Multiple sequence alignment - TraesCS7B01G413000

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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 TraesCS7B01G413000 chr7B 100.000 3221 0 0 1 3221 680855457 680852237 0.000000e+00 5949.0
1 TraesCS7B01G413000 chr7B 77.334 1328 256 27 968 2274 680541717 680540414 0.000000e+00 743.0
2 TraesCS7B01G413000 chr7B 79.401 534 83 14 1706 2213 732647940 732648472 5.110000e-93 351.0
3 TraesCS7B01G413000 chr7B 95.000 60 3 0 92 151 680659318 680659259 9.510000e-16 95.3
4 TraesCS7B01G413000 chr7D 86.891 2647 230 66 635 3206 601787409 601784805 0.000000e+00 2857.0
5 TraesCS7B01G413000 chr7D 88.228 1648 154 22 633 2258 601700164 601698535 0.000000e+00 1932.0
6 TraesCS7B01G413000 chr7D 89.609 818 70 7 2273 3088 601698489 601697685 0.000000e+00 1026.0
7 TraesCS7B01G413000 chr7D 77.351 1329 254 28 968 2274 601494398 601493095 0.000000e+00 743.0
8 TraesCS7B01G413000 chr7D 79.141 652 104 18 1652 2274 601589660 601589012 3.840000e-114 422.0
9 TraesCS7B01G413000 chr7D 76.577 555 105 21 1001 1545 601584154 601583615 6.800000e-72 281.0
10 TraesCS7B01G413000 chr7D 80.542 406 30 17 238 623 601787838 601787462 1.910000e-67 267.0
11 TraesCS7B01G413000 chr7D 76.640 381 39 23 255 625 601700555 601700215 7.150000e-37 165.0
12 TraesCS7B01G413000 chr7A 90.346 2051 157 14 238 2273 693399728 693397704 0.000000e+00 2652.0
13 TraesCS7B01G413000 chr7A 89.670 697 51 14 2273 2963 693397674 693396993 0.000000e+00 869.0
14 TraesCS7B01G413000 chr7A 76.147 1329 268 30 968 2274 693197900 693196599 0.000000e+00 652.0
15 TraesCS7B01G413000 chr7A 94.488 254 11 3 1 253 693400110 693399859 3.900000e-104 388.0
16 TraesCS7B01G413000 chr7A 75.285 789 147 24 1512 2257 667937595 667938378 1.850000e-87 333.0
17 TraesCS7B01G413000 chr7A 79.556 450 75 7 1736 2184 725925784 725926217 4.040000e-79 305.0
18 TraesCS7B01G413000 chr1D 79.073 1295 237 18 961 2247 414568435 414567167 0.000000e+00 859.0
19 TraesCS7B01G413000 chr2D 77.803 1311 237 33 969 2255 33544522 33545802 0.000000e+00 760.0
20 TraesCS7B01G413000 chr2D 77.557 1310 246 28 970 2255 33340667 33341952 0.000000e+00 747.0
21 TraesCS7B01G413000 chr6D 74.444 1303 280 33 996 2275 1373130 1374402 2.220000e-141 512.0
22 TraesCS7B01G413000 chr6B 74.979 1195 255 27 995 2176 5555577 5554414 7.970000e-141 510.0
23 TraesCS7B01G413000 chr1A 81.693 508 87 4 1754 2255 511450299 511449792 4.970000e-113 418.0
24 TraesCS7B01G413000 chr3B 100.000 28 0 0 2289 2316 15761975 15762002 6.000000e-03 52.8
25 TraesCS7B01G413000 chr3B 100.000 28 0 0 2289 2316 25665248 25665221 6.000000e-03 52.8


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 TraesCS7B01G413000 chr7B 680852237 680855457 3220 True 5949 5949 100.000000 1 3221 1 chr7B.!!$R3 3220
1 TraesCS7B01G413000 chr7B 680540414 680541717 1303 True 743 743 77.334000 968 2274 1 chr7B.!!$R1 1306
2 TraesCS7B01G413000 chr7B 732647940 732648472 532 False 351 351 79.401000 1706 2213 1 chr7B.!!$F1 507
