Multiple sequence alignment - TraesCS2A01G150000

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 TraesCS2A01G150000 chr2A 100.000 5400 0 0 1 5400 97840114 97845513 0.000000e+00 9973.0
1 TraesCS2A01G150000 chr2A 78.788 132 20 5 6 131 158517594 158517723 1.250000e-11 82.4
2 TraesCS2A01G150000 chr2D 94.704 3059 106 27 656 3689 98903645 98906672 0.000000e+00 4700.0
3 TraesCS2A01G150000 chr2D 92.185 1625 69 25 3694 5295 98906739 98908328 0.000000e+00 2244.0
4 TraesCS2A01G150000 chr2D 88.417 518 42 5 1 517 98902706 98903206 4.620000e-170 608.0
5 TraesCS2A01G150000 chr2D 90.756 119 5 5 5283 5397 98985944 98986060 2.600000e-33 154.0
6 TraesCS2A01G150000 chr2D 78.125 128 19 8 6 127 520641642 520641766 7.500000e-09 73.1
7 TraesCS2A01G150000 chr2B 97.650 1404 30 3 1887 3289 150597009 150598410 0.000000e+00 2407.0
8 TraesCS2A01G150000 chr2B 94.824 1024 50 3 3694 4715 150598923 150599945 0.000000e+00 1594.0
9 TraesCS2A01G150000 chr2B 92.252 968 53 9 929 1890 150595802 150596753 0.000000e+00 1352.0
10 TraesCS2A01G150000 chr2B 95.098 408 14 5 3286 3689 150598453 150598858 5.900000e-179 638.0
11 TraesCS2A01G150000 chr2B 88.641 537 36 12 4719 5254 150599980 150600492 9.870000e-177 630.0
12 TraesCS2A01G150000 chr2B 87.216 352 25 5 549 900 150595211 150595542 3.050000e-102 383.0
13 TraesCS2A01G150000 chr2B 88.449 303 32 3 2 302 150542277 150542578 3.980000e-96 363.0
14 TraesCS2A01G150000 chr2B 91.200 125 10 1 286 410 150585045 150585168 9.300000e-38 169.0
15 TraesCS2A01G150000 chr2B 91.736 121 10 0 397 517 150595014 150595134 9.300000e-38 169.0
16 TraesCS2A01G150000 chr3D 77.647 1190 163 52 1715 2887 608300355 608299252 3.550000e-176 628.0
17 TraesCS2A01G150000 chr3D 78.125 128 19 6 6 127 10696900 10697024 7.500000e-09 73.1
18 TraesCS2A01G150000 chr5A 84.124 548 81 4 1875 2421 3316399 3316941 4.790000e-145 525.0
19 TraesCS2A01G150000 chr5D 84.066 546 74 8 1878 2421 9918652 9918118 1.040000e-141 514.0
20 TraesCS2A01G150000 chr5D 78.125 128 19 8 6 127 112842108 112841984 7.500000e-09 73.1
21 TraesCS2A01G150000 chr1D 78.696 690 103 22 1733 2416 392565231 392564580 2.330000e-113 420.0
22 TraesCS2A01G150000 chr1D 82.160 426 53 11 2472 2887 392564574 392564162 1.440000e-90 344.0
23 TraesCS2A01G150000 chr3A 79.851 134 17 7 6 132 515916916 515916786 7.450000e-14 89.8
24 TraesCS2A01G150000 chr3B 90.000 50 5 0 4668 4717 704578514 704578465 1.260000e-06 65.8


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 TraesCS2A01G150000 chr2A 97840114 97845513 5399 False 9973.000000 9973 100.000000 1 5400 1 chr2A.!!$F1 5399
1 TraesCS2A01G150000 chr2D 98902706 98908328 5622 False 2517.333333 4700 91.768667 1 5295 3 chr2D.!!$F3 5294
2 TraesCS2A01G150000 chr2B 150595014 150600492 5478 False 1024.714286 2407 92.488143 397 5254 7 chr2B.!!$F3 4857
3 TraesCS2A01G150000 chr3D 608299252 608300355 1103 True 628.000000 628 77.647000 1715 2887 1 chr3D.!!$R1 1172
4 TraesCS2A01G150000 chr5A 3316399 3316941 542 False 525.000000 525 84.124000 1875 2421 1 chr5A.!!$F1 546
5 TraesCS2A01G150000 chr5D 9918118 9918652 534 True 514.000000 514 84.066000 1878 2421 1 chr5D.!!$R1 543
6 TraesCS2A01G150000 chr1D 392564162 392565231 1069 True 382.000000 420 80.428000 1733 2887 2 chr1D.!!$R1 1154

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
676 979 0.103026 TAAGCTCATGCGCGATCTGT 59.897 50.000 12.10 0.0 45.42 3.41 F
1279 1813 0.031857 TGCGCTGATTTTGGTGGTTG 59.968 50.000 9.73 0.0 0.00 3.77 F
1549 2096 0.460284 GGATTCGATGCGGTGTCAGT 60.460 55.000 0.00 0.0 0.00 3.41 F
2002 2821 1.202879 TGTGGGACTGATGGTTTGTCC 60.203 52.381 0.00 0.0 46.83 4.02 F
3962 4923 0.251165 ACCATTCCCAAGGGTCGTTG 60.251 55.000 4.80 0.0 43.03 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2882 0.179000 CCCGATTCCTCACTTCTGGG 59.821 60.000 0.00 0.0 0.00 4.45 R
2382 3209 3.698040 AGAAAAGGCACATGATCCATCAC 59.302 43.478 0.00 0.0 40.03 3.06 R
3306 4200 5.107875 GCAATGTTTTAGTAACTGCTTGTGC 60.108 40.000 0.00 0.0 40.20 4.57 R
4001 4962 1.470979 CCACTTCTCCGTATTCCACCG 60.471 57.143 0.00 0.0 0.00 4.94 R
5303 6308 0.035739 GTTACTGCCAGGAAACCGGA 59.964 55.000 9.46 0.0 0.00 5.14 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
75 76 9.553064 TTTTTGCTACCATGTTTTATTTGATGT 57.447 25.926 0.00 0.00 0.00 3.06
84 85 8.087750 CCATGTTTTATTTGATGTAACCACTGT 58.912 33.333 0.00 0.00 0.00 3.55
102 103 5.415701 CCACTGTATCAATTTTGCTACCACT 59.584 40.000 2.80 0.00 30.82 4.00
104 105 7.283127 CCACTGTATCAATTTTGCTACCACTAT 59.717 37.037 2.80 0.00 30.82 2.12
118 119 5.181245 GCTACCACTATCTTCAGTTTTTGCA 59.819 40.000 0.00 0.00 0.00 4.08
123 124 6.376978 CACTATCTTCAGTTTTTGCAGGAAG 58.623 40.000 0.00 0.00 37.03 3.46
160 161 3.450115 GGTCGACAGGCGCCTAGT 61.450 66.667 32.30 28.00 40.61 2.57
184 185 6.104146 ACGGCCCTATTGTAAAACAAATTT 57.896 33.333 0.00 0.00 41.96 1.82
196 197 7.556844 TGTAAAACAAATTTGCTTGAAGGGTA 58.443 30.769 18.12 0.00 34.99 3.69
218 219 5.705609 AACCAAGTTCATAGAACGCATTT 57.294 34.783 4.43 0.00 0.00 2.32
219 220 5.705609 ACCAAGTTCATAGAACGCATTTT 57.294 34.783 4.43 0.00 0.00 1.82
