Multiple sequence alignment - TraesCS5A01G207400

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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 TraesCS5A01G207400 chr5A 100.000 7165 0 0 1 7165 419369877 419362713 0.000000e+00 13232.0
1 TraesCS5A01G207400 chr5A 95.035 141 7 0 6635 6775 419360289 419360429 9.360000e-54 222.0
2 TraesCS5A01G207400 chr5A 97.701 87 2 0 3369 3455 419366423 419366337 4.480000e-32 150.0
3 TraesCS5A01G207400 chr5A 97.701 87 2 0 3455 3541 419366509 419366423 4.480000e-32 150.0
4 TraesCS5A01G207400 chr5D 92.374 3501 141 42 11 3455 322792003 322788573 0.000000e+00 4870.0
5 TraesCS5A01G207400 chr5D 93.727 1865 81 14 4786 6615 322787282 322785419 0.000000e+00 2763.0
6 TraesCS5A01G207400 chr5D 93.912 1347 61 12 3455 4784 322788659 322787317 0.000000e+00 2013.0
7 TraesCS5A01G207400 chr5B 92.104 2001 83 30 4676 6640 374446429 374444468 0.000000e+00 2750.0
8 TraesCS5A01G207400 chr5B 96.154 1586 41 7 3125 4690 374449702 374448117 0.000000e+00 2573.0
9 TraesCS5A01G207400 chr5B 90.996 1877 62 33 100 1913 374453189 374451357 0.000000e+00 2431.0
10 TraesCS5A01G207400 chr5B 91.986 861 47 14 2271 3126 374451326 374450483 0.000000e+00 1188.0
11 TraesCS5A01G207400 chr5B 96.552 87 3 0 3369 3455 374449369 374449283 2.080000e-30 145.0
12 TraesCS5A01G207400 chr5B 96.552 87 3 0 3455 3541 374449455 374449369 2.080000e-30 145.0
13 TraesCS5A01G207400 chr5B 82.143 140 19 5 6635 6771 710872124 710871988 1.630000e-21 115.0
14 TraesCS5A01G207400 chr5B 97.368 38 1 0 1871 1908 374451360 374451323 1.670000e-06 65.8
15 TraesCS5A01G207400 chr4A 96.196 368 14 0 6770 7137 541324197 541324564 2.860000e-168 603.0
16 TraesCS5A01G207400 chr4A 92.908 141 10 0 6635 6775 541323993 541324133 9.420000e-49 206.0
17 TraesCS5A01G207400 chr4A 92.754 138 8 2 6631 6767 541337489 541337353 1.580000e-46 198.0
18 TraesCS5A01G207400 chr4A 100.000 36 0 0 7130 7165 541324575 541324610 4.640000e-07 67.6
19 TraesCS5A01G207400 chr7B 93.750 368 23 0 6770 7137 667433667 667434034 2.920000e-153 553.0
20 TraesCS5A01G207400 chr7B 93.478 368 24 0 6770 7137 541491504 541491137 1.360000e-151 547.0
21 TraesCS5A01G207400 chr7B 94.326 141 8 0 6635 6775 541491708 541491568 4.350000e-52 217.0
22 TraesCS5A01G207400 chr7B 94.253 87 5 0 6689 6775 667433517 667433603 4.510000e-27 134.0
23 TraesCS5A01G207400 chr7B 94.231 52 2 1 2149 2200 724730023 724729973 2.140000e-10 78.7
24 TraesCS5A01G207400 chr1B 93.478 368 24 0 6770 7137 491700956 491700589 1.360000e-151 547.0
25 TraesCS5A01G207400 chr1B 91.837 98 8 0 6678 6775 676245870 676245967 3.490000e-28 137.0
26 TraesCS5A01G207400 chr1B 83.673 147 20 4 6630 6775 676248610 676248467 1.250000e-27 135.0
27 TraesCS5A01G207400 chr2B 93.103 58 3 1 2136 2193 323085365 323085421 4.610000e-12 84.2
28 TraesCS5A01G207400 chr2A 93.103 58 3 1 2136 2193 285622293 285622349 4.610000e-12 84.2
29 TraesCS5A01G207400 chrUn 92.727 55 3 1 2146 2200 75920475 75920528 2.140000e-10 78.7
30 TraesCS5A01G207400 chr6B 94.231 52 2 1 2149 2200 9990278 9990228 2.140000e-10 78.7
31 TraesCS5A01G207400 chr6A 94.231 52 2 1 2149 2200 432824797 432824747 2.140000e-10 78.7
32 TraesCS5A01G207400 chr1A 92.727 55 3 1 2146 2200 208881706 208881759 2.140000e-10 78.7