3 TraesCS7B01G413000 chr7D 601784805 601787838 3033 True 1562 2857 83.716500 238 3206 2 chr7D.!!$R5 2968
4 TraesCS7B01G413000 chr7D 601697685 601700555 2870 True 1041 1932 84.825667 255 3088 3 chr7D.!!$R4 2833
5 TraesCS7B01G413000 chr7D 601493095 601494398 1303 True 743 743 77.351000 968 2274 1 chr7D.!!$R1 1306
6 TraesCS7B01G413000 chr7D 601589012 601589660 648 True 422 422 79.141000 1652 2274 1 chr7D.!!$R3 622
7 TraesCS7B01G413000 chr7D 601583615 601584154 539 True 281 281 76.577000 1001 1545 1 chr7D.!!$R2 544
8 TraesCS7B01G413000 chr7A 693396993 693400110 3117 True 1303 2652 91.501333 1 2963 3 chr7A.!!$R2 2962
9 TraesCS7B01G413000 chr7A 693196599 693197900 1301 True 652 652 76.147000 968 2274 1 chr7A.!!$R1 1306
10 TraesCS7B01G413000 chr7A 667937595 667938378 783 False 333 333 75.285000 1512 2257 1 chr7A.!!$F1 745
11 TraesCS7B01G413000 chr1D 414567167 414568435 1268 True 859 859 79.073000 961 2247 1 chr1D.!!$R1 1286
12 TraesCS7B01G413000 chr2D 33544522 33545802 1280 False 760 760 77.803000 969 2255 1 chr2D.!!$F2 1286
13 TraesCS7B01G413000 chr2D 33340667 33341952 1285 False 747 747 77.557000 970 2255 1 chr2D.!!$F1 1285
14 TraesCS7B01G413000 chr6D 1373130 1374402 1272 False 512 512 74.444000 996 2275 1 chr6D.!!$F1 1279
15 TraesCS7B01G413000 chr6B 5554414 5555577 1163 True 510 510 74.979000 995 2176 1 chr6B.!!$R1 1181
16 TraesCS7B01G413000 chr1A 511449792 511450299 507 True 418 418 81.693000 1754 2255 1 chr1A.!!$R1 501

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
106 107 0.463833 CGCGCCCCCTTTTATCTTCT 60.464 55.0 0.00 0.0 0.0 2.85 F
1294 1548 0.250166 AAGCTCCAAACGCCGTTACT 60.250 50.0 1.51 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 1787 0.610174 TGTCAGATCCCACTGTGAGC 59.390 55.0 9.86 0.00 38.79 4.26 R
3130 3558 0.039165 CAGCAAGCCTTTTCCGGAAC 60.039 55.0 18.64 5.26 0.00 3.62 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
30 31 2.746279 TTCCAAATGATACCCGCCAT 57.254 45.000 0.00 0.00 0.00 4.40
68 69 2.757099 CTTGCACATGGAGGCCCC 60.757 66.667 0.00 0.03 0.00 5.80
70 71 1.925285 CTTGCACATGGAGGCCCCTA 61.925 60.000 0.00 0.00 35.38 3.53
106 107 0.463833 CGCGCCCCCTTTTATCTTCT 60.464 55.000 0.00 0.00 0.00 2.85
181 182 8.655651 ACAAAATTTGGAAATTATGTCACGTT 57.344 26.923 10.71 0.00 37.62 3.99
194 195 8.810652 ATTATGTCACGTTGCAATTTTAAACT 57.189 26.923 0.59 0.00 0.00 2.66
197 198 6.983910 TGTCACGTTGCAATTTTAAACTTTC 58.016 32.000 0.59 0.00 0.00 2.62
408 568 8.996024 TGTAAAAGACAAAAAGGAAAAGGAAG 57.004 30.769 0.00 0.00 34.15 3.46
449 615 2.940994 TCCTCTATCCTCGAGGTGAG 57.059 55.000 30.17 28.93 46.49 3.51
473 639 2.756042 CCCCATCCCCATTCGAGCA 61.756 63.158 0.00 0.00 0.00 4.26
479 645 1.153289 CCCCATTCGAGCAGACCAG 60.153 63.158 0.00 0.00 0.00 4.00
500 667 2.422127 GGCGCTGCAAGACCTAATTTTA 59.578 45.455 7.64 0.00 34.07 1.52
756 993 1.141881 ATCTACCGTTGGCGCTCAG 59.858 57.895 7.64 0.00 36.67 3.35
876 1113 1.203087 TCCAGTCTCCGAGGGTAAACA 60.203 52.381 0.00 0.00 0.00 2.83
