 1404 1549 733272410 733272555 3.190000e-45 193
6 TraesCS3B01G027600 chr3D 89.838 925 63 13 736 1657 5802613 5803509 0.000000e+00 1158
7 TraesCS3B01G027600 chr3D 94.918 610 29 2 123 730 17116974 17116365 0.000000e+00 953
8 TraesCS3B01G027600 chr3D 93.290 611 38 3 123 730 339180214 339180824 0.000000e+00 898
9 TraesCS3B01G027600 chr3D 91.630 454 24 5 1699 2152 5803753 5804192 1.600000e-172 616
10 TraesCS3B01G027600 chr3D 93.478 138 9 0 1412 1549 519930956 519931093 4.100000e-49 206
11 TraesCS3B01G027600 chr3D 96.154 78 2 1 39 116 5802534 5802610 3.290000e-25 126
12 TraesCS3B01G027600 chr2D 95.246 610 27 2 123 730 31475075 31474466 0.000000e+00 965
13 TraesCS3B01G027600 chr1D 94.590 610 30 3 123 730 326240683 326240075 0.000000e+00 941
14 TraesCS3B01G027600 chr1D 94.127 613 28 4 123 732 377015628 377015021 0.000000e+00 926
15 TraesCS3B01G027600 chr1A 94.262 610 31 4 123 730 577586926 577587533 0.000000e+00 929
16 TraesCS3B01G027600 chr1A 94.521 73 4 0 1305 1377 439491623 439491695 2.560000e-21 113
17 TraesCS3B01G027600 chr1A 94.286 70 4 0 1308 1377 11022971 11022902 1.190000e-19 108
18 TraesCS3B01G027600 chr5A 93.770 610 32 4 123 730 225268337 225268942 0.000000e+00 911
19 TraesCS3B01G027600 chr5A 88.182 110 11 2 1832 1941 540350901 540350794 2.540000e-26 130
20 TraesCS3B01G027600 chr5A 93.151 73 5 0 1308 1380 431434514 431434442 1.190000e-19 108
21 TraesCS3B01G027600 chr6D 93.443 610 32 8 123 730 127668650 127669253 0.000000e+00 898
22 TraesCS3B01G027600 chr6D 83.158 190 29 3 1945 2131 804664 804853 1.500000e-38 171
23 TraesCS3B01G027600 chr5D 82.215 596 73 16 857 1446 426044224 426043656 1.690000e-132 483
24 TraesCS3B01G027600 chr5D 81.104 598 81 18 855 1446 426034629 426034058 1.720000e-122 449
25 TraesCS3B01G027600 chr5D 85.397 315 35 4 1832 2146 426042049 426041746 1.820000e-82 316
26 TraesCS3B01G027600 chr5B 83.260 454 67 7 927 1377 515715774 515715327 2.910000e-110 409
27 TraesCS3B01G027600 chr5B 93.023 129 8 1 1421 1549 702325403 702325276 1.490000e-43 187
28 TraesCS3B01G027600 chr6B 93.151 146 10 0 1404 1549 248526880 248527025 6.820000e-52 215
29 TraesCS3B01G027600 chr6B 94.309 123 7 0 1427 1549 149657676 149657554 4.130000e-44 189
30 TraesCS3B01G027600 chr4A 91.781 146 12 0 1404 1549 313506779 313506924 1.480000e-48 204
31 TraesCS3B01G027600 chr4A 82.584 178 30 1 1955 2131 732780517 732780694 4.190000e-34 156
32 TraesCS3B01G027600 chr7B 92.754 138 10 0 1412 1549 318148837 318148974 1.910000e-47 200
33 TraesCS3B01G027600 chr7B 95.714 70 3 0 1308 1377 645437217 645437148 2.560000e-21 113
34 TraesCS3B01G027600 chr7D 81.250 192 33 3 1943 2131 7455482 7455673 5.420000e-33 152
35 TraesCS3B01G027600 chr7A 81.250 192 33 3 1943 2131 8382851 8383042 5.420000e-33 152
36 TraesCS3B01G027600 chr4B 93.151 73 5 0 1305 1377 626991588 626991660 1.190000e-19 108


