Multiple sequence alignment - TraesCS6D01G192100

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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 TraesCS6D01G192100 chr6D 100.000 7127 0 0 1 7127 265174114 265181240 0.000000e+00 13162.0
1 TraesCS6D01G192100 chr6D 92.560 1492 71 9 2023 3492 352826555 352825082 0.000000e+00 2104.0
2 TraesCS6D01G192100 chr6A 97.060 3299 71 12 3480 6778 374889458 374892730 0.000000e+00 5531.0
3 TraesCS6D01G192100 chr6A 97.075 1778 47 4 1 1775 374887201 374888976 0.000000e+00 2990.0
4 TraesCS6D01G192100 chr6A 98.824 170 2 0 1824 1993 374889191 374889360 3.230000e-78 303.0
5 TraesCS6D01G192100 chr6A 97.414 116 3 0 7012 7127 374974555 374974670 1.570000e-46 198.0
6 TraesCS6D01G192100 chr6A 82.143 224 17 6 6793 7016 374892718 374892918 3.420000e-38 171.0
7 TraesCS6D01G192100 chr6B 95.814 2413 62 21 4565 6959 412157609 412155218 0.000000e+00 3860.0
8 TraesCS6D01G192100 chr6B 96.038 1262 23 8 508 1744 412162556 412161297 0.000000e+00 2028.0
9 TraesCS6D01G192100 chr6B 96.897 709 22 0 3480 4188 412161024 412160316 0.000000e+00 1188.0
10 TraesCS6D01G192100 chr6B 96.374 524 18 1 1 523 412163233 412162710 0.000000e+00 861.0
11 TraesCS6D01G192100 chr6B 98.137 161 3 0 6967 7127 412154931 412154771 1.510000e-71 281.0
12 TraesCS6D01G192100 chr6B 95.429 175 8 0 1819 1993 412161296 412161122 5.440000e-71 279.0
13 TraesCS6D01G192100 chr5D 94.733 1481 51 10 2023 3480 322583620 322582144 0.000000e+00 2278.0
14 TraesCS6D01G192100 chr5D 91.231 1072 71 4 2023 3072 521102656 521103726 0.000000e+00 1437.0
15 TraesCS6D01G192100 chrUn 94.217 1487 53 12 2023 3481 33042584 33041103 0.000000e+00 2239.0
16 TraesCS6D01G192100 chr1D 92.963 1478 67 11 2024 3479 10628736 10630198 0.000000e+00 2119.0
17 TraesCS6D01G192100 chr3A 92.260 1460 100 6 2025 3482 743546767 743548215 0.000000e+00 2058.0
18 TraesCS6D01G192100 chr3A 90.811 1480 99 7 2023 3480 340811374 340812838 0.000000e+00 1945.0
19 TraesCS6D01G192100 chr3A 91.828 930 51 4 2023 2931 596508144 596507219 0.000000e+00 1273.0
20 TraesCS6D01G192100 chr3A 92.176 818 40 6 2037 2830 10596692 10597509 0.000000e+00 1134.0
21 TraesCS6D01G192100 chr3D 93.706 1287 50 6 2216 3480 608484208 608482931 0.000000e+00 1899.0
22 TraesCS6D01G192100 chr3D 89.948 965 73 4 2539 3481 149236964 149236002 0.000000e+00 1223.0
23 TraesCS6D01G192100 chr3D 90.654 107 10 0 6598 6704 532994071 532994177 7.450000e-30 143.0
24 TraesCS6D01G192100 chr2A 91.576 1282 80 10 2222 3480 712551074 712552350 0.000000e+00 1744.0
25 TraesCS6D01G192100 chr2A 94.394 1106 40 3 2395 3479 666986234 666987338 0.000000e+00 1679.0
