Multiple sequence alignment - TraesCS4B01G036800

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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 TraesCS4B01G036800 chr4B 100.000 7419 0 0 1 7419 26485605 26493023 0.000000e+00 13701.0
1 TraesCS4B01G036800 chr4B 82.828 99 16 1 7254 7352 33075139 33075042 3.690000e-13 87.9
2 TraesCS4B01G036800 chr4A 92.572 7162 334 83 327 7419 585033997 585026965 0.000000e+00 10096.0
3 TraesCS4B01G036800 chr4A 90.278 72 3 1 243 310 585034210 585034139 2.850000e-14 91.6
4 TraesCS4B01G036800 chr4A 82.828 99 16 1 7254 7352 580622687 580622784 3.690000e-13 87.9
5 TraesCS4B01G036800 chr4D 95.183 4090 137 28 324 4395 15551458 15555505 0.000000e+00 6407.0
6 TraesCS4B01G036800 chr4D 94.166 2331 83 19 4455 6768 15555750 15558044 0.000000e+00 3502.0
7 TraesCS4B01G036800 chr4D 88.209 670 42 9 6763 7419 15558748 15559393 0.000000e+00 765.0
8 TraesCS4B01G036800 chr4D 85.075 134 9 3 188 310 15551275 15551408 7.810000e-25 126.0
9 TraesCS4B01G036800 chr4D 79.851 134 25 2 7221 7352 21682820 21682953 6.130000e-16 97.1
10 TraesCS4B01G036800 chr3D 83.333 240 36 4 1369 1606 587597467 587597230 1.250000e-52 219.0
11 TraesCS4B01G036800 chr3D 78.049 123 23 2 4839 4960 460446780 460446899 2.870000e-09 75.0
12 TraesCS4B01G036800 chr7B 82.969 229 35 4 1384 1610 602639128 602638902 3.510000e-48 204.0
13 TraesCS4B01G036800 chr5D 82.278 237 40 2 1371 1606 214614310 214614545 3.510000e-48 204.0
14 TraesCS4B01G036800 chr5B 82.969 229 35 3 1379 1606 229375825 229376050 3.510000e-48 204.0
15 TraesCS4B01G036800 chr5B 81.818 242 39 5 1367 1606 366053612 366053374 1.630000e-46 198.0
16 TraesCS4B01G036800 chr1D 81.818 242 39 5 1367 1606 18888913 18889151 1.630000e-46 198.0
17 TraesCS4B01G036800 chr2D 81.328 241 42 3 1368 1606 584529936 584529697 7.600000e-45 193.0
18 TraesCS4B01G036800 chrUn 80.392 153 19 8 2258 2403 100518661 100518809 1.020000e-18 106.0
19 TraesCS4B01G036800 chr6A 78.453 181 26 9 2261 2435 35943598 35943425 1.020000e-18 106.0
20 TraesCS4B01G036800 chr6A 78.512 121 11 6 6741 6860 205100393 205100287 1.730000e-06 65.8
21 TraesCS4B01G036800 chr6B 79.545 132 17 8 2209 2340 684764329 684764450 1.330000e-12 86.1
22 TraesCS4B01G036800 chr6D 85.333 75 10 1 2271 2344 451027511 451027585 7.980000e-10 76.8
23 TraesCS4B01G036800 chr7A 95.000 40 2 0 7309 7348 91358031 91357992 6.210000e-06 63.9


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 TraesCS4B01G036800 chr4B 26485605 26493023 7418 False 13701.0 13701 100.00000 1 7419 1 chr4B.!!$F1 7418
1 TraesCS4B01G036800 chr4A 585026965 585034210 7245 True 5093.8 10096 91.42500 243 7419 2 chr4A.!!$R1 7176
2 TraesCS4B01G036800 chr4D 15551275 15559393 8118 False 2700.0 6407 90.65825 188 7419 4 chr4D.!!$F2 7231

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
796 954 0.108585 TTGAGTGGCCTTCGCTTTCT 59.891 50.000 3.32 0.0 36.15 2.52 F
1723 1913 1.159285 CCAGCCTACATGTGTGTGTG 58.841 55.000 9.11 0.0 39.39 3.82 F
2208 2400 1.273327 CATGGAGTTTTGGTTCCCAGC 59.727 52.381 0.00 0.0 33.81 4.85 F
2950 3146 5.017294 ACTTCAGATAGCCACTTAAGCTC 57.983 43.478 1.29 0.0 41.83 4.09 F
4492 4884 0.036732 TGTAGCCTGCTTGGTCTTGG 59.963 55.000 0.00 0.0 38.35 3.61 F
4493 4885 0.036875 GTAGCCTGCTTGGTCTTGGT 59.963 55.000 0.00 0.0 38.35 3.67 F
5911 6320 0.037447 GTGCCCTCAGAAAGCTCCTT 59.963 55.000 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2544 2740 3.359950 CTCCCAAGCTTAAATGCTCCTT 58.640 45.455 0.00 0.00 43.24 3.36 R
3223 3419 0.299895 CTACAATGAAGAGCGCGCAG 59.700 55.000 35.10 13.84 0.00 5.18 R
3274 3470 1.556911 TGACTGGAGGAATCAAGGAGC 59.443 52.381 0.00 0.00 0.00 4.70 R
4573 4967 0.807496 GCCCATCTTGCAGACTGTTC 59.193 55.000 3.99 0.00 0.00 3.18 R
5776 6185 0.385223 CGACTTGCTGTGCTTGCTTC 60.385 55.000 0.00 0.00 0.00 3.86 R
6348 6757 0.401738 TGGTCTCTTGGGCTCTTTGG 59.598 55.000 0.00 0.00 0.00 3.28 R
7398 8532 0.175989 GCCGAGGAAAGGAGAACGAT 59.824 55.000 0.00 0.00 0.00 3.73 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
46 47 9.519191 ACTATTGGCTATTTATATCACATTGCA 57.481 29.630 0.00 0.00 0.00 4.08
49 50 9.647797 ATTGGCTATTTATATCACATTGCAATG 57.352 29.630 32.74 32.74 42.10 2.82
50 51 7.092079 TGGCTATTTATATCACATTGCAATGC 58.908 34.615 33.94 17.78 40.04 3.56
51 52 7.092079 GGCTATTTATATCACATTGCAATGCA 58.908 34.615 33.94 23.19 40.04 3.96
52 53 7.062605 GGCTATTTATATCACATTGCAATGCAC 59.937 37.037 33.94 9.72 38.71 4.57
53 54 6.996562 ATTTATATCACATTGCAATGCACG 57.003 33.333 33.94 23.67 38.71 5.34
54 55 5.747951 TTATATCACATTGCAATGCACGA 57.252 34.783 33.94 27.27 38.71 4.35
55 56 2.554806 ATCACATTGCAATGCACGAG 57.445 45.000 33.94 20.26 38.71 4.18
