Multiple sequence alignment - TraesCS5D01G341200

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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 TraesCS5D01G341200 chr5D 100.000 6981 0 0 1 6981 429360152 429353172 0.000000e+00 12892.0
1 TraesCS5D01G341200 chr5A 94.884 5141 189 43 729 5823 545217941 545212829 0.000000e+00 7969.0
2 TraesCS5D01G341200 chr5A 95.126 636 25 5 5802 6437 545212820 545212191 0.000000e+00 998.0
3 TraesCS5D01G341200 chr5A 89.441 483 25 14 281 739 545218635 545218155 2.810000e-163 586.0
4 TraesCS5D01G341200 chr5A 89.665 358 27 8 6626 6981 545212194 545211845 1.380000e-121 448.0
5 TraesCS5D01G341200 chr5A 89.524 210 16 5 6431 6638 397506073 397505868 1.930000e-65 261.0
6 TraesCS5D01G341200 chr5A 96.721 61 1 1 2608 2668 705520669 705520610 4.460000e-17 100.0
7 TraesCS5D01G341200 chr5B 95.052 3840 172 12 994 4824 518684863 518681033 0.000000e+00 6023.0
8 TraesCS5D01G341200 chr5B 93.988 998 33 14 4833 5829 518680962 518679991 0.000000e+00 1485.0
9 TraesCS5D01G341200 chr5B 88.126 1019 64 25 1 995 518685877 518684892 0.000000e+00 1158.0
10 TraesCS5D01G341200 chr5B 96.494 542 17 1 5814 6355 518679976 518679437 0.000000e+00 894.0
11 TraesCS5D01G341200 chr5B 88.154 363 29 5 6624 6981 518679390 518679037 3.010000e-113 420.0
12 TraesCS5D01G341200 chr5B 96.610 59 2 0 6374 6432 518679446 518679388 1.600000e-16 99.0
13 TraesCS5D01G341200 chr7D 93.548 186 8 4 6430 6614 44802275 44802093 2.480000e-69 274.0
14 TraesCS5D01G341200 chr4A 91.500 200 13 4 6431 6628 594365107 594364910 8.920000e-69 272.0
15 TraesCS5D01G341200 chr2D 93.048 187 11 2 6435 6621 101884248 101884064 8.920000e-69 272.0
16 TraesCS5D01G341200 chr2D 89.372 207 19 3 6420 6624 540163571 540163776 2.500000e-64 257.0
17 TraesCS5D01G341200 chr3A 91.795 195 15 1 6434 6628 78529649 78529456 3.210000e-68 270.0
18 TraesCS5D01G341200 chr3A 96.721 61 1 1 2608 2668 300788090 300788031 4.460000e-17 100.0
19 TraesCS5D01G341200 chr6A 90.955 199 15 3 6429 6625 494463089 494463286 1.490000e-66 265.0
20 TraesCS5D01G341200 chr3D 91.710 193 13 3 6436 6626 25294121 25293930 1.490000e-66 265.0
21 TraesCS5D01G341200 chr3D 96.721 61 1 1 2608 2668 168503528 168503587 4.460000e-17 100.0
22 TraesCS5D01G341200 chr1A 90.500 200 15 4 6435 6631 557897512 557897710 1.930000e-65 261.0
23 TraesCS5D01G341200 chr3B 84.264 197 19 11 2282 2468 28336118 28336312 1.550000e-41 182.0
24 TraesCS5D01G341200 chr2A 89.109 101 2 5 3768 3859 615291579 615291479 4.420000e-22 117.0
25 TraesCS5D01G341200 chr7B 96.721 61 1 1 2608 2668 215236735 215236794 4.460000e-17 100.0
26 TraesCS5D01G341200 chr7B 91.803 61 4 1 2608 2668 636396204 636396263 4.490000e-12 84.2
27 TraesCS5D01G341200 chr1D 96.721 61 1 1 2608 2668 46104206 46104147 4.460000e-17 100.0


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 TraesCS5D01G341200 chr5D 429353172 429360152 6980 True 12892.000000 12892 100.000000 1 6981 1 chr5D.!!$R1 6980
1 TraesCS5D01G341200 chr5A 545211845 545218635 6790 True 2500.250000 7969 92.279000 281 6981 4 chr5A.!!$R3 6700
2 TraesCS5D01G341200 chr5B 518679037 518685877 6840 True 1679.833333 6023 93.070667 1 6981 6 chr5B.!!$R1 6980

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
96 97 0.307760 GCTGAGACCAACCAAACACG 59.692 55.000 0.00 0.0 0.00 4.49 F
170 171 0.454196 TCGCATCGACCGAGAATTGA 59.546 50.000 5.97 0.0 0.00 2.57 F
321 332 0.456221 AATCCGTCTCACTGCGTAGG 59.544 55.000 5.26 0.0 0.00 3.18 F
2249 2557 0.030638 ACATTCAAAGGTGTGTGCGC 59.969 50.000 0.00 0.0 0.00 6.09 F
3345 3662 0.681733 AGCGTCTTGAGAAGGAAGCA 59.318 50.000 0.00 0.0 38.89 3.91 F
4598 4915 0.620556 CCAAGCATGTCCCTACCACT 59.379 55.000 0.00 0.0 0.00 4.00 F
5088 5468 3.119352 CCAACTTAGCTCATGAAAAGGCC 60.119 47.826 13.66 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 2389 0.385223 GAGCTGACAAAGTTGCTGCG 60.385 55.000 0.00 0.00 35.76 5.18 R
2216 2522 6.368516 ACCTTTGAATGTTGTTCTTTTGTGTG 59.631 34.615 0.00 0.00 0.00 3.82 R
2298 2606 4.584327 GCTTCAAAGCCTTAAGGTTCAA 57.416 40.909 22.55 9.65 46.20 2.69 R
3458 3775 0.035630 AGTGCCTGGATCAACAGAGC 60.036 55.000 0.00 0.93 40.97 4.09 R
4821 5139 0.105555 TTGGGAATGGGGATGCATCC 60.106 55.000 33.90 33.90 46.41 3.51 R
5842 6256 1.001633 TCTGGAGGTAAACACCGCTTC 59.998 52.381 0.00 0.00 34.28 3.86 R
6765 7218 1.203287 GCTCTGGTTTCATGCTTTCCC 59.797 52.381 0.00 0.00 0.00 3.97 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
