Multiple sequence alignment - TraesCS7A01G006900

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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 TraesCS7A01G006900 chr7A 100.000 4145 0 0 1 4145 3272097 3276241 0.000000e+00 7655.0
1 TraesCS7A01G006900 chr7A 98.157 597 9 1 1 595 2082475 2083071 0.000000e+00 1040.0
2 TraesCS7A01G006900 chr7A 99.585 482 0 2 1 482 3297993 3298472 0.000000e+00 878.0
3 TraesCS7A01G006900 chr7A 77.709 803 149 17 1120 1901 2827338 2828131 8.120000e-127 464.0
4 TraesCS7A01G006900 chr7A 77.290 797 158 12 1121 1901 2093388 2094177 8.170000e-122 448.0
5 TraesCS7A01G006900 chr7A 80.000 335 46 15 637 954 3217564 3217234 1.160000e-55 228.0
6 TraesCS7A01G006900 chr7D 91.697 2216 117 20 601 2782 2649539 2651721 0.000000e+00 3011.0
7 TraesCS7A01G006900 chr7D 85.519 953 112 11 1127 2071 3685928 3686862 0.000000e+00 972.0
8 TraesCS7A01G006900 chr7D 77.940 961 163 32 1046 1977 3858796 3857856 4.680000e-154 555.0
9 TraesCS7A01G006900 chr7D 80.952 315 49 7 637 947 3796258 3795951 5.360000e-59 239.0
10 TraesCS7A01G006900 chr7D 75.567 397 77 14 1163 1546 9309706 9310095 1.180000e-40 178.0
11 TraesCS7A01G006900 chr7D 78.495 186 21 15 2615 2782 3688219 3688403 2.040000e-18 104.0
12 TraesCS7A01G006900 chr7D 73.606 269 52 15 1162 1416 10501205 10500942 7.380000e-13 86.1
13 TraesCS7A01G006900 chr4A 86.061 1399 114 30 2788 4145 741585257 741586615 0.000000e+00 1428.0
14 TraesCS7A01G006900 chr4A 85.042 956 112 21 1117 2053 740219874 740218931 0.000000e+00 944.0
15 TraesCS7A01G006900 chr4A 86.253 902 87 16 2788 3666 742044098 742044985 0.000000e+00 944.0
16 TraesCS7A01G006900 chr4A 86.108 907 89 16 2782 3665 739851445 739852337 0.000000e+00 942.0
17 TraesCS7A01G006900 chr4A 85.870 920 80 17 2788 3666 739638953 739639863 0.000000e+00 933.0
18 TraesCS7A01G006900 chr4A 87.989 741 74 7 3408 4145 739640740 739641468 0.000000e+00 861.0
19 TraesCS7A01G006900 chr4A 87.989 741 74 7 3408 4145 742045863 742046591 0.000000e+00 861.0
20 TraesCS7A01G006900 chr4A 90.159 630 45 8 3044 3666 740027029 740026410 0.000000e+00 804.0
21 TraesCS7A01G006900 chr4A 87.678 633 59 12 3044 3666 740549174 740549797 0.000000e+00 719.0
22 TraesCS7A01G006900 chr4A 88.497 539 53 6 3408 3943 739853212 739853744 0.000000e+00 643.0
23 TraesCS7A01G006900 chr4A 88.126 539 55 6 3408 3943 740550674 740551206 2.100000e-177 632.0
24 TraesCS7A01G006900 chr4A 88.613 483 43 5 3659 4141 741496831 741496361 9.990000e-161 577.0
25 TraesCS7A01G006900 chr4A 89.318 440 35 4 3706 4145 740025474 740025047 3.640000e-150 542.0
26 TraesCS7A01G006900 chr4A 77.122 813 154 15 1111 1901 742036061 742035259 3.800000e-120 442.0
27 TraesCS7A01G006900 chr4A 77.037 810 154 15 1114 1901 740541138 740540339 1.770000e-118 436.0
28 TraesCS7A01G006900 chr4A 76.790 810 154 17 1114 1901 739630468 739629671 1.380000e-114 424.0
29 TraesCS7A01G006900 chr4A 81.264 459 73 7 82 536 739730165 739729716 3.940000e-95 359.0
30 TraesCS7A01G006900 chr4A 78.175 559 90 12 1 536 742125499 742124950 1.110000e-85 327.0
31 TraesCS7A01G006900 chr4A 88.211 246 23 1 2788 3027 740548882 740549127 5.240000e-74 289.0
32 TraesCS7A01G006900 chr4A 87.398 246 25 1 2788 3027 740037461 740037216 1.130000e-70 278.0
33 TraesCS7A01G006900 chr4A 87.923 207 19 1 3939 4145 740564412 740564612 5.360000e-59 239.0
34 TraesCS7A01G006900 chr4A 87.440 207 20 1 3939 4145 739858639 739858839 2.490000e-57 233.0
35 TraesCS7A01G006900 chr4A 82.400 125 15 4 845 963 739728513 739728390 7.330000e-18 102.0
