Multiple sequence alignment - TraesCS7B01G336600

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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 TraesCS7B01G336600 chr7B 100.000 3939 0 0 1 3939 591702031 591705969 0.000000e+00 7275.0
1 TraesCS7B01G336600 chr7B 84.211 551 77 8 2 547 695067273 695066728 9.690000e-146 527.0
2 TraesCS7B01G336600 chr7B 85.241 332 33 8 1693 2022 34614440 34614123 1.060000e-85 327.0
3 TraesCS7B01G336600 chr7A 89.610 1155 73 21 2139 3271 632379233 632380362 0.000000e+00 1424.0
4 TraesCS7B01G336600 chr7A 87.177 1006 85 14 545 1528 632377452 632378435 0.000000e+00 1103.0
5 TraesCS7B01G336600 chr7A 92.462 398 23 3 1628 2022 632378623 632379016 2.660000e-156 562.0
6 TraesCS7B01G336600 chr7A 90.244 328 15 7 3343 3660 632380445 632380765 2.830000e-111 412.0
7 TraesCS7B01G336600 chr7A 87.955 357 32 7 1674 2022 86052476 86052123 1.020000e-110 411.0
8 TraesCS7B01G336600 chr7A 87.500 352 39 3 1673 2022 86074079 86073731 6.130000e-108 401.0
9 TraesCS7B01G336600 chr7A 90.714 280 14 8 3660 3939 632380836 632381103 2.890000e-96 363.0
10 TraesCS7B01G336600 chr7A 85.311 354 40 5 1674 2019 86071890 86071541 4.840000e-94 355.0
11 TraesCS7B01G336600 chr7A 94.286 70 4 0 2021 2090 632379046 632379115 1.500000e-19 108.0
12 TraesCS7B01G336600 chr7A 86.364 66 7 2 2021 2085 86071505 86071441 1.960000e-08 71.3
13 TraesCS7B01G336600 chr7D 88.087 1192 73 26 2189 3342 548604732 548605892 0.000000e+00 1351.0
14 TraesCS7B01G336600 chr7D 89.821 894 54 15 739 1610 548603220 548604098 0.000000e+00 1112.0
15 TraesCS7B01G336600 chr7D 87.184 554 59 10 1 544 165665945 165665394 1.550000e-173 619.0
16 TraesCS7B01G336600 chr7D 94.154 325 12 5 1677 1996 548604151 548604473 4.570000e-134 488.0
17 TraesCS7B01G336600 chr7D 78.253 538 75 27 3390 3906 548606074 548606590 1.370000e-79 307.0
18 TraesCS7B01G336600 chr7D 93.548 62 3 1 2021 2082 84990686 84990626 1.510000e-14 91.6
19 TraesCS7B01G336600 chr7D 91.935 62 4 1 2021 2082 84990457 84990397 7.010000e-13 86.1
20 TraesCS7B01G336600 chr7D 97.778 45 0 1 1648 1692 548604150 548604107 4.220000e-10 76.8
21 TraesCS7B01G336600 chr7D 89.474 57 4 2 2021 2075 85026209 85026153 1.960000e-08 71.3
22 TraesCS7B01G336600 chr5B 91.713 543 38 3 1 543 489915775 489916310 0.000000e+00 747.0
23 TraesCS7B01G336600 chr5B 91.009 545 47 2 1 544 676624918 676624375 0.000000e+00 734.0
24 TraesCS7B01G336600 chr5B 88.504 548 56 7 1 544 642289846 642290390 0.000000e+00 656.0
25 TraesCS7B01G336600 chr3A 89.821 560 52 4 1 556 303544673 303545231 0.000000e+00 713.0
26 TraesCS7B01G336600 chr2D 90.146 548 50 3 1 544 263052334 263052881 0.000000e+00 710.0
27 TraesCS7B01G336600 chr2B 88.483 547 58 5 1 544 146628531 146627987 0.000000e+00 656.0
28 TraesCS7B01G336600 chr2A 84.353 556 71 14 5 549 89962437 89961887 7.490000e-147 531.0
29 TraesCS7B01G336600 chr2A 94.737 38 1 1 2021 2057 20293439 20293476 1.530000e-04 58.4
30 TraesCS7B01G336600 chr6A 84.756 328 45 5 1680 2005 105591588 105591264 1.370000e-84 324.0
31 TraesCS7B01G336600 chr6A 81.744 367 48 18 1673 2026 106073025 106073385 4.980000e-74 289.0
32 TraesCS7B01G336600 chr6A 92.500 40 2 1 2021 2060 105591233 105591195 5.500000e-04 56.5
33 TraesCS7B01G336600 chr6B 83.626 342 47 7 1680 2018 166117554 166117219 2.960000e-81 313.0
34 TraesCS7B01G336600 chr6D 82.544 338 35 16 1700 2019 87463662 87463331 3.880000e-70 276.0
35 TraesCS7B01G336600 chr6D 95.122 41 1 1 2021 2061 87465800 87465761 3.290000e-06 63.9


