Multiple sequence alignment - TraesCS5B01G208200

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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 TraesCS5B01G208200 chr5B 100.000 4217 0 0 1 4217 377697587 377701803 0.000000e+00 7788.0
1 TraesCS5B01G208200 chr5B 85.964 2572 261 63 1001 3522 377843634 377846155 0.000000e+00 2658.0
2 TraesCS5B01G208200 chr5B 83.645 642 66 24 1001 1608 378510565 378511201 6.120000e-158 568.0
3 TraesCS5B01G208200 chr5B 86.837 509 52 10 1112 1608 377978340 377978845 4.760000e-154 555.0
4 TraesCS5B01G208200 chr5B 86.154 520 50 13 1112 1609 378068455 378068974 3.710000e-150 542.0
5 TraesCS5B01G208200 chr5B 93.567 171 10 1 532 702 102630143 102629974 1.950000e-63 254.0
6 TraesCS5B01G208200 chr5B 84.979 233 30 5 1815 2045 378069267 378069496 9.120000e-57 231.0
7 TraesCS5B01G208200 chr5B 81.673 251 42 4 1815 2064 377979110 377979357 5.530000e-49 206.0
8 TraesCS5B01G208200 chr5B 94.792 96 3 2 3547 3641 290895025 290894931 9.450000e-32 148.0
9 TraesCS5B01G208200 chr5D 94.492 2778 99 20 704 3470 325422428 325425162 0.000000e+00 4233.0
10 TraesCS5B01G208200 chr5D 94.020 602 18 5 3631 4217 325425506 325426104 0.000000e+00 896.0
11 TraesCS5B01G208200 chr5D 86.320 519 49 15 1112 1608 326118243 326118761 2.870000e-151 545.0
12 TraesCS5B01G208200 chr5D 86.200 500 53 12 1112 1609 325663796 325664281 1.040000e-145 527.0
13 TraesCS5B01G208200 chr5D 85.714 504 60 9 1112 1609 325646957 325647454 4.830000e-144 521.0
14 TraesCS5B01G208200 chr5D 88.400 250 26 2 1815 2064 326119080 326119326 8.860000e-77 298.0
15 TraesCS5B01G208200 chr5D 86.667 195 19 5 3961 4154 325374577 325374765 4.270000e-50 209.0
16 TraesCS5B01G208200 chr5D 98.824 85 1 0 3467 3551 325425425 325425509 7.300000e-33 152.0
17 TraesCS5B01G208200 chr5D 95.402 87 4 0 3546 3632 21789113 21789199 5.690000e-29 139.0
18 TraesCS5B01G208200 chr5D 88.393 112 7 4 3524 3633 337703218 337703325 3.420000e-26 130.0
19 TraesCS5B01G208200 chr5A 92.286 1750 108 7 1828 3551 423681159 423682907 0.000000e+00 2459.0
20 TraesCS5B01G208200 chr5A 84.031 2605 265 77 1001 3535 423744978 423747501 0.000000e+00 2366.0
21 TraesCS5B01G208200 chr5A 93.123 1047 47 12 704 1725 423680107 423681153 0.000000e+00 1511.0
22 TraesCS5B01G208200 chr5A 87.525 505 49 12 1112 1608 430508317 430507819 4.730000e-159 571.0
23 TraesCS5B01G208200 chr5A 83.798 574 68 20 3631 4199 423682904 423683457 4.830000e-144 521.0
24 TraesCS5B01G208200 chr5A 85.772 492 50 11 1121 1609 430958477 430958003 1.750000e-138 503.0
25 TraesCS5B01G208200 chr5A 93.985 133 7 1 4023 4154 423664071 423664203 2.570000e-47 200.0
26 TraesCS5B01G208200 chr5A 87.302 63 6 2 2003 2064 666933475 666933414 2.100000e-08 71.3
27 TraesCS5B01G208200 chr2B 93.384 529 35 0 1 529 374217763 374217235 0.000000e+00 784.0
28 TraesCS5B01G208200 chr2B 92.030 527 42 0 1 527 94345870 94345344 0.000000e+00 741.0
29 TraesCS5B01G208200 chr2B 85.938 192 21 5 519 707 797329985 797329797 2.570000e-47 200.0
30 TraesCS5B01G208200 chr7B 92.453 530 39 1 1 529 284959235 284958706 0.000000e+00 756.0
31 TraesCS5B01G208200 chr7B 92.075 530 39 3 1 529 194597118 194596591 0.000000e+00 743.0
32 TraesCS5B01G208200 chr3D 91.871 529 43 0 1 529 28272520 28273048 0.000000e+00 739.0
33 TraesCS5B01G208200 chr3D 93.293 164 11 0 540 703 459077268 459077431 4.210000e-60 243.0
34 TraesCS5B01G208200 chr3D 91.279 172 15 0 535 706 6667270 6667441 7.050000e-58 235.0
35 TraesCS5B01G208200 chr3D 95.556 90 3 1 3545 3634 296034413 296034501 4.400000e-30 143.0
36 TraesCS5B01G208200 chr3D 93.750 96 5 1 3548 3642 505557393 505557298 4.400000e-30 143.0
37 TraesCS5B01G208200 chr6B 91.698 530 43 1 1 529 21938517 21937988 0.000000e+00 734.0
38 TraesCS5B01G208200 chr6B 91.682 529 44 0 1 529 714185330 714184802 0.000000e+00 734.0
39 TraesCS5B01G208200 chr6B 92.941 170 10 2 537 705 314547152 314546984 3.260000e-61 246.0
40 TraesCS5B01G208200 chr6B 92.398 171 12 1 537 706 119526975 119526805 4.210000e-60 243.0
41 TraesCS5B01G208200 chr6B 92.073 164 13 0 541 704 98892445 98892608 9.120000e-57 231.0
42 TraesCS5B01G208200 chr6B 87.097 186 19 5 524 705 656279215 656279399 5.530000e-49 206.0
43 TraesCS5B01G208200 chr6B 96.774 93 3 0 3547 3639 68002400 68002308 5.650000e-34 156.0
44 TraesCS5B01G208200 chr6B 92.929 99 6 1 3537 3635 38004042 38003945 4.400000e-30 143.0
45 TraesCS5B01G208200 chr3B 91.682 529 43 1 1 529 242480663 242480136 0.000000e+00 732.0
46 TraesCS5B01G208200 chr3B 85.484 186 23 3 522 704 456554366 456554182 1.550000e-44 191.0
47 TraesCS5B01G208200 chr3B 96.809 94 3 0 3542 3635 748777085 748777178 1.570000e-34 158.0
48 TraesCS5B01G208200 chr1B 91.493 529 45 0 1 529 645415369 645415897 0.000000e+00 728.0
