Multiple sequence alignment - TraesCS3B01G011900

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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 TraesCS3B01G011900 chr3B 100.000 3560 0 0 1 3560 5324635 5321076 0.000000e+00 6575.0
1 TraesCS3B01G011900 chr3B 90.273 1357 85 21 124 1465 3406353 3407677 0.000000e+00 1731.0
2 TraesCS3B01G011900 chr3B 89.218 1048 87 15 1905 2927 3408114 3409160 0.000000e+00 1286.0
3 TraesCS3B01G011900 chr3B 93.690 523 27 6 947 1465 3667380 3666860 0.000000e+00 778.0
4 TraesCS3B01G011900 chr3B 90.249 523 29 14 947 1465 5168986 5169490 0.000000e+00 664.0
5 TraesCS3B01G011900 chr3B 82.766 441 70 6 175 612 3610485 3610922 4.310000e-104 388.0
6 TraesCS3B01G011900 chr3B 82.766 441 70 6 175 612 5226207 5225770 4.310000e-104 388.0
7 TraesCS3B01G011900 chr3B 93.506 231 15 0 3330 3560 3409578 3409808 9.460000e-91 344.0
8 TraesCS3B01G011900 chr3B 94.211 190 11 0 2491 2680 3625833 3626022 1.250000e-74 291.0
9 TraesCS3B01G011900 chr3B 90.566 212 19 1 1982 2192 3666375 3666164 2.710000e-71 279.0
10 TraesCS3B01G011900 chr3B 81.250 288 15 11 3042 3299 3409204 3409482 2.800000e-46 196.0
11 TraesCS3B01G011900 chr3B 89.404 151 12 3 2471 2617 3665786 3665636 1.690000e-43 187.0
12 TraesCS3B01G011900 chr3B 88.125 160 15 3 2462 2617 5170554 5170713 1.690000e-43 187.0
13 TraesCS3B01G011900 chr3B 88.312 154 18 0 609 762 3610958 3611111 6.070000e-43 185.0
14 TraesCS3B01G011900 chr3B 87.898 157 19 0 612 768 5225731 5225575 6.070000e-43 185.0
15 TraesCS3B01G011900 chr3D 87.101 1628 99 50 612 2192 1641015 1639452 0.000000e+00 1740.0
16 TraesCS3B01G011900 chr3D 90.151 863 44 24 609 1465 1337145 1337972 0.000000e+00 1085.0
17 TraesCS3B01G011900 chr3D 87.923 621 61 9 1 612 1336494 1337109 0.000000e+00 719.0
18 TraesCS3B01G011900 chr3D 87.903 620 63 7 1 612 1641669 1641054 0.000000e+00 719.0
19 TraesCS3B01G011900 chr3D 84.174 575 65 14 1638 2191 546540895 546541464 5.230000e-148 534.0
20 TraesCS3B01G011900 chr3D 89.150 341 23 10 2299 2627 1338984 1339322 2.560000e-111 412.0
21 TraesCS3B01G011900 chr3D 88.302 265 21 6 2660 2922 1339323 1339579 3.450000e-80 309.0
22 TraesCS3B01G011900 chr3D 94.531 128 7 0 3332 3459 1340116 1340243 7.800000e-47 198.0
23 TraesCS3B01G011900 chr3D 90.066 151 11 3 2471 2617 1639064 1638914 3.630000e-45 193.0
24 TraesCS3B01G011900 chr3D 84.422 199 7 3 3126 3300 1339821 1340019 1.310000e-39 174.0
25 TraesCS3B01G011900 chr3D 81.522 184 23 8 1 177 542996445 542996266 1.330000e-29 141.0
26 TraesCS3B01G011900 chr3D 81.871 171 23 2 5 169 606398791 606398959 1.720000e-28 137.0
27 TraesCS3B01G011900 chr3A 85.018 821 66 29 657 1465 7477206 7476431 0.000000e+00 782.0
28 TraesCS3B01G011900 chr3A 85.574 714 61 22 1480 2191 7476370 7475697 0.000000e+00 710.0
29 TraesCS3B01G011900 chr3A 94.603 315 12 5 293 604 7477528 7477216 1.920000e-132 483.0
30 TraesCS3B01G011900 chr3A 86.102 295 31 4 6 291 7478069 7477776 3.450000e-80 309.0
31 TraesCS3B01G011900 chr3A 90.066 151 11 3 2471 2617 7475331 7475181 3.630000e-45 193.0
32 TraesCS3B01G011900 chr3A 91.129 124 10 1 2918 3041 371626719 371626597 2.200000e-37 167.0
33 TraesCS3B01G011900 chr6B 84.076 741 91 15 1480 2198 94240838 94240103 0.000000e+00 689.0
34 TraesCS3B01G011900 chr6B 94.737 95 4 1 2474 2568 265677438 265677345 2.860000e-31 147.0
35 TraesCS3B01G011900 chr6B 83.030 165 20 2 12 170 694625699 694625537 3.700000e-30 143.0
36 TraesCS3B01G011900 chr4A 96.306 379 14 0 1075 1453 732517271 732516893 1.090000e-174 623.0
37 TraesCS3B01G011900 chr7A 96.063 381 15 0 1082 1462 8262588 8262208 3.900000e-174 621.0
