Multiple sequence alignment - TraesCS7D01G357400

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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 TraesCS7D01G357400 chr7D 100.000 3290 0 0 1 3290 460795224 460791935 0.000000e+00 6076.0
1 TraesCS7D01G357400 chr7D 99.462 744 4 0 1 744 530757699 530756956 0.000000e+00 1352.0
2 TraesCS7D01G357400 chr7D 77.676 327 36 20 1549 1856 461142332 461142640 7.300000e-37 165.0
3 TraesCS7D01G357400 chr7D 92.661 109 8 0 2948 3056 460792175 460792067 1.220000e-34 158.0
4 TraesCS7D01G357400 chr7D 92.661 109 8 0 3050 3158 460792277 460792169 1.220000e-34 158.0
5 TraesCS7D01G357400 chr7D 77.116 319 38 24 1549 1856 461130980 461131274 5.690000e-33 152.0
6 TraesCS7D01G357400 chr7D 76.730 318 41 23 1549 1856 460795966 460796260 2.650000e-31 147.0
7 TraesCS7D01G357400 chr7D 92.045 88 6 1 934 1021 461129926 461129840 4.460000e-24 122.0
8 TraesCS7D01G357400 chr7A 86.322 1623 148 36 766 2354 538821938 538823520 0.000000e+00 1700.0
9 TraesCS7D01G357400 chr7A 76.993 439 61 28 330 744 68910520 68910942 7.150000e-52 215.0
10 TraesCS7D01G357400 chr7A 76.947 321 37 24 1552 1860 538807584 538807289 7.360000e-32 148.0
11 TraesCS7D01G357400 chr7B 86.342 1501 121 47 741 2190 483329852 483328385 0.000000e+00 1559.0
12 TraesCS7D01G357400 chr7B 86.044 867 94 18 2199 3056 483327742 483326894 0.000000e+00 905.0
13 TraesCS7D01G357400 chr7B 87.701 374 29 3 1307 1666 483343357 483342987 1.410000e-113 420.0
14 TraesCS7D01G357400 chr7B 86.992 246 26 3 3051 3290 483327002 483326757 4.180000e-69 272.0
15 TraesCS7D01G357400 chr7B 78.414 454 58 27 1418 1856 483329988 483330416 3.260000e-65 259.0
16 TraesCS7D01G357400 chr7B 77.070 314 43 22 1549 1856 483759681 483759971 1.580000e-33 154.0
17 TraesCS7D01G357400 chr7B 96.296 81 3 0 1780 1860 483766105 483766185 2.060000e-27 134.0
18 TraesCS7D01G357400 chr3D 100.000 747 0 0 1 747 346057792 346057046 0.000000e+00 1380.0
19 TraesCS7D01G357400 chr3D 78.680 197 27 12 330 513 529497508 529497314 2.070000e-22 117.0
20 TraesCS7D01G357400 chr6D 98.925 744 8 0 1 744 2161856 2162599 0.000000e+00 1330.0
21 TraesCS7D01G357400 chr3B 95.688 603 22 2 144 745 803188965 803188366 0.000000e+00 966.0
22 TraesCS7D01G357400 chr3B 94.000 150 9 0 1 150 803189198 803189049 9.180000e-56 228.0
23 TraesCS7D01G357400 chr2B 79.091 440 64 18 330 744 787524301 787523865 8.990000e-71 278.0
24 TraesCS7D01G357400 chr1A 79.279 444 56 25 330 744 589120328 589119892 8.990000e-71 278.0
25 TraesCS7D01G357400 chr6A 78.384 458 65 25 330 759 578655048 578655499 1.950000e-67 267.0
26 TraesCS7D01G357400 chr6A 77.273 176 27 9 575 743 593013318 593013487 1.260000e-14 91.6
27 TraesCS7D01G357400 chr2D 81.865 193 25 9 561 744 634584531 634584722 1.580000e-33 154.0
28 TraesCS7D01G357400 chr5D 77.160 162 36 1 458 618 352939454 352939615 3.500000e-15 93.5
29 TraesCS7D01G357400 chr5B 73.009 226 54 6 399 618 415997563 415997787 4.550000e-09 73.1


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 TraesCS7D01G357400 chr7D 460791935 460795224 3289 True 2130.666667 6076 95.107333 1 3290 3 chr7D.!!$R3 3289
1 TraesCS7D01G357400 chr7D 530756956 530757699 743 True 1352.000000 1352 99.462000 1 744 1 chr7D.!!$R2 743
2 TraesCS7D01G357400 chr7A 538821938 538823520 1582 False 1700.000000 1700 86.322000 766 2354 1 chr7A.!!$F2 1588
3 TraesCS7D01G357400 chr7B 483326757 483329852 3095 True 912.000000 1559 86.459333 741 3290 3 chr7B.!!$R2 2549
4 TraesCS7D01G357400 chr3D 346057046 346057792 746 True 1380.000000 1380 100.000000 1 747 1 chr3D.!!$R1 746
5 TraesCS7D01G357400 chr6D 2161856 2162599 743 False 1330.000000 1330 98.925000 1 744 1 chr6D.!!$F1 743
6 TraesCS7D01G357400 chr3B 803188366 803189198 832 True 597.000000 966 94.844000 1 745 2 chr3B.!!$R1 744

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
858 960 0.826715 CATCCTTCCTTCCTCGCTGA 59.173 55.0 0.00 0.0 0.0 4.26 F
1059 1167 0.041312 GGCATAATTACACGCGCTGG 60.041 55.0 5.73 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1864 0.105964 CCACGGGAAGGATGCGATTA 59.894 55.0 0.00 0.0 0.0 1.75 R
2850 3669 0.167908 TTGAACATGAATCGTGCGCC 59.832 50.0 4.18 0.0 0.0 6.53 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
754 846 3.771160 GCCACTGGGTCGACGGAT 61.771 66.667 9.92 0.00 36.17 4.18
765 857 2.537401 GTCGACGGATCCCTTAAACTG 58.463 52.381 6.06 0.00 0.00 3.16
766 858 1.479323 TCGACGGATCCCTTAAACTGG 59.521 52.381 6.06 0.00 0.00 4.00
768 860 2.093869 CGACGGATCCCTTAAACTGGAA 60.094 50.000 6.06 0.00 33.54 3.53
769 861 3.431766 CGACGGATCCCTTAAACTGGAAT 60.432 47.826 6.06 0.00 33.54 3.01
772 864 6.069705 ACGGATCCCTTAAACTGGAATAAA 57.930 37.500 6.06 0.00 33.54 1.40
773 865 6.120220 ACGGATCCCTTAAACTGGAATAAAG 58.880 40.000 6.06 0.00 33.54 1.85
809 903 3.063084 GGCGTCTCTCTCGTGGGT 61.063 66.667 0.00 0.00 0.00 4.51
840 934 2.425592 CTGCAGGTGACGGTTCCA 59.574 61.111 5.57 0.00 0.00 3.53
