Multiple sequence alignment - TraesCS1A01G410900

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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 TraesCS1A01G410900 chr1A 100.000 2432 0 0 1 2432 571865865 571863434 0.000000e+00 4492.0
1 TraesCS1A01G410900 chr1A 84.946 93 12 2 1501 1592 517327209 517327300 2.570000e-15 93.5
2 TraesCS1A01G410900 chr1A 93.220 59 3 1 1679 1737 456370340 456370397 4.310000e-13 86.1
3 TraesCS1A01G410900 chr1A 100.000 33 0 0 1672 1704 571871707 571871675 7.260000e-06 62.1
4 TraesCS1A01G410900 chr2D 95.737 1595 58 7 3 1592 103241654 103240065 0.000000e+00 2560.0
5 TraesCS1A01G410900 chr2D 96.000 75 2 1 1593 1667 126850462 126850535 1.180000e-23 121.0
6 TraesCS1A01G410900 chr3D 95.630 1602 57 8 1 1592 49966474 49964876 0.000000e+00 2558.0
7 TraesCS1A01G410900 chr3D 87.899 595 45 18 1021 1592 134640366 134640956 0.000000e+00 675.0
8 TraesCS1A01G410900 chr3D 83.442 459 46 3 594 1023 14356596 14356139 1.350000e-107 399.0
9 TraesCS1A01G410900 chr5B 92.486 1597 103 12 1 1592 178915767 178914183 0.000000e+00 2268.0
10 TraesCS1A01G410900 chr5B 81.331 616 89 15 1 595 607480537 607481147 6.080000e-131 477.0
11 TraesCS1A01G410900 chr5B 90.686 204 18 1 822 1025 5103698 5103496 1.110000e-68 270.0
12 TraesCS1A01G410900 chr3B 85.272 1066 93 21 1 1021 775177376 775176330 0.000000e+00 1040.0
13 TraesCS1A01G410900 chr3B 90.000 660 58 6 1 656 769386625 769385970 0.000000e+00 846.0
14 TraesCS1A01G410900 chr3B 97.333 75 2 0 1593 1667 418686636 418686562 7.060000e-26 128.0
15 TraesCS1A01G410900 chr4A 88.133 691 63 7 145 816 709876034 709875344 0.000000e+00 804.0
16 TraesCS1A01G410900 chr4A 86.275 459 33 5 594 1023 718008537 718008080 2.830000e-129 472.0
17 TraesCS1A01G410900 chr4A 88.514 296 21 6 1310 1592 709875355 709875060 1.790000e-91 346.0
18 TraesCS1A01G410900 chr4A 89.506 162 14 2 1 159 709876211 709876050 4.100000e-48 202.0
19 TraesCS1A01G410900 chr6B 87.536 690 68 7 145 816 203463253 203462564 0.000000e+00 782.0
20 TraesCS1A01G410900 chr6B 86.710 459 31 5 594 1023 132658482 132658025 1.310000e-132 483.0
21 TraesCS1A01G410900 chr6B 89.506 162 14 2 1 159 203463432 203463271 4.100000e-48 202.0
22 TraesCS1A01G410900 chr5A 92.899 507 33 3 1021 1524 697889952 697890458 0.000000e+00 734.0
23 TraesCS1A01G410900 chr5A 86.710 459 31 9 594 1023 697889419 697889876 1.310000e-132 483.0
24 TraesCS1A01G410900 chr5A 86.275 459 33 3 594 1023 651581534 651581077 2.830000e-129 472.0
25 TraesCS1A01G410900 chr2B 92.276 479 34 1 1021 1499 138737317 138736842 0.000000e+00 676.0
26 TraesCS1A01G410900 chr2B 90.291 309 25 2 318 621 227898103 227897795 1.350000e-107 399.0
27 TraesCS1A01G410900 chr2B 92.670 191 14 0 1 191 227898320 227898130 2.380000e-70 276.0
28 TraesCS1A01G410900 chr2B 93.333 75 5 0 1593 1667 10117140 10117214 7.110000e-21 111.0
29 TraesCS1A01G410900 chr2B 87.097 62 8 0 5 66 25468399 25468338 1.210000e-08 71.3
30 TraesCS1A01G410900 chr1D 91.129 496 40 4 1021 1515 481612242 481612734 0.000000e+00 669.0
31 TraesCS1A01G410900 chr1D 88.319 565 44 9 1740 2299 475954591 475954044 0.000000e+00 658.0
32 TraesCS1A01G410900 chr1D 88.816 152 7 3 2288 2432 475953912 475953764 6.910000e-41 178.0
33 TraesCS1A01G410900 chr1D 100.000 57 0 0 1537 1593 481612789 481612845 3.310000e-19 106.0
34 TraesCS1A01G410900 chr1D 94.118 51 3 0 1733 1783 475954655 475954605 7.210000e-11 78.7
35 TraesCS1A01G410900 chr1D 86.957 69 8 1 1669 1737 355750823 355750890 2.590000e-10 76.8
36 TraesCS1A01G410900 chr4D 90.135 517 45 6 1021 1533 398867666 398868180 0.000000e+00 667.0
37 TraesCS1A01G410900 chr4D 87.174 460 28 4 594 1023 398867132 398867590 6.040000e-136 494.0
38 TraesCS1A01G410900 chr5D 90.078 514 48 3 1021 1533 292726620 292726109 0.000000e+00 664.0
39 TraesCS1A01G410900 chr5D 93.333 75 5 0 1593 1667 240793375 240793301 7.110000e-21 111.0
40 TraesCS1A01G410900 chr5D 93.333 75 5 0 1593 1667 439297033 439296959 7.110000e-21 111.0
41 TraesCS1A01G410900 chr5D 93.333 75 5 0 1593 1667 565826701 565826627 7.110000e-21 111.0
42 TraesCS1A01G410900 chr1B 85.974 606 49 17 1021 1592 46156487 46155884 1.240000e-172 616.0
43 TraesCS1A01G410900 chr1B 81.788 604 82 14 5 595 414554852 414555440 4.700000e-132 481.0
44 TraesCS1A01G410900 chr1B 93.956 182 10 1 2040 2220 662032823 662032642 8.570000e-70 274.0
45 TraesCS1A01G410900 chr1B 97.260 73 2 0 2213 2285 662031714 662031642 9.130000e-25 124.0
46 TraesCS1A01G410900 chr1B 96.000 75 3 0 1593 1667 629685566 629685492 3.280000e-24 122.0
47 TraesCS1A01G410900 chr1B 94.667 75 4 0 1593 1667 671236263 671236189 1.530000e-22 117.0
48 TraesCS1A01G410900 chr1B 87.097 62 8 0 5 66 287697045 287697106 1.210000e-08 71.3
49 TraesCS1A01G410900 chr7A 84.946 558 52 15 52 595 729166619 729167158 9.900000e-149 536.0
