Multiple sequence alignment - TraesCS5B01G465900

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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 TraesCS5B01G465900 chr5B 100.000 3936 0 0 1 3936 640157148 640153213 0.000000e+00 7269.0
1 TraesCS5B01G465900 chr5B 91.635 1040 82 4 1 1040 419477366 419478400 0.000000e+00 1434.0
2 TraesCS5B01G465900 chr5B 88.652 141 16 0 1200 1340 43884298 43884438 5.230000e-39 172.0
3 TraesCS5B01G465900 chr5B 89.630 135 14 0 1209 1343 44231450 44231316 5.230000e-39 172.0
4 TraesCS5B01G465900 chr5D 94.486 1324 53 6 1429 2738 509529975 509528658 0.000000e+00 2023.0
5 TraesCS5B01G465900 chr5D 86.753 1238 67 38 2765 3936 509528667 509527461 0.000000e+00 1288.0
6 TraesCS5B01G465900 chr5D 93.857 293 18 0 1139 1431 509537343 509537051 3.610000e-120 442.0
7 TraesCS5B01G465900 chr5D 88.652 141 16 0 1200 1340 44488974 44489114 5.230000e-39 172.0
8 TraesCS5B01G465900 chr3B 91.765 1020 84 0 1 1020 671877151 671878170 0.000000e+00 1419.0
9 TraesCS5B01G465900 chr1B 91.309 1024 89 0 1 1024 587967559 587966536 0.000000e+00 1399.0
10 TraesCS5B01G465900 chr7B 91.105 1023 91 0 1 1023 245997609 245996587 0.000000e+00 1386.0
11 TraesCS5B01G465900 chr2D 90.820 1024 94 0 1 1024 382461705 382460682 0.000000e+00 1371.0
12 TraesCS5B01G465900 chr6B 89.699 1029 104 2 1 1028 569032304 569033331 0.000000e+00 1312.0
13 TraesCS5B01G465900 chr5A 93.253 830 52 3 1084 1909 636695905 636695076 0.000000e+00 1219.0
14 TraesCS5B01G465900 chr5A 85.442 996 102 19 1914 2870 636677798 636676807 0.000000e+00 996.0
15 TraesCS5B01G465900 chr5A 82.197 719 79 21 2886 3590 636676761 636676078 1.230000e-159 573.0
16 TraesCS5B01G465900 chr5A 87.943 141 17 0 1200 1340 34903678 34903818 2.430000e-37 167.0
17 TraesCS5B01G465900 chr5A 100.000 33 0 0 3182 3214 636673192 636673160 1.180000e-05 62.1
18 TraesCS5B01G465900 chr7A 87.671 1022 122 4 1 1020 74731134 74732153 0.000000e+00 1186.0
19 TraesCS5B01G465900 chr3D 85.050 1010 151 0 16 1025 524678770 524679779 0.000000e+00 1029.0
20 TraesCS5B01G465900 chr3A 83.366 1022 167 3 2 1022 17266820 17265801 0.000000e+00 942.0


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 TraesCS5B01G465900 chr5B 640153213 640157148 3935 True 7269.0 7269 100.0000 1 3936 1 chr5B.!!$R2 3935
1 TraesCS5B01G465900 chr5B 419477366 419478400 1034 False 1434.0 1434 91.6350 1 1040 1 chr5B.!!$F2 1039
2 TraesCS5B01G465900 chr5D 509527461 509529975 2514 True 1655.5 2023 90.6195 1429 3936 2 chr5D.!!$R2 2507
3 TraesCS5B01G465900 chr3B 671877151 671878170 1019 False 1419.0 1419 91.7650 1 1020 1 chr3B.!!$F1 1019
4 TraesCS5B01G465900 chr1B 587966536 587967559 1023 True 1399.0 1399 91.3090 1 1024 1 chr1B.!!$R1 1023
5 TraesCS5B01G465900 chr7B 245996587 245997609 1022 True 1386.0 1386 91.1050 1 1023 1 chr7B.!!$R1 1022
6 TraesCS5B01G465900 chr2D 382460682 382461705 1023 True 1371.0 1371 90.8200 1 1024 1 chr2D.!!$R1 1023
7 TraesCS5B01G465900 chr6B 569032304 569033331 1027 False 1312.0 1312 89.6990 1 1028 1 chr6B.!!$F1 1027
8 TraesCS5B01G465900 chr5A 636695076 636695905 829 True 1219.0 1219 93.2530 1084 1909 1 chr5A.!!$R1 825
9 TraesCS5B01G465900 chr5A 636673160 636677798 4638 True 543.7 996 89.2130 1914 3590 3 chr5A.!!$R2 1676
10 TraesCS5B01G465900 chr7A 74731134 74732153 1019 False 1186.0 1186 87.6710 1 1020 1 chr7A.!!$F1 1019
11 TraesCS5B01G465900 chr3D 524678770 524679779 1009 False 1029.0 1029 85.0500 16 1025 1 chr3D.!!$F1 1009