26 TraesCS6D01G192100 chr2A 91.625 800 42 5 2023 2799 102105235 102104438 0.000000e+00 1083.0
27 TraesCS6D01G192100 chr4A 92.227 862 42 10 2640 3479 93902439 93903297 0.000000e+00 1197.0
28 TraesCS6D01G192100 chr7B 93.003 686 46 2 2023 2707 607302609 607301925 0.000000e+00 1000.0
29 TraesCS6D01G192100 chr5B 90.816 98 9 0 6607 6704 592354916 592355013 1.610000e-26 132.0
30 TraesCS6D01G192100 chr4D 90.099 101 8 2 6608 6708 112074085 112073987 5.800000e-26 130.0
31 TraesCS6D01G192100 chr4D 90.541 74 5 1 6865 6938 362125594 362125665 5.880000e-16 97.1
32 TraesCS6D01G192100 chr4B 88.073 109 13 0 6604 6712 541857880 541857772 5.800000e-26 130.0
33 TraesCS6D01G192100 chr4B 89.109 101 9 2 6608 6708 172735589 172735491 2.700000e-24 124.0
34 TraesCS6D01G192100 chr1A 87.719 114 9 4 6599 6708 82720006 82720118 2.090000e-25 128.0
35 TraesCS6D01G192100 chr7D 88.462 104 12 0 6605 6708 530896940 530897043 7.510000e-25 126.0


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 TraesCS6D01G192100 chr6D 265174114 265181240 7126 False 13162.000000 13162 100.000000 1 7127 1 chr6D.!!$F1 7126
1 TraesCS6D01G192100 chr6D 352825082 352826555 1473 True 2104.000000 2104 92.560000 2023 3492 1 chr6D.!!$R1 1469
2 TraesCS6D01G192100 chr6A 374887201 374892918 5717 False 2248.750000 5531 93.775500 1 7016 4 chr6A.!!$F2 7015
3 TraesCS6D01G192100 chr6B 412154771 412163233 8462 True 1416.166667 3860 96.448167 1 7127 6 chr6B.!!$R1 7126
4 TraesCS6D01G192100 chr5D 322582144 322583620 1476 True 2278.000000 2278 94.733000 2023 3480 1 chr5D.!!$R1 1457
5 TraesCS6D01G192100 chr5D 521102656 521103726 1070 False 1437.000000 1437 91.231000 2023 3072 1 chr5D.!!$F1 1049
6 TraesCS6D01G192100 chrUn 33041103 33042584 1481 True 2239.000000 2239 94.217000 2023 3481 1 chrUn.!!$R1 1458
7 TraesCS6D01G192100 chr1D 10628736 10630198 1462 False 2119.000000 2119 92.963000 2024 3479 1 chr1D.!!$F1 1455
8 TraesCS6D01G192100 chr3A 743546767 743548215 1448 False 2058.000000 2058 92.260000 2025 3482 1 chr3A.!!$F3 1457
9 TraesCS6D01G192100 chr3A 340811374 340812838 1464 False 1945.000000 1945 90.811000 2023 3480 1 chr3A.!!$F2 1457
10 TraesCS6D01G192100 chr3A 596507219 596508144 925 True 1273.000000 1273 91.828000 2023 2931 1 chr3A.!!$R1 908
11 TraesCS6D01G192100 chr3A 10596692 10597509 817 False 1134.000000 1134 92.176000 2037 2830 1 chr3A.!!$F1 793
12 TraesCS6D01G192100 chr3D 608482931 608484208 1277 True 1899.000000 1899 93.706000 2216 3480 1 chr3D.!!$R2 1264
13 TraesCS6D01G192100 chr3D 149236002 149236964 962 True 1223.000000 1223 89.948000 2539 3481 1 chr3D.!!$R1 942