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 TraesCS3B01G027600 chr3B 11942060 11945197 3137 True 5795.000000 5795 100.000000 1 3138 1 chr3B.!!$R1 3137
1 TraesCS3B01G027600 chr3B 4503336 4504304 968 False 1650.000000 1650 97.423000 2171 3138 1 chr3B.!!$F1 967
2 TraesCS3B01G027600 chr2B 25741472 25742427 955 False 1245.000000 1245 90.103000 2171 3138 1 chr2B.!!$F1 967
3 TraesCS3B01G027600 chr2B 90447662 90448273 611 True 896.000000 896 93.148000 123 733 1 chr2B.!!$R1 610
4 TraesCS3B01G027600 chr3D 17116365 17116974 609 True 953.000000 953 94.918000 123 730 1 chr3D.!!$R1 607
5 TraesCS3B01G027600 chr3D 339180214 339180824 610 False 898.000000 898 93.290000 123 730 1 chr3D.!!$F1 607
6 TraesCS3B01G027600 chr3D 5802534 5804192 1658 False 633.333333 1158 92.540667 39 2152 3 chr3D.!!$F3 2113
7 TraesCS3B01G027600 chr2D 31474466 31475075 609 True 965.000000 965 95.246000 123 730 1 chr2D.!!$R1 607
8 TraesCS3B01G027600 chr1D 326240075 326240683 608 True 941.000000 941 94.590000 123 730 1 chr1D.!!$R1 607
9 TraesCS3B01G027600 chr1D 377015021 377015628 607 True 926.000000 926 94.127000 123 732 1 chr1D.!!$R2 609
10 TraesCS3B01G027600 chr1A 577586926 577587533 607 False 929.000000 929 94.262000 123 730 1 chr1A.!!$F2 607
11 TraesCS3B01G027600 chr5A 225268337 225268942 605 False 911.000000 911 93.770000 123 730 1 chr5A.!!$F1 607
12 TraesCS3B01G027600 chr6D 127668650 127669253 603 False 898.000000 898 93.443000 123 730 1 chr6D.!!$F2 607
13 TraesCS3B01G027600 chr5D 426034058 426034629 571 True 449.000000 449 81.104000 855 1446 1 chr5D.!!$R1 591
14 TraesCS3B01G027600 chr5D 426041746 426044224 2478 True 399.500000 483 83.806000 857 2146 2 chr5D.!!$R2 1289

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
24 25 0.322187 ATGTTTGTACTCCCACCGCC 60.322 55.0 0.00 0.0 0.00 6.13 F
169 170 0.380378 GAGCTGCTCGAGATCGACTT 59.620 55.0 18.75 0.0 44.22 3.01 F
779 787 0.669619 TTGGACGTACGCTTGACTGA 59.330 50.0 16.72 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1381 1392 0.039911 AGAGCCCCTTGACGAGTACT 59.960 55.0 0.00 0.0 0.00 2.73 R
1976 3492 0.112995 AGCAGCCCCTTGATGTTCAA 59.887 50.0 0.00 0.0 34.79 2.69 R
2148 3664 0.327591 AGGAGGTAAGACCGTCTCGT 59.672 55.0 0.35 0.0 44.90 4.18 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
23 24 2.389962 TATGTTTGTACTCCCACCGC 57.610 50.000 0.00 0.00 0.00 5.68
24 25 0.322187 ATGTTTGTACTCCCACCGCC 60.322 55.000 0.00 0.00 0.00 6.13
25 26 1.673337 GTTTGTACTCCCACCGCCC 60.673 63.158 0.00 0.00 0.00 6.13
26 27 3.242897 TTTGTACTCCCACCGCCCG 62.243 63.158 0.00 0.00 0.00 6.13
33 34 4.499633 CCCACCGCCCGGCTTTAT 62.500 66.667 8.05 0.00 39.32 1.40
34 35 2.439519 CCACCGCCCGGCTTTATT 60.440 61.111 8.05 0.00 39.32 1.40
35 36 2.770589 CCACCGCCCGGCTTTATTG 61.771 63.158 8.05 0.00 39.32 1.90
