Multiple sequence alignment - TraesCS7B01G001000

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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 TraesCS7B01G001000 chr7B 100.000 3451 0 0 1 3451 260219 263669 0.000000e+00 6373.0
1 TraesCS7B01G001000 chr5D 90.312 1280 55 19 1884 3145 562345875 562344647 0.000000e+00 1613.0
2 TraesCS7B01G001000 chr5D 92.434 978 40 20 913 1872 562346878 562345917 0.000000e+00 1365.0
3 TraesCS7B01G001000 chr5D 87.722 619 27 17 6 596 562347867 562347270 0.000000e+00 676.0
4 TraesCS7B01G001000 chr5D 78.760 871 122 32 924 1759 562344159 562343317 3.050000e-145 525.0
5 TraesCS7B01G001000 chr5D 76.252 699 129 25 922 1601 562349284 562348604 1.530000e-88 337.0
6 TraesCS7B01G001000 chr5D 95.238 210 10 0 676 885 562347084 562346875 1.980000e-87 333.0
7 TraesCS7B01G001000 chr5D 89.706 136 7 6 3313 3447 562344447 562344318 2.130000e-37 167.0
8 TraesCS7B01G001000 chr5D 100.000 64 0 0 613 676 562347124 562347061 6.050000e-23 119.0
9 TraesCS7B01G001000 chr5B 83.724 1665 98 72 1869 3447 712858656 712857079 0.000000e+00 1413.0
10 TraesCS7B01G001000 chr5B 88.126 1019 49 13 915 1872 712859697 712858690 0.000000e+00 1146.0
11 TraesCS7B01G001000 chr5B 85.314 606 44 26 6 596 712860581 712860006 4.960000e-163 584.0
12 TraesCS7B01G001000 chr5B 78.129 887 119 35 919 1759 712856946 712856089 8.600000e-136 494.0
13 TraesCS7B01G001000 chr5B 88.820 161 8 1 676 836 712859876 712859726 4.550000e-44 189.0
14 TraesCS7B01G001000 chr5B 92.105 38 2 1 855 892 712859726 712859690 6.000000e-03 52.8


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 TraesCS7B01G001000 chr7B 260219 263669 3450 False 6373.000000 6373 100.000000 1 3451 1 chr7B.!!$F1 3450
1 TraesCS7B01G001000 chr5D 562343317 562349284 5967 True 641.875000 1613 88.803000 6 3447 8 chr5D.!!$R1 3441
2 TraesCS7B01G001000 chr5B 712856089 712860581 4492 True 646.466667 1413 86.036333 6 3447 6 chr5B.!!$R1 3441

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
773 2352 0.615331 TCTTACCTTGCCAGCCTCTG 59.385 55.000 0.0 0.0 0.0 3.35 F
1571 3184 1.067071 CAAGGAGTAGAACCCACCGTC 60.067 57.143 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 3472 0.111061 AACAGCTTGCCTGACATGGA 59.889 50.0 0.00 0.00 44.64 3.41 R
2915 4609 0.320771 GTGCAGACTGTACTGTGGGG 60.321 60.0 15.61 0.97 39.73 4.96 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
80 1493 6.866010 TTGTATAGCATATGCAAGGAGTTG 57.134 37.500 28.62 0.00 45.16 3.16
92 1505 3.274288 CAAGGAGTTGATGTAAGGAGGC 58.726 50.000 0.00 0.00 35.46 4.70
93 1506 2.551270 AGGAGTTGATGTAAGGAGGCA 58.449 47.619 0.00 0.00 0.00 4.75
94 1507 2.912956 AGGAGTTGATGTAAGGAGGCAA 59.087 45.455 0.00 0.00 0.00 4.52
95 1508 3.525199 AGGAGTTGATGTAAGGAGGCAAT 59.475 43.478 0.00 0.00 0.00 3.56
96 1509 4.721776 AGGAGTTGATGTAAGGAGGCAATA 59.278 41.667 0.00 0.00 0.00 1.90
103 1516 6.894682 TGATGTAAGGAGGCAATACAATACA 58.105 36.000 0.00 0.00 33.63 2.29
136 1549 5.649395 TCCCACATTTTCAGAAGAATAGCAG 59.351 40.000 0.00 0.00 32.89 4.24
137 1550 5.338365 CCACATTTTCAGAAGAATAGCAGC 58.662 41.667 0.00 0.00 32.89 5.25
138 1551 5.106038 CCACATTTTCAGAAGAATAGCAGCA 60.106 40.000 0.00 0.00 32.89 4.41
158 1571 4.777896 AGCAGTTCTCAAAGATACCCTGTA 59.222 41.667 0.00 0.00 0.00 2.74
192 1606 3.482156 TCATCCTATTCTTGCTCCTGC 57.518 47.619 0.00 0.00 40.20 4.85
203 1617 2.202295 TGCTCCTGCGAAACAAAAAC 57.798 45.000 0.00 0.00 43.34 2.43
204 1618 1.120437 GCTCCTGCGAAACAAAAACG 58.880 50.000 0.00 0.00 0.00 3.60
207 1621 1.212455 CCTGCGAAACAAAAACGGGC 61.212 55.000 0.00 0.00 0.00 6.13
238 1653 8.731275 TTCACTCTTAAAGAAAATGACTGACA 57.269 30.769 0.00 0.00 0.00 3.58
240 1655 7.041780 TCACTCTTAAAGAAAATGACTGACAGC 60.042 37.037 1.25 0.00 0.00 4.40
241 1656 6.767902 ACTCTTAAAGAAAATGACTGACAGCA 59.232 34.615 1.25 2.12 0.00 4.41
255 1670 4.225042 ACTGACAGCATTTGTAGGGATGTA 59.775 41.667 1.25 0.00 41.05 2.29
259 1674 8.201242 TGACAGCATTTGTAGGGATGTATATA 57.799 34.615 0.00 0.00 41.05 0.86
260 1675 8.825774 TGACAGCATTTGTAGGGATGTATATAT 58.174 33.333 0.00 0.00 41.05 0.86
309 1724 5.757320 ACTGAGCAATGCTACTATCACATTC 59.243 40.000 8.12 0.00 39.88 2.67
310 1725 5.922053 TGAGCAATGCTACTATCACATTCT 58.078 37.500 8.12 0.00 39.88 2.40
311 1726 7.054491 TGAGCAATGCTACTATCACATTCTA 57.946 36.000 8.12 0.00 39.88 2.10
312 1727 7.500141 TGAGCAATGCTACTATCACATTCTAA 58.500 34.615 8.12 0.00 39.88 2.10
353 1768 3.242739 GCGTGCCTATGTGTTATTCCTTG 60.243 47.826 0.00 0.00 0.00 3.61
354 1769 3.312421 CGTGCCTATGTGTTATTCCTTGG 59.688 47.826 0.00 0.00 0.00 3.61
