Multiple sequence alignment - TraesCS2B01G443400

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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 TraesCS2B01G443400 chr2B 100.000 2752 0 0 1544 4295 636469283 636472034 0.000000e+00 5083.0
1 TraesCS2B01G443400 chr2B 100.000 1257 0 0 1 1257 636467740 636468996 0.000000e+00 2322.0
2 TraesCS2B01G443400 chr2B 96.505 1030 15 2 1544 2553 391902823 391903851 0.000000e+00 1683.0
3 TraesCS2B01G443400 chr2A 93.811 1438 71 4 2549 3969 678364900 678366336 0.000000e+00 2146.0
4 TraesCS2B01G443400 chr2A 95.644 1125 41 2 1 1124 678363795 678364912 0.000000e+00 1799.0
5 TraesCS2B01G443400 chr2A 94.386 285 16 0 4010 4294 678366335 678366619 5.100000e-119 438.0
6 TraesCS2B01G443400 chr2D 92.659 1444 74 9 2549 3969 535100488 535101922 0.000000e+00 2050.0
7 TraesCS2B01G443400 chr2D 95.911 1125 38 2 1 1124 535099383 535100500 0.000000e+00 1816.0
8 TraesCS2B01G443400 chr2D 91.509 212 16 1 4010 4221 535101921 535102130 1.510000e-74 291.0
9 TraesCS2B01G443400 chr3B 96.990 1030 9 1 1544 2551 199542620 199543649 0.000000e+00 1711.0
10 TraesCS2B01G443400 chr3B 96.696 1029 13 1 1544 2551 550987373 550986345 0.000000e+00 1692.0
11 TraesCS2B01G443400 chr3B 73.991 1115 246 31 17 1118 690430910 690431993 3.090000e-111 412.0
12 TraesCS2B01G443400 chr3B 72.865 1124 256 33 17 1124 690443232 690444322 1.480000e-89 340.0
13 TraesCS2B01G443400 chr5B 97.079 1027 7 1 1544 2547 640284302 640285328 0.000000e+00 1709.0
14 TraesCS2B01G443400 chr5B 92.105 38 1 1 3971 4006 650338120 650338157 8.000000e-03 52.8
15 TraesCS2B01G443400 chr7A 96.702 1031 12 1 1544 2552 34525469 34526499 0.000000e+00 1696.0
16 TraesCS2B01G443400 chr7A 96.512 1032 13 1 1544 2552 15785634 15786665 0.000000e+00 1685.0
17 TraesCS2B01G443400 chr7A 98.683 911 12 0 1544 2454 15813515 15814425 0.000000e+00 1616.0
18 TraesCS2B01G443400 chr7A 99.123 114 1 0 2439 2552 15814435 15814548 5.630000e-49 206.0
19 TraesCS2B01G443400 chr4A 96.702 1031 10 1 1544 2550 735689186 735688156 0.000000e+00 1694.0
20 TraesCS2B01G443400 chr4A 96.696 1029 11 1 1544 2549 626008689 626009717 0.000000e+00 1690.0
21 TraesCS2B01G443400 chr4A 96.599 1029 13 1 1544 2550 740321437 740322465 0.000000e+00 1687.0
22 TraesCS2B01G443400 chr4A 94.669 1013 14 2 1560 2550 740286694 740287688 0.000000e+00 1535.0
23 TraesCS2B01G443400 chrUn 96.512 1032 13 1 1544 2552 318849907 318850938 0.000000e+00 1685.0
24 TraesCS2B01G443400 chr1B 96.132 1034 20 1 1544 2557 675362030 675363063 0.000000e+00 1670.0
25 TraesCS2B01G443400 chr3D 80.303 594 111 5 2648 3236 523562704 523563296 1.100000e-120 444.0
26 TraesCS2B01G443400 chr3A 74.400 1125 236 35 17 1124 658303980 658305069 6.600000e-118 435.0


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 TraesCS2B01G443400 chr2B 636467740 636472034 4294 False 3702.500000 5083 100.000000 1 4295 2 chr2B.!!$F2 4294
