Multiple sequence alignment - TraesCS3A01G206400

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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 TraesCS3A01G206400 chr3A 100.000 4310 0 0 1 4310 363414982 363419291 0.000000e+00 7960.0
1 TraesCS3A01G206400 chr3D 91.315 3811 148 71 261 4000 276577963 276574265 0.000000e+00 5035.0
2 TraesCS3A01G206400 chr3D 97.959 49 1 0 188 236 276578079 276578031 7.680000e-13 86.1
3 TraesCS3A01G206400 chr3D 96.154 52 1 1 95 146 85213716 85213766 2.760000e-12 84.2
4 TraesCS3A01G206400 chr3B 91.661 1559 63 27 1983 3506 373843594 373845120 0.000000e+00 2097.0
5 TraesCS3A01G206400 chr3B 83.143 1750 102 82 267 1921 373841856 373843507 0.000000e+00 1419.0
6 TraesCS3A01G206400 chr3B 88.191 796 54 23 3538 4310 373845121 373845899 0.000000e+00 913.0
7 TraesCS3A01G206400 chr3B 85.897 78 10 1 65 142 41010210 41010134 9.930000e-12 82.4
8 TraesCS3A01G206400 chr3B 88.060 67 6 2 81 146 499755089 499755154 1.290000e-10 78.7
9 TraesCS3A01G206400 chr3B 89.831 59 6 0 85 143 581127770 581127828 4.620000e-10 76.8
10 TraesCS3A01G206400 chr6A 86.667 90 12 0 85 174 30205618 30205529 2.740000e-17 100.0
11 TraesCS3A01G206400 chr7A 88.462 78 7 2 68 144 637335868 637335792 4.590000e-15 93.5
12 TraesCS3A01G206400 chr7A 89.655 58 6 0 87 144 637613593 637613536 1.660000e-09 75.0
13 TraesCS3A01G206400 chr2A 91.803 61 3 2 87 146 3522758 3522699 2.760000e-12 84.2
14 TraesCS3A01G206400 chr4A 84.000 75 10 2 101 174 552844337 552844410 2.150000e-08 71.3


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 TraesCS3A01G206400 chr3A 363414982 363419291 4309 False 7960.000000 7960 100.000 1 4310 1 chr3A.!!$F1 4309
1 TraesCS3A01G206400 chr3D 276574265 276578079 3814 True 2560.550000 5035 94.637 188 4000 2 chr3D.!!$R1 3812
2 TraesCS3A01G206400 chr3B 373841856 373845899 4043 False 1476.333333 2097 87.665 267 4310 3 chr3B.!!$F3 4043

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
184 185 0.037232 GAGGGAGTAACTGCAACGCT 60.037 55.0 0.00 0.00 0.00 5.07 F
241 259 0.042448 AGCGCGTGAAAACGTTCTTC 60.042 50.0 8.43 8.59 34.60 2.87 F
760 884 0.110192 GGTTAAACAGAGCTGCGTGC 60.110 55.0 0.00 0.00 43.29 5.34 F
2315 2554 0.883833 TCGTAGAAACCACCGAGGAC 59.116 55.0 0.00 0.00 41.22 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 1990 0.613260 CGGGTCAATCTGGAGAACCA 59.387 55.0 0.0 0.0 41.82 3.67 R
1803 1991 0.744771 GCGGGTCAATCTGGAGAACC 60.745 60.0 0.0 0.0 38.28 3.62 R
2400 2650 0.673985 TGCACGACTGCTGAACTAGT 59.326 50.0 0.0 0.0 44.57 2.57 R
4274 4606 0.039527 CGTGTTTTACCCCTTGCAGC 60.040 55.0 0.0 0.0 0.00 5.25 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
34 35 4.406844 CGCAAATTAATTAGCGTTGCAG 57.593 40.909 20.54 13.56 43.71 4.41
35 36 4.094911 CGCAAATTAATTAGCGTTGCAGA 58.905 39.130 20.54 0.00 43.71 4.26
36 37 4.202959 CGCAAATTAATTAGCGTTGCAGAG 59.797 41.667 20.54 8.50 43.71 3.35
37 38 4.027377 GCAAATTAATTAGCGTTGCAGAGC 60.027 41.667 17.91 7.31 43.17 4.09
38 39 4.963276 AATTAATTAGCGTTGCAGAGCA 57.037 36.364 16.09 0.00 36.47 4.26
39 40 4.542662 ATTAATTAGCGTTGCAGAGCAG 57.457 40.909 16.09 0.00 40.61 4.24
40 41 0.449388 AATTAGCGTTGCAGAGCAGC 59.551 50.000 16.09 5.71 40.61 5.25
41 42 1.372087 ATTAGCGTTGCAGAGCAGCC 61.372 55.000 16.09 0.00 40.61 4.85
49 50 4.399395 CAGAGCAGCCGCCTGGAA 62.399 66.667 0.00 0.00 39.54 3.53
50 51 3.406200 AGAGCAGCCGCCTGGAAT 61.406 61.111 0.00 0.00 39.54 3.01
51 52 2.439156 GAGCAGCCGCCTGGAATT 60.439 61.111 0.00 0.00 39.54 2.17
52 53 1.153168 GAGCAGCCGCCTGGAATTA 60.153 57.895 0.00 0.00 39.54 1.40
53 54 1.153086 AGCAGCCGCCTGGAATTAG 60.153 57.895 0.00 0.00 39.54 1.73
54 55 1.452108 GCAGCCGCCTGGAATTAGT 60.452 57.895 0.00 0.00 39.54 2.24
55 56 1.032114 GCAGCCGCCTGGAATTAGTT 61.032 55.000 0.00 0.00 39.54 2.24
56 57 1.745827 GCAGCCGCCTGGAATTAGTTA 60.746 52.381 0.00 0.00 39.54 2.24
57 58 1.940613 CAGCCGCCTGGAATTAGTTAC 59.059 52.381 0.00 0.00 37.49 2.50
58 59 0.935196 GCCGCCTGGAATTAGTTACG 59.065 55.000 0.00 0.00 37.49 3.18
59 60 1.472026 GCCGCCTGGAATTAGTTACGA 60.472 52.381 0.00 0.00 37.49 3.43
60 61 2.805657 GCCGCCTGGAATTAGTTACGAT 60.806 50.000 0.00 0.00 37.49 3.73
61 62 2.800544 CCGCCTGGAATTAGTTACGATG 59.199 50.000 0.00 0.00 37.49 3.84
62 63 2.800544 CGCCTGGAATTAGTTACGATGG 59.199 50.000 0.00 0.00 0.00 3.51
63 64 3.139077 GCCTGGAATTAGTTACGATGGG 58.861 50.000 0.00 0.00 0.00 4.00
64 65 3.433173 GCCTGGAATTAGTTACGATGGGT 60.433 47.826 0.00 0.00 0.00 4.51
65 66 4.202284 GCCTGGAATTAGTTACGATGGGTA 60.202 45.833 0.00 0.00 0.00 3.69
66 67 5.295152 CCTGGAATTAGTTACGATGGGTAC 58.705 45.833 0.00 0.00 0.00 3.34
67 68 5.070047 CCTGGAATTAGTTACGATGGGTACT 59.930 44.000 0.00 0.00 0.00 2.73