38 TraesCS3B01G011900 chr7D 96.237 372 14 0 1082 1453 7302268 7301897 8.450000e-171 610.0
39 TraesCS3B01G011900 chr7D 94.737 95 4 1 2474 2568 7300734 7300641 2.860000e-31 147.0
40 TraesCS3B01G011900 chr2B 86.897 435 51 4 1758 2191 727307380 727307809 1.920000e-132 483.0
41 TraesCS3B01G011900 chr2B 90.000 130 11 2 2913 3041 721714640 721714768 2.200000e-37 167.0
42 TraesCS3B01G011900 chr2D 86.810 326 36 5 1867 2191 56853121 56853440 1.220000e-94 357.0
43 TraesCS3B01G011900 chr2D 86.293 321 36 6 1872 2191 547752785 547752472 3.400000e-90 342.0
44 TraesCS3B01G011900 chr2D 84.091 176 20 6 4 173 16083652 16083479 2.840000e-36 163.0
45 TraesCS3B01G011900 chr5B 94.017 117 7 0 2926 3042 382489069 382488953 1.020000e-40 178.0
46 TraesCS3B01G011900 chr5B 92.500 120 9 0 2922 3041 375738239 375738120 4.730000e-39 172.0
47 TraesCS3B01G011900 chr5B 80.804 224 32 6 3330 3551 457082023 457082237 7.910000e-37 165.0
48 TraesCS3B01G011900 chr5B 80.460 174 23 6 1 166 710199171 710199341 4.830000e-24 122.0
49 TraesCS3B01G011900 chr5D 93.162 117 8 0 2925 3041 90314142 90314258 4.730000e-39 172.0
50 TraesCS3B01G011900 chr5D 97.297 37 1 0 3524 3560 548968955 548968991 2.970000e-06 63.9
51 TraesCS3B01G011900 chr7B 93.103 116 8 0 2926 3041 332242888 332242773 1.700000e-38 171.0
52 TraesCS3B01G011900 chr7B 89.844 128 12 1 2915 3042 123402008 123402134 2.840000e-36 163.0
53 TraesCS3B01G011900 chr7B 81.768 181 22 6 4 177 554757720 554757544 1.330000e-29 141.0
54 TraesCS3B01G011900 chr7B 82.946 129 15 5 50 177 599881503 599881381 3.760000e-20 110.0
55 TraesCS3B01G011900 chr5A 92.500 120 7 1 2924 3041 556685015 556685134 1.700000e-38 171.0
56 TraesCS3B01G011900 chr2A 89.394 132 10 3 2912 3041 65193131 65193002 2.840000e-36 163.0
57 TraesCS3B01G011900 chr4D 80.814 172 22 6 6 170 469912966 469913133 1.340000e-24 124.0


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 TraesCS3B01G011900 chr3B 5321076 5324635 3559 True 6575.000000 6575 100.000000 1 3560 1 chr3B.!!$R1 3559
1 TraesCS3B01G011900 chr3B 3406353 3409808 3455 False 889.250000 1731 88.561750 124 3560 4 chr3B.!!$F2 3436
2 TraesCS3B01G011900 chr3B 5168986 5170713 1727 False 425.500000 664 89.187000 947 2617 2 chr3B.!!$F4 1670
3 TraesCS3B01G011900 chr3B 3665636 3667380 1744 True 414.666667 778 91.220000 947 2617 3 chr3B.!!$R2 1670
4 TraesCS3B01G011900 chr3B 3610485 3611111 626 False 286.500000 388 85.539000 175 762 2 chr3B.!!$F3 587
5 TraesCS3B01G011900 chr3B 5225575 5226207 632 True 286.500000 388 85.332000 175 768 2 chr3B.!!$R3 593
6 TraesCS3B01G011900 chr3D 1638914 1641669 2755 True 884.000000 1740 88.356667 1 2617 3 chr3D.!!$R2 2616
7 TraesCS3B01G011900 chr3D 546540895 546541464 569 False 534.000000 534 84.174000 1638 2191 1 chr3D.!!$F1 553
8 TraesCS3B01G011900 chr3D 1336494 1340243 3749 False 482.833333 1085 89.079833 1 3459 6 chr3D.!!$F3 3458
9 TraesCS3B01G011900 chr3A 7475181 7478069 2888 True 495.400000 782 88.272600 6 2617 5 chr3A.!!$R2 2611
10 TraesCS3B01G011900 chr6B 94240103 94240838 735 True 689.000000 689 84.076000 1480 2198 1 chr6B.!!$R1 718
11 TraesCS3B01G011900 chr7D 7300641 7302268 1627 True 378.500000 610 95.487000 1082 2568 2 chr7D.!!$R1 1486

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
24 25 1.127213 GTTTAAGATTTGGACGCGCGA 59.873 47.619 39.36 14.91 0.00 5.87 F
461 719 1.222115 GACCATTATGGCGTCGGAGC 61.222 60.000 11.72 0.00 42.67 4.70 F
1329 1687 0.243907 ACGTCCAGAACCTCATCACG 59.756 55.000 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1107 1465 0.538516 CCGGGATCTCCATCGTCTCT 60.539 60.000 0.00 0.0 37.91 3.10 R