858 960 0.826715 CATCCTTCCTTCCTCGCTGA 59.173 55.000 0.00 0.00 0.00 4.26
859 961 1.208052 CATCCTTCCTTCCTCGCTGAA 59.792 52.381 0.00 0.00 0.00 3.02
860 962 1.348064 TCCTTCCTTCCTCGCTGAAA 58.652 50.000 0.00 0.00 0.00 2.69
875 977 2.600792 GCTGAAATTATCTGCGGCGAAG 60.601 50.000 12.98 10.94 42.15 3.79
876 978 2.866156 CTGAAATTATCTGCGGCGAAGA 59.134 45.455 21.79 21.79 0.00 2.87
880 982 1.865865 TTATCTGCGGCGAAGATTCC 58.134 50.000 33.54 3.35 35.92 3.01
923 1025 1.549203 AGGCTCGCATTGGTCAAATT 58.451 45.000 0.00 0.00 0.00 1.82
932 1034 4.101942 GCATTGGTCAAATTAAATCGCGA 58.898 39.130 13.09 13.09 0.00 5.87
977 1085 2.894387 GCAGAGGAGATGCCACGC 60.894 66.667 0.00 0.00 40.02 5.34
978 1086 2.584418 CAGAGGAGATGCCACGCG 60.584 66.667 3.53 3.53 40.02 6.01
979 1087 3.842923 AGAGGAGATGCCACGCGG 61.843 66.667 12.47 0.00 40.02 6.46
1059 1167 0.041312 GGCATAATTACACGCGCTGG 60.041 55.000 5.73 0.00 0.00 4.85
1061 1169 1.332904 GCATAATTACACGCGCTGGTC 60.333 52.381 5.73 0.00 0.00 4.02
1110 1218 3.118956 CGTCTTGGATTTCTGCTCTAGGT 60.119 47.826 0.00 0.00 0.00 3.08
1113 1221 4.532126 TCTTGGATTTCTGCTCTAGGTTCA 59.468 41.667 0.00 0.00 0.00 3.18
1253 1365 1.355210 CAACACCTGAAAGCGCGTT 59.645 52.632 8.72 8.72 0.00 4.84
1300 1412 3.312404 GGCAGTTCAGCTGTCTTCA 57.688 52.632 14.67 0.00 45.87 3.02
1301 1413 1.818642 GGCAGTTCAGCTGTCTTCAT 58.181 50.000 14.67 0.00 45.87 2.57
1302 1414 2.977914 GGCAGTTCAGCTGTCTTCATA 58.022 47.619 14.67 0.00 45.87 2.15
1303 1415 2.675348 GGCAGTTCAGCTGTCTTCATAC 59.325 50.000 14.67 2.32 45.87 2.39
1304 1416 3.594134 GCAGTTCAGCTGTCTTCATACT 58.406 45.455 14.67 4.48 46.64 2.12
1305 1417 3.370366 GCAGTTCAGCTGTCTTCATACTG 59.630 47.826 14.67 15.62 46.64 2.74
1306 1418 3.931468 CAGTTCAGCTGTCTTCATACTGG 59.069 47.826 14.67 0.00 40.27 4.00
1307 1419 3.580458 AGTTCAGCTGTCTTCATACTGGT 59.420 43.478 14.67 0.00 32.23 4.00
1308 1420 4.040952 AGTTCAGCTGTCTTCATACTGGTT 59.959 41.667 14.67 0.00 32.23 3.67
1309 1421 4.623932 TCAGCTGTCTTCATACTGGTTT 57.376 40.909 14.67 0.00 32.23 3.27
1322 1434 2.932261 ACTGGTTTCCTTTCGCTTTCT 58.068 42.857 0.00 0.00 0.00 2.52
1323 1435 2.879026 ACTGGTTTCCTTTCGCTTTCTC 59.121 45.455 0.00 0.00 0.00 2.87
1324 1436 3.142174 CTGGTTTCCTTTCGCTTTCTCT 58.858 45.455 0.00 0.00 0.00 3.10
1411 1524 1.675310 CCCGGCAATGCAGTCTTCA 60.675 57.895 7.79 0.00 0.00 3.02
1469 1582 1.133945 GCCTCTTTTCCTCATCCTCCC 60.134 57.143 0.00 0.00 0.00 4.30
1724 1864 3.390280 AGGCTGGTAAGTCTCTGCT 57.610 52.632 0.00 0.00 30.42 4.24
1725 1865 2.534042 AGGCTGGTAAGTCTCTGCTA 57.466 50.000 0.00 0.00 30.42 3.49
1726 1866 2.821437 AGGCTGGTAAGTCTCTGCTAA 58.179 47.619 0.00 0.00 30.42 3.09
1743 1913 0.105964 TAATCGCATCCTTCCCGTGG 59.894 55.000 0.00 0.00 0.00 4.94
1761 1931 2.762327 GTGGATGGCCTTGTTCATGAAT 59.238 45.455 12.12 0.00 34.31 2.57
1762 1932 3.025978 TGGATGGCCTTGTTCATGAATC 58.974 45.455 12.12 6.28 34.31 2.52
1763 1933 3.025978 GGATGGCCTTGTTCATGAATCA 58.974 45.455 12.12 8.83 0.00 2.57
1764 1934 3.640029 GGATGGCCTTGTTCATGAATCAT 59.360 43.478 12.12 8.76 0.00 2.45
1765 1935 4.500887 GGATGGCCTTGTTCATGAATCATG 60.501 45.833 16.63 16.63 42.60 3.07
1796 1966 6.798959 GCTTAACTATGTTTGTCTGCTTCTTG 59.201 38.462 0.00 0.00 0.00 3.02
1814 1984 4.610890 TGTTGTTGCAGCTGCGCG 62.611 61.111 32.11 0.00 45.83 6.86
1875 2045 0.102300 AAGCCAATTTTATCCGCCGC 59.898 50.000 0.00 0.00 0.00 6.53
1927 2097 0.798776 CCTGCTGTTCATCACGGTTC 59.201 55.000 0.00 0.00 33.70 3.62
2040 2212 2.095567 GCAGCACCATTTCTGTGTAGTG 60.096 50.000 0.00 0.00 36.11 2.74
2144 2326 4.154918 ACAATCGCTTCACCTCTTCAATTC 59.845 41.667 0.00 0.00 0.00 2.17
2145 2327 2.337583 TCGCTTCACCTCTTCAATTCG 58.662 47.619 0.00 0.00 0.00 3.34
2153 2335 7.386299 GCTTCACCTCTTCAATTCGTATATGAT 59.614 37.037 0.00 0.00 0.00 2.45
2159 2341 8.226448 CCTCTTCAATTCGTATATGATTTGCTC 58.774 37.037 18.54 0.00 32.17 4.26
2166 2348 6.101650 TCGTATATGATTTGCTCATGGAGT 57.898 37.500 0.00 0.00 44.48 3.85
2183 2365 1.681793 GAGTCATAACCCAGCTCGCTA 59.318 52.381 0.00 0.00 0.00 4.26
2251 3068 3.364889 TGTTGTCTCAAGTCACTACGG 57.635 47.619 0.00 0.00 0.00 4.02
2274 3091 3.292460 ACCGTTTGATTCACCCTTTTGA 58.708 40.909 0.00 0.00 0.00 2.69
2276 3093 4.343814 ACCGTTTGATTCACCCTTTTGAAT 59.656 37.500 0.00 0.00 46.73 2.57
2349 3166 4.481368 TTAGTGATGGCCGAACAACTAT 57.519 40.909 0.00 0.00 0.00 2.12
2383 3200 1.271597 ACTTGACTTGAGACATGCCCC 60.272 52.381 0.00 0.00 0.00 5.80
2438 3255 4.098654 TGTCCAGCTCTAGAAAGACTATGC 59.901 45.833 0.00 0.00 33.72 3.14
2447 3264 4.720649 AGAAAGACTATGCGAGCACTAA 57.279 40.909 0.00 0.00 0.00 2.24
2452 3269 7.436673 AGAAAGACTATGCGAGCACTAAATTAG 59.563 37.037 0.00 0.00 0.00 1.73
2473 3290 3.711190 AGGGCCAAAACCATTGAATATCC 59.289 43.478 6.18 0.00 0.00 2.59
2477 3294 5.351458 GCCAAAACCATTGAATATCCAGTC 58.649 41.667 0.00 0.00 0.00 3.51
2478 3295 5.682212 GCCAAAACCATTGAATATCCAGTCC 60.682 44.000 0.00 0.00 0.00 3.85
2479 3296 5.421693 CCAAAACCATTGAATATCCAGTCCA 59.578 40.000 0.00 0.00 0.00 4.02
