Multiple sequence alignment - TraesCS3B01G097100

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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 TraesCS3B01G097100 chr3B 100.000 4548 0 0 1 4548 64810084 64814631 0 8399
1 TraesCS3B01G097100 chr3B 93.561 2609 141 21 996 3592 276876380 276873787 0 3862
2 TraesCS3B01G097100 chr3B 91.625 1003 59 20 1 995 82773254 82774239 0 1363
3 TraesCS3B01G097100 chr3B 78.824 1327 221 38 2296 3590 564646422 564645124 0 839
4 TraesCS3B01G097100 chr4B 94.118 2601 138 13 996 3589 141555330 141552738 0 3941
5 TraesCS3B01G097100 chr4B 93.065 2610 151 22 996 3592 362753310 362750718 0 3790
6 TraesCS3B01G097100 chr4B 91.650 1006 70 12 1 995 436427421 436426419 0 1380
7 TraesCS3B01G097100 chr3A 93.784 2606 141 16 996 3592 148660110 148657517 0 3895
8 TraesCS3B01G097100 chr2B 93.433 2604 154 13 996 3592 546747570 546750163 0 3845
9 TraesCS3B01G097100 chr2B 93.802 2049 110 13 996 3033 761798011 761800053 0 3064
10 TraesCS3B01G097100 chr2B 96.555 958 28 5 3592 4548 167955990 167956943 0 1581
11 TraesCS3B01G097100 chr2B 91.617 1002 57 12 1 995 441048208 441047227 0 1360
12 TraesCS3B01G097100 chr2B 91.252 1006 64 21 1 995 381241542 381240550 0 1349
13 TraesCS3B01G097100 chr5B 92.567 2610 167 22 996 3592 78453592 78450997 0 3720
14 TraesCS3B01G097100 chr5B 92.493 2611 158 32 996 3592 565763184 565760598 0 3701
15 TraesCS3B01G097100 chr1B 91.239 2614 179 29 996 3592 218459077 218456497 0 3513
16 TraesCS3B01G097100 chr1B 96.559 959 30 3 3592 4548 292390509 292391466 0 1585
17 TraesCS3B01G097100 chr1B 96.555 958 29 4 3592 4548 132105067 132106021 0 1583
18 TraesCS3B01G097100 chr1B 96.466 962 27 6 3592 4548 292327619 292328578 0 1581
19 TraesCS3B01G097100 chr1B 92.024 1003 67 9 1 995 168511495 168510498 0 1397
20 TraesCS3B01G097100 chr1B 91.608 1001 63 17 1 995 327157471 327158456 0 1363
21 TraesCS3B01G097100 chr7B 97.083 960 22 6 3592 4548 202597500 202598456 0 1613
22 TraesCS3B01G097100 chr7B 96.868 958 25 5 3592 4548 659361540 659360587 0 1598
23 TraesCS3B01G097100 chrUn 96.555 958 30 3 3593 4548 155340197 155341153 0 1583
24 TraesCS3B01G097100 chr6B 96.555 958 30 3 3593 4548 246435577 246436533 0 1583
25 TraesCS3B01G097100 chr6B 95.803 977 31 9 3577 4547 221681335 221682307 0 1568
26 TraesCS3B01G097100 chr6B 91.865 1008 53 24 1 995 206029040 206030031 0 1380
27 TraesCS3B01G097100 chr7D 91.261 1007 60 22 1 995 626388582 626387592 0 1347
28 TraesCS3B01G097100 chr4D 91.179 1009 57 24 1 995 371784144 371783154 0 1341


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 TraesCS3B01G097100 chr3B 64810084 64814631 4547 False 8399 8399 100.000 1 4548 1 chr3B.!!$F1 4547
1 TraesCS3B01G097100 chr3B 276873787 276876380 2593 True 3862 3862 93.561 996 3592 1 chr3B.!!$R1 2596
2 TraesCS3B01G097100 chr3B 82773254 82774239 985 False 1363 1363 91.625 1 995 1 chr3B.!!$F2 994
3 TraesCS3B01G097100 chr3B 564645124 564646422 1298 True 839 839 78.824 2296 3590 1 chr3B.!!$R2 1294
4 TraesCS3B01G097100 chr4B 141552738 141555330 2592 True 3941 3941 94.118 996 3589 1 chr4B.!!$R1 2593
5 TraesCS3B01G097100 chr4B 362750718 362753310 2592 True 3790 3790 93.065 996 3592 1 chr4B.!!$R2 2596
