Multiple sequence alignment - TraesCS7D01G342500

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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 TraesCS7D01G342500 chr7D 100.000 3107 0 0 1 3107 438746676 438749782 0.000000e+00 5738.0
1 TraesCS7D01G342500 chr7A 84.947 2438 157 88 23 2362 490163651 490165976 0.000000e+00 2276.0
2 TraesCS7D01G342500 chr7A 84.536 679 76 8 2398 3050 490166107 490166782 0.000000e+00 645.0
3 TraesCS7D01G342500 chr7A 100.000 39 0 0 3069 3107 490166783 490166821 4.300000e-09 73.1
4 TraesCS7D01G342500 chr7B 90.188 1488 98 16 639 2117 454791427 454789979 0.000000e+00 1895.0
5 TraesCS7D01G342500 chr7B 86.945 743 84 6 2375 3107 454729807 454729068 0.000000e+00 822.0
6 TraesCS7D01G342500 chr7B 87.224 634 32 17 23 639 454793165 454792564 0.000000e+00 676.0
7 TraesCS7D01G342500 chr7B 88.462 52 4 2 2302 2352 454729853 454729803 9.300000e-06 62.1


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 TraesCS7D01G342500 chr7D 438746676 438749782 3106 False 5738.000000 5738 100.000000 1 3107 1 chr7D.!!$F1 3106
1 TraesCS7D01G342500 chr7A 490163651 490166821 3170 False 998.033333 2276 89.827667 23 3107 3 chr7A.!!$F1 3084
2 TraesCS7D01G342500 chr7B 454789979 454793165 3186 True 1285.500000 1895 88.706000 23 2117 2 chr7B.!!$R2 2094
3 TraesCS7D01G342500 chr7B 454729068 454729853 785 True 442.050000 822 87.703500 2302 3107 2 chr7B.!!$R1 805

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
733 1906 0.110486 AACTCACCCACCATGTCACC 59.89 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2445 3801 0.033796 ATGGCCCATCACTCTTGGTG 60.034 55.0 0.0 0.0 46.6 4.17 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
41 42 5.698545 AGCTCCTCTATCGATGCAATAAAAC 59.301 40.000 8.54 0.00 0.00 2.43
86 89 4.884744 TGAAGAAGAAAATTCGGAACACCA 59.115 37.500 0.00 0.00 0.00 4.17
90 93 2.946990 AGAAAATTCGGAACACCAACGT 59.053 40.909 0.00 0.00 0.00 3.99
95 98 2.886862 TCGGAACACCAACGTAAGAA 57.113 45.000 0.00 0.00 43.62 2.52
107 110 8.098912 ACACCAACGTAAGAATACCTCTTTATT 58.901 33.333 0.00 0.00 41.97 1.40
202 209 4.028993 GTTCCCACCATTCAAGAACCTA 57.971 45.455 0.00 0.00 32.53 3.08
225 232 5.698741 TGGGAATTGAATCTTCTGAGCTA 57.301 39.130 0.00 0.00 0.00 3.32
230 237 7.387397 GGGAATTGAATCTTCTGAGCTATAGTG 59.613 40.741 0.84 0.00 0.00 2.74
231 238 8.147058 GGAATTGAATCTTCTGAGCTATAGTGA 58.853 37.037 0.84 0.00 0.00 3.41
256 263 2.831685 TCAGCGCTTTCCTTGTTCTA 57.168 45.000 7.50 0.00 0.00 2.10
257 264 2.413837 TCAGCGCTTTCCTTGTTCTAC 58.586 47.619 7.50 0.00 0.00 2.59
258 265 2.143122 CAGCGCTTTCCTTGTTCTACA 58.857 47.619 7.50 0.00 0.00 2.74
259 266 2.158449 CAGCGCTTTCCTTGTTCTACAG 59.842 50.000 7.50 0.00 0.00 2.74
260 267 2.037251 AGCGCTTTCCTTGTTCTACAGA 59.963 45.455 2.64 0.00 0.00 3.41
261 268 2.806244 GCGCTTTCCTTGTTCTACAGAA 59.194 45.455 0.00 0.00 0.00 3.02
262 269 3.120511 GCGCTTTCCTTGTTCTACAGAAG 60.121 47.826 0.00 0.00 34.27 2.85
263 270 4.058817 CGCTTTCCTTGTTCTACAGAAGT 58.941 43.478 0.00 0.00 34.27 3.01
264 271 5.227908 CGCTTTCCTTGTTCTACAGAAGTA 58.772 41.667 0.00 0.00 34.27 2.24
310 318 2.038975 ACTTGGCGCCCCTCTCTA 59.961 61.111 26.77 0.00 0.00 2.43
313 321 1.048601 CTTGGCGCCCCTCTCTATTA 58.951 55.000 26.77 0.00 0.00 0.98
315 323 1.729586 TGGCGCCCCTCTCTATTATT 58.270 50.000 26.77 0.00 0.00 1.40
317 325 2.565834 TGGCGCCCCTCTCTATTATTAC 59.434 50.000 26.77 0.00 0.00 1.89
318 326 2.832733 GGCGCCCCTCTCTATTATTACT 59.167 50.000 18.11 0.00 0.00 2.24
