Multiple sequence alignment - TraesCS5B01G500900

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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 TraesCS5B01G500900 chr5B 100.000 3115 0 0 797 3911 668195374 668198488 0.000000e+00 5753
1 TraesCS5B01G500900 chr5B 100.000 335 0 0 1 335 668194578 668194912 1.540000e-173 619
2 TraesCS5B01G500900 chr5D 95.098 1326 37 7 1690 2989 529356100 529357423 0.000000e+00 2063
3 TraesCS5B01G500900 chr5D 93.691 745 27 9 955 1692 529355283 529356014 0.000000e+00 1098
4 TraesCS5B01G500900 chr5D 89.607 866 55 15 3074 3911 529357425 529358283 0.000000e+00 1068
5 TraesCS5B01G500900 chr5D 83.533 334 24 18 5 335 529354775 529355080 2.300000e-72 283
6 TraesCS5B01G500900 chr5D 93.478 92 6 0 2985 3076 367998175 367998084 1.900000e-28 137
7 TraesCS5B01G500900 chr5D 85.000 120 6 5 797 916 529355107 529355214 1.150000e-20 111
8 TraesCS5B01G500900 chr5A 90.401 1271 84 18 1751 2990 657491245 657492508 0.000000e+00 1637
9 TraesCS5B01G500900 chr5A 87.100 876 58 25 3069 3911 657492504 657493357 0.000000e+00 941
10 TraesCS5B01G500900 chr5A 88.131 792 50 16 908 1688 657490331 657491089 0.000000e+00 902
11 TraesCS5B01G500900 chr5A 89.189 333 22 7 5 335 657489840 657490160 1.690000e-108 403
12 TraesCS5B01G500900 chr2A 79.675 492 66 19 3414 3880 282967021 282967503 1.360000e-84 324
13 TraesCS5B01G500900 chr3D 95.455 88 4 0 2986 3073 43577841 43577928 1.470000e-29 141
14 TraesCS5B01G500900 chr3D 93.617 94 6 0 2989 3082 607079211 607079118 1.470000e-29 141
15 TraesCS5B01G500900 chr2B 95.402 87 4 0 2989 3075 756555370 756555456 5.270000e-29 139
16 TraesCS5B01G500900 chr7B 93.478 92 5 1 2988 3079 203031544 203031454 6.820000e-28 135
17 TraesCS5B01G500900 chr4D 93.407 91 6 0 2989 3079 449455616 449455706 6.820000e-28 135
18 TraesCS5B01G500900 chr3B 91.667 96 8 0 2989 3084 804117569 804117474 2.450000e-27 134
19 TraesCS5B01G500900 chr2D 91.667 96 8 0 2989 3084 25037968 25037873 2.450000e-27 134
20 TraesCS5B01G500900 chr7D 87.719 114 9 4 2986 3098 98275771 98275880 1.140000e-25 128


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 TraesCS5B01G500900 chr5B 668194578 668198488 3910 False 3186.00 5753 100.00000 1 3911 2 chr5B.!!$F1 3910
1 TraesCS5B01G500900 chr5D 529354775 529358283 3508 False 924.60 2063 89.38580 5 3911 5 chr5D.!!$F1 3906
2 TraesCS5B01G500900 chr5A 657489840 657493357 3517 False 970.75 1637 88.70525 5 3911 4 chr5A.!!$F1 3906

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
931 974 0.596083 CGAGGTGATAAGCGGCTCTG 60.596 60.0 1.45 0.00 0.00 3.35 F
1529 1585 0.318107 GATGCGTAATGTGCCATGGC 60.318 55.0 30.54 30.54 42.35 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2652 2850 1.084370 GCCCGGAGAGAACATGAACG 61.084 60.0 0.73 0.0 0.00 3.95 R
3058 3267 0.107654 AATGCTACTGCCTTCGTCCC 60.108 55.0 0.00 0.0 38.71 4.46 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
51 52 0.811616 AATCGAAGAGGATGGCGCAC 60.812 55.000 10.83 0.00 43.63 5.34
52 53 1.960040 ATCGAAGAGGATGGCGCACA 61.960 55.000 10.83 5.20 43.63 4.57
97 98 2.106683 GTAGCAAAGATGGGCGCGT 61.107 57.895 8.43 0.00 34.54 6.01
160 161 3.554692 CCATTGTCGCGACGCCTC 61.555 66.667 31.88 10.78 0.00 4.70
246 247 3.213402 GGAGAGAGACGGGGAGCG 61.213 72.222 0.00 0.00 0.00 5.03
