Multiple sequence alignment - TraesCS6D01G217100

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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 TraesCS6D01G217100 chr6D 100.000 7222 0 0 1 7222 306719044 306711823 0.000000e+00 13337.0
1 TraesCS6D01G217100 chr6D 90.822 730 52 11 1 721 58834364 58833641 0.000000e+00 963.0
2 TraesCS6D01G217100 chr6D 87.640 89 1 5 3864 3942 277318502 277318590 2.140000e-15 95.3
3 TraesCS6D01G217100 chr6A 94.411 3990 168 31 2367 6330 442404462 442400502 0.000000e+00 6082.0
4 TraesCS6D01G217100 chr6A 92.605 1528 71 15 752 2258 442405969 442404463 0.000000e+00 2158.0
5 TraesCS6D01G217100 chr6A 85.714 651 68 18 6579 7222 442400072 442399440 0.000000e+00 664.0
6 TraesCS6D01G217100 chr6B 93.311 2392 106 25 2077 4448 474191641 474189284 0.000000e+00 3482.0
7 TraesCS6D01G217100 chr6B 94.324 1427 55 12 4443 5867 474189206 474187804 0.000000e+00 2163.0
8 TraesCS6D01G217100 chr6B 85.341 1187 82 50 827 1975 474192766 474191634 0.000000e+00 1144.0
9 TraesCS6D01G217100 chr6B 91.429 770 57 7 5875 6641 474187745 474186982 0.000000e+00 1048.0
10 TraesCS6D01G217100 chr6B 91.132 733 55 8 1 726 523507318 523508047 0.000000e+00 985.0
11 TraesCS6D01G217100 chr6B 89.024 656 39 17 6593 7222 474180225 474179577 0.000000e+00 782.0
12 TraesCS6D01G217100 chr6B 96.629 89 3 0 6493 6581 474183003 474182915 1.620000e-31 148.0
13 TraesCS6D01G217100 chr3D 91.713 724 49 9 1 716 604796353 604795633 0.000000e+00 994.0
14 TraesCS6D01G217100 chr3D 90.934 728 56 8 1 721 607327287 607326563 0.000000e+00 970.0
15 TraesCS6D01G217100 chr4D 91.389 720 48 11 1 711 329141827 329142541 0.000000e+00 974.0
16 TraesCS6D01G217100 chr4D 91.148 723 54 10 1 716 318591833 318592552 0.000000e+00 972.0
17 TraesCS6D01G217100 chr4D 86.517 89 2 3 3864 3942 123308716 123308804 9.980000e-14 89.8
18 TraesCS6D01G217100 chr4D 86.517 89 2 3 3864 3942 123459713 123459625 9.980000e-14 89.8
19 TraesCS6D01G217100 chr1A 91.396 709 53 8 12 716 73810670 73811374 0.000000e+00 965.0
20 TraesCS6D01G217100 chr1A 90.947 718 59 6 1 716 218120455 218121168 0.000000e+00 961.0
21 TraesCS6D01G217100 chr7D 90.884 724 54 9 1 715 51419629 51420349 0.000000e+00 961.0
22 TraesCS6D01G217100 chr7B 81.350 311 36 12 1668 1972 478472387 478472093 4.360000e-57 233.0
23 TraesCS6D01G217100 chrUn 86.517 89 2 3 3864 3942 45118825 45118737 9.980000e-14 89.8
24 TraesCS6D01G217100 chrUn 86.517 89 2 3 3864 3942 441344438 441344350 9.980000e-14 89.8
25 TraesCS6D01G217100 chrUn 85.393 89 3 3 3864 3942 222665690 222665778 4.640000e-12 84.2
26 TraesCS6D01G217100 chr2B 86.022 93 2 4 3864 3945 526477376 526477284 9.980000e-14 89.8


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 TraesCS6D01G217100 chr6D 306711823 306719044 7221 True 13337.000000 13337 100.000000 1 7222 1 chr6D.!!$R2 7221
1 TraesCS6D01G217100 chr6D 58833641 58834364 723 True 963.000000 963 90.822000 1 721 1 chr6D.!!$R1 720
2 TraesCS6D01G217100 chr6A 442399440 442405969 6529 True 2968.000000 6082 90.910000 752 7222 3 chr6A.!!$R1 6470
3 TraesCS6D01G217100 chr6B 474179577 474192766 13189 True 1461.166667 3482 91.676333 827 7222 6 chr6B.!!$R1 6395
4 TraesCS6D01G217100 chr6B 523507318 523508047 729 False 985.000000 985 91.132000 1 726 1 chr6B.!!$F1 725
5 TraesCS6D01G217100 chr3D 604795633 604796353 720 True 994.000000 994 91.713000 1 716 1 chr3D.!!$R1 715
6 TraesCS6D01G217100 chr3D 607326563 607327287 724 True 970.000000 970 90.934000 1 721 1 chr3D.!!$R2 720
7 TraesCS6D01G217100 chr4D 329141827 329142541 714 False 974.000000 974 91.389000 1 711 1 chr4D.!!$F3 710
8 TraesCS6D01G217100 chr4D 318591833 318592552 719 False 972.000000 972 91.148000 1 716 1 chr4D.!!$F2 715
9 TraesCS6D01G217100 chr1A 73810670 73811374 704 False 965.000000 965 91.396000 12 716 1 chr1A.!!$F1 704
10 TraesCS6D01G217100 chr1A 218120455 218121168 713 False 961.000000 961 90.947000 1 716 1 chr1A.!!$F2 715
11 TraesCS6D01G217100 chr7D 51419629 51420349 720 False 961.000000 961 90.884000 1 715 1 chr7D.!!$F1 714

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
824 844 0.326927 GCTGGCCCTACAGTTGGTTA 59.673 55.000 0.00 0.00 40.59 2.85 F
1350 1390 0.033228 TGCTTGCCCCAAATTCGTTG 59.967 50.000 0.00 0.00 36.94 4.10 F
2568 2633 0.187361 AAGTTGTGGCCCCTAGCAAA 59.813 50.000 0.00 0.00 46.50 3.68 F
3021 3089 0.466922 ACTGCTGCCACAAAGCTCTT 60.467 50.000 0.00 0.00 41.42 2.85 F
3112 3180 0.758685 TGCTTGGGAAAACCCAGGTG 60.759 55.000 16.52 9.08 41.27 4.00 F
3616 3689 2.359850 TGTTCATCTGGTGGCCGC 60.360 61.111 8.12 8.12 0.00 6.53 F
5445 5619 2.288579 CGGGCTTGTCAGTTACACTGTA 60.289 50.000 3.87 0.00 46.03 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2753 2820 1.140852 TGGGAGCGAATAAGGGTGATG 59.859 52.381 0.00 0.0 0.00 3.07 R
2755 2822 1.281419 TTGGGAGCGAATAAGGGTGA 58.719 50.000 0.00 0.0 0.00 4.02 R
3810 3884 2.710096 ACACCTAATGCCGCAACTAT 57.290 45.000 0.00 0.0 0.00 2.12 R
4083 4167 3.561725 GGCTTGTCACCATCAATAGCTAC 59.438 47.826 0.00 0.0 0.00 3.58 R
5062 5236 4.392940 CTTCCACCTTCACTTGATCAACT 58.607 43.478 3.38 0.0 0.00 3.16 R
