Multiple sequence alignment - TraesCS4B01G220100

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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 TraesCS4B01G220100 chr4B 100.000 2646 0 0 1 2646 462695811 462698456 0.000000e+00 4887.0
1 TraesCS4B01G220100 chr4B 76.868 562 87 30 1046 1603 462592291 462592813 7.210000e-71 278.0
2 TraesCS4B01G220100 chr4B 95.968 124 5 0 2523 2646 349913514 349913391 4.470000e-48 202.0
3 TraesCS4B01G220100 chr4B 95.968 124 5 0 2523 2646 484496362 484496485 4.470000e-48 202.0
4 TraesCS4B01G220100 chr4B 95.968 124 5 0 2523 2646 544466458 544466335 4.470000e-48 202.0
5 TraesCS4B01G220100 chr4D 93.698 2158 96 22 1 2142 375507808 375509941 0.000000e+00 3195.0
6 TraesCS4B01G220100 chr4D 93.399 303 14 4 2229 2527 375510069 375510369 6.720000e-121 444.0
7 TraesCS4B01G220100 chr4D 81.915 188 31 2 1076 1263 375445379 375445563 3.530000e-34 156.0
8 TraesCS4B01G220100 chr4D 88.636 44 4 1 2153 2196 94372770 94372728 5.000000e-03 52.8
9 TraesCS4B01G220100 chr4A 93.196 1411 54 16 565 1963 88541829 88540449 0.000000e+00 2036.0
10 TraesCS4B01G220100 chr4A 90.939 309 13 7 2229 2527 88540170 88539867 4.100000e-108 401.0
11 TraesCS4B01G220100 chr4A 88.346 266 15 7 148 398 88542428 88542164 3.310000e-79 305.0
12 TraesCS4B01G220100 chr4A 76.357 571 97 28 1046 1612 88705013 88704477 3.360000e-69 272.0
13 TraesCS4B01G220100 chr4A 93.210 162 9 1 1989 2148 88540453 88540292 1.220000e-58 237.0
14 TraesCS4B01G220100 chr4A 95.349 43 0 2 522 562 88542163 88542121 1.700000e-07 67.6
15 TraesCS4B01G220100 chr7B 96.774 124 4 0 2523 2646 524454917 524455040 9.600000e-50 207.0
16 TraesCS4B01G220100 chr7B 95.968 124 5 0 2523 2646 428499841 428499964 4.470000e-48 202.0
17 TraesCS4B01G220100 chr7B 95.968 124 5 0 2523 2646 530141245 530141368 4.470000e-48 202.0
18 TraesCS4B01G220100 chr6B 96.774 124 4 0 2523 2646 76213935 76213812 9.600000e-50 207.0
19 TraesCS4B01G220100 chr6B 95.968 124 5 0 2523 2646 121639623 121639746 4.470000e-48 202.0
20 TraesCS4B01G220100 chr1B 96.774 124 4 0 2523 2646 593661593 593661470 9.600000e-50 207.0
21 TraesCS4B01G220100 chr6D 97.143 35 0 1 2153 2187 78782103 78782136 1.020000e-04 58.4


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 TraesCS4B01G220100 chr4B 462695811 462698456 2645 False 4887.00 4887 100.0000 1 2646 1 chr4B.!!$F2 2645
1 TraesCS4B01G220100 chr4B 462592291 462592813 522 False 278.00 278 76.8680 1046 1603 1 chr4B.!!$F1 557
2 TraesCS4B01G220100 chr4D 375507808 375510369 2561 False 1819.50 3195 93.5485 1 2527 2 chr4D.!!$F2 2526
3 TraesCS4B01G220100 chr4A 88539867 88542428 2561 True 609.32 2036 92.2080 148 2527 5 chr4A.!!$R2 2379
4 TraesCS4B01G220100 chr4A 88704477 88705013 536 True 272.00 272 76.3570 1046 1612 1 chr4A.!!$R1 566

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
462 480 1.150827 CATCCGACATATGCATGCGT 58.849 50.0 18.07 18.07 35.39 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 2167 0.107654 GGCAGAAGGATTGCGTACCT 60.108 55.0 0.0 0.0 42.42 3.08 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
86 87 7.225145 CCCATATTAATTGGCACTGATGTTTTG 59.775 37.037 9.79 0.00 32.60 2.44
97 98 7.013750 TGGCACTGATGTTTTGTACTAAATCAA 59.986 33.333 5.78 0.00 0.00 2.57
315 328 9.681062 AACTTGTACATACAAAAGGTATATGCT 57.319 29.630 0.00 0.00 44.67 3.79
452 470 2.321263 CTGGCCTCTGCATCCGACAT 62.321 60.000 3.32 0.00 40.13 3.06
462 480 1.150827 CATCCGACATATGCATGCGT 58.849 50.000 18.07 18.07 35.39 5.24
481 499 7.648142 CATGCGTCCATATTATTAAAAGGTGT 58.352 34.615 0.00 0.00 0.00 4.16