50 TraesCS1A01G410900 chr7A 84.532 459 41 3 594 1023 729168459 729168916 6.210000e-116 427.0
51 TraesCS1A01G410900 chr7A 94.030 67 2 2 1537 1602 712074614 712074679 1.540000e-17 100.0
52 TraesCS1A01G410900 chr7A 96.429 56 2 0 1537 1592 706402698 706402643 2.570000e-15 93.5
53 TraesCS1A01G410900 chr7A 85.542 83 9 2 1511 1593 732322788 732322867 1.550000e-12 84.2
54 TraesCS1A01G410900 chr4B 97.333 75 2 0 1593 1667 639590319 639590245 7.060000e-26 128.0


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 TraesCS1A01G410900 chr1A 571863434 571865865 2431 True 4492.000000 4492 100.000000 1 2432 1 chr1A.!!$R1 2431
1 TraesCS1A01G410900 chr2D 103240065 103241654 1589 True 2560.000000 2560 95.737000 3 1592 1 chr2D.!!$R1 1589
2 TraesCS1A01G410900 chr3D 49964876 49966474 1598 True 2558.000000 2558 95.630000 1 1592 1 chr3D.!!$R2 1591
3 TraesCS1A01G410900 chr3D 134640366 134640956 590 False 675.000000 675 87.899000 1021 1592 1 chr3D.!!$F1 571
4 TraesCS1A01G410900 chr5B 178914183 178915767 1584 True 2268.000000 2268 92.486000 1 1592 1 chr5B.!!$R2 1591
5 TraesCS1A01G410900 chr5B 607480537 607481147 610 False 477.000000 477 81.331000 1 595 1 chr5B.!!$F1 594
6 TraesCS1A01G410900 chr3B 775176330 775177376 1046 True 1040.000000 1040 85.272000 1 1021 1 chr3B.!!$R3 1020
7 TraesCS1A01G410900 chr3B 769385970 769386625 655 True 846.000000 846 90.000000 1 656 1 chr3B.!!$R2 655
8 TraesCS1A01G410900 chr4A 709875060 709876211 1151 True 450.666667 804 88.717667 1 1592 3 chr4A.!!$R2 1591
9 TraesCS1A01G410900 chr6B 203462564 203463432 868 True 492.000000 782 88.521000 1 816 2 chr6B.!!$R2 815
10 TraesCS1A01G410900 chr5A 697889419 697890458 1039 False 608.500000 734 89.804500 594 1524 2 chr5A.!!$F1 930
11 TraesCS1A01G410900 chr2B 227897795 227898320 525 True 337.500000 399 91.480500 1 621 2 chr2B.!!$R3 620
12 TraesCS1A01G410900 chr1D 481612242 481612845 603 False 387.500000 669 95.564500 1021 1593 2 chr1D.!!$F2 572
13 TraesCS1A01G410900 chr1D 475953764 475954655 891 True 304.900000 658 90.417667 1733 2432 3 chr1D.!!$R1 699
14 TraesCS1A01G410900 chr4D 398867132 398868180 1048 False 580.500000 667 88.654500 594 1533 2 chr4D.!!$F1 939
15 TraesCS1A01G410900 chr5D 292726109 292726620 511 True 664.000000 664 90.078000 1021 1533 1 chr5D.!!$R2 512
16 TraesCS1A01G410900 chr1B 46155884 46156487 603 True 616.000000 616 85.974000 1021 1592 1 chr1B.!!$R1 571
17 TraesCS1A01G410900 chr1B 414554852 414555440 588 False 481.000000 481 81.788000 5 595 1 chr1B.!!$F2 590
18 TraesCS1A01G410900 chr7A 729166619 729168916 2297 False 481.500000 536 84.739000 52 1023 2 chr7A.!!$F3 971

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
27 31 1.21671 CTCACCTTGCCGTCCTCTC 59.783 63.158 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 3173 0.174845 TTCGGGAGGCTTGTATGTCG 59.825 55.0 0.0 0.0 0.0 4.35 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
27 31 1.216710 CTCACCTTGCCGTCCTCTC 59.783 63.158 0.00 0.00 0.00 3.20
169 222 5.779922 TGCAGACTTTAGAAACGTACAGAT 58.220 37.500 0.00 0.00 0.00 2.90
172 225 8.033038 TGCAGACTTTAGAAACGTACAGATTAT 58.967 33.333 0.00 0.00 0.00 1.28
192 247 8.519526 AGATTATAGAAGTTCGATCATCAGGAC 58.480 37.037 17.28 0.00 0.00 3.85
196 251 4.464244 AGAAGTTCGATCATCAGGACTCAA 59.536 41.667 0.00 0.00 0.00 3.02
345 431 9.162451 GGAAATATCCATCGCTAGCGACAAAAT 62.162 40.741 39.66 28.98 45.79 1.82
384 481 7.931407 AGTGAATAAACTGATACACTCACAACA 59.069 33.333 0.00 0.00 35.50 3.33
395 492 5.036117 ACACTCACAACACAGAGGTATTT 57.964 39.130 0.00 0.00 36.20 1.40
453 550 4.876107 CACTACTTCGCCAAACCAAGATAT 59.124 41.667 0.00 0.00 0.00 1.63
505 606 9.248291 GAAGAGCAACAAACTAATGAAAATTCA 57.752 29.630 0.00 0.00 42.14 2.57
561 664 6.655425 TCCAACATCGGTGATAACAATGTAAA 59.345 34.615 0.65 0.00 30.71 2.01
693 2099 7.671495 AAAAATTATTTGATGCACTTGGTCC 57.329 32.000 0.00 0.00 0.00 4.46
861 2307 7.333423 TGAGCATCGCTAAAGTTATTGTAACTT 59.667 33.333 8.81 8.81 39.88 2.66
887 2333 2.708325 GGGAATAGAGCCATTGTCTCCT 59.292 50.000 0.00 0.00 0.00 3.69
988 2438 8.752254 GGCTTTCCGAGTTAAATATTTTAATGC 58.248 33.333 5.91 0.00 0.00 3.56
1010 2460 3.778619 TGGTTGATATGGCGACCAG 57.221 52.632 0.00 0.00 45.27 4.00
1045 2573 5.291971 ACAATGAACTTGAAGAATGTTGCC 58.708 37.500 0.00 0.00 38.29 4.52
1174 2708 2.771943 TCTGCTATGGAGATTTTCGGGT 59.228 45.455 0.00 0.00 0.00 5.28
1175 2709 2.874701 CTGCTATGGAGATTTTCGGGTG 59.125 50.000 0.00 0.00 0.00 4.61
1189 2723 2.557317 TCGGGTGTGTCAAAGAAGTTC 58.443 47.619 0.00 0.00 0.00 3.01
1234 2768 5.270893 TGCCTATCGCATCTTGTTTACTA 57.729 39.130 0.00 0.00 44.64 1.82
1362 2896 6.309712 ACATTATGCATCGAGGAGAAATTG 57.690 37.500 0.19 0.00 0.00 2.32
1376 2910 5.655532 AGGAGAAATTGTTGGATGAGATTGG 59.344 40.000 0.00 0.00 0.00 3.16
1608 3179 3.845259 GACTGCCGCCCCGACATA 61.845 66.667 0.00 0.00 0.00 2.29
1609 3180 4.157120 ACTGCCGCCCCGACATAC 62.157 66.667 0.00 0.00 0.00 2.39
