Multiple sequence alignment - TraesCS2A01G246400

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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 TraesCS2A01G246400 chr2A 100.000 3221 0 0 1 3221 360751993 360748773 0.000000e+00 5949.0
1 TraesCS2A01G246400 chr2A 95.652 92 2 1 2998 3089 360748904 360748815 2.590000e-31 147.0
2 TraesCS2A01G246400 chr2A 95.652 92 2 1 3090 3179 360748996 360748905 2.590000e-31 147.0
3 TraesCS2A01G246400 chr2B 95.747 1881 35 15 756 2598 369501874 369500001 0.000000e+00 2988.0
4 TraesCS2A01G246400 chr2B 95.292 616 14 7 114 728 369502543 369501942 0.000000e+00 963.0
5 TraesCS2A01G246400 chr2B 93.187 455 22 7 2598 3052 369499971 369499526 0.000000e+00 660.0
6 TraesCS2A01G246400 chr2B 89.032 155 17 0 2597 2751 359531487 359531641 3.280000e-45 193.0
7 TraesCS2A01G246400 chr2B 84.375 160 24 1 2597 2756 4846286 4846444 4.300000e-34 156.0
8 TraesCS2A01G246400 chr2B 84.375 160 24 1 2597 2756 11120530 11120688 4.300000e-34 156.0
9 TraesCS2A01G246400 chr2B 98.507 67 1 0 3155 3221 369499530 369499464 5.640000e-23 119.0
10 TraesCS2A01G246400 chr2B 90.000 70 6 1 3133 3202 52407591 52407523 4.430000e-14 89.8
11 TraesCS2A01G246400 chr2B 95.745 47 2 0 3043 3089 52407591 52407545 3.450000e-10 76.8
12 TraesCS2A01G246400 chr2B 88.679 53 4 2 6 58 433118171 433118121 2.680000e-06 63.9
13 TraesCS2A01G246400 chr2B 88.235 51 5 1 6 56 526840060 526840011 3.470000e-05 60.2
14 TraesCS2A01G246400 chr2D 96.112 1183 33 4 1299 2478 293683393 293682221 0.000000e+00 1917.0
15 TraesCS2A01G246400 chr2D 95.347 1182 23 13 91 1249 293684528 293683356 0.000000e+00 1849.0
16 TraesCS2A01G246400 chr2D 91.385 325 19 4 2772 3089 293682123 293681801 1.370000e-118 436.0
17 TraesCS2A01G246400 chr4A 88.125 160 17 2 2597 2755 738878164 738878006 4.240000e-44 189.0
18 TraesCS2A01G246400 chr4A 90.625 128 11 1 2471 2598 738878319 738878193 5.530000e-38 169.0
19 TraesCS2A01G246400 chr7D 94.215 121 7 0 2478 2598 4787767 4787647 5.490000e-43 185.0
20 TraesCS2A01G246400 chr6B 87.342 158 17 1 2597 2751 26396147 26396304 9.180000e-41 178.0
21 TraesCS2A01G246400 chr6B 84.810 158 22 2 2597 2753 534911345 534911189 1.200000e-34 158.0
22 TraesCS2A01G246400 chrUn 87.234 141 18 0 2597 2737 355029641 355029501 9.250000e-36 161.0
23 TraesCS2A01G246400 chr7B 86.131 137 19 0 2598 2734 733133815 733133951 7.200000e-32 148.0
24 TraesCS2A01G246400 chr7B 96.970 33 1 0 3095 3127 675012124 675012092 4.490000e-04 56.5
25 TraesCS2A01G246400 chr6A 90.667 75 7 0 3133 3207 73561996 73562070 2.040000e-17 100.0
26 TraesCS2A01G246400 chr6A 97.826 46 1 0 3043 3088 73561996 73562041 2.660000e-11 80.5
27 TraesCS2A01G246400 chr6A 90.385 52 4 1 6 57 123442047 123441997 2.070000e-07 67.6
28 TraesCS2A01G246400 chr6A 91.837 49 3 1 6 54 577004681 577004728 2.070000e-07 67.6
29 TraesCS2A01G246400 chr6D 91.549 71 6 0 3133 3203 58245379 58245449 7.350000e-17 99.0
30 TraesCS2A01G246400 chr6D 97.826 46 1 0 3043 3088 58245379 58245424 2.660000e-11 80.5
31 TraesCS2A01G246400 chr6D 95.556 45 2 0 3039 3083 35626737 35626781 4.460000e-09 73.1
32 TraesCS2A01G246400 chr6D 100.000 28 0 0 3097 3124 340903853 340903880 6.000000e-03 52.8
33 TraesCS2A01G246400 chr1D 89.189 74 8 0 3134 3207 141706055 141705982 3.420000e-15 93.5
34 TraesCS2A01G246400 chr1D 97.561 41 1 0 6 46 411194902 411194942 1.600000e-08 71.3
35 TraesCS2A01G246400 chr1D 86.885 61 7 1 3028 3088 141706070 141706011 2.070000e-07 67.6
36 TraesCS2A01G246400 chr1D 100.000 28 0 0 3100 3127 193126405 193126432 6.000000e-03 52.8
37 TraesCS2A01G246400 chr1B 89.189 74 8 0 3134 3207 195591279 195591206 3.420000e-15 93.5
38 TraesCS2A01G246400 chr1B 86.885 61 7 1 3028 3088 195591294 195591235 2.070000e-07 67.6
39 TraesCS2A01G246400 chr1B 100.000 28 0 0 3005 3032 177469139 177469112 6.000000e-03 52.8
40 TraesCS2A01G246400 chr4B 88.000 75 9 0 3133 3207 270831751 270831677 4.430000e-14 89.8
41 TraesCS2A01G246400 chr4B 95.652 46 2 0 3043 3088 270831751 270831706 1.240000e-09 75.0
42 TraesCS2A01G246400 chr1A 87.838 74 9 0 3134 3207 148958895 148958968 1.590000e-13 87.9
43 TraesCS2A01G246400 chr3D 90.385 52 4 1 6 57 492121994 492121944 2.070000e-07 67.6
44 TraesCS2A01G246400 chr3D 96.774 31 1 0 3097 3127 93257513 93257483 6.000000e-03 52.8
45 TraesCS2A01G246400 chr3D 100.000 28 0 0 3097 3124 231226740 231226767 6.000000e-03 52.8
46 TraesCS2A01G246400 chr7A 93.182 44 3 0 6 49 688847950 688847907 7.460000e-07 65.8
47 TraesCS2A01G246400 chr7A 89.796 49 4 1 6 54 62186380 62186333 9.650000e-06 62.1
48 TraesCS2A01G246400 chr3A 95.122 41 2 0 6 46 45864795 45864835 7.460000e-07 65.8
49 TraesCS2A01G246400 chr5B 96.970 33 1 0 3095 3127 608638032 608638000 4.490000e-04 56.5