52 53 7.649306 GCGCATGAGGAACTAAATCATTTTTAT 59.351 33.333 0.30 0.00 41.55 1.40
53 54 9.520204 CGCATGAGGAACTAAATCATTTTTATT 57.480 29.630 0.00 0.00 41.55 1.40
68 69 2.631160 TTATTTCATCCATCGGGCGT 57.369 45.000 0.00 0.00 0.00 5.68
96 97 0.307760 GCTGAGACCAACCAAACACG 59.692 55.000 0.00 0.00 0.00 4.49
98 99 1.098712 TGAGACCAACCAAACACGCC 61.099 55.000 0.00 0.00 0.00 5.68
110 111 3.056179 CCAAACACGCCCCAAAATAGAAT 60.056 43.478 0.00 0.00 0.00 2.40
117 118 3.242936 CGCCCCAAAATAGAATACCAACG 60.243 47.826 0.00 0.00 0.00 4.10
118 119 3.490249 GCCCCAAAATAGAATACCAACGC 60.490 47.826 0.00 0.00 0.00 4.84
119 120 3.697045 CCCCAAAATAGAATACCAACGCA 59.303 43.478 0.00 0.00 0.00 5.24
120 121 4.340950 CCCCAAAATAGAATACCAACGCAT 59.659 41.667 0.00 0.00 0.00 4.73
121 122 5.533154 CCCCAAAATAGAATACCAACGCATA 59.467 40.000 0.00 0.00 0.00 3.14
122 123 6.039941 CCCCAAAATAGAATACCAACGCATAA 59.960 38.462 0.00 0.00 0.00 1.90
123 124 7.416890 CCCCAAAATAGAATACCAACGCATAAA 60.417 37.037 0.00 0.00 0.00 1.40
124 125 7.976734 CCCAAAATAGAATACCAACGCATAAAA 59.023 33.333 0.00 0.00 0.00 1.52
125 126 9.360093 CCAAAATAGAATACCAACGCATAAAAA 57.640 29.630 0.00 0.00 0.00 1.94
128 129 9.783256 AAATAGAATACCAACGCATAAAAAGTC 57.217 29.630 0.00 0.00 0.00 3.01
129 130 8.732746 ATAGAATACCAACGCATAAAAAGTCT 57.267 30.769 0.00 0.00 0.00 3.24
140 141 9.797556 AACGCATAAAAAGTCTTAAAAAGTCTT 57.202 25.926 0.00 0.00 38.27 3.01
153 154 4.663636 AAAAGTCTTGACGCCTAAATCG 57.336 40.909 0.00 0.00 0.00 3.34
170 171 0.454196 TCGCATCGACCGAGAATTGA 59.546 50.000 5.97 0.00 0.00 2.57
171 172 0.848942 CGCATCGACCGAGAATTGAG 59.151 55.000 1.37 0.00 0.00 3.02
172 173 1.533965 CGCATCGACCGAGAATTGAGA 60.534 52.381 1.37 0.00 0.00 3.27
173 174 2.540515 GCATCGACCGAGAATTGAGAA 58.459 47.619 0.00 0.00 0.00 2.87
174 175 3.126831 GCATCGACCGAGAATTGAGAAT 58.873 45.455 0.00 0.00 0.00 2.40
175 176 3.557595 GCATCGACCGAGAATTGAGAATT 59.442 43.478 0.00 0.00 0.00 2.17
176 177 4.551603 GCATCGACCGAGAATTGAGAATTG 60.552 45.833 0.00 0.00 0.00 2.32
188 189 4.497473 TTGAGAATTGGCAAAACCGTAG 57.503 40.909 3.01 0.00 43.94 3.51
199 200 3.426292 GCAAAACCGTAGCTCATTTCTCC 60.426 47.826 0.00 0.00 0.00 3.71
205 206 3.304257 CGTAGCTCATTTCTCCGATCTG 58.696 50.000 0.00 0.00 0.00 2.90
216 220 3.165875 TCTCCGATCTGAGACTGGTTTT 58.834 45.455 12.36 0.00 36.48 2.43
230 234 1.964223 TGGTTTTCTTGGGCGCATTTA 59.036 42.857 10.83 0.00 0.00 1.40
262 266 9.837525 CAGAAATAGAAAGGAGAAATCAACAAG 57.162 33.333 0.00 0.00 0.00 3.16
265 269 7.951347 ATAGAAAGGAGAAATCAACAAGCAT 57.049 32.000 0.00 0.00 0.00 3.79
284 288 2.223803 TTCGCTTTCTCTCCCTCTCT 57.776 50.000 0.00 0.00 0.00 3.10
285 289 2.223803 TCGCTTTCTCTCCCTCTCTT 57.776 50.000 0.00 0.00 0.00 2.85
288 292 2.495669 CGCTTTCTCTCCCTCTCTTCTT 59.504 50.000 0.00 0.00 0.00 2.52
289 293 3.428862 CGCTTTCTCTCCCTCTCTTCTTC 60.429 52.174 0.00 0.00 0.00 2.87
290 294 3.769300 GCTTTCTCTCCCTCTCTTCTTCT 59.231 47.826 0.00 0.00 0.00 2.85
291 295 4.953579 GCTTTCTCTCCCTCTCTTCTTCTA 59.046 45.833 0.00 0.00 0.00 2.10
321 332 0.456221 AATCCGTCTCACTGCGTAGG 59.544 55.000 5.26 0.00 0.00 3.18
372 387 2.076863 ACCATAGTTTTGACTCGCTGC 58.923 47.619 0.00 0.00 0.00 5.25
397 412 1.038681 AGTTTCGTTTTTGGCGGGGT 61.039 50.000 0.00 0.00 0.00 4.95
527 555 0.831307 GGCGTGGGAGTAGAAATCCT 59.169 55.000 0.00 0.00 37.01 3.24
622 652 3.174265 CTCCTGCCTCCCCCATCC 61.174 72.222 0.00 0.00 0.00 3.51
657 697 3.368501 CCTCCCCTCCCCTCTCCA 61.369 72.222 0.00 0.00 0.00 3.86
743 783 0.743345 CCACGGGAAGGAATTCGGTC 60.743 60.000 0.00 0.00 0.00 4.79
753 1017 3.636679 AGGAATTCGGTCATCTCTCTCA 58.363 45.455 0.00 0.00 0.00 3.27
824 1088 4.404715 CGGTAAGGAACCCTAGATTTCTGA 59.595 45.833 0.00 0.00 46.62 3.27
834 1098 5.163395 ACCCTAGATTTCTGATCGTTTCCTC 60.163 44.000 0.00 0.00 0.00 3.71
837 1101 5.017294 AGATTTCTGATCGTTTCCTCCTC 57.983 43.478 0.00 0.00 0.00 3.71
887 1151 4.599047 ATCCGACCAGATCTTGATTCTC 57.401 45.455 0.00 0.00 0.00 2.87
888 1152 2.695666 TCCGACCAGATCTTGATTCTCC 59.304 50.000 0.00 0.00 0.00 3.71
889 1153 2.224161 CCGACCAGATCTTGATTCTCCC 60.224 54.545 0.00 0.00 0.00 4.30
951 1215 2.125512 CCGTGCCTGTACCTGAGC 60.126 66.667 0.00 0.00 0.00 4.26
1061 1355 4.697756 CGAAGGCGCCAGGTTGGA 62.698 66.667 31.54 0.00 40.96 3.53
1078 1372 2.811066 GAGCAGTCGCAGATGCAGC 61.811 63.158 5.55 0.00 41.23 5.25
1122 1416 1.001240 GATCTGCCGAGCTCGAATCG 61.001 60.000 36.59 20.69 43.02 3.34
1172 1466 2.684843 CGCAAGCCCTGAAGCAGAC 61.685 63.158 0.00 0.00 32.44 3.51
1380 1674 1.263484 CACAAGATGCAGATCGATGGC 59.737 52.381 0.54 7.22 33.34 4.40