504 522 7.222611 GTGTCAACAAAATACAAAGTCTGCAAT 59.777 33.333 0.00 0.00 0.00 3.56
514 532 9.624373 AATACAAAGTCTGCAATCTAGATGATT 57.376 29.630 5.86 0.00 45.52 2.57
590 900 6.328641 TGTTAGGTCACTCTTACTCAAGAC 57.671 41.667 0.00 0.00 35.82 3.01
609 919 6.320926 TCAAGACTGATCTTAGATCACTCCAG 59.679 42.308 19.74 12.62 43.69 3.86
617 927 7.450014 TGATCTTAGATCACTCCAGGTAATCTC 59.550 40.741 19.74 0.00 0.00 2.75
919 1235 1.405797 CCGCCCGTCCTATAAACACAA 60.406 52.381 0.00 0.00 0.00 3.33
953 1269 2.039084 AGTCGACCAGATCAAAGCCTTT 59.961 45.455 13.01 0.00 0.00 3.11
967 1283 1.493311 CCTTTTGTCAGTCGCTCGC 59.507 57.895 0.00 0.00 0.00 5.03
1020 1343 1.302993 GAGCGGCCAAGTTTACCCA 60.303 57.895 2.24 0.00 0.00 4.51
1189 1512 3.589654 TACTGGCAGGACACGCTGC 62.590 63.158 20.34 4.37 45.04 5.25
1269 1592 1.599797 GCAAAGGTACGCACAGGGT 60.600 57.895 0.00 0.00 0.00 4.34
1302 1625 8.478877 TCCTGGTTAGAAACTTAGATTCTGATC 58.521 37.037 13.83 7.51 37.67 2.92
1303 1626 7.436673 CCTGGTTAGAAACTTAGATTCTGATCG 59.563 40.741 13.83 4.36 37.67 3.69
1304 1627 8.063200 TGGTTAGAAACTTAGATTCTGATCGA 57.937 34.615 13.83 0.00 37.67 3.59
1429 1752 2.997315 ACGCTGAGCCTGCTGGTA 60.997 61.111 11.69 0.00 35.27 3.25
1483 1806 2.749044 TTCGCCGTCGCCTACTCT 60.749 61.111 0.00 0.00 35.26 3.24
1658 1981 1.152756 AACTGACGCCCCAAGCTTT 60.153 52.632 0.00 0.00 40.39 3.51
1667 1990 2.239400 GCCCCAAGCTTTAGTGTTCTT 58.761 47.619 0.00 0.00 38.99 2.52
1680 2003 7.416154 TTTAGTGTTCTTATGTCTTTGTCGG 57.584 36.000 0.00 0.00 0.00 4.79
1780 2105 0.037734 AACAAAAGGGGACGCCTAGG 59.962 55.000 12.12 3.67 0.00 3.02
1845 2171 3.706600 AGCCGTTTGGATTTACAGGTA 57.293 42.857 0.00 0.00 37.49 3.08
1846 2172 3.340928 AGCCGTTTGGATTTACAGGTAC 58.659 45.455 0.00 0.00 37.49 3.34
1847 2173 2.094734 GCCGTTTGGATTTACAGGTACG 59.905 50.000 0.00 0.00 37.49 3.67
1848 2174 2.094734 CCGTTTGGATTTACAGGTACGC 59.905 50.000 0.00 0.00 37.49 4.42
1849 2175 2.737783 CGTTTGGATTTACAGGTACGCA 59.262 45.455 0.00 0.00 0.00 5.24
1850 2176 3.186817 CGTTTGGATTTACAGGTACGCAA 59.813 43.478 0.00 0.00 0.00 4.85
1857 2186 4.546829 TTTACAGGTACGCAATCCTTCT 57.453 40.909 0.00 0.00 30.91 2.85
1913 2242 1.078918 CATTCTGCCGAGCCTGACA 60.079 57.895 0.00 0.00 0.00 3.58
1957 2286 3.970640 GACCTGATCATCCCTCTAAACCT 59.029 47.826 0.00 0.00 0.00 3.50
2143 2474 1.404477 CGACCGATGCAAACAAAACC 58.596 50.000 0.00 0.00 0.00 3.27
2144 2475 1.001815 CGACCGATGCAAACAAAACCT 60.002 47.619 0.00 0.00 0.00 3.50
2145 2476 2.542824 CGACCGATGCAAACAAAACCTT 60.543 45.455 0.00 0.00 0.00 3.50
2146 2477 3.304123 CGACCGATGCAAACAAAACCTTA 60.304 43.478 0.00 0.00 0.00 2.69
2147 2478 4.612943 GACCGATGCAAACAAAACCTTAA 58.387 39.130 0.00 0.00 0.00 1.85
2148 2479 4.364860 ACCGATGCAAACAAAACCTTAAC 58.635 39.130 0.00 0.00 0.00 2.01
2149 2480 4.098807 ACCGATGCAAACAAAACCTTAACT 59.901 37.500 0.00 0.00 0.00 2.24
2150 2481 5.047188 CCGATGCAAACAAAACCTTAACTT 58.953 37.500 0.00 0.00 0.00 2.66
2151 2482 5.522097 CCGATGCAAACAAAACCTTAACTTT 59.478 36.000 0.00 0.00 0.00 2.66
2152 2483 6.036626 CCGATGCAAACAAAACCTTAACTTTT 59.963 34.615 0.00 0.00 0.00 2.27
2153 2484 7.413548 CCGATGCAAACAAAACCTTAACTTTTT 60.414 33.333 0.00 0.00 0.00 1.94
2179 2510 9.722184 TTTTGAAATTGATTGGATTGCTTATCA 57.278 25.926 2.57 0.00 34.77 2.15
2180 2511 8.706492 TTGAAATTGATTGGATTGCTTATCAC 57.294 30.769 0.00 0.00 34.77 3.06
2181 2512 7.838884 TGAAATTGATTGGATTGCTTATCACA 58.161 30.769 0.00 0.00 34.77 3.58
2182 2513 8.479689 TGAAATTGATTGGATTGCTTATCACAT 58.520 29.630 0.00 0.00 34.77 3.21
2183 2514 8.657074 AAATTGATTGGATTGCTTATCACATG 57.343 30.769 0.00 0.00 34.77 3.21
2184 2515 6.778834 TTGATTGGATTGCTTATCACATGT 57.221 33.333 0.00 0.00 34.77 3.21