320 328 4.142204 GGCGCCCCTCTCTATTATTACTAC 60.142 50.000 18.11 0.00 0.00 2.73
321 329 4.705991 GCGCCCCTCTCTATTATTACTACT 59.294 45.833 0.00 0.00 0.00 2.57
322 330 5.884792 GCGCCCCTCTCTATTATTACTACTA 59.115 44.000 0.00 0.00 0.00 1.82
323 331 6.376581 GCGCCCCTCTCTATTATTACTACTAA 59.623 42.308 0.00 0.00 0.00 2.24
324 332 7.094032 GCGCCCCTCTCTATTATTACTACTAAA 60.094 40.741 0.00 0.00 0.00 1.85
325 333 8.242739 CGCCCCTCTCTATTATTACTACTAAAC 58.757 40.741 0.00 0.00 0.00 2.01
356 364 2.827555 GTCTTTGAGACGTTGATTGCG 58.172 47.619 0.00 0.00 35.28 4.85
412 427 2.670934 GAGTGGGTGTGCAGGCAG 60.671 66.667 0.00 0.00 0.00 4.85
413 428 4.275508 AGTGGGTGTGCAGGCAGG 62.276 66.667 0.00 0.00 0.00 4.85
447 462 3.588955 CCGGCCCGTACCTAATAAATAC 58.411 50.000 0.85 0.00 0.00 1.89
450 465 4.488879 GGCCCGTACCTAATAAATACTCG 58.511 47.826 0.00 0.00 0.00 4.18
454 469 6.317857 CCCGTACCTAATAAATACTCGTAGC 58.682 44.000 0.00 0.00 0.00 3.58
464 493 1.731433 TACTCGTAGCGGTCATGGGC 61.731 60.000 0.00 0.00 0.00 5.36
476 505 0.824109 TCATGGGCGGAGTAACTCTG 59.176 55.000 0.00 0.00 39.66 3.35
710 1880 2.664185 CATGGCCGGATCGAGCTG 60.664 66.667 5.05 1.51 0.00 4.24
727 1900 1.279271 GCTGACTAACTCACCCACCAT 59.721 52.381 0.00 0.00 0.00 3.55
728 1901 2.936993 GCTGACTAACTCACCCACCATG 60.937 54.545 0.00 0.00 0.00 3.66
729 1902 2.303022 CTGACTAACTCACCCACCATGT 59.697 50.000 0.00 0.00 0.00 3.21
731 1904 2.301870 GACTAACTCACCCACCATGTCA 59.698 50.000 0.00 0.00 0.00 3.58
732 1905 2.038557 ACTAACTCACCCACCATGTCAC 59.961 50.000 0.00 0.00 0.00 3.67
733 1906 0.110486 AACTCACCCACCATGTCACC 59.890 55.000 0.00 0.00 0.00 4.02
734 1907 1.059584 ACTCACCCACCATGTCACCA 61.060 55.000 0.00 0.00 0.00 4.17
735 1908 0.329261 CTCACCCACCATGTCACCAT 59.671 55.000 0.00 0.00 0.00 3.55
748 1921 5.048782 CCATGTCACCATTATCCATTAACGG 60.049 44.000 0.00 0.00 0.00 4.44
945 2149 4.552365 ATGCTCCCATCCGCGGTG 62.552 66.667 27.15 21.41 0.00 4.94
1022 2230 2.202797 CGGCACCTGACCTGATCG 60.203 66.667 0.00 0.00 0.00 3.69
1085 2300 2.568956 TGGAGATGGAGGTGAGTCAAAG 59.431 50.000 0.00 0.00 0.00 2.77
1086 2301 2.834549 GGAGATGGAGGTGAGTCAAAGA 59.165 50.000 0.00 0.00 0.00 2.52
1087 2302 3.368948 GGAGATGGAGGTGAGTCAAAGAC 60.369 52.174 0.00 0.00 0.00 3.01
1088 2303 3.513515 GAGATGGAGGTGAGTCAAAGACT 59.486 47.826 0.00 0.00 46.42 3.24
1143 2361 5.407995 AGCTCGTACTAGTATATCGTTGGAC 59.592 44.000 5.75 0.00 0.00 4.02
1254 2475 0.036164 TGCCCATCACGCAGTACTTT 59.964 50.000 0.00 0.00 41.61 2.66
1394 2615 4.293626 GGCACGCACACACGACAC 62.294 66.667 0.00 0.00 36.70 3.67
1395 2616 4.627114 GCACGCACACACGACACG 62.627 66.667 0.00 0.00 36.70 4.49
1396 2617 2.952264 CACGCACACACGACACGA 60.952 61.111 0.00 0.00 36.70 4.35
1397 2618 2.952783 ACGCACACACGACACGAC 60.953 61.111 0.00 0.00 36.70 4.34
1398 2619 2.952264 CGCACACACGACACGACA 60.952 61.111 0.00 0.00 34.06 4.35
1410 2632 0.667993 ACACGACATGCTTGGGTTTG 59.332 50.000 4.44 0.00 0.00 2.93
1450 2672 4.652822 GTCACCTTTTAGGATGGAGTTGT 58.347 43.478 0.00 0.00 37.67 3.32
1453 2675 5.783360 TCACCTTTTAGGATGGAGTTGTCTA 59.217 40.000 0.00 0.00 37.67 2.59
1457 2679 7.829706 ACCTTTTAGGATGGAGTTGTCTAATTC 59.170 37.037 0.00 0.00 37.67 2.17
1466 2689 4.159135 GGAGTTGTCTAATTCGGTCTGGTA 59.841 45.833 0.00 0.00 0.00 3.25
1595 2818 2.970324 GCTGACACCGCGACCAAA 60.970 61.111 8.23 0.00 0.00 3.28
1598 2821 2.963320 GACACCGCGACCAAACGT 60.963 61.111 8.23 0.00 35.59 3.99
1602 2825 4.659874 CCGCGACCAAACGTGTGC 62.660 66.667 8.23 0.00 41.30 4.57