33 TraesCS5A01G207400 chr4D 87.500 64 6 2 2148 2211 87721755 87721816 9.970000e-09 73.1


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 TraesCS5A01G207400 chr5A 419362713 419369877 7164 True 4510.666667 13232 98.467333 1 7165 3 chr5A.!!$R1 7164
1 TraesCS5A01G207400 chr5D 322785419 322792003 6584 True 3215.333333 4870 93.337667 11 6615 3 chr5D.!!$R1 6604
2 TraesCS5A01G207400 chr5B 374444468 374453189 8721 True 1328.257143 2750 94.530286 100 6640 7 chr5B.!!$R2 6540
3 TraesCS5A01G207400 chr4A 541323993 541324610 617 False 292.200000 603 96.368000 6635 7165 3 chr4A.!!$F1 530
4 TraesCS5A01G207400 chr7B 541491137 541491708 571 True 382.000000 547 93.902000 6635 7137 2 chr7B.!!$R2 502
5 TraesCS5A01G207400 chr7B 667433517 667434034 517 False 343.500000 553 94.001500 6689 7137 2 chr7B.!!$F1 448

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
207 210 0.038618 GGAACGGTGGCAATCAAACC 60.039 55.0 0.00 0.0 0.00 3.27 F
463 484 0.505655 CGAACCTCCGTCGAAACAAC 59.494 55.0 0.00 0.0 0.00 3.32 F
767 808 0.523335 GCTGCCATTAAAACCGCGAG 60.523 55.0 8.23 0.0 0.00 5.03 F
2385 2476 0.035739 TTTAACCCCTCACGTGCTCC 59.964 55.0 11.67 0.0 0.00 4.70 F
2906 3000 0.532115 CTGCCACCCTATTTTGCCAC 59.468 55.0 0.00 0.0 0.00 5.01 F
3604 4488 0.667184 GCAAACAAACATGGCCCTCG 60.667 55.0 0.00 0.0 0.00 4.63 F
4135 5023 0.875059 GGCTTAACCACTGCACACTC 59.125 55.0 0.00 0.0 38.86 3.51 F
5459 8112 0.668706 CACTGGACAAGGAGCGAGTG 60.669 60.0 0.00 0.0 35.18 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1833 0.249120 ATCGGATGCGTTTGAGGTCA 59.751 50.000 6.49 0.00 0.00 4.02 R
1952 2042 0.393402 TGCGCTTCATCCTTCTGCAT 60.393 50.000 9.73 0.00 0.00 3.96 R
2513 2604 0.548926 TGGACTTGCCCCCACATAGA 60.549 55.000 0.00 0.00 34.97 1.98 R
3837 4724 1.073763 TCAACATAGCTGGCCACAAGT 59.926 47.619 0.00 0.00 0.00 3.16 R
4182 5070 1.273838 ACAGAAGGAGATGGCCCACTA 60.274 52.381 0.00 0.00 0.00 2.74 R
5162 7815 0.802222 CTCACGGCTGTCATACACCG 60.802 60.000 14.96 14.96 43.40 4.94 R
5696 8349 0.323816 AGAGCTCATCGGACCTGTCA 60.324 55.000 17.77 0.00 0.00 3.58 R
6459 9152 1.202746 GGGAATTGGTTTTGGCAAGCA 60.203 47.619 0.00 0.00 0.00 3.91 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
32 33 2.223572 GCGTTGGAGATGCCCTTAAATG 60.224 50.000 0.00 0.00 34.03 2.32
33 34 3.278574 CGTTGGAGATGCCCTTAAATGA 58.721 45.455 0.00 0.00 34.97 2.57
207 210 0.038618 GGAACGGTGGCAATCAAACC 60.039 55.000 0.00 0.00 0.00 3.27
404 420 6.072673 GGAAAAATTACACTCCTCACGACATT 60.073 38.462 0.00 0.00 0.00 2.71
406 422 6.877611 AAATTACACTCCTCACGACATTTT 57.122 33.333 0.00 0.00 0.00 1.82
411 428 2.800544 ACTCCTCACGACATTTTGAACG 59.199 45.455 0.00 0.00 0.00 3.95
440 457 1.901464 CCCTTTTCACCCACCACCG 60.901 63.158 0.00 0.00 0.00 4.94
450 471 3.622826 CACCACCGACCCGAACCT 61.623 66.667 0.00 0.00 0.00 3.50
462 483 0.598158 CCGAACCTCCGTCGAAACAA 60.598 55.000 0.00 0.00 0.00 2.83
463 484 0.505655 CGAACCTCCGTCGAAACAAC 59.494 55.000 0.00 0.00 0.00 3.32
464 485 1.574134 GAACCTCCGTCGAAACAACA 58.426 50.000 0.00 0.00 0.00 3.33
465 486 1.259770 GAACCTCCGTCGAAACAACAC 59.740 52.381 0.00 0.00 0.00 3.32
466 487 0.872881 ACCTCCGTCGAAACAACACG 60.873 55.000 0.00 0.00 0.00 4.49
467 488 1.200839 CTCCGTCGAAACAACACGC 59.799 57.895 0.00 0.00 32.03 5.34
468 489 1.213094 CTCCGTCGAAACAACACGCT 61.213 55.000 0.00 0.00 32.03 5.07