2185 2516 6.139048 TGATTGGATTGCTTATCACATGTG 57.861 37.500 20.18 20.18 34.77 3.21
2186 2517 5.653330 TGATTGGATTGCTTATCACATGTGT 59.347 36.000 24.63 14.61 34.77 3.72
2187 2518 5.981088 TTGGATTGCTTATCACATGTGTT 57.019 34.783 24.63 18.96 34.77 3.32
2188 2519 7.338957 TGATTGGATTGCTTATCACATGTGTTA 59.661 33.333 24.63 17.92 34.77 2.41
2189 2520 6.435430 TGGATTGCTTATCACATGTGTTAC 57.565 37.500 24.63 10.79 34.77 2.50
2190 2521 5.064579 TGGATTGCTTATCACATGTGTTACG 59.935 40.000 24.63 18.28 34.77 3.18
2191 2522 5.064707 GGATTGCTTATCACATGTGTTACGT 59.935 40.000 24.63 9.96 34.77 3.57
2192 2523 4.919677 TGCTTATCACATGTGTTACGTG 57.080 40.909 24.63 13.69 40.80 4.49
2193 2524 3.124466 TGCTTATCACATGTGTTACGTGC 59.876 43.478 24.63 20.95 38.65 5.34
2194 2525 3.370978 GCTTATCACATGTGTTACGTGCT 59.629 43.478 24.63 4.45 38.65 4.40
2195 2526 4.565166 GCTTATCACATGTGTTACGTGCTA 59.435 41.667 24.63 3.11 38.65 3.49
2196 2527 5.062934 GCTTATCACATGTGTTACGTGCTAA 59.937 40.000 24.63 5.91 38.65 3.09
2197 2528 4.921470 ATCACATGTGTTACGTGCTAAC 57.079 40.909 24.63 0.00 38.65 2.34
2198 2529 3.718815 TCACATGTGTTACGTGCTAACA 58.281 40.909 24.63 0.00 42.13 2.41
2199 2530 4.120589 TCACATGTGTTACGTGCTAACAA 58.879 39.130 24.63 0.00 45.16 2.83
2200 2531 4.571176 TCACATGTGTTACGTGCTAACAAA 59.429 37.500 24.63 0.00 45.16 2.83
2201 2532 5.064834 TCACATGTGTTACGTGCTAACAAAA 59.935 36.000 24.63 0.00 45.16 2.44
2202 2533 5.739630 CACATGTGTTACGTGCTAACAAAAA 59.260 36.000 18.03 0.00 45.16 1.94
2206 2537 4.663091 GTGTTACGTGCTAACAAAAACTCG 59.337 41.667 4.03 0.00 45.16 4.18
2217 2548 5.437289 AACAAAAACTCGATTGCATGAGA 57.563 34.783 15.55 2.42 36.11 3.27
2228 2559 5.972973 TCGATTGCATGAGAAATAAATGTGC 59.027 36.000 0.00 0.00 0.00 4.57
2229 2560 5.174398 CGATTGCATGAGAAATAAATGTGCC 59.826 40.000 0.00 0.00 0.00 5.01
2234 2667 6.935771 TGCATGAGAAATAAATGTGCCTTTTT 59.064 30.769 0.00 0.00 0.00 1.94
2321 2761 0.389391 ATAGGAATGCGCTGCGTACT 59.611 50.000 24.04 9.28 0.00 2.73
2329 2769 0.723129 GCGCTGCGTACTCTAGATCG 60.723 60.000 24.04 0.32 0.00 3.69
2543 2987 8.910351 ATTTTACTCCATAGTTAGGATCTTGC 57.090 34.615 0.00 0.00 37.15 4.01
2544 2988 4.965200 ACTCCATAGTTAGGATCTTGCC 57.035 45.455 0.00 0.00 33.99 4.52
2545 2989 4.561752 ACTCCATAGTTAGGATCTTGCCT 58.438 43.478 0.00 0.00 42.15 4.75
2546 2990 4.591072 ACTCCATAGTTAGGATCTTGCCTC 59.409 45.833 0.00 0.00 39.50 4.70
2547 2991 4.820775 TCCATAGTTAGGATCTTGCCTCT 58.179 43.478 0.00 0.00 39.50 3.69
2548 2992 4.835615 TCCATAGTTAGGATCTTGCCTCTC 59.164 45.833 0.00 0.00 39.50 3.20
2549 2993 4.020662 CCATAGTTAGGATCTTGCCTCTCC 60.021 50.000 0.00 0.00 39.50 3.71
2550 2994 3.121929 AGTTAGGATCTTGCCTCTCCA 57.878 47.619 0.00 0.00 39.50 3.86
2551 2995 3.663198 AGTTAGGATCTTGCCTCTCCAT 58.337 45.455 0.00 0.00 39.50 3.41
2552 2996 4.043596 AGTTAGGATCTTGCCTCTCCATT 58.956 43.478 0.00 0.00 39.50 3.16
2553 2997 5.219739 AGTTAGGATCTTGCCTCTCCATTA 58.780 41.667 0.00 0.00 39.50 1.90
2554 2998 5.306678 AGTTAGGATCTTGCCTCTCCATTAG 59.693 44.000 0.00 0.00 39.50 1.73
2555 2999 3.663198 AGGATCTTGCCTCTCCATTAGT 58.337 45.455 0.00 0.00 30.76 2.24
2556 3000 4.820775 AGGATCTTGCCTCTCCATTAGTA 58.179 43.478 0.00 0.00 30.76 1.82
2557 3001 5.410602 AGGATCTTGCCTCTCCATTAGTAT 58.589 41.667 0.00 0.00 30.76 2.12
2558 3002 5.483583 AGGATCTTGCCTCTCCATTAGTATC 59.516 44.000 0.00 0.00 30.76 2.24
2559 3003 5.337975 GGATCTTGCCTCTCCATTAGTATCC 60.338 48.000 0.00 0.00 0.00 2.59
2560 3004 3.904339 TCTTGCCTCTCCATTAGTATCCC 59.096 47.826 0.00 0.00 0.00 3.85
2561 3005 2.621070 TGCCTCTCCATTAGTATCCCC 58.379 52.381 0.00 0.00 0.00 4.81