232 233 2.486203 ACGCATTTTGAAGTATTGGCGA 59.514 40.909 9.77 0.00 45.42 5.54
246 247 2.673074 GGCGAAATTCCGATCGACA 58.327 52.632 18.66 2.16 46.23 4.35
249 250 1.858458 GCGAAATTCCGATCGACATGA 59.142 47.619 18.66 1.59 41.43 3.07
252 253 3.305897 CGAAATTCCGATCGACATGAACA 59.694 43.478 18.66 0.00 41.43 3.18
293 295 4.874970 ACATGAAAGGTGATCAAGTTTGC 58.125 39.130 0.00 0.00 0.00 3.68
297 299 4.276678 TGAAAGGTGATCAAGTTTGCAGAG 59.723 41.667 0.00 0.00 0.00 3.35
314 316 3.306088 GCAGAGTGCACCTTGAAGTAGTA 60.306 47.826 14.63 0.00 44.26 1.82
336 338 7.246674 GTAGCAAAATTCTCATTGATACGGA 57.753 36.000 1.50 0.00 38.26 4.69
338 340 5.647658 AGCAAAATTCTCATTGATACGGACA 59.352 36.000 0.00 0.00 0.00 4.02
365 367 4.768145 TGTAAAACAGATTCGCGTGAAAG 58.232 39.130 16.40 11.07 37.71 2.62
366 368 2.969443 AAACAGATTCGCGTGAAAGG 57.031 45.000 16.40 10.38 37.71 3.11
384 386 7.095229 CGTGAAAGGTGATCAAGTTCATAGAAA 60.095 37.037 15.93 0.00 31.38 2.52
419 421 2.936498 ACCGGCGAAATTCTAACAGATG 59.064 45.455 9.30 0.00 0.00 2.90
499 502 4.275196 GCTCACCTAGACGGTTTTTCTTTT 59.725 41.667 0.00 0.00 46.37 2.27
506 509 7.201705 ACCTAGACGGTTTTTCTTTTCAAGAAG 60.202 37.037 0.00 0.00 46.37 2.85
517 520 7.496529 TTCTTTTCAAGAAGGTACACTGATG 57.503 36.000 0.00 0.00 42.31 3.07
518 521 5.470098 TCTTTTCAAGAAGGTACACTGATGC 59.530 40.000 0.00 0.00 33.83 3.91
520 523 3.930336 TCAAGAAGGTACACTGATGCAG 58.070 45.455 0.00 0.00 37.52 4.41
521 524 3.324846 TCAAGAAGGTACACTGATGCAGT 59.675 43.478 0.00 0.00 46.51 4.40
523 526 5.011635 TCAAGAAGGTACACTGATGCAGTAA 59.988 40.000 0.00 0.00 43.43 2.24
526 551 5.877012 AGAAGGTACACTGATGCAGTAAATG 59.123 40.000 0.00 0.00 43.43 2.32
530 555 6.490040 AGGTACACTGATGCAGTAAATGTTTT 59.510 34.615 0.00 0.00 43.43 2.43
539 564 8.579006 TGATGCAGTAAATGTTTTCAAAGAGAT 58.421 29.630 0.00 0.00 0.00 2.75
551 576 9.206870 TGTTTTCAAAGAGATTAATTTGCCATC 57.793 29.630 0.00 0.00 36.55 3.51
602 657 7.295201 TGATCGTGTTAGAACATTTTAGTTGC 58.705 34.615 0.00 0.00 41.59 4.17
604 659 4.317291 CGTGTTAGAACATTTTAGTTGCGC 59.683 41.667 0.00 0.00 41.59 6.09
622 677 1.200716 CGCAACCTGGTACTACTCGAA 59.799 52.381 0.00 0.00 0.00 3.71
623 678 2.159282 CGCAACCTGGTACTACTCGAAT 60.159 50.000 0.00 0.00 0.00 3.34
624 679 3.675228 CGCAACCTGGTACTACTCGAATT 60.675 47.826 0.00 0.00 0.00 2.17
625 680 3.864003 GCAACCTGGTACTACTCGAATTC 59.136 47.826 0.00 0.00 0.00 2.17
626 681 4.381718 GCAACCTGGTACTACTCGAATTCT 60.382 45.833 0.00 0.00 0.00 2.40
627 682 4.985538 ACCTGGTACTACTCGAATTCTG 57.014 45.455 0.00 0.00 0.00 3.02
628 683 3.130693 ACCTGGTACTACTCGAATTCTGC 59.869 47.826 0.00 0.00 0.00 4.26
629 684 3.491104 CCTGGTACTACTCGAATTCTGCC 60.491 52.174 3.52 0.00 0.00 4.85
630 685 2.429610 TGGTACTACTCGAATTCTGCCC 59.570 50.000 3.52 0.00 0.00 5.36
631 686 2.543238 GGTACTACTCGAATTCTGCCCG 60.543 54.545 3.52 0.00 0.00 6.13
632 687 0.460311 ACTACTCGAATTCTGCCCGG 59.540 55.000 3.52 0.00 0.00 5.73
633 688 0.744874 CTACTCGAATTCTGCCCGGA 59.255 55.000 0.73 0.00 0.00 5.14
634 689 1.341531 CTACTCGAATTCTGCCCGGAT 59.658 52.381 0.73 0.00 0.00 4.18
635 690 0.541863 ACTCGAATTCTGCCCGGATT 59.458 50.000 0.73 0.00 0.00 3.01
636 691 1.065418 ACTCGAATTCTGCCCGGATTT 60.065 47.619 0.73 0.00 0.00 2.17
676 979 0.103026 TAAGCTCATGCGCGATCTGT 59.897 50.000 12.10 0.00 45.42 3.41
678 981 2.879070 GCTCATGCGCGATCTGTGG 61.879 63.158 12.10 2.75 0.00 4.17
679 982 2.202919 TCATGCGCGATCTGTGGG 60.203 61.111 12.10 0.00 0.00 4.61
680 983 3.945434 CATGCGCGATCTGTGGGC 61.945 66.667 12.10 1.89 44.67 5.36
790 1093 0.806102 CCACTGGCAGATACCGTTCG 60.806 60.000 23.66 0.00 0.00 3.95
827 1130 2.279784 GAGCCCAGCGAAGATCCG 60.280 66.667 0.00 0.00 0.00 4.18
920 1223 1.654774 GCCTTAATTAGCCGCCTGC 59.345 57.895 0.00 0.00 41.71 4.85
921 1224 1.796190 GCCTTAATTAGCCGCCTGCC 61.796 60.000 0.00 0.00 42.71 4.85
1246 1780 1.144936 GCCATCCTCAAGGTCTCCG 59.855 63.158 0.00 0.00 36.34 4.63
1248 1782 1.144936 CATCCTCAAGGTCTCCGCC 59.855 63.158 0.00 0.00 36.34 6.13
1249 1783 2.066999 ATCCTCAAGGTCTCCGCCC 61.067 63.158 0.00 0.00 36.34 6.13
1250 1784 3.787001 CCTCAAGGTCTCCGCCCC 61.787 72.222 0.00 0.00 0.00 5.80
1251 1785 3.003173 CTCAAGGTCTCCGCCCCA 61.003 66.667 0.00 0.00 0.00 4.96
1279 1813 0.031857 TGCGCTGATTTTGGTGGTTG 59.968 50.000 9.73 0.00 0.00 3.77
1350 1885 2.036217 TGTCCTTGATGGCTTGCTTTTG 59.964 45.455 0.00 0.00 35.26 2.44
1380 1915 1.003545 CCCGTCGATGATTTGACATGC 60.004 52.381 6.11 0.00 36.21 4.06
1429 1964 1.409241 GCTTGCTTGGGGAGATGATGA 60.409 52.381 0.00 0.00 0.00 2.92
1443 1978 5.448768 GGAGATGATGATTTTGCTGTCTGTG 60.449 44.000 0.00 0.00 0.00 3.66
1450 1985 4.515191 TGATTTTGCTGTCTGTGTCCTTAC 59.485 41.667 0.00 0.00 0.00 2.34
1452 1987 2.820059 TGCTGTCTGTGTCCTTACTG 57.180 50.000 0.00 0.00 0.00 2.74
1457 1997 4.302455 CTGTCTGTGTCCTTACTGTCTTG 58.698 47.826 0.00 0.00 0.00 3.02
1473 2013 4.579869 TGTCTTGCTAGGATGTTTTCTCC 58.420 43.478 0.00 0.00 0.00 3.71
1539 2086 5.005394 CCGTGTTTACTGTTAGGATTCGATG 59.995 44.000 0.00 0.00 0.00 3.84
1549 2096 0.460284 GGATTCGATGCGGTGTCAGT 60.460 55.000 0.00 0.00 0.00 3.41