2480 3297 6.406177 CCAAAACCATTGAATATCCAGTCCAG 60.406 42.308 0.00 0.00 0.00 3.86
2481 3298 4.443978 ACCATTGAATATCCAGTCCAGG 57.556 45.455 0.00 0.00 0.00 4.45
2482 3299 4.047166 ACCATTGAATATCCAGTCCAGGA 58.953 43.478 0.00 0.00 43.01 3.86
2483 3300 4.103785 ACCATTGAATATCCAGTCCAGGAG 59.896 45.833 0.00 0.00 41.90 3.69
2484 3301 4.349048 CCATTGAATATCCAGTCCAGGAGA 59.651 45.833 0.00 0.00 41.90 3.71
2485 3302 5.512749 CCATTGAATATCCAGTCCAGGAGAG 60.513 48.000 0.00 0.00 41.90 3.20
2486 3303 2.968574 TGAATATCCAGTCCAGGAGAGC 59.031 50.000 0.00 0.00 41.90 4.09
2487 3304 3.238597 GAATATCCAGTCCAGGAGAGCT 58.761 50.000 0.00 0.00 41.90 4.09
2488 3305 2.373335 TATCCAGTCCAGGAGAGCTC 57.627 55.000 5.27 5.27 41.90 4.09
2489 3306 0.636101 ATCCAGTCCAGGAGAGCTCT 59.364 55.000 18.28 18.28 41.90 4.09
2490 3307 0.324183 TCCAGTCCAGGAGAGCTCTG 60.324 60.000 23.91 7.83 32.77 3.35
2496 3313 0.258484 CCAGGAGAGCTCTGAGGAGA 59.742 60.000 23.91 0.00 41.86 3.71
2508 3325 0.884514 TGAGGAGAGCTCTGAACACG 59.115 55.000 23.91 0.00 0.00 4.49
2529 3346 3.016736 GGATAAGTGGATTGTGTGGGTG 58.983 50.000 0.00 0.00 0.00 4.61
2530 3347 3.561313 GGATAAGTGGATTGTGTGGGTGT 60.561 47.826 0.00 0.00 0.00 4.16
2583 3402 5.809562 CCTCACTAATGTCTCAGACACATTC 59.190 44.000 10.48 0.00 45.65 2.67
2584 3403 5.724328 TCACTAATGTCTCAGACACATTCC 58.276 41.667 10.48 0.00 45.65 3.01
2587 3406 2.724977 TGTCTCAGACACATTCCGTC 57.275 50.000 2.36 0.00 37.67 4.79
2589 3408 2.029918 TGTCTCAGACACATTCCGTCAG 60.030 50.000 2.36 0.00 37.67 3.51
2600 3419 4.328440 CACATTCCGTCAGAAGTTGATCTC 59.672 45.833 0.00 0.00 38.07 2.75
2602 3421 1.472878 TCCGTCAGAAGTTGATCTCGG 59.527 52.381 0.00 0.00 41.71 4.63
2621 3440 5.188948 TCTCGGGTTTTCAGGATCAAATCTA 59.811 40.000 0.00 0.00 0.00 1.98
2657 3476 5.941948 ATCAACTTTAAACAAGTCTCCCG 57.058 39.130 0.00 0.00 0.00 5.14
2660 3479 5.648960 TCAACTTTAAACAAGTCTCCCGTTT 59.351 36.000 0.00 0.00 36.79 3.60
2664 3483 6.598850 ACTTTAAACAAGTCTCCCGTTTACAA 59.401 34.615 0.00 0.00 35.45 2.41
2669 3488 2.830104 AGTCTCCCGTTTACAACACAC 58.170 47.619 0.00 0.00 0.00 3.82
2673 3492 4.209911 GTCTCCCGTTTACAACACACTTAC 59.790 45.833 0.00 0.00 0.00 2.34
2688 3507 7.500720 ACACACTTACAAAATAAGTACCACC 57.499 36.000 0.00 0.00 36.14 4.61
2705 3524 9.907229 AAGTACCACCCAAAATTAAAATTTTCA 57.093 25.926 6.72 0.00 44.38 2.69
2711 3530 8.844244 CACCCAAAATTAAAATTTTCATGTGGA 58.156 29.630 20.00 0.00 44.38 4.02
2743 3562 9.984190 CATAGGGGAGTTATTCTTACTAAAGAC 57.016 37.037 0.00 0.00 41.48 3.01
2767 3586 9.677567 GACAATATAACGAAATGTAAATGGCAT 57.322 29.630 0.00 0.00 0.00 4.40
2768 3587 9.462174 ACAATATAACGAAATGTAAATGGCATG 57.538 29.630 0.00 0.00 0.00 4.06
2782 3601 2.630158 TGGCATGGCAATAAACAATGC 58.370 42.857 21.13 0.00 41.82 3.56
2799 3618 4.142534 ACAATGCTGCTTATGTGATCACAC 60.143 41.667 30.09 17.69 45.05 3.82
2818 3637 4.803088 CACACGAAAACATCACACCATTTT 59.197 37.500 0.00 0.00 0.00 1.82
2843 3662 3.921119 TTGCATGTCCATTTGTCACTC 57.079 42.857 0.00 0.00 0.00 3.51
2850 3669 7.012610 TGCATGTCCATTTGTCACTCTATTATG 59.987 37.037 0.00 0.00 0.00 1.90
2852 3671 5.822519 TGTCCATTTGTCACTCTATTATGGC 59.177 40.000 0.00 0.00 32.92 4.40
2866 3685 1.662517 TATGGCGCACGATTCATGTT 58.337 45.000 10.83 0.00 0.00 2.71
2867 3686 0.378257 ATGGCGCACGATTCATGTTC 59.622 50.000 10.83 0.00 0.00 3.18
2868 3687 0.952984 TGGCGCACGATTCATGTTCA 60.953 50.000 10.83 0.00 0.00 3.18
2869 3688 0.167908 GGCGCACGATTCATGTTCAA 59.832 50.000 10.83 0.00 0.00 2.69
2944 3768 4.051237 GTTGAAGCCAAAACTAAAGCAGG 58.949 43.478 0.00 0.00 33.49 4.85
2949 3773 1.893137 CCAAAACTAAAGCAGGGACCC 59.107 52.381 0.59 0.59 0.00 4.46
2950 3774 1.539827 CAAAACTAAAGCAGGGACCCG 59.460 52.381 4.40 1.05 0.00 5.28
2951 3775 0.769247 AAACTAAAGCAGGGACCCGT 59.231 50.000 4.40 0.00 0.00 5.28
2952 3776 1.648116 AACTAAAGCAGGGACCCGTA 58.352 50.000 4.40 0.00 0.00 4.02
2953 3777 1.875488 ACTAAAGCAGGGACCCGTAT 58.125 50.000 4.40 0.00 0.00 3.06
2954 3778 2.193993 ACTAAAGCAGGGACCCGTATT 58.806 47.619 4.40 2.09 0.00 1.89
2955 3779 3.377573 ACTAAAGCAGGGACCCGTATTA 58.622 45.455 4.40 3.19 0.00 0.98
2956 3780 2.704464 AAAGCAGGGACCCGTATTAC 57.296 50.000 4.40 0.00 0.00 1.89
2957 3781 1.575419 AAGCAGGGACCCGTATTACA 58.425 50.000 4.40 0.00 0.00 2.41
2958 3782 1.575419 AGCAGGGACCCGTATTACAA 58.425 50.000 4.40 0.00 0.00 2.41
2959 3783 1.910671 AGCAGGGACCCGTATTACAAA 59.089 47.619 4.40 0.00 0.00 2.83
2960 3784 2.011947 GCAGGGACCCGTATTACAAAC 58.988 52.381 4.40 0.00 0.00 2.93
2961 3785 2.616001 GCAGGGACCCGTATTACAAACA 60.616 50.000 4.40 0.00 0.00 2.83
2962 3786 3.267483 CAGGGACCCGTATTACAAACAG 58.733 50.000 4.40 0.00 0.00 3.16
2963 3787 2.011947 GGGACCCGTATTACAAACAGC 58.988 52.381 0.00 0.00 0.00 4.40
2964 3788 2.616001 GGGACCCGTATTACAAACAGCA 60.616 50.000 0.00 0.00 0.00 4.41
2965 3789 3.275999 GGACCCGTATTACAAACAGCAT 58.724 45.455 0.00 0.00 0.00 3.79
2966 3790 3.692593 GGACCCGTATTACAAACAGCATT 59.307 43.478 0.00 0.00 0.00 3.56