355 1770 3.632145 GTGCCTATGTGTTATTCCTTGGG 59.368 47.826 0.00 0.00 0.00 4.12
529 1971 2.590645 CAGCAGCAGGAGCAGGAT 59.409 61.111 0.00 0.00 45.49 3.24
596 2038 7.831691 TCCATGTGGAAAGTATTCAAAGAAA 57.168 32.000 0.00 0.00 42.18 2.52
597 2039 7.657336 TCCATGTGGAAAGTATTCAAAGAAAC 58.343 34.615 0.00 0.00 42.18 2.78
598 2040 7.286546 TCCATGTGGAAAGTATTCAAAGAAACA 59.713 33.333 0.00 0.00 42.18 2.83
652 2231 2.499693 AGTCTTAGCAGGCTTCTCCTTC 59.500 50.000 0.00 0.00 44.75 3.46
653 2232 2.499693 GTCTTAGCAGGCTTCTCCTTCT 59.500 50.000 0.00 0.00 44.75 2.85
654 2233 3.055458 GTCTTAGCAGGCTTCTCCTTCTT 60.055 47.826 0.00 0.00 44.75 2.52
655 2234 3.196685 TCTTAGCAGGCTTCTCCTTCTTC 59.803 47.826 0.00 0.00 44.75 2.87
656 2235 1.356124 AGCAGGCTTCTCCTTCTTCA 58.644 50.000 0.00 0.00 44.75 3.02
657 2236 1.278699 AGCAGGCTTCTCCTTCTTCAG 59.721 52.381 0.00 0.00 44.75 3.02
658 2237 1.678425 GCAGGCTTCTCCTTCTTCAGG 60.678 57.143 0.00 0.00 44.75 3.86
659 2238 1.065564 CAGGCTTCTCCTTCTTCAGGG 60.066 57.143 0.00 0.00 44.75 4.45
660 2239 1.203364 AGGCTTCTCCTTCTTCAGGGA 60.203 52.381 0.00 0.00 44.75 4.20
661 2240 1.630878 GGCTTCTCCTTCTTCAGGGAA 59.369 52.381 0.00 0.00 44.12 3.97
662 2241 2.040412 GGCTTCTCCTTCTTCAGGGAAA 59.960 50.000 0.00 0.00 44.12 3.13
663 2242 3.078097 GCTTCTCCTTCTTCAGGGAAAC 58.922 50.000 0.00 0.00 44.12 2.78
664 2243 3.244735 GCTTCTCCTTCTTCAGGGAAACT 60.245 47.826 0.00 0.00 44.12 2.66
665 2244 4.574892 CTTCTCCTTCTTCAGGGAAACTC 58.425 47.826 0.00 0.00 44.12 3.01
666 2245 3.587498 TCTCCTTCTTCAGGGAAACTCA 58.413 45.455 0.00 0.00 44.12 3.41
667 2246 3.973973 TCTCCTTCTTCAGGGAAACTCAA 59.026 43.478 0.00 0.00 44.12 3.02
668 2247 4.599241 TCTCCTTCTTCAGGGAAACTCAAT 59.401 41.667 0.00 0.00 44.12 2.57
669 2248 4.655963 TCCTTCTTCAGGGAAACTCAATG 58.344 43.478 0.00 0.00 44.12 2.82
670 2249 4.104738 TCCTTCTTCAGGGAAACTCAATGT 59.895 41.667 0.00 0.00 44.12 2.71
671 2250 5.309543 TCCTTCTTCAGGGAAACTCAATGTA 59.690 40.000 0.00 0.00 44.12 2.29
672 2251 6.003950 CCTTCTTCAGGGAAACTCAATGTAA 58.996 40.000 0.00 0.00 39.39 2.41
673 2252 6.490040 CCTTCTTCAGGGAAACTCAATGTAAA 59.510 38.462 0.00 0.00 39.39 2.01
674 2253 7.308830 CCTTCTTCAGGGAAACTCAATGTAAAG 60.309 40.741 0.00 0.00 39.39 1.85
711 2290 6.855836 TCAATGTAAAGCATAGCAAAAGGAG 58.144 36.000 0.00 0.00 36.67 3.69
712 2291 4.701956 TGTAAAGCATAGCAAAAGGAGC 57.298 40.909 0.00 0.00 0.00 4.70
766 2345 2.378038 GGCATGATTCTTACCTTGCCA 58.622 47.619 12.47 0.00 46.60 4.92
773 2352 0.615331 TCTTACCTTGCCAGCCTCTG 59.385 55.000 0.00 0.00 0.00 3.35
847 2426 1.572447 CTTTAACGGTGCACCACGG 59.428 57.895 34.16 20.92 39.91 4.94
885 2464 3.326297 CCAGGAAGCTTCTTCCCCTATAG 59.674 52.174 25.05 4.06 39.39 1.31
887 2466 2.039216 GGAAGCTTCTTCCCCTATAGGC 59.961 54.545 25.05 0.00 32.48 3.93
888 2467 2.805290 AGCTTCTTCCCCTATAGGCT 57.195 50.000 13.85 1.66 0.00 4.58
889 2468 3.925261 AGCTTCTTCCCCTATAGGCTA 57.075 47.619 13.85 0.00 0.00 3.93
890 2469 4.427956 AGCTTCTTCCCCTATAGGCTAT 57.572 45.455 13.85 12.41 0.00 2.97
891 2470 5.554034 AGCTTCTTCCCCTATAGGCTATA 57.446 43.478 13.85 13.39 0.00 1.31
892 2471 6.111564 AGCTTCTTCCCCTATAGGCTATAT 57.888 41.667 13.85 0.00 0.00 0.86
893 2472 7.240390 AGCTTCTTCCCCTATAGGCTATATA 57.760 40.000 13.85 0.00 0.00 0.86
894 2473 7.842454 AGCTTCTTCCCCTATAGGCTATATAT 58.158 38.462 13.85 0.00 0.00 0.86
895 2474 8.971894 AGCTTCTTCCCCTATAGGCTATATATA 58.028 37.037 13.85 0.00 0.00 0.86
896 2475 9.777008 GCTTCTTCCCCTATAGGCTATATATAT 57.223 37.037 13.85 0.00 0.00 0.86
953 2532 3.126001 TCTCTAACCACCAAGCAACTG 57.874 47.619 0.00 0.00 0.00 3.16
954 2533 2.703536 TCTCTAACCACCAAGCAACTGA 59.296 45.455 0.00 0.00 0.00 3.41
967 2546 1.606224 GCAACTGAAAATGCCCACCAG 60.606 52.381 0.00 0.00 36.56 4.00
970 2549 1.075374 ACTGAAAATGCCCACCAGCTA 59.925 47.619 0.00 0.00 0.00 3.32
971 2550 2.291800 ACTGAAAATGCCCACCAGCTAT 60.292 45.455 0.00 0.00 0.00 2.97
1044 2628 3.194062 CAAACACCCAAACACCATGAAC 58.806 45.455 0.00 0.00 0.00 3.18
1193 2777 1.228245 CCATACCAGGGCCGAATGG 60.228 63.158 16.49 16.49 42.60 3.16
1278 2862 4.889780 AGTTCTACTCCTCCCTCAATGAT 58.110 43.478 0.00 0.00 0.00 2.45
1400 3013 5.189342 CCAATATCTCCAGTCCTCTGCATAT 59.811 44.000 0.00 0.00 40.09 1.78
1443 3056 4.668138 TTAAAGCCAGGTTCCCATACTT 57.332 40.909 0.00 0.00 0.00 2.24
1568 3181 1.975680 TGTCAAGGAGTAGAACCCACC 59.024 52.381 0.00 0.00 0.00 4.61
1571 3184 1.067071 CAAGGAGTAGAACCCACCGTC 60.067 57.143 0.00 0.00 0.00 4.79
1681 3312 3.058160 ATGTTGCAGAGTGGCGCC 61.058 61.111 22.73 22.73 36.28 6.53
1725 3356 1.668047 GGCTGCAGTTTCTTCATGTGC 60.668 52.381 16.64 0.00 34.62 4.57
1829 3472 4.279169 CAGTGTTTCAGTGTTTCCATCCAT 59.721 41.667 0.00 0.00 30.89 3.41
