Multiple sequence alignment - TraesCS7A01G362600

Loading Multiple Alignment...

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 TraesCS7A01G362600 chr7A 100.000 5590 0 0 1 5590 536985248 536979659 0.000000e+00 10323.0
1 TraesCS7A01G362600 chr7B 88.822 2639 148 57 2987 5585 488412395 488409864 0.000000e+00 3103.0
2 TraesCS7A01G362600 chr7B 89.393 1829 91 43 1 1744 488415469 488413659 0.000000e+00 2207.0
3 TraesCS7A01G362600 chr7B 96.517 1177 38 2 1747 2921 488413581 488412406 0.000000e+00 1943.0
4 TraesCS7A01G362600 chr7D 89.290 2521 145 37 1 2460 463260618 463263074 0.000000e+00 3044.0
5 TraesCS7A01G362600 chr7D 89.623 2043 106 29 3594 5585 463264130 463266117 0.000000e+00 2501.0
6 TraesCS7A01G362600 chr7D 95.238 462 20 1 3048 3509 463263672 463264131 0.000000e+00 730.0
7 TraesCS7A01G362600 chr7D 93.534 464 26 3 2459 2919 463263156 463263618 0.000000e+00 688.0
8 TraesCS7A01G362600 chr7D 89.908 109 9 1 1672 1780 454079182 454079076 7.550000e-29 139.0
9 TraesCS7A01G362600 chr4D 90.909 110 8 1 1671 1780 74079457 74079350 4.510000e-31 147.0
10 TraesCS7A01G362600 chr1D 91.589 107 7 1 1673 1779 193504487 193504383 4.510000e-31 147.0
11 TraesCS7A01G362600 chr1B 90.265 113 7 2 1671 1783 667230521 667230629 1.620000e-30 145.0
12 TraesCS7A01G362600 chr6D 90.826 109 7 1 1671 1779 221843041 221843146 5.840000e-30 143.0
13 TraesCS7A01G362600 chr6D 98.333 60 1 0 2922 2981 472379886 472379945 7.660000e-19 106.0
14 TraesCS7A01G362600 chr4A 90.826 109 7 1 1671 1779 490599658 490599553 5.840000e-30 143.0
15 TraesCS7A01G362600 chr3D 88.596 114 9 2 1671 1784 73853134 73853243 9.770000e-28 135.0
16 TraesCS7A01G362600 chr3D 98.361 61 1 0 2922 2982 313603933 313603873 2.130000e-19 108.0
17 TraesCS7A01G362600 chr3D 89.855 69 4 3 2922 2987 303792846 303792778 9.980000e-13 86.1
18 TraesCS7A01G362600 chr3B 96.970 66 2 0 2922 2987 405955490 405955555 1.650000e-20 111.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G362600 chr7A 536979659 536985248 5589 True 10323.000000 10323 100.000000 1 5590 1 chr7A.!!$R1 5589
1 TraesCS7A01G362600 chr7B 488409864 488415469 5605 True 2417.666667 3103 91.577333 1 5585 3 chr7B.!!$R1 5584
2 TraesCS7A01G362600 chr7D 463260618 463266117 5499 False 1740.750000 3044 91.921250 1 5585 4 chr7D.!!$F1 5584

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
737 796 0.561141 CGCGTAAATTGCATTCGTGC 59.439 50.000 0.00 0.00 0.00 5.34 F
1931 2125 0.171455 GTGCTCCCGTCTGTACTGAG 59.829 60.000 2.23 0.00 0.00 3.35 F
2632 2909 0.737367 ACGATGACACAGTGATGCCG 60.737 55.000 7.81 7.94 0.00 5.69 F
4034 4330 1.556911 ACTCCCTGTGCAGAATGTAGG 59.443 52.381 0.02 0.00 39.31 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2317 0.239347 GCAAACTGAATGCAGAGCGT 59.761 50.0 8.02 0.0 45.17 5.07 R
3861 4157 0.311790 CGACCTGCAAACAACATGCT 59.688 50.0 0.00 0.0 44.14 3.79 R
4482 4788 0.325671 TAGCCTCCTGAGAAGGGGTG 60.326 60.0 0.00 0.0 0.00 4.61 R
5184 5507 0.179000 GGATGATGAAGCTCGGTGGT 59.821 55.0 0.00 0.0 0.00 4.16 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
33 35 5.185828 AGTCCTGGAGAAAATGGTAAAATGC 59.814 40.000 0.00 0.00 0.00 3.56
75 77 0.645868 GCTGATTCCGTTCACGCTAC 59.354 55.000 0.00 0.00 38.18 3.58
111 113 2.771372 TCTTATGTGGTATCCTGCAGCA 59.229 45.455 8.66 0.00 0.00 4.41
112 114 3.392285 TCTTATGTGGTATCCTGCAGCAT 59.608 43.478 8.66 0.25 0.00 3.79
125 127 2.947652 CTGCAGCATTAACTGGCACTAT 59.052 45.455 0.00 0.00 38.16 2.12
134 136 7.041098 AGCATTAACTGGCACTATTAAGCATAC 60.041 37.037 0.00 0.00 0.00 2.39
139 141 4.450976 TGGCACTATTAAGCATACACAGG 58.549 43.478 0.00 0.00 0.00 4.00
144 174 6.260936 GCACTATTAAGCATACACAGGACATT 59.739 38.462 0.00 0.00 0.00 2.71
155 185 2.492088 CACAGGACATTCTAGACCGTGA 59.508 50.000 12.53 0.00 33.59 4.35
205 237 8.440059 TGTTACAATCTTTAAGCACTGATAACG 58.560 33.333 0.00 0.00 0.00 3.18
207 239 5.354234 ACAATCTTTAAGCACTGATAACGGG 59.646 40.000 0.00 0.00 0.00 5.28
213 245 3.460857 AGCACTGATAACGGGATTCTC 57.539 47.619 0.00 0.00 0.00 2.87
237 283 5.561679 GTTTCCTAATCTCCTTGGAGTTGT 58.438 41.667 15.44 5.85 0.00 3.32
272 318 4.692625 ACAATGCAGTTAGAGCTTACAGTG 59.307 41.667 0.00 0.00 0.00 3.66
275 321 3.067106 GCAGTTAGAGCTTACAGTGCAA 58.933 45.455 12.53 0.00 0.00 4.08
302 348 0.867746 TCACAAGTCACAATGCGAGC 59.132 50.000 0.00 0.00 0.00 5.03
498 547 2.930385 ATTGGATCGTCAGCAGGGCG 62.930 60.000 0.00 0.00 0.00 6.13
542 593 4.452733 GAGGGGTGGAAGGCGTCG 62.453 72.222 0.00 0.00 0.00 5.12
