Multiple sequence alignment - TraesCS6B01G245100

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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 TraesCS6B01G245100 chr6B 100.000 3956 0 0 1 3956 437487873 437483918 0.000000e+00 7306.0
1 TraesCS6B01G245100 chr6B 100.000 2394 0 0 4324 6717 437483550 437481157 0.000000e+00 4421.0
2 TraesCS6B01G245100 chr6B 100.000 1605 0 0 6979 8583 437480895 437479291 0.000000e+00 2964.0
3 TraesCS6B01G245100 chr6B 91.353 266 20 1 8318 8583 424088625 424088887 2.280000e-95 361.0
4 TraesCS6B01G245100 chr6B 91.353 266 20 1 8318 8583 424314123 424314385 2.280000e-95 361.0
5 TraesCS6B01G245100 chr6B 79.638 221 29 9 7391 7603 229680351 229680563 2.500000e-30 145.0
6 TraesCS6B01G245100 chr6D 95.695 3972 103 26 12 3956 275679306 275675376 0.000000e+00 6325.0
7 TraesCS6B01G245100 chr6D 96.448 1126 22 7 4332 5450 275675022 275673908 0.000000e+00 1842.0
8 TraesCS6B01G245100 chr6D 95.005 961 41 4 6979 7937 275673594 275672639 0.000000e+00 1502.0
9 TraesCS6B01G245100 chr6D 91.101 663 39 9 7925 8582 275671271 275670624 0.000000e+00 880.0
10 TraesCS6B01G245100 chr6D 82.519 389 43 7 3290 3678 57278671 57278308 1.390000e-82 318.0
11 TraesCS6B01G245100 chr6D 96.581 117 4 0 6601 6717 275673916 275673800 2.440000e-45 195.0
12 TraesCS6B01G245100 chr6D 80.455 220 28 10 7391 7603 132047430 132047641 4.150000e-33 154.0
13 TraesCS6B01G245100 chr6D 82.550 149 24 2 7881 8028 275672932 275672785 6.990000e-26 130.0
14 TraesCS6B01G245100 chr6A 92.250 4026 178 49 10 3956 396302421 396298451 0.000000e+00 5583.0
15 TraesCS6B01G245100 chr6A 93.489 1029 36 4 6979 8005 396297156 396296157 0.000000e+00 1500.0
16 TraesCS6B01G245100 chr6A 96.075 535 21 0 4333 4867 396298379 396297845 0.000000e+00 872.0
17 TraesCS6B01G245100 chr6A 91.486 599 37 7 7991 8582 396295838 396295247 0.000000e+00 811.0
18 TraesCS6B01G245100 chr6A 94.695 509 18 3 4951 5450 396297844 396297336 0.000000e+00 782.0
19 TraesCS6B01G245100 chr6A 86.095 338 39 3 3545 3877 107616527 107616193 2.950000e-94 357.0
20 TraesCS6B01G245100 chr6A 81.062 433 62 10 3474 3895 571270707 571271130 2.310000e-85 327.0
21 TraesCS6B01G245100 chr6A 83.103 290 28 8 3106 3395 105043692 105043424 2.390000e-60 244.0
22 TraesCS6B01G245100 chr6A 94.783 115 6 0 6601 6715 396297344 396297230 6.850000e-41 180.0
23 TraesCS6B01G245100 chr4B 92.487 1158 83 3 5448 6601 660662840 660663997 0.000000e+00 1653.0
24 TraesCS6B01G245100 chr4B 90.870 1172 97 8 5441 6604 74673280 74674449 0.000000e+00 1563.0
25 TraesCS6B01G245100 chr4B 85.235 298 36 4 3543 3833 512662588 512662292 5.040000e-77 300.0
26 TraesCS6B01G245100 chr4B 79.032 434 68 13 3474 3895 471270763 471270341 8.490000e-70 276.0
27 TraesCS6B01G245100 chr4B 82.414 290 30 8 3106 3395 471271068 471270800 5.180000e-57 233.0
28 TraesCS6B01G245100 chr4B 90.000 40 4 0 7841 7880 6394397 6394436 1.600000e-02 52.8
29 TraesCS6B01G245100 chr7B 92.468 1155 80 5 5451 6601 690597265 690596114 0.000000e+00 1644.0
30 TraesCS6B01G245100 chr7B 92.114 1154 85 4 5451 6601 690566570 690565420 0.000000e+00 1622.0
31 TraesCS6B01G245100 chr7B 85.401 137 16 3 3108 3242 116381198 116381064 1.160000e-28 139.0
32 TraesCS6B01G245100 chr7B 87.629 97 7 4 4865 4958 321681525 321681619 3.280000e-19 108.0
33 TraesCS6B01G245100 chr3B 92.069 1160 87 5 5447 6601 23784325 23785484 0.000000e+00 1628.0
34 TraesCS6B01G245100 chr3B 89.474 95 9 1 4856 4950 156646824 156646731 1.510000e-22 119.0
35 TraesCS6B01G245100 chr3B 86.585 82 9 2 4592 4672 125857705 125857785 1.190000e-13 89.8
36 TraesCS6B01G245100 chr5B 92.194 1153 85 5 5451 6602 490123329 490122181 0.000000e+00 1626.0
37 TraesCS6B01G245100 chr5B 90.259 1160 104 8 5450 6601 33950810 33951968 0.000000e+00 1507.0
38 TraesCS6B01G245100 chr1B 91.090 1156 100 3 5441 6594 146770775 146771929 0.000000e+00 1561.0
39 TraesCS6B01G245100 chr1B 91.344 1109 92 3 5496 6600 408617227 408618335 0.000000e+00 1513.0
40 TraesCS6B01G245100 chr1B 90.805 87 7 1 4865 4950 424216149 424216063 1.960000e-21 115.0
41 TraesCS6B01G245100 chr3D 86.683 398 49 3 2972 3365 44215439 44215836 1.020000e-118 438.0