248 249 2.124487 AGAGAGACGGGGAGCGAG 60.124 66.667 0.00 0.00 0.00 5.03
249 250 2.124653 GAGAGACGGGGAGCGAGA 60.125 66.667 0.00 0.00 0.00 4.04
250 251 1.527380 GAGAGACGGGGAGCGAGAT 60.527 63.158 0.00 0.00 0.00 2.75
271 274 1.180029 CGTCTCTTACCGGGAAGGAA 58.820 55.000 26.45 11.90 45.00 3.36
848 851 2.826488 TCTTTCTTGGAGGAGGAGGAG 58.174 52.381 0.00 0.00 0.00 3.69
851 854 1.383803 CTTGGAGGAGGAGGAGGGG 60.384 68.421 0.00 0.00 0.00 4.79
884 887 1.202533 CGTCCTCATATGGGCTTCGTT 60.203 52.381 2.13 0.00 0.00 3.85
889 892 3.244353 CCTCATATGGGCTTCGTTCTGAT 60.244 47.826 2.13 0.00 0.00 2.90
890 893 3.732212 TCATATGGGCTTCGTTCTGATG 58.268 45.455 2.13 0.00 0.00 3.07
895 898 2.846371 GCTTCGTTCTGATGCCACT 58.154 52.632 0.00 0.00 40.83 4.00
931 974 0.596083 CGAGGTGATAAGCGGCTCTG 60.596 60.000 1.45 0.00 0.00 3.35
937 980 3.492313 GTGATAAGCGGCTCTGTTTTTG 58.508 45.455 1.45 0.00 0.00 2.44
942 985 3.245518 AGCGGCTCTGTTTTTGTTTTT 57.754 38.095 0.00 0.00 0.00 1.94
943 986 2.929398 AGCGGCTCTGTTTTTGTTTTTG 59.071 40.909 0.00 0.00 0.00 2.44
1094 1137 3.036084 GTCGGTGGTGTCGCTGTG 61.036 66.667 0.00 0.00 0.00 3.66
1423 1478 3.317455 TCAAGGTAGTATCGCCCCTAA 57.683 47.619 0.00 0.00 0.00 2.69
1424 1479 3.645434 TCAAGGTAGTATCGCCCCTAAA 58.355 45.455 0.00 0.00 0.00 1.85
1437 1492 2.753507 GCCCCTAAATCTCTCCTCTCGA 60.754 54.545 0.00 0.00 0.00 4.04
1456 1512 1.227102 CCCCGAATGGAGCAATGGA 59.773 57.895 0.00 0.00 37.49 3.41
1467 1523 0.729116 AGCAATGGATCGCTCGTTTG 59.271 50.000 0.00 0.00 31.16 2.93
1477 1533 0.670546 CGCTCGTTTGGATCACTGGT 60.671 55.000 0.00 0.00 0.00 4.00
1480 1536 2.341257 CTCGTTTGGATCACTGGTCTG 58.659 52.381 0.00 0.00 0.00 3.51
1481 1537 0.798776 CGTTTGGATCACTGGTCTGC 59.201 55.000 0.00 0.00 0.00 4.26
1482 1538 1.609061 CGTTTGGATCACTGGTCTGCT 60.609 52.381 0.00 0.00 0.00 4.24
1483 1539 2.079925 GTTTGGATCACTGGTCTGCTC 58.920 52.381 0.00 0.00 0.00 4.26
1484 1540 1.649321 TTGGATCACTGGTCTGCTCT 58.351 50.000 0.00 0.00 0.00 4.09
1485 1541 1.189752 TGGATCACTGGTCTGCTCTC 58.810 55.000 0.00 0.00 0.00 3.20
1487 1543 1.408702 GGATCACTGGTCTGCTCTCTC 59.591 57.143 0.00 0.00 0.00 3.20
1488 1544 2.098614 GATCACTGGTCTGCTCTCTCA 58.901 52.381 0.00 0.00 0.00 3.27
1489 1545 1.252175 TCACTGGTCTGCTCTCTCAC 58.748 55.000 0.00 0.00 0.00 3.51
1490 1546 0.964700 CACTGGTCTGCTCTCTCACA 59.035 55.000 0.00 0.00 0.00 3.58
1512 1568 1.067635 GCATTTTGCCGAACACCTGAT 60.068 47.619 0.00 0.00 37.42 2.90
1529 1585 0.318107 GATGCGTAATGTGCCATGGC 60.318 55.000 30.54 30.54 42.35 4.40
1530 1586 1.737355 ATGCGTAATGTGCCATGGCC 61.737 55.000 33.44 23.83 41.09 5.36
1531 1587 3.119193 CGTAATGTGCCATGGCCC 58.881 61.111 33.44 23.88 41.09 5.80
1532 1588 2.489275 CGTAATGTGCCATGGCCCC 61.489 63.158 33.44 23.44 41.09 5.80
1533 1589 1.381056 GTAATGTGCCATGGCCCCA 60.381 57.895 33.44 28.02 41.09 4.96
1534 1590 0.760189 GTAATGTGCCATGGCCCCAT 60.760 55.000 33.44 28.87 41.09 4.00
1553 1609 1.377690 TGGGGGTATGTGGATTGTGT 58.622 50.000 0.00 0.00 0.00 3.72
1578 1638 1.953138 CAATGCCGCCGTGCAAAAA 60.953 52.632 4.46 0.00 45.84 1.94
1608 1668 6.908825 TCACCACTACTTAAATTTCACATGC 58.091 36.000 0.00 0.00 0.00 4.06
1693 1753 4.021650 GACACTTGCCGTCGTGAA 57.978 55.556 0.00 0.00 35.23 3.18
1734 1882 3.046374 GCCTTCAACTCCCCCTCTTATA 58.954 50.000 0.00 0.00 0.00 0.98
1735 1883 3.653352 GCCTTCAACTCCCCCTCTTATAT 59.347 47.826 0.00 0.00 0.00 0.86
