Multiple sequence alignment - TraesCS7D01G058100

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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 TraesCS7D01G058100 chr7D 100.000 3441 0 0 1 3441 31112360 31115800 0.000000e+00 6355.0
1 TraesCS7D01G058100 chr7D 80.186 323 54 8 986 1301 31281455 31281774 2.060000e-57 233.0
2 TraesCS7D01G058100 chr7D 96.774 31 1 0 760 790 31113056 31113086 6.000000e-03 52.8
3 TraesCS7D01G058100 chr7D 96.774 31 1 0 697 727 31113119 31113149 6.000000e-03 52.8
4 TraesCS7D01G058100 chr7A 88.760 1210 126 8 1784 2989 31582397 31581194 0.000000e+00 1472.0
5 TraesCS7D01G058100 chr7A 88.718 975 67 20 1 965 31583996 31583055 0.000000e+00 1151.0
6 TraesCS7D01G058100 chr7A 88.128 876 99 4 1938 2809 31687393 31688267 0.000000e+00 1037.0
7 TraesCS7D01G058100 chr7A 82.083 1133 122 44 441 1514 31686103 31687213 0.000000e+00 893.0
8 TraesCS7D01G058100 chr7A 89.715 632 48 8 965 1591 31583013 31582394 0.000000e+00 791.0
9 TraesCS7D01G058100 chr7A 86.562 640 63 9 2806 3438 31692214 31692837 0.000000e+00 684.0
10 TraesCS7D01G058100 chr7A 89.294 411 38 4 3034 3441 25876671 25877078 8.520000e-141 510.0
11 TraesCS7D01G058100 chr7A 89.349 338 34 1 3104 3441 31575507 31575172 1.140000e-114 424.0
12 TraesCS7D01G058100 chr7A 90.123 324 26 4 1784 2107 31536968 31536651 1.910000e-112 416.0
13 TraesCS7D01G058100 chr7A 89.506 324 28 4 1784 2107 31518527 31518210 4.140000e-109 405.0
14 TraesCS7D01G058100 chr7A 89.506 324 28 4 1784 2107 31555409 31555092 4.140000e-109 405.0
15 TraesCS7D01G058100 chr7A 80.617 454 56 20 984 1408 31693442 31693892 4.280000e-84 322.0
16 TraesCS7D01G058100 chr7A 91.538 130 9 2 2984 3112 31580914 31580786 9.810000e-41 178.0
17 TraesCS7D01G058100 chr7A 85.294 136 13 7 1662 1796 5678351 5678222 2.150000e-27 134.0
18 TraesCS7D01G058100 chr7A 88.889 63 5 2 1587 1648 649077694 649077633 3.680000e-10 76.8
19 TraesCS7D01G058100 chr7A 94.444 36 2 0 3204 3239 546594026 546593991 4.800000e-04 56.5
20 TraesCS7D01G058100 chrUn 90.123 324 26 4 1784 2107 350569251 350568934 1.910000e-112 416.0
21 TraesCS7D01G058100 chrUn 91.964 224 14 2 1884 2107 359467981 359467762 9.270000e-81 311.0
22 TraesCS7D01G058100 chrUn 87.903 124 12 3 1667 1790 112299266 112299386 3.580000e-30 143.0
23 TraesCS7D01G058100 chrUn 87.500 56 6 1 78 132 287694894 287694949 2.870000e-06 63.9
24 TraesCS7D01G058100 chrUn 87.500 56 6 1 78 132 287707098 287707153 2.870000e-06 63.9
25 TraesCS7D01G058100 chrUn 87.500 56 6 1 78 132 294703111 294703166 2.870000e-06 63.9
26 TraesCS7D01G058100 chr5D 81.643 414 65 10 1010 1417 34063953 34064361 1.980000e-87 333.0
27 TraesCS7D01G058100 chr5D 76.660 497 93 20 2803 3286 458249105 458249591 1.590000e-63 254.0
28 TraesCS7D01G058100 chr5D 88.889 126 9 3 1667 1792 377988115 377987995 2.140000e-32 150.0
29 TraesCS7D01G058100 chr4B 79.287 449 56 18 985 1408 531479133 531479569 2.620000e-71 279.0
30 TraesCS7D01G058100 chr4B 90.476 63 5 1 1585 1647 613157256 613157317 7.910000e-12 82.4
31 TraesCS7D01G058100 chr4B 90.164 61 6 0 1587 1647 527372255 527372315 2.850000e-11 80.5
32 TraesCS7D01G058100 chr5B 79.467 375 66 8 2933 3300 228115602 228115972 4.410000e-64 255.0
33 TraesCS7D01G058100 chr5B 76.653 484 92 15 2816 3287 288320190 288319716 7.370000e-62 248.0
34 TraesCS7D01G058100 chr5B 74.664 446 104 6 2863 3300 614834189 614833745 4.530000e-44 189.0
35 TraesCS7D01G058100 chr4D 78.242 455 56 20 985 1408 433365498 433365940 5.700000e-63 252.0
36 TraesCS7D01G058100 chr4D 77.089 371 68 15 2918 3279 172013441 172013803 7.530000e-47 198.0
37 TraesCS7D01G058100 chr4D 84.783 138 16 5 1667 1803 316527406 316527539 2.150000e-27 134.0
38 TraesCS7D01G058100 chr4D 93.220 59 2 2 1589 1647 170334045 170333989 6.120000e-13 86.1
39 TraesCS7D01G058100 chr4A 83.103 290 35 8 984 1260 34677939 34678227 5.700000e-63 252.0
40 TraesCS7D01G058100 chr4A 90.000 80 8 0 1204 1283 696576847 696576926 1.690000e-18 104.0
41 TraesCS7D01G058100 chr5A 76.376 436 86 17 2860 3286 576306528 576306955 5.780000e-53 219.0
42 TraesCS7D01G058100 chr5A 91.525 59 4 1 1590 1648 385316393 385316336 2.850000e-11 80.5
43 TraesCS7D01G058100 chr3A 73.673 471 97 20 2828 3286 164935581 164935126 1.280000e-34 158.0
44 TraesCS7D01G058100 chr6A 86.232 138 13 3 1667 1804 595172399 595172268 9.950000e-31 145.0
45 TraesCS7D01G058100 chr6A 87.903 124 10 5 1667 1789 328167471 328167590 1.290000e-29 141.0
46 TraesCS7D01G058100 chr1D 87.903 124 10 5 1667 1789 311411491 311411372 1.290000e-29 141.0
47 TraesCS7D01G058100 chr2A 79.426 209 33 6 1588 1794 343448417 343448617 4.630000e-29 139.0
48 TraesCS7D01G058100 chr7B 85.185 135 16 4 1667 1800 66258018 66257887 5.990000e-28 135.0
49 TraesCS7D01G058100 chr7B 94.444 36 2 0 3204 3239 467453320 467453355 4.800000e-04 56.5
50 TraesCS7D01G058100 chr6B 91.803 61 4 1 1587 1647 650598703 650598644 2.200000e-12 84.2
51 TraesCS7D01G058100 chr6D 90.164 61 5 1 1587 1647 431160831 431160772 1.020000e-10 78.7
52 TraesCS7D01G058100 chr2D 91.228 57 5 0 1590 1646 31668911 31668967 1.020000e-10 78.7
53 TraesCS7D01G058100 chr3B 84.000 75 11 1 3212 3286 8631914 8631841 1.710000e-08 71.3