953 1196 2.603021 AGCTGGTCTGAACTCTGAAGA 58.397 47.619 0.00 0.00 0.00 2.87
959 1202 6.672266 TGGTCTGAACTCTGAAGAAGTTAT 57.328 37.500 0.00 0.00 0.00 1.89
1076 1323 2.233922 ACAAGATACTCGTCCTGTTGGG 59.766 50.000 0.00 0.00 0.00 4.12
1276 1530 1.145738 AGCTTTGGCCTTTCCTCTCAA 59.854 47.619 3.32 0.00 39.73 3.02
1294 1548 0.250166 AAGCTCCAAACGCCGTTACT 60.250 50.000 1.51 0.00 0.00 2.24
1332 1586 3.069586 CCGTCTGTGATGGCTTCCTTATA 59.930 47.826 0.00 0.00 31.58 0.98
1368 1628 5.711506 ACACAAATTCTACATCTGCAATCCA 59.288 36.000 0.00 0.00 0.00 3.41
1424 1684 1.607178 TTGGGCAAGGCATCCACAG 60.607 57.895 0.00 0.00 0.00 3.66
1431 1691 2.726821 CAAGGCATCCACAGTACCATT 58.273 47.619 0.00 0.00 0.00 3.16
1494 1754 0.757561 TCTGGGTCTCACGGTCACAA 60.758 55.000 0.00 0.00 0.00 3.33
1495 1755 0.321671 CTGGGTCTCACGGTCACAAT 59.678 55.000 0.00 0.00 0.00 2.71
1496 1756 0.320374 TGGGTCTCACGGTCACAATC 59.680 55.000 0.00 0.00 0.00 2.67
1497 1757 0.320374 GGGTCTCACGGTCACAATCA 59.680 55.000 0.00 0.00 0.00 2.57
1498 1758 1.429463 GGTCTCACGGTCACAATCAC 58.571 55.000 0.00 0.00 0.00 3.06
1499 1759 1.270094 GGTCTCACGGTCACAATCACA 60.270 52.381 0.00 0.00 0.00 3.58
1500 1760 2.479837 GTCTCACGGTCACAATCACAA 58.520 47.619 0.00 0.00 0.00 3.33
1501 1761 3.067106 GTCTCACGGTCACAATCACAAT 58.933 45.455 0.00 0.00 0.00 2.71
1506 1766 3.370978 CACGGTCACAATCACAATACTCC 59.629 47.826 0.00 0.00 0.00 3.85
1527 1787 6.106648 TCCTCTGAATCCAGCTTATATGTG 57.893 41.667 0.00 0.00 40.20 3.21
1553 1813 0.038166 GTGGGATCTGACAGGCCAAA 59.962 55.000 5.01 2.98 0.00 3.28
1556 1816 1.272147 GGGATCTGACAGGCCAAAGTT 60.272 52.381 5.01 0.00 0.00 2.66
1597 1857 2.029828 ACAGTCTCATCGTCTTCCACAC 60.030 50.000 0.00 0.00 0.00 3.82
1615 1881 5.298276 TCCACACAACAGAAGTTATTGAACC 59.702 40.000 1.99 0.00 35.85 3.62
1622 1888 3.084786 AGAAGTTATTGAACCAGCTGCC 58.915 45.455 8.66 0.00 36.08 4.85
1665 1937 2.358247 GTACACCACCGTGGCAGG 60.358 66.667 17.99 9.92 44.86 4.85
1693 1974 2.225467 GGCTTCCTTATGATGACAGCC 58.775 52.381 0.00 0.00 0.00 4.85
1703 1984 3.701205 TGATGACAGCCACATTACAGT 57.299 42.857 0.00 0.00 0.00 3.55
1750 2031 4.051237 CGACACAGAAACAGAGTCATTCA 58.949 43.478 0.00 0.00 0.00 2.57
1759 2040 2.909006 ACAGAGTCATTCAGGTGGATGT 59.091 45.455 0.00 0.00 0.00 3.06
1815 2123 0.616395 TTGACATGGAGGGGACGCTA 60.616 55.000 0.00 0.00 0.00 4.26
2014 2360 5.748152 GCGGTGCAATTGTTTAATGATATGT 59.252 36.000 7.40 0.00 0.00 2.29
2161 2519 1.018226 CCACTGCCTCAAAGAGAGCG 61.018 60.000 0.00 0.00 43.31 5.03
2192 2559 0.458669 CCAGGCCATGAGATGCAAAC 59.541 55.000 5.01 0.00 0.00 2.93
2218 2585 2.172293 GAGGAGGCTCCATTCTTCACAT 59.828 50.000 33.86 10.36 39.61 3.21
2219 2586 3.387962 AGGAGGCTCCATTCTTCACATA 58.612 45.455 33.86 0.00 39.61 2.29
2230 2597 5.236695 CCATTCTTCACATAGCATGTCTGAG 59.763 44.000 0.00 0.00 42.70 3.35
2243 2614 4.679905 GCATGTCTGAGTGATCATGACTCA 60.680 45.833 6.78 6.78 46.01 3.41
2258 2629 2.694628 TGACTCATGGTTTGCTTTGCTT 59.305 40.909 0.00 0.00 0.00 3.91
