Multiple sequence alignment - TraesCS4D01G208900

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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 TraesCS4D01G208900 chr4D 100.000 4310 0 0 1 4310 360449841 360454150 0.000000e+00 7960
1 TraesCS4D01G208900 chr4A 88.881 2707 148 45 1646 4310 104410991 104408396 0.000000e+00 3190
2 TraesCS4D01G208900 chr4A 87.539 1292 94 25 5 1259 104413121 104411860 0.000000e+00 1432
3 TraesCS4D01G208900 chr4A 93.214 280 16 1 1263 1542 104411595 104411319 4.010000e-110 409
4 TraesCS4D01G208900 chr4B 92.664 1554 91 13 2070 3619 445229925 445231459 0.000000e+00 2217
5 TraesCS4D01G208900 chr4B 91.023 1593 84 24 1 1554 445227688 445229260 0.000000e+00 2095
6 TraesCS4D01G208900 chr4B 94.646 523 17 6 1557 2078 445229382 445229894 0.000000e+00 800
7 TraesCS4D01G208900 chr4B 88.224 518 39 10 3796 4310 445231692 445232190 2.220000e-167 599
8 TraesCS4D01G208900 chr4B 90.780 141 11 1 3624 3764 445231494 445231632 2.050000e-43 187
9 TraesCS4D01G208900 chr1A 77.081 973 173 35 2134 3075 481674509 481675462 2.300000e-142 516
10 TraesCS4D01G208900 chr1A 74.502 1204 246 46 2132 3302 480935160 480933985 2.350000e-127 466
11 TraesCS4D01G208900 chr3D 74.631 1218 245 38 2130 3313 465027154 465025967 3.010000e-131 479
12 TraesCS4D01G208900 chr3D 81.673 251 44 2 1675 1924 465509504 465509753 1.570000e-49 207
13 TraesCS4D01G208900 chr1D 76.190 1008 180 36 2134 3099 381019561 381020550 1.080000e-130 477
14 TraesCS4D01G208900 chr1D 74.399 1207 242 52 2132 3302 379911999 379910824 5.080000e-124 455
15 TraesCS4D01G208900 chr1B 75.944 1006 186 35 2134 3099 510809344 510810333 2.350000e-127 466
16 TraesCS4D01G208900 chr1B 74.825 1001 200 42 2132 3110 509902338 509901368 5.190000e-109 405
17 TraesCS4D01G208900 chr3A 74.798 988 204 34 2132 3101 608751173 608752133 1.870000e-108 403
18 TraesCS4D01G208900 chr3A 82.996 247 42 0 1678 1924 608347931 608347685 1.560000e-54 224
19 TraesCS4D01G208900 chr3A 82.072 251 43 2 1675 1924 608750570 608750819 3.380000e-51 213
20 TraesCS4D01G208900 chr3B 81.545 233 41 2 1675 1906 618869784 618870015 1.580000e-44 191
21 TraesCS4D01G208900 chr3B 81.000 200 32 5 2132 2328 618870681 618870877 2.080000e-33 154
22 TraesCS4D01G208900 chr3B 83.088 136 21 2 3176 3310 618441101 618440967 5.850000e-24 122


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 TraesCS4D01G208900 chr4D 360449841 360454150 4309 False 7960.0 7960 100.0000 1 4310 1 chr4D.!!$F1 4309
1 TraesCS4D01G208900 chr4A 104408396 104413121 4725 True 1677.0 3190 89.8780 5 4310 3 chr4A.!!$R1 4305
2 TraesCS4D01G208900 chr4B 445227688 445232190 4502 False 1179.6 2217 91.4674 1 4310 5 chr4B.!!$F1 4309
3 TraesCS4D01G208900 chr1A 481674509 481675462 953 False 516.0 516 77.0810 2134 3075 1 chr1A.!!$F1 941
4 TraesCS4D01G208900 chr1A 480933985 480935160 1175 True 466.0 466 74.5020 2132 3302 1 chr1A.!!$R1 1170
5 TraesCS4D01G208900 chr3D 465025967 465027154 1187 True 479.0 479 74.6310 2130 3313 1 chr3D.!!$R1 1183
6 TraesCS4D01G208900 chr1D 381019561 381020550 989 False 477.0 477 76.1900 2134 3099 1 chr1D.!!$F1 965
7 TraesCS4D01G208900 chr1D 379910824 379911999 1175 True 455.0 455 74.3990 2132 3302 1 chr1D.!!$R1 1170
