Multiple sequence alignment - TraesCS7A01G059100

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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 TraesCS7A01G059100 chr7A 100.000 2469 0 0 1434 3902 28556970 28559438 0.000000e+00 4560.0
1 TraesCS7A01G059100 chr7A 100.000 1125 0 0 1 1125 28555537 28556661 0.000000e+00 2078.0
2 TraesCS7A01G059100 chr7A 90.909 1529 113 9 2371 3893 577871044 577872552 0.000000e+00 2030.0
3 TraesCS7A01G059100 chr7A 93.843 1007 58 4 78 1082 577854429 577855433 0.000000e+00 1513.0
4 TraesCS7A01G059100 chr7A 92.408 922 69 1 1454 2375 577855799 577856719 0.000000e+00 1314.0
5 TraesCS7A01G059100 chr7A 95.349 86 2 1 1 86 577854323 577854406 6.800000e-28 135.0
6 TraesCS7A01G059100 chr7B 82.909 1375 212 13 1631 3000 65744669 65746025 0.000000e+00 1216.0
7 TraesCS7A01G059100 chr7B 89.070 860 87 7 3036 3890 65746205 65747062 0.000000e+00 1061.0
8 TraesCS7A01G059100 chr2D 75.090 277 61 7 1528 1800 598847131 598846859 5.290000e-24 122.0
9 TraesCS7A01G059100 chr6D 92.683 41 3 0 472 512 81582229 81582269 4.210000e-05 60.2


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 TraesCS7A01G059100 chr7A 28555537 28559438 3901 False 3319.000000 4560 100.000000 1 3902 2 chr7A.!!$F2 3901
1 TraesCS7A01G059100 chr7A 577871044 577872552 1508 False 2030.000000 2030 90.909000 2371 3893 1 chr7A.!!$F1 1522
2 TraesCS7A01G059100 chr7A 577854323 577856719 2396 False 987.333333 1513 93.866667 1 2375 3 chr7A.!!$F3 2374
3 TraesCS7A01G059100 chr7B 65744669 65747062 2393 False 1138.500000 1216 85.989500 1631 3890 2 chr7B.!!$F1 2259

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
571 603 0.038343 TTCTTTCTTGCAATGCCCGC 60.038 50.0 1.53 0.0 0.0 6.13 F
1103 1135 0.033504 CCAACCCCTATCATCCGTCG 59.966 60.0 0.00 0.0 0.0 5.12 F
1776 1808 0.032515 TCGTCCAGCTTCCTCCCATA 60.033 55.0 0.00 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1558 1590 0.241481 ACGAGTTCGGAGAAGACAGC 59.759 55.0 6.48 0.0 45.90 4.40 R
2395 2427 0.250727 GTGAACCCACCAGCTAGCAA 60.251 55.0 18.83 0.0 37.33 3.91 R
3689 3890 0.468226 AAGTGAAACGGCAGTCCAGA 59.532 50.0 0.00 0.0 45.86 3.86 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
59 60 0.544357 TCCTTCTCTTCTTCCCCGCA 60.544 55.000 0.00 0.00 0.00 5.69
75 76 1.227943 GCACAACCTGACCAGCTCA 60.228 57.895 0.00 0.00 0.00 4.26
76 77 1.510480 GCACAACCTGACCAGCTCAC 61.510 60.000 0.00 0.00 0.00 3.51
90 120 1.153489 CTCACGAGCCACTCCCATG 60.153 63.158 0.00 0.00 0.00 3.66
115 145 0.934496 TCAACCGCTCAAAACTGACG 59.066 50.000 0.00 0.00 0.00 4.35
170 200 0.319728 CACATCAGCCCCTCCTATCG 59.680 60.000 0.00 0.00 0.00 2.92
174 204 2.040884 AGCCCCTCCTATCGCCAA 60.041 61.111 0.00 0.00 0.00 4.52
186 216 3.964875 CGCCAAGCCACAAACGCT 61.965 61.111 0.00 0.00 38.53 5.07
200 230 3.064820 ACAAACGCTAACAGTTCAACCTG 59.935 43.478 0.00 0.00 38.45 4.00
225 255 2.279517 CGCCAGCCCTATCGTCAC 60.280 66.667 0.00 0.00 0.00 3.67
237 267 0.458543 ATCGTCACGACACAGGCATC 60.459 55.000 0.00 0.00 39.18 3.91
301 332 2.632996 CCCATGATACACCGGTCATACT 59.367 50.000 2.59 0.00 33.52 2.12
308 339 0.528924 CACCGGTCATACTTGGACGA 59.471 55.000 2.59 0.00 36.12 4.20
