Multiple sequence alignment - TraesCS6D01G398100

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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 TraesCS6D01G398100 chr6D 100.000 5866 0 0 1 5866 469539332 469533467 0.000000e+00 10833.0
1 TraesCS6D01G398100 chr6D 87.619 210 20 2 1495 1704 60795646 60795849 7.600000e-59 239.0
2 TraesCS6D01G398100 chr6B 90.762 1981 131 34 2609 4554 715679258 715677295 0.000000e+00 2597.0
3 TraesCS6D01G398100 chr6B 84.393 1935 191 58 5 1901 715682212 715680351 0.000000e+00 1797.0
4 TraesCS6D01G398100 chr6B 90.601 766 35 5 4509 5271 715677294 715676563 0.000000e+00 981.0
5 TraesCS6D01G398100 chr6B 92.956 653 41 3 1961 2612 715680165 715679517 0.000000e+00 946.0
6 TraesCS6D01G398100 chr6B 89.628 511 43 8 5325 5831 715676563 715676059 4.960000e-180 641.0
7 TraesCS6D01G398100 chr6B 84.894 331 43 5 2199 2528 71978846 71979170 1.580000e-85 327.0
8 TraesCS6D01G398100 chr6B 90.476 189 15 2 1046 1231 703675183 703675371 4.540000e-61 246.0
9 TraesCS6D01G398100 chr6B 79.624 319 39 16 1903 2217 16907794 16907498 7.710000e-49 206.0
10 TraesCS6D01G398100 chr6A 85.914 1860 166 58 1 1848 614590554 614588779 0.000000e+00 1895.0
11 TraesCS6D01G398100 chr6A 86.063 1557 163 34 3035 4553 614587801 614586261 0.000000e+00 1624.0
12 TraesCS6D01G398100 chr6A 81.424 576 63 22 4509 5051 614586260 614585696 1.170000e-116 431.0
13 TraesCS6D01G398100 chr6A 80.400 250 28 13 5351 5582 614584361 614584115 2.810000e-38 171.0
14 TraesCS6D01G398100 chr6A 89.899 99 10 0 1907 2005 614588767 614588669 1.720000e-25 128.0
15 TraesCS6D01G398100 chr6A 87.500 112 11 3 2926 3037 61004947 61004839 6.170000e-25 126.0
16 TraesCS6D01G398100 chr6A 95.082 61 2 1 5599 5659 614584123 614584064 1.740000e-15 95.3
17 TraesCS6D01G398100 chr6A 79.562 137 21 5 2038 2174 614588662 614588533 2.250000e-14 91.6
18 TraesCS6D01G398100 chr7B 90.556 720 53 11 1907 2620 139398073 139398783 0.000000e+00 939.0
19 TraesCS6D01G398100 chr7B 83.929 280 38 5 2250 2528 473006203 473006476 1.620000e-65 261.0
20 TraesCS6D01G398100 chr7B 83.630 281 38 6 2250 2528 593845424 593845150 2.100000e-64 257.0
21 TraesCS6D01G398100 chr5D 84.700 817 111 12 3153 3963 432443680 432444488 0.000000e+00 804.0
22 TraesCS6D01G398100 chr5D 86.473 207 22 2 1498 1704 471426119 471425919 7.650000e-54 222.0
23 TraesCS6D01G398100 chr5D 89.189 111 8 3 2930 3037 255685635 255685744 1.030000e-27 135.0
24 TraesCS6D01G398100 chr5A 84.088 817 113 13 3153 3963 552590411 552591216 0.000000e+00 773.0
25 TraesCS6D01G398100 chr5A 94.505 91 5 0 2930 3020 519884863 519884773 2.200000e-29 141.0
26 TraesCS6D01G398100 chr2A 84.049 815 113 13 3153 3963 753471477 753470676 0.000000e+00 769.0
27 TraesCS6D01G398100 chr2A 77.806 775 103 33 2132 2871 728995278 728996018 1.180000e-111 414.0
28 TraesCS6D01G398100 chr2A 77.619 420 40 23 2471 2866 709590790 709590401 7.710000e-49 206.0
29 TraesCS6D01G398100 chr4A 83.354 817 116 14 3153 3963 102390806 102390004 0.000000e+00 737.0
30 TraesCS6D01G398100 chr2B 89.251 307 28 3 1264 1569 661841879 661842181 4.290000e-101 379.0
31 TraesCS6D01G398100 chr2B 91.979 187 14 1 1046 1231 661841698 661841884 1.620000e-65 261.0
32 TraesCS6D01G398100 chr2B 83.051 236 33 3 1469 1704 5923079 5922851 2.140000e-49 207.0
33 TraesCS6D01G398100 chr2B 92.708 96 6 1 2921 3016 691994689 691994783 2.850000e-28 137.0
34 TraesCS6D01G398100 chr5B 89.262 298 27 3 1273 1569 37791549 37791256 9.290000e-98 368.0
35 TraesCS6D01G398100 chr5B 84.286 280 38 4 2250 2528 381220822 381220548 9.690000e-68 268.0
36 TraesCS6D01G398100 chr5B 91.444 187 15 1 1046 1231 37791739 37791553 7.540000e-64 255.0
37 TraesCS6D01G398100 chr5B 95.556 90 2 2 2930 3018 138777619 138777531 6.130000e-30 143.0
38 TraesCS6D01G398100 chr5B 89.362 47 4 1 5765 5811 525597912 525597867 2.280000e-04 58.4
39 TraesCS6D01G398100 chr1B 78.485 581 68 32 2270 2826 601494625 601495172 1.580000e-85 327.0
40 TraesCS6D01G398100 chr1B 79.941 339 45 12 1903 2238 114006879 114006561 1.640000e-55 228.0
41 TraesCS6D01G398100 chr1B 86.869 198 20 2 1507 1704 637285085 637284894 3.560000e-52 217.0
42 TraesCS6D01G398100 chr2D 88.571 210 17 3 1495 1704 29139770 29139972 1.260000e-61 248.0
43 TraesCS6D01G398100 chr2D 94.624 93 2 3 2930 3021 420176093 420176003 2.200000e-29 141.0
44 TraesCS6D01G398100 chr4B 85.253 217 26 2 1488 1704 11348654 11348444 9.900000e-53 219.0
45 TraesCS6D01G398100 chr4B 93.617 94 5 1 2927 3019 91298402 91298309 7.930000e-29 139.0
46 TraesCS6D01G398100 chr3A 79.208 303 39 12 1479 1766 103682981 103683274 7.760000e-44 189.0
47 TraesCS6D01G398100 chr7A 78.761 226 40 4 1479 1704 341984262 341984479 1.700000e-30 145.0
48 TraesCS6D01G398100 chr4D 93.548 93 5 1 2925 3016 28237803 28237895 2.850000e-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 TraesCS6D01G398100 chr6D 469533467 469539332 5865 True 10833.0 10833 100.000000 1 5866 1 chr6D.!!$R1 5865
1 TraesCS6D01G398100 chr6B 715676059 715682212 6153 True 1392.4 2597 89.668000 5 5831 5 chr6B.!!$R2 5826
2 TraesCS6D01G398100 chr6A 614584064 614590554 6490 True 633.7 1895 85.477714 1 5659 7 chr6A.!!$R2 5658
3 TraesCS6D01G398100 chr7B 139398073 139398783 710 False 939.0 939 90.556000 1907 2620 1 chr7B.!!$F1 713
4 TraesCS6D01G398100 chr5D 432443680 432444488 808 False 804.0 804 84.700000 3153 3963 1 chr5D.!!$F2 810
