Multiple sequence alignment - TraesCS6B01G308400

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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 TraesCS6B01G308400 chr6B 100.000 5378 0 0 1 5378 552398224 552403601 0.000000e+00 9932.0
1 TraesCS6B01G308400 chr6A 95.902 1342 50 3 1316 2652 507115026 507116367 0.000000e+00 2169.0
2 TraesCS6B01G308400 chr6A 93.160 1345 59 11 3263 4575 507117011 507118354 0.000000e+00 1943.0
3 TraesCS6B01G308400 chr6A 92.348 575 23 5 2690 3264 507116364 507116917 0.000000e+00 798.0
4 TraesCS6B01G308400 chr6A 94.292 473 20 4 846 1313 507114503 507114973 0.000000e+00 717.0
5 TraesCS6B01G308400 chr6A 84.565 758 72 21 6 734 507113759 507114500 0.000000e+00 710.0
6 TraesCS6B01G308400 chr6A 94.146 205 11 1 4654 4857 507118480 507118684 1.450000e-80 311.0
7 TraesCS6B01G308400 chr6A 78.278 511 60 24 4848 5339 507118881 507119359 1.140000e-71 281.0
8 TraesCS6B01G308400 chr6A 87.778 90 4 2 19 107 560695185 560695102 1.230000e-16 99.0
9 TraesCS6B01G308400 chr6D 93.696 1285 41 14 1316 2585 366677538 366678797 0.000000e+00 1888.0
10 TraesCS6B01G308400 chr6D 86.544 1635 162 41 2970 4571 366679179 366680788 0.000000e+00 1748.0
11 TraesCS6B01G308400 chr6D 90.753 876 36 19 458 1313 366676635 366677485 0.000000e+00 1127.0
12 TraesCS6B01G308400 chr6D 88.136 472 44 7 2 463 366545933 366546402 7.870000e-153 551.0
13 TraesCS6B01G308400 chr6D 86.595 373 27 6 4654 5016 366680916 366681275 1.820000e-104 390.0
14 TraesCS6B01G308400 chr6D 86.614 254 19 9 994 1232 24030757 24031010 3.190000e-67 267.0
15 TraesCS6B01G308400 chr6D 100.000 29 0 0 2672 2700 55924911 55924939 3.000000e-03 54.7
16 TraesCS6B01G308400 chr6D 100.000 28 0 0 5019 5046 366681860 366681887 1.000000e-02 52.8
17 TraesCS6B01G308400 chr2B 81.960 449 47 22 5 426 373982661 373983102 3.080000e-92 350.0
18 TraesCS6B01G308400 chr1D 85.846 325 37 6 109 426 399042870 399043192 2.400000e-88 337.0
19 TraesCS6B01G308400 chr1D 84.663 326 40 7 109 426 398987341 398987664 3.130000e-82 316.0
20 TraesCS6B01G308400 chr1D 94.643 56 1 2 7 61 42982597 42982543 9.600000e-13 86.1
21 TraesCS6B01G308400 chr1D 90.164 61 6 0 2808 2868 283615455 283615395 4.470000e-11 80.5
22 TraesCS6B01G308400 chr2D 80.846 449 53 22 5 426 305865749 305866191 6.720000e-84 322.0
23 TraesCS6B01G308400 chr2D 86.192 239 30 3 191 426 270844660 270844898 6.910000e-64 255.0
24 TraesCS6B01G308400 chr2D 85.577 104 12 3 5 107 646590746 646590847 7.370000e-19 106.0
25 TraesCS6B01G308400 chr2D 82.432 74 10 2 110 182 106968036 106967965 1.620000e-05 62.1
26 TraesCS6B01G308400 chr1A 85.489 317 35 8 118 426 495716012 495716325 2.420000e-83 320.0
27 TraesCS6B01G308400 chr1A 96.875 64 2 0 2808 2871 64714393 64714330 2.050000e-19 108.0
28 TraesCS6B01G308400 chr1A 92.857 70 2 3 2808 2875 64714369 64714437 1.230000e-16 99.0
29 TraesCS6B01G308400 chr2A 80.044 451 56 16 5 426 384677744 384678189 2.430000e-78 303.0
30 TraesCS6B01G308400 chr2A 84.615 104 12 4 5 107 773222767 773222667 3.430000e-17 100.0
31 TraesCS6B01G308400 chr2A 98.113 53 0 1 2818 2870 607487827 607487776 2.060000e-14 91.6
32 TraesCS6B01G308400 chr4D 86.458 288 19 10 960 1232 450714566 450714848 1.130000e-76 298.0
33 TraesCS6B01G308400 chr4D 100.000 29 0 0 2672 2700 476314631 476314603 3.000000e-03 54.7
34 TraesCS6B01G308400 chr3B 85.911 291 21 9 960 1235 782651018 782650733 5.270000e-75 292.0
35 TraesCS6B01G308400 chr3B 88.412 233 20 2 960 1192 49404775 49404550 1.910000e-69 274.0
36 TraesCS6B01G308400 chr3D 87.747 253 16 9 998 1235 40718608 40718356 1.140000e-71 281.0
37 TraesCS6B01G308400 chr3D 86.614 254 19 9 994 1232 28478970 28479223 3.190000e-67 267.0
38 TraesCS6B01G308400 chr3D 100.000 29 0 0 2672 2700 462452731 462452703 3.000000e-03 54.7
39 TraesCS6B01G308400 chr7D 87.200 250 17 9 994 1228 548208580 548208829 2.470000e-68 270.0
40 TraesCS6B01G308400 chr7D 100.000 30 0 0 2671 2700 20726901 20726930 7.520000e-04 56.5
41 TraesCS6B01G308400 chr4A 85.882 255 22 7 960 1205 343933337 343933586 5.340000e-65 259.0
42 TraesCS6B01G308400 chr7B 95.455 66 2 1 2808 2873 245070383 245070447 2.650000e-18 104.0
43 TraesCS6B01G308400 chr7B 93.939 66 2 2 2808 2872 245070407 245070343 1.230000e-16 99.0
44 TraesCS6B01G308400 chr5D 86.458 96 4 3 4 98 237602449 237602536 4.430000e-16 97.1
45 TraesCS6B01G308400 chr5D 93.220 59 2 2 4 61 514971785 514971842 9.600000e-13 86.1
46 TraesCS6B01G308400 chr7A 84.375 96 6 3 4 98 101466716 101466803 9.600000e-13 86.1
47 TraesCS6B01G308400 chr5B 89.062 64 7 0 2809 2872 101153434 101153497 4.470000e-11 80.5
48 TraesCS6B01G308400 chr5B 96.875 32 1 0 65 96 267874481 267874512 3.000000e-03 54.7
49 TraesCS6B01G308400 chr3A 90.164 61 6 0 2808 2868 37344012 37344072 4.470000e-11 80.5
50 TraesCS6B01G308400 chr3A 100.000 29 0 0 2672 2700 109148109 109148081 3.000000e-03 54.7
51 TraesCS6B01G308400 chr4B 74.346 191 29 14 5093 5276 147143166 147142989 4.500000e-06 63.9


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 TraesCS6B01G308400 chr6B 552398224 552403601 5377 False 9932.000000 9932 100.000000 1 5378 1 chr6B.!!$F1 5377
1 TraesCS6B01G308400 chr6A 507113759 507119359 5600 False 989.857143 2169 90.384429 6 5339 7 chr6A.!!$F1 5333