1610 3181 4.155733 CTGCCGCCCCGACATACA 62.156 66.667 0.00 0.00 0.00 2.29
1611 3182 3.673956 CTGCCGCCCCGACATACAA 62.674 63.158 0.00 0.00 0.00 2.41
1612 3183 2.895372 GCCGCCCCGACATACAAG 60.895 66.667 0.00 0.00 0.00 3.16
1613 3184 2.895372 CCGCCCCGACATACAAGC 60.895 66.667 0.00 0.00 0.00 4.01
1614 3185 2.895372 CGCCCCGACATACAAGCC 60.895 66.667 0.00 0.00 0.00 4.35
1615 3186 2.590092 GCCCCGACATACAAGCCT 59.410 61.111 0.00 0.00 0.00 4.58
1616 3187 1.523938 GCCCCGACATACAAGCCTC 60.524 63.158 0.00 0.00 0.00 4.70
1617 3188 1.146263 CCCCGACATACAAGCCTCC 59.854 63.158 0.00 0.00 0.00 4.30
1618 3189 1.146263 CCCGACATACAAGCCTCCC 59.854 63.158 0.00 0.00 0.00 4.30
1619 3190 1.227263 CCGACATACAAGCCTCCCG 60.227 63.158 0.00 0.00 0.00 5.14
1620 3191 1.672854 CCGACATACAAGCCTCCCGA 61.673 60.000 0.00 0.00 0.00 5.14
1621 3192 0.174845 CGACATACAAGCCTCCCGAA 59.825 55.000 0.00 0.00 0.00 4.30
1622 3193 1.802880 CGACATACAAGCCTCCCGAAG 60.803 57.143 0.00 0.00 0.00 3.79
1623 3194 1.480954 GACATACAAGCCTCCCGAAGA 59.519 52.381 0.00 0.00 0.00 2.87
1624 3195 2.103263 GACATACAAGCCTCCCGAAGAT 59.897 50.000 0.00 0.00 0.00 2.40
1625 3196 2.103263 ACATACAAGCCTCCCGAAGATC 59.897 50.000 0.00 0.00 0.00 2.75
1626 3197 1.120530 TACAAGCCTCCCGAAGATCC 58.879 55.000 0.00 0.00 0.00 3.36
1627 3198 0.909610 ACAAGCCTCCCGAAGATCCA 60.910 55.000 0.00 0.00 0.00 3.41
1628 3199 0.253044 CAAGCCTCCCGAAGATCCAA 59.747 55.000 0.00 0.00 0.00 3.53
1629 3200 0.991920 AAGCCTCCCGAAGATCCAAA 59.008 50.000 0.00 0.00 0.00 3.28
1630 3201 0.253327 AGCCTCCCGAAGATCCAAAC 59.747 55.000 0.00 0.00 0.00 2.93
1631 3202 0.253327 GCCTCCCGAAGATCCAAACT 59.747 55.000 0.00 0.00 0.00 2.66
1632 3203 2.014068 GCCTCCCGAAGATCCAAACTG 61.014 57.143 0.00 0.00 0.00 3.16
1633 3204 1.279271 CCTCCCGAAGATCCAAACTGT 59.721 52.381 0.00 0.00 0.00 3.55
1634 3205 2.622436 CTCCCGAAGATCCAAACTGTC 58.378 52.381 0.00 0.00 0.00 3.51
1635 3206 1.974957 TCCCGAAGATCCAAACTGTCA 59.025 47.619 0.00 0.00 0.00 3.58
1636 3207 2.370519 TCCCGAAGATCCAAACTGTCAA 59.629 45.455 0.00 0.00 0.00 3.18
1637 3208 3.009033 TCCCGAAGATCCAAACTGTCAAT 59.991 43.478 0.00 0.00 0.00 2.57
1638 3209 3.758554 CCCGAAGATCCAAACTGTCAATT 59.241 43.478 0.00 0.00 0.00 2.32
1639 3210 4.941263 CCCGAAGATCCAAACTGTCAATTA 59.059 41.667 0.00 0.00 0.00 1.40
1640 3211 5.163754 CCCGAAGATCCAAACTGTCAATTAC 60.164 44.000 0.00 0.00 0.00 1.89
1641 3212 5.411361 CCGAAGATCCAAACTGTCAATTACA 59.589 40.000 0.00 0.00 36.42 2.41
1642 3213 6.072728 CCGAAGATCCAAACTGTCAATTACAA 60.073 38.462 0.00 0.00 37.74 2.41
1643 3214 6.797033 CGAAGATCCAAACTGTCAATTACAAC 59.203 38.462 0.00 0.00 37.74 3.32
1644 3215 7.519809 CGAAGATCCAAACTGTCAATTACAACA 60.520 37.037 0.00 0.00 37.74 3.33
1645 3216 7.765695 AGATCCAAACTGTCAATTACAACAT 57.234 32.000 0.00 0.00 37.74 2.71
1646 3217 8.181904 AGATCCAAACTGTCAATTACAACATT 57.818 30.769 0.00 0.00 37.74 2.71
1647 3218 8.084073 AGATCCAAACTGTCAATTACAACATTG 58.916 33.333 0.00 0.00 37.74 2.82
1648 3219 7.340122 TCCAAACTGTCAATTACAACATTGA 57.660 32.000 0.00 0.00 40.23 2.57
1649 3220 7.776107 TCCAAACTGTCAATTACAACATTGAA 58.224 30.769 0.00 0.00 43.30 2.69
1650 3221 8.420222 TCCAAACTGTCAATTACAACATTGAAT 58.580 29.630 0.00 0.00 43.30 2.57
1651 3222 9.689976 CCAAACTGTCAATTACAACATTGAATA 57.310 29.630 0.00 0.00 43.30 1.75
1653 3224 9.912634 AAACTGTCAATTACAACATTGAATAGG 57.087 29.630 0.00 0.00 43.30 2.57
1654 3225 8.862325 ACTGTCAATTACAACATTGAATAGGA 57.138 30.769 0.00 0.00 43.30 2.94
1655 3226 9.295825 ACTGTCAATTACAACATTGAATAGGAA 57.704 29.630 0.00 0.00 43.30 3.36
1659 3230 9.585099 TCAATTACAACATTGAATAGGAAATGC 57.415 29.630 0.00 0.00 39.69 3.56
1660 3231 8.819974 CAATTACAACATTGAATAGGAAATGCC 58.180 33.333 0.00 0.00 37.30 4.40
1661 3232 5.999205 ACAACATTGAATAGGAAATGCCA 57.001 34.783 0.00 0.00 37.30 4.92
1662 3233 6.357579 ACAACATTGAATAGGAAATGCCAA 57.642 33.333 0.00 0.00 37.30 4.52
1663 3234 6.949715 ACAACATTGAATAGGAAATGCCAAT 58.050 32.000 0.00 0.00 37.30 3.16
1664 3235 6.819649 ACAACATTGAATAGGAAATGCCAATG 59.180 34.615 0.00 0.00 43.60 2.82
1665 3236 6.795144 ACATTGAATAGGAAATGCCAATGA 57.205 33.333 16.62 0.00 41.75 2.57
1666 3237 6.812998 ACATTGAATAGGAAATGCCAATGAG 58.187 36.000 16.62 0.00 41.75 2.90
1667 3238 6.608405 ACATTGAATAGGAAATGCCAATGAGA 59.392 34.615 16.62 0.00 41.75 3.27
1668 3239 7.289317 ACATTGAATAGGAAATGCCAATGAGAT 59.711 33.333 16.62 0.00 41.75 2.75
1669 3240 8.799367 CATTGAATAGGAAATGCCAATGAGATA 58.201 33.333 0.00 0.00 41.75 1.98
1670 3241 8.765488 TTGAATAGGAAATGCCAATGAGATAA 57.235 30.769 0.00 0.00 40.02 1.75
1671 3242 8.765488 TGAATAGGAAATGCCAATGAGATAAA 57.235 30.769 0.00 0.00 40.02 1.40
1672 3243 9.370930 TGAATAGGAAATGCCAATGAGATAAAT 57.629 29.630 0.00 0.00 40.02 1.40
1673 3244 9.635520 GAATAGGAAATGCCAATGAGATAAATG 57.364 33.333 0.00 0.00 40.02 2.32
1674 3245 8.716674 ATAGGAAATGCCAATGAGATAAATGT 57.283 30.769 0.00 0.00 40.02 2.71