1553 2100 1.588674 TCGATGCGGTGTCAGTTTTT 58.411 45.000 0.00 0.00 0.00 1.94
1558 2105 2.020720 TGCGGTGTCAGTTTTTGTCAT 58.979 42.857 0.00 0.00 0.00 3.06
1566 2113 5.463061 GTGTCAGTTTTTGTCATGGGATTTG 59.537 40.000 0.00 0.00 0.00 2.32
1575 2122 2.033801 GTCATGGGATTTGGAATGCGAG 59.966 50.000 0.00 0.00 0.00 5.03
1583 2130 4.453819 GGATTTGGAATGCGAGGAAGATAG 59.546 45.833 0.00 0.00 0.00 2.08
1584 2131 3.475566 TTGGAATGCGAGGAAGATAGG 57.524 47.619 0.00 0.00 0.00 2.57
1585 2132 2.677914 TGGAATGCGAGGAAGATAGGA 58.322 47.619 0.00 0.00 0.00 2.94
1606 2158 4.020485 GGACCACTGTGTCAGTACCTAAAT 60.020 45.833 7.08 0.00 43.43 1.40
1607 2159 5.512576 GGACCACTGTGTCAGTACCTAAATT 60.513 44.000 7.08 0.00 43.43 1.82
1609 2161 4.154195 CCACTGTGTCAGTACCTAAATTGC 59.846 45.833 7.08 0.00 43.43 3.56
1611 2163 4.997395 ACTGTGTCAGTACCTAAATTGCTG 59.003 41.667 0.27 0.00 43.46 4.41
1614 2166 5.929992 TGTGTCAGTACCTAAATTGCTGTAC 59.070 40.000 0.00 0.00 35.04 2.90
1623 2177 5.882557 ACCTAAATTGCTGTACTGATTCAGG 59.117 40.000 17.66 3.36 35.51 3.86
1678 2233 8.165239 ACTGATGTGCTGTTTAGTTTATTTCA 57.835 30.769 0.00 0.00 0.00 2.69
1700 2255 7.872163 TCATTTTTCATTTCCACTTCAATCG 57.128 32.000 0.00 0.00 0.00 3.34
2002 2821 1.202879 TGTGGGACTGATGGTTTGTCC 60.203 52.381 0.00 0.00 46.83 4.02
2057 2876 3.391160 CTCGTTCCGCGACATCCGA 62.391 63.158 8.23 6.91 45.68 4.55
2063 2882 2.060326 TCCGCGACATCCGATATTTC 57.940 50.000 8.23 0.00 41.76 2.17
2237 3056 1.321074 ACGAGATCCACGGGTTCCTC 61.321 60.000 13.06 0.00 34.93 3.71
2382 3209 3.250762 TCTTGCTTGTGATTCGGAACAAG 59.749 43.478 13.99 13.99 42.67 3.16
2621 3462 9.620259 TGGCTTAAAAACTGAAAAATGGTAAAT 57.380 25.926 0.00 0.00 0.00 1.40
3306 4200 6.222038 TGGTACATTCTAGGCTAAAGAGTG 57.778 41.667 7.92 7.92 36.91 3.51
3423 4317 1.480137 CCTCATCGAGGCTTCTGAACT 59.520 52.381 0.00 0.00 43.29 3.01
3454 4348 7.789831 TCCATGTATATGAACCTCTCTACCTTT 59.210 37.037 0.25 0.00 36.36 3.11
3472 4366 6.232581 ACCTTTCCAATGAAATGAAACACA 57.767 33.333 0.00 0.00 39.65 3.72
3492 4386 6.601264 ACACAAAGTGTTTTTGCATTTCTTG 58.399 32.000 0.00 0.00 45.08 3.02
3493 4387 6.426328 ACACAAAGTGTTTTTGCATTTCTTGA 59.574 30.769 0.00 0.00 45.08 3.02
3494 4388 6.957077 CACAAAGTGTTTTTGCATTTCTTGAG 59.043 34.615 0.00 0.00 32.93 3.02
3495 4389 6.873076 ACAAAGTGTTTTTGCATTTCTTGAGA 59.127 30.769 0.00 0.00 32.93 3.27
3496 4390 7.063780 ACAAAGTGTTTTTGCATTTCTTGAGAG 59.936 33.333 0.00 0.00 32.93 3.20
3562 4458 1.535226 CGCGTTACTAGGCTGTGCATA 60.535 52.381 0.00 0.00 33.08 3.14
3675 4572 7.011857 TGCAAATCTAAACCAAAACACCAATTC 59.988 33.333 0.00 0.00 0.00 2.17
3689 4586 3.025978 ACCAATTCGAATGCATGTCCAT 58.974 40.909 12.25 0.00 0.00 3.41
3690 4587 3.448301 ACCAATTCGAATGCATGTCCATT 59.552 39.130 12.25 0.00 38.09 3.16
3691 4588 4.046462 CCAATTCGAATGCATGTCCATTC 58.954 43.478 12.25 13.24 44.74 2.67
3692 4589 4.202080 CCAATTCGAATGCATGTCCATTCT 60.202 41.667 12.25 3.69 45.56 2.40
3962 4923 0.251165 ACCATTCCCAAGGGTCGTTG 60.251 55.000 4.80 0.00 43.03 4.10
4001 4962 0.321919 TGCAGGTCAGTGATGAAGGC 60.322 55.000 0.00 0.00 0.00 4.35
4109 5070 2.111384 GAAGGAGTGACTATGGCTGGA 58.889 52.381 0.00 0.00 0.00 3.86
4298 5259 6.920210 TGTATATCTTTCTGCTTCTGTCATCG 59.080 38.462 0.00 0.00 0.00 3.84
4308 5271 5.178061 TGCTTCTGTCATCGTGATGTATTT 58.822 37.500 9.51 0.00 39.72 1.40
4328 5291 2.372264 TGGCTGATCATTCTTGCCTTC 58.628 47.619 20.08 0.00 40.44 3.46
4369 5332 1.000506 GCTTACCTCCACTTGTCACGA 59.999 52.381 0.00 0.00 0.00 4.35
4408 5371 1.005924 CCATTGCCTTAGTGACCCCTT 59.994 52.381 0.00 0.00 0.00 3.95
4411 5374 2.634639 TGCCTTAGTGACCCCTTCTA 57.365 50.000 0.00 0.00 0.00 2.10
4421 5384 3.256136 GTGACCCCTTCTATCCTGATACG 59.744 52.174 0.00 0.00 0.00 3.06
4688 5655 1.030457 ACTGCCTCCGTCCTATAACG 58.970 55.000 0.00 0.00 42.24 3.18
4785 5783 0.042708 CTGCACGCGACTATTCATGC 60.043 55.000 15.93 10.51 0.00 4.06
4826 5824 4.838423 TCTGATCAGTGTACCTCAAGGAAA 59.162 41.667 21.92 0.00 38.94 3.13
4828 5826 6.013379 TCTGATCAGTGTACCTCAAGGAAATT 60.013 38.462 21.92 0.00 38.94 1.82
4834 5832 4.217767 GTGTACCTCAAGGAAATTTGGTCC 59.782 45.833 2.30 0.00 38.94 4.46
4855 5853 9.974980 TGGTCCTTTTTCAAATATTGTTAACTC 57.025 29.630 7.22 0.00 0.00 3.01
4873 5871 7.715249 TGTTAACTCTTGATAGCTTGTCACTTT 59.285 33.333 7.22 0.00 0.00 2.66
4922 5920 8.887717 GCATTTGGTAGATGCTATAAGATTAGG 58.112 37.037 2.07 0.00 44.92 2.69
4923 5921 9.950496 CATTTGGTAGATGCTATAAGATTAGGT 57.050 33.333 0.00 0.00 0.00 3.08
4971 5970 6.369629 TCATTTCCTGTTTCCTACTTTTCCA 58.630 36.000 0.00 0.00 0.00 3.53
5012 6011 2.093235 GGAATCAGTTCCCTGTCCTGAG 60.093 54.545 0.00 0.00 46.84 3.35
5041 6040 2.541556 GCTTCCAATCAGTAGGTCGTC 58.458 52.381 0.00 0.00 0.00 4.20
5052 6051 4.876652 GGTCGTCGACCCTTGTAC 57.123 61.111 30.44 6.48 46.19 2.90
5133 6133 2.962253 GCTGGGCGTGCTCGATAC 60.962 66.667 13.13 1.41 39.71 2.24
5261 6266 3.591789 AGCCCCACATCTACATGTATCT 58.408 45.455 5.91 0.00 41.69 1.98
5263 6268 4.413520 AGCCCCACATCTACATGTATCTTT 59.586 41.667 5.91 0.00 41.69 2.52
5271 6276 5.604758 TCTACATGTATCTTTGCAGCTCT 57.395 39.130 5.91 0.00 0.00 4.09
5295 6300 1.762957 GCTAGGAGCCTTCCACACATA 59.237 52.381 0.00 0.00 46.64 2.29