1709 2937 0.535335 TACAAACCCCTGCTCTAGCG 59.465 55.000 0.00 0.00 45.83 4.26
1765 2994 4.705110 TTTGTTCAGATGAGGAAGGTGA 57.295 40.909 0.00 0.00 0.00 4.02
1851 3080 6.207025 GGCTTATCATCTTCAAGCTTCATCAT 59.793 38.462 0.00 0.00 43.33 2.45
1852 3081 7.299586 GCTTATCATCTTCAAGCTTCATCATC 58.700 38.462 0.00 0.00 41.14 2.92
1853 3082 7.041303 GCTTATCATCTTCAAGCTTCATCATCA 60.041 37.037 0.00 0.00 41.14 3.07
1854 3083 6.869315 ATCATCTTCAAGCTTCATCATCAG 57.131 37.500 0.00 0.00 0.00 2.90
1855 3084 5.985911 TCATCTTCAAGCTTCATCATCAGA 58.014 37.500 0.00 0.00 0.00 3.27
1856 3085 6.412214 TCATCTTCAAGCTTCATCATCAGAA 58.588 36.000 0.00 0.00 0.00 3.02
1857 3086 7.054751 TCATCTTCAAGCTTCATCATCAGAAT 58.945 34.615 0.00 0.00 0.00 2.40
1921 3150 1.640917 ACTTCTCTGTTCGCCCCTAA 58.359 50.000 0.00 0.00 0.00 2.69
1927 3156 1.626321 TCTGTTCGCCCCTAATTGTCA 59.374 47.619 0.00 0.00 0.00 3.58
1951 3180 4.563786 GGCTCTACAACTAGCTTCCACTTT 60.564 45.833 0.00 0.00 38.80 2.66
1957 3186 4.338400 ACAACTAGCTTCCACTTTTCAACC 59.662 41.667 0.00 0.00 0.00 3.77
1962 3191 2.031944 GCTTCCACTTTTCAACCGAGTC 60.032 50.000 0.00 0.00 0.00 3.36
1964 3193 3.107642 TCCACTTTTCAACCGAGTCTC 57.892 47.619 0.00 0.00 0.00 3.36
2036 3269 8.508883 AACTTGTGTGTGTATTACTACCAAAA 57.491 30.769 0.00 0.00 0.00 2.44
2039 3272 7.956420 TGTGTGTGTATTACTACCAAAAGAG 57.044 36.000 0.00 0.00 0.00 2.85
2117 3350 3.243535 GCTAAAGCCAGCACTTTTGTTCT 60.244 43.478 4.95 0.00 40.32 3.01
2119 3352 2.355010 AGCCAGCACTTTTGTTCTCT 57.645 45.000 0.00 0.00 0.00 3.10
2125 3358 4.800471 CCAGCACTTTTGTTCTCTTTGTTC 59.200 41.667 0.00 0.00 0.00 3.18
2128 3361 4.351192 CACTTTTGTTCTCTTTGTTCCCG 58.649 43.478 0.00 0.00 0.00 5.14
2134 3367 3.263261 GTTCTCTTTGTTCCCGGATCTC 58.737 50.000 0.73 0.00 0.00 2.75
2138 3371 0.248289 TTTGTTCCCGGATCTCGACC 59.752 55.000 0.73 0.00 42.43 4.79
2154 3387 0.586802 GACCACCAACTTGAACTCGC 59.413 55.000 0.00 0.00 0.00 5.03
2155 3388 0.107410 ACCACCAACTTGAACTCGCA 60.107 50.000 0.00 0.00 0.00 5.10
2156 3389 1.021202 CCACCAACTTGAACTCGCAA 58.979 50.000 0.00 0.00 0.00 4.85
2157 3390 1.608590 CCACCAACTTGAACTCGCAAT 59.391 47.619 0.00 0.00 0.00 3.56
2196 3429 5.612725 AGGCTTGAAAATTCCTTGTTTCA 57.387 34.783 0.00 0.00 40.93 2.69
2198 3431 5.817296 AGGCTTGAAAATTCCTTGTTTCAAC 59.183 36.000 7.32 5.62 44.63 3.18
2200 3433 6.238184 GGCTTGAAAATTCCTTGTTTCAACTG 60.238 38.462 7.32 2.03 44.63 3.16
2210 3443 5.768164 TCCTTGTTTCAACTGGTAAATCCTC 59.232 40.000 0.00 0.00 37.07 3.71
2217 3450 5.902681 TCAACTGGTAAATCCTCGTATGAG 58.097 41.667 4.85 4.85 42.18 2.90
2226 3459 7.648510 GGTAAATCCTCGTATGAGTTAGAGTTG 59.351 40.741 11.03 0.00 40.85 3.16
2228 3461 5.814764 TCCTCGTATGAGTTAGAGTTGTC 57.185 43.478 11.03 0.00 40.85 3.18
2229 3462 5.498393 TCCTCGTATGAGTTAGAGTTGTCT 58.502 41.667 11.03 0.00 40.85 3.41
2232 3465 6.528423 CCTCGTATGAGTTAGAGTTGTCTTTG 59.472 42.308 11.03 0.00 40.85 2.77
2233 3466 7.210718 TCGTATGAGTTAGAGTTGTCTTTGA 57.789 36.000 0.00 0.00 33.84 2.69
2234 3467 7.306213 TCGTATGAGTTAGAGTTGTCTTTGAG 58.694 38.462 0.00 0.00 33.84 3.02
2236 3469 5.871396 TGAGTTAGAGTTGTCTTTGAGGT 57.129 39.130 0.00 0.00 33.84 3.85
2237 3470 5.601662 TGAGTTAGAGTTGTCTTTGAGGTG 58.398 41.667 0.00 0.00 33.84 4.00
2238 3471 5.128827 TGAGTTAGAGTTGTCTTTGAGGTGT 59.871 40.000 0.00 0.00 33.84 4.16
2239 3472 5.360591 AGTTAGAGTTGTCTTTGAGGTGTG 58.639 41.667 0.00 0.00 33.84 3.82
2240 3473 3.914426 AGAGTTGTCTTTGAGGTGTGT 57.086 42.857 0.00 0.00 0.00 3.72
2241 3474 6.097839 AGTTAGAGTTGTCTTTGAGGTGTGTA 59.902 38.462 0.00 0.00 33.84 2.90
