Multiple sequence alignment - TraesCS6B01G112100

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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 TraesCS6B01G112100 chr6B 100.000 4758 0 0 1 4758 93915105 93910348 0.000000e+00 8787.0
1 TraesCS6B01G112100 chr6B 92.827 962 44 14 19 958 712098900 712097942 0.000000e+00 1371.0
2 TraesCS6B01G112100 chr6B 96.818 660 12 2 4105 4758 241181956 241181300 0.000000e+00 1094.0
3 TraesCS6B01G112100 chr6B 84.985 333 39 4 1191 1523 93840091 93839770 1.280000e-85 327.0
4 TraesCS6B01G112100 chr6B 85.437 309 40 4 3754 4059 226195932 226195626 2.760000e-82 316.0
5 TraesCS6B01G112100 chr6B 79.907 428 68 11 1107 1533 45617537 45617127 1.000000e-76 298.0
6 TraesCS6B01G112100 chr6B 81.503 346 55 3 1182 1527 93831807 93831471 4.690000e-70 276.0
7 TraesCS6B01G112100 chr6B 86.574 216 24 3 1103 1317 45599293 45599082 2.860000e-57 233.0
8 TraesCS6B01G112100 chr6B 84.834 211 21 4 1089 1292 45573271 45573065 8.070000e-48 202.0
9 TraesCS6B01G112100 chr6B 79.392 296 51 7 1167 1462 45596952 45596667 2.900000e-47 200.0
10 TraesCS6B01G112100 chr6A 93.340 1877 95 10 965 2828 58009954 58008095 0.000000e+00 2747.0
11 TraesCS6B01G112100 chr6A 82.393 443 60 10 1093 1534 26621765 26621340 2.090000e-98 370.0
12 TraesCS6B01G112100 chr6A 85.231 325 39 3 1191 1515 57931008 57930693 4.590000e-85 326.0
13 TraesCS6B01G112100 chrUn 93.838 1347 70 6 1586 2922 18918418 18919761 0.000000e+00 2015.0
14 TraesCS6B01G112100 chrUn 92.843 1020 57 8 3089 4105 18919762 18920768 0.000000e+00 1465.0
15 TraesCS6B01G112100 chrUn 95.893 633 19 3 957 1587 18917701 18918328 0.000000e+00 1018.0
16 TraesCS6B01G112100 chrUn 80.088 452 66 11 1089 1533 95233329 95232895 9.940000e-82 315.0
17 TraesCS6B01G112100 chrUn 87.662 154 16 2 3755 3906 368559786 368559938 4.890000e-40 176.0
18 TraesCS6B01G112100 chrUn 76.305 249 45 12 2382 2624 19130043 19130283 2.330000e-23 121.0
19 TraesCS6B01G112100 chrUn 91.026 78 7 0 2382 2459 95232171 95232094 6.510000e-19 106.0
20 TraesCS6B01G112100 chr2B 93.869 946 40 6 19 961 123176371 123175441 0.000000e+00 1410.0
21 TraesCS6B01G112100 chr2B 93.006 958 48 12 19 960 105381134 105380180 0.000000e+00 1380.0
22 TraesCS6B01G112100 chr2B 93.269 936 37 6 19 954 545165935 545166844 0.000000e+00 1356.0
23 TraesCS6B01G112100 chr2B 91.614 942 53 7 19 958 631333757 631334674 0.000000e+00 1279.0
24 TraesCS6B01G112100 chr2B 97.269 659 9 2 4106 4758 219750825 219750170 0.000000e+00 1109.0
25 TraesCS6B01G112100 chr2B 96.364 660 15 2 4105 4758 182490391 182489735 0.000000e+00 1077.0
26 TraesCS6B01G112100 chr2B 96.078 663 19 2 4103 4758 702552776 702553438 0.000000e+00 1074.0
27 TraesCS6B01G112100 chr1B 93.050 964 47 10 19 964 562616933 562617894 0.000000e+00 1391.0
28 TraesCS6B01G112100 chr1B 91.935 186 13 2 2914 3097 486835808 486835623 4.720000e-65 259.0
29 TraesCS6B01G112100 chr5B 92.842 964 40 11 1 963 596980437 596981372 0.000000e+00 1371.0
30 TraesCS6B01G112100 chr5B 92.534 951 52 11 26 961 284158713 284157767 0.000000e+00 1345.0
31 TraesCS6B01G112100 chr5B 93.013 916 39 8 43 958 64718009 64718899 0.000000e+00 1314.0
32 TraesCS6B01G112100 chr5B 89.831 354 32 3 3755 4105 352396874 352397226 7.260000e-123 451.0
33 TraesCS6B01G112100 chr4B 92.604 960 51 11 19 961 422782914 422783870 0.000000e+00 1362.0
34 TraesCS6B01G112100 chr4B 85.567 97 11 2 815 910 391158849 391158755 1.090000e-16 99.0
35 TraesCS6B01G112100 chr7B 97.117 659 13 1 4106 4758 576464150 576464808 0.000000e+00 1107.0
36 TraesCS6B01G112100 chr7B 96.358 659 15 2 4106 4758 677248574 677247919 0.000000e+00 1075.0
37 TraesCS6B01G112100 chr7B 96.084 664 17 2 4101 4758 679159579 679160239 0.000000e+00 1074.0
38 TraesCS6B01G112100 chr7B 87.395 357 38 6 3750 4100 676159801 676160156 2.060000e-108 403.0
39 TraesCS6B01G112100 chr7B 87.117 326 33 5 3783 4105 332114939 332115258 1.260000e-95 361.0
40 TraesCS6B01G112100 chr7B 82.353 119 16 5 813 929 7564518 7564403 1.090000e-16 99.0
41 TraesCS6B01G112100 chr7B 100.000 29 0 0 3763 3791 362444204 362444232 2.000000e-03 54.7
42 TraesCS6B01G112100 chr3B 96.369 661 15 2 4104 4758 14456803 14457460 0.000000e+00 1079.0
43 TraesCS6B01G112100 chr3B 96.358 659 18 1 4106 4758 570042140 570042798 0.000000e+00 1079.0