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 TraesCS7D01G058100 chr7D 31112360 31115800 3440 False 2153.533333 6355 97.849333 1 3441 3 chr7D.!!$F2 3440
1 TraesCS7D01G058100 chr7A 31580786 31583996 3210 True 898.000000 1472 89.682750 1 3112 4 chr7A.!!$R8 3111
2 TraesCS7D01G058100 chr7A 31686103 31693892 7789 False 734.000000 1037 84.347500 441 3438 4 chr7A.!!$F2 2997

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
316 317 0.030235 GGTCCTTGTGTTCGTTTGCC 59.970 55.0 0.0 0.00 0.00 4.52 F
317 318 0.316689 GTCCTTGTGTTCGTTTGCCG 60.317 55.0 0.0 0.00 38.13 5.69 F
321 322 0.317436 TTGTGTTCGTTTGCCGATGC 60.317 50.0 0.0 0.00 46.75 3.91 F
2197 2295 0.108424 AGAAGGCATCAGTGAGCGTC 60.108 55.0 0.0 4.36 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2103 0.108898 CAGCACTCTCGGAAGACCTG 60.109 60.000 0.0 0.0 35.39 4.00 R
2161 2259 0.178068 TCTGGACCGGCAATTCTAGC 59.822 55.000 0.0 0.0 0.00 3.42 R
2202 2300 0.673437 CTTGCGGATTTGGTGGTTGT 59.327 50.000 0.0 0.0 0.00 3.32 R
3113 7451 1.600916 GCAAAGGGACGCCTCAACT 60.601 57.895 0.0 0.0 0.00 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 139 6.325596 TCTCCGAATATGAATTCAGCGATAG 58.674 40.000 14.54 13.48 41.44 2.08
225 226 4.163458 TGTGCATGCAACTTATTCACTG 57.837 40.909 24.58 0.00 0.00 3.66
226 227 3.057386 TGTGCATGCAACTTATTCACTGG 60.057 43.478 24.58 0.00 0.00 4.00
227 228 3.191162 GTGCATGCAACTTATTCACTGGA 59.809 43.478 24.58 0.00 0.00 3.86
228 229 3.825585 TGCATGCAACTTATTCACTGGAA 59.174 39.130 20.30 0.00 37.45 3.53
229 230 4.168760 GCATGCAACTTATTCACTGGAAC 58.831 43.478 14.21 0.00 35.46 3.62
230 231 4.406069 CATGCAACTTATTCACTGGAACG 58.594 43.478 0.00 0.00 35.46 3.95
231 232 2.811431 TGCAACTTATTCACTGGAACGG 59.189 45.455 0.00 0.00 42.99 4.44
232 233 2.414161 GCAACTTATTCACTGGAACGGC 60.414 50.000 0.00 0.00 39.14 5.68
233 234 3.074412 CAACTTATTCACTGGAACGGCT 58.926 45.455 0.00 0.00 39.14 5.52
234 235 2.699954 ACTTATTCACTGGAACGGCTG 58.300 47.619 0.00 0.00 39.14 4.85
235 236 2.009774 CTTATTCACTGGAACGGCTGG 58.990 52.381 0.00 0.00 39.14 4.85
236 237 1.271856 TATTCACTGGAACGGCTGGA 58.728 50.000 0.00 0.00 39.14 3.86
237 238 0.400213 ATTCACTGGAACGGCTGGAA 59.600 50.000 0.00 0.00 39.14 3.53
238 239 0.534203 TTCACTGGAACGGCTGGAAC 60.534 55.000 0.00 0.00 39.14 3.62
242 243 3.119096 GGAACGGCTGGAACGAGC 61.119 66.667 0.00 0.35 38.34 5.03
256 257 0.533755 ACGAGCCTGCCTGATATTGC 60.534 55.000 0.00 0.00 0.00 3.56
257 258 1.563435 CGAGCCTGCCTGATATTGCG 61.563 60.000 0.00 0.00 0.00 4.85
278 279 2.636893 GTGATGATAGAGGTGCCATCCT 59.363 50.000 0.00 0.00 40.97 3.24
279 280 3.072184 GTGATGATAGAGGTGCCATCCTT 59.928 47.826 0.00 0.00 38.02 3.36
280 281 3.718434 TGATGATAGAGGTGCCATCCTTT 59.282 43.478 0.00 0.00 38.02 3.11
309 310 1.966451 CTGGCCGGTCCTTGTGTTC 60.966 63.158 2.12 0.00 35.26 3.18
311 312 2.280592 GCCGGTCCTTGTGTTCGT 60.281 61.111 1.90 0.00 0.00 3.85
312 313 1.890510 GCCGGTCCTTGTGTTCGTT 60.891 57.895 1.90 0.00 0.00 3.85
313 314 1.441732 GCCGGTCCTTGTGTTCGTTT 61.442 55.000 1.90 0.00 0.00 3.60
314 315 0.306533 CCGGTCCTTGTGTTCGTTTG 59.693 55.000 0.00 0.00 0.00 2.93
315 316 0.316689 CGGTCCTTGTGTTCGTTTGC 60.317 55.000 0.00 0.00 0.00 3.68
316 317 0.030235 GGTCCTTGTGTTCGTTTGCC 59.970 55.000 0.00 0.00 0.00 4.52
317 318 0.316689 GTCCTTGTGTTCGTTTGCCG 60.317 55.000 0.00 0.00 38.13 5.69
318 319 0.462225 TCCTTGTGTTCGTTTGCCGA 60.462 50.000 0.00 0.00 45.66 5.54
319 320 0.591170 CCTTGTGTTCGTTTGCCGAT 59.409 50.000 0.00 0.00 46.75 4.18
320 321 1.662876 CCTTGTGTTCGTTTGCCGATG 60.663 52.381 0.00 0.00 46.75 3.84
321 322 0.317436 TTGTGTTCGTTTGCCGATGC 60.317 50.000 0.00 0.00 46.75 3.91
322 323 1.792057 GTGTTCGTTTGCCGATGCG 60.792 57.895 0.00 0.00 46.75 4.73
323 324 2.248135 TGTTCGTTTGCCGATGCGT 61.248 52.632 0.00 0.00 46.75 5.24
364 365 0.379669 GCAATGAGGGCTCACATTCG 59.620 55.000 6.24 4.38 43.11 3.34
372 373 1.580942 GCTCACATTCGCCTTGCAA 59.419 52.632 0.00 0.00 0.00 4.08
383 384 1.034292 GCCTTGCAATGGACCTCTCC 61.034 60.000 16.28 0.00 37.04 3.71
432 433 2.646798 AGAGGCCAAGAACCTGATTTCT 59.353 45.455 5.01 0.00 37.77 2.52
527 528 1.746787 TGAAGATCACACATGCCATGC 59.253 47.619 4.17 0.00 0.00 4.06
654 674 9.474920 TTGCCACTTGATTTTGAGTAATAAAAG 57.525 29.630 0.00 0.00 31.31 2.27
668 688 7.767198 TGAGTAATAAAAGACACCCTATTTCCG 59.233 37.037 0.00 0.00 0.00 4.30
669 689 7.052248 AGTAATAAAAGACACCCTATTTCCGG 58.948 38.462 0.00 0.00 0.00 5.14
709 729 5.894298 AGCAGAACATATCCACTGGAATA 57.106 39.130 0.66 0.00 34.34 1.75
735 755 2.289547 GAGTAAAACAAAGCCGCTGACA 59.710 45.455 0.00 0.00 0.00 3.58
758 778 3.423154 CGACCCGCCAAGTCTTGC 61.423 66.667 7.09 2.39 31.83 4.01
763 783 2.109126 CCGCCAAGTCTTGCTAGCC 61.109 63.158 13.29 0.00 0.00 3.93
764 784 1.375908 CGCCAAGTCTTGCTAGCCA 60.376 57.895 13.29 0.00 0.00 4.75
766 786 0.322008 GCCAAGTCTTGCTAGCCACT 60.322 55.000 13.29 8.73 0.00 4.00
767 787 1.446907 CCAAGTCTTGCTAGCCACTG 58.553 55.000 13.29 6.64 0.00 3.66
768 788 1.446907 CAAGTCTTGCTAGCCACTGG 58.553 55.000 13.29 5.44 0.00 4.00
772 792 3.107601 AGTCTTGCTAGCCACTGGAATA 58.892 45.455 13.29 0.00 0.00 1.75
773 793 3.133721 AGTCTTGCTAGCCACTGGAATAG 59.866 47.826 13.29 1.49 0.00 1.73
