Multiple sequence alignment - TraesCS7D01G474200

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 TraesCS7D01G474200 chr7D 100.000 2511 0 0 1 2511 586764717 586767227 0.000000e+00 4638.0
1 TraesCS7D01G474200 chr7D 92.162 1161 54 16 1 1132 586782517 586783669 0.000000e+00 1605.0
2 TraesCS7D01G474200 chr7D 95.228 461 13 5 1141 1597 586783721 586784176 0.000000e+00 721.0
3 TraesCS7D01G474200 chr7D 98.020 101 2 0 2129 2229 511614664 511614564 2.570000e-40 176.0
4 TraesCS7D01G474200 chr7D 96.970 99 3 0 2131 2229 3233187 3233089 1.540000e-37 167.0
5 TraesCS7D01G474200 chr7D 98.438 64 1 0 1667 1730 586784311 586784374 2.040000e-21 113.0
6 TraesCS7D01G474200 chr7A 88.020 818 49 21 742 1522 677871128 677871933 0.000000e+00 922.0
7 TraesCS7D01G474200 chr7A 86.885 305 21 10 1728 2016 677872355 677872656 8.660000e-85 324.0
8 TraesCS7D01G474200 chr7A 85.345 116 8 4 2024 2130 677872724 677872839 7.340000e-21 111.0
9 TraesCS7D01G474200 chr7B 91.418 536 24 12 1122 1645 657479498 657480023 0.000000e+00 715.0
10 TraesCS7D01G474200 chr7B 91.045 536 26 12 1122 1645 657496432 657496957 0.000000e+00 704.0
11 TraesCS7D01G474200 chr7B 89.615 520 29 8 640 1145 657495912 657496420 2.720000e-179 638.0
12 TraesCS7D01G474200 chr7B 89.423 520 30 8 640 1145 657478978 657479486 1.270000e-177 632.0
13 TraesCS7D01G474200 chr7B 95.588 340 15 0 1189 1528 657500720 657501059 1.700000e-151 545.0
14 TraesCS7D01G474200 chr7B 84.615 312 32 14 1828 2132 657497124 657497426 1.890000e-76 296.0
15 TraesCS7D01G474200 chr7B 98.165 109 2 0 2024 2132 657480460 657480568 9.170000e-45 191.0
16 TraesCS7D01G474200 chr7B 98.058 103 2 0 147 249 657478874 657478976 1.980000e-41 180.0
17 TraesCS7D01G474200 chr7B 98.058 103 2 0 147 249 657495808 657495910 1.980000e-41 180.0
18 TraesCS7D01G474200 chr7B 92.727 110 8 0 998 1107 43949109 43949000 2.590000e-35 159.0
19 TraesCS7D01G474200 chr7B 97.222 36 1 0 1108 1143 657500607 657500642 7.500000e-06 62.1
20 TraesCS7D01G474200 chr3D 95.167 269 9 2 2244 2511 492123321 492123586 2.990000e-114 422.0
21 TraesCS7D01G474200 chr3D 96.970 99 3 0 2131 2229 511660014 511660112 1.540000e-37 167.0
22 TraesCS7D01G474200 chrUn 94.796 269 10 2 2244 2511 104044413 104044678 1.390000e-112 416.0
23 TraesCS7D01G474200 chrUn 96.970 99 3 0 2131 2229 347565139 347565041 1.540000e-37 167.0
24 TraesCS7D01G474200 chrUn 94.286 105 6 0 2125 2229 104049732 104049836 7.190000e-36 161.0
25 TraesCS7D01G474200 chrUn 88.462 104 10 2 999 1101 20705502 20705604 9.430000e-25 124.0
26 TraesCS7D01G474200 chrUn 86.538 104 12 2 999 1101 20430140 20430242 2.040000e-21 113.0
27 TraesCS7D01G474200 chrUn 85.938 64 9 0 1031 1094 23975077 23975014 4.480000e-08 69.4
28 TraesCS7D01G474200 chr6D 94.796 269 10 2 2244 2511 458101591 458101326 1.390000e-112 416.0