2242 3475 4.950050 AGAGTTGTCTTTGAGGTGTGTAG 58.050 43.478 0.00 0.00 0.00 2.74
2251 3484 6.586844 GTCTTTGAGGTGTGTAGTATGAGTTC 59.413 42.308 0.00 0.00 0.00 3.01
2253 3486 4.329392 TGAGGTGTGTAGTATGAGTTCGA 58.671 43.478 0.00 0.00 0.00 3.71
2362 3596 4.193240 AACCAGATTTGGGTTAACACCT 57.807 40.909 5.16 0.00 43.82 4.00
2363 3597 4.552674 AACCAGATTTGGGTTAACACCTT 58.447 39.130 5.16 0.00 43.82 3.50
2364 3598 4.966168 AACCAGATTTGGGTTAACACCTTT 59.034 37.500 5.16 0.00 43.82 3.11
2365 3599 5.427157 AACCAGATTTGGGTTAACACCTTTT 59.573 36.000 5.16 0.00 43.82 2.27
2366 3600 5.924356 CCAGATTTGGGTTAACACCTTTTT 58.076 37.500 5.16 0.00 43.65 1.94
2388 3622 7.687005 TTTTAGGCAAATTTGAGTTAACACG 57.313 32.000 22.31 0.00 0.00 4.49
2424 3780 0.676782 GGCCAACGATTGTAGTGCCT 60.677 55.000 0.00 0.00 34.83 4.75
2425 3781 0.447801 GCCAACGATTGTAGTGCCTG 59.552 55.000 0.00 0.00 0.00 4.85
2430 3786 1.269166 CGATTGTAGTGCCTGTCGAC 58.731 55.000 9.11 9.11 0.00 4.20
2433 3789 0.973632 TTGTAGTGCCTGTCGACCAT 59.026 50.000 14.12 0.00 0.00 3.55
2438 3794 4.587262 TGTAGTGCCTGTCGACCATATTAT 59.413 41.667 14.12 0.00 0.00 1.28
2445 3801 7.063544 GTGCCTGTCGACCATATTATAATTCTC 59.936 40.741 14.12 0.00 0.00 2.87
2446 3802 7.097192 GCCTGTCGACCATATTATAATTCTCA 58.903 38.462 14.12 0.00 0.00 3.27
2447 3803 7.063544 GCCTGTCGACCATATTATAATTCTCAC 59.936 40.741 14.12 0.00 0.00 3.51
2466 3822 0.754217 CCAAGAGTGATGGGCCATGG 60.754 60.000 26.77 15.15 34.15 3.66
2470 3826 0.548031 GAGTGATGGGCCATGGAAGA 59.452 55.000 26.77 0.00 0.00 2.87
2474 3830 3.205056 AGTGATGGGCCATGGAAGATTTA 59.795 43.478 26.77 0.00 0.00 1.40
2485 3841 6.539464 GCCATGGAAGATTTATGCAAATGAAA 59.461 34.615 18.40 0.00 34.44 2.69
2486 3842 7.066043 GCCATGGAAGATTTATGCAAATGAAAA 59.934 33.333 18.40 0.00 34.44 2.29
2520 3876 1.922447 TGTCTCACCTGGCCCATTTAT 59.078 47.619 0.00 0.00 0.00 1.40
2521 3877 2.301346 GTCTCACCTGGCCCATTTATG 58.699 52.381 0.00 0.00 0.00 1.90
2540 3898 2.610873 TGGGCCATATATACACCGTCA 58.389 47.619 0.00 0.00 0.00 4.35
2543 3901 3.765511 GGGCCATATATACACCGTCACTA 59.234 47.826 4.39 0.00 0.00 2.74
2547 3905 6.127423 GGCCATATATACACCGTCACTAAGAT 60.127 42.308 0.00 0.00 0.00 2.40
2590 3971 0.761802 TACACACCACAGGCACATCA 59.238 50.000 0.00 0.00 0.00 3.07
2609 3990 3.807553 TCAAGCTTGACATGAACACAGA 58.192 40.909 25.16 0.00 31.01 3.41
2610 3991 4.392047 TCAAGCTTGACATGAACACAGAT 58.608 39.130 25.16 0.00 31.01 2.90
2619 4000 7.742556 TGACATGAACACAGATTCAACATAA 57.257 32.000 0.00 0.00 41.78 1.90
2627 4008 4.094887 CACAGATTCAACATAAAGGACCCG 59.905 45.833 0.00 0.00 0.00 5.28
2628 4009 4.019681 ACAGATTCAACATAAAGGACCCGA 60.020 41.667 0.00 0.00 0.00 5.14
2629 4010 4.941263 CAGATTCAACATAAAGGACCCGAA 59.059 41.667 0.00 0.00 0.00 4.30
2630 4011 5.065218 CAGATTCAACATAAAGGACCCGAAG 59.935 44.000 0.00 0.00 0.00 3.79
2638 4020 6.779860 ACATAAAGGACCCGAAGCATATATT 58.220 36.000 0.00 0.00 0.00 1.28
2654 4036 5.066375 GCATATATTGGTGTCAAGCAGTCAA 59.934 40.000 0.00 0.00 36.19 3.18
2655 4037 6.238842 GCATATATTGGTGTCAAGCAGTCAAT 60.239 38.462 0.00 0.00 36.19 2.57
2674 4056 2.743752 CGTGCAACCAGATCGCCTG 61.744 63.158 0.00 0.00 42.55 4.85
2686 4068 1.534595 GATCGCCTGATCCTTGATTGC 59.465 52.381 0.00 0.00 44.39 3.56
2690 4072 2.479049 CGCCTGATCCTTGATTGCAAAG 60.479 50.000 1.71 0.00 32.73 2.77
2691 4073 2.737679 GCCTGATCCTTGATTGCAAAGC 60.738 50.000 1.71 0.00 32.73 3.51
2712 4094 4.017499 AGCTTCCCCAACAGTACCATATTT 60.017 41.667 0.00 0.00 0.00 1.40