571 622 3.174790 CCGGAGTAGATTAACGGCG 57.825 57.895 4.80 4.80 37.93 6.46
591 642 1.747774 GAGGAGGATGAGGAGCAGC 59.252 63.158 0.00 0.00 0.00 5.25
676 735 1.139947 CGAGAGCGAGTTTCCCCTC 59.860 63.158 0.00 0.00 40.82 4.30
729 788 1.520368 CGTTCTTCCGCGTAAATTGC 58.480 50.000 4.92 0.00 0.00 3.56
737 796 0.561141 CGCGTAAATTGCATTCGTGC 59.439 50.000 0.00 0.00 0.00 5.34
759 818 2.898705 CTCCAAACTCCAGAGATTCCG 58.101 52.381 0.70 0.00 0.00 4.30
762 821 2.028112 CCAAACTCCAGAGATTCCGTGA 60.028 50.000 0.70 0.00 0.00 4.35
784 843 1.082954 AAGGGAAGGAGGGCTAGCA 59.917 57.895 18.24 0.00 0.00 3.49
804 863 5.413499 AGCAATGCAAATATCCAACTTCAC 58.587 37.500 8.35 0.00 0.00 3.18
808 867 6.839124 ATGCAAATATCCAACTTCACAAGA 57.161 33.333 0.00 0.00 0.00 3.02
812 871 7.147976 GCAAATATCCAACTTCACAAGAACTT 58.852 34.615 0.00 0.00 0.00 2.66
817 876 5.496556 TCCAACTTCACAAGAACTTTCTCA 58.503 37.500 0.00 0.00 36.28 3.27
818 877 5.586243 TCCAACTTCACAAGAACTTTCTCAG 59.414 40.000 0.00 0.00 36.28 3.35
827 886 8.883731 TCACAAGAACTTTCTCAGAAAAAGTAG 58.116 33.333 2.15 0.00 44.13 2.57
837 896 1.071699 AGAAAAAGTAGAGCACCGCCA 59.928 47.619 0.00 0.00 0.00 5.69
1129 1209 1.524863 CTCCAAGGTCAGTCGTCCGT 61.525 60.000 0.00 0.00 0.00 4.69
1211 1304 2.424733 GGCTCCGGTGGTCTACTCC 61.425 68.421 0.00 0.00 0.00 3.85
1275 1368 2.498726 CTCTGCTTCCCGCCTCTC 59.501 66.667 0.00 0.00 38.05 3.20
1285 1378 3.827898 CGCCTCTCCTCCACCGTC 61.828 72.222 0.00 0.00 0.00 4.79
1294 1387 2.037367 TCCACCGTCTGCCTAGCT 59.963 61.111 0.00 0.00 0.00 3.32
1295 1388 2.185350 CCACCGTCTGCCTAGCTG 59.815 66.667 0.00 0.00 0.00 4.24
1297 1390 4.135153 ACCGTCTGCCTAGCTGCG 62.135 66.667 0.00 0.00 0.00 5.18
1353 1446 2.672996 ATGTGCAGGCACCCGTTC 60.673 61.111 20.60 0.00 45.63 3.95
1640 1758 2.610438 AGTTGAATTGGTGGCCTGAT 57.390 45.000 3.32 0.00 0.00 2.90
1641 1759 2.893424 AGTTGAATTGGTGGCCTGATT 58.107 42.857 3.32 0.00 0.00 2.57
1642 1760 2.564062 AGTTGAATTGGTGGCCTGATTG 59.436 45.455 3.32 0.00 0.00 2.67
1643 1761 2.562298 GTTGAATTGGTGGCCTGATTGA 59.438 45.455 3.32 0.00 0.00 2.57
1644 1762 3.104519 TGAATTGGTGGCCTGATTGAT 57.895 42.857 3.32 0.00 0.00 2.57
1645 1763 4.248174 TGAATTGGTGGCCTGATTGATA 57.752 40.909 3.32 0.00 0.00 2.15
1646 1764 4.209538 TGAATTGGTGGCCTGATTGATAG 58.790 43.478 3.32 0.00 0.00 2.08
1647 1765 3.959495 ATTGGTGGCCTGATTGATAGT 57.041 42.857 3.32 0.00 0.00 2.12
1724 1843 6.197276 ACACACTAAAGCGTGTCTATATACG 58.803 40.000 0.00 0.00 45.74 3.06
1845 2039 3.054361 AGGTTCCTCCATTAACGCTCATT 60.054 43.478 0.00 0.00 39.02 2.57
1910 2104 3.791973 ACAGGTGATCTCTCGTGATTC 57.208 47.619 8.44 0.00 0.00 2.52
1931 2125 0.171455 GTGCTCCCGTCTGTACTGAG 59.829 60.000 2.23 0.00 0.00 3.35
1991 2185 6.369340 GGGAAACTCTGTAAGCTAGTTCTTTC 59.631 42.308 0.00 0.00 32.42 2.62
2123 2317 6.484977 TGGATTTTGTGCATACGCTGATATTA 59.515 34.615 0.00 0.00 39.64 0.98
2268 2462 2.495155 ACATATGTGCTTGCCTGACA 57.505 45.000 7.78 0.00 0.00 3.58
2380 2574 2.393768 CGCATCTTCGCAAGCACCT 61.394 57.895 0.00 0.00 37.18 4.00
2564 2841 4.012374 TGGTCATGAGAAGGATTTTGCTC 58.988 43.478 0.00 0.00 0.00 4.26
2632 2909 0.737367 ACGATGACACAGTGATGCCG 60.737 55.000 7.81 7.94 0.00 5.69
2921 3203 5.779241 TTTGGAAGATACCATCCAGTTCT 57.221 39.130 0.00 0.00 45.94 3.01
2922 3204 5.779241 TTGGAAGATACCATCCAGTTCTT 57.221 39.130 0.00 0.00 45.94 2.52
2923 3205 5.779241 TGGAAGATACCATCCAGTTCTTT 57.221 39.130 0.00 0.00 40.74 2.52
2925 3207 6.552008 TGGAAGATACCATCCAGTTCTTTTT 58.448 36.000 0.00 0.00 40.74 1.94
2945 3227 6.879188 TTTTTCGAGAAAACGCAAAAAGAT 57.121 29.167 10.18 0.00 39.70 2.40
2946 3228 6.879188 TTTTCGAGAAAACGCAAAAAGATT 57.121 29.167 6.89 0.00 35.57 2.40
2947 3229 6.879188 TTTCGAGAAAACGCAAAAAGATTT 57.121 29.167 0.00 0.00 0.00 2.17
2948 3230 6.879188 TTCGAGAAAACGCAAAAAGATTTT 57.121 29.167 0.00 0.00 0.00 1.82
2949 3231 6.254600 TCGAGAAAACGCAAAAAGATTTTG 57.745 33.333 10.42 10.42 0.00 2.44
2960 3242 7.069829 GCAAAAAGATTTTGCGTTTCATTTC 57.930 32.000 20.62 0.00 44.13 2.17
2961 3243 6.686253 GCAAAAAGATTTTGCGTTTCATTTCA 59.314 30.769 20.62 0.00 44.13 2.69
2962 3244 7.376601 GCAAAAAGATTTTGCGTTTCATTTCAT 59.623 29.630 20.62 0.00 44.13 2.57
2963 3245 9.224058 CAAAAAGATTTTGCGTTTCATTTCATT 57.776 25.926 2.95 0.00 0.00 2.57
2964 3246 8.770850 AAAAGATTTTGCGTTTCATTTCATTG 57.229 26.923 0.00 0.00 0.00 2.82
2965 3247 7.712264 AAGATTTTGCGTTTCATTTCATTGA 57.288 28.000 0.00 0.00 0.00 2.57