49 TraesCS5B01G208200 chr1B 86.857 175 23 0 528 702 687090925 687091099 3.330000e-46 196.0
50 TraesCS5B01G208200 chr1B 85.915 142 20 0 1461 1602 121404862 121405003 7.300000e-33 152.0
51 TraesCS5B01G208200 chr1B 95.604 91 4 0 3545 3635 234252677 234252587 3.400000e-31 147.0
52 TraesCS5B01G208200 chr1B 93.684 95 6 0 3542 3636 28500414 28500508 4.400000e-30 143.0
53 TraesCS5B01G208200 chrUn 93.976 166 10 0 537 702 141680742 141680907 7.000000e-63 252.0
54 TraesCS5B01G208200 chrUn 94.444 90 5 0 3544 3633 244923808 244923897 5.690000e-29 139.0
55 TraesCS5B01G208200 chrUn 94.444 90 5 0 3544 3633 287095696 287095785 5.690000e-29 139.0
56 TraesCS5B01G208200 chrUn 93.407 91 6 0 3548 3638 371558133 371558043 7.350000e-28 135.0
57 TraesCS5B01G208200 chrUn 93.407 91 6 0 3548 3638 371616940 371616850 7.350000e-28 135.0
58 TraesCS5B01G208200 chrUn 92.473 93 7 0 3542 3634 27475949 27476041 2.650000e-27 134.0
59 TraesCS5B01G208200 chrUn 93.333 90 6 0 3545 3634 55723609 55723698 2.650000e-27 134.0
60 TraesCS5B01G208200 chrUn 88.596 114 7 5 3527 3639 335557631 335557739 2.650000e-27 134.0
61 TraesCS5B01G208200 chrUn 93.258 89 6 0 3544 3632 2693318 2693230 9.510000e-27 132.0
62 TraesCS5B01G208200 chrUn 94.118 85 5 0 3548 3632 13209427 13209343 3.420000e-26 130.0
63 TraesCS5B01G208200 chrUn 93.182 88 6 0 3548 3635 16901709 16901622 3.420000e-26 130.0
64 TraesCS5B01G208200 chrUn 87.302 63 6 2 2003 2064 30412927 30412866 2.100000e-08 71.3
65 TraesCS5B01G208200 chr2D 93.902 164 10 0 540 703 87407526 87407363 9.050000e-62 248.0
66 TraesCS5B01G208200 chr2D 88.506 174 14 4 526 697 565312765 565312596 5.530000e-49 206.0
67 TraesCS5B01G208200 chr2D 93.617 94 6 0 3547 3640 572049125 572049218 1.580000e-29 141.0
68 TraesCS5B01G208200 chr4A 92.857 168 11 1 537 703 517406637 517406470 4.210000e-60 243.0
69 TraesCS5B01G208200 chr4A 87.931 116 11 3 3538 3653 34261960 34262072 2.650000e-27 134.0
70 TraesCS5B01G208200 chr4A 88.034 117 8 5 3527 3642 632934475 632934364 2.650000e-27 134.0
71 TraesCS5B01G208200 chr4D 89.831 177 15 3 528 703 23312045 23312219 1.530000e-54 224.0
72 TraesCS5B01G208200 chr4D 94.444 90 5 0 3544 3633 436376805 436376716 5.690000e-29 139.0
73 TraesCS5B01G208200 chr1A 87.912 182 21 1 522 702 139560037 139560218 3.300000e-51 213.0
74 TraesCS5B01G208200 chr1A 96.512 86 3 0 3548 3633 542440397 542440312 4.400000e-30 143.0
75 TraesCS5B01G208200 chr1A 93.548 93 6 0 3542 3634 498811738 498811646 5.690000e-29 139.0
76 TraesCS5B01G208200 chr1A 91.919 99 6 2 3544 3642 551465803 551465707 2.040000e-28 137.0
77 TraesCS5B01G208200 chr1A 77.253 233 49 3 1820 2052 50749026 50748798 2.650000e-27 134.0
78 TraesCS5B01G208200 chr1A 89.524 105 9 2 3541 3643 448911830 448911934 9.510000e-27 132.0
79 TraesCS5B01G208200 chr1A 87.719 114 8 5 3527 3639 555691336 555691444 1.230000e-25 128.0
80 TraesCS5B01G208200 chr3A 87.709 179 21 1 528 706 659527403 659527226 1.540000e-49 207.0
81 TraesCS5B01G208200 chr3A 91.429 105 7 2 3546 3648 709065498 709065602 4.400000e-30 143.0
82 TraesCS5B01G208200 chr7A 86.932 176 23 0 527 702 727851110 727851285 9.250000e-47 198.0
83 TraesCS5B01G208200 chr6A 84.868 152 21 2 1820 1971 57963272 57963123 7.300000e-33 152.0
84 TraesCS5B01G208200 chr6A 95.556 90 4 0 3548 3637 439517401 439517312 1.220000e-30 145.0
85 TraesCS5B01G208200 chr6A 94.505 91 5 0 3544 3634 7099612 7099702 1.580000e-29 141.0
86 TraesCS5B01G208200 chr6A 92.708 96 6 1 3548 3643 89971069 89971163 2.040000e-28 137.0
87 TraesCS5B01G208200 chr4B 97.701 87 2 0 3548 3634 248358333 248358247 2.630000e-32 150.0
88 TraesCS5B01G208200 chr2A 89.256 121 8 4 3547 3667 386732356 386732241 3.400000e-31 147.0
89 TraesCS5B01G208200 chr7D 90.826 109 8 2 3544 3650 53485498 53485606 1.220000e-30 145.0
90 TraesCS5B01G208200 chr7D 93.684 95 6 0 3544 3638 511659434 511659528 4.400000e-30 143.0
91 TraesCS5B01G208200 chr7D 86.066 122 14 3 3535 3653 37655966 37655845 1.230000e-25 128.0
92 TraesCS5B01G208200 chr6D 96.512 86 3 0 3547 3632 36675481 36675396 4.400000e-30 143.0
93 TraesCS5B01G208200 chr6D 94.565 92 4 1 3548 3638 157328025 157328116 1.580000e-29 141.0
94 TraesCS5B01G208200 chr6D 94.444 90 5 0 3545 3634 31474853 31474942 5.690000e-29 139.0
95 TraesCS5B01G208200 chr6D 92.784 97 6 1 3547 3642 206553954 206553858 5.690000e-29 139.0
96 TraesCS5B01G208200 chr6D 94.382 89 5 0 3547 3635 199144927 199144839 2.040000e-28 137.0
97 TraesCS5B01G208200 chr6D 94.382 89 5 0 3548 3636 380781868 380781780 2.040000e-28 137.0
98 TraesCS5B01G208200 chr6D 91.000 100 7 2 3541 3639 58042851 58042753 2.650000e-27 134.0
99 TraesCS5B01G208200 chr1D 92.929 99 5 2 3548 3646 234329042 234329138 4.400000e-30 143.0
100 TraesCS5B01G208200 chr1D 95.455 88 4 0 3547 3634 85191512 85191599 1.580000e-29 141.0
