Multiple sequence alignment - TraesCS6B01G034600

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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 TraesCS6B01G034600 chr6B 100.000 3395 0 0 1 3395 20760458 20763852 0.000000e+00 6270.0
1 TraesCS6B01G034600 chr6B 82.444 2250 301 55 198 2393 20922983 20925192 0.000000e+00 1881.0
2 TraesCS6B01G034600 chr6B 83.406 2055 274 43 395 2398 20826216 20828254 0.000000e+00 1844.0
3 TraesCS6B01G034600 chr6B 81.512 2315 341 54 154 2398 20783531 20785828 0.000000e+00 1823.0
4 TraesCS6B01G034600 chr6B 92.362 1283 93 2 190 1468 20694317 20695598 0.000000e+00 1821.0
5 TraesCS6B01G034600 chr6B 81.428 2213 350 36 154 2317 21004041 21006241 0.000000e+00 1753.0
6 TraesCS6B01G034600 chr6B 81.453 2243 325 47 139 2323 21043321 21045530 0.000000e+00 1753.0
7 TraesCS6B01G034600 chr6B 81.329 1971 307 44 389 2317 20976723 20978674 0.000000e+00 1544.0
8 TraesCS6B01G034600 chr6B 91.444 187 9 3 1 187 20694169 20694348 2.020000e-62 250.0
9 TraesCS6B01G034600 chr6B 84.034 119 11 6 2224 2339 23313646 23313533 1.290000e-19 108.0
10 TraesCS6B01G034600 chr6D 92.439 1997 136 8 395 2379 11058498 11060491 0.000000e+00 2837.0
11 TraesCS6B01G034600 chr6D 82.275 2251 312 49 198 2398 11046275 11048488 0.000000e+00 1866.0
12 TraesCS6B01G034600 chr6D 81.620 2334 308 74 148 2398 10943650 10945945 0.000000e+00 1821.0
13 TraesCS6B01G034600 chr6D 82.558 2041 296 33 414 2403 11089654 11091685 0.000000e+00 1742.0
14 TraesCS6B01G034600 chr6D 83.079 1968 271 40 395 2322 11113369 11115314 0.000000e+00 1733.0
15 TraesCS6B01G034600 chr6D 92.760 442 23 6 2375 2811 11065906 11066343 6.180000e-177 630.0
16 TraesCS6B01G034600 chr6D 91.189 227 13 2 3167 3393 11066926 11067145 5.510000e-78 302.0
17 TraesCS6B01G034600 chr6D 78.193 509 84 18 1675 2166 12474388 12473890 1.980000e-77 300.0
18 TraesCS6B01G034600 chr6D 92.896 183 13 0 2813 2995 11066636 11066818 2.010000e-67 267.0
19 TraesCS6B01G034600 chr6D 83.065 124 20 1 1904 2026 12198969 12199092 9.960000e-21 111.0
20 TraesCS6B01G034600 chr6D 80.882 136 14 11 2228 2359 12618541 12618414 2.790000e-16 97.1
21 TraesCS6B01G034600 chr6A 83.001 2159 288 50 198 2322 12410175 12412288 0.000000e+00 1881.0
22 TraesCS6B01G034600 chr6A 77.238 659 122 18 1675 2317 13890403 13889757 8.960000e-96 361.0


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 TraesCS6B01G034600 chr6B 20760458 20763852 3394 False 6270.000000 6270 100.000000 1 3395 1 chr6B.!!$F1 3394
1 TraesCS6B01G034600 chr6B 20922983 20925192 2209 False 1881.000000 1881 82.444000 198 2393 1 chr6B.!!$F4 2195
2 TraesCS6B01G034600 chr6B 20826216 20828254 2038 False 1844.000000 1844 83.406000 395 2398 1 chr6B.!!$F3 2003
3 TraesCS6B01G034600 chr6B 20783531 20785828 2297 False 1823.000000 1823 81.512000 154 2398 1 chr6B.!!$F2 2244
4 TraesCS6B01G034600 chr6B 21004041 21006241 2200 False 1753.000000 1753 81.428000 154 2317 1 chr6B.!!$F6 2163
5 TraesCS6B01G034600 chr6B 21043321 21045530 2209 False 1753.000000 1753 81.453000 139 2323 1 chr6B.!!$F7 2184
6 TraesCS6B01G034600 chr6B 20976723 20978674 1951 False 1544.000000 1544 81.329000 389 2317 1 chr6B.!!$F5 1928
7 TraesCS6B01G034600 chr6B 20694169 20695598 1429 False 1035.500000 1821 91.903000 1 1468 2 chr6B.!!$F8 1467
8 TraesCS6B01G034600 chr6D 11058498 11060491 1993 False 2837.000000 2837 92.439000 395 2379 1 chr6D.!!$F3 1984
9 TraesCS6B01G034600 chr6D 11046275 11048488 2213 False 1866.000000 1866 82.275000 198 2398 1 chr6D.!!$F2 2200