1383 1677 2.667536 ATGCAGATCGATGGCGGC 60.668 61.111 0.54 0.00 38.28 6.53
1401 1695 0.521735 GCGGGAATCTGTCAACCAAC 59.478 55.000 0.00 0.00 0.00 3.77
1506 1800 1.003233 GGGTGTCTCTGTGGCTTCC 60.003 63.158 0.00 0.00 0.00 3.46
1563 1857 1.117150 TGTACGGACAATCTAGCCCC 58.883 55.000 0.00 0.00 30.68 5.80
1569 1863 0.603975 GACAATCTAGCCCCGATGCC 60.604 60.000 0.00 0.00 0.00 4.40
1575 1869 1.532078 TAGCCCCGATGCCGATGTA 60.532 57.895 0.00 0.00 38.22 2.29
1576 1870 1.812686 TAGCCCCGATGCCGATGTAC 61.813 60.000 0.00 0.00 38.22 2.90
1659 1953 6.019779 TCATTTACAAGTTGGTGCCATAAC 57.980 37.500 7.96 0.00 0.00 1.89
1661 1955 5.854010 TTTACAAGTTGGTGCCATAACAA 57.146 34.783 7.96 0.00 0.00 2.83
1666 1960 5.011943 ACAAGTTGGTGCCATAACAATTCAT 59.988 36.000 7.96 0.00 0.00 2.57
1697 1991 7.057894 TGCTATTTTAATCCAGAAATACCGGT 58.942 34.615 13.98 13.98 0.00 5.28
1700 1994 7.948034 ATTTTAATCCAGAAATACCGGTTCA 57.052 32.000 15.04 0.00 0.00 3.18
1704 1998 3.934068 TCCAGAAATACCGGTTCAGTTC 58.066 45.455 15.04 11.31 0.00 3.01
1853 2149 1.009829 CACCGCTCTCCATTGTAAGC 58.990 55.000 0.00 0.00 0.00 3.09
1993 2291 8.212317 ACATGCTTTGCTGTTAATTTTTCTTT 57.788 26.923 0.00 0.00 0.00 2.52
2022 2320 5.261209 TGTTGCAAGTTAGCTTTCATTGT 57.739 34.783 0.00 0.00 31.49 2.71
2090 2389 6.800543 TCTGTTCACTAAGTGCATCTCTATC 58.199 40.000 0.00 0.00 32.98 2.08
2216 2522 6.484977 GGATTAGATCAATGGTGGAAAGAGTC 59.515 42.308 0.00 0.00 0.00 3.36
2249 2557 0.030638 ACATTCAAAGGTGTGTGCGC 59.969 50.000 0.00 0.00 0.00 6.09
2283 2591 3.868077 TGTGTTTTGTTTGTAGGCATTGC 59.132 39.130 0.00 0.00 0.00 3.56
2311 2619 6.095440 TGCTCATCTTATTTGAACCTTAAGGC 59.905 38.462 21.92 6.81 39.32 4.35
2447 2755 1.022735 GATGCTGTGAATGGCTCTGG 58.977 55.000 0.00 0.00 0.00 3.86
2496 2807 9.825109 GCTAATGTTAGTATCTCTTTCCTTTCT 57.175 33.333 2.11 0.00 33.32 2.52
2588 2901 9.425577 TCTATAGACACTATGAAGATACTGACG 57.574 37.037 0.00 0.00 0.00 4.35
2688 3001 3.287222 ACATACACACAACCAAGCTGTT 58.713 40.909 0.00 0.00 0.00 3.16
2739 3054 2.847327 TCTGAGCCATATAGCCTTGC 57.153 50.000 0.00 0.00 0.00 4.01
2759 3074 8.687242 GCCTTGCTTCTTCCTAAATAAATTAGT 58.313 33.333 0.00 0.00 39.56 2.24
2788 3103 8.347004 TCATAATAGACCTGCTAATCTGAGAG 57.653 38.462 0.00 0.00 31.66 3.20
2793 3108 5.265191 AGACCTGCTAATCTGAGAGTGTTA 58.735 41.667 0.00 0.00 0.00 2.41
2801 3116 6.147821 GCTAATCTGAGAGTGTTAGTTTTGCA 59.852 38.462 0.00 0.00 0.00 4.08
3006 3323 9.853921 GAACAAGTAATTCTGAAAATGCAAAAG 57.146 29.630 0.00 0.00 0.00 2.27
3345 3662 0.681733 AGCGTCTTGAGAAGGAAGCA 59.318 50.000 0.00 0.00 38.89 3.91
3348 3665 1.606480 CGTCTTGAGAAGGAAGCAGCA 60.606 52.381 0.00 0.00 0.00 4.41
3480 3797 2.499289 CTCTGTTGATCCAGGCACTACT 59.501 50.000 0.00 0.00 36.02 2.57
3656 3973 6.257849 GGTCACTCGAAAACAGAATATGCATA 59.742 38.462 9.27 9.27 0.00 3.14
3989 4306 1.683943 TTGATATGCTTCCAGCCAGC 58.316 50.000 0.00 0.00 41.51 4.85
4308 4625 3.159472 TGCCAATGATCTTGCTTTGTCT 58.841 40.909 0.00 0.00 0.00 3.41
4459 4776 6.773638 TGAAGAAGAGGAAGATAGCTTTGTT 58.226 36.000 0.00 0.00 33.61 2.83
4571 4888 5.543507 TTCCACATGTTTTTGCCTGTATT 57.456 34.783 0.00 0.00 0.00 1.89
4598 4915 0.620556 CCAAGCATGTCCCTACCACT 59.379 55.000 0.00 0.00 0.00 4.00
4711 5029 4.917385 ACCTGCAATACTTGTGTTATCCA 58.083 39.130 0.00 0.00 0.00 3.41
4712 5030 5.321102 ACCTGCAATACTTGTGTTATCCAA 58.679 37.500 0.00 0.00 0.00 3.53
4821 5139 8.671921 AGAAATACACATGCTCTTTGTTGATAG 58.328 33.333 0.00 0.00 0.00 2.08
5088 5468 3.119352 CCAACTTAGCTCATGAAAAGGCC 60.119 47.826 13.66 0.00 0.00 5.19
5123 5503 3.815757 GCCCAAGATCTCAAGGGAAGTTT 60.816 47.826 24.59 0.00 44.30 2.66
5130 5510 6.413892 AGATCTCAAGGGAAGTTTGAAGATC 58.586 40.000 13.45 13.45 38.20 2.75
5358 5738 8.415950 TTTGAATGGAGGTAGCATTTTTAAGA 57.584 30.769 0.00 0.00 0.00 2.10
5673 6053 4.373156 AGGTGTTCTGCTCTTATTTGGT 57.627 40.909 0.00 0.00 0.00 3.67
5746 6130 5.303845 CACCTGGTAAGTACCCTATACTTCC 59.696 48.000 0.00 5.76 45.87 3.46
5747 6131 5.197395 ACCTGGTAAGTACCCTATACTTCCT 59.803 44.000 0.00 0.00 45.87 3.36
5748 6132 6.141790 CCTGGTAAGTACCCTATACTTCCTT 58.858 44.000 5.05 0.00 45.87 3.36
5749 6133 6.041751 CCTGGTAAGTACCCTATACTTCCTTG 59.958 46.154 5.05 3.74 45.87 3.61
5842 6256 4.592485 AGGAATAGGCATGTACTTCTCG 57.408 45.455 0.00 0.00 0.00 4.04
5875 6289 0.539051 CTCCAGAAGAGGCCGTCAAT 59.461 55.000 0.00 0.00 39.13 2.57
5956 6370 2.116983 TTGCTGGTGCTCCTCAGGTC 62.117 60.000 6.34 0.00 40.48 3.85
5981 6395 0.670854 GTTCCCCTCGCAGAAGTGAC 60.671 60.000 0.00 0.00 34.09 3.67
