Multiple sequence alignment - TraesCS2D01G124600

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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 TraesCS2D01G124600 chr2D 100.000 3064 0 0 1 3064 72997670 73000733 0.000000e+00 5659
1 TraesCS2D01G124600 chr2D 96.262 642 23 1 2304 2944 617082844 617082203 0.000000e+00 1051
2 TraesCS2D01G124600 chr2D 90.753 757 64 4 1264 2020 72594734 72593984 0.000000e+00 1005
3 TraesCS2D01G124600 chr2D 87.708 781 85 10 1258 2034 23168268 23167495 0.000000e+00 900
4 TraesCS2D01G124600 chr2B 89.856 2090 163 20 5 2064 110369671 110371741 0.000000e+00 2639
5 TraesCS2D01G124600 chr2B 93.381 846 56 0 1221 2066 110406358 110407203 0.000000e+00 1253
6 TraesCS2D01G124600 chr2B 95.231 650 29 2 2303 2951 40324390 40323742 0.000000e+00 1027
7 TraesCS2D01G124600 chr2B 89.704 777 74 4 1258 2034 110043960 110043190 0.000000e+00 987
8 TraesCS2D01G124600 chr2B 86.207 145 17 1 2114 2258 110371752 110371893 1.470000e-33 154
9 TraesCS2D01G124600 chr2A 96.254 1148 35 6 1164 2304 71587143 71588289 0.000000e+00 1875
10 TraesCS2D01G124600 chr2A 89.704 777 74 5 1258 2034 71435595 71434825 0.000000e+00 987
11 TraesCS2D01G124600 chr2A 77.220 777 119 20 10 758 71585816 71586562 4.760000e-108 401
12 TraesCS2D01G124600 chr3D 96.291 647 22 2 2303 2947 559109487 559108841 0.000000e+00 1061
13 TraesCS2D01G124600 chr3D 95.356 646 29 1 2303 2947 533718405 533719050 0.000000e+00 1026
14 TraesCS2D01G124600 chr1B 95.981 647 24 2 2303 2947 269218257 269218903 0.000000e+00 1050
15 TraesCS2D01G124600 chr1B 95.497 644 28 1 2305 2947 390273123 390272480 0.000000e+00 1027
16 TraesCS2D01G124600 chr4D 95.853 651 20 5 2300 2944 8274413 8275062 0.000000e+00 1046
17 TraesCS2D01G124600 chr6B 95.666 646 27 1 2303 2947 21064050 21063405 0.000000e+00 1037
18 TraesCS2D01G124600 chr4B 95.666 646 27 1 2303 2947 629957935 629957290 0.000000e+00 1037
19 TraesCS2D01G124600 chrUn 90.407 761 67 4 1258 2018 287773580 287772826 0.000000e+00 996
20 TraesCS2D01G124600 chrUn 90.407 761 67 4 1258 2018 297962705 297961951 0.000000e+00 996


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 TraesCS2D01G124600 chr2D 72997670 73000733 3063 False 5659.0 5659 100.0000 1 3064 1 chr2D.!!$F1 3063
1 TraesCS2D01G124600 chr2D 617082203 617082844 641 True 1051.0 1051 96.2620 2304 2944 1 chr2D.!!$R3 640
2 TraesCS2D01G124600 chr2D 72593984 72594734 750 True 1005.0 1005 90.7530 1264 2020 1 chr2D.!!$R2 756
3 TraesCS2D01G124600 chr2D 23167495 23168268 773 True 900.0 900 87.7080 1258 2034 1 chr2D.!!$R1 776
4 TraesCS2D01G124600 chr2B 110369671 110371893 2222 False 1396.5 2639 88.0315 5 2258 2 chr2B.!!$F2 2253
5 TraesCS2D01G124600 chr2B 110406358 110407203 845 False 1253.0 1253 93.3810 1221 2066 1 chr2B.!!$F1 845
6 TraesCS2D01G124600 chr2B 40323742 40324390 648 True 1027.0 1027 95.2310 2303 2951 1 chr2B.!!$R1 648
7 TraesCS2D01G124600 chr2B 110043190 110043960 770 True 987.0 987 89.7040 1258 2034 1 chr2B.!!$R2 776
8 TraesCS2D01G124600 chr2A 71585816 71588289 2473 False 1138.0 1875 86.7370 10 2304 2 chr2A.!!$F1 2294
9 TraesCS2D01G124600 chr2A 71434825 71435595 770 True 987.0 987 89.7040 1258 2034 1 chr2A.!!$R1 776