1926 2425 2.393768 GCCACACAGGACATCGCAG 61.394 63.158 0.00 0.0 41.22 5.18 R
3124 4765 0.686789 ATGGCCGCATGTAGCATCTA 59.313 50.000 10.63 0.0 46.13 1.98 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
24 25 1.127213 GTTTAAGATTTGGACGCGCGA 59.873 47.619 39.36 14.91 0.00 5.87
39 40 5.333111 GGACGCGCGATTTAAGAGATAAAAT 60.333 40.000 39.36 7.14 37.06 1.82
40 41 5.432157 ACGCGCGATTTAAGAGATAAAATG 58.568 37.500 39.36 0.00 37.06 2.32
42 43 5.556665 CGCGCGATTTAAGAGATAAAATGTC 59.443 40.000 28.94 0.00 37.06 3.06
122 131 3.670377 GGCCACTTGTCGCAACCC 61.670 66.667 0.00 0.00 0.00 4.11
159 168 7.740805 AGTGATCTTTGAAAGAAGTACTCCTT 58.259 34.615 12.10 0.00 41.63 3.36
223 232 1.739750 TTGGTTCAAAATGGGCCCAT 58.260 45.000 32.75 32.75 38.46 4.00
246 255 4.601406 TCTAGCCCATAACCACCAATTT 57.399 40.909 0.00 0.00 0.00 1.82
383 640 4.488136 CCCGCATAGCCCAGCACA 62.488 66.667 0.00 0.00 0.00 4.57
405 662 1.310933 CCGCCACACTACTCTACCGT 61.311 60.000 0.00 0.00 0.00 4.83
461 719 1.222115 GACCATTATGGCGTCGGAGC 61.222 60.000 11.72 0.00 42.67 4.70
462 720 2.310233 CCATTATGGCGTCGGAGCG 61.310 63.158 0.00 0.00 38.18 5.03
463 721 1.299850 CATTATGGCGTCGGAGCGA 60.300 57.895 0.00 0.00 38.18 4.93
580 839 7.063780 CACTTACAAATGGGCAAGATTGAAATC 59.936 37.037 0.00 0.00 35.64 2.17
775 1088 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
776 1089 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
777 1090 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
778 1091 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
779 1092 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
780 1093 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
781 1094 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
782 1095 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
783 1096 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
784 1097 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
785 1098 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
786 1099 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
787 1100 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
788 1101 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
789 1102 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
790 1103 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
791 1104 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
792 1105 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
793 1106 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
794 1107 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
795 1108 8.887036 AGAAGAAGAAGAAGAAGAAGAAGAAC 57.113 34.615 0.00 0.00 0.00 3.01
829 1148 2.628106 CCGCCGCAGATTGATTCG 59.372 61.111 0.00 0.00 0.00 3.34
980 1308 5.013547 ACGCCAGCTATATAAGATCTCACT 58.986 41.667 0.00 0.00 0.00 3.41
983 1311 6.127758 CGCCAGCTATATAAGATCTCACTTCT 60.128 42.308 0.00 0.00 0.00 2.85
984 1312 7.576666 CGCCAGCTATATAAGATCTCACTTCTT 60.577 40.741 0.00 0.00 37.25 2.52
986 1314 8.250332 CCAGCTATATAAGATCTCACTTCTTCC 58.750 40.741 0.00 0.00 35.19 3.46
987 1315 9.023962 CAGCTATATAAGATCTCACTTCTTCCT 57.976 37.037 0.00 0.00 35.19 3.36
988 1316 9.600432 AGCTATATAAGATCTCACTTCTTCCTT 57.400 33.333 0.00 0.00 35.19 3.36
992 1320 2.167487 AGATCTCACTTCTTCCTTCGCC 59.833 50.000 0.00 0.00 0.00 5.54
993 1321 1.633774 TCTCACTTCTTCCTTCGCCT 58.366 50.000 0.00 0.00 0.00 5.52
1287 1645 3.965258 ACCCGCAAGACCATGGCA 61.965 61.111 13.04 0.00 43.02 4.92
1329 1687 0.243907 ACGTCCAGAACCTCATCACG 59.756 55.000 0.00 0.00 0.00 4.35
1428 1786 1.037579 ACCGTGGCATCGAGATCAGA 61.038 55.000 10.33 0.00 0.00 3.27
