Multiple sequence alignment - TraesCS7B01G446300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G446300 chr7B 100.000 2435 0 0 1576 4010 709515979 709513545 0.000000e+00 4497.0
1 TraesCS7B01G446300 chr7B 100.000 1048 0 0 1 1048 709517554 709516507 0.000000e+00 1936.0
2 TraesCS7B01G446300 chr7B 85.631 1204 145 15 1883 3070 709591895 709590704 0.000000e+00 1240.0
3 TraesCS7B01G446300 chr7B 82.332 1132 166 18 1883 3005 709530586 709529480 0.000000e+00 952.0
4 TraesCS7B01G446300 chr7B 86.621 725 80 9 2350 3067 711205588 711206302 0.000000e+00 785.0
5 TraesCS7B01G446300 chr7B 82.343 572 74 17 3117 3668 709590731 709590167 4.690000e-129 472.0
6 TraesCS7B01G446300 chr7B 82.768 383 19 19 685 1039 709531310 709530947 8.430000e-77 298.0
7 TraesCS7B01G446300 chr7B 81.848 303 32 10 284 565 173868717 173868417 2.410000e-57 233.0
8 TraesCS7B01G446300 chr7B 78.544 261 40 11 3330 3577 711206550 711206807 1.490000e-34 158.0
9 TraesCS7B01G446300 chr7B 98.246 57 1 0 3070 3126 323849595 323849651 2.550000e-17 100.0
10 TraesCS7B01G446300 chr7B 93.333 45 3 0 910 954 709592462 709592418 2.590000e-07 67.6
11 TraesCS7B01G446300 chr1D 92.542 1180 67 8 1888 3067 408625996 408627154 0.000000e+00 1672.0
12 TraesCS7B01G446300 chr1D 78.750 1200 198 39 1884 3067 486240467 486241625 0.000000e+00 750.0
13 TraesCS7B01G446300 chr1D 87.945 506 48 9 3515 4010 408627952 408628454 5.780000e-163 584.0
14 TraesCS7B01G446300 chr1D 94.211 380 20 1 3112 3489 408627125 408627504 2.690000e-161 579.0
15 TraesCS7B01G446300 chr1D 74.554 224 26 19 750 958 408625281 408625488 7.190000e-08 69.4
16 TraesCS7B01G446300 chr7D 88.917 1191 115 10 1888 3067 617027829 617029013 0.000000e+00 1452.0
17 TraesCS7B01G446300 chr7D 85.417 1200 147 18 1883 3067 616276415 616275229 0.000000e+00 1221.0
18 TraesCS7B01G446300 chr7D 85.821 938 115 14 2139 3067 616331554 616330626 0.000000e+00 979.0
19 TraesCS7B01G446300 chr7D 82.010 995 156 11 2070 3049 616220145 616221131 0.000000e+00 824.0
20 TraesCS7B01G446300 chr7D 77.778 1179 221 31 1888 3045 617009972 617011130 0.000000e+00 688.0
21 TraesCS7B01G446300 chr7D 81.571 700 100 14 1 690 616259004 616258324 5.860000e-153 551.0
22 TraesCS7B01G446300 chr7D 85.072 556 53 12 3117 3651 617028989 617029535 1.270000e-149 540.0
23 TraesCS7B01G446300 chr7D 81.593 565 73 15 3117 3658 616275253 616274697 4.760000e-119 438.0
24 TraesCS7B01G446300 chr7D 94.488 254 14 0 1883 2136 616333248 616332995 3.760000e-105 392.0
25 TraesCS7B01G446300 chr7D 86.389 360 11 8 708 1039 616258237 616257888 3.810000e-95 359.0
26 TraesCS7B01G446300 chr7D 84.655 391 19 11 685 1039 616219181 616219566 6.380000e-93 351.0
27 TraesCS7B01G446300 chr7D 78.328 586 86 20 3117 3669 616330650 616330073 1.380000e-89 340.0
28 TraesCS7B01G446300 chr7D 79.398 432 60 18 1606 2018 616257856 616257435 1.100000e-70 278.0
29 TraesCS7B01G446300 chr7D 84.950 299 13 8 1606 1887 616219598 616219881 1.420000e-69 274.0
30 TraesCS7B01G446300 chr7D 77.273 264 48 4 2125 2377 588073541 588073279 1.160000e-30 145.0
31 TraesCS7B01G446300 chr7D 75.439 228 32 17 750 958 616277080 616276858 5.520000e-14 89.8
32 TraesCS7B01G446300 chr7A 88.758 1192 115 11 1888 3067 709755301 709756485 0.000000e+00 1441.0
33 TraesCS7B01G446300 chr7A 77.778 1179 221 31 1888 3045 709726004 709727162 0.000000e+00 688.0
34 TraesCS7B01G446300 chr7A 85.252 556 55 12 3117 3651 709756461 709757010 7.580000e-152 547.0
35 TraesCS7B01G446300 chr7A 80.719 612 79 23 3117 3704 709284536 709283940 1.320000e-119 440.0
36 TraesCS7B01G446300 chr7A 83.077 390 24 19 685 1039 709266323 709265941 2.330000e-82 316.0
37 TraesCS7B01G446300 chr7A 82.886 298 49 1 3247 3542 709264344 709264047 2.380000e-67 267.0
38 TraesCS7B01G446300 chr7A 83.601 311 20 9 754 1039 709286233 709285929 3.070000e-66 263.0
39 TraesCS7B01G446300 chr7A 79.412 306 40 11 281 565 237515758 237516061 1.140000e-45 195.0
40 TraesCS7B01G446300 chr7A 87.425 167 21 0 1883 2049 709788140 709788306 4.090000e-45 193.0
41 TraesCS7B01G446300 chr7A 90.805 87 6 2 1799 1885 709285805 709285721 9.110000e-22 115.0
42 TraesCS7B01G446300 chr7A 90.769 65 5 1 1823 1887 709265796 709265733 7.140000e-13 86.1
43 TraesCS7B01G446300 chr1A 79.150 1012 184 21 2071 3067 583924637 583925636 0.000000e+00 675.0
44 TraesCS7B01G446300 chr1A 96.721 61 1 1 3069 3128 142857275 142857215 2.550000e-17 100.0
45 TraesCS7B01G446300 chr1B 78.441 603 87 22 3117 3694 677255856 677256440 1.770000e-93 353.0
46 TraesCS7B01G446300 chr6B 98.246 57 1 0 3070 3126 49701483 49701427 2.550000e-17 100.0
47 TraesCS7B01G446300 chr5B 96.667 60 2 0 3070 3129 515818788 515818847 2.550000e-17 100.0
48 TraesCS7B01G446300 chr5B 98.246 57 1 0 3070 3126 566505731 566505675 2.550000e-17 100.0
49 TraesCS7B01G446300 chr5A 98.246 57 1 0 3070 3126 596662294 596662350 2.550000e-17 100.0
50 TraesCS7B01G446300 chr2B 98.246 57 1 0 3070 3126 784193598 784193542 2.550000e-17 100.0
51 TraesCS7B01G446300 chr2B 96.491 57 2 0 3070 3126 423659790 423659846 1.190000e-15 95.3