2 TraesCS6B01G308400 chr6D 366676635 366681887 5252 False 1041.160000 1888 91.517600 458 5046 5 chr6D.!!$F4 4588

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
397 406 0.601057 AACCCAATAACAGCAACGGC 59.399 50.000 0.00 0.0 41.61 5.68 F
1722 1839 0.179000 CGGAAGAAGGAGGATGTGGG 59.821 60.000 0.00 0.0 0.00 4.61 F
2395 2517 1.063417 AGCATCTTTCAGGATTGGGGG 60.063 52.381 0.00 0.0 0.00 5.40 F
3542 3923 0.599060 GGCTATCCTGTACCTCGAGC 59.401 60.000 6.99 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 1942 0.321210 CCAGTACATTGCACGTCCCA 60.321 55.000 0.00 0.0 0.00 4.37 R
2691 2911 0.253044 ACCATGCAGGCACGTCTTAT 59.747 50.000 0.00 0.0 43.14 1.73 R
4368 4780 1.620819 GACTATCCGGATCACCAGCAT 59.379 52.381 23.08 0.0 35.59 3.79 R
4646 5077 0.456221 AGGCGACGGACATCTTACAG 59.544 55.000 0.00 0.0 0.00 2.74 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
32 33 4.264352 TGAGGCCTCCAATTTAGAATTGGT 60.264 41.667 29.95 10.77 46.47 3.67
33 34 4.281657 AGGCCTCCAATTTAGAATTGGTC 58.718 43.478 24.16 16.71 46.47 4.02
45 47 3.761897 AGAATTGGTCACCCGATTTTGA 58.238 40.909 0.00 0.00 43.71 2.69
71 73 6.926272 CCGGGTCAACAATTTTATTTTTCTCA 59.074 34.615 0.00 0.00 0.00 3.27
77 79 9.260002 TCAACAATTTTATTTTTCTCAAGGAGC 57.740 29.630 0.00 0.00 0.00 4.70
92 94 5.183969 TCAAGGAGCTCTCTCATTCAATTG 58.816 41.667 14.64 0.00 40.92 2.32
98 100 7.667219 AGGAGCTCTCTCATTCAATTGTTTTAA 59.333 33.333 14.64 0.00 41.13 1.52
207 209 5.938322 ACATGTAAAAACATCGACATCCAC 58.062 37.500 0.00 0.00 30.13 4.02
397 406 0.601057 AACCCAATAACAGCAACGGC 59.399 50.000 0.00 0.00 41.61 5.68
426 435 1.745489 GCGCCCAACCCTTCTAGTG 60.745 63.158 0.00 0.00 0.00 2.74
447 456 9.243637 CTAGTGAATAGTCAAAGTGAATAGAGC 57.756 37.037 0.00 0.00 34.87 4.09
448 457 6.754209 AGTGAATAGTCAAAGTGAATAGAGCG 59.246 38.462 0.00 0.00 34.87 5.03
454 463 8.989811 ATAGTCAAAGTGAATAGAGCGGAAGGT 61.990 40.741 0.00 0.00 34.82 3.50
625 647 8.546597 AAAGCACAACATTTTAAGTGAAAAGT 57.453 26.923 0.00 0.00 40.34 2.66
626 648 9.646427 AAAGCACAACATTTTAAGTGAAAAGTA 57.354 25.926 0.00 0.00 40.34 2.24
627 649 9.816354 AAGCACAACATTTTAAGTGAAAAGTAT 57.184 25.926 0.00 0.00 40.34 2.12
667 689 1.674519 CGCCTAGGCACACACATAACA 60.675 52.381 32.47 0.00 42.06 2.41
668 690 2.643551 GCCTAGGCACACACATAACAT 58.356 47.619 29.33 0.00 41.49 2.71
670 692 3.065371 GCCTAGGCACACACATAACATTC 59.935 47.826 29.33 0.00 41.49 2.67
671 693 4.260985 CCTAGGCACACACATAACATTCA 58.739 43.478 0.00 0.00 0.00 2.57
672 694 4.094887 CCTAGGCACACACATAACATTCAC 59.905 45.833 0.00 0.00 0.00 3.18
692 718 6.139679 TCACCAAAATACTCCAATCCTTCT 57.860 37.500 0.00 0.00 0.00 2.85
716 745 8.764558 TCTAAGGGTATTTGAGTGTAATTAGCA 58.235 33.333 0.00 0.00 0.00 3.49
774 805 2.071778 AGATGTGTTTGGGTGCAAGT 57.928 45.000 0.00 0.00 0.00 3.16
775 806 3.222173 AGATGTGTTTGGGTGCAAGTA 57.778 42.857 0.00 0.00 0.00 2.24
776 807 3.561143 AGATGTGTTTGGGTGCAAGTAA 58.439 40.909 0.00 0.00 0.00 2.24
777 808 3.569701 AGATGTGTTTGGGTGCAAGTAAG 59.430 43.478 0.00 0.00 0.00 2.34
778 809 1.407258 TGTGTTTGGGTGCAAGTAAGC 59.593 47.619 0.00 0.00 0.00 3.09
779 810 1.407258 GTGTTTGGGTGCAAGTAAGCA 59.593 47.619 0.00 0.00 43.35 3.91
788 819 1.086696 GCAAGTAAGCATTCAGGCGA 58.913 50.000 0.00 0.00 39.27 5.54
798 829 1.352156 ATTCAGGCGACGCGAGAAAC 61.352 55.000 23.21 6.55 0.00 2.78
930 975 2.395690 CAACAAGATCGTCGGCGC 59.604 61.111 3.52 0.00 38.14 6.53
967 1012 1.520666 CTTGTTATCTCCGCCCCGT 59.479 57.895 0.00 0.00 0.00 5.28
972 1017 0.687098 TTATCTCCGCCCCGTAACCA 60.687 55.000 0.00 0.00 0.00 3.67
983 1029 2.377310 CGTAACCACACGCCCGAAG 61.377 63.158 0.00 0.00 34.78 3.79
1050 1101 2.586635 GTGCGGTTCGTGGTGACA 60.587 61.111 0.00 0.00 38.70 3.58
1193 1244 1.157585 GTCCGCTTCTTCCAAGGTTC 58.842 55.000 0.00 0.00 0.00 3.62
1197 1252 1.270839 CGCTTCTTCCAAGGTTCCTCA 60.271 52.381 0.00 0.00 0.00 3.86
1209 1264 2.046864 TTCCTCACTCCCTCGCTCG 61.047 63.158 0.00 0.00 0.00 5.03
1264 1319 3.640029 GTCCCCGTCTAATGGAGTTCATA 59.360 47.826 0.00 0.00 34.44 2.15
1313 1368 6.237384 GCACATATTTGACAGAATTGCTTTCG 60.237 38.462 0.00 0.00 39.46 3.46
1314 1369 6.252015 CACATATTTGACAGAATTGCTTTCGG 59.748 38.462 0.00 0.00 39.46 4.30
1366 1473 4.997395 TGTTCCACAGAGATTTTACTCAGC 59.003 41.667 0.00 0.00 39.14 4.26
1505 1612 4.521639 ACTGCTCTGAATTCATCTGCAAAA 59.478 37.500 21.82 7.96 32.40 2.44
1506 1615 4.801891 TGCTCTGAATTCATCTGCAAAAC 58.198 39.130 20.36 2.83 30.78 2.43
1524 1633 6.149633 GCAAAACTGTCGGAGATTTTACATT 58.850 36.000 0.00 0.00 40.67 2.71
1525 1634 6.088085 GCAAAACTGTCGGAGATTTTACATTG 59.912 38.462 0.00 0.00 40.67 2.82
1564 1681 6.374333 TGTTTGTTTTGCTTCAAGTAGAGAGT 59.626 34.615 0.00 0.00 0.00 3.24
1573 1690 3.902150 TCAAGTAGAGAGTGTTCTTGCG 58.098 45.455 0.00 0.00 36.47 4.85
1637 1754 4.091549 ACCATCATGCCTTGAATTGTCTT 58.908 39.130 0.00 0.00 38.03 3.01
1691 1808 7.620880 AGTATCTGCTGGATTACTTTGTGTTA 58.379 34.615 0.00 0.00 35.98 2.41
1722 1839 0.179000 CGGAAGAAGGAGGATGTGGG 59.821 60.000 0.00 0.00 0.00 4.61
1825 1942 7.657761 GGACGAACAGATGAGGTCAATATAAAT 59.342 37.037 0.00 0.00 0.00 1.40
1885 2002 4.760204 GGTGTTAGAAGGCTTGTGTATGTT 59.240 41.667 3.46 0.00 0.00 2.71
1957 2074 4.086457 AGACGTTGCCTTATTTTCCCATT 58.914 39.130 0.00 0.00 0.00 3.16