14 TraesCS6D01G192100 chr2A 712551074 712552350 1276 False 1744.000000 1744 91.576000 2222 3480 1 chr2A.!!$F2 1258
15 TraesCS6D01G192100 chr2A 666986234 666987338 1104 False 1679.000000 1679 94.394000 2395 3479 1 chr2A.!!$F1 1084
16 TraesCS6D01G192100 chr2A 102104438 102105235 797 True 1083.000000 1083 91.625000 2023 2799 1 chr2A.!!$R1 776
17 TraesCS6D01G192100 chr4A 93902439 93903297 858 False 1197.000000 1197 92.227000 2640 3479 1 chr4A.!!$F1 839
18 TraesCS6D01G192100 chr7B 607301925 607302609 684 True 1000.000000 1000 93.003000 2023 2707 1 chr7B.!!$R1 684

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
130 131 0.249911 ACAGAGAAAAGCTTCGCGGT 60.250 50.000 6.13 0.0 36.56 5.68 F
1033 1211 0.719465 CACGTTCTATGCGGGTGAAC 59.281 55.000 0.00 0.0 37.36 3.18 F
2001 2364 0.904394 TTGGATTTCTTGGGGGCTGC 60.904 55.000 0.00 0.0 0.00 5.25 F
3040 3467 0.174389 CTACGCTGAGTCATGCCTGT 59.826 55.000 0.00 0.0 0.00 4.00 F
3823 4251 0.166814 GCAAAGTGCACGCCTTCTAG 59.833 55.000 12.01 0.0 44.26 2.43 F
5644 8409 1.810151 TGCCGCTTTCAAGGTAACATC 59.190 47.619 0.00 0.0 41.41 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 2013 0.196118 ACAGGGAAGAGGGGGAAAGA 59.804 55.000 0.00 0.0 0.0 2.52 R
2802 3214 0.250727 CCGTCAAGGACCCACACAAT 60.251 55.000 0.00 0.0 45.0 2.71 R
3598 4026 1.078497 CACTACATGCTTCCCCGCA 60.078 57.895 0.00 0.0 45.1 5.69 R
4956 7716 2.161855 CAGGACTATGCTGCACCAAAA 58.838 47.619 3.57 0.0 0.0 2.44 R
5814 8579 2.104622 TGCACTTGGTCTGATGTTCTGA 59.895 45.455 0.00 0.0 0.0 3.27 R
6783 9561 0.171903 GCCATGCTTGCCAACTACAG 59.828 55.000 0.00 0.0 0.0 2.74 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
86 87 0.397816 CGGTTCCATCTCCCTCTCCT 60.398 60.000 0.00 0.00 0.00 3.69
97 98 1.847968 CCTCTCCTGGGGTGGTTGT 60.848 63.158 6.51 0.00 0.00 3.32
130 131 0.249911 ACAGAGAAAAGCTTCGCGGT 60.250 50.000 6.13 0.00 36.56 5.68
435 436 4.460948 ACTCATGGGTTTTCAATGCATC 57.539 40.909 0.00 0.00 0.00 3.91
522 694 5.296531 GGGTCGTAGTTGGTTCTTTTTGTTA 59.703 40.000 0.00 0.00 0.00 2.41
651 824 4.830015 GTTCGTATACCAACTTCCGAAC 57.170 45.455 6.15 6.93 44.57 3.95
1033 1211 0.719465 CACGTTCTATGCGGGTGAAC 59.281 55.000 0.00 0.00 37.36 3.18
1154 1332 4.803098 AAGGCTCGTCTGTTTACACTAT 57.197 40.909 0.00 0.00 0.00 2.12
1578 1763 2.496817 CTGGAGCCTCGTGTAGCC 59.503 66.667 0.00 0.00 0.00 3.93
1629 1814 2.151881 TGGAATGTTTGCATGCACAC 57.848 45.000 26.37 26.37 35.15 3.82
1677 1874 4.864247 CCTGGTAAGATTTTCCATTTTGCG 59.136 41.667 0.00 0.00 0.00 4.85
1712 1909 6.430007 AGGTGAATTTCTGCAAAGAGGATAT 58.570 36.000 0.00 0.00 0.00 1.63
1730 1927 2.978156 ATTGGCTTTCCTTCTGTCCA 57.022 45.000 0.00 0.00 0.00 4.02
1766 1963 4.707448 AGTGGTACTGTTGTAGGATCTCTG 59.293 45.833 0.00 0.00 0.00 3.35