50 TraesCS2A01G246400 chr5D 100.000 28 0 0 3097 3124 211342423 211342450 6.000000e-03 52.8
51 TraesCS2A01G246400 chr3B 96.875 32 0 1 3093 3124 252062493 252062463 6.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G246400 chr2A 360748773 360751993 3220 True 2081.000000 5949 97.101333 1 3221 3 chr2A.!!$R1 3220
1 TraesCS2A01G246400 chr2B 369499464 369502543 3079 True 1182.500000 2988 95.683250 114 3221 4 chr2B.!!$R4 3107
2 TraesCS2A01G246400 chr2D 293681801 293684528 2727 True 1400.666667 1917 94.281333 91 3089 3 chr2D.!!$R1 2998

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
58 59 0.558712 ACCAAACTGGGGCCTTAACA 59.441 50.0 0.84 0.0 43.37 2.41 F
880 931 0.609131 ATAGCCTTGGCGCAGTTGTT 60.609 50.0 10.83 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1301 1460 1.833630 TCCCGTCATCTTCATGCTTCT 59.166 47.619 0.00 0.0 0.0 2.85 R
2396 2563 0.890683 CCAGGGGAGCAAACATGTTC 59.109 55.000 12.39 0.0 0.0 3.18 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
45 46 7.679659 GTCAGATGACTTGTTAAAACCAAAC 57.320 36.000 5.72 0.00 41.65 2.93
46 47 7.480810 GTCAGATGACTTGTTAAAACCAAACT 58.519 34.615 5.72 0.00 41.65 2.66
47 48 7.432252 GTCAGATGACTTGTTAAAACCAAACTG 59.568 37.037 5.72 0.00 41.65 3.16
48 49 6.697019 CAGATGACTTGTTAAAACCAAACTGG 59.303 38.462 0.00 0.00 45.02 4.00
49 50 5.331876 TGACTTGTTAAAACCAAACTGGG 57.668 39.130 0.00 0.00 43.37 4.45
50 51 4.160626 TGACTTGTTAAAACCAAACTGGGG 59.839 41.667 0.00 0.00 43.37 4.96
51 52 3.118555 ACTTGTTAAAACCAAACTGGGGC 60.119 43.478 0.00 0.00 43.37 5.80
52 53 1.763545 TGTTAAAACCAAACTGGGGCC 59.236 47.619 0.00 0.00 43.37 5.80
53 54 2.043992 GTTAAAACCAAACTGGGGCCT 58.956 47.619 0.84 0.00 43.37 5.19
54 55 2.436542 GTTAAAACCAAACTGGGGCCTT 59.563 45.455 0.84 0.00 43.37 4.35
55 56 2.480642 AAAACCAAACTGGGGCCTTA 57.519 45.000 0.84 0.00 43.37 2.69
56 57 2.480642 AAACCAAACTGGGGCCTTAA 57.519 45.000 0.84 0.00 43.37 1.85
57 58 1.712056 AACCAAACTGGGGCCTTAAC 58.288 50.000 0.84 0.00 43.37 2.01
58 59 0.558712 ACCAAACTGGGGCCTTAACA 59.441 50.000 0.84 0.00 43.37 2.41
59 60 1.149077 ACCAAACTGGGGCCTTAACAT 59.851 47.619 0.84 0.00 43.37 2.71
60 61 1.550072 CCAAACTGGGGCCTTAACATG 59.450 52.381 0.84 0.00 32.67 3.21
61 62 2.247358 CAAACTGGGGCCTTAACATGT 58.753 47.619 0.84 0.00 0.00 3.21
62 63 2.632512 CAAACTGGGGCCTTAACATGTT 59.367 45.455 16.68 16.68 0.00 2.71
63 64 2.215942 ACTGGGGCCTTAACATGTTC 57.784 50.000 15.85 0.00 0.00 3.18
64 65 1.427368 ACTGGGGCCTTAACATGTTCA 59.573 47.619 15.85 2.83 0.00 3.18
65 66 1.818674 CTGGGGCCTTAACATGTTCAC 59.181 52.381 15.85 1.02 0.00 3.18
66 67 1.145945 TGGGGCCTTAACATGTTCACA 59.854 47.619 15.85 4.58 0.00 3.58
67 68 1.544246 GGGGCCTTAACATGTTCACAC 59.456 52.381 15.85 4.11 0.00 3.82
68 69 2.514803 GGGCCTTAACATGTTCACACT 58.485 47.619 15.85 0.00 0.00 3.55
69 70 2.890945 GGGCCTTAACATGTTCACACTT 59.109 45.455 15.85 0.00 0.00 3.16
70 71 3.305335 GGGCCTTAACATGTTCACACTTG 60.305 47.826 15.85 0.00 34.81 3.16
71 72 3.317993 GGCCTTAACATGTTCACACTTGT 59.682 43.478 15.85 0.00 41.81 3.16
72 73 4.537015 GCCTTAACATGTTCACACTTGTC 58.463 43.478 15.85 0.00 39.72 3.18
73 74 4.275936 GCCTTAACATGTTCACACTTGTCT 59.724 41.667 15.85 0.00 39.72 3.41
74 75 5.751680 CCTTAACATGTTCACACTTGTCTG 58.248 41.667 15.85 0.00 39.72 3.51
75 76 5.527214 CCTTAACATGTTCACACTTGTCTGA 59.473 40.000 15.85 0.00 39.72 3.27
76 77 6.293081 CCTTAACATGTTCACACTTGTCTGAG 60.293 42.308 15.85 0.00 39.72 3.35
77 78 4.406648 ACATGTTCACACTTGTCTGAGA 57.593 40.909 0.00 0.00 36.77 3.27
78 79 4.769688 ACATGTTCACACTTGTCTGAGAA 58.230 39.130 0.00 0.00 36.77 2.87
79 80 4.813161 ACATGTTCACACTTGTCTGAGAAG 59.187 41.667 12.51 12.51 36.77 2.85
80 81 3.797039 TGTTCACACTTGTCTGAGAAGG 58.203 45.455 17.53 9.66 0.00 3.46
81 82 3.134458 GTTCACACTTGTCTGAGAAGGG 58.866 50.000 14.59 14.59 0.00 3.95
82 83 1.070758 TCACACTTGTCTGAGAAGGGC 59.929 52.381 15.93 0.00 0.00 5.19
83 84 1.131638 ACACTTGTCTGAGAAGGGCA 58.868 50.000 15.93 0.00 0.00 5.36
84 85 1.490490 ACACTTGTCTGAGAAGGGCAA 59.510 47.619 15.93 0.00 0.00 4.52
85 86 2.092429 ACACTTGTCTGAGAAGGGCAAA 60.092 45.455 15.93 0.00 0.00 3.68
86 87 2.551459 CACTTGTCTGAGAAGGGCAAAG 59.449 50.000 17.53 0.00 0.00 2.77
87 88 2.173569 ACTTGTCTGAGAAGGGCAAAGT 59.826 45.455 17.53 0.00 0.00 2.66
88 89 2.260844 TGTCTGAGAAGGGCAAAGTG 57.739 50.000 0.00 0.00 0.00 3.16
89 90 1.768275 TGTCTGAGAAGGGCAAAGTGA 59.232 47.619 0.00 0.00 0.00 3.41
177 178 2.185350 CGCGGCTGATCTCCACTT 59.815 61.111 0.00 0.00 0.00 3.16
188 189 5.397334 GCTGATCTCCACTTCCCTTCTTATT 60.397 44.000 0.00 0.00 0.00 1.40
189 190 6.642733 TGATCTCCACTTCCCTTCTTATTT 57.357 37.500 0.00 0.00 0.00 1.40
190 191 6.653989 TGATCTCCACTTCCCTTCTTATTTC 58.346 40.000 0.00 0.00 0.00 2.17
465 467 4.677182 ACCTTGGCATAGGTCATTTTCTT 58.323 39.130 13.43 0.00 45.44 2.52