2562 3006 1.909986 GCCTCTCCATTAGTATCCCCC 59.090 57.143 0.00 0.00 0.00 5.40
2563 3007 2.495572 GCCTCTCCATTAGTATCCCCCT 60.496 54.545 0.00 0.00 0.00 4.79
2564 3008 3.246021 GCCTCTCCATTAGTATCCCCCTA 60.246 52.174 0.00 0.00 0.00 3.53
2565 3009 4.354662 CCTCTCCATTAGTATCCCCCTAC 58.645 52.174 0.00 0.00 0.00 3.18
2566 3010 4.202792 CCTCTCCATTAGTATCCCCCTACA 60.203 50.000 0.00 0.00 0.00 2.74
2567 3011 4.748701 TCTCCATTAGTATCCCCCTACAC 58.251 47.826 0.00 0.00 0.00 2.90
2568 3012 4.422592 TCTCCATTAGTATCCCCCTACACT 59.577 45.833 0.00 0.00 0.00 3.55
2569 3013 5.618284 TCTCCATTAGTATCCCCCTACACTA 59.382 44.000 0.00 0.00 0.00 2.74
2570 3014 6.279682 TCTCCATTAGTATCCCCCTACACTAT 59.720 42.308 0.00 0.00 0.00 2.12
2571 3015 6.882155 TCCATTAGTATCCCCCTACACTATT 58.118 40.000 0.00 0.00 0.00 1.73
2572 3016 6.729100 TCCATTAGTATCCCCCTACACTATTG 59.271 42.308 0.00 0.00 0.00 1.90
2573 3017 6.500751 CCATTAGTATCCCCCTACACTATTGT 59.499 42.308 0.00 0.00 40.02 2.71
2574 3018 7.310485 CCATTAGTATCCCCCTACACTATTGTC 60.310 44.444 0.00 0.00 37.15 3.18
2575 3019 5.152306 AGTATCCCCCTACACTATTGTCA 57.848 43.478 0.00 0.00 37.15 3.58
2576 3020 5.148502 AGTATCCCCCTACACTATTGTCAG 58.851 45.833 0.00 0.00 37.15 3.51
2577 3021 3.769189 TCCCCCTACACTATTGTCAGA 57.231 47.619 0.00 0.00 37.15 3.27
2578 3022 3.371965 TCCCCCTACACTATTGTCAGAC 58.628 50.000 0.00 0.00 37.15 3.51
2579 3023 3.012502 TCCCCCTACACTATTGTCAGACT 59.987 47.826 1.31 0.00 37.15 3.24
2580 3024 3.775316 CCCCCTACACTATTGTCAGACTT 59.225 47.826 1.31 0.00 37.15 3.01
2581 3025 4.960469 CCCCCTACACTATTGTCAGACTTA 59.040 45.833 1.31 0.00 37.15 2.24
2582 3026 5.069251 CCCCCTACACTATTGTCAGACTTAG 59.931 48.000 1.31 5.93 37.15 2.18
2583 3027 5.892119 CCCCTACACTATTGTCAGACTTAGA 59.108 44.000 14.53 0.00 37.15 2.10
2584 3028 6.380274 CCCCTACACTATTGTCAGACTTAGAA 59.620 42.308 14.53 0.00 37.15 2.10
2585 3029 7.259161 CCCTACACTATTGTCAGACTTAGAAC 58.741 42.308 14.53 0.00 37.15 3.01
2586 3030 7.259161 CCTACACTATTGTCAGACTTAGAACC 58.741 42.308 14.53 0.00 37.15 3.62
2587 3031 6.665992 ACACTATTGTCAGACTTAGAACCA 57.334 37.500 14.53 0.00 0.00 3.67
2588 3032 6.456501 ACACTATTGTCAGACTTAGAACCAC 58.543 40.000 14.53 0.00 0.00 4.16
2589 3033 5.573282 CACTATTGTCAGACTTAGAACCACG 59.427 44.000 14.53 0.00 0.00 4.94
2590 3034 4.866508 ATTGTCAGACTTAGAACCACGA 57.133 40.909 1.31 0.00 0.00 4.35
2591 3035 3.637998 TGTCAGACTTAGAACCACGAC 57.362 47.619 1.31 0.00 0.00 4.34
2592 3036 2.953648 TGTCAGACTTAGAACCACGACA 59.046 45.455 1.31 0.00 0.00 4.35
2593 3037 3.004419 TGTCAGACTTAGAACCACGACAG 59.996 47.826 1.31 0.00 0.00 3.51
2594 3038 3.004524 GTCAGACTTAGAACCACGACAGT 59.995 47.826 0.00 0.00 0.00 3.55
2595 3039 3.635373 TCAGACTTAGAACCACGACAGTT 59.365 43.478 0.00 0.00 0.00 3.16
2596 3040 3.736252 CAGACTTAGAACCACGACAGTTG 59.264 47.826 0.00 0.00 0.00 3.16
2597 3041 3.057734 GACTTAGAACCACGACAGTTGG 58.942 50.000 0.00 0.00 0.00 3.77
2598 3042 1.798813 CTTAGAACCACGACAGTTGGC 59.201 52.381 0.00 0.00 0.00 4.52
2622 3066 3.697747 CGTGGGGCGGGTGTCTTA 61.698 66.667 0.00 0.00 36.85 2.10
2623 3067 2.267961 GTGGGGCGGGTGTCTTAG 59.732 66.667 0.00 0.00 0.00 2.18
2624 3068 3.712907 TGGGGCGGGTGTCTTAGC 61.713 66.667 0.00 0.00 0.00 3.09
2625 3069 4.832608 GGGGCGGGTGTCTTAGCG 62.833 72.222 0.00 0.00 0.00 4.26
2626 3070 3.766691 GGGCGGGTGTCTTAGCGA 61.767 66.667 0.00 0.00 0.00 4.93
2627 3071 2.508663 GGCGGGTGTCTTAGCGAC 60.509 66.667 0.00 0.00 43.14 5.19
2628 3072 2.572284 GCGGGTGTCTTAGCGACT 59.428 61.111 0.00 0.00 43.25 4.18
2629 3073 1.080025 GCGGGTGTCTTAGCGACTT 60.080 57.895 0.00 0.00 43.25 3.01