56 57 0.109643 TCACATTGCAATGCACGAGC 60.110 50.000 33.94 0.00 38.71 5.03
71 72 5.769967 GCACGAGCATTGTCCTAATATAG 57.230 43.478 0.00 0.00 41.58 1.31
72 73 5.230942 GCACGAGCATTGTCCTAATATAGT 58.769 41.667 0.00 0.00 41.58 2.12
73 74 5.119279 GCACGAGCATTGTCCTAATATAGTG 59.881 44.000 0.00 0.00 41.58 2.74
74 75 5.635280 CACGAGCATTGTCCTAATATAGTGG 59.365 44.000 0.00 0.00 0.00 4.00
75 76 5.538813 ACGAGCATTGTCCTAATATAGTGGA 59.461 40.000 0.00 0.00 0.00 4.02
76 77 6.096036 CGAGCATTGTCCTAATATAGTGGAG 58.904 44.000 0.00 0.00 0.00 3.86
77 78 6.294787 CGAGCATTGTCCTAATATAGTGGAGT 60.295 42.308 0.00 0.00 0.00 3.85
78 79 7.094334 CGAGCATTGTCCTAATATAGTGGAGTA 60.094 40.741 0.00 0.00 0.00 2.59
79 80 8.671987 AGCATTGTCCTAATATAGTGGAGTAT 57.328 34.615 0.00 0.00 0.00 2.12
80 81 9.769677 AGCATTGTCCTAATATAGTGGAGTATA 57.230 33.333 0.00 0.00 0.00 1.47
106 107 9.803507 ATCATCATCATTATAGAAAGCCTGAAA 57.196 29.630 0.00 0.00 0.00 2.69
107 108 9.281371 TCATCATCATTATAGAAAGCCTGAAAG 57.719 33.333 0.00 0.00 0.00 2.62
120 121 2.749280 CTGAAAGGGGCAAATCCAAC 57.251 50.000 0.00 0.00 36.21 3.77
121 122 2.250924 CTGAAAGGGGCAAATCCAACT 58.749 47.619 0.00 0.00 36.21 3.16
122 123 3.430453 CTGAAAGGGGCAAATCCAACTA 58.570 45.455 0.00 0.00 36.21 2.24
123 124 4.026052 CTGAAAGGGGCAAATCCAACTAT 58.974 43.478 0.00 0.00 36.21 2.12
124 125 4.023291 TGAAAGGGGCAAATCCAACTATC 58.977 43.478 0.00 0.00 36.21 2.08
125 126 4.264352 TGAAAGGGGCAAATCCAACTATCT 60.264 41.667 0.00 0.00 36.21 1.98
126 127 4.337264 AAGGGGCAAATCCAACTATCTT 57.663 40.909 0.00 0.00 36.21 2.40
127 128 4.337264 AGGGGCAAATCCAACTATCTTT 57.663 40.909 0.00 0.00 36.21 2.52
128 129 4.687976 AGGGGCAAATCCAACTATCTTTT 58.312 39.130 0.00 0.00 36.21 2.27
129 130 5.093677 AGGGGCAAATCCAACTATCTTTTT 58.906 37.500 0.00 0.00 36.21 1.94
155 156 8.528044 TTGAACTATCAATTAATACCCAACCC 57.472 34.615 0.00 0.00 40.59 4.11
156 157 7.064229 TGAACTATCAATTAATACCCAACCCC 58.936 38.462 0.00 0.00 30.99 4.95
157 158 6.858792 ACTATCAATTAATACCCAACCCCT 57.141 37.500 0.00 0.00 0.00 4.79
158 159 7.233855 ACTATCAATTAATACCCAACCCCTT 57.766 36.000 0.00 0.00 0.00 3.95
159 160 7.658260 ACTATCAATTAATACCCAACCCCTTT 58.342 34.615 0.00 0.00 0.00 3.11
160 161 8.126385 ACTATCAATTAATACCCAACCCCTTTT 58.874 33.333 0.00 0.00 0.00 2.27
161 162 7.822749 ATCAATTAATACCCAACCCCTTTTT 57.177 32.000 0.00 0.00 0.00 1.94
202 203 7.873719 TTCCATGTTAAGAGAAAACTGTCAA 57.126 32.000 0.00 0.00 0.00 3.18
203 204 8.463930 TTCCATGTTAAGAGAAAACTGTCAAT 57.536 30.769 0.00 0.00 0.00 2.57
209 211 4.843220 AGAGAAAACTGTCAATTGCTGG 57.157 40.909 0.00 0.00 0.00 4.85
231 239 6.826668 TGGTTAAGTCACTCTTCATTCTTGA 58.173 36.000 0.00 0.00 37.56 3.02
270 282 4.022589 CACAGATTGTCTTGCACCAATTCT 60.023 41.667 6.83 4.15 31.67 2.40
277 289 6.258230 TGTCTTGCACCAATTCTGAAATAG 57.742 37.500 0.00 0.00 0.00 1.73
321 471 7.967303 GGCTGAGAACTTCTTAATTCTTGATTG 59.033 37.037 0.00 0.00 35.29 2.67
322 472 8.725148 GCTGAGAACTTCTTAATTCTTGATTGA 58.275 33.333 0.00 0.00 35.29 2.57
405 555 0.249073 CATAACTCCTCGGTCGGCTG 60.249 60.000 0.00 0.00 0.00 4.85
494 645 0.174617 CCTCTTGCCTTCTCCGTCTC 59.825 60.000 0.00 0.00 0.00 3.36
495 646 0.174617 CTCTTGCCTTCTCCGTCTCC 59.825 60.000 0.00 0.00 0.00 3.71
513 664 3.157949 CTCCCTTCCGCCCCTCTC 61.158 72.222 0.00 0.00 0.00 3.20
602 753 2.270205 CCGTCCAGCAAGGCTCAT 59.730 61.111 0.00 0.00 36.40 2.90
625 777 7.996066 TCATATGGTTTCCTAATTTCGATCCAA 59.004 33.333 2.13 0.00 0.00 3.53
656 810 1.633774 TCTCCTCTGTTCCCACTCAC 58.366 55.000 0.00 0.00 0.00 3.51
692 846 2.157738 GCATCTGGAACACTGCTTCTT 58.842 47.619 0.00 0.00 38.44 2.52
693 847 2.095364 GCATCTGGAACACTGCTTCTTG 60.095 50.000 0.00 0.00 38.44 3.02
694 848 1.597742 TCTGGAACACTGCTTCTTGC 58.402 50.000 0.00 0.00 43.25 4.01
695 849 0.595095 CTGGAACACTGCTTCTTGCC 59.405 55.000 0.00 0.00 42.00 4.52
711 869 3.462954 TCTTGCCTGGATTGGATTGGATA 59.537 43.478 0.00 0.00 0.00 2.59
726 884 5.278315 GGATTGGATATCCCGTTTTACTTGC 60.278 44.000 19.34 0.00 37.93 4.01
757 915 1.512694 GGGCAAATTTCAGGAGCCG 59.487 57.895 9.62 0.00 46.12 5.52
796 954 0.108585 TTGAGTGGCCTTCGCTTTCT 59.891 50.000 3.32 0.00 36.15 2.52
797 955 0.108585 TGAGTGGCCTTCGCTTTCTT 59.891 50.000 3.32 0.00 36.15 2.52
798 956 1.239347 GAGTGGCCTTCGCTTTCTTT 58.761 50.000 3.32 0.00 36.15 2.52
799 957 1.197949 GAGTGGCCTTCGCTTTCTTTC 59.802 52.381 3.32 0.00 36.15 2.62
815 973 2.731691 TTTCCACCTCAGGAGCGCAC 62.732 60.000 11.47 1.97 39.25 5.34
822 980 4.093952 CAGGAGCGCACGCCTTTG 62.094 66.667 11.47 3.74 44.85 2.77
824 982 4.090057 GGAGCGCACGCCTTTGAC 62.090 66.667 11.47 0.00 43.17 3.18
856 1016 4.392138 CCTTTCTTACTTGACGCCTTTAGG 59.608 45.833 0.00 0.00 38.53 2.69