313 345 1.202268 GGTCATACTTGGACGACTCCG 60.202 57.143 0.00 0.00 39.88 4.63
337 369 0.391661 AACAGACCACGGCTGCTATG 60.392 55.000 0.00 0.00 36.86 2.23
350 382 1.336440 CTGCTATGTCCCTCTCACTCG 59.664 57.143 0.00 0.00 0.00 4.18
420 452 3.349022 CTCTTCTCTACAACCTCTCCGT 58.651 50.000 0.00 0.00 0.00 4.69
424 456 1.153823 CTACAACCTCTCCGTGCCG 60.154 63.158 0.00 0.00 0.00 5.69
429 461 1.827399 AACCTCTCCGTGCCGAACAT 61.827 55.000 0.00 0.00 0.00 2.71
433 465 2.741985 TCCGTGCCGAACATGCTG 60.742 61.111 0.00 0.00 33.60 4.41
476 508 2.665185 AAAGTCGACCAGTGCCGC 60.665 61.111 13.01 0.00 0.00 6.53
504 536 2.103042 CGCTGCTCTAGGTGTTGGC 61.103 63.158 0.00 0.00 0.00 4.52
505 537 1.003355 GCTGCTCTAGGTGTTGGCA 60.003 57.895 0.00 0.00 0.00 4.92
517 549 1.024046 TGTTGGCATTCCGGTCATCG 61.024 55.000 0.00 0.00 38.88 3.84
548 580 1.234615 GCAGGTTGGCTCGTTTGCTA 61.235 55.000 0.00 0.00 0.00 3.49
571 603 0.038343 TTCTTTCTTGCAATGCCCGC 60.038 50.000 1.53 0.00 0.00 6.13
594 626 3.322466 CCTCTCACAACCCCGCCT 61.322 66.667 0.00 0.00 0.00 5.52
599 631 2.359975 CACAACCCCGCCTTCTCC 60.360 66.667 0.00 0.00 0.00 3.71
617 649 1.044790 CCCCCATTTGCAGGATGGAC 61.045 60.000 24.89 0.00 45.59 4.02
621 653 1.471119 CATTTGCAGGATGGACAGCT 58.529 50.000 4.66 0.00 34.66 4.24
633 665 0.531974 GGACAGCTCCAACGTCAACA 60.532 55.000 3.82 0.00 36.42 3.33
640 672 1.541147 CTCCAACGTCAACAATGCCAT 59.459 47.619 0.00 0.00 0.00 4.40
656 688 2.438975 ATGACCATGCCACGCCAG 60.439 61.111 0.00 0.00 0.00 4.85
674 706 0.040351 AGTCACTAGCTCCTCTGCCA 59.960 55.000 0.00 0.00 0.00 4.92
689 721 2.774799 GCCACCCGTCATCATTGCC 61.775 63.158 0.00 0.00 0.00 4.52
729 761 2.203938 TCCCCACTCCACACCCTC 60.204 66.667 0.00 0.00 0.00 4.30
738 770 1.080354 CCACACCCTCCCTCCTACA 59.920 63.158 0.00 0.00 0.00 2.74
767 799 0.658897 CGGAGGACTCTCTTCGCTAC 59.341 60.000 0.00 0.00 39.86 3.58
801 833 0.324830 ACTCCCCTAGCCTGACTCAC 60.325 60.000 0.00 0.00 0.00 3.51
838 870 1.635817 GGCTTCCACTCCCTATGCCA 61.636 60.000 0.00 0.00 38.79 4.92
864 896 0.739813 CACCATCTTTCCCCGTCGAC 60.740 60.000 5.18 5.18 0.00 4.20
906 938 1.664151 CTCCAAGACGTATTTTCCGCC 59.336 52.381 0.00 0.00 0.00 6.13
956 988 1.588404 CACCATATCAGTTGACGACGC 59.412 52.381 0.00 0.00 0.00 5.19
1018 1050 1.449246 ATGCTCCTCGCTGTTGCTC 60.449 57.895 0.00 0.00 40.11 4.26
1027 1059 2.670934 CTGTTGCTCCGCCTTGCT 60.671 61.111 0.00 0.00 0.00 3.91
1068 1100 2.653115 GCCTTTGCTCACCTTGCC 59.347 61.111 0.00 0.00 33.53 4.52
1082 1114 1.679139 CTTGCCACTCCAACTCACAA 58.321 50.000 0.00 0.00 0.00 3.33
1083 1115 1.334869 CTTGCCACTCCAACTCACAAC 59.665 52.381 0.00 0.00 0.00 3.32
1084 1116 0.465460 TGCCACTCCAACTCACAACC 60.465 55.000 0.00 0.00 0.00 3.77
1085 1117 1.172812 GCCACTCCAACTCACAACCC 61.173 60.000 0.00 0.00 0.00 4.11
1086 1118 0.182537 CCACTCCAACTCACAACCCA 59.817 55.000 0.00 0.00 0.00 4.51
1087 1119 1.409521 CCACTCCAACTCACAACCCAA 60.410 52.381 0.00 0.00 0.00 4.12
1088 1120 1.676006 CACTCCAACTCACAACCCAAC 59.324 52.381 0.00 0.00 0.00 3.77
1089 1121 1.318576 CTCCAACTCACAACCCAACC 58.681 55.000 0.00 0.00 0.00 3.77
1090 1122 0.106419 TCCAACTCACAACCCAACCC 60.106 55.000 0.00 0.00 0.00 4.11