2630 3074 0.171903 GCGGGTGTCTTAGCGACTTA 59.828 55.000 0.00 0.00 43.25 2.24
2631 3075 1.905449 CGGGTGTCTTAGCGACTTAC 58.095 55.000 0.00 0.00 43.25 2.34
2632 3076 1.471684 CGGGTGTCTTAGCGACTTACT 59.528 52.381 0.00 0.00 43.25 2.24
2633 3077 2.731341 CGGGTGTCTTAGCGACTTACTG 60.731 54.545 0.00 0.00 43.25 2.74
2634 3078 2.416972 GGGTGTCTTAGCGACTTACTGG 60.417 54.545 0.00 0.00 43.25 4.00
2635 3079 2.490903 GGTGTCTTAGCGACTTACTGGA 59.509 50.000 0.00 0.00 43.25 3.86
2636 3080 3.427773 GGTGTCTTAGCGACTTACTGGAG 60.428 52.174 0.00 0.00 43.25 3.86
2637 3081 3.439476 GTGTCTTAGCGACTTACTGGAGA 59.561 47.826 0.00 0.00 43.25 3.71
2638 3082 4.077108 TGTCTTAGCGACTTACTGGAGAA 58.923 43.478 0.00 0.00 43.25 2.87
2639 3083 4.156190 TGTCTTAGCGACTTACTGGAGAAG 59.844 45.833 0.00 0.00 43.25 2.85
2640 3084 4.156373 GTCTTAGCGACTTACTGGAGAAGT 59.844 45.833 0.00 0.00 40.06 3.01
2641 3085 4.765856 TCTTAGCGACTTACTGGAGAAGTT 59.234 41.667 0.00 0.00 40.56 2.66
2642 3086 3.305398 AGCGACTTACTGGAGAAGTTG 57.695 47.619 0.00 0.00 40.56 3.16
2644 3088 3.026630 CGACTTACTGGAGAAGTTGCA 57.973 47.619 0.00 0.00 40.56 4.08
2645 3089 3.390135 CGACTTACTGGAGAAGTTGCAA 58.610 45.455 0.00 0.00 40.56 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.229131 ATGGGTCGGAGGGAGTAGTA 58.771 55.000 0.00 0.00 0.00 1.82
46 47 1.229131 TATGGGTCGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
47 48 2.606751 ATATGGGTCGGAGGGAGTAG 57.393 55.000 0.00 0.00 0.00 2.57
117 118 9.656323 TGGGATTAACATACTCTAGTACATCTT 57.344 33.333 0.00 0.00 32.72 2.40
130 131 9.701098 TCGACTATGTATTTGGGATTAACATAC 57.299 33.333 0.00 0.00 33.15 2.39
132 133 9.621629 TTTCGACTATGTATTTGGGATTAACAT 57.378 29.630 0.00 0.00 35.16 2.71
133 134 8.885722 GTTTCGACTATGTATTTGGGATTAACA 58.114 33.333 0.00 0.00 0.00 2.41
134 135 8.340443 GGTTTCGACTATGTATTTGGGATTAAC 58.660 37.037 0.00 0.00 0.00 2.01
415 432 3.044156 CCAGGATGATCCTCCTTCTCAA 58.956 50.000 16.24 0.00 45.66 3.02
416 433 2.687297 CCAGGATGATCCTCCTTCTCA 58.313 52.381 16.24 0.00 45.66 3.27
417 434 1.347378 GCCAGGATGATCCTCCTTCTC 59.653 57.143 16.24 5.69 45.66 2.87
418 435 1.433121 GCCAGGATGATCCTCCTTCT 58.567 55.000 16.24 0.00 45.66 2.85
419 436 0.399833 GGCCAGGATGATCCTCCTTC 59.600 60.000 16.24 11.08 45.66 3.46
420 437 0.029267 AGGCCAGGATGATCCTCCTT 60.029 55.000 16.24 0.00 45.66 3.36
431 448 3.473647 CGGATGCAGAGGCCAGGA 61.474 66.667 5.01 0.00 40.13 3.86
434 451 1.048160 TATGTCGGATGCAGAGGCCA 61.048 55.000 5.01 0.00 40.13 5.36
452 470 8.458052 CCTTTTAATAATATGGACGCATGCATA 58.542 33.333 19.57 8.21 42.60 3.14
477 495 5.458779 GCAGACTTTGTATTTTGTTGACACC 59.541 40.000 0.00 0.00 0.00 4.16
481 499 7.715657 AGATTGCAGACTTTGTATTTTGTTGA 58.284 30.769 0.00 0.00 0.00 3.18
590 900 6.968263 TTACCTGGAGTGATCTAAGATCAG 57.032 41.667 0.00 0.00 0.00 2.90
919 1235 0.526662 GTCGACTCTGATGGAACGGT 59.473 55.000 8.70 0.00 0.00 4.83
953 1269 1.371758 GACAGCGAGCGACTGACAA 60.372 57.895 16.82 0.00 38.55 3.18
1074 1397 3.222855 TTGCCCGCCCAGTTGTTG 61.223 61.111 0.00 0.00 0.00 3.33
1224 1547 3.780173 TCGCGCATGATGGGGTCA 61.780 61.111 8.75 0.00 42.06 4.02
1269 1592 5.499004 AAGTTTCTAACCAGGAGCATGTA 57.501 39.130 0.00 0.00 0.00 2.29
1302 1625 2.046314 ATGACCACCGGGCTTTCG 60.046 61.111 6.32 0.00 37.90 3.46
1303 1626 2.700773 GCATGACCACCGGGCTTTC 61.701 63.158 6.32 0.00 37.90 2.62
1304 1627 2.676471 GCATGACCACCGGGCTTT 60.676 61.111 6.32 0.00 37.90 3.51
1564 1887 2.942752 GCTGATCATGAGCCACAGGAAA 60.943 50.000 8.78 0.00 42.50 3.13
1612 1935 0.392706 TGCAGCAGAAGAAACGGAGA 59.607 50.000 0.00 0.00 0.00 3.71
1658 1981 5.011329 ACCCGACAAAGACATAAGAACACTA 59.989 40.000 0.00 0.00 0.00 2.74