1675 3246 7.047460 AGGAAATGCCAATGAGATAAATGTC 57.953 36.000 0.00 0.00 40.02 3.06
1676 3247 6.837568 AGGAAATGCCAATGAGATAAATGTCT 59.162 34.615 0.00 0.00 40.02 3.41
1677 3248 8.000709 AGGAAATGCCAATGAGATAAATGTCTA 58.999 33.333 0.00 0.00 40.02 2.59
1678 3249 8.295288 GGAAATGCCAATGAGATAAATGTCTAG 58.705 37.037 0.00 0.00 36.34 2.43
1679 3250 8.985315 AAATGCCAATGAGATAAATGTCTAGA 57.015 30.769 0.00 0.00 0.00 2.43
1680 3251 8.618702 AATGCCAATGAGATAAATGTCTAGAG 57.381 34.615 0.00 0.00 0.00 2.43
1681 3252 7.365497 TGCCAATGAGATAAATGTCTAGAGA 57.635 36.000 0.00 0.00 0.00 3.10
1682 3253 7.971201 TGCCAATGAGATAAATGTCTAGAGAT 58.029 34.615 0.00 0.00 0.00 2.75
1683 3254 8.435187 TGCCAATGAGATAAATGTCTAGAGATT 58.565 33.333 9.25 9.25 0.00 2.40
1684 3255 8.934825 GCCAATGAGATAAATGTCTAGAGATTC 58.065 37.037 14.94 4.03 0.00 2.52
1692 3263 8.900983 ATAAATGTCTAGAGATTCTTGAAGGC 57.099 34.615 14.94 0.00 30.60 4.35
1693 3264 6.558488 AATGTCTAGAGATTCTTGAAGGCT 57.442 37.500 9.25 0.00 30.60 4.58
1694 3265 6.558488 ATGTCTAGAGATTCTTGAAGGCTT 57.442 37.500 0.00 0.00 30.60 4.35
1695 3266 7.667575 ATGTCTAGAGATTCTTGAAGGCTTA 57.332 36.000 0.00 0.00 30.60 3.09
1696 3267 7.106439 TGTCTAGAGATTCTTGAAGGCTTAG 57.894 40.000 0.00 0.00 30.60 2.18
1697 3268 6.665680 TGTCTAGAGATTCTTGAAGGCTTAGT 59.334 38.462 0.00 0.00 30.60 2.24
1698 3269 6.978080 GTCTAGAGATTCTTGAAGGCTTAGTG 59.022 42.308 0.00 0.00 30.60 2.74
1699 3270 5.753721 AGAGATTCTTGAAGGCTTAGTGT 57.246 39.130 0.00 0.00 0.00 3.55
1700 3271 5.486526 AGAGATTCTTGAAGGCTTAGTGTG 58.513 41.667 0.00 0.00 0.00 3.82
1701 3272 4.583871 AGATTCTTGAAGGCTTAGTGTGG 58.416 43.478 0.00 0.00 0.00 4.17
1702 3273 2.185004 TCTTGAAGGCTTAGTGTGGC 57.815 50.000 0.00 0.00 0.00 5.01
1703 3274 1.419762 TCTTGAAGGCTTAGTGTGGCA 59.580 47.619 0.00 0.00 0.00 4.92
1704 3275 2.158682 TCTTGAAGGCTTAGTGTGGCAA 60.159 45.455 0.00 0.00 0.00 4.52
1705 3276 2.356665 TGAAGGCTTAGTGTGGCAAA 57.643 45.000 0.00 0.00 0.00 3.68
1706 3277 2.660572 TGAAGGCTTAGTGTGGCAAAA 58.339 42.857 0.00 0.00 0.00 2.44
1707 3278 2.622942 TGAAGGCTTAGTGTGGCAAAAG 59.377 45.455 0.00 0.00 0.00 2.27
1708 3279 2.656947 AGGCTTAGTGTGGCAAAAGA 57.343 45.000 0.00 0.00 0.00 2.52
1709 3280 2.944129 AGGCTTAGTGTGGCAAAAGAA 58.056 42.857 0.00 0.00 0.00 2.52
1710 3281 3.295973 AGGCTTAGTGTGGCAAAAGAAA 58.704 40.909 0.00 0.00 0.00 2.52
1711 3282 3.704061 AGGCTTAGTGTGGCAAAAGAAAA 59.296 39.130 0.00 0.00 0.00 2.29
1712 3283 4.051237 GGCTTAGTGTGGCAAAAGAAAAG 58.949 43.478 0.00 0.00 0.00 2.27
1713 3284 3.490896 GCTTAGTGTGGCAAAAGAAAAGC 59.509 43.478 0.00 0.00 0.00 3.51
1714 3285 4.681744 CTTAGTGTGGCAAAAGAAAAGCA 58.318 39.130 0.00 0.00 0.00 3.91
1715 3286 3.825143 AGTGTGGCAAAAGAAAAGCAT 57.175 38.095 0.00 0.00 0.00 3.79
1716 3287 3.721035 AGTGTGGCAAAAGAAAAGCATC 58.279 40.909 0.00 0.00 0.00 3.91
1717 3288 3.385755 AGTGTGGCAAAAGAAAAGCATCT 59.614 39.130 0.00 0.00 0.00 2.90
1718 3289 3.737774 GTGTGGCAAAAGAAAAGCATCTC 59.262 43.478 0.00 0.00 0.00 2.75
1719 3290 3.638160 TGTGGCAAAAGAAAAGCATCTCT 59.362 39.130 0.00 0.00 0.00 3.10
1720 3291 4.233005 GTGGCAAAAGAAAAGCATCTCTC 58.767 43.478 0.00 0.00 0.00 3.20
1721 3292 3.256631 TGGCAAAAGAAAAGCATCTCTCC 59.743 43.478 0.00 0.00 0.00 3.71
1722 3293 3.256631 GGCAAAAGAAAAGCATCTCTCCA 59.743 43.478 0.00 0.00 0.00 3.86
1723 3294 4.483311 GCAAAAGAAAAGCATCTCTCCAG 58.517 43.478 0.00 0.00 0.00 3.86
1724 3295 4.617762 GCAAAAGAAAAGCATCTCTCCAGG 60.618 45.833 0.00 0.00 0.00 4.45
1725 3296 4.647564 AAAGAAAAGCATCTCTCCAGGA 57.352 40.909 0.00 0.00 0.00 3.86
1726 3297 3.910568 AGAAAAGCATCTCTCCAGGAG 57.089 47.619 10.70 10.70 43.12 3.69
1727 3298 3.180507 AGAAAAGCATCTCTCCAGGAGT 58.819 45.455 16.65 0.00 42.40 3.85
1728 3299 4.357325 AGAAAAGCATCTCTCCAGGAGTA 58.643 43.478 16.65 6.55 42.40 2.59
1729 3300 4.405358 AGAAAAGCATCTCTCCAGGAGTAG 59.595 45.833 16.65 12.10 42.40 2.57
1730 3301 2.380064 AGCATCTCTCCAGGAGTAGG 57.620 55.000 16.65 8.85 42.40 3.18
1731 3302 1.856259 AGCATCTCTCCAGGAGTAGGA 59.144 52.381 16.65 12.93 42.40 2.94
1732 3303 2.246067 AGCATCTCTCCAGGAGTAGGAA 59.754 50.000 16.65 0.00 42.40 3.36
1733 3304 3.034635 GCATCTCTCCAGGAGTAGGAAA 58.965 50.000 16.65 0.00 42.40 3.13
1734 3305 3.645687 GCATCTCTCCAGGAGTAGGAAAT 59.354 47.826 16.65 0.68 42.40 2.17
1735 3306 4.835615 GCATCTCTCCAGGAGTAGGAAATA 59.164 45.833 16.65 0.00 42.40 1.40
1736 3307 5.279256 GCATCTCTCCAGGAGTAGGAAATAC 60.279 48.000 16.65 2.53 42.40 1.89
1738 3309 5.450453 TCTCTCCAGGAGTAGGAAATACTG 58.550 45.833 16.65 0.00 45.06 2.74
1750 3321 7.775120 AGTAGGAAATACTGGCATCAAATTTG 58.225 34.615 12.15 12.15 43.35 2.32
1792 3415 6.339587 AGTTTGTCAAGAACCAACTTCAAA 57.660 33.333 0.00 0.00 40.04 2.69
1798 3421 6.183360 TGTCAAGAACCAACTTCAAATCCTTC 60.183 38.462 0.00 0.00 0.00 3.46
1812 3435 7.214467 TCAAATCCTTCATTTTCTGTGTACC 57.786 36.000 0.00 0.00 31.79 3.34
1820 3443 6.817765 TCATTTTCTGTGTACCCTTCATTC 57.182 37.500 0.00 0.00 0.00 2.67