1768 1965 5.047235 GTGGTACTGTTGTAGGATCTCTGTT 60.047 44.000 0.00 0.00 0.00 3.16
1775 1972 4.271696 TGTAGGATCTCTGTTTGTGTGG 57.728 45.455 0.00 0.00 0.00 4.17
1776 1973 3.901222 TGTAGGATCTCTGTTTGTGTGGA 59.099 43.478 0.00 0.00 0.00 4.02
1777 1974 3.409026 AGGATCTCTGTTTGTGTGGAC 57.591 47.619 0.00 0.00 0.00 4.02
1778 1975 2.705658 AGGATCTCTGTTTGTGTGGACA 59.294 45.455 0.00 0.00 0.00 4.02
1779 1976 3.328931 AGGATCTCTGTTTGTGTGGACAT 59.671 43.478 0.00 0.00 30.13 3.06
1780 1977 3.438087 GGATCTCTGTTTGTGTGGACATG 59.562 47.826 0.00 0.00 30.13 3.21
1781 1978 3.558931 TCTCTGTTTGTGTGGACATGT 57.441 42.857 0.00 0.00 30.13 3.21
1782 1979 3.884895 TCTCTGTTTGTGTGGACATGTT 58.115 40.909 0.00 0.00 30.13 2.71
1783 1980 3.876914 TCTCTGTTTGTGTGGACATGTTC 59.123 43.478 0.00 0.00 30.13 3.18
1784 1981 3.615155 TCTGTTTGTGTGGACATGTTCA 58.385 40.909 1.52 1.52 30.13 3.18
1785 1982 3.627123 TCTGTTTGTGTGGACATGTTCAG 59.373 43.478 7.20 0.00 30.13 3.02
1786 1983 2.687425 TGTTTGTGTGGACATGTTCAGG 59.313 45.455 7.20 0.00 30.13 3.86
1787 1984 2.687935 GTTTGTGTGGACATGTTCAGGT 59.312 45.455 7.20 0.00 30.13 4.00
1788 1985 2.727123 TGTGTGGACATGTTCAGGTT 57.273 45.000 7.20 0.00 0.00 3.50
1789 1986 3.011566 TGTGTGGACATGTTCAGGTTT 57.988 42.857 7.20 0.00 0.00 3.27
1790 1987 3.360867 TGTGTGGACATGTTCAGGTTTT 58.639 40.909 7.20 0.00 0.00 2.43
1791 1988 3.766591 TGTGTGGACATGTTCAGGTTTTT 59.233 39.130 7.20 0.00 0.00 1.94
1970 2333 4.981674 CGTACTGTTACTTTTACCGTTGGA 59.018 41.667 0.00 0.00 0.00 3.53
1993 2356 8.415553 TGGAATAGCAATGTATTGGATTTCTTG 58.584 33.333 6.72 0.00 38.21 3.02
1994 2357 7.869429 GGAATAGCAATGTATTGGATTTCTTGG 59.131 37.037 6.72 0.00 38.21 3.61
1995 2358 5.603170 AGCAATGTATTGGATTTCTTGGG 57.397 39.130 6.72 0.00 38.21 4.12
1996 2359 4.406649 AGCAATGTATTGGATTTCTTGGGG 59.593 41.667 6.72 0.00 38.21 4.96
1998 2361 2.745968 TGTATTGGATTTCTTGGGGGC 58.254 47.619 0.00 0.00 0.00 5.80
2000 2363 1.870064 ATTGGATTTCTTGGGGGCTG 58.130 50.000 0.00 0.00 0.00 4.85
2001 2364 0.904394 TTGGATTTCTTGGGGGCTGC 60.904 55.000 0.00 0.00 0.00 5.25
2002 2365 2.418083 GGATTTCTTGGGGGCTGCG 61.418 63.158 0.00 0.00 0.00 5.18
2003 2366 3.068729 GATTTCTTGGGGGCTGCGC 62.069 63.158 8.35 8.35 0.00 6.09
2708 3094 1.107114 CGGTCTATGTCTGCTCCTGT 58.893 55.000 0.00 0.00 0.00 4.00
2795 3207 1.002868 CCTTGAGGGCTGAGTGGTG 60.003 63.158 0.00 0.00 0.00 4.17
2796 3208 1.002868 CTTGAGGGCTGAGTGGTGG 60.003 63.158 0.00 0.00 0.00 4.61
2797 3209 1.770110 TTGAGGGCTGAGTGGTGGT 60.770 57.895 0.00 0.00 0.00 4.16
2798 3210 2.055689 TTGAGGGCTGAGTGGTGGTG 62.056 60.000 0.00 0.00 0.00 4.17
2799 3211 3.252284 AGGGCTGAGTGGTGGTGG 61.252 66.667 0.00 0.00 0.00 4.61