36 37 2.439519 ACCGCCCGGCTTTATTGG 60.440 61.111 8.05 2.33 39.32 3.16
37 38 3.216292 CCGCCCGGCTTTATTGGG 61.216 66.667 8.05 0.00 46.22 4.12
40 41 2.837758 CCCGGCTTTATTGGGCCC 60.838 66.667 17.59 17.59 45.01 5.80
41 42 2.043450 CCGGCTTTATTGGGCCCA 60.043 61.111 24.45 24.45 45.01 5.36
42 43 1.457455 CCGGCTTTATTGGGCCCAT 60.457 57.895 29.23 18.30 45.01 4.00
43 44 1.048160 CCGGCTTTATTGGGCCCATT 61.048 55.000 29.23 25.26 45.01 3.16
68 69 3.875134 ACAGACGTGTTTACTTTTCCCTG 59.125 43.478 0.00 0.00 30.30 4.45
82 83 1.377333 CCCTGGTTCCTTCCGCTTC 60.377 63.158 0.00 0.00 0.00 3.86
116 117 2.965572 AATGGAATTGGCAATGGTCG 57.034 45.000 14.47 0.00 33.44 4.79
117 118 0.461135 ATGGAATTGGCAATGGTCGC 59.539 50.000 14.47 3.90 0.00 5.19
118 119 0.897401 TGGAATTGGCAATGGTCGCA 60.897 50.000 14.47 6.29 0.00 5.10
119 120 0.461135 GGAATTGGCAATGGTCGCAT 59.539 50.000 14.47 0.00 0.00 4.73
120 121 1.563111 GAATTGGCAATGGTCGCATG 58.437 50.000 14.47 0.00 0.00 4.06
121 122 0.460635 AATTGGCAATGGTCGCATGC 60.461 50.000 14.47 7.91 39.33 4.06
169 170 0.380378 GAGCTGCTCGAGATCGACTT 59.620 55.000 18.75 0.00 44.22 3.01
197 200 6.712241 TTTGACTCGACTCAAGATCAATTC 57.288 37.500 7.42 0.00 31.76 2.17
202 205 7.226523 TGACTCGACTCAAGATCAATTCAAAAA 59.773 33.333 0.00 0.00 0.00 1.94
203 206 8.103948 ACTCGACTCAAGATCAATTCAAAAAT 57.896 30.769 0.00 0.00 0.00 1.82
246 249 6.313905 CACTTTATGTAGCTTGACCGAGAAAT 59.686 38.462 0.00 0.00 0.00 2.17
280 283 1.203928 CTAATGTTGGCTCGCTCGAG 58.796 55.000 8.45 8.45 44.56 4.04
478 484 7.644945 CACGTGGTCGACTATGTGTTAAATATA 59.355 37.037 33.81 0.00 38.87 0.86
672 679 3.251004 AGTTTGAGCTCGCTCGAATTTTT 59.749 39.130 20.94 8.05 45.11 1.94
689 697 7.768582 TCGAATTTTTATATGAGTTGGCTGAGA 59.231 33.333 0.00 0.00 0.00 3.27
733 741 1.068474 CTCGTTTGCAACCCTAGTCG 58.932 55.000 0.00 0.00 0.00 4.18
734 742 0.947180 TCGTTTGCAACCCTAGTCGC 60.947 55.000 0.00 0.00 0.00 5.19
749 757 2.905075 AGTCGCATGCTGTAATTGCTA 58.095 42.857 17.13 0.00 34.23 3.49
777 785 1.710013 CATTGGACGTACGCTTGACT 58.290 50.000 16.72 0.00 0.00 3.41
779 787 0.669619 TTGGACGTACGCTTGACTGA 59.330 50.000 16.72 0.00 0.00 3.41
780 788 0.669619 TGGACGTACGCTTGACTGAA 59.330 50.000 16.72 0.00 0.00 3.02
800 808 2.897271 TGGAGGCAAATATGTGGTGT 57.103 45.000 0.00 0.00 0.00 4.16
817 825 2.547855 GGTGTATGATCGGCTACATGCA 60.548 50.000 0.00 0.00 45.15 3.96
863 871 5.103043 TGACTATTCTCATAGACCCTTCCCT 60.103 44.000 0.00 0.00 36.58 4.20
894 902 4.526650 TCTGAAAAATAAAAGCACCTCCCC 59.473 41.667 0.00 0.00 0.00 4.81
924 932 1.152839 CCCCTCAAACACCACCGTT 60.153 57.895 0.00 0.00 0.00 4.44
939 947 2.388232 CGTTTCCCCTTCGCCTTCG 61.388 63.158 0.00 0.00 0.00 3.79
954 962 2.622436 CCTTCGCTCCTAAGGTTTCTG 58.378 52.381 0.00 0.00 38.98 3.02
1068 1079 1.014564 CCGACGGCAAGGAGTTCTTC 61.015 60.000 0.00 0.00 32.41 2.87