52 TraesCS7B01G446300 chr3B 93.846 65 2 2 3062 3125 385469721 385469658 3.300000e-16 97.1


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 TraesCS7B01G446300 chr7B 709513545 709517554 4009 True 3216.500000 4497 100.000000 1 4010 2 chr7B.!!$R2 4009
1 TraesCS7B01G446300 chr7B 709529480 709531310 1830 True 625.000000 952 82.550000 685 3005 2 chr7B.!!$R3 2320
2 TraesCS7B01G446300 chr7B 709590167 709592462 2295 True 593.200000 1240 87.102333 910 3668 3 chr7B.!!$R4 2758
3 TraesCS7B01G446300 chr7B 711205588 711206807 1219 False 471.500000 785 82.582500 2350 3577 2 chr7B.!!$F2 1227
4 TraesCS7B01G446300 chr1D 486240467 486241625 1158 False 750.000000 750 78.750000 1884 3067 1 chr1D.!!$F1 1183
5 TraesCS7B01G446300 chr1D 408625281 408628454 3173 False 726.100000 1672 87.313000 750 4010 4 chr1D.!!$F2 3260
6 TraesCS7B01G446300 chr7D 617027829 617029535 1706 False 996.000000 1452 86.994500 1888 3651 2 chr7D.!!$F3 1763
7 TraesCS7B01G446300 chr7D 617009972 617011130 1158 False 688.000000 688 77.778000 1888 3045 1 chr7D.!!$F1 1157
8 TraesCS7B01G446300 chr7D 616274697 616277080 2383 True 582.933333 1221 80.816333 750 3658 3 chr7D.!!$R3 2908
9 TraesCS7B01G446300 chr7D 616330073 616333248 3175 True 570.333333 979 86.212333 1883 3669 3 chr7D.!!$R4 1786
10 TraesCS7B01G446300 chr7D 616219181 616221131 1950 False 483.000000 824 83.871667 685 3049 3 chr7D.!!$F2 2364
11 TraesCS7B01G446300 chr7D 616257435 616259004 1569 True 396.000000 551 82.452667 1 2018 3 chr7D.!!$R2 2017
12 TraesCS7B01G446300 chr7A 709755301 709757010 1709 False 994.000000 1441 87.005000 1888 3651 2 chr7A.!!$F4 1763
13 TraesCS7B01G446300 chr7A 709726004 709727162 1158 False 688.000000 688 77.778000 1888 3045 1 chr7A.!!$F2 1157
14 TraesCS7B01G446300 chr7A 709283940 709286233 2293 True 272.666667 440 85.041667 754 3704 3 chr7A.!!$R2 2950
15 TraesCS7B01G446300 chr7A 709264047 709266323 2276 True 223.033333 316 85.577333 685 3542 3 chr7A.!!$R1 2857
16 TraesCS7B01G446300 chr1A 583924637 583925636 999 False 675.000000 675 79.150000 2071 3067 1 chr1A.!!$F1 996
17 TraesCS7B01G446300 chr1B 677255856 677256440 584 False 353.000000 353 78.441000 3117 3694 1 chr1B.!!$F1 577

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
440 449 0.178950 AGATGGAGGCAGAGGCGATA 60.179 55.0 0.00 0.0 42.47 2.92 F
759 841 0.465460 CTCTGGTCGGAGAGGAGAGG 60.465 65.0 0.65 0.0 38.65 3.69 F
822 910 0.980231 CTCCTCCCCCTTCTCCACTG 60.980 65.0 0.00 0.0 0.00 3.66 F
2527 4459 1.072266 AAGCATACCCCACCAACTCA 58.928 50.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1971 0.536006 GAGTTGAAGGCCACAGCAGT 60.536 55.000 5.01 0.00 42.56 4.40 R
2167 4091 0.884704 TGAGCGTCTTCTTTGGGCAC 60.885 55.000 0.00 0.00 0.00 5.01 R
2570 4505 1.806542 CATGAAACTCAACCACCTCGG 59.193 52.381 0.00 0.00 42.50 4.63 R
3565 6083 0.459934 CTGAGCTGCTGCAGACTACC 60.460 60.000 32.30 14.39 42.74 3.18 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
31 32 1.690352 ACCTGTATATTTCGTCCCCCG 59.310 52.381 0.00 0.00 38.13 5.73
52 53 4.315803 CGTCCGCCATATTTCTAGGATTT 58.684 43.478 0.00 0.00 0.00 2.17
57 58 4.938226 CGCCATATTTCTAGGATTTCTCCC 59.062 45.833 0.00 0.00 43.21 4.30
68 69 8.214721 TCTAGGATTTCTCCCTCTTTTTACAA 57.785 34.615 0.00 0.00 43.21 2.41
69 70 8.836735 TCTAGGATTTCTCCCTCTTTTTACAAT 58.163 33.333 0.00 0.00 43.21 2.71
70 71 7.709149 AGGATTTCTCCCTCTTTTTACAATG 57.291 36.000 0.00 0.00 43.21 2.82
73 74 3.697166 TCTCCCTCTTTTTACAATGCCC 58.303 45.455 0.00 0.00 0.00 5.36
74 75 3.333680 TCTCCCTCTTTTTACAATGCCCT 59.666 43.478 0.00 0.00 0.00 5.19
75 76 3.696548 CTCCCTCTTTTTACAATGCCCTC 59.303 47.826 0.00 0.00 0.00 4.30
78 79 5.193728 TCCCTCTTTTTACAATGCCCTCTAT 59.806 40.000 0.00 0.00 0.00 1.98
79 80 5.893824 CCCTCTTTTTACAATGCCCTCTATT 59.106 40.000 0.00 0.00 0.00 1.73
80 81 6.381133 CCCTCTTTTTACAATGCCCTCTATTT 59.619 38.462 0.00 0.00 0.00 1.40
81 82 7.093333 CCCTCTTTTTACAATGCCCTCTATTTT 60.093 37.037 0.00 0.00 0.00 1.82
82 83 8.314021 CCTCTTTTTACAATGCCCTCTATTTTT 58.686 33.333 0.00 0.00 0.00 1.94
114 115 1.250840 ATTTCAGCCCCAACCGCTTC 61.251 55.000 0.00 0.00 33.17 3.86
115 116 2.351924 TTTCAGCCCCAACCGCTTCT 62.352 55.000 0.00 0.00 33.17 2.85
126 127 3.793144 CGCTTCTGTTCTGCGCCC 61.793 66.667 4.18 0.00 43.08 6.13
144 145 1.227823 CCCGCCGCCATTAATCTCA 60.228 57.895 0.00 0.00 0.00 3.27
146 147 0.532862 CCGCCGCCATTAATCTCACT 60.533 55.000 0.00 0.00 0.00 3.41
148 149 1.668419 GCCGCCATTAATCTCACTGT 58.332 50.000 0.00 0.00 0.00 3.55
156 157 2.941453 TAATCTCACTGTCGCCTCAC 57.059 50.000 0.00 0.00 0.00 3.51
167 168 2.435059 GCCTCACCGTTGCTCCTC 60.435 66.667 0.00 0.00 0.00 3.71
172 173 3.382832 ACCGTTGCTCCTCCCTCG 61.383 66.667 0.00 0.00 0.00 4.63
174 175 3.382832 CGTTGCTCCTCCCTCGGT 61.383 66.667 0.00 0.00 0.00 4.69
175 176 2.943978 CGTTGCTCCTCCCTCGGTT 61.944 63.158 0.00 0.00 0.00 4.44
176 177 1.376037 GTTGCTCCTCCCTCGGTTG 60.376 63.158 0.00 0.00 0.00 3.77
178 179 4.475135 GCTCCTCCCTCGGTTGGC 62.475 72.222 0.00 0.00 0.00 4.52
179 180 4.148825 CTCCTCCCTCGGTTGGCG 62.149 72.222 0.00 0.00 0.00 5.69
198 199 1.965930 GCACGACACCATGGAGCAA 60.966 57.895 21.47 0.00 0.00 3.91