12 TraesCS5B01G465900 chr3A 17265801 17266820 1019 True 942.0 942 83.3660 2 1022 1 chr3A.!!$R1 1020

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
585 586 0.393077 CAAGGAACAGACGAGTGGGT 59.607 55.0 0.0 0.0 0.00 4.51 F
1394 1399 0.109365 CTATCTCTGCCCATCGCTCG 60.109 60.0 0.0 0.0 38.78 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 1665 0.388649 AGACGTGGACACATTCGAGC 60.389 55.0 0.00 0.0 0.0 5.03 R
3347 3435 0.729116 CACAACCCTCGATGCATGTC 59.271 55.0 2.46 0.0 0.0 3.06 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
38 39 2.142292 GAGAAGGAAGCTTGGGGCCA 62.142 60.000 2.10 0.00 43.05 5.36
144 145 0.751643 ATAGGCGGAACATGGCAACC 60.752 55.000 0.00 0.00 0.00 3.77
229 230 3.451894 CGAGGTGCATTTGGGCCC 61.452 66.667 17.59 17.59 0.00 5.80
247 248 1.344763 CCCTGTCGGATGATACCCTTC 59.655 57.143 0.00 0.00 0.00 3.46
300 301 4.582701 TGCGAAGAATTGGTTGTTTGAT 57.417 36.364 0.00 0.00 0.00 2.57
356 357 3.071892 AGAATGGTCGTTACTTTGTGGGA 59.928 43.478 0.00 0.00 0.00 4.37
420 421 3.264450 TCCAAAACCCACACCAAACAATT 59.736 39.130 0.00 0.00 0.00 2.32
484 485 3.045688 GCTGCTAAACAAAGAGTGCAAC 58.954 45.455 0.00 0.00 0.00 4.17
585 586 0.393077 CAAGGAACAGACGAGTGGGT 59.607 55.000 0.00 0.00 0.00 4.51
600 601 2.127232 GGGTGTGGTTGCTGCAGTT 61.127 57.895 16.64 0.00 0.00 3.16
606 607 2.355009 GTTGCTGCAGTTTGCCGG 60.355 61.111 16.64 0.00 44.23 6.13
623 624 3.249986 CCGGGACTCAAACGGTAATTA 57.750 47.619 0.00 0.00 42.53 1.40
630 631 5.395990 GGACTCAAACGGTAATTATCTGGGA 60.396 44.000 0.00 0.00 0.00 4.37
633 634 6.099845 ACTCAAACGGTAATTATCTGGGATCT 59.900 38.462 0.00 0.00 0.00 2.75
658 659 5.473504 TCAGCAGTTGTCTTTAAGGGAATTC 59.526 40.000 0.00 0.00 0.00 2.17
660 661 4.379499 GCAGTTGTCTTTAAGGGAATTCGG 60.379 45.833 0.00 0.00 0.00 4.30
666 667 0.921166 TTAAGGGAATTCGGGACCCC 59.079 55.000 4.46 0.00 44.21 4.95
669 670 1.384924 GGGAATTCGGGACCCCCTA 60.385 63.158 4.46 0.00 42.67 3.53
697 698 0.739813 AACATACGCCTGCCGAGAAC 60.740 55.000 0.00 0.00 41.02 3.01
783 784 4.641989 GTGGTGCAAGATATCAATGAAGGT 59.358 41.667 5.32 0.00 0.00 3.50
826 827 7.409026 CGGCTGTTATACGTGAAATAATAGACG 60.409 40.741 20.14 20.14 46.19 4.18
840 841 9.747293 GAAATAATAGACGGTAGAGCTAGTTTT 57.253 33.333 0.00 0.00 0.00 2.43
914 915 5.643339 AATCTCGCTAAATTCGCTTGTAG 57.357 39.130 0.00 0.00 0.00 2.74
954 955 0.467290 TTTGGTTGGGCACTCCTCAC 60.467 55.000 2.79 0.00 36.20 3.51
975 976 2.426738 CGACCCAAACCGTGTACCTATA 59.573 50.000 0.00 0.00 0.00 1.31
1061 1062 3.323136 CAGCGCGCGTCTCCATAC 61.323 66.667 32.35 11.90 0.00 2.39
1062 1063 4.570663 AGCGCGCGTCTCCATACC 62.571 66.667 32.35 11.09 0.00 2.73
1063 1064 4.570663 GCGCGCGTCTCCATACCT 62.571 66.667 32.35 0.00 0.00 3.08
1064 1065 2.104331 CGCGCGTCTCCATACCTT 59.896 61.111 24.19 0.00 0.00 3.50
1065 1066 1.944676 CGCGCGTCTCCATACCTTC 60.945 63.158 24.19 0.00 0.00 3.46
1066 1067 1.591863 GCGCGTCTCCATACCTTCC 60.592 63.158 8.43 0.00 0.00 3.46
1067 1068 2.017559 GCGCGTCTCCATACCTTCCT 62.018 60.000 8.43 0.00 0.00 3.36
1068 1069 0.460311 CGCGTCTCCATACCTTCCTT 59.540 55.000 0.00 0.00 0.00 3.36
1069 1070 1.536284 CGCGTCTCCATACCTTCCTTC 60.536 57.143 0.00 0.00 0.00 3.46
1070 1071 1.202545 GCGTCTCCATACCTTCCTTCC 60.203 57.143 0.00 0.00 0.00 3.46
1071 1072 2.389715 CGTCTCCATACCTTCCTTCCT 58.610 52.381 0.00 0.00 0.00 3.36
1072 1073 2.766828 CGTCTCCATACCTTCCTTCCTT 59.233 50.000 0.00 0.00 0.00 3.36
1073 1074 3.181474 CGTCTCCATACCTTCCTTCCTTC 60.181 52.174 0.00 0.00 0.00 3.46