10 TraesCS2D01G124600 chr3D 559108841 559109487 646 True 1061.0 1061 96.2910 2303 2947 1 chr3D.!!$R1 644
11 TraesCS2D01G124600 chr3D 533718405 533719050 645 False 1026.0 1026 95.3560 2303 2947 1 chr3D.!!$F1 644
12 TraesCS2D01G124600 chr1B 269218257 269218903 646 False 1050.0 1050 95.9810 2303 2947 1 chr1B.!!$F1 644
13 TraesCS2D01G124600 chr1B 390272480 390273123 643 True 1027.0 1027 95.4970 2305 2947 1 chr1B.!!$R1 642
14 TraesCS2D01G124600 chr4D 8274413 8275062 649 False 1046.0 1046 95.8530 2300 2944 1 chr4D.!!$F1 644
15 TraesCS2D01G124600 chr6B 21063405 21064050 645 True 1037.0 1037 95.6660 2303 2947 1 chr6B.!!$R1 644
16 TraesCS2D01G124600 chr4B 629957290 629957935 645 True 1037.0 1037 95.6660 2303 2947 1 chr4B.!!$R1 644
17 TraesCS2D01G124600 chrUn 287772826 287773580 754 True 996.0 996 90.4070 1258 2018 1 chrUn.!!$R1 760
18 TraesCS2D01G124600 chrUn 297961951 297962705 754 True 996.0 996 90.4070 1258 2018 1 chrUn.!!$R2 760

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
510 517 0.105964 TTTGCTACCAGACACTGCGT 59.894 50.0 0.0 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 2459 2.026822 ACTTGACTGGTGGATGTGGATC 60.027 50.0 0.0 0.0 0.0 3.36 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
19 20 1.587613 GCACTCCGACTGCTCGATC 60.588 63.158 0.00 0.00 43.06 3.69
22 23 4.237809 TCCGACTGCTCGATCGCG 62.238 66.667 11.09 5.24 43.06 5.87
46 47 0.749454 GGATTGCCTTGGCGAGTGAT 60.749 55.000 7.70 0.00 0.00 3.06
193 194 1.809619 CGCGAGCCTCCGATTTCAA 60.810 57.895 0.00 0.00 0.00 2.69
194 195 1.154205 CGCGAGCCTCCGATTTCAAT 61.154 55.000 0.00 0.00 0.00 2.57
195 196 0.305922 GCGAGCCTCCGATTTCAATG 59.694 55.000 0.00 0.00 0.00 2.82
197 198 2.821546 CGAGCCTCCGATTTCAATGTA 58.178 47.619 0.00 0.00 0.00 2.29
198 199 3.393800 CGAGCCTCCGATTTCAATGTAT 58.606 45.455 0.00 0.00 0.00 2.29
211 218 4.729227 TCAATGTATACCTCTGCGTTCA 57.271 40.909 0.00 0.00 0.00 3.18
225 232 4.858680 TTCACGGCGGCACCAACA 62.859 61.111 13.24 0.00 39.03 3.33
243 250 3.314331 CAGGCACGAGGACCCAGT 61.314 66.667 0.00 0.00 0.00 4.00
342 349 0.663269 CAGCGTCGTTGTCTGCACTA 60.663 55.000 0.28 0.00 0.00 2.74
358 365 1.248785 ACTACGCCACCGAGTGATGT 61.249 55.000 5.71 6.14 35.23 3.06
368 375 2.046892 AGTGATGTGGGACAGCGC 60.047 61.111 0.00 0.00 44.50 5.92
402 409 3.884774 TTGCCGCCCTTGTCCAGT 61.885 61.111 0.00 0.00 0.00 4.00
461 468 2.599281 TCGTCCGCCTTCACCTCA 60.599 61.111 0.00 0.00 0.00 3.86
464 471 2.915659 TCCGCCTTCACCTCACGT 60.916 61.111 0.00 0.00 0.00 4.49
465 472 2.030562 CCGCCTTCACCTCACGTT 59.969 61.111 0.00 0.00 0.00 3.99
510 517 0.105964 TTTGCTACCAGACACTGCGT 59.894 50.000 0.00 0.00 0.00 5.24
514 521 1.617755 CTACCAGACACTGCGTTGCG 61.618 60.000 0.00 0.00 0.00 4.85
537 544 3.935203 GGAGCTCGACATTGAATCAGAAA 59.065 43.478 7.83 0.00 0.00 2.52
540 547 3.486542 GCTCGACATTGAATCAGAAAGGC 60.487 47.826 0.00 0.00 0.00 4.35
547 554 1.710244 TGAATCAGAAAGGCAAGGGGA 59.290 47.619 0.00 0.00 0.00 4.81
632 642 1.748732 TCTGGGTGGTATTTGTGGGA 58.251 50.000 0.00 0.00 0.00 4.37
676 704 3.749064 GACGCGTCTGAGCCTCCA 61.749 66.667 31.12 0.00 0.00 3.86
705 733 6.154534 TCCTCAAATTCGTCTCAGATTTAGGA 59.845 38.462 0.00 0.00 0.00 2.94