36 TraesCS7A01G006900 chr4A 82.258 124 17 2 845 963 742123748 742123625 7.330000e-18 102.0
37 TraesCS7A01G006900 chr4A 96.667 60 2 0 2726 2785 740209426 740209367 2.640000e-17 100.0
38 TraesCS7A01G006900 chr4A 73.704 270 50 16 1162 1416 728503788 728503525 7.380000e-13 86.1


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 TraesCS7A01G006900 chr7A 3272097 3276241 4144 False 7655.000000 7655 100.0000 1 4145 1 chr7A.!!$F4 4144
1 TraesCS7A01G006900 chr7A 2082475 2083071 596 False 1040.000000 1040 98.1570 1 595 1 chr7A.!!$F1 594
2 TraesCS7A01G006900 chr7A 2827338 2828131 793 False 464.000000 464 77.7090 1120 1901 1 chr7A.!!$F3 781
3 TraesCS7A01G006900 chr7A 2093388 2094177 789 False 448.000000 448 77.2900 1121 1901 1 chr7A.!!$F2 780
4 TraesCS7A01G006900 chr7D 2649539 2651721 2182 False 3011.000000 3011 91.6970 601 2782 1 chr7D.!!$F1 2181
5 TraesCS7A01G006900 chr7D 3857856 3858796 940 True 555.000000 555 77.9400 1046 1977 1 chr7D.!!$R2 931
6 TraesCS7A01G006900 chr7D 3685928 3688403 2475 False 538.000000 972 82.0070 1127 2782 2 chr7D.!!$F3 1655
7 TraesCS7A01G006900 chr4A 741585257 741586615 1358 False 1428.000000 1428 86.0610 2788 4145 1 chr4A.!!$F3 1357
8 TraesCS7A01G006900 chr4A 740218931 740219874 943 True 944.000000 944 85.0420 1117 2053 1 chr4A.!!$R5 936
9 TraesCS7A01G006900 chr4A 742044098 742046591 2493 False 902.500000 944 87.1210 2788 4145 2 chr4A.!!$F7 1357
10 TraesCS7A01G006900 chr4A 739638953 739641468 2515 False 897.000000 933 86.9295 2788 4145 2 chr4A.!!$F4 1357
11 TraesCS7A01G006900 chr4A 739851445 739853744 2299 False 792.500000 942 87.3025 2782 3943 2 chr4A.!!$F5 1161
12 TraesCS7A01G006900 chr4A 740025047 740027029 1982 True 673.000000 804 89.7385 3044 4145 2 chr4A.!!$R10 1101
13 TraesCS7A01G006900 chr4A 740548882 740551206 2324 False 546.666667 719 88.0050 2788 3943 3 chr4A.!!$F6 1155
14 TraesCS7A01G006900 chr4A 742035259 742036061 802 True 442.000000 442 77.1220 1111 1901 1 chr4A.!!$R8 790
15 TraesCS7A01G006900 chr4A 740540339 740541138 799 True 436.000000 436 77.0370 1114 1901 1 chr4A.!!$R6 787
16 TraesCS7A01G006900 chr4A 739629671 739630468 797 True 424.000000 424 76.7900 1114 1901 1 chr4A.!!$R2 787
17 TraesCS7A01G006900 chr4A 739728390 739730165 1775 True 230.500000 359 81.8320 82 963 2 chr4A.!!$R9 881
18 TraesCS7A01G006900 chr4A 742123625 742125499 1874 True 214.500000 327 80.2165 1 963 2 chr4A.!!$R11 962

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
600 653 0.037232 GTTTCTCCTCCTCGGTGGTG 60.037 60.0 4.15 2.42 37.07 4.17 F
967 1965 0.107017 GCTAATTGGCTGGCTCCTCA 60.107 55.0 6.53 0.00 0.00 3.86 F
1901 2947 0.320374 TACTCCGACAACTTGGCCAG 59.680 55.0 5.11 2.72 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 3196 0.521735 GACCGTGGGAGCAAACAATC 59.478 55.0 0.00 0.0 0.0 2.67 R
2858 4840 0.613777 ACTTCCCCATCGAGTGTTCC 59.386 55.0 0.00 0.0 0.0 3.62 R
3610 6785 0.177836 TGGACGTTGCATGGATCGAT 59.822 50.0 22.25 0.0 0.0 3.59 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
379 404 0.326264 CTGACTCAAGGGTGAAGGGG 59.674 60.000 0.00 0.00 31.88 4.79
570 623 0.811281 CCTCATTCTTTTGCCGTCCC 59.189 55.000 0.00 0.00 0.00 4.46
595 648 1.797025 GTGTTGTTTCTCCTCCTCGG 58.203 55.000 0.00 0.00 0.00 4.63
596 649 1.070289 GTGTTGTTTCTCCTCCTCGGT 59.930 52.381 0.00 0.00 0.00 4.69
597 650 1.070134 TGTTGTTTCTCCTCCTCGGTG 59.930 52.381 0.00 0.00 0.00 4.94
598 651 0.685097 TTGTTTCTCCTCCTCGGTGG 59.315 55.000 0.00 0.00 37.10 4.61
599 652 0.471211 TGTTTCTCCTCCTCGGTGGT 60.471 55.000 4.15 0.00 37.07 4.16
