Multiple sequence alignment - TraesCS2D01G475800

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 TraesCS2D01G475800 chr2D 100.000 3491 0 0 1 3491 578335363 578331873 0.000000e+00 6447.0
1 TraesCS2D01G475800 chr2D 96.136 1527 36 6 1 1525 578369269 578367764 0.000000e+00 2471.0
2 TraesCS2D01G475800 chr2D 95.098 1530 27 12 3 1525 578350683 578349195 0.000000e+00 2366.0
3 TraesCS2D01G475800 chr2B 93.014 1918 83 13 808 2710 793893951 793895832 0.000000e+00 2752.0
4 TraesCS2D01G475800 chr2B 82.563 757 114 16 4 753 776660107 776659362 0.000000e+00 651.0
5 TraesCS2D01G475800 chr2B 92.771 166 9 2 2942 3105 793899615 793899779 1.620000e-58 237.0
6 TraesCS2D01G475800 chr2B 93.651 126 7 1 2748 2873 793895837 793895961 1.650000e-43 187.0
7 TraesCS2D01G475800 chr2B 75.954 262 50 8 2719 2978 793277597 793277347 4.730000e-24 122.0
8 TraesCS2D01G475800 chr2B 97.826 46 1 0 2898 2943 793895964 793896009 2.890000e-11 80.5
9 TraesCS2D01G475800 chr3A 80.338 1419 244 22 1031 2436 641172317 641170921 0.000000e+00 1042.0
10 TraesCS2D01G475800 chr3A 78.928 1381 223 29 1029 2397 641638949 641640273 0.000000e+00 876.0
11 TraesCS2D01G475800 chr3A 87.273 330 26 8 3167 3491 714876615 714876933 2.560000e-96 363.0
12 TraesCS2D01G475800 chr3A 89.189 148 13 3 3347 3491 278850810 278850957 7.700000e-42 182.0
13 TraesCS2D01G475800 chr3A 76.628 261 48 8 2724 2982 83238896 83239145 7.860000e-27 132.0
14 TraesCS2D01G475800 chr3A 83.871 93 7 6 2477 2567 720370649 720370563 8.030000e-12 82.4
15 TraesCS2D01G475800 chr3B 79.930 1425 244 22 1029 2438 663086542 663085145 0.000000e+00 1009.0
16 TraesCS2D01G475800 chr3B 80.072 1380 241 19 1029 2397 663037797 663039153 0.000000e+00 994.0
17 TraesCS2D01G475800 chr3B 83.451 284 25 12 3211 3491 757471405 757471141 9.680000e-61 244.0
18 TraesCS2D01G475800 chr3B 84.932 146 13 5 3230 3375 757471546 757471410 4.700000e-29 139.0
19 TraesCS2D01G475800 chr3B 91.071 56 0 2 3121 3175 43783427 43783376 1.740000e-08 71.3
20 TraesCS2D01G475800 chr3D 79.817 1422 251 20 1029 2438 501478701 501477304 0.000000e+00 1003.0
21 TraesCS2D01G475800 chr3D 79.775 1424 248 21 1029 2438 501790691 501789294 0.000000e+00 998.0
22 TraesCS2D01G475800 chr3D 79.381 1421 259 19 1029 2438 501512965 501511568 0.000000e+00 970.0
23 TraesCS2D01G475800 chr7D 77.530 1433 269 34 1029 2439 40033352 40031951 0.000000e+00 813.0
24 TraesCS2D01G475800 chr7D 84.367 742 94 18 1 734 34493040 34493767 0.000000e+00 708.0
25 TraesCS2D01G475800 chr7D 83.038 790 106 21 1 781 381345956 381346726 0.000000e+00 691.0
26 TraesCS2D01G475800 chr6B 77.452 1397 289 15 1046 2438 11246658 11245284 0.000000e+00 811.0
27 TraesCS2D01G475800 chr6B 96.970 33 0 1 767 798 715648226 715648194 2.000000e-03 54.7
28 TraesCS2D01G475800 chr6D 83.712 792 104 20 2 785 440591407 440592181 0.000000e+00 725.0
29 TraesCS2D01G475800 chr7A 83.755 751 100 14 1 740 429473988 429474727 0.000000e+00 691.0
30 TraesCS2D01G475800 chr7A 87.879 330 25 7 3167 3491 115307220 115307539 1.180000e-99 374.0
31 TraesCS2D01G475800 chrUn 83.377 764 98 25 3 757 7637347 7636604 0.000000e+00 680.0
32 TraesCS2D01G475800 chr5A 83.198 738 102 16 64 795 428993508 428994229 0.000000e+00 656.0
33 TraesCS2D01G475800 chr6A 87.879 330 25 7 3167 3491 169250636 169250317 1.180000e-99 374.0
34 TraesCS2D01G475800 chr6A 97.619 42 1 0 3113 3154 54080984 54081025 4.830000e-09 73.1
35 TraesCS2D01G475800 chr4A 87.879 330 25 7 3167 3491 708998866 708998547 1.180000e-99 374.0
36 TraesCS2D01G475800 chr4A 74.906 267 52 12 2718 2982 564953370 564953117 1.330000e-19 108.0
37 TraesCS2D01G475800 chr5B 86.689 293 27 6 3202 3491 605797895 605797612 7.270000e-82 315.0
38 TraesCS2D01G475800 chr5B 89.865 148 12 3 3347 3491 253154328 253154181 1.650000e-43 187.0
39 TraesCS2D01G475800 chr5B 97.619 42 1 0 3113 3154 253154466 253154425 4.830000e-09 73.1
40 TraesCS2D01G475800 chr5B 97.619 42 1 0 3113 3154 605797959 605797918 4.830000e-09 73.1
41 TraesCS2D01G475800 chr5B 91.071 56 0 2 3121 3175 20043780 20043729 1.740000e-08 71.3
42 TraesCS2D01G475800 chr4D 92.593 135 7 3 3359 3491 267247378 267247245 1.280000e-44 191.0
43 TraesCS2D01G475800 chr4D 86.047 172 15 3 3193 3362 267259354 267259190 3.580000e-40 176.0
44 TraesCS2D01G475800 chr4D 97.619 42 1 0 3113 3154 267259407 267259366 4.830000e-09 73.1
45 TraesCS2D01G475800 chr4D 100.000 32 0 0 2854 2885 346380774 346380805 3.760000e-05 60.2
46 TraesCS2D01G475800 chr1A 88.966 145 13 3 3350 3491 273194543 273194399 3.580000e-40 176.0
47 TraesCS2D01G475800 chr1B 92.661 109 4 3 3167 3272 679242259 679242366 1.680000e-33 154.0
48 TraesCS2D01G475800 chr2A 75.191 262 56 5 2716 2975 66580573 66580319 7.920000e-22 115.0
49 TraesCS2D01G475800 chr4B 100.000 32 0 0 2854 2885 427409430 427409461 3.760000e-05 60.2


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 TraesCS2D01G475800 chr2D 578331873 578335363 3490 True 6447.000 6447 100.0000 1 3491 1 chr2D.!!$R1 3490
1 TraesCS2D01G475800 chr2D 578367764 578369269 1505 True 2471.000 2471 96.1360 1 1525 1 chr2D.!!$R3 1524