6 TraesCS3B01G097100 chr4B 436426419 436427421 1002 True 1380 1380 91.650 1 995 1 chr4B.!!$R3 994
7 TraesCS3B01G097100 chr3A 148657517 148660110 2593 True 3895 3895 93.784 996 3592 1 chr3A.!!$R1 2596
8 TraesCS3B01G097100 chr2B 546747570 546750163 2593 False 3845 3845 93.433 996 3592 1 chr2B.!!$F2 2596
9 TraesCS3B01G097100 chr2B 761798011 761800053 2042 False 3064 3064 93.802 996 3033 1 chr2B.!!$F3 2037
10 TraesCS3B01G097100 chr2B 167955990 167956943 953 False 1581 1581 96.555 3592 4548 1 chr2B.!!$F1 956
11 TraesCS3B01G097100 chr2B 441047227 441048208 981 True 1360 1360 91.617 1 995 1 chr2B.!!$R2 994
12 TraesCS3B01G097100 chr2B 381240550 381241542 992 True 1349 1349 91.252 1 995 1 chr2B.!!$R1 994
13 TraesCS3B01G097100 chr5B 78450997 78453592 2595 True 3720 3720 92.567 996 3592 1 chr5B.!!$R1 2596
14 TraesCS3B01G097100 chr5B 565760598 565763184 2586 True 3701 3701 92.493 996 3592 1 chr5B.!!$R2 2596
15 TraesCS3B01G097100 chr1B 218456497 218459077 2580 True 3513 3513 91.239 996 3592 1 chr1B.!!$R2 2596
16 TraesCS3B01G097100 chr1B 292390509 292391466 957 False 1585 1585 96.559 3592 4548 1 chr1B.!!$F3 956
17 TraesCS3B01G097100 chr1B 132105067 132106021 954 False 1583 1583 96.555 3592 4548 1 chr1B.!!$F1 956
18 TraesCS3B01G097100 chr1B 292327619 292328578 959 False 1581 1581 96.466 3592 4548 1 chr1B.!!$F2 956
19 TraesCS3B01G097100 chr1B 168510498 168511495 997 True 1397 1397 92.024 1 995 1 chr1B.!!$R1 994
20 TraesCS3B01G097100 chr1B 327157471 327158456 985 False 1363 1363 91.608 1 995 1 chr1B.!!$F4 994
21 TraesCS3B01G097100 chr7B 202597500 202598456 956 False 1613 1613 97.083 3592 4548 1 chr7B.!!$F1 956
22 TraesCS3B01G097100 chr7B 659360587 659361540 953 True 1598 1598 96.868 3592 4548 1 chr7B.!!$R1 956
23 TraesCS3B01G097100 chrUn 155340197 155341153 956 False 1583 1583 96.555 3593 4548 1 chrUn.!!$F1 955
24 TraesCS3B01G097100 chr6B 246435577 246436533 956 False 1583 1583 96.555 3593 4548 1 chr6B.!!$F3 955
25 TraesCS3B01G097100 chr6B 221681335 221682307 972 False 1568 1568 95.803 3577 4547 1 chr6B.!!$F2 970
26 TraesCS3B01G097100 chr6B 206029040 206030031 991 False 1380 1380 91.865 1 995 1 chr6B.!!$F1 994
27 TraesCS3B01G097100 chr7D 626387592 626388582 990 True 1347 1347 91.261 1 995 1 chr7D.!!$R1 994
28 TraesCS3B01G097100 chr4D 371783154 371784144 990 True 1341 1341 91.179 1 995 1 chr4D.!!$R1 994

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
892 917 0.179222 GTGCTAACGCTTCCGCTTTC 60.179 55.0 0.00 0.0 38.22 2.62 F
897 922 0.389948 AACGCTTCCGCTTTCGATCT 60.390 50.0 0.00 0.0 38.22 2.75 F
898 923 0.454600 ACGCTTCCGCTTTCGATCTA 59.545 50.0 0.00 0.0 38.22 1.98 F
911 936 0.585357 CGATCTACGAGGGTACGTGG 59.415 60.0 0.00 0.0 46.02 4.94 F
917 942 0.752054 ACGAGGGTACGTGGAAAACA 59.248 50.0 0.00 0.0 44.84 2.83 F
934 959 0.885196 ACACTCTCTCCTCTCGTTGC 59.115 55.0 0.00 0.0 0.00 4.17 F
935 960 1.173043 CACTCTCTCCTCTCGTTGCT 58.827 55.0 0.00 0.0 0.00 3.91 F
3149 3408 0.524414 ACCGACGACGATGAACATGA 59.476 50.0 9.28 0.0 42.66 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 2306 0.958876 CAGCCTTGACAGCAGCATCA 60.959 55.000 0.00 0.00 0.00 3.07 R