2139 2259 9.591792 TTCTAGTGATGATGTGTTTATTCTCTG 57.408 33.333 0.00 0.00 0.00 3.35
2148 2268 7.936847 TGATGTGTTTATTCTCTGGTACAACTT 59.063 33.333 0.00 0.00 38.70 2.66
2269 2391 4.160439 TCTGATGTTTGCCTACAGGAGTAG 59.840 45.833 0.00 0.00 45.90 2.57
2282 2404 3.693578 ACAGGAGTAGTAAAGGTACTCGC 59.306 47.826 4.61 0.00 45.06 5.03
2395 2517 1.063417 AGCATCTTTCAGGATTGGGGG 60.063 52.381 0.00 0.00 0.00 5.40
2677 2897 3.974642 ACCTGATGGTAATTCCTACTCCC 59.025 47.826 0.00 0.00 46.43 4.30
2678 2898 4.235372 CCTGATGGTAATTCCTACTCCCT 58.765 47.826 0.00 0.00 37.07 4.20
2679 2899 4.284746 CCTGATGGTAATTCCTACTCCCTC 59.715 50.000 0.00 0.00 37.07 4.30
2680 2900 5.151454 CTGATGGTAATTCCTACTCCCTCT 58.849 45.833 0.00 0.00 37.07 3.69
2681 2901 4.901849 TGATGGTAATTCCTACTCCCTCTG 59.098 45.833 0.00 0.00 37.07 3.35
2682 2902 4.348020 TGGTAATTCCTACTCCCTCTGT 57.652 45.455 0.00 0.00 37.07 3.41
2683 2903 5.476950 TGGTAATTCCTACTCCCTCTGTA 57.523 43.478 0.00 0.00 37.07 2.74
2684 2904 5.206587 TGGTAATTCCTACTCCCTCTGTAC 58.793 45.833 0.00 0.00 37.07 2.90
2685 2905 5.206587 GGTAATTCCTACTCCCTCTGTACA 58.793 45.833 0.00 0.00 0.00 2.90
2686 2906 5.068855 GGTAATTCCTACTCCCTCTGTACAC 59.931 48.000 0.00 0.00 0.00 2.90
2687 2907 4.611564 ATTCCTACTCCCTCTGTACACT 57.388 45.455 0.00 0.00 0.00 3.55
2688 2908 5.728937 ATTCCTACTCCCTCTGTACACTA 57.271 43.478 0.00 0.00 0.00 2.74
2689 2909 5.525454 TTCCTACTCCCTCTGTACACTAA 57.475 43.478 0.00 0.00 0.00 2.24
2690 2910 5.728937 TCCTACTCCCTCTGTACACTAAT 57.271 43.478 0.00 0.00 0.00 1.73
2691 2911 6.836714 TCCTACTCCCTCTGTACACTAATA 57.163 41.667 0.00 0.00 0.00 0.98
2692 2912 7.403837 TCCTACTCCCTCTGTACACTAATAT 57.596 40.000 0.00 0.00 0.00 1.28
2796 3016 7.488187 CATGGTACCATGTTCTGAATTCTAG 57.512 40.000 36.87 14.14 46.20 2.43
2805 3025 6.777213 TGTTCTGAATTCTAGTACTCCCTC 57.223 41.667 7.05 0.00 0.00 4.30
2806 3026 5.357314 TGTTCTGAATTCTAGTACTCCCTCG 59.643 44.000 7.05 0.00 0.00 4.63
2942 3167 6.019152 CGTACATGTAACATGTTTAGTTGGC 58.981 40.000 17.78 2.70 33.76 4.52
2946 3171 6.150474 ACATGTAACATGTTTAGTTGGCTACC 59.850 38.462 17.78 0.00 0.00 3.18
3069 3315 1.021968 ACTTGTTCGGTGGCTGTTTC 58.978 50.000 0.00 0.00 0.00 2.78
3070 3316 1.308998 CTTGTTCGGTGGCTGTTTCT 58.691 50.000 0.00 0.00 0.00 2.52
3084 3330 5.003804 GGCTGTTTCTTTACCAGAATCTGA 58.996 41.667 12.53 0.00 41.42 3.27
3105 3351 5.113383 TGAGAACGTTTTGTAGTGATGTGT 58.887 37.500 0.46 0.00 0.00 3.72
3126 3372 5.065474 GTGTGTGTTTTAGCTGTGAACCTTA 59.935 40.000 0.00 0.00 0.00 2.69
3134 3380 9.043079 GTTTTAGCTGTGAACCTTATAGTATCC 57.957 37.037 0.00 0.00 0.00 2.59
3230 3479 8.130307 GCTAAAAGCACTTCAGAAATTTTCAA 57.870 30.769 11.53 0.00 41.89 2.69
3283 3627 8.383947 AGTACTATTTTGCTACTTTTCCTTCCT 58.616 33.333 0.00 0.00 0.00 3.36
3290 3652 5.794894 TGCTACTTTTCCTTCCTAGTTCAG 58.205 41.667 0.00 0.00 0.00 3.02
3342 3709 7.940850 AGCATGTACTTGATGTTTTACTGTTT 58.059 30.769 12.65 0.00 0.00 2.83
3383 3750 7.094677 ACGTTCAATATACCCACAACCTTTAAC 60.095 37.037 0.00 0.00 0.00 2.01
3388 3755 8.581578 CAATATACCCACAACCTTTAACAAAGT 58.418 33.333 0.00 0.00 36.77 2.66
3510 3891 8.526147 AGTTTTGATTTTATCATCAGTCCCTTG 58.474 33.333 0.00 0.00 39.39 3.61
3534 3915 3.101437 TCGAAGTTTGGGCTATCCTGTA 58.899 45.455 0.00 0.00 36.20 2.74
3542 3923 0.599060 GGCTATCCTGTACCTCGAGC 59.401 60.000 6.99 0.00 0.00 5.03
3567 3948 3.452627 CACTAGATACCTCTGTTGCCCTT 59.547 47.826 0.00 0.00 32.66 3.95
3677 4058 5.974108 TGCTGAAGTATACAAGGTAAGTCC 58.026 41.667 5.50 0.00 0.00 3.85
3807 4190 9.851686 TTTTCATACTATCTTCATATGGCAACT 57.148 29.630 2.13 0.00 37.61 3.16
3809 4192 8.193953 TCATACTATCTTCATATGGCAACTGA 57.806 34.615 2.13 0.00 37.61 3.41
3844 4227 7.179872 TGCTGAGGCATGAATAACTATAGATCT 59.820 37.037 6.78 0.00 44.28 2.75
3919 4304 5.369685 ACGACAGATCTGCAGTATATGAG 57.630 43.478 22.83 16.41 0.00 2.90
3973 4379 7.993183 TCATTTTCAAGGGATATCTGTAGTTCC 59.007 37.037 2.05 0.00 0.00 3.62
4299 4710 1.364626 GGATGCTGGCTGTGTTCTCG 61.365 60.000 0.00 0.00 0.00 4.04
4347 4759 1.001020 AAATGGGTGCTCGCCATCA 60.001 52.632 8.59 0.00 0.00 3.07
4368 4780 0.031043 TCTGTTCGTTTTCCGCTCGA 59.969 50.000 0.00 0.00 36.19 4.04
4445 4857 2.925706 TACGCCTGGTTCCTGGCA 60.926 61.111 29.49 15.15 46.84 4.92
4493 4905 0.673985 GGTGGTTTTGGCAGACCTTC 59.326 55.000 18.94 13.12 36.86 3.46
4506 4918 4.426313 CCTTCGCCCTGGGGTTCC 62.426 72.222 16.03 0.00 37.65 3.62
4508 4920 3.327404 TTCGCCCTGGGGTTCCTC 61.327 66.667 16.03 0.00 37.65 3.71
4532 4944 0.321671 TCCGGTTTCTGCTCAAGAGG 59.678 55.000 0.00 0.00 35.91 3.69
4538 4950 1.892819 TTCTGCTCAAGAGGGCGAGG 61.893 60.000 0.00 0.00 35.91 4.63
4589 5020 7.936847 TGTTGTACTTCAGTAACAATGGATTCT 59.063 33.333 0.00 0.00 31.52 2.40
4606 5037 6.209774 TGGATTCTAGTAGAAATTCCCCAGA 58.790 40.000 21.92 7.68 37.82 3.86
4611 5042 4.846168 AGTAGAAATTCCCCAGAGGTTC 57.154 45.455 0.00 0.00 36.75 3.62
4614 5045 5.663556 AGTAGAAATTCCCCAGAGGTTCTAG 59.336 44.000 0.00 0.00 33.37 2.43
4615 5046 3.783082 AGAAATTCCCCAGAGGTTCTAGG 59.217 47.826 0.00 0.00 36.75 3.02
4616 5047 2.972153 ATTCCCCAGAGGTTCTAGGT 57.028 50.000 0.00 0.00 36.75 3.08
4617 5048 2.735259 TTCCCCAGAGGTTCTAGGTT 57.265 50.000 0.00 0.00 36.75 3.50
4618 5049 2.735259 TCCCCAGAGGTTCTAGGTTT 57.265 50.000 0.00 0.00 36.75 3.27