8 TraesCS4D01G208900 chr1B 510809344 510810333 989 False 466.0 466 75.9440 2134 3099 1 chr1B.!!$F1 965
9 TraesCS4D01G208900 chr1B 509901368 509902338 970 True 405.0 405 74.8250 2132 3110 1 chr1B.!!$R1 978
10 TraesCS4D01G208900 chr3A 608750570 608752133 1563 False 308.0 403 78.4350 1675 3101 2 chr3A.!!$F1 1426

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
162 163 0.178987 TTTGGGGTACGTGCAATGGT 60.179 50.0 5.86 0.0 0.00 3.55 F
506 539 0.249447 CGGCAGATTCCAGTCGCATA 60.249 55.0 0.00 0.0 0.00 3.14 F
1367 1704 0.410270 AGTTCCCCGGCCCAAAAATA 59.590 50.0 0.00 0.0 0.00 1.40 F
2099 2932 0.953960 GGTTTCGGCTTCCATGTCGT 60.954 55.0 0.00 0.0 36.35 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1891 0.109342 AAGTGGCTGCAGTTGCTAGT 59.891 50.0 16.64 0.00 42.66 2.57 R
2079 2912 0.673644 CGACATGGAAGCCGAAACCT 60.674 55.0 0.00 0.00 0.00 3.50 R
3265 4195 0.747283 GGAGGCATCAGCTTCTGGTG 60.747 60.0 0.00 2.87 45.39 4.17 R
3684 4653 0.164647 GCGCATTGCTGATATCGACC 59.835 55.0 0.30 0.00 41.73 4.79 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
162 163 0.178987 TTTGGGGTACGTGCAATGGT 60.179 50.000 5.86 0.00 0.00 3.55
167 168 1.459450 GGTACGTGCAATGGTGGAAT 58.541 50.000 5.86 0.00 0.00 3.01
190 211 7.597288 ATTTAGGAACTTAAACCAAGCTTGT 57.403 32.000 24.35 9.39 41.75 3.16
203 224 5.003804 ACCAAGCTTGTACCTTATCTTGTG 58.996 41.667 24.35 6.84 31.64 3.33
277 300 6.126768 CCCATGAAGAACAGAACCCTATAAGA 60.127 42.308 0.00 0.00 0.00 2.10
347 370 6.331369 TGAAACTCTTGAATGAATCAACCC 57.669 37.500 0.00 0.00 43.08 4.11
374 397 3.876914 GCGAACCAATCATCTCCACATTA 59.123 43.478 0.00 0.00 0.00 1.90
416 442 3.130164 ACTGACGAGATGACAAGGAGATG 59.870 47.826 0.00 0.00 0.00 2.90
440 466 3.146104 ACAAATGCTAGCTGTCAAGGT 57.854 42.857 17.23 2.41 37.95 3.50
444 470 2.175236 GCTAGCTGTCAAGGTTGCC 58.825 57.895 7.70 0.00 43.85 4.52
505 538 1.522355 CGGCAGATTCCAGTCGCAT 60.522 57.895 0.00 0.00 0.00 4.73
506 539 0.249447 CGGCAGATTCCAGTCGCATA 60.249 55.000 0.00 0.00 0.00 3.14
507 540 1.221414 GGCAGATTCCAGTCGCATAC 58.779 55.000 0.00 0.00 0.00 2.39
508 541 0.855349 GCAGATTCCAGTCGCATACG 59.145 55.000 0.00 0.00 42.01 3.06
514 547 2.554806 TCCAGTCGCATACGTACTTG 57.445 50.000 0.00 0.00 41.18 3.16
567 600 3.145212 ACCAACTGTTCAAAAGCGAAC 57.855 42.857 0.00 0.00 44.56 3.95
568 601 2.108700 CCAACTGTTCAAAAGCGAACG 58.891 47.619 0.00 0.00 46.77 3.95
569 602 2.223157 CCAACTGTTCAAAAGCGAACGA 60.223 45.455 0.00 0.00 46.77 3.85
570 603 3.548014 CCAACTGTTCAAAAGCGAACGAT 60.548 43.478 0.00 0.00 46.77 3.73
571 604 3.521524 ACTGTTCAAAAGCGAACGATC 57.478 42.857 0.00 0.00 46.77 3.69
572 605 2.869801 ACTGTTCAAAAGCGAACGATCA 59.130 40.909 0.00 0.00 46.77 2.92
611 649 2.890808 GGAGAATATCCGTGTGAGCA 57.109 50.000 0.00 0.00 38.67 4.26
612 650 2.748605 GGAGAATATCCGTGTGAGCAG 58.251 52.381 0.00 0.00 38.67 4.24
613 651 2.101582 GGAGAATATCCGTGTGAGCAGT 59.898 50.000 0.00 0.00 38.67 4.40
614 652 3.119291 GAGAATATCCGTGTGAGCAGTG 58.881 50.000 0.00 0.00 0.00 3.66
615 653 1.594862 GAATATCCGTGTGAGCAGTGC 59.405 52.381 7.13 7.13 0.00 4.40
616 654 0.826715 ATATCCGTGTGAGCAGTGCT 59.173 50.000 19.86 19.86 43.88 4.40
