Multiple sequence alignment - TraesCS1D01G026400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G026400 chr1D 100.000 2311 0 0 1 2311 10737153 10739463 0.000000e+00 4268
1 TraesCS1D01G026400 chr1A 87.792 942 74 20 597 1509 12915889 12916818 0.000000e+00 1064
2 TraesCS1D01G026400 chr1A 90.608 543 50 1 1 542 12915257 12915799 0.000000e+00 719
3 TraesCS1D01G026400 chr1A 89.597 471 42 5 80 543 592218820 592218350 1.980000e-165 592
4 TraesCS1D01G026400 chr1A 85.567 388 39 4 1922 2308 12917215 12917586 7.740000e-105 390
5 TraesCS1D01G026400 chr1A 84.951 206 23 7 1934 2131 12917973 12918178 3.890000e-48 202
6 TraesCS1D01G026400 chr1A 80.682 264 28 9 559 816 592218368 592218122 1.410000e-42 183
7 TraesCS1D01G026400 chr1A 89.744 117 11 1 105 220 104551046 104551162 5.140000e-32 148
8 TraesCS1D01G026400 chr1B 86.674 953 85 29 590 1509 23980820 23979877 0.000000e+00 1018
9 TraesCS1D01G026400 chr1B 88.525 671 49 16 670 1333 16214647 16215296 0.000000e+00 787
10 TraesCS1D01G026400 chr1B 81.159 207 29 8 1922 2118 16215808 16216014 8.550000e-35 158
11 TraesCS1D01G026400 chr7A 90.446 471 38 5 80 543 168318726 168318256 4.220000e-172 614
12 TraesCS1D01G026400 chr7A 88.596 228 20 4 80 301 114220393 114220620 2.930000e-69 272
13 TraesCS1D01G026400 chr7A 80.682 264 28 10 559 816 114220623 114220869 1.410000e-42 183
14 TraesCS1D01G026400 chr7A 80.682 264 28 10 559 816 168318274 168318028 1.410000e-42 183
15 TraesCS1D01G026400 chr6A 89.597 471 42 5 80 543 426029407 426028937 1.980000e-165 592
16 TraesCS1D01G026400 chr6A 80.303 264 29 11 559 816 426028955 426028709 6.560000e-41 178
17 TraesCS1D01G026400 chr5B 79.518 249 37 10 1891 2129 262353385 262353141 5.110000e-37 165
18 TraesCS1D01G026400 chr5A 80.645 217 34 8 1917 2129 311000421 311000633 6.610000e-36 161
19 TraesCS1D01G026400 chr5D 79.630 216 38 6 1917 2129 241275463 241275675 1.430000e-32 150


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 TraesCS1D01G026400 chr1D 10737153 10739463 2310 False 4268.00 4268 100.0000 1 2311 1 chr1D.!!$F1 2310
1 TraesCS1D01G026400 chr1A 12915257 12918178 2921 False 593.75 1064 87.2295 1 2308 4 chr1A.!!$F2 2307
2 TraesCS1D01G026400 chr1A 592218122 592218820 698 True 387.50 592 85.1395 80 816 2 chr1A.!!$R1 736
3 TraesCS1D01G026400 chr1B 23979877 23980820 943 True 1018.00 1018 86.6740 590 1509 1 chr1B.!!$R1 919
4 TraesCS1D01G026400 chr1B 16214647 16216014 1367 False 472.50 787 84.8420 670 2118 2 chr1B.!!$F1 1448
5 TraesCS1D01G026400 chr7A 168318028 168318726 698 True 398.50 614 85.5640 80 816 2 chr7A.!!$R1 736
6 TraesCS1D01G026400 chr6A 426028709 426029407 698 True 385.00 592 84.9500 80 816 2 chr6A.!!$R1 736

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
558 566 0.031449 TCTTTTCTTTTTGCGCGGGG 59.969 50.0 8.83 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1812 0.036875 GGTGCAGCTCCTACTTGGTT 59.963 55.0 9.07 0.0 37.07 3.67 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
63 64 2.371306 GATCCGCCCTATACTCTCCTC 58.629 57.143 0.00 0.00 0.00 3.71
67 68 1.614850 CGCCCTATACTCTCCTCTCCC 60.615 61.905 0.00 0.00 0.00 4.30
71 72 3.054948 CCCTATACTCTCCTCTCCCGTAG 60.055 56.522 0.00 0.00 0.00 3.51
105 106 5.532406 TCTTGACTGGTTTGGATCTTTTCTG 59.468 40.000 0.00 0.00 0.00 3.02
121 127 4.591321 TTTCTGGGATAGACTGGCATTT 57.409 40.909 0.00 0.00 34.43 2.32
157 163 6.554334 TTGCTTGATTCTAGTACCAAACAC 57.446 37.500 0.00 0.00 0.00 3.32
182 188 6.561294 TCTTTGGGGAAGTGGAATTAGAATT 58.439 36.000 0.00 0.00 36.70 2.17
187 193 4.335594 GGGAAGTGGAATTAGAATTGGTCG 59.664 45.833 0.00 0.00 0.00 4.79
189 195 3.279434 AGTGGAATTAGAATTGGTCGCC 58.721 45.455 0.00 0.00 0.00 5.54
190 196 3.013921 GTGGAATTAGAATTGGTCGCCA 58.986 45.455 0.00 0.00 0.00 5.69
203 209 2.067013 GGTCGCCAAGTTCACTTAGAC 58.933 52.381 10.98 10.98 35.38 2.59
211 217 1.199558 AGTTCACTTAGACGTCGCTCC 59.800 52.381 10.46 0.00 0.00 4.70
217 223 1.331138 CTTAGACGTCGCTCCGAATCT 59.669 52.381 10.46 7.51 37.72 2.40
229 235 1.550524 TCCGAATCTCACTTCACCCTG 59.449 52.381 0.00 0.00 0.00 4.45
247 253 4.838959 CAACCGATCGTTGTTGGC 57.161 55.556 22.15 0.00 45.79 4.52
268 274 4.637091 GGCGTAAATTAAGGTTGGAGCTTA 59.363 41.667 0.00 0.00 37.16 3.09
290 297 1.132640 GCTGCCGTTGACGTCAATC 59.867 57.895 31.81 22.83 38.24 2.67
355 362 5.231702 TGATTTTGTAGCTTAGCGTGTGTA 58.768 37.500 0.00 0.00 0.00 2.90
366 373 0.530744 GCGTGTGTACCCTGATCTGA 59.469 55.000 0.38 0.00 0.00 3.27
406 414 5.984926 ACAATTAAACTTTGATGCCTGTGTG 59.015 36.000 0.00 0.00 0.00 3.82
410 418 2.387757 ACTTTGATGCCTGTGTGGTTT 58.612 42.857 0.00 0.00 38.35 3.27
411 419 3.561143 ACTTTGATGCCTGTGTGGTTTA 58.439 40.909 0.00 0.00 38.35 2.01
420 428 4.173256 GCCTGTGTGGTTTATTTACATGC 58.827 43.478 0.00 0.00 38.35 4.06
421 429 4.321601 GCCTGTGTGGTTTATTTACATGCA 60.322 41.667 0.00 0.00 38.35 3.96
428 436 5.514914 GTGGTTTATTTACATGCAATCCACG 59.485 40.000 0.00 0.00 33.46 4.94
452 460 7.067129 ACGATTTGCACTCAGTTATCTAGTCTA 59.933 37.037 0.00 0.00 0.00 2.59
507 515 0.114954 AATCTGCTGCCTTCCCCAAA 59.885 50.000 0.00 0.00 0.00 3.28
547 555 9.396022 TCTGACAGATTGTTTAACTCTTTTCTT 57.604 29.630 0.00 0.00 0.00 2.52
552 560 9.906111 CAGATTGTTTAACTCTTTTCTTTTTGC 57.094 29.630 0.00 0.00 0.00 3.68
553 561 8.807581 AGATTGTTTAACTCTTTTCTTTTTGCG 58.192 29.630 0.00 0.00 0.00 4.85
554 562 6.325849 TGTTTAACTCTTTTCTTTTTGCGC 57.674 33.333 0.00 0.00 0.00 6.09
