Multiple sequence alignment - TraesCS3D01G235700

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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 TraesCS3D01G235700 chr3D 100.000 3805 0 0 1 3805 326128618 326124814 0.000000e+00 7027
1 TraesCS3D01G235700 chr3B 97.087 2712 72 6 447 3155 423537021 423534314 0.000000e+00 4564
2 TraesCS3D01G235700 chr3B 96.305 433 12 1 1 429 423537436 423537004 0.000000e+00 708
3 TraesCS3D01G235700 chr3B 91.228 285 22 3 3372 3654 423528435 423528152 5.960000e-103 385
4 TraesCS3D01G235700 chr3B 94.470 217 12 0 3164 3380 423534159 423533943 6.090000e-88 335
5 TraesCS3D01G235700 chr3B 96.053 152 5 1 3653 3803 326997370 326997219 2.940000e-61 246
6 TraesCS3D01G235700 chr3A 97.388 1378 30 4 447 1820 438778962 438780337 0.000000e+00 2340
7 TraesCS3D01G235700 chr3A 95.148 1319 55 6 2187 3503 438780623 438781934 0.000000e+00 2073
8 TraesCS3D01G235700 chr3A 96.471 255 9 0 1849 2103 438780338 438780592 4.540000e-114 422
9 TraesCS3D01G235700 chr3A 96.078 153 5 1 3654 3805 585605638 585605790 8.160000e-62 248
10 TraesCS3D01G235700 chr3A 93.151 146 7 2 3510 3654 438782213 438782356 1.070000e-50 211
11 TraesCS3D01G235700 chr3A 97.368 76 2 0 354 429 438778904 438778979 3.080000e-26 130
12 TraesCS3D01G235700 chr5B 96.689 151 4 1 3654 3803 82505895 82506045 2.270000e-62 250
13 TraesCS3D01G235700 chr2D 96.078 153 5 1 3652 3803 192752402 192752554 8.160000e-62 248
14 TraesCS3D01G235700 chr2D 96.053 152 5 1 3653 3803 647970258 647970107 2.940000e-61 246
15 TraesCS3D01G235700 chr7A 93.865 163 7 3 3643 3803 115807698 115807537 3.800000e-60 243
16 TraesCS3D01G235700 chr5D 90.761 184 13 3 3622 3803 274577981 274578162 3.800000e-60 243
17 TraesCS3D01G235700 chr1D 95.425 153 5 2 3653 3803 39871980 39871828 3.800000e-60 243
18 TraesCS3D01G235700 chr7B 93.293 164 8 3 3641 3803 588861671 588861832 4.910000e-59 239


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 TraesCS3D01G235700 chr3D 326124814 326128618 3804 True 7027.0 7027 100.0000 1 3805 1 chr3D.!!$R1 3804
1 TraesCS3D01G235700 chr3B 423533943 423537436 3493 True 1869.0 4564 95.9540 1 3380 3 chr3B.!!$R3 3379
2 TraesCS3D01G235700 chr3A 438778904 438782356 3452 False 1035.2 2340 95.9052 354 3654 5 chr3A.!!$F2 3300

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
843 849 0.034089 GGGTGAGAGATTTGGTGGGG 60.034 60.0 0.00 0.0 0.0 4.96 F
1917 1925 0.104304 AGCGAGTCGTTGGTGTTTCT 59.896 50.0 15.08 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2516 2524 1.408340 CCTGTGTCGATCATGAGCTCT 59.592 52.381 16.19 0.0 0.00 4.09 R
3047 3056 0.251121 TGCGGGGAAATGTCACACAT 60.251 50.000 0.00 0.0 41.31 3.21 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
113 114 1.170919 GGCAGATGCTGGGCTGTATG 61.171 60.000 4.59 0.00 41.70 2.39
127 128 4.884164 GGGCTGTATGCAGATAAGAAAACT 59.116 41.667 15.68 0.00 45.28 2.66
177 178 9.319143 CATCTAGACCTGTCTTAACCTAAAATG 57.681 37.037 4.94 0.00 40.93 2.32
183 184 5.281037 CCTGTCTTAACCTAAAATGGAGGGT 60.281 44.000 0.00 0.00 38.52 4.34
199 200 4.412199 TGGAGGGTATCTTTAGGTGGAATG 59.588 45.833 0.00 0.00 0.00 2.67