709 737 4.672587 TTCGTCTCAGATTTAGGATGGG 57.327 45.455 0.00 0.00 0.00 4.00
719 747 4.166919 AGATTTAGGATGGGTTTGAGAGGG 59.833 45.833 0.00 0.00 0.00 4.30
727 755 1.674651 GTTTGAGAGGGGCCGGTTC 60.675 63.158 1.90 0.00 0.00 3.62
728 756 3.248446 TTTGAGAGGGGCCGGTTCG 62.248 63.158 1.90 0.00 0.00 3.95
771 799 2.158871 ACTGGCTTGGTCACGTTTTCTA 60.159 45.455 0.00 0.00 0.00 2.10
817 845 0.552615 ATGGGTAGTTTGGGGAGCCT 60.553 55.000 0.00 0.00 0.00 4.58
821 849 2.612493 TAGTTTGGGGAGCCTGGCC 61.612 63.158 16.57 6.85 0.00 5.36
861 1030 0.249405 GATCAAGAGGGAGCTGCGAG 60.249 60.000 0.00 0.00 0.00 5.03
862 1031 2.308968 ATCAAGAGGGAGCTGCGAGC 62.309 60.000 0.00 0.47 42.84 5.03
902 1078 0.586802 GCCGGCGTCTTGATAAATCC 59.413 55.000 12.58 0.00 0.00 3.01
923 1115 1.478510 CCTCGCCAAGTCACAGTATCT 59.521 52.381 0.00 0.00 0.00 1.98
950 1142 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
952 1144 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
953 1145 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
954 1146 1.136000 CACACACACACACACACACAG 60.136 52.381 0.00 0.00 0.00 3.66
955 1147 0.447406 CACACACACACACACACAGG 59.553 55.000 0.00 0.00 0.00 4.00
980 1185 5.652014 ACACACATCAACTTGAAAGGAGAAA 59.348 36.000 0.00 0.00 0.00 2.52
999 1204 0.173708 AGCTCCGAAGATCCACGAAC 59.826 55.000 10.08 1.01 0.00 3.95
1010 1215 3.133003 AGATCCACGAACATGTTCCTAGG 59.867 47.826 28.40 25.32 36.27 3.02
1012 1217 1.406887 CCACGAACATGTTCCTAGGGG 60.407 57.143 28.40 21.94 36.27 4.79
1073 1278 8.998377 TGATTTCTGAACAAGAACAAATCGATA 58.002 29.630 0.00 0.00 44.77 2.92
1078 1283 7.843401 TCTGAACAAGAACAAATCGATATCCGA 60.843 37.037 0.00 0.00 41.25 4.55
1120 1325 7.177832 TCCTGGATTACGAATAAGAAGTGAA 57.822 36.000 0.00 0.00 0.00 3.18
1139 1344 4.679197 GTGAAGCACGATATGATCTCTCAC 59.321 45.833 0.00 0.00 33.22 3.51
1161 1366 4.825085 ACACCCGAATTTCTATGTGTTTGT 59.175 37.500 8.67 0.00 33.47 2.83
1162 1367 5.048991 ACACCCGAATTTCTATGTGTTTGTC 60.049 40.000 8.67 0.00 33.47 3.18
1172 1439 0.724549 TGTGTTTGTCTGCGTGTGTC 59.275 50.000 0.00 0.00 0.00 3.67
1191 1458 0.449388 CTGCAGGAGAAATGCCGTTC 59.551 55.000 5.57 0.00 43.18 3.95
1833 2103 3.726517 CCACGCAGTTCGGGCTTG 61.727 66.667 0.00 0.00 41.61 4.01
2112 2385 1.081892 TGCCGTAGTAGTGAGTCGAC 58.918 55.000 7.70 7.70 0.00 4.20
2279 2554 3.804873 GGCGTTGCAATAAAGGTGAAAAA 59.195 39.130 0.59 0.00 0.00 1.94
2353 2628 8.380867 TCTATTCATCTTCAATCATGGCAGTAT 58.619 33.333 0.00 0.00 0.00 2.12
2362 2637 6.054941 TCAATCATGGCAGTATAACGAACAT 58.945 36.000 0.00 0.00 0.00 2.71
2417 2692 1.065701 CCTAGCGACGACTACAAGCAT 59.934 52.381 0.00 0.00 0.00 3.79
2875 3154 1.074167 CCCTAGGGCCACCAGAGAT 60.074 63.158 16.90 0.00 40.13 2.75
2922 3201 1.275573 AGAGGCACGAACCCTAACTTC 59.724 52.381 0.00 0.00 31.41 3.01
2947 3226 2.123033 GGAGGAGGAGGAGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
2950 3229 0.618968 GAGGAGGAGGAGGAGGCAAA 60.619 60.000 0.00 0.00 0.00 3.68
2951 3230 0.620121 AGGAGGAGGAGGAGGCAAAG 60.620 60.000 0.00 0.00 0.00 2.77
2952 3231 1.223211 GAGGAGGAGGAGGCAAAGC 59.777 63.158 0.00 0.00 0.00 3.51
2976 3255 6.243811 CGTAGGGTAAATAAAACTGCAACA 57.756 37.500 0.00 0.00 0.00 3.33