617 655 1.470051 TATCCGTGTGAGCAGTGCTA 58.530 50.000 19.77 0.00 39.88 3.49
727 776 3.737850 CACTGGCAACTCTCTTTTCTCT 58.262 45.455 0.00 0.00 37.61 3.10
760 809 1.401931 CCCAAACAAGCTTCGCTGATG 60.402 52.381 0.00 0.00 39.62 3.07
791 840 3.432782 GAAAAAGCTTGGCTGATCATCG 58.567 45.455 0.00 0.00 39.62 3.84
814 863 7.383687 TCGACACCTAACACTTCTCATATTTT 58.616 34.615 0.00 0.00 0.00 1.82
816 865 7.330946 CGACACCTAACACTTCTCATATTTTCA 59.669 37.037 0.00 0.00 0.00 2.69
832 884 7.609918 TCATATTTTCAATCACCTCGGAAGAAA 59.390 33.333 0.00 0.00 41.32 2.52
833 885 6.648879 ATTTTCAATCACCTCGGAAGAAAA 57.351 33.333 0.00 0.00 41.32 2.29
916 968 6.659668 TCCTCCATATATAACCTGTTCTCTCG 59.340 42.308 0.00 0.00 0.00 4.04
933 985 0.523968 TCGTGTTATGGTACGAGCGC 60.524 55.000 0.00 0.00 43.54 5.92
934 986 1.794455 CGTGTTATGGTACGAGCGCG 61.794 60.000 8.75 8.75 42.54 6.86
970 1022 2.480593 GTTTGCGAAACGTCTGCAC 58.519 52.632 8.59 0.00 34.52 4.57
1005 1057 1.377229 GGTTGGGACGACAATGGGA 59.623 57.895 0.00 0.00 32.24 4.37
1103 1155 2.157668 CCTTCAATGTGCGTACTGTGTC 59.842 50.000 4.97 0.00 0.00 3.67
1119 1171 2.743664 TGTGTCCATGCATTTTCTCTCG 59.256 45.455 0.00 0.00 0.00 4.04
1130 1182 6.835914 TGCATTTTCTCTCGATCTCTTTTTC 58.164 36.000 0.00 0.00 0.00 2.29
1132 1184 6.676700 GCATTTTCTCTCGATCTCTTTTTCCC 60.677 42.308 0.00 0.00 0.00 3.97
1133 1185 4.473477 TTCTCTCGATCTCTTTTTCCCC 57.527 45.455 0.00 0.00 0.00 4.81
1138 1190 2.642807 TCGATCTCTTTTTCCCCTTGGT 59.357 45.455 0.00 0.00 0.00 3.67
1139 1191 2.749621 CGATCTCTTTTTCCCCTTGGTG 59.250 50.000 0.00 0.00 0.00 4.17
1140 1192 1.995376 TCTCTTTTTCCCCTTGGTGC 58.005 50.000 0.00 0.00 0.00 5.01
1144 1196 1.762370 CTTTTTCCCCTTGGTGCTTGT 59.238 47.619 0.00 0.00 0.00 3.16
1147 1199 1.650242 TTCCCCTTGGTGCTTGTGGA 61.650 55.000 0.00 0.00 0.00 4.02
1148 1200 1.152567 CCCCTTGGTGCTTGTGGAA 60.153 57.895 0.00 0.00 0.00 3.53
1174 1226 2.221286 GCTGCATCTCAACATCGATCTG 59.779 50.000 0.00 0.00 0.00 2.90
1179 1231 2.802256 TCTCAACATCGATCTGAAGCG 58.198 47.619 0.00 0.00 35.07 4.68
1232 1302 1.068588 TGAGTTGTCCAGTTGAGACCG 59.931 52.381 0.00 0.00 33.09 4.79
1253 1325 2.223144 GTGCTGCGTGTATTTGTTCTGA 59.777 45.455 0.00 0.00 0.00 3.27
1275 1612 0.464036 GATACCGCCTGATGTGTGGA 59.536 55.000 0.00 0.00 36.85 4.02
1307 1644 0.943673 TGACAATGCACAAGGTGACG 59.056 50.000 0.00 0.00 35.23 4.35
1367 1704 0.410270 AGTTCCCCGGCCCAAAAATA 59.590 50.000 0.00 0.00 0.00 1.40
1472 1809 1.736681 GCCTTGCTCAGTTGCTCTTAG 59.263 52.381 0.00 0.00 0.00 2.18
1473 1810 2.873649 GCCTTGCTCAGTTGCTCTTAGT 60.874 50.000 0.00 0.00 0.00 2.24
1474 1811 3.617531 GCCTTGCTCAGTTGCTCTTAGTA 60.618 47.826 0.00 0.00 0.00 1.82
1483 1820 7.762159 GCTCAGTTGCTCTTAGTACTTAATTCT 59.238 37.037 0.00 0.00 0.00 2.40
1541 1878 5.443185 AAACAAAGTCATGGTCATCACAG 57.557 39.130 0.00 0.00 0.00 3.66
1554 1891 4.708421 GGTCATCACAGTTGGGTAGTACTA 59.292 45.833 0.00 0.00 0.00 1.82
1594 2050 4.920640 TTTCTGAAGACGACTCAGTTCT 57.079 40.909 11.14 0.00 33.57 3.01
1595 2051 6.039493 ACTTTTCTGAAGACGACTCAGTTCTA 59.961 38.462 11.14 0.00 33.57 2.10
1596 2052 5.614923 TTCTGAAGACGACTCAGTTCTAG 57.385 43.478 11.14 0.00 33.57 2.43
1627 2083 3.751175 TGCGAAAAATTACTCCACCTCTG 59.249 43.478 0.00 0.00 0.00 3.35