5505 5679 4.142381 ACTTCAAGCACTTCCAACAGTTTC 60.142 41.667 0.00 0.0 0.00 2.78 R
7125 14403 0.247460 TGGCGATCAGACAAGACTGG 59.753 55.000 0.00 0.0 32.75 4.00 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
170 182 5.731957 TTACACTGTAGTTGCCATAGTGA 57.268 39.130 9.39 0.00 40.80 3.41
185 197 8.630054 TGCCATAGTGATTAAACTAAAGTTGT 57.370 30.769 0.00 0.00 38.44 3.32
196 208 2.621055 ACTAAAGTTGTCATGCGGCAAA 59.379 40.909 6.82 0.00 0.00 3.68
212 224 4.556699 GCGGCAAATTTCAGTTTGTAGAGT 60.557 41.667 0.00 0.00 40.38 3.24
327 340 8.976353 TGTATCATGGCAATTTTAGTTTATGGT 58.024 29.630 0.00 0.00 0.00 3.55
339 352 4.192429 AGTTTATGGTTTCATGGCAAGC 57.808 40.909 0.00 0.00 34.96 4.01
361 374 6.129874 AGCCTAGTTTCTTAATTCCCCATTC 58.870 40.000 0.00 0.00 0.00 2.67
454 470 1.551430 ACACCATGGCAATTCATGTGG 59.449 47.619 13.04 0.00 42.02 4.17
461 477 5.245301 CCATGGCAATTCATGTGGAATAGAT 59.755 40.000 0.00 0.00 45.46 1.98
648 668 3.498834 GCATGCGATGTCGTGGCA 61.499 61.111 0.00 4.07 45.88 4.92
677 697 2.037381 TGTGTTATAAGACGTGTGGGCA 59.963 45.455 8.11 0.00 0.00 5.36
688 708 2.032681 GTGGGCAGGTTTCGCTCT 59.967 61.111 0.00 0.00 0.00 4.09
726 746 4.283678 CGTTAGCGTTGTTCAAATGGAAA 58.716 39.130 0.00 0.00 37.23 3.13
727 747 4.735822 CGTTAGCGTTGTTCAAATGGAAAA 59.264 37.500 0.00 0.00 37.23 2.29
728 748 5.230306 CGTTAGCGTTGTTCAAATGGAAAAA 59.770 36.000 0.00 0.00 37.23 1.94
746 766 4.718940 AAAAAGAACACCTTCCACTGTG 57.281 40.909 0.00 0.00 38.44 3.66
747 767 1.680338 AAGAACACCTTCCACTGTGC 58.320 50.000 1.29 0.00 35.90 4.57
748 768 0.839946 AGAACACCTTCCACTGTGCT 59.160 50.000 1.29 0.00 35.90 4.40
749 769 0.947244 GAACACCTTCCACTGTGCTG 59.053 55.000 1.29 0.00 35.90 4.41
750 770 0.466189 AACACCTTCCACTGTGCTGG 60.466 55.000 1.29 6.36 35.90 4.85
790 810 2.203209 CTACCTGGCCGCATTCCC 60.203 66.667 0.00 0.00 0.00 3.97
811 831 3.880846 GCGCATACACAGCTGGCC 61.881 66.667 19.93 0.00 0.00 5.36
813 833 2.273449 GCATACACAGCTGGCCCT 59.727 61.111 19.93 0.00 0.00 5.19
822 842 1.847968 AGCTGGCCCTACAGTTGGT 60.848 57.895 0.00 0.00 40.59 3.67
823 843 1.074951 GCTGGCCCTACAGTTGGTT 59.925 57.895 0.00 0.00 40.59 3.67
824 844 0.326927 GCTGGCCCTACAGTTGGTTA 59.673 55.000 0.00 0.00 40.59 2.85
992 1026 3.213402 GGAGTCGAGGGAGAGCGG 61.213 72.222 0.00 0.00 0.00 5.52
1170 1210 4.421479 CCGCAGCTCTCGTCCGTT 62.421 66.667 4.47 0.00 0.00 4.44
1236 1276 0.600255 CAACCTCAAACTCGCTCCGT 60.600 55.000 0.00 0.00 0.00 4.69
1237 1277 0.963962 AACCTCAAACTCGCTCCGTA 59.036 50.000 0.00 0.00 0.00 4.02
1238 1278 1.183549 ACCTCAAACTCGCTCCGTAT 58.816 50.000 0.00 0.00 0.00 3.06
1239 1279 2.372264 ACCTCAAACTCGCTCCGTATA 58.628 47.619 0.00 0.00 0.00 1.47
1240 1280 2.358267 ACCTCAAACTCGCTCCGTATAG 59.642 50.000 0.00 0.00 0.00 1.31
1242 1282 3.066342 CCTCAAACTCGCTCCGTATAGAA 59.934 47.826 0.00 0.00 0.00 2.10
1243 1283 4.283678 CTCAAACTCGCTCCGTATAGAAG 58.716 47.826 0.00 0.00 0.00 2.85
1245 1285 3.967203 AACTCGCTCCGTATAGAAGAC 57.033 47.619 0.00 0.00 0.00 3.01
1246 1286 3.196939 ACTCGCTCCGTATAGAAGACT 57.803 47.619 0.00 0.00 0.00 3.24
1350 1390 0.033228 TGCTTGCCCCAAATTCGTTG 59.967 50.000 0.00 0.00 36.94 4.10
1386 1426 0.804989 GCGTGTGCTTAAATGCTCCT 59.195 50.000 0.00 0.00 38.39 3.69
1476 1519 2.157863 GCTTAATTCGATAGGAAGCGCC 59.842 50.000 2.29 0.00 38.24 6.53
1508 1551 8.121086 GCGTTTCTGTATTACTTATTTTCTCCC 58.879 37.037 0.00 0.00 0.00 4.30
1513 1556 9.901172 TCTGTATTACTTATTTTCTCCCCTTTC 57.099 33.333 0.00 0.00 0.00 2.62
1519 1562 7.683437 ACTTATTTTCTCCCCTTTCGTTAAG 57.317 36.000 0.00 0.00 0.00 1.85
1553 1596 2.159653 GCGTGCTTTCAATCTCATCGTT 60.160 45.455 0.00 0.00 0.00 3.85
1557 1600 2.789092 GCTTTCAATCTCATCGTTGGCG 60.789 50.000 0.00 0.00 39.92 5.69
1580 1623 5.503683 CGGTAGACAGTAGTTATTGTCCTCG 60.504 48.000 10.14 8.49 41.98 4.63
1610 1653 6.016108 GGGTAGAGTACAGGAGTTGATGTATC 60.016 46.154 0.00 0.00 34.60 2.24
1699 1757 4.466015 GGGATTCACATGGTTTTGGTGTAT 59.534 41.667 0.00 0.00 34.27 2.29
1700 1758 5.654650 GGGATTCACATGGTTTTGGTGTATA 59.345 40.000 0.00 0.00 34.27 1.47
1701 1759 6.323739 GGGATTCACATGGTTTTGGTGTATAT 59.676 38.462 0.00 0.00 34.27 0.86
1702 1760 7.504238 GGGATTCACATGGTTTTGGTGTATATA 59.496 37.037 0.00 0.00 34.27 0.86
1752 1812 6.824305 GCATAGGGCATAATGTCTGTAATT 57.176 37.500 0.00 0.00 43.97 1.40
1764 1824 3.985279 TGTCTGTAATTTCGACTTCACCG 59.015 43.478 0.00 0.00 0.00 4.94
1821 1882 3.622163 GCATCTCCAAGATTCACTGACTG 59.378 47.826 0.00 0.00 31.32 3.51
1829 1890 7.000472 TCCAAGATTCACTGACTGAAAAGAAT 59.000 34.615 0.00 0.00 42.37 2.40
1951 2015 7.161404 TCTCTGCATAAACTGTTACATTCTGT 58.839 34.615 0.00 0.00 0.00 3.41
1994 2058 3.815401 GCCTGTATGCAAAATATCGTCCT 59.185 43.478 0.00 0.00 0.00 3.85
2060 2124 5.163530 TGGCCGATCAATTACTAGTTAACGA 60.164 40.000 0.00 0.00 0.00 3.85
2071 2135 9.715121 AATTACTAGTTAACGATTTCCTGAACA 57.285 29.630 0.00 0.00 0.00 3.18
2150 2214 2.022764 TGCCCACATGTCATTACTCG 57.977 50.000 0.00 0.00 0.00 4.18
2265 2330 9.865321 CTGAATGAATTCTTACATTGTGGAAAT 57.135 29.630 7.05 0.00 36.94 2.17
2272 2337 5.547465 TCTTACATTGTGGAAATCGAGTGT 58.453 37.500 0.00 0.00 0.00 3.55