199 200 1.868997 CACGACACCATGGAGCAAC 59.131 57.895 21.47 5.18 0.00 4.17
200 201 0.603707 CACGACACCATGGAGCAACT 60.604 55.000 21.47 0.00 0.00 3.16
211 212 1.439644 GAGCAACTAGAGCCTCCCG 59.560 63.158 0.00 0.00 0.00 5.14
215 216 1.040646 CAACTAGAGCCTCCCGCATA 58.959 55.000 0.00 0.00 41.38 3.14
222 231 2.280186 CCTCCCGCATAAGGTCGC 60.280 66.667 0.00 0.00 0.00 5.19
233 242 3.069778 AGGTCGCCCCTTCAGAAC 58.930 61.111 0.00 0.00 42.73 3.01
236 245 2.602267 TCGCCCCTTCAGAACCGA 60.602 61.111 0.00 0.00 0.00 4.69
272 281 1.891060 GAGAGCGTCGTTTGGCACAG 61.891 60.000 0.00 0.00 42.39 3.66
275 284 2.052237 CGTCGTTTGGCACAGCAC 60.052 61.111 0.00 0.00 42.39 4.40
276 285 2.331451 GTCGTTTGGCACAGCACC 59.669 61.111 0.00 0.00 42.39 5.01
279 288 2.616330 CGTTTGGCACAGCACCGAT 61.616 57.895 0.00 0.00 42.39 4.18
280 289 1.081242 GTTTGGCACAGCACCGATG 60.081 57.895 0.00 0.00 42.39 3.84
282 291 0.608856 TTTGGCACAGCACCGATGAT 60.609 50.000 0.00 0.00 42.39 2.45
284 293 2.406401 GCACAGCACCGATGATGC 59.594 61.111 0.00 0.00 46.57 3.91
295 304 3.995526 GATGATGCCATCGAGGACA 57.004 52.632 0.00 0.00 39.70 4.02
299 308 0.604780 GATGCCATCGAGGACATGGG 60.605 60.000 2.91 0.00 41.23 4.00
300 309 2.060567 ATGCCATCGAGGACATGGGG 62.061 60.000 0.00 0.00 41.23 4.96
333 342 1.911766 GGTCGTCTGGAGGGTGGAA 60.912 63.158 0.00 0.00 0.00 3.53
337 346 1.599576 GTCTGGAGGGTGGAAGAGC 59.400 63.158 0.00 0.00 0.00 4.09
375 384 4.204028 ACCACCACCAAAGCCGCT 62.204 61.111 0.00 0.00 0.00 5.52
377 386 3.673484 CACCACCAAAGCCGCTGG 61.673 66.667 0.00 0.00 40.05 4.85
401 410 2.030562 CCAGGTGCGACGGTTTCT 59.969 61.111 0.00 0.00 0.00 2.52
402 411 2.317609 CCAGGTGCGACGGTTTCTG 61.318 63.158 0.00 0.00 0.00 3.02
408 417 2.127758 CGACGGTTTCTGCGTTGC 60.128 61.111 0.00 0.00 0.00 4.17
410 419 2.877974 GACGGTTTCTGCGTTGCGT 61.878 57.895 0.00 0.00 0.00 5.24
414 423 3.205536 TTTCTGCGTTGCGTGCCA 61.206 55.556 0.00 0.00 0.00 4.92
416 425 1.231296 TTTCTGCGTTGCGTGCCATA 61.231 50.000 0.00 0.00 0.00 2.74
431 440 1.550524 GCCATATACGAGATGGAGGCA 59.449 52.381 15.91 0.00 45.89 4.75
440 449 0.178950 AGATGGAGGCAGAGGCGATA 60.179 55.000 0.00 0.00 42.47 2.92
454 463 1.887707 CGATACGCTTCAAGGGCCC 60.888 63.158 16.46 16.46 0.00 5.80
492 501 1.045350 CGGCCTCCAGGATCTCTTCA 61.045 60.000 0.00 0.00 37.39 3.02
505 514 2.177594 CTCTTCAAGGCGGTCCTGCT 62.178 60.000 5.82 0.00 43.40 4.24
532 541 1.450848 CCATGCCTGCAGACGATGT 60.451 57.895 17.39 0.00 0.00 3.06
534 543 1.520120 ATGCCTGCAGACGATGTCG 60.520 57.895 17.39 0.11 46.33 4.35
566 575 2.161808 CGACACAGACGAGTATGAACCT 59.838 50.000 4.77 0.00 0.00 3.50
603 612 8.800370 ATATTTTGTTTTCAGGGTTTTTGTGT 57.200 26.923 0.00 0.00 0.00 3.72
605 614 8.622948 ATTTTGTTTTCAGGGTTTTTGTGTTA 57.377 26.923 0.00 0.00 0.00 2.41
606 615 7.422878 TTTGTTTTCAGGGTTTTTGTGTTAC 57.577 32.000 0.00 0.00 0.00 2.50
608 617 6.760291 TGTTTTCAGGGTTTTTGTGTTACTT 58.240 32.000 0.00 0.00 0.00 2.24
610 619 7.385478 TGTTTTCAGGGTTTTTGTGTTACTTTC 59.615 33.333 0.00 0.00 0.00 2.62
612 621 7.941431 TTCAGGGTTTTTGTGTTACTTTCTA 57.059 32.000 0.00 0.00 0.00 2.10
613 622 7.941431 TCAGGGTTTTTGTGTTACTTTCTAA 57.059 32.000 0.00 0.00 0.00 2.10
614 623 7.992008 TCAGGGTTTTTGTGTTACTTTCTAAG 58.008 34.615 0.00 0.00 0.00 2.18
618 627 7.423199 GGTTTTTGTGTTACTTTCTAAGAGGG 58.577 38.462 0.00 0.00 0.00 4.30
622 631 6.295719 TGTGTTACTTTCTAAGAGGGATCC 57.704 41.667 1.92 1.92 0.00 3.36
624 633 4.404715 TGTTACTTTCTAAGAGGGATCCGG 59.595 45.833 5.45 0.00 0.00 5.14
627 636 3.197983 ACTTTCTAAGAGGGATCCGGTTG 59.802 47.826 5.45 0.00 0.00 3.77
641 650 6.825213 GGGATCCGGTTGTAAATTTAACTACT 59.175 38.462 5.45 0.00 0.00 2.57
642 651 7.201670 GGGATCCGGTTGTAAATTTAACTACTG 60.202 40.741 5.45 6.79 0.00 2.74
647 656 8.013378 CCGGTTGTAAATTTAACTACTGACAAG 58.987 37.037 15.56 2.84 32.76 3.16
657 666 3.714144 ACTACTGACAAGTGGGCTCTAT 58.286 45.455 0.00 0.00 39.14 1.98
662 671 5.706447 ACTGACAAGTGGGCTCTATATCTA 58.294 41.667 0.00 0.00 34.48 1.98
665 674 5.009710 TGACAAGTGGGCTCTATATCTAACG 59.990 44.000 0.00 0.00 0.00 3.18
683 692 3.268013 ACGTGAAAGATTTTTGCGGAG 57.732 42.857 0.00 0.00 0.00 4.63
758 840 3.094386 CTCTGGTCGGAGAGGAGAG 57.906 63.158 0.65 0.00 36.93 3.20
759 841 0.465460 CTCTGGTCGGAGAGGAGAGG 60.465 65.000 0.65 0.00 38.65 3.69
822 910 0.980231 CTCCTCCCCCTTCTCCACTG 60.980 65.000 0.00 0.00 0.00 3.66
881 1001 3.822192 GTTTTCCCGGCGGATGGC 61.822 66.667 30.79 9.63 38.24 4.40
954 1086 2.119655 CAGCAGCCCATGGAAGAGC 61.120 63.158 15.22 8.10 0.00 4.09
1039 1359 7.362574 CGGCGGTAATTTCCATTCCATTATTAT 60.363 37.037 0.00 0.00 0.00 1.28
1600 1920 8.454570 AAGAAAAATACTAAAAGTGTTCCGGA 57.545 30.769 0.00 0.00 27.77 5.14
1601 1921 8.631480 AGAAAAATACTAAAAGTGTTCCGGAT 57.369 30.769 4.15 0.00 27.77 4.18
1602 1922 8.512138 AGAAAAATACTAAAAGTGTTCCGGATG 58.488 33.333 4.15 0.00 27.77 3.51
1603 1923 6.753107 AAATACTAAAAGTGTTCCGGATGG 57.247 37.500 4.15 0.00 27.77 3.51
1604 1924 5.687166 ATACTAAAAGTGTTCCGGATGGA 57.313 39.130 4.15 0.00 44.61 3.41
1651 1971 2.554893 GACCGCTGTTTTGTGGGATTTA 59.445 45.455 0.00 0.00 41.59 1.40
1689 2009 5.757850 ACTCTTGTTCACCTCATGTTTTC 57.242 39.130 0.00 0.00 0.00 2.29