1526 2000 5.303589 CCATTCATCAGATGCCTGGTTTATT 59.696 40.000 17.19 0.00 40.76 1.40
1546 2020 9.241317 GTTTATTAGTGATTGCTGATGAATTGG 57.759 33.333 0.00 0.00 0.00 3.16
1552 2026 4.400251 TGATTGCTGATGAATTGGGAGTTC 59.600 41.667 0.00 0.00 0.00 3.01
1592 2066 9.107177 GAATCTCTGTTCACATATCATTCTGTT 57.893 33.333 0.00 0.00 0.00 3.16
1650 2126 4.600111 ACTGGTGTAAATTGGGGAACTCTA 59.400 41.667 0.00 0.00 0.00 2.43
1753 2233 2.501723 GGGATCACAGCCTTACTTGAGA 59.498 50.000 0.00 0.00 0.00 3.27
1754 2234 3.055094 GGGATCACAGCCTTACTTGAGAA 60.055 47.826 0.00 0.00 0.00 2.87
1755 2235 4.187694 GGATCACAGCCTTACTTGAGAAG 58.812 47.826 0.00 0.00 0.00 2.85
1756 2236 3.045601 TCACAGCCTTACTTGAGAAGC 57.954 47.619 0.00 0.00 0.00 3.86
1770 2269 5.411977 ACTTGAGAAGCTGAGATGTTTGATG 59.588 40.000 0.00 0.00 0.00 3.07
1806 2305 4.348020 TTCCTAGAACAGGGGTCACTAT 57.652 45.455 0.00 0.00 45.58 2.12
1832 2331 2.236395 ACTGTAGTAGTGGTGCCATTCC 59.764 50.000 0.00 0.00 38.49 3.01
1835 2334 0.844661 AGTAGTGGTGCCATTCCCCA 60.845 55.000 0.00 0.00 0.00 4.96
1865 2364 1.587547 GGCTCATAGTGCTGTTAGCC 58.412 55.000 5.61 5.61 41.51 3.93
1869 2368 3.494048 GCTCATAGTGCTGTTAGCCTCAT 60.494 47.826 0.00 0.00 41.51 2.90
1877 2376 4.397417 GTGCTGTTAGCCTCATTGAATCTT 59.603 41.667 0.00 0.00 41.51 2.40
1881 2380 6.986817 GCTGTTAGCCTCATTGAATCTTAGTA 59.013 38.462 0.00 0.00 34.48 1.82
1903 2402 8.630054 AGTATGGTATACTCTAGAGAAGCAAG 57.370 38.462 26.57 0.00 0.00 4.01
1926 2425 1.267806 CCACTCTTGGCATTGTGTGTC 59.732 52.381 16.31 0.00 35.56 3.67
1960 2459 4.341806 TGTGTGGCTTTCATCTGTTTTGAT 59.658 37.500 0.00 0.00 0.00 2.57
2428 3895 5.757320 GCTGTATCTTGATATTGCAGTGACT 59.243 40.000 0.00 0.00 0.00 3.41
2578 4102 2.731571 GGGTGCGACCTATCTGCCA 61.732 63.158 5.48 0.00 38.64 4.92
2661 4192 1.542472 TCACATGAGTTGGCTGCAATG 59.458 47.619 0.00 0.00 0.00 2.82
2680 4211 3.012934 TGTGTACTGGATCGATCAGGA 57.987 47.619 25.93 15.17 36.62 3.86
2682 4213 3.381590 TGTGTACTGGATCGATCAGGAAG 59.618 47.826 25.93 18.21 36.62 3.46
2707 4238 5.531287 GTCATGTAACTGGAGAAGGTTGTTT 59.469 40.000 0.00 0.00 0.00 2.83
2741 4273 7.040340 TGTGTTTGTTTCACCGGTTGATAATAT 60.040 33.333 2.97 0.00 32.84 1.28
2860 4400 3.190744 GTGATTGACGTGTCCTCTGACTA 59.809 47.826 0.00 0.00 42.28 2.59
2862 4402 4.462834 TGATTGACGTGTCCTCTGACTAAT 59.537 41.667 0.00 0.00 42.28 1.73
2863 4403 4.866508 TTGACGTGTCCTCTGACTAATT 57.133 40.909 0.00 0.00 42.28 1.40
2864 4404 4.866508 TGACGTGTCCTCTGACTAATTT 57.133 40.909 0.00 0.00 42.28 1.82
2865 4405 5.209818 TGACGTGTCCTCTGACTAATTTT 57.790 39.130 0.00 0.00 42.28 1.82
2866 4406 5.607477 TGACGTGTCCTCTGACTAATTTTT 58.393 37.500 0.00 0.00 42.28 1.94
2927 4467 7.549488 AGTCAGCCAAGTTTTGTATCTATGTAC 59.451 37.037 0.00 0.00 0.00 2.90
2929 4469 7.764443 TCAGCCAAGTTTTGTATCTATGTACTC 59.236 37.037 0.00 0.00 0.00 2.59
2930 4470 7.011482 CAGCCAAGTTTTGTATCTATGTACTCC 59.989 40.741 0.00 0.00 0.00 3.85
2933 4473 7.711339 CCAAGTTTTGTATCTATGTACTCCCTC 59.289 40.741 0.00 0.00 0.00 4.30
2934 4474 8.478877 CAAGTTTTGTATCTATGTACTCCCTCT 58.521 37.037 0.00 0.00 0.00 3.69
2936 4476 9.884814 AGTTTTGTATCTATGTACTCCCTCTAT 57.115 33.333 0.00 0.00 0.00 1.98
2944 4484 9.836179 ATCTATGTACTCCCTCTATCTGAAAAT 57.164 33.333 0.00 0.00 0.00 1.82
2948 4488 8.840200 TGTACTCCCTCTATCTGAAAATACTT 57.160 34.615 0.00 0.00 0.00 2.24
2949 4489 8.696374 TGTACTCCCTCTATCTGAAAATACTTG 58.304 37.037 0.00 0.00 0.00 3.16
2950 4490 7.741554 ACTCCCTCTATCTGAAAATACTTGT 57.258 36.000 0.00 0.00 0.00 3.16
2951 4491 7.787028 ACTCCCTCTATCTGAAAATACTTGTC 58.213 38.462 0.00 0.00 0.00 3.18
2954 4494 8.424918 TCCCTCTATCTGAAAATACTTGTCATC 58.575 37.037 0.00 0.00 0.00 2.92
