Multiple sequence alignment - TraesCS5B01G303800

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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 TraesCS5B01G303800 chr5B 100.000 3713 0 0 1 3713 488110547 488114259 0.000000e+00 6857.0
1 TraesCS5B01G303800 chr5B 91.162 1471 84 27 1366 2825 488015162 488016597 0.000000e+00 1954.0
2 TraesCS5B01G303800 chr5B 87.651 332 21 4 952 1268 488014557 488014883 5.860000e-98 368.0
3 TraesCS5B01G303800 chr5B 88.318 214 21 1 73 282 225021804 225022017 1.710000e-63 254.0
4 TraesCS5B01G303800 chr5D 92.789 1567 84 16 1266 2825 407021306 407019762 0.000000e+00 2241.0
5 TraesCS5B01G303800 chr5D 91.877 1268 79 8 12 1268 407022755 407021501 0.000000e+00 1749.0
6 TraesCS5B01G303800 chr5D 88.068 704 66 11 2120 2823 407107031 407106346 0.000000e+00 819.0
7 TraesCS5B01G303800 chr5D 87.636 550 39 14 3184 3713 407014739 407014199 2.450000e-171 612.0
8 TraesCS5B01G303800 chr5D 87.963 324 20 5 958 1268 407108681 407108364 7.580000e-97 364.0
9 TraesCS5B01G303800 chr5D 82.548 361 41 13 1345 1699 407108072 407107728 7.800000e-77 298.0
10 TraesCS5B01G303800 chr5A 89.844 1477 97 28 1366 2823 512458973 512460415 0.000000e+00 1847.0
11 TraesCS5B01G303800 chr5A 93.676 1012 56 7 1817 2823 512600780 512601788 0.000000e+00 1507.0
12 TraesCS5B01G303800 chr5A 89.079 1227 62 23 580 1788 512599608 512600780 0.000000e+00 1458.0
13 TraesCS5B01G303800 chr5A 86.601 612 40 17 3118 3698 512619082 512619682 4.040000e-179 638.0
14 TraesCS5B01G303800 chr5A 89.086 339 25 7 1 327 512583027 512583365 9.600000e-111 411.0
15 TraesCS5B01G303800 chr5A 82.456 171 12 8 2893 3063 512604779 512604931 2.330000e-27 134.0
16 TraesCS5B01G303800 chr5A 98.182 55 1 0 952 1006 512458536 512458590 3.050000e-16 97.1
17 TraesCS5B01G303800 chr2D 80.712 674 101 19 2116 2781 28896083 28896735 7.160000e-137 497.0
18 TraesCS5B01G303800 chr2D 81.433 614 96 13 2116 2723 28828683 28829284 1.550000e-133 486.0
19 TraesCS5B01G303800 chr2D 85.463 227 30 1 1003 1229 28827641 28827864 2.230000e-57 233.0
20 TraesCS5B01G303800 chr2A 81.656 616 89 14 2116 2726 30858344 30858940 1.200000e-134 490.0
21 TraesCS5B01G303800 chr2A 81.059 623 101 11 2110 2728 30765792 30766401 7.210000e-132 481.0
22 TraesCS5B01G303800 chr2A 85.950 242 29 3 989 1228 30764403 30764641 1.710000e-63 254.0
23 TraesCS5B01G303800 chr2A 87.963 216 22 1 74 285 680259453 680259238 6.160000e-63 252.0
24 TraesCS5B01G303800 chr2A 90.909 66 6 0 284 349 41172398 41172463 5.110000e-14 89.8
25 TraesCS5B01G303800 chr2B 79.792 673 105 17 2116 2781 46672929 46673577 9.400000e-126 460.0
26 TraesCS5B01G303800 chr2B 79.605 608 102 14 2110 2713 46505456 46506045 2.060000e-112 416.0
27 TraesCS5B01G303800 chr2B 87.558 217 23 1 73 285 640515872 640515656 7.960000e-62 248.0
28 TraesCS5B01G303800 chr2B 86.344 227 26 3 61 282 797407191 797406965 3.700000e-60 243.0
29 TraesCS5B01G303800 chr2B 85.345 232 31 1 998 1229 46504374 46504602 1.720000e-58 237.0
30 TraesCS5B01G303800 chr2B 90.141 71 6 1 279 349 63186881 63186950 1.420000e-14 91.6
31 TraesCS5B01G303800 chr4B 87.131 373 34 8 3210 3568 185241057 185240685 9.600000e-111 411.0
32 TraesCS5B01G303800 chr4B 83.904 292 39 3 3285 3568 672244142 672243851 4.730000e-69 272.0
33 TraesCS5B01G303800 chr4A 87.131 373 34 7 3210 3568 448509059 448509431 9.600000e-111 411.0
34 TraesCS5B01G303800 chr4D 86.595 373 36 7 3210 3568 122206118 122205746 2.080000e-107 399.0
35 TraesCS5B01G303800 chr7A 84.677 372 46 5 3205 3568 213114639 213114271 9.800000e-96 361.0
36 TraesCS5B01G303800 chr7B 84.682 346 45 3 3231 3568 171984449 171984794 4.590000e-89 339.0
37 TraesCS5B01G303800 chrUn 81.421 366 48 9 3211 3568 100076686 100077039 7.850000e-72 281.0
38 TraesCS5B01G303800 chrUn 82.624 282 38 6 12 282 39759799 39760080 4.790000e-59 239.0
39 TraesCS5B01G303800 chr3B 83.513 279 33 4 12 279 289599144 289599420 7.960000e-62 248.0
40 TraesCS5B01G303800 chr3B 86.283 226 27 1 61 282 289629870 289630095 3.700000e-60 243.0
41 TraesCS5B01G303800 chr3D 90.625 64 4 2 1121 1184 511326614 511326553 2.380000e-12 84.2
42 TraesCS5B01G303800 chr3A 90.625 64 4 2 1121 1184 647453231 647453170 2.380000e-12 84.2


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 TraesCS5B01G303800 chr5B 488110547 488114259 3712 False 6857.000000 6857 100.000000 1 3713 1 chr5B.!!$F2 3712
1 TraesCS5B01G303800 chr5B 488014557 488016597 2040 False 1161.000000 1954 89.406500 952 2825 2 chr5B.!!$F3 1873
2 TraesCS5B01G303800 chr5D 407019762 407022755 2993 True 1995.000000 2241 92.333000 12 2825 2 chr5D.!!$R2 2813
3 TraesCS5B01G303800 chr5D 407014199 407014739 540 True 612.000000 612 87.636000 3184 3713 1 chr5D.!!$R1 529