2977 3256 6.311723 CGTAGGGTAAATAAAACTGCAACAG 58.688 40.000 0.00 0.00 37.52 3.16
2978 3257 6.148150 CGTAGGGTAAATAAAACTGCAACAGA 59.852 38.462 0.78 0.00 35.18 3.41
2979 3258 6.575162 AGGGTAAATAAAACTGCAACAGAG 57.425 37.500 0.78 0.00 35.18 3.35
2980 3259 6.068670 AGGGTAAATAAAACTGCAACAGAGT 58.931 36.000 0.78 0.00 35.18 3.24
2981 3260 6.549736 AGGGTAAATAAAACTGCAACAGAGTT 59.450 34.615 0.78 0.00 35.08 3.01
2982 3261 6.861572 GGGTAAATAAAACTGCAACAGAGTTC 59.138 38.462 0.78 0.00 32.33 3.01
2983 3262 7.422399 GGTAAATAAAACTGCAACAGAGTTCA 58.578 34.615 0.78 0.00 32.33 3.18
2984 3263 8.082242 GGTAAATAAAACTGCAACAGAGTTCAT 58.918 33.333 0.78 0.00 32.33 2.57
2985 3264 9.463443 GTAAATAAAACTGCAACAGAGTTCATT 57.537 29.630 0.78 0.00 32.33 2.57
2986 3265 8.947055 AAATAAAACTGCAACAGAGTTCATTT 57.053 26.923 0.78 0.00 32.33 2.32
2987 3266 8.579682 AATAAAACTGCAACAGAGTTCATTTC 57.420 30.769 0.78 0.00 32.33 2.17
2988 3267 5.581126 AAACTGCAACAGAGTTCATTTCA 57.419 34.783 0.78 0.00 32.33 2.69
2989 3268 5.779529 AACTGCAACAGAGTTCATTTCAT 57.220 34.783 0.78 0.00 35.18 2.57
2990 3269 5.779529 ACTGCAACAGAGTTCATTTCATT 57.220 34.783 0.78 0.00 35.18 2.57
2991 3270 6.152932 ACTGCAACAGAGTTCATTTCATTT 57.847 33.333 0.78 0.00 35.18 2.32
2992 3271 6.576185 ACTGCAACAGAGTTCATTTCATTTT 58.424 32.000 0.78 0.00 35.18 1.82
2993 3272 6.698766 ACTGCAACAGAGTTCATTTCATTTTC 59.301 34.615 0.78 0.00 35.18 2.29
2994 3273 6.571605 TGCAACAGAGTTCATTTCATTTTCA 58.428 32.000 0.00 0.00 0.00 2.69
2995 3274 7.040494 TGCAACAGAGTTCATTTCATTTTCAA 58.960 30.769 0.00 0.00 0.00 2.69
2996 3275 7.010367 TGCAACAGAGTTCATTTCATTTTCAAC 59.990 33.333 0.00 0.00 0.00 3.18
2997 3276 7.517259 GCAACAGAGTTCATTTCATTTTCAACC 60.517 37.037 0.00 0.00 0.00 3.77
2998 3277 6.515832 ACAGAGTTCATTTCATTTTCAACCC 58.484 36.000 0.00 0.00 0.00 4.11
2999 3278 6.098124 ACAGAGTTCATTTCATTTTCAACCCA 59.902 34.615 0.00 0.00 0.00 4.51
3000 3279 6.643770 CAGAGTTCATTTCATTTTCAACCCAG 59.356 38.462 0.00 0.00 0.00 4.45
3001 3280 6.324770 AGAGTTCATTTCATTTTCAACCCAGT 59.675 34.615 0.00 0.00 0.00 4.00
3002 3281 6.888105 AGTTCATTTCATTTTCAACCCAGTT 58.112 32.000 0.00 0.00 0.00 3.16
3003 3282 6.762661 AGTTCATTTCATTTTCAACCCAGTTG 59.237 34.615 0.96 0.96 43.99 3.16
3004 3283 6.232581 TCATTTCATTTTCAACCCAGTTGT 57.767 33.333 7.30 0.00 43.23 3.32
3005 3284 7.353414 TCATTTCATTTTCAACCCAGTTGTA 57.647 32.000 7.30 0.00 43.23 2.41
3006 3285 7.432869 TCATTTCATTTTCAACCCAGTTGTAG 58.567 34.615 7.30 0.00 43.23 2.74
3007 3286 7.286546 TCATTTCATTTTCAACCCAGTTGTAGA 59.713 33.333 7.30 0.00 43.23 2.59
3008 3287 6.385649 TTCATTTTCAACCCAGTTGTAGAC 57.614 37.500 7.30 0.00 43.23 2.59
3009 3288 4.513692 TCATTTTCAACCCAGTTGTAGACG 59.486 41.667 7.30 0.00 43.23 4.18
3010 3289 1.873698 TTCAACCCAGTTGTAGACGC 58.126 50.000 7.30 0.00 43.23 5.19
3011 3290 0.753867 TCAACCCAGTTGTAGACGCA 59.246 50.000 7.30 0.00 43.23 5.24
3012 3291 1.148310 CAACCCAGTTGTAGACGCAG 58.852 55.000 0.00 0.00 38.56 5.18
3013 3292 1.045407 AACCCAGTTGTAGACGCAGA 58.955 50.000 0.00 0.00 0.00 4.26
3014 3293 1.267121 ACCCAGTTGTAGACGCAGAT 58.733 50.000 0.00 0.00 0.00 2.90
3015 3294 1.204941 ACCCAGTTGTAGACGCAGATC 59.795 52.381 0.00 0.00 0.00 2.75