1091 1123 1.112916 CCAACTCACAACCCAACCCC 61.113 60.000 0.00 0.00 0.00 4.95
1092 1124 0.106217 CAACTCACAACCCAACCCCT 60.106 55.000 0.00 0.00 0.00 4.79
1093 1125 1.144093 CAACTCACAACCCAACCCCTA 59.856 52.381 0.00 0.00 0.00 3.53
1094 1126 1.755200 ACTCACAACCCAACCCCTAT 58.245 50.000 0.00 0.00 0.00 2.57
1095 1127 1.633945 ACTCACAACCCAACCCCTATC 59.366 52.381 0.00 0.00 0.00 2.08
1096 1128 1.633432 CTCACAACCCAACCCCTATCA 59.367 52.381 0.00 0.00 0.00 2.15
1097 1129 2.242196 CTCACAACCCAACCCCTATCAT 59.758 50.000 0.00 0.00 0.00 2.45
1098 1130 2.241176 TCACAACCCAACCCCTATCATC 59.759 50.000 0.00 0.00 0.00 2.92
1099 1131 1.569072 ACAACCCAACCCCTATCATCC 59.431 52.381 0.00 0.00 0.00 3.51
1100 1132 0.843984 AACCCAACCCCTATCATCCG 59.156 55.000 0.00 0.00 0.00 4.18
1101 1133 0.327191 ACCCAACCCCTATCATCCGT 60.327 55.000 0.00 0.00 0.00 4.69
1102 1134 0.396811 CCCAACCCCTATCATCCGTC 59.603 60.000 0.00 0.00 0.00 4.79
1103 1135 0.033504 CCAACCCCTATCATCCGTCG 59.966 60.000 0.00 0.00 0.00 5.12
1104 1136 0.750850 CAACCCCTATCATCCGTCGT 59.249 55.000 0.00 0.00 0.00 4.34
1105 1137 0.750850 AACCCCTATCATCCGTCGTG 59.249 55.000 0.00 0.00 0.00 4.35
1106 1138 1.006102 CCCCTATCATCCGTCGTGC 60.006 63.158 0.00 0.00 0.00 5.34
1107 1139 1.006102 CCCTATCATCCGTCGTGCC 60.006 63.158 0.00 0.00 0.00 5.01
1108 1140 1.739667 CCTATCATCCGTCGTGCCA 59.260 57.895 0.00 0.00 0.00 4.92
1109 1141 0.318441 CCTATCATCCGTCGTGCCAT 59.682 55.000 0.00 0.00 0.00 4.40
1110 1142 1.670087 CCTATCATCCGTCGTGCCATC 60.670 57.143 0.00 0.00 0.00 3.51
1111 1143 0.317160 TATCATCCGTCGTGCCATCC 59.683 55.000 0.00 0.00 0.00 3.51
1112 1144 1.685355 ATCATCCGTCGTGCCATCCA 61.685 55.000 0.00 0.00 0.00 3.41
1113 1145 1.449423 CATCCGTCGTGCCATCCAA 60.449 57.895 0.00 0.00 0.00 3.53
1114 1146 1.024046 CATCCGTCGTGCCATCCAAA 61.024 55.000 0.00 0.00 0.00 3.28
1115 1147 1.024579 ATCCGTCGTGCCATCCAAAC 61.025 55.000 0.00 0.00 0.00 2.93
1116 1148 2.686816 CCGTCGTGCCATCCAAACC 61.687 63.158 0.00 0.00 0.00 3.27
1117 1149 2.686816 CGTCGTGCCATCCAAACCC 61.687 63.158 0.00 0.00 0.00 4.11
1118 1150 1.303317 GTCGTGCCATCCAAACCCT 60.303 57.895 0.00 0.00 0.00 4.34
1119 1151 1.002624 TCGTGCCATCCAAACCCTC 60.003 57.895 0.00 0.00 0.00 4.30
1120 1152 2.398554 CGTGCCATCCAAACCCTCG 61.399 63.158 0.00 0.00 0.00 4.63
1121 1153 2.361104 TGCCATCCAAACCCTCGC 60.361 61.111 0.00 0.00 0.00 5.03
1122 1154 2.044946 GCCATCCAAACCCTCGCT 60.045 61.111 0.00 0.00 0.00 4.93
1123 1155 2.409870 GCCATCCAAACCCTCGCTG 61.410 63.158 0.00 0.00 0.00 5.18
1124 1156 1.750399 CCATCCAAACCCTCGCTGG 60.750 63.158 0.00 0.00 0.00 4.85
1454 1486 0.400594 GGTGTCACCTGCCTAACCTT 59.599 55.000 15.22 0.00 34.73 3.50
1455 1487 1.610886 GGTGTCACCTGCCTAACCTTC 60.611 57.143 15.22 0.00 34.73 3.46
1456 1488 1.348036 GTGTCACCTGCCTAACCTTCT 59.652 52.381 0.00 0.00 0.00 2.85
1459 1491 1.203313 TCACCTGCCTAACCTTCTCCT 60.203 52.381 0.00 0.00 0.00 3.69
1460 1492 1.208293 CACCTGCCTAACCTTCTCCTC 59.792 57.143 0.00 0.00 0.00 3.71
1461 1493 0.833949 CCTGCCTAACCTTCTCCTCC 59.166 60.000 0.00 0.00 0.00 4.30
1462 1494 0.833949 CTGCCTAACCTTCTCCTCCC 59.166 60.000 0.00 0.00 0.00 4.30
1463 1495 0.620700 TGCCTAACCTTCTCCTCCCC 60.621 60.000 0.00 0.00 0.00 4.81
