Multiple sequence alignment - TraesCS6D01G149800

Loading Multiple Alignment...

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 TraesCS6D01G149800 chr6D 100.000 9458 0 0 1 9458 123772569 123782026 0.000000e+00 17466.0
1 TraesCS6D01G149800 chr6D 89.901 505 33 8 8969 9458 269898387 269898888 1.340000e-177 634.0
2 TraesCS6D01G149800 chr6D 89.823 452 33 5 9017 9458 163346395 163345947 1.380000e-157 568.0
3 TraesCS6D01G149800 chr6B 94.725 4891 153 24 1568 6453 218666264 218671054 0.000000e+00 7505.0
4 TraesCS6D01G149800 chr6B 95.047 1373 46 10 7392 8759 218673380 218674735 0.000000e+00 2139.0
5 TraesCS6D01G149800 chr6B 96.660 958 26 3 6449 7402 218671236 218672191 0.000000e+00 1587.0
6 TraesCS6D01G149800 chr6B 91.619 704 58 1 4 706 534869041 534868338 0.000000e+00 972.0
7 TraesCS6D01G149800 chr6B 93.961 563 29 4 886 1445 218665706 218666266 0.000000e+00 846.0
8 TraesCS6D01G149800 chr6B 93.197 147 9 1 1427 1573 68120845 68120700 2.070000e-51 215.0
9 TraesCS6D01G149800 chr6B 87.565 193 12 3 8760 8950 218674979 218675161 7.440000e-51 213.0
10 TraesCS6D01G149800 chr6A 97.305 4304 80 19 4668 8953 157637091 157632806 0.000000e+00 7273.0
11 TraesCS6D01G149800 chr6A 97.303 3115 58 11 1568 4677 157640451 157637358 0.000000e+00 5264.0
12 TraesCS6D01G149800 chr6A 91.796 707 57 1 1 706 416179845 416180551 0.000000e+00 983.0
13 TraesCS6D01G149800 chr6A 93.345 556 23 6 746 1291 157641115 157640564 0.000000e+00 809.0
14 TraesCS6D01G149800 chr6A 89.873 474 26 9 8994 9458 37710366 37710826 2.940000e-164 590.0
15 TraesCS6D01G149800 chr6A 87.879 264 13 8 8969 9223 136946732 136946479 9.290000e-75 292.0
16 TraesCS6D01G149800 chr6A 96.721 122 4 0 1324 1445 157640570 157640449 4.480000e-48 204.0
17 TraesCS6D01G149800 chr5D 84.369 2623 304 66 2027 4613 442101706 442099154 0.000000e+00 2475.0
18 TraesCS6D01G149800 chr5D 84.516 930 116 18 5349 6271 442098811 442097903 0.000000e+00 894.0
19 TraesCS6D01G149800 chr5D 90.948 464 32 6 9003 9458 482168931 482169392 4.850000e-172 616.0
20 TraesCS6D01G149800 chr5D 82.516 612 58 28 6744 7327 442096762 442096172 8.530000e-135 492.0
21 TraesCS6D01G149800 chr5D 87.097 403 42 7 6340 6739 442097817 442097422 1.870000e-121 448.0
22 TraesCS6D01G149800 chr5D 93.667 300 18 1 5018 5317 449151102 449150804 1.870000e-121 448.0
23 TraesCS6D01G149800 chr5D 85.663 279 15 11 939 1203 442102520 442102253 4.350000e-68 270.0
24 TraesCS6D01G149800 chr5D 82.993 294 23 16 8248 8532 442095464 442095189 3.410000e-59 241.0
25 TraesCS6D01G149800 chr5D 92.617 149 8 3 1426 1574 460652901 460652756 2.680000e-50 211.0
26 TraesCS6D01G149800 chr5B 84.062 2629 304 65 2026 4621 538300145 538297599 0.000000e+00 2427.0
27 TraesCS6D01G149800 chr5B 83.251 609 56 25 6744 7327 538295192 538294605 1.410000e-142 518.0
28 TraesCS6D01G149800 chr5B 85.211 426 43 12 6340 6762 538296238 538295830 4.080000e-113 420.0
29 TraesCS6D01G149800 chr5B 88.031 259 12 10 954 1203 538300893 538300645 1.200000e-73 289.0
30 TraesCS6D01G149800 chr5B 83.219 292 27 15 8248 8532 538293859 538293583 2.040000e-61 248.0
31 TraesCS6D01G149800 chr5B 85.556 90 8 4 6935 7019 537781480 537781391 1.310000e-13 89.8
32 TraesCS6D01G149800 chr5A 84.465 1738 207 35 2886 4609 558329205 558327517 0.000000e+00 1655.0
33 TraesCS6D01G149800 chr5A 92.504 707 52 1 1 706 534812593 534811887 0.000000e+00 1011.0
34 TraesCS6D01G149800 chr5A 84.247 1022 96 29 6276 7273 558325110 558324130 0.000000e+00 935.0
35 TraesCS6D01G149800 chr5A 92.072 555 43 1 2 555 344235346 344234792 0.000000e+00 780.0
36 TraesCS6D01G149800 chr5A 87.500 624 59 13 2287 2908 558329820 558329214 0.000000e+00 702.0
37 TraesCS6D01G149800 chr5A 89.058 329 35 1 5349 5677 558327185 558326858 3.180000e-109 407.0
38 TraesCS6D01G149800 chr5A 82.730 359 52 8 5894 6250 558325455 558325105 2.560000e-80 311.0
39 TraesCS6D01G149800 chr5A 84.561 285 21 11 942 1206 558331237 558330956 2.620000e-65 261.0
40 TraesCS6D01G149800 chr5A 79.830 352 40 18 8191 8532 558322043 558321713 2.660000e-55 228.0
41 TraesCS6D01G149800 chr5A 94.366 142 6 2 1431 1570 508283796 508283655 5.750000e-52 217.0
42 TraesCS6D01G149800 chr2D 95.191 707 33 1 1 706 406706171 406706877 0.000000e+00 1116.0
43 TraesCS6D01G149800 chr2D 94.333 300 16 1 5018 5317 630267366 630267068 8.660000e-125 459.0
44 TraesCS6D01G149800 chr2D 93.667 300 18 1 5018 5317 196965600 196965898 1.870000e-121 448.0
45 TraesCS6D01G149800 chr2D 96.296 135 5 0 1436 1570 450745501 450745635 1.240000e-53 222.0
46 TraesCS6D01G149800 chr1A 91.926 706 56 1 1 705 30554656 30555361 0.000000e+00 987.0
47 TraesCS6D01G149800 chr1A 89.109 707 76 1 1 706 466438927 466438221 0.000000e+00 878.0
48 TraesCS6D01G149800 chr1A 90.600 500 33 7 8969 9458 126549890 126550385 0.000000e+00 651.0
49 TraesCS6D01G149800 chr1A 83.417 199 28 5 3469 3662 523391580 523391382 7.550000e-41 180.0
50 TraesCS6D01G149800 chr1A 87.879 132 16 0 3469 3600 525178792 525178661 1.270000e-33 156.0
51 TraesCS6D01G149800 chr2B 91.335 704 59 2 4 706 574644635 574645337 0.000000e+00 961.0
52 TraesCS6D01G149800 chr2B 97.710 131 3 0 1440 1570 378986164 378986034 9.560000e-55 226.0
