Multiple sequence alignment - TraesCS7A01G126600

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 TraesCS7A01G126600 chr7A 100.000 3563 0 0 1 3563 81547238 81550800 0.000000e+00 6580.0
1 TraesCS7A01G126600 chr7D 95.135 2672 90 15 1 2662 78114509 78117150 0.000000e+00 4178.0
2 TraesCS7A01G126600 chr7D 87.840 1546 182 2 1006 2551 477641653 477643192 0.000000e+00 1808.0
3 TraesCS7A01G126600 chr7D 90.214 562 28 12 2646 3183 78117168 78117726 0.000000e+00 708.0
4 TraesCS7A01G126600 chr7D 91.000 100 9 0 3289 3388 78117728 78117827 6.200000e-28 135.0
5 TraesCS7A01G126600 chr7B 87.130 1554 182 9 1007 2551 501965667 501967211 0.000000e+00 1746.0
6 TraesCS7A01G126600 chr7B 93.569 1104 60 7 1792 2892 25340416 25341511 0.000000e+00 1635.0
7 TraesCS7A01G126600 chr7B 96.621 799 27 0 1005 1803 25339166 25339964 0.000000e+00 1327.0
8 TraesCS7A01G126600 chr7B 77.394 1504 298 38 1070 2554 502316790 502318270 0.000000e+00 856.0
9 TraesCS7A01G126600 chr7B 93.571 140 9 0 675 814 25338834 25338973 3.600000e-50 209.0
10 TraesCS7A01G126600 chr7B 94.355 124 7 0 870 993 25338982 25339105 1.310000e-44 191.0
11 TraesCS7A01G126600 chr3A 86.623 1383 170 11 1175 2551 33137240 33138613 0.000000e+00 1515.0
12 TraesCS7A01G126600 chr3A 95.968 124 4 1 3440 3563 534187789 534187911 2.170000e-47 200.0
13 TraesCS7A01G126600 chr3A 95.161 124 5 1 3440 3563 742883204 742883326 1.010000e-45 195.0
14 TraesCS7A01G126600 chr2A 82.310 1498 228 26 1085 2550 72814090 72812598 0.000000e+00 1264.0
15 TraesCS7A01G126600 chr2A 96.774 124 3 1 3440 3563 28448618 28448496 4.660000e-49 206.0
16 TraesCS7A01G126600 chr2A 93.893 131 7 1 3433 3563 4120352 4120223 2.810000e-46 196.0
17 TraesCS7A01G126600 chr2A 95.200 125 4 2 3440 3563 118452550 118452427 2.810000e-46 196.0
18 TraesCS7A01G126600 chr2D 82.255 1499 230 23 1085 2550 73417409 73415914 0.000000e+00 1262.0
19 TraesCS7A01G126600 chr2B 82.062 1494 236 22 1085 2550 111081870 111080381 0.000000e+00 1245.0
20 TraesCS7A01G126600 chr3B 83.863 818 121 10 1741 2553 41848991 41849802 0.000000e+00 769.0
21 TraesCS7A01G126600 chr3B 77.689 251 52 4 232 479 776354361 776354610 2.220000e-32 150.0
22 TraesCS7A01G126600 chr5A 96.774 124 3 1 3440 3563 639206189 639206311 4.660000e-49 206.0
23 TraesCS7A01G126600 chr5A 95.868 121 4 1 3443 3563 680192646 680192527 1.010000e-45 195.0
24 TraesCS7A01G126600 chr5A 93.077 130 8 1 3434 3563 18536096 18536224 4.700000e-44 189.0
25 TraesCS7A01G126600 chr5A 91.304 138 10 2 3426 3563 690431858 690431723 1.690000e-43 187.0
26 TraesCS7A01G126600 chr5A 78.363 171 36 1 11 180 245435059 245434889 3.760000e-20 110.0
27 TraesCS7A01G126600 chr5D 79.070 172 30 4 11 180 205566345 205566178 2.910000e-21 113.0
28 TraesCS7A01G126600 chr4D 77.922 154 25 8 432 581 209103038 209103186 1.760000e-13 87.9
29 TraesCS7A01G126600 chr1B 92.500 40 2 1 2916 2954 97509705 97509744 4.970000e-04 56.5


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 TraesCS7A01G126600 chr7A 81547238 81550800 3562 False 6580.000000 6580 100.000000 1 3563 1 chr7A.!!$F1 3562
1 TraesCS7A01G126600 chr7D 477641653 477643192 1539 False 1808.000000 1808 87.840000 1006 2551 1 chr7D.!!$F1 1545
2 TraesCS7A01G126600 chr7D 78114509 78117827 3318 False 1673.666667 4178 92.116333 1 3388 3 chr7D.!!$F2 3387
3 TraesCS7A01G126600 chr7B 501965667 501967211 1544 False 1746.000000 1746 87.130000 1007 2551 1 chr7B.!!$F1 1544
4 TraesCS7A01G126600 chr7B 502316790 502318270 1480 False 856.000000 856 77.394000 1070 2554 1 chr7B.!!$F2 1484
5 TraesCS7A01G126600 chr7B 25338834 25341511 2677 False 840.500000 1635 94.529000 675 2892 4 chr7B.!!$F3 2217
6 TraesCS7A01G126600 chr3A 33137240 33138613 1373 False 1515.000000 1515 86.623000 1175 2551 1 chr3A.!!$F1 1376
7 TraesCS7A01G126600 chr2A 72812598 72814090 1492 True 1264.000000 1264 82.310000 1085 2550 1 chr2A.!!$R3 1465
8 TraesCS7A01G126600 chr2D 73415914 73417409 1495 True 1262.000000 1262 82.255000 1085 2550 1 chr2D.!!$R1 1465
9 TraesCS7A01G126600 chr2B 111080381 111081870 1489 True 1245.000000 1245 82.062000 1085 2550 1 chr2B.!!$R1 1465
10 TraesCS7A01G126600 chr3B 41848991 41849802 811 False 769.000000 769 83.863000 1741 2553 1 chr3B.!!$F1 812

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
148 149 0.447801 CTTACAACCATCGGTGCAGC 59.552 55.000 5.64 5.64 35.34 5.25 F
448 450 0.748005 AACGATTCGGCCATTCCTGG 60.748 55.000 11.29 0.00 46.17 4.45 F
1111 1170 0.749091 CGATGGCTTCCTCCAATGCA 60.749 55.000 0.00 0.00 39.96 3.96 F
1993 2536 1.064906 ACTGCAAGGAGATGACATGGG 60.065 52.381 0.00 0.00 39.30 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 2552 1.692749 GTGGGGCCCAGGTAGATGA 60.693 63.158 29.66 0.0 32.34 2.92 R
2366 2924 0.795735 CCTGTAGTTCACGTACGCCG 60.796 60.000 16.72 7.1 44.03 6.46 R
2556 3117 1.226717 GCATCGTCCTCGTCACTCC 60.227 63.158 0.00 0.0 38.33 3.85 R
3474 4096 0.106149 CGGCGGCTAGGGTTTTAGAT 59.894 55.000 7.61 0.0 0.00 1.98 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