1960 2756 1.938657 ATCCCGAGGCGATCATAGCG 61.939 60.000 0.00 0.00 35.00 4.26
2091 2924 4.569761 AAAAAGAGAAGGTTTCGGCTTC 57.430 40.909 0.00 0.00 31.81 3.86
2099 2932 0.953960 GGTTTCGGCTTCCATGTCGT 60.954 55.000 0.00 0.00 36.35 4.34
3148 4072 6.427441 TGCACAAGTTATATGGGGTTGATTA 58.573 36.000 0.00 0.00 0.00 1.75
3156 4086 9.707957 AGTTATATGGGGTTGATTAATTCACAA 57.292 29.630 0.00 0.00 32.84 3.33
3174 4104 1.067000 CAATTTTCCTTGCATGCCGGA 60.067 47.619 16.68 17.90 0.00 5.14
3265 4195 2.264794 ACGATGGTCCGTTGCCTC 59.735 61.111 0.00 0.00 40.17 4.70
3322 4252 0.108329 ATGTTAGAGACCGGCCGTTG 60.108 55.000 26.12 12.62 0.00 4.10
3353 4283 8.149647 TGACCAACATTGCTATTCATTTCTTTT 58.850 29.630 0.00 0.00 0.00 2.27
3355 4285 7.329226 ACCAACATTGCTATTCATTTCTTTTCG 59.671 33.333 0.00 0.00 0.00 3.46
3356 4286 7.541783 CCAACATTGCTATTCATTTCTTTTCGA 59.458 33.333 0.00 0.00 0.00 3.71
3401 4331 6.183360 TGGTGGATAAATTAATTACCGCACAC 60.183 38.462 22.17 16.41 31.93 3.82
3426 4356 8.878769 ACACATAAGCACAAAAAGGTTAAAAAG 58.121 29.630 0.00 0.00 33.30 2.27
3427 4357 9.092876 CACATAAGCACAAAAAGGTTAAAAAGA 57.907 29.630 0.00 0.00 33.30 2.52
3432 4362 8.642908 AGCACAAAAAGGTTAAAAAGATGTAC 57.357 30.769 0.00 0.00 0.00 2.90
3433 4363 8.474831 AGCACAAAAAGGTTAAAAAGATGTACT 58.525 29.630 0.00 0.00 0.00 2.73
3478 4411 9.971922 GTATTTTCCCATTATCATTCTTTCCAG 57.028 33.333 0.00 0.00 0.00 3.86
3484 4417 8.281531 TCCCATTATCATTCTTTCCAGTGTTAT 58.718 33.333 0.00 0.00 0.00 1.89
3492 4425 4.569943 TCTTTCCAGTGTTATGCTCTGTC 58.430 43.478 0.00 0.00 37.08 3.51
3498 4431 3.434641 CAGTGTTATGCTCTGTCCTTGTG 59.565 47.826 0.00 0.00 34.86 3.33
3513 4446 2.296752 CCTTGTGACATGTTGCCATTGA 59.703 45.455 0.00 0.00 0.00 2.57
3515 4448 3.579335 TGTGACATGTTGCCATTGATG 57.421 42.857 0.00 0.00 0.00 3.07
3517 4450 2.094390 GTGACATGTTGCCATTGATGCT 60.094 45.455 0.00 0.00 0.00 3.79
3518 4451 2.563620 TGACATGTTGCCATTGATGCTT 59.436 40.909 0.00 0.00 0.00 3.91
3520 4453 3.331150 ACATGTTGCCATTGATGCTTTG 58.669 40.909 0.00 0.00 0.00 2.77
3521 4454 1.798283 TGTTGCCATTGATGCTTTGC 58.202 45.000 0.00 0.00 0.00 3.68
3522 4455 1.345089 TGTTGCCATTGATGCTTTGCT 59.655 42.857 0.00 0.00 0.00 3.91
3524 4457 2.087501 TGCCATTGATGCTTTGCTTG 57.912 45.000 0.00 0.00 0.00 4.01
3525 4458 0.725117 GCCATTGATGCTTTGCTTGC 59.275 50.000 0.00 0.00 0.00 4.01
3526 4459 1.674817 GCCATTGATGCTTTGCTTGCT 60.675 47.619 0.00 0.00 0.00 3.91
3527 4460 2.695359 CCATTGATGCTTTGCTTGCTT 58.305 42.857 0.00 0.00 0.00 3.91
3528 4461 3.071479 CCATTGATGCTTTGCTTGCTTT 58.929 40.909 0.00 0.00 0.00 3.51
3529 4462 3.500680 CCATTGATGCTTTGCTTGCTTTT 59.499 39.130 0.00 0.00 0.00 2.27
3530 4463 4.691685 CCATTGATGCTTTGCTTGCTTTTA 59.308 37.500 0.00 0.00 0.00 1.52
3531 4464 5.390145 CCATTGATGCTTTGCTTGCTTTTAC 60.390 40.000 0.00 0.00 0.00 2.01
3532 4465 4.589216 TGATGCTTTGCTTGCTTTTACT 57.411 36.364 0.00 0.00 0.00 2.24
3533 4466 4.549458 TGATGCTTTGCTTGCTTTTACTC 58.451 39.130 0.00 0.00 0.00 2.59
3534 4467 3.369546 TGCTTTGCTTGCTTTTACTCC 57.630 42.857 0.00 0.00 0.00 3.85
3684 4653 2.102252 GAGAGGGACCAGAGCAGTATTG 59.898 54.545 0.00 0.00 0.00 1.90
3700 4669 5.390251 GCAGTATTGGTCGATATCAGCAATG 60.390 44.000 25.86 18.51 41.08 2.82