555 563 5.003967 TGTTTAACTCTTTTCTTTTTGCGCG 59.996 36.000 0.00 0.00 0.00 6.86
556 564 2.119671 ACTCTTTTCTTTTTGCGCGG 57.880 45.000 8.83 0.00 0.00 6.46
557 565 1.269051 ACTCTTTTCTTTTTGCGCGGG 60.269 47.619 8.83 0.00 0.00 6.13
558 566 0.031449 TCTTTTCTTTTTGCGCGGGG 59.969 50.000 8.83 0.00 0.00 5.73
559 567 0.031449 CTTTTCTTTTTGCGCGGGGA 59.969 50.000 8.83 0.00 0.00 4.81
560 568 0.249114 TTTTCTTTTTGCGCGGGGAC 60.249 50.000 8.83 0.00 0.00 4.46
561 569 1.384989 TTTCTTTTTGCGCGGGGACA 61.385 50.000 8.83 0.00 0.00 4.02
562 570 1.791103 TTCTTTTTGCGCGGGGACAG 61.791 55.000 8.83 0.00 0.00 3.51
563 571 2.203224 TTTTTGCGCGGGGACAGA 60.203 55.556 8.83 0.00 0.00 3.41
564 572 1.586154 CTTTTTGCGCGGGGACAGAT 61.586 55.000 8.83 0.00 0.00 2.90
565 573 1.175983 TTTTTGCGCGGGGACAGATT 61.176 50.000 8.83 0.00 0.00 2.40
566 574 1.861542 TTTTGCGCGGGGACAGATTG 61.862 55.000 8.83 0.00 0.00 2.67
569 577 2.436646 CGCGGGGACAGATTGCTT 60.437 61.111 0.00 0.00 0.00 3.91
570 578 1.153449 CGCGGGGACAGATTGCTTA 60.153 57.895 0.00 0.00 0.00 3.09
571 579 0.742990 CGCGGGGACAGATTGCTTAA 60.743 55.000 0.00 0.00 0.00 1.85
572 580 1.459450 GCGGGGACAGATTGCTTAAA 58.541 50.000 0.00 0.00 0.00 1.52
573 581 2.024414 GCGGGGACAGATTGCTTAAAT 58.976 47.619 0.00 0.00 0.00 1.40
574 582 2.033424 GCGGGGACAGATTGCTTAAATC 59.967 50.000 0.00 0.00 44.44 2.17
611 688 7.754475 TGTGATGTAATGTAACACATTTGCATC 59.246 33.333 23.98 23.98 45.80 3.91
615 692 8.054152 TGTAATGTAACACATTTGCATCATCT 57.946 30.769 9.61 0.00 45.80 2.90
702 783 2.057922 AGTCCAACTGAAGGTGTGGAT 58.942 47.619 0.00 0.00 37.41 3.41
711 792 4.783227 ACTGAAGGTGTGGATAGTTGGTAT 59.217 41.667 0.00 0.00 0.00 2.73
723 804 6.069673 TGGATAGTTGGTATTTGTGTCCAGAT 60.070 38.462 0.00 0.00 32.63 2.90
772 853 3.613737 CACCATTGTGATTTCGGCATTTC 59.386 43.478 0.00 0.00 45.76 2.17
792 876 7.254932 GCATTTCGCTCTTCTTAGTCCATTTAT 60.255 37.037 0.00 0.00 37.77 1.40
798 882 7.218963 CGCTCTTCTTAGTCCATTTATTTTTGC 59.781 37.037 0.00 0.00 0.00 3.68
821 944 9.823647 TTGCTACTTTTTAACCATGAAAATTCA 57.176 25.926 0.00 0.00 42.14 2.57
852 999 2.173356 TGCTGCTGGCTAAATGGTATCT 59.827 45.455 0.00 0.00 42.39 1.98
853 1000 3.390967 TGCTGCTGGCTAAATGGTATCTA 59.609 43.478 0.00 0.00 42.39 1.98
854 1001 4.042062 TGCTGCTGGCTAAATGGTATCTAT 59.958 41.667 0.00 0.00 42.39 1.98
857 1004 5.551233 TGCTGGCTAAATGGTATCTATCAC 58.449 41.667 0.00 0.00 0.00 3.06
858 1005 4.938226 GCTGGCTAAATGGTATCTATCACC 59.062 45.833 0.00 0.00 36.54 4.02
859 1006 5.491982 CTGGCTAAATGGTATCTATCACCC 58.508 45.833 0.00 0.00 34.99 4.61
860 1007 4.910913 TGGCTAAATGGTATCTATCACCCA 59.089 41.667 0.00 0.00 34.99 4.51
861 1008 5.551583 TGGCTAAATGGTATCTATCACCCAT 59.448 40.000 0.00 0.00 39.34 4.00
862 1009 6.045459 TGGCTAAATGGTATCTATCACCCATT 59.955 38.462 0.00 0.00 46.84 3.16
863 1010 6.375455 GGCTAAATGGTATCTATCACCCATTG 59.625 42.308 3.70 0.00 44.74 2.82
872 1019 3.774766 TCTATCACCCATTGCACTGTAGT 59.225 43.478 3.14 0.00 0.00 2.73
891 1038 6.904498 TGTAGTAACACCATTGTTTACATGC 58.096 36.000 0.00 0.00 43.89 4.06
952 1099 9.912634 ATTACTATTTGAAATGACTTGGTTGTG 57.087 29.630 0.00 0.00 0.00 3.33
958 1105 3.715628 AATGACTTGGTTGTGCTGTTC 57.284 42.857 0.00 0.00 0.00 3.18
985 1132 6.357367 CAAACAGGTAATATTCTACTGCCCT 58.643 40.000 11.64 0.00 0.00 5.19
1079 1230 6.527722 CAGGATCAACCGTTTTGTTCATTATG 59.472 38.462 0.00 0.00 44.74 1.90
1172 1323 8.133627 GCTCAGTTCATTGTTAATATGAATGCT 58.866 33.333 15.00 8.71 42.22 3.79
1262 1413 8.734386 CCTAATATGGGAGATTACATCAAAAGC 58.266 37.037 0.00 0.00 0.00 3.51
1301 1452 2.891580 AGACCAGAACAGCTACGAGAAA 59.108 45.455 0.00 0.00 0.00 2.52
1317 1468 0.608130 GAAACCAACATGAAGGGCCC 59.392 55.000 16.46 16.46 0.00 5.80
1333 1484 2.978010 CCCCATCCATTACCGCGC 60.978 66.667 0.00 0.00 0.00 6.86
1334 1485 3.345808 CCCATCCATTACCGCGCG 61.346 66.667 25.67 25.67 0.00 6.86
1354 1533 2.875933 CGGTTGTAGCTTCAAACTCCAA 59.124 45.455 17.63 0.00 33.40 3.53
1364 1543 5.045286 AGCTTCAAACTCCAACCAGAGATAT 60.045 40.000 0.00 0.00 37.33 1.63
1368 1547 7.733773 TCAAACTCCAACCAGAGATATCTAA 57.266 36.000 4.89 0.00 37.33 2.10
1393 1572 8.034058 AGTTGATTATCGCTATTTAGAATGGC 57.966 34.615 0.00 0.00 0.00 4.40
1406 1585 6.942163 TTTAGAATGGCTATAGGCTGAGAT 57.058 37.500 25.03 9.17 41.69 2.75
1417 1596 7.279758 GGCTATAGGCTGAGATTGAACATTATC 59.720 40.741 18.61 0.00 41.46 1.75
1421 1600 6.897986 AGGCTGAGATTGAACATTATCTCTT 58.102 36.000 13.86 1.13 44.51 2.85
1448 1633 4.516321 TGTGATGTTCTGGAATGACAGTTG 59.484 41.667 0.00 0.00 39.48 3.16
1465 1656 6.713450 TGACAGTTGTGTAGTATCACAGAGTA 59.287 38.462 0.00 0.00 46.66 2.59
1470 1661 6.524101 TGTGTAGTATCACAGAGTATTGCA 57.476 37.500 0.00 0.00 42.36 4.08
1472 1663 8.232913 TGTGTAGTATCACAGAGTATTGCATA 57.767 34.615 0.00 0.00 42.36 3.14
1498 1690 4.141711 TGCATCTTCGGAGTAAGCCTTTAT 60.142 41.667 0.00 0.00 0.00 1.40
1534 1731 3.930229 TGCTTAACACTTATACTGTGCGG 59.070 43.478 5.30 0.00 38.86 5.69
1535 1732 4.178540 GCTTAACACTTATACTGTGCGGA 58.821 43.478 5.30 0.00 38.86 5.54
1536 1733 4.809426 GCTTAACACTTATACTGTGCGGAT 59.191 41.667 5.30 0.00 38.86 4.18
1541 1738 7.941795 AACACTTATACTGTGCGGATAATAC 57.058 36.000 5.30 0.00 38.86 1.89
1552 1749 4.506654 GTGCGGATAATACAGTACCACTTG 59.493 45.833 0.00 0.00 0.00 3.16
1558 1762 8.975439 CGGATAATACAGTACCACTTGTTATTC 58.025 37.037 0.00 0.00 0.00 1.75
1564 1768 6.838382 ACAGTACCACTTGTTATTCCTCTTT 58.162 36.000 0.00 0.00 0.00 2.52