30 31 4.587891 TGCCACAACATCATATTCTCACA 58.412 39.130 0.00 0.00 0.00 3.58
36 37 6.910972 CACAACATCATATTCTCACAGATTGC 59.089 38.462 0.00 0.00 0.00 3.56
40 41 5.363562 TCATATTCTCACAGATTGCCAGT 57.636 39.130 0.00 0.00 0.00 4.00
85 86 8.358582 TCACATATCTACTCATATCACATGCT 57.641 34.615 0.00 0.00 0.00 3.79
103 104 7.069208 TCACATGCTCACAGATCTAGTTAGAAT 59.931 37.037 0.00 0.00 35.69 2.40
105 106 5.595885 TGCTCACAGATCTAGTTAGAATGC 58.404 41.667 0.00 0.00 35.69 3.56
106 107 5.362143 TGCTCACAGATCTAGTTAGAATGCT 59.638 40.000 0.00 0.00 35.69 3.79
142 143 3.306166 GTGATCGAACTTACAACCATCGG 59.694 47.826 0.00 0.00 34.47 4.18
143 144 3.056393 TGATCGAACTTACAACCATCGGT 60.056 43.478 0.00 0.00 37.65 4.69
144 145 2.679450 TCGAACTTACAACCATCGGTG 58.321 47.619 0.00 0.00 35.34 4.94
145 146 1.127951 CGAACTTACAACCATCGGTGC 59.872 52.381 0.00 0.00 35.34 5.01
146 147 2.147958 GAACTTACAACCATCGGTGCA 58.852 47.619 0.00 0.00 35.34 4.57
147 148 1.808411 ACTTACAACCATCGGTGCAG 58.192 50.000 0.00 0.00 35.34 4.41
148 149 0.447801 CTTACAACCATCGGTGCAGC 59.552 55.000 5.64 5.64 35.34 5.25
149 150 0.958382 TTACAACCATCGGTGCAGCC 60.958 55.000 10.90 2.64 35.34 4.85
166 167 2.434359 CGGAAGGAGGCGTGGAAC 60.434 66.667 0.00 0.00 0.00 3.62
197 198 0.937231 GACGCGCCTCTTATCTGCTC 60.937 60.000 5.73 0.00 0.00 4.26
220 221 4.229432 TCGATGACGATCCGCATGGAAT 62.229 50.000 0.00 0.00 41.86 3.01
228 229 1.452651 CCGCATGGAATGGTGAGCT 60.453 57.895 0.00 0.00 46.86 4.09
291 293 6.726764 GGTGAGGGTGACTATATTAGGAGATT 59.273 42.308 0.00 0.00 0.00 2.40
307 309 1.137086 AGATTGATTCGACGGGAGGTG 59.863 52.381 0.00 0.00 0.00 4.00
325 327 1.299976 GACCCCAATTCGTCCTGCT 59.700 57.895 0.00 0.00 0.00 4.24
345 347 6.165659 TGCTAAATTTTTAGAGACTCGCAC 57.834 37.500 13.02 0.00 42.05 5.34
368 370 0.951558 GTTGTGCCATCTTCGTGGTT 59.048 50.000 0.00 0.00 41.47 3.67
380 382 1.737735 CGTGGTTGCATGAGCTCGA 60.738 57.895 9.64 0.00 42.74 4.04
390 392 2.512515 GAGCTCGATGCCGCCTTT 60.513 61.111 0.00 0.00 44.23 3.11
407 409 1.852157 TTTCCTTCCCCTGCATCGCT 61.852 55.000 0.00 0.00 0.00 4.93
448 450 0.748005 AACGATTCGGCCATTCCTGG 60.748 55.000 11.29 0.00 46.17 4.45
456 458 3.642078 CCATTCCTGGCGGGTCTA 58.358 61.111 13.14 0.00 35.23 2.59
457 459 1.447643 CCATTCCTGGCGGGTCTAG 59.552 63.158 13.14 1.18 35.23 2.43
539 541 1.612950 AGCCATTTTTGCATCACGTGA 59.387 42.857 22.48 22.48 0.00 4.35
561 563 1.001020 TGGTTGGGCTGTATGCAGG 60.001 57.895 13.03 0.00 45.15 4.85
590 592 6.018588 CCAAACACGTCACTAATGTTTCACTA 60.019 38.462 0.00 0.00 43.02 2.74
948 952 4.452733 GGAAGGTGGAGCCGGACG 62.453 72.222 5.05 0.00 43.70 4.79
982 986 1.790387 GAGGTTGCAACAGCTAGCG 59.210 57.895 29.55 7.05 36.78 4.26
1066 1125 4.129737 TCCTGTCCTGCTACGCGC 62.130 66.667 5.73 0.00 39.77 6.86
1111 1170 0.749091 CGATGGCTTCCTCCAATGCA 60.749 55.000 0.00 0.00 39.96 3.96
1993 2536 1.064906 ACTGCAAGGAGATGACATGGG 60.065 52.381 0.00 0.00 39.30 4.00
2009 2552 3.637273 GGTCCAGTCCGTGCCCTT 61.637 66.667 0.00 0.00 0.00 3.95
2146 2701 3.217017 CGGAGATCTTCGCCCGGA 61.217 66.667 11.20 0.00 35.15 5.14
2366 2924 2.361737 GAGCAAGAACCCCAGGGC 60.362 66.667 0.00 0.00 39.32 5.19
2430 2988 2.203153 GTGGGCAACGTCACCAGT 60.203 61.111 8.87 0.00 34.39 4.00
2555 3116 1.956636 GCAGAGCATCCCACCATTCAA 60.957 52.381 0.00 0.00 33.66 2.69
2556 3117 2.022195 CAGAGCATCCCACCATTCAAG 58.978 52.381 0.00 0.00 33.66 3.02
2569 3130 2.611518 CATTCAAGGAGTGACGAGGAC 58.388 52.381 0.00 0.00 35.39 3.85
2651 3215 6.367983 AGATGGCAGGTGAATATTACATTGT 58.632 36.000 0.00 0.00 0.00 2.71
2762 3360 2.899303 ACTTTCCCTGGTATGTTGGG 57.101 50.000 0.00 0.00 42.20 4.12
2892 3496 9.631257 ATTGTTATATTCATGATGTGTTGGAGA 57.369 29.630 0.00 0.00 0.00 3.71
2957 3561 8.624776 CCCATTCATTAATTAAGAGAGGACAAC 58.375 37.037 3.94 0.00 0.00 3.32
2977 3581 2.358898 ACAGAGTTTGGCACACACATTC 59.641 45.455 6.55 0.00 42.21 2.67
2985 3589 6.437162 AGTTTGGCACACACATTCCTTATTAT 59.563 34.615 6.55 0.00 42.21 1.28
2992 3609 8.285394 GCACACACATTCCTTATTATACTGATG 58.715 37.037 0.00 0.00 0.00 3.07
2999 3616 9.449719 CATTCCTTATTATACTGATGTTACCCC 57.550 37.037 0.00 0.00 0.00 4.95
3000 3617 8.570038 TTCCTTATTATACTGATGTTACCCCA 57.430 34.615 0.00 0.00 0.00 4.96
3020 3637 3.170810 TTTTTGCGCCCGTCGTGAC 62.171 57.895 4.18 0.00 41.07 3.67
3026 3643 3.376078 GCCCGTCGTGACCCACTA 61.376 66.667 0.00 0.00 31.34 2.74
3027 3644 2.718073 GCCCGTCGTGACCCACTAT 61.718 63.158 0.00 0.00 31.34 2.12
3046 3663 4.952335 ACTATTTTTGCCTCCCTCTTGATG 59.048 41.667 0.00 0.00 0.00 3.07
3053 3670 2.402564 CCTCCCTCTTGATGGAGCTAA 58.597 52.381 14.04 0.00 45.64 3.09
3065 3682 5.536260 TGATGGAGCTAAAGATGATCGAAG 58.464 41.667 0.00 0.00 0.00 3.79
3098 3715 4.077300 TGAGTCAATCATGAGGTATGCC 57.923 45.455 0.09 0.00 35.88 4.40
3110 3732 4.277476 TGAGGTATGCCCAAACATTTAGG 58.723 43.478 0.00 0.00 34.66 2.69
3203 3825 4.569719 GGGGGTGTTAAGAAGATCTTCA 57.430 45.455 31.79 13.89 41.84 3.02
3204 3826 4.918588 GGGGGTGTTAAGAAGATCTTCAA 58.081 43.478 31.79 18.51 41.84 2.69
3205 3827 5.510430 GGGGGTGTTAAGAAGATCTTCAAT 58.490 41.667 31.79 23.19 41.84 2.57