600 653 0.037232 GTTTCTCCTCCTCGGTGGTG 60.037 60.000 4.15 2.42 37.07 4.17
602 1570 2.283966 CTCCTCCTCGGTGGTGGT 60.284 66.667 14.78 0.00 46.71 4.16
616 1584 1.574702 GGTGGTGACAAGGCGCTAAC 61.575 60.000 7.64 0.00 46.06 2.34
651 1619 9.884636 AGTTAATTAGTGTGCATCTAATGTGTA 57.115 29.630 20.12 11.23 37.90 2.90
679 1647 1.863267 TTTCAAATTTGGGCACGCAG 58.137 45.000 17.90 0.00 0.00 5.18
757 1729 0.537188 TGAGGTCGAGAAATGGGAGC 59.463 55.000 0.00 0.00 0.00 4.70
799 1771 0.689055 TGTGAGGCAGCTGTTGAGAT 59.311 50.000 16.64 0.00 0.00 2.75
800 1772 1.085091 GTGAGGCAGCTGTTGAGATG 58.915 55.000 16.64 0.00 38.73 2.90
904 1902 2.507058 TGAACCCTAAGCTGCATCTGAT 59.493 45.455 1.02 0.00 0.00 2.90
963 1961 1.135721 CTTTGGCTAATTGGCTGGCTC 59.864 52.381 13.90 0.00 42.34 4.70
967 1965 0.107017 GCTAATTGGCTGGCTCCTCA 60.107 55.000 6.53 0.00 0.00 3.86
968 1966 1.673168 CTAATTGGCTGGCTCCTCAC 58.327 55.000 2.00 0.00 0.00 3.51
980 1978 1.433534 CTCCTCACGGCTTGTTTCTC 58.566 55.000 0.00 0.00 0.00 2.87
981 1979 1.001406 CTCCTCACGGCTTGTTTCTCT 59.999 52.381 0.00 0.00 0.00 3.10
987 1985 2.673368 CACGGCTTGTTTCTCTGGTATC 59.327 50.000 0.00 0.00 0.00 2.24
1008 2006 4.072131 TCCAGAACAAGGAACAGCATTAC 58.928 43.478 0.00 0.00 30.71 1.89
1040 2038 4.821805 CAGTGCTTTCAGTTCCTTCCTTAA 59.178 41.667 0.00 0.00 0.00 1.85
1088 2096 2.289382 ACTGAGAACACACACACACACA 60.289 45.455 0.00 0.00 0.00 3.72
1089 2097 2.073056 TGAGAACACACACACACACAC 58.927 47.619 0.00 0.00 0.00 3.82
1090 2098 2.073056 GAGAACACACACACACACACA 58.927 47.619 0.00 0.00 0.00 3.72
1091 2099 1.804151 AGAACACACACACACACACAC 59.196 47.619 0.00 0.00 0.00 3.82
1092 2100 1.533299 GAACACACACACACACACACA 59.467 47.619 0.00 0.00 0.00 3.72
1093 2101 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1094 2102 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1095 2103 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1096 2104 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1097 2105 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1098 2106 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1099 2107 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1100 2108 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1101 2109 1.136000 CACACACACACACACACACAG 60.136 52.381 0.00 0.00 0.00 3.66
1102 2110 1.270571 ACACACACACACACACACAGA 60.271 47.619 0.00 0.00 0.00 3.41
1103 2111 1.394572 CACACACACACACACACAGAG 59.605 52.381 0.00 0.00 0.00 3.35
1104 2112 1.275010 ACACACACACACACACAGAGA 59.725 47.619 0.00 0.00 0.00 3.10
1105 2113 1.929169 CACACACACACACACAGAGAG 59.071 52.381 0.00 0.00 0.00 3.20
1106 2114 1.824852 ACACACACACACACAGAGAGA 59.175 47.619 0.00 0.00 0.00 3.10
1107 2115 2.159184 ACACACACACACACAGAGAGAG 60.159 50.000 0.00 0.00 0.00 3.20
1108 2116 2.099756 CACACACACACACAGAGAGAGA 59.900 50.000 0.00 0.00 0.00 3.10
1109 2117 2.360483 ACACACACACACAGAGAGAGAG 59.640 50.000 0.00 0.00 0.00 3.20
1315 2325 3.831323 TCCAGGATGAGCAAAAAGTTCA 58.169 40.909 0.00 0.00 41.89 3.18
1370 2386 3.635373 GGATCAAGATGGTACGTGAGGTA 59.365 47.826 0.00 0.00 32.68 3.08
1665 2693 0.536687 CCATTCAGCAGCATCCGGAT 60.537 55.000 12.38 12.38 0.00 4.18
1704 2732 2.665603 GTCCCCTCAGCGAGCTTT 59.334 61.111 0.00 0.00 0.00 3.51
1901 2947 0.320374 TACTCCGACAACTTGGCCAG 59.680 55.000 5.11 2.72 0.00 4.85
2025 3080 7.445402 CCTCCTTCAATATATTCGTGTCCAATT 59.555 37.037 0.00 0.00 0.00 2.32
2032 3087 9.546909 CAATATATTCGTGTCCAATTAATCTGC 57.453 33.333 0.00 0.00 0.00 4.26
2090 3145 0.962356 GTGAGGTGACCCAGGCATTG 60.962 60.000 0.00 0.00 0.00 2.82
2092 3147 3.443045 GGTGACCCAGGCATTGCG 61.443 66.667 1.91 0.00 0.00 4.85