1830 3473 4.520492 AGTGTTTCAGTGTTTCCATCCATC 59.480 41.667 0.00 0.00 0.00 3.51
1831 3474 3.826157 TGTTTCAGTGTTTCCATCCATCC 59.174 43.478 0.00 0.00 0.00 3.51
1832 3475 3.805066 TTCAGTGTTTCCATCCATCCA 57.195 42.857 0.00 0.00 0.00 3.41
1853 3496 0.595095 GTCAGGCAAGCTGTTGGAAG 59.405 55.000 0.00 0.00 33.87 3.46
1865 3508 6.199937 AGCTGTTGGAAGTATAATGCTTTG 57.800 37.500 0.00 0.00 0.00 2.77
1872 3515 5.777732 TGGAAGTATAATGCTTTGGTGGTTT 59.222 36.000 0.00 0.00 0.00 3.27
1873 3516 6.099341 GGAAGTATAATGCTTTGGTGGTTTG 58.901 40.000 0.00 0.00 0.00 2.93
1874 3517 5.659440 AGTATAATGCTTTGGTGGTTTGG 57.341 39.130 0.00 0.00 0.00 3.28
1875 3518 2.829741 TAATGCTTTGGTGGTTTGGC 57.170 45.000 0.00 0.00 0.00 4.52
1876 3519 0.108396 AATGCTTTGGTGGTTTGGCC 59.892 50.000 0.00 0.00 37.90 5.36
1877 3520 0.763986 ATGCTTTGGTGGTTTGGCCT 60.764 50.000 3.32 0.00 38.35 5.19
1879 3522 1.115326 GCTTTGGTGGTTTGGCCTCT 61.115 55.000 3.32 0.00 38.35 3.69
1880 3523 1.821666 GCTTTGGTGGTTTGGCCTCTA 60.822 52.381 3.32 0.00 38.35 2.43
1881 3524 2.162681 CTTTGGTGGTTTGGCCTCTAG 58.837 52.381 3.32 0.00 38.35 2.43
1882 3525 1.440618 TTGGTGGTTTGGCCTCTAGA 58.559 50.000 3.32 0.00 38.35 2.43
1940 3621 4.339247 CCTTGACCTGACACAGAAATGTTT 59.661 41.667 0.00 0.00 32.44 2.83
1941 3622 5.163519 CCTTGACCTGACACAGAAATGTTTT 60.164 40.000 0.00 0.00 32.44 2.43
1942 3623 5.499139 TGACCTGACACAGAAATGTTTTC 57.501 39.130 0.00 0.00 32.44 2.29
1943 3624 4.946772 TGACCTGACACAGAAATGTTTTCA 59.053 37.500 0.00 0.00 32.44 2.69
2067 3748 3.088532 CCTGCTGCACCCAACTAAAATA 58.911 45.455 0.00 0.00 0.00 1.40
2187 3868 6.939132 AAGGTATGCTCTTCATCAAATCAG 57.061 37.500 0.00 0.00 36.63 2.90
2192 3873 3.439129 TGCTCTTCATCAAATCAGCTGTG 59.561 43.478 14.67 4.92 0.00 3.66
2193 3874 3.731264 GCTCTTCATCAAATCAGCTGTGC 60.731 47.826 14.67 0.00 0.00 4.57
2205 3886 7.278646 TCAAATCAGCTGTGCAGTATAAACTAG 59.721 37.037 14.67 0.00 33.48 2.57
2210 3891 8.909923 TCAGCTGTGCAGTATAAACTAGTATTA 58.090 33.333 14.67 0.00 33.48 0.98
2211 3892 9.698309 CAGCTGTGCAGTATAAACTAGTATTAT 57.302 33.333 5.25 5.79 33.48 1.28
2212 3893 9.698309 AGCTGTGCAGTATAAACTAGTATTATG 57.302 33.333 15.06 5.12 33.48 1.90
2213 3894 8.926710 GCTGTGCAGTATAAACTAGTATTATGG 58.073 37.037 15.06 9.11 33.48 2.74
2214 3895 9.982651 CTGTGCAGTATAAACTAGTATTATGGT 57.017 33.333 15.06 5.18 33.48 3.55
2291 3972 0.109272 CACTAGCTCGGTTCTTCGCA 60.109 55.000 0.00 0.00 0.00 5.10
2354 4035 2.892215 TGCATATTATACCGACGTCCCA 59.108 45.455 10.58 0.00 0.00 4.37
2432 4113 5.527214 GGTGCTCAACATGCTGTATAACATA 59.473 40.000 0.00 0.00 0.00 2.29
2451 4132 5.437060 ACATATTCAAGCGGTTCCTGTAAT 58.563 37.500 0.00 0.00 0.00 1.89
2454 4135 2.972625 TCAAGCGGTTCCTGTAATGAG 58.027 47.619 0.00 0.00 0.00 2.90
2455 4136 2.009774 CAAGCGGTTCCTGTAATGAGG 58.990 52.381 0.00 0.00 0.00 3.86
2456 4137 1.568504 AGCGGTTCCTGTAATGAGGA 58.431 50.000 0.00 0.00 40.62 3.71
2490 4182 8.652810 AACATTCAGAAGAAAAACAAATCTGG 57.347 30.769 0.00 0.00 38.39 3.86
2491 4183 8.010733 ACATTCAGAAGAAAAACAAATCTGGA 57.989 30.769 0.00 0.00 38.39 3.86
2492 4184 8.477256 ACATTCAGAAGAAAAACAAATCTGGAA 58.523 29.630 0.00 0.00 38.39 3.53
2519 4211 0.388659 GCCTGTGTGGTTGCAATCAA 59.611 50.000 15.37 2.10 38.35 2.57
2520 4212 1.001181 GCCTGTGTGGTTGCAATCAAT 59.999 47.619 15.37 0.00 38.35 2.57
2521 4213 2.548493 GCCTGTGTGGTTGCAATCAATT 60.548 45.455 15.37 0.00 38.35 2.32
2522 4214 3.305950 GCCTGTGTGGTTGCAATCAATTA 60.306 43.478 15.37 0.90 38.35 1.40
2523 4215 4.798924 GCCTGTGTGGTTGCAATCAATTAA 60.799 41.667 15.37 0.00 38.35 1.40
2532 4224 5.006261 GGTTGCAATCAATTAAATTACCGGC 59.994 40.000 4.39 0.00 34.29 6.13
2564 4256 0.528684 GAAGGATCAGCGAAGGACCG 60.529 60.000 0.00 0.00 0.00 4.79
2565 4257 1.961180 AAGGATCAGCGAAGGACCGG 61.961 60.000 0.00 0.00 0.00 5.28
2566 4258 2.423898 GGATCAGCGAAGGACCGGA 61.424 63.158 9.46 0.00 0.00 5.14
2567 4259 1.227002 GATCAGCGAAGGACCGGAC 60.227 63.158 9.46 0.00 0.00 4.79
2568 4260 2.630592 GATCAGCGAAGGACCGGACC 62.631 65.000 15.76 15.76 0.00 4.46
2585 4277 0.884704 ACCTACAACAACCAGCTGCG 60.885 55.000 8.66 4.27 0.00 5.18
2593 4285 1.146263 AACCAGCTGCGGTATAGGC 59.854 57.895 8.66 0.00 38.76 3.93
2604 4296 2.483013 GCGGTATAGGCACTGTCAATGA 60.483 50.000 0.00 0.00 41.52 2.57
2621 4313 5.355071 GTCAATGACTCAGAATATGCCACAA 59.645 40.000 6.07 0.00 0.00 3.33
2627 4319 5.121811 ACTCAGAATATGCCACAAGATGTC 58.878 41.667 0.00 0.00 0.00 3.06
2669 4362 2.480419 CCTACTTTGCTCCTGTGAAACG 59.520 50.000 0.00 0.00 42.39 3.60
2706 4399 8.748380 CATTTCACTCTTAAAAGGAAATGGTC 57.252 34.615 16.86 0.00 45.39 4.02