553 555 5.775701 AGCTCTCGGGTATTACTATCATGTT 59.224 40.000 0.00 0.00 0.00 2.71
571 574 5.748630 TCATGTTATCGTGTCAGTTCTATGC 59.251 40.000 0.00 0.00 32.85 3.14
670 673 6.174760 TCACTCTGTCTAGTTTCTACTCTCC 58.825 44.000 0.00 0.00 35.78 3.71
740 743 9.487442 TTTTTGCCTTTCCCTTCATATAAGTAT 57.513 29.630 0.00 0.00 0.00 2.12
796 840 7.459394 CATTTTATGCTGATTGGAATGTGTC 57.541 36.000 0.00 0.00 0.00 3.67
857 908 3.702548 CCATTTGCTCATCCCTGAAATCA 59.297 43.478 0.00 0.00 0.00 2.57
880 931 0.609131 ATAGCCTTGGCGCAGTTGTT 60.609 50.000 10.83 0.00 0.00 2.83
883 934 2.489275 CCTTGGCGCAGTTGTTGGT 61.489 57.895 10.83 0.00 0.00 3.67
1176 1230 2.364002 TGCAGGCAAAGTTAAGGAAACC 59.636 45.455 0.00 0.00 39.03 3.27
1237 1396 4.498241 TGAACATGAAGACGATCAGAAGG 58.502 43.478 0.00 0.00 31.76 3.46
1239 1398 1.857217 CATGAAGACGATCAGAAGGCG 59.143 52.381 0.00 0.00 31.76 5.52
1240 1399 1.173913 TGAAGACGATCAGAAGGCGA 58.826 50.000 0.00 0.00 0.00 5.54
1241 1400 1.133216 TGAAGACGATCAGAAGGCGAG 59.867 52.381 0.00 0.00 0.00 5.03
1242 1401 1.133407 GAAGACGATCAGAAGGCGAGT 59.867 52.381 0.00 0.00 0.00 4.18
1243 1402 2.039818 AGACGATCAGAAGGCGAGTA 57.960 50.000 0.00 0.00 0.00 2.59
1244 1403 2.366533 AGACGATCAGAAGGCGAGTAA 58.633 47.619 0.00 0.00 0.00 2.24
1245 1404 2.356382 AGACGATCAGAAGGCGAGTAAG 59.644 50.000 0.00 0.00 0.00 2.34
1246 1405 2.355132 GACGATCAGAAGGCGAGTAAGA 59.645 50.000 0.00 0.00 0.00 2.10
1247 1406 2.753452 ACGATCAGAAGGCGAGTAAGAA 59.247 45.455 0.00 0.00 0.00 2.52
1248 1407 3.181495 ACGATCAGAAGGCGAGTAAGAAG 60.181 47.826 0.00 0.00 0.00 2.85
1249 1408 3.065510 CGATCAGAAGGCGAGTAAGAAGA 59.934 47.826 0.00 0.00 0.00 2.87
1250 1409 4.438880 CGATCAGAAGGCGAGTAAGAAGAA 60.439 45.833 0.00 0.00 0.00 2.52
1251 1410 4.442375 TCAGAAGGCGAGTAAGAAGAAG 57.558 45.455 0.00 0.00 0.00 2.85
1252 1411 3.193691 TCAGAAGGCGAGTAAGAAGAAGG 59.806 47.826 0.00 0.00 0.00 3.46
1253 1412 3.193691 CAGAAGGCGAGTAAGAAGAAGGA 59.806 47.826 0.00 0.00 0.00 3.36
1254 1413 3.833070 AGAAGGCGAGTAAGAAGAAGGAA 59.167 43.478 0.00 0.00 0.00 3.36
1255 1414 4.283722 AGAAGGCGAGTAAGAAGAAGGAAA 59.716 41.667 0.00 0.00 0.00 3.13
1256 1415 4.618920 AGGCGAGTAAGAAGAAGGAAAA 57.381 40.909 0.00 0.00 0.00 2.29
1257 1416 5.167303 AGGCGAGTAAGAAGAAGGAAAAT 57.833 39.130 0.00 0.00 0.00 1.82
1258 1417 6.295719 AGGCGAGTAAGAAGAAGGAAAATA 57.704 37.500 0.00 0.00 0.00 1.40
1259 1418 6.708285 AGGCGAGTAAGAAGAAGGAAAATAA 58.292 36.000 0.00 0.00 0.00 1.40
1260 1419 6.819146 AGGCGAGTAAGAAGAAGGAAAATAAG 59.181 38.462 0.00 0.00 0.00 1.73
1261 1420 6.037281 GGCGAGTAAGAAGAAGGAAAATAAGG 59.963 42.308 0.00 0.00 0.00 2.69
1262 1421 6.457122 GCGAGTAAGAAGAAGGAAAATAAGGC 60.457 42.308 0.00 0.00 0.00 4.35
1263 1422 6.594159 CGAGTAAGAAGAAGGAAAATAAGGCA 59.406 38.462 0.00 0.00 0.00 4.75
1264 1423 7.201565 CGAGTAAGAAGAAGGAAAATAAGGCAG 60.202 40.741 0.00 0.00 0.00 4.85
1265 1424 7.690256 AGTAAGAAGAAGGAAAATAAGGCAGA 58.310 34.615 0.00 0.00 0.00 4.26
1266 1425 7.826744 AGTAAGAAGAAGGAAAATAAGGCAGAG 59.173 37.037 0.00 0.00 0.00 3.35
1267 1426 6.380079 AGAAGAAGGAAAATAAGGCAGAGA 57.620 37.500 0.00 0.00 0.00 3.10
1268 1427 6.784031 AGAAGAAGGAAAATAAGGCAGAGAA 58.216 36.000 0.00 0.00 0.00 2.87
1269 1428 7.234355 AGAAGAAGGAAAATAAGGCAGAGAAA 58.766 34.615 0.00 0.00 0.00 2.52
1270 1429 6.825944 AGAAGGAAAATAAGGCAGAGAAAC 57.174 37.500 0.00 0.00 0.00 2.78
1271 1430 6.306987 AGAAGGAAAATAAGGCAGAGAAACA 58.693 36.000 0.00 0.00 0.00 2.83
1272 1431 6.950619 AGAAGGAAAATAAGGCAGAGAAACAT 59.049 34.615 0.00 0.00 0.00 2.71
1273 1432 6.521151 AGGAAAATAAGGCAGAGAAACATG 57.479 37.500 0.00 0.00 0.00 3.21
1274 1433 6.248433 AGGAAAATAAGGCAGAGAAACATGA 58.752 36.000 0.00 0.00 0.00 3.07
1275 1434 6.721208 AGGAAAATAAGGCAGAGAAACATGAA 59.279 34.615 0.00 0.00 0.00 2.57
1276 1435 7.031975 GGAAAATAAGGCAGAGAAACATGAAG 58.968 38.462 0.00 0.00 0.00 3.02
1277 1436 7.094205 GGAAAATAAGGCAGAGAAACATGAAGA 60.094 37.037 0.00 0.00 0.00 2.87
1278 1437 7.951347 AAATAAGGCAGAGAAACATGAAGAT 57.049 32.000 0.00 0.00 0.00 2.40
1279 1438 6.939132 ATAAGGCAGAGAAACATGAAGATG 57.061 37.500 0.00 0.00 35.49 2.90
1280 1439 3.618351 AGGCAGAGAAACATGAAGATGG 58.382 45.455 0.00 0.00 33.39 3.51
1281 1440 3.009916 AGGCAGAGAAACATGAAGATGGT 59.990 43.478 0.00 0.00 33.39 3.55
1282 1441 4.225942 AGGCAGAGAAACATGAAGATGGTA 59.774 41.667 0.00 0.00 33.39 3.25
1283 1442 4.943705 GGCAGAGAAACATGAAGATGGTAA 59.056 41.667 0.00 0.00 33.39 2.85
1284 1443 5.065731 GGCAGAGAAACATGAAGATGGTAAG 59.934 44.000 0.00 0.00 33.39 2.34
1285 1444 5.877012 GCAGAGAAACATGAAGATGGTAAGA 59.123 40.000 0.00 0.00 33.39 2.10
1286 1445 6.372659 GCAGAGAAACATGAAGATGGTAAGAA 59.627 38.462 0.00 0.00 33.39 2.52
1287 1446 7.413877 GCAGAGAAACATGAAGATGGTAAGAAG 60.414 40.741 0.00 0.00 33.39 2.85
1288 1447 7.065563 CAGAGAAACATGAAGATGGTAAGAAGG 59.934 40.741 0.00 0.00 33.39 3.46