101 TraesCS5B01G208200 chr1D 92.708 96 6 1 3548 3642 200825983 200826078 2.040000e-28 137.0
102 TraesCS5B01G208200 chr1D 88.785 107 10 2 3531 3636 253197637 253197532 3.420000e-26 130.0


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 TraesCS5B01G208200 chr5B 377697587 377701803 4216 False 7788.000000 7788 100.000000 1 4217 1 chr5B.!!$F1 4216
1 TraesCS5B01G208200 chr5B 377843634 377846155 2521 False 2658.000000 2658 85.964000 1001 3522 1 chr5B.!!$F2 2521
2 TraesCS5B01G208200 chr5B 378510565 378511201 636 False 568.000000 568 83.645000 1001 1608 1 chr5B.!!$F3 607
3 TraesCS5B01G208200 chr5B 378068455 378069496 1041 False 386.500000 542 85.566500 1112 2045 2 chr5B.!!$F5 933
4 TraesCS5B01G208200 chr5B 377978340 377979357 1017 False 380.500000 555 84.255000 1112 2064 2 chr5B.!!$F4 952
5 TraesCS5B01G208200 chr5D 325422428 325426104 3676 False 1760.333333 4233 95.778667 704 4217 3 chr5D.!!$F6 3513
6 TraesCS5B01G208200 chr5D 326118243 326119326 1083 False 421.500000 545 87.360000 1112 2064 2 chr5D.!!$F7 952
7 TraesCS5B01G208200 chr5A 423744978 423747501 2523 False 2366.000000 2366 84.031000 1001 3535 1 chr5A.!!$F2 2534
8 TraesCS5B01G208200 chr5A 423680107 423683457 3350 False 1497.000000 2459 89.735667 704 4199 3 chr5A.!!$F3 3495
9 TraesCS5B01G208200 chr2B 374217235 374217763 528 True 784.000000 784 93.384000 1 529 1 chr2B.!!$R2 528
10 TraesCS5B01G208200 chr2B 94345344 94345870 526 True 741.000000 741 92.030000 1 527 1 chr2B.!!$R1 526
11 TraesCS5B01G208200 chr7B 284958706 284959235 529 True 756.000000 756 92.453000 1 529 1 chr7B.!!$R2 528
12 TraesCS5B01G208200 chr7B 194596591 194597118 527 True 743.000000 743 92.075000 1 529 1 chr7B.!!$R1 528
13 TraesCS5B01G208200 chr3D 28272520 28273048 528 False 739.000000 739 91.871000 1 529 1 chr3D.!!$F2 528
14 TraesCS5B01G208200 chr6B 21937988 21938517 529 True 734.000000 734 91.698000 1 529 1 chr6B.!!$R1 528
15 TraesCS5B01G208200 chr6B 714184802 714185330 528 True 734.000000 734 91.682000 1 529 1 chr6B.!!$R6 528
16 TraesCS5B01G208200 chr3B 242480136 242480663 527 True 732.000000 732 91.682000 1 529 1 chr3B.!!$R1 528
17 TraesCS5B01G208200 chr1B 645415369 645415897 528 False 728.000000 728 91.493000 1 529 1 chr1B.!!$F3 528

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
522 525 0.608130 ACCACAGAGTGCGCAATCTA 59.392 50.0 36.48 0.0 33.56 1.98 F
752 756 0.877071 GCAACCACATCAGACACCAG 59.123 55.0 0.00 0.0 0.00 4.00 F
1697 1880 0.322008 CTGTTCTTGTCCCCTGCCTC 60.322 60.0 0.00 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 1428 1.258720 TCGCAAGCATTTCATCGATCG 59.741 47.619 9.36 9.36 37.18 3.69 R
2698 2976 1.004394 TCGTCCTGAGAGTAGCTCCAA 59.996 52.381 0.00 0.00 43.26 3.53 R
3224 3503 2.238898 GCACACTTCCCCTACCATACTT 59.761 50.000 0.00 0.00 0.00 2.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 2.673043 CGCTTTTGCCAAATCATGCTCT 60.673 45.455 0.00 0.00 43.93 4.09
137 139 2.338500 CTACTTGACCAGCGTCCTTTC 58.662 52.381 0.00 0.00 38.32 2.62
155 157 6.557633 GTCCTTTCCCCTACCTATTAGAATGA 59.442 42.308 0.00 0.00 0.00 2.57
213 215 2.428890 ACATCGGATCTCCTTGTCTCAC 59.571 50.000 0.00 0.00 0.00 3.51
236 238 4.260784 CGCCTTTATGTGTCTGGAAATAGC 60.261 45.833 0.00 0.00 0.00 2.97
264 266 6.313658 CCTATGTCGTCATTCACTTTGATTCA 59.686 38.462 0.00 0.00 35.70 2.57
351 353 1.614903 CAAGGCCTGTTGCAGAAATGA 59.385 47.619 5.69 0.00 43.89 2.57
453 456 2.228822 GCGTTTCATGAAGGACCACAAT 59.771 45.455 8.41 0.00 0.00 2.71
454 457 3.305335 GCGTTTCATGAAGGACCACAATT 60.305 43.478 8.41 0.00 0.00 2.32
455 458 4.795962 GCGTTTCATGAAGGACCACAATTT 60.796 41.667 8.41 0.00 0.00 1.82
459 462 5.710513 TCATGAAGGACCACAATTTCTTG 57.289 39.130 0.00 0.00 38.39 3.02
474 477 8.137437 CACAATTTCTTGTAGGATGTTTCTGTT 58.863 33.333 0.00 0.00 43.76 3.16
522 525 0.608130 ACCACAGAGTGCGCAATCTA 59.392 50.000 36.48 0.00 33.56 1.98
529 532 2.428530 AGAGTGCGCAATCTATGTGAGA 59.571 45.455 36.32 0.00 42.32 3.27
530 533 2.793790 GAGTGCGCAATCTATGTGAGAG 59.206 50.000 29.00 0.00 42.32 3.20
531 534 1.260033 GTGCGCAATCTATGTGAGAGC 59.740 52.381 14.00 0.00 42.32 4.09
532 535 1.137675 TGCGCAATCTATGTGAGAGCT 59.862 47.619 8.16 0.00 42.32 4.09
533 536 2.362077 TGCGCAATCTATGTGAGAGCTA 59.638 45.455 8.16 0.00 42.32 3.32
534 537 2.985809 GCGCAATCTATGTGAGAGCTAG 59.014 50.000 0.30 0.00 42.32 3.42
535 538 2.985809 CGCAATCTATGTGAGAGCTAGC 59.014 50.000 6.62 6.62 42.32 3.42
536 539 3.551659 CGCAATCTATGTGAGAGCTAGCA 60.552 47.826 18.83 0.00 42.32 3.49
537 540 4.375272 GCAATCTATGTGAGAGCTAGCAA 58.625 43.478 18.83 0.00 37.70 3.91
538 541 4.996122 GCAATCTATGTGAGAGCTAGCAAT 59.004 41.667 18.83 4.15 37.70 3.56
539 542 5.107026 GCAATCTATGTGAGAGCTAGCAATG 60.107 44.000 18.83 0.00 37.70 2.82
540 543 5.804944 ATCTATGTGAGAGCTAGCAATGT 57.195 39.130 18.83 0.00 37.70 2.71