68 69 6.266103 CCTGGAATTAGTTACGATGGGTACTA 59.734 42.308 0.00 0.00 0.00 1.82
69 70 7.042797 TGGAATTAGTTACGATGGGTACTAC 57.957 40.000 0.00 0.00 0.00 2.73
70 71 6.835488 TGGAATTAGTTACGATGGGTACTACT 59.165 38.462 0.00 0.00 0.00 2.57
71 72 7.342799 TGGAATTAGTTACGATGGGTACTACTT 59.657 37.037 0.00 0.00 0.00 2.24
72 73 7.864882 GGAATTAGTTACGATGGGTACTACTTC 59.135 40.741 0.00 0.00 32.07 3.01
73 74 6.699575 TTAGTTACGATGGGTACTACTTCC 57.300 41.667 0.00 0.00 0.00 3.46
74 75 4.864726 AGTTACGATGGGTACTACTTCCT 58.135 43.478 0.00 0.00 0.00 3.36
75 76 5.267587 AGTTACGATGGGTACTACTTCCTT 58.732 41.667 0.00 0.00 0.00 3.36
76 77 5.718607 AGTTACGATGGGTACTACTTCCTTT 59.281 40.000 0.00 0.00 0.00 3.11
77 78 6.891908 AGTTACGATGGGTACTACTTCCTTTA 59.108 38.462 0.00 0.00 0.00 1.85
78 79 7.562821 AGTTACGATGGGTACTACTTCCTTTAT 59.437 37.037 0.00 0.00 0.00 1.40
79 80 6.803366 ACGATGGGTACTACTTCCTTTATT 57.197 37.500 0.00 0.00 0.00 1.40
80 81 6.814043 ACGATGGGTACTACTTCCTTTATTC 58.186 40.000 0.00 0.00 0.00 1.75
81 82 5.919141 CGATGGGTACTACTTCCTTTATTCG 59.081 44.000 0.00 0.00 0.00 3.34
82 83 5.603170 TGGGTACTACTTCCTTTATTCGG 57.397 43.478 0.00 0.00 0.00 4.30
83 84 4.406649 TGGGTACTACTTCCTTTATTCGGG 59.593 45.833 0.00 0.00 0.00 5.14
84 85 4.651045 GGGTACTACTTCCTTTATTCGGGA 59.349 45.833 0.00 0.00 0.00 5.14
85 86 5.306419 GGGTACTACTTCCTTTATTCGGGAT 59.694 44.000 0.00 0.00 0.00 3.85
86 87 6.183361 GGGTACTACTTCCTTTATTCGGGATT 60.183 42.308 0.00 0.00 0.00 3.01
87 88 7.015584 GGGTACTACTTCCTTTATTCGGGATTA 59.984 40.741 0.00 0.00 0.00 1.75
88 89 7.869937 GGTACTACTTCCTTTATTCGGGATTAC 59.130 40.741 0.00 0.00 0.00 1.89
89 90 7.672122 ACTACTTCCTTTATTCGGGATTACT 57.328 36.000 0.00 0.00 0.00 2.24
90 91 8.087303 ACTACTTCCTTTATTCGGGATTACTT 57.913 34.615 0.00 0.00 0.00 2.24
91 92 7.985752 ACTACTTCCTTTATTCGGGATTACTTG 59.014 37.037 0.00 0.00 0.00 3.16
92 93 6.718294 ACTTCCTTTATTCGGGATTACTTGT 58.282 36.000 0.00 0.00 0.00 3.16
93 94 6.822170 ACTTCCTTTATTCGGGATTACTTGTC 59.178 38.462 0.00 0.00 0.00 3.18
94 95 6.555463 TCCTTTATTCGGGATTACTTGTCT 57.445 37.500 0.00 0.00 0.00 3.41
95 96 6.954232 TCCTTTATTCGGGATTACTTGTCTT 58.046 36.000 0.00 0.00 0.00 3.01
96 97 6.821665 TCCTTTATTCGGGATTACTTGTCTTG 59.178 38.462 0.00 0.00 0.00 3.02
97 98 6.821665 CCTTTATTCGGGATTACTTGTCTTGA 59.178 38.462 0.00 0.00 0.00 3.02
98 99 7.335924 CCTTTATTCGGGATTACTTGTCTTGAA 59.664 37.037 0.00 0.00 0.00 2.69
99 100 8.624367 TTTATTCGGGATTACTTGTCTTGAAA 57.376 30.769 0.00 0.00 0.00 2.69
100 101 8.624367 TTATTCGGGATTACTTGTCTTGAAAA 57.376 30.769 0.00 0.00 0.00 2.29
101 102 7.703058 ATTCGGGATTACTTGTCTTGAAAAT 57.297 32.000 0.00 0.00 0.00 1.82
102 103 6.494893 TCGGGATTACTTGTCTTGAAAATG 57.505 37.500 0.00 0.00 0.00 2.32
103 104 6.234920 TCGGGATTACTTGTCTTGAAAATGA 58.765 36.000 0.00 0.00 0.00 2.57
104 105 6.712998 TCGGGATTACTTGTCTTGAAAATGAA 59.287 34.615 0.00 0.00 0.00 2.57
105 106 7.393234 TCGGGATTACTTGTCTTGAAAATGAAT 59.607 33.333 0.00 0.00 0.00 2.57
106 107 8.673711 CGGGATTACTTGTCTTGAAAATGAATA 58.326 33.333 0.00 0.00 0.00 1.75
172 173 8.996651 AATAAATAATTTCGAATGGAGGGAGT 57.003 30.769 0.00 0.00 0.00 3.85
175 176 7.803279 AATAATTTCGAATGGAGGGAGTAAC 57.197 36.000 0.00 0.00 0.00 2.50
176 177 5.437191 AATTTCGAATGGAGGGAGTAACT 57.563 39.130 0.00 0.00 0.00 2.24
177 178 3.887621 TTCGAATGGAGGGAGTAACTG 57.112 47.619 0.00 0.00 0.00 3.16
178 179 1.480954 TCGAATGGAGGGAGTAACTGC 59.519 52.381 0.00 0.00 0.00 4.40
179 180 1.207089 CGAATGGAGGGAGTAACTGCA 59.793 52.381 0.00 0.00 40.59 4.41
180 181 2.354704 CGAATGGAGGGAGTAACTGCAA 60.355 50.000 0.00 0.00 39.73 4.08
181 182 2.789409 ATGGAGGGAGTAACTGCAAC 57.211 50.000 0.00 0.00 39.73 4.17
182 183 0.320374 TGGAGGGAGTAACTGCAACG 59.680 55.000 0.00 0.00 33.20 4.10
183 184 1.019805 GGAGGGAGTAACTGCAACGC 61.020 60.000 0.00 0.00 0.00 4.84
184 185 0.037232 GAGGGAGTAACTGCAACGCT 60.037 55.000 0.00 0.00 0.00 5.07
185 186 0.320771 AGGGAGTAACTGCAACGCTG 60.321 55.000 0.00 0.00 0.00 5.18
186 187 0.602905 GGGAGTAACTGCAACGCTGT 60.603 55.000 0.00 0.00 42.21 4.40
187 188 0.790814 GGAGTAACTGCAACGCTGTC 59.209 55.000 0.00 0.00 39.66 3.51
188 189 1.605712 GGAGTAACTGCAACGCTGTCT 60.606 52.381 0.00 0.00 39.66 3.41
189 190 1.457303 GAGTAACTGCAACGCTGTCTG 59.543 52.381 0.00 0.00 39.66 3.51
190 191 1.202533 AGTAACTGCAACGCTGTCTGT 60.203 47.619 0.00 0.00 39.66 3.41
191 192 1.192534 GTAACTGCAACGCTGTCTGTC 59.807 52.381 0.00 0.00 39.66 3.51
192 193 1.160329 AACTGCAACGCTGTCTGTCC 61.160 55.000 0.00 0.00 39.66 4.02
193 194 2.280797 TGCAACGCTGTCTGTCCC 60.281 61.111 0.00 0.00 0.00 4.46
241 259 0.042448 AGCGCGTGAAAACGTTCTTC 60.042 50.000 8.43 8.59 34.60 2.87
242 260 0.990295 GCGCGTGAAAACGTTCTTCC 60.990 55.000 8.43 2.38 34.60 3.46