469 490 1.200839 CCGTCGAAACAACACGCTC 59.799 57.895 0.00 0.00 32.03 5.03
470 491 1.155087 CGTCGAAACAACACGCTCG 60.155 57.895 0.00 0.00 0.00 5.03
510 541 4.711399 TCTACTACTACTATTGCCGCTGA 58.289 43.478 0.00 0.00 0.00 4.26
535 566 3.350219 ACTCACTCTCACTCTCTCTCC 57.650 52.381 0.00 0.00 0.00 3.71
684 725 0.745845 ATCCAGTCGAGCCACAATGC 60.746 55.000 0.00 0.00 0.00 3.56
685 726 2.743752 CCAGTCGAGCCACAATGCG 61.744 63.158 0.00 0.00 36.02 4.73
694 735 3.803082 CACAATGCGGCGTGGAGG 61.803 66.667 9.37 0.00 0.00 4.30
767 808 0.523335 GCTGCCATTAAAACCGCGAG 60.523 55.000 8.23 0.00 0.00 5.03
959 1001 3.876589 TTTCCGGGTCTGTCGCTGC 62.877 63.158 0.00 0.00 0.00 5.25
1204 1259 2.011046 GCATCTCTTGCCACTGGAGTC 61.011 57.143 0.00 0.00 46.15 3.36
1218 1273 3.152341 CTGGAGTCCTGCTTGAAATGTT 58.848 45.455 11.33 0.00 0.00 2.71
1219 1274 2.886523 TGGAGTCCTGCTTGAAATGTTG 59.113 45.455 11.33 0.00 0.00 3.33
1256 1311 4.600692 TTCTCTTGTTCTGTTCATCCGA 57.399 40.909 0.00 0.00 0.00 4.55
1257 1312 4.600692 TCTCTTGTTCTGTTCATCCGAA 57.399 40.909 0.00 0.00 0.00 4.30
1842 1930 4.456911 CAGTGCATTACTCTGATTGTTGGT 59.543 41.667 0.00 0.00 41.48 3.67
1852 1940 6.981722 ACTCTGATTGTTGGTTGGAAAATAC 58.018 36.000 0.00 0.00 0.00 1.89
1901 1991 7.063898 TCAGAAAATGTGATCGAGATTTGAGAC 59.936 37.037 0.00 0.00 0.00 3.36
1913 2003 2.496899 TTTGAGACCCTCCTGCATTC 57.503 50.000 0.00 0.00 0.00 2.67
1914 2004 1.361204 TTGAGACCCTCCTGCATTCA 58.639 50.000 0.00 0.00 0.00 2.57
1975 2065 1.741706 CAGAAGGATGAAGCGCAATGT 59.258 47.619 11.47 0.00 0.00 2.71
1980 2070 1.621107 GATGAAGCGCAATGTGTTGG 58.379 50.000 11.47 0.00 35.83 3.77
1990 2080 3.243035 CGCAATGTGTTGGAAAACTCTCA 60.243 43.478 0.00 0.00 35.83 3.27
2008 2098 5.237344 ACTCTCAACGAATTGAAGTTCCAAG 59.763 40.000 0.00 0.00 44.28 3.61
2261 2351 4.150897 TGTGCTACACTTTTTCCTCACT 57.849 40.909 0.00 0.00 35.11 3.41
2267 2357 6.106673 GCTACACTTTTTCCTCACTGCTATA 58.893 40.000 0.00 0.00 0.00 1.31
2385 2476 0.035739 TTTAACCCCTCACGTGCTCC 59.964 55.000 11.67 0.00 0.00 4.70
2456 2547 3.564225 CGGTAGATTTAGAATTGCCCACC 59.436 47.826 0.00 0.00 0.00 4.61
2504 2595 7.329962 TGCATCAACTTGCTATGAATTTTGAAG 59.670 33.333 0.00 0.00 43.18 3.02
2513 2604 8.177119 TGCTATGAATTTTGAAGTTACCAGTT 57.823 30.769 0.00 0.00 0.00 3.16
2681 2772 6.256819 TCCTATCTGGGTATCCAATACAGAG 58.743 44.000 0.00 0.00 43.51 3.35
2694 2785 7.391148 TCCAATACAGAGGCTTAATTGAAAC 57.609 36.000 11.33 0.00 30.77 2.78
2695 2786 7.175104 TCCAATACAGAGGCTTAATTGAAACT 58.825 34.615 11.33 0.00 30.77 2.66
2696 2787 7.669722 TCCAATACAGAGGCTTAATTGAAACTT 59.330 33.333 11.33 0.00 30.77 2.66
2697 2788 8.306761 CCAATACAGAGGCTTAATTGAAACTTT 58.693 33.333 11.33 0.00 30.77 2.66
2698 2789 9.132521 CAATACAGAGGCTTAATTGAAACTTTG 57.867 33.333 0.00 0.00 30.77 2.77
2699 2790 6.959639 ACAGAGGCTTAATTGAAACTTTGA 57.040 33.333 0.00 0.00 0.00 2.69
2700 2791 7.346751 ACAGAGGCTTAATTGAAACTTTGAA 57.653 32.000 0.00 0.00 0.00 2.69
2701 2792 7.781056 ACAGAGGCTTAATTGAAACTTTGAAA 58.219 30.769 0.00 0.00 0.00 2.69
2704 2795 8.864087 AGAGGCTTAATTGAAACTTTGAAAGAT 58.136 29.630 12.53 0.00 0.00 2.40
2742 2833 2.968574 TCTGCTCCTCTCACTTCTTTGT 59.031 45.455 0.00 0.00 0.00 2.83
2906 3000 0.532115 CTGCCACCCTATTTTGCCAC 59.468 55.000 0.00 0.00 0.00 5.01
2909 3003 1.474330 CCACCCTATTTTGCCACTCC 58.526 55.000 0.00 0.00 0.00 3.85