10 TraesCS6B01G034600 chr6D 10943650 10945945 2295 False 1821.000000 1821 81.620000 148 2398 1 chr6D.!!$F1 2250
11 TraesCS6B01G034600 chr6D 11089654 11091685 2031 False 1742.000000 1742 82.558000 414 2403 1 chr6D.!!$F4 1989
12 TraesCS6B01G034600 chr6D 11113369 11115314 1945 False 1733.000000 1733 83.079000 395 2322 1 chr6D.!!$F5 1927
13 TraesCS6B01G034600 chr6D 11065906 11067145 1239 False 399.666667 630 92.281667 2375 3393 3 chr6D.!!$F7 1018
14 TraesCS6B01G034600 chr6A 12410175 12412288 2113 False 1881.000000 1881 83.001000 198 2322 1 chr6A.!!$F1 2124
15 TraesCS6B01G034600 chr6A 13889757 13890403 646 True 361.000000 361 77.238000 1675 2317 1 chr6A.!!$R1 642

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
262 271 1.210478 AGTGCACACCCAGGATACATC 59.790 52.381 21.04 0.0 41.41 3.06 F
2102 2197 0.459237 CTTGCAGTCCTACGCCTCTG 60.459 60.000 0.00 0.0 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 2230 0.827368 ACTCGGGAAAGATGAGCTCC 59.173 55.0 12.15 0.0 32.98 4.70 R
3218 3648 0.178990 AAGAAGAAGCTTGCCCCGTT 60.179 50.0 2.10 0.0 0.00 4.44 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
55 56 6.590234 ACAAATTTCAAGGGCTAAAGTAGG 57.410 37.500 0.00 0.00 0.00 3.18
91 92 7.040823 GCCCACAAATTTGTTTTCCATTTCATA 60.041 33.333 21.10 0.00 39.91 2.15
180 181 4.142116 TGCTTCTGGGTGCATATTTGAATG 60.142 41.667 0.00 0.00 33.94 2.67
213 214 2.819608 GCTCCTAGGTGCACATTTGAAA 59.180 45.455 27.04 0.00 35.06 2.69
262 271 1.210478 AGTGCACACCCAGGATACATC 59.790 52.381 21.04 0.00 41.41 3.06
277 286 5.471456 AGGATACATCGAAATTCCAATGCTC 59.529 40.000 9.00 2.26 41.41 4.26
387 419 8.222637 AGTTTTATCACAAACTTACCCTAAGGT 58.777 33.333 0.00 0.00 43.17 3.50
538 571 5.389859 TGCAGGTATTCAAGGACAATTTG 57.610 39.130 0.00 0.00 0.00 2.32
619 652 2.225343 TGATGGACTTCCCCTTGCAATT 60.225 45.455 0.00 0.00 34.29 2.32
624 657 2.755103 GACTTCCCCTTGCAATTTCGAT 59.245 45.455 0.00 0.00 0.00 3.59
686 719 3.897505 TGAATGGAGGAAGATGAGCGATA 59.102 43.478 0.00 0.00 0.00 2.92
736 769 6.415573 TCCTGAGCTTAGGAAAATAAAGACC 58.584 40.000 24.17 0.00 43.71 3.85
972 1009 3.248024 AGGGACAGACCAATACAGTCAA 58.752 45.455 0.00 0.00 41.20 3.18
1140 1177 6.377146 GCAACTGGAAAAGGGATAAAGATGTA 59.623 38.462 0.00 0.00 0.00 2.29
1191 1228 0.596082 GGTCATTGACCGTGTTTGGG 59.404 55.000 19.65 0.00 43.14 4.12
1203 1240 1.630878 GTGTTTGGGGAGTGGAGATCT 59.369 52.381 0.00 0.00 0.00 2.75
1206 1243 3.244911 TGTTTGGGGAGTGGAGATCTTTC 60.245 47.826 0.00 0.00 0.00 2.62
1284 1321 6.158520 TGGGGTTAAGAGATCATCATCTTGAA 59.841 38.462 5.44 0.00 39.71 2.69
1358 1395 6.036300 CACAACATTTTATGCCTGCCTAATTG 59.964 38.462 0.00 0.00 0.00 2.32
1524 1564 9.499479 GGAGATGACATAGTTCAAATGTATGAT 57.501 33.333 0.00 0.00 37.69 2.45
1574 1644 1.337703 TGCCAATTGTGTGTTCAGCTC 59.662 47.619 4.43 0.00 0.00 4.09
1975 2061 3.366396 CTCACTCTGGAAGGTAGGCTAA 58.634 50.000 0.00 0.00 0.00 3.09
1984 2070 4.080751 TGGAAGGTAGGCTAACCAATGTAC 60.081 45.833 5.82 0.00 42.40 2.90
2053 2145 3.118445 GGAGAGCTACTTGAGGCAAGATT 60.118 47.826 13.56 0.00 43.42 2.40
2102 2197 0.459237 CTTGCAGTCCTACGCCTCTG 60.459 60.000 0.00 0.00 0.00 3.35
2107 2202 0.757188 AGTCCTACGCCTCTGGGATG 60.757 60.000 0.00 0.00 33.58 3.51
2135 2230 1.668419 GGGACACATCTCCAATTCCG 58.332 55.000 0.00 0.00 30.97 4.30
2169 2264 1.959985 CCGAGTCTCATGGAGCTACAT 59.040 52.381 5.29 5.29 0.00 2.29
2186 2281 7.148154 GGAGCTACATCTCTCACGATTATACAT 60.148 40.741 0.00 0.00 33.70 2.29
2201 2296 1.376543 TACATCCTCGAGTCGGTGTC 58.623 55.000 13.54 0.00 0.00 3.67
2218 2313 2.221055 GTGTCGTTTGAAGAAGACGCAT 59.779 45.455 3.52 0.00 41.94 4.73