1845 3468 5.406780 GCATCCAAGATAAATGAGTAGTCCG 59.593 44.000 0.00 0.00 0.00 4.79
1846 3469 5.531122 TCCAAGATAAATGAGTAGTCCGG 57.469 43.478 0.00 0.00 0.00 5.14
1849 3472 7.008332 TCCAAGATAAATGAGTAGTCCGGATA 58.992 38.462 7.81 0.00 0.00 2.59
1858 3481 4.080469 TGAGTAGTCCGGATAGACAAGACT 60.080 45.833 7.81 0.00 39.34 3.24
1860 3483 4.641094 AGTAGTCCGGATAGACAAGACTTG 59.359 45.833 7.81 13.77 39.34 3.16
1867 3490 8.958506 GTCCGGATAGACAAGACTTGTATATAT 58.041 37.037 27.23 20.83 45.21 0.86
1890 3513 6.405278 TCATTCAGAACAGCTATATCCGAA 57.595 37.500 0.00 0.00 0.00 4.30
1896 3519 7.272244 TCAGAACAGCTATATCCGAATTCAAA 58.728 34.615 6.22 0.00 0.00 2.69
1901 3524 9.736023 AACAGCTATATCCGAATTCAAATTTTC 57.264 29.630 6.22 0.00 0.00 2.29
1911 3534 8.856103 TCCGAATTCAAATTTTCTCCTACTTTT 58.144 29.630 6.22 0.00 0.00 2.27
1931 3554 4.634012 TTAGCTAGCTTCAAGGTTCCAA 57.366 40.909 24.88 3.65 0.00 3.53
1940 3564 3.946242 AAGGTTCCAAGCCCTTGTT 57.054 47.368 7.21 0.00 39.59 2.83
1963 3587 3.789224 GTCGTTATTTTGCGGCCAATTAG 59.211 43.478 2.24 0.00 0.00 1.73
1965 3589 4.336993 TCGTTATTTTGCGGCCAATTAGAT 59.663 37.500 2.24 0.00 0.00 1.98
1976 3600 6.321181 TGCGGCCAATTAGATTCTTATTTTCT 59.679 34.615 2.24 0.00 0.00 2.52
2004 3628 7.772332 ATACTACCTAACTTCAGCAATTTCG 57.228 36.000 0.00 0.00 0.00 3.46
2015 3639 5.878332 TCAGCAATTTCGATTAAGCAAGA 57.122 34.783 0.00 0.00 0.00 3.02
2068 3693 3.063084 ACCTCGCACTCCGGACTC 61.063 66.667 0.00 0.00 37.59 3.36
2094 3719 0.865111 TGGATCACACTTCAAACGCG 59.135 50.000 3.53 3.53 0.00 6.01
2174 3802 4.126437 CACCTACATGTATGGCGATTTCA 58.874 43.478 5.91 0.00 0.00 2.69
2176 3804 4.997395 ACCTACATGTATGGCGATTTCATC 59.003 41.667 5.91 0.00 0.00 2.92
2193 3821 1.741706 CATCATGGCCAATATCCTCGC 59.258 52.381 10.96 0.00 0.00 5.03
2200 3828 2.029073 AATATCCTCGCGGTGCCG 59.971 61.111 6.13 6.22 43.09 5.69
2205 3833 4.745751 CCTCGCGGTGCCGGTTTA 62.746 66.667 6.13 0.00 40.19 2.01
2214 3842 1.424403 GTGCCGGTTTATTTGTTGCC 58.576 50.000 1.90 0.00 0.00 4.52
2223 3851 7.262048 CCGGTTTATTTGTTGCCTACATAAAT 58.738 34.615 0.00 0.00 36.44 1.40
2224 3852 7.434013 CCGGTTTATTTGTTGCCTACATAAATC 59.566 37.037 0.00 0.00 36.44 2.17
2238 3866 9.952188 GCCTACATAAATCAGTAAATTCCTTTC 57.048 33.333 0.00 0.00 0.00 2.62
2282 3910 6.976934 TGAGTTGTCTATGCATATCCAGTA 57.023 37.500 6.92 0.00 0.00 2.74
2286 3914 3.572255 TGTCTATGCATATCCAGTACGCA 59.428 43.478 6.92 0.00 36.95 5.24
2305 4075 2.728846 GCAGCACCACAATAACGACATG 60.729 50.000 0.00 0.00 0.00 3.21
2306 4076 2.083774 AGCACCACAATAACGACATGG 58.916 47.619 0.00 0.00 36.46 3.66
2320 4090 2.418628 CGACATGGTTACTTTCCGCAAT 59.581 45.455 0.00 0.00 0.00 3.56
2328 4098 4.976116 GGTTACTTTCCGCAATTATCATGC 59.024 41.667 0.00 0.00 40.41 4.06
2329 4099 3.715628 ACTTTCCGCAATTATCATGCC 57.284 42.857 0.00 0.00 40.72 4.40
2330 4100 3.290710 ACTTTCCGCAATTATCATGCCT 58.709 40.909 0.00 0.00 40.72 4.75
2331 4101 4.460263 ACTTTCCGCAATTATCATGCCTA 58.540 39.130 0.00 0.00 40.72 3.93
2337 4107 7.124573 TCCGCAATTATCATGCCTACTATAT 57.875 36.000 0.00 0.00 40.72 0.86
2347 4117 5.484998 TCATGCCTACTATATGCAATCTCCA 59.515 40.000 0.00 0.00 38.69 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 14 2.636412 CGAGAGGACGGCAAGGTGA 61.636 63.158 0.00 0.00 0.00 4.02
16 20 1.134907 GGAAATTACGAGAGGACGGCA 60.135 52.381 0.00 0.00 37.61 5.69
27 31 8.774586 CATAACCAGATTAGGAAGGAAATTACG 58.225 37.037 0.00 0.00 0.00 3.18
169 222 7.502561 TGAGTCCTGATGATCGAACTTCTATAA 59.497 37.037 9.47 0.00 0.00 0.98
172 225 5.193679 TGAGTCCTGATGATCGAACTTCTA 58.806 41.667 9.47 0.00 0.00 2.10
192 247 3.672808 ACCTCAAAGCTGATGTCTTGAG 58.327 45.455 14.14 14.14 0.00 3.02
196 251 9.717942 GAATAATATACCTCAAAGCTGATGTCT 57.282 33.333 0.00 0.00 33.15 3.41
245 323 2.904866 GTTGAACGGTGCCAGCCA 60.905 61.111 0.00 0.00 0.00 4.75
384 481 8.515414 GCTTGAGAAATTTGTAAATACCTCTGT 58.485 33.333 0.00 0.00 32.68 3.41
453 550 1.659954 GCAACAATCGCCAACGCAA 60.660 52.632 0.00 0.00 39.84 4.85
561 664 1.794714 ACCTACATTCTCGGAGCCAT 58.205 50.000 0.00 0.00 0.00 4.40
585 688 1.557099 TAACTCAGTGGCATCCGACT 58.443 50.000 0.00 0.00 0.00 4.18
693 2099 7.824289 TGATCATACCAACTAGAAACTCAAAGG 59.176 37.037 0.00 0.00 0.00 3.11
749 2177 5.505489 GCATATGGTTGACGATTGCAACATA 60.505 40.000 0.00 2.83 45.58 2.29
861 2307 4.721776 AGACAATGGCTCTATTCCCACTTA 59.278 41.667 0.00 0.00 33.17 2.24
887 2333 0.029167 TCGTAGCACGACGTTTCACA 59.971 50.000 0.00 0.00 46.73 3.58
988 2438 2.752354 TGGTCGCCATATCAACCAAAAG 59.248 45.455 0.00 0.00 38.80 2.27
1045 2573 6.982724 AGAGAGAAAGTTTCTGCAAATTTTGG 59.017 34.615 22.68 0.00 40.87 3.28
1174 2708 7.502226 AGGATAACAATGAACTTCTTTGACACA 59.498 33.333 19.27 6.16 35.74 3.72
1175 2709 7.875971 AGGATAACAATGAACTTCTTTGACAC 58.124 34.615 19.27 10.08 35.74 3.67
1189 2723 8.680903 GGCAATGGAGATATTAGGATAACAATG 58.319 37.037 0.00 0.00 0.00 2.82