5982 6396 1.118965 TTCCCCTCGCAGAAGTGACA 61.119 55.000 0.00 0.00 34.09 3.58
6036 6450 2.817665 TGAATTGGGTCCATGCATTGA 58.182 42.857 0.00 0.00 0.00 2.57
6349 6790 9.671279 TTGTCAGATTTTCTAAAGATGCATAGA 57.329 29.630 0.00 0.00 0.00 1.98
6350 6791 9.842775 TGTCAGATTTTCTAAAGATGCATAGAT 57.157 29.630 0.00 0.00 0.00 1.98
6363 6804 9.692325 AAAGATGCATAGATCTTAGTTTTTCCT 57.308 29.630 0.00 0.00 41.02 3.36
6364 6805 8.674263 AGATGCATAGATCTTAGTTTTTCCTG 57.326 34.615 0.00 0.00 27.38 3.86
6365 6806 8.489489 AGATGCATAGATCTTAGTTTTTCCTGA 58.511 33.333 0.00 0.00 27.38 3.86
6366 6807 8.674263 ATGCATAGATCTTAGTTTTTCCTGAG 57.326 34.615 0.00 0.00 0.00 3.35
6367 6808 7.851228 TGCATAGATCTTAGTTTTTCCTGAGA 58.149 34.615 0.00 0.00 32.39 3.27
6368 6809 7.984050 TGCATAGATCTTAGTTTTTCCTGAGAG 59.016 37.037 0.00 0.00 31.49 3.20
6369 6810 8.200792 GCATAGATCTTAGTTTTTCCTGAGAGA 58.799 37.037 0.00 0.00 31.49 3.10
6372 6813 8.201242 AGATCTTAGTTTTTCCTGAGAGAAGT 57.799 34.615 0.00 0.00 31.49 3.01
6373 6814 9.315363 AGATCTTAGTTTTTCCTGAGAGAAGTA 57.685 33.333 0.00 0.00 31.49 2.24
6414 6855 9.822185 AAAAACCAGAAAATATATGAGAATGCC 57.178 29.630 0.00 0.00 0.00 4.40
6418 6859 6.082338 CAGAAAATATATGAGAATGCCGCAC 58.918 40.000 0.00 0.00 0.00 5.34
6430 6871 0.539518 TGCCGCACAAGCTAGGATTA 59.460 50.000 0.00 0.00 39.10 1.75
6431 6872 1.065782 TGCCGCACAAGCTAGGATTAA 60.066 47.619 0.00 0.00 39.10 1.40
6432 6873 2.222027 GCCGCACAAGCTAGGATTAAT 58.778 47.619 0.00 0.00 39.10 1.40
6433 6874 3.181459 TGCCGCACAAGCTAGGATTAATA 60.181 43.478 0.00 0.00 39.10 0.98
6434 6875 3.813166 GCCGCACAAGCTAGGATTAATAA 59.187 43.478 0.00 0.00 39.10 1.40
6435 6876 4.274950 GCCGCACAAGCTAGGATTAATAAA 59.725 41.667 0.00 0.00 39.10 1.40
6436 6877 5.748592 CCGCACAAGCTAGGATTAATAAAC 58.251 41.667 0.00 0.00 39.10 2.01
6437 6878 5.295787 CCGCACAAGCTAGGATTAATAAACA 59.704 40.000 0.00 0.00 39.10 2.83
6438 6879 6.422223 CGCACAAGCTAGGATTAATAAACAG 58.578 40.000 0.00 0.00 39.10 3.16
6439 6880 6.037172 CGCACAAGCTAGGATTAATAAACAGT 59.963 38.462 0.00 0.00 39.10 3.55
6440 6881 7.414098 CGCACAAGCTAGGATTAATAAACAGTT 60.414 37.037 0.00 0.00 39.10 3.16
6441 6882 8.244113 GCACAAGCTAGGATTAATAAACAGTTT 58.756 33.333 3.49 3.49 37.91 2.66
6442 6883 9.559958 CACAAGCTAGGATTAATAAACAGTTTG 57.440 33.333 8.93 10.89 0.00 2.93
6443 6884 9.297037 ACAAGCTAGGATTAATAAACAGTTTGT 57.703 29.630 8.93 0.00 33.14 2.83
6444 6885 9.774742 CAAGCTAGGATTAATAAACAGTTTGTC 57.225 33.333 8.93 0.00 0.00 3.18
6445 6886 9.740710 AAGCTAGGATTAATAAACAGTTTGTCT 57.259 29.630 8.93 0.00 0.00 3.41
6459 6900 9.778741 AAACAGTTTGTCTAATTCACATCTAGA 57.221 29.630 0.00 0.00 0.00 2.43
6460 6901 9.950496 AACAGTTTGTCTAATTCACATCTAGAT 57.050 29.630 0.00 0.00 0.00 1.98
6461 6902 9.376075 ACAGTTTGTCTAATTCACATCTAGATG 57.624 33.333 27.63 27.63 44.15 2.90
6488 6929 8.561738 TTTTTAAGGATGTCACATCTAACCTC 57.438 34.615 17.46 0.00 0.00 3.85
6489 6930 7.496346 TTTAAGGATGTCACATCTAACCTCT 57.504 36.000 17.46 2.09 0.00 3.69
6490 6931 5.606348 AAGGATGTCACATCTAACCTCTC 57.394 43.478 17.46 0.00 0.00 3.20
6491 6932 4.614475 AGGATGTCACATCTAACCTCTCA 58.386 43.478 17.46 0.00 0.00 3.27
6492 6933 4.404073 AGGATGTCACATCTAACCTCTCAC 59.596 45.833 17.46 0.00 0.00 3.51
6493 6934 4.160439 GGATGTCACATCTAACCTCTCACA 59.840 45.833 17.46 0.00 0.00 3.58
6494 6935 5.337571 GGATGTCACATCTAACCTCTCACAA 60.338 44.000 17.46 0.00 0.00 3.33
6495 6936 5.545063 TGTCACATCTAACCTCTCACAAA 57.455 39.130 0.00 0.00 0.00 2.83
6496 6937 6.114187 TGTCACATCTAACCTCTCACAAAT 57.886 37.500 0.00 0.00 0.00 2.32
6497 6938 7.239763 TGTCACATCTAACCTCTCACAAATA 57.760 36.000 0.00 0.00 0.00 1.40
6498 6939 7.851228 TGTCACATCTAACCTCTCACAAATAT 58.149 34.615 0.00 0.00 0.00 1.28
6499 6940 8.977412 TGTCACATCTAACCTCTCACAAATATA 58.023 33.333 0.00 0.00 0.00 0.86
6500 6941 9.988815 GTCACATCTAACCTCTCACAAATATAT 57.011 33.333 0.00 0.00 0.00 0.86
6508 6949 7.678947 ACCTCTCACAAATATATAATGCAGC 57.321 36.000 0.00 0.00 0.00 5.25
6509 6950 7.226441 ACCTCTCACAAATATATAATGCAGCA 58.774 34.615 0.00 0.00 0.00 4.41
6510 6951 7.720957 ACCTCTCACAAATATATAATGCAGCAA 59.279 33.333 0.00 0.00 0.00 3.91
6511 6952 8.019669 CCTCTCACAAATATATAATGCAGCAAC 58.980 37.037 0.00 0.00 0.00 4.17
6512 6953 8.449251 TCTCACAAATATATAATGCAGCAACA 57.551 30.769 0.00 0.00 0.00 3.33
6513 6954 8.901793 TCTCACAAATATATAATGCAGCAACAA 58.098 29.630 0.00 0.00 0.00 2.83
6514 6955 9.177304 CTCACAAATATATAATGCAGCAACAAG 57.823 33.333 0.00 0.00 0.00 3.16