2966 3248 7.712264 AGATTTTGCGTTTCATTTCATTGAA 57.288 28.000 0.00 0.00 33.89 2.69
2967 3249 8.140677 AGATTTTGCGTTTCATTTCATTGAAA 57.859 26.923 13.88 13.88 41.92 2.69
2968 3250 8.610896 AGATTTTGCGTTTCATTTCATTGAAAA 58.389 25.926 15.34 0.00 44.71 2.29
2969 3251 8.770850 ATTTTGCGTTTCATTTCATTGAAAAG 57.229 26.923 15.34 11.41 44.71 2.27
2970 3252 5.903764 TGCGTTTCATTTCATTGAAAAGG 57.096 34.783 15.34 10.89 44.71 3.11
2971 3253 5.595885 TGCGTTTCATTTCATTGAAAAGGA 58.404 33.333 15.34 12.80 44.71 3.36
2972 3254 5.691305 TGCGTTTCATTTCATTGAAAAGGAG 59.309 36.000 15.34 6.85 44.71 3.69
2973 3255 5.920273 GCGTTTCATTTCATTGAAAAGGAGA 59.080 36.000 15.34 8.97 44.71 3.71
2974 3256 6.420604 GCGTTTCATTTCATTGAAAAGGAGAA 59.579 34.615 15.34 13.28 44.71 2.87
2975 3257 7.358683 GCGTTTCATTTCATTGAAAAGGAGAAG 60.359 37.037 15.34 13.25 44.71 2.85
2976 3258 7.862372 CGTTTCATTTCATTGAAAAGGAGAAGA 59.138 33.333 15.34 3.74 44.71 2.87
2977 3259 9.189723 GTTTCATTTCATTGAAAAGGAGAAGAG 57.810 33.333 15.34 0.00 44.71 2.85
2978 3260 8.469309 TTCATTTCATTGAAAAGGAGAAGAGT 57.531 30.769 15.34 0.00 38.16 3.24
2979 3261 8.469309 TCATTTCATTGAAAAGGAGAAGAGTT 57.531 30.769 15.34 0.00 38.16 3.01
2980 3262 8.571336 TCATTTCATTGAAAAGGAGAAGAGTTC 58.429 33.333 15.34 0.00 38.16 3.01
2984 3266 5.540400 TTGAAAAGGAGAAGAGTTCGGTA 57.460 39.130 0.00 0.00 34.02 4.02
3017 3300 6.582672 GCATTTACCAGAACTAAAAGAACAGC 59.417 38.462 0.00 0.00 0.00 4.40
3038 3323 5.149054 GCAGTCAGCTGTGTACATAAATC 57.851 43.478 14.67 0.00 44.32 2.17
3076 3361 6.153510 TGCTATGATATCTATGACACCCACTC 59.846 42.308 3.98 0.00 0.00 3.51
3110 3395 3.058224 GTCTGTTGTTATTGTCACCAGCC 60.058 47.826 0.00 0.00 0.00 4.85
3238 3524 8.930760 GCTAAGCGATATATTGATCAGAAAGTT 58.069 33.333 3.97 0.00 0.00 2.66
3514 3800 9.778479 TGTTAGGTGCCATATATTATACTACCT 57.222 33.333 0.00 0.00 39.23 3.08
3517 3803 8.540507 AGGTGCCATATATTATACTACCTCTG 57.459 38.462 0.00 0.00 30.66 3.35
3519 3805 9.417561 GGTGCCATATATTATACTACCTCTGTA 57.582 37.037 0.00 0.00 0.00 2.74
3521 3807 9.417561 TGCCATATATTATACTACCTCTGTACC 57.582 37.037 0.00 0.00 0.00 3.34
3522 3808 9.417561 GCCATATATTATACTACCTCTGTACCA 57.582 37.037 0.00 0.00 0.00 3.25
3530 3816 9.570468 TTATACTACCTCTGTACCAAGATGTAG 57.430 37.037 17.06 17.06 44.50 2.74
3531 3817 6.075949 ACTACCTCTGTACCAAGATGTAGA 57.924 41.667 21.86 4.56 43.00 2.59
3532 3818 5.887035 ACTACCTCTGTACCAAGATGTAGAC 59.113 44.000 21.86 0.00 43.00 2.59
3533 3819 3.695060 ACCTCTGTACCAAGATGTAGACG 59.305 47.826 0.00 0.00 0.00 4.18
3534 3820 3.695060 CCTCTGTACCAAGATGTAGACGT 59.305 47.826 0.00 0.00 0.00 4.34
3535 3821 4.158025 CCTCTGTACCAAGATGTAGACGTT 59.842 45.833 0.00 0.00 0.00 3.99
3537 3823 6.092955 TCTGTACCAAGATGTAGACGTTTT 57.907 37.500 0.00 0.00 0.00 2.43
3538 3824 6.518493 TCTGTACCAAGATGTAGACGTTTTT 58.482 36.000 0.00 0.00 0.00 1.94
3563 3849 6.919721 TGGTTTTGCATAGGACATAGAAAAC 58.080 36.000 0.00 0.00 33.22 2.43
3584 3870 7.739498 AAACGTCTTACAGTTTGTTATGGAT 57.261 32.000 0.00 0.00 38.90 3.41
3585 3871 7.739498 AACGTCTTACAGTTTGTTATGGATT 57.261 32.000 0.00 0.00 0.00 3.01
3586 3872 7.129109 ACGTCTTACAGTTTGTTATGGATTG 57.871 36.000 0.00 0.00 0.00 2.67
3587 3873 6.932400 ACGTCTTACAGTTTGTTATGGATTGA 59.068 34.615 0.00 0.00 0.00 2.57
3598 3884 9.003658 GTTTGTTATGGATTGAGGGAGTATATG 57.996 37.037 0.00 0.00 0.00 1.78
3635 3921 8.540388 TGTTCTGAAGCTTATACTAAACTGGAT 58.460 33.333 0.00 0.00 0.00 3.41
3636 3922 8.821894 GTTCTGAAGCTTATACTAAACTGGATG 58.178 37.037 0.00 0.00 0.00 3.51
3744 4030 4.344968 ACTGAAAAGGAGGTTTGAAATGGG 59.655 41.667 0.00 0.00 0.00 4.00
3796 4089 7.175990 CAGTTGGCACTTTCCCTTTAACTATTA 59.824 37.037 0.00 0.00 0.00 0.98
3810 4106 9.769093 CCTTTAACTATTAATTCTTGTTGTCCG 57.231 33.333 0.00 0.00 0.00 4.79
4034 4330 1.556911 ACTCCCTGTGCAGAATGTAGG 59.443 52.381 0.02 0.00 39.31 3.18
4060 4356 7.832503 GCAACCTGCATAATTTTTCTAATGT 57.167 32.000 0.00 0.00 44.26 2.71
4098 4394 3.472652 ACTGAACTTAACCATGAACGCA 58.527 40.909 0.00 0.00 0.00 5.24
4105 4401 5.339990 ACTTAACCATGAACGCATAATTGC 58.660 37.500 0.00 0.00 45.78 3.56
4121 4417 7.688478 CATAATTGCAACATGACTTGGTATG 57.312 36.000 14.82 0.00 0.00 2.39
4122 4418 5.726980 AATTGCAACATGACTTGGTATGT 57.273 34.783 0.00 0.00 39.08 2.29
4159 4455 5.700402 TCCTAAGCTAGAATTTTCTGCCT 57.300 39.130 3.07 0.00 38.19 4.75
4252 4556 8.031848 ACATATTATTGCCTTTGTTTTGCTTG 57.968 30.769 0.00 0.00 0.00 4.01
4426 4731 2.817396 GAGCGGCTTCTCCTGCAC 60.817 66.667 2.97 0.00 37.01 4.57
