Multiple sequence alignment - TraesCS3B01G002700

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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 TraesCS3B01G002700 chr3B 100.000 4708 0 0 1 4708 2173216 2168509 0.000000e+00 8695
1 TraesCS3B01G002700 chr3B 95.853 2098 76 7 1982 4077 2297711 2299799 0.000000e+00 3382
2 TraesCS3B01G002700 chr3B 79.953 2130 309 73 2073 4129 2309400 2311484 0.000000e+00 1459
3 TraesCS3B01G002700 chr3B 91.309 1001 49 15 660 1633 2296354 2297343 0.000000e+00 1332
4 TraesCS3B01G002700 chr3B 97.956 587 11 1 4122 4708 2299795 2300380 0.000000e+00 1016
5 TraesCS3B01G002700 chr3B 81.298 1310 191 36 2424 3697 2161961 2160670 0.000000e+00 1013
6 TraesCS3B01G002700 chr3B 93.375 317 17 4 1631 1946 2297399 2297712 2.570000e-127 466
7 TraesCS3B01G002700 chr3B 87.189 281 33 3 225 504 2296079 2296357 2.730000e-82 316
8 TraesCS3B01G002700 chr3B 76.682 639 68 45 996 1571 2163429 2162809 3.590000e-71 279
9 TraesCS3B01G002700 chr3B 97.516 161 4 0 502 662 243784205 243784045 4.640000e-70 276
10 TraesCS3B01G002700 chr3B 84.962 266 34 5 996 1257 2308481 2308744 1.000000e-66 265
11 TraesCS3B01G002700 chr3B 76.771 353 56 14 1383 1715 2308996 2309342 1.740000e-39 174
12 TraesCS3B01G002700 chr3B 92.784 97 5 2 1 95 2295905 2296001 6.350000e-29 139
13 TraesCS3B01G002700 chr3D 90.828 1690 124 17 2442 4119 3223496 3221826 0.000000e+00 2233
14 TraesCS3B01G002700 chr3D 93.011 787 36 8 660 1431 3224803 3224021 0.000000e+00 1131
15 TraesCS3B01G002700 chr3D 83.269 1034 143 24 2073 3089 3198305 3197285 0.000000e+00 924
16 TraesCS3B01G002700 chr3D 90.941 563 37 7 4155 4708 3221825 3221268 0.000000e+00 745
17 TraesCS3B01G002700 chr3D 76.334 1331 182 76 502 1751 3199631 3198353 1.460000e-164 590
18 TraesCS3B01G002700 chr3D 87.329 513 49 8 1535 2034 3224009 3223500 1.470000e-159 573
19 TraesCS3B01G002700 chr3D 82.759 464 74 6 3250 3712 3197168 3196710 4.390000e-110 409
20 TraesCS3B01G002700 chr3D 87.356 348 34 6 137 479 3225175 3224833 1.590000e-104 390
21 TraesCS3B01G002700 chr3D 85.185 108 16 0 2672 2779 3152029 3151922 1.380000e-20 111
22 TraesCS3B01G002700 chr3A 80.528 1818 264 57 2085 3834 373000 371205 0.000000e+00 1314
23 TraesCS3B01G002700 chr3A 89.613 982 88 12 3146 4119 398620 397645 0.000000e+00 1236
24 TraesCS3B01G002700 chr3A 93.952 744 40 4 2407 3147 399645 398904 0.000000e+00 1120
25 TraesCS3B01G002700 chr3A 92.755 773 43 4 665 1429 401057 400290 0.000000e+00 1105
26 TraesCS3B01G002700 chr3A 87.188 640 52 11 1415 2034 400271 399642 0.000000e+00 701
27 TraesCS3B01G002700 chr3A 92.348 379 26 2 4331 4708 397219 396843 1.930000e-148 536
28 TraesCS3B01G002700 chr3A 76.895 818 110 49 996 1751 373863 373063 1.590000e-104 390
29 TraesCS3B01G002700 chr3A 85.559 367 39 7 136 500 401419 401065 5.750000e-99 372
30 TraesCS3B01G002700 chr3A 74.140 785 121 43 3943 4677 270176 269424 2.810000e-62 250
31 TraesCS3B01G002700 chr1B 99.390 164 1 0 501 664 401623605 401623442 9.900000e-77 298
32 TraesCS3B01G002700 chr1B 96.951 164 5 0 499 662 543805940 543806103 4.640000e-70 276
33 TraesCS3B01G002700 chr2B 97.024 168 4 1 502 669 650282214 650282380 9.970000e-72 281
34 TraesCS3B01G002700 chr7B 96.951 164 5 0 499 662 424979912 424980075 4.640000e-70 276
35 TraesCS3B01G002700 chr5B 95.238 168 8 0 496 663 474318340 474318507 2.790000e-67 267