541 544 6.907853 ATCTATGTGAGAGCTAGCAATGTA 57.092 37.500 18.83 0.00 37.70 2.29
542 545 6.078202 TCTATGTGAGAGCTAGCAATGTAC 57.922 41.667 18.83 9.56 0.00 2.90
543 546 5.830457 TCTATGTGAGAGCTAGCAATGTACT 59.170 40.000 18.83 5.93 0.00 2.73
544 547 4.377839 TGTGAGAGCTAGCAATGTACTC 57.622 45.455 18.83 14.35 0.00 2.59
545 548 3.131223 TGTGAGAGCTAGCAATGTACTCC 59.869 47.826 18.83 9.43 0.00 3.85
546 549 2.695666 TGAGAGCTAGCAATGTACTCCC 59.304 50.000 18.83 0.00 0.00 4.30
547 550 2.962421 GAGAGCTAGCAATGTACTCCCT 59.038 50.000 18.83 0.00 0.00 4.20
548 551 2.962421 AGAGCTAGCAATGTACTCCCTC 59.038 50.000 18.83 0.50 0.00 4.30
549 552 2.036604 GAGCTAGCAATGTACTCCCTCC 59.963 54.545 18.83 0.00 0.00 4.30
550 553 1.269831 GCTAGCAATGTACTCCCTCCG 60.270 57.143 10.63 0.00 0.00 4.63
551 554 2.032620 CTAGCAATGTACTCCCTCCGT 58.967 52.381 0.00 0.00 0.00 4.69
552 555 1.276622 AGCAATGTACTCCCTCCGTT 58.723 50.000 0.00 0.00 0.00 4.44
553 556 1.207329 AGCAATGTACTCCCTCCGTTC 59.793 52.381 0.00 0.00 0.00 3.95
554 557 1.742750 GCAATGTACTCCCTCCGTTCC 60.743 57.143 0.00 0.00 0.00 3.62
555 558 1.831736 CAATGTACTCCCTCCGTTCCT 59.168 52.381 0.00 0.00 0.00 3.36
556 559 3.028850 CAATGTACTCCCTCCGTTCCTA 58.971 50.000 0.00 0.00 0.00 2.94
557 560 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
558 561 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
559 562 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
560 563 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
561 564 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
562 565 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
563 566 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
564 567 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
565 568 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
566 569 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
567 570 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
568 571 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
569 572 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
570 573 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
571 574 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
602 605 9.672673 ATTCCACTATAAACTACATATGGATGC 57.327 33.333 7.80 0.00 36.43 3.91
603 606 8.201242 TCCACTATAAACTACATATGGATGCA 57.799 34.615 7.80 0.00 36.43 3.96
604 607 8.825774 TCCACTATAAACTACATATGGATGCAT 58.174 33.333 7.80 4.68 36.43 3.96
610 613 7.834068 AAACTACATATGGATGCATATCGAC 57.166 36.000 16.09 0.00 36.43 4.20
611 614 6.530019 ACTACATATGGATGCATATCGACA 57.470 37.500 16.09 2.48 36.43 4.35
612 615 7.117285 ACTACATATGGATGCATATCGACAT 57.883 36.000 16.09 2.53 36.43 3.06
613 616 8.237811 ACTACATATGGATGCATATCGACATA 57.762 34.615 16.09 4.73 36.43 2.29
614 617 8.138074 ACTACATATGGATGCATATCGACATAC 58.862 37.037 16.09 0.00 36.43 2.39
615 618 7.117285 ACATATGGATGCATATCGACATACT 57.883 36.000 16.09 0.00 36.43 2.12
616 619 7.559486 ACATATGGATGCATATCGACATACTT 58.441 34.615 16.09 0.00 36.43 2.24
617 620 8.043113 ACATATGGATGCATATCGACATACTTT 58.957 33.333 16.09 0.00 36.43 2.66
618 621 9.533253 CATATGGATGCATATCGACATACTTTA 57.467 33.333 16.09 0.00 33.98 1.85
619 622 9.755804 ATATGGATGCATATCGACATACTTTAG 57.244 33.333 13.50 0.00 33.98 1.85
620 623 7.227049 TGGATGCATATCGACATACTTTAGA 57.773 36.000 0.00 0.00 33.98 2.10
621 624 7.315890 TGGATGCATATCGACATACTTTAGAG 58.684 38.462 0.00 0.00 33.98 2.43
622 625 7.039714 TGGATGCATATCGACATACTTTAGAGT 60.040 37.037 0.00 0.00 35.69 3.24
623 626 7.274468 GGATGCATATCGACATACTTTAGAGTG 59.726 40.741 0.00 0.00 34.37 3.51
624 627 7.039313 TGCATATCGACATACTTTAGAGTGT 57.961 36.000 0.00 0.00 36.60 3.55
625 628 8.161699 TGCATATCGACATACTTTAGAGTGTA 57.838 34.615 0.00 0.00 36.60 2.90
626 629 8.290325 TGCATATCGACATACTTTAGAGTGTAG 58.710 37.037 0.00 0.00 36.60 2.74
627 630 8.504815 GCATATCGACATACTTTAGAGTGTAGA 58.495 37.037 0.00 0.00 36.60 2.59
631 634 8.502105 TCGACATACTTTAGAGTGTAGATTCA 57.498 34.615 0.00 0.00 36.60 2.57
632 635 8.396390 TCGACATACTTTAGAGTGTAGATTCAC 58.604 37.037 0.00 0.00 36.60 3.18
643 646 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
644 647 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
645 648 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
646 649 6.003326 TGTAGATTCACTCATTTTGCTCCAA 58.997 36.000 0.00 0.00 0.00 3.53
647 650 6.489700 TGTAGATTCACTCATTTTGCTCCAAA 59.510 34.615 0.00 0.00 0.00 3.28
648 651 6.600882 AGATTCACTCATTTTGCTCCAAAT 57.399 33.333 0.00 0.00 33.19 2.32
649 652 6.395629 AGATTCACTCATTTTGCTCCAAATG 58.604 36.000 9.18 9.18 33.19 2.32
650 653 5.534207 TTCACTCATTTTGCTCCAAATGT 57.466 34.783 13.08 0.00 33.19 2.71
651 654 6.647334 TTCACTCATTTTGCTCCAAATGTA 57.353 33.333 13.08 4.05 33.19 2.29
