Multiple sequence alignment - TraesCS5B01G067400

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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 TraesCS5B01G067400 chr5B 100.000 2701 0 0 1 2701 75333390 75330690 0.000000e+00 4988.0
1 TraesCS5B01G067400 chr5B 93.524 664 34 7 2041 2701 508623267 508622610 0.000000e+00 979.0
2 TraesCS5B01G067400 chr5B 85.789 380 33 8 1142 1518 75736942 75736581 1.520000e-102 383.0
3 TraesCS5B01G067400 chr5B 86.897 290 27 6 525 806 538261733 538261447 5.610000e-82 315.0
4 TraesCS5B01G067400 chr5B 96.471 170 6 0 1731 1900 6590861 6590692 5.690000e-72 281.0
5 TraesCS5B01G067400 chr5B 89.952 209 6 6 935 1137 75737333 75737134 3.450000e-64 255.0
6 TraesCS5B01G067400 chr5B 83.333 78 10 3 413 489 536520532 536520607 4.830000e-08 69.4
7 TraesCS5B01G067400 chr1B 95.215 815 29 5 1 807 106898779 106899591 0.000000e+00 1280.0
8 TraesCS5B01G067400 chr1B 92.632 665 37 4 2041 2701 586308086 586307430 0.000000e+00 946.0
9 TraesCS5B01G067400 chr1B 77.804 428 53 23 2041 2440 55443507 55443094 2.710000e-55 226.0
10 TraesCS5B01G067400 chr1B 87.342 79 4 1 1969 2041 14440397 14440319 4.790000e-13 86.1
11 TraesCS5B01G067400 chr6A 98.792 662 6 2 2041 2701 13783792 13783132 0.000000e+00 1177.0
12 TraesCS5B01G067400 chr6A 92.542 590 36 5 2039 2627 48377048 48377630 0.000000e+00 839.0
13 TraesCS5B01G067400 chr6A 87.241 290 24 7 525 806 548399153 548398869 4.340000e-83 318.0
14 TraesCS5B01G067400 chr2A 96.352 603 9 5 219 813 192219483 192220080 0.000000e+00 979.0
15 TraesCS5B01G067400 chr2A 95.294 170 8 0 1731 1900 214445207 214445376 1.230000e-68 270.0
16 TraesCS5B01G067400 chr2A 77.108 166 22 6 2018 2180 256216941 256216789 6.200000e-12 82.4
17 TraesCS5B01G067400 chr2A 76.860 121 23 5 2014 2131 353954428 353954310 2.250000e-06 63.9
18 TraesCS5B01G067400 chr5A 92.922 664 39 7 2041 2701 629816728 629817386 0.000000e+00 959.0
19 TraesCS5B01G067400 chr5A 92.832 572 35 4 1169 1737 60250955 60250387 0.000000e+00 824.0
20 TraesCS5B01G067400 chr5A 89.320 412 36 7 1 409 31581755 31581349 6.670000e-141 510.0
21 TraesCS5B01G067400 chr5A 86.495 311 34 8 2041 2346 707871106 707871413 4.310000e-88 335.0
22 TraesCS5B01G067400 chr5A 90.047 211 9 3 931 1137 60251344 60251142 2.060000e-66 263.0
23 TraesCS5B01G067400 chr5A 89.764 127 6 4 819 938 60251496 60251370 3.600000e-34 156.0
24 TraesCS5B01G067400 chr5A 89.474 76 7 1 11 85 323259851 323259926 7.960000e-16 95.3
25 TraesCS5B01G067400 chr7A 91.691 686 33 10 2037 2701 690977752 690978434 0.000000e+00 929.0
26 TraesCS5B01G067400 chr7A 86.333 300 30 7 516 806 514711201 514711498 1.560000e-82 316.0
27 TraesCS5B01G067400 chr7A 97.674 43 1 0 413 455 16929504 16929462 1.040000e-09 75.0
28 TraesCS5B01G067400 chr5D 93.322 599 27 8 1142 1737 69504779 69504191 0.000000e+00 872.0
29 TraesCS5B01G067400 chr5D 91.028 613 32 8 1142 1737 70402840 70402234 0.000000e+00 806.0
30 TraesCS5B01G067400 chr5D 88.131 337 38 1 75 409 286419906 286420242 1.510000e-107 399.0
31 TraesCS5B01G067400 chr5D 80.325 554 70 27 2031 2571 167942685 167942158 1.520000e-102 383.0
32 TraesCS5B01G067400 chr5D 80.289 553 70 28 2031 2571 167858871 167858346 5.460000e-102 381.0
33 TraesCS5B01G067400 chr5D 86.350 337 23 12 810 1137 70403345 70403023 1.990000e-91 346.0
34 TraesCS5B01G067400 chr5D 95.294 170 8 0 1731 1900 327998540 327998371 1.230000e-68 270.0
35 TraesCS5B01G067400 chr5D 86.869 99 4 5 834 927 69505220 69505126 4.760000e-18 102.0
36 TraesCS5B01G067400 chrUn 89.781 411 38 3 1 409 46064128 46063720 8.570000e-145 523.0
37 TraesCS5B01G067400 chr2B 88.378 413 40 7 1 409 581452809 581452401 8.690000e-135 490.0
38 TraesCS5B01G067400 chr2B 87.440 414 44 6 1 409 780043495 780043905 1.130000e-128 470.0
39 TraesCS5B01G067400 chr2B 86.620 284 28 4 532 807 10815215 10815496 3.380000e-79 305.0
40 TraesCS5B01G067400 chr2B 83.849 291 28 7 525 807 794750439 794750160 2.670000e-65 259.0
41 TraesCS5B01G067400 chr2B 90.184 163 14 2 1 163 525833185 525833025 7.580000e-51 211.0
42 TraesCS5B01G067400 chr2B 84.375 128 12 2 688 807 30518585 30518458 4.720000e-23 119.0
43 TraesCS5B01G067400 chr2B 100.000 42 0 0 413 454 594260256 594260297 8.020000e-11 78.7
44 TraesCS5B01G067400 chr4B 87.651 413 44 6 1 409 623016993 623016584 8.750000e-130 473.0
45 TraesCS5B01G067400 chr4B 86.395 294 23 5 525 810 45203304 45203020 3.380000e-79 305.0
46 TraesCS5B01G067400 chr4B 86.207 290 28 6 525 806 413819405 413819120 1.220000e-78 303.0
47 TraesCS5B01G067400 chr4B 97.727 44 1 0 413 456 45203391 45203348 2.880000e-10 76.8
48 TraesCS5B01G067400 chr1A 87.250 400 20 10 2305 2701 77789160 77789531 6.910000e-116 427.0
49 TraesCS5B01G067400 chr6D 86.875 320 39 2 92 409 87372764 87373082 3.310000e-94 355.0
50 TraesCS5B01G067400 chr6D 94.118 170 10 0 1731 1900 169577825 169577656 2.670000e-65 259.0
51 TraesCS5B01G067400 chr3D 88.256 281 23 6 532 804 577804929 577805207 7.210000e-86 327.0
52 TraesCS5B01G067400 chr3B 86.897 290 26 5 525 806 810340094 810340379 5.610000e-82 315.0
53 TraesCS5B01G067400 chr6B 83.871 341 32 14 486 806 612272864 612272527 1.220000e-78 303.0
54 TraesCS5B01G067400 chr6B 86.159 289 29 6 526 806 559350057 559349772 4.370000e-78 302.0
55 TraesCS5B01G067400 chr6B 100.000 42 0 0 413 454 79274015 79273974 8.020000e-11 78.7