4 TraesCS5B01G303800 chr5D 407106346 407108681 2335 True 493.666667 819 86.193000 958 2823 3 chr5D.!!$R3 1865
5 TraesCS5B01G303800 chr5A 512599608 512604931 5323 False 1033.000000 1507 88.403667 580 3063 3 chr5A.!!$F4 2483
6 TraesCS5B01G303800 chr5A 512458536 512460415 1879 False 972.050000 1847 94.013000 952 2823 2 chr5A.!!$F3 1871
7 TraesCS5B01G303800 chr5A 512619082 512619682 600 False 638.000000 638 86.601000 3118 3698 1 chr5A.!!$F2 580
8 TraesCS5B01G303800 chr2D 28896083 28896735 652 False 497.000000 497 80.712000 2116 2781 1 chr2D.!!$F1 665
9 TraesCS5B01G303800 chr2D 28827641 28829284 1643 False 359.500000 486 83.448000 1003 2723 2 chr2D.!!$F2 1720
10 TraesCS5B01G303800 chr2A 30858344 30858940 596 False 490.000000 490 81.656000 2116 2726 1 chr2A.!!$F1 610
11 TraesCS5B01G303800 chr2A 30764403 30766401 1998 False 367.500000 481 83.504500 989 2728 2 chr2A.!!$F3 1739
12 TraesCS5B01G303800 chr2B 46672929 46673577 648 False 460.000000 460 79.792000 2116 2781 1 chr2B.!!$F1 665
13 TraesCS5B01G303800 chr2B 46504374 46506045 1671 False 326.500000 416 82.475000 998 2713 2 chr2B.!!$F3 1715

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
456 468 0.038166 ATGGTCCAGGTGAAACGCAT 59.962 50.0 0.00 0.0 38.12 4.73 F
1625 1932 0.323725 ACCATCCTGAATTGCCGCTT 60.324 50.0 0.00 0.0 0.00 4.68 F
2295 3210 0.776810 TTCCAATGAACAGGGCCAGA 59.223 50.0 6.18 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2855 0.036105 TCATTGTCTGGCGATGTGCT 60.036 50.0 9.21 0.0 45.43 4.40 R
2534 3453 0.032267 GTAGCTGCCGTAGTGATCCC 59.968 60.0 0.00 0.0 0.00 3.85 R
3141 6993 0.250166 GCCGGGGAAACGCATACTAT 60.250 55.0 2.18 0.0 45.02 2.12 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
31 32 4.070552 GGCCAGAACGGAGCGTCT 62.071 66.667 0.00 0.00 39.99 4.18
35 36 0.242825 CCAGAACGGAGCGTCTACAA 59.757 55.000 0.00 0.00 39.99 2.41
38 39 1.338973 AGAACGGAGCGTCTACAACAA 59.661 47.619 0.00 0.00 39.99 2.83
70 71 0.668706 CATCTTCATCCCTAGCCGCG 60.669 60.000 0.00 0.00 0.00 6.46
111 112 3.708451 TCACCACTATAGTGCTTCCTCA 58.292 45.455 24.85 3.64 44.34 3.86
113 114 4.716784 TCACCACTATAGTGCTTCCTCATT 59.283 41.667 24.85 0.20 44.34 2.57
123 124 8.894768 ATAGTGCTTCCTCATTTAGTTCATAC 57.105 34.615 0.00 0.00 0.00 2.39
139 140 5.232202 AGTTCATACTTGTAATCGTGCATCG 59.768 40.000 0.00 0.00 41.41 3.84
158 159 5.765176 CATCGCACAATTCATCCATTGTAT 58.235 37.500 0.00 0.00 44.08 2.29
164 165 7.306341 CGCACAATTCATCCATTGTATGATTTG 60.306 37.037 17.93 17.93 44.08 2.32
190 191 7.220300 GCAATCAATCAATCTTCAAGATGTGTC 59.780 37.037 0.00 0.00 34.65 3.67
194 195 7.449395 TCAATCAATCTTCAAGATGTGTCCTTT 59.551 33.333 0.00 0.00 34.65 3.11
196 197 7.912056 TCAATCTTCAAGATGTGTCCTTTAG 57.088 36.000 0.00 0.00 34.65 1.85
205 206 7.556275 TCAAGATGTGTCCTTTAGTGTTTTCTT 59.444 33.333 0.00 0.00 0.00 2.52
208 209 7.775561 AGATGTGTCCTTTAGTGTTTTCTTCTT 59.224 33.333 0.00 0.00 0.00 2.52
209 210 7.083875 TGTGTCCTTTAGTGTTTTCTTCTTG 57.916 36.000 0.00 0.00 0.00 3.02
210 211 5.971792 GTGTCCTTTAGTGTTTTCTTCTTGC 59.028 40.000 0.00 0.00 0.00 4.01
219 220 5.121454 AGTGTTTTCTTCTTGCGATCTGATC 59.879 40.000 7.60 7.60 0.00 2.92
221 222 6.311445 GTGTTTTCTTCTTGCGATCTGATCTA 59.689 38.462 15.16 2.19 0.00 1.98
226 227 3.646946 TCTTGCGATCTGATCTACATGC 58.353 45.455 15.16 10.92 0.00 4.06
227 228 3.320256 TCTTGCGATCTGATCTACATGCT 59.680 43.478 15.16 0.00 0.00 3.79
237 238 6.800543 TCTGATCTACATGCTTGAGTAGTTC 58.199 40.000 6.60 7.74 38.97 3.01
239 240 4.371855 TCTACATGCTTGAGTAGTTCGG 57.628 45.455 6.60 0.00 38.97 4.30
251 252 5.263599 TGAGTAGTTCGGTAAGGTATGGAA 58.736 41.667 0.00 0.00 0.00 3.53
258 259 2.104111 CGGTAAGGTATGGAATGAGGCA 59.896 50.000 0.00 0.00 0.00 4.75
282 283 6.731292 TGAGCCTTGCAACTCTCTATATTA 57.269 37.500 18.55 1.60 33.92 0.98
283 284 6.753180 TGAGCCTTGCAACTCTCTATATTAG 58.247 40.000 18.55 0.00 33.92 1.73
288 289 7.255801 GCCTTGCAACTCTCTATATTAGTCTCT 60.256 40.741 0.00 0.00 0.00 3.10
364 365 8.792830 TCTACCTTTGGTTGAAGATAATCTTG 57.207 34.615 0.00 0.00 35.39 3.02
366 367 7.454260 ACCTTTGGTTGAAGATAATCTTGAC 57.546 36.000 0.00 0.00 31.37 3.18
370 371 5.175859 TGGTTGAAGATAATCTTGACGTCC 58.824 41.667 14.12 0.00 36.73 4.79
384 385 0.108804 ACGTCCATACAAGGCTCACG 60.109 55.000 0.00 0.00 33.94 4.35
396 397 0.602638 GGCTCACGTGAACACCATCA 60.603 55.000 20.49 0.00 0.00 3.07
397 398 1.225855 GCTCACGTGAACACCATCAA 58.774 50.000 20.49 0.00 0.00 2.57
433 445 6.953743 GTCACAACATCACAACAATCGTATAC 59.046 38.462 0.00 0.00 0.00 1.47
456 468 0.038166 ATGGTCCAGGTGAAACGCAT 59.962 50.000 0.00 0.00 38.12 4.73
467 479 0.452784 GAAACGCATCGTGAACCAGC 60.453 55.000 0.00 0.00 39.99 4.85
471 483 1.965930 GCATCGTGAACCAGCCACA 60.966 57.895 0.00 0.00 34.36 4.17