1690 2010 5.192927 ACTCTTGTTCACCTCATGTTTTCA 58.807 37.500 0.00 0.00 0.00 2.69
1692 2012 4.338118 TCTTGTTCACCTCATGTTTTCACC 59.662 41.667 0.00 0.00 0.00 4.02
1693 2013 3.897239 TGTTCACCTCATGTTTTCACCT 58.103 40.909 0.00 0.00 0.00 4.00
1694 2014 3.882888 TGTTCACCTCATGTTTTCACCTC 59.117 43.478 0.00 0.00 0.00 3.85
1696 2016 4.437682 TCACCTCATGTTTTCACCTCTT 57.562 40.909 0.00 0.00 0.00 2.85
1818 2196 6.829229 AACTAAACCCCTATACAGCAAAAC 57.171 37.500 0.00 0.00 0.00 2.43
1857 2236 5.995282 TCTGCTCGTATTTCTCCTTCAAAAA 59.005 36.000 0.00 0.00 0.00 1.94
1879 2258 3.900966 ACATGCACTCTGAGCTCATTA 57.099 42.857 18.63 7.82 0.00 1.90
1991 2425 3.181440 ACAAGTTGGAGAATGCTCTGGAA 60.181 43.478 7.96 0.00 41.06 3.53
2022 2468 5.015515 TGCAATCTATGTTTTGATGGTCCA 58.984 37.500 0.00 0.00 0.00 4.02
2028 2474 7.773489 TCTATGTTTTGATGGTCCAAATGAA 57.227 32.000 0.00 0.00 36.12 2.57
2040 2486 4.952335 GGTCCAAATGAACCAGATTCTGAT 59.048 41.667 15.36 3.56 38.25 2.90
2042 2488 6.261826 GGTCCAAATGAACCAGATTCTGATAG 59.738 42.308 15.36 1.24 38.25 2.08
2108 2593 7.065894 CGAACAAAGTTCATTGAGACTGTAAG 58.934 38.462 10.15 0.00 35.37 2.34
2167 4091 4.758251 TCAGCATCCGGTGTGGCG 62.758 66.667 0.00 0.00 41.52 5.69
2252 4176 9.455847 GGCAAAGATAATACATTTTGATCTGAC 57.544 33.333 0.00 0.00 33.50 3.51
2306 4237 1.488393 CTTCCCTCTTGAGGCCTTAGG 59.512 57.143 6.77 11.94 0.00 2.69
2527 4459 1.072266 AAGCATACCCCACCAACTCA 58.928 50.000 0.00 0.00 0.00 3.41
2628 4563 2.450609 TTGAGTACAAAGGGCGAGTC 57.549 50.000 0.00 0.00 32.73 3.36
2639 4574 0.533032 GGGCGAGTCATCCCTATAGC 59.467 60.000 9.62 0.00 39.46 2.97
2716 4657 2.726821 CACTGGCCCATACATTCACTT 58.273 47.619 0.00 0.00 0.00 3.16
2751 4692 6.498304 CATTTTGGCAGTGAGGATATTACAC 58.502 40.000 0.00 0.00 35.15 2.90
2762 4703 4.621991 AGGATATTACACGTGCAAGCTAG 58.378 43.478 17.22 0.00 0.00 3.42
2831 4807 8.463930 TCAAAGTTCTTCAGAATTGGTGTTAT 57.536 30.769 0.00 0.00 36.33 1.89
2894 4870 1.447317 AAGCTGCCAACAAGACCACG 61.447 55.000 0.00 0.00 0.00 4.94
2946 4922 4.935808 ACTTGCCAACTAAGTGTATACTGC 59.064 41.667 4.17 0.00 37.03 4.40
2954 4936 6.037786 ACTAAGTGTATACTGCAGCAAAGA 57.962 37.500 15.27 0.00 37.19 2.52
2955 4937 6.102663 ACTAAGTGTATACTGCAGCAAAGAG 58.897 40.000 15.27 4.09 37.19 2.85
3007 4990 0.469705 TTGTTTGGATGCTGCACCCT 60.470 50.000 15.44 0.00 0.00 4.34
3049 5032 5.549347 TGCATGTGAGTGCCATTTTATTTT 58.451 33.333 0.00 0.00 44.43 1.82
3050 5033 6.695429 TGCATGTGAGTGCCATTTTATTTTA 58.305 32.000 0.00 0.00 44.43 1.52
3051 5034 7.329499 TGCATGTGAGTGCCATTTTATTTTAT 58.671 30.769 0.00 0.00 44.43 1.40
3052 5035 7.823310 TGCATGTGAGTGCCATTTTATTTTATT 59.177 29.630 0.00 0.00 44.43 1.40
3053 5036 8.667463 GCATGTGAGTGCCATTTTATTTTATTT 58.333 29.630 0.00 0.00 39.18 1.40
3076 5059 9.853177 ATTTAGAAAGACTAATACATTCCCCAG 57.147 33.333 0.00 0.00 40.24 4.45
3077 5060 8.618240 TTAGAAAGACTAATACATTCCCCAGA 57.382 34.615 0.00 0.00 36.33 3.86
3078 5061 6.890293 AGAAAGACTAATACATTCCCCAGAC 58.110 40.000 0.00 0.00 0.00 3.51
3079 5062 5.632034 AAGACTAATACATTCCCCAGACC 57.368 43.478 0.00 0.00 0.00 3.85
3080 5063 3.974642 AGACTAATACATTCCCCAGACCC 59.025 47.826 0.00 0.00 0.00 4.46
3081 5064 3.974642 GACTAATACATTCCCCAGACCCT 59.025 47.826 0.00 0.00 0.00 4.34
3082 5065 3.716872 ACTAATACATTCCCCAGACCCTG 59.283 47.826 0.00 0.00 0.00 4.45
3083 5066 2.286935 ATACATTCCCCAGACCCTGT 57.713 50.000 0.00 0.00 0.00 4.00
3084 5067 1.285280 TACATTCCCCAGACCCTGTG 58.715 55.000 0.00 0.00 0.00 3.66
3085 5068 1.379044 CATTCCCCAGACCCTGTGC 60.379 63.158 0.00 0.00 0.00 4.57
3086 5069 1.852157 ATTCCCCAGACCCTGTGCA 60.852 57.895 0.00 0.00 0.00 4.57
3087 5070 1.434513 ATTCCCCAGACCCTGTGCAA 61.435 55.000 0.00 0.00 0.00 4.08
3088 5071 2.034687 CCCCAGACCCTGTGCAAG 59.965 66.667 0.00 0.00 0.00 4.01
3089 5072 2.674380 CCCAGACCCTGTGCAAGC 60.674 66.667 0.00 0.00 0.00 4.01
3090 5073 3.052082 CCAGACCCTGTGCAAGCG 61.052 66.667 0.00 0.00 0.00 4.68
3091 5074 3.052082 CAGACCCTGTGCAAGCGG 61.052 66.667 0.00 0.00 0.00 5.52
3092 5075 4.335647 AGACCCTGTGCAAGCGGG 62.336 66.667 13.19 13.19 43.79 6.13
3093 5076 4.329545 GACCCTGTGCAAGCGGGA 62.330 66.667 19.81 0.00 40.55 5.14
3094 5077 4.335647 ACCCTGTGCAAGCGGGAG 62.336 66.667 19.81 6.26 40.55 4.30
3106 5089 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
3107 5090 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
3108 5091 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
3109 5092 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
3110 5093 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
3111 5094 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
3112 5095 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
3113 5096 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
3114 5097 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
3120 5103 1.838396 CACTGGGGCTGCCCTTTTT 60.838 57.895 34.99 15.74 44.66 1.94
3310 5327 0.394938 TTCGCTGTTACAGGGCTCAA 59.605 50.000 22.16 10.54 42.87 3.02
3460 5540 1.448540 GGATCTGTGAGTGGGCACG 60.449 63.158 0.00 0.00 41.63 5.34
3482 5562 3.541713 ATCTCGGAGGGCTTCGGC 61.542 66.667 4.96 0.00 40.88 5.54