44 TraesCS6B01G112100 chr3B 92.391 184 11 3 2914 3095 655849407 655849589 4.720000e-65 259.0
45 TraesCS6B01G112100 chr5A 84.887 933 111 17 34 958 460471344 460470434 0.000000e+00 915.0
46 TraesCS6B01G112100 chr5A 88.818 313 33 2 3751 4062 69552312 69552623 2.690000e-102 383.0
47 TraesCS6B01G112100 chr3A 87.606 355 33 8 3755 4105 8731713 8731366 7.420000e-108 401.0
48 TraesCS6B01G112100 chr3A 89.781 274 24 3 3835 4105 8740695 8740423 9.800000e-92 348.0
49 TraesCS6B01G112100 chr7D 87.640 356 27 6 3754 4105 188163888 188164230 9.590000e-107 398.0
50 TraesCS6B01G112100 chr1D 94.798 173 8 1 2924 3095 238940384 238940212 7.850000e-68 268.0
51 TraesCS6B01G112100 chr5D 94.767 172 8 1 2924 3094 274578180 274578009 2.820000e-67 267.0
52 TraesCS6B01G112100 chr5D 93.258 178 11 1 2919 3095 61715391 61715214 1.310000e-65 261.0
53 TraesCS6B01G112100 chr5D 82.550 149 22 4 815 962 552635571 552635426 1.390000e-25 128.0
54 TraesCS6B01G112100 chr2A 94.253 174 9 1 2920 3092 746756982 746757155 1.020000e-66 265.0
55 TraesCS6B01G112100 chr2A 82.877 146 25 0 816 961 160035575 160035720 1.070000e-26 132.0
56 TraesCS6B01G112100 chr4D 92.391 184 10 4 2917 3097 46028714 46028532 4.720000e-65 259.0
57 TraesCS6B01G112100 chr1A 90.769 195 13 4 2903 3095 354304540 354304731 6.110000e-64 255.0
58 TraesCS6B01G112100 chr3D 91.489 188 11 5 2906 3092 304588283 304588100 2.200000e-63 254.0
59 TraesCS6B01G112100 chr7A 86.014 143 20 0 818 960 719617092 719616950 2.290000e-33 154.0
60 TraesCS6B01G112100 chr7A 84.000 150 16 7 813 960 516920837 516920694 2.310000e-28 137.0
61 TraesCS6B01G112100 chr7A 83.673 147 22 1 813 959 662139423 662139567 2.310000e-28 137.0


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 TraesCS6B01G112100 chr6B 93910348 93915105 4757 True 8787.000000 8787 100.000000 1 4758 1 chr6B.!!$R5 4757
1 TraesCS6B01G112100 chr6B 712097942 712098900 958 True 1371.000000 1371 92.827000 19 958 1 chr6B.!!$R8 939
2 TraesCS6B01G112100 chr6B 241181300 241181956 656 True 1094.000000 1094 96.818000 4105 4758 1 chr6B.!!$R7 653
3 TraesCS6B01G112100 chr6B 45596667 45599293 2626 True 216.500000 233 82.983000 1103 1462 2 chr6B.!!$R9 359
4 TraesCS6B01G112100 chr6A 58008095 58009954 1859 True 2747.000000 2747 93.340000 965 2828 1 chr6A.!!$R3 1863
5 TraesCS6B01G112100 chrUn 18917701 18920768 3067 False 1499.333333 2015 94.191333 957 4105 3 chrUn.!!$F3 3148
6 TraesCS6B01G112100 chrUn 95232094 95233329 1235 True 210.500000 315 85.557000 1089 2459 2 chrUn.!!$R1 1370
7 TraesCS6B01G112100 chr2B 123175441 123176371 930 True 1410.000000 1410 93.869000 19 961 1 chr2B.!!$R2 942
8 TraesCS6B01G112100 chr2B 105380180 105381134 954 True 1380.000000 1380 93.006000 19 960 1 chr2B.!!$R1 941
9 TraesCS6B01G112100 chr2B 545165935 545166844 909 False 1356.000000 1356 93.269000 19 954 1 chr2B.!!$F1 935
10 TraesCS6B01G112100 chr2B 631333757 631334674 917 False 1279.000000 1279 91.614000 19 958 1 chr2B.!!$F2 939
11 TraesCS6B01G112100 chr2B 219750170 219750825 655 True 1109.000000 1109 97.269000 4106 4758 1 chr2B.!!$R4 652
12 TraesCS6B01G112100 chr2B 182489735 182490391 656 True 1077.000000 1077 96.364000 4105 4758 1 chr2B.!!$R3 653
13 TraesCS6B01G112100 chr2B 702552776 702553438 662 False 1074.000000 1074 96.078000 4103 4758 1 chr2B.!!$F3 655
14 TraesCS6B01G112100 chr1B 562616933 562617894 961 False 1391.000000 1391 93.050000 19 964 1 chr1B.!!$F1 945
15 TraesCS6B01G112100 chr5B 596980437 596981372 935 False 1371.000000 1371 92.842000 1 963 1 chr5B.!!$F3 962
16 TraesCS6B01G112100 chr5B 284157767 284158713 946 True 1345.000000 1345 92.534000 26 961 1 chr5B.!!$R1 935
17 TraesCS6B01G112100 chr5B 64718009 64718899 890 False 1314.000000 1314 93.013000 43 958 1 chr5B.!!$F1 915
18 TraesCS6B01G112100 chr4B 422782914 422783870 956 False 1362.000000 1362 92.604000 19 961 1 chr4B.!!$F1 942
19 TraesCS6B01G112100 chr7B 576464150 576464808 658 False 1107.000000 1107 97.117000 4106 4758 1 chr7B.!!$F3 652
20 TraesCS6B01G112100 chr7B 677247919 677248574 655 True 1075.000000 1075 96.358000 4106 4758 1 chr7B.!!$R2 652
21 TraesCS6B01G112100 chr7B 679159579 679160239 660 False 1074.000000 1074 96.084000 4101 4758 1 chr7B.!!$F5 657
22 TraesCS6B01G112100 chr3B 14456803 14457460 657 False 1079.000000 1079 96.369000 4104 4758 1 chr3B.!!$F1 654