2 TraesCS2D01G475800 chr2D 578349195 578350683 1488 True 2366.000 2366 95.0980 3 1525 1 chr2D.!!$R2 1522
3 TraesCS2D01G475800 chr2B 793893951 793899779 5828 False 814.125 2752 94.3155 808 3105 4 chr2B.!!$F1 2297
4 TraesCS2D01G475800 chr2B 776659362 776660107 745 True 651.000 651 82.5630 4 753 1 chr2B.!!$R1 749
5 TraesCS2D01G475800 chr3A 641170921 641172317 1396 True 1042.000 1042 80.3380 1031 2436 1 chr3A.!!$R1 1405
6 TraesCS2D01G475800 chr3A 641638949 641640273 1324 False 876.000 876 78.9280 1029 2397 1 chr3A.!!$F3 1368
7 TraesCS2D01G475800 chr3B 663085145 663086542 1397 True 1009.000 1009 79.9300 1029 2438 1 chr3B.!!$R2 1409
8 TraesCS2D01G475800 chr3B 663037797 663039153 1356 False 994.000 994 80.0720 1029 2397 1 chr3B.!!$F1 1368
9 TraesCS2D01G475800 chr3D 501477304 501478701 1397 True 1003.000 1003 79.8170 1029 2438 1 chr3D.!!$R1 1409
10 TraesCS2D01G475800 chr3D 501789294 501790691 1397 True 998.000 998 79.7750 1029 2438 1 chr3D.!!$R3 1409
11 TraesCS2D01G475800 chr3D 501511568 501512965 1397 True 970.000 970 79.3810 1029 2438 1 chr3D.!!$R2 1409
12 TraesCS2D01G475800 chr7D 40031951 40033352 1401 True 813.000 813 77.5300 1029 2439 1 chr7D.!!$R1 1410
13 TraesCS2D01G475800 chr7D 34493040 34493767 727 False 708.000 708 84.3670 1 734 1 chr7D.!!$F1 733
14 TraesCS2D01G475800 chr7D 381345956 381346726 770 False 691.000 691 83.0380 1 781 1 chr7D.!!$F2 780
15 TraesCS2D01G475800 chr6B 11245284 11246658 1374 True 811.000 811 77.4520 1046 2438 1 chr6B.!!$R1 1392
16 TraesCS2D01G475800 chr6D 440591407 440592181 774 False 725.000 725 83.7120 2 785 1 chr6D.!!$F1 783
17 TraesCS2D01G475800 chr7A 429473988 429474727 739 False 691.000 691 83.7550 1 740 1 chr7A.!!$F2 739
18 TraesCS2D01G475800 chrUn 7636604 7637347 743 True 680.000 680 83.3770 3 757 1 chrUn.!!$R1 754
19 TraesCS2D01G475800 chr5A 428993508 428994229 721 False 656.000 656 83.1980 64 795 1 chr5A.!!$F1 731

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
536 549 2.857748 GTGGTTCTTGTTTTCTTTGGCG 59.142 45.455 0.0 0.0 0.00 5.69 F
1441 1470 1.553690 TTTCCTCTTCTCAGGCGGGG 61.554 60.000 0.0 0.0 32.91 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2327 0.179084 ATGGTCGCCTTCATACCGTG 60.179 55.0 0.00 0.00 35.98 4.94 R
2808 2869 0.109272 TCGAGCGCTCACCACTAAAG 60.109 55.0 34.69 16.44 0.00 1.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
434 446 5.923204 TCAAGAAGCCAATAGAGAGAATCC 58.077 41.667 0.00 0.00 33.66 3.01
536 549 2.857748 GTGGTTCTTGTTTTCTTTGGCG 59.142 45.455 0.00 0.00 0.00 5.69
1441 1470 1.553690 TTTCCTCTTCTCAGGCGGGG 61.554 60.000 0.00 0.00 32.91 5.73
1442 1471 3.474570 CCTCTTCTCAGGCGGGGG 61.475 72.222 0.00 0.00 0.00 5.40
1443 1472 4.168291 CTCTTCTCAGGCGGGGGC 62.168 72.222 0.00 0.00 0.00 5.80
1656 1694 2.180204 CCGCATCATCCCAACGTCC 61.180 63.158 0.00 0.00 0.00 4.79
1968 2006 2.113433 CATGGACTGCTGCTGCCTC 61.113 63.158 13.47 7.40 38.71 4.70
2004 2043 2.125512 CAGCTTACCTCCGCGCTT 60.126 61.111 5.56 0.00 0.00 4.68
2027 2066 3.764434 TCCATCACTTCAGAGTACCTCAC 59.236 47.826 0.00 0.00 33.90 3.51
2031 2070 2.755655 CACTTCAGAGTACCTCACCGAT 59.244 50.000 0.00 0.00 33.90 4.18
2247 2295 2.125106 GTCGCGCCCAGGAGATTT 60.125 61.111 0.00 0.00 0.00 2.17
2397 2448 2.159747 GGACAACAAGTTCGTTATCCGC 60.160 50.000 1.46 0.00 33.05 5.54
2400 2451 2.005971 ACAAGTTCGTTATCCGCCTC 57.994 50.000 0.00 0.00 36.19 4.70
2454 2505 1.136057 GTCCGAAACGCATTTCACCTC 60.136 52.381 6.04 0.00 43.90 3.85
2459 2510 2.198827 AACGCATTTCACCTCATCCA 57.801 45.000 0.00 0.00 0.00 3.41
2469 2520 5.209318 TTCACCTCATCCAGGAGAAAGCC 62.209 52.174 0.00 0.00 45.88 4.35
2473 2524 0.394899 CATCCAGGAGAAAGCCACCC 60.395 60.000 0.00 0.00 0.00 4.61
2482 2533 3.017442 GAGAAAGCCACCCAAATACTCC 58.983 50.000 0.00 0.00 0.00 3.85
2487 2538 1.295020 CCACCCAAATACTCCCTCCA 58.705 55.000 0.00 0.00 0.00 3.86
2505 2561 8.239038 TCCCTCCATAGAAATATATAAGAGCG 57.761 38.462 0.00 0.00 0.00 5.03
2558 2619 5.530171 ACGCTCTTATATTTCCGTACAGAGA 59.470 40.000 5.52 0.00 0.00 3.10
2564 2625 1.183549 TTTCCGTACAGAGAGGGAGC 58.816 55.000 0.00 0.00 34.94 4.70
2568 2629 0.965866 CGTACAGAGAGGGAGCACCA 60.966 60.000 1.58 0.00 43.89 4.17
2580 2641 2.093869 GGGAGCACCACGTGACTAATAA 60.094 50.000 19.30 0.00 39.85 1.40
2593 2654 9.443283 CACGTGACTAATAATAGTACTTGTACC 57.557 37.037 10.90 0.00 42.47 3.34
2596 2657 9.140874 GTGACTAATAATAGTACTTGTACCCCT 57.859 37.037 0.00 0.00 42.47 4.79
2625 2686 0.481567 AATAGCCATGCCTCATGCCT 59.518 50.000 1.47 0.00 40.20 4.75
2630 2691 1.315690 CCATGCCTCATGCCTTACTG 58.684 55.000 1.47 0.00 40.20 2.74
2644 2705 5.412640 TGCCTTACTGCAAAATCAATCATG 58.587 37.500 0.00 0.00 38.56 3.07
2694 2755 2.229675 TGTCTCTATCGCCTTGCATG 57.770 50.000 0.00 0.00 0.00 4.06
2703 2764 0.600782 CGCCTTGCATGTTTGGCTTT 60.601 50.000 17.94 0.00 42.90 3.51
2710 2771 1.403249 GCATGTTTGGCTTTCGCATCT 60.403 47.619 0.00 0.00 38.10 2.90
2711 2772 2.927871 GCATGTTTGGCTTTCGCATCTT 60.928 45.455 0.00 0.00 38.10 2.40
2712 2773 3.673052 GCATGTTTGGCTTTCGCATCTTA 60.673 43.478 0.00 0.00 38.10 2.10
2713 2774 4.675510 CATGTTTGGCTTTCGCATCTTAT 58.324 39.130 0.00 0.00 38.10 1.73
2715 2776 4.009675 TGTTTGGCTTTCGCATCTTATCT 58.990 39.130 0.00 0.00 38.10 1.98