2434 2492 0.963856 CATGTGCAGACAGCCATGGT 60.964 55.000 14.67 0.00 42.85 3.55 R
2595 2668 3.870538 ATAGCATTCTTGGCCATCAGA 57.129 42.857 6.09 4.16 0.00 3.27 R
2837 2928 4.479993 GTGCCCTCGCCTGAGCAT 62.480 66.667 0.00 0.00 41.13 3.79 R
3108 3367 2.805845 GCATGTTGCACATTCTCCATC 58.194 47.619 0.00 0.00 44.26 3.51 R
3149 3408 2.592102 ACCACCTGCATGAACTTCAT 57.408 45.000 0.00 0.00 37.65 2.57 R
3158 3417 1.198759 ACCCTTCGTACCACCTGCAT 61.199 55.000 0.00 0.00 0.00 3.96 R
3992 4273 2.254546 ATTGTGTTTCGTCTGCTCCA 57.745 45.000 0.00 0.00 0.00 3.86 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
548 566 4.548513 CCTCCTCCTAGGCCGGCT 62.549 72.222 28.56 15.07 34.61 5.52
632 654 0.894835 TGATCTCTTAGCCGTGTGCA 59.105 50.000 0.00 0.00 44.83 4.57
633 655 1.482182 TGATCTCTTAGCCGTGTGCAT 59.518 47.619 0.00 0.00 44.83 3.96
634 656 1.863454 GATCTCTTAGCCGTGTGCATG 59.137 52.381 0.00 0.00 44.83 4.06
676 700 1.536766 TCGGTAATATCGTAGCGGTGG 59.463 52.381 0.00 0.00 43.40 4.61
733 757 1.798813 CGTCATCACGCTGTCATGCTA 60.799 52.381 0.00 0.00 39.69 3.49
734 758 2.477825 GTCATCACGCTGTCATGCTAT 58.522 47.619 0.00 0.00 0.00 2.97
746 771 2.435805 GTCATGCTATGGAACTCTCCCA 59.564 50.000 0.00 0.00 41.64 4.37
777 802 0.686441 TGGATCGGAGTTCGTGGGAT 60.686 55.000 0.00 0.00 40.32 3.85
867 892 4.453478 TGAAGACGTACGACTACATCAACT 59.547 41.667 24.41 2.94 0.00 3.16
870 895 2.227149 ACGTACGACTACATCAACTGCA 59.773 45.455 24.41 0.00 0.00 4.41
880 905 4.164822 ACATCAACTGCATTGTGCTAAC 57.835 40.909 3.41 0.00 45.31 2.34
881 906 2.967459 TCAACTGCATTGTGCTAACG 57.033 45.000 3.41 0.00 45.31 3.18
882 907 1.069296 TCAACTGCATTGTGCTAACGC 60.069 47.619 3.41 0.00 45.31 4.84
883 908 1.069022 CAACTGCATTGTGCTAACGCT 60.069 47.619 3.41 0.00 45.31 5.07
884 909 1.238439 ACTGCATTGTGCTAACGCTT 58.762 45.000 3.41 0.00 45.31 4.68
885 910 1.197721 ACTGCATTGTGCTAACGCTTC 59.802 47.619 3.41 0.00 45.31 3.86
886 911 0.521291 TGCATTGTGCTAACGCTTCC 59.479 50.000 3.41 0.00 45.31 3.46
887 912 0.521242 GCATTGTGCTAACGCTTCCG 60.521 55.000 0.00 0.00 40.96 4.30
888 913 0.521242 CATTGTGCTAACGCTTCCGC 60.521 55.000 0.00 0.00 38.22 5.54
889 914 0.673644 ATTGTGCTAACGCTTCCGCT 60.674 50.000 0.00 0.00 38.22 5.52
890 915 0.882927 TTGTGCTAACGCTTCCGCTT 60.883 50.000 0.00 0.00 38.22 4.68
891 916 0.882927 TGTGCTAACGCTTCCGCTTT 60.883 50.000 0.00 0.00 38.22 3.51
892 917 0.179222 GTGCTAACGCTTCCGCTTTC 60.179 55.000 0.00 0.00 38.22 2.62
893 918 1.058903 GCTAACGCTTCCGCTTTCG 59.941 57.895 0.00 0.00 38.22 3.46
894 919 1.349259 GCTAACGCTTCCGCTTTCGA 61.349 55.000 0.00 0.00 38.22 3.71
895 920 1.278238 CTAACGCTTCCGCTTTCGAT 58.722 50.000 0.00 0.00 38.22 3.59
896 921 1.255600 CTAACGCTTCCGCTTTCGATC 59.744 52.381 0.00 0.00 38.22 3.69
897 922 0.389948 AACGCTTCCGCTTTCGATCT 60.390 50.000 0.00 0.00 38.22 2.75
898 923 0.454600 ACGCTTCCGCTTTCGATCTA 59.545 50.000 0.00 0.00 38.22 1.98
899 924 0.847035 CGCTTCCGCTTTCGATCTAC 59.153 55.000 0.00 0.00 38.10 2.59
900 925 0.847035 GCTTCCGCTTTCGATCTACG 59.153 55.000 0.00 0.00 44.09 3.51
910 935 1.575244 TCGATCTACGAGGGTACGTG 58.425 55.000 0.00 0.00 46.45 4.49
911 936 0.585357 CGATCTACGAGGGTACGTGG 59.415 60.000 0.00 0.00 46.02 4.94