3206 3828 5.358160 GGGGGTGTTAAGAAGATCTTCAATG 59.642 44.000 31.79 0.00 41.84 2.82
3207 3829 5.946377 GGGGTGTTAAGAAGATCTTCAATGT 59.054 40.000 31.79 18.32 41.84 2.71
3208 3830 6.434340 GGGGTGTTAAGAAGATCTTCAATGTT 59.566 38.462 31.79 21.05 41.84 2.71
3209 3831 7.308435 GGGTGTTAAGAAGATCTTCAATGTTG 58.692 38.462 31.79 0.00 41.84 3.33
3210 3832 7.174946 GGGTGTTAAGAAGATCTTCAATGTTGA 59.825 37.037 31.79 14.76 41.84 3.18
3211 3833 8.017946 GGTGTTAAGAAGATCTTCAATGTTGAC 58.982 37.037 31.79 23.25 41.84 3.18
3212 3834 7.742089 GTGTTAAGAAGATCTTCAATGTTGACG 59.258 37.037 31.79 0.00 41.84 4.35
3213 3835 4.935885 AGAAGATCTTCAATGTTGACGC 57.064 40.909 31.79 6.29 41.84 5.19
3214 3836 4.573900 AGAAGATCTTCAATGTTGACGCT 58.426 39.130 31.79 8.62 41.84 5.07
3215 3837 4.999950 AGAAGATCTTCAATGTTGACGCTT 59.000 37.500 31.79 8.44 41.84 4.68
3216 3838 4.675190 AGATCTTCAATGTTGACGCTTG 57.325 40.909 0.00 0.00 36.83 4.01
3217 3839 4.318332 AGATCTTCAATGTTGACGCTTGA 58.682 39.130 0.00 0.00 36.83 3.02
3218 3840 3.878086 TCTTCAATGTTGACGCTTGAC 57.122 42.857 0.00 0.00 36.83 3.18
3219 3841 3.202097 TCTTCAATGTTGACGCTTGACA 58.798 40.909 0.00 0.00 36.83 3.58
3220 3842 3.814842 TCTTCAATGTTGACGCTTGACAT 59.185 39.130 0.00 0.00 36.83 3.06
3221 3843 4.994217 TCTTCAATGTTGACGCTTGACATA 59.006 37.500 0.00 0.00 36.83 2.29
3222 3844 4.926860 TCAATGTTGACGCTTGACATAG 57.073 40.909 0.00 0.00 33.88 2.23
3223 3845 4.314961 TCAATGTTGACGCTTGACATAGT 58.685 39.130 0.00 0.00 33.88 2.12
3224 3846 4.152223 TCAATGTTGACGCTTGACATAGTG 59.848 41.667 0.00 0.00 33.88 2.74
3225 3847 2.412870 TGTTGACGCTTGACATAGTGG 58.587 47.619 0.00 0.00 0.00 4.00
3226 3848 2.036604 TGTTGACGCTTGACATAGTGGA 59.963 45.455 0.00 0.00 0.00 4.02
3227 3849 3.262420 GTTGACGCTTGACATAGTGGAT 58.738 45.455 0.00 0.00 0.00 3.41
3228 3850 3.610040 TGACGCTTGACATAGTGGATT 57.390 42.857 0.00 0.00 0.00 3.01
3229 3851 3.937814 TGACGCTTGACATAGTGGATTT 58.062 40.909 0.00 0.00 0.00 2.17
3230 3852 4.323417 TGACGCTTGACATAGTGGATTTT 58.677 39.130 0.00 0.00 0.00 1.82
3231 3853 4.154015 TGACGCTTGACATAGTGGATTTTG 59.846 41.667 0.00 0.00 0.00 2.44
3232 3854 4.323417 ACGCTTGACATAGTGGATTTTGA 58.677 39.130 0.00 0.00 0.00 2.69
3233 3855 4.759693 ACGCTTGACATAGTGGATTTTGAA 59.240 37.500 0.00 0.00 0.00 2.69
3234 3856 5.106555 ACGCTTGACATAGTGGATTTTGAAG 60.107 40.000 0.00 0.00 0.00 3.02
3235 3857 5.106555 CGCTTGACATAGTGGATTTTGAAGT 60.107 40.000 0.00 0.00 0.00 3.01
3236 3858 6.568462 CGCTTGACATAGTGGATTTTGAAGTT 60.568 38.462 0.00 0.00 0.00 2.66
3237 3859 6.803807 GCTTGACATAGTGGATTTTGAAGTTC 59.196 38.462 0.00 0.00 0.00 3.01
3238 3860 7.308830 GCTTGACATAGTGGATTTTGAAGTTCT 60.309 37.037 4.17 0.00 0.00 3.01
3239 3861 8.463930 TTGACATAGTGGATTTTGAAGTTCTT 57.536 30.769 4.17 0.00 0.00 2.52
3240 3862 7.874940 TGACATAGTGGATTTTGAAGTTCTTG 58.125 34.615 4.17 0.00 0.00 3.02
3241 3863 6.681777 ACATAGTGGATTTTGAAGTTCTTGC 58.318 36.000 4.17 0.00 0.00 4.01
3242 3864 6.491403 ACATAGTGGATTTTGAAGTTCTTGCT 59.509 34.615 4.17 0.00 0.00 3.91
3243 3865 7.665559 ACATAGTGGATTTTGAAGTTCTTGCTA 59.334 33.333 4.17 0.00 0.00 3.49
3244 3866 6.959639 AGTGGATTTTGAAGTTCTTGCTAA 57.040 33.333 4.17 0.00 0.00 3.09
3245 3867 7.346751 AGTGGATTTTGAAGTTCTTGCTAAA 57.653 32.000 4.17 0.00 0.00 1.85
3246 3868 7.203218 AGTGGATTTTGAAGTTCTTGCTAAAC 58.797 34.615 4.17 0.00 0.00 2.01
3247 3869 6.978080 GTGGATTTTGAAGTTCTTGCTAAACA 59.022 34.615 4.17 0.00 0.00 2.83
3248 3870 7.491048 GTGGATTTTGAAGTTCTTGCTAAACAA 59.509 33.333 4.17 0.00 36.62 2.83
3249 3871 8.203485 TGGATTTTGAAGTTCTTGCTAAACAAT 58.797 29.630 4.17 0.00 37.72 2.71
3250 3872 8.490355 GGATTTTGAAGTTCTTGCTAAACAATG 58.510 33.333 4.17 0.00 37.72 2.82
3251 3873 7.769272 TTTTGAAGTTCTTGCTAAACAATGG 57.231 32.000 4.17 0.00 37.72 3.16
3252 3874 4.870363 TGAAGTTCTTGCTAAACAATGGC 58.130 39.130 4.17 0.00 37.72 4.40
3253 3875 4.340666 TGAAGTTCTTGCTAAACAATGGCA 59.659 37.500 4.17 0.00 37.72 4.92
3254 3876 5.010922 TGAAGTTCTTGCTAAACAATGGCAT 59.989 36.000 4.17 0.00 37.72 4.40
3255 3877 5.473066 AGTTCTTGCTAAACAATGGCATT 57.527 34.783 6.96 6.96 37.72 3.56
3256 3878 5.857268 AGTTCTTGCTAAACAATGGCATTT 58.143 33.333 10.65 0.00 37.72 2.32
3257 3879 6.290605 AGTTCTTGCTAAACAATGGCATTTT 58.709 32.000 10.65 6.18 37.72 1.82
3258 3880 6.767423 AGTTCTTGCTAAACAATGGCATTTTT 59.233 30.769 10.65 15.48 37.72 1.94
3286 3908 8.839310 AGATAGCTGCATATACCTTTAACAAG 57.161 34.615 1.02 0.00 0.00 3.16
3287 3909 8.651389 AGATAGCTGCATATACCTTTAACAAGA 58.349 33.333 1.02 0.00 30.57 3.02
3290 3912 6.763610 AGCTGCATATACCTTTAACAAGAGTC 59.236 38.462 1.02 0.00 30.57 3.36
3309 3931 8.935844 CAAGAGTCTGTTACAAATATAGCACAA 58.064 33.333 0.00 0.00 0.00 3.33
3312 3934 7.739295 AGTCTGTTACAAATATAGCACAAACG 58.261 34.615 0.00 0.00 0.00 3.60
3318 3940 5.153513 ACAAATATAGCACAAACGCAACAG 58.846 37.500 0.00 0.00 0.00 3.16
3319 3941 5.153513 CAAATATAGCACAAACGCAACAGT 58.846 37.500 0.00 0.00 0.00 3.55
3323 3945 1.193665 GCACAAACGCAACAGTGTCG 61.194 55.000 0.00 0.00 34.59 4.35
3353 3975 5.456619 CCACAAGAGATAATAGGCATCCCAA 60.457 44.000 0.00 0.00 0.00 4.12