2259 2630 3.888323 TGACTCATGGTTTGCTTTGCTTA 59.112 39.130 0.00 0.00 0.00 3.09
2333 2741 1.841450 GCAGTAGCACCTATGACGTC 58.159 55.000 9.11 9.11 41.58 4.34
2344 2752 4.635765 CACCTATGACGTCATCATTTGGTT 59.364 41.667 33.11 10.95 46.54 3.67
2345 2753 4.876107 ACCTATGACGTCATCATTTGGTTC 59.124 41.667 33.11 0.00 46.54 3.62
2349 2757 3.676172 TGACGTCATCATTTGGTTCGTAC 59.324 43.478 15.76 0.00 31.72 3.67
2350 2758 2.664568 ACGTCATCATTTGGTTCGTACG 59.335 45.455 9.53 9.53 0.00 3.67
2370 2778 4.313282 ACGATGATGTGCTGAATATCCTG 58.687 43.478 0.00 0.00 0.00 3.86
2391 2799 9.739276 ATCCTGTTAATGTTCTGAAGTATCAAA 57.261 29.630 0.00 0.00 34.49 2.69
2460 2869 4.303282 TCCCAAATTTGCTTTAGTTTCGC 58.697 39.130 12.92 0.00 0.00 4.70
2487 2896 4.436050 GGTTAAGATGCACGAGTGACATTG 60.436 45.833 7.50 0.00 31.15 2.82
2492 2901 4.389992 AGATGCACGAGTGACATTGTTAAG 59.610 41.667 7.50 0.00 31.15 1.85
2531 2940 3.479489 TCTTTTGCTGCAAGATGAGACA 58.521 40.909 15.39 0.00 34.07 3.41
2534 2943 3.842732 TTGCTGCAAGATGAGACATTG 57.157 42.857 11.69 0.00 34.07 2.82
2535 2944 2.786777 TGCTGCAAGATGAGACATTGT 58.213 42.857 0.00 0.00 34.07 2.71
2536 2945 3.151554 TGCTGCAAGATGAGACATTGTT 58.848 40.909 0.00 0.00 34.07 2.83
2537 2946 4.325972 TGCTGCAAGATGAGACATTGTTA 58.674 39.130 0.00 0.00 34.07 2.41
2538 2947 4.761227 TGCTGCAAGATGAGACATTGTTAA 59.239 37.500 0.00 0.00 34.07 2.01
2539 2948 5.106436 TGCTGCAAGATGAGACATTGTTAAG 60.106 40.000 0.00 0.00 34.07 1.85
2540 2949 5.122869 GCTGCAAGATGAGACATTGTTAAGA 59.877 40.000 0.00 0.00 34.07 2.10
2541 2950 6.486253 TGCAAGATGAGACATTGTTAAGAC 57.514 37.500 0.00 0.00 0.00 3.01
2542 2951 5.120674 TGCAAGATGAGACATTGTTAAGACG 59.879 40.000 0.00 0.00 0.00 4.18
2545 2954 6.274157 AGATGAGACATTGTTAAGACGAGT 57.726 37.500 0.00 0.00 0.00 4.18
2546 2955 6.096036 AGATGAGACATTGTTAAGACGAGTG 58.904 40.000 0.00 0.00 0.00 3.51
2548 2957 3.326747 AGACATTGTTAAGACGAGTGCC 58.673 45.455 0.00 0.00 0.00 5.01
2549 2958 2.066262 ACATTGTTAAGACGAGTGCCG 58.934 47.619 0.00 0.00 45.44 5.69
2616 3027 1.209019 AGCACTTCCATAGCCTGTCAG 59.791 52.381 0.00 0.00 0.00 3.51
2638 3049 6.650807 TCAGTTTGATCTCTGTTGTCCATTAC 59.349 38.462 10.92 0.00 33.89 1.89
2656 3068 5.748152 CCATTACGCAATTTGGGATAACAAG 59.252 40.000 19.08 8.23 34.12 3.16
2692 3104 1.070376 CAGATGCTGTGTGTGTCAACG 60.070 52.381 0.00 0.00 0.00 4.10
2699 3111 2.908009 CTGTGTGTGTCAACGTGTTTTG 59.092 45.455 0.00 0.00 0.00 2.44
2739 3152 5.182001 GTGTATCATGGCCCTTAATTAGCAG 59.818 44.000 0.00 0.00 0.00 4.24
2786 3199 4.552378 GCTGCTATGATTGAAGAAAGAGCG 60.552 45.833 0.00 0.00 0.00 5.03
2825 3239 3.090037 TGTTGGAGTACTGCTAGTCCTC 58.910 50.000 15.92 4.89 41.60 3.71
2892 3306 7.090953 TCCTTTGTTCATTTACAAACGAGTT 57.909 32.000 0.00 0.00 41.65 3.01
2921 3348 2.810439 CTCTCCGGGAGCAAGATAAG 57.190 55.000 19.48 5.75 35.08 1.73
2970 3397 5.065988 CCCCGGATAAAACATCTGTAACTTG 59.934 44.000 0.73 0.00 0.00 3.16
2988 3415 7.651304 TGTAACTTGCTTACATGTTTGGATTTG 59.349 33.333 2.30 0.00 42.37 2.32
2997 3424 6.363167 ACATGTTTGGATTTGAATGGTGAT 57.637 33.333 0.00 0.00 0.00 3.06