4619 5050 2.266279 TCCCCAGAGGTTCTAGGTTTG 58.734 52.381 0.00 0.00 36.75 2.93
4620 5051 1.985895 CCCCAGAGGTTCTAGGTTTGT 59.014 52.381 0.00 0.00 0.00 2.83
4643 5074 3.494336 CGGTGCTGCTGCTACTGC 61.494 66.667 17.00 1.02 40.48 4.40
4644 5075 2.046507 GGTGCTGCTGCTACTGCT 60.047 61.111 17.00 0.00 40.48 4.24
4645 5076 2.396955 GGTGCTGCTGCTACTGCTG 61.397 63.158 17.00 0.00 40.48 4.41
4722 5195 0.885879 CTGCAGCACATGGACACATT 59.114 50.000 0.00 0.00 34.35 2.71
4724 5197 0.734942 GCAGCACATGGACACATTGC 60.735 55.000 0.00 0.00 39.36 3.56
4875 5563 3.662247 AGTAGCACTACACACTGAACC 57.338 47.619 10.30 0.00 38.48 3.62
4895 5583 4.028825 ACCGTATAATATCTGGGGGCTAC 58.971 47.826 0.00 0.00 0.00 3.58
4897 5585 4.099573 CCGTATAATATCTGGGGGCTACAG 59.900 50.000 3.15 3.15 37.30 2.74
4919 5607 3.370061 GGCAGCTCGTTTTTCTTACGTAT 59.630 43.478 0.00 0.00 39.84 3.06
4922 5610 5.220416 GCAGCTCGTTTTTCTTACGTATCAT 60.220 40.000 0.00 0.00 39.84 2.45
4925 5613 6.198591 AGCTCGTTTTTCTTACGTATCATAGC 59.801 38.462 0.00 0.00 39.84 2.97
4929 5617 3.293311 TTCTTACGTATCATAGCCGGC 57.707 47.619 21.89 21.89 0.00 6.13
5015 6287 4.388499 CTGCGGCGTACCAACCCT 62.388 66.667 9.37 0.00 34.57 4.34
5052 6329 1.821216 ACACGAAAATGCCTAGTGGG 58.179 50.000 0.00 0.00 37.16 4.61
5078 6366 4.217983 GGATGGGATAGTCAAGTACCGTAG 59.782 50.000 0.00 0.00 0.00 3.51
5080 6368 5.372343 TGGGATAGTCAAGTACCGTAGTA 57.628 43.478 0.00 0.00 0.00 1.82
5082 6370 4.759183 GGGATAGTCAAGTACCGTAGTAGG 59.241 50.000 0.00 0.00 37.30 3.18
5089 6377 5.819901 GTCAAGTACCGTAGTAGGAGTACAT 59.180 44.000 16.79 8.07 38.01 2.29
5090 6378 6.018343 GTCAAGTACCGTAGTAGGAGTACATC 60.018 46.154 16.79 0.00 38.01 3.06
5093 6381 4.226427 ACCGTAGTAGGAGTACATCACA 57.774 45.455 0.00 0.00 34.73 3.58
5096 6384 5.105997 ACCGTAGTAGGAGTACATCACAAAC 60.106 44.000 0.00 0.00 34.73 2.93
5099 6387 6.527023 CGTAGTAGGAGTACATCACAAACAAG 59.473 42.308 0.00 0.00 0.00 3.16
5100 6388 5.794894 AGTAGGAGTACATCACAAACAAGG 58.205 41.667 0.00 0.00 0.00 3.61
5101 6389 4.021102 AGGAGTACATCACAAACAAGGG 57.979 45.455 0.00 0.00 0.00 3.95
5102 6390 3.650942 AGGAGTACATCACAAACAAGGGA 59.349 43.478 0.00 0.00 0.00 4.20
5103 6391 4.104102 AGGAGTACATCACAAACAAGGGAA 59.896 41.667 0.00 0.00 0.00 3.97
5104 6392 4.825085 GGAGTACATCACAAACAAGGGAAA 59.175 41.667 0.00 0.00 0.00 3.13
5105 6393 5.300792 GGAGTACATCACAAACAAGGGAAAA 59.699 40.000 0.00 0.00 0.00 2.29
5138 6427 7.275920 TGCATACACAATACATGTATACCACA 58.724 34.615 18.56 5.48 40.51 4.17
5174 6463 8.433585 TTTTCATAATAATGTATTCGCATGCG 57.566 30.769 33.61 33.61 36.24 4.73
5175 6464 6.720012 TCATAATAATGTATTCGCATGCGT 57.280 33.333 36.50 22.86 36.29 5.24
5191 6480 4.317069 GCATGCGTACACAAAAAGACAAAC 60.317 41.667 0.00 0.00 0.00 2.93
5197 6486 6.140108 GCGTACACAAAAAGACAAACATGTAG 59.860 38.462 0.00 0.00 0.00 2.74
5198 6487 7.184106 CGTACACAAAAAGACAAACATGTAGT 58.816 34.615 0.00 0.25 0.00 2.73
5199 6488 8.329583 CGTACACAAAAAGACAAACATGTAGTA 58.670 33.333 0.00 0.00 0.00 1.82
5200 6489 9.429600 GTACACAAAAAGACAAACATGTAGTAC 57.570 33.333 0.00 0.00 0.00 2.73
5202 6491 8.682710 ACACAAAAAGACAAACATGTAGTACAT 58.317 29.630 10.10 10.10 39.91 2.29
5213 6502 2.702261 TGTAGTACATGAAAACGGGCC 58.298 47.619 0.00 0.00 0.00 5.80
5229 6518 2.705730 GGGCCTTTTTGTTGTTGTTGT 58.294 42.857 0.84 0.00 0.00 3.32
5230 6519 3.078097 GGGCCTTTTTGTTGTTGTTGTT 58.922 40.909 0.84 0.00 0.00 2.83
5231 6520 3.120025 GGGCCTTTTTGTTGTTGTTGTTG 60.120 43.478 0.84 0.00 0.00 3.33
5233 6522 4.023622 GGCCTTTTTGTTGTTGTTGTTGTT 60.024 37.500 0.00 0.00 0.00 2.83
5235 6524 5.504830 GCCTTTTTGTTGTTGTTGTTGTTGT 60.505 36.000 0.00 0.00 0.00 3.32
5236 6525 6.490534 CCTTTTTGTTGTTGTTGTTGTTGTT 58.509 32.000 0.00 0.00 0.00 2.83
5237 6526 6.413235 CCTTTTTGTTGTTGTTGTTGTTGTTG 59.587 34.615 0.00 0.00 0.00 3.33
5239 6528 6.422776 TTTGTTGTTGTTGTTGTTGTTGTT 57.577 29.167 0.00 0.00 0.00 2.83
5240 6529 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
5241 6530 4.271049 TGTTGTTGTTGTTGTTGTTGTTGG 59.729 37.500 0.00 0.00 0.00 3.77
5242 6531 3.393800 TGTTGTTGTTGTTGTTGTTGGG 58.606 40.909 0.00 0.00 0.00 4.12
5243 6532 3.181465 TGTTGTTGTTGTTGTTGTTGGGT 60.181 39.130 0.00 0.00 0.00 4.51
5244 6533 3.032017 TGTTGTTGTTGTTGTTGGGTG 57.968 42.857 0.00 0.00 0.00 4.61
5245 6534 2.289072 TGTTGTTGTTGTTGTTGGGTGG 60.289 45.455 0.00 0.00 0.00 4.61
5246 6535 0.898320 TGTTGTTGTTGTTGGGTGGG 59.102 50.000 0.00 0.00 0.00 4.61
5247 6536 1.187087 GTTGTTGTTGTTGGGTGGGA 58.813 50.000 0.00 0.00 0.00 4.37
5250 6539 2.472029 TGTTGTTGTTGGGTGGGATTT 58.528 42.857 0.00 0.00 0.00 2.17
5258 6547 4.742012 TGTTGGGTGGGATTTTTAGCTTA 58.258 39.130 0.00 0.00 0.00 3.09
5259 6548 4.525100 TGTTGGGTGGGATTTTTAGCTTAC 59.475 41.667 0.00 0.00 0.00 2.34
5306 6595 7.972832 AAAAATTACAGATCCGTAGTGAACA 57.027 32.000 0.00 0.00 0.00 3.18
5307 6596 6.963049 AAATTACAGATCCGTAGTGAACAC 57.037 37.500 0.00 0.00 0.00 3.32
5308 6597 2.631418 ACAGATCCGTAGTGAACACG 57.369 50.000 0.00 0.00 39.10 4.49
5310 6599 2.095364 ACAGATCCGTAGTGAACACGAC 60.095 50.000 7.85 7.85 41.91 4.34
5318 6607 2.857592 AGTGAACACGACGTACAAGT 57.142 45.000 0.00 0.00 36.20 3.16
5330 6619 3.200483 ACGTACAAGTTTCCACAGGTTC 58.800 45.455 0.00 0.00 0.00 3.62
