Multiple sequence alignment - TraesCS3D01G388500

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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 TraesCS3D01G388500 chr3D 100.000 3596 0 0 1 3596 503855709 503859304 0.000000e+00 6641.0
1 TraesCS3D01G388500 chr3B 86.807 1948 146 56 1157 3065 665257814 665259689 0.000000e+00 2071.0
2 TraesCS3D01G388500 chr3B 86.600 597 46 16 4 583 665256475 665257054 2.360000e-176 628.0
3 TraesCS3D01G388500 chr3B 88.433 536 30 10 3086 3596 665259773 665260301 5.100000e-173 617.0
4 TraesCS3D01G388500 chr3B 100.000 41 0 0 1866 1906 753954754 753954714 3.850000e-10 76.8
5 TraesCS3D01G388500 chr3A 83.829 2016 165 88 4 1926 642157626 642159573 0.000000e+00 1768.0
6 TraesCS3D01G388500 chr3A 94.112 1087 46 12 1982 3063 642159584 642160657 0.000000e+00 1637.0
7 TraesCS3D01G388500 chr3A 86.131 548 35 5 3073 3596 642160742 642161272 1.460000e-153 553.0


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 TraesCS3D01G388500 chr3D 503855709 503859304 3595 False 6641.000000 6641 100.000 1 3596 1 chr3D.!!$F1 3595
1 TraesCS3D01G388500 chr3B 665256475 665260301 3826 False 1105.333333 2071 87.280 4 3596 3 chr3B.!!$F1 3592
2 TraesCS3D01G388500 chr3A 642157626 642161272 3646 False 1319.333333 1768 88.024 4 3596 3 chr3A.!!$F1 3592

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
102 105 0.035152 TTGCCGCCTTCTCATGACAT 60.035 50.0 0.00 0.00 0.00 3.06 F
378 397 0.393820 TATCATCGGCTGCTGATGCA 59.606 50.0 35.50 26.67 44.35 3.96 F
1060 1196 0.394488 TACGCCCTCTGTCTCTCCAG 60.394 60.0 0.00 0.00 0.00 3.86 F
1593 2011 0.106335 CTGATCGAGCTGGCCATCTT 59.894 55.0 11.11 0.00 0.00 2.40 F
2464 2886 0.665835 ACTGCGCAAAATCCGACAAA 59.334 45.0 13.05 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1184 1489 0.042013 CTCGAGACCGTACTGATCGC 60.042 60.0 6.58 0.00 37.05 4.58 R
1185 1490 0.042013 GCTCGAGACCGTACTGATCG 60.042 60.0 18.75 9.22 37.05 3.69 R
2060 2479 0.104304 GGAACCTATCATCGCACCGT 59.896 55.0 0.00 0.00 0.00 4.83 R
2512 2934 0.107945 ACGCTCCTCTCCTGCAAATC 60.108 55.0 0.00 0.00 0.00 2.17 R
3357 3912 0.767375 TGCTTCAGCCCTTTGAGTCT 59.233 50.0 0.00 0.00 41.18 3.24 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
102 105 0.035152 TTGCCGCCTTCTCATGACAT 60.035 50.000 0.00 0.00 0.00 3.06
146 149 3.242543 GCCTTGTTACGAGATGATGCTTG 60.243 47.826 0.31 0.00 0.00 4.01
150 153 4.424626 TGTTACGAGATGATGCTTGTCTC 58.575 43.478 0.00 0.00 34.43 3.36
181 189 2.612212 TCAAGCAACCGTTTGTTCTCTC 59.388 45.455 0.00 0.00 34.00 3.20
190 198 4.881850 ACCGTTTGTTCTCTCTTGTCAATT 59.118 37.500 0.00 0.00 0.00 2.32
212 227 1.680735 GACGATCCTCTGCTCACTGAT 59.319 52.381 0.00 0.00 0.00 2.90
227 242 0.773014 CTGATATGTGGGCCCCATGA 59.227 55.000 27.12 15.75 35.28 3.07
228 243 1.356738 CTGATATGTGGGCCCCATGAT 59.643 52.381 27.12 18.56 35.28 2.45
229 244 1.075861 TGATATGTGGGCCCCATGATG 59.924 52.381 27.12 0.00 35.28 3.07
237 252 1.352622 GGCCCCATGATGGTCCTGTA 61.353 60.000 11.09 0.00 35.17 2.74
244 259 4.202503 CCCATGATGGTCCTGTAAAGCTAT 60.203 45.833 11.09 0.00 35.17 2.97
254 270 7.084486 GGTCCTGTAAAGCTATTTTGTTCTTG 58.916 38.462 0.00 0.00 0.00 3.02
266 282 0.979665 TGTTCTTGAGGGAGGCTCAG 59.020 55.000 17.69 4.58 31.98 3.35
274 290 3.478274 GGAGGCTCAGCTCCCCAG 61.478 72.222 17.69 0.00 33.81 4.45
294 310 7.623278 TCCCCAGCAAGGAGATTTATTTATTTT 59.377 33.333 0.00 0.00 41.22 1.82
355 371 2.361119 GGTTCCTTTTTGTCCTGTCACC 59.639 50.000 0.00 0.00 0.00 4.02
378 397 0.393820 TATCATCGGCTGCTGATGCA 59.606 50.000 35.50 26.67 44.35 3.96
412 431 2.298593 GCCTCGCCAAGATAACGAC 58.701 57.895 0.00 0.00 0.00 4.34
413 432 1.480219 GCCTCGCCAAGATAACGACG 61.480 60.000 0.00 0.00 0.00 5.12
457 485 1.144298 TGAATGGATGCATGAGAGGGG 59.856 52.381 2.46 0.00 0.00 4.79
507 540 1.533033 TGACAGCACGGAGGAAGGA 60.533 57.895 0.00 0.00 0.00 3.36
508 541 1.118965 TGACAGCACGGAGGAAGGAA 61.119 55.000 0.00 0.00 0.00 3.36