36 TraesCS3B01G002700 chr4B 95.238 168 7 1 496 662 352835566 352835399 1.000000e-66 265
37 TraesCS3B01G002700 chr4B 81.159 207 27 8 3628 3828 653428015 653427815 6.310000e-34 156
38 TraesCS3B01G002700 chr4B 80.000 210 27 11 3625 3828 653012796 653012996 1.770000e-29 141
39 TraesCS3B01G002700 chr6B 95.706 163 7 0 502 664 332382715 332382877 3.610000e-66 263
40 TraesCS3B01G002700 chr7D 92.737 179 8 4 489 663 235502392 235502569 2.170000e-63 254
41 TraesCS3B01G002700 chr5A 78.680 197 28 12 3638 3828 690565582 690565770 8.280000e-23 119


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 TraesCS3B01G002700 chr3B 2168509 2173216 4707 True 8695.000000 8695 100.000000 1 4708 1 chr3B.!!$R1 4707
1 TraesCS3B01G002700 chr3B 2295905 2300380 4475 False 1108.500000 3382 93.077667 1 4708 6 chr3B.!!$F1 4707
2 TraesCS3B01G002700 chr3B 2160670 2163429 2759 True 646.000000 1013 78.990000 996 3697 2 chr3B.!!$R3 2701
3 TraesCS3B01G002700 chr3B 2308481 2311484 3003 False 632.666667 1459 80.562000 996 4129 3 chr3B.!!$F2 3133
4 TraesCS3B01G002700 chr3D 3221268 3225175 3907 True 1014.400000 2233 89.893000 137 4708 5 chr3D.!!$R3 4571
5 TraesCS3B01G002700 chr3D 3196710 3199631 2921 True 641.000000 924 80.787333 502 3712 3 chr3D.!!$R2 3210
6 TraesCS3B01G002700 chr3A 371205 373863 2658 True 852.000000 1314 78.711500 996 3834 2 chr3A.!!$R2 2838
7 TraesCS3B01G002700 chr3A 396843 401419 4576 True 845.000000 1236 90.235833 136 4708 6 chr3A.!!$R3 4572
8 TraesCS3B01G002700 chr3A 269424 270176 752 True 250.000000 250 74.140000 3943 4677 1 chr3A.!!$R1 734

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
132 134 0.167908 CCACACACACACACACACAC 59.832 55.000 0.00 0.0 0.00 3.82 F
133 135 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.0 0.00 4.16 F
808 855 0.679640 CCTCCCATTTAAGCCACGCA 60.680 55.000 0.00 0.0 0.00 5.24 F
1261 1414 0.251634 GTTAGCTGCTTCTCTGGCCT 59.748 55.000 7.79 0.0 0.00 5.19 F
1584 1946 1.271856 TGGACAACCGAATCTAGCCA 58.728 50.000 0.00 0.0 39.42 4.75 F
2832 3632 1.683365 GTGCCTCAATGCCCACCAT 60.683 57.895 0.00 0.0 35.06 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1122 1230 2.109126 GGTAAGCTTGGCGCAGAGG 61.109 63.158 10.83 0.0 42.61 3.69 R
1216 1326 2.378547 TGTCCCATTCAGCTAAAAGGGT 59.621 45.455 9.78 0.0 37.61 4.34 R
2152 2690 1.340568 GTCTAGTACGGCCCATCCTTC 59.659 57.143 0.00 0.0 0.00 3.46 R
2958 3758 0.392336 GAGCATGATCGGCCTCTCTT 59.608 55.000 0.00 0.0 0.00 2.85 R
3459 4576 2.355010 AATTGTAGCAGATGGAGGGC 57.645 50.000 0.00 0.0 0.00 5.19 R
3925 5072 0.871163 CAGCAACCAACAACAAGCCG 60.871 55.000 0.00 0.0 0.00 5.52 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
35 36 1.004277 CCAACCTAGCCTAGCCACAAA 59.996 52.381 0.00 0.00 0.00 2.83
39 40 2.290323 ACCTAGCCTAGCCACAAAACTG 60.290 50.000 0.00 0.00 0.00 3.16
91 93 9.989296 TTCATATTATAAGGATTATTGTGGGGG 57.011 33.333 0.00 0.00 38.31 5.40
92 94 9.134504 TCATATTATAAGGATTATTGTGGGGGT 57.865 33.333 0.00 0.00 38.31 4.95
93 95 9.189156 CATATTATAAGGATTATTGTGGGGGTG 57.811 37.037 0.00 0.00 38.31 4.61
94 96 6.599986 TTATAAGGATTATTGTGGGGGTGT 57.400 37.500 0.00 0.00 38.31 4.16
95 97 7.709024 TTATAAGGATTATTGTGGGGGTGTA 57.291 36.000 0.00 0.00 38.31 2.90
96 98 3.945640 AGGATTATTGTGGGGGTGTAC 57.054 47.619 0.00 0.00 0.00 2.90
97 99 3.194620 AGGATTATTGTGGGGGTGTACA 58.805 45.455 0.00 0.00 0.00 2.90
98 100 3.053917 AGGATTATTGTGGGGGTGTACAC 60.054 47.826 18.01 18.01 38.08 2.90