2986 3080 4.141914 GGACTCTAATGAGAACAATCGGGT 60.142 45.833 0.00 0.00 42.73 5.28
2987 3081 5.420409 GACTCTAATGAGAACAATCGGGTT 58.580 41.667 0.00 0.00 42.73 4.11
2988 3082 6.406624 GGACTCTAATGAGAACAATCGGGTTA 60.407 42.308 0.00 0.00 42.73 2.85
2990 3084 6.817140 ACTCTAATGAGAACAATCGGGTTAAC 59.183 38.462 0.00 0.00 42.73 2.01
2992 3086 7.039882 TCTAATGAGAACAATCGGGTTAACTC 58.960 38.462 5.42 0.00 0.00 3.01
2998 3092 7.881232 TGAGAACAATCGGGTTAACTCTAAATT 59.119 33.333 3.52 0.00 0.00 1.82
2999 3093 8.265165 AGAACAATCGGGTTAACTCTAAATTC 57.735 34.615 3.52 1.72 0.00 2.17
3000 3094 7.881232 AGAACAATCGGGTTAACTCTAAATTCA 59.119 33.333 3.52 0.00 0.00 2.57
3040 3137 3.520317 TCAACTCTAAATTTAGCCCCCGA 59.480 43.478 18.68 9.37 0.00 5.14
3041 3138 4.165372 TCAACTCTAAATTTAGCCCCCGAT 59.835 41.667 18.68 0.41 0.00 4.18
3054 3151 2.046023 CCGATGTGCTCCAGCCAA 60.046 61.111 0.00 0.00 41.18 4.52
3076 3173 6.402983 CCAAGTTGAATTCTAGATGTGTCAGC 60.403 42.308 3.87 0.00 0.00 4.26
3151 4031 2.099141 ACGGGATCATGTCAGTTGTG 57.901 50.000 0.00 0.00 0.00 3.33
3154 4034 1.470098 GGGATCATGTCAGTTGTGCAC 59.530 52.381 10.75 10.75 0.00 4.57
3159 4039 1.194547 CATGTCAGTTGTGCACGGTAC 59.805 52.381 13.13 10.21 0.00 3.34
3184 4064 2.428530 TGTAGCAGCTCCAGTGTATCAG 59.571 50.000 0.00 0.00 0.00 2.90
3262 4142 9.102757 CACATTTGTACTTTATGCTATCAGAGT 57.897 33.333 0.00 0.00 0.00 3.24
3289 4172 1.108132 TTGCTGTGCTGGCAATGACA 61.108 50.000 0.00 0.00 43.50 3.58
3492 4376 6.409704 TGGAAAGATGAGTGTTGGATTAGAG 58.590 40.000 0.00 0.00 0.00 2.43
3495 4379 7.279758 GGAAAGATGAGTGTTGGATTAGAGAAG 59.720 40.741 0.00 0.00 0.00 2.85
3497 4381 7.251321 AGATGAGTGTTGGATTAGAGAAGTT 57.749 36.000 0.00 0.00 0.00 2.66
3564 4448 7.839705 TCTTACTGATATGTAGTTGGGTCTCTT 59.160 37.037 0.00 0.00 0.00 2.85
3587 4471 1.483827 CACTGGCTTATCAGGAGAGCA 59.516 52.381 8.93 0.00 38.98 4.26
3604 4488 0.667184 GCAAACAAACATGGCCCTCG 60.667 55.000 0.00 0.00 0.00 4.63
3607 4491 0.958822 AACAAACATGGCCCTCGAAC 59.041 50.000 0.00 0.00 0.00 3.95
3709 4595 6.712998 TGCAAACTTAGTCTTGGCACTATAAA 59.287 34.615 0.00 0.00 0.00 1.40
3837 4724 5.514500 AATAAGGTTCTTGTTGGGAGCTA 57.486 39.130 0.00 0.00 0.00 3.32
3862 4749 3.953201 GCCAGCTATGTTGATTGGC 57.047 52.632 0.00 0.00 46.39 4.52
3919 4806 3.788227 TGGTTGAAACAGTAGCTGGAT 57.212 42.857 0.00 0.00 35.51 3.41
4051 4939 1.359848 GTTGTCACGGGATGCACTAG 58.640 55.000 0.00 0.00 0.00 2.57
4135 5023 0.875059 GGCTTAACCACTGCACACTC 59.125 55.000 0.00 0.00 38.86 3.51
4182 5070 5.321102 TGGGCAACACAGTAAATTGATAGT 58.679 37.500 0.00 0.00 39.74 2.12
4866 7509 7.361201 GCATTCATAACTCTTCACAGCTTTGTA 60.361 37.037 0.00 0.00 0.00 2.41
4871 7514 8.598924 CATAACTCTTCACAGCTTTGTATACAG 58.401 37.037 5.56 0.00 0.00 2.74
4904 7548 8.262227 AGTAGAGTACTATACAGCTATAGCCAG 58.738 40.741 25.30 16.07 38.48 4.85
4909 7553 1.399714 TACAGCTATAGCCAGCGTGT 58.600 50.000 21.17 19.05 46.52 4.49
5074 7719 6.580041 GTGAATTCATAGACAAACAGCAACAG 59.420 38.462 12.12 0.00 0.00 3.16
5142 7795 3.397849 TCCATCTGTATCTCATGCTGC 57.602 47.619 0.00 0.00 0.00 5.25
5459 8112 0.668706 CACTGGACAAGGAGCGAGTG 60.669 60.000 0.00 0.00 35.18 3.51
5696 8349 3.194542 CGAGTTCATCTCCAGAAGAGGTT 59.805 47.826 0.00 0.00 43.44 3.50
5707 8360 0.966920 GAAGAGGTTGACAGGTCCGA 59.033 55.000 0.00 0.00 0.00 4.55
