Multiple sequence alignment - TraesCS4A01G019000

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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 TraesCS4A01G019000 chr4A 100.000 4268 0 0 1 4268 12391763 12396030 0.000000e+00 7882.0
1 TraesCS4A01G019000 chr4A 95.766 803 27 4 2 798 534589711 534590512 0.000000e+00 1288.0
2 TraesCS4A01G019000 chr4A 82.973 370 42 12 1046 1406 12525273 12524916 8.910000e-82 315.0
3 TraesCS4A01G019000 chr4A 84.348 230 19 9 925 1152 12551989 12551775 4.320000e-50 209.0
4 TraesCS4A01G019000 chr4D 92.762 2473 146 20 807 3261 455484634 455487091 0.000000e+00 3544.0
5 TraesCS4A01G019000 chr4D 84.477 831 87 20 924 1736 455477914 455478720 0.000000e+00 782.0
6 TraesCS4A01G019000 chr4D 78.184 793 107 43 3526 4268 455487221 455487997 3.030000e-121 446.0
7 TraesCS4A01G019000 chr4B 92.952 1816 100 17 1490 3294 568553099 568554897 0.000000e+00 2619.0
8 TraesCS4A01G019000 chr4B 94.397 696 29 4 807 1496 568552289 568552980 0.000000e+00 1061.0
9 TraesCS4A01G019000 chr4B 84.101 868 98 17 974 1833 568446282 568447117 0.000000e+00 802.0
10 TraesCS4A01G019000 chr4B 80.156 514 41 29 3786 4259 568555298 568555790 1.140000e-85 327.0
11 TraesCS4A01G019000 chr4B 86.842 76 7 2 3449 3521 381378312 381378237 9.840000e-12 82.4
12 TraesCS4A01G019000 chr4B 95.918 49 2 0 3444 3492 1994975 1994927 3.540000e-11 80.5
13 TraesCS4A01G019000 chr4B 94.118 51 3 0 3443 3493 60699515 60699465 1.270000e-10 78.7
14 TraesCS4A01G019000 chr3A 96.020 804 24 3 1 798 548832016 548832817 0.000000e+00 1301.0
15 TraesCS4A01G019000 chr3A 95.143 803 33 3 1 798 167868653 167867852 0.000000e+00 1262.0
16 TraesCS4A01G019000 chr2A 95.500 800 31 4 2 798 733187040 733186243 0.000000e+00 1273.0
17 TraesCS4A01G019000 chr2A 95.019 803 34 3 2 798 163845176 163845978 0.000000e+00 1256.0
18 TraesCS4A01G019000 chr5A 95.387 802 31 3 2 798 347188506 347189306 0.000000e+00 1271.0
19 TraesCS4A01G019000 chr7A 95.375 800 34 2 2 798 730657109 730656310 0.000000e+00 1269.0
20 TraesCS4A01G019000 chr7A 86.420 81 5 3 3444 3518 60725514 60725594 2.730000e-12 84.2
21 TraesCS4A01G019000 chr1A 95.375 800 32 4 2 798 254705904 254705107 0.000000e+00 1267.0
22 TraesCS4A01G019000 chr1A 92.982 57 4 0 3438 3494 245535582 245535638 2.730000e-12 84.2
23 TraesCS4A01G019000 chr1A 95.745 47 2 0 3446 3492 448929829 448929783 4.580000e-10 76.8
24 TraesCS4A01G019000 chr1A 94.000 50 3 0 3443 3492 486046168 486046119 4.580000e-10 76.8
25 TraesCS4A01G019000 chr6A 95.137 802 34 3 2 798 480716748 480715947 0.000000e+00 1260.0
26 TraesCS4A01G019000 chr5B 91.429 70 4 2 3450 3517 50521338 50521407 1.260000e-15 95.3
27 TraesCS4A01G019000 chr1B 88.312 77 5 3 3445 3517 344044762 344044838 5.880000e-14 89.8
28 TraesCS4A01G019000 chr5D 88.000 75 5 2 3450 3520 498669759 498669833 7.600000e-13 86.1
29 TraesCS4A01G019000 chr5D 87.500 72 5 3 3450 3517 26518300 26518229 3.540000e-11 80.5
30 TraesCS4A01G019000 chr5D 86.765 68 5 3 3454 3520 464401325 464401261 5.920000e-09 73.1
31 TraesCS4A01G019000 chr7B 88.000 75 3 3 3449 3517 8923355 8923429 2.730000e-12 84.2
32 TraesCS4A01G019000 chr7B 100.000 32 0 0 3373 3404 539218343 539218374 4.610000e-05 60.2
33 TraesCS4A01G019000 chr2D 88.571 70 7 1 3450 3518 580704209 580704140 2.730000e-12 84.2
34 TraesCS4A01G019000 chr6B 87.324 71 9 0 3449 3519 641047901 641047831 9.840000e-12 82.4
35 TraesCS4A01G019000 chr3D 88.235 68 5 1 3453 3520 152483685 152483621 1.270000e-10 78.7
36 TraesCS4A01G019000 chr3D 85.135 74 6 3 3450 3518 515014773 515014846 2.130000e-08 71.3
37 TraesCS4A01G019000 chr3D 85.135 74 5 3 3448 3521 611910952 611910885 2.130000e-08 71.3
38 TraesCS4A01G019000 chr6D 94.000 50 3 0 3443 3492 149721658 149721707 4.580000e-10 76.8
39 TraesCS4A01G019000 chr6D 88.889 63 3 2 3450 3512 446215209 446215267 1.650000e-09 75.0
40 TraesCS4A01G019000 chr6D 85.507 69 7 2 3450 3518 32921719 32921654 7.660000e-08 69.4
41 TraesCS4A01G019000 chr1D 95.745 47 2 0 3446 3492 298576989 298577035 4.580000e-10 76.8
42 TraesCS4A01G019000 chr1D 83.333 78 7 3 3449 3520 86107143 86107066 2.750000e-07 67.6
43 TraesCS4A01G019000 chrUn 95.745 47 0 2 3449 3494 83814017 83813972 1.650000e-09 75.0
44 TraesCS4A01G019000 chrUn 95.745 47 0 2 3449 3494 83861290 83861245 1.650000e-09 75.0
45 TraesCS4A01G019000 chrUn 95.652 46 2 0 3447 3492 242182863 242182908 1.650000e-09 75.0
46 TraesCS4A01G019000 chrUn 95.745 47 0 2 3449 3494 254176109 254176064 1.650000e-09 75.0
47 TraesCS4A01G019000 chrUn 94.000 50 1 2 3446 3494 391446218 391446266 1.650000e-09 75.0
48 TraesCS4A01G019000 chrUn 94.000 50 1 2 3446 3494 391518070 391518118 1.650000e-09 75.0
49 TraesCS4A01G019000 chrUn 95.745 47 0 2 3449 3494 456291365 456291320 1.650000e-09 75.0
50 TraesCS4A01G019000 chrUn 92.157 51 4 0 3444 3494 42635420 42635370 5.920000e-09 73.1
51 TraesCS4A01G019000 chrUn 92.157 51 4 0 3444 3494 42892575 42892625 5.920000e-09 73.1