3358 3980 5.132648 AGAGATAATAGGCATCCCAACACAA 59.867 40.000 0.00 0.00 0.00 3.33
3375 3997 1.069978 ACAAATGCAAAAAGACCCCCG 59.930 47.619 0.00 0.00 0.00 5.73
3388 4010 4.114015 AGACCCCCGAAGAAAAAGAAAT 57.886 40.909 0.00 0.00 0.00 2.17
3389 4011 4.079970 AGACCCCCGAAGAAAAAGAAATC 58.920 43.478 0.00 0.00 0.00 2.17
3390 4012 3.824443 GACCCCCGAAGAAAAAGAAATCA 59.176 43.478 0.00 0.00 0.00 2.57
3391 4013 4.416516 ACCCCCGAAGAAAAAGAAATCAT 58.583 39.130 0.00 0.00 0.00 2.45
3392 4014 4.220602 ACCCCCGAAGAAAAAGAAATCATG 59.779 41.667 0.00 0.00 0.00 3.07
3393 4015 4.176271 CCCCGAAGAAAAAGAAATCATGC 58.824 43.478 0.00 0.00 0.00 4.06
3394 4016 4.321899 CCCCGAAGAAAAAGAAATCATGCA 60.322 41.667 0.00 0.00 0.00 3.96
3395 4017 4.622740 CCCGAAGAAAAAGAAATCATGCAC 59.377 41.667 0.00 0.00 0.00 4.57
3396 4018 5.221880 CCGAAGAAAAAGAAATCATGCACA 58.778 37.500 0.00 0.00 0.00 4.57
3397 4019 5.344128 CCGAAGAAAAAGAAATCATGCACAG 59.656 40.000 0.00 0.00 0.00 3.66
3398 4020 6.144854 CGAAGAAAAAGAAATCATGCACAGA 58.855 36.000 0.00 0.00 0.00 3.41
3399 4021 6.087291 CGAAGAAAAAGAAATCATGCACAGAC 59.913 38.462 0.00 0.00 0.00 3.51
3400 4022 6.395426 AGAAAAAGAAATCATGCACAGACA 57.605 33.333 0.00 0.00 0.00 3.41
3401 4023 6.808829 AGAAAAAGAAATCATGCACAGACAA 58.191 32.000 0.00 0.00 0.00 3.18
3402 4024 6.698766 AGAAAAAGAAATCATGCACAGACAAC 59.301 34.615 0.00 0.00 0.00 3.32
3403 4025 5.518848 AAAGAAATCATGCACAGACAACA 57.481 34.783 0.00 0.00 0.00 3.33
3404 4026 4.761235 AGAAATCATGCACAGACAACAG 57.239 40.909 0.00 0.00 0.00 3.16
3405 4027 4.392047 AGAAATCATGCACAGACAACAGA 58.608 39.130 0.00 0.00 0.00 3.41
3406 4028 4.214971 AGAAATCATGCACAGACAACAGAC 59.785 41.667 0.00 0.00 0.00 3.51
3407 4029 2.618442 TCATGCACAGACAACAGACA 57.382 45.000 0.00 0.00 0.00 3.41
3408 4030 3.130280 TCATGCACAGACAACAGACAT 57.870 42.857 0.00 0.00 0.00 3.06
3409 4031 2.809696 TCATGCACAGACAACAGACATG 59.190 45.455 0.00 0.00 35.81 3.21
3410 4032 1.596603 TGCACAGACAACAGACATGG 58.403 50.000 0.00 0.00 0.00 3.66
3411 4033 1.140652 TGCACAGACAACAGACATGGA 59.859 47.619 0.00 0.00 0.00 3.41
3412 4034 2.224597 TGCACAGACAACAGACATGGAT 60.225 45.455 0.00 0.00 0.00 3.41
3413 4035 2.816087 GCACAGACAACAGACATGGATT 59.184 45.455 0.00 0.00 0.00 3.01
3414 4036 3.120060 GCACAGACAACAGACATGGATTC 60.120 47.826 0.00 0.00 0.00 2.52
3415 4037 4.067192 CACAGACAACAGACATGGATTCA 58.933 43.478 0.00 0.00 0.00 2.57
3416 4038 4.516321 CACAGACAACAGACATGGATTCAA 59.484 41.667 0.00 0.00 0.00 2.69
3417 4039 5.008911 CACAGACAACAGACATGGATTCAAA 59.991 40.000 0.00 0.00 0.00 2.69
3418 4040 5.771666 ACAGACAACAGACATGGATTCAAAT 59.228 36.000 0.00 0.00 0.00 2.32
3419 4041 6.090783 CAGACAACAGACATGGATTCAAATG 58.909 40.000 0.00 0.00 0.00 2.32
3420 4042 6.005823 AGACAACAGACATGGATTCAAATGA 58.994 36.000 0.00 0.00 0.00 2.57
3421 4043 6.491062 AGACAACAGACATGGATTCAAATGAA 59.509 34.615 0.00 0.00 38.56 2.57
3422 4044 7.014518 AGACAACAGACATGGATTCAAATGAAA 59.985 33.333 0.00 0.00 37.61 2.69
3423 4045 7.499292 ACAACAGACATGGATTCAAATGAAAA 58.501 30.769 0.00 0.00 37.61 2.29
3424 4046 7.439056 ACAACAGACATGGATTCAAATGAAAAC 59.561 33.333 0.00 0.00 37.61 2.43
3425 4047 7.294017 ACAGACATGGATTCAAATGAAAACT 57.706 32.000 0.00 0.00 37.61 2.66
3426 4048 7.373493 ACAGACATGGATTCAAATGAAAACTC 58.627 34.615 0.00 0.00 37.61 3.01
3427 4049 7.014518 ACAGACATGGATTCAAATGAAAACTCA 59.985 33.333 0.00 0.00 37.61 3.41
3428 4050 7.868922 CAGACATGGATTCAAATGAAAACTCAA 59.131 33.333 0.00 0.00 37.61 3.02
3429 4051 8.086522 AGACATGGATTCAAATGAAAACTCAAG 58.913 33.333 0.00 0.00 37.61 3.02
3430 4052 7.954835 ACATGGATTCAAATGAAAACTCAAGA 58.045 30.769 0.00 0.00 37.61 3.02
3431 4053 8.086522 ACATGGATTCAAATGAAAACTCAAGAG 58.913 33.333 0.00 0.00 37.61 2.85
3432 4054 6.985117 TGGATTCAAATGAAAACTCAAGAGG 58.015 36.000 0.00 0.00 37.61 3.69
3433 4055 6.777091 TGGATTCAAATGAAAACTCAAGAGGA 59.223 34.615 0.00 0.00 37.61 3.71
3434 4056 7.040201 TGGATTCAAATGAAAACTCAAGAGGAG 60.040 37.037 0.00 0.00 42.47 3.69
3435 4057 7.224522 ATTCAAATGAAAACTCAAGAGGAGG 57.775 36.000 0.00 0.00 41.74 4.30
3436 4058 6.294955 ATTCAAATGAAAACTCAAGAGGAGGC 60.295 38.462 0.00 0.00 41.74 4.70
3437 4059 8.613826 ATTCAAATGAAAACTCAAGAGGAGGCA 61.614 37.037 0.00 0.00 41.74 4.75
3478 4100 2.593725 CGACTCGGGCGGGATCTA 60.594 66.667 0.00 0.00 0.00 1.98
3479 4101 2.191513 CGACTCGGGCGGGATCTAA 61.192 63.158 0.00 0.00 0.00 2.10
3480 4102 1.731433 CGACTCGGGCGGGATCTAAA 61.731 60.000 0.00 0.00 0.00 1.85
3481 4103 0.462789 GACTCGGGCGGGATCTAAAA 59.537 55.000 0.00 0.00 0.00 1.52
3482 4104 0.177373 ACTCGGGCGGGATCTAAAAC 59.823 55.000 0.00 0.00 0.00 2.43
3483 4105 0.532196 CTCGGGCGGGATCTAAAACC 60.532 60.000 0.00 0.00 0.00 3.27
3484 4106 1.525306 CGGGCGGGATCTAAAACCC 60.525 63.158 0.00 0.00 42.43 4.11
3485 4107 1.920532 GGGCGGGATCTAAAACCCT 59.079 57.895 0.00 0.00 43.57 4.34
3486 4108 1.134228 GGGCGGGATCTAAAACCCTA 58.866 55.000 0.00 0.00 43.57 3.53
3487 4109 1.071857 GGGCGGGATCTAAAACCCTAG 59.928 57.143 0.00 0.00 43.57 3.02
3488 4110 1.542767 GGCGGGATCTAAAACCCTAGC 60.543 57.143 0.00 0.00 43.57 3.42