5735 8388 1.965930 GGTGTCCATCAGCAACGCA 60.966 57.895 0.00 0.00 43.22 5.24
5842 8495 1.289109 CGCCGTGTTCGATTCAGGTT 61.289 55.000 0.00 0.00 39.71 3.50
5849 8502 4.527564 GTGTTCGATTCAGGTTTGTCTTG 58.472 43.478 0.00 0.00 0.00 3.02
5859 8512 1.680338 GTTTGTCTTGTGTCCTGCCT 58.320 50.000 0.00 0.00 0.00 4.75
5891 8545 7.669304 TGATTTCTTTGTGAATGAGATTACCCA 59.331 33.333 0.00 0.00 34.24 4.51
5897 8551 4.019411 TGTGAATGAGATTACCCAAGAGCA 60.019 41.667 0.00 0.00 0.00 4.26
5914 8568 1.301401 CAGTTTTCGAGGCGGTCCA 60.301 57.895 0.00 0.00 33.74 4.02
6047 8714 6.435277 AGGGTATGAATTATGATCATGGCAAC 59.565 38.462 18.72 7.03 38.01 4.17
6197 8867 7.446625 AGAAGAAGCACAGATGAAAACAATACT 59.553 33.333 0.00 0.00 0.00 2.12
6201 8871 6.233434 AGCACAGATGAAAACAATACTGAGA 58.767 36.000 0.00 0.00 0.00 3.27
6268 8938 5.371115 TTGCAGTTTGAGCTAACATTACC 57.629 39.130 2.35 0.00 0.00 2.85
6316 9004 7.093771 TGAGAAACTGAACTATACTGATCTGCA 60.094 37.037 0.00 0.00 0.00 4.41
6350 9042 0.697658 TGGCCATCCACATGTTCTCA 59.302 50.000 0.00 0.00 37.47 3.27
6395 9088 1.063469 CGCAGGAACTTCGTTTGTGTT 59.937 47.619 0.00 0.00 40.82 3.32
6428 9121 0.796312 GGGTGCGTACTGTGTCATTG 59.204 55.000 3.01 0.00 0.00 2.82
6459 9152 6.773638 AGATACCATCTGTTCTGAAACTGTT 58.226 36.000 0.00 0.00 38.44 3.16
6575 9268 2.439837 CCTCAAGCAGGCCCAAAAA 58.560 52.632 0.00 0.00 34.56 1.94
6585 9278 3.202097 CAGGCCCAAAAATGTTCGTTTT 58.798 40.909 0.00 0.00 32.94 2.43
6586 9279 4.372656 CAGGCCCAAAAATGTTCGTTTTA 58.627 39.130 0.00 0.00 31.43 1.52
6617 9311 2.373540 TTCGTCTACAATCCAACCGG 57.626 50.000 0.00 0.00 0.00 5.28
6664 9358 9.816787 AAAATTCACTATAGGTCCCAAAACTTA 57.183 29.630 4.43 0.00 0.00 2.24
6671 9365 1.612676 GTCCCAAAACTTAAGCCGGT 58.387 50.000 1.90 0.00 0.00 5.28
7005 9768 4.419939 AGTGCAGCGCATCGACGA 62.420 61.111 11.47 0.00 41.91 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.844946 TCTCCAACGCTCATGTTCAAA 58.155 42.857 0.00 0.00 0.00 2.69
1 2 2.542020 TCTCCAACGCTCATGTTCAA 57.458 45.000 0.00 0.00 0.00 2.69
2 3 2.349590 CATCTCCAACGCTCATGTTCA 58.650 47.619 0.00 0.00 0.00 3.18
3 4 1.063174 GCATCTCCAACGCTCATGTTC 59.937 52.381 0.00 0.00 0.00 3.18
4 5 1.089920 GCATCTCCAACGCTCATGTT 58.910 50.000 0.00 0.00 0.00 2.71
5 6 0.745845 GGCATCTCCAACGCTCATGT 60.746 55.000 0.00 0.00 34.01 3.21
6 7 1.442526 GGGCATCTCCAACGCTCATG 61.443 60.000 0.00 0.00 36.21 3.07
7 8 1.153086 GGGCATCTCCAACGCTCAT 60.153 57.895 0.00 0.00 36.21 2.90
8 9 1.841302 AAGGGCATCTCCAACGCTCA 61.841 55.000 0.00 0.00 36.21 4.26
9 10 0.178068 TAAGGGCATCTCCAACGCTC 59.822 55.000 0.00 0.00 36.21 5.03
46 47 6.379703 TCAAGAAAAGACATGTTCCCTCAAAA 59.620 34.615 0.00 0.00 0.00 2.44
47 48 5.890985 TCAAGAAAAGACATGTTCCCTCAAA 59.109 36.000 0.00 0.00 0.00 2.69
48 49 5.299279 GTCAAGAAAAGACATGTTCCCTCAA 59.701 40.000 0.00 0.00 36.06 3.02
50 51 4.821805 TGTCAAGAAAAGACATGTTCCCTC 59.178 41.667 0.00 0.00 40.80 4.30
51 52 4.792068 TGTCAAGAAAAGACATGTTCCCT 58.208 39.130 0.00 0.00 40.80 4.20
125 126 5.116882 GTGGATTCTACGGATAAGCAAACT 58.883 41.667 0.00 0.00 0.00 2.66
189 192 0.671251 TGGTTTGATTGCCACCGTTC 59.329 50.000 0.00 0.00 32.71 3.95
207 210 0.179129 GCGCCTGGTTTTGGATCATG 60.179 55.000 0.00 0.00 0.00 3.07
326 335 7.938490 ACTCCCGGTGTTAATTTTAACTTAAGA 59.062 33.333 10.09 4.87 42.61 2.10
344 353 1.489230 GGTTTCATATGGACTCCCGGT 59.511 52.381 0.00 0.00 34.29 5.28
