Multiple sequence alignment - TraesCS4B01G006500

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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 TraesCS4B01G006500 chr4B 100.000 4944 0 0 1 4944 4334282 4329339 0.000000e+00 9130.0
1 TraesCS4B01G006500 chr4B 91.068 2922 192 27 1896 4758 4301749 4298838 0.000000e+00 3886.0
2 TraesCS4B01G006500 chr4B 89.378 932 62 16 1 911 4303230 4302315 0.000000e+00 1138.0
3 TraesCS4B01G006500 chr4B 94.046 571 33 1 1296 1865 4302320 4301750 0.000000e+00 865.0
4 TraesCS4B01G006500 chr4A 92.035 3729 223 23 1 3671 599647365 599643653 0.000000e+00 5173.0
5 TraesCS4B01G006500 chr4A 89.631 704 63 6 3698 4399 599643598 599642903 0.000000e+00 887.0
6 TraesCS4B01G006500 chr4A 78.777 556 91 15 58 590 600279831 600280382 1.020000e-91 348.0
7 TraesCS4B01G006500 chr4D 93.202 2589 127 13 2 2557 4245828 4248400 0.000000e+00 3760.0
8 TraesCS4B01G006500 chr4D 91.549 1846 102 16 2568 4399 4248452 4250257 0.000000e+00 2495.0
9 TraesCS4B01G006500 chr4D 85.489 1709 160 22 139 1803 4287940 4286276 0.000000e+00 1701.0
10 TraesCS4B01G006500 chr4D 88.421 1045 89 18 2891 3912 4285342 4284307 0.000000e+00 1230.0
11 TraesCS4B01G006500 chr4D 77.458 1251 222 39 2810 4027 4273340 4272117 0.000000e+00 693.0
12 TraesCS4B01G006500 chr4D 86.190 630 56 11 982 1602 4333064 4332457 0.000000e+00 652.0
13 TraesCS4B01G006500 chr4D 89.516 496 44 3 1598 2086 4331976 4331482 5.440000e-174 621.0
14 TraesCS4B01G006500 chr4D 96.175 366 14 0 4400 4765 74616139 74616504 2.550000e-167 599.0
15 TraesCS4B01G006500 chr4D 95.924 368 14 1 4400 4766 397161801 397162168 3.290000e-166 595.0
16 TraesCS4B01G006500 chr4D 86.595 373 42 2 2 374 4333511 4333147 5.960000e-109 405.0
17 TraesCS4B01G006500 chr4D 79.672 610 68 33 1944 2527 4286231 4285652 6.000000e-104 388.0
18 TraesCS4B01G006500 chr4D 93.956 182 9 1 4765 4944 4226307 4226488 1.750000e-69 274.0
19 TraesCS4B01G006500 chr4D 73.839 818 158 39 1274 2075 4321142 4320365 1.750000e-69 274.0
20 TraesCS4B01G006500 chr4D 94.702 151 8 0 2568 2718 4285554 4285404 8.270000e-58 235.0
21 TraesCS4B01G006500 chr5A 83.534 747 99 12 1060 1801 555596479 555595752 0.000000e+00 676.0
22 TraesCS4B01G006500 chr6D 96.216 370 13 1 4397 4765 14797890 14798259 5.470000e-169 604.0
23 TraesCS4B01G006500 chr6D 93.923 181 9 1 4765 4943 307837163 307836983 6.310000e-69 272.0
24 TraesCS4B01G006500 chr6D 81.416 226 40 1 110 333 34086925 34086700 3.040000e-42 183.0
25 TraesCS4B01G006500 chr2B 96.216 370 13 1 4398 4766 579608093 579608462 5.470000e-169 604.0
26 TraesCS4B01G006500 chr2D 96.438 365 13 0 4402 4766 445283594 445283230 1.970000e-168 603.0
27 TraesCS4B01G006500 chr2D 96.185 367 14 0 4400 4766 198163479 198163113 7.080000e-168 601.0
28 TraesCS4B01G006500 chr7B 96.175 366 14 0 4401 4766 497030065 497029700 2.550000e-167 599.0
29 TraesCS4B01G006500 chr7B 74.640 347 72 10 1288 1632 732749249 732748917 6.670000e-29 139.0
30 TraesCS4B01G006500 chr1D 95.913 367 15 0 4400 4766 297301214 297301580 3.290000e-166 595.0
31 TraesCS4B01G006500 chr1D 94.475 181 8 1 4765 4943 446057456 446057636 1.360000e-70 278.0
32 TraesCS4B01G006500 chr1D 93.956 182 8 2 4765 4943 174762485 174762666 6.310000e-69 272.0
33 TraesCS4B01G006500 chr5B 82.399 642 94 7 1164 1800 534487951 534487324 4.350000e-150 542.0
34 TraesCS4B01G006500 chr5B 81.250 304 44 7 1060 1357 534605461 534605165 2.980000e-57 233.0
35 TraesCS4B01G006500 chr3D 94.475 181 8 1 4765 4943 308007542 308007362 1.360000e-70 278.0
36 TraesCS4B01G006500 chr3D 94.475 181 7 2 4765 4943 442245647 442245468 4.880000e-70 276.0
37 TraesCS4B01G006500 chr3D 93.923 181 9 1 4765 4943 158521925 158521745 6.310000e-69 272.0
38 TraesCS4B01G006500 chr3D 94.595 37 2 0 61 97 539707422 539707386 1.920000e-04 58.4
39 TraesCS4B01G006500 chr7D 94.444 180 9 1 4765 4943 445951715 445951536 4.880000e-70 276.0
40 TraesCS4B01G006500 chr7D 92.683 41 1 2 63 102 499524336 499524375 1.920000e-04 58.4
41 TraesCS4B01G006500 chr5D 93.923 181 9 1 4765 4943 114728739 114728919 6.310000e-69 272.0
42 TraesCS4B01G006500 chr6B 79.137 278 55 2 59 333 16445390 16445113 6.530000e-44 189.0
43 TraesCS4B01G006500 chr6B 89.796 49 3 2 60 107 69963447 69963494 1.490000e-05 62.1
44 TraesCS4B01G006500 chr7A 86.154 65 4 5 64 125 565333169 565333231 1.150000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G006500 chr4B 4329339 4334282 4943 True 9130.000000 9130 100.000000 1 4944 1 chr4B.!!$R1 4943
1 TraesCS4B01G006500 chr4B 4298838 4303230 4392 True 1963.000000 3886 91.497333 1 4758 3 chr4B.!!$R2 4757
2 TraesCS4B01G006500 chr4A 599642903 599647365 4462 True 3030.000000 5173 90.833000 1 4399 2 chr4A.!!$R1 4398
3 TraesCS4B01G006500 chr4A 600279831 600280382 551 False 348.000000 348 78.777000 58 590 1 chr4A.!!$F1 532