99 101 3.308545 GGATTATTGTGGGGGTGTACACA 60.309 47.826 26.51 5.37 45.06 3.72
101 103 0.847373 ATTGTGGGGGTGTACACACA 59.153 50.000 28.62 19.66 46.25 3.72
113 115 3.459145 TGTACACACACATACACACACC 58.541 45.455 0.00 0.00 0.00 4.16
114 116 1.961793 ACACACACATACACACACCC 58.038 50.000 0.00 0.00 0.00 4.61
115 117 1.210722 ACACACACATACACACACCCA 59.789 47.619 0.00 0.00 0.00 4.51
116 118 1.601903 CACACACATACACACACCCAC 59.398 52.381 0.00 0.00 0.00 4.61
117 119 1.210722 ACACACATACACACACCCACA 59.789 47.619 0.00 0.00 0.00 4.17
118 120 1.601903 CACACATACACACACCCACAC 59.398 52.381 0.00 0.00 0.00 3.82
119 121 1.210722 ACACATACACACACCCACACA 59.789 47.619 0.00 0.00 0.00 3.72
120 122 1.601903 CACATACACACACCCACACAC 59.398 52.381 0.00 0.00 0.00 3.82
121 123 1.210722 ACATACACACACCCACACACA 59.789 47.619 0.00 0.00 0.00 3.72
122 124 1.601903 CATACACACACCCACACACAC 59.398 52.381 0.00 0.00 0.00 3.82
123 125 0.613777 TACACACACCCACACACACA 59.386 50.000 0.00 0.00 0.00 3.72
124 126 0.958382 ACACACACCCACACACACAC 60.958 55.000 0.00 0.00 0.00 3.82
125 127 0.957888 CACACACCCACACACACACA 60.958 55.000 0.00 0.00 0.00 3.72
126 128 0.958382 ACACACCCACACACACACAC 60.958 55.000 0.00 0.00 0.00 3.82
127 129 0.957888 CACACCCACACACACACACA 60.958 55.000 0.00 0.00 0.00 3.72
128 130 0.958382 ACACCCACACACACACACAC 60.958 55.000 0.00 0.00 0.00 3.82
129 131 0.957888 CACCCACACACACACACACA 60.958 55.000 0.00 0.00 0.00 3.72
130 132 0.958382 ACCCACACACACACACACAC 60.958 55.000 0.00 0.00 0.00 3.82
131 133 0.957888 CCCACACACACACACACACA 60.958 55.000 0.00 0.00 0.00 3.72
132 134 0.167908 CCACACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
133 135 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.00 0.00 4.16
134 136 1.295357 ACACACACACACACACACCG 61.295 55.000 0.00 0.00 0.00 4.94
148 150 6.366877 ACACACACACCGTTATAACTACATTC 59.633 38.462 13.56 0.00 0.00 2.67
154 156 9.485591 CACACCGTTATAACTACATTCATTTTC 57.514 33.333 13.56 0.00 0.00 2.29
262 264 2.638480 TTGCTGGTGTTGCTCTTACT 57.362 45.000 0.00 0.00 0.00 2.24
263 265 1.882912 TGCTGGTGTTGCTCTTACTG 58.117 50.000 0.00 0.00 0.00 2.74
264 266 1.140852 TGCTGGTGTTGCTCTTACTGT 59.859 47.619 0.00 0.00 0.00 3.55
266 268 2.061773 CTGGTGTTGCTCTTACTGTCG 58.938 52.381 0.00 0.00 0.00 4.35
300 303 1.903877 ATGACAAGAGGGACCCAGCG 61.904 60.000 14.60 0.09 0.00 5.18
409 418 5.300411 ACCCGTCGATATTTCCCTAAAAT 57.700 39.130 0.00 0.00 40.67 1.82
412 421 7.455891 ACCCGTCGATATTTCCCTAAAATAAT 58.544 34.615 0.00 0.00 41.85 1.28
413 422 8.596293 ACCCGTCGATATTTCCCTAAAATAATA 58.404 33.333 0.00 0.00 41.85 0.98
414 423 9.439500 CCCGTCGATATTTCCCTAAAATAATAA 57.561 33.333 0.00 0.00 41.85 1.40
454 464 2.550277 TCTTGGTGCTCCCTATCTCA 57.450 50.000 1.59 0.00 0.00 3.27
456 466 0.824109 TTGGTGCTCCCTATCTCACG 59.176 55.000 1.59 0.00 0.00 4.35
497 515 9.616634 CAAGTGCATCCACATATATTTCATAAC 57.383 33.333 0.00 0.00 44.53 1.89
522 542 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
523 543 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
524 544 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
531 551 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
547 567 7.840342 AAGTCTTTGTAGAGATTGCACTATG 57.160 36.000 0.00 0.00 0.00 2.23
548 568 7.175347 AGTCTTTGTAGAGATTGCACTATGA 57.825 36.000 0.00 0.00 0.00 2.15
549 569 7.615403 AGTCTTTGTAGAGATTGCACTATGAA 58.385 34.615 0.00 0.00 0.00 2.57