543 577 1.594293 ACGTGCTGTCCCGTTCTTG 60.594 57.895 0.00 0.00 32.50 3.02
583 617 1.615107 CGTTTCGAGTTCGGCAGGAC 61.615 60.000 1.26 0.00 40.29 3.85
585 619 1.750341 TTTCGAGTTCGGCAGGACCA 61.750 55.000 1.26 0.00 39.03 4.02
586 620 2.125912 CGAGTTCGGCAGGACCAG 60.126 66.667 0.00 0.00 39.03 4.00
587 621 2.636412 CGAGTTCGGCAGGACCAGA 61.636 63.158 0.00 0.00 39.03 3.86
590 624 0.472471 AGTTCGGCAGGACCAGAAAA 59.528 50.000 0.00 0.00 39.03 2.29
595 629 1.669795 CGGCAGGACCAGAAAATTTGC 60.670 52.381 0.00 0.00 39.03 3.68
606 640 4.497300 CAGAAAATTTGCCATCATCCGTT 58.503 39.130 0.00 0.00 0.00 4.44
608 642 4.220382 AGAAAATTTGCCATCATCCGTTGA 59.780 37.500 0.00 0.00 39.12 3.18
615 649 2.484417 GCCATCATCCGTTGAGTCTCAT 60.484 50.000 2.68 0.00 37.89 2.90
621 655 4.931601 TCATCCGTTGAGTCTCATTTTCAG 59.068 41.667 2.68 0.00 0.00 3.02
625 659 4.214437 CGTTGAGTCTCATTTTCAGTTGC 58.786 43.478 2.68 0.00 0.00 4.17
638 672 1.373497 AGTTGCTCGAGCGGTTCTG 60.373 57.895 30.75 0.00 45.83 3.02
659 698 2.436824 GAGGGGAGCACCGAAAGC 60.437 66.667 0.00 0.00 41.60 3.51
703 755 0.841961 AATTAGGAGCCCCCGGTTAC 59.158 55.000 0.00 0.00 40.87 2.50
837 934 4.641989 CCTGAAAAGTGAATCCGATTCCAT 59.358 41.667 16.82 4.39 38.50 3.41
950 1051 1.304617 CTTGCTTCCCCTTCCCCTC 59.695 63.158 0.00 0.00 0.00 4.30
952 1053 3.421386 GCTTCCCCTTCCCCTCCC 61.421 72.222 0.00 0.00 0.00 4.30
969 1070 2.373707 CCTGCCCTGGAAGAGGAGG 61.374 68.421 0.00 0.00 46.33 4.30
971 1072 1.306482 TGCCCTGGAAGAGGAGGAG 60.306 63.158 0.00 0.00 46.33 3.69
974 1075 2.069430 CCTGGAAGAGGAGGAGGGC 61.069 68.421 0.00 0.00 46.33 5.19
975 1076 1.306482 CTGGAAGAGGAGGAGGGCA 60.306 63.158 0.00 0.00 34.07 5.36
1052 1180 2.423898 CCATCCGTACGCCCTCTGT 61.424 63.158 10.49 0.00 0.00 3.41
1053 1181 1.065928 CATCCGTACGCCCTCTGTC 59.934 63.158 10.49 0.00 0.00 3.51
1058 1186 1.716826 CGTACGCCCTCTGTCTCTCC 61.717 65.000 0.52 0.00 0.00 3.71
1059 1187 0.680280 GTACGCCCTCTGTCTCTCCA 60.680 60.000 0.00 0.00 0.00 3.86
1060 1196 0.394488 TACGCCCTCTGTCTCTCCAG 60.394 60.000 0.00 0.00 0.00 3.86
1065 1201 1.554836 CCTCTGTCTCTCCAGCTTGA 58.445 55.000 0.00 0.00 32.32 3.02
1068 1204 3.703556 CCTCTGTCTCTCCAGCTTGATTA 59.296 47.826 0.00 0.00 32.32 1.75
1069 1205 4.344679 CCTCTGTCTCTCCAGCTTGATTAT 59.655 45.833 0.00 0.00 32.32 1.28
1070 1206 5.509501 CCTCTGTCTCTCCAGCTTGATTATC 60.510 48.000 0.00 0.00 32.32 1.75
1071 1207 4.037327 TCTGTCTCTCCAGCTTGATTATCG 59.963 45.833 0.00 0.00 32.32 2.92
1072 1208 3.056304 GTCTCTCCAGCTTGATTATCGC 58.944 50.000 0.00 0.00 0.00 4.58
1073 1209 2.695147 TCTCTCCAGCTTGATTATCGCA 59.305 45.455 0.00 0.00 0.00 5.10
1077 1213 1.605232 CCAGCTTGATTATCGCATGCA 59.395 47.619 19.57 5.34 38.46 3.96
1079 1215 3.234386 CAGCTTGATTATCGCATGCATG 58.766 45.455 22.70 22.70 38.46 4.06
1091 1227 1.471119 CATGCATGCTCCTTGTCCTT 58.529 50.000 20.33 0.00 0.00 3.36
1111 1251 7.071824 TGTCCTTATGAAAAGGGGAATTGTTTT 59.928 33.333 4.05 0.00 37.99 2.43
1128 1268 9.361315 GAATTGTTTTGATGATGATCATGACAA 57.639 29.630 14.30 18.80 42.19 3.18
1132 1272 9.198837 TGTTTTGATGATGATCATGACAAAAAG 57.801 29.630 24.43 0.00 39.78 2.27
1140 1280 8.509690 TGATGATCATGACAAAAAGAGAGTTTC 58.490 33.333 14.30 0.00 0.00 2.78
1144 1284 8.688747 ATCATGACAAAAAGAGAGTTTCTTCT 57.311 30.769 0.00 0.00 45.41 2.85
1145 1285 8.511604 TCATGACAAAAAGAGAGTTTCTTCTT 57.488 30.769 0.00 0.00 45.41 2.52
1146 1286 8.616076 TCATGACAAAAAGAGAGTTTCTTCTTC 58.384 33.333 0.00 0.00 45.41 2.87
1147 1287 8.619546 CATGACAAAAAGAGAGTTTCTTCTTCT 58.380 33.333 0.00 0.00 45.41 2.85
1148 1288 8.567285 TGACAAAAAGAGAGTTTCTTCTTCTT 57.433 30.769 0.00 0.00 45.41 2.52
1149 1289 8.669243 TGACAAAAAGAGAGTTTCTTCTTCTTC 58.331 33.333 0.00 0.00 45.41 2.87
1150 1290 7.990917 ACAAAAAGAGAGTTTCTTCTTCTTCC 58.009 34.615 0.00 0.00 45.41 3.46
1151 1291 7.831690 ACAAAAAGAGAGTTTCTTCTTCTTCCT 59.168 33.333 0.00 0.00 45.41 3.36
1165 1466 7.976175 TCTTCTTCTTCCTTTTTGCTTCTTTTC 59.024 33.333 0.00 0.00 0.00 2.29