652 655 6.258230 TCACTCATTTTGCTCCAAATGTAG 57.742 37.500 13.08 11.71 33.19 2.74
653 656 5.769662 TCACTCATTTTGCTCCAAATGTAGT 59.230 36.000 13.08 12.12 33.19 2.73
654 657 6.265196 TCACTCATTTTGCTCCAAATGTAGTT 59.735 34.615 13.08 0.02 33.19 2.24
655 658 6.583806 CACTCATTTTGCTCCAAATGTAGTTC 59.416 38.462 13.08 0.00 33.19 3.01
656 659 6.265196 ACTCATTTTGCTCCAAATGTAGTTCA 59.735 34.615 13.08 0.00 33.19 3.18
657 660 7.039504 ACTCATTTTGCTCCAAATGTAGTTCAT 60.040 33.333 13.08 0.00 38.57 2.57
658 661 8.347004 TCATTTTGCTCCAAATGTAGTTCATA 57.653 30.769 13.08 0.00 35.48 2.15
659 662 8.461222 TCATTTTGCTCCAAATGTAGTTCATAG 58.539 33.333 13.08 0.00 35.48 2.23
660 663 7.759489 TTTTGCTCCAAATGTAGTTCATAGT 57.241 32.000 0.00 0.00 35.48 2.12
661 664 6.741992 TTGCTCCAAATGTAGTTCATAGTG 57.258 37.500 0.00 0.00 35.48 2.74
662 665 6.048732 TGCTCCAAATGTAGTTCATAGTGA 57.951 37.500 0.00 0.00 35.48 3.41
663 666 6.472016 TGCTCCAAATGTAGTTCATAGTGAA 58.528 36.000 0.00 0.00 35.48 3.18
664 667 6.939730 TGCTCCAAATGTAGTTCATAGTGAAA 59.060 34.615 0.00 0.00 38.22 2.69
665 668 7.611467 TGCTCCAAATGTAGTTCATAGTGAAAT 59.389 33.333 0.00 0.00 38.22 2.17
666 669 8.125448 GCTCCAAATGTAGTTCATAGTGAAATC 58.875 37.037 0.00 0.00 38.22 2.17
667 670 9.388506 CTCCAAATGTAGTTCATAGTGAAATCT 57.611 33.333 0.00 0.00 38.22 2.40
668 671 9.383519 TCCAAATGTAGTTCATAGTGAAATCTC 57.616 33.333 0.00 0.00 38.22 2.75
669 672 9.388506 CCAAATGTAGTTCATAGTGAAATCTCT 57.611 33.333 0.00 0.00 38.22 3.10
697 700 9.907229 AAAAGACTTATATTTAGGAACTGAGGG 57.093 33.333 0.00 0.00 41.52 4.30
698 701 8.855804 AAGACTTATATTTAGGAACTGAGGGA 57.144 34.615 0.00 0.00 41.52 4.20
699 702 8.485578 AGACTTATATTTAGGAACTGAGGGAG 57.514 38.462 0.00 0.00 41.52 4.30
700 703 8.068733 AGACTTATATTTAGGAACTGAGGGAGT 58.931 37.037 0.00 0.00 41.52 3.85
701 704 9.364653 GACTTATATTTAGGAACTGAGGGAGTA 57.635 37.037 0.00 0.00 41.52 2.59
702 705 9.145442 ACTTATATTTAGGAACTGAGGGAGTAC 57.855 37.037 0.00 0.00 41.52 2.73
709 712 3.949113 GGAACTGAGGGAGTACTAGAGTG 59.051 52.174 0.00 0.00 33.09 3.51
714 717 3.267291 TGAGGGAGTACTAGAGTGCTTCT 59.733 47.826 6.09 5.47 41.05 2.85
732 735 2.032528 CCTCTTCGGCTGTTGGCA 59.967 61.111 0.00 0.00 44.01 4.92
752 756 0.877071 GCAACCACATCAGACACCAG 59.123 55.000 0.00 0.00 0.00 4.00
778 785 2.102252 GGTTTGACAACAAGCCCATCAA 59.898 45.455 0.00 0.00 46.74 2.57
883 891 1.546476 TCTCCTCAAGTCTTTCTCCGC 59.454 52.381 0.00 0.00 0.00 5.54
921 930 1.539827 CACAACCCCGGAACATTTCTC 59.460 52.381 0.73 0.00 0.00 2.87
949 958 1.214589 CTCGATCGGTTCCGGTTGT 59.785 57.895 16.41 0.00 0.00 3.32
1403 1476 0.387202 AAGCAGAGTCCCGATCGATG 59.613 55.000 18.66 7.52 0.00 3.84
1420 1497 3.374988 TCGATGAAATGCTTGCGAGATTT 59.625 39.130 4.70 7.97 0.00 2.17
1450 1536 6.790825 GGCTGCTAATTAACGACGATTATTTC 59.209 38.462 0.00 0.00 0.00 2.17
1697 1880 0.322008 CTGTTCTTGTCCCCTGCCTC 60.322 60.000 0.00 0.00 0.00 4.70
1699 1882 0.322008 GTTCTTGTCCCCTGCCTCTG 60.322 60.000 0.00 0.00 0.00 3.35
1712 1904 1.270305 TGCCTCTGTTCTCTGTTTCCG 60.270 52.381 0.00 0.00 0.00 4.30
1752 1947 1.662629 CAGAAGAGCTGTTATGTGCCG 59.337 52.381 9.92 0.00 39.85 5.69
1771 1968 1.822581 GTGCAAAGGAACACGTCAAC 58.177 50.000 0.00 0.00 0.00 3.18
1776 1973 3.181500 GCAAAGGAACACGTCAACTTCTT 60.181 43.478 0.00 0.00 0.00 2.52
1777 1974 4.034742 GCAAAGGAACACGTCAACTTCTTA 59.965 41.667 0.00 0.00 0.00 2.10
1780 1977 6.541111 AAGGAACACGTCAACTTCTTATTC 57.459 37.500 0.00 0.00 0.00 1.75
1788 1985 9.878599 ACACGTCAACTTCTTATTCTTAAATTG 57.121 29.630 0.00 0.00 0.00 2.32
1855 2096 8.369424 TGCTTACAAGTTATACAACTCTTGGTA 58.631 33.333 0.00 0.00 44.41 3.25
2022 2267 1.264288 GTGACTTCAAAGCCTCCAACG 59.736 52.381 0.00 0.00 0.00 4.10
2118 2364 1.031235 TCTGGGAACAACACGTCGTA 58.969 50.000 0.00 0.00 42.06 3.43
2147 2398 7.079700 TCCCATGACTAGAATTATTACAGGGA 58.920 38.462 0.00 0.00 36.77 4.20
2313 2591 2.094675 CGGAAGGTTCTTGGATGCATT 58.905 47.619 0.00 0.00 0.00 3.56
2391 2669 5.440234 AACATAGCTACCTATCACTGTCG 57.560 43.478 0.00 0.00 31.92 4.35
2486 2764 7.994911 TCTTTCTATGATAATGTCAACTGCCAT 59.005 33.333 0.00 0.00 40.97 4.40
2487 2765 7.500720 TTCTATGATAATGTCAACTGCCATG 57.499 36.000 0.00 0.00 40.97 3.66
2489 2767 2.355444 TGATAATGTCAACTGCCATGCG 59.645 45.455 0.00 0.00 32.78 4.73
2698 2976 0.882042 CAGCTTCGGTGTTGTGCTCT 60.882 55.000 0.00 0.00 0.00 4.09
3224 3503 5.516062 GGGAAAGAGGGGCTTAAAAGTTAGA 60.516 44.000 0.00 0.00 35.24 2.10
3243 3526 4.076175 AGAAGTATGGTAGGGGAAGTGT 57.924 45.455 0.00 0.00 0.00 3.55
3262 3547 7.280876 GGAAGTGTGCATGATTGTAGATAGAAA 59.719 37.037 0.00 0.00 0.00 2.52
3322 3608 9.961266 CGTATCACATCGTTTGTTTAGAAATTA 57.039 29.630 0.00 0.00 36.00 1.40
3330 3616 7.254852 TCGTTTGTTTAGAAATTATGGATGGC 58.745 34.615 0.00 0.00 0.00 4.40
3417 3703 6.476380 AGTTTGTTGTTCAAATATGTGTGCAG 59.524 34.615 0.00 0.00 45.88 4.41