2717 2778 5.822519 TGTTTGGCTTTCGCATCTTATCTAT 59.177 36.000 0.00 0.00 38.10 1.98
2718 2779 6.989759 TGTTTGGCTTTCGCATCTTATCTATA 59.010 34.615 0.00 0.00 38.10 1.31
2720 2781 7.834068 TTGGCTTTCGCATCTTATCTATATC 57.166 36.000 0.00 0.00 38.10 1.63
2721 2782 7.175347 TGGCTTTCGCATCTTATCTATATCT 57.825 36.000 0.00 0.00 38.10 1.98
2722 2783 8.293699 TGGCTTTCGCATCTTATCTATATCTA 57.706 34.615 0.00 0.00 38.10 1.98
2723 2784 8.918116 TGGCTTTCGCATCTTATCTATATCTAT 58.082 33.333 0.00 0.00 38.10 1.98
2797 2858 5.518487 GCCATTAAACCATGTTAATCCAACG 59.482 40.000 0.00 0.00 40.26 4.10
2807 2868 8.647796 ACCATGTTAATCCAACGATCTAGATTA 58.352 33.333 6.70 0.00 40.26 1.75
2808 2869 8.926710 CCATGTTAATCCAACGATCTAGATTAC 58.073 37.037 6.70 0.00 40.26 1.89
2851 2912 7.464830 ACATGTTCAGCGTGTAATTAGTATC 57.535 36.000 0.00 0.00 44.85 2.24
2873 2934 9.450807 GTATCAACCAAATATCAACTTATGTGC 57.549 33.333 0.00 0.00 0.00 4.57
2875 2936 8.800370 TCAACCAAATATCAACTTATGTGCTA 57.200 30.769 0.00 0.00 0.00 3.49
2876 2937 9.237187 TCAACCAAATATCAACTTATGTGCTAA 57.763 29.630 0.00 0.00 0.00 3.09
2879 2940 9.407380 ACCAAATATCAACTTATGTGCTAATCA 57.593 29.630 0.00 0.00 0.00 2.57
2880 2941 9.669353 CCAAATATCAACTTATGTGCTAATCAC 57.331 33.333 0.00 0.00 45.82 3.06
2955 6623 8.648557 TTCTTCTCTAATATCAACGTCCATTG 57.351 34.615 0.00 0.00 0.00 2.82
2960 6628 2.371910 TATCAACGTCCATTGCACGA 57.628 45.000 7.21 0.00 39.75 4.35
2981 6649 7.324375 GCACGAACGCATTTACTAGTATATACA 59.676 37.037 15.18 0.94 0.00 2.29
2984 6652 8.019669 CGAACGCATTTACTAGTATATACAGGT 58.980 37.037 15.18 13.85 0.00 4.00
3046 6714 3.844211 TGGTAAACTATGCCTGTCCTTCT 59.156 43.478 0.00 0.00 34.34 2.85
3048 6716 3.356529 AAACTATGCCTGTCCTTCTGG 57.643 47.619 0.00 0.00 38.06 3.86
3055 6723 0.761802 CCTGTCCTTCTGGCCTATCC 59.238 60.000 3.32 0.00 0.00 2.59
3056 6724 1.500474 CTGTCCTTCTGGCCTATCCA 58.500 55.000 3.32 0.00 44.18 3.41
3062 6730 0.178068 TTCTGGCCTATCCAACGCTC 59.822 55.000 3.32 0.00 46.01 5.03
3097 6765 4.742201 CTGGCCAGTACGCGCTGT 62.742 66.667 25.53 8.05 34.84 4.40
3098 6766 3.350909 CTGGCCAGTACGCGCTGTA 62.351 63.158 25.53 6.93 34.84 2.74
3099 6767 2.125832 GGCCAGTACGCGCTGTAA 60.126 61.111 5.73 0.00 34.07 2.41
3100 6768 2.450345 GGCCAGTACGCGCTGTAAC 61.450 63.158 5.73 5.12 34.07 2.50
3101 6769 2.450345 GCCAGTACGCGCTGTAACC 61.450 63.158 5.73 0.00 34.07 2.85
3103 6771 2.156446 CAGTACGCGCTGTAACCCG 61.156 63.158 5.73 0.00 34.07 5.28
3104 6772 2.179018 GTACGCGCTGTAACCCGA 59.821 61.111 5.73 0.00 34.07 5.14
3105 6773 1.226773 GTACGCGCTGTAACCCGAT 60.227 57.895 5.73 0.00 34.07 4.18
3106 6774 1.226745 TACGCGCTGTAACCCGATG 60.227 57.895 5.73 0.00 0.00 3.84
3107 6775 2.616786 TACGCGCTGTAACCCGATGG 62.617 60.000 5.73 0.00 37.80 3.51
3108 6776 3.573491 GCGCTGTAACCCGATGGC 61.573 66.667 0.00 0.00 33.59 4.40
3109 6777 2.186903 CGCTGTAACCCGATGGCT 59.813 61.111 0.00 0.00 33.59 4.75
3110 6778 1.440060 CGCTGTAACCCGATGGCTA 59.560 57.895 0.00 0.00 33.59 3.93
3111 6779 0.033504 CGCTGTAACCCGATGGCTAT 59.966 55.000 0.00 0.00 33.59 2.97
3112 6780 1.512926 GCTGTAACCCGATGGCTATG 58.487 55.000 0.00 0.00 33.59 2.23
3113 6781 1.202651 GCTGTAACCCGATGGCTATGT 60.203 52.381 0.00 0.00 33.59 2.29
3114 6782 2.036733 GCTGTAACCCGATGGCTATGTA 59.963 50.000 0.00 0.00 33.59 2.29
3115 6783 3.861131 GCTGTAACCCGATGGCTATGTAG 60.861 52.174 0.00 0.00 33.59 2.74
3116 6784 3.302161 TGTAACCCGATGGCTATGTAGT 58.698 45.455 0.00 0.00 33.59 2.73
3117 6785 3.707611 TGTAACCCGATGGCTATGTAGTT 59.292 43.478 0.00 0.00 33.59 2.24
3118 6786 4.894705 TGTAACCCGATGGCTATGTAGTTA 59.105 41.667 0.00 0.00 33.59 2.24
3119 6787 4.602340 AACCCGATGGCTATGTAGTTAG 57.398 45.455 0.00 0.00 33.59 2.34
3120 6788 2.897969 ACCCGATGGCTATGTAGTTAGG 59.102 50.000 0.00 0.00 33.59 2.69
3121 6789 2.233922 CCCGATGGCTATGTAGTTAGGG 59.766 54.545 0.00 0.00 0.00 3.53
3122 6790 3.162666 CCGATGGCTATGTAGTTAGGGA 58.837 50.000 0.00 0.00 0.00 4.20
3123 6791 3.769844 CCGATGGCTATGTAGTTAGGGAT 59.230 47.826 0.00 0.00 0.00 3.85
3124 6792 4.223032 CCGATGGCTATGTAGTTAGGGATT 59.777 45.833 0.00 0.00 0.00 3.01
3125 6793 5.421056 CCGATGGCTATGTAGTTAGGGATTA 59.579 44.000 0.00 0.00 0.00 1.75
3126 6794 6.331061 CGATGGCTATGTAGTTAGGGATTAC 58.669 44.000 0.00 0.00 0.00 1.89
3127 6795 6.622427 ATGGCTATGTAGTTAGGGATTACC 57.378 41.667 0.00 0.00 40.67 2.85
3128 6796 5.469579 TGGCTATGTAGTTAGGGATTACCA 58.530 41.667 0.00 0.00 43.89 3.25
3129 6797 6.088819 TGGCTATGTAGTTAGGGATTACCAT 58.911 40.000 0.00 0.00 43.89 3.55
3130 6798 6.212791 TGGCTATGTAGTTAGGGATTACCATC 59.787 42.308 0.00 0.00 43.89 3.51
3131 6799 6.212791 GGCTATGTAGTTAGGGATTACCATCA 59.787 42.308 0.00 0.00 43.89 3.07
3132 6800 7.097834 GCTATGTAGTTAGGGATTACCATCAC 58.902 42.308 0.00 0.00 43.89 3.06
3133 6801 5.524971 TGTAGTTAGGGATTACCATCACG 57.475 43.478 0.00 0.00 43.89 4.35
3134 6802 4.957954 TGTAGTTAGGGATTACCATCACGT 59.042 41.667 0.00 0.00 43.89 4.49
3135 6803 6.128486 TGTAGTTAGGGATTACCATCACGTA 58.872 40.000 0.00 0.00 43.89 3.57
3136 6804 5.526506 AGTTAGGGATTACCATCACGTAC 57.473 43.478 0.00 0.00 43.89 3.67
3137 6805 4.957954 AGTTAGGGATTACCATCACGTACA 59.042 41.667 0.00 0.00 43.89 2.90