1171 1472 4.279671 TCCTTTTTGCTTCTTTTCGCCATA 59.720 37.500 0.00 0.00 0.00 2.74
1178 1479 4.922692 TGCTTCTTTTCGCCATAATTTGTG 59.077 37.500 0.00 0.00 0.00 3.33
1182 1487 5.457140 TCTTTTCGCCATAATTTGTGTGTC 58.543 37.500 0.00 0.00 0.00 3.67
1183 1488 5.240623 TCTTTTCGCCATAATTTGTGTGTCT 59.759 36.000 0.00 0.00 0.00 3.41
1184 1489 4.418013 TTCGCCATAATTTGTGTGTCTG 57.582 40.909 0.00 0.00 0.00 3.51
1185 1490 2.161410 TCGCCATAATTTGTGTGTCTGC 59.839 45.455 0.00 0.00 0.00 4.26
1196 1501 0.170339 TGTGTCTGCGATCAGTACGG 59.830 55.000 0.00 0.00 41.10 4.02
1225 1530 2.360854 CCTGGTCTAGAGGGGAGGAAAT 60.361 54.545 0.00 0.00 0.00 2.17
1226 1531 3.388913 CTGGTCTAGAGGGGAGGAAATT 58.611 50.000 0.00 0.00 0.00 1.82
1227 1532 4.557705 CTGGTCTAGAGGGGAGGAAATTA 58.442 47.826 0.00 0.00 0.00 1.40
1228 1533 4.967871 TGGTCTAGAGGGGAGGAAATTAA 58.032 43.478 0.00 0.00 0.00 1.40
1229 1534 5.355711 TGGTCTAGAGGGGAGGAAATTAAA 58.644 41.667 0.00 0.00 0.00 1.52
1243 1548 4.941873 GGAAATTAAAGAGCGGGAGAAAGA 59.058 41.667 0.00 0.00 0.00 2.52
1244 1549 5.065346 GGAAATTAAAGAGCGGGAGAAAGAG 59.935 44.000 0.00 0.00 0.00 2.85
1271 1576 6.730960 TTAGGTGTTGATTTGAATCGGTAC 57.269 37.500 0.00 0.00 38.26 3.34
1283 1588 7.760131 TTTGAATCGGTACTAAACTAATCGG 57.240 36.000 0.00 0.00 0.00 4.18
1346 1651 4.720649 TTGCTATCTCTGTCCACTGTAC 57.279 45.455 0.00 0.00 0.00 2.90
1366 1678 3.991367 ACGACTAGTTTAAAGCAGCAGT 58.009 40.909 0.00 0.00 0.00 4.40
1390 1702 6.651225 GTCTTTGCATAACTGGGTATCTATCC 59.349 42.308 0.00 0.00 0.00 2.59
1398 1726 9.206690 CATAACTGGGTATCTATCCATCTATGT 57.793 37.037 8.51 0.00 35.56 2.29
1404 1732 9.019542 TGGGTATCTATCCATCTATGTATCTCT 57.980 37.037 0.00 0.00 29.75 3.10
1412 1740 6.763355 TCCATCTATGTATCTCTTTTGAGGC 58.237 40.000 0.00 0.00 46.22 4.70
1413 1741 6.556495 TCCATCTATGTATCTCTTTTGAGGCT 59.444 38.462 0.00 0.00 46.22 4.58
1414 1742 7.071698 TCCATCTATGTATCTCTTTTGAGGCTT 59.928 37.037 0.00 0.00 46.22 4.35
1415 1743 7.718753 CCATCTATGTATCTCTTTTGAGGCTTT 59.281 37.037 0.00 0.00 46.22 3.51
1416 1744 8.557864 CATCTATGTATCTCTTTTGAGGCTTTG 58.442 37.037 0.00 0.00 46.22 2.77
1417 1745 7.851228 TCTATGTATCTCTTTTGAGGCTTTGA 58.149 34.615 0.00 0.00 46.22 2.69
1420 1748 6.240894 TGTATCTCTTTTGAGGCTTTGACAT 58.759 36.000 0.00 0.00 46.22 3.06
1421 1749 7.394016 TGTATCTCTTTTGAGGCTTTGACATA 58.606 34.615 0.00 0.00 46.22 2.29
1422 1750 8.049117 TGTATCTCTTTTGAGGCTTTGACATAT 58.951 33.333 0.00 0.00 46.22 1.78
1423 1751 7.951347 ATCTCTTTTGAGGCTTTGACATATT 57.049 32.000 0.00 0.00 46.22 1.28
1424 1752 7.383102 TCTCTTTTGAGGCTTTGACATATTC 57.617 36.000 0.00 0.00 46.22 1.75
1425 1753 6.942005 TCTCTTTTGAGGCTTTGACATATTCA 59.058 34.615 0.00 0.00 46.22 2.57
1426 1754 6.913170 TCTTTTGAGGCTTTGACATATTCAC 58.087 36.000 0.00 0.00 32.26 3.18
1427 1755 5.643379 TTTGAGGCTTTGACATATTCACC 57.357 39.130 0.00 0.00 32.26 4.02
1442 1770 8.859236 ACATATTCACCAGGAAGATCAATATG 57.141 34.615 11.91 11.91 35.31 1.78
1448 1835 8.547481 TCACCAGGAAGATCAATATGTAACTA 57.453 34.615 0.00 0.00 0.00 2.24
1483 1871 0.251787 AAAAGGATGACCCCACCTGC 60.252 55.000 0.00 0.00 36.73 4.85
1546 1935 2.634940 TGGTTCCTCTGAAACTCTCCAG 59.365 50.000 0.00 0.00 39.06 3.86
1565 1954 2.751259 CAGGTGGTTGATTCTGATGTGG 59.249 50.000 0.00 0.00 0.00 4.17
1583 1972 2.413453 GTGGTTTTCAGACTGATCGAGC 59.587 50.000 5.87 5.84 0.00 5.03
1592 2010 1.047596 ACTGATCGAGCTGGCCATCT 61.048 55.000 9.33 9.33 0.00 2.90
1593 2011 0.106335 CTGATCGAGCTGGCCATCTT 59.894 55.000 11.11 0.00 0.00 2.40
1594 2012 1.342496 CTGATCGAGCTGGCCATCTTA 59.658 52.381 11.11 2.75 0.00 2.10
1595 2013 1.342496 TGATCGAGCTGGCCATCTTAG 59.658 52.381 11.11 8.49 0.00 2.18
1603 2021 2.941720 GCTGGCCATCTTAGTTTCTGAG 59.058 50.000 5.51 0.00 0.00 3.35
1616 2034 4.836125 GTTTCTGAGCATTGGAAACTGA 57.164 40.909 13.43 0.00 42.87 3.41
1620 2038 4.464008 TCTGAGCATTGGAAACTGAACTT 58.536 39.130 0.00 0.00 0.00 2.66
1621 2039 5.620206 TCTGAGCATTGGAAACTGAACTTA 58.380 37.500 0.00 0.00 0.00 2.24