2253 2348 3.885297 AGCTGCTACAAGTTGATTTGTGT 59.115 39.130 10.54 0.00 41.18 3.72
2256 2351 5.574891 TGCTACAAGTTGATTTGTGTGTT 57.425 34.783 10.54 0.00 41.18 3.32
2284 2379 2.203126 GATTCTCCGGGCTGCCAG 60.203 66.667 22.05 17.07 0.00 4.85
2285 2380 4.496336 ATTCTCCGGGCTGCCAGC 62.496 66.667 22.05 8.55 41.46 4.85
2403 2517 9.226345 GTGAATTTTGTTGACTAAACTCTCTTG 57.774 33.333 2.43 0.00 39.70 3.02
2404 2518 8.956426 TGAATTTTGTTGACTAAACTCTCTTGT 58.044 29.630 2.43 0.00 39.70 3.16
2406 2520 8.738645 ATTTTGTTGACTAAACTCTCTTGTCT 57.261 30.769 0.00 0.00 39.70 3.41
2420 2534 5.192927 TCTCTTGTCTCTCTCTCTGGATTC 58.807 45.833 0.00 0.00 0.00 2.52
2436 2550 0.948623 ATTCGTGTGCGCACTTGCTA 60.949 50.000 37.59 20.78 43.16 3.49
2478 2593 6.650427 AGTAGATACCGAAATGCTGACATA 57.350 37.500 0.00 0.00 34.62 2.29
2552 2667 5.008316 GTCGTTGACTTCCAGGTTTACAAAT 59.992 40.000 0.00 0.00 0.00 2.32
2558 2673 4.827284 ACTTCCAGGTTTACAAATCTGTGG 59.173 41.667 12.68 1.57 43.89 4.17
2567 2682 5.689383 TTACAAATCTGTGGCTTGACTTC 57.311 39.130 0.00 0.00 36.96 3.01
2570 2685 4.586001 ACAAATCTGTGGCTTGACTTCAAT 59.414 37.500 0.00 0.00 32.71 2.57
2605 2720 8.191446 TCAGTAGTCATTGCAGAACTACTTATC 58.809 37.037 24.08 7.79 40.85 1.75
2606 2721 7.976175 CAGTAGTCATTGCAGAACTACTTATCA 59.024 37.037 24.08 0.00 40.85 2.15
2610 2725 7.826252 AGTCATTGCAGAACTACTTATCAATGT 59.174 33.333 10.55 0.00 38.25 2.71
2663 2782 1.444553 CACTCTCACTCGGCCGAAC 60.445 63.158 30.53 0.00 0.00 3.95
2692 2811 7.488322 TGCTGCAAGTATTTCTTTTGTTTACT 58.512 30.769 0.00 0.00 35.30 2.24
2728 2847 2.168106 AGCAAGCATTCAACACCACAAA 59.832 40.909 0.00 0.00 0.00 2.83
2734 2853 4.099881 AGCATTCAACACCACAAAGACATT 59.900 37.500 0.00 0.00 0.00 2.71
2738 2857 4.780815 TCAACACCACAAAGACATTCTCT 58.219 39.130 0.00 0.00 0.00 3.10
2780 2899 0.671781 AAGACGAGCACACAGATGGC 60.672 55.000 0.00 0.00 0.00 4.40
2811 2930 2.300152 TCAAGACTGCTTCGATGGTTCT 59.700 45.455 0.00 0.00 30.14 3.01
2824 3234 4.391830 TCGATGGTTCTGCATAAAACACTC 59.608 41.667 2.12 2.21 0.00 3.51
2852 3262 2.072298 GCAACGGGCAGAGATATCATC 58.928 52.381 5.32 0.05 43.97 2.92
2866 3276 4.346418 AGATATCATCCCCACAGACTTGTC 59.654 45.833 5.32 0.00 34.62 3.18
2867 3277 0.608130 TCATCCCCACAGACTTGTCG 59.392 55.000 0.00 0.00 34.62 4.35
2899 3309 7.456725 TCTTTCTTGAGAAGAATCAACATCCT 58.543 34.615 0.00 0.00 46.15 3.24
2914 3324 7.345422 TCAACATCCTGACAATGAAAGAAAA 57.655 32.000 0.00 0.00 0.00 2.29
2919 3329 8.086522 ACATCCTGACAATGAAAGAAAATTCTG 58.913 33.333 0.00 0.00 37.65 3.02
2947 3357 5.737290 CCAACAAACAGTTCTTCAACTTACG 59.263 40.000 0.00 0.00 41.24 3.18
2970 3380 4.792068 ACTGAATCTTTCAAGTTGGGTCA 58.208 39.130 2.34 0.00 39.58 4.02
2989 3399 3.002656 GTCATAATCCACCAACAGCATCG 59.997 47.826 0.00 0.00 0.00 3.84
2995 3405 1.079819 ACCAACAGCATCGTCCTCG 60.080 57.895 0.00 0.00 38.55 4.63
2996 3406 2.456119 CCAACAGCATCGTCCTCGC 61.456 63.158 0.00 0.00 36.96 5.03
3002 3412 2.987593 CATCGTCCTCGCGAAACG 59.012 61.111 28.09 28.09 44.38 3.60
3010 3420 2.606272 GTCCTCGCGAAACGGAATATTT 59.394 45.455 16.26 0.00 43.89 1.40
3060 3490 6.775939 AGTTTAGTTAGTTCTTACGGTTGC 57.224 37.500 0.00 0.00 0.00 4.17
3061 3491 6.519382 AGTTTAGTTAGTTCTTACGGTTGCT 58.481 36.000 0.00 0.00 0.00 3.91
3062 3492 6.423001 AGTTTAGTTAGTTCTTACGGTTGCTG 59.577 38.462 0.00 0.00 0.00 4.41
3063 3493 3.660865 AGTTAGTTCTTACGGTTGCTGG 58.339 45.455 0.00 0.00 0.00 4.85
3064 3494 2.740447 GTTAGTTCTTACGGTTGCTGGG 59.260 50.000 0.00 0.00 0.00 4.45
3065 3495 0.763035 AGTTCTTACGGTTGCTGGGT 59.237 50.000 0.00 0.00 0.00 4.51
3066 3496 1.142262 AGTTCTTACGGTTGCTGGGTT 59.858 47.619 0.00 0.00 0.00 4.11