776 796 3.758755 TGCTAGCCACTGGAATAGATG 57.241 47.619 13.29 0.00 0.00 2.90
777 797 2.369860 TGCTAGCCACTGGAATAGATGG 59.630 50.000 13.29 0.00 33.41 3.51
778 798 2.634940 GCTAGCCACTGGAATAGATGGA 59.365 50.000 2.29 0.00 32.55 3.41
779 799 3.306641 GCTAGCCACTGGAATAGATGGAG 60.307 52.174 2.29 0.00 32.55 3.86
781 801 3.928754 AGCCACTGGAATAGATGGAGTA 58.071 45.455 0.00 0.00 32.55 2.59
782 802 4.298626 AGCCACTGGAATAGATGGAGTAA 58.701 43.478 0.00 0.00 32.55 2.24
783 803 4.721776 AGCCACTGGAATAGATGGAGTAAA 59.278 41.667 0.00 0.00 32.55 2.01
784 804 5.191722 AGCCACTGGAATAGATGGAGTAAAA 59.808 40.000 0.00 0.00 32.55 1.52
833 860 4.262635 GGTCTCTGACTCTCAACCAATCAA 60.263 45.833 0.00 0.00 32.47 2.57
836 863 5.246883 TCTCTGACTCTCAACCAATCAATGA 59.753 40.000 0.00 0.00 0.00 2.57
840 867 5.106038 TGACTCTCAACCAATCAATGAATGC 60.106 40.000 0.00 0.00 0.00 3.56
847 874 2.169769 CCAATCAATGAATGCAAGGCCT 59.830 45.455 0.00 0.00 0.00 5.19
848 875 3.194861 CAATCAATGAATGCAAGGCCTG 58.805 45.455 5.69 1.10 0.00 4.85
849 876 1.187974 TCAATGAATGCAAGGCCTGG 58.812 50.000 5.69 3.35 0.00 4.45
853 880 1.324740 TGAATGCAAGGCCTGGATGC 61.325 55.000 19.17 19.17 36.01 3.91
855 882 2.361992 TGCAAGGCCTGGATGCAG 60.362 61.111 23.69 7.35 44.52 4.41
887 915 4.082463 AGACCTCGAGAAGACTTGACATTC 60.082 45.833 15.71 0.00 33.48 2.67
897 925 6.433404 AGAAGACTTGACATTCTCAAATGCAT 59.567 34.615 0.00 0.00 45.16 3.96
898 926 6.192234 AGACTTGACATTCTCAAATGCATC 57.808 37.500 0.00 0.00 45.16 3.91
905 933 4.705507 ACATTCTCAAATGCATCTGCTTCT 59.294 37.500 0.00 0.00 45.16 2.85
914 942 2.241941 TGCATCTGCTTCTCCCCAAATA 59.758 45.455 3.53 0.00 42.66 1.40
923 951 9.707957 TCTGCTTCTCCCCAAATAAAATAAATA 57.292 29.630 0.00 0.00 0.00 1.40
952 980 3.648339 TTTCATCTTGCAAGTGCTTCC 57.352 42.857 25.19 0.00 42.66 3.46
954 982 2.156917 TCATCTTGCAAGTGCTTCCTG 58.843 47.619 25.19 12.26 42.66 3.86
955 983 0.886563 ATCTTGCAAGTGCTTCCTGC 59.113 50.000 25.19 0.00 42.66 4.85
993 1063 1.077858 GGCTGCAAAGGAGGAGGAG 60.078 63.158 0.50 0.00 0.00 3.69
995 1065 1.557269 GCTGCAAAGGAGGAGGAGGA 61.557 60.000 0.00 0.00 0.00 3.71
1018 1088 1.005275 ATGGAGGCATGCGAGATCG 60.005 57.895 12.44 0.00 43.27 3.69
1261 1331 4.779733 TCCTCCCAGGCGGACTCC 62.780 72.222 0.00 0.00 34.86 3.85
1488 1566 0.744874 TCCGTCGCAGCTAGCTTATT 59.255 50.000 16.46 0.00 42.61 1.40
1514 1592 4.337555 GGTCAATGAACAATGATGCTAGCT 59.662 41.667 17.23 0.83 0.00 3.32
1515 1593 5.528690 GGTCAATGAACAATGATGCTAGCTA 59.471 40.000 17.23 2.58 0.00 3.32
1516 1594 6.293298 GGTCAATGAACAATGATGCTAGCTAG 60.293 42.308 16.84 16.84 0.00 3.42
1539 1617 7.437793 AGCTCGTCTAATTCCATACTAGTAC 57.562 40.000 4.31 0.00 0.00 2.73
1541 1619 7.666388 AGCTCGTCTAATTCCATACTAGTACAT 59.334 37.037 4.31 0.00 0.00 2.29
1577 1655 1.892819 CGTGGCCCATGACTGAGTCT 61.893 60.000 14.42 0.00 33.15 3.24
1591 1669 9.457110 CATGACTGAGTCTTGACTACATTATAC 57.543 37.037 20.14 0.00 39.17 1.47
1592 1670 8.809468 TGACTGAGTCTTGACTACATTATACT 57.191 34.615 14.42 0.00 33.15 2.12
1594 1672 9.724839 GACTGAGTCTTGACTACATTATACTTC 57.275 37.037 5.12 0.00 0.00 3.01
1595 1673 8.688151 ACTGAGTCTTGACTACATTATACTTCC 58.312 37.037 3.00 0.00 0.00 3.46
1596 1674 8.824756 TGAGTCTTGACTACATTATACTTCCT 57.175 34.615 3.00 0.00 0.00 3.36
1597 1675 8.904834 TGAGTCTTGACTACATTATACTTCCTC 58.095 37.037 3.00 0.00 0.00 3.71
1598 1676 9.127277 GAGTCTTGACTACATTATACTTCCTCT 57.873 37.037 3.00 0.00 0.00 3.69
1599 1677 8.908903 AGTCTTGACTACATTATACTTCCTCTG 58.091 37.037 0.89 0.00 0.00 3.35
1600 1678 7.650104 GTCTTGACTACATTATACTTCCTCTGC 59.350 40.741 0.00 0.00 0.00 4.26
1601 1679 7.561722 TCTTGACTACATTATACTTCCTCTGCT 59.438 37.037 0.00 0.00 0.00 4.24
1602 1680 7.278461 TGACTACATTATACTTCCTCTGCTC 57.722 40.000 0.00 0.00 0.00 4.26
1603 1681 6.265649 TGACTACATTATACTTCCTCTGCTCC 59.734 42.308 0.00 0.00 0.00 4.70
1604 1682 6.377912 ACTACATTATACTTCCTCTGCTCCT 58.622 40.000 0.00 0.00 0.00 3.69
1605 1683 7.527796 ACTACATTATACTTCCTCTGCTCCTA 58.472 38.462 0.00 0.00 0.00 2.94
1606 1684 8.005388 ACTACATTATACTTCCTCTGCTCCTAA 58.995 37.037 0.00 0.00 0.00 2.69
1607 1685 7.676683 ACATTATACTTCCTCTGCTCCTAAA 57.323 36.000 0.00 0.00 0.00 1.85
1608 1686 8.268878 ACATTATACTTCCTCTGCTCCTAAAT 57.731 34.615 0.00 0.00 0.00 1.40
1609 1687 9.381038 ACATTATACTTCCTCTGCTCCTAAATA 57.619 33.333 0.00 0.00 0.00 1.40
1614 1692 7.922699 ACTTCCTCTGCTCCTAAATATAAGT 57.077 36.000 0.00 0.00 0.00 2.24
1615 1693 7.958088 ACTTCCTCTGCTCCTAAATATAAGTC 58.042 38.462 0.00 0.00 0.00 3.01
1616 1694 6.919775 TCCTCTGCTCCTAAATATAAGTCC 57.080 41.667 0.00 0.00 0.00 3.85
1617 1695 6.625267 TCCTCTGCTCCTAAATATAAGTCCT 58.375 40.000 0.00 0.00 0.00 3.85
1618 1696 7.076446 TCCTCTGCTCCTAAATATAAGTCCTT 58.924 38.462 0.00 0.00 0.00 3.36
1619 1697 7.569111 TCCTCTGCTCCTAAATATAAGTCCTTT 59.431 37.037 0.00 0.00 0.00 3.11
1620 1698 8.214364 CCTCTGCTCCTAAATATAAGTCCTTTT 58.786 37.037 0.00 0.00 0.00 2.27
1688 1766 9.816354 AAAAACTACATACAAAGCAAAATGAGT 57.184 25.926 0.00 0.00 0.00 3.41
1689 1767 8.801715 AAACTACATACAAAGCAAAATGAGTG 57.198 30.769 0.00 0.00 0.00 3.51
1690 1768 7.744087 ACTACATACAAAGCAAAATGAGTGA 57.256 32.000 0.00 0.00 0.00 3.41
1691 1769 8.165239 ACTACATACAAAGCAAAATGAGTGAA 57.835 30.769 0.00 0.00 0.00 3.18