2109 3164 1.724623 TGCGTGCTCGATTTTCTGTAC 59.275 47.619 13.13 0.00 39.71 2.90
2118 3173 5.651172 TCGATTTTCTGTACTGTGTTGTG 57.349 39.130 0.00 0.00 0.00 3.33
2125 3180 6.468333 TTCTGTACTGTGTTGTGGTTACTA 57.532 37.500 0.00 0.00 0.00 1.82
2126 3181 5.835257 TCTGTACTGTGTTGTGGTTACTAC 58.165 41.667 0.00 0.00 33.89 2.73
2138 3193 9.081204 TGTTGTGGTTACTACTAATTAGTCTCA 57.919 33.333 21.25 10.14 40.48 3.27
2141 3196 8.737175 TGTGGTTACTACTAATTAGTCTCACTG 58.263 37.037 21.25 8.69 40.48 3.66
2169 3224 2.290641 TGCTCCCACGGTCAATTGTTAT 60.291 45.455 5.13 0.00 0.00 1.89
2198 3260 8.623903 CATTTAGCCTGCTTCAAAGTATTATCA 58.376 33.333 0.00 0.00 0.00 2.15
2313 3446 1.299089 GTTGTCAAAGCCACACCGC 60.299 57.895 0.00 0.00 0.00 5.68
2363 3496 2.290323 GGCACTTAGTCCATTGTCCACT 60.290 50.000 0.00 0.00 0.00 4.00
2369 3502 5.071250 ACTTAGTCCATTGTCCACTGTACAA 59.929 40.000 0.00 0.00 40.85 2.41
2378 3511 4.133820 TGTCCACTGTACAAAAGTCATGG 58.866 43.478 0.00 0.00 0.00 3.66
2388 3521 9.778993 CTGTACAAAAGTCATGGAAAATCATAG 57.221 33.333 0.00 0.00 0.00 2.23
2444 3581 2.371923 GCGCACGCCCATTGTTTTC 61.372 57.895 0.30 0.00 34.56 2.29
2445 3582 1.285641 CGCACGCCCATTGTTTTCT 59.714 52.632 0.00 0.00 0.00 2.52
2468 3605 7.083858 TCTTTTTCTCGCAAATGTTATTCTGG 58.916 34.615 0.00 0.00 0.00 3.86
2512 3649 5.750352 ATGAAAGCATCTTTTGTGGGAAT 57.250 34.783 0.00 0.00 0.00 3.01
2571 3711 1.511850 TTCTCCACATGTTGCGTCTG 58.488 50.000 0.00 0.00 0.00 3.51
2573 3713 1.202639 TCTCCACATGTTGCGTCTGTT 60.203 47.619 0.00 0.00 0.00 3.16
2720 4700 8.319881 TCATTCATTCAGATCCCTATTCATCTC 58.680 37.037 0.00 0.00 0.00 2.75
2722 4702 6.329404 TCATTCAGATCCCTATTCATCTCCT 58.671 40.000 0.00 0.00 0.00 3.69
2784 4764 5.565509 TGGTACATAGGTTCTTCATTGCAA 58.434 37.500 0.00 0.00 0.00 4.08
2786 4766 6.072175 TGGTACATAGGTTCTTCATTGCAAAC 60.072 38.462 1.71 0.00 0.00 2.93
2797 4779 8.482429 GTTCTTCATTGCAAACAGACAAATTAG 58.518 33.333 1.71 0.00 0.00 1.73
2803 4785 6.389830 TGCAAACAGACAAATTAGTCATGT 57.610 33.333 0.00 0.00 40.98 3.21
2811 4793 8.342634 ACAGACAAATTAGTCATGTGTTGTAAC 58.657 33.333 0.00 0.00 40.98 2.50
2858 4840 6.342111 GGAACACTTGGAGTAGAGATAAAGG 58.658 44.000 0.00 0.00 0.00 3.11
2859 4841 5.941555 ACACTTGGAGTAGAGATAAAGGG 57.058 43.478 0.00 0.00 0.00 3.95
2869 4851 6.130569 AGTAGAGATAAAGGGAACACTCGAT 58.869 40.000 0.00 0.00 0.00 3.59
2879 4861 1.550976 GAACACTCGATGGGGAAGTCT 59.449 52.381 0.00 0.00 0.00 3.24
2885 4867 6.494952 ACACTCGATGGGGAAGTCTATATAT 58.505 40.000 0.00 0.00 0.00 0.86
2888 4870 8.572185 CACTCGATGGGGAAGTCTATATATATG 58.428 40.741 5.44 0.00 0.00 1.78
2889 4871 7.231722 ACTCGATGGGGAAGTCTATATATATGC 59.768 40.741 5.44 0.00 0.00 3.14
2890 4872 7.298374 TCGATGGGGAAGTCTATATATATGCT 58.702 38.462 5.44 0.00 0.00 3.79
2913 4895 7.040617 TGCTAGATTCCGAGAGATTTACGTAAT 60.041 37.037 9.18 0.00 0.00 1.89
2989 4977 1.620822 CTGCCAGTTAGCCAAGGTTT 58.379 50.000 0.00 0.00 0.00 3.27
2998 4986 2.489938 AGCCAAGGTTTAGATGCGAA 57.510 45.000 0.00 0.00 0.00 4.70
3042 5052 0.445436 GGATTCACAAGACGCTGCTG 59.555 55.000 0.00 0.00 0.00 4.41
3050 5068 0.036010 AAGACGCTGCTGGTATTGCT 60.036 50.000 0.00 0.00 0.00 3.91
3145 5168 2.096909 CGCAGTTCACGGTTAAACAGAG 60.097 50.000 6.08 0.00 0.00 3.35
3198 5221 1.815003 CCACTCCCTCTGCAAATTGTC 59.185 52.381 0.00 0.00 0.00 3.18
3211 5234 4.584325 TGCAAATTGTCAAACTTAGCTCCT 59.416 37.500 0.00 0.00 0.00 3.69
3298 5321 1.911057 TGCTACGGGATCGATCTGAT 58.089 50.000 23.96 12.19 41.06 2.90
3349 5373 6.268825 AGACAGACGACAGTGTTACAATAT 57.731 37.500 0.00 0.00 0.00 1.28
3456 6627 3.376859 ACTTTGCATTGAGTCGAAACACA 59.623 39.130 0.00 0.00 0.00 3.72