1565 1769 6.710744 ACAGTACCACTTGTTATTCCTCTTTG 59.289 38.462 0.00 0.00 0.00 2.77
1569 1773 5.539955 ACCACTTGTTATTCCTCTTTGCAAT 59.460 36.000 0.00 0.00 0.00 3.56
1576 1780 8.347004 TGTTATTCCTCTTTGCAATATGTTCA 57.653 30.769 0.00 0.00 0.00 3.18
1579 1783 5.885230 TCCTCTTTGCAATATGTTCAGTG 57.115 39.130 0.00 0.00 0.00 3.66
1580 1784 4.701651 TCCTCTTTGCAATATGTTCAGTGG 59.298 41.667 0.00 3.39 0.00 4.00
1581 1785 4.701651 CCTCTTTGCAATATGTTCAGTGGA 59.298 41.667 0.00 0.00 0.00 4.02
1587 1794 4.941263 TGCAATATGTTCAGTGGACTTACC 59.059 41.667 2.55 0.00 39.54 2.85
1597 1804 0.039180 TGGACTTACCGGAGCTCTGA 59.961 55.000 24.60 1.40 42.61 3.27
1615 1822 6.155475 CTCTGAATAGAGGAACCAAGTAGG 57.845 45.833 0.00 0.00 45.47 3.18
1620 1827 2.183679 AGAGGAACCAAGTAGGAGCTG 58.816 52.381 0.00 0.00 41.22 4.24
1621 1828 0.615850 AGGAACCAAGTAGGAGCTGC 59.384 55.000 0.00 0.00 41.22 5.25
1624 1831 0.036875 AACCAAGTAGGAGCTGCACC 59.963 55.000 8.35 8.14 41.22 5.01
1627 1834 1.446907 CAAGTAGGAGCTGCACCAAG 58.553 55.000 18.31 0.00 0.00 3.61
1639 1846 2.009051 TGCACCAAGATTGCAGATACG 58.991 47.619 0.00 0.00 45.06 3.06
1645 1852 5.740569 CACCAAGATTGCAGATACGAAAATG 59.259 40.000 0.00 0.00 0.00 2.32
1651 1858 6.648310 AGATTGCAGATACGAAAATGATCGAT 59.352 34.615 0.00 0.00 45.48 3.59
1655 1862 6.093404 GCAGATACGAAAATGATCGATCCTA 58.907 40.000 22.31 5.39 45.48 2.94
1658 1865 9.227490 CAGATACGAAAATGATCGATCCTATAC 57.773 37.037 22.31 10.22 45.48 1.47
1682 1894 8.845942 ACTAAAATACGAAAAACAACTCCAAC 57.154 30.769 0.00 0.00 0.00 3.77
1685 1897 7.692908 AAATACGAAAAACAACTCCAACATG 57.307 32.000 0.00 0.00 0.00 3.21
1688 1900 6.197364 ACGAAAAACAACTCCAACATGTAA 57.803 33.333 0.00 0.00 0.00 2.41
1697 1909 7.648142 ACAACTCCAACATGTAATTGTGTTAG 58.352 34.615 0.00 0.00 36.48 2.34
1703 1915 9.072375 TCCAACATGTAATTGTGTTAGAATTCA 57.928 29.630 8.44 0.00 36.48 2.57
1704 1916 9.128107 CCAACATGTAATTGTGTTAGAATTCAC 57.872 33.333 8.44 0.00 36.48 3.18
1721 1933 8.812513 AGAATTCACAAATATCATGTCTCCAA 57.187 30.769 8.44 0.00 0.00 3.53
1726 1938 7.774134 TCACAAATATCATGTCTCCAATTTGG 58.226 34.615 9.28 9.28 38.18 3.28
1727 1939 6.477688 CACAAATATCATGTCTCCAATTTGGC 59.522 38.462 10.76 0.00 38.18 4.52
1728 1940 6.154877 ACAAATATCATGTCTCCAATTTGGCA 59.845 34.615 10.76 3.74 38.18 4.92
1730 1942 6.989155 ATATCATGTCTCCAATTTGGCAAT 57.011 33.333 10.76 0.00 37.47 3.56
1731 1943 5.687166 ATCATGTCTCCAATTTGGCAATT 57.313 34.783 10.76 0.00 37.47 2.32
1733 1945 5.239351 TCATGTCTCCAATTTGGCAATTTG 58.761 37.500 21.88 21.88 37.47 2.32
1735 1947 5.798125 TGTCTCCAATTTGGCAATTTGTA 57.202 34.783 24.89 14.25 37.47 2.41
1736 1948 6.166984 TGTCTCCAATTTGGCAATTTGTAA 57.833 33.333 24.89 15.70 37.47 2.41
1737 1949 6.222389 TGTCTCCAATTTGGCAATTTGTAAG 58.778 36.000 24.89 21.50 37.47 2.34
1738 1950 6.041409 TGTCTCCAATTTGGCAATTTGTAAGA 59.959 34.615 24.89 22.79 37.47 2.10
1739 1951 6.366061 GTCTCCAATTTGGCAATTTGTAAGAC 59.634 38.462 28.31 28.31 37.47 3.01
1741 1953 6.222389 TCCAATTTGGCAATTTGTAAGACTG 58.778 36.000 24.89 13.16 37.47 3.51
1742 1954 5.990996 CCAATTTGGCAATTTGTAAGACTGT 59.009 36.000 24.89 0.00 29.41 3.55
1743 1955 7.014711 TCCAATTTGGCAATTTGTAAGACTGTA 59.985 33.333 24.89 0.00 37.47 2.74
1744 1956 7.329226 CCAATTTGGCAATTTGTAAGACTGTAG 59.671 37.037 24.89 8.98 29.41 2.74
1745 1957 5.371115 TTGGCAATTTGTAAGACTGTAGC 57.629 39.130 0.00 0.00 0.00 3.58
1746 1958 3.756434 TGGCAATTTGTAAGACTGTAGCC 59.244 43.478 0.00 0.00 38.82 3.93
1747 1959 4.010349 GGCAATTTGTAAGACTGTAGCCT 58.990 43.478 0.00 0.00 35.63 4.58
1748 1960 4.095036 GGCAATTTGTAAGACTGTAGCCTC 59.905 45.833 0.00 0.00 35.63 4.70
1749 1961 4.938226 GCAATTTGTAAGACTGTAGCCTCT 59.062 41.667 0.00 0.00 0.00 3.69
1750 1962 5.163814 GCAATTTGTAAGACTGTAGCCTCTG 60.164 44.000 0.00 0.00 0.00 3.35
1751 1963 5.746990 ATTTGTAAGACTGTAGCCTCTGT 57.253 39.130 0.00 0.00 0.00 3.41
1752 1964 6.852420 ATTTGTAAGACTGTAGCCTCTGTA 57.148 37.500 0.00 0.00 0.00 2.74
1753 1965 5.899120 TTGTAAGACTGTAGCCTCTGTAG 57.101 43.478 0.00 0.00 0.00 2.74
1754 1966 3.695060 TGTAAGACTGTAGCCTCTGTAGC 59.305 47.826 0.00 0.00 0.00 3.58
1755 1967 2.516227 AGACTGTAGCCTCTGTAGCA 57.484 50.000 0.00 0.00 0.00 3.49
1756 1968 3.025322 AGACTGTAGCCTCTGTAGCAT 57.975 47.619 0.00 0.00 0.00 3.79
1757 1969 3.370104 AGACTGTAGCCTCTGTAGCATT 58.630 45.455 0.00 0.00 0.00 3.56
1758 1970 4.537751 AGACTGTAGCCTCTGTAGCATTA 58.462 43.478 0.00 0.00 0.00 1.90
1759 1971 5.144100 AGACTGTAGCCTCTGTAGCATTAT 58.856 41.667 0.00 0.00 0.00 1.28
1760 1972 6.307776 AGACTGTAGCCTCTGTAGCATTATA 58.692 40.000 0.00 0.00 0.00 0.98
1761 1973 6.951198 AGACTGTAGCCTCTGTAGCATTATAT 59.049 38.462 0.00 0.00 0.00 0.86
1762 1974 7.453126 AGACTGTAGCCTCTGTAGCATTATATT 59.547 37.037 0.00 0.00 0.00 1.28
1763 1975 7.967908 ACTGTAGCCTCTGTAGCATTATATTT 58.032 34.615 0.00 0.00 0.00 1.40
1764 1976 8.432805 ACTGTAGCCTCTGTAGCATTATATTTT 58.567 33.333 0.00 0.00 0.00 1.82
1765 1977 9.277783 CTGTAGCCTCTGTAGCATTATATTTTT 57.722 33.333 0.00 0.00 0.00 1.94
1766 1978 9.056005 TGTAGCCTCTGTAGCATTATATTTTTG 57.944 33.333 0.00 0.00 0.00 2.44
1767 1979 9.057089 GTAGCCTCTGTAGCATTATATTTTTGT 57.943 33.333 0.00 0.00 0.00 2.83
1768 1980 8.525290 AGCCTCTGTAGCATTATATTTTTGTT 57.475 30.769 0.00 0.00 0.00 2.83
1769 1981 8.624776 AGCCTCTGTAGCATTATATTTTTGTTC 58.375 33.333 0.00 0.00 0.00 3.18
1770 1982 8.405531 GCCTCTGTAGCATTATATTTTTGTTCA 58.594 33.333 0.00 0.00 0.00 3.18