5 TraesCS6D01G398100 chr5A 552590411 552591216 805 False 773.0 773 84.088000 3153 3963 1 chr5A.!!$F1 810
6 TraesCS6D01G398100 chr2A 753470676 753471477 801 True 769.0 769 84.049000 3153 3963 1 chr2A.!!$R2 810
7 TraesCS6D01G398100 chr2A 728995278 728996018 740 False 414.0 414 77.806000 2132 2871 1 chr2A.!!$F1 739
8 TraesCS6D01G398100 chr4A 102390004 102390806 802 True 737.0 737 83.354000 3153 3963 1 chr4A.!!$R1 810
9 TraesCS6D01G398100 chr1B 601494625 601495172 547 False 327.0 327 78.485000 2270 2826 1 chr1B.!!$F1 556

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
64 65 0.109597 GCTGGGCTCGAATGTTGTTG 60.110 55.0 0.00 0.0 0.00 3.33 F
1248 1295 0.982852 TCCAGATGGATCCTTGCCGT 60.983 55.0 14.23 0.0 39.78 5.68 F
1854 1921 0.040058 TGAGGCCATTGCTGGATGTT 59.960 50.0 5.01 0.0 46.37 2.71 F
3366 3900 0.886563 ATTCTGCTGAAACTGCTGCC 59.113 50.0 10.27 0.0 35.63 4.85 F
3787 4337 0.037975 GCCCCTTGCAAACACTCATG 60.038 55.0 0.00 0.0 40.77 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 1459 0.320421 GCGTACATATGGCGGGTGAT 60.320 55.0 18.82 0.0 0.00 3.06 R
2136 2333 1.085091 CTAAGCCAGCTGCACAGAAG 58.915 55.0 8.66 0.0 44.83 2.85 R
3769 4319 0.037975 GCATGAGTGTTTGCAAGGGG 60.038 55.0 0.00 0.0 38.72 4.79 R
4300 4867 0.035317 GCACACCATGGTCACTCTCA 59.965 55.0 16.53 0.0 0.00 3.27 R
5272 6174 0.251916 CTCCCTACGTGGATTTGCCA 59.748 55.0 0.00 0.0 46.96 4.92 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
63 64 1.577328 CGCTGGGCTCGAATGTTGTT 61.577 55.000 0.00 0.00 0.00 2.83
64 65 0.109597 GCTGGGCTCGAATGTTGTTG 60.110 55.000 0.00 0.00 0.00 3.33
65 66 1.238439 CTGGGCTCGAATGTTGTTGT 58.762 50.000 0.00 0.00 0.00 3.32
354 365 8.870879 AGTAGAATTTTCTATTCTGTAACACGC 58.129 33.333 9.63 0.00 41.43 5.34
361 372 1.045407 TTCTGTAACACGCTGGACCT 58.955 50.000 0.00 0.00 0.00 3.85
371 382 1.812571 ACGCTGGACCTTTTTAGCATG 59.187 47.619 2.07 0.00 35.98 4.06
444 460 8.603242 ATTTTTCTAACTTGAAAGTCTCGCTA 57.397 30.769 0.00 0.00 38.57 4.26
453 469 3.243636 TGAAAGTCTCGCTAGGTCGTTTT 60.244 43.478 0.00 0.00 0.00 2.43
454 470 4.022935 TGAAAGTCTCGCTAGGTCGTTTTA 60.023 41.667 0.00 0.00 0.00 1.52
467 483 7.440255 GCTAGGTCGTTTTAAATATAGAAGGCA 59.560 37.037 0.00 0.00 0.00 4.75
489 505 8.718656 AGGCATACATATTTTATCCTAGGATCC 58.281 37.037 27.86 16.76 36.17 3.36
491 507 9.905713 GCATACATATTTTATCCTAGGATCCAA 57.094 33.333 27.86 20.35 36.17 3.53
561 577 8.556213 ACAATACCGAACAAACAATATAGTGT 57.444 30.769 0.00 0.00 0.00 3.55
604 620 2.751036 TCATGGTACGTCGCCGGA 60.751 61.111 5.05 0.00 38.78 5.14
651 667 2.095263 CGCCCCAAATATATGGCTTTCG 60.095 50.000 9.44 0.00 41.80 3.46
664 680 2.793278 GCTTTCGGCCTCTTTTTCAA 57.207 45.000 0.00 0.00 34.27 2.69
665 681 2.666026 GCTTTCGGCCTCTTTTTCAAG 58.334 47.619 0.00 0.00 34.27 3.02
744 762 7.673810 AATTTTGTTTTGACACTTACGTAGC 57.326 32.000 0.00 0.00 0.00 3.58
755 773 7.349711 TGACACTTACGTAGCAAAGAATTTTC 58.650 34.615 2.89 0.00 35.03 2.29
756 774 6.665465 ACACTTACGTAGCAAAGAATTTTCC 58.335 36.000 2.89 0.00 35.03 3.13
757 775 6.485648 ACACTTACGTAGCAAAGAATTTTCCT 59.514 34.615 2.89 0.00 35.03 3.36
760 778 8.410912 ACTTACGTAGCAAAGAATTTTCCTTTT 58.589 29.630 2.89 0.00 35.03 2.27
794 822 4.790962 CTCACCGGCTGCTGGCAT 62.791 66.667 27.03 6.07 44.01 4.40
836 864 1.302351 GCTGCTGGCAGTTGACTCT 60.302 57.895 21.34 0.00 45.24 3.24
841 869 1.959042 CTGGCAGTTGACTCTTGTGT 58.041 50.000 6.28 0.00 0.00 3.72
855 883 1.057275 TTGTGTAGCAGGGACCCACA 61.057 55.000 14.60 5.18 34.47 4.17
865 893 1.377725 GGACCCACATGTCAGCCAG 60.378 63.158 0.00 0.00 36.97 4.85
932 965 1.544686 GTGTATTTCCCGCGCATTTG 58.455 50.000 8.75 0.00 0.00 2.32
970 1003 2.447959 GCCCCCTCTTATCCCCGT 60.448 66.667 0.00 0.00 0.00 5.28
984 1018 3.288290 CCGTCTCCTCCGATCCCG 61.288 72.222 0.00 0.00 0.00 5.14
985 1019 2.203167 CGTCTCCTCCGATCCCGA 60.203 66.667 0.00 0.00 38.22 5.14
986 1020 2.544698 CGTCTCCTCCGATCCCGAC 61.545 68.421 0.00 0.00 38.22 4.79
987 1021 2.194889 GTCTCCTCCGATCCCGACC 61.195 68.421 0.00 0.00 38.22 4.79
988 1022 2.913060 CTCCTCCGATCCCGACCC 60.913 72.222 0.00 0.00 38.22 4.46
989 1023 4.534824 TCCTCCGATCCCGACCCC 62.535 72.222 0.00 0.00 38.22 4.95
991 1025 4.889112 CTCCGATCCCGACCCCGA 62.889 72.222 0.00 0.00 38.22 5.14
1039 1082 2.279784 GCCGCCAGAAGAGATCCG 60.280 66.667 0.00 0.00 0.00 4.18
1043 1086 1.667154 CGCCAGAAGAGATCCGTCCA 61.667 60.000 0.00 0.00 0.00 4.02
1098 1141 1.454295 GAGACGGGAGAGAGGACCC 60.454 68.421 0.00 0.00 42.43 4.46
1196 1239 2.917227 CACCCCCAACAAGGTGCC 60.917 66.667 0.00 0.00 46.55 5.01
1197 1240 4.233558 ACCCCCAACAAGGTGCCC 62.234 66.667 0.00 0.00 34.20 5.36
1215 1258 2.525381 CCCTCCTCCCATCCTCCG 60.525 72.222 0.00 0.00 0.00 4.63
1225 1272 3.155167 ATCCTCCGTCCCCGCTTC 61.155 66.667 0.00 0.00 0.00 3.86
1228 1275 3.839432 CTCCGTCCCCGCTTCCTC 61.839 72.222 0.00 0.00 0.00 3.71
1229 1276 4.377760 TCCGTCCCCGCTTCCTCT 62.378 66.667 0.00 0.00 0.00 3.69
1231 1278 3.839432 CGTCCCCGCTTCCTCTCC 61.839 72.222 0.00 0.00 0.00 3.71
1248 1295 0.982852 TCCAGATGGATCCTTGCCGT 60.983 55.000 14.23 0.00 39.78 5.68
1268 1315 5.123979 GCCGTTTTCCTGATGTAGATCTTTT 59.876 40.000 0.00 0.00 0.00 2.27
1271 1318 6.403636 CGTTTTCCTGATGTAGATCTTTTGGG 60.404 42.308 0.00 0.00 0.00 4.12
1273 1320 5.779241 TCCTGATGTAGATCTTTTGGGTT 57.221 39.130 0.00 0.00 0.00 4.11
1274 1321 5.500234 TCCTGATGTAGATCTTTTGGGTTG 58.500 41.667 0.00 0.00 0.00 3.77
1276 1323 5.255397 TGATGTAGATCTTTTGGGTTGGT 57.745 39.130 0.00 0.00 0.00 3.67