4 TraesCS4B01G006500 chr4D 4245828 4250257 4429 False 3127.500000 3760 92.375500 2 4399 2 chr4D.!!$F4 4397
5 TraesCS4B01G006500 chr4D 4284307 4287940 3633 True 888.500000 1701 87.071000 139 3912 4 chr4D.!!$R3 3773
6 TraesCS4B01G006500 chr4D 4272117 4273340 1223 True 693.000000 693 77.458000 2810 4027 1 chr4D.!!$R1 1217
7 TraesCS4B01G006500 chr4D 4331482 4333511 2029 True 559.333333 652 87.433667 2 2086 3 chr4D.!!$R4 2084
8 TraesCS4B01G006500 chr4D 4320365 4321142 777 True 274.000000 274 73.839000 1274 2075 1 chr4D.!!$R2 801
9 TraesCS4B01G006500 chr5A 555595752 555596479 727 True 676.000000 676 83.534000 1060 1801 1 chr5A.!!$R1 741
10 TraesCS4B01G006500 chr5B 534487324 534487951 627 True 542.000000 542 82.399000 1164 1800 1 chr5B.!!$R1 636

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
54 55 0.102120 CTGCCGTGCAAACTTGGAAA 59.898 50.0 0.0 0.0 38.41 3.13 F
688 747 0.905357 AGTTCGGCAAGGCTACTGAT 59.095 50.0 0.0 0.0 0.00 2.90 F
1198 1260 0.461163 CATCCATGTTCGCCACGGTA 60.461 55.0 0.0 0.0 0.00 4.02 F
1222 1294 0.826256 CATCCCCTCGTCGTCCCATA 60.826 60.0 0.0 0.0 0.00 2.74 F
2944 3637 0.908198 ACCTGAGATGGCTGGAGTTC 59.092 55.0 0.0 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1150 1212 0.966179 TGTTTAGCCGTGCTCTGAGA 59.034 50.000 9.28 0.00 40.44 3.27 R
2318 2923 0.455464 TAACAGCACGATCGACACGG 60.455 55.000 24.34 13.02 34.93 4.94 R
2926 3619 1.202330 AGAACTCCAGCCATCTCAGG 58.798 55.000 0.00 0.00 0.00 3.86 R
3003 3698 3.188048 GCAGTCAAATTCTGGACAGAGTG 59.812 47.826 1.92 3.37 38.88 3.51 R
4311 5063 0.038159 GCACGAGCACTGGTACTCTT 60.038 55.000 0.00 0.00 41.58 2.85 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
49 50 3.964875 CCGCTGCCGTGCAAACTT 61.965 61.111 0.00 0.00 38.41 2.66
50 51 2.726912 CGCTGCCGTGCAAACTTG 60.727 61.111 0.00 0.00 38.41 3.16
51 52 2.355009 GCTGCCGTGCAAACTTGG 60.355 61.111 0.00 0.00 38.41 3.61
52 53 2.844451 GCTGCCGTGCAAACTTGGA 61.844 57.895 0.00 0.00 38.41 3.53
53 54 1.732917 CTGCCGTGCAAACTTGGAA 59.267 52.632 0.00 0.00 38.41 3.53
54 55 0.102120 CTGCCGTGCAAACTTGGAAA 59.898 50.000 0.00 0.00 38.41 3.13
146 149 2.731691 GAAACCACAGCGCCCTCTCA 62.732 60.000 2.29 0.00 0.00 3.27
204 209 2.922503 TCCGAGCAACTCTGGCCA 60.923 61.111 4.71 4.71 0.00 5.36
236 241 1.455773 TCCACGAGGCGGAGATCAT 60.456 57.895 0.00 0.00 33.74 2.45
313 326 3.950794 GAGGCGGCGAATGTGGACA 62.951 63.158 12.98 0.00 0.00 4.02
333 346 2.711922 CGAGCTCGCCTACACCCTT 61.712 63.158 25.07 0.00 0.00 3.95
390 417 2.997986 GCCGTTCCTCAGTCGATTAAAA 59.002 45.455 0.00 0.00 0.00 1.52
393 420 5.292589 GCCGTTCCTCAGTCGATTAAAATTA 59.707 40.000 0.00 0.00 0.00 1.40
688 747 0.905357 AGTTCGGCAAGGCTACTGAT 59.095 50.000 0.00 0.00 0.00 2.90
796 855 2.352651 CCAGACAGTTCACACACACAAG 59.647 50.000 0.00 0.00 0.00 3.16
804 863 5.121611 CAGTTCACACACACAAGAGTACAAA 59.878 40.000 0.00 0.00 0.00 2.83
836 895 4.563630 CGAACGACGGAACCATCA 57.436 55.556 0.00 0.00 38.46 3.07
886 945 2.113433 CATCTGGCTGCAGCTGTCC 61.113 63.158 35.82 20.88 41.70 4.02
939 998 2.182496 CATGCATGCCGTCTCCAAA 58.818 52.632 14.93 0.00 0.00 3.28
980 1040 1.278127 TGGCCAAGCAAGTAGAGGTAC 59.722 52.381 0.61 0.00 0.00 3.34
990 1050 3.362870 AGTAGAGGTACCGTAGCACTT 57.637 47.619 12.06 0.00 0.00 3.16
1024 1084 3.749064 GCGGGAGAGTCTCGTGCA 61.749 66.667 23.05 0.00 43.50 4.57
1053 1113 4.017867 CCACATAAAGGTTTCCTTCCCCTA 60.018 45.833 1.36 0.00 43.92 3.53
1198 1260 0.461163 CATCCATGTTCGCCACGGTA 60.461 55.000 0.00 0.00 0.00 4.02
1202 1264 1.404449 CCATGTTCGCCACGGTAAGTA 60.404 52.381 0.00 0.00 0.00 2.24
1222 1294 0.826256 CATCCCCTCGTCGTCCCATA 60.826 60.000 0.00 0.00 0.00 2.74
1282 1361 5.952347 TGACTAGTCTATCTTTGCCTTCTCA 59.048 40.000 23.01 0.00 0.00 3.27
1358 1437 1.227764 CATGGAGGAGGATGGCACG 60.228 63.158 0.00 0.00 0.00 5.34
1558 1641 1.988015 CCAACCCGTGGTGGACTAT 59.012 57.895 0.00 0.00 43.20 2.12
1622 2190 9.725019 CCAGCTACAGGTATAATGATGATAAAA 57.275 33.333 0.00 0.00 0.00 1.52
1677 2250 3.773860 TGATTGTTTCTGTGTTGCGTT 57.226 38.095 0.00 0.00 0.00 4.84
1780 2363 3.729163 GCCGAATTTAGCTGTGCTTCTTC 60.729 47.826 0.00 0.00 40.44 2.87
1783 2366 5.525378 CCGAATTTAGCTGTGCTTCTTCTAT 59.475 40.000 0.00 0.00 40.44 1.98
1991 2580 7.970061 TGTCGTATACACTCAAGTATAACAACC 59.030 37.037 3.32 0.00 38.34 3.77
1992 2581 7.970061 GTCGTATACACTCAAGTATAACAACCA 59.030 37.037 3.32 0.00 38.34 3.67
2012 2601 4.099824 CCAAGTTTTGTTGTGTCGTTACC 58.900 43.478 0.00 0.00 0.00 2.85
2139 2735 2.224523 TGGAATATTCTAGGCCGGCAAG 60.225 50.000 30.85 24.28 0.00 4.01
2171 2767 5.008217 TGAGTTGGGATTCTACAAACGTTTG 59.992 40.000 33.52 33.52 43.62 2.93
2231 2828 4.467795 TGGTCATTTTTCTGGTTTGTCCAA 59.532 37.500 0.00 0.00 46.59 3.53
2260 2857 7.543520 GCTACTAGAAAAACCACGTACTGTATT 59.456 37.037 0.00 0.00 0.00 1.89
2311 2916 4.088762 GTGTGCACGTCATGGGCG 62.089 66.667 13.13 8.61 0.00 6.13