245 263 1.596220 GCGTGAAAACGTTCTTCCACC 60.596 52.381 0.00 0.00 34.60 4.61
314 358 7.276438 AGCAACAACAAGAGAAAAGAAATGAAC 59.724 33.333 0.00 0.00 0.00 3.18
471 537 2.038557 TCTAACTTGGACTTGTGCTCCC 59.961 50.000 0.00 0.00 0.00 4.30
472 538 0.535102 AACTTGGACTTGTGCTCCCG 60.535 55.000 0.00 0.00 0.00 5.14
473 539 1.071471 CTTGGACTTGTGCTCCCGT 59.929 57.895 0.00 0.00 0.00 5.28
542 630 4.523173 TCCTAGTATATAGCTGCGCAACTT 59.477 41.667 19.80 9.38 0.00 2.66
556 644 3.995048 GCGCAACTTCTAACCTTAACTCT 59.005 43.478 0.30 0.00 0.00 3.24
569 670 3.388308 CTTAACTCTCATCCATCGCCTG 58.612 50.000 0.00 0.00 0.00 4.85
617 741 3.583380 CCCCGCCCATCCATCCAT 61.583 66.667 0.00 0.00 0.00 3.41
618 742 2.034687 CCCGCCCATCCATCCATC 59.965 66.667 0.00 0.00 0.00 3.51
619 743 2.034687 CCGCCCATCCATCCATCC 59.965 66.667 0.00 0.00 0.00 3.51
620 744 2.832778 CCGCCCATCCATCCATCCA 61.833 63.158 0.00 0.00 0.00 3.41
621 745 1.381463 CGCCCATCCATCCATCCAT 59.619 57.895 0.00 0.00 0.00 3.41
622 746 0.679002 CGCCCATCCATCCATCCATC 60.679 60.000 0.00 0.00 0.00 3.51
623 747 0.324091 GCCCATCCATCCATCCATCC 60.324 60.000 0.00 0.00 0.00 3.51
637 761 2.997980 TCCATCCTTGGTACGTACGTA 58.002 47.619 23.60 23.60 44.06 3.57
656 780 6.917217 ACGTACACCATCTACTAGTTCTAC 57.083 41.667 0.00 0.00 0.00 2.59
657 781 6.648192 ACGTACACCATCTACTAGTTCTACT 58.352 40.000 0.00 0.00 0.00 2.57
658 782 7.108847 ACGTACACCATCTACTAGTTCTACTT 58.891 38.462 0.00 0.00 0.00 2.24
659 783 7.279758 ACGTACACCATCTACTAGTTCTACTTC 59.720 40.741 0.00 0.00 0.00 3.01
660 784 7.495279 CGTACACCATCTACTAGTTCTACTTCT 59.505 40.741 0.00 0.00 0.00 2.85
661 785 9.829507 GTACACCATCTACTAGTTCTACTTCTA 57.170 37.037 0.00 0.00 0.00 2.10
662 786 8.735692 ACACCATCTACTAGTTCTACTTCTAC 57.264 38.462 0.00 0.00 0.00 2.59
663 787 8.550585 ACACCATCTACTAGTTCTACTTCTACT 58.449 37.037 0.00 0.00 0.00 2.57
689 813 4.489810 ACTTCTAGTCGATTGTTGCTCTG 58.510 43.478 0.00 0.00 0.00 3.35
690 814 4.021894 ACTTCTAGTCGATTGTTGCTCTGT 60.022 41.667 0.00 0.00 0.00 3.41
694 818 2.808543 AGTCGATTGTTGCTCTGTTTCC 59.191 45.455 0.00 0.00 0.00 3.13
695 819 2.808543 GTCGATTGTTGCTCTGTTTCCT 59.191 45.455 0.00 0.00 0.00 3.36
697 821 3.070018 CGATTGTTGCTCTGTTTCCTCT 58.930 45.455 0.00 0.00 0.00 3.69
698 822 3.124297 CGATTGTTGCTCTGTTTCCTCTC 59.876 47.826 0.00 0.00 0.00 3.20
699 823 3.845781 TTGTTGCTCTGTTTCCTCTCT 57.154 42.857 0.00 0.00 0.00 3.10
757 881 2.076100 TCATGGTTAAACAGAGCTGCG 58.924 47.619 0.00 0.00 0.00 5.18
760 884 0.110192 GGTTAAACAGAGCTGCGTGC 60.110 55.000 0.00 0.00 43.29 5.34
780 904 6.381801 CGTGCTTGTTATTTTCTTCCTTCAT 58.618 36.000 0.00 0.00 0.00 2.57
781 905 6.524586 CGTGCTTGTTATTTTCTTCCTTCATC 59.475 38.462 0.00 0.00 0.00 2.92
782 906 7.370383 GTGCTTGTTATTTTCTTCCTTCATCA 58.630 34.615 0.00 0.00 0.00 3.07
783 907 7.540055 GTGCTTGTTATTTTCTTCCTTCATCAG 59.460 37.037 0.00 0.00 0.00 2.90
785 909 7.752686 GCTTGTTATTTTCTTCCTTCATCAGTC 59.247 37.037 0.00 0.00 0.00 3.51
786 910 8.924511 TTGTTATTTTCTTCCTTCATCAGTCT 57.075 30.769 0.00 0.00 0.00 3.24
787 911 8.924511 TGTTATTTTCTTCCTTCATCAGTCTT 57.075 30.769 0.00 0.00 0.00 3.01
788 912 9.354673 TGTTATTTTCTTCCTTCATCAGTCTTT 57.645 29.630 0.00 0.00 0.00 2.52
791 915 6.639632 TTTCTTCCTTCATCAGTCTTTTGG 57.360 37.500 0.00 0.00 0.00 3.28
792 916 5.310409 TCTTCCTTCATCAGTCTTTTGGT 57.690 39.130 0.00 0.00 0.00 3.67
793 917 5.694995 TCTTCCTTCATCAGTCTTTTGGTT 58.305 37.500 0.00 0.00 0.00 3.67
794 918 6.837312 TCTTCCTTCATCAGTCTTTTGGTTA 58.163 36.000 0.00 0.00 0.00 2.85
841 982 3.837213 CTGTGCTTTCATAACCCACAG 57.163 47.619 4.91 4.91 44.79 3.66
885 1039 7.520798 TCCCATGACATAATGAGCTTATCTTT 58.479 34.615 0.00 0.00 0.00 2.52
886 1040 8.000709 TCCCATGACATAATGAGCTTATCTTTT 58.999 33.333 0.00 0.00 0.00 2.27
887 1041 8.636213 CCCATGACATAATGAGCTTATCTTTTT 58.364 33.333 0.00 0.00 0.00 1.94
995 1170 4.974721 AAAGGGGTGCCACAGCGG 62.975 66.667 0.00 0.00 44.31 5.52
1049 1224 1.478654 GCCAAGTTTTCTCCACTCCCA 60.479 52.381 0.00 0.00 0.00 4.37
1294 1469 3.745803 GCAAGCAGCAGCAGTCCC 61.746 66.667 3.17 0.00 45.49 4.46
1295 1470 3.060615 CAAGCAGCAGCAGTCCCC 61.061 66.667 3.17 0.00 45.49 4.81
1296 1471 4.711949 AAGCAGCAGCAGTCCCCG 62.712 66.667 3.17 0.00 45.49 5.73
1445 1620 1.679305 TCGTGGAGGAGCTCTGGTC 60.679 63.158 14.64 8.11 0.00 4.02
1446 1621 1.680651 CGTGGAGGAGCTCTGGTCT 60.681 63.158 14.64 1.19 0.00 3.85
1448 1623 1.986757 TGGAGGAGCTCTGGTCTGC 60.987 63.158 14.64 7.95 0.00 4.26
1450 1625 1.336632 GGAGGAGCTCTGGTCTGCAT 61.337 60.000 14.64 0.00 0.00 3.96
1492 1676 3.955551 TGCATGCATGTTGATTGGAGTAT 59.044 39.130 26.79 0.00 0.00 2.12
1704 1892 1.008079 GAAACTGGCACTGCAGCAC 60.008 57.895 15.27 5.74 35.83 4.40
1803 1991 7.816945 ACTCAAGTCAAAATCTTTGTTTGTG 57.183 32.000 13.47 13.36 37.28 3.33