884 1047 3.760684 CCTTTCTTTCTGTGGGGATCTTG 59.239 47.826 0.00 0.00 0.00 3.02
893 1056 2.514824 GGGATCTTGGGCTCGTGC 60.515 66.667 0.00 0.00 38.76 5.34
934 1097 4.048504 GTTTGATCGGTTTGGTTTTGGAG 58.951 43.478 0.00 0.00 0.00 3.86
935 1098 2.235016 TGATCGGTTTGGTTTTGGAGG 58.765 47.619 0.00 0.00 0.00 4.30
937 1100 2.668144 TCGGTTTGGTTTTGGAGGAT 57.332 45.000 0.00 0.00 0.00 3.24
1088 1273 1.517832 CCGACGAGGGCTCTTTGAT 59.482 57.895 0.00 0.00 35.97 2.57
1104 1289 6.479660 GCTCTTTGATATCTCTGGTCAAGAAG 59.520 42.308 3.98 0.00 33.37 2.85
1200 1385 7.389607 TCTTTGGTTAGCTAGTTCATTTGTACC 59.610 37.037 0.00 0.00 0.00 3.34
1294 1480 7.264947 AGTTTTTCCATTGCTAAATATTCCCG 58.735 34.615 0.00 0.00 0.00 5.14
1397 1583 6.091555 TCTCTATCATGGTTTATTAGCCCCT 58.908 40.000 0.00 0.00 0.00 4.79
1399 1585 6.542821 TCTATCATGGTTTATTAGCCCCTTG 58.457 40.000 0.00 0.00 0.00 3.61
1401 1587 3.270960 TCATGGTTTATTAGCCCCTTGGT 59.729 43.478 0.00 0.00 0.00 3.67
1402 1588 4.479056 TCATGGTTTATTAGCCCCTTGGTA 59.521 41.667 0.00 0.00 0.00 3.25
1403 1589 4.513406 TGGTTTATTAGCCCCTTGGTAG 57.487 45.455 0.00 0.00 0.00 3.18
1408 1594 6.211986 GGTTTATTAGCCCCTTGGTAGTTTTT 59.788 38.462 0.00 0.00 0.00 1.94
1456 1643 3.210358 ACAAAATGTTAATGCCCGTCG 57.790 42.857 0.00 0.00 0.00 5.12
1457 1644 2.554893 ACAAAATGTTAATGCCCGTCGT 59.445 40.909 0.00 0.00 0.00 4.34
1458 1645 3.752222 ACAAAATGTTAATGCCCGTCGTA 59.248 39.130 0.00 0.00 0.00 3.43
1501 1689 3.740044 ATTTGAACATAGTTGCCGACG 57.260 42.857 0.00 0.00 0.00 5.12
1580 1770 7.998964 ACAATATGACTCTAAATACAAAGGGGG 59.001 37.037 0.00 0.00 0.00 5.40
1635 1825 7.065324 TCGGCACCTCTTATTTTTGTATTACTG 59.935 37.037 0.00 0.00 0.00 2.74
1671 1861 4.450976 TGTGATTTGTATCTTCCCATCCG 58.549 43.478 0.00 0.00 0.00 4.18
1723 1913 1.159285 CCAGCCTACATGTGTGTGTG 58.841 55.000 9.11 0.00 39.39 3.82
1992 2182 5.299949 TGCATCATAGCGTAATCAGTTCAT 58.700 37.500 0.00 0.00 37.31 2.57
2037 2227 6.569179 TTTCAAGAGTGCAATAGTTTACCC 57.431 37.500 0.00 0.00 0.00 3.69
2106 2297 3.004171 GGTGACAACCAAAACCCAAAAC 58.996 45.455 0.00 0.00 46.75 2.43
2122 2313 6.292150 ACCCAAAACAGAAAAACAGAAACAA 58.708 32.000 0.00 0.00 0.00 2.83
2208 2400 1.273327 CATGGAGTTTTGGTTCCCAGC 59.727 52.381 0.00 0.00 33.81 4.85
2288 2483 6.665474 TTTTATGGCAAACATTGATGCATC 57.335 33.333 20.14 20.14 44.32 3.91
2458 2654 5.805994 GGAAGTTTACATGTACGGAGAGAAG 59.194 44.000 4.68 0.00 0.00 2.85
2475 2671 7.307751 CGGAGAGAAGTAAGCAACATTTGTTTA 60.308 37.037 0.00 0.00 35.83 2.01
2540 2736 7.171508 TGCTATTTTCTGGAGTTATGCTATTCG 59.828 37.037 0.00 0.00 0.00 3.34
2544 2740 6.954487 TTCTGGAGTTATGCTATTCGTAGA 57.046 37.500 0.00 0.00 0.00 2.59
2555 2751 6.156748 TGCTATTCGTAGAAGGAGCATTTA 57.843 37.500 14.32 0.00 45.90 1.40
2560 2756 5.086104 TCGTAGAAGGAGCATTTAAGCTT 57.914 39.130 3.48 3.48 46.75 3.74
2726 2922 7.489160 AGAGTGGTTAATTGTTTTCTTTGGTC 58.511 34.615 0.00 0.00 0.00 4.02
2763 2959 5.587388 ATGAATTGCTTGAATGATCGGTT 57.413 34.783 0.00 0.00 0.00 4.44
2905 3101 6.451292 TGTTTGTAAGGAACTATAACCCCA 57.549 37.500 0.00 0.00 38.49 4.96
2950 3146 5.017294 ACTTCAGATAGCCACTTAAGCTC 57.983 43.478 1.29 0.00 41.83 4.09
3223 3419 9.694137 TTCTTAACTCAGCTTCTTAACTACTTC 57.306 33.333 0.00 0.00 0.00 3.01
3260 3456 8.836413 TCATTGTAGGCAAACTATTTATGCTAC 58.164 33.333 0.00 0.00 39.94 3.58
3261 3457 6.838198 TGTAGGCAAACTATTTATGCTACG 57.162 37.500 0.00 0.00 39.94 3.51
3262 3458 6.342906 TGTAGGCAAACTATTTATGCTACGT 58.657 36.000 0.00 0.00 39.94 3.57
3263 3459 7.490840 TGTAGGCAAACTATTTATGCTACGTA 58.509 34.615 0.00 0.00 39.94 3.57
3523 3721 6.148315 GCCCACTACGTACAGATAAAGTTTTT 59.852 38.462 0.00 0.00 0.00 1.94
3559 3757 3.871006 TCATACGTGATGCTCCATGTTTC 59.129 43.478 0.00 0.00 37.46 2.78
3731 3929 1.440708 CTCAGTCAGGCTGCTTGAAG 58.559 55.000 16.40 11.87 44.66 3.02
3761 3959 5.413213 TCGGATTGGCGAAGAAATTTCTTTA 59.587 36.000 29.24 16.03 46.84 1.85
3998 4196 8.066668 TGTGCGTAGGTTGATTTTTATTTTTG 57.933 30.769 0.00 0.00 0.00 2.44
3999 4197 7.707035 TGTGCGTAGGTTGATTTTTATTTTTGT 59.293 29.630 0.00 0.00 0.00 2.83
4027 4225 4.873010 TCTTCCTACAGCCTTGATAGTCT 58.127 43.478 0.00 0.00 0.00 3.24
4035 4233 3.701542 CAGCCTTGATAGTCTGTGTCCTA 59.298 47.826 0.00 0.00 0.00 2.94
4299 4498 1.483004 GAGACCACTTCCTAGGCCTTC 59.517 57.143 12.58 0.00 0.00 3.46
4375 4574 5.233050 CAGACGAGTATTGTTGTGGATGATC 59.767 44.000 0.00 0.00 28.27 2.92
4379 4578 6.092670 ACGAGTATTGTTGTGGATGATCTTTG 59.907 38.462 0.00 0.00 0.00 2.77
4401 4602 2.108075 TCACAGAAAGCAGGGGAATTCA 59.892 45.455 7.93 0.00 0.00 2.57
4409 4610 3.094572 AGCAGGGGAATTCATTGAAGTG 58.905 45.455 7.93 0.00 0.00 3.16
4432 4633 3.550692 AAAAACTTGGGTGGGAGGG 57.449 52.632 0.00 0.00 0.00 4.30
4433 4634 0.105194 AAAAACTTGGGTGGGAGGGG 60.105 55.000 0.00 0.00 0.00 4.79