3067 3497 1.265905 GTTCTTACGGTTGCTGGGTTG 59.734 52.381 0.00 0.00 0.00 3.77
3068 3498 0.250553 TCTTACGGTTGCTGGGTTGG 60.251 55.000 0.00 0.00 0.00 3.77
3069 3499 1.862602 CTTACGGTTGCTGGGTTGGC 61.863 60.000 0.00 0.00 0.00 4.52
3070 3500 2.346284 TTACGGTTGCTGGGTTGGCT 62.346 55.000 0.00 0.00 0.00 4.75
3071 3501 3.673484 CGGTTGCTGGGTTGGCTG 61.673 66.667 0.00 0.00 0.00 4.85
3072 3502 2.521708 GGTTGCTGGGTTGGCTGT 60.522 61.111 0.00 0.00 0.00 4.40
3073 3503 2.133641 GGTTGCTGGGTTGGCTGTT 61.134 57.895 0.00 0.00 0.00 3.16
3074 3504 1.067916 GTTGCTGGGTTGGCTGTTG 59.932 57.895 0.00 0.00 0.00 3.33
3075 3505 2.795110 TTGCTGGGTTGGCTGTTGC 61.795 57.895 0.00 0.00 38.76 4.17
3076 3506 2.914097 GCTGGGTTGGCTGTTGCT 60.914 61.111 0.00 0.00 39.59 3.91
3077 3507 2.924105 GCTGGGTTGGCTGTTGCTC 61.924 63.158 0.00 0.00 39.59 4.26
3078 3508 1.228367 CTGGGTTGGCTGTTGCTCT 60.228 57.895 0.00 0.00 39.59 4.09
3079 3509 1.521450 CTGGGTTGGCTGTTGCTCTG 61.521 60.000 0.00 0.00 39.59 3.35
3080 3510 2.647297 GGTTGGCTGTTGCTCTGC 59.353 61.111 0.00 0.00 39.59 4.26
3081 3511 1.900498 GGTTGGCTGTTGCTCTGCT 60.900 57.895 9.93 0.00 40.19 4.24
3082 3512 0.606401 GGTTGGCTGTTGCTCTGCTA 60.606 55.000 9.93 3.34 40.19 3.49
3083 3513 1.238439 GTTGGCTGTTGCTCTGCTAA 58.762 50.000 9.93 8.07 38.60 3.09
3084 3514 1.238439 TTGGCTGTTGCTCTGCTAAC 58.762 50.000 9.93 0.00 36.80 2.34
3085 3515 0.397941 TGGCTGTTGCTCTGCTAACT 59.602 50.000 9.93 0.00 40.19 2.24
3086 3516 0.801251 GGCTGTTGCTCTGCTAACTG 59.199 55.000 9.93 0.00 40.19 3.16
3087 3517 1.609061 GGCTGTTGCTCTGCTAACTGA 60.609 52.381 9.93 0.00 40.19 3.41
3094 3524 1.466558 GCTCTGCTAACTGAAGCCAAC 59.533 52.381 4.75 0.00 42.05 3.77
3097 3527 4.569943 CTCTGCTAACTGAAGCCAACTAA 58.430 43.478 4.75 0.00 42.05 2.24
3114 3544 2.226437 ACTAACGGCATCAGCAACAAAG 59.774 45.455 0.00 0.00 44.61 2.77
3117 3547 1.680735 ACGGCATCAGCAACAAAGAAA 59.319 42.857 0.00 0.00 44.61 2.52
3126 3556 5.890334 TCAGCAACAAAGAAAGTTACAAGG 58.110 37.500 0.00 0.00 0.00 3.61
3127 3557 5.043248 CAGCAACAAAGAAAGTTACAAGGG 58.957 41.667 0.00 0.00 0.00 3.95
3128 3558 4.709886 AGCAACAAAGAAAGTTACAAGGGT 59.290 37.500 0.00 0.00 0.00 4.34
3129 3559 4.803613 GCAACAAAGAAAGTTACAAGGGTG 59.196 41.667 0.00 0.00 0.00 4.61
3130 3560 4.649088 ACAAAGAAAGTTACAAGGGTGC 57.351 40.909 0.00 0.00 0.00 5.01
3131 3561 4.020543 ACAAAGAAAGTTACAAGGGTGCA 58.979 39.130 0.00 0.00 0.00 4.57
3132 3562 4.464597 ACAAAGAAAGTTACAAGGGTGCAA 59.535 37.500 0.00 0.00 0.00 4.08
3133 3563 5.128663 ACAAAGAAAGTTACAAGGGTGCAAT 59.871 36.000 0.00 0.00 0.00 3.56
3134 3564 4.853924 AGAAAGTTACAAGGGTGCAATG 57.146 40.909 0.00 0.00 0.00 2.82
3135 3565 4.469657 AGAAAGTTACAAGGGTGCAATGA 58.530 39.130 0.00 0.00 0.00 2.57
3136 3566 4.278419 AGAAAGTTACAAGGGTGCAATGAC 59.722 41.667 0.00 0.00 0.00 3.06
3137 3567 2.151202 AGTTACAAGGGTGCAATGACG 58.849 47.619 0.00 0.00 0.00 4.35
3138 3568 1.877443 GTTACAAGGGTGCAATGACGT 59.123 47.619 0.00 0.00 0.00 4.34
3139 3569 3.068560 GTTACAAGGGTGCAATGACGTA 58.931 45.455 0.00 0.00 0.00 3.57
3140 3570 1.519408 ACAAGGGTGCAATGACGTAC 58.481 50.000 0.00 0.00 0.00 3.67
3141 3571 1.071699 ACAAGGGTGCAATGACGTACT 59.928 47.619 0.00 0.00 0.00 2.73
3142 3572 2.300723 ACAAGGGTGCAATGACGTACTA 59.699 45.455 0.00 0.00 0.00 1.82
3143 3573 2.667473 AGGGTGCAATGACGTACTAC 57.333 50.000 0.00 0.00 0.00 2.73
3159 3589 6.124088 CGTACTACGTTTATTCAGGGTACT 57.876 41.667 0.00 0.00 36.74 2.73
3160 3590 7.246674 CGTACTACGTTTATTCAGGGTACTA 57.753 40.000 0.00 0.00 36.74 1.82
3161 3591 7.865707 CGTACTACGTTTATTCAGGGTACTAT 58.134 38.462 0.00 0.00 36.74 2.12