202 203 4.660771 AGGGTATCTTTAGGTGGAATGGAG 59.339 45.833 0.00 0.00 0.00 3.86
271 276 5.538053 TGGTTTGCCATCTTTTTCATACAGA 59.462 36.000 0.00 0.00 40.46 3.41
314 319 4.889409 TCTCAATAACAGGGAAATGATGGC 59.111 41.667 0.00 0.00 0.00 4.40
344 349 4.706842 ACACTGGTGGTTATGTCTTTCT 57.293 40.909 5.70 0.00 34.19 2.52
399 404 8.031864 AGTGTCACTATCTGTAATTCTTCTGTG 58.968 37.037 2.87 0.00 0.00 3.66
416 421 6.897966 TCTTCTGTGAAGGAACTAGGTATCAT 59.102 38.462 7.37 0.00 38.49 2.45
417 422 8.059461 TCTTCTGTGAAGGAACTAGGTATCATA 58.941 37.037 7.37 0.00 38.49 2.15
418 423 8.783660 TTCTGTGAAGGAACTAGGTATCATAT 57.216 34.615 0.00 0.00 38.49 1.78
419 424 9.877222 TTCTGTGAAGGAACTAGGTATCATATA 57.123 33.333 0.00 0.00 38.49 0.86
556 561 6.202188 TCGTTTGGAAAATGTCTTACAGACTC 59.798 38.462 5.53 0.00 45.27 3.36
557 562 6.202954 CGTTTGGAAAATGTCTTACAGACTCT 59.797 38.462 5.53 0.00 45.27 3.24
588 593 3.255642 ACACAATCACTGGTGTTATTGGC 59.744 43.478 14.95 0.00 45.39 4.52
600 605 5.417580 TGGTGTTATTGGCCAGAGTAAAATC 59.582 40.000 5.11 3.46 0.00 2.17
608 613 2.825532 GCCAGAGTAAAATCTTGGGCAA 59.174 45.455 4.46 0.00 37.11 4.52
821 826 2.307496 ACAGGATGAATGGTTGCCAA 57.693 45.000 0.00 0.00 39.69 4.52
843 849 0.034089 GGGTGAGAGATTTGGTGGGG 60.034 60.000 0.00 0.00 0.00 4.96
861 867 1.273098 GGGTAGAGAGTGACAGGGGAA 60.273 57.143 0.00 0.00 0.00 3.97
917 923 1.460699 GTTTCCTGGGGAAGCCAGT 59.539 57.895 0.00 0.00 43.06 4.00
947 955 9.823647 CTAGCATGTCCTATATATACAAAAGGG 57.176 37.037 0.00 0.00 0.00 3.95
950 958 9.297037 GCATGTCCTATATATACAAAAGGGTTT 57.703 33.333 0.00 0.00 0.00 3.27
976 984 1.142870 TGGGCTCTTGTAAGCAACACT 59.857 47.619 0.00 0.00 44.35 3.55
1281 1289 8.770828 ACGAAGTTTATATATGCAATGTGTACC 58.229 33.333 0.00 0.00 37.78 3.34
1314 1322 4.520111 CCGGATGATTTCATGATAAAGCCA 59.480 41.667 0.00 0.00 36.57 4.75
1341 1349 4.189188 GCCGCATGGAGCAAGCAG 62.189 66.667 0.00 0.00 46.13 4.24
1475 1483 4.279420 GGATGACCTTGATATTTCCTTGGC 59.721 45.833 0.00 0.00 0.00 4.52
1503 1511 4.683832 CTTCAGAAATAGTACGACCAGGG 58.316 47.826 0.00 0.00 0.00 4.45
1515 1523 0.257039 GACCAGGGAGTGCCAATGAT 59.743 55.000 2.50 0.00 35.15 2.45
1579 1587 0.178068 CCCAGGGTCTCGGTACAATG 59.822 60.000 0.00 0.00 0.00 2.82
1647 1655 8.650490 TCAGCATTAGTATATCACCAGAATCAA 58.350 33.333 0.00 0.00 0.00 2.57
1662 1670 8.680903 CACCAGAATCAATATTATAGATTGCCC 58.319 37.037 4.67 0.00 34.82 5.36
1687 1695 4.127171 TGTTCTGAAGCACAAACCTCTAC 58.873 43.478 0.00 0.00 0.00 2.59
1766 1774 5.786311 AGTTTGTAATGATGCATGTGCTTT 58.214 33.333 2.46 0.00 42.66 3.51
1774 1782 4.475028 TGATGCATGTGCTTTAAGTTTCG 58.525 39.130 2.46 0.00 42.66 3.46
1866 1874 5.612725 TGTCCATGCATATTAGTCTGTCA 57.387 39.130 0.00 0.00 0.00 3.58
1917 1925 0.104304 AGCGAGTCGTTGGTGTTTCT 59.896 50.000 15.08 0.00 0.00 2.52
1918 1926 0.507358 GCGAGTCGTTGGTGTTTCTC 59.493 55.000 15.08 0.00 0.00 2.87
2146 2154 6.459066 TGCCTCTTACTAGTCATGCATATTC 58.541 40.000 0.00 0.00 0.00 1.75
2174 2182 5.175673 GTGGCTTTTTAGTTTTGCTCATCAC 59.824 40.000 0.00 0.00 0.00 3.06
2175 2183 5.163468 TGGCTTTTTAGTTTTGCTCATCACA 60.163 36.000 0.00 0.00 0.00 3.58
2235 2243 3.678289 CATCAGGTGTTGGATGAAGTCA 58.322 45.455 0.00 0.00 42.73 3.41