2346 2411 5.334414 CGATTTTGATACTCTGCTAATGCCC 60.334 44.000 0.00 0.00 38.71 5.36
2354 2419 1.281577 TCTGCTAATGCCCACATGTCA 59.718 47.619 0.00 0.00 36.36 3.58
2355 2420 2.092267 TCTGCTAATGCCCACATGTCAT 60.092 45.455 0.00 0.00 36.36 3.06
2365 2430 4.904853 TGCCCACATGTCATTACTCCTATA 59.095 41.667 0.00 0.00 0.00 1.31
2369 2434 7.448469 GCCCACATGTCATTACTCCTATAAAAT 59.552 37.037 0.00 0.00 0.00 1.82
2391 2456 9.669887 AAAATGTGATAATTGGTTGTTGCATAT 57.330 25.926 0.00 0.00 0.00 1.78
2393 2458 7.401955 TGTGATAATTGGTTGTTGCATATGA 57.598 32.000 6.97 0.00 0.00 2.15
2401 2466 4.821260 TGGTTGTTGCATATGATTCGCTAT 59.179 37.500 6.97 0.00 0.00 2.97
2415 2480 4.471904 TTCGCTATCAATGGTTGAGACT 57.528 40.909 0.00 0.00 43.98 3.24
2416 2481 3.785486 TCGCTATCAATGGTTGAGACTG 58.215 45.455 0.00 0.00 43.98 3.51
2487 2552 3.838565 AGACACCCTGATCTATCACGAT 58.161 45.455 0.00 0.00 32.50 3.73
2499 2564 9.860898 CTGATCTATCACGATTTTGTGGATATA 57.139 33.333 0.00 0.00 40.31 0.86
2526 2591 4.082026 AGCAACACCTCAATTCCATAAAGC 60.082 41.667 0.00 0.00 0.00 3.51
2536 2601 8.133627 CCTCAATTCCATAAAGCAATTAGTCTG 58.866 37.037 0.00 0.00 0.00 3.51
2561 2626 3.224269 TGTAGTAAAAAGTTGTGGCCCC 58.776 45.455 0.00 0.00 0.00 5.80
2568 2633 0.187361 AAGTTGTGGCCCCTAGCAAA 59.813 50.000 0.00 0.00 46.50 3.68
2584 2649 1.408702 GCAAAGCACCAGGTTTCTTGA 59.591 47.619 8.05 0.00 43.10 3.02
2635 2700 4.689612 ACTGTATCTGGTCTTGTTGTGT 57.310 40.909 0.00 0.00 0.00 3.72
2639 2704 1.953559 TCTGGTCTTGTTGTGTGAGC 58.046 50.000 0.00 0.00 0.00 4.26
2685 2751 4.437239 CCACAGTCGAATCAGCTAAATCT 58.563 43.478 0.00 0.00 0.00 2.40
2748 2815 7.053710 AGAACGTCGTAATTAGCCTTAAAAC 57.946 36.000 0.00 0.00 0.00 2.43
2749 2816 6.646240 AGAACGTCGTAATTAGCCTTAAAACA 59.354 34.615 0.00 0.00 0.00 2.83
2750 2817 6.973229 ACGTCGTAATTAGCCTTAAAACAT 57.027 33.333 0.00 0.00 0.00 2.71
2751 2818 6.768078 ACGTCGTAATTAGCCTTAAAACATG 58.232 36.000 0.00 0.00 0.00 3.21
2752 2819 6.591062 ACGTCGTAATTAGCCTTAAAACATGA 59.409 34.615 0.00 0.00 0.00 3.07
2753 2820 6.898189 CGTCGTAATTAGCCTTAAAACATGAC 59.102 38.462 0.00 0.00 0.00 3.06
2754 2821 7.412129 CGTCGTAATTAGCCTTAAAACATGACA 60.412 37.037 0.00 0.00 0.00 3.58
2755 2822 8.395633 GTCGTAATTAGCCTTAAAACATGACAT 58.604 33.333 0.00 0.00 0.00 3.06
2756 2823 8.609176 TCGTAATTAGCCTTAAAACATGACATC 58.391 33.333 0.00 0.00 0.00 3.06
2757 2824 8.394877 CGTAATTAGCCTTAAAACATGACATCA 58.605 33.333 0.00 0.00 0.00 3.07
2758 2825 9.503427 GTAATTAGCCTTAAAACATGACATCAC 57.497 33.333 0.00 0.00 0.00 3.06
2772 2839 1.141053 ACATCACCCTTATTCGCTCCC 59.859 52.381 0.00 0.00 0.00 4.30
2785 2852 1.885887 TCGCTCCCAAAATTTCCACTG 59.114 47.619 0.00 0.00 0.00 3.66
2828 2895 2.874701 GTTGCTGTGATGTCTGACAAGT 59.125 45.455 15.31 0.00 0.00 3.16
2879 2946 7.653767 TTAGTTCTAAAGTCAAGTGCTTAGC 57.346 36.000 0.00 0.00 0.00 3.09
3021 3089 0.466922 ACTGCTGCCACAAAGCTCTT 60.467 50.000 0.00 0.00 41.42 2.85
3052 3120 5.464030 AACTACACGTCCAGACTATTTGT 57.536 39.130 0.04 0.00 0.00 2.83
3112 3180 0.758685 TGCTTGGGAAAACCCAGGTG 60.759 55.000 16.52 9.08 41.27 4.00
3155 3223 5.988310 AATGTGAGAAATCTTCATTGCCA 57.012 34.783 11.28 0.00 33.29 4.92
3179 3247 5.045213 ACAGTTGGTCACCATATACCATTCA 60.045 40.000 0.00 0.00 44.98 2.57
3324 3393 7.856145 ATTGTGATTGTCAGAATTCTACCTC 57.144 36.000 7.86 7.43 37.08 3.85
3391 3460 5.295431 TCTATGCGAATTCCACAAGTTTG 57.705 39.130 0.00 0.00 0.00 2.93
3417 3486 7.255139 GGCTGTTCAAGTTAGTTCTGTTTACAT 60.255 37.037 0.00 0.00 0.00 2.29
3493 3566 8.296713 TGATTTAGTGCTGTTCATTTTTAGGTC 58.703 33.333 0.00 0.00 0.00 3.85
3616 3689 2.359850 TGTTCATCTGGTGGCCGC 60.360 61.111 8.12 8.12 0.00 6.53
3628 3701 3.093057 TGGTGGCCGCTTACATTATTTT 58.907 40.909 17.49 0.00 0.00 1.82
3676 3749 6.610075 TTAGACCGGTAAGGAATACAGTTT 57.390 37.500 7.34 0.00 45.00 2.66
3810 3884 7.392673 AGACCAAGTTCGTATTCTCTACAACTA 59.607 37.037 0.00 0.00 0.00 2.24
3872 3946 9.780186 ATACTTTATTGGTAGTGCTTTCTATCC 57.220 33.333 0.00 0.00 0.00 2.59
4043 4127 4.517285 TCAAAGGAGTTATGCAGTCATCC 58.483 43.478 0.00 0.00 34.22 3.51
4083 4167 2.549064 TGATGCTGGGGAATGTATCG 57.451 50.000 0.00 0.00 0.00 2.92
5193 5367 8.889717 GGTGTATTGTACAAGTACATTATTGCT 58.110 33.333 22.39 5.02 44.54 3.91
5360 5534 2.952978 AGGTAATTTCGTTGTGGTTGCA 59.047 40.909 0.00 0.00 0.00 4.08
5400 5574 5.401376 TGCTTACGTATATCGCTTTGCTTAG 59.599 40.000 0.00 0.00 44.19 2.18
5445 5619 2.288579 CGGGCTTGTCAGTTACACTGTA 60.289 50.000 3.87 0.00 46.03 2.74
5505 5679 4.192317 GGCATAAGTACAGTGAAGAAGGG 58.808 47.826 0.00 0.00 0.00 3.95
5542 5716 1.952621 TGAAGTAAGACCCCCTCCAG 58.047 55.000 0.00 0.00 0.00 3.86
5572 5746 2.611292 CCTGTCGAGCAAATCTTGATCC 59.389 50.000 0.00 0.00 42.82 3.36
5689 5863 2.860136 GTTTGTCCTTGCTGTTGCTTTC 59.140 45.455 0.00 0.00 40.48 2.62
5695 5869 3.188460 TCCTTGCTGTTGCTTTCGAATAC 59.812 43.478 0.00 0.00 40.48 1.89
5696 5870 2.873170 TGCTGTTGCTTTCGAATACG 57.127 45.000 0.00 0.00 40.48 3.06
5697 5871 1.463056 TGCTGTTGCTTTCGAATACGG 59.537 47.619 0.00 1.96 40.48 4.02
5720 5895 6.174049 GGGTCTGTTTATTGAGGGATATAGC 58.826 44.000 0.00 0.00 0.00 2.97
5732 5907 4.493618 AGGGATATAGCCTAGCAAACTCA 58.506 43.478 7.03 0.00 0.00 3.41