1125 1136 1.221840 GCACATCGTGGAGGATGGT 59.778 57.895 12.61 0.00 46.38 3.55
1167 1178 2.482333 CCCCAACGTCAACGCCAAA 61.482 57.895 1.81 0.00 44.43 3.28
1197 1208 3.261643 ACATGGTCATCAAGTACTGCAGA 59.738 43.478 23.35 0.48 0.00 4.26
1275 1286 0.818296 CGGACCTCAAGACCTTCGAT 59.182 55.000 0.00 0.00 0.00 3.59
1345 1356 3.202151 GGTGAGATTTCCATCCAACCCTA 59.798 47.826 0.00 0.00 32.53 3.53
1349 1360 1.761711 TTTCCATCCAACCCTACCCA 58.238 50.000 0.00 0.00 0.00 4.51
1350 1361 1.994399 TTCCATCCAACCCTACCCAT 58.006 50.000 0.00 0.00 0.00 4.00
1351 1362 2.899906 TCCATCCAACCCTACCCATA 57.100 50.000 0.00 0.00 0.00 2.74
1377 1388 5.333513 CGTGGTGCTCTTTCTAGTTAGTAG 58.666 45.833 0.00 0.00 0.00 2.57
1378 1389 5.106237 CGTGGTGCTCTTTCTAGTTAGTAGT 60.106 44.000 0.00 0.00 0.00 2.73
1379 1390 6.569994 CGTGGTGCTCTTTCTAGTTAGTAGTT 60.570 42.308 0.00 0.00 0.00 2.24
1380 1391 7.153315 GTGGTGCTCTTTCTAGTTAGTAGTTT 58.847 38.462 0.00 0.00 0.00 2.66
1381 1392 8.302438 GTGGTGCTCTTTCTAGTTAGTAGTTTA 58.698 37.037 0.00 0.00 0.00 2.01
1382 1393 8.521176 TGGTGCTCTTTCTAGTTAGTAGTTTAG 58.479 37.037 0.00 0.00 0.00 1.85
1383 1394 8.522003 GGTGCTCTTTCTAGTTAGTAGTTTAGT 58.478 37.037 0.00 0.00 0.00 2.24
1429 1445 3.496884 TGTCTAGATGCGGTTTTGTTGTC 59.503 43.478 0.00 0.00 0.00 3.18
1430 1446 3.071479 TCTAGATGCGGTTTTGTTGTCC 58.929 45.455 0.00 0.00 0.00 4.02
1435 1451 3.320673 TGCGGTTTTGTTGTCCTTTTT 57.679 38.095 0.00 0.00 0.00 1.94
1446 1462 4.106909 GTTGTCCTTTTTAACGGTTGGTG 58.893 43.478 3.07 0.00 0.00 4.17
1461 1483 1.745489 GGTGCCCCAGATTCGTGTC 60.745 63.158 0.00 0.00 0.00 3.67
1507 1851 6.967135 TGTGTTTACTGTAGAGTGTAGACTG 58.033 40.000 2.10 0.00 33.21 3.51
1540 1922 6.272822 ACTCTGACAAAATATTTGAAGGGC 57.727 37.500 9.62 0.00 0.00 5.19
1542 1924 7.175104 ACTCTGACAAAATATTTGAAGGGCTA 58.825 34.615 9.62 0.00 0.00 3.93
1573 1955 6.490566 TTTTAAGCGTTTGTAATCTCTCCC 57.509 37.500 0.00 0.00 0.00 4.30
1581 1993 5.301555 GTTTGTAATCTCTCCCTAGGATGC 58.698 45.833 11.48 0.00 0.00 3.91
1583 1995 2.390225 AATCTCTCCCTAGGATGCGT 57.610 50.000 11.48 0.00 0.00 5.24
1595 2007 4.508124 CCTAGGATGCGTGTTATTTCTCAC 59.492 45.833 1.05 0.00 0.00 3.51
1633 2046 7.598493 GGTTGCATGTCATAAGTGTTTGTAATT 59.402 33.333 0.00 0.00 0.00 1.40
1635 2051 8.741101 TGCATGTCATAAGTGTTTGTAATTTC 57.259 30.769 0.00 0.00 0.00 2.17
1639 2055 7.881142 TGTCATAAGTGTTTGTAATTTCCCTG 58.119 34.615 0.00 0.00 0.00 4.45
1783 2425 6.467677 AGCTATGCTTCTGTTTTCAGTTCTA 58.532 36.000 0.00 0.00 46.98 2.10
1786 2428 5.947228 TGCTTCTGTTTTCAGTTCTATGG 57.053 39.130 0.00 0.00 46.98 2.74
1790 2432 6.094048 GCTTCTGTTTTCAGTTCTATGGCATA 59.906 38.462 7.06 7.06 46.98 3.14
1791 2433 7.201767 GCTTCTGTTTTCAGTTCTATGGCATAT 60.202 37.037 7.81 0.00 46.98 1.78
1805 2447 9.688091 TTCTATGGCATATTTAACCAGTGTAAA 57.312 29.630 7.81 0.00 36.78 2.01
1811 2453 7.010091 GGCATATTTAACCAGTGTAAATTGCAC 59.990 37.037 19.95 6.08 33.80 4.57