3162 3592 8.345565 CGTACTACGTTTATTCAGGGTACTATT 58.654 37.037 0.00 0.00 36.74 1.73
3163 3593 9.455847 GTACTACGTTTATTCAGGGTACTATTG 57.544 37.037 0.00 0.00 0.00 1.90
3164 3594 6.982724 ACTACGTTTATTCAGGGTACTATTGC 59.017 38.462 0.00 0.00 0.00 3.56
3165 3595 4.807304 ACGTTTATTCAGGGTACTATTGCG 59.193 41.667 0.00 0.00 0.00 4.85
3166 3596 5.045215 CGTTTATTCAGGGTACTATTGCGA 58.955 41.667 0.00 0.00 0.00 5.10
3167 3597 5.521010 CGTTTATTCAGGGTACTATTGCGAA 59.479 40.000 0.00 0.00 0.00 4.70
3168 3598 6.292168 CGTTTATTCAGGGTACTATTGCGAAG 60.292 42.308 0.00 0.00 0.00 3.79
3209 3639 0.258774 ACACCAGCCAAACAGTCCTT 59.741 50.000 0.00 0.00 0.00 3.36
3210 3640 0.670162 CACCAGCCAAACAGTCCTTG 59.330 55.000 0.00 0.00 0.00 3.61
3212 3642 1.064017 ACCAGCCAAACAGTCCTTGAA 60.064 47.619 0.00 0.00 0.00 2.69
3218 3648 3.278574 CCAAACAGTCCTTGAACACAGA 58.721 45.455 0.00 0.00 0.00 3.41
3241 3671 1.815613 GGGGCAAGCTTCTTCTTCTTC 59.184 52.381 0.00 0.00 0.00 2.87
3242 3672 2.554124 GGGGCAAGCTTCTTCTTCTTCT 60.554 50.000 0.00 0.00 0.00 2.85
3243 3673 3.153130 GGGCAAGCTTCTTCTTCTTCTT 58.847 45.455 0.00 0.00 0.00 2.52
3244 3674 3.190327 GGGCAAGCTTCTTCTTCTTCTTC 59.810 47.826 0.00 0.00 0.00 2.87
3245 3675 4.071423 GGCAAGCTTCTTCTTCTTCTTCT 58.929 43.478 0.00 0.00 0.00 2.85
3246 3676 4.518590 GGCAAGCTTCTTCTTCTTCTTCTT 59.481 41.667 0.00 0.00 0.00 2.52
3247 3677 5.334802 GGCAAGCTTCTTCTTCTTCTTCTTC 60.335 44.000 0.00 0.00 0.00 2.87
3262 3692 5.695851 TCTTCTTCTTGCACATTTCCTTC 57.304 39.130 0.00 0.00 0.00 3.46
3281 3711 4.507021 CCTTCGATGACAGTGATCTGATTG 59.493 45.833 0.00 0.00 43.76 2.67
3292 3722 3.573967 GTGATCTGATTGGTGGTTTTGGT 59.426 43.478 0.00 0.00 0.00 3.67
3301 3731 5.461032 TTGGTGGTTTTGGTTATGCTTAG 57.539 39.130 0.00 0.00 0.00 2.18
3307 3737 2.137810 TTGGTTATGCTTAGGCCACC 57.862 50.000 5.01 0.64 37.74 4.61
3315 3745 1.429148 GCTTAGGCCACCGAATCGTG 61.429 60.000 5.01 0.14 0.00 4.35
3346 3776 8.319146 ACGGATTTGGAACTCTAAAGATAGAAA 58.681 33.333 0.00 0.00 37.70 2.52
3388 3818 1.534595 GCAGGCTTCAGTTCAGAGTTG 59.465 52.381 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.955471 TGGAAAACAAATTTGTGGGCAA 58.045 36.364 23.93 7.46 41.31 4.52
66 67 6.690194 TGAAATGGAAAACAAATTTGTGGG 57.310 33.333 23.93 0.00 41.31 4.61
77 78 7.728847 ACTTTTTGCCTATGAAATGGAAAAC 57.271 32.000 0.00 0.00 31.07 2.43
262 271 2.368439 TCCCTGAGCATTGGAATTTCG 58.632 47.619 0.00 0.00 0.00 3.46
349 379 6.419484 TGTGATAAAACTTGTCTCTCCTCA 57.581 37.500 0.00 0.00 0.00 3.86
387 419 0.540365 CTGGAAGCCAAAGCCCTGAA 60.540 55.000 0.00 0.00 41.25 3.02
462 494 9.638176 ATCTGGATTAAAGATTTACTGATGCTT 57.362 29.630 0.00 0.00 29.94 3.91
504 537 6.154203 TGAATACCTGCAAACAAACATGAA 57.846 33.333 0.00 0.00 0.00 2.57
514 547 6.222389 CAAATTGTCCTTGAATACCTGCAAA 58.778 36.000 0.00 0.00 0.00 3.68
538 571 6.085555 GCTGGGGCTAAATAATTTACTTCC 57.914 41.667 0.00 0.00 35.22 3.46
619 652 3.931907 AGGAATCCACCAATGATCGAA 57.068 42.857 0.61 0.00 0.00 3.71
624 657 1.076841 TGGCAAGGAATCCACCAATGA 59.923 47.619 0.61 0.00 0.00 2.57
686 719 4.226427 TCTCCAGTTCAATGCTAATGCT 57.774 40.909 0.00 0.00 40.48 3.79
726 759 8.277918 AGCTCCTCATAAGAATGGTCTTTATTT 58.722 33.333 0.00 0.00 41.55 1.40
736 769 5.167121 CCATCGTAGCTCCTCATAAGAATG 58.833 45.833 0.00 0.00 0.00 2.67
1140 1177 2.157640 AGTCTAGCATGCTCTCCAGT 57.842 50.000 26.57 6.55 0.00 4.00
1191 1228 5.600696 GAGATGAAGAAAGATCTCCACTCC 58.399 45.833 0.00 0.00 39.06 3.85
1203 1240 7.338710 ACCTCATATTTTCGGAGATGAAGAAA 58.661 34.615 0.00 0.00 35.04 2.52
1206 1243 7.066284 ACAAACCTCATATTTTCGGAGATGAAG 59.934 37.037 0.00 0.00 35.04 3.02