3489 4111 1.542767 GCGGGATCTAAAACCCTAGCC 60.543 57.143 0.00 0.00 43.57 3.93
3490 4112 1.270147 CGGGATCTAAAACCCTAGCCG 60.270 57.143 0.00 0.00 43.57 5.52
3491 4113 1.542767 GGGATCTAAAACCCTAGCCGC 60.543 57.143 0.00 0.00 42.56 6.53
3492 4114 1.542767 GGATCTAAAACCCTAGCCGCC 60.543 57.143 0.00 0.00 0.00 6.13
3493 4115 0.106149 ATCTAAAACCCTAGCCGCCG 59.894 55.000 0.00 0.00 0.00 6.46
3494 4116 1.523032 CTAAAACCCTAGCCGCCGG 60.523 63.158 0.00 0.00 0.00 6.13
3495 4117 2.935627 CTAAAACCCTAGCCGCCGGG 62.936 65.000 4.77 12.66 46.26 5.73
3511 4133 4.817909 GGGGTCCCCATCCGTCCT 62.818 72.222 23.53 0.00 44.65 3.85
3512 4134 3.162154 GGGTCCCCATCCGTCCTC 61.162 72.222 0.00 0.00 35.81 3.71
3513 4135 3.162154 GGTCCCCATCCGTCCTCC 61.162 72.222 0.00 0.00 0.00 4.30
3514 4136 3.162154 GTCCCCATCCGTCCTCCC 61.162 72.222 0.00 0.00 0.00 4.30
3515 4137 4.492303 TCCCCATCCGTCCTCCCC 62.492 72.222 0.00 0.00 0.00 4.81
3516 4138 4.499116 CCCCATCCGTCCTCCCCT 62.499 72.222 0.00 0.00 0.00 4.79
3517 4139 2.844839 CCCATCCGTCCTCCCCTC 60.845 72.222 0.00 0.00 0.00 4.30
3518 4140 2.844839 CCATCCGTCCTCCCCTCC 60.845 72.222 0.00 0.00 0.00 4.30
3519 4141 2.844839 CATCCGTCCTCCCCTCCC 60.845 72.222 0.00 0.00 0.00 4.30
3520 4142 3.036959 ATCCGTCCTCCCCTCCCT 61.037 66.667 0.00 0.00 0.00 4.20
3521 4143 3.089419 ATCCGTCCTCCCCTCCCTC 62.089 68.421 0.00 0.00 0.00 4.30
3522 4144 3.756783 CCGTCCTCCCCTCCCTCT 61.757 72.222 0.00 0.00 0.00 3.69
3523 4145 2.443016 CGTCCTCCCCTCCCTCTG 60.443 72.222 0.00 0.00 0.00 3.35
3524 4146 2.766229 GTCCTCCCCTCCCTCTGC 60.766 72.222 0.00 0.00 0.00 4.26
3525 4147 4.095400 TCCTCCCCTCCCTCTGCC 62.095 72.222 0.00 0.00 0.00 4.85
3526 4148 4.421554 CCTCCCCTCCCTCTGCCA 62.422 72.222 0.00 0.00 0.00 4.92
3527 4149 3.086600 CTCCCCTCCCTCTGCCAC 61.087 72.222 0.00 0.00 0.00 5.01
3528 4150 4.741239 TCCCCTCCCTCTGCCACC 62.741 72.222 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.587891 TGTGAGAATATGATGTTGTGGCA 58.412 39.130 0.00 0.00 0.00 4.92
9 10 4.877823 TCTGTGAGAATATGATGTTGTGGC 59.122 41.667 0.00 0.00 0.00 5.01
30 31 1.842562 AGCATGGTAGACTGGCAATCT 59.157 47.619 3.16 3.16 0.00 2.40
36 37 1.831106 TGTGGTAGCATGGTAGACTGG 59.169 52.381 4.51 0.00 0.00 4.00
40 41 2.620251 GCATGTGGTAGCATGGTAGA 57.380 50.000 4.51 0.00 44.58 2.59
85 86 8.753497 TCTAAGCATTCTAACTAGATCTGTGA 57.247 34.615 5.18 0.00 31.40 3.58
103 104 1.641192 TCACTCCCTCCTCTCTAAGCA 59.359 52.381 0.00 0.00 0.00 3.91
105 106 3.146066 CGATCACTCCCTCCTCTCTAAG 58.854 54.545 0.00 0.00 0.00 2.18
106 107 2.778270 TCGATCACTCCCTCCTCTCTAA 59.222 50.000 0.00 0.00 0.00 2.10
148 149 3.702048 TTCCACGCCTCCTTCCGG 61.702 66.667 0.00 0.00 0.00 5.14
149 150 2.434359 GTTCCACGCCTCCTTCCG 60.434 66.667 0.00 0.00 0.00 4.30
150 151 1.376037 CTGTTCCACGCCTCCTTCC 60.376 63.158 0.00 0.00 0.00 3.46
151 152 1.376037 CCTGTTCCACGCCTCCTTC 60.376 63.158 0.00 0.00 0.00 3.46
152 153 1.841556 TCCTGTTCCACGCCTCCTT 60.842 57.895 0.00 0.00 0.00 3.36
153 154 2.203788 TCCTGTTCCACGCCTCCT 60.204 61.111 0.00 0.00 0.00 3.69
154 155 2.047179 GTCCTGTTCCACGCCTCC 60.047 66.667 0.00 0.00 0.00 4.30
155 156 2.432628 CGTCCTGTTCCACGCCTC 60.433 66.667 0.00 0.00 0.00 4.70
156 157 4.003788 CCGTCCTGTTCCACGCCT 62.004 66.667 0.00 0.00 34.58 5.52
157 158 3.934391 CTCCGTCCTGTTCCACGCC 62.934 68.421 0.00 0.00 34.58 5.68
158 159 2.430382 TTCTCCGTCCTGTTCCACGC 62.430 60.000 0.00 0.00 34.58 5.34
159 160 0.388649 CTTCTCCGTCCTGTTCCACG 60.389 60.000 0.00 0.00 35.72 4.94
160 161 0.966920 TCTTCTCCGTCCTGTTCCAC 59.033 55.000 0.00 0.00 0.00 4.02
166 167 2.202492 CGCGTCTTCTCCGTCCTG 60.202 66.667 0.00 0.00 0.00 3.86
220 221 2.592993 CCCCCTTTCGAGCTCACCA 61.593 63.158 15.40 0.00 0.00 4.17
291 293 1.601419 GGTCACCTCCCGTCGAATCA 61.601 60.000 0.00 0.00 0.00 2.57
307 309 0.539986 TAGCAGGACGAATTGGGGTC 59.460 55.000 0.00 0.00 0.00 4.46
325 327 5.575606 CCTCGTGCGAGTCTCTAAAAATTTA 59.424 40.000 18.51 0.00 40.44 1.40
380 382 2.043953 GGGAAGGAAAGGCGGCAT 60.044 61.111 13.08 0.00 0.00 4.40
390 392 2.688666 AGCGATGCAGGGGAAGGA 60.689 61.111 0.00 0.00 0.00 3.36
439 441 1.447643 CTAGACCCGCCAGGAATGG 59.552 63.158 0.00 0.00 41.02 3.16
441 443 1.383248 AGCTAGACCCGCCAGGAAT 60.383 57.895 0.00 0.00 41.02 3.01
445 447 3.854669 CCCAGCTAGACCCGCCAG 61.855 72.222 0.00 0.00 0.00 4.85
448 450 3.541713 CCTCCCAGCTAGACCCGC 61.542 72.222 0.00 0.00 0.00 6.13
449 451 2.042843 ACCTCCCAGCTAGACCCG 60.043 66.667 0.00 0.00 0.00 5.28
450 452 0.910088 AACACCTCCCAGCTAGACCC 60.910 60.000 0.00 0.00 0.00 4.46
451 453 0.984995 AAACACCTCCCAGCTAGACC 59.015 55.000 0.00 0.00 0.00 3.85
452 454 2.861147 AAAACACCTCCCAGCTAGAC 57.139 50.000 0.00 0.00 0.00 2.59
453 455 3.263425 CCTTAAAACACCTCCCAGCTAGA 59.737 47.826 0.00 0.00 0.00 2.43
454 456 3.009143 ACCTTAAAACACCTCCCAGCTAG 59.991 47.826 0.00 0.00 0.00 3.42
455 457 2.983898 ACCTTAAAACACCTCCCAGCTA 59.016 45.455 0.00 0.00 0.00 3.32
456 458 1.780919 ACCTTAAAACACCTCCCAGCT 59.219 47.619 0.00 0.00 0.00 4.24
457 459 2.287977 ACCTTAAAACACCTCCCAGC 57.712 50.000 0.00 0.00 0.00 4.85