3491 5571 1.223487 GGGCTTCGGCAAGGTGATA 59.777 57.895 0.00 0.00 43.96 2.15
3598 6129 2.292103 GCTCAGTGTAGCTGGAAGAG 57.708 55.000 0.00 0.00 45.08 2.85
3627 6166 6.887376 TTCGTTCATGTAGTAATGCTTCTC 57.113 37.500 0.00 0.00 0.00 2.87
3628 6167 5.961272 TCGTTCATGTAGTAATGCTTCTCA 58.039 37.500 0.00 0.00 0.00 3.27
3686 6227 2.015456 TGCCCTCTTCTCTTCACAGA 57.985 50.000 0.00 0.00 0.00 3.41
3694 6235 6.658391 CCCTCTTCTCTTCACAGATGAAAAAT 59.342 38.462 0.00 0.00 44.28 1.82
3697 6238 8.320396 TCTTCTCTTCACAGATGAAAAATCAG 57.680 34.615 0.00 0.00 44.28 2.90
3733 6274 5.116084 TGGCACAGCTTTATTTCTCCTAT 57.884 39.130 0.00 0.00 0.00 2.57
3740 6281 7.280876 CACAGCTTTATTTCTCCTATTGTGCTA 59.719 37.037 0.00 0.00 0.00 3.49
3748 6289 3.069586 TCTCCTATTGTGCTATCGTTGGG 59.930 47.826 0.00 0.00 0.00 4.12
3764 6305 3.487372 GTTGGGGCTACTGAAAGAACTT 58.513 45.455 0.00 0.00 37.43 2.66
3768 6309 3.008704 GGGGCTACTGAAAGAACTTGGTA 59.991 47.826 0.00 0.00 37.43 3.25
3792 6333 7.429636 AATGGAATCTCAAACAAAATTGCAG 57.570 32.000 0.00 0.00 33.80 4.41
3802 6343 2.818432 ACAAAATTGCAGCTCTCCTCTG 59.182 45.455 0.00 0.00 34.79 3.35
3827 6368 8.988934 TGTTCATGTACATTTCTCAACTCTTAC 58.011 33.333 5.37 0.00 0.00 2.34
3834 6375 9.170584 GTACATTTCTCAACTCTTACAAAAAGC 57.829 33.333 0.00 0.00 0.00 3.51
3854 6395 2.815478 CTGAACTATCTCCTGGTTCGC 58.185 52.381 0.00 0.00 45.59 4.70
3857 6398 1.404843 ACTATCTCCTGGTTCGCCTC 58.595 55.000 0.00 0.00 38.36 4.70
3861 6402 1.933021 TCTCCTGGTTCGCCTCTTTA 58.067 50.000 0.00 0.00 38.36 1.85
3863 6404 1.825474 CTCCTGGTTCGCCTCTTTAGA 59.175 52.381 0.00 0.00 38.36 2.10
3872 6413 5.048991 GGTTCGCCTCTTTAGATGAAAAACA 60.049 40.000 0.00 0.00 0.00 2.83
3876 6417 7.974675 TCGCCTCTTTAGATGAAAAACATAAG 58.025 34.615 0.00 0.00 39.56 1.73
3877 6418 7.606456 TCGCCTCTTTAGATGAAAAACATAAGT 59.394 33.333 0.00 0.00 39.56 2.24
3931 6472 5.995282 TGTATCTTGGACAAAACACCTACAG 59.005 40.000 0.00 0.00 0.00 2.74
3975 6516 1.361543 TGTACTCCTTGGGTAGCCTCT 59.638 52.381 13.11 0.00 0.00 3.69
3982 6523 0.324943 TTGGGTAGCCTCTGAGTTGC 59.675 55.000 13.11 0.81 0.00 4.17
3986 6527 1.984570 TAGCCTCTGAGTTGCCGCT 60.985 57.895 9.70 9.70 0.00 5.52
3989 6530 3.485431 CTCTGAGTTGCCGCTGCG 61.485 66.667 16.34 16.34 41.78 5.18
4002 6543 2.357517 CTGCGCAACCGAGGAGTT 60.358 61.111 13.05 0.00 36.29 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.701951 GGACGAAATATACAGGTCCCCA 59.298 50.000 0.00 0.00 40.97 4.96
24 25 2.333701 AAATATGGCGGACGGGGGAC 62.334 60.000 0.00 0.00 0.00 4.46
25 26 2.047213 GAAATATGGCGGACGGGGGA 62.047 60.000 0.00 0.00 0.00 4.81
31 32 5.552178 AGAAATCCTAGAAATATGGCGGAC 58.448 41.667 0.00 0.00 0.00 4.79
52 53 3.333680 AGGGCATTGTAAAAAGAGGGAGA 59.666 43.478 0.00 0.00 0.00 3.71
79 80 4.367450 CTGAAATTTCACTCCCGCAAAAA 58.633 39.130 16.91 0.00 32.90 1.94
80 81 3.798548 GCTGAAATTTCACTCCCGCAAAA 60.799 43.478 16.91 0.00 32.90 2.44
81 82 2.288152 GCTGAAATTTCACTCCCGCAAA 60.288 45.455 16.91 0.00 32.90 3.68
82 83 1.269448 GCTGAAATTTCACTCCCGCAA 59.731 47.619 16.91 0.00 32.90 4.85
83 84 0.881118 GCTGAAATTTCACTCCCGCA 59.119 50.000 16.91 0.00 32.90 5.69
84 85 0.171231 GGCTGAAATTTCACTCCCGC 59.829 55.000 16.91 16.87 32.90 6.13
85 86 0.811281 GGGCTGAAATTTCACTCCCG 59.189 55.000 26.06 15.42 36.08 5.14
86 87 1.186200 GGGGCTGAAATTTCACTCCC 58.814 55.000 29.23 29.23 41.04 4.30
125 126 1.966451 GAGATTAATGGCGGCGGGG 60.966 63.158 9.78 0.00 0.00 5.73
126 127 1.227823 TGAGATTAATGGCGGCGGG 60.228 57.895 9.78 0.00 0.00 6.13
136 137 2.094182 GGTGAGGCGACAGTGAGATTAA 60.094 50.000 0.00 0.00 0.00 1.40
140 141 2.626780 CGGTGAGGCGACAGTGAGA 61.627 63.158 0.00 0.00 0.00 3.27
144 145 2.029073 CAACGGTGAGGCGACAGT 59.971 61.111 0.00 0.00 0.00 3.55
146 147 3.858868 GAGCAACGGTGAGGCGACA 62.859 63.158 3.55 0.00 0.00 4.35
148 149 4.373116 GGAGCAACGGTGAGGCGA 62.373 66.667 3.55 0.00 0.00 5.54
156 157 4.148825 CCGAGGGAGGAGCAACGG 62.149 72.222 0.00 0.00 34.77 4.44
178 179 2.815211 CTCCATGGTGTCGTGCCG 60.815 66.667 12.58 0.00 0.00 5.69
179 180 3.127533 GCTCCATGGTGTCGTGCC 61.128 66.667 12.58 0.00 0.00 5.01
180 181 1.965930 TTGCTCCATGGTGTCGTGC 60.966 57.895 12.58 8.38 0.00 5.34
181 182 0.603707 AGTTGCTCCATGGTGTCGTG 60.604 55.000 12.58 0.00 0.00 4.35
182 183 0.973632 TAGTTGCTCCATGGTGTCGT 59.026 50.000 12.58 0.00 0.00 4.34
185 186 1.065854 GCTCTAGTTGCTCCATGGTGT 60.066 52.381 12.58 0.00 0.00 4.16
187 188 0.543749 GGCTCTAGTTGCTCCATGGT 59.456 55.000 12.58 0.00 0.00 3.55
198 199 1.333177 CTTATGCGGGAGGCTCTAGT 58.667 55.000 15.23 0.00 44.05 2.57
199 200 0.605589 CCTTATGCGGGAGGCTCTAG 59.394 60.000 15.23 9.75 44.05 2.43
200 201 0.105658 ACCTTATGCGGGAGGCTCTA 60.106 55.000 15.23 0.00 44.05 2.43
222 231 2.990479 CCCTCGGTTCTGAAGGGG 59.010 66.667 4.50 4.32 36.21 4.79
226 235 0.537188 GAGATGCCCTCGGTTCTGAA 59.463 55.000 0.00 0.00 31.32 3.02
233 242 2.507944 CCTTGGAGATGCCCTCGG 59.492 66.667 0.00 0.00 42.89 4.63
236 245 3.801997 CCGCCTTGGAGATGCCCT 61.802 66.667 0.00 0.00 42.00 5.19
261 270 2.616330 ATCGGTGCTGTGCCAAACG 61.616 57.895 0.00 0.00 0.00 3.60
279 288 0.107268 CCATGTCCTCGATGGCATCA 59.893 55.000 25.88 12.74 34.21 3.07
280 289 0.604780 CCCATGTCCTCGATGGCATC 60.605 60.000 17.58 17.58 39.36 3.91