4482 4788 1.679559 GATTTGCTCATGCCCCACCC 61.680 60.000 0.00 0.00 38.71 4.61
4483 4789 2.458969 ATTTGCTCATGCCCCACCCA 62.459 55.000 0.00 0.00 38.71 4.51
4622 4928 2.010582 GCCACCCACAAGCGTTCAAA 62.011 55.000 0.00 0.00 0.00 2.69
4631 4937 0.668535 AAGCGTTCAAACTGAAGGGC 59.331 50.000 10.19 7.46 41.17 5.19
4632 4938 0.465460 AGCGTTCAAACTGAAGGGCA 60.465 50.000 10.19 0.00 41.17 5.36
4633 4939 0.317854 GCGTTCAAACTGAAGGGCAC 60.318 55.000 10.19 0.00 41.17 5.01
4634 4940 1.021202 CGTTCAAACTGAAGGGCACA 58.979 50.000 0.00 0.00 37.00 4.57
4635 4941 1.608590 CGTTCAAACTGAAGGGCACAT 59.391 47.619 0.00 0.00 37.00 3.21
4636 4942 2.350772 CGTTCAAACTGAAGGGCACATC 60.351 50.000 0.00 0.00 37.00 3.06
4682 4988 6.984474 TGTGTAAGAAGAGGTTTACAGTTCTG 59.016 38.462 0.00 0.00 39.63 3.02
4698 5004 9.529325 TTACAGTTCTGTCATATTAGCATGTAC 57.471 33.333 8.80 0.00 0.00 2.90
4699 5005 7.786030 ACAGTTCTGTCATATTAGCATGTACT 58.214 34.615 0.00 0.00 0.00 2.73
4700 5006 8.914011 ACAGTTCTGTCATATTAGCATGTACTA 58.086 33.333 0.00 0.00 0.00 1.82
4772 5078 7.441890 TTGTTTCCAAGAAGATTACGCAATA 57.558 32.000 0.00 0.00 0.00 1.90
4806 5112 2.806019 GCGCCATGATGACAAGAGAGAT 60.806 50.000 0.00 0.00 0.00 2.75
4813 5119 5.344743 TGATGACAAGAGAGATAACACCC 57.655 43.478 0.00 0.00 0.00 4.61
4852 5158 7.891712 TGATCCCCATCGTCAAACTATACTATA 59.108 37.037 0.00 0.00 0.00 1.31
4907 5217 4.402155 TGGGAAGCCAATAAATACTGCTTG 59.598 41.667 0.00 0.00 41.97 4.01
4912 5222 7.362920 GGAAGCCAATAAATACTGCTTGAAGAA 60.363 37.037 0.00 0.00 41.97 2.52
4914 5224 7.710896 AGCCAATAAATACTGCTTGAAGAATC 58.289 34.615 0.00 0.00 0.00 2.52
4997 5307 1.611673 CGGCTTTCCTGACAAGACCAT 60.612 52.381 0.00 0.00 0.00 3.55
5064 5387 5.488341 TGTAATTCCTGCTACTTGGAACTC 58.512 41.667 0.00 0.00 44.02 3.01
5184 5507 3.411446 CATCTTGGTAGTTGGCACTGAA 58.589 45.455 0.00 0.00 34.06 3.02
5210 5533 2.211806 GAGCTTCATCATCCAGTGCTC 58.788 52.381 0.00 0.00 38.58 4.26
5228 5551 1.065102 CTCGAATTTGATGCCAGGCTG 59.935 52.381 14.15 7.75 0.00 4.85
5229 5552 0.526954 CGAATTTGATGCCAGGCTGC 60.527 55.000 14.15 5.00 0.00 5.25
5237 5560 2.034687 GCCAGGCTGCTCCTTTCA 59.965 61.111 9.56 0.00 44.75 2.69
5240 5563 0.600057 CCAGGCTGCTCCTTTCAAAC 59.400 55.000 9.56 0.00 44.75 2.93
5251 5577 5.040635 GCTCCTTTCAAACAAAATTCGTCA 58.959 37.500 0.00 0.00 0.00 4.35
5264 5590 1.934220 TTCGTCAGTGCCTAGAGCCG 61.934 60.000 0.00 0.00 42.71 5.52
5265 5591 2.407428 CGTCAGTGCCTAGAGCCGA 61.407 63.158 0.00 0.00 42.71 5.54
5321 5663 3.059665 GTGCCAGCAAAAAGGAAAATTCG 60.060 43.478 0.00 0.00 0.00 3.34
5384 5726 5.647589 CCTTGCATAGACGACAAGTAACTA 58.352 41.667 0.00 0.00 39.30 2.24
5385 5727 5.515626 CCTTGCATAGACGACAAGTAACTAC 59.484 44.000 0.00 0.00 39.30 2.73
5386 5728 5.892160 TGCATAGACGACAAGTAACTACT 57.108 39.130 0.00 0.00 38.39 2.57
5387 5729 5.637809 TGCATAGACGACAAGTAACTACTG 58.362 41.667 0.00 0.00 36.50 2.74
5388 5730 5.182570 TGCATAGACGACAAGTAACTACTGT 59.817 40.000 0.00 0.00 36.50 3.55
5389 5731 6.372381 TGCATAGACGACAAGTAACTACTGTA 59.628 38.462 0.00 0.00 36.50 2.74
5390 5732 6.686253 GCATAGACGACAAGTAACTACTGTAC 59.314 42.308 0.00 0.00 36.50 2.90
5391 5733 7.413877 GCATAGACGACAAGTAACTACTGTACT 60.414 40.741 0.00 0.00 36.50 2.73
5406 5748 5.012328 ACTGTACTAACTATCAGCAAGCC 57.988 43.478 0.00 0.00 0.00 4.35
5445 5787 6.830838 CACTAAAATAGGAGGCCTTCAATCTT 59.169 38.462 15.31 3.75 34.61 2.40
5451 5793 0.035056 AGGCCTTCAATCTTGACCCG 60.035 55.000 0.00 0.00 36.83 5.28
5463 5806 2.435069 TCTTGACCCGACACTACCAAAA 59.565 45.455 0.00 0.00 0.00 2.44
5472 5815 4.495184 CCGACACTACCAAAACTCAACAAC 60.495 45.833 0.00 0.00 0.00 3.32
5474 5817 5.391097 CGACACTACCAAAACTCAACAACAA 60.391 40.000 0.00 0.00 0.00 2.83
5475 5818 6.524101 ACACTACCAAAACTCAACAACAAT 57.476 33.333 0.00 0.00 0.00 2.71
5476 5819 6.329496 ACACTACCAAAACTCAACAACAATG 58.671 36.000 0.00 0.00 0.00 2.82
5485 5832 3.507233 ACTCAACAACAATGCTACATGGG 59.493 43.478 0.00 0.00 0.00 4.00
5537 5884 4.243383 GCCATTGCGACCAAACAC 57.757 55.556 0.00 0.00 34.05 3.32
5585 5932 1.822990 TCCCTGACACGGTCAATACTC 59.177 52.381 7.90 0.00 42.26 2.59
5586 5933 1.548719 CCCTGACACGGTCAATACTCA 59.451 52.381 7.90 0.00 42.26 3.41
5587 5934 2.028476 CCCTGACACGGTCAATACTCAA 60.028 50.000 7.90 0.00 42.26 3.02
5588 5935 3.369471 CCCTGACACGGTCAATACTCAAT 60.369 47.826 7.90 0.00 42.26 2.57
5589 5936 4.142026 CCCTGACACGGTCAATACTCAATA 60.142 45.833 7.90 0.00 42.26 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.583806 CACTGACTGCATTTTACCATTTTCTC 59.416 38.462 0.00 0.00 0.00 2.87