1284 1321 1.084289 GACGTAGCTGCCCGATTTTT 58.916 50.000 14.99 0.00 0.00 1.94
1358 1395 1.001974 GGTGCCTCAAATTCCCCAAAC 59.998 52.381 0.00 0.00 0.00 2.93
1524 1564 1.885887 CCTTCGGAAAAACCATCAGCA 59.114 47.619 0.00 0.00 38.90 4.41
1559 1629 3.748083 ACATGAGAGCTGAACACACAAT 58.252 40.909 0.00 0.00 0.00 2.71
1574 1644 5.297776 ACTTGTGGTCTCAAGAAAACATGAG 59.702 40.000 16.53 0.00 45.11 2.90
1975 2061 4.682563 TGGATCCATTTTGGTACATTGGT 58.317 39.130 11.44 0.00 39.30 3.67
1984 2070 5.537295 TCTGAAGCATATGGATCCATTTTGG 59.463 40.000 31.70 18.63 39.43 3.28
2053 2145 1.005450 GAACCCAAGGGCTTGTATGGA 59.995 52.381 4.70 0.00 38.85 3.41
2102 2197 4.090588 TCCCCGTGAACGCATCCC 62.091 66.667 0.00 0.00 38.18 3.85
2107 2202 2.358247 ATGTGTCCCCGTGAACGC 60.358 61.111 0.00 0.00 38.18 4.84
2135 2230 0.827368 ACTCGGGAAAGATGAGCTCC 59.173 55.000 12.15 0.00 32.98 4.70
2186 2281 1.168407 AAACGACACCGACTCGAGGA 61.168 55.000 18.41 0.00 39.50 3.71
2201 2296 1.971962 GCAATGCGTCTTCTTCAAACG 59.028 47.619 0.00 0.00 39.33 3.60
2284 2379 2.435059 GAGGCTTGTGAGGACCGC 60.435 66.667 0.00 0.00 0.00 5.68
2285 2380 0.671781 CTTGAGGCTTGTGAGGACCG 60.672 60.000 0.00 0.00 0.00 4.79
2286 2381 0.322008 CCTTGAGGCTTGTGAGGACC 60.322 60.000 0.00 0.00 0.00 4.46
2403 2517 3.013921 ACACGAATCCAGAGAGAGAGAC 58.986 50.000 0.00 0.00 0.00 3.36
2404 2518 3.013219 CACACGAATCCAGAGAGAGAGA 58.987 50.000 0.00 0.00 0.00 3.10
2406 2520 1.474478 GCACACGAATCCAGAGAGAGA 59.526 52.381 0.00 0.00 0.00 3.10
2526 2641 2.930826 AACCTGGAAGTCAACGACAT 57.069 45.000 0.00 0.00 34.60 3.06
2529 2644 3.823281 TGTAAACCTGGAAGTCAACGA 57.177 42.857 0.00 0.00 0.00 3.85
2530 2645 4.886247 TTTGTAAACCTGGAAGTCAACG 57.114 40.909 0.00 0.00 0.00 4.10
2552 2667 5.596836 AAAAATTGAAGTCAAGCCACAGA 57.403 34.783 0.00 0.00 39.47 3.41
2579 2694 5.984695 AGTAGTTCTGCAATGACTACTGA 57.015 39.130 24.34 0.06 41.14 3.41
2634 2749 2.102084 GAGTGAGAGTGGCATGCATAGA 59.898 50.000 21.36 0.00 0.00 1.98
2663 2782 8.524870 AACAAAAGAAATACTTGCAGCATTAG 57.475 30.769 0.00 0.00 38.98 1.73
2765 2884 1.375140 AGTGCCATCTGTGTGCTCG 60.375 57.895 0.00 0.00 0.00 5.03
2811 2930 3.253188 GCTCCACTTGAGTGTTTTATGCA 59.747 43.478 10.03 0.00 44.21 3.96
2824 3234 2.594303 TGCCCGTTGCTCCACTTG 60.594 61.111 0.00 0.00 42.00 3.16
2837 3247 1.280421 GTGGGGATGATATCTCTGCCC 59.720 57.143 21.06 21.06 35.76 5.36
2852 3262 0.535102 AAAGCGACAAGTCTGTGGGG 60.535 55.000 0.00 0.00 35.30 4.96
2888 3298 7.528996 TTCTTTCATTGTCAGGATGTTGATT 57.471 32.000 0.00 0.00 37.40 2.57
2893 3303 8.086522 CAGAATTTTCTTTCATTGTCAGGATGT 58.913 33.333 0.00 0.00 34.74 3.06
2899 3309 7.147932 TGGTCACAGAATTTTCTTTCATTGTCA 60.148 33.333 0.00 0.00 34.74 3.58
2914 3324 4.949856 AGAACTGTTTGTTGGTCACAGAAT 59.050 37.500 5.57 0.00 39.30 2.40
2919 3329 4.695217 TGAAGAACTGTTTGTTGGTCAC 57.305 40.909 0.00 0.00 39.30 3.67
2947 3357 4.821805 TGACCCAACTTGAAAGATTCAGTC 59.178 41.667 0.00 0.00 41.38 3.51
2970 3380 3.206150 GACGATGCTGTTGGTGGATTAT 58.794 45.455 0.00 0.00 0.00 1.28
2989 3399 1.849097 ATATTCCGTTTCGCGAGGAC 58.151 50.000 14.53 13.67 44.77 3.85
2995 3405 1.462791 CGCCAAATATTCCGTTTCGC 58.537 50.000 0.00 0.00 0.00 4.70
2996 3406 1.666700 TCCGCCAAATATTCCGTTTCG 59.333 47.619 0.00 0.00 0.00 3.46
3002 3412 5.514274 TCAAAGATTCCGCCAAATATTCC 57.486 39.130 0.00 0.00 0.00 3.01
3010 3420 1.543607 TGCATTCAAAGATTCCGCCA 58.456 45.000 0.00 0.00 0.00 5.69
3041 3471 4.322198 CCCAGCAACCGTAAGAACTAACTA 60.322 45.833 0.00 0.00 43.02 2.24
3042 3472 3.556423 CCCAGCAACCGTAAGAACTAACT 60.556 47.826 0.00 0.00 43.02 2.24