1804 1992 6.813152 ACTCAAGTCAAAATCTTTGTTTGTGG 59.187 34.615 16.11 12.79 37.28 4.17
1809 1997 7.035612 AGTCAAAATCTTTGTTTGTGGTTCTC 58.964 34.615 0.00 0.00 37.28 2.87
1842 2030 2.461110 CCATCGCTACGGCCACAAC 61.461 63.158 2.24 0.00 34.44 3.32
1870 2058 3.433882 CCTCTACTACGACATCTGGTCCT 60.434 52.174 0.00 0.00 43.95 3.85
1979 2214 2.890945 GTGCAATTACAGGGAGGTTTGT 59.109 45.455 0.00 0.00 0.00 2.83
2012 2251 1.003223 AGCGCGTTCCTTGTTTTGTAC 60.003 47.619 8.43 0.00 0.00 2.90
2013 2252 1.003223 GCGCGTTCCTTGTTTTGTACT 60.003 47.619 8.43 0.00 0.00 2.73
2014 2253 2.899977 CGCGTTCCTTGTTTTGTACTC 58.100 47.619 0.00 0.00 0.00 2.59
2015 2254 2.349155 CGCGTTCCTTGTTTTGTACTCC 60.349 50.000 0.00 0.00 0.00 3.85
2065 2304 2.290641 AGACGTTCATCACCAAAAGTGC 59.709 45.455 0.00 0.00 46.81 4.40
2089 2328 2.941720 GAGAAGCAAGCTGTATTCCCAG 59.058 50.000 0.00 0.00 35.49 4.45
2144 2383 6.918067 TCCTCTTTTCTGTCTCAAGATACA 57.082 37.500 0.00 0.00 0.00 2.29
2145 2384 6.692486 TCCTCTTTTCTGTCTCAAGATACAC 58.308 40.000 0.00 0.00 0.00 2.90
2146 2385 6.267699 TCCTCTTTTCTGTCTCAAGATACACA 59.732 38.462 0.00 0.00 0.00 3.72
2147 2386 6.589523 CCTCTTTTCTGTCTCAAGATACACAG 59.410 42.308 0.00 0.00 38.09 3.66
2173 2412 4.276678 CAGACCTCAAAGTTGAATCTTGCA 59.723 41.667 5.23 0.00 36.64 4.08
2315 2554 0.883833 TCGTAGAAACCACCGAGGAC 59.116 55.000 0.00 0.00 41.22 3.85
2399 2649 7.502060 TGTTCCATCCTTTTCTTCTCTCTAT 57.498 36.000 0.00 0.00 0.00 1.98
2400 2650 8.609617 TGTTCCATCCTTTTCTTCTCTCTATA 57.390 34.615 0.00 0.00 0.00 1.31
2401 2651 8.478877 TGTTCCATCCTTTTCTTCTCTCTATAC 58.521 37.037 0.00 0.00 0.00 1.47
2402 2652 8.700973 GTTCCATCCTTTTCTTCTCTCTATACT 58.299 37.037 0.00 0.00 0.00 2.12
2403 2653 9.937876 TTCCATCCTTTTCTTCTCTCTATACTA 57.062 33.333 0.00 0.00 0.00 1.82
2509 2760 4.003648 AGAAGGGTAAATTTCAGCACTCG 58.996 43.478 0.00 0.00 0.00 4.18
2518 2769 4.537135 ATTTCAGCACTCGAGTTTCCTA 57.463 40.909 17.26 0.20 0.00 2.94
2614 2865 0.690762 GCCACTACCTCCCAACAGAA 59.309 55.000 0.00 0.00 0.00 3.02
2701 2952 6.091123 GTAAATTTACCACTCGTGCTACAG 57.909 41.667 16.14 0.00 0.00 2.74
2704 2955 3.837213 TTACCACTCGTGCTACAGTAC 57.163 47.619 0.00 0.00 0.00 2.73
2706 2957 3.063510 ACCACTCGTGCTACAGTACTA 57.936 47.619 0.00 0.00 0.00 1.82
2707 2958 3.618351 ACCACTCGTGCTACAGTACTAT 58.382 45.455 0.00 0.00 0.00 2.12
2709 2960 4.461781 ACCACTCGTGCTACAGTACTATTT 59.538 41.667 0.00 0.00 0.00 1.40
2710 2961 5.047519 ACCACTCGTGCTACAGTACTATTTT 60.048 40.000 0.00 0.00 0.00 1.82
2711 2962 5.867716 CCACTCGTGCTACAGTACTATTTTT 59.132 40.000 0.00 0.00 0.00 1.94
2766 3017 4.661125 TCTGATACGCATTTGCAATTCAC 58.339 39.130 0.00 0.00 42.21 3.18
2769 3020 5.094812 TGATACGCATTTGCAATTCACTTC 58.905 37.500 0.00 0.00 42.21 3.01
2784 3035 0.680061 ACTTCCAGAGGTGTTCCGTC 59.320 55.000 0.00 0.00 39.05 4.79
2837 3088 2.416162 CCTCAGACGAGCCTACTGAAAC 60.416 54.545 0.00 0.00 39.60 2.78
2991 3245 1.153289 CAAGATGGCCAGTCTCCCG 60.153 63.158 13.05 3.68 0.00 5.14
3345 3607 0.252284 ACCTACTACCAGGCTGCTGT 60.252 55.000 9.56 9.51 39.53 4.40
3411 3687 7.551035 AGATCAGAGATACTCACAATTTTGC 57.449 36.000 0.00 0.00 32.06 3.68
3440 3716 3.445805 TGGTTGGTTCTTTGGTTCTGTTC 59.554 43.478 0.00 0.00 0.00 3.18
3441 3717 3.699538 GGTTGGTTCTTTGGTTCTGTTCT 59.300 43.478 0.00 0.00 0.00 3.01
3483 3766 9.606631 AGTATGTTCATCTTCTTATTTGACCTC 57.393 33.333 0.00 0.00 0.00 3.85
3507 3790 1.269673 TGCGTCGGCTGTAGTGTAAAA 60.270 47.619 0.00 0.00 40.82 1.52
3581 3864 6.200854 CCATGTAACTTTCCAGCTTTGTTTTC 59.799 38.462 0.00 0.00 0.00 2.29
3629 3927 4.696877 TCATGTTGATGTGTCTGAACCATC 59.303 41.667 9.64 9.64 35.42 3.51
3651 3949 2.665056 TTTTGTTGCATGCATTTGCG 57.335 40.000 23.37 0.00 45.77 4.85
3682 3980 9.685828 GAATGTAGGACACTCTCTAATGTTATC 57.314 37.037 0.00 0.00 0.00 1.75
3752 4055 2.635427 TGCACATCTAACTGTACCACCA 59.365 45.455 0.00 0.00 0.00 4.17
3755 4058 5.046231 TGCACATCTAACTGTACCACCATTA 60.046 40.000 0.00 0.00 0.00 1.90
3764 4067 6.374417 ACTGTACCACCATTAGATGAAAGT 57.626 37.500 0.00 0.00 0.00 2.66
3867 4172 1.577922 GCAGATGGCATGCATACCG 59.422 57.895 21.36 5.65 43.31 4.02
3868 4173 1.577922 CAGATGGCATGCATACCGC 59.422 57.895 21.36 5.21 42.89 5.68
3874 4179 0.165944 GGCATGCATACCGCGATAAC 59.834 55.000 21.36 0.00 46.97 1.89
3882 4187 0.248907 TACCGCGATAACTGCAGAGC 60.249 55.000 23.35 15.43 0.00 4.09
3884 4189 2.580470 CGCGATAACTGCAGAGCCG 61.580 63.158 23.35 17.73 0.00 5.52
3912 4240 2.629051 GGCTAGTTAAATGTCTGCCGT 58.371 47.619 0.00 0.00 0.00 5.68
4039 4368 2.806945 TCTTCCGCCCAATGAGAAAT 57.193 45.000 0.00 0.00 0.00 2.17
4058 4387 7.559897 TGAGAAATAATAATTCAAGACCCACCC 59.440 37.037 0.00 0.00 0.00 4.61
4204 4536 1.368019 CACGACGCAACTGCAACTG 60.368 57.895 2.12 0.00 42.21 3.16