2967 3791 4.877251 GGACCCGTATTACAAACAGCATTA 59.123 41.667 0.00 0.00 0.00 1.90
2968 3792 5.220719 GGACCCGTATTACAAACAGCATTAC 60.221 44.000 0.00 0.00 0.00 1.89
2969 3793 5.493809 ACCCGTATTACAAACAGCATTACT 58.506 37.500 0.00 0.00 0.00 2.24
2970 3794 6.642430 ACCCGTATTACAAACAGCATTACTA 58.358 36.000 0.00 0.00 0.00 1.82
2971 3795 7.104939 ACCCGTATTACAAACAGCATTACTAA 58.895 34.615 0.00 0.00 0.00 2.24
2972 3796 7.771826 ACCCGTATTACAAACAGCATTACTAAT 59.228 33.333 0.00 0.00 0.00 1.73
2973 3797 8.067784 CCCGTATTACAAACAGCATTACTAATG 58.932 37.037 4.61 4.61 41.85 1.90
2974 3798 8.067784 CCGTATTACAAACAGCATTACTAATGG 58.932 37.037 10.24 0.00 39.31 3.16
2975 3799 7.586300 CGTATTACAAACAGCATTACTAATGGC 59.414 37.037 10.24 3.81 39.31 4.40
2976 3800 6.825944 TTACAAACAGCATTACTAATGGCA 57.174 33.333 10.24 0.00 39.31 4.92
2977 3801 5.314923 ACAAACAGCATTACTAATGGCAG 57.685 39.130 10.24 3.56 39.31 4.85
2978 3802 4.766891 ACAAACAGCATTACTAATGGCAGT 59.233 37.500 10.24 0.00 39.31 4.40
2979 3803 5.943416 ACAAACAGCATTACTAATGGCAGTA 59.057 36.000 10.24 0.00 39.31 2.74
2980 3804 6.603201 ACAAACAGCATTACTAATGGCAGTAT 59.397 34.615 10.24 0.00 39.31 2.12
2981 3805 7.122650 ACAAACAGCATTACTAATGGCAGTATT 59.877 33.333 10.24 0.00 39.31 1.89
2982 3806 8.620416 CAAACAGCATTACTAATGGCAGTATTA 58.380 33.333 10.24 0.00 39.31 0.98
2983 3807 8.924511 AACAGCATTACTAATGGCAGTATTAT 57.075 30.769 10.24 0.00 39.31 1.28
2987 3811 9.672673 AGCATTACTAATGGCAGTATTATAAGG 57.327 33.333 10.24 0.00 39.31 2.69
2988 3812 9.449719 GCATTACTAATGGCAGTATTATAAGGT 57.550 33.333 10.24 0.00 39.31 3.50
2990 3814 9.871238 ATTACTAATGGCAGTATTATAAGGTCG 57.129 33.333 0.00 0.00 31.24 4.79
2991 3815 7.299246 ACTAATGGCAGTATTATAAGGTCGT 57.701 36.000 0.00 0.00 0.00 4.34
2992 3816 7.376615 ACTAATGGCAGTATTATAAGGTCGTC 58.623 38.462 0.00 0.00 0.00 4.20
2993 3817 5.801531 ATGGCAGTATTATAAGGTCGTCA 57.198 39.130 0.00 0.00 0.00 4.35
2994 3818 4.940463 TGGCAGTATTATAAGGTCGTCAC 58.060 43.478 0.00 0.00 0.00 3.67
2995 3819 4.403113 TGGCAGTATTATAAGGTCGTCACA 59.597 41.667 0.00 0.00 0.00 3.58
2996 3820 5.105269 TGGCAGTATTATAAGGTCGTCACAA 60.105 40.000 0.00 0.00 0.00 3.33
2997 3821 5.813672 GGCAGTATTATAAGGTCGTCACAAA 59.186 40.000 0.00 0.00 0.00 2.83
2998 3822 6.238022 GGCAGTATTATAAGGTCGTCACAAAC 60.238 42.308 0.00 0.00 0.00 2.93
2999 3823 6.311935 GCAGTATTATAAGGTCGTCACAAACA 59.688 38.462 0.00 0.00 0.00 2.83
3000 3824 7.464178 GCAGTATTATAAGGTCGTCACAAACAG 60.464 40.741 0.00 0.00 0.00 3.16
3001 3825 7.544566 CAGTATTATAAGGTCGTCACAAACAGT 59.455 37.037 0.00 0.00 0.00 3.55
3002 3826 8.092687 AGTATTATAAGGTCGTCACAAACAGTT 58.907 33.333 0.00 0.00 0.00 3.16
3003 3827 6.533819 TTATAAGGTCGTCACAAACAGTTG 57.466 37.500 0.00 0.00 40.84 3.16
3005 3829 2.706890 AGGTCGTCACAAACAGTTGTT 58.293 42.857 0.00 0.00 46.01 2.83
3006 3830 3.078837 AGGTCGTCACAAACAGTTGTTT 58.921 40.909 4.48 4.48 46.01 2.83
3007 3831 3.504520 AGGTCGTCACAAACAGTTGTTTT 59.495 39.130 7.48 0.00 46.01 2.43
3008 3832 3.606346 GGTCGTCACAAACAGTTGTTTTG 59.394 43.478 7.48 9.51 46.01 2.44
3009 3833 4.468643 GTCGTCACAAACAGTTGTTTTGA 58.531 39.130 7.48 11.26 46.01 2.69
3010 3834 4.912766 GTCGTCACAAACAGTTGTTTTGAA 59.087 37.500 7.48 0.92 46.01 2.69
3011 3835 5.399892 GTCGTCACAAACAGTTGTTTTGAAA 59.600 36.000 7.48 5.41 46.01 2.69
3012 3836 5.977725 TCGTCACAAACAGTTGTTTTGAAAA 59.022 32.000 7.48 0.00 46.01 2.29
3013 3837 6.475727 TCGTCACAAACAGTTGTTTTGAAAAA 59.524 30.769 7.48 3.36 46.01 1.94
3028 3852 2.603915 AAAAATTGTGCGTGCCTGC 58.396 47.368 0.00 0.00 0.00 4.85
3029 3853 0.879839 AAAAATTGTGCGTGCCTGCC 60.880 50.000 0.00 0.00 0.00 4.85
3030 3854 2.713927 AAAATTGTGCGTGCCTGCCC 62.714 55.000 0.00 0.00 0.00 5.36
3031 3855 4.666253 ATTGTGCGTGCCTGCCCT 62.666 61.111 0.00 0.00 0.00 5.19
3032 3856 2.762969 AATTGTGCGTGCCTGCCCTA 62.763 55.000 0.00 0.00 0.00 3.53
3033 3857 4.697756 TGTGCGTGCCTGCCCTAC 62.698 66.667 0.00 0.00 0.00 3.18
3034 3858 4.394712 GTGCGTGCCTGCCCTACT 62.395 66.667 0.00 0.00 0.00 2.57
3035 3859 2.682136 TGCGTGCCTGCCCTACTA 60.682 61.111 0.00 0.00 0.00 1.82
3036 3860 2.287274 TGCGTGCCTGCCCTACTAA 61.287 57.895 0.00 0.00 0.00 2.24
3037 3861 1.146263 GCGTGCCTGCCCTACTAAT 59.854 57.895 0.00 0.00 0.00 1.73
3038 3862 0.880718 GCGTGCCTGCCCTACTAATC 60.881 60.000 0.00 0.00 0.00 1.75
3039 3863 0.597637 CGTGCCTGCCCTACTAATCG 60.598 60.000 0.00 0.00 0.00 3.34
3040 3864 0.750850 GTGCCTGCCCTACTAATCGA 59.249 55.000 0.00 0.00 0.00 3.59
3041 3865 1.138266 GTGCCTGCCCTACTAATCGAA 59.862 52.381 0.00 0.00 0.00 3.71
3042 3866 1.412710 TGCCTGCCCTACTAATCGAAG 59.587 52.381 0.00 0.00 0.00 3.79
3043 3867 1.687123 GCCTGCCCTACTAATCGAAGA 59.313 52.381 0.00 0.00 45.75 2.87
3044 3868 2.300437 GCCTGCCCTACTAATCGAAGAT 59.700 50.000 0.00 0.00 45.12 2.40
3045 3869 3.862642 GCCTGCCCTACTAATCGAAGATG 60.863 52.174 0.00 0.00 45.12 2.90
3046 3870 3.574396 CCTGCCCTACTAATCGAAGATGA 59.426 47.826 0.00 0.00 45.12 2.92