1316 1363 2.954868 GGTACGATGCCGCTGACG 60.955 66.667 0.00 0.00 39.95 4.35
1424 1471 2.923619 TGAAGGATCACCCGCCATA 58.076 52.632 0.00 0.00 40.87 2.74
1425 1472 1.434188 TGAAGGATCACCCGCCATAT 58.566 50.000 0.00 0.00 40.87 1.78
1428 1475 2.024176 AGGATCACCCGCCATATGTA 57.976 50.000 1.24 0.00 40.87 2.29
1432 1479 1.959226 CACCCGCCATATGTACGCC 60.959 63.158 9.28 0.00 0.00 5.68
1435 1482 1.374252 CCGCCATATGTACGCCTCC 60.374 63.158 9.28 0.00 0.00 4.30
1436 1483 1.733041 CGCCATATGTACGCCTCCG 60.733 63.158 1.24 0.00 41.14 4.63
1467 1514 0.391661 GCTCGTCTGGATTGGCTTCA 60.392 55.000 0.00 0.00 0.00 3.02
1561 1609 1.442184 CACGGACGTCTCCTTCACG 60.442 63.158 16.46 10.88 43.13 4.35
1621 1669 2.052766 GCGCATCTCGGCAAATCG 60.053 61.111 0.30 0.00 38.94 3.34
1623 1671 2.528743 CGCATCTCGGCAAATCGCT 61.529 57.895 0.00 0.00 41.91 4.93
1625 1673 0.590732 GCATCTCGGCAAATCGCTTG 60.591 55.000 0.00 0.00 41.91 4.01
1637 1685 5.486095 CAAATCGCTTGCTTTTCACTTAC 57.514 39.130 0.00 0.00 0.00 2.34
1638 1686 5.215160 CAAATCGCTTGCTTTTCACTTACT 58.785 37.500 0.00 0.00 0.00 2.24
1639 1687 5.438761 AATCGCTTGCTTTTCACTTACTT 57.561 34.783 0.00 0.00 0.00 2.24
1652 1700 5.808366 TCACTTACTTGAGTTCCAGATGT 57.192 39.130 0.00 0.00 0.00 3.06
1653 1701 5.541845 TCACTTACTTGAGTTCCAGATGTG 58.458 41.667 0.00 0.00 0.00 3.21
1656 1704 5.992217 ACTTACTTGAGTTCCAGATGTGTTC 59.008 40.000 0.00 0.00 0.00 3.18
1657 1705 4.696479 ACTTGAGTTCCAGATGTGTTCT 57.304 40.909 0.00 0.00 33.90 3.01
1658 1706 5.808366 ACTTGAGTTCCAGATGTGTTCTA 57.192 39.130 0.00 0.00 31.77 2.10
1659 1707 5.788450 ACTTGAGTTCCAGATGTGTTCTAG 58.212 41.667 0.00 0.00 31.77 2.43
1660 1708 4.808414 TGAGTTCCAGATGTGTTCTAGG 57.192 45.455 0.00 0.00 31.77 3.02
1661 1709 3.515502 TGAGTTCCAGATGTGTTCTAGGG 59.484 47.826 0.00 0.00 31.77 3.53
1662 1710 2.840651 AGTTCCAGATGTGTTCTAGGGG 59.159 50.000 0.00 0.00 31.77 4.79
1663 1711 2.572104 GTTCCAGATGTGTTCTAGGGGT 59.428 50.000 0.00 0.00 31.77 4.95
1664 1712 2.187958 TCCAGATGTGTTCTAGGGGTG 58.812 52.381 0.00 0.00 31.77 4.61
1665 1713 1.210478 CCAGATGTGTTCTAGGGGTGG 59.790 57.143 0.00 0.00 31.77 4.61
1666 1714 1.909302 CAGATGTGTTCTAGGGGTGGT 59.091 52.381 0.00 0.00 31.77 4.16
1667 1715 3.104512 CAGATGTGTTCTAGGGGTGGTA 58.895 50.000 0.00 0.00 31.77 3.25
1668 1716 3.105283 AGATGTGTTCTAGGGGTGGTAC 58.895 50.000 0.00 0.00 30.96 3.34
1669 1717 2.402182 TGTGTTCTAGGGGTGGTACA 57.598 50.000 0.00 0.00 0.00 2.90
1670 1718 2.692024 TGTGTTCTAGGGGTGGTACAA 58.308 47.619 0.00 0.00 44.16 2.41
1671 1719 3.253220 TGTGTTCTAGGGGTGGTACAAT 58.747 45.455 0.00 0.00 44.16 2.71
1672 1720 3.653836 TGTGTTCTAGGGGTGGTACAATT 59.346 43.478 0.00 0.00 44.16 2.32
1673 1721 4.105057 TGTGTTCTAGGGGTGGTACAATTT 59.895 41.667 0.00 0.00 44.16 1.82
1674 1722 5.074804 GTGTTCTAGGGGTGGTACAATTTT 58.925 41.667 0.00 0.00 44.16 1.82
1675 1723 6.183361 TGTGTTCTAGGGGTGGTACAATTTTA 60.183 38.462 0.00 0.00 44.16 1.52
1676 1724 6.373495 GTGTTCTAGGGGTGGTACAATTTTAG 59.627 42.308 0.00 0.00 44.16 1.85
1677 1725 5.703730 TCTAGGGGTGGTACAATTTTAGG 57.296 43.478 0.00 0.00 44.16 2.69
1678 1726 3.095912 AGGGGTGGTACAATTTTAGGC 57.904 47.619 0.00 0.00 44.16 3.93
1679 1727 2.104967 GGGGTGGTACAATTTTAGGCC 58.895 52.381 0.00 0.00 44.16 5.19
1687 1735 7.435305 GTGGTACAATTTTAGGCCTTTGTTTA 58.565 34.615 22.29 6.20 44.16 2.01
1689 1737 7.094631 GGTACAATTTTAGGCCTTTGTTTAGG 58.905 38.462 22.29 4.94 38.40 2.69
1695 1743 3.322191 AGGCCTTTGTTTAGGTTCCAA 57.678 42.857 0.00 0.00 37.63 3.53
1719 1785 3.132160 CTGGATCTGTCTAATGCTGCAG 58.868 50.000 10.11 10.11 0.00 4.41
1744 1811 9.545105 AGCTTCAATCTTCACTAGATAGAAATG 57.455 33.333 0.00 1.08 42.90 2.32
1757 1824 5.500234 AGATAGAAATGCTGTTGGCTGTTA 58.500 37.500 0.00 0.00 42.39 2.41
1766 1833 3.386486 CTGTTGGCTGTTAGTACGACAA 58.614 45.455 6.58 0.00 0.00 3.18
1802 1869 3.553511 CAGTAATCGAGTTCCAGATGTGC 59.446 47.826 0.00 0.00 0.00 4.57
1810 1877 4.187694 GAGTTCCAGATGTGCTTTAGGAG 58.812 47.826 0.00 0.00 0.00 3.69
1811 1878 3.584848 AGTTCCAGATGTGCTTTAGGAGT 59.415 43.478 0.00 0.00 0.00 3.85
1829 1896 5.306394 AGGAGTACAAGTTTAGACCTTTGC 58.694 41.667 0.00 0.00 0.00 3.68
1837 1904 0.973632 TTAGACCTTTGCGCTCCTGA 59.026 50.000 9.73 0.00 0.00 3.86
1850 1917 1.918467 CTCCTGAGGCCATTGCTGGA 61.918 60.000 5.01 9.24 46.37 3.86
1854 1921 0.040058 TGAGGCCATTGCTGGATGTT 59.960 50.000 5.01 0.00 46.37 2.71
1868 1938 5.118990 GCTGGATGTTAGCTGTTAGATTCA 58.881 41.667 0.00 0.00 38.14 2.57
1876 1946 6.092122 TGTTAGCTGTTAGATTCATCAAACCG 59.908 38.462 0.00 0.00 0.00 4.44
1886 1956 5.995282 AGATTCATCAAACCGTACAAGTTCA 59.005 36.000 0.00 0.00 0.00 3.18
1887 1957 6.485313 AGATTCATCAAACCGTACAAGTTCAA 59.515 34.615 0.00 0.00 0.00 2.69
1888 1958 6.627395 TTCATCAAACCGTACAAGTTCAAT 57.373 33.333 0.00 0.00 0.00 2.57
1889 1959 6.627395 TCATCAAACCGTACAAGTTCAATT 57.373 33.333 0.00 0.00 0.00 2.32
1898 1968 5.178623 CCGTACAAGTTCAATTTGCACTAGA 59.821 40.000 2.08 0.00 0.00 2.43
1901 1971 7.111593 CGTACAAGTTCAATTTGCACTAGAAAC 59.888 37.037 2.08 0.00 0.00 2.78
1905 2017 9.462174 CAAGTTCAATTTGCACTAGAAACAATA 57.538 29.630 2.08 0.00 0.00 1.90
1932 2044 6.238320 GCAATTGCTTTACCATCTCTGACTAG 60.238 42.308 23.21 0.00 38.21 2.57
1970 2166 7.521115 AGGGAGGGACATTAGTGGAATATATTT 59.479 37.037 0.00 0.00 0.00 1.40
1979 2175 9.599322 CATTAGTGGAATATATTTCTGCGAAAC 57.401 33.333 5.34 0.00 0.00 2.78
1980 2176 8.725405 TTAGTGGAATATATTTCTGCGAAACA 57.275 30.769 5.34 0.00 0.00 2.83