23 TraesCS6B01G112100 chr3B 570042140 570042798 658 False 1079.000000 1079 96.358000 4106 4758 1 chr3B.!!$F2 652
24 TraesCS6B01G112100 chr5A 460470434 460471344 910 True 915.000000 915 84.887000 34 958 1 chr5A.!!$R1 924

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
292 293 1.674057 CTCAACTTCGCCCCTCTGT 59.326 57.895 0.00 0.00 0.00 3.41 F
1067 1134 0.170561 ATGCTCGCTCGTCGTTAACT 59.829 50.000 3.71 0.00 39.67 2.24 F
1153 1226 0.321671 TTCCAAGAGAAGAGCACGGG 59.678 55.000 0.00 0.00 0.00 5.28 F
2213 2621 0.452987 ATTACAACCTACGCGCGAGA 59.547 50.000 39.36 22.51 0.00 4.04 F
2989 3512 1.204941 ACAAGTGACTACATCCGGAGC 59.795 52.381 11.34 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 1588 1.746615 CTTCCGCACCATGGACCTG 60.747 63.158 21.47 7.72 34.56 4.00 R
2970 3493 1.204704 TGCTCCGGATGTAGTCACTTG 59.795 52.381 3.57 0.00 0.00 3.16 R
2980 3503 2.358957 TCACTCATTTTGCTCCGGATG 58.641 47.619 3.57 0.00 0.00 3.51 R
3304 3827 0.255033 ATTACCTCGACCAAAGGGCC 59.745 55.000 0.00 0.00 38.29 5.80 R
4288 4985 0.323725 TACCGCGGGTAAGGAGAAGT 60.324 55.000 31.76 5.83 34.97 3.01 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
292 293 1.674057 CTCAACTTCGCCCCTCTGT 59.326 57.895 0.00 0.00 0.00 3.41
605 606 1.674962 GCTAACTACCTCGGACGACAT 59.325 52.381 0.00 0.00 0.00 3.06
912 977 2.745785 CGATGGGCGCGCACTAAAA 61.746 57.895 35.65 15.34 0.00 1.52
954 1019 2.511600 GGCGTCCGTTGGAGATGG 60.512 66.667 0.00 0.00 35.59 3.51
978 1043 2.736670 AGACAGCCCAAGAAAACAGT 57.263 45.000 0.00 0.00 0.00 3.55
1067 1134 0.170561 ATGCTCGCTCGTCGTTAACT 59.829 50.000 3.71 0.00 39.67 2.24
1153 1226 0.321671 TTCCAAGAGAAGAGCACGGG 59.678 55.000 0.00 0.00 0.00 5.28
1248 1321 1.299468 GATCTCGCGCATCTTCCGT 60.299 57.895 8.75 0.00 0.00 4.69
1410 1588 1.614317 CCCATGTTCAACCTGGAGACC 60.614 57.143 13.17 0.00 36.17 3.85
1563 1746 3.881688 CCCCGATCTCTTTCGTACTCTTA 59.118 47.826 0.00 0.00 37.42 2.10
1651 2052 1.979809 TCTCTTGCCCCCTCCAATTA 58.020 50.000 0.00 0.00 0.00 1.40
1713 2115 2.143925 GGAGGAAAGGTCGTTTCTGTG 58.856 52.381 15.57 0.00 43.73 3.66
1860 2268 3.738982 TCGTTGAAAAGCCTTCATCTCA 58.261 40.909 0.01 0.00 0.00 3.27
1964 2372 7.598278 TGCTTTCAAAAACGTATACATTGGAT 58.402 30.769 3.32 0.00 0.00 3.41
2006 2414 2.025863 GCCTGCCCACTATTGAAGCAT 61.026 52.381 0.00 0.00 33.10 3.79
2021 2429 4.454678 TGAAGCATTTCAGACTTGTCACT 58.545 39.130 3.49 0.00 38.37 3.41
2033 2441 5.186021 CAGACTTGTCACTGGAAGGTACTAT 59.814 44.000 3.49 0.00 38.49 2.12
2099 2507 4.134563 AGTTACGTTCCTTGCATCTTGTT 58.865 39.130 0.00 0.00 0.00 2.83
2207 2615 4.280174 TCTCCTATGGATTACAACCTACGC 59.720 45.833 0.00 0.00 0.00 4.42
2213 2621 0.452987 ATTACAACCTACGCGCGAGA 59.547 50.000 39.36 22.51 0.00 4.04
2300 2711 3.735820 CGTATTACCGCTTCAAGCCTACA 60.736 47.826 3.08 0.00 38.18 2.74
2403 2820 3.244840 TGGTGATGGTGATGATGTTGACA 60.245 43.478 0.00 0.00 0.00 3.58
2459 2876 3.070159 ACATCAAGAGCATGCGTAGGTAT 59.930 43.478 13.01 0.30 0.00 2.73
2488 2921 9.796180 AAGTAGATGAAACGATATACTAGAGGT 57.204 33.333 0.00 0.00 30.73 3.85
2489 2922 9.221933 AGTAGATGAAACGATATACTAGAGGTG 57.778 37.037 0.00 0.00 30.31 4.00
2505 2938 7.551585 ACTAGAGGTGTAATGTCTTGATGAAG 58.448 38.462 0.00 0.00 0.00 3.02
2506 2939 6.365970 AGAGGTGTAATGTCTTGATGAAGT 57.634 37.500 0.00 0.00 0.00 3.01
2509 2942 6.299141 AGGTGTAATGTCTTGATGAAGTTGT 58.701 36.000 0.00 0.00 0.00 3.32
2584 3017 2.206576 AGTTTTGCCCCATGAGACTC 57.793 50.000 0.00 0.00 0.00 3.36
2681 3114 4.503007 CGACAATCATTTTATCCGAGTCGT 59.497 41.667 12.31 0.00 40.75 4.34
2840 3278 6.266558 AGCACAAACATATTGTAAACCCAAGA 59.733 34.615 0.00 0.00 0.00 3.02
2889 3327 8.723942 AAAACTCTAACATCTCATACCACATC 57.276 34.615 0.00 0.00 0.00 3.06
2891 3329 7.048629 ACTCTAACATCTCATACCACATCTG 57.951 40.000 0.00 0.00 0.00 2.90
2941 3464 7.898014 AATTTGTTTATACTCCCTCCATTCC 57.102 36.000 0.00 0.00 0.00 3.01
2942 3465 6.652205 TTTGTTTATACTCCCTCCATTCCT 57.348 37.500 0.00 0.00 0.00 3.36
2945 3468 7.758820 TGTTTATACTCCCTCCATTCCTAAA 57.241 36.000 0.00 0.00 0.00 1.85
2947 3470 9.455144 TGTTTATACTCCCTCCATTCCTAAATA 57.545 33.333 0.00 0.00 0.00 1.40
2952 3475 7.226059 ACTCCCTCCATTCCTAAATATTTGT 57.774 36.000 11.05 0.00 0.00 2.83
2957 3480 8.633561 CCCTCCATTCCTAAATATTTGTCTTTC 58.366 37.037 11.05 0.00 0.00 2.62
2973 3496 7.510549 TTGTCTTTCTAGGGATTTCAACAAG 57.489 36.000 0.00 0.00 0.00 3.16