1623 2041 6.149973 TCTGAGCATTGGAAACTGAACTTATG 59.850 38.462 0.00 0.00 0.00 1.90
1624 2042 5.064441 AGCATTGGAAACTGAACTTATGC 57.936 39.130 0.00 0.00 37.88 3.14
1625 2043 4.523943 AGCATTGGAAACTGAACTTATGCA 59.476 37.500 0.00 0.00 39.54 3.96
1626 2044 4.860907 GCATTGGAAACTGAACTTATGCAG 59.139 41.667 0.00 0.00 37.62 4.41
1627 2045 5.565439 GCATTGGAAACTGAACTTATGCAGT 60.565 40.000 0.00 0.00 46.59 4.40
1643 2061 1.825090 CAGTTATGCTGCCCTTGACA 58.175 50.000 0.00 0.00 38.52 3.58
1644 2062 2.372264 CAGTTATGCTGCCCTTGACAT 58.628 47.619 0.00 0.00 38.52 3.06
1645 2063 2.357009 CAGTTATGCTGCCCTTGACATC 59.643 50.000 0.00 0.00 38.52 3.06
1655 2073 2.948315 GCCCTTGACATCTTCAGGAATC 59.052 50.000 0.00 0.00 32.96 2.52
1670 2088 0.976073 GAATCACAGGGGACGGGAGA 60.976 60.000 0.00 0.00 0.00 3.71
1688 2106 3.605749 ATGCCTGTTCCGGTCCGTG 62.606 63.158 11.06 1.77 0.00 4.94
1691 2109 4.003788 CTGTTCCGGTCCGTGGCT 62.004 66.667 11.06 0.00 0.00 4.75
1776 2194 1.630244 CGAGCTTCGAGCAAAGGTGG 61.630 60.000 9.09 0.00 45.56 4.61
1781 2199 0.669318 TTCGAGCAAAGGTGGCTACG 60.669 55.000 0.00 0.00 42.78 3.51
1956 2374 2.831685 TTGTGTACATCAGAGCCGTT 57.168 45.000 0.00 0.00 0.00 4.44
1958 2376 2.412870 TGTGTACATCAGAGCCGTTTG 58.587 47.619 0.00 0.00 0.00 2.93
1963 2381 2.571212 ACATCAGAGCCGTTTGTTTCA 58.429 42.857 0.00 0.00 0.00 2.69
2060 2479 9.112725 ACATGATCATTTTTCGATGTGAATCTA 57.887 29.630 5.16 0.00 36.22 1.98
2061 2480 9.378597 CATGATCATTTTTCGATGTGAATCTAC 57.621 33.333 5.16 0.00 36.22 2.59
2069 2488 2.743938 GATGTGAATCTACGGTGCGAT 58.256 47.619 0.00 0.00 0.00 4.58
2135 2555 2.505364 GAAAGCCTCATGCCTGGGGT 62.505 60.000 9.87 2.88 45.79 4.95
2162 2582 3.810812 GAGCTGCTCATGTGCTCC 58.189 61.111 24.02 10.79 45.12 4.70
2165 2585 2.404995 GCTGCTCATGTGCTCCCAC 61.405 63.158 19.60 2.57 42.40 4.61
2168 2588 2.103042 GCTCATGTGCTCCCACGTC 61.103 63.158 12.42 0.00 45.04 4.34
2193 2613 3.653836 TGGGTAGCCACCTTTCTTTCTTA 59.346 43.478 10.27 0.00 45.04 2.10
2227 2649 6.817270 TCGTAGGTTTATATTCTGAAACGC 57.183 37.500 0.00 0.00 36.59 4.84
2238 2660 4.560136 TTCTGAAACGCAATTGCTTACA 57.440 36.364 26.86 18.90 39.32 2.41
2251 2673 4.481930 TTGCTTACAAGGAATGTCAACG 57.518 40.909 0.00 0.00 42.70 4.10
2464 2886 0.665835 ACTGCGCAAAATCCGACAAA 59.334 45.000 13.05 0.00 0.00 2.83
2476 2898 3.080300 TCCGACAAACATTTGGCCTAT 57.920 42.857 3.32 0.00 43.30 2.57
2512 2934 1.302511 CCAACGTTCCCTCCTGTGG 60.303 63.158 0.00 0.00 0.00 4.17
2597 3025 2.203098 TAGGGCCGCCGCATAAAC 60.203 61.111 2.55 0.00 36.38 2.01
2709 3137 1.402259 TCGATCTTCTTCGAGGCTGAC 59.598 52.381 0.00 0.00 42.81 3.51
2819 3250 7.382218 GGAGTGTTTTGTGTAAATTCTGGAATG 59.618 37.037 0.00 0.00 0.00 2.67
2866 3298 4.688879 GGACATATGATTCGCCGACAATTA 59.311 41.667 10.38 0.00 0.00 1.40
2912 3344 5.106317 ACGGCGAATGTGAATACAATCTTTT 60.106 36.000 16.62 0.00 40.84 2.27
2914 3346 6.021468 CGGCGAATGTGAATACAATCTTTTTC 60.021 38.462 0.00 0.00 40.84 2.29
2921 3353 7.874940 TGTGAATACAATCTTTTTCCAGAGTG 58.125 34.615 0.00 0.00 43.19 3.51
2952 3384 6.811170 ACAATCTTATTTTGTTATGTTGGCCG 59.189 34.615 0.00 0.00 33.64 6.13
2973 3405 3.812053 CGCTGATTTTCCTCTAGGATTGG 59.188 47.826 0.00 0.00 44.98 3.16
3058 3490 3.491447 GCCAATTTGACACATGCCTATCC 60.491 47.826 0.00 0.00 0.00 2.59
3065 3497 3.132824 TGACACATGCCTATCCAGTACTG 59.867 47.826 16.34 16.34 0.00 2.74
3082 3589 5.924825 CAGTACTGGTGAACTACTAACCAAC 59.075 44.000 15.49 0.00 43.21 3.77
3090 3597 5.233689 GTGAACTACTAACCAACACAGTGAC 59.766 44.000 7.81 0.00 0.00 3.67
3102 3609 5.924254 CCAACACAGTGACGATTAGTAAAGA 59.076 40.000 7.81 0.00 0.00 2.52
3115 3622 5.945144 TTAGTAAAGAACTAGCCCGGAAT 57.055 39.130 0.73 0.00 41.70 3.01
3116 3623 4.403585 AGTAAAGAACTAGCCCGGAATC 57.596 45.455 0.73 0.00 36.36 2.52
3117 3624 2.311124 AAAGAACTAGCCCGGAATCG 57.689 50.000 0.73 0.00 0.00 3.34
3118 3625 6.241362 AGTAAAGAACTAGCCCGGAATCGG 62.241 50.000 0.73 0.00 46.08 4.18