1 TraesCS2B01G443400 chr2B 391902823 391903851 1028 False 1683.000000 1683 96.505000 1544 2553 1 chr2B.!!$F1 1009
2 TraesCS2B01G443400 chr2A 678363795 678366619 2824 False 1461.000000 2146 94.613667 1 4294 3 chr2A.!!$F1 4293
3 TraesCS2B01G443400 chr2D 535099383 535102130 2747 False 1385.666667 2050 93.359667 1 4221 3 chr2D.!!$F1 4220
4 TraesCS2B01G443400 chr3B 199542620 199543649 1029 False 1711.000000 1711 96.990000 1544 2551 1 chr3B.!!$F1 1007
5 TraesCS2B01G443400 chr3B 550986345 550987373 1028 True 1692.000000 1692 96.696000 1544 2551 1 chr3B.!!$R1 1007
6 TraesCS2B01G443400 chr3B 690430910 690431993 1083 False 412.000000 412 73.991000 17 1118 1 chr3B.!!$F2 1101
7 TraesCS2B01G443400 chr3B 690443232 690444322 1090 False 340.000000 340 72.865000 17 1124 1 chr3B.!!$F3 1107
8 TraesCS2B01G443400 chr5B 640284302 640285328 1026 False 1709.000000 1709 97.079000 1544 2547 1 chr5B.!!$F1 1003
9 TraesCS2B01G443400 chr7A 34525469 34526499 1030 False 1696.000000 1696 96.702000 1544 2552 1 chr7A.!!$F2 1008
10 TraesCS2B01G443400 chr7A 15785634 15786665 1031 False 1685.000000 1685 96.512000 1544 2552 1 chr7A.!!$F1 1008
11 TraesCS2B01G443400 chr7A 15813515 15814548 1033 False 911.000000 1616 98.903000 1544 2552 2 chr7A.!!$F3 1008
12 TraesCS2B01G443400 chr4A 735688156 735689186 1030 True 1694.000000 1694 96.702000 1544 2550 1 chr4A.!!$R1 1006
13 TraesCS2B01G443400 chr4A 626008689 626009717 1028 False 1690.000000 1690 96.696000 1544 2549 1 chr4A.!!$F1 1005
14 TraesCS2B01G443400 chr4A 740321437 740322465 1028 False 1687.000000 1687 96.599000 1544 2550 1 chr4A.!!$F3 1006
15 TraesCS2B01G443400 chr4A 740286694 740287688 994 False 1535.000000 1535 94.669000 1560 2550 1 chr4A.!!$F2 990
16 TraesCS2B01G443400 chrUn 318849907 318850938 1031 False 1685.000000 1685 96.512000 1544 2552 1 chrUn.!!$F1 1008
17 TraesCS2B01G443400 chr1B 675362030 675363063 1033 False 1670.000000 1670 96.132000 1544 2557 1 chr1B.!!$F1 1013
18 TraesCS2B01G443400 chr3D 523562704 523563296 592 False 444.000000 444 80.303000 2648 3236 1 chr3D.!!$F1 588
19 TraesCS2B01G443400 chr3A 658303980 658305069 1089 False 435.000000 435 74.400000 17 1124 1 chr3A.!!$F1 1107

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
253 254 0.758734 CATCCCGCTGGAGATTGGTA 59.241 55.0 2.45 0.0 46.08 3.25 F
1138 1142 0.527817 GTTCAGATACCGCCAGGACG 60.528 60.0 0.00 0.0 41.02 4.79 F
2574 2625 0.326264 AGTGCACTGGACAGATTCCC 59.674 55.0 20.97 0.0 45.17 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2085 0.748005 GTCCACCAATATGCGCCACT 60.748 55.0 4.18 0.0 0.0 4.00 R
2992 3043 0.259938 ATTGAAGGATCTGGGGGTGC 59.740 55.0 0.00 0.0 0.0 5.01 R
3967 4046 0.250901 TTTTGAGAGGGAGGCAGCAC 60.251 55.0 0.00 0.0 0.0 4.40 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
31 32 2.645802 GTACAATTCCCCGTGGCATTA 58.354 47.619 0.00 0.00 0.00 1.90
250 251 2.249535 CGCATCCCGCTGGAGATTG 61.250 63.158 2.45 0.00 46.08 2.67