2354 2362 2.215196 GTCTCCAACGGCTACAACAAA 58.785 47.619 0.00 0.00 0.00 2.83
2432 2440 2.313234 CAGAAAGCATTTGACAGTGCG 58.687 47.619 8.64 0.00 45.69 5.34
2870 2878 1.600413 GCAACCAACGAGCTTTCCTTG 60.600 52.381 0.00 0.00 0.00 3.61
2880 2888 2.163211 GAGCTTTCCTTGAGAACATGGC 59.837 50.000 0.00 0.00 39.99 4.40
2894 2902 6.127281 TGAGAACATGGCAAATATTCTGCATT 60.127 34.615 18.16 10.22 41.78 3.56
2895 2903 7.068470 TGAGAACATGGCAAATATTCTGCATTA 59.932 33.333 18.16 8.97 41.78 1.90
2943 2951 5.490139 AGAAATGCATCCTGTTATGTTCG 57.510 39.130 0.00 0.00 0.00 3.95
2964 2972 8.067784 TGTTCGAACTCATATTTTTCAGTGAAC 58.932 33.333 27.32 0.00 0.00 3.18
3031 3040 9.817809 TCGATCTTGCTGTAATAAAGTCTTAAT 57.182 29.630 0.00 0.00 0.00 1.40
3099 3109 2.446435 AGGAACTTGTGTGCTTTGTGT 58.554 42.857 0.00 0.00 27.25 3.72
3138 3148 7.372451 TCCTAATAACAAGTAACATGCACAC 57.628 36.000 0.00 0.00 0.00 3.82
3142 3152 7.737972 AATAACAAGTAACATGCACACAGTA 57.262 32.000 0.00 0.00 0.00 2.74
3143 3153 7.921786 ATAACAAGTAACATGCACACAGTAT 57.078 32.000 0.00 0.00 0.00 2.12
3168 3324 7.178573 TCATGTTAGGTGTATCAATTTTCCCA 58.821 34.615 0.00 0.00 0.00 4.37
3177 3333 7.973944 GGTGTATCAATTTTCCCAGTATCAAAC 59.026 37.037 0.00 0.00 0.00 2.93
3230 3386 1.169577 AATTATTGCCCGTGCGTTGA 58.830 45.000 0.00 0.00 41.78 3.18
3259 3415 8.465999 TGAGGCCACAAATATTTTGTACATAAG 58.534 33.333 5.01 0.00 0.00 1.73
3260 3416 7.781056 AGGCCACAAATATTTTGTACATAAGG 58.219 34.615 5.01 3.64 0.00 2.69
3276 3432 5.057149 ACATAAGGACCGTGATTTATCTGC 58.943 41.667 2.21 0.00 0.00 4.26
3280 3436 2.808543 GGACCGTGATTTATCTGCCATC 59.191 50.000 0.00 0.00 0.00 3.51
3301 3457 9.664332 GCCATCTTAGTATGAATGAATATGTCT 57.336 33.333 0.00 0.00 0.00 3.41
3380 3536 3.279434 GGTAAGCCAATAAGTGAGGTGG 58.721 50.000 0.00 0.00 34.09 4.61
3386 3542 3.365969 GCCAATAAGTGAGGTGGTTTTCG 60.366 47.826 0.00 0.00 33.43 3.46
3401 3557 3.967203 TTTTCGAGTAAAACCGTTGGG 57.033 42.857 0.00 0.00 40.11 4.12
3402 3558 1.881591 TTCGAGTAAAACCGTTGGGG 58.118 50.000 0.00 0.00 43.62 4.96
3408 3564 4.261698 CGAGTAAAACCGTTGGGGAAAATT 60.262 41.667 0.00 0.00 39.97 1.82
3417 3573 2.621055 GTTGGGGAAAATTGGCAAAACC 59.379 45.455 3.01 5.46 39.84 3.27
3421 3577 3.206964 GGGAAAATTGGCAAAACCGAAA 58.793 40.909 3.01 0.00 43.94 3.46
3422 3578 3.628032 GGGAAAATTGGCAAAACCGAAAA 59.372 39.130 3.01 0.00 43.94 2.29
3426 3582 0.806492 TTGGCAAAACCGAAAACGGC 60.806 50.000 8.59 0.00 43.94 5.68
3427 3583 1.952133 GGCAAAACCGAAAACGGCC 60.952 57.895 8.59 0.00 0.00 6.13
3444 3600 2.660064 CCGTGGGTTGAGGAGGGAG 61.660 68.421 0.00 0.00 0.00 4.30
3448 3604 2.359967 GGGTTGAGGAGGGAGGACG 61.360 68.421 0.00 0.00 0.00 4.79
3472 3628 7.119846 ACGAAAGGAATGAATGTTTTAGGAGAG 59.880 37.037 0.00 0.00 0.00 3.20
3489 3646 3.385577 GAGAGATTAATGCACGGGTCTC 58.614 50.000 11.15 11.15 33.94 3.36
3498 3655 2.203451 ACGGGTCTCACTCACGGT 60.203 61.111 0.00 0.00 0.00 4.83
3503 3660 2.440409 GGGTCTCACTCACGGTACTTA 58.560 52.381 0.00 0.00 0.00 2.24
3504 3661 2.821969 GGGTCTCACTCACGGTACTTAA 59.178 50.000 0.00 0.00 0.00 1.85
3505 3662 3.366781 GGGTCTCACTCACGGTACTTAAC 60.367 52.174 0.00 0.00 0.00 2.01
3507 3664 4.379290 GGTCTCACTCACGGTACTTAACTC 60.379 50.000 0.00 0.00 0.00 3.01