3466 6638 7.402811 TTGAGTCGAAACACAGTGTATTAAG 57.597 36.000 6.63 0.00 0.00 1.85
3478 6650 5.944007 ACAGTGTATTAAGGTTGAATGGACC 59.056 40.000 0.00 0.00 37.44 4.46
3483 6655 0.609131 AAGGTTGAATGGACCAGCGG 60.609 55.000 0.00 0.00 39.71 5.52
3569 6742 0.838554 TGGTACCTTGCCACCTGCTA 60.839 55.000 14.36 0.00 42.00 3.49
3571 6744 1.475213 GGTACCTTGCCACCTGCTATC 60.475 57.143 4.06 0.00 42.00 2.08
3572 6745 0.464036 TACCTTGCCACCTGCTATCG 59.536 55.000 0.00 0.00 42.00 2.92
3589 6762 5.579511 TGCTATCGGAGTTGTTAAACTTAGC 59.420 40.000 10.81 10.81 46.84 3.09
3597 6770 5.128205 AGTTGTTAAACTTAGCTCCCGTTT 58.872 37.500 11.21 11.21 44.47 3.60
3603 6778 1.229723 TTAGCTCCCGTTTCCCCCT 60.230 57.895 0.00 0.00 0.00 4.79
3610 6785 0.913924 CCCGTTTCCCCCTTAGCTTA 59.086 55.000 0.00 0.00 0.00 3.09
3622 6797 3.306989 CCCTTAGCTTATCGATCCATGCA 60.307 47.826 0.00 0.00 0.00 3.96
3653 6829 4.961438 AAAAGTTGGTGGATTCAAGCAT 57.039 36.364 0.00 0.00 0.00 3.79
3704 6880 5.238583 AGGCAGACAGTGTTACATTAGTTC 58.761 41.667 0.00 0.00 0.00 3.01
3730 6906 7.009631 CGACTAATCAACTCACGAATCTTTCAT 59.990 37.037 0.00 0.00 0.00 2.57
3797 6973 9.462174 CACTAGTTTAATTTCACTTTGCATTGA 57.538 29.630 0.00 0.00 0.00 2.57
3849 7025 7.875971 ACTTTTAGAAAGTTCAAATCTCGCAT 58.124 30.769 0.44 0.00 0.00 4.73
3859 7035 3.686241 TCAAATCTCGCATTGTTCTGGAG 59.314 43.478 0.00 0.00 0.00 3.86
3863 7039 3.476552 TCTCGCATTGTTCTGGAGTTTT 58.523 40.909 0.00 0.00 0.00 2.43
3912 7088 6.802834 TGCATATGCTTGCGTGATATATTTTG 59.197 34.615 27.13 0.00 45.77 2.44
3932 7108 4.112634 TGGCAAAAGAATCAAGGTAGGT 57.887 40.909 0.00 0.00 0.00 3.08
3956 7132 1.227102 GCCCCACCATGCACTATGA 59.773 57.895 0.00 0.00 39.21 2.15
3991 7167 1.687660 TGTTGGTGTTAGCCTACGTCA 59.312 47.619 0.00 0.00 37.13 4.35
4000 7176 1.004918 GCCTACGTCAAGGTGCACT 60.005 57.895 17.98 0.00 39.02 4.40
4001 7177 0.245539 GCCTACGTCAAGGTGCACTA 59.754 55.000 17.98 0.00 39.02 2.74
4002 7178 1.337447 GCCTACGTCAAGGTGCACTAA 60.337 52.381 17.98 0.00 39.02 2.24
4003 7179 2.334838 CCTACGTCAAGGTGCACTAAC 58.665 52.381 17.98 8.83 31.46 2.34
4004 7180 2.334838 CTACGTCAAGGTGCACTAACC 58.665 52.381 17.98 0.00 40.85 2.85
4043 7219 3.817084 CAGTGCAAGTTTCCTCAATCTCA 59.183 43.478 0.00 0.00 0.00 3.27
4051 7227 6.581171 AGTTTCCTCAATCTCAATGAAACC 57.419 37.500 8.76 0.00 41.34 3.27
4055 7231 6.070951 TCCTCAATCTCAATGAAACCTCAT 57.929 37.500 0.00 0.00 44.54 2.90
4107 7283 5.892568 AGAGAGAAATTGCATTGATTCTGC 58.107 37.500 8.09 0.00 40.10 4.26
4138 7314 2.410322 CTGTAGTGCCCCACAAGCCA 62.410 60.000 0.00 0.00 36.74 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
241 260 5.833082 TCAAGATCTTACGGTTAGATGAGC 58.167 41.667 13.82 1.09 32.64 4.26
379 404 4.439057 TCATTGTCCTAGTTATTGACCGC 58.561 43.478 0.00 0.00 0.00 5.68
435 460 8.970020 AGAGTGATGCCAATAATTTATCAAACA 58.030 29.630 0.00 0.00 30.43 2.83
436 461 9.807649 AAGAGTGATGCCAATAATTTATCAAAC 57.192 29.630 0.00 0.00 30.43 2.93
570 623 0.600255 AGGAGAAACAACACGGAGCG 60.600 55.000 0.00 0.00 0.00 5.03
595 648 2.725203 TAGCGCCTTGTCACCACCAC 62.725 60.000 2.29 0.00 0.00 4.16
596 649 2.046009 TTAGCGCCTTGTCACCACCA 62.046 55.000 2.29 0.00 0.00 4.17
597 650 1.302192 TTAGCGCCTTGTCACCACC 60.302 57.895 2.29 0.00 0.00 4.61
598 651 1.866925 GTTAGCGCCTTGTCACCAC 59.133 57.895 2.29 0.00 0.00 4.16
599 652 1.666553 CGTTAGCGCCTTGTCACCA 60.667 57.895 2.29 0.00 0.00 4.17
600 653 0.739813 ATCGTTAGCGCCTTGTCACC 60.740 55.000 2.29 0.00 38.14 4.02
602 1570 0.245266 TCATCGTTAGCGCCTTGTCA 59.755 50.000 2.29 0.00 38.14 3.58