550 570 7.547370 AGTCTTTGTAGAGATTGCACTATGAAC 59.453 37.037 0.00 0.00 0.00 3.18
562 583 4.342665 TGCACTATGAACCACATACGGATA 59.657 41.667 0.00 0.00 40.07 2.59
566 587 8.410912 GCACTATGAACCACATACGGATATATA 58.589 37.037 0.00 0.00 40.07 0.86
573 594 9.627395 GAACCACATACGGATATATATAGATGC 57.373 37.037 0.00 0.00 0.00 3.91
593 615 5.627499 TGCATTTTGAGTGTAGATTCACC 57.373 39.130 0.00 0.00 38.91 4.02
600 622 6.573664 TTGAGTGTAGATTCACCCATTTTG 57.426 37.500 0.00 0.00 38.91 2.44
614 636 3.560068 CCCATTTTGCTCCGTATGTAGTC 59.440 47.826 0.00 0.00 0.00 2.59
615 637 3.560068 CCATTTTGCTCCGTATGTAGTCC 59.440 47.826 0.00 0.00 0.00 3.85
616 638 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
618 640 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
620 642 2.557056 TGCTCCGTATGTAGTCCATAGC 59.443 50.000 0.00 0.00 36.71 2.97
621 643 2.414293 GCTCCGTATGTAGTCCATAGCG 60.414 54.545 0.00 0.00 36.71 4.26
622 644 3.072211 CTCCGTATGTAGTCCATAGCGA 58.928 50.000 0.00 0.00 36.71 4.93
625 647 4.521639 TCCGTATGTAGTCCATAGCGAAAT 59.478 41.667 0.00 0.00 36.71 2.17
626 648 4.857588 CCGTATGTAGTCCATAGCGAAATC 59.142 45.833 0.00 0.00 36.71 2.17
627 649 5.335740 CCGTATGTAGTCCATAGCGAAATCT 60.336 44.000 0.00 0.00 36.71 2.40
631 654 6.315091 TGTAGTCCATAGCGAAATCTCTAC 57.685 41.667 0.00 0.00 0.00 2.59
638 661 6.096987 TCCATAGCGAAATCTCTACAAAGACT 59.903 38.462 0.00 0.00 0.00 3.24
639 662 6.758886 CCATAGCGAAATCTCTACAAAGACTT 59.241 38.462 0.00 0.00 0.00 3.01
640 663 7.921214 CCATAGCGAAATCTCTACAAAGACTTA 59.079 37.037 0.00 0.00 0.00 2.24
641 664 8.747666 CATAGCGAAATCTCTACAAAGACTTAC 58.252 37.037 0.00 0.00 0.00 2.34
657 680 5.021458 AGACTTACATTTAGGAACGGAGGA 58.979 41.667 0.00 0.00 0.00 3.71
747 789 2.149973 ATTTTCCACATCCTGGCCTC 57.850 50.000 3.32 0.00 40.39 4.70
808 855 0.679640 CCTCCCATTTAAGCCACGCA 60.680 55.000 0.00 0.00 0.00 5.24
899 947 5.975693 TGAAAAACAAAACACTCACTCCT 57.024 34.783 0.00 0.00 0.00 3.69
940 991 5.304686 TCTTGTGTTCATAAACCCTCACT 57.695 39.130 0.00 0.00 34.28 3.41
941 992 5.305585 TCTTGTGTTCATAAACCCTCACTC 58.694 41.667 0.00 0.00 34.28 3.51
942 993 4.015872 TGTGTTCATAAACCCTCACTCC 57.984 45.455 0.00 0.00 34.28 3.85
966 1017 1.316266 CTCACCCATCTCCCCCTCT 59.684 63.158 0.00 0.00 0.00 3.69
1122 1230 2.362120 AGGCAGCACATGAAGGCC 60.362 61.111 0.00 7.02 44.92 5.19
1185 1293 1.697432 TCCAACCCTGTAAGACCACAG 59.303 52.381 0.00 0.00 44.60 3.66
1261 1414 0.251634 GTTAGCTGCTTCTCTGGCCT 59.748 55.000 7.79 0.00 0.00 5.19
1306 1496 8.443937 AGCACGTTTAGTTATTCTGAAATCTTC 58.556 33.333 0.00 0.00 0.00 2.87
1413 1706 5.906113 AGTATATAGCCCTTCTCATCACG 57.094 43.478 0.00 0.00 0.00 4.35
1506 1848 4.713553 TGTGTTGCTTTCCTCATGAACTA 58.286 39.130 0.00 0.00 31.05 2.24
1577 1939 3.338249 CTGTTGAGATGGACAACCGAAT 58.662 45.455 0.00 0.00 44.49 3.34
1584 1946 1.271856 TGGACAACCGAATCTAGCCA 58.728 50.000 0.00 0.00 39.42 4.75
1633 2004 4.753107 CACGTCCAGGTGTACAAAATAGTT 59.247 41.667 0.00 0.00 33.24 2.24
1687 2184 3.122948 CACCTCGATATATTTTTCCGGCG 59.877 47.826 0.00 0.00 0.00 6.46
1735 2234 4.170053 TCCCAGGAGATATCCAAGACAGTA 59.830 45.833 9.50 0.00 0.00 2.74
1902 2402 2.159282 CGTACGAGGTCTTATGTGGCTT 60.159 50.000 10.44 0.00 0.00 4.35
1953 2453 8.455903 AATAATATTCGCTCCATCCCATATTG 57.544 34.615 0.00 0.00 0.00 1.90
1960 2460 3.688126 GCTCCATCCCATATTGGTTGTCA 60.688 47.826 3.83 0.00 35.17 3.58
1961 2461 3.885297 CTCCATCCCATATTGGTTGTCAC 59.115 47.826 3.83 0.00 35.17 3.67