1952 2129 5.046520 GGTTCTATGTGGGTACTTCTCAACT 60.047 44.000 0.00 0.00 0.00 3.16
1977 2154 6.944290 TCATTCATCAAACCTCTGTCTGAAAT 59.056 34.615 0.00 0.00 0.00 2.17
1987 2164 7.288810 ACCTCTGTCTGAAATTTTATTTGCA 57.711 32.000 0.00 0.00 0.00 4.08
2075 2266 6.612247 TTTTCAAGTGTTTGCGATCTAGAA 57.388 33.333 0.00 0.00 34.21 2.10
2177 2371 5.897824 TCAGTACCCAATTTACCCAAAACAA 59.102 36.000 0.00 0.00 0.00 2.83
2211 2405 7.148069 ACCAATTTAATGATCCGGACTTCTTTC 60.148 37.037 6.12 0.00 0.00 2.62
2260 2454 4.447290 TCACATGAAGGTCTTGTTCGAAA 58.553 39.130 0.00 0.00 33.21 3.46
2388 2586 3.544684 TCTTGTGGCTGCCATTATACTG 58.455 45.455 26.22 10.89 35.28 2.74
2400 2598 5.368230 TGCCATTATACTGATACTTCCACCA 59.632 40.000 0.00 0.00 0.00 4.17
2652 2850 2.240612 CTTTTACGCTCGGTGCCAGC 62.241 60.000 0.00 3.62 38.78 4.85
2773 2979 2.476854 GCTAATTGCCTTGCTGTTCTCG 60.477 50.000 0.00 0.00 35.15 4.04
2901 3110 6.628185 AGATTTTGATCAAATTGAGGCACTC 58.372 36.000 21.10 2.22 45.15 3.51
2922 3131 7.928706 GCACTCAATACTTAATGGTACTGAGAT 59.071 37.037 15.96 3.19 44.06 2.75
2929 3138 9.823647 ATACTTAATGGTACTGAGATTTGTCTG 57.176 33.333 0.00 0.00 0.00 3.51
2938 3147 7.921745 GGTACTGAGATTTGTCTGTAATACCTC 59.078 40.741 0.00 0.00 33.99 3.85
2961 3170 5.824429 CAGCACTTCTGAATTCTGTTTTCA 58.176 37.500 7.05 0.00 45.72 2.69
2985 3194 5.720041 ACTTACCTATGACTAAGCACTGGAA 59.280 40.000 0.00 0.00 0.00 3.53
2986 3195 6.212791 ACTTACCTATGACTAAGCACTGGAAA 59.787 38.462 0.00 0.00 0.00 3.13
2987 3196 5.499004 ACCTATGACTAAGCACTGGAAAA 57.501 39.130 0.00 0.00 0.00 2.29
2988 3197 6.067217 ACCTATGACTAAGCACTGGAAAAT 57.933 37.500 0.00 0.00 0.00 1.82
2989 3198 7.195374 ACCTATGACTAAGCACTGGAAAATA 57.805 36.000 0.00 0.00 0.00 1.40
2990 3199 7.048512 ACCTATGACTAAGCACTGGAAAATAC 58.951 38.462 0.00 0.00 0.00 1.89
2991 3200 7.092846 ACCTATGACTAAGCACTGGAAAATACT 60.093 37.037 0.00 0.00 0.00 2.12
2992 3201 7.439655 CCTATGACTAAGCACTGGAAAATACTC 59.560 40.741 0.00 0.00 0.00 2.59
2993 3202 5.488341 TGACTAAGCACTGGAAAATACTCC 58.512 41.667 0.00 0.00 35.88 3.85
2994 3203 4.844884 ACTAAGCACTGGAAAATACTCCC 58.155 43.478 0.00 0.00 34.22 4.30
2995 3204 4.536489 ACTAAGCACTGGAAAATACTCCCT 59.464 41.667 0.00 0.00 34.22 4.20
2996 3205 3.636153 AGCACTGGAAAATACTCCCTC 57.364 47.619 0.00 0.00 34.22 4.30
2997 3206 2.239907 AGCACTGGAAAATACTCCCTCC 59.760 50.000 0.00 0.00 34.22 4.30
2998 3207 2.906354 CACTGGAAAATACTCCCTCCG 58.094 52.381 0.00 0.00 34.22 4.63
2999 3208 2.236395 CACTGGAAAATACTCCCTCCGT 59.764 50.000 0.00 0.00 34.22 4.69
3000 3209 2.500504 ACTGGAAAATACTCCCTCCGTC 59.499 50.000 0.00 0.00 34.22 4.79
3001 3210 1.835531 TGGAAAATACTCCCTCCGTCC 59.164 52.381 0.00 0.00 34.22 4.79
3002 3211 1.140452 GGAAAATACTCCCTCCGTCCC 59.860 57.143 0.00 0.00 0.00 4.46
3003 3212 1.835531 GAAAATACTCCCTCCGTCCCA 59.164 52.381 0.00 0.00 0.00 4.37
3004 3213 1.961133 AAATACTCCCTCCGTCCCAA 58.039 50.000 0.00 0.00 0.00 4.12
3005 3214 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
3006 3215 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
3007 3216 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3008 3217 0.328258 ACTCCCTCCGTCCCAAAATG 59.672 55.000 0.00 0.00 0.00 2.32
3009 3218 0.328258 CTCCCTCCGTCCCAAAATGT 59.672 55.000 0.00 0.00 0.00 2.71
3010 3219 1.557832 CTCCCTCCGTCCCAAAATGTA 59.442 52.381 0.00 0.00 0.00 2.29