42 TraesCS6B01G245100 chr3D 84.133 271 42 1 3426 3696 44215850 44216119 2.380000e-65 261.0
43 TraesCS6B01G245100 chr4D 86.284 401 51 3 2972 3368 23281425 23281025 4.760000e-117 433.0
44 TraesCS6B01G245100 chr4D 83.764 271 42 2 3426 3696 23281014 23280746 1.110000e-63 255.0
45 TraesCS6B01G245100 chr3A 85.638 376 45 4 3528 3896 55056060 55055687 3.760000e-103 387.0
46 TraesCS6B01G245100 chr3A 81.986 433 58 10 3474 3895 91457598 91457175 4.930000e-92 350.0
47 TraesCS6B01G245100 chr3A 80.600 433 64 10 3474 3895 425601323 425600900 5.000000e-82 316.0
48 TraesCS6B01G245100 chr3A 82.759 290 29 9 3106 3395 91457903 91457635 1.110000e-58 239.0
49 TraesCS6B01G245100 chr3A 78.966 290 26 10 3106 3395 425601614 425601360 1.920000e-36 165.0
50 TraesCS6B01G245100 chr3A 87.629 97 8 3 4865 4958 167878256 167878161 9.110000e-20 110.0
51 TraesCS6B01G245100 chr3A 88.571 70 6 2 4604 4672 93562264 93562332 5.520000e-12 84.2
52 TraesCS6B01G245100 chr1A 86.686 338 38 3 3545 3877 58236853 58236518 1.360000e-97 368.0
53 TraesCS6B01G245100 chr1A 90.000 90 9 0 4861 4950 522462459 522462370 5.440000e-22 117.0
54 TraesCS6B01G245100 chr7A 81.293 433 61 10 3474 3895 501091620 501092043 4.970000e-87 333.0
55 TraesCS6B01G245100 chr7A 89.655 87 9 0 4865 4951 4000684 4000770 2.530000e-20 111.0
56 TraesCS6B01G245100 chr7A 97.143 35 0 1 7846 7880 18292581 18292614 3.350000e-04 58.4
57 TraesCS6B01G245100 chr7A 97.143 35 0 1 7846 7880 303473983 303474016 3.350000e-04 58.4
58 TraesCS6B01G245100 chr5D 82.474 388 43 7 3291 3678 459324102 459323740 5.000000e-82 316.0
59 TraesCS6B01G245100 chr5D 92.105 38 3 0 7843 7880 437637244 437637281 4.000000e-03 54.7
60 TraesCS6B01G245100 chr4A 90.909 231 20 1 5451 5680 659019279 659019049 8.370000e-80 309.0
61 TraesCS6B01G245100 chr4A 80.896 424 40 14 2973 3395 669814889 669815272 6.510000e-76 296.0
62 TraesCS6B01G245100 chr4A 100.000 33 0 0 7848 7880 643435561 643435529 2.590000e-05 62.1
63 TraesCS6B01G245100 chr4A 94.872 39 1 1 7842 7880 645259497 645259460 9.300000e-05 60.2
64 TraesCS6B01G245100 chr4A 92.308 39 1 2 7843 7880 613849640 613849603 4.000000e-03 54.7
65 TraesCS6B01G245100 chr2D 83.209 268 44 1 3426 3693 634883593 634883859 2.390000e-60 244.0
66 TraesCS6B01G245100 chr2D 90.588 85 8 0 4865 4949 566557840 566557924 7.040000e-21 113.0
67 TraesCS6B01G245100 chr7D 87.629 97 7 4 4865 4958 32112976 32113070 3.280000e-19 108.0
68 TraesCS6B01G245100 chr7D 94.595 37 1 1 7844 7880 565280538 565280573 1.000000e-03 56.5
69 TraesCS6B01G245100 chr2A 87.234 94 12 0 4863 4956 492513862 492513769 3.280000e-19 108.0
70 TraesCS6B01G245100 chrUn 88.571 70 6 2 4604 4672 272886445 272886377 5.520000e-12 84.2
71 TraesCS6B01G245100 chrUn 88.571 70 6 2 4604 4672 299203897 299203965 5.520000e-12 84.2


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 TraesCS6B01G245100 chr6B 437479291 437487873 8582 True 4897.000000 7306 100.000000 1 8583 3 chr6B.!!$R1 8582
1 TraesCS6B01G245100 chr6D 275670624 275679306 8682 True 1812.333333 6325 92.896667 12 8582 6 chr6D.!!$R2 8570
2 TraesCS6B01G245100 chr6A 396295247 396302421 7174 True 1621.333333 5583 93.796333 10 8582 6 chr6A.!!$R3 8572
3 TraesCS6B01G245100 chr4B 660662840 660663997 1157 False 1653.000000 1653 92.487000 5448 6601 1 chr4B.!!$F3 1153
4 TraesCS6B01G245100 chr4B 74673280 74674449 1169 False 1563.000000 1563 90.870000 5441 6604 1 chr4B.!!$F2 1163
5 TraesCS6B01G245100 chr4B 471270341 471271068 727 True 254.500000 276 80.723000 3106 3895 2 chr4B.!!$R2 789
6 TraesCS6B01G245100 chr7B 690596114 690597265 1151 True 1644.000000 1644 92.468000 5451 6601 1 chr7B.!!$R3 1150
7 TraesCS6B01G245100 chr7B 690565420 690566570 1150 True 1622.000000 1622 92.114000 5451 6601 1 chr7B.!!$R2 1150
8 TraesCS6B01G245100 chr3B 23784325 23785484 1159 False 1628.000000 1628 92.069000 5447 6601 1 chr3B.!!$F1 1154
9 TraesCS6B01G245100 chr5B 490122181 490123329 1148 True 1626.000000 1626 92.194000 5451 6602 1 chr5B.!!$R1 1151
10 TraesCS6B01G245100 chr5B 33950810 33951968 1158 False 1507.000000 1507 90.259000 5450 6601 1 chr5B.!!$F1 1151