2974 3497 6.601332 TGTCTTTCTAGGGATTTCAACAAGT 58.399 36.000 0.00 0.00 0.00 3.16
2976 3499 6.710744 GTCTTTCTAGGGATTTCAACAAGTGA 59.289 38.462 0.00 0.00 0.00 3.41
2977 3500 6.710744 TCTTTCTAGGGATTTCAACAAGTGAC 59.289 38.462 0.00 0.00 35.39 3.67
2978 3501 5.825593 TCTAGGGATTTCAACAAGTGACT 57.174 39.130 0.00 0.00 35.39 3.41
2980 3503 6.698380 TCTAGGGATTTCAACAAGTGACTAC 58.302 40.000 0.00 0.00 35.39 2.73
2982 3505 5.880901 AGGGATTTCAACAAGTGACTACAT 58.119 37.500 0.00 0.00 35.39 2.29
2983 3506 5.940470 AGGGATTTCAACAAGTGACTACATC 59.060 40.000 0.00 0.00 35.39 3.06
2984 3507 5.123979 GGGATTTCAACAAGTGACTACATCC 59.876 44.000 0.00 0.00 35.39 3.51
2985 3508 5.163854 GGATTTCAACAAGTGACTACATCCG 60.164 44.000 0.00 0.00 35.39 4.18
2986 3509 3.313012 TCAACAAGTGACTACATCCGG 57.687 47.619 0.00 0.00 0.00 5.14
2987 3510 2.894765 TCAACAAGTGACTACATCCGGA 59.105 45.455 6.61 6.61 0.00 5.14
2988 3511 3.056821 TCAACAAGTGACTACATCCGGAG 60.057 47.826 11.34 4.72 0.00 4.63
2989 3512 1.204941 ACAAGTGACTACATCCGGAGC 59.795 52.381 11.34 0.00 0.00 4.70
2991 3514 1.557099 AGTGACTACATCCGGAGCAA 58.443 50.000 11.34 0.00 0.00 3.91
2992 3515 1.899814 AGTGACTACATCCGGAGCAAA 59.100 47.619 11.34 0.00 0.00 3.68
2993 3516 2.301870 AGTGACTACATCCGGAGCAAAA 59.698 45.455 11.34 0.00 0.00 2.44
2994 3517 3.055094 AGTGACTACATCCGGAGCAAAAT 60.055 43.478 11.34 0.00 0.00 1.82
2995 3518 3.063997 GTGACTACATCCGGAGCAAAATG 59.936 47.826 11.34 4.36 0.00 2.32
2996 3519 3.055458 TGACTACATCCGGAGCAAAATGA 60.055 43.478 11.34 0.00 0.00 2.57
2997 3520 3.535561 ACTACATCCGGAGCAAAATGAG 58.464 45.455 11.34 4.60 0.00 2.90
2998 3521 2.496899 ACATCCGGAGCAAAATGAGT 57.503 45.000 11.34 0.00 0.00 3.41
2999 3522 2.086869 ACATCCGGAGCAAAATGAGTG 58.913 47.619 11.34 0.98 0.00 3.51
3000 3523 2.290260 ACATCCGGAGCAAAATGAGTGA 60.290 45.455 11.34 0.00 0.00 3.41
3001 3524 2.559698 TCCGGAGCAAAATGAGTGAA 57.440 45.000 0.00 0.00 0.00 3.18
3002 3525 3.071874 TCCGGAGCAAAATGAGTGAAT 57.928 42.857 0.00 0.00 0.00 2.57
3003 3526 3.009723 TCCGGAGCAAAATGAGTGAATC 58.990 45.455 0.00 0.00 0.00 2.52
3004 3527 3.012518 CCGGAGCAAAATGAGTGAATCT 58.987 45.455 0.00 0.00 0.00 2.40
3005 3528 4.081142 TCCGGAGCAAAATGAGTGAATCTA 60.081 41.667 0.00 0.00 0.00 1.98
3006 3529 4.034510 CCGGAGCAAAATGAGTGAATCTAC 59.965 45.833 0.00 0.00 0.00 2.59
3007 3530 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3008 3531 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3041 3564 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
3043 3566 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
3045 3568 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
3046 3569 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
3047 3570 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
3048 3571 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
3049 3572 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
3051 3574 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
3052 3575 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
3053 3576 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
3054 3577 5.104693 TCCGTATGTGGTAGTCCATTTGAAT 60.105 40.000 0.00 0.00 46.20 2.57
3055 3578 6.098552 TCCGTATGTGGTAGTCCATTTGAATA 59.901 38.462 0.00 0.00 46.20 1.75
3056 3579 6.934645 CCGTATGTGGTAGTCCATTTGAATAT 59.065 38.462 0.00 0.00 46.20 1.28
3057 3580 7.117812 CCGTATGTGGTAGTCCATTTGAATATC 59.882 40.741 0.00 0.00 46.20 1.63
3058 3581 7.872993 CGTATGTGGTAGTCCATTTGAATATCT 59.127 37.037 0.00 0.00 46.20 1.98
3059 3582 8.993121 GTATGTGGTAGTCCATTTGAATATCTG 58.007 37.037 0.00 0.00 46.20 2.90
3060 3583 7.194112 TGTGGTAGTCCATTTGAATATCTGA 57.806 36.000 0.00 0.00 46.20 3.27
3061 3584 7.629157 TGTGGTAGTCCATTTGAATATCTGAA 58.371 34.615 0.00 0.00 46.20 3.02
3062 3585 8.106462 TGTGGTAGTCCATTTGAATATCTGAAA 58.894 33.333 0.00 0.00 46.20 2.69
3063 3586 8.956426 GTGGTAGTCCATTTGAATATCTGAAAA 58.044 33.333 0.00 0.00 46.20 2.29
3064 3587 8.956426 TGGTAGTCCATTTGAATATCTGAAAAC 58.044 33.333 0.00 0.00 39.03 2.43
3065 3588 8.956426 GGTAGTCCATTTGAATATCTGAAAACA 58.044 33.333 0.00 0.00 0.00 2.83
3066 3589 9.774742 GTAGTCCATTTGAATATCTGAAAACAC 57.225 33.333 0.00 0.00 0.00 3.32
3067 3590 8.408043 AGTCCATTTGAATATCTGAAAACACA 57.592 30.769 0.00 0.00 0.00 3.72
3068 3591 8.859090 AGTCCATTTGAATATCTGAAAACACAA 58.141 29.630 0.00 0.00 0.00 3.33