3138 6806 5.068723 AGTTAGGGATTACCATCACGTACAG 59.931 44.000 0.00 0.00 43.89 2.74
3139 6807 3.371965 AGGGATTACCATCACGTACAGT 58.628 45.455 0.00 0.00 43.89 3.55
3140 6808 3.773119 AGGGATTACCATCACGTACAGTT 59.227 43.478 0.00 0.00 43.89 3.16
3141 6809 4.224370 AGGGATTACCATCACGTACAGTTT 59.776 41.667 0.00 0.00 43.89 2.66
3142 6810 4.939439 GGGATTACCATCACGTACAGTTTT 59.061 41.667 0.00 0.00 39.85 2.43
3143 6811 5.064325 GGGATTACCATCACGTACAGTTTTC 59.936 44.000 0.00 0.00 39.85 2.29
3144 6812 5.064325 GGATTACCATCACGTACAGTTTTCC 59.936 44.000 0.00 0.00 35.97 3.13
3145 6813 3.764237 ACCATCACGTACAGTTTTCCT 57.236 42.857 0.00 0.00 0.00 3.36
3146 6814 4.081322 ACCATCACGTACAGTTTTCCTT 57.919 40.909 0.00 0.00 0.00 3.36
3147 6815 5.217978 ACCATCACGTACAGTTTTCCTTA 57.782 39.130 0.00 0.00 0.00 2.69
3148 6816 5.613329 ACCATCACGTACAGTTTTCCTTAA 58.387 37.500 0.00 0.00 0.00 1.85
3149 6817 6.056884 ACCATCACGTACAGTTTTCCTTAAA 58.943 36.000 0.00 0.00 0.00 1.52
3150 6818 6.543100 ACCATCACGTACAGTTTTCCTTAAAA 59.457 34.615 0.00 0.00 32.15 1.52
3151 6819 7.229907 ACCATCACGTACAGTTTTCCTTAAAAT 59.770 33.333 0.00 0.00 36.96 1.82
3152 6820 8.723311 CCATCACGTACAGTTTTCCTTAAAATA 58.277 33.333 0.00 0.00 36.96 1.40
3187 6855 8.960064 ACTCCAATTATATTAGGGATGAAACCT 58.040 33.333 0.00 0.00 42.15 3.50
3188 6856 9.236006 CTCCAATTATATTAGGGATGAAACCTG 57.764 37.037 0.00 0.00 39.12 4.00
3189 6857 8.732854 TCCAATTATATTAGGGATGAAACCTGT 58.267 33.333 0.00 0.00 39.12 4.00
3197 6865 8.742125 ATTAGGGATGAAACCTGTATATCTCA 57.258 34.615 0.00 0.00 39.12 3.27
3198 6866 6.678568 AGGGATGAAACCTGTATATCTCAG 57.321 41.667 0.00 2.08 36.85 3.35
3199 6867 5.012561 AGGGATGAAACCTGTATATCTCAGC 59.987 44.000 0.00 0.00 36.85 4.26
3200 6868 4.926238 GGATGAAACCTGTATATCTCAGCG 59.074 45.833 3.23 0.00 0.00 5.18
3201 6869 3.717707 TGAAACCTGTATATCTCAGCGC 58.282 45.455 0.00 0.00 0.00 5.92
3202 6870 3.132111 TGAAACCTGTATATCTCAGCGCA 59.868 43.478 11.47 0.00 0.00 6.09
3203 6871 3.377346 AACCTGTATATCTCAGCGCAG 57.623 47.619 11.47 0.00 0.00 5.18
3204 6872 2.311463 ACCTGTATATCTCAGCGCAGT 58.689 47.619 11.47 0.00 0.00 4.40
3205 6873 3.487372 ACCTGTATATCTCAGCGCAGTA 58.513 45.455 11.47 0.00 0.00 2.74
3206 6874 3.889538 ACCTGTATATCTCAGCGCAGTAA 59.110 43.478 11.47 0.00 0.00 2.24
3207 6875 4.341235 ACCTGTATATCTCAGCGCAGTAAA 59.659 41.667 11.47 0.00 0.00 2.01
3208 6876 5.163447 ACCTGTATATCTCAGCGCAGTAAAA 60.163 40.000 11.47 0.00 0.00 1.52
3209 6877 5.753438 CCTGTATATCTCAGCGCAGTAAAAA 59.247 40.000 11.47 0.00 0.00 1.94
3241 6909 7.944729 GTCCATTACCATCCATGCTTAATAT 57.055 36.000 0.00 0.00 0.00 1.28
3242 6910 7.765307 GTCCATTACCATCCATGCTTAATATG 58.235 38.462 0.00 0.00 0.00 1.78
3243 6911 7.394359 GTCCATTACCATCCATGCTTAATATGT 59.606 37.037 0.00 0.00 0.00 2.29
3244 6912 7.949565 TCCATTACCATCCATGCTTAATATGTT 59.050 33.333 0.00 0.00 0.00 2.71
3245 6913 9.241919 CCATTACCATCCATGCTTAATATGTTA 57.758 33.333 0.00 0.00 0.00 2.41
3275 6943 7.334574 GTAATACATTACTACATGTCTGGCG 57.665 40.000 0.00 0.00 39.53 5.69
3276 6944 5.784578 ATACATTACTACATGTCTGGCGA 57.215 39.130 0.00 0.00 38.40 5.54
3277 6945 4.465632 ACATTACTACATGTCTGGCGAA 57.534 40.909 0.00 0.00 31.26 4.70
3278 6946 4.433615 ACATTACTACATGTCTGGCGAAG 58.566 43.478 0.00 0.00 31.26 3.79
3279 6947 3.520290 TTACTACATGTCTGGCGAAGG 57.480 47.619 0.00 0.00 0.00 3.46
3280 6948 1.267121 ACTACATGTCTGGCGAAGGT 58.733 50.000 0.00 0.00 0.00 3.50
3281 6949 1.623811 ACTACATGTCTGGCGAAGGTT 59.376 47.619 0.00 0.00 0.00 3.50
3282 6950 2.038557 ACTACATGTCTGGCGAAGGTTT 59.961 45.455 0.00 0.00 0.00 3.27
3283 6951 1.981256 ACATGTCTGGCGAAGGTTTT 58.019 45.000 0.00 0.00 0.00 2.43
3284 6952 3.134574 ACATGTCTGGCGAAGGTTTTA 57.865 42.857 0.00 0.00 0.00 1.52
3285 6953 2.812011 ACATGTCTGGCGAAGGTTTTAC 59.188 45.455 0.00 0.00 0.00 2.01
3286 6954 2.922740 TGTCTGGCGAAGGTTTTACT 57.077 45.000 0.00 0.00 0.00 2.24
3287 6955 4.250464 CATGTCTGGCGAAGGTTTTACTA 58.750 43.478 0.00 0.00 0.00 1.82
3288 6956 4.546829 TGTCTGGCGAAGGTTTTACTAT 57.453 40.909 0.00 0.00 0.00 2.12
3289 6957 5.664294 TGTCTGGCGAAGGTTTTACTATA 57.336 39.130 0.00 0.00 0.00 1.31
3290 6958 6.229936 TGTCTGGCGAAGGTTTTACTATAT 57.770 37.500 0.00 0.00 0.00 0.86
3291 6959 6.646267 TGTCTGGCGAAGGTTTTACTATATT 58.354 36.000 0.00 0.00 0.00 1.28
3292 6960 7.107542 TGTCTGGCGAAGGTTTTACTATATTT 58.892 34.615 0.00 0.00 0.00 1.40
3293 6961 8.259411 TGTCTGGCGAAGGTTTTACTATATTTA 58.741 33.333 0.00 0.00 0.00 1.40
3294 6962 9.269453 GTCTGGCGAAGGTTTTACTATATTTAT 57.731 33.333 0.00 0.00 0.00 1.40
3322 6990 8.888836 TTAGGGATATAACCATCGATAACTCA 57.111 34.615 0.00 0.00 0.00 3.41
3323 6991 7.792364 AGGGATATAACCATCGATAACTCAA 57.208 36.000 0.00 0.00 0.00 3.02
3324 6992 8.380742 AGGGATATAACCATCGATAACTCAAT 57.619 34.615 0.00 0.00 0.00 2.57
3325 6993 8.260818 AGGGATATAACCATCGATAACTCAATG 58.739 37.037 0.00 0.00 0.00 2.82
3326 6994 7.011482 GGGATATAACCATCGATAACTCAATGC 59.989 40.741 0.00 0.00 0.00 3.56
3327 6995 7.011482 GGATATAACCATCGATAACTCAATGCC 59.989 40.741 0.00 0.00 0.00 4.40
3328 6996 2.483876 ACCATCGATAACTCAATGCCG 58.516 47.619 0.00 0.00 0.00 5.69