1842 3358 1.555075 TCAGTATTGTGCTCCCTCACC 59.445 52.381 0.00 0.00 36.17 4.02
1946 3462 5.047802 ACCTGACCATCTTGCTTGTATTTTG 60.048 40.000 0.00 0.00 0.00 2.44
1976 3492 0.244994 CTGACAGGCTGCGAACTACT 59.755 55.000 15.89 0.00 0.00 2.57
2065 3581 1.208293 GAGGAGATCCGCAAGACCTTT 59.792 52.381 0.00 0.00 42.08 3.11
2078 3594 4.036734 GCAAGACCTTTGACATCAAGAACA 59.963 41.667 0.00 0.00 37.15 3.18
2112 3628 1.478916 GGAAGAGGAGGAAGTTCGGAG 59.521 57.143 0.00 0.00 0.00 4.63
2128 3644 1.575447 GGAGGGAGAACCAATGGGCT 61.575 60.000 3.55 0.00 43.89 5.19
2158 3674 3.559024 TCGAGTGACGAGACGGTC 58.441 61.111 0.00 0.00 46.45 4.79
2159 3675 1.005275 TCGAGTGACGAGACGGTCT 60.005 57.895 11.09 11.09 46.45 3.85
2160 3676 0.602106 TCGAGTGACGAGACGGTCTT 60.602 55.000 12.67 0.00 46.45 3.01
2161 3677 1.073964 CGAGTGACGAGACGGTCTTA 58.926 55.000 12.67 0.00 45.77 2.10
2162 3678 1.201899 CGAGTGACGAGACGGTCTTAC 60.202 57.143 12.67 9.37 45.77 2.34
2163 3679 1.130186 GAGTGACGAGACGGTCTTACC 59.870 57.143 12.67 5.06 37.81 2.85
2164 3680 1.163554 GTGACGAGACGGTCTTACCT 58.836 55.000 12.67 0.00 35.66 3.08
2165 3681 1.130186 GTGACGAGACGGTCTTACCTC 59.870 57.143 12.67 5.43 35.66 3.85
2166 3682 0.731994 GACGAGACGGTCTTACCTCC 59.268 60.000 12.67 0.00 35.66 4.30
2167 3683 0.327591 ACGAGACGGTCTTACCTCCT 59.672 55.000 12.67 0.00 35.66 3.69
2168 3684 1.015868 CGAGACGGTCTTACCTCCTC 58.984 60.000 12.67 0.00 35.66 3.71
2169 3685 1.678123 CGAGACGGTCTTACCTCCTCA 60.678 57.143 12.67 0.00 35.49 3.86
2192 3710 4.095400 TCCTCCAGCTCCCCTCCC 62.095 72.222 0.00 0.00 0.00 4.30
2434 3952 1.078214 TCCGCCATTCTTCAGCCAG 60.078 57.895 0.00 0.00 0.00 4.85
2445 3963 0.687354 TTCAGCCAGTCACTCCCTTC 59.313 55.000 0.00 0.00 0.00 3.46
2499 4017 4.175489 GTCGAGCGCGCTGTCCTA 62.175 66.667 41.82 13.95 37.46 2.94
2876 4394 0.527817 CTACGCCTTGACCCATCGAC 60.528 60.000 0.00 0.00 0.00 4.20
3001 4519 2.689034 GCAGCCTACCCCTGGACT 60.689 66.667 0.00 0.00 0.00 3.85
3002 4520 3.036429 GCAGCCTACCCCTGGACTG 62.036 68.421 0.00 0.00 34.33 3.51
3106 4624 2.048222 CCTTCTGCGTGGCTTCGA 60.048 61.111 6.82 0.00 0.00 3.71
3117 4635 2.472049 GCTTCGACTTCTGCGCAC 59.528 61.111 5.66 0.00 0.00 5.34
3128 4646 1.164411 TCTGCGCACGAATGGATTTT 58.836 45.000 5.66 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.061179 GCGGTGGGAGTACAAACATATAAT 58.939 41.667 0.00 0.00 0.00 1.28
1 2 4.444536 GCGGTGGGAGTACAAACATATAA 58.555 43.478 0.00 0.00 0.00 0.98
2 3 3.181463 GGCGGTGGGAGTACAAACATATA 60.181 47.826 0.00 0.00 0.00 0.86
3 4 2.420967 GGCGGTGGGAGTACAAACATAT 60.421 50.000 0.00 0.00 0.00 1.78
5 6 0.322187 GGCGGTGGGAGTACAAACAT 60.322 55.000 0.00 0.00 0.00 2.71
6 7 1.071814 GGCGGTGGGAGTACAAACA 59.928 57.895 0.00 0.00 0.00 2.83
7 8 1.673337 GGGCGGTGGGAGTACAAAC 60.673 63.158 0.00 0.00 0.00 2.93
8 9 2.751688 GGGCGGTGGGAGTACAAA 59.248 61.111 0.00 0.00 0.00 2.83