4434 4635 2.031123 AAAACTTGGGTGGGAGGGGG 62.031 60.000 0.00 0.00 0.00 5.40
4448 4649 2.534533 GGGGGAGGGGGTTCTGTT 60.535 66.667 0.00 0.00 0.00 3.16
4449 4650 2.763902 GGGGAGGGGGTTCTGTTG 59.236 66.667 0.00 0.00 0.00 3.33
4450 4651 2.160853 GGGGAGGGGGTTCTGTTGT 61.161 63.158 0.00 0.00 0.00 3.32
4452 4653 1.069775 GGGAGGGGGTTCTGTTGTTA 58.930 55.000 0.00 0.00 0.00 2.41
4453 4654 1.004394 GGGAGGGGGTTCTGTTGTTAG 59.996 57.143 0.00 0.00 0.00 2.34
4488 4880 2.029918 CCTTTTTGTAGCCTGCTTGGTC 60.030 50.000 0.00 0.00 38.35 4.02
4489 4881 2.656947 TTTTGTAGCCTGCTTGGTCT 57.343 45.000 0.00 0.00 38.35 3.85
4490 4882 2.656947 TTTGTAGCCTGCTTGGTCTT 57.343 45.000 0.00 0.00 38.35 3.01
4491 4883 1.896220 TTGTAGCCTGCTTGGTCTTG 58.104 50.000 0.00 0.00 38.35 3.02
4492 4884 0.036732 TGTAGCCTGCTTGGTCTTGG 59.963 55.000 0.00 0.00 38.35 3.61
4493 4885 0.036875 GTAGCCTGCTTGGTCTTGGT 59.963 55.000 0.00 0.00 38.35 3.67
4514 4906 3.472283 TTTGTACTTGCGGGTTCACTA 57.528 42.857 0.00 0.00 0.00 2.74
4515 4907 3.472283 TTGTACTTGCGGGTTCACTAA 57.528 42.857 0.00 0.00 0.00 2.24
4516 4908 3.688694 TGTACTTGCGGGTTCACTAAT 57.311 42.857 0.00 0.00 0.00 1.73
4518 4910 4.497300 TGTACTTGCGGGTTCACTAATAC 58.503 43.478 0.00 0.00 0.00 1.89
4525 4917 4.762765 TGCGGGTTCACTAATACACAAAAT 59.237 37.500 0.00 0.00 0.00 1.82
4526 4918 5.241949 TGCGGGTTCACTAATACACAAAATT 59.758 36.000 0.00 0.00 0.00 1.82
4527 4919 5.798434 GCGGGTTCACTAATACACAAAATTC 59.202 40.000 0.00 0.00 0.00 2.17
4672 5066 1.915078 ATTTACCGAGCCTGCTGCCT 61.915 55.000 0.00 0.00 42.71 4.75
4863 5260 7.562821 AGGATTTCCAAATCAAAGGAATAGGAG 59.437 37.037 12.91 0.00 45.10 3.69
4877 5274 9.453830 AAAGGAATAGGAGAAGTATAGGATTGT 57.546 33.333 0.00 0.00 0.00 2.71
5144 5548 5.984926 TGTACCTGTACTTCACTTTTAACCG 59.015 40.000 8.75 0.00 37.00 4.44
5534 5940 0.179134 ACGCGAGTACCAGCATTCTC 60.179 55.000 15.93 0.00 46.88 2.87
5603 6009 2.697751 CTCCCTGAGAATCCCACTGTAG 59.302 54.545 0.00 0.00 0.00 2.74
5626 6035 3.618690 AATCCTCTGGCAGTCACTAAC 57.381 47.619 15.27 0.00 0.00 2.34
5702 6111 3.018423 AGGTGGATAATCTTGCAACCC 57.982 47.619 0.00 0.00 0.00 4.11
5776 6185 3.570125 TCACTAGTCCTGACAGAACAGTG 59.430 47.826 14.10 14.10 36.30 3.66
5799 6208 1.335324 GCAAGCACAGCAAGTCGAAAT 60.335 47.619 0.00 0.00 0.00 2.17
5896 6305 2.089980 AGATCTGCAAACATCAGTGCC 58.910 47.619 0.00 0.00 40.14 5.01
5911 6320 0.037447 GTGCCCTCAGAAAGCTCCTT 59.963 55.000 0.00 0.00 0.00 3.36
5925 6334 7.013083 CAGAAAGCTCCTTAGTTATGATGCAAT 59.987 37.037 0.00 0.00 0.00 3.56
5941 6350 1.945819 GCAATGTCGGAAGAAGGCAGA 60.946 52.381 0.00 0.00 45.01 4.26
5974 6383 1.392589 AAAATTCGCATGCCCTCGAT 58.607 45.000 13.15 0.00 34.48 3.59
6020 6429 0.911769 TGGGTATCCTCTTGCCACAG 59.088 55.000 0.00 0.00 0.00 3.66
6034 6443 1.012086 CCACAGCACCTCATGATTCG 58.988 55.000 0.00 0.00 0.00 3.34
6153 6562 4.993584 GTGTCTTCTTTCATGCAGAGAGAA 59.006 41.667 14.17 14.17 43.07 2.87
6205 6614 4.821589 CGCGACAGGGAGGAAGGC 62.822 72.222 0.00 0.00 0.00 4.35
6210 6619 1.383248 ACAGGGAGGAAGGCGCTAT 60.383 57.895 7.64 0.00 0.00 2.97
6213 6622 2.340443 GGAGGAAGGCGCTATCGG 59.660 66.667 7.64 0.00 35.95 4.18
6220 6629 0.179108 AAGGCGCTATCGGAAGTGAC 60.179 55.000 7.64 0.05 35.08 3.67
6313 6722 3.269178 GCATGAAGAAGAGACCCTGAAG 58.731 50.000 0.00 0.00 0.00 3.02
6348 6757 0.307760 CAGAACGGTTTCCACAGTGC 59.692 55.000 0.00 0.00 30.88 4.40
6495 6906 5.399858 TCAGAAAATAGACGAGCTACACAC 58.600 41.667 0.00 0.00 0.00 3.82
6606 7019 9.329913 GAAGTTATGTTGTTGTAACATCATGTC 57.670 33.333 22.29 16.69 44.59 3.06
6644 7057 9.807649 GAGCATCTCCAACAAATAATGTAAAAT 57.192 29.630 0.00 0.00 42.99 1.82
6677 7091 5.722021 AAAACGTTTTTAGGGCATGAGAT 57.278 34.783 20.26 0.00 0.00 2.75
6690 7104 4.273318 GGCATGAGATAGAAGGTTTTGGT 58.727 43.478 0.00 0.00 0.00 3.67
6716 7130 3.486708 CGCAGCAGTTGTCACTTTAACAA 60.487 43.478 0.00 0.00 34.37 2.83
6719 7133 5.505286 CAGCAGTTGTCACTTTAACAAGAG 58.495 41.667 0.00 0.00 37.30 2.85
6733 7147 8.257306 ACTTTAACAAGAGGATTTGCTCAAAAA 58.743 29.630 1.84 0.00 32.32 1.94
6820 7943 1.003866 GACTTTGCGAGACCACAACAC 60.004 52.381 0.00 0.00 0.00 3.32
6821 7944 1.299541 CTTTGCGAGACCACAACACT 58.700 50.000 0.00 0.00 0.00 3.55
6890 8020 2.192624 GTGCATCACAACCACAAACAC 58.807 47.619 0.00 0.00 34.08 3.32
6965 8099 4.654915 TCTTCATCATTTGCTTCCACTCA 58.345 39.130 0.00 0.00 0.00 3.41
6968 8102 5.988310 TCATCATTTGCTTCCACTCAATT 57.012 34.783 0.00 0.00 0.00 2.32
7000 8134 0.032912 TCCATTGCCATCAGTGCCAT 60.033 50.000 0.00 0.00 0.00 4.40
7003 8137 1.108776 ATTGCCATCAGTGCCATCAC 58.891 50.000 0.00 0.00 43.44 3.06
7029 8163 3.507103 TCATTTTCATCCATTGCACCG 57.493 42.857 0.00 0.00 0.00 4.94