1464 1496 0.326713 GCCTAACCTTCTCCTCCCCT 60.327 60.000 0.00 0.00 0.00 4.79
1493 1525 4.803426 GAGCGTCCTCTGCCGTGG 62.803 72.222 0.00 0.00 35.16 4.94
1521 1553 1.831389 CGTTCGAGGGCAACACTGTG 61.831 60.000 6.19 6.19 39.74 3.66
1526 1558 2.597510 GGGCAACACTGTGACCCC 60.598 66.667 15.86 15.56 41.37 4.95
1558 1590 2.353492 TCGCCGATCGCTCAATCG 60.353 61.111 10.32 5.77 46.28 3.34
1563 1595 1.543941 CCGATCGCTCAATCGCTGTC 61.544 60.000 10.32 0.00 45.56 3.51
1569 1601 1.285578 GCTCAATCGCTGTCTTCTCC 58.714 55.000 0.00 0.00 0.00 3.71
1626 1658 1.244019 AACTTTGGCATGACGAGGGC 61.244 55.000 2.48 0.00 0.00 5.19
1634 1666 0.379669 CATGACGAGGGCATTTGCTC 59.620 55.000 2.12 0.00 43.28 4.26
1641 1673 1.223487 GGGCATTTGCTCCGTCCTA 59.777 57.895 2.12 0.00 41.70 2.94
1776 1808 0.032515 TCGTCCAGCTTCCTCCCATA 60.033 55.000 0.00 0.00 0.00 2.74
1793 1825 6.317789 TCCCATAAATGAAATCAAGATCGC 57.682 37.500 0.00 0.00 0.00 4.58
1797 1829 6.979817 CCATAAATGAAATCAAGATCGCCAAA 59.020 34.615 0.00 0.00 0.00 3.28
1806 1838 0.037326 AGATCGCCAAAGTCGCTGAA 60.037 50.000 0.00 0.00 0.00 3.02
2004 2036 2.185608 GCCTCTCCTCGTCTTGCC 59.814 66.667 0.00 0.00 0.00 4.52
2106 2138 2.673523 GTGCCCCTGTGCATCTCT 59.326 61.111 0.00 0.00 44.30 3.10
2115 2147 3.370209 CCCTGTGCATCTCTTCTGATGAA 60.370 47.826 8.46 0.00 44.71 2.57
2248 2280 1.375396 CCAATCGTCGCACCCTTCA 60.375 57.895 0.00 0.00 0.00 3.02
2259 2291 1.152030 ACCCTTCACCTCTGCCTCA 60.152 57.895 0.00 0.00 0.00 3.86
2341 2373 1.153289 GACGCCTGCATCACCATCT 60.153 57.895 0.00 0.00 0.00 2.90
2358 2390 4.388499 TCGCCCTCGCCAAACTCC 62.388 66.667 0.00 0.00 35.26 3.85
2395 2427 1.616921 CCACCTGCCATTCCATCCT 59.383 57.895 0.00 0.00 0.00 3.24
2401 2433 2.228059 CTGCCATTCCATCCTTGCTAG 58.772 52.381 0.00 0.00 0.00 3.42
2406 2441 1.289160 TTCCATCCTTGCTAGCTGGT 58.711 50.000 17.23 6.47 0.00 4.00
2426 2461 1.133637 TGGGTTCACCTTTGCTGCTAA 60.134 47.619 0.00 0.00 41.11 3.09
2461 2496 4.601084 TGTTCAGGGTAAGTCCAAAACAA 58.399 39.130 0.00 0.00 38.11 2.83
2469 2504 5.535030 GGGTAAGTCCAAAACAATTCAGTCT 59.465 40.000 0.00 0.00 38.11 3.24
2530 2565 1.065418 CGTTGCCCATACTCCCTTCTT 60.065 52.381 0.00 0.00 0.00 2.52
2579 2614 2.178273 CGAGTGTGCGATCCGTCA 59.822 61.111 0.00 0.00 0.00 4.35
2585 2620 3.690280 TGCGATCCGTCACCAGCA 61.690 61.111 0.00 0.00 0.00 4.41
2616 2651 1.303398 TCGCGACCACTCCTTCTCT 60.303 57.895 3.71 0.00 0.00 3.10
2622 2657 1.137825 CCACTCCTTCTCTCGCGAC 59.862 63.158 3.71 0.00 0.00 5.19
2780 2815 0.253044 ACCCGTCTGGATGACAATGG 59.747 55.000 0.00 0.00 45.60 3.16
2790 2825 1.630126 ATGACAATGGCGCTCCTCCT 61.630 55.000 7.64 0.00 0.00 3.69
2889 2924 0.972983 CCTCCGACTCAGGTGTGGAT 60.973 60.000 0.00 0.00 0.00 3.41
2891 2926 1.219124 CCGACTCAGGTGTGGATGG 59.781 63.158 0.00 0.00 0.00 3.51
3005 3203 9.841880 CCTTCTCTTAGGTTTTTAATTTGTAGC 57.158 33.333 0.00 0.00 0.00 3.58
3029 3227 4.937201 AATTATCAAATCGGGCCCTTTC 57.063 40.909 22.43 0.00 0.00 2.62
3071 3269 2.102588 CCCGTCCACTACTATTTCCCTG 59.897 54.545 0.00 0.00 0.00 4.45
3099 3297 5.987347 CGTTCAGTCTTTCCCTTACTGTTAA 59.013 40.000 0.00 0.00 41.12 2.01
3124 3322 2.495409 CCGGCGGCCATGTAGTCTA 61.495 63.158 20.71 0.00 0.00 2.59