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 TraesCS7B01G336600 chr7B 591702031 591705969 3938 False 7275.000000 7275 100.000000 1 3939 1 chr7B.!!$F1 3938
1 TraesCS7B01G336600 chr7B 695066728 695067273 545 True 527.000000 527 84.211000 2 547 1 chr7B.!!$R2 545
2 TraesCS7B01G336600 chr7A 632377452 632381103 3651 False 662.000000 1424 90.748833 545 3939 6 chr7A.!!$F1 3394
3 TraesCS7B01G336600 chr7A 86071441 86074079 2638 True 275.766667 401 86.391667 1673 2085 3 chr7A.!!$R2 412
4 TraesCS7B01G336600 chr7D 548603220 548606590 3370 False 814.500000 1351 87.578750 739 3906 4 chr7D.!!$F1 3167
5 TraesCS7B01G336600 chr7D 165665394 165665945 551 True 619.000000 619 87.184000 1 544 1 chr7D.!!$R2 543
6 TraesCS7B01G336600 chr5B 489915775 489916310 535 False 747.000000 747 91.713000 1 543 1 chr5B.!!$F1 542
7 TraesCS7B01G336600 chr5B 676624375 676624918 543 True 734.000000 734 91.009000 1 544 1 chr5B.!!$R1 543
8 TraesCS7B01G336600 chr5B 642289846 642290390 544 False 656.000000 656 88.504000 1 544 1 chr5B.!!$F2 543
9 TraesCS7B01G336600 chr3A 303544673 303545231 558 False 713.000000 713 89.821000 1 556 1 chr3A.!!$F1 555
10 TraesCS7B01G336600 chr2D 263052334 263052881 547 False 710.000000 710 90.146000 1 544 1 chr2D.!!$F1 543
11 TraesCS7B01G336600 chr2B 146627987 146628531 544 True 656.000000 656 88.483000 1 544 1 chr2B.!!$R1 543
12 TraesCS7B01G336600 chr2A 89961887 89962437 550 True 531.000000 531 84.353000 5 549 1 chr2A.!!$R1 544

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
213 214 0.036875 CCTGGGAAGACAAGGTGACC 59.963 60.0 0.00 0.0 0.00 4.02 F
671 686 0.306228 CCACAAACGTCATTGCACGA 59.694 50.0 13.15 0.0 42.69 4.35 F
703 718 0.613012 AGCATCCAGAAGTTTGCCCC 60.613 55.0 0.00 0.0 35.71 5.80 F
2180 4206 0.107945 CCTAGAGCCCTGAACACTGC 60.108 60.0 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 1798 0.179468 GCTTCCACGGCCCAGTATTA 59.821 55.0 0.00 0.0 0.0 0.98 R
1813 3722 0.337773 TCCACCTCTCTGCTCTCCAT 59.662 55.0 0.00 0.0 0.0 3.41 R
2692 4768 0.037160 TGATGGCTGATGTGCTGTGT 59.963 50.0 0.00 0.0 0.0 3.72 R
3869 6224 0.886490 CCCGAGGCCACTGATATTGC 60.886 60.0 5.01 0.0 0.0 3.56 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
213 214 0.036875 CCTGGGAAGACAAGGTGACC 59.963 60.000 0.00 0.00 0.00 4.02
260 261 3.615509 CTCGGGGGCAAGCCGTTTA 62.616 63.158 4.80 0.00 36.85 2.01
330 331 3.071206 GAGACGAGCAGGCCCAGA 61.071 66.667 0.00 0.00 0.00 3.86
549 564 6.607019 ACAAACCCTAGACCTCACATAAAAA 58.393 36.000 0.00 0.00 0.00 1.94
550 565 7.238710 ACAAACCCTAGACCTCACATAAAAAT 58.761 34.615 0.00 0.00 0.00 1.82
551 566 7.176690 ACAAACCCTAGACCTCACATAAAAATG 59.823 37.037 0.00 0.00 0.00 2.32
552 567 6.636454 ACCCTAGACCTCACATAAAAATGA 57.364 37.500 0.00 0.00 0.00 2.57
564 579 9.426837 CTCACATAAAAATGACATTTGTGGAAT 57.573 29.630 21.89 5.36 34.40 3.01
570 585 8.503458 AAAAATGACATTTGTGGAATTTGTGA 57.497 26.923 14.05 0.00 31.77 3.58
572 587 5.588958 TGACATTTGTGGAATTTGTGACA 57.411 34.783 0.00 0.00 0.00 3.58
659 674 2.574018 GGCCAGGGCTTCCACAAAC 61.574 63.158 10.60 0.00 41.60 2.93
660 675 2.919494 GCCAGGGCTTCCACAAACG 61.919 63.158 2.30 0.00 38.26 3.60
666 681 1.335872 GGGCTTCCACAAACGTCATTG 60.336 52.381 0.00 0.00 36.37 2.82
671 686 0.306228 CCACAAACGTCATTGCACGA 59.694 50.000 13.15 0.00 42.69 4.35
679 694 2.157668 ACGTCATTGCACGATGAAACTC 59.842 45.455 10.73 0.00 42.69 3.01
695 710 2.110901 ACTCTGCAAGCATCCAGAAG 57.889 50.000 0.00 0.91 37.61 2.85