498 510 9.784680 GTAGATCGAGTACAAAATAGAAAGACA 57.215 33.333 0.00 0.00 0.00 3.41
500 512 9.360093 AGATCGAGTACAAAATAGAAAGACAAG 57.640 33.333 0.00 0.00 0.00 3.16
524 536 4.684703 AGTTAACTCGTGAATGAAGAACGG 59.315 41.667 1.12 0.00 37.87 4.44
563 575 1.162085 ACTCTGGCCCCCTCTTCTT 59.838 57.895 0.00 0.00 0.00 2.52
595 607 2.662791 GCATTAACACACGTGACTGCTG 60.663 50.000 25.01 12.24 0.00 4.41
663 675 1.014352 ACAACGTCACAACAAGCTCC 58.986 50.000 0.00 0.00 0.00 4.70
683 695 0.689623 GGCCAGATGGTCCAGATAGG 59.310 60.000 0.00 0.00 37.57 2.57
715 750 2.173669 CAGCCACATTAGACCGCGG 61.174 63.158 26.86 26.86 0.00 6.46
716 751 2.895372 GCCACATTAGACCGCGGG 60.895 66.667 31.76 13.10 0.00 6.13
717 752 2.897207 CCACATTAGACCGCGGGA 59.103 61.111 31.76 11.78 0.00 5.14
718 753 1.227263 CCACATTAGACCGCGGGAG 60.227 63.158 31.76 14.16 0.00 4.30
730 765 3.136123 CGGGAGCCAGCCACATTG 61.136 66.667 0.00 0.00 0.00 2.82
731 766 2.757099 GGGAGCCAGCCACATTGG 60.757 66.667 0.00 0.00 41.55 3.16
732 767 2.356278 GGAGCCAGCCACATTGGA 59.644 61.111 0.00 0.00 40.96 3.53
733 768 2.048603 GGAGCCAGCCACATTGGAC 61.049 63.158 0.00 0.00 40.96 4.02
734 769 2.036256 AGCCAGCCACATTGGACC 59.964 61.111 0.00 0.00 40.96 4.46
735 770 3.443045 GCCAGCCACATTGGACCG 61.443 66.667 0.00 0.00 40.96 4.79
736 771 3.443045 CCAGCCACATTGGACCGC 61.443 66.667 0.00 0.00 40.96 5.68
737 772 3.803082 CAGCCACATTGGACCGCG 61.803 66.667 0.00 0.00 40.96 6.46
738 773 4.329545 AGCCACATTGGACCGCGT 62.330 61.111 4.92 0.00 40.96 6.01
739 774 2.435234 GCCACATTGGACCGCGTA 60.435 61.111 4.92 0.00 40.96 4.42
740 775 2.746803 GCCACATTGGACCGCGTAC 61.747 63.158 4.92 0.00 40.96 3.67
814 849 2.586635 GGTGTCGTCCAACGCACA 60.587 61.111 20.18 12.13 44.34 4.57
942 980 4.942944 TCCCTCACTTTCATAGTACTCCA 58.057 43.478 0.00 0.00 34.56 3.86
1065 1122 2.285144 GGGTTCCCCTCCGAGGAA 60.285 66.667 16.69 0.18 41.34 3.36
1266 1327 9.830975 AATTTGTTTTAACCTAGCATCAAACTT 57.169 25.926 0.00 0.00 0.00 2.66
1267 1328 8.641499 TTTGTTTTAACCTAGCATCAAACTTG 57.359 30.769 0.00 0.00 0.00 3.16
1268 1329 7.341445 TGTTTTAACCTAGCATCAAACTTGT 57.659 32.000 0.00 0.00 0.00 3.16
1269 1330 7.777095 TGTTTTAACCTAGCATCAAACTTGTT 58.223 30.769 0.00 0.00 0.00 2.83
1270 1331 7.704472 TGTTTTAACCTAGCATCAAACTTGTTG 59.296 33.333 0.00 0.00 0.00 3.33
1271 1332 4.853924 AACCTAGCATCAAACTTGTTGG 57.146 40.909 3.40 0.00 0.00 3.77
1272 1333 4.098914 ACCTAGCATCAAACTTGTTGGA 57.901 40.909 3.40 0.00 0.00 3.53
1273 1334 4.666512 ACCTAGCATCAAACTTGTTGGAT 58.333 39.130 0.00 0.00 0.00 3.41
1274 1335 4.702131 ACCTAGCATCAAACTTGTTGGATC 59.298 41.667 0.70 0.00 0.00 3.36
1275 1336 4.946157 CCTAGCATCAAACTTGTTGGATCT 59.054 41.667 0.70 4.88 0.00 2.75
1276 1337 4.778534 AGCATCAAACTTGTTGGATCTG 57.221 40.909 0.70 0.00 0.00 2.90
1277 1338 4.147321 AGCATCAAACTTGTTGGATCTGT 58.853 39.130 0.70 0.00 0.00 3.41
1278 1339 5.316167 AGCATCAAACTTGTTGGATCTGTA 58.684 37.500 0.70 0.00 0.00 2.74
1279 1340 5.413833 AGCATCAAACTTGTTGGATCTGTAG 59.586 40.000 0.70 0.00 0.00 2.74
1280 1341 5.634896 CATCAAACTTGTTGGATCTGTAGC 58.365 41.667 0.70 0.00 0.00 3.58
1400 1705 7.233348 ACATGGATTCAGCCTTTTCTTTTTCTA 59.767 33.333 0.00 0.00 0.00 2.10
1439 1746 2.156917 CTGAAGCTGAAGGCATGACAA 58.843 47.619 0.00 0.00 44.79 3.18
1625 1932 0.323725 ACCATCCTGAATTGCCGCTT 60.324 50.000 0.00 0.00 0.00 4.68
1702 2010 6.702329 CCAGGTCTGGTTATCATTATACTCC 58.298 44.000 8.78 0.00 45.53 3.85
1799 2334 3.874392 ATCAAATGTAACCTTGGCTGC 57.126 42.857 0.00 0.00 0.00 5.25
1812 2347 2.088104 TGGCTGCTATACTGGCTAGT 57.912 50.000 8.18 8.18 42.47 2.57
1813 2348 3.238788 TGGCTGCTATACTGGCTAGTA 57.761 47.619 12.75 12.75 43.19 1.82
1831 2366 6.644592 GGCTAGTATATTTTCTCTGACTGCTG 59.355 42.308 0.00 0.00 0.00 4.41
1839 2374 3.117491 TCTCTGACTGCTGGAAACTTG 57.883 47.619 0.00 0.00 0.00 3.16
1985 2805 1.809651 GCCAAGATCTCTGGCTGCTAC 60.810 57.143 27.75 9.75 44.72 3.58
2035 2855 4.098914 AGGTTTGTGCCTACTCATTTGA 57.901 40.909 0.00 0.00 37.04 2.69
2043 2880 2.286294 GCCTACTCATTTGAGCACATCG 59.714 50.000 7.48 0.00 45.79 3.84
2075 2912 8.815189 CAATGAGTAGTTCTGTTCATACTGATG 58.185 37.037 0.00 0.00 33.04 3.07
2114 3022 6.037062 GCTGTTGGCAAAACTTTCTATTTTGT 59.963 34.615 0.00 0.00 45.03 2.83
2163 3071 6.096423 AGGTCAACCTCCTAAAAACAAAGTTC 59.904 38.462 0.00 0.00 44.77 3.01
2235 3143 3.441572 CACTGAAGAGGTTAATTGCAGGG 59.558 47.826 0.00 0.00 0.00 4.45
2295 3210 0.776810 TTCCAATGAACAGGGCCAGA 59.223 50.000 6.18 0.00 0.00 3.86
2413 3331 1.338105 CGGTGCTTCTCAACATGAGGA 60.338 52.381 0.00 0.00 44.39 3.71
2534 3453 0.833287 ATGGAGGGGTTCATCGTGAG 59.167 55.000 0.00 0.00 0.00 3.51
2752 3678 2.025155 TCCTGGATCGAGAAGTACTGC 58.975 52.381 6.27 0.00 0.00 4.40
2755 3681 1.135139 TGGATCGAGAAGTACTGCTGC 59.865 52.381 8.55 0.00 0.00 5.25