1984 2180 8.609176 GTGGAATATATTTCTGCGAAACACTTA 58.391 33.333 5.34 0.00 0.00 2.24
1990 2186 8.687824 ATATTTCTGCGAAACACTTAATTTGG 57.312 30.769 5.99 0.00 0.00 3.28
2021 2218 6.233905 TCAGTATGAACAGGCTAAGCATAA 57.766 37.500 0.00 0.00 45.97 1.90
2022 2219 6.830912 TCAGTATGAACAGGCTAAGCATAAT 58.169 36.000 0.00 0.00 45.97 1.28
2023 2220 7.962441 TCAGTATGAACAGGCTAAGCATAATA 58.038 34.615 0.00 0.00 45.97 0.98
2024 2221 8.090831 TCAGTATGAACAGGCTAAGCATAATAG 58.909 37.037 0.00 0.00 45.97 1.73
2035 2232 9.553064 AGGCTAAGCATAATAGTATGATAATGC 57.447 33.333 14.15 11.61 39.72 3.56
2246 2454 4.463070 TGTGTTTTAGGGGGTACAGTTTC 58.537 43.478 0.00 0.00 0.00 2.78
2344 2553 3.539604 AGAAATGCTGCTAGCTGTTAGG 58.460 45.455 21.03 4.25 42.97 2.69
2550 2767 6.207928 TCACAGTGCAAACAATTCAATAGTG 58.792 36.000 0.00 0.00 0.00 2.74
2628 3112 6.259387 GGCATTACTTATTAGGGTGTGTGTAC 59.741 42.308 0.00 0.00 0.00 2.90
2672 3156 4.759782 TCTTAGAACTGGCTAAGCATGAC 58.240 43.478 0.00 0.00 44.39 3.06
2683 3167 6.118852 TGGCTAAGCATGACATATTTGTACA 58.881 36.000 0.00 0.00 35.79 2.90
2702 3186 6.398095 TGTACAACTGAGATTCATGTACCAG 58.602 40.000 15.15 0.00 39.93 4.00
2862 3358 6.044682 CCAAGAATGGGAAATCTGCAAATAC 58.955 40.000 0.00 0.00 43.51 1.89
3026 3549 7.366371 GGGACGGAGGGAGTATATTAGTATAGT 60.366 44.444 0.00 0.00 0.00 2.12
3366 3900 0.886563 ATTCTGCTGAAACTGCTGCC 59.113 50.000 10.27 0.00 35.63 4.85
3441 3979 8.695456 ACAATCACTATTTGTTGAGGAAAGTTT 58.305 29.630 0.00 0.00 33.64 2.66
3455 3993 2.869101 AAGTTTCTGCCTTCCTCTCC 57.131 50.000 0.00 0.00 0.00 3.71
3456 3994 0.988063 AGTTTCTGCCTTCCTCTCCC 59.012 55.000 0.00 0.00 0.00 4.30
3515 4053 9.316730 TGTTAATTAAGGAATGGTATGTACGTC 57.683 33.333 0.00 0.00 0.00 4.34
3625 4171 4.002906 TGTTCCTGTTCCACTGATGTAC 57.997 45.455 0.00 0.00 0.00 2.90
3628 4174 2.567169 TCCTGTTCCACTGATGTACTGG 59.433 50.000 0.00 0.00 32.95 4.00
3761 4310 1.510776 GTATGCTCCTGATCTGCAGC 58.489 55.000 9.47 8.50 43.50 5.25
3785 4335 3.854856 GCCCCTTGCAAACACTCA 58.145 55.556 0.00 0.00 40.77 3.41
3786 4336 2.354902 GCCCCTTGCAAACACTCAT 58.645 52.632 0.00 0.00 40.77 2.90
3787 4337 0.037975 GCCCCTTGCAAACACTCATG 60.038 55.000 0.00 0.00 40.77 3.07
3792 4342 2.333926 CTTGCAAACACTCATGCCATG 58.666 47.619 0.00 0.00 41.87 3.66
3793 4343 0.604073 TGCAAACACTCATGCCATGG 59.396 50.000 7.63 7.63 41.87 3.66
3794 4344 0.604578 GCAAACACTCATGCCATGGT 59.395 50.000 14.67 0.00 36.56 3.55
3812 4365 5.066505 CCATGGTAGTCTTTTGGTCATTAGC 59.933 44.000 2.57 0.00 0.00 3.09
3818 4371 7.389607 GGTAGTCTTTTGGTCATTAGCTACAAA 59.610 37.037 0.00 0.00 0.00 2.83
3844 4397 9.259832 AGCCTGGTTAAAAGAATTATTCTGATT 57.740 29.630 8.34 9.32 40.59 2.57
3968 4521 2.355310 CCAACCCGGTAAGCTGTGATTA 60.355 50.000 0.00 0.00 0.00 1.75
3972 4525 2.676342 CCCGGTAAGCTGTGATTACAAC 59.324 50.000 0.00 0.00 36.14 3.32
3973 4526 3.596214 CCGGTAAGCTGTGATTACAACT 58.404 45.455 7.79 0.00 34.82 3.16
3974 4527 3.370978 CCGGTAAGCTGTGATTACAACTG 59.629 47.826 7.79 0.00 33.70 3.16
4015 4572 9.268268 CAATACAACTCTTCTGGTGTTAACTAA 57.732 33.333 7.22 0.00 31.48 2.24
4029 4586 9.308000 TGGTGTTAACTAATCATTCATTTCCTT 57.692 29.630 7.22 0.00 0.00 3.36
4067 4624 1.238439 CAGTGACCAGCGGAACAAAT 58.762 50.000 1.50 0.00 0.00 2.32
4073 4630 0.740737 CCAGCGGAACAAATGGATCC 59.259 55.000 4.20 4.20 34.60 3.36
4085 4642 5.256474 ACAAATGGATCCGAGACTGATTTT 58.744 37.500 7.39 0.00 0.00 1.82
4139 4696 2.053627 GCAAACATGTAAGCTGTGCAC 58.946 47.619 10.75 10.75 0.00 4.57
4161 4718 2.621668 CCACCAATCCTTCCTTCCCTTC 60.622 54.545 0.00 0.00 0.00 3.46
4276 4842 8.918658 CACTGGTGATTTGTTTTCATCTTTATG 58.081 33.333 0.00 0.00 0.00 1.90
4300 4867 7.051623 TGTAACCACTCTGTTTAATTGACAGT 58.948 34.615 17.89 4.23 43.80 3.55
4315 4882 1.620819 GACAGTGAGAGTGACCATGGT 59.379 52.381 19.89 19.89 0.00 3.55
4376 4943 3.262915 AGCACTCAAGATCAAGTAAGCCT 59.737 43.478 0.00 0.00 0.00 4.58
4385 4952 7.230510 TCAAGATCAAGTAAGCCTATCTCTCTC 59.769 40.741 0.00 0.00 0.00 3.20
4387 4954 7.984475 AGATCAAGTAAGCCTATCTCTCTCTA 58.016 38.462 0.00 0.00 0.00 2.43
4390 4957 7.750655 TCAAGTAAGCCTATCTCTCTCTATCA 58.249 38.462 0.00 0.00 0.00 2.15
4404 4975 3.260884 TCTCTATCAAACCCAGACACACC 59.739 47.826 0.00 0.00 0.00 4.16
4472 5044 1.674962 GAGGCTATCGACTACCACGTT 59.325 52.381 0.00 0.00 0.00 3.99
4475 5047 2.448219 GCTATCGACTACCACGTTGAC 58.552 52.381 0.00 0.00 30.47 3.18
4499 5071 1.139058 GGGCACATCTACTCGACCATT 59.861 52.381 0.00 0.00 0.00 3.16
4554 5172 1.177256 AGTCTGTAACCGAGTGCCGT 61.177 55.000 0.00 0.00 36.31 5.68
4556 5174 1.800315 CTGTAACCGAGTGCCGTCG 60.800 63.158 0.00 0.00 39.77 5.12
4600 5220 2.840651 AGATGTGCTGTTTAGGTAGCCT 59.159 45.455 0.00 0.00 39.15 4.58
4603 5223 0.909623 TGCTGTTTAGGTAGCCTCCC 59.090 55.000 0.00 0.00 39.15 4.30
4604 5224 0.909623 GCTGTTTAGGTAGCCTCCCA 59.090 55.000 0.00 0.00 34.61 4.37
4620 5240 3.277715 CTCCCAAAGGAAGCATCTTCTC 58.722 50.000 6.54 0.00 43.40 2.87
4647 5268 4.021544 GGAGTTTGAGAGACATGACTCACT 60.022 45.833 23.85 18.19 41.82 3.41
4740 5369 1.454201 TGCGATGAGAGTCTCGTCTT 58.546 50.000 30.54 11.43 42.47 3.01
4748 5377 5.201713 TGAGAGTCTCGTCTTGTGAAATT 57.798 39.130 15.34 0.00 32.35 1.82
4759 5388 5.163893 CGTCTTGTGAAATTATGGTTAGCGT 60.164 40.000 0.00 0.00 0.00 5.07
4760 5389 6.248631 GTCTTGTGAAATTATGGTTAGCGTC 58.751 40.000 0.00 0.00 0.00 5.19
4835 5464 5.090652 TCAAAGTTTGACAGTTACATCGC 57.909 39.130 14.35 0.00 34.08 4.58
4889 5539 6.395426 TTGAGACAAAGTGCAAAGATTGAT 57.605 33.333 8.47 0.00 0.00 2.57