5746 5921 3.372206 GCAAACTCACAGTGCTTCGATAT 59.628 43.478 0.00 0.00 35.36 1.63
5748 5923 5.500931 GCAAACTCACAGTGCTTCGATATAC 60.501 44.000 0.00 0.00 35.36 1.47
5751 5926 5.131067 ACTCACAGTGCTTCGATATACCTA 58.869 41.667 0.00 0.00 0.00 3.08
5753 5928 6.013842 TCACAGTGCTTCGATATACCTATG 57.986 41.667 0.00 0.00 0.00 2.23
5754 5929 5.768164 TCACAGTGCTTCGATATACCTATGA 59.232 40.000 0.00 0.00 0.00 2.15
5755 5930 6.434340 TCACAGTGCTTCGATATACCTATGAT 59.566 38.462 0.00 0.00 0.00 2.45
5756 5931 7.610305 TCACAGTGCTTCGATATACCTATGATA 59.390 37.037 0.00 0.00 0.00 2.15
5757 5932 8.244113 CACAGTGCTTCGATATACCTATGATAA 58.756 37.037 0.00 0.00 0.00 1.75
5758 5933 8.803235 ACAGTGCTTCGATATACCTATGATAAA 58.197 33.333 0.00 0.00 0.00 1.40
5759 5934 9.077674 CAGTGCTTCGATATACCTATGATAAAC 57.922 37.037 0.00 0.00 0.00 2.01
5760 5935 7.968956 AGTGCTTCGATATACCTATGATAAACG 59.031 37.037 0.00 0.00 0.00 3.60
5761 5936 7.966753 GTGCTTCGATATACCTATGATAAACGA 59.033 37.037 0.00 0.00 0.00 3.85
5763 5938 9.171701 GCTTCGATATACCTATGATAAACGATC 57.828 37.037 0.00 0.00 34.84 3.69
5767 5942 8.630917 CGATATACCTATGATAAACGATCCCTT 58.369 37.037 0.00 0.00 33.07 3.95
5768 5943 9.751542 GATATACCTATGATAAACGATCCCTTG 57.248 37.037 0.00 0.00 33.07 3.61
5769 5944 7.792364 ATACCTATGATAAACGATCCCTTGA 57.208 36.000 0.00 0.00 33.07 3.02
5770 5945 5.855045 ACCTATGATAAACGATCCCTTGAC 58.145 41.667 0.00 0.00 33.07 3.18
5771 5946 5.365605 ACCTATGATAAACGATCCCTTGACA 59.634 40.000 0.00 0.00 33.07 3.58
5772 5947 6.043243 ACCTATGATAAACGATCCCTTGACAT 59.957 38.462 0.00 0.00 33.07 3.06
5773 5948 6.369890 CCTATGATAAACGATCCCTTGACATG 59.630 42.308 0.00 0.00 33.07 3.21
5774 5949 5.351948 TGATAAACGATCCCTTGACATGA 57.648 39.130 0.00 0.00 33.07 3.07
5775 5950 5.116180 TGATAAACGATCCCTTGACATGAC 58.884 41.667 0.00 0.00 33.07 3.06
5776 5951 3.703001 AAACGATCCCTTGACATGACT 57.297 42.857 0.00 0.00 0.00 3.41
5777 5952 4.819105 AAACGATCCCTTGACATGACTA 57.181 40.909 0.00 0.00 0.00 2.59
5778 5953 4.819105 AACGATCCCTTGACATGACTAA 57.181 40.909 0.00 0.00 0.00 2.24
5779 5954 4.124851 ACGATCCCTTGACATGACTAAC 57.875 45.455 0.00 0.00 0.00 2.34
5780 5955 3.513912 ACGATCCCTTGACATGACTAACA 59.486 43.478 0.00 0.00 0.00 2.41
5781 5956 3.865745 CGATCCCTTGACATGACTAACAC 59.134 47.826 0.00 0.00 0.00 3.32
5785 5960 3.753272 CCCTTGACATGACTAACACTTGG 59.247 47.826 0.00 0.00 0.00 3.61
5871 6046 4.401022 TGAGCCATTTCTAGCCCAATATG 58.599 43.478 0.00 0.00 0.00 1.78
5872 6047 3.160269 AGCCATTTCTAGCCCAATATGC 58.840 45.455 0.00 0.00 0.00 3.14
5873 6048 2.892852 GCCATTTCTAGCCCAATATGCA 59.107 45.455 0.00 0.00 0.00 3.96
5878 6104 6.660521 CCATTTCTAGCCCAATATGCATCTAA 59.339 38.462 0.19 0.00 0.00 2.10
5883 6109 5.972107 AGCCCAATATGCATCTAAACATC 57.028 39.130 0.19 0.00 0.00 3.06
5892 6118 9.445878 AATATGCATCTAAACATCTGTGATAGG 57.554 33.333 0.19 0.00 0.00 2.57
5917 6143 7.278424 GGTTACATTTAGCATTGCACATCATTT 59.722 33.333 11.91 0.00 0.00 2.32
5951 6177 7.715249 AGTTTTCTTTGTAACTATGCAGTGAGA 59.285 33.333 0.00 0.00 34.36 3.27
5954 6180 6.935167 TCTTTGTAACTATGCAGTGAGATCA 58.065 36.000 0.00 0.00 34.36 2.92
5956 6182 7.877612 TCTTTGTAACTATGCAGTGAGATCAAA 59.122 33.333 0.00 0.00 34.36 2.69
5958 6184 5.874810 TGTAACTATGCAGTGAGATCAAACC 59.125 40.000 0.00 0.00 34.36 3.27
5960 6186 2.479566 ATGCAGTGAGATCAAACCGT 57.520 45.000 0.00 0.00 0.00 4.83
5963 6189 2.289631 TGCAGTGAGATCAAACCGTCAT 60.290 45.455 0.00 0.00 0.00 3.06
5978 6204 5.290493 ACCGTCATAATGCTAATCTCCAA 57.710 39.130 0.00 0.00 0.00 3.53
5979 6205 5.869579 ACCGTCATAATGCTAATCTCCAAT 58.130 37.500 0.00 0.00 0.00 3.16
5984 6210 8.961092 CGTCATAATGCTAATCTCCAATTTTTG 58.039 33.333 0.00 0.00 0.00 2.44
6108 6334 1.496060 TTACACGAGGGAGATGCCAT 58.504 50.000 0.00 0.00 38.95 4.40
6200 6426 5.830457 TCCTGTACAGATGATCAGACCTAAG 59.170 44.000 24.68 1.53 0.00 2.18
6271 6497 4.162651 AGAGCTCACAATTTTCCCCAATT 58.837 39.130 17.77 0.00 0.00 2.32
6373 6729 8.985315 AATGCTAATGATGTCTCCTGATTAAA 57.015 30.769 0.00 0.00 0.00 1.52
6424 6780 7.630026 TGTTATCGATGCATAAAAAGCTACAG 58.370 34.615 8.54 0.00 0.00 2.74
6451 6807 4.212425 TGTCTATACAAACAGTTGCGTTGG 59.788 41.667 0.00 0.00 38.39 3.77
6492 6848 2.094894 CCGATGCAAGTTCTGTAAGCAG 59.905 50.000 0.00 0.00 43.87 4.24
6540 6898 3.321497 GCTATGAAGGTTGCCTAGATCG 58.679 50.000 0.00 0.00 31.13 3.69
6545 6903 3.512329 TGAAGGTTGCCTAGATCGTGTTA 59.488 43.478 0.00 0.00 31.13 2.41
6555 6913 1.400494 AGATCGTGTTATTTTGCGGCC 59.600 47.619 0.00 0.00 0.00 6.13
6610 7034 1.643832 CTTATGCGCGCTCTTTCCC 59.356 57.895 33.29 0.00 0.00 3.97
6651 13880 4.632538 AGTTTCTTGTTACAGTGTTGGC 57.367 40.909 0.00 0.00 0.00 4.52
6652 13881 3.064820 AGTTTCTTGTTACAGTGTTGGCG 59.935 43.478 0.00 0.00 0.00 5.69
6655 13884 1.448922 TTGTTACAGTGTTGGCGGGC 61.449 55.000 0.00 0.00 0.00 6.13
6709 13939 1.976404 GGGGCATTCCTACCTACCTAC 59.024 57.143 0.00 0.00 35.33 3.18
6892 14131 2.480426 CTTCTGGTTTCGTCGCGTGC 62.480 60.000 5.77 0.00 0.00 5.34
6893 14132 4.409588 CTGGTTTCGTCGCGTGCG 62.410 66.667 16.80 16.80 41.35 5.34
6918 14174 1.772182 GTGTGTGTTCTCCTGACTCG 58.228 55.000 0.00 0.00 0.00 4.18