1692 1770 8.796475 ACTACATACAAAGCAAAATGAGTGAAT 58.204 29.630 0.00 0.00 0.00 2.57
1693 1771 9.282247 CTACATACAAAGCAAAATGAGTGAATC 57.718 33.333 0.00 0.00 0.00 2.52
1694 1772 7.889469 ACATACAAAGCAAAATGAGTGAATCT 58.111 30.769 0.00 0.00 0.00 2.40
1695 1773 9.013229 ACATACAAAGCAAAATGAGTGAATCTA 57.987 29.630 0.00 0.00 0.00 1.98
1696 1774 9.282247 CATACAAAGCAAAATGAGTGAATCTAC 57.718 33.333 0.00 0.00 0.00 2.59
1697 1775 7.275888 ACAAAGCAAAATGAGTGAATCTACA 57.724 32.000 0.00 0.00 0.00 2.74
1698 1776 7.141363 ACAAAGCAAAATGAGTGAATCTACAC 58.859 34.615 0.00 0.00 40.60 2.90
1712 1790 8.958506 AGTGAATCTACACTCTAAAATACGTCT 58.041 33.333 0.00 0.00 46.36 4.18
1715 1793 9.367717 GAATCTACACTCTAAAATACGTCTACG 57.632 37.037 0.00 0.04 46.33 3.51
1741 1819 7.898014 ACATCTGTATGTATGTAGTTCCTCA 57.102 36.000 0.00 0.00 44.66 3.86
1742 1820 8.484214 ACATCTGTATGTATGTAGTTCCTCAT 57.516 34.615 0.00 0.00 44.66 2.90
1743 1821 8.928448 ACATCTGTATGTATGTAGTTCCTCATT 58.072 33.333 0.00 0.00 44.66 2.57
1744 1822 9.201127 CATCTGTATGTATGTAGTTCCTCATTG 57.799 37.037 0.00 0.00 0.00 2.82
1745 1823 7.210174 TCTGTATGTATGTAGTTCCTCATTGC 58.790 38.462 0.00 0.00 0.00 3.56
1746 1824 6.883744 TGTATGTATGTAGTTCCTCATTGCA 58.116 36.000 0.00 0.00 0.00 4.08
1747 1825 7.334858 TGTATGTATGTAGTTCCTCATTGCAA 58.665 34.615 0.00 0.00 0.00 4.08
1748 1826 7.992608 TGTATGTATGTAGTTCCTCATTGCAAT 59.007 33.333 5.99 5.99 0.00 3.56
1749 1827 6.925610 TGTATGTAGTTCCTCATTGCAATC 57.074 37.500 9.53 0.00 0.00 2.67
1750 1828 6.653020 TGTATGTAGTTCCTCATTGCAATCT 58.347 36.000 9.53 5.13 0.00 2.40
1751 1829 7.112122 TGTATGTAGTTCCTCATTGCAATCTT 58.888 34.615 9.53 0.00 0.00 2.40
1752 1830 7.611467 TGTATGTAGTTCCTCATTGCAATCTTT 59.389 33.333 9.53 0.00 0.00 2.52
1753 1831 9.109393 GTATGTAGTTCCTCATTGCAATCTTTA 57.891 33.333 9.53 0.00 0.00 1.85
1754 1832 7.994425 TGTAGTTCCTCATTGCAATCTTTAA 57.006 32.000 9.53 0.00 0.00 1.52
1755 1833 8.402798 TGTAGTTCCTCATTGCAATCTTTAAA 57.597 30.769 9.53 0.00 0.00 1.52
1756 1834 8.855110 TGTAGTTCCTCATTGCAATCTTTAAAA 58.145 29.630 9.53 0.00 0.00 1.52
1757 1835 9.691362 GTAGTTCCTCATTGCAATCTTTAAAAA 57.309 29.630 9.53 0.00 0.00 1.94
1758 1836 8.822652 AGTTCCTCATTGCAATCTTTAAAAAG 57.177 30.769 9.53 0.00 37.36 2.27
1760 1838 8.703336 GTTCCTCATTGCAATCTTTAAAAAGAC 58.297 33.333 9.53 0.00 46.80 3.01
1761 1839 8.181904 TCCTCATTGCAATCTTTAAAAAGACT 57.818 30.769 9.53 0.00 46.80 3.24
1762 1840 8.641541 TCCTCATTGCAATCTTTAAAAAGACTT 58.358 29.630 9.53 1.95 46.80 3.01
1763 1841 9.912634 CCTCATTGCAATCTTTAAAAAGACTTA 57.087 29.630 9.53 0.00 46.80 2.24
1829 1907 7.234355 ACAATCATGAAAGAAAGTACTCCCTT 58.766 34.615 0.00 0.00 0.00 3.95
1843 1921 8.631480 AAGTACTCCCTTCGAAAATAAATGTT 57.369 30.769 0.00 0.00 0.00 2.71
1845 1923 6.267496 ACTCCCTTCGAAAATAAATGTTGG 57.733 37.500 0.00 0.00 0.00 3.77
1848 1926 4.221924 CCCTTCGAAAATAAATGTTGGGGT 59.778 41.667 0.00 0.00 0.00 4.95
1861 1939 9.762381 ATAAATGTTGGGGTTTTAGATCTAACA 57.238 29.630 14.85 9.93 0.00 2.41
1894 1972 4.095483 GCAGTTAGTTCCCATCATCAGTTG 59.905 45.833 0.00 0.00 0.00 3.16
1916 1994 3.270027 GCTTTGCAACTTTTGTTCCCTT 58.730 40.909 0.00 0.00 41.35 3.95
2005 2103 8.958119 TCCTAAATGTATATGTGTTCAACTCC 57.042 34.615 0.00 0.00 0.00 3.85
2010 2108 5.730550 TGTATATGTGTTCAACTCCAGGTC 58.269 41.667 0.00 0.00 0.00 3.85
2094 2192 0.924823 ATGCTCTCCCAAGGCTCAAT 59.075 50.000 0.00 0.00 0.00 2.57
2109 2207 6.398234 AGGCTCAATATACTCAGTGTACAG 57.602 41.667 0.00 0.00 33.45 2.74
2128 2226 2.627699 CAGGGTGTACAAGTTTGCCAAT 59.372 45.455 0.00 0.00 0.00 3.16
2129 2227 3.069443 CAGGGTGTACAAGTTTGCCAATT 59.931 43.478 0.00 0.00 0.00 2.32
2133 2231 6.042666 AGGGTGTACAAGTTTGCCAATTATTT 59.957 34.615 0.00 0.00 0.00 1.40
2134 2232 6.147000 GGGTGTACAAGTTTGCCAATTATTTG 59.853 38.462 0.00 0.00 0.00 2.32
2140 2238 7.675062 ACAAGTTTGCCAATTATTTGTATGGA 58.325 30.769 0.00 0.00 34.82 3.41
2144 2242 8.320617 AGTTTGCCAATTATTTGTATGGATTGT 58.679 29.630 0.00 0.00 34.82 2.71
2161 2259 1.305219 TGTCCGACGGTTACTACGGG 61.305 60.000 14.79 0.00 44.57 5.28
2197 2295 0.108424 AGAAGGCATCAGTGAGCGTC 60.108 55.000 0.00 4.36 0.00 5.19
2202 2300 1.803289 CATCAGTGAGCGTCGGAGA 59.197 57.895 0.00 0.00 0.00 3.71
2241 2339 1.490490 GGTCTGCATCCATCCTAACCA 59.510 52.381 0.00 0.00 0.00 3.67
2283 2381 0.250252 TGTCATGCAACGCTTCCTCA 60.250 50.000 0.00 0.00 0.00 3.86
2359 2457 0.175760 ATGAAGATGGGGACGTGTCG 59.824 55.000 0.00 0.00 0.00 4.35
2368 2466 1.577328 GGGACGTGTCGTTCGGTCTA 61.577 60.000 0.00 0.00 41.37 2.59
2389 2487 8.203485 GGTCTATCAGAGATGAAAGATTTGAGT 58.797 37.037 0.00 0.00 36.29 3.41
2497 2596 3.767309 AGACAGGGAGATAGACAACCT 57.233 47.619 0.00 0.00 0.00 3.50
2512 2611 1.264749 AACCTAGTGGCTGGCGATGA 61.265 55.000 0.00 0.00 36.63 2.92
2519 2618 1.337384 TGGCTGGCGATGACCTACAT 61.337 55.000 0.00 0.00 42.47 2.29
2559 2659 3.027170 GCGCTCATCACACCGTTGG 62.027 63.158 0.00 0.00 0.00 3.77
2570 2670 4.452825 TCACACCGTTGGTTAAATCAGAA 58.547 39.130 0.00 0.00 31.02 3.02
2617 2720 7.107639 TCACTCCGATATTGTCACTAATGAA 57.892 36.000 0.00 0.00 36.31 2.57
2641 2744 4.198473 ACGAATACGAGAGATCGTGAAG 57.802 45.455 13.14 5.07 46.53 3.02
2651 2754 4.310769 AGAGATCGTGAAGTCTTTGGTTG 58.689 43.478 0.00 0.00 0.00 3.77