6515 6956 8.901793 TCACAAATATATAATGCAGCAACAAGA 58.098 29.630 0.00 0.00 0.00 3.02
6516 6957 9.518906 CACAAATATATAATGCAGCAACAAGAA 57.481 29.630 0.00 0.00 0.00 2.52
6568 7009 9.998106 AAGACTACAAACAAAGTGTATATCAGT 57.002 29.630 0.00 0.00 31.27 3.41
6569 7010 9.998106 AGACTACAAACAAAGTGTATATCAGTT 57.002 29.630 0.00 0.00 40.95 3.16
6616 7057 5.916661 TCTAGATGTGTCCTAAACAGACC 57.083 43.478 0.00 0.00 38.97 3.85
6617 7058 3.983044 AGATGTGTCCTAAACAGACCC 57.017 47.619 0.00 0.00 38.97 4.46
6618 7059 3.248024 AGATGTGTCCTAAACAGACCCA 58.752 45.455 0.00 0.00 38.97 4.51
6619 7060 3.846588 AGATGTGTCCTAAACAGACCCAT 59.153 43.478 0.00 0.00 38.97 4.00
6620 7061 5.030147 AGATGTGTCCTAAACAGACCCATA 58.970 41.667 0.00 0.00 38.97 2.74
6621 7062 5.487488 AGATGTGTCCTAAACAGACCCATAA 59.513 40.000 0.00 0.00 38.97 1.90
6622 7063 5.570205 TGTGTCCTAAACAGACCCATAAA 57.430 39.130 0.00 0.00 38.97 1.40
6623 7064 6.134535 TGTGTCCTAAACAGACCCATAAAT 57.865 37.500 0.00 0.00 38.97 1.40
6729 7170 3.192633 CCCTTTGTTCGGAAATAAGTGGG 59.807 47.826 10.41 10.82 30.74 4.61
6763 7216 5.523188 TCAAATTGTTTGTCATCAAAGCACC 59.477 36.000 2.74 0.00 43.04 5.01
6764 7217 4.669206 ATTGTTTGTCATCAAAGCACCA 57.331 36.364 0.00 0.00 43.04 4.17
6765 7218 3.713858 TGTTTGTCATCAAAGCACCAG 57.286 42.857 0.00 0.00 43.04 4.00
6766 7219 2.361757 TGTTTGTCATCAAAGCACCAGG 59.638 45.455 0.00 0.00 43.04 4.45
6767 7220 1.619654 TTGTCATCAAAGCACCAGGG 58.380 50.000 0.00 0.00 0.00 4.45
6768 7221 0.770499 TGTCATCAAAGCACCAGGGA 59.230 50.000 0.00 0.00 0.00 4.20
6769 7222 1.144708 TGTCATCAAAGCACCAGGGAA 59.855 47.619 0.00 0.00 0.00 3.97
6770 7223 2.238521 GTCATCAAAGCACCAGGGAAA 58.761 47.619 0.00 0.00 0.00 3.13
6771 7224 2.229784 GTCATCAAAGCACCAGGGAAAG 59.770 50.000 0.00 0.00 0.00 2.62
6772 7225 1.067354 CATCAAAGCACCAGGGAAAGC 60.067 52.381 0.00 0.00 0.00 3.51
6781 7234 1.133199 ACCAGGGAAAGCATGAAACCA 60.133 47.619 0.00 0.00 0.00 3.67
6870 7326 2.363306 TCACTTTTGTCATGGGCTGT 57.637 45.000 0.00 0.00 0.00 4.40
6894 7350 0.037605 CGGACGGCCTAGTCTTGTTT 60.038 55.000 5.33 0.00 40.76 2.83
6908 7364 3.088532 TCTTGTTTGTGTTGTCAAGCCT 58.911 40.909 0.00 0.00 37.68 4.58
6915 7371 2.945008 TGTGTTGTCAAGCCTCTTCTTG 59.055 45.455 0.00 0.00 43.53 3.02
6924 7380 3.393360 CTCTTCTTGAGGGCCGGT 58.607 61.111 1.90 0.00 39.08 5.28
6959 7415 0.465824 GCTCTGGATGCATCTGCCTT 60.466 55.000 25.28 0.00 41.18 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 9.979578 CCCGATGGATGAAATAAAAATGATTTA 57.020 29.630 0.00 0.00 0.00 1.40
52 53 0.322098 AACACGCCCGATGGATGAAA 60.322 50.000 0.00 0.00 0.00 2.69
53 54 0.322098 AAACACGCCCGATGGATGAA 60.322 50.000 0.00 0.00 0.00 2.57
54 55 1.024046 CAAACACGCCCGATGGATGA 61.024 55.000 0.00 0.00 0.00 2.92
68 69 1.650242 TTGGTCTCAGCCCCCAAACA 61.650 55.000 0.00 0.00 35.38 2.83
96 97 3.490249 GCGTTGGTATTCTATTTTGGGGC 60.490 47.826 0.00 0.00 0.00 5.80
98 99 4.974368 TGCGTTGGTATTCTATTTTGGG 57.026 40.909 0.00 0.00 0.00 4.12
110 111 9.453325 CTTTTTAAGACTTTTTATGCGTTGGTA 57.547 29.630 0.00 0.00 0.00 3.25
119 120 9.447040 GCGTCAAGACTTTTTAAGACTTTTTAT 57.553 29.630 0.00 0.00 40.59 1.40
120 121 7.911727 GGCGTCAAGACTTTTTAAGACTTTTTA 59.088 33.333 0.00 0.00 40.59 1.52
121 122 6.750501 GGCGTCAAGACTTTTTAAGACTTTTT 59.249 34.615 0.00 0.00 40.59 1.94
122 123 6.095021 AGGCGTCAAGACTTTTTAAGACTTTT 59.905 34.615 0.00 0.00 40.59 2.27
123 124 5.589050 AGGCGTCAAGACTTTTTAAGACTTT 59.411 36.000 0.00 0.00 40.59 2.66
124 125 5.123936 AGGCGTCAAGACTTTTTAAGACTT 58.876 37.500 0.00 0.00 42.68 3.01
125 126 4.704965 AGGCGTCAAGACTTTTTAAGACT 58.295 39.130 0.00 0.00 30.60 3.24
126 127 6.535274 TTAGGCGTCAAGACTTTTTAAGAC 57.465 37.500 0.00 0.00 40.13 3.01
127 128 7.359765 CGATTTAGGCGTCAAGACTTTTTAAGA 60.360 37.037 0.00 0.00 40.13 2.10
128 129 6.736853 CGATTTAGGCGTCAAGACTTTTTAAG 59.263 38.462 0.00 0.00 40.13 1.85
129 130 6.595794 CGATTTAGGCGTCAAGACTTTTTAA 58.404 36.000 0.00 0.00 40.13 1.52
140 141 0.101579 TCGATGCGATTTAGGCGTCA 59.898 50.000 6.77 0.00 44.68 4.35
153 154 2.209838 TCTCAATTCTCGGTCGATGC 57.790 50.000 0.00 0.00 0.00 3.91
170 171 2.488153 GAGCTACGGTTTTGCCAATTCT 59.512 45.455 0.00 0.00 36.97 2.40
171 172 2.227865 TGAGCTACGGTTTTGCCAATTC 59.772 45.455 0.00 0.00 36.97 2.17
172 173 2.235016 TGAGCTACGGTTTTGCCAATT 58.765 42.857 0.00 0.00 36.97 2.32
173 174 1.904287 TGAGCTACGGTTTTGCCAAT 58.096 45.000 0.00 0.00 36.97 3.16
174 175 1.904287 ATGAGCTACGGTTTTGCCAA 58.096 45.000 0.00 0.00 36.97 4.52
175 176 1.904287 AATGAGCTACGGTTTTGCCA 58.096 45.000 0.00 0.00 36.97 4.92