2719 4412 3.181458 GGAAATGGTCGTTAGCATAGGGA 60.181 47.826 0.00 0.00 42.93 4.20
2720 4413 4.505039 GGAAATGGTCGTTAGCATAGGGAT 60.505 45.833 0.00 0.00 42.93 3.85
2721 4414 3.685139 ATGGTCGTTAGCATAGGGATG 57.315 47.619 0.00 0.00 41.96 3.51
2740 4433 4.943705 GGATGCATGTATATAACCACAGGG 59.056 45.833 2.46 0.00 41.29 4.45
2763 4456 6.128634 GGGTATTGTTGTAAGAAGAACTGACG 60.129 42.308 0.00 0.00 32.75 4.35
2769 4462 6.643770 TGTTGTAAGAAGAACTGACGAATACC 59.356 38.462 0.00 0.00 32.75 2.73
2783 4476 7.606456 ACTGACGAATACCATTGTTACATTCTT 59.394 33.333 0.00 0.00 0.00 2.52
2809 4502 4.122776 CTGCGTACTAATTTCCAGCATCT 58.877 43.478 0.00 0.00 32.49 2.90
2825 4518 4.525912 GCATCTAATAAAATGCCCCCAG 57.474 45.455 0.00 0.00 41.92 4.45
2831 4524 6.731467 TCTAATAAAATGCCCCCAGGATATC 58.269 40.000 0.00 0.00 33.47 1.63
2915 4609 9.926751 GTGTAGTTGTAGGTTTTTCTTTAAGAC 57.073 33.333 0.00 0.00 0.00 3.01
2916 4610 9.112725 TGTAGTTGTAGGTTTTTCTTTAAGACC 57.887 33.333 0.00 0.00 0.00 3.85
2917 4611 7.578310 AGTTGTAGGTTTTTCTTTAAGACCC 57.422 36.000 0.00 0.00 0.00 4.46
3036 4759 8.725046 CGTGTGCTTTATCGAAAAATCTATTTC 58.275 33.333 0.00 0.00 36.24 2.17
3040 4763 8.120465 TGCTTTATCGAAAAATCTATTTCCGTC 58.880 33.333 0.00 0.00 36.21 4.79
3051 4774 7.948278 AATCTATTTCCGTCTGTAGCATTAC 57.052 36.000 0.00 0.00 0.00 1.89
3084 4808 5.381174 TGAAGCTTGAAATTGACTCCATG 57.619 39.130 2.10 0.00 0.00 3.66
3147 4898 5.416952 CAGGTAAAGAATGCTTCAGTCCAAT 59.583 40.000 0.00 0.00 31.82 3.16
3162 4913 4.869297 CAGTCCAATGCAAGACAAAACAAA 59.131 37.500 14.91 0.00 35.38 2.83
3170 4921 9.409312 CAATGCAAGACAAAACAAATATCACTA 57.591 29.630 0.00 0.00 0.00 2.74
3177 4929 9.003658 AGACAAAACAAATATCACTAGAGTTGG 57.996 33.333 0.00 0.00 0.00 3.77
3179 4931 8.784043 ACAAAACAAATATCACTAGAGTTGGAC 58.216 33.333 0.00 0.00 0.00 4.02
3207 4959 8.579850 AATGCTTACCAGAACTCAAATCATTA 57.420 30.769 0.00 0.00 0.00 1.90
3211 4963 7.148474 GCTTACCAGAACTCAAATCATTAACGA 60.148 37.037 0.00 0.00 0.00 3.85
3212 4964 6.481954 ACCAGAACTCAAATCATTAACGAC 57.518 37.500 0.00 0.00 0.00 4.34
3213 4965 5.995282 ACCAGAACTCAAATCATTAACGACA 59.005 36.000 0.00 0.00 0.00 4.35
3214 4966 6.655003 ACCAGAACTCAAATCATTAACGACAT 59.345 34.615 0.00 0.00 0.00 3.06
3220 4972 9.773328 AACTCAAATCATTAACGACATTGTATG 57.227 29.630 0.00 0.00 0.00 2.39
3232 4984 4.679106 CGACATTGTATGAGAGGCAGTCTT 60.679 45.833 0.00 0.00 34.71 3.01
3235 4987 5.163364 ACATTGTATGAGAGGCAGTCTTAGG 60.163 44.000 0.00 0.00 34.71 2.69
3243 4995 1.557371 AGGCAGTCTTAGGCTTCTTCC 59.443 52.381 0.00 0.00 38.98 3.46
3256 5008 2.678324 CTTCTTCCGGAAGTGACAGAC 58.322 52.381 36.74 0.00 44.59 3.51
3258 5010 2.036387 TCTTCCGGAAGTGACAGACAA 58.964 47.619 36.74 16.77 39.38 3.18
3260 5012 0.391597 TCCGGAAGTGACAGACAACC 59.608 55.000 0.00 0.00 0.00 3.77
3281 5072 3.069586 CCAAACTTTCCCTTTCCCAAGAC 59.930 47.826 0.00 0.00 30.57 3.01
3313 5105 5.997129 CAGCCTTCTCTTTCTCTTTCTCTTT 59.003 40.000 0.00 0.00 0.00 2.52
3322 5114 9.196552 CTCTTTCTCTTTCTCTTTCTCTTTCTC 57.803 37.037 0.00 0.00 0.00 2.87
3323 5115 8.923270 TCTTTCTCTTTCTCTTTCTCTTTCTCT 58.077 33.333 0.00 0.00 0.00 3.10
3324 5116 9.546428 CTTTCTCTTTCTCTTTCTCTTTCTCTT 57.454 33.333 0.00 0.00 0.00 2.85
3326 5118 9.541143 TTCTCTTTCTCTTTCTCTTTCTCTTTC 57.459 33.333 0.00 0.00 0.00 2.62
3327 5119 8.923270 TCTCTTTCTCTTTCTCTTTCTCTTTCT 58.077 33.333 0.00 0.00 0.00 2.52
3331 5123 9.898152 TTTCTCTTTCTCTTTCTCTTTCTCTTT 57.102 29.630 0.00 0.00 0.00 2.52
3332 5124 9.541143 TTCTCTTTCTCTTTCTCTTTCTCTTTC 57.459 33.333 0.00 0.00 0.00 2.62
3333 5125 8.923270 TCTCTTTCTCTTTCTCTTTCTCTTTCT 58.077 33.333 0.00 0.00 0.00 2.52
3334 5126 9.196552 CTCTTTCTCTTTCTCTTTCTCTTTCTC 57.803 37.037 0.00 0.00 0.00 2.87
3335 5127 8.923270 TCTTTCTCTTTCTCTTTCTCTTTCTCT 58.077 33.333 0.00 0.00 0.00 3.10
3336 5128 9.546428 CTTTCTCTTTCTCTTTCTCTTTCTCTT 57.454 33.333 0.00 0.00 0.00 2.85
3338 5130 9.898152 TTCTCTTTCTCTTTCTCTTTCTCTTTT 57.102 29.630 0.00 0.00 0.00 2.27
3339 5131 9.898152 TCTCTTTCTCTTTCTCTTTCTCTTTTT 57.102 29.630 0.00 0.00 0.00 1.94
3344 5136 8.669946 TCTCTTTCTCTTTCTCTTTTTCTTCC 57.330 34.615 0.00 0.00 0.00 3.46
3345 5137 8.490311 TCTCTTTCTCTTTCTCTTTTTCTTCCT 58.510 33.333 0.00 0.00 0.00 3.36
3346 5138 8.669946 TCTTTCTCTTTCTCTTTTTCTTCCTC 57.330 34.615 0.00 0.00 0.00 3.71
3347 5139 7.717436 TCTTTCTCTTTCTCTTTTTCTTCCTCC 59.283 37.037 0.00 0.00 0.00 4.30
3348 5140 5.870706 TCTCTTTCTCTTTTTCTTCCTCCC 58.129 41.667 0.00 0.00 0.00 4.30
3349 5141 5.608860 TCTCTTTCTCTTTTTCTTCCTCCCT 59.391 40.000 0.00 0.00 0.00 4.20
3350 5142 6.101881 TCTCTTTCTCTTTTTCTTCCTCCCTT 59.898 38.462 0.00 0.00 0.00 3.95