3329 6997 1.800586 CCATCGATAACTCAATGCCGG 59.199 52.381 0.00 0.00 0.00 6.13
3330 6998 2.483876 CATCGATAACTCAATGCCGGT 58.516 47.619 1.90 0.00 0.00 5.28
3331 6999 3.554129 CCATCGATAACTCAATGCCGGTA 60.554 47.826 1.90 0.00 0.00 4.02
3332 7000 3.804786 TCGATAACTCAATGCCGGTAA 57.195 42.857 1.90 0.00 0.00 2.85
3333 7001 4.126208 TCGATAACTCAATGCCGGTAAA 57.874 40.909 1.90 0.00 0.00 2.01
3334 7002 4.505808 TCGATAACTCAATGCCGGTAAAA 58.494 39.130 1.90 0.00 0.00 1.52
3335 7003 4.569162 TCGATAACTCAATGCCGGTAAAAG 59.431 41.667 1.90 0.06 0.00 2.27
3336 7004 4.569162 CGATAACTCAATGCCGGTAAAAGA 59.431 41.667 1.90 0.00 0.00 2.52
3337 7005 5.064198 CGATAACTCAATGCCGGTAAAAGAA 59.936 40.000 1.90 0.00 0.00 2.52
3338 7006 6.402766 CGATAACTCAATGCCGGTAAAAGAAA 60.403 38.462 1.90 0.00 0.00 2.52
3339 7007 5.523438 AACTCAATGCCGGTAAAAGAAAA 57.477 34.783 1.90 0.00 0.00 2.29
3340 7008 5.722021 ACTCAATGCCGGTAAAAGAAAAT 57.278 34.783 1.90 0.00 0.00 1.82
3341 7009 6.827586 ACTCAATGCCGGTAAAAGAAAATA 57.172 33.333 1.90 0.00 0.00 1.40
3342 7010 6.852664 ACTCAATGCCGGTAAAAGAAAATAG 58.147 36.000 1.90 0.00 0.00 1.73
3343 7011 6.127730 ACTCAATGCCGGTAAAAGAAAATAGG 60.128 38.462 1.90 0.00 0.00 2.57
3344 7012 5.712917 TCAATGCCGGTAAAAGAAAATAGGT 59.287 36.000 1.90 0.00 0.00 3.08
3345 7013 6.209788 TCAATGCCGGTAAAAGAAAATAGGTT 59.790 34.615 1.90 0.00 0.00 3.50
3346 7014 6.599356 ATGCCGGTAAAAGAAAATAGGTTT 57.401 33.333 1.90 0.00 0.00 3.27
3347 7015 7.706100 ATGCCGGTAAAAGAAAATAGGTTTA 57.294 32.000 1.90 0.00 0.00 2.01
3348 7016 7.706100 TGCCGGTAAAAGAAAATAGGTTTAT 57.294 32.000 1.90 0.00 0.00 1.40
3349 7017 8.124808 TGCCGGTAAAAGAAAATAGGTTTATT 57.875 30.769 1.90 0.00 31.96 1.40
3350 7018 9.240734 TGCCGGTAAAAGAAAATAGGTTTATTA 57.759 29.630 1.90 0.00 30.47 0.98
3351 7019 9.507280 GCCGGTAAAAGAAAATAGGTTTATTAC 57.493 33.333 1.90 0.00 30.47 1.89
3389 7057 8.627208 ATCTATTACTGGCAATGTTTAGGATG 57.373 34.615 0.00 0.00 0.00 3.51
3390 7058 7.801104 TCTATTACTGGCAATGTTTAGGATGA 58.199 34.615 0.00 0.00 0.00 2.92
3391 7059 8.271458 TCTATTACTGGCAATGTTTAGGATGAA 58.729 33.333 0.00 0.00 0.00 2.57
3392 7060 7.716799 ATTACTGGCAATGTTTAGGATGAAA 57.283 32.000 0.00 0.00 0.00 2.69
3393 7061 5.391312 ACTGGCAATGTTTAGGATGAAAC 57.609 39.130 0.00 0.00 39.35 2.78
3394 7062 4.220602 ACTGGCAATGTTTAGGATGAAACC 59.779 41.667 0.00 0.00 38.33 3.27
3395 7063 4.415596 TGGCAATGTTTAGGATGAAACCT 58.584 39.130 0.00 0.00 43.32 3.50
3396 7064 4.837860 TGGCAATGTTTAGGATGAAACCTT 59.162 37.500 0.00 0.00 41.00 3.50
3397 7065 5.170748 GGCAATGTTTAGGATGAAACCTTG 58.829 41.667 10.70 10.70 42.77 3.61
3398 7066 5.047377 GGCAATGTTTAGGATGAAACCTTGA 60.047 40.000 16.26 0.00 42.64 3.02
3399 7067 6.454795 GCAATGTTTAGGATGAAACCTTGAA 58.545 36.000 16.26 0.00 42.64 2.69
3400 7068 7.099120 GCAATGTTTAGGATGAAACCTTGAAT 58.901 34.615 16.26 0.00 42.64 2.57
3401 7069 8.250332 GCAATGTTTAGGATGAAACCTTGAATA 58.750 33.333 16.26 0.00 42.64 1.75
3409 7077 8.915057 AGGATGAAACCTTGAATATATCAGTG 57.085 34.615 0.00 0.00 39.77 3.66
3410 7078 7.446625 AGGATGAAACCTTGAATATATCAGTGC 59.553 37.037 0.00 0.00 39.77 4.40
3411 7079 6.942532 TGAAACCTTGAATATATCAGTGCC 57.057 37.500 0.00 0.00 39.77 5.01
3412 7080 5.827797 TGAAACCTTGAATATATCAGTGCCC 59.172 40.000 0.00 0.00 39.77 5.36
3413 7081 4.008074 ACCTTGAATATATCAGTGCCCG 57.992 45.455 0.00 0.00 39.77 6.13
3414 7082 3.391296 ACCTTGAATATATCAGTGCCCGT 59.609 43.478 0.00 0.00 39.77 5.28
3415 7083 4.591498 ACCTTGAATATATCAGTGCCCGTA 59.409 41.667 0.00 0.00 39.77 4.02
3416 7084 5.071250 ACCTTGAATATATCAGTGCCCGTAA 59.929 40.000 0.00 0.00 39.77 3.18
3417 7085 5.995282 CCTTGAATATATCAGTGCCCGTAAA 59.005 40.000 0.00 0.00 39.77 2.01
3418 7086 6.485313 CCTTGAATATATCAGTGCCCGTAAAA 59.515 38.462 0.00 0.00 39.77 1.52
3419 7087 7.012894 CCTTGAATATATCAGTGCCCGTAAAAA 59.987 37.037 0.00 0.00 39.77 1.94
3473 7141 8.978874 ATATTACTGCAATGAATAGTGACCAA 57.021 30.769 0.00 0.00 0.00 3.67
3474 7142 6.494893 TTACTGCAATGAATAGTGACCAAC 57.505 37.500 0.00 0.00 0.00 3.77
3475 7143 4.397420 ACTGCAATGAATAGTGACCAACA 58.603 39.130 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
211 213 3.999001 TGAGCAAACAATGAGCTACAGAG 59.001 43.478 0.00 0.00 39.02 3.35
536 549 4.989168 ACCAATTCTTCACTACGAGAACAC 59.011 41.667 0.00 0.00 0.00 3.32
1656 1694 2.028190 CCGTAGCTGGATGAGGCG 59.972 66.667 0.00 0.00 0.00 5.52
1884 1922 4.201679 TCGGCGCCGTGGATGTAG 62.202 66.667 44.16 17.22 40.74 2.74
2027 2066 0.674581 TTCTTGGCAGCTGACATCGG 60.675 55.000 26.07 16.61 30.06 4.18
2031 2070 1.165907 CGGTTTCTTGGCAGCTGACA 61.166 55.000 21.20 21.20 0.00 3.58
2238 2286 2.229784 GCACACAAGGGAAAATCTCCTG 59.770 50.000 0.00 0.00 44.68 3.86
2247 2295 4.473643 CGGAAGCACACAAGGGAA 57.526 55.556 0.00 0.00 0.00 3.97
2279 2327 0.179084 ATGGTCGCCTTCATACCGTG 60.179 55.000 0.00 0.00 35.98 4.94
2280 2328 0.179084 CATGGTCGCCTTCATACCGT 60.179 55.000 0.00 0.00 35.98 4.83
2281 2329 1.498865 GCATGGTCGCCTTCATACCG 61.499 60.000 0.00 0.00 35.98 4.02
2454 2505 0.394899 GGGTGGCTTTCTCCTGGATG 60.395 60.000 0.00 0.00 0.00 3.51
2459 2510 2.649816 AGTATTTGGGTGGCTTTCTCCT 59.350 45.455 0.00 0.00 0.00 3.69
2469 2520 3.973973 TCTATGGAGGGAGTATTTGGGTG 59.026 47.826 0.00 0.00 0.00 4.61