1667 1990 5.813672 GCAGTTTATACCCGACAAAGACATA 59.186 40.000 0.00 0.00 0.00 2.29
1680 2003 5.479306 TCTGAACTCACAGCAGTTTATACC 58.521 41.667 0.00 0.00 36.71 2.73
1798 2123 7.535139 TGACAAAATCGACTGAAAGACTTTTT 58.465 30.769 1.12 0.00 37.43 1.94
1841 2167 0.107654 GGCAGAAGGATTGCGTACCT 60.108 55.000 0.00 0.00 42.42 3.08
1843 2169 1.009829 CTGGCAGAAGGATTGCGTAC 58.990 55.000 9.42 0.00 42.42 3.67
1845 2171 2.042831 GCTGGCAGAAGGATTGCGT 61.043 57.895 20.86 0.00 42.42 5.24
1846 2172 2.768492 GGCTGGCAGAAGGATTGCG 61.768 63.158 20.86 0.00 42.42 4.85
1847 2173 1.679977 TGGCTGGCAGAAGGATTGC 60.680 57.895 20.86 0.00 40.80 3.56
1848 2174 0.323178 AGTGGCTGGCAGAAGGATTG 60.323 55.000 20.86 0.00 0.00 2.67
1849 2175 1.289160 TAGTGGCTGGCAGAAGGATT 58.711 50.000 20.86 0.22 0.00 3.01
1850 2176 1.516110 ATAGTGGCTGGCAGAAGGAT 58.484 50.000 20.86 0.95 0.00 3.24
1857 2186 2.421952 GGAAGATGAATAGTGGCTGGCA 60.422 50.000 0.00 0.00 0.00 4.92
1926 2255 3.562176 GGGATGATCAGGTCAAACAAGGT 60.562 47.826 0.09 0.00 40.97 3.50
2153 2484 9.722184 TGATAAGCAATCCAATCAATTTCAAAA 57.278 25.926 0.00 0.00 33.22 2.44
2154 2485 9.153721 GTGATAAGCAATCCAATCAATTTCAAA 57.846 29.630 0.00 0.00 33.22 2.69
2155 2486 8.312564 TGTGATAAGCAATCCAATCAATTTCAA 58.687 29.630 0.00 0.00 33.22 2.69
2156 2487 7.838884 TGTGATAAGCAATCCAATCAATTTCA 58.161 30.769 0.00 0.00 33.22 2.69
2157 2488 8.761497 CATGTGATAAGCAATCCAATCAATTTC 58.239 33.333 0.00 0.00 33.22 2.17
2158 2489 8.262227 ACATGTGATAAGCAATCCAATCAATTT 58.738 29.630 0.00 0.00 33.22 1.82
2159 2490 7.709182 CACATGTGATAAGCAATCCAATCAATT 59.291 33.333 21.64 0.00 33.22 2.32
2160 2491 7.147794 ACACATGTGATAAGCAATCCAATCAAT 60.148 33.333 31.94 0.00 33.22 2.57
2161 2492 6.153170 ACACATGTGATAAGCAATCCAATCAA 59.847 34.615 31.94 0.00 33.22 2.57
2162 2493 5.653330 ACACATGTGATAAGCAATCCAATCA 59.347 36.000 31.94 0.00 33.22 2.57
2163 2494 6.140303 ACACATGTGATAAGCAATCCAATC 57.860 37.500 31.94 0.00 33.22 2.67
2164 2495 6.534475 AACACATGTGATAAGCAATCCAAT 57.466 33.333 31.94 1.18 33.22 3.16
2165 2496 5.981088 AACACATGTGATAAGCAATCCAA 57.019 34.783 31.94 0.00 33.22 3.53
2166 2497 5.064579 CGTAACACATGTGATAAGCAATCCA 59.935 40.000 31.94 0.00 33.22 3.41
2167 2498 5.064707 ACGTAACACATGTGATAAGCAATCC 59.935 40.000 31.94 9.74 33.22 3.01
2168 2499 5.959527 CACGTAACACATGTGATAAGCAATC 59.040 40.000 31.94 10.41 45.57 2.67
2169 2500 5.673568 GCACGTAACACATGTGATAAGCAAT 60.674 40.000 31.94 8.58 45.57 3.56
2170 2501 4.377943 GCACGTAACACATGTGATAAGCAA 60.378 41.667 31.94 1.87 45.57 3.91
2171 2502 3.124466 GCACGTAACACATGTGATAAGCA 59.876 43.478 31.94 2.28 45.57 3.91
2172 2503 3.370978 AGCACGTAACACATGTGATAAGC 59.629 43.478 31.94 24.38 45.57 3.09
2173 2504 6.641176 TTAGCACGTAACACATGTGATAAG 57.359 37.500 31.94 25.96 45.49 1.73
2175 2506 5.471257 TGTTAGCACGTAACACATGTGATA 58.529 37.500 31.94 21.57 45.07 2.15
2176 2507 4.311606 TGTTAGCACGTAACACATGTGAT 58.688 39.130 31.94 22.71 45.07 3.06
2177 2508 3.718815 TGTTAGCACGTAACACATGTGA 58.281 40.909 31.94 8.09 45.07 3.58
2185 2516 5.069485 TCGAGTTTTTGTTAGCACGTAAC 57.931 39.130 0.00 0.00 41.45 2.50
2186 2517 5.910637 ATCGAGTTTTTGTTAGCACGTAA 57.089 34.783 0.00 0.00 0.00 3.18
2187 2518 5.672051 CAATCGAGTTTTTGTTAGCACGTA 58.328 37.500 0.00 0.00 0.00 3.57
2188 2519 4.523813 CAATCGAGTTTTTGTTAGCACGT 58.476 39.130 0.00 0.00 0.00 4.49
2189 2520 3.357823 GCAATCGAGTTTTTGTTAGCACG 59.642 43.478 0.00 0.00 0.00 5.34
2190 2521 4.286910 TGCAATCGAGTTTTTGTTAGCAC 58.713 39.130 0.00 0.00 0.00 4.40
2191 2522 4.560136 TGCAATCGAGTTTTTGTTAGCA 57.440 36.364 0.00 0.00 0.00 3.49