2781 3707 5.746245 CGTTCAGAGACCAGAATTCAGATAC 59.254 44.000 8.44 0.00 0.00 2.24
2782 3708 6.625960 CGTTCAGAGACCAGAATTCAGATACA 60.626 42.308 8.44 0.00 0.00 2.29
2783 3709 6.462552 TCAGAGACCAGAATTCAGATACAG 57.537 41.667 8.44 0.00 0.00 2.74
2789 3721 9.853555 GAGACCAGAATTCAGATACAGTATATG 57.146 37.037 8.44 8.68 0.00 1.78
2810 3742 0.896226 AGAGAAGTACTTGGTCCGGC 59.104 55.000 14.14 0.00 0.00 6.13
2859 3838 8.348507 GGAAGCTGGAATGAACTATAATCTTTG 58.651 37.037 0.00 0.00 0.00 2.77
2864 3843 8.383318 TGGAATGAACTATAATCTTTGCTAGC 57.617 34.615 8.10 8.10 0.00 3.42
2865 3844 8.213679 TGGAATGAACTATAATCTTTGCTAGCT 58.786 33.333 17.23 0.00 0.00 3.32
2866 3845 9.712305 GGAATGAACTATAATCTTTGCTAGCTA 57.288 33.333 17.23 5.31 0.00 3.32
2916 6768 2.540383 TGGTACTCATCCTGCACTCTT 58.460 47.619 0.00 0.00 0.00 2.85
2941 6793 2.203684 CCCAGCAAAGGGCCAGTT 60.204 61.111 6.18 0.00 46.50 3.16
2955 6807 0.096976 CCAGTTTAGGCGACGCATTG 59.903 55.000 23.09 9.57 0.00 2.82
2958 6810 2.607635 CAGTTTAGGCGACGCATTGTAT 59.392 45.455 23.09 0.00 0.00 2.29
2959 6811 3.799963 CAGTTTAGGCGACGCATTGTATA 59.200 43.478 23.09 0.00 0.00 1.47
2969 6821 5.320723 CGACGCATTGTATAACACACAAAT 58.679 37.500 0.00 0.00 39.22 2.32
2975 6827 8.483218 CGCATTGTATAACACACAAATTTTGAA 58.517 29.630 15.81 0.00 39.22 2.69
2985 6837 8.647143 ACACACAAATTTTGAATTACAGAAGG 57.353 30.769 15.81 0.00 0.00 3.46
2986 6838 7.710475 ACACACAAATTTTGAATTACAGAAGGG 59.290 33.333 15.81 0.00 0.00 3.95
2987 6839 7.925483 CACACAAATTTTGAATTACAGAAGGGA 59.075 33.333 15.81 0.00 0.00 4.20
2988 6840 8.650490 ACACAAATTTTGAATTACAGAAGGGAT 58.350 29.630 15.81 0.00 0.00 3.85
2989 6841 9.143631 CACAAATTTTGAATTACAGAAGGGATC 57.856 33.333 15.81 0.00 0.00 3.36
2990 6842 8.314021 ACAAATTTTGAATTACAGAAGGGATCC 58.686 33.333 15.81 1.92 0.00 3.36
2991 6843 7.423844 AATTTTGAATTACAGAAGGGATCCC 57.576 36.000 24.59 24.59 0.00 3.85
2998 6850 5.630415 TTACAGAAGGGATCCCATTACAG 57.370 43.478 32.69 18.12 38.92 2.74
3002 6854 4.884164 CAGAAGGGATCCCATTACAGAAAC 59.116 45.833 32.69 6.27 38.92 2.78
3004 6856 5.194537 AGAAGGGATCCCATTACAGAAACAT 59.805 40.000 32.69 3.83 38.92 2.71
3005 6857 6.389869 AGAAGGGATCCCATTACAGAAACATA 59.610 38.462 32.69 0.00 38.92 2.29
3056 6908 6.479006 TCTTCACAGAGAAATCAATGACCAT 58.521 36.000 0.00 0.00 35.40 3.55
3057 6909 6.373495 TCTTCACAGAGAAATCAATGACCATG 59.627 38.462 0.00 0.00 35.40 3.66
3058 6910 5.807909 TCACAGAGAAATCAATGACCATGA 58.192 37.500 0.00 0.00 0.00 3.07
3059 6911 5.645067 TCACAGAGAAATCAATGACCATGAC 59.355 40.000 0.00 0.00 0.00 3.06
3061 6913 6.150641 CACAGAGAAATCAATGACCATGACTT 59.849 38.462 0.00 0.00 0.00 3.01
3062 6914 6.150641 ACAGAGAAATCAATGACCATGACTTG 59.849 38.462 0.00 0.00 0.00 3.16
3063 6915 5.125097 AGAGAAATCAATGACCATGACTTGC 59.875 40.000 0.00 0.00 0.00 4.01
3064 6916 4.768448 AGAAATCAATGACCATGACTTGCA 59.232 37.500 0.00 0.00 0.00 4.08
3065 6917 4.713824 AATCAATGACCATGACTTGCAG 57.286 40.909 0.00 0.00 0.00 4.41
3066 6918 2.439409 TCAATGACCATGACTTGCAGG 58.561 47.619 0.00 0.00 0.00 4.85
3070 6922 3.136123 CCATGACTTGCAGGGCCG 61.136 66.667 0.00 0.00 42.18 6.13
3071 6923 3.136123 CATGACTTGCAGGGCCGG 61.136 66.667 0.00 0.00 0.00 6.13
3072 6924 4.431131 ATGACTTGCAGGGCCGGG 62.431 66.667 2.18 0.00 0.00 5.73
3074 6926 4.660938 GACTTGCAGGGCCGGGTT 62.661 66.667 2.18 0.00 0.00 4.11
3075 6927 3.253838 ACTTGCAGGGCCGGGTTA 61.254 61.111 2.18 0.00 0.00 2.85
3076 6928 2.438434 CTTGCAGGGCCGGGTTAG 60.438 66.667 2.18 0.00 0.00 2.34
3077 6929 4.733542 TTGCAGGGCCGGGTTAGC 62.734 66.667 2.18 1.62 0.00 3.09
3079 6931 3.476419 GCAGGGCCGGGTTAGCTA 61.476 66.667 2.18 0.00 0.00 3.32
3080 6932 2.504519 CAGGGCCGGGTTAGCTAC 59.495 66.667 2.18 0.00 0.00 3.58
3081 6933 2.767073 AGGGCCGGGTTAGCTACC 60.767 66.667 2.18 0.00 46.99 3.18
3091 6943 3.162202 GGTTAGCTACCGAAGAGAACC 57.838 52.381 0.00 0.00 37.12 3.62
3092 6944 2.759535 GGTTAGCTACCGAAGAGAACCT 59.240 50.000 0.00 0.00 37.98 3.50
3093 6945 3.195182 GGTTAGCTACCGAAGAGAACCTT 59.805 47.826 0.00 0.00 37.98 3.50
3094 6946 4.422840 GTTAGCTACCGAAGAGAACCTTC 58.577 47.826 0.00 0.00 46.05 3.46
3104 6956 4.464069 AAGAGAACCTTCAGAATCCGAG 57.536 45.455 0.00 0.00 0.00 4.63
3105 6957 3.436243 AGAGAACCTTCAGAATCCGAGT 58.564 45.455 0.00 0.00 0.00 4.18
3106 6958 4.601084 AGAGAACCTTCAGAATCCGAGTA 58.399 43.478 0.00 0.00 0.00 2.59
3107 6959 4.399934 AGAGAACCTTCAGAATCCGAGTAC 59.600 45.833 0.00 0.00 0.00 2.73
3108 6960 3.128938 AGAACCTTCAGAATCCGAGTACG 59.871 47.826 0.00 0.00 39.43 3.67
3109 6961 2.444421 ACCTTCAGAATCCGAGTACGT 58.556 47.619 0.00 0.00 37.88 3.57
3110 6962 2.422832 ACCTTCAGAATCCGAGTACGTC 59.577 50.000 0.00 0.00 37.88 4.34
3111 6963 2.223525 CCTTCAGAATCCGAGTACGTCC 60.224 54.545 0.00 0.00 37.88 4.79