3085 3512 1.078918 CCGCTCAACTGAGATGCCA 60.079 57.895 10.95 0.00 44.74 4.92
3104 3531 3.120060 GCCAGACTGAACAATTAGCACTG 60.120 47.826 3.32 0.00 0.00 3.66
3105 3532 4.318332 CCAGACTGAACAATTAGCACTGA 58.682 43.478 3.32 0.00 0.00 3.41
3107 3534 5.413833 CCAGACTGAACAATTAGCACTGAAT 59.586 40.000 3.32 0.00 0.00 2.57
3108 3535 6.312487 CAGACTGAACAATTAGCACTGAATG 58.688 40.000 0.00 0.00 0.00 2.67
3109 3536 6.148315 CAGACTGAACAATTAGCACTGAATGA 59.852 38.462 0.00 0.00 0.00 2.57
3110 3537 6.883217 AGACTGAACAATTAGCACTGAATGAT 59.117 34.615 0.00 0.00 0.00 2.45
3111 3538 7.065563 AGACTGAACAATTAGCACTGAATGATC 59.934 37.037 0.00 0.00 0.00 2.92
3114 3542 6.880529 TGAACAATTAGCACTGAATGATCTCA 59.119 34.615 0.00 0.00 0.00 3.27
3119 3547 9.073368 CAATTAGCACTGAATGATCTCAAAAAG 57.927 33.333 0.00 0.00 0.00 2.27
3130 3558 4.991056 TGATCTCAAAAAGAAGACGACCTG 59.009 41.667 0.00 0.00 37.61 4.00
3134 3562 3.875134 TCAAAAAGAAGACGACCTGTTCC 59.125 43.478 0.00 0.00 0.00 3.62
3141 3569 1.145803 GACGACCTGTTCCGGAAAAG 58.854 55.000 25.34 25.34 0.00 2.27
3145 3577 3.036431 CCTGTTCCGGAAAAGGCTT 57.964 52.632 35.35 0.00 38.84 4.35
3153 3585 0.519077 CGGAAAAGGCTTGCTGAGTC 59.481 55.000 0.00 0.00 0.00 3.36
3173 3605 4.844655 AGTCGGCCTAACCTTGGATTATAT 59.155 41.667 0.00 0.00 35.61 0.86
3174 3606 5.309806 AGTCGGCCTAACCTTGGATTATATT 59.690 40.000 0.00 0.00 35.61 1.28
3180 3612 7.337942 GGCCTAACCTTGGATTATATTGATGAG 59.662 40.741 0.00 0.00 34.51 2.90
3199 3631 9.965824 TTGATGAGAAACAGAGTTTTTATTTCC 57.034 29.630 0.00 0.00 31.05 3.13
3203 3635 7.920682 TGAGAAACAGAGTTTTTATTTCCAAGC 59.079 33.333 0.00 0.00 31.05 4.01
3206 3638 5.842907 ACAGAGTTTTTATTTCCAAGCACC 58.157 37.500 0.00 0.00 0.00 5.01
3207 3639 5.221441 ACAGAGTTTTTATTTCCAAGCACCC 60.221 40.000 0.00 0.00 0.00 4.61
3208 3640 4.022329 AGAGTTTTTATTTCCAAGCACCCG 60.022 41.667 0.00 0.00 0.00 5.28
3209 3641 3.639561 AGTTTTTATTTCCAAGCACCCGT 59.360 39.130 0.00 0.00 0.00 5.28
3210 3642 4.100344 AGTTTTTATTTCCAAGCACCCGTT 59.900 37.500 0.00 0.00 0.00 4.44
3211 3643 4.674281 TTTTATTTCCAAGCACCCGTTT 57.326 36.364 0.00 0.00 0.00 3.60
3212 3644 5.786264 TTTTATTTCCAAGCACCCGTTTA 57.214 34.783 0.00 0.00 0.00 2.01
3213 3645 4.769859 TTATTTCCAAGCACCCGTTTAC 57.230 40.909 0.00 0.00 0.00 2.01
3214 3646 1.320507 TTTCCAAGCACCCGTTTACC 58.679 50.000 0.00 0.00 0.00 2.85
3215 3647 0.183014 TTCCAAGCACCCGTTTACCA 59.817 50.000 0.00 0.00 0.00 3.25
3216 3648 0.402504 TCCAAGCACCCGTTTACCAT 59.597 50.000 0.00 0.00 0.00 3.55
3217 3649 1.202952 TCCAAGCACCCGTTTACCATT 60.203 47.619 0.00 0.00 0.00 3.16
3218 3650 2.040012 TCCAAGCACCCGTTTACCATTA 59.960 45.455 0.00 0.00 0.00 1.90
3219 3651 2.162809 CCAAGCACCCGTTTACCATTAC 59.837 50.000 0.00 0.00 0.00 1.89
3220 3652 2.118313 AGCACCCGTTTACCATTACC 57.882 50.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.374184 TGGCGGGTATCATTTGGAAAG 58.626 47.619 0.00 0.00 0.00 2.62
19 20 1.166531 GCAAGTGGATGGCGGGTATC 61.167 60.000 0.00 0.00 0.00 2.24