1967 2467 5.579047 TCCCATATTGGTTGTCACTGAAAT 58.421 37.500 0.00 0.00 35.17 2.17
1968 2468 5.418524 TCCCATATTGGTTGTCACTGAAATG 59.581 40.000 0.00 0.00 35.17 2.32
1979 2479 7.716998 GGTTGTCACTGAAATGGATGTATCTAT 59.283 37.037 0.00 0.00 0.00 1.98
2032 2543 5.687166 AATATGTGACGGAGGGAAAGTAA 57.313 39.130 0.00 0.00 0.00 2.24
2042 2554 8.156165 TGACGGAGGGAAAGTAAATTAACTAAA 58.844 33.333 0.00 0.00 0.00 1.85
2123 2659 4.184629 AGGACAAATATCTCACTCGTTGC 58.815 43.478 0.00 0.00 0.00 4.17
2152 2690 2.862541 TCAGGGTGACAAATGGAACTG 58.137 47.619 0.00 0.00 0.00 3.16
2192 2737 8.035984 ACTAGACAGCTAGAAATAGGACAAAAC 58.964 37.037 6.92 0.00 45.71 2.43
2197 2745 7.119846 ACAGCTAGAAATAGGACAAAACATCAC 59.880 37.037 0.00 0.00 0.00 3.06
2233 2877 5.978814 ACTCCGTTGCAGATATTAAGAAGT 58.021 37.500 0.00 0.00 0.00 3.01
2242 2886 8.498054 TGCAGATATTAAGAAGTTTTCTGAGG 57.502 34.615 2.59 0.00 40.59 3.86
2278 2923 5.906772 ATCCGGGATTAAGAACCAACTAT 57.093 39.130 2.97 0.00 0.00 2.12
2336 2981 7.096885 GCACATTTGACGAAAATATCATACAGC 60.097 37.037 0.00 0.00 36.28 4.40
2566 3358 9.055689 AGGATGCATAGATCCAGAAAATATAGT 57.944 33.333 0.00 0.00 44.08 2.12
2702 3502 2.958818 AGGATACGATGACCCAGCTAA 58.041 47.619 0.00 0.00 46.39 3.09
2832 3632 1.683365 GTGCCTCAATGCCCACCAT 60.683 57.895 0.00 0.00 35.06 3.55
3169 4255 3.618698 CACACATGAGTCCGAGTATACG 58.381 50.000 0.00 0.00 0.00 3.06
3184 4271 6.020121 CCGAGTATACGTTTTGACCATAACTG 60.020 42.308 0.00 0.00 0.00 3.16
3201 4288 6.347402 CCATAACTGTTTACTTTCTGTGTCCG 60.347 42.308 0.00 0.00 0.00 4.79
3459 4576 3.751518 TCCTTTCTTTTTCTCTTCCCGG 58.248 45.455 0.00 0.00 0.00 5.73
3474 4591 2.423446 CGGCCCTCCATCTGCTAC 59.577 66.667 0.00 0.00 0.00 3.58
3587 4707 7.703058 ATTTGGTACTACCTTTTCCATGAAG 57.297 36.000 6.79 0.00 39.58 3.02
3811 4940 1.123928 AGCTAGAAGAACGGGATGGG 58.876 55.000 0.00 0.00 0.00 4.00
3903 5032 6.243900 AGGATGTTGACTGATCTGTGATTTT 58.756 36.000 10.29 0.00 0.00 1.82
3925 5072 0.394565 ACTGACTTCTGGGCTGTCAC 59.605 55.000 0.00 0.00 36.03 3.67
3936 5083 1.724582 GGCTGTCACGGCTTGTTGTT 61.725 55.000 8.93 0.00 35.82 2.83
3937 5084 0.592247 GCTGTCACGGCTTGTTGTTG 60.592 55.000 0.00 0.00 32.24 3.33
3963 5112 6.683974 TGCTGGAGTATTTTCAGAATAAGC 57.316 37.500 0.00 0.00 0.00 3.09
4022 5171 0.744874 GCATGGTGCAGATGCTCAAT 59.255 50.000 19.13 0.00 44.26 2.57
4119 5270 2.089980 CACATCTGGGAGCAAAAGAGG 58.910 52.381 0.00 0.00 0.00 3.69
4320 5499 3.270027 GAAAGCAAACCTTGGCAAAACT 58.730 40.909 0.00 0.00 33.01 2.66
4322 5501 1.830477 AGCAAACCTTGGCAAAACTGA 59.170 42.857 0.00 0.00 0.00 3.41
4325 5504 3.438434 GCAAACCTTGGCAAAACTGAAAA 59.562 39.130 0.00 0.00 0.00 2.29
4359 5785 3.189921 CCATGTGGGCGTCATGTG 58.810 61.111 15.57 7.00 40.43 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.681062 AATACATAATAGTACAGTTTTGTGGCT 57.319 29.630 12.94 0.00 38.23 4.75
74 76 4.789159 TGTACACCCCCACAATAATCCTTA 59.211 41.667 0.00 0.00 0.00 2.69
78 80 3.692593 GTGTGTACACCCCCACAATAATC 59.307 47.826 22.91 0.00 42.73 1.75
92 94 3.459145 GGTGTGTGTATGTGTGTGTACA 58.541 45.455 0.00 0.00 34.63 2.90
93 95 2.803956 GGGTGTGTGTATGTGTGTGTAC 59.196 50.000 0.00 0.00 0.00 2.90
94 96 2.434702 TGGGTGTGTGTATGTGTGTGTA 59.565 45.455 0.00 0.00 0.00 2.90
95 97 1.210722 TGGGTGTGTGTATGTGTGTGT 59.789 47.619 0.00 0.00 0.00 3.72
96 98 1.601903 GTGGGTGTGTGTATGTGTGTG 59.398 52.381 0.00 0.00 0.00 3.82
97 99 1.210722 TGTGGGTGTGTGTATGTGTGT 59.789 47.619 0.00 0.00 0.00 3.72