913 938 3.955145 TCTACGAGGGTACGTGGAA 57.045 52.632 0.00 0.00 46.84 3.53
914 939 2.198827 TCTACGAGGGTACGTGGAAA 57.801 50.000 0.00 0.00 46.84 3.13
915 940 2.513753 TCTACGAGGGTACGTGGAAAA 58.486 47.619 0.00 0.00 46.84 2.29
916 941 2.228822 TCTACGAGGGTACGTGGAAAAC 59.771 50.000 0.00 0.00 46.84 2.43
917 942 0.752054 ACGAGGGTACGTGGAAAACA 59.248 50.000 0.00 0.00 44.84 2.83
918 943 1.142474 CGAGGGTACGTGGAAAACAC 58.858 55.000 0.00 0.00 46.78 3.32
929 954 3.920446 GTGGAAAACACTCTCTCCTCTC 58.080 50.000 0.00 0.00 46.72 3.20
930 955 2.558795 TGGAAAACACTCTCTCCTCTCG 59.441 50.000 0.00 0.00 0.00 4.04
931 956 2.559231 GGAAAACACTCTCTCCTCTCGT 59.441 50.000 0.00 0.00 0.00 4.18
932 957 3.006003 GGAAAACACTCTCTCCTCTCGTT 59.994 47.826 0.00 0.00 0.00 3.85
933 958 3.651803 AAACACTCTCTCCTCTCGTTG 57.348 47.619 0.00 0.00 0.00 4.10
934 959 0.885196 ACACTCTCTCCTCTCGTTGC 59.115 55.000 0.00 0.00 0.00 4.17
935 960 1.173043 CACTCTCTCCTCTCGTTGCT 58.827 55.000 0.00 0.00 0.00 3.91
936 961 2.290387 ACACTCTCTCCTCTCGTTGCTA 60.290 50.000 0.00 0.00 0.00 3.49
937 962 2.948979 CACTCTCTCCTCTCGTTGCTAT 59.051 50.000 0.00 0.00 0.00 2.97
938 963 2.948979 ACTCTCTCCTCTCGTTGCTATG 59.051 50.000 0.00 0.00 0.00 2.23
939 964 1.678627 TCTCTCCTCTCGTTGCTATGC 59.321 52.381 0.00 0.00 0.00 3.14
940 965 1.406898 CTCTCCTCTCGTTGCTATGCA 59.593 52.381 0.00 0.00 36.47 3.96
941 966 2.034878 TCTCCTCTCGTTGCTATGCAT 58.965 47.619 3.79 3.79 38.76 3.96
942 967 2.035193 TCTCCTCTCGTTGCTATGCATC 59.965 50.000 0.19 0.00 38.76 3.91
943 968 1.756538 TCCTCTCGTTGCTATGCATCA 59.243 47.619 0.19 0.00 38.76 3.07
944 969 2.366590 TCCTCTCGTTGCTATGCATCAT 59.633 45.455 0.19 0.00 38.76 2.45
945 970 2.479275 CCTCTCGTTGCTATGCATCATG 59.521 50.000 0.19 0.00 38.76 3.07
946 971 3.387397 CTCTCGTTGCTATGCATCATGA 58.613 45.455 0.19 0.00 38.76 3.07
947 972 3.995048 CTCTCGTTGCTATGCATCATGAT 59.005 43.478 0.19 1.18 38.76 2.45
948 973 3.992427 TCTCGTTGCTATGCATCATGATC 59.008 43.478 4.86 1.82 38.76 2.92
949 974 3.995048 CTCGTTGCTATGCATCATGATCT 59.005 43.478 4.86 0.00 38.76 2.75
950 975 4.383173 TCGTTGCTATGCATCATGATCTT 58.617 39.130 4.86 2.55 38.76 2.40
951 976 4.212636 TCGTTGCTATGCATCATGATCTTG 59.787 41.667 4.86 2.18 38.76 3.02
952 977 4.227538 GTTGCTATGCATCATGATCTTGC 58.772 43.478 4.86 9.09 38.76 4.01
953 978 2.482721 TGCTATGCATCATGATCTTGCG 59.517 45.455 4.86 0.00 39.23 4.85
954 979 2.483106 GCTATGCATCATGATCTTGCGT 59.517 45.455 16.49 16.49 39.23 5.24
955 980 3.667166 GCTATGCATCATGATCTTGCGTG 60.667 47.826 19.96 12.81 39.23 5.34
956 981 1.741528 TGCATCATGATCTTGCGTGT 58.258 45.000 4.86 0.00 39.23 4.49
957 982 1.399089 TGCATCATGATCTTGCGTGTG 59.601 47.619 4.86 0.00 39.23 3.82
958 983 1.858798 GCATCATGATCTTGCGTGTGC 60.859 52.381 4.86 0.37 43.20 4.57
970 995 2.325509 GCGTGTGCGTAGGAATTTTT 57.674 45.000 0.00 0.00 40.81 1.94
991 1016 6.956202 TTTTTGAAATTACTACGTTCCCCA 57.044 33.333 0.00 0.00 0.00 4.96
992 1017 6.956202 TTTTGAAATTACTACGTTCCCCAA 57.044 33.333 0.00 0.00 0.00 4.12
993 1018 5.945466 TTGAAATTACTACGTTCCCCAAC 57.055 39.130 0.00 0.00 0.00 3.77
994 1019 4.970711 TGAAATTACTACGTTCCCCAACA 58.029 39.130 0.00 0.00 32.14 3.33
1119 1145 1.812686 TTGCGCCTACCACGTCTCTT 61.813 55.000 4.18 0.00 0.00 2.85