7066 8200 3.660571 CTCCCATGGCACCACCCA 61.661 66.667 6.09 0.00 39.65 4.51
7067 8201 2.946084 TCCCATGGCACCACCCAT 60.946 61.111 6.09 0.00 46.35 4.00
7074 8208 0.040942 TGGCACCACCCATATGCTTT 59.959 50.000 0.00 0.00 39.38 3.51
7119 8253 2.666190 CGCATGCCTCCCATACCG 60.666 66.667 13.15 0.00 31.47 4.02
7124 8258 1.481056 ATGCCTCCCATACCGCCTAC 61.481 60.000 0.00 0.00 30.69 3.18
7186 8320 5.203528 CCATAAATCCTCCCATGTCAAACT 58.796 41.667 0.00 0.00 0.00 2.66
7286 8420 6.065976 TCATCAAGACCACTTATGTCCATT 57.934 37.500 0.00 0.00 34.70 3.16
7364 8498 1.201429 TCTCCTCAACCCCTGCCTTC 61.201 60.000 0.00 0.00 0.00 3.46
7398 8532 1.613630 GCCCTCCTCTCCTTGGTCA 60.614 63.158 0.00 0.00 0.00 4.02
7401 8535 0.749649 CCTCCTCTCCTTGGTCATCG 59.250 60.000 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.519191 TGCAATGTGATATAAATAGCCAATAGT 57.481 29.630 0.00 0.00 0.00 2.12
23 24 9.647797 CATTGCAATGTGATATAAATAGCCAAT 57.352 29.630 27.81 0.00 0.00 3.16
24 25 7.599621 GCATTGCAATGTGATATAAATAGCCAA 59.400 33.333 33.67 0.00 38.65 4.52
25 26 7.092079 GCATTGCAATGTGATATAAATAGCCA 58.908 34.615 33.67 0.00 38.65 4.75
26 27 7.062605 GTGCATTGCAATGTGATATAAATAGCC 59.937 37.037 33.67 16.31 41.47 3.93
27 28 7.201291 CGTGCATTGCAATGTGATATAAATAGC 60.201 37.037 33.67 18.71 41.47 2.97
28 29 8.016801 TCGTGCATTGCAATGTGATATAAATAG 58.983 33.333 33.67 15.50 41.47 1.73
29 30 7.869800 TCGTGCATTGCAATGTGATATAAATA 58.130 30.769 33.67 11.22 41.47 1.40
30 31 6.737118 TCGTGCATTGCAATGTGATATAAAT 58.263 32.000 33.67 0.00 41.47 1.40
31 32 6.129053 TCGTGCATTGCAATGTGATATAAA 57.871 33.333 33.67 13.57 41.47 1.40
32 33 5.747951 TCGTGCATTGCAATGTGATATAA 57.252 34.783 33.67 14.92 41.47 0.98
33 34 4.319694 GCTCGTGCATTGCAATGTGATATA 60.320 41.667 33.67 17.31 41.47 0.86
34 35 3.549423 GCTCGTGCATTGCAATGTGATAT 60.549 43.478 33.67 0.63 41.47 1.63
35 36 2.223317 GCTCGTGCATTGCAATGTGATA 60.223 45.455 33.67 19.36 41.47 2.15
36 37 1.468565 GCTCGTGCATTGCAATGTGAT 60.469 47.619 33.67 2.21 41.47 3.06
37 38 0.109643 GCTCGTGCATTGCAATGTGA 60.110 50.000 33.67 26.89 41.47 3.58
38 39 0.387494 TGCTCGTGCATTGCAATGTG 60.387 50.000 33.67 24.80 45.31 3.21
39 40 1.958323 TGCTCGTGCATTGCAATGT 59.042 47.368 33.67 3.82 45.31 2.71
40 41 4.872418 TGCTCGTGCATTGCAATG 57.128 50.000 30.92 30.92 45.31 2.82
49 50 5.119279 CACTATATTAGGACAATGCTCGTGC 59.881 44.000 1.71 1.71 40.20 5.34
50 51 5.635280 CCACTATATTAGGACAATGCTCGTG 59.365 44.000 0.00 0.00 0.00 4.35
51 52 5.538813 TCCACTATATTAGGACAATGCTCGT 59.461 40.000 0.00 0.00 0.00 4.18
52 53 6.025749 TCCACTATATTAGGACAATGCTCG 57.974 41.667 0.00 0.00 0.00 5.03
53 54 6.998802 ACTCCACTATATTAGGACAATGCTC 58.001 40.000 0.00 0.00 0.00 4.26
54 55 8.671987 ATACTCCACTATATTAGGACAATGCT 57.328 34.615 0.00 0.00 0.00 3.79
80 81 9.803507 TTTCAGGCTTTCTATAATGATGATGAT 57.196 29.630 0.00 0.00 0.00 2.45
81 82 9.281371 CTTTCAGGCTTTCTATAATGATGATGA 57.719 33.333 0.00 0.00 0.00 2.92
82 83 8.512956 CCTTTCAGGCTTTCTATAATGATGATG 58.487 37.037 0.00 0.00 0.00 3.07
83 84 7.668886 CCCTTTCAGGCTTTCTATAATGATGAT 59.331 37.037 0.00 0.00 32.73 2.45
84 85 7.000472 CCCTTTCAGGCTTTCTATAATGATGA 59.000 38.462 0.00 0.00 32.73 2.92
85 86 6.208204 CCCCTTTCAGGCTTTCTATAATGATG 59.792 42.308 0.00 0.00 32.73 3.07
86 87 6.310149 CCCCTTTCAGGCTTTCTATAATGAT 58.690 40.000 0.00 0.00 32.73 2.45
87 88 5.694995 CCCCTTTCAGGCTTTCTATAATGA 58.305 41.667 0.00 0.00 32.73 2.57
100 101 1.276138 GTTGGATTTGCCCCTTTCAGG 59.724 52.381 0.00 0.00 34.97 3.86
101 102 2.250924 AGTTGGATTTGCCCCTTTCAG 58.749 47.619 0.00 0.00 34.97 3.02
102 103 2.397044 AGTTGGATTTGCCCCTTTCA 57.603 45.000 0.00 0.00 34.97 2.69
103 104 4.281657 AGATAGTTGGATTTGCCCCTTTC 58.718 43.478 0.00 0.00 34.97 2.62
104 105 4.337264 AGATAGTTGGATTTGCCCCTTT 57.663 40.909 0.00 0.00 34.97 3.11
105 106 4.337264 AAGATAGTTGGATTTGCCCCTT 57.663 40.909 0.00 0.00 34.97 3.95
106 107 4.337264 AAAGATAGTTGGATTTGCCCCT 57.663 40.909 0.00 0.00 34.97 4.79
107 108 5.420725 AAAAAGATAGTTGGATTTGCCCC 57.579 39.130 0.00 0.00 34.97 5.80
129 130 8.973182 GGGTTGGGTATTAATTGATAGTTCAAA 58.027 33.333 0.00 0.00 44.70 2.69
130 131 7.562088 GGGGTTGGGTATTAATTGATAGTTCAA 59.438 37.037 0.00 0.00 45.57 2.69
131 132 7.064229 GGGGTTGGGTATTAATTGATAGTTCA 58.936 38.462 0.00 0.00 0.00 3.18
132 133 7.295340 AGGGGTTGGGTATTAATTGATAGTTC 58.705 38.462 0.00 0.00 0.00 3.01
133 134 7.233855 AGGGGTTGGGTATTAATTGATAGTT 57.766 36.000 0.00 0.00 0.00 2.24
134 135 6.858792 AGGGGTTGGGTATTAATTGATAGT 57.141 37.500 0.00 0.00 0.00 2.12
135 136 8.547481 AAAAGGGGTTGGGTATTAATTGATAG 57.453 34.615 0.00 0.00 0.00 2.08
136 137 8.919018 AAAAAGGGGTTGGGTATTAATTGATA 57.081 30.769 0.00 0.00 0.00 2.15
137 138 7.822749 AAAAAGGGGTTGGGTATTAATTGAT 57.177 32.000 0.00 0.00 0.00 2.57