52 TraesCS4A01G019000 chrUn 92.157 51 4 0 3444 3494 367959446 367959396 5.920000e-09 73.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G019000 chr4A 12391763 12396030 4267 False 7882.000000 7882 100.000000 1 4268 1 chr4A.!!$F1 4267
1 TraesCS4A01G019000 chr4A 534589711 534590512 801 False 1288.000000 1288 95.766000 2 798 1 chr4A.!!$F2 796
2 TraesCS4A01G019000 chr4D 455484634 455487997 3363 False 1995.000000 3544 85.473000 807 4268 2 chr4D.!!$F2 3461
3 TraesCS4A01G019000 chr4D 455477914 455478720 806 False 782.000000 782 84.477000 924 1736 1 chr4D.!!$F1 812
4 TraesCS4A01G019000 chr4B 568552289 568555790 3501 False 1335.666667 2619 89.168333 807 4259 3 chr4B.!!$F2 3452
5 TraesCS4A01G019000 chr4B 568446282 568447117 835 False 802.000000 802 84.101000 974 1833 1 chr4B.!!$F1 859
6 TraesCS4A01G019000 chr3A 548832016 548832817 801 False 1301.000000 1301 96.020000 1 798 1 chr3A.!!$F1 797
7 TraesCS4A01G019000 chr3A 167867852 167868653 801 True 1262.000000 1262 95.143000 1 798 1 chr3A.!!$R1 797
8 TraesCS4A01G019000 chr2A 733186243 733187040 797 True 1273.000000 1273 95.500000 2 798 1 chr2A.!!$R1 796
9 TraesCS4A01G019000 chr2A 163845176 163845978 802 False 1256.000000 1256 95.019000 2 798 1 chr2A.!!$F1 796
10 TraesCS4A01G019000 chr5A 347188506 347189306 800 False 1271.000000 1271 95.387000 2 798 1 chr5A.!!$F1 796
11 TraesCS4A01G019000 chr7A 730656310 730657109 799 True 1269.000000 1269 95.375000 2 798 1 chr7A.!!$R1 796
12 TraesCS4A01G019000 chr1A 254705107 254705904 797 True 1267.000000 1267 95.375000 2 798 1 chr1A.!!$R1 796
13 TraesCS4A01G019000 chr6A 480715947 480716748 801 True 1260.000000 1260 95.137000 2 798 1 chr6A.!!$R1 796

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
804 819 0.960364 GCGCTTGTTGGGAAGATGGA 60.960 55.000 0.0 0.0 0.00 3.41 F
1148 1184 0.035152 TGGACTCACCATCATGCCAC 60.035 55.000 0.0 0.0 44.64 5.01 F
2749 2934 1.228644 TGCAAGTGCCTTCATGCCT 60.229 52.632 0.0 0.0 41.18 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2122 0.772926 GCGTCGACAAGCATATCTCG 59.227 55.0 17.16 0.0 0.00 4.04 R
2847 3032 0.107017 ATACCACAGCAGGGACATGC 60.107 55.0 0.00 0.0 46.88 4.06 R
4056 4496 0.041312 CACCAACCAAAACTCGCTCG 60.041 55.0 0.00 0.0 0.00 5.03 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
66 67 5.304357 TCACAATCCCTATCTCTCGCATTAA 59.696 40.000 0.00 0.00 0.00 1.40
277 290 9.448438 AAACAAAAGCAAGGAGAAAACTTAAAT 57.552 25.926 0.00 0.00 0.00 1.40
338 351 6.721318 TGCACCCTAGAAGTAAATTTCAGAT 58.279 36.000 0.00 0.00 0.00 2.90
685 700 3.136992 TGAAGGGAAACGTAAGGAACCTT 59.863 43.478 10.97 10.97 41.61 3.50
713 728 7.465379 CGGATTCGAGCATAACATCACTAAAAA 60.465 37.037 0.00 0.00 39.00 1.94
761 776 6.722129 ACCTAGATCTATCCTCGCTTTTATGT 59.278 38.462 2.11 0.00 0.00 2.29
772 787 4.212716 TCGCTTTTATGTCTAGCTAGGGA 58.787 43.478 20.58 7.92 32.80 4.20
780 795 7.592885 TTATGTCTAGCTAGGGACGTTAAAT 57.407 36.000 20.58 2.89 35.45 1.40
798 813 2.418368 ATGATAGCGCTTGTTGGGAA 57.582 45.000 18.68 0.00 0.00 3.97
799 814 1.737838 TGATAGCGCTTGTTGGGAAG 58.262 50.000 18.68 0.00 0.00 3.46
800 815 1.277842 TGATAGCGCTTGTTGGGAAGA 59.722 47.619 18.68 0.00 0.00 2.87
801 816 2.092968 TGATAGCGCTTGTTGGGAAGAT 60.093 45.455 18.68 0.00 0.00 2.40
802 817 1.737838 TAGCGCTTGTTGGGAAGATG 58.262 50.000 18.68 0.00 0.00 2.90
803 818 0.962356 AGCGCTTGTTGGGAAGATGG 60.962 55.000 2.64 0.00 0.00 3.51
804 819 0.960364 GCGCTTGTTGGGAAGATGGA 60.960 55.000 0.00 0.00 0.00 3.41
805 820 1.755179 CGCTTGTTGGGAAGATGGAT 58.245 50.000 0.00 0.00 0.00 3.41
832 847 4.770010 GGATACTCTAACCAGCTGAGCTAT 59.230 45.833 17.39 0.00 36.40 2.97
852 867 3.043465 TGGGACCCATACGTATAACCA 57.957 47.619 9.95 9.33 0.00 3.67
1148 1184 0.035152 TGGACTCACCATCATGCCAC 60.035 55.000 0.00 0.00 44.64 5.01
1196 1232 4.316823 AGTCCCTCGTGCTCCCCA 62.317 66.667 0.00 0.00 0.00 4.96
1267 1303 3.515901 AGAAGAAGGTCTCGTGGCTTATT 59.484 43.478 0.00 0.00 0.00 1.40
1337 1375 2.427506 GTTTCGGTGATCTCTTTGCCT 58.572 47.619 0.00 0.00 0.00 4.75
1345 1383 2.816087 TGATCTCTTTGCCTTTGCTGTC 59.184 45.455 0.00 0.00 38.71 3.51
1346 1384 1.229428 TCTCTTTGCCTTTGCTGTCG 58.771 50.000 0.00 0.00 38.71 4.35
1445 1483 4.133820 ACATGTCGAAATGTTTCACCAGA 58.866 39.130 15.72 0.00 37.50 3.86
1462 1504 5.053145 CACCAGAGGAACATAGTTGATAGC 58.947 45.833 0.00 0.00 0.00 2.97
1510 1677 6.704493 TGTTGATTACTTGGTAGTTCAGTGAC 59.296 38.462 0.00 0.00 35.78 3.67
1576 1744 7.176690 CACAAAGTCTTATTCAGGGGTATGTTT 59.823 37.037 0.00 0.00 0.00 2.83
1665 1838 6.726230 CAAATTTGCCAAAATGTGATGAACA 58.274 32.000 5.01 0.00 41.73 3.18
1782 1959 7.767261 ACTATCTATGTGTTCTTCAGACAGAC 58.233 38.462 0.00 0.00 0.00 3.51
1800 1977 2.952310 AGACTGTTCTTTGGTTTCTGCC 59.048 45.455 0.00 0.00 0.00 4.85
1920 2097 3.307691 CCTGAAGCCTGTTCCAGTGATTA 60.308 47.826 0.00 0.00 0.00 1.75
1945 2122 3.673809 CGTTGCAGGTACAGTTAGAACTC 59.326 47.826 0.00 0.00 37.08 3.01
2146 2324 9.698617 GTGATACAATTACCTTTTCGAATGTAC 57.301 33.333 0.00 0.00 0.00 2.90
2185 2363 4.036262 TGCCACTTTGAGTTTGTGTATGTC 59.964 41.667 0.00 0.00 0.00 3.06
2292 2470 8.066612 CCACTTTTATGGTCCAAATACAGATT 57.933 34.615 0.00 0.00 34.77 2.40