3136 3644 3.408634 TCGGAATCACCAGAGGAAAAAC 58.591 45.455 0.00 0.00 38.90 2.43
3139 3647 3.500471 GGAATCACCAGAGGAAAAACCCT 60.500 47.826 0.00 0.00 37.78 4.34
3175 3683 2.602217 CGTTCAAAGGTGGCTCTTTTCG 60.602 50.000 4.19 6.27 35.04 3.46
3232 3787 3.041508 AGGTGGCTCTTTTCTACGAAC 57.958 47.619 0.00 0.00 0.00 3.95
3238 3793 5.517054 GTGGCTCTTTTCTACGAACATAGAG 59.483 44.000 0.00 0.00 32.78 2.43
3336 3891 2.091541 GGTTCCGAATGGATTTGCTCA 58.908 47.619 0.00 0.00 45.91 4.26
3406 3961 2.166270 GCTCGAAAGTGCCAGGAAG 58.834 57.895 0.00 0.00 44.29 3.46
3426 3981 7.119699 CAGGAAGAAGTTATGCTCAAATGTACA 59.880 37.037 0.00 0.00 0.00 2.90
3465 4020 4.801330 TCTCAAAGGAAACATAGCTCGA 57.199 40.909 0.00 0.00 0.00 4.04
3513 4069 6.542735 CAGTTCTTACTAGGGAAAAATAGGGC 59.457 42.308 0.00 0.00 31.96 5.19
3541 4097 0.109086 CAGAGCACACACCCTACTCG 60.109 60.000 0.00 0.00 32.60 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.777850 TTCAACTTACTTAACCCAAAGGC 57.222 39.130 0.00 0.00 36.11 4.35
1 2 7.501225 TCTCTTTCAACTTACTTAACCCAAAGG 59.499 37.037 0.00 0.00 40.04 3.11
2 3 8.343366 GTCTCTTTCAACTTACTTAACCCAAAG 58.657 37.037 0.00 0.00 0.00 2.77
102 105 8.146053 AGGCAGGCTATATATACATTGTACAA 57.854 34.615 11.41 11.41 0.00 2.41
146 149 2.851195 TGCTTGACTGAAAAGGGAGAC 58.149 47.619 0.00 0.00 0.00 3.36
150 153 1.001378 CGGTTGCTTGACTGAAAAGGG 60.001 52.381 0.00 0.00 0.00 3.95
190 198 0.393132 AGTGAGCAGAGGATCGTCGA 60.393 55.000 9.64 0.00 42.67 4.20
212 227 0.998398 ACCATCATGGGGCCCACATA 60.998 55.000 31.54 17.07 43.37 2.29
221 236 2.092212 AGCTTTACAGGACCATCATGGG 60.092 50.000 9.04 0.00 43.37 4.00
227 242 6.948309 AGAACAAAATAGCTTTACAGGACCAT 59.052 34.615 0.00 0.00 0.00 3.55
228 243 6.303839 AGAACAAAATAGCTTTACAGGACCA 58.696 36.000 0.00 0.00 0.00 4.02
229 244 6.819397 AGAACAAAATAGCTTTACAGGACC 57.181 37.500 0.00 0.00 0.00 4.46
237 252 5.478332 CCTCCCTCAAGAACAAAATAGCTTT 59.522 40.000 0.00 0.00 0.00 3.51
244 259 2.863809 GAGCCTCCCTCAAGAACAAAA 58.136 47.619 0.00 0.00 40.45 2.44
271 287 9.741647 GAGAAAATAAATAAATCTCCTTGCTGG 57.258 33.333 0.00 0.00 32.30 4.85
294 310 2.598565 AGCAGCGGGATTATAGTGAGA 58.401 47.619 0.00 0.00 0.00 3.27
355 371 2.070262 TCAGCAGCCGATGATAATCG 57.930 50.000 5.38 5.38 43.15 3.34
378 397 1.773653 GAGGCCTCTGGATCCTTTCAT 59.226 52.381 26.25 0.00 0.00 2.57
412 431 2.693762 CCCTTGCCATGTCAGTGCG 61.694 63.158 0.00 0.00 0.00 5.34
413 432 2.998279 GCCCTTGCCATGTCAGTGC 61.998 63.158 0.00 0.00 0.00 4.40
507 540 3.551846 ACGTGAGTGAAAATGAACCCTT 58.448 40.909 0.00 0.00 46.97 3.95
508 541 3.208747 ACGTGAGTGAAAATGAACCCT 57.791 42.857 0.00 0.00 46.97 4.34
583 617 3.119029 ACGGATGATGGCAAATTTTCTGG 60.119 43.478 0.00 0.00 0.00 3.86
585 619 4.220382 TCAACGGATGATGGCAAATTTTCT 59.780 37.500 0.00 0.00 31.50 2.52
586 620 4.493547 TCAACGGATGATGGCAAATTTTC 58.506 39.130 0.00 0.00 31.50 2.29
587 621 4.021192 ACTCAACGGATGATGGCAAATTTT 60.021 37.500 0.00 0.00 37.44 1.82
590 624 2.684881 GACTCAACGGATGATGGCAAAT 59.315 45.455 0.00 0.00 37.44 2.32
595 629 2.967599 TGAGACTCAACGGATGATGG 57.032 50.000 1.64 0.00 37.44 3.51
606 640 3.742882 CGAGCAACTGAAAATGAGACTCA 59.257 43.478 7.80 7.80 0.00 3.41
608 642 3.993081 CTCGAGCAACTGAAAATGAGACT 59.007 43.478 0.00 0.00 0.00 3.24
615 649 0.531974 ACCGCTCGAGCAACTGAAAA 60.532 50.000 34.69 0.00 42.21 2.29
621 655 1.372997 TCAGAACCGCTCGAGCAAC 60.373 57.895 34.69 21.55 42.21 4.17
625 659 2.202492 CCGTCAGAACCGCTCGAG 60.202 66.667 8.45 8.45 0.00 4.04
758 828 2.884207 GCGTCCCATCGAACCGAC 60.884 66.667 0.00 0.00 39.18 4.79
950 1051 2.285668 TCCTCTTCCAGGGCAGGG 60.286 66.667 0.00 0.00 43.67 4.45
952 1053 1.306482 TCCTCCTCTTCCAGGGCAG 60.306 63.158 0.00 0.00 43.67 4.85
969 1070 2.273776 GCCCTCTTCCTTGCCCTC 59.726 66.667 0.00 0.00 0.00 4.30
971 1072 4.803908 CGGCCCTCTTCCTTGCCC 62.804 72.222 0.00 0.00 40.87 5.36
974 1075 2.269241 GGTCGGCCCTCTTCCTTG 59.731 66.667 0.00 0.00 0.00 3.61
1045 1173 0.536260 CAAGCTGGAGAGACAGAGGG 59.464 60.000 0.00 0.00 40.97 4.30