7128 14406 6.764877 GCATTTGCATCTTATTCATTCCAG 57.235 37.500 0.00 0.00 41.59 3.86
7129 14407 6.278363 GCATTTGCATCTTATTCATTCCAGT 58.722 36.000 0.00 0.00 41.59 4.00
7130 14408 6.420008 GCATTTGCATCTTATTCATTCCAGTC 59.580 38.462 0.00 0.00 41.59 3.51
7131 14409 7.683704 GCATTTGCATCTTATTCATTCCAGTCT 60.684 37.037 0.00 0.00 41.59 3.24
7132 14410 7.707624 TTTGCATCTTATTCATTCCAGTCTT 57.292 32.000 0.00 0.00 0.00 3.01
7133 14411 6.688637 TGCATCTTATTCATTCCAGTCTTG 57.311 37.500 0.00 0.00 0.00 3.02
7134 14412 6.182627 TGCATCTTATTCATTCCAGTCTTGT 58.817 36.000 0.00 0.00 0.00 3.16
7135 14413 6.317140 TGCATCTTATTCATTCCAGTCTTGTC 59.683 38.462 0.00 0.00 0.00 3.18
7136 14414 6.541641 GCATCTTATTCATTCCAGTCTTGTCT 59.458 38.462 0.00 0.00 0.00 3.41
7137 14415 7.466996 GCATCTTATTCATTCCAGTCTTGTCTG 60.467 40.741 0.00 0.00 35.45 3.51
7138 14416 7.244886 TCTTATTCATTCCAGTCTTGTCTGA 57.755 36.000 0.00 0.00 37.61 3.27
7139 14417 7.855375 TCTTATTCATTCCAGTCTTGTCTGAT 58.145 34.615 0.00 0.00 37.61 2.90
7140 14418 7.984050 TCTTATTCATTCCAGTCTTGTCTGATC 59.016 37.037 0.00 0.00 37.61 2.92
7141 14419 4.115401 TCATTCCAGTCTTGTCTGATCG 57.885 45.455 0.00 0.00 37.61 3.69
7142 14420 2.370281 TTCCAGTCTTGTCTGATCGC 57.630 50.000 0.00 0.00 37.61 4.58
7143 14421 0.532573 TCCAGTCTTGTCTGATCGCC 59.467 55.000 0.00 0.00 37.61 5.54
7144 14422 0.247460 CCAGTCTTGTCTGATCGCCA 59.753 55.000 0.00 0.00 37.61 5.69
7148 14426 2.100584 AGTCTTGTCTGATCGCCATCTC 59.899 50.000 0.00 0.00 0.00 2.75
7153 14431 1.000385 GTCTGATCGCCATCTCCTCTG 60.000 57.143 0.00 0.00 0.00 3.35
7158 14437 1.107114 TCGCCATCTCCTCTGAACTC 58.893 55.000 0.00 0.00 0.00 3.01
7161 14440 1.830477 GCCATCTCCTCTGAACTCTGT 59.170 52.381 0.00 0.00 0.00 3.41
7165 14444 2.530701 TCTCCTCTGAACTCTGTTCCC 58.469 52.381 7.81 0.00 0.00 3.97
7168 14447 2.368875 TCCTCTGAACTCTGTTCCCAAC 59.631 50.000 7.81 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 142 9.062524 ACAGTGTAAACATCATAGCAACTTTTA 57.937 29.630 0.00 0.00 0.00 1.52
140 152 6.468543 TGGCAACTACAGTGTAAACATCATA 58.531 36.000 4.21 0.00 37.61 2.15
170 182 5.048364 TGCCGCATGACAACTTTAGTTTAAT 60.048 36.000 0.00 0.00 35.83 1.40
185 197 3.058450 CAAACTGAAATTTGCCGCATGA 58.942 40.909 0.00 0.00 33.07 3.07
190 202 5.108385 ACTCTACAAACTGAAATTTGCCG 57.892 39.130 0.00 0.00 42.29 5.69
278 291 4.712476 TGCACTTAAAATTGCCATGGTTT 58.288 34.783 14.67 8.41 38.00 3.27
327 340 3.766545 AGAAACTAGGCTTGCCATGAAA 58.233 40.909 14.54 0.00 0.00 2.69
648 668 7.027760 CACACGTCTTATAACACATAGACTGT 58.972 38.462 0.00 0.00 39.20 3.55
677 697 0.249911 GTGTGGTGAGAGCGAAACCT 60.250 55.000 0.00 0.00 34.90 3.50
703 723 4.201930 TTTCCATTTGAACAACGCTAACGT 60.202 37.500 0.00 0.00 43.74 3.99
726 746 2.427095 GCACAGTGGAAGGTGTTCTTTT 59.573 45.455 1.84 0.00 37.35 2.27
727 747 2.024414 GCACAGTGGAAGGTGTTCTTT 58.976 47.619 1.84 0.00 37.35 2.52
728 748 1.212935 AGCACAGTGGAAGGTGTTCTT 59.787 47.619 1.84 0.00 37.35 2.52
729 749 0.839946 AGCACAGTGGAAGGTGTTCT 59.160 50.000 1.84 0.00 37.35 3.01
730 750 0.947244 CAGCACAGTGGAAGGTGTTC 59.053 55.000 1.84 0.00 37.35 3.18
731 751 0.466189 CCAGCACAGTGGAAGGTGTT 60.466 55.000 1.84 0.00 40.44 3.32
732 752 1.149174 CCAGCACAGTGGAAGGTGT 59.851 57.895 1.84 0.00 40.44 4.16
733 753 2.263741 GCCAGCACAGTGGAAGGTG 61.264 63.158 1.84 0.00 40.44 4.00
734 754 2.113986 GCCAGCACAGTGGAAGGT 59.886 61.111 1.84 0.00 40.44 3.50
735 755 3.052082 CGCCAGCACAGTGGAAGG 61.052 66.667 1.84 0.00 40.44 3.46
736 756 3.052082 CCGCCAGCACAGTGGAAG 61.052 66.667 1.84 0.00 40.44 3.46
764 784 2.064581 GGCCAGGTAGGATGACGGT 61.065 63.158 0.00 0.00 41.22 4.83
798 818 0.833287 CTGTAGGGCCAGCTGTGTAT 59.167 55.000 13.81 0.00 0.00 2.29
799 819 0.544357 ACTGTAGGGCCAGCTGTGTA 60.544 55.000 13.81 0.00 35.83 2.90
811 831 7.263496 GGTGTATCTTACTAACCAACTGTAGG 58.737 42.308 0.00 0.00 0.00 3.18
813 833 6.625740 GCGGTGTATCTTACTAACCAACTGTA 60.626 42.308 0.00 0.00 0.00 2.74
822 842 2.099592 CCACCGCGGTGTATCTTACTAA 59.900 50.000 45.63 0.00 44.02 2.24
823 843 1.677576 CCACCGCGGTGTATCTTACTA 59.322 52.381 45.63 0.00 44.02 1.82
824 844 0.458669 CCACCGCGGTGTATCTTACT 59.541 55.000 45.63 14.62 44.02 2.24
973 994 2.477176 CGCTCTCCCTCGACTCCTG 61.477 68.421 0.00 0.00 0.00 3.86
992 1026 4.626081 CGATCCCCATGCCGACCC 62.626 72.222 0.00 0.00 0.00 4.46
1085 1119 4.410400 GGGAGGTGGTGGAAGCGG 62.410 72.222 0.00 0.00 36.92 5.52
1089 1123 3.319198 GAGCGGGAGGTGGTGGAA 61.319 66.667 0.00 0.00 43.00 3.53
1170 1210 2.649034 GAGACGACCGAGTTGGCA 59.351 61.111 0.00 0.00 43.94 4.92
1236 1276 9.320295 GACCCCTACTACTAGTAGTCTTCTATA 57.680 40.741 33.47 16.74 45.12 1.31
1237 1277 7.039082 CGACCCCTACTACTAGTAGTCTTCTAT 60.039 44.444 33.47 18.48 45.12 1.98
1238 1278 6.266558 CGACCCCTACTACTAGTAGTCTTCTA 59.733 46.154 33.47 18.02 45.12 2.10
1239 1279 5.070313 CGACCCCTACTACTAGTAGTCTTCT 59.930 48.000 33.47 16.51 45.12 2.85
1240 1280 5.069781 TCGACCCCTACTACTAGTAGTCTTC 59.930 48.000 33.47 21.90 45.12 2.87
1242 1282 4.551671 TCGACCCCTACTACTAGTAGTCT 58.448 47.826 33.47 16.74 45.12 3.24
1243 1283 4.262420 CCTCGACCCCTACTACTAGTAGTC 60.262 54.167 33.47 19.56 45.12 2.59