2956 4496 9.775854 CCTCTATCTGAAAATACTTGTCATCAT 57.224 33.333 0.00 0.00 0.00 2.45
2962 4502 9.904198 TCTGAAAATACTTGTCATCATAATGGA 57.096 29.630 0.00 0.00 33.42 3.41
2971 4511 8.917088 ACTTGTCATCATAATGGATAAAAAGGG 58.083 33.333 0.00 0.00 33.42 3.95
2972 4512 9.135189 CTTGTCATCATAATGGATAAAAAGGGA 57.865 33.333 0.00 0.00 33.42 4.20
2973 4513 9.659135 TTGTCATCATAATGGATAAAAAGGGAT 57.341 29.630 0.00 0.00 33.42 3.85
2974 4514 9.081204 TGTCATCATAATGGATAAAAAGGGATG 57.919 33.333 0.00 0.00 33.42 3.51
3011 4551 8.927675 AGAATACGTCTAGATACATCTCCTTT 57.072 34.615 0.00 0.00 38.32 3.11
3012 4552 9.357161 AGAATACGTCTAGATACATCTCCTTTT 57.643 33.333 0.00 0.00 38.32 2.27
3017 4557 9.132923 ACGTCTAGATACATCTCCTTTTATTCA 57.867 33.333 0.00 0.00 38.32 2.57
3031 4571 9.918630 CTCCTTTTATTCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
3039 4579 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
3040 4580 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
3041 4581 8.739039 TCATTTTGATGACAAGTATTTTCGGAT 58.261 29.630 0.00 0.00 37.32 4.18
3042 4582 9.013490 CATTTTGATGACAAGTATTTTCGGATC 57.987 33.333 0.00 0.00 37.32 3.36
3043 4583 6.677781 TTGATGACAAGTATTTTCGGATCC 57.322 37.500 0.00 0.00 0.00 3.36
3044 4584 5.739959 TGATGACAAGTATTTTCGGATCCA 58.260 37.500 13.41 0.00 0.00 3.41
3045 4585 6.356556 TGATGACAAGTATTTTCGGATCCAT 58.643 36.000 13.41 0.00 0.00 3.41
3046 4586 6.260714 TGATGACAAGTATTTTCGGATCCATG 59.739 38.462 13.41 0.00 0.00 3.66
3047 4587 4.881273 TGACAAGTATTTTCGGATCCATGG 59.119 41.667 13.41 4.97 0.00 3.66
3048 4588 3.632145 ACAAGTATTTTCGGATCCATGGC 59.368 43.478 13.41 0.00 0.00 4.40
3049 4589 3.864789 AGTATTTTCGGATCCATGGCT 57.135 42.857 13.41 0.00 0.00 4.75
3068 4608 2.072298 CTTTCTTCCCTTGTCTCAGCG 58.928 52.381 0.00 0.00 0.00 5.18
3075 4615 1.153939 CTTGTCTCAGCGACCTCCG 60.154 63.158 0.00 0.00 42.13 4.63
3088 4628 2.650116 CCTCCGTGACTCCACCCAG 61.650 68.421 0.00 0.00 40.12 4.45
3124 4765 1.374190 CCACTTGAGCTGCCTGTCT 59.626 57.895 0.00 0.00 0.00 3.41
3312 5047 0.958822 GTGCGACCAAGGGAATTTGT 59.041 50.000 0.00 0.00 0.00 2.83
3353 5105 1.982612 GGCAGACGATTTTCTTTGCC 58.017 50.000 0.00 0.00 43.54 4.52
3373 5125 1.065436 GAACCGGCTACTAGCGGAC 59.935 63.158 19.52 12.02 43.27 4.79
3375 5127 3.603671 CCGGCTACTAGCGGACCC 61.604 72.222 15.40 0.00 43.27 4.46
3454 5206 2.887568 GACGACGGATGCTGCTGG 60.888 66.667 0.00 0.00 0.00 4.85
3495 5247 2.906354 ACCGGCATCAACTAAAGCTAG 58.094 47.619 0.00 0.00 0.00 3.42
3504 5256 6.352516 CATCAACTAAAGCTAGATCCACCTT 58.647 40.000 0.00 0.00 0.00 3.50
3515 5267 4.071961 AGATCCACCTTTTTGTTTTGCC 57.928 40.909 0.00 0.00 0.00 4.52
3524 5276 0.103208 TTTGTTTTGCCGCGATGGTT 59.897 45.000 8.23 0.00 41.21 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.802494 AAATCGCGCGTCCAAATCTT 59.198 45.000 30.98 9.38 0.00 2.40
105 114 3.670377 GGGTTGCGACAAGTGGCC 61.670 66.667 6.39 0.00 33.12 5.36
122 131 1.407936 AGATCACTCCCACATCCTCG 58.592 55.000 0.00 0.00 0.00 4.63
128 137 4.705110 TCTTTCAAAGATCACTCCCACA 57.295 40.909 0.00 0.00 31.20 4.17
223 232 4.601406 ATTGGTGGTTATGGGCTAGAAA 57.399 40.909 0.00 0.00 0.00 2.52
235 244 2.819348 GCAGGAGAGGAAATTGGTGGTT 60.819 50.000 0.00 0.00 0.00 3.67
246 255 3.071206 GTGGCTCGCAGGAGAGGA 61.071 66.667 2.29 0.00 43.27 3.71
269 278 3.812156 TCATATAACGTGGGGTCACTG 57.188 47.619 0.00 0.00 41.53 3.66
383 640 1.274447 GGTAGAGTAGTGTGGCGGTTT 59.726 52.381 0.00 0.00 0.00 3.27
405 662 1.566211 CTCCTCTTCCTCCTCAGCAA 58.434 55.000 0.00 0.00 0.00 3.91
461 719 0.665835 CTCCTCCAGGATCTTCGTCG 59.334 60.000 0.00 0.00 44.46 5.12