2716 4098 3.381272 CCCCAACAGTACCATATTTGCAG 59.619 47.826 0.00 0.00 0.00 4.41
2720 4102 4.701956 ACAGTACCATATTTGCAGCAAC 57.298 40.909 7.54 0.00 0.00 4.17
2735 4117 3.181497 GCAGCAACATGTACCAATACCAG 60.181 47.826 0.00 0.00 0.00 4.00
2745 4127 6.740944 TGTACCAATACCAGTACATAGCAT 57.259 37.500 0.00 0.00 42.87 3.79
2762 4144 3.942377 ATCCATTGCGCCTGCCACA 62.942 57.895 4.18 0.00 41.78 4.17
2763 4145 3.682885 CCATTGCGCCTGCCACAA 61.683 61.111 4.18 0.00 41.78 3.33
2768 4150 2.144833 TTGCGCCTGCCACAAAGATG 62.145 55.000 4.18 0.00 41.78 2.90
2769 4151 2.334946 GCGCCTGCCACAAAGATGA 61.335 57.895 0.00 0.00 33.98 2.92
2783 4165 6.034591 CACAAAGATGAGAGGATGCAATTTC 58.965 40.000 0.00 0.00 0.00 2.17
2784 4166 5.713389 ACAAAGATGAGAGGATGCAATTTCA 59.287 36.000 0.00 0.00 0.00 2.69
2790 4172 3.159472 AGAGGATGCAATTTCACAGCAA 58.841 40.909 0.00 0.00 42.15 3.91
2791 4173 3.575256 AGAGGATGCAATTTCACAGCAAA 59.425 39.130 0.00 0.00 42.15 3.68
2797 4179 6.361214 GGATGCAATTTCACAGCAAATTTTTG 59.639 34.615 0.00 0.00 42.15 2.44
2827 4210 8.137210 GCTTTTGCTTTTAAACCACAGAAATA 57.863 30.769 0.00 0.00 43.35 1.40
2839 4222 8.635765 AAACCACAGAAATACTCACATATGTT 57.364 30.769 5.37 0.00 0.00 2.71
2909 4292 2.358003 GTTGCTGCTCCTGTCGCT 60.358 61.111 0.00 0.00 0.00 4.93
3029 4412 9.450807 CAGAGTTAAAACTTTACCATGTTTGAG 57.549 33.333 0.00 0.00 39.88 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.602924 GATAGAGGAGCTCCGCGCG 62.603 68.421 27.99 25.67 45.59 6.86
11 12 2.257067 GATAGAGGAGCTCCGCGC 59.743 66.667 27.99 20.30 40.98 6.86
12 13 1.961791 TCGATAGAGGAGCTCCGCG 60.962 63.158 27.99 23.88 42.67 6.46
13 14 4.066694 TCGATAGAGGAGCTCCGC 57.933 61.111 27.43 27.43 42.67 5.54
29 30 8.220434 ACAAATAACTTTGCGTTTTATTGCATC 58.780 29.630 0.00 0.00 44.63 3.91
41 42 7.215696 TCAAGAAAACACAAATAACTTTGCG 57.784 32.000 0.00 0.00 44.63 4.85
107 110 4.431378 TCTTTGTAACCTGTCCCCTCATA 58.569 43.478 0.00 0.00 0.00 2.15
202 209 5.126699 AGCTCAGAAGATTCAATTCCCAT 57.873 39.130 0.00 0.00 0.00 4.00
225 232 2.322355 AGCGCTGAAATGCTCACTAT 57.678 45.000 10.39 0.00 36.53 2.12
230 237 0.807496 AGGAAAGCGCTGAAATGCTC 59.193 50.000 12.58 0.00 41.46 4.26
231 238 1.068055 CAAGGAAAGCGCTGAAATGCT 60.068 47.619 12.58 5.77 44.97 3.79
256 263 3.314693 TGGAGGGTTCTGTTACTTCTGT 58.685 45.455 0.00 0.00 0.00 3.41
257 264 4.319177 CTTGGAGGGTTCTGTTACTTCTG 58.681 47.826 0.00 0.00 0.00 3.02
258 265 3.244596 GCTTGGAGGGTTCTGTTACTTCT 60.245 47.826 0.00 0.00 0.00 2.85
259 266 3.075148 GCTTGGAGGGTTCTGTTACTTC 58.925 50.000 0.00 0.00 0.00 3.01
260 267 2.711547 AGCTTGGAGGGTTCTGTTACTT 59.288 45.455 0.00 0.00 0.00 2.24
261 268 2.039084 CAGCTTGGAGGGTTCTGTTACT 59.961 50.000 0.00 0.00 0.00 2.24
262 269 2.427506 CAGCTTGGAGGGTTCTGTTAC 58.572 52.381 0.00 0.00 0.00 2.50
263 270 1.351017 CCAGCTTGGAGGGTTCTGTTA 59.649 52.381 0.00 0.00 40.96 2.41
264 271 0.111253 CCAGCTTGGAGGGTTCTGTT 59.889 55.000 0.00 0.00 40.96 3.16
294 302 1.048601 TAATAGAGAGGGGCGCCAAG 58.951 55.000 30.85 0.00 0.00 3.61
313 321 7.835181 AGACTCTGCTAGGTGTTTAGTAGTAAT 59.165 37.037 0.00 0.00 35.60 1.89
315 323 6.719301 AGACTCTGCTAGGTGTTTAGTAGTA 58.281 40.000 0.00 0.00 35.60 1.82
317 325 6.518208 AAGACTCTGCTAGGTGTTTAGTAG 57.482 41.667 0.00 0.00 35.47 2.57
318 326 6.492429 TCAAAGACTCTGCTAGGTGTTTAGTA 59.508 38.462 0.00 0.00 29.87 1.82
320 328 5.784177 TCAAAGACTCTGCTAGGTGTTTAG 58.216 41.667 0.00 0.00 29.87 1.85
321 329 5.538813 TCTCAAAGACTCTGCTAGGTGTTTA 59.461 40.000 0.00 0.00 29.87 2.01
