Multiple sequence alignment - TraesCS6B01G393400

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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 TraesCS6B01G393400 chr6B 100.000 4734 0 0 1 4734 668251686 668246953 0.000000e+00 8743.0
1 TraesCS6B01G393400 chr6D 92.843 4569 179 66 112 4612 443850923 443846435 0.000000e+00 6490.0
2 TraesCS6B01G393400 chr6D 92.920 113 7 1 1 113 443851148 443851037 3.790000e-36 163.0
3 TraesCS6B01G393400 chr6D 97.826 46 1 0 4460 4505 363038121 363038076 3.930000e-11 80.5
4 TraesCS6B01G393400 chr6D 94.231 52 2 1 4460 4511 387886031 387886081 1.410000e-10 78.7
5 TraesCS6B01G393400 chr6D 93.182 44 3 0 4460 4503 287026459 287026502 1.100000e-06 65.8
6 TraesCS6B01G393400 chr6A 93.803 4228 134 48 426 4613 591440650 591436511 0.000000e+00 6239.0
7 TraesCS6B01G393400 chr6A 89.253 977 46 30 3595 4534 591436502 591435548 0.000000e+00 1168.0
8 TraesCS6B01G393400 chr6A 81.467 259 30 8 4292 4534 591435547 591435291 3.740000e-46 196.0
9 TraesCS6B01G393400 chr6A 82.081 173 23 5 1 170 591440971 591440804 1.780000e-29 141.0
10 TraesCS6B01G393400 chr6A 86.154 130 6 3 4290 4407 591431385 591431256 3.840000e-26 130.0
11 TraesCS6B01G393400 chr7D 90.439 2165 197 10 1059 3218 93791680 93789521 0.000000e+00 2843.0
12 TraesCS6B01G393400 chr7D 85.421 1509 198 18 1719 3219 606636159 606637653 0.000000e+00 1548.0
13 TraesCS6B01G393400 chr7D 85.984 371 50 2 3335 3704 93789522 93789153 3.430000e-106 396.0
14 TraesCS6B01G393400 chr7D 82.769 325 52 4 3355 3677 606637781 606638103 2.160000e-73 287.0
15 TraesCS6B01G393400 chr7D 78.746 287 49 8 3784 4070 93789058 93788784 1.050000e-41 182.0
16 TraesCS6B01G393400 chr7D 86.275 153 15 3 3920 4069 606638255 606638404 1.360000e-35 161.0
17 TraesCS6B01G393400 chr7D 94.118 51 2 1 4460 4510 4644034 4644083 5.080000e-10 76.8
18 TraesCS6B01G393400 chr7A 90.443 2166 195 12 1059 3218 96570516 96568357 0.000000e+00 2843.0
19 TraesCS6B01G393400 chr7A 85.620 1516 196 21 1712 3219 698679382 698677881 0.000000e+00 1572.0
20 TraesCS6B01G393400 chr7A 87.017 362 45 2 3335 3695 96568358 96567998 1.590000e-109 407.0
21 TraesCS6B01G393400 chr7A 84.641 306 45 2 3373 3677 698677728 698677424 2.140000e-78 303.0
22 TraesCS6B01G393400 chr7A 79.791 287 46 8 3784 4070 96567891 96567617 1.040000e-46 198.0
23 TraesCS6B01G393400 chr7A 86.897 145 17 2 3926 4069 698677266 698677123 1.360000e-35 161.0
24 TraesCS6B01G393400 chr7B 89.658 2166 212 12 1059 3218 47003652 47001493 0.000000e+00 2748.0
25 TraesCS6B01G393400 chr7B 85.648 1512 193 21 1717 3219 690754917 690753421 0.000000e+00 1568.0
26 TraesCS6B01G393400 chr7B 88.203 551 61 4 1168 1716 690755575 690755027 0.000000e+00 654.0
27 TraesCS6B01G393400 chr7B 87.293 362 44 2 3335 3695 47001494 47001134 3.410000e-111 412.0
28 TraesCS6B01G393400 chr7B 84.590 305 47 0 3373 3677 690753260 690752956 2.140000e-78 303.0
29 TraesCS6B01G393400 chr7B 79.791 287 46 8 3784 4070 47001005 47000731 1.040000e-46 198.0
30 TraesCS6B01G393400 chr7B 86.806 144 17 2 3928 4070 690752796 690752654 4.900000e-35 159.0
31 TraesCS6B01G393400 chr7B 92.632 95 7 0 4513 4607 620325714 620325808 2.300000e-28 137.0
32 TraesCS6B01G393400 chr7B 92.537 67 5 0 4665 4731 620325821 620325887 3.900000e-16 97.1
33 TraesCS6B01G393400 chr1D 82.934 1793 277 26 1168 2941 349794639 349792857 0.000000e+00 1589.0
34 TraesCS6B01G393400 chr1D 83.871 186 29 1 170 354 24208943 24208758 4.870000e-40 176.0
35 TraesCS6B01G393400 chr1B 82.599 1793 283 26 1168 2941 471763387 471761605 0.000000e+00 1555.0
36 TraesCS6B01G393400 chr1B 83.962 106 15 2 1 105 651876998 651877102 3.010000e-17 100.0
37 TraesCS6B01G393400 chr1A 82.524 1791 288 23 1168 2941 450096395 450094613 0.000000e+00 1550.0
38 TraesCS6B01G393400 chr2A 86.257 342 19 10 580 906 348213529 348213201 3.510000e-91 346.0
39 TraesCS6B01G393400 chr5B 92.537 67 5 0 4665 4731 633625059 633625125 3.900000e-16 97.1
40 TraesCS6B01G393400 chr2D 97.826 46 1 0 4458 4503 468866591 468866546 3.930000e-11 80.5
41 TraesCS6B01G393400 chr4A 97.778 45 1 0 4460 4504 37066315 37066359 1.410000e-10 78.7
42 TraesCS6B01G393400 chr4A 95.833 48 2 0 4460 4507 539300672 539300719 1.410000e-10 78.7
43 TraesCS6B01G393400 chr3D 95.833 48 2 0 4460 4507 526509340 526509293 1.410000e-10 78.7
44 TraesCS6B01G393400 chr2B 97.778 45 1 0 4460 4504 8499661 8499705 1.410000e-10 78.7
45 TraesCS6B01G393400 chr5D 95.745 47 2 0 4460 4506 267846640 267846594 5.080000e-10 76.8
46 TraesCS6B01G393400 chr5D 100.000 30 0 0 4403 4432 535579490 535579461 6.620000e-04 56.5
47 TraesCS6B01G393400 chr5A 100.000 31 0 0 4404 4434 634071655 634071625 1.840000e-04 58.4
48 TraesCS6B01G393400 chr4B 100.000 31 0 0 4404 4434 57444002 57443972 1.840000e-04 58.4
49 TraesCS6B01G393400 chr4B 100.000 31 0 0 4404 4434 524861293 524861323 1.840000e-04 58.4
50 TraesCS6B01G393400 chr3B 94.286 35 2 0 4396 4430 527655630 527655664 2.000000e-03 54.7


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 TraesCS6B01G393400 chr6B 668246953 668251686 4733 True 8743.000000 8743 100.000000 1 4734 1 chr6B.!!$R1 4733
1 TraesCS6B01G393400 chr6D 443846435 443851148 4713 True 3326.500000 6490 92.881500 1 4612 2 chr6D.!!$R2 4611
2 TraesCS6B01G393400 chr6A 591431256 591440971 9715 True 1574.800000 6239 86.551600 1 4613 5 chr6A.!!$R1 4612
3 TraesCS6B01G393400 chr7D 93788784 93791680 2896 True 1140.333333 2843 85.056333 1059 4070 3 chr7D.!!$R1 3011