11 TraesCS6B01G245100 chr1B 146770775 146771929 1154 False 1561.000000 1561 91.090000 5441 6594 1 chr1B.!!$F1 1153
12 TraesCS6B01G245100 chr1B 408617227 408618335 1108 False 1513.000000 1513 91.344000 5496 6600 1 chr1B.!!$F2 1104
13 TraesCS6B01G245100 chr3D 44215439 44216119 680 False 349.500000 438 85.408000 2972 3696 2 chr3D.!!$F1 724
14 TraesCS6B01G245100 chr4D 23280746 23281425 679 True 344.000000 433 85.024000 2972 3696 2 chr4D.!!$R1 724
15 TraesCS6B01G245100 chr3A 91457175 91457903 728 True 294.500000 350 82.372500 3106 3895 2 chr3A.!!$R3 789
16 TraesCS6B01G245100 chr3A 425600900 425601614 714 True 240.500000 316 79.783000 3106 3895 2 chr3A.!!$R4 789

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
682 707 1.138883 CGCGGTTTCATCTCGAGGA 59.861 57.895 13.56 0.0 0.00 3.71 F
992 1027 1.407437 CCTTCGAAGCTTGGGCATAGT 60.407 52.381 19.99 0.0 41.70 2.12 F
1612 1670 2.040813 ACTGTTGCAGGTGATGAGGATT 59.959 45.455 1.08 0.0 35.51 3.01 F
3249 3328 4.592942 TGCCTTATCTGATTGTTTGAGCT 58.407 39.130 0.00 0.0 0.00 4.09 F
3579 3669 0.035458 GTGTGACCCCACCAGAAGAG 59.965 60.000 0.00 0.0 42.53 2.85 F
4885 5067 1.423921 ACTCCCTCCGTTCCAAAATGT 59.576 47.619 0.00 0.0 0.00 2.71 F
4946 5128 0.328258 ACATTTTGGGACGGAGGGAG 59.672 55.000 0.00 0.0 0.00 4.30 F
5940 6139 0.035317 CTACTGCCTTGTGCTCCACA 59.965 55.000 0.00 0.0 43.02 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 1652 1.133790 GCAATCCTCATCACCTGCAAC 59.866 52.381 0.00 0.0 0.00 4.17 R
1909 1967 1.135315 CCAACGCAAATGGGAGACATG 60.135 52.381 4.34 0.0 40.44 3.21 R
3512 3602 0.969409 AAGGGCAAGGAAGATGCAGC 60.969 55.000 0.00 0.0 45.60 5.25 R
4927 5109 0.328258 CTCCCTCCGTCCCAAAATGT 59.672 55.000 0.00 0.0 0.00 2.71 R
4928 5110 0.328258 ACTCCCTCCGTCCCAAAATG 59.672 55.000 0.00 0.0 0.00 2.32 R
5940 6139 0.036199 ACGAGCGTGTCTCTAGGACT 60.036 55.000 11.21 0.0 44.74 3.85 R
6275 6477 0.532862 CCGGCGCTATGAACTCCATT 60.533 55.000 7.64 0.0 36.71 3.16 R
7587 7791 0.759959 TGAACTACCGGAAACAGCCA 59.240 50.000 9.46 0.0 0.00 4.75 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
39 40 2.906354 ACGAAGCATCCTCAATGGTAC 58.094 47.619 0.00 0.00 45.23 3.34
42 43 4.202161 ACGAAGCATCCTCAATGGTACTAG 60.202 45.833 0.00 0.00 45.23 2.57
67 72 2.000447 GTAACTCGGAAAGATTGCGCT 59.000 47.619 9.73 0.00 44.57 5.92
149 154 5.392767 TGCACTTTCACCAGTAAACAAAA 57.607 34.783 0.00 0.00 0.00 2.44
178 183 6.324819 ACTCGAACCGTAGAAAATCGAATAA 58.675 36.000 0.00 0.00 41.39 1.40
182 187 7.914871 TCGAACCGTAGAAAATCGAATAATACA 59.085 33.333 0.00 0.00 39.33 2.29
186 191 9.674824 ACCGTAGAAAATCGAATAATACAGTAG 57.325 33.333 0.00 0.00 0.00 2.57
187 192 9.674824 CCGTAGAAAATCGAATAATACAGTAGT 57.325 33.333 0.00 0.00 0.00 2.73
326 331 1.371183 CCGAGTCCAGCAAGACCAA 59.629 57.895 2.77 0.00 37.49 3.67
682 707 1.138883 CGCGGTTTCATCTCGAGGA 59.861 57.895 13.56 0.00 0.00 3.71
707 732 3.052036 CAATTTGAACCAAAGCTGTCCG 58.948 45.455 0.00 0.00 36.76 4.79
758 783 4.142600 CGAATTGAGCCGGAATTCTCTTTT 60.143 41.667 19.31 8.98 37.57 2.27
759 784 5.064707 CGAATTGAGCCGGAATTCTCTTTTA 59.935 40.000 19.31 1.69 37.57 1.52
760 785 5.819825 ATTGAGCCGGAATTCTCTTTTAC 57.180 39.130 5.05 0.00 0.00 2.01
761 786 3.259064 TGAGCCGGAATTCTCTTTTACG 58.741 45.455 5.05 0.00 0.00 3.18
848 873 2.203337 TCCTGTTGCTGCACACCC 60.203 61.111 0.00 0.00 0.00 4.61
914 949 3.517100 ACCACACAGAAGATGAGCTACAT 59.483 43.478 0.00 0.00 42.47 2.29
927 962 4.861196 TGAGCTACATCTCACCTCTAACT 58.139 43.478 0.00 0.00 38.11 2.24
992 1027 1.407437 CCTTCGAAGCTTGGGCATAGT 60.407 52.381 19.99 0.00 41.70 2.12
1290 1347 6.016610 TGGAGTTATTTTGTGCCTTTGTACTC 60.017 38.462 0.00 0.00 0.00 2.59
1326 1383 6.451064 AATACTGAATGATTTTCCCCGTTC 57.549 37.500 0.00 0.00 0.00 3.95
1456 1514 4.262808 CCCATGAGGATTCAGACTATGACC 60.263 50.000 0.00 0.00 35.88 4.02
1546 1604 6.886459 GCCCTGCATAATCCTCTTATCATTTA 59.114 38.462 0.00 0.00 0.00 1.40
1547 1605 7.148171 GCCCTGCATAATCCTCTTATCATTTAC 60.148 40.741 0.00 0.00 0.00 2.01
1594 1652 7.366513 ACTGATGAAGTATATCGATCACACTG 58.633 38.462 0.00 0.00 37.36 3.66
1612 1670 2.040813 ACTGTTGCAGGTGATGAGGATT 59.959 45.455 1.08 0.00 35.51 3.01