1052 1180 2.695147 TGCGATAATCAAGCTGGAGAGA 59.305 45.455 0.00 0.00 0.00 3.10
1053 1181 3.103447 TGCGATAATCAAGCTGGAGAG 57.897 47.619 0.00 0.00 0.00 3.20
1058 1186 3.234386 CATGCATGCGATAATCAAGCTG 58.766 45.455 14.93 0.00 0.00 4.24
1059 1187 2.351447 GCATGCATGCGATAATCAAGCT 60.351 45.455 33.99 0.00 44.67 3.74
1060 1196 1.983605 GCATGCATGCGATAATCAAGC 59.016 47.619 33.99 8.68 44.67 4.01
1072 1208 1.471119 AAGGACAAGGAGCATGCATG 58.529 50.000 22.70 22.70 0.00 4.06
1073 1209 3.117776 TCATAAGGACAAGGAGCATGCAT 60.118 43.478 21.98 4.75 0.00 3.96
1089 1225 8.938906 CATCAAAACAATTCCCCTTTTCATAAG 58.061 33.333 0.00 0.00 0.00 1.73
1091 1227 8.200024 TCATCAAAACAATTCCCCTTTTCATA 57.800 30.769 0.00 0.00 0.00 2.15
1103 1243 9.713713 TTTGTCATGATCATCATCAAAACAATT 57.286 25.926 18.69 0.00 42.53 2.32
1111 1251 7.827729 ACTCTCTTTTTGTCATGATCATCATCA 59.172 33.333 4.86 2.71 43.45 3.07
1128 1268 8.815565 AAAGGAAGAAGAAGAAACTCTCTTTT 57.184 30.769 0.00 0.00 44.82 2.27
1132 1272 6.915300 GCAAAAAGGAAGAAGAAGAAACTCTC 59.085 38.462 0.00 0.00 0.00 3.20
1140 1280 7.043788 CGAAAAGAAGCAAAAAGGAAGAAGAAG 60.044 37.037 0.00 0.00 0.00 2.85
1144 1284 4.803613 GCGAAAAGAAGCAAAAAGGAAGAA 59.196 37.500 0.00 0.00 0.00 2.52
1145 1285 4.359706 GCGAAAAGAAGCAAAAAGGAAGA 58.640 39.130 0.00 0.00 0.00 2.87
1146 1286 3.490896 GGCGAAAAGAAGCAAAAAGGAAG 59.509 43.478 0.00 0.00 34.54 3.46
1147 1287 3.118956 TGGCGAAAAGAAGCAAAAAGGAA 60.119 39.130 0.00 0.00 34.54 3.36
1148 1288 2.428890 TGGCGAAAAGAAGCAAAAAGGA 59.571 40.909 0.00 0.00 34.54 3.36
1149 1289 2.820330 TGGCGAAAAGAAGCAAAAAGG 58.180 42.857 0.00 0.00 34.54 3.11
1150 1290 6.710692 ATTATGGCGAAAAGAAGCAAAAAG 57.289 33.333 0.00 0.00 34.54 2.27
1151 1291 7.011857 ACAAATTATGGCGAAAAGAAGCAAAAA 59.988 29.630 0.00 0.00 34.54 1.94
1165 1466 2.518949 GCAGACACACAAATTATGGCG 58.481 47.619 0.00 0.00 0.00 5.69
1171 1472 3.141398 ACTGATCGCAGACACACAAATT 58.859 40.909 0.00 0.00 45.17 1.82
1178 1479 0.170561 ACCGTACTGATCGCAGACAC 59.829 55.000 0.00 0.00 45.17 3.67
1182 1487 2.661878 TCGAGACCGTACTGATCGCAG 61.662 57.143 10.19 0.00 41.37 5.18
1183 1488 0.741927 TCGAGACCGTACTGATCGCA 60.742 55.000 10.19 0.00 37.05 5.10
1184 1489 0.042013 CTCGAGACCGTACTGATCGC 60.042 60.000 6.58 0.00 37.05 4.58
1185 1490 0.042013 GCTCGAGACCGTACTGATCG 60.042 60.000 18.75 9.22 37.05 3.69
1196 1501 1.305201 CTCTAGACCAGGCTCGAGAC 58.695 60.000 18.75 15.26 31.39 3.36
1225 1530 3.170717 TCCTCTTTCTCCCGCTCTTTAA 58.829 45.455 0.00 0.00 0.00 1.52
1226 1531 2.816411 TCCTCTTTCTCCCGCTCTTTA 58.184 47.619 0.00 0.00 0.00 1.85
1227 1532 1.645710 TCCTCTTTCTCCCGCTCTTT 58.354 50.000 0.00 0.00 0.00 2.52
1228 1533 1.872773 ATCCTCTTTCTCCCGCTCTT 58.127 50.000 0.00 0.00 0.00 2.85
1229 1534 1.872773 AATCCTCTTTCTCCCGCTCT 58.127 50.000 0.00 0.00 0.00 4.09
1243 1548 6.095440 CCGATTCAAATCAACACCTAAATCCT 59.905 38.462 3.81 0.00 35.11 3.24
1244 1549 6.127730 ACCGATTCAAATCAACACCTAAATCC 60.128 38.462 3.81 0.00 35.11 3.01
1271 1576 7.116519 GGCATCTTAACTAGCCGATTAGTTTAG 59.883 40.741 14.08 13.99 40.11 1.85
1283 1588 2.224402 CCAGGGAGGCATCTTAACTAGC 60.224 54.545 0.00 0.00 0.00 3.42
1346 1651 4.238514 AGACTGCTGCTTTAAACTAGTCG 58.761 43.478 0.00 0.00 38.39 4.18
1366 1678 6.328934 TGGATAGATACCCAGTTATGCAAAGA 59.671 38.462 0.00 0.00 0.00 2.52
1390 1702 8.557864 CAAAGCCTCAAAAGAGATACATAGATG 58.442 37.037 0.00 0.00 0.00 2.90
1398 1726 9.113838 GAATATGTCAAAGCCTCAAAAGAGATA 57.886 33.333 0.00 0.00 0.00 1.98
1404 1732 5.538053 TGGTGAATATGTCAAAGCCTCAAAA 59.462 36.000 0.00 0.00 38.23 2.44
1410 1738 3.620488 TCCTGGTGAATATGTCAAAGCC 58.380 45.455 0.00 0.00 38.23 4.35
1411 1739 4.943705 TCTTCCTGGTGAATATGTCAAAGC 59.056 41.667 0.00 0.00 38.23 3.51
1412 1740 6.825213 TGATCTTCCTGGTGAATATGTCAAAG 59.175 38.462 0.00 0.00 38.23 2.77
1413 1741 6.720309 TGATCTTCCTGGTGAATATGTCAAA 58.280 36.000 0.00 0.00 38.23 2.69