5296 6301 2.483889 GCTAGGAGCCTTCCACACATAC 60.484 54.545 0.00 0.00 46.64 2.39
5297 6302 0.912486 AGGAGCCTTCCACACATACC 59.088 55.000 0.00 0.00 46.64 2.73
5298 6303 0.912486 GGAGCCTTCCACACATACCT 59.088 55.000 0.00 0.00 43.45 3.08
5299 6304 1.134371 GGAGCCTTCCACACATACCTC 60.134 57.143 0.00 0.00 43.45 3.85
5300 6305 1.834263 GAGCCTTCCACACATACCTCT 59.166 52.381 0.00 0.00 0.00 3.69
5301 6306 1.834263 AGCCTTCCACACATACCTCTC 59.166 52.381 0.00 0.00 0.00 3.20
5302 6307 1.834263 GCCTTCCACACATACCTCTCT 59.166 52.381 0.00 0.00 0.00 3.10
5303 6308 2.237392 GCCTTCCACACATACCTCTCTT 59.763 50.000 0.00 0.00 0.00 2.85
5304 6309 3.680196 GCCTTCCACACATACCTCTCTTC 60.680 52.174 0.00 0.00 0.00 2.87
5305 6310 3.118592 CCTTCCACACATACCTCTCTTCC 60.119 52.174 0.00 0.00 0.00 3.46
5306 6311 2.100197 TCCACACATACCTCTCTTCCG 58.900 52.381 0.00 0.00 0.00 4.30
5307 6312 1.137086 CCACACATACCTCTCTTCCGG 59.863 57.143 0.00 0.00 0.00 5.14
5308 6313 1.825474 CACACATACCTCTCTTCCGGT 59.175 52.381 0.00 0.00 37.31 5.28
5309 6314 2.233922 CACACATACCTCTCTTCCGGTT 59.766 50.000 0.00 0.00 34.76 4.44
5310 6315 2.904434 ACACATACCTCTCTTCCGGTTT 59.096 45.455 0.00 0.00 34.76 3.27
5311 6316 3.056035 ACACATACCTCTCTTCCGGTTTC 60.056 47.826 0.00 0.00 34.76 2.78
5312 6317 2.500504 ACATACCTCTCTTCCGGTTTCC 59.499 50.000 0.00 0.00 34.76 3.13
5313 6318 2.617840 TACCTCTCTTCCGGTTTCCT 57.382 50.000 0.00 0.00 34.76 3.36
5314 6319 0.977395 ACCTCTCTTCCGGTTTCCTG 59.023 55.000 0.00 0.00 0.00 3.86
5315 6320 0.250513 CCTCTCTTCCGGTTTCCTGG 59.749 60.000 0.00 0.00 0.00 4.45
5316 6321 0.391793 CTCTCTTCCGGTTTCCTGGC 60.392 60.000 0.00 0.00 0.00 4.85
5317 6322 1.125093 TCTCTTCCGGTTTCCTGGCA 61.125 55.000 0.00 0.00 0.00 4.92
5318 6323 0.674895 CTCTTCCGGTTTCCTGGCAG 60.675 60.000 7.75 7.75 0.00 4.85
5319 6324 1.073199 CTTCCGGTTTCCTGGCAGT 59.927 57.895 14.43 0.00 0.00 4.40
5320 6325 0.323629 CTTCCGGTTTCCTGGCAGTA 59.676 55.000 14.43 0.00 0.00 2.74
5321 6326 0.766131 TTCCGGTTTCCTGGCAGTAA 59.234 50.000 14.43 0.00 0.00 2.24
5322 6327 0.035739 TCCGGTTTCCTGGCAGTAAC 59.964 55.000 14.43 15.92 0.00 2.50
5323 6328 0.036306 CCGGTTTCCTGGCAGTAACT 59.964 55.000 21.53 0.00 0.00 2.24
5324 6329 1.439679 CGGTTTCCTGGCAGTAACTC 58.560 55.000 21.53 14.17 0.00 3.01
5325 6330 1.270625 CGGTTTCCTGGCAGTAACTCA 60.271 52.381 21.53 0.00 0.00 3.41
5326 6331 2.808933 CGGTTTCCTGGCAGTAACTCAA 60.809 50.000 21.53 2.66 0.00 3.02
5327 6332 2.814336 GGTTTCCTGGCAGTAACTCAAG 59.186 50.000 21.53 3.86 0.00 3.02
5328 6333 3.477530 GTTTCCTGGCAGTAACTCAAGT 58.522 45.455 14.43 0.00 0.00 3.16
5329 6334 3.857157 TTCCTGGCAGTAACTCAAGTT 57.143 42.857 14.43 0.46 41.73 2.66
5330 6335 3.857157 TCCTGGCAGTAACTCAAGTTT 57.143 42.857 14.43 0.00 39.31 2.66
5331 6336 3.476552 TCCTGGCAGTAACTCAAGTTTG 58.523 45.455 14.43 0.00 39.31 2.93
5332 6337 2.030805 CCTGGCAGTAACTCAAGTTTGC 60.031 50.000 14.43 9.91 39.66 3.68
5333 6338 2.618241 CTGGCAGTAACTCAAGTTTGCA 59.382 45.455 16.99 6.67 41.22 4.08
5334 6339 2.618241 TGGCAGTAACTCAAGTTTGCAG 59.382 45.455 16.99 4.45 41.22 4.41
5335 6340 2.878406 GGCAGTAACTCAAGTTTGCAGA 59.122 45.455 16.99 0.00 41.22 4.26
5336 6341 3.315191 GGCAGTAACTCAAGTTTGCAGAA 59.685 43.478 16.99 0.00 41.22 3.02
5337 6342 4.282873 GCAGTAACTCAAGTTTGCAGAAC 58.717 43.478 12.46 4.26 39.96 3.01
5338 6343 4.201910 GCAGTAACTCAAGTTTGCAGAACA 60.202 41.667 12.46 0.00 39.96 3.18
5339 6344 5.506317 GCAGTAACTCAAGTTTGCAGAACAT 60.506 40.000 12.46 0.70 39.96 2.71
5340 6345 5.911280 CAGTAACTCAAGTTTGCAGAACATG 59.089 40.000 0.00 10.75 39.31 3.21
5341 6346 5.822519 AGTAACTCAAGTTTGCAGAACATGA 59.177 36.000 0.00 14.46 39.31 3.07
5342 6347 5.779529 AACTCAAGTTTGCAGAACATGAT 57.220 34.783 15.14 0.00 33.93 2.45
5343 6348 5.779529 ACTCAAGTTTGCAGAACATGATT 57.220 34.783 15.14 10.06 29.17 2.57
5344 6349 6.152932 ACTCAAGTTTGCAGAACATGATTT 57.847 33.333 15.14 7.32 29.17 2.17
5345 6350 6.211515 ACTCAAGTTTGCAGAACATGATTTC 58.788 36.000 15.14 0.00 29.17 2.17
5346 6351 6.040166 ACTCAAGTTTGCAGAACATGATTTCT 59.960 34.615 15.14 0.00 36.18 2.52
5347 6352 6.441274 TCAAGTTTGCAGAACATGATTTCTC 58.559 36.000 0.00 0.00 33.31 2.87
5348 6353 5.039480 AGTTTGCAGAACATGATTTCTCG 57.961 39.130 0.00 0.00 33.31 4.04
5349 6354 3.476295 TTGCAGAACATGATTTCTCGC 57.524 42.857 0.00 6.63 33.31 5.03
5350 6355 1.394572 TGCAGAACATGATTTCTCGCG 59.605 47.619 0.00 0.00 33.31 5.87
5351 6356 1.660607 GCAGAACATGATTTCTCGCGA 59.339 47.619 9.26 9.26 33.31 5.87
5352 6357 2.285486 GCAGAACATGATTTCTCGCGAG 60.285 50.000 30.03 30.03 33.31 5.03
5353 6358 3.182182 CAGAACATGATTTCTCGCGAGA 58.818 45.455 33.84 33.84 33.31 4.04
5368 6373 1.961793 CGAGAGCCTGTAGAGTAGCT 58.038 55.000 0.00 0.00 38.56 3.32
5369 6374 3.114668 CGAGAGCCTGTAGAGTAGCTA 57.885 52.381 0.00 0.00 35.23 3.32
5370 6375 3.064207 CGAGAGCCTGTAGAGTAGCTAG 58.936 54.545 0.00 0.00 35.23 3.42
5371 6376 2.812011 GAGAGCCTGTAGAGTAGCTAGC 59.188 54.545 6.62 6.62 35.23 3.42
5372 6377 2.441750 AGAGCCTGTAGAGTAGCTAGCT 59.558 50.000 23.12 23.12 35.23 3.32
5373 6378 2.812011 GAGCCTGTAGAGTAGCTAGCTC 59.188 54.545 23.26 13.06 37.59 4.09