2123 2181 9.102757 GAACATATCATGTGTCATCTTACTTGT 57.897 33.333 0.00 0.00 44.07 3.16
2158 2216 7.559590 AATATCATTTCAGGTCTTTTCTCCG 57.440 36.000 0.00 0.00 0.00 4.63
2651 2709 9.614792 AGTGTTCTTAAAGTGAGTTGAATTACT 57.385 29.630 0.00 0.00 0.00 2.24
2652 2710 9.651718 GTGTTCTTAAAGTGAGTTGAATTACTG 57.348 33.333 0.00 0.00 0.00 2.74
2653 2711 9.607988 TGTTCTTAAAGTGAGTTGAATTACTGA 57.392 29.630 0.00 0.00 0.00 3.41
3249 3328 4.592942 TGCCTTATCTGATTGTTTGAGCT 58.407 39.130 0.00 0.00 0.00 4.09
3512 3602 6.814146 GTGTCCTTAGATCAGTTGAAGGTAAG 59.186 42.308 0.00 0.00 39.62 2.34
3574 3664 1.228245 CCTTGTGTGACCCCACCAG 60.228 63.158 0.00 0.00 42.53 4.00
3579 3669 0.035458 GTGTGACCCCACCAGAAGAG 59.965 60.000 0.00 0.00 42.53 2.85
4352 4452 8.455903 TGCTCTATTCCTTTATGAAAGATTGG 57.544 34.615 0.47 0.00 41.02 3.16
4588 4688 7.012327 TGTGTGTAAAGATATAGATTTGCCTGC 59.988 37.037 0.00 0.00 0.00 4.85
4870 5052 9.543783 CTAAATGGTCAAGTATAAACTACTCCC 57.456 37.037 0.00 0.00 33.75 4.30
4871 5053 7.750947 AATGGTCAAGTATAAACTACTCCCT 57.249 36.000 0.00 0.00 33.75 4.20
4872 5054 6.786967 TGGTCAAGTATAAACTACTCCCTC 57.213 41.667 0.00 0.00 33.75 4.30
4873 5055 5.659971 TGGTCAAGTATAAACTACTCCCTCC 59.340 44.000 0.00 0.00 33.75 4.30
4874 5056 5.221204 GGTCAAGTATAAACTACTCCCTCCG 60.221 48.000 0.00 0.00 33.75 4.63
4875 5057 5.359292 GTCAAGTATAAACTACTCCCTCCGT 59.641 44.000 0.00 0.00 33.75 4.69
4876 5058 5.954150 TCAAGTATAAACTACTCCCTCCGTT 59.046 40.000 0.00 0.00 33.75 4.44
4877 5059 6.096001 TCAAGTATAAACTACTCCCTCCGTTC 59.904 42.308 0.00 0.00 33.75 3.95
4878 5060 4.892345 AGTATAAACTACTCCCTCCGTTCC 59.108 45.833 0.00 0.00 32.84 3.62
4879 5061 2.019807 AAACTACTCCCTCCGTTCCA 57.980 50.000 0.00 0.00 0.00 3.53
4880 5062 2.019807 AACTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
4881 5063 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
4882 5064 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
4883 5065 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
4884 5066 2.200373 ACTCCCTCCGTTCCAAAATG 57.800 50.000 0.00 0.00 0.00 2.32
4885 5067 1.423921 ACTCCCTCCGTTCCAAAATGT 59.576 47.619 0.00 0.00 0.00 2.71
4886 5068 2.640826 ACTCCCTCCGTTCCAAAATGTA 59.359 45.455 0.00 0.00 0.00 2.29
4887 5069 3.073356 ACTCCCTCCGTTCCAAAATGTAA 59.927 43.478 0.00 0.00 0.00 2.41
4888 5070 3.681593 TCCCTCCGTTCCAAAATGTAAG 58.318 45.455 0.00 0.00 0.00 2.34
4889 5071 3.328343 TCCCTCCGTTCCAAAATGTAAGA 59.672 43.478 0.00 0.00 0.00 2.10
4890 5072 3.439129 CCCTCCGTTCCAAAATGTAAGAC 59.561 47.826 0.00 0.00 0.00 3.01
4891 5073 3.439129 CCTCCGTTCCAAAATGTAAGACC 59.561 47.826 0.00 0.00 0.00 3.85
4892 5074 4.324267 CTCCGTTCCAAAATGTAAGACCT 58.676 43.478 0.00 0.00 0.00 3.85
4893 5075 4.721132 TCCGTTCCAAAATGTAAGACCTT 58.279 39.130 0.00 0.00 0.00 3.50
4894 5076 5.134661 TCCGTTCCAAAATGTAAGACCTTT 58.865 37.500 0.00 0.00 0.00 3.11
4895 5077 5.595133 TCCGTTCCAAAATGTAAGACCTTTT 59.405 36.000 0.00 0.00 0.00 2.27
4896 5078 6.097129 TCCGTTCCAAAATGTAAGACCTTTTT 59.903 34.615 0.00 0.00 0.00 1.94
4929 5111 8.862325 ATGATAGTGTCAAAAATGGTCTTACA 57.138 30.769 0.00 0.00 40.97 2.41
4930 5112 8.862325 TGATAGTGTCAAAAATGGTCTTACAT 57.138 30.769 0.00 0.00 32.78 2.29
4931 5113 9.295825 TGATAGTGTCAAAAATGGTCTTACATT 57.704 29.630 0.00 0.00 36.95 2.71
4939 5121 5.385509 AAATGGTCTTACATTTTGGGACG 57.614 39.130 0.00 0.00 45.94 4.79
4940 5122 2.785562 TGGTCTTACATTTTGGGACGG 58.214 47.619 0.00 0.00 0.00 4.79
4941 5123 2.372504 TGGTCTTACATTTTGGGACGGA 59.627 45.455 0.00 0.00 0.00 4.69
4942 5124 3.007635 GGTCTTACATTTTGGGACGGAG 58.992 50.000 0.00 0.00 0.00 4.63
4943 5125 3.007635 GTCTTACATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4944 5126 2.026636 TCTTACATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
4945 5127 1.659022 TACATTTTGGGACGGAGGGA 58.341 50.000 0.00 0.00 0.00 4.20
4946 5128 0.328258 ACATTTTGGGACGGAGGGAG 59.672 55.000 0.00 0.00 0.00 4.30
4947 5129 0.328258 CATTTTGGGACGGAGGGAGT 59.672 55.000 0.00 0.00 0.00 3.85
4948 5130 1.557832 CATTTTGGGACGGAGGGAGTA 59.442 52.381 0.00 0.00 0.00 2.59
4949 5131 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