3047 3871 4.221703 CCTGCCCTACTAATCGAAGATGAT 59.778 45.833 0.00 0.00 45.12 2.45
3048 3872 5.279708 CCTGCCCTACTAATCGAAGATGATT 60.280 44.000 0.00 0.00 45.12 2.57
3049 3873 5.784177 TGCCCTACTAATCGAAGATGATTC 58.216 41.667 0.00 0.00 45.12 2.52
3050 3874 5.172205 GCCCTACTAATCGAAGATGATTCC 58.828 45.833 0.00 0.00 45.12 3.01
3051 3875 5.725362 CCCTACTAATCGAAGATGATTCCC 58.275 45.833 0.00 0.00 45.12 3.97
3067 3891 7.556275 AGATGATTCCCGTATTACAAACAACAT 59.444 33.333 0.00 0.00 0.00 2.71
3073 3897 9.499479 TTCCCGTATTACAAACAACATTACTAA 57.501 29.630 0.00 0.00 0.00 2.24
3134 3959 0.538516 AATTGTGCGTGGTTGCCCTA 60.539 50.000 0.00 0.00 0.00 3.53
3166 3991 2.039418 TGATTCCCGCATAGCTACACT 58.961 47.619 0.00 0.00 0.00 3.55
3170 3995 2.380941 TCCCGCATAGCTACACTTGTA 58.619 47.619 0.00 0.00 0.00 2.41
3199 4024 7.644490 TGGTACAGTCATTGTTGTCATTTTAC 58.356 34.615 0.00 0.00 41.29 2.01
3212 4037 4.876679 TGTCATTTTACGTTTGGTCAGTGA 59.123 37.500 0.00 0.00 0.00 3.41
3215 4040 4.822036 TTTTACGTTTGGTCAGTGATGG 57.178 40.909 0.00 0.00 0.00 3.51
3275 4105 1.216178 ATTGTCTGCAATTGGGCGC 59.784 52.632 7.72 0.00 42.19 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
747 839 1.479323 TCCAGTTTAAGGGATCCGTCG 59.521 52.381 7.56 0.00 0.00 5.12
748 840 3.622166 TTCCAGTTTAAGGGATCCGTC 57.378 47.619 7.56 0.00 32.15 4.79
749 841 5.703730 TTATTCCAGTTTAAGGGATCCGT 57.296 39.130 5.45 2.61 32.15 4.69
750 842 6.120220 ACTTTATTCCAGTTTAAGGGATCCG 58.880 40.000 5.45 0.00 32.15 4.18
751 843 6.546403 GGACTTTATTCCAGTTTAAGGGATCC 59.454 42.308 1.92 1.92 35.49 3.36
752 844 7.067129 GTGGACTTTATTCCAGTTTAAGGGATC 59.933 40.741 0.00 0.00 46.75 3.36
753 845 6.890268 GTGGACTTTATTCCAGTTTAAGGGAT 59.110 38.462 0.00 0.00 46.75 3.85
754 846 6.243148 GTGGACTTTATTCCAGTTTAAGGGA 58.757 40.000 0.00 0.00 46.75 4.20
765 857 1.022451 TGCCGCGTGGACTTTATTCC 61.022 55.000 21.76 0.00 37.49 3.01
766 858 0.800012 TTGCCGCGTGGACTTTATTC 59.200 50.000 21.76 0.00 37.49 1.75
768 860 0.732571 CATTGCCGCGTGGACTTTAT 59.267 50.000 21.76 0.42 37.49 1.40
769 861 1.302383 CCATTGCCGCGTGGACTTTA 61.302 55.000 21.76 0.00 37.72 1.85
827 921 0.613777 GAAGGATGGAACCGTCACCT 59.386 55.000 13.96 2.10 38.10 4.00
840 934 1.573108 TTCAGCGAGGAAGGAAGGAT 58.427 50.000 0.00 0.00 0.00 3.24
858 960 3.251004 GGAATCTTCGCCGCAGATAATTT 59.749 43.478 0.00 0.00 30.35 1.82
859 961 2.808543 GGAATCTTCGCCGCAGATAATT 59.191 45.455 0.00 0.00 30.35 1.40
860 962 2.037772 AGGAATCTTCGCCGCAGATAAT 59.962 45.455 0.00 0.00 30.35 1.28
899 1001 0.946221 GACCAATGCGAGCCTATCCG 60.946 60.000 0.00 0.00 0.00 4.18
900 1002 0.106708 TGACCAATGCGAGCCTATCC 59.893 55.000 0.00 0.00 0.00 2.59
902 1004 2.418368 TTTGACCAATGCGAGCCTAT 57.582 45.000 0.00 0.00 0.00 2.57
908 1010 4.101942 GCGATTTAATTTGACCAATGCGA 58.898 39.130 0.00 0.00 0.00 5.10
923 1025 2.390938 CAGCTACGGATTCGCGATTTA 58.609 47.619 10.88 0.00 40.63 1.40
932 1034 1.676014 GCAGTTGACCAGCTACGGATT 60.676 52.381 0.00 0.00 0.00 3.01
977 1085 1.300931 ATGCATCGATTCGTCCCCG 60.301 57.895 5.89 0.00 0.00 5.73
978 1086 1.845809 GCATGCATCGATTCGTCCCC 61.846 60.000 14.21 0.00 0.00 4.81
979 1087 1.571460 GCATGCATCGATTCGTCCC 59.429 57.895 14.21 0.00 0.00 4.46
990 1098 2.512286 CTCCGTCGTGGCATGCAT 60.512 61.111 21.36 0.00 37.80 3.96
1059 1167 1.064208 TCGTCTCTGCTAATCGCTGAC 59.936 52.381 0.00 0.00 41.01 3.51
1061 1169 1.471964 GTCGTCTCTGCTAATCGCTG 58.528 55.000 0.00 0.00 40.11 5.18
1064 1172 1.732528 GACGTCGTCTCTGCTAATCG 58.267 55.000 18.09 0.00 0.00 3.34
1110 1218 1.608055 CACCACACCAAGCAGATGAA 58.392 50.000 0.00 0.00 0.00 2.57
1113 1221 0.892358 CAGCACCACACCAAGCAGAT 60.892 55.000 0.00 0.00 0.00 2.90
1152 1262 1.303236 CCGCCATTGGTCCAACTGA 60.303 57.895 6.41 0.00 0.00 3.41
1298 1410 3.695830 AGCGAAAGGAAACCAGTATGA 57.304 42.857 0.00 0.00 39.69 2.15
1299 1411 4.455877 AGAAAGCGAAAGGAAACCAGTATG 59.544 41.667 0.00 0.00 0.00 2.39
1300 1412 4.652822 AGAAAGCGAAAGGAAACCAGTAT 58.347 39.130 0.00 0.00 0.00 2.12
1301 1413 4.062991 GAGAAAGCGAAAGGAAACCAGTA 58.937 43.478 0.00 0.00 0.00 2.74
1302 1414 2.879026 GAGAAAGCGAAAGGAAACCAGT 59.121 45.455 0.00 0.00 0.00 4.00
1303 1415 3.142174 AGAGAAAGCGAAAGGAAACCAG 58.858 45.455 0.00 0.00 0.00 4.00
1304 1416 3.208747 AGAGAAAGCGAAAGGAAACCA 57.791 42.857 0.00 0.00 0.00 3.67
1305 1417 3.815962 AGAAGAGAAAGCGAAAGGAAACC 59.184 43.478 0.00 0.00 0.00 3.27
1306 1418 5.237561 AGAAGAAGAGAAAGCGAAAGGAAAC 59.762 40.000 0.00 0.00 0.00 2.78
1307 1419 5.368989 AGAAGAAGAGAAAGCGAAAGGAAA 58.631 37.500 0.00 0.00 0.00 3.13
1308 1420 4.962155 AGAAGAAGAGAAAGCGAAAGGAA 58.038 39.130 0.00 0.00 0.00 3.36
1309 1421 4.561105 GAGAAGAAGAGAAAGCGAAAGGA 58.439 43.478 0.00 0.00 0.00 3.36
1367 1480 1.943340 GCCTTTATAGGAGCTGCACAC 59.057 52.381 8.35 0.00 45.05 3.82
1394 1507 1.667236 TATGAAGACTGCATTGCCGG 58.333 50.000 0.00 0.00 0.00 6.13
1405 1518 5.310857 AGGGAATGGGTAGGATTATGAAGAC 59.689 44.000 0.00 0.00 0.00 3.01
1411 1524 6.101223 AGATGAAGGGAATGGGTAGGATTAT 58.899 40.000 0.00 0.00 0.00 1.28