1819 2031 8.668510 ATGTACTCCATTATGCACTAAAGAAG 57.331 34.615 0.00 0.00 0.00 2.85
1825 2037 9.113838 CTCCATTATGCACTAAAGAAGTATGTT 57.886 33.333 0.00 0.00 35.76 2.71
1831 2053 5.700832 TGCACTAAAGAAGTATGTTCCTGTG 59.299 40.000 0.00 0.00 35.76 3.66
1842 2064 3.140325 TGTTCCTGTGGAGCTAAAAGG 57.860 47.619 0.00 0.00 33.98 3.11
1846 2068 1.271597 CCTGTGGAGCTAAAAGGTGCT 60.272 52.381 0.00 0.00 42.82 4.40
1848 2070 3.003480 CTGTGGAGCTAAAAGGTGCTAC 58.997 50.000 0.00 0.00 39.91 3.58
1849 2071 2.370519 TGTGGAGCTAAAAGGTGCTACA 59.629 45.455 0.00 0.00 46.65 2.74
1852 2074 4.465886 TGGAGCTAAAAGGTGCTACAAAA 58.534 39.130 0.00 0.00 45.94 2.44
1854 2076 5.220381 GGAGCTAAAAGGTGCTACAAAAAC 58.780 41.667 0.00 0.00 39.77 2.43
1855 2077 5.009710 GGAGCTAAAAGGTGCTACAAAAACT 59.990 40.000 0.00 0.00 39.77 2.66
1856 2078 6.461092 GGAGCTAAAAGGTGCTACAAAAACTT 60.461 38.462 0.00 0.00 39.77 2.66
1857 2079 7.255346 GGAGCTAAAAGGTGCTACAAAAACTTA 60.255 37.037 0.00 0.00 39.77 2.24
1858 2080 7.423199 AGCTAAAAGGTGCTACAAAAACTTAC 58.577 34.615 0.00 0.00 37.81 2.34
1860 2082 7.865889 GCTAAAAGGTGCTACAAAAACTTACAT 59.134 33.333 0.00 0.00 0.00 2.29
1861 2083 9.744468 CTAAAAGGTGCTACAAAAACTTACATT 57.256 29.630 0.00 0.00 0.00 2.71
1862 2084 8.419076 AAAAGGTGCTACAAAAACTTACATTG 57.581 30.769 0.00 0.00 0.00 2.82
1863 2085 6.952773 AGGTGCTACAAAAACTTACATTGA 57.047 33.333 0.00 0.00 0.00 2.57
1870 2096 9.083080 GCTACAAAAACTTACATTGACTTTTGT 57.917 29.630 13.37 13.37 44.64 2.83
1874 2100 9.049974 CAAAAACTTACATTGACTTTTGTTTGC 57.950 29.630 0.00 0.00 32.00 3.68
1879 2105 8.629158 ACTTACATTGACTTTTGTTTGCATCTA 58.371 29.630 0.00 0.00 0.00 1.98
1884 2110 6.875948 TGACTTTTGTTTGCATCTAGCTTA 57.124 33.333 0.00 0.00 45.94 3.09
1885 2111 6.668323 TGACTTTTGTTTGCATCTAGCTTAC 58.332 36.000 0.00 0.00 45.94 2.34
1891 2117 6.486253 TGTTTGCATCTAGCTTACTTTGAG 57.514 37.500 0.00 0.00 45.94 3.02
1892 2118 6.230472 TGTTTGCATCTAGCTTACTTTGAGA 58.770 36.000 0.00 0.00 45.94 3.27
1893 2119 6.147821 TGTTTGCATCTAGCTTACTTTGAGAC 59.852 38.462 0.00 0.00 45.94 3.36
1894 2120 5.405935 TGCATCTAGCTTACTTTGAGACA 57.594 39.130 0.00 0.00 45.94 3.41
1895 2121 5.793817 TGCATCTAGCTTACTTTGAGACAA 58.206 37.500 0.00 0.00 45.94 3.18
1896 2122 6.230472 TGCATCTAGCTTACTTTGAGACAAA 58.770 36.000 0.00 0.00 45.94 2.83
1899 2125 8.883731 GCATCTAGCTTACTTTGAGACAAATAA 58.116 33.333 0.00 0.00 41.15 1.40
1902 2128 9.424319 TCTAGCTTACTTTGAGACAAATAAGTG 57.576 33.333 0.00 12.21 33.28 3.16
1904 2130 7.865707 AGCTTACTTTGAGACAAATAAGTGTG 58.134 34.615 16.95 0.00 33.28 3.82
1905 2131 7.499232 AGCTTACTTTGAGACAAATAAGTGTGT 59.501 33.333 16.95 0.00 33.28 3.72
1911 2137 6.993786 TGAGACAAATAAGTGTGTCACAAA 57.006 33.333 7.38 0.00 44.32 2.83
1913 2139 7.995289 TGAGACAAATAAGTGTGTCACAAAAT 58.005 30.769 7.38 0.00 44.32 1.82
1914 2140 7.914871 TGAGACAAATAAGTGTGTCACAAAATG 59.085 33.333 7.38 4.37 44.32 2.32
1915 2141 7.202526 AGACAAATAAGTGTGTCACAAAATGG 58.797 34.615 7.38 1.62 45.40 3.16
1916 2142 6.872920 ACAAATAAGTGTGTCACAAAATGGT 58.127 32.000 7.38 2.16 36.74 3.55
1917 2143 6.756074 ACAAATAAGTGTGTCACAAAATGGTG 59.244 34.615 7.38 5.44 36.74 4.17
1918 2144 6.463995 AATAAGTGTGTCACAAAATGGTGT 57.536 33.333 7.38 0.00 39.76 4.16
1920 2146 7.759489 ATAAGTGTGTCACAAAATGGTGTAT 57.241 32.000 7.38 0.00 39.76 2.29
1929 2155 5.185442 TCACAAAATGGTGTATGCACATGAT 59.815 36.000 16.11 1.74 46.95 2.45
1940 2166 7.919690 GTGTATGCACATGATACAGTATGTTT 58.080 34.615 9.26 0.00 46.56 2.83
1977 2203 5.925509 TCTTTTACTCCAAGTAGCAAGTGT 58.074 37.500 0.00 0.00 31.47 3.55
1978 2204 5.758296 TCTTTTACTCCAAGTAGCAAGTGTG 59.242 40.000 0.00 0.00 31.47 3.82
1986 2212 1.070758 AGTAGCAAGTGTGGTCACCAG 59.929 52.381 0.00 0.00 44.83 4.00
2014 2240 8.149647 AGATAGCATTCCTTTACATCTTCTGAG 58.850 37.037 0.00 0.00 0.00 3.35
2020 2246 6.688073 TCCTTTACATCTTCTGAGAAAGGT 57.312 37.500 10.19 4.12 43.90 3.50
2027 2253 4.223923 CATCTTCTGAGAAAGGTACACCCT 59.776 45.833 0.00 0.00 38.44 4.34
2038 2264 4.100279 AGGTACACCCTTTTTCTCCAAG 57.900 45.455 0.00 0.00 42.73 3.61
2039 2265 3.154710 GGTACACCCTTTTTCTCCAAGG 58.845 50.000 0.00 0.00 40.67 3.61
2040 2266 1.704641 ACACCCTTTTTCTCCAAGGC 58.295 50.000 0.00 0.00 39.78 4.35
2041 2267 1.063266 ACACCCTTTTTCTCCAAGGCA 60.063 47.619 0.00 0.00 39.78 4.75
2042 2268 1.615392 CACCCTTTTTCTCCAAGGCAG 59.385 52.381 0.00 0.00 39.78 4.85
2043 2269 0.605083 CCCTTTTTCTCCAAGGCAGC 59.395 55.000 0.00 0.00 39.78 5.25
2044 2270 1.331214 CCTTTTTCTCCAAGGCAGCA 58.669 50.000 0.00 0.00 34.59 4.41
2045 2271 1.688197 CCTTTTTCTCCAAGGCAGCAA 59.312 47.619 0.00 0.00 34.59 3.91
2046 2272 2.102925 CCTTTTTCTCCAAGGCAGCAAA 59.897 45.455 0.00 0.00 34.59 3.68
2047 2273 2.888834 TTTTCTCCAAGGCAGCAAAC 57.111 45.000 0.00 0.00 0.00 2.93
2053 2279 1.419762 TCCAAGGCAGCAAACTACTGA 59.580 47.619 0.00 0.00 37.32 3.41
2068 2294 7.010923 GCAAACTACTGATCTGAAACTATCTGG 59.989 40.741 6.60 0.00 0.00 3.86
2088 2314 4.385825 TGGTGAACAGATGTAGAAACCAC 58.614 43.478 5.40 0.00 0.00 4.16
2094 2320 2.744202 CAGATGTAGAAACCACTGCACC 59.256 50.000 0.00 0.00 35.59 5.01
2147 2373 7.222000 AGCATTAAGAGATACCTACACTAGC 57.778 40.000 0.00 0.00 0.00 3.42
2148 2374 6.072397 AGCATTAAGAGATACCTACACTAGCG 60.072 42.308 0.00 0.00 0.00 4.26
2157 2383 2.167900 ACCTACACTAGCGGTTGATTCC 59.832 50.000 2.41 0.00 0.00 3.01
2159 2385 2.386661 ACACTAGCGGTTGATTCCTG 57.613 50.000 2.41 0.00 0.00 3.86