4 TraesCS6B01G393400 chr7D 606636159 606638404 2245 False 665.333333 1548 84.821667 1719 4069 3 chr7D.!!$F2 2350
5 TraesCS6B01G393400 chr7A 96567617 96570516 2899 True 1149.333333 2843 85.750333 1059 4070 3 chr7A.!!$R1 3011
6 TraesCS6B01G393400 chr7A 698677123 698679382 2259 True 678.666667 1572 85.719333 1712 4069 3 chr7A.!!$R2 2357
7 TraesCS6B01G393400 chr7B 47000731 47003652 2921 True 1119.333333 2748 85.580667 1059 4070 3 chr7B.!!$R1 3011
8 TraesCS6B01G393400 chr7B 690752654 690755575 2921 True 671.000000 1568 86.311750 1168 4070 4 chr7B.!!$R2 2902
9 TraesCS6B01G393400 chr1D 349792857 349794639 1782 True 1589.000000 1589 82.934000 1168 2941 1 chr1D.!!$R2 1773
10 TraesCS6B01G393400 chr1B 471761605 471763387 1782 True 1555.000000 1555 82.599000 1168 2941 1 chr1B.!!$R1 1773
11 TraesCS6B01G393400 chr1A 450094613 450096395 1782 True 1550.000000 1550 82.524000 1168 2941 1 chr1A.!!$R1 1773

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
223 339 0.109342 CCAAGCCTCAGTCAACTGGT 59.891 55.000 10.13 0.00 43.91 4.00 F
502 708 1.039856 TGGAAGAAAAACCCAGCTGC 58.960 50.000 8.66 0.00 0.00 5.25 F
757 971 1.073474 TCCCTCCTCCCCATCCATG 60.073 63.158 0.00 0.00 0.00 3.66 F
1470 1723 0.466543 TGCCCGGCGACATTATTAGT 59.533 50.000 9.30 0.00 0.00 2.24 F
2085 2450 0.037303 ACAAGGACATGGTGCTCCTG 59.963 55.000 6.34 4.74 36.97 3.86 F
3232 3603 0.178978 CCCGGTACCTACCTACCTCC 60.179 65.000 10.90 0.00 44.25 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1392 1645 0.550914 TCAAGCACTTGGTCTTGGGT 59.449 50.000 10.35 0.0 39.92 4.51 R
1470 1723 1.788229 TGATGTCCCCGAGCTTGATA 58.212 50.000 1.22 0.0 0.00 2.15 R
2061 2426 1.977854 AGCACCATGTCCTTGTCTACA 59.022 47.619 0.00 0.0 0.00 2.74 R
3250 3621 0.179029 GAGAGGAGGAGGAGGAGTCG 60.179 65.000 0.00 0.0 0.00 4.18 R
3251 3622 0.185175 GGAGAGGAGGAGGAGGAGTC 59.815 65.000 0.00 0.0 0.00 3.36 R
4516 6141 0.322456 TGTACATTGTCTGCTGGGGC 60.322 55.000 0.00 0.0 39.26 5.80 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
71 72 7.995463 TTTCATAACAACCAAAGTAAAGCAC 57.005 32.000 0.00 0.00 0.00 4.40
83 84 0.180642 TAAAGCACCACACCAACGGA 59.819 50.000 0.00 0.00 0.00 4.69
164 280 7.325694 AGATCAAATAAGGACATTGGCTTTTG 58.674 34.615 0.00 0.00 0.00 2.44
168 284 7.178983 TCAAATAAGGACATTGGCTTTTGAGAT 59.821 33.333 0.00 0.00 30.72 2.75
172 288 3.259123 GGACATTGGCTTTTGAGATTGGT 59.741 43.478 0.00 0.00 0.00 3.67
178 294 2.407090 GCTTTTGAGATTGGTTGTGGC 58.593 47.619 0.00 0.00 0.00 5.01
185 301 1.282157 AGATTGGTTGTGGCTAGGTCC 59.718 52.381 0.00 0.00 0.00 4.46
187 303 0.770557 TTGGTTGTGGCTAGGTCCCT 60.771 55.000 0.00 0.00 0.00 4.20
209 325 1.066858 TCGACTGAGATCCAACCAAGC 60.067 52.381 0.00 0.00 0.00 4.01
212 328 1.280421 ACTGAGATCCAACCAAGCCTC 59.720 52.381 0.00 0.00 0.00 4.70
219 335 0.954452 CCAACCAAGCCTCAGTCAAC 59.046 55.000 0.00 0.00 0.00 3.18
223 339 0.109342 CCAAGCCTCAGTCAACTGGT 59.891 55.000 10.13 0.00 43.91 4.00
254 370 8.758715 CATACAAGAAAGAAAAAGGAAAAGCTG 58.241 33.333 0.00 0.00 0.00 4.24
258 374 8.720562 CAAGAAAGAAAAAGGAAAAGCTGAAAA 58.279 29.630 0.00 0.00 0.00 2.29
259 375 8.484641 AGAAAGAAAAAGGAAAAGCTGAAAAG 57.515 30.769 0.00 0.00 0.00 2.27
304 420 3.674682 GCAGGATCTCACGGATATAGCAC 60.675 52.174 0.00 0.00 34.33 4.40
314 430 3.562567 GGATATAGCACCGACTGAGAC 57.437 52.381 0.00 0.00 0.00 3.36
316 432 3.570550 GGATATAGCACCGACTGAGACTT 59.429 47.826 0.00 0.00 0.00 3.01
317 433 4.760715 GGATATAGCACCGACTGAGACTTA 59.239 45.833 0.00 0.00 0.00 2.24
318 434 5.241064 GGATATAGCACCGACTGAGACTTAA 59.759 44.000 0.00 0.00 0.00 1.85
319 435 2.726832 AGCACCGACTGAGACTTAAC 57.273 50.000 0.00 0.00 0.00 2.01
320 436 2.240279 AGCACCGACTGAGACTTAACT 58.760 47.619 0.00 0.00 0.00 2.24
321 437 3.418995 AGCACCGACTGAGACTTAACTA 58.581 45.455 0.00 0.00 0.00 2.24
322 438 3.825014 AGCACCGACTGAGACTTAACTAA 59.175 43.478 0.00 0.00 0.00 2.24
323 439 4.082679 AGCACCGACTGAGACTTAACTAAG 60.083 45.833 0.00 0.00 39.18 2.18
362 478 7.025963 GGATTTAGCAAGACTGTTTGAGATTG 58.974 38.462 6.82 0.00 0.00 2.67
377 493 1.713078 AGATTGCCCAAAGAACTCCCT 59.287 47.619 0.00 0.00 0.00 4.20
407 523 7.170658 ACATTCCAAAACGATTTTACCATGTTG 59.829 33.333 0.00 0.00 0.00 3.33
439 645 6.814506 AGAGAAAAGATGTTCATGTGAAGG 57.185 37.500 0.00 0.00 34.27 3.46
440 646 6.302269 AGAGAAAAGATGTTCATGTGAAGGT 58.698 36.000 0.00 0.00 34.27 3.50
502 708 1.039856 TGGAAGAAAAACCCAGCTGC 58.960 50.000 8.66 0.00 0.00 5.25
506 712 1.661509 GAAAAACCCAGCTGCGTGC 60.662 57.895 8.66 0.00 43.29 5.34
684 890 1.180029 GGCGCGGTATAAGGATCCTA 58.820 55.000 16.55 3.95 0.00 2.94
693 899 2.320830 TAAGGATCCTAGGGCGCCCA 62.321 60.000 45.13 29.46 38.92 5.36
717 931 1.270305 CCTCGTCTTCTTCAAGCACCA 60.270 52.381 0.00 0.00 0.00 4.17
752 966 3.795924 CCCCTCCCTCCTCCCCAT 61.796 72.222 0.00 0.00 0.00 4.00
753 967 2.122189 CCCTCCCTCCTCCCCATC 60.122 72.222 0.00 0.00 0.00 3.51
754 968 2.122189 CCTCCCTCCTCCCCATCC 60.122 72.222 0.00 0.00 0.00 3.51
755 969 2.705410 CTCCCTCCTCCCCATCCA 59.295 66.667 0.00 0.00 0.00 3.41
756 970 1.241327 CTCCCTCCTCCCCATCCAT 59.759 63.158 0.00 0.00 0.00 3.41
757 971 1.073474 TCCCTCCTCCCCATCCATG 60.073 63.158 0.00 0.00 0.00 3.66
758 972 1.073474 CCCTCCTCCCCATCCATGA 60.073 63.158 0.00 0.00 0.00 3.07
759 973 1.132554 CCCTCCTCCCCATCCATGAG 61.133 65.000 0.00 0.00 0.00 2.90
814 1055 3.595758 GCCACCAGCACACCACAC 61.596 66.667 0.00 0.00 42.97 3.82
1359 1612 2.654877 GAGGAGAACAACGCCGGA 59.345 61.111 5.05 0.00 43.25 5.14