1289 1448 7.020827 AGAAACATGAAGATGGTAAGAAGGA 57.979 36.000 0.00 0.00 33.39 3.36
1290 1449 7.461749 AGAAACATGAAGATGGTAAGAAGGAA 58.538 34.615 0.00 0.00 33.39 3.36
1291 1450 7.944554 AGAAACATGAAGATGGTAAGAAGGAAA 59.055 33.333 0.00 0.00 33.39 3.13
1292 1451 8.477419 AAACATGAAGATGGTAAGAAGGAAAA 57.523 30.769 0.00 0.00 33.39 2.29
1293 1452 7.693969 ACATGAAGATGGTAAGAAGGAAAAG 57.306 36.000 0.00 0.00 33.39 2.27
1294 1453 7.461749 ACATGAAGATGGTAAGAAGGAAAAGA 58.538 34.615 0.00 0.00 33.39 2.52
1295 1454 7.944554 ACATGAAGATGGTAAGAAGGAAAAGAA 59.055 33.333 0.00 0.00 33.39 2.52
1296 1455 7.986085 TGAAGATGGTAAGAAGGAAAAGAAG 57.014 36.000 0.00 0.00 0.00 2.85
1297 1456 7.518188 TGAAGATGGTAAGAAGGAAAAGAAGT 58.482 34.615 0.00 0.00 0.00 3.01
1298 1457 7.998964 TGAAGATGGTAAGAAGGAAAAGAAGTT 59.001 33.333 0.00 0.00 0.00 2.66
1299 1458 9.503399 GAAGATGGTAAGAAGGAAAAGAAGTTA 57.497 33.333 0.00 0.00 0.00 2.24
1300 1459 9.508642 AAGATGGTAAGAAGGAAAAGAAGTTAG 57.491 33.333 0.00 0.00 0.00 2.34
1301 1460 8.881262 AGATGGTAAGAAGGAAAAGAAGTTAGA 58.119 33.333 0.00 0.00 0.00 2.10
1302 1461 9.157104 GATGGTAAGAAGGAAAAGAAGTTAGAG 57.843 37.037 0.00 0.00 0.00 2.43
1303 1462 8.258850 TGGTAAGAAGGAAAAGAAGTTAGAGA 57.741 34.615 0.00 0.00 0.00 3.10
1304 1463 8.711170 TGGTAAGAAGGAAAAGAAGTTAGAGAA 58.289 33.333 0.00 0.00 0.00 2.87
1305 1464 9.210329 GGTAAGAAGGAAAAGAAGTTAGAGAAG 57.790 37.037 0.00 0.00 0.00 2.85
1306 1465 7.737972 AAGAAGGAAAAGAAGTTAGAGAAGC 57.262 36.000 0.00 0.00 0.00 3.86
1307 1466 6.831976 AGAAGGAAAAGAAGTTAGAGAAGCA 58.168 36.000 0.00 0.00 0.00 3.91
1308 1467 7.457561 AGAAGGAAAAGAAGTTAGAGAAGCAT 58.542 34.615 0.00 0.00 0.00 3.79
1309 1468 7.390162 AGAAGGAAAAGAAGTTAGAGAAGCATG 59.610 37.037 0.00 0.00 0.00 4.06
1310 1469 6.773638 AGGAAAAGAAGTTAGAGAAGCATGA 58.226 36.000 0.00 0.00 0.00 3.07
1311 1470 7.227156 AGGAAAAGAAGTTAGAGAAGCATGAA 58.773 34.615 0.00 0.00 0.00 2.57
1312 1471 7.390162 AGGAAAAGAAGTTAGAGAAGCATGAAG 59.610 37.037 0.00 0.00 0.00 3.02
1313 1472 7.389053 GGAAAAGAAGTTAGAGAAGCATGAAGA 59.611 37.037 0.00 0.00 0.00 2.87
1314 1473 8.860780 AAAAGAAGTTAGAGAAGCATGAAGAT 57.139 30.769 0.00 0.00 0.00 2.40
1315 1474 7.846644 AAGAAGTTAGAGAAGCATGAAGATG 57.153 36.000 0.00 0.00 0.00 2.90
1316 1475 7.180322 AGAAGTTAGAGAAGCATGAAGATGA 57.820 36.000 0.00 0.00 0.00 2.92
1317 1476 7.041107 AGAAGTTAGAGAAGCATGAAGATGAC 58.959 38.462 0.00 0.00 0.00 3.06
1318 1477 5.347342 AGTTAGAGAAGCATGAAGATGACG 58.653 41.667 0.00 0.00 0.00 4.35
1319 1478 3.176552 AGAGAAGCATGAAGATGACGG 57.823 47.619 0.00 0.00 0.00 4.79
1320 1479 2.158986 AGAGAAGCATGAAGATGACGGG 60.159 50.000 0.00 0.00 0.00 5.28
1321 1480 1.833630 AGAAGCATGAAGATGACGGGA 59.166 47.619 0.00 0.00 0.00 5.14
1322 1481 2.237143 AGAAGCATGAAGATGACGGGAA 59.763 45.455 0.00 0.00 0.00 3.97
1323 1482 2.322355 AGCATGAAGATGACGGGAAG 57.678 50.000 0.00 0.00 0.00 3.46
1324 1483 1.833630 AGCATGAAGATGACGGGAAGA 59.166 47.619 0.00 0.00 0.00 2.87
1325 1484 1.936547 GCATGAAGATGACGGGAAGAC 59.063 52.381 0.00 0.00 0.00 3.01
1326 1485 2.419297 GCATGAAGATGACGGGAAGACT 60.419 50.000 0.00 0.00 0.00 3.24
1340 1499 6.063404 ACGGGAAGACTAGTAAGAAGGATAG 58.937 44.000 0.00 0.00 0.00 2.08
1445 1604 6.917217 CGAGAGCAAAGAGAAGGATAAAAT 57.083 37.500 0.00 0.00 0.00 1.82
1563 1722 9.230932 GATGAAAAACAAGAGAAAGACAAAGAG 57.769 33.333 0.00 0.00 0.00 2.85
1604 1763 4.213564 AGAAGAAGCATGTAGAAGTGGG 57.786 45.455 0.00 0.00 0.00 4.61
1829 1988 0.848053 AAAACCGACAAGAAGGGGGA 59.152 50.000 0.00 0.00 0.00 4.81
2020 2179 2.815647 GCGGCAAGGAGAAGACCG 60.816 66.667 0.00 0.00 46.50 4.79
2028 2187 0.034380 AGGAGAAGACCGACGATCCA 60.034 55.000 0.00 0.00 34.73 3.41
2396 2563 7.361971 GCCCAGAAAAATAAAATGAACCCATTG 60.362 37.037 0.00 0.00 41.84 2.82
2412 2579 2.354003 CCATTGAACATGTTTGCTCCCC 60.354 50.000 13.36 0.00 0.00 4.81
2470 2637 0.181114 AGCTGGAATTCCGCTGCATA 59.819 50.000 30.23 9.87 41.69 3.14
2500 2667 0.109226 GTGGTAGTGCAGTCGGACTC 60.109 60.000 7.89 4.32 40.19 3.36
2648 2846 2.338620 CGCACCGAGAGAACCACA 59.661 61.111 0.00 0.00 0.00 4.17
2652 2850 0.888619 CACCGAGAGAACCACAGCTA 59.111 55.000 0.00 0.00 0.00 3.32
2670 2868 4.973051 CAGCTATGTGAGTACACTCGATTC 59.027 45.833 4.98 0.00 45.72 2.52
2681 2879 4.553330 ACACTCGATTCCACCTTGTATT 57.447 40.909 0.00 0.00 0.00 1.89
2707 2905 5.888161 AGGATTTGTGGCCTCTTAATTGTAG 59.112 40.000 3.32 0.00 0.00 2.74
2718 2916 5.349817 CCTCTTAATTGTAGCACTGTGACAG 59.650 44.000 11.70 11.70 37.52 3.51
2732 2930 5.821204 ACTGTGACAGTGCAATAAAAACTC 58.179 37.500 18.72 0.00 43.63 3.01
2737 2935 5.009610 TGACAGTGCAATAAAAACTCCCTTC 59.990 40.000 0.00 0.00 0.00 3.46
2742 2940 3.447586 GCAATAAAAACTCCCTTCTCCCC 59.552 47.826 0.00 0.00 0.00 4.81
2744 2942 0.404426 AAAAACTCCCTTCTCCCCGG 59.596 55.000 0.00 0.00 0.00 5.73