56 TraesCS5B01G067400 chr6B 100.000 41 0 0 413 453 534227555 534227595 2.880000e-10 76.8
57 TraesCS5B01G067400 chr2D 95.294 170 8 0 1731 1900 37298614 37298445 1.230000e-68 270.0
58 TraesCS5B01G067400 chr2D 95.294 170 8 0 1731 1900 587740293 587740462 1.230000e-68 270.0
59 TraesCS5B01G067400 chr2D 94.706 170 9 0 1731 1900 57150457 57150626 5.730000e-67 265.0
60 TraesCS5B01G067400 chr2D 94.706 170 9 0 1731 1900 591569405 591569236 5.730000e-67 265.0
61 TraesCS5B01G067400 chr2D 83.486 218 27 5 1 212 446329645 446329431 7.630000e-46 195.0
62 TraesCS5B01G067400 chr1D 95.210 167 8 0 1734 1900 475979323 475979489 5.730000e-67 265.0
63 TraesCS5B01G067400 chr7B 77.632 304 40 14 1 279 125761066 125760766 2.780000e-35 159.0
64 TraesCS5B01G067400 chr4A 100.000 41 0 0 413 453 710418531 710418571 2.880000e-10 76.8


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 TraesCS5B01G067400 chr5B 75330690 75333390 2700 True 4988.000000 4988 100.0000 1 2701 1 chr5B.!!$R2 2700
1 TraesCS5B01G067400 chr5B 508622610 508623267 657 True 979.000000 979 93.5240 2041 2701 1 chr5B.!!$R3 660
2 TraesCS5B01G067400 chr5B 75736581 75737333 752 True 319.000000 383 87.8705 935 1518 2 chr5B.!!$R5 583
3 TraesCS5B01G067400 chr1B 106898779 106899591 812 False 1280.000000 1280 95.2150 1 807 1 chr1B.!!$F1 806
4 TraesCS5B01G067400 chr1B 586307430 586308086 656 True 946.000000 946 92.6320 2041 2701 1 chr1B.!!$R3 660
5 TraesCS5B01G067400 chr6A 13783132 13783792 660 True 1177.000000 1177 98.7920 2041 2701 1 chr6A.!!$R1 660
6 TraesCS5B01G067400 chr6A 48377048 48377630 582 False 839.000000 839 92.5420 2039 2627 1 chr6A.!!$F1 588
7 TraesCS5B01G067400 chr2A 192219483 192220080 597 False 979.000000 979 96.3520 219 813 1 chr2A.!!$F1 594
8 TraesCS5B01G067400 chr5A 629816728 629817386 658 False 959.000000 959 92.9220 2041 2701 1 chr5A.!!$F2 660
9 TraesCS5B01G067400 chr5A 60250387 60251496 1109 True 414.333333 824 90.8810 819 1737 3 chr5A.!!$R2 918
10 TraesCS5B01G067400 chr7A 690977752 690978434 682 False 929.000000 929 91.6910 2037 2701 1 chr7A.!!$F2 664
11 TraesCS5B01G067400 chr5D 70402234 70403345 1111 True 576.000000 806 88.6890 810 1737 2 chr5D.!!$R5 927
12 TraesCS5B01G067400 chr5D 69504191 69505220 1029 True 487.000000 872 90.0955 834 1737 2 chr5D.!!$R4 903
13 TraesCS5B01G067400 chr5D 167942158 167942685 527 True 383.000000 383 80.3250 2031 2571 1 chr5D.!!$R2 540
14 TraesCS5B01G067400 chr5D 167858346 167858871 525 True 381.000000 381 80.2890 2031 2571 1 chr5D.!!$R1 540

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
966 1027 0.249489 CGATCCCACAGACGGAATCC 60.249 60.0 0.0 0.0 31.75 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 2046 0.167251 CGCCAAATAACGACCACCAC 59.833 55.0 0.0 0.0 0.0 4.16 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
92 93 7.011016 GTGAAGAATTTTTGAAACGGAACCAAT 59.989 33.333 0.00 0.00 0.00 3.16
212 213 9.801873 ATATTATTTTGAAAATCTGGTTCACGG 57.198 29.630 6.40 0.00 34.78 4.94
319 320 6.525628 TCGAACTCGCGGAAAATATATGATAC 59.474 38.462 6.13 0.00 39.60 2.24
611 612 7.550906 CCCTTGGTGAATTTTTGTTTCTTAACA 59.449 33.333 0.00 0.00 42.34 2.41
763 772 3.498082 GACCGGGATTTCAATTCGTTTG 58.502 45.455 6.32 0.00 36.61 2.93
777 786 1.605165 GTTTGGCCGAACCCATCCA 60.605 57.895 23.59 0.00 37.83 3.41
836 847 8.484008 TCATTTCGTTATTAAAAAGCAGCAAAC 58.516 29.630 0.00 0.00 0.00 2.93
837 848 6.427300 TTCGTTATTAAAAAGCAGCAAACG 57.573 33.333 0.00 0.00 39.67 3.60
886 899 0.956902 GAAACGTTATGCCCCACGGT 60.957 55.000 0.00 0.00 40.84 4.83
889 902 2.672295 GTTATGCCCCACGGTCCA 59.328 61.111 0.00 0.00 0.00 4.02
914 930 1.939838 GCCTTATATGAACGGCCCGAG 60.940 57.143 11.71 0.00 36.56 4.63
917 933 2.758770 TATATGAACGGCCCGAGCGC 62.759 60.000 11.71 0.00 41.24 5.92
938 993 2.352814 CCTCGTCTCCAACAGAACGATT 60.353 50.000 0.00 0.00 35.50 3.34
966 1027 0.249489 CGATCCCACAGACGGAATCC 60.249 60.000 0.00 0.00 31.75 3.01
1072 1133 3.235200 CATCTCCCGTCCCTCTCTTAAT 58.765 50.000 0.00 0.00 0.00 1.40
1137 1204 4.771577 ACCCACAAGCATGTTTTGATATGA 59.228 37.500 15.89 0.00 37.82 2.15
1140 1397 5.286797 CCACAAGCATGTTTTGATATGAACG 59.713 40.000 15.89 0.00 37.82 3.95
1165 1422 6.599638 GTCCATTCTAACTTAATCTTGGCTGT 59.400 38.462 0.00 0.00 0.00 4.40
1166 1423 6.599244 TCCATTCTAACTTAATCTTGGCTGTG 59.401 38.462 0.00 0.00 0.00 3.66
1167 1424 6.183360 CCATTCTAACTTAATCTTGGCTGTGG 60.183 42.308 0.00 0.00 0.00 4.17
1168 1425 4.261801 TCTAACTTAATCTTGGCTGTGGC 58.738 43.478 0.00 0.00 37.82 5.01
1169 1426 2.887151 ACTTAATCTTGGCTGTGGCT 57.113 45.000 0.00 0.00 38.73 4.75
1170 1427 2.440409 ACTTAATCTTGGCTGTGGCTG 58.560 47.619 0.00 0.00 38.73 4.85
1171 1428 1.747355 CTTAATCTTGGCTGTGGCTGG 59.253 52.381 0.00 0.00 38.73 4.85
1172 1429 0.034186 TAATCTTGGCTGTGGCTGGG 60.034 55.000 0.00 0.00 38.73 4.45
1300 1557 2.995466 AATGCTCATCAACAACACCG 57.005 45.000 0.00 0.00 0.00 4.94
1441 1707 0.107459 GAAGACCTGGTGGAGGATGC 60.107 60.000 2.82 0.00 46.33 3.91
1444 1710 2.262774 GACCTGGTGGAGGATGCCAG 62.263 65.000 2.82 0.00 46.33 4.85
1595 1861 1.333177 GCAGGAGGAGTATGGATCGT 58.667 55.000 0.00 0.00 0.00 3.73
1608 1874 1.066430 TGGATCGTAGGTGGTTTGCTC 60.066 52.381 0.00 0.00 0.00 4.26
1669 1942 1.140589 CTGCTGGAGACTACGGCTG 59.859 63.158 19.43 14.99 40.81 4.85