5334 6623 4.983671 ACAAGTTTCCACAGGTTCTTTC 57.016 40.909 0.00 0.00 0.00 2.62
5336 6625 5.016831 ACAAGTTTCCACAGGTTCTTTCTT 58.983 37.500 0.00 0.00 0.00 2.52
5337 6626 5.480422 ACAAGTTTCCACAGGTTCTTTCTTT 59.520 36.000 0.00 0.00 0.00 2.52
5338 6627 6.661805 ACAAGTTTCCACAGGTTCTTTCTTTA 59.338 34.615 0.00 0.00 0.00 1.85
5339 6628 7.177744 ACAAGTTTCCACAGGTTCTTTCTTTAA 59.822 33.333 0.00 0.00 0.00 1.52
5340 6629 7.712204 AGTTTCCACAGGTTCTTTCTTTAAA 57.288 32.000 0.00 0.00 0.00 1.52
5341 6630 7.544622 AGTTTCCACAGGTTCTTTCTTTAAAC 58.455 34.615 0.00 0.00 0.00 2.01
5342 6631 7.396339 AGTTTCCACAGGTTCTTTCTTTAAACT 59.604 33.333 0.00 0.00 0.00 2.66
5343 6632 7.712204 TTCCACAGGTTCTTTCTTTAAACTT 57.288 32.000 0.00 0.00 0.00 2.66
5344 6633 7.712204 TCCACAGGTTCTTTCTTTAAACTTT 57.288 32.000 0.00 0.00 0.00 2.66
5345 6634 7.543756 TCCACAGGTTCTTTCTTTAAACTTTG 58.456 34.615 0.00 0.00 0.00 2.77
5346 6635 7.394923 TCCACAGGTTCTTTCTTTAAACTTTGA 59.605 33.333 0.00 0.00 0.00 2.69
5347 6636 8.032451 CCACAGGTTCTTTCTTTAAACTTTGAA 58.968 33.333 0.00 0.00 0.00 2.69
5348 6637 9.418045 CACAGGTTCTTTCTTTAAACTTTGAAA 57.582 29.630 1.75 1.75 0.00 2.69
5349 6638 9.990360 ACAGGTTCTTTCTTTAAACTTTGAAAA 57.010 25.926 3.01 0.00 0.00 2.29
5352 6641 9.702726 GGTTCTTTCTTTAAACTTTGAAAATGC 57.297 29.630 3.01 0.00 0.00 3.56
5353 6642 9.408731 GTTCTTTCTTTAAACTTTGAAAATGCG 57.591 29.630 3.01 0.00 0.00 4.73
5354 6643 8.918961 TCTTTCTTTAAACTTTGAAAATGCGA 57.081 26.923 0.00 0.00 0.00 5.10
5355 6644 9.528018 TCTTTCTTTAAACTTTGAAAATGCGAT 57.472 25.926 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.006564 TCTAAATTGGAGGCCTCAATTGATATT 58.993 33.333 33.29 15.90 42.06 1.28
1 2 7.529555 TCTAAATTGGAGGCCTCAATTGATAT 58.470 34.615 33.29 20.47 42.06 1.63
2 3 6.910191 TCTAAATTGGAGGCCTCAATTGATA 58.090 36.000 33.29 21.29 42.06 2.15
3 4 5.769835 TCTAAATTGGAGGCCTCAATTGAT 58.230 37.500 33.29 21.31 42.06 2.57
4 5 5.191727 TCTAAATTGGAGGCCTCAATTGA 57.808 39.130 33.29 24.48 42.06 2.57
32 33 4.705746 CCGGTCAAAATCGGGTGA 57.294 55.556 0.00 0.00 42.32 4.02
45 47 6.822442 AGAAAAATAAAATTGTTGACCCGGT 58.178 32.000 0.00 0.00 0.00 5.28
51 53 9.260002 GCTCCTTGAGAAAAATAAAATTGTTGA 57.740 29.630 0.00 0.00 0.00 3.18
52 54 9.264719 AGCTCCTTGAGAAAAATAAAATTGTTG 57.735 29.630 0.00 0.00 0.00 3.33
71 73 5.176741 ACAATTGAATGAGAGAGCTCCTT 57.823 39.130 13.59 0.00 40.55 3.36
77 79 9.565213 GTGGATTAAAACAATTGAATGAGAGAG 57.435 33.333 13.59 0.00 0.00 3.20
92 94 8.882415 TCGAATGAGGTATAGTGGATTAAAAC 57.118 34.615 0.00 0.00 0.00 2.43
98 100 6.918067 TCAATCGAATGAGGTATAGTGGAT 57.082 37.500 0.00 0.00 0.00 3.41
188 190 7.748847 AGTATTGTGGATGTCGATGTTTTTAC 58.251 34.615 0.00 0.00 0.00 2.01
189 191 7.915293 AGTATTGTGGATGTCGATGTTTTTA 57.085 32.000 0.00 0.00 0.00 1.52
407 416 2.511600 CTAGAAGGGTTGGGCGCG 60.512 66.667 0.00 0.00 34.93 6.86
408 417 1.745489 CACTAGAAGGGTTGGGCGC 60.745 63.158 0.00 0.00 0.00 6.53
413 422 7.118390 CACTTTGACTATTCACTAGAAGGGTTG 59.882 40.741 0.00 0.00 37.14 3.77
421 430 9.243637 GCTCTATTCACTTTGACTATTCACTAG 57.756 37.037 0.00 0.00 0.00 2.57
422 431 7.915923 CGCTCTATTCACTTTGACTATTCACTA 59.084 37.037 0.00 0.00 0.00 2.74
426 435 6.273825 TCCGCTCTATTCACTTTGACTATTC 58.726 40.000 0.00 0.00 0.00 1.75
445 454 2.971452 GGTTCTCGACCTTCCGCT 59.029 61.111 0.00 0.00 45.55 5.52
628 650 9.924650 CCTAGGCGATATTACAAGTTATAAGTT 57.075 33.333 0.00 0.00 0.00 2.66
629 651 8.033626 GCCTAGGCGATATTACAAGTTATAAGT 58.966 37.037 20.16 0.00 0.00 2.24
630 652 8.033038 TGCCTAGGCGATATTACAAGTTATAAG 58.967 37.037 28.28 0.00 45.51 1.73
631 653 7.816031 GTGCCTAGGCGATATTACAAGTTATAA 59.184 37.037 28.28 1.22 45.51 0.98
667 689 7.184862 AGAAGGATTGGAGTATTTTGGTGAAT 58.815 34.615 0.00 0.00 0.00 2.57
668 690 6.552008 AGAAGGATTGGAGTATTTTGGTGAA 58.448 36.000 0.00 0.00 0.00 3.18
670 692 7.938140 TTAGAAGGATTGGAGTATTTTGGTG 57.062 36.000 0.00 0.00 0.00 4.17
692 718 8.545472 ACTGCTAATTACACTCAAATACCCTTA 58.455 33.333 0.00 0.00 0.00 2.69
774 805 2.164663 CGCGTCGCCTGAATGCTTA 61.165 57.895 12.44 0.00 0.00 3.09
775 806 3.490759 CGCGTCGCCTGAATGCTT 61.491 61.111 12.44 0.00 0.00 3.91
776 807 4.435436 TCGCGTCGCCTGAATGCT 62.435 61.111 12.44 0.00 0.00 3.79
777 808 3.918220 CTCGCGTCGCCTGAATGC 61.918 66.667 12.44 0.00 0.00 3.56
778 809 1.351430 TTTCTCGCGTCGCCTGAATG 61.351 55.000 12.44 0.00 0.00 2.67
779 810 1.080093 TTTCTCGCGTCGCCTGAAT 60.080 52.632 12.44 0.00 0.00 2.57
780 811 2.019951 GTTTCTCGCGTCGCCTGAA 61.020 57.895 12.44 12.97 0.00 3.02
781 812 2.430244 GTTTCTCGCGTCGCCTGA 60.430 61.111 12.44 7.18 0.00 3.86
782 813 3.479269 GGTTTCTCGCGTCGCCTG 61.479 66.667 12.44 4.66 0.00 4.85
783 814 4.736896 GGGTTTCTCGCGTCGCCT 62.737 66.667 12.44 0.00 0.00 5.52
820 851 3.345808 CTTCCCGTGTGTGTGGCG 61.346 66.667 0.00 0.00 0.00 5.69
967 1012 2.357760 GCTTCGGGCGTGTGGTTA 60.358 61.111 0.00 0.00 0.00 2.85
988 1034 3.512223 GATGCATCTCGGCTCGGCT 62.512 63.158 19.70 0.00 34.04 5.52
989 1035 3.040763 GATGCATCTCGGCTCGGC 61.041 66.667 19.70 0.00 34.04 5.54
990 1036 1.664017 CAGATGCATCTCGGCTCGG 60.664 63.158 26.44 9.78 34.22 4.63
991 1037 0.663867 CTCAGATGCATCTCGGCTCG 60.664 60.000 26.44 14.08 34.22 5.03
992 1038 0.945265 GCTCAGATGCATCTCGGCTC 60.945 60.000 28.76 15.09 34.22 4.70
1193 1244 1.388065 ATTCGAGCGAGGGAGTGAGG 61.388 60.000 0.00 0.00 0.00 3.86