2336 2941 1.733041 CCGTGTCGATCGTGCTGTT 60.733 57.895 15.94 0.00 0.00 3.16
2379 2984 3.057526 GCCCCATTTACTTGTGTTCTGTC 60.058 47.826 0.00 0.00 0.00 3.51
2464 3080 8.786937 TTATAAAAATGTCTAGTACTACCGCG 57.213 34.615 0.00 0.00 0.00 6.46
2547 3194 7.218393 CGTGATTATCATCGCTAGTATGGTTAC 59.782 40.741 0.00 0.00 37.72 2.50
2557 3204 3.530265 AGTATGGTTACGCGGATCAAA 57.470 42.857 12.47 0.00 33.32 2.69
2558 3205 3.192466 AGTATGGTTACGCGGATCAAAC 58.808 45.455 12.47 6.53 33.32 2.93
2559 3206 2.102070 ATGGTTACGCGGATCAAACA 57.898 45.000 12.47 8.16 0.00 2.83
2560 3207 1.880271 TGGTTACGCGGATCAAACAA 58.120 45.000 12.47 0.00 0.00 2.83
2561 3208 2.428491 TGGTTACGCGGATCAAACAAT 58.572 42.857 12.47 0.00 0.00 2.71
2562 3209 3.597255 TGGTTACGCGGATCAAACAATA 58.403 40.909 12.47 0.00 0.00 1.90
2563 3210 4.193090 TGGTTACGCGGATCAAACAATAT 58.807 39.130 12.47 0.00 0.00 1.28
2564 3211 5.358090 TGGTTACGCGGATCAAACAATATA 58.642 37.500 12.47 0.00 0.00 0.86
2565 3212 5.992829 TGGTTACGCGGATCAAACAATATAT 59.007 36.000 12.47 0.00 0.00 0.86
2566 3213 6.483974 TGGTTACGCGGATCAAACAATATATT 59.516 34.615 12.47 0.00 0.00 1.28
2608 3296 7.936847 TCTTCTTTGTATGTATCAGTGTTGGTT 59.063 33.333 0.00 0.00 0.00 3.67
2629 3317 6.889019 GTTCTAAGAAAGTGAACCTATCCG 57.111 41.667 0.00 0.00 35.41 4.18
2722 3414 9.986157 ATATCTTGCACAATCATTATTATCCCT 57.014 29.630 0.00 0.00 0.00 4.20
2797 3489 8.138928 TGATGGCACTATATTTAGCTCATAGT 57.861 34.615 0.00 0.00 36.21 2.12
2938 3631 3.616956 TGACTAAACCTGAGATGGCTG 57.383 47.619 0.00 0.00 0.00 4.85
2944 3637 0.908198 ACCTGAGATGGCTGGAGTTC 59.092 55.000 0.00 0.00 0.00 3.01
2983 3678 4.007659 GGTTATGATTTCCGAACCACTGT 58.992 43.478 0.00 0.00 40.91 3.55
2999 3694 3.303132 CCACTGTTTAGTTCAGTTCACGC 60.303 47.826 0.00 0.00 43.14 5.34
3003 3698 3.427528 TGTTTAGTTCAGTTCACGCGATC 59.572 43.478 15.93 0.00 0.00 3.69
3090 3786 2.224137 TGCTTGGAGTGAGTTCTGTGAG 60.224 50.000 0.00 0.00 0.00 3.51
3128 3824 0.689623 GCTATGATGCAGGTAGCCCT 59.310 55.000 13.79 0.00 44.83 5.19
3155 3852 4.041723 GTGCGTATGTTTGCTTTGACTTT 58.958 39.130 0.00 0.00 0.00 2.66
3251 3955 7.085746 TCTGATTGTTGTTGCTGTTGATATTG 58.914 34.615 0.00 0.00 0.00 1.90
3338 4042 7.664318 TCACGATTCAGTAGCTATATGAGGTAA 59.336 37.037 10.44 0.00 39.82 2.85
3378 4082 7.678194 TTTCTTTGTTTCTCAGCGTAAATTG 57.322 32.000 0.00 0.00 0.00 2.32
3472 4181 2.880890 GCCACCAATATGCACCTTAGAG 59.119 50.000 0.00 0.00 0.00 2.43
3488 4197 9.640963 GCACCTTAGAGATGTCGTAATAATTAT 57.359 33.333 0.00 0.00 0.00 1.28
3664 4375 3.489229 GCTTTGGAGGGCGATTATGAAAC 60.489 47.826 0.00 0.00 0.00 2.78
3732 4471 5.852827 TGTTGTCATGTGTCAATGTCTCTA 58.147 37.500 0.00 0.00 0.00 2.43
3747 4486 9.072375 TCAATGTCTCTATCAACTCTATACCAG 57.928 37.037 0.00 0.00 0.00 4.00
3748 4487 6.885952 TGTCTCTATCAACTCTATACCAGC 57.114 41.667 0.00 0.00 0.00 4.85
3749 4488 5.770663 TGTCTCTATCAACTCTATACCAGCC 59.229 44.000 0.00 0.00 0.00 4.85
3750 4489 5.004448 TCTCTATCAACTCTATACCAGCCG 58.996 45.833 0.00 0.00 0.00 5.52
3807 4549 4.903045 TTAAACTCTCTACCTGGTTGGG 57.097 45.455 3.84 2.45 41.11 4.12
3808 4550 0.984995 AACTCTCTACCTGGTTGGGC 59.015 55.000 3.84 0.00 41.11 5.36
3816 4558 4.169666 TCTACCTGGTTGGGCTTTTACTA 58.830 43.478 3.84 0.00 41.11 1.82
3870 4620 3.396560 CCCGTCTCTTTACCGTCTTTTT 58.603 45.455 0.00 0.00 0.00 1.94
3875 4625 6.366877 CCGTCTCTTTACCGTCTTTTTGAATA 59.633 38.462 0.00 0.00 0.00 1.75
3876 4626 7.411588 CCGTCTCTTTACCGTCTTTTTGAATAG 60.412 40.741 0.00 0.00 0.00 1.73
3913 4664 1.801242 AAGGGGAAAGGTTTGTTGGG 58.199 50.000 0.00 0.00 0.00 4.12
3951 4702 2.211250 AGTGAGTGCATGGCTTGATT 57.789 45.000 4.32 0.00 0.00 2.57
4003 4754 2.210013 TGTCGCTTGCTGACCTCCT 61.210 57.895 12.30 0.00 35.46 3.69
4013 4764 1.619977 GCTGACCTCCTCCACCTCTAA 60.620 57.143 0.00 0.00 0.00 2.10
4072 4823 1.205179 TGCGGGCGAACAAGATACTAA 59.795 47.619 0.00 0.00 0.00 2.24
4078 4829 5.508489 CGGGCGAACAAGATACTAATAGGAA 60.508 44.000 0.00 0.00 0.00 3.36
4089 4840 8.025299 AGATACTAATAGGAAGGGGAGGTAAT 57.975 38.462 0.00 0.00 0.00 1.89
4118 4869 1.798223 ACGATGTGTGAAATGGTGTCG 59.202 47.619 0.00 0.00 0.00 4.35
4132 4883 2.569853 TGGTGTCGGGTAGAACATCAAT 59.430 45.455 0.00 0.00 0.00 2.57
4141 4892 3.118038 GGTAGAACATCAATAGGGCCACA 60.118 47.826 6.18 0.00 0.00 4.17
4161 4912 4.095483 CACAAATCAAGTGATCTAGTGGCC 59.905 45.833 0.00 0.00 39.30 5.36
4162 4913 4.263462 ACAAATCAAGTGATCTAGTGGCCA 60.263 41.667 0.00 0.00 32.75 5.36
4198 4949 2.992114 AAGCGCCGGAGTCTCTGT 60.992 61.111 5.05 0.00 0.00 3.41
4209 4960 3.305676 CGGAGTCTCTGTGTGTCTTCAAT 60.306 47.826 0.00 0.00 0.00 2.57
4214 4965 2.740981 CTCTGTGTGTCTTCAATGCCTC 59.259 50.000 0.00 0.00 0.00 4.70
4311 5063 2.100087 TGCCATCTACGCGATCAAGTAA 59.900 45.455 15.93 0.00 0.00 2.24
4335 5087 4.767255 CCAGTGCTCGTGCCCTCC 62.767 72.222 7.05 0.00 38.71 4.30
4347 5099 3.801997 CCCTCCATGGCTTCCGCT 61.802 66.667 6.96 0.00 36.09 5.52