5089 5274 6.578944 TGTTGTGCCTACCTAACACATATAG 58.421 40.000 0.00 0.00 43.34 1.31
5441 5632 4.829064 AACTGTACGTTCATGCATTGTT 57.171 36.364 0.00 0.00 0.00 2.83
5442 5633 4.829064 ACTGTACGTTCATGCATTGTTT 57.171 36.364 0.00 0.00 0.00 2.83
5443 5634 5.181690 ACTGTACGTTCATGCATTGTTTT 57.818 34.783 0.00 0.00 0.00 2.43
5444 5635 5.212194 ACTGTACGTTCATGCATTGTTTTC 58.788 37.500 0.00 0.00 0.00 2.29
5445 5636 5.008613 ACTGTACGTTCATGCATTGTTTTCT 59.991 36.000 0.00 0.00 0.00 2.52
5567 5758 9.659830 CAACTTATAACACTTTACCACAACTTC 57.340 33.333 0.00 0.00 0.00 3.01
5631 5823 5.508567 TCAACATTGAGCCCAAATCTATCA 58.491 37.500 0.00 0.00 35.67 2.15
5760 5952 3.119779 TGTGCATACAACATCGTCGTCTA 60.120 43.478 0.00 0.00 32.88 2.59
5779 5971 2.126228 TCGACGATGCGTTCACCC 60.126 61.111 0.00 0.00 41.37 4.61
5781 5973 2.431942 GACGATGCGTTCACCCGT 60.432 61.111 0.00 0.00 41.37 5.28
5800 5992 2.289820 CGTAGCTTCTACGCCATCTACA 59.710 50.000 12.53 0.00 34.07 2.74
5914 6113 4.965042 CACTATATCGCGTTGTGCATAA 57.035 40.909 5.77 0.00 46.97 1.90
5923 6122 3.822594 CGTTGTGCATAAACAAGGCTA 57.177 42.857 13.64 0.00 40.60 3.93
5940 6139 0.035317 CTACTGCCTTGTGCTCCACA 59.965 55.000 0.00 0.00 43.02 4.17
5944 6143 1.968540 GCCTTGTGCTCCACAGTCC 60.969 63.158 0.00 0.00 45.39 3.85
6013 6212 2.980233 GCCCGACCATGCCATAGC 60.980 66.667 0.00 0.00 40.48 2.97
6015 6214 2.822637 CCCGACCATGCCATAGCCT 61.823 63.158 0.00 0.00 38.69 4.58
6073 6272 1.604308 CACAATCAGGGCTGCCACA 60.604 57.895 22.05 3.22 0.00 4.17
6086 6286 1.226491 GCCACATCGTGCTTCATGC 60.226 57.895 0.00 0.00 43.25 4.06
6092 6292 0.322816 ATCGTGCTTCATGCCCACTT 60.323 50.000 8.05 0.00 42.00 3.16
6240 6441 2.228582 TCATGTGGCAGAATTTTGACCG 59.771 45.455 0.00 0.00 0.00 4.79
6275 6477 1.078918 CTCCCTGCTCAATGCGTCA 60.079 57.895 0.00 0.00 46.63 4.35
6340 6542 0.396556 TAGGCCACGTAGGAGATGCA 60.397 55.000 5.01 0.00 41.22 3.96
6708 6912 6.323482 TCCCTGTCACAATGAAAATTTGAGAA 59.677 34.615 0.00 0.00 0.00 2.87
7111 7315 1.681793 GCCTGGCGTCTCTGTAATCTA 59.318 52.381 1.35 0.00 0.00 1.98
7220 7424 0.179076 GCATTGTTAATGGGCCAGGC 60.179 55.000 13.78 1.26 39.31 4.85
7346 7550 7.945134 ACCAGATGGATATTTTGCTACAATTC 58.055 34.615 5.72 0.00 38.94 2.17
7401 7605 3.634568 CACACCTTTTAATTGTGCGGA 57.365 42.857 0.00 0.00 34.64 5.54
7464 7668 3.255642 CGTTTCCTTCCATTGACACCATT 59.744 43.478 0.00 0.00 0.00 3.16
7651 7855 4.570772 GCTAGCGGAAAATTCAGTGTATCA 59.429 41.667 0.00 0.00 0.00 2.15
7653 7857 5.296813 AGCGGAAAATTCAGTGTATCAAC 57.703 39.130 0.00 0.00 0.00 3.18
7654 7858 4.759693 AGCGGAAAATTCAGTGTATCAACA 59.240 37.500 0.00 0.00 0.00 3.33
7655 7859 5.088739 GCGGAAAATTCAGTGTATCAACAG 58.911 41.667 0.00 0.00 35.91 3.16
7656 7860 5.106712 GCGGAAAATTCAGTGTATCAACAGA 60.107 40.000 0.00 0.00 35.91 3.41
7657 7861 6.307155 CGGAAAATTCAGTGTATCAACAGAC 58.693 40.000 0.00 0.00 35.91 3.51
7665 7869 4.161189 CAGTGTATCAACAGACCAGAGGAT 59.839 45.833 0.00 0.00 35.91 3.24
7720 7926 2.177394 TAGAAACAATGTCGGCTGCA 57.823 45.000 0.50 0.00 0.00 4.41
7787 7993 6.929049 TCTTGAAATCACATCACGGTATATCC 59.071 38.462 0.00 0.00 0.00 2.59
7913 8119 2.892852 ACAAAGGACATCCCAACACATG 59.107 45.455 0.00 0.00 37.41 3.21
7933 8139 8.250332 ACACATGTTGTATATCAATTGGGAAAC 58.750 33.333 5.42 3.55 36.32 2.78
7953 9539 2.162681 CAAAGTAGAAACAGGGCTGGG 58.837 52.381 0.00 0.00 34.19 4.45
8095 10018 4.734398 TTTGATTTGTTCCAAGCTGTGT 57.266 36.364 0.00 0.00 0.00 3.72
8110 10033 0.822944 TGTGTGGCTGGACATGGTTG 60.823 55.000 0.00 0.00 0.00 3.77
8114 10037 0.827089 TGGCTGGACATGGTTGTTGG 60.827 55.000 0.00 0.00 35.79 3.77
8134 10057 5.682943 TGGAAAACACGGTAGAAATCAAG 57.317 39.130 0.00 0.00 0.00 3.02
8175 10098 6.055588 CCTGTTCAACTTCTTCTAGAACCAA 58.944 40.000 0.00 0.00 38.17 3.67
8255 10181 6.127842 GGAGAACCTCTTTGTTGTGTTTGTTA 60.128 38.462 0.00 0.00 0.00 2.41
8260 10186 8.458573 ACCTCTTTGTTGTGTTTGTTATATCA 57.541 30.769 0.00 0.00 0.00 2.15
8270 10196 7.598278 TGTGTTTGTTATATCATTTGTCCACC 58.402 34.615 0.00 0.00 0.00 4.61
8273 10199 9.467796 TGTTTGTTATATCATTTGTCCACCATA 57.532 29.630 0.00 0.00 0.00 2.74
8280 10206 8.859236 ATATCATTTGTCCACCATATCTGAAG 57.141 34.615 0.00 0.00 0.00 3.02