404 420 0.658897 GGTGAGGCGAAACGTTCAAA 59.341 50.000 0.00 0.00 0.00 2.69
406 422 1.595929 GGGTGAGGCGAAACGTTCA 60.596 57.895 0.00 0.00 0.00 3.18
411 428 1.001706 GTGAAAAGGGTGAGGCGAAAC 60.002 52.381 0.00 0.00 0.00 2.78
440 457 2.146073 TTTCGACGGAGGTTCGGGTC 62.146 60.000 0.00 0.00 0.00 4.46
450 471 1.210545 GAGCGTGTTGTTTCGACGGA 61.211 55.000 0.00 0.00 33.68 4.69
462 483 1.697772 TTGTTTGTTCGCGAGCGTGT 61.698 50.000 18.23 0.00 40.74 4.49
463 484 0.587737 TTTGTTTGTTCGCGAGCGTG 60.588 50.000 18.23 4.85 40.74 5.34
464 485 0.097325 TTTTGTTTGTTCGCGAGCGT 59.903 45.000 18.23 0.00 40.74 5.07
465 486 1.184349 TTTTTGTTTGTTCGCGAGCG 58.816 45.000 18.23 11.64 41.35 5.03
489 520 5.630661 ATCAGCGGCAATAGTAGTAGTAG 57.369 43.478 1.45 0.00 0.00 2.57
490 521 6.236409 AGTATCAGCGGCAATAGTAGTAGTA 58.764 40.000 1.45 0.00 0.00 1.82
491 522 5.071370 AGTATCAGCGGCAATAGTAGTAGT 58.929 41.667 1.45 0.00 0.00 2.73
492 523 5.630661 AGTATCAGCGGCAATAGTAGTAG 57.369 43.478 1.45 0.00 0.00 2.57
493 524 6.236409 AGTAGTATCAGCGGCAATAGTAGTA 58.764 40.000 1.45 0.00 0.00 1.82
494 525 5.071370 AGTAGTATCAGCGGCAATAGTAGT 58.929 41.667 1.45 7.17 0.00 2.73
510 541 6.183360 GGAGAGAGAGTGAGAGTGAGTAGTAT 60.183 46.154 0.00 0.00 0.00 2.12
535 566 1.327690 ATTGCCATTGCCAGCAGAGG 61.328 55.000 7.77 7.77 40.73 3.69
696 737 1.109323 AATTTATGGAGCGGCTGCCC 61.109 55.000 19.11 15.72 44.31 5.36
697 738 1.604604 TAATTTATGGAGCGGCTGCC 58.395 50.000 19.11 9.11 44.31 4.85
698 739 3.708563 TTTAATTTATGGAGCGGCTGC 57.291 42.857 15.13 15.13 43.24 5.25
699 740 4.321230 GGGATTTAATTTATGGAGCGGCTG 60.321 45.833 7.50 0.00 0.00 4.85
700 741 3.826729 GGGATTTAATTTATGGAGCGGCT 59.173 43.478 0.00 0.00 0.00 5.52
747 788 1.867373 CGCGGTTTTAATGGCAGCG 60.867 57.895 0.00 0.00 39.88 5.18
767 808 6.204882 GGCATTAATGGCCGGATTAGTATATC 59.795 42.308 27.12 0.71 46.49 1.63
936 978 1.446272 GACAGACCCGGAAAGCGAG 60.446 63.158 0.73 0.00 0.00 5.03
1231 1286 4.750098 GGATGAACAGAACAAGAGAAACGA 59.250 41.667 0.00 0.00 0.00 3.85
1232 1287 4.376413 CGGATGAACAGAACAAGAGAAACG 60.376 45.833 0.00 0.00 0.00 3.60
1269 1337 3.506810 CTTCCAGACAGATTCAGACGAC 58.493 50.000 0.00 0.00 0.00 4.34
1307 1375 2.288825 ACGCTCGAGACAAGATTCCAAA 60.289 45.455 18.75 0.00 0.00 3.28
1751 1833 0.249120 ATCGGATGCGTTTGAGGTCA 59.751 50.000 6.49 0.00 0.00 4.02
1842 1930 5.836358 ACTAAGCCAACAAGGTATTTTCCAA 59.164 36.000 0.00 0.00 40.61 3.53
1852 1940 7.206687 TGAAAATGTAAACTAAGCCAACAAGG 58.793 34.615 0.00 0.00 41.84 3.61
1901 1991 2.392662 TCTACTCTGAATGCAGGAGGG 58.607 52.381 0.00 1.79 42.53 4.30
1952 2042 0.393402 TGCGCTTCATCCTTCTGCAT 60.393 50.000 9.73 0.00 0.00 3.96
1959 2049 1.200716 CAACACATTGCGCTTCATCCT 59.799 47.619 9.73 0.00 0.00 3.24
1975 2065 5.355630 TCAATTCGTTGAGAGTTTTCCAACA 59.644 36.000 0.00 0.00 39.90 3.33
1980 2070 6.633234 GGAACTTCAATTCGTTGAGAGTTTTC 59.367 38.462 14.10 9.60 35.04 2.29
1990 2080 8.095169 AGATACTACTTGGAACTTCAATTCGTT 58.905 33.333 0.00 0.00 0.00 3.85
2032 2122 3.191581 TGTAGTAACTCTGAGCACTGAGC 59.808 47.826 16.03 10.93 42.97 4.26
2099 2189 5.073280 AGAGGTTAACCAAGAAAGCCTTAGT 59.927 40.000 26.26 0.00 38.89 2.24
2304 2394 4.566004 GTTTACAGCTCATCCAGTGTGTA 58.434 43.478 0.00 0.00 0.00 2.90
2385 2476 1.464734 TCTAGACTTCGACCTGGCTG 58.535 55.000 0.00 0.00 0.00 4.85