3069 3592 9.474920 GTCCATTTGAATATCTGAAAACACAAA 57.525 29.630 0.00 0.00 0.00 2.83
3081 3604 9.840427 ATCTGAAAACACAAATATTTAGGAACG 57.160 29.630 0.00 0.00 0.00 3.95
3082 3605 8.293867 TCTGAAAACACAAATATTTAGGAACGG 58.706 33.333 0.00 0.00 0.00 4.44
3083 3606 8.167605 TGAAAACACAAATATTTAGGAACGGA 57.832 30.769 0.00 0.00 0.00 4.69
3084 3607 8.293867 TGAAAACACAAATATTTAGGAACGGAG 58.706 33.333 0.00 0.00 0.00 4.63
3085 3608 6.753107 AACACAAATATTTAGGAACGGAGG 57.247 37.500 0.00 0.00 0.00 4.30
3086 3609 5.190677 ACACAAATATTTAGGAACGGAGGG 58.809 41.667 0.00 0.00 0.00 4.30
3087 3610 5.045432 ACACAAATATTTAGGAACGGAGGGA 60.045 40.000 0.00 0.00 0.00 4.20
3091 3614 8.445588 ACAAATATTTAGGAACGGAGGGAATAT 58.554 33.333 0.00 0.00 0.00 1.28
3108 3631 6.335311 AGGGAATATAATCTTGGGATGGTTCA 59.665 38.462 0.00 0.00 31.75 3.18
3158 3681 7.935755 TGAATCTTTACAATTTGCATTTTCCCA 59.064 29.630 0.00 0.00 0.00 4.37
3163 3686 4.142790 ACAATTTGCATTTTCCCATTGCA 58.857 34.783 0.00 0.00 44.12 4.08
3165 3688 2.924757 TTGCATTTTCCCATTGCACA 57.075 40.000 0.00 0.00 45.35 4.57
3168 3691 2.302157 TGCATTTTCCCATTGCACATCA 59.698 40.909 0.00 0.00 41.18 3.07
3217 3740 4.380531 ACATGTGAGAAATGAGTGTCGTT 58.619 39.130 0.00 0.00 0.00 3.85
3252 3775 5.850614 ACAATACCCATACGAGGATAACAC 58.149 41.667 0.00 0.00 0.00 3.32
3303 3826 7.016268 ACACAAAGAGAGATTTACCTAGGTTCA 59.984 37.037 22.11 7.52 0.00 3.18
3304 3827 7.547370 CACAAAGAGAGATTTACCTAGGTTCAG 59.453 40.741 22.11 6.44 0.00 3.02
3306 3829 4.651962 AGAGAGATTTACCTAGGTTCAGGC 59.348 45.833 22.11 6.55 39.53 4.85
3311 3834 2.354261 TACCTAGGTTCAGGCCCTTT 57.646 50.000 22.11 0.00 39.53 3.11
3350 3873 8.532819 ACCCTACTTTCTACTTGTCTTTGATAG 58.467 37.037 0.00 0.00 0.00 2.08
3392 3915 5.944007 AGTGCTAGGGTTTGTATTTACAAGG 59.056 40.000 3.60 0.00 45.77 3.61
3395 3918 5.589050 GCTAGGGTTTGTATTTACAAGGGAG 59.411 44.000 3.60 1.36 45.77 4.30
3402 3925 4.928601 TGTATTTACAAGGGAGTCGATCG 58.071 43.478 9.36 9.36 32.40 3.69
3426 3949 5.687441 GCAAGATCATATAGGGGTTGACACA 60.687 44.000 0.00 0.00 0.00 3.72
3433 3956 8.966155 TCATATAGGGGTTGACACATTAGATA 57.034 34.615 0.00 0.00 0.00 1.98
3547 4070 5.885912 GGAGTTTTCCTATGCTACATTTGGA 59.114 40.000 0.00 0.00 40.58 3.53
3548 4071 6.547510 GGAGTTTTCCTATGCTACATTTGGAT 59.452 38.462 3.83 0.00 40.58 3.41
3549 4072 7.068716 GGAGTTTTCCTATGCTACATTTGGATT 59.931 37.037 3.83 0.00 40.58 3.01
3550 4073 8.366359 AGTTTTCCTATGCTACATTTGGATTT 57.634 30.769 3.83 0.00 0.00 2.17
3551 4074 8.253113 AGTTTTCCTATGCTACATTTGGATTTG 58.747 33.333 3.83 0.00 0.00 2.32
3552 4075 6.713762 TTCCTATGCTACATTTGGATTTGG 57.286 37.500 3.83 0.00 0.00 3.28
3653 4347 0.463295 AAGATGGCGATGCACTCCAG 60.463 55.000 8.99 0.00 36.78 3.86
3727 4422 1.300233 CATTCGTAGCCTCCGAGCC 60.300 63.158 0.00 0.00 35.49 4.70
3736 4431 2.294078 CCTCCGAGCCCTTCAAGGT 61.294 63.158 1.78 0.00 31.93 3.50
3740 4435 0.391793 CCGAGCCCTTCAAGGTCTTC 60.392 60.000 1.78 0.00 31.93 2.87
3743 4438 2.705730 GAGCCCTTCAAGGTCTTCTTC 58.294 52.381 1.78 0.00 31.93 2.87
3746 4441 3.139211 AGCCCTTCAAGGTCTTCTTCTTT 59.861 43.478 1.78 0.00 31.93 2.52
3747 4442 3.504134 GCCCTTCAAGGTCTTCTTCTTTC 59.496 47.826 1.78 0.00 31.93 2.62
3748 4443 4.748239 GCCCTTCAAGGTCTTCTTCTTTCT 60.748 45.833 1.78 0.00 31.93 2.52
3749 4444 5.380900 CCCTTCAAGGTCTTCTTCTTTCTT 58.619 41.667 1.78 0.00 31.93 2.52
3750 4445 5.240403 CCCTTCAAGGTCTTCTTCTTTCTTG 59.760 44.000 1.78 0.00 31.93 3.02
3758 4453 8.480133 AGGTCTTCTTCTTTCTTGACTACTAA 57.520 34.615 0.00 0.00 0.00 2.24
3771 4466 5.125100 TGACTACTAATAAATACCCCGCG 57.875 43.478 0.00 0.00 0.00 6.46
3778 4473 2.855880 TAAATACCCCGCGCGTTGCT 62.856 55.000 29.95 10.35 43.27 3.91
3793 4488 1.810151 GTTGCTGCGGGATTTCTTGTA 59.190 47.619 0.00 0.00 0.00 2.41
3798 4493 4.515191 TGCTGCGGGATTTCTTGTATTATC 59.485 41.667 0.00 0.00 0.00 1.75
3826 4521 9.581289 TGGTATGAGAAAGGAAGAATTAAAACA 57.419 29.630 0.00 0.00 0.00 2.83
3910 4605 3.971971 AGGCCCGATGGTAGTAATAGTTT 59.028 43.478 0.00 0.00 0.00 2.66
3912 4607 4.753610 GGCCCGATGGTAGTAATAGTTTTC 59.246 45.833 0.00 0.00 0.00 2.29
3915 4610 5.919141 CCCGATGGTAGTAATAGTTTTCTCG 59.081 44.000 0.00 0.00 0.00 4.04
3929 4624 6.296365 AGTTTTCTCGTGTAACTTAAAGCC 57.704 37.500 0.00 0.00 31.75 4.35
3949 4644 6.124316 AGCCTCATATGCTTGATACAGAAT 57.876 37.500 0.00 0.00 34.87 2.40