3011 3220 1.986631 TCCCTCCGTCCCAAAATGTAA 59.013 47.619 0.00 0.00 0.00 2.41
3012 3221 2.026636 TCCCTCCGTCCCAAAATGTAAG 60.027 50.000 0.00 0.00 0.00 2.34
3013 3222 2.026636 CCCTCCGTCCCAAAATGTAAGA 60.027 50.000 0.00 0.00 0.00 2.10
3014 3223 3.007635 CCTCCGTCCCAAAATGTAAGAC 58.992 50.000 0.00 0.00 0.00 3.01
3016 3225 2.037511 TCCGTCCCAAAATGTAAGACGT 59.962 45.455 9.63 0.00 46.62 4.34
3017 3226 2.809696 CCGTCCCAAAATGTAAGACGTT 59.190 45.455 9.63 0.00 46.62 3.99
3018 3227 3.251487 CCGTCCCAAAATGTAAGACGTTT 59.749 43.478 9.63 0.00 46.62 3.60
3019 3228 4.261280 CCGTCCCAAAATGTAAGACGTTTT 60.261 41.667 9.63 4.14 45.25 2.43
3020 3229 4.907582 CGTCCCAAAATGTAAGACGTTTTC 59.092 41.667 6.57 0.00 43.26 2.29
3021 3230 5.277634 CGTCCCAAAATGTAAGACGTTTTCT 60.278 40.000 6.57 0.00 43.26 2.52
3022 3231 6.140786 GTCCCAAAATGTAAGACGTTTTCTC 58.859 40.000 6.57 0.00 43.26 2.87
3023 3232 5.823570 TCCCAAAATGTAAGACGTTTTCTCA 59.176 36.000 6.57 0.00 43.26 3.27
3024 3233 5.912955 CCCAAAATGTAAGACGTTTTCTCAC 59.087 40.000 6.57 0.00 43.26 3.51
3025 3234 6.459024 CCCAAAATGTAAGACGTTTTCTCACA 60.459 38.462 6.57 0.00 43.26 3.58
3026 3235 6.413818 CCAAAATGTAAGACGTTTTCTCACAC 59.586 38.462 6.57 0.00 43.26 3.82
3027 3236 6.920569 AAATGTAAGACGTTTTCTCACACT 57.079 33.333 0.00 0.00 35.10 3.55
3028 3237 8.332464 CAAAATGTAAGACGTTTTCTCACACTA 58.668 33.333 6.57 0.00 43.26 2.74
3029 3238 7.639162 AATGTAAGACGTTTTCTCACACTAG 57.361 36.000 0.00 0.00 35.10 2.57
3030 3239 6.140303 TGTAAGACGTTTTCTCACACTAGT 57.860 37.500 0.00 0.00 25.97 2.57
3032 3241 4.650754 AGACGTTTTCTCACACTAGTGT 57.349 40.909 22.95 22.95 46.01 3.55
3033 3242 5.762825 AGACGTTTTCTCACACTAGTGTA 57.237 39.130 27.48 10.55 46.01 2.90
3034 3243 5.759963 AGACGTTTTCTCACACTAGTGTAG 58.240 41.667 27.48 22.14 46.01 2.74
3035 3244 5.298777 AGACGTTTTCTCACACTAGTGTAGT 59.701 40.000 27.48 15.91 46.01 2.73
3070 3279 2.332063 ACATTATGGGACGAAGGCAG 57.668 50.000 0.00 0.00 0.00 4.85
3084 3293 3.063997 CGAAGGCAGTAGCATTTAACCAG 59.936 47.826 0.00 0.00 45.98 4.00
3108 3317 5.706916 CAGTTTCCAAGAATCAACATCTGG 58.293 41.667 0.00 0.00 0.00 3.86
3239 3448 7.014518 TGGTTATGGCCTGAAAAGAATCATATG 59.985 37.037 3.32 0.00 0.00 1.78
3355 3576 4.801147 TCATTCGTTATCATTGCTGCTC 57.199 40.909 0.00 0.00 0.00 4.26
3469 3690 3.231207 TCAAATCGACTTTTTCCCCCA 57.769 42.857 0.00 0.00 0.00 4.96
3470 3691 2.888414 TCAAATCGACTTTTTCCCCCAC 59.112 45.455 0.00 0.00 0.00 4.61
3471 3692 2.625790 CAAATCGACTTTTTCCCCCACA 59.374 45.455 0.00 0.00 0.00 4.17
3472 3693 2.200373 ATCGACTTTTTCCCCCACAG 57.800 50.000 0.00 0.00 0.00 3.66
3511 3734 0.902984 TCCTCTAAGCTTCGTGGGCA 60.903 55.000 16.44 0.00 0.00 5.36
3512 3735 0.179000 CCTCTAAGCTTCGTGGGCAT 59.821 55.000 0.00 0.00 0.00 4.40
3588 3835 0.321671 GAACAGCTAGGCACAGACCA 59.678 55.000 0.00 0.00 0.00 4.02
3609 3856 7.441458 AGACCAACTGTATCAGTAGTTTTGTTC 59.559 37.037 2.80 0.00 44.62 3.18
3610 3857 7.051623 ACCAACTGTATCAGTAGTTTTGTTCA 58.948 34.615 2.80 0.00 44.62 3.18
3612 3859 8.567948 CCAACTGTATCAGTAGTTTTGTTCATT 58.432 33.333 2.80 0.00 44.62 2.57
3645 3892 2.159179 AAGTTTTGTCAGTTGGGCCT 57.841 45.000 4.53 0.00 0.00 5.19
3655 3902 2.852449 TCAGTTGGGCCTTGGAGATATT 59.148 45.455 4.53 0.00 0.00 1.28
3656 3903 2.954318 CAGTTGGGCCTTGGAGATATTG 59.046 50.000 4.53 0.00 0.00 1.90