1467 1720 2.177580 CGTGCCCGGCGACATTATT 61.178 57.895 9.30 0.00 0.00 1.40
1470 1723 0.466543 TGCCCGGCGACATTATTAGT 59.533 50.000 9.30 0.00 0.00 2.24
1760 2125 2.224233 ACTTCTGCATCATCTCCATCGG 60.224 50.000 0.00 0.00 0.00 4.18
2061 2426 1.005394 CGAGGTGTACGGCAAAGGT 60.005 57.895 0.00 0.00 0.00 3.50
2085 2450 0.037303 ACAAGGACATGGTGCTCCTG 59.963 55.000 6.34 4.74 36.97 3.86
2644 3012 0.671472 CAAGAGCACGGACATGAGCA 60.671 55.000 0.00 0.00 0.00 4.26
3229 3600 1.215423 TCTTCCCGGTACCTACCTACC 59.785 57.143 10.90 0.00 44.25 3.18
3230 3601 1.216427 CTTCCCGGTACCTACCTACCT 59.784 57.143 10.90 0.00 44.25 3.08
3231 3602 0.846693 TCCCGGTACCTACCTACCTC 59.153 60.000 10.90 0.00 44.25 3.85
3232 3603 0.178978 CCCGGTACCTACCTACCTCC 60.179 65.000 10.90 0.00 44.25 4.30
3233 3604 0.536006 CCGGTACCTACCTACCTCCG 60.536 65.000 10.90 0.00 44.25 4.63
3234 3605 0.469917 CGGTACCTACCTACCTCCGA 59.530 60.000 10.90 0.00 44.25 4.55
3235 3606 1.811941 CGGTACCTACCTACCTCCGAC 60.812 61.905 10.90 0.00 44.25 4.79
3236 3607 1.492599 GGTACCTACCTACCTCCGACT 59.507 57.143 4.06 0.00 43.10 4.18
3237 3608 2.486370 GGTACCTACCTACCTCCGACTC 60.486 59.091 4.06 0.00 43.10 3.36
3238 3609 1.594129 ACCTACCTACCTCCGACTCT 58.406 55.000 0.00 0.00 0.00 3.24
3239 3610 1.921748 ACCTACCTACCTCCGACTCTT 59.078 52.381 0.00 0.00 0.00 2.85
3240 3611 2.092484 ACCTACCTACCTCCGACTCTTC 60.092 54.545 0.00 0.00 0.00 2.87
3241 3612 2.173143 CCTACCTACCTCCGACTCTTCT 59.827 54.545 0.00 0.00 0.00 2.85
3242 3613 2.903375 ACCTACCTCCGACTCTTCTT 57.097 50.000 0.00 0.00 0.00 2.52
3243 3614 2.725637 ACCTACCTCCGACTCTTCTTC 58.274 52.381 0.00 0.00 0.00 2.87
3244 3615 2.309458 ACCTACCTCCGACTCTTCTTCT 59.691 50.000 0.00 0.00 0.00 2.85
3245 3616 3.245336 ACCTACCTCCGACTCTTCTTCTT 60.245 47.826 0.00 0.00 0.00 2.52
3246 3617 3.379057 CCTACCTCCGACTCTTCTTCTTC 59.621 52.174 0.00 0.00 0.00 2.87
3247 3618 2.172679 ACCTCCGACTCTTCTTCTTCC 58.827 52.381 0.00 0.00 0.00 3.46
3248 3619 2.225167 ACCTCCGACTCTTCTTCTTCCT 60.225 50.000 0.00 0.00 0.00 3.36
3249 3620 2.425668 CCTCCGACTCTTCTTCTTCCTC 59.574 54.545 0.00 0.00 0.00 3.71
3250 3621 2.425668 CTCCGACTCTTCTTCTTCCTCC 59.574 54.545 0.00 0.00 0.00 4.30
3251 3622 1.133407 CCGACTCTTCTTCTTCCTCCG 59.867 57.143 0.00 0.00 0.00 4.63
3252 3623 2.085320 CGACTCTTCTTCTTCCTCCGA 58.915 52.381 0.00 0.00 0.00 4.55
3253 3624 2.159490 CGACTCTTCTTCTTCCTCCGAC 60.159 54.545 0.00 0.00 0.00 4.79
3256 3627 2.425668 CTCTTCTTCTTCCTCCGACTCC 59.574 54.545 0.00 0.00 0.00 3.85
3263 3634 1.215679 TTCCTCCGACTCCTCCTCCT 61.216 60.000 0.00 0.00 0.00 3.69
3264 3635 1.152839 CCTCCGACTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
3279 3650 2.519541 CTCCTCTCCGGCGATCCA 60.520 66.667 9.30 0.00 0.00 3.41
3291 3662 2.233271 GGCGATCCACCATGAATGATT 58.767 47.619 0.00 0.00 0.00 2.57
3292 3663 2.030540 GGCGATCCACCATGAATGATTG 60.031 50.000 0.00 0.00 0.00 2.67
3293 3664 2.880268 GCGATCCACCATGAATGATTGA 59.120 45.455 0.00 0.00 0.00 2.57
3294 3665 3.504906 GCGATCCACCATGAATGATTGAT 59.495 43.478 0.00 0.00 0.00 2.57
3295 3666 4.022589 GCGATCCACCATGAATGATTGATT 60.023 41.667 0.00 0.00 0.00 2.57
3296 3667 5.181811 GCGATCCACCATGAATGATTGATTA 59.818 40.000 0.00 0.00 0.00 1.75
3297 3668 6.127814 GCGATCCACCATGAATGATTGATTAT 60.128 38.462 0.00 0.00 0.00 1.28
3298 3669 7.066163 GCGATCCACCATGAATGATTGATTATA 59.934 37.037 0.00 0.00 0.00 0.98
3299 3670 8.610035 CGATCCACCATGAATGATTGATTATAG 58.390 37.037 0.00 0.00 0.00 1.31
3300 3671 8.818622 ATCCACCATGAATGATTGATTATAGG 57.181 34.615 0.00 0.00 0.00 2.57
3322 3693 7.443302 AGGGAAGATAACTGAGATGATGAAA 57.557 36.000 0.00 0.00 0.00 2.69
3323 3694 8.043429 AGGGAAGATAACTGAGATGATGAAAT 57.957 34.615 0.00 0.00 0.00 2.17
3324 3695 7.937942 AGGGAAGATAACTGAGATGATGAAATG 59.062 37.037 0.00 0.00 0.00 2.32
3325 3696 7.935755 GGGAAGATAACTGAGATGATGAAATGA 59.064 37.037 0.00 0.00 0.00 2.57
3326 3697 9.334947 GGAAGATAACTGAGATGATGAAATGAA 57.665 33.333 0.00 0.00 0.00 2.57
3601 4121 0.252881 TCTCCATCTGGGCCTTCACT 60.253 55.000 4.53 0.00 36.21 3.41
3707 4235 1.606531 GCAAGCCACTCCCATCTCT 59.393 57.895 0.00 0.00 0.00 3.10
3708 4236 0.463474 GCAAGCCACTCCCATCTCTC 60.463 60.000 0.00 0.00 0.00 3.20
3715 4243 2.406559 CACTCCCATCTCTCCTCCATT 58.593 52.381 0.00 0.00 0.00 3.16
3716 4244 2.104451 CACTCCCATCTCTCCTCCATTG 59.896 54.545 0.00 0.00 0.00 2.82
3718 4246 0.110104 CCCATCTCTCCTCCATTGCC 59.890 60.000 0.00 0.00 0.00 4.52
3730 4270 0.826062 CCATTGCCCACCTCCATTTC 59.174 55.000 0.00 0.00 0.00 2.17
3731 4271 1.620524 CCATTGCCCACCTCCATTTCT 60.621 52.381 0.00 0.00 0.00 2.52
3775 4315 5.358725 TCATCTCATGTTTGTCCATGGAATG 59.641 40.000 18.20 16.08 46.21 2.67
4149 5735 6.827727 TCTACACTTCTAAGTTCTTTTGCCT 58.172 36.000 0.00 0.00 37.08 4.75
4153 5739 3.053831 TCTAAGTTCTTTTGCCTCCCG 57.946 47.619 0.00 0.00 0.00 5.14
4154 5740 2.084546 CTAAGTTCTTTTGCCTCCCGG 58.915 52.381 0.00 0.00 0.00 5.73
4187 5791 0.676782 AAGCGGGGAAGATTGGTTCG 60.677 55.000 0.00 0.00 0.00 3.95
4203 5807 0.618458 TTCGGATTCTCAGGGTTGGG 59.382 55.000 0.00 0.00 0.00 4.12
4239 5845 7.016268 TGACCTAGATGTTAAGAAGAAGTTGGT 59.984 37.037 0.00 0.00 0.00 3.67
4321 5927 5.861727 AGGAGTACGGTTTTGAGTTTATGT 58.138 37.500 0.00 0.00 0.00 2.29
4323 5929 6.426025 AGGAGTACGGTTTTGAGTTTATGTTC 59.574 38.462 0.00 0.00 0.00 3.18
4409 6027 5.907391 GTGAAACTTGTTCAAACATACTCCG 59.093 40.000 0.00 0.00 38.95 4.63
4431 6049 4.082408 CGTCCGTCCCATAATATAAGAGCA 60.082 45.833 0.00 0.00 0.00 4.26