1234 2768 3.315142 ATGCGACCGTCACAGGCAT 62.315 57.895 5.96 5.96 39.35 4.40
1362 2896 2.289002 GTCGATGCCAATCTCATCCAAC 59.711 50.000 0.00 0.00 37.60 3.77
1376 2910 2.146342 CACTTATGATGGGGTCGATGC 58.854 52.381 0.00 0.00 0.00 3.91
1593 3164 3.673956 TTGTATGTCGGGGCGGCAG 62.674 63.158 12.47 4.04 46.78 4.85
1595 3166 2.895372 CTTGTATGTCGGGGCGGC 60.895 66.667 0.00 0.00 0.00 6.53
1596 3167 2.895372 GCTTGTATGTCGGGGCGG 60.895 66.667 0.00 0.00 0.00 6.13
1597 3168 2.895372 GGCTTGTATGTCGGGGCG 60.895 66.667 0.00 0.00 0.00 6.13
1598 3169 1.523938 GAGGCTTGTATGTCGGGGC 60.524 63.158 0.00 0.00 0.00 5.80
1599 3170 1.146263 GGAGGCTTGTATGTCGGGG 59.854 63.158 0.00 0.00 0.00 5.73
1600 3171 1.146263 GGGAGGCTTGTATGTCGGG 59.854 63.158 0.00 0.00 0.00 5.14
1601 3172 1.227263 CGGGAGGCTTGTATGTCGG 60.227 63.158 0.00 0.00 0.00 4.79
1602 3173 0.174845 TTCGGGAGGCTTGTATGTCG 59.825 55.000 0.00 0.00 0.00 4.35
1603 3174 1.480954 TCTTCGGGAGGCTTGTATGTC 59.519 52.381 0.00 0.00 0.00 3.06
1604 3175 1.568504 TCTTCGGGAGGCTTGTATGT 58.431 50.000 0.00 0.00 0.00 2.29
1605 3176 2.548920 GGATCTTCGGGAGGCTTGTATG 60.549 54.545 0.00 0.00 0.00 2.39
1606 3177 1.694696 GGATCTTCGGGAGGCTTGTAT 59.305 52.381 0.00 0.00 0.00 2.29
1607 3178 1.120530 GGATCTTCGGGAGGCTTGTA 58.879 55.000 0.00 0.00 0.00 2.41
1608 3179 0.909610 TGGATCTTCGGGAGGCTTGT 60.910 55.000 0.00 0.00 0.00 3.16
1609 3180 0.253044 TTGGATCTTCGGGAGGCTTG 59.747 55.000 0.00 0.00 0.00 4.01
1610 3181 0.991920 TTTGGATCTTCGGGAGGCTT 59.008 50.000 0.00 0.00 0.00 4.35
1611 3182 0.253327 GTTTGGATCTTCGGGAGGCT 59.747 55.000 0.00 0.00 0.00 4.58
1612 3183 0.253327 AGTTTGGATCTTCGGGAGGC 59.747 55.000 0.00 0.00 0.00 4.70
1613 3184 1.279271 ACAGTTTGGATCTTCGGGAGG 59.721 52.381 0.00 0.00 0.00 4.30
1614 3185 2.028112 TGACAGTTTGGATCTTCGGGAG 60.028 50.000 0.00 0.00 0.00 4.30
1615 3186 1.974957 TGACAGTTTGGATCTTCGGGA 59.025 47.619 0.00 0.00 0.00 5.14
1616 3187 2.472695 TGACAGTTTGGATCTTCGGG 57.527 50.000 0.00 0.00 0.00 5.14
1617 3188 5.411361 TGTAATTGACAGTTTGGATCTTCGG 59.589 40.000 0.00 0.00 32.86 4.30
1618 3189 6.480524 TGTAATTGACAGTTTGGATCTTCG 57.519 37.500 0.00 0.00 32.86 3.79
1619 3190 7.648142 TGTTGTAATTGACAGTTTGGATCTTC 58.352 34.615 0.00 0.00 39.88 2.87
1620 3191 7.581213 TGTTGTAATTGACAGTTTGGATCTT 57.419 32.000 0.00 0.00 39.88 2.40
1621 3192 7.765695 ATGTTGTAATTGACAGTTTGGATCT 57.234 32.000 0.00 0.00 39.88 2.75
1622 3193 8.081633 TCAATGTTGTAATTGACAGTTTGGATC 58.918 33.333 0.00 0.00 40.72 3.36
1623 3194 7.950512 TCAATGTTGTAATTGACAGTTTGGAT 58.049 30.769 0.00 0.00 40.72 3.41
1624 3195 7.340122 TCAATGTTGTAATTGACAGTTTGGA 57.660 32.000 0.00 0.00 40.72 3.53
1625 3196 8.592105 ATTCAATGTTGTAATTGACAGTTTGG 57.408 30.769 0.00 0.00 44.26 3.28
1627 3198 9.912634 CCTATTCAATGTTGTAATTGACAGTTT 57.087 29.630 0.00 0.00 44.26 2.66
1628 3199 9.295825 TCCTATTCAATGTTGTAATTGACAGTT 57.704 29.630 0.00 0.00 44.26 3.16
1629 3200 8.862325 TCCTATTCAATGTTGTAATTGACAGT 57.138 30.769 0.00 0.00 44.26 3.55
1633 3204 9.585099 GCATTTCCTATTCAATGTTGTAATTGA 57.415 29.630 0.00 0.00 43.20 2.57
1634 3205 8.819974 GGCATTTCCTATTCAATGTTGTAATTG 58.180 33.333 0.00 0.00 38.63 2.32
1635 3206 8.538701 TGGCATTTCCTATTCAATGTTGTAATT 58.461 29.630 0.00 0.00 33.58 1.40
1636 3207 8.076910 TGGCATTTCCTATTCAATGTTGTAAT 57.923 30.769 0.00 0.00 33.58 1.89
1637 3208 7.473735 TGGCATTTCCTATTCAATGTTGTAA 57.526 32.000 0.00 0.00 33.58 2.41
1638 3209 7.473735 TTGGCATTTCCTATTCAATGTTGTA 57.526 32.000 0.00 0.00 33.58 2.41
1639 3210 5.999205 TGGCATTTCCTATTCAATGTTGT 57.001 34.783 0.00 0.00 33.58 3.32
1640 3211 7.042950 TCATTGGCATTTCCTATTCAATGTTG 58.957 34.615 11.81 0.00 40.99 3.33
1641 3212 7.124599 TCTCATTGGCATTTCCTATTCAATGTT 59.875 33.333 11.81 0.00 40.99 2.71
1642 3213 6.608405 TCTCATTGGCATTTCCTATTCAATGT 59.392 34.615 11.81 0.00 40.99 2.71
1643 3214 7.046292 TCTCATTGGCATTTCCTATTCAATG 57.954 36.000 0.00 0.00 41.33 2.82
1644 3215 7.850935 ATCTCATTGGCATTTCCTATTCAAT 57.149 32.000 0.00 0.00 35.26 2.57
1645 3216 8.765488 TTATCTCATTGGCATTTCCTATTCAA 57.235 30.769 0.00 0.00 35.26 2.69
1646 3217 8.765488 TTTATCTCATTGGCATTTCCTATTCA 57.235 30.769 0.00 0.00 35.26 2.57
1647 3218 9.635520 CATTTATCTCATTGGCATTTCCTATTC 57.364 33.333 0.00 0.00 35.26 1.75
1648 3219 9.151177 ACATTTATCTCATTGGCATTTCCTATT 57.849 29.630 0.00 0.00 35.26 1.73
1649 3220 8.716674 ACATTTATCTCATTGGCATTTCCTAT 57.283 30.769 0.00 0.00 35.26 2.57
1650 3221 8.000709 AGACATTTATCTCATTGGCATTTCCTA 58.999 33.333 0.00 0.00 35.26 2.94
1651 3222 6.837568 AGACATTTATCTCATTGGCATTTCCT 59.162 34.615 0.00 0.00 35.26 3.36
1652 3223 7.047460 AGACATTTATCTCATTGGCATTTCC 57.953 36.000 0.00 0.00 0.00 3.13
1653 3224 9.060347 TCTAGACATTTATCTCATTGGCATTTC 57.940 33.333 0.00 0.00 0.00 2.17
1654 3225 8.985315 TCTAGACATTTATCTCATTGGCATTT 57.015 30.769 0.00 0.00 0.00 2.32
1655 3226 8.435187 TCTCTAGACATTTATCTCATTGGCATT 58.565 33.333 0.00 0.00 0.00 3.56