4219 4551 2.111878 CTGGGATGGGATGTCGGC 59.888 66.667 0.00 0.00 0.00 5.54
4229 4561 0.249155 GGATGTCGGCCAATTGCATG 60.249 55.000 2.24 0.00 43.89 4.06
4233 4565 1.303970 TCGGCCAATTGCATGTCCA 60.304 52.632 2.24 0.00 43.89 4.02
4251 4583 4.710865 TGTCCAACACCCGATATGTAACTA 59.289 41.667 0.00 0.00 0.00 2.24
4273 4605 4.102649 ACACATGACATACATACGACACG 58.897 43.478 0.00 0.00 37.46 4.49
4274 4606 3.485743 CACATGACATACATACGACACGG 59.514 47.826 0.00 0.00 37.46 4.94
4275 4607 2.197792 TGACATACATACGACACGGC 57.802 50.000 0.00 0.00 0.00 5.68
4295 4627 1.265905 CTGCAAGGGGTAAAACACGAC 59.734 52.381 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.830591 GCTAATTAATTTGCGTCGTACGTAC 59.169 40.000 15.90 15.90 44.73 3.67
4 5 5.950580 GCTAATTAATTTGCGTCGTACGTA 58.049 37.500 16.05 0.00 44.73 3.57
5 6 4.814465 GCTAATTAATTTGCGTCGTACGT 58.186 39.130 16.05 0.00 44.73 3.57
14 15 4.027377 GCTCTGCAACGCTAATTAATTTGC 60.027 41.667 20.39 20.39 42.37 3.68
15 16 5.094812 TGCTCTGCAACGCTAATTAATTTG 58.905 37.500 5.91 5.62 34.76 2.32
16 17 5.309323 TGCTCTGCAACGCTAATTAATTT 57.691 34.783 5.91 0.00 34.76 1.82
17 18 4.731773 GCTGCTCTGCAACGCTAATTAATT 60.732 41.667 5.89 5.89 38.41 1.40
18 19 3.242870 GCTGCTCTGCAACGCTAATTAAT 60.243 43.478 8.18 0.00 38.41 1.40
19 20 2.095853 GCTGCTCTGCAACGCTAATTAA 59.904 45.455 8.18 0.00 38.41 1.40
20 21 1.665679 GCTGCTCTGCAACGCTAATTA 59.334 47.619 8.18 0.00 38.41 1.40
21 22 0.449388 GCTGCTCTGCAACGCTAATT 59.551 50.000 8.18 0.00 38.41 1.40
22 23 1.372087 GGCTGCTCTGCAACGCTAAT 61.372 55.000 0.00 0.00 38.41 1.73
23 24 2.034879 GGCTGCTCTGCAACGCTAA 61.035 57.895 0.00 0.00 38.41 3.09
24 25 2.434884 GGCTGCTCTGCAACGCTA 60.435 61.111 0.00 0.00 38.41 4.26
32 33 3.694058 ATTCCAGGCGGCTGCTCTG 62.694 63.158 31.99 22.18 42.25 3.35
33 34 1.626356 TAATTCCAGGCGGCTGCTCT 61.626 55.000 31.99 17.76 42.25 4.09
34 35 1.153168 TAATTCCAGGCGGCTGCTC 60.153 57.895 31.99 7.73 42.25 4.26
35 36 1.153086 CTAATTCCAGGCGGCTGCT 60.153 57.895 31.99 17.77 42.25 4.24
36 37 1.032114 AACTAATTCCAGGCGGCTGC 61.032 55.000 31.99 9.72 41.71 5.25
37 38 1.940613 GTAACTAATTCCAGGCGGCTG 59.059 52.381 30.63 30.63 0.00 4.85
38 39 1.472728 CGTAACTAATTCCAGGCGGCT 60.473 52.381 5.25 5.25 0.00 5.52
39 40 0.935196 CGTAACTAATTCCAGGCGGC 59.065 55.000 0.00 0.00 0.00 6.53
40 41 2.589798 TCGTAACTAATTCCAGGCGG 57.410 50.000 0.00 0.00 0.00 6.13
41 42 2.800544 CCATCGTAACTAATTCCAGGCG 59.199 50.000 0.00 0.00 0.00 5.52
42 43 3.139077 CCCATCGTAACTAATTCCAGGC 58.861 50.000 0.00 0.00 0.00 4.85
43 44 4.417426 ACCCATCGTAACTAATTCCAGG 57.583 45.455 0.00 0.00 0.00 4.45
44 45 6.158023 AGTACCCATCGTAACTAATTCCAG 57.842 41.667 0.00 0.00 0.00 3.86
45 46 6.835488 AGTAGTACCCATCGTAACTAATTCCA 59.165 38.462 0.00 0.00 0.00 3.53
46 47 7.282332 AGTAGTACCCATCGTAACTAATTCC 57.718 40.000 0.00 0.00 0.00 3.01
47 48 7.864882 GGAAGTAGTACCCATCGTAACTAATTC 59.135 40.741 11.15 11.15 36.39 2.17
48 49 7.562821 AGGAAGTAGTACCCATCGTAACTAATT 59.437 37.037 0.00 0.00 29.57 1.40
49 50 7.065504 AGGAAGTAGTACCCATCGTAACTAAT 58.934 38.462 0.00 0.00 0.00 1.73
50 51 6.426587 AGGAAGTAGTACCCATCGTAACTAA 58.573 40.000 0.00 0.00 0.00 2.24
51 52 6.006275 AGGAAGTAGTACCCATCGTAACTA 57.994 41.667 0.00 0.00 0.00 2.24
52 53 4.864726 AGGAAGTAGTACCCATCGTAACT 58.135 43.478 0.00 0.00 0.00 2.24
53 54 5.588958 AAGGAAGTAGTACCCATCGTAAC 57.411 43.478 0.00 0.00 0.00 2.50
54 55 7.902920 ATAAAGGAAGTAGTACCCATCGTAA 57.097 36.000 0.00 0.00 0.00 3.18
55 56 7.255242 CGAATAAAGGAAGTAGTACCCATCGTA 60.255 40.741 0.00 0.00 0.00 3.43
56 57 6.460676 CGAATAAAGGAAGTAGTACCCATCGT 60.461 42.308 0.00 0.00 0.00 3.73
57 58 5.919141 CGAATAAAGGAAGTAGTACCCATCG 59.081 44.000 0.00 0.00 0.00 3.84
58 59 6.221659 CCGAATAAAGGAAGTAGTACCCATC 58.778 44.000 0.00 0.00 0.00 3.51
59 60 5.071384 CCCGAATAAAGGAAGTAGTACCCAT 59.929 44.000 0.00 0.00 0.00 4.00
60 61 4.406649 CCCGAATAAAGGAAGTAGTACCCA 59.593 45.833 0.00 0.00 0.00 4.51
61 62 4.651045 TCCCGAATAAAGGAAGTAGTACCC 59.349 45.833 0.00 0.00 0.00 3.69
62 63 5.859205 TCCCGAATAAAGGAAGTAGTACC 57.141 43.478 0.00 0.00 0.00 3.34
63 64 8.637099 AGTAATCCCGAATAAAGGAAGTAGTAC 58.363 37.037 0.00 0.00 35.30 2.73
64 65 8.773033 AGTAATCCCGAATAAAGGAAGTAGTA 57.227 34.615 0.00 0.00 35.30 1.82
65 66 7.672122 AGTAATCCCGAATAAAGGAAGTAGT 57.328 36.000 0.00 0.00 35.30 2.73
66 67 7.985752 ACAAGTAATCCCGAATAAAGGAAGTAG 59.014 37.037 0.00 0.00 35.30 2.57
67 68 7.854337 ACAAGTAATCCCGAATAAAGGAAGTA 58.146 34.615 0.00 0.00 35.30 2.24
68 69 6.718294 ACAAGTAATCCCGAATAAAGGAAGT 58.282 36.000 0.00 0.00 35.30 3.01
69 70 7.048512 AGACAAGTAATCCCGAATAAAGGAAG 58.951 38.462 0.00 0.00 35.30 3.46
70 71 6.954232 AGACAAGTAATCCCGAATAAAGGAA 58.046 36.000 0.00 0.00 35.30 3.36