696 711 1.350351 ACTCTGCAAGCATCCAGAAGT 59.650 47.619 0.00 1.38 37.61 3.01
699 714 2.555325 TCTGCAAGCATCCAGAAGTTTG 59.445 45.455 0.00 0.00 35.32 2.93
700 715 1.706443 GCAAGCATCCAGAAGTTTGC 58.294 50.000 8.34 8.34 42.91 3.68
703 718 0.613012 AGCATCCAGAAGTTTGCCCC 60.613 55.000 0.00 0.00 35.71 5.80
946 961 2.048127 AGCGCCGTCTTCTTCCAC 60.048 61.111 2.29 0.00 0.00 4.02
950 965 2.890766 GCCGTCTTCTTCCACCCCA 61.891 63.158 0.00 0.00 0.00 4.96
1042 1077 1.658686 GAAGCCGCTCTTCTCTCCGA 61.659 60.000 0.00 0.00 45.99 4.55
1122 1158 1.830477 GTCAGGCACAGAGAGGAATCT 59.170 52.381 0.00 0.00 0.00 2.40
1144 1180 7.411486 TCTTCATTCCTCGTCTTTAGATTCT 57.589 36.000 0.00 0.00 0.00 2.40
1163 1199 3.791320 TCTGTTGGTTAGGAGATCTGGT 58.209 45.455 0.00 0.00 0.00 4.00
1164 1200 4.168101 TCTGTTGGTTAGGAGATCTGGTT 58.832 43.478 0.00 0.00 0.00 3.67
1169 1205 2.026262 GGTTAGGAGATCTGGTTTGGCA 60.026 50.000 0.00 0.00 0.00 4.92
1178 1214 5.021458 AGATCTGGTTTGGCATTCTTGATT 58.979 37.500 0.00 0.00 0.00 2.57
1181 1217 3.401182 TGGTTTGGCATTCTTGATTTGC 58.599 40.909 0.00 0.00 35.64 3.68
1218 1254 4.268359 CTCTCCCCTTTTCCTCTGATTTG 58.732 47.826 0.00 0.00 0.00 2.32
1350 1386 6.773638 TCTGCTTTAGTTCTGGATTTCTTCT 58.226 36.000 0.00 0.00 0.00 2.85
1351 1387 6.652481 TCTGCTTTAGTTCTGGATTTCTTCTG 59.348 38.462 0.00 0.00 0.00 3.02
1365 1401 7.147966 TGGATTTCTTCTGATTCATCCATTGTG 60.148 37.037 0.00 0.00 36.16 3.33
1371 1407 3.688235 TGATTCATCCATTGTGTGCTCA 58.312 40.909 0.00 0.00 0.00 4.26
1473 1510 1.807142 GCTTCAGTAGTTGGGACTTGC 59.193 52.381 0.00 0.00 37.33 4.01
1511 1548 7.815068 CAGAATAGTTGGAAATATAGGAGACCG 59.185 40.741 0.00 0.00 0.00 4.79
1533 1570 5.149054 GACTTATCGAAAATGCTCACTGG 57.851 43.478 0.00 0.00 0.00 4.00
1548 1612 1.153086 CTGGGACATGGTGCTAGGC 60.153 63.158 0.00 0.00 38.20 3.93
1573 1637 1.071314 TGGAATCCCAACCACACCCT 61.071 55.000 0.00 0.00 40.09 4.34
1576 1640 0.702316 AATCCCAACCACACCCTACC 59.298 55.000 0.00 0.00 0.00 3.18
1673 1798 1.273781 CCCCCAATGGATTTTCCCTGT 60.274 52.381 0.00 0.00 35.03 4.00
1674 1799 2.023501 CCCCCAATGGATTTTCCCTGTA 60.024 50.000 0.00 0.00 35.03 2.74
1675 1800 3.567663 CCCCCAATGGATTTTCCCTGTAA 60.568 47.826 0.00 0.00 35.03 2.41
1676 1801 4.297768 CCCCAATGGATTTTCCCTGTAAT 58.702 43.478 0.00 0.00 35.03 1.89
1785 3689 0.885196 GTGAAGCACGGACTCTCTCT 59.115 55.000 0.00 0.00 0.00 3.10
1813 3722 1.200716 CGTTTAGTACCACCTCGCTGA 59.799 52.381 0.00 0.00 0.00 4.26
1998 3907 0.178828 TTTGTGGGGGAGGGTCCATA 60.179 55.000 0.00 0.00 38.64 2.74
2098 4054 7.781324 AGAATTGTCATGTTTTATTCCCTGT 57.219 32.000 0.00 0.00 0.00 4.00
2099 4055 7.605449 AGAATTGTCATGTTTTATTCCCTGTG 58.395 34.615 0.00 0.00 0.00 3.66
2100 4056 4.782019 TGTCATGTTTTATTCCCTGTGC 57.218 40.909 0.00 0.00 0.00 4.57
2101 4057 4.148079 TGTCATGTTTTATTCCCTGTGCA 58.852 39.130 0.00 0.00 0.00 4.57
2103 4059 4.923281 GTCATGTTTTATTCCCTGTGCAAC 59.077 41.667 0.00 0.00 37.35 4.17
2125 4106 4.236935 CAGTTGCAACTAAATCGCCATTT 58.763 39.130 30.67 2.39 37.08 2.32
2180 4206 0.107945 CCTAGAGCCCTGAACACTGC 60.108 60.000 0.00 0.00 0.00 4.40
2181 4207 0.901124 CTAGAGCCCTGAACACTGCT 59.099 55.000 0.00 0.00 36.62 4.24
2182 4208 2.103373 CTAGAGCCCTGAACACTGCTA 58.897 52.381 0.00 0.00 33.41 3.49
2225 4256 5.986135 CGCTGGCTCTATTTTCTTACTATGT 59.014 40.000 0.00 0.00 0.00 2.29
2226 4257 7.013942 TCGCTGGCTCTATTTTCTTACTATGTA 59.986 37.037 0.00 0.00 0.00 2.29
2269 4305 7.777910 TCATTTGTTTCCCTCAGAGAAGTAAAA 59.222 33.333 0.00 0.00 0.00 1.52
2284 4320 3.778265 AGTAAAAGGGCCAACATCATGT 58.222 40.909 6.18 0.00 0.00 3.21