580 839 3.126001 TGGAGCTACTTCAACAGTTGG 57.874 47.619 13.52 0.79 36.88 3.77
615 913 1.441729 GGATTGCCGATCTCCGTCA 59.558 57.895 0.00 0.00 35.02 4.35
775 1088 9.320352 GTTACTGTTCTTCTTCTTCTTCTTCTT 57.680 33.333 0.00 0.00 0.00 2.52
776 1089 8.700973 AGTTACTGTTCTTCTTCTTCTTCTTCT 58.299 33.333 0.00 0.00 0.00 2.85
777 1090 8.760569 CAGTTACTGTTCTTCTTCTTCTTCTTC 58.239 37.037 3.88 0.00 0.00 2.87
778 1091 8.478877 TCAGTTACTGTTCTTCTTCTTCTTCTT 58.521 33.333 12.41 0.00 32.61 2.52
779 1092 8.012957 TCAGTTACTGTTCTTCTTCTTCTTCT 57.987 34.615 12.41 0.00 32.61 2.85
780 1093 8.707839 CATCAGTTACTGTTCTTCTTCTTCTTC 58.292 37.037 12.41 0.00 32.61 2.87
781 1094 8.207545 ACATCAGTTACTGTTCTTCTTCTTCTT 58.792 33.333 12.41 0.00 32.61 2.52
782 1095 7.731054 ACATCAGTTACTGTTCTTCTTCTTCT 58.269 34.615 12.41 0.00 32.61 2.85
783 1096 7.954788 ACATCAGTTACTGTTCTTCTTCTTC 57.045 36.000 12.41 0.00 32.61 2.87
784 1097 7.227512 CCAACATCAGTTACTGTTCTTCTTCTT 59.772 37.037 12.41 0.00 35.85 2.52
785 1098 6.708054 CCAACATCAGTTACTGTTCTTCTTCT 59.292 38.462 12.41 0.00 35.85 2.85
786 1099 6.073003 CCCAACATCAGTTACTGTTCTTCTTC 60.073 42.308 12.41 0.00 35.85 2.87
787 1100 5.765182 CCCAACATCAGTTACTGTTCTTCTT 59.235 40.000 12.41 0.00 35.85 2.52
788 1101 5.308825 CCCAACATCAGTTACTGTTCTTCT 58.691 41.667 12.41 0.00 35.85 2.85
789 1102 4.083271 GCCCAACATCAGTTACTGTTCTTC 60.083 45.833 12.41 0.00 35.85 2.87
790 1103 3.821033 GCCCAACATCAGTTACTGTTCTT 59.179 43.478 12.41 0.00 35.85 2.52
791 1104 3.412386 GCCCAACATCAGTTACTGTTCT 58.588 45.455 12.41 0.00 35.85 3.01
792 1105 2.488153 GGCCCAACATCAGTTACTGTTC 59.512 50.000 12.41 0.00 35.85 3.18
793 1106 2.514803 GGCCCAACATCAGTTACTGTT 58.485 47.619 12.41 0.76 35.85 3.16
794 1107 1.610624 CGGCCCAACATCAGTTACTGT 60.611 52.381 12.41 0.00 35.85 3.55
795 1108 1.086696 CGGCCCAACATCAGTTACTG 58.913 55.000 5.94 5.94 35.85 2.74
903 1224 1.767088 TGGCAGAGATGAGAGGGAATG 59.233 52.381 0.00 0.00 0.00 2.67
914 1235 2.194388 CTGTGGGCTGTGGCAGAGAT 62.194 60.000 16.83 0.00 40.87 2.75
980 1308 2.264794 GGCGAGGCGAAGGAAGAA 59.735 61.111 0.00 0.00 0.00 2.52
1107 1465 0.538516 CCGGGATCTCCATCGTCTCT 60.539 60.000 0.00 0.00 37.91 3.10
1239 1597 1.376037 GTCCACCTTGAGCTTCCGG 60.376 63.158 0.00 0.00 0.00 5.14
1329 1687 3.585525 GAAGCCCTTGGTGACCCCC 62.586 68.421 0.00 0.00 0.00 5.40
1413 1771 3.525537 GAAGTTTCTGATCTCGATGCCA 58.474 45.455 0.00 0.00 0.00 4.92
1428 1786 4.529109 CTTCTTCTCTCCGAGGAAGTTT 57.471 45.455 18.49 0.00 45.66 2.66
1477 1951 7.335924 GGAACACTACACTATCAGGCAATTAAA 59.664 37.037 0.00 0.00 0.00 1.52
1478 1952 6.821665 GGAACACTACACTATCAGGCAATTAA 59.178 38.462 0.00 0.00 0.00 1.40
1526 2000 5.114764 TCCCAATTCATCAGCAATCACTA 57.885 39.130 0.00 0.00 0.00 2.74
1546 2020 5.662674 TTCTACTGCCTAGAAAGAACTCC 57.337 43.478 0.00 0.00 38.35 3.85
1552 2026 6.463995 ACAGAGATTCTACTGCCTAGAAAG 57.536 41.667 10.96 0.00 43.41 2.62
1592 2066 9.073475 AGGTAAAAAGCTACACAAATCACATAA 57.927 29.630 0.00 0.00 0.00 1.90
1636 2112 7.928873 TCATTTCTAAGTAGAGTTCCCCAATT 58.071 34.615 0.00 0.00 33.21 2.32
1650 2126 7.721399 ACTCACAAGAACCATTCATTTCTAAGT 59.279 33.333 0.00 0.00 31.62 2.24
1742 2222 5.083533 ACATCTCAGCTTCTCAAGTAAGG 57.916 43.478 0.00 0.00 0.00 2.69
1743 2223 6.648310 TCAAACATCTCAGCTTCTCAAGTAAG 59.352 38.462 0.00 0.00 0.00 2.34
1744 2224 6.524734 TCAAACATCTCAGCTTCTCAAGTAA 58.475 36.000 0.00 0.00 0.00 2.24
1746 2226 4.965814 TCAAACATCTCAGCTTCTCAAGT 58.034 39.130 0.00 0.00 0.00 3.16
1747 2227 5.642491 TCATCAAACATCTCAGCTTCTCAAG 59.358 40.000 0.00 0.00 0.00 3.02
1748 2228 5.410746 GTCATCAAACATCTCAGCTTCTCAA 59.589 40.000 0.00 0.00 0.00 3.02