1323 1352 5.757850 AGCTGAAAGACGTGAAGAAAATT 57.242 34.783 0.00 0.00 34.07 1.82
1382 1411 4.263462 TGCATTCTCAACCAAGATGTACCT 60.263 41.667 0.00 0.00 0.00 3.08
1439 1469 5.812286 TCCCCACTCTTTTACAAATACTCC 58.188 41.667 0.00 0.00 0.00 3.85
1475 1505 9.571810 TCAATGATTTTTCCTAAATCAACATCG 57.428 29.630 14.64 4.97 46.06 3.84
1476 1506 9.357652 CAATGATTTTTCCTAAATCAACATCGT 57.642 29.630 14.64 0.00 46.06 3.73
1481 1511 4.380841 TCCTAAATCAACATCGTAGCGT 57.619 40.909 0.00 0.00 0.00 5.07
1496 1526 5.165676 TCGTAGCGTTTGATAAGTGTGAAT 58.834 37.500 0.00 0.00 0.00 2.57
1547 1577 1.518056 ATCGTGCACAGCAACCCTTG 61.518 55.000 18.64 0.00 41.47 3.61
1650 1682 6.232692 ACAAGGCAATAGCATTTTCAACAAT 58.767 32.000 0.00 0.00 43.04 2.71
1858 1894 4.710865 TGGCAATCATCATGCTTCCTTTTA 59.289 37.500 0.00 0.00 43.34 1.52
2082 2123 5.123502 CCATTCTCTTCAACTTGATGACTGG 59.876 44.000 3.75 7.29 0.00 4.00
2190 2244 1.351076 TGCTCTTGATCTGTCCACCA 58.649 50.000 0.00 0.00 0.00 4.17
2252 2306 2.880890 GTTTGTTGTCTCTGCATGGACT 59.119 45.455 16.50 0.00 34.01 3.85
2301 2355 3.703420 GCAGACAGAATAACCGATACGT 58.297 45.455 0.00 0.00 0.00 3.57
2360 2416 4.827304 TGCACGACATTCTTCAATTTCA 57.173 36.364 0.00 0.00 0.00 2.69
2434 2492 7.775053 AACAAGAGATAAATACCTTTGGCAA 57.225 32.000 0.00 0.00 0.00 4.52
2815 2895 5.178252 CGCACATGACTCTAATATCTTTGGG 59.822 44.000 0.00 0.00 0.00 4.12
3040 3299 3.505464 GGTACGACTACAACAGCTCAT 57.495 47.619 0.00 0.00 0.00 2.90
3108 3367 3.048501 CGACAAGGACGATGATGATGAG 58.951 50.000 0.00 0.00 0.00 2.90
3149 3408 0.524414 ACCGACGACGATGAACATGA 59.476 50.000 9.28 0.00 42.66 3.07
3229 3488 3.489229 GGAAGCAGTTGAACAAACAGGTC 60.489 47.826 0.00 0.00 41.61 3.85
3340 3599 1.801309 CGTAGCTGCTAGGAGGAGGC 61.801 65.000 21.39 0.00 33.92 4.70
3353 3612 2.230266 GGAGGAGGCTCGACATCTATTC 59.770 54.545 8.69 0.00 0.00 1.75
3360 3622 3.799420 GGCTCGACATCTATTCAGTGTTC 59.201 47.826 0.00 0.00 0.00 3.18
3366 3630 9.140286 CTCGACATCTATTCAGTGTTCTTTTTA 57.860 33.333 0.00 0.00 0.00 1.52
3521 3794 5.417580 AGTTAAGAAGAAACAAGCACCAACA 59.582 36.000 0.00 0.00 0.00 3.33
3535 3808 0.820074 CCAACACCAACCCGTGCTTA 60.820 55.000 0.00 0.00 37.25 3.09
3992 4273 3.662759 ATGTACCCCGAAAACATCCAT 57.337 42.857 0.00 0.00 0.00 3.41
4037 4318 3.194968 CACCACCGTAACCTTCTGTATCT 59.805 47.826 0.00 0.00 0.00 1.98
4051 4333 4.331108 TCTGTATCTCGAGATCCCATCTG 58.669 47.826 30.49 18.26 40.38 2.90
4270 4553 2.844122 ACTCTTTTTGCGGTGTGTTC 57.156 45.000 0.00 0.00 0.00 3.18
4496 4780 0.971386 CAGAAAGGGTTGCAAGGCAT 59.029 50.000 0.00 0.00 38.76 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 132 1.628846 ACTCCAAACTACCTTCGGCAT 59.371 47.619 0.00 0.00 0.00 4.40
133 134 1.675116 GGACTCCAAACTACCTTCGGC 60.675 57.143 0.00 0.00 0.00 5.54
146 147 2.248248 GTGATCATATCCGGGACTCCA 58.752 52.381 0.00 0.00 0.00 3.86
548 566 3.706373 GGAGCAAGACGGGAGGCA 61.706 66.667 0.00 0.00 44.00 4.75
556 575 4.562963 CCCCCGTATATAAAGGAGCAAGAC 60.563 50.000 7.00 0.00 0.00 3.01
557 576 3.581332 CCCCCGTATATAAAGGAGCAAGA 59.419 47.826 7.00 0.00 0.00 3.02
632 654 0.779997 GAATATGGTGGAGGGGGCAT 59.220 55.000 0.00 0.00 0.00 4.40
633 655 1.360393 GGAATATGGTGGAGGGGGCA 61.360 60.000 0.00 0.00 0.00 5.36