2800 3212 4.351054 GGGCTGAGTGGTGGTGGG 62.351 72.222 0.00 0.00 0.00 4.61
2802 3214 4.269523 GCTGAGTGGTGGTGGGCA 62.270 66.667 0.00 0.00 0.00 5.36
2803 3215 2.759114 CTGAGTGGTGGTGGGCAT 59.241 61.111 0.00 0.00 0.00 4.40
2804 3216 1.075482 CTGAGTGGTGGTGGGCATT 59.925 57.895 0.00 0.00 0.00 3.56
2805 3217 1.228521 TGAGTGGTGGTGGGCATTG 60.229 57.895 0.00 0.00 0.00 2.82
2806 3218 1.228552 GAGTGGTGGTGGGCATTGT 60.229 57.895 0.00 0.00 0.00 2.71
2807 3219 1.526575 GAGTGGTGGTGGGCATTGTG 61.527 60.000 0.00 0.00 0.00 3.33
2808 3220 1.832167 GTGGTGGTGGGCATTGTGT 60.832 57.895 0.00 0.00 0.00 3.72
3040 3467 0.174389 CTACGCTGAGTCATGCCTGT 59.826 55.000 0.00 0.00 0.00 4.00
3083 3510 0.800300 CTCTTCCAGAGTCTTCGCGC 60.800 60.000 0.00 0.00 37.57 6.86
3282 3709 5.173774 TGTTAGTCCCGATACGTTATGTC 57.826 43.478 0.00 0.00 0.00 3.06
3823 4251 0.166814 GCAAAGTGCACGCCTTCTAG 59.833 55.000 12.01 0.00 44.26 2.43
3847 4275 6.149474 AGGTTATAAATGTGTGTGACTTCTGC 59.851 38.462 0.00 0.00 0.00 4.26
3925 4353 3.752796 GCACATGCATTGGCTGATT 57.247 47.368 11.19 0.00 41.91 2.57
3990 4418 6.369065 ACACACTTAGTAAATAGCTTGCACTC 59.631 38.462 0.00 0.00 0.00 3.51
4067 4495 4.383118 CCGACTTGGATTCAGGTGTTCTAT 60.383 45.833 0.00 0.00 42.00 1.98
4227 4655 4.702131 GCATACACCCATCTCTTTTGTCTT 59.298 41.667 0.00 0.00 0.00 3.01
4239 4667 4.843147 TCTTTTGTCTTGTTGCATGTACG 58.157 39.130 0.00 0.00 0.00 3.67
4374 4802 6.510960 GCATGTGCCTTTTATTGTTTTCGTTT 60.511 34.615 0.00 0.00 34.31 3.60
4375 4803 6.576551 TGTGCCTTTTATTGTTTTCGTTTC 57.423 33.333 0.00 0.00 0.00 2.78
4387 4815 4.038080 CGTTTCGGGCAACTGGGC 62.038 66.667 0.00 0.00 45.79 5.36
4649 7407 6.470877 TGTGAACGTCTTCAAAATTTGTTAGC 59.529 34.615 5.56 1.87 38.17 3.09
4660 7418 2.300956 TTTGTTAGCTCCATTGGCCA 57.699 45.000 0.00 0.00 0.00 5.36
4843 7602 6.259608 CGTAAGGTCGAGAAAGAGGAGTTATA 59.740 42.308 0.00 0.00 0.00 0.98
4956 7716 9.737427 CAAAGAGACGTTGACAGATAGTTATAT 57.263 33.333 0.00 0.00 0.00 0.86
4965 7725 8.673711 GTTGACAGATAGTTATATTTTGGTGCA 58.326 33.333 0.00 0.00 0.00 4.57
4966 7726 8.437360 TGACAGATAGTTATATTTTGGTGCAG 57.563 34.615 0.00 0.00 0.00 4.41
5203 7967 5.369409 AATCTCAAATGATCTGCCTGAGA 57.631 39.130 15.13 15.13 44.78 3.27
5223 7987 8.610896 CCTGAGAAAATGTTTGTGCAAATAAAA 58.389 29.630 0.46 0.00 32.36 1.52
5371 8135 3.270877 GACCGCAGAAACAGGAACATAT 58.729 45.455 0.00 0.00 0.00 1.78
5442 8207 7.483307 TCAGTTCTTGAACCTTTTCATTTCTG 58.517 34.615 9.58 0.00 41.50 3.02
5561 8326 2.124011 ACAGCTTTGCGATTGTGTTG 57.876 45.000 0.00 0.00 0.00 3.33
5644 8409 1.810151 TGCCGCTTTCAAGGTAACATC 59.190 47.619 0.00 0.00 41.41 3.06
5682 8447 9.248291 GTATAATCATACCCATTTGCTGTTTTG 57.752 33.333 0.00 0.00 32.33 2.44