68 69 2.810650 CGGTCTTGGGATTCGAACTAG 58.189 52.381 0.00 0.00 0.00 2.57
70 71 0.391263 GCGGTCTTGGGATTCGAACT 60.391 55.000 0.00 0.00 0.00 3.01
106 107 7.622713 AGAAATATGCCATCATGGTTCAAAAA 58.377 30.769 5.31 0.00 40.46 1.94
263 410 5.596845 TGTTTTGCTTTACTTGGTCCATTC 58.403 37.500 0.00 0.00 0.00 2.67
399 559 1.002087 TCGGCAGAGTCCTTCCTTTTC 59.998 52.381 0.00 0.00 0.00 2.29
449 615 1.963515 CGAATGGGGATGGGGAATTTC 59.036 52.381 0.00 0.00 0.00 2.17
473 639 3.630013 TCTTGCAGCGCCTGGTCT 61.630 61.111 2.29 0.00 31.21 3.85
479 645 0.811281 AAATTAGGTCTTGCAGCGCC 59.189 50.000 2.29 0.00 0.00 6.53
718 955 6.557291 AGATGCAGAGAAAAACAAAGAGAG 57.443 37.500 0.00 0.00 0.00 3.20
756 993 3.187700 AGGCACGAATACACGAAAGATC 58.812 45.455 0.00 0.00 37.03 2.75
876 1113 0.178958 AAGGAGGTGAGGTGAGACGT 60.179 55.000 0.00 0.00 0.00 4.34
924 1165 5.483583 AGAGTTCAGACCAGCTTCTAATCTT 59.516 40.000 0.00 0.00 0.00 2.40
953 1196 3.003897 TGAAAAGACGCGGCAAATAACTT 59.996 39.130 17.71 0.00 0.00 2.66
959 1202 0.736053 AACTGAAAAGACGCGGCAAA 59.264 45.000 17.71 0.00 0.00 3.68
1076 1323 4.754667 GGCCGACGTCCTTGGACC 62.755 72.222 10.58 7.67 0.00 4.46
1101 1348 1.334960 CGCCATGAAGTGTTCACAACC 60.335 52.381 5.74 0.00 43.48 3.77
1172 1420 1.561769 ATCCACAATGGGGAGCGACA 61.562 55.000 11.06 0.00 38.32 4.35
1194 1442 1.422531 AATTGGCAGGCTTTCCACAA 58.577 45.000 4.84 0.00 33.74 3.33
1276 1530 0.949105 CAGTAACGGCGTTTGGAGCT 60.949 55.000 31.53 17.06 34.52 4.09
1294 1548 3.001514 GGCTCTGGGCTGATTCCA 58.998 61.111 0.00 0.00 41.46 3.53
1332 1586 8.429237 TGTAGAATTTGTGTCCCCAATAAATT 57.571 30.769 0.00 0.00 34.72 1.82
1368 1628 3.590824 GCATGCTTGCGGGTAACT 58.409 55.556 11.37 0.00 39.49 2.24
1494 1754 5.454471 GCTGGATTCAGAGGAGTATTGTGAT 60.454 44.000 4.75 0.00 43.49 3.06
1495 1755 4.141846 GCTGGATTCAGAGGAGTATTGTGA 60.142 45.833 4.75 0.00 43.49 3.58
1496 1756 4.125703 GCTGGATTCAGAGGAGTATTGTG 58.874 47.826 4.75 0.00 43.49 3.33
1497 1757 4.036518 AGCTGGATTCAGAGGAGTATTGT 58.963 43.478 4.75 0.00 43.49 2.71
1498 1758 4.686191 AGCTGGATTCAGAGGAGTATTG 57.314 45.455 4.75 0.00 43.49 1.90
1499 1759 8.538701 CATATAAGCTGGATTCAGAGGAGTATT 58.461 37.037 4.75 0.00 43.49 1.89
1500 1760 7.677745 ACATATAAGCTGGATTCAGAGGAGTAT 59.322 37.037 4.75 0.00 43.49 2.12
1501 1761 7.013220 ACATATAAGCTGGATTCAGAGGAGTA 58.987 38.462 4.75 0.00 43.49 2.59
1506 1766 5.549347 AGCACATATAAGCTGGATTCAGAG 58.451 41.667 4.75 0.00 43.49 3.35
1527 1787 0.610174 TGTCAGATCCCACTGTGAGC 59.390 55.000 9.86 0.00 38.79 4.26
1553 1813 3.244665 TGGCATTCTGACACTGATGAACT 60.245 43.478 0.00 0.00 24.43 3.01
1556 1816 3.076621 GTTGGCATTCTGACACTGATGA 58.923 45.455 0.00 0.00 33.32 2.92
1597 1857 5.455392 CAGCTGGTTCAATAACTTCTGTTG 58.545 41.667 5.57 0.00 37.59 3.33
1615 1881 3.082165 CAGATGAAGAGGGCAGCTG 57.918 57.895 10.11 10.11 42.41 4.24
1622 1888 4.869297 GTGATGAACAGTCAGATGAAGAGG 59.131 45.833 0.00 0.00 37.14 3.69
1665 1937 0.737219 CATAAGGAAGCCAGTGCAGC 59.263 55.000 0.00 0.00 41.13 5.25