4434 6052 7.553334 GTCCGTCCCATAATATAAGAGCATTA 58.447 38.462 0.00 0.00 0.00 1.90
4435 6053 8.038944 GTCCGTCCCATAATATAAGAGCATTAA 58.961 37.037 0.00 0.00 0.00 1.40
4436 6054 8.258007 TCCGTCCCATAATATAAGAGCATTAAG 58.742 37.037 0.00 0.00 0.00 1.85
4437 6055 7.011482 CCGTCCCATAATATAAGAGCATTAAGC 59.989 40.741 0.00 0.00 46.19 3.09
4449 6067 3.984018 GCATTAAGCGTTTAGTGTCGA 57.016 42.857 14.29 0.00 31.28 4.20
4450 6068 4.316375 GCATTAAGCGTTTAGTGTCGAA 57.684 40.909 14.29 0.00 31.28 3.71
4451 6069 4.704457 GCATTAAGCGTTTAGTGTCGAAA 58.296 39.130 14.29 0.00 31.28 3.46
4452 6070 5.141568 GCATTAAGCGTTTAGTGTCGAAAA 58.858 37.500 14.29 0.00 31.28 2.29
4461 6081 0.299597 AGTGTCGAAAACGAACGCAC 59.700 50.000 0.00 0.00 37.08 5.34
4496 6121 4.082354 ACGCTCTTATATTATGGGACGGAC 60.082 45.833 0.00 0.00 0.00 4.79
4534 6159 0.035056 AGCCCCAGCAGACAATGTAC 60.035 55.000 0.00 0.00 43.56 2.90
4552 6177 3.936453 TGTACACCAGTAATTTCATCGCC 59.064 43.478 0.00 0.00 30.67 5.54
4553 6178 2.006888 ACACCAGTAATTTCATCGCCG 58.993 47.619 0.00 0.00 0.00 6.46
4558 6183 2.540101 CAGTAATTTCATCGCCGGAGAC 59.460 50.000 11.10 0.00 0.00 3.36
4564 6189 1.226802 CATCGCCGGAGACTGTCAG 60.227 63.158 11.10 0.00 0.00 3.51
4567 6192 2.343758 GCCGGAGACTGTCAGCAA 59.656 61.111 5.05 0.00 0.00 3.91
4570 6195 1.151668 CCGGAGACTGTCAGCAAAAG 58.848 55.000 10.88 0.00 0.00 2.27
4596 6221 4.947388 AGACAGTTTAACAGAGCAAAACCA 59.053 37.500 0.00 0.00 34.39 3.67
4599 6224 3.954258 AGTTTAACAGAGCAAAACCAGCT 59.046 39.130 0.00 0.00 46.82 4.24
4608 6233 3.785486 AGCAAAACCAGCTGAAAGAAAC 58.215 40.909 17.39 0.00 41.61 2.78
4614 6239 0.961753 CAGCTGAAAGAAACCCCCAC 59.038 55.000 8.42 0.00 34.07 4.61
4615 6240 0.555769 AGCTGAAAGAAACCCCCACA 59.444 50.000 0.00 0.00 34.07 4.17
4616 6241 0.673985 GCTGAAAGAAACCCCCACAC 59.326 55.000 0.00 0.00 34.07 3.82
4619 6244 2.100749 CTGAAAGAAACCCCCACACAAC 59.899 50.000 0.00 0.00 34.07 3.32
4620 6245 1.411246 GAAAGAAACCCCCACACAACC 59.589 52.381 0.00 0.00 0.00 3.77
4622 6247 1.075896 GAAACCCCCACACAACCCA 60.076 57.895 0.00 0.00 0.00 4.51
4623 6248 0.688087 GAAACCCCCACACAACCCAA 60.688 55.000 0.00 0.00 0.00 4.12
4624 6249 0.978667 AAACCCCCACACAACCCAAC 60.979 55.000 0.00 0.00 0.00 3.77
4625 6250 2.169590 AACCCCCACACAACCCAACA 62.170 55.000 0.00 0.00 0.00 3.33
4626 6251 1.832167 CCCCCACACAACCCAACAG 60.832 63.158 0.00 0.00 0.00 3.16
4627 6252 1.228793 CCCCACACAACCCAACAGA 59.771 57.895 0.00 0.00 0.00 3.41
4628 6253 0.396417 CCCCACACAACCCAACAGAA 60.396 55.000 0.00 0.00 0.00 3.02
4629 6254 1.032014 CCCACACAACCCAACAGAAG 58.968 55.000 0.00 0.00 0.00 2.85
4630 6255 1.684869 CCCACACAACCCAACAGAAGT 60.685 52.381 0.00 0.00 0.00 3.01
4631 6256 1.405105 CCACACAACCCAACAGAAGTG 59.595 52.381 0.00 0.00 0.00 3.16
4632 6257 1.102978 ACACAACCCAACAGAAGTGC 58.897 50.000 0.00 0.00 0.00 4.40
4633 6258 0.385390 CACAACCCAACAGAAGTGCC 59.615 55.000 0.00 0.00 0.00 5.01
4634 6259 1.101049 ACAACCCAACAGAAGTGCCG 61.101 55.000 0.00 0.00 0.00 5.69
4635 6260 1.101049 CAACCCAACAGAAGTGCCGT 61.101 55.000 0.00 0.00 0.00 5.68
4636 6261 1.101049 AACCCAACAGAAGTGCCGTG 61.101 55.000 0.00 0.00 0.00 4.94
4637 6262 2.260869 CCCAACAGAAGTGCCGTGG 61.261 63.158 0.00 0.00 0.00 4.94
4639 6264 0.606401 CCAACAGAAGTGCCGTGGAT 60.606 55.000 0.00 0.00 0.00 3.41
4640 6265 0.798776 CAACAGAAGTGCCGTGGATC 59.201 55.000 0.00 0.00 0.00 3.36
4641 6266 0.396435 AACAGAAGTGCCGTGGATCA 59.604 50.000 0.00 0.00 0.00 2.92
4643 6268 1.081892 CAGAAGTGCCGTGGATCAAG 58.918 55.000 0.00 0.00 0.00 3.02
4646 6271 2.151202 GAAGTGCCGTGGATCAAGAAA 58.849 47.619 0.00 0.00 0.00 2.52
4647 6272 1.813513 AGTGCCGTGGATCAAGAAAG 58.186 50.000 0.00 0.00 0.00 2.62
4648 6273 0.804989 GTGCCGTGGATCAAGAAAGG 59.195 55.000 0.00 0.00 0.00 3.11
4649 6274 0.400213 TGCCGTGGATCAAGAAAGGT 59.600 50.000 0.00 0.00 0.00 3.50
4651 6276 2.039216 TGCCGTGGATCAAGAAAGGTTA 59.961 45.455 0.00 0.00 0.00 2.85
4652 6277 2.678336 GCCGTGGATCAAGAAAGGTTAG 59.322 50.000 0.00 0.00 0.00 2.34
4653 6278 2.678336 CCGTGGATCAAGAAAGGTTAGC 59.322 50.000 0.00 0.00 0.00 3.09
4655 6280 3.941483 CGTGGATCAAGAAAGGTTAGCAT 59.059 43.478 0.00 0.00 0.00 3.79
4657 6282 4.034510 GTGGATCAAGAAAGGTTAGCATCG 59.965 45.833 0.00 0.00 0.00 3.84
4658 6283 3.002759 GGATCAAGAAAGGTTAGCATCGC 59.997 47.826 0.00 0.00 0.00 4.58
4659 6284 3.334583 TCAAGAAAGGTTAGCATCGCT 57.665 42.857 0.00 0.00 43.41 4.93
4660 6285 3.674997 TCAAGAAAGGTTAGCATCGCTT 58.325 40.909 0.00 0.00 40.44 4.68
4661 6286 3.436704 TCAAGAAAGGTTAGCATCGCTTG 59.563 43.478 0.00 0.00 40.44 4.01
4662 6287 3.334583 AGAAAGGTTAGCATCGCTTGA 57.665 42.857 0.00 0.00 40.44 3.02
4663 6288 3.674997 AGAAAGGTTAGCATCGCTTGAA 58.325 40.909 0.00 0.00 40.44 2.69
4664 6289 3.437049 AGAAAGGTTAGCATCGCTTGAAC 59.563 43.478 0.00 0.00 40.44 3.18
4665 6290 2.472695 AGGTTAGCATCGCTTGAACA 57.527 45.000 0.00 0.00 40.44 3.18
4667 6292 1.804151 GGTTAGCATCGCTTGAACACA 59.196 47.619 0.00 0.00 40.44 3.72
4670 6295 2.455674 AGCATCGCTTGAACACAGTA 57.544 45.000 0.00 0.00 33.89 2.74
4671 6296 2.341257 AGCATCGCTTGAACACAGTAG 58.659 47.619 0.00 0.00 33.89 2.57
4673 6298 1.394917 CATCGCTTGAACACAGTAGCC 59.605 52.381 0.00 0.00 0.00 3.93
4675 6300 1.071605 CGCTTGAACACAGTAGCCTC 58.928 55.000 0.00 0.00 0.00 4.70
4677 6302 2.072298 GCTTGAACACAGTAGCCTCAG 58.928 52.381 0.00 0.00 0.00 3.35
4679 6304 3.583806 CTTGAACACAGTAGCCTCAGAG 58.416 50.000 0.00 0.00 0.00 3.35
4680 6305 1.273606 TGAACACAGTAGCCTCAGAGC 59.726 52.381 0.00 0.00 0.00 4.09