33 35 5.464722 GCATCTATTGTGTATCCACTGACTG 59.535 44.000 0.00 0.00 42.34 3.51
51 53 2.809446 CGTGAACGGAATCAGCATCTA 58.191 47.619 0.00 0.00 35.37 1.98
111 113 7.773224 TGTGTATGCTTAATAGTGCCAGTTAAT 59.227 33.333 0.00 0.00 0.00 1.40
112 114 7.106890 TGTGTATGCTTAATAGTGCCAGTTAA 58.893 34.615 0.00 0.00 0.00 2.01
125 127 7.265673 GTCTAGAATGTCCTGTGTATGCTTAA 58.734 38.462 0.00 0.00 0.00 1.85
134 136 2.492088 TCACGGTCTAGAATGTCCTGTG 59.508 50.000 11.31 11.31 0.00 3.66
139 141 6.910536 AAATTGATCACGGTCTAGAATGTC 57.089 37.500 0.00 0.00 0.00 3.06
144 174 8.038351 TGAATGTAAAATTGATCACGGTCTAGA 58.962 33.333 0.00 0.00 0.00 2.43
155 185 8.308931 ACATGCTGTTCTGAATGTAAAATTGAT 58.691 29.630 0.00 0.00 34.62 2.57
182 212 6.537301 CCCGTTATCAGTGCTTAAAGATTGTA 59.463 38.462 0.00 0.00 0.00 2.41
183 213 5.354234 CCCGTTATCAGTGCTTAAAGATTGT 59.646 40.000 0.00 0.00 0.00 2.71
184 214 5.584649 TCCCGTTATCAGTGCTTAAAGATTG 59.415 40.000 0.00 0.00 0.00 2.67
186 216 5.353394 TCCCGTTATCAGTGCTTAAAGAT 57.647 39.130 0.00 0.00 0.00 2.40
187 217 4.811969 TCCCGTTATCAGTGCTTAAAGA 57.188 40.909 0.00 0.00 0.00 2.52
188 218 5.817816 AGAATCCCGTTATCAGTGCTTAAAG 59.182 40.000 0.00 0.00 0.00 1.85
191 221 4.499188 CGAGAATCCCGTTATCAGTGCTTA 60.499 45.833 0.00 0.00 0.00 3.09
205 237 4.345547 AGGAGATTAGGAAACGAGAATCCC 59.654 45.833 0.00 0.00 36.31 3.85
207 239 5.755861 CCAAGGAGATTAGGAAACGAGAATC 59.244 44.000 0.00 0.00 32.38 2.52
213 245 4.473477 ACTCCAAGGAGATTAGGAAACG 57.527 45.455 22.34 0.00 44.53 3.60
237 283 5.590530 AACTGCATTGTACCAGTTTGAAA 57.409 34.783 8.82 0.00 46.86 2.69
272 318 5.112220 TGTGACTTGTGATTCTCATTTGC 57.888 39.130 0.00 0.00 0.00 3.68
275 321 5.618418 CGCATTGTGACTTGTGATTCTCATT 60.618 40.000 0.00 0.00 0.00 2.57
302 348 4.451435 GGTTTCTCCTCTTAGTTTCGGTTG 59.549 45.833 0.00 0.00 0.00 3.77
449 498 1.268899 CTTCTTGCAGTTTCCAGGCTG 59.731 52.381 7.75 7.75 35.93 4.85
498 547 3.269347 ACACACACTGCGCGGTTC 61.269 61.111 21.75 0.00 0.00 3.62
570 621 3.038280 CTCCTCATCCTCCTCGCG 58.962 66.667 0.00 0.00 0.00 5.87
571 622 2.086251 CTGCTCCTCATCCTCCTCGC 62.086 65.000 0.00 0.00 0.00 5.03
591 642 3.866582 GTCCCCCTCATCCCGCTG 61.867 72.222 0.00 0.00 0.00 5.18
729 788 0.179215 GAGTTTGGAGCGCACGAATG 60.179 55.000 11.47 0.00 0.00 2.67
737 796 2.275318 GAATCTCTGGAGTTTGGAGCG 58.725 52.381 0.00 0.00 0.00 5.03
759 818 0.322906 CCCTCCTTCCCTTGCTTCAC 60.323 60.000 0.00 0.00 0.00 3.18
762 821 0.550147 TAGCCCTCCTTCCCTTGCTT 60.550 55.000 0.00 0.00 0.00 3.91
784 843 7.230849 TCTTGTGAAGTTGGATATTTGCATT 57.769 32.000 0.00 0.00 0.00 3.56
804 863 8.067189 GCTCTACTTTTTCTGAGAAAGTTCTTG 58.933 37.037 25.29 16.13 42.90 3.02
808 867 6.261158 GGTGCTCTACTTTTTCTGAGAAAGTT 59.739 38.462 25.29 13.36 42.90 2.66
812 871 4.307432 CGGTGCTCTACTTTTTCTGAGAA 58.693 43.478 0.00 0.00 0.00 2.87
817 876 1.071699 TGGCGGTGCTCTACTTTTTCT 59.928 47.619 0.00 0.00 0.00 2.52
818 877 1.197036 GTGGCGGTGCTCTACTTTTTC 59.803 52.381 0.00 0.00 0.00 2.29
837 896 1.079819 CAGAATCACTCGGTGGCGT 60.080 57.895 4.52 0.00 33.87 5.68
847 907 2.478831 GCTCGGGAGAATCAGAATCAC 58.521 52.381 0.00 0.00 39.18 3.06
1138 1218 4.452733 GGGGTGAACGGAGGAGCG 62.453 72.222 0.00 0.00 0.00 5.03
1275 1368 3.082579 GCTAGGCAGACGGTGGAGG 62.083 68.421 0.00 0.00 0.00 4.30
1285 1378 1.298713 CGTCTACGCAGCTAGGCAG 60.299 63.158 0.00 0.00 0.00 4.85
1294 1387 2.202557 CCGATGCACGTCTACGCA 60.203 61.111 1.74 0.39 44.43 5.24
1295 1388 2.101575 TCCGATGCACGTCTACGC 59.898 61.111 1.74 0.00 44.43 4.42
1297 1390 0.102481 ATGGTCCGATGCACGTCTAC 59.898 55.000 0.00 0.00 40.78 2.59
1353 1446 1.109323 GGCCCCATTTGGAGGAATCG 61.109 60.000 0.00 0.00 37.39 3.34
1452 1545 0.400213 TGTTTCCTACCACCAGCAGG 59.600 55.000 0.00 0.00 42.21 4.85
1640 1758 4.960469 ACGGAGGGAGTATCAAACTATCAA 59.040 41.667 0.00 0.00 39.07 2.57
1641 1759 4.543689 ACGGAGGGAGTATCAAACTATCA 58.456 43.478 0.00 0.00 39.07 2.15
1642 1760 5.068723 TGAACGGAGGGAGTATCAAACTATC 59.931 44.000 0.00 0.00 39.07 2.08
1643 1761 4.960469 TGAACGGAGGGAGTATCAAACTAT 59.040 41.667 0.00 0.00 39.07 2.12
1644 1762 4.159135 GTGAACGGAGGGAGTATCAAACTA 59.841 45.833 0.00 0.00 39.07 2.24
1645 1763 3.056035 GTGAACGGAGGGAGTATCAAACT 60.056 47.826 0.00 0.00 42.80 2.66
1646 1764 3.259902 GTGAACGGAGGGAGTATCAAAC 58.740 50.000 0.00 0.00 36.25 2.93
1647 1765 2.901192 TGTGAACGGAGGGAGTATCAAA 59.099 45.455 0.00 0.00 36.25 2.69