3483 4057 6.725246 ACTTTCACTTTCAAATAGTTGGTCG 58.275 36.000 2.65 0.00 35.29 4.79
3547 4121 7.776969 AGAGGAAATTGACACATACAAGCATAT 59.223 33.333 0.00 0.00 0.00 1.78
3548 4122 8.978874 AGGAAATTGACACATACAAGCATATA 57.021 30.769 0.00 0.00 0.00 0.86
3549 4123 8.840321 AGGAAATTGACACATACAAGCATATAC 58.160 33.333 0.00 0.00 0.00 1.47
3550 4124 8.840321 GGAAATTGACACATACAAGCATATACT 58.160 33.333 0.00 0.00 0.00 2.12
3551 4125 9.869844 GAAATTGACACATACAAGCATATACTC 57.130 33.333 0.00 0.00 0.00 2.59
3552 4126 7.969536 ATTGACACATACAAGCATATACTCC 57.030 36.000 0.00 0.00 0.00 3.85
3553 4127 5.853936 TGACACATACAAGCATATACTCCC 58.146 41.667 0.00 0.00 0.00 4.30
3554 4128 5.602561 TGACACATACAAGCATATACTCCCT 59.397 40.000 0.00 0.00 0.00 4.20
3555 4129 6.102897 ACACATACAAGCATATACTCCCTC 57.897 41.667 0.00 0.00 0.00 4.30
3556 4130 5.841237 ACACATACAAGCATATACTCCCTCT 59.159 40.000 0.00 0.00 0.00 3.69
3557 4131 6.162079 CACATACAAGCATATACTCCCTCTG 58.838 44.000 0.00 0.00 0.00 3.35
3558 4132 5.841237 ACATACAAGCATATACTCCCTCTGT 59.159 40.000 0.00 0.00 0.00 3.41
3559 4133 7.010771 ACATACAAGCATATACTCCCTCTGTA 58.989 38.462 0.00 0.00 0.00 2.74
3560 4134 7.509318 ACATACAAGCATATACTCCCTCTGTAA 59.491 37.037 0.00 0.00 0.00 2.41
3561 4135 6.808321 ACAAGCATATACTCCCTCTGTAAA 57.192 37.500 0.00 0.00 0.00 2.01
3562 4136 6.583562 ACAAGCATATACTCCCTCTGTAAAC 58.416 40.000 0.00 0.00 0.00 2.01
3563 4137 6.384305 ACAAGCATATACTCCCTCTGTAAACT 59.616 38.462 0.00 0.00 0.00 2.66
3564 4138 7.563924 ACAAGCATATACTCCCTCTGTAAACTA 59.436 37.037 0.00 0.00 0.00 2.24
3565 4139 8.421784 CAAGCATATACTCCCTCTGTAAACTAA 58.578 37.037 0.00 0.00 0.00 2.24
3566 4140 8.728596 AGCATATACTCCCTCTGTAAACTAAT 57.271 34.615 0.00 0.00 0.00 1.73
3567 4141 9.824216 AGCATATACTCCCTCTGTAAACTAATA 57.176 33.333 0.00 0.00 0.00 0.98
3574 4148 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
3576 4150 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
3670 4244 5.841957 ATTAGAGGCAAAATACTGCAAGG 57.158 39.130 0.00 0.00 44.52 3.61
3764 4338 4.530710 AACAGTAATGTGTTCTAGCCGA 57.469 40.909 0.00 0.00 35.71 5.54
3892 4479 8.531622 TTTTTATCGTTCGGATGTGTACTTTA 57.468 30.769 0.00 0.00 36.55 1.85
3977 4564 6.600350 GTTTAGGCCTCGTTAAGAAAGAAAG 58.400 40.000 9.68 0.00 0.00 2.62
4024 4612 6.491745 TCTTACTAGCCAGATCGATCAGAATT 59.508 38.462 26.47 10.68 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.550842 GGCAAAAGCGAGAAACATGAAGT 60.551 43.478 0.00 0.00 0.00 3.01
137 139 7.316393 TGTTGATCATTCTAATAGGTAGGGG 57.684 40.000 0.00 0.00 0.00 4.79
155 157 5.931724 TCAACATTGTAGTCGACATGTTGAT 59.068 36.000 34.92 16.02 46.88 2.57
213 215 4.260784 GCTATTTCCAGACACATAAAGGCG 60.261 45.833 0.00 0.00 0.00 5.52
264 266 2.096248 TCACGCAAAAAGGGAGTGTTT 58.904 42.857 0.00 0.00 37.35 2.83
351 353 3.619929 GGCGTACGATAAAGTCAAATGGT 59.380 43.478 21.65 0.00 0.00 3.55
453 456 5.468746 CCGAACAGAAACATCCTACAAGAAA 59.531 40.000 0.00 0.00 0.00 2.52
454 457 4.994852 CCGAACAGAAACATCCTACAAGAA 59.005 41.667 0.00 0.00 0.00 2.52
455 458 4.566004 CCGAACAGAAACATCCTACAAGA 58.434 43.478 0.00 0.00 0.00 3.02
459 462 2.695359 TGCCGAACAGAAACATCCTAC 58.305 47.619 0.00 0.00 0.00 3.18
474 477 0.597568 CCAAACTGCTTTCATGCCGA 59.402 50.000 0.00 0.00 0.00 5.54
522 525 4.202202 GGAGTACATTGCTAGCTCTCACAT 60.202 45.833 17.23 0.00 0.00 3.21
529 532 2.043227 GGAGGGAGTACATTGCTAGCT 58.957 52.381 17.23 0.00 0.00 3.32
530 533 1.269831 CGGAGGGAGTACATTGCTAGC 60.270 57.143 8.10 8.10 0.00 3.42
531 534 2.032620 ACGGAGGGAGTACATTGCTAG 58.967 52.381 0.00 0.00 0.00 3.42
532 535 2.154567 ACGGAGGGAGTACATTGCTA 57.845 50.000 0.00 0.00 0.00 3.49
533 536 1.207329 GAACGGAGGGAGTACATTGCT 59.793 52.381 0.00 0.00 0.00 3.91
534 537 1.653151 GAACGGAGGGAGTACATTGC 58.347 55.000 0.00 0.00 0.00 3.56
535 538 1.831736 AGGAACGGAGGGAGTACATTG 59.168 52.381 0.00 0.00 0.00 2.82
536 539 2.249309 AGGAACGGAGGGAGTACATT 57.751 50.000 0.00 0.00 0.00 2.71
537 540 3.393426 TTAGGAACGGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
538 541 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
539 542 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
540 543 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
541 544 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
542 545 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
543 546 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
544 547 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
545 548 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
576 579 9.672673 GCATCCATATGTAGTTTATAGTGGAAT 57.327 33.333 1.24 0.00 37.96 3.01
577 580 8.655901 TGCATCCATATGTAGTTTATAGTGGAA 58.344 33.333 1.24 0.00 37.96 3.53
578 581 8.201242 TGCATCCATATGTAGTTTATAGTGGA 57.799 34.615 1.24 0.00 38.70 4.02
584 587 9.534565 GTCGATATGCATCCATATGTAGTTTAT 57.465 33.333 0.19 0.00 43.07 1.40