1469 1582 3.849911 TGAAGCGATCAAGAACAGTAGG 58.150 45.455 0.00 0.00 34.30 3.18
1568 1705 4.790962 TAGGCCTGCTGCTGCTGC 62.791 66.667 22.51 22.51 40.92 5.25
1569 1706 2.823147 GTAGGCCTGCTGCTGCTG 60.823 66.667 17.99 15.58 40.92 4.41
1723 1863 1.502231 CACGGGAAGGATGCGATTAG 58.498 55.000 0.00 0.00 0.00 1.73
1724 1864 0.105964 CCACGGGAAGGATGCGATTA 59.894 55.000 0.00 0.00 0.00 1.75
1725 1865 1.153168 CCACGGGAAGGATGCGATT 60.153 57.895 0.00 0.00 0.00 3.34
1726 1866 1.410850 ATCCACGGGAAGGATGCGAT 61.411 55.000 0.00 0.00 44.04 4.58
1743 1913 4.340097 TCATGATTCATGAACAAGGCCATC 59.660 41.667 23.72 2.35 46.17 3.51
1761 1931 8.510243 ACAAACATAGTTAAGCATCATCATGA 57.490 30.769 0.00 0.00 30.57 3.07
1762 1932 8.618677 AGACAAACATAGTTAAGCATCATCATG 58.381 33.333 0.00 0.00 0.00 3.07
1763 1933 8.618677 CAGACAAACATAGTTAAGCATCATCAT 58.381 33.333 0.00 0.00 0.00 2.45
1764 1934 7.414429 GCAGACAAACATAGTTAAGCATCATCA 60.414 37.037 0.00 0.00 0.00 3.07
1765 1935 6.909357 GCAGACAAACATAGTTAAGCATCATC 59.091 38.462 0.00 0.00 0.00 2.92
1766 1936 6.600822 AGCAGACAAACATAGTTAAGCATCAT 59.399 34.615 0.00 0.00 0.00 2.45
1767 1937 5.939883 AGCAGACAAACATAGTTAAGCATCA 59.060 36.000 0.00 0.00 0.00 3.07
1777 1947 5.679734 ACACAAGAAGCAGACAAACATAG 57.320 39.130 0.00 0.00 0.00 2.23
1778 1948 5.356751 ACAACACAAGAAGCAGACAAACATA 59.643 36.000 0.00 0.00 0.00 2.29
1859 2029 1.657181 GCGCGGCGGATAAAATTGG 60.657 57.895 25.03 0.00 0.00 3.16
1875 2045 1.202110 ACCACGTATCGTAACTGAGCG 60.202 52.381 0.00 0.00 38.32 5.03
1927 2097 1.153823 GACGTCCGGACTCCACATG 60.154 63.158 30.92 16.47 0.00 3.21
2001 2173 3.427503 GCTGCGCAACCAACAAATAGTAT 60.428 43.478 13.05 0.00 0.00 2.12
2040 2212 3.457234 TCGAGCAACATCACCATGATAC 58.543 45.455 0.00 0.00 34.28 2.24
2108 2285 2.416547 AGCGATTGTTGCACAGTGATAC 59.583 45.455 4.15 1.52 33.85 2.24
2153 2335 3.010027 TGGGTTATGACTCCATGAGCAAA 59.990 43.478 0.00 0.00 38.18 3.68
2159 2341 2.804572 CGAGCTGGGTTATGACTCCATG 60.805 54.545 0.00 0.00 34.31 3.66
2166 2348 0.384309 CGTAGCGAGCTGGGTTATGA 59.616 55.000 5.55 0.00 0.00 2.15
2183 2365 4.714632 CAATAATTGTATCCACCCTCCGT 58.285 43.478 0.00 0.00 0.00 4.69
2248 3065 1.232119 GGTGAATCAAACGGTTCCGT 58.768 50.000 11.27 11.27 45.08 4.69
2251 3068 4.048504 CAAAAGGGTGAATCAAACGGTTC 58.951 43.478 0.00 0.00 0.00 3.62
2274 3091 7.676004 CAACCCTAGTTTTTATCAAACCCATT 58.324 34.615 0.00 0.00 32.45 3.16
2276 3093 5.011227 GCAACCCTAGTTTTTATCAAACCCA 59.989 40.000 0.00 0.00 32.45 4.51
2317 3134 4.452455 CGGCCATCACTAATATGAAACCTC 59.548 45.833 2.24 0.00 30.82 3.85
2349 3166 3.698289 AGTCAAGTATCCTCTCGGAACA 58.302 45.455 0.00 0.00 44.02 3.18
2354 3171 4.396478 TGTCTCAAGTCAAGTATCCTCTCG 59.604 45.833 0.00 0.00 0.00 4.04
2356 3173 5.395103 GCATGTCTCAAGTCAAGTATCCTCT 60.395 44.000 0.00 0.00 0.00 3.69
2383 3200 7.440523 ACAAAGAAAGATACTGTAAAGCCAG 57.559 36.000 0.00 0.00 38.45 4.85
2413 3230 4.799564 AGTCTTTCTAGAGCTGGACAAG 57.200 45.455 0.00 5.80 0.00 3.16
2418 3235 3.316588 TCGCATAGTCTTTCTAGAGCTGG 59.683 47.826 0.00 0.00 33.98 4.85
2438 3255 2.325583 TGGCCCTAATTTAGTGCTCG 57.674 50.000 10.15 0.00 29.52 5.03
2447 3264 5.777526 ATTCAATGGTTTTGGCCCTAATT 57.222 34.783 0.00 0.00 0.00 1.40
2452 3269 3.454082 TGGATATTCAATGGTTTTGGCCC 59.546 43.478 0.00 0.00 0.00 5.80
2455 3272 5.421693 TGGACTGGATATTCAATGGTTTTGG 59.578 40.000 0.00 0.00 0.00 3.28
2456 3273 6.406177 CCTGGACTGGATATTCAATGGTTTTG 60.406 42.308 0.00 0.00 0.00 2.44
2459 3276 4.478317 TCCTGGACTGGATATTCAATGGTT 59.522 41.667 0.00 0.00 0.00 3.67
2460 3277 4.047166 TCCTGGACTGGATATTCAATGGT 58.953 43.478 0.00 0.00 0.00 3.55
2473 3290 1.105457 CTCAGAGCTCTCCTGGACTG 58.895 60.000 14.96 0.53 32.73 3.51
2477 3294 0.258484 TCTCCTCAGAGCTCTCCTGG 59.742 60.000 14.96 15.71 40.22 4.45
2478 3295 1.683943 CTCTCCTCAGAGCTCTCCTG 58.316 60.000 14.96 3.89 40.00 3.86
2487 3304 2.166829 GTGTTCAGAGCTCTCCTCAGA 58.833 52.381 14.96 4.77 43.31 3.27
2488 3305 1.135431 CGTGTTCAGAGCTCTCCTCAG 60.135 57.143 14.96 1.93 43.31 3.35
2489 3306 0.884514 CGTGTTCAGAGCTCTCCTCA 59.115 55.000 14.96 10.04 43.31 3.86
2490 3307 0.172352 CCGTGTTCAGAGCTCTCCTC 59.828 60.000 14.96 7.41 41.07 3.71
2496 3313 2.093973 CCACTTATCCGTGTTCAGAGCT 60.094 50.000 0.00 0.00 33.07 4.09
2504 3321 3.334691 CACACAATCCACTTATCCGTGT 58.665 45.455 0.00 0.00 36.61 4.49
2508 3325 3.016736 CACCCACACAATCCACTTATCC 58.983 50.000 0.00 0.00 0.00 2.59
2571 3390 3.249091 CTTCTGACGGAATGTGTCTGAG 58.751 50.000 0.00 0.00 42.63 3.35
2573 3392 3.032017 ACTTCTGACGGAATGTGTCTG 57.968 47.619 0.00 0.00 37.26 3.51
2583 3402 1.469940 CCCGAGATCAACTTCTGACGG 60.470 57.143 0.00 0.00 39.67 4.79
2584 3403 1.202582 ACCCGAGATCAACTTCTGACG 59.797 52.381 0.00 0.00 36.69 4.35
2587 3406 4.065088 TGAAAACCCGAGATCAACTTCTG 58.935 43.478 0.00 0.00 0.00 3.02
2589 3408 3.437049 CCTGAAAACCCGAGATCAACTTC 59.563 47.826 0.00 0.00 0.00 3.01
2600 3419 5.590259 ACATAGATTTGATCCTGAAAACCCG 59.410 40.000 0.00 0.00 0.00 5.28