2410 2590 3.256631 GTCATTGAAGCCACATGTTTCCT 59.743 43.478 0.00 0.00 0.00 3.36
2430 2610 7.589958 TTCCTGTGGTACAAATACACAAATT 57.410 32.000 0.00 0.00 44.16 1.82
2489 2669 5.071519 ACAAGCTCTCAGTGGCATATAAGAT 59.928 40.000 0.00 0.00 0.00 2.40
2491 2671 7.038445 ACAAGCTCTCAGTGGCATATAAGATAT 60.038 37.037 0.00 0.00 0.00 1.63
2492 2672 7.111247 AGCTCTCAGTGGCATATAAGATATC 57.889 40.000 0.00 0.00 0.00 1.63
2493 2673 6.098124 AGCTCTCAGTGGCATATAAGATATCC 59.902 42.308 0.00 0.00 0.00 2.59
2605 2790 1.555075 GGTTCAGACAGTAGGCCATGA 59.445 52.381 5.01 0.00 0.00 3.07
2620 2805 4.529377 AGGCCATGAGATGTTTGACATTTT 59.471 37.500 5.01 0.00 39.27 1.82
2736 2921 8.175069 TGCTAGTAATATTTCTTTTCGTGCAAG 58.825 33.333 0.00 0.00 0.00 4.01
2739 2924 6.801862 AGTAATATTTCTTTTCGTGCAAGTGC 59.198 34.615 0.00 0.00 42.50 4.40
2749 2934 1.228644 TGCAAGTGCCTTCATGCCT 60.229 52.632 0.00 0.00 41.18 4.75
2755 2940 1.342174 AGTGCCTTCATGCCTTTGTTG 59.658 47.619 0.00 0.00 0.00 3.33
2792 2977 4.499696 GGGAATGCGGAACATAGAAAATGG 60.500 45.833 0.00 0.00 38.34 3.16
2802 2987 6.774656 GGAACATAGAAAATGGATCCAGTGAT 59.225 38.462 21.33 10.53 32.68 3.06
2847 3032 1.131883 GCCACAAGCAAGCTACATCTG 59.868 52.381 0.00 0.00 42.97 2.90
2897 3086 3.632145 GGGCGTGACTGGATATGATTTTT 59.368 43.478 0.00 0.00 0.00 1.94
2898 3087 4.498009 GGGCGTGACTGGATATGATTTTTG 60.498 45.833 0.00 0.00 0.00 2.44
2899 3088 4.037690 GCGTGACTGGATATGATTTTTGC 58.962 43.478 0.00 0.00 0.00 3.68
2973 3165 0.887836 GAGAAAAAGGGAACGCCGGT 60.888 55.000 1.90 0.00 33.83 5.28
3012 3204 1.153958 GAGTTTGCGCATGAAGCCC 60.154 57.895 12.75 0.00 41.38 5.19
3019 3211 2.044650 GCATGAAGCCCTGGCAGA 60.045 61.111 17.94 0.00 44.88 4.26
3089 3283 3.865745 GCTATCTCTTTGCGAGCAGTAAA 59.134 43.478 0.00 0.00 39.70 2.01
3090 3284 4.509600 GCTATCTCTTTGCGAGCAGTAAAT 59.490 41.667 0.00 0.00 39.70 1.40
3091 3285 5.007136 GCTATCTCTTTGCGAGCAGTAAATT 59.993 40.000 0.00 0.00 39.70 1.82
3092 3286 4.668576 TCTCTTTGCGAGCAGTAAATTG 57.331 40.909 0.00 0.00 39.70 2.32
3140 3334 2.851263 TTCCATGGCGAACTTAGTGT 57.149 45.000 6.96 0.00 0.00 3.55
3174 3369 0.969917 AGCGTGGATGCTCTCTGAGT 60.970 55.000 4.32 0.00 42.95 3.41
3188 3383 3.897505 TCTCTGAGTTGAGTGATGGTTGA 59.102 43.478 4.32 0.00 35.68 3.18
3189 3384 4.529769 TCTCTGAGTTGAGTGATGGTTGAT 59.470 41.667 4.32 0.00 35.68 2.57
3190 3385 5.012458 TCTCTGAGTTGAGTGATGGTTGATT 59.988 40.000 4.32 0.00 35.68 2.57
3205 3400 9.183368 TGATGGTTGATTATTATGTGTTGCTAA 57.817 29.630 0.00 0.00 0.00 3.09
3219 3414 7.416154 TGTGTTGCTAACTTTCAGTATGTAC 57.584 36.000 0.00 0.00 37.40 2.90
3231 3426 1.139308 TATGTACGACGCCCCGTTG 59.861 57.895 3.36 3.62 45.61 4.10
3279 3474 5.181690 TGGTAGCATGTCTTTGTTTTGAC 57.818 39.130 0.00 0.00 0.00 3.18
3283 3478 6.072175 GGTAGCATGTCTTTGTTTTGACCATA 60.072 38.462 0.00 0.00 32.67 2.74
3308 3503 2.932261 AGAACCCCAGTGTGAGAAAAC 58.068 47.619 0.00 0.00 0.00 2.43
3315 3510 5.131475 ACCCCAGTGTGAGAAAACTAAACTA 59.869 40.000 0.00 0.00 0.00 2.24
3336 3531 2.483014 TGTTCTGTTTCGTATGGGGG 57.517 50.000 0.00 0.00 0.00 5.40
3355 3550 2.041755 GGGAAAAATGACACTCCCTCCT 59.958 50.000 0.00 0.00 43.74 3.69
3372 3567 5.844516 TCCCTCCTATCCGAATTAATTGACT 59.155 40.000 5.17 0.00 0.00 3.41
3373 3568 7.014449 TCCCTCCTATCCGAATTAATTGACTA 58.986 38.462 5.17 0.00 0.00 2.59
3374 3569 7.178628 TCCCTCCTATCCGAATTAATTGACTAG 59.821 40.741 5.17 1.89 0.00 2.57
3376 3571 8.247562 CCTCCTATCCGAATTAATTGACTAGAG 58.752 40.741 5.17 4.96 0.00 2.43
3378 3573 6.814146 CCTATCCGAATTAATTGACTAGAGGC 59.186 42.308 5.17 0.00 0.00 4.70
3379 3574 5.871396 TCCGAATTAATTGACTAGAGGCT 57.129 39.130 5.17 0.00 0.00 4.58
3380 3575 5.601662 TCCGAATTAATTGACTAGAGGCTG 58.398 41.667 5.17 0.00 0.00 4.85
3381 3576 5.128827 TCCGAATTAATTGACTAGAGGCTGT 59.871 40.000 5.17 0.00 0.00 4.40
3382 3577 5.235186 CCGAATTAATTGACTAGAGGCTGTG 59.765 44.000 5.17 0.00 0.00 3.66
3383 3578 5.812642 CGAATTAATTGACTAGAGGCTGTGT 59.187 40.000 5.17 0.00 0.00 3.72
3384 3579 6.019479 CGAATTAATTGACTAGAGGCTGTGTC 60.019 42.308 5.17 0.00 0.00 3.67
3385 3580 5.738619 TTAATTGACTAGAGGCTGTGTCA 57.261 39.130 11.09 11.09 37.62 3.58
3388 3583 4.623932 TTGACTAGAGGCTGTGTCAATT 57.376 40.909 18.58 0.00 42.25 2.32
3389 3584 5.738619 TTGACTAGAGGCTGTGTCAATTA 57.261 39.130 18.58 5.03 42.25 1.40
3390 3585 5.738619 TGACTAGAGGCTGTGTCAATTAA 57.261 39.130 12.22 0.00 36.64 1.40
3391 3586 6.299805 TGACTAGAGGCTGTGTCAATTAAT 57.700 37.500 12.22 0.00 36.64 1.40
3392 3587 6.711277 TGACTAGAGGCTGTGTCAATTAATT 58.289 36.000 12.22 0.00 36.64 1.40
3393 3588 6.818644 TGACTAGAGGCTGTGTCAATTAATTC 59.181 38.462 12.22 0.00 36.64 2.17
3394 3589 5.812642 ACTAGAGGCTGTGTCAATTAATTCG 59.187 40.000 0.00 0.00 0.00 3.34
3395 3590 3.941483 AGAGGCTGTGTCAATTAATTCGG 59.059 43.478 0.00 0.00 0.00 4.30
3396 3591 3.938963 GAGGCTGTGTCAATTAATTCGGA 59.061 43.478 0.00 0.00 0.00 4.55
3397 3592 4.526970 AGGCTGTGTCAATTAATTCGGAT 58.473 39.130 0.00 0.00 0.00 4.18
3398 3593 4.576463 AGGCTGTGTCAATTAATTCGGATC 59.424 41.667 0.00 0.00 0.00 3.36