9 10 3.697747 CGGGCGGTGGGAGTACAA 61.698 66.667 0.00 0.00 0.00 2.41
16 17 4.499633 ATAAAGCCGGGCGGTGGG 62.500 66.667 14.39 0.00 37.65 4.61
17 18 2.439519 AATAAAGCCGGGCGGTGG 60.440 61.111 14.39 0.00 37.65 4.61
18 19 2.770589 CCAATAAAGCCGGGCGGTG 61.771 63.158 14.39 8.26 37.65 4.94
19 20 2.439519 CCAATAAAGCCGGGCGGT 60.440 61.111 14.39 8.09 37.65 5.68
20 21 3.216292 CCCAATAAAGCCGGGCGG 61.216 66.667 14.39 7.40 31.89 6.13
27 28 2.235898 TGTTCAATGGGCCCAATAAAGC 59.764 45.455 32.58 17.79 0.00 3.51
28 29 3.768757 TCTGTTCAATGGGCCCAATAAAG 59.231 43.478 32.58 20.81 0.00 1.85
29 30 3.513515 GTCTGTTCAATGGGCCCAATAAA 59.486 43.478 32.58 19.86 0.00 1.40
30 31 3.096092 GTCTGTTCAATGGGCCCAATAA 58.904 45.455 32.58 20.28 0.00 1.40
31 32 2.733956 GTCTGTTCAATGGGCCCAATA 58.266 47.619 32.58 14.85 0.00 1.90
32 33 1.560505 GTCTGTTCAATGGGCCCAAT 58.439 50.000 32.58 20.33 0.00 3.16
33 34 0.893270 CGTCTGTTCAATGGGCCCAA 60.893 55.000 32.58 10.32 0.00 4.12
34 35 1.303236 CGTCTGTTCAATGGGCCCA 60.303 57.895 30.92 30.92 0.00 5.36
35 36 1.303317 ACGTCTGTTCAATGGGCCC 60.303 57.895 17.59 17.59 0.00 5.80
36 37 0.889186 ACACGTCTGTTCAATGGGCC 60.889 55.000 0.00 0.00 0.00 5.80
37 38 0.951558 AACACGTCTGTTCAATGGGC 59.048 50.000 0.00 0.00 35.57 5.36
38 39 3.813166 AGTAAACACGTCTGTTCAATGGG 59.187 43.478 0.00 0.00 39.88 4.00
39 40 5.418310 AAGTAAACACGTCTGTTCAATGG 57.582 39.130 0.00 0.00 39.88 3.16
40 41 6.413818 GGAAAAGTAAACACGTCTGTTCAATG 59.586 38.462 6.49 0.00 39.88 2.82
41 42 6.459161 GGGAAAAGTAAACACGTCTGTTCAAT 60.459 38.462 6.49 0.00 39.88 2.57
42 43 5.163733 GGGAAAAGTAAACACGTCTGTTCAA 60.164 40.000 6.49 0.00 39.88 2.69
43 44 4.333372 GGGAAAAGTAAACACGTCTGTTCA 59.667 41.667 6.49 0.00 39.88 3.18
68 69 0.875059 CTGTTGAAGCGGAAGGAACC 59.125 55.000 0.00 0.00 0.00 3.62
82 83 2.768698 TCCATTTTTGCATGCCTGTTG 58.231 42.857 16.68 6.50 0.00 3.33
121 122 0.243095 GAGCTTTTCTTGCAGCCCTG 59.757 55.000 0.00 0.00 36.62 4.45
207 210 9.382244 GCTACATAAAGTGTTTAAACTCAACTG 57.618 33.333 18.72 12.85 42.29 3.16
218 221 5.302360 TCGGTCAAGCTACATAAAGTGTTT 58.698 37.500 0.00 0.00 42.29 2.83
246 249 2.432146 ACATTAGCTCAAGATCGGCTCA 59.568 45.455 0.00 0.72 37.50 4.26
386 392 5.407995 CCATGTTCGTTGGCAAATAAAATGT 59.592 36.000 17.88 0.00 0.00 2.71
397 403 2.793278 AAGTTTCCATGTTCGTTGGC 57.207 45.000 0.00 0.00 34.06 4.52
478 484 9.154847 GCTGAGAACTTTTGCCAAAAATATAAT 57.845 29.630 3.91 0.00 34.81 1.28
689 697 0.039074 CTCGAGCGAGTTGGAGTTGT 60.039 55.000 11.50 0.00 37.47 3.32
733 741 2.684881 ACCAGTAGCAATTACAGCATGC 59.315 45.455 10.51 10.51 42.53 4.06
734 742 3.940852 TGACCAGTAGCAATTACAGCATG 59.059 43.478 0.00 0.00 46.00 4.06
749 757 0.973632 TACGTCCAATGCTGACCAGT 59.026 50.000 0.00 0.00 0.00 4.00
777 785 3.700539 CACCACATATTTGCCTCCATTCA 59.299 43.478 0.00 0.00 0.00 2.57
779 787 3.711863 ACACCACATATTTGCCTCCATT 58.288 40.909 0.00 0.00 0.00 3.16