1245 1285 3.007831 CCCTCGACCCCTACTACTAGTAG 59.992 56.522 25.30 25.30 45.93 2.57
1246 1286 2.975489 CCCTCGACCCCTACTACTAGTA 59.025 54.545 1.89 1.89 0.00 1.82
1350 1390 0.598680 CGCCTCAGATGAACCGATCC 60.599 60.000 0.00 0.00 0.00 3.36
1386 1426 9.935241 GAACAGGCTAAGATGATTTCAGATATA 57.065 33.333 0.00 0.00 0.00 0.86
1476 1519 2.666508 AGTAATACAGAAACGCACGCAG 59.333 45.455 0.00 0.00 0.00 5.18
1484 1527 9.682465 AGGGGAGAAAATAAGTAATACAGAAAC 57.318 33.333 0.00 0.00 0.00 2.78
1543 1586 1.067212 GTCTACCGCCAACGATGAGAT 59.933 52.381 0.00 0.00 43.93 2.75
1553 1596 3.765511 ACAATAACTACTGTCTACCGCCA 59.234 43.478 0.00 0.00 0.00 5.69
1557 1600 5.221009 CCGAGGACAATAACTACTGTCTACC 60.221 48.000 2.56 0.00 41.43 3.18
1580 1623 0.337428 TCCTGTACTCTACCCACCCC 59.663 60.000 0.00 0.00 0.00 4.95
1699 1757 9.725019 AAGAAAGTCAATGTCAACAGTCATATA 57.275 29.630 0.00 0.00 0.00 0.86
1700 1758 8.627208 AAGAAAGTCAATGTCAACAGTCATAT 57.373 30.769 0.00 0.00 0.00 1.78
1701 1759 7.714813 TGAAGAAAGTCAATGTCAACAGTCATA 59.285 33.333 0.00 0.00 0.00 2.15
1702 1760 6.543465 TGAAGAAAGTCAATGTCAACAGTCAT 59.457 34.615 0.00 0.00 0.00 3.06
1752 1812 1.658994 AGCAAAACGGTGAAGTCGAA 58.341 45.000 0.00 0.00 0.00 3.71
1805 1866 6.624352 TTCTTTTCAGTCAGTGAATCTTGG 57.376 37.500 0.00 0.00 44.89 3.61
1821 1882 4.789012 TGCTGATTGGTCCATTCTTTTC 57.211 40.909 13.58 3.11 0.00 2.29
1829 1890 4.513442 GTGTAACTATGCTGATTGGTCCA 58.487 43.478 0.00 0.00 0.00 4.02
1913 1977 6.683974 TTATGCAGAGAAAATTAGCAGTCC 57.316 37.500 0.00 0.00 38.75 3.85
1978 2042 9.507329 ACTGATTTATAGGACGATATTTTGCAT 57.493 29.630 0.00 0.00 0.00 3.96
2043 2107 9.932207 TTCAGGAAATCGTTAACTAGTAATTGA 57.068 29.630 3.71 0.00 0.00 2.57
2060 2124 8.275040 ACTAGCTATTACCAATGTTCAGGAAAT 58.725 33.333 0.00 0.00 0.00 2.17
2094 2158 5.825151 TGAAGTGTGTCATACAAATGTCCAA 59.175 36.000 2.32 0.00 41.89 3.53
2095 2159 5.372373 TGAAGTGTGTCATACAAATGTCCA 58.628 37.500 2.32 0.00 41.89 4.02
2309 2374 8.948631 AGTATCAAAATCGAAGTGTGTCATAT 57.051 30.769 0.00 0.00 0.00 1.78
2310 2375 8.251026 AGAGTATCAAAATCGAAGTGTGTCATA 58.749 33.333 0.00 0.00 37.82 2.15
2311 2376 7.063898 CAGAGTATCAAAATCGAAGTGTGTCAT 59.936 37.037 0.00 0.00 37.82 3.06
2312 2377 6.366061 CAGAGTATCAAAATCGAAGTGTGTCA 59.634 38.462 0.00 0.00 37.82 3.58
2365 2430 7.982761 ATGCAACAACCAATTATCACATTTT 57.017 28.000 0.00 0.00 0.00 1.82
2369 2434 7.401955 TCATATGCAACAACCAATTATCACA 57.598 32.000 0.00 0.00 0.00 3.58
2372 2437 7.148918 GCGAATCATATGCAACAACCAATTATC 60.149 37.037 0.00 0.00 0.00 1.75
2380 2445 5.989249 TGATAGCGAATCATATGCAACAAC 58.011 37.500 0.00 0.00 39.77 3.32
2385 2450 5.247862 ACCATTGATAGCGAATCATATGCA 58.752 37.500 0.00 0.00 44.13 3.96
2386 2451 5.808042 ACCATTGATAGCGAATCATATGC 57.192 39.130 0.00 0.00 44.13 3.14
2391 2456 4.811024 GTCTCAACCATTGATAGCGAATCA 59.189 41.667 1.14 1.14 43.03 2.57
2393 2458 4.813161 CAGTCTCAACCATTGATAGCGAAT 59.187 41.667 0.00 0.00 39.30 3.34
2401 2466 3.054875 CCCATCTCAGTCTCAACCATTGA 60.055 47.826 0.00 0.00 38.17 2.57
2415 2480 2.940158 CAATCTGGCAATCCCATCTCA 58.060 47.619 0.00 0.00 44.33 3.27
2416 2481 1.612463 GCAATCTGGCAATCCCATCTC 59.388 52.381 0.00 0.00 44.33 2.75
2487 2552 5.883673 GGTGTTGCTAGGTATATCCACAAAA 59.116 40.000 0.00 0.00 39.02 2.44
2499 2564 2.375174 TGGAATTGAGGTGTTGCTAGGT 59.625 45.455 0.00 0.00 0.00 3.08
2536 2601 5.458015 GGCCACAACTTTTTACTACATGTC 58.542 41.667 0.00 0.00 0.00 3.06
2561 2626 2.508526 AGAAACCTGGTGCTTTGCTAG 58.491 47.619 0.00 0.00 0.00 3.42
2568 2633 5.499004 TTACTATCAAGAAACCTGGTGCT 57.501 39.130 0.00 0.00 0.00 4.40
2635 2700 5.241506 ACTTATGCTGCTTTACTTTTGCTCA 59.758 36.000 0.00 0.00 0.00 4.26
2639 2704 6.528072 GGCTAACTTATGCTGCTTTACTTTTG 59.472 38.462 0.00 0.00 0.00 2.44
2685 2751 2.948979 ACTTGATCAAAAGGTGCGTTCA 59.051 40.909 9.88 0.00 0.00 3.18
2729 2796 7.745015 TGTCATGTTTTAAGGCTAATTACGAC 58.255 34.615 0.00 0.00 0.00 4.34
2748 2815 3.470709 AGCGAATAAGGGTGATGTCATG 58.529 45.455 0.00 0.00 0.00 3.07
2749 2816 3.495100 GGAGCGAATAAGGGTGATGTCAT 60.495 47.826 0.00 0.00 0.00 3.06
2750 2817 2.158957 GGAGCGAATAAGGGTGATGTCA 60.159 50.000 0.00 0.00 0.00 3.58
2751 2818 2.484889 GGAGCGAATAAGGGTGATGTC 58.515 52.381 0.00 0.00 0.00 3.06
2752 2819 1.141053 GGGAGCGAATAAGGGTGATGT 59.859 52.381 0.00 0.00 0.00 3.06
2753 2820 1.140852 TGGGAGCGAATAAGGGTGATG 59.859 52.381 0.00 0.00 0.00 3.07
2754 2821 1.507140 TGGGAGCGAATAAGGGTGAT 58.493 50.000 0.00 0.00 0.00 3.06
2755 2822 1.281419 TTGGGAGCGAATAAGGGTGA 58.719 50.000 0.00 0.00 0.00 4.02
2756 2823 2.122783 TTTGGGAGCGAATAAGGGTG 57.877 50.000 0.00 0.00 0.00 4.61
2757 2824 2.891191 TTTTGGGAGCGAATAAGGGT 57.109 45.000 0.00 0.00 0.00 4.34
2758 2825 4.441495 GGAAATTTTGGGAGCGAATAAGGG 60.441 45.833 0.00 0.00 0.00 3.95
2772 2839 7.039363 TGGAAGGGTATAACAGTGGAAATTTTG 60.039 37.037 0.00 0.00 0.00 2.44
2785 2852 7.360946 GCAACGATATGAATGGAAGGGTATAAC 60.361 40.741 0.00 0.00 0.00 1.89
2828 2895 8.210946 TCATTTTGAGAGGAACTGAAGTAGAAA 58.789 33.333 0.00 0.00 41.55 2.52
2879 2946 7.693969 ATCCTGAAATGTAAAACTGAGGAAG 57.306 36.000 0.00 0.00 32.24 3.46