3399 3594 4.335315 GGCTGTGTCAATTAATTCGGATCA 59.665 41.667 0.00 0.00 0.00 2.92
3400 3595 5.504665 GGCTGTGTCAATTAATTCGGATCAG 60.505 44.000 0.00 8.02 0.00 2.90
3401 3596 5.294306 GCTGTGTCAATTAATTCGGATCAGA 59.706 40.000 17.51 0.00 0.00 3.27
3402 3597 6.510799 GCTGTGTCAATTAATTCGGATCAGAG 60.511 42.308 17.51 13.21 0.00 3.35
3403 3598 5.817296 TGTGTCAATTAATTCGGATCAGAGG 59.183 40.000 0.00 0.00 0.00 3.69
3404 3599 5.817816 GTGTCAATTAATTCGGATCAGAGGT 59.182 40.000 0.00 0.00 0.00 3.85
3405 3600 6.984474 GTGTCAATTAATTCGGATCAGAGGTA 59.016 38.462 0.00 0.00 0.00 3.08
3406 3601 7.494625 GTGTCAATTAATTCGGATCAGAGGTAA 59.505 37.037 0.00 0.00 0.00 2.85
3407 3602 8.210946 TGTCAATTAATTCGGATCAGAGGTAAT 58.789 33.333 0.00 1.66 0.00 1.89
3408 3603 9.706691 GTCAATTAATTCGGATCAGAGGTAATA 57.293 33.333 0.00 0.00 0.00 0.98
3453 3648 8.738645 AATCCCAGTGTGAGAAAATTATACTC 57.261 34.615 0.00 0.00 0.00 2.59
3454 3649 6.650120 TCCCAGTGTGAGAAAATTATACTCC 58.350 40.000 0.00 0.00 0.00 3.85
3455 3650 5.823045 CCCAGTGTGAGAAAATTATACTCCC 59.177 44.000 0.00 0.00 0.00 4.30
3456 3651 6.353082 CCCAGTGTGAGAAAATTATACTCCCT 60.353 42.308 0.00 0.00 0.00 4.20
3457 3652 6.763610 CCAGTGTGAGAAAATTATACTCCCTC 59.236 42.308 0.00 0.00 0.00 4.30
3458 3653 6.763610 CAGTGTGAGAAAATTATACTCCCTCC 59.236 42.308 0.00 0.00 0.00 4.30
3459 3654 5.753921 GTGTGAGAAAATTATACTCCCTCCG 59.246 44.000 0.00 0.00 0.00 4.63
3460 3655 4.750598 GTGAGAAAATTATACTCCCTCCGC 59.249 45.833 0.00 0.00 0.00 5.54
3461 3656 4.654262 TGAGAAAATTATACTCCCTCCGCT 59.346 41.667 0.00 0.00 0.00 5.52
3462 3657 5.216614 AGAAAATTATACTCCCTCCGCTC 57.783 43.478 0.00 0.00 0.00 5.03
3463 3658 4.040584 AGAAAATTATACTCCCTCCGCTCC 59.959 45.833 0.00 0.00 0.00 4.70
3464 3659 2.696526 ATTATACTCCCTCCGCTCCA 57.303 50.000 0.00 0.00 0.00 3.86
3465 3660 2.696526 TTATACTCCCTCCGCTCCAT 57.303 50.000 0.00 0.00 0.00 3.41
3466 3661 3.820195 TTATACTCCCTCCGCTCCATA 57.180 47.619 0.00 0.00 0.00 2.74
3467 3662 2.696526 ATACTCCCTCCGCTCCATAA 57.303 50.000 0.00 0.00 0.00 1.90
3468 3663 2.696526 TACTCCCTCCGCTCCATAAT 57.303 50.000 0.00 0.00 0.00 1.28
3469 3664 2.696526 ACTCCCTCCGCTCCATAATA 57.303 50.000 0.00 0.00 0.00 0.98
3470 3665 3.191888 ACTCCCTCCGCTCCATAATAT 57.808 47.619 0.00 0.00 0.00 1.28
3471 3666 4.332683 ACTCCCTCCGCTCCATAATATA 57.667 45.455 0.00 0.00 0.00 0.86
3472 3667 4.684724 ACTCCCTCCGCTCCATAATATAA 58.315 43.478 0.00 0.00 0.00 0.98
3473 3668 4.712337 ACTCCCTCCGCTCCATAATATAAG 59.288 45.833 0.00 0.00 0.00 1.73
3474 3669 4.942944 TCCCTCCGCTCCATAATATAAGA 58.057 43.478 0.00 0.00 0.00 2.10
3475 3670 5.338632 TCCCTCCGCTCCATAATATAAGAA 58.661 41.667 0.00 0.00 0.00 2.52
3476 3671 5.187186 TCCCTCCGCTCCATAATATAAGAAC 59.813 44.000 0.00 0.00 0.00 3.01
3477 3672 5.103000 CCTCCGCTCCATAATATAAGAACG 58.897 45.833 0.00 0.00 0.00 3.95
3478 3673 5.336531 CCTCCGCTCCATAATATAAGAACGT 60.337 44.000 0.00 0.00 0.00 3.99
3479 3674 6.092955 TCCGCTCCATAATATAAGAACGTT 57.907 37.500 0.00 0.00 0.00 3.99
3480 3675 6.518493 TCCGCTCCATAATATAAGAACGTTT 58.482 36.000 0.46 0.00 0.00 3.60
3481 3676 6.987992 TCCGCTCCATAATATAAGAACGTTTT 59.012 34.615 0.46 0.00 0.00 2.43
3482 3677 7.496591 TCCGCTCCATAATATAAGAACGTTTTT 59.503 33.333 9.22 9.22 0.00 1.94
3483 3678 7.586300 CCGCTCCATAATATAAGAACGTTTTTG 59.414 37.037 13.87 0.00 0.00 2.44
3484 3679 8.332464 CGCTCCATAATATAAGAACGTTTTTGA 58.668 33.333 13.87 2.81 0.00 2.69
3485 3680 9.434559 GCTCCATAATATAAGAACGTTTTTGAC 57.565 33.333 13.87 0.00 0.00 3.18
3507 3702 9.537192 TTGACACTAGTATTTTATTATGGGACG 57.463 33.333 0.00 0.00 0.00 4.79
3508 3703 8.145767 TGACACTAGTATTTTATTATGGGACGG 58.854 37.037 0.00 0.00 0.00 4.79
3509 3704 8.253867 ACACTAGTATTTTATTATGGGACGGA 57.746 34.615 0.00 0.00 0.00 4.69
3510 3705 8.365647 ACACTAGTATTTTATTATGGGACGGAG 58.634 37.037 0.00 0.00 0.00 4.63
3511 3706 7.817962 CACTAGTATTTTATTATGGGACGGAGG 59.182 40.741 0.00 0.00 0.00 4.30
3512 3707 7.731688 ACTAGTATTTTATTATGGGACGGAGGA 59.268 37.037 0.00 0.00 0.00 3.71
3513 3708 7.383156 AGTATTTTATTATGGGACGGAGGAA 57.617 36.000 0.00 0.00 0.00 3.36
3514 3709 7.450903 AGTATTTTATTATGGGACGGAGGAAG 58.549 38.462 0.00 0.00 0.00 3.46
3515 3710 5.703730 TTTTATTATGGGACGGAGGAAGT 57.296 39.130 0.00 0.00 0.00 3.01
3516 3711 6.811634 TTTTATTATGGGACGGAGGAAGTA 57.188 37.500 0.00 0.00 0.00 2.24
3517 3712 5.796424 TTATTATGGGACGGAGGAAGTAC 57.204 43.478 0.00 0.00 0.00 2.73
3518 3713 3.393426 TTATGGGACGGAGGAAGTACT 57.607 47.619 0.00 0.00 0.00 2.73
3519 3714 2.249309 ATGGGACGGAGGAAGTACTT 57.751 50.000 8.13 8.13 0.00 2.24
3520 3715 2.905415 TGGGACGGAGGAAGTACTTA 57.095 50.000 8.42 0.00 0.00 2.24
3521 3716 2.450476 TGGGACGGAGGAAGTACTTAC 58.550 52.381 10.07 10.07 0.00 2.34
3522 3717 2.042162 TGGGACGGAGGAAGTACTTACT 59.958 50.000 20.70 20.70 36.20 2.24
3524 3719 3.513119 GGGACGGAGGAAGTACTTACTTT 59.487 47.826 21.45 9.27 45.84 2.66
3528 3723 5.922053 ACGGAGGAAGTACTTACTTTTTGT 58.078 37.500 21.45 13.91 45.84 2.83
3536 3731 7.641411 GGAAGTACTTACTTTTTGTTCCGTTTC 59.359 37.037 10.83 0.00 45.84 2.78