2745 2943 0.770948 AAAACTCCCTTCTCCCCGGT 60.771 55.000 0.00 0.00 0.00 5.28
2751 2949 1.631898 TCCCTTCTCCCCGGTAAAAAG 59.368 52.381 0.00 0.00 0.00 2.27
2958 3163 3.692257 ATGATGTATGCACCTCCTAGC 57.308 47.619 0.00 0.00 0.00 3.42
2990 3195 5.637104 TTTTCTATTATCTCGTTGCGCTC 57.363 39.130 9.73 0.35 0.00 5.03
2991 3196 4.569761 TTCTATTATCTCGTTGCGCTCT 57.430 40.909 9.73 0.00 0.00 4.09
3018 3223 8.344939 TCAGTCTCAATAAAATTATACCCCCT 57.655 34.615 0.00 0.00 0.00 4.79
3085 3290 6.347696 AGATGTTTTGGCAGTTCAATTTCAA 58.652 32.000 0.00 0.00 0.00 2.69
3089 3294 7.271511 TGTTTTGGCAGTTCAATTTCAACTAT 58.728 30.769 0.18 0.00 32.61 2.12
3090 3295 7.437862 TGTTTTGGCAGTTCAATTTCAACTATC 59.562 33.333 0.18 0.00 32.61 2.08
3091 3296 6.899393 TTGGCAGTTCAATTTCAACTATCT 57.101 33.333 0.18 0.00 32.61 1.98
3092 3297 6.500684 TGGCAGTTCAATTTCAACTATCTC 57.499 37.500 0.18 0.00 32.61 2.75
3093 3298 6.003326 TGGCAGTTCAATTTCAACTATCTCA 58.997 36.000 0.18 0.00 32.61 3.27
3094 3299 6.489700 TGGCAGTTCAATTTCAACTATCTCAA 59.510 34.615 0.18 0.00 32.61 3.02
3095 3300 7.177216 TGGCAGTTCAATTTCAACTATCTCAAT 59.823 33.333 0.18 0.00 32.61 2.57
3096 3301 8.677300 GGCAGTTCAATTTCAACTATCTCAATA 58.323 33.333 0.18 0.00 32.61 1.90
3117 3322 9.847224 TCAATAAAATTATACTCCCTCTGTTCC 57.153 33.333 0.00 0.00 0.00 3.62
3118 3323 9.853177 CAATAAAATTATACTCCCTCTGTTCCT 57.147 33.333 0.00 0.00 0.00 3.36
3130 3335 9.907229 ACTCCCTCTGTTCCTAAATAAAATTAG 57.093 33.333 0.00 0.00 33.54 1.73
3131 3336 9.907229 CTCCCTCTGTTCCTAAATAAAATTAGT 57.093 33.333 0.00 0.00 32.16 2.24
3132 3337 9.901172 TCCCTCTGTTCCTAAATAAAATTAGTC 57.099 33.333 0.00 0.00 32.16 2.59
3133 3338 9.121658 CCCTCTGTTCCTAAATAAAATTAGTCC 57.878 37.037 0.00 0.00 32.16 3.85
3134 3339 9.121658 CCTCTGTTCCTAAATAAAATTAGTCCC 57.878 37.037 0.00 0.00 32.16 4.46
3135 3340 9.907229 CTCTGTTCCTAAATAAAATTAGTCCCT 57.093 33.333 0.00 0.00 32.16 4.20
3136 3341 9.901172 TCTGTTCCTAAATAAAATTAGTCCCTC 57.099 33.333 0.00 0.00 32.16 4.30
3137 3342 9.907229 CTGTTCCTAAATAAAATTAGTCCCTCT 57.093 33.333 0.00 0.00 32.16 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 7.432252 CAGTTTGGTTTTAACAAGTCATCTGAC 59.568 37.037 2.01 2.01 45.08 3.51
22 23 7.416213 CCAGTTTGGTTTTAACAAGTCATCTGA 60.416 37.037 0.00 0.00 31.35 3.27
23 24 6.697019 CCAGTTTGGTTTTAACAAGTCATCTG 59.303 38.462 0.00 0.00 31.35 2.90
24 25 6.183360 CCCAGTTTGGTTTTAACAAGTCATCT 60.183 38.462 0.00 0.00 35.17 2.90
25 26 5.983118 CCCAGTTTGGTTTTAACAAGTCATC 59.017 40.000 0.00 0.00 35.17 2.92
26 27 5.163353 CCCCAGTTTGGTTTTAACAAGTCAT 60.163 40.000 0.00 0.00 35.17 3.06
27 28 4.160626 CCCCAGTTTGGTTTTAACAAGTCA 59.839 41.667 0.00 0.00 35.17 3.41
28 29 4.689071 CCCCAGTTTGGTTTTAACAAGTC 58.311 43.478 0.00 0.00 35.17 3.01
29 30 3.118555 GCCCCAGTTTGGTTTTAACAAGT 60.119 43.478 0.00 0.00 35.17 3.16
30 31 3.462982 GCCCCAGTTTGGTTTTAACAAG 58.537 45.455 0.00 0.00 35.17 3.16
31 32 2.170817 GGCCCCAGTTTGGTTTTAACAA 59.829 45.455 0.00 0.00 35.17 2.83
32 33 1.763545 GGCCCCAGTTTGGTTTTAACA 59.236 47.619 0.00 0.00 35.17 2.41
33 34 2.043992 AGGCCCCAGTTTGGTTTTAAC 58.956 47.619 0.00 0.00 35.17 2.01
34 35 2.480642 AGGCCCCAGTTTGGTTTTAA 57.519 45.000 0.00 0.00 35.17 1.52
35 36 2.480642 AAGGCCCCAGTTTGGTTTTA 57.519 45.000 0.00 0.00 35.17 1.52
36 37 2.436542 GTTAAGGCCCCAGTTTGGTTTT 59.563 45.455 0.00 0.00 35.17 2.43
37 38 2.043992 GTTAAGGCCCCAGTTTGGTTT 58.956 47.619 0.00 0.00 35.17 3.27
38 39 1.062810 TGTTAAGGCCCCAGTTTGGTT 60.063 47.619 0.00 0.00 35.17 3.67
39 40 0.558712 TGTTAAGGCCCCAGTTTGGT 59.441 50.000 0.00 0.00 35.17 3.67
40 41 1.550072 CATGTTAAGGCCCCAGTTTGG 59.450 52.381 0.00 0.00 37.25 3.28
41 42 2.247358 ACATGTTAAGGCCCCAGTTTG 58.753 47.619 0.00 0.00 0.00 2.93
42 43 2.694616 ACATGTTAAGGCCCCAGTTT 57.305 45.000 0.00 0.00 0.00 2.66
43 44 2.158385 TGAACATGTTAAGGCCCCAGTT 60.158 45.455 11.95 0.00 0.00 3.16
44 45 1.427368 TGAACATGTTAAGGCCCCAGT 59.573 47.619 11.95 0.00 0.00 4.00
45 46 1.818674 GTGAACATGTTAAGGCCCCAG 59.181 52.381 11.95 0.00 0.00 4.45
46 47 1.145945 TGTGAACATGTTAAGGCCCCA 59.854 47.619 11.95 0.02 0.00 4.96
47 48 1.544246 GTGTGAACATGTTAAGGCCCC 59.456 52.381 11.95 0.00 0.00 5.80
48 49 2.514803 AGTGTGAACATGTTAAGGCCC 58.485 47.619 11.95 0.00 0.00 5.80
49 50 3.317993 ACAAGTGTGAACATGTTAAGGCC 59.682 43.478 11.95 0.00 0.00 5.19
50 51 4.275936 AGACAAGTGTGAACATGTTAAGGC 59.724 41.667 11.95 0.00 0.00 4.35
51 52 5.527214 TCAGACAAGTGTGAACATGTTAAGG 59.473 40.000 11.95 0.11 29.36 2.69
52 53 6.479990 TCTCAGACAAGTGTGAACATGTTAAG 59.520 38.462 11.95 0.00 32.24 1.85
53 54 6.345298 TCTCAGACAAGTGTGAACATGTTAA 58.655 36.000 11.95 0.00 32.24 2.01
54 55 5.912892 TCTCAGACAAGTGTGAACATGTTA 58.087 37.500 11.95 0.00 32.24 2.41
55 56 4.769688 TCTCAGACAAGTGTGAACATGTT 58.230 39.130 11.78 11.78 32.24 2.71
56 57 4.406648 TCTCAGACAAGTGTGAACATGT 57.593 40.909 0.00 0.00 32.24 3.21