3657 3904 2.091665 AGTTGGGCCTTGGAGATATTGG 60.092 50.000 4.53 0.00 0.00 3.16
3674 3922 6.772716 AGATATTGGTAAAGCACTTGGGTATG 59.227 38.462 0.00 0.00 0.00 2.39
3677 3925 3.181438 TGGTAAAGCACTTGGGTATGTGT 60.181 43.478 0.00 0.00 35.16 3.72
3691 3939 4.804139 GGGTATGTGTATCTGTTGAAGACG 59.196 45.833 0.00 0.00 37.88 4.18
3696 3944 2.000447 GTATCTGTTGAAGACGCACCC 59.000 52.381 0.00 0.00 37.88 4.61
3713 3961 3.495124 CCGATTGGGCAACAAACAG 57.505 52.632 0.00 0.00 43.46 3.16
3716 3964 2.393764 CGATTGGGCAACAAACAGAAC 58.606 47.619 0.00 0.00 43.46 3.01
3721 3969 3.030291 TGGGCAACAAACAGAACAGAAT 58.970 40.909 0.00 0.00 39.74 2.40
3723 3971 4.646945 TGGGCAACAAACAGAACAGAATAA 59.353 37.500 0.00 0.00 39.74 1.40
3733 3981 7.617041 AACAGAACAGAATAATTAGCCTGTC 57.383 36.000 17.57 12.87 38.75 3.51
3735 3983 7.341805 ACAGAACAGAATAATTAGCCTGTCAT 58.658 34.615 17.57 10.08 38.75 3.06
3737 3985 7.714377 CAGAACAGAATAATTAGCCTGTCATCT 59.286 37.037 17.57 15.22 38.75 2.90
3738 3986 8.928448 AGAACAGAATAATTAGCCTGTCATCTA 58.072 33.333 17.57 0.00 38.75 1.98
3769 4017 5.363005 ACATTAAGCCGTAAGTACTCTCCAT 59.637 40.000 0.00 0.00 0.00 3.41
3796 4044 6.183360 ACCATGTGTTTGAACAACTAAACGAT 60.183 34.615 0.00 0.00 41.21 3.73
3806 4054 6.200286 TGAACAACTAAACGATCTCTGTGAAC 59.800 38.462 0.00 0.00 0.00 3.18
3807 4055 5.844004 ACAACTAAACGATCTCTGTGAACT 58.156 37.500 0.00 0.00 0.00 3.01
3818 4066 3.259374 TCTCTGTGAACTGATCCTGAACC 59.741 47.826 0.00 0.00 0.00 3.62
3846 4095 1.065997 AGGTGGGGGCAGTAAACAGT 61.066 55.000 0.00 0.00 0.00 3.55
3847 4096 0.178973 GGTGGGGGCAGTAAACAGTT 60.179 55.000 0.00 0.00 0.00 3.16
3852 4101 4.820173 GTGGGGGCAGTAAACAGTTATATC 59.180 45.833 0.00 0.00 0.00 1.63
3856 4105 5.995897 GGGGCAGTAAACAGTTATATCGAAT 59.004 40.000 0.00 0.00 0.00 3.34
3885 4135 4.707030 TGCAGCCTTATTCATGTTGAAG 57.293 40.909 0.00 0.00 40.05 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.851263 TGAGGTTAATTGACGGCAGT 57.149 45.000 0.00 0.00 0.00 4.40
1 2 3.063997 GTGATGAGGTTAATTGACGGCAG 59.936 47.826 0.00 0.00 0.00 4.85
2 3 3.006940 GTGATGAGGTTAATTGACGGCA 58.993 45.455 0.00 0.00 0.00 5.69
3 4 3.006940 TGTGATGAGGTTAATTGACGGC 58.993 45.455 0.00 0.00 0.00 5.68
10 11 7.413000 CGATTTCGAGTTTGTGATGAGGTTAAT 60.413 37.037 0.00 0.00 43.02 1.40
67 68 5.336372 CCATCTTTGCTACCGGATTTTTCAA 60.336 40.000 9.46 0.08 0.00 2.69
70 71 3.447229 CCCATCTTTGCTACCGGATTTTT 59.553 43.478 9.46 0.00 0.00 1.94
80 81 2.106074 CACGCGCCCATCTTTGCTA 61.106 57.895 5.73 0.00 0.00 3.49
139 140 3.853330 CGTCGCGACAATGGCTGG 61.853 66.667 35.71 15.34 0.00 4.85
160 161 1.085091 GATTCTGTCTGTGCAGGCTG 58.915 55.000 10.94 10.94 37.12 4.85
232 233 1.527380 ATCTCGCTCCCCGTCTCTC 60.527 63.158 0.00 0.00 38.35 3.20
248 249 0.458669 TTCCCGGTAAGAGACGCATC 59.541 55.000 0.00 0.00 0.00 3.91
249 250 0.460311 CTTCCCGGTAAGAGACGCAT 59.540 55.000 0.00 0.00 0.00 4.73
250 251 1.601419 CCTTCCCGGTAAGAGACGCA 61.601 60.000 8.60 0.00 0.00 5.24
255 258 1.481363 GGTCTTCCTTCCCGGTAAGAG 59.519 57.143 8.60 0.00 32.93 2.85
262 265 2.722201 CCTCCGGTCTTCCTTCCCG 61.722 68.421 0.00 0.00 41.37 5.14
890 893 1.227853 CCGTAGGCCCATTAGTGGC 60.228 63.158 0.00 0.00 46.14 5.01
1179 1234 4.388499 TTCCAGTCCCGCGCCTTC 62.388 66.667 0.00 0.00 0.00 3.46
1423 1478 0.466555 CGGGGTCGAGAGGAGAGATT 60.467 60.000 0.00 0.00 39.00 2.40
1424 1479 1.149627 CGGGGTCGAGAGGAGAGAT 59.850 63.158 0.00 0.00 39.00 2.75