3351 5143 6.299922 TCTTTCTCTTTTTCTTCCTCCCTTC 58.700 40.000 0.00 0.00 0.00 3.46
3352 5144 5.646692 TTCTCTTTTTCTTCCTCCCTTCA 57.353 39.130 0.00 0.00 0.00 3.02
3353 5145 4.974399 TCTCTTTTTCTTCCTCCCTTCAC 58.026 43.478 0.00 0.00 0.00 3.18
3354 5146 4.412199 TCTCTTTTTCTTCCTCCCTTCACA 59.588 41.667 0.00 0.00 0.00 3.58
3355 5147 5.104109 TCTCTTTTTCTTCCTCCCTTCACAA 60.104 40.000 0.00 0.00 0.00 3.33
3356 5148 5.705400 TCTTTTTCTTCCTCCCTTCACAAT 58.295 37.500 0.00 0.00 0.00 2.71
3357 5149 5.770162 TCTTTTTCTTCCTCCCTTCACAATC 59.230 40.000 0.00 0.00 0.00 2.67
3358 5150 4.722526 TTTCTTCCTCCCTTCACAATCA 57.277 40.909 0.00 0.00 0.00 2.57
3359 5151 3.703001 TCTTCCTCCCTTCACAATCAC 57.297 47.619 0.00 0.00 0.00 3.06
3360 5152 2.978978 TCTTCCTCCCTTCACAATCACA 59.021 45.455 0.00 0.00 0.00 3.58
3361 5153 3.394274 TCTTCCTCCCTTCACAATCACAA 59.606 43.478 0.00 0.00 0.00 3.33
3362 5154 3.423539 TCCTCCCTTCACAATCACAAG 57.576 47.619 0.00 0.00 0.00 3.16
3363 5155 2.711009 TCCTCCCTTCACAATCACAAGT 59.289 45.455 0.00 0.00 0.00 3.16
3364 5156 3.077359 CCTCCCTTCACAATCACAAGTC 58.923 50.000 0.00 0.00 0.00 3.01
3365 5157 3.496692 CCTCCCTTCACAATCACAAGTCA 60.497 47.826 0.00 0.00 0.00 3.41
3447 5239 8.942338 AAAGAAAACCAAGGAACAAAGTTATC 57.058 30.769 0.00 0.00 0.00 1.75
3449 5241 5.801531 AAACCAAGGAACAAAGTTATCCC 57.198 39.130 0.00 0.00 33.55 3.85
3450 5242 4.741928 ACCAAGGAACAAAGTTATCCCT 57.258 40.909 0.00 0.00 33.55 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.351465 ACAAATCTGAAAAGACGTGCGATAT 59.649 36.000 0.00 0.00 0.00 1.63
3 4 3.498397 ACAAATCTGAAAAGACGTGCGAT 59.502 39.130 0.00 0.00 0.00 4.58
4 5 2.869801 ACAAATCTGAAAAGACGTGCGA 59.130 40.909 0.00 0.00 0.00 5.10
5 6 2.966708 CACAAATCTGAAAAGACGTGCG 59.033 45.455 0.00 0.00 0.00 5.34
6 7 3.300009 CCACAAATCTGAAAAGACGTGC 58.700 45.455 0.00 0.00 0.00 5.34
7 8 3.300009 GCCACAAATCTGAAAAGACGTG 58.700 45.455 0.00 0.00 0.00 4.49
8 9 2.032030 CGCCACAAATCTGAAAAGACGT 60.032 45.455 0.00 0.00 0.00 4.34
80 1493 7.282224 TGTTGTATTGTATTGCCTCCTTACATC 59.718 37.037 0.00 0.00 0.00 3.06
92 1505 7.093988 TGTGGGATTTCCTGTTGTATTGTATTG 60.094 37.037 0.00 0.00 36.20 1.90
93 1506 6.951198 TGTGGGATTTCCTGTTGTATTGTATT 59.049 34.615 0.00 0.00 36.20 1.89
94 1507 6.489603 TGTGGGATTTCCTGTTGTATTGTAT 58.510 36.000 0.00 0.00 36.20 2.29
95 1508 5.882040 TGTGGGATTTCCTGTTGTATTGTA 58.118 37.500 0.00 0.00 36.20 2.41
96 1509 4.735369 TGTGGGATTTCCTGTTGTATTGT 58.265 39.130 0.00 0.00 36.20 2.71
103 1516 5.147032 TCTGAAAATGTGGGATTTCCTGTT 58.853 37.500 0.00 0.00 35.23 3.16
136 1549 3.944087 ACAGGGTATCTTTGAGAACTGC 58.056 45.455 0.00 0.00 0.00 4.40
137 1550 6.037610 GCATTACAGGGTATCTTTGAGAACTG 59.962 42.308 0.00 0.00 0.00 3.16
138 1551 6.069963 AGCATTACAGGGTATCTTTGAGAACT 60.070 38.462 0.00 0.00 0.00 3.01
158 1571 8.773033 AGAATAGGATGAAATAAACCAGCATT 57.227 30.769 0.00 0.00 0.00 3.56
192 1606 0.248134 TGACGCCCGTTTTTGTTTCG 60.248 50.000 0.00 0.00 0.00 3.46
203 1617 2.004583 TAAGAGTGAAATGACGCCCG 57.995 50.000 0.00 0.00 0.00 6.13
204 1618 4.000988 TCTTTAAGAGTGAAATGACGCCC 58.999 43.478 0.00 0.00 0.00 6.13
207 1621 9.107367 GTCATTTTCTTTAAGAGTGAAATGACG 57.893 33.333 28.49 11.08 45.65 4.35
260 1675 9.485206 GTACTTCCTGTCTTTCTTACAACAATA 57.515 33.333 0.00 0.00 0.00 1.90
261 1676 8.211629 AGTACTTCCTGTCTTTCTTACAACAAT 58.788 33.333 0.00 0.00 0.00 2.71
262 1677 7.494625 CAGTACTTCCTGTCTTTCTTACAACAA 59.505 37.037 0.00 0.00 0.00 2.83
311 1726 8.932791 GGCACGCACAATATAGTAATATTAGTT 58.067 33.333 8.10 0.00 36.36 2.24
312 1727 8.311836 AGGCACGCACAATATAGTAATATTAGT 58.688 33.333 7.91 7.91 36.36 2.24
330 1745 2.093181 AGGAATAACACATAGGCACGCA 60.093 45.455 0.00 0.00 0.00 5.24
331 1746 2.561569 AGGAATAACACATAGGCACGC 58.438 47.619 0.00 0.00 0.00 5.34
332 1747 3.312421 CCAAGGAATAACACATAGGCACG 59.688 47.826 0.00 0.00 0.00 5.34
333 1748 3.632145 CCCAAGGAATAACACATAGGCAC 59.368 47.826 0.00 0.00 0.00 5.01
353 1768 1.603455 CACCATCCCACACACACCC 60.603 63.158 0.00 0.00 0.00 4.61
354 1769 0.179004 TTCACCATCCCACACACACC 60.179 55.000 0.00 0.00 0.00 4.16
355 1770 1.909700 ATTCACCATCCCACACACAC 58.090 50.000 0.00 0.00 0.00 3.82
391 1806 5.084818 TGGTATGATGGTATCCGCTTATG 57.915 43.478 0.00 0.00 0.00 1.90
397 1812 8.138074 CAGAGTTATATGGTATGATGGTATCCG 58.862 40.741 0.00 0.00 0.00 4.18
529 1971 4.099266 GCCATAGGTAATTGTTCCAATGCA 59.901 41.667 0.00 0.00 0.00 3.96
582 2024 7.654022 TCCCAACTTGTTTCTTTGAATACTT 57.346 32.000 0.00 0.00 0.00 2.24
596 2038 0.250338 GGCTCGACTTCCCAACTTGT 60.250 55.000 0.00 0.00 0.00 3.16
597 2039 0.250295 TGGCTCGACTTCCCAACTTG 60.250 55.000 0.00 0.00 0.00 3.16