1701 1974 2.644299 TGCCCCGAAGATGATGGATAAT 59.356 45.455 0.00 0.00 0.00 1.28
1742 2015 9.915629 ATTAATCTCTTATTTCTAGTGGTAGCG 57.084 33.333 0.00 0.00 0.00 4.26
1743 2016 5.184340 TCTCTTATTTCTAGTGGTAGCGC 57.816 43.478 0.00 0.00 0.00 5.92
1744 2017 4.888239 TCTCTTATTTCTAGTGGTAGCGCT 59.112 41.667 17.26 17.26 0.00 5.92
1745 2018 5.008811 TCTCTTATTTCTAGTGGTAGCGCTC 59.991 44.000 16.34 5.63 0.00 5.03
1746 2019 2.892784 ATTTCTAGTGGTAGCGCTCC 57.107 50.000 16.34 16.25 0.00 4.70
1747 2020 1.848652 TTTCTAGTGGTAGCGCTCCT 58.151 50.000 16.34 8.70 0.00 3.69
1748 2021 1.848652 TTCTAGTGGTAGCGCTCCTT 58.151 50.000 16.34 10.43 0.00 3.36
1749 2022 1.390565 TCTAGTGGTAGCGCTCCTTC 58.609 55.000 16.34 12.35 0.00 3.46
1750 2023 0.029567 CTAGTGGTAGCGCTCCTTCG 59.970 60.000 16.34 2.38 0.00 3.79
1751 2024 1.381928 TAGTGGTAGCGCTCCTTCGG 61.382 60.000 16.34 0.00 0.00 4.30
1752 2025 4.143333 TGGTAGCGCTCCTTCGGC 62.143 66.667 16.34 0.00 0.00 5.54
1753 2026 3.839432 GGTAGCGCTCCTTCGGCT 61.839 66.667 16.34 0.00 40.68 5.52
1754 2027 2.184579 GTAGCGCTCCTTCGGCTT 59.815 61.111 16.34 0.00 38.19 4.35
1755 2028 2.167861 GTAGCGCTCCTTCGGCTTG 61.168 63.158 16.34 0.00 38.19 4.01
1756 2029 3.371097 TAGCGCTCCTTCGGCTTGG 62.371 63.158 16.34 0.00 38.19 3.61
1757 2030 4.760047 GCGCTCCTTCGGCTTGGA 62.760 66.667 0.00 0.00 0.00 3.53
1762 2035 1.907739 TCCTTCGGCTTGGAGATGG 59.092 57.895 0.00 0.00 34.22 3.51
1763 2036 0.617535 TCCTTCGGCTTGGAGATGGA 60.618 55.000 0.00 0.00 38.06 3.41
1764 2037 0.462759 CCTTCGGCTTGGAGATGGAC 60.463 60.000 0.00 0.00 34.67 4.02
1765 2038 0.539051 CTTCGGCTTGGAGATGGACT 59.461 55.000 0.00 0.00 0.00 3.85
1766 2039 0.250234 TTCGGCTTGGAGATGGACTG 59.750 55.000 0.00 0.00 0.00 3.51
1767 2040 1.153289 CGGCTTGGAGATGGACTGG 60.153 63.158 0.00 0.00 0.00 4.00
1768 2041 1.452833 GGCTTGGAGATGGACTGGC 60.453 63.158 0.00 0.00 0.00 4.85
1769 2042 1.300963 GCTTGGAGATGGACTGGCA 59.699 57.895 0.00 0.00 0.00 4.92
1770 2043 0.106819 GCTTGGAGATGGACTGGCAT 60.107 55.000 0.00 0.00 0.00 4.40
1771 2044 1.141657 GCTTGGAGATGGACTGGCATA 59.858 52.381 0.00 0.00 0.00 3.14
1772 2045 2.809665 GCTTGGAGATGGACTGGCATAG 60.810 54.545 0.00 0.00 0.00 2.23
1773 2046 1.427809 TGGAGATGGACTGGCATAGG 58.572 55.000 0.00 0.00 0.00 2.57
1774 2047 1.344393 TGGAGATGGACTGGCATAGGT 60.344 52.381 0.00 0.00 0.00 3.08
1775 2048 1.071385 GGAGATGGACTGGCATAGGTG 59.929 57.143 0.00 0.00 0.00 4.00
1776 2049 1.071385 GAGATGGACTGGCATAGGTGG 59.929 57.143 0.00 0.00 0.00 4.61
1777 2050 0.839946 GATGGACTGGCATAGGTGGT 59.160 55.000 0.00 0.00 0.00 4.16
1778 2051 0.548031 ATGGACTGGCATAGGTGGTG 59.452 55.000 0.00 0.00 0.00 4.17
1779 2052 1.224592 GGACTGGCATAGGTGGTGG 59.775 63.158 0.00 0.00 0.00 4.61
1780 2053 1.562672 GGACTGGCATAGGTGGTGGT 61.563 60.000 0.00 0.00 0.00 4.16
1781 2054 0.107654 GACTGGCATAGGTGGTGGTC 60.108 60.000 0.00 0.00 0.00 4.02
1782 2055 1.153369 CTGGCATAGGTGGTGGTCG 60.153 63.158 0.00 0.00 0.00 4.79
1783 2056 1.899437 CTGGCATAGGTGGTGGTCGT 61.899 60.000 0.00 0.00 0.00 4.34
1784 2057 1.298667 GGCATAGGTGGTGGTCGTT 59.701 57.895 0.00 0.00 0.00 3.85
1785 2058 0.538118 GGCATAGGTGGTGGTCGTTA 59.462 55.000 0.00 0.00 0.00 3.18
1786 2059 1.140252 GGCATAGGTGGTGGTCGTTAT 59.860 52.381 0.00 0.00 0.00 1.89
1787 2060 2.420967 GGCATAGGTGGTGGTCGTTATT 60.421 50.000 0.00 0.00 0.00 1.40
1788 2061 3.275999 GCATAGGTGGTGGTCGTTATTT 58.724 45.455 0.00 0.00 0.00 1.40
1789 2062 3.064820 GCATAGGTGGTGGTCGTTATTTG 59.935 47.826 0.00 0.00 0.00 2.32
1790 2063 2.194201 AGGTGGTGGTCGTTATTTGG 57.806 50.000 0.00 0.00 0.00 3.28
1791 2064 0.524414 GGTGGTGGTCGTTATTTGGC 59.476 55.000 0.00 0.00 0.00 4.52
1792 2065 0.167251 GTGGTGGTCGTTATTTGGCG 59.833 55.000 0.00 0.00 0.00 5.69
1793 2066 0.250381 TGGTGGTCGTTATTTGGCGT 60.250 50.000 0.00 0.00 0.00 5.68
1794 2067 0.445043 GGTGGTCGTTATTTGGCGTC 59.555 55.000 0.00 0.00 0.00 5.19
1795 2068 1.149987 GTGGTCGTTATTTGGCGTCA 58.850 50.000 0.00 0.00 0.00 4.35
1796 2069 1.735571 GTGGTCGTTATTTGGCGTCAT 59.264 47.619 0.00 0.00 0.00 3.06
1797 2070 1.735018 TGGTCGTTATTTGGCGTCATG 59.265 47.619 0.00 0.00 0.00 3.07
1798 2071 1.063469 GGTCGTTATTTGGCGTCATGG 59.937 52.381 0.00 0.00 0.00 3.66
1799 2072 1.735571 GTCGTTATTTGGCGTCATGGT 59.264 47.619 0.00 0.00 0.00 3.55
1800 2073 1.735018 TCGTTATTTGGCGTCATGGTG 59.265 47.619 0.00 0.00 0.00 4.17
1801 2074 1.202132 CGTTATTTGGCGTCATGGTGG 60.202 52.381 0.00 0.00 0.00 4.61
1802 2075 0.814457 TTATTTGGCGTCATGGTGGC 59.186 50.000 0.00 0.00 0.00 5.01
1808 2081 2.202743 CGTCATGGTGGCGTCGAT 60.203 61.111 0.00 0.00 41.12 3.59
1809 2082 2.516589 CGTCATGGTGGCGTCGATG 61.517 63.158 0.00 0.00 41.12 3.84
1810 2083 2.173669 GTCATGGTGGCGTCGATGG 61.174 63.158 6.79 0.00 0.00 3.51
1811 2084 3.576356 CATGGTGGCGTCGATGGC 61.576 66.667 23.33 23.33 0.00 4.40
1818 2091 4.508128 GCGTCGATGGCGGAGGAA 62.508 66.667 6.79 0.00 38.28 3.36
1819 2092 2.582498 CGTCGATGGCGGAGGAAC 60.582 66.667 0.00 0.00 38.28 3.62
1820 2093 2.202892 GTCGATGGCGGAGGAACC 60.203 66.667 0.00 0.00 38.28 3.62
1821 2094 2.363795 TCGATGGCGGAGGAACCT 60.364 61.111 0.00 0.00 38.28 3.50
1822 2095 2.202932 CGATGGCGGAGGAACCTG 60.203 66.667 0.00 0.00 36.31 4.00
1823 2096 2.514824 GATGGCGGAGGAACCTGC 60.515 66.667 0.00 0.00 37.42 4.85
1827 2100 2.747855 GCGGAGGAACCTGCCAAG 60.748 66.667 6.78 0.00 36.31 3.61
1848 2121 4.287766 GGTTGGTACCTCAATCTGTTCT 57.712 45.455 14.36 0.00 41.53 3.01