3751 4720 7.508636 ACATACTGGATCTTGTACATGATCTCT 59.491 37.037 33.44 23.59 40.10 3.10
3809 4806 1.945354 ATGTCGTCCGACCAAGCGAT 61.945 55.000 16.39 0.39 43.97 4.58
3839 4837 2.244695 TCCCAACATGAGTACACGTCT 58.755 47.619 0.00 0.00 0.00 4.18
3845 4843 1.989966 ATGAGTACACGTCTCGCCCG 61.990 60.000 0.00 0.00 34.99 6.13
3891 4894 1.801178 CGTGGCCTTCTTTTCTGTCTC 59.199 52.381 3.32 0.00 0.00 3.36
3892 4895 1.801178 GTGGCCTTCTTTTCTGTCTCG 59.199 52.381 3.32 0.00 0.00 4.04
3893 4896 1.691976 TGGCCTTCTTTTCTGTCTCGA 59.308 47.619 3.32 0.00 0.00 4.04
3959 4966 3.170585 CGAGTTCGAACCCGCGAC 61.171 66.667 24.22 8.51 43.02 5.19
4018 5025 5.201713 TCAGCTATAACTATCACTGCACC 57.798 43.478 0.00 0.00 0.00 5.01
4037 5044 6.806751 TGCACCATTTATCTCTCTACACTAC 58.193 40.000 0.00 0.00 0.00 2.73
4038 5045 6.379988 TGCACCATTTATCTCTCTACACTACA 59.620 38.462 0.00 0.00 0.00 2.74
4039 5046 6.920758 GCACCATTTATCTCTCTACACTACAG 59.079 42.308 0.00 0.00 0.00 2.74
4040 5047 6.920758 CACCATTTATCTCTCTACACTACAGC 59.079 42.308 0.00 0.00 0.00 4.40
4041 5048 6.607600 ACCATTTATCTCTCTACACTACAGCA 59.392 38.462 0.00 0.00 0.00 4.41
4107 5117 0.910338 ATGACTCATGACAGGCAGCT 59.090 50.000 0.00 0.00 33.80 4.24
4120 5130 2.667536 CAGCTCGCCTGCTTGTGT 60.668 61.111 0.00 0.00 41.98 3.72
4128 5138 1.815196 CCTGCTTGTGTGCCAACAA 59.185 52.632 1.81 1.81 38.27 2.83
4152 5162 2.563427 GGCTGCGCTTGGTTTCTC 59.437 61.111 9.73 0.00 0.00 2.87
4164 5174 1.072648 TGGTTTCTCTTGGTAACCCGG 59.927 52.381 0.00 0.00 40.44 5.73
4166 5176 2.026542 GGTTTCTCTTGGTAACCCGGAT 60.027 50.000 0.73 0.00 36.21 4.18
4195 5205 2.926200 CTGTCATCGACCACTGCTTAAG 59.074 50.000 0.00 0.00 0.00 1.85
4209 5219 2.302733 TGCTTAAGTGCAGAGATGGACA 59.697 45.455 4.02 0.00 38.12 4.02
4215 5225 1.818785 GCAGAGATGGACAGCCTGC 60.819 63.158 12.65 12.65 42.52 4.85
4216 5226 1.521010 CAGAGATGGACAGCCTGCG 60.521 63.158 0.00 0.00 34.31 5.18
4217 5227 2.202987 GAGATGGACAGCCTGCGG 60.203 66.667 0.00 0.00 34.31 5.69
4251 5266 0.038526 ACGAAGCTTCACGGACGAAT 60.039 50.000 25.47 0.00 0.00 3.34
4292 5307 2.316108 GGTGAGTGGGGATTGTTTGTT 58.684 47.619 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 163 6.780522 AGCTTGGTTTAAGTTCCTAAATTCCA 59.219 34.615 0.00 0.00 38.70 3.53
167 168 7.013559 GGTACAAGCTTGGTTTAAGTTCCTAAA 59.986 37.037 29.18 0.00 38.70 1.85
190 211 5.596763 AGGGACCTAACACAAGATAAGGTA 58.403 41.667 0.00 0.00 0.00 3.08
203 224 5.665459 CATAGCTGCATATAGGGACCTAAC 58.335 45.833 1.02 0.00 31.73 2.34
235 258 5.650283 TCATGGGGTCCAACTAAAAGATTT 58.350 37.500 0.00 0.00 36.95 2.17
277 300 3.814504 ACTGGGATTGGAACACTTCAT 57.185 42.857 0.00 0.00 39.29 2.57
347 370 0.179073 AGATGATTGGTTCGCTCGGG 60.179 55.000 0.00 0.00 0.00 5.14
374 397 4.024670 AGTTCAGTAGCGACCTTAAGGAT 58.975 43.478 28.52 12.18 38.94 3.24
440 466 1.544825 CCTCTGGAAGGTCGAGGCAA 61.545 60.000 0.00 0.00 40.67 4.52
444 470 1.203523 CAGTTCCTCTGGAAGGTCGAG 59.796 57.143 0.00 0.00 42.88 4.04
478 510 1.889573 GAATCTGCCGTGCCTAGCC 60.890 63.158 0.00 0.00 0.00 3.93
505 538 5.276461 AGAATCATGATGCCAAGTACGTA 57.724 39.130 9.46 0.00 0.00 3.57
506 539 4.142609 AGAATCATGATGCCAAGTACGT 57.857 40.909 9.46 0.00 0.00 3.57
507 540 4.571984 TCAAGAATCATGATGCCAAGTACG 59.428 41.667 9.46 0.00 0.00 3.67