322 330 4.345257 TCTCAAAGACTCTGCTAGGTGTTT 59.655 41.667 0.00 0.00 30.80 2.83
323 331 3.898123 TCTCAAAGACTCTGCTAGGTGTT 59.102 43.478 0.00 0.00 0.00 3.32
324 332 3.257127 GTCTCAAAGACTCTGCTAGGTGT 59.743 47.826 0.00 0.00 41.88 4.16
325 333 3.671971 CGTCTCAAAGACTCTGCTAGGTG 60.672 52.174 5.63 0.00 42.92 4.00
447 462 2.279517 GCCCATGACCGCTACGAG 60.280 66.667 0.00 0.00 0.00 4.18
450 465 3.792053 CTCCGCCCATGACCGCTAC 62.792 68.421 0.00 0.00 0.00 3.58
454 469 1.520787 GTTACTCCGCCCATGACCG 60.521 63.158 0.00 0.00 0.00 4.79
464 493 1.464734 TCTCTGCCAGAGTTACTCCG 58.535 55.000 20.67 0.00 42.83 4.63
476 505 2.559440 AGAAAGATTGCGATCTCTGCC 58.441 47.619 17.02 6.79 41.78 4.85
710 1880 2.301870 TGACATGGTGGGTGAGTTAGTC 59.698 50.000 0.00 0.00 0.00 2.59
733 1906 4.055360 TGCTCGACCGTTAATGGATAATG 58.945 43.478 20.84 7.29 0.00 1.90
734 1907 4.330944 TGCTCGACCGTTAATGGATAAT 57.669 40.909 20.84 0.00 0.00 1.28
735 1908 3.804786 TGCTCGACCGTTAATGGATAA 57.195 42.857 20.84 3.92 0.00 1.75
859 2041 2.820037 GCACGTAGAAGGGCAGGC 60.820 66.667 0.00 0.00 0.00 4.85
945 2149 3.855950 CGGATTCGCGGATTTATACTACC 59.144 47.826 6.13 0.00 0.00 3.18
1022 2230 2.799917 CGAGGTGGTCTTTCGATGGATC 60.800 54.545 0.00 0.00 36.49 3.36
1038 2246 2.842462 TCTGTGTGTGGGCGAGGT 60.842 61.111 0.00 0.00 0.00 3.85
1039 2247 2.357517 GTCTGTGTGTGGGCGAGG 60.358 66.667 0.00 0.00 0.00 4.63
1159 2377 0.599558 TGCTGGACACAGGTACGTAC 59.400 55.000 17.56 17.56 45.04 3.67
1379 2600 2.952264 TCGTGTCGTGTGTGCGTG 60.952 61.111 0.00 0.00 0.00 5.34
1394 2615 0.387622 CTGCAAACCCAAGCATGTCG 60.388 55.000 0.00 0.00 40.42 4.35
1395 2616 0.037975 CCTGCAAACCCAAGCATGTC 60.038 55.000 0.00 0.00 40.42 3.06
1396 2617 2.051941 CCTGCAAACCCAAGCATGT 58.948 52.632 0.00 0.00 40.42 3.21
1397 2618 1.375013 GCCTGCAAACCCAAGCATG 60.375 57.895 0.00 0.00 40.42 4.06
1398 2619 1.123246 AAGCCTGCAAACCCAAGCAT 61.123 50.000 0.00 0.00 40.42 3.79
1410 2632 2.287547 TGACGAAAAATGACAAGCCTGC 60.288 45.455 0.00 0.00 0.00 4.85
1450 2672 7.713507 CCAAAATGTATACCAGACCGAATTAGA 59.286 37.037 0.00 0.00 0.00 2.10
1453 2675 5.592688 CCCAAAATGTATACCAGACCGAATT 59.407 40.000 0.00 0.00 0.00 2.17
1457 2679 3.625764 CACCCAAAATGTATACCAGACCG 59.374 47.826 0.00 0.00 0.00 4.79
1466 2689 2.307686 ACCGAGACCACCCAAAATGTAT 59.692 45.455 0.00 0.00 0.00 2.29
1585 2808 4.659874 GCACACGTTTGGTCGCGG 62.660 66.667 6.13 0.00 0.00 6.46
1655 2878 5.059161 ACTACCTTTCGAGGTTTTTGGTAC 58.941 41.667 3.08 0.00 42.99 3.34
1765 2994 1.064166 CCCAATCCACAAGCTCCAGAT 60.064 52.381 0.00 0.00 0.00 2.90
1921 3150 3.772025 AGCTAGTTGTAGAGCCTGACAAT 59.228 43.478 0.00 0.00 39.65 2.71
1927 3156 2.498078 GTGGAAGCTAGTTGTAGAGCCT 59.502 50.000 0.00 0.00 39.65 4.58
1951 3180 9.584008 AAGTTATATATAGGAGACTCGGTTGAA 57.416 33.333 0.00 0.00 43.67 2.69
2058 3291 3.513662 TGCAAATTTTCGCATCCATGAG 58.486 40.909 0.00 0.00 31.95 2.90
2117 3350 1.203994 GTCGAGATCCGGGAACAAAGA 59.796 52.381 0.00 0.00 39.14 2.52
2119 3352 0.248289 GGTCGAGATCCGGGAACAAA 59.752 55.000 0.00 0.00 39.14 2.83
2125 3358 2.355986 TTGGTGGTCGAGATCCGGG 61.356 63.158 0.00 0.00 39.14 5.73
2128 3361 1.275291 TCAAGTTGGTGGTCGAGATCC 59.725 52.381 2.34 0.00 0.00 3.36
2134 3367 0.859232 CGAGTTCAAGTTGGTGGTCG 59.141 55.000 2.34 3.56 0.00 4.79
2138 3371 4.481930 TTATTGCGAGTTCAAGTTGGTG 57.518 40.909 2.34 0.00 0.00 4.17
2183 3416 7.290014 AGGATTTACCAGTTGAAACAAGGAATT 59.710 33.333 10.51 0.00 42.04 2.17
2194 3427 5.421056 ACTCATACGAGGATTTACCAGTTGA 59.579 40.000 0.00 0.00 44.17 3.18