5685 8450 6.849085 TCATACCCATTTGCTGTTTTGTAT 57.151 33.333 0.00 0.00 0.00 2.29
5786 8551 8.428852 TGCATACACCTGTGTCATATATTAGTT 58.571 33.333 6.14 0.00 43.74 2.24
5910 8675 1.676006 CCAAGCGACAGACCAAACTTT 59.324 47.619 0.00 0.00 0.00 2.66
6578 9348 4.938226 AGAGCCAGAGAAAAAGAATAACCG 59.062 41.667 0.00 0.00 0.00 4.44
6611 9381 8.742777 ACAAAACACTGATGCAATGATATACTT 58.257 29.630 0.00 0.00 0.00 2.24
6765 9543 4.698201 TGGAATCTGATAACGCCCAATA 57.302 40.909 0.00 0.00 0.00 1.90
6777 9555 1.472552 CGCCCAATACGAGGATGACAA 60.473 52.381 0.00 0.00 0.00 3.18
6778 9556 2.806745 CGCCCAATACGAGGATGACAAT 60.807 50.000 0.00 0.00 0.00 2.71
6781 9559 4.097892 GCCCAATACGAGGATGACAATTTT 59.902 41.667 0.00 0.00 0.00 1.82
6782 9560 5.298276 GCCCAATACGAGGATGACAATTTTA 59.702 40.000 0.00 0.00 0.00 1.52
6783 9561 6.725246 CCCAATACGAGGATGACAATTTTAC 58.275 40.000 0.00 0.00 0.00 2.01
6784 9562 6.542370 CCCAATACGAGGATGACAATTTTACT 59.458 38.462 0.00 0.00 0.00 2.24
6785 9563 7.409697 CCAATACGAGGATGACAATTTTACTG 58.590 38.462 0.00 0.00 0.00 2.74
6792 9570 7.413000 CGAGGATGACAATTTTACTGTAGTTGG 60.413 40.741 11.62 0.00 0.00 3.77
6810 9588 2.831597 GCAAGCATGGCAACTTTCC 58.168 52.632 3.61 0.00 32.79 3.13
6849 9627 4.116747 TGACAGAAAATTGCCGTTTGTT 57.883 36.364 0.00 0.00 0.00 2.83
6911 9689 5.352284 CATCCTTACGTCACTAGAATTGCT 58.648 41.667 0.00 0.00 0.00 3.91
6933 9711 5.619981 GCTGTCGAAAACATTAGATTTGCCT 60.620 40.000 0.00 0.00 37.23 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 3.659092 CTGTCAAAAGCGGCGGCA 61.659 61.111 19.21 0.00 43.41 5.69
130 131 1.395608 GCGCATTTTAGTCCACGCTTA 59.604 47.619 0.30 0.00 42.81 3.09
257 258 3.906720 TCTTGTAACTACTCATGGCCC 57.093 47.619 0.00 0.00 0.00 5.80
260 261 5.891451 TCACGATCTTGTAACTACTCATGG 58.109 41.667 0.00 0.00 0.00 3.66
355 356 7.385752 AGTCCAGCACAAAATCACATAAATTTG 59.614 33.333 0.00 0.00 38.42 2.32
482 483 2.496070 CGACCCTGTTCACATAGAGGAA 59.504 50.000 0.00 0.00 0.00 3.36
783 959 4.887071 ACAAGTTGCTCCAAAGAATGTACA 59.113 37.500 1.81 0.00 0.00 2.90
841 1019 3.248363 GCGCAGAACATAGATGCATTACA 59.752 43.478 0.30 0.00 39.97 2.41
1033 1211 1.667724 GCTGGGATCAATGTGAAGACG 59.332 52.381 0.00 0.00 0.00 4.18
1154 1332 9.176460 TCATACAAATCAGCAAATTGTAGATCA 57.824 29.630 0.00 0.00 41.34 2.92
1204 1389 5.048013 CCCATCATCATGAATCATCAACTGG 60.048 44.000 0.00 0.00 39.49 4.00
1578 1763 2.721274 TGTCCAATGCAAATCCAACG 57.279 45.000 0.00 0.00 0.00 4.10
1677 1874 7.816640 TGCAGAAATTCACCTAGTATTCAAAC 58.183 34.615 0.00 0.00 0.00 2.93
1712 1909 2.746279 TTGGACAGAAGGAAAGCCAA 57.254 45.000 0.00 0.00 36.29 4.52
1730 1927 7.567622 ACAACAGTACCACTCAGGGTATATATT 59.432 37.037 0.00 0.00 44.78 1.28