98 100 1.601903 GTGTGGGTGTGTGTATGTGTG 59.398 52.381 0.00 0.00 0.00 3.82
99 101 1.210722 TGTGTGGGTGTGTGTATGTGT 59.789 47.619 0.00 0.00 0.00 3.72
101 103 1.210722 TGTGTGTGGGTGTGTGTATGT 59.789 47.619 0.00 0.00 0.00 2.29
102 104 1.601903 GTGTGTGTGGGTGTGTGTATG 59.398 52.381 0.00 0.00 0.00 2.39
103 105 1.210722 TGTGTGTGTGGGTGTGTGTAT 59.789 47.619 0.00 0.00 0.00 2.29
104 106 0.613777 TGTGTGTGTGGGTGTGTGTA 59.386 50.000 0.00 0.00 0.00 2.90
105 107 0.958382 GTGTGTGTGTGGGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
106 108 0.957888 TGTGTGTGTGTGGGTGTGTG 60.958 55.000 0.00 0.00 0.00 3.82
107 109 0.958382 GTGTGTGTGTGTGGGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
108 110 0.957888 TGTGTGTGTGTGTGGGTGTG 60.958 55.000 0.00 0.00 0.00 3.82
109 111 0.958382 GTGTGTGTGTGTGTGGGTGT 60.958 55.000 0.00 0.00 0.00 4.16
110 112 0.957888 TGTGTGTGTGTGTGTGGGTG 60.958 55.000 0.00 0.00 0.00 4.61
111 113 0.958382 GTGTGTGTGTGTGTGTGGGT 60.958 55.000 0.00 0.00 0.00 4.51
112 114 0.957888 TGTGTGTGTGTGTGTGTGGG 60.958 55.000 0.00 0.00 0.00 4.61
113 115 0.167908 GTGTGTGTGTGTGTGTGTGG 59.832 55.000 0.00 0.00 0.00 4.17
114 116 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
115 117 1.295357 CGGTGTGTGTGTGTGTGTGT 61.295 55.000 0.00 0.00 0.00 3.72
116 118 1.295357 ACGGTGTGTGTGTGTGTGTG 61.295 55.000 0.00 0.00 0.00 3.82
117 119 0.604243 AACGGTGTGTGTGTGTGTGT 60.604 50.000 0.00 0.00 0.00 3.72
118 120 1.360820 TAACGGTGTGTGTGTGTGTG 58.639 50.000 0.00 0.00 0.00 3.82
119 121 2.319136 ATAACGGTGTGTGTGTGTGT 57.681 45.000 0.00 0.00 0.00 3.72
120 122 3.805422 AGTTATAACGGTGTGTGTGTGTG 59.195 43.478 9.91 0.00 0.00 3.82
121 123 4.062677 AGTTATAACGGTGTGTGTGTGT 57.937 40.909 9.91 0.00 0.00 3.72
122 124 4.983538 TGTAGTTATAACGGTGTGTGTGTG 59.016 41.667 9.91 0.00 0.00 3.82
123 125 5.199024 TGTAGTTATAACGGTGTGTGTGT 57.801 39.130 9.91 0.00 0.00 3.72
124 126 6.366604 TGAATGTAGTTATAACGGTGTGTGTG 59.633 38.462 9.91 0.00 0.00 3.82
125 127 6.457355 TGAATGTAGTTATAACGGTGTGTGT 58.543 36.000 9.91 0.00 0.00 3.72
126 128 6.954616 TGAATGTAGTTATAACGGTGTGTG 57.045 37.500 9.91 0.00 0.00 3.82
127 129 8.556213 AAATGAATGTAGTTATAACGGTGTGT 57.444 30.769 9.91 0.00 0.00 3.72
128 130 9.485591 GAAAATGAATGTAGTTATAACGGTGTG 57.514 33.333 9.91 0.00 0.00 3.82
129 131 9.221933 TGAAAATGAATGTAGTTATAACGGTGT 57.778 29.630 9.91 0.00 0.00 4.16
154 156 8.673711 TCGAAATGTCCCTGAATATAGTTTTTG 58.326 33.333 0.00 0.00 0.00 2.44
191 193 2.032681 AAAGCCCGACAGACTGGC 59.967 61.111 7.51 1.93 46.86 4.85
192 194 1.672356 CCAAAGCCCGACAGACTGG 60.672 63.158 7.51 0.00 0.00 4.00
262 264 5.350091 TGTCATAGATTCGAAAAATGCGACA 59.650 36.000 0.00 8.58 37.52 4.35
263 265 5.795766 TGTCATAGATTCGAAAAATGCGAC 58.204 37.500 0.00 6.03 37.52 5.19
264 266 6.312672 TCTTGTCATAGATTCGAAAAATGCGA 59.687 34.615 0.00 2.91 35.76 5.10
266 268 6.909357 CCTCTTGTCATAGATTCGAAAAATGC 59.091 38.462 0.00 4.13 0.00 3.56
300 303 1.272490 GGCAAGGTTTCCTTTGTAGCC 59.728 52.381 10.38 10.38 41.69 3.93
352 356 8.311836 TCACAACCAAAACTTAATTTAACACCA 58.688 29.630 0.00 0.00 0.00 4.17
414 423 9.396022 CCAAGAAATATCCACGGCTATTATTAT 57.604 33.333 0.00 0.00 0.00 1.28
416 425 7.174946 CACCAAGAAATATCCACGGCTATTATT 59.825 37.037 0.00 0.00 0.00 1.40
423 432 1.065551 GCACCAAGAAATATCCACGGC 59.934 52.381 0.00 0.00 0.00 5.68
472 482 9.353431 TGTTATGAAATATATGTGGATGCACTT 57.647 29.630 18.75 14.46 0.00 3.16