539 541 1.304282 CATACAGCCCAACCAGCCT 59.696 57.895 0.00 0.00 0.00 4.58
561 563 3.242936 ACATTAGTGACGTGTTTGGTTGC 60.243 43.478 0.00 0.00 0.00 4.17
948 952 2.154462 ACCTCGCTATATTTGCATGGC 58.846 47.619 0.00 0.00 0.00 4.40
1066 1125 2.358247 CACGGAAGGGACAACGGG 60.358 66.667 0.00 0.00 35.60 5.28
1071 1130 2.747686 GAAGCCACGGAAGGGACA 59.252 61.111 0.00 0.00 35.60 4.02
1320 1379 3.066190 CCCTCGTAGTCGTGCCCA 61.066 66.667 0.00 0.00 38.33 5.36
1377 1436 3.934391 GAGGTTGGCCAGGTCGACG 62.934 68.421 5.11 0.00 37.19 5.12
1993 2536 2.047179 GAAGGGCACGGACTGGAC 60.047 66.667 0.00 0.00 0.00 4.02
2009 2552 1.692749 GTGGGGCCCAGGTAGATGA 60.693 63.158 29.66 0.00 32.34 2.92
2366 2924 0.795735 CCTGTAGTTCACGTACGCCG 60.796 60.000 16.72 7.10 44.03 6.46
2430 2988 1.906105 AAATCCTGCCGGCCTCGTAA 61.906 55.000 26.77 2.02 33.95 3.18
2503 3064 1.381928 TAGTCGTCAGGATCCGCCAC 61.382 60.000 5.98 3.41 40.02 5.01
2555 3116 1.658686 GCATCGTCCTCGTCACTCCT 61.659 60.000 0.00 0.00 38.33 3.69
2556 3117 1.226717 GCATCGTCCTCGTCACTCC 60.227 63.158 0.00 0.00 38.33 3.85
2608 3169 5.396101 CCATCTCAACTCCAAGATCAAGCTA 60.396 44.000 0.00 0.00 29.77 3.32
2616 3180 1.280133 CCTGCCATCTCAACTCCAAGA 59.720 52.381 0.00 0.00 0.00 3.02
2651 3215 6.299922 TGGAACTATACATTGAACACCAACA 58.700 36.000 0.00 0.00 37.63 3.33
2740 3338 3.509967 CCCAACATACCAGGGAAAGTTTC 59.490 47.826 7.09 7.09 45.80 2.78
2744 3342 1.357761 ACCCCAACATACCAGGGAAAG 59.642 52.381 0.00 0.00 45.80 2.62
2847 3451 1.521580 TGATGAACACTTGCATGCGA 58.478 45.000 14.09 10.84 0.00 5.10
2936 3540 8.816894 ACTCTGTTGTCCTCTCTTAATTAATGA 58.183 33.333 0.00 0.31 0.00 2.57
2957 3561 2.287788 GGAATGTGTGTGCCAAACTCTG 60.288 50.000 0.00 0.00 0.00 3.35
2977 3581 9.807921 AAATGGGGTAACATCAGTATAATAAGG 57.192 33.333 0.00 0.00 39.74 2.69
3014 3631 2.156098 GGCAAAAATAGTGGGTCACGA 58.844 47.619 0.00 0.00 39.64 4.35
3020 3637 2.024941 AGAGGGAGGCAAAAATAGTGGG 60.025 50.000 0.00 0.00 0.00 4.61
3024 3641 4.340381 CCATCAAGAGGGAGGCAAAAATAG 59.660 45.833 0.00 0.00 33.27 1.73
3026 3643 3.102204 CCATCAAGAGGGAGGCAAAAAT 58.898 45.455 0.00 0.00 33.27 1.82
3027 3644 2.109834 TCCATCAAGAGGGAGGCAAAAA 59.890 45.455 0.00 0.00 36.20 1.94
3046 3663 3.070302 ACCCTTCGATCATCTTTAGCTCC 59.930 47.826 0.00 0.00 0.00 4.70
3053 3670 8.597167 TCAAATATATCACCCTTCGATCATCTT 58.403 33.333 0.00 0.00 0.00 2.40
3065 3682 8.853077 TCATGATTGACTCAAATATATCACCC 57.147 34.615 0.00 0.00 37.44 4.61
3094 3711 2.566724 CACACCCTAAATGTTTGGGCAT 59.433 45.455 7.33 0.00 44.56 4.40
3096 3713 1.967779 ACACACCCTAAATGTTTGGGC 59.032 47.619 7.33 0.00 44.56 5.36
3098 3715 4.927978 TGAACACACCCTAAATGTTTGG 57.072 40.909 0.00 0.00 36.70 3.28
3110 3732 3.188460 ACTGATAACGCAATGAACACACC 59.812 43.478 0.00 0.00 0.00 4.16
3149 3771 7.818930 CCAAACCAATCTAGTTACAATGCATTT 59.181 33.333 9.83 4.36 0.00 2.32
3161 3783 1.923148 CCCCCTCCAAACCAATCTAGT 59.077 52.381 0.00 0.00 0.00 2.57
3183 3805 5.946377 ACATTGAAGATCTTCTTAACACCCC 59.054 40.000 30.45 6.75 36.73 4.95
3184 3806 7.174946 TCAACATTGAAGATCTTCTTAACACCC 59.825 37.037 30.45 7.42 36.73 4.61
3185 3807 8.017946 GTCAACATTGAAGATCTTCTTAACACC 58.982 37.037 30.45 12.63 36.73 4.16
3186 3808 7.742089 CGTCAACATTGAAGATCTTCTTAACAC 59.258 37.037 30.45 18.34 36.73 3.32
3187 3809 7.571244 GCGTCAACATTGAAGATCTTCTTAACA 60.571 37.037 30.45 12.50 36.73 2.41
3188 3810 6.738649 GCGTCAACATTGAAGATCTTCTTAAC 59.261 38.462 30.45 15.15 36.73 2.01
3189 3811 6.650807 AGCGTCAACATTGAAGATCTTCTTAA 59.349 34.615 30.45 20.23 36.73 1.85
3190 3812 6.166279 AGCGTCAACATTGAAGATCTTCTTA 58.834 36.000 30.45 20.71 36.73 2.10
3191 3813 4.999950 AGCGTCAACATTGAAGATCTTCTT 59.000 37.500 30.45 16.97 39.87 2.52
3192 3814 4.573900 AGCGTCAACATTGAAGATCTTCT 58.426 39.130 30.45 13.29 38.67 2.85
3193 3815 4.935885 AGCGTCAACATTGAAGATCTTC 57.064 40.909 25.68 25.68 38.67 2.87
3194 3816 4.756642 TCAAGCGTCAACATTGAAGATCTT 59.243 37.500 7.95 7.95 38.67 2.40
3195 3817 4.153117 GTCAAGCGTCAACATTGAAGATCT 59.847 41.667 11.12 0.00 38.67 2.75
3196 3818 4.083855 TGTCAAGCGTCAACATTGAAGATC 60.084 41.667 11.12 0.00 38.67 2.75
3197 3819 3.814842 TGTCAAGCGTCAACATTGAAGAT 59.185 39.130 11.12 2.31 38.67 2.40
3198 3820 3.202097 TGTCAAGCGTCAACATTGAAGA 58.798 40.909 11.12 0.00 38.67 2.87
3199 3821 3.607422 TGTCAAGCGTCAACATTGAAG 57.393 42.857 3.50 3.50 39.21 3.02
3200 3822 4.754618 ACTATGTCAAGCGTCAACATTGAA 59.245 37.500 10.97 0.00 39.21 2.69
3201 3823 4.152223 CACTATGTCAAGCGTCAACATTGA 59.848 41.667 10.97 0.00 35.38 2.57
3202 3824 4.397382 CACTATGTCAAGCGTCAACATTG 58.603 43.478 3.14 4.29 35.38 2.82
3203 3825 3.436704 CCACTATGTCAAGCGTCAACATT 59.563 43.478 3.14 0.00 35.38 2.71
3204 3826 3.002791 CCACTATGTCAAGCGTCAACAT 58.997 45.455 3.32 3.32 37.40 2.71
3205 3827 2.036604 TCCACTATGTCAAGCGTCAACA 59.963 45.455 0.00 0.00 0.00 3.33
3206 3828 2.683968 TCCACTATGTCAAGCGTCAAC 58.316 47.619 0.00 0.00 0.00 3.18
3207 3829 3.610040 ATCCACTATGTCAAGCGTCAA 57.390 42.857 0.00 0.00 0.00 3.18
3208 3830 3.610040 AATCCACTATGTCAAGCGTCA 57.390 42.857 0.00 0.00 0.00 4.35