1197 1252 1.405821 CAGTAATTCGAGCGAGGGAGT 59.594 52.381 0.00 0.00 0.00 3.85
1227 1282 5.046159 AGACGGGGACATTTTACACTGAATA 60.046 40.000 0.00 0.00 0.00 1.75
1228 1283 4.007659 GACGGGGACATTTTACACTGAAT 58.992 43.478 0.00 0.00 0.00 2.57
1229 1284 3.071892 AGACGGGGACATTTTACACTGAA 59.928 43.478 0.00 0.00 0.00 3.02
1264 1319 7.671819 TGCATCTAAGAGCAACCTATCTACTAT 59.328 37.037 0.00 0.00 37.90 2.12
1287 1342 5.648178 AGCAATTCTGTCAAATATGTGCA 57.352 34.783 0.00 0.00 31.95 4.57
1313 1368 0.599558 TTGCAGCTTGATTCAGTGCC 59.400 50.000 12.52 1.40 32.99 5.01
1314 1369 2.427232 TTTGCAGCTTGATTCAGTGC 57.573 45.000 9.58 9.58 34.62 4.40
1366 1473 1.663695 AACAAACACACCGAGGAGTG 58.336 50.000 16.25 16.25 43.65 3.51
1409 1516 9.698617 GTTACTATTTTAAGAAGTAACCATGCG 57.301 33.333 17.56 0.00 44.97 4.73
1450 1557 2.672961 TTCAAGGCACGATGGTCTAG 57.327 50.000 0.00 0.00 0.00 2.43
1505 1612 4.906618 ACCAATGTAAAATCTCCGACAGT 58.093 39.130 0.00 0.00 0.00 3.55
1506 1615 6.106673 AGTACCAATGTAAAATCTCCGACAG 58.893 40.000 0.00 0.00 0.00 3.51
1524 1633 2.240160 ACAAACACACCAAGGAGTACCA 59.760 45.455 0.00 0.00 38.94 3.25
1525 1634 2.927028 ACAAACACACCAAGGAGTACC 58.073 47.619 0.00 0.00 0.00 3.34
1564 1681 3.188159 AGAAGTAACCACGCAAGAACA 57.812 42.857 0.00 0.00 43.62 3.18
1637 1754 4.729227 TCAGTGTATATCTGGCGTTGAA 57.271 40.909 7.65 0.00 34.15 2.69
1691 1808 1.279271 CTTCTTCCGAACATCCCCTGT 59.721 52.381 0.00 0.00 40.84 4.00
1722 1839 1.336795 CCACATTGCGGAAAACCTTCC 60.337 52.381 0.00 0.00 46.85 3.46
1825 1942 0.321210 CCAGTACATTGCACGTCCCA 60.321 55.000 0.00 0.00 0.00 4.37
1957 2074 4.641541 CCATAAGCATCAACATGGTCTTCA 59.358 41.667 0.00 0.00 39.96 3.02
2395 2517 4.082571 CCCAATCTGTCTTCACATTTGGAC 60.083 45.833 14.23 0.00 42.81 4.02
2656 2876 4.235372 AGGGAGTAGGAATTACCATCAGG 58.765 47.826 0.00 0.00 42.04 3.86
2657 2877 5.011533 CAGAGGGAGTAGGAATTACCATCAG 59.988 48.000 0.00 0.00 42.04 2.90
2662 2882 5.068855 GTGTACAGAGGGAGTAGGAATTACC 59.931 48.000 0.00 0.00 39.35 2.85
2665 2885 4.949121 AGTGTACAGAGGGAGTAGGAATT 58.051 43.478 0.00 0.00 0.00 2.17
2672 2892 7.444792 CGTCTTATATTAGTGTACAGAGGGAGT 59.555 40.741 0.00 0.00 0.00 3.85
2673 2893 7.444792 ACGTCTTATATTAGTGTACAGAGGGAG 59.555 40.741 0.00 0.00 0.00 4.30
2675 2895 7.361127 CACGTCTTATATTAGTGTACAGAGGG 58.639 42.308 0.00 0.00 0.00 4.30
2676 2896 6.856938 GCACGTCTTATATTAGTGTACAGAGG 59.143 42.308 0.00 0.00 35.46 3.69
2677 2897 6.856938 GGCACGTCTTATATTAGTGTACAGAG 59.143 42.308 0.00 0.00 35.46 3.35
2678 2898 6.544931 AGGCACGTCTTATATTAGTGTACAGA 59.455 38.462 0.00 0.00 35.46 3.41
2679 2899 6.637254 CAGGCACGTCTTATATTAGTGTACAG 59.363 42.308 0.00 0.00 35.46 2.74
2680 2900 6.500910 CAGGCACGTCTTATATTAGTGTACA 58.499 40.000 0.00 0.00 35.46 2.90
2681 2901 5.401674 GCAGGCACGTCTTATATTAGTGTAC 59.598 44.000 0.00 0.00 35.46 2.90
2682 2902 5.068067 TGCAGGCACGTCTTATATTAGTGTA 59.932 40.000 0.00 0.00 35.46 2.90
2683 2903 4.142026 TGCAGGCACGTCTTATATTAGTGT 60.142 41.667 0.00 0.00 35.46 3.55
2684 2904 4.368315 TGCAGGCACGTCTTATATTAGTG 58.632 43.478 0.00 0.00 36.05 2.74
2685 2905 4.665833 TGCAGGCACGTCTTATATTAGT 57.334 40.909 0.00 0.00 0.00 2.24
2686 2906 4.389992 CCATGCAGGCACGTCTTATATTAG 59.610 45.833 0.00 0.00 0.00 1.73
2687 2907 4.202315 ACCATGCAGGCACGTCTTATATTA 60.202 41.667 0.00 0.00 43.14 0.98
2688 2908 3.141398 CCATGCAGGCACGTCTTATATT 58.859 45.455 0.00 0.00 0.00 1.28
2689 2909 2.104792 ACCATGCAGGCACGTCTTATAT 59.895 45.455 0.00 0.00 43.14 0.86
2690 2910 1.484653 ACCATGCAGGCACGTCTTATA 59.515 47.619 0.00 0.00 43.14 0.98
2691 2911 0.253044 ACCATGCAGGCACGTCTTAT 59.747 50.000 0.00 0.00 43.14 1.73
2692 2912 0.391130 GACCATGCAGGCACGTCTTA 60.391 55.000 13.30 0.00 43.14 2.10
2793 3013 4.268359 ACTTTGTACCGAGGGAGTACTAG 58.732 47.826 0.00 0.00 40.61 2.57
2796 3016 3.006217 ACAACTTTGTACCGAGGGAGTAC 59.994 47.826 0.00 0.00 40.16 2.73
2824 3049 4.510340 ACTTGTCGCTGGTTTAGTACAAAG 59.490 41.667 0.00 0.00 35.46 2.77
2825 3050 4.444536 ACTTGTCGCTGGTTTAGTACAAA 58.555 39.130 0.00 0.00 35.46 2.83
2826 3051 4.062677 ACTTGTCGCTGGTTTAGTACAA 57.937 40.909 0.00 0.00 34.99 2.41
2827 3052 3.738830 ACTTGTCGCTGGTTTAGTACA 57.261 42.857 0.00 0.00 0.00 2.90
2829 3054 6.982141 CCATATTACTTGTCGCTGGTTTAGTA 59.018 38.462 0.00 0.00 0.00 1.82
2975 3200 6.764308 TTGTGAAGATCAAGGGATGAATTC 57.236 37.500 0.00 0.00 42.54 2.17
2977 3223 7.501559 CACTATTGTGAAGATCAAGGGATGAAT 59.498 37.037 0.50 0.00 46.55 2.57
3069 3315 6.787085 AAACGTTCTCAGATTCTGGTAAAG 57.213 37.500 13.59 11.86 31.51 1.85
3070 3316 6.540914 ACAAAACGTTCTCAGATTCTGGTAAA 59.459 34.615 13.59 3.53 31.51 2.01
3084 3330 4.873827 ACACACATCACTACAAAACGTTCT 59.126 37.500 0.00 0.00 0.00 3.01
3105 3351 7.221450 ACTATAAGGTTCACAGCTAAAACACA 58.779 34.615 7.19 0.00 0.00 3.72
3134 3380 8.931775 CCCCCGATTTTTAATTAAAAGAAACTG 58.068 33.333 19.74 10.93 39.00 3.16
3184 3430 4.083802 AGCAGATGAGTTACGTGCTTTTTC 60.084 41.667 0.00 0.00 41.72 2.29
3230 3479 3.068590 GGCTTATGCAATGTAGTGCCATT 59.931 43.478 1.61 0.00 44.26 3.16
3353 3720 6.941436 AGGTTGTGGGTATATTGAACGTAAAA 59.059 34.615 0.00 0.00 0.00 1.52
3510 3891 3.127030 CAGGATAGCCCAAACTTCGAAAC 59.873 47.826 0.00 0.00 37.41 2.78