2196 3429 5.934402 ACTCATACGAGGATTTACCAGTT 57.066 39.130 0.00 0.00 44.17 3.16
2198 3431 7.013464 ACTCTAACTCATACGAGGATTTACCAG 59.987 40.741 0.00 0.00 44.17 4.00
2200 3433 7.274603 ACTCTAACTCATACGAGGATTTACC 57.725 40.000 0.00 0.00 44.17 2.85
2210 3443 6.528423 CCTCAAAGACAACTCTAACTCATACG 59.472 42.308 0.00 0.00 0.00 3.06
2217 3450 5.116882 ACACACCTCAAAGACAACTCTAAC 58.883 41.667 0.00 0.00 0.00 2.34
2226 3459 6.026947 ACTCATACTACACACCTCAAAGAC 57.973 41.667 0.00 0.00 0.00 3.01
2228 3461 5.573282 CGAACTCATACTACACACCTCAAAG 59.427 44.000 0.00 0.00 0.00 2.77
2229 3462 5.242171 TCGAACTCATACTACACACCTCAAA 59.758 40.000 0.00 0.00 0.00 2.69
2232 3465 4.959596 TCGAACTCATACTACACACCTC 57.040 45.455 0.00 0.00 0.00 3.85
2233 3466 4.765856 AGTTCGAACTCATACTACACACCT 59.234 41.667 24.93 0.00 32.86 4.00
2234 3467 5.056894 AGTTCGAACTCATACTACACACC 57.943 43.478 24.93 0.00 32.86 4.16
2236 3469 9.701098 ATTTTTAGTTCGAACTCATACTACACA 57.299 29.630 32.86 9.94 40.37 3.72
2237 3470 9.953825 CATTTTTAGTTCGAACTCATACTACAC 57.046 33.333 32.86 0.16 40.37 2.90
2238 3471 9.917129 TCATTTTTAGTTCGAACTCATACTACA 57.083 29.630 32.86 11.45 40.37 2.74
2242 3475 9.543018 CCTTTCATTTTTAGTTCGAACTCATAC 57.457 33.333 32.86 4.07 40.37 2.39
2251 3484 8.970691 AATGTGATCCTTTCATTTTTAGTTCG 57.029 30.769 0.00 0.00 36.54 3.95
2305 3539 6.407202 GGAACTAAGAGCTCCAATCAGTTTA 58.593 40.000 10.93 0.00 0.00 2.01
2313 3547 4.657814 AATTGGGAACTAAGAGCTCCAA 57.342 40.909 10.93 5.87 38.43 3.53
2314 3548 4.657814 AAATTGGGAACTAAGAGCTCCA 57.342 40.909 10.93 0.00 0.00 3.86
2315 3549 7.646548 ATTAAAATTGGGAACTAAGAGCTCC 57.353 36.000 10.93 0.00 0.00 4.70
2363 3597 7.760340 ACGTGTTAACTCAAATTTGCCTAAAAA 59.240 29.630 13.54 0.68 0.00 1.94
2364 3598 7.259161 ACGTGTTAACTCAAATTTGCCTAAAA 58.741 30.769 13.54 3.50 0.00 1.52
2365 3599 6.797454 ACGTGTTAACTCAAATTTGCCTAAA 58.203 32.000 13.54 3.00 0.00 1.85
2366 3600 6.380095 ACGTGTTAACTCAAATTTGCCTAA 57.620 33.333 13.54 7.62 0.00 2.69
2367 3601 6.707161 AGTACGTGTTAACTCAAATTTGCCTA 59.293 34.615 13.54 1.96 0.00 3.93
2368 3602 4.911514 ACGTGTTAACTCAAATTTGCCT 57.088 36.364 13.54 2.89 0.00 4.75
2369 3603 5.754778 AGTACGTGTTAACTCAAATTTGCC 58.245 37.500 13.54 0.00 0.00 4.52
2370 3604 6.423862 TGAGTACGTGTTAACTCAAATTTGC 58.576 36.000 14.87 0.00 46.82 3.68
2378 3612 5.306532 TCATCCTGAGTACGTGTTAACTC 57.693 43.478 7.22 8.90 42.04 3.01
2379 3613 5.417894 TCATCATCCTGAGTACGTGTTAACT 59.582 40.000 7.22 0.00 0.00 2.24
2380 3614 5.515626 GTCATCATCCTGAGTACGTGTTAAC 59.484 44.000 0.00 0.00 0.00 2.01
2381 3615 5.647589 GTCATCATCCTGAGTACGTGTTAA 58.352 41.667 0.00 0.00 0.00 2.01
2382 3616 4.201881 CGTCATCATCCTGAGTACGTGTTA 60.202 45.833 0.00 0.00 35.24 2.41
2388 3622 1.269831 GGCCGTCATCATCCTGAGTAC 60.270 57.143 0.00 0.00 0.00 2.73
2396 3630 1.003545 CAATCGTTGGCCGTCATCATC 60.004 52.381 0.00 0.00 37.94 2.92
2415 3771 1.842052 TATGGTCGACAGGCACTACA 58.158 50.000 18.91 3.48 36.02 2.74
2416 3772 3.454371 AATATGGTCGACAGGCACTAC 57.546 47.619 18.91 0.00 36.02 2.73
2424 3780 7.958088 TGGTGAGAATTATAATATGGTCGACA 58.042 34.615 18.91 3.91 0.00 4.35
2425 3781 8.827177 TTGGTGAGAATTATAATATGGTCGAC 57.173 34.615 7.13 7.13 0.00 4.20
2445 3801 0.033796 ATGGCCCATCACTCTTGGTG 60.034 55.000 0.00 0.00 46.60 4.17
2446 3802 0.033796 CATGGCCCATCACTCTTGGT 60.034 55.000 0.00 0.00 31.99 3.67
2447 3803 0.754217 CCATGGCCCATCACTCTTGG 60.754 60.000 0.00 0.00 0.00 3.61
2457 3813 2.318908 GCATAAATCTTCCATGGCCCA 58.681 47.619 6.96 0.00 0.00 5.36