4357 5109 0.034616 GGCTTCCGCTGCTAGATCAT 59.965 55.000 0.00 0.00 36.09 2.45
4404 5156 7.493971 TGTTTTACCATGACAACATTTTGAAGG 59.506 33.333 0.00 0.00 36.48 3.46
4411 5163 8.875803 CCATGACAACATTTTGAAGGAAATATG 58.124 33.333 0.00 0.00 36.48 1.78
4413 5165 6.873076 TGACAACATTTTGAAGGAAATATGCC 59.127 34.615 0.00 0.00 36.48 4.40
4549 5301 5.681639 ACAAATACCATGTCCCTAGTAAGC 58.318 41.667 0.00 0.00 0.00 3.09
4567 5319 4.781775 AAGCCTCTACTAGACTAGCTCA 57.218 45.455 9.52 0.00 0.00 4.26
4570 5322 5.070001 AGCCTCTACTAGACTAGCTCATTG 58.930 45.833 9.52 0.00 0.00 2.82
4594 5346 6.659242 TGATCAAAGATGGTTAAGGTTTCCTC 59.341 38.462 0.00 0.00 30.89 3.71
4596 5348 6.552008 TCAAAGATGGTTAAGGTTTCCTCAT 58.448 36.000 0.00 0.00 30.89 2.90
4632 5384 6.092122 TGTTGTCATTTGATAACGAGATCACC 59.908 38.462 13.29 0.00 45.39 4.02
4642 5394 6.207614 TGATAACGAGATCACCTCATTAGGAG 59.792 42.308 0.00 0.00 46.70 3.69
4687 5439 6.148480 CCCATCTGTTAGCTTAGCATAATGAC 59.852 42.308 7.07 0.00 0.00 3.06
4692 5444 5.878116 TGTTAGCTTAGCATAATGACCGTTT 59.122 36.000 7.07 0.00 0.00 3.60
4703 5455 7.067008 AGCATAATGACCGTTTAGTTTATTGCT 59.933 33.333 0.00 0.00 0.00 3.91
4712 5464 7.540745 ACCGTTTAGTTTATTGCTATTGCTTTG 59.459 33.333 0.00 0.00 40.48 2.77
4722 5474 5.050644 TGCTATTGCTTTGTTCATGTCAG 57.949 39.130 0.00 0.00 40.48 3.51
4742 5494 8.637196 TGTCAGATACATATTCCTTCGACTAT 57.363 34.615 0.00 0.00 31.43 2.12
4758 5510 5.773575 TCGACTATGAGATTATGCAACTCC 58.226 41.667 0.00 0.00 0.00 3.85
4759 5511 4.926238 CGACTATGAGATTATGCAACTCCC 59.074 45.833 0.00 0.00 0.00 4.30
4760 5512 4.887748 ACTATGAGATTATGCAACTCCCG 58.112 43.478 0.00 0.00 0.00 5.14
4761 5513 4.588951 ACTATGAGATTATGCAACTCCCGA 59.411 41.667 0.00 0.00 0.00 5.14
4762 5514 3.904800 TGAGATTATGCAACTCCCGAA 57.095 42.857 0.00 0.00 0.00 4.30
4763 5515 4.422073 TGAGATTATGCAACTCCCGAAT 57.578 40.909 0.00 0.00 0.00 3.34
4764 5516 5.545063 TGAGATTATGCAACTCCCGAATA 57.455 39.130 0.00 0.00 0.00 1.75
4765 5517 5.297547 TGAGATTATGCAACTCCCGAATAC 58.702 41.667 0.00 0.00 0.00 1.89
4766 5518 5.163353 TGAGATTATGCAACTCCCGAATACA 60.163 40.000 0.00 0.00 0.00 2.29
4767 5519 5.057149 AGATTATGCAACTCCCGAATACAC 58.943 41.667 0.00 0.00 0.00 2.90
4768 5520 1.651987 ATGCAACTCCCGAATACACG 58.348 50.000 0.00 0.00 0.00 4.49
4769 5521 1.017177 TGCAACTCCCGAATACACGC 61.017 55.000 0.00 0.00 0.00 5.34
4770 5522 1.017177 GCAACTCCCGAATACACGCA 61.017 55.000 0.00 0.00 0.00 5.24
4771 5523 1.651987 CAACTCCCGAATACACGCAT 58.348 50.000 0.00 0.00 0.00 4.73
4772 5524 2.006888 CAACTCCCGAATACACGCATT 58.993 47.619 0.00 0.00 0.00 3.56
4773 5525 3.191669 CAACTCCCGAATACACGCATTA 58.808 45.455 0.00 0.00 0.00 1.90
4774 5526 3.530265 ACTCCCGAATACACGCATTAA 57.470 42.857 0.00 0.00 0.00 1.40
4775 5527 4.067972 ACTCCCGAATACACGCATTAAT 57.932 40.909 0.00 0.00 0.00 1.40
4776 5528 4.056050 ACTCCCGAATACACGCATTAATC 58.944 43.478 0.00 0.00 0.00 1.75
4777 5529 3.054166 TCCCGAATACACGCATTAATCG 58.946 45.455 5.96 5.96 0.00 3.34
4778 5530 2.798283 CCCGAATACACGCATTAATCGT 59.202 45.455 7.00 7.00 41.28 3.73
4823 5575 6.611381 TGTGCTTCACTTATATGTTTTGAGC 58.389 36.000 0.00 0.00 35.11 4.26
4824 5576 6.430925 TGTGCTTCACTTATATGTTTTGAGCT 59.569 34.615 0.00 0.00 35.11 4.09
4825 5577 7.606073 TGTGCTTCACTTATATGTTTTGAGCTA 59.394 33.333 0.00 0.00 35.11 3.32
4826 5578 8.119226 GTGCTTCACTTATATGTTTTGAGCTAG 58.881 37.037 0.00 0.00 0.00 3.42
4827 5579 7.280876 TGCTTCACTTATATGTTTTGAGCTAGG 59.719 37.037 0.00 0.00 0.00 3.02
4828 5580 7.495934 GCTTCACTTATATGTTTTGAGCTAGGA 59.504 37.037 0.00 0.00 0.00 2.94
4829 5581 9.383519 CTTCACTTATATGTTTTGAGCTAGGAA 57.616 33.333 0.00 0.00 0.00 3.36
4830 5582 8.948631 TCACTTATATGTTTTGAGCTAGGAAG 57.051 34.615 0.00 0.00 0.00 3.46
4831 5583 8.540388 TCACTTATATGTTTTGAGCTAGGAAGT 58.460 33.333 0.00 0.00 0.00 3.01
4832 5584 9.167311 CACTTATATGTTTTGAGCTAGGAAGTT 57.833 33.333 0.00 0.00 0.00 2.66
4833 5585 9.740710 ACTTATATGTTTTGAGCTAGGAAGTTT 57.259 29.630 0.00 0.00 0.00 2.66
4834 5586 9.994432 CTTATATGTTTTGAGCTAGGAAGTTTG 57.006 33.333 0.00 0.00 0.00 2.93
4835 5587 4.568152 TGTTTTGAGCTAGGAAGTTTGC 57.432 40.909 0.00 0.00 0.00 3.68
4836 5588 4.207165 TGTTTTGAGCTAGGAAGTTTGCT 58.793 39.130 0.00 0.00 38.59 3.91
4841 5593 4.729227 GAGCTAGGAAGTTTGCTCTAGT 57.271 45.455 6.58 0.00 45.78 2.57
4842 5594 4.429108 GAGCTAGGAAGTTTGCTCTAGTG 58.571 47.826 6.58 0.00 45.78 2.74
4843 5595 2.933260 GCTAGGAAGTTTGCTCTAGTGC 59.067 50.000 9.86 9.86 33.65 4.40
4844 5596 3.368948 GCTAGGAAGTTTGCTCTAGTGCT 60.369 47.826 17.08 0.00 33.65 4.40
4845 5597 3.778954 AGGAAGTTTGCTCTAGTGCTT 57.221 42.857 17.08 3.78 0.00 3.91
4846 5598 3.669536 AGGAAGTTTGCTCTAGTGCTTC 58.330 45.455 17.08 11.81 33.63 3.86
4847 5599 3.326297 AGGAAGTTTGCTCTAGTGCTTCT 59.674 43.478 17.08 9.82 34.50 2.85
4848 5600 4.068599 GGAAGTTTGCTCTAGTGCTTCTT 58.931 43.478 17.08 16.16 34.50 2.52