4682 6307 1.342074 ACACAGTAGCCTCAGAGCAA 58.658 50.000 0.00 0.00 34.23 3.91
4683 6308 1.905215 ACACAGTAGCCTCAGAGCAAT 59.095 47.619 0.00 0.00 34.23 3.56
4684 6309 2.093764 ACACAGTAGCCTCAGAGCAATC 60.094 50.000 0.00 0.00 34.23 2.67
4686 6311 3.382865 CACAGTAGCCTCAGAGCAATCTA 59.617 47.826 0.00 0.00 34.23 1.98
4687 6312 4.026744 ACAGTAGCCTCAGAGCAATCTAA 58.973 43.478 0.00 0.00 34.23 2.10
4688 6313 4.467795 ACAGTAGCCTCAGAGCAATCTAAA 59.532 41.667 0.00 0.00 34.23 1.85
4689 6314 5.049167 CAGTAGCCTCAGAGCAATCTAAAG 58.951 45.833 0.00 0.00 34.23 1.85
4690 6315 3.557228 AGCCTCAGAGCAATCTAAAGG 57.443 47.619 0.00 0.00 34.23 3.11
4691 6316 3.110705 AGCCTCAGAGCAATCTAAAGGA 58.889 45.455 9.08 0.00 34.23 3.36
4692 6317 3.521126 AGCCTCAGAGCAATCTAAAGGAA 59.479 43.478 9.08 0.00 34.23 3.36
4693 6318 3.625313 GCCTCAGAGCAATCTAAAGGAAC 59.375 47.826 9.08 0.00 0.00 3.62
4694 6319 6.810312 AGCCTCAGAGCAATCTAAAGGAACT 61.810 44.000 9.08 0.00 35.52 3.01
4695 6320 5.115480 CCTCAGAGCAATCTAAAGGAACTC 58.885 45.833 0.00 0.00 38.49 3.01
4696 6321 5.337894 CCTCAGAGCAATCTAAAGGAACTCA 60.338 44.000 0.00 0.00 38.49 3.41
4697 6322 6.114187 TCAGAGCAATCTAAAGGAACTCAA 57.886 37.500 0.00 0.00 38.49 3.02
4699 6324 6.998074 TCAGAGCAATCTAAAGGAACTCAAAA 59.002 34.615 0.00 0.00 38.49 2.44
4700 6325 7.041098 TCAGAGCAATCTAAAGGAACTCAAAAC 60.041 37.037 0.00 0.00 38.49 2.43
4701 6326 6.772716 AGAGCAATCTAAAGGAACTCAAAACA 59.227 34.615 0.00 0.00 38.49 2.83
4702 6327 6.974965 AGCAATCTAAAGGAACTCAAAACAG 58.025 36.000 0.00 0.00 38.49 3.16
4704 6329 6.681777 CAATCTAAAGGAACTCAAAACAGGG 58.318 40.000 0.00 0.00 38.49 4.45
4705 6330 4.725490 TCTAAAGGAACTCAAAACAGGGG 58.275 43.478 0.00 0.00 38.49 4.79
4707 6332 4.529716 AAAGGAACTCAAAACAGGGGTA 57.470 40.909 0.00 0.00 38.49 3.69
4709 6334 2.781174 AGGAACTCAAAACAGGGGTACA 59.219 45.455 0.00 0.00 0.00 2.90
4710 6335 3.146847 GGAACTCAAAACAGGGGTACAG 58.853 50.000 0.00 0.00 0.00 2.74
4711 6336 3.181448 GGAACTCAAAACAGGGGTACAGA 60.181 47.826 0.00 0.00 0.00 3.41
4712 6337 3.771577 ACTCAAAACAGGGGTACAGAG 57.228 47.619 0.00 0.00 0.00 3.35
4713 6338 3.314693 ACTCAAAACAGGGGTACAGAGA 58.685 45.455 0.00 0.00 0.00 3.10
4714 6339 3.714798 ACTCAAAACAGGGGTACAGAGAA 59.285 43.478 0.00 0.00 0.00 2.87
4716 6341 4.714632 TCAAAACAGGGGTACAGAGAAAG 58.285 43.478 0.00 0.00 0.00 2.62
4717 6342 2.861147 AACAGGGGTACAGAGAAAGC 57.139 50.000 0.00 0.00 0.00 3.51
4718 6343 1.729586 ACAGGGGTACAGAGAAAGCA 58.270 50.000 0.00 0.00 0.00 3.91
4719 6344 2.054799 ACAGGGGTACAGAGAAAGCAA 58.945 47.619 0.00 0.00 0.00 3.91
4721 6346 3.074538 ACAGGGGTACAGAGAAAGCAAAT 59.925 43.478 0.00 0.00 0.00 2.32
4723 6348 4.156739 CAGGGGTACAGAGAAAGCAAATTC 59.843 45.833 0.00 0.00 0.00 2.17
4724 6349 3.127030 GGGGTACAGAGAAAGCAAATTCG 59.873 47.826 0.00 0.00 34.46 3.34
4726 6351 3.437049 GGTACAGAGAAAGCAAATTCGCT 59.563 43.478 0.00 0.00 46.67 4.93
4728 6353 2.860062 CAGAGAAAGCAAATTCGCTGG 58.140 47.619 17.03 5.09 46.81 4.85
4730 6355 2.485814 AGAGAAAGCAAATTCGCTGGAC 59.514 45.455 0.00 0.00 42.89 4.02
4731 6356 2.226437 GAGAAAGCAAATTCGCTGGACA 59.774 45.455 0.00 0.00 42.89 4.02
4732 6357 2.030805 AGAAAGCAAATTCGCTGGACAC 60.031 45.455 0.00 0.00 42.89 3.67
4733 6358 1.317613 AAGCAAATTCGCTGGACACA 58.682 45.000 0.00 0.00 42.89 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 2.429250 GGTGTGGTGCTTTACTTTGGTT 59.571 45.455 0.00 0.00 0.00 3.67
71 72 1.470112 GGTTGTTTTCCGTTGGTGTGG 60.470 52.381 0.00 0.00 0.00 4.17
83 84 1.314730 AAGATCGTGCCGGTTGTTTT 58.685 45.000 1.90 0.00 0.00 2.43
127 243 7.548075 GTCCTTATTTGATCTTTGTCGGAACTA 59.452 37.037 0.00 0.00 0.00 2.24
133 249 6.968904 CCAATGTCCTTATTTGATCTTTGTCG 59.031 38.462 0.00 0.00 0.00 4.35
164 280 2.633488 GACCTAGCCACAACCAATCTC 58.367 52.381 0.00 0.00 0.00 2.75
168 284 0.770557 AGGGACCTAGCCACAACCAA 60.771 55.000 0.00 0.00 0.00 3.67
172 288 1.541310 CGACAGGGACCTAGCCACAA 61.541 60.000 0.00 0.00 0.00 3.33
178 294 1.065345 TCTCAGTCGACAGGGACCTAG 60.065 57.143 19.50 2.02 37.66 3.02
185 301 1.134965 GGTTGGATCTCAGTCGACAGG 60.135 57.143 19.50 9.68 0.00 4.00
187 303 1.627864 TGGTTGGATCTCAGTCGACA 58.372 50.000 19.50 0.00 0.00 4.35
209 325 6.873997 TGTATGTTATACCAGTTGACTGAGG 58.126 40.000 12.54 0.00 46.59 3.86
212 328 8.771920 TTCTTGTATGTTATACCAGTTGACTG 57.228 34.615 4.15 4.15 43.40 3.51
254 370 6.769608 AGATCCGTGCAAAATTTTCTTTTC 57.230 33.333 0.00 0.00 0.00 2.29
258 374 6.311200 GCATTAAGATCCGTGCAAAATTTTCT 59.689 34.615 0.00 0.00 37.52 2.52
259 375 6.090628 TGCATTAAGATCCGTGCAAAATTTTC 59.909 34.615 0.00 0.00 43.83 2.29
285 401 2.159366 CGGTGCTATATCCGTGAGATCC 60.159 54.545 0.00 0.00 41.58 3.36
314 430 9.892130 ATCCCAGTCAATTAAGACTTAGTTAAG 57.108 33.333 2.95 0.00 46.26 1.85
318 434 9.892130 CTAAATCCCAGTCAATTAAGACTTAGT 57.108 33.333 0.00 0.00 46.26 2.24
319 435 8.831550 GCTAAATCCCAGTCAATTAAGACTTAG 58.168 37.037 0.00 0.00 46.26 2.18
320 436 8.325787 TGCTAAATCCCAGTCAATTAAGACTTA 58.674 33.333 0.00 0.00 46.26 2.24
321 437 7.175104 TGCTAAATCCCAGTCAATTAAGACTT 58.825 34.615 0.00 0.00 46.26 3.01
323 439 7.336931 TCTTGCTAAATCCCAGTCAATTAAGAC 59.663 37.037 0.00 0.00 38.81 3.01
324 440 7.336931 GTCTTGCTAAATCCCAGTCAATTAAGA 59.663 37.037 0.00 0.00 0.00 2.10
325 441 7.337942 AGTCTTGCTAAATCCCAGTCAATTAAG 59.662 37.037 0.00 0.00 0.00 1.85
326 442 7.121168 CAGTCTTGCTAAATCCCAGTCAATTAA 59.879 37.037 0.00 0.00 0.00 1.40
327 443 6.599244 CAGTCTTGCTAAATCCCAGTCAATTA 59.401 38.462 0.00 0.00 0.00 1.40