3554 3749 4.625324 CGTTTCATATTGGGGGAGAAGACA 60.625 45.833 0.00 0.00 0.00 3.41
3564 3759 3.960755 GGGGGAGAAGACAATAAATTGGG 59.039 47.826 7.56 0.00 41.96 4.12
3575 3899 5.372373 ACAATAAATTGGGTTTGGTTGTGG 58.628 37.500 7.56 0.00 41.96 4.17
3606 3930 2.420022 GTCTGCACTGATAAATTGGCGT 59.580 45.455 0.00 0.00 0.00 5.68
3611 3935 5.119694 TGCACTGATAAATTGGCGTGTATA 58.880 37.500 0.00 0.00 0.00 1.47
3618 3942 6.587226 TGATAAATTGGCGTGTATATCGTACC 59.413 38.462 0.00 0.00 0.00 3.34
3621 3945 0.244721 GGCGTGTATATCGTACCCCC 59.755 60.000 0.00 0.00 0.00 5.40
3622 3946 1.251251 GCGTGTATATCGTACCCCCT 58.749 55.000 0.00 0.00 0.00 4.79
3623 3947 1.200948 GCGTGTATATCGTACCCCCTC 59.799 57.143 0.00 0.00 0.00 4.30
3624 3948 1.815003 CGTGTATATCGTACCCCCTCC 59.185 57.143 0.00 0.00 0.00 4.30
3651 3988 1.479323 CCCTCCGGAATTAGTTGACGA 59.521 52.381 5.23 0.00 0.00 4.20
3666 4003 1.132453 TGACGAATCTAGCACAGACGG 59.868 52.381 0.00 0.00 35.62 4.79
3692 4029 4.530857 GATCCGGTCCCTGTGGCG 62.531 72.222 0.00 0.00 0.00 5.69
3707 4044 1.135575 GTGGCGCATCAGGAAAGAAAG 60.136 52.381 10.83 0.00 0.00 2.62
3717 4054 0.375106 GGAAAGAAAGAGATGCCGCG 59.625 55.000 0.00 0.00 0.00 6.46
3719 4056 1.026718 AAAGAAAGAGATGCCGCGGG 61.027 55.000 29.38 8.95 0.00 6.13
3820 4210 4.021925 GGTCGTTGGCCTGGCTCT 62.022 66.667 19.68 0.00 0.00 4.09
3906 4317 3.084579 CGTGGAGACGCTGCAATC 58.915 61.111 0.00 0.00 39.10 2.67
3919 4330 2.005451 CTGCAATCTCTGTGTGGCTAC 58.995 52.381 0.00 0.00 0.00 3.58
3942 4355 1.471964 GTCAGCGAGCAGATAACGAG 58.528 55.000 0.00 0.00 0.00 4.18
3946 4359 0.930742 GCGAGCAGATAACGAGACGG 60.931 60.000 0.00 0.00 0.00 4.79
3947 4360 0.656259 CGAGCAGATAACGAGACGGA 59.344 55.000 0.00 0.00 0.00 4.69
3948 4361 1.333347 CGAGCAGATAACGAGACGGAG 60.333 57.143 0.00 0.00 0.00 4.63
3949 4362 0.382515 AGCAGATAACGAGACGGAGC 59.617 55.000 0.00 0.00 0.00 4.70
3950 4363 0.595310 GCAGATAACGAGACGGAGCC 60.595 60.000 0.00 0.00 0.00 4.70
3951 4364 0.317103 CAGATAACGAGACGGAGCCG 60.317 60.000 7.48 7.48 46.03 5.52
4017 4456 2.755469 CCCCCACCAAATCGGCAG 60.755 66.667 0.00 0.00 39.03 4.85
4020 4460 3.055719 CCACCAAATCGGCAGCGT 61.056 61.111 0.00 0.00 39.03 5.07
4081 4540 2.096248 GAGTTTTGGTTGGTGGACACA 58.904 47.619 4.69 0.00 0.00 3.72
4082 4541 2.099098 GAGTTTTGGTTGGTGGACACAG 59.901 50.000 4.69 0.00 0.00 3.66
4086 4545 0.107410 TGGTTGGTGGACACAGACAC 60.107 55.000 4.69 0.00 36.89 3.67
4087 4546 0.107410 GGTTGGTGGACACAGACACA 60.107 55.000 4.69 0.00 39.31 3.72
4088 4547 1.014352 GTTGGTGGACACAGACACAC 58.986 55.000 4.69 0.00 39.31 3.82
4089 4548 0.615850 TTGGTGGACACAGACACACA 59.384 50.000 4.69 0.00 39.31 3.72
4090 4549 0.615850 TGGTGGACACAGACACACAA 59.384 50.000 4.69 0.00 39.31 3.33
4091 4550 1.299541 GGTGGACACAGACACACAAG 58.700 55.000 4.69 0.00 39.31 3.16
4092 4551 1.134521 GGTGGACACAGACACACAAGA 60.135 52.381 4.69 0.00 39.31 3.02
4093 4552 1.933853 GTGGACACAGACACACAAGAC 59.066 52.381 0.00 0.00 37.54 3.01
4094 4553 1.209128 GGACACAGACACACAAGACG 58.791 55.000 0.00 0.00 0.00 4.18
4095 4554 1.202371 GGACACAGACACACAAGACGA 60.202 52.381 0.00 0.00 0.00 4.20
4096 4555 2.536365 GACACAGACACACAAGACGAA 58.464 47.619 0.00 0.00 0.00 3.85
4097 4556 2.268298 ACACAGACACACAAGACGAAC 58.732 47.619 0.00 0.00 0.00 3.95
4098 4557 2.267426 CACAGACACACAAGACGAACA 58.733 47.619 0.00 0.00 0.00 3.18
4099 4558 2.029244 CACAGACACACAAGACGAACAC 59.971 50.000 0.00 0.00 0.00 3.32
4100 4559 1.255342 CAGACACACAAGACGAACACG 59.745 52.381 0.00 0.00 0.00 4.49
4101 4560 0.575390 GACACACAAGACGAACACGG 59.425 55.000 0.00 0.00 0.00 4.94
4102 4561 1.275657 CACACAAGACGAACACGGC 59.724 57.895 0.00 0.00 35.00 5.68
4103 4562 2.235016 ACACAAGACGAACACGGCG 61.235 57.895 4.80 4.80 40.30 6.46
4118 4577 2.585247 GCGGTACAGATGGCGTCC 60.585 66.667 2.37 0.00 0.00 4.79
4121 4580 2.106332 GTACAGATGGCGTCCCCG 59.894 66.667 2.37 0.00 35.87 5.73
4229 4688 2.125225 GTCCACTTCCCCTCCCCT 59.875 66.667 0.00 0.00 0.00 4.79
4259 4718 0.840617 CCTAGGCCTTTTCTCCTCCC 59.159 60.000 12.58 0.00 34.02 4.30
4260 4719 1.626631 CCTAGGCCTTTTCTCCTCCCT 60.627 57.143 12.58 0.00 34.02 4.20
4262 4721 0.916845 AGGCCTTTTCTCCTCCCTCC 60.917 60.000 0.00 0.00 0.00 4.30
4263 4722 1.610327 GCCTTTTCTCCTCCCTCCC 59.390 63.158 0.00 0.00 0.00 4.30
4265 4724 0.915364 CCTTTTCTCCTCCCTCCCTG 59.085 60.000 0.00 0.00 0.00 4.45
4266 4725 1.662686 CTTTTCTCCTCCCTCCCTGT 58.337 55.000 0.00 0.00 0.00 4.00
4267 4726 2.562214 CCTTTTCTCCTCCCTCCCTGTA 60.562 54.545 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
247 260 6.934083 AGTTTTCTCCTTGCTTTTGTTTGAAA 59.066 30.769 0.00 0.00 0.00 2.69
277 290 7.953005 TTCCATTATTCTAAACCAAGCATCA 57.047 32.000 0.00 0.00 0.00 3.07
430 443 7.148507 CCTTCCATAATTTCATGAGCGATACTC 60.149 40.741 0.00 0.00 46.45 2.59
488 503 3.849574 TGTTTCCTCTTGGGTATGATGGA 59.150 43.478 0.00 0.00 36.25 3.41
685 700 2.364002 TGATGTTATGCTCGAATCCGGA 59.636 45.455 6.61 6.61 36.24 5.14
731 746 5.822204 AGCGAGGATAGATCTAGGTATTGT 58.178 41.667 8.70 0.00 0.00 2.71
761 776 6.072064 GCTATCATTTAACGTCCCTAGCTAGA 60.072 42.308 22.70 0.00 0.00 2.43