4849 5601 5.012148 AGGAAGTTTGCTCTAGTGCTTCTTA 59.988 40.000 17.08 0.00 34.50 2.10
4850 5602 5.877564 GGAAGTTTGCTCTAGTGCTTCTTAT 59.122 40.000 17.08 0.73 34.50 1.73
4851 5603 7.042335 GGAAGTTTGCTCTAGTGCTTCTTATA 58.958 38.462 17.08 0.00 34.50 0.98
4852 5604 7.713073 GGAAGTTTGCTCTAGTGCTTCTTATAT 59.287 37.037 17.08 0.04 34.50 0.86
4853 5605 8.655651 AAGTTTGCTCTAGTGCTTCTTATATC 57.344 34.615 17.08 0.01 0.00 1.63
4854 5606 8.017418 AGTTTGCTCTAGTGCTTCTTATATCT 57.983 34.615 17.08 1.92 0.00 1.98
4855 5607 8.482128 AGTTTGCTCTAGTGCTTCTTATATCTT 58.518 33.333 17.08 0.00 0.00 2.40
4856 5608 9.103861 GTTTGCTCTAGTGCTTCTTATATCTTT 57.896 33.333 17.08 0.00 0.00 2.52
4857 5609 9.672673 TTTGCTCTAGTGCTTCTTATATCTTTT 57.327 29.630 17.08 0.00 0.00 2.27
4858 5610 9.672673 TTGCTCTAGTGCTTCTTATATCTTTTT 57.327 29.630 17.08 0.00 0.00 1.94
4865 5617 9.844257 AGTGCTTCTTATATCTTTTTAGAGCAT 57.156 29.630 0.00 0.00 0.00 3.79
4866 5618 9.875675 GTGCTTCTTATATCTTTTTAGAGCATG 57.124 33.333 0.00 0.00 0.00 4.06
4867 5619 9.060347 TGCTTCTTATATCTTTTTAGAGCATGG 57.940 33.333 0.00 0.00 0.00 3.66
4868 5620 8.020244 GCTTCTTATATCTTTTTAGAGCATGGC 58.980 37.037 0.00 0.00 0.00 4.40
4869 5621 7.658179 TCTTATATCTTTTTAGAGCATGGCG 57.342 36.000 0.00 0.00 0.00 5.69
4870 5622 6.650807 TCTTATATCTTTTTAGAGCATGGCGG 59.349 38.462 0.00 0.00 0.00 6.13
4871 5623 2.489938 TCTTTTTAGAGCATGGCGGT 57.510 45.000 0.00 0.00 0.00 5.68
4872 5624 2.083774 TCTTTTTAGAGCATGGCGGTG 58.916 47.619 0.00 0.00 0.00 4.94
4873 5625 1.133025 CTTTTTAGAGCATGGCGGTGG 59.867 52.381 0.00 0.00 0.00 4.61
4874 5626 1.312371 TTTTAGAGCATGGCGGTGGC 61.312 55.000 0.00 0.00 38.90 5.01
4875 5627 2.196997 TTTAGAGCATGGCGGTGGCT 62.197 55.000 0.00 0.00 41.35 4.75
4876 5628 2.196997 TTAGAGCATGGCGGTGGCTT 62.197 55.000 0.00 0.00 38.15 4.35
4877 5629 2.196997 TAGAGCATGGCGGTGGCTTT 62.197 55.000 0.00 0.00 38.15 3.51
4878 5630 1.748879 GAGCATGGCGGTGGCTTTA 60.749 57.895 0.00 0.00 38.15 1.85
4879 5631 1.076777 AGCATGGCGGTGGCTTTAT 60.077 52.632 0.00 0.00 39.81 1.40
4880 5632 0.684153 AGCATGGCGGTGGCTTTATT 60.684 50.000 0.00 0.00 39.81 1.40
4881 5633 0.175531 GCATGGCGGTGGCTTTATTT 59.824 50.000 0.00 0.00 39.81 1.40
4882 5634 1.405391 GCATGGCGGTGGCTTTATTTT 60.405 47.619 0.00 0.00 39.81 1.82
4883 5635 2.159170 GCATGGCGGTGGCTTTATTTTA 60.159 45.455 0.00 0.00 39.81 1.52
4884 5636 3.492482 GCATGGCGGTGGCTTTATTTTAT 60.492 43.478 0.00 0.00 39.81 1.40
4885 5637 4.261825 GCATGGCGGTGGCTTTATTTTATA 60.262 41.667 0.00 0.00 39.81 0.98
4886 5638 5.460646 CATGGCGGTGGCTTTATTTTATAG 58.539 41.667 0.00 0.00 39.81 1.31
4887 5639 4.783055 TGGCGGTGGCTTTATTTTATAGA 58.217 39.130 0.00 0.00 39.81 1.98
4888 5640 5.194432 TGGCGGTGGCTTTATTTTATAGAA 58.806 37.500 0.00 0.00 39.81 2.10
4889 5641 5.652891 TGGCGGTGGCTTTATTTTATAGAAA 59.347 36.000 0.00 0.00 39.81 2.52
4890 5642 6.322712 TGGCGGTGGCTTTATTTTATAGAAAT 59.677 34.615 0.00 0.00 39.81 2.17
4891 5643 7.147811 TGGCGGTGGCTTTATTTTATAGAAATT 60.148 33.333 0.00 0.00 39.81 1.82
4892 5644 7.169140 GGCGGTGGCTTTATTTTATAGAAATTG 59.831 37.037 0.00 0.00 39.81 2.32
4893 5645 7.169140 GCGGTGGCTTTATTTTATAGAAATTGG 59.831 37.037 0.00 0.00 35.83 3.16
4894 5646 8.194769 CGGTGGCTTTATTTTATAGAAATTGGT 58.805 33.333 0.00 0.00 0.00 3.67
4895 5647 9.313118 GGTGGCTTTATTTTATAGAAATTGGTG 57.687 33.333 0.00 0.00 0.00 4.17
4906 5658 6.690194 ATAGAAATTGGTGAACTCTCATGC 57.310 37.500 0.00 0.00 33.05 4.06
4907 5659 4.660168 AGAAATTGGTGAACTCTCATGCT 58.340 39.130 0.00 0.00 33.05 3.79
4908 5660 5.075493 AGAAATTGGTGAACTCTCATGCTT 58.925 37.500 0.00 0.00 33.05 3.91
4909 5661 5.182760 AGAAATTGGTGAACTCTCATGCTTC 59.817 40.000 0.00 0.00 33.05 3.86
4910 5662 3.490439 TTGGTGAACTCTCATGCTTCA 57.510 42.857 0.00 0.00 33.05 3.02
4911 5663 2.771089 TGGTGAACTCTCATGCTTCAC 58.229 47.619 13.02 13.02 42.02 3.18
4912 5664 2.369860 TGGTGAACTCTCATGCTTCACT 59.630 45.455 17.48 0.00 42.27 3.41
4913 5665 3.181451 TGGTGAACTCTCATGCTTCACTT 60.181 43.478 17.48 0.00 42.27 3.16
4914 5666 4.040339 TGGTGAACTCTCATGCTTCACTTA 59.960 41.667 17.48 9.71 42.27 2.24
4915 5667 5.181748 GGTGAACTCTCATGCTTCACTTAT 58.818 41.667 17.48 0.00 42.27 1.73
4916 5668 6.070824 TGGTGAACTCTCATGCTTCACTTATA 60.071 38.462 17.48 6.67 42.27 0.98
4917 5669 6.989169 GGTGAACTCTCATGCTTCACTTATAT 59.011 38.462 17.48 0.00 42.27 0.86
4918 5670 7.497249 GGTGAACTCTCATGCTTCACTTATATT 59.503 37.037 17.48 0.00 42.27 1.28
4919 5671 9.534565 GTGAACTCTCATGCTTCACTTATATTA 57.465 33.333 13.68 0.00 40.37 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.513158 CACATCCGCGACCTTCTCT 59.487 57.895 8.23 0.00 0.00 3.10
41 42 0.383949 GCCGAGTTTCCAAGTTTGCA 59.616 50.000 0.00 0.00 0.00 4.08
47 48 3.431725 GCCGGCCGAGTTTCCAAG 61.432 66.667 30.73 7.40 0.00 3.61
48 49 4.257654 TGCCGGCCGAGTTTCCAA 62.258 61.111 30.73 0.00 0.00 3.53