598 2040 0.250338 GTGGCTCGACTTCCCAACTT 60.250 55.000 0.00 0.00 0.00 2.66
652 2231 5.474876 AGCTTTACATTGAGTTTCCCTGAAG 59.525 40.000 0.00 0.00 0.00 3.02
653 2232 5.385198 AGCTTTACATTGAGTTTCCCTGAA 58.615 37.500 0.00 0.00 0.00 3.02
654 2233 4.985538 AGCTTTACATTGAGTTTCCCTGA 58.014 39.130 0.00 0.00 0.00 3.86
655 2234 5.241506 TGAAGCTTTACATTGAGTTTCCCTG 59.758 40.000 0.00 0.00 33.72 4.45
656 2235 5.385198 TGAAGCTTTACATTGAGTTTCCCT 58.615 37.500 0.00 0.00 33.72 4.20
657 2236 5.335976 CCTGAAGCTTTACATTGAGTTTCCC 60.336 44.000 0.00 0.00 33.72 3.97
658 2237 5.335976 CCCTGAAGCTTTACATTGAGTTTCC 60.336 44.000 0.00 0.00 33.72 3.13
659 2238 5.473504 TCCCTGAAGCTTTACATTGAGTTTC 59.526 40.000 0.00 0.00 34.79 2.78
660 2239 5.385198 TCCCTGAAGCTTTACATTGAGTTT 58.615 37.500 0.00 0.00 0.00 2.66
661 2240 4.985538 TCCCTGAAGCTTTACATTGAGTT 58.014 39.130 0.00 0.00 0.00 3.01
662 2241 4.640771 TCCCTGAAGCTTTACATTGAGT 57.359 40.909 0.00 0.00 0.00 3.41
663 2242 5.474876 AGTTTCCCTGAAGCTTTACATTGAG 59.525 40.000 0.00 0.00 29.13 3.02
664 2243 5.385198 AGTTTCCCTGAAGCTTTACATTGA 58.615 37.500 0.00 0.00 29.13 2.57
665 2244 5.241506 TGAGTTTCCCTGAAGCTTTACATTG 59.758 40.000 0.00 0.00 33.49 2.82
666 2245 5.385198 TGAGTTTCCCTGAAGCTTTACATT 58.615 37.500 0.00 0.00 33.49 2.71
667 2246 4.985538 TGAGTTTCCCTGAAGCTTTACAT 58.014 39.130 0.00 0.00 33.49 2.29
668 2247 4.431416 TGAGTTTCCCTGAAGCTTTACA 57.569 40.909 0.00 0.00 33.49 2.41
669 2248 5.241728 ACATTGAGTTTCCCTGAAGCTTTAC 59.758 40.000 0.00 0.00 33.49 2.01
670 2249 5.385198 ACATTGAGTTTCCCTGAAGCTTTA 58.615 37.500 0.00 0.00 33.49 1.85
671 2250 4.218312 ACATTGAGTTTCCCTGAAGCTTT 58.782 39.130 0.00 0.00 33.49 3.51
672 2251 3.837355 ACATTGAGTTTCCCTGAAGCTT 58.163 40.909 0.00 0.00 33.49 3.74
673 2252 3.515602 ACATTGAGTTTCCCTGAAGCT 57.484 42.857 0.00 0.00 35.90 3.74
674 2253 5.703876 CTTTACATTGAGTTTCCCTGAAGC 58.296 41.667 0.00 0.00 0.00 3.86
711 2290 2.531522 ATTGCTTTGTTCCTTGGTGC 57.468 45.000 0.00 0.00 0.00 5.01
712 2291 3.573967 AGGTATTGCTTTGTTCCTTGGTG 59.426 43.478 0.00 0.00 0.00 4.17
766 2345 7.950684 TCACTTCCACTATAATATACAGAGGCT 59.049 37.037 0.00 0.00 0.00 4.58
836 2415 1.175983 TGGAATTTCCGTGGTGCACC 61.176 55.000 29.67 29.67 40.17 5.01
847 2426 4.741321 TCCTGGCATCAAATGGAATTTC 57.259 40.909 0.00 0.00 44.81 2.17
943 2522 1.070445 TGGGCATTTTCAGTTGCTTGG 59.930 47.619 0.00 0.00 38.88 3.61
953 2532 3.287222 TGTATAGCTGGTGGGCATTTTC 58.713 45.455 0.00 0.00 34.17 2.29
954 2533 3.380471 TGTATAGCTGGTGGGCATTTT 57.620 42.857 0.00 0.00 34.17 1.82
967 2546 8.056407 TGAGGTGTGATATAGTCATGTATAGC 57.944 38.462 0.00 0.00 39.48 2.97
970 2549 8.535335 GGAATGAGGTGTGATATAGTCATGTAT 58.465 37.037 0.00 0.00 39.48 2.29
971 2550 7.508977 TGGAATGAGGTGTGATATAGTCATGTA 59.491 37.037 0.00 0.00 39.48 2.29
1044 2628 2.036992 GGAGATATGTGTGAGGGCAGAG 59.963 54.545 0.00 0.00 0.00 3.35
1278 2862 2.418976 CTCGAGTCGTGTGATGTCCTTA 59.581 50.000 13.12 0.00 0.00 2.69
1443 3056 6.522625 TCAAAGTTGTTTCTGTGAATTCCA 57.477 33.333 2.27 0.00 29.84 3.53
1568 3181 1.419922 GTGCCACATTACTGCGACG 59.580 57.895 0.00 0.00 0.00 5.12
1571 3184 0.168788 CAAGGTGCCACATTACTGCG 59.831 55.000 0.00 0.00 0.00 5.18
1638 3269 7.094506 TGCAGCATGATGATACAATTATCCTTC 60.095 37.037 16.67 0.00 39.69 3.46
1639 3270 6.717997 TGCAGCATGATGATACAATTATCCTT 59.282 34.615 16.67 0.00 39.69 3.36
1640 3271 6.243148 TGCAGCATGATGATACAATTATCCT 58.757 36.000 16.67 0.00 39.69 3.24
1683 3314 2.369983 TGGCAAATGGGATCATCTCC 57.630 50.000 0.00 0.00 44.11 3.71
1725 3356 1.664321 GGGCTGCTCCATTTGCTGAG 61.664 60.000 0.00 0.00 36.21 3.35
1829 3472 0.111061 AACAGCTTGCCTGACATGGA 59.889 50.000 0.00 0.00 44.64 3.41
1830 3473 0.242825 CAACAGCTTGCCTGACATGG 59.757 55.000 0.00 0.00 44.64 3.66
1831 3474 0.242825 CCAACAGCTTGCCTGACATG 59.757 55.000 0.00 0.00 44.64 3.21
1832 3475 0.111061 TCCAACAGCTTGCCTGACAT 59.889 50.000 0.00 0.00 44.64 3.06
1853 3496 4.180817 GCCAAACCACCAAAGCATTATAC 58.819 43.478 0.00 0.00 0.00 1.47
1865 3508 3.039011 TCTATCTAGAGGCCAAACCACC 58.961 50.000 5.01 0.00 43.14 4.61
1872 3515 8.964533 AGAGAAAAATATCTATCTAGAGGCCA 57.035 34.615 5.01 0.00 35.50 5.36
1906 3587 0.919710 AGGTCAAGGGGAGCATTACC 59.080 55.000 0.00 0.00 46.51 2.85
1907 3588 1.559682 TCAGGTCAAGGGGAGCATTAC 59.440 52.381 0.00 0.00 46.51 1.89
1908 3589 1.559682 GTCAGGTCAAGGGGAGCATTA 59.440 52.381 0.00 0.00 46.51 1.90
1909 3590 0.329596 GTCAGGTCAAGGGGAGCATT 59.670 55.000 0.00 0.00 46.51 3.56
1940 3621 0.251297 CTGCAGGGTGGGTGAATGAA 60.251 55.000 5.57 0.00 0.00 2.57
1941 3622 1.379916 CTGCAGGGTGGGTGAATGA 59.620 57.895 5.57 0.00 0.00 2.57