1656 3227 7.971201 TCTCTAGACATTTATCTCATTGGCAT 58.029 34.615 0.00 0.00 0.00 4.40
1657 3228 7.365497 TCTCTAGACATTTATCTCATTGGCA 57.635 36.000 0.00 0.00 0.00 4.92
1658 3229 8.845413 AATCTCTAGACATTTATCTCATTGGC 57.155 34.615 0.00 0.00 0.00 4.52
1666 3237 8.987890 GCCTTCAAGAATCTCTAGACATTTATC 58.012 37.037 0.00 0.00 0.00 1.75
1667 3238 8.713036 AGCCTTCAAGAATCTCTAGACATTTAT 58.287 33.333 0.00 0.00 0.00 1.40
1668 3239 8.083828 AGCCTTCAAGAATCTCTAGACATTTA 57.916 34.615 0.00 0.00 0.00 1.40
1669 3240 6.956497 AGCCTTCAAGAATCTCTAGACATTT 58.044 36.000 0.00 0.00 0.00 2.32
1670 3241 6.558488 AGCCTTCAAGAATCTCTAGACATT 57.442 37.500 0.00 0.00 0.00 2.71
1671 3242 6.558488 AAGCCTTCAAGAATCTCTAGACAT 57.442 37.500 0.00 0.00 0.00 3.06
1672 3243 6.665680 ACTAAGCCTTCAAGAATCTCTAGACA 59.334 38.462 0.00 0.00 0.00 3.41
1673 3244 6.978080 CACTAAGCCTTCAAGAATCTCTAGAC 59.022 42.308 0.00 0.00 0.00 2.59
1674 3245 6.665680 ACACTAAGCCTTCAAGAATCTCTAGA 59.334 38.462 0.00 0.00 0.00 2.43
1675 3246 6.756074 CACACTAAGCCTTCAAGAATCTCTAG 59.244 42.308 0.00 0.00 0.00 2.43
1676 3247 6.351371 CCACACTAAGCCTTCAAGAATCTCTA 60.351 42.308 0.00 0.00 0.00 2.43
1677 3248 5.486526 CACACTAAGCCTTCAAGAATCTCT 58.513 41.667 0.00 0.00 0.00 3.10
1678 3249 4.633565 CCACACTAAGCCTTCAAGAATCTC 59.366 45.833 0.00 0.00 0.00 2.75
1679 3250 4.583871 CCACACTAAGCCTTCAAGAATCT 58.416 43.478 0.00 0.00 0.00 2.40
1680 3251 3.127721 GCCACACTAAGCCTTCAAGAATC 59.872 47.826 0.00 0.00 0.00 2.52
1681 3252 3.084786 GCCACACTAAGCCTTCAAGAAT 58.915 45.455 0.00 0.00 0.00 2.40
1682 3253 2.158682 TGCCACACTAAGCCTTCAAGAA 60.159 45.455 0.00 0.00 0.00 2.52
1683 3254 1.419762 TGCCACACTAAGCCTTCAAGA 59.580 47.619 0.00 0.00 0.00 3.02
1684 3255 1.896220 TGCCACACTAAGCCTTCAAG 58.104 50.000 0.00 0.00 0.00 3.02
1685 3256 2.356665 TTGCCACACTAAGCCTTCAA 57.643 45.000 0.00 0.00 0.00 2.69
1686 3257 2.356665 TTTGCCACACTAAGCCTTCA 57.643 45.000 0.00 0.00 0.00 3.02
1687 3258 2.884639 TCTTTTGCCACACTAAGCCTTC 59.115 45.455 0.00 0.00 0.00 3.46
1688 3259 2.944129 TCTTTTGCCACACTAAGCCTT 58.056 42.857 0.00 0.00 0.00 4.35
1689 3260 2.656947 TCTTTTGCCACACTAAGCCT 57.343 45.000 0.00 0.00 0.00 4.58
1690 3261 3.726291 TTTCTTTTGCCACACTAAGCC 57.274 42.857 0.00 0.00 0.00 4.35
1691 3262 3.490896 GCTTTTCTTTTGCCACACTAAGC 59.509 43.478 0.00 0.00 0.00 3.09
1692 3263 4.681744 TGCTTTTCTTTTGCCACACTAAG 58.318 39.130 0.00 0.00 0.00 2.18
1693 3264 4.727507 TGCTTTTCTTTTGCCACACTAA 57.272 36.364 0.00 0.00 0.00 2.24
1694 3265 4.584325 AGATGCTTTTCTTTTGCCACACTA 59.416 37.500 0.00 0.00 0.00 2.74
1695 3266 3.385755 AGATGCTTTTCTTTTGCCACACT 59.614 39.130 0.00 0.00 0.00 3.55
1696 3267 3.721035 AGATGCTTTTCTTTTGCCACAC 58.279 40.909 0.00 0.00 0.00 3.82
1697 3268 3.638160 AGAGATGCTTTTCTTTTGCCACA 59.362 39.130 0.00 0.00 0.00 4.17
1698 3269 4.233005 GAGAGATGCTTTTCTTTTGCCAC 58.767 43.478 0.00 0.00 0.00 5.01
1699 3270 3.256631 GGAGAGATGCTTTTCTTTTGCCA 59.743 43.478 0.00 0.00 0.00 4.92
1700 3271 3.256631 TGGAGAGATGCTTTTCTTTTGCC 59.743 43.478 0.00 0.00 0.00 4.52
1701 3272 4.483311 CTGGAGAGATGCTTTTCTTTTGC 58.517 43.478 0.00 0.00 0.00 3.68
1702 3273 4.763793 TCCTGGAGAGATGCTTTTCTTTTG 59.236 41.667 0.00 0.00 0.00 2.44
1703 3274 4.990526 TCCTGGAGAGATGCTTTTCTTTT 58.009 39.130 0.00 0.00 0.00 2.27
1704 3275 4.042684 ACTCCTGGAGAGATGCTTTTCTTT 59.957 41.667 29.71 0.00 46.50 2.52
1705 3276 3.586618 ACTCCTGGAGAGATGCTTTTCTT 59.413 43.478 29.71 0.00 46.50 2.52
1706 3277 3.180507 ACTCCTGGAGAGATGCTTTTCT 58.819 45.455 29.71 0.00 46.50 2.52
1707 3278 3.625649 ACTCCTGGAGAGATGCTTTTC 57.374 47.619 29.71 0.00 46.50 2.29
1708 3279 3.454082 CCTACTCCTGGAGAGATGCTTTT 59.546 47.826 29.71 6.80 46.50 2.27
1709 3280 3.037549 CCTACTCCTGGAGAGATGCTTT 58.962 50.000 29.71 7.54 46.50 3.51
1710 3281 2.246067 TCCTACTCCTGGAGAGATGCTT 59.754 50.000 29.71 8.28 46.50 3.91
1711 3282 1.856259 TCCTACTCCTGGAGAGATGCT 59.144 52.381 29.71 9.02 46.50 3.79
1712 3283 2.373335 TCCTACTCCTGGAGAGATGC 57.627 55.000 29.71 0.00 46.50 3.91
1713 3284 6.015519 CAGTATTTCCTACTCCTGGAGAGATG 60.016 46.154 29.71 14.29 46.50 2.90
1714 3285 6.074648 CAGTATTTCCTACTCCTGGAGAGAT 58.925 44.000 29.71 10.53 46.50 2.75
1715 3286 5.450453 CAGTATTTCCTACTCCTGGAGAGA 58.550 45.833 29.71 18.76 46.50 3.10
1717 3288 4.547671 CCAGTATTTCCTACTCCTGGAGA 58.452 47.826 29.71 12.43 38.68 3.71
1718 3289 3.070302 GCCAGTATTTCCTACTCCTGGAG 59.930 52.174 22.00 22.00 38.68 3.86
1719 3290 3.039011 GCCAGTATTTCCTACTCCTGGA 58.961 50.000 7.64 0.00 38.68 3.86
1720 3291 2.771943 TGCCAGTATTTCCTACTCCTGG 59.228 50.000 0.00 0.00 38.68 4.45
1721 3292 4.101585 TGATGCCAGTATTTCCTACTCCTG 59.898 45.833 0.00 0.00 38.68 3.86
1722 3293 4.298626 TGATGCCAGTATTTCCTACTCCT 58.701 43.478 0.00 0.00 38.68 3.69
1723 3294 4.689612 TGATGCCAGTATTTCCTACTCC 57.310 45.455 0.00 0.00 38.68 3.85
1724 3295 7.573968 AATTTGATGCCAGTATTTCCTACTC 57.426 36.000 0.00 0.00 38.68 2.59