5374 6379 2.173782 AGCCTGTAGAGTAGCTAGCTCA 59.826 50.000 23.26 10.99 35.55 4.26
5375 6380 2.552315 GCCTGTAGAGTAGCTAGCTCAG 59.448 54.545 23.26 19.78 35.55 3.35
5376 6381 3.746114 GCCTGTAGAGTAGCTAGCTCAGA 60.746 52.174 23.26 0.00 35.55 3.27
5377 6382 4.065088 CCTGTAGAGTAGCTAGCTCAGAG 58.935 52.174 23.26 10.89 35.55 3.35
5378 6383 4.202315 CCTGTAGAGTAGCTAGCTCAGAGA 60.202 50.000 23.26 0.00 35.55 3.10
5379 6384 5.513094 CCTGTAGAGTAGCTAGCTCAGAGAT 60.513 48.000 23.26 6.42 35.55 2.75
5380 6385 5.304778 TGTAGAGTAGCTAGCTCAGAGATG 58.695 45.833 23.26 0.00 35.55 2.90
5381 6386 4.705110 AGAGTAGCTAGCTCAGAGATGA 57.295 45.455 23.26 0.00 35.55 2.92
5382 6387 5.047566 AGAGTAGCTAGCTCAGAGATGAA 57.952 43.478 23.26 0.00 35.55 2.57
5383 6388 5.445069 AGAGTAGCTAGCTCAGAGATGAAA 58.555 41.667 23.26 0.00 35.55 2.69
5384 6389 5.532406 AGAGTAGCTAGCTCAGAGATGAAAG 59.468 44.000 23.26 0.00 35.55 2.62
5385 6390 5.445069 AGTAGCTAGCTCAGAGATGAAAGA 58.555 41.667 23.26 0.00 0.00 2.52
5386 6391 4.924305 AGCTAGCTCAGAGATGAAAGAG 57.076 45.455 12.68 0.00 0.00 2.85
5387 6392 4.280819 AGCTAGCTCAGAGATGAAAGAGT 58.719 43.478 12.68 0.00 0.00 3.24
5388 6393 4.711355 AGCTAGCTCAGAGATGAAAGAGTT 59.289 41.667 12.68 0.00 0.00 3.01
5389 6394 4.805192 GCTAGCTCAGAGATGAAAGAGTTG 59.195 45.833 7.70 0.00 0.00 3.16
5390 6395 5.394005 GCTAGCTCAGAGATGAAAGAGTTGA 60.394 44.000 7.70 0.00 0.00 3.18
5391 6396 4.819769 AGCTCAGAGATGAAAGAGTTGAC 58.180 43.478 0.00 0.00 0.00 3.18
5392 6397 3.611986 GCTCAGAGATGAAAGAGTTGACG 59.388 47.826 0.00 0.00 0.00 4.35
5393 6398 4.617067 GCTCAGAGATGAAAGAGTTGACGA 60.617 45.833 0.00 0.00 0.00 4.20
5394 6399 5.453567 TCAGAGATGAAAGAGTTGACGAA 57.546 39.130 0.00 0.00 0.00 3.85
5395 6400 5.842907 TCAGAGATGAAAGAGTTGACGAAA 58.157 37.500 0.00 0.00 0.00 3.46
5396 6401 5.923114 TCAGAGATGAAAGAGTTGACGAAAG 59.077 40.000 0.00 0.00 0.00 2.62
5397 6402 5.923114 CAGAGATGAAAGAGTTGACGAAAGA 59.077 40.000 0.00 0.00 0.00 2.52
5398 6403 6.089283 CAGAGATGAAAGAGTTGACGAAAGAG 59.911 42.308 0.00 0.00 0.00 2.85
5399 6404 5.848406 AGATGAAAGAGTTGACGAAAGAGT 58.152 37.500 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.792538 GTTCGATTCTAGCAAAAATTGAAGATG 58.207 33.333 5.28 0.00 36.44 2.90
20 21 7.083858 TGGTTCGATTCTAGCAAAAATTGAAG 58.916 34.615 5.28 0.00 36.44 3.02
68 69 9.689976 CAAAATTGATACAGTGGTTACATCAAA 57.310 29.630 0.00 0.00 38.65 2.69
69 70 7.812191 GCAAAATTGATACAGTGGTTACATCAA 59.188 33.333 0.00 2.44 39.27 2.57
70 71 7.176515 AGCAAAATTGATACAGTGGTTACATCA 59.823 33.333 0.00 0.00 0.00 3.07
71 72 7.538575 AGCAAAATTGATACAGTGGTTACATC 58.461 34.615 0.00 0.00 0.00 3.06
72 73 7.466746 AGCAAAATTGATACAGTGGTTACAT 57.533 32.000 0.00 0.00 0.00 2.29
73 74 6.892658 AGCAAAATTGATACAGTGGTTACA 57.107 33.333 0.00 0.00 0.00 2.41
84 85 9.330063 CTGAAGATAGTGGTAGCAAAATTGATA 57.670 33.333 0.00 0.00 0.00 2.15
86 87 7.168219 ACTGAAGATAGTGGTAGCAAAATTGA 58.832 34.615 0.00 0.00 0.00 2.57
102 103 5.376854 GCTTCCTGCAAAAACTGAAGATA 57.623 39.130 0.00 0.00 42.31 1.98
104 105 3.715628 GCTTCCTGCAAAAACTGAAGA 57.284 42.857 0.00 0.00 42.31 2.87
160 161 6.837471 AATTTGTTTTACAATAGGGCCGTA 57.163 33.333 7.78 7.78 38.00 4.02
184 185 3.219281 GAACTTGGTTACCCTTCAAGCA 58.781 45.455 0.00 0.00 40.90 3.91
196 197 5.705609 AAATGCGTTCTATGAACTTGGTT 57.294 34.783 8.51 0.00 0.00 3.67
208 209 4.485163 GCCAATACTTCAAAATGCGTTCT 58.515 39.130 0.00 0.00 0.00 3.01
212 213 3.129852 TCGCCAATACTTCAAAATGCG 57.870 42.857 0.00 0.00 41.90 4.73
213 214 6.407475 AATTTCGCCAATACTTCAAAATGC 57.593 33.333 0.00 0.00 0.00 3.56
218 219 4.004314 TCGGAATTTCGCCAATACTTCAA 58.996 39.130 0.00 0.00 0.00 2.69
219 220 3.601435 TCGGAATTTCGCCAATACTTCA 58.399 40.909 0.00 0.00 0.00 3.02
232 233 5.818136 AATGTTCATGTCGATCGGAATTT 57.182 34.783 16.41 6.29 0.00 1.82
293 295 3.393089 ACTACTTCAAGGTGCACTCTG 57.607 47.619 17.98 14.00 0.00 3.35
297 299 3.040147 TGCTACTACTTCAAGGTGCAC 57.960 47.619 8.80 8.80 0.00 4.57
314 316 5.647658 TGTCCGTATCAATGAGAATTTTGCT 59.352 36.000 0.00 0.00 0.00 3.91
336 338 6.740905 CACGCGAATCTGTTTTACAATAATGT 59.259 34.615 15.93 0.00 43.74 2.71
338 340 7.067532 TCACGCGAATCTGTTTTACAATAAT 57.932 32.000 15.93 0.00 0.00 1.28
356 358 1.148310 ACTTGATCACCTTTCACGCG 58.852 50.000 3.53 3.53 0.00 6.01
365 367 6.441093 TGCATTTCTATGAACTTGATCACC 57.559 37.500 0.00 0.00 33.37 4.02
366 368 7.928103 AGATGCATTTCTATGAACTTGATCAC 58.072 34.615 0.00 0.00 33.37 3.06
384 386 1.603802 CGCCGGTAATTCAAGATGCAT 59.396 47.619 1.90 0.00 0.00 3.96
419 421 4.650545 TCTGTTTTACAATAACGTCCGC 57.349 40.909 0.00 0.00 0.00 5.54
499 502 3.324846 ACTGCATCAGTGTACCTTCTTGA 59.675 43.478 0.00 0.00 43.63 3.02
506 509 5.880054 AACATTTACTGCATCAGTGTACC 57.120 39.130 9.52 0.00 45.01 3.34
512 515 8.077991 TCTCTTTGAAAACATTTACTGCATCAG 58.922 33.333 0.00 0.00 37.52 2.90
523 526 9.558396 TGGCAAATTAATCTCTTTGAAAACATT 57.442 25.926 3.92 0.00 34.93 2.71
526 551 9.206870 TGATGGCAAATTAATCTCTTTGAAAAC 57.793 29.630 0.00 0.00 34.93 2.43
576 631 7.478667 GCAACTAAAATGTTCTAACACGATCAG 59.521 37.037 0.00 0.00 42.51 2.90