1849 2122 4.003648 GGTTGGTACCTCAATCTGTTCTG 58.996 47.826 14.36 0.00 41.53 3.02
1850 2123 4.262894 GGTTGGTACCTCAATCTGTTCTGA 60.263 45.833 14.36 0.00 41.53 3.27
1851 2124 5.305585 GTTGGTACCTCAATCTGTTCTGAA 58.694 41.667 14.36 0.00 0.00 3.02
1852 2125 5.152623 TGGTACCTCAATCTGTTCTGAAG 57.847 43.478 14.36 0.00 0.00 3.02
1853 2126 4.838423 TGGTACCTCAATCTGTTCTGAAGA 59.162 41.667 14.36 0.00 0.00 2.87
1854 2127 5.485353 TGGTACCTCAATCTGTTCTGAAGAT 59.515 40.000 14.36 0.00 35.89 2.40
1855 2128 5.814705 GGTACCTCAATCTGTTCTGAAGATG 59.185 44.000 4.06 0.00 34.59 2.90
1856 2129 4.841422 ACCTCAATCTGTTCTGAAGATGG 58.159 43.478 0.00 0.00 34.59 3.51
1857 2130 4.533707 ACCTCAATCTGTTCTGAAGATGGA 59.466 41.667 0.00 0.00 34.59 3.41
1858 2131 4.874966 CCTCAATCTGTTCTGAAGATGGAC 59.125 45.833 0.00 0.00 34.59 4.02
1859 2132 5.485620 CTCAATCTGTTCTGAAGATGGACA 58.514 41.667 0.00 0.00 34.59 4.02
1860 2133 5.868454 TCAATCTGTTCTGAAGATGGACAA 58.132 37.500 0.00 0.00 34.59 3.18
1861 2134 5.936372 TCAATCTGTTCTGAAGATGGACAAG 59.064 40.000 0.00 0.00 34.59 3.16
1862 2135 4.963318 TCTGTTCTGAAGATGGACAAGT 57.037 40.909 0.00 0.00 0.00 3.16
1863 2136 6.611613 ATCTGTTCTGAAGATGGACAAGTA 57.388 37.500 0.00 0.00 33.08 2.24
1864 2137 6.030548 TCTGTTCTGAAGATGGACAAGTAG 57.969 41.667 0.00 0.00 0.00 2.57
1865 2138 5.775195 TCTGTTCTGAAGATGGACAAGTAGA 59.225 40.000 0.00 0.00 0.00 2.59
1866 2139 6.267699 TCTGTTCTGAAGATGGACAAGTAGAA 59.732 38.462 0.00 0.00 0.00 2.10
1867 2140 6.459066 TGTTCTGAAGATGGACAAGTAGAAG 58.541 40.000 0.00 0.00 0.00 2.85
1868 2141 6.267699 TGTTCTGAAGATGGACAAGTAGAAGA 59.732 38.462 0.00 0.00 0.00 2.87
1869 2142 7.038729 TGTTCTGAAGATGGACAAGTAGAAGAT 60.039 37.037 0.00 0.00 0.00 2.40
1870 2143 6.871844 TCTGAAGATGGACAAGTAGAAGATG 58.128 40.000 0.00 0.00 0.00 2.90
1871 2144 5.982356 TGAAGATGGACAAGTAGAAGATGG 58.018 41.667 0.00 0.00 0.00 3.51
1872 2145 5.485353 TGAAGATGGACAAGTAGAAGATGGT 59.515 40.000 0.00 0.00 0.00 3.55
1873 2146 5.350504 AGATGGACAAGTAGAAGATGGTG 57.649 43.478 0.00 0.00 0.00 4.17
1874 2147 5.026121 AGATGGACAAGTAGAAGATGGTGA 58.974 41.667 0.00 0.00 0.00 4.02
1875 2148 5.664908 AGATGGACAAGTAGAAGATGGTGAT 59.335 40.000 0.00 0.00 0.00 3.06
1876 2149 5.089970 TGGACAAGTAGAAGATGGTGATG 57.910 43.478 0.00 0.00 0.00 3.07
1877 2150 4.777366 TGGACAAGTAGAAGATGGTGATGA 59.223 41.667 0.00 0.00 0.00 2.92
1878 2151 5.112686 GGACAAGTAGAAGATGGTGATGAC 58.887 45.833 0.00 0.00 0.00 3.06
1879 2152 5.337571 GGACAAGTAGAAGATGGTGATGACA 60.338 44.000 0.00 0.00 0.00 3.58
1880 2153 6.114187 ACAAGTAGAAGATGGTGATGACAA 57.886 37.500 0.00 0.00 0.00 3.18
1881 2154 5.934625 ACAAGTAGAAGATGGTGATGACAAC 59.065 40.000 0.00 0.00 0.00 3.32
1883 2156 5.482908 AGTAGAAGATGGTGATGACAACAC 58.517 41.667 7.29 7.29 46.89 3.32
1884 2157 4.356405 AGAAGATGGTGATGACAACACA 57.644 40.909 16.57 4.70 46.89 3.72
1885 2158 4.914983 AGAAGATGGTGATGACAACACAT 58.085 39.130 16.57 8.76 46.89 3.21
1886 2159 4.698780 AGAAGATGGTGATGACAACACATG 59.301 41.667 16.57 0.00 46.89 3.21
1887 2160 4.025040 AGATGGTGATGACAACACATGT 57.975 40.909 16.57 0.00 46.89 3.21
1888 2161 3.754850 AGATGGTGATGACAACACATGTG 59.245 43.478 24.25 24.25 46.89 3.21
1889 2162 3.205784 TGGTGATGACAACACATGTGA 57.794 42.857 31.94 9.84 44.12 3.58
1890 2163 3.140623 TGGTGATGACAACACATGTGAG 58.859 45.455 31.94 23.60 44.12 3.51
1891 2164 3.141398 GGTGATGACAACACATGTGAGT 58.859 45.455 31.94 26.40 44.12 3.41
1892 2165 3.058708 GGTGATGACAACACATGTGAGTG 60.059 47.826 31.94 27.02 44.12 3.51
1899 2172 3.586430 CACATGTGAGTGTGTCGGA 57.414 52.632 21.64 0.00 43.43 4.55
1900 2173 2.084610 CACATGTGAGTGTGTCGGAT 57.915 50.000 21.64 0.00 43.43 4.18
1901 2174 1.995484 CACATGTGAGTGTGTCGGATC 59.005 52.381 21.64 0.00 43.43 3.36
1902 2175 1.895798 ACATGTGAGTGTGTCGGATCT 59.104 47.619 0.00 0.00 0.00 2.75
1903 2176 2.300152 ACATGTGAGTGTGTCGGATCTT 59.700 45.455 0.00 0.00 0.00 2.40
1904 2177 2.438868 TGTGAGTGTGTCGGATCTTG 57.561 50.000 0.00 0.00 0.00 3.02
1905 2178 1.686587 TGTGAGTGTGTCGGATCTTGT 59.313 47.619 0.00 0.00 0.00 3.16
1906 2179 2.061773 GTGAGTGTGTCGGATCTTGTG 58.938 52.381 0.00 0.00 0.00 3.33
1907 2180 1.960689 TGAGTGTGTCGGATCTTGTGA 59.039 47.619 0.00 0.00 0.00 3.58
1908 2181 2.364002 TGAGTGTGTCGGATCTTGTGAA 59.636 45.455 0.00 0.00 0.00 3.18
1909 2182 2.989840 GAGTGTGTCGGATCTTGTGAAG 59.010 50.000 0.00 0.00 0.00 3.02
1910 2183 1.461127 GTGTGTCGGATCTTGTGAAGC 59.539 52.381 0.00 0.00 0.00 3.86
1911 2184 1.069978 TGTGTCGGATCTTGTGAAGCA 59.930 47.619 0.00 0.00 0.00 3.91
1912 2185 2.143122 GTGTCGGATCTTGTGAAGCAA 58.857 47.619 0.00 0.00 35.50 3.91
1913 2186 2.744202 GTGTCGGATCTTGTGAAGCAAT 59.256 45.455 0.00 0.00 36.36 3.56
1914 2187 3.189287 GTGTCGGATCTTGTGAAGCAATT 59.811 43.478 0.00 0.00 36.36 2.32
1915 2188 3.820467 TGTCGGATCTTGTGAAGCAATTT 59.180 39.130 0.00 0.00 36.36 1.82
1916 2189 5.000591 TGTCGGATCTTGTGAAGCAATTTA 58.999 37.500 0.00 0.00 36.36 1.40
1917 2190 5.647658 TGTCGGATCTTGTGAAGCAATTTAT 59.352 36.000 0.00 0.00 36.36 1.40
1918 2191 5.967674 GTCGGATCTTGTGAAGCAATTTATG 59.032 40.000 0.00 0.00 36.36 1.90
1919 2192 5.647658 TCGGATCTTGTGAAGCAATTTATGT 59.352 36.000 0.00 0.00 36.36 2.29
1920 2193 5.740569 CGGATCTTGTGAAGCAATTTATGTG 59.259 40.000 0.00 0.00 36.36 3.21
1921 2194 6.623549 CGGATCTTGTGAAGCAATTTATGTGT 60.624 38.462 0.00 0.00 36.36 3.72