8310 10238 1.047002 CCCTCTGAGGTGGCTGATAG 58.953 60.000 21.70 0.00 31.93 2.08
8353 10281 2.660064 GGGAGGAGCGCAAGAGGAA 61.660 63.158 11.47 0.00 43.02 3.36
8406 10334 5.493809 AGAGGTAGTAGTGAGACTTCTGTC 58.506 45.833 0.00 0.00 43.22 3.51
8454 10384 8.533965 CATGTCATTTTTGTGTCACTAAAACAG 58.466 33.333 22.04 18.04 36.11 3.16
8467 10397 3.930848 ACTAAAACAGGTTTATCGAGCCG 59.069 43.478 0.00 0.00 33.10 5.52
8550 10480 9.352784 TCAACTTGTGTTTGAAATGAAGTTTAG 57.647 29.630 8.35 2.25 32.66 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.448615 GGATGCTTCGTTTGTTTAGTTATTACT 58.551 33.333 0.00 0.00 38.44 2.24
4 5 8.448615 AGGATGCTTCGTTTGTTTAGTTATTAC 58.551 33.333 0.00 0.00 0.00 1.89
6 7 7.174253 TGAGGATGCTTCGTTTGTTTAGTTATT 59.826 33.333 0.00 0.00 0.00 1.40
7 8 6.653320 TGAGGATGCTTCGTTTGTTTAGTTAT 59.347 34.615 0.00 0.00 0.00 1.89
39 40 6.074782 GCAATCTTTCCGAGTTACGAATCTAG 60.075 42.308 0.00 0.00 45.77 2.43
42 43 4.548346 CGCAATCTTTCCGAGTTACGAATC 60.548 45.833 0.00 0.00 45.77 2.52
67 72 1.447838 GAGAATGTTCGCGAGCCCA 60.448 57.895 20.56 13.49 0.00 5.36
149 154 4.326504 TTTTCTACGGTTCGAGTTTCCT 57.673 40.909 0.00 0.00 0.00 3.36
182 187 8.081025 CCGTCTTCTGTTAGTTTTTCTACTACT 58.919 37.037 0.00 0.00 30.62 2.57
185 190 6.041296 TCCCGTCTTCTGTTAGTTTTTCTACT 59.959 38.462 0.00 0.00 0.00 2.57
186 191 6.218746 TCCCGTCTTCTGTTAGTTTTTCTAC 58.781 40.000 0.00 0.00 0.00 2.59
187 192 6.409524 TCCCGTCTTCTGTTAGTTTTTCTA 57.590 37.500 0.00 0.00 0.00 2.10
188 193 5.286267 TCCCGTCTTCTGTTAGTTTTTCT 57.714 39.130 0.00 0.00 0.00 2.52
189 194 4.451435 CCTCCCGTCTTCTGTTAGTTTTTC 59.549 45.833 0.00 0.00 0.00 2.29
190 195 4.386711 CCTCCCGTCTTCTGTTAGTTTTT 58.613 43.478 0.00 0.00 0.00 1.94
196 201 1.888018 CGCCTCCCGTCTTCTGTTA 59.112 57.895 0.00 0.00 0.00 2.41
345 351 3.334691 CTTTTCATGCTCCGTTAGGTCA 58.665 45.455 0.00 0.00 39.05 4.02
349 355 1.401905 GGGCTTTTCATGCTCCGTTAG 59.598 52.381 0.00 0.00 0.00 2.34
350 356 1.459450 GGGCTTTTCATGCTCCGTTA 58.541 50.000 0.00 0.00 0.00 3.18
395 401 4.593956 CCTTGCCTTCCTTTTATCTCTGT 58.406 43.478 0.00 0.00 0.00 3.41
682 707 5.759763 GGACAGCTTTGGTTCAAATTGATTT 59.240 36.000 0.00 0.00 32.70 2.17
758 783 6.703607 TGAACCGGAAACAAAATTAGTACGTA 59.296 34.615 9.46 0.00 0.00 3.57
759 784 5.526846 TGAACCGGAAACAAAATTAGTACGT 59.473 36.000 9.46 0.00 0.00 3.57
760 785 5.988092 TGAACCGGAAACAAAATTAGTACG 58.012 37.500 9.46 0.00 0.00 3.67
761 786 8.806177 AAATGAACCGGAAACAAAATTAGTAC 57.194 30.769 9.46 0.00 0.00 2.73
799 824 6.207810 TGGTGTTTTGTTTTCTAAGTGACAGT 59.792 34.615 0.00 0.00 0.00 3.55
848 873 2.503331 TGGTATATTCGCCCATTGCTG 58.497 47.619 0.00 0.00 38.05 4.41
914 949 3.496160 GGCAACCAAAGTTAGAGGTGAGA 60.496 47.826 0.00 0.00 35.42 3.27
973 1008 1.936547 GACTATGCCCAAGCTTCGAAG 59.063 52.381 21.02 21.02 40.80 3.79
992 1027 4.854924 CGGTGGCCATGGCGATGA 62.855 66.667 29.90 11.30 43.06 2.92
1065 1100 0.663568 CGAAGTCGACGCTCTTGGTT 60.664 55.000 10.46 0.00 43.02 3.67
1149 1184 3.088532 AGACTCTGTACTTGAGCTCCTG 58.911 50.000 12.15 6.38 35.12 3.86
1326 1383 3.486383 TGCCTGGGAACTAAAGAACAAG 58.514 45.455 0.00 0.00 0.00 3.16
1456 1514 4.194640 CAACATCCTTGGTATCTGAGGTG 58.805 47.826 0.00 0.00 32.33 4.00
1546 1604 9.046296 CAGTTGACTAAACAGAAAACATCTAGT 57.954 33.333 0.00 0.00 41.61 2.57
1547 1605 9.261180 TCAGTTGACTAAACAGAAAACATCTAG 57.739 33.333 0.00 0.00 41.61 2.43
1594 1652 1.133790 GCAATCCTCATCACCTGCAAC 59.866 52.381 0.00 0.00 0.00 4.17
1612 1670 2.042686 AATCAGCGCCTTTATCTGCA 57.957 45.000 2.29 0.00 0.00 4.41
1909 1967 1.135315 CCAACGCAAATGGGAGACATG 60.135 52.381 4.34 0.00 40.44 3.21
1917 1975 3.848726 AGAATTTAGCCAACGCAAATGG 58.151 40.909 0.00 0.00 41.08 3.16
2123 2181 1.877637 AATGATATTACAGCGGCGCA 58.122 45.000 35.02 14.17 0.00 6.09
2158 2216 4.936891 ACTTCTTGCATTTCTCAACCAAC 58.063 39.130 0.00 0.00 0.00 3.77
2328 2386 6.037610 GCAGACTCAACCTGAAATTAGTATGG 59.962 42.308 0.00 0.00 33.65 2.74
2794 2868 5.122869 TCAATCAGCTCACTGCAAACTATTC 59.877 40.000 0.00 0.00 44.10 1.75
2978 3053 3.074538 AGGCCTTACAACCTGTTCAAGAT 59.925 43.478 0.00 0.00 34.07 2.40
3058 3133 1.971357 TCTTCCTCTGGTGGTTCTGTC 59.029 52.381 0.00 0.00 0.00 3.51