3168 3366 6.561614 TCATGAGTACTGTAATCTCGGTTTC 58.438 40.000 15.28 0.00 0.00 2.78
3187 3386 4.982241 TTCTTCTTGGAATGTGAGAGGT 57.018 40.909 0.00 0.00 0.00 3.85
3212 3411 8.243426 GTCTTGGTGATAATGAAAAATGTGCTA 58.757 33.333 0.00 0.00 0.00 3.49
3248 3447 4.412528 AGTTAATCTCTATCAACCCCCACC 59.587 45.833 0.00 0.00 0.00 4.61
3356 3555 0.323629 CCTCCCTGCTAACGGAACAA 59.676 55.000 0.00 0.00 0.00 2.83
3363 3562 1.373246 CTAACGGAACAACGGGCGA 60.373 57.895 0.00 0.00 38.39 5.54
3430 3631 3.841845 ACTAACCACACCTATGCCACTAA 59.158 43.478 0.00 0.00 0.00 2.24
3446 3647 3.191371 CCACTAAGCTCACCATCAAAACC 59.809 47.826 0.00 0.00 0.00 3.27
3488 3689 6.315144 ACATTGCAATTACTAACGTCTATGCA 59.685 34.615 9.83 0.00 0.00 3.96
3498 3699 0.537188 CGTCTATGCACCCTCCTGTT 59.463 55.000 0.00 0.00 0.00 3.16
3503 3704 0.251341 ATGCACCCTCCTGTTGTTCC 60.251 55.000 0.00 0.00 0.00 3.62
3557 3758 2.315925 TCAAGCAGGATGATTCGACC 57.684 50.000 0.00 0.00 44.15 4.79
3567 3768 2.041265 ATTCGACCCCCTGGCTCT 59.959 61.111 0.00 0.00 33.59 4.09
3608 3809 1.790623 CTTCGCTTCTCGGACGAAAAA 59.209 47.619 0.00 0.00 44.30 1.94
3659 3860 4.211374 GCTACGGCCTTTAATGACACTATG 59.789 45.833 0.00 0.00 0.00 2.23
3677 3878 7.806180 ACACTATGAATGAACTAGCCCTAATT 58.194 34.615 0.00 0.00 0.00 1.40
3689 3890 2.649816 AGCCCTAATTGAACTCCCACTT 59.350 45.455 0.00 0.00 0.00 3.16
3696 3897 2.103153 TGAACTCCCACTTCTGGACT 57.897 50.000 0.00 0.00 40.55 3.85
3751 3952 5.105473 CCCCTACTTTAGAACGACTTGATCA 60.105 44.000 0.00 0.00 0.00 2.92
3753 3954 7.042335 CCCTACTTTAGAACGACTTGATCATT 58.958 38.462 0.00 0.00 0.00 2.57
3772 3973 7.833682 TGATCATTCTTTTATCAACTTGGCCTA 59.166 33.333 3.32 0.00 0.00 3.93
3893 4094 5.047188 TCAAACTTTTTCAAATTCGAGCCC 58.953 37.500 0.00 0.00 0.00 5.19
3894 4095 3.282831 ACTTTTTCAAATTCGAGCCCG 57.717 42.857 0.00 0.00 37.07 6.13
3895 4096 2.030274 ACTTTTTCAAATTCGAGCCCGG 60.030 45.455 0.00 0.00 36.24 5.73
3896 4097 0.242555 TTTTCAAATTCGAGCCCGGC 59.757 50.000 0.00 0.00 36.24 6.13
3897 4098 0.608035 TTTCAAATTCGAGCCCGGCT 60.608 50.000 13.16 13.16 43.88 5.52
3898 4099 0.250793 TTCAAATTCGAGCCCGGCTA 59.749 50.000 13.29 0.00 39.88 3.93
3899 4100 0.179084 TCAAATTCGAGCCCGGCTAG 60.179 55.000 13.29 13.18 39.88 3.42
3900 4101 1.146263 AAATTCGAGCCCGGCTAGG 59.854 57.895 13.29 7.81 39.88 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 1.069765 CGTGAGCTGGTCAGGTTGT 59.930 57.895 18.41 0.00 39.57 3.32
75 76 4.101448 GGCATGGGAGTGGCTCGT 62.101 66.667 0.00 0.00 41.09 4.18
76 77 3.411114 ATGGCATGGGAGTGGCTCG 62.411 63.158 0.00 0.00 44.29 5.03
90 120 0.881118 TTTTGAGCGGTTGAGATGGC 59.119 50.000 0.00 0.00 0.00 4.40
115 145 1.893919 GAGACTGGTCAGGAGTGGGC 61.894 65.000 3.51 0.00 0.00 5.36
153 183 1.294780 GCGATAGGAGGGGCTGATG 59.705 63.158 0.00 0.00 0.00 3.07
170 200 0.663269 GTTAGCGTTTGTGGCTTGGC 60.663 55.000 0.00 0.00 41.80 4.52
174 204 1.602377 GAACTGTTAGCGTTTGTGGCT 59.398 47.619 0.00 0.00 44.35 4.75
186 216 2.506231 TGGGTGTCAGGTTGAACTGTTA 59.494 45.455 0.00 0.00 39.48 2.41
262 293 2.243264 GCTGAGCTGATACTGGCGC 61.243 63.158 0.00 0.00 0.00 6.53
301 332 0.524862 GTTAGCTCGGAGTCGTCCAA 59.475 55.000 6.90 0.00 44.18 3.53