1074 1075 4.034410 GTCTCCATACCTTCCTTCCTTCT 58.966 47.826 0.00 0.00 0.00 2.85
1075 1076 4.471747 GTCTCCATACCTTCCTTCCTTCTT 59.528 45.833 0.00 0.00 0.00 2.52
1076 1077 5.045505 GTCTCCATACCTTCCTTCCTTCTTT 60.046 44.000 0.00 0.00 0.00 2.52
1077 1078 5.189934 TCTCCATACCTTCCTTCCTTCTTTC 59.810 44.000 0.00 0.00 0.00 2.62
1078 1079 4.227527 TCCATACCTTCCTTCCTTCTTTCC 59.772 45.833 0.00 0.00 0.00 3.13
1079 1080 4.527944 CATACCTTCCTTCCTTCTTTCCC 58.472 47.826 0.00 0.00 0.00 3.97
1080 1081 1.711375 ACCTTCCTTCCTTCTTTCCCC 59.289 52.381 0.00 0.00 0.00 4.81
1081 1082 1.710809 CCTTCCTTCCTTCTTTCCCCA 59.289 52.381 0.00 0.00 0.00 4.96
1082 1083 2.110011 CCTTCCTTCCTTCTTTCCCCAA 59.890 50.000 0.00 0.00 0.00 4.12
1099 1100 0.798776 CAAACACAAGAGCCCTAGCG 59.201 55.000 0.00 0.00 46.67 4.26
1100 1101 0.955919 AAACACAAGAGCCCTAGCGC 60.956 55.000 0.00 0.00 46.67 5.92
1101 1102 2.512515 CACAAGAGCCCTAGCGCC 60.513 66.667 2.29 0.00 46.67 6.53
1102 1103 4.148825 ACAAGAGCCCTAGCGCCG 62.149 66.667 2.29 0.00 46.67 6.46
1152 1157 3.857038 GCCCGGCGGTCCTATTGA 61.857 66.667 26.32 0.00 0.00 2.57
1169 1174 1.388174 TGAGAGGAGGAGGAGGAAGT 58.612 55.000 0.00 0.00 0.00 3.01
1186 1191 1.366319 AGTTGGAGTTGGAGGAGCAT 58.634 50.000 0.00 0.00 0.00 3.79
1191 1196 1.680249 GGAGTTGGAGGAGCATGAACC 60.680 57.143 0.00 0.00 0.00 3.62
1248 1253 0.521291 CTCCTCGGCGAGATCATCTC 59.479 60.000 36.47 4.35 40.06 2.75
1271 1276 1.014352 CCTCCAAATTAAGGACGCCG 58.986 55.000 0.00 0.00 34.35 6.46
1355 1360 3.141398 GACTGCTGTCATTTGTTCTCCA 58.859 45.455 17.89 0.00 42.48 3.86
1362 1367 4.984295 TGTCATTTGTTCTCCATCAAGGA 58.016 39.130 0.00 0.00 46.75 3.36
1387 1392 2.042464 GACATGTCCTATCTCTGCCCA 58.958 52.381 15.31 0.00 0.00 5.36
1389 1394 2.636893 ACATGTCCTATCTCTGCCCATC 59.363 50.000 0.00 0.00 0.00 3.51
1394 1399 0.109365 CTATCTCTGCCCATCGCTCG 60.109 60.000 0.00 0.00 38.78 5.03
1401 1406 2.174319 GCCCATCGCTCGTCCTTTC 61.174 63.158 0.00 0.00 0.00 2.62
1412 1417 3.646715 TCCTTTCAGCCCACCCGG 61.647 66.667 0.00 0.00 0.00 5.73
1466 1471 2.590611 TCCTCAATGACTACCCCTACCT 59.409 50.000 0.00 0.00 0.00 3.08
1523 1528 1.743252 CAGGAGCTTGAGTTCGCCC 60.743 63.158 0.00 0.00 0.00 6.13
1543 1548 3.246112 CACGGGTTCACCTCCCCA 61.246 66.667 0.00 0.00 41.30 4.96
1560 1565 1.442526 CCAGTGCCGGCATCAATCTC 61.443 60.000 35.23 18.12 0.00 2.75
1563 1568 2.192979 GCCGGCATCAATCTCCCA 59.807 61.111 24.80 0.00 0.00 4.37
1575 1580 1.901591 ATCTCCCACTTTGCACACAG 58.098 50.000 0.00 0.00 0.00 3.66
1691 1696 2.436292 ACGTCTCGGAGTCCTCGG 60.436 66.667 7.77 0.00 0.00 4.63
1897 1902 9.565090 TTGATTCATCTGTATAAGATTTGGAGG 57.435 33.333 0.00 0.00 43.52 4.30
1961 1966 3.507162 TGGACTTCCTTGCTGATTTGA 57.493 42.857 0.00 0.00 36.82 2.69
2013 2018 8.058667 TCACGGTCTTAAGTTATATGTCTTGA 57.941 34.615 1.63 0.00 0.00 3.02
2014 2019 8.692710 TCACGGTCTTAAGTTATATGTCTTGAT 58.307 33.333 1.63 0.00 0.00 2.57
2016 2021 9.530633 ACGGTCTTAAGTTATATGTCTTGATTC 57.469 33.333 1.63 0.00 0.00 2.52
2017 2022 9.529325 CGGTCTTAAGTTATATGTCTTGATTCA 57.471 33.333 1.63 0.00 0.00 2.57
2111 2141 2.838736 TGCTCGATTAAGGGATTGCTC 58.161 47.619 0.00 0.00 0.00 4.26
2128 2158 1.411394 CTCGTTTTTAGCACGACGGA 58.589 50.000 0.00 0.00 41.66 4.69
2174 2210 2.934887 TCCGTCAATATGGGTCGACTA 58.065 47.619 16.46 5.48 32.02 2.59
2240 2276 2.089980 GAGGAGCTACACGTGAAGGTA 58.910 52.381 25.01 2.66 0.00 3.08
2272 2308 8.299262 TCGTAGCTTTTGATATTCTTGCTATC 57.701 34.615 0.00 0.00 34.70 2.08