3021 3089 4.763279 TCTGGACGTGTAGTTACTTCATGA 59.237 41.667 16.17 0.00 0.00 3.07
3052 3120 8.968242 CATTAAACGACGAAGATTCATATCAGA 58.032 33.333 0.00 0.00 32.95 3.27
3215 3284 9.185192 GCAGGTGTCATTTATTTATTTATGCTC 57.815 33.333 0.00 0.00 0.00 4.26
3391 3460 5.500645 AAACAGAACTAACTTGAACAGCC 57.499 39.130 0.00 0.00 0.00 4.85
3493 3566 3.130633 TCCAACTGTCTTCATGTCGTTG 58.869 45.455 0.00 0.00 33.47 4.10
3628 3701 9.701098 AAACTTTTGAGATACTTGTCGTATACA 57.299 29.630 3.32 0.00 38.90 2.29
3690 3763 7.591821 AGGGTAGGGCAAATAAATAATGAGAA 58.408 34.615 0.00 0.00 0.00 2.87
3706 3779 3.964411 AGACATTAACAAAGGGTAGGGC 58.036 45.455 0.00 0.00 0.00 5.19
3810 3884 2.710096 ACACCTAATGCCGCAACTAT 57.290 45.000 0.00 0.00 0.00 2.12
3818 3892 6.031751 TCCACAATAAAAACACCTAATGCC 57.968 37.500 0.00 0.00 0.00 4.40
3890 3964 5.163509 GGAAAGCTTCTAAATCAATGTCCCC 60.164 44.000 0.00 0.00 0.00 4.81
3891 3965 5.163509 GGGAAAGCTTCTAAATCAATGTCCC 60.164 44.000 0.00 3.88 33.51 4.46
3894 3968 6.916360 TTGGGAAAGCTTCTAAATCAATGT 57.084 33.333 0.00 0.00 0.00 2.71
3895 3969 7.153985 TGTTTGGGAAAGCTTCTAAATCAATG 58.846 34.615 0.00 0.00 0.00 2.82
3896 3970 7.301868 TGTTTGGGAAAGCTTCTAAATCAAT 57.698 32.000 0.00 0.00 0.00 2.57
3897 3971 6.723298 TGTTTGGGAAAGCTTCTAAATCAA 57.277 33.333 0.00 0.00 0.00 2.57
4001 4085 8.820831 CCTTTGATAGATCTGAATACCCTACAT 58.179 37.037 5.18 0.00 0.00 2.29
4083 4167 3.561725 GGCTTGTCACCATCAATAGCTAC 59.438 47.826 0.00 0.00 0.00 3.58
4953 5127 5.048434 ACAGCACAAAAGCTTATCTCCTTTC 60.048 40.000 0.00 0.00 43.70 2.62
5062 5236 4.392940 CTTCCACCTTCACTTGATCAACT 58.607 43.478 3.38 0.00 0.00 3.16
5193 5367 4.405358 GGGCCAACCATCAGAAATCAAATA 59.595 41.667 4.39 0.00 39.85 1.40
5360 5534 7.291411 ACGTAAGCATACTTGATAAGATCCT 57.709 36.000 0.00 0.00 45.62 3.24
5400 5574 7.903431 CCGCTACATAACAAAGAAAAGACATAC 59.097 37.037 0.00 0.00 0.00 2.39
5445 5619 4.762251 GCAAAGACTATGAAAACAGAGGGT 59.238 41.667 0.00 0.00 0.00 4.34
5505 5679 4.142381 ACTTCAAGCACTTCCAACAGTTTC 60.142 41.667 0.00 0.00 0.00 2.78
5542 5716 4.419522 TTTGCTCGACAGGATTTTTAGC 57.580 40.909 0.00 0.00 0.00 3.09
5572 5746 4.348863 ACTTGGATATAGCTTCCTGCAG 57.651 45.455 6.78 6.78 45.94 4.41
5689 5863 4.506654 CCTCAATAAACAGACCCGTATTCG 59.493 45.833 0.00 0.00 0.00 3.34
5695 5869 3.560636 ATCCCTCAATAAACAGACCCG 57.439 47.619 0.00 0.00 0.00 5.28
5696 5870 6.174049 GCTATATCCCTCAATAAACAGACCC 58.826 44.000 0.00 0.00 0.00 4.46
5697 5871 6.013293 AGGCTATATCCCTCAATAAACAGACC 60.013 42.308 0.00 0.00 0.00 3.85
5720 5895 2.175878 AGCACTGTGAGTTTGCTAGG 57.824 50.000 12.86 0.00 44.82 3.02
5732 5907 6.842437 ATCATAGGTATATCGAAGCACTGT 57.158 37.500 0.00 0.00 0.00 3.55
5739 5914 8.627403 GGGATCGTTTATCATAGGTATATCGAA 58.373 37.037 0.00 0.00 36.20 3.71
5746 5921 6.551975 TGTCAAGGGATCGTTTATCATAGGTA 59.448 38.462 0.00 0.00 36.20 3.08
5748 5923 5.853936 TGTCAAGGGATCGTTTATCATAGG 58.146 41.667 0.00 0.00 36.20 2.57
5751 5926 5.760253 GTCATGTCAAGGGATCGTTTATCAT 59.240 40.000 0.00 0.00 36.20 2.45
5753 5928 5.360591 AGTCATGTCAAGGGATCGTTTATC 58.639 41.667 0.00 0.00 0.00 1.75
5754 5929 5.359194 AGTCATGTCAAGGGATCGTTTAT 57.641 39.130 0.00 0.00 0.00 1.40
5755 5930 4.819105 AGTCATGTCAAGGGATCGTTTA 57.181 40.909 0.00 0.00 0.00 2.01
5756 5931 3.703001 AGTCATGTCAAGGGATCGTTT 57.297 42.857 0.00 0.00 0.00 3.60
5757 5932 4.020573 TGTTAGTCATGTCAAGGGATCGTT 60.021 41.667 0.00 0.00 0.00 3.85
5758 5933 3.513912 TGTTAGTCATGTCAAGGGATCGT 59.486 43.478 0.00 0.00 0.00 3.73
5759 5934 3.865745 GTGTTAGTCATGTCAAGGGATCG 59.134 47.826 0.00 0.00 0.00 3.69
5760 5935 5.091261 AGTGTTAGTCATGTCAAGGGATC 57.909 43.478 0.00 0.00 0.00 3.36
5761 5936 5.248640 CAAGTGTTAGTCATGTCAAGGGAT 58.751 41.667 0.00 0.00 0.00 3.85
5763 5938 3.753272 CCAAGTGTTAGTCATGTCAAGGG 59.247 47.826 0.00 0.00 0.00 3.95
5767 5942 4.415881 ACACCAAGTGTTAGTCATGTCA 57.584 40.909 0.00 0.00 45.08 3.58
5768 5943 7.435068 AAATACACCAAGTGTTAGTCATGTC 57.565 36.000 5.59 0.00 45.08 3.06
5769 5944 7.284489 ACAAAATACACCAAGTGTTAGTCATGT 59.716 33.333 5.59 2.62 45.08 3.21
5770 5945 7.648142 ACAAAATACACCAAGTGTTAGTCATG 58.352 34.615 5.59 2.07 45.08 3.07
5771 5946 7.817418 ACAAAATACACCAAGTGTTAGTCAT 57.183 32.000 5.59 0.00 45.08 3.06
5772 5947 7.633193 AACAAAATACACCAAGTGTTAGTCA 57.367 32.000 5.59 0.00 45.08 3.41
5773 5948 8.920509 AAAACAAAATACACCAAGTGTTAGTC 57.079 30.769 5.59 0.00 45.08 2.59
5774 5949 9.791820 GTAAAACAAAATACACCAAGTGTTAGT 57.208 29.630 5.59 0.00 45.08 2.24
5775 5950 9.790389 TGTAAAACAAAATACACCAAGTGTTAG 57.210 29.630 5.59 0.00 45.08 2.34
5777 5952 9.660180 ATTGTAAAACAAAATACACCAAGTGTT 57.340 25.926 5.59 0.00 41.87 3.32
5778 5953 9.660180 AATTGTAAAACAAAATACACCAAGTGT 57.340 25.926 5.60 5.60 44.44 3.55
5837 6012 6.874288 AGAAATGGCTCATATCTAACAAGC 57.126 37.500 0.00 0.00 0.00 4.01
5840 6015 6.467677 GGCTAGAAATGGCTCATATCTAACA 58.532 40.000 0.00 0.00 0.00 2.41
5841 6016 5.877564 GGGCTAGAAATGGCTCATATCTAAC 59.122 44.000 0.00 0.00 0.00 2.34
5843 6018 5.093677 TGGGCTAGAAATGGCTCATATCTA 58.906 41.667 0.00 0.00 33.66 1.98
5871 6046 7.710907 TGTAACCTATCACAGATGTTTAGATGC 59.289 37.037 0.00 0.00 0.00 3.91