29 TraesCS7D01G474200 chr6D 94.424 269 11 2 2244 2511 20834440 20834705 6.460000e-111 411.0
30 TraesCS7D01G474200 chr6D 94.286 105 6 0 2125 2229 23745109 23745213 7.190000e-36 161.0
31 TraesCS7D01G474200 chr6D 88.785 107 12 0 1001 1107 89329294 89329188 5.640000e-27 132.0
32 TraesCS7D01G474200 chr6D 87.324 71 9 0 1399 1469 106049383 106049453 5.760000e-12 82.4
33 TraesCS7D01G474200 chr4D 94.796 269 10 2 2244 2511 451053948 451054213 1.390000e-112 416.0
34 TraesCS7D01G474200 chr4D 77.644 331 57 12 996 1320 394384206 394384525 4.270000e-43 185.0
35 TraesCS7D01G474200 chr4D 95.327 107 5 0 999 1105 3588702 3588596 1.190000e-38 171.0
36 TraesCS7D01G474200 chr4D 94.286 105 6 0 2125 2229 451053859 451053963 7.190000e-36 161.0
37 TraesCS7D01G474200 chr4D 92.593 108 8 0 999 1106 373933836 373933729 3.340000e-34 156.0
38 TraesCS7D01G474200 chr4D 85.965 57 8 0 1039 1095 353570830 353570886 7.500000e-06 62.1
39 TraesCS7D01G474200 chr2D 94.796 269 10 2 2244 2511 420579531 420579796 1.390000e-112 416.0
40 TraesCS7D01G474200 chr2D 94.796 269 10 2 2244 2511 606945770 606945505 1.390000e-112 416.0
41 TraesCS7D01G474200 chr2D 82.192 146 20 3 202 347 272236285 272236146 1.220000e-23 121.0
42 TraesCS7D01G474200 chr2D 85.057 87 13 0 1399 1485 565860990 565860904 3.440000e-14 89.8
43 TraesCS7D01G474200 chr2D 86.154 65 9 0 427 491 649592933 649592997 1.250000e-08 71.3
44 TraesCS7D01G474200 chr1D 94.796 269 10 2 2244 2511 83874886 83874621 1.390000e-112 416.0
45 TraesCS7D01G474200 chr1D 86.111 216 30 0 1189 1404 316678681 316678896 1.500000e-57 233.0
46 TraesCS7D01G474200 chr1D 88.824 170 15 3 962 1131 316678400 316678565 3.270000e-49 206.0
47 TraesCS7D01G474200 chr1D 96.190 105 4 0 2125 2229 24201251 24201355 3.320000e-39 172.0
48 TraesCS7D01G474200 chr1D 76.062 259 49 10 41 293 426744767 426744516 3.390000e-24 122.0
49 TraesCS7D01G474200 chr1D 87.255 102 11 2 1400 1500 316679100 316679200 5.680000e-22 115.0
50 TraesCS7D01G474200 chr5D 94.776 268 10 2 2245 2511 286324794 286324530 5.000000e-112 414.0
51 TraesCS7D01G474200 chr5D 95.575 113 5 0 998 1110 373763090 373763202 5.520000e-42 182.0
52 TraesCS7D01G474200 chr5D 89.189 74 2 4 1399 1469 373763625 373763695 1.240000e-13 87.9
53 TraesCS7D01G474200 chr5D 75.472 159 36 3 443 600 406522417 406522573 9.630000e-10 75.0
54 TraesCS7D01G474200 chr1B 86.111 216 30 0 1189 1404 428801992 428802207 1.500000e-57 233.0
55 TraesCS7D01G474200 chr1B 89.157 166 12 3 955 1120 428801678 428801837 4.240000e-48 202.0
56 TraesCS7D01G474200 chr1B 87.255 102 11 2 1400 1500 428802292 428802392 5.680000e-22 115.0
57 TraesCS7D01G474200 chr1B 83.133 83 13 1 229 311 576551121 576551040 9.630000e-10 75.0
58 TraesCS7D01G474200 chr1A 84.914 232 33 2 1174 1404 397770000 397770230 1.500000e-57 233.0