616 1584 7.003939 TGCACACTAATTAACTCATTCATCG 57.996 36.000 0.00 0.00 0.00 3.84
676 1644 2.796425 CTGTCGAGATGCGCACTGC 61.796 63.158 14.90 5.24 46.70 4.40
679 1647 3.558411 GGCTGTCGAGATGCGCAC 61.558 66.667 14.90 7.11 40.61 5.34
680 1648 3.763356 AGGCTGTCGAGATGCGCA 61.763 61.111 14.96 14.96 40.61 6.09
682 1650 3.260483 GCAGGCTGTCGAGATGCG 61.260 66.667 17.16 0.00 42.69 4.73
685 1653 0.036732 TTTTGGCAGGCTGTCGAGAT 59.963 50.000 15.29 0.00 0.00 2.75
686 1654 0.036732 ATTTTGGCAGGCTGTCGAGA 59.963 50.000 15.29 8.48 0.00 4.04
687 1655 0.169672 CATTTTGGCAGGCTGTCGAG 59.830 55.000 15.29 0.00 0.00 4.04
744 1716 6.737254 TTTTAACTTAGCTCCCATTTCTCG 57.263 37.500 0.00 0.00 0.00 4.04
784 1756 0.677098 CTGCATCTCAACAGCTGCCT 60.677 55.000 15.27 0.00 40.49 4.75
799 1771 2.231721 TGCATAGTACACGGTTACTGCA 59.768 45.455 8.14 8.01 0.00 4.41
800 1772 2.858344 CTGCATAGTACACGGTTACTGC 59.142 50.000 8.14 5.94 0.00 4.40
801 1773 4.352039 CTCTGCATAGTACACGGTTACTG 58.648 47.826 8.14 0.00 0.00 2.74
802 1774 3.380637 CCTCTGCATAGTACACGGTTACT 59.619 47.826 0.00 3.94 0.00 2.24
829 1822 8.134202 TCCTCAATCTCTATGTAAGTTCACAA 57.866 34.615 0.00 0.00 30.84 3.33
904 1902 7.291991 TGGGAAGGGAGAAAAATATAAAGGA 57.708 36.000 0.00 0.00 0.00 3.36
967 1965 2.354805 GGATACCAGAGAAACAAGCCGT 60.355 50.000 0.00 0.00 0.00 5.68
968 1966 2.280628 GGATACCAGAGAAACAAGCCG 58.719 52.381 0.00 0.00 0.00 5.52
981 1979 3.559171 GCTGTTCCTTGTTCTGGATACCA 60.559 47.826 0.00 0.00 33.09 3.25
987 1985 3.120199 CGTAATGCTGTTCCTTGTTCTGG 60.120 47.826 0.00 0.00 0.00 3.86
1059 2057 2.677836 TGTGTGTTCTCAGTTGCAAGAC 59.322 45.455 0.00 0.00 0.00 3.01
1088 2096 2.360483 CTCTCTCTCTGTGTGTGTGTGT 59.640 50.000 0.00 0.00 0.00 3.72
1089 2097 2.620585 TCTCTCTCTCTGTGTGTGTGTG 59.379 50.000 0.00 0.00 0.00 3.82
1090 2098 2.884012 CTCTCTCTCTCTGTGTGTGTGT 59.116 50.000 0.00 0.00 0.00 3.72
1091 2099 3.145286 TCTCTCTCTCTCTGTGTGTGTG 58.855 50.000 0.00 0.00 0.00 3.82
1092 2100 3.072330 TCTCTCTCTCTCTCTGTGTGTGT 59.928 47.826 0.00 0.00 0.00 3.72
1093 2101 3.673902 TCTCTCTCTCTCTCTGTGTGTG 58.326 50.000 0.00 0.00 0.00 3.82
1094 2102 3.582647 TCTCTCTCTCTCTCTCTGTGTGT 59.417 47.826 0.00 0.00 0.00 3.72
1095 2103 4.081476 TCTCTCTCTCTCTCTCTCTGTGTG 60.081 50.000 0.00 0.00 0.00 3.82
1096 2104 4.096681 TCTCTCTCTCTCTCTCTCTGTGT 58.903 47.826 0.00 0.00 0.00 3.72
1097 2105 4.403752 TCTCTCTCTCTCTCTCTCTCTGTG 59.596 50.000 0.00 0.00 0.00 3.66
1098 2106 4.614475 TCTCTCTCTCTCTCTCTCTCTGT 58.386 47.826 0.00 0.00 0.00 3.41
1099 2107 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
1100 2108 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1101 2109 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1102 2110 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1103 2111 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1104 2112 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1105 2113 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1106 2114 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1107 2115 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1108 2116 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1109 2117 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1159 2169 4.697756 CGAAAGAGGTGGCCGCCA 62.698 66.667 36.17 8.43 0.00 5.69
1238 2248 0.969149 ACTTGATGTCACGCTCCAGA 59.031 50.000 0.00 0.00 0.00 3.86
1370 2386 4.435436 TCTTCGATGGCGTGCGCT 62.435 61.111 16.21 0.00 41.60 5.92
1496 2512 1.452833 GAGCTCCTGGATGGCCAAC 60.453 63.158 10.96 7.12 45.41 3.77
1497 2513 1.499913 TTGAGCTCCTGGATGGCCAA 61.500 55.000 10.96 2.72 45.41 4.52