4917 5567 0.679505 TGCTCGCCACTAGTTTGAGT 59.320 50.000 14.13 0.00 0.00 3.41
4945 5597 3.131396 GGGATTATTACACTGTCTGCGG 58.869 50.000 0.00 0.00 0.00 5.69
5008 5661 1.602311 AGCAAGTGCACTTTCCTCTG 58.398 50.000 29.23 18.49 45.16 3.35
5009 5662 1.141657 AGCAAGTGCACTTTCCTCTGA 59.858 47.619 29.23 0.00 45.16 3.27
5010 5663 1.949525 GCAAGTGCACTTTCCTCTGAA 59.050 47.619 29.23 0.00 41.59 3.02
5011 5664 2.031333 GCAAGTGCACTTTCCTCTGAAG 60.031 50.000 29.23 15.35 41.59 3.02
5012 5665 3.470709 CAAGTGCACTTTCCTCTGAAGA 58.529 45.455 29.23 0.00 33.11 2.87
5013 5666 4.070716 CAAGTGCACTTTCCTCTGAAGAT 58.929 43.478 29.23 0.65 33.11 2.40
5014 5667 3.672808 AGTGCACTTTCCTCTGAAGATG 58.327 45.455 15.25 0.00 0.00 2.90
5015 5668 3.326006 AGTGCACTTTCCTCTGAAGATGA 59.674 43.478 15.25 0.00 0.00 2.92
5016 5669 4.067896 GTGCACTTTCCTCTGAAGATGAA 58.932 43.478 10.32 0.00 0.00 2.57
5017 5670 4.153835 GTGCACTTTCCTCTGAAGATGAAG 59.846 45.833 10.32 0.00 31.96 3.02
5018 5671 4.040829 TGCACTTTCCTCTGAAGATGAAGA 59.959 41.667 0.00 0.00 31.96 2.87
5019 5672 5.184711 GCACTTTCCTCTGAAGATGAAGAT 58.815 41.667 0.00 0.00 31.96 2.40
5020 5673 5.647225 GCACTTTCCTCTGAAGATGAAGATT 59.353 40.000 0.00 0.00 31.96 2.40
5021 5674 6.820656 GCACTTTCCTCTGAAGATGAAGATTA 59.179 38.462 0.00 0.00 31.96 1.75
5022 5675 7.201600 GCACTTTCCTCTGAAGATGAAGATTAC 60.202 40.741 0.00 0.00 31.96 1.89
5023 5676 8.040132 CACTTTCCTCTGAAGATGAAGATTACT 58.960 37.037 0.00 0.00 31.96 2.24
5024 5677 8.257306 ACTTTCCTCTGAAGATGAAGATTACTC 58.743 37.037 0.00 0.00 31.96 2.59
5025 5678 7.969690 TTCCTCTGAAGATGAAGATTACTCT 57.030 36.000 0.00 0.00 0.00 3.24
5119 6017 4.625028 TGAGACGAGCATTTCATATGAGG 58.375 43.478 5.39 1.47 0.00 3.86
5270 6172 3.443037 GAATGTCTCTCGGTCAGTCATG 58.557 50.000 0.00 0.00 0.00 3.07
5271 6173 0.528017 TGTCTCTCGGTCAGTCATGC 59.472 55.000 0.00 0.00 0.00 4.06
5272 6174 0.814457 GTCTCTCGGTCAGTCATGCT 59.186 55.000 0.00 0.00 0.00 3.79
5274 6176 0.179116 CTCTCGGTCAGTCATGCTGG 60.179 60.000 14.50 2.78 45.08 4.85
5287 6995 1.064505 CATGCTGGCAAATCCACGTAG 59.935 52.381 0.00 0.00 40.72 3.51
5291 6999 0.251916 TGGCAAATCCACGTAGGGAG 59.748 55.000 0.78 0.00 40.72 4.30
5470 7220 4.668289 ACAAAACAAACAACATCGACTCC 58.332 39.130 0.00 0.00 0.00 3.85
5556 7309 4.827304 TCTCGATGAAATTTTGCACACA 57.173 36.364 0.00 0.00 0.00 3.72
5565 7318 0.375454 TTTTGCACACACCTCGAACG 59.625 50.000 0.00 0.00 0.00 3.95
5582 7335 5.382303 TCGAACGCTCAAGAATTTTTCATC 58.618 37.500 0.00 0.00 0.00 2.92
5619 7374 7.662604 AAGATTTGTTCATGCCAAGAAATTC 57.337 32.000 4.43 0.00 31.27 2.17
5628 7383 4.439305 TGCCAAGAAATTCCAGATTTCG 57.561 40.909 6.00 0.00 41.49 3.46
5688 7443 1.452108 GCTCGGGGTCCAGAAATGG 60.452 63.158 0.00 0.00 0.00 3.16
5698 7453 2.094854 GTCCAGAAATGGCAGCTCTTTG 60.095 50.000 0.00 0.00 0.00 2.77
5703 7458 3.638160 AGAAATGGCAGCTCTTTGAACAA 59.362 39.130 0.00 0.00 0.00 2.83
5709 7464 3.375642 GCAGCTCTTTGAACAAAAGGTC 58.624 45.455 1.76 0.00 44.69 3.85
5711 7466 3.381272 CAGCTCTTTGAACAAAAGGTCCA 59.619 43.478 1.76 0.00 44.69 4.02
5714 7469 5.241728 AGCTCTTTGAACAAAAGGTCCATAC 59.758 40.000 1.76 0.00 44.69 2.39
5715 7470 5.009610 GCTCTTTGAACAAAAGGTCCATACA 59.990 40.000 1.76 0.00 44.69 2.29
5760 7515 8.001881 ACATTTACATATATCTAGCTCCTCCG 57.998 38.462 0.00 0.00 0.00 4.63
5761 7516 6.452494 TTTACATATATCTAGCTCCTCCGC 57.548 41.667 0.00 0.00 0.00 5.54
5774 7529 0.688487 CCTCCGCCGGGGATTATTAA 59.312 55.000 21.95 0.00 46.04 1.40
5776 7531 0.688487 TCCGCCGGGGATTATTAAGG 59.312 55.000 21.95 0.00 40.94 2.69
5778 7533 0.958876 CGCCGGGGATTATTAAGGCC 60.959 60.000 14.46 0.00 41.36 5.19
5793 7548 1.212250 AGGCCCCTCGTATTTTGGGT 61.212 55.000 0.00 0.00 40.36 4.51
5798 7553 2.490509 CCCCTCGTATTTTGGGTCAAAC 59.509 50.000 0.00 0.00 39.31 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.001674 TGTTCTTTCATGGAAAGCCTAGTTAA 58.998 34.615 12.63 0.00 45.86 2.01
19 20 4.461781 CAGATGTTCTTTCATGGAAAGCCT 59.538 41.667 12.63 3.83 45.86 4.58
63 64 7.118723 ACAGAAATATAAAATCAGCCTCCACA 58.881 34.615 0.00 0.00 0.00 4.17
64 65 7.573968 ACAGAAATATAAAATCAGCCTCCAC 57.426 36.000 0.00 0.00 0.00 4.02
65 66 9.866655 ATTACAGAAATATAAAATCAGCCTCCA 57.133 29.630 0.00 0.00 0.00 3.86
99 100 7.915293 TTCCTCTCAAAGCATAAACGAAATA 57.085 32.000 0.00 0.00 0.00 1.40
112 113 9.829507 AGAAGATATGTGTATTTCCTCTCAAAG 57.170 33.333 0.00 0.00 0.00 2.77
344 355 1.878953 AAAGGTCCAGCGTGTTACAG 58.121 50.000 0.00 0.00 0.00 2.74
354 365 8.230472 AGAATAATCATGCTAAAAAGGTCCAG 57.770 34.615 0.00 0.00 0.00 3.86
424 440 4.765856 ACCTAGCGAGACTTTCAAGTTAGA 59.234 41.667 0.00 0.00 39.88 2.10
440 456 7.359014 GCCTTCTATATTTAAAACGACCTAGCG 60.359 40.741 0.00 0.00 37.29 4.26
444 460 9.269453 GTATGCCTTCTATATTTAAAACGACCT 57.731 33.333 0.00 0.00 0.00 3.85
561 577 6.706270 GCAAAGCTCTAATACCATAGCAGTAA 59.294 38.462 0.00 0.00 37.44 2.24
604 620 6.381420 TCGAAATCTTCTTCTTCCTACATCCT 59.619 38.462 0.00 0.00 0.00 3.24
674 690 8.282801 TCCCAAATGTAAAGCCTATAAGGATA 57.717 34.615 0.00 0.00 37.67 2.59
684 702 3.132824 CCATCCTTCCCAAATGTAAAGCC 59.867 47.826 0.00 0.00 0.00 4.35
760 778 6.759827 GCCGGTGAGATTAATCAAGTAAGTTA 59.240 38.462 17.56 0.00 0.00 2.24
771 789 1.475751 CCAGCAGCCGGTGAGATTAAT 60.476 52.381 1.90 0.00 43.56 1.40
774 792 2.270205 CCAGCAGCCGGTGAGATT 59.730 61.111 1.90 0.00 43.56 2.40
807 835 1.747325 GCCAGCAGCCAAACCTCAAA 61.747 55.000 0.00 0.00 34.35 2.69