2670 2773 3.342377 TGAATATGTTTCTGCGGGACA 57.658 42.857 5.34 5.34 0.00 4.02
2687 2790 5.640732 CGGGACATAAACATGGAAAGAAAG 58.359 41.667 0.00 0.00 0.00 2.62
2698 2801 8.579850 AACATGGAAAGAAAGCATCACTTATA 57.420 30.769 0.00 0.00 37.75 0.98
2740 2843 4.603610 AGGAAGAAAGGAAGGAATTGGAGA 59.396 41.667 0.00 0.00 0.00 3.71
2750 2853 4.918810 AGGAATTGGAGACACAACAAAC 57.081 40.909 0.00 0.00 42.67 2.93
2769 2872 0.249868 CCAACCAGAGTGCAAGACGA 60.250 55.000 0.00 0.00 0.00 4.20
2799 2902 3.776656 GCGAACGCTTGTACCGAT 58.223 55.556 11.97 0.00 38.26 4.18
2853 6907 3.240302 AGGGGTCAATACTAGAATCCCG 58.760 50.000 0.00 0.00 36.45 5.14
2854 6908 2.302157 GGGGTCAATACTAGAATCCCGG 59.698 54.545 0.00 0.00 34.78 5.73
2856 6910 2.633481 GGTCAATACTAGAATCCCGGCT 59.367 50.000 0.00 0.00 0.00 5.52
2883 6937 2.365293 AGCACCATTTGGGAAACAGAAC 59.635 45.455 0.96 0.00 41.15 3.01
2887 6941 2.288152 CCATTTGGGAAACAGAACACCG 60.288 50.000 0.00 0.00 40.01 4.94
2890 6944 0.547075 TGGGAAACAGAACACCGGAA 59.453 50.000 9.46 0.00 0.00 4.30
2903 6957 1.064825 ACCGGAACCATCTTCCAACT 58.935 50.000 9.46 0.00 38.49 3.16
2912 6966 0.827368 ATCTTCCAACTCTCGCCCTC 59.173 55.000 0.00 0.00 0.00 4.30
2913 6967 0.541998 TCTTCCAACTCTCGCCCTCA 60.542 55.000 0.00 0.00 0.00 3.86
2930 6984 4.287067 GCCCTCACTATTTCCCATCTCATA 59.713 45.833 0.00 0.00 0.00 2.15
2938 6992 8.820831 CACTATTTCCCATCTCATATCCTTAGT 58.179 37.037 0.00 0.00 0.00 2.24
2939 6993 9.041354 ACTATTTCCCATCTCATATCCTTAGTC 57.959 37.037 0.00 0.00 0.00 2.59
2992 7330 7.618117 TCTCCAAGTTAGTCATACCTGTAATCA 59.382 37.037 0.00 0.00 0.00 2.57
3010 7348 3.443099 TCATGTATCTCAGCCGACAAG 57.557 47.619 0.00 0.00 0.00 3.16
3102 7440 5.178252 CCGATCATCATGTGTGAGTAATTCC 59.822 44.000 8.93 0.00 37.87 3.01
3136 7474 3.680786 GGCGTCCCTTTGCAACCC 61.681 66.667 0.00 0.00 0.00 4.11
3154 7492 1.199097 CCCGATGTGTTTGTACAAGGC 59.801 52.381 8.56 6.83 35.69 4.35
3157 7495 3.426159 CCGATGTGTTTGTACAAGGCATC 60.426 47.826 24.03 24.03 35.69 3.91
3160 7498 2.546368 TGTGTTTGTACAAGGCATCGAC 59.454 45.455 8.56 3.02 35.69 4.20
3161 7499 2.806244 GTGTTTGTACAAGGCATCGACT 59.194 45.455 8.56 0.00 35.69 4.18
3174 7512 4.631813 AGGCATCGACTAAATGACTTTGAC 59.368 41.667 0.00 0.00 39.52 3.18
3203 7541 2.192664 TCATGTATGTGCCCGTTTGT 57.807 45.000 0.00 0.00 0.00 2.83
3206 7544 4.072839 TCATGTATGTGCCCGTTTGTAAA 58.927 39.130 0.00 0.00 0.00 2.01
3222 7560 6.509677 CGTTTGTAAAGGAGTTGTCTCTTGTC 60.510 42.308 0.00 0.00 40.29 3.18
3245 7583 1.550976 CTTCTCGTTCTAAGGCCCTGT 59.449 52.381 0.00 0.00 0.00 4.00
3246 7584 0.895530 TCTCGTTCTAAGGCCCTGTG 59.104 55.000 0.00 0.00 0.00 3.66
3251 7589 2.701107 GTTCTAAGGCCCTGTGAGTTC 58.299 52.381 0.00 0.00 0.00 3.01
3254 7592 2.043939 TCTAAGGCCCTGTGAGTTCCTA 59.956 50.000 0.00 0.00 0.00 2.94
3258 7596 1.501582 GCCCTGTGAGTTCCTAGGAT 58.498 55.000 13.57 0.00 31.91 3.24
3289 7632 6.987403 ATCTATCAAGGAGGAGGTAAGAAC 57.013 41.667 0.00 0.00 0.00 3.01
3309 7652 5.419471 AGAACTGAGGAGGACACATAACTAC 59.581 44.000 0.00 0.00 0.00 2.73
3321 7664 2.120232 CATAACTACGCTGCTCCTTCG 58.880 52.381 0.00 0.00 0.00 3.79
3327 7670 2.896443 GCTGCTCCTTCGCCTACT 59.104 61.111 0.00 0.00 0.00 2.57
3328 7671 1.725557 CGCTGCTCCTTCGCCTACTA 61.726 60.000 0.00 0.00 0.00 1.82
3346 7689 7.661847 CGCCTACTAATTCCTTTAGATTGGATT 59.338 37.037 0.00 0.00 39.86 3.01
3351 7694 8.689972 ACTAATTCCTTTAGATTGGATTTGCAG 58.310 33.333 0.00 0.00 39.86 4.41
3360 7703 8.635765 TTAGATTGGATTTGCAGAAAACTAGT 57.364 30.769 0.00 0.00 0.00 2.57
3374 7717 9.129209 GCAGAAAACTAGTTTGAATACCAAATC 57.871 33.333 21.22 10.72 45.48 2.17
3380 7723 9.816787 AACTAGTTTGAATACCAAATCCCTTTA 57.183 29.630 1.12 0.00 45.48 1.85
3385 7728 9.419297 GTTTGAATACCAAATCCCTTTACTTTC 57.581 33.333 0.00 0.00 45.48 2.62
3386 7729 8.950007 TTGAATACCAAATCCCTTTACTTTCT 57.050 30.769 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.826720 TGGCCCATCTTCTGAAAATGC 59.173 47.619 0.00 0.00 0.00 3.56
24 25 2.123982 GCCCTGGCCCATCTTCTG 60.124 66.667 0.00 0.00 34.56 3.02
104 105 9.495754 GAATTCATATTCGGAGAAAGTTTTCAG 57.504 33.333 0.00 0.00 45.90 3.02
188 189 6.311690 TGCATGCACATTTCATGAATTTACTG 59.688 34.615 18.46 5.18 42.84 2.74
225 226 3.119096 GCTCGTTCCAGCCGTTCC 61.119 66.667 0.00 0.00 32.76 3.62
231 232 4.400961 AGGCAGGCTCGTTCCAGC 62.401 66.667 0.00 4.95 37.84 4.85
232 233 2.249413 ATCAGGCAGGCTCGTTCCAG 62.249 60.000 0.00 0.00 0.00 3.86
233 234 0.975556 TATCAGGCAGGCTCGTTCCA 60.976 55.000 0.00 0.00 0.00 3.53
234 235 0.394565 ATATCAGGCAGGCTCGTTCC 59.605 55.000 0.00 0.00 0.00 3.62
235 236 1.869767 CAATATCAGGCAGGCTCGTTC 59.130 52.381 0.00 0.00 0.00 3.95
236 237 1.959042 CAATATCAGGCAGGCTCGTT 58.041 50.000 0.00 0.00 0.00 3.85
237 238 0.533755 GCAATATCAGGCAGGCTCGT 60.534 55.000 0.00 0.00 0.00 4.18
238 239 1.563435 CGCAATATCAGGCAGGCTCG 61.563 60.000 0.00 0.00 0.00 5.03
242 243 1.534163 CATCACGCAATATCAGGCAGG 59.466 52.381 0.00 0.00 0.00 4.85
256 257 2.611473 GGATGGCACCTCTATCATCACG 60.611 54.545 0.00 0.00 38.11 4.35
257 258 2.636893 AGGATGGCACCTCTATCATCAC 59.363 50.000 0.00 0.00 38.11 3.06
309 310 2.252127 ATCCAACGCATCGGCAAACG 62.252 55.000 0.00 0.00 46.11 3.60
311 312 1.674359 ATATCCAACGCATCGGCAAA 58.326 45.000 0.00 0.00 41.24 3.68