2194 2420 5.919755 TGGTTACAGACTGAACAACATGTA 58.080 37.500 10.08 0.00 0.00 2.29
2196 2422 5.989777 GGTTACAGACTGAACAACATGTACT 59.010 40.000 10.08 0.00 0.00 2.73
2197 2423 6.145696 GGTTACAGACTGAACAACATGTACTC 59.854 42.308 10.08 0.00 0.00 2.59
2198 2424 5.537300 ACAGACTGAACAACATGTACTCT 57.463 39.130 10.08 0.00 0.00 3.24
2199 2425 6.650427 ACAGACTGAACAACATGTACTCTA 57.350 37.500 10.08 0.00 0.00 2.43
2200 2426 6.682746 ACAGACTGAACAACATGTACTCTAG 58.317 40.000 10.08 0.00 0.00 2.43
2201 2427 6.265649 ACAGACTGAACAACATGTACTCTAGT 59.734 38.462 10.08 1.56 0.00 2.57
2202 2428 6.584184 CAGACTGAACAACATGTACTCTAGTG 59.416 42.308 0.00 0.00 0.00 2.74
2203 2429 6.490381 AGACTGAACAACATGTACTCTAGTGA 59.510 38.462 0.00 0.00 0.00 3.41
2204 2430 7.177568 AGACTGAACAACATGTACTCTAGTGAT 59.822 37.037 0.00 0.00 0.00 3.06
2205 2431 7.093354 ACTGAACAACATGTACTCTAGTGATG 58.907 38.462 0.00 0.00 0.00 3.07
2206 2432 6.993079 TGAACAACATGTACTCTAGTGATGT 58.007 36.000 0.00 0.00 35.36 3.06
2207 2433 8.117813 TGAACAACATGTACTCTAGTGATGTA 57.882 34.615 0.00 0.00 33.83 2.29
2208 2434 8.027189 TGAACAACATGTACTCTAGTGATGTAC 58.973 37.037 0.00 5.28 33.83 2.90
2209 2435 7.704578 ACAACATGTACTCTAGTGATGTACT 57.295 36.000 0.00 0.00 43.56 2.73
2210 2436 7.539436 ACAACATGTACTCTAGTGATGTACTG 58.461 38.462 0.00 7.87 40.65 2.74
2211 2437 7.176865 ACAACATGTACTCTAGTGATGTACTGT 59.823 37.037 0.00 8.30 40.65 3.55
2212 2438 8.674607 CAACATGTACTCTAGTGATGTACTGTA 58.325 37.037 0.00 0.00 40.65 2.74
2213 2439 8.803397 ACATGTACTCTAGTGATGTACTGTAA 57.197 34.615 0.00 0.00 40.65 2.41
2214 2440 9.409918 ACATGTACTCTAGTGATGTACTGTAAT 57.590 33.333 0.00 0.00 40.65 1.89
2215 2441 9.670719 CATGTACTCTAGTGATGTACTGTAATG 57.329 37.037 0.00 2.00 40.65 1.90
2256 2483 8.270030 TCAATGTATTGAATCTTCATGTCCTCT 58.730 33.333 4.89 0.00 43.26 3.69
2258 2485 6.351711 TGTATTGAATCTTCATGTCCTCTGG 58.648 40.000 0.00 0.00 37.00 3.86
2259 2486 4.916041 TTGAATCTTCATGTCCTCTGGT 57.084 40.909 0.00 0.00 37.00 4.00
2263 2490 3.685139 TCTTCATGTCCTCTGGTTGAC 57.315 47.619 0.00 0.00 0.00 3.18
2265 2492 0.984230 TCATGTCCTCTGGTTGACCC 59.016 55.000 0.00 0.00 34.29 4.46
2275 2502 1.886542 CTGGTTGACCCTTTACTTGGC 59.113 52.381 0.00 0.00 34.29 4.52
2276 2503 1.215673 TGGTTGACCCTTTACTTGGCA 59.784 47.619 0.00 0.00 34.29 4.92
2303 2530 6.437162 TGAAATTGCCTTATTTTAGCTGGACT 59.563 34.615 0.00 0.00 0.00 3.85
2308 2535 5.104109 TGCCTTATTTTAGCTGGACTGGTAT 60.104 40.000 0.00 0.00 0.00 2.73
2309 2536 5.470437 GCCTTATTTTAGCTGGACTGGTATC 59.530 44.000 0.00 0.00 0.00 2.24
2310 2537 6.591935 CCTTATTTTAGCTGGACTGGTATCA 58.408 40.000 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 3.264964 GGATCTACGGGAGAGGAGAGTAT 59.735 52.174 0.00 0.00 37.70 2.12
58 59 0.108963 ACGGATCTACGGGAGAGGAG 59.891 60.000 0.00 0.00 37.70 3.69
60 61 0.953003 GAACGGATCTACGGGAGAGG 59.047 60.000 0.00 0.00 37.70 3.69
63 64 0.953003 GAGGAACGGATCTACGGGAG 59.047 60.000 0.00 0.00 38.39 4.30
67 68 2.683867 AGTCAAGAGGAACGGATCTACG 59.316 50.000 0.00 0.00 40.31 3.51
71 72 1.550976 ACCAGTCAAGAGGAACGGATC 59.449 52.381 0.00 0.00 0.00 3.36
105 106 4.092116 AGCTTAAATGCCAGTCTATCCC 57.908 45.455 0.00 0.00 0.00 3.85
121 127 4.778213 ATCAAGCAATCAGGGTAGCTTA 57.222 40.909 0.00 0.00 44.77 3.09
157 163 5.179452 TCTAATTCCACTTCCCCAAAGAG 57.821 43.478 0.00 0.00 38.44 2.85
182 188 1.689813 TCTAAGTGAACTTGGCGACCA 59.310 47.619 5.95 0.00 37.40 4.02
187 193 1.719780 CGACGTCTAAGTGAACTTGGC 59.280 52.381 14.70 0.00 37.40 4.52
189 195 2.657372 GAGCGACGTCTAAGTGAACTTG 59.343 50.000 14.70 0.00 37.40 3.16
190 196 2.351544 GGAGCGACGTCTAAGTGAACTT 60.352 50.000 14.70 0.71 39.85 2.66
203 209 0.179161 AAGTGAGATTCGGAGCGACG 60.179 55.000 0.00 0.00 34.89 5.12
211 217 1.338105 TGCAGGGTGAAGTGAGATTCG 60.338 52.381 0.00 0.00 31.52 3.34
217 223 1.227823 CGGTTGCAGGGTGAAGTGA 60.228 57.895 0.00 0.00 0.00 3.41
246 252 4.696899 AAGCTCCAACCTTAATTTACGC 57.303 40.909 0.00 0.00 0.00 4.42
283 290 6.494893 TCAGGGAACAAAATTAGATTGACG 57.505 37.500 0.00 0.00 0.00 4.35
290 297 6.271488 TGCTGAATCAGGGAACAAAATTAG 57.729 37.500 12.66 0.00 31.21 1.73
355 362 3.972638 AGCAATATCTGTCAGATCAGGGT 59.027 43.478 18.74 11.50 36.20 4.34
406 414 5.885881 TCGTGGATTGCATGTAAATAAACC 58.114 37.500 0.00 1.02 0.00 3.27
410 418 5.976534 GCAAATCGTGGATTGCATGTAAATA 59.023 36.000 0.00 0.00 32.14 1.40
411 419 4.805192 GCAAATCGTGGATTGCATGTAAAT 59.195 37.500 0.00 0.00 32.14 1.40
420 428 2.485426 ACTGAGTGCAAATCGTGGATTG 59.515 45.455 0.00 0.00 30.38 2.67
421 429 2.783135 ACTGAGTGCAAATCGTGGATT 58.217 42.857 0.00 0.00 30.38 3.01
428 436 9.405587 GATAGACTAGATAACTGAGTGCAAATC 57.594 37.037 0.00 0.00 0.00 2.17
452 460 4.098807 AGGCAAATAAAATTAACGCGGGAT 59.901 37.500 12.47 0.00 0.00 3.85
507 515 8.475639 ACAATCTGTCAGAATAAACGGTACTAT 58.524 33.333 6.64 0.00 0.00 2.12
543 551 1.791103 CTGTCCCCGCGCAAAAAGAA 61.791 55.000 8.75 0.00 0.00 2.52
545 553 1.586154 ATCTGTCCCCGCGCAAAAAG 61.586 55.000 8.75 0.00 0.00 2.27
547 555 1.602323 AATCTGTCCCCGCGCAAAA 60.602 52.632 8.75 0.00 0.00 2.44
548 556 2.033448 AATCTGTCCCCGCGCAAA 59.967 55.556 8.75 0.00 0.00 3.68
549 557 2.745884 CAATCTGTCCCCGCGCAA 60.746 61.111 8.75 0.00 0.00 4.85
552 560 0.742990 TTAAGCAATCTGTCCCCGCG 60.743 55.000 0.00 0.00 0.00 6.46
553 561 1.459450 TTTAAGCAATCTGTCCCCGC 58.541 50.000 0.00 0.00 0.00 6.13
554 562 3.971032 GATTTAAGCAATCTGTCCCCG 57.029 47.619 0.00 0.00 38.69 5.73