2602 3421 8.506168 TGTACATAGATTTGATCCTGAAAACC 57.494 34.615 0.00 0.00 0.00 3.27
2635 3454 5.374071 ACGGGAGACTTGTTTAAAGTTGAT 58.626 37.500 0.00 0.00 0.00 2.57
2644 3463 4.888038 GTTGTAAACGGGAGACTTGTTT 57.112 40.909 6.64 6.64 36.92 2.83
2660 3479 9.610705 TGGTACTTATTTTGTAAGTGTGTTGTA 57.389 29.630 9.96 0.00 38.16 2.41
2664 3483 6.487668 GGGTGGTACTTATTTTGTAAGTGTGT 59.512 38.462 9.96 0.00 38.16 3.72
2669 3488 9.990360 AATTTTGGGTGGTACTTATTTTGTAAG 57.010 29.630 0.00 0.00 0.00 2.34
2698 3517 7.364939 CCCCTATGAACAATCCACATGAAAATT 60.365 37.037 0.00 0.00 0.00 1.82
2699 3518 6.098695 CCCCTATGAACAATCCACATGAAAAT 59.901 38.462 0.00 0.00 0.00 1.82
2705 3524 3.788142 ACTCCCCTATGAACAATCCACAT 59.212 43.478 0.00 0.00 0.00 3.21
2706 3525 3.189606 ACTCCCCTATGAACAATCCACA 58.810 45.455 0.00 0.00 0.00 4.17
2711 3530 9.004231 AGTAAGAATAACTCCCCTATGAACAAT 57.996 33.333 0.00 0.00 0.00 2.71
2720 3539 8.445361 TTGTCTTTAGTAAGAATAACTCCCCT 57.555 34.615 0.00 0.00 41.86 4.79
2743 3562 8.914654 CCATGCCATTTACATTTCGTTATATTG 58.085 33.333 0.00 0.00 0.00 1.90
2756 3575 5.411831 TGTTTATTGCCATGCCATTTACA 57.588 34.783 0.00 0.00 0.00 2.41
2767 3586 3.681593 AAGCAGCATTGTTTATTGCCA 57.318 38.095 0.00 0.00 39.72 4.92
2768 3587 5.005971 CACATAAGCAGCATTGTTTATTGCC 59.994 40.000 0.00 0.00 38.26 4.52
2782 3601 4.926860 TTTCGTGTGATCACATAAGCAG 57.073 40.909 30.10 16.86 43.97 4.24
2799 3618 8.427012 CAATAAGAAAATGGTGTGATGTTTTCG 58.573 33.333 0.00 0.00 42.42 3.46
2801 3620 7.714377 TGCAATAAGAAAATGGTGTGATGTTTT 59.286 29.630 0.00 0.00 0.00 2.43
2807 3626 6.343716 ACATGCAATAAGAAAATGGTGTGA 57.656 33.333 0.00 0.00 0.00 3.58
2818 3637 5.711506 AGTGACAAATGGACATGCAATAAGA 59.288 36.000 0.00 0.00 0.00 2.10
2843 3662 3.433274 ACATGAATCGTGCGCCATAATAG 59.567 43.478 4.18 0.00 0.00 1.73
2850 3669 0.167908 TTGAACATGAATCGTGCGCC 59.832 50.000 4.18 0.00 0.00 6.53
2852 3671 4.495472 GGTAAATTGAACATGAATCGTGCG 59.505 41.667 0.00 0.00 0.00 5.34
2866 3685 2.041081 CTGGTGGGTGGAGGTAAATTGA 59.959 50.000 0.00 0.00 0.00 2.57
2867 3686 2.225017 ACTGGTGGGTGGAGGTAAATTG 60.225 50.000 0.00 0.00 0.00 2.32
2868 3687 2.070573 ACTGGTGGGTGGAGGTAAATT 58.929 47.619 0.00 0.00 0.00 1.82
2869 3688 1.755200 ACTGGTGGGTGGAGGTAAAT 58.245 50.000 0.00 0.00 0.00 1.40
2920 3744 3.181470 TGCTTTAGTTTTGGCTTCAACCC 60.181 43.478 0.00 0.00 0.00 4.11
2944 3768 2.702261 TGCTGTTTGTAATACGGGTCC 58.298 47.619 0.00 0.00 0.00 4.46
2949 3773 7.586300 GCCATTAGTAATGCTGTTTGTAATACG 59.414 37.037 16.17 0.66 37.57 3.06
2950 3774 8.402472 TGCCATTAGTAATGCTGTTTGTAATAC 58.598 33.333 16.17 0.00 37.57 1.89
2951 3775 8.512966 TGCCATTAGTAATGCTGTTTGTAATA 57.487 30.769 16.17 0.00 37.57 0.98
2952 3776 7.122650 ACTGCCATTAGTAATGCTGTTTGTAAT 59.877 33.333 16.17 0.00 37.57 1.89
2953 3777 6.432783 ACTGCCATTAGTAATGCTGTTTGTAA 59.567 34.615 16.17 0.00 37.57 2.41
2954 3778 5.943416 ACTGCCATTAGTAATGCTGTTTGTA 59.057 36.000 16.17 2.19 37.57 2.41
2955 3779 4.766891 ACTGCCATTAGTAATGCTGTTTGT 59.233 37.500 16.17 6.80 37.57 2.83
2956 3780 5.314923 ACTGCCATTAGTAATGCTGTTTG 57.685 39.130 16.17 4.21 37.57 2.93
2957 3781 7.645058 AATACTGCCATTAGTAATGCTGTTT 57.355 32.000 22.20 16.47 36.78 2.83
2958 3782 8.924511 ATAATACTGCCATTAGTAATGCTGTT 57.075 30.769 22.20 14.33 36.78 3.16
2961 3785 9.672673 CCTTATAATACTGCCATTAGTAATGCT 57.327 33.333 16.17 2.57 36.78 3.79
2962 3786 9.449719 ACCTTATAATACTGCCATTAGTAATGC 57.550 33.333 16.17 12.23 36.78 3.56
2964 3788 9.871238 CGACCTTATAATACTGCCATTAGTAAT 57.129 33.333 0.00 0.00 36.78 1.89
2965 3789 8.863086 ACGACCTTATAATACTGCCATTAGTAA 58.137 33.333 0.00 0.00 36.78 2.24
2966 3790 8.413309 ACGACCTTATAATACTGCCATTAGTA 57.587 34.615 0.00 0.00 37.54 1.82
2967 3791 7.014905 TGACGACCTTATAATACTGCCATTAGT 59.985 37.037 0.00 0.00 34.71 2.24
2968 3792 7.328737 GTGACGACCTTATAATACTGCCATTAG 59.671 40.741 0.00 0.00 0.00 1.73
2969 3793 7.149973 GTGACGACCTTATAATACTGCCATTA 58.850 38.462 0.00 0.00 0.00 1.90
2970 3794 5.989777 GTGACGACCTTATAATACTGCCATT 59.010 40.000 0.00 0.00 0.00 3.16
2971 3795 5.069914 TGTGACGACCTTATAATACTGCCAT 59.930 40.000 0.00 0.00 0.00 4.40
2972 3796 4.403113 TGTGACGACCTTATAATACTGCCA 59.597 41.667 0.00 0.00 0.00 4.92
2973 3797 4.940463 TGTGACGACCTTATAATACTGCC 58.060 43.478 0.00 0.00 0.00 4.85
2974 3798 6.311935 TGTTTGTGACGACCTTATAATACTGC 59.688 38.462 0.00 0.00 0.00 4.40
2975 3799 7.544566 ACTGTTTGTGACGACCTTATAATACTG 59.455 37.037 0.00 0.00 0.00 2.74
2976 3800 7.609056 ACTGTTTGTGACGACCTTATAATACT 58.391 34.615 0.00 0.00 0.00 2.12
2977 3801 7.823149 ACTGTTTGTGACGACCTTATAATAC 57.177 36.000 0.00 0.00 0.00 1.89
2978 3802 7.874016 ACAACTGTTTGTGACGACCTTATAATA 59.126 33.333 0.00 0.00 44.66 0.98
2979 3803 6.708949 ACAACTGTTTGTGACGACCTTATAAT 59.291 34.615 0.00 0.00 44.66 1.28
2980 3804 6.050432 ACAACTGTTTGTGACGACCTTATAA 58.950 36.000 0.00 0.00 44.66 0.98
2981 3805 5.603596 ACAACTGTTTGTGACGACCTTATA 58.396 37.500 0.00 0.00 44.66 0.98