1414 1742 6.312141 TGATCTTCCTGGTGAATATGTCAA 57.688 37.500 0.00 0.00 38.23 3.18
1415 1743 5.955961 TGATCTTCCTGGTGAATATGTCA 57.044 39.130 0.00 0.00 31.06 3.58
1416 1744 8.944029 CATATTGATCTTCCTGGTGAATATGTC 58.056 37.037 0.00 0.00 31.84 3.06
1417 1745 8.443176 ACATATTGATCTTCCTGGTGAATATGT 58.557 33.333 11.44 11.44 39.20 2.29
1420 1748 9.778741 GTTACATATTGATCTTCCTGGTGAATA 57.221 33.333 0.00 0.00 31.06 1.75
1421 1749 8.497745 AGTTACATATTGATCTTCCTGGTGAAT 58.502 33.333 0.00 0.00 31.06 2.57
1422 1750 7.861629 AGTTACATATTGATCTTCCTGGTGAA 58.138 34.615 0.00 0.00 0.00 3.18
1423 1751 7.437713 AGTTACATATTGATCTTCCTGGTGA 57.562 36.000 0.00 0.00 0.00 4.02
1467 1855 3.402681 CGCAGGTGGGGTCATCCT 61.403 66.667 0.00 0.00 35.33 3.24
1468 1856 2.746375 ATCGCAGGTGGGGTCATCC 61.746 63.158 0.00 0.00 0.00 3.51
1469 1857 1.524621 CATCGCAGGTGGGGTCATC 60.525 63.158 0.00 0.00 0.00 2.92
1470 1858 2.300967 ACATCGCAGGTGGGGTCAT 61.301 57.895 0.00 0.00 0.00 3.06
1483 1871 1.200474 CGCGGTACTAGCACACATCG 61.200 60.000 0.00 0.00 34.19 3.84
1521 1910 4.887655 GGAGAGTTTCAGAGGAACCAAAAA 59.112 41.667 0.00 0.00 31.35 1.94
1522 1911 4.080015 TGGAGAGTTTCAGAGGAACCAAAA 60.080 41.667 0.00 0.00 31.35 2.44
1523 1912 3.458118 TGGAGAGTTTCAGAGGAACCAAA 59.542 43.478 0.00 0.00 31.35 3.28
1526 1915 2.027653 CCTGGAGAGTTTCAGAGGAACC 60.028 54.545 0.00 0.00 31.52 3.62
1533 1922 2.104792 TCAACCACCTGGAGAGTTTCAG 59.895 50.000 0.00 0.00 38.94 3.02
1546 1935 2.795329 ACCACATCAGAATCAACCACC 58.205 47.619 0.00 0.00 0.00 4.61
1565 1954 2.670414 CCAGCTCGATCAGTCTGAAAAC 59.330 50.000 6.64 1.20 31.43 2.43
1583 1972 2.941720 GCTCAGAAACTAAGATGGCCAG 59.058 50.000 13.05 0.00 0.00 4.85
1595 2013 4.836125 TCAGTTTCCAATGCTCAGAAAC 57.164 40.909 6.72 6.72 46.20 2.78
1603 2021 4.808558 TGCATAAGTTCAGTTTCCAATGC 58.191 39.130 0.00 0.00 39.08 3.56
1625 2043 2.240667 AGATGTCAAGGGCAGCATAACT 59.759 45.455 0.00 0.00 0.00 2.24
1626 2044 2.648059 AGATGTCAAGGGCAGCATAAC 58.352 47.619 0.00 0.00 0.00 1.89
1627 2045 3.282021 GAAGATGTCAAGGGCAGCATAA 58.718 45.455 0.00 0.00 0.00 1.90
1628 2046 2.239402 TGAAGATGTCAAGGGCAGCATA 59.761 45.455 0.00 0.00 31.51 3.14
1629 2047 1.005097 TGAAGATGTCAAGGGCAGCAT 59.995 47.619 0.00 0.00 31.51 3.79
1630 2048 0.401356 TGAAGATGTCAAGGGCAGCA 59.599 50.000 0.00 0.00 31.51 4.41
1631 2049 1.093159 CTGAAGATGTCAAGGGCAGC 58.907 55.000 0.00 0.00 35.22 5.25
1632 2050 1.280133 TCCTGAAGATGTCAAGGGCAG 59.720 52.381 0.00 0.00 35.22 4.85
1633 2051 1.361204 TCCTGAAGATGTCAAGGGCA 58.639 50.000 0.00 0.00 35.22 5.36
1634 2052 2.496899 TTCCTGAAGATGTCAAGGGC 57.503 50.000 0.00 0.00 35.22 5.19
1635 2053 3.944015 GTGATTCCTGAAGATGTCAAGGG 59.056 47.826 0.00 0.00 35.22 3.95
1636 2054 4.582869 TGTGATTCCTGAAGATGTCAAGG 58.417 43.478 0.00 0.00 35.22 3.61
1637 2055 4.634883 CCTGTGATTCCTGAAGATGTCAAG 59.365 45.833 0.00 0.00 35.22 3.02
1638 2056 4.566278 CCCTGTGATTCCTGAAGATGTCAA 60.566 45.833 0.00 0.00 35.22 3.18
1639 2057 3.054875 CCCTGTGATTCCTGAAGATGTCA 60.055 47.826 0.00 0.00 34.17 3.58
1640 2058 3.539604 CCCTGTGATTCCTGAAGATGTC 58.460 50.000 0.00 0.00 0.00 3.06
1641 2059 2.240667 CCCCTGTGATTCCTGAAGATGT 59.759 50.000 0.00 0.00 0.00 3.06
1642 2060 2.507058 TCCCCTGTGATTCCTGAAGATG 59.493 50.000 0.00 0.00 0.00 2.90
1643 2061 2.507471 GTCCCCTGTGATTCCTGAAGAT 59.493 50.000 0.00 0.00 0.00 2.40
1644 2062 1.909302 GTCCCCTGTGATTCCTGAAGA 59.091 52.381 0.00 0.00 0.00 2.87
1645 2063 1.406069 CGTCCCCTGTGATTCCTGAAG 60.406 57.143 0.00 0.00 0.00 3.02
1655 2073 2.903357 CATCTCCCGTCCCCTGTG 59.097 66.667 0.00 0.00 0.00 3.66
1670 2088 3.319198 ACGGACCGGAACAGGCAT 61.319 61.111 20.00 0.00 33.69 4.40
1691 2109 1.522806 CCTTATGCAGGCGCCGTAA 60.523 57.895 23.20 16.97 35.13 3.18
1781 2199 1.234821 TCAAGTGATGAACCGGTTGC 58.765 50.000 27.87 16.58 34.30 4.17
2048 2467 0.846401 CGCACCGTAGATTCACATCG 59.154 55.000 0.00 0.00 34.17 3.84
2060 2479 0.104304 GGAACCTATCATCGCACCGT 59.896 55.000 0.00 0.00 0.00 4.83