1437 1492 1.076777 CCATTGCTCCATTCGGGGT 60.077 57.895 0.00 0.00 33.89 4.95
1456 1512 1.645034 CAGTGATCCAAACGAGCGAT 58.355 50.000 0.00 0.00 0.00 4.58
1467 1523 1.408702 GAGAGAGCAGACCAGTGATCC 59.591 57.143 0.00 0.00 33.09 3.36
1480 1536 2.593257 GCAAAATGCTTGTGAGAGAGC 58.407 47.619 0.00 0.00 40.96 4.09
1481 1537 2.413765 CGGCAAAATGCTTGTGAGAGAG 60.414 50.000 2.00 0.00 44.28 3.20
1482 1538 1.536766 CGGCAAAATGCTTGTGAGAGA 59.463 47.619 2.00 0.00 44.28 3.10
1483 1539 1.536766 TCGGCAAAATGCTTGTGAGAG 59.463 47.619 2.00 0.00 44.28 3.20
1484 1540 1.603456 TCGGCAAAATGCTTGTGAGA 58.397 45.000 2.00 0.00 44.28 3.27
1485 1541 2.053627 GTTCGGCAAAATGCTTGTGAG 58.946 47.619 2.00 0.00 44.28 3.51
1487 1543 1.522258 GTGTTCGGCAAAATGCTTGTG 59.478 47.619 2.00 0.00 44.28 3.33
1488 1544 1.537990 GGTGTTCGGCAAAATGCTTGT 60.538 47.619 2.00 0.00 44.28 3.16
1489 1545 1.139163 GGTGTTCGGCAAAATGCTTG 58.861 50.000 2.00 0.00 44.28 4.01
1490 1546 1.039856 AGGTGTTCGGCAAAATGCTT 58.960 45.000 2.00 0.00 44.28 3.91
1531 1587 1.217689 ACAATCCACATACCCCCATGG 59.782 52.381 4.14 4.14 41.37 3.66
1532 1588 2.309613 CACAATCCACATACCCCCATG 58.690 52.381 0.00 0.00 0.00 3.66
1533 1589 1.929494 ACACAATCCACATACCCCCAT 59.071 47.619 0.00 0.00 0.00 4.00
1534 1590 1.377690 ACACAATCCACATACCCCCA 58.622 50.000 0.00 0.00 0.00 4.96
1535 1591 2.525105 AACACAATCCACATACCCCC 57.475 50.000 0.00 0.00 0.00 5.40
1536 1592 4.787551 TCATAACACAATCCACATACCCC 58.212 43.478 0.00 0.00 0.00 4.95
1537 1593 4.275936 GCTCATAACACAATCCACATACCC 59.724 45.833 0.00 0.00 0.00 3.69
1543 1599 4.107622 GCATTGCTCATAACACAATCCAC 58.892 43.478 0.16 0.00 31.82 4.02
1553 1609 1.451207 ACGGCGGCATTGCTCATAA 60.451 52.632 13.24 0.00 34.52 1.90
1578 1638 8.784043 GTGAAATTTAAGTAGTGGTGATCAGTT 58.216 33.333 0.00 0.00 0.00 3.16
1579 1639 7.936847 TGTGAAATTTAAGTAGTGGTGATCAGT 59.063 33.333 0.00 0.00 0.00 3.41
1617 1677 5.473846 TCTCACCGGTTTTGTTATGCATAAA 59.526 36.000 20.46 4.86 0.00 1.40
1635 1695 4.365723 CAATAGCCAAATGCATTCTCACC 58.634 43.478 13.38 0.21 44.83 4.02
1692 1752 2.943033 CTGTCTTTCGTTGGGTTCACTT 59.057 45.455 0.00 0.00 0.00 3.16
1693 1753 2.561569 CTGTCTTTCGTTGGGTTCACT 58.438 47.619 0.00 0.00 0.00 3.41
1952 2129 5.488262 TCAGACAGAGGTTTGATGAATGA 57.512 39.130 0.00 0.00 33.61 2.57
1987 2164 4.552767 CGAACAAGAACATCGAAGCAAAGT 60.553 41.667 0.00 0.00 38.82 2.66
2075 2266 7.064134 CGGCATACGGTTGTACAATATCAATAT 59.936 37.037 12.26 2.42 39.42 1.28
2146 2339 6.012333 TGGGTAAATTGGGTACTGAGTAATGT 60.012 38.462 0.00 0.00 0.00 2.71
2177 2371 5.694910 CGGATCATTAAATTGGTACGCTAGT 59.305 40.000 0.00 0.00 0.00 2.57
2388 2586 5.066505 CCTTTTACTGCATGGTGGAAGTATC 59.933 44.000 0.00 0.00 0.00 2.24
2400 2598 6.405176 GCTTCTTAATCTGCCTTTTACTGCAT 60.405 38.462 0.00 0.00 36.79 3.96
2598 2796 6.183360 TGGAGGCATCTTTTGAAGTTGATTTT 60.183 34.615 0.00 0.00 31.36 1.82
2652 2850 1.084370 GCCCGGAGAGAACATGAACG 61.084 60.000 0.73 0.00 0.00 3.95
2773 2979 9.032420 CAGATAATACGAGAAGAAAAGGTAACC 57.968 37.037 0.00 0.00 37.17 2.85
2916 3125 6.478344 GCTGAGGTATTACAGACAAATCTCAG 59.522 42.308 13.61 13.61 44.77 3.35
2922 3131 5.483685 AGTGCTGAGGTATTACAGACAAA 57.516 39.130 0.00 0.00 36.38 2.83
2938 3147 5.684626 GTGAAAACAGAATTCAGAAGTGCTG 59.315 40.000 8.44 0.00 46.31 4.41