71 72 6.555463 AGACAAGTAATCCCGAATAAAGGA 57.445 37.500 0.00 0.00 36.36 3.36
72 73 6.821665 TCAAGACAAGTAATCCCGAATAAAGG 59.178 38.462 0.00 0.00 0.00 3.11
73 74 7.843490 TCAAGACAAGTAATCCCGAATAAAG 57.157 36.000 0.00 0.00 0.00 1.85
74 75 8.624367 TTTCAAGACAAGTAATCCCGAATAAA 57.376 30.769 0.00 0.00 0.00 1.40
75 76 8.624367 TTTTCAAGACAAGTAATCCCGAATAA 57.376 30.769 0.00 0.00 0.00 1.40
76 77 8.673711 CATTTTCAAGACAAGTAATCCCGAATA 58.326 33.333 0.00 0.00 0.00 1.75
77 78 7.393234 TCATTTTCAAGACAAGTAATCCCGAAT 59.607 33.333 0.00 0.00 0.00 3.34
78 79 6.712998 TCATTTTCAAGACAAGTAATCCCGAA 59.287 34.615 0.00 0.00 0.00 4.30
79 80 6.234920 TCATTTTCAAGACAAGTAATCCCGA 58.765 36.000 0.00 0.00 0.00 5.14
80 81 6.494893 TCATTTTCAAGACAAGTAATCCCG 57.505 37.500 0.00 0.00 0.00 5.14
146 147 9.421399 ACTCCCTCCATTCGAAATTATTTATTT 57.579 29.630 0.00 0.00 39.15 1.40
147 148 8.996651 ACTCCCTCCATTCGAAATTATTTATT 57.003 30.769 0.00 0.00 0.00 1.40
149 150 9.333724 GTTACTCCCTCCATTCGAAATTATTTA 57.666 33.333 0.00 0.00 0.00 1.40
150 151 8.053355 AGTTACTCCCTCCATTCGAAATTATTT 58.947 33.333 0.00 0.00 0.00 1.40
151 152 7.499232 CAGTTACTCCCTCCATTCGAAATTATT 59.501 37.037 0.00 0.00 0.00 1.40
152 153 6.992715 CAGTTACTCCCTCCATTCGAAATTAT 59.007 38.462 0.00 0.00 0.00 1.28
153 154 6.346096 CAGTTACTCCCTCCATTCGAAATTA 58.654 40.000 0.00 0.00 0.00 1.40
154 155 5.186198 CAGTTACTCCCTCCATTCGAAATT 58.814 41.667 0.00 0.00 0.00 1.82
155 156 4.770795 CAGTTACTCCCTCCATTCGAAAT 58.229 43.478 0.00 0.00 0.00 2.17
156 157 3.618997 GCAGTTACTCCCTCCATTCGAAA 60.619 47.826 0.00 0.00 0.00 3.46
157 158 2.093658 GCAGTTACTCCCTCCATTCGAA 60.094 50.000 0.00 0.00 0.00 3.71
158 159 1.480954 GCAGTTACTCCCTCCATTCGA 59.519 52.381 0.00 0.00 0.00 3.71
159 160 1.207089 TGCAGTTACTCCCTCCATTCG 59.793 52.381 0.00 0.00 0.00 3.34
160 161 3.010420 GTTGCAGTTACTCCCTCCATTC 58.990 50.000 0.00 0.00 0.00 2.67
161 162 2.615493 CGTTGCAGTTACTCCCTCCATT 60.615 50.000 0.00 0.00 0.00 3.16
162 163 1.066143 CGTTGCAGTTACTCCCTCCAT 60.066 52.381 0.00 0.00 0.00 3.41
163 164 0.320374 CGTTGCAGTTACTCCCTCCA 59.680 55.000 0.00 0.00 0.00 3.86
164 165 1.019805 GCGTTGCAGTTACTCCCTCC 61.020 60.000 0.00 0.00 0.00 4.30
165 166 0.037232 AGCGTTGCAGTTACTCCCTC 60.037 55.000 0.00 0.00 0.00 4.30
166 167 0.320771 CAGCGTTGCAGTTACTCCCT 60.321 55.000 0.00 0.00 0.00 4.20
167 168 0.602905 ACAGCGTTGCAGTTACTCCC 60.603 55.000 0.00 0.00 0.00 4.30
168 169 0.790814 GACAGCGTTGCAGTTACTCC 59.209 55.000 0.00 0.00 0.00 3.85
169 170 1.457303 CAGACAGCGTTGCAGTTACTC 59.543 52.381 0.00 0.00 0.00 2.59
170 171 1.202533 ACAGACAGCGTTGCAGTTACT 60.203 47.619 0.00 0.00 0.00 2.24
171 172 1.192534 GACAGACAGCGTTGCAGTTAC 59.807 52.381 0.00 0.00 0.00 2.50
172 173 1.497991 GACAGACAGCGTTGCAGTTA 58.502 50.000 0.00 0.00 0.00 2.24
173 174 1.160329 GGACAGACAGCGTTGCAGTT 61.160 55.000 0.00 0.00 0.00 3.16
174 175 1.595382 GGACAGACAGCGTTGCAGT 60.595 57.895 0.00 0.00 0.00 4.40
175 176 2.320587 GGGACAGACAGCGTTGCAG 61.321 63.158 0.00 0.00 0.00 4.41
176 177 2.280797 GGGACAGACAGCGTTGCA 60.281 61.111 0.00 0.00 0.00 4.08
177 178 3.414700 CGGGACAGACAGCGTTGC 61.415 66.667 0.00 0.00 0.00 4.17
178 179 2.149803 TACCGGGACAGACAGCGTTG 62.150 60.000 6.32 0.00 0.00 4.10
179 180 1.466025 TTACCGGGACAGACAGCGTT 61.466 55.000 6.32 0.00 0.00 4.84
180 181 1.466025 TTTACCGGGACAGACAGCGT 61.466 55.000 6.32 0.00 0.00 5.07
181 182 0.320073 TTTTACCGGGACAGACAGCG 60.320 55.000 6.32 0.00 0.00 5.18
182 183 1.154197 GTTTTACCGGGACAGACAGC 58.846 55.000 6.32 0.00 0.00 4.40
183 184 1.071071 TGGTTTTACCGGGACAGACAG 59.929 52.381 6.32 0.00 42.58 3.51
184 185 1.071071 CTGGTTTTACCGGGACAGACA 59.929 52.381 6.32 0.00 42.58 3.41
185 186 1.345415 TCTGGTTTTACCGGGACAGAC 59.655 52.381 6.32 0.00 44.85 3.51
186 187 1.719529 TCTGGTTTTACCGGGACAGA 58.280 50.000 6.32 2.97 44.85 3.41
187 188 2.423577 CTTCTGGTTTTACCGGGACAG 58.576 52.381 6.32 0.00 44.85 3.51
188 189 1.072648 CCTTCTGGTTTTACCGGGACA 59.927 52.381 6.32 0.00 44.85 4.02
189 190 1.348696 TCCTTCTGGTTTTACCGGGAC 59.651 52.381 6.32 0.00 44.85 4.46
190 191 1.732117 TCCTTCTGGTTTTACCGGGA 58.268 50.000 6.32 0.00 44.85 5.14
191 192 2.801077 ATCCTTCTGGTTTTACCGGG 57.199 50.000 6.32 0.00 44.85 5.73
192 193 3.014623 GGAATCCTTCTGGTTTTACCGG 58.985 50.000 0.00 0.00 46.14 5.28
193 194 2.676342 CGGAATCCTTCTGGTTTTACCG 59.324 50.000 0.00 0.00 42.58 4.02
241 259 2.444624 CGAATGACAGCGACGGTGG 61.445 63.158 28.55 12.50 35.13 4.61
242 260 3.071459 GCGAATGACAGCGACGGTG 62.071 63.158 24.39 24.39 37.06 4.94
245 263 2.508891 GGAGCGAATGACAGCGACG 61.509 63.158 4.85 0.00 38.61 5.12
314 358 4.088648 CACGCTTAAACTGCTATTTTCCG 58.911 43.478 0.00 0.00 0.00 4.30
440 506 3.196685 AGTCCAAGTTAGATGCAGAGGAC 59.803 47.826 0.00 0.00 43.44 3.85