562 570 5.252969 TGGCACATCAGATTTAAGCAATC 57.747 39.130 0.00 0.00 41.73 2.67
611 688 6.427150 GGTAACATAAACCAACGCATAGATG 58.573 40.000 0.00 0.00 36.96 2.90
615 692 4.846040 AGGGTAACATAAACCAACGCATA 58.154 39.130 0.00 0.00 38.87 3.14
683 763 2.568623 ATCCACACCTTCAGTTGGAC 57.431 50.000 0.00 0.00 38.01 4.02
699 780 5.741011 TCTGGACACAAATACCAACTATCC 58.259 41.667 0.00 0.00 33.14 2.59
723 804 7.016153 TGGTCTGGCTTCTTCTCTTTATTTA 57.984 36.000 0.00 0.00 0.00 1.40
772 853 7.218963 GCAAAAATAAATGGACTAAGAAGAGCG 59.781 37.037 0.00 0.00 0.00 5.03
810 933 7.690637 GCAGCATGTAAACAATGAATTTTCATG 59.309 33.333 6.56 10.80 42.42 3.07
811 934 7.604927 AGCAGCATGTAAACAATGAATTTTCAT 59.395 29.630 0.00 0.00 44.08 2.57
812 935 6.930164 AGCAGCATGTAAACAATGAATTTTCA 59.070 30.769 0.00 0.00 39.25 2.69
813 936 7.231607 CAGCAGCATGTAAACAATGAATTTTC 58.768 34.615 0.00 0.00 39.31 2.29
815 938 5.640357 CCAGCAGCATGTAAACAATGAATTT 59.360 36.000 0.00 0.00 39.31 1.82
816 939 5.172934 CCAGCAGCATGTAAACAATGAATT 58.827 37.500 0.00 0.00 39.31 2.17
817 940 4.751060 CCAGCAGCATGTAAACAATGAAT 58.249 39.130 0.00 0.00 39.31 2.57
819 942 2.094597 GCCAGCAGCATGTAAACAATGA 60.095 45.455 0.00 0.00 42.97 2.57
820 943 2.264813 GCCAGCAGCATGTAAACAATG 58.735 47.619 0.00 0.00 42.97 2.82
821 944 2.660189 GCCAGCAGCATGTAAACAAT 57.340 45.000 0.00 0.00 42.97 2.71
852 999 5.046231 TGTTACTACAGTGCAATGGGTGATA 60.046 40.000 19.57 8.98 0.00 2.15
853 1000 4.261801 GTTACTACAGTGCAATGGGTGAT 58.738 43.478 19.57 0.00 0.00 3.06
854 1001 3.071747 TGTTACTACAGTGCAATGGGTGA 59.928 43.478 19.57 10.52 0.00 4.02
857 1004 2.747446 GGTGTTACTACAGTGCAATGGG 59.253 50.000 19.57 12.88 34.24 4.00
858 1005 3.407698 TGGTGTTACTACAGTGCAATGG 58.592 45.455 19.57 3.87 34.24 3.16
859 1006 5.048782 ACAATGGTGTTACTACAGTGCAATG 60.049 40.000 13.51 13.51 32.58 2.82
860 1007 5.070001 ACAATGGTGTTACTACAGTGCAAT 58.930 37.500 7.07 0.00 32.58 3.56
861 1008 4.456535 ACAATGGTGTTACTACAGTGCAA 58.543 39.130 7.07 0.00 32.58 4.08
862 1009 4.079980 ACAATGGTGTTACTACAGTGCA 57.920 40.909 7.07 0.00 32.58 4.57
872 1019 7.175816 ACACATAGCATGTAAACAATGGTGTTA 59.824 33.333 0.00 0.00 43.84 2.41
891 1038 9.897744 AACATTTACAAACAATCTGACACATAG 57.102 29.630 0.00 0.00 0.00 2.23
933 1080 4.081752 ACAGCACAACCAAGTCATTTCAAA 60.082 37.500 0.00 0.00 0.00 2.69
935 1082 3.023119 ACAGCACAACCAAGTCATTTCA 58.977 40.909 0.00 0.00 0.00 2.69
936 1083 3.715628 ACAGCACAACCAAGTCATTTC 57.284 42.857 0.00 0.00 0.00 2.17
958 1105 5.277345 GCAGTAGAATATTACCTGTTTGGCG 60.277 44.000 9.14 0.00 40.22 5.69
985 1132 6.623486 CATTAACCATCTTTCAATGTGCTCA 58.377 36.000 0.00 0.00 0.00 4.26
1079 1230 3.077359 AGTAAAACTGCAGAGTGATGGC 58.923 45.455 23.35 2.62 30.61 4.40
1262 1413 1.205655 TCTCTGAACTCCGCCATCTTG 59.794 52.381 0.00 0.00 0.00 3.02
1301 1452 2.445155 GGGGCCCTTCATGTTGGT 59.555 61.111 24.38 0.00 0.00 3.67
1317 1468 3.345808 CGCGCGGTAATGGATGGG 61.346 66.667 24.84 0.00 0.00 4.00
1333 1484 2.489971 TGGAGTTTGAAGCTACAACCG 58.510 47.619 0.00 0.00 0.00 4.44
1334 1485 4.224715 GTTGGAGTTTGAAGCTACAACC 57.775 45.455 22.00 7.97 46.64 3.77
1336 1487 3.882888 CTGGTTGGAGTTTGAAGCTACAA 59.117 43.478 2.32 2.32 34.68 2.41
1337 1488 3.135712 TCTGGTTGGAGTTTGAAGCTACA 59.864 43.478 0.00 0.00 0.00 2.74
1338 1489 3.740115 TCTGGTTGGAGTTTGAAGCTAC 58.260 45.455 0.00 0.00 0.00 3.58
1354 1533 8.247562 GCGATAATCAACTTAGATATCTCTGGT 58.752 37.037 8.95 4.06 32.66 4.00
1368 1547 7.880195 AGCCATTCTAAATAGCGATAATCAACT 59.120 33.333 0.00 0.00 0.00 3.16
1384 1563 6.498303 TCAATCTCAGCCTATAGCCATTCTAA 59.502 38.462 0.00 0.00 45.47 2.10
1393 1572 9.585099 GAGATAATGTTCAATCTCAGCCTATAG 57.415 37.037 7.31 0.00 44.94 1.31
1398 1577 7.498570 AGAAAGAGATAATGTTCAATCTCAGCC 59.501 37.037 13.22 3.58 46.99 4.85
1406 1585 9.288576 ACATCACAAGAAAGAGATAATGTTCAA 57.711 29.630 0.00 0.00 0.00 2.69
1417 1596 6.429078 TCATTCCAGAACATCACAAGAAAGAG 59.571 38.462 0.00 0.00 0.00 2.85
1421 1600 5.375773 TGTCATTCCAGAACATCACAAGAA 58.624 37.500 0.00 0.00 0.00 2.52
1470 1661 5.423610 AGGCTTACTCCGAAGATGCATATAT 59.576 40.000 0.00 0.00 0.00 0.86
1472 1663 3.580458 AGGCTTACTCCGAAGATGCATAT 59.420 43.478 0.00 0.00 0.00 1.78
1477 1669 5.694006 CAGATAAAGGCTTACTCCGAAGATG 59.306 44.000 0.00 0.00 0.00 2.90
1509 1701 6.403200 CCGCACAGTATAAGTGTTAAGCAAAT 60.403 38.462 8.01 0.00 39.17 2.32
1511 1703 4.390603 CCGCACAGTATAAGTGTTAAGCAA 59.609 41.667 8.01 0.00 39.17 3.91
1514 1706 7.997107 TTATCCGCACAGTATAAGTGTTAAG 57.003 36.000 8.01 0.30 39.17 1.85
1517 1714 7.494211 TGTATTATCCGCACAGTATAAGTGTT 58.506 34.615 8.01 0.00 39.17 3.32
1519 1716 7.568267 CTGTATTATCCGCACAGTATAAGTG 57.432 40.000 2.92 2.92 39.92 3.16
1528 1725 3.702548 AGTGGTACTGTATTATCCGCACA 59.297 43.478 8.04 0.00 0.00 4.57
1536 1733 9.263446 AGAGGAATAACAAGTGGTACTGTATTA 57.737 33.333 0.00 0.00 0.00 0.98
1541 1738 6.348540 GCAAAGAGGAATAACAAGTGGTACTG 60.349 42.308 0.00 0.00 0.00 2.74
1552 1749 8.462016 ACTGAACATATTGCAAAGAGGAATAAC 58.538 33.333 1.71 0.00 42.68 1.89
1558 1762 4.701651 TCCACTGAACATATTGCAAAGAGG 59.298 41.667 1.71 2.56 0.00 3.69
1564 1768 4.941263 GGTAAGTCCACTGAACATATTGCA 59.059 41.667 0.00 0.00 35.97 4.08
1565 1769 4.034048 CGGTAAGTCCACTGAACATATTGC 59.966 45.833 0.00 0.00 35.57 3.56
1569 1773 3.433343 TCCGGTAAGTCCACTGAACATA 58.567 45.455 0.00 0.00 35.57 2.29
1576 1780 0.039911 AGAGCTCCGGTAAGTCCACT 59.960 55.000 10.93 0.00 35.57 4.00