53 TraesCS6D01G149800 chr2B 97.692 130 3 0 1441 1570 25948923 25948794 3.440000e-54 224.0
54 TraesCS6D01G149800 chr2B 91.925 161 9 4 8977 9136 787747761 787747918 1.240000e-53 222.0
55 TraesCS6D01G149800 chr2A 89.675 707 71 2 1 706 575276231 575276936 0.000000e+00 900.0
56 TraesCS6D01G149800 chr2A 90.345 435 31 7 9033 9458 733535507 733535939 2.310000e-155 560.0
57 TraesCS6D01G149800 chr7D 91.093 494 35 5 8969 9458 269036461 269036949 0.000000e+00 660.0
58 TraesCS6D01G149800 chr7D 96.269 134 5 0 1440 1573 13018450 13018583 4.450000e-53 220.0
59 TraesCS6D01G149800 chr7D 91.772 158 8 5 8977 9132 194212215 194212061 2.070000e-51 215.0
60 TraesCS6D01G149800 chr1D 89.868 454 33 5 9015 9458 359483081 359482631 1.070000e-158 571.0
61 TraesCS6D01G149800 chr1D 93.667 300 18 1 5018 5317 254534335 254534037 1.870000e-121 448.0
62 TraesCS6D01G149800 chr1D 77.459 488 78 29 8977 9448 126670187 126670658 7.280000e-66 263.0
63 TraesCS6D01G149800 chr3D 87.665 454 30 6 9013 9458 218569669 218569234 1.100000e-138 505.0
64 TraesCS6D01G149800 chr7B 93.667 300 18 1 5018 5317 662735652 662735354 1.870000e-121 448.0
65 TraesCS6D01G149800 chr7B 89.222 167 16 2 8977 9143 712066276 712066440 3.460000e-49 207.0
66 TraesCS6D01G149800 chrUn 93.333 300 19 1 5018 5317 351213250 351213548 8.720000e-120 442.0
67 TraesCS6D01G149800 chrUn 93.333 300 18 2 5018 5317 416132780 416133077 8.720000e-120 442.0
68 TraesCS6D01G149800 chr1B 98.450 129 2 0 1442 1570 623950956 623951084 2.660000e-55 228.0
69 TraesCS6D01G149800 chr4B 97.692 130 3 0 1441 1570 300811319 300811448 3.440000e-54 224.0


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 TraesCS6D01G149800 chr6D 123772569 123782026 9457 False 17466.000000 17466 100.000000 1 9458 1 chr6D.!!$F1 9457
1 TraesCS6D01G149800 chr6D 269898387 269898888 501 False 634.000000 634 89.901000 8969 9458 1 chr6D.!!$F2 489
2 TraesCS6D01G149800 chr6B 218665706 218675161 9455 False 2458.000000 7505 93.591600 886 8950 5 chr6B.!!$F1 8064
3 TraesCS6D01G149800 chr6B 534868338 534869041 703 True 972.000000 972 91.619000 4 706 1 chr6B.!!$R2 702
4 TraesCS6D01G149800 chr6A 157632806 157641115 8309 True 3387.500000 7273 96.168500 746 8953 4 chr6A.!!$R2 8207
5 TraesCS6D01G149800 chr6A 416179845 416180551 706 False 983.000000 983 91.796000 1 706 1 chr6A.!!$F2 705
6 TraesCS6D01G149800 chr5D 442095189 442102520 7331 True 803.333333 2475 84.525667 939 8532 6 chr5D.!!$R3 7593
7 TraesCS6D01G149800 chr5B 538293583 538300893 7310 True 780.400000 2427 84.754800 954 8532 5 chr5B.!!$R2 7578
8 TraesCS6D01G149800 chr5A 534811887 534812593 706 True 1011.000000 1011 92.504000 1 706 1 chr5A.!!$R3 705
9 TraesCS6D01G149800 chr5A 344234792 344235346 554 True 780.000000 780 92.072000 2 555 1 chr5A.!!$R1 553
10 TraesCS6D01G149800 chr5A 558321713 558331237 9524 True 642.714286 1655 84.627286 942 8532 7 chr5A.!!$R4 7590
11 TraesCS6D01G149800 chr2D 406706171 406706877 706 False 1116.000000 1116 95.191000 1 706 1 chr2D.!!$F2 705
12 TraesCS6D01G149800 chr1A 30554656 30555361 705 False 987.000000 987 91.926000 1 705 1 chr1A.!!$F1 704
13 TraesCS6D01G149800 chr1A 466438221 466438927 706 True 878.000000 878 89.109000 1 706 1 chr1A.!!$R1 705
14 TraesCS6D01G149800 chr2B 574644635 574645337 702 False 961.000000 961 91.335000 4 706 1 chr2B.!!$F1 702
15 TraesCS6D01G149800 chr2A 575276231 575276936 705 False 900.000000 900 89.675000 1 706 1 chr2A.!!$F1 705

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
708 710 0.037303 CCTGGCACTCCATTGACTGT 59.963 55.000 0.00 0.00 42.51 3.55 F
771 773 0.099791 CCACCGCACGAAAACAAGTT 59.900 50.000 0.00 0.00 0.00 2.66 F
1566 1676 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 F
2232 2378 1.000938 CCTTTGCCTGAACAGTGCTTC 60.001 52.381 13.25 0.00 0.00 3.86 F
3481 4241 0.386731 CCCTTTTTGCCACGTTAGCG 60.387 55.000 0.00 0.00 44.93 4.26 F
4600 5410 1.302832 AGCAAACAGAAGAGGGGCG 60.303 57.895 0.00 0.00 0.00 6.13 F
6125 8465 0.100682 TCGTGCGCTCTTACTCCATC 59.899 55.000 9.73 0.00 0.00 3.51 F
6300 8678 1.281287 ACTTGGATCTGCTCATGTGCT 59.719 47.619 19.60 0.52 0.00 4.40 F
6926 10164 2.673368 GTCACTATACAGTTGTGCAGCC 59.327 50.000 0.00 0.00 34.19 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1547 1657 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12 R
2575 3297 0.547954 AGTGGGGAGGGGAAGAGAAC 60.548 60.000 0.00 0.00 0.00 3.01 R
2576 3298 1.098589 TAGTGGGGAGGGGAAGAGAA 58.901 55.000 0.00 0.00 0.00 2.87 R
4189 4992 1.132262 ACTGCCACGTGAAAACAAGTG 59.868 47.619 19.30 8.73 35.00 3.16 R
4622 5432 0.031449 CGTGGCGTTTTTCCATGGTT 59.969 50.000 12.58 0.00 37.05 3.67 R
6300 8678 1.277842 TCGAGGCTCCACTAAAATGCA 59.722 47.619 9.32 0.00 0.00 3.96 R
7980 13790 3.750130 TCATTCAAACTGCTCTGCTTCTC 59.250 43.478 0.00 0.00 0.00 2.87 R
8060 13873 7.101054 ACAATATGTGTTAAAGCTACTCGGAA 58.899 34.615 0.00 0.00 37.01 4.30 R
8865 14971 0.388006 CCACAAACGCCGGAAAATCC 60.388 55.000 5.05 0.00 0.00 3.01 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
106 107 1.349688 ACACCATAAGAACCCTCGCAA 59.650 47.619 0.00 0.00 0.00 4.85
136 137 4.524802 TGATGGCCTTGATTATCTTGGT 57.475 40.909 3.32 0.00 0.00 3.67
377 379 5.358298 GGTGTCAACAACCACTTCTATTC 57.642 43.478 0.00 0.00 0.00 1.75