308 339 0.889306 GTGGTCTGTTAGCTCGGAGT 59.111 55.000 6.90 0.00 0.00 3.85
313 345 0.737715 CAGCCGTGGTCTGTTAGCTC 60.738 60.000 0.00 0.00 0.00 4.09
337 369 2.179517 CGTGCGAGTGAGAGGGAC 59.820 66.667 0.00 0.00 0.00 4.46
350 382 1.732259 CGAGGATTTATATGGGCGTGC 59.268 52.381 0.00 0.00 0.00 5.34
420 452 1.580942 GAAAGCAGCATGTTCGGCA 59.419 52.632 0.00 0.00 39.31 5.69
491 523 1.656652 CGGAATGCCAACACCTAGAG 58.343 55.000 0.00 0.00 0.00 2.43
492 524 0.251916 CCGGAATGCCAACACCTAGA 59.748 55.000 0.00 0.00 0.00 2.43
504 536 1.594862 GAAGCTTCGATGACCGGAATG 59.405 52.381 9.46 0.00 39.14 2.67
505 537 1.941325 GAAGCTTCGATGACCGGAAT 58.059 50.000 9.46 0.00 39.14 3.01
517 549 0.514691 CAACCTGCAGTCGAAGCTTC 59.485 55.000 16.84 16.84 0.00 3.86
548 580 1.620323 GGCATTGCAAGAAAGAAGGGT 59.380 47.619 11.39 0.00 0.00 4.34
571 603 2.266055 GGTTGTGAGAGGGAGCGG 59.734 66.667 0.00 0.00 0.00 5.52
594 626 1.009997 ATCCTGCAAATGGGGGAGAA 58.990 50.000 0.00 0.00 0.00 2.87
599 631 0.324552 TGTCCATCCTGCAAATGGGG 60.325 55.000 21.69 5.39 43.30 4.96
617 649 1.664016 GCATTGTTGACGTTGGAGCTG 60.664 52.381 0.00 0.00 0.00 4.24
621 653 1.269174 CATGGCATTGTTGACGTTGGA 59.731 47.619 0.00 0.00 31.31 3.53
627 659 2.883574 CATGGTCATGGCATTGTTGAC 58.116 47.619 9.86 9.86 39.19 3.18
640 672 3.899981 GACTGGCGTGGCATGGTCA 62.900 63.158 9.08 2.11 0.00 4.02
656 688 0.174617 GTGGCAGAGGAGCTAGTGAC 59.825 60.000 0.00 0.00 34.17 3.67
689 721 0.539669 AAAGGGCTGGGAAAGGTTCG 60.540 55.000 0.00 0.00 0.00 3.95
711 743 2.529389 AGGGTGTGGAGTGGGGAC 60.529 66.667 0.00 0.00 0.00 4.46
738 770 1.133009 AGAGTCCTCCGGCATTCCTAT 60.133 52.381 0.00 0.00 0.00 2.57
747 779 0.464013 TAGCGAAGAGAGTCCTCCGG 60.464 60.000 0.00 0.00 40.30 5.14
754 786 4.358810 GGGGGTAGCGAAGAGAGT 57.641 61.111 0.00 0.00 0.00 3.24
823 855 2.731571 GCGTGGCATAGGGAGTGGA 61.732 63.158 0.00 0.00 0.00 4.02
838 870 0.889186 GGGAAAGATGGTGTGTGCGT 60.889 55.000 0.00 0.00 0.00 5.24
930 962 1.138859 TCAACTGATATGGTGGAGGCG 59.861 52.381 0.00 0.00 0.00 5.52
956 988 0.890683 GGCCTCATGAGTGTTTTGGG 59.109 55.000 21.11 5.52 0.00 4.12
987 1019 1.748403 GAGCATGTCGCCATAGGGA 59.252 57.895 0.00 0.00 44.04 4.20
1018 1050 0.101759 CATTGGATGAAGCAAGGCGG 59.898 55.000 0.00 0.00 0.00 6.13
1027 1059 1.321805 CGCTTGGGGCATTGGATGAA 61.322 55.000 0.00 0.00 41.91 2.57
1068 1100 1.676006 GTTGGGTTGTGAGTTGGAGTG 59.324 52.381 0.00 0.00 0.00 3.51
1082 1114 0.327191 ACGGATGATAGGGGTTGGGT 60.327 55.000 0.00 0.00 0.00 4.51
1083 1115 0.396811 GACGGATGATAGGGGTTGGG 59.603 60.000 0.00 0.00 0.00 4.12
1084 1116 0.033504 CGACGGATGATAGGGGTTGG 59.966 60.000 0.00 0.00 0.00 3.77
1085 1117 0.750850 ACGACGGATGATAGGGGTTG 59.249 55.000 0.00 0.00 0.00 3.77
1086 1118 0.750850 CACGACGGATGATAGGGGTT 59.249 55.000 0.00 0.00 0.00 4.11
1087 1119 1.745320 GCACGACGGATGATAGGGGT 61.745 60.000 0.00 0.00 0.00 4.95
1088 1120 1.006102 GCACGACGGATGATAGGGG 60.006 63.158 0.00 0.00 0.00 4.79
1089 1121 1.006102 GGCACGACGGATGATAGGG 60.006 63.158 0.00 0.00 0.00 3.53
1090 1122 0.318441 ATGGCACGACGGATGATAGG 59.682 55.000 0.00 0.00 0.00 2.57
1091 1123 1.670087 GGATGGCACGACGGATGATAG 60.670 57.143 0.00 0.00 0.00 2.08