3112 6964 1.386533 TCAGAATCCGAGTACGTCCC 58.613 55.000 0.00 0.00 37.88 4.46
3113 6965 0.029035 CAGAATCCGAGTACGTCCCG 59.971 60.000 0.00 0.00 37.88 5.14
3114 6966 0.393537 AGAATCCGAGTACGTCCCGT 60.394 55.000 0.00 0.00 44.35 5.28
3115 6967 0.028637 GAATCCGAGTACGTCCCGTC 59.971 60.000 0.00 0.00 41.54 4.79
3116 6968 1.709147 AATCCGAGTACGTCCCGTCG 61.709 60.000 0.00 0.00 41.54 5.12
3135 6987 1.066587 GCCGTCTCCAGAATCCGAG 59.933 63.158 0.00 0.00 0.00 4.63
3137 6989 1.323412 CCGTCTCCAGAATCCGAGAT 58.677 55.000 1.65 0.00 37.46 2.75
3138 6990 1.683917 CCGTCTCCAGAATCCGAGATT 59.316 52.381 1.65 0.00 37.46 2.40
3139 6991 2.544694 CCGTCTCCAGAATCCGAGATTG 60.545 54.545 4.18 0.00 37.46 2.67
3140 6992 2.099921 CGTCTCCAGAATCCGAGATTGT 59.900 50.000 4.18 0.00 37.46 2.71
3141 6993 3.315470 CGTCTCCAGAATCCGAGATTGTA 59.685 47.826 4.18 0.00 37.46 2.41
3142 6994 4.022762 CGTCTCCAGAATCCGAGATTGTAT 60.023 45.833 4.18 0.00 37.46 2.29
3143 6995 5.181433 CGTCTCCAGAATCCGAGATTGTATA 59.819 44.000 4.18 0.00 37.46 1.47
3156 7008 5.345202 CGAGATTGTATAGTATGCGTTTCCC 59.655 44.000 0.00 0.00 0.00 3.97
3174 7026 1.170290 CCCGGCTTCCGTTTTCAACT 61.170 55.000 0.00 0.00 46.80 3.16
3175 7027 0.040425 CCGGCTTCCGTTTTCAACTG 60.040 55.000 4.47 0.00 46.80 3.16
3176 7028 0.040425 CGGCTTCCGTTTTCAACTGG 60.040 55.000 0.00 0.00 42.73 4.00
3177 7029 0.313987 GGCTTCCGTTTTCAACTGGG 59.686 55.000 0.00 0.00 0.00 4.45
3178 7030 1.029681 GCTTCCGTTTTCAACTGGGT 58.970 50.000 0.00 0.00 0.00 4.51
3179 7031 1.407618 GCTTCCGTTTTCAACTGGGTT 59.592 47.619 0.00 0.00 0.00 4.11
3181 7033 3.677700 GCTTCCGTTTTCAACTGGGTTTT 60.678 43.478 0.00 0.00 0.00 2.43
3182 7034 4.500127 CTTCCGTTTTCAACTGGGTTTTT 58.500 39.130 0.00 0.00 0.00 1.94
3225 7087 1.338107 AAACTAGGGTTTTGCCTGCC 58.662 50.000 0.00 0.00 42.28 4.85
3226 7088 0.893727 AACTAGGGTTTTGCCTGCCG 60.894 55.000 0.00 0.00 37.43 5.69
3227 7089 1.002624 CTAGGGTTTTGCCTGCCGA 60.003 57.895 0.00 0.00 37.43 5.54
3228 7090 1.302993 TAGGGTTTTGCCTGCCGAC 60.303 57.895 0.00 0.00 37.43 4.79
3369 7232 3.887110 TCAACTACTTCGAGTCCAAGTCA 59.113 43.478 6.40 0.00 35.63 3.41
3370 7233 4.523173 TCAACTACTTCGAGTCCAAGTCAT 59.477 41.667 6.40 0.00 35.63 3.06
3371 7234 4.442375 ACTACTTCGAGTCCAAGTCATG 57.558 45.455 6.40 2.31 35.63 3.07
3392 7270 3.745803 GTCGTCGTCGAGCCCCTT 61.746 66.667 4.68 0.00 46.96 3.95
3396 7274 2.036098 TCGTCGAGCCCCTTGGTA 59.964 61.111 0.00 0.00 0.00 3.25
3403 7281 4.462280 GCCCCTTGGTACCCGTCG 62.462 72.222 10.07 0.00 0.00 5.12
3493 7374 3.126879 CCGATTCGCAGCTTGGCA 61.127 61.111 0.00 0.00 0.00 4.92
3575 7456 3.953652 TGGGGAAGGAGGAGGCCA 61.954 66.667 5.01 0.00 0.00 5.36
3586 7470 2.357517 GAGGCCATCGGGTATGCG 60.358 66.667 5.01 0.00 36.17 4.73
3625 7509 2.771328 CTTGCCTTCGCTCCCCCTTT 62.771 60.000 0.00 0.00 35.36 3.11
3631 7515 0.965363 TTCGCTCCCCCTTTTGATGC 60.965 55.000 0.00 0.00 0.00 3.91
3638 7522 3.696548 CTCCCCCTTTTGATGCTAGTTTC 59.303 47.826 0.00 0.00 0.00 2.78
3645 7529 5.705441 CCTTTTGATGCTAGTTTCTACCACA 59.295 40.000 0.00 0.00 0.00 4.17
3648 7532 4.820897 TGATGCTAGTTTCTACCACACTG 58.179 43.478 0.00 0.00 0.00 3.66
3696 7580 7.499895 TGGATCGGTAAAGTTTAAGTGAAAAGT 59.500 33.333 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.541863 CTGGCCTCCCTCGTTGTATT 59.458 55.000 3.32 0.00 0.00 1.89
2 3 0.543410 TTCTGGCCTCCCTCGTTGTA 60.543 55.000 3.32 0.00 0.00 2.41
3 4 1.841556 TTCTGGCCTCCCTCGTTGT 60.842 57.895 3.32 0.00 0.00 3.32
4 5 1.376037 GTTCTGGCCTCCCTCGTTG 60.376 63.158 3.32 0.00 0.00 4.10
5 6 2.943978 CGTTCTGGCCTCCCTCGTT 61.944 63.158 3.32 0.00 0.00 3.85
6 7 3.382832 CGTTCTGGCCTCCCTCGT 61.383 66.667 3.32 0.00 0.00 4.18
7 8 4.148825 CCGTTCTGGCCTCCCTCG 62.149 72.222 3.32 2.57 0.00 4.63
8 9 2.683933 TCCGTTCTGGCCTCCCTC 60.684 66.667 3.32 0.00 37.80 4.30
9 10 2.685380 CTCCGTTCTGGCCTCCCT 60.685 66.667 3.32 0.00 37.80 4.20
10 11 4.475135 GCTCCGTTCTGGCCTCCC 62.475 72.222 3.32 0.00 37.80 4.30
31 32 4.092116 TGATGGTGATGTGGTTGTTGTA 57.908 40.909 0.00 0.00 0.00 2.41
35 36 3.726557 AGATGATGGTGATGTGGTTGT 57.273 42.857 0.00 0.00 0.00 3.32
38 39 4.458397 GATGAAGATGATGGTGATGTGGT 58.542 43.478 0.00 0.00 0.00 4.16
111 112 8.487313 TGCACGATTACAAGTATGAACTAAAT 57.513 30.769 0.00 0.00 33.75 1.40
113 114 7.043656 CGATGCACGATTACAAGTATGAACTAA 60.044 37.037 0.00 0.00 45.77 2.24
158 159 8.308207 TCTTGAAGATTGATTGATTGCAAATCA 58.692 29.630 1.71 5.64 37.59 2.57
164 165 7.033791 ACACATCTTGAAGATTGATTGATTGC 58.966 34.615 17.86 0.00 31.32 3.56
208 209 3.068590 TCAAGCATGTAGATCAGATCGCA 59.931 43.478 4.67 8.65 0.00 5.10
209 210 3.646946 TCAAGCATGTAGATCAGATCGC 58.353 45.455 4.67 2.23 0.00 4.58
210 211 4.869215 ACTCAAGCATGTAGATCAGATCG 58.131 43.478 4.67 0.00 0.00 3.69