2482 2533 9.877178 AAACGCTCTTATATATTTCTATGGAGG 57.123 33.333 0.00 0.00 0.00 4.30
2514 2570 8.578151 AGAGCGTTTAGATTACTCCTTTATAGG 58.422 37.037 0.00 0.00 43.46 2.57
2558 2619 0.830444 TTAGTCACGTGGTGCTCCCT 60.830 55.000 17.00 3.35 32.98 4.20
2564 2625 7.972277 ACAAGTACTATTATTAGTCACGTGGTG 59.028 37.037 17.00 0.00 39.42 4.17
2568 2629 8.624776 GGGTACAAGTACTATTATTAGTCACGT 58.375 37.037 9.94 0.00 39.42 4.49
2593 2654 6.948309 AGGCATGGCTATTAACTAATTTAGGG 59.052 38.462 22.00 0.00 0.00 3.53
2596 2657 9.013229 CATGAGGCATGGCTATTAACTAATTTA 57.987 33.333 23.39 0.00 38.11 1.40
2601 2662 4.326826 GCATGAGGCATGGCTATTAACTA 58.673 43.478 23.39 3.35 41.64 2.24
2625 2686 7.828712 TGATGTCATGATTGATTTTGCAGTAA 58.171 30.769 0.00 0.00 33.56 2.24
2630 2691 7.764695 TCATTGATGTCATGATTGATTTTGC 57.235 32.000 0.00 0.00 33.56 3.68
2675 2736 1.482182 ACATGCAAGGCGATAGAGACA 59.518 47.619 0.00 0.00 39.76 3.41
2680 2741 1.534595 GCCAAACATGCAAGGCGATAG 60.535 52.381 7.08 0.00 37.41 2.08
2681 2742 0.455410 GCCAAACATGCAAGGCGATA 59.545 50.000 7.08 0.00 37.41 2.92
2731 2792 9.859427 CTGCCTGTTTGAATCTTTTTATATTGA 57.141 29.630 0.00 0.00 0.00 2.57
2732 2793 9.859427 TCTGCCTGTTTGAATCTTTTTATATTG 57.141 29.630 0.00 0.00 0.00 1.90
2735 2796 8.686334 GGATCTGCCTGTTTGAATCTTTTTATA 58.314 33.333 0.00 0.00 0.00 0.98
2736 2797 7.178983 TGGATCTGCCTGTTTGAATCTTTTTAT 59.821 33.333 0.00 0.00 37.63 1.40
2737 2798 6.493115 TGGATCTGCCTGTTTGAATCTTTTTA 59.507 34.615 0.00 0.00 37.63 1.52
2738 2799 5.305128 TGGATCTGCCTGTTTGAATCTTTTT 59.695 36.000 0.00 0.00 37.63 1.94
2739 2800 4.834496 TGGATCTGCCTGTTTGAATCTTTT 59.166 37.500 0.00 0.00 37.63 2.27
2740 2801 4.410099 TGGATCTGCCTGTTTGAATCTTT 58.590 39.130 0.00 0.00 37.63 2.52
2741 2802 4.038271 TGGATCTGCCTGTTTGAATCTT 57.962 40.909 0.00 0.00 37.63 2.40
2742 2803 3.726557 TGGATCTGCCTGTTTGAATCT 57.273 42.857 0.00 0.00 37.63 2.40
2743 2804 4.996788 ATTGGATCTGCCTGTTTGAATC 57.003 40.909 0.00 0.00 37.63 2.52
2744 2805 6.855763 TTAATTGGATCTGCCTGTTTGAAT 57.144 33.333 0.00 0.00 37.63 2.57
2745 2806 6.664816 AGATTAATTGGATCTGCCTGTTTGAA 59.335 34.615 5.62 0.00 37.63 2.69
2746 2807 6.189859 AGATTAATTGGATCTGCCTGTTTGA 58.810 36.000 5.62 0.00 37.63 2.69
2747 2808 6.095860 TGAGATTAATTGGATCTGCCTGTTTG 59.904 38.462 9.96 0.00 34.13 2.93
2748 2809 6.189859 TGAGATTAATTGGATCTGCCTGTTT 58.810 36.000 9.96 0.00 34.13 2.83
2749 2810 5.759059 TGAGATTAATTGGATCTGCCTGTT 58.241 37.500 9.96 0.00 34.13 3.16
2750 2811 5.374921 CTGAGATTAATTGGATCTGCCTGT 58.625 41.667 9.96 0.00 34.13 4.00
2751 2812 4.215827 GCTGAGATTAATTGGATCTGCCTG 59.784 45.833 9.96 4.11 34.13 4.85
2752 2813 4.396522 GCTGAGATTAATTGGATCTGCCT 58.603 43.478 9.96 0.00 34.13 4.75
2753 2814 3.505293 GGCTGAGATTAATTGGATCTGCC 59.495 47.826 17.61 17.61 44.28 4.85
2797 2858 6.858993 CGCTCACCACTAAAGTAATCTAGATC 59.141 42.308 5.51 0.00 0.00 2.75
2807 2868 0.388649 CGAGCGCTCACCACTAAAGT 60.389 55.000 34.69 0.00 0.00 2.66
2808 2869 0.109272 TCGAGCGCTCACCACTAAAG 60.109 55.000 34.69 16.44 0.00 1.85
2811 2872 1.313091 ATGTCGAGCGCTCACCACTA 61.313 55.000 34.69 17.99 0.00 2.74
2892 2953 5.659971 TCTTATTAGGTAGGGTGTCCTTCAC 59.340 44.000 0.00 0.00 41.56 3.18
2893 2954 5.845734 TCTTATTAGGTAGGGTGTCCTTCA 58.154 41.667 0.00 0.00 41.56 3.02
2894 2955 6.155737 TGTTCTTATTAGGTAGGGTGTCCTTC 59.844 42.308 0.00 0.00 41.56 3.46
2895 2956 6.027482 TGTTCTTATTAGGTAGGGTGTCCTT 58.973 40.000 0.00 0.00 41.56 3.36
2896 2957 5.596763 TGTTCTTATTAGGTAGGGTGTCCT 58.403 41.667 0.00 0.00 46.96 3.85
2955 6623 6.686130 ATATACTAGTAAATGCGTTCGTGC 57.314 37.500 6.70 0.00 0.00 5.34
2960 6628 9.688592 GAACCTGTATATACTAGTAAATGCGTT 57.311 33.333 13.89 4.14 0.00 4.84
3022 6690 4.222124 AGGACAGGCATAGTTTACCAAG 57.778 45.455 0.00 0.00 0.00 3.61
3026 6694 4.192317 CCAGAAGGACAGGCATAGTTTAC 58.808 47.826 0.00 0.00 36.89 2.01
3048 6716 2.280186 CCGGAGCGTTGGATAGGC 60.280 66.667 0.00 0.00 37.91 3.93
3050 6718 2.280186 GGCCGGAGCGTTGGATAG 60.280 66.667 5.05 0.00 41.24 2.08
3051 6719 3.078196 TGGCCGGAGCGTTGGATA 61.078 61.111 5.05 0.00 41.24 2.59
3052 6720 4.778143 GTGGCCGGAGCGTTGGAT 62.778 66.667 5.05 0.00 41.24 3.41
3055 6723 3.423154 GAAGTGGCCGGAGCGTTG 61.423 66.667 5.05 0.00 41.24 4.10
3056 6724 3.469863 TTGAAGTGGCCGGAGCGTT 62.470 57.895 5.05 0.00 41.24 4.84
3096 6764 4.332428 AACTACATAGCCATCGGGTTAC 57.668 45.455 0.00 0.00 32.20 2.50
3097 6765 4.525487 CCTAACTACATAGCCATCGGGTTA 59.475 45.833 0.00 0.00 34.28 2.85
3098 6766 3.323979 CCTAACTACATAGCCATCGGGTT 59.676 47.826 0.00 0.00 34.28 4.11
3099 6767 2.897969 CCTAACTACATAGCCATCGGGT 59.102 50.000 0.00 0.00 37.19 5.28
3100 6768 2.233922 CCCTAACTACATAGCCATCGGG 59.766 54.545 0.00 0.00 37.18 5.14
3101 6769 3.162666 TCCCTAACTACATAGCCATCGG 58.837 50.000 0.00 0.00 0.00 4.18
3103 6771 6.212791 TGGTAATCCCTAACTACATAGCCATC 59.787 42.308 0.00 0.00 0.00 3.51
3104 6772 6.088819 TGGTAATCCCTAACTACATAGCCAT 58.911 40.000 0.00 0.00 0.00 4.40
3105 6773 5.469579 TGGTAATCCCTAACTACATAGCCA 58.530 41.667 0.00 0.00 0.00 4.75
3106 6774 6.212791 TGATGGTAATCCCTAACTACATAGCC 59.787 42.308 0.00 0.00 31.15 3.93