2280 2316 8.866970 TTTGATATTCTTGCTATCCATGCATA 57.133 30.769 0.00 0.00 40.34 3.14
2333 2373 3.960755 TCAGTCTGGTGTATCATCCGAAT 59.039 43.478 0.00 0.00 0.00 3.34
2341 2381 6.118852 TGGTGTATCATCCGAATCAAATTGA 58.881 36.000 0.00 0.00 0.00 2.57
2348 2388 3.536570 TCCGAATCAAATTGATGGCGTA 58.463 40.909 21.43 10.17 37.15 4.42
2504 2544 4.343814 TGACATTTCATATCGAGGCCAGTA 59.656 41.667 5.01 0.00 0.00 2.74
2579 2619 1.293498 GCTTCAAGAGGTGCTCGGA 59.707 57.895 0.00 0.00 35.36 4.55
2600 2640 3.781341 TTCGTTTTACAACTGCTAGCG 57.219 42.857 10.77 7.61 0.00 4.26
2734 2774 5.858581 GCATATCACCTTTTGTGTGTTCTTC 59.141 40.000 0.00 0.00 45.61 2.87
2751 2791 5.067283 TGTTCTTCTTCTTTTACTTGTGGGC 59.933 40.000 0.00 0.00 0.00 5.36
2757 2797 5.584649 TCTTCTTTTACTTGTGGGCATATCG 59.415 40.000 0.00 0.00 0.00 2.92
2803 2846 5.369833 TGGATTAGTTTTCGTGTTTCCAGA 58.630 37.500 0.00 0.00 0.00 3.86
2821 2864 5.263599 TCCAGATTGCATATGTTTGGTTCT 58.736 37.500 4.29 0.00 0.00 3.01
2845 2888 3.181493 GCATCAATTAAGTGGCCTCACAG 60.181 47.826 3.32 0.00 45.91 3.66
2872 2915 3.881089 TCTGTAGTGTCACTCTTCAACGA 59.119 43.478 9.26 1.74 0.00 3.85
2905 2978 6.454795 TGGGAAGTGTTTATTTCTTGAATGC 58.545 36.000 0.00 0.00 0.00 3.56
2999 3072 7.953710 GCTTAATTTTGACTTTGCATTCATGAC 59.046 33.333 0.00 0.00 0.00 3.06
3038 3112 0.742505 CCCTACTTCGGTCGCACATA 59.257 55.000 0.00 0.00 0.00 2.29
3067 3142 0.178950 TATGCTTGGGTTGTGGCCAA 60.179 50.000 7.24 0.00 0.00 4.52
3161 3240 7.580910 ACCCAATTAAATGAGATGAGATGACT 58.419 34.615 0.00 0.00 0.00 3.41
3218 3304 6.324770 TGAGTGCATGATCCTGAATAGACTTA 59.675 38.462 0.00 0.00 0.00 2.24
3219 3305 7.129457 AGTGCATGATCCTGAATAGACTTAA 57.871 36.000 0.00 0.00 0.00 1.85
3222 3308 9.494271 GTGCATGATCCTGAATAGACTTAATTA 57.506 33.333 0.00 0.00 0.00 1.40
3278 3364 6.558909 TGACATGCGCATTGTTTATTATTCA 58.441 32.000 22.81 10.57 0.00 2.57
3282 3368 8.329583 ACATGCGCATTGTTTATTATTCATTTG 58.670 29.630 22.81 6.79 0.00 2.32
3347 3435 0.320073 TCAGGTAAACCTTGCGGACG 60.320 55.000 0.00 0.00 46.09 4.79
3367 3459 0.324614 ACATGCATCGAGGGTTGTGA 59.675 50.000 0.00 0.00 0.00 3.58
3376 3468 1.478510 CGAGGGTTGTGAGAGTAGCAT 59.521 52.381 0.00 0.00 0.00 3.79
3397 3489 5.639506 GCATCTTCAGTTTACTGCTTCACTA 59.360 40.000 5.00 0.00 43.46 2.74
3403 3495 6.288294 TCAGTTTACTGCTTCACTACACAAT 58.712 36.000 5.00 0.00 43.46 2.71
3404 3496 6.202762 TCAGTTTACTGCTTCACTACACAATG 59.797 38.462 5.00 0.00 43.46 2.82
3405 3497 6.017934 CAGTTTACTGCTTCACTACACAATGT 60.018 38.462 0.00 0.00 37.15 2.71
3408 3500 3.071602 ACTGCTTCACTACACAATGTCCT 59.928 43.478 0.00 0.00 0.00 3.85
3410 3502 3.070878 TGCTTCACTACACAATGTCCTCA 59.929 43.478 0.00 0.00 0.00 3.86
3413 3505 3.990092 TCACTACACAATGTCCTCACAC 58.010 45.455 0.00 0.00 34.48 3.82
3418 3510 6.091305 CACTACACAATGTCCTCACACTTATG 59.909 42.308 0.00 0.00 34.48 1.90
3421 3513 3.244875 ACAATGTCCTCACACTTATGCCA 60.245 43.478 0.00 0.00 34.48 4.92
3443 3535 1.024271 CATTGGGGCTATGTCGTTGG 58.976 55.000 0.00 0.00 0.00 3.77
3468 3560 8.456471 GGTAACACTTTAAAGGTCATTATGTCC 58.544 37.037 19.14 7.31 0.00 4.02
3555 3647 7.707624 TGCTTGAAATATCTTGTGGAGATTT 57.292 32.000 0.00 0.00 45.14 2.17
3590 3682 4.875536 AGCGCTACAAATGATTACACATGA 59.124 37.500 8.99 0.00 0.00 3.07
3595 3687 7.028962 GCTACAAATGATTACACATGAAGCAA 58.971 34.615 0.00 0.00 0.00 3.91
3610 3702 8.244113 CACATGAAGCAATGCTATCATATGAAT 58.756 33.333 22.24 1.63 38.25 2.57
3611 3703 8.244113 ACATGAAGCAATGCTATCATATGAATG 58.756 33.333 22.60 16.67 38.25 2.67