282 291 2.745308 CCCCATGTCCTCGATGGCA 61.745 63.158 0.00 0.00 39.36 4.92
284 293 2.831770 CCCCCATGTCCTCGATGG 59.168 66.667 0.00 0.00 40.25 3.51
289 298 4.489771 CCACGCCCCCATGTCCTC 62.490 72.222 0.00 0.00 0.00 3.71
294 303 3.727258 TCTTCCCACGCCCCCATG 61.727 66.667 0.00 0.00 0.00 3.66
295 304 3.728373 GTCTTCCCACGCCCCCAT 61.728 66.667 0.00 0.00 0.00 4.00
299 308 4.452733 CCTCGTCTTCCCACGCCC 62.453 72.222 0.00 0.00 39.74 6.13
300 309 3.644399 GACCTCGTCTTCCCACGCC 62.644 68.421 0.00 0.00 39.74 5.68
322 331 3.003173 CGGCTCTTCCACCCTCCA 61.003 66.667 0.00 0.00 34.01 3.86
383 392 2.280592 GAAACCGTCGCACCTGGT 60.281 61.111 0.00 0.00 37.68 4.00
386 395 2.665185 GCAGAAACCGTCGCACCT 60.665 61.111 0.00 0.00 0.00 4.00
388 397 2.877974 AACGCAGAAACCGTCGCAC 61.878 57.895 0.00 0.00 38.06 5.34
393 402 2.893404 ACGCAACGCAGAAACCGT 60.893 55.556 0.00 0.00 41.24 4.83
401 410 1.757346 CGTATATGGCACGCAACGCA 61.757 55.000 0.00 0.00 31.94 5.24
402 411 1.083657 CGTATATGGCACGCAACGC 60.084 57.895 0.00 0.00 31.94 4.84
408 417 2.416027 CCTCCATCTCGTATATGGCACG 60.416 54.545 0.00 0.00 43.11 5.34
410 419 1.550524 GCCTCCATCTCGTATATGGCA 59.449 52.381 0.00 0.00 43.11 4.92
414 423 3.360867 CCTCTGCCTCCATCTCGTATAT 58.639 50.000 0.00 0.00 0.00 0.86
416 425 1.626686 CCTCTGCCTCCATCTCGTAT 58.373 55.000 0.00 0.00 0.00 3.06
454 463 3.965701 GCAGCGATTCGTCGAGCG 61.966 66.667 8.03 13.21 43.01 5.03
463 472 4.537433 GGAGGCCGAGCAGCGATT 62.537 66.667 0.00 0.00 44.57 3.34
474 483 1.140652 CTTGAAGAGATCCTGGAGGCC 59.859 57.143 1.52 0.00 34.44 5.19
492 501 2.348998 CTTGAGCAGGACCGCCTT 59.651 61.111 4.93 0.00 43.90 4.35
517 526 2.125952 CGACATCGTCTGCAGGCA 60.126 61.111 20.11 6.00 34.11 4.75
518 527 2.887568 CCGACATCGTCTGCAGGC 60.888 66.667 15.13 12.04 37.74 4.85
524 533 3.838271 ATGGCGCCGACATCGTCT 61.838 61.111 23.90 0.00 37.74 4.18
544 553 1.912110 GTTCATACTCGTCTGTGTCGC 59.088 52.381 0.00 0.00 0.00 5.19
546 555 3.851976 AGGTTCATACTCGTCTGTGTC 57.148 47.619 0.00 0.00 0.00 3.67
579 588 8.622948 AACACAAAAACCCTGAAAACAAAATA 57.377 26.923 0.00 0.00 0.00 1.40
584 593 6.347859 AGTAACACAAAAACCCTGAAAACA 57.652 33.333 0.00 0.00 0.00 2.83
596 605 7.664318 GGATCCCTCTTAGAAAGTAACACAAAA 59.336 37.037 0.00 0.00 0.00 2.44
600 609 5.349809 CGGATCCCTCTTAGAAAGTAACAC 58.650 45.833 6.06 0.00 0.00 3.32
601 610 4.404715 CCGGATCCCTCTTAGAAAGTAACA 59.595 45.833 6.06 0.00 0.00 2.41
602 611 4.405036 ACCGGATCCCTCTTAGAAAGTAAC 59.595 45.833 9.46 0.00 0.00 2.50
603 612 4.617593 ACCGGATCCCTCTTAGAAAGTAA 58.382 43.478 9.46 0.00 0.00 2.24
605 614 3.117552 ACCGGATCCCTCTTAGAAAGT 57.882 47.619 9.46 0.00 0.00 2.66
606 615 3.197983 ACAACCGGATCCCTCTTAGAAAG 59.802 47.826 9.46 0.00 0.00 2.62
608 617 2.829023 ACAACCGGATCCCTCTTAGAA 58.171 47.619 9.46 0.00 0.00 2.10
610 619 4.748277 TTTACAACCGGATCCCTCTTAG 57.252 45.455 9.46 0.00 0.00 2.18
612 621 4.586306 AATTTACAACCGGATCCCTCTT 57.414 40.909 9.46 0.00 0.00 2.85
613 622 4.586306 AAATTTACAACCGGATCCCTCT 57.414 40.909 9.46 0.00 0.00 3.69
614 623 5.884232 AGTTAAATTTACAACCGGATCCCTC 59.116 40.000 9.46 0.00 0.00 4.30
618 627 8.385858 GTCAGTAGTTAAATTTACAACCGGATC 58.614 37.037 9.46 0.00 0.00 3.36
622 631 8.553696 ACTTGTCAGTAGTTAAATTTACAACCG 58.446 33.333 0.00 0.00 0.00 4.44
624 633 9.659830 CCACTTGTCAGTAGTTAAATTTACAAC 57.340 33.333 0.00 0.00 0.00 3.32
627 636 7.174426 AGCCCACTTGTCAGTAGTTAAATTTAC 59.826 37.037 0.00 0.00 0.00 2.01
641 650 5.009710 CGTTAGATATAGAGCCCACTTGTCA 59.990 44.000 0.00 0.00 0.00 3.58
642 651 5.009811 ACGTTAGATATAGAGCCCACTTGTC 59.990 44.000 0.00 0.00 0.00 3.18
647 656 5.449107 TTCACGTTAGATATAGAGCCCAC 57.551 43.478 0.00 0.00 0.00 4.61
657 666 6.369340 TCCGCAAAAATCTTTCACGTTAGATA 59.631 34.615 5.33 0.00 31.10 1.98
662 671 3.066203 ACTCCGCAAAAATCTTTCACGTT 59.934 39.130 0.00 0.00 0.00 3.99
665 674 3.004315 TGGACTCCGCAAAAATCTTTCAC 59.996 43.478 0.00 0.00 0.00 3.18
678 687 0.740737 CAATGGGAAATGGACTCCGC 59.259 55.000 0.00 0.00 33.36 5.54
683 692 2.767960 AGGAATGCAATGGGAAATGGAC 59.232 45.455 0.00 0.00 0.00 4.02
758 840 1.227615 GCCATCTCTGCTCTGCTCC 60.228 63.158 0.00 0.00 0.00 4.70
759 841 1.227615 GGCCATCTCTGCTCTGCTC 60.228 63.158 0.00 0.00 0.00 4.26
822 910 0.249657 GGATGCTCACCTGTCGATCC 60.250 60.000 0.00 0.00 0.00 3.36
881 1001 2.279120 GGCACTCCGCAGATCGAG 60.279 66.667 0.00 0.00 45.17 4.04
1575 1895 8.454570 TCCGGAACACTTTTAGTATTTTTCTT 57.545 30.769 0.00 0.00 0.00 2.52
1576 1896 8.512138 CATCCGGAACACTTTTAGTATTTTTCT 58.488 33.333 9.01 0.00 0.00 2.52
1577 1897 7.753580 CCATCCGGAACACTTTTAGTATTTTTC 59.246 37.037 9.01 0.00 0.00 2.29
1578 1898 7.449086 TCCATCCGGAACACTTTTAGTATTTTT 59.551 33.333 9.01 0.00 38.83 1.94
1579 1899 6.943718 TCCATCCGGAACACTTTTAGTATTTT 59.056 34.615 9.01 0.00 38.83 1.82
1580 1900 6.478129 TCCATCCGGAACACTTTTAGTATTT 58.522 36.000 9.01 0.00 38.83 1.40
1581 1901 6.057321 TCCATCCGGAACACTTTTAGTATT 57.943 37.500 9.01 0.00 38.83 1.89
1582 1902 5.396436 CCTCCATCCGGAACACTTTTAGTAT 60.396 44.000 9.01 0.00 42.21 2.12
1583 1903 4.081309 CCTCCATCCGGAACACTTTTAGTA 60.081 45.833 9.01 0.00 42.21 1.82