497 515 1.486211 AGGAACGGAGGGAGTACATG 58.514 55.000 0.00 0.00 0.00 3.21
522 542 8.749354 TCATAGTGCAATCTCTACAAAGACTTA 58.251 33.333 0.00 0.00 0.00 2.24
523 543 7.615403 TCATAGTGCAATCTCTACAAAGACTT 58.385 34.615 0.00 0.00 0.00 3.01
524 544 7.175347 TCATAGTGCAATCTCTACAAAGACT 57.825 36.000 0.00 0.00 0.00 3.24
531 551 5.419542 TGTGGTTCATAGTGCAATCTCTAC 58.580 41.667 0.00 0.00 0.00 2.59
535 555 4.811024 CGTATGTGGTTCATAGTGCAATCT 59.189 41.667 0.00 0.00 39.36 2.40
536 556 4.024893 CCGTATGTGGTTCATAGTGCAATC 60.025 45.833 0.00 0.00 39.36 2.67
540 560 3.173668 TCCGTATGTGGTTCATAGTGC 57.826 47.619 0.00 0.00 39.36 4.40
547 567 9.627395 GCATCTATATATATCCGTATGTGGTTC 57.373 37.037 0.00 0.00 0.00 3.62
548 568 9.143155 TGCATCTATATATATCCGTATGTGGTT 57.857 33.333 0.00 0.00 0.00 3.67
549 569 8.706322 TGCATCTATATATATCCGTATGTGGT 57.294 34.615 0.00 0.00 0.00 4.16
566 587 8.834465 GTGAATCTACACTCAAAATGCATCTAT 58.166 33.333 0.00 0.00 37.73 1.98
571 592 4.458989 GGGTGAATCTACACTCAAAATGCA 59.541 41.667 0.00 0.00 40.56 3.96
572 593 4.458989 TGGGTGAATCTACACTCAAAATGC 59.541 41.667 0.00 0.00 46.35 3.56
593 615 3.560068 GGACTACATACGGAGCAAAATGG 59.440 47.826 0.00 0.00 0.00 3.16
600 622 2.414293 CGCTATGGACTACATACGGAGC 60.414 54.545 0.00 0.00 41.03 4.70
614 636 6.276847 AGTCTTTGTAGAGATTTCGCTATGG 58.723 40.000 0.00 0.00 31.23 2.74
615 637 7.763172 AAGTCTTTGTAGAGATTTCGCTATG 57.237 36.000 0.00 0.00 31.23 2.23
616 638 8.467598 TGTAAGTCTTTGTAGAGATTTCGCTAT 58.532 33.333 0.00 0.00 31.23 2.97
618 640 6.688578 TGTAAGTCTTTGTAGAGATTTCGCT 58.311 36.000 0.00 0.00 29.76 4.93
625 647 9.924650 GTTCCTAAATGTAAGTCTTTGTAGAGA 57.075 33.333 0.00 0.00 0.00 3.10
626 648 8.861101 CGTTCCTAAATGTAAGTCTTTGTAGAG 58.139 37.037 0.00 0.00 0.00 2.43
627 649 7.816031 CCGTTCCTAAATGTAAGTCTTTGTAGA 59.184 37.037 0.00 0.00 0.00 2.59
631 654 6.092259 CCTCCGTTCCTAAATGTAAGTCTTTG 59.908 42.308 0.00 0.00 0.00 2.77
638 661 5.750352 ACTTCCTCCGTTCCTAAATGTAA 57.250 39.130 0.00 0.00 0.00 2.41
639 662 5.954150 AGTACTTCCTCCGTTCCTAAATGTA 59.046 40.000 0.00 0.00 0.00 2.29
640 663 4.776308 AGTACTTCCTCCGTTCCTAAATGT 59.224 41.667 0.00 0.00 0.00 2.71
641 664 5.340439 AGTACTTCCTCCGTTCCTAAATG 57.660 43.478 0.00 0.00 0.00 2.32
808 855 2.583566 AGCTAGTAGGAGGACTGGAGTT 59.416 50.000 0.00 0.00 29.77 3.01
940 991 0.263172 GAGATGGGTGAGGAGGAGGA 59.737 60.000 0.00 0.00 0.00 3.71
941 992 0.762461 GGAGATGGGTGAGGAGGAGG 60.762 65.000 0.00 0.00 0.00 4.30
942 993 0.762461 GGGAGATGGGTGAGGAGGAG 60.762 65.000 0.00 0.00 0.00 3.69
966 1017 1.879380 CGAAATGCAACCAGAAGGACA 59.121 47.619 0.00 0.00 38.69 4.02
1122 1230 2.109126 GGTAAGCTTGGCGCAGAGG 61.109 63.158 10.83 0.00 42.61 3.69
1137 1245 3.214694 TCTTTTGGGATGAGGGAGGTA 57.785 47.619 0.00 0.00 0.00 3.08
1185 1293 8.718102 ATTGTACAACATATGGAGTACTGTTC 57.282 34.615 26.45 12.14 38.09 3.18
1216 1326 2.378547 TGTCCCATTCAGCTAAAAGGGT 59.621 45.455 9.78 0.00 37.61 4.34
1261 1414 5.179368 CGTGCTCATCTTGTTCCTTTTTCTA 59.821 40.000 0.00 0.00 0.00 2.10
1306 1496 6.231211 ACACACAATAAACCCTTCTGACTAG 58.769 40.000 0.00 0.00 0.00 2.57
1395 1688 3.562182 TCACGTGATGAGAAGGGCTATA 58.438 45.455 15.76 0.00 31.91 1.31
1396 1689 2.388735 TCACGTGATGAGAAGGGCTAT 58.611 47.619 15.76 0.00 31.91 2.97
1400 1693 4.445718 CGATATTTCACGTGATGAGAAGGG 59.554 45.833 20.80 1.52 38.99 3.95
1577 1939 4.580167 GCATGATTGTACCAATTGGCTAGA 59.420 41.667 24.79 11.40 39.32 2.43