3616 3708 5.651139 GCAATGCTATCATATGAATGGACCT 59.349 40.000 9.99 0.00 33.61 3.85
3617 3709 6.152323 GCAATGCTATCATATGAATGGACCTT 59.848 38.462 9.99 0.00 33.61 3.50
3618 3710 7.337689 GCAATGCTATCATATGAATGGACCTTA 59.662 37.037 9.99 0.00 33.61 2.69
3619 3711 9.234827 CAATGCTATCATATGAATGGACCTTAA 57.765 33.333 9.99 0.00 33.61 1.85
3648 3740 9.538508 ACAGAAAGTTTACGTACTACTTCAATT 57.461 29.630 17.80 6.93 31.26 2.32
3655 3747 3.195661 CGTACTACTTCAATTGGGAGGC 58.804 50.000 5.42 0.00 0.00 4.70
3658 3750 2.009774 CTACTTCAATTGGGAGGCGTG 58.990 52.381 5.42 0.00 0.00 5.34
3659 3751 0.609131 ACTTCAATTGGGAGGCGTGG 60.609 55.000 5.42 0.00 0.00 4.94
3660 3752 1.937546 CTTCAATTGGGAGGCGTGGC 61.938 60.000 5.42 0.00 0.00 5.01
3686 3778 2.741759 AAATCATGGGGCGAACAAAC 57.258 45.000 0.00 0.00 0.00 2.93
3690 3782 0.808755 CATGGGGCGAACAAACTACC 59.191 55.000 0.00 0.00 0.00 3.18
3695 3787 1.467342 GGGCGAACAAACTACCACATC 59.533 52.381 0.00 0.00 0.00 3.06
3698 3790 2.159881 GCGAACAAACTACCACATCGAC 60.160 50.000 0.00 0.00 0.00 4.20
3704 3796 5.816919 ACAAACTACCACATCGACTTTTTG 58.183 37.500 0.00 0.00 0.00 2.44
3735 3852 7.775120 AGGTGTATGCAGGAATAGAATTTTTG 58.225 34.615 0.00 0.00 0.00 2.44
3741 3858 8.652810 ATGCAGGAATAGAATTTTTGTTATGC 57.347 30.769 0.00 0.00 0.00 3.14
3763 3880 4.634443 GCGTGTGACCTATTATGGAGTTTT 59.366 41.667 0.00 0.00 0.00 2.43
3764 3881 5.447279 GCGTGTGACCTATTATGGAGTTTTG 60.447 44.000 0.00 0.00 0.00 2.44
3793 3910 3.523606 TTAATTGCATGTGGTGGATGC 57.476 42.857 0.00 0.00 45.45 3.91
3830 3961 8.622948 AGGAAACTCTACTGAAATTTTGTAGG 57.377 34.615 21.52 16.99 32.90 3.18
3843 3974 9.148879 TGAAATTTTGTAGGTTTCCCTTGATAA 57.851 29.630 0.00 0.00 42.66 1.75
3860 3991 7.231317 CCCTTGATAATGTATGTGGTAGCATTT 59.769 37.037 0.00 0.00 34.05 2.32
3902 4047 2.619013 GGTGCAGACCAAAAGATTCG 57.381 50.000 0.00 0.00 42.59 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.044894 CCCCAAGCTTCCTTCTCTCTAT 58.955 50.000 0.00 0.00 0.00 1.98
21 22 1.000866 ATGGCCCCAAGCTTCCTTC 59.999 57.895 0.00 0.00 43.05 3.46
38 39 2.158696 GGGACTTTGAGCTGCCATAGAT 60.159 50.000 12.68 0.00 0.00 1.98
51 52 5.251764 ACTCTGATCTTTGATGGGACTTTG 58.748 41.667 0.00 0.00 0.00 2.77
162 163 0.615331 ACGAGTCTTGGCATCCACAT 59.385 50.000 0.00 0.00 30.78 3.21
229 230 2.695666 ACAGAAGGGTATCATCCGACAG 59.304 50.000 0.00 0.00 0.00 3.51
300 301 5.869344 CACGTGGTCTAAAATCTCATGAAGA 59.131 40.000 7.95 0.00 38.72 2.87
311 312 3.128349 GTGAAGCTCACGTGGTCTAAAA 58.872 45.455 17.00 0.00 37.67 1.52
356 357 0.319083 TCGCCTCACGTACCAAACAT 59.681 50.000 0.00 0.00 44.19 2.71
420 421 8.156820 TCCTGAAGATAAGAGTCAACAAATGAA 58.843 33.333 0.00 0.00 40.50 2.57
484 485 2.157738 CTGCCCTGAAACTTCAAGGAG 58.842 52.381 10.68 4.32 40.49 3.69
585 586 1.141449 GCAAACTGCAGCAACCACA 59.859 52.632 15.27 0.00 44.26 4.17
600 601 1.756408 TACCGTTTGAGTCCCGGCAA 61.756 55.000 11.59 0.00 45.49 4.52
606 607 4.814771 CCCAGATAATTACCGTTTGAGTCC 59.185 45.833 0.00 0.00 0.00 3.85
623 624 2.575279 ACAACTGCTGAAGATCCCAGAT 59.425 45.455 14.76 0.00 33.65 2.90
630 631 5.006386 CCCTTAAAGACAACTGCTGAAGAT 58.994 41.667 0.00 0.00 0.00 2.40
633 634 4.431416 TCCCTTAAAGACAACTGCTGAA 57.569 40.909 0.00 0.00 0.00 3.02
660 661 3.512496 TGTTTCCAAAATTAGGGGGTCC 58.488 45.455 0.00 0.00 0.00 4.46
666 667 5.339990 CAGGCGTATGTTTCCAAAATTAGG 58.660 41.667 0.00 0.00 0.00 2.69
669 670 3.584834 GCAGGCGTATGTTTCCAAAATT 58.415 40.909 0.00 0.00 0.00 1.82
697 698 1.414158 TCCTCCGCCAAAGATAGAGG 58.586 55.000 0.00 0.00 44.59 3.69