204 209 1.080434 GTGGAGCTTCTTCGTCGCT 60.080 57.895 0.00 0.00 36.57 4.93
306 319 2.355837 GCGAGCTCGTTGTCCACA 60.356 61.111 34.46 0.00 42.22 4.17
313 326 2.572284 GGTGTAGGCGAGCTCGTT 59.428 61.111 34.46 25.12 42.22 3.85
390 417 8.889717 CACACACGGAGGAACTAAAATTATAAT 58.110 33.333 0.00 0.00 41.55 1.28
393 420 6.148811 CACACACACGGAGGAACTAAAATTAT 59.851 38.462 0.00 0.00 41.55 1.28
405 432 1.148310 GTTCATCACACACACGGAGG 58.852 55.000 0.00 0.00 0.00 4.30
406 433 2.061773 GAGTTCATCACACACACGGAG 58.938 52.381 0.00 0.00 0.00 4.63
533 573 4.555906 CGTTTCGCCCTAAGACAATTTTGT 60.556 41.667 0.00 0.00 45.65 2.83
688 747 8.586744 GTGGGTTTTGTTGGGTTTAAGATTATA 58.413 33.333 0.00 0.00 0.00 0.98
773 832 2.498078 TGTGTGTGTGAACTGTCTGGTA 59.502 45.455 0.00 0.00 0.00 3.25
796 855 5.003590 CGTCTGCGATACTCTTTTTGTACTC 59.996 44.000 0.00 0.00 41.33 2.59
836 895 2.490991 GAGTGTAGGGCGTGTTCTTTT 58.509 47.619 0.00 0.00 0.00 2.27
886 945 0.610174 TGCAGCTACTGGTTGAGGAG 59.390 55.000 0.00 0.00 35.37 3.69
1000 1060 1.599606 GAGACTCTCCCGCAGAAGCA 61.600 60.000 0.00 0.00 42.27 3.91
1024 1084 2.375146 GAAACCTTTATGTGGCCGGAT 58.625 47.619 5.05 0.00 0.00 4.18
1053 1113 0.977395 GTGGTGGTGAAGGAGTAGCT 59.023 55.000 0.00 0.00 0.00 3.32
1150 1212 0.966179 TGTTTAGCCGTGCTCTGAGA 59.034 50.000 9.28 0.00 40.44 3.27
1198 1260 1.101331 GACGACGAGGGGATGTACTT 58.899 55.000 0.00 0.00 0.00 2.24
1202 1264 2.758737 GGGACGACGAGGGGATGT 60.759 66.667 0.00 0.00 0.00 3.06
1222 1294 2.577059 CACACGGCCGAGGTGTAT 59.423 61.111 35.90 3.57 46.27 2.29
1358 1437 3.462199 GACATAGCCCCGGTCTGCC 62.462 68.421 0.00 0.00 0.00 4.85
1558 1641 1.873270 CGAGGACGTCCACCATGTCA 61.873 60.000 35.00 0.00 42.27 3.58
1622 2190 1.777272 ACTGAGCAGGGAAAGAAAGGT 59.223 47.619 2.20 0.00 0.00 3.50
1677 2250 4.142469 ACACGTCTGAATCACACGATATGA 60.142 41.667 17.30 0.00 0.00 2.15
1747 2326 5.967674 CAGCTAAATTCGGCAATTCTACTTG 59.032 40.000 0.00 0.00 30.37 3.16
1991 2580 4.099824 GGGTAACGACACAACAAAACTTG 58.900 43.478 0.00 0.00 37.60 3.16
1992 2581 3.757493 TGGGTAACGACACAACAAAACTT 59.243 39.130 0.00 0.00 35.49 2.66
2171 2767 8.973378 GTAGAATATAGCAAATCACTGAGACAC 58.027 37.037 0.00 0.00 0.00 3.67
2175 2771 9.678941 TTACGTAGAATATAGCAAATCACTGAG 57.321 33.333 0.00 0.00 0.00 3.35
2179 2776 8.485591 GGTGTTACGTAGAATATAGCAAATCAC 58.514 37.037 0.00 0.00 0.00 3.06
2231 2828 4.184079 ACGTGGTTTTTCTAGTAGCGAT 57.816 40.909 0.00 0.00 0.00 4.58
2260 2857 7.984422 ACACATCAGAATAGAAACAACATCA 57.016 32.000 0.00 0.00 0.00 3.07
2311 2916 2.813908 GATCGACACGGGCCACAC 60.814 66.667 4.39 0.00 0.00 3.82
2318 2923 0.455464 TAACAGCACGATCGACACGG 60.455 55.000 24.34 13.02 34.93 4.94
2336 2941 9.279233 TGGGGCTCTTCTAATTATTGCTATATA 57.721 33.333 0.00 0.00 0.00 0.86
2361 2966 8.322906 TCCATTAGACAGAACACAAGTAAATG 57.677 34.615 0.00 0.00 0.00 2.32
2379 2984 6.857964 GGCACGAATATCAACAATTCCATTAG 59.142 38.462 0.00 0.00 30.98 1.73
2418 3023 5.520376 AATACAGCAAAGTTTCACTTGCT 57.480 34.783 3.54 3.54 40.52 3.91
2449 3054 3.311048 AGCTAAACGCGGTAGTACTAGAC 59.689 47.826 12.47 0.00 45.59 2.59
2558 3205 8.373981 AGAGGAAGATCAGGACACAATATATTG 58.626 37.037 21.42 21.42 43.26 1.90
2559 3206 8.503428 AGAGGAAGATCAGGACACAATATATT 57.497 34.615 0.00 0.00 0.00 1.28
2560 3207 8.503428 AAGAGGAAGATCAGGACACAATATAT 57.497 34.615 0.00 0.00 0.00 0.86
2561 3208 7.786943 AGAAGAGGAAGATCAGGACACAATATA 59.213 37.037 0.00 0.00 0.00 0.86
2562 3209 6.614906 AGAAGAGGAAGATCAGGACACAATAT 59.385 38.462 0.00 0.00 0.00 1.28
2563 3210 5.960811 AGAAGAGGAAGATCAGGACACAATA 59.039 40.000 0.00 0.00 0.00 1.90
2564 3211 4.782156 AGAAGAGGAAGATCAGGACACAAT 59.218 41.667 0.00 0.00 0.00 2.71
2565 3212 4.163427 AGAAGAGGAAGATCAGGACACAA 58.837 43.478 0.00 0.00 0.00 3.33
2566 3213 3.784178 AGAAGAGGAAGATCAGGACACA 58.216 45.455 0.00 0.00 0.00 3.72
2608 3296 4.142004 GCCGGATAGGTTCACTTTCTTAGA 60.142 45.833 5.05 0.00 43.70 2.10
2629 3317 1.933115 AACCGACGGAATTGCATGCC 61.933 55.000 23.38 0.00 0.00 4.40
2700 3392 7.094205 GGGTAGGGATAATAATGATTGTGCAAG 60.094 40.741 0.00 0.00 0.00 4.01
2797 3489 3.570975 TGAAGTGAACGAGCAGGTTAGTA 59.429 43.478 0.00 0.00 0.00 1.82
2844 3536 7.106239 AGAGGCATATTTAGATAATGAACCGG 58.894 38.462 0.00 0.00 0.00 5.28
2910 3603 7.095910 CCATCTCAGGTTTAGTCATGCTATAG 58.904 42.308 0.00 0.00 0.00 1.31
2926 3619 1.202330 AGAACTCCAGCCATCTCAGG 58.798 55.000 0.00 0.00 0.00 3.86
2983 3678 3.427528 GTGATCGCGTGAACTGAACTAAA 59.572 43.478 5.77 0.00 0.00 1.85
2999 3694 4.328440 GTCAAATTCTGGACAGAGTGATCG 59.672 45.833 12.50 0.00 38.88 3.69
3003 3698 3.188048 GCAGTCAAATTCTGGACAGAGTG 59.812 47.826 1.92 3.37 38.88 3.51
3128 3824 5.627367 GTCAAAGCAAACATACGCACATAAA 59.373 36.000 0.00 0.00 0.00 1.40
3179 3876 5.373812 AAGGATCCATGTCCGTTCTTTAT 57.626 39.130 15.82 0.00 43.27 1.40
3186 3883 6.494666 TTATCTTAAAGGATCCATGTCCGT 57.505 37.500 15.82 0.00 43.27 4.69