808 836 2.202395 GCCAGCAGCCAAACCTCAA 61.202 57.895 0.00 0.00 34.35 3.02
809 837 2.598394 GCCAGCAGCCAAACCTCA 60.598 61.111 0.00 0.00 34.35 3.86
829 857 2.037251 GTCCCTGCTACACAAGAGTCAA 59.963 50.000 0.00 0.00 0.00 3.18
836 864 1.057275 TGTGGGTCCCTGCTACACAA 61.057 55.000 10.00 0.00 38.91 3.33
841 869 0.546507 TGACATGTGGGTCCCTGCTA 60.547 55.000 10.00 0.00 36.97 3.49
855 883 0.957395 CCTTCGTTGCTGGCTGACAT 60.957 55.000 0.00 0.00 0.00 3.06
916 949 1.435515 GGCAAATGCGCGGGAAATA 59.564 52.632 8.83 0.00 43.26 1.40
970 1003 2.195139 GGTCGGGATCGGAGGAGA 59.805 66.667 0.00 0.00 36.95 3.71
1067 1110 0.760945 CCGTCTCCTTCCCCTGCTAT 60.761 60.000 0.00 0.00 0.00 2.97
1068 1111 1.381327 CCGTCTCCTTCCCCTGCTA 60.381 63.158 0.00 0.00 0.00 3.49
1098 1141 0.745486 TGGAGAACATCATGGCTGCG 60.745 55.000 0.00 0.00 0.00 5.18
1196 1239 2.122189 GAGGATGGGAGGAGGGGG 60.122 72.222 0.00 0.00 0.00 5.40
1197 1240 2.122189 GGAGGATGGGAGGAGGGG 60.122 72.222 0.00 0.00 0.00 4.79
1198 1241 2.525381 CGGAGGATGGGAGGAGGG 60.525 72.222 0.00 0.00 0.00 4.30
1199 1242 1.834822 GACGGAGGATGGGAGGAGG 60.835 68.421 0.00 0.00 0.00 4.30
1200 1243 1.834822 GGACGGAGGATGGGAGGAG 60.835 68.421 0.00 0.00 0.00 3.69
1201 1244 2.282446 GGACGGAGGATGGGAGGA 59.718 66.667 0.00 0.00 0.00 3.71
1202 1245 2.844839 GGGACGGAGGATGGGAGG 60.845 72.222 0.00 0.00 0.00 4.30
1203 1246 2.844839 GGGGACGGAGGATGGGAG 60.845 72.222 0.00 0.00 0.00 4.30
1215 1258 2.683933 TGGAGAGGAAGCGGGGAC 60.684 66.667 0.00 0.00 0.00 4.46
1231 1278 1.755179 AAACGGCAAGGATCCATCTG 58.245 50.000 15.82 9.26 0.00 2.90
1248 1295 6.552008 ACCCAAAAGATCTACATCAGGAAAA 58.448 36.000 0.00 0.00 0.00 2.29
1268 1315 1.525077 GAACTGCGACACCAACCCA 60.525 57.895 0.00 0.00 0.00 4.51
1271 1318 2.604174 CCGGAACTGCGACACCAAC 61.604 63.158 0.00 0.00 0.00 3.77
1273 1320 4.308458 CCCGGAACTGCGACACCA 62.308 66.667 0.73 0.00 0.00 4.17
1316 1363 2.167861 GTCCGCGATCTGCTTCACC 61.168 63.158 8.23 0.00 43.27 4.02
1409 1456 1.623811 GTACATATGGCGGGTGATCCT 59.376 52.381 7.80 0.00 0.00 3.24
1411 1458 1.710013 CGTACATATGGCGGGTGATC 58.290 55.000 7.80 0.00 0.00 2.92
1412 1459 0.320421 GCGTACATATGGCGGGTGAT 60.320 55.000 18.82 0.00 0.00 3.06
1418 1465 1.733041 CGGAGGCGTACATATGGCG 60.733 63.158 7.80 12.02 42.04 5.69
1424 1471 3.900892 CCGAGCGGAGGCGTACAT 61.901 66.667 2.00 0.00 46.35 2.29
1467 1514 1.923356 CCCAAACAACAGCAGGGTAT 58.077 50.000 0.00 0.00 34.75 2.73
1621 1669 5.175090 ACTCAAGTAAGTGAAAAGCAAGC 57.825 39.130 0.00 0.00 0.00 4.01
1623 1671 5.650266 TGGAACTCAAGTAAGTGAAAAGCAA 59.350 36.000 0.00 0.00 0.00 3.91
1625 1673 5.527582 TCTGGAACTCAAGTAAGTGAAAAGC 59.472 40.000 0.00 0.00 0.00 3.51
1631 1679 5.300752 ACACATCTGGAACTCAAGTAAGTG 58.699 41.667 0.00 0.00 0.00 3.16
1633 1681 6.226787 AGAACACATCTGGAACTCAAGTAAG 58.773 40.000 0.00 0.00 36.88 2.34
1634 1682 6.174720 AGAACACATCTGGAACTCAAGTAA 57.825 37.500 0.00 0.00 36.88 2.24
1635 1683 5.808366 AGAACACATCTGGAACTCAAGTA 57.192 39.130 0.00 0.00 36.88 2.24
1636 1684 4.696479 AGAACACATCTGGAACTCAAGT 57.304 40.909 0.00 0.00 36.88 3.16
1637 1685 5.174395 CCTAGAACACATCTGGAACTCAAG 58.826 45.833 0.00 0.00 38.88 3.02
1638 1686 4.020218 CCCTAGAACACATCTGGAACTCAA 60.020 45.833 0.00 0.00 38.88 3.02
1639 1687 3.515502 CCCTAGAACACATCTGGAACTCA 59.484 47.826 0.00 0.00 38.88 3.41
1652 1700 5.327737 AAAATTGTACCACCCCTAGAACA 57.672 39.130 0.00 0.00 0.00 3.18
1653 1701 5.884232 CCTAAAATTGTACCACCCCTAGAAC 59.116 44.000 0.00 0.00 0.00 3.01
1656 1704 4.204799 GCCTAAAATTGTACCACCCCTAG 58.795 47.826 0.00 0.00 0.00 3.02
1657 1705 3.053470 GGCCTAAAATTGTACCACCCCTA 60.053 47.826 0.00 0.00 0.00 3.53
1658 1706 2.291996 GGCCTAAAATTGTACCACCCCT 60.292 50.000 0.00 0.00 0.00 4.79
1659 1707 2.104967 GGCCTAAAATTGTACCACCCC 58.895 52.381 0.00 0.00 0.00 4.95
1660 1708 3.095912 AGGCCTAAAATTGTACCACCC 57.904 47.619 1.29 0.00 0.00 4.61
1661 1709 4.282449 ACAAAGGCCTAAAATTGTACCACC 59.718 41.667 17.15 0.00 34.45 4.61
1662 1710 5.462530 ACAAAGGCCTAAAATTGTACCAC 57.537 39.130 17.15 0.00 34.45 4.16
1663 1711 6.487299 AAACAAAGGCCTAAAATTGTACCA 57.513 33.333 18.58 0.00 35.09 3.25
1664 1712 7.094631 CCTAAACAAAGGCCTAAAATTGTACC 58.905 38.462 18.58 0.00 35.09 3.34
1665 1713 7.663827 ACCTAAACAAAGGCCTAAAATTGTAC 58.336 34.615 18.58 0.00 40.62 2.90
1666 1714 7.842887 ACCTAAACAAAGGCCTAAAATTGTA 57.157 32.000 18.58 5.82 40.62 2.41
1667 1715 6.740944 ACCTAAACAAAGGCCTAAAATTGT 57.259 33.333 13.69 13.69 40.62 2.71
1668 1716 6.649141 GGAACCTAAACAAAGGCCTAAAATTG 59.351 38.462 5.16 9.86 40.62 2.32
1669 1717 6.327887 TGGAACCTAAACAAAGGCCTAAAATT 59.672 34.615 5.16 1.98 40.62 1.82
1670 1718 5.841783 TGGAACCTAAACAAAGGCCTAAAAT 59.158 36.000 5.16 0.00 40.62 1.82
1671 1719 5.209659 TGGAACCTAAACAAAGGCCTAAAA 58.790 37.500 5.16 0.00 40.62 1.52
1672 1720 4.805744 TGGAACCTAAACAAAGGCCTAAA 58.194 39.130 5.16 0.00 40.62 1.85
1673 1721 4.456662 TGGAACCTAAACAAAGGCCTAA 57.543 40.909 5.16 0.00 40.62 2.69
1674 1722 4.456662 TTGGAACCTAAACAAAGGCCTA 57.543 40.909 5.16 0.00 40.62 3.93
1675 1723 3.322191 TTGGAACCTAAACAAAGGCCT 57.678 42.857 0.00 0.00 40.62 5.19
1676 1724 3.864540 GCATTGGAACCTAAACAAAGGCC 60.865 47.826 0.00 0.00 40.62 5.19
1677 1725 3.006859 AGCATTGGAACCTAAACAAAGGC 59.993 43.478 0.00 0.00 40.62 4.35
1678 1726 4.559153 CAGCATTGGAACCTAAACAAAGG 58.441 43.478 0.00 0.00 42.82 3.11
1695 1743 3.741249 CAGCATTAGACAGATCCAGCAT 58.259 45.455 0.00 0.00 0.00 3.79
1704 1752 2.353323 TGAAGCTGCAGCATTAGACAG 58.647 47.619 38.24 0.00 45.16 3.51