812 813 7.873910 ACTAGCTCTACCGTCTATTATTTCAC 58.126 38.462 0.00 0.00 0.00 3.18
826 827 5.935206 AGCAAGAAGAAAAACTAGCTCTACC 59.065 40.000 0.00 0.00 0.00 3.18
840 841 5.704888 TCAAAAACAAACGAGCAAGAAGAA 58.295 33.333 0.00 0.00 0.00 2.52
914 915 8.329502 ACCAAATATGCCTCCCTATATCTAAAC 58.670 37.037 0.00 0.00 0.00 2.01
954 955 0.602562 TAGGTACACGGTTTGGGTCG 59.397 55.000 0.00 0.00 0.00 4.79
975 976 9.039870 TCGCTTTATTGATTCAAAACAATGTTT 57.960 25.926 5.41 5.41 37.32 2.83
1044 1045 3.323136 GTATGGAGACGCGCGCTG 61.323 66.667 32.58 23.88 0.00 5.18
1045 1046 4.570663 GGTATGGAGACGCGCGCT 62.571 66.667 32.58 27.12 0.00 5.92
1046 1047 4.570663 AGGTATGGAGACGCGCGC 62.571 66.667 32.58 23.91 0.00 6.86
1047 1048 1.944676 GAAGGTATGGAGACGCGCG 60.945 63.158 30.96 30.96 0.00 6.86
1048 1049 1.591863 GGAAGGTATGGAGACGCGC 60.592 63.158 5.73 0.00 0.00 6.86
1049 1050 0.460311 AAGGAAGGTATGGAGACGCG 59.540 55.000 3.53 3.53 0.00 6.01
1050 1051 1.202545 GGAAGGAAGGTATGGAGACGC 60.203 57.143 0.00 0.00 0.00 5.19
1051 1052 2.389715 AGGAAGGAAGGTATGGAGACG 58.610 52.381 0.00 0.00 0.00 4.18
1052 1053 4.034410 AGAAGGAAGGAAGGTATGGAGAC 58.966 47.826 0.00 0.00 0.00 3.36
1053 1054 4.354208 AGAAGGAAGGAAGGTATGGAGA 57.646 45.455 0.00 0.00 0.00 3.71
1054 1055 5.432645 GAAAGAAGGAAGGAAGGTATGGAG 58.567 45.833 0.00 0.00 0.00 3.86
1055 1056 4.227527 GGAAAGAAGGAAGGAAGGTATGGA 59.772 45.833 0.00 0.00 0.00 3.41
1056 1057 4.527944 GGAAAGAAGGAAGGAAGGTATGG 58.472 47.826 0.00 0.00 0.00 2.74
1057 1058 4.527944 GGGAAAGAAGGAAGGAAGGTATG 58.472 47.826 0.00 0.00 0.00 2.39
1058 1059 3.528078 GGGGAAAGAAGGAAGGAAGGTAT 59.472 47.826 0.00 0.00 0.00 2.73
1059 1060 2.917600 GGGGAAAGAAGGAAGGAAGGTA 59.082 50.000 0.00 0.00 0.00 3.08
1060 1061 1.711375 GGGGAAAGAAGGAAGGAAGGT 59.289 52.381 0.00 0.00 0.00 3.50
1061 1062 1.710809 TGGGGAAAGAAGGAAGGAAGG 59.289 52.381 0.00 0.00 0.00 3.46
1062 1063 3.525800 TTGGGGAAAGAAGGAAGGAAG 57.474 47.619 0.00 0.00 0.00 3.46
1063 1064 3.052490 TGTTTGGGGAAAGAAGGAAGGAA 60.052 43.478 0.00 0.00 0.00 3.36
1064 1065 2.516277 TGTTTGGGGAAAGAAGGAAGGA 59.484 45.455 0.00 0.00 0.00 3.36
1065 1066 2.628178 GTGTTTGGGGAAAGAAGGAAGG 59.372 50.000 0.00 0.00 0.00 3.46
1066 1067 3.295973 TGTGTTTGGGGAAAGAAGGAAG 58.704 45.455 0.00 0.00 0.00 3.46
1067 1068 3.390175 TGTGTTTGGGGAAAGAAGGAA 57.610 42.857 0.00 0.00 0.00 3.36
1068 1069 3.053245 TCTTGTGTTTGGGGAAAGAAGGA 60.053 43.478 0.00 0.00 0.00 3.36
1069 1070 3.295973 TCTTGTGTTTGGGGAAAGAAGG 58.704 45.455 0.00 0.00 0.00 3.46
1070 1071 3.243535 GCTCTTGTGTTTGGGGAAAGAAG 60.244 47.826 0.00 0.00 0.00 2.85
1071 1072 2.693074 GCTCTTGTGTTTGGGGAAAGAA 59.307 45.455 0.00 0.00 0.00 2.52
1072 1073 2.306847 GCTCTTGTGTTTGGGGAAAGA 58.693 47.619 0.00 0.00 0.00 2.52
1073 1074 1.341209 GGCTCTTGTGTTTGGGGAAAG 59.659 52.381 0.00 0.00 0.00 2.62
1074 1075 1.408969 GGCTCTTGTGTTTGGGGAAA 58.591 50.000 0.00 0.00 0.00 3.13
1075 1076 0.469144 GGGCTCTTGTGTTTGGGGAA 60.469 55.000 0.00 0.00 0.00 3.97
1076 1077 1.152830 GGGCTCTTGTGTTTGGGGA 59.847 57.895 0.00 0.00 0.00 4.81
1077 1078 0.404040 TAGGGCTCTTGTGTTTGGGG 59.596 55.000 0.00 0.00 0.00 4.96
1078 1079 1.826385 CTAGGGCTCTTGTGTTTGGG 58.174 55.000 0.00 0.00 0.00 4.12
1079 1080 1.168714 GCTAGGGCTCTTGTGTTTGG 58.831 55.000 0.00 0.00 35.22 3.28
1080 1081 0.798776 CGCTAGGGCTCTTGTGTTTG 59.201 55.000 0.00 0.00 36.09 2.93
1081 1082 0.955919 GCGCTAGGGCTCTTGTGTTT 60.956 55.000 23.47 0.00 36.09 2.83
1082 1083 1.376037 GCGCTAGGGCTCTTGTGTT 60.376 57.895 23.47 0.00 36.09 3.32