459 461 0.380378 GCGGCAGCGAAAATATCCAA 59.620 50.000 0.00 0.00 0.00 3.53
706 708 1.067295 TTCCTGGCACTCCATTGACT 58.933 50.000 0.00 0.00 42.51 3.41
707 709 0.325933 TCCTGGCACTCCATTGACTG 59.674 55.000 0.00 0.00 42.51 3.51
708 710 0.037303 CCTGGCACTCCATTGACTGT 59.963 55.000 0.00 0.00 42.51 3.55
709 711 1.446907 CTGGCACTCCATTGACTGTC 58.553 55.000 0.00 0.00 42.51 3.51
710 712 1.002888 CTGGCACTCCATTGACTGTCT 59.997 52.381 9.51 0.00 42.51 3.41
711 713 1.002430 TGGCACTCCATTGACTGTCTC 59.998 52.381 9.51 0.00 37.47 3.36
712 714 1.002430 GGCACTCCATTGACTGTCTCA 59.998 52.381 9.51 0.00 0.00 3.27
713 715 2.344950 GCACTCCATTGACTGTCTCAG 58.655 52.381 9.51 0.77 37.52 3.35
723 725 2.898729 ACTGTCTCAGTCCACACTTG 57.101 50.000 0.00 0.00 41.21 3.16
724 726 2.111384 ACTGTCTCAGTCCACACTTGT 58.889 47.619 0.00 0.00 41.21 3.16
725 727 2.101582 ACTGTCTCAGTCCACACTTGTC 59.898 50.000 0.00 0.00 41.21 3.18
726 728 1.067060 TGTCTCAGTCCACACTTGTCG 59.933 52.381 0.00 0.00 0.00 4.35
727 729 1.067212 GTCTCAGTCCACACTTGTCGT 59.933 52.381 0.00 0.00 0.00 4.34
728 730 2.292569 GTCTCAGTCCACACTTGTCGTA 59.707 50.000 0.00 0.00 0.00 3.43
729 731 3.057456 GTCTCAGTCCACACTTGTCGTAT 60.057 47.826 0.00 0.00 0.00 3.06
730 732 4.155462 GTCTCAGTCCACACTTGTCGTATA 59.845 45.833 0.00 0.00 0.00 1.47
731 733 4.948004 TCTCAGTCCACACTTGTCGTATAT 59.052 41.667 0.00 0.00 0.00 0.86
732 734 5.417894 TCTCAGTCCACACTTGTCGTATATT 59.582 40.000 0.00 0.00 0.00 1.28
733 735 5.407502 TCAGTCCACACTTGTCGTATATTG 58.592 41.667 0.00 0.00 0.00 1.90
734 736 4.566759 CAGTCCACACTTGTCGTATATTGG 59.433 45.833 0.00 0.00 0.00 3.16
735 737 3.308866 GTCCACACTTGTCGTATATTGGC 59.691 47.826 0.00 0.00 0.00 4.52
736 738 3.196901 TCCACACTTGTCGTATATTGGCT 59.803 43.478 0.00 0.00 0.00 4.75
737 739 3.938963 CCACACTTGTCGTATATTGGCTT 59.061 43.478 0.00 0.00 0.00 4.35
738 740 4.394920 CCACACTTGTCGTATATTGGCTTT 59.605 41.667 0.00 0.00 0.00 3.51
739 741 5.106317 CCACACTTGTCGTATATTGGCTTTT 60.106 40.000 0.00 0.00 0.00 2.27
740 742 6.021596 CACACTTGTCGTATATTGGCTTTTC 58.978 40.000 0.00 0.00 0.00 2.29
741 743 5.123344 ACACTTGTCGTATATTGGCTTTTCC 59.877 40.000 0.00 0.00 0.00 3.13
742 744 4.638865 ACTTGTCGTATATTGGCTTTTCCC 59.361 41.667 0.00 0.00 0.00 3.97
743 745 4.223556 TGTCGTATATTGGCTTTTCCCA 57.776 40.909 0.00 0.00 0.00 4.37
744 746 4.787551 TGTCGTATATTGGCTTTTCCCAT 58.212 39.130 0.00 0.00 34.21 4.00
771 773 0.099791 CCACCGCACGAAAACAAGTT 59.900 50.000 0.00 0.00 0.00 2.66
823 827 0.940126 GCACGGCTATCCAGTTCATG 59.060 55.000 0.00 0.00 0.00 3.07
860 864 2.434134 CGACGAACTGGCAGCGTAC 61.434 63.158 17.96 11.58 38.51 3.67
861 865 2.048503 ACGAACTGGCAGCGTACC 60.049 61.111 15.89 0.00 36.37 3.34
862 866 2.048597 CGAACTGGCAGCGTACCA 60.049 61.111 15.89 0.00 35.40 3.25
988 1000 4.465446 CCGAGCCCTCCCTCTCCA 62.465 72.222 0.00 0.00 0.00 3.86
1257 1288 1.729838 GTGTCTCGTCGTGACCAGC 60.730 63.158 21.11 10.26 33.83 4.85
1270 1345 3.211045 GTGACCAGCCTGTTTTAGTTCA 58.789 45.455 0.00 0.00 0.00 3.18
1283 1358 3.663995 TTAGTTCATTCGTTGACCCGA 57.336 42.857 0.00 0.00 32.84 5.14
1316 1406 4.101790 GTGCATCGCAACCGTGGG 62.102 66.667 0.00 0.00 41.47 4.61
1322 1412 1.153127 TCGCAACCGTGGGAGTTTT 60.153 52.632 0.00 0.00 41.45 2.43
1446 1556 8.918202 TCTGGTCAAATCATAAACTTTGTACT 57.082 30.769 0.00 0.00 34.66 2.73
1447 1557 8.999431 TCTGGTCAAATCATAAACTTTGTACTC 58.001 33.333 0.00 0.00 34.66 2.59
1448 1558 8.106247 TGGTCAAATCATAAACTTTGTACTCC 57.894 34.615 0.00 0.00 34.66 3.85
1449 1559 7.175990 TGGTCAAATCATAAACTTTGTACTCCC 59.824 37.037 0.00 0.00 34.66 4.30
1450 1560 7.393515 GGTCAAATCATAAACTTTGTACTCCCT 59.606 37.037 0.00 0.00 34.66 4.20
1451 1561 8.451748 GTCAAATCATAAACTTTGTACTCCCTC 58.548 37.037 0.00 0.00 34.66 4.30
1452 1562 7.610305 TCAAATCATAAACTTTGTACTCCCTCC 59.390 37.037 0.00 0.00 34.66 4.30
1453 1563 5.080969 TCATAAACTTTGTACTCCCTCCG 57.919 43.478 0.00 0.00 0.00 4.63
1454 1564 4.529377 TCATAAACTTTGTACTCCCTCCGT 59.471 41.667 0.00 0.00 0.00 4.69
1455 1565 3.397849 AAACTTTGTACTCCCTCCGTC 57.602 47.619 0.00 0.00 0.00 4.79
1456 1566 1.264295 ACTTTGTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
1457 1567 0.172803 CTTTGTACTCCCTCCGTCCG 59.827 60.000 0.00 0.00 0.00 4.79
1458 1568 0.251297 TTTGTACTCCCTCCGTCCGA 60.251 55.000 0.00 0.00 0.00 4.55
1459 1569 0.251297 TTGTACTCCCTCCGTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
1460 1570 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
1461 1571 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
1462 1572 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
1463 1573 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
1464 1574 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
1465 1575 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
1466 1576 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
1467 1577 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1468 1578 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1469 1579 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1470 1580 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
1471 1581 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
1472 1582 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