3016 3295 1.471676 CCCAGTTGTAGACGCAGATCC 60.472 57.143 0.00 0.00 0.00 3.36
3017 3296 1.478510 CCAGTTGTAGACGCAGATCCT 59.521 52.381 0.00 0.00 0.00 3.24
3018 3297 2.093973 CCAGTTGTAGACGCAGATCCTT 60.094 50.000 0.00 0.00 0.00 3.36
3019 3298 3.182967 CAGTTGTAGACGCAGATCCTTC 58.817 50.000 0.00 0.00 0.00 3.46
3020 3299 2.826128 AGTTGTAGACGCAGATCCTTCA 59.174 45.455 0.00 0.00 0.00 3.02
3021 3300 3.258372 AGTTGTAGACGCAGATCCTTCAA 59.742 43.478 0.00 0.00 0.00 2.69
3022 3301 3.953712 TGTAGACGCAGATCCTTCAAA 57.046 42.857 0.00 0.00 0.00 2.69
3023 3302 4.265904 TGTAGACGCAGATCCTTCAAAA 57.734 40.909 0.00 0.00 0.00 2.44
3024 3303 4.637276 TGTAGACGCAGATCCTTCAAAAA 58.363 39.130 0.00 0.00 0.00 1.94
3042 3321 0.996727 AAAATCGCAAACGCAGACGC 60.997 50.000 0.00 0.00 45.53 5.19
3043 3322 1.841663 AAATCGCAAACGCAGACGCT 61.842 50.000 0.00 0.00 45.53 5.07
3044 3323 2.227968 AATCGCAAACGCAGACGCTC 62.228 55.000 0.00 0.00 45.53 5.03
3045 3324 3.701530 CGCAAACGCAGACGCTCA 61.702 61.111 0.00 0.00 45.53 4.26
3046 3325 2.127609 GCAAACGCAGACGCTCAC 60.128 61.111 0.00 0.00 45.53 3.51
3047 3326 2.881266 GCAAACGCAGACGCTCACA 61.881 57.895 0.00 0.00 45.53 3.58
3048 3327 1.083401 CAAACGCAGACGCTCACAC 60.083 57.895 0.00 0.00 45.53 3.82
3049 3328 1.520564 AAACGCAGACGCTCACACA 60.521 52.632 0.00 0.00 45.53 3.72
3050 3329 1.762222 AAACGCAGACGCTCACACAC 61.762 55.000 0.00 0.00 45.53 3.82
3051 3330 2.658268 CGCAGACGCTCACACACA 60.658 61.111 0.00 0.00 35.30 3.72
3052 3331 2.652079 CGCAGACGCTCACACACAG 61.652 63.158 0.00 0.00 35.30 3.66
3053 3332 2.313172 GCAGACGCTCACACACAGG 61.313 63.158 0.00 0.00 34.30 4.00
3054 3333 1.068083 CAGACGCTCACACACAGGT 59.932 57.895 0.00 0.00 0.00 4.00
3055 3334 0.313987 CAGACGCTCACACACAGGTA 59.686 55.000 0.00 0.00 0.00 3.08
3056 3335 0.598562 AGACGCTCACACACAGGTAG 59.401 55.000 0.00 0.00 0.00 3.18
3057 3336 0.596577 GACGCTCACACACAGGTAGA 59.403 55.000 0.00 0.00 0.00 2.59
3058 3337 1.202582 GACGCTCACACACAGGTAGAT 59.797 52.381 0.00 0.00 0.00 1.98
3059 3338 1.202582 ACGCTCACACACAGGTAGATC 59.797 52.381 0.00 0.00 0.00 2.75
3060 3339 1.474478 CGCTCACACACAGGTAGATCT 59.526 52.381 0.00 0.00 0.00 2.75
3061 3340 2.683362 CGCTCACACACAGGTAGATCTA 59.317 50.000 0.00 0.00 0.00 1.98
3062 3341 3.487711 CGCTCACACACAGGTAGATCTAC 60.488 52.174 22.47 22.47 35.40 2.59
3063 3342 3.444034 GCTCACACACAGGTAGATCTACA 59.556 47.826 29.36 8.95 37.78 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.587613 GATCGAGCAGTCGGAGTGC 60.588 63.158 26.43 26.43 46.80 4.40
2 3 1.297967 CGATCGAGCAGTCGGAGTG 60.298 63.158 10.26 8.49 46.80 3.51
3 4 3.102985 CGATCGAGCAGTCGGAGT 58.897 61.111 10.26 0.00 46.80 3.85
30 31 1.741401 CGATCACTCGCCAAGGCAA 60.741 57.895 12.19 0.00 42.06 4.52
108 109 1.596934 GAAGTGATGTCCTCCCGCA 59.403 57.895 0.00 0.00 0.00 5.69
137 138 3.167414 CGGGGAAAGGTTGAGGGT 58.833 61.111 0.00 0.00 0.00 4.34
142 143 3.373565 GGCAGCGGGGAAAGGTTG 61.374 66.667 0.00 0.00 0.00 3.77
143 144 3.569200 GAGGCAGCGGGGAAAGGTT 62.569 63.158 0.00 0.00 0.00 3.50
144 145 4.035102 GAGGCAGCGGGGAAAGGT 62.035 66.667 0.00 0.00 0.00 3.50
186 187 6.257849 TGAACGCAGAGGTATACATTGAAATC 59.742 38.462 5.01 0.00 0.00 2.17