3209 3831 4.391830 TCAAAATCCACTATGTCAAGCGTC 59.608 41.667 0.00 0.00 0.00 5.19
3210 3832 4.323417 TCAAAATCCACTATGTCAAGCGT 58.677 39.130 0.00 0.00 0.00 5.07
3211 3833 4.944962 TCAAAATCCACTATGTCAAGCG 57.055 40.909 0.00 0.00 0.00 4.68
3212 3834 6.259550 ACTTCAAAATCCACTATGTCAAGC 57.740 37.500 0.00 0.00 0.00 4.01
3213 3835 8.103948 AGAACTTCAAAATCCACTATGTCAAG 57.896 34.615 0.00 0.00 0.00 3.02
3214 3836 8.352201 CAAGAACTTCAAAATCCACTATGTCAA 58.648 33.333 0.00 0.00 0.00 3.18
3215 3837 7.522073 GCAAGAACTTCAAAATCCACTATGTCA 60.522 37.037 0.00 0.00 0.00 3.58
3216 3838 6.803807 GCAAGAACTTCAAAATCCACTATGTC 59.196 38.462 0.00 0.00 0.00 3.06
3217 3839 6.491403 AGCAAGAACTTCAAAATCCACTATGT 59.509 34.615 0.00 0.00 0.00 2.29
3218 3840 6.917533 AGCAAGAACTTCAAAATCCACTATG 58.082 36.000 0.00 0.00 0.00 2.23
3219 3841 8.635765 TTAGCAAGAACTTCAAAATCCACTAT 57.364 30.769 0.00 0.00 0.00 2.12
3220 3842 8.349983 GTTTAGCAAGAACTTCAAAATCCACTA 58.650 33.333 0.00 0.00 0.00 2.74
3221 3843 6.959639 TTAGCAAGAACTTCAAAATCCACT 57.040 33.333 0.00 0.00 0.00 4.00
3222 3844 6.978080 TGTTTAGCAAGAACTTCAAAATCCAC 59.022 34.615 0.00 0.00 0.00 4.02
3223 3845 7.106439 TGTTTAGCAAGAACTTCAAAATCCA 57.894 32.000 0.00 0.00 0.00 3.41
3224 3846 8.490355 CATTGTTTAGCAAGAACTTCAAAATCC 58.510 33.333 0.00 0.00 40.86 3.01
3225 3847 8.490355 CCATTGTTTAGCAAGAACTTCAAAATC 58.510 33.333 0.00 0.00 40.86 2.17
3226 3848 7.041848 GCCATTGTTTAGCAAGAACTTCAAAAT 60.042 33.333 0.00 0.00 40.86 1.82
3227 3849 6.257630 GCCATTGTTTAGCAAGAACTTCAAAA 59.742 34.615 0.00 0.00 40.86 2.44
3228 3850 5.752955 GCCATTGTTTAGCAAGAACTTCAAA 59.247 36.000 0.00 0.00 40.86 2.69
3229 3851 5.163468 TGCCATTGTTTAGCAAGAACTTCAA 60.163 36.000 0.00 0.00 40.86 2.69
3230 3852 4.340666 TGCCATTGTTTAGCAAGAACTTCA 59.659 37.500 0.00 0.00 40.86 3.02
3231 3853 4.870363 TGCCATTGTTTAGCAAGAACTTC 58.130 39.130 0.00 0.00 40.86 3.01
3232 3854 4.935352 TGCCATTGTTTAGCAAGAACTT 57.065 36.364 0.00 0.00 40.86 2.66
3233 3855 5.473066 AATGCCATTGTTTAGCAAGAACT 57.527 34.783 0.00 0.00 40.86 3.01
3234 3856 6.544038 AAAATGCCATTGTTTAGCAAGAAC 57.456 33.333 0.00 0.00 40.86 3.01
3260 3882 9.277783 CTTGTTAAAGGTATATGCAGCTATCTT 57.722 33.333 0.00 0.00 0.00 2.40
3261 3883 8.651389 TCTTGTTAAAGGTATATGCAGCTATCT 58.349 33.333 0.00 0.00 33.90 1.98
3262 3884 8.833231 TCTTGTTAAAGGTATATGCAGCTATC 57.167 34.615 0.00 0.00 33.90 2.08
3263 3885 8.432805 ACTCTTGTTAAAGGTATATGCAGCTAT 58.567 33.333 0.00 0.00 33.90 2.97
3264 3886 7.792032 ACTCTTGTTAAAGGTATATGCAGCTA 58.208 34.615 0.00 0.00 33.90 3.32
3265 3887 6.653989 ACTCTTGTTAAAGGTATATGCAGCT 58.346 36.000 0.00 0.00 33.90 4.24
3266 3888 6.763610 AGACTCTTGTTAAAGGTATATGCAGC 59.236 38.462 0.00 0.00 33.90 5.25
3267 3889 7.766278 ACAGACTCTTGTTAAAGGTATATGCAG 59.234 37.037 0.00 0.00 33.90 4.41
3268 3890 7.620880 ACAGACTCTTGTTAAAGGTATATGCA 58.379 34.615 0.00 0.00 33.90 3.96
3269 3891 8.494016 AACAGACTCTTGTTAAAGGTATATGC 57.506 34.615 0.00 0.00 39.40 3.14
3273 3895 9.841295 TTTGTAACAGACTCTTGTTAAAGGTAT 57.159 29.630 0.64 0.00 43.11 2.73
3274 3896 9.841295 ATTTGTAACAGACTCTTGTTAAAGGTA 57.159 29.630 0.64 0.00 43.11 3.08
3275 3897 8.747538 ATTTGTAACAGACTCTTGTTAAAGGT 57.252 30.769 0.64 0.00 43.11 3.50
3281 3903 8.936864 GTGCTATATTTGTAACAGACTCTTGTT 58.063 33.333 0.00 0.00 43.34 2.83
3282 3904 8.094548 TGTGCTATATTTGTAACAGACTCTTGT 58.905 33.333 0.00 0.00 0.00 3.16
3283 3905 8.479313 TGTGCTATATTTGTAACAGACTCTTG 57.521 34.615 0.00 0.00 0.00 3.02
3284 3906 9.502091 TTTGTGCTATATTTGTAACAGACTCTT 57.498 29.630 0.00 0.00 0.00 2.85
3285 3907 8.936864 GTTTGTGCTATATTTGTAACAGACTCT 58.063 33.333 0.00 0.00 0.00 3.24
3286 3908 7.898309 CGTTTGTGCTATATTTGTAACAGACTC 59.102 37.037 0.00 0.00 0.00 3.36
3287 3909 7.623506 GCGTTTGTGCTATATTTGTAACAGACT 60.624 37.037 0.00 0.00 0.00 3.24
3290 3912 6.310960 TGCGTTTGTGCTATATTTGTAACAG 58.689 36.000 0.00 0.00 35.36 3.16
3309 3931 0.928229 GTTCTCGACACTGTTGCGTT 59.072 50.000 0.00 0.00 0.00 4.84
3312 3934 0.531974 TGGGTTCTCGACACTGTTGC 60.532 55.000 0.00 0.00 30.98 4.17
3318 3940 1.340248 TCTCTTGTGGGTTCTCGACAC 59.660 52.381 0.00 0.00 33.82 3.67
3319 3941 1.699730 TCTCTTGTGGGTTCTCGACA 58.300 50.000 0.00 0.00 32.20 4.35
3323 3945 5.163301 TGCCTATTATCTCTTGTGGGTTCTC 60.163 44.000 0.00 0.00 0.00 2.87
3353 3975 2.158827 GGGGGTCTTTTTGCATTTGTGT 60.159 45.455 0.00 0.00 0.00 3.72
3358 3980 1.618343 CTTCGGGGGTCTTTTTGCATT 59.382 47.619 0.00 0.00 0.00 3.56
3375 3997 6.919662 TGTCTGTGCATGATTTCTTTTTCTTC 59.080 34.615 0.00 0.00 0.00 2.87
3388 4010 2.618442 TGTCTGTTGTCTGTGCATGA 57.382 45.000 0.00 0.00 0.00 3.07
3389 4011 2.095415 CCATGTCTGTTGTCTGTGCATG 60.095 50.000 0.00 0.00 33.98 4.06
3390 4012 2.156917 CCATGTCTGTTGTCTGTGCAT 58.843 47.619 0.00 0.00 0.00 3.96
3391 4013 1.140652 TCCATGTCTGTTGTCTGTGCA 59.859 47.619 0.00 0.00 0.00 4.57
3392 4014 1.882912 TCCATGTCTGTTGTCTGTGC 58.117 50.000 0.00 0.00 0.00 4.57
3393 4015 4.067192 TGAATCCATGTCTGTTGTCTGTG 58.933 43.478 0.00 0.00 0.00 3.66
3394 4016 4.356405 TGAATCCATGTCTGTTGTCTGT 57.644 40.909 0.00 0.00 0.00 3.41