1144 1149 2.448961 CCTCCTCCTCCTCTCAATAGGA 59.551 54.545 0.00 0.00 43.58 2.94
1149 1154 1.719378 ACTTCCTCCTCCTCCTCTCAA 59.281 52.381 0.00 0.00 0.00 3.02
1152 1157 1.273552 CCAACTTCCTCCTCCTCCTCT 60.274 57.143 0.00 0.00 0.00 3.69
1169 1174 1.361204 TCATGCTCCTCCAACTCCAA 58.639 50.000 0.00 0.00 0.00 3.53
1186 1191 1.070786 GTCAACAGGCGGAGGTTCA 59.929 57.895 0.00 0.00 0.00 3.18
1191 1196 0.460987 GATGAGGTCAACAGGCGGAG 60.461 60.000 0.00 0.00 0.00 4.63
1248 1253 2.919228 CGTCCTTAATTTGGAGGAGGG 58.081 52.381 11.92 3.01 42.49 4.30
1271 1276 3.161450 TAGGATCTGGGTGCGGGC 61.161 66.667 0.00 0.00 0.00 6.13
1321 1326 2.982130 CAGTCGAGGTTGAGGGGG 59.018 66.667 0.00 0.00 0.00 5.40
1355 1360 3.252974 GGACATGTCTTCGTCCTTGAT 57.747 47.619 24.50 0.00 46.83 2.57
1362 1367 3.067461 GCAGAGATAGGACATGTCTTCGT 59.933 47.826 24.50 10.31 27.89 3.85
1387 1392 1.153549 GGCTGAAAGGACGAGCGAT 60.154 57.895 0.00 0.00 33.26 4.58
1389 1394 2.815647 GGGCTGAAAGGACGAGCG 60.816 66.667 0.00 0.00 33.26 5.03
1394 1399 2.359975 CGGGTGGGCTGAAAGGAC 60.360 66.667 0.00 0.00 0.00 3.85
1466 1471 2.391724 GACCGAAGCCAGTGGTCCAA 62.392 60.000 11.74 0.00 45.14 3.53
1539 1544 4.738998 TTGATGCCGGCACTGGGG 62.739 66.667 35.50 0.00 0.00 4.96
1543 1548 1.153086 GGAGATTGATGCCGGCACT 60.153 57.895 35.50 24.55 0.00 4.40
1560 1565 1.799258 GAGGCTGTGTGCAAAGTGGG 61.799 60.000 0.00 0.00 45.15 4.61
1563 1568 1.893808 CGGAGGCTGTGTGCAAAGT 60.894 57.895 0.00 0.00 45.15 2.66
1575 1580 2.240612 GATGTTTGCGACACGGAGGC 62.241 60.000 0.00 0.00 42.04 4.70
1621 1626 1.202348 GGAAAATGAAGCCCTTGGACG 59.798 52.381 0.00 0.00 0.00 4.79
1660 1665 0.388649 AGACGTGGACACATTCGAGC 60.389 55.000 0.00 0.00 0.00 5.03
1700 1705 4.996434 GGGGCATCCGGCGATCAG 62.996 72.222 9.30 0.00 46.16 2.90
1961 1966 6.356186 ACTAGTTACCTGACGAAATCCTTT 57.644 37.500 0.00 0.00 0.00 3.11
2095 2125 4.616181 AAAACGAGCAATCCCTTAATCG 57.384 40.909 0.00 0.00 36.32 3.34
2111 2141 0.437295 CCTCCGTCGTGCTAAAAACG 59.563 55.000 0.00 0.00 42.36 3.60
2128 2158 1.968017 CTGACATTGCGCACCACCT 60.968 57.895 11.12 0.00 0.00 4.00
2240 2276 6.480320 AGAATATCAAAAGCTACGAAATCGCT 59.520 34.615 2.15 0.00 44.43 4.93
2306 2346 4.878397 GGATGATACACCAGACTGAAAAGG 59.122 45.833 3.32 0.00 0.00 3.11
2333 2373 5.470437 TGTGTTTACTACGCCATCAATTTGA 59.530 36.000 0.75 0.75 36.40 2.69
2341 2381 3.688694 TCCTTGTGTTTACTACGCCAT 57.311 42.857 0.00 0.00 36.40 4.40
2424 2464 2.916716 GTGGCAAAGTTAACATGCGATG 59.083 45.455 22.32 8.40 40.94 3.84
2504 2544 2.993899 CCAAGAACTCGTCGCTGTAAAT 59.006 45.455 0.00 0.00 0.00 1.40
2579 2619 3.124636 CCGCTAGCAGTTGTAAAACGAAT 59.875 43.478 16.45 0.00 0.00 3.34
2734 2774 5.730568 GCGATATGCCCACAAGTAAAAGAAG 60.731 44.000 0.00 0.00 37.76 2.85
2769 2809 5.336372 CGAAAACTAATCCATCTTGGGCAAA 60.336 40.000 0.00 0.00 38.32 3.68
2770 2810 4.157656 CGAAAACTAATCCATCTTGGGCAA 59.842 41.667 0.00 0.00 38.32 4.52
2803 2846 6.321945 TGATGCTAGAACCAAACATATGCAAT 59.678 34.615 1.58 0.00 0.00 3.56
2821 2864 4.199310 GTGAGGCCACTTAATTGATGCTA 58.801 43.478 5.01 0.00 40.10 3.49
2845 2888 4.218635 TGAAGAGTGACACTACAGATGGTC 59.781 45.833 8.41 0.00 0.00 4.02
2872 2915 9.039165 AGAAATAAACACTTCCCAATTGATCAT 57.961 29.630 7.12 0.00 0.00 2.45
2952 3025 0.966179 CAACCAAACACCCCCTTAGC 59.034 55.000 0.00 0.00 0.00 3.09
2999 3072 2.190981 GTACACTATCTTCCGTTGCCG 58.809 52.381 0.00 0.00 0.00 5.69
3012 3085 2.632377 CGACCGAAGTAGGGTACACTA 58.368 52.381 0.00 0.00 38.07 2.74