772 787 4.436852 CCAACAAGCGCTATCATTTAACGT 60.437 41.667 12.05 0.00 0.00 3.99
780 795 1.277842 TCTTCCCAACAAGCGCTATCA 59.722 47.619 12.05 0.00 0.00 2.15
798 813 4.767928 GGTTAGAGTATCCGTCATCCATCT 59.232 45.833 0.00 0.00 33.66 2.90
799 814 4.523173 TGGTTAGAGTATCCGTCATCCATC 59.477 45.833 0.00 0.00 33.66 3.51
800 815 4.480115 TGGTTAGAGTATCCGTCATCCAT 58.520 43.478 0.00 0.00 33.66 3.41
801 816 3.889538 CTGGTTAGAGTATCCGTCATCCA 59.110 47.826 0.00 0.00 33.66 3.41
802 817 3.305471 GCTGGTTAGAGTATCCGTCATCC 60.305 52.174 0.00 0.00 33.66 3.51
803 818 3.570550 AGCTGGTTAGAGTATCCGTCATC 59.429 47.826 0.00 0.00 33.66 2.92
804 819 3.319405 CAGCTGGTTAGAGTATCCGTCAT 59.681 47.826 5.57 0.00 33.66 3.06
805 820 2.688446 CAGCTGGTTAGAGTATCCGTCA 59.312 50.000 5.57 0.00 33.66 4.35
832 847 3.043465 TGGTTATACGTATGGGTCCCA 57.957 47.619 14.64 14.64 38.19 4.37
898 913 3.817148 TTAAAGGTTCGCCATCGTTTC 57.183 42.857 0.00 0.00 40.60 2.78
1041 1074 3.310860 CTTCGGGGTTCGGGGAGTG 62.311 68.421 0.00 0.00 39.77 3.51
1177 1213 2.997897 GGGAGCACGAGGGACTGT 60.998 66.667 0.00 0.00 41.55 3.55
1267 1303 0.691904 ACACGGAATAAAACGGGGGA 59.308 50.000 0.00 0.00 37.93 4.81
1337 1375 0.314618 TGGTACTACGCGACAGCAAA 59.685 50.000 15.93 0.00 45.49 3.68
1345 1383 3.620374 TCTTAGAGTCTTGGTACTACGCG 59.380 47.826 3.53 3.53 0.00 6.01
1346 1384 4.035441 CCTCTTAGAGTCTTGGTACTACGC 59.965 50.000 8.55 0.00 0.00 4.42
1445 1483 7.663081 CACCATAATGCTATCAACTATGTTCCT 59.337 37.037 0.00 0.00 0.00 3.36
1510 1677 7.064134 TGACTTAAACGCCAAACACTATATCTG 59.936 37.037 0.00 0.00 0.00 2.90
1681 1854 8.924511 AGGTTCTCCATATGTTGGTAATATTG 57.075 34.615 1.24 0.00 46.52 1.90
1713 1886 7.618117 TCCTAATAAGTAGTGTTGAGGATGTGA 59.382 37.037 0.00 0.00 0.00 3.58
1742 1915 9.896645 CACATAGATAGTAGGCCAAAATATGAT 57.103 33.333 5.01 0.00 0.00 2.45
1757 1934 7.613801 AGTCTGTCTGAAGAACACATAGATAGT 59.386 37.037 0.00 0.00 31.24 2.12
1782 1959 2.689983 ACAGGCAGAAACCAAAGAACAG 59.310 45.455 0.00 0.00 0.00 3.16
1800 1977 5.937540 TGGTGATTATGTACAAGGACAACAG 59.062 40.000 0.00 0.00 31.83 3.16
1920 2097 2.829720 TCTAACTGTACCTGCAACGGAT 59.170 45.455 2.85 0.00 0.00 4.18
1945 2122 0.772926 GCGTCGACAAGCATATCTCG 59.227 55.000 17.16 0.00 0.00 4.04
2035 2212 9.896645 ATCAGAATCAAGAATACTGTTACACAT 57.103 29.630 0.00 0.00 0.00 3.21
2146 2324 9.716531 TCAAAGTGGCATATAAGATATTCTCTG 57.283 33.333 0.00 0.00 33.29 3.35
2195 2373 4.269183 TCAGTGCCATATGTTTTTCCGAT 58.731 39.130 1.24 0.00 0.00 4.18
2410 2590 5.069119 TGCCAATTTGTGTATTTGTACCACA 59.931 36.000 0.00 0.00 0.00 4.17
2430 2610 1.894466 CCATGACATCCAAGTTTGCCA 59.106 47.619 0.00 0.00 0.00 4.92
2493 2673 3.650942 TGGTAGCATTACATTCTAGGGGG 59.349 47.826 0.00 0.00 0.00 5.40
2530 2714 6.734871 GTGGCTCCACTAAAACCTAAAGTTTG 60.735 42.308 11.61 0.00 44.17 2.93
2633 2818 5.907662 TCCTCTGGGAAGAACTGATATGATT 59.092 40.000 0.00 0.00 38.93 2.57
2739 2924 2.552315 ACGTACAACAAAGGCATGAAGG 59.448 45.455 0.00 0.00 0.00 3.46
2755 2940 1.931172 CATTCCCGAATGGTGACGTAC 59.069 52.381 9.19 0.00 43.25 3.67
2802 2987 7.361201 GCACTGAAAAATGCTCATTACTAGTGA 60.361 37.037 20.53 0.00 38.84 3.41
2806 2991 5.709631 TGGCACTGAAAAATGCTCATTACTA 59.290 36.000 0.00 0.00 41.74 1.82
2847 3032 0.107017 ATACCACAGCAGGGACATGC 60.107 55.000 0.00 0.00 46.88 4.06
2897 3086 1.359833 CAGCACCTGAAAAAGCGCA 59.640 52.632 11.47 0.00 32.44 6.09
2898 3087 2.018324 GCAGCACCTGAAAAAGCGC 61.018 57.895 0.00 0.00 32.44 5.92
2899 3088 1.727022 CGCAGCACCTGAAAAAGCG 60.727 57.895 0.00 0.00 37.68 4.68
2934 3126 1.792941 GCTGCAGCAGTAGAAGTGC 59.207 57.895 33.36 3.66 44.65 4.40
3012 3204 1.002366 GCACTACGATGTTCTGCCAG 58.998 55.000 0.00 0.00 0.00 4.85
3019 3211 4.096382 GGATTTCCATTGCACTACGATGTT 59.904 41.667 0.00 0.00 38.36 2.71
3091 3285 9.616156 TGAAAACCAAACTAAAGTCTACATACA 57.384 29.630 0.00 0.00 0.00 2.29
3111 3305 5.650543 AGTTCGCCATGGAATTATGAAAAC 58.349 37.500 18.40 5.36 0.00 2.43
3140 3334 1.600636 CGCTCCTGGCAAAGACCAA 60.601 57.895 0.97 0.00 39.86 3.67
3162 3357 3.118702 CCATCACTCAACTCAGAGAGCAT 60.119 47.826 3.79 0.00 38.98 3.79
3174 3369 8.806429 ACACATAATAATCAACCATCACTCAA 57.194 30.769 0.00 0.00 0.00 3.02
3219 3414 4.728102 TGTAGCAACGGGGCGTCG 62.728 66.667 0.00 0.00 39.99 5.12
3279 3474 6.270000 TCTCACACTGGGGTTCTATATTATGG 59.730 42.308 0.00 0.00 0.00 2.74
3283 3478 6.636454 TTTCTCACACTGGGGTTCTATATT 57.364 37.500 0.00 0.00 0.00 1.28
3308 3503 8.388103 CCCATACGAAACAGAACAATAGTTTAG 58.612 37.037 0.00 0.00 38.30 1.85
3315 3510 3.009695 TCCCCCATACGAAACAGAACAAT 59.990 43.478 0.00 0.00 0.00 2.71
3332 3527 1.557099 GGGAGTGTCATTTTTCCCCC 58.443 55.000 0.00 0.00 42.88 5.40
3336 3531 5.126779 GGATAGGAGGGAGTGTCATTTTTC 58.873 45.833 0.00 0.00 0.00 2.29
3355 3550 7.015292 ACAGCCTCTAGTCAATTAATTCGGATA 59.985 37.037 0.00 0.00 0.00 2.59
3372 3567 5.105106 TCCGAATTAATTGACACAGCCTCTA 60.105 40.000 5.17 0.00 0.00 2.43
3373 3568 3.941483 CCGAATTAATTGACACAGCCTCT 59.059 43.478 5.17 0.00 0.00 3.69
3374 3569 3.938963 TCCGAATTAATTGACACAGCCTC 59.061 43.478 5.17 0.00 0.00 4.70