251 252 1.895707 GCATCCCGCTGGAGATTGG 60.896 63.158 2.45 0.00 46.08 3.16
252 253 1.528824 CATCCCGCTGGAGATTGGT 59.471 57.895 2.45 0.00 46.08 3.67
253 254 0.758734 CATCCCGCTGGAGATTGGTA 59.241 55.000 2.45 0.00 46.08 3.25
254 255 1.349026 CATCCCGCTGGAGATTGGTAT 59.651 52.381 2.45 0.00 46.08 2.73
255 256 1.507140 TCCCGCTGGAGATTGGTATT 58.493 50.000 0.00 0.00 35.03 1.89
256 257 1.843851 TCCCGCTGGAGATTGGTATTT 59.156 47.619 0.00 0.00 35.03 1.40
325 326 2.300152 ACATGGCCAGATACCAGATACG 59.700 50.000 13.05 0.00 41.46 3.06
372 373 4.452455 CCGCTTGTTACTGTCAGAAAATCT 59.548 41.667 6.91 0.00 0.00 2.40
397 398 1.678728 GGAGGCAACATCATCCACGAA 60.679 52.381 0.00 0.00 41.41 3.85
476 477 3.851897 TTCCCGCCGTCCATTTGCA 62.852 57.895 0.00 0.00 0.00 4.08
515 516 2.093181 ACGGTCCTTGCTGCATACAATA 60.093 45.455 1.84 0.00 0.00 1.90
757 758 6.071616 TGGACCTATCAAACAATGCCTTAAAC 60.072 38.462 0.00 0.00 0.00 2.01
928 930 2.163509 GGAGCCTTTCCTTGGTTCTTC 58.836 52.381 0.00 0.00 43.16 2.87
933 935 3.254411 GCCTTTCCTTGGTTCTTCAGAAG 59.746 47.826 3.45 3.45 34.27 2.85
971 975 4.220382 CACTCTAGATCTGGGAGGCAATAG 59.780 50.000 22.69 8.40 0.00 1.73
1002 1006 6.002653 GGTGGAATACCTTCTTGGATAAGT 57.997 41.667 0.00 0.00 46.51 2.24
1074 1078 2.779430 TGGCATCATACCCTCACAGATT 59.221 45.455 0.00 0.00 0.00 2.40
1132 1136 4.499037 AAAAACAAGTTCAGATACCGCC 57.501 40.909 0.00 0.00 0.00 6.13
1133 1137 2.851263 AACAAGTTCAGATACCGCCA 57.149 45.000 0.00 0.00 0.00 5.69
1134 1138 2.386661 ACAAGTTCAGATACCGCCAG 57.613 50.000 0.00 0.00 0.00 4.85
1135 1139 1.066143 ACAAGTTCAGATACCGCCAGG 60.066 52.381 0.00 0.00 45.13 4.45
1136 1140 1.207089 CAAGTTCAGATACCGCCAGGA 59.793 52.381 0.00 0.00 41.02 3.86
1137 1141 0.824759 AGTTCAGATACCGCCAGGAC 59.175 55.000 0.00 0.00 41.02 3.85
1138 1142 0.527817 GTTCAGATACCGCCAGGACG 60.528 60.000 0.00 0.00 41.02 4.79
1139 1143 0.681887 TTCAGATACCGCCAGGACGA 60.682 55.000 4.99 0.00 41.02 4.20
1140 1144 1.101635 TCAGATACCGCCAGGACGAG 61.102 60.000 4.99 0.00 41.02 4.18
1141 1145 2.027751 GATACCGCCAGGACGAGC 59.972 66.667 4.99 0.00 41.02 5.03
1149 1153 4.504916 CAGGACGAGCGGCTCCTG 62.505 72.222 23.36 20.79 45.97 3.86
1152 1156 3.518998 GACGAGCGGCTCCTGCTA 61.519 66.667 23.36 0.00 44.18 3.49
1153 1157 3.477224 GACGAGCGGCTCCTGCTAG 62.477 68.421 23.36 11.12 44.18 3.42
1154 1158 4.277593 CGAGCGGCTCCTGCTAGG 62.278 72.222 23.36 4.48 44.18 3.02
1155 1159 3.922640 GAGCGGCTCCTGCTAGGG 61.923 72.222 19.20 0.00 44.18 3.53
1156 1160 4.787280 AGCGGCTCCTGCTAGGGT 62.787 66.667 0.00 0.00 41.87 4.34
1157 1161 3.787001 GCGGCTCCTGCTAGGGTT 61.787 66.667 0.00 0.00 39.59 4.11
1158 1162 2.990479 CGGCTCCTGCTAGGGTTT 59.010 61.111 0.00 0.00 39.59 3.27
1159 1163 1.153349 CGGCTCCTGCTAGGGTTTC 60.153 63.158 0.00 0.00 39.59 2.78
1160 1164 1.224870 GGCTCCTGCTAGGGTTTCC 59.775 63.158 0.00 0.00 39.59 3.13
1161 1165 1.224870 GCTCCTGCTAGGGTTTCCC 59.775 63.158 0.00 0.00 39.12 3.97