3107 6775 7.097834 GTGATGGTAATCCCTAACTACATAGC 58.902 42.308 0.00 0.00 31.15 2.97
3108 6776 7.039923 ACGTGATGGTAATCCCTAACTACATAG 60.040 40.741 0.00 0.00 31.15 2.23
3109 6777 6.779049 ACGTGATGGTAATCCCTAACTACATA 59.221 38.462 0.00 0.00 31.15 2.29
3110 6778 5.601313 ACGTGATGGTAATCCCTAACTACAT 59.399 40.000 0.00 0.00 31.15 2.29
3111 6779 4.957954 ACGTGATGGTAATCCCTAACTACA 59.042 41.667 0.00 0.00 31.15 2.74
3112 6780 5.526506 ACGTGATGGTAATCCCTAACTAC 57.473 43.478 0.00 0.00 31.15 2.73
3113 6781 6.128486 TGTACGTGATGGTAATCCCTAACTA 58.872 40.000 0.00 0.00 31.15 2.24
3114 6782 4.957954 TGTACGTGATGGTAATCCCTAACT 59.042 41.667 0.00 0.00 31.15 2.24
3115 6783 5.163478 ACTGTACGTGATGGTAATCCCTAAC 60.163 44.000 0.00 0.00 31.15 2.34
3116 6784 4.957954 ACTGTACGTGATGGTAATCCCTAA 59.042 41.667 0.00 0.00 31.15 2.69
3117 6785 4.539726 ACTGTACGTGATGGTAATCCCTA 58.460 43.478 0.00 0.00 31.15 3.53
3118 6786 3.371965 ACTGTACGTGATGGTAATCCCT 58.628 45.455 0.00 0.00 31.15 4.20
3119 6787 3.814005 ACTGTACGTGATGGTAATCCC 57.186 47.619 0.00 0.00 31.15 3.85
3120 6788 5.064325 GGAAAACTGTACGTGATGGTAATCC 59.936 44.000 0.00 0.57 31.15 3.01
3121 6789 5.873164 AGGAAAACTGTACGTGATGGTAATC 59.127 40.000 0.00 0.00 0.00 1.75
3122 6790 5.801380 AGGAAAACTGTACGTGATGGTAAT 58.199 37.500 0.00 0.00 0.00 1.89
3123 6791 5.217978 AGGAAAACTGTACGTGATGGTAA 57.782 39.130 0.00 0.00 0.00 2.85
3124 6792 4.877378 AGGAAAACTGTACGTGATGGTA 57.123 40.909 0.00 0.00 0.00 3.25
3125 6793 3.764237 AGGAAAACTGTACGTGATGGT 57.236 42.857 0.00 0.00 0.00 3.55
3126 6794 6.548441 TTTAAGGAAAACTGTACGTGATGG 57.452 37.500 0.00 0.00 0.00 3.51
3161 6829 8.960064 AGGTTTCATCCCTAATATAATTGGAGT 58.040 33.333 0.00 0.00 0.00 3.85
3162 6830 9.236006 CAGGTTTCATCCCTAATATAATTGGAG 57.764 37.037 0.00 0.00 0.00 3.86
3163 6831 8.732854 ACAGGTTTCATCCCTAATATAATTGGA 58.267 33.333 0.00 0.00 0.00 3.53
3164 6832 8.940397 ACAGGTTTCATCCCTAATATAATTGG 57.060 34.615 0.00 0.00 0.00 3.16
3171 6839 9.837681 TGAGATATACAGGTTTCATCCCTAATA 57.162 33.333 0.00 0.00 0.00 0.98
3172 6840 8.742125 TGAGATATACAGGTTTCATCCCTAAT 57.258 34.615 0.00 0.00 0.00 1.73
3173 6841 7.256332 GCTGAGATATACAGGTTTCATCCCTAA 60.256 40.741 10.18 0.00 36.09 2.69
3174 6842 6.211584 GCTGAGATATACAGGTTTCATCCCTA 59.788 42.308 10.18 0.00 36.09 3.53
3175 6843 5.012561 GCTGAGATATACAGGTTTCATCCCT 59.987 44.000 10.18 0.00 36.09 4.20
3176 6844 5.241662 GCTGAGATATACAGGTTTCATCCC 58.758 45.833 10.18 0.00 36.09 3.85
3177 6845 4.926238 CGCTGAGATATACAGGTTTCATCC 59.074 45.833 10.18 0.00 36.09 3.51
3178 6846 4.387256 GCGCTGAGATATACAGGTTTCATC 59.613 45.833 0.00 0.00 36.09 2.92
3179 6847 4.202253 TGCGCTGAGATATACAGGTTTCAT 60.202 41.667 9.73 0.00 36.09 2.57
3180 6848 3.132111 TGCGCTGAGATATACAGGTTTCA 59.868 43.478 9.73 0.00 36.09 2.69
3181 6849 3.717707 TGCGCTGAGATATACAGGTTTC 58.282 45.455 9.73 0.00 36.09 2.78
3182 6850 3.133003 ACTGCGCTGAGATATACAGGTTT 59.867 43.478 21.92 0.00 36.09 3.27
3183 6851 2.695666 ACTGCGCTGAGATATACAGGTT 59.304 45.455 21.92 0.00 36.09 3.50
3184 6852 2.311463 ACTGCGCTGAGATATACAGGT 58.689 47.619 21.92 0.00 36.09 4.00
3185 6853 4.505313 TTACTGCGCTGAGATATACAGG 57.495 45.455 21.92 3.82 36.09 4.00
3186 6854 6.828502 TTTTTACTGCGCTGAGATATACAG 57.171 37.500 21.92 1.55 38.27 2.74
3217 6885 7.394359 ACATATTAAGCATGGATGGTAATGGAC 59.606 37.037 0.00 0.00 37.57 4.02
3218 6886 7.469343 ACATATTAAGCATGGATGGTAATGGA 58.531 34.615 0.00 0.00 37.57 3.41
3219 6887 7.707624 ACATATTAAGCATGGATGGTAATGG 57.292 36.000 0.00 0.00 37.57 3.16
3251 6919 7.143340 TCGCCAGACATGTAGTAATGTATTAC 58.857 38.462 0.00 6.65 40.87 1.89
3252 6920 7.279750 TCGCCAGACATGTAGTAATGTATTA 57.720 36.000 0.00 0.00 40.87 0.98
3253 6921 6.156748 TCGCCAGACATGTAGTAATGTATT 57.843 37.500 0.00 0.00 40.87 1.89
3254 6922 5.784578 TCGCCAGACATGTAGTAATGTAT 57.215 39.130 0.00 0.00 40.87 2.29
3255 6923 5.451381 CCTTCGCCAGACATGTAGTAATGTA 60.451 44.000 0.00 0.00 40.87 2.29
3256 6924 4.433615 CTTCGCCAGACATGTAGTAATGT 58.566 43.478 0.00 0.00 43.47 2.71
3257 6925 3.804325 CCTTCGCCAGACATGTAGTAATG 59.196 47.826 0.00 0.00 0.00 1.90
3258 6926 3.451178 ACCTTCGCCAGACATGTAGTAAT 59.549 43.478 0.00 0.00 0.00 1.89
3259 6927 2.829720 ACCTTCGCCAGACATGTAGTAA 59.170 45.455 0.00 0.00 0.00 2.24
3260 6928 2.453521 ACCTTCGCCAGACATGTAGTA 58.546 47.619 0.00 0.00 0.00 1.82
3261 6929 1.267121 ACCTTCGCCAGACATGTAGT 58.733 50.000 0.00 0.00 0.00 2.73
3262 6930 2.386661 AACCTTCGCCAGACATGTAG 57.613 50.000 0.00 0.00 0.00 2.74
3263 6931 2.851263 AAACCTTCGCCAGACATGTA 57.149 45.000 0.00 0.00 0.00 2.29
3264 6932 1.981256 AAAACCTTCGCCAGACATGT 58.019 45.000 0.00 0.00 0.00 3.21
3265 6933 3.074412 AGTAAAACCTTCGCCAGACATG 58.926 45.455 0.00 0.00 0.00 3.21
3266 6934 3.418684 AGTAAAACCTTCGCCAGACAT 57.581 42.857 0.00 0.00 0.00 3.06
3267 6935 2.922740 AGTAAAACCTTCGCCAGACA 57.077 45.000 0.00 0.00 0.00 3.41
3268 6936 7.549615 AAATATAGTAAAACCTTCGCCAGAC 57.450 36.000 0.00 0.00 0.00 3.51
3296 6964 9.316594 TGAGTTATCGATGGTTATATCCCTAAA 57.683 33.333 8.54 0.00 0.00 1.85
3297 6965 8.888836 TGAGTTATCGATGGTTATATCCCTAA 57.111 34.615 8.54 0.00 0.00 2.69
3298 6966 8.888836 TTGAGTTATCGATGGTTATATCCCTA 57.111 34.615 8.54 0.00 0.00 3.53