1473 1583 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
1474 1584 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
1475 1585 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
1476 1586 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
1477 1587 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
1478 1588 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
1479 1589 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
1480 1590 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
1481 1591 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
1489 1599 8.096414 ACTTGTCATCAAAATGGATAAAAAGGG 58.904 33.333 0.00 0.00 33.42 3.95
1490 1600 7.789202 TGTCATCAAAATGGATAAAAAGGGA 57.211 32.000 0.00 0.00 33.42 4.20
1491 1601 8.378115 TGTCATCAAAATGGATAAAAAGGGAT 57.622 30.769 0.00 0.00 33.42 3.85
1492 1602 8.259411 TGTCATCAAAATGGATAAAAAGGGATG 58.741 33.333 0.00 0.00 33.42 3.51
1493 1603 8.260114 GTCATCAAAATGGATAAAAAGGGATGT 58.740 33.333 0.00 0.00 33.42 3.06
1494 1604 9.486123 TCATCAAAATGGATAAAAAGGGATGTA 57.514 29.630 0.00 0.00 33.42 2.29
1497 1607 9.713684 TCAAAATGGATAAAAAGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
1498 1608 9.754382 CAAAATGGATAAAAAGGGATGTATCTG 57.246 33.333 0.00 0.00 0.00 2.90
1499 1609 8.482852 AAATGGATAAAAAGGGATGTATCTGG 57.517 34.615 0.00 0.00 0.00 3.86
1500 1610 6.840090 TGGATAAAAAGGGATGTATCTGGA 57.160 37.500 0.00 0.00 0.00 3.86
1501 1611 7.219601 TGGATAAAAAGGGATGTATCTGGAA 57.780 36.000 0.00 0.00 0.00 3.53
1502 1612 7.060421 TGGATAAAAAGGGATGTATCTGGAAC 58.940 38.462 0.00 0.00 0.00 3.62
1503 1613 7.091993 TGGATAAAAAGGGATGTATCTGGAACT 60.092 37.037 0.00 0.00 0.00 3.01
1504 1614 8.437575 GGATAAAAAGGGATGTATCTGGAACTA 58.562 37.037 0.00 0.00 0.00 2.24
1505 1615 9.847224 GATAAAAAGGGATGTATCTGGAACTAA 57.153 33.333 0.00 0.00 0.00 2.24
1511 1621 9.615660 AAGGGATGTATCTGGAACTAATATACA 57.384 33.333 0.00 0.00 37.42 2.29
1512 1622 9.790297 AGGGATGTATCTGGAACTAATATACAT 57.210 33.333 0.00 0.00 43.13 2.29
1545 1655 9.657419 ACATCCCTTTTTATTCATTTTGATGAC 57.343 29.630 0.00 0.00 32.39 3.06
1546 1656 9.656040 CATCCCTTTTTATTCATTTTGATGACA 57.344 29.630 0.00 0.00 0.00 3.58
1548 1658 9.709495 TCCCTTTTTATTCATTTTGATGACAAG 57.291 29.630 0.00 0.00 37.32 3.16
1549 1659 9.492973 CCCTTTTTATTCATTTTGATGACAAGT 57.507 29.630 0.00 0.00 37.32 3.16
1556 1666 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
1557 1667 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
1558 1668 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
1559 1669 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
1560 1670 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
1561 1671 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
1562 1672 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
1563 1673 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
1564 1674 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1565 1675 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1566 1676 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1802 1933 2.965147 GCACCGCGAGTCAAATGCA 61.965 57.895 8.23 0.00 33.27 3.96
1936 2074 9.734620 TTTGAAATGTGAAGTTCAGTTTATCTG 57.265 29.630 5.62 0.00 44.85 2.90
2134 2274 8.680001 TCATGTGATAACATTCAGAGAAAATGG 58.320 33.333 0.00 0.00 38.23 3.16
2211 2357 2.619646 TGGGTTTAGCACGTTTTCTTCC 59.380 45.455 0.00 0.00 0.00 3.46
2232 2378 1.000938 CCTTTGCCTGAACAGTGCTTC 60.001 52.381 13.25 0.00 0.00 3.86
2486 3194 7.492344 CGCAAATTTTATCTAGGCCAAGAATTT 59.508 33.333 5.01 4.99 0.00 1.82
3004 3762 6.398234 TTTGTTGGAGTTGCTATTGCTTTA 57.602 33.333 0.00 0.00 40.48 1.85
3221 3980 5.620738 TTTCCATGTTCTATAGAGCAGCT 57.379 39.130 21.70 6.21 38.62 4.24
3446 4205 4.151883 TCTGCAACCTGCTATTTTCCTTT 58.848 39.130 0.00 0.00 45.31 3.11
3481 4241 0.386731 CCCTTTTTGCCACGTTAGCG 60.387 55.000 0.00 0.00 44.93 4.26
3618 4378 1.462616 TTGTGGAGCAATTCATCCGG 58.537 50.000 0.00 0.00 38.52 5.14
3624 4385 2.632377 GAGCAATTCATCCGGACAAGA 58.368 47.619 6.12 1.89 0.00 3.02
3685 4466 6.091305 GCTAAAATTTCCATTTTCTCTGTGCC 59.909 38.462 0.00 0.00 41.00 5.01
3781 4578 8.726988 GTGTCATTAGATTTTAACAAGCTGGTA 58.273 33.333 0.00 0.00 0.00 3.25
3794 4591 3.895232 AGCTGGTATTGAACATCGACT 57.105 42.857 0.00 0.00 0.00 4.18
3797 4594 5.918608 AGCTGGTATTGAACATCGACTAAT 58.081 37.500 0.00 0.00 0.00 1.73
3858 4655 7.692460 TGTCATGAGAGAAATTGCTGTATTT 57.308 32.000 0.00 0.00 0.00 1.40
3982 4779 5.520376 ACTGATTTTCAAAGGGAAGTGTG 57.480 39.130 0.00 0.00 36.72 3.82
4600 5410 1.302832 AGCAAACAGAAGAGGGGCG 60.303 57.895 0.00 0.00 0.00 6.13
4740 5832 2.030451 CCCTTGCTGAGTTCTTTTCTGC 60.030 50.000 0.00 0.00 39.21 4.26
4741 5833 2.620115 CCTTGCTGAGTTCTTTTCTGCA 59.380 45.455 3.21 3.21 44.36 4.41
5247 6340 6.487668 TGTCATGATATCAGCCGATTTCATTT 59.512 34.615 11.78 0.00 43.60 2.32
5850 8186 6.372981 TCATTCATTTGACTGATTTGACACG 58.627 36.000 0.00 0.00 30.25 4.49
6125 8465 0.100682 TCGTGCGCTCTTACTCCATC 59.899 55.000 9.73 0.00 0.00 3.51
6300 8678 1.281287 ACTTGGATCTGCTCATGTGCT 59.719 47.619 19.60 0.52 0.00 4.40
6334 8712 4.933400 GGAGCCTCGAGTTGTAATTTAACA 59.067 41.667 12.31 0.00 0.00 2.41