2417 4467 3.567670 CAAATGTTTGTGTTCCGTTGC 57.432 42.857 0.00 0.00 33.59 4.17
2418 4468 1.833860 AATGTTTGTGTTCCGTTGCG 58.166 45.000 0.00 0.00 0.00 4.85
2419 4469 0.736053 ATGTTTGTGTTCCGTTGCGT 59.264 45.000 0.00 0.00 0.00 5.24
2464 4537 6.721571 TCACACTAGCCTTTTATTCTTTCG 57.278 37.500 0.00 0.00 0.00 3.46
2544 4617 8.927675 AGTTTAACCAATGGACAATAACTGTA 57.072 30.769 6.16 0.00 38.84 2.74
2580 4653 2.494870 GGCATGGCTTTCAAAGTGATCT 59.505 45.455 12.86 0.00 0.00 2.75
2589 4662 7.448161 TGGCTTTCAAAGTGATCTATCTGAAAA 59.552 33.333 0.00 0.62 33.68 2.29
2604 4680 5.404466 TCTGAAAAGGGCATACCAAATTG 57.596 39.130 0.00 0.00 43.89 2.32
2692 4768 2.555227 GGAGGCTTTTGAAGATGTGGGA 60.555 50.000 0.00 0.00 0.00 4.37
2784 4860 2.665185 AACGAAGGACGCCACAGC 60.665 61.111 0.00 0.00 46.94 4.40
2786 4862 1.812686 AACGAAGGACGCCACAGCTA 61.813 55.000 0.00 0.00 46.94 3.32
2787 4863 1.141881 CGAAGGACGCCACAGCTAT 59.858 57.895 0.00 0.00 36.60 2.97
2842 4918 0.988063 AGAGGAACAAAGGCTCTCCC 59.012 55.000 0.00 0.00 0.00 4.30
2881 4957 2.354805 GGACTTCGTGCTCCCTTTATGT 60.355 50.000 0.00 0.00 0.00 2.29
2889 4965 3.316308 GTGCTCCCTTTATGTATGCTTGG 59.684 47.826 0.00 0.00 0.00 3.61
2891 4967 3.554934 CTCCCTTTATGTATGCTTGGCA 58.445 45.455 0.00 0.00 44.86 4.92
2920 4996 2.901192 TGCAGCTTGGTACTACCTAACA 59.099 45.455 6.79 0.00 39.58 2.41
2940 5016 1.934220 TTCGTGGCCGAGAGCTAGTG 61.934 60.000 0.00 0.00 45.24 2.74
2949 5025 2.722071 CGAGAGCTAGTGAATTCGGAC 58.278 52.381 0.04 0.00 0.00 4.79
2979 5055 8.978564 TTCATATCATTGCACATTTTTACGTT 57.021 26.923 0.00 0.00 0.00 3.99
2995 5071 6.489127 TTTACGTTAATAGTGTTGCTGCAT 57.511 33.333 1.84 0.00 0.00 3.96
3005 5081 3.064408 AGTGTTGCTGCATCGATACATTG 59.936 43.478 1.84 0.00 0.00 2.82
3007 5083 3.310501 TGTTGCTGCATCGATACATTGAG 59.689 43.478 1.84 0.00 0.00 3.02
3011 5087 3.732212 CTGCATCGATACATTGAGGGAA 58.268 45.455 0.00 0.00 0.00 3.97
3013 5089 3.118445 TGCATCGATACATTGAGGGAACA 60.118 43.478 0.00 0.00 0.00 3.18
3026 5102 4.394729 TGAGGGAACATAAACTTGGTCAC 58.605 43.478 0.00 0.00 36.97 3.67
3031 5107 5.278315 GGGAACATAAACTTGGTCACAGAAC 60.278 44.000 0.00 0.00 36.70 3.01
3099 5182 5.897377 GGCATATTTCGCCCTACATATTT 57.103 39.130 0.00 0.00 44.22 1.40
3112 5195 7.327214 GCCCTACATATTTCAAATTTGTTGGA 58.673 34.615 25.09 5.51 35.93 3.53
3151 5234 3.381272 CCTGCCTATAACACAAACCATGG 59.619 47.826 11.19 11.19 0.00 3.66
3156 5239 3.940209 ATAACACAAACCATGGCAGTG 57.060 42.857 22.91 22.91 36.34 3.66
3157 5240 1.774110 AACACAAACCATGGCAGTGA 58.226 45.000 28.31 0.00 34.47 3.41
3158 5241 1.032014 ACACAAACCATGGCAGTGAC 58.968 50.000 28.31 0.00 34.47 3.67
3159 5242 1.031235 CACAAACCATGGCAGTGACA 58.969 50.000 21.06 0.00 32.14 3.58
3160 5243 1.032014 ACAAACCATGGCAGTGACAC 58.968 50.000 13.04 0.00 0.00 3.67
3161 5244 1.321474 CAAACCATGGCAGTGACACT 58.679 50.000 13.04 1.07 0.00 3.55
3254 5337 6.260936 AGAATTTATCTTAGTTGCGTGATGGG 59.739 38.462 0.00 0.00 33.39 4.00
3296 5421 9.998106 AGTACTTATTCACTTGACACATAAAGT 57.002 29.630 0.00 0.00 37.09 2.66
3324 5449 1.770658 TGGATCCACTGGGCAATCTAG 59.229 52.381 11.44 0.00 0.00 2.43
3349 5474 8.200792 AGAACTCTAGGAAAACATGCAGTATAG 58.799 37.037 0.00 0.00 0.00 1.31
3356 5481 5.765182 GGAAAACATGCAGTATAGGCTATGT 59.235 40.000 17.24 4.14 35.80 2.29
3435 5700 6.377327 TTTCTTCTGAGTGAACAATGTTCC 57.623 37.500 21.75 13.55 0.00 3.62
3436 5701 5.034852 TCTTCTGAGTGAACAATGTTCCA 57.965 39.130 21.75 12.34 0.00 3.53
3437 5702 5.624159 TCTTCTGAGTGAACAATGTTCCAT 58.376 37.500 21.75 11.20 0.00 3.41