173 174 9.574516 ACAGTTTTCTCTTAACATGGAATACTT 57.425 29.630 0.00 0.00 31.37 2.24
174 175 9.220767 GACAGTTTTCTCTTAACATGGAATACT 57.779 33.333 0.00 0.00 32.97 2.12
175 176 8.999431 TGACAGTTTTCTCTTAACATGGAATAC 58.001 33.333 0.00 0.00 0.00 1.89
176 177 9.567776 TTGACAGTTTTCTCTTAACATGGAATA 57.432 29.630 0.00 0.00 0.00 1.75
177 178 8.463930 TTGACAGTTTTCTCTTAACATGGAAT 57.536 30.769 0.00 0.00 0.00 3.01
178 179 7.873719 TTGACAGTTTTCTCTTAACATGGAA 57.126 32.000 0.00 0.00 0.00 3.53
179 180 8.352201 CAATTGACAGTTTTCTCTTAACATGGA 58.648 33.333 0.00 0.00 0.00 3.41
180 181 7.115378 GCAATTGACAGTTTTCTCTTAACATGG 59.885 37.037 10.34 0.00 0.00 3.66
181 182 7.864379 AGCAATTGACAGTTTTCTCTTAACATG 59.136 33.333 10.34 0.00 0.00 3.21
182 183 7.864379 CAGCAATTGACAGTTTTCTCTTAACAT 59.136 33.333 10.34 0.00 0.00 2.71
183 184 7.195646 CAGCAATTGACAGTTTTCTCTTAACA 58.804 34.615 10.34 0.00 0.00 2.41
184 185 6.638468 CCAGCAATTGACAGTTTTCTCTTAAC 59.362 38.462 10.34 0.00 0.00 2.01
185 186 6.321181 ACCAGCAATTGACAGTTTTCTCTTAA 59.679 34.615 10.34 0.00 0.00 1.85
186 187 5.827797 ACCAGCAATTGACAGTTTTCTCTTA 59.172 36.000 10.34 0.00 0.00 2.10
190 191 6.096846 ACTTAACCAGCAATTGACAGTTTTCT 59.903 34.615 10.34 0.00 0.00 2.52
197 198 4.460263 AGTGACTTAACCAGCAATTGACA 58.540 39.130 10.34 0.00 0.00 3.58
202 203 4.973168 TGAAGAGTGACTTAACCAGCAAT 58.027 39.130 0.00 0.00 39.13 3.56
203 204 4.415881 TGAAGAGTGACTTAACCAGCAA 57.584 40.909 0.00 0.00 39.13 3.91
209 211 8.770438 AGATCAAGAATGAAGAGTGACTTAAC 57.230 34.615 0.00 0.00 39.49 2.01
237 245 7.907045 GTGCAAGACAATCTGTGAATACATAAG 59.093 37.037 0.00 0.00 35.97 1.73
277 289 6.431234 TCTCAGCCTGAAGTTTAGAAAATTCC 59.569 38.462 11.43 0.00 40.98 3.01
321 471 4.151798 GTGCGCTGTATTTCAAGAGTTTC 58.848 43.478 9.73 0.00 0.00 2.78
322 472 3.563808 TGTGCGCTGTATTTCAAGAGTTT 59.436 39.130 9.73 0.00 0.00 2.66
323 473 3.138304 TGTGCGCTGTATTTCAAGAGTT 58.862 40.909 9.73 0.00 0.00 3.01
324 474 2.738846 CTGTGCGCTGTATTTCAAGAGT 59.261 45.455 9.73 0.00 0.00 3.24
325 475 2.995939 TCTGTGCGCTGTATTTCAAGAG 59.004 45.455 9.73 0.00 0.00 2.85
326 476 3.038788 TCTGTGCGCTGTATTTCAAGA 57.961 42.857 9.73 0.00 0.00 3.02
327 477 3.811722 TTCTGTGCGCTGTATTTCAAG 57.188 42.857 9.73 0.00 0.00 3.02
328 478 4.455533 AGATTTCTGTGCGCTGTATTTCAA 59.544 37.500 9.73 0.00 0.00 2.69
329 479 4.002982 AGATTTCTGTGCGCTGTATTTCA 58.997 39.130 9.73 0.00 0.00 2.69
330 480 4.337763 CAGATTTCTGTGCGCTGTATTTC 58.662 43.478 9.73 0.00 39.09 2.17
331 481 4.346734 CAGATTTCTGTGCGCTGTATTT 57.653 40.909 9.73 0.00 39.09 1.40
357 507 0.850100 TTTCCCTCTTCTGCCCACAA 59.150 50.000 0.00 0.00 0.00 3.33
358 508 0.850100 TTTTCCCTCTTCTGCCCACA 59.150 50.000 0.00 0.00 0.00 4.17
495 646 4.806339 AGAGGGGCGGAAGGGAGG 62.806 72.222 0.00 0.00 0.00 4.30
513 664 2.284798 CTGGTGGTGATCGACGAGGG 62.285 65.000 3.01 0.00 0.00 4.30
587 738 1.133976 ACCATATGAGCCTTGCTGGAC 60.134 52.381 3.65 0.00 39.88 4.02
588 739 1.216064 ACCATATGAGCCTTGCTGGA 58.784 50.000 3.65 0.00 39.88 3.86
589 740 2.062971 AACCATATGAGCCTTGCTGG 57.937 50.000 3.65 0.00 39.88 4.85
590 741 2.360165 GGAAACCATATGAGCCTTGCTG 59.640 50.000 3.65 0.00 39.88 4.41
602 753 7.447238 GGATTGGATCGAAATTAGGAAACCATA 59.553 37.037 0.00 0.00 0.00 2.74
625 777 1.979308 CAGAGGAGATGCCAGATGGAT 59.021 52.381 2.18 0.00 40.02 3.41
656 810 3.123620 GCAGAACAGAGCAGCCCG 61.124 66.667 0.00 0.00 0.00 6.13
692 846 3.245371 GGATATCCAATCCAATCCAGGCA 60.245 47.826 17.34 0.00 38.23 4.75
693 847 3.359950 GGATATCCAATCCAATCCAGGC 58.640 50.000 17.34 0.00 38.23 4.85
694 848 3.623203 CGGGATATCCAATCCAATCCAGG 60.623 52.174 23.27 0.00 39.79 4.45
695 849 3.009473 ACGGGATATCCAATCCAATCCAG 59.991 47.826 23.27 0.00 39.79 3.86
711 869 1.173913 GCCAGCAAGTAAAACGGGAT 58.826 50.000 0.00 0.00 0.00 3.85
757 915 6.009115 TCAAACGGAAAAATTAAGGAGCTC 57.991 37.500 4.71 4.71 0.00 4.09
796 954 2.347490 GCGCTCCTGAGGTGGAAA 59.653 61.111 0.00 0.00 35.43 3.13
797 955 2.922503 TGCGCTCCTGAGGTGGAA 60.923 61.111 9.73 0.00 35.43 3.53
798 956 3.695606 GTGCGCTCCTGAGGTGGA 61.696 66.667 9.73 0.00 34.52 4.02
815 973 2.076863 AGGAAAGAATCGTCAAAGGCG 58.923 47.619 0.00 0.00 0.00 5.52
822 980 7.511463 GTCAAGTAAGAAAGGAAAGAATCGTC 58.489 38.462 0.00 0.00 0.00 4.20
824 982 6.526222 CGTCAAGTAAGAAAGGAAAGAATCG 58.474 40.000 0.00 0.00 0.00 3.34
856 1016 1.889170 CCACAGAAAGAAAGGAAGGGC 59.111 52.381 0.00 0.00 0.00 5.19
893 1056 2.942710 ACGAATATAGAATCCGCACGG 58.057 47.619 1.73 1.73 0.00 4.94
898 1061 5.862323 ACCGATCAAACGAATATAGAATCCG 59.138 40.000 0.00 0.00 35.09 4.18
934 1097 4.509600 TGACAACCAAAATCGCAAAAATCC 59.490 37.500 0.00 0.00 0.00 3.01
935 1098 5.649602 TGACAACCAAAATCGCAAAAATC 57.350 34.783 0.00 0.00 0.00 2.17