1092 1124 0.317160 GGATGGCACGACGGATGATA 59.683 55.000 0.00 0.00 0.00 2.15
1093 1125 1.069765 GGATGGCACGACGGATGAT 59.930 57.895 0.00 0.00 0.00 2.45
1094 1126 1.893919 TTGGATGGCACGACGGATGA 61.894 55.000 0.00 0.00 0.00 2.92
1095 1127 1.024046 TTTGGATGGCACGACGGATG 61.024 55.000 0.00 0.00 0.00 3.51
1096 1128 1.024579 GTTTGGATGGCACGACGGAT 61.025 55.000 0.00 0.00 0.00 4.18
1097 1129 1.669760 GTTTGGATGGCACGACGGA 60.670 57.895 0.00 0.00 0.00 4.69
1098 1130 2.686816 GGTTTGGATGGCACGACGG 61.687 63.158 0.00 0.00 0.00 4.79
1099 1131 2.686816 GGGTTTGGATGGCACGACG 61.687 63.158 0.00 0.00 0.00 5.12
1100 1132 1.303317 AGGGTTTGGATGGCACGAC 60.303 57.895 0.00 0.00 0.00 4.34
1101 1133 1.002624 GAGGGTTTGGATGGCACGA 60.003 57.895 0.00 0.00 0.00 4.35
1102 1134 2.398554 CGAGGGTTTGGATGGCACG 61.399 63.158 0.00 0.00 0.00 5.34
1103 1135 2.700773 GCGAGGGTTTGGATGGCAC 61.701 63.158 0.00 0.00 0.00 5.01
1104 1136 2.361104 GCGAGGGTTTGGATGGCA 60.361 61.111 0.00 0.00 0.00 4.92
1105 1137 2.044946 AGCGAGGGTTTGGATGGC 60.045 61.111 0.00 0.00 0.00 4.40
1106 1138 1.750399 CCAGCGAGGGTTTGGATGG 60.750 63.158 0.00 0.00 33.76 3.51
1107 1139 3.909662 CCAGCGAGGGTTTGGATG 58.090 61.111 0.00 0.00 33.76 3.51
1433 1465 0.605589 GGTTAGGCAGGTGACACCAC 60.606 60.000 26.30 17.05 41.95 4.16
1434 1466 0.766674 AGGTTAGGCAGGTGACACCA 60.767 55.000 26.30 2.15 41.95 4.17
1435 1467 0.400594 AAGGTTAGGCAGGTGACACC 59.599 55.000 17.43 17.43 38.99 4.16
1436 1468 1.348036 AGAAGGTTAGGCAGGTGACAC 59.652 52.381 0.00 0.00 0.00 3.67
1437 1469 1.623811 GAGAAGGTTAGGCAGGTGACA 59.376 52.381 0.00 0.00 0.00 3.58
1438 1470 1.066071 GGAGAAGGTTAGGCAGGTGAC 60.066 57.143 0.00 0.00 0.00 3.67
1439 1471 1.203313 AGGAGAAGGTTAGGCAGGTGA 60.203 52.381 0.00 0.00 0.00 4.02
1440 1472 1.208293 GAGGAGAAGGTTAGGCAGGTG 59.792 57.143 0.00 0.00 0.00 4.00
1441 1473 1.574263 GAGGAGAAGGTTAGGCAGGT 58.426 55.000 0.00 0.00 0.00 4.00
1442 1474 0.833949 GGAGGAGAAGGTTAGGCAGG 59.166 60.000 0.00 0.00 0.00 4.85
1443 1475 0.833949 GGGAGGAGAAGGTTAGGCAG 59.166 60.000 0.00 0.00 0.00 4.85
1444 1476 0.620700 GGGGAGGAGAAGGTTAGGCA 60.621 60.000 0.00 0.00 0.00 4.75
1445 1477 0.326713 AGGGGAGGAGAAGGTTAGGC 60.327 60.000 0.00 0.00 0.00 3.93
1446 1478 1.008449 TCAGGGGAGGAGAAGGTTAGG 59.992 57.143 0.00 0.00 0.00 2.69
1447 1479 2.393646 CTCAGGGGAGGAGAAGGTTAG 58.606 57.143 0.00 0.00 37.51 2.34
1449 1481 3.408251 CTCAGGGGAGGAGAAGGTT 57.592 57.895 0.00 0.00 37.51 3.50
1558 1590 0.241481 ACGAGTTCGGAGAAGACAGC 59.759 55.000 6.48 0.00 45.90 4.40
1585 1617 2.657066 GGGGGAACTCGGACACCTC 61.657 68.421 0.00 0.00 0.00 3.85
1626 1658 2.403252 ACCTTAGGACGGAGCAAATG 57.597 50.000 4.77 0.00 0.00 2.32
1634 1666 1.732417 GCCGAGGTACCTTAGGACGG 61.732 65.000 30.46 28.66 41.44 4.79
1641 1673 0.968901 TGACATCGCCGAGGTACCTT 60.969 55.000 17.53 0.00 0.00 3.50
1776 1808 6.029346 ACTTTGGCGATCTTGATTTCATTT 57.971 33.333 0.00 0.00 0.00 2.32
1793 1825 1.795286 GAGTCAGTTCAGCGACTTTGG 59.205 52.381 0.00 0.00 42.48 3.28
1797 1829 1.173444 ACCGAGTCAGTTCAGCGACT 61.173 55.000 0.00 0.00 45.07 4.18
1851 1883 2.179517 GCCGAGTCACCGTCAGAG 59.820 66.667 0.00 0.00 0.00 3.35
2016 2048 2.584418 CTGCTGGAGTCGGATGCG 60.584 66.667 0.00 0.00 0.00 4.73