312 313 2.036604 TCTATATCCAACGCATCGGCAA 59.963 45.455 0.00 0.00 41.24 4.52
313 314 1.616374 TCTATATCCAACGCATCGGCA 59.384 47.619 0.00 0.00 41.24 5.69
314 315 2.263077 CTCTATATCCAACGCATCGGC 58.737 52.381 0.00 0.00 0.00 5.54
315 316 2.263077 GCTCTATATCCAACGCATCGG 58.737 52.381 0.00 0.00 0.00 4.18
316 317 2.946564 TGCTCTATATCCAACGCATCG 58.053 47.619 0.00 0.00 0.00 3.84
317 318 4.331168 GGATTGCTCTATATCCAACGCATC 59.669 45.833 0.00 0.00 40.08 3.91
318 319 4.256920 GGATTGCTCTATATCCAACGCAT 58.743 43.478 0.00 0.00 40.08 4.73
319 320 3.664107 GGATTGCTCTATATCCAACGCA 58.336 45.455 0.00 0.00 40.08 5.24
320 321 2.668457 CGGATTGCTCTATATCCAACGC 59.332 50.000 0.00 0.00 40.30 4.84
321 322 2.668457 GCGGATTGCTCTATATCCAACG 59.332 50.000 0.00 0.00 40.30 4.10
322 323 3.003480 GGCGGATTGCTCTATATCCAAC 58.997 50.000 0.00 0.00 45.43 3.77
323 324 2.906389 AGGCGGATTGCTCTATATCCAA 59.094 45.455 0.00 0.00 45.43 3.53
364 365 1.034292 GGAGAGGTCCATTGCAAGGC 61.034 60.000 5.36 0.00 43.31 4.35
383 384 1.942657 CAGCCTCCGGTACAATTCATG 59.057 52.381 0.00 0.00 0.00 3.07
384 385 1.837439 TCAGCCTCCGGTACAATTCAT 59.163 47.619 0.00 0.00 0.00 2.57
400 401 0.321671 TTGGCCTCTGTACAGTCAGC 59.678 55.000 21.99 20.51 35.63 4.26
405 406 1.625818 AGGTTCTTGGCCTCTGTACAG 59.374 52.381 17.17 17.17 0.00 2.74
432 433 1.913951 ATCGCCCTGCATGTCCTTGA 61.914 55.000 0.00 0.00 0.00 3.02
527 528 3.358700 CACATCATTTTGTTCACGCTTCG 59.641 43.478 0.00 0.00 0.00 3.79
595 596 5.163426 ACAAAGTTCTGCATGAAATCCACAA 60.163 36.000 0.00 0.00 36.30 3.33
654 674 2.773993 TTGACCGGAAATAGGGTGTC 57.226 50.000 9.46 0.00 36.46 3.67
678 698 6.721668 AGTGGATATGTTCTGCTAGCTGTATA 59.278 38.462 17.23 14.85 0.00 1.47
680 700 4.895889 AGTGGATATGTTCTGCTAGCTGTA 59.104 41.667 17.23 6.55 0.00 2.74
681 701 3.708631 AGTGGATATGTTCTGCTAGCTGT 59.291 43.478 17.23 1.97 0.00 4.40
682 702 4.056740 CAGTGGATATGTTCTGCTAGCTG 58.943 47.826 17.23 16.05 0.00 4.24
683 703 3.070734 CCAGTGGATATGTTCTGCTAGCT 59.929 47.826 17.23 0.00 0.00 3.32
684 704 3.070159 TCCAGTGGATATGTTCTGCTAGC 59.930 47.826 8.12 8.10 0.00 3.42
686 706 5.894298 ATTCCAGTGGATATGTTCTGCTA 57.106 39.130 14.00 0.00 0.00 3.49
709 729 2.488153 GCGGCTTTGTTTTACTCCATCT 59.512 45.455 0.00 0.00 0.00 2.90
758 778 3.900601 ACTCCATCTATTCCAGTGGCTAG 59.099 47.826 3.51 8.19 0.00 3.42
763 783 7.921786 TTGTTTTACTCCATCTATTCCAGTG 57.078 36.000 0.00 0.00 0.00 3.66
764 784 8.383175 TCTTTGTTTTACTCCATCTATTCCAGT 58.617 33.333 0.00 0.00 0.00 4.00
766 786 8.383175 AGTCTTTGTTTTACTCCATCTATTCCA 58.617 33.333 0.00 0.00 0.00 3.53
767 787 8.794335 AGTCTTTGTTTTACTCCATCTATTCC 57.206 34.615 0.00 0.00 0.00 3.01
772 792 7.060421 TCCAAAGTCTTTGTTTTACTCCATCT 58.940 34.615 21.12 0.00 38.98 2.90
773 793 7.013369 ACTCCAAAGTCTTTGTTTTACTCCATC 59.987 37.037 21.12 0.00 38.98 3.51
776 796 6.694877 ACTCCAAAGTCTTTGTTTTACTCC 57.305 37.500 21.12 0.00 38.98 3.85
777 797 8.434733 AGTACTCCAAAGTCTTTGTTTTACTC 57.565 34.615 21.12 7.85 38.98 2.59
778 798 8.434733 GAGTACTCCAAAGTCTTTGTTTTACT 57.565 34.615 21.12 20.35 38.98 2.24
833 860 1.410004 CATCCAGGCCTTGCATTCAT 58.590 50.000 0.00 0.00 0.00 2.57
836 863 1.305465 TGCATCCAGGCCTTGCATT 60.305 52.632 23.69 0.00 41.18 3.56
840 867 0.971386 AAAACTGCATCCAGGCCTTG 59.029 50.000 0.00 0.00 43.53 3.61
847 874 2.224018 GGTCTTTGCAAAACTGCATCCA 60.224 45.455 13.84 0.00 44.94 3.41
848 875 2.036346 AGGTCTTTGCAAAACTGCATCC 59.964 45.455 13.84 7.80 44.94 3.51
849 876 3.311966 GAGGTCTTTGCAAAACTGCATC 58.688 45.455 13.84 7.02 44.94 3.91
853 880 2.872245 TCTCGAGGTCTTTGCAAAACTG 59.128 45.455 13.84 1.77 0.00 3.16
855 882 3.560068 TCTTCTCGAGGTCTTTGCAAAAC 59.440 43.478 13.84 13.33 0.00 2.43
887 915 2.358267 GGGAGAAGCAGATGCATTTGAG 59.642 50.000 20.67 3.09 45.16 3.02
897 925 8.608185 ATTTATTTTATTTGGGGAGAAGCAGA 57.392 30.769 0.00 0.00 0.00 4.26
923 951 6.626623 GCACTTGCAAGATGAAATGTAAGGAT 60.627 38.462 32.50 1.12 41.67 3.24
929 957 4.553323 GAAGCACTTGCAAGATGAAATGT 58.447 39.130 32.50 5.62 45.16 2.71
973 1043 3.130160 CTCCTCCTTTGCAGCCGC 61.130 66.667 0.00 0.00 39.24 6.53
982 1052 0.641601 ATCTGCTCCTCCTCCTCCTT 59.358 55.000 0.00 0.00 0.00 3.36
993 1063 1.897615 GCATGCCTCCATCTGCTCC 60.898 63.158 6.36 0.00 0.00 4.70
995 1065 2.203167 CGCATGCCTCCATCTGCT 60.203 61.111 13.15 0.00 0.00 4.24
1488 1566 5.471556 AGCATCATTGTTCATTGACCAAA 57.528 34.783 0.48 0.00 0.00 3.28
1514 1592 8.152898 TGTACTAGTATGGAATTAGACGAGCTA 58.847 37.037 5.75 0.00 0.00 3.32
1515 1593 6.996879 TGTACTAGTATGGAATTAGACGAGCT 59.003 38.462 5.75 0.00 0.00 4.09
1516 1594 7.199541 TGTACTAGTATGGAATTAGACGAGC 57.800 40.000 5.75 0.00 0.00 5.03
1539 1617 7.148407 GGGCCACGATTAAATATTCAGAGTATG 60.148 40.741 4.39 0.00 0.00 2.39
1541 1619 6.183361 TGGGCCACGATTAAATATTCAGAGTA 60.183 38.462 0.00 0.00 0.00 2.59
1546 1624 5.240623 GTCATGGGCCACGATTAAATATTCA 59.759 40.000 9.28 0.00 0.00 2.57
1562 1640 1.277557 AGTCAAGACTCAGTCATGGGC 59.722 52.381 10.11 4.19 36.92 5.36
1577 1655 7.201920 GGAGCAGAGGAAGTATAATGTAGTCAA 60.202 40.741 0.00 0.00 0.00 3.18
1591 1669 7.234577 AGGACTTATATTTAGGAGCAGAGGAAG 59.765 40.741 0.00 0.00 0.00 3.46
1592 1670 7.076446 AGGACTTATATTTAGGAGCAGAGGAA 58.924 38.462 0.00 0.00 0.00 3.36