6818 10049 6.424207 ACTTGTCTTCCTCACGAATTAACTTC 59.576 38.462 0.00 0.00 0.00 3.01
6926 10164 2.673368 GTCACTATACAGTTGTGCAGCC 59.327 50.000 0.00 0.00 34.19 4.85
7065 10308 5.909621 AGACATTATCAAGTGCTGCATTT 57.090 34.783 5.27 4.79 0.00 2.32
7243 10486 6.037500 CGTCATCAATCCTGCAGATAAAAGAA 59.962 38.462 17.39 0.00 33.66 2.52
7377 10631 2.923655 CGTCAACCACTAGCATACACAG 59.076 50.000 0.00 0.00 0.00 3.66
7429 11882 6.939730 TGATAGCAGGTTTGTCATGAAAAGTA 59.060 34.615 0.00 0.00 0.00 2.24
7484 11937 8.486210 ACATCAATTTTGCTATAGAGGTAGTGA 58.514 33.333 3.21 1.40 0.00 3.41
7606 13395 4.767409 AGACAAGCTTTCCACCTTATTTCC 59.233 41.667 0.00 0.00 0.00 3.13
7709 13517 9.131791 ACAATGGTTACTTAGTCTTGATTTTGT 57.868 29.630 0.00 0.00 0.00 2.83
7710 13518 9.965824 CAATGGTTACTTAGTCTTGATTTTGTT 57.034 29.630 0.00 0.00 0.00 2.83
7713 13521 9.841295 TGGTTACTTAGTCTTGATTTTGTTAGT 57.159 29.630 0.00 0.00 0.00 2.24
7980 13790 3.941483 GGCTATATTCAATGGATCCCGTG 59.059 47.826 9.90 7.38 0.00 4.94
8096 13921 0.618458 ACATATTGTCGTGGCCCTGT 59.382 50.000 0.00 0.00 0.00 4.00
8534 14394 1.614317 GGGCAACAGTTAGATGCACCT 60.614 52.381 0.00 0.00 46.81 4.00
8535 14395 2.162681 GGCAACAGTTAGATGCACCTT 58.837 47.619 0.00 0.00 46.81 3.50
8536 14396 2.095059 GGCAACAGTTAGATGCACCTTG 60.095 50.000 0.00 0.00 46.81 3.61
8613 14473 1.576421 CGCAAGTTGAGGACAAGCC 59.424 57.895 7.16 0.00 36.64 4.35
8637 14497 4.529897 AGCTGATACTTTGCCATTGATGA 58.470 39.130 0.00 0.00 0.00 2.92
8703 14564 4.357142 ACCGAGTACTGTATTATGCAACG 58.643 43.478 0.00 0.00 0.00 4.10
8793 14897 0.097674 CCATCTTGTTACGCAGCTGC 59.902 55.000 29.12 29.12 37.78 5.25
8859 14965 5.093849 TGAACTTACTGTTATAGGTGGCC 57.906 43.478 0.00 0.00 39.30 5.36
8861 14967 3.102204 ACTTACTGTTATAGGTGGCCGT 58.898 45.455 0.00 0.00 0.00 5.68
8865 14971 2.006888 CTGTTATAGGTGGCCGTTGTG 58.993 52.381 0.00 0.00 0.00 3.33
8956 15062 9.822727 ATGAGAAAGTAAAAAGAAAATAGGGGA 57.177 29.630 0.00 0.00 0.00 4.81
8957 15063 9.649316 TGAGAAAGTAAAAAGAAAATAGGGGAA 57.351 29.630 0.00 0.00 0.00 3.97
8960 15066 9.871238 GAAAGTAAAAAGAAAATAGGGGAATCC 57.129 33.333 0.00 0.00 0.00 3.01
8970 15076 0.178990 AGGGGAATCCTATTTGCCGC 60.179 55.000 0.00 0.00 45.98 6.53
8971 15077 0.178990 GGGGAATCCTATTTGCCGCT 60.179 55.000 0.00 0.00 37.93 5.52
8972 15078 1.239347 GGGAATCCTATTTGCCGCTC 58.761 55.000 0.00 0.00 0.00 5.03
8973 15079 0.868406 GGAATCCTATTTGCCGCTCG 59.132 55.000 0.00 0.00 0.00 5.03
8974 15080 0.235926 GAATCCTATTTGCCGCTCGC 59.764 55.000 0.00 0.00 38.31 5.03
8975 15081 0.179045 AATCCTATTTGCCGCTCGCT 60.179 50.000 0.00 0.00 38.78 4.93
8976 15082 0.882042 ATCCTATTTGCCGCTCGCTG 60.882 55.000 0.00 0.00 38.78 5.18
9037 15143 6.062095 TCTGGTTTTGGGAAACTTCTAGAAG 58.938 40.000 27.41 27.41 43.68 2.85
9162 15274 8.749841 TTTTCATAATGTTCGTGGTTTAATGG 57.250 30.769 0.00 0.00 0.00 3.16
9209 15329 7.818493 TGAATTTGAAATTTGTTCGTGTTCA 57.182 28.000 4.46 0.00 0.00 3.18
9245 15365 6.960431 CACAATTCAAAAATGTTCACGCTTTT 59.040 30.769 0.00 0.00 0.00 2.27
9246 15366 7.162385 CACAATTCAAAAATGTTCACGCTTTTC 59.838 33.333 0.00 0.00 0.00 2.29
9249 15369 6.712241 TCAAAAATGTTCACGCTTTTCAAA 57.288 29.167 0.00 0.00 0.00 2.69
9250 15370 7.121974 TCAAAAATGTTCACGCTTTTCAAAA 57.878 28.000 0.00 0.00 0.00 2.44
9262 15382 5.918011 ACGCTTTTCAAAATTTATTCGCAGA 59.082 32.000 0.00 0.00 0.00 4.26
9373 15493 6.428385 AATGCGGTTTCAAAATTTGTTCAA 57.572 29.167 5.56 0.00 0.00 2.69
9380 15500 9.334693 CGGTTTCAAAATTTGTTCAAAATTCAA 57.665 25.926 5.56 0.00 0.00 2.69
9430 15550 7.670916 TGTTCACGAATTTGAAATTTGTTCAC 58.329 30.769 18.37 16.95 37.24 3.18
9437 15557 8.055402 CGAATTTGAAATTTGTTCACGTTTCAT 58.945 29.630 4.46 1.04 39.48 2.57
9455 15575 7.858382 ACGTTTCATAATTTGTTCACAATTCGA 59.142 29.630 0.00 0.00 35.55 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 8.323567 AGATAATCAAGGCCATCAACAAAATTT 58.676 29.630 5.01 0.00 0.00 1.82
377 379 3.716006 CAGGTGCACGCAAGACCG 61.716 66.667 11.45 0.00 43.62 4.79
706 708 1.067060 CGACAAGTGTGGACTGAGACA 59.933 52.381 0.00 0.00 30.61 3.41
707 709 1.067212 ACGACAAGTGTGGACTGAGAC 59.933 52.381 0.08 0.00 30.61 3.36
708 710 1.399714 ACGACAAGTGTGGACTGAGA 58.600 50.000 0.08 0.00 30.61 3.27
709 711 3.577649 ATACGACAAGTGTGGACTGAG 57.422 47.619 0.08 0.00 30.61 3.35
710 712 5.407502 CAATATACGACAAGTGTGGACTGA 58.592 41.667 0.08 0.00 30.61 3.41
711 713 4.566759 CCAATATACGACAAGTGTGGACTG 59.433 45.833 0.08 0.00 30.61 3.51
712 714 4.755411 CCAATATACGACAAGTGTGGACT 58.245 43.478 0.08 0.00 0.00 3.85
713 715 3.308866 GCCAATATACGACAAGTGTGGAC 59.691 47.826 0.08 0.00 0.00 4.02
714 716 3.196901 AGCCAATATACGACAAGTGTGGA 59.803 43.478 0.08 0.00 0.00 4.02
715 717 3.531538 AGCCAATATACGACAAGTGTGG 58.468 45.455 0.00 0.00 0.00 4.17
716 718 5.545658 AAAGCCAATATACGACAAGTGTG 57.454 39.130 0.00 0.00 0.00 3.82
717 719 5.123344 GGAAAAGCCAATATACGACAAGTGT 59.877 40.000 0.00 0.00 36.34 3.55
718 720 5.448632 GGGAAAAGCCAATATACGACAAGTG 60.449 44.000 0.00 0.00 38.95 3.16
719 721 4.638865 GGGAAAAGCCAATATACGACAAGT 59.361 41.667 0.00 0.00 38.95 3.16
720 722 4.638421 TGGGAAAAGCCAATATACGACAAG 59.362 41.667 0.00 0.00 38.95 3.16
721 723 4.590918 TGGGAAAAGCCAATATACGACAA 58.409 39.130 0.00 0.00 38.95 3.18
722 724 4.223556 TGGGAAAAGCCAATATACGACA 57.776 40.909 0.00 0.00 38.95 4.35