328 444 5.416952 CAGTCTTGCTAAATCCCAGTCAATT 59.583 40.000 0.00 0.00 0.00 2.32
329 445 4.946157 CAGTCTTGCTAAATCCCAGTCAAT 59.054 41.667 0.00 0.00 0.00 2.57
337 453 6.749923 ATCTCAAACAGTCTTGCTAAATCC 57.250 37.500 0.00 0.00 0.00 3.01
362 478 2.160205 GTTGTAGGGAGTTCTTTGGGC 58.840 52.381 0.00 0.00 0.00 5.36
377 493 7.713750 TGGTAAAATCGTTTTGGAATGTTGTA 58.286 30.769 6.13 0.00 34.19 2.41
439 645 1.340017 ACCATCACATAGCCCACACAC 60.340 52.381 0.00 0.00 0.00 3.82
440 646 0.991146 ACCATCACATAGCCCACACA 59.009 50.000 0.00 0.00 0.00 3.72
662 868 0.317479 GATCCTTATACCGCGCCACT 59.683 55.000 0.00 0.00 0.00 4.00
693 899 1.273886 GCTTGAAGAAGACGAGGAGGT 59.726 52.381 0.00 0.00 0.00 3.85
746 960 0.567687 TAGGAGCTCATGGATGGGGA 59.432 55.000 17.19 0.00 0.00 4.81
747 961 1.072965 GTTAGGAGCTCATGGATGGGG 59.927 57.143 17.19 0.00 0.00 4.96
748 962 1.072965 GGTTAGGAGCTCATGGATGGG 59.927 57.143 17.19 0.00 0.00 4.00
749 963 1.072965 GGGTTAGGAGCTCATGGATGG 59.927 57.143 17.19 0.00 0.00 3.51
750 964 1.072965 GGGGTTAGGAGCTCATGGATG 59.927 57.143 17.19 0.00 0.00 3.51
751 965 1.439543 GGGGTTAGGAGCTCATGGAT 58.560 55.000 17.19 0.00 0.00 3.41
752 966 0.694444 GGGGGTTAGGAGCTCATGGA 60.694 60.000 17.19 0.00 0.00 3.41
753 967 1.839894 GGGGGTTAGGAGCTCATGG 59.160 63.158 17.19 0.00 0.00 3.66
810 1051 2.670934 GGGCTGAGCTGTGGTGTG 60.671 66.667 3.72 0.00 0.00 3.82
811 1052 3.170672 TGGGCTGAGCTGTGGTGT 61.171 61.111 3.72 0.00 0.00 4.16
812 1053 2.670934 GTGGGCTGAGCTGTGGTG 60.671 66.667 3.72 0.00 0.00 4.17
813 1054 3.958860 GGTGGGCTGAGCTGTGGT 61.959 66.667 3.72 0.00 0.00 4.16
814 1055 3.914579 CTGGTGGGCTGAGCTGTGG 62.915 68.421 3.72 0.00 0.00 4.17
843 1084 4.648626 TGCTGCTGCTGGTGGTCC 62.649 66.667 17.00 0.00 40.48 4.46
1392 1645 0.550914 TCAAGCACTTGGTCTTGGGT 59.449 50.000 10.35 0.00 39.92 4.51
1464 1717 4.476297 TGTCCCCGAGCTTGATACTAATA 58.524 43.478 1.22 0.00 0.00 0.98
1467 1720 2.447408 TGTCCCCGAGCTTGATACTA 57.553 50.000 1.22 0.00 0.00 1.82
1470 1723 1.788229 TGATGTCCCCGAGCTTGATA 58.212 50.000 1.22 0.00 0.00 2.15
2061 2426 1.977854 AGCACCATGTCCTTGTCTACA 59.022 47.619 0.00 0.00 0.00 2.74
2553 2921 2.586357 GCCGTCTCCTTGCCGATC 60.586 66.667 0.00 0.00 0.00 3.69
2644 3012 2.835431 CTCGTCGATGGGGAGGCT 60.835 66.667 4.48 0.00 0.00 4.58
3229 3600 2.425668 GGAGGAAGAAGAAGAGTCGGAG 59.574 54.545 0.00 0.00 0.00 4.63
3230 3601 2.448453 GGAGGAAGAAGAAGAGTCGGA 58.552 52.381 0.00 0.00 0.00 4.55
3231 3602 1.133407 CGGAGGAAGAAGAAGAGTCGG 59.867 57.143 0.00 0.00 0.00 4.79
3232 3603 2.085320 TCGGAGGAAGAAGAAGAGTCG 58.915 52.381 0.00 0.00 0.00 4.18
3233 3604 3.086282 AGTCGGAGGAAGAAGAAGAGTC 58.914 50.000 0.00 0.00 0.00 3.36
3234 3605 3.086282 GAGTCGGAGGAAGAAGAAGAGT 58.914 50.000 0.00 0.00 0.00 3.24
3235 3606 2.425668 GGAGTCGGAGGAAGAAGAAGAG 59.574 54.545 0.00 0.00 0.00 2.85
3236 3607 2.041891 AGGAGTCGGAGGAAGAAGAAGA 59.958 50.000 0.00 0.00 0.00 2.87
3237 3608 2.425668 GAGGAGTCGGAGGAAGAAGAAG 59.574 54.545 0.00 0.00 0.00 2.85
3238 3609 2.448453 GAGGAGTCGGAGGAAGAAGAA 58.552 52.381 0.00 0.00 0.00 2.52
3239 3610 1.341187 GGAGGAGTCGGAGGAAGAAGA 60.341 57.143 0.00 0.00 0.00 2.87
3240 3611 1.107945 GGAGGAGTCGGAGGAAGAAG 58.892 60.000 0.00 0.00 0.00 2.85
3241 3612 0.705253 AGGAGGAGTCGGAGGAAGAA 59.295 55.000 0.00 0.00 0.00 2.52
3242 3613 0.256464 GAGGAGGAGTCGGAGGAAGA 59.744 60.000 0.00 0.00 0.00 2.87
3243 3614 0.753848 GGAGGAGGAGTCGGAGGAAG 60.754 65.000 0.00 0.00 0.00 3.46
3244 3615 1.215679 AGGAGGAGGAGTCGGAGGAA 61.216 60.000 0.00 0.00 0.00 3.36
3245 3616 1.619975 AGGAGGAGGAGTCGGAGGA 60.620 63.158 0.00 0.00 0.00 3.71
3246 3617 1.152839 GAGGAGGAGGAGTCGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
3247 3618 1.152839 GGAGGAGGAGGAGTCGGAG 60.153 68.421 0.00 0.00 0.00 4.63
3248 3619 1.619975 AGGAGGAGGAGGAGTCGGA 60.620 63.158 0.00 0.00 0.00 4.55
3249 3620 1.152839 GAGGAGGAGGAGGAGTCGG 60.153 68.421 0.00 0.00 0.00 4.79
3250 3621 0.179029 GAGAGGAGGAGGAGGAGTCG 60.179 65.000 0.00 0.00 0.00 4.18
3251 3622 0.185175 GGAGAGGAGGAGGAGGAGTC 59.815 65.000 0.00 0.00 0.00 3.36
3252 3623 1.641552 CGGAGAGGAGGAGGAGGAGT 61.642 65.000 0.00 0.00 0.00 3.85
3253 3624 1.150536 CGGAGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
3256 3627 2.520741 GCCGGAGAGGAGGAGGAG 60.521 72.222 5.05 0.00 45.00 3.69
3263 3634 2.833582 GTGGATCGCCGGAGAGGA 60.834 66.667 14.81 0.38 45.00 3.71
3264 3635 3.917760 GGTGGATCGCCGGAGAGG 61.918 72.222 14.81 0.00 44.97 3.69
3279 3650 8.672329 TCTTCCCTATAATCAATCATTCATGGT 58.328 33.333 0.00 0.00 0.00 3.55
3291 3662 9.828691 TCATCTCAGTTATCTTCCCTATAATCA 57.171 33.333 0.00 0.00 0.00 2.57
3294 3665 9.828691 TCATCATCTCAGTTATCTTCCCTATAA 57.171 33.333 0.00 0.00 0.00 0.98
3295 3666 9.828691 TTCATCATCTCAGTTATCTTCCCTATA 57.171 33.333 0.00 0.00 0.00 1.31
3296 3667 8.733092 TTCATCATCTCAGTTATCTTCCCTAT 57.267 34.615 0.00 0.00 0.00 2.57
3297 3668 8.553085 TTTCATCATCTCAGTTATCTTCCCTA 57.447 34.615 0.00 0.00 0.00 3.53
3298 3669 7.443302 TTTCATCATCTCAGTTATCTTCCCT 57.557 36.000 0.00 0.00 0.00 4.20
3299 3670 7.935755 TCATTTCATCATCTCAGTTATCTTCCC 59.064 37.037 0.00 0.00 0.00 3.97
3300 3671 8.899427 TCATTTCATCATCTCAGTTATCTTCC 57.101 34.615 0.00 0.00 0.00 3.46
3313 3684 7.222224 GTCTCCTGCATTTTTCATTTCATCATC 59.778 37.037 0.00 0.00 0.00 2.92
3318 3689 4.278170 ACGTCTCCTGCATTTTTCATTTCA 59.722 37.500 0.00 0.00 0.00 2.69
3322 3693 3.120199 CGAACGTCTCCTGCATTTTTCAT 60.120 43.478 0.00 0.00 0.00 2.57