1766 1963 2.687935 ACCTGAACATGTCCACACAAAC 59.312 45.455 0.00 0.00 35.64 2.93
1768 1965 2.727123 ACCTGAACATGTCCACACAA 57.273 45.000 0.00 0.00 35.64 3.33
1813 2010 1.078356 GGAAGAGGGGGAAAGACGC 60.078 63.158 0.00 0.00 0.00 5.19
1814 2011 0.910088 AGGGAAGAGGGGGAAAGACG 60.910 60.000 0.00 0.00 0.00 4.18
1815 2012 0.621082 CAGGGAAGAGGGGGAAAGAC 59.379 60.000 0.00 0.00 0.00 3.01
1816 2013 0.196118 ACAGGGAAGAGGGGGAAAGA 59.804 55.000 0.00 0.00 0.00 2.52
1817 2014 0.329596 CACAGGGAAGAGGGGGAAAG 59.670 60.000 0.00 0.00 0.00 2.62
1970 2333 7.202029 CCCCAAGAAATCCAATACATTGCTATT 60.202 37.037 0.00 0.00 36.48 1.73
2007 2370 2.358737 GTCCCCACCTGCTTGACG 60.359 66.667 0.00 0.00 0.00 4.35
2008 2371 2.034221 GGTCCCCACCTGCTTGAC 59.966 66.667 0.00 0.00 40.00 3.18
2010 2373 3.579302 TGGGTCCCCACCTGCTTG 61.579 66.667 5.13 0.00 43.22 4.01
2795 3207 2.203625 ACCCACACAATGCCCACC 60.204 61.111 0.00 0.00 0.00 4.61
2796 3208 2.275380 GGACCCACACAATGCCCAC 61.275 63.158 0.00 0.00 0.00 4.61
2797 3209 2.017668 AAGGACCCACACAATGCCCA 62.018 55.000 0.00 0.00 0.00 5.36
2798 3210 1.228862 AAGGACCCACACAATGCCC 60.229 57.895 0.00 0.00 0.00 5.36
2799 3211 0.539438 TCAAGGACCCACACAATGCC 60.539 55.000 0.00 0.00 0.00 4.40
2800 3212 0.598065 GTCAAGGACCCACACAATGC 59.402 55.000 0.00 0.00 0.00 3.56
2801 3213 0.874390 CGTCAAGGACCCACACAATG 59.126 55.000 0.00 0.00 0.00 2.82
2802 3214 0.250727 CCGTCAAGGACCCACACAAT 60.251 55.000 0.00 0.00 45.00 2.71
2803 3215 1.147376 CCGTCAAGGACCCACACAA 59.853 57.895 0.00 0.00 45.00 3.33
2804 3216 1.628238 AACCGTCAAGGACCCACACA 61.628 55.000 0.00 0.00 45.00 3.72
2805 3217 1.147600 AACCGTCAAGGACCCACAC 59.852 57.895 0.00 0.00 45.00 3.82
2806 3218 1.147376 CAACCGTCAAGGACCCACA 59.853 57.895 0.00 0.00 45.00 4.17
2807 3219 2.258726 GCAACCGTCAAGGACCCAC 61.259 63.158 0.00 0.00 45.00 4.61
2808 3220 2.112297 GCAACCGTCAAGGACCCA 59.888 61.111 0.00 0.00 45.00 4.51
3282 3709 2.726180 GTCGTCGCCGATCCATCG 60.726 66.667 0.00 1.77 46.30 3.84
3598 4026 1.078497 CACTACATGCTTCCCCGCA 60.078 57.895 0.00 0.00 45.10 5.69
3815 4243 6.821665 TCACACACATTTATAACCTAGAAGGC 59.178 38.462 0.00 0.00 39.63 4.35
3823 4251 6.072728 TGCAGAAGTCACACACATTTATAACC 60.073 38.462 0.00 0.00 0.00 2.85
3990 4418 7.285401 AGGCATTGTTTCCTGGTTATAGTTATG 59.715 37.037 0.00 0.00 0.00 1.90
4067 4495 5.183713 CCATGTTTAGCAACCTTCATCTGAA 59.816 40.000 0.00 0.00 31.02 3.02
4227 4655 4.024725 GGTCTAAACAACGTACATGCAACA 60.025 41.667 0.00 0.00 0.00 3.33
4239 4667 6.368213 CCAATAACTTGACGGTCTAAACAAC 58.632 40.000 9.88 0.00 34.04 3.32
4387 4815 4.278170 TGTTAGTCATGAAAACAAGCAGGG 59.722 41.667 18.00 0.00 30.54 4.45