1746 1865 9.888878 CTCCGTTCATAAATATAAGACGTTCTA 57.111 33.333 0.00 0.00 0.00 2.10
1748 1867 7.115947 CCCTCCGTTCATAAATATAAGACGTTC 59.884 40.741 0.00 0.00 0.00 3.95
1749 1868 6.927381 CCCTCCGTTCATAAATATAAGACGTT 59.073 38.462 0.00 0.00 0.00 3.99
1750 1869 6.266103 TCCCTCCGTTCATAAATATAAGACGT 59.734 38.462 0.00 0.00 0.00 4.34
1751 1870 6.684686 TCCCTCCGTTCATAAATATAAGACG 58.315 40.000 0.00 0.00 0.00 4.18
1845 2039 2.596904 GCTGTACGAGCCAATTAGGA 57.403 50.000 6.14 0.00 42.54 2.94
1931 2125 4.097892 CCCAAATTATGCACCTGGTACTTC 59.902 45.833 0.00 0.00 0.00 3.01
2098 2292 2.431454 TCAGCGTATGCACAAAATCCA 58.569 42.857 10.11 0.00 46.23 3.41
2123 2317 0.239347 GCAAACTGAATGCAGAGCGT 59.761 50.000 8.02 0.00 45.17 5.07
2195 2389 9.384764 AGATTAAAGGAACATAGTTTCTACAGC 57.615 33.333 0.00 0.00 0.00 4.40
2247 2441 3.940852 CTGTCAGGCAAGCACATATGTTA 59.059 43.478 5.37 0.00 0.00 2.41
2251 2445 1.064906 AGCTGTCAGGCAAGCACATAT 60.065 47.619 1.14 0.00 34.17 1.78
2380 2574 3.541632 GGTAACTAGCCAAGCAGCATAA 58.458 45.455 0.00 0.00 34.23 1.90
2592 2869 6.074642 TCGTAGTGAAAACAAAATGCATACG 58.925 36.000 0.00 1.13 35.02 3.06
2632 2909 2.893489 ACCCTTCCTGCAAGTGAAAATC 59.107 45.455 0.00 0.00 0.00 2.17
2828 3108 1.340211 ACACCAGGACACGGACAAAAA 60.340 47.619 0.00 0.00 0.00 1.94
2922 3204 6.879188 ATCTTTTTGCGTTTTCTCGAAAAA 57.121 29.167 6.41 1.59 43.62 1.94
2923 3205 6.879188 AATCTTTTTGCGTTTTCTCGAAAA 57.121 29.167 0.93 0.93 36.69 2.29
2925 3207 6.691442 CAAAATCTTTTTGCGTTTTCTCGAA 58.309 32.000 0.26 0.00 0.00 3.71
2926 3208 5.276161 GCAAAATCTTTTTGCGTTTTCTCGA 60.276 36.000 18.52 0.00 44.13 4.04
2927 3209 4.892323 GCAAAATCTTTTTGCGTTTTCTCG 59.108 37.500 18.52 0.00 44.13 4.04
2937 3219 8.770850 ATGAAATGAAACGCAAAATCTTTTTG 57.229 26.923 8.07 8.07 0.00 2.44
2938 3220 9.224058 CAATGAAATGAAACGCAAAATCTTTTT 57.776 25.926 0.00 0.00 0.00 1.94
2939 3221 8.610896 TCAATGAAATGAAACGCAAAATCTTTT 58.389 25.926 0.00 0.00 0.00 2.27
2940 3222 8.140677 TCAATGAAATGAAACGCAAAATCTTT 57.859 26.923 0.00 0.00 0.00 2.52
2941 3223 7.712264 TCAATGAAATGAAACGCAAAATCTT 57.288 28.000 0.00 0.00 0.00 2.40
2942 3224 7.712264 TTCAATGAAATGAAACGCAAAATCT 57.288 28.000 0.00 0.00 36.42 2.40
2943 3225 8.765044 TTTTCAATGAAATGAAACGCAAAATC 57.235 26.923 9.41 0.00 46.06 2.17
2944 3226 7.856894 CCTTTTCAATGAAATGAAACGCAAAAT 59.143 29.630 19.20 0.00 46.06 1.82
2945 3227 7.065085 TCCTTTTCAATGAAATGAAACGCAAAA 59.935 29.630 19.20 0.00 46.06 2.44
2946 3228 6.536582 TCCTTTTCAATGAAATGAAACGCAAA 59.463 30.769 19.20 0.00 46.06 3.68
2947 3229 6.045318 TCCTTTTCAATGAAATGAAACGCAA 58.955 32.000 19.20 0.00 46.06 4.85
2948 3230 5.595885 TCCTTTTCAATGAAATGAAACGCA 58.404 33.333 19.20 0.00 46.06 5.24
2949 3231 5.920273 TCTCCTTTTCAATGAAATGAAACGC 59.080 36.000 19.20 0.00 46.06 4.84
2950 3232 7.862372 TCTTCTCCTTTTCAATGAAATGAAACG 59.138 33.333 19.20 6.32 46.06 3.60
2951 3233 9.189723 CTCTTCTCCTTTTCAATGAAATGAAAC 57.810 33.333 19.20 0.00 46.06 2.78
2952 3234 8.917088 ACTCTTCTCCTTTTCAATGAAATGAAA 58.083 29.630 19.20 11.17 45.07 2.69
2953 3235 8.469309 ACTCTTCTCCTTTTCAATGAAATGAA 57.531 30.769 19.20 14.43 37.53 2.57
2954 3236 8.469309 AACTCTTCTCCTTTTCAATGAAATGA 57.531 30.769 19.20 13.29 31.34 2.57
2955 3237 7.536622 CGAACTCTTCTCCTTTTCAATGAAATG 59.463 37.037 9.41 11.40 31.34 2.32
2956 3238 7.308830 CCGAACTCTTCTCCTTTTCAATGAAAT 60.309 37.037 9.41 0.00 31.34 2.17
2957 3239 6.017109 CCGAACTCTTCTCCTTTTCAATGAAA 60.017 38.462 4.03 4.03 0.00 2.69
2958 3240 5.470098 CCGAACTCTTCTCCTTTTCAATGAA 59.530 40.000 0.00 0.00 0.00 2.57
2959 3241 4.997395 CCGAACTCTTCTCCTTTTCAATGA 59.003 41.667 0.00 0.00 0.00 2.57
2960 3242 4.757149 ACCGAACTCTTCTCCTTTTCAATG 59.243 41.667 0.00 0.00 0.00 2.82
2961 3243 4.974399 ACCGAACTCTTCTCCTTTTCAAT 58.026 39.130 0.00 0.00 0.00 2.57
2962 3244 4.417426 ACCGAACTCTTCTCCTTTTCAA 57.583 40.909 0.00 0.00 0.00 2.69
2963 3245 4.342951 TGTACCGAACTCTTCTCCTTTTCA 59.657 41.667 0.00 0.00 0.00 2.69
2964 3246 4.879598 TGTACCGAACTCTTCTCCTTTTC 58.120 43.478 0.00 0.00 0.00 2.29
2965 3247 4.950205 TGTACCGAACTCTTCTCCTTTT 57.050 40.909 0.00 0.00 0.00 2.27
2966 3248 4.950205 TTGTACCGAACTCTTCTCCTTT 57.050 40.909 0.00 0.00 0.00 3.11
2967 3249 4.950205 TTTGTACCGAACTCTTCTCCTT 57.050 40.909 0.00 0.00 0.00 3.36
2968 3250 5.127356 CCTATTTGTACCGAACTCTTCTCCT 59.873 44.000 0.00 0.00 0.00 3.69
2969 3251 5.349809 CCTATTTGTACCGAACTCTTCTCC 58.650 45.833 0.00 0.00 0.00 3.71
2970 3252 4.804665 GCCTATTTGTACCGAACTCTTCTC 59.195 45.833 0.00 0.00 0.00 2.87