1579 1783 1.183549 TTCAGAGCTCCGGTAAGTCC 58.816 55.000 10.93 0.00 0.00 3.85
1580 1784 3.884091 TCTATTCAGAGCTCCGGTAAGTC 59.116 47.826 10.93 0.00 0.00 3.01
1581 1785 3.886505 CTCTATTCAGAGCTCCGGTAAGT 59.113 47.826 10.93 0.00 41.91 2.24
1587 1794 2.035321 GGTTCCTCTATTCAGAGCTCCG 59.965 54.545 10.93 0.00 46.08 4.63
1597 1804 4.407296 CAGCTCCTACTTGGTTCCTCTATT 59.593 45.833 0.00 0.00 37.07 1.73
1604 1811 1.443802 GTGCAGCTCCTACTTGGTTC 58.556 55.000 0.00 0.00 37.07 3.62
1605 1812 0.036875 GGTGCAGCTCCTACTTGGTT 59.963 55.000 9.07 0.00 37.07 3.67
1606 1813 1.127567 TGGTGCAGCTCCTACTTGGT 61.128 55.000 18.08 0.00 37.07 3.67
1615 1822 2.260247 TGCAATCTTGGTGCAGCTC 58.740 52.632 18.08 0.00 46.76 4.09
1620 1827 2.279741 TCGTATCTGCAATCTTGGTGC 58.720 47.619 0.00 0.00 42.55 5.01
1621 1828 4.944962 TTTCGTATCTGCAATCTTGGTG 57.055 40.909 0.00 0.00 0.00 4.17
1624 1831 6.572621 CGATCATTTTCGTATCTGCAATCTTG 59.427 38.462 0.00 0.00 34.46 3.02
1627 1834 6.215477 TCGATCATTTTCGTATCTGCAATC 57.785 37.500 0.00 0.00 40.03 2.67
1633 1840 9.179909 AGTATAGGATCGATCATTTTCGTATCT 57.820 33.333 25.93 12.19 40.03 1.98
1637 1844 9.976511 TTTTAGTATAGGATCGATCATTTTCGT 57.023 29.630 25.93 4.89 40.03 3.85
1658 1865 8.844441 TGTTGGAGTTGTTTTTCGTATTTTAG 57.156 30.769 0.00 0.00 0.00 1.85
1660 1867 7.762159 ACATGTTGGAGTTGTTTTTCGTATTTT 59.238 29.630 0.00 0.00 0.00 1.82
1664 1871 5.821516 ACATGTTGGAGTTGTTTTTCGTA 57.178 34.783 0.00 0.00 0.00 3.43
1667 1874 8.327429 CACAATTACATGTTGGAGTTGTTTTTC 58.673 33.333 2.30 0.00 0.00 2.29
1670 1877 6.872920 ACACAATTACATGTTGGAGTTGTTT 58.127 32.000 2.30 0.00 0.00 2.83
1671 1878 6.463995 ACACAATTACATGTTGGAGTTGTT 57.536 33.333 2.30 0.00 0.00 2.83
1675 1882 8.635765 ATTCTAACACAATTACATGTTGGAGT 57.364 30.769 2.30 8.94 44.09 3.85
1676 1883 9.559958 GAATTCTAACACAATTACATGTTGGAG 57.440 33.333 2.30 0.00 44.09 3.86
1677 1884 9.072375 TGAATTCTAACACAATTACATGTTGGA 57.928 29.630 2.30 9.84 42.44 3.53
1678 1885 9.128107 GTGAATTCTAACACAATTACATGTTGG 57.872 33.333 2.30 8.52 39.36 3.77
1679 1886 9.676195 TGTGAATTCTAACACAATTACATGTTG 57.324 29.630 2.30 0.00 42.72 3.33
1703 1915 6.154877 TGCCAAATTGGAGACATGATATTTGT 59.845 34.615 17.47 0.00 40.63 2.83
1704 1916 6.575267 TGCCAAATTGGAGACATGATATTTG 58.425 36.000 17.47 5.97 40.96 2.32
1709 1921 5.687166 AATTGCCAAATTGGAGACATGAT 57.313 34.783 17.47 0.00 40.96 2.45
1713 1925 4.686191 ACAAATTGCCAAATTGGAGACA 57.314 36.364 17.47 1.03 40.96 3.41
1721 1933 6.389906 GCTACAGTCTTACAAATTGCCAAAT 58.610 36.000 0.00 0.00 0.00 2.32
1724 1936 3.756434 GGCTACAGTCTTACAAATTGCCA 59.244 43.478 0.00 0.00 36.91 4.92
1726 1938 4.938226 AGAGGCTACAGTCTTACAAATTGC 59.062 41.667 0.00 0.00 0.00 3.56
1727 1939 5.934625 ACAGAGGCTACAGTCTTACAAATTG 59.065 40.000 0.00 0.00 0.00 2.32
1728 1940 6.115448 ACAGAGGCTACAGTCTTACAAATT 57.885 37.500 0.00 0.00 0.00 1.82
1730 1942 5.336531 GCTACAGAGGCTACAGTCTTACAAA 60.337 44.000 0.00 0.00 0.00 2.83
1731 1943 4.158025 GCTACAGAGGCTACAGTCTTACAA 59.842 45.833 0.00 0.00 0.00 2.41
1733 1945 3.695060 TGCTACAGAGGCTACAGTCTTAC 59.305 47.826 0.00 0.00 0.00 2.34
1735 1947 2.808919 TGCTACAGAGGCTACAGTCTT 58.191 47.619 0.00 0.00 0.00 3.01
1736 1948 2.516227 TGCTACAGAGGCTACAGTCT 57.484 50.000 0.00 0.00 0.00 3.24
1737 1949 3.810310 AATGCTACAGAGGCTACAGTC 57.190 47.619 0.00 0.00 0.00 3.51
1738 1950 7.546250 AATATAATGCTACAGAGGCTACAGT 57.454 36.000 0.00 0.00 0.00 3.55
1739 1951 8.839310 AAAATATAATGCTACAGAGGCTACAG 57.161 34.615 0.00 0.00 0.00 2.74
1741 1953 9.057089 ACAAAAATATAATGCTACAGAGGCTAC 57.943 33.333 0.00 0.00 0.00 3.58
1742 1954 9.627123 AACAAAAATATAATGCTACAGAGGCTA 57.373 29.630 0.00 0.00 0.00 3.93
1743 1955 8.525290 AACAAAAATATAATGCTACAGAGGCT 57.475 30.769 0.00 0.00 0.00 4.58
1744 1956 8.405531 TGAACAAAAATATAATGCTACAGAGGC 58.594 33.333 0.00 0.00 0.00 4.70
1806 2018 6.372659 CACAGGAACATACTTCTTTAGTGCAT 59.627 38.462 0.00 0.00 37.73 3.96
1810 2022 6.681729 TCCACAGGAACATACTTCTTTAGT 57.318 37.500 0.00 0.00 41.04 2.24
1812 2024 5.248477 AGCTCCACAGGAACATACTTCTTTA 59.752 40.000 0.00 0.00 0.00 1.85
1813 2025 4.042187 AGCTCCACAGGAACATACTTCTTT 59.958 41.667 0.00 0.00 0.00 2.52
1819 2031 4.636206 CCTTTTAGCTCCACAGGAACATAC 59.364 45.833 0.00 0.00 0.00 2.39
1825 2037 1.271379 GCACCTTTTAGCTCCACAGGA 60.271 52.381 7.90 0.00 0.00 3.86
1831 2053 5.009710 AGTTTTTGTAGCACCTTTTAGCTCC 59.990 40.000 0.00 0.00 42.05 4.70
1842 2064 8.628882 AAAGTCAATGTAAGTTTTTGTAGCAC 57.371 30.769 0.00 0.00 0.00 4.40
1848 2070 9.049974 GCAAACAAAAGTCAATGTAAGTTTTTG 57.950 29.630 6.09 6.09 39.87 2.44
1849 2071 8.778358 TGCAAACAAAAGTCAATGTAAGTTTTT 58.222 25.926 0.00 0.00 29.07 1.94
1852 2074 7.981225 AGATGCAAACAAAAGTCAATGTAAGTT 59.019 29.630 0.00 0.00 0.00 2.66
1854 2076 7.935338 AGATGCAAACAAAAGTCAATGTAAG 57.065 32.000 0.00 0.00 0.00 2.34
1855 2077 7.594758 GCTAGATGCAAACAAAAGTCAATGTAA 59.405 33.333 0.00 0.00 42.31 2.41
1856 2078 7.040478 AGCTAGATGCAAACAAAAGTCAATGTA 60.040 33.333 0.00 0.00 45.94 2.29
1857 2079 5.922544 GCTAGATGCAAACAAAAGTCAATGT 59.077 36.000 0.00 0.00 42.31 2.71
1858 2080 6.154445 AGCTAGATGCAAACAAAAGTCAATG 58.846 36.000 0.00 0.00 45.94 2.82
1860 2082 5.772825 AGCTAGATGCAAACAAAAGTCAA 57.227 34.783 0.00 0.00 45.94 3.18
1861 2083 5.772825 AAGCTAGATGCAAACAAAAGTCA 57.227 34.783 0.00 0.00 45.94 3.41
1862 2084 6.903419 AGTAAGCTAGATGCAAACAAAAGTC 58.097 36.000 0.00 0.00 45.94 3.01