3222 3926 4.761235 ACAGCAACAACAATCAGATCTG 57.239 40.909 17.07 17.07 0.00 2.90
3223 3927 4.823442 TCAACAGCAACAACAATCAGATCT 59.177 37.500 0.00 0.00 0.00 2.75
3233 3937 8.201554 TCTAGATCAATATCAACAGCAACAAC 57.798 34.615 0.00 0.00 34.28 3.32
3305 4009 5.016051 AGCTACTGAATCGTGATGACAAT 57.984 39.130 0.00 0.00 0.00 2.71
3472 4181 8.530269 AAGAACGGGATAATTATTACGACATC 57.470 34.615 21.80 16.93 0.00 3.06
3488 4197 3.502211 GCTTCATCAAAAGAAGAACGGGA 59.498 43.478 7.08 0.00 44.00 5.14
3489 4198 3.503748 AGCTTCATCAAAAGAAGAACGGG 59.496 43.478 7.08 0.00 44.00 5.28
3533 4242 4.649692 TCCATAGCTACTACTTAGGACCG 58.350 47.826 0.00 0.00 0.00 4.79
3664 4375 2.468532 GTGTTCCTACGCGCGTTG 59.531 61.111 42.10 36.67 0.00 4.10
3732 4471 1.971357 CCCGGCTGGTATAGAGTTGAT 59.029 52.381 11.58 0.00 0.00 2.57
3750 4489 3.292159 GCCCAACGGACACAACCC 61.292 66.667 0.00 0.00 0.00 4.11
3807 4549 8.642908 AACAAAACCAATTCACTAGTAAAAGC 57.357 30.769 0.00 0.00 0.00 3.51
3870 4620 2.039818 AGGAGAGACGTCGCTATTCA 57.960 50.000 22.18 0.00 0.00 2.57
3875 4625 0.959553 TTTCAAGGAGAGACGTCGCT 59.040 50.000 22.32 22.32 0.00 4.93
3876 4626 1.721926 CTTTTCAAGGAGAGACGTCGC 59.278 52.381 11.72 11.72 0.00 5.19
4003 4754 3.269592 TCTGGAGGTTTTAGAGGTGGA 57.730 47.619 0.00 0.00 0.00 4.02
4013 4764 1.886542 GCGATGGTTTTCTGGAGGTTT 59.113 47.619 0.00 0.00 0.00 3.27
4072 4823 3.050564 TCACCATTACCTCCCCTTCCTAT 60.051 47.826 0.00 0.00 0.00 2.57
4078 4829 1.082194 TCCTTCACCATTACCTCCCCT 59.918 52.381 0.00 0.00 0.00 4.79
4089 4840 1.044611 TCACACATCGTCCTTCACCA 58.955 50.000 0.00 0.00 0.00 4.17
4118 4869 2.441750 TGGCCCTATTGATGTTCTACCC 59.558 50.000 0.00 0.00 0.00 3.69
4132 4883 3.266772 AGATCACTTGATTTGTGGCCCTA 59.733 43.478 0.00 0.00 36.21 3.53
4141 4892 4.225942 TCTGGCCACTAGATCACTTGATTT 59.774 41.667 0.00 0.00 34.37 2.17
4198 4949 2.715046 GATGGAGGCATTGAAGACACA 58.285 47.619 0.00 0.00 0.00 3.72
4209 4960 0.249120 CAACACTACCGATGGAGGCA 59.751 55.000 0.00 0.00 33.69 4.75
4311 5063 0.038159 GCACGAGCACTGGTACTCTT 60.038 55.000 0.00 0.00 41.58 2.85
4347 5099 5.766670 GGGTCATGAATTTGATGATCTAGCA 59.233 40.000 8.68 0.00 32.40 3.49
4357 5109 1.912731 TCGAGGGGGTCATGAATTTGA 59.087 47.619 0.00 0.00 0.00 2.69
4492 5244 7.970384 TCACACATGTATTTAAGTTTCCGATC 58.030 34.615 0.00 0.00 0.00 3.69
4534 5286 4.475345 AGTAGAGGCTTACTAGGGACATG 58.525 47.826 7.35 0.00 32.25 3.21
4535 5287 4.817874 AGTAGAGGCTTACTAGGGACAT 57.182 45.455 7.35 0.00 32.25 3.06
4549 5301 6.939730 TGATCAATGAGCTAGTCTAGTAGAGG 59.060 42.308 8.68 0.00 0.00 3.69
4560 5312 6.939132 AACCATCTTTGATCAATGAGCTAG 57.061 37.500 23.52 11.87 0.00 3.42
4567 5319 7.675619 AGGAAACCTTAACCATCTTTGATCAAT 59.324 33.333 9.40 0.00 0.00 2.57
4570 5322 6.659242 TGAGGAAACCTTAACCATCTTTGATC 59.341 38.462 0.00 0.00 31.76 2.92
4624 5376 6.662865 TCATTCTCCTAATGAGGTGATCTC 57.337 41.667 1.52 0.00 43.31 2.75
4632 5384 6.649973 GTCCATCACATCATTCTCCTAATGAG 59.350 42.308 6.58 2.51 39.69 2.90
4642 5394 3.629398 GGGTCTTGTCCATCACATCATTC 59.371 47.826 0.00 0.00 33.90 2.67
4668 5420 5.018539 ACGGTCATTATGCTAAGCTAACA 57.981 39.130 0.00 0.00 0.00 2.41
4687 5439 7.540745 ACAAAGCAATAGCAATAAACTAAACGG 59.459 33.333 0.00 0.00 45.49 4.44
4692 5444 9.571810 CATGAACAAAGCAATAGCAATAAACTA 57.428 29.630 0.00 0.00 45.49 2.24
4703 5455 7.920160 TGTATCTGACATGAACAAAGCAATA 57.080 32.000 0.00 0.00 31.20 1.90
4730 5482 6.405278 TGCATAATCTCATAGTCGAAGGAA 57.595 37.500 0.00 0.00 0.00 3.36
4742 5494 3.904800 TTCGGGAGTTGCATAATCTCA 57.095 42.857 0.00 0.00 0.00 3.27
4797 5549 8.397906 GCTCAAAACATATAAGTGAAGCACATA 58.602 33.333 0.00 0.00 36.74 2.29
4798 5550 7.121759 AGCTCAAAACATATAAGTGAAGCACAT 59.878 33.333 0.00 0.00 36.74 3.21
4799 5551 6.430925 AGCTCAAAACATATAAGTGAAGCACA 59.569 34.615 0.00 0.00 36.74 4.57
4800 5552 6.846350 AGCTCAAAACATATAAGTGAAGCAC 58.154 36.000 0.00 0.00 34.10 4.40
4801 5553 7.280876 CCTAGCTCAAAACATATAAGTGAAGCA 59.719 37.037 0.00 0.00 0.00 3.91
4802 5554 7.495934 TCCTAGCTCAAAACATATAAGTGAAGC 59.504 37.037 0.00 0.00 0.00 3.86
4803 5555 8.948631 TCCTAGCTCAAAACATATAAGTGAAG 57.051 34.615 0.00 0.00 0.00 3.02
4804 5556 9.383519 CTTCCTAGCTCAAAACATATAAGTGAA 57.616 33.333 0.00 0.00 0.00 3.18
4805 5557 8.540388 ACTTCCTAGCTCAAAACATATAAGTGA 58.460 33.333 0.00 0.00 0.00 3.41
4806 5558 8.723942 ACTTCCTAGCTCAAAACATATAAGTG 57.276 34.615 0.00 0.00 0.00 3.16
4807 5559 9.740710 AAACTTCCTAGCTCAAAACATATAAGT 57.259 29.630 0.00 0.00 0.00 2.24
4808 5560 9.994432 CAAACTTCCTAGCTCAAAACATATAAG 57.006 33.333 0.00 0.00 0.00 1.73
4809 5561 8.458843 GCAAACTTCCTAGCTCAAAACATATAA 58.541 33.333 0.00 0.00 0.00 0.98
4810 5562 7.829211 AGCAAACTTCCTAGCTCAAAACATATA 59.171 33.333 0.00 0.00 30.05 0.86
4811 5563 6.660949 AGCAAACTTCCTAGCTCAAAACATAT 59.339 34.615 0.00 0.00 30.05 1.78
4812 5564 6.003950 AGCAAACTTCCTAGCTCAAAACATA 58.996 36.000 0.00 0.00 30.05 2.29