780 788 3.386932 ACACCACATATTTGCCTCCAT 57.613 42.857 0.00 0.00 0.00 3.41
800 808 3.996363 GTCATTGCATGTAGCCGATCATA 59.004 43.478 0.00 0.00 44.83 2.15
844 852 4.101741 CGAAAGGGAAGGGTCTATGAGAAT 59.898 45.833 0.00 0.00 0.00 2.40
863 871 7.381139 GGTGCTTTTATTTTTCAGATCACGAAA 59.619 33.333 6.30 6.30 0.00 3.46
894 902 1.204146 TTGAGGGGATCGAAGGGAAG 58.796 55.000 0.00 0.00 0.00 3.46
924 932 3.310860 GAGCGAAGGCGAAGGGGAA 62.311 63.158 0.00 0.00 46.35 3.97
939 947 0.621082 AGGCCAGAAACCTTAGGAGC 59.379 55.000 4.77 0.00 31.87 4.70
968 976 2.626467 GGGGAGATTGGGGTGGCTT 61.626 63.158 0.00 0.00 0.00 4.35
1057 1068 1.896465 CTCCTCCACGAAGAACTCCTT 59.104 52.381 0.00 0.00 37.93 3.36
1125 1136 0.243365 GGATGATGTTGTTGGCGCAA 59.757 50.000 10.83 0.00 0.00 4.85
1197 1208 2.037136 GCGCTTCTGGATGTGCTGT 61.037 57.895 0.00 0.00 38.47 4.40
1204 1215 4.537433 GGCTCCGCGCTTCTGGAT 62.537 66.667 5.56 0.00 39.13 3.41
1275 1286 4.637091 TGGTCGACGTCTATGAACTTATCA 59.363 41.667 14.70 0.00 43.67 2.15
1345 1356 2.609610 AGCACCACGGGTATGGGT 60.610 61.111 0.00 0.00 44.81 4.51
1349 1360 1.276622 AGAAAGAGCACCACGGGTAT 58.723 50.000 0.00 0.00 32.11 2.73
1350 1361 1.822990 CTAGAAAGAGCACCACGGGTA 59.177 52.381 0.00 0.00 32.11 3.69
1351 1362 0.608640 CTAGAAAGAGCACCACGGGT 59.391 55.000 0.00 0.00 35.62 5.28
1377 1388 2.233186 AGCCCCTTGACGAGTACTAAAC 59.767 50.000 0.00 0.00 0.00 2.01
1378 1389 2.494870 GAGCCCCTTGACGAGTACTAAA 59.505 50.000 0.00 0.00 0.00 1.85
1379 1390 2.097825 GAGCCCCTTGACGAGTACTAA 58.902 52.381 0.00 0.00 0.00 2.24
1380 1391 1.284198 AGAGCCCCTTGACGAGTACTA 59.716 52.381 0.00 0.00 0.00 1.82
1381 1392 0.039911 AGAGCCCCTTGACGAGTACT 59.960 55.000 0.00 0.00 0.00 2.73
1382 1393 0.896226 AAGAGCCCCTTGACGAGTAC 59.104 55.000 0.00 0.00 32.92 2.73
1383 1394 3.376082 AAGAGCCCCTTGACGAGTA 57.624 52.632 0.00 0.00 32.92 2.59
1384 1395 4.217112 AAGAGCCCCTTGACGAGT 57.783 55.556 0.00 0.00 32.92 4.18
1410 1426 3.074412 AGGACAACAAAACCGCATCTAG 58.926 45.455 0.00 0.00 0.00 2.43
1429 1445 2.143008 GGCACCAACCGTTAAAAAGG 57.857 50.000 0.00 0.00 0.00 3.11
1446 1462 1.519455 CGAGACACGAATCTGGGGC 60.519 63.158 0.00 0.00 45.77 5.80
1488 1510 5.008331 CCACCAGTCTACACTCTACAGTAA 58.992 45.833 0.00 0.00 0.00 2.24
1490 1512 3.422796 CCACCAGTCTACACTCTACAGT 58.577 50.000 0.00 0.00 0.00 3.55
1507 1851 0.685097 TTGTCAGAGTACCTGCCACC 59.315 55.000 6.51 0.00 42.62 4.61
1557 1939 5.533482 CATCCTAGGGAGAGATTACAAACG 58.467 45.833 9.46 0.00 34.05 3.60
1570 1952 3.709653 AGAAATAACACGCATCCTAGGGA 59.290 43.478 9.46 0.00 35.55 4.20
1573 1955 4.508124 GGTGAGAAATAACACGCATCCTAG 59.492 45.833 0.00 0.00 37.82 3.02
1581 1993 9.650371 CATGTAAATATGGTGAGAAATAACACG 57.350 33.333 0.00 0.00 37.82 4.49
1633 2046 1.455822 AGTTGTTCCATCCCAGGGAA 58.544 50.000 13.94 0.00 41.98 3.97