3993 4688 4.201910 CCAATGACCGCGTCAGATTATTTT 60.202 41.667 4.92 0.00 46.04 1.82
4048 4743 9.516546 AATAGATATGGCATGCAAGATATATGG 57.483 33.333 21.36 0.00 0.00 2.74
4255 4952 1.544246 TGACTTAGTAGCAGCGCTTCA 59.456 47.619 7.50 2.12 40.44 3.02
4305 5002 1.153628 CACTTCTCCTTACCCGCGG 60.154 63.158 21.04 21.04 0.00 6.46
4316 5013 3.319122 CCTTACCCGCGGTACTACTATTT 59.681 47.826 26.12 0.00 37.97 1.40
4656 5365 8.642908 TCATTATCAACTCTAACACATTACCG 57.357 34.615 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 3.764466 CCAGAGTTCGCCGGAGCT 61.764 66.667 5.05 0.00 36.32 4.09
292 293 2.254350 CGCCGTGTTCAGACGAGA 59.746 61.111 0.00 0.00 42.10 4.04
399 400 4.100084 TAGGCGACGTCCTCCGGA 62.100 66.667 10.58 2.93 42.24 5.14
565 566 2.045926 GATGTCCAGCCACCGCTT 60.046 61.111 0.00 0.00 45.55 4.68
605 606 0.467474 ACCACTATCATCCTCGGCGA 60.467 55.000 10.14 10.14 0.00 5.54
841 906 1.154054 CAGCCGCGCTAAAATGCAA 60.154 52.632 5.56 0.00 36.40 4.08
882 947 0.605319 GCCCATCGTCTGGTTTGACA 60.605 55.000 6.14 0.00 44.30 3.58
943 1008 3.775202 CTGTCTTAGACCATCTCCAACG 58.225 50.000 10.10 0.00 0.00 4.10
954 1019 4.134563 TGTTTTCTTGGGCTGTCTTAGAC 58.865 43.478 5.27 5.27 0.00 2.59
1067 1134 0.679640 GATGCGGAATTGTGGTGGGA 60.680 55.000 0.00 0.00 0.00 4.37
1248 1321 4.392166 TCGGCCTGGTCCAGCCTA 62.392 66.667 22.40 13.69 38.35 3.93
1410 1588 1.746615 CTTCCGCACCATGGACCTG 60.747 63.158 21.47 7.72 34.56 4.00
1534 1717 2.623889 CGAAAGAGATCGGGGTGATAGT 59.376 50.000 0.00 0.00 37.47 2.12
1860 2268 5.762179 TTGTCAGAGATAAGGGTCACAAT 57.238 39.130 0.00 0.00 0.00 2.71
1964 2372 3.485394 TCTAGCAGCAATTTCAACCACA 58.515 40.909 0.00 0.00 0.00 4.17
2006 2414 3.199946 ACCTTCCAGTGACAAGTCTGAAA 59.800 43.478 1.53 0.00 34.02 2.69
2021 2429 7.691213 TGTTACCATTTTCATAGTACCTTCCA 58.309 34.615 0.00 0.00 0.00 3.53
2033 2441 6.909550 AATGCTACCTTGTTACCATTTTCA 57.090 33.333 0.00 0.00 0.00 2.69
2207 2615 2.544267 GGTTATCCAGGAAAATCTCGCG 59.456 50.000 0.00 0.00 0.00 5.87
2213 2621 6.001449 TCATCGAAGGTTATCCAGGAAAAT 57.999 37.500 0.00 0.00 35.89 1.82
2403 2820 2.391616 TGCTTGTCGAGATCTGCATT 57.608 45.000 0.00 0.00 0.00 3.56
2481 2914 7.551585 ACTTCATCAAGACATTACACCTCTAG 58.448 38.462 0.00 0.00 33.34 2.43
2482 2915 7.482169 ACTTCATCAAGACATTACACCTCTA 57.518 36.000 0.00 0.00 33.34 2.43
2483 2916 6.365970 ACTTCATCAAGACATTACACCTCT 57.634 37.500 0.00 0.00 33.34 3.69
2485 2918 6.299141 ACAACTTCATCAAGACATTACACCT 58.701 36.000 0.00 0.00 33.34 4.00
2487 2920 6.348540 GGGACAACTTCATCAAGACATTACAC 60.349 42.308 0.00 0.00 33.34 2.90
2488 2921 5.705441 GGGACAACTTCATCAAGACATTACA 59.295 40.000 0.00 0.00 33.34 2.41
2489 2922 5.123979 GGGGACAACTTCATCAAGACATTAC 59.876 44.000 0.00 0.00 33.34 1.89
2505 2938 2.698274 ACACATTCCAAAAGGGGACAAC 59.302 45.455 0.00 0.00 36.46 3.32
2506 2939 2.697751 CACACATTCCAAAAGGGGACAA 59.302 45.455 0.00 0.00 36.46 3.18
2509 2942 1.337118 GCACACATTCCAAAAGGGGA 58.663 50.000 0.00 0.00 37.22 4.81
2674 3107 6.678663 CACAAGCATCTAAAATTAACGACTCG 59.321 38.462 0.00 0.00 0.00 4.18
2813 3251 7.710676 TGGGTTTACAATATGTTTGTGCTAT 57.289 32.000 6.21 0.00 34.11 2.97
2840 3278 4.976864 AGTAAACACGGGGTTACAATCTT 58.023 39.130 26.56 3.33 39.29 2.40
2850 3288 6.482973 TGTTAGAGTTTTAAGTAAACACGGGG 59.517 38.462 0.00 0.00 46.93 5.73
2918 3356 7.226059 AGGAATGGAGGGAGTATAAACAAAT 57.774 36.000 0.00 0.00 0.00 2.32
2927 3365 8.344939 ACAAATATTTAGGAATGGAGGGAGTA 57.655 34.615 0.00 0.00 0.00 2.59
2928 3366 7.129504 AGACAAATATTTAGGAATGGAGGGAGT 59.870 37.037 0.00 0.00 0.00 3.85
2929 3367 7.521669 AGACAAATATTTAGGAATGGAGGGAG 58.478 38.462 0.00 0.00 0.00 4.30
2930 3368 7.465900 AGACAAATATTTAGGAATGGAGGGA 57.534 36.000 0.00 0.00 0.00 4.20
2931 3369 8.539117 AAAGACAAATATTTAGGAATGGAGGG 57.461 34.615 0.00 0.00 0.00 4.30
2932 3370 9.413734 AGAAAGACAAATATTTAGGAATGGAGG 57.586 33.333 0.00 0.00 0.00 4.30
2945 3468 9.753674 TGTTGAAATCCCTAGAAAGACAAATAT 57.246 29.630 0.00 0.00 0.00 1.28
2947 3470 8.477419 TTGTTGAAATCCCTAGAAAGACAAAT 57.523 30.769 0.00 0.00 0.00 2.32
2948 3471 7.559897 ACTTGTTGAAATCCCTAGAAAGACAAA 59.440 33.333 0.00 0.00 0.00 2.83
2951 3474 6.710744 TCACTTGTTGAAATCCCTAGAAAGAC 59.289 38.462 0.00 0.00 0.00 3.01
2952 3475 6.710744 GTCACTTGTTGAAATCCCTAGAAAGA 59.289 38.462 0.00 0.00 35.39 2.52
2957 3480 6.464222 TGTAGTCACTTGTTGAAATCCCTAG 58.536 40.000 0.00 0.00 35.39 3.02