1744 1811 1.725164 GTCGTACTAACAGCCAACAGC 59.275 52.381 0.00 0.00 44.25 4.40
1757 1824 8.529476 ACTGAATTAATCTTACCTTGTCGTACT 58.471 33.333 0.00 0.00 0.00 2.73
1787 1854 2.932614 CCTAAAGCACATCTGGAACTCG 59.067 50.000 0.00 0.00 0.00 4.18
1802 1869 8.989980 CAAAGGTCTAAACTTGTACTCCTAAAG 58.010 37.037 0.00 0.00 0.00 1.85
1810 1877 3.497262 AGCGCAAAGGTCTAAACTTGTAC 59.503 43.478 11.47 0.00 0.00 2.90
1811 1878 3.735591 AGCGCAAAGGTCTAAACTTGTA 58.264 40.909 11.47 0.00 0.00 2.41
1829 1896 3.207669 GCAATGGCCTCAGGAGCG 61.208 66.667 3.32 0.00 0.00 5.03
1837 1904 2.025863 GCTAACATCCAGCAATGGCCT 61.026 52.381 3.32 0.00 42.56 5.19
1850 1917 7.201644 CGGTTTGATGAATCTAACAGCTAACAT 60.202 37.037 15.98 0.00 41.92 2.71
1854 1921 5.730550 ACGGTTTGATGAATCTAACAGCTA 58.269 37.500 15.98 0.00 41.92 3.32
1868 1938 5.689961 GCAAATTGAACTTGTACGGTTTGAT 59.310 36.000 0.00 1.97 0.00 2.57
1876 1946 7.913297 TGTTTCTAGTGCAAATTGAACTTGTAC 59.087 33.333 12.45 12.46 37.46 2.90
1898 1968 8.042515 AGATGGTAAAGCAATTGCATATTGTTT 58.957 29.630 30.89 21.88 45.16 2.83
1901 1971 7.381408 CAGAGATGGTAAAGCAATTGCATATTG 59.619 37.037 30.89 13.83 45.16 1.90
1905 2017 4.951715 TCAGAGATGGTAAAGCAATTGCAT 59.048 37.500 30.89 18.15 45.16 3.96
1932 2044 3.245122 TGTCCCTCCCTCAAATGGTTAAC 60.245 47.826 0.00 0.00 0.00 2.01
1970 2166 5.508200 AACCAAATTAAGTGTTTCGCAGA 57.492 34.783 0.00 0.00 0.00 4.26
1979 2175 9.398170 CATACTGACTCAAAACCAAATTAAGTG 57.602 33.333 0.00 0.00 0.00 3.16
1980 2176 9.349713 TCATACTGACTCAAAACCAAATTAAGT 57.650 29.630 0.00 0.00 0.00 2.24
1984 2180 8.006298 TGTTCATACTGACTCAAAACCAAATT 57.994 30.769 0.00 0.00 0.00 1.82
1989 2185 4.083271 GCCTGTTCATACTGACTCAAAACC 60.083 45.833 0.00 0.00 0.00 3.27
1990 2186 4.757149 AGCCTGTTCATACTGACTCAAAAC 59.243 41.667 0.00 0.00 0.00 2.43
2009 2206 9.553064 GCATTATCATACTATTATGCTTAGCCT 57.447 33.333 0.29 0.00 38.33 4.58
2050 2247 6.932356 AATATGGTGTCTATGAACTTGCAG 57.068 37.500 0.00 0.00 0.00 4.41
2136 2333 1.085091 CTAAGCCAGCTGCACAGAAG 58.915 55.000 8.66 0.00 44.83 2.85
2137 2334 3.238232 CTAAGCCAGCTGCACAGAA 57.762 52.632 8.66 0.00 44.83 3.02
2161 2358 9.396022 AGGACACCTGAAATGTATACTAATTTG 57.604 33.333 4.17 0.00 29.57 2.32
2344 2553 2.019249 TGGATAGCTTGCATTGCTGTC 58.981 47.619 21.94 21.94 44.37 3.51
2512 2729 3.921257 TGTGATGAGAGCCACAGTG 57.079 52.632 0.00 0.00 38.26 3.66
2550 2767 3.889538 GGTAAAGTAATTGCAGATCCCCC 59.110 47.826 0.00 0.00 0.00 5.40
2628 3112 4.685169 ATTGAAGCGTTCCACAGTAATG 57.315 40.909 0.00 0.00 0.00 1.90
2683 3167 5.481824 TCTCACTGGTACATGAATCTCAGTT 59.518 40.000 0.00 0.00 38.20 3.16
2909 3432 6.927381 GGAGTATAATCTTAGCCAGCGTTAAA 59.073 38.462 0.00 0.00 0.00 1.52
2913 3436 3.258622 GGGAGTATAATCTTAGCCAGCGT 59.741 47.826 0.00 0.00 0.00 5.07
3441 3979 0.972983 CTTCGGGAGAGGAAGGCAGA 60.973 60.000 0.00 0.00 41.75 4.26
3456 3994 3.546714 AAAGGGTGGCGGTCCTTCG 62.547 63.158 6.35 0.00 42.06 3.79
3463 4001 3.277142 AGTATTAGAAAAGGGTGGCGG 57.723 47.619 0.00 0.00 0.00 6.13
3465 4003 4.856509 AGGAAGTATTAGAAAAGGGTGGC 58.143 43.478 0.00 0.00 0.00 5.01
3515 4053 1.299468 GAGGCTACCGATGACAGCG 60.299 63.158 6.03 6.03 36.12 5.18
3769 4319 0.037975 GCATGAGTGTTTGCAAGGGG 60.038 55.000 0.00 0.00 38.72 4.79
3773 4323 1.001068 CCATGGCATGAGTGTTTGCAA 59.999 47.619 28.43 0.00 40.66 4.08
3785 4335 3.245229 TGACCAAAAGACTACCATGGCAT 60.245 43.478 13.04 0.00 34.45 4.40
3786 4336 2.107378 TGACCAAAAGACTACCATGGCA 59.893 45.455 13.04 0.00 34.45 4.92
3787 4337 2.790433 TGACCAAAAGACTACCATGGC 58.210 47.619 13.04 0.00 34.45 4.40
3792 4342 6.403878 TGTAGCTAATGACCAAAAGACTACC 58.596 40.000 0.00 0.00 0.00 3.18
3793 4343 7.900782 TTGTAGCTAATGACCAAAAGACTAC 57.099 36.000 0.00 0.00 0.00 2.73
3794 4344 7.119262 GCTTTGTAGCTAATGACCAAAAGACTA 59.881 37.037 0.00 0.00 44.27 2.59
3818 4371 8.829373 ATCAGAATAATTCTTTTAACCAGGCT 57.171 30.769 0.00 0.00 38.11 4.58
3844 4397 2.632028 TGCCAACCTACAGTTAACCGTA 59.368 45.455 0.88 1.44 36.18 4.02
3853 4406 3.540211 CAGGACTGCCAACCTACAG 57.460 57.895 0.00 0.00 39.86 2.74
3968 4521 3.761218 TGTTTGATCCACACAACAGTTGT 59.239 39.130 13.53 13.53 46.75 3.32
3972 4525 6.070897 TGTATTGTTTGATCCACACAACAG 57.929 37.500 1.41 0.00 36.96 3.16
3973 4526 6.096141 AGTTGTATTGTTTGATCCACACAACA 59.904 34.615 19.01 12.84 36.96 3.33
3974 4527 6.503524 AGTTGTATTGTTTGATCCACACAAC 58.496 36.000 13.74 13.74 36.96 3.32
3978 4531 6.998074 AGAAGAGTTGTATTGTTTGATCCACA 59.002 34.615 0.00 0.00 0.00 4.17
4015 4572 7.551617 GCAGGAATGAAAAAGGAAATGAATGAT 59.448 33.333 0.00 0.00 0.00 2.45
4029 4586 0.968405 GGTGCCTGCAGGAATGAAAA 59.032 50.000 37.21 8.75 37.39 2.29
4030 4587 0.178967 TGGTGCCTGCAGGAATGAAA 60.179 50.000 37.21 12.84 37.39 2.69
4031 4588 0.609957 CTGGTGCCTGCAGGAATGAA 60.610 55.000 37.21 14.53 37.39 2.57
4067 4624 5.175859 GTGTAAAAATCAGTCTCGGATCCA 58.824 41.667 13.41 0.00 0.00 3.41
4073 4630 3.181530 CCTGCGTGTAAAAATCAGTCTCG 60.182 47.826 0.00 0.00 0.00 4.04
4139 4696 0.033109 GGGAAGGAAGGATTGGTGGG 60.033 60.000 0.00 0.00 0.00 4.61
4161 4718 3.356529 AAGACAAGCATCCTACAAGGG 57.643 47.619 0.00 0.00 35.59 3.95
4276 4842 7.225931 TCACTGTCAATTAAACAGAGTGGTTAC 59.774 37.037 21.02 0.00 45.64 2.50
4300 4867 0.035317 GCACACCATGGTCACTCTCA 59.965 55.000 16.53 0.00 0.00 3.27
4315 4882 1.202817 GCAATGTCATCCACATGCACA 59.797 47.619 0.00 0.00 45.77 4.57
4376 4943 6.547880 GTGTCTGGGTTTGATAGAGAGAGATA 59.452 42.308 0.00 0.00 0.00 1.98