1584 1904 3.307480 CCTCCATCCGGAACACTTTTAGT 60.307 47.826 9.01 0.00 42.21 2.24
1585 1905 3.055385 TCCTCCATCCGGAACACTTTTAG 60.055 47.826 9.01 0.00 42.21 1.85
1586 1906 2.907696 TCCTCCATCCGGAACACTTTTA 59.092 45.455 9.01 0.00 42.21 1.52
1587 1907 1.702957 TCCTCCATCCGGAACACTTTT 59.297 47.619 9.01 0.00 42.21 2.27
1588 1908 1.358152 TCCTCCATCCGGAACACTTT 58.642 50.000 9.01 0.00 42.21 2.66
1589 1909 1.486726 GATCCTCCATCCGGAACACTT 59.513 52.381 9.01 0.00 42.21 3.16
1590 1910 1.123928 GATCCTCCATCCGGAACACT 58.876 55.000 9.01 0.00 42.21 3.55
1591 1911 1.123928 AGATCCTCCATCCGGAACAC 58.876 55.000 9.01 0.00 42.21 3.32
1592 1912 1.123077 CAGATCCTCCATCCGGAACA 58.877 55.000 9.01 0.00 42.21 3.18
1593 1913 1.123928 ACAGATCCTCCATCCGGAAC 58.876 55.000 9.01 0.00 42.21 3.62
1594 1914 2.698797 GTTACAGATCCTCCATCCGGAA 59.301 50.000 9.01 0.00 42.21 4.30
1595 1915 2.091278 AGTTACAGATCCTCCATCCGGA 60.091 50.000 6.61 6.61 39.79 5.14
1596 1916 2.297597 GAGTTACAGATCCTCCATCCGG 59.702 54.545 0.00 0.00 30.71 5.14
1597 1917 3.005261 CAGAGTTACAGATCCTCCATCCG 59.995 52.174 0.00 0.00 30.71 4.18
1598 1918 3.323403 CCAGAGTTACAGATCCTCCATCC 59.677 52.174 0.00 0.00 30.71 3.51
1599 1919 3.323403 CCCAGAGTTACAGATCCTCCATC 59.677 52.174 0.00 0.00 0.00 3.51
1600 1920 3.051803 TCCCAGAGTTACAGATCCTCCAT 60.052 47.826 0.00 0.00 0.00 3.41
1601 1921 2.314852 TCCCAGAGTTACAGATCCTCCA 59.685 50.000 0.00 0.00 0.00 3.86
1602 1922 2.696187 GTCCCAGAGTTACAGATCCTCC 59.304 54.545 0.00 0.00 0.00 4.30
1603 1923 3.366396 TGTCCCAGAGTTACAGATCCTC 58.634 50.000 0.00 0.00 0.00 3.71
1604 1924 3.474798 TGTCCCAGAGTTACAGATCCT 57.525 47.619 0.00 0.00 0.00 3.24
1633 1953 3.564511 CAGTAAATCCCACAAAACAGCG 58.435 45.455 0.00 0.00 0.00 5.18
1651 1971 0.536006 GAGTTGAAGGCCACAGCAGT 60.536 55.000 5.01 0.00 42.56 4.40
1689 2009 3.441572 CCCTAAACATTGAGCAAGAGGTG 59.558 47.826 0.00 0.00 0.00 4.00
1690 2010 3.074538 ACCCTAAACATTGAGCAAGAGGT 59.925 43.478 0.00 0.00 0.00 3.85
1692 2012 6.352516 AGATACCCTAAACATTGAGCAAGAG 58.647 40.000 0.00 0.00 0.00 2.85
1693 2013 6.313519 AGATACCCTAAACATTGAGCAAGA 57.686 37.500 0.00 0.00 0.00 3.02
1694 2014 6.678900 GCAAGATACCCTAAACATTGAGCAAG 60.679 42.308 0.00 0.00 0.00 4.01
1696 2016 4.640201 GCAAGATACCCTAAACATTGAGCA 59.360 41.667 0.00 0.00 0.00 4.26
1807 2185 2.704725 CTGCAACCGTTTTGCTGTAT 57.295 45.000 17.12 0.00 45.13 2.29
1857 2236 4.418973 AATGAGCTCAGAGTGCATGTAT 57.581 40.909 22.96 0.00 0.00 2.29
1879 2258 4.973168 TGTAACAAGAAAGGAGCTGACAT 58.027 39.130 0.00 0.00 0.00 3.06
1991 2425 7.230849 TCAAAACATAGATTGCAGTGGAATT 57.769 32.000 11.49 4.62 0.00 2.17
2022 2468 5.674525 TCGCTATCAGAATCTGGTTCATTT 58.325 37.500 10.71 0.00 39.39 2.32
2028 2474 3.304996 CGTCATCGCTATCAGAATCTGGT 60.305 47.826 10.71 5.74 31.51 4.00
2108 2593 3.250040 ACTGTGCTGTTGAATAACCGAAC 59.750 43.478 0.00 0.00 35.92 3.95
2167 4091 0.884704 TGAGCGTCTTCTTTGGGCAC 60.885 55.000 0.00 0.00 0.00 5.01
2252 4176 7.572523 TCTTCTAATGGCCAATCAACTATTG 57.427 36.000 10.96 0.00 43.99 1.90
2306 4237 3.077359 ACAAATGAGCTACCTTGAGCAC 58.923 45.455 7.85 0.00 45.43 4.40
2570 4505 1.806542 CATGAAACTCAACCACCTCGG 59.193 52.381 0.00 0.00 42.50 4.63
2628 4563 2.027745 ACCATGAAGCGCTATAGGGATG 60.028 50.000 25.28 13.46 0.00 3.51
2639 4574 2.420628 TTTTGAGCAACCATGAAGCG 57.579 45.000 0.00 0.00 0.00 4.68
2716 4657 2.036217 CTGCCAAAATGCTTGGAACTGA 59.964 45.455 7.37 0.00 42.06 3.41
2751 4692 7.689812 GCATATTTTGATATACTAGCTTGCACG 59.310 37.037 0.00 0.00 0.00 5.34
2809 4785 8.237811 ACAATAACACCAATTCTGAAGAACTT 57.762 30.769 0.00 0.00 36.80 2.66
2831 4807 6.401688 CCGAACAAATAAGATGACGCTAACAA 60.402 38.462 0.00 0.00 0.00 2.83
2894 4870 3.460103 CTCAAATGCATAAACATGCCCC 58.540 45.455 0.00 0.00 46.43 5.80
2946 4922 4.274214 TCATTATCGCCATTCTCTTTGCTG 59.726 41.667 0.00 0.00 0.00 4.41
2954 4936 6.115446 TGAAGAACTTCATTATCGCCATTCT 58.885 36.000 12.40 0.00 43.90 2.40
2955 4937 6.363577 TGAAGAACTTCATTATCGCCATTC 57.636 37.500 12.40 0.00 43.90 2.67
3007 4990 0.035317 AAGCGCAATGTCTCCAGTCA 59.965 50.000 11.47 0.00 0.00 3.41
3050 5033 9.853177 CTGGGGAATGTATTAGTCTTTCTAAAT 57.147 33.333 0.00 0.00 41.25 1.40
3051 5034 9.053472 TCTGGGGAATGTATTAGTCTTTCTAAA 57.947 33.333 0.00 0.00 41.25 1.85
3052 5035 8.483758 GTCTGGGGAATGTATTAGTCTTTCTAA 58.516 37.037 0.00 0.00 41.98 2.10
3053 5036 7.070821 GGTCTGGGGAATGTATTAGTCTTTCTA 59.929 40.741 0.00 0.00 0.00 2.10
3054 5037 6.126739 GGTCTGGGGAATGTATTAGTCTTTCT 60.127 42.308 0.00 0.00 0.00 2.52
3055 5038 6.056236 GGTCTGGGGAATGTATTAGTCTTTC 58.944 44.000 0.00 0.00 0.00 2.62
3056 5039 5.104067 GGGTCTGGGGAATGTATTAGTCTTT 60.104 44.000 0.00 0.00 0.00 2.52
3057 5040 4.412528 GGGTCTGGGGAATGTATTAGTCTT 59.587 45.833 0.00 0.00 0.00 3.01
3058 5041 3.974642 GGGTCTGGGGAATGTATTAGTCT 59.025 47.826 0.00 0.00 0.00 3.24
3059 5042 3.974642 AGGGTCTGGGGAATGTATTAGTC 59.025 47.826 0.00 0.00 0.00 2.59
3060 5043 3.716872 CAGGGTCTGGGGAATGTATTAGT 59.283 47.826 0.00 0.00 0.00 2.24
3061 5044 3.716872 ACAGGGTCTGGGGAATGTATTAG 59.283 47.826 0.00 0.00 35.51 1.73
3062 5045 3.458118 CACAGGGTCTGGGGAATGTATTA 59.542 47.826 0.00 0.00 35.51 0.98