3219 3298 4.397417 ACAATCAGATAAGGCAAAGCACTC 59.603 41.667 0.00 0.00 0.00 3.51
3249 3328 9.507329 AGAGCACAAGATAAATGTTTTAAGAGA 57.493 29.630 0.00 0.00 0.00 3.10
3418 3500 1.771854 TGCCTCACCCTGTTGTAAGAA 59.228 47.619 0.00 0.00 0.00 2.52
3512 3602 0.969409 AAGGGCAAGGAAGATGCAGC 60.969 55.000 0.00 0.00 45.60 5.25
3574 3664 8.090214 AGAAAATAGCTGCATAGAGATCTCTTC 58.910 37.037 29.54 18.53 40.93 2.87
3579 3669 9.874205 AGATTAGAAAATAGCTGCATAGAGATC 57.126 33.333 1.02 0.00 0.00 2.75
3846 3946 9.498176 GAAGTCCCTCTAAAAATAGTTGTGTAA 57.502 33.333 0.00 0.00 0.00 2.41
3896 3996 5.808540 CAGTTGCCAAATCCTAATGTTCATG 59.191 40.000 0.00 0.00 0.00 3.07
4326 4426 9.075678 CCAATCTTTCATAAAGGAATAGAGCAT 57.924 33.333 0.00 0.00 39.01 3.79
4327 4427 7.013655 GCCAATCTTTCATAAAGGAATAGAGCA 59.986 37.037 0.00 0.00 39.01 4.26
4328 4428 7.013655 TGCCAATCTTTCATAAAGGAATAGAGC 59.986 37.037 0.00 0.00 39.01 4.09
4329 4429 8.455903 TGCCAATCTTTCATAAAGGAATAGAG 57.544 34.615 0.00 0.00 39.01 2.43
4330 4430 7.013655 GCTGCCAATCTTTCATAAAGGAATAGA 59.986 37.037 0.00 0.00 39.01 1.98
4352 4452 9.869844 CTGTACAGAAATACAAATTATAGCTGC 57.130 33.333 18.45 0.00 34.68 5.25
4577 4677 7.016072 AGAGTAAGTCATATAGCAGGCAAATCT 59.984 37.037 0.00 0.00 0.00 2.40
4609 4709 4.848357 ACAGCAAATCTAGTGCCTACAAT 58.152 39.130 0.46 0.00 43.27 2.71
4867 5049 3.328343 TCTTACATTTTGGAACGGAGGGA 59.672 43.478 0.00 0.00 0.00 4.20
4868 5050 3.439129 GTCTTACATTTTGGAACGGAGGG 59.561 47.826 0.00 0.00 0.00 4.30
4869 5051 3.439129 GGTCTTACATTTTGGAACGGAGG 59.561 47.826 0.00 0.00 0.00 4.30
4870 5052 4.324267 AGGTCTTACATTTTGGAACGGAG 58.676 43.478 0.00 0.00 0.00 4.63
4871 5053 4.360951 AGGTCTTACATTTTGGAACGGA 57.639 40.909 0.00 0.00 0.00 4.69
4872 5054 5.447624 AAAGGTCTTACATTTTGGAACGG 57.552 39.130 0.00 0.00 26.15 4.44
4903 5085 9.952030 TGTAAGACCATTTTTGACACTATCATA 57.048 29.630 0.00 0.00 37.11 2.15
4904 5086 8.862325 TGTAAGACCATTTTTGACACTATCAT 57.138 30.769 0.00 0.00 37.11 2.45
4905 5087 8.862325 ATGTAAGACCATTTTTGACACTATCA 57.138 30.769 0.00 0.00 34.65 2.15
4917 5099 4.219725 CCGTCCCAAAATGTAAGACCATTT 59.780 41.667 0.00 0.00 44.71 2.32
4918 5100 3.761752 CCGTCCCAAAATGTAAGACCATT 59.238 43.478 0.00 0.00 36.62 3.16
4919 5101 3.009695 TCCGTCCCAAAATGTAAGACCAT 59.990 43.478 0.00 0.00 0.00 3.55
4920 5102 2.372504 TCCGTCCCAAAATGTAAGACCA 59.627 45.455 0.00 0.00 0.00 4.02
4921 5103 3.007635 CTCCGTCCCAAAATGTAAGACC 58.992 50.000 0.00 0.00 0.00 3.85
4922 5104 3.007635 CCTCCGTCCCAAAATGTAAGAC 58.992 50.000 0.00 0.00 0.00 3.01
4923 5105 2.026636 CCCTCCGTCCCAAAATGTAAGA 60.027 50.000 0.00 0.00 0.00 2.10
4924 5106 2.026636 TCCCTCCGTCCCAAAATGTAAG 60.027 50.000 0.00 0.00 0.00 2.34
4925 5107 1.986631 TCCCTCCGTCCCAAAATGTAA 59.013 47.619 0.00 0.00 0.00 2.41
4926 5108 1.557832 CTCCCTCCGTCCCAAAATGTA 59.442 52.381 0.00 0.00 0.00 2.29
4927 5109 0.328258 CTCCCTCCGTCCCAAAATGT 59.672 55.000 0.00 0.00 0.00 2.71
4928 5110 0.328258 ACTCCCTCCGTCCCAAAATG 59.672 55.000 0.00 0.00 0.00 2.32
4929 5111 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4930 5112 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
4931 5113 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
4932 5114 0.337082 TCATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
4933 5115 0.561184 ATCATACTCCCTCCGTCCCA 59.439 55.000 0.00 0.00 0.00 4.37
4934 5116 1.718280 AATCATACTCCCTCCGTCCC 58.282 55.000 0.00 0.00 0.00 4.46
4935 5117 4.799917 GCTTAAATCATACTCCCTCCGTCC 60.800 50.000 0.00 0.00 0.00 4.79
4936 5118 4.202223 TGCTTAAATCATACTCCCTCCGTC 60.202 45.833 0.00 0.00 0.00 4.79
4937 5119 3.709653 TGCTTAAATCATACTCCCTCCGT 59.290 43.478 0.00 0.00 0.00 4.69
4938 5120 4.336889 TGCTTAAATCATACTCCCTCCG 57.663 45.455 0.00 0.00 0.00 4.63
4939 5121 5.930135 TCTTGCTTAAATCATACTCCCTCC 58.070 41.667 0.00 0.00 0.00 4.30
4940 5122 7.865706 TTTCTTGCTTAAATCATACTCCCTC 57.134 36.000 0.00 0.00 0.00 4.30
4941 5123 8.650143 TTTTTCTTGCTTAAATCATACTCCCT 57.350 30.769 0.00 0.00 0.00 4.20
4942 5124 8.523658 ACTTTTTCTTGCTTAAATCATACTCCC 58.476 33.333 0.00 0.00 0.00 4.30
4943 5125 9.561270 GACTTTTTCTTGCTTAAATCATACTCC 57.439 33.333 0.00 0.00 0.00 3.85