2456 2547 5.782047 CACTGGAGCTTCTATGATTCTAGG 58.218 45.833 0.00 0.00 0.00 3.02
2504 2595 2.682858 GCCCCCACATAGAACTGGTAAC 60.683 54.545 0.00 0.00 0.00 2.50
2513 2604 0.548926 TGGACTTGCCCCCACATAGA 60.549 55.000 0.00 0.00 34.97 1.98
2574 2665 2.110967 GCATCATCGCCAGCACACT 61.111 57.895 0.00 0.00 0.00 3.55
2575 2666 1.651240 AAGCATCATCGCCAGCACAC 61.651 55.000 0.00 0.00 0.00 3.82
2681 2772 8.593492 ACATCTTTCAAAGTTTCAATTAAGCC 57.407 30.769 0.00 0.00 0.00 4.35
2694 2785 8.477984 TTTTTCTGTTCCAACATCTTTCAAAG 57.522 30.769 0.00 0.00 38.41 2.77
2695 2786 9.447157 AATTTTTCTGTTCCAACATCTTTCAAA 57.553 25.926 0.00 0.00 38.41 2.69
2696 2787 9.097257 GAATTTTTCTGTTCCAACATCTTTCAA 57.903 29.630 0.00 0.00 38.41 2.69
2697 2788 8.477256 AGAATTTTTCTGTTCCAACATCTTTCA 58.523 29.630 0.00 0.00 38.91 2.69
2698 2789 8.877808 AGAATTTTTCTGTTCCAACATCTTTC 57.122 30.769 0.00 0.00 38.91 2.62
2733 2824 3.493176 GCCAAGCAAATGGACAAAGAAGT 60.493 43.478 7.33 0.00 43.54 3.01
2742 2833 1.186917 CCACCAGCCAAGCAAATGGA 61.187 55.000 7.33 0.00 43.54 3.41
2874 2968 9.784376 AAATAGGGTGGCAGATATATACTAGAA 57.216 33.333 0.00 0.00 0.00 2.10
2879 2973 6.318900 GGCAAAATAGGGTGGCAGATATATAC 59.681 42.308 0.00 0.00 39.93 1.47
2880 2974 6.012069 TGGCAAAATAGGGTGGCAGATATATA 60.012 38.462 0.00 0.00 44.48 0.86
2883 2977 3.117169 TGGCAAAATAGGGTGGCAGATAT 60.117 43.478 0.00 0.00 44.48 1.63
2953 3047 5.026121 TCTCATTAGAGTCCATCCAGTTGT 58.974 41.667 0.00 0.00 42.66 3.32
2964 3058 5.012328 ACCCGATTGTTCTCATTAGAGTC 57.988 43.478 0.00 0.00 42.66 3.36
2965 3059 5.422214 AACCCGATTGTTCTCATTAGAGT 57.578 39.130 0.00 0.00 42.66 3.24
2998 3092 8.918202 AGTTGACAATTAGTACCATTTTCTGA 57.082 30.769 0.00 0.00 0.00 3.27
2999 3093 9.003658 AGAGTTGACAATTAGTACCATTTTCTG 57.996 33.333 0.00 0.00 0.00 3.02
3027 3124 0.258774 AGCACATCGGGGGCTAAATT 59.741 50.000 2.79 0.00 35.82 1.82
3040 3137 0.111061 TCAACTTGGCTGGAGCACAT 59.889 50.000 0.20 0.00 44.36 3.21
3041 3138 0.106769 TTCAACTTGGCTGGAGCACA 60.107 50.000 0.20 0.00 44.36 4.57
3054 3151 5.798132 TGCTGACACATCTAGAATTCAACT 58.202 37.500 8.44 0.00 0.00 3.16
3076 3173 7.725818 ATCTGACAACTCTATAACATGCATG 57.274 36.000 25.09 25.09 0.00 4.06
3151 4031 0.736325 CTGCTACACCTGTACCGTGC 60.736 60.000 9.47 0.00 34.45 5.34
3154 4034 0.179134 GAGCTGCTACACCTGTACCG 60.179 60.000 0.15 0.00 0.00 4.02
3159 4039 0.390866 CACTGGAGCTGCTACACCTG 60.391 60.000 11.31 10.53 0.00 4.00
3184 4064 6.036470 GGTAAGTTCAAAATTCATAGCCAGC 58.964 40.000 0.00 0.00 0.00 4.85
3262 4142 1.473677 GCCAGCACAGCAAATGTATGA 59.526 47.619 0.00 0.00 41.41 2.15
3492 4376 6.530019 AAGAAGAGAGAGGATCAGAACTTC 57.470 41.667 0.00 0.00 37.82 3.01
3495 4379 5.418676 CCAAAGAAGAGAGAGGATCAGAAC 58.581 45.833 0.00 0.00 37.82 3.01
3497 4381 3.450457 GCCAAAGAAGAGAGAGGATCAGA 59.550 47.826 0.00 0.00 37.82 3.27
3564 4448 1.908619 TCTCCTGATAAGCCAGTGCAA 59.091 47.619 0.00 0.00 41.13 4.08
3587 4471 1.339929 GTTCGAGGGCCATGTTTGTTT 59.660 47.619 6.18 0.00 0.00 2.83
3604 4488 3.981211 TGAGCAAAAATGCTTCCAGTTC 58.019 40.909 4.64 0.00 46.36 3.01
3607 4491 3.678072 CACATGAGCAAAAATGCTTCCAG 59.322 43.478 0.00 0.00 46.36 3.86
3829 4716 1.841302 CTGGCCACAAGTAGCTCCCA 61.841 60.000 0.00 0.00 0.00 4.37
3837 4724 1.073763 TCAACATAGCTGGCCACAAGT 59.926 47.619 0.00 0.00 0.00 3.16