176 177 2.488153 AGAAATGAGCTACGGTTTTGCC 59.512 45.455 0.00 0.00 0.00 4.52
188 189 3.068024 AGTCTCAGATCGGAGAAATGAGC 59.932 47.826 24.50 12.63 46.27 4.26
199 200 3.681897 CCAAGAAAACCAGTCTCAGATCG 59.318 47.826 0.00 0.00 0.00 3.69
205 206 0.875059 CGCCCAAGAAAACCAGTCTC 59.125 55.000 0.00 0.00 0.00 3.36
216 220 1.067915 GCAACTTAAATGCGCCCAAGA 60.068 47.619 4.18 0.00 33.57 3.02
230 234 7.823745 TTTCTCCTTTCTATTTCTGCAACTT 57.176 32.000 0.00 0.00 0.00 2.66
262 266 1.134551 AGAGGGAGAGAAAGCGAATGC 60.135 52.381 0.00 0.00 43.24 3.56
265 269 2.223803 AGAGAGGGAGAGAAAGCGAA 57.776 50.000 0.00 0.00 0.00 4.70
328 339 2.930562 GTGGGCCAGTGAGGGAGT 60.931 66.667 6.40 0.00 38.09 3.85
329 340 3.721706 GGTGGGCCAGTGAGGGAG 61.722 72.222 6.40 0.00 38.09 4.30
354 369 2.349886 GGAGCAGCGAGTCAAAACTATG 59.650 50.000 0.00 0.00 35.28 2.23
372 387 2.602217 CGCCAAAAACGAAACTGAGGAG 60.602 50.000 0.00 0.00 0.00 3.69
397 412 2.819595 GATTGCTTCGCGGGCTCA 60.820 61.111 21.15 11.41 0.00 4.26
478 496 2.637025 CCACAAGTTTCGCCCACG 59.363 61.111 0.00 0.00 42.01 4.94
479 497 2.335011 GCCACAAGTTTCGCCCAC 59.665 61.111 0.00 0.00 0.00 4.61
480 498 3.283684 CGCCACAAGTTTCGCCCA 61.284 61.111 0.00 0.00 0.00 5.36
550 578 1.817099 GGAGAATGGAGCGCAGGTG 60.817 63.158 11.47 0.00 39.88 4.00
555 583 4.105486 GTTTAATTTGGAGAATGGAGCGC 58.895 43.478 0.00 0.00 0.00 5.92
694 734 3.822192 CGCCTCGGTGTGGATCGA 61.822 66.667 0.00 0.00 32.48 3.59
743 783 1.144565 CGCCGCTTGTGAGAGAGATG 61.145 60.000 0.00 0.00 0.00 2.90
753 1017 4.719369 GTCGAGGACGCCGCTTGT 62.719 66.667 0.00 0.00 39.58 3.16
791 1055 3.948735 TCCTTACCGGCAAAAGGAG 57.051 52.632 23.02 5.83 44.96 3.69
824 1088 0.324460 AGACGGGAGGAGGAAACGAT 60.324 55.000 0.00 0.00 0.00 3.73
834 1098 0.035458 AGCAACAGAAAGACGGGAGG 59.965 55.000 0.00 0.00 0.00 4.30
837 1101 2.972625 TCATAGCAACAGAAAGACGGG 58.027 47.619 0.00 0.00 0.00 5.28
1061 1355 2.799814 AAGCTGCATCTGCGACTGCT 62.800 55.000 1.02 2.43 45.83 4.24
1122 1416 1.195347 CGATATCCATCGCATCGCTC 58.805 55.000 0.00 0.00 46.80 5.03
1161 1455 2.743928 GGCACCGTCTGCTTCAGG 60.744 66.667 2.66 0.00 46.25 3.86
1239 1533 1.557269 ATGCCCTCTTCCGCTTCAGT 61.557 55.000 0.00 0.00 0.00 3.41
1372 1666 3.883744 GATTCCCGCCGCCATCGAT 62.884 63.158 0.00 0.00 38.10 3.59
1380 1674 2.106683 GGTTGACAGATTCCCGCCG 61.107 63.158 0.00 0.00 0.00 6.46
1383 1677 0.796312 CGTTGGTTGACAGATTCCCG 59.204 55.000 0.00 0.00 0.00 5.14
1386 1680 1.234821 TGGCGTTGGTTGACAGATTC 58.765 50.000 0.00 0.00 0.00 2.52
1401 1695 1.140161 CAAGCACCCAATCATGGCG 59.860 57.895 0.00 0.00 46.09 5.69
1563 1857 1.067060 TCTTCCAGTACATCGGCATCG 59.933 52.381 0.00 0.00 37.82 3.84
1569 1863 5.836347 TCTGATTCATCTTCCAGTACATCG 58.164 41.667 0.00 0.00 0.00 3.84
1575 1869 4.840716 AAGCTCTGATTCATCTTCCAGT 57.159 40.909 0.00 0.00 0.00 4.00
1576 1870 5.430007 AGAAAGCTCTGATTCATCTTCCAG 58.570 41.667 0.00 0.00 0.00 3.86
1634 1928 5.543507 ATGGCACCAACTTGTAAATGAAA 57.456 34.783 0.00 0.00 0.00 2.69
1649 1943 6.457257 GCATTGAAATGAATTGTTATGGCACC 60.457 38.462 7.21 0.00 38.70 5.01
1691 1985 9.754382 GACATATTAATTAGAACTGAACCGGTA 57.246 33.333 8.00 0.00 0.00 4.02
1693 1987 8.888579 AGACATATTAATTAGAACTGAACCGG 57.111 34.615 0.00 0.00 0.00 5.28
1837 2133 1.959042 ATGGCTTACAATGGAGAGCG 58.041 50.000 0.00 0.00 36.02 5.03
1853 2149 5.125900 TCAAACATGGTGCAAGAAGATATGG 59.874 40.000 0.00 0.00 0.00 2.74
1933 2229 0.395586 TGGGCACAACTTGAGCTGTT 60.396 50.000 10.50 0.00 34.36 3.16
1935 2231 0.963962 AATGGGCACAACTTGAGCTG 59.036 50.000 10.50 0.00 34.36 4.24
1993 2291 7.261325 TGAAAGCTAACTTGCAACAACATTTA 58.739 30.769 0.00 0.00 38.59 1.40
2022 2320 8.677300 GGCAATTTCACAGTTCTAATTAGATGA 58.323 33.333 18.66 14.86 31.40 2.92
2043 2341 5.832539 ATACAAGCTATGGAGTAGGCAAT 57.167 39.130 0.00 0.00 0.00 3.56
2090 2389 0.385223 GAGCTGACAAAGTTGCTGCG 60.385 55.000 0.00 0.00 35.76 5.18
2216 2522 6.368516 ACCTTTGAATGTTGTTCTTTTGTGTG 59.631 34.615 0.00 0.00 0.00 3.82
2283 2591 6.461110 AAGGTTCAAATAAGATGAGCATGG 57.539 37.500 0.00 0.00 30.54 3.66
2298 2606 4.584327 GCTTCAAAGCCTTAAGGTTCAA 57.416 40.909 22.55 9.65 46.20 2.69
2311 2619 7.807977 ATACACATGTATTAGGGCTTCAAAG 57.192 36.000 0.00 0.00 37.97 2.77
2447 2755 0.251073 AGCATTTCCATTTGGCAGCC 59.749 50.000 3.66 3.66 34.44 4.85
2513 2824 8.963130 TGAAATTCTTTAAATACTTGCACGTTG 58.037 29.630 0.00 0.00 0.00 4.10
2515 2826 8.564574 TCTGAAATTCTTTAAATACTTGCACGT 58.435 29.630 0.05 0.05 0.00 4.49
2516 2827 8.948853 TCTGAAATTCTTTAAATACTTGCACG 57.051 30.769 0.00 0.00 0.00 5.34