577 632 7.295201 GCAACTAAAATGTTCTAACACGATCA 58.705 34.615 0.00 0.00 42.51 2.92
580 635 5.672051 CGCAACTAAAATGTTCTAACACGA 58.328 37.500 0.00 0.00 42.51 4.35
581 636 4.317291 GCGCAACTAAAATGTTCTAACACG 59.683 41.667 0.30 0.00 42.51 4.49
582 637 5.209240 TGCGCAACTAAAATGTTCTAACAC 58.791 37.500 8.16 0.00 42.51 3.32
584 639 5.116528 GGTTGCGCAACTAAAATGTTCTAAC 59.883 40.000 42.08 22.61 40.94 2.34
596 651 0.682852 AGTACCAGGTTGCGCAACTA 59.317 50.000 42.08 28.34 40.94 2.24
602 657 0.806868 TCGAGTAGTACCAGGTTGCG 59.193 55.000 0.00 0.00 0.00 4.85
604 659 5.103000 CAGAATTCGAGTAGTACCAGGTTG 58.897 45.833 0.00 0.00 0.00 3.77
632 687 4.286808 CCATGGGGATTTGGGGAATAAATC 59.713 45.833 2.85 0.00 41.53 2.17
633 688 4.077506 TCCATGGGGATTTGGGGAATAAAT 60.078 41.667 13.02 0.00 38.64 1.40
634 689 3.276037 TCCATGGGGATTTGGGGAATAAA 59.724 43.478 13.02 0.00 38.64 1.40
635 690 2.868393 TCCATGGGGATTTGGGGAATAA 59.132 45.455 13.02 0.00 38.64 1.40
636 691 2.519084 TCCATGGGGATTTGGGGAATA 58.481 47.619 13.02 0.00 38.64 1.75
688 991 4.460873 GTGTGCGGGCGCTTTAGC 62.461 66.667 7.64 8.68 42.51 3.09
689 992 3.027170 CTGTGTGCGGGCGCTTTAG 62.027 63.158 7.64 0.00 42.51 1.85
696 999 4.980805 TCGGTTCTGTGTGCGGGC 62.981 66.667 0.00 0.00 0.00 6.13
790 1093 1.004440 GGTGTCAGTGAGTGGCCTC 60.004 63.158 3.32 0.00 38.27 4.70
827 1130 3.991121 GGCGATTTATAGAGGAGTGAAGC 59.009 47.826 0.00 0.00 0.00 3.86
990 1524 4.996434 GCCATCATCCCTCCGCCG 62.996 72.222 0.00 0.00 0.00 6.46
1279 1813 2.866762 AGCCTAGCGTCAAATCGAAATC 59.133 45.455 0.00 0.00 0.00 2.17
1350 1885 0.179161 CATCGACGGGACAGACTGAC 60.179 60.000 10.08 2.35 0.00 3.51
1380 1915 1.586154 AAATTGGGCGCTCACCGAAG 61.586 55.000 11.03 0.00 40.02 3.79
1402 1937 1.904865 CCCCAAGCAAGCAGAGCAA 60.905 57.895 0.00 0.00 0.00 3.91
1403 1938 2.282674 CCCCAAGCAAGCAGAGCA 60.283 61.111 0.00 0.00 0.00 4.26
1429 1964 4.516698 CAGTAAGGACACAGACAGCAAAAT 59.483 41.667 0.00 0.00 0.00 1.82
1443 1978 4.160626 ACATCCTAGCAAGACAGTAAGGAC 59.839 45.833 0.00 0.00 36.03 3.85
1450 1985 4.633565 GGAGAAAACATCCTAGCAAGACAG 59.366 45.833 0.00 0.00 33.77 3.51
1452 1987 3.619038 CGGAGAAAACATCCTAGCAAGAC 59.381 47.826 0.00 0.00 34.45 3.01
1457 1997 2.981859 TCCGGAGAAAACATCCTAGC 57.018 50.000 0.00 0.00 34.45 3.42
1473 2013 4.793216 CGCTGACCTTTTAAAAATGATCCG 59.207 41.667 1.66 0.00 0.00 4.18
1539 2086 2.384382 CATGACAAAAACTGACACCGC 58.616 47.619 0.00 0.00 32.44 5.68
1549 2096 5.002516 GCATTCCAAATCCCATGACAAAAA 58.997 37.500 0.00 0.00 0.00 1.94
1553 2100 1.750206 CGCATTCCAAATCCCATGACA 59.250 47.619 0.00 0.00 0.00 3.58
1558 2105 0.623194 TCCTCGCATTCCAAATCCCA 59.377 50.000 0.00 0.00 0.00 4.37
1566 2113 2.289133 GGTCCTATCTTCCTCGCATTCC 60.289 54.545 0.00 0.00 0.00 3.01
1575 2122 2.832129 TGACACAGTGGTCCTATCTTCC 59.168 50.000 5.31 0.00 36.97 3.46
1583 2130 1.339097 AGGTACTGACACAGTGGTCC 58.661 55.000 13.62 12.29 45.01 4.46
1584 2131 4.595762 TTTAGGTACTGACACAGTGGTC 57.404 45.455 13.62 0.00 45.01 4.02
1585 2132 5.305585 CAATTTAGGTACTGACACAGTGGT 58.694 41.667 13.62 0.00 45.01 4.16
1606 2158 4.824479 TCATCCTGAATCAGTACAGCAA 57.176 40.909 9.63 0.00 33.40 3.91
1607 2159 5.600069 AGTATCATCCTGAATCAGTACAGCA 59.400 40.000 9.63 0.00 33.40 4.41
1609 2161 8.402798 ACTAGTATCATCCTGAATCAGTACAG 57.597 38.462 9.63 7.40 0.00 2.74
1611 2163 8.851145 TCAACTAGTATCATCCTGAATCAGTAC 58.149 37.037 9.63 4.86 0.00 2.73
1614 2166 8.420222 AGTTCAACTAGTATCATCCTGAATCAG 58.580 37.037 2.68 2.68 0.00 2.90
1623 2177 8.462811 TCACTCAAGAGTTCAACTAGTATCATC 58.537 37.037 0.00 0.00 40.20 2.92
1630 2184 5.201713 TGGTCACTCAAGAGTTCAACTAG 57.798 43.478 0.00 0.00 40.20 2.57
1678 2233 6.758254 ACCGATTGAAGTGGAAATGAAAAAT 58.242 32.000 0.00 0.00 0.00 1.82
1689 2244 3.073678 TGTTGATGACCGATTGAAGTGG 58.926 45.455 0.00 0.00 0.00 4.00
1699 2254 6.035650 ACGATAACTTTACATGTTGATGACCG 59.964 38.462 2.30 2.58 33.36 4.79
1700 2255 7.303634 ACGATAACTTTACATGTTGATGACC 57.696 36.000 2.30 0.00 33.36 4.02
1787 2346 3.573110 CCCACTACCGAACTCCTATTAGG 59.427 52.174 3.07 3.07 36.46 2.69
2002 2821 2.131972 TCACCTTCACAATCGTCAACG 58.868 47.619 0.00 0.00 41.45 4.10
2057 2876 5.455326 CCGATTCCTCACTTCTGGGAAATAT 60.455 44.000 0.00 0.00 41.60 1.28
2063 2882 0.179000 CCCGATTCCTCACTTCTGGG 59.821 60.000 0.00 0.00 0.00 4.45
2237 3056 5.966636 TCCTTGACATGTAAAATCGATCG 57.033 39.130 9.36 9.36 0.00 3.69
2382 3209 3.698040 AGAAAAGGCACATGATCCATCAC 59.302 43.478 0.00 0.00 40.03 3.06
2949 3797 6.449635 TGCTAACACATGATTTAATCCACC 57.550 37.500 0.00 0.00 0.00 4.61
3261 4109 6.101150 ACCAAATAGATGCTAGGTGGTATCAA 59.899 38.462 9.05 0.00 36.15 2.57
3306 4200 5.107875 GCAATGTTTTAGTAACTGCTTGTGC 60.108 40.000 0.00 0.00 40.20 4.57
3354 4248 6.704050 ACAAACCAAACAAGGGAATTTTATCG 59.296 34.615 0.00 0.00 0.00 2.92
3423 4317 8.324191 AGAGAGGTTCATATACATGGAGAAAA 57.676 34.615 0.00 0.00 32.61 2.29
3454 4348 6.638610 ACACTTTGTGTTTCATTTCATTGGA 58.361 32.000 0.00 0.00 45.08 3.53
3472 4366 7.322664 TCTCTCAAGAAATGCAAAAACACTTT 58.677 30.769 0.00 0.00 0.00 2.66
3604 4500 9.042450 TCCATATCTTTCTTAGTCAGGTTGTAA 57.958 33.333 0.00 0.00 0.00 2.41