2081 2085 1.529152 ATGGTGACTGCGTGTCCGTA 61.529 55.000 7.12 0.00 44.75 4.02
2185 2189 2.665185 GTCGGCTTGTTCGGCACT 60.665 61.111 0.00 0.00 31.94 4.40
2334 2338 2.287009 GCGTTCCTTCTTGAAGGTGTTG 60.287 50.000 23.78 15.22 40.81 3.33
2553 2604 3.064271 GGAAACCCTTTTTCGGCAAAAAC 59.936 43.478 4.27 0.00 36.70 2.43
2557 2608 3.266636 CCCTTTTTCGGCAAAAACAAGT 58.733 40.909 4.27 0.00 36.70 3.16
2558 2609 3.063316 CCCTTTTTCGGCAAAAACAAGTG 59.937 43.478 4.27 0.00 36.70 3.16
2559 2610 3.485051 CCTTTTTCGGCAAAAACAAGTGC 60.485 43.478 4.27 0.00 36.70 4.40
2560 2611 2.370281 TTTCGGCAAAAACAAGTGCA 57.630 40.000 0.00 0.00 42.74 4.57
2567 2618 2.673610 GCAAAAACAAGTGCACTGGACA 60.674 45.455 28.22 0.00 40.58 4.02
2574 2625 0.326264 AGTGCACTGGACAGATTCCC 59.674 55.000 20.97 0.00 45.17 3.97
2622 2673 6.572898 GCATGATCCAAGAACAGAAAAATGGA 60.573 38.462 0.00 0.00 40.90 3.41
2655 2706 1.297689 CTACCTGCCAGCAGAGCAA 59.702 57.895 21.01 2.62 46.30 3.91
2696 2747 9.886132 GAAGAATGAGGGTTATCTTTACAACTA 57.114 33.333 0.00 0.00 32.54 2.24
2793 2844 2.633481 ACTTGTTGGACTCAGGTACCTC 59.367 50.000 12.84 0.02 0.00 3.85
2830 2881 2.940514 TCTCTCAGGTGGTATTCCCA 57.059 50.000 0.00 0.00 42.51 4.37
2876 2927 1.282157 AGAATCCTTGGACCTTTCGGG 59.718 52.381 0.00 0.00 41.89 5.14
2946 2997 3.706373 GGCGCCCTGAACCTCTCA 61.706 66.667 18.11 0.00 0.00 3.27
2948 2999 1.743252 GCGCCCTGAACCTCTCAAG 60.743 63.158 0.00 0.00 32.17 3.02
2962 3013 4.191544 CCTCTCAAGCAATGGTTTATCGA 58.808 43.478 0.00 0.00 0.00 3.59
3031 3082 7.090319 TCAATATACAGCAATAATCCAGGGT 57.910 36.000 0.00 0.00 0.00 4.34
3068 3119 1.812708 GCAGGACTGTGTAAACCCGTT 60.813 52.381 0.82 0.00 0.00 4.44
3098 3150 2.568509 ACCAAAATCAAATGAGCCAGGG 59.431 45.455 0.00 0.00 0.00 4.45
3100 3152 1.941377 AAATCAAATGAGCCAGGGCA 58.059 45.000 13.63 0.00 44.88 5.36
3289 3344 1.134098 GCACCTCCAAGCTAAGGCATA 60.134 52.381 9.12 0.00 41.70 3.14
3343 3398 7.051623 AGTCGGTCATTGCCTGTTATATTTTA 58.948 34.615 0.00 0.00 0.00 1.52
3374 3444 6.280643 TGATCTACATTTCTTACATGACCGG 58.719 40.000 0.00 0.00 0.00 5.28
3460 3531 2.979813 GGCAGTTGCACATTTCTTAACG 59.020 45.455 6.43 0.00 44.36 3.18
3479 3550 3.753842 ACGTAAAGTTGTGCACAGTTTG 58.246 40.909 27.22 18.66 0.00 2.93
3595 3666 0.618458 TTGCCCCTTACTCGCTGAAT 59.382 50.000 0.00 0.00 0.00 2.57
3665 3736 9.918630 TCAGTAGGAATGTTACTGTAGTTTAAC 57.081 33.333 11.01 0.00 45.20 2.01
3934 4012 3.751767 TCTGGTTTTGGCAGCAGAT 57.248 47.368 1.54 0.00 44.51 2.90
3973 4052 8.133627 ACTTTATTCAATCATCTATTGTGCTGC 58.866 33.333 0.00 0.00 44.58 5.25
3974 4053 4.906065 TTCAATCATCTATTGTGCTGCC 57.094 40.909 0.00 0.00 44.58 4.85
3975 4054 4.160642 TCAATCATCTATTGTGCTGCCT 57.839 40.909 0.00 0.00 44.58 4.75
3976 4055 4.132336 TCAATCATCTATTGTGCTGCCTC 58.868 43.478 0.00 0.00 44.58 4.70
3977 4056 2.627515 TCATCTATTGTGCTGCCTCC 57.372 50.000 0.00 0.00 0.00 4.30
3978 4057 1.141657 TCATCTATTGTGCTGCCTCCC 59.858 52.381 0.00 0.00 0.00 4.30