3323 3694 2.223144 CGAACGTCTCCTGCATTTTTCA 59.777 45.455 0.00 0.00 0.00 2.69
3324 3695 2.412847 CCGAACGTCTCCTGCATTTTTC 60.413 50.000 0.00 0.00 0.00 2.29
3325 3696 1.535462 CCGAACGTCTCCTGCATTTTT 59.465 47.619 0.00 0.00 0.00 1.94
3326 3697 1.156736 CCGAACGTCTCCTGCATTTT 58.843 50.000 0.00 0.00 0.00 1.82
3327 3698 0.673644 CCCGAACGTCTCCTGCATTT 60.674 55.000 0.00 0.00 0.00 2.32
3328 3699 1.079127 CCCGAACGTCTCCTGCATT 60.079 57.895 0.00 0.00 0.00 3.56
3707 4235 2.308722 GGAGGTGGGCAATGGAGGA 61.309 63.158 0.00 0.00 0.00 3.71
3708 4236 1.941403 ATGGAGGTGGGCAATGGAGG 61.941 60.000 0.00 0.00 0.00 4.30
3715 4243 1.340991 GCTTAGAAATGGAGGTGGGCA 60.341 52.381 0.00 0.00 0.00 5.36
3716 4244 1.064389 AGCTTAGAAATGGAGGTGGGC 60.064 52.381 0.00 0.00 0.00 5.36
3718 4246 2.239654 TGGAGCTTAGAAATGGAGGTGG 59.760 50.000 0.00 0.00 0.00 4.61
3775 4315 1.087501 GAAGGCCGTCTGTTGGATTC 58.912 55.000 11.87 0.00 0.00 2.52
3777 4317 0.321653 GTGAAGGCCGTCTGTTGGAT 60.322 55.000 19.81 0.00 0.00 3.41
3778 4318 1.070786 GTGAAGGCCGTCTGTTGGA 59.929 57.895 19.81 0.00 0.00 3.53
3779 4319 1.966451 GGTGAAGGCCGTCTGTTGG 60.966 63.158 19.81 0.00 0.00 3.77
3780 4320 0.817634 TTGGTGAAGGCCGTCTGTTG 60.818 55.000 19.81 0.00 0.00 3.33
3781 4321 0.818040 GTTGGTGAAGGCCGTCTGTT 60.818 55.000 19.81 0.00 0.00 3.16
4078 5664 2.716244 CGACGAGGAGGATGGTCG 59.284 66.667 0.00 0.00 43.28 4.79
4079 5665 1.728672 GACGACGAGGAGGATGGTC 59.271 63.158 0.00 0.00 0.00 4.02
4080 5666 2.113433 CGACGACGAGGAGGATGGT 61.113 63.158 0.00 0.00 42.66 3.55
4081 5667 2.716244 CGACGACGAGGAGGATGG 59.284 66.667 0.00 0.00 42.66 3.51
4082 5668 2.716244 CCGACGACGAGGAGGATG 59.284 66.667 9.28 0.00 42.66 3.51
4083 5669 3.210528 GCCGACGACGAGGAGGAT 61.211 66.667 9.28 0.00 42.66 3.24
4111 5697 0.668535 TGTAGATATCGCTGCGCTGT 59.331 50.000 18.65 5.90 0.00 4.40
4112 5698 1.056103 GTGTAGATATCGCTGCGCTG 58.944 55.000 18.65 10.04 0.00 5.18
4113 5699 0.955178 AGTGTAGATATCGCTGCGCT 59.045 50.000 18.65 10.91 36.68 5.92
4114 5700 1.716581 GAAGTGTAGATATCGCTGCGC 59.283 52.381 18.65 0.00 0.00 6.09
4115 5701 3.275400 AGAAGTGTAGATATCGCTGCG 57.725 47.619 17.25 17.25 0.00 5.18
4132 5718 3.408634 CGGGAGGCAAAAGAACTTAGAA 58.591 45.455 0.00 0.00 0.00 2.10
4153 5739 4.168291 CTTCCAGCCTCCCTCGCC 62.168 72.222 0.00 0.00 0.00 5.54
4154 5740 4.847444 GCTTCCAGCCTCCCTCGC 62.847 72.222 0.00 0.00 34.48 5.03
4168 5772 0.676782 CGAACCAATCTTCCCCGCTT 60.677 55.000 0.00 0.00 0.00 4.68
4187 5791 2.604912 AAACCCAACCCTGAGAATCC 57.395 50.000 0.00 0.00 0.00 3.01
4239 5845 8.371699 CCTCCCCACTGAAAAATACAAATAAAA 58.628 33.333 0.00 0.00 0.00 1.52
4321 5927 9.840427 GCTAACATATTACAAGCAAAAGAAGAA 57.160 29.630 0.00 0.00 33.38 2.52
4323 5929 7.962918 ACGCTAACATATTACAAGCAAAAGAAG 59.037 33.333 0.00 0.00 32.69 2.85
4409 6027 5.401531 TGCTCTTATATTATGGGACGGAC 57.598 43.478 0.00 0.00 0.00 4.79
4431 6049 5.368374 CGTTTTCGACACTAAACGCTTAAT 58.632 37.500 16.96 0.00 46.45 1.40
4434 6052 3.228878 CGTTTTCGACACTAAACGCTT 57.771 42.857 16.96 0.00 46.45 4.68
4435 6053 2.916735 CGTTTTCGACACTAAACGCT 57.083 45.000 16.96 0.00 46.45 5.07
4447 6065 1.519758 ACACTAGTGCGTTCGTTTTCG 59.480 47.619 22.90 0.00 45.64 3.46
4449 6067 5.467902 TTTAACACTAGTGCGTTCGTTTT 57.532 34.783 22.90 9.29 0.00 2.43
4450 6068 5.467902 TTTTAACACTAGTGCGTTCGTTT 57.532 34.783 22.90 10.00 0.00 3.60
4451 6069 5.257864 GTTTTTAACACTAGTGCGTTCGTT 58.742 37.500 22.90 10.70 0.00 3.85
4452 6070 4.548726 CGTTTTTAACACTAGTGCGTTCGT 60.549 41.667 22.90 0.00 0.00 3.85
4456 6074 2.867975 AGCGTTTTTAACACTAGTGCGT 59.132 40.909 22.90 13.34 0.00 5.24
4457 6075 3.183775 AGAGCGTTTTTAACACTAGTGCG 59.816 43.478 22.90 16.17 0.00 5.34
4458 6076 4.727235 AGAGCGTTTTTAACACTAGTGC 57.273 40.909 22.90 5.36 0.00 4.40
4468 6088 7.385752 CCGTCCCATAATATAAGAGCGTTTTTA 59.614 37.037 0.00 0.00 0.00 1.52
4475 6095 4.421948 CGTCCGTCCCATAATATAAGAGC 58.578 47.826 0.00 0.00 0.00 4.09
4516 6141 0.322456 TGTACATTGTCTGCTGGGGC 60.322 55.000 0.00 0.00 39.26 5.80
4534 6159 1.330521 CCGGCGATGAAATTACTGGTG 59.669 52.381 9.30 0.00 0.00 4.17
4552 6177 2.064762 CTCTTTTGCTGACAGTCTCCG 58.935 52.381 3.99 0.00 0.00 4.63
4553 6178 3.006323 TCTCTCTTTTGCTGACAGTCTCC 59.994 47.826 3.99 0.00 0.00 3.71
4564 6189 6.604735 TCTGTTAAACTGTCTCTCTTTTGC 57.395 37.500 0.00 0.00 0.00 3.68
4567 6192 5.918608 TGCTCTGTTAAACTGTCTCTCTTT 58.081 37.500 0.00 0.00 0.00 2.52
4570 6195 6.423042 GTTTTGCTCTGTTAAACTGTCTCTC 58.577 40.000 0.00 0.00 0.00 3.20
4596 6221 0.555769 TGTGGGGGTTTCTTTCAGCT 59.444 50.000 0.00 0.00 0.00 4.24
4599 6224 2.104170 GTTGTGTGGGGGTTTCTTTCA 58.896 47.619 0.00 0.00 0.00 2.69
4608 6233 1.832167 CTGTTGGGTTGTGTGGGGG 60.832 63.158 0.00 0.00 0.00 5.40
4614 6239 0.385390 GGCACTTCTGTTGGGTTGTG 59.615 55.000 0.00 0.00 0.00 3.33
4615 6240 1.101049 CGGCACTTCTGTTGGGTTGT 61.101 55.000 0.00 0.00 0.00 3.32
4616 6241 1.101049 ACGGCACTTCTGTTGGGTTG 61.101 55.000 0.00 0.00 0.00 3.77
4619 6244 2.260869 CCACGGCACTTCTGTTGGG 61.261 63.158 0.00 0.00 30.14 4.12
4620 6245 0.606401 ATCCACGGCACTTCTGTTGG 60.606 55.000 0.00 0.00 30.14 3.77
4622 6247 0.396435 TGATCCACGGCACTTCTGTT 59.604 50.000 0.00 0.00 30.14 3.16
4623 6248 0.396435 TTGATCCACGGCACTTCTGT 59.604 50.000 0.00 0.00 33.70 3.41
4624 6249 1.081892 CTTGATCCACGGCACTTCTG 58.918 55.000 0.00 0.00 0.00 3.02
4625 6250 0.976641 TCTTGATCCACGGCACTTCT 59.023 50.000 0.00 0.00 0.00 2.85
4626 6251 1.808411 TTCTTGATCCACGGCACTTC 58.192 50.000 0.00 0.00 0.00 3.01