219 220 4.111375 ACCGAACTACTCAAGCATGTAG 57.889 45.455 0.00 0.00 41.18 2.74
221 222 4.495422 CTTACCGAACTACTCAAGCATGT 58.505 43.478 0.00 0.00 0.00 3.21
226 227 5.359009 TCCATACCTTACCGAACTACTCAAG 59.641 44.000 0.00 0.00 0.00 3.02
227 228 5.263599 TCCATACCTTACCGAACTACTCAA 58.736 41.667 0.00 0.00 0.00 3.02
237 238 2.104111 TGCCTCATTCCATACCTTACCG 59.896 50.000 0.00 0.00 0.00 4.02
239 240 4.973168 TCATGCCTCATTCCATACCTTAC 58.027 43.478 0.00 0.00 0.00 2.34
258 259 5.822132 ATATAGAGAGTTGCAAGGCTCAT 57.178 39.130 23.12 17.53 34.39 2.90
282 283 8.743714 ACAAAATCAAACAAGAGAAAAGAGACT 58.256 29.630 0.00 0.00 0.00 3.24
283 284 8.801913 CACAAAATCAAACAAGAGAAAAGAGAC 58.198 33.333 0.00 0.00 0.00 3.36
288 289 7.664082 TTGCACAAAATCAAACAAGAGAAAA 57.336 28.000 0.00 0.00 0.00 2.29
300 301 5.664294 ATATGCTCCTTTGCACAAAATCA 57.336 34.783 0.00 0.00 46.33 2.57
329 330 9.503399 CTTCAACCAAAGGTAGAGTAGTTTTAT 57.497 33.333 0.00 0.00 33.12 1.40
364 365 1.641577 GTGAGCCTTGTATGGACGTC 58.358 55.000 7.13 7.13 0.00 4.34
366 367 0.108804 ACGTGAGCCTTGTATGGACG 60.109 55.000 0.00 0.00 33.08 4.79
370 371 2.157668 GTGTTCACGTGAGCCTTGTATG 59.842 50.000 26.65 0.00 0.00 2.39
384 385 3.974401 CGTCAAACATTGATGGTGTTCAC 59.026 43.478 4.72 0.00 42.47 3.18
396 397 4.095632 TGATGTTGTGACACGTCAAACATT 59.904 37.500 24.76 16.42 43.16 2.71
397 398 3.625313 TGATGTTGTGACACGTCAAACAT 59.375 39.130 24.50 24.50 44.25 2.71
433 445 1.826385 GTTTCACCTGGACCATCTGG 58.174 55.000 0.00 0.00 42.17 3.86
456 468 0.317160 CTACTGTGGCTGGTTCACGA 59.683 55.000 0.00 0.00 37.91 4.35
467 479 7.704271 TCTATTTTGTACTCGATCTACTGTGG 58.296 38.462 0.00 0.00 0.00 4.17
498 510 6.144080 CGTTCTTCATTCACGAGTTAACTCTT 59.856 38.462 28.30 19.49 40.75 2.85
500 512 5.164080 CCGTTCTTCATTCACGAGTTAACTC 60.164 44.000 23.25 23.25 39.55 3.01
510 522 0.165944 CCGCACCGTTCTTCATTCAC 59.834 55.000 0.00 0.00 0.00 3.18
548 560 1.301293 GTGAAGAAGAGGGGGCCAG 59.699 63.158 4.39 0.00 0.00 4.85
595 607 1.207593 GTGTTCATGCGAGCCACAC 59.792 57.895 0.00 0.00 0.00 3.82
663 675 0.319728 CTATCTGGACCATCTGGCCG 59.680 60.000 0.00 0.00 39.32 6.13
715 750 2.048603 GTCCAATGTGGCTGGCTCC 61.049 63.158 2.00 0.00 37.47 4.70
716 751 2.048603 GGTCCAATGTGGCTGGCTC 61.049 63.158 2.00 0.00 37.47 4.70
717 752 2.036256 GGTCCAATGTGGCTGGCT 59.964 61.111 2.00 0.00 37.47 4.75
718 753 3.443045 CGGTCCAATGTGGCTGGC 61.443 66.667 0.00 0.00 37.47 4.85
719 754 3.443045 GCGGTCCAATGTGGCTGG 61.443 66.667 0.00 0.00 37.47 4.85
720 755 3.803082 CGCGGTCCAATGTGGCTG 61.803 66.667 0.00 0.00 37.47 4.85
721 756 2.949909 TACGCGGTCCAATGTGGCT 61.950 57.895 12.47 0.00 37.47 4.75
722 757 2.435234 TACGCGGTCCAATGTGGC 60.435 61.111 12.47 0.00 37.47 5.01
723 758 2.104253 GGTACGCGGTCCAATGTGG 61.104 63.158 12.47 0.00 39.43 4.17
724 759 0.951525 TTGGTACGCGGTCCAATGTG 60.952 55.000 25.48 0.00 38.57 3.21
725 760 0.250381 TTTGGTACGCGGTCCAATGT 60.250 50.000 28.14 2.74 42.25 2.71
726 761 0.875728 TTTTGGTACGCGGTCCAATG 59.124 50.000 28.14 0.00 42.25 2.82
727 762 1.828979 ATTTTGGTACGCGGTCCAAT 58.171 45.000 28.14 17.09 42.25 3.16
728 763 2.028294 TCTATTTTGGTACGCGGTCCAA 60.028 45.455 25.48 25.48 41.22 3.53
729 764 1.549620 TCTATTTTGGTACGCGGTCCA 59.450 47.619 18.00 18.00 0.00 4.02
730 765 2.298411 TCTATTTTGGTACGCGGTCC 57.702 50.000 12.47 13.13 0.00 4.46
731 766 3.928375 TCTTTCTATTTTGGTACGCGGTC 59.072 43.478 12.47 2.10 0.00 4.79
732 767 3.929094 TCTTTCTATTTTGGTACGCGGT 58.071 40.909 12.47 0.00 0.00 5.68
733 768 4.178540 TCTCTTTCTATTTTGGTACGCGG 58.821 43.478 12.47 0.00 0.00 6.46
734 769 5.575606 TCTTCTCTTTCTATTTTGGTACGCG 59.424 40.000 3.53 3.53 0.00 6.01
735 770 6.812160 TCTCTTCTCTTTCTATTTTGGTACGC 59.188 38.462 0.00 0.00 0.00 4.42
736 771 7.008447 CGTCTCTTCTCTTTCTATTTTGGTACG 59.992 40.741 0.00 0.00 0.00 3.67
737 772 8.027771 TCGTCTCTTCTCTTTCTATTTTGGTAC 58.972 37.037 0.00 0.00 0.00 3.34
738 773 8.118976 TCGTCTCTTCTCTTTCTATTTTGGTA 57.881 34.615 0.00 0.00 0.00 3.25
739 774 6.994221 TCGTCTCTTCTCTTTCTATTTTGGT 58.006 36.000 0.00 0.00 0.00 3.67
740 775 7.815068 TCTTCGTCTCTTCTCTTTCTATTTTGG 59.185 37.037 0.00 0.00 0.00 3.28
788 823 2.558286 GGACGACACCAGACCGTGA 61.558 63.158 0.00 0.00 37.20 4.35
793 828 2.308039 GCGTTGGACGACACCAGAC 61.308 63.158 4.46 0.00 46.05 3.51
797 832 2.174969 TTGTGCGTTGGACGACACC 61.175 57.895 18.11 0.00 46.05 4.16
814 849 2.165030 CCGGACTTGTGAGGTATACGTT 59.835 50.000 0.00 0.00 0.00 3.99
821 856 3.637273 GGGCCGGACTTGTGAGGT 61.637 66.667 7.57 0.00 0.00 3.85
942 980 7.332430 GTGATCTGCAGTAGTCTACGTAGATAT 59.668 40.741 27.02 20.31 36.10 1.63
949 987 2.683362 TGGTGATCTGCAGTAGTCTACG 59.317 50.000 14.67 1.60 0.00 3.51
1065 1122 2.060980 GGGGACGAGCTCCATGTCT 61.061 63.158 16.60 0.00 41.63 3.41