2971 3253 4.222145 TGCCTATTTGTACCGAACTCTTCT 59.778 41.667 0.00 0.00 0.00 2.85
2972 3254 4.501071 TGCCTATTTGTACCGAACTCTTC 58.499 43.478 0.00 0.00 0.00 2.87
2973 3255 4.546829 TGCCTATTTGTACCGAACTCTT 57.453 40.909 0.00 0.00 0.00 2.85
2974 3256 4.755266 ATGCCTATTTGTACCGAACTCT 57.245 40.909 0.00 0.00 0.00 3.24
2975 3257 5.813080 AAATGCCTATTTGTACCGAACTC 57.187 39.130 0.00 0.00 35.26 3.01
2976 3258 5.587443 GGTAAATGCCTATTTGTACCGAACT 59.413 40.000 0.00 0.00 37.12 3.01
2977 3259 5.354792 TGGTAAATGCCTATTTGTACCGAAC 59.645 40.000 0.00 0.00 37.57 3.95
2978 3260 5.498393 TGGTAAATGCCTATTTGTACCGAA 58.502 37.500 0.00 0.00 37.57 4.30
2979 3261 5.100344 TGGTAAATGCCTATTTGTACCGA 57.900 39.130 0.00 0.00 37.57 4.69
2980 3262 5.120399 TCTGGTAAATGCCTATTTGTACCG 58.880 41.667 0.00 0.00 37.57 4.02
2984 3266 8.644374 TTTAGTTCTGGTAAATGCCTATTTGT 57.356 30.769 0.00 0.00 37.12 2.83
3076 3361 8.926710 ACAATAACAACAGACTAATCTTCGAAG 58.073 33.333 19.35 19.35 30.42 3.79
3238 3524 6.037830 GCAAAGTCCAACTTACAACTAACTCA 59.962 38.462 0.00 0.00 37.47 3.41
3396 3682 2.260822 AGCGAGCACCCCATCTATAAT 58.739 47.619 0.00 0.00 0.00 1.28
3437 3723 2.099141 TGCAGTGCATAGGACAACTC 57.901 50.000 15.37 0.00 31.71 3.01
3505 3791 8.942033 TCTACATCTTGGTACAGAGGTAGTATA 58.058 37.037 23.44 10.61 43.75 1.47
3512 3798 3.695060 ACGTCTACATCTTGGTACAGAGG 59.305 47.826 0.00 0.00 42.39 3.69
3513 3799 4.966965 ACGTCTACATCTTGGTACAGAG 57.033 45.455 0.00 0.00 42.39 3.35
3514 3800 5.717078 AAACGTCTACATCTTGGTACAGA 57.283 39.130 0.00 0.00 42.39 3.41
3515 3801 6.780706 AAAAACGTCTACATCTTGGTACAG 57.219 37.500 0.00 0.00 42.39 2.74
3535 3821 7.531857 TCTATGTCCTATGCAAAACCAAAAA 57.468 32.000 0.00 0.00 0.00 1.94
3537 3823 7.531857 TTTCTATGTCCTATGCAAAACCAAA 57.468 32.000 0.00 0.00 0.00 3.28
3538 3824 7.375053 GTTTTCTATGTCCTATGCAAAACCAA 58.625 34.615 0.00 0.00 0.00 3.67
3539 3825 6.348950 CGTTTTCTATGTCCTATGCAAAACCA 60.349 38.462 0.00 0.00 31.49 3.67
3540 3826 6.027749 CGTTTTCTATGTCCTATGCAAAACC 58.972 40.000 0.00 0.00 31.49 3.27
3541 3827 6.608610 ACGTTTTCTATGTCCTATGCAAAAC 58.391 36.000 0.00 0.00 0.00 2.43
3542 3828 6.653320 AGACGTTTTCTATGTCCTATGCAAAA 59.347 34.615 0.00 0.00 42.68 2.44
3543 3829 6.170506 AGACGTTTTCTATGTCCTATGCAAA 58.829 36.000 0.00 0.00 42.68 3.68
3544 3830 5.730550 AGACGTTTTCTATGTCCTATGCAA 58.269 37.500 0.00 0.00 42.68 4.08
3545 3831 5.339008 AGACGTTTTCTATGTCCTATGCA 57.661 39.130 0.00 0.00 42.68 3.96
3546 3832 6.755141 TGTAAGACGTTTTCTATGTCCTATGC 59.245 38.462 0.00 0.00 42.68 3.14
3547 3833 7.974501 ACTGTAAGACGTTTTCTATGTCCTATG 59.025 37.037 0.00 0.00 42.68 2.23
3548 3834 8.064336 ACTGTAAGACGTTTTCTATGTCCTAT 57.936 34.615 0.00 0.00 42.68 2.57
3549 3835 7.458409 ACTGTAAGACGTTTTCTATGTCCTA 57.542 36.000 0.00 0.00 42.68 2.94
3550 3836 6.342338 ACTGTAAGACGTTTTCTATGTCCT 57.658 37.500 0.00 0.00 42.68 3.85
3551 3837 7.042254 ACAAACTGTAAGACGTTTTCTATGTCC 60.042 37.037 0.00 0.00 42.68 4.02
3552 3838 7.848491 ACAAACTGTAAGACGTTTTCTATGTC 58.152 34.615 0.00 0.00 42.13 3.06
3553 3839 7.781548 ACAAACTGTAAGACGTTTTCTATGT 57.218 32.000 0.00 0.00 37.43 2.29
3556 3842 8.767085 CCATAACAAACTGTAAGACGTTTTCTA 58.233 33.333 0.00 0.00 37.43 2.10
3557 3843 7.496591 TCCATAACAAACTGTAAGACGTTTTCT 59.503 33.333 0.00 0.00 37.43 2.52
3558 3844 7.632721 TCCATAACAAACTGTAAGACGTTTTC 58.367 34.615 0.00 0.00 37.43 2.29
3563 3849 7.359262 TCAATCCATAACAAACTGTAAGACG 57.641 36.000 0.00 0.00 37.43 4.18
3584 3870 9.948964 CATAAATCATGTCATATACTCCCTCAA 57.051 33.333 0.00 0.00 0.00 3.02
3585 3871 9.104713 ACATAAATCATGTCATATACTCCCTCA 57.895 33.333 0.00 0.00 44.99 3.86
3674 3960 8.394971 TCATTCAATACCATCGATGCTTTTAT 57.605 30.769 20.25 9.92 0.00 1.40
3716 4002 5.835113 TCAAACCTCCTTTTCAGTTGAAG 57.165 39.130 0.00 0.00 35.21 3.02
3796 4089 7.961325 ATTTAAATTGCGGACAACAAGAATT 57.039 28.000 0.00 0.00 38.99 2.17
3850 4146 4.961438 AACAACATGCTCCAAAAGGAAT 57.039 36.364 0.00 0.00 0.00 3.01
3861 4157 0.311790 CGACCTGCAAACAACATGCT 59.688 50.000 0.00 0.00 44.14 3.79
4079 4375 6.751514 ATTATGCGTTCATGGTTAAGTTCA 57.248 33.333 0.00 0.00 34.22 3.18
4098 4394 7.408756 ACATACCAAGTCATGTTGCAATTAT 57.591 32.000 0.59 0.00 31.32 1.28
4105 4401 9.859427 ATTATTGAAACATACCAAGTCATGTTG 57.141 29.630 1.06 0.00 42.93 3.33
4137 4433 5.700402 AGGCAGAAAATTCTAGCTTAGGA 57.300 39.130 0.00 0.00 35.34 2.94
4149 4445 6.016276 CCAGTTTACTGTTGTAGGCAGAAAAT 60.016 38.462 8.91 0.00 42.27 1.82