634 656 1.360393 TGGAATATGGTGGAGGGGGC 61.360 60.000 0.00 0.00 0.00 5.80
733 757 1.707427 AGCTTTGTGGGAGAGTTCCAT 59.293 47.619 0.00 0.00 45.98 3.41
734 758 1.140312 AGCTTTGTGGGAGAGTTCCA 58.860 50.000 0.00 0.00 45.98 3.53
746 771 0.883833 CCGATCCAGCAAAGCTTTGT 59.116 50.000 33.47 20.67 36.40 2.83
777 802 0.313987 ACACGTTCAGCTCGATGACA 59.686 50.000 0.00 0.00 0.00 3.58
819 844 1.066605 CCGACCGATCAAGTACCGAAT 59.933 52.381 0.00 0.00 0.00 3.34
824 849 1.332997 ACGATCCGACCGATCAAGTAC 59.667 52.381 0.00 0.00 46.85 2.73
882 907 2.470196 TCGTAGATCGAAAGCGGAAG 57.530 50.000 0.00 0.00 45.98 3.46
891 916 1.575244 CACGTACCCTCGTAGATCGA 58.425 55.000 0.00 0.00 46.83 3.59
892 917 0.585357 CCACGTACCCTCGTAGATCG 59.415 60.000 0.00 0.00 42.27 3.69
893 918 1.959042 TCCACGTACCCTCGTAGATC 58.041 55.000 0.00 0.00 42.27 2.75
894 919 2.425143 TTCCACGTACCCTCGTAGAT 57.575 50.000 0.00 0.00 42.27 1.98
895 920 2.198827 TTTCCACGTACCCTCGTAGA 57.801 50.000 0.00 0.00 42.27 2.59
896 921 2.030007 TGTTTTCCACGTACCCTCGTAG 60.030 50.000 0.00 0.00 42.27 3.51
897 922 1.959985 TGTTTTCCACGTACCCTCGTA 59.040 47.619 0.00 0.00 42.27 3.43
898 923 0.752054 TGTTTTCCACGTACCCTCGT 59.248 50.000 0.00 0.00 45.10 4.18
899 924 1.142474 GTGTTTTCCACGTACCCTCG 58.858 55.000 0.00 0.00 33.61 4.63
908 933 3.612955 CGAGAGGAGAGAGTGTTTTCCAC 60.613 52.174 0.00 0.00 44.89 4.02
909 934 2.558795 CGAGAGGAGAGAGTGTTTTCCA 59.441 50.000 0.00 0.00 32.02 3.53
910 935 2.559231 ACGAGAGGAGAGAGTGTTTTCC 59.441 50.000 0.00 0.00 0.00 3.13
911 936 3.926821 ACGAGAGGAGAGAGTGTTTTC 57.073 47.619 0.00 0.00 0.00 2.29
912 937 3.800604 GCAACGAGAGGAGAGAGTGTTTT 60.801 47.826 0.00 0.00 0.00 2.43
913 938 2.288518 GCAACGAGAGGAGAGAGTGTTT 60.289 50.000 0.00 0.00 0.00 2.83
914 939 1.271102 GCAACGAGAGGAGAGAGTGTT 59.729 52.381 0.00 0.00 0.00 3.32
915 940 0.885196 GCAACGAGAGGAGAGAGTGT 59.115 55.000 0.00 0.00 0.00 3.55
916 941 1.173043 AGCAACGAGAGGAGAGAGTG 58.827 55.000 0.00 0.00 0.00 3.51
917 942 2.791347 TAGCAACGAGAGGAGAGAGT 57.209 50.000 0.00 0.00 0.00 3.24
918 943 2.287547 GCATAGCAACGAGAGGAGAGAG 60.288 54.545 0.00 0.00 0.00 3.20
919 944 1.678627 GCATAGCAACGAGAGGAGAGA 59.321 52.381 0.00 0.00 0.00 3.10
920 945 1.406898 TGCATAGCAACGAGAGGAGAG 59.593 52.381 0.00 0.00 34.76 3.20
921 946 1.474330 TGCATAGCAACGAGAGGAGA 58.526 50.000 0.00 0.00 34.76 3.71
922 947 2.223900 TGATGCATAGCAACGAGAGGAG 60.224 50.000 0.00 0.00 43.62 3.69
923 948 1.756538 TGATGCATAGCAACGAGAGGA 59.243 47.619 0.00 0.00 43.62 3.71
924 949 2.229675 TGATGCATAGCAACGAGAGG 57.770 50.000 0.00 0.00 43.62 3.69
925 950 3.387397 TCATGATGCATAGCAACGAGAG 58.613 45.455 0.00 0.00 43.62 3.20
926 951 3.457610 TCATGATGCATAGCAACGAGA 57.542 42.857 0.00 0.00 43.62 4.04
927 952 3.995048 AGATCATGATGCATAGCAACGAG 59.005 43.478 14.30 0.00 43.62 4.18
928 953 3.999046 AGATCATGATGCATAGCAACGA 58.001 40.909 14.30 0.00 43.62 3.85
929 954 4.464112 CAAGATCATGATGCATAGCAACG 58.536 43.478 14.30 0.00 43.62 4.10
930 955 4.227538 GCAAGATCATGATGCATAGCAAC 58.772 43.478 14.30 0.00 43.62 4.17
931 956 3.058501 CGCAAGATCATGATGCATAGCAA 60.059 43.478 14.30 0.00 41.13 3.91
932 957 2.482721 CGCAAGATCATGATGCATAGCA 59.517 45.455 14.30 0.00 41.92 3.49