3508 3665 3.755378 TCTCACTCACGGTACTTAACTCC 59.245 47.826 0.00 0.00 0.00 3.85
3513 3942 5.012239 ACTCACGGTACTTAACTCCACATA 58.988 41.667 0.00 0.00 0.00 2.29
3542 3971 4.510340 TCTTCGTCAAAAAGCTAACCTCAC 59.490 41.667 0.00 0.00 0.00 3.51
3551 3980 9.344772 TCAAAAAGCTAACCTCACAAGTTAATA 57.655 29.630 0.00 0.00 29.68 0.98
3552 3981 9.394477 CAAAAAGCTAACCTCACAAGTTAATAC 57.606 33.333 0.00 0.00 29.68 1.89
3553 3982 8.919777 AAAAGCTAACCTCACAAGTTAATACT 57.080 30.769 0.00 0.00 35.68 2.12
3554 3983 8.549338 AAAGCTAACCTCACAAGTTAATACTC 57.451 34.615 0.00 0.00 31.99 2.59
3555 3984 6.641474 AGCTAACCTCACAAGTTAATACTCC 58.359 40.000 0.00 0.00 31.99 3.85
3556 3985 6.212791 AGCTAACCTCACAAGTTAATACTCCA 59.787 38.462 0.00 0.00 31.99 3.86
3558 3987 7.148457 GCTAACCTCACAAGTTAATACTCCAAC 60.148 40.741 0.00 0.00 31.99 3.77
3654 4084 7.039011 GGTATCAGACCCATGTTATGATGTCTA 60.039 40.741 10.48 4.71 43.25 2.59
3655 4085 6.161855 TCAGACCCATGTTATGATGTCTAC 57.838 41.667 11.12 0.00 38.93 2.59
3656 4086 5.899547 TCAGACCCATGTTATGATGTCTACT 59.100 40.000 11.12 0.00 38.93 2.57
3657 4087 6.040955 TCAGACCCATGTTATGATGTCTACTC 59.959 42.308 11.12 0.00 38.93 2.59
3658 4088 5.305644 AGACCCATGTTATGATGTCTACTCC 59.694 44.000 10.28 0.00 39.08 3.85
3659 4089 4.348168 ACCCATGTTATGATGTCTACTCCC 59.652 45.833 0.00 0.00 0.00 4.30
3660 4090 4.594920 CCCATGTTATGATGTCTACTCCCT 59.405 45.833 0.00 0.00 0.00 4.20
3661 4091 5.279708 CCCATGTTATGATGTCTACTCCCTC 60.280 48.000 0.00 0.00 0.00 4.30
3662 4092 5.279708 CCATGTTATGATGTCTACTCCCTCC 60.280 48.000 0.00 0.00 0.00 4.30
3663 4093 3.889538 TGTTATGATGTCTACTCCCTCCG 59.110 47.826 0.00 0.00 0.00 4.63
3664 4094 2.757894 ATGATGTCTACTCCCTCCGT 57.242 50.000 0.00 0.00 0.00 4.69
3665 4095 2.526888 TGATGTCTACTCCCTCCGTT 57.473 50.000 0.00 0.00 0.00 4.44
3666 4096 2.376109 TGATGTCTACTCCCTCCGTTC 58.624 52.381 0.00 0.00 0.00 3.95
3667 4097 1.682323 GATGTCTACTCCCTCCGTTCC 59.318 57.143 0.00 0.00 0.00 3.62
3668 4098 0.702902 TGTCTACTCCCTCCGTTCCT 59.297 55.000 0.00 0.00 0.00 3.36
3669 4099 1.918262 TGTCTACTCCCTCCGTTCCTA 59.082 52.381 0.00 0.00 0.00 2.94
3670 4100 2.309755 TGTCTACTCCCTCCGTTCCTAA 59.690 50.000 0.00 0.00 0.00 2.69
3671 4101 3.245371 TGTCTACTCCCTCCGTTCCTAAA 60.245 47.826 0.00 0.00 0.00 1.85
3672 4102 3.959449 GTCTACTCCCTCCGTTCCTAAAT 59.041 47.826 0.00 0.00 0.00 1.40
3673 4103 5.136105 GTCTACTCCCTCCGTTCCTAAATA 58.864 45.833 0.00 0.00 0.00 1.40
3674 4104 5.774184 GTCTACTCCCTCCGTTCCTAAATAT 59.226 44.000 0.00 0.00 0.00 1.28
3675 4105 6.267242 GTCTACTCCCTCCGTTCCTAAATATT 59.733 42.308 0.00 0.00 0.00 1.28
3676 4106 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3677 4107 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3678 4108 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3679 4109 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3680 4110 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3681 4111 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3682 4112 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3683 4113 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