1753 2233 4.260170 GGAGTCATCAAACATCTCAGCTT 58.740 43.478 0.00 0.00 0.00 3.74
1754 2234 3.262660 TGGAGTCATCAAACATCTCAGCT 59.737 43.478 0.00 0.00 0.00 4.24
1755 2235 3.603532 TGGAGTCATCAAACATCTCAGC 58.396 45.455 0.00 0.00 0.00 4.26
1756 2236 4.035324 GCATGGAGTCATCAAACATCTCAG 59.965 45.833 0.00 0.00 0.00 3.35
1770 2269 5.991933 TCTAGGAATATCAGCATGGAGTC 57.008 43.478 0.00 0.00 36.16 3.36
1832 2331 5.582269 CACTATGAGCCAATTACGATATGGG 59.418 44.000 0.00 0.00 34.71 4.00
1835 2334 5.871524 CAGCACTATGAGCCAATTACGATAT 59.128 40.000 0.00 0.00 0.00 1.63
1877 2376 9.727859 CTTGCTTCTCTAGAGTATACCATACTA 57.272 37.037 19.21 0.00 0.00 1.82
1881 2380 6.239176 GCACTTGCTTCTCTAGAGTATACCAT 60.239 42.308 19.21 0.00 38.21 3.55
1926 2425 2.393768 GCCACACAGGACATCGCAG 61.394 63.158 0.00 0.00 41.22 5.18
1960 2459 6.540551 TGACTCAAGTAACACACATAAAAGCA 59.459 34.615 0.00 0.00 0.00 3.91
2279 2900 2.987149 CGCATCGACAGAACTAAACAGT 59.013 45.455 0.00 0.00 0.00 3.55
2428 3895 3.870538 ATGGCCAGCATAGAGATGAAA 57.129 42.857 13.05 0.00 35.00 2.69
2469 3940 0.950836 TCACGTGGCATTTCTGGTTG 59.049 50.000 17.00 0.00 0.00 3.77
2648 4179 1.881973 CAGTACACATTGCAGCCAACT 59.118 47.619 0.00 0.00 32.95 3.16
2654 4185 2.892374 TCGATCCAGTACACATTGCAG 58.108 47.619 0.00 0.00 0.00 4.41
2661 4192 3.243569 CCTTCCTGATCGATCCAGTACAC 60.244 52.174 22.31 0.00 0.00 2.90
2680 4211 3.910627 ACCTTCTCCAGTTACATGACCTT 59.089 43.478 0.00 0.00 0.00 3.50
2682 4213 3.983044 ACCTTCTCCAGTTACATGACC 57.017 47.619 0.00 0.00 0.00 4.02
2707 4238 4.035091 CGGTGAAACAAACACATCTCAAGA 59.965 41.667 0.00 0.00 39.98 3.02
2741 4273 8.621532 AAAACATTGCAGTAGATAACAAGAGA 57.378 30.769 0.00 0.00 0.00 3.10
2832 4372 3.131396 AGGACACGTCAATCACTTGTTC 58.869 45.455 0.00 0.00 37.60 3.18
2833 4373 3.131396 GAGGACACGTCAATCACTTGTT 58.869 45.455 0.00 0.00 37.60 2.83
2834 4374 2.365617 AGAGGACACGTCAATCACTTGT 59.634 45.455 0.00 0.00 40.12 3.16
2867 4407 1.603802 CAAGTGCCTCGCTCTGAAAAA 59.396 47.619 0.00 0.00 32.56 1.94
2868 4408 1.229428 CAAGTGCCTCGCTCTGAAAA 58.771 50.000 0.00 0.00 32.56 2.29
2869 4409 1.230635 GCAAGTGCCTCGCTCTGAAA 61.231 55.000 0.00 0.00 32.56 2.69
2870 4410 1.669115 GCAAGTGCCTCGCTCTGAA 60.669 57.895 0.00 0.00 32.56 3.02
2927 4467 7.786030 TGACAAGTATTTTCAGATAGAGGGAG 58.214 38.462 0.00 0.00 0.00 4.30
2929 4469 8.206867 TGATGACAAGTATTTTCAGATAGAGGG 58.793 37.037 0.00 0.00 0.00 4.30
2930 4470 9.775854 ATGATGACAAGTATTTTCAGATAGAGG 57.224 33.333 0.00 0.00 0.00 3.69
2936 4476 9.904198 TCCATTATGATGACAAGTATTTTCAGA 57.096 29.630 0.00 0.00 35.16 3.27
2945 4485 8.917088 CCCTTTTTATCCATTATGATGACAAGT 58.083 33.333 0.00 0.00 35.16 3.16
2946 4486 9.135189 TCCCTTTTTATCCATTATGATGACAAG 57.865 33.333 0.00 0.00 35.16 3.16
2948 4488 9.081204 CATCCCTTTTTATCCATTATGATGACA 57.919 33.333 0.00 0.00 35.16 3.58
2949 4489 9.082313 ACATCCCTTTTTATCCATTATGATGAC 57.918 33.333 0.00 0.00 35.16 3.06
2986 4526 8.927675 AAAGGAGATGTATCTAGACGTATTCT 57.072 34.615 0.00 0.00 37.25 2.40
2991 4531 9.132923 TGAATAAAAGGAGATGTATCTAGACGT 57.867 33.333 0.00 0.00 37.25 4.34
3005 4545 9.918630 ACTTGTCATCAAAATGAATAAAAGGAG 57.081 29.630 0.00 0.00 43.42 3.69
3013 4553 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
3014 4554 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
3015 4555 8.105097 TCCGAAAATACTTGTCATCAAAATGA 57.895 30.769 0.00 0.00 39.63 2.57
3016 4556 8.915871 ATCCGAAAATACTTGTCATCAAAATG 57.084 30.769 0.00 0.00 32.87 2.32
3017 4557 8.190784 GGATCCGAAAATACTTGTCATCAAAAT 58.809 33.333 0.00 0.00 32.87 1.82
3018 4558 7.175816 TGGATCCGAAAATACTTGTCATCAAAA 59.824 33.333 7.39 0.00 32.87 2.44