2982 3806 4.448210 ACAACTGTTTGTGACGACCTTAT 58.552 39.130 0.00 0.00 44.66 1.73
2983 3807 3.864243 ACAACTGTTTGTGACGACCTTA 58.136 40.909 0.00 0.00 44.66 2.69
2984 3808 2.706890 ACAACTGTTTGTGACGACCTT 58.293 42.857 0.00 0.00 44.66 3.50
2985 3809 2.396590 ACAACTGTTTGTGACGACCT 57.603 45.000 0.00 0.00 44.66 3.85
2986 3810 3.481112 AAACAACTGTTTGTGACGACC 57.519 42.857 7.02 0.00 45.69 4.79
2987 3811 4.468643 TCAAAACAACTGTTTGTGACGAC 58.531 39.130 8.53 0.00 45.69 4.34
2988 3812 4.750952 TCAAAACAACTGTTTGTGACGA 57.249 36.364 8.53 0.00 45.69 4.20
2989 3813 5.814314 TTTCAAAACAACTGTTTGTGACG 57.186 34.783 8.53 0.00 45.69 4.35
3010 3834 0.879839 GGCAGGCACGCACAATTTTT 60.880 50.000 1.26 0.00 0.00 1.94
3011 3835 1.300853 GGCAGGCACGCACAATTTT 60.301 52.632 1.26 0.00 0.00 1.82
3012 3836 2.339712 GGCAGGCACGCACAATTT 59.660 55.556 1.26 0.00 0.00 1.82
3013 3837 2.762969 TAGGGCAGGCACGCACAATT 62.763 55.000 3.92 0.00 37.96 2.32
3014 3838 3.266686 TAGGGCAGGCACGCACAAT 62.267 57.895 3.92 0.00 37.96 2.71
3015 3839 3.947459 TAGGGCAGGCACGCACAA 61.947 61.111 3.92 0.00 37.96 3.33
3016 3840 4.697756 GTAGGGCAGGCACGCACA 62.698 66.667 3.92 0.00 37.96 4.57
3017 3841 2.515996 TTAGTAGGGCAGGCACGCAC 62.516 60.000 0.00 0.00 34.65 5.34
3018 3842 1.622607 ATTAGTAGGGCAGGCACGCA 61.623 55.000 0.00 0.00 0.00 5.24
3019 3843 0.880718 GATTAGTAGGGCAGGCACGC 60.881 60.000 0.00 0.00 0.00 5.34
3020 3844 0.597637 CGATTAGTAGGGCAGGCACG 60.598 60.000 0.00 0.00 0.00 5.34
3021 3845 0.750850 TCGATTAGTAGGGCAGGCAC 59.249 55.000 0.00 0.00 0.00 5.01
3022 3846 1.412710 CTTCGATTAGTAGGGCAGGCA 59.587 52.381 0.00 0.00 0.00 4.75
3023 3847 1.687123 TCTTCGATTAGTAGGGCAGGC 59.313 52.381 0.00 0.00 0.00 4.85
3024 3848 3.574396 TCATCTTCGATTAGTAGGGCAGG 59.426 47.826 0.00 0.00 0.00 4.85
3025 3849 4.855715 TCATCTTCGATTAGTAGGGCAG 57.144 45.455 0.00 0.00 0.00 4.85
3026 3850 5.279506 GGAATCATCTTCGATTAGTAGGGCA 60.280 44.000 0.00 0.00 35.74 5.36
3027 3851 5.172205 GGAATCATCTTCGATTAGTAGGGC 58.828 45.833 0.00 0.00 35.74 5.19
3028 3852 5.622460 CGGGAATCATCTTCGATTAGTAGGG 60.622 48.000 0.00 0.00 35.74 3.53
3029 3853 5.047943 ACGGGAATCATCTTCGATTAGTAGG 60.048 44.000 0.00 0.00 35.74 3.18
3030 3854 6.015027 ACGGGAATCATCTTCGATTAGTAG 57.985 41.667 0.00 0.00 35.74 2.57
3031 3855 7.698506 ATACGGGAATCATCTTCGATTAGTA 57.301 36.000 0.00 0.00 35.74 1.82
3032 3856 4.939052 ACGGGAATCATCTTCGATTAGT 57.061 40.909 0.00 0.00 35.74 2.24
3033 3857 8.027189 TGTAATACGGGAATCATCTTCGATTAG 58.973 37.037 0.00 0.00 35.74 1.73
3034 3858 7.888424 TGTAATACGGGAATCATCTTCGATTA 58.112 34.615 0.00 0.00 35.74 1.75
3035 3859 6.755206 TGTAATACGGGAATCATCTTCGATT 58.245 36.000 0.00 0.00 38.32 3.34
3036 3860 6.340962 TGTAATACGGGAATCATCTTCGAT 57.659 37.500 0.00 0.00 0.00 3.59
3037 3861 5.777850 TGTAATACGGGAATCATCTTCGA 57.222 39.130 0.00 0.00 0.00 3.71
3038 3862 6.256975 TGTTTGTAATACGGGAATCATCTTCG 59.743 38.462 0.00 0.00 0.00 3.79
3039 3863 7.548196 TGTTTGTAATACGGGAATCATCTTC 57.452 36.000 0.00 0.00 0.00 2.87
3040 3864 7.392113 TGTTGTTTGTAATACGGGAATCATCTT 59.608 33.333 0.00 0.00 0.00 2.40
3041 3865 6.882140 TGTTGTTTGTAATACGGGAATCATCT 59.118 34.615 0.00 0.00 0.00 2.90
3042 3866 7.079182 TGTTGTTTGTAATACGGGAATCATC 57.921 36.000 0.00 0.00 0.00 2.92
3043 3867 7.639113 ATGTTGTTTGTAATACGGGAATCAT 57.361 32.000 0.00 0.00 0.00 2.45
3044 3868 7.455641 AATGTTGTTTGTAATACGGGAATCA 57.544 32.000 0.00 0.00 0.00 2.57
3045 3869 8.671028 AGTAATGTTGTTTGTAATACGGGAATC 58.329 33.333 0.00 0.00 0.00 2.52
3046 3870 8.570068 AGTAATGTTGTTTGTAATACGGGAAT 57.430 30.769 0.00 0.00 0.00 3.01
3047 3871 7.982761 AGTAATGTTGTTTGTAATACGGGAA 57.017 32.000 0.00 0.00 0.00 3.97
3048 3872 9.669887 ATTAGTAATGTTGTTTGTAATACGGGA 57.330 29.630 0.00 0.00 0.00 5.14
3049 3873 9.710979 CATTAGTAATGTTGTTTGTAATACGGG 57.289 33.333 13.80 0.00 34.18 5.28
3073 3897 7.058023 TGCCACGACCTTATAATACTAACAT 57.942 36.000 0.00 0.00 0.00 2.71
3077 3901 6.876155 TGTTTGCCACGACCTTATAATACTA 58.124 36.000 0.00 0.00 0.00 1.82
3086 3910 0.738389 CAACTGTTTGCCACGACCTT 59.262 50.000 0.00 0.00 0.00 3.50
3134 3959 3.069586 TGCGGGAATCATCTTCGATTAGT 59.930 43.478 0.00 0.00 35.74 2.24
3166 3991 5.755409 ACAATGACTGTACCATCCTACAA 57.245 39.130 0.00 0.00 36.10 2.41
3170 3995 4.041567 TGACAACAATGACTGTACCATCCT 59.958 41.667 0.00 0.00 37.23 3.24
3187 4012 5.454232 CACTGACCAAACGTAAAATGACAAC 59.546 40.000 0.00 0.00 0.00 3.32
3188 4013 5.354513 TCACTGACCAAACGTAAAATGACAA 59.645 36.000 0.00 0.00 0.00 3.18
3189 4014 4.876679 TCACTGACCAAACGTAAAATGACA 59.123 37.500 0.00 0.00 0.00 3.58
3190 4015 5.412526 TCACTGACCAAACGTAAAATGAC 57.587 39.130 0.00 0.00 0.00 3.06
3191 4016 5.049060 CCATCACTGACCAAACGTAAAATGA 60.049 40.000 0.00 0.00 0.00 2.57
3193 4018 5.067273 TCCATCACTGACCAAACGTAAAAT 58.933 37.500 0.00 0.00 0.00 1.82
3199 4024 2.032030 GTGTTCCATCACTGACCAAACG 60.032 50.000 0.00 0.00 35.68 3.60


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

AutoCloner maintained by Alex Coulton.