3462 5740 3.425858 GTCGCTTTATCCGTAGAATCAGC 59.574 47.826 0.00 0.00 0.00 4.26
3473 5751 2.270434 AGAATCAGCCTCCAGGGTAA 57.730 50.000 0.00 0.00 45.47 2.85
3660 5944 7.272244 TGAATTAGAACAAAGACTGACAGTGA 58.728 34.615 14.14 0.00 0.00 3.41
3661 5945 7.768582 TGAATTAGAACAAAGACTGACAGTGAA 59.231 33.333 14.14 0.00 0.00 3.18
3662 5946 8.682936 AATTAGAACAAAGACTGACAGTGAAT 57.317 30.769 14.14 0.00 0.00 2.57
3663 5947 5.998454 AGAACAAAGACTGACAGTGAATG 57.002 39.130 14.14 10.73 0.00 2.67
3666 5950 3.562973 ACAAAGACTGACAGTGAATGCAG 59.437 43.478 14.14 1.44 38.35 4.41
3667 5951 2.469274 AGACTGACAGTGAATGCAGG 57.531 50.000 14.14 0.00 37.37 4.85
3668 5952 1.696336 AGACTGACAGTGAATGCAGGT 59.304 47.619 14.14 0.00 37.37 4.00
3669 5953 2.899900 AGACTGACAGTGAATGCAGGTA 59.100 45.455 14.14 0.00 37.37 3.08
3693 6048 9.209175 GTAATAGTTGTCAAGAGTGAAATCTGT 57.791 33.333 0.00 0.00 34.87 3.41
3750 6105 9.474313 TGACAAATAGGCTAATTCAATTAAGGT 57.526 29.630 0.00 0.00 0.00 3.50
3757 6112 8.738645 AGGCTAATTCAATTAAGGTAGACAAG 57.261 34.615 0.00 0.00 0.00 3.16
3758 6113 7.775561 AGGCTAATTCAATTAAGGTAGACAAGG 59.224 37.037 0.00 0.00 0.00 3.61
3759 6114 7.773690 GGCTAATTCAATTAAGGTAGACAAGGA 59.226 37.037 0.00 0.00 0.00 3.36
3760 6115 9.343539 GCTAATTCAATTAAGGTAGACAAGGAT 57.656 33.333 0.00 0.00 0.00 3.24
3762 6117 8.438676 AATTCAATTAAGGTAGACAAGGATCG 57.561 34.615 0.00 0.00 0.00 3.69
3785 6140 5.799936 CGACATTATTGTTTTGGATCCACAC 59.200 40.000 15.91 14.88 35.79 3.82
3786 6141 6.036577 ACATTATTGTTTTGGATCCACACC 57.963 37.500 15.91 0.00 29.55 4.16
3814 6169 1.612442 GCTCACCTGGTCACCCCTA 60.612 63.158 0.00 0.00 0.00 3.53
3815 6170 1.617947 GCTCACCTGGTCACCCCTAG 61.618 65.000 0.00 0.00 0.00 3.02
3816 6171 0.252284 CTCACCTGGTCACCCCTAGT 60.252 60.000 0.00 0.00 0.00 2.57
3817 6172 0.252103 TCACCTGGTCACCCCTAGTC 60.252 60.000 0.00 0.00 0.00 2.59
3861 6216 8.327941 TGGTAAATCATTTATGCAGAGATAGC 57.672 34.615 0.00 0.00 0.00 2.97
3863 6218 8.449397 GGTAAATCATTTATGCAGAGATAGCTG 58.551 37.037 0.00 0.00 38.91 4.24
3869 6224 5.474578 TTATGCAGAGATAGCTGGGTAAG 57.525 43.478 0.00 0.00 36.41 2.34
3888 6243 0.886490 GCAATATCAGTGGCCTCGGG 60.886 60.000 3.32 0.00 0.00 5.14
3923 6280 4.949856 GCTCTAGGGTCATTTTCCATTTCA 59.050 41.667 0.00 0.00 0.00 2.69
3931 6288 8.605065 AGGGTCATTTTCCATTTCATTTTATGT 58.395 29.630 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 180 1.339631 CCCAGGTAGCCATTTCGACAA 60.340 52.381 0.00 0.00 0.00 3.18
260 261 2.780010 CTGACAATCCCACCCTCCTTAT 59.220 50.000 0.00 0.00 0.00 1.73
549 564 6.159299 TGTCACAAATTCCACAAATGTCAT 57.841 33.333 0.00 0.00 0.00 3.06
550 565 5.588958 TGTCACAAATTCCACAAATGTCA 57.411 34.783 0.00 0.00 0.00 3.58
551 566 6.900568 TTTGTCACAAATTCCACAAATGTC 57.099 33.333 0.00 0.00 34.56 3.06
552 567 7.678947 TTTTTGTCACAAATTCCACAAATGT 57.321 28.000 3.17 0.00 38.27 2.71
639 654 2.595954 TTTGTGGAAGCCCTGGCCAA 62.596 55.000 7.01 0.00 43.17 4.52
659 674 2.413112 AGAGTTTCATCGTGCAATGACG 59.587 45.455 0.42 0.00 40.83 4.35
660 675 3.740590 CAGAGTTTCATCGTGCAATGAC 58.259 45.455 0.42 0.00 35.44 3.06
666 681 1.727213 GCTTGCAGAGTTTCATCGTGC 60.727 52.381 0.00 0.00 34.62 5.34
671 686 2.753452 CTGGATGCTTGCAGAGTTTCAT 59.247 45.455 14.95 0.00 43.52 2.57
679 694 2.925306 GCAAACTTCTGGATGCTTGCAG 60.925 50.000 14.05 14.05 42.29 4.41
728 743 6.093633 ACGCAGAGTAAAATAGGACAATTTCC 59.906 38.462 0.00 0.00 46.33 3.13
729 744 7.073342 ACGCAGAGTAAAATAGGACAATTTC 57.927 36.000 0.00 0.00 0.00 2.17