723 725 5.767816 AATGGGAAAAGCCAATATACGAC 57.232 39.130 0.00 0.00 38.95 4.34
724 726 7.721842 TGATAAATGGGAAAAGCCAATATACGA 59.278 33.333 0.00 0.00 38.95 3.43
725 727 7.881142 TGATAAATGGGAAAAGCCAATATACG 58.119 34.615 0.00 0.00 38.95 3.06
726 728 9.476202 GTTGATAAATGGGAAAAGCCAATATAC 57.524 33.333 0.00 0.00 38.95 1.47
727 729 8.646900 GGTTGATAAATGGGAAAAGCCAATATA 58.353 33.333 0.00 0.00 38.95 0.86
728 730 7.127032 TGGTTGATAAATGGGAAAAGCCAATAT 59.873 33.333 0.00 0.00 38.95 1.28
729 731 6.441924 TGGTTGATAAATGGGAAAAGCCAATA 59.558 34.615 0.00 0.00 38.95 1.90
730 732 5.250313 TGGTTGATAAATGGGAAAAGCCAAT 59.750 36.000 0.00 0.00 38.95 3.16
731 733 4.594920 TGGTTGATAAATGGGAAAAGCCAA 59.405 37.500 0.00 0.00 38.95 4.52
732 734 4.020662 GTGGTTGATAAATGGGAAAAGCCA 60.021 41.667 0.00 0.00 38.95 4.75
733 735 4.503910 GTGGTTGATAAATGGGAAAAGCC 58.496 43.478 0.00 0.00 0.00 4.35
734 736 4.503910 GGTGGTTGATAAATGGGAAAAGC 58.496 43.478 0.00 0.00 0.00 3.51
735 737 4.743493 CGGTGGTTGATAAATGGGAAAAG 58.257 43.478 0.00 0.00 0.00 2.27
736 738 3.056465 GCGGTGGTTGATAAATGGGAAAA 60.056 43.478 0.00 0.00 0.00 2.29
737 739 2.494073 GCGGTGGTTGATAAATGGGAAA 59.506 45.455 0.00 0.00 0.00 3.13
738 740 2.096248 GCGGTGGTTGATAAATGGGAA 58.904 47.619 0.00 0.00 0.00 3.97
739 741 1.004862 TGCGGTGGTTGATAAATGGGA 59.995 47.619 0.00 0.00 0.00 4.37
740 742 1.134175 GTGCGGTGGTTGATAAATGGG 59.866 52.381 0.00 0.00 0.00 4.00
741 743 1.202132 CGTGCGGTGGTTGATAAATGG 60.202 52.381 0.00 0.00 0.00 3.16
742 744 1.735018 TCGTGCGGTGGTTGATAAATG 59.265 47.619 0.00 0.00 0.00 2.32
743 745 2.102070 TCGTGCGGTGGTTGATAAAT 57.898 45.000 0.00 0.00 0.00 1.40
744 746 1.880271 TTCGTGCGGTGGTTGATAAA 58.120 45.000 0.00 0.00 0.00 1.40
780 782 4.463515 GACCTTGTCGTCCTTTGTAAAC 57.536 45.455 0.00 0.00 0.00 2.01
810 814 3.551863 GGTCGAGCTCATGAACTGGATAG 60.552 52.174 15.40 0.00 0.00 2.08
823 827 1.270068 GTTTCGCTTAGGTCGAGCTC 58.730 55.000 22.33 2.73 37.99 4.09
860 864 1.127567 TCAACTCCCACCTCCACTGG 61.128 60.000 0.00 0.00 0.00 4.00
861 865 0.035458 GTCAACTCCCACCTCCACTG 59.965 60.000 0.00 0.00 0.00 3.66
862 866 0.399949 TGTCAACTCCCACCTCCACT 60.400 55.000 0.00 0.00 0.00 4.00
863 867 0.472471 TTGTCAACTCCCACCTCCAC 59.528 55.000 0.00 0.00 0.00 4.02
988 1000 1.043816 CCGTACATGGCTGGAGATCT 58.956 55.000 0.00 0.00 0.00 2.75
1213 1244 8.595567 TCGGAAGAAACAGAAAATCTGACCCA 62.596 42.308 13.93 0.00 41.71 4.51
1248 1279 1.878953 ACTAAAACAGGCTGGTCACG 58.121 50.000 20.34 6.42 0.00 4.35
1257 1288 5.449304 GGTCAACGAATGAACTAAAACAGG 58.551 41.667 4.18 0.00 42.82 4.00
1283 1358 1.026718 GCACGCAGATTTAGCACCCT 61.027 55.000 0.00 0.00 0.00 4.34
1322 1412 5.596836 ACTTGGAAATTTTGAAGCACTCA 57.403 34.783 9.09 0.00 0.00 3.41
1421 1526 8.918202 AGTACAAAGTTTATGATTTGACCAGA 57.082 30.769 4.79 0.00 38.42 3.86
1426 1531 7.610305 GGAGGGAGTACAAAGTTTATGATTTGA 59.390 37.037 4.79 0.00 38.42 2.69
1431 1536 4.529377 ACGGAGGGAGTACAAAGTTTATGA 59.471 41.667 0.00 0.00 0.00 2.15
1442 1552 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
1443 1553 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
1444 1554 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
1445 1555 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
1446 1556 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
1447 1557 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1448 1558 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1449 1559 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
1450 1560 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
1451 1561 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
1452 1562 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
1453 1563 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
1454 1564 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
1455 1565 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
1456 1566 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
1463 1573 8.096414 CCCTTTTTATCCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
1464 1574 8.313292 TCCCTTTTTATCCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
1465 1575 8.200024 TCCCTTTTTATCCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
1466 1576 7.789202 TCCCTTTTTATCCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
1467 1577 8.260114 ACATCCCTTTTTATCCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
1468 1578 8.378115 ACATCCCTTTTTATCCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
1471 1581 9.713684 AGATACATCCCTTTTTATCCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
1472 1582 9.754382 CAGATACATCCCTTTTTATCCATTTTG 57.246 33.333 0.00 0.00 0.00 2.44
1473 1583 8.927411 CCAGATACATCCCTTTTTATCCATTTT 58.073 33.333 0.00 0.00 0.00 1.82
1474 1584 8.288812 TCCAGATACATCCCTTTTTATCCATTT 58.711 33.333 0.00 0.00 0.00 2.32
1475 1585 7.825709 TCCAGATACATCCCTTTTTATCCATT 58.174 34.615 0.00 0.00 0.00 3.16
1476 1586 7.406620 TCCAGATACATCCCTTTTTATCCAT 57.593 36.000 0.00 0.00 0.00 3.41
1477 1587 6.840090 TCCAGATACATCCCTTTTTATCCA 57.160 37.500 0.00 0.00 0.00 3.41
1478 1588 7.290813 AGTTCCAGATACATCCCTTTTTATCC 58.709 38.462 0.00 0.00 0.00 2.59
1479 1589 9.847224 TTAGTTCCAGATACATCCCTTTTTATC 57.153 33.333 0.00 0.00 0.00 1.75