187 188 6.037172 GTGAACGCAGAGGTATACATTGAAAT 59.963 38.462 5.01 0.00 0.00 2.17
188 189 5.350365 GTGAACGCAGAGGTATACATTGAAA 59.650 40.000 5.01 0.00 0.00 2.69
189 190 4.868171 GTGAACGCAGAGGTATACATTGAA 59.132 41.667 5.01 0.00 0.00 2.69
193 194 2.223735 CCGTGAACGCAGAGGTATACAT 60.224 50.000 5.01 0.00 38.18 2.29
194 195 1.133598 CCGTGAACGCAGAGGTATACA 59.866 52.381 5.01 0.00 38.18 2.29
195 196 1.836383 CCGTGAACGCAGAGGTATAC 58.164 55.000 0.00 0.00 38.18 1.47
197 198 1.153628 GCCGTGAACGCAGAGGTAT 60.154 57.895 0.00 0.00 38.18 2.73
198 199 2.260434 GCCGTGAACGCAGAGGTA 59.740 61.111 0.00 0.00 38.18 3.08
225 232 3.314331 CTGGGTCCTCGTGCCTGT 61.314 66.667 0.00 0.00 0.00 4.00
250 257 2.759973 CTCCTGCTAGCGTCCCCA 60.760 66.667 10.77 0.00 0.00 4.96
259 266 3.774528 CCGCACCTGCTCCTGCTA 61.775 66.667 0.00 0.00 40.48 3.49
342 349 2.048222 CACATCACTCGGTGGCGT 60.048 61.111 4.52 0.51 33.87 5.68
368 375 3.031417 AACGGAAGATCTGGGCCCG 62.031 63.158 19.37 12.57 45.09 6.13
371 378 2.115291 GGCAACGGAAGATCTGGGC 61.115 63.158 0.00 0.00 0.00 5.36
372 379 4.225497 GGCAACGGAAGATCTGGG 57.775 61.111 0.00 0.00 0.00 4.45
413 420 3.929948 GCTGTACGCATCCGCAGC 61.930 66.667 0.00 0.00 41.11 5.25
426 433 0.171455 GACGATGAGGAGTTCGCTGT 59.829 55.000 0.00 0.00 38.91 4.40
430 437 0.248134 GGACGACGATGAGGAGTTCG 60.248 60.000 0.00 0.00 41.04 3.95
461 468 2.429236 CGAGAGTCGCTGCAACGT 60.429 61.111 9.64 0.00 31.14 3.99
464 471 2.258591 GACCGAGAGTCGCTGCAA 59.741 61.111 0.00 0.00 38.82 4.08
510 517 1.741401 CAATGTCGAGCTCCCGCAA 60.741 57.895 8.47 0.00 39.10 4.85
514 521 2.159043 TCTGATTCAATGTCGAGCTCCC 60.159 50.000 8.47 0.00 0.00 4.30
537 544 1.842381 CTTTCCTCGTCCCCTTGCCT 61.842 60.000 0.00 0.00 0.00 4.75
540 547 0.250513 CTCCTTTCCTCGTCCCCTTG 59.749 60.000 0.00 0.00 0.00 3.61
547 554 2.291930 ACTCTCCATCTCCTTTCCTCGT 60.292 50.000 0.00 0.00 0.00 4.18
676 704 5.152623 TCTGAGACGAATTTGAGGATTGT 57.847 39.130 0.00 0.00 0.00 2.71
705 733 2.983879 CGGCCCCTCTCAAACCCAT 61.984 63.158 0.00 0.00 0.00 4.00
709 737 1.674651 GAACCGGCCCCTCTCAAAC 60.675 63.158 0.00 0.00 0.00 2.93
719 747 4.038521 GCCTTATACGAACCGGCC 57.961 61.111 0.00 0.00 34.75 6.13
727 755 1.688197 TCCCTAAACCGGCCTTATACG 59.312 52.381 0.00 0.00 0.00 3.06
728 756 3.389002 TCTTCCCTAAACCGGCCTTATAC 59.611 47.826 0.00 0.00 0.00 1.47
799 827 1.151677 AGGCTCCCCAAACTACCCA 60.152 57.895 0.00 0.00 0.00 4.51
803 831 2.612493 GGCCAGGCTCCCCAAACTA 61.612 63.158 12.43 0.00 0.00 2.24
832 860 4.197750 CTCCCTCTTGATCATTGACAAGG 58.802 47.826 19.63 13.82 42.27 3.61
834 862 3.265221 AGCTCCCTCTTGATCATTGACAA 59.735 43.478 0.00 0.00 0.00 3.18
861 1030 1.514873 CCAAGTACGTACGTCCCGC 60.515 63.158 26.53 13.47 0.00 6.13
862 1031 1.514873 GCCAAGTACGTACGTCCCG 60.515 63.158 26.53 11.79 0.00 5.14
863 1032 1.514873 CGCCAAGTACGTACGTCCC 60.515 63.158 26.53 16.61 0.00 4.46
864 1033 1.514873 CCGCCAAGTACGTACGTCC 60.515 63.158 26.53 14.52 0.00 4.79
865 1034 1.514873 CCCGCCAAGTACGTACGTC 60.515 63.158 26.53 16.16 0.00 4.34
866 1035 2.568090 CCCGCCAAGTACGTACGT 59.432 61.111 25.98 25.98 0.00 3.57
867 1036 2.882301 GCCCGCCAAGTACGTACG 60.882 66.667 19.49 15.01 0.00 3.67
902 1078 0.537188 ATACTGTGACTTGGCGAGGG 59.463 55.000 6.71 0.00 0.00 4.30