3038 3112 5.010012 CACAACCCAAGCATAAAGTTCTCTT 59.990 40.000 0.00 0.00 35.14 2.85
3067 3142 1.927487 TGTGCAGATTGCCTCCAAAT 58.073 45.000 0.00 0.00 44.23 2.32
3082 3157 3.319137 TCTACTCACTCCAACATGTGC 57.681 47.619 0.00 0.00 34.49 4.57
3161 3240 5.196695 TGTATTGGTGTGCCTAAATGCATA 58.803 37.500 0.00 0.00 44.30 3.14
3181 3267 4.577875 TCATGCACTCATCAACACATGTA 58.422 39.130 0.00 0.00 36.96 2.29
3261 3347 7.631750 GCACACAAATGAATAATAAACAATGCG 59.368 33.333 0.00 0.00 0.00 4.73
3278 3364 4.989279 AAGACTCAACAAGCACACAAAT 57.011 36.364 0.00 0.00 0.00 2.32
3282 3368 3.764885 ACAAAGACTCAACAAGCACAC 57.235 42.857 0.00 0.00 0.00 3.82
3347 3435 0.729116 CACAACCCTCGATGCATGTC 59.271 55.000 2.46 0.00 0.00 3.06
3367 3459 5.186797 AGCAGTAAACTGAAGATGCTACTCT 59.813 40.000 14.21 0.00 46.59 3.24
3376 3468 5.983720 GTGTAGTGAAGCAGTAAACTGAAGA 59.016 40.000 14.21 0.00 46.59 2.87
3397 3489 3.753272 GCATAAGTGTGAGGACATTGTGT 59.247 43.478 0.00 0.00 33.63 3.72
3403 3495 3.517500 TGTATGGCATAAGTGTGAGGACA 59.482 43.478 9.14 0.00 0.00 4.02
3404 3496 4.137116 TGTATGGCATAAGTGTGAGGAC 57.863 45.455 9.14 0.00 0.00 3.85
3405 3497 5.125356 CAATGTATGGCATAAGTGTGAGGA 58.875 41.667 9.14 0.00 36.67 3.71
3421 3513 3.476552 CAACGACATAGCCCCAATGTAT 58.523 45.455 0.00 0.00 37.69 2.29
3443 3535 9.227777 AGGACATAATGACCTTTAAAGTGTTAC 57.772 33.333 14.03 7.22 39.42 2.50
3454 3546 5.707298 CAGTTCAACAGGACATAATGACCTT 59.293 40.000 0.00 0.00 39.42 3.50
3468 3560 8.322906 TCAAATACTCCATAACAGTTCAACAG 57.677 34.615 0.00 0.00 0.00 3.16
3563 3655 7.135089 TGTGTAATCATTTGTAGCGCTAAAA 57.865 32.000 20.73 18.31 0.00 1.52
3566 3658 6.045955 TCATGTGTAATCATTTGTAGCGCTA 58.954 36.000 14.45 14.45 0.00 4.26
3576 3668 6.216801 AGCATTGCTTCATGTGTAATCATT 57.783 33.333 5.03 0.00 33.89 2.57
3585 3677 7.754851 TTCATATGATAGCATTGCTTCATGT 57.245 32.000 27.87 23.21 40.44 3.21
3590 3682 6.152323 GGTCCATTCATATGATAGCATTGCTT 59.848 38.462 17.71 4.77 35.50 3.91
3595 3687 9.986157 AATTAAGGTCCATTCATATGATAGCAT 57.014 29.630 6.17 0.00 38.54 3.79
3610 3702 7.933033 ACGTAAACTTTCTGTAATTAAGGTCCA 59.067 33.333 0.00 0.00 0.00 4.02
3611 3703 8.315391 ACGTAAACTTTCTGTAATTAAGGTCC 57.685 34.615 0.00 0.00 0.00 4.46
3641 3733 1.937546 GCCACGCCTCCCAATTGAAG 61.938 60.000 7.12 3.95 0.00 3.02
3655 3747 1.003545 CCATGATTTTAGCTCGCCACG 60.004 52.381 0.00 0.00 0.00 4.94
3658 3750 0.954452 CCCCATGATTTTAGCTCGCC 59.046 55.000 0.00 0.00 0.00 5.54
3659 3751 0.312102 GCCCCATGATTTTAGCTCGC 59.688 55.000 0.00 0.00 0.00 5.03
3660 3752 0.588252 CGCCCCATGATTTTAGCTCG 59.412 55.000 0.00 0.00 0.00 5.03
3686 3778 8.488979 CTTTTTACAAAAAGTCGATGTGGTAG 57.511 34.615 15.81 0.00 46.03 3.18
3704 3796 7.859325 TCTATTCCTGCATACACCTTTTTAC 57.141 36.000 0.00 0.00 0.00 2.01
3735 3852 5.294356 TCCATAATAGGTCACACGCATAAC 58.706 41.667 0.00 0.00 0.00 1.89
3741 3858 5.064707 CCAAAACTCCATAATAGGTCACACG 59.935 44.000 0.00 0.00 0.00 4.49
3763 3880 7.039152 CCACCACATGCAATTAATATATTCCCA 60.039 37.037 0.00 0.00 0.00 4.37
3764 3881 7.178274 TCCACCACATGCAATTAATATATTCCC 59.822 37.037 0.00 0.00 0.00 3.97
3830 3961 7.255139 GCTACCACATACATTATCAAGGGAAAC 60.255 40.741 0.00 0.00 0.00 2.78
3843 3974 5.163622 GCACTTGAAATGCTACCACATACAT 60.164 40.000 0.00 0.00 40.08 2.29
3860 3991 2.092103 ACTTAACACCCCAAGCACTTGA 60.092 45.455 11.94 0.00 42.93 3.02
3902 4047 0.391597 TTGTTCCGAGGGACTGTCAC 59.608 55.000 10.38 5.95 41.55 3.67


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

AutoCloner maintained by Alex Coulton.