2192 2523 5.153513 TCATGCAATCGAGTTTTTGTTAGC 58.846 37.500 0.00 0.00 0.00 3.09
2193 2524 6.602179 TCTCATGCAATCGAGTTTTTGTTAG 58.398 36.000 10.03 0.00 0.00 2.34
2194 2525 6.552859 TCTCATGCAATCGAGTTTTTGTTA 57.447 33.333 10.03 0.00 0.00 2.41
2195 2526 5.437289 TCTCATGCAATCGAGTTTTTGTT 57.563 34.783 10.03 0.00 0.00 2.83
2196 2527 5.437289 TTCTCATGCAATCGAGTTTTTGT 57.563 34.783 10.03 0.00 0.00 2.83
2197 2528 6.939551 ATTTCTCATGCAATCGAGTTTTTG 57.060 33.333 10.03 0.00 0.00 2.44
2198 2529 9.643693 ATTTATTTCTCATGCAATCGAGTTTTT 57.356 25.926 10.03 0.00 0.00 1.94
2199 2530 9.079833 CATTTATTTCTCATGCAATCGAGTTTT 57.920 29.630 10.03 1.57 0.00 2.43
2200 2531 8.246180 ACATTTATTTCTCATGCAATCGAGTTT 58.754 29.630 10.03 1.83 0.00 2.66
2201 2532 7.699391 CACATTTATTTCTCATGCAATCGAGTT 59.301 33.333 10.03 2.09 0.00 3.01
2202 2533 7.191551 CACATTTATTTCTCATGCAATCGAGT 58.808 34.615 10.03 0.00 0.00 4.18
2206 2537 6.278363 AGGCACATTTATTTCTCATGCAATC 58.722 36.000 0.00 0.00 33.24 2.67
2258 2698 7.206687 GGTTACTTGTCAACCATCATTTTCAA 58.793 34.615 0.00 0.00 44.12 2.69
2259 2699 6.514212 CGGTTACTTGTCAACCATCATTTTCA 60.514 38.462 5.21 0.00 44.80 2.69
2262 2702 5.048991 GTCGGTTACTTGTCAACCATCATTT 60.049 40.000 5.21 0.00 44.80 2.32
2278 2718 2.414161 GCTGCAAGGATTTGTCGGTTAC 60.414 50.000 0.00 0.00 36.65 2.50
2321 2761 3.224324 GGCCGGCCACGATCTAGA 61.224 66.667 40.73 0.00 44.60 2.43
2527 2971 4.590647 TGGAGAGGCAAGATCCTAACTATG 59.409 45.833 0.00 0.00 36.38 2.23
2528 2972 4.820775 TGGAGAGGCAAGATCCTAACTAT 58.179 43.478 0.00 0.00 36.38 2.12
2529 2973 4.265856 TGGAGAGGCAAGATCCTAACTA 57.734 45.455 0.00 0.00 36.38 2.24
2530 2974 3.121929 TGGAGAGGCAAGATCCTAACT 57.878 47.619 0.00 0.00 36.38 2.24
2531 2975 4.429854 AATGGAGAGGCAAGATCCTAAC 57.570 45.455 0.00 0.00 36.38 2.34
2532 2976 5.219739 ACTAATGGAGAGGCAAGATCCTAA 58.780 41.667 0.00 0.00 36.38 2.69
2533 2977 4.820775 ACTAATGGAGAGGCAAGATCCTA 58.179 43.478 0.00 0.00 36.38 2.94
2534 2978 3.663198 ACTAATGGAGAGGCAAGATCCT 58.337 45.455 0.00 0.00 39.67 3.24
2535 2979 5.337975 GGATACTAATGGAGAGGCAAGATCC 60.338 48.000 0.00 0.00 0.00 3.36
2536 2980 5.337975 GGGATACTAATGGAGAGGCAAGATC 60.338 48.000 0.00 0.00 0.00 2.75
2537 2981 4.534103 GGGATACTAATGGAGAGGCAAGAT 59.466 45.833 0.00 0.00 0.00 2.40
2538 2982 3.904339 GGGATACTAATGGAGAGGCAAGA 59.096 47.826 0.00 0.00 0.00 3.02
2539 2983 3.008485 GGGGATACTAATGGAGAGGCAAG 59.992 52.174 0.00 0.00 0.00 4.01
2540 2984 2.979678 GGGGATACTAATGGAGAGGCAA 59.020 50.000 0.00 0.00 0.00 4.52
2541 2985 2.621070 GGGGATACTAATGGAGAGGCA 58.379 52.381 0.00 0.00 0.00 4.75
2542 2986 1.909986 GGGGGATACTAATGGAGAGGC 59.090 57.143 0.00 0.00 0.00 4.70
2543 2987 3.569135 AGGGGGATACTAATGGAGAGG 57.431 52.381 0.00 0.00 0.00 3.69
2544 2988 4.773149 GTGTAGGGGGATACTAATGGAGAG 59.227 50.000 0.00 0.00 0.00 3.20
2545 2989 4.422592 AGTGTAGGGGGATACTAATGGAGA 59.577 45.833 0.00 0.00 0.00 3.71
2546 2990 4.753186 AGTGTAGGGGGATACTAATGGAG 58.247 47.826 0.00 0.00 0.00 3.86
2547 2991 4.845530 AGTGTAGGGGGATACTAATGGA 57.154 45.455 0.00 0.00 0.00 3.41
2548 2992 6.500751 ACAATAGTGTAGGGGGATACTAATGG 59.499 42.308 0.00 0.00 35.72 3.16
2549 2993 7.234782 TGACAATAGTGTAGGGGGATACTAATG 59.765 40.741 0.00 0.00 38.41 1.90
2550 2994 7.310634 TGACAATAGTGTAGGGGGATACTAAT 58.689 38.462 0.00 0.00 38.41 1.73
2551 2995 6.685541 TGACAATAGTGTAGGGGGATACTAA 58.314 40.000 0.00 0.00 38.41 2.24
2552 2996 6.103649 TCTGACAATAGTGTAGGGGGATACTA 59.896 42.308 0.00 0.00 38.41 1.82
2553 2997 5.103215 TCTGACAATAGTGTAGGGGGATACT 60.103 44.000 0.00 0.00 38.41 2.12
2554 2998 5.010820 GTCTGACAATAGTGTAGGGGGATAC 59.989 48.000 2.24 0.00 38.41 2.24