4385 4952 3.417069 TGGTGTGTCTGGGTTTGATAG 57.583 47.619 0.00 0.00 0.00 2.08
4387 4954 2.108075 TCATGGTGTGTCTGGGTTTGAT 59.892 45.455 0.00 0.00 0.00 2.57
4390 4957 2.158475 ACATCATGGTGTGTCTGGGTTT 60.158 45.455 11.75 0.00 0.00 3.27
4404 4975 2.417339 GCCAGCAGCAATACATCATG 57.583 50.000 0.00 0.00 42.97 3.07
4472 5044 0.963856 AGTAGATGTGCCCGACGTCA 60.964 55.000 17.16 0.00 42.39 4.35
4475 5047 1.298413 CGAGTAGATGTGCCCGACG 60.298 63.158 0.00 0.00 0.00 5.12
4499 5071 4.937620 GCTGACTTGTAGTGGAAATCATCA 59.062 41.667 0.00 0.00 0.00 3.07
4554 5172 0.378610 CAGATGCTAGCGAGTGACGA 59.621 55.000 10.77 0.00 45.77 4.20
4556 5174 1.535015 GGACAGATGCTAGCGAGTGAC 60.535 57.143 10.77 7.04 0.00 3.67
4600 5220 2.355108 CGAGAAGATGCTTCCTTTGGGA 60.355 50.000 3.71 0.00 40.36 4.37
4603 5223 2.095532 CAGCGAGAAGATGCTTCCTTTG 59.904 50.000 3.71 0.00 40.03 2.77
4604 5224 2.354259 CAGCGAGAAGATGCTTCCTTT 58.646 47.619 3.71 0.00 40.03 3.11
4620 5240 1.998315 CATGTCTCTCAAACTCCAGCG 59.002 52.381 0.00 0.00 0.00 5.18
4647 5268 1.203441 AGCATCCTCTCAGGCCAACA 61.203 55.000 5.01 0.00 34.61 3.33
4740 5369 5.730550 AGAGACGCTAACCATAATTTCACA 58.269 37.500 0.00 0.00 0.00 3.58
4748 5377 4.645136 AGAACATGAGAGACGCTAACCATA 59.355 41.667 0.00 0.00 0.00 2.74
4759 5388 3.193056 CACTCAGAGCAGAACATGAGAGA 59.807 47.826 0.00 0.00 41.35 3.10
4760 5389 3.056678 ACACTCAGAGCAGAACATGAGAG 60.057 47.826 0.00 2.90 41.35 3.20
4829 5458 5.533482 GGTTATTCAGATGTAGAGCGATGT 58.467 41.667 0.00 0.00 0.00 3.06
4835 5464 7.921214 ACACATAACGGTTATTCAGATGTAGAG 59.079 37.037 10.59 0.03 0.00 2.43
4889 5539 1.079819 GTGGCGAGCAGAGTTAGCA 60.080 57.895 0.00 0.00 0.00 3.49
4917 5567 4.917385 ACAGTGTAATAATCCCTTGTGCA 58.083 39.130 0.00 0.00 0.00 4.57
4945 5597 5.445142 CGCTCAGTGTAAGTGATGATGTTTC 60.445 44.000 0.00 0.00 46.90 2.78
5008 5661 6.815641 TGCACTTCAGAGTAATCTTCATCTTC 59.184 38.462 0.00 0.00 33.90 2.87
5009 5662 6.593382 GTGCACTTCAGAGTAATCTTCATCTT 59.407 38.462 10.32 0.00 33.90 2.40
5010 5663 6.105333 GTGCACTTCAGAGTAATCTTCATCT 58.895 40.000 10.32 0.00 33.90 2.90
5011 5664 5.871524 TGTGCACTTCAGAGTAATCTTCATC 59.128 40.000 19.41 0.00 33.90 2.92
5012 5665 5.798132 TGTGCACTTCAGAGTAATCTTCAT 58.202 37.500 19.41 0.00 33.90 2.57
5013 5666 5.213891 TGTGCACTTCAGAGTAATCTTCA 57.786 39.130 19.41 0.00 33.90 3.02
5014 5667 6.348050 CCTTTGTGCACTTCAGAGTAATCTTC 60.348 42.308 19.41 0.00 33.90 2.87
5015 5668 5.471456 CCTTTGTGCACTTCAGAGTAATCTT 59.529 40.000 19.41 0.00 33.90 2.40
5016 5669 4.999950 CCTTTGTGCACTTCAGAGTAATCT 59.000 41.667 19.41 0.00 33.90 2.40
5017 5670 4.154918 CCCTTTGTGCACTTCAGAGTAATC 59.845 45.833 19.41 0.00 33.90 1.75
5018 5671 4.074970 CCCTTTGTGCACTTCAGAGTAAT 58.925 43.478 19.41 0.00 33.90 1.89
5019 5672 3.135712 TCCCTTTGTGCACTTCAGAGTAA 59.864 43.478 19.41 0.00 33.90 2.24
5020 5673 2.703536 TCCCTTTGTGCACTTCAGAGTA 59.296 45.455 19.41 0.00 33.90 2.59
5021 5674 1.490490 TCCCTTTGTGCACTTCAGAGT 59.510 47.619 19.41 0.00 36.25 3.24
5022 5675 2.260844 TCCCTTTGTGCACTTCAGAG 57.739 50.000 19.41 8.24 0.00 3.35
5023 5676 2.957402 ATCCCTTTGTGCACTTCAGA 57.043 45.000 19.41 8.85 0.00 3.27
5024 5677 3.820467 TGTAATCCCTTTGTGCACTTCAG 59.180 43.478 19.41 10.63 0.00 3.02
5025 5678 3.568007 GTGTAATCCCTTTGTGCACTTCA 59.432 43.478 19.41 0.00 0.00 3.02
5119 6017 2.167487 TGAACAGACAAGGGGCAAAAAC 59.833 45.455 0.00 0.00 0.00 2.43
5239 6141 2.544694 CGAGAGACATTCCGGATTCTGG 60.545 54.545 4.15 5.04 0.00 3.86
5240 6142 2.544694 CCGAGAGACATTCCGGATTCTG 60.545 54.545 4.15 6.30 40.15 3.02
5272 6174 0.251916 CTCCCTACGTGGATTTGCCA 59.748 55.000 0.00 0.00 46.96 4.92
5274 6176 1.095807 GCCTCCCTACGTGGATTTGC 61.096 60.000 0.00 0.00 38.35 3.68
5278 6986 2.446036 GGGCCTCCCTACGTGGAT 60.446 66.667 0.84 0.00 41.34 3.41
5287 6995 1.073706 TCCCTTATCTGGGCCTCCC 60.074 63.158 4.53 0.00 46.67 4.30
5291 6999 2.427753 CGCTCCCTTATCTGGGCC 59.572 66.667 0.00 0.00 46.67 5.80
5299 7007 3.006728 CCCACCACCGCTCCCTTA 61.007 66.667 0.00 0.00 0.00 2.69
5430 7180 3.128852 TGTCTAGAGCTCCCGAGATAC 57.871 52.381 10.93 1.92 0.00 2.24
5437 7187 4.134563 TGTTTGTTTTGTCTAGAGCTCCC 58.865 43.478 10.93 0.00 0.00 4.30
5556 7309 2.457366 AATTCTTGAGCGTTCGAGGT 57.543 45.000 15.66 3.54 35.79 3.85
5565 7318 5.405797 GGGACAGATGAAAAATTCTTGAGC 58.594 41.667 0.00 0.00 0.00 4.26
5599 7354 5.070180 TCTGGAATTTCTTGGCATGAACAAA 59.930 36.000 14.62 2.30 0.00 2.83
5600 7355 4.588106 TCTGGAATTTCTTGGCATGAACAA 59.412 37.500 14.62 2.99 0.00 2.83
5602 7357 4.789012 TCTGGAATTTCTTGGCATGAAC 57.211 40.909 14.62 5.18 0.00 3.18
5604 7359 5.393352 CGAAATCTGGAATTTCTTGGCATGA 60.393 40.000 0.00 0.00 36.24 3.07
5659 7414 1.918293 CCCCGAGCTATATGCCCCA 60.918 63.158 0.00 0.00 44.23 4.96
5688 7443 3.375642 GACCTTTTGTTCAAAGAGCTGC 58.624 45.455 0.00 0.00 44.40 5.25
5735 7490 7.416890 GCGGAGGAGCTAGATATATGTAAATGT 60.417 40.741 0.00 0.00 0.00 2.71
5746 7501 1.303398 CCGGCGGAGGAGCTAGATA 60.303 63.158 24.41 0.00 37.29 1.98
5759 7514 0.958876 GGCCTTAATAATCCCCGGCG 60.959 60.000 0.00 0.00 38.39 6.46
5760 7515 0.611062 GGGCCTTAATAATCCCCGGC 60.611 60.000 0.84 0.00 36.83 6.13
5761 7516 3.664240 GGGCCTTAATAATCCCCGG 57.336 57.895 0.84 0.00 32.60 5.73
5766 7521 6.072119 CCAAAATACGAGGGGCCTTAATAATC 60.072 42.308 0.84 0.00 0.00 1.75
5774 7529 1.613061 CCCAAAATACGAGGGGCCT 59.387 57.895 0.84 0.00 38.98 5.19


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

AutoCloner maintained by Alex Coulton.