542 630 5.221263 GCGATGGATGAGAGTTAAGGTTAGA 60.221 44.000 0.00 0.00 0.00 2.10
556 644 1.752358 GAGGAGCAGGCGATGGATGA 61.752 60.000 0.00 0.00 0.00 2.92
569 670 0.175531 GAAGTGGAGCAGAGAGGAGC 59.824 60.000 0.00 0.00 0.00 4.70
637 761 8.550585 AGTAGAAGTAGAACTAGTAGATGGTGT 58.449 37.037 3.59 0.00 0.00 4.16
656 780 8.885722 ACAATCGACTAGAAGTAGAAGTAGAAG 58.114 37.037 0.00 0.00 33.67 2.85
657 781 8.789825 ACAATCGACTAGAAGTAGAAGTAGAA 57.210 34.615 0.00 0.00 33.67 2.10
658 782 8.666573 CAACAATCGACTAGAAGTAGAAGTAGA 58.333 37.037 0.00 0.00 33.67 2.59
659 783 7.429920 GCAACAATCGACTAGAAGTAGAAGTAG 59.570 40.741 0.00 0.00 33.67 2.57
660 784 7.120873 AGCAACAATCGACTAGAAGTAGAAGTA 59.879 37.037 0.00 0.00 33.67 2.24
661 785 6.071840 AGCAACAATCGACTAGAAGTAGAAGT 60.072 38.462 0.00 0.00 33.67 3.01
662 786 6.326375 AGCAACAATCGACTAGAAGTAGAAG 58.674 40.000 0.00 0.00 33.67 2.85
663 787 6.151312 AGAGCAACAATCGACTAGAAGTAGAA 59.849 38.462 0.00 0.00 33.67 2.10
689 813 2.550180 GCCAAGTTCACAGAGAGGAAAC 59.450 50.000 0.00 0.00 0.00 2.78
690 814 2.487265 GGCCAAGTTCACAGAGAGGAAA 60.487 50.000 0.00 0.00 0.00 3.13
694 818 2.082231 CATGGCCAAGTTCACAGAGAG 58.918 52.381 10.96 0.00 0.00 3.20
695 819 1.421268 ACATGGCCAAGTTCACAGAGA 59.579 47.619 10.96 0.00 0.00 3.10
697 821 2.363306 AACATGGCCAAGTTCACAGA 57.637 45.000 20.35 0.00 0.00 3.41
698 822 2.624838 AGAAACATGGCCAAGTTCACAG 59.375 45.455 25.45 3.85 0.00 3.66
699 823 2.665165 AGAAACATGGCCAAGTTCACA 58.335 42.857 25.45 0.00 0.00 3.58
757 881 7.370383 TGATGAAGGAAGAAAATAACAAGCAC 58.630 34.615 0.00 0.00 0.00 4.40
760 884 9.007901 AGACTGATGAAGGAAGAAAATAACAAG 57.992 33.333 0.00 0.00 0.00 3.16
804 932 3.056607 GCACAGCCAACCTAAACATCATT 60.057 43.478 0.00 0.00 0.00 2.57
816 944 2.352715 GGGTTATGAAAGCACAGCCAAC 60.353 50.000 0.00 0.00 34.70 3.77
818 946 1.202989 TGGGTTATGAAAGCACAGCCA 60.203 47.619 0.00 0.00 36.40 4.75
841 982 4.525100 TGGGAAACTAATTGGTTTGGTAGC 59.475 41.667 22.77 9.11 39.20 3.58
885 1039 4.819769 GCAAGGGCAAATCACATAAGAAA 58.180 39.130 0.00 0.00 40.72 2.52
886 1040 4.454728 GCAAGGGCAAATCACATAAGAA 57.545 40.909 0.00 0.00 40.72 2.52
995 1170 3.639162 CTCAGCGAGGACATCTCAC 57.361 57.895 0.00 0.00 42.55 3.51
1029 1204 1.248486 GGGAGTGGAGAAAACTTGGC 58.752 55.000 0.00 0.00 0.00 4.52
1049 1224 2.999648 TCGGGCTCTGCAGCTTCT 61.000 61.111 9.47 0.00 46.03 2.85
1156 1331 1.244697 AAGCTGAGCGACCTCTCGAA 61.245 55.000 0.00 0.00 43.06 3.71
1272 1447 1.972223 CTGCTGCTGCTTGCTTCCT 60.972 57.895 17.00 0.00 43.37 3.36
1448 1623 1.746470 TGCAGGTGAAGATGCAGATG 58.254 50.000 0.00 0.00 46.97 2.90
1492 1676 1.234821 GTTTTGGTCAGGCACGATGA 58.765 50.000 0.00 0.00 0.00 2.92
1704 1892 2.378028 GCTTACAGCTTCGAGCCAG 58.622 57.895 3.66 0.82 43.77 4.85
1799 1987 2.224769 GGGTCAATCTGGAGAACCACAA 60.225 50.000 0.00 0.00 41.36 3.33
1800 1988 1.351017 GGGTCAATCTGGAGAACCACA 59.649 52.381 0.00 0.00 41.36 4.17
1801 1989 1.676014 CGGGTCAATCTGGAGAACCAC 60.676 57.143 0.00 0.00 41.82 4.16
1802 1990 0.613260 CGGGTCAATCTGGAGAACCA 59.387 55.000 0.00 0.00 41.82 3.67
1803 1991 0.744771 GCGGGTCAATCTGGAGAACC 60.745 60.000 0.00 0.00 38.28 3.62
1804 1992 1.084370 CGCGGGTCAATCTGGAGAAC 61.084 60.000 0.00 0.00 0.00 3.01
1809 1997 4.776322 TGGCGCGGGTCAATCTGG 62.776 66.667 8.83 0.00 0.00 3.86
1842 2030 3.378742 AGATGTCGTAGTAGAGGTGCAAG 59.621 47.826 0.00 0.00 0.00 4.01
1870 2058 1.290324 GCTCTGTGCTGGAACTCGA 59.710 57.895 0.00 0.00 38.95 4.04
1979 2214 1.313091 ACGCGCTGTCAGGATCACTA 61.313 55.000 5.73 0.00 0.00 2.74
2012 2251 3.397482 CGATATCCAGCCTGAAAAGGAG 58.603 50.000 0.00 0.00 32.91 3.69
2013 2252 2.104792 CCGATATCCAGCCTGAAAAGGA 59.895 50.000 0.00 0.00 34.12 3.36
2014 2253 2.104792 TCCGATATCCAGCCTGAAAAGG 59.895 50.000 0.00 0.00 0.00 3.11
2015 2254 3.397482 CTCCGATATCCAGCCTGAAAAG 58.603 50.000 0.00 0.00 0.00 2.27
2065 2304 1.936547 GAATACAGCTTGCTTCTCGGG 59.063 52.381 0.00 0.00 0.00 5.14
2089 2328 4.142004 ACTGGTCCGAGGTACATAATCAAC 60.142 45.833 0.00 0.00 0.00 3.18
2144 2383 2.092968 TCAACTTTGAGGTCTGTGCTGT 60.093 45.455 0.00 0.00 32.50 4.40
2145 2384 2.564771 TCAACTTTGAGGTCTGTGCTG 58.435 47.619 0.00 0.00 32.50 4.41
2146 2385 3.281727 TTCAACTTTGAGGTCTGTGCT 57.718 42.857 0.00 0.00 38.61 4.40
2147 2386 3.817647 AGATTCAACTTTGAGGTCTGTGC 59.182 43.478 7.69 0.00 38.61 4.57
2315 2554 5.739752 TCAGCACAAATATCCATTTCGAG 57.260 39.130 0.00 0.00 31.82 4.04
2399 2649 1.883926 TGCACGACTGCTGAACTAGTA 59.116 47.619 0.00 0.00 44.57 1.82
2400 2650 0.673985 TGCACGACTGCTGAACTAGT 59.326 50.000 0.00 0.00 44.57 2.57
2401 2651 1.657594 CATGCACGACTGCTGAACTAG 59.342 52.381 0.00 0.00 44.57 2.57
2402 2652 1.672737 CCATGCACGACTGCTGAACTA 60.673 52.381 0.00 0.00 44.57 2.24