4627 6252 2.154462 CTTTCTTGATCCACGGCACTT 58.846 47.619 0.00 0.00 0.00 3.16
4628 6253 1.611673 CCTTTCTTGATCCACGGCACT 60.612 52.381 0.00 0.00 0.00 4.40
4629 6254 0.804989 CCTTTCTTGATCCACGGCAC 59.195 55.000 0.00 0.00 0.00 5.01
4630 6255 0.400213 ACCTTTCTTGATCCACGGCA 59.600 50.000 0.00 0.00 0.00 5.69
4631 6256 1.534729 AACCTTTCTTGATCCACGGC 58.465 50.000 0.00 0.00 0.00 5.68
4632 6257 2.678336 GCTAACCTTTCTTGATCCACGG 59.322 50.000 0.00 0.00 0.00 4.94
4633 6258 3.334691 TGCTAACCTTTCTTGATCCACG 58.665 45.455 0.00 0.00 0.00 4.94
4634 6259 4.034510 CGATGCTAACCTTTCTTGATCCAC 59.965 45.833 0.00 0.00 0.00 4.02
4635 6260 4.191544 CGATGCTAACCTTTCTTGATCCA 58.808 43.478 0.00 0.00 0.00 3.41
4636 6261 3.002759 GCGATGCTAACCTTTCTTGATCC 59.997 47.826 0.00 0.00 0.00 3.36
4637 6262 3.873952 AGCGATGCTAACCTTTCTTGATC 59.126 43.478 0.00 0.00 36.99 2.92
4639 6264 3.334583 AGCGATGCTAACCTTTCTTGA 57.665 42.857 0.00 0.00 36.99 3.02
4640 6265 3.436704 TCAAGCGATGCTAACCTTTCTTG 59.563 43.478 0.00 0.00 38.25 3.02
4641 6266 3.674997 TCAAGCGATGCTAACCTTTCTT 58.325 40.909 0.00 0.00 38.25 2.52
4643 6268 3.188460 TGTTCAAGCGATGCTAACCTTTC 59.812 43.478 0.00 0.00 38.25 2.62
4646 6271 2.076863 GTGTTCAAGCGATGCTAACCT 58.923 47.619 0.00 0.00 38.25 3.50
4647 6272 1.804151 TGTGTTCAAGCGATGCTAACC 59.196 47.619 0.00 0.00 38.25 2.85
4648 6273 2.480419 ACTGTGTTCAAGCGATGCTAAC 59.520 45.455 0.00 0.00 38.25 2.34
4649 6274 2.766313 ACTGTGTTCAAGCGATGCTAA 58.234 42.857 0.00 0.00 38.25 3.09
4651 6276 2.341257 CTACTGTGTTCAAGCGATGCT 58.659 47.619 0.00 0.00 42.56 3.79
4652 6277 1.201965 GCTACTGTGTTCAAGCGATGC 60.202 52.381 0.00 0.00 0.00 3.91
4653 6278 1.394917 GGCTACTGTGTTCAAGCGATG 59.605 52.381 0.00 0.00 35.79 3.84
4655 6280 0.679505 AGGCTACTGTGTTCAAGCGA 59.320 50.000 0.00 0.00 35.79 4.93
4657 6282 2.072298 CTGAGGCTACTGTGTTCAAGC 58.928 52.381 0.00 0.00 0.00 4.01
4658 6283 3.583806 CTCTGAGGCTACTGTGTTCAAG 58.416 50.000 0.00 0.00 0.00 3.02
4659 6284 2.289072 GCTCTGAGGCTACTGTGTTCAA 60.289 50.000 6.83 0.00 0.00 2.69
4660 6285 1.273606 GCTCTGAGGCTACTGTGTTCA 59.726 52.381 6.83 0.00 0.00 3.18
4661 6286 1.273606 TGCTCTGAGGCTACTGTGTTC 59.726 52.381 6.83 0.00 0.00 3.18
4662 6287 1.342074 TGCTCTGAGGCTACTGTGTT 58.658 50.000 6.83 0.00 0.00 3.32
4663 6288 1.342074 TTGCTCTGAGGCTACTGTGT 58.658 50.000 6.83 0.00 0.00 3.72
4664 6289 2.168106 AGATTGCTCTGAGGCTACTGTG 59.832 50.000 6.83 0.00 0.00 3.66
4665 6290 2.465813 AGATTGCTCTGAGGCTACTGT 58.534 47.619 6.83 0.00 0.00 3.55
4667 6292 4.100808 CCTTTAGATTGCTCTGAGGCTACT 59.899 45.833 6.83 3.64 32.66 2.57
4670 6295 3.110705 TCCTTTAGATTGCTCTGAGGCT 58.889 45.455 6.83 0.00 36.67 4.58
4671 6296 3.550437 TCCTTTAGATTGCTCTGAGGC 57.450 47.619 6.83 0.00 36.67 4.70
4673 6298 5.728471 TGAGTTCCTTTAGATTGCTCTGAG 58.272 41.667 0.00 0.00 32.66 3.35
4675 6300 6.808008 TTTGAGTTCCTTTAGATTGCTCTG 57.192 37.500 0.00 0.00 32.66 3.35
4677 6302 6.970484 TGTTTTGAGTTCCTTTAGATTGCTC 58.030 36.000 0.00 0.00 0.00 4.26
4679 6304 6.152379 CCTGTTTTGAGTTCCTTTAGATTGC 58.848 40.000 0.00 0.00 0.00 3.56
4680 6305 6.294731 CCCCTGTTTTGAGTTCCTTTAGATTG 60.295 42.308 0.00 0.00 0.00 2.67
4682 6307 5.162980 ACCCCTGTTTTGAGTTCCTTTAGAT 60.163 40.000 0.00 0.00 0.00 1.98
4683 6308 4.167307 ACCCCTGTTTTGAGTTCCTTTAGA 59.833 41.667 0.00 0.00 0.00 2.10
4684 6309 4.470602 ACCCCTGTTTTGAGTTCCTTTAG 58.529 43.478 0.00 0.00 0.00 1.85
4686 6311 3.398318 ACCCCTGTTTTGAGTTCCTTT 57.602 42.857 0.00 0.00 0.00 3.11
4687 6312 3.203487 TGTACCCCTGTTTTGAGTTCCTT 59.797 43.478 0.00 0.00 0.00 3.36
4688 6313 2.781174 TGTACCCCTGTTTTGAGTTCCT 59.219 45.455 0.00 0.00 0.00 3.36
4689 6314 3.146847 CTGTACCCCTGTTTTGAGTTCC 58.853 50.000 0.00 0.00 0.00 3.62
4690 6315 4.065789 CTCTGTACCCCTGTTTTGAGTTC 58.934 47.826 0.00 0.00 0.00 3.01
4691 6316 3.714798 TCTCTGTACCCCTGTTTTGAGTT 59.285 43.478 0.00 0.00 0.00 3.01
4692 6317 3.314693 TCTCTGTACCCCTGTTTTGAGT 58.685 45.455 0.00 0.00 0.00 3.41
4693 6318 4.351874 TTCTCTGTACCCCTGTTTTGAG 57.648 45.455 0.00 0.00 0.00 3.02
4694 6319 4.714632 CTTTCTCTGTACCCCTGTTTTGA 58.285 43.478 0.00 0.00 0.00 2.69
4695 6320 3.253432 GCTTTCTCTGTACCCCTGTTTTG 59.747 47.826 0.00 0.00 0.00 2.44
4696 6321 3.117663 TGCTTTCTCTGTACCCCTGTTTT 60.118 43.478 0.00 0.00 0.00 2.43
4697 6322 2.441750 TGCTTTCTCTGTACCCCTGTTT 59.558 45.455 0.00 0.00 0.00 2.83
4699 6324 1.729586 TGCTTTCTCTGTACCCCTGT 58.270 50.000 0.00 0.00 0.00 4.00
4700 6325 2.859165 TTGCTTTCTCTGTACCCCTG 57.141 50.000 0.00 0.00 0.00 4.45
4701 6326 4.336280 GAATTTGCTTTCTCTGTACCCCT 58.664 43.478 0.00 0.00 0.00 4.79
4702 6327 3.127030 CGAATTTGCTTTCTCTGTACCCC 59.873 47.826 0.00 0.00 0.00 4.95
4704 6329 3.437049 AGCGAATTTGCTTTCTCTGTACC 59.563 43.478 14.80 0.00 44.46 3.34
4705 6330 4.398247 CAGCGAATTTGCTTTCTCTGTAC 58.602 43.478 17.93 0.00 44.46 2.90
4707 6332 2.227388 CCAGCGAATTTGCTTTCTCTGT 59.773 45.455 17.93 0.00 44.46 3.41
4709 6334 2.485814 GTCCAGCGAATTTGCTTTCTCT 59.514 45.455 17.93 0.00 44.46 3.10
4710 6335 2.226437 TGTCCAGCGAATTTGCTTTCTC 59.774 45.455 17.93 9.18 44.46 2.87
4711 6336 2.030805 GTGTCCAGCGAATTTGCTTTCT 60.031 45.455 17.93 0.00 44.46 2.52
4712 6337 2.287547 TGTGTCCAGCGAATTTGCTTTC 60.288 45.455 17.93 11.12 44.46 2.62
4713 6338 1.680735 TGTGTCCAGCGAATTTGCTTT 59.319 42.857 17.93 0.00 44.46 3.51
4714 6339 1.317613 TGTGTCCAGCGAATTTGCTT 58.682 45.000 17.93 0.68 44.46 3.91


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

AutoCloner maintained by Alex Coulton.