3684 4114 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
3700 4130 9.965824 TTTGTCTTTTTAGAGATTTCAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
3701 4131 8.924511 TGTCTTTTTAGAGATTTCAATGGACT 57.075 30.769 0.00 0.00 0.00 3.85
3704 4134 9.449719 TCTTTTTAGAGATTTCAATGGACTACC 57.550 33.333 0.00 0.00 0.00 3.18
3744 4174 8.804688 ATAGACGTATTTTAGAGTGCAGATTC 57.195 34.615 0.00 0.00 0.00 2.52
3745 4175 6.631016 AGACGTATTTTAGAGTGCAGATTCA 58.369 36.000 0.00 0.00 0.00 2.57
3746 4176 6.531948 AGACGTATTTTAGAGTGCAGATTCAC 59.468 38.462 0.00 0.00 37.24 3.18
3755 4185 4.170292 AGTGCAGATTCACTCATTTTGC 57.830 40.909 0.00 0.00 43.28 3.68
3756 4186 3.825014 AGTGCAGATTCACTCATTTTGCT 59.175 39.130 0.00 0.00 43.28 3.91
3757 4187 4.082895 AGTGCAGATTCACTCATTTTGCTC 60.083 41.667 0.00 0.00 43.28 4.26
3758 4188 3.192001 TGCAGATTCACTCATTTTGCTCC 59.808 43.478 0.00 0.00 0.00 4.70
3759 4189 3.730061 GCAGATTCACTCATTTTGCTCCG 60.730 47.826 0.00 0.00 0.00 4.63
3760 4190 3.438087 CAGATTCACTCATTTTGCTCCGT 59.562 43.478 0.00 0.00 0.00 4.69
3761 4191 4.631377 CAGATTCACTCATTTTGCTCCGTA 59.369 41.667 0.00 0.00 0.00 4.02
3762 4192 5.295292 CAGATTCACTCATTTTGCTCCGTAT 59.705 40.000 0.00 0.00 0.00 3.06
3763 4193 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3764 4194 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3765 4195 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3766 4196 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3767 4197 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3768 4198 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3769 4199 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
3770 4200 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
3771 4201 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
3772 4202 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
3773 4203 4.530710 TTGCTCCGTATGTAGTCACTTT 57.469 40.909 0.00 0.00 0.00 2.66
3774 4204 4.530710 TGCTCCGTATGTAGTCACTTTT 57.469 40.909 0.00 0.00 0.00 2.27
3775 4205 4.890088 TGCTCCGTATGTAGTCACTTTTT 58.110 39.130 0.00 0.00 0.00 1.94
3776 4206 4.688879 TGCTCCGTATGTAGTCACTTTTTG 59.311 41.667 0.00 0.00 0.00 2.44
3777 4207 4.927425 GCTCCGTATGTAGTCACTTTTTGA 59.073 41.667 0.00 0.00 0.00 2.69
3778 4208 5.407387 GCTCCGTATGTAGTCACTTTTTGAA 59.593 40.000 0.00 0.00 35.39 2.69
3779 4209 6.073440 GCTCCGTATGTAGTCACTTTTTGAAA 60.073 38.462 0.00 0.00 35.39 2.69
3780 4210 7.360946 GCTCCGTATGTAGTCACTTTTTGAAAT 60.361 37.037 0.00 0.00 35.39 2.17
3781 4211 8.025243 TCCGTATGTAGTCACTTTTTGAAATC 57.975 34.615 0.00 0.00 35.39 2.17
3782 4212 7.876068 TCCGTATGTAGTCACTTTTTGAAATCT 59.124 33.333 0.00 0.00 35.39 2.40
3783 4213 8.169268 CCGTATGTAGTCACTTTTTGAAATCTC 58.831 37.037 0.00 0.00 35.39 2.75
3784 4214 8.926710 CGTATGTAGTCACTTTTTGAAATCTCT 58.073 33.333 0.00 0.00 35.39 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.202818 GGCCTACTAATTCCCAGCAGG 60.203 57.143 0.00 0.00 30.70 4.85
127 128 8.415950 TGGCTCAAGGTTTTTCAATTATAGAA 57.584 30.769 0.00 0.00 0.00 2.10
177 178 4.202472 CCATTCCACCTAAAGATACCCTCC 60.202 50.000 0.00 0.00 0.00 4.30
183 184 7.635089 GCAGTAACTCCATTCCACCTAAAGATA 60.635 40.741 0.00 0.00 0.00 1.98