1265 1326 3.181445 ACCACAAGCTACAGATCCAACAA 60.181 43.478 0.00 0.00 0.00 2.83
1266 1327 2.371841 ACCACAAGCTACAGATCCAACA 59.628 45.455 0.00 0.00 0.00 3.33
1267 1328 3.059352 ACCACAAGCTACAGATCCAAC 57.941 47.619 0.00 0.00 0.00 3.77
1268 1329 3.674997 GAACCACAAGCTACAGATCCAA 58.325 45.455 0.00 0.00 0.00 3.53
1269 1330 2.353704 CGAACCACAAGCTACAGATCCA 60.354 50.000 0.00 0.00 0.00 3.41
1270 1331 2.271800 CGAACCACAAGCTACAGATCC 58.728 52.381 0.00 0.00 0.00 3.36
1271 1332 1.661112 GCGAACCACAAGCTACAGATC 59.339 52.381 0.00 0.00 0.00 2.75
1272 1333 1.001974 TGCGAACCACAAGCTACAGAT 59.998 47.619 0.00 0.00 0.00 2.90
1273 1334 0.391228 TGCGAACCACAAGCTACAGA 59.609 50.000 0.00 0.00 0.00 3.41
1274 1335 1.129251 CATGCGAACCACAAGCTACAG 59.871 52.381 0.00 0.00 0.00 2.74
1275 1336 1.155889 CATGCGAACCACAAGCTACA 58.844 50.000 0.00 0.00 0.00 2.74
1276 1337 1.394917 CTCATGCGAACCACAAGCTAC 59.605 52.381 0.00 0.00 0.00 3.58
1277 1338 1.725641 CTCATGCGAACCACAAGCTA 58.274 50.000 0.00 0.00 0.00 3.32
1278 1339 1.580845 GCTCATGCGAACCACAAGCT 61.581 55.000 0.00 0.00 33.64 3.74
1279 1340 1.154150 GCTCATGCGAACCACAAGC 60.154 57.895 0.00 0.00 0.00 4.01
1280 1341 0.167470 CTGCTCATGCGAACCACAAG 59.833 55.000 0.00 0.00 43.34 3.16
1400 1705 4.750941 TCAGGTGGGGAAAAATTCAGATT 58.249 39.130 0.00 0.00 0.00 2.40
1439 1746 1.019278 CACGTACGGAGGCAGCAAAT 61.019 55.000 21.06 0.00 0.00 2.32
1625 1932 5.542635 ACCAAGAACTCCTGTGTAGTATGAA 59.457 40.000 0.00 0.00 0.00 2.57
1716 2027 6.598064 ACCATAACTTTCCGGTTTCAGAATAG 59.402 38.462 0.00 0.00 0.00 1.73
1812 2347 7.624549 AGTTTCCAGCAGTCAGAGAAAATATA 58.375 34.615 0.00 0.00 0.00 0.86
1813 2348 6.479884 AGTTTCCAGCAGTCAGAGAAAATAT 58.520 36.000 0.00 0.00 0.00 1.28
1831 2366 5.045872 GCATGCCTGAATTATCAAGTTTCC 58.954 41.667 6.36 0.00 34.49 3.13
1896 2716 1.666189 GACATAGTCGCCCTTCTTTGC 59.334 52.381 0.00 0.00 0.00 3.68
1985 2805 2.740826 CCGGCACTACCAACCACG 60.741 66.667 0.00 0.00 39.03 4.94
2035 2855 0.036105 TCATTGTCTGGCGATGTGCT 60.036 50.000 9.21 0.00 45.43 4.40
2043 2880 3.931578 ACAGAACTACTCATTGTCTGGC 58.068 45.455 4.20 0.00 0.00 4.85
2075 2912 4.662145 GCCAACAGCAGTGACATAATTAC 58.338 43.478 0.00 0.00 42.97 1.89
2114 3022 6.015918 TGAGGAGAAGGCAAATTTATTCCAA 58.984 36.000 0.00 0.00 0.00 3.53
2163 3071 0.953471 TGAAGGCATCGTCAAACCCG 60.953 55.000 0.00 0.00 0.00 5.28
2235 3143 2.025636 TATGGTAGCTAGGGAAGGGC 57.974 55.000 0.00 0.00 0.00 5.19
2295 3210 4.513442 TGGCACGCAGAACTCTTTATTAT 58.487 39.130 0.00 0.00 0.00 1.28
2534 3453 0.032267 GTAGCTGCCGTAGTGATCCC 59.968 60.000 0.00 0.00 0.00 3.85
2628 3547 2.279784 GCCGGGAAGCTCTCGATG 60.280 66.667 2.18 0.00 44.60 3.84
2752 3678 2.049156 TGGTCTCTGAACGCGCAG 60.049 61.111 5.73 6.73 37.24 5.18
2755 3681 1.656095 GAATTCTGGTCTCTGAACGCG 59.344 52.381 3.53 3.53 34.46 6.01
2781 3707 8.569641 GGACCAAGTACTTCTCTACATATACTG 58.430 40.741 4.77 0.00 0.00 2.74
2782 3708 7.444792 CGGACCAAGTACTTCTCTACATATACT 59.555 40.741 4.77 0.00 0.00 2.12
2783 3709 7.308469 CCGGACCAAGTACTTCTCTACATATAC 60.308 44.444 4.77 0.00 0.00 1.47
2789 3721 2.159268 GCCGGACCAAGTACTTCTCTAC 60.159 54.545 5.05 0.00 0.00 2.59
2796 3728 0.605589 GCAAAGCCGGACCAAGTACT 60.606 55.000 5.05 0.00 0.00 2.73
2803 3735 1.657751 GAATCCAGCAAAGCCGGACC 61.658 60.000 5.05 0.00 0.00 4.46
2810 3742 2.229784 GGTTCACCTGAATCCAGCAAAG 59.770 50.000 0.00 0.00 39.07 2.77
2941 6793 3.552699 GTGTTATACAATGCGTCGCCTAA 59.447 43.478 15.88 0.00 0.00 2.69
2946 6798 3.982127 TGTGTGTTATACAATGCGTCG 57.018 42.857 0.00 0.00 41.89 5.12
2949 6801 8.001358 TCAAAATTTGTGTGTTATACAATGCG 57.999 30.769 5.56 0.00 41.89 4.73
2959 6811 9.097257 CCTTCTGTAATTCAAAATTTGTGTGTT 57.903 29.630 5.56 0.50 0.00 3.32
2969 6821 5.898120 TGGGATCCCTTCTGTAATTCAAAA 58.102 37.500 31.05 2.00 36.94 2.44
2975 6827 5.911178 TCTGTAATGGGATCCCTTCTGTAAT 59.089 40.000 31.05 11.94 36.94 1.89
2976 6828 5.285401 TCTGTAATGGGATCCCTTCTGTAA 58.715 41.667 31.05 9.90 36.94 2.41
2977 6829 4.890988 TCTGTAATGGGATCCCTTCTGTA 58.109 43.478 31.05 10.70 36.94 2.74
2978 6830 3.736094 TCTGTAATGGGATCCCTTCTGT 58.264 45.455 31.05 12.91 36.94 3.41
2979 6831 4.778213 TTCTGTAATGGGATCCCTTCTG 57.222 45.455 31.05 19.52 36.94 3.02
2980 6832 4.540099 TGTTTCTGTAATGGGATCCCTTCT 59.460 41.667 31.05 17.26 36.94 2.85
2981 6833 4.855340 TGTTTCTGTAATGGGATCCCTTC 58.145 43.478 31.05 17.76 36.94 3.46
2982 6834 4.946160 TGTTTCTGTAATGGGATCCCTT 57.054 40.909 31.05 22.58 36.94 3.95
2983 6835 6.069088 TGTTATGTTTCTGTAATGGGATCCCT 60.069 38.462 31.05 15.06 36.94 4.20
2984 6836 6.126409 TGTTATGTTTCTGTAATGGGATCCC 58.874 40.000 25.22 25.22 0.00 3.85
2985 6837 7.339466 ACTTGTTATGTTTCTGTAATGGGATCC 59.661 37.037 1.92 1.92 0.00 3.36
2986 6838 8.184192 CACTTGTTATGTTTCTGTAATGGGATC 58.816 37.037 0.00 0.00 0.00 3.36