1693 1974 1.206132 TCCACCGCCTACTGTAATGTG 59.794 52.381 0.00 0.00 0.00 3.21
1703 1984 4.591498 ACACAATAATATCTCCACCGCCTA 59.409 41.667 0.00 0.00 0.00 3.93
1750 2031 1.847506 TGGGACTGCACATCCACCT 60.848 57.895 13.15 0.00 38.06 4.00
2133 2491 0.472925 TGAGGCAGTGGTGGGTAAGA 60.473 55.000 0.00 0.00 0.00 2.10
2192 2559 2.048601 AGAATGGAGCCTCCTCATCTG 58.951 52.381 12.94 0.00 39.96 2.90
2218 2585 4.648307 AGTCATGATCACTCAGACATGCTA 59.352 41.667 16.77 0.00 36.53 3.49
2219 2586 3.451540 AGTCATGATCACTCAGACATGCT 59.548 43.478 16.77 0.00 36.53 3.79
2230 2597 3.693085 AGCAAACCATGAGTCATGATCAC 59.307 43.478 30.63 16.77 43.81 3.06
2243 2614 5.477984 TCTGAATCTAAGCAAAGCAAACCAT 59.522 36.000 0.00 0.00 0.00 3.55
2258 2629 7.175816 GGTCTGCTAGTACATGATCTGAATCTA 59.824 40.741 0.00 0.00 32.75 1.98
2259 2630 6.015519 GGTCTGCTAGTACATGATCTGAATCT 60.016 42.308 0.00 0.00 32.75 2.40
2330 2738 2.918600 TCGTACGAACCAAATGATGACG 59.081 45.455 17.11 0.00 0.00 4.35
2333 2741 5.434706 CATCATCGTACGAACCAAATGATG 58.565 41.667 28.62 28.62 42.09 3.07
2344 2752 2.931512 TTCAGCACATCATCGTACGA 57.068 45.000 21.93 21.93 0.00 3.43
2345 2753 4.324669 GGATATTCAGCACATCATCGTACG 59.675 45.833 9.53 9.53 0.00 3.67
2349 2757 4.313282 ACAGGATATTCAGCACATCATCG 58.687 43.478 0.00 0.00 0.00 3.84
2350 2758 7.734924 TTAACAGGATATTCAGCACATCATC 57.265 36.000 0.00 0.00 0.00 2.92
2414 2823 5.670361 AGGCAGGGAGGAACAGTAATATAAA 59.330 40.000 0.00 0.00 0.00 1.40
2417 2826 3.648545 GAGGCAGGGAGGAACAGTAATAT 59.351 47.826 0.00 0.00 0.00 1.28
2460 2869 1.752501 CTCGTGCATCTTAACCGCGG 61.753 60.000 26.86 26.86 33.70 6.46
2492 2901 8.563732 AGCAAAAGAAAGACTGAATTTCTAGTC 58.436 33.333 15.40 15.40 44.25 2.59
2516 2925 3.844577 AACAATGTCTCATCTTGCAGC 57.155 42.857 0.00 0.00 0.00 5.25
2541 2950 1.621301 CTCAAAGAGCACGGCACTCG 61.621 60.000 0.00 0.00 45.88 4.18
2542 2951 0.601311 ACTCAAAGAGCACGGCACTC 60.601 55.000 0.00 0.00 32.04 3.51
2545 2954 1.597854 CCACTCAAAGAGCACGGCA 60.598 57.895 0.00 0.00 32.04 5.69
2546 2955 1.294659 CTCCACTCAAAGAGCACGGC 61.295 60.000 0.00 0.00 32.04 5.68
2548 2957 1.294659 GCCTCCACTCAAAGAGCACG 61.295 60.000 0.00 0.00 32.04 5.34
2549 2958 0.250467 TGCCTCCACTCAAAGAGCAC 60.250 55.000 0.00 0.00 32.04 4.40
2597 3008 1.065854 ACTGACAGGCTATGGAAGTGC 60.066 52.381 7.51 0.00 30.09 4.40
2616 3027 5.671329 GCGTAATGGACAACAGAGATCAAAC 60.671 44.000 0.00 0.00 0.00 2.93
2638 3049 3.866883 ACCTTGTTATCCCAAATTGCG 57.133 42.857 0.00 0.00 0.00 4.85
2656 3068 3.440522 GCATCTGTTAACCTCCTGAAACC 59.559 47.826 2.48 0.00 0.00 3.27
2692 3104 7.918562 ACACATGTTGTAATCCTAACAAAACAC 59.081 33.333 0.00 0.00 39.89 3.32
2721 3133 3.825328 ACTCTGCTAATTAAGGGCCATG 58.175 45.455 6.18 0.00 0.00 3.66
2786 3199 4.236935 CAACATATGACCAAAGCACCAAC 58.763 43.478 10.38 0.00 0.00 3.77
2825 3239 4.805719 GGAAACAGAAAACAGCAGGAAAAG 59.194 41.667 0.00 0.00 0.00 2.27
2880 3294 3.496884 GCACATCCTCAACTCGTTTGTAA 59.503 43.478 0.54 0.00 36.49 2.41
2883 3297 2.146342 AGCACATCCTCAACTCGTTTG 58.854 47.619 0.00 0.00 36.42 2.93