1725 3296 7.631377 GCAAATTTGATGCCAGTATTTCCTACT 60.631 37.037 22.31 0.00 36.19 2.57
1726 3297 6.476706 GCAAATTTGATGCCAGTATTTCCTAC 59.523 38.462 22.31 0.00 37.85 3.18
1727 3298 6.154192 TGCAAATTTGATGCCAGTATTTCCTA 59.846 34.615 22.31 0.00 43.16 2.94
1728 3299 5.046448 TGCAAATTTGATGCCAGTATTTCCT 60.046 36.000 22.31 0.00 43.16 3.36
1729 3300 5.063817 GTGCAAATTTGATGCCAGTATTTCC 59.936 40.000 22.31 0.00 43.16 3.13
1730 3301 5.220265 CGTGCAAATTTGATGCCAGTATTTC 60.220 40.000 22.31 0.00 43.16 2.17
1731 3302 4.626604 CGTGCAAATTTGATGCCAGTATTT 59.373 37.500 22.31 0.00 43.16 1.40
1732 3303 4.082300 TCGTGCAAATTTGATGCCAGTATT 60.082 37.500 22.31 0.00 43.16 1.89
1733 3304 3.443329 TCGTGCAAATTTGATGCCAGTAT 59.557 39.130 22.31 0.00 43.16 2.12
1734 3305 2.816672 TCGTGCAAATTTGATGCCAGTA 59.183 40.909 22.31 0.00 43.16 2.74
1735 3306 1.612950 TCGTGCAAATTTGATGCCAGT 59.387 42.857 22.31 0.00 43.16 4.00
1736 3307 2.256174 CTCGTGCAAATTTGATGCCAG 58.744 47.619 22.31 6.32 43.16 4.85
1737 3308 1.612950 ACTCGTGCAAATTTGATGCCA 59.387 42.857 22.31 7.22 43.16 4.92
1738 3309 2.352503 ACTCGTGCAAATTTGATGCC 57.647 45.000 22.31 4.54 43.16 4.40
1750 3321 5.352643 AACTAAATGGTTTGTACTCGTGC 57.647 39.130 0.00 0.00 0.00 5.34
1779 3350 7.928167 AGAAAATGAAGGATTTGAAGTTGGTTC 59.072 33.333 0.00 0.00 34.30 3.62
1783 3354 7.707893 ACACAGAAAATGAAGGATTTGAAGTTG 59.292 33.333 0.00 0.00 34.30 3.16
1792 3415 5.520748 AGGGTACACAGAAAATGAAGGAT 57.479 39.130 0.00 0.00 0.00 3.24
1798 3421 5.631026 CGAATGAAGGGTACACAGAAAATG 58.369 41.667 0.00 0.00 0.00 2.32
1812 3435 5.756195 TTTATCTTGGATGCGAATGAAGG 57.244 39.130 0.00 0.00 0.00 3.46
1820 3443 5.406780 GGACTACTCATTTATCTTGGATGCG 59.593 44.000 0.00 0.00 0.00 4.73
1867 3490 6.405278 TTCGGATATAGCTGTTCTGAATGA 57.595 37.500 0.00 0.00 31.52 2.57
1896 3519 8.322091 TGAAGCTAGCTAAAAGTAGGAGAAAAT 58.678 33.333 19.70 0.00 0.00 1.82
1901 3524 6.045955 CCTTGAAGCTAGCTAAAAGTAGGAG 58.954 44.000 25.97 13.99 0.00 3.69
1911 3534 3.619979 GCTTGGAACCTTGAAGCTAGCTA 60.620 47.826 19.70 0.00 39.24 3.32
1912 3535 2.877708 GCTTGGAACCTTGAAGCTAGCT 60.878 50.000 12.68 12.68 39.24 3.32
1913 3536 1.470494 GCTTGGAACCTTGAAGCTAGC 59.530 52.381 6.62 6.62 39.24 3.42
1914 3537 2.087646 GGCTTGGAACCTTGAAGCTAG 58.912 52.381 12.00 0.00 41.55 3.42
1931 3554 3.552068 GCAAAATAACGACAACAAGGGCT 60.552 43.478 0.00 0.00 0.00 5.19
1940 3564 0.952280 TTGGCCGCAAAATAACGACA 59.048 45.000 0.00 0.00 0.00 4.35
1976 3600 9.515226 AAATTGCTGAAGTTAGGTAGTATTTCA 57.485 29.630 0.00 0.00 0.00 2.69
1981 3605 6.927416 TCGAAATTGCTGAAGTTAGGTAGTA 58.073 36.000 0.00 0.00 0.00 1.82
1982 3606 5.790593 TCGAAATTGCTGAAGTTAGGTAGT 58.209 37.500 0.00 0.00 0.00 2.73
1983 3607 6.910536 ATCGAAATTGCTGAAGTTAGGTAG 57.089 37.500 0.00 0.00 0.00 3.18
2004 3628 4.113354 CCCTAGACACGTCTTGCTTAATC 58.887 47.826 4.79 0.00 40.93 1.75
2015 3639 1.001760 ATGCCCTCCCTAGACACGT 59.998 57.895 0.00 0.00 0.00 4.49
2065 3690 1.362932 AGTGTGATCCACCTAGGGAGT 59.637 52.381 14.81 0.00 45.74 3.85
2068 3693 2.187958 TGAAGTGTGATCCACCTAGGG 58.812 52.381 14.81 1.73 45.74 3.53
2094 3719 6.194325 CGCAAATTCCAAAACAAAACATTGTC 59.806 34.615 0.00 0.00 33.35 3.18
2142 3767 2.054799 ACATGTAGGTGGACAGTTGGT 58.945 47.619 0.00 0.00 31.51 3.67
2174 3802 1.676916 CGCGAGGATATTGGCCATGAT 60.677 52.381 6.09 2.13 0.00 2.45
2176 3804 2.165380 CGCGAGGATATTGGCCATG 58.835 57.895 6.09 0.00 0.00 3.66
2193 3821 1.692296 CAACAAATAAACCGGCACCG 58.308 50.000 0.00 1.02 39.44 4.94
2200 3828 9.301153 CTGATTTATGTAGGCAACAAATAAACC 57.699 33.333 0.00 0.00 42.70 3.27
2223 3851 9.057089 GTCTTCTTCTTGAAAGGAATTTACTGA 57.943 33.333 0.00 0.00 33.79 3.41
2224 3852 8.840321 TGTCTTCTTCTTGAAAGGAATTTACTG 58.160 33.333 0.00 0.00 33.79 2.74
2232 3860 9.573166 TGATTTATTGTCTTCTTCTTGAAAGGA 57.427 29.630 0.00 0.00 33.79 3.36
2256 3884 6.042437 ACTGGATATGCATAGACAACTCATGA 59.958 38.462 12.79 0.00 0.00 3.07
2271 3899 0.861837 GTGCTGCGTACTGGATATGC 59.138 55.000 0.00 0.00 44.89 3.14
2272 3900 1.202521 TGGTGCTGCGTACTGGATATG 60.203 52.381 0.00 0.00 0.00 1.78
2282 3910 0.601576 TCGTTATTGTGGTGCTGCGT 60.602 50.000 0.00 0.00 0.00 5.24
2286 3914 2.083774 CCATGTCGTTATTGTGGTGCT 58.916 47.619 0.00 0.00 0.00 4.40
2305 4075 4.976116 GCATGATAATTGCGGAAAGTAACC 59.024 41.667 0.00 0.00 0.00 2.85
2306 4076 4.976116 GGCATGATAATTGCGGAAAGTAAC 59.024 41.667 0.00 0.00 41.07 2.50
2320 4090 8.206867 GGAGATTGCATATAGTAGGCATGATAA 58.793 37.037 0.00 0.00 45.52 1.75
2328 4098 9.725019 TTATGTTTGGAGATTGCATATAGTAGG 57.275 33.333 0.00 0.00 0.00 3.18
2331 4101 9.632638 ACTTTATGTTTGGAGATTGCATATAGT 57.367 29.630 0.00 0.00 33.10 2.12
2337 4107 6.839124 ATCACTTTATGTTTGGAGATTGCA 57.161 33.333 0.00 0.00 0.00 4.08
2409 4186 2.066262 GCTAACTAACGAGCTGTTGCA 58.934 47.619 10.59 0.00 42.01 4.08


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

AutoCloner maintained by Alex Coulton.