730 745 6.183360 CGACGCAGAGTAAAATAGGACAATTT 60.183 38.462 0.00 0.00 0.00 1.82
731 746 5.291128 CGACGCAGAGTAAAATAGGACAATT 59.709 40.000 0.00 0.00 0.00 2.32
732 747 4.804139 CGACGCAGAGTAAAATAGGACAAT 59.196 41.667 0.00 0.00 0.00 2.71
737 752 3.114065 GACCGACGCAGAGTAAAATAGG 58.886 50.000 0.00 0.00 0.00 2.57
946 961 1.490574 GGGGAGAGATATCGATGGGG 58.509 60.000 8.54 0.00 0.00 4.96
950 965 1.683629 GGAGCGGGGAGAGATATCGAT 60.684 57.143 2.16 2.16 0.00 3.59
996 1031 1.153349 GGTCTCCTCCGCCATTGAC 60.153 63.158 0.00 0.00 0.00 3.18
1042 1077 1.508545 CGTGGAGCGAGACATCTGT 59.491 57.895 0.00 0.00 44.77 3.41
1122 1158 6.936279 ACAGAATCTAAAGACGAGGAATGAA 58.064 36.000 0.00 0.00 0.00 2.57
1129 1165 6.531948 CCTAACCAACAGAATCTAAAGACGAG 59.468 42.308 0.00 0.00 0.00 4.18
1140 1176 4.785376 ACCAGATCTCCTAACCAACAGAAT 59.215 41.667 0.00 0.00 0.00 2.40
1144 1180 4.506625 CCAAACCAGATCTCCTAACCAACA 60.507 45.833 0.00 0.00 0.00 3.33
1169 1205 4.082125 AGAGAAACGGGCAAATCAAGAAT 58.918 39.130 0.00 0.00 0.00 2.40
1178 1214 0.984230 AGGATCAGAGAAACGGGCAA 59.016 50.000 0.00 0.00 0.00 4.52
1181 1217 1.410882 GGAGAGGATCAGAGAAACGGG 59.589 57.143 0.00 0.00 37.82 5.28
1183 1219 1.410882 GGGGAGAGGATCAGAGAAACG 59.589 57.143 0.00 0.00 37.82 3.60
1350 1386 3.688235 TGAGCACACAATGGATGAATCA 58.312 40.909 0.00 0.00 0.00 2.57
1351 1387 4.707030 TTGAGCACACAATGGATGAATC 57.293 40.909 0.00 0.00 0.00 2.52
1365 1401 6.368791 TCAGTAGTAACATGACAATTGAGCAC 59.631 38.462 13.59 1.44 0.00 4.40
1473 1510 5.534654 TCCAACTATTCTGGTTGACCTTTTG 59.465 40.000 7.96 0.00 44.58 2.44
1511 1548 4.034510 CCCAGTGAGCATTTTCGATAAGTC 59.965 45.833 0.00 0.00 0.00 3.01
1533 1570 1.227380 CTCGCCTAGCACCATGTCC 60.227 63.158 0.00 0.00 0.00 4.02
1606 1680 6.308566 AGGCAGGGTGTGTTACTAAAAATTA 58.691 36.000 0.00 0.00 0.00 1.40
1610 1684 3.868619 AGGCAGGGTGTGTTACTAAAA 57.131 42.857 0.00 0.00 0.00 1.52
1611 1685 4.978438 TTAGGCAGGGTGTGTTACTAAA 57.022 40.909 0.00 0.00 0.00 1.85
1612 1686 4.978438 TTTAGGCAGGGTGTGTTACTAA 57.022 40.909 0.00 0.00 0.00 2.24
1613 1687 4.532916 TCATTTAGGCAGGGTGTGTTACTA 59.467 41.667 0.00 0.00 0.00 1.82
1615 1689 3.681593 TCATTTAGGCAGGGTGTGTTAC 58.318 45.455 0.00 0.00 0.00 2.50
1616 1690 4.263727 ACATCATTTAGGCAGGGTGTGTTA 60.264 41.667 0.00 0.00 0.00 2.41
1617 1691 2.969821 TCATTTAGGCAGGGTGTGTT 57.030 45.000 0.00 0.00 0.00 3.32
1618 1692 2.041620 ACATCATTTAGGCAGGGTGTGT 59.958 45.455 0.00 0.00 0.00 3.72
1619 1693 2.684881 GACATCATTTAGGCAGGGTGTG 59.315 50.000 0.00 0.00 0.00 3.82
1620 1694 2.680805 CGACATCATTTAGGCAGGGTGT 60.681 50.000 0.00 0.00 0.00 4.16
1622 1696 1.559682 ACGACATCATTTAGGCAGGGT 59.440 47.619 0.00 0.00 0.00 4.34
1623 1697 2.213499 GACGACATCATTTAGGCAGGG 58.787 52.381 0.00 0.00 0.00 4.45
1625 1699 3.126831 GAGGACGACATCATTTAGGCAG 58.873 50.000 0.00 0.00 0.00 4.85
1657 1782 6.040842 CCCAGTATTACAGGGAAAATCCATTG 59.959 42.308 17.26 0.00 46.93 2.82
1673 1798 0.179468 GCTTCCACGGCCCAGTATTA 59.821 55.000 0.00 0.00 0.00 0.98
1674 1799 1.077716 GCTTCCACGGCCCAGTATT 60.078 57.895 0.00 0.00 0.00 1.89
1675 1800 1.635817 ATGCTTCCACGGCCCAGTAT 61.636 55.000 0.00 0.00 0.00 2.12
1676 1801 1.847798 AATGCTTCCACGGCCCAGTA 61.848 55.000 0.00 0.00 0.00 2.74
1785 3689 5.280654 AGGTGGTACTAAACGAAAGAACA 57.719 39.130 0.00 0.00 0.00 3.18
1813 3722 0.337773 TCCACCTCTCTGCTCTCCAT 59.662 55.000 0.00 0.00 0.00 3.41
1865 3774 4.202050 GCCGAGAAAGGTATGATTTGCAAT 60.202 41.667 0.00 0.00 0.00 3.56
1943 3852 3.122480 TCATTGTGAGGATGTACCCCAT 58.878 45.455 4.49 0.00 40.05 4.00