1922 2195 6.749118 GGATCTTGTGAAGCAATTTATGTGTC 59.251 38.462 0.00 0.00 36.36 3.67
1923 2196 6.882610 TCTTGTGAAGCAATTTATGTGTCT 57.117 33.333 0.00 0.00 36.36 3.41
1924 2197 7.275888 TCTTGTGAAGCAATTTATGTGTCTT 57.724 32.000 0.00 0.00 36.36 3.01
1925 2198 7.715657 TCTTGTGAAGCAATTTATGTGTCTTT 58.284 30.769 0.00 0.00 36.36 2.52
1926 2199 7.862372 TCTTGTGAAGCAATTTATGTGTCTTTC 59.138 33.333 0.00 0.00 36.36 2.62
1927 2200 7.036996 TGTGAAGCAATTTATGTGTCTTTCA 57.963 32.000 0.00 0.00 0.00 2.69
1928 2201 7.487484 TGTGAAGCAATTTATGTGTCTTTCAA 58.513 30.769 0.00 0.00 0.00 2.69
1929 2202 7.978414 TGTGAAGCAATTTATGTGTCTTTCAAA 59.022 29.630 0.00 0.00 0.00 2.69
1930 2203 8.816144 GTGAAGCAATTTATGTGTCTTTCAAAA 58.184 29.630 0.00 0.00 0.00 2.44
1931 2204 9.376075 TGAAGCAATTTATGTGTCTTTCAAAAA 57.624 25.926 0.00 0.00 0.00 1.94
1958 2231 9.618890 ATTAATCTCTTATTTCTAGTGCAAGCA 57.381 29.630 0.00 0.00 0.00 3.91
1959 2232 9.618890 TTAATCTCTTATTTCTAGTGCAAGCAT 57.381 29.630 0.00 0.00 0.00 3.79
1960 2233 6.915544 TCTCTTATTTCTAGTGCAAGCATG 57.084 37.500 0.00 0.00 0.00 4.06
1961 2234 5.819379 TCTCTTATTTCTAGTGCAAGCATGG 59.181 40.000 0.00 0.00 0.00 3.66
1962 2235 5.744171 TCTTATTTCTAGTGCAAGCATGGA 58.256 37.500 0.00 0.00 0.00 3.41
1963 2236 6.359804 TCTTATTTCTAGTGCAAGCATGGAT 58.640 36.000 0.00 0.00 0.00 3.41
1964 2237 6.484643 TCTTATTTCTAGTGCAAGCATGGATC 59.515 38.462 0.00 0.00 0.00 3.36
1965 2238 3.920231 TTCTAGTGCAAGCATGGATCT 57.080 42.857 0.00 0.00 0.00 2.75
1966 2239 3.920231 TCTAGTGCAAGCATGGATCTT 57.080 42.857 0.00 0.00 0.00 2.40
1967 2240 3.538591 TCTAGTGCAAGCATGGATCTTG 58.461 45.455 0.00 7.07 42.72 3.02
1968 2241 2.211250 AGTGCAAGCATGGATCTTGT 57.789 45.000 11.62 0.00 42.06 3.16
1969 2242 1.816835 AGTGCAAGCATGGATCTTGTG 59.183 47.619 11.62 0.00 42.06 3.33
1970 2243 1.542915 GTGCAAGCATGGATCTTGTGT 59.457 47.619 11.62 0.00 42.06 3.72
1971 2244 2.749076 GTGCAAGCATGGATCTTGTGTA 59.251 45.455 11.62 0.00 42.06 2.90
1972 2245 3.011818 TGCAAGCATGGATCTTGTGTAG 58.988 45.455 11.62 0.00 42.06 2.74
1973 2246 2.223433 GCAAGCATGGATCTTGTGTAGC 60.223 50.000 11.62 0.00 42.06 3.58
1974 2247 3.011818 CAAGCATGGATCTTGTGTAGCA 58.988 45.455 0.00 0.00 36.93 3.49
1975 2248 3.354948 AGCATGGATCTTGTGTAGCAA 57.645 42.857 0.00 0.00 35.50 3.91
1976 2249 3.894759 AGCATGGATCTTGTGTAGCAAT 58.105 40.909 0.00 0.00 36.36 3.56
1977 2250 4.275810 AGCATGGATCTTGTGTAGCAATT 58.724 39.130 0.00 0.00 36.36 2.32
1978 2251 4.708421 AGCATGGATCTTGTGTAGCAATTT 59.292 37.500 0.00 0.00 36.36 1.82
1979 2252 5.887598 AGCATGGATCTTGTGTAGCAATTTA 59.112 36.000 0.00 0.00 36.36 1.40
1980 2253 6.548622 AGCATGGATCTTGTGTAGCAATTTAT 59.451 34.615 0.00 0.00 36.36 1.40
1981 2254 6.639686 GCATGGATCTTGTGTAGCAATTTATG 59.360 38.462 0.00 0.00 36.36 1.90
1982 2255 7.682741 GCATGGATCTTGTGTAGCAATTTATGT 60.683 37.037 0.00 0.00 36.36 2.29
1983 2256 7.087409 TGGATCTTGTGTAGCAATTTATGTG 57.913 36.000 0.00 0.00 36.36 3.21
1984 2257 6.658816 TGGATCTTGTGTAGCAATTTATGTGT 59.341 34.615 0.00 0.00 36.36 3.72
1985 2258 7.148255 TGGATCTTGTGTAGCAATTTATGTGTC 60.148 37.037 0.00 0.00 36.36 3.67
1986 2259 7.066284 GGATCTTGTGTAGCAATTTATGTGTCT 59.934 37.037 0.00 0.00 36.36 3.41
1987 2260 7.744087 TCTTGTGTAGCAATTTATGTGTCTT 57.256 32.000 0.00 0.00 36.36 3.01
1988 2261 8.165239 TCTTGTGTAGCAATTTATGTGTCTTT 57.835 30.769 0.00 0.00 36.36 2.52
1989 2262 8.289618 TCTTGTGTAGCAATTTATGTGTCTTTC 58.710 33.333 0.00 0.00 36.36 2.62
1990 2263 7.503521 TGTGTAGCAATTTATGTGTCTTTCA 57.496 32.000 0.00 0.00 0.00 2.69
1991 2264 7.935520 TGTGTAGCAATTTATGTGTCTTTCAA 58.064 30.769 0.00 0.00 0.00 2.69
1992 2265 8.409371 TGTGTAGCAATTTATGTGTCTTTCAAA 58.591 29.630 0.00 0.00 0.00 2.69
1993 2266 8.690840 GTGTAGCAATTTATGTGTCTTTCAAAC 58.309 33.333 0.00 0.00 0.00 2.93
1994 2267 8.409371 TGTAGCAATTTATGTGTCTTTCAAACA 58.591 29.630 0.00 0.00 0.00 2.83
1995 2268 9.410556 GTAGCAATTTATGTGTCTTTCAAACAT 57.589 29.630 0.00 0.00 38.13 2.71
1996 2269 8.891671 AGCAATTTATGTGTCTTTCAAACATT 57.108 26.923 0.00 0.00 36.08 2.71
1997 2270 9.979578 AGCAATTTATGTGTCTTTCAAACATTA 57.020 25.926 0.00 0.00 36.08 1.90
2006 2279 9.772973 TGTGTCTTTCAAACATTATACTACAGT 57.227 29.630 0.00 0.00 0.00 3.55
2585 2893 0.034476 CACTTCTCAGCAGCCAGACA 59.966 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 9.553418 CCGTTTCAAAAATTCTTCACAAATTTT 57.447 25.926 0.00 1.75 44.21 1.82
64 65 6.311690 GGTTCCGTTTCAAAAATTCTTCACAA 59.688 34.615 0.00 0.00 0.00 3.33
452 453 7.283127 GCCATCTTAGTAGGAAATGACAAATGA 59.717 37.037 0.00 0.00 0.00 2.57
763 772 0.459899 GAATTTGGATGGGTTCGGCC 59.540 55.000 0.00 0.00 0.00 6.13
777 786 9.693739 AAAAAGTCCATTTTAAACCCTGAATTT 57.306 25.926 0.00 0.00 40.27 1.82
808 817 9.847706 TTGCTGCTTTTTAATAACGAAATGATA 57.152 25.926 0.00 0.00 0.00 2.15
817 826 4.143200 GGGCGTTTGCTGCTTTTTAATAAC 60.143 41.667 0.00 0.00 42.25 1.89
836 847 2.106683 GTGTCCGAATTCAGGGGCG 61.107 63.158 6.22 0.00 0.00 6.13
837 848 1.749258 GGTGTCCGAATTCAGGGGC 60.749 63.158 6.22 1.51 0.00 5.80
886 899 1.071699 GTTCATATAAGGCCGGCTGGA 59.928 52.381 28.56 12.01 37.49 3.86
889 902 0.034896 CCGTTCATATAAGGCCGGCT 59.965 55.000 28.56 10.45 0.00 5.52
914 930 2.765250 TTCTGTTGGAGACGAGGCGC 62.765 60.000 0.00 0.00 0.00 6.53
917 933 0.596577 TCGTTCTGTTGGAGACGAGG 59.403 55.000 0.00 0.00 32.68 4.63
1137 1204 6.093633 GCCAAGATTAAGTTAGAATGGACGTT 59.906 38.462 0.00 0.00 0.00 3.99