923 1115 1.152510 GTGTGTGTGTGTGTGTGTGA 58.847 50.000 0.00 0.00 0.00 3.58
950 1142 3.205338 TCAAGTTGATGTGTGTCCTGTG 58.795 45.455 0.08 0.00 0.00 3.66
952 1144 4.261322 CCTTTCAAGTTGATGTGTGTCCTG 60.261 45.833 6.36 0.00 0.00 3.86
953 1145 3.885297 CCTTTCAAGTTGATGTGTGTCCT 59.115 43.478 6.36 0.00 0.00 3.85
954 1146 3.882888 TCCTTTCAAGTTGATGTGTGTCC 59.117 43.478 6.36 0.00 0.00 4.02
955 1147 4.816385 TCTCCTTTCAAGTTGATGTGTGTC 59.184 41.667 6.36 0.00 0.00 3.67
980 1185 0.173708 GTTCGTGGATCTTCGGAGCT 59.826 55.000 9.35 0.00 0.00 4.09
985 1190 2.348666 GGAACATGTTCGTGGATCTTCG 59.651 50.000 27.69 0.00 40.37 3.79
999 1204 0.107017 CCTGCACCCCTAGGAACATG 60.107 60.000 11.48 3.76 36.11 3.21
1098 1303 6.535150 TGCTTCACTTCTTATTCGTAATCCAG 59.465 38.462 0.00 0.00 0.00 3.86
1120 1325 3.005261 GGTGTGAGAGATCATATCGTGCT 59.995 47.826 0.00 0.00 0.00 4.40
1139 1344 5.181245 AGACAAACACATAGAAATTCGGGTG 59.819 40.000 11.21 11.21 0.00 4.61
1172 1439 0.449388 GAACGGCATTTCTCCTGCAG 59.551 55.000 6.78 6.78 41.47 4.41
2186 2459 2.026822 ACTTGACTGGTGGATGTGGATC 60.027 50.000 0.00 0.00 0.00 3.36
2417 2692 2.261671 GCCTTCGGCTCACTTCGA 59.738 61.111 0.00 0.00 46.69 3.71
2697 2972 2.653087 GCCTAGTCCCCGTTTCGGT 61.653 63.158 7.40 0.00 46.80 4.69
2870 3149 2.430610 GCAGGTCCGCCTCATCTCT 61.431 63.158 0.00 0.00 44.97 3.10
2899 3178 0.896940 TTAGGGTTCGTGCCTCTCGT 60.897 55.000 0.00 0.00 0.00 4.18
2922 3201 1.836802 CTCCTCCTCCTCCAAGAAAGG 59.163 57.143 0.00 0.00 35.05 3.11
2947 3226 6.319399 CAGTTTTATTTACCCTACGGCTTTG 58.681 40.000 0.00 0.00 0.00 2.77
2950 3229 3.943381 GCAGTTTTATTTACCCTACGGCT 59.057 43.478 0.00 0.00 0.00 5.52
2951 3230 3.690628 TGCAGTTTTATTTACCCTACGGC 59.309 43.478 0.00 0.00 0.00 5.68
2952 3231 5.181622 TGTTGCAGTTTTATTTACCCTACGG 59.818 40.000 0.00 0.00 0.00 4.02
2953 3232 6.148150 TCTGTTGCAGTTTTATTTACCCTACG 59.852 38.462 0.00 0.00 32.61 3.51
2954 3233 7.174426 ACTCTGTTGCAGTTTTATTTACCCTAC 59.826 37.037 0.00 0.00 32.61 3.18
2955 3234 7.228590 ACTCTGTTGCAGTTTTATTTACCCTA 58.771 34.615 0.00 0.00 32.61 3.53
2956 3235 6.068670 ACTCTGTTGCAGTTTTATTTACCCT 58.931 36.000 0.00 0.00 32.61 4.34
2957 3236 6.327279 ACTCTGTTGCAGTTTTATTTACCC 57.673 37.500 0.00 0.00 32.61 3.69
2958 3237 7.422399 TGAACTCTGTTGCAGTTTTATTTACC 58.578 34.615 0.00 0.00 34.10 2.85
2959 3238 9.463443 AATGAACTCTGTTGCAGTTTTATTTAC 57.537 29.630 0.00 0.00 34.10 2.01
2961 3240 8.947055 AAATGAACTCTGTTGCAGTTTTATTT 57.053 26.923 0.00 0.00 34.10 1.40
2962 3241 8.196771 TGAAATGAACTCTGTTGCAGTTTTATT 58.803 29.630 0.00 0.00 34.10 1.40
2963 3242 7.715657 TGAAATGAACTCTGTTGCAGTTTTAT 58.284 30.769 0.00 0.00 34.10 1.40
2964 3243 7.094508 TGAAATGAACTCTGTTGCAGTTTTA 57.905 32.000 0.00 0.00 34.10 1.52
2965 3244 5.964758 TGAAATGAACTCTGTTGCAGTTTT 58.035 33.333 0.00 0.00 34.10 2.43
2966 3245 5.581126 TGAAATGAACTCTGTTGCAGTTT 57.419 34.783 0.00 0.00 34.10 2.66
2967 3246 5.779529 ATGAAATGAACTCTGTTGCAGTT 57.220 34.783 0.00 0.00 36.77 3.16
2968 3247 5.779529 AATGAAATGAACTCTGTTGCAGT 57.220 34.783 0.00 0.00 32.61 4.40
2969 3248 6.698329 TGAAAATGAAATGAACTCTGTTGCAG 59.302 34.615 0.00 0.00 0.00 4.41