1594 1672 6.926630 AGGACTTATATTTAGGAGCAGAGG 57.073 41.667 0.00 0.00 0.00 3.69
1662 1740 9.816354 ACTCATTTTGCTTTGTATGTAGTTTTT 57.184 25.926 0.00 0.00 0.00 1.94
1663 1741 9.248291 CACTCATTTTGCTTTGTATGTAGTTTT 57.752 29.630 0.00 0.00 0.00 2.43
1664 1742 8.629158 TCACTCATTTTGCTTTGTATGTAGTTT 58.371 29.630 0.00 0.00 0.00 2.66
1665 1743 8.165239 TCACTCATTTTGCTTTGTATGTAGTT 57.835 30.769 0.00 0.00 0.00 2.24
1666 1744 7.744087 TCACTCATTTTGCTTTGTATGTAGT 57.256 32.000 0.00 0.00 0.00 2.73
1667 1745 9.282247 GATTCACTCATTTTGCTTTGTATGTAG 57.718 33.333 0.00 0.00 0.00 2.74
1668 1746 9.013229 AGATTCACTCATTTTGCTTTGTATGTA 57.987 29.630 0.00 0.00 0.00 2.29
1669 1747 7.889469 AGATTCACTCATTTTGCTTTGTATGT 58.111 30.769 0.00 0.00 0.00 2.29
1670 1748 9.282247 GTAGATTCACTCATTTTGCTTTGTATG 57.718 33.333 0.00 0.00 0.00 2.39
1671 1749 9.013229 TGTAGATTCACTCATTTTGCTTTGTAT 57.987 29.630 0.00 0.00 0.00 2.29
1672 1750 8.289618 GTGTAGATTCACTCATTTTGCTTTGTA 58.710 33.333 0.00 0.00 35.68 2.41
1673 1751 7.013655 AGTGTAGATTCACTCATTTTGCTTTGT 59.986 33.333 0.00 0.00 44.07 2.83
1674 1752 7.365741 AGTGTAGATTCACTCATTTTGCTTTG 58.634 34.615 0.00 0.00 44.07 2.77
1675 1753 7.516198 AGTGTAGATTCACTCATTTTGCTTT 57.484 32.000 0.00 0.00 44.07 3.51
1689 1767 9.367717 CGTAGACGTATTTTAGAGTGTAGATTC 57.632 37.037 0.00 0.00 34.11 2.52
1713 1791 7.501559 AGGAACTACATACATACAGATGTACGT 59.498 37.037 0.00 0.00 44.13 3.57
1714 1792 7.872881 AGGAACTACATACATACAGATGTACG 58.127 38.462 0.04 0.00 44.13 3.67
1715 1793 8.847196 TGAGGAACTACATACATACAGATGTAC 58.153 37.037 0.04 0.00 45.25 2.90
1716 1794 8.990163 TGAGGAACTACATACATACAGATGTA 57.010 34.615 0.54 0.54 46.01 2.29
1717 1795 7.898014 TGAGGAACTACATACATACAGATGT 57.102 36.000 0.00 0.00 44.83 3.06
1718 1796 9.201127 CAATGAGGAACTACATACATACAGATG 57.799 37.037 0.00 0.00 41.55 2.90
1719 1797 7.875041 GCAATGAGGAACTACATACATACAGAT 59.125 37.037 0.00 0.00 41.55 2.90
1720 1798 7.147742 TGCAATGAGGAACTACATACATACAGA 60.148 37.037 0.00 0.00 41.55 3.41
1721 1799 6.986231 TGCAATGAGGAACTACATACATACAG 59.014 38.462 0.00 0.00 41.55 2.74
1722 1800 6.883744 TGCAATGAGGAACTACATACATACA 58.116 36.000 0.00 0.00 41.55 2.29
1723 1801 7.786178 TTGCAATGAGGAACTACATACATAC 57.214 36.000 0.00 0.00 41.55 2.39
1724 1802 8.432013 AGATTGCAATGAGGAACTACATACATA 58.568 33.333 18.59 0.00 41.55 2.29
1725 1803 7.285566 AGATTGCAATGAGGAACTACATACAT 58.714 34.615 18.59 0.00 41.55 2.29
1726 1804 6.653020 AGATTGCAATGAGGAACTACATACA 58.347 36.000 18.59 0.00 41.55 2.29
1727 1805 7.559590 AAGATTGCAATGAGGAACTACATAC 57.440 36.000 18.59 0.00 41.55 2.39
1728 1806 9.679661 TTAAAGATTGCAATGAGGAACTACATA 57.320 29.630 18.59 0.00 41.55 2.29
1729 1807 8.579850 TTAAAGATTGCAATGAGGAACTACAT 57.420 30.769 18.59 0.05 41.55 2.29
1730 1808 7.994425 TTAAAGATTGCAATGAGGAACTACA 57.006 32.000 18.59 0.00 41.55 2.74
1731 1809 9.691362 TTTTTAAAGATTGCAATGAGGAACTAC 57.309 29.630 18.59 0.00 41.55 2.73
1732 1810 9.912634 CTTTTTAAAGATTGCAATGAGGAACTA 57.087 29.630 18.59 0.00 37.13 2.24
1733 1811 8.641541 TCTTTTTAAAGATTGCAATGAGGAACT 58.358 29.630 18.59 3.22 40.34 3.01
1734 1812 8.703336 GTCTTTTTAAAGATTGCAATGAGGAAC 58.297 33.333 18.59 0.51 45.83 3.62
1735 1813 8.641541 AGTCTTTTTAAAGATTGCAATGAGGAA 58.358 29.630 18.59 3.05 45.83 3.36
1736 1814 8.181904 AGTCTTTTTAAAGATTGCAATGAGGA 57.818 30.769 18.59 0.00 45.83 3.71
1737 1815 8.822652 AAGTCTTTTTAAAGATTGCAATGAGG 57.177 30.769 18.59 0.00 45.83 3.86
1806 1884 6.595716 CGAAGGGAGTACTTTCTTTCATGATT 59.404 38.462 16.37 0.00 0.00 2.57
1826 1904 5.400066 ACCCCAACATTTATTTTCGAAGG 57.600 39.130 0.00 0.00 0.00 3.46
1829 1907 8.179509 TCTAAAACCCCAACATTTATTTTCGA 57.820 30.769 0.00 0.00 0.00 3.71
1843 1921 4.473559 CCCTCTGTTAGATCTAAAACCCCA 59.526 45.833 16.73 9.24 0.00 4.96
1845 1923 5.425862 ACTCCCTCTGTTAGATCTAAAACCC 59.574 44.000 16.73 5.42 0.00 4.11
1848 1926 6.895756 TGCTACTCCCTCTGTTAGATCTAAAA 59.104 38.462 16.73 10.88 0.00 1.52
1857 1935 4.931914 ACTAACTGCTACTCCCTCTGTTA 58.068 43.478 0.00 0.00 0.00 2.41
1861 1939 3.367321 GGAACTAACTGCTACTCCCTCT 58.633 50.000 0.00 0.00 0.00 3.69
1894 1972 1.939934 GGGAACAAAAGTTGCAAAGCC 59.060 47.619 0.00 0.00 0.00 4.35
1916 1994 5.186256 TGGATAAAACCCATCTAGCACAA 57.814 39.130 0.00 0.00 0.00 3.33
1987 2085 5.483937 AGACCTGGAGTTGAACACATATACA 59.516 40.000 0.00 0.00 0.00 2.29
2000 2098 1.203075 ACTCTCGGAAGACCTGGAGTT 60.203 52.381 0.00 0.00 40.10 3.01
2005 2103 0.108898 CAGCACTCTCGGAAGACCTG 60.109 60.000 0.00 0.00 35.39 4.00
2031 2129 5.278808 CGGATATACAGCCAGCAAACTAGTA 60.279 44.000 0.00 0.00 0.00 1.82
2109 2207 3.744238 AATTGGCAAACTTGTACACCC 57.256 42.857 3.01 0.00 0.00 4.61
2122 2220 6.460814 CGGACAATCCATACAAATAATTGGCA 60.461 38.462 0.00 0.00 37.13 4.92
2128 2226 4.812091 CCGTCGGACAATCCATACAAATAA 59.188 41.667 4.91 0.00 35.91 1.40
2129 2227 4.141892 ACCGTCGGACAATCCATACAAATA 60.142 41.667 20.51 0.00 35.91 1.40
2133 2231 1.187974 ACCGTCGGACAATCCATACA 58.812 50.000 20.51 0.00 35.91 2.29
2134 2232 2.304751 AACCGTCGGACAATCCATAC 57.695 50.000 20.51 0.00 35.91 2.39
2140 2238 1.133025 CCGTAGTAACCGTCGGACAAT 59.867 52.381 20.51 6.67 44.86 2.71
2144 2242 2.406616 GCCCGTAGTAACCGTCGGA 61.407 63.158 20.51 0.00 44.86 4.55