2061 2480 0.389391 AGGAACCTATCATCGCACCG 59.611 55.000 0.00 0.00 0.00 4.94
2069 2488 1.860641 TGCCTTCGAGGAACCTATCA 58.139 50.000 0.00 0.00 37.67 2.15
2126 2546 3.256960 GGTTCTCCACCCCAGGCA 61.257 66.667 0.00 0.00 40.19 4.75
2135 2555 0.833409 TGAGCAGCTCAGGTTCTCCA 60.833 55.000 21.85 0.00 35.39 3.86
2162 2582 2.267961 GGCTACCCAAGGACGTGG 59.732 66.667 0.00 0.00 38.51 4.94
2165 2585 2.267961 GGTGGCTACCCAAGGACG 59.732 66.667 8.31 0.00 44.33 4.79
2205 2627 6.578020 TGCGTTTCAGAATATAAACCTACG 57.422 37.500 0.00 0.00 33.05 3.51
2225 2647 3.836949 ACATTCCTTGTAAGCAATTGCG 58.163 40.909 24.02 9.12 40.93 4.85
2227 2649 5.343058 CGTTGACATTCCTTGTAAGCAATTG 59.657 40.000 0.00 0.00 39.18 2.32
2238 2660 1.267806 CAAGCAGCGTTGACATTCCTT 59.732 47.619 2.38 0.00 0.00 3.36
2464 2886 6.267471 TCAACTCAAAAGAATAGGCCAAATGT 59.733 34.615 5.01 0.00 0.00 2.71
2476 2898 4.095782 CGTTGGTTCCTCAACTCAAAAGAA 59.904 41.667 6.23 0.00 43.36 2.52
2512 2934 0.107945 ACGCTCCTCTCCTGCAAATC 60.108 55.000 0.00 0.00 0.00 2.17
2597 3025 0.390866 AGTTGCAGCAGATGTCGGAG 60.391 55.000 2.55 0.00 0.00 4.63
2819 3250 6.309737 CCATCAGCAAGCTTTCAGAATAAAAC 59.690 38.462 0.00 0.00 0.00 2.43
2825 3256 2.816087 GTCCATCAGCAAGCTTTCAGAA 59.184 45.455 0.00 0.00 0.00 3.02
2866 3298 4.212214 GTGAGAATTCAGTTGCTTCGAAGT 59.788 41.667 25.24 3.51 32.98 3.01
2912 3344 9.739276 AAATAAGATTGTATTCACACTCTGGAA 57.261 29.630 0.00 0.00 42.17 3.53
2914 3346 9.778993 CAAAATAAGATTGTATTCACACTCTGG 57.221 33.333 0.00 0.00 42.17 3.86
3058 3490 5.717078 TGGTTAGTAGTTCACCAGTACTG 57.283 43.478 16.34 16.34 41.18 2.74
3065 3497 4.510340 CACTGTGTTGGTTAGTAGTTCACC 59.490 45.833 0.00 0.00 0.00 4.02
3066 3498 5.233689 GTCACTGTGTTGGTTAGTAGTTCAC 59.766 44.000 7.79 0.00 0.00 3.18
3068 3500 4.443394 CGTCACTGTGTTGGTTAGTAGTTC 59.557 45.833 7.79 0.00 0.00 3.01
3069 3501 4.098349 TCGTCACTGTGTTGGTTAGTAGTT 59.902 41.667 7.79 0.00 0.00 2.24
3070 3502 3.633525 TCGTCACTGTGTTGGTTAGTAGT 59.366 43.478 7.79 0.00 0.00 2.73
3071 3503 4.233123 TCGTCACTGTGTTGGTTAGTAG 57.767 45.455 7.79 0.00 0.00 2.57
3082 3589 7.008447 GCTAGTTCTTTACTAATCGTCACTGTG 59.992 40.741 0.17 0.17 38.84 3.66
3090 3597 4.037208 TCCGGGCTAGTTCTTTACTAATCG 59.963 45.833 0.00 0.00 38.84 3.34
3115 3622 3.408634 GTTTTTCCTCTGGTGATTCCGA 58.591 45.455 0.00 0.00 39.52 4.55
3116 3623 2.488153 GGTTTTTCCTCTGGTGATTCCG 59.512 50.000 0.00 0.00 39.52 4.30
3117 3624 2.826128 GGGTTTTTCCTCTGGTGATTCC 59.174 50.000 0.00 0.00 36.25 3.01
3118 3625 3.767711 AGGGTTTTTCCTCTGGTGATTC 58.232 45.455 0.00 0.00 36.25 2.52
3119 3626 3.903530 AGGGTTTTTCCTCTGGTGATT 57.096 42.857 0.00 0.00 36.25 2.57
3120 3627 4.175962 TCTAGGGTTTTTCCTCTGGTGAT 58.824 43.478 0.00 0.00 38.30 3.06
3121 3628 3.593942 TCTAGGGTTTTTCCTCTGGTGA 58.406 45.455 0.00 0.00 38.30 4.02
3136 3644 0.393077 CGTGCCCCATAGTTCTAGGG 59.607 60.000 3.85 3.85 42.94 3.53
3139 3647 2.181125 TGAACGTGCCCCATAGTTCTA 58.819 47.619 8.35 0.00 42.29 2.10
3175 3683 4.938080 TCCAAGCATCTTCTATCTTCGTC 58.062 43.478 0.00 0.00 0.00 4.20
3232 3787 4.636249 GGTACTTCCAAGCATCCTCTATG 58.364 47.826 0.00 0.00 35.98 2.23
3238 3793 0.463833 CCCGGTACTTCCAAGCATCC 60.464 60.000 0.00 0.00 35.57 3.51
3288 3843 1.134401 TGGGATCTAGCCTTTTCTGCG 60.134 52.381 0.00 0.00 0.00 5.18
3336 3891 6.103501 AGTCTCATTATAGGTCCAGTACTCCT 59.896 42.308 6.81 6.81 35.60 3.69
3357 3912 0.767375 TGCTTCAGCCCTTTGAGTCT 59.233 50.000 0.00 0.00 41.18 3.24
3401 3956 7.168219 TGTACATTTGAGCATAACTTCTTCCT 58.832 34.615 0.00 0.00 0.00 3.36
3426 3981 7.336427 CCTTTGAGATCATCTTTGTTAGCTCTT 59.664 37.037 0.00 0.00 0.00 2.85
3437 3992 7.344913 AGCTATGTTTCCTTTGAGATCATCTT 58.655 34.615 0.00 0.00 0.00 2.40
3485 4040 3.604875 TTTCCCTAGTAAGAACTGCCG 57.395 47.619 0.00 0.00 36.36 5.69
3495 4051 3.070590 GCGAGCCCTATTTTTCCCTAGTA 59.929 47.826 0.00 0.00 0.00 1.82
3541 4097 3.268023 ACCCAGTACTATTGAGCTTGC 57.732 47.619 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.