3979 4058 1.142465 CATCTATTGTGCTGCCTCCCT 59.858 52.381 0.00 0.00 0.00 4.20
3980 4059 0.833287 TCTATTGTGCTGCCTCCCTC 59.167 55.000 0.00 0.00 0.00 4.30
3981 4060 0.835941 CTATTGTGCTGCCTCCCTCT 59.164 55.000 0.00 0.00 0.00 3.69
3982 4061 0.833287 TATTGTGCTGCCTCCCTCTC 59.167 55.000 0.00 0.00 0.00 3.20
3983 4062 1.203441 ATTGTGCTGCCTCCCTCTCA 61.203 55.000 0.00 0.00 0.00 3.27
3984 4063 1.418097 TTGTGCTGCCTCCCTCTCAA 61.418 55.000 0.00 0.00 0.00 3.02
3985 4064 1.376466 GTGCTGCCTCCCTCTCAAA 59.624 57.895 0.00 0.00 0.00 2.69
3986 4065 0.250901 GTGCTGCCTCCCTCTCAAAA 60.251 55.000 0.00 0.00 0.00 2.44
3987 4066 0.700564 TGCTGCCTCCCTCTCAAAAT 59.299 50.000 0.00 0.00 0.00 1.82
3988 4067 1.915489 TGCTGCCTCCCTCTCAAAATA 59.085 47.619 0.00 0.00 0.00 1.40
3989 4068 2.511218 TGCTGCCTCCCTCTCAAAATAT 59.489 45.455 0.00 0.00 0.00 1.28
3990 4069 3.716353 TGCTGCCTCCCTCTCAAAATATA 59.284 43.478 0.00 0.00 0.00 0.86
3991 4070 4.165950 TGCTGCCTCCCTCTCAAAATATAA 59.834 41.667 0.00 0.00 0.00 0.98
3992 4071 4.759183 GCTGCCTCCCTCTCAAAATATAAG 59.241 45.833 0.00 0.00 0.00 1.73
3993 4072 5.455326 GCTGCCTCCCTCTCAAAATATAAGA 60.455 44.000 0.00 0.00 0.00 2.10
3994 4073 5.930135 TGCCTCCCTCTCAAAATATAAGAC 58.070 41.667 0.00 0.00 0.00 3.01
3995 4074 4.991687 GCCTCCCTCTCAAAATATAAGACG 59.008 45.833 0.00 0.00 0.00 4.18
3996 4075 5.453480 GCCTCCCTCTCAAAATATAAGACGT 60.453 44.000 0.00 0.00 0.00 4.34
3997 4076 6.583562 CCTCCCTCTCAAAATATAAGACGTT 58.416 40.000 0.00 0.00 0.00 3.99
3998 4077 7.048512 CCTCCCTCTCAAAATATAAGACGTTT 58.951 38.462 0.00 0.00 0.00 3.60
3999 4078 7.553044 CCTCCCTCTCAAAATATAAGACGTTTT 59.447 37.037 0.00 0.00 0.00 2.43
4000 4079 8.857694 TCCCTCTCAAAATATAAGACGTTTTT 57.142 30.769 0.00 0.00 0.00 1.94
4001 4080 8.726988 TCCCTCTCAAAATATAAGACGTTTTTG 58.273 33.333 12.50 12.50 39.33 2.44
4002 4081 8.512138 CCCTCTCAAAATATAAGACGTTTTTGT 58.488 33.333 16.32 4.99 39.13 2.83
4006 4085 9.769093 CTCAAAATATAAGACGTTTTTGTAGGG 57.231 33.333 16.32 6.32 39.13 3.53
4007 4086 9.504708 TCAAAATATAAGACGTTTTTGTAGGGA 57.495 29.630 16.32 0.17 39.13 4.20
4008 4087 9.769093 CAAAATATAAGACGTTTTTGTAGGGAG 57.231 33.333 11.08 0.00 35.41 4.30
4034 4113 6.515512 AGTACAATGGATTGCTACCCTTAT 57.484 37.500 0.00 0.00 41.38 1.73
4050 4129 4.227527 ACCCTTATGAAAAGGAGGTAGGTG 59.772 45.833 5.35 0.00 39.81 4.00
4059 4138 0.472898 GGAGGTAGGTGCCCATTACC 59.527 60.000 0.00 0.00 37.66 2.85
4075 4154 1.507140 TACCCCTGAACTATGGCCTG 58.493 55.000 3.32 0.00 0.00 4.85
4091 4170 4.922206 TGGCCTGAGTTTCATATTTGTCT 58.078 39.130 3.32 0.00 0.00 3.41
4144 4223 2.552315 TCAACTTCCAAAATCGGTCTGC 59.448 45.455 0.00 0.00 0.00 4.26
4172 4251 2.117051 CCCTCTACCCCTAACTGGAAC 58.883 57.143 0.00 0.00 38.35 3.62
4173 4252 2.117051 CCTCTACCCCTAACTGGAACC 58.883 57.143 0.00 0.00 38.35 3.62
4179 4258 0.618393 CCCTAACTGGAACCGGGGTA 60.618 60.000 6.32 0.00 38.35 3.69