4813 5565 4.829492 AGCAAACTTCCTAGCTCAAAACAT 59.171 37.500 0.00 0.00 30.05 2.71
4814 5566 4.207165 AGCAAACTTCCTAGCTCAAAACA 58.793 39.130 0.00 0.00 30.05 2.83
4815 5567 4.837896 AGCAAACTTCCTAGCTCAAAAC 57.162 40.909 0.00 0.00 30.05 2.43
4821 5573 3.368948 GCACTAGAGCAAACTTCCTAGCT 60.369 47.826 7.33 0.00 40.60 3.32
4822 5574 2.933260 GCACTAGAGCAAACTTCCTAGC 59.067 50.000 7.33 0.00 33.70 3.42
4823 5575 4.464069 AGCACTAGAGCAAACTTCCTAG 57.536 45.455 14.80 0.00 36.85 3.02
4824 5576 4.528596 AGAAGCACTAGAGCAAACTTCCTA 59.471 41.667 14.80 0.00 35.28 2.94
4825 5577 3.326297 AGAAGCACTAGAGCAAACTTCCT 59.674 43.478 14.80 0.00 35.28 3.36
4826 5578 3.669536 AGAAGCACTAGAGCAAACTTCC 58.330 45.455 14.80 0.00 35.28 3.46
4827 5579 6.976636 ATAAGAAGCACTAGAGCAAACTTC 57.023 37.500 14.80 8.97 36.85 3.01
4828 5580 8.482128 AGATATAAGAAGCACTAGAGCAAACTT 58.518 33.333 14.80 16.04 36.85 2.66
4829 5581 8.017418 AGATATAAGAAGCACTAGAGCAAACT 57.983 34.615 14.80 7.32 36.85 2.66
4830 5582 8.655651 AAGATATAAGAAGCACTAGAGCAAAC 57.344 34.615 14.80 5.24 36.85 2.93
4831 5583 9.672673 AAAAGATATAAGAAGCACTAGAGCAAA 57.327 29.630 14.80 0.00 36.85 3.68
4832 5584 9.672673 AAAAAGATATAAGAAGCACTAGAGCAA 57.327 29.630 14.80 0.00 36.85 3.91
4839 5591 9.844257 ATGCTCTAAAAAGATATAAGAAGCACT 57.156 29.630 0.00 0.00 0.00 4.40
4840 5592 9.875675 CATGCTCTAAAAAGATATAAGAAGCAC 57.124 33.333 0.00 0.00 0.00 4.40
4841 5593 9.060347 CCATGCTCTAAAAAGATATAAGAAGCA 57.940 33.333 0.00 0.00 0.00 3.91
4842 5594 8.020244 GCCATGCTCTAAAAAGATATAAGAAGC 58.980 37.037 0.00 0.00 0.00 3.86
4843 5595 8.226448 CGCCATGCTCTAAAAAGATATAAGAAG 58.774 37.037 0.00 0.00 0.00 2.85
4844 5596 7.173218 CCGCCATGCTCTAAAAAGATATAAGAA 59.827 37.037 0.00 0.00 0.00 2.52
4845 5597 6.650807 CCGCCATGCTCTAAAAAGATATAAGA 59.349 38.462 0.00 0.00 0.00 2.10
4846 5598 6.428159 ACCGCCATGCTCTAAAAAGATATAAG 59.572 38.462 0.00 0.00 0.00 1.73
4847 5599 6.204688 CACCGCCATGCTCTAAAAAGATATAA 59.795 38.462 0.00 0.00 0.00 0.98
4848 5600 5.700832 CACCGCCATGCTCTAAAAAGATATA 59.299 40.000 0.00 0.00 0.00 0.86
4849 5601 4.516698 CACCGCCATGCTCTAAAAAGATAT 59.483 41.667 0.00 0.00 0.00 1.63
4850 5602 3.876914 CACCGCCATGCTCTAAAAAGATA 59.123 43.478 0.00 0.00 0.00 1.98
4851 5603 2.684881 CACCGCCATGCTCTAAAAAGAT 59.315 45.455 0.00 0.00 0.00 2.40
4852 5604 2.083774 CACCGCCATGCTCTAAAAAGA 58.916 47.619 0.00 0.00 0.00 2.52
4853 5605 1.133025 CCACCGCCATGCTCTAAAAAG 59.867 52.381 0.00 0.00 0.00 2.27
4854 5606 1.173043 CCACCGCCATGCTCTAAAAA 58.827 50.000 0.00 0.00 0.00 1.94
4855 5607 1.312371 GCCACCGCCATGCTCTAAAA 61.312 55.000 0.00 0.00 0.00 1.52
4856 5608 1.748879 GCCACCGCCATGCTCTAAA 60.749 57.895 0.00 0.00 0.00 1.85
4857 5609 2.124736 GCCACCGCCATGCTCTAA 60.125 61.111 0.00 0.00 0.00 2.10
4858 5610 2.196997 AAAGCCACCGCCATGCTCTA 62.197 55.000 0.00 0.00 33.36 2.43
4859 5611 2.196997 TAAAGCCACCGCCATGCTCT 62.197 55.000 0.00 0.00 33.36 4.09
4860 5612 1.103398 ATAAAGCCACCGCCATGCTC 61.103 55.000 0.00 0.00 33.36 4.26
4861 5613 0.684153 AATAAAGCCACCGCCATGCT 60.684 50.000 0.00 0.00 36.79 3.79
4862 5614 0.175531 AAATAAAGCCACCGCCATGC 59.824 50.000 0.00 0.00 34.57 4.06
4863 5615 2.671130 AAAATAAAGCCACCGCCATG 57.329 45.000 0.00 0.00 34.57 3.66
4864 5616 5.381757 TCTATAAAATAAAGCCACCGCCAT 58.618 37.500 0.00 0.00 34.57 4.40
4865 5617 4.783055 TCTATAAAATAAAGCCACCGCCA 58.217 39.130 0.00 0.00 34.57 5.69
4866 5618 5.761165 TTCTATAAAATAAAGCCACCGCC 57.239 39.130 0.00 0.00 34.57 6.13
4867 5619 7.169140 CCAATTTCTATAAAATAAAGCCACCGC 59.831 37.037 0.00 0.00 0.00 5.68
4868 5620 8.194769 ACCAATTTCTATAAAATAAAGCCACCG 58.805 33.333 0.00 0.00 0.00 4.94
4869 5621 9.313118 CACCAATTTCTATAAAATAAAGCCACC 57.687 33.333 0.00 0.00 0.00 4.61
4880 5632 8.677300 GCATGAGAGTTCACCAATTTCTATAAA 58.323 33.333 0.00 0.00 35.83 1.40
4881 5633 8.049117 AGCATGAGAGTTCACCAATTTCTATAA 58.951 33.333 0.00 0.00 35.83 0.98
4882 5634 7.568349 AGCATGAGAGTTCACCAATTTCTATA 58.432 34.615 0.00 0.00 35.83 1.31
4883 5635 6.421485 AGCATGAGAGTTCACCAATTTCTAT 58.579 36.000 0.00 0.00 35.83 1.98
4884 5636 5.809001 AGCATGAGAGTTCACCAATTTCTA 58.191 37.500 0.00 0.00 35.83 2.10
4885 5637 4.660168 AGCATGAGAGTTCACCAATTTCT 58.340 39.130 0.00 0.00 35.83 2.52
4886 5638 5.048504 TGAAGCATGAGAGTTCACCAATTTC 60.049 40.000 0.00 0.00 35.83 2.17
4887 5639 4.828939 TGAAGCATGAGAGTTCACCAATTT 59.171 37.500 0.00 0.00 35.83 1.82
4888 5640 4.217118 GTGAAGCATGAGAGTTCACCAATT 59.783 41.667 14.82 0.00 42.79 2.32
4889 5641 3.755378 GTGAAGCATGAGAGTTCACCAAT 59.245 43.478 14.82 0.00 42.79 3.16
4890 5642 3.141398 GTGAAGCATGAGAGTTCACCAA 58.859 45.455 14.82 0.00 42.79 3.67
4891 5643 2.771089 GTGAAGCATGAGAGTTCACCA 58.229 47.619 14.82 0.00 42.79 4.17
4893 5645 8.430801 AATATAAGTGAAGCATGAGAGTTCAC 57.569 34.615 16.70 16.70 46.93 3.18


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

AutoCloner maintained by Alex Coulton.