1665 2693 2.665089 CCATACCCACGGGCACAGA 61.665 63.158 0.69 0.00 39.32 3.41
1693 2721 3.541996 TCATATCCAAAAGCTCGCTGA 57.458 42.857 0.00 0.00 0.00 4.26
1998 3053 5.600898 TGGACACGAATATATTGAAGGAGGA 59.399 40.000 1.78 0.00 0.00 3.71
2025 3080 9.019656 ACACACTAAATTAAACATGGCAGATTA 57.980 29.630 0.00 0.00 0.00 1.75
2090 3145 1.993370 AGTACAGAAAATCGAGCACGC 59.007 47.619 0.00 0.00 39.58 5.34
2092 3147 3.741344 ACACAGTACAGAAAATCGAGCAC 59.259 43.478 0.00 0.00 0.00 4.40
2109 3164 9.136952 GACTAATTAGTAGTAACCACAACACAG 57.863 37.037 18.03 0.00 43.45 3.66
2125 3180 7.880195 AGCAAACAATCAGTGAGACTAATTAGT 59.120 33.333 18.05 18.05 39.71 2.24
2126 3181 8.261492 AGCAAACAATCAGTGAGACTAATTAG 57.739 34.615 11.05 11.05 0.00 1.73
2138 3193 1.238439 CGTGGGAGCAAACAATCAGT 58.762 50.000 0.00 0.00 0.00 3.41
2141 3196 0.521735 GACCGTGGGAGCAAACAATC 59.478 55.000 0.00 0.00 0.00 2.67
2169 3224 5.789643 ACTTTGAAGCAGGCTAAATGAAA 57.210 34.783 0.00 0.00 0.00 2.69
2291 3421 2.481104 CGGTGTGGCTTTGACAACAATT 60.481 45.455 0.00 0.00 35.85 2.32
2292 3422 1.066908 CGGTGTGGCTTTGACAACAAT 59.933 47.619 0.00 0.00 35.85 2.71
2330 3463 4.081642 GGACTAAGTGCCACTGAATAGTCA 60.082 45.833 25.39 0.00 37.61 3.41
2363 3496 9.295825 ACTATGATTTTCCATGACTTTTGTACA 57.704 29.630 0.00 0.00 0.00 2.90
2369 3502 7.177216 TGAGCAACTATGATTTTCCATGACTTT 59.823 33.333 0.00 0.00 0.00 2.66
2388 3521 6.705381 AGAAGCAAGATGATAGTATGAGCAAC 59.295 38.462 0.00 0.00 0.00 4.17
2390 3523 6.416631 AGAAGCAAGATGATAGTATGAGCA 57.583 37.500 0.00 0.00 0.00 4.26
2444 3581 7.083858 TCCAGAATAACATTTGCGAGAAAAAG 58.916 34.615 0.00 0.00 0.00 2.27
2445 3582 6.976088 TCCAGAATAACATTTGCGAGAAAAA 58.024 32.000 0.00 0.00 0.00 1.94
2483 3620 9.434420 CCCACAAAAGATGCTTTCATTTAAATA 57.566 29.630 0.00 0.00 31.96 1.40
2550 3687 3.261580 CAGACGCAACATGTGGAGAATA 58.738 45.455 11.32 0.00 30.87 1.75
2551 3688 2.079158 CAGACGCAACATGTGGAGAAT 58.921 47.619 11.32 0.00 30.87 2.40
2657 4617 1.069513 ACAGGACAAACGTGAATCGGA 59.930 47.619 0.00 0.00 44.69 4.55
2720 4700 6.150140 GCTAATTAGCCAAGGATTACATCAGG 59.850 42.308 24.34 0.00 43.39 3.86
2784 4764 7.333528 ACAACACATGACTAATTTGTCTGTT 57.666 32.000 18.63 16.83 35.03 3.16
2786 4766 7.530525 CGTTACAACACATGACTAATTTGTCTG 59.469 37.037 18.63 15.73 37.79 3.51
2797 4779 3.955771 ACAACCGTTACAACACATGAC 57.044 42.857 0.00 0.00 0.00 3.06
2803 4785 5.220892 GGATGAAGAAACAACCGTTACAACA 60.221 40.000 0.00 0.00 33.99 3.33
2811 4793 3.367292 CCCAATGGATGAAGAAACAACCG 60.367 47.826 0.00 0.00 35.85 4.44
2858 4840 0.613777 ACTTCCCCATCGAGTGTTCC 59.386 55.000 0.00 0.00 0.00 3.62
2859 4841 1.550976 AGACTTCCCCATCGAGTGTTC 59.449 52.381 0.00 0.00 0.00 3.18
2885 4867 6.430308 ACGTAAATCTCTCGGAATCTAGCATA 59.570 38.462 0.00 0.00 0.00 3.14
2888 4870 5.110940 ACGTAAATCTCTCGGAATCTAGC 57.889 43.478 0.00 0.00 0.00 3.42
2913 4895 5.138276 AGCTCCACATCTCCGTAAACTATA 58.862 41.667 0.00 0.00 0.00 1.31
2922 4904 1.373570 GGAAAAGCTCCACATCTCCG 58.626 55.000 0.00 0.00 44.67 4.63
2989 4977 0.830648 CCCTCCCAAGTTCGCATCTA 59.169 55.000 0.00 0.00 0.00 1.98
2998 4986 1.007118 CTATTTTGGCCCCTCCCAAGT 59.993 52.381 0.00 0.00 45.03 3.16
3042 5052 3.081710 ACTACACCCCAAAGCAATACC 57.918 47.619 0.00 0.00 0.00 2.73
3050 5068 5.892524 ACAAGTTAGTACTACACCCCAAA 57.107 39.130 0.91 0.00 33.17 3.28
3145 5168 9.632807 AGCAGTCGATAAACAATATAATCTCTC 57.367 33.333 0.00 0.00 0.00 3.20
3211 5234 1.511305 CGAGTTAGGCGGAGAAGCA 59.489 57.895 0.00 0.00 39.27 3.91
3298 5321 0.601046 CAGTCTGGCAAGCAGTTCGA 60.601 55.000 0.00 0.00 0.00 3.71
3299 5322 1.864862 CAGTCTGGCAAGCAGTTCG 59.135 57.895 0.00 0.00 0.00 3.95