2970 3249 6.571605 TGAAAATGAAATGAACTCTGTTGCA 58.428 32.000 0.00 0.00 0.00 4.08
2971 3250 7.339953 GTTGAAAATGAAATGAACTCTGTTGC 58.660 34.615 0.00 0.00 0.00 4.17
2972 3251 7.042523 GGGTTGAAAATGAAATGAACTCTGTTG 60.043 37.037 0.00 0.00 0.00 3.33
2973 3252 6.986231 GGGTTGAAAATGAAATGAACTCTGTT 59.014 34.615 0.00 0.00 0.00 3.16
2974 3253 6.098124 TGGGTTGAAAATGAAATGAACTCTGT 59.902 34.615 0.00 0.00 0.00 3.41
2975 3254 6.514947 TGGGTTGAAAATGAAATGAACTCTG 58.485 36.000 0.00 0.00 0.00 3.35
2976 3255 6.324770 ACTGGGTTGAAAATGAAATGAACTCT 59.675 34.615 0.00 0.00 0.00 3.24
2977 3256 6.515832 ACTGGGTTGAAAATGAAATGAACTC 58.484 36.000 0.00 0.00 0.00 3.01
2978 3257 6.484364 ACTGGGTTGAAAATGAAATGAACT 57.516 33.333 0.00 0.00 0.00 3.01
2979 3258 6.538381 ACAACTGGGTTGAAAATGAAATGAAC 59.462 34.615 15.89 0.00 45.28 3.18
2980 3259 6.648192 ACAACTGGGTTGAAAATGAAATGAA 58.352 32.000 15.89 0.00 45.28 2.57
2981 3260 6.232581 ACAACTGGGTTGAAAATGAAATGA 57.767 33.333 15.89 0.00 45.28 2.57
2982 3261 7.382218 GTCTACAACTGGGTTGAAAATGAAATG 59.618 37.037 15.89 0.00 45.28 2.32
2983 3262 7.433680 GTCTACAACTGGGTTGAAAATGAAAT 58.566 34.615 15.89 0.00 45.28 2.17
2984 3263 6.459024 CGTCTACAACTGGGTTGAAAATGAAA 60.459 38.462 15.89 0.00 45.28 2.69
2985 3264 5.008217 CGTCTACAACTGGGTTGAAAATGAA 59.992 40.000 15.89 0.00 45.28 2.57
2986 3265 4.513692 CGTCTACAACTGGGTTGAAAATGA 59.486 41.667 15.89 5.05 45.28 2.57
2987 3266 4.783242 CGTCTACAACTGGGTTGAAAATG 58.217 43.478 15.89 3.90 45.28 2.32
2988 3267 3.252458 GCGTCTACAACTGGGTTGAAAAT 59.748 43.478 15.89 0.00 45.28 1.82
2989 3268 2.614983 GCGTCTACAACTGGGTTGAAAA 59.385 45.455 15.89 2.28 45.28 2.29
2990 3269 2.215196 GCGTCTACAACTGGGTTGAAA 58.785 47.619 15.89 4.35 45.28 2.69
2991 3270 1.139256 TGCGTCTACAACTGGGTTGAA 59.861 47.619 15.89 0.51 45.28 2.69
2992 3271 0.753867 TGCGTCTACAACTGGGTTGA 59.246 50.000 15.89 1.25 45.28 3.18
2994 3273 1.045407 TCTGCGTCTACAACTGGGTT 58.955 50.000 0.00 0.00 0.00 4.11
2995 3274 1.204941 GATCTGCGTCTACAACTGGGT 59.795 52.381 0.00 0.00 0.00 4.51
2996 3275 1.471676 GGATCTGCGTCTACAACTGGG 60.472 57.143 0.00 0.00 0.00 4.45
2997 3276 1.478510 AGGATCTGCGTCTACAACTGG 59.521 52.381 0.00 0.00 0.00 4.00
2998 3277 2.949451 AGGATCTGCGTCTACAACTG 57.051 50.000 0.00 0.00 0.00 3.16
2999 3278 2.826128 TGAAGGATCTGCGTCTACAACT 59.174 45.455 0.00 0.00 0.00 3.16
3000 3279 3.232213 TGAAGGATCTGCGTCTACAAC 57.768 47.619 0.00 0.00 0.00 3.32
3001 3280 3.953712 TTGAAGGATCTGCGTCTACAA 57.046 42.857 0.00 0.00 0.00 2.41
3002 3281 3.953712 TTTGAAGGATCTGCGTCTACA 57.046 42.857 0.00 0.00 0.00 2.74
3035 3314 2.313172 CCTGTGTGTGAGCGTCTGC 61.313 63.158 0.00 0.00 43.24 4.26
3036 3315 0.313987 TACCTGTGTGTGAGCGTCTG 59.686 55.000 0.00 0.00 0.00 3.51
3037 3316 0.598562 CTACCTGTGTGTGAGCGTCT 59.401 55.000 0.00 0.00 0.00 4.18
3038 3317 0.596577 TCTACCTGTGTGTGAGCGTC 59.403 55.000 0.00 0.00 0.00 5.19
3039 3318 1.202582 GATCTACCTGTGTGTGAGCGT 59.797 52.381 0.00 0.00 0.00 5.07
3040 3319 1.474478 AGATCTACCTGTGTGTGAGCG 59.526 52.381 0.00 0.00 0.00 5.03
3041 3320 3.444034 TGTAGATCTACCTGTGTGTGAGC 59.556 47.826 26.37 1.39 35.26 4.26


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

AutoCloner maintained by Alex Coulton.