2403 2653 0.952497 CCATGCACGACTGCTGAACT 60.952 55.000 0.00 0.00 44.57 3.01
2407 2657 1.372582 ATTACCATGCACGACTGCTG 58.627 50.000 0.00 0.00 44.57 4.41
2467 2718 4.818642 TCTTCTTCTGCTCACAAGAGATG 58.181 43.478 0.00 0.00 44.98 2.90
2509 2760 2.189784 GCCCCGGCTAGGAAACTC 59.810 66.667 0.00 0.00 45.00 3.01
2530 2781 2.358247 CTACCGGCAGCGGTTGTT 60.358 61.111 12.38 0.00 42.86 2.83
2693 2944 8.403606 ACGATACAAAAATAGTACTGTAGCAC 57.596 34.615 5.39 0.00 31.71 4.40
2695 2946 8.853469 AGACGATACAAAAATAGTACTGTAGC 57.147 34.615 5.39 0.80 0.00 3.58
2706 2957 9.233649 TGGTGGTTATTAAGACGATACAAAAAT 57.766 29.630 0.00 0.00 0.00 1.82
2707 2958 8.618702 TGGTGGTTATTAAGACGATACAAAAA 57.381 30.769 0.00 0.00 0.00 1.94
2709 2960 6.819649 CCTGGTGGTTATTAAGACGATACAAA 59.180 38.462 0.00 0.00 0.00 2.83
2710 2961 6.342906 CCTGGTGGTTATTAAGACGATACAA 58.657 40.000 0.00 0.00 0.00 2.41
2711 2962 5.163385 CCCTGGTGGTTATTAAGACGATACA 60.163 44.000 0.00 0.00 0.00 2.29
2751 3002 2.664568 CTGGAAGTGAATTGCAAATGCG 59.335 45.455 1.71 0.00 45.83 4.73
2766 3017 0.388649 CGACGGAACACCTCTGGAAG 60.389 60.000 0.00 0.00 34.34 3.46
2769 3020 1.080705 GTCGACGGAACACCTCTGG 60.081 63.158 0.00 0.00 34.34 3.86
2784 3035 1.699656 ATGGGTACTCGTCGTCGTCG 61.700 60.000 5.50 5.50 38.33 5.12
2837 3088 2.412089 GGTTTCTCGTCATGTTCTTCCG 59.588 50.000 0.00 0.00 0.00 4.30
2869 3123 3.937706 CTGTTGAGGGTCTCATCATGTTC 59.062 47.826 8.54 0.00 40.39 3.18
2958 3212 4.704833 TTGGTCGCTGCTGCCTCC 62.705 66.667 10.24 12.44 35.36 4.30
2991 3245 0.243636 CGGTTGCCCATTTGAAGGAC 59.756 55.000 0.00 0.00 0.00 3.85
3234 3488 0.251354 TGAACTGCTGCCTCCTGATC 59.749 55.000 0.00 0.00 0.00 2.92
3277 3531 1.220477 GCTTGGGGAGAGTGAGAGC 59.780 63.158 0.00 0.00 0.00 4.09
3411 3687 6.265422 AGAACCAAAGAACCAACCATAAGAAG 59.735 38.462 0.00 0.00 0.00 2.85
3483 3766 2.507102 CTACAGCCGACGCACCTG 60.507 66.667 6.79 6.79 37.52 4.00
3536 3819 2.094545 GGCTTATTTGCAGAGTTGTGGG 60.095 50.000 0.00 0.00 34.04 4.61
3636 3934 1.962092 CTGCCGCAAATGCATGCAAC 61.962 55.000 26.68 13.44 46.76 4.17
3651 3949 1.834263 AGAGTGTCCTACATTCCTGCC 59.166 52.381 0.00 0.00 35.71 4.85
3726 4029 5.523916 GTGGTACAGTTAGATGTGCAATAGG 59.476 44.000 0.00 0.00 41.80 2.57
3752 4055 8.919145 ACGAATCTTAGAGGACTTTCATCTAAT 58.081 33.333 9.94 0.00 45.14 1.73
3755 4058 6.568869 CACGAATCTTAGAGGACTTTCATCT 58.431 40.000 0.00 0.00 40.90 2.90
3764 4067 5.407407 AAGAAAGCACGAATCTTAGAGGA 57.593 39.130 0.00 0.00 31.88 3.71
3803 4108 2.014018 GCCGCGCGAAAACAACAAT 61.014 52.632 34.63 0.00 0.00 2.71
3854 4159 0.250081 TTATCGCGGTATGCATGCCA 60.250 50.000 29.97 13.99 46.97 4.92
3855 4160 0.165944 GTTATCGCGGTATGCATGCC 59.834 55.000 22.79 22.79 46.97 4.40
3856 4161 1.136252 CAGTTATCGCGGTATGCATGC 60.136 52.381 11.82 11.82 46.97 4.06
3857 4162 1.136252 GCAGTTATCGCGGTATGCATG 60.136 52.381 17.74 7.89 46.97 4.06
3866 4171 2.580470 CGGCTCTGCAGTTATCGCG 61.580 63.158 14.67 0.00 0.00 5.87
3867 4172 2.240500 CCGGCTCTGCAGTTATCGC 61.241 63.158 14.67 9.50 0.00 4.58
3868 4173 1.592669 CCCGGCTCTGCAGTTATCG 60.593 63.158 14.67 13.01 0.00 2.92
3874 4179 2.202987 GACATCCCGGCTCTGCAG 60.203 66.667 7.63 7.63 0.00 4.41
3884 4189 3.805207 ACATTTAACTAGCCGACATCCC 58.195 45.455 0.00 0.00 0.00 3.85
4014 4343 2.819608 CTCATTGGGCGGAAGAAAGAAA 59.180 45.455 0.00 0.00 0.00 2.52
4017 4346 2.113860 TCTCATTGGGCGGAAGAAAG 57.886 50.000 0.00 0.00 0.00 2.62
4039 4368 4.123745 AGGGGGTGGGTCTTGAATTATTA 58.876 43.478 0.00 0.00 0.00 0.98
4092 4421 1.344087 TGGCCCCTGGTGGTTTAAAAA 60.344 47.619 0.00 0.00 0.00 1.94
4093 4422 0.264955 TGGCCCCTGGTGGTTTAAAA 59.735 50.000 0.00 0.00 0.00 1.52
4096 4425 1.365105 AACTGGCCCCTGGTGGTTTA 61.365 55.000 0.00 0.00 0.00 2.01
4101 4430 3.892104 ATGCAACTGGCCCCTGGTG 62.892 63.158 0.00 5.01 43.89 4.17
4103 4432 3.072468 CATGCAACTGGCCCCTGG 61.072 66.667 0.00 0.00 43.89 4.45
4106 4435 2.658422 CAACATGCAACTGGCCCC 59.342 61.111 0.00 0.00 43.89 5.80
4136 4468 6.859508 CACCATATGCACATGTTATAGCAAAG 59.140 38.462 12.02 5.86 40.76 2.77
4186 4518 1.368019 CAGTTGCAGTTGCGTCGTG 60.368 57.895 0.00 0.00 45.83 4.35
4204 4536 2.357593 ATTGGCCGACATCCCATCCC 62.358 60.000 0.00 0.00 0.00 3.85
4219 4551 1.338011 GGGTGTTGGACATGCAATTGG 60.338 52.381 7.72 0.00 0.00 3.16
4229 4561 4.133013 AGTTACATATCGGGTGTTGGAC 57.867 45.455 0.00 0.00 0.00 4.02
4233 4565 5.664294 TGTGTAGTTACATATCGGGTGTT 57.336 39.130 0.00 0.00 38.63 3.32
4251 4583 4.102649 CGTGTCGTATGTATGTCATGTGT 58.897 43.478 0.00 0.00 37.91 3.72
4273 4605 0.317160 GTGTTTTACCCCTTGCAGCC 59.683 55.000 0.00 0.00 0.00 4.85
4274 4606 0.039527 CGTGTTTTACCCCTTGCAGC 60.040 55.000 0.00 0.00 0.00 5.25
4275 4607 1.265905 GTCGTGTTTTACCCCTTGCAG 59.734 52.381 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.