3300 5323 1.578423 GCAGTCTGGCAAGCAGTTC 59.422 57.895 1.14 0.00 0.00 3.01
3301 5324 1.900498 GGCAGTCTGGCAAGCAGTT 60.900 57.895 20.87 0.00 43.14 3.16
3349 5373 7.594351 AGACTCATGAGCTGATTAGTCAATA 57.406 36.000 23.74 0.00 31.97 1.90
3456 6627 6.134535 TGGTCCATTCAACCTTAATACACT 57.865 37.500 0.00 0.00 37.69 3.55
3466 6638 1.002624 TCCGCTGGTCCATTCAACC 60.003 57.895 0.00 0.00 37.31 3.77
3502 6674 7.442969 TGTGAAAATGTAGTTTGGTAGGTGTAG 59.557 37.037 0.00 0.00 0.00 2.74
3569 6742 5.176592 GGAGCTAAGTTTAACAACTCCGAT 58.823 41.667 8.96 0.00 42.89 4.18
3571 6744 3.683340 GGGAGCTAAGTTTAACAACTCCG 59.317 47.826 14.71 0.00 42.89 4.63
3572 6745 3.683340 CGGGAGCTAAGTTTAACAACTCC 59.317 47.826 13.56 13.56 42.89 3.85
3589 6762 1.223763 GCTAAGGGGGAAACGGGAG 59.776 63.158 0.00 0.00 0.00 4.30
3597 6770 2.158219 TGGATCGATAAGCTAAGGGGGA 60.158 50.000 0.00 0.00 0.00 4.81
3603 6778 3.740832 CGTTGCATGGATCGATAAGCTAA 59.259 43.478 11.78 0.00 0.00 3.09
3610 6785 0.177836 TGGACGTTGCATGGATCGAT 59.822 50.000 22.25 0.00 0.00 3.59
3642 6818 7.587757 CGCTAAACTAATACAATGCTTGAATCC 59.412 37.037 3.37 0.00 0.00 3.01
3646 6822 5.584649 AGCGCTAAACTAATACAATGCTTGA 59.415 36.000 8.99 0.00 0.00 3.02
3653 6829 2.940410 GGCCAGCGCTAAACTAATACAA 59.060 45.455 10.99 0.00 34.44 2.41
3704 6880 6.308041 TGAAAGATTCGTGAGTTGATTAGTCG 59.692 38.462 0.00 0.00 0.00 4.18
3784 6960 3.625313 TGTTTCGAGTCAATGCAAAGTGA 59.375 39.130 0.00 0.00 0.00 3.41
3838 7014 3.438087 ACTCCAGAACAATGCGAGATTTG 59.562 43.478 0.00 0.00 0.00 2.32
3849 7025 5.220777 CGCTACTTTCAAAACTCCAGAACAA 60.221 40.000 0.00 0.00 0.00 2.83
3859 7035 5.153513 TCATTGCATCGCTACTTTCAAAAC 58.846 37.500 0.00 0.00 0.00 2.43
3863 7039 4.541085 CATCATTGCATCGCTACTTTCA 57.459 40.909 0.00 0.00 0.00 2.69
3889 7065 6.252015 GCCAAAATATATCACGCAAGCATATG 59.748 38.462 0.00 0.00 45.62 1.78
3890 7066 6.072008 TGCCAAAATATATCACGCAAGCATAT 60.072 34.615 0.00 0.00 45.62 1.78
3891 7067 5.240403 TGCCAAAATATATCACGCAAGCATA 59.760 36.000 0.00 0.00 45.62 3.14
3892 7068 4.037803 TGCCAAAATATATCACGCAAGCAT 59.962 37.500 0.00 0.00 45.62 3.79
3893 7069 3.379688 TGCCAAAATATATCACGCAAGCA 59.620 39.130 0.00 0.00 45.62 3.91
3894 7070 3.963665 TGCCAAAATATATCACGCAAGC 58.036 40.909 0.00 0.00 45.62 4.01
3899 7075 8.854979 TGATTCTTTTGCCAAAATATATCACG 57.145 30.769 2.58 0.00 0.00 4.35
3912 7088 4.321974 CCAACCTACCTTGATTCTTTTGCC 60.322 45.833 0.00 0.00 0.00 4.52
3946 7122 1.781786 ACGAGGACCTCATAGTGCAT 58.218 50.000 21.49 0.00 0.00 3.96
3950 7126 4.710375 ACATGTTAACGAGGACCTCATAGT 59.290 41.667 21.49 8.42 0.00 2.12
3956 7132 2.370849 ACCAACATGTTAACGAGGACCT 59.629 45.455 11.53 0.00 0.00 3.85
4000 7176 6.708949 CACTGCTTTGAAGTAGGTTAAGGTTA 59.291 38.462 12.41 0.00 42.21 2.85
4001 7177 5.531287 CACTGCTTTGAAGTAGGTTAAGGTT 59.469 40.000 12.41 0.00 42.21 3.50
4002 7178 5.063880 CACTGCTTTGAAGTAGGTTAAGGT 58.936 41.667 12.41 0.00 42.21 3.50
4003 7179 4.083271 GCACTGCTTTGAAGTAGGTTAAGG 60.083 45.833 12.41 0.00 42.21 2.69
4004 7180 4.515191 TGCACTGCTTTGAAGTAGGTTAAG 59.485 41.667 12.41 0.00 42.21 1.85
4005 7181 4.456535 TGCACTGCTTTGAAGTAGGTTAA 58.543 39.130 12.41 0.00 42.21 2.01
4043 7219 5.136105 GGAGGCATCTTATGAGGTTTCATT 58.864 41.667 0.00 0.00 41.24 2.57
4051 7227 4.038042 TGAACTACGGAGGCATCTTATGAG 59.962 45.833 0.00 0.00 0.00 2.90
4055 7231 3.069586 CCATGAACTACGGAGGCATCTTA 59.930 47.826 0.00 0.00 0.00 2.10
4107 7283 3.126343 GGGCACTACAGTTTGTATTTCCG 59.874 47.826 0.00 0.00 31.66 4.30


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

AutoCloner maintained by Alex Coulton.