1584 1946 5.536161 GGTCCATAGCATGATTGTACCAATT 59.464 40.000 0.00 0.00 0.00 2.32
1683 2180 3.235195 GCTGTATATTCAGAGTACGCCG 58.765 50.000 13.07 0.00 37.61 6.46
1687 2184 5.070580 ACTTGGGGCTGTATATTCAGAGTAC 59.929 44.000 13.07 1.33 37.61 2.73
1853 2352 4.384940 TGGAGGCAAAAATTAACAAAGCC 58.615 39.130 0.00 0.00 40.85 4.35
1859 2358 4.625311 CGTCCAATGGAGGCAAAAATTAAC 59.375 41.667 9.18 0.00 30.80 2.01
1953 2453 5.882557 AGATACATCCATTTCAGTGACAACC 59.117 40.000 0.00 0.00 0.00 3.77
1960 2460 7.231519 TCTCGACATAGATACATCCATTTCAGT 59.768 37.037 0.00 0.00 0.00 3.41
1961 2461 7.597386 TCTCGACATAGATACATCCATTTCAG 58.403 38.462 0.00 0.00 0.00 3.02
1979 2479 4.443913 TTGAAACGGATGTATCTCGACA 57.556 40.909 8.87 0.00 0.00 4.35
2123 2659 6.828273 TCCATTTGTCACCCTGATAGTAATTG 59.172 38.462 0.00 0.00 0.00 2.32
2152 2690 1.340568 GTCTAGTACGGCCCATCCTTC 59.659 57.143 0.00 0.00 0.00 3.46
2192 2737 3.612860 GGAGTTGTACTTGCTACGTGATG 59.387 47.826 0.00 0.00 0.00 3.07
2197 2745 2.342910 ACGGAGTTGTACTTGCTACG 57.657 50.000 12.57 12.57 37.78 3.51
2233 2877 9.892130 GGATTAGTTCTTCTATTCCTCAGAAAA 57.108 33.333 7.92 0.00 41.89 2.29
2242 2886 9.425577 CTTAATCCCGGATTAGTTCTTCTATTC 57.574 37.037 17.52 0.00 36.15 1.75
2317 2962 7.264947 TCTCTTGCTGTATGATATTTTCGTCA 58.735 34.615 0.00 0.00 0.00 4.35
2336 2981 7.360776 GCTTCCTTAACAGTTGAGAATCTCTTG 60.361 40.741 11.92 9.55 34.92 3.02
2670 3470 8.136165 GGGTCATCGTATCCTATATACACATTC 58.864 40.741 0.00 0.00 0.00 2.67
2795 3595 2.284699 ACTAGCCCCTCTTGCGGT 60.285 61.111 0.00 0.00 0.00 5.68
2832 3632 1.608336 CCACTCGTGGTAGGGGTGA 60.608 63.158 7.93 0.00 45.53 4.02
2958 3758 0.392336 GAGCATGATCGGCCTCTCTT 59.608 55.000 0.00 0.00 0.00 2.85
3169 4255 9.233232 CAGAAAGTAAACAGTTATGGTCAAAAC 57.767 33.333 0.00 0.00 0.00 2.43
3184 4271 8.699283 AATAGATACGGACACAGAAAGTAAAC 57.301 34.615 0.00 0.00 0.00 2.01
3201 4288 8.142551 ACAAACGTGAATCCCTCTAATAGATAC 58.857 37.037 0.00 0.00 0.00 2.24
3265 4376 8.017373 CCTTTGTGTCTTTCACTTGTGTATATG 58.983 37.037 0.46 0.00 46.27 1.78
3459 4576 2.355010 AATTGTAGCAGATGGAGGGC 57.645 50.000 0.00 0.00 0.00 5.19
3492 4609 4.755123 ACTTTTTCCAGTCACGGTAGATTG 59.245 41.667 0.00 0.00 0.00 2.67
3560 4678 9.762381 TTCATGGAAAAGGTAGTACCAAATTAT 57.238 29.630 21.49 5.77 41.95 1.28
3568 4686 8.611654 TGTTAACTTCATGGAAAAGGTAGTAC 57.388 34.615 7.22 0.00 28.20 2.73
3587 4707 6.614160 ACGCAACTAATTAACCCATGTTAAC 58.386 36.000 0.00 0.00 46.65 2.01
3811 4940 7.723324 TGTTATATAGCTACTGAAGGGTGTTC 58.277 38.462 0.00 0.00 0.00 3.18
3903 5032 1.070758 GACAGCCCAGAAGTCAGTGAA 59.929 52.381 0.00 0.00 32.68 3.18
3925 5072 0.871163 CAGCAACCAACAACAAGCCG 60.871 55.000 0.00 0.00 0.00 5.52
3936 5083 4.365514 TCTGAAAATACTCCAGCAACCA 57.634 40.909 0.00 0.00 0.00 3.67
3937 5084 5.904362 ATTCTGAAAATACTCCAGCAACC 57.096 39.130 0.00 0.00 0.00 3.77
4018 5167 7.131907 TCGAGAAAGTTGGGGATAATATTGA 57.868 36.000 0.00 0.00 0.00 2.57
4022 5171 6.895782 ACATTCGAGAAAGTTGGGGATAATA 58.104 36.000 0.00 0.00 0.00 0.98
4087 5238 2.225019 CCCAGATGTGCGATGATTAAGC 59.775 50.000 0.00 0.00 0.00 3.09
4088 5239 3.732212 TCCCAGATGTGCGATGATTAAG 58.268 45.455 0.00 0.00 0.00 1.85
4119 5270 9.765795 ATGCTAGAATAACTTACAGTATTGACC 57.234 33.333 0.00 0.00 0.00 4.02
4325 5504 6.347696 CCACATGGCCACATATTGTATTTTT 58.652 36.000 8.16 0.00 34.99 1.94


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

AutoCloner maintained by Alex Coulton.