2961 3170 5.269991 TCCAGTGCTTAGTCATAGGTAAGT 58.730 41.667 0.00 0.00 0.00 2.24
2975 3184 3.308473 GGAGGGAGTATTTTCCAGTGCTT 60.308 47.826 0.00 0.00 39.09 3.91
2985 3194 1.961133 TTGGGACGGAGGGAGTATTT 58.039 50.000 0.00 0.00 0.00 1.40
2986 3195 1.961133 TTTGGGACGGAGGGAGTATT 58.039 50.000 0.00 0.00 0.00 1.89
2987 3196 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
2988 3197 1.557832 CATTTTGGGACGGAGGGAGTA 59.442 52.381 0.00 0.00 0.00 2.59
2989 3198 0.328258 CATTTTGGGACGGAGGGAGT 59.672 55.000 0.00 0.00 0.00 3.85
2990 3199 0.328258 ACATTTTGGGACGGAGGGAG 59.672 55.000 0.00 0.00 0.00 4.30
2991 3200 1.659022 TACATTTTGGGACGGAGGGA 58.341 50.000 0.00 0.00 0.00 4.20
2992 3201 2.026636 TCTTACATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
2993 3202 3.007635 GTCTTACATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2994 3203 2.671396 CGTCTTACATTTTGGGACGGAG 59.329 50.000 0.00 0.00 43.69 4.63
2995 3204 2.690786 CGTCTTACATTTTGGGACGGA 58.309 47.619 0.00 0.00 43.69 4.69
2998 3207 6.068473 AGAAAACGTCTTACATTTTGGGAC 57.932 37.500 0.00 0.00 29.66 4.46
2999 3208 5.823570 TGAGAAAACGTCTTACATTTTGGGA 59.176 36.000 0.00 0.00 36.41 4.37
3000 3209 5.912955 GTGAGAAAACGTCTTACATTTTGGG 59.087 40.000 0.00 0.00 41.45 4.12
3001 3210 6.491394 TGTGAGAAAACGTCTTACATTTTGG 58.509 36.000 0.00 0.00 45.30 3.28
3008 3217 5.975939 ACACTAGTGTGAGAAAACGTCTTAC 59.024 40.000 27.41 0.00 46.55 2.34
3009 3218 6.140303 ACACTAGTGTGAGAAAACGTCTTA 57.860 37.500 27.41 0.00 46.55 2.10
3010 3219 5.007385 ACACTAGTGTGAGAAAACGTCTT 57.993 39.130 27.41 0.00 46.55 3.01
3011 3220 4.650754 ACACTAGTGTGAGAAAACGTCT 57.349 40.909 27.41 0.00 46.55 4.18
3012 3221 5.517904 ACTACACTAGTGTGAGAAAACGTC 58.482 41.667 33.77 0.00 46.55 4.34
3013 3222 5.511234 ACTACACTAGTGTGAGAAAACGT 57.489 39.130 33.77 16.01 46.55 3.99
3040 3249 6.173191 CGTCCCATAATGTAAGACGTTTTT 57.827 37.500 0.00 0.00 43.89 1.94
3041 3250 5.789710 CGTCCCATAATGTAAGACGTTTT 57.210 39.130 0.00 0.00 43.89 2.43
3046 3255 3.808174 GCCTTCGTCCCATAATGTAAGAC 59.192 47.826 0.00 0.00 0.00 3.01
3047 3256 3.452990 TGCCTTCGTCCCATAATGTAAGA 59.547 43.478 0.00 0.00 0.00 2.10
3048 3257 3.804036 TGCCTTCGTCCCATAATGTAAG 58.196 45.455 0.00 0.00 0.00 2.34
3049 3258 3.199071 ACTGCCTTCGTCCCATAATGTAA 59.801 43.478 0.00 0.00 0.00 2.41
3050 3259 2.769663 ACTGCCTTCGTCCCATAATGTA 59.230 45.455 0.00 0.00 0.00 2.29
3051 3260 1.559682 ACTGCCTTCGTCCCATAATGT 59.440 47.619 0.00 0.00 0.00 2.71
3052 3261 2.332063 ACTGCCTTCGTCCCATAATG 57.668 50.000 0.00 0.00 0.00 1.90
3053 3262 2.224305 GCTACTGCCTTCGTCCCATAAT 60.224 50.000 0.00 0.00 0.00 1.28
3054 3263 1.138266 GCTACTGCCTTCGTCCCATAA 59.862 52.381 0.00 0.00 0.00 1.90
3055 3264 0.750850 GCTACTGCCTTCGTCCCATA 59.249 55.000 0.00 0.00 0.00 2.74
3056 3265 1.264749 TGCTACTGCCTTCGTCCCAT 61.265 55.000 0.00 0.00 38.71 4.00
3057 3266 1.264749 ATGCTACTGCCTTCGTCCCA 61.265 55.000 0.00 0.00 38.71 4.37
3058 3267 0.107654 AATGCTACTGCCTTCGTCCC 60.108 55.000 0.00 0.00 38.71 4.46
3059 3268 1.739067 AAATGCTACTGCCTTCGTCC 58.261 50.000 0.00 0.00 38.71 4.79
3060 3269 3.063588 GGTTAAATGCTACTGCCTTCGTC 59.936 47.826 0.00 0.00 38.71 4.20
3061 3270 3.007635 GGTTAAATGCTACTGCCTTCGT 58.992 45.455 0.00 0.00 38.71 3.85
3062 3271 3.006940 TGGTTAAATGCTACTGCCTTCG 58.993 45.455 0.00 0.00 38.71 3.79
3063 3272 3.181496 GCTGGTTAAATGCTACTGCCTTC 60.181 47.826 0.00 0.00 38.71 3.46