508 541 5.008415 CCTCAAGAATCATGATGCCAAGTAC 59.992 44.000 9.46 0.00 0.00 2.73
514 547 1.266175 CGCCTCAAGAATCATGATGCC 59.734 52.381 9.46 4.62 35.73 4.40
567 600 1.205655 TCAGGAGCCAGAACTTGATCG 59.794 52.381 0.00 0.00 0.00 3.69
568 601 3.204526 CATCAGGAGCCAGAACTTGATC 58.795 50.000 0.00 0.00 32.12 2.92
569 602 2.575279 ACATCAGGAGCCAGAACTTGAT 59.425 45.455 0.00 0.00 34.14 2.57
570 603 1.980765 ACATCAGGAGCCAGAACTTGA 59.019 47.619 0.00 0.00 0.00 3.02
571 604 2.486472 ACATCAGGAGCCAGAACTTG 57.514 50.000 0.00 0.00 0.00 3.16
572 605 2.553904 CCAACATCAGGAGCCAGAACTT 60.554 50.000 0.00 0.00 0.00 2.66
610 648 2.462456 TTTGACAGGAGCTAGCACTG 57.538 50.000 27.73 27.73 38.19 3.66
611 649 3.492102 TTTTTGACAGGAGCTAGCACT 57.508 42.857 18.83 11.89 0.00 4.40
679 718 1.645034 CTGGTGATGCAGTACGAAGG 58.355 55.000 0.00 0.00 0.00 3.46
727 776 3.874383 TGTTTGGGAGGAAGATGACAA 57.126 42.857 0.00 0.00 0.00 3.18
791 840 8.547967 TGAAAATATGAGAAGTGTTAGGTGTC 57.452 34.615 0.00 0.00 0.00 3.67
832 884 6.640907 GTGAAGATACGATGTTTTGCCTTTTT 59.359 34.615 0.00 0.00 0.00 1.94
833 885 6.149633 GTGAAGATACGATGTTTTGCCTTTT 58.850 36.000 0.00 0.00 0.00 2.27
916 968 1.915093 CGCGCTCGTACCATAACAC 59.085 57.895 5.56 0.00 0.00 3.32
952 1004 0.027586 AGTGCAGACGTTTCGCAAAC 59.972 50.000 8.76 2.75 34.52 2.93
970 1022 2.322355 ACCCTTTGATCGATCTGCAG 57.678 50.000 25.02 16.81 0.00 4.41
1119 1171 2.493675 GCACCAAGGGGAAAAAGAGATC 59.506 50.000 0.00 0.00 38.05 2.75
1130 1182 0.542702 ATTCCACAAGCACCAAGGGG 60.543 55.000 0.00 0.00 41.29 4.79
1132 1184 3.676873 GCATAATTCCACAAGCACCAAGG 60.677 47.826 0.00 0.00 0.00 3.61
1133 1185 3.194116 AGCATAATTCCACAAGCACCAAG 59.806 43.478 0.00 0.00 0.00 3.61
1138 1190 2.169330 TGCAGCATAATTCCACAAGCA 58.831 42.857 0.00 0.00 0.00 3.91
1139 1191 2.945447 TGCAGCATAATTCCACAAGC 57.055 45.000 0.00 0.00 0.00 4.01
1140 1192 4.337274 TGAGATGCAGCATAATTCCACAAG 59.663 41.667 8.22 0.00 0.00 3.16
1144 1196 4.271661 TGTTGAGATGCAGCATAATTCCA 58.728 39.130 8.22 0.07 32.40 3.53
1147 1199 4.818005 TCGATGTTGAGATGCAGCATAATT 59.182 37.500 8.22 0.00 46.68 1.40
1148 1200 4.383173 TCGATGTTGAGATGCAGCATAAT 58.617 39.130 8.22 0.00 46.68 1.28
1174 1226 1.059994 CAATCTGTGCGCTCGCTTC 59.940 57.895 9.73 9.01 42.51 3.86
1232 1302 2.223144 TCAGAACAAATACACGCAGCAC 59.777 45.455 0.00 0.00 0.00 4.40
1253 1325 1.134699 CACACATCAGGCGGTATCTGT 60.135 52.381 0.00 0.00 34.15 3.41
1275 1612 5.149973 TGCATTGTCACCTGCAAATTAAT 57.850 34.783 6.77 0.00 44.87 1.40
1298 1635 2.813179 GCATAGCCGCGTCACCTTG 61.813 63.158 4.92 0.00 0.00 3.61
1361 1698 3.506067 CGCCTTCCCTTGTGACTATTTTT 59.494 43.478 0.00 0.00 0.00 1.94
1367 1704 1.371558 GTCGCCTTCCCTTGTGACT 59.628 57.895 0.00 0.00 38.60 3.41
1472 1809 7.503549 GGTTATCGCCGATAGAATTAAGTAC 57.496 40.000 6.93 0.00 39.76 2.73
1541 1878 5.648572 CAGTTGCTAGTAGTACTACCCAAC 58.351 45.833 30.59 30.59 38.66 3.77
1554 1891 0.109342 AAGTGGCTGCAGTTGCTAGT 59.891 50.000 16.64 0.00 42.66 2.57
1594 2050 9.095065 GGAGTAATTTTTCGCAGAAAGATACTA 57.905 33.333 15.94 4.94 45.90 1.82
1595 2051 7.606456 TGGAGTAATTTTTCGCAGAAAGATACT 59.394 33.333 15.92 15.92 45.90 2.12
1596 2052 7.692705 GTGGAGTAATTTTTCGCAGAAAGATAC 59.307 37.037 7.22 9.31 45.90 2.24