2055 2087 4.393778 GGGGAGAGGTCCACCGGA 62.394 72.222 9.46 0.00 46.07 5.14
2106 2138 1.299648 CCCCGTGCCTTCATCAGAA 59.700 57.895 0.00 0.00 0.00 3.02
2178 2210 3.934391 GACTGGTTCCACGCCGAGG 62.934 68.421 0.00 0.00 0.00 4.63
2341 2373 4.388499 GGAGTTTGGCGAGGGCGA 62.388 66.667 0.00 0.00 41.24 5.54
2358 2390 0.438830 GGTCGTAAGCAGTGAAAGCG 59.561 55.000 0.00 0.00 37.01 4.68
2395 2427 0.250727 GTGAACCCACCAGCTAGCAA 60.251 55.000 18.83 0.00 37.33 3.91
2406 2441 0.476338 TAGCAGCAAAGGTGAACCCA 59.524 50.000 0.00 0.00 36.42 4.51
2426 2461 1.228894 TGAACAGAGGACGAGGCCT 60.229 57.895 3.86 3.86 42.17 5.19
2461 2496 5.337788 AGAAGTACAGGGAGAAGACTGAAT 58.662 41.667 0.00 0.00 38.09 2.57
2469 2504 4.281182 GTGTTCAGAGAAGTACAGGGAGAA 59.719 45.833 0.00 0.00 0.00 2.87
2530 2565 2.685017 AGAGACCGGCATGGCTGA 60.685 61.111 17.57 0.00 43.94 4.26
2571 2606 2.509336 CGGTGCTGGTGACGGATC 60.509 66.667 0.00 0.00 39.98 3.36
2651 2686 2.054799 TGTAGGACTTTGGCTCCTTGT 58.945 47.619 0.00 0.00 39.09 3.16
2711 2746 2.543687 ATCGTCCGCACCGTTGAGAG 62.544 60.000 0.00 0.00 0.00 3.20
2780 2815 4.527583 CAGAGGCAGGAGGAGCGC 62.528 72.222 0.00 0.00 0.00 5.92
2790 2825 2.601666 AGGTCGTCAGCAGAGGCA 60.602 61.111 0.00 0.00 44.61 4.75
2826 2861 3.189921 GCATCATCTGCGCCACAA 58.810 55.556 4.18 0.00 41.97 3.33
3005 3203 4.034285 AGGGCCCGATTTGATAATTAGG 57.966 45.455 18.44 0.00 0.00 2.69
3071 3269 1.594331 AGGGAAAGACTGAACGCAAC 58.406 50.000 0.00 0.00 0.00 4.17
3124 3322 8.712228 TCATGAGATACTAATGTGACACCTAT 57.288 34.615 2.45 0.00 0.00 2.57
3168 3366 4.550076 AGACCTCTCACATTCCAAGAAG 57.450 45.455 0.00 0.00 0.00 2.85
3187 3386 7.230849 AGCACATTTTTCATTATCACCAAGA 57.769 32.000 0.00 0.00 0.00 3.02
3248 3447 3.025978 TGGATTCTTGCAATAAGGCCAG 58.974 45.455 5.01 0.00 0.00 4.85
3363 3562 0.668535 GAGTTGGCAGCCGAAACTTT 59.331 50.000 16.40 0.00 34.37 2.66
3430 3631 2.242043 CCAAGGTTTTGATGGTGAGCT 58.758 47.619 0.00 0.00 36.36 4.09
3446 3647 1.118838 TGTTTTGTCCAAGGGCCAAG 58.881 50.000 6.18 0.00 0.00 3.61
3488 3689 4.430388 TGGGAACAACAGGAGGGT 57.570 55.556 0.00 0.00 37.44 4.34
3498 3699 5.396213 CCAAGAAGGATTGTTTTTGGGAACA 60.396 40.000 0.00 0.00 41.22 3.18
3557 3758 2.370445 ACCGATCAAGAGCCAGGGG 61.370 63.158 0.00 0.00 0.00 4.79
3567 3768 5.957842 AGCAAGTTAAAATCACCGATCAA 57.042 34.783 0.00 0.00 0.00 2.57
3638 3839 5.601583 TCATAGTGTCATTAAAGGCCGTA 57.398 39.130 0.00 0.00 0.00 4.02
3659 3860 6.261158 GGAGTTCAATTAGGGCTAGTTCATTC 59.739 42.308 0.00 0.00 0.00 2.67
3677 3878 1.694150 CAGTCCAGAAGTGGGAGTTCA 59.306 52.381 0.00 0.00 45.11 3.18
3689 3890 0.468226 AAGTGAAACGGCAGTCCAGA 59.532 50.000 0.00 0.00 45.86 3.86
3696 3897 1.464734 TTTGACCAAGTGAAACGGCA 58.535 45.000 0.00 0.00 45.86 5.69
3751 3952 8.689972 CATTCTAGGCCAAGTTGATAAAAGAAT 58.310 33.333 5.01 8.99 31.87 2.40
3753 3954 7.336931 GTCATTCTAGGCCAAGTTGATAAAAGA 59.663 37.037 5.01 0.00 0.00 2.52
3772 3973 1.196012 GTCGGGGAAGGAGTCATTCT 58.804 55.000 16.45 0.00 0.00 2.40
3837 4038 4.390264 TGGGTGTTAATGTGAACGATCAA 58.610 39.130 0.00 0.00 37.30 2.57


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

AutoCloner maintained by Alex Coulton.