1863 2085 6.884280 AGTAAGCTAGATGCAAACAAAAGT 57.116 33.333 0.00 0.00 45.94 2.66
1870 2096 6.230472 TGTCTCAAAGTAAGCTAGATGCAAA 58.770 36.000 0.00 0.00 45.94 3.68
1879 2105 7.499232 ACACACTTATTTGTCTCAAAGTAAGCT 59.501 33.333 15.46 0.00 34.43 3.74
1884 2110 6.597672 TGTGACACACTTATTTGTCTCAAAGT 59.402 34.615 3.56 0.00 41.10 2.66
1885 2111 7.015226 TGTGACACACTTATTTGTCTCAAAG 57.985 36.000 3.56 0.00 41.10 2.77
1891 2117 6.978080 ACCATTTTGTGACACACTTATTTGTC 59.022 34.615 8.05 0.00 42.18 3.18
1892 2118 6.756074 CACCATTTTGTGACACACTTATTTGT 59.244 34.615 8.05 0.00 38.55 2.83
1893 2119 6.756074 ACACCATTTTGTGACACACTTATTTG 59.244 34.615 8.05 4.96 39.57 2.32
1894 2120 6.872920 ACACCATTTTGTGACACACTTATTT 58.127 32.000 8.05 0.00 39.57 1.40
1895 2121 6.463995 ACACCATTTTGTGACACACTTATT 57.536 33.333 8.05 0.00 39.57 1.40
1896 2122 7.592938 CATACACCATTTTGTGACACACTTAT 58.407 34.615 8.05 0.00 39.57 1.73
1899 2125 4.261572 GCATACACCATTTTGTGACACACT 60.262 41.667 8.05 0.00 39.57 3.55
1901 2127 3.633986 TGCATACACCATTTTGTGACACA 59.366 39.130 3.56 3.56 39.57 3.72
1902 2128 3.980775 GTGCATACACCATTTTGTGACAC 59.019 43.478 0.00 0.00 41.21 3.67
1904 2130 4.235939 TGTGCATACACCATTTTGTGAC 57.764 40.909 0.00 0.00 46.86 3.67
1905 2131 4.522022 TCATGTGCATACACCATTTTGTGA 59.478 37.500 0.00 0.00 46.86 3.58
1908 2134 6.562518 TGTATCATGTGCATACACCATTTTG 58.437 36.000 0.00 0.00 46.86 2.44
1911 2137 5.439721 ACTGTATCATGTGCATACACCATT 58.560 37.500 0.00 0.00 46.86 3.16
1913 2139 4.486125 ACTGTATCATGTGCATACACCA 57.514 40.909 0.00 0.00 46.86 4.17
1914 2140 5.991606 ACATACTGTATCATGTGCATACACC 59.008 40.000 0.00 0.00 46.86 4.16
1916 2142 9.606631 TTAAACATACTGTATCATGTGCATACA 57.393 29.630 0.00 5.80 41.89 2.29
1917 2143 9.864034 GTTAAACATACTGTATCATGTGCATAC 57.136 33.333 0.00 0.00 35.59 2.39
1918 2144 9.830975 AGTTAAACATACTGTATCATGTGCATA 57.169 29.630 0.00 0.00 35.59 3.14
1920 2146 8.450180 CAAGTTAAACATACTGTATCATGTGCA 58.550 33.333 0.00 0.00 35.59 4.57
1929 2155 5.883673 GGGGCATCAAGTTAAACATACTGTA 59.116 40.000 0.00 0.00 0.00 2.74
1938 2164 6.311735 AGTAAAAGAGGGGCATCAAGTTAAA 58.688 36.000 0.00 0.00 0.00 1.52
1940 2166 5.497474 GAGTAAAAGAGGGGCATCAAGTTA 58.503 41.667 0.00 0.00 0.00 2.24
1977 2203 2.180946 ATGCTATCTCCTGGTGACCA 57.819 50.000 3.40 3.40 0.00 4.02
1978 2204 2.224402 GGAATGCTATCTCCTGGTGACC 60.224 54.545 0.00 0.00 0.00 4.02
1986 2212 7.387397 CAGAAGATGTAAAGGAATGCTATCTCC 59.613 40.741 0.00 0.00 0.00 3.71
2020 2246 2.175931 TGCCTTGGAGAAAAAGGGTGTA 59.824 45.455 4.48 0.00 43.80 2.90
2027 2253 2.765699 AGTTTGCTGCCTTGGAGAAAAA 59.234 40.909 0.00 0.00 30.54 1.94
2029 2255 2.071778 AGTTTGCTGCCTTGGAGAAA 57.928 45.000 0.00 0.00 0.00 2.52
2032 2258 1.808945 CAGTAGTTTGCTGCCTTGGAG 59.191 52.381 0.00 0.00 0.00 3.86
2033 2259 1.419762 TCAGTAGTTTGCTGCCTTGGA 59.580 47.619 0.00 0.00 34.21 3.53
2034 2260 1.896220 TCAGTAGTTTGCTGCCTTGG 58.104 50.000 0.00 0.00 34.21 3.61
2035 2261 3.126514 CAGATCAGTAGTTTGCTGCCTTG 59.873 47.826 0.00 0.00 34.21 3.61
2036 2262 3.008375 TCAGATCAGTAGTTTGCTGCCTT 59.992 43.478 0.00 0.00 34.21 4.35
2037 2263 2.568956 TCAGATCAGTAGTTTGCTGCCT 59.431 45.455 0.00 0.00 34.21 4.75
2038 2264 2.977914 TCAGATCAGTAGTTTGCTGCC 58.022 47.619 0.00 0.00 34.21 4.85
2039 2265 4.453819 AGTTTCAGATCAGTAGTTTGCTGC 59.546 41.667 0.00 0.00 34.21 5.25
2040 2266 7.763528 AGATAGTTTCAGATCAGTAGTTTGCTG 59.236 37.037 0.00 0.00 35.43 4.41
2041 2267 7.763528 CAGATAGTTTCAGATCAGTAGTTTGCT 59.236 37.037 0.00 0.00 0.00 3.91
2042 2268 7.010923 CCAGATAGTTTCAGATCAGTAGTTTGC 59.989 40.741 0.00 0.00 0.00 3.68
2043 2269 8.037758 ACCAGATAGTTTCAGATCAGTAGTTTG 58.962 37.037 0.00 0.00 0.00 2.93
2044 2270 8.037758 CACCAGATAGTTTCAGATCAGTAGTTT 58.962 37.037 0.00 0.00 0.00 2.66
2045 2271 7.397476 TCACCAGATAGTTTCAGATCAGTAGTT 59.603 37.037 0.00 0.00 0.00 2.24
2046 2272 6.892456 TCACCAGATAGTTTCAGATCAGTAGT 59.108 38.462 0.00 0.00 0.00 2.73
2047 2273 7.340122 TCACCAGATAGTTTCAGATCAGTAG 57.660 40.000 0.00 0.00 0.00 2.57
2053 2279 6.611613 TCTGTTCACCAGATAGTTTCAGAT 57.388 37.500 0.00 0.00 45.34 2.90
2068 2294 4.083802 GCAGTGGTTTCTACATCTGTTCAC 60.084 45.833 0.00 0.00 32.73 3.18
2094 2320 1.863454 CGGCTAGCTGAACATAGCAAG 59.137 52.381 19.34 0.00 45.03 4.01
2129 2355 4.167652 ACCGCTAGTGTAGGTATCTCTT 57.832 45.455 1.99 0.00 36.34 2.85
2147 2373 1.942657 CACATAGCCAGGAATCAACCG 59.057 52.381 0.00 0.00 34.73 4.44
2148 2374 2.092429 TCCACATAGCCAGGAATCAACC 60.092 50.000 0.00 0.00 0.00 3.77
2157 2383 3.879295 CTGTAACCATTCCACATAGCCAG 59.121 47.826 0.00 0.00 0.00 4.85
2159 2385 3.877508 GTCTGTAACCATTCCACATAGCC 59.122 47.826 0.00 0.00 0.00 3.93
2194 2420 8.818622 TTACCATTACAGTACATCACTAGAGT 57.181 34.615 0.00 0.00 34.98 3.24
2199 2425 8.540388 ACAGAATTACCATTACAGTACATCACT 58.460 33.333 0.00 0.00 38.32 3.41
2200 2426 8.718102 ACAGAATTACCATTACAGTACATCAC 57.282 34.615 0.00 0.00 0.00 3.06
2233 2460 6.996879 CCAGAGGACATGAAGATTCAATACAT 59.003 38.462 0.00 0.00 41.13 2.29
2256 2483 1.215673 TGCCAAGTAAAGGGTCAACCA 59.784 47.619 0.89 0.00 43.89 3.67
2258 2485 3.572255 TCATTGCCAAGTAAAGGGTCAAC 59.428 43.478 0.00 0.00 0.00 3.18
2259 2486 3.838565 TCATTGCCAAGTAAAGGGTCAA 58.161 40.909 0.00 0.00 0.00 3.18
2275 2502 7.765360 TCCAGCTAAAATAAGGCAATTTCATTG 59.235 33.333 0.00 0.00 43.06 2.82
2276 2503 7.765819 GTCCAGCTAAAATAAGGCAATTTCATT 59.234 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.