57 58 4.212847 CCTTCTCAGACAAGTGTGAACATG 59.787 45.833 1.62 0.00 32.24 3.21
58 59 4.384056 CCTTCTCAGACAAGTGTGAACAT 58.616 43.478 1.62 0.00 32.24 2.71
59 60 3.432186 CCCTTCTCAGACAAGTGTGAACA 60.432 47.826 1.62 0.00 32.24 3.18
60 61 3.134458 CCCTTCTCAGACAAGTGTGAAC 58.866 50.000 1.62 0.00 32.24 3.18
61 62 2.485479 GCCCTTCTCAGACAAGTGTGAA 60.485 50.000 1.62 0.00 32.24 3.18
62 63 1.070758 GCCCTTCTCAGACAAGTGTGA 59.929 52.381 0.00 0.00 0.00 3.58
63 64 1.202687 TGCCCTTCTCAGACAAGTGTG 60.203 52.381 0.00 0.00 0.00 3.82
64 65 1.131638 TGCCCTTCTCAGACAAGTGT 58.868 50.000 0.00 0.00 0.00 3.55
65 66 2.260844 TTGCCCTTCTCAGACAAGTG 57.739 50.000 0.00 0.00 0.00 3.16
66 67 2.173569 ACTTTGCCCTTCTCAGACAAGT 59.826 45.455 0.00 0.00 0.00 3.16
67 68 2.551459 CACTTTGCCCTTCTCAGACAAG 59.449 50.000 0.00 0.00 0.00 3.16
68 69 2.172505 TCACTTTGCCCTTCTCAGACAA 59.827 45.455 0.00 0.00 0.00 3.18
69 70 1.768275 TCACTTTGCCCTTCTCAGACA 59.232 47.619 0.00 0.00 0.00 3.41
70 71 2.224402 ACTCACTTTGCCCTTCTCAGAC 60.224 50.000 0.00 0.00 0.00 3.51
71 72 2.050144 ACTCACTTTGCCCTTCTCAGA 58.950 47.619 0.00 0.00 0.00 3.27
72 73 2.149578 CACTCACTTTGCCCTTCTCAG 58.850 52.381 0.00 0.00 0.00 3.35
73 74 1.815408 GCACTCACTTTGCCCTTCTCA 60.815 52.381 0.00 0.00 33.58 3.27
74 75 0.877743 GCACTCACTTTGCCCTTCTC 59.122 55.000 0.00 0.00 33.58 2.87
75 76 3.027419 GCACTCACTTTGCCCTTCT 57.973 52.632 0.00 0.00 33.58 2.85
81 82 2.159272 GACGTCGGCACTCACTTTGC 62.159 60.000 0.00 0.00 39.41 3.68
82 83 1.853319 GACGTCGGCACTCACTTTG 59.147 57.895 0.00 0.00 0.00 2.77
83 84 1.660575 CGACGTCGGCACTCACTTT 60.661 57.895 29.70 0.00 35.37 2.66
84 85 2.050351 CGACGTCGGCACTCACTT 60.050 61.111 29.70 0.00 35.37 3.16
177 178 8.103935 GGAAGAAGAAGAAGAAATAAGAAGGGA 58.896 37.037 0.00 0.00 0.00 4.20
188 189 4.166144 ACACAAGGGGAAGAAGAAGAAGAA 59.834 41.667 0.00 0.00 0.00 2.52
189 190 3.716872 ACACAAGGGGAAGAAGAAGAAGA 59.283 43.478 0.00 0.00 0.00 2.87
190 191 3.817647 CACACAAGGGGAAGAAGAAGAAG 59.182 47.826 0.00 0.00 0.00 2.85
355 357 1.453155 AATCAAATCTGGCGCTTCGT 58.547 45.000 7.64 0.00 0.00 3.85
459 461 9.131791 AGGTAGCAAAGAACAAGATAAAGAAAA 57.868 29.630 0.00 0.00 0.00 2.29
465 467 6.121776 TGGAGGTAGCAAAGAACAAGATAA 57.878 37.500 0.00 0.00 0.00 1.75
476 478 1.144913 AGCTTGGTTGGAGGTAGCAAA 59.855 47.619 0.00 0.00 33.16 3.68
553 555 2.686405 ACCGCATAGAACTGACACGATA 59.314 45.455 0.00 0.00 0.00 2.92
571 574 1.681780 ATGCACACATTAGGGGAACCG 60.682 52.381 0.00 0.00 46.13 4.44
670 673 8.453238 AACTGTACTGTCATATACTCCTACTG 57.547 38.462 5.81 0.00 0.00 2.74
675 678 6.037940 TGACGAACTGTACTGTCATATACTCC 59.962 42.308 5.81 0.00 36.50 3.85
676 679 7.012959 TGACGAACTGTACTGTCATATACTC 57.987 40.000 5.81 0.00 36.50 2.59
685 688 3.147629 ACTAGCTGACGAACTGTACTGT 58.852 45.455 0.00 0.00 0.00 3.55
796 840 4.848562 TGACGAACCATAGGCTACATAG 57.151 45.455 0.00 0.00 0.00 2.23
857 908 3.740128 CTGCGCCAAGGCTATCGGT 62.740 63.158 4.18 0.00 39.32 4.69
880 931 7.125659 TGGAGAATCATATAGTCTGTTCAACCA 59.874 37.037 0.00 0.00 36.25 3.67
883 934 8.927411 TGATGGAGAATCATATAGTCTGTTCAA 58.073 33.333 0.00 0.00 40.50 2.69
1237 1396 6.457122 GCCTTATTTTCCTTCTTCTTACTCGC 60.457 42.308 0.00 0.00 0.00 5.03
1239 1398 7.824779 TCTGCCTTATTTTCCTTCTTCTTACTC 59.175 37.037 0.00 0.00 0.00 2.59
1240 1399 7.690256 TCTGCCTTATTTTCCTTCTTCTTACT 58.310 34.615 0.00 0.00 0.00 2.24
1241 1400 7.824779 TCTCTGCCTTATTTTCCTTCTTCTTAC 59.175 37.037 0.00 0.00 0.00 2.34
1242 1401 7.918076 TCTCTGCCTTATTTTCCTTCTTCTTA 58.082 34.615 0.00 0.00 0.00 2.10
1243 1402 6.784031 TCTCTGCCTTATTTTCCTTCTTCTT 58.216 36.000 0.00 0.00 0.00 2.52
1244 1403 6.380079 TCTCTGCCTTATTTTCCTTCTTCT 57.620 37.500 0.00 0.00 0.00 2.85
1245 1404 7.040409 TGTTTCTCTGCCTTATTTTCCTTCTTC 60.040 37.037 0.00 0.00 0.00 2.87
1246 1405 6.777580 TGTTTCTCTGCCTTATTTTCCTTCTT 59.222 34.615 0.00 0.00 0.00 2.52
1247 1406 6.306987 TGTTTCTCTGCCTTATTTTCCTTCT 58.693 36.000 0.00 0.00 0.00 2.85
1248 1407 6.575162 TGTTTCTCTGCCTTATTTTCCTTC 57.425 37.500 0.00 0.00 0.00 3.46
1249 1408 6.721208 TCATGTTTCTCTGCCTTATTTTCCTT 59.279 34.615 0.00 0.00 0.00 3.36
1250 1409 6.248433 TCATGTTTCTCTGCCTTATTTTCCT 58.752 36.000 0.00 0.00 0.00 3.36
1251 1410 6.515272 TCATGTTTCTCTGCCTTATTTTCC 57.485 37.500 0.00 0.00 0.00 3.13
1252 1411 7.820648 TCTTCATGTTTCTCTGCCTTATTTTC 58.179 34.615 0.00 0.00 0.00 2.29
1253 1412 7.765695 TCTTCATGTTTCTCTGCCTTATTTT 57.234 32.000 0.00 0.00 0.00 1.82
1254 1413 7.147949 CCATCTTCATGTTTCTCTGCCTTATTT 60.148 37.037 0.00 0.00 0.00 1.40
1255 1414 6.320672 CCATCTTCATGTTTCTCTGCCTTATT 59.679 38.462 0.00 0.00 0.00 1.40
1256 1415 5.826737 CCATCTTCATGTTTCTCTGCCTTAT 59.173 40.000 0.00 0.00 0.00 1.73
1257 1416 5.188434 CCATCTTCATGTTTCTCTGCCTTA 58.812 41.667 0.00 0.00 0.00 2.69