2161 2259 0.178068 TCTGGACCGGCAATTCTAGC 59.822 55.000 0.00 0.00 0.00 3.42
2197 2295 1.165270 GGATTTGGTGGTTGTCTCCG 58.835 55.000 0.00 0.00 0.00 4.63
2202 2300 0.673437 CTTGCGGATTTGGTGGTTGT 59.327 50.000 0.00 0.00 0.00 3.32
2205 2303 0.893727 GACCTTGCGGATTTGGTGGT 60.894 55.000 1.88 0.00 32.30 4.16
2228 2326 4.530875 CTTCTTTGCTGGTTAGGATGGAT 58.469 43.478 0.00 0.00 0.00 3.41
2233 2331 2.949177 TGCTTCTTTGCTGGTTAGGA 57.051 45.000 0.00 0.00 0.00 2.94
2241 2339 1.002430 TCCGTCTCATGCTTCTTTGCT 59.998 47.619 0.00 0.00 0.00 3.91
2283 2381 3.228188 TCCAACCATCAGCTCTTTTGT 57.772 42.857 0.00 0.00 0.00 2.83
2359 2457 6.137794 TCTTTCATCTCTGATAGACCGAAC 57.862 41.667 0.00 0.00 35.39 3.95
2368 2466 8.316497 TCCTACTCAAATCTTTCATCTCTGAT 57.684 34.615 0.00 0.00 0.00 2.90
2389 2487 3.181493 GCACGATAAGACCGTTCTTCCTA 60.181 47.826 0.00 0.00 41.48 2.94
2477 2575 3.767309 AGGTTGTCTATCTCCCTGTCT 57.233 47.619 0.00 0.00 0.00 3.41
2485 2583 3.034635 CCAGCCACTAGGTTGTCTATCT 58.965 50.000 0.00 0.00 43.95 1.98
2488 2587 0.902531 GCCAGCCACTAGGTTGTCTA 59.097 55.000 0.00 0.00 43.95 2.59
2490 2589 1.741770 CGCCAGCCACTAGGTTGTC 60.742 63.158 0.00 0.00 43.95 3.18
2497 2596 0.396556 TAGGTCATCGCCAGCCACTA 60.397 55.000 0.00 0.00 0.00 2.74
2512 2611 1.757118 CACCCATCACTCGATGTAGGT 59.243 52.381 2.07 0.66 46.54 3.08
2519 2618 4.062293 CAAAAACTACACCCATCACTCGA 58.938 43.478 0.00 0.00 0.00 4.04
2534 2634 1.001378 GGTGTGATGAGCGCAAAAACT 60.001 47.619 11.47 0.00 39.02 2.66
2583 2686 9.613428 TGACAATATCGGAGTGAATTTCTAAAT 57.387 29.630 0.00 0.00 0.00 1.40
2641 2744 5.569059 CGCAGAAACATATTCAACCAAAGAC 59.431 40.000 0.00 0.00 0.00 3.01
2651 2754 6.371809 TTTATGTCCCGCAGAAACATATTC 57.628 37.500 0.00 0.00 35.68 1.75
2670 2773 7.472334 AGTGATGCTTTCTTTCCATGTTTAT 57.528 32.000 0.00 0.00 0.00 1.40
2740 2843 2.491693 CACTCTGGTTGGTTTGTTGTGT 59.508 45.455 0.00 0.00 0.00 3.72
2750 2853 0.249868 TCGTCTTGCACTCTGGTTGG 60.250 55.000 0.00 0.00 0.00 3.77
2841 6895 4.653868 CTCTCTTAGCCGGGATTCTAGTA 58.346 47.826 2.18 0.00 0.00 1.82
2856 6910 4.079253 GTTTCCCAAATGGTGCTCTCTTA 58.921 43.478 0.00 0.00 34.77 2.10
2871 6925 0.547075 TTCCGGTGTTCTGTTTCCCA 59.453 50.000 0.00 0.00 0.00 4.37
2873 6927 0.949397 GGTTCCGGTGTTCTGTTTCC 59.051 55.000 0.00 0.00 0.00 3.13
2883 6937 1.165270 GTTGGAAGATGGTTCCGGTG 58.835 55.000 0.00 0.00 41.43 4.94
2887 6941 2.622436 CGAGAGTTGGAAGATGGTTCC 58.378 52.381 0.00 0.00 39.03 3.62
2890 6944 0.250513 GGCGAGAGTTGGAAGATGGT 59.749 55.000 0.00 0.00 0.00 3.55
2903 6957 1.120530 GGGAAATAGTGAGGGCGAGA 58.879 55.000 0.00 0.00 0.00 4.04
2912 6966 8.820831 ACTAAGGATATGAGATGGGAAATAGTG 58.179 37.037 0.00 0.00 0.00 2.74
2913 6967 8.980832 ACTAAGGATATGAGATGGGAAATAGT 57.019 34.615 0.00 0.00 0.00 2.12
2930 6984 1.496060 TGATGGTGGCGACTAAGGAT 58.504 50.000 0.00 0.00 0.00 3.24
2938 6992 1.450134 GCAGTGATGATGGTGGCGA 60.450 57.895 0.00 0.00 0.00 5.54
2939 6993 1.712018 CTGCAGTGATGATGGTGGCG 61.712 60.000 5.25 0.00 0.00 5.69
2992 7330 5.163405 ACAATACTTGTCGGCTGAGATACAT 60.163 40.000 0.00 0.00 40.56 2.29
3038 7376 7.382110 TCACTGAAGAAGACATAAAGAGGAAG 58.618 38.462 0.00 0.00 0.00 3.46
3102 7440 4.037858 ACGCCTCAACTATTACCTTACG 57.962 45.455 0.00 0.00 0.00 3.18
3109 7447 3.869065 CAAAGGGACGCCTCAACTATTA 58.131 45.455 0.00 0.00 0.00 0.98
3110 7448 2.711542 CAAAGGGACGCCTCAACTATT 58.288 47.619 0.00 0.00 0.00 1.73
3113 7451 1.600916 GCAAAGGGACGCCTCAACT 60.601 57.895 0.00 0.00 0.00 3.16
3118 7456 2.597510 GGTTGCAAAGGGACGCCT 60.598 61.111 0.00 0.00 0.00 5.52
3136 7474 3.724716 CGATGCCTTGTACAAACACATCG 60.725 47.826 31.36 31.36 45.47 3.84
3199 7537 6.650120 AGACAAGAGACAACTCCTTTACAAA 58.350 36.000 0.00 0.00 43.53 2.83
3203 7541 6.732896 AGAAGACAAGAGACAACTCCTTTA 57.267 37.500 0.00 0.00 43.53 1.85
3206 7544 4.898861 AGAAGAAGACAAGAGACAACTCCT 59.101 41.667 0.00 0.00 43.53 3.69
3222 7560 2.498078 AGGGCCTTAGAACGAGAAGAAG 59.502 50.000 0.00 0.00 0.00 2.85
3245 7583 3.897657 ATACGGGATCCTAGGAACTCA 57.102 47.619 17.30 0.00 41.75 3.41
3246 7584 5.757988 AGATATACGGGATCCTAGGAACTC 58.242 45.833 17.30 12.76 41.75 3.01
3251 7589 6.717540 CCTTGATAGATATACGGGATCCTAGG 59.282 46.154 12.58 0.82 0.00 3.02
3254 7592 6.342819 TCCTTGATAGATATACGGGATCCT 57.657 41.667 12.58 0.00 0.00 3.24
3258 7596 5.340110 CCTCCTCCTTGATAGATATACGGGA 60.340 48.000 0.00 0.00 0.00 5.14
3289 7632 3.489398 GCGTAGTTATGTGTCCTCCTCAG 60.489 52.174 0.00 0.00 0.00 3.35
3309 7652 1.725557 TAGTAGGCGAAGGAGCAGCG 61.726 60.000 0.00 0.00 39.27 5.18
3321 7664 8.926092 AATCCAATCTAAAGGAATTAGTAGGC 57.074 34.615 0.00 0.00 41.54 3.93
3327 7670 8.821686 TCTGCAAATCCAATCTAAAGGAATTA 57.178 30.769 0.00 0.00 37.48 1.40
3328 7671 7.722949 TCTGCAAATCCAATCTAAAGGAATT 57.277 32.000 0.00 0.00 37.48 2.17
3346 7689 7.575414 TGGTATTCAAACTAGTTTTCTGCAA 57.425 32.000 18.25 6.94 0.00 4.08
3351 7694 8.803235 AGGGATTTGGTATTCAAACTAGTTTTC 58.197 33.333 18.25 9.07 46.72 2.29
3385 7728 9.878667 AGCTCATCTGATTCTCATTGAATATAG 57.121 33.333 0.00 0.00 44.70 1.31
3396 7739 6.598850 AGAAAAAGGAAGCTCATCTGATTCTC 59.401 38.462 0.00 0.00 33.41 2.87


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

AutoCloner maintained by Alex Coulton.