2987 6839 7.362920 GCACTTGTTATGTTTCTGTAATGGGAT 60.363 37.037 0.00 0.00 0.00 3.85
2988 6840 6.072175 GCACTTGTTATGTTTCTGTAATGGGA 60.072 38.462 0.00 0.00 0.00 4.37
2989 6841 6.071952 AGCACTTGTTATGTTTCTGTAATGGG 60.072 38.462 0.00 0.00 0.00 4.00
2990 6842 6.913170 AGCACTTGTTATGTTTCTGTAATGG 58.087 36.000 0.00 0.00 0.00 3.16
2991 6843 8.075574 TGAAGCACTTGTTATGTTTCTGTAATG 58.924 33.333 3.76 0.00 37.93 1.90
2998 6850 5.570589 GCAGATGAAGCACTTGTTATGTTTC 59.429 40.000 0.00 0.00 37.68 2.78
3002 6854 4.690184 TGCAGATGAAGCACTTGTTATG 57.310 40.909 0.00 0.00 37.02 1.90
3025 6877 2.099141 TTCTCTGTGAAGATTGGGCG 57.901 50.000 0.00 0.00 0.00 6.13
3027 6879 6.376299 TCATTGATTTCTCTGTGAAGATTGGG 59.624 38.462 0.00 0.00 35.89 4.12
3057 6909 3.262448 TAACCCGGCCCTGCAAGTC 62.262 63.158 0.00 0.00 0.00 3.01
3058 6910 3.253838 TAACCCGGCCCTGCAAGT 61.254 61.111 0.00 0.00 0.00 3.16
3059 6911 2.438434 CTAACCCGGCCCTGCAAG 60.438 66.667 0.00 0.00 0.00 4.01
3062 6914 3.476419 TAGCTAACCCGGCCCTGC 61.476 66.667 0.00 0.00 0.00 4.85
3063 6915 2.504519 GTAGCTAACCCGGCCCTG 59.495 66.667 0.00 0.00 0.00 4.45
3064 6916 2.767073 GGTAGCTAACCCGGCCCT 60.767 66.667 0.00 0.00 43.16 5.19
3065 6917 4.231439 CGGTAGCTAACCCGGCCC 62.231 72.222 13.60 0.09 46.62 5.80
3066 6918 2.639883 CTTCGGTAGCTAACCCGGCC 62.640 65.000 19.40 4.60 46.62 6.13
3067 6919 1.227176 CTTCGGTAGCTAACCCGGC 60.227 63.158 19.40 0.00 46.62 6.13
3068 6920 0.384669 CTCTTCGGTAGCTAACCCGG 59.615 60.000 19.40 7.57 46.62 5.73
3069 6921 1.386533 TCTCTTCGGTAGCTAACCCG 58.613 55.000 14.93 14.93 46.62 5.28
3070 6922 2.159128 GGTTCTCTTCGGTAGCTAACCC 60.159 54.545 2.43 0.00 46.62 4.11
3071 6923 2.759535 AGGTTCTCTTCGGTAGCTAACC 59.240 50.000 2.43 2.02 45.77 2.85
3072 6924 4.422840 GAAGGTTCTCTTCGGTAGCTAAC 58.577 47.826 0.00 0.00 41.95 2.34
3073 6925 4.715527 GAAGGTTCTCTTCGGTAGCTAA 57.284 45.455 0.00 0.00 41.95 3.09
3083 6935 3.835395 ACTCGGATTCTGAAGGTTCTCTT 59.165 43.478 0.00 0.00 38.65 2.85
3084 6936 3.436243 ACTCGGATTCTGAAGGTTCTCT 58.564 45.455 0.00 0.00 0.00 3.10
3085 6937 3.878160 ACTCGGATTCTGAAGGTTCTC 57.122 47.619 0.00 0.00 0.00 2.87
3086 6938 3.128938 CGTACTCGGATTCTGAAGGTTCT 59.871 47.826 0.00 0.00 0.00 3.01
3087 6939 3.119566 ACGTACTCGGATTCTGAAGGTTC 60.120 47.826 0.00 0.00 41.85 3.62
3088 6940 2.824341 ACGTACTCGGATTCTGAAGGTT 59.176 45.455 0.00 0.00 41.85 3.50
3089 6941 2.422832 GACGTACTCGGATTCTGAAGGT 59.577 50.000 0.00 0.00 41.85 3.50
3090 6942 2.223525 GGACGTACTCGGATTCTGAAGG 60.224 54.545 0.00 0.00 41.85 3.46
3091 6943 2.223525 GGGACGTACTCGGATTCTGAAG 60.224 54.545 0.00 0.00 41.85 3.02
3092 6944 1.747355 GGGACGTACTCGGATTCTGAA 59.253 52.381 0.00 0.00 41.85 3.02
3093 6945 1.386533 GGGACGTACTCGGATTCTGA 58.613 55.000 0.00 0.00 41.85 3.27
3094 6946 3.940723 GGGACGTACTCGGATTCTG 57.059 57.895 0.00 0.00 41.85 3.02
3113 6965 1.227002 GATTCTGGAGACGGCCGAC 60.227 63.158 35.90 27.70 36.33 4.79
3114 6966 2.423898 GGATTCTGGAGACGGCCGA 61.424 63.158 35.90 7.96 36.33 5.54
3115 6967 2.107141 GGATTCTGGAGACGGCCG 59.893 66.667 26.86 26.86 36.33 6.13
3116 6968 2.107141 CGGATTCTGGAGACGGCC 59.893 66.667 0.00 0.00 36.33 6.13
3135 6987 4.387862 CGGGGAAACGCATACTATACAATC 59.612 45.833 0.00 0.00 45.02 2.67
3137 6989 3.493002 CCGGGGAAACGCATACTATACAA 60.493 47.826 0.00 0.00 45.02 2.41
3138 6990 2.036217 CCGGGGAAACGCATACTATACA 59.964 50.000 0.00 0.00 45.02 2.29
3139 6991 2.680577 CCGGGGAAACGCATACTATAC 58.319 52.381 0.00 0.00 45.02 1.47
3140 6992 1.001181 GCCGGGGAAACGCATACTATA 59.999 52.381 2.18 0.00 45.02 1.31
3141 6993 0.250166 GCCGGGGAAACGCATACTAT 60.250 55.000 2.18 0.00 45.02 2.12
3142 6994 1.144496 GCCGGGGAAACGCATACTA 59.856 57.895 2.18 0.00 45.02 1.82
3143 6995 2.124860 GCCGGGGAAACGCATACT 60.125 61.111 2.18 0.00 45.02 2.12
3184 7036 8.375506 AGTTTTTCTTTTTCTTTCTTGACCCTT 58.624 29.630 0.00 0.00 0.00 3.95
3341 7204 5.849510 TGGACTCGAAGTAGTTGATGAAAA 58.150 37.500 0.00 0.00 0.00 2.29
3369 7232 4.175489 CTCGACGACGACGGCCAT 62.175 66.667 18.73 0.00 45.81 4.40
3376 7239 3.744719 CAAGGGGCTCGACGACGA 61.745 66.667 9.98 9.98 46.56 4.20
3377 7240 4.796231 CCAAGGGGCTCGACGACG 62.796 72.222 0.00 0.00 41.26 5.12
3575 7456 3.138625 CTCCCACGCATACCCGAT 58.861 61.111 0.00 0.00 0.00 4.18
3586 7470 2.185310 AATCCGACAGGTGCTCCCAC 62.185 60.000 0.00 0.00 41.32 4.61
3625 7509 5.237815 CAGTGTGGTAGAAACTAGCATCAA 58.762 41.667 12.53 1.93 0.00 2.57
3631 7515 4.258702 ACAGCAGTGTGGTAGAAACTAG 57.741 45.455 0.00 0.00 34.75 2.57
3638 7522 2.094494 CAGAGGTACAGCAGTGTGGTAG 60.094 54.545 0.00 0.00 37.52 3.18
3662 7546 6.619801 AAACTTTACCGATCCATAATCTGC 57.380 37.500 0.00 0.00 31.68 4.26


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

AutoCloner maintained by Alex Coulton.