1258 1417 4.015084 CCATCTTCATGTTTCTCTGCCTT 58.985 43.478 0.00 0.00 0.00 4.35
1259 1418 3.009916 ACCATCTTCATGTTTCTCTGCCT 59.990 43.478 0.00 0.00 0.00 4.75
1260 1419 3.350833 ACCATCTTCATGTTTCTCTGCC 58.649 45.455 0.00 0.00 0.00 4.85
1261 1420 5.877012 TCTTACCATCTTCATGTTTCTCTGC 59.123 40.000 0.00 0.00 0.00 4.26
1262 1421 7.065563 CCTTCTTACCATCTTCATGTTTCTCTG 59.934 40.741 0.00 0.00 0.00 3.35
1263 1422 7.038017 TCCTTCTTACCATCTTCATGTTTCTCT 60.038 37.037 0.00 0.00 0.00 3.10
1264 1423 7.106239 TCCTTCTTACCATCTTCATGTTTCTC 58.894 38.462 0.00 0.00 0.00 2.87
1265 1424 7.020827 TCCTTCTTACCATCTTCATGTTTCT 57.979 36.000 0.00 0.00 0.00 2.52
1266 1425 7.687941 TTCCTTCTTACCATCTTCATGTTTC 57.312 36.000 0.00 0.00 0.00 2.78
1267 1426 8.477419 TTTTCCTTCTTACCATCTTCATGTTT 57.523 30.769 0.00 0.00 0.00 2.83
1268 1427 7.944554 TCTTTTCCTTCTTACCATCTTCATGTT 59.055 33.333 0.00 0.00 0.00 2.71
1269 1428 7.461749 TCTTTTCCTTCTTACCATCTTCATGT 58.538 34.615 0.00 0.00 0.00 3.21
1270 1429 7.928307 TCTTTTCCTTCTTACCATCTTCATG 57.072 36.000 0.00 0.00 0.00 3.07
1271 1430 8.166726 ACTTCTTTTCCTTCTTACCATCTTCAT 58.833 33.333 0.00 0.00 0.00 2.57
1272 1431 7.518188 ACTTCTTTTCCTTCTTACCATCTTCA 58.482 34.615 0.00 0.00 0.00 3.02
1273 1432 7.987750 ACTTCTTTTCCTTCTTACCATCTTC 57.012 36.000 0.00 0.00 0.00 2.87
1274 1433 9.508642 CTAACTTCTTTTCCTTCTTACCATCTT 57.491 33.333 0.00 0.00 0.00 2.40
1275 1434 8.881262 TCTAACTTCTTTTCCTTCTTACCATCT 58.119 33.333 0.00 0.00 0.00 2.90
1276 1435 9.157104 CTCTAACTTCTTTTCCTTCTTACCATC 57.843 37.037 0.00 0.00 0.00 3.51
1277 1436 8.881262 TCTCTAACTTCTTTTCCTTCTTACCAT 58.119 33.333 0.00 0.00 0.00 3.55
1278 1437 8.258850 TCTCTAACTTCTTTTCCTTCTTACCA 57.741 34.615 0.00 0.00 0.00 3.25
1279 1438 9.210329 CTTCTCTAACTTCTTTTCCTTCTTACC 57.790 37.037 0.00 0.00 0.00 2.85
1280 1439 8.714179 GCTTCTCTAACTTCTTTTCCTTCTTAC 58.286 37.037 0.00 0.00 0.00 2.34
1281 1440 8.429641 TGCTTCTCTAACTTCTTTTCCTTCTTA 58.570 33.333 0.00 0.00 0.00 2.10
1282 1441 7.283329 TGCTTCTCTAACTTCTTTTCCTTCTT 58.717 34.615 0.00 0.00 0.00 2.52
1283 1442 6.831976 TGCTTCTCTAACTTCTTTTCCTTCT 58.168 36.000 0.00 0.00 0.00 2.85
1284 1443 7.389053 TCATGCTTCTCTAACTTCTTTTCCTTC 59.611 37.037 0.00 0.00 0.00 3.46
1285 1444 7.227156 TCATGCTTCTCTAACTTCTTTTCCTT 58.773 34.615 0.00 0.00 0.00 3.36
1286 1445 6.773638 TCATGCTTCTCTAACTTCTTTTCCT 58.226 36.000 0.00 0.00 0.00 3.36
1287 1446 7.389053 TCTTCATGCTTCTCTAACTTCTTTTCC 59.611 37.037 0.00 0.00 0.00 3.13
1288 1447 8.316640 TCTTCATGCTTCTCTAACTTCTTTTC 57.683 34.615 0.00 0.00 0.00 2.29
1289 1448 8.728833 CATCTTCATGCTTCTCTAACTTCTTTT 58.271 33.333 0.00 0.00 0.00 2.27
1290 1449 8.099537 TCATCTTCATGCTTCTCTAACTTCTTT 58.900 33.333 0.00 0.00 0.00 2.52
1291 1450 7.548780 GTCATCTTCATGCTTCTCTAACTTCTT 59.451 37.037 0.00 0.00 0.00 2.52
1292 1451 7.041107 GTCATCTTCATGCTTCTCTAACTTCT 58.959 38.462 0.00 0.00 0.00 2.85
1293 1452 6.019961 CGTCATCTTCATGCTTCTCTAACTTC 60.020 42.308 0.00 0.00 0.00 3.01
1294 1453 5.809562 CGTCATCTTCATGCTTCTCTAACTT 59.190 40.000 0.00 0.00 0.00 2.66
1295 1454 5.347342 CGTCATCTTCATGCTTCTCTAACT 58.653 41.667 0.00 0.00 0.00 2.24
1296 1455 4.505922 CCGTCATCTTCATGCTTCTCTAAC 59.494 45.833 0.00 0.00 0.00 2.34
1297 1456 4.442052 CCCGTCATCTTCATGCTTCTCTAA 60.442 45.833 0.00 0.00 0.00 2.10
1298 1457 3.068732 CCCGTCATCTTCATGCTTCTCTA 59.931 47.826 0.00 0.00 0.00 2.43
1299 1458 2.158986 CCCGTCATCTTCATGCTTCTCT 60.159 50.000 0.00 0.00 0.00 3.10
1300 1459 2.159043 TCCCGTCATCTTCATGCTTCTC 60.159 50.000 0.00 0.00 0.00 2.87
1301 1460 1.833630 TCCCGTCATCTTCATGCTTCT 59.166 47.619 0.00 0.00 0.00 2.85
1302 1461 2.315925 TCCCGTCATCTTCATGCTTC 57.684 50.000 0.00 0.00 0.00 3.86
1303 1462 2.237143 TCTTCCCGTCATCTTCATGCTT 59.763 45.455 0.00 0.00 0.00 3.91
1304 1463 1.833630 TCTTCCCGTCATCTTCATGCT 59.166 47.619 0.00 0.00 0.00 3.79
1305 1464 1.936547 GTCTTCCCGTCATCTTCATGC 59.063 52.381 0.00 0.00 0.00 4.06
1306 1465 3.533606 AGTCTTCCCGTCATCTTCATG 57.466 47.619 0.00 0.00 0.00 3.07
1307 1466 4.282496 ACTAGTCTTCCCGTCATCTTCAT 58.718 43.478 0.00 0.00 0.00 2.57
1308 1467 3.698289 ACTAGTCTTCCCGTCATCTTCA 58.302 45.455 0.00 0.00 0.00 3.02
1309 1468 5.589452 TCTTACTAGTCTTCCCGTCATCTTC 59.411 44.000 0.00 0.00 0.00 2.87
1310 1469 5.507637 TCTTACTAGTCTTCCCGTCATCTT 58.492 41.667 0.00 0.00 0.00 2.40
1311 1470 5.113446 TCTTACTAGTCTTCCCGTCATCT 57.887 43.478 0.00 0.00 0.00 2.90
1312 1471 5.221087 CCTTCTTACTAGTCTTCCCGTCATC 60.221 48.000 0.00 0.00 0.00 2.92
1313 1472 4.645588 CCTTCTTACTAGTCTTCCCGTCAT 59.354 45.833 0.00 0.00 0.00 3.06
1314 1473 4.015084 CCTTCTTACTAGTCTTCCCGTCA 58.985 47.826 0.00 0.00 0.00 4.35
1315 1474 4.268359 TCCTTCTTACTAGTCTTCCCGTC 58.732 47.826 0.00 0.00 0.00 4.79
1316 1475 4.313020 TCCTTCTTACTAGTCTTCCCGT 57.687 45.455 0.00 0.00 0.00 5.28
1317 1476 6.297582 TCTATCCTTCTTACTAGTCTTCCCG 58.702 44.000 0.00 0.00 0.00 5.14