3534 3915 3.391955 AGGTATCTAGTGTAGCTCGAGGT 59.608 47.826 22.31 22.31 0.00 3.85
3542 3923 4.038162 GGGCAACAGAGGTATCTAGTGTAG 59.962 50.000 0.00 0.00 33.22 2.74
3567 3948 8.434733 TGAACAAAATGATTCTTGAAATTGCA 57.565 26.923 6.95 0.00 0.00 4.08
3785 4167 8.093307 ACTCAGTTGCCATATGAAGATAGTATG 58.907 37.037 3.65 0.00 0.00 2.39
3852 4237 5.964958 TCAAGCTCATAGAAAACCAAAGG 57.035 39.130 0.00 0.00 0.00 3.11
3973 4379 8.610896 ACTAGTAAAGCATAAGTAGTCAGTACG 58.389 37.037 0.00 0.00 36.66 3.67
4065 4476 9.502091 GCATTAGTTTATGATCCCTGTATACAA 57.498 33.333 7.06 0.00 0.00 2.41
4203 4614 2.411904 CGCTCTTGCCAATAGGAGATC 58.588 52.381 0.00 0.00 36.89 2.75
4368 4780 1.620819 GACTATCCGGATCACCAGCAT 59.379 52.381 23.08 0.00 35.59 3.79
4445 4857 0.541296 TCCTCGGGTCGACCTTCTTT 60.541 55.000 32.52 0.00 36.97 2.52
4493 4905 3.787001 GAGAGGAACCCCAGGGCG 61.787 72.222 0.00 0.00 39.32 6.13
4551 4963 4.034626 TGAAGTACAACACACAAATCACGG 59.965 41.667 0.00 0.00 0.00 4.94
4589 5020 5.600749 AGAACCTCTGGGGAATTTCTACTA 58.399 41.667 0.00 0.00 38.76 1.82
4615 5046 1.953772 CAGCACCGGGGTTACAAAC 59.046 57.895 5.12 0.00 0.00 2.93
4616 5047 1.899534 GCAGCACCGGGGTTACAAA 60.900 57.895 5.12 0.00 0.00 2.83
4617 5048 2.281900 GCAGCACCGGGGTTACAA 60.282 61.111 5.12 0.00 0.00 2.41
4618 5049 3.246112 AGCAGCACCGGGGTTACA 61.246 61.111 5.12 0.00 0.00 2.41
4619 5050 2.746277 CAGCAGCACCGGGGTTAC 60.746 66.667 5.12 0.00 0.00 2.50
4620 5051 4.715523 GCAGCAGCACCGGGGTTA 62.716 66.667 5.12 0.00 41.58 2.85
4639 5070 1.404717 CGGACATCTTACAGCAGCAGT 60.405 52.381 0.00 0.00 0.00 4.40
4643 5074 1.550065 CGACGGACATCTTACAGCAG 58.450 55.000 0.00 0.00 0.00 4.24
4644 5075 0.457853 GCGACGGACATCTTACAGCA 60.458 55.000 0.00 0.00 0.00 4.41
4645 5076 1.146358 GGCGACGGACATCTTACAGC 61.146 60.000 0.00 0.00 0.00 4.40
4646 5077 0.456221 AGGCGACGGACATCTTACAG 59.544 55.000 0.00 0.00 0.00 2.74
4647 5078 0.892755 AAGGCGACGGACATCTTACA 59.107 50.000 0.00 0.00 0.00 2.41
4648 5079 1.278238 CAAGGCGACGGACATCTTAC 58.722 55.000 0.00 0.00 0.00 2.34
4649 5080 0.459585 GCAAGGCGACGGACATCTTA 60.460 55.000 0.00 0.00 0.00 2.10
4650 5081 1.741770 GCAAGGCGACGGACATCTT 60.742 57.895 0.00 0.00 0.00 2.40
4651 5082 2.125512 GCAAGGCGACGGACATCT 60.126 61.111 0.00 0.00 0.00 2.90
4669 5142 1.202076 GCCAAGCTCGTGTAAAGCATC 60.202 52.381 0.00 0.00 42.35 3.91
4703 5176 0.885879 AATGTGTCCATGTGCTGCAG 59.114 50.000 10.11 10.11 0.00 4.41
4707 5180 1.588824 CGGCAATGTGTCCATGTGCT 61.589 55.000 2.72 0.00 36.35 4.40
4738 5212 5.003804 ACATTTGATACTTGAGGGTCACAC 58.996 41.667 0.00 0.00 0.00 3.82
4773 5255 3.432252 CGACAGTGATTGTTACAACCTCC 59.568 47.826 0.00 0.00 41.05 4.30
4875 5563 4.099573 CCTGTAGCCCCCAGATATTATACG 59.900 50.000 0.00 0.00 31.38 3.06
4895 5583 2.411547 CGTAAGAAAAACGAGCTGCCTG 60.412 50.000 0.00 0.00 42.90 4.85
4897 5585 1.529865 ACGTAAGAAAAACGAGCTGCC 59.470 47.619 0.00 0.00 42.90 4.85
4919 5607 2.349969 CTGCTACGTGCCGGCTATGA 62.350 60.000 29.70 3.37 42.00 2.15
4922 5610 3.833645 CCTGCTACGTGCCGGCTA 61.834 66.667 29.70 11.13 39.14 3.93
4925 5613 1.940883 TAGTTCCTGCTACGTGCCGG 61.941 60.000 12.07 12.07 45.85 6.13
4929 5617 4.650754 ATAACCTAGTTCCTGCTACGTG 57.349 45.455 0.00 0.00 0.00 4.49
5000 5689 3.887335 TTCAGGGTTGGTACGCCGC 62.887 63.158 0.00 0.00 37.92 6.53
5015 6287 7.851387 TTCGTGTATAATATGCCTTTGTTCA 57.149 32.000 0.00 0.00 0.00 3.18
5052 6329 1.821088 ACTTGACTATCCCATCCCCC 58.179 55.000 0.00 0.00 0.00 5.40
5056 6333 4.826183 ACTACGGTACTTGACTATCCCATC 59.174 45.833 0.00 0.00 0.00 3.51
5057 6334 4.801164 ACTACGGTACTTGACTATCCCAT 58.199 43.478 0.00 0.00 0.00 4.00
5058 6335 4.240881 ACTACGGTACTTGACTATCCCA 57.759 45.455 0.00 0.00 0.00 4.37
5059 6336 4.759183 CCTACTACGGTACTTGACTATCCC 59.241 50.000 0.00 0.00 0.00 3.85
5060 6337 5.615289 TCCTACTACGGTACTTGACTATCC 58.385 45.833 0.00 0.00 0.00 2.59
5061 6338 6.287525 ACTCCTACTACGGTACTTGACTATC 58.712 44.000 0.00 0.00 0.00 2.08
5062 6339 6.245890 ACTCCTACTACGGTACTTGACTAT 57.754 41.667 0.00 0.00 0.00 2.12
5065 6353 5.178797 TGTACTCCTACTACGGTACTTGAC 58.821 45.833 0.00 0.00 36.48 3.18
5078 6366 4.935808 CCCTTGTTTGTGATGTACTCCTAC 59.064 45.833 0.00 0.00 0.00 3.18
5080 6368 3.650942 TCCCTTGTTTGTGATGTACTCCT 59.349 43.478 0.00 0.00 0.00 3.69
5082 6370 6.385649 TTTTCCCTTGTTTGTGATGTACTC 57.614 37.500 0.00 0.00 0.00 2.59
5112 6401 7.936301 TGTGGTATACATGTATTGTGTATGCAT 59.064 33.333 22.90 3.79 42.94 3.96
5151 6440 7.127917 ACGCATGCGAATACATTATTATGAA 57.872 32.000 43.72 0.00 42.83 2.57
5158 6447 4.113354 TGTGTACGCATGCGAATACATTA 58.887 39.130 43.72 28.07 42.83 1.90
5161 6450 1.997669 TGTGTACGCATGCGAATACA 58.002 45.000 43.72 35.35 42.83 2.29
5162 6451 3.377434 TTTGTGTACGCATGCGAATAC 57.623 42.857 43.72 33.41 42.83 1.89
5163 6452 4.152580 TCTTTTTGTGTACGCATGCGAATA 59.847 37.500 43.72 25.24 42.83 1.75
5164 6453 2.979401 TTTTGTGTACGCATGCGAAT 57.021 40.000 43.72 26.37 42.83 3.34
5165 6454 2.288186 TCTTTTTGTGTACGCATGCGAA 59.712 40.909 43.72 25.42 42.83 4.70
5166 6455 1.867865 TCTTTTTGTGTACGCATGCGA 59.132 42.857 43.72 25.29 42.83 5.10
5167 6456 1.969256 GTCTTTTTGTGTACGCATGCG 59.031 47.619 36.79 36.79 46.03 4.73
5168 6457 2.993545 TGTCTTTTTGTGTACGCATGC 58.006 42.857 10.45 7.91 0.00 4.06
5169 6458 4.795795 TGTTTGTCTTTTTGTGTACGCATG 59.204 37.500 10.45 1.83 0.00 4.06