1942 3623 1.679977 CCTGCAGGGTGGGTGAATG 60.680 63.158 26.14 0.00 0.00 2.67
1943 3624 1.434513 TTCCTGCAGGGTGGGTGAAT 61.435 55.000 32.23 0.00 36.25 2.57
2093 3774 9.289782 AGTATTTCCTGTAAGCATTGGAATATC 57.710 33.333 0.00 0.00 38.24 1.63
2187 3868 8.926710 CCATAATACTAGTTTATACTGCACAGC 58.073 37.037 0.00 0.00 35.78 4.40
2210 3891 5.016173 TGCTTAGCTGGATTTTAACACCAT 58.984 37.500 5.60 0.00 33.08 3.55
2211 3892 4.402829 TGCTTAGCTGGATTTTAACACCA 58.597 39.130 5.60 0.00 0.00 4.17
2212 3893 5.343249 CATGCTTAGCTGGATTTTAACACC 58.657 41.667 5.60 0.00 0.00 4.16
2213 3894 5.125417 TCCATGCTTAGCTGGATTTTAACAC 59.875 40.000 17.19 0.00 36.63 3.32
2214 3895 5.260424 TCCATGCTTAGCTGGATTTTAACA 58.740 37.500 17.19 0.00 36.63 2.41
2291 3972 4.142026 GGCCCGCAGAATTTATAAAACCTT 60.142 41.667 1.21 0.00 0.00 3.50
2354 4035 6.942576 AGAAGCGGGTATAATATGCAAGAATT 59.057 34.615 0.00 0.00 0.00 2.17
2432 4113 3.941483 CTCATTACAGGAACCGCTTGAAT 59.059 43.478 0.00 0.00 0.00 2.57
2464 4145 9.748708 CCAGATTTGTTTTTCTTCTGAATGTTA 57.251 29.630 0.00 0.00 36.72 2.41
2489 4181 2.237392 ACCACACAGGCTATCTTCTTCC 59.763 50.000 0.00 0.00 43.14 3.46
2490 4182 3.618690 ACCACACAGGCTATCTTCTTC 57.381 47.619 0.00 0.00 43.14 2.87
2491 4183 3.679389 CAACCACACAGGCTATCTTCTT 58.321 45.455 0.00 0.00 43.14 2.52
2492 4184 2.616510 GCAACCACACAGGCTATCTTCT 60.617 50.000 0.00 0.00 43.14 2.85
2500 4192 0.388659 TTGATTGCAACCACACAGGC 59.611 50.000 0.00 0.00 43.14 4.85
2519 4211 4.201970 CCGTGATGTTGCCGGTAATTTAAT 60.202 41.667 8.64 0.33 37.00 1.40
2520 4212 3.127203 CCGTGATGTTGCCGGTAATTTAA 59.873 43.478 8.64 0.00 37.00 1.52
2521 4213 2.678836 CCGTGATGTTGCCGGTAATTTA 59.321 45.455 8.64 0.00 37.00 1.40
2522 4214 1.470890 CCGTGATGTTGCCGGTAATTT 59.529 47.619 8.64 0.00 37.00 1.82
2523 4215 1.091537 CCGTGATGTTGCCGGTAATT 58.908 50.000 8.64 0.00 37.00 1.40
2532 4224 2.009774 GATCCTTCACCCGTGATGTTG 58.990 52.381 0.00 0.00 39.64 3.33
2564 4256 1.523758 CAGCTGGTTGTTGTAGGTCC 58.476 55.000 5.57 0.00 0.00 4.46
2565 4257 0.875059 GCAGCTGGTTGTTGTAGGTC 59.125 55.000 17.12 0.00 0.00 3.85
2566 4258 0.884704 CGCAGCTGGTTGTTGTAGGT 60.885 55.000 17.12 0.00 0.00 3.08
2567 4259 1.577328 CCGCAGCTGGTTGTTGTAGG 61.577 60.000 17.12 0.00 0.00 3.18
2568 4260 0.884704 ACCGCAGCTGGTTGTTGTAG 60.885 55.000 17.12 0.00 39.99 2.74
2585 4277 4.141937 TGAGTCATTGACAGTGCCTATACC 60.142 45.833 18.57 0.00 34.60 2.73
2593 4285 5.007430 GGCATATTCTGAGTCATTGACAGTG 59.993 44.000 18.57 7.84 34.60 3.66
2604 4296 5.108187 ACATCTTGTGGCATATTCTGAGT 57.892 39.130 0.00 0.00 0.00 3.41
2621 4313 2.105821 TCTGGGAAACAAACCGACATCT 59.894 45.455 0.00 0.00 0.00 2.90
2627 4319 0.537371 AGCCTCTGGGAAACAAACCG 60.537 55.000 0.00 0.00 33.58 4.44
2693 4386 5.357032 CCTATGCTAACGACCATTTCCTTTT 59.643 40.000 0.00 0.00 0.00 2.27
2719 4412 5.582950 ACCCTGTGGTTATATACATGCAT 57.417 39.130 0.00 0.00 44.75 3.96
2720 4413 6.696042 ATACCCTGTGGTTATATACATGCA 57.304 37.500 0.00 0.00 44.75 3.96
2721 4414 6.940298 ACAATACCCTGTGGTTATATACATGC 59.060 38.462 0.00 0.00 44.75 4.06
2722 4415 8.783093 CAACAATACCCTGTGGTTATATACATG 58.217 37.037 0.00 0.00 44.75 3.21
2740 4433 7.633361 TCGTCAGTTCTTCTTACAACAATAC 57.367 36.000 0.00 0.00 0.00 1.89
2787 4480 4.122776 AGATGCTGGAAATTAGTACGCAG 58.877 43.478 0.00 0.00 0.00 5.18
2789 4482 6.787085 ATTAGATGCTGGAAATTAGTACGC 57.213 37.500 0.00 0.00 0.00 4.42
2809 4502 5.559545 AGGATATCCTGGGGGCATTTTATTA 59.440 40.000 23.95 0.00 46.55 0.98
2824 4517 4.421131 AGAATCCGTAAGCAGGATATCCT 58.579 43.478 19.18 19.18 46.99 3.24
2825 4518 4.810191 AGAATCCGTAAGCAGGATATCC 57.190 45.455 14.41 14.41 46.99 2.59
2831 4524 2.699954 ACACAAGAATCCGTAAGCAGG 58.300 47.619 0.00 0.00 0.00 4.85
2841 4534 3.499918 ACTGCAGCTGTTACACAAGAATC 59.500 43.478 15.27 0.00 0.00 2.52
2915 4609 0.320771 GTGCAGACTGTACTGTGGGG 60.321 60.000 15.61 0.97 39.73 4.96
2916 4610 0.681733 AGTGCAGACTGTACTGTGGG 59.318 55.000 23.39 3.37 41.73 4.61
2917 4611 2.224042 TGAAGTGCAGACTGTACTGTGG 60.224 50.000 24.49 3.72 42.47 4.17
3036 4759 5.538118 TGGAATATGTAATGCTACAGACGG 58.462 41.667 0.00 0.00 41.33 4.79
3040 4763 9.888878 CTTCAAATGGAATATGTAATGCTACAG 57.111 33.333 0.00 0.00 36.84 2.74
3051 4774 9.373603 TCAATTTCAAGCTTCAAATGGAATATG 57.626 29.630 10.19 3.89 34.32 1.78
3084 4808 7.387673 CCACAAAAAGGGAAAATAATCTGGAAC 59.612 37.037 0.00 0.00 0.00 3.62
3147 4898 8.389779 TCTAGTGATATTTGTTTTGTCTTGCA 57.610 30.769 0.00 0.00 0.00 4.08
3162 4913 8.200024 AGCATTATGTCCAACTCTAGTGATAT 57.800 34.615 0.00 0.00 0.00 1.63
3170 4921 5.189736 TCTGGTAAGCATTATGTCCAACTCT 59.810 40.000 0.00 0.00 30.46 3.24