1318 1477 8.536340 TTTCTATCCTTCTTACTAGTCTTCCC 57.464 38.462 0.00 0.00 0.00 3.97
1319 1478 8.635328 CCTTTCTATCCTTCTTACTAGTCTTCC 58.365 40.741 0.00 0.00 0.00 3.46
1320 1479 9.411189 TCCTTTCTATCCTTCTTACTAGTCTTC 57.589 37.037 0.00 0.00 0.00 2.87
1321 1480 9.416284 CTCCTTTCTATCCTTCTTACTAGTCTT 57.584 37.037 0.00 0.00 0.00 3.01
1322 1481 8.783903 TCTCCTTTCTATCCTTCTTACTAGTCT 58.216 37.037 0.00 0.00 0.00 3.24
1323 1482 8.983702 TCTCCTTTCTATCCTTCTTACTAGTC 57.016 38.462 0.00 0.00 0.00 2.59
1324 1483 9.416284 CTTCTCCTTTCTATCCTTCTTACTAGT 57.584 37.037 0.00 0.00 0.00 2.57
1325 1484 8.856103 CCTTCTCCTTTCTATCCTTCTTACTAG 58.144 40.741 0.00 0.00 0.00 2.57
1326 1485 8.566979 TCCTTCTCCTTTCTATCCTTCTTACTA 58.433 37.037 0.00 0.00 0.00 1.82
1340 1499 7.751768 TTCTTTTTCTCATCCTTCTCCTTTC 57.248 36.000 0.00 0.00 0.00 2.62
1563 1722 4.899502 TCTTGTTCTCATGTTCCTCCTTC 58.100 43.478 0.00 0.00 0.00 3.46
1604 1763 3.080319 AGCTTGATTTCTCTTGCCTGAC 58.920 45.455 0.00 0.00 0.00 3.51
1829 1988 1.844687 GCCATCCTTCTTCTTGCCTT 58.155 50.000 0.00 0.00 0.00 4.35
2020 2179 3.262420 TCTTAAGCTTTGCTGGATCGTC 58.738 45.455 3.20 0.00 39.62 4.20
2260 2425 8.120465 AGAAATTATTCGCGTTACAACCATAAG 58.880 33.333 5.77 0.00 40.63 1.73
2387 2554 3.989817 GAGCAAACATGTTCAATGGGTTC 59.010 43.478 12.39 2.18 0.00 3.62
2396 2563 0.890683 CCAGGGGAGCAAACATGTTC 59.109 55.000 12.39 0.00 0.00 3.18
2412 2579 3.310774 CAGATGCATAACGAAAGGACCAG 59.689 47.826 0.00 0.00 0.00 4.00
2587 2755 3.451178 TGCAACACTATTCTCCCTCCTAC 59.549 47.826 0.00 0.00 0.00 3.18
2591 2759 3.895232 TCTGCAACACTATTCTCCCTC 57.105 47.619 0.00 0.00 0.00 4.30
2648 2846 4.036971 GGAATCGAGTGTACTCACATAGCT 59.963 45.833 12.11 0.00 46.01 3.32
2652 2850 3.119101 GGTGGAATCGAGTGTACTCACAT 60.119 47.826 12.11 1.08 46.01 3.21
2657 2855 2.897969 ACAAGGTGGAATCGAGTGTACT 59.102 45.455 0.00 0.00 0.00 2.73
2670 2868 4.158394 CCACAAATCCTCAATACAAGGTGG 59.842 45.833 0.00 0.00 36.49 4.61
2718 2916 4.082190 GGGAGAAGGGAGTTTTTATTGCAC 60.082 45.833 0.00 0.00 0.00 4.57
2732 2930 1.631898 TCTTTTTACCGGGGAGAAGGG 59.368 52.381 6.32 0.00 0.00 3.95
2737 2935 5.777850 TTTTTCTTCTTTTTACCGGGGAG 57.222 39.130 6.32 0.00 0.00 4.30
2760 2958 9.310716 CAGAGCTTTCATTTTCTTTTCTTTTCT 57.689 29.630 0.00 0.00 0.00 2.52
2766 2964 6.743110 AGACCAGAGCTTTCATTTTCTTTTC 58.257 36.000 0.00 0.00 0.00 2.29
2767 2965 6.721704 AGACCAGAGCTTTCATTTTCTTTT 57.278 33.333 0.00 0.00 0.00 2.27
2768 2966 6.322201 TGAAGACCAGAGCTTTCATTTTCTTT 59.678 34.615 0.00 0.00 0.00 2.52
2769 2967 5.829924 TGAAGACCAGAGCTTTCATTTTCTT 59.170 36.000 0.00 0.00 0.00 2.52
2770 2968 5.240403 GTGAAGACCAGAGCTTTCATTTTCT 59.760 40.000 0.00 0.00 0.00 2.52
2976 3181 2.879026 ACTGATAGAGCGCAACGAGATA 59.121 45.455 11.47 0.00 0.00 1.98
3061 3266 5.916318 TGAAATTGAACTGCCAAAACATCT 58.084 33.333 0.00 0.00 0.00 2.90
3091 3296 9.847224 GGAACAGAGGGAGTATAATTTTATTGA 57.153 33.333 0.00 0.00 0.00 2.57
3092 3297 9.853177 AGGAACAGAGGGAGTATAATTTTATTG 57.147 33.333 0.00 0.00 0.00 1.90
3104 3309 9.907229 CTAATTTTATTTAGGAACAGAGGGAGT 57.093 33.333 0.00 0.00 0.00 3.85
3105 3310 9.907229 ACTAATTTTATTTAGGAACAGAGGGAG 57.093 33.333 0.00 0.00 34.19 4.30
3106 3311 9.901172 GACTAATTTTATTTAGGAACAGAGGGA 57.099 33.333 0.00 0.00 34.19 4.20
3107 3312 9.121658 GGACTAATTTTATTTAGGAACAGAGGG 57.878 37.037 0.00 0.00 34.19 4.30
3108 3313 9.121658 GGGACTAATTTTATTTAGGAACAGAGG 57.878 37.037 0.00 0.00 34.19 3.69
3109 3314 9.907229 AGGGACTAATTTTATTTAGGAACAGAG 57.093 33.333 0.00 0.00 36.02 3.35
3110 3315 9.901172 GAGGGACTAATTTTATTTAGGAACAGA 57.099 33.333 0.00 0.00 41.55 3.41
3111 3316 9.907229 AGAGGGACTAATTTTATTTAGGAACAG 57.093 33.333 0.00 0.00 41.55 3.16
3139 3344 9.474313 ACTGCCAAAACATCTTATATTTAGGAA 57.526 29.630 0.00 0.00 0.00 3.36
3140 3345 9.474313 AACTGCCAAAACATCTTATATTTAGGA 57.526 29.630 0.00 0.00 0.00 2.94
3141 3346 9.736023 GAACTGCCAAAACATCTTATATTTAGG 57.264 33.333 0.00 0.00 0.00 2.69
3147 3352 9.638239 GAAATTGAACTGCCAAAACATCTTATA 57.362 29.630 0.00 0.00 0.00 0.98
3148 3353 8.149647 TGAAATTGAACTGCCAAAACATCTTAT 58.850 29.630 0.00 0.00 0.00 1.73
3149 3354 7.495901 TGAAATTGAACTGCCAAAACATCTTA 58.504 30.769 0.00 0.00 0.00 2.10
3150 3355 6.347696 TGAAATTGAACTGCCAAAACATCTT 58.652 32.000 0.00 0.00 0.00 2.40
3151 3356 5.916318 TGAAATTGAACTGCCAAAACATCT 58.084 33.333 0.00 0.00 0.00 2.90
3152 3357 6.258507 AGTTGAAATTGAACTGCCAAAACATC 59.741 34.615 0.00 0.00 32.30 3.06
3153 3358 6.114767 AGTTGAAATTGAACTGCCAAAACAT 58.885 32.000 0.00 0.00 32.30 2.71
3154 3359 5.486526 AGTTGAAATTGAACTGCCAAAACA 58.513 33.333 0.00 0.00 32.30 2.83
3155 3360 6.933130 GTAGTTGAAATTGAACTGCCAAAAC 58.067 36.000 8.07 0.00 35.30 2.43


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

AutoCloner maintained by Alex Coulton.