937 1100 5.672321 GCTTTGACAACCAAAATCGCAAAAA 60.672 36.000 0.00 0.00 43.50 1.94
1050 1235 1.882167 GAGATCAGAGCACGCCAGC 60.882 63.158 0.00 0.00 0.00 4.85
1088 1273 5.946942 AATCTGCTTCTTGACCAGAGATA 57.053 39.130 0.00 0.00 38.82 1.98
1104 1289 2.670414 CAGAGACGACTCCAAAATCTGC 59.330 50.000 11.32 0.00 43.53 4.26
1200 1385 6.235231 ACAGTTATGACTATTAGTGGTGGG 57.765 41.667 0.00 0.00 33.90 4.61
1373 1559 6.091555 AGGGGCTAATAAACCATGATAGAGA 58.908 40.000 0.00 0.00 0.00 3.10
1377 1563 5.135362 ACCAAGGGGCTAATAAACCATGATA 59.865 40.000 0.00 0.00 37.90 2.15
1378 1564 4.078630 ACCAAGGGGCTAATAAACCATGAT 60.079 41.667 0.00 0.00 37.90 2.45
1381 1567 4.480908 ACTACCAAGGGGCTAATAAACCAT 59.519 41.667 0.00 0.00 37.90 3.55
1580 1770 6.990798 ACTACCTCCGTCCTAATTTATTAGC 58.009 40.000 4.33 0.00 38.69 3.09
1607 1797 7.404671 AATACAAAAATAAGAGGTGCCGATT 57.595 32.000 0.00 0.00 0.00 3.34
1671 1861 9.798994 AATGAATCTACAATGAGAAGCAAATTC 57.201 29.630 0.00 0.00 38.28 2.17
1723 1913 6.230472 AGAAGGCATAACCCAAAATGAAAAC 58.770 36.000 0.00 0.00 40.58 2.43
1963 2153 6.128035 ACTGATTACGCTATGATGCAAAACAA 60.128 34.615 0.00 0.00 0.00 2.83
2106 2297 9.928236 TCTTTTGTTTTTGTTTCTGTTTTTCTG 57.072 25.926 0.00 0.00 0.00 3.02
2122 2313 9.509855 GTTCCTGTTTTGTTTTTCTTTTGTTTT 57.490 25.926 0.00 0.00 0.00 2.43
2272 2467 4.092383 GGTGAAAGATGCATCAATGTTTGC 59.908 41.667 27.81 12.39 39.33 3.68
2288 2483 3.441496 AACATTGCACACAGGTGAAAG 57.559 42.857 6.40 0.00 45.63 2.62
2349 2544 8.389779 TCACAAATAGTCTTTTTGTAGCATCA 57.610 30.769 17.60 0.80 43.51 3.07
2525 2721 6.328641 TCCTTCTACGAATAGCATAACTCC 57.671 41.667 0.00 0.00 0.00 3.85
2540 2736 4.336713 CCCAAGCTTAAATGCTCCTTCTAC 59.663 45.833 0.00 0.00 43.24 2.59
2544 2740 3.359950 CTCCCAAGCTTAAATGCTCCTT 58.640 45.455 0.00 0.00 43.24 3.36
2726 2922 4.728882 GCAATTCATAGAACTTGCACGGAG 60.729 45.833 15.42 0.00 42.66 4.63
2763 2959 7.857456 TCCTGCTTCACCTACAAAATAGAATA 58.143 34.615 0.00 0.00 0.00 1.75
2920 3116 6.299805 AGTGGCTATCTGAAGTTATTGTGA 57.700 37.500 0.00 0.00 0.00 3.58
2950 3146 7.639850 CACATGTACCTATGAATAAAAACAGCG 59.360 37.037 0.00 0.00 0.00 5.18
3223 3419 0.299895 CTACAATGAAGAGCGCGCAG 59.700 55.000 35.10 13.84 0.00 5.18
3260 3456 5.201713 TCAAGGAGCAGGATTCTAATACG 57.798 43.478 0.00 0.00 0.00 3.06
3261 3457 6.652900 GGAATCAAGGAGCAGGATTCTAATAC 59.347 42.308 11.87 0.00 43.92 1.89
3262 3458 6.560304 AGGAATCAAGGAGCAGGATTCTAATA 59.440 38.462 11.87 0.00 43.92 0.98
3263 3459 5.372066 AGGAATCAAGGAGCAGGATTCTAAT 59.628 40.000 11.87 0.00 43.92 1.73
3274 3470 1.556911 TGACTGGAGGAATCAAGGAGC 59.443 52.381 0.00 0.00 0.00 4.70
3523 3721 7.201522 GCATCACGTATGAATCAACACTCTTTA 60.202 37.037 8.57 0.00 38.69 1.85
3559 3757 3.049206 CGGGCAACATGTTTACTTTGTG 58.951 45.455 8.77 0.00 39.74 3.33
3731 3929 2.550978 TCTTCGCCAATCCGAATCTTC 58.449 47.619 0.00 0.00 45.03 2.87
3761 3959 7.839680 AATTTAGTCTTCAACCAACCTGATT 57.160 32.000 0.00 0.00 0.00 2.57
3998 4196 1.903183 AGGCTGTAGGAAGAGGTTCAC 59.097 52.381 0.00 0.00 33.93 3.18
3999 4197 2.303022 CAAGGCTGTAGGAAGAGGTTCA 59.697 50.000 0.00 0.00 33.93 3.18
4027 4225 7.717875 AGCAGTAAATAAACAAACTAGGACACA 59.282 33.333 0.00 0.00 0.00 3.72
4090 4288 3.979101 TCCATGTGTCTGCATACTGAA 57.021 42.857 3.71 0.00 0.00 3.02
4299 4498 6.086765 GTGAAAAGATAGTGTGCACAATTTCG 59.913 38.462 26.24 0.00 29.62 3.46
4375 4574 1.610522 CCCCTGCTTTCTGTGACAAAG 59.389 52.381 0.00 0.00 34.47 2.77
4379 4578 2.206576 ATTCCCCTGCTTTCTGTGAC 57.793 50.000 0.00 0.00 0.00 3.67
4416 4617 2.478803 CCCCCTCCCACCCAAGTTT 61.479 63.158 0.00 0.00 0.00 2.66
4417 4618 2.863988 CCCCCTCCCACCCAAGTT 60.864 66.667 0.00 0.00 0.00 2.66
4431 4632 2.534533 AACAGAACCCCCTCCCCC 60.535 66.667 0.00 0.00 0.00 5.40
4432 4633 1.726192 AACAACAGAACCCCCTCCCC 61.726 60.000 0.00 0.00 0.00 4.81
4433 4634 1.004394 CTAACAACAGAACCCCCTCCC 59.996 57.143 0.00 0.00 0.00 4.30
4434 4635 1.703513 ACTAACAACAGAACCCCCTCC 59.296 52.381 0.00 0.00 0.00 4.30
4435 4636 3.503800 AACTAACAACAGAACCCCCTC 57.496 47.619 0.00 0.00 0.00 4.30
4436 4637 3.329814 CCTAACTAACAACAGAACCCCCT 59.670 47.826 0.00 0.00 0.00 4.79
4438 4639 3.079578 GCCTAACTAACAACAGAACCCC 58.920 50.000 0.00 0.00 0.00 4.95
4439 4640 3.079578 GGCCTAACTAACAACAGAACCC 58.920 50.000 0.00 0.00 0.00 4.11
4440 4641 3.751698 CAGGCCTAACTAACAACAGAACC 59.248 47.826 3.98 0.00 0.00 3.62
4441 4642 4.386711 ACAGGCCTAACTAACAACAGAAC 58.613 43.478 3.98 0.00 0.00 3.01
4442 4643 4.699925 ACAGGCCTAACTAACAACAGAA 57.300 40.909 3.98 0.00 0.00 3.02
4444 4645 4.504858 CCTACAGGCCTAACTAACAACAG 58.495 47.826 3.98 0.00 0.00 3.16
4488 4880 1.679153 ACCCGCAAGTACAAAACCAAG 59.321 47.619 0.00 0.00 0.00 3.61