2963 3486 4.695455 CCGGATGTAGTCACTTGTTGAAAT 59.305 41.667 0.00 0.00 35.39 2.17
2964 3487 4.062293 CCGGATGTAGTCACTTGTTGAAA 58.938 43.478 0.00 0.00 35.39 2.69
2965 3488 3.322541 TCCGGATGTAGTCACTTGTTGAA 59.677 43.478 0.00 0.00 35.39 2.69
2966 3489 2.894765 TCCGGATGTAGTCACTTGTTGA 59.105 45.455 0.00 0.00 0.00 3.18
2967 3490 3.254060 CTCCGGATGTAGTCACTTGTTG 58.746 50.000 3.57 0.00 0.00 3.33
2968 3491 2.353803 GCTCCGGATGTAGTCACTTGTT 60.354 50.000 3.57 0.00 0.00 2.83
2969 3492 1.204941 GCTCCGGATGTAGTCACTTGT 59.795 52.381 3.57 0.00 0.00 3.16
2970 3493 1.204704 TGCTCCGGATGTAGTCACTTG 59.795 52.381 3.57 0.00 0.00 3.16
2973 3496 2.380084 TTTGCTCCGGATGTAGTCAC 57.620 50.000 3.57 0.00 0.00 3.67
2974 3497 3.055458 TCATTTTGCTCCGGATGTAGTCA 60.055 43.478 3.57 0.00 0.00 3.41
2976 3499 3.055094 ACTCATTTTGCTCCGGATGTAGT 60.055 43.478 3.57 2.45 0.00 2.73
2977 3500 3.310774 CACTCATTTTGCTCCGGATGTAG 59.689 47.826 3.57 0.00 0.00 2.74
2978 3501 3.055458 TCACTCATTTTGCTCCGGATGTA 60.055 43.478 3.57 0.00 0.00 2.29
2980 3503 2.358957 TCACTCATTTTGCTCCGGATG 58.641 47.619 3.57 0.00 0.00 3.51
2982 3505 2.559698 TTCACTCATTTTGCTCCGGA 57.440 45.000 2.93 2.93 0.00 5.14
2983 3506 3.012518 AGATTCACTCATTTTGCTCCGG 58.987 45.455 0.00 0.00 0.00 5.14
2984 3507 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2985 3508 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2986 3509 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3015 3538 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
3017 3540 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
3018 3541 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
3019 3542 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
3020 3543 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
3021 3544 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
3022 3545 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
3023 3546 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
3024 3547 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
3025 3548 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
3039 3562 8.956426 TGTTTTCAGATATTCAAATGGACTACC 58.044 33.333 0.00 0.00 0.00 3.18
3041 3564 9.513906 TGTGTTTTCAGATATTCAAATGGACTA 57.486 29.630 0.00 0.00 0.00 2.59
3042 3565 8.408043 TGTGTTTTCAGATATTCAAATGGACT 57.592 30.769 0.00 0.00 0.00 3.85
3043 3566 9.474920 TTTGTGTTTTCAGATATTCAAATGGAC 57.525 29.630 0.00 0.00 0.00 4.02
3055 3578 9.840427 CGTTCCTAAATATTTGTGTTTTCAGAT 57.160 29.630 11.05 0.00 0.00 2.90
3056 3579 8.293867 CCGTTCCTAAATATTTGTGTTTTCAGA 58.706 33.333 11.05 0.00 0.00 3.27
3057 3580 8.293867 TCCGTTCCTAAATATTTGTGTTTTCAG 58.706 33.333 11.05 0.00 0.00 3.02
3058 3581 8.167605 TCCGTTCCTAAATATTTGTGTTTTCA 57.832 30.769 11.05 0.00 0.00 2.69
3059 3582 7.753580 CCTCCGTTCCTAAATATTTGTGTTTTC 59.246 37.037 11.05 0.00 0.00 2.29
3060 3583 7.309560 CCCTCCGTTCCTAAATATTTGTGTTTT 60.310 37.037 11.05 0.00 0.00 2.43
3061 3584 6.152154 CCCTCCGTTCCTAAATATTTGTGTTT 59.848 38.462 11.05 0.00 0.00 2.83
3062 3585 5.650703 CCCTCCGTTCCTAAATATTTGTGTT 59.349 40.000 11.05 0.00 0.00 3.32
3063 3586 5.045432 TCCCTCCGTTCCTAAATATTTGTGT 60.045 40.000 11.05 0.00 0.00 3.72
3064 3587 5.433526 TCCCTCCGTTCCTAAATATTTGTG 58.566 41.667 11.05 3.85 0.00 3.33
3065 3588 5.703730 TCCCTCCGTTCCTAAATATTTGT 57.296 39.130 11.05 0.00 0.00 2.83
3066 3589 8.863872 ATATTCCCTCCGTTCCTAAATATTTG 57.136 34.615 11.05 1.40 0.00 2.32
3070 3593 9.556772 AGATTATATTCCCTCCGTTCCTAAATA 57.443 33.333 0.00 0.00 0.00 1.40
3071 3594 8.450780 AGATTATATTCCCTCCGTTCCTAAAT 57.549 34.615 0.00 0.00 0.00 1.40
3072 3595 7.867160 AGATTATATTCCCTCCGTTCCTAAA 57.133 36.000 0.00 0.00 0.00 1.85
3073 3596 7.256547 CCAAGATTATATTCCCTCCGTTCCTAA 60.257 40.741 0.00 0.00 0.00 2.69
3074 3597 6.212791 CCAAGATTATATTCCCTCCGTTCCTA 59.787 42.308 0.00 0.00 0.00 2.94
3075 3598 5.013183 CCAAGATTATATTCCCTCCGTTCCT 59.987 44.000 0.00 0.00 0.00 3.36
3076 3599 5.246307 CCAAGATTATATTCCCTCCGTTCC 58.754 45.833 0.00 0.00 0.00 3.62
3077 3600 5.012768 TCCCAAGATTATATTCCCTCCGTTC 59.987 44.000 0.00 0.00 0.00 3.95
3078 3601 4.911522 TCCCAAGATTATATTCCCTCCGTT 59.088 41.667 0.00 0.00 0.00 4.44
3079 3602 4.499472 TCCCAAGATTATATTCCCTCCGT 58.501 43.478 0.00 0.00 0.00 4.69
3080 3603 5.431765 CATCCCAAGATTATATTCCCTCCG 58.568 45.833 0.00 0.00 0.00 4.63