3376 3571 4.335315 TGATCCGAATTAATTGACACAGCC 59.665 41.667 5.17 0.00 0.00 4.85
3378 3573 6.018425 CCTCTGATCCGAATTAATTGACACAG 60.018 42.308 5.17 10.50 0.00 3.66
3379 3574 5.817296 CCTCTGATCCGAATTAATTGACACA 59.183 40.000 5.17 2.24 0.00 3.72
3380 3575 5.817816 ACCTCTGATCCGAATTAATTGACAC 59.182 40.000 5.17 0.00 0.00 3.67
3381 3576 5.989477 ACCTCTGATCCGAATTAATTGACA 58.011 37.500 5.17 0.00 0.00 3.58
3382 3577 8.608844 ATTACCTCTGATCCGAATTAATTGAC 57.391 34.615 5.17 0.00 0.00 3.18
3389 3584 8.980481 ACAATTTATTACCTCTGATCCGAATT 57.020 30.769 0.00 0.00 0.00 2.17
3390 3585 8.980481 AACAATTTATTACCTCTGATCCGAAT 57.020 30.769 0.00 0.00 0.00 3.34
3391 3586 8.801882 AAACAATTTATTACCTCTGATCCGAA 57.198 30.769 0.00 0.00 0.00 4.30
3392 3587 8.673711 CAAAACAATTTATTACCTCTGATCCGA 58.326 33.333 0.00 0.00 0.00 4.55
3393 3588 8.673711 TCAAAACAATTTATTACCTCTGATCCG 58.326 33.333 0.00 0.00 0.00 4.18
3394 3589 9.788960 GTCAAAACAATTTATTACCTCTGATCC 57.211 33.333 0.00 0.00 0.00 3.36
3395 3590 9.788960 GGTCAAAACAATTTATTACCTCTGATC 57.211 33.333 0.00 0.00 0.00 2.92
3396 3591 9.308000 TGGTCAAAACAATTTATTACCTCTGAT 57.692 29.630 0.00 0.00 31.31 2.90
3397 3592 8.573035 GTGGTCAAAACAATTTATTACCTCTGA 58.427 33.333 0.00 0.00 31.31 3.27
3398 3593 8.356657 TGTGGTCAAAACAATTTATTACCTCTG 58.643 33.333 0.00 0.00 31.31 3.35
3399 3594 8.357402 GTGTGGTCAAAACAATTTATTACCTCT 58.643 33.333 0.00 0.00 31.31 3.69
3400 3595 8.138712 TGTGTGGTCAAAACAATTTATTACCTC 58.861 33.333 0.00 0.00 31.31 3.85
3401 3596 8.012957 TGTGTGGTCAAAACAATTTATTACCT 57.987 30.769 0.00 0.00 31.31 3.08
3402 3597 8.138712 TCTGTGTGGTCAAAACAATTTATTACC 58.861 33.333 0.00 0.00 0.00 2.85
3403 3598 9.522804 TTCTGTGTGGTCAAAACAATTTATTAC 57.477 29.630 0.00 0.00 0.00 1.89
3405 3600 9.260002 GATTCTGTGTGGTCAAAACAATTTATT 57.740 29.630 0.00 0.00 0.00 1.40
3406 3601 7.872483 GGATTCTGTGTGGTCAAAACAATTTAT 59.128 33.333 0.00 0.00 0.00 1.40
3407 3602 7.206687 GGATTCTGTGTGGTCAAAACAATTTA 58.793 34.615 0.00 0.00 0.00 1.40
3408 3603 6.048509 GGATTCTGTGTGGTCAAAACAATTT 58.951 36.000 0.00 0.00 0.00 1.82
3430 3625 6.352737 GGGAGTATAATTTTCTCACACTGGGA 60.353 42.308 0.00 0.00 32.56 4.37
3453 3648 5.420409 GTTCTTATATTATGGAGCGGAGGG 58.580 45.833 0.00 0.00 0.00 4.30
3454 3649 5.103000 CGTTCTTATATTATGGAGCGGAGG 58.897 45.833 8.61 0.00 0.00 4.30
3455 3650 5.710984 ACGTTCTTATATTATGGAGCGGAG 58.289 41.667 15.75 0.00 36.89 4.63
3456 3651 5.717078 ACGTTCTTATATTATGGAGCGGA 57.283 39.130 15.75 0.00 36.89 5.54
3457 3652 6.780706 AAACGTTCTTATATTATGGAGCGG 57.219 37.500 0.00 5.21 36.89 5.52
3458 3653 8.332464 TCAAAAACGTTCTTATATTATGGAGCG 58.668 33.333 0.00 12.37 38.13 5.03
3459 3654 9.434559 GTCAAAAACGTTCTTATATTATGGAGC 57.565 33.333 0.00 0.00 0.00 4.70
3481 3676 9.537192 CGTCCCATAATAAAATACTAGTGTCAA 57.463 33.333 5.39 0.00 0.00 3.18
3482 3677 8.145767 CCGTCCCATAATAAAATACTAGTGTCA 58.854 37.037 5.39 0.00 0.00 3.58
3483 3678 8.362639 TCCGTCCCATAATAAAATACTAGTGTC 58.637 37.037 5.39 0.00 0.00 3.67
3484 3679 8.253867 TCCGTCCCATAATAAAATACTAGTGT 57.746 34.615 5.39 0.00 0.00 3.55
3485 3680 7.817962 CCTCCGTCCCATAATAAAATACTAGTG 59.182 40.741 5.39 0.00 0.00 2.74
3486 3681 7.731688 TCCTCCGTCCCATAATAAAATACTAGT 59.268 37.037 0.00 0.00 0.00 2.57
3487 3682 8.130671 TCCTCCGTCCCATAATAAAATACTAG 57.869 38.462 0.00 0.00 0.00 2.57
3488 3683 8.495160 TTCCTCCGTCCCATAATAAAATACTA 57.505 34.615 0.00 0.00 0.00 1.82
3489 3684 7.072076 ACTTCCTCCGTCCCATAATAAAATACT 59.928 37.037 0.00 0.00 0.00 2.12
3490 3685 7.222161 ACTTCCTCCGTCCCATAATAAAATAC 58.778 38.462 0.00 0.00 0.00 1.89
3491 3686 7.383156 ACTTCCTCCGTCCCATAATAAAATA 57.617 36.000 0.00 0.00 0.00 1.40
3492 3687 6.262056 ACTTCCTCCGTCCCATAATAAAAT 57.738 37.500 0.00 0.00 0.00 1.82
3493 3688 5.703730 ACTTCCTCCGTCCCATAATAAAA 57.296 39.130 0.00 0.00 0.00 1.52
3494 3689 5.901276 AGTACTTCCTCCGTCCCATAATAAA 59.099 40.000 0.00 0.00 0.00 1.40
3495 3690 5.461327 AGTACTTCCTCCGTCCCATAATAA 58.539 41.667 0.00 0.00 0.00 1.40
3496 3691 5.070823 AGTACTTCCTCCGTCCCATAATA 57.929 43.478 0.00 0.00 0.00 0.98
3497 3692 3.924922 AGTACTTCCTCCGTCCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
3498 3693 3.393426 AGTACTTCCTCCGTCCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
3499 3694 3.393426 AAGTACTTCCTCCGTCCCATA 57.607 47.619 1.12 0.00 0.00 2.74
3500 3695 2.249309 AAGTACTTCCTCCGTCCCAT 57.751 50.000 1.12 0.00 0.00 4.00
3501 3696 2.042162 AGTAAGTACTTCCTCCGTCCCA 59.958 50.000 12.39 0.00 31.13 4.37
3502 3697 2.732763 AGTAAGTACTTCCTCCGTCCC 58.267 52.381 12.39 0.00 31.13 4.46
3503 3698 4.797800 AAAGTAAGTACTTCCTCCGTCC 57.202 45.455 12.39 0.00 45.17 4.79
3504 3699 5.987953 ACAAAAAGTAAGTACTTCCTCCGTC 59.012 40.000 12.39 0.00 45.17 4.79
3505 3700 5.922053 ACAAAAAGTAAGTACTTCCTCCGT 58.078 37.500 12.39 0.00 45.17 4.69
3506 3701 6.073385 GGAACAAAAAGTAAGTACTTCCTCCG 60.073 42.308 12.39 0.00 45.17 4.63
3507 3702 6.073385 CGGAACAAAAAGTAAGTACTTCCTCC 60.073 42.308 12.39 1.06 45.17 4.30
3508 3703 6.481313 ACGGAACAAAAAGTAAGTACTTCCTC 59.519 38.462 12.39 4.45 45.17 3.71