199 200 7.677511 GCAAAAATAGAGCTTAGCAGTAACTCC 60.678 40.741 7.07 0.00 0.00 3.85
202 203 6.842163 TGCAAAAATAGAGCTTAGCAGTAAC 58.158 36.000 7.07 0.00 0.00 2.50
271 276 0.603065 GCATGCTTCCCGGAAAGTTT 59.397 50.000 11.37 0.00 0.00 2.66
314 319 1.573108 ACCACCAGTGTAGGATCCAG 58.427 55.000 15.82 0.00 0.00 3.86
549 554 4.937201 TGTGTACACAATCAGAGTCTGT 57.063 40.909 26.07 4.83 38.56 3.41
588 593 5.243730 TCTTTTGCCCAAGATTTTACTCTGG 59.756 40.000 0.00 0.00 0.00 3.86
600 605 2.426738 TGAACAGTGTCTTTTGCCCAAG 59.573 45.455 0.00 0.00 0.00 3.61
608 613 3.290710 ACCAGCAATGAACAGTGTCTTT 58.709 40.909 0.00 0.00 0.00 2.52
821 826 1.352352 CCACCAAATCTCTCACCCACT 59.648 52.381 0.00 0.00 0.00 4.00
843 849 2.756207 GAGTTCCCCTGTCACTCTCTAC 59.244 54.545 0.00 0.00 35.10 2.59
861 867 4.758688 TGATATGCGTGTTGAAGATGAGT 58.241 39.130 0.00 0.00 0.00 3.41
917 923 9.709387 TTTGTATATATAGGACATGCTAGGCTA 57.291 33.333 0.00 0.00 0.00 3.93
947 955 4.320275 GCTTACAAGAGCCCACAACTAAAC 60.320 45.833 0.00 0.00 36.66 2.01
950 958 2.370519 TGCTTACAAGAGCCCACAACTA 59.629 45.455 0.00 0.00 42.01 2.24
976 984 6.899393 ATTTGACAGGAAATGCTTCTGTTA 57.101 33.333 0.00 0.00 0.00 2.41
1053 1061 1.339631 CCCTTCCAGTAATTCGCACCA 60.340 52.381 0.00 0.00 0.00 4.17
1281 1289 1.091771 AATCATCCGGCAAGCTCACG 61.092 55.000 0.00 0.00 0.00 4.35
1314 1322 1.973281 CCATGCGGCCTTTGACAGT 60.973 57.895 0.00 0.00 0.00 3.55
1341 1349 4.064388 CAACAAACCCCATCCAATTTGAC 58.936 43.478 0.00 0.00 35.93 3.18
1475 1483 2.535984 CGTACTATTTCTGAAGCAGGCG 59.464 50.000 0.00 5.70 31.51 5.52
1503 1511 1.097547 CACGGGGATCATTGGCACTC 61.098 60.000 0.00 0.00 0.00 3.51
1515 1523 0.620410 ATCCTCCATGAACACGGGGA 60.620 55.000 0.00 0.00 0.00 4.81
1579 1587 3.119291 CCTGATATCGTGCACTCTGTTC 58.881 50.000 16.19 6.05 0.00 3.18
1647 1655 7.932134 TCAGAACATGGGGCAATCTATAATAT 58.068 34.615 0.00 0.00 0.00 1.28
1662 1670 2.624838 AGGTTTGTGCTTCAGAACATGG 59.375 45.455 0.00 0.00 32.71 3.66
1687 1695 8.438513 CGCACAAAGATCAACTATATCCTAATG 58.561 37.037 0.00 0.00 0.00 1.90
1766 1774 7.336161 TCAAATGGAAGAAAACCGAAACTTA 57.664 32.000 0.00 0.00 0.00 2.24
1889 1897 1.455786 CAACGACTCGCTGGTGTAAAG 59.544 52.381 0.00 0.00 0.00 1.85
1917 1925 3.838244 AGTGCAGTAAGGTTGAACAGA 57.162 42.857 0.00 0.00 0.00 3.41
1918 1926 3.428870 CGTAGTGCAGTAAGGTTGAACAG 59.571 47.826 1.96 0.00 0.00 3.16
2033 2041 4.265893 TCCAAACTGTCTTAAAGTGCACA 58.734 39.130 21.04 0.00 0.00 4.57
2146 2154 2.466205 GCAAAACTAAAAAGCCACGTCG 59.534 45.455 0.00 0.00 0.00 5.12
2235 2243 2.040278 TGTACAGATCCTGCAGCCTTTT 59.960 45.455 8.66 0.00 34.37 2.27
2432 2440 1.472376 CGGAGCAACCTCAGATCTTCC 60.472 57.143 0.00 0.00 39.96 3.46
2516 2524 1.408340 CCTGTGTCGATCATGAGCTCT 59.592 52.381 16.19 0.00 0.00 4.09
2870 2878 5.252969 TGCAGAATATTTGCCATGTTCTC 57.747 39.130 15.43 1.16 40.81 2.87
2964 2972 3.997021 ACTGGTCTCGAAAGCAATAACAG 59.003 43.478 0.00 0.00 0.00 3.16
3035 3044 6.389830 AATGTCACACATGAACAGCTAAAA 57.610 33.333 0.00 0.00 37.97 1.52
3045 3054 1.819928 CGGGGAAATGTCACACATGA 58.180 50.000 0.00 0.00 37.97 3.07
3047 3056 0.251121 TGCGGGGAAATGTCACACAT 60.251 50.000 0.00 0.00 41.31 3.21