585 588 8.527810 TGTCGATATGCATCCATATGTAGTTTA 58.472 33.333 0.19 0.00 43.07 2.01
586 589 7.386059 TGTCGATATGCATCCATATGTAGTTT 58.614 34.615 0.19 0.00 43.07 2.66
587 590 6.935167 TGTCGATATGCATCCATATGTAGTT 58.065 36.000 0.19 0.00 43.07 2.24
588 591 6.530019 TGTCGATATGCATCCATATGTAGT 57.470 37.500 0.19 0.00 43.07 2.73
589 592 8.355913 AGTATGTCGATATGCATCCATATGTAG 58.644 37.037 12.40 0.00 43.07 2.74
590 593 8.237811 AGTATGTCGATATGCATCCATATGTA 57.762 34.615 12.40 0.00 43.07 2.29
591 594 7.117285 AGTATGTCGATATGCATCCATATGT 57.883 36.000 12.40 0.00 43.07 2.29
592 595 8.429493 AAAGTATGTCGATATGCATCCATATG 57.571 34.615 12.40 0.00 43.07 1.78
593 596 9.755804 CTAAAGTATGTCGATATGCATCCATAT 57.244 33.333 12.40 0.00 45.10 1.78
594 597 8.966868 TCTAAAGTATGTCGATATGCATCCATA 58.033 33.333 12.40 0.90 38.25 2.74
595 598 7.840931 TCTAAAGTATGTCGATATGCATCCAT 58.159 34.615 12.40 1.88 35.44 3.41
596 599 7.039714 ACTCTAAAGTATGTCGATATGCATCCA 60.040 37.037 12.40 0.00 32.59 3.41
597 600 7.274468 CACTCTAAAGTATGTCGATATGCATCC 59.726 40.741 12.40 0.00 33.25 3.51
598 601 7.810282 ACACTCTAAAGTATGTCGATATGCATC 59.190 37.037 12.40 0.00 33.25 3.91
599 602 7.661968 ACACTCTAAAGTATGTCGATATGCAT 58.338 34.615 12.40 3.79 33.25 3.96
600 603 7.039313 ACACTCTAAAGTATGTCGATATGCA 57.961 36.000 12.40 0.00 33.25 3.96
601 604 8.504815 TCTACACTCTAAAGTATGTCGATATGC 58.495 37.037 4.73 3.31 33.25 3.14
605 608 9.121658 TGAATCTACACTCTAAAGTATGTCGAT 57.878 33.333 0.00 0.00 33.25 3.59
606 609 8.396390 GTGAATCTACACTCTAAAGTATGTCGA 58.604 37.037 0.00 0.00 37.73 4.20
607 610 8.399425 AGTGAATCTACACTCTAAAGTATGTCG 58.601 37.037 0.00 0.00 46.36 4.35
621 624 5.412594 TGGAGCAAAATGAGTGAATCTACAC 59.587 40.000 0.00 0.00 40.60 2.90
622 625 5.559770 TGGAGCAAAATGAGTGAATCTACA 58.440 37.500 0.00 0.00 0.00 2.74
623 626 6.500684 TTGGAGCAAAATGAGTGAATCTAC 57.499 37.500 0.00 0.00 0.00 2.59
624 627 7.177216 ACATTTGGAGCAAAATGAGTGAATCTA 59.823 33.333 20.02 0.00 46.13 1.98
625 628 6.014840 ACATTTGGAGCAAAATGAGTGAATCT 60.015 34.615 20.02 0.33 46.13 2.40
626 629 6.161381 ACATTTGGAGCAAAATGAGTGAATC 58.839 36.000 20.02 0.00 46.13 2.52
627 630 6.105397 ACATTTGGAGCAAAATGAGTGAAT 57.895 33.333 20.02 1.41 46.13 2.57
628 631 5.534207 ACATTTGGAGCAAAATGAGTGAA 57.466 34.783 20.02 0.00 46.13 3.18
629 632 5.769662 ACTACATTTGGAGCAAAATGAGTGA 59.230 36.000 20.02 7.02 46.13 3.41
630 633 6.017400 ACTACATTTGGAGCAAAATGAGTG 57.983 37.500 20.02 13.37 46.13 3.51
631 634 6.265196 TGAACTACATTTGGAGCAAAATGAGT 59.735 34.615 20.02 16.01 46.13 3.41
632 635 6.680810 TGAACTACATTTGGAGCAAAATGAG 58.319 36.000 20.02 15.59 46.13 2.90
633 636 6.647334 TGAACTACATTTGGAGCAAAATGA 57.353 33.333 20.02 8.14 46.13 2.57
635 638 8.246180 CACTATGAACTACATTTGGAGCAAAAT 58.754 33.333 0.00 0.00 40.07 1.82
636 639 7.446931 TCACTATGAACTACATTTGGAGCAAAA 59.553 33.333 0.00 0.00 40.07 2.44
637 640 6.939730 TCACTATGAACTACATTTGGAGCAAA 59.060 34.615 0.00 0.00 40.07 3.68
638 641 6.472016 TCACTATGAACTACATTTGGAGCAA 58.528 36.000 0.00 0.00 40.07 3.91
639 642 6.048732 TCACTATGAACTACATTTGGAGCA 57.951 37.500 0.00 0.00 40.07 4.26
640 643 6.985188 TTCACTATGAACTACATTTGGAGC 57.015 37.500 0.00 0.00 40.07 4.70
641 644 9.388506 AGATTTCACTATGAACTACATTTGGAG 57.611 33.333 0.00 0.00 35.89 3.86
642 645 9.383519 GAGATTTCACTATGAACTACATTTGGA 57.616 33.333 0.00 0.00 35.89 3.53
643 646 9.388506 AGAGATTTCACTATGAACTACATTTGG 57.611 33.333 0.00 0.00 35.89 3.28
671 674 9.907229 CCCTCAGTTCCTAAATATAAGTCTTTT 57.093 33.333 0.00 0.00 0.00 2.27
672 675 9.280456 TCCCTCAGTTCCTAAATATAAGTCTTT 57.720 33.333 0.00 0.00 0.00 2.52
673 676 8.855804 TCCCTCAGTTCCTAAATATAAGTCTT 57.144 34.615 0.00 0.00 0.00 3.01
674 677 8.068733 ACTCCCTCAGTTCCTAAATATAAGTCT 58.931 37.037 0.00 0.00 26.56 3.24
675 678 8.252624 ACTCCCTCAGTTCCTAAATATAAGTC 57.747 38.462 0.00 0.00 26.56 3.01
676 679 9.145442 GTACTCCCTCAGTTCCTAAATATAAGT 57.855 37.037 0.00 0.00 36.43 2.24
677 680 9.369672 AGTACTCCCTCAGTTCCTAAATATAAG 57.630 37.037 0.00 0.00 36.43 1.73
680 683 8.734763 TCTAGTACTCCCTCAGTTCCTAAATAT 58.265 37.037 0.00 0.00 36.43 1.28
681 684 8.110743 TCTAGTACTCCCTCAGTTCCTAAATA 57.889 38.462 0.00 0.00 36.43 1.40
682 685 6.982899 TCTAGTACTCCCTCAGTTCCTAAAT 58.017 40.000 0.00 0.00 36.43 1.40
683 686 6.011805 ACTCTAGTACTCCCTCAGTTCCTAAA 60.012 42.308 0.00 0.00 36.43 1.85
684 687 5.491800 ACTCTAGTACTCCCTCAGTTCCTAA 59.508 44.000 0.00 0.00 36.43 2.69
685 688 5.038279 ACTCTAGTACTCCCTCAGTTCCTA 58.962 45.833 0.00 0.00 36.43 2.94
686 689 3.853784 ACTCTAGTACTCCCTCAGTTCCT 59.146 47.826 0.00 0.00 36.43 3.36
687 690 3.949113 CACTCTAGTACTCCCTCAGTTCC 59.051 52.174 0.00 0.00 36.43 3.62
688 691 3.379057 GCACTCTAGTACTCCCTCAGTTC 59.621 52.174 0.00 0.00 36.43 3.01
689 692 3.010808 AGCACTCTAGTACTCCCTCAGTT 59.989 47.826 0.00 0.00 36.43 3.16