1140 1397 6.599638 ACAGCCAAGATTAAGTTAGAATGGAC 59.400 38.462 9.14 3.25 0.00 4.02
1157 1414 2.203538 AACCCAGCCACAGCCAAG 60.204 61.111 0.00 0.00 41.25 3.61
1168 1425 1.592400 CCACTCATGCTGCAACCCAG 61.592 60.000 6.36 2.71 44.67 4.45
1169 1426 1.604308 CCACTCATGCTGCAACCCA 60.604 57.895 6.36 0.00 0.00 4.51
1170 1427 1.303561 TCCACTCATGCTGCAACCC 60.304 57.895 6.36 0.00 0.00 4.11
1171 1428 0.607489 AGTCCACTCATGCTGCAACC 60.607 55.000 6.36 0.00 0.00 3.77
1172 1429 0.801251 GAGTCCACTCATGCTGCAAC 59.199 55.000 6.36 0.00 42.42 4.17
1300 1557 0.458260 GGTGGTGGTGGTGTTTGTTC 59.542 55.000 0.00 0.00 0.00 3.18
1441 1707 1.568612 TTTGCGCGCTTCTTCTCTGG 61.569 55.000 33.29 0.00 0.00 3.86
1444 1710 1.135972 TGAATTTGCGCGCTTCTTCTC 60.136 47.619 33.29 19.77 0.00 2.87
1595 1861 1.980052 CCTCCGAGCAAACCACCTA 59.020 57.895 0.00 0.00 0.00 3.08
1608 1874 2.821366 AGCAGCAATTCGCCTCCG 60.821 61.111 0.00 0.00 44.04 4.63
1669 1942 1.870055 TTCGGGGCAGTCTACGTCAC 61.870 60.000 0.00 0.00 0.00 3.67
1746 2019 0.539051 AGTCCATCTCCAAGCCGAAG 59.461 55.000 0.00 0.00 0.00 3.79
1747 2020 0.250234 CAGTCCATCTCCAAGCCGAA 59.750 55.000 0.00 0.00 0.00 4.30
1748 2021 1.617018 CCAGTCCATCTCCAAGCCGA 61.617 60.000 0.00 0.00 0.00 5.54
1749 2022 1.153289 CCAGTCCATCTCCAAGCCG 60.153 63.158 0.00 0.00 0.00 5.52
1750 2023 1.452833 GCCAGTCCATCTCCAAGCC 60.453 63.158 0.00 0.00 0.00 4.35
1751 2024 0.106819 ATGCCAGTCCATCTCCAAGC 60.107 55.000 0.00 0.00 0.00 4.01
1752 2025 2.224475 CCTATGCCAGTCCATCTCCAAG 60.224 54.545 0.00 0.00 0.00 3.61
1753 2026 1.770658 CCTATGCCAGTCCATCTCCAA 59.229 52.381 0.00 0.00 0.00 3.53
1754 2027 1.344393 ACCTATGCCAGTCCATCTCCA 60.344 52.381 0.00 0.00 0.00 3.86
1755 2028 1.071385 CACCTATGCCAGTCCATCTCC 59.929 57.143 0.00 0.00 0.00 3.71
1756 2029 1.071385 CCACCTATGCCAGTCCATCTC 59.929 57.143 0.00 0.00 0.00 2.75
1757 2030 1.135094 CCACCTATGCCAGTCCATCT 58.865 55.000 0.00 0.00 0.00 2.90
1758 2031 0.839946 ACCACCTATGCCAGTCCATC 59.160 55.000 0.00 0.00 0.00 3.51
1759 2032 0.548031 CACCACCTATGCCAGTCCAT 59.452 55.000 0.00 0.00 0.00 3.41
1760 2033 1.561769 CCACCACCTATGCCAGTCCA 61.562 60.000 0.00 0.00 0.00 4.02
1761 2034 1.224592 CCACCACCTATGCCAGTCC 59.775 63.158 0.00 0.00 0.00 3.85
1762 2035 0.107654 GACCACCACCTATGCCAGTC 60.108 60.000 0.00 0.00 0.00 3.51
1763 2036 1.899437 CGACCACCACCTATGCCAGT 61.899 60.000 0.00 0.00 0.00 4.00
1764 2037 1.153369 CGACCACCACCTATGCCAG 60.153 63.158 0.00 0.00 0.00 4.85
1765 2038 1.485294 AACGACCACCACCTATGCCA 61.485 55.000 0.00 0.00 0.00 4.92
1766 2039 0.538118 TAACGACCACCACCTATGCC 59.462 55.000 0.00 0.00 0.00 4.40
1767 2040 2.614829 ATAACGACCACCACCTATGC 57.385 50.000 0.00 0.00 0.00 3.14
1768 2041 3.625764 CCAAATAACGACCACCACCTATG 59.374 47.826 0.00 0.00 0.00 2.23
1769 2042 3.881220 CCAAATAACGACCACCACCTAT 58.119 45.455 0.00 0.00 0.00 2.57
1770 2043 2.616001 GCCAAATAACGACCACCACCTA 60.616 50.000 0.00 0.00 0.00 3.08
1771 2044 1.884928 GCCAAATAACGACCACCACCT 60.885 52.381 0.00 0.00 0.00 4.00
1772 2045 0.524414 GCCAAATAACGACCACCACC 59.476 55.000 0.00 0.00 0.00 4.61
1773 2046 0.167251 CGCCAAATAACGACCACCAC 59.833 55.000 0.00 0.00 0.00 4.16
1774 2047 0.250381 ACGCCAAATAACGACCACCA 60.250 50.000 0.00 0.00 0.00 4.17
1775 2048 0.445043 GACGCCAAATAACGACCACC 59.555 55.000 0.00 0.00 0.00 4.61
1776 2049 1.149987 TGACGCCAAATAACGACCAC 58.850 50.000 0.00 0.00 0.00 4.16
1777 2050 1.735018 CATGACGCCAAATAACGACCA 59.265 47.619 0.00 0.00 0.00 4.02
1778 2051 1.063469 CCATGACGCCAAATAACGACC 59.937 52.381 0.00 0.00 0.00 4.79
1779 2052 1.735571 ACCATGACGCCAAATAACGAC 59.264 47.619 0.00 0.00 0.00 4.34
1780 2053 1.735018 CACCATGACGCCAAATAACGA 59.265 47.619 0.00 0.00 0.00 3.85
1781 2054 1.202132 CCACCATGACGCCAAATAACG 60.202 52.381 0.00 0.00 0.00 3.18
1782 2055 1.469079 GCCACCATGACGCCAAATAAC 60.469 52.381 0.00 0.00 0.00 1.89
1783 2056 0.814457 GCCACCATGACGCCAAATAA 59.186 50.000 0.00 0.00 0.00 1.40
1784 2057 1.372838 CGCCACCATGACGCCAAATA 61.373 55.000 0.00 0.00 0.00 1.40
1785 2058 2.699768 CGCCACCATGACGCCAAAT 61.700 57.895 0.00 0.00 0.00 2.32
1786 2059 3.361158 CGCCACCATGACGCCAAA 61.361 61.111 0.00 0.00 0.00 3.28
1787 2060 4.634703 ACGCCACCATGACGCCAA 62.635 61.111 0.00 0.00 0.00 4.52
1791 2064 2.202743 ATCGACGCCACCATGACG 60.203 61.111 0.00 0.00 0.00 4.35
1792 2065 2.173669 CCATCGACGCCACCATGAC 61.174 63.158 0.00 0.00 0.00 3.06
1793 2066 2.186644 CCATCGACGCCACCATGA 59.813 61.111 0.00 0.00 0.00 3.07
1794 2067 3.576356 GCCATCGACGCCACCATG 61.576 66.667 0.00 0.00 0.00 3.66
1801 2074 4.508128 TTCCTCCGCCATCGACGC 62.508 66.667 0.00 0.00 38.10 5.19
1802 2075 2.582498 GTTCCTCCGCCATCGACG 60.582 66.667 0.00 0.00 38.10 5.12
1803 2076 2.202892 GGTTCCTCCGCCATCGAC 60.203 66.667 0.00 0.00 38.10 4.20
1804 2077 2.363795 AGGTTCCTCCGCCATCGA 60.364 61.111 0.00 0.00 41.99 3.59
1805 2078 2.202932 CAGGTTCCTCCGCCATCG 60.203 66.667 0.00 0.00 41.99 3.84
1806 2079 2.514824 GCAGGTTCCTCCGCCATC 60.515 66.667 0.00 0.00 41.99 3.51
1807 2080 4.115199 GGCAGGTTCCTCCGCCAT 62.115 66.667 13.22 0.00 46.89 4.40
1810 2083 2.747855 CTTGGCAGGTTCCTCCGC 60.748 66.667 0.00 0.00 41.99 5.54
1811 2084 2.045926 CCTTGGCAGGTTCCTCCG 60.046 66.667 0.00 0.00 41.99 4.63
1828 2101 4.894784 TCAGAACAGATTGAGGTACCAAC 58.105 43.478 15.94 8.42 0.00 3.77
1829 2102 5.306937 TCTTCAGAACAGATTGAGGTACCAA 59.693 40.000 15.94 0.02 0.00 3.67