933 958 2.483106 ACGCAAGATCATGATGCATAGC 59.517 45.455 14.30 8.77 40.04 2.97
934 959 3.497262 ACACGCAAGATCATGATGCATAG 59.503 43.478 14.30 7.17 40.04 2.23
935 960 3.249080 CACACGCAAGATCATGATGCATA 59.751 43.478 14.30 0.00 40.04 3.14
936 961 2.032924 CACACGCAAGATCATGATGCAT 59.967 45.455 14.30 0.00 40.04 3.96
937 962 1.399089 CACACGCAAGATCATGATGCA 59.601 47.619 14.30 0.00 40.04 3.96
938 963 1.858798 GCACACGCAAGATCATGATGC 60.859 52.381 14.30 11.40 43.62 3.91
939 964 1.593793 CGCACACGCAAGATCATGATG 60.594 52.381 14.30 1.04 43.62 3.07
940 965 0.654160 CGCACACGCAAGATCATGAT 59.346 50.000 8.25 8.25 43.62 2.45
941 966 0.670239 ACGCACACGCAAGATCATGA 60.670 50.000 1.25 0.00 45.53 3.07
942 967 0.998669 TACGCACACGCAAGATCATG 59.001 50.000 0.00 0.00 45.53 3.07
943 968 1.280982 CTACGCACACGCAAGATCAT 58.719 50.000 0.00 0.00 45.53 2.45
944 969 0.735978 CCTACGCACACGCAAGATCA 60.736 55.000 0.00 0.00 45.53 2.92
945 970 0.457853 TCCTACGCACACGCAAGATC 60.458 55.000 0.00 0.00 45.53 2.75
946 971 0.037697 TTCCTACGCACACGCAAGAT 60.038 50.000 0.00 0.00 45.53 2.40
947 972 0.037697 ATTCCTACGCACACGCAAGA 60.038 50.000 0.00 0.00 45.53 3.02
948 973 0.796312 AATTCCTACGCACACGCAAG 59.204 50.000 0.00 0.00 45.53 4.01
949 974 1.231221 AAATTCCTACGCACACGCAA 58.769 45.000 0.00 0.00 45.53 4.85
950 975 1.231221 AAAATTCCTACGCACACGCA 58.769 45.000 0.00 0.00 45.53 5.24
951 976 2.325509 AAAAATTCCTACGCACACGC 57.674 45.000 0.00 0.00 45.53 5.34
968 993 6.956202 TGGGGAACGTAGTAATTTCAAAAA 57.044 33.333 0.00 0.00 45.00 1.94
969 994 6.320672 TGTTGGGGAACGTAGTAATTTCAAAA 59.679 34.615 0.00 0.00 45.00 2.44
970 995 5.826737 TGTTGGGGAACGTAGTAATTTCAAA 59.173 36.000 0.00 0.00 45.00 2.69
971 996 5.239087 GTGTTGGGGAACGTAGTAATTTCAA 59.761 40.000 0.00 0.00 45.00 2.69
972 997 4.756135 GTGTTGGGGAACGTAGTAATTTCA 59.244 41.667 0.00 0.00 45.00 2.69
973 998 4.756135 TGTGTTGGGGAACGTAGTAATTTC 59.244 41.667 0.00 0.00 45.00 2.17
974 999 4.716794 TGTGTTGGGGAACGTAGTAATTT 58.283 39.130 0.00 0.00 45.00 1.82
975 1000 4.354893 TGTGTTGGGGAACGTAGTAATT 57.645 40.909 0.00 0.00 45.00 1.40
976 1001 4.067192 GTTGTGTTGGGGAACGTAGTAAT 58.933 43.478 0.00 0.00 45.00 1.89
977 1002 3.465871 GTTGTGTTGGGGAACGTAGTAA 58.534 45.455 0.00 0.00 45.00 2.24
978 1003 2.224257 GGTTGTGTTGGGGAACGTAGTA 60.224 50.000 0.00 0.00 45.00 1.82
980 1005 1.232119 GGTTGTGTTGGGGAACGTAG 58.768 55.000 0.00 0.00 0.00 3.51
981 1006 0.545171 TGGTTGTGTTGGGGAACGTA 59.455 50.000 0.00 0.00 0.00 3.57
982 1007 0.106419 ATGGTTGTGTTGGGGAACGT 60.106 50.000 0.00 0.00 0.00 3.99
983 1008 0.313672 CATGGTTGTGTTGGGGAACG 59.686 55.000 0.00 0.00 0.00 3.95
984 1009 0.033366 GCATGGTTGTGTTGGGGAAC 59.967 55.000 0.00 0.00 0.00 3.62
985 1010 1.118356 GGCATGGTTGTGTTGGGGAA 61.118 55.000 0.00 0.00 0.00 3.97
986 1011 1.532794 GGCATGGTTGTGTTGGGGA 60.533 57.895 0.00 0.00 0.00 4.81
987 1012 2.929903 CGGCATGGTTGTGTTGGGG 61.930 63.158 0.00 0.00 0.00 4.96
988 1013 1.459455 TTCGGCATGGTTGTGTTGGG 61.459 55.000 0.00 0.00 0.00 4.12
989 1014 0.602562 ATTCGGCATGGTTGTGTTGG 59.397 50.000 0.00 0.00 0.00 3.77
990 1015 2.727607 CGTATTCGGCATGGTTGTGTTG 60.728 50.000 0.00 0.00 0.00 3.33