5170 6459 4.987832 TGTTTGTCTTTTTGTGTACGCAT 58.012 34.783 10.45 0.00 0.00 4.73
5171 6460 4.421033 TGTTTGTCTTTTTGTGTACGCA 57.579 36.364 4.65 4.65 0.00 5.24
5172 6461 4.796312 ACATGTTTGTCTTTTTGTGTACGC 59.204 37.500 0.00 0.00 0.00 4.42
5173 6462 7.184106 ACTACATGTTTGTCTTTTTGTGTACG 58.816 34.615 2.30 0.00 37.28 3.67
5174 6463 9.429600 GTACTACATGTTTGTCTTTTTGTGTAC 57.570 33.333 2.30 0.00 37.28 2.90
5175 6464 9.163899 TGTACTACATGTTTGTCTTTTTGTGTA 57.836 29.630 2.30 0.00 37.28 2.90
5197 6486 3.653539 AAAAGGCCCGTTTTCATGTAC 57.346 42.857 0.00 0.00 0.00 2.90
5198 6487 3.385111 ACAAAAAGGCCCGTTTTCATGTA 59.615 39.130 10.99 0.00 0.00 2.29
5199 6488 2.169561 ACAAAAAGGCCCGTTTTCATGT 59.830 40.909 10.99 6.72 0.00 3.21
5200 6489 2.832563 ACAAAAAGGCCCGTTTTCATG 58.167 42.857 10.99 6.18 0.00 3.07
5202 6491 2.028020 ACAACAAAAAGGCCCGTTTTCA 60.028 40.909 10.99 0.00 0.00 2.69
5203 6492 2.623535 ACAACAAAAAGGCCCGTTTTC 58.376 42.857 10.99 0.00 0.00 2.29
5204 6493 2.744741 CAACAACAAAAAGGCCCGTTTT 59.255 40.909 0.00 3.70 0.00 2.43
5205 6494 2.289756 ACAACAACAAAAAGGCCCGTTT 60.290 40.909 0.00 0.00 0.00 3.60
5206 6495 1.276705 ACAACAACAAAAAGGCCCGTT 59.723 42.857 0.00 0.00 0.00 4.44
5207 6496 0.899019 ACAACAACAAAAAGGCCCGT 59.101 45.000 0.00 0.00 0.00 5.28
5208 6497 1.663135 CAACAACAACAAAAAGGCCCG 59.337 47.619 0.00 0.00 0.00 6.13
5209 6498 2.705730 ACAACAACAACAAAAAGGCCC 58.294 42.857 0.00 0.00 0.00 5.80
5210 6499 3.500299 ACAACAACAACAACAAAAAGGCC 59.500 39.130 0.00 0.00 0.00 5.19
5211 6500 4.740741 ACAACAACAACAACAAAAAGGC 57.259 36.364 0.00 0.00 0.00 4.35
5212 6501 6.054035 ACAACAACAACAACAACAAAAAGG 57.946 33.333 0.00 0.00 0.00 3.11
5213 6502 6.963805 ACAACAACAACAACAACAACAAAAAG 59.036 30.769 0.00 0.00 0.00 2.27
5229 6518 2.166907 ATCCCACCCAACAACAACAA 57.833 45.000 0.00 0.00 0.00 2.83
5230 6519 2.166907 AATCCCACCCAACAACAACA 57.833 45.000 0.00 0.00 0.00 3.33
5231 6520 3.552132 AAAATCCCACCCAACAACAAC 57.448 42.857 0.00 0.00 0.00 3.32
5233 6522 3.070302 GCTAAAAATCCCACCCAACAACA 59.930 43.478 0.00 0.00 0.00 3.33
5235 6524 3.582164 AGCTAAAAATCCCACCCAACAA 58.418 40.909 0.00 0.00 0.00 2.83
5236 6525 3.252554 AGCTAAAAATCCCACCCAACA 57.747 42.857 0.00 0.00 0.00 3.33
5237 6526 4.525100 TGTAAGCTAAAAATCCCACCCAAC 59.475 41.667 0.00 0.00 0.00 3.77
5239 6528 4.390129 TGTAAGCTAAAAATCCCACCCA 57.610 40.909 0.00 0.00 0.00 4.51
5240 6529 5.731957 TTTGTAAGCTAAAAATCCCACCC 57.268 39.130 0.00 0.00 0.00 4.61
5241 6530 6.811665 GTGATTTGTAAGCTAAAAATCCCACC 59.188 38.462 18.62 7.20 38.81 4.61
5242 6531 7.602753 AGTGATTTGTAAGCTAAAAATCCCAC 58.397 34.615 18.62 14.09 38.81 4.61
5243 6532 7.775053 AGTGATTTGTAAGCTAAAAATCCCA 57.225 32.000 18.62 6.27 38.81 4.37
5285 6574 5.100259 CGTGTTCACTACGGATCTGTAATT 58.900 41.667 15.21 3.08 37.86 1.40
5286 6575 4.397103 TCGTGTTCACTACGGATCTGTAAT 59.603 41.667 15.21 2.60 41.58 1.89
5287 6576 3.752747 TCGTGTTCACTACGGATCTGTAA 59.247 43.478 15.21 0.00 41.58 2.41
5288 6577 3.125829 GTCGTGTTCACTACGGATCTGTA 59.874 47.826 13.75 13.75 41.58 2.74
5289 6578 2.095364 GTCGTGTTCACTACGGATCTGT 60.095 50.000 12.79 12.79 41.58 3.41
5290 6579 2.516923 GTCGTGTTCACTACGGATCTG 58.483 52.381 0.00 0.00 41.58 2.90
5291 6580 1.129998 CGTCGTGTTCACTACGGATCT 59.870 52.381 17.84 0.00 41.58 2.75
5292 6581 1.135859 ACGTCGTGTTCACTACGGATC 60.136 52.381 25.20 0.00 41.58 3.36
5293 6582 0.877071 ACGTCGTGTTCACTACGGAT 59.123 50.000 25.20 9.86 41.58 4.18
5294 6583 1.194547 GTACGTCGTGTTCACTACGGA 59.805 52.381 25.20 18.56 41.58 4.69
5295 6584 1.069973 TGTACGTCGTGTTCACTACGG 60.070 52.381 25.20 13.02 41.58 4.02
5296 6585 2.299085 TGTACGTCGTGTTCACTACG 57.701 50.000 21.89 21.89 42.56 3.51
5297 6586 3.621794 ACTTGTACGTCGTGTTCACTAC 58.378 45.455 8.47 0.00 0.00 2.73
5298 6587 3.969117 ACTTGTACGTCGTGTTCACTA 57.031 42.857 8.47 0.00 0.00 2.74
5299 6588 2.857592 ACTTGTACGTCGTGTTCACT 57.142 45.000 8.47 0.00 0.00 3.41
5300 6589 3.302028 GGAAACTTGTACGTCGTGTTCAC 60.302 47.826 8.47 0.00 0.00 3.18
5301 6590 2.859538 GGAAACTTGTACGTCGTGTTCA 59.140 45.455 8.47 1.97 0.00 3.18
5302 6591 2.859538 TGGAAACTTGTACGTCGTGTTC 59.140 45.455 8.47 2.29 0.00 3.18
5305 6594 2.195096 TGTGGAAACTTGTACGTCGTG 58.805 47.619 8.47 0.00 0.00 4.35
5306 6595 2.466846 CTGTGGAAACTTGTACGTCGT 58.533 47.619 2.21 2.21 0.00 4.34
5307 6596 1.790623 CCTGTGGAAACTTGTACGTCG 59.209 52.381 0.00 0.00 0.00 5.12
5308 6597 2.830104 ACCTGTGGAAACTTGTACGTC 58.170 47.619 0.00 0.00 0.00 4.34
5310 6599 3.463944 AGAACCTGTGGAAACTTGTACG 58.536 45.455 0.00 0.00 0.00 3.67
5311 6600 5.589050 AGAAAGAACCTGTGGAAACTTGTAC 59.411 40.000 0.00 0.00 0.00 2.90
5312 6601 5.751586 AGAAAGAACCTGTGGAAACTTGTA 58.248 37.500 0.00 0.00 0.00 2.41
5313 6602 4.600062 AGAAAGAACCTGTGGAAACTTGT 58.400 39.130 0.00 0.00 0.00 3.16
5314 6603 5.582689 AAGAAAGAACCTGTGGAAACTTG 57.417 39.130 0.00 0.00 0.00 3.16
5315 6604 7.712204 TTAAAGAAAGAACCTGTGGAAACTT 57.288 32.000 0.00 0.00 0.00 2.66
5316 6605 7.396339 AGTTTAAAGAAAGAACCTGTGGAAACT 59.604 33.333 0.00 0.00 0.00 2.66
5317 6606 7.544622 AGTTTAAAGAAAGAACCTGTGGAAAC 58.455 34.615 0.00 0.00 0.00 2.78
5318 6607 7.712204 AGTTTAAAGAAAGAACCTGTGGAAA 57.288 32.000 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.