4489 4881 1.765230 ACCCGCAAGTACAAAACCAA 58.235 45.000 0.00 0.00 0.00 3.67
4490 4882 1.677052 GAACCCGCAAGTACAAAACCA 59.323 47.619 0.00 0.00 0.00 3.67
4491 4883 1.677052 TGAACCCGCAAGTACAAAACC 59.323 47.619 0.00 0.00 0.00 3.27
4492 4884 2.356695 AGTGAACCCGCAAGTACAAAAC 59.643 45.455 0.00 0.00 0.00 2.43
4493 4885 2.645802 AGTGAACCCGCAAGTACAAAA 58.354 42.857 0.00 0.00 0.00 2.44
4573 4967 0.807496 GCCCATCTTGCAGACTGTTC 59.193 55.000 3.99 0.00 0.00 3.18
4672 5066 1.061735 TGCCCATGGGTGATAGGAGTA 60.062 52.381 31.58 0.00 37.65 2.59
4731 5125 1.209747 GTAGGCTCAGTAAAGTGGGGG 59.790 57.143 0.00 0.00 0.00 5.40
4796 5190 4.984146 AGGGTGGAGCTTAATCCTTATC 57.016 45.455 0.00 0.00 40.29 1.75
4863 5260 5.012561 AGAGGGCATCACAATCCTATACTTC 59.987 44.000 0.58 0.00 0.00 3.01
4877 5274 1.198713 GAAGTGGAGAGAGGGCATCA 58.801 55.000 0.58 0.00 0.00 3.07
5144 5548 2.996631 ACTGCCCTGAATGAGTGATTC 58.003 47.619 0.00 0.00 40.99 2.52
5534 5940 0.951040 GTCACCTTCGCCTTGTCAGG 60.951 60.000 0.00 0.00 44.28 3.86
5603 6009 5.293560 GTTAGTGACTGCCAGAGGATTATC 58.706 45.833 0.00 0.00 0.00 1.75
5702 6111 1.068541 GGCTGGTTGGTTAGAAAAGCG 60.069 52.381 0.00 0.00 35.82 4.68
5776 6185 0.385223 CGACTTGCTGTGCTTGCTTC 60.385 55.000 0.00 0.00 0.00 3.86
5799 6208 6.934645 CACCTCAGGACTAATCAACTGTTTAA 59.065 38.462 0.00 0.00 32.92 1.52
5896 6305 6.227298 TCATAACTAAGGAGCTTTCTGAGG 57.773 41.667 7.16 0.00 0.00 3.86
5911 6320 5.912892 TCTTCCGACATTGCATCATAACTA 58.087 37.500 0.00 0.00 0.00 2.24
5925 6334 1.293498 GCTCTGCCTTCTTCCGACA 59.707 57.895 0.00 0.00 0.00 4.35
5955 6364 1.066002 CATCGAGGGCATGCGAATTTT 59.934 47.619 12.44 0.00 40.20 1.82
5962 6371 2.315246 GAGAACATCGAGGGCATGC 58.685 57.895 9.90 9.90 0.00 4.06
5974 6383 4.098044 GGGAGATTGTCTGTATCGAGAACA 59.902 45.833 3.63 3.63 0.00 3.18
6034 6443 7.731054 AGTTCATATCTCTTAATGTGGACCTC 58.269 38.462 0.00 0.00 29.00 3.85
6071 6480 8.253810 TGACCATCAACTGAAACACAAATTTTA 58.746 29.630 0.00 0.00 0.00 1.52
6072 6481 7.102346 TGACCATCAACTGAAACACAAATTTT 58.898 30.769 0.00 0.00 0.00 1.82
6141 6550 0.674581 TTGGCGGTTCTCTCTGCATG 60.675 55.000 0.00 0.00 41.03 4.06
6153 6562 2.029380 GGCAAGAAATAAGTTTGGCGGT 60.029 45.455 0.00 0.00 37.58 5.68
6205 6614 1.002251 GGAGAGTCACTTCCGATAGCG 60.002 57.143 0.00 0.00 37.24 4.26
6210 6619 4.342951 TGTTTTTAGGAGAGTCACTTCCGA 59.657 41.667 0.00 0.00 0.00 4.55
6213 6622 6.147985 GGTCATGTTTTTAGGAGAGTCACTTC 59.852 42.308 0.00 0.00 0.00 3.01
6220 6629 3.600388 AGCGGTCATGTTTTTAGGAGAG 58.400 45.455 0.00 0.00 0.00 3.20
6313 6722 1.252175 TCTGATAGAGGCCATCGCTC 58.748 55.000 5.01 0.00 34.44 5.03
6348 6757 0.401738 TGGTCTCTTGGGCTCTTTGG 59.598 55.000 0.00 0.00 0.00 3.28
6495 6906 1.417517 TCTGATCCCCATGTTCCATCG 59.582 52.381 0.00 0.00 0.00 3.84
6514 6925 1.450531 CTGCCTCCGGAATTGCCATC 61.451 60.000 5.23 0.00 35.94 3.51
6606 7019 7.988737 TGTTGGAGATGCTCTAATAATGTTTG 58.011 34.615 0.00 0.00 33.81 2.93
6644 7057 5.348997 CCTAAAAACGTTTTTGAGCACCAAA 59.651 36.000 36.92 19.71 42.56 3.28
6677 7091 1.141254 TGCGGTGACCAAAACCTTCTA 59.859 47.619 1.11 0.00 35.39 2.10
6690 7104 1.887242 GTGACAACTGCTGCGGTGA 60.887 57.895 15.95 0.00 0.00 4.02
6733 7147 8.841300 GTGGAGTAAAAGAGAAGAAGTCAATTT 58.159 33.333 0.00 0.00 0.00 1.82
6800 7923 1.003866 GTGTTGTGGTCTCGCAAAGTC 60.004 52.381 0.00 0.00 43.87 3.01
6812 7935 6.502652 TGTTGTTTGATTATGAGTGTTGTGG 58.497 36.000 0.00 0.00 0.00 4.17
6914 8044 3.818180 AGAGGCAATGCTATTTGAGAGG 58.182 45.455 4.82 0.00 0.00 3.69
6965 8099 4.400567 GCAATGGAGAGGAAGTAAGCAATT 59.599 41.667 0.00 0.00 0.00 2.32
6968 8102 2.356125 GGCAATGGAGAGGAAGTAAGCA 60.356 50.000 0.00 0.00 0.00 3.91
7000 8134 6.424509 GCAATGGATGAAAATGAAAACAGTGA 59.575 34.615 0.00 0.00 0.00 3.41
7003 8137 6.347888 GGTGCAATGGATGAAAATGAAAACAG 60.348 38.462 0.00 0.00 0.00 3.16
7014 8148 1.902938 TGAACGGTGCAATGGATGAA 58.097 45.000 0.00 0.00 0.00 2.57
7029 8163 1.663695 CCACGGGTGATGGTATGAAC 58.336 55.000 0.00 0.00 32.08 3.18
7066 8200 6.591834 GGTATCTAGCGACATGAAAAGCATAT 59.408 38.462 0.00 0.00 34.82 1.78
7067 8201 5.926542 GGTATCTAGCGACATGAAAAGCATA 59.073 40.000 0.00 0.00 34.82 3.14
7074 8208 3.006859 CCATGGGTATCTAGCGACATGAA 59.993 47.826 2.85 0.00 38.29 2.57
7124 8258 4.394712 GAGGACTGGGTGGTGCCG 62.395 72.222 0.00 0.00 38.44 5.69
7186 8320 1.492176 GGGAGGCTTCATGATGGAAGA 59.508 52.381 10.35 0.00 45.66 2.87
7286 8420 1.614903 CAAGGGCAAAAGCTCATGACA 59.385 47.619 6.85 0.00 0.00 3.58
7313 8447 3.703052 CCATGGAAGAAAGAATCAAGGGG 59.297 47.826 5.56 0.00 0.00 4.79
7398 8532 0.175989 GCCGAGGAAAGGAGAACGAT 59.824 55.000 0.00 0.00 0.00 3.73
7401 8535 4.619852 GGCCGAGGAAAGGAGAAC 57.380 61.111 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.