2892 3306 2.060383 CCCGGAGAGCACATCCTCA 61.060 63.158 0.73 0.00 34.45 3.86
2915 3342 6.156949 TGAACCAAGAAGAGGCATACTTATCT 59.843 38.462 0.00 0.00 0.00 1.98
2921 3348 2.680339 GCTGAACCAAGAAGAGGCATAC 59.320 50.000 0.00 0.00 0.00 2.39
2970 3397 6.091169 CACCATTCAAATCCAAACATGTAAGC 59.909 38.462 0.00 0.00 0.00 3.09
3010 3437 7.270793 GCAATCGAGACATAACCGTATAACTAG 59.729 40.741 0.00 0.00 0.00 2.57
3013 3440 5.688621 TGCAATCGAGACATAACCGTATAAC 59.311 40.000 0.00 0.00 0.00 1.89
3014 3441 5.834169 TGCAATCGAGACATAACCGTATAA 58.166 37.500 0.00 0.00 0.00 0.98
3015 3442 5.441709 TGCAATCGAGACATAACCGTATA 57.558 39.130 0.00 0.00 0.00 1.47
3017 3444 3.786516 TGCAATCGAGACATAACCGTA 57.213 42.857 0.00 0.00 0.00 4.02
3018 3445 2.665649 TGCAATCGAGACATAACCGT 57.334 45.000 0.00 0.00 0.00 4.83
3019 3446 2.866156 ACATGCAATCGAGACATAACCG 59.134 45.455 0.00 0.00 0.00 4.44
3020 3447 5.120830 GGATACATGCAATCGAGACATAACC 59.879 44.000 0.00 0.00 0.00 2.85
3021 3448 5.696270 TGGATACATGCAATCGAGACATAAC 59.304 40.000 0.00 0.00 46.17 1.89
3022 3449 5.852827 TGGATACATGCAATCGAGACATAA 58.147 37.500 0.00 0.00 46.17 1.90
3024 3451 4.341366 TGGATACATGCAATCGAGACAT 57.659 40.909 0.00 0.00 46.17 3.06
3025 3452 3.817709 TGGATACATGCAATCGAGACA 57.182 42.857 0.00 0.00 46.17 3.41
3085 3512 6.233434 TCATTCAGTGCTAATTGTTCAGTCT 58.767 36.000 0.00 0.00 0.00 3.24
3104 3531 6.370166 AGGTCGTCTTCTTTTTGAGATCATTC 59.630 38.462 0.00 0.00 33.49 2.67
3105 3532 6.148480 CAGGTCGTCTTCTTTTTGAGATCATT 59.852 38.462 0.00 0.00 33.49 2.57
3107 3534 4.991056 CAGGTCGTCTTCTTTTTGAGATCA 59.009 41.667 0.00 0.00 33.49 2.92
3108 3535 4.991687 ACAGGTCGTCTTCTTTTTGAGATC 59.008 41.667 0.00 0.00 33.49 2.75
3109 3536 4.962155 ACAGGTCGTCTTCTTTTTGAGAT 58.038 39.130 0.00 0.00 33.49 2.75
3110 3537 4.402056 ACAGGTCGTCTTCTTTTTGAGA 57.598 40.909 0.00 0.00 0.00 3.27
3111 3538 4.024809 GGAACAGGTCGTCTTCTTTTTGAG 60.025 45.833 0.00 0.00 0.00 3.02
3114 3542 2.870411 CGGAACAGGTCGTCTTCTTTTT 59.130 45.455 0.00 0.00 0.00 1.94
3119 3547 0.316204 TTCCGGAACAGGTCGTCTTC 59.684 55.000 14.35 0.00 0.00 2.87
3130 3558 0.039165 CAGCAAGCCTTTTCCGGAAC 60.039 55.000 18.64 5.26 0.00 3.62
3134 3562 0.519077 GACTCAGCAAGCCTTTTCCG 59.481 55.000 0.00 0.00 0.00 4.30
3141 3569 2.521958 TTAGGCCGACTCAGCAAGCC 62.522 60.000 0.00 0.00 44.20 4.35
3142 3570 1.079127 TTAGGCCGACTCAGCAAGC 60.079 57.895 0.00 0.00 0.00 4.01
3145 3577 1.192146 AAGGTTAGGCCGACTCAGCA 61.192 55.000 11.37 0.00 43.70 4.41
3153 3585 5.556915 TCAATATAATCCAAGGTTAGGCCG 58.443 41.667 0.00 0.00 43.70 6.13
3173 3605 9.965824 GGAAATAAAAACTCTGTTTCTCATCAA 57.034 29.630 0.00 0.00 0.00 2.57
3174 3606 9.130661 TGGAAATAAAAACTCTGTTTCTCATCA 57.869 29.630 0.00 0.00 0.00 3.07
3180 3612 7.042725 GGTGCTTGGAAATAAAAACTCTGTTTC 60.043 37.037 0.00 0.00 0.00 2.78
3194 3626 1.890489 GGTAAACGGGTGCTTGGAAAT 59.110 47.619 0.00 0.00 0.00 2.17
3199 3631 2.162809 GGTAATGGTAAACGGGTGCTTG 59.837 50.000 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.