3063 5046 2.242196 CACAGGGTCTGGGGAATGTATT 59.758 50.000 0.00 0.00 35.51 1.89
3064 5047 1.846439 CACAGGGTCTGGGGAATGTAT 59.154 52.381 0.00 0.00 35.51 2.29
3065 5048 1.285280 CACAGGGTCTGGGGAATGTA 58.715 55.000 0.00 0.00 35.51 2.29
3066 5049 2.078452 CACAGGGTCTGGGGAATGT 58.922 57.895 0.00 0.00 35.51 2.71
3067 5050 1.379044 GCACAGGGTCTGGGGAATG 60.379 63.158 0.00 0.00 35.08 2.67
3068 5051 1.434513 TTGCACAGGGTCTGGGGAAT 61.435 55.000 0.00 0.00 40.13 3.01
3069 5052 2.067932 CTTGCACAGGGTCTGGGGAA 62.068 60.000 4.20 4.20 42.60 3.97
3070 5053 2.449518 TTGCACAGGGTCTGGGGA 60.450 61.111 0.00 0.00 35.08 4.81
3071 5054 2.034687 CTTGCACAGGGTCTGGGG 59.965 66.667 0.00 0.00 35.08 4.96
3072 5055 2.674380 GCTTGCACAGGGTCTGGG 60.674 66.667 0.00 0.00 38.04 4.45
3073 5056 3.052082 CGCTTGCACAGGGTCTGG 61.052 66.667 0.00 0.00 35.51 3.86
3074 5057 3.052082 CCGCTTGCACAGGGTCTG 61.052 66.667 10.46 0.00 37.52 3.51
3075 5058 4.335647 CCCGCTTGCACAGGGTCT 62.336 66.667 11.20 0.00 40.27 3.85
3076 5059 4.329545 TCCCGCTTGCACAGGGTC 62.330 66.667 17.06 0.00 45.27 4.46
3077 5060 4.335647 CTCCCGCTTGCACAGGGT 62.336 66.667 17.06 0.00 45.27 4.34
3079 5062 3.315142 TAGCTCCCGCTTGCACAGG 62.315 63.158 0.00 0.00 46.47 4.00
3080 5063 2.103042 GTAGCTCCCGCTTGCACAG 61.103 63.158 0.00 0.00 46.47 3.66
3081 5064 2.047274 GTAGCTCCCGCTTGCACA 60.047 61.111 0.00 0.00 46.47 4.57
3082 5065 1.450312 ATGTAGCTCCCGCTTGCAC 60.450 57.895 0.00 0.00 46.47 4.57
3083 5066 1.450134 CATGTAGCTCCCGCTTGCA 60.450 57.895 0.00 0.00 46.47 4.08
3084 5067 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
3085 5068 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
3086 5069 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
3088 5071 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
3089 5072 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
3090 5073 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
3091 5074 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
3092 5075 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
3093 5076 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
3094 5077 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
3095 5078 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
3096 5079 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
3135 5118 8.669243 GTTCTTTCTTGAAGGTCCATGTATTAG 58.331 37.037 0.00 0.00 35.98 1.73
3141 5124 7.609532 AGAATAGTTCTTTCTTGAAGGTCCATG 59.390 37.037 0.00 0.00 36.36 3.66
3212 5209 1.349026 ACTGGAGACACCACTGGATTG 59.651 52.381 0.71 0.00 44.64 2.67
3310 5327 0.764890 TACAACAGGCCAGCTCAGTT 59.235 50.000 5.01 0.00 0.00 3.16
3322 5339 5.047802 ACAAGCATTTCCCAAGATACAACAG 60.048 40.000 0.00 0.00 0.00 3.16
3435 5515 1.414158 CACTCACAGATCCCCGGTAT 58.586 55.000 0.00 0.00 0.00 2.73
3460 5540 2.034048 GAAGCCCTCCGAGATGACCC 62.034 65.000 0.00 0.00 0.00 4.46
3482 5562 4.181578 CACCTAAGACGGTTATCACCTTG 58.818 47.826 0.00 0.00 41.64 3.61
3561 6079 1.150567 GCTGCTGCAGACTACCGATG 61.151 60.000 32.30 3.79 39.41 3.84
3565 6083 0.459934 CTGAGCTGCTGCAGACTACC 60.460 60.000 32.30 14.39 42.74 3.18
3598 6129 7.916552 AGCATTACTACATGAACGAATAAACC 58.083 34.615 0.00 0.00 0.00 3.27
3694 6235 4.642437 TGTGCCAACTCACAAATTAACTGA 59.358 37.500 0.00 0.00 43.27 3.41
3697 6238 3.735746 GCTGTGCCAACTCACAAATTAAC 59.264 43.478 0.00 0.00 45.22 2.01
3703 6244 1.473258 AAAGCTGTGCCAACTCACAA 58.527 45.000 0.00 0.00 45.22 3.33
3709 6250 3.507622 AGGAGAAATAAAGCTGTGCCAAC 59.492 43.478 0.00 0.00 0.00 3.77
3711 6252 3.439857 AGGAGAAATAAAGCTGTGCCA 57.560 42.857 0.00 0.00 0.00 4.92
3718 6259 7.171678 ACGATAGCACAATAGGAGAAATAAAGC 59.828 37.037 0.00 0.00 42.67 3.51
3729 6270 2.494059 CCCCAACGATAGCACAATAGG 58.506 52.381 0.00 0.00 42.67 2.57
3733 6274 0.906066 TAGCCCCAACGATAGCACAA 59.094 50.000 0.00 0.00 42.67 3.33
3740 6281 1.906574 TCTTTCAGTAGCCCCAACGAT 59.093 47.619 0.00 0.00 0.00 3.73
3748 6289 5.123979 CCATTACCAAGTTCTTTCAGTAGCC 59.876 44.000 0.00 0.00 0.00 3.93
3764 6305 7.387397 GCAATTTTGTTTGAGATTCCATTACCA 59.613 33.333 0.00 0.00 0.00 3.25
3768 6309 6.072893 GCTGCAATTTTGTTTGAGATTCCATT 60.073 34.615 0.00 0.00 0.00 3.16
3792 6333 3.876274 TGTACATGAACAGAGGAGAGC 57.124 47.619 0.00 0.00 0.00 4.09
3802 6343 8.988934 TGTAAGAGTTGAGAAATGTACATGAAC 58.011 33.333 9.63 7.77 0.00 3.18
3827 6368 5.006386 ACCAGGAGATAGTTCAGCTTTTTG 58.994 41.667 0.00 0.00 0.00 2.44
3834 6375 2.482142 GGCGAACCAGGAGATAGTTCAG 60.482 54.545 0.00 0.00 39.89 3.02
3877 6418 9.658799 GCTTACCATATATGCTTTGAAGAGATA 57.341 33.333 7.24 0.00 0.00 1.98
3895 6436 7.136822 TGTCCAAGATACAATAGCTTACCAT 57.863 36.000 0.00 0.00 31.74 3.55
3896 6437 6.553953 TGTCCAAGATACAATAGCTTACCA 57.446 37.500 0.00 0.00 31.74 3.25
3897 6438 7.859325 TTTGTCCAAGATACAATAGCTTACC 57.141 36.000 0.00 0.00 36.75 2.85
3898 6439 8.726988 TGTTTTGTCCAAGATACAATAGCTTAC 58.273 33.333 0.00 0.00 36.75 2.34
3931 6472 7.812669 ACAAAAATGTCAATCTACGAAATTCCC 59.187 33.333 0.00 0.00 0.00 3.97
3986 6527 2.664851 CAACTCCTCGGTTGCGCA 60.665 61.111 5.66 5.66 39.76 6.09


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

AutoCloner maintained by Alex Coulton.