3176 4928 5.428253 TGAGTTCTGGTAAGCATTATGTCC 58.572 41.667 0.00 0.00 30.46 4.02
3177 4929 6.985188 TTGAGTTCTGGTAAGCATTATGTC 57.015 37.500 0.00 0.00 30.46 3.06
3179 4931 7.988737 TGATTTGAGTTCTGGTAAGCATTATG 58.011 34.615 0.00 0.00 30.46 1.90
3184 4936 7.360861 CGTTAATGATTTGAGTTCTGGTAAGCA 60.361 37.037 0.00 0.00 0.00 3.91
3207 4959 3.055819 ACTGCCTCTCATACAATGTCGTT 60.056 43.478 0.00 0.00 0.00 3.85
3211 4963 4.833478 AAGACTGCCTCTCATACAATGT 57.167 40.909 0.00 0.00 0.00 2.71
3212 4964 5.295950 CCTAAGACTGCCTCTCATACAATG 58.704 45.833 0.00 0.00 0.00 2.82
3213 4965 4.202305 GCCTAAGACTGCCTCTCATACAAT 60.202 45.833 0.00 0.00 0.00 2.71
3214 4966 3.133003 GCCTAAGACTGCCTCTCATACAA 59.867 47.826 0.00 0.00 0.00 2.41
3220 4972 2.107366 AGAAGCCTAAGACTGCCTCTC 58.893 52.381 0.00 0.00 0.00 3.20
3243 4995 1.948104 TTGGTTGTCTGTCACTTCCG 58.052 50.000 0.00 0.00 0.00 4.30
3253 5005 3.704566 GGAAAGGGAAAGTTTGGTTGTCT 59.295 43.478 0.00 0.00 0.00 3.41
3254 5006 3.181469 GGGAAAGGGAAAGTTTGGTTGTC 60.181 47.826 0.00 0.00 0.00 3.18
3255 5007 2.769663 GGGAAAGGGAAAGTTTGGTTGT 59.230 45.455 0.00 0.00 0.00 3.32
3256 5008 2.769095 TGGGAAAGGGAAAGTTTGGTTG 59.231 45.455 0.00 0.00 0.00 3.77
3258 5010 2.858787 TGGGAAAGGGAAAGTTTGGT 57.141 45.000 0.00 0.00 0.00 3.67
3260 5012 3.704061 TGTCTTGGGAAAGGGAAAGTTTG 59.296 43.478 0.00 0.00 0.00 2.93
3281 5072 6.815089 AGAGAAAGAGAAGGCTGTATGTATG 58.185 40.000 0.00 0.00 0.00 2.39
3313 5105 9.898152 AAAAAGAGAAAGAGAAAGAGAAAGAGA 57.102 29.630 0.00 0.00 0.00 3.10
3322 5114 7.040755 GGGAGGAAGAAAAAGAGAAAGAGAAAG 60.041 40.741 0.00 0.00 0.00 2.62
3323 5115 6.773200 GGGAGGAAGAAAAAGAGAAAGAGAAA 59.227 38.462 0.00 0.00 0.00 2.52
3324 5116 6.101881 AGGGAGGAAGAAAAAGAGAAAGAGAA 59.898 38.462 0.00 0.00 0.00 2.87
3326 5118 5.875224 AGGGAGGAAGAAAAAGAGAAAGAG 58.125 41.667 0.00 0.00 0.00 2.85
3327 5119 5.913946 AGGGAGGAAGAAAAAGAGAAAGA 57.086 39.130 0.00 0.00 0.00 2.52
3331 5123 4.412199 TGTGAAGGGAGGAAGAAAAAGAGA 59.588 41.667 0.00 0.00 0.00 3.10
3332 5124 4.718961 TGTGAAGGGAGGAAGAAAAAGAG 58.281 43.478 0.00 0.00 0.00 2.85
3333 5125 4.788925 TGTGAAGGGAGGAAGAAAAAGA 57.211 40.909 0.00 0.00 0.00 2.52
3334 5126 5.536161 TGATTGTGAAGGGAGGAAGAAAAAG 59.464 40.000 0.00 0.00 0.00 2.27
3335 5127 5.301805 GTGATTGTGAAGGGAGGAAGAAAAA 59.698 40.000 0.00 0.00 0.00 1.94
3336 5128 4.827284 GTGATTGTGAAGGGAGGAAGAAAA 59.173 41.667 0.00 0.00 0.00 2.29
3338 5130 3.394274 TGTGATTGTGAAGGGAGGAAGAA 59.606 43.478 0.00 0.00 0.00 2.52
3339 5131 2.978978 TGTGATTGTGAAGGGAGGAAGA 59.021 45.455 0.00 0.00 0.00 2.87
3342 5134 2.711009 ACTTGTGATTGTGAAGGGAGGA 59.289 45.455 0.00 0.00 0.00 3.71
3343 5135 3.077359 GACTTGTGATTGTGAAGGGAGG 58.923 50.000 0.00 0.00 0.00 4.30
3344 5136 3.499918 GTGACTTGTGATTGTGAAGGGAG 59.500 47.826 0.00 0.00 0.00 4.30
3345 5137 3.136443 AGTGACTTGTGATTGTGAAGGGA 59.864 43.478 0.00 0.00 0.00 4.20
3346 5138 3.480470 AGTGACTTGTGATTGTGAAGGG 58.520 45.455 0.00 0.00 0.00 3.95
3347 5139 6.652481 AGATAAGTGACTTGTGATTGTGAAGG 59.348 38.462 8.33 0.00 0.00 3.46
3348 5140 7.664082 AGATAAGTGACTTGTGATTGTGAAG 57.336 36.000 8.33 0.00 0.00 3.02
3349 5141 7.933577 AGAAGATAAGTGACTTGTGATTGTGAA 59.066 33.333 8.33 0.00 0.00 3.18
3350 5142 7.445121 AGAAGATAAGTGACTTGTGATTGTGA 58.555 34.615 8.33 0.00 0.00 3.58
3351 5143 7.664082 AGAAGATAAGTGACTTGTGATTGTG 57.336 36.000 8.33 0.00 0.00 3.33
3352 5144 8.682936 AAAGAAGATAAGTGACTTGTGATTGT 57.317 30.769 8.33 0.00 0.00 2.71
3353 5145 9.604626 GAAAAGAAGATAAGTGACTTGTGATTG 57.395 33.333 8.33 0.00 0.00 2.67
3354 5146 9.566432 AGAAAAGAAGATAAGTGACTTGTGATT 57.434 29.630 8.33 0.00 0.00 2.57
3355 5147 8.997323 CAGAAAAGAAGATAAGTGACTTGTGAT 58.003 33.333 8.33 0.00 0.00 3.06
3356 5148 7.987458 ACAGAAAAGAAGATAAGTGACTTGTGA 59.013 33.333 8.33 0.00 0.00 3.58
3357 5149 8.147642 ACAGAAAAGAAGATAAGTGACTTGTG 57.852 34.615 8.33 0.00 0.00 3.33
3358 5150 9.482627 CTACAGAAAAGAAGATAAGTGACTTGT 57.517 33.333 8.33 0.00 0.00 3.16
3359 5151 9.698309 TCTACAGAAAAGAAGATAAGTGACTTG 57.302 33.333 8.33 0.00 0.00 3.16
3360 5152 9.699703 GTCTACAGAAAAGAAGATAAGTGACTT 57.300 33.333 2.37 2.37 0.00 3.01
3361 5153 8.861086 TGTCTACAGAAAAGAAGATAAGTGACT 58.139 33.333 0.00 0.00 0.00 3.41
3362 5154 9.477484 TTGTCTACAGAAAAGAAGATAAGTGAC 57.523 33.333 0.00 0.00 0.00 3.67
3363 5155 9.477484 GTTGTCTACAGAAAAGAAGATAAGTGA 57.523 33.333 0.00 0.00 0.00 3.41
3364 5156 8.713271 GGTTGTCTACAGAAAAGAAGATAAGTG 58.287 37.037 0.00 0.00 0.00 3.16
3365 5157 8.429641 TGGTTGTCTACAGAAAAGAAGATAAGT 58.570 33.333 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.