3019 4559 6.657117 TGGATCCGAAAATACTTGTCATCAAA 59.343 34.615 7.39 0.00 32.87 2.69
3020 4560 6.176896 TGGATCCGAAAATACTTGTCATCAA 58.823 36.000 7.39 0.00 0.00 2.57
3021 4561 5.739959 TGGATCCGAAAATACTTGTCATCA 58.260 37.500 7.39 0.00 0.00 3.07
3022 4562 6.293626 CCATGGATCCGAAAATACTTGTCATC 60.294 42.308 5.56 0.00 0.00 2.92
3023 4563 5.532406 CCATGGATCCGAAAATACTTGTCAT 59.468 40.000 5.56 0.00 0.00 3.06
3024 4564 4.881273 CCATGGATCCGAAAATACTTGTCA 59.119 41.667 5.56 0.00 0.00 3.58
3025 4565 4.261197 GCCATGGATCCGAAAATACTTGTC 60.261 45.833 18.40 0.00 0.00 3.18
3026 4566 3.632145 GCCATGGATCCGAAAATACTTGT 59.368 43.478 18.40 0.00 0.00 3.16
3027 4567 3.885297 AGCCATGGATCCGAAAATACTTG 59.115 43.478 18.40 0.00 0.00 3.16
3028 4568 4.170468 AGCCATGGATCCGAAAATACTT 57.830 40.909 18.40 0.00 0.00 2.24
3029 4569 3.864789 AGCCATGGATCCGAAAATACT 57.135 42.857 18.40 0.00 0.00 2.12
3030 4570 4.580580 AGAAAGCCATGGATCCGAAAATAC 59.419 41.667 18.40 0.00 0.00 1.89
3031 4571 4.792068 AGAAAGCCATGGATCCGAAAATA 58.208 39.130 18.40 0.00 0.00 1.40
3032 4572 3.635591 AGAAAGCCATGGATCCGAAAAT 58.364 40.909 18.40 0.00 0.00 1.82
3033 4573 3.085952 AGAAAGCCATGGATCCGAAAA 57.914 42.857 18.40 0.00 0.00 2.29
3034 4574 2.806945 AGAAAGCCATGGATCCGAAA 57.193 45.000 18.40 0.00 0.00 3.46
3035 4575 2.643551 GAAGAAAGCCATGGATCCGAA 58.356 47.619 18.40 0.00 0.00 4.30
3036 4576 1.134098 GGAAGAAAGCCATGGATCCGA 60.134 52.381 18.40 0.00 0.00 4.55
3037 4577 1.312815 GGAAGAAAGCCATGGATCCG 58.687 55.000 18.40 0.00 0.00 4.18
3038 4578 1.216427 AGGGAAGAAAGCCATGGATCC 59.784 52.381 18.40 4.20 0.00 3.36
3039 4579 2.692041 CAAGGGAAGAAAGCCATGGATC 59.308 50.000 18.40 10.24 0.00 3.36
3040 4580 2.043526 ACAAGGGAAGAAAGCCATGGAT 59.956 45.455 18.40 6.18 0.00 3.41
3041 4581 1.428912 ACAAGGGAAGAAAGCCATGGA 59.571 47.619 18.40 0.00 0.00 3.41
3042 4582 1.821136 GACAAGGGAAGAAAGCCATGG 59.179 52.381 7.63 7.63 0.00 3.66
3043 4583 2.751806 GAGACAAGGGAAGAAAGCCATG 59.248 50.000 0.00 0.00 0.00 3.66
3044 4584 2.376518 TGAGACAAGGGAAGAAAGCCAT 59.623 45.455 0.00 0.00 0.00 4.40
3045 4585 1.774254 TGAGACAAGGGAAGAAAGCCA 59.226 47.619 0.00 0.00 0.00 4.75
3046 4586 2.431454 CTGAGACAAGGGAAGAAAGCC 58.569 52.381 0.00 0.00 0.00 4.35
3047 4587 1.809547 GCTGAGACAAGGGAAGAAAGC 59.190 52.381 0.00 0.00 0.00 3.51
3048 4588 2.072298 CGCTGAGACAAGGGAAGAAAG 58.928 52.381 0.00 0.00 32.03 2.62
3049 4589 1.691976 TCGCTGAGACAAGGGAAGAAA 59.308 47.619 0.00 0.00 36.31 2.52
3068 4608 2.647158 GGGTGGAGTCACGGAGGTC 61.647 68.421 0.00 0.00 44.50 3.85
3075 4615 3.612247 ATGCGCTGGGTGGAGTCAC 62.612 63.158 9.73 0.00 42.91 3.67
3124 4765 0.686789 ATGGCCGCATGTAGCATCTA 59.313 50.000 10.63 0.00 46.13 1.98
3227 4898 7.433680 CATTTTTACCTCTGGTTGTAGCTTTT 58.566 34.615 0.00 0.00 37.09 2.27
3300 4987 6.588719 TGAAGGATGTAACAAATTCCCTTG 57.411 37.500 0.00 0.00 33.19 3.61
3301 4988 6.155049 CCATGAAGGATGTAACAAATTCCCTT 59.845 38.462 0.00 0.00 41.22 3.95
3312 5047 1.134220 GGTCCGCCATGAAGGATGTAA 60.134 52.381 11.41 0.00 41.22 2.41
3353 5105 2.025727 CGCTAGTAGCCGGTTCCG 59.974 66.667 16.51 4.08 38.18 4.30
3381 5133 3.511595 CAGCACCCGCATCGCATT 61.512 61.111 0.00 0.00 42.27 3.56
3454 5206 1.227205 CAGCTCATCGAGGCAGGAC 60.227 63.158 9.78 0.00 0.00 3.85
3487 5239 7.833285 AAACAAAAAGGTGGATCTAGCTTTA 57.167 32.000 29.15 0.00 44.83 1.85
3495 5247 2.799978 CGGCAAAACAAAAAGGTGGATC 59.200 45.455 0.00 0.00 0.00 3.36
3504 5256 0.103208 ACCATCGCGGCAAAACAAAA 59.897 45.000 6.13 0.00 39.03 2.44
3515 5267 1.067974 TCACCCACTATAACCATCGCG 59.932 52.381 0.00 0.00 0.00 5.87
3524 5276 2.766263 CTCCACTGCTTCACCCACTATA 59.234 50.000 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.