1633 2089 8.178313 CAGTTACCCGTAGTAAAAGAGTACTAC 58.822 40.741 10.98 10.98 46.99 2.73
1634 2090 7.336931 CCAGTTACCCGTAGTAAAAGAGTACTA 59.663 40.741 0.00 0.00 42.56 1.82
1635 2091 6.151817 CCAGTTACCCGTAGTAAAAGAGTACT 59.848 42.308 0.00 0.00 42.56 2.73
1636 2092 6.325596 CCAGTTACCCGTAGTAAAAGAGTAC 58.674 44.000 0.00 0.00 42.56 2.73
1637 2093 5.105756 GCCAGTTACCCGTAGTAAAAGAGTA 60.106 44.000 0.00 0.00 42.56 2.59
1638 2094 4.322273 GCCAGTTACCCGTAGTAAAAGAGT 60.322 45.833 0.00 0.00 42.56 3.24
1650 2106 1.813753 CATCACCGCCAGTTACCCG 60.814 63.158 0.00 0.00 0.00 5.28
1663 2378 2.743538 TGCCTGCGCTCACATCAC 60.744 61.111 9.73 0.00 35.36 3.06
1975 2771 4.636435 ACGTTTGGGCCTCCACCG 62.636 66.667 4.53 1.48 43.94 4.94
2075 2908 1.740025 CATGGAAGCCGAAACCTTCTC 59.260 52.381 0.00 0.00 38.91 2.87
2079 2912 0.673644 CGACATGGAAGCCGAAACCT 60.674 55.000 0.00 0.00 0.00 3.50
2084 2917 1.600023 AAAAACGACATGGAAGCCGA 58.400 45.000 0.00 0.00 0.00 5.54
2120 2954 3.314913 TGAACGTGTCTGCAAATGTTCAT 59.685 39.130 19.74 0.00 37.96 2.57
2399 3266 1.070105 GTTGTCGTAGGTGCCCACA 59.930 57.895 0.40 0.00 0.00 4.17
2974 3881 3.976902 GACGGGTCGTAGTTGCCGG 62.977 68.421 0.00 0.00 41.37 6.13
3148 4072 4.456566 GGCATGCAAGGAAAATTGTGAATT 59.543 37.500 21.36 0.00 32.56 2.17
3156 4086 0.819582 CTCCGGCATGCAAGGAAAAT 59.180 50.000 27.02 0.00 33.10 1.82
3174 4104 1.004628 TGCATGAACCATACACCTGCT 59.995 47.619 0.00 0.00 0.00 4.24
3265 4195 0.747283 GGAGGCATCAGCTTCTGGTG 60.747 60.000 0.00 2.87 45.39 4.17
3322 4252 4.458989 TGAATAGCAATGTTGGTCAAGGTC 59.541 41.667 0.10 0.00 39.88 3.85
3353 4283 4.277174 ACTGTGTTTATGCAAACCAATCGA 59.723 37.500 0.00 0.00 42.88 3.59
3355 4285 4.685628 CCACTGTGTTTATGCAAACCAATC 59.314 41.667 7.08 0.00 42.88 2.67
3356 4286 4.100808 ACCACTGTGTTTATGCAAACCAAT 59.899 37.500 7.08 0.00 42.88 3.16
3384 4314 6.750039 GCTTATGTGTGTGCGGTAATTAATTT 59.250 34.615 5.91 0.00 0.00 1.82
3394 4324 0.590682 TTGTGCTTATGTGTGTGCGG 59.409 50.000 0.00 0.00 0.00 5.69
3401 4331 9.092876 TCTTTTTAACCTTTTTGTGCTTATGTG 57.907 29.630 0.00 0.00 0.00 3.21
3465 4398 6.318144 CAGAGCATAACACTGGAAAGAATGAT 59.682 38.462 0.00 0.00 33.72 2.45
3478 4411 3.433615 GTCACAAGGACAGAGCATAACAC 59.566 47.826 0.00 0.00 46.19 3.32
3505 4438 1.942127 GCAAGCAAAGCATCAATGGCA 60.942 47.619 0.00 0.00 0.00 4.92
3513 4446 3.575687 AGGAGTAAAAGCAAGCAAAGCAT 59.424 39.130 0.00 0.00 0.00 3.79
3515 4448 3.650070 AGGAGTAAAAGCAAGCAAAGC 57.350 42.857 0.00 0.00 0.00 3.51
3517 4450 5.825679 TCAAGTAGGAGTAAAAGCAAGCAAA 59.174 36.000 0.00 0.00 0.00 3.68
3518 4451 5.238650 GTCAAGTAGGAGTAAAAGCAAGCAA 59.761 40.000 0.00 0.00 0.00 3.91
3520 4453 4.755123 TGTCAAGTAGGAGTAAAAGCAAGC 59.245 41.667 0.00 0.00 0.00 4.01
3521 4454 7.041098 ACAATGTCAAGTAGGAGTAAAAGCAAG 60.041 37.037 0.00 0.00 0.00 4.01
3522 4455 6.770785 ACAATGTCAAGTAGGAGTAAAAGCAA 59.229 34.615 0.00 0.00 0.00 3.91
3524 4457 6.803154 ACAATGTCAAGTAGGAGTAAAAGC 57.197 37.500 0.00 0.00 0.00 3.51
3525 4458 8.076178 CCAAACAATGTCAAGTAGGAGTAAAAG 58.924 37.037 0.00 0.00 0.00 2.27
3526 4459 7.776030 TCCAAACAATGTCAAGTAGGAGTAAAA 59.224 33.333 0.00 0.00 0.00 1.52
3527 4460 7.284074 TCCAAACAATGTCAAGTAGGAGTAAA 58.716 34.615 0.00 0.00 0.00 2.01