3299 6967 7.792364 TTGAGTTATCGATGGTTATATCCCT 57.208 36.000 8.54 0.00 0.00 4.20
3300 6968 7.011482 GCATTGAGTTATCGATGGTTATATCCC 59.989 40.741 8.54 0.00 44.56 3.85
3301 6969 7.011482 GGCATTGAGTTATCGATGGTTATATCC 59.989 40.741 8.54 0.00 44.56 2.59
3302 6970 7.254117 CGGCATTGAGTTATCGATGGTTATATC 60.254 40.741 8.54 0.00 44.56 1.63
3303 6971 6.535150 CGGCATTGAGTTATCGATGGTTATAT 59.465 38.462 8.54 0.00 44.56 0.86
3304 6972 5.867174 CGGCATTGAGTTATCGATGGTTATA 59.133 40.000 8.54 0.00 44.56 0.98
3305 6973 4.690748 CGGCATTGAGTTATCGATGGTTAT 59.309 41.667 8.54 0.00 44.56 1.89
3306 6974 4.055360 CGGCATTGAGTTATCGATGGTTA 58.945 43.478 8.54 0.00 44.56 2.85
3307 6975 2.872245 CGGCATTGAGTTATCGATGGTT 59.128 45.455 8.54 0.00 44.56 3.67
3308 6976 2.483876 CGGCATTGAGTTATCGATGGT 58.516 47.619 8.54 0.00 44.56 3.55
3309 6977 1.800586 CCGGCATTGAGTTATCGATGG 59.199 52.381 8.54 0.00 44.56 3.51
3310 6978 2.483876 ACCGGCATTGAGTTATCGATG 58.516 47.619 8.54 1.76 46.39 3.84
3311 6979 2.910688 ACCGGCATTGAGTTATCGAT 57.089 45.000 0.00 2.16 0.00 3.59
3312 6980 3.804786 TTACCGGCATTGAGTTATCGA 57.195 42.857 0.00 0.00 0.00 3.59
3313 6981 4.569162 TCTTTTACCGGCATTGAGTTATCG 59.431 41.667 0.00 0.00 0.00 2.92
3314 6982 6.431198 TTCTTTTACCGGCATTGAGTTATC 57.569 37.500 0.00 0.00 0.00 1.75
3315 6983 6.827586 TTTCTTTTACCGGCATTGAGTTAT 57.172 33.333 0.00 0.00 0.00 1.89
3316 6984 6.636562 TTTTCTTTTACCGGCATTGAGTTA 57.363 33.333 0.00 0.00 0.00 2.24
3317 6985 5.523438 TTTTCTTTTACCGGCATTGAGTT 57.477 34.783 0.00 0.00 0.00 3.01
3318 6986 5.722021 ATTTTCTTTTACCGGCATTGAGT 57.278 34.783 0.00 0.00 0.00 3.41
3319 6987 6.127730 ACCTATTTTCTTTTACCGGCATTGAG 60.128 38.462 0.00 0.00 0.00 3.02
3320 6988 5.712917 ACCTATTTTCTTTTACCGGCATTGA 59.287 36.000 0.00 0.00 0.00 2.57
3321 6989 5.961272 ACCTATTTTCTTTTACCGGCATTG 58.039 37.500 0.00 0.00 0.00 2.82
3322 6990 6.599356 AACCTATTTTCTTTTACCGGCATT 57.401 33.333 0.00 0.00 0.00 3.56
3323 6991 6.599356 AAACCTATTTTCTTTTACCGGCAT 57.401 33.333 0.00 0.00 0.00 4.40
3324 6992 7.706100 ATAAACCTATTTTCTTTTACCGGCA 57.294 32.000 0.00 0.00 0.00 5.69
3325 6993 9.507280 GTAATAAACCTATTTTCTTTTACCGGC 57.493 33.333 0.00 0.00 0.00 6.13
3363 7031 9.071276 CATCCTAAACATTGCCAGTAATAGATT 57.929 33.333 0.00 0.00 0.00 2.40
3364 7032 8.439971 TCATCCTAAACATTGCCAGTAATAGAT 58.560 33.333 0.00 0.00 0.00 1.98
3365 7033 7.801104 TCATCCTAAACATTGCCAGTAATAGA 58.199 34.615 0.00 0.00 0.00 1.98
3366 7034 8.450578 TTCATCCTAAACATTGCCAGTAATAG 57.549 34.615 0.00 0.00 0.00 1.73
3367 7035 8.682710 GTTTCATCCTAAACATTGCCAGTAATA 58.317 33.333 0.00 0.00 38.85 0.98
3368 7036 7.363793 GGTTTCATCCTAAACATTGCCAGTAAT 60.364 37.037 0.00 0.00 40.42 1.89
3369 7037 6.071616 GGTTTCATCCTAAACATTGCCAGTAA 60.072 38.462 0.00 0.00 40.42 2.24
3370 7038 5.417580 GGTTTCATCCTAAACATTGCCAGTA 59.582 40.000 0.00 0.00 40.42 2.74
3371 7039 4.220602 GGTTTCATCCTAAACATTGCCAGT 59.779 41.667 0.00 0.00 40.42 4.00
3372 7040 4.463891 AGGTTTCATCCTAAACATTGCCAG 59.536 41.667 0.00 0.00 40.42 4.85
3373 7041 4.415596 AGGTTTCATCCTAAACATTGCCA 58.584 39.130 0.00 0.00 40.42 4.92
3374 7042 5.405935 AAGGTTTCATCCTAAACATTGCC 57.594 39.130 0.00 0.00 40.63 4.52
3384 7052 7.446625 GCACTGATATATTCAAGGTTTCATCCT 59.553 37.037 0.00 0.00 39.84 3.24
3385 7053 7.308830 GGCACTGATATATTCAAGGTTTCATCC 60.309 40.741 0.00 0.00 32.78 3.51
3386 7054 7.308830 GGGCACTGATATATTCAAGGTTTCATC 60.309 40.741 0.00 0.00 32.78 2.92
3387 7055 6.491403 GGGCACTGATATATTCAAGGTTTCAT 59.509 38.462 0.00 0.00 32.78 2.57
3388 7056 5.827797 GGGCACTGATATATTCAAGGTTTCA 59.172 40.000 0.00 0.00 32.78 2.69
3389 7057 5.049405 CGGGCACTGATATATTCAAGGTTTC 60.049 44.000 0.00 0.00 36.31 2.78
3390 7058 4.821805 CGGGCACTGATATATTCAAGGTTT 59.178 41.667 0.00 0.00 36.31 3.27
3391 7059 4.141482 ACGGGCACTGATATATTCAAGGTT 60.141 41.667 0.00 0.00 38.67 3.50
3392 7060 3.391296 ACGGGCACTGATATATTCAAGGT 59.609 43.478 0.00 0.00 38.67 3.50
3393 7061 4.008074 ACGGGCACTGATATATTCAAGG 57.992 45.455 0.00 0.00 38.67 3.61
3394 7062 7.490962 TTTTACGGGCACTGATATATTCAAG 57.509 36.000 0.00 0.00 38.67 3.02
3395 7063 7.867305 TTTTTACGGGCACTGATATATTCAA 57.133 32.000 0.00 0.00 38.67 2.69
3448 7116 8.840321 GTTGGTCACTATTCATTGCAGTAATAT 58.160 33.333 0.00 0.00 0.00 1.28
3449 7117 7.826744 TGTTGGTCACTATTCATTGCAGTAATA 59.173 33.333 0.00 0.00 0.00 0.98
3450 7118 6.658816 TGTTGGTCACTATTCATTGCAGTAAT 59.341 34.615 0.00 0.00 0.00 1.89
3451 7119 6.000840 TGTTGGTCACTATTCATTGCAGTAA 58.999 36.000 0.00 0.00 0.00 2.24
3452 7120 5.411361 GTGTTGGTCACTATTCATTGCAGTA 59.589 40.000 0.00 0.00 43.13 2.74
3453 7121 4.216257 GTGTTGGTCACTATTCATTGCAGT 59.784 41.667 0.00 0.00 43.13 4.40
3454 7122 4.216042 TGTGTTGGTCACTATTCATTGCAG 59.784 41.667 0.00 0.00 46.27 4.41
3455 7123 4.140536 TGTGTTGGTCACTATTCATTGCA 58.859 39.130 0.00 0.00 46.27 4.08
3456 7124 4.764679 TGTGTTGGTCACTATTCATTGC 57.235 40.909 0.00 0.00 46.27 3.56
3457 7125 5.643664 CCATGTGTTGGTCACTATTCATTG 58.356 41.667 0.00 0.00 46.27 2.82
3458 7126 5.902613 CCATGTGTTGGTCACTATTCATT 57.097 39.130 0.00 0.00 46.27 2.57


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

AutoCloner maintained by Alex Coulton.