3862 4749 4.141990 TCCCTAATGATACTAGTGGGGG 57.858 50.000 5.39 6.47 37.10 5.40
3910 4797 4.130118 CACCCATGTTAAGATCCAGCTAC 58.870 47.826 0.00 0.00 0.00 3.58
3919 4806 1.423541 ACACCTGCACCCATGTTAAGA 59.576 47.619 0.00 0.00 0.00 2.10
4069 4957 4.753610 AGCACATTAATCGACTGATCCATG 59.246 41.667 0.00 0.00 32.24 3.66
4135 5023 4.154737 TGCTCCATTCAGAAAGAAATCACG 59.845 41.667 0.00 0.00 40.22 4.35
4182 5070 1.273838 ACAGAAGGAGATGGCCCACTA 60.274 52.381 0.00 0.00 0.00 2.74
4556 5458 4.615588 TTTATTTTGAAAGGGTGGCAGG 57.384 40.909 0.00 0.00 0.00 4.85
4594 5501 4.077108 GCCTCATAAATCATGATGCCTGA 58.923 43.478 9.46 10.86 44.86 3.86
4625 5532 3.708403 TGCTATTCCTATGCATCAGGG 57.292 47.619 0.19 4.61 33.66 4.45
4904 7548 4.599047 AGTAGTGAATCGATAAGACACGC 58.401 43.478 0.00 6.45 36.71 5.34
5074 7719 3.560896 ACAAGCATGCATTTTGTTTCCAC 59.439 39.130 21.98 0.00 31.38 4.02
5123 7776 2.067013 CGCAGCATGAGATACAGATGG 58.933 52.381 0.00 0.00 38.60 3.51
5162 7815 0.802222 CTCACGGCTGTCATACACCG 60.802 60.000 14.96 14.96 43.40 4.94
5386 8039 4.042809 TCTGTAGGAAAAGAAAGGCCATGA 59.957 41.667 5.01 0.00 0.00 3.07
5459 8112 2.029290 TGGTCTCTGTAAAGAACGAGGC 60.029 50.000 0.00 0.00 35.65 4.70
5499 8152 6.098124 AGAGAATCAGATGAAGAGTAACCCAG 59.902 42.308 0.00 0.00 37.82 4.45
5666 8319 2.690497 TGGAGATGAACTCGTCCTCATC 59.310 50.000 12.45 12.45 45.54 2.92
5696 8349 0.323816 AGAGCTCATCGGACCTGTCA 60.324 55.000 17.77 0.00 0.00 3.58
5707 8360 0.749649 GATGGACACCGAGAGCTCAT 59.250 55.000 17.77 0.29 0.00 2.90
5735 8388 1.065854 CATTCCCTCTCTTGGTCGCTT 60.066 52.381 0.00 0.00 0.00 4.68
5842 8495 2.435372 AAAGGCAGGACACAAGACAA 57.565 45.000 0.00 0.00 0.00 3.18
5849 8502 6.272822 AGAAATCAAATAAAGGCAGGACAC 57.727 37.500 0.00 0.00 0.00 3.67
5891 8545 0.951040 CCGCCTCGAAAACTGCTCTT 60.951 55.000 0.00 0.00 0.00 2.85
5897 8551 0.899720 TATGGACCGCCTCGAAAACT 59.100 50.000 0.00 0.00 34.31 2.66
6197 8867 0.103390 TGTCAACGGCGAAGTTCTCA 59.897 50.000 16.62 0.18 30.96 3.27
6201 8871 1.148310 CTCATGTCAACGGCGAAGTT 58.852 50.000 16.62 0.00 34.15 2.66
6268 8938 2.993853 GCCTTCACCAGAGAGGGG 59.006 66.667 0.00 0.00 44.73 4.79
6316 9004 1.565759 TGGCCACATAATCAGAGCCTT 59.434 47.619 0.00 0.00 41.08 4.35
6350 9042 4.888326 TCTAAAGCCAAAAACCATGCAT 57.112 36.364 0.00 0.00 0.00 3.96
6395 9088 1.980052 CACCCTTTCGAGCTACCCA 59.020 57.895 0.00 0.00 0.00 4.51
6428 9121 4.021544 CAGAACAGATGGTATCTCTAGGCC 60.022 50.000 0.00 0.00 37.58 5.19
6459 9152 1.202746 GGGAATTGGTTTTGGCAAGCA 60.203 47.619 0.00 0.00 0.00 3.91
6537 9230 1.591619 GCGTACGCCTTGGTAAGAATC 59.408 52.381 29.51 0.00 34.56 2.52
6570 9263 7.837446 GGACGAAACTTAAAACGAACATTTTTG 59.163 33.333 0.00 0.00 33.80 2.44
6575 9268 5.738118 TGGACGAAACTTAAAACGAACAT 57.262 34.783 0.00 0.00 0.00 2.71
6585 9278 5.375417 TGTAGACGAATGGACGAAACTTA 57.625 39.130 0.00 0.00 37.03 2.24
6586 9279 4.247267 TGTAGACGAATGGACGAAACTT 57.753 40.909 0.00 0.00 37.03 2.66
6664 9358 2.158871 TGACTAAAGTGTCAACCGGCTT 60.159 45.455 0.00 0.00 43.08 4.35
6671 9365 6.869695 TGAAGTACAGTGACTAAAGTGTCAA 58.130 36.000 0.00 0.00 46.77 3.18
6992 9755 3.918220 GGCTTCGTCGATGCGCTG 61.918 66.667 22.25 0.00 34.22 5.18
7051 9814 1.257675 CGCGCATCGTCAATATGTTCA 59.742 47.619 8.75 0.00 0.00 3.18
7076 9839 2.996395 CTCAGCATCCACCAGCCT 59.004 61.111 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.