3528 4461 6.833041 TCCAAACAATGTCAAGTAGGAGTAA 58.167 36.000 0.00 0.00 0.00 2.24
3529 4462 6.428083 TCCAAACAATGTCAAGTAGGAGTA 57.572 37.500 0.00 0.00 0.00 2.59
3530 4463 5.304686 TCCAAACAATGTCAAGTAGGAGT 57.695 39.130 0.00 0.00 0.00 3.85
3531 4464 5.335191 GCTTCCAAACAATGTCAAGTAGGAG 60.335 44.000 0.00 0.00 0.00 3.69
3532 4465 4.518970 GCTTCCAAACAATGTCAAGTAGGA 59.481 41.667 0.00 0.00 0.00 2.94
3533 4466 4.520492 AGCTTCCAAACAATGTCAAGTAGG 59.480 41.667 0.00 0.00 0.00 3.18
3534 4467 5.695851 AGCTTCCAAACAATGTCAAGTAG 57.304 39.130 0.00 0.00 0.00 2.57
3570 4503 3.741388 GCAGGTAGCGTATCAACCATTCT 60.741 47.826 0.00 0.00 35.64 2.40
3684 4653 0.164647 GCGCATTGCTGATATCGACC 59.835 55.000 0.30 0.00 41.73 4.79
3816 4814 2.193447 CGTGTACTCATGTTGGGATCG 58.807 52.381 0.00 0.00 0.00 3.69
3817 4815 3.119101 AGACGTGTACTCATGTTGGGATC 60.119 47.826 0.00 0.00 42.94 3.36
3818 4816 2.832129 AGACGTGTACTCATGTTGGGAT 59.168 45.455 0.00 0.00 42.94 3.85
3819 4817 2.230508 GAGACGTGTACTCATGTTGGGA 59.769 50.000 0.00 0.00 42.94 4.37
3820 4818 2.607187 GAGACGTGTACTCATGTTGGG 58.393 52.381 0.00 0.00 42.94 4.12
3847 4845 2.819595 CACGTGGGAGCGATTGGG 60.820 66.667 7.95 0.00 35.59 4.12
3848 4846 3.499737 GCACGTGGGAGCGATTGG 61.500 66.667 18.88 0.00 35.59 3.16
3849 4847 3.499737 GGCACGTGGGAGCGATTG 61.500 66.667 18.88 0.00 35.59 2.67
3850 4848 3.545124 TTGGCACGTGGGAGCGATT 62.545 57.895 18.88 0.00 35.59 3.34
3851 4849 4.015406 TTGGCACGTGGGAGCGAT 62.015 61.111 18.88 0.00 35.59 4.58
3879 4882 3.984508 ACTTCGTCGAGACAGAAAAGA 57.015 42.857 4.02 0.00 0.00 2.52
3881 4884 3.795101 GTCAACTTCGTCGAGACAGAAAA 59.205 43.478 7.31 0.00 0.00 2.29
3891 4894 1.606350 GGAGCGTGTCAACTTCGTCG 61.606 60.000 0.00 0.00 0.00 5.12
3892 4895 0.318784 AGGAGCGTGTCAACTTCGTC 60.319 55.000 0.00 0.00 0.00 4.20
3893 4896 0.597637 CAGGAGCGTGTCAACTTCGT 60.598 55.000 0.00 0.00 0.00 3.85
4018 5025 7.935520 TCTGCTGTAGTGTAGAGAGATAAATG 58.064 38.462 0.00 0.00 0.00 2.32
4037 5044 1.088340 CAGCCGGAACTGATCTGCTG 61.088 60.000 5.05 12.59 42.82 4.41
4038 5045 1.220206 CAGCCGGAACTGATCTGCT 59.780 57.895 5.05 0.00 40.25 4.24
4039 5046 1.817099 CCAGCCGGAACTGATCTGC 60.817 63.158 5.05 0.00 40.25 4.26
4040 5047 1.817099 GCCAGCCGGAACTGATCTG 60.817 63.158 5.05 0.00 40.25 2.90
4041 5048 1.992277 AGCCAGCCGGAACTGATCT 60.992 57.895 5.05 1.85 40.25 2.75
4107 5117 4.560743 TGGCACACAAGCAGGCGA 62.561 61.111 0.00 0.00 35.83 5.54
4115 5125 1.333308 CGAGACATTGTTGGCACACAA 59.667 47.619 14.49 14.49 39.29 3.33
4120 5130 3.667087 GCCGAGACATTGTTGGCA 58.333 55.556 18.28 0.00 45.06 4.92
4152 5162 2.781681 ACTCAATCCGGGTTACCAAG 57.218 50.000 0.00 0.00 36.13 3.61
4164 5174 3.190874 GGTCGATGACAGGAACTCAATC 58.809 50.000 0.00 0.00 34.60 2.67
4166 5176 1.967779 TGGTCGATGACAGGAACTCAA 59.032 47.619 0.00 0.00 34.60 3.02
4195 5205 0.743701 CAGGCTGTCCATCTCTGCAC 60.744 60.000 6.28 0.00 33.74 4.57
4219 5229 2.430244 TTCGTCGCAAGCGGAGAC 60.430 61.111 14.98 4.71 42.22 3.36
4220 5230 2.126463 CTTCGTCGCAAGCGGAGA 60.126 61.111 14.98 11.13 42.50 3.71
4221 5231 3.843240 GCTTCGTCGCAAGCGGAG 61.843 66.667 14.98 8.96 42.68 4.63
4251 5266 1.125093 AGTCATTCCACCCCGACACA 61.125 55.000 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.