4186 4265 1.072648 CTGGAACCGGGGTAGTTTTGA 59.927 52.381 6.32 0.00 0.00 2.69
4210 4289 2.076863 GTGTGGCACCTAACTGTCATC 58.923 52.381 16.26 0.00 0.00 2.92
4260 4339 5.471456 GTGGACAAAAGTCATTGAGTCAGAT 59.529 40.000 0.00 0.00 34.38 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 181 1.343069 ACCGGAGCTTCTTCAGTCTT 58.657 50.000 9.46 0.00 0.00 3.01
250 251 8.952278 TGTAATTCTGTCATGTTACCAAATACC 58.048 33.333 0.00 0.00 0.00 2.73
251 252 9.769093 GTGTAATTCTGTCATGTTACCAAATAC 57.231 33.333 0.00 0.00 0.00 1.89
252 253 8.952278 GGTGTAATTCTGTCATGTTACCAAATA 58.048 33.333 0.00 0.00 0.00 1.40
253 254 7.361713 CGGTGTAATTCTGTCATGTTACCAAAT 60.362 37.037 0.00 0.00 0.00 2.32
254 255 6.072948 CGGTGTAATTCTGTCATGTTACCAAA 60.073 38.462 0.00 0.00 0.00 3.28
255 256 5.410132 CGGTGTAATTCTGTCATGTTACCAA 59.590 40.000 0.00 0.00 0.00 3.67
256 257 4.932799 CGGTGTAATTCTGTCATGTTACCA 59.067 41.667 0.00 0.00 0.00 3.25
325 326 3.041508 AGCTTTACCAAACGAGAGACC 57.958 47.619 0.00 0.00 0.00 3.85
372 373 0.462581 GATGATGTTGCCTCCGAGCA 60.463 55.000 0.00 0.00 42.17 4.26
397 398 1.826024 CCTGCTGCTATTCCCGAGT 59.174 57.895 0.00 0.00 0.00 4.18
476 477 1.151899 TAACCAGTGCCCCTCCTGT 60.152 57.895 0.00 0.00 0.00 4.00
515 516 1.740025 GCTGCGAAGGCTTGTAAATCT 59.260 47.619 3.46 0.00 40.82 2.40
794 795 5.186942 CAAATCCATGAATTCCAAATGCCA 58.813 37.500 2.27 0.00 0.00 4.92
928 930 6.873076 AGAGTGATAAGTTTCTTGCTCTTCTG 59.127 38.462 0.00 0.00 0.00 3.02
933 935 8.413229 AGATCTAGAGTGATAAGTTTCTTGCTC 58.587 37.037 0.00 0.00 0.00 4.26
1002 1006 5.683876 ATCTTAGTTCAGGCAAGCTCTTA 57.316 39.130 0.00 0.00 0.00 2.10
1074 1078 4.819630 AGCTGGAGTTGACGAAATTGTAAA 59.180 37.500 0.00 0.00 0.00 2.01
1124 1128 2.027751 GCTCGTCCTGGCGGTATC 59.972 66.667 9.91 0.00 0.00 2.24
1125 1129 3.900892 CGCTCGTCCTGGCGGTAT 61.901 66.667 9.91 0.00 46.42 2.73
1135 1139 3.477224 CTAGCAGGAGCCGCTCGTC 62.477 68.421 12.62 8.18 43.56 4.20
1136 1140 3.522731 CTAGCAGGAGCCGCTCGT 61.523 66.667 14.21 12.03 43.56 4.18
1137 1141 4.277593 CCTAGCAGGAGCCGCTCG 62.278 72.222 14.21 2.70 43.56 5.03
1138 1142 3.922640 CCCTAGCAGGAGCCGCTC 61.923 72.222 12.27 12.27 43.56 5.03
1139 1143 4.787280 ACCCTAGCAGGAGCCGCT 62.787 66.667 0.00 0.00 43.56 5.52
1140 1144 3.330992 AAACCCTAGCAGGAGCCGC 62.331 63.158 4.00 0.00 43.56 6.53
1141 1145 1.153349 GAAACCCTAGCAGGAGCCG 60.153 63.158 4.00 0.00 43.56 5.52
1142 1146 1.224870 GGAAACCCTAGCAGGAGCC 59.775 63.158 4.00 0.00 43.56 4.70
1143 1147 4.966123 GGAAACCCTAGCAGGAGC 57.034 61.111 4.00 0.00 37.67 4.70
1952 1956 1.151587 AGGGGACAACCTCCACCAT 60.152 57.895 0.00 0.00 45.06 3.55
2081 2085 0.748005 GTCCACCAATATGCGCCACT 60.748 55.000 4.18 0.00 0.00 4.00
2334 2338 1.226295 GAAACGCCGCATACCAAGC 60.226 57.895 0.00 0.00 0.00 4.01
2553 2604 1.808945 GGAATCTGTCCAGTGCACTTG 59.191 52.381 18.94 14.93 46.97 3.16
2696 2747 9.390582 CCATACCCACTATGAACGATATCGTGT 62.391 44.444 30.01 19.86 41.91 4.49
2793 2844 5.528690 TGAGAGATGGTTTCTTGACAAGTTG 59.471 40.000 14.75 0.00 33.74 3.16