3043 3473 2.740447 CCCAGCAACCGTAAGAACTAAC 59.260 50.000 0.00 0.00 43.02 2.34
3044 3474 2.369532 ACCCAGCAACCGTAAGAACTAA 59.630 45.455 0.00 0.00 43.02 2.24
3045 3475 1.972795 ACCCAGCAACCGTAAGAACTA 59.027 47.619 0.00 0.00 43.02 2.24
3046 3476 0.763035 ACCCAGCAACCGTAAGAACT 59.237 50.000 0.00 0.00 43.02 3.01
3047 3477 1.265905 CAACCCAGCAACCGTAAGAAC 59.734 52.381 0.00 0.00 43.02 3.01
3048 3478 1.600023 CAACCCAGCAACCGTAAGAA 58.400 50.000 0.00 0.00 43.02 2.52
3049 3479 0.250553 CCAACCCAGCAACCGTAAGA 60.251 55.000 0.00 0.00 43.02 2.10
3050 3480 1.862602 GCCAACCCAGCAACCGTAAG 61.863 60.000 0.00 0.00 0.00 2.34
3051 3481 1.899534 GCCAACCCAGCAACCGTAA 60.900 57.895 0.00 0.00 0.00 3.18
3052 3482 2.281900 GCCAACCCAGCAACCGTA 60.282 61.111 0.00 0.00 0.00 4.02
3053 3483 4.204028 AGCCAACCCAGCAACCGT 62.204 61.111 0.00 0.00 0.00 4.83
3054 3484 3.673484 CAGCCAACCCAGCAACCG 61.673 66.667 0.00 0.00 0.00 4.44
3055 3485 2.133641 AACAGCCAACCCAGCAACC 61.134 57.895 0.00 0.00 0.00 3.77
3056 3486 1.067916 CAACAGCCAACCCAGCAAC 59.932 57.895 0.00 0.00 0.00 4.17
3057 3487 2.795110 GCAACAGCCAACCCAGCAA 61.795 57.895 0.00 0.00 0.00 3.91
3058 3488 3.225798 GCAACAGCCAACCCAGCA 61.226 61.111 0.00 0.00 0.00 4.41
3059 3489 2.914097 AGCAACAGCCAACCCAGC 60.914 61.111 0.00 0.00 0.00 4.85
3060 3490 1.228367 AGAGCAACAGCCAACCCAG 60.228 57.895 0.00 0.00 0.00 4.45
3061 3491 1.529010 CAGAGCAACAGCCAACCCA 60.529 57.895 0.00 0.00 0.00 4.51
3062 3492 2.924105 GCAGAGCAACAGCCAACCC 61.924 63.158 0.00 0.00 0.00 4.11
3063 3493 0.606401 TAGCAGAGCAACAGCCAACC 60.606 55.000 0.00 0.00 0.00 3.77
3064 3494 1.068954 GTTAGCAGAGCAACAGCCAAC 60.069 52.381 0.00 0.00 0.00 3.77
3065 3495 1.202806 AGTTAGCAGAGCAACAGCCAA 60.203 47.619 0.00 0.00 0.00 4.52
3066 3496 0.397941 AGTTAGCAGAGCAACAGCCA 59.602 50.000 0.00 0.00 0.00 4.75
3067 3497 0.801251 CAGTTAGCAGAGCAACAGCC 59.199 55.000 0.00 0.00 0.00 4.85
3068 3498 1.800805 TCAGTTAGCAGAGCAACAGC 58.199 50.000 0.00 0.00 0.00 4.40
3069 3499 2.159234 GCTTCAGTTAGCAGAGCAACAG 59.841 50.000 0.00 0.00 40.89 3.16
3070 3500 2.146342 GCTTCAGTTAGCAGAGCAACA 58.854 47.619 0.00 0.00 40.89 3.33
3071 3501 1.466558 GGCTTCAGTTAGCAGAGCAAC 59.533 52.381 0.00 0.00 43.02 4.17
3072 3502 1.072173 TGGCTTCAGTTAGCAGAGCAA 59.928 47.619 0.00 0.00 43.02 3.91
3073 3503 0.686789 TGGCTTCAGTTAGCAGAGCA 59.313 50.000 0.00 0.00 43.02 4.26
3074 3504 1.466558 GTTGGCTTCAGTTAGCAGAGC 59.533 52.381 0.00 0.00 43.02 4.09
3075 3505 3.051081 AGTTGGCTTCAGTTAGCAGAG 57.949 47.619 0.00 0.00 43.02 3.35
3076 3506 4.315803 GTTAGTTGGCTTCAGTTAGCAGA 58.684 43.478 0.00 0.00 43.02 4.26
3077 3507 3.123621 CGTTAGTTGGCTTCAGTTAGCAG 59.876 47.826 0.00 0.00 43.02 4.24
3078 3508 3.064207 CGTTAGTTGGCTTCAGTTAGCA 58.936 45.455 0.00 0.00 43.02 3.49
3079 3509 2.415512 CCGTTAGTTGGCTTCAGTTAGC 59.584 50.000 0.00 0.00 40.48 3.09
3094 3524 2.483877 TCTTTGTTGCTGATGCCGTTAG 59.516 45.455 0.00 0.00 38.71 2.34
3097 3527 1.317613 TTCTTTGTTGCTGATGCCGT 58.682 45.000 0.00 0.00 38.71 5.68
3105 3535 4.709886 ACCCTTGTAACTTTCTTTGTTGCT 59.290 37.500 0.00 0.00 32.58 3.91
3114 3544 4.546570 GTCATTGCACCCTTGTAACTTTC 58.453 43.478 0.00 0.00 29.21 2.62
3117 3547 2.151202 CGTCATTGCACCCTTGTAACT 58.849 47.619 0.00 0.00 29.21 2.24
3136 3566 6.124088 AGTACCCTGAATAAACGTAGTACG 57.876 41.667 20.82 20.82 45.00 3.67
3137 3567 9.455847 CAATAGTACCCTGAATAAACGTAGTAC 57.544 37.037 0.00 0.00 45.00 2.73
3138 3568 8.137437 GCAATAGTACCCTGAATAAACGTAGTA 58.863 37.037 0.00 0.00 45.00 1.82
3140 3570 6.143438 CGCAATAGTACCCTGAATAAACGTAG 59.857 42.308 0.00 0.00 0.00 3.51