1485 1595 9.615660 TGTATATTAGTTCCAGATACATCCCTT 57.384 33.333 0.00 0.00 30.11 3.95
1486 1596 9.790297 ATGTATATTAGTTCCAGATACATCCCT 57.210 33.333 0.00 0.00 38.67 4.20
1519 1629 9.657419 GTCATCAAAATGAATAAAAAGGGATGT 57.343 29.630 0.00 0.00 43.42 3.06
1520 1630 9.656040 TGTCATCAAAATGAATAAAAAGGGATG 57.344 29.630 0.00 0.00 43.42 3.51
1522 1632 9.709495 CTTGTCATCAAAATGAATAAAAAGGGA 57.291 29.630 0.00 0.00 43.42 4.20
1523 1633 9.492973 ACTTGTCATCAAAATGAATAAAAAGGG 57.507 29.630 0.00 0.00 43.42 3.95
1531 1641 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
1532 1642 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
1533 1643 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
1534 1644 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
1535 1645 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
1536 1646 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
1537 1647 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
1538 1648 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1539 1649 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
1540 1650 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
1541 1651 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
1542 1652 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
1543 1653 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1544 1654 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1545 1655 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1546 1656 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1547 1657 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1548 1658 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1549 1659 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1550 1660 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1551 1661 0.251742 TTACTCCCTCCGTCCGGAAA 60.252 55.000 5.23 0.00 44.66 3.13
1552 1662 0.967380 GTTACTCCCTCCGTCCGGAA 60.967 60.000 5.23 0.00 44.66 4.30
1553 1663 1.379044 GTTACTCCCTCCGTCCGGA 60.379 63.158 0.00 0.00 42.90 5.14
1554 1664 1.664321 CTGTTACTCCCTCCGTCCGG 61.664 65.000 0.00 0.00 0.00 5.14
1555 1665 1.664321 CCTGTTACTCCCTCCGTCCG 61.664 65.000 0.00 0.00 0.00 4.79
1556 1666 1.957765 GCCTGTTACTCCCTCCGTCC 61.958 65.000 0.00 0.00 0.00 4.79
1557 1667 1.516423 GCCTGTTACTCCCTCCGTC 59.484 63.158 0.00 0.00 0.00 4.79
1558 1668 2.348888 CGCCTGTTACTCCCTCCGT 61.349 63.158 0.00 0.00 0.00 4.69
1559 1669 2.494918 CGCCTGTTACTCCCTCCG 59.505 66.667 0.00 0.00 0.00 4.63
1560 1670 2.187163 GCGCCTGTTACTCCCTCC 59.813 66.667 0.00 0.00 0.00 4.30
1561 1671 2.202756 CGCGCCTGTTACTCCCTC 60.203 66.667 0.00 0.00 0.00 4.30
1562 1672 4.452733 GCGCGCCTGTTACTCCCT 62.453 66.667 23.24 0.00 0.00 4.20
1565 1675 3.072486 TAGGGCGCGCCTGTTACTC 62.072 63.158 45.23 28.67 36.10 2.59
1566 1676 3.072468 TAGGGCGCGCCTGTTACT 61.072 61.111 45.23 34.66 36.10 2.24
1936 2074 4.574599 ATTCTCCAACTCAACAACTTGC 57.425 40.909 0.00 0.00 0.00 4.01
2134 2274 8.767478 TTAGTGCTAATTTACACAGTACTTCC 57.233 34.615 11.69 0.00 39.30 3.46
2211 2357 0.825010 AGCACTGTTCAGGCAAAGGG 60.825 55.000 12.86 0.00 0.00 3.95
2232 2378 9.627395 TTGAACCAACAAAATAACATAATACCG 57.373 29.630 0.00 0.00 0.00 4.02
2486 3194 5.164897 TCCATATGATCCCTCCTGAATTCA 58.835 41.667 8.12 8.12 0.00 2.57
2564 3286 4.017130 AGGGGAAGAGAACCAATAAGCAAT 60.017 41.667 0.00 0.00 0.00 3.56
2565 3287 3.333680 AGGGGAAGAGAACCAATAAGCAA 59.666 43.478 0.00 0.00 0.00 3.91
2566 3288 2.919602 AGGGGAAGAGAACCAATAAGCA 59.080 45.455 0.00 0.00 0.00 3.91
2567 3289 3.546724 GAGGGGAAGAGAACCAATAAGC 58.453 50.000 0.00 0.00 0.00 3.09
2569 3291 2.850568 GGGAGGGGAAGAGAACCAATAA 59.149 50.000 0.00 0.00 0.00 1.40
2571 3293 1.299939 GGGAGGGGAAGAGAACCAAT 58.700 55.000 0.00 0.00 0.00 3.16
2572 3294 0.845102 GGGGAGGGGAAGAGAACCAA 60.845 60.000 0.00 0.00 0.00 3.67
2573 3295 1.229853 GGGGAGGGGAAGAGAACCA 60.230 63.158 0.00 0.00 0.00 3.67
2574 3296 1.229853 TGGGGAGGGGAAGAGAACC 60.230 63.158 0.00 0.00 0.00 3.62
2575 3297 0.547954 AGTGGGGAGGGGAAGAGAAC 60.548 60.000 0.00 0.00 0.00 3.01
2576 3298 1.098589 TAGTGGGGAGGGGAAGAGAA 58.901 55.000 0.00 0.00 0.00 2.87
2925 3679 9.211485 GTACTTAATCAACCTTAGCTGTTACAA 57.789 33.333 0.00 0.00 0.00 2.41
3004 3762 6.240894 AGTGAGTGTGACAATACAATGGAAT 58.759 36.000 0.00 0.00 31.36 3.01
3161 3920 2.412591 AGGCACTCATATGGGTTAGCT 58.587 47.619 15.47 0.00 0.00 3.32
3221 3980 9.391006 ACTTTGTACTTCTCAAACATAAGTTCA 57.609 29.630 0.00 0.00 36.84 3.18
3446 4205 6.351796 GCAAAAAGGGGCCTTCATTTATCTAA 60.352 38.462 0.84 0.00 34.84 2.10
3481 4241 4.737765 TGCACTTGTTCAAAAACTAATCGC 59.262 37.500 0.00 0.00 36.30 4.58
3618 4378 7.352719 ACTTCGTCATGAGTATTTTCTTGTC 57.647 36.000 0.00 0.00 0.00 3.18
3624 4385 6.710744 AGAACCAACTTCGTCATGAGTATTTT 59.289 34.615 0.00 0.00 33.60 1.82
3685 4466 3.875727 CCAGATTAAGGTGCTCACATCAG 59.124 47.826 2.21 0.00 0.00 2.90
3858 4655 5.507817 GCACCAAAAATGATCACTCAGTCAA 60.508 40.000 0.00 0.00 34.12 3.18
3982 4779 6.696441 AGATACAGGTAAGTAGTGTAGTGC 57.304 41.667 0.00 0.00 30.43 4.40
3996 4793 5.482175 GGGCAGATCACTATTAGATACAGGT 59.518 44.000 0.00 0.00 0.00 4.00
4189 4992 1.132262 ACTGCCACGTGAAAACAAGTG 59.868 47.619 19.30 8.73 35.00 3.16