4180 4484 1.549203 ACTTCTGCGCCCAATGATTT 58.451 45.000 4.18 0.00 0.00 2.17
4181 4485 2.418368 TACTTCTGCGCCCAATGATT 57.582 45.000 4.18 0.00 0.00 2.57
4182 4486 2.645838 ATACTTCTGCGCCCAATGAT 57.354 45.000 4.18 0.00 0.00 2.45
4183 4487 3.552132 TTATACTTCTGCGCCCAATGA 57.448 42.857 4.18 0.00 0.00 2.57
4184 4488 5.940192 TTATTATACTTCTGCGCCCAATG 57.060 39.130 4.18 0.00 0.00 2.82
4225 4529 8.031848 AGCAAAACAAAGGCAATAATATGTTG 57.968 30.769 0.00 0.00 31.90 3.33
4227 4531 7.661027 ACAAGCAAAACAAAGGCAATAATATGT 59.339 29.630 0.00 0.00 0.00 2.29
4252 4556 4.946784 CACTAATTAGTGCAGGGAACAC 57.053 45.455 27.90 0.00 46.03 3.32
4445 4750 2.951457 TCGGTATGTCATTCGCAGAA 57.049 45.000 0.00 0.00 45.90 3.02
4455 4761 2.031682 GGCATGAGCAAATCGGTATGTC 60.032 50.000 0.00 0.00 44.61 3.06
4482 4788 0.325671 TAGCCTCCTGAGAAGGGGTG 60.326 60.000 0.00 0.00 0.00 4.61
4483 4789 0.325765 GTAGCCTCCTGAGAAGGGGT 60.326 60.000 0.00 0.00 0.00 4.95
4622 4928 0.700564 ATGTGGATGTGCCCTTCAGT 59.299 50.000 0.00 0.00 34.97 3.41
4698 5004 9.612620 GGTGACAAGACTTTTTGTGATTTATAG 57.387 33.333 0.00 0.00 41.15 1.31
4699 5005 9.349713 AGGTGACAAGACTTTTTGTGATTTATA 57.650 29.630 0.00 0.00 41.15 0.98
4700 5006 8.237811 AGGTGACAAGACTTTTTGTGATTTAT 57.762 30.769 0.00 0.00 41.15 1.40
4772 5078 3.780173 GGCGCTCTCAGCTTCCCT 61.780 66.667 7.64 0.00 39.60 4.20
4806 5112 2.777972 CGGCGATCTCCGGGTGTTA 61.778 63.158 16.46 0.00 45.38 2.41
4907 5217 8.140628 TCAAGATCTATACAGTGCAGATTCTTC 58.859 37.037 0.00 0.00 0.00 2.87
4912 5222 6.326064 ACCTTCAAGATCTATACAGTGCAGAT 59.674 38.462 0.00 2.93 0.00 2.90
4914 5224 5.911752 ACCTTCAAGATCTATACAGTGCAG 58.088 41.667 0.00 0.00 0.00 4.41
5003 5313 1.134946 CAAACCGATGATGAAAGCCCC 59.865 52.381 0.00 0.00 0.00 5.80
5015 5325 4.199310 CAGATACCATCCAACAAACCGAT 58.801 43.478 0.00 0.00 0.00 4.18
5064 5387 5.570320 TGATTCTAAAAGGGAAGGAACCAG 58.430 41.667 0.00 0.00 0.00 4.00
5167 5490 1.213182 TGGTTCAGTGCCAACTACCAA 59.787 47.619 0.00 0.00 40.55 3.67
5184 5507 0.179000 GGATGATGAAGCTCGGTGGT 59.821 55.000 0.00 0.00 0.00 4.16
5210 5533 0.526954 GCAGCCTGGCATCAAATTCG 60.527 55.000 22.65 0.00 0.00 3.34
5228 5551 5.040635 TGACGAATTTTGTTTGAAAGGAGC 58.959 37.500 0.00 0.00 0.00 4.70
5229 5552 6.197096 CACTGACGAATTTTGTTTGAAAGGAG 59.803 38.462 0.00 0.00 0.00 3.69
5237 5560 4.819630 TCTAGGCACTGACGAATTTTGTTT 59.180 37.500 0.00 0.00 41.52 2.83
5240 5563 3.181516 GCTCTAGGCACTGACGAATTTTG 60.182 47.826 0.00 0.00 41.52 2.44
5251 5577 0.396417 ATGAGTCGGCTCTAGGCACT 60.396 55.000 19.37 6.38 44.01 4.40
5264 5590 5.269505 ACTTCCTGCACAGTATATGAGTC 57.730 43.478 0.00 0.00 0.00 3.36
5265 5591 5.187772 TCAACTTCCTGCACAGTATATGAGT 59.812 40.000 0.00 0.00 0.00 3.41
5321 5663 4.635765 TGACATGAGATGAATCGGTTTTCC 59.364 41.667 0.00 0.00 0.00 3.13
5384 5726 4.440250 CGGCTTGCTGATAGTTAGTACAGT 60.440 45.833 0.00 0.00 33.57 3.55
5385 5727 4.045104 CGGCTTGCTGATAGTTAGTACAG 58.955 47.826 0.00 0.00 0.00 2.74
5386 5728 3.697542 TCGGCTTGCTGATAGTTAGTACA 59.302 43.478 0.00 0.00 0.00 2.90
5387 5729 4.291783 CTCGGCTTGCTGATAGTTAGTAC 58.708 47.826 4.48 0.00 0.00 2.73
5388 5730 3.318275 CCTCGGCTTGCTGATAGTTAGTA 59.682 47.826 4.48 0.00 0.00 1.82
5389 5731 2.101582 CCTCGGCTTGCTGATAGTTAGT 59.898 50.000 4.48 0.00 0.00 2.24
5390 5732 2.362397 TCCTCGGCTTGCTGATAGTTAG 59.638 50.000 4.48 0.00 0.00 2.34
5391 5733 2.100916 GTCCTCGGCTTGCTGATAGTTA 59.899 50.000 4.48 0.00 0.00 2.24
5406 5748 6.909357 CCTATTTTAGTGTAACGTAGTCCTCG 59.091 42.308 0.00 0.00 45.00 4.63
5445 5787 1.764134 AGTTTTGGTAGTGTCGGGTCA 59.236 47.619 0.00 0.00 0.00 4.02
5451 5793 5.554822 TGTTGTTGAGTTTTGGTAGTGTC 57.445 39.130 0.00 0.00 0.00 3.67
5463 5806 3.507233 CCCATGTAGCATTGTTGTTGAGT 59.493 43.478 0.00 0.00 0.00 3.41
5472 5815 4.634004 TCGTCTTTTACCCATGTAGCATTG 59.366 41.667 0.00 0.00 0.00 2.82
5474 5817 4.161565 TCTCGTCTTTTACCCATGTAGCAT 59.838 41.667 0.00 0.00 0.00 3.79
5475 5818 3.512329 TCTCGTCTTTTACCCATGTAGCA 59.488 43.478 0.00 0.00 0.00 3.49
5476 5819 4.113354 CTCTCGTCTTTTACCCATGTAGC 58.887 47.826 0.00 0.00 0.00 3.58
5509 5856 2.048603 GCAATGGCGGCCTCTCTTT 61.049 57.895 21.46 3.44 0.00 2.52
5510 5857 2.439156 GCAATGGCGGCCTCTCTT 60.439 61.111 21.46 5.77 0.00 2.85
5528 5875 4.610945 CAGGAAAATGACTGTGTTTGGTC 58.389 43.478 0.00 0.00 0.00 4.02
5537 5884 2.503895 AGGAGGCAGGAAAATGACTG 57.496 50.000 0.00 0.00 39.20 3.51


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

AutoCloner maintained by Alex Coulton.