3142 3152 7.838696 TGGGAAAATTGATACACCTAACATGAT 59.161 33.333 0.00 0.00 0.00 2.45
3143 3153 7.178573 TGGGAAAATTGATACACCTAACATGA 58.821 34.615 0.00 0.00 0.00 3.07
3230 3386 7.675062 TGTACAAAATATTTGTGGCCTCATTT 58.325 30.769 16.47 3.37 34.11 2.32
3259 3415 2.325583 TGGCAGATAAATCACGGTCC 57.674 50.000 0.00 0.00 0.00 4.46
3260 3416 3.733337 AGATGGCAGATAAATCACGGTC 58.267 45.455 0.00 0.00 0.00 4.79
3301 3457 3.153369 TGGCAGCTAAGTCCATTTTCA 57.847 42.857 0.00 0.00 0.00 2.69
3386 3542 4.859304 ATTTTCCCCAACGGTTTTACTC 57.141 40.909 0.00 0.00 0.00 2.59
3401 3557 4.593157 GTTTTCGGTTTTGCCAATTTTCC 58.407 39.130 0.00 0.00 36.97 3.13
3402 3558 4.267733 CGTTTTCGGTTTTGCCAATTTTC 58.732 39.130 0.00 0.00 39.94 2.29
3417 3573 3.281395 AACCCACGGCCGTTTTCG 61.281 61.111 32.11 17.94 43.67 3.46
3421 3577 4.636435 CCTCAACCCACGGCCGTT 62.636 66.667 32.11 12.67 0.00 4.44
3426 3582 2.606519 TCCCTCCTCAACCCACGG 60.607 66.667 0.00 0.00 0.00 4.94
3427 3583 2.660064 CCTCCCTCCTCAACCCACG 61.660 68.421 0.00 0.00 0.00 4.94
3433 3589 1.267121 CTTTCGTCCTCCCTCCTCAA 58.733 55.000 0.00 0.00 0.00 3.02
3444 3600 6.150474 TCCTAAAACATTCATTCCTTTCGTCC 59.850 38.462 0.00 0.00 0.00 4.79
3448 3604 8.567285 TCTCTCCTAAAACATTCATTCCTTTC 57.433 34.615 0.00 0.00 0.00 2.62
3472 3628 2.866762 GAGTGAGACCCGTGCATTAATC 59.133 50.000 0.00 0.00 0.00 1.75
3489 3646 3.005050 TGTGGAGTTAAGTACCGTGAGTG 59.995 47.826 0.00 0.00 0.00 3.51
3508 3665 5.621197 TTTTGACGAAGACCCATTATGTG 57.379 39.130 0.00 0.00 0.00 3.21
3513 3942 3.222603 AGCTTTTTGACGAAGACCCATT 58.777 40.909 0.00 0.00 0.00 3.16
3520 3949 4.272504 TGTGAGGTTAGCTTTTTGACGAAG 59.727 41.667 0.00 0.00 0.00 3.79
3551 3980 7.993183 TCTTTGAAGAATTTCTAGTGTTGGAGT 59.007 33.333 0.00 0.00 34.31 3.85
3552 3981 8.383318 TCTTTGAAGAATTTCTAGTGTTGGAG 57.617 34.615 0.00 0.00 34.31 3.86
3553 3982 8.746052 TTCTTTGAAGAATTTCTAGTGTTGGA 57.254 30.769 0.00 0.00 39.95 3.53
3554 3983 9.801873 TTTTCTTTGAAGAATTTCTAGTGTTGG 57.198 29.630 6.98 0.00 43.92 3.77
3632 4062 5.899547 AGTAGACATCATAACATGGGTCTGA 59.100 40.000 17.23 0.00 41.74 3.27
3654 4084 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3655 4085 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3656 4086 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3657 4087 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3658 4088 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
3674 4104 9.965824 GTCCATTGAAATCTCTAAAAAGACAAA 57.034 29.630 0.00 0.00 0.00 2.83
3675 4105 9.354673 AGTCCATTGAAATCTCTAAAAAGACAA 57.645 29.630 0.00 0.00 0.00 3.18
3676 4106 8.924511 AGTCCATTGAAATCTCTAAAAAGACA 57.075 30.769 0.00 0.00 0.00 3.41
3678 4108 9.449719 GGTAGTCCATTGAAATCTCTAAAAAGA 57.550 33.333 0.00 0.00 0.00 2.52
3679 4109 9.231297 TGGTAGTCCATTGAAATCTCTAAAAAG 57.769 33.333 0.00 0.00 39.03 2.27
3680 4110 9.010029 GTGGTAGTCCATTGAAATCTCTAAAAA 57.990 33.333 0.00 0.00 46.20 1.94
3681 4111 8.160765 TGTGGTAGTCCATTGAAATCTCTAAAA 58.839 33.333 0.00 0.00 46.20 1.52
3682 4112 7.685481 TGTGGTAGTCCATTGAAATCTCTAAA 58.315 34.615 0.00 0.00 46.20 1.85
3683 4113 7.252612 TGTGGTAGTCCATTGAAATCTCTAA 57.747 36.000 0.00 0.00 46.20 2.10