991 1016 1.466950 CGTATTCGGCATGGTTGTGTT 59.533 47.619 0.00 0.00 0.00 3.32
992 1017 1.083489 CGTATTCGGCATGGTTGTGT 58.917 50.000 0.00 0.00 0.00 3.72
993 1018 1.062002 GTCGTATTCGGCATGGTTGTG 59.938 52.381 0.00 0.00 41.67 3.33
994 1019 1.066430 AGTCGTATTCGGCATGGTTGT 60.066 47.619 0.00 0.00 44.74 3.32
1119 1145 3.431055 CACTTGTTGCTTGGGCGA 58.569 55.556 0.00 0.00 42.25 5.54
1323 1352 6.597672 AGTCAGCGATGAATTTACACCAATTA 59.402 34.615 4.22 0.00 0.00 1.40
1382 1411 1.153066 TGCAAGCGACAACCCTTCA 60.153 52.632 0.00 0.00 0.00 3.02
1439 1469 7.088589 AGGAAAAATCATTGAACCGTGATAG 57.911 36.000 0.00 0.00 34.14 2.08
1475 1505 5.061808 ACGATTCACACTTATCAAACGCTAC 59.938 40.000 0.00 0.00 0.00 3.58
1476 1506 5.165676 ACGATTCACACTTATCAAACGCTA 58.834 37.500 0.00 0.00 0.00 4.26
1481 1511 8.771920 ATCTTGTACGATTCACACTTATCAAA 57.228 30.769 0.00 0.00 0.00 2.69
1496 1526 1.921243 CCATGCACGATCTTGTACGA 58.079 50.000 0.73 0.00 0.00 3.43
1580 1610 9.533253 CATGGATTAAACAAAAGTCACTTTCTT 57.467 29.630 2.45 0.75 31.99 2.52
1581 1611 8.143835 CCATGGATTAAACAAAAGTCACTTTCT 58.856 33.333 5.56 0.00 31.99 2.52
1696 1730 2.026641 AGCATCATGGTTGCCATACAC 58.973 47.619 15.23 0.00 43.15 2.90
1737 1771 6.000840 TGTTGACAGTTGCCATCTTGTTATA 58.999 36.000 0.00 0.00 0.00 0.98
2190 2244 3.646637 CCTCCTATCCCGGTAAAGTCAAT 59.353 47.826 0.00 0.00 0.00 2.57
2219 2273 4.207165 AGACAACAAACTTATGTGCAGGT 58.793 39.130 0.00 0.00 32.81 4.00
2252 2306 0.958876 CAGCCTTGACAGCAGCATCA 60.959 55.000 0.00 0.00 0.00 3.07
2288 2342 9.768662 AGTTTTCCATATTACGTATCGGTTATT 57.231 29.630 0.00 0.00 0.00 1.40
2301 2355 8.107095 AGAACTAACCTGCAGTTTTCCATATTA 58.893 33.333 13.81 0.00 40.05 0.98
2434 2492 0.963856 CATGTGCAGACAGCCATGGT 60.964 55.000 14.67 0.00 42.85 3.55
2541 2613 4.284490 AGAGAGAAATAAGGTGCACTGACA 59.716 41.667 17.98 0.00 0.00 3.58
2595 2668 3.870538 ATAGCATTCTTGGCCATCAGA 57.129 42.857 6.09 4.16 0.00 3.27
2796 2876 7.836183 AGCAAAACCCAAAGATATTAGAGTCAT 59.164 33.333 0.00 0.00 0.00 3.06
2837 2928 4.479993 GTGCCCTCGCCTGAGCAT 62.480 66.667 0.00 0.00 41.13 3.79
3108 3367 2.805845 GCATGTTGCACATTCTCCATC 58.194 47.619 0.00 0.00 44.26 3.51
3149 3408 2.592102 ACCACCTGCATGAACTTCAT 57.408 45.000 0.00 0.00 37.65 2.57
3158 3417 1.198759 ACCCTTCGTACCACCTGCAT 61.199 55.000 0.00 0.00 0.00 3.96
3340 3599 7.588143 AAAAGAACACTGAATAGATGTCGAG 57.412 36.000 0.00 0.00 0.00 4.04
3353 3612 9.971922 ATTGAAAAGGAGATAAAAAGAACACTG 57.028 29.630 0.00 0.00 0.00 3.66
3360 3622 9.162764 TCGGTCTATTGAAAAGGAGATAAAAAG 57.837 33.333 0.00 0.00 0.00 2.27
3366 3630 4.141688 GGGTCGGTCTATTGAAAAGGAGAT 60.142 45.833 0.00 0.00 0.00 2.75
3521 3794 0.676782 GAGCATAAGCACGGGTTGGT 60.677 55.000 0.00 0.00 45.49 3.67
3535 3808 2.945668 GCTCCCTTGTTTATTCGAGCAT 59.054 45.455 0.00 0.00 41.80 3.79
3694 3967 2.311542 TCCGGTTAGTAGGTTAGTCCCA 59.688 50.000 0.00 0.00 36.75 4.37
3739 4012 9.912634 TTCTTTGAAATACTGAAATAGGCAAAG 57.087 29.630 0.00 0.00 40.35 2.77
3992 4273 2.254546 ATTGTGTTTCGTCTGCTCCA 57.745 45.000 0.00 0.00 0.00 3.86
4174 4456 6.619329 AAAAGAGAGAAGAAGCCATCTAGT 57.381 37.500 0.00 0.00 37.42 2.57


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

AutoCloner maintained by Alex Coulton.