3509 3704 6.351711 ACGGAACAAAAAGTAAGTACTTCCT 58.648 36.000 12.39 2.48 45.17 3.36
3510 3705 6.609237 ACGGAACAAAAAGTAAGTACTTCC 57.391 37.500 12.39 0.00 45.17 3.46
3511 3706 8.177013 TGAAACGGAACAAAAAGTAAGTACTTC 58.823 33.333 12.39 4.24 45.17 3.01
3513 3708 7.614124 TGAAACGGAACAAAAAGTAAGTACT 57.386 32.000 0.00 0.00 38.39 2.73
3516 3711 9.458374 CAATATGAAACGGAACAAAAAGTAAGT 57.542 29.630 0.00 0.00 0.00 2.24
3517 3712 8.911662 CCAATATGAAACGGAACAAAAAGTAAG 58.088 33.333 0.00 0.00 0.00 2.34
3518 3713 7.868415 CCCAATATGAAACGGAACAAAAAGTAA 59.132 33.333 0.00 0.00 0.00 2.24
3519 3714 7.371936 CCCAATATGAAACGGAACAAAAAGTA 58.628 34.615 0.00 0.00 0.00 2.24
3520 3715 6.220201 CCCAATATGAAACGGAACAAAAAGT 58.780 36.000 0.00 0.00 0.00 2.66
3521 3716 5.637387 CCCCAATATGAAACGGAACAAAAAG 59.363 40.000 0.00 0.00 0.00 2.27
3522 3717 5.511545 CCCCCAATATGAAACGGAACAAAAA 60.512 40.000 0.00 0.00 0.00 1.94
3523 3718 4.021016 CCCCCAATATGAAACGGAACAAAA 60.021 41.667 0.00 0.00 0.00 2.44
3524 3719 3.511934 CCCCCAATATGAAACGGAACAAA 59.488 43.478 0.00 0.00 0.00 2.83
3528 3723 2.847449 TCTCCCCCAATATGAAACGGAA 59.153 45.455 0.00 0.00 0.00 4.30
3536 3731 8.362639 CAATTTATTGTCTTCTCCCCCAATATG 58.637 37.037 0.00 0.00 31.80 1.78
3554 3749 4.393834 GCCACAACCAAACCCAATTTATT 58.606 39.130 0.00 0.00 0.00 1.40
3564 3759 1.226831 CACACGGCCACAACCAAAC 60.227 57.895 2.24 0.00 0.00 2.93
3575 3899 2.180204 AGTGCAGACAACACACGGC 61.180 57.895 0.00 0.00 40.59 5.68
3606 3930 2.042162 GAGGGAGGGGGTACGATATACA 59.958 54.545 0.00 0.00 0.00 2.29
3611 3935 2.613421 GGAGGGAGGGGGTACGAT 59.387 66.667 0.00 0.00 0.00 3.73
3618 3942 4.179599 GAGGGAGGGAGGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
3651 3988 4.207955 TCATACTCCGTCTGTGCTAGATT 58.792 43.478 0.00 0.00 37.83 2.40
3666 4003 2.232452 CAGGGACCGGATCATCATACTC 59.768 54.545 9.46 0.00 0.00 2.59
3675 4012 4.530857 CGCCACAGGGACCGGATC 62.531 72.222 9.46 1.18 35.59 3.36
3692 4029 4.290104 GCATCTCTTTCTTTCCTGATGC 57.710 45.455 9.46 9.46 45.97 3.91
3693 4030 3.311871 CGGCATCTCTTTCTTTCCTGATG 59.688 47.826 0.00 0.00 35.69 3.07
3695 4032 2.936993 GCGGCATCTCTTTCTTTCCTGA 60.937 50.000 0.00 0.00 0.00 3.86
3707 4044 3.581687 GATCTCCCCGCGGCATCTC 62.582 68.421 22.85 8.43 0.00 2.75
3734 4072 0.521735 GGCACGGAATGGACAGAAAC 59.478 55.000 0.00 0.00 0.00 2.78
3903 4314 0.537188 CCCGTAGCCACACAGAGATT 59.463 55.000 0.00 0.00 0.00 2.40
3905 4316 1.982395 CCCCGTAGCCACACAGAGA 60.982 63.158 0.00 0.00 0.00 3.10
3906 4317 2.227089 GACCCCGTAGCCACACAGAG 62.227 65.000 0.00 0.00 0.00 3.35
3919 4330 2.016393 TTATCTGCTCGCTGACCCCG 62.016 60.000 0.46 0.00 0.00 5.73
3996 4435 1.152963 CCGATTTGGTGGGGGCTAG 60.153 63.158 0.00 0.00 0.00 3.42
4016 4455 1.094785 CGGAATGGAATGGAAACGCT 58.905 50.000 0.00 0.00 0.00 5.07
4017 4456 0.525455 GCGGAATGGAATGGAAACGC 60.525 55.000 0.00 0.00 38.94 4.84
4020 4460 1.005332 TCTGGCGGAATGGAATGGAAA 59.995 47.619 0.00 0.00 0.00 3.13
4056 4496 0.041312 CACCAACCAAAACTCGCTCG 60.041 55.000 0.00 0.00 0.00 5.03
4060 4516 1.064952 GTGTCCACCAACCAAAACTCG 59.935 52.381 0.00 0.00 0.00 4.18
4081 4540 1.556564 CGTGTTCGTCTTGTGTGTCT 58.443 50.000 0.00 0.00 0.00 3.41
4082 4541 0.575390 CCGTGTTCGTCTTGTGTGTC 59.425 55.000 0.00 0.00 35.01 3.67
4086 4545 2.544359 CGCCGTGTTCGTCTTGTG 59.456 61.111 0.00 0.00 35.01 3.33
4087 4546 2.074230 TACCGCCGTGTTCGTCTTGT 62.074 55.000 0.00 0.00 35.01 3.16
4088 4547 1.372004 TACCGCCGTGTTCGTCTTG 60.372 57.895 0.00 0.00 35.01 3.02
4089 4548 1.372128 GTACCGCCGTGTTCGTCTT 60.372 57.895 0.00 0.00 35.01 3.01
4090 4549 2.256461 GTACCGCCGTGTTCGTCT 59.744 61.111 0.00 0.00 35.01 4.18
4091 4550 2.050168 TGTACCGCCGTGTTCGTC 60.050 61.111 0.00 0.00 35.01 4.20
4092 4551 1.870055 ATCTGTACCGCCGTGTTCGT 61.870 55.000 0.00 0.00 35.01 3.85
4093 4552 1.153901 ATCTGTACCGCCGTGTTCG 60.154 57.895 0.00 0.00 0.00 3.95
4094 4553 1.082117 CCATCTGTACCGCCGTGTTC 61.082 60.000 0.00 0.00 0.00 3.18
4095 4554 1.079405 CCATCTGTACCGCCGTGTT 60.079 57.895 0.00 0.00 0.00 3.32
4096 4555 2.577059 CCATCTGTACCGCCGTGT 59.423 61.111 0.00 0.00 0.00 4.49
4097 4556 2.890474 GCCATCTGTACCGCCGTG 60.890 66.667 0.00 0.00 0.00 4.94
4098 4557 4.508128 CGCCATCTGTACCGCCGT 62.508 66.667 0.00 0.00 0.00 5.68
4099 4558 4.508128 ACGCCATCTGTACCGCCG 62.508 66.667 0.00 0.00 0.00 6.46
4100 4559 2.585247 GACGCCATCTGTACCGCC 60.585 66.667 0.00 0.00 0.00 6.13
4101 4560 2.585247 GGACGCCATCTGTACCGC 60.585 66.667 0.00 0.00 0.00 5.68
4102 4561 2.106332 GGGACGCCATCTGTACCG 59.894 66.667 0.00 0.00 28.74 4.02
4103 4562 2.504519 GGGGACGCCATCTGTACC 59.495 66.667 3.14 0.00 39.81 3.34
4118 4577 4.180946 CAGAGCGACGAGGACGGG 62.181 72.222 0.00 0.00 44.46 5.28
4121 4580 2.101380 GAGCAGAGCGACGAGGAC 59.899 66.667 0.00 0.00 0.00 3.85
4237 4696 1.820056 GGAGAAAAGGCCTAGGCGC 60.820 63.158 27.24 19.43 43.06 6.53
4240 4699 0.840617 GGGAGGAGAAAAGGCCTAGG 59.159 60.000 5.16 3.67 33.84 3.02
4242 4701 1.625508 GGAGGGAGGAGAAAAGGCCTA 60.626 57.143 5.16 0.00 33.84 3.93


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

AutoCloner maintained by Alex Coulton.