3606 4502 7.496346 TCCATATCTTTCTTAGTCAGGTTGT 57.504 36.000 0.00 0.00 0.00 3.32
3607 4503 8.970859 AATCCATATCTTTCTTAGTCAGGTTG 57.029 34.615 0.00 0.00 0.00 3.77
3663 4560 4.630111 ACATGCATTCGAATTGGTGTTTT 58.370 34.783 8.21 0.00 0.00 2.43
3675 4572 5.490139 AAACTAGAATGGACATGCATTCG 57.510 39.130 17.21 9.12 41.31 3.34
3737 4697 2.071540 TGTCTGCAGCTTCATCGAAAG 58.928 47.619 9.47 0.00 0.00 2.62
3912 4873 5.302568 TGATGAATATTTGACAGGAATGGGC 59.697 40.000 0.00 0.00 0.00 5.36
3952 4913 2.158667 ACAATGAACTCCAACGACCCTT 60.159 45.455 0.00 0.00 0.00 3.95
3962 4923 5.879237 TGCATTATCGAAACAATGAACTCC 58.121 37.500 17.20 4.61 34.69 3.85
4001 4962 1.470979 CCACTTCTCCGTATTCCACCG 60.471 57.143 0.00 0.00 0.00 4.94
4097 5058 4.520492 CCAAAACCATATCCAGCCATAGTC 59.480 45.833 0.00 0.00 0.00 2.59
4269 5230 7.924947 TGACAGAAGCAGAAAGATATACATGAG 59.075 37.037 0.00 0.00 0.00 2.90
4298 5259 6.630444 AGAATGATCAGCCAAATACATCAC 57.370 37.500 0.09 0.00 0.00 3.06
4308 5271 2.025605 AGAAGGCAAGAATGATCAGCCA 60.026 45.455 21.21 0.00 45.95 4.75
4328 5291 0.241749 TCGGTGCCTACGTAACACAG 59.758 55.000 22.72 19.88 36.00 3.66
4369 5332 1.304952 CTCCTCCGAGTCTCCCAGT 59.695 63.158 0.00 0.00 0.00 4.00
4408 5371 7.834881 ATTACAGAAACCGTATCAGGATAGA 57.165 36.000 0.00 0.00 34.73 1.98
4411 5374 7.070821 ACCTAATTACAGAAACCGTATCAGGAT 59.929 37.037 0.00 0.00 34.73 3.24
4421 5384 6.206829 ACAAGAGCAACCTAATTACAGAAACC 59.793 38.462 0.00 0.00 0.00 3.27
4534 5501 6.349611 GGCAGAAAAGCAGAAACAATGAGATA 60.350 38.462 0.00 0.00 35.83 1.98
4535 5502 5.467705 GCAGAAAAGCAGAAACAATGAGAT 58.532 37.500 0.00 0.00 0.00 2.75
4602 5569 2.579873 ACTATGTACCGTCTACCGCAT 58.420 47.619 0.00 0.00 34.38 4.73
4603 5570 2.042686 ACTATGTACCGTCTACCGCA 57.957 50.000 0.00 0.00 34.38 5.69
4715 5682 0.323999 TTGCTACTGCCTCCGTCCTA 60.324 55.000 0.00 0.00 38.71 2.94
4717 5684 0.107654 AATTGCTACTGCCTCCGTCC 60.108 55.000 0.00 0.00 38.71 4.79
4803 5801 4.047627 TCCTTGAGGTACACTGATCAGA 57.952 45.455 29.27 3.89 36.34 3.27
4845 5843 7.880195 AGTGACAAGCTATCAAGAGTTAACAAT 59.120 33.333 8.61 0.00 0.00 2.71
4849 5847 8.150945 AGAAAGTGACAAGCTATCAAGAGTTAA 58.849 33.333 2.28 0.00 0.00 2.01
4855 5853 7.254387 GCAGATAGAAAGTGACAAGCTATCAAG 60.254 40.741 15.72 10.96 39.72 3.02
4873 5871 5.395768 GCTAGGAGAAACAAAGGCAGATAGA 60.396 44.000 0.00 0.00 0.00 1.98
4934 5933 5.449553 ACAGGAAATGAAAAGACTTCCAGT 58.550 37.500 2.78 0.00 39.91 4.00
4971 5970 9.504708 TGATTCCAAATAAAATCAAACTGCATT 57.495 25.926 0.00 0.00 38.57 3.56
5005 6004 2.416893 GGAAGCGACATTTTCTCAGGAC 59.583 50.000 0.00 0.00 0.00 3.85
5012 6011 4.425577 ACTGATTGGAAGCGACATTTTC 57.574 40.909 0.00 0.00 0.00 2.29
5041 6040 4.174762 GAGCTTTCTTAGTACAAGGGTCG 58.825 47.826 0.00 0.00 0.00 4.79
5049 6048 3.193056 ACGGGAGTGAGCTTTCTTAGTAC 59.807 47.826 0.00 0.00 44.82 2.73
5115 6115 4.221422 TATCGAGCACGCCCAGCC 62.221 66.667 0.00 0.00 39.58 4.85
5116 6116 2.962253 GTATCGAGCACGCCCAGC 60.962 66.667 0.00 0.00 39.58 4.85
5117 6117 2.655364 CGTATCGAGCACGCCCAG 60.655 66.667 9.11 0.00 39.58 4.45
5118 6118 3.120979 CTCGTATCGAGCACGCCCA 62.121 63.158 15.40 1.00 46.75 5.36
5119 6119 2.353607 CTCGTATCGAGCACGCCC 60.354 66.667 15.40 0.00 46.75 6.13
5133 6133 2.040544 GCCACATTCACCCACCTCG 61.041 63.158 0.00 0.00 0.00 4.63
5141 6141 1.081242 CCTGCAACGCCACATTCAC 60.081 57.895 0.00 0.00 0.00 3.18
5213 6216 2.036089 GGGATGTCGGTACAGAGAATCC 59.964 54.545 20.64 20.64 39.49 3.01
5261 6266 1.219124 CTAGCCCGAGAGCTGCAAA 59.781 57.895 1.02 0.00 44.67 3.68
5263 6268 3.150335 CCTAGCCCGAGAGCTGCA 61.150 66.667 1.02 0.00 44.67 4.41
5295 6300 0.977395 CAGGAAACCGGAAGAGAGGT 59.023 55.000 9.46 0.00 43.68 3.85
5296 6301 0.250513 CCAGGAAACCGGAAGAGAGG 59.749 60.000 9.46 0.00 0.00 3.69
5297 6302 0.391793 GCCAGGAAACCGGAAGAGAG 60.392 60.000 9.46 0.00 0.00 3.20
5298 6303 1.125093 TGCCAGGAAACCGGAAGAGA 61.125 55.000 9.46 0.00 0.00 3.10
5299 6304 0.674895 CTGCCAGGAAACCGGAAGAG 60.675 60.000 9.46 0.00 28.62 2.85
5300 6305 1.374947 CTGCCAGGAAACCGGAAGA 59.625 57.895 9.46 0.00 28.62 2.87
5301 6306 0.323629 TACTGCCAGGAAACCGGAAG 59.676 55.000 9.46 0.00 31.95 3.46
5302 6307 0.766131 TTACTGCCAGGAAACCGGAA 59.234 50.000 9.46 0.00 0.00 4.30
5303 6308 0.035739 GTTACTGCCAGGAAACCGGA 59.964 55.000 9.46 0.00 0.00 5.14
5304 6309 0.036306 AGTTACTGCCAGGAAACCGG 59.964 55.000 0.00 0.00 0.00 5.28
5305 6310 1.270625 TGAGTTACTGCCAGGAAACCG 60.271 52.381 0.00 0.00 0.00 4.44
5306 6311 2.561478 TGAGTTACTGCCAGGAAACC 57.439 50.000 0.00 0.00 0.00 3.27
5307 6312 3.477530 ACTTGAGTTACTGCCAGGAAAC 58.522 45.455 0.00 0.00 0.00 2.78
5308 6313 3.857157 ACTTGAGTTACTGCCAGGAAA 57.143 42.857 0.00 0.00 0.00 3.13
5309 6314 3.857157 AACTTGAGTTACTGCCAGGAA 57.143 42.857 0.00 0.00 36.32 3.36
5310 6315 3.476552 CAAACTTGAGTTACTGCCAGGA 58.523 45.455 0.00 0.00 37.25 3.86
5311 6316 2.030805 GCAAACTTGAGTTACTGCCAGG 60.031 50.000 8.63 0.00 36.36 4.45
5312 6317 2.618241 TGCAAACTTGAGTTACTGCCAG 59.382 45.455 14.56 0.00 39.65 4.85
5313 6318 2.618241 CTGCAAACTTGAGTTACTGCCA 59.382 45.455 14.56 5.76 39.65 4.92