2830 2881 1.005097 TGCCAGATTGCCAATGTCTCT 59.995 47.619 0.00 0.00 0.00 3.10
2876 2927 5.392703 GGAATTTCACCGGATAGTTGGTTTC 60.393 44.000 9.46 0.17 35.96 2.78
2886 2937 2.945890 GCTTGGAGGAATTTCACCGGAT 60.946 50.000 9.46 0.00 0.00 4.18
2889 2940 0.811281 GGCTTGGAGGAATTTCACCG 59.189 55.000 0.00 0.00 0.00 4.94
2892 2943 1.895131 GCAAGGCTTGGAGGAATTTCA 59.105 47.619 27.25 0.00 0.00 2.69
2934 2985 2.089980 CCATTGCTTGAGAGGTTCAGG 58.910 52.381 0.00 0.00 37.07 3.86
2946 2997 3.199946 TCCTCCTCGATAAACCATTGCTT 59.800 43.478 0.00 0.00 0.00 3.91
2948 2999 3.194005 TCCTCCTCGATAAACCATTGC 57.806 47.619 0.00 0.00 0.00 3.56
2962 3013 1.759562 GCTGCCTGTAGGTATCCTCCT 60.760 57.143 0.00 0.00 41.20 3.69
2992 3043 0.259938 ATTGAAGGATCTGGGGGTGC 59.740 55.000 0.00 0.00 0.00 5.01
2996 3047 4.042062 TGCTGTATATTGAAGGATCTGGGG 59.958 45.833 0.00 0.00 0.00 4.96
3031 3082 0.461548 TGCAATGGAAAACCGCACAA 59.538 45.000 0.00 0.00 0.00 3.33
3068 3119 6.293516 GCTCATTTGATTTTGGTTTGATGCAA 60.294 34.615 0.00 0.00 0.00 4.08
3098 3150 4.125703 CCAGAGTGTCTCCATATCTTTGC 58.874 47.826 0.00 0.00 0.00 3.68
3100 3152 5.249393 ACAACCAGAGTGTCTCCATATCTTT 59.751 40.000 0.00 0.00 0.00 2.52
3289 3344 2.183478 TGTGATGCACGTCCTCATTT 57.817 45.000 0.00 0.00 37.14 2.32
3343 3398 9.823647 CATGTAAGAAATGTAGATCAGTAAGGT 57.176 33.333 0.00 0.00 0.00 3.50
3374 3444 1.896220 TCAACTTGAGATGTGCCACC 58.104 50.000 0.00 0.00 0.00 4.61
3460 3531 7.569677 TTTTACAAACTGTGCACAACTTTAC 57.430 32.000 21.98 0.00 0.00 2.01
3479 3550 7.812648 TGGTAACAGATAGTTGCACATTTTAC 58.187 34.615 0.00 0.00 46.17 2.01
3566 3637 4.755123 CGAGTAAGGGGCAAATATTACAGG 59.245 45.833 0.00 0.00 31.90 4.00
3665 3736 4.707030 TGCTGACATTTGGAATAGCTTG 57.293 40.909 0.00 0.00 32.66 4.01
3962 4041 0.835941 AGAGGGAGGCAGCACAATAG 59.164 55.000 0.00 0.00 0.00 1.73
3963 4042 0.833287 GAGAGGGAGGCAGCACAATA 59.167 55.000 0.00 0.00 0.00 1.90
3967 4046 0.250901 TTTTGAGAGGGAGGCAGCAC 60.251 55.000 0.00 0.00 0.00 4.40
3968 4047 0.700564 ATTTTGAGAGGGAGGCAGCA 59.299 50.000 0.00 0.00 0.00 4.41
3969 4048 2.717639 TATTTTGAGAGGGAGGCAGC 57.282 50.000 0.00 0.00 0.00 5.25
3970 4049 5.994668 GTCTTATATTTTGAGAGGGAGGCAG 59.005 44.000 0.00 0.00 0.00 4.85
3971 4050 5.453339 CGTCTTATATTTTGAGAGGGAGGCA 60.453 44.000 0.00 0.00 0.00 4.75
3972 4051 4.991687 CGTCTTATATTTTGAGAGGGAGGC 59.008 45.833 0.00 0.00 0.00 4.70
3973 4052 6.163135 ACGTCTTATATTTTGAGAGGGAGG 57.837 41.667 0.00 0.00 31.49 4.30
3974 4053 8.494016 AAAACGTCTTATATTTTGAGAGGGAG 57.506 34.615 0.00 0.00 31.49 4.30
3975 4054 8.726988 CAAAAACGTCTTATATTTTGAGAGGGA 58.273 33.333 13.15 0.00 42.48 4.20
3976 4055 8.512138 ACAAAAACGTCTTATATTTTGAGAGGG 58.488 33.333 21.46 1.66 42.48 4.30
3980 4059 9.769093 CCCTACAAAAACGTCTTATATTTTGAG 57.231 33.333 21.46 15.15 42.48 3.02
3981 4060 9.504708 TCCCTACAAAAACGTCTTATATTTTGA 57.495 29.630 21.46 9.08 42.48 2.69