4649 7407 8.130671 AGAAATATATTCATTGGCCAATGGAG 57.869 34.615 43.41 27.40 46.08 3.86
4843 7602 8.509690 CAAGTCATCATTCACTGAACAACTATT 58.490 33.333 0.00 0.00 37.44 1.73
4956 7716 2.161855 CAGGACTATGCTGCACCAAAA 58.838 47.619 3.57 0.00 0.00 2.44
4965 7725 6.711277 TGTCTAATGAAAACAGGACTATGCT 58.289 36.000 0.00 0.00 0.00 3.79
4966 7726 6.985188 TGTCTAATGAAAACAGGACTATGC 57.015 37.500 0.00 0.00 0.00 3.14
5097 7861 6.553100 AGGAAATGGTAGATCAACAAAACCAA 59.447 34.615 0.00 0.00 43.10 3.67
5223 7987 7.363268 GGCAAAAACTATGGACTCAGAATCAAT 60.363 37.037 0.00 0.00 0.00 2.57
5561 8326 6.527057 AGTCTATTGTGTAGTAGTTCCCAC 57.473 41.667 0.00 0.00 0.00 4.61
5668 8433 8.702438 CAAGAAAGTATACAAAACAGCAAATGG 58.298 33.333 5.50 0.00 0.00 3.16
5685 8450 9.290988 TGCAACATAAATAGGTTCAAGAAAGTA 57.709 29.630 0.00 0.00 0.00 2.24
5756 8521 8.777865 ATATATGACACAGGTGTATGCATTAC 57.222 34.615 3.54 4.78 45.05 1.89
5793 8558 8.924511 TCTGAAGAAAATGAGGTTTCATAAGT 57.075 30.769 0.97 0.00 43.20 2.24
5801 8566 7.000472 TCTGATGTTCTGAAGAAAATGAGGTT 59.000 34.615 9.09 0.00 34.86 3.50
5814 8579 2.104622 TGCACTTGGTCTGATGTTCTGA 59.895 45.455 0.00 0.00 0.00 3.27
5910 8675 6.313519 AGAAGCATTTGAACTATCTGGGTA 57.686 37.500 0.00 0.00 0.00 3.69
6435 9202 3.269538 TGGAACAAAGGAAGTCGTCAA 57.730 42.857 0.00 0.00 31.92 3.18
6436 9203 2.992124 TGGAACAAAGGAAGTCGTCA 57.008 45.000 0.00 0.00 31.92 4.35
6578 9348 1.980844 CATCAGTGTTTTGTGCATCGC 59.019 47.619 0.00 0.00 0.00 4.58
6611 9381 4.946160 ACACTTATTTTGGGATGGAGGA 57.054 40.909 0.00 0.00 0.00 3.71
6726 9504 9.740239 CAGATTCCAAAATCATTACCATTAGTG 57.260 33.333 1.41 0.00 43.21 2.74
6765 9543 6.698380 ACTACAGTAAAATTGTCATCCTCGT 58.302 36.000 0.00 0.00 0.00 4.18
6777 9555 5.336690 CCATGCTTGCCAACTACAGTAAAAT 60.337 40.000 0.00 0.00 0.00 1.82
6778 9556 4.022416 CCATGCTTGCCAACTACAGTAAAA 60.022 41.667 0.00 0.00 0.00 1.52
6781 9559 2.710377 CCATGCTTGCCAACTACAGTA 58.290 47.619 0.00 0.00 0.00 2.74
6782 9560 1.538047 CCATGCTTGCCAACTACAGT 58.462 50.000 0.00 0.00 0.00 3.55
6783 9561 0.171903 GCCATGCTTGCCAACTACAG 59.828 55.000 0.00 0.00 0.00 2.74
6784 9562 0.539207 TGCCATGCTTGCCAACTACA 60.539 50.000 0.00 0.00 0.00 2.74
6785 9563 0.602562 TTGCCATGCTTGCCAACTAC 59.397 50.000 0.00 0.00 0.00 2.73
6792 9570 0.319405 AGGAAAGTTGCCATGCTTGC 59.681 50.000 1.70 0.00 0.00 4.01
6911 9689 5.957842 AGGCAAATCTAATGTTTTCGACA 57.042 34.783 0.00 0.00 43.71 4.35
6933 9711 4.651585 GCAAATGGCGCTTCACAA 57.348 50.000 7.64 0.00 0.00 3.33
7020 10077 8.030692 CACTTGATAATTTGATGTCACATTGGT 58.969 33.333 0.00 0.00 29.99 3.67


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

AutoCloner maintained by Alex Coulton.