2570 2883 8.873830 ACAAAATTCGTCAGTATCTTCATAGTG 58.126 33.333 0.00 0.00 37.29 2.74
2588 2901 9.352784 TGCAGCAACTTAATGTATACAAAATTC 57.647 29.630 10.14 0.00 0.00 2.17
2696 3009 8.728833 AGAATTCAGAAAAGTGCTAAGAATCTG 58.271 33.333 8.44 0.00 35.35 2.90
2697 3010 8.728833 CAGAATTCAGAAAAGTGCTAAGAATCT 58.271 33.333 8.44 0.00 0.00 2.40
2788 3103 6.200665 TGCAGATCAAATTGCAAAACTAACAC 59.799 34.615 1.71 0.00 46.42 3.32
2801 3116 8.525316 TGAATCATTGTAGTTGCAGATCAAATT 58.475 29.630 0.00 0.00 36.26 1.82
3006 3323 4.058124 GTTTTGTTTCCTTCTGGGATTGC 58.942 43.478 0.00 0.00 44.66 3.56
3345 3662 3.129287 CCAGTTGTTTCTTGAGTTGTGCT 59.871 43.478 0.00 0.00 0.00 4.40
3348 3665 2.427095 GGCCAGTTGTTTCTTGAGTTGT 59.573 45.455 0.00 0.00 0.00 3.32
3457 3774 0.321919 GTGCCTGGATCAACAGAGCA 60.322 55.000 0.00 9.44 40.97 4.26
3458 3775 0.035630 AGTGCCTGGATCAACAGAGC 60.036 55.000 0.00 0.93 40.97 4.09
3656 3973 5.838521 TGTTAATTTTCTCTGGGAAAGCCTT 59.161 36.000 2.55 2.13 43.68 4.35
3686 4003 5.581085 GGGCACAGTAAGACTACAATAGTTG 59.419 44.000 0.00 0.00 39.59 3.16
3989 4306 2.416547 GGTGACATGACATTCAACCTCG 59.583 50.000 0.00 0.00 0.00 4.63
4236 4553 9.117183 CTGTCAATTTCATAATCAAGATCAGGA 57.883 33.333 0.00 0.00 0.00 3.86
4308 4625 3.598264 TCTCTTGGGAGAAAGGAAGGAA 58.402 45.455 0.00 0.00 44.62 3.36
4338 4655 1.200716 CCACCTGTGCAGCAAACATAG 59.799 52.381 0.00 0.00 0.00 2.23
4459 4776 2.467880 GAGAGGTAACCATCAGGGACA 58.532 52.381 0.00 0.00 41.15 4.02
4571 4888 2.846206 AGGGACATGCTTGGATGTAAGA 59.154 45.455 7.71 0.00 36.67 2.10
4598 4915 4.334203 TCTTGCGCTTTTGTTAACTCTGAA 59.666 37.500 9.73 0.00 0.00 3.02
4821 5139 0.105555 TTGGGAATGGGGATGCATCC 60.106 55.000 33.90 33.90 46.41 3.51
5088 5468 1.006832 CTTGGGCGGTCAATAAGTCG 58.993 55.000 0.00 0.00 0.00 4.18
5123 5503 3.742882 CAGACAAAGTTGCTCGATCTTCA 59.257 43.478 0.00 0.00 0.00 3.02
5130 5510 1.331756 ACTTGCAGACAAAGTTGCTCG 59.668 47.619 0.00 0.00 40.87 5.03
5383 5763 0.182537 CACCTGAACCTGTGGTGGAA 59.817 55.000 0.00 0.00 45.29 3.53
5673 6053 5.048846 AGAACCTCTTTCTTAACCTGCAA 57.951 39.130 0.00 0.00 42.37 4.08
5732 6112 7.093421 ACTGAGAAACAAGGAAGTATAGGGTAC 60.093 40.741 0.00 0.00 0.00 3.34
5746 6130 5.239306 TGCAACATTCCTACTGAGAAACAAG 59.761 40.000 0.00 0.00 0.00 3.16
5747 6131 5.008613 GTGCAACATTCCTACTGAGAAACAA 59.991 40.000 0.00 0.00 36.32 2.83
5748 6132 4.515191 GTGCAACATTCCTACTGAGAAACA 59.485 41.667 0.00 0.00 36.32 2.83
5749 6133 4.083271 GGTGCAACATTCCTACTGAGAAAC 60.083 45.833 0.00 0.00 39.98 2.78
5842 6256 1.001633 TCTGGAGGTAAACACCGCTTC 59.998 52.381 0.00 0.00 34.28 3.86
5956 6370 1.227089 CTGCGAGGGGAACAGATCG 60.227 63.158 0.00 0.00 38.19 3.69
5981 6395 1.554160 AGGATCAGCTTGTCAGGACTG 59.446 52.381 0.65 0.00 0.00 3.51
5982 6396 1.554160 CAGGATCAGCTTGTCAGGACT 59.446 52.381 0.65 0.00 0.00 3.85
6009 6423 3.853475 CATGGACCCAATTCAAGAAAGC 58.147 45.455 0.00 0.00 0.00 3.51
6036 6450 4.426416 GGTTTCTGCTTGTTTTAAACCGT 58.574 39.130 5.32 0.00 39.60 4.83
6263 6679 8.254508 CCGGTCCATCCAATTTAAAAATTAAGA 58.745 33.333 0.00 2.44 36.52 2.10
6264 6680 7.011016 GCCGGTCCATCCAATTTAAAAATTAAG 59.989 37.037 1.90 0.00 36.52 1.85
6265 6681 6.819146 GCCGGTCCATCCAATTTAAAAATTAA 59.181 34.615 1.90 0.00 36.52 1.40
6346 6787 9.315363 ACTTCTCTCAGGAAAAACTAAGATCTA 57.685 33.333 0.00 0.00 0.00 1.98
6347 6788 8.201242 ACTTCTCTCAGGAAAAACTAAGATCT 57.799 34.615 0.00 0.00 0.00 2.75
6354 6795 9.487442 AGATCTATACTTCTCTCAGGAAAAACT 57.513 33.333 0.00 0.00 0.00 2.66
6414 6855 6.037172 ACTGTTTATTAATCCTAGCTTGTGCG 59.963 38.462 0.00 0.00 45.42 5.34
6418 6859 9.774742 GACAAACTGTTTATTAATCCTAGCTTG 57.225 33.333 5.31 0.00 0.00 4.01
6433 6874 9.778741 TCTAGATGTGAATTAGACAAACTGTTT 57.221 29.630 0.00 0.00 0.00 2.83
6434 6875 9.950496 ATCTAGATGTGAATTAGACAAACTGTT 57.050 29.630 3.89 0.00 0.00 3.16
6435 6876 9.376075 CATCTAGATGTGAATTAGACAAACTGT 57.624 33.333 22.42 0.00 34.23 3.55
6463 6904 8.383175 AGAGGTTAGATGTGACATCCTTAAAAA 58.617 33.333 21.05 4.81 0.00 1.94
6464 6905 7.918076 AGAGGTTAGATGTGACATCCTTAAAA 58.082 34.615 21.05 6.42 0.00 1.52
6465 6906 7.180229 TGAGAGGTTAGATGTGACATCCTTAAA 59.820 37.037 21.05 8.69 0.00 1.52
6466 6907 6.667848 TGAGAGGTTAGATGTGACATCCTTAA 59.332 38.462 21.05 11.73 0.00 1.85
6467 6908 6.096987 GTGAGAGGTTAGATGTGACATCCTTA 59.903 42.308 21.05 6.22 0.00 2.69
6468 6909 5.026121 TGAGAGGTTAGATGTGACATCCTT 58.974 41.667 21.05 7.22 0.00 3.36
6469 6910 4.404073 GTGAGAGGTTAGATGTGACATCCT 59.596 45.833 21.05 12.23 0.00 3.24