5872 6047 9.770097 ATGTAACCTATCACAGATGTTTAGATG 57.230 33.333 0.00 0.00 0.00 2.90
5878 6104 8.046708 TGCTAAATGTAACCTATCACAGATGTT 58.953 33.333 0.00 0.00 0.00 2.71
5883 6109 7.134815 GCAATGCTAAATGTAACCTATCACAG 58.865 38.462 0.00 0.00 0.00 3.66
5892 6118 7.760131 AATGATGTGCAATGCTAAATGTAAC 57.240 32.000 6.82 0.00 0.00 2.50
5899 6125 7.908827 ATTTTGAAATGATGTGCAATGCTAA 57.091 28.000 6.82 0.00 0.00 3.09
5900 6126 8.999220 TTATTTTGAAATGATGTGCAATGCTA 57.001 26.923 6.82 0.00 0.00 3.49
5929 6155 7.386059 TGATCTCACTGCATAGTTACAAAGAA 58.614 34.615 0.00 0.00 34.07 2.52
5943 6169 1.795768 TGACGGTTTGATCTCACTGC 58.204 50.000 0.00 0.00 0.00 4.40
5946 6172 4.572389 AGCATTATGACGGTTTGATCTCAC 59.428 41.667 0.00 0.00 0.00 3.51
5947 6173 4.769688 AGCATTATGACGGTTTGATCTCA 58.230 39.130 0.00 0.00 0.00 3.27
5951 6177 6.428159 GGAGATTAGCATTATGACGGTTTGAT 59.572 38.462 0.00 0.00 0.00 2.57
5954 6180 5.680619 TGGAGATTAGCATTATGACGGTTT 58.319 37.500 0.00 0.00 0.00 3.27
5956 6182 4.955811 TGGAGATTAGCATTATGACGGT 57.044 40.909 0.00 0.00 0.00 4.83
5958 6184 8.961092 CAAAAATTGGAGATTAGCATTATGACG 58.039 33.333 0.00 0.00 0.00 4.35
5978 6204 2.905736 AGTTGCCTGCATACCCAAAAAT 59.094 40.909 0.00 0.00 0.00 1.82
5979 6205 2.036992 CAGTTGCCTGCATACCCAAAAA 59.963 45.455 0.00 0.00 0.00 1.94
5984 6210 1.544724 TTTCAGTTGCCTGCATACCC 58.455 50.000 0.00 0.00 38.66 3.69
5985 6211 3.947834 ACTATTTCAGTTGCCTGCATACC 59.052 43.478 0.00 0.00 38.66 2.73
5986 6212 4.260375 CGACTATTTCAGTTGCCTGCATAC 60.260 45.833 0.00 0.00 37.72 2.39
6108 6334 4.415881 TCTCTGTGTGTTGCTTCCTTAA 57.584 40.909 0.00 0.00 0.00 1.85
6424 6780 7.464830 ACGCAACTGTTTGTATAGACATATC 57.535 36.000 0.00 0.00 34.86 1.63
6540 6898 0.800012 TCGAGGCCGCAAAATAACAC 59.200 50.000 7.44 0.00 35.37 3.32
6545 6903 1.135402 GTCAATTCGAGGCCGCAAAAT 60.135 47.619 7.44 2.65 35.37 1.82
6555 6913 4.319766 CCACCTGAAGTTTGTCAATTCGAG 60.320 45.833 0.00 0.00 0.00 4.04
6610 7034 8.548721 AGAAACTTGAACAACTTATTACTGTCG 58.451 33.333 0.00 0.00 0.00 4.35
6651 13880 4.189188 GCTCAATGCTGCTGCCCG 62.189 66.667 13.47 1.51 38.71 6.13
6652 13881 2.642254 TTGCTCAATGCTGCTGCCC 61.642 57.895 13.47 0.00 43.37 5.36
6655 13884 1.154093 CCGTTGCTCAATGCTGCTG 60.154 57.895 0.00 0.00 43.37 4.41
6674 13903 3.912907 CCCTGCCGCTACCTACCG 61.913 72.222 0.00 0.00 0.00 4.02
6709 13939 0.398098 TCGCTTTAGTAGGGGAGGGG 60.398 60.000 0.00 0.00 37.41 4.79
6893 14132 2.245532 GAGAACACACACGCGCAC 59.754 61.111 5.73 0.00 0.00 5.34
6898 14137 1.772182 GAGTCAGGAGAACACACACG 58.228 55.000 0.00 0.00 0.00 4.49
6900 14139 1.337071 GACGAGTCAGGAGAACACACA 59.663 52.381 0.00 0.00 0.00 3.72
6918 14174 2.898343 ACGCCACCAAACACCGAC 60.898 61.111 0.00 0.00 0.00 4.79
7092 14348 0.745845 CAAATGCAGGGGAGTCGGAG 60.746 60.000 0.00 0.00 0.00 4.63
7093 14349 1.299648 CAAATGCAGGGGAGTCGGA 59.700 57.895 0.00 0.00 0.00 4.55
7095 14351 3.190878 GCAAATGCAGGGGAGTCG 58.809 61.111 0.00 0.00 41.59 4.18
7122 14400 2.419297 GGCGATCAGACAAGACTGGAAT 60.419 50.000 0.00 0.00 38.31 3.01
7123 14401 1.066858 GGCGATCAGACAAGACTGGAA 60.067 52.381 0.00 0.00 38.31 3.53
7124 14402 0.532573 GGCGATCAGACAAGACTGGA 59.467 55.000 0.00 0.00 38.31 3.86
7125 14403 0.247460 TGGCGATCAGACAAGACTGG 59.753 55.000 0.00 0.00 32.75 4.00
7126 14404 2.159128 AGATGGCGATCAGACAAGACTG 60.159 50.000 11.55 0.00 44.01 3.51
7127 14405 2.100584 GAGATGGCGATCAGACAAGACT 59.899 50.000 11.55 0.00 44.01 3.24
7128 14406 2.468831 GAGATGGCGATCAGACAAGAC 58.531 52.381 11.55 0.00 44.01 3.01
7129 14407 1.410517 GGAGATGGCGATCAGACAAGA 59.589 52.381 11.55 0.00 44.01 3.02
7130 14408 1.411977 AGGAGATGGCGATCAGACAAG 59.588 52.381 11.55 0.00 44.01 3.16
7131 14409 1.410517 GAGGAGATGGCGATCAGACAA 59.589 52.381 11.55 0.00 44.01 3.18
7132 14410 1.035923 GAGGAGATGGCGATCAGACA 58.964 55.000 11.55 0.00 45.56 3.41
7133 14411 1.000385 CAGAGGAGATGGCGATCAGAC 60.000 57.143 11.55 0.75 0.00 3.51
7134 14412 1.133668 TCAGAGGAGATGGCGATCAGA 60.134 52.381 11.55 0.00 0.00 3.27
7135 14413 1.326328 TCAGAGGAGATGGCGATCAG 58.674 55.000 11.55 0.00 0.00 2.90
7136 14414 1.410517 GTTCAGAGGAGATGGCGATCA 59.589 52.381 11.55 0.00 0.00 2.92
7137 14415 1.686052 AGTTCAGAGGAGATGGCGATC 59.314 52.381 0.00 0.00 0.00 3.69
7138 14416 1.686052 GAGTTCAGAGGAGATGGCGAT 59.314 52.381 0.00 0.00 0.00 4.58
7139 14417 1.107114 GAGTTCAGAGGAGATGGCGA 58.893 55.000 0.00 0.00 0.00 5.54
7140 14418 1.110442 AGAGTTCAGAGGAGATGGCG 58.890 55.000 0.00 0.00 0.00 5.69
7141 14419 1.830477 ACAGAGTTCAGAGGAGATGGC 59.170 52.381 0.00 0.00 0.00 4.40
7142 14420 3.118811 GGAACAGAGTTCAGAGGAGATGG 60.119 52.174 11.51 0.00 0.00 3.51
7143 14421 3.118811 GGGAACAGAGTTCAGAGGAGATG 60.119 52.174 11.51 0.00 0.00 2.90
7144 14422 3.103742 GGGAACAGAGTTCAGAGGAGAT 58.896 50.000 11.51 0.00 0.00 2.75
7148 14426 2.551071 GGTTGGGAACAGAGTTCAGAGG 60.551 54.545 11.51 0.00 44.54 3.69
7153 14431 0.534203 TGCGGTTGGGAACAGAGTTC 60.534 55.000 1.37 1.37 44.54 3.01
7158 14437 3.365265 GCCTGCGGTTGGGAACAG 61.365 66.667 0.00 0.00 44.54 3.16


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

AutoCloner maintained by Alex Coulton.