5314 6319 2.878406 TCTGCAAACTTGAGTTACTGCC 59.122 45.455 14.56 2.49 39.65 4.85
5315 6320 4.201910 TGTTCTGCAAACTTGAGTTACTGC 60.202 41.667 11.67 11.67 40.37 4.40
5316 6321 5.484173 TGTTCTGCAAACTTGAGTTACTG 57.516 39.130 11.34 0.00 37.25 2.74
5317 6322 5.822519 TCATGTTCTGCAAACTTGAGTTACT 59.177 36.000 17.91 0.00 37.25 2.24
5318 6323 6.060028 TCATGTTCTGCAAACTTGAGTTAC 57.940 37.500 17.91 0.00 37.25 2.50
5319 6324 6.882610 ATCATGTTCTGCAAACTTGAGTTA 57.117 33.333 22.23 10.12 37.61 2.24
5320 6325 5.779529 ATCATGTTCTGCAAACTTGAGTT 57.220 34.783 22.23 12.47 37.61 3.01
5321 6326 5.779529 AATCATGTTCTGCAAACTTGAGT 57.220 34.783 22.23 19.61 37.61 3.41
5322 6327 6.444633 AGAAATCATGTTCTGCAAACTTGAG 58.555 36.000 22.23 9.49 37.61 3.02
5323 6328 6.395426 AGAAATCATGTTCTGCAAACTTGA 57.605 33.333 21.14 21.14 36.48 3.02
5324 6329 5.341462 CGAGAAATCATGTTCTGCAAACTTG 59.659 40.000 15.28 15.28 37.98 3.16
5325 6330 5.455392 CGAGAAATCATGTTCTGCAAACTT 58.545 37.500 3.45 4.59 37.98 2.66
5326 6331 4.614535 GCGAGAAATCATGTTCTGCAAACT 60.615 41.667 3.45 0.00 37.98 2.66
5327 6332 3.605486 GCGAGAAATCATGTTCTGCAAAC 59.395 43.478 3.45 0.00 37.98 2.93
5328 6333 3.667695 CGCGAGAAATCATGTTCTGCAAA 60.668 43.478 0.00 0.00 37.98 3.68
5329 6334 2.159667 CGCGAGAAATCATGTTCTGCAA 60.160 45.455 0.00 0.00 37.98 4.08
5330 6335 1.394572 CGCGAGAAATCATGTTCTGCA 59.605 47.619 0.00 0.00 37.98 4.41
5331 6336 1.660607 TCGCGAGAAATCATGTTCTGC 59.339 47.619 3.71 6.80 37.98 4.26
5332 6337 3.182182 TCTCGCGAGAAATCATGTTCTG 58.818 45.455 35.16 6.10 37.98 3.02
5333 6338 3.443037 CTCTCGCGAGAAATCATGTTCT 58.557 45.455 35.84 0.00 40.62 3.01
5334 6339 2.034170 GCTCTCGCGAGAAATCATGTTC 60.034 50.000 35.84 14.43 41.32 3.18
5335 6340 1.929836 GCTCTCGCGAGAAATCATGTT 59.070 47.619 35.84 0.00 41.32 2.71
5336 6341 1.565305 GCTCTCGCGAGAAATCATGT 58.435 50.000 35.84 0.00 41.32 3.21
5337 6342 0.857935 GGCTCTCGCGAGAAATCATG 59.142 55.000 35.84 24.70 41.32 3.07
5338 6343 0.749649 AGGCTCTCGCGAGAAATCAT 59.250 50.000 35.84 23.06 41.32 2.45
5339 6344 0.179127 CAGGCTCTCGCGAGAAATCA 60.179 55.000 35.84 16.59 41.32 2.57
5340 6345 0.179124 ACAGGCTCTCGCGAGAAATC 60.179 55.000 35.84 26.45 41.32 2.17
5341 6346 1.066303 CTACAGGCTCTCGCGAGAAAT 59.934 52.381 35.84 22.76 41.32 2.17
5342 6347 0.452184 CTACAGGCTCTCGCGAGAAA 59.548 55.000 35.84 18.08 41.32 2.52
5343 6348 0.392595 TCTACAGGCTCTCGCGAGAA 60.393 55.000 35.84 21.01 41.32 2.87
5344 6349 0.812014 CTCTACAGGCTCTCGCGAGA 60.812 60.000 34.65 34.65 39.74 4.04
5345 6350 1.092921 ACTCTACAGGCTCTCGCGAG 61.093 60.000 30.03 30.03 40.35 5.03
5346 6351 0.177373 TACTCTACAGGCTCTCGCGA 59.823 55.000 9.26 9.26 36.88 5.87
5347 6352 0.584396 CTACTCTACAGGCTCTCGCG 59.416 60.000 0.00 0.00 36.88 5.87
5348 6353 0.309612 GCTACTCTACAGGCTCTCGC 59.690 60.000 0.00 0.00 0.00 5.03
5349 6354 1.961793 AGCTACTCTACAGGCTCTCG 58.038 55.000 0.00 0.00 0.00 4.04
5350 6355 2.812011 GCTAGCTACTCTACAGGCTCTC 59.188 54.545 7.70 0.00 36.40 3.20
5351 6356 2.441750 AGCTAGCTACTCTACAGGCTCT 59.558 50.000 17.69 0.00 36.40 4.09
5352 6357 2.812011 GAGCTAGCTACTCTACAGGCTC 59.188 54.545 19.38 10.46 36.55 4.70
5353 6358 2.173782 TGAGCTAGCTACTCTACAGGCT 59.826 50.000 19.38 10.87 38.62 4.58
5354 6359 2.552315 CTGAGCTAGCTACTCTACAGGC 59.448 54.545 19.38 1.13 35.12 4.85
5355 6360 4.065088 CTCTGAGCTAGCTACTCTACAGG 58.935 52.174 19.38 9.52 35.12 4.00
5356 6361 4.956085 TCTCTGAGCTAGCTACTCTACAG 58.044 47.826 19.38 18.68 35.12 2.74
5357 6362 5.071115 TCATCTCTGAGCTAGCTACTCTACA 59.929 44.000 19.38 9.33 35.12 2.74
5358 6363 5.547465 TCATCTCTGAGCTAGCTACTCTAC 58.453 45.833 19.38 4.39 35.12 2.59
5359 6364 5.816955 TCATCTCTGAGCTAGCTACTCTA 57.183 43.478 19.38 4.02 35.12 2.43
5360 6365 4.705110 TCATCTCTGAGCTAGCTACTCT 57.295 45.455 19.38 0.00 35.12 3.24
5361 6366 5.530915 TCTTTCATCTCTGAGCTAGCTACTC 59.469 44.000 19.38 6.35 31.68 2.59
5362 6367 5.445069 TCTTTCATCTCTGAGCTAGCTACT 58.555 41.667 19.38 0.00 31.68 2.57
5363 6368 5.299279 ACTCTTTCATCTCTGAGCTAGCTAC 59.701 44.000 19.38 11.96 31.68 3.58
5364 6369 5.445069 ACTCTTTCATCTCTGAGCTAGCTA 58.555 41.667 19.38 0.97 31.68 3.32
5365 6370 4.280819 ACTCTTTCATCTCTGAGCTAGCT 58.719 43.478 19.45 19.45 31.68 3.32
5366 6371 4.654091 ACTCTTTCATCTCTGAGCTAGC 57.346 45.455 6.62 6.62 31.68 3.42
5367 6372 6.035843 GTCAACTCTTTCATCTCTGAGCTAG 58.964 44.000 0.00 0.00 31.68 3.42
5368 6373 5.392487 CGTCAACTCTTTCATCTCTGAGCTA 60.392 44.000 0.00 0.00 31.68 3.32
5369 6374 4.617995 CGTCAACTCTTTCATCTCTGAGCT 60.618 45.833 0.00 0.00 31.68 4.09
5370 6375 3.611986 CGTCAACTCTTTCATCTCTGAGC 59.388 47.826 0.00 0.00 31.68 4.26
5371 6376 5.053140 TCGTCAACTCTTTCATCTCTGAG 57.947 43.478 0.00 0.00 31.68 3.35
5372 6377 5.453567 TTCGTCAACTCTTTCATCTCTGA 57.546 39.130 0.00 0.00 0.00 3.27
5373 6378 5.923114 TCTTTCGTCAACTCTTTCATCTCTG 59.077 40.000 0.00 0.00 0.00 3.35
5374 6379 6.090483 TCTTTCGTCAACTCTTTCATCTCT 57.910 37.500 0.00 0.00 0.00 3.10
5375 6380 5.923684 ACTCTTTCGTCAACTCTTTCATCTC 59.076 40.000 0.00 0.00 0.00 2.75
5376 6381 5.848406 ACTCTTTCGTCAACTCTTTCATCT 58.152 37.500 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.