3141 3571 5.978919 CGCAATAGTACCCTGAATAAACGTA 59.021 40.000 0.00 0.00 0.00 3.57
3142 3572 4.807304 CGCAATAGTACCCTGAATAAACGT 59.193 41.667 0.00 0.00 0.00 3.99
3143 3573 5.045215 TCGCAATAGTACCCTGAATAAACG 58.955 41.667 0.00 0.00 0.00 3.60
3144 3574 6.511282 GCTTCGCAATAGTACCCTGAATAAAC 60.511 42.308 0.00 0.00 0.00 2.01
3145 3575 5.526111 GCTTCGCAATAGTACCCTGAATAAA 59.474 40.000 0.00 0.00 0.00 1.40
3146 3576 5.054477 GCTTCGCAATAGTACCCTGAATAA 58.946 41.667 0.00 0.00 0.00 1.40
3147 3577 4.100344 TGCTTCGCAATAGTACCCTGAATA 59.900 41.667 0.00 0.00 34.76 1.75
3148 3578 3.118408 TGCTTCGCAATAGTACCCTGAAT 60.118 43.478 0.00 0.00 34.76 2.57
3149 3579 2.235155 TGCTTCGCAATAGTACCCTGAA 59.765 45.455 0.00 0.00 34.76 3.02
3150 3580 1.828595 TGCTTCGCAATAGTACCCTGA 59.171 47.619 0.00 0.00 34.76 3.86
3151 3581 1.933853 GTGCTTCGCAATAGTACCCTG 59.066 52.381 0.00 0.00 41.47 4.45
3152 3582 1.831736 AGTGCTTCGCAATAGTACCCT 59.168 47.619 0.00 0.00 41.47 4.34
3153 3583 1.933853 CAGTGCTTCGCAATAGTACCC 59.066 52.381 0.00 0.00 41.47 3.69
3154 3584 2.618053 ACAGTGCTTCGCAATAGTACC 58.382 47.619 0.00 0.00 41.47 3.34
3155 3585 4.669318 TCTACAGTGCTTCGCAATAGTAC 58.331 43.478 0.00 0.00 41.47 2.73
3156 3586 4.976224 TCTACAGTGCTTCGCAATAGTA 57.024 40.909 0.00 0.00 41.47 1.82
3157 3587 3.868757 TCTACAGTGCTTCGCAATAGT 57.131 42.857 0.00 0.00 41.47 2.12
3158 3588 4.627467 ACTTTCTACAGTGCTTCGCAATAG 59.373 41.667 0.00 0.00 41.47 1.73
3159 3589 4.566004 ACTTTCTACAGTGCTTCGCAATA 58.434 39.130 0.00 0.00 41.47 1.90
3160 3590 3.403038 ACTTTCTACAGTGCTTCGCAAT 58.597 40.909 0.00 0.00 41.47 3.56
3161 3591 2.800544 GACTTTCTACAGTGCTTCGCAA 59.199 45.455 0.00 0.00 41.47 4.85
3162 3592 2.223947 TGACTTTCTACAGTGCTTCGCA 60.224 45.455 0.00 0.00 35.60 5.10
3163 3593 2.404215 TGACTTTCTACAGTGCTTCGC 58.596 47.619 0.00 0.00 0.00 4.70
3164 3594 2.410053 GCTGACTTTCTACAGTGCTTCG 59.590 50.000 0.00 0.00 36.62 3.79
3165 3595 3.185391 GTGCTGACTTTCTACAGTGCTTC 59.815 47.826 0.00 0.00 36.62 3.86
3166 3596 3.134458 GTGCTGACTTTCTACAGTGCTT 58.866 45.455 0.00 0.00 36.62 3.91
3167 3597 2.103094 TGTGCTGACTTTCTACAGTGCT 59.897 45.455 0.00 0.00 36.62 4.40
3168 3598 2.221981 GTGTGCTGACTTTCTACAGTGC 59.778 50.000 0.00 0.00 36.62 4.40
3169 3599 3.246226 GTGTGTGCTGACTTTCTACAGTG 59.754 47.826 0.00 0.00 36.62 3.66
3209 3639 0.817634 CTTGCCCCGTTCTGTGTTCA 60.818 55.000 0.00 0.00 0.00 3.18
3210 3640 1.949257 CTTGCCCCGTTCTGTGTTC 59.051 57.895 0.00 0.00 0.00 3.18
3212 3642 2.594592 GCTTGCCCCGTTCTGTGT 60.595 61.111 0.00 0.00 0.00 3.72
3218 3648 0.178990 AAGAAGAAGCTTGCCCCGTT 60.179 50.000 2.10 0.00 0.00 4.44
3241 3671 4.214119 TCGAAGGAAATGTGCAAGAAGAAG 59.786 41.667 0.00 0.00 0.00 2.85
3242 3672 4.133820 TCGAAGGAAATGTGCAAGAAGAA 58.866 39.130 0.00 0.00 0.00 2.52
3243 3673 3.738982 TCGAAGGAAATGTGCAAGAAGA 58.261 40.909 0.00 0.00 0.00 2.87
3244 3674 4.154737 TCATCGAAGGAAATGTGCAAGAAG 59.845 41.667 0.00 0.00 0.00 2.85
3245 3675 4.071423 TCATCGAAGGAAATGTGCAAGAA 58.929 39.130 0.00 0.00 0.00 2.52
3246 3676 3.436704 GTCATCGAAGGAAATGTGCAAGA 59.563 43.478 0.00 0.00 0.00 3.02
3247 3677 3.189080 TGTCATCGAAGGAAATGTGCAAG 59.811 43.478 0.00 0.00 0.00 4.01
3262 3692 3.554731 CACCAATCAGATCACTGTCATCG 59.445 47.826 0.00 0.00 43.81 3.84
3281 3711 3.368013 GCCTAAGCATAACCAAAACCACC 60.368 47.826 0.00 0.00 39.53 4.61
3292 3722 2.805295 CGATTCGGTGGCCTAAGCATAA 60.805 50.000 3.32 0.00 42.56 1.90
3315 3745 1.004595 GAGTTCCAAATCCGTACCGC 58.995 55.000 0.00 0.00 0.00 5.68
3346 3776 1.133823 TGCCTCAACCATGTTCAGTGT 60.134 47.619 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.