3684 4114 6.867519 TGTGGTAGTCCATTGAAATCTCTA 57.132 37.500 0.00 0.00 46.20 2.43
3685 4115 5.762179 TGTGGTAGTCCATTGAAATCTCT 57.238 39.130 0.00 0.00 46.20 3.10
3686 4116 9.429359 CTATATGTGGTAGTCCATTGAAATCTC 57.571 37.037 0.00 0.00 46.20 2.75
3687 4117 9.159254 TCTATATGTGGTAGTCCATTGAAATCT 57.841 33.333 0.00 0.00 46.20 2.40
3688 4118 9.950496 ATCTATATGTGGTAGTCCATTGAAATC 57.050 33.333 0.00 0.00 46.20 2.17
3689 4119 9.730705 CATCTATATGTGGTAGTCCATTGAAAT 57.269 33.333 0.00 0.00 46.20 2.17
3690 4120 8.713971 ACATCTATATGTGGTAGTCCATTGAAA 58.286 33.333 0.00 0.00 44.79 2.69
3691 4121 8.262601 ACATCTATATGTGGTAGTCCATTGAA 57.737 34.615 0.00 0.00 44.79 2.69
3692 4122 7.855784 ACATCTATATGTGGTAGTCCATTGA 57.144 36.000 0.00 0.00 44.79 2.57
3718 4148 9.894783 GAATCTGCACTCTAAAATACGTCTATA 57.105 33.333 0.00 0.00 0.00 1.31
3719 4149 8.414003 TGAATCTGCACTCTAAAATACGTCTAT 58.586 33.333 0.00 0.00 0.00 1.98
3720 4150 7.701078 GTGAATCTGCACTCTAAAATACGTCTA 59.299 37.037 0.00 0.00 35.91 2.59
3721 4151 6.531948 GTGAATCTGCACTCTAAAATACGTCT 59.468 38.462 0.00 0.00 35.91 4.18
3722 4152 6.531948 AGTGAATCTGCACTCTAAAATACGTC 59.468 38.462 0.00 0.00 45.54 4.34
3723 4153 6.398918 AGTGAATCTGCACTCTAAAATACGT 58.601 36.000 0.00 0.00 45.54 3.57
3724 4154 6.893958 AGTGAATCTGCACTCTAAAATACG 57.106 37.500 0.00 0.00 45.54 3.06
3735 4165 4.164294 GAGCAAAATGAGTGAATCTGCAC 58.836 43.478 0.00 0.00 39.05 4.57
3736 4166 3.192001 GGAGCAAAATGAGTGAATCTGCA 59.808 43.478 0.00 0.00 0.00 4.41
3737 4167 3.730061 CGGAGCAAAATGAGTGAATCTGC 60.730 47.826 0.00 0.00 0.00 4.26
3738 4168 3.438087 ACGGAGCAAAATGAGTGAATCTG 59.562 43.478 0.00 0.00 0.00 2.90
3739 4169 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3740 4170 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3741 4171 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3742 4172 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3743 4173 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3744 4174 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3745 4175 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3746 4176 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
3747 4177 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
3748 4178 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
3749 4179 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
3750 4180 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
3751 4181 4.530710 AAGTGACTACATACGGAGCAAA 57.469 40.909 0.00 0.00 0.00 3.68
3752 4182 4.530710 AAAGTGACTACATACGGAGCAA 57.469 40.909 0.00 0.00 0.00 3.91
3753 4183 4.530710 AAAAGTGACTACATACGGAGCA 57.469 40.909 0.00 0.00 0.00 4.26
3754 4184 4.927425 TCAAAAAGTGACTACATACGGAGC 59.073 41.667 0.00 0.00 0.00 4.70
3755 4185 7.416154 TTTCAAAAAGTGACTACATACGGAG 57.584 36.000 0.00 0.00 35.39 4.63
3756 4186 7.876068 AGATTTCAAAAAGTGACTACATACGGA 59.124 33.333 0.00 0.00 35.39 4.69
3757 4187 8.029642 AGATTTCAAAAAGTGACTACATACGG 57.970 34.615 0.00 0.00 35.39 4.02
3758 4188 8.926710 AGAGATTTCAAAAAGTGACTACATACG 58.073 33.333 0.00 0.00 35.39 3.06


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

AutoCloner maintained by Alex Coulton.