1830 2103 4.838423 TCTTCAGAACAGATTGAGGTACCA 59.162 41.667 15.94 0.00 0.00 3.25
1831 2104 5.407407 TCTTCAGAACAGATTGAGGTACC 57.593 43.478 2.73 2.73 0.00 3.34
1832 2105 5.814705 CCATCTTCAGAACAGATTGAGGTAC 59.185 44.000 0.00 0.00 0.00 3.34
1833 2106 5.721480 TCCATCTTCAGAACAGATTGAGGTA 59.279 40.000 0.00 0.00 0.00 3.08
1834 2107 4.533707 TCCATCTTCAGAACAGATTGAGGT 59.466 41.667 0.00 0.00 0.00 3.85
1835 2108 4.874966 GTCCATCTTCAGAACAGATTGAGG 59.125 45.833 0.00 0.00 0.00 3.86
1836 2109 5.485620 TGTCCATCTTCAGAACAGATTGAG 58.514 41.667 0.00 0.00 0.00 3.02
1837 2110 5.488262 TGTCCATCTTCAGAACAGATTGA 57.512 39.130 0.00 0.00 0.00 2.57
1838 2111 5.704515 ACTTGTCCATCTTCAGAACAGATTG 59.295 40.000 0.00 0.00 0.00 2.67
1839 2112 5.874093 ACTTGTCCATCTTCAGAACAGATT 58.126 37.500 0.00 0.00 0.00 2.40
1840 2113 5.495926 ACTTGTCCATCTTCAGAACAGAT 57.504 39.130 0.00 0.00 0.00 2.90
1841 2114 4.963318 ACTTGTCCATCTTCAGAACAGA 57.037 40.909 0.00 0.00 0.00 3.41
1842 2115 6.030548 TCTACTTGTCCATCTTCAGAACAG 57.969 41.667 0.00 0.00 0.00 3.16
1843 2116 6.267699 TCTTCTACTTGTCCATCTTCAGAACA 59.732 38.462 0.00 0.00 0.00 3.18
1844 2117 6.692486 TCTTCTACTTGTCCATCTTCAGAAC 58.308 40.000 0.00 0.00 0.00 3.01
1845 2118 6.918067 TCTTCTACTTGTCCATCTTCAGAA 57.082 37.500 0.00 0.00 0.00 3.02
1846 2119 6.127225 CCATCTTCTACTTGTCCATCTTCAGA 60.127 42.308 0.00 0.00 0.00 3.27
1847 2120 6.047870 CCATCTTCTACTTGTCCATCTTCAG 58.952 44.000 0.00 0.00 0.00 3.02
1848 2121 5.485353 ACCATCTTCTACTTGTCCATCTTCA 59.515 40.000 0.00 0.00 0.00 3.02
1849 2122 5.814705 CACCATCTTCTACTTGTCCATCTTC 59.185 44.000 0.00 0.00 0.00 2.87
1850 2123 5.485353 TCACCATCTTCTACTTGTCCATCTT 59.515 40.000 0.00 0.00 0.00 2.40
1851 2124 5.026121 TCACCATCTTCTACTTGTCCATCT 58.974 41.667 0.00 0.00 0.00 2.90
1852 2125 5.344743 TCACCATCTTCTACTTGTCCATC 57.655 43.478 0.00 0.00 0.00 3.51
1853 2126 5.426509 TCATCACCATCTTCTACTTGTCCAT 59.573 40.000 0.00 0.00 0.00 3.41
1854 2127 4.777366 TCATCACCATCTTCTACTTGTCCA 59.223 41.667 0.00 0.00 0.00 4.02
1855 2128 5.112686 GTCATCACCATCTTCTACTTGTCC 58.887 45.833 0.00 0.00 0.00 4.02
1856 2129 5.724328 TGTCATCACCATCTTCTACTTGTC 58.276 41.667 0.00 0.00 0.00 3.18
1857 2130 5.745312 TGTCATCACCATCTTCTACTTGT 57.255 39.130 0.00 0.00 0.00 3.16
1858 2131 5.934043 TGTTGTCATCACCATCTTCTACTTG 59.066 40.000 0.00 0.00 0.00 3.16
1859 2132 5.934625 GTGTTGTCATCACCATCTTCTACTT 59.065 40.000 3.04 0.00 0.00 2.24
1860 2133 5.012046 TGTGTTGTCATCACCATCTTCTACT 59.988 40.000 10.78 0.00 35.25 2.57
1861 2134 5.237815 TGTGTTGTCATCACCATCTTCTAC 58.762 41.667 10.78 0.00 35.25 2.59
1862 2135 5.482163 TGTGTTGTCATCACCATCTTCTA 57.518 39.130 10.78 0.00 35.25 2.10
1863 2136 4.356405 TGTGTTGTCATCACCATCTTCT 57.644 40.909 10.78 0.00 35.25 2.85
1864 2137 4.456911 ACATGTGTTGTCATCACCATCTTC 59.543 41.667 10.78 0.00 30.89 2.87
1865 2138 4.216902 CACATGTGTTGTCATCACCATCTT 59.783 41.667 18.03 0.00 36.00 2.40
1866 2139 3.754850 CACATGTGTTGTCATCACCATCT 59.245 43.478 18.03 0.00 36.00 2.90
1867 2140 3.752747 TCACATGTGTTGTCATCACCATC 59.247 43.478 24.63 0.00 36.00 3.51
1868 2141 3.753815 TCACATGTGTTGTCATCACCAT 58.246 40.909 24.63 3.38 36.00 3.55
1869 2142 3.140623 CTCACATGTGTTGTCATCACCA 58.859 45.455 24.63 0.63 36.00 4.17
1870 2143 3.058708 CACTCACATGTGTTGTCATCACC 60.059 47.826 24.63 0.00 36.00 4.02
1871 2144 4.137849 CACTCACATGTGTTGTCATCAC 57.862 45.455 24.63 7.03 36.00 3.06
1882 2155 1.895798 AGATCCGACACACTCACATGT 59.104 47.619 0.00 0.00 0.00 3.21
1883 2156 2.662006 AGATCCGACACACTCACATG 57.338 50.000 0.00 0.00 0.00 3.21
1884 2157 2.300152 ACAAGATCCGACACACTCACAT 59.700 45.455 0.00 0.00 0.00 3.21
1885 2158 1.686587 ACAAGATCCGACACACTCACA 59.313 47.619 0.00 0.00 0.00 3.58
1886 2159 2.061773 CACAAGATCCGACACACTCAC 58.938 52.381 0.00 0.00 0.00 3.51
1887 2160 1.960689 TCACAAGATCCGACACACTCA 59.039 47.619 0.00 0.00 0.00 3.41
1888 2161 2.724977 TCACAAGATCCGACACACTC 57.275 50.000 0.00 0.00 0.00 3.51
1889 2162 2.868044 GCTTCACAAGATCCGACACACT 60.868 50.000 0.00 0.00 0.00 3.55
1890 2163 1.461127 GCTTCACAAGATCCGACACAC 59.539 52.381 0.00 0.00 0.00 3.82
1891 2164 1.069978 TGCTTCACAAGATCCGACACA 59.930 47.619 0.00 0.00 0.00 3.72
1892 2165 1.795768 TGCTTCACAAGATCCGACAC 58.204 50.000 0.00 0.00 0.00 3.67
1893 2166 2.542020 TTGCTTCACAAGATCCGACA 57.458 45.000 0.00 0.00 33.24 4.35
1894 2167 4.425577 AAATTGCTTCACAAGATCCGAC 57.574 40.909 0.00 0.00 42.87 4.79
1895 2168 5.647658 ACATAAATTGCTTCACAAGATCCGA 59.352 36.000 0.00 0.00 42.87 4.55
1896 2169 5.740569 CACATAAATTGCTTCACAAGATCCG 59.259 40.000 0.00 0.00 42.87 4.18
1897 2170 6.624423 ACACATAAATTGCTTCACAAGATCC 58.376 36.000 0.00 0.00 42.87 3.36
1898 2171 7.533426 AGACACATAAATTGCTTCACAAGATC 58.467 34.615 0.00 0.00 42.87 2.75
1899 2172 7.458409 AGACACATAAATTGCTTCACAAGAT 57.542 32.000 0.00 0.00 42.87 2.40
1900 2173 6.882610 AGACACATAAATTGCTTCACAAGA 57.117 33.333 0.00 0.00 42.87 3.02
1901 2174 7.648908 TGAAAGACACATAAATTGCTTCACAAG 59.351 33.333 0.00 0.00 42.87 3.16
1902 2175 7.487484 TGAAAGACACATAAATTGCTTCACAA 58.513 30.769 0.00 0.00 44.01 3.33
1903 2176 7.036996 TGAAAGACACATAAATTGCTTCACA 57.963 32.000 0.00 0.00 0.00 3.58
1904 2177 7.928908 TTGAAAGACACATAAATTGCTTCAC 57.071 32.000 0.00 0.00 0.00 3.18
1905 2178 8.939201 TTTTGAAAGACACATAAATTGCTTCA 57.061 26.923 0.00 0.00 0.00 3.02