4949 5131 9.301153 GTCAAAGACTTTTTCTTGCTTAAATCA 57.699 29.630 0.00 0.00 44.41 2.57
5047 5232 4.082571 ACAACAAATCAGAAGCACCATAGC 60.083 41.667 0.00 0.00 0.00 2.97
5089 5274 5.867174 ACAGCCTGTAAAACAAGAACAAAAC 59.133 36.000 0.00 0.00 0.00 2.43
5631 5823 6.833933 AGATTGGGTGTTAAAAGAAGTTGACT 59.166 34.615 0.00 0.00 0.00 3.41
5760 5952 1.443872 GGTGAACGCATCGTCGAGT 60.444 57.895 0.00 0.00 39.99 4.18
5769 5961 1.373748 GAAGCTACGGGTGAACGCA 60.374 57.895 0.00 0.00 37.37 5.24
5779 5971 2.289820 TGTAGATGGCGTAGAAGCTACG 59.710 50.000 19.38 19.38 37.40 3.51
5781 5973 2.621998 GGTGTAGATGGCGTAGAAGCTA 59.378 50.000 0.00 0.00 37.29 3.32
5877 6071 2.102438 GTGCATGTGCTAGCTGCGA 61.102 57.895 17.23 5.96 46.63 5.10
5923 6122 1.228063 CTGTGGAGCACAAGGCAGT 60.228 57.895 0.00 0.00 44.08 4.40
5940 6139 0.036199 ACGAGCGTGTCTCTAGGACT 60.036 55.000 11.21 0.00 44.74 3.85
5944 6143 0.653636 GAGGACGAGCGTGTCTCTAG 59.346 60.000 0.00 0.00 39.70 2.43
6039 6238 1.067749 GTGCACAATGTGGCAGCAA 59.932 52.632 15.78 0.00 41.35 3.91
6086 6286 3.244105 CGAGCACGTTGAAGTGGG 58.756 61.111 0.00 0.00 42.09 4.61
6240 6441 3.615709 GCTGGGTGTTGTTGGGGC 61.616 66.667 0.00 0.00 0.00 5.80
6275 6477 0.532862 CCGGCGCTATGAACTCCATT 60.533 55.000 7.64 0.00 36.71 3.16
6340 6542 1.619827 CAGGAAAATGGTGGCATGTGT 59.380 47.619 0.00 0.00 0.00 3.72
6568 6772 2.757868 CACAAAACCACAACTTCAGGGA 59.242 45.455 0.00 0.00 0.00 4.20
7111 7315 6.016360 TGAATGGAAACAATCAAGTGTTCGAT 60.016 34.615 0.00 0.00 46.88 3.59
7142 7346 4.832266 AGTGAATCAGGCCAATGTTTTACA 59.168 37.500 5.01 0.00 0.00 2.41
7401 7605 8.730680 GGTTTCATATATTTATTCACGCCATCT 58.269 33.333 0.00 0.00 0.00 2.90
7464 7668 7.639039 CACAACAGTCTACAGCAAAAAGATAA 58.361 34.615 0.00 0.00 0.00 1.75
7537 7741 0.916086 AACGGCCATGGTCCTTGATA 59.084 50.000 11.65 0.00 0.00 2.15
7587 7791 0.759959 TGAACTACCGGAAACAGCCA 59.240 50.000 9.46 0.00 0.00 4.75
7641 7845 3.511540 CCTCTGGTCTGTTGATACACTGA 59.488 47.826 0.00 0.00 0.00 3.41
7651 7855 3.312890 CTGGGATATCCTCTGGTCTGTT 58.687 50.000 21.18 0.00 36.20 3.16
7653 7857 1.622811 GCTGGGATATCCTCTGGTCTG 59.377 57.143 21.18 8.51 36.20 3.51
7654 7858 1.221523 TGCTGGGATATCCTCTGGTCT 59.778 52.381 21.18 0.00 36.20 3.85
7655 7859 1.346068 GTGCTGGGATATCCTCTGGTC 59.654 57.143 21.18 4.19 36.20 4.02
7656 7860 1.344393 TGTGCTGGGATATCCTCTGGT 60.344 52.381 21.18 0.00 36.20 4.00
7657 7861 1.427809 TGTGCTGGGATATCCTCTGG 58.572 55.000 21.18 9.87 36.20 3.86
7665 7869 8.267183 CCAACTGATATAATATGTGCTGGGATA 58.733 37.037 0.00 0.00 0.00 2.59
7720 7926 3.548745 TCATCAGGATGTCGCAGAATT 57.451 42.857 8.97 0.00 39.69 2.17
7734 7940 4.995487 TCTATGCTGCTTATGCTTCATCAG 59.005 41.667 0.00 0.00 40.48 2.90
7787 7993 8.942338 TTACAAATGTACTCCTACATGCTTAG 57.058 34.615 0.00 0.00 41.92 2.18
7933 8139 2.162681 CCCAGCCCTGTTTCTACTTTG 58.837 52.381 0.00 0.00 0.00 2.77
7953 9539 1.002366 AAGATGTCGCAGAATCGTGC 58.998 50.000 0.00 0.00 39.69 5.34
8008 9594 9.862371 ACCTTCTTTAAGATATATAGCGACATG 57.138 33.333 0.00 0.00 34.37 3.21
8095 10018 0.827089 CCAACAACCATGTCCAGCCA 60.827 55.000 0.00 0.00 39.40 4.75
8110 10033 5.427036 TGATTTCTACCGTGTTTTCCAAC 57.573 39.130 0.00 0.00 0.00 3.77
8114 10037 4.082949 CCCCTTGATTTCTACCGTGTTTTC 60.083 45.833 0.00 0.00 0.00 2.29
8175 10098 2.426738 CGCACACATAATTGGATTGGGT 59.573 45.455 0.00 0.00 0.00 4.51
8242 10168 8.633561 TGGACAAATGATATAACAAACACAACA 58.366 29.630 0.00 0.00 0.00 3.33
8255 10181 7.392673 GCTTCAGATATGGTGGACAAATGATAT 59.607 37.037 0.00 0.00 0.00 1.63
8260 10186 5.121380 AGCTTCAGATATGGTGGACAAAT 57.879 39.130 0.00 0.00 0.00 2.32
8265 10191 2.421952 GCCAAGCTTCAGATATGGTGGA 60.422 50.000 0.00 0.00 33.63 4.02
8310 10238 1.933853 GTGCATGTTGATCGTCCCTAC 59.066 52.381 0.00 0.00 0.00 3.18
8386 10314 4.002316 ACGACAGAAGTCTCACTACTACC 58.998 47.826 0.00 0.00 42.73 3.18
8406 10334 7.904977 ACATGATATGAAACAAAAATCGAGACG 59.095 33.333 0.00 0.00 0.00 4.18
8409 10337 9.726232 ATGACATGATATGAAACAAAAATCGAG 57.274 29.630 0.00 0.00 0.00 4.04
8454 10384 1.949465 AATCCACGGCTCGATAAACC 58.051 50.000 1.50 0.00 0.00 3.27
8467 10397 7.700656 GGTTAACATGCACTAAACATAATCCAC 59.299 37.037 8.10 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.