2555 2999 5.103215 AGTCTGACAATAGTGTAGGGGGATA 60.103 44.000 10.88 0.00 38.41 2.59
2556 3000 3.967987 GTCTGACAATAGTGTAGGGGGAT 59.032 47.826 2.24 0.00 38.41 3.85
2557 3001 3.012502 AGTCTGACAATAGTGTAGGGGGA 59.987 47.826 10.88 0.00 38.41 4.81
2558 3002 3.375699 AGTCTGACAATAGTGTAGGGGG 58.624 50.000 10.88 0.00 38.41 5.40
2559 3003 5.892119 TCTAAGTCTGACAATAGTGTAGGGG 59.108 44.000 10.88 0.00 38.41 4.79
2560 3004 7.259161 GTTCTAAGTCTGACAATAGTGTAGGG 58.741 42.308 10.88 0.00 38.41 3.53
2561 3005 7.093902 TGGTTCTAAGTCTGACAATAGTGTAGG 60.094 40.741 10.88 0.00 38.41 3.18
2562 3006 7.755822 GTGGTTCTAAGTCTGACAATAGTGTAG 59.244 40.741 10.88 0.00 38.41 2.74
2563 3007 7.574404 CGTGGTTCTAAGTCTGACAATAGTGTA 60.574 40.741 10.88 1.22 38.41 2.90
2564 3008 6.456501 GTGGTTCTAAGTCTGACAATAGTGT 58.543 40.000 10.88 0.00 42.10 3.55
2565 3009 5.573282 CGTGGTTCTAAGTCTGACAATAGTG 59.427 44.000 10.88 0.00 0.00 2.74
2566 3010 5.475909 TCGTGGTTCTAAGTCTGACAATAGT 59.524 40.000 10.88 0.00 0.00 2.12
2567 3011 5.800941 GTCGTGGTTCTAAGTCTGACAATAG 59.199 44.000 10.88 11.57 0.00 1.73
2568 3012 5.242171 TGTCGTGGTTCTAAGTCTGACAATA 59.758 40.000 10.88 2.15 32.68 1.90
2569 3013 4.038763 TGTCGTGGTTCTAAGTCTGACAAT 59.961 41.667 10.88 0.96 32.68 2.71
2570 3014 3.382227 TGTCGTGGTTCTAAGTCTGACAA 59.618 43.478 10.88 0.00 32.68 3.18
2571 3015 2.953648 TGTCGTGGTTCTAAGTCTGACA 59.046 45.455 10.88 0.00 33.14 3.58
2572 3016 3.004524 ACTGTCGTGGTTCTAAGTCTGAC 59.995 47.826 0.00 0.00 0.00 3.51
2573 3017 3.220110 ACTGTCGTGGTTCTAAGTCTGA 58.780 45.455 0.00 0.00 0.00 3.27
2574 3018 3.644884 ACTGTCGTGGTTCTAAGTCTG 57.355 47.619 0.00 0.00 0.00 3.51
2575 3019 3.243771 CCAACTGTCGTGGTTCTAAGTCT 60.244 47.826 0.00 0.00 0.00 3.24
2576 3020 3.057734 CCAACTGTCGTGGTTCTAAGTC 58.942 50.000 0.00 0.00 0.00 3.01
2577 3021 2.805657 GCCAACTGTCGTGGTTCTAAGT 60.806 50.000 0.84 0.00 0.00 2.24
2578 3022 1.798813 GCCAACTGTCGTGGTTCTAAG 59.201 52.381 0.84 0.00 0.00 2.18
2579 3023 1.870580 CGCCAACTGTCGTGGTTCTAA 60.871 52.381 0.84 0.00 0.00 2.10
2580 3024 0.319211 CGCCAACTGTCGTGGTTCTA 60.319 55.000 0.84 0.00 0.00 2.10
2581 3025 1.594293 CGCCAACTGTCGTGGTTCT 60.594 57.895 0.84 0.00 0.00 3.01
2582 3026 2.935955 CGCCAACTGTCGTGGTTC 59.064 61.111 0.84 0.00 0.00 3.62
2583 3027 3.276846 GCGCCAACTGTCGTGGTT 61.277 61.111 0.00 0.00 0.00 3.67
2605 3049 3.659089 CTAAGACACCCGCCCCACG 62.659 68.421 0.00 0.00 43.15 4.94
2606 3050 2.267961 CTAAGACACCCGCCCCAC 59.732 66.667 0.00 0.00 0.00 4.61
2607 3051 3.712907 GCTAAGACACCCGCCCCA 61.713 66.667 0.00 0.00 0.00 4.96
2608 3052 4.832608 CGCTAAGACACCCGCCCC 62.833 72.222 0.00 0.00 0.00 5.80
2609 3053 3.766691 TCGCTAAGACACCCGCCC 61.767 66.667 0.00 0.00 0.00 6.13
2615 3059 8.223951 ACTTCTCCAGTAAGTCGCTAAGACAC 62.224 46.154 1.00 0.00 42.74 3.67
2616 3060 6.265967 ACTTCTCCAGTAAGTCGCTAAGACA 61.266 44.000 1.00 0.00 42.74 3.41
2617 3061 4.156373 ACTTCTCCAGTAAGTCGCTAAGAC 59.844 45.833 0.00 0.00 41.47 3.01
2618 3062 4.333690 ACTTCTCCAGTAAGTCGCTAAGA 58.666 43.478 0.00 0.00 31.56 2.10
2619 3063 4.705337 ACTTCTCCAGTAAGTCGCTAAG 57.295 45.455 0.00 0.00 31.56 2.18
2620 3064 4.806330 CAACTTCTCCAGTAAGTCGCTAA 58.194 43.478 0.00 0.00 36.17 3.09
2621 3065 3.367087 GCAACTTCTCCAGTAAGTCGCTA 60.367 47.826 0.00 0.00 34.71 4.26
2622 3066 2.610727 GCAACTTCTCCAGTAAGTCGCT 60.611 50.000 0.00 0.00 34.71 4.93
2623 3067 1.727335 GCAACTTCTCCAGTAAGTCGC 59.273 52.381 0.00 0.00 36.17 5.19
2624 3068 3.026630 TGCAACTTCTCCAGTAAGTCG 57.973 47.619 0.00 0.00 36.17 4.18


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

AutoCloner maintained by Alex Coulton.