3395 4017 5.694231 TTTGAATCCATGTCTGTTGTCTG 57.306 39.130 0.00 0.00 0.00 3.51
3396 4018 6.005823 TCATTTGAATCCATGTCTGTTGTCT 58.994 36.000 0.00 0.00 0.00 3.41
3397 4019 6.258230 TCATTTGAATCCATGTCTGTTGTC 57.742 37.500 0.00 0.00 0.00 3.18
3398 4020 6.653526 TTCATTTGAATCCATGTCTGTTGT 57.346 33.333 0.00 0.00 0.00 3.32
3399 4021 7.654520 AGTTTTCATTTGAATCCATGTCTGTTG 59.345 33.333 0.00 0.00 33.54 3.33
3400 4022 7.729116 AGTTTTCATTTGAATCCATGTCTGTT 58.271 30.769 0.00 0.00 33.54 3.16
3401 4023 7.014518 TGAGTTTTCATTTGAATCCATGTCTGT 59.985 33.333 0.00 0.00 33.54 3.41
3402 4024 7.372714 TGAGTTTTCATTTGAATCCATGTCTG 58.627 34.615 0.00 0.00 33.54 3.51
3403 4025 7.528996 TGAGTTTTCATTTGAATCCATGTCT 57.471 32.000 0.00 0.00 33.54 3.41
3404 4026 8.084073 TCTTGAGTTTTCATTTGAATCCATGTC 58.916 33.333 0.00 0.00 33.54 3.06
3405 4027 7.954835 TCTTGAGTTTTCATTTGAATCCATGT 58.045 30.769 0.00 0.00 33.54 3.21
3406 4028 7.544566 CCTCTTGAGTTTTCATTTGAATCCATG 59.455 37.037 0.00 0.00 33.54 3.66
3407 4029 7.452501 TCCTCTTGAGTTTTCATTTGAATCCAT 59.547 33.333 0.00 0.00 33.54 3.41
3408 4030 6.777091 TCCTCTTGAGTTTTCATTTGAATCCA 59.223 34.615 0.00 0.00 33.54 3.41
3409 4031 7.219484 TCCTCTTGAGTTTTCATTTGAATCC 57.781 36.000 0.00 0.00 33.54 3.01
3410 4032 7.311408 CCTCCTCTTGAGTTTTCATTTGAATC 58.689 38.462 0.00 0.00 39.65 2.52
3411 4033 6.294955 GCCTCCTCTTGAGTTTTCATTTGAAT 60.295 38.462 0.00 0.00 39.65 2.57
3412 4034 5.010012 GCCTCCTCTTGAGTTTTCATTTGAA 59.990 40.000 0.00 0.00 39.65 2.69
3413 4035 4.520492 GCCTCCTCTTGAGTTTTCATTTGA 59.480 41.667 0.00 0.00 39.65 2.69
3414 4036 4.279169 TGCCTCCTCTTGAGTTTTCATTTG 59.721 41.667 0.00 0.00 39.65 2.32
3415 4037 4.473444 TGCCTCCTCTTGAGTTTTCATTT 58.527 39.130 0.00 0.00 39.65 2.32
3416 4038 4.104383 TGCCTCCTCTTGAGTTTTCATT 57.896 40.909 0.00 0.00 39.65 2.57
3417 4039 3.795688 TGCCTCCTCTTGAGTTTTCAT 57.204 42.857 0.00 0.00 39.65 2.57
3418 4040 3.560025 GGATGCCTCCTCTTGAGTTTTCA 60.560 47.826 0.00 0.00 39.65 2.69
3419 4041 3.013219 GGATGCCTCCTCTTGAGTTTTC 58.987 50.000 0.00 0.00 39.65 2.29
3420 4042 2.291217 GGGATGCCTCCTCTTGAGTTTT 60.291 50.000 8.03 0.00 41.74 2.43
3421 4043 1.283321 GGGATGCCTCCTCTTGAGTTT 59.717 52.381 8.03 0.00 41.74 2.66
3422 4044 0.915364 GGGATGCCTCCTCTTGAGTT 59.085 55.000 8.03 0.00 41.74 3.01
3423 4045 1.333636 CGGGATGCCTCCTCTTGAGT 61.334 60.000 8.03 0.00 41.74 3.41
3424 4046 1.445095 CGGGATGCCTCCTCTTGAG 59.555 63.158 8.03 0.00 41.74 3.02
3425 4047 2.735772 GCGGGATGCCTCCTCTTGA 61.736 63.158 8.03 0.00 41.74 3.02
3426 4048 2.203126 GCGGGATGCCTCCTCTTG 60.203 66.667 8.03 0.00 41.74 3.02
3427 4049 3.854669 CGCGGGATGCCTCCTCTT 61.855 66.667 8.03 0.00 41.74 2.85
3429 4051 4.593864 GACGCGGGATGCCTCCTC 62.594 72.222 12.47 0.00 41.74 3.71
3461 4083 1.731433 TTTAGATCCCGCCCGAGTCG 61.731 60.000 5.29 5.29 0.00 4.18
3462 4084 0.462789 TTTTAGATCCCGCCCGAGTC 59.537 55.000 0.00 0.00 0.00 3.36
3463 4085 0.177373 GTTTTAGATCCCGCCCGAGT 59.823 55.000 0.00 0.00 0.00 4.18
3464 4086 0.532196 GGTTTTAGATCCCGCCCGAG 60.532 60.000 0.00 0.00 0.00 4.63
3465 4087 1.523524 GGTTTTAGATCCCGCCCGA 59.476 57.895 0.00 0.00 0.00 5.14
3466 4088 1.525306 GGGTTTTAGATCCCGCCCG 60.525 63.158 0.00 0.00 33.97 6.13
3467 4089 4.573210 GGGTTTTAGATCCCGCCC 57.427 61.111 0.00 0.00 33.97 6.13
3471 4093 1.542767 GCGGCTAGGGTTTTAGATCCC 60.543 57.143 0.00 0.00 43.71 3.85
3472 4094 1.542767 GGCGGCTAGGGTTTTAGATCC 60.543 57.143 0.00 0.00 0.00 3.36
3473 4095 1.872653 CGGCGGCTAGGGTTTTAGATC 60.873 57.143 7.61 0.00 0.00 2.75
3474 4096 0.106149 CGGCGGCTAGGGTTTTAGAT 59.894 55.000 7.61 0.00 0.00 1.98
3475 4097 1.518774 CGGCGGCTAGGGTTTTAGA 59.481 57.895 7.61 0.00 0.00 2.10
3476 4098 1.523032 CCGGCGGCTAGGGTTTTAG 60.523 63.158 15.42 0.00 0.00 1.85
3477 4099 2.585698 CCGGCGGCTAGGGTTTTA 59.414 61.111 15.42 0.00 0.00 1.52
3478 4100 4.419921 CCCGGCGGCTAGGGTTTT 62.420 66.667 23.20 0.00 42.67 2.43
3497 4119 3.162154 GGGAGGACGGATGGGGAC 61.162 72.222 0.00 0.00 0.00 4.46
3498 4120 4.492303 GGGGAGGACGGATGGGGA 62.492 72.222 0.00 0.00 0.00 4.81
3499 4121 4.499116 AGGGGAGGACGGATGGGG 62.499 72.222 0.00 0.00 0.00 4.96
3500 4122 2.844839 GAGGGGAGGACGGATGGG 60.845 72.222 0.00 0.00 0.00 4.00
3501 4123 2.844839 GGAGGGGAGGACGGATGG 60.845 72.222 0.00 0.00 0.00 3.51
3502 4124 2.844839 GGGAGGGGAGGACGGATG 60.845 72.222 0.00 0.00 0.00 3.51
3503 4125 3.036959 AGGGAGGGGAGGACGGAT 61.037 66.667 0.00 0.00 0.00 4.18
3504 4126 3.752167 GAGGGAGGGGAGGACGGA 61.752 72.222 0.00 0.00 0.00 4.69
3505 4127 3.756783 AGAGGGAGGGGAGGACGG 61.757 72.222 0.00 0.00 0.00 4.79
3506 4128 2.443016 CAGAGGGAGGGGAGGACG 60.443 72.222 0.00 0.00 0.00 4.79
3507 4129 2.766229 GCAGAGGGAGGGGAGGAC 60.766 72.222 0.00 0.00 0.00 3.85
3508 4130 4.095400 GGCAGAGGGAGGGGAGGA 62.095 72.222 0.00 0.00 0.00 3.71
3509 4131 4.421554 TGGCAGAGGGAGGGGAGG 62.422 72.222 0.00 0.00 0.00 4.30
3510 4132 3.086600 GTGGCAGAGGGAGGGGAG 61.087 72.222 0.00 0.00 0.00 4.30
3511 4133 4.741239 GGTGGCAGAGGGAGGGGA 62.741 72.222 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.