1932 2205 9.618890 TGCTTGCACTAGAAATAAGAGATTAAT 57.381 29.630 0.00 0.00 0.00 1.40
1933 2206 9.618890 ATGCTTGCACTAGAAATAAGAGATTAA 57.381 29.630 0.00 0.00 0.00 1.40
1934 2207 9.049523 CATGCTTGCACTAGAAATAAGAGATTA 57.950 33.333 0.00 0.00 0.00 1.75
1935 2208 7.013083 CCATGCTTGCACTAGAAATAAGAGATT 59.987 37.037 0.00 0.00 0.00 2.40
1936 2209 6.485984 CCATGCTTGCACTAGAAATAAGAGAT 59.514 38.462 0.00 0.00 0.00 2.75
1937 2210 5.819379 CCATGCTTGCACTAGAAATAAGAGA 59.181 40.000 0.00 0.00 0.00 3.10
1938 2211 5.819379 TCCATGCTTGCACTAGAAATAAGAG 59.181 40.000 0.00 0.00 0.00 2.85
1939 2212 5.744171 TCCATGCTTGCACTAGAAATAAGA 58.256 37.500 0.00 0.00 0.00 2.10
1940 2213 6.485984 AGATCCATGCTTGCACTAGAAATAAG 59.514 38.462 0.00 0.00 0.00 1.73
1941 2214 6.359804 AGATCCATGCTTGCACTAGAAATAA 58.640 36.000 0.00 0.00 0.00 1.40
1942 2215 5.933617 AGATCCATGCTTGCACTAGAAATA 58.066 37.500 0.00 0.00 0.00 1.40
1943 2216 4.789807 AGATCCATGCTTGCACTAGAAAT 58.210 39.130 0.00 0.00 0.00 2.17
1944 2217 4.226427 AGATCCATGCTTGCACTAGAAA 57.774 40.909 0.00 0.00 0.00 2.52
1945 2218 3.920231 AGATCCATGCTTGCACTAGAA 57.080 42.857 0.00 0.00 0.00 2.10
1946 2219 3.054875 ACAAGATCCATGCTTGCACTAGA 60.055 43.478 10.42 0.00 45.00 2.43
1947 2220 3.064958 CACAAGATCCATGCTTGCACTAG 59.935 47.826 10.42 0.00 45.00 2.57
1948 2221 3.011818 CACAAGATCCATGCTTGCACTA 58.988 45.455 10.42 0.00 45.00 2.74
1949 2222 1.816835 CACAAGATCCATGCTTGCACT 59.183 47.619 10.42 0.00 45.00 4.40
1950 2223 1.542915 ACACAAGATCCATGCTTGCAC 59.457 47.619 10.42 0.00 45.00 4.57
1951 2224 1.913778 ACACAAGATCCATGCTTGCA 58.086 45.000 10.42 0.00 45.00 4.08
1952 2225 2.223433 GCTACACAAGATCCATGCTTGC 60.223 50.000 10.42 0.00 45.00 4.01
1953 2226 3.011818 TGCTACACAAGATCCATGCTTG 58.988 45.455 9.28 9.28 46.20 4.01
1954 2227 3.354948 TGCTACACAAGATCCATGCTT 57.645 42.857 0.00 0.00 0.00 3.91
1955 2228 3.354948 TTGCTACACAAGATCCATGCT 57.645 42.857 0.00 0.00 33.24 3.79
1956 2229 4.644103 AATTGCTACACAAGATCCATGC 57.356 40.909 0.00 0.00 42.87 4.06
1957 2230 7.646526 CACATAAATTGCTACACAAGATCCATG 59.353 37.037 0.00 0.00 42.87 3.66
1958 2231 7.340232 ACACATAAATTGCTACACAAGATCCAT 59.660 33.333 0.00 0.00 42.87 3.41
1959 2232 6.658816 ACACATAAATTGCTACACAAGATCCA 59.341 34.615 0.00 0.00 42.87 3.41
1960 2233 7.066284 AGACACATAAATTGCTACACAAGATCC 59.934 37.037 0.00 0.00 42.87 3.36
1961 2234 7.978982 AGACACATAAATTGCTACACAAGATC 58.021 34.615 0.00 0.00 42.87 2.75
1962 2235 7.928307 AGACACATAAATTGCTACACAAGAT 57.072 32.000 0.00 0.00 42.87 2.40
1963 2236 7.744087 AAGACACATAAATTGCTACACAAGA 57.256 32.000 0.00 0.00 42.87 3.02
1964 2237 8.075574 TGAAAGACACATAAATTGCTACACAAG 58.924 33.333 0.00 0.00 42.87 3.16
1965 2238 7.935520 TGAAAGACACATAAATTGCTACACAA 58.064 30.769 0.00 0.00 44.01 3.33
1966 2239 7.503521 TGAAAGACACATAAATTGCTACACA 57.496 32.000 0.00 0.00 0.00 3.72
1967 2240 8.690840 GTTTGAAAGACACATAAATTGCTACAC 58.309 33.333 0.00 0.00 0.00 2.90
1968 2241 8.409371 TGTTTGAAAGACACATAAATTGCTACA 58.591 29.630 0.00 0.00 0.00 2.74
1969 2242 8.795786 TGTTTGAAAGACACATAAATTGCTAC 57.204 30.769 0.00 0.00 0.00 3.58
1970 2243 9.979578 AATGTTTGAAAGACACATAAATTGCTA 57.020 25.926 0.00 0.00 0.00 3.49
1971 2244 8.891671 AATGTTTGAAAGACACATAAATTGCT 57.108 26.923 0.00 0.00 0.00 3.91
1980 2253 9.772973 ACTGTAGTATAATGTTTGAAAGACACA 57.227 29.630 0.00 0.00 0.00 3.72
2013 2286 9.874205 CAAACACAATTTCCATAATGAGGTATT 57.126 29.630 0.00 0.00 0.00 1.89
2014 2287 9.253832 TCAAACACAATTTCCATAATGAGGTAT 57.746 29.630 0.00 0.00 0.00 2.73
2015 2288 8.519526 GTCAAACACAATTTCCATAATGAGGTA 58.480 33.333 0.00 0.00 0.00 3.08
2016 2289 7.233348 AGTCAAACACAATTTCCATAATGAGGT 59.767 33.333 0.00 0.00 0.00 3.85
2017 2290 7.605449 AGTCAAACACAATTTCCATAATGAGG 58.395 34.615 0.00 0.00 0.00 3.86
2018 2291 9.778993 CTAGTCAAACACAATTTCCATAATGAG 57.221 33.333 0.00 0.00 0.00 2.90
2019 2292 9.295825 ACTAGTCAAACACAATTTCCATAATGA 57.704 29.630 0.00 0.00 0.00 2.57
2022 2295 9.562408 TGTACTAGTCAAACACAATTTCCATAA 57.438 29.630 0.00 0.00 0.00 1.90
2023 2296 9.562408 TTGTACTAGTCAAACACAATTTCCATA 57.438 29.630 0.00 0.00 0.00 2.74
2024 2297 8.458573 TTGTACTAGTCAAACACAATTTCCAT 57.541 30.769 0.00 0.00 0.00 3.41
2025 2298 7.867305 TTGTACTAGTCAAACACAATTTCCA 57.133 32.000 0.00 0.00 0.00 3.53
2026 2299 9.180678 CATTTGTACTAGTCAAACACAATTTCC 57.819 33.333 17.21 0.00 37.56 3.13
2027 2300 8.690840 GCATTTGTACTAGTCAAACACAATTTC 58.309 33.333 17.21 4.40 37.56 2.17
2028 2301 7.651704 GGCATTTGTACTAGTCAAACACAATTT 59.348 33.333 17.21 4.88 37.56 1.82
2029 2302 7.145323 GGCATTTGTACTAGTCAAACACAATT 58.855 34.615 17.21 8.87 37.56 2.32
2030 2303 6.294508 GGGCATTTGTACTAGTCAAACACAAT 60.295 38.462 17.21 9.24 37.56 2.71
2031 2304 5.009210 GGGCATTTGTACTAGTCAAACACAA 59.991 40.000 17.21 11.66 37.56 3.33
2032 2305 4.517453 GGGCATTTGTACTAGTCAAACACA 59.483 41.667 17.21 6.91 37.56 3.72
2033 2306 4.378046 CGGGCATTTGTACTAGTCAAACAC 60.378 45.833 17.21 13.43 37.56 3.32
2034 2307 3.749088 CGGGCATTTGTACTAGTCAAACA 59.251 43.478 17.21 7.53 37.56 2.83
2035 2308 3.749609 ACGGGCATTTGTACTAGTCAAAC 59.250 43.478 17.21 5.28 37.56 2.93
2036 2309 3.749088 CACGGGCATTTGTACTAGTCAAA 59.251 43.478 17.19 17.19 38.77 2.69
2037 2310 3.331150 CACGGGCATTTGTACTAGTCAA 58.669 45.455 0.00 0.93 0.00 3.18
2585 2893 0.969149 TGATTGTGACGAGGCTGAGT 59.031 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.