3081 3604 5.254032 ACCATCCCAAGATTATATTCCCTCC 59.746 44.000 0.00 0.00 0.00 4.30
3082 3605 6.394345 ACCATCCCAAGATTATATTCCCTC 57.606 41.667 0.00 0.00 0.00 4.30
3083 3606 6.335311 TGAACCATCCCAAGATTATATTCCCT 59.665 38.462 0.00 0.00 0.00 4.20
3084 3607 6.552008 TGAACCATCCCAAGATTATATTCCC 58.448 40.000 0.00 0.00 0.00 3.97
3085 3608 9.927081 ATATGAACCATCCCAAGATTATATTCC 57.073 33.333 0.00 0.00 0.00 3.01
3123 3646 7.951565 GCAAATTGTAAAGATTCAATGTTTCGG 59.048 33.333 0.00 0.00 34.98 4.30
3124 3647 8.486383 TGCAAATTGTAAAGATTCAATGTTTCG 58.514 29.630 0.00 0.00 34.98 3.46
3158 3681 4.708421 AGGACTTGCTATTTGATGTGCAAT 59.292 37.500 0.00 0.00 43.17 3.56
3163 3686 5.564550 AGTCAAGGACTTGCTATTTGATGT 58.435 37.500 7.18 0.00 40.28 3.06
3165 3688 5.189180 GGAGTCAAGGACTTGCTATTTGAT 58.811 41.667 7.18 0.00 43.53 2.57
3168 3691 4.640771 TGGAGTCAAGGACTTGCTATTT 57.359 40.909 7.18 0.00 43.53 1.40
3217 3740 3.772387 TGGGTATTGTTGAGGAAATGCA 58.228 40.909 0.00 0.00 0.00 3.96
3252 3775 2.159476 CCATTTGGTTCTCTGATGTGCG 60.159 50.000 0.00 0.00 0.00 5.34
3303 3826 0.838987 TTACCTCGACCAAAGGGCCT 60.839 55.000 0.00 0.00 38.29 5.19
3304 3827 0.255033 ATTACCTCGACCAAAGGGCC 59.745 55.000 0.00 0.00 38.29 5.80
3306 3829 2.158856 GGGTATTACCTCGACCAAAGGG 60.159 54.545 12.54 0.00 38.64 3.95
3311 3834 3.959495 AGTAGGGTATTACCTCGACCA 57.041 47.619 12.54 0.00 42.09 4.02
3350 3873 4.036971 AGCACTCACACGAGGATAGATTAC 59.963 45.833 0.00 0.00 44.17 1.89
3402 3925 4.757149 GTGTCAACCCCTATATGATCTTGC 59.243 45.833 0.00 0.00 0.00 4.01
3433 3956 6.153680 CGATAGGTCCCTTATTCTAGCAAGAT 59.846 42.308 0.00 0.00 0.00 2.40
3518 4041 0.651031 GCATAGGAAAACTCCGCGAC 59.349 55.000 8.23 0.00 34.28 5.19
3522 4045 5.220854 CCAAATGTAGCATAGGAAAACTCCG 60.221 44.000 0.00 0.00 34.28 4.63
3641 4164 2.159043 ACCTACAATCTGGAGTGCATCG 60.159 50.000 0.00 0.00 0.00 3.84
3653 4347 2.213499 CTCGAATGCCCACCTACAATC 58.787 52.381 0.00 0.00 0.00 2.67
3712 4407 3.657038 AAGGGCTCGGAGGCTACGA 62.657 63.158 27.72 22.42 41.09 3.43
3727 4422 6.017523 GTCAAGAAAGAAGAAGACCTTGAAGG 60.018 42.308 10.24 10.24 40.77 3.46
3743 4438 9.257651 CGGGGTATTTATTAGTAGTCAAGAAAG 57.742 37.037 0.00 0.00 0.00 2.62
3746 4441 6.515531 CGCGGGGTATTTATTAGTAGTCAAGA 60.516 42.308 0.00 0.00 0.00 3.02
3747 4442 5.632347 CGCGGGGTATTTATTAGTAGTCAAG 59.368 44.000 0.00 0.00 0.00 3.02
3748 4443 5.531634 CGCGGGGTATTTATTAGTAGTCAA 58.468 41.667 0.00 0.00 0.00 3.18
3749 4444 4.559300 GCGCGGGGTATTTATTAGTAGTCA 60.559 45.833 8.83 0.00 0.00 3.41
3750 4445 3.922850 GCGCGGGGTATTTATTAGTAGTC 59.077 47.826 8.83 0.00 0.00 2.59
3758 4453 1.778027 GCAACGCGCGGGGTATTTAT 61.778 55.000 35.22 6.31 0.00 1.40
3771 4466 2.200170 AAGAAATCCCGCAGCAACGC 62.200 55.000 0.00 0.00 0.00 4.84
3778 4473 5.063204 CAGGATAATACAAGAAATCCCGCA 58.937 41.667 0.00 0.00 38.99 5.69
3787 4482 8.651389 CCTTTCTCATACCAGGATAATACAAGA 58.349 37.037 0.00 0.00 0.00 3.02
3793 4488 7.937700 TCTTCCTTTCTCATACCAGGATAAT 57.062 36.000 0.00 0.00 35.30 1.28
3798 4493 8.807948 TTTAATTCTTCCTTTCTCATACCAGG 57.192 34.615 0.00 0.00 0.00 4.45
3825 4520 6.524239 GCATATGACAACAGTTGTAATGTGTG 59.476 38.462 28.53 21.66 45.52 3.82
3826 4521 6.206438 TGCATATGACAACAGTTGTAATGTGT 59.794 34.615 28.53 13.83 45.52 3.72
3893 4588 6.971184 ACACGAGAAAACTATTACTACCATCG 59.029 38.462 0.00 0.00 0.00 3.84
3910 4605 5.204409 TGAGGCTTTAAGTTACACGAGAA 57.796 39.130 0.00 0.00 0.00 2.87
3912 4607 6.292381 GCATATGAGGCTTTAAGTTACACGAG 60.292 42.308 6.97 0.00 0.00 4.18
3915 4610 6.927294 AGCATATGAGGCTTTAAGTTACAC 57.073 37.500 6.97 0.00 38.81 2.90
3949 4644 8.748412 CATTGGATCCAAAACCTTACTATTTCA 58.252 33.333 30.28 2.05 39.55 2.69
3958 4653 2.825532 CGGTCATTGGATCCAAAACCTT 59.174 45.455 35.91 20.67 40.57 3.50
4026 4721 6.301486 TCCCATATATCTTGCATGCCATATC 58.699 40.000 16.68 0.00 0.00 1.63
4047 4742 8.160106 ACATGTTATAGAATCTCCATCTTTCCC 58.840 37.037 0.00 0.00 0.00 3.97
4048 4743 9.566432 AACATGTTATAGAATCTCCATCTTTCC 57.434 33.333 9.97 0.00 0.00 3.13
4098 4795 2.921834 TTCCCTAGTAGTGAGGTGCT 57.078 50.000 0.00 0.00 31.52 4.40
4255 4952 4.402793 AGTTACCAGTAGCGATGTTCTGAT 59.597 41.667 4.44 0.00 0.00 2.90
4288 4985 0.323725 TACCGCGGGTAAGGAGAAGT 60.324 55.000 31.76 5.83 34.97 3.01
4538 5247 9.836076 CAATGATGTATTATGATGCTAAGTTGG 57.164 33.333 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.