690 693 2.578940 AGCACTCTAGTACTCCCTCAGT 59.421 50.000 0.00 0.00 39.41 3.41
691 694 3.290948 AGCACTCTAGTACTCCCTCAG 57.709 52.381 0.00 0.00 0.00 3.35
692 695 3.267291 AGAAGCACTCTAGTACTCCCTCA 59.733 47.826 0.00 0.00 30.22 3.86
693 696 3.881089 GAGAAGCACTCTAGTACTCCCTC 59.119 52.174 0.00 0.00 41.94 4.30
694 697 3.372241 GGAGAAGCACTCTAGTACTCCCT 60.372 52.174 0.00 1.51 44.37 4.20
695 698 2.953648 GGAGAAGCACTCTAGTACTCCC 59.046 54.545 0.00 0.00 44.37 4.30
696 699 3.881089 GAGGAGAAGCACTCTAGTACTCC 59.119 52.174 0.00 0.00 44.37 3.85
697 700 4.777463 AGAGGAGAAGCACTCTAGTACTC 58.223 47.826 0.00 7.90 42.00 2.59
698 701 4.855298 AGAGGAGAAGCACTCTAGTACT 57.145 45.455 0.00 0.00 42.00 2.73
699 702 4.034742 CGAAGAGGAGAAGCACTCTAGTAC 59.965 50.000 10.00 0.00 42.93 2.73
700 703 4.193090 CGAAGAGGAGAAGCACTCTAGTA 58.807 47.826 10.00 0.00 42.93 1.82
701 704 3.013921 CGAAGAGGAGAAGCACTCTAGT 58.986 50.000 10.00 0.00 42.93 2.57
702 705 2.357637 CCGAAGAGGAGAAGCACTCTAG 59.642 54.545 10.00 0.00 42.93 2.43
709 712 0.036858 AACAGCCGAAGAGGAGAAGC 60.037 55.000 0.00 0.00 45.00 3.86
714 717 2.347490 GCCAACAGCCGAAGAGGA 59.653 61.111 0.00 0.00 45.00 3.71
732 735 0.473755 TGGTGTCTGATGTGGTTGCT 59.526 50.000 0.00 0.00 0.00 3.91
752 756 0.869880 GCTTGTTGTCAAACCACGGC 60.870 55.000 0.00 0.00 35.25 5.68
778 785 4.335647 CCTTGGCTGCCAGACGGT 62.336 66.667 22.17 0.00 33.81 4.83
883 891 2.236382 GCGGATGCAAGAGAGCTCG 61.236 63.158 8.37 0.00 42.15 5.03
921 930 1.874019 CCGATCGAGCAACAGACCG 60.874 63.158 18.66 0.00 0.00 4.79
949 958 5.030147 AGGTGGATGTACTAATGGTGAAGA 58.970 41.667 0.00 0.00 0.00 2.87
982 991 4.536489 AGCCATAGGAAACAAGAACTAGGT 59.464 41.667 0.00 0.00 0.00 3.08
1104 1125 1.004440 GCTCAGGTTCTTCAGCGGT 60.004 57.895 0.00 0.00 0.00 5.68
1395 1428 1.258720 TCGCAAGCATTTCATCGATCG 59.741 47.619 9.36 9.36 37.18 3.69
1403 1476 4.672413 CCGAATAAATCTCGCAAGCATTTC 59.328 41.667 0.00 0.00 34.95 2.17
1420 1497 3.732219 CGTCGTTAATTAGCAGCCGAATA 59.268 43.478 0.06 0.00 0.00 1.75
1697 1880 4.616181 ACAAAACGGAAACAGAGAACAG 57.384 40.909 0.00 0.00 0.00 3.16
1699 1882 6.468000 CACTTAACAAAACGGAAACAGAGAAC 59.532 38.462 0.00 0.00 0.00 3.01
1712 1904 4.885325 TCTGTCCCCTTCACTTAACAAAAC 59.115 41.667 0.00 0.00 0.00 2.43
1752 1947 1.400494 AGTTGACGTGTTCCTTTGCAC 59.600 47.619 0.00 0.00 0.00 4.57
1855 2096 3.368116 GGTCAGCTACGTACTCCACATTT 60.368 47.826 0.00 0.00 0.00 2.32
2022 2267 1.897641 CTTACCGAGTCGAGCAAGAC 58.102 55.000 15.64 3.71 41.23 3.01
2118 2364 8.331931 TGTAATAATTCTAGTCATGGGAGGTT 57.668 34.615 0.00 0.00 0.00 3.50
2147 2398 7.551262 GGAACCAAGATTTAACTTTTTGTTGGT 59.449 33.333 0.00 0.00 46.53 3.67
2313 2591 7.335924 GGGCACACTGTATTTCTCAAGTTTATA 59.664 37.037 0.00 0.00 0.00 0.98
2334 2612 2.305607 TGATGTGGGGGTAGGGCAC 61.306 63.158 0.00 0.00 0.00 5.01
2391 2669 5.467063 GCAGGGTATCTATTTGTGTAAGCTC 59.533 44.000 0.00 0.00 0.00 4.09
2467 2745 3.004002 CGCATGGCAGTTGACATTATCAT 59.996 43.478 0.00 0.00 42.08 2.45
2486 2764 5.010112 TCAAATTTGGTTAGGTGAAATCGCA 59.990 36.000 17.90 0.00 0.00 5.10
2487 2765 5.465935 TCAAATTTGGTTAGGTGAAATCGC 58.534 37.500 17.90 0.00 0.00 4.58
2489 2767 8.887036 AAGTTCAAATTTGGTTAGGTGAAATC 57.113 30.769 17.90 0.00 0.00 2.17
2580 2858 1.014564 TTGTCACGTGTGTTGCGTCA 61.015 50.000 16.51 1.15 40.90 4.35
2698 2976 1.004394 TCGTCCTGAGAGTAGCTCCAA 59.996 52.381 0.00 0.00 43.26 3.53
3224 3503 2.238898 GCACACTTCCCCTACCATACTT 59.761 50.000 0.00 0.00 0.00 2.24
3272 3557 8.512956 ACGTATCACATCTCAATAGTATGTACC 58.487 37.037 0.00 0.00 32.70 3.34
3322 3608 3.690460 AGAAGAAAGAAACGCCATCCAT 58.310 40.909 0.00 0.00 0.00 3.41
3330 3616 9.374960 CACTATTTTGAAGAGAAGAAAGAAACG 57.625 33.333 0.00 0.00 0.00 3.60
3417 3703 5.645497 AGGTAGACTCATTCATTTGCAGTTC 59.355 40.000 0.00 0.00 0.00 3.01
3483 4057 5.571357 CACTTGCCAACGGTTTACAATATTC 59.429 40.000 5.95 0.00 0.00 1.75
3548 4122 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
3550 4124 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
3604 4178 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
3614 4188 9.765295 AGAAATAAGTACTCCCTCTGTAAACTA 57.235 33.333 0.00 0.00 0.00 2.24
3615 4189 8.667592 AGAAATAAGTACTCCCTCTGTAAACT 57.332 34.615 0.00 0.00 0.00 2.66
3643 4217 9.807649 CTTGCAGTATTTTGCCTCTAATATTTT 57.192 29.630 0.00 0.00 43.43 1.82
3670 4244 2.738314 GCCATCAATTTCAACTTGTGGC 59.262 45.455 14.06 14.06 40.31 5.01
3914 4501 6.260050 AGTCTTGAATTACGCTTTCACTTCAA 59.740 34.615 0.00 0.00 33.03 2.69
3958 4545 5.684550 TTTCTTTCTTTCTTAACGAGGCC 57.315 39.130 0.00 0.00 0.00 5.19
3996 4584 5.565509 TGATCGATCTGGCTAGTAAGAGAT 58.434 41.667 25.02 0.00 0.00 2.75
4006 4594 3.577848 AGCTAATTCTGATCGATCTGGCT 59.422 43.478 26.16 22.67 0.00 4.75


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

AutoCloner maintained by Alex Coulton.