2100 4056 2.979813 GGCGATTTAGTTGCAACTGTTG 59.020 45.455 36.50 25.66 40.07 3.33
2101 4057 2.621055 TGGCGATTTAGTTGCAACTGTT 59.379 40.909 36.50 22.62 40.07 3.16
2103 4059 2.987413 TGGCGATTTAGTTGCAACTG 57.013 45.000 36.50 22.67 40.07 3.16
2104 4060 4.236935 CAAATGGCGATTTAGTTGCAACT 58.763 39.130 32.97 32.97 42.91 3.16
2125 4106 0.767998 TACCACACAATGACTGCCCA 59.232 50.000 0.00 0.00 0.00 5.36
2180 4206 3.990469 CGAAGCAATAGTGGGTATGCTAG 59.010 47.826 0.00 0.00 30.13 3.42
2181 4207 3.990092 CGAAGCAATAGTGGGTATGCTA 58.010 45.455 0.00 0.00 30.13 3.49
2182 4208 2.838736 CGAAGCAATAGTGGGTATGCT 58.161 47.619 0.00 0.00 30.98 3.79
2245 4279 7.231519 CCTTTTACTTCTCTGAGGGAAACAAAT 59.768 37.037 4.59 0.00 0.00 2.32
2260 4296 4.112634 TGATGTTGGCCCTTTTACTTCT 57.887 40.909 0.00 0.00 0.00 2.85
2269 4305 5.129368 ACTTTATACATGATGTTGGCCCT 57.871 39.130 2.29 0.00 0.00 5.19
2284 4320 9.653287 CTGTCCTGTGATTCACTAAACTTTATA 57.347 33.333 17.26 0.00 35.11 0.98
2340 4378 1.571215 GACGCGGATTTTTGGGACGT 61.571 55.000 12.47 0.00 34.58 4.34
2407 4457 1.865970 ACGATTTTACGCAACGGAACA 59.134 42.857 0.00 0.00 36.70 3.18
2413 4463 2.095919 AGGCTTGACGATTTTACGCAAC 60.096 45.455 0.00 0.00 36.70 4.17
2414 4464 2.147958 AGGCTTGACGATTTTACGCAA 58.852 42.857 0.00 0.00 36.70 4.85
2417 4467 4.600012 AATGAGGCTTGACGATTTTACG 57.400 40.909 0.00 0.00 39.31 3.18
2418 4468 7.640240 GTGATTAATGAGGCTTGACGATTTTAC 59.360 37.037 0.00 0.00 0.00 2.01
2419 4469 7.335673 TGTGATTAATGAGGCTTGACGATTTTA 59.664 33.333 0.00 0.00 0.00 1.52
2464 4537 3.273434 TCATGGAACTAATGCAGCTGTC 58.727 45.455 16.64 8.39 30.55 3.51
2544 4617 4.711355 AGCCATGCCAAGTGTGTAAATATT 59.289 37.500 0.00 0.00 0.00 1.28
2548 4621 1.993956 AGCCATGCCAAGTGTGTAAA 58.006 45.000 0.00 0.00 0.00 2.01
2557 4630 2.037901 TCACTTTGAAAGCCATGCCAA 58.962 42.857 4.57 0.00 0.00 4.52
2580 4653 6.406849 GCAATTTGGTATGCCCTTTTCAGATA 60.407 38.462 0.00 0.00 36.56 1.98
2589 4662 2.530460 TCAGCAATTTGGTATGCCCT 57.470 45.000 0.00 0.00 43.57 5.19
2604 4680 8.368126 CGAAATAAAATTGAACAACTCATCAGC 58.632 33.333 0.00 0.00 32.78 4.26
2692 4768 0.037160 TGATGGCTGATGTGCTGTGT 59.963 50.000 0.00 0.00 0.00 3.72
2734 4810 1.338337 ACATAGTCCTCGATGCTTCCG 59.662 52.381 0.00 0.00 31.45 4.30
2842 4918 1.879380 TCCAGAAATGTGTTTGGAGCG 59.121 47.619 0.00 0.00 0.00 5.03
2889 4965 1.740296 CAAGCTGCAAAGGCCATGC 60.740 57.895 22.68 22.68 44.08 4.06
2891 4967 0.251742 TACCAAGCTGCAAAGGCCAT 60.252 50.000 5.01 0.00 40.13 4.40
2940 5016 7.536622 GCAATGATATGAATCTTGTCCGAATTC 59.463 37.037 0.00 0.00 32.93 2.17
2979 5055 5.596845 TGTATCGATGCAGCAACACTATTA 58.403 37.500 12.50 0.00 0.00 0.98
2981 5057 4.058721 TGTATCGATGCAGCAACACTAT 57.941 40.909 12.50 0.00 0.00 2.12
2995 5071 6.884832 AGTTTATGTTCCCTCAATGTATCGA 58.115 36.000 0.00 0.00 0.00 3.59
3005 5081 4.394729 TGTGACCAAGTTTATGTTCCCTC 58.605 43.478 0.00 0.00 0.00 4.30
3007 5083 4.394729 TCTGTGACCAAGTTTATGTTCCC 58.605 43.478 0.00 0.00 0.00 3.97
3011 5087 4.787551 TGGTTCTGTGACCAAGTTTATGT 58.212 39.130 3.75 0.00 46.33 2.29
3026 5102 3.760151 TCCATCAAGAGCAAATGGTTCTG 59.240 43.478 0.00 0.00 40.69 3.02
3031 5107 2.731572 ACCTCCATCAAGAGCAAATGG 58.268 47.619 0.00 0.00 41.12 3.16
3099 5182 6.015180 CCTCCAAGAAGATCCAACAAATTTGA 60.015 38.462 24.64 2.30 0.00 2.69
3112 5195 0.918310 AGGCCAGCCTCCAAGAAGAT 60.918 55.000 5.04 0.00 44.43 2.40
3136 5219 3.255642 GTCACTGCCATGGTTTGTGTTAT 59.744 43.478 23.20 0.00 0.00 1.89
3151 5234 3.207677 CACTCCTCAGTGTCACTGC 57.792 57.895 25.45 0.00 45.54 4.40