2466 3822 9.516091 GAAACGTTTTCATTTGCATAAATCTTC 57.484 29.630 15.89 0.00 34.34 2.87
2470 3826 8.487176 GTGAGAAACGTTTTCATTTGCATAAAT 58.513 29.630 15.89 0.00 36.97 1.40
2474 3830 5.347342 TGTGAGAAACGTTTTCATTTGCAT 58.653 33.333 15.89 0.00 0.00 3.96
2485 3841 4.051922 GTGAGACATCTGTGAGAAACGTT 58.948 43.478 0.00 0.00 0.00 3.99
2486 3842 3.553096 GGTGAGACATCTGTGAGAAACGT 60.553 47.826 0.00 0.00 0.00 3.99
2520 3876 2.300723 GTGACGGTGTATATATGGCCCA 59.699 50.000 0.00 0.00 0.00 5.36
2521 3877 2.565834 AGTGACGGTGTATATATGGCCC 59.434 50.000 0.00 0.00 0.00 5.80
2522 3878 3.955650 AGTGACGGTGTATATATGGCC 57.044 47.619 0.00 0.00 0.00 5.36
2523 3879 6.263516 TCTTAGTGACGGTGTATATATGGC 57.736 41.667 0.00 0.00 0.00 4.40
2524 3880 8.051901 TCATCTTAGTGACGGTGTATATATGG 57.948 38.462 0.00 0.00 0.00 2.74
2530 3888 5.508153 GCATCTCATCTTAGTGACGGTGTAT 60.508 44.000 0.00 0.00 0.00 2.29
2531 3889 4.202020 GCATCTCATCTTAGTGACGGTGTA 60.202 45.833 0.00 0.00 0.00 2.90
2590 3971 4.823442 TGAATCTGTGTTCATGTCAAGCTT 59.177 37.500 0.00 0.00 33.41 3.74
2609 3990 3.694566 GCTTCGGGTCCTTTATGTTGAAT 59.305 43.478 0.00 0.00 0.00 2.57
2610 3991 3.078837 GCTTCGGGTCCTTTATGTTGAA 58.921 45.455 0.00 0.00 0.00 2.69
2619 4000 3.394606 ACCAATATATGCTTCGGGTCCTT 59.605 43.478 0.00 0.00 0.00 3.36
2627 4008 5.297776 ACTGCTTGACACCAATATATGCTTC 59.702 40.000 0.00 0.00 0.00 3.86
2628 4009 5.195940 ACTGCTTGACACCAATATATGCTT 58.804 37.500 0.00 0.00 0.00 3.91
2629 4010 4.785301 ACTGCTTGACACCAATATATGCT 58.215 39.130 0.00 0.00 0.00 3.79
2630 4011 4.576053 TGACTGCTTGACACCAATATATGC 59.424 41.667 0.00 0.00 0.00 3.14
2638 4020 1.202639 ACGATTGACTGCTTGACACCA 60.203 47.619 0.00 0.00 0.00 4.17
2654 4036 1.815421 GGCGATCTGGTTGCACGAT 60.815 57.895 2.00 0.00 39.13 3.73
2655 4037 2.434185 GGCGATCTGGTTGCACGA 60.434 61.111 2.00 0.00 39.13 4.35
2674 4056 3.429960 GGGAAGCTTTGCAATCAAGGATC 60.430 47.826 0.00 0.00 31.65 3.36
2677 4059 1.066645 GGGGAAGCTTTGCAATCAAGG 60.067 52.381 0.00 0.00 33.12 3.61
2686 4068 1.886542 GGTACTGTTGGGGAAGCTTTG 59.113 52.381 0.00 0.00 0.00 2.77
2690 4072 3.577805 ATATGGTACTGTTGGGGAAGC 57.422 47.619 0.00 0.00 0.00 3.86
2691 4073 4.097892 GCAAATATGGTACTGTTGGGGAAG 59.902 45.833 0.00 0.00 0.00 3.46
2712 4094 2.752354 GGTATTGGTACATGTTGCTGCA 59.248 45.455 2.30 0.00 39.30 4.41
2716 4098 4.938832 TGTACTGGTATTGGTACATGTTGC 59.061 41.667 2.30 0.00 41.90 4.17
2745 4127 4.657408 TGTGGCAGGCGCAATGGA 62.657 61.111 10.83 0.00 41.24 3.41
2762 4144 5.713389 TGTGAAATTGCATCCTCTCATCTTT 59.287 36.000 0.00 0.00 0.00 2.52
2763 4145 5.258841 TGTGAAATTGCATCCTCTCATCTT 58.741 37.500 0.00 0.00 0.00 2.40
2768 4150 2.751259 TGCTGTGAAATTGCATCCTCTC 59.249 45.455 0.00 0.00 0.00 3.20
2769 4151 2.799017 TGCTGTGAAATTGCATCCTCT 58.201 42.857 0.00 0.00 0.00 3.69
2797 4179 6.374578 TGTGGTTTAAAAGCAAAAGCAAAAC 58.625 32.000 2.40 0.00 43.57 2.43
2813 4196 9.733556 AACATATGTGAGTATTTCTGTGGTTTA 57.266 29.630 9.63 0.00 0.00 2.01
2827 4210 2.715046 CAGGTGCCAACATATGTGAGT 58.285 47.619 9.63 0.00 0.00 3.41
2850 4233 2.001159 GACAAGCTGTCTCATGAGCAG 58.999 52.381 28.36 28.36 43.73 4.24
2909 4292 4.412199 CAGGAATTCAGAGGGGGTAATACA 59.588 45.833 7.93 0.00 0.00 2.29
2966 4349 1.808390 CCTTCGTTTCCGCGGTAGG 60.808 63.158 27.15 19.11 0.00 3.18
3029 4412 7.095816 GGGCTGTATCACAATTTGTTGTTTTAC 60.096 37.037 0.00 0.00 31.86 2.01


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

AutoCloner maintained by Alex Coulton.