1635 2051 3.669939 AATAGTTGTTCCATCCCAGGG 57.330 47.619 0.00 0.00 0.00 4.45
1639 2055 9.388506 CTCATCATATAATAGTTGTTCCATCCC 57.611 37.037 0.00 0.00 0.00 3.85
1783 2425 7.710475 GCAATTTACACTGGTTAAATATGCCAT 59.290 33.333 12.71 0.00 30.46 4.40
1786 2428 7.759433 AGTGCAATTTACACTGGTTAAATATGC 59.241 33.333 9.55 14.59 46.38 3.14
1805 2447 9.231297 ACAATACTGAAGTTATACAAGTGCAAT 57.769 29.630 0.00 0.00 0.00 3.56
1811 2453 7.011482 GGGAGCACAATACTGAAGTTATACAAG 59.989 40.741 0.00 0.00 0.00 3.16
1830 3346 1.377725 CCACATGGTGAGGGAGCAC 60.378 63.158 0.00 0.00 35.23 4.40
1842 3358 4.340097 AGATATTGTTGCATCACCCACATG 59.660 41.667 0.00 0.00 0.00 3.21
1946 3462 4.106925 CTGTCAGGGGCTCAGGGC 62.107 72.222 0.00 0.00 40.90 5.19
1976 3492 0.112995 AGCAGCCCCTTGATGTTCAA 59.887 50.000 0.00 0.00 34.79 2.69
2065 3581 4.522114 TGGTGAAGTTGTTCTTGATGTCA 58.478 39.130 0.00 0.00 36.40 3.58
2078 3594 3.716872 TCCTCTTCCTCTTTGGTGAAGTT 59.283 43.478 0.00 0.00 37.39 2.66
2112 3628 1.186200 GAAAGCCCATTGGTTCTCCC 58.814 55.000 1.20 0.00 32.32 4.30
2128 3644 3.314553 GTCACTCGACCTTCATTCGAAA 58.685 45.455 0.00 0.00 44.52 3.46
2148 3664 0.327591 AGGAGGTAAGACCGTCTCGT 59.672 55.000 0.35 0.00 44.90 4.18
2152 3668 2.159085 CCATTGAGGAGGTAAGACCGTC 60.159 54.545 0.00 0.00 44.90 4.79
2153 3669 1.831736 CCATTGAGGAGGTAAGACCGT 59.168 52.381 0.00 0.00 44.90 4.83
2154 3670 1.473434 GCCATTGAGGAGGTAAGACCG 60.473 57.143 0.00 0.00 39.97 4.79
2155 3671 1.840635 AGCCATTGAGGAGGTAAGACC 59.159 52.381 0.00 0.00 41.22 3.85
2156 3672 2.158885 GGAGCCATTGAGGAGGTAAGAC 60.159 54.545 0.00 0.00 41.22 3.01
2157 3673 2.119495 GGAGCCATTGAGGAGGTAAGA 58.881 52.381 0.00 0.00 41.22 2.10
2158 3674 2.103941 GAGGAGCCATTGAGGAGGTAAG 59.896 54.545 0.00 0.00 41.22 2.34
2159 3675 2.119495 GAGGAGCCATTGAGGAGGTAA 58.881 52.381 0.00 0.00 41.22 2.85
2160 3676 1.692762 GGAGGAGCCATTGAGGAGGTA 60.693 57.143 0.00 0.00 41.22 3.08
2161 3677 0.985490 GGAGGAGCCATTGAGGAGGT 60.985 60.000 0.00 0.00 41.22 3.85
2162 3678 0.984961 TGGAGGAGCCATTGAGGAGG 60.985 60.000 0.00 0.00 43.33 4.30
2163 3679 2.612760 TGGAGGAGCCATTGAGGAG 58.387 57.895 0.00 0.00 43.33 3.69
2164 3680 4.917476 TGGAGGAGCCATTGAGGA 57.083 55.556 0.00 0.00 43.33 3.71
2192 3710 3.535962 GAGCAGGAGGGAGGAGCG 61.536 72.222 0.00 0.00 0.00 5.03
2331 3849 1.380403 CGAGCACCGGAGAGTCATCT 61.380 60.000 9.46 0.00 38.98 2.90
2434 3952 0.391597 TTGTGTCGGAAGGGAGTGAC 59.608 55.000 0.00 0.00 0.00 3.67
2445 3963 2.328099 GCCTGAGCCTTTGTGTCGG 61.328 63.158 0.00 0.00 0.00 4.79
2499 4017 4.201891 GCAATCATGAGCGAGTCAATTTCT 60.202 41.667 0.09 0.00 39.19 2.52
3001 4519 3.052620 GAGCTGCGACGAGGTAGCA 62.053 63.158 18.42 3.64 46.47 3.49
3002 4520 2.272918 AAGAGCTGCGACGAGGTAGC 62.273 60.000 0.00 11.19 44.71 3.58
3106 4624 0.391661 ATCCATTCGTGCGCAGAAGT 60.392 50.000 12.22 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.