3159 5242 1.145945 TCTCAGTGTCCACTCCTCAGT 59.854 52.381 0.00 0.00 40.20 3.41
3160 5243 1.916506 TCTCAGTGTCCACTCCTCAG 58.083 55.000 0.00 0.00 40.20 3.35
3161 5244 2.174360 CATCTCAGTGTCCACTCCTCA 58.826 52.381 0.00 0.00 40.20 3.86
3162 5245 2.175202 ACATCTCAGTGTCCACTCCTC 58.825 52.381 0.00 0.00 40.20 3.71
3163 5246 2.317371 ACATCTCAGTGTCCACTCCT 57.683 50.000 0.00 0.00 40.20 3.69
3164 5247 3.181471 CCATACATCTCAGTGTCCACTCC 60.181 52.174 0.00 0.00 40.20 3.85
3165 5248 3.701542 TCCATACATCTCAGTGTCCACTC 59.298 47.826 0.00 0.00 40.20 3.51
3166 5249 3.713003 TCCATACATCTCAGTGTCCACT 58.287 45.455 0.00 0.00 43.61 4.00
3167 5250 4.679373 ATCCATACATCTCAGTGTCCAC 57.321 45.455 0.00 0.00 33.62 4.02
3168 5251 4.835056 CCTATCCATACATCTCAGTGTCCA 59.165 45.833 0.00 0.00 33.62 4.02
3169 5252 4.221703 CCCTATCCATACATCTCAGTGTCC 59.778 50.000 0.00 0.00 33.62 4.02
3254 5337 9.303537 GAATAAGTACTAGATCACTTGGAACAC 57.696 37.037 14.98 0.00 39.29 3.32
3312 5437 4.219115 TCCTAGAGTTCTAGATTGCCCAG 58.781 47.826 15.97 0.00 46.80 4.45
3324 5449 7.439655 CCTATACTGCATGTTTTCCTAGAGTTC 59.560 40.741 0.00 0.00 0.00 3.01
3349 5474 8.432805 AGAGGTGGCATATTATTATACATAGCC 58.567 37.037 0.00 0.00 39.95 3.93
3356 5481 6.573434 CGAGCAGAGGTGGCATATTATTATA 58.427 40.000 0.00 0.00 0.00 0.98
3435 5700 3.702330 TCTACGGATAAAGCGACACATG 58.298 45.455 0.00 0.00 0.00 3.21
3436 5701 4.380841 TTCTACGGATAAAGCGACACAT 57.619 40.909 0.00 0.00 0.00 3.21
3437 5702 3.853831 TTCTACGGATAAAGCGACACA 57.146 42.857 0.00 0.00 0.00 3.72
3462 5740 7.336176 GTGTACTAGAAATTTTTACCCTGGAGG 59.664 40.741 0.00 0.00 43.78 4.30
3641 5925 4.274459 GCATTCACTGTCAGTCTTTGTTCT 59.726 41.667 1.37 0.00 0.00 3.01
3660 5944 6.372659 CACTCTTGACAACTATTACCTGCATT 59.627 38.462 0.00 0.00 0.00 3.56
3661 5945 5.877012 CACTCTTGACAACTATTACCTGCAT 59.123 40.000 0.00 0.00 0.00 3.96
3662 5946 5.011635 TCACTCTTGACAACTATTACCTGCA 59.988 40.000 0.00 0.00 0.00 4.41
3663 5947 5.479306 TCACTCTTGACAACTATTACCTGC 58.521 41.667 0.00 0.00 0.00 4.85
3666 5950 8.660373 CAGATTTCACTCTTGACAACTATTACC 58.340 37.037 0.00 0.00 0.00 2.85
3667 5951 9.209175 ACAGATTTCACTCTTGACAACTATTAC 57.791 33.333 0.00 0.00 0.00 1.89
3669 5953 9.950496 ATACAGATTTCACTCTTGACAACTATT 57.050 29.630 0.00 0.00 0.00 1.73
3693 6048 7.333423 GGTACACACTTTGCTCTTAATGTGATA 59.667 37.037 9.02 0.00 39.83 2.15
3750 6105 8.664798 CAAAACAATAATGTCGATCCTTGTCTA 58.335 33.333 0.00 0.00 39.40 2.59
3756 6111 6.263168 GGATCCAAAACAATAATGTCGATCCT 59.737 38.462 6.95 0.00 40.45 3.24
3757 6112 6.039270 TGGATCCAAAACAATAATGTCGATCC 59.961 38.462 13.46 15.65 41.91 3.36
3758 6113 6.912591 GTGGATCCAAAACAATAATGTCGATC 59.087 38.462 18.20 0.00 39.40 3.69
3759 6114 6.376864 TGTGGATCCAAAACAATAATGTCGAT 59.623 34.615 18.20 0.00 39.40 3.59
3760 6115 5.707764 TGTGGATCCAAAACAATAATGTCGA 59.292 36.000 18.20 0.00 39.40 4.20
3761 6116 5.799936 GTGTGGATCCAAAACAATAATGTCG 59.200 40.000 18.20 0.00 39.40 4.35
3762 6117 6.071391 AGGTGTGGATCCAAAACAATAATGTC 60.071 38.462 22.46 3.03 39.40 3.06
3785 6140 2.092212 ACCAGGTGAGCATTTCCATAGG 60.092 50.000 0.00 0.00 0.00 2.57
3786 6141 3.209410 GACCAGGTGAGCATTTCCATAG 58.791 50.000 0.00 0.00 0.00 2.23
3861 6216 2.880890 GCCACTGATATTGCTTACCCAG 59.119 50.000 0.00 0.00 0.00 4.45
3863 6218 2.158608 AGGCCACTGATATTGCTTACCC 60.159 50.000 5.01 0.00 0.00 3.69
3869 6224 0.886490 CCCGAGGCCACTGATATTGC 60.886 60.000 5.01 0.00 0.00 3.56
3888 6243 7.992754 ATGACCCTAGAGCATTGATTTATTC 57.007 36.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.