3982 4061 9.769093 CTCCCTACAAAAACGTCTTATATTTTG 57.231 33.333 15.70 15.70 44.34 2.44
3983 4062 8.953313 CCTCCCTACAAAAACGTCTTATATTTT 58.047 33.333 0.00 0.00 0.00 1.82
3984 4063 8.105197 ACCTCCCTACAAAAACGTCTTATATTT 58.895 33.333 0.00 0.00 0.00 1.40
3985 4064 7.627311 ACCTCCCTACAAAAACGTCTTATATT 58.373 34.615 0.00 0.00 0.00 1.28
3986 4065 7.191593 ACCTCCCTACAAAAACGTCTTATAT 57.808 36.000 0.00 0.00 0.00 0.86
3987 4066 6.610075 ACCTCCCTACAAAAACGTCTTATA 57.390 37.500 0.00 0.00 0.00 0.98
3988 4067 5.494390 ACCTCCCTACAAAAACGTCTTAT 57.506 39.130 0.00 0.00 0.00 1.73
3989 4068 4.961438 ACCTCCCTACAAAAACGTCTTA 57.039 40.909 0.00 0.00 0.00 2.10
3990 4069 3.851458 ACCTCCCTACAAAAACGTCTT 57.149 42.857 0.00 0.00 0.00 3.01
3991 4070 3.899980 ACTACCTCCCTACAAAAACGTCT 59.100 43.478 0.00 0.00 0.00 4.18
3992 4071 4.263018 ACTACCTCCCTACAAAAACGTC 57.737 45.455 0.00 0.00 0.00 4.34
3993 4072 4.588528 TGTACTACCTCCCTACAAAAACGT 59.411 41.667 0.00 0.00 0.00 3.99
3994 4073 5.138125 TGTACTACCTCCCTACAAAAACG 57.862 43.478 0.00 0.00 0.00 3.60
3995 4074 6.373495 CCATTGTACTACCTCCCTACAAAAAC 59.627 42.308 0.00 0.00 34.79 2.43
3996 4075 6.272792 TCCATTGTACTACCTCCCTACAAAAA 59.727 38.462 0.00 0.00 34.79 1.94
3997 4076 5.786457 TCCATTGTACTACCTCCCTACAAAA 59.214 40.000 0.00 0.00 34.79 2.44
3998 4077 5.343715 TCCATTGTACTACCTCCCTACAAA 58.656 41.667 0.00 0.00 34.79 2.83
3999 4078 4.950361 TCCATTGTACTACCTCCCTACAA 58.050 43.478 0.00 0.00 35.42 2.41
4000 4079 4.613265 TCCATTGTACTACCTCCCTACA 57.387 45.455 0.00 0.00 0.00 2.74
4001 4080 5.742255 GCAATCCATTGTACTACCTCCCTAC 60.742 48.000 1.37 0.00 39.88 3.18
4002 4081 4.347000 GCAATCCATTGTACTACCTCCCTA 59.653 45.833 1.37 0.00 39.88 3.53
4003 4082 3.136626 GCAATCCATTGTACTACCTCCCT 59.863 47.826 1.37 0.00 39.88 4.20
4004 4083 3.136626 AGCAATCCATTGTACTACCTCCC 59.863 47.826 1.37 0.00 39.88 4.30
4005 4084 4.423625 AGCAATCCATTGTACTACCTCC 57.576 45.455 1.37 0.00 39.88 4.30
4006 4085 5.298347 GGTAGCAATCCATTGTACTACCTC 58.702 45.833 19.24 4.56 43.12 3.85
4007 4086 4.102681 GGGTAGCAATCCATTGTACTACCT 59.897 45.833 22.50 7.57 44.34 3.08
4008 4087 4.102681 AGGGTAGCAATCCATTGTACTACC 59.897 45.833 18.75 18.75 44.28 3.18
4050 4129 2.489073 CCATAGTTCAGGGGTAATGGGC 60.489 54.545 0.00 0.00 32.07 5.36
4059 4138 1.207791 ACTCAGGCCATAGTTCAGGG 58.792 55.000 5.01 0.00 0.00 4.45
4075 4154 9.342308 TGGAATCCATAGACAAATATGAAACTC 57.658 33.333 0.00 0.00 35.54 3.01
4091 4170 9.053472 TCCTTCTAGTTAGTTTTGGAATCCATA 57.947 33.333 1.39 0.00 31.53 2.74
4144 4223 2.817379 AGGGGTAGAGGGGGATAAAG 57.183 55.000 0.00 0.00 0.00 1.85
4172 4251 1.816224 CACCAATCAAAACTACCCCGG 59.184 52.381 0.00 0.00 0.00 5.73
4173 4252 2.227865 CACACCAATCAAAACTACCCCG 59.772 50.000 0.00 0.00 0.00 5.73
4179 4258 2.888834 GTGCCACACCAATCAAAACT 57.111 45.000 0.00 0.00 0.00 2.66
4210 4289 5.643348 TGGACATGATACTAGCACACAAAAG 59.357 40.000 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.