6470 6911 4.160439 TGTGAGAGGTTAGATGTGACATCC 59.840 45.833 21.05 7.40 0.00 3.51
6471 6912 5.330455 TGTGAGAGGTTAGATGTGACATC 57.670 43.478 17.46 17.46 0.00 3.06
6472 6913 5.745312 TTGTGAGAGGTTAGATGTGACAT 57.255 39.130 0.00 0.00 0.00 3.06
6473 6914 5.545063 TTTGTGAGAGGTTAGATGTGACA 57.455 39.130 0.00 0.00 0.00 3.58
6474 6915 9.988815 ATATATTTGTGAGAGGTTAGATGTGAC 57.011 33.333 0.00 0.00 0.00 3.67
6482 6923 9.219603 GCTGCATTATATATTTGTGAGAGGTTA 57.780 33.333 0.00 0.00 0.00 2.85
6483 6924 7.720957 TGCTGCATTATATATTTGTGAGAGGTT 59.279 33.333 0.00 0.00 0.00 3.50
6484 6925 7.226441 TGCTGCATTATATATTTGTGAGAGGT 58.774 34.615 0.00 0.00 0.00 3.85
6485 6926 7.677454 TGCTGCATTATATATTTGTGAGAGG 57.323 36.000 0.00 0.00 0.00 3.69
6486 6927 8.562052 TGTTGCTGCATTATATATTTGTGAGAG 58.438 33.333 1.84 0.00 0.00 3.20
6487 6928 8.449251 TGTTGCTGCATTATATATTTGTGAGA 57.551 30.769 1.84 0.00 0.00 3.27
6488 6929 9.177304 CTTGTTGCTGCATTATATATTTGTGAG 57.823 33.333 1.84 0.00 0.00 3.51
6489 6930 8.901793 TCTTGTTGCTGCATTATATATTTGTGA 58.098 29.630 1.84 0.00 0.00 3.58
6490 6931 9.518906 TTCTTGTTGCTGCATTATATATTTGTG 57.481 29.630 1.84 0.00 0.00 3.33
6542 6983 9.998106 ACTGATATACACTTTGTTTGTAGTCTT 57.002 29.630 0.00 0.00 33.01 3.01
6543 6984 9.998106 AACTGATATACACTTTGTTTGTAGTCT 57.002 29.630 0.00 0.00 33.01 3.24
6592 7033 6.276847 GGTCTGTTTAGGACACATCTAGATG 58.723 44.000 27.63 27.63 44.15 2.90
6593 7034 5.364157 GGGTCTGTTTAGGACACATCTAGAT 59.636 44.000 0.00 0.00 37.11 1.98
6594 7035 4.710375 GGGTCTGTTTAGGACACATCTAGA 59.290 45.833 0.00 0.00 37.11 2.43
6595 7036 4.466370 TGGGTCTGTTTAGGACACATCTAG 59.534 45.833 0.00 0.00 41.46 2.43
6596 7037 4.422057 TGGGTCTGTTTAGGACACATCTA 58.578 43.478 0.00 0.00 41.46 1.98
6597 7038 3.248024 TGGGTCTGTTTAGGACACATCT 58.752 45.455 0.00 0.00 41.46 2.90
6598 7039 3.695830 TGGGTCTGTTTAGGACACATC 57.304 47.619 0.00 0.00 41.46 3.06
6601 7042 8.570068 TTTATTTATGGGTCTGTTTAGGACAC 57.430 34.615 0.00 0.00 37.60 3.67
6602 7043 9.016438 GTTTTATTTATGGGTCTGTTTAGGACA 57.984 33.333 0.00 0.00 35.61 4.02
6603 7044 8.464404 GGTTTTATTTATGGGTCTGTTTAGGAC 58.536 37.037 0.00 0.00 0.00 3.85
6604 7045 7.616542 GGGTTTTATTTATGGGTCTGTTTAGGA 59.383 37.037 0.00 0.00 0.00 2.94
6605 7046 7.618117 AGGGTTTTATTTATGGGTCTGTTTAGG 59.382 37.037 0.00 0.00 0.00 2.69
6606 7047 8.466798 CAGGGTTTTATTTATGGGTCTGTTTAG 58.533 37.037 0.00 0.00 0.00 1.85
6607 7048 8.171400 TCAGGGTTTTATTTATGGGTCTGTTTA 58.829 33.333 0.00 0.00 0.00 2.01
6608 7049 7.013834 TCAGGGTTTTATTTATGGGTCTGTTT 58.986 34.615 0.00 0.00 0.00 2.83
6609 7050 6.557568 TCAGGGTTTTATTTATGGGTCTGTT 58.442 36.000 0.00 0.00 0.00 3.16
6610 7051 6.147437 TCAGGGTTTTATTTATGGGTCTGT 57.853 37.500 0.00 0.00 0.00 3.41
6611 7052 5.067805 GCTCAGGGTTTTATTTATGGGTCTG 59.932 44.000 0.00 0.00 0.00 3.51
6612 7053 5.201243 GCTCAGGGTTTTATTTATGGGTCT 58.799 41.667 0.00 0.00 0.00 3.85
6613 7054 4.341235 GGCTCAGGGTTTTATTTATGGGTC 59.659 45.833 0.00 0.00 0.00 4.46
6614 7055 4.264623 TGGCTCAGGGTTTTATTTATGGGT 60.265 41.667 0.00 0.00 0.00 4.51
6615 7056 4.285863 TGGCTCAGGGTTTTATTTATGGG 58.714 43.478 0.00 0.00 0.00 4.00
6616 7057 5.520376 CTGGCTCAGGGTTTTATTTATGG 57.480 43.478 0.00 0.00 0.00 2.74
6729 7170 7.835634 TGACAAACAATTTGAACTAAAACCC 57.164 32.000 8.24 0.00 43.26 4.11
6763 7216 2.490903 CTCTGGTTTCATGCTTTCCCTG 59.509 50.000 0.00 0.00 0.00 4.45
6764 7217 2.800250 CTCTGGTTTCATGCTTTCCCT 58.200 47.619 0.00 0.00 0.00 4.20
6765 7218 1.203287 GCTCTGGTTTCATGCTTTCCC 59.797 52.381 0.00 0.00 0.00 3.97
6766 7219 2.094854 CAGCTCTGGTTTCATGCTTTCC 60.095 50.000 0.00 0.00 32.86 3.13
6767 7220 2.094854 CCAGCTCTGGTTTCATGCTTTC 60.095 50.000 7.75 0.00 45.53 2.62
6768 7221 1.891150 CCAGCTCTGGTTTCATGCTTT 59.109 47.619 7.75 0.00 45.53 3.51
6769 7222 1.542492 CCAGCTCTGGTTTCATGCTT 58.458 50.000 7.75 0.00 45.53 3.91
6770 7223 3.261250 CCAGCTCTGGTTTCATGCT 57.739 52.632 7.75 0.00 45.53 3.79
6781 7234 8.914011 AGTTTGAACTTAAATAAAACCAGCTCT 58.086 29.630 0.00 0.00 35.21 4.09
6870 7326 3.711059 GACTAGGCCGTCCGGGAGA 62.711 68.421 7.97 0.00 38.47 3.71
6894 7350 2.945008 CAAGAAGAGGCTTGACAACACA 59.055 45.455 0.00 0.00 46.31 3.72
6908 7364 3.068881 CACCGGCCCTCAAGAAGA 58.931 61.111 0.00 0.00 0.00 2.87
6915 7371 4.821589 CGAGAAGCACCGGCCCTC 62.822 72.222 0.00 0.00 42.56 4.30
6921 7377 4.796231 CGTCCCCGAGAAGCACCG 62.796 72.222 0.00 0.00 35.63 4.94


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

AutoCloner maintained by Alex Coulton.