4622 5432 0.031449 CGTGGCGTTTTTCCATGGTT 59.969 50.000 12.58 0.00 37.05 3.67
4740 5832 6.648725 CCATGTGGTAAAACTTAATTGGGTTG 59.351 38.462 0.00 0.00 0.00 3.77
4741 5833 6.742926 GCCATGTGGTAAAACTTAATTGGGTT 60.743 38.462 0.35 0.00 37.57 4.11
4934 6026 5.340439 AATTCAGAACCTTAGGTAGACCG 57.660 43.478 3.55 0.00 42.08 4.79
5022 6115 6.261381 ACTTGTAATTGCGTGGTTAGAAAGAA 59.739 34.615 0.00 0.00 0.00 2.52
5288 6381 3.642938 TGGAGAATTTGTCCACCCG 57.357 52.632 11.05 0.00 39.28 5.28
6125 8465 2.414481 CTGAAGTGAAGAGGCATGAACG 59.586 50.000 0.00 0.00 0.00 3.95
6231 8571 5.124776 TGAGTTGAAACTTTGTGGTTACCAG 59.875 40.000 3.45 0.00 39.88 4.00
6300 8678 1.277842 TCGAGGCTCCACTAAAATGCA 59.722 47.619 9.32 0.00 0.00 3.96
6334 8712 2.562738 GGTCTACCAGGCTGCAAAATTT 59.437 45.455 9.56 0.00 35.64 1.82
6818 10049 4.125703 GCCAGGAATAGTCTGTTGATCAG 58.874 47.826 0.00 0.00 44.85 2.90
7065 10308 4.222145 ACGGGAACATTTAGAGAGTAGCAA 59.778 41.667 0.00 0.00 0.00 3.91
7243 10486 4.282703 TCCAGTACTTCTTTTTCTAGGCGT 59.717 41.667 0.00 0.00 0.00 5.68
7357 10611 4.188247 TCTGTGTATGCTAGTGGTTGAC 57.812 45.455 0.00 0.00 0.00 3.18
7377 10631 8.709386 TTCTATGTGAGAAGTCTAAATGCTTC 57.291 34.615 0.00 0.00 39.36 3.86
7706 13514 9.005777 GGAACCATTATTAACAGTCACTAACAA 57.994 33.333 0.00 0.00 0.00 2.83
7707 13515 8.380099 AGGAACCATTATTAACAGTCACTAACA 58.620 33.333 0.00 0.00 0.00 2.41
7708 13516 8.788325 AGGAACCATTATTAACAGTCACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
7711 13519 8.603304 ACTAAGGAACCATTATTAACAGTCACT 58.397 33.333 0.00 0.00 0.00 3.41
7712 13520 8.788325 ACTAAGGAACCATTATTAACAGTCAC 57.212 34.615 0.00 0.00 0.00 3.67
7713 13521 8.822805 AGACTAAGGAACCATTATTAACAGTCA 58.177 33.333 0.00 0.00 0.00 3.41
7757 13565 5.845953 GTCACAACATTGTAATCACTGTTCG 59.154 40.000 0.00 2.22 42.62 3.95
7980 13790 3.750130 TCATTCAAACTGCTCTGCTTCTC 59.250 43.478 0.00 0.00 0.00 2.87
8060 13873 7.101054 ACAATATGTGTTAAAGCTACTCGGAA 58.899 34.615 0.00 0.00 37.01 4.30
8096 13921 7.167924 TGATAAGCATGTTTTCAGCCAATTA 57.832 32.000 0.00 0.00 0.00 1.40
8486 14345 1.001378 ACATCTTTCGGCAGCACAAAC 60.001 47.619 0.00 0.00 0.00 2.93
8534 14394 7.893302 AGAATAAACATCCCCAGATAACAACAA 59.107 33.333 0.00 0.00 0.00 2.83
8535 14395 7.410174 AGAATAAACATCCCCAGATAACAACA 58.590 34.615 0.00 0.00 0.00 3.33
8536 14396 7.881775 AGAATAAACATCCCCAGATAACAAC 57.118 36.000 0.00 0.00 0.00 3.32
8606 14466 3.311048 GCAAAGTATCAGCTAGGCTTGTC 59.689 47.826 0.00 0.00 36.40 3.18
8613 14473 5.761726 TCATCAATGGCAAAGTATCAGCTAG 59.238 40.000 0.00 0.00 0.00 3.42
8614 14474 5.683681 TCATCAATGGCAAAGTATCAGCTA 58.316 37.500 0.00 0.00 0.00 3.32
8637 14497 6.266330 TCAGCACATGAACTGCTACTATCTAT 59.734 38.462 8.80 0.00 43.34 1.98
8703 14564 5.181622 CCCGGATAGTACATGAGAGTAACTC 59.818 48.000 0.73 0.00 45.11 3.01
8754 14615 2.157085 GGCTAAAGACTTCGTTTGTCCG 59.843 50.000 0.00 0.00 35.21 4.79
8859 14965 1.154301 CGCCGGAAAATCCACAACG 60.154 57.895 5.05 0.00 35.91 4.10
8861 14967 1.033574 AAACGCCGGAAAATCCACAA 58.966 45.000 5.05 0.00 35.91 3.33
8865 14971 0.388006 CCACAAACGCCGGAAAATCC 60.388 55.000 5.05 0.00 0.00 3.01
8953 15059 1.239347 GAGCGGCAAATAGGATTCCC 58.761 55.000 1.45 0.00 0.00 3.97
8954 15060 0.868406 CGAGCGGCAAATAGGATTCC 59.132 55.000 1.45 0.00 0.00 3.01
8955 15061 0.235926 GCGAGCGGCAAATAGGATTC 59.764 55.000 1.45 0.00 42.87 2.52
8956 15062 2.321213 GCGAGCGGCAAATAGGATT 58.679 52.632 1.45 0.00 42.87 3.01
8957 15063 4.049393 GCGAGCGGCAAATAGGAT 57.951 55.556 1.45 0.00 42.87 3.24
8966 15072 4.404654 CCCAAAACAGCGAGCGGC 62.405 66.667 0.00 0.00 44.05 6.53
8967 15073 2.258013 TTCCCAAAACAGCGAGCGG 61.258 57.895 0.00 0.00 0.00 5.52
8968 15074 1.082104 GTTCCCAAAACAGCGAGCG 60.082 57.895 0.00 0.00 0.00 5.03
8969 15075 1.172812 AGGTTCCCAAAACAGCGAGC 61.173 55.000 0.00 0.00 0.00 5.03
8970 15076 1.266989 GAAGGTTCCCAAAACAGCGAG 59.733 52.381 0.00 0.00 0.00 5.03
8971 15077 1.133915 AGAAGGTTCCCAAAACAGCGA 60.134 47.619 0.00 0.00 0.00 4.93
8972 15078 1.318576 AGAAGGTTCCCAAAACAGCG 58.681 50.000 0.00 0.00 0.00 5.18
8973 15079 3.751518 TCTAGAAGGTTCCCAAAACAGC 58.248 45.455 0.00 0.00 0.00 4.40
8974 15080 4.327680 CCTCTAGAAGGTTCCCAAAACAG 58.672 47.826 0.00 0.00 40.67 3.16
8975 15081 4.367039 CCTCTAGAAGGTTCCCAAAACA 57.633 45.455 0.00 0.00 40.67 2.83
9182 15294 8.417780 AACACGAACAAATTTCAAATTCATGA 57.582 26.923 0.00 0.00 0.00 3.07
9183 15295 8.326713 TGAACACGAACAAATTTCAAATTCATG 58.673 29.630 0.00 0.00 0.00 3.07
9184 15296 8.417780 TGAACACGAACAAATTTCAAATTCAT 57.582 26.923 0.00 0.00 0.00 2.57
9256 15376 5.586339 TGTGAACAATTTTTGAATCTGCGA 58.414 33.333 0.00 0.00 0.00 5.10
9290 15410 8.755941 TGAATAAATTTCAAATTCGCGAACAAA 58.244 25.926 26.00 19.31 33.28 2.83
9291 15411 8.286996 TGAATAAATTTCAAATTCGCGAACAA 57.713 26.923 26.00 11.71 33.28 2.83
9351 15471 6.428385 TTTGAACAAATTTTGAAACCGCAT 57.572 29.167 15.81 0.00 0.00 4.73
9421 15541 9.307121 TGAACAAATTATGAAACGTGAACAAAT 57.693 25.926 0.00 0.00 0.00 2.32
9425 15545 7.672351 TGTGAACAAATTATGAAACGTGAAC 57.328 32.000 0.00 0.00 0.00 3.18
9430 15550 8.210026 TCGAATTGTGAACAAATTATGAAACG 57.790 30.769 0.00 0.00 39.55 3.60


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

AutoCloner maintained by Alex Coulton.