3064 3273 2.755103 GCTGGTTAAATGCTACTGCCTT 59.245 45.455 0.00 0.00 38.71 4.35
3065 3274 2.290896 TGCTGGTTAAATGCTACTGCCT 60.291 45.455 0.00 0.00 38.71 4.75
3066 3275 2.091541 TGCTGGTTAAATGCTACTGCC 58.908 47.619 0.00 0.00 38.71 4.85
3067 3276 2.749621 ACTGCTGGTTAAATGCTACTGC 59.250 45.455 0.00 0.00 40.20 4.40
3070 3279 4.217550 TGGAAACTGCTGGTTAAATGCTAC 59.782 41.667 0.00 0.00 37.12 3.58
3084 3293 5.159209 CAGATGTTGATTCTTGGAAACTGC 58.841 41.667 0.00 0.00 0.00 4.40
3108 3317 2.744202 CCACCTGATGCAAGTTGAGTAC 59.256 50.000 7.16 0.00 0.00 2.73
3181 3390 5.648247 AGACTCCCCACTTGTACTAGTAAA 58.352 41.667 9.68 0.00 0.00 2.01
3239 3448 7.391148 TGAAAAATATGCAAGTCTTCTACCC 57.609 36.000 0.00 0.00 0.00 3.69
3437 3658 3.517901 AGTCGATTTGATGGACACCCTAA 59.482 43.478 5.98 0.00 40.03 2.69
3469 3690 8.943085 AGGATCTCAAATATATGAAAGTCCTGT 58.057 33.333 0.00 0.00 35.20 4.00
3470 3691 9.434420 GAGGATCTCAAATATATGAAAGTCCTG 57.566 37.037 9.33 0.00 35.95 3.86
3542 3768 5.748152 ACATGAAAAACAAATGTGAGAACCG 59.252 36.000 0.00 0.00 33.37 4.44
3588 3835 9.337396 TCAATGAACAAAACTACTGATACAGTT 57.663 29.630 9.63 0.00 42.59 3.16
3609 3856 9.853921 GACAAAACTTTTGCTTCTATTTCAATG 57.146 29.630 13.22 0.00 0.00 2.82
3610 3857 9.598517 TGACAAAACTTTTGCTTCTATTTCAAT 57.401 25.926 13.22 0.00 0.00 2.57
3612 3859 8.250332 ACTGACAAAACTTTTGCTTCTATTTCA 58.750 29.630 13.22 6.87 0.00 2.69
3622 3869 2.351418 GCCCAACTGACAAAACTTTTGC 59.649 45.455 13.22 7.64 0.00 3.68
3625 3872 2.466846 AGGCCCAACTGACAAAACTTT 58.533 42.857 0.00 0.00 0.00 2.66
3645 3892 5.652014 CCAAGTGCTTTACCAATATCTCCAA 59.348 40.000 0.00 0.00 0.00 3.53
3655 3902 3.181438 ACACATACCCAAGTGCTTTACCA 60.181 43.478 0.00 0.00 39.30 3.25
3656 3903 3.418047 ACACATACCCAAGTGCTTTACC 58.582 45.455 0.00 0.00 39.30 2.85
3657 3904 6.037172 CAGATACACATACCCAAGTGCTTTAC 59.963 42.308 0.00 0.00 39.30 2.01
3674 3922 2.412089 GGTGCGTCTTCAACAGATACAC 59.588 50.000 0.00 0.00 38.55 2.90
3677 3925 1.403647 CGGGTGCGTCTTCAACAGATA 60.404 52.381 0.00 0.00 32.60 1.98
3696 3944 2.223688 TGTTCTGTTTGTTGCCCAATCG 60.224 45.455 0.00 0.00 31.81 3.34
3704 3952 8.299570 AGGCTAATTATTCTGTTCTGTTTGTTG 58.700 33.333 0.00 0.00 0.00 3.33
3705 3953 8.299570 CAGGCTAATTATTCTGTTCTGTTTGTT 58.700 33.333 0.00 0.00 0.00 2.83
3713 3961 8.983724 GTAGATGACAGGCTAATTATTCTGTTC 58.016 37.037 16.80 12.97 40.13 3.18
3733 3981 6.903883 ACGGCTTAATGTTTACTGTAGATG 57.096 37.500 0.00 0.00 0.00 2.90
3735 3983 7.605449 ACTTACGGCTTAATGTTTACTGTAGA 58.395 34.615 0.00 0.00 0.00 2.59
3737 3985 8.522830 AGTACTTACGGCTTAATGTTTACTGTA 58.477 33.333 0.00 0.00 0.00 2.74
3738 3986 7.381323 AGTACTTACGGCTTAATGTTTACTGT 58.619 34.615 0.00 0.00 0.00 3.55
3769 4017 6.326375 GTTTAGTTGTTCAAACACATGGTGA 58.674 36.000 2.98 0.00 38.92 4.02
3796 4044 3.259374 GGTTCAGGATCAGTTCACAGAGA 59.741 47.826 0.00 0.00 0.00 3.10
3806 4054 6.540189 CACCTAGTAATTTGGTTCAGGATCAG 59.460 42.308 0.00 0.00 32.21 2.90
3807 4055 6.414732 CACCTAGTAATTTGGTTCAGGATCA 58.585 40.000 0.00 0.00 32.21 2.92
3818 4066 2.025321 ACTGCCCCCACCTAGTAATTTG 60.025 50.000 0.00 0.00 0.00 2.32
3852 4101 9.630098 ATGAATAAGGCTGCAAAAATATATTCG 57.370 29.630 0.50 0.00 33.40 3.34
3856 4105 9.531942 CAACATGAATAAGGCTGCAAAAATATA 57.468 29.630 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.