59 TraesCS7D01G474200 chr1A 88.235 170 16 2 962 1131 397769736 397769901 1.520000e-47 200.0
60 TraesCS7D01G474200 chr4B 93.077 130 9 0 1191 1320 5466302 5466431 9.170000e-45 191.0
61 TraesCS7D01G474200 chr4B 92.437 119 8 1 987 1105 5466067 5466184 4.300000e-38 169.0
62 TraesCS7D01G474200 chr4B 91.818 110 8 1 996 1105 484580259 484580367 4.330000e-33 152.0
63 TraesCS7D01G474200 chr4B 91.667 108 9 0 999 1106 459947249 459947142 1.560000e-32 150.0
64 TraesCS7D01G474200 chr4B 90.741 108 10 0 999 1106 460032324 460032217 7.240000e-31 145.0
65 TraesCS7D01G474200 chr5B 97.248 109 3 0 998 1106 445173802 445173910 4.270000e-43 185.0
66 TraesCS7D01G474200 chr5B 88.889 72 6 2 1399 1469 445176991 445177061 1.240000e-13 87.9
67 TraesCS7D01G474200 chr4A 95.327 107 5 0 999 1105 601059809 601059915 1.190000e-38 171.0
68 TraesCS7D01G474200 chr4A 95.960 99 4 0 2131 2229 620483991 620483893 7.190000e-36 161.0
69 TraesCS7D01G474200 chr4A 81.061 132 22 2 147 277 479421465 479421336 4.420000e-18 102.0
70 TraesCS7D01G474200 chr6B 92.523 107 8 0 998 1104 192738186 192738292 1.200000e-33 154.0
71 TraesCS7D01G474200 chr6B 88.235 68 8 0 436 503 152192258 152192191 5.760000e-12 82.4
72 TraesCS7D01G474200 chr6B 87.324 71 9 0 1399 1469 192738725 192738795 5.760000e-12 82.4
73 TraesCS7D01G474200 chr5A 78.261 230 41 8 66 289 701474780 701475006 3.370000e-29 139.0
74 TraesCS7D01G474200 chr6A 88.889 72 8 0 1398 1469 129317539 129317610 3.440000e-14 89.8
75 TraesCS7D01G474200 chr6A 85.185 81 12 0 417 497 515380104 515380184 1.600000e-12 84.2
76 TraesCS7D01G474200 chr2A 85.057 87 13 0 1399 1485 706200530 706200444 3.440000e-14 89.8
77 TraesCS7D01G474200 chr2A 83.908 87 14 0 1399 1485 705926733 705926647 1.600000e-12 84.2
78 TraesCS7D01G474200 chr2A 84.337 83 13 0 1403 1485 706001037 706000955 5.760000e-12 82.4
79 TraesCS7D01G474200 chr2B 85.542 83 12 0 1403 1485 678198041 678197959 1.240000e-13 87.9
80 TraesCS7D01G474200 chr3A 78.846 104 20 2 436 537 547407467 547407364 4.480000e-08 69.4


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 TraesCS7D01G474200 chr7D 586764717 586767227 2510 False 4638.000000 4638 100.0000 1 2511 1 chr7D.!!$F1 2510
1 TraesCS7D01G474200 chr7D 586782517 586784374 1857 False 813.000000 1605 95.2760 1 1730 3 chr7D.!!$F2 1729
2 TraesCS7D01G474200 chr7A 677871128 677872839 1711 False 452.333333 922 86.7500 742 2130 3 chr7A.!!$F1 1388
3 TraesCS7D01G474200 chr7B 657478874 657480568 1694 False 429.500000 715 94.2660 147 2132 4 chr7B.!!$F1 1985
4 TraesCS7D01G474200 chr7B 657495808 657501059 5251 False 404.183333 704 92.6905 147 2132 6 chr7B.!!$F2 1985

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
399 402 0.321564 CTCCCTGACAATGTTCCGCA 60.322 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 2833 0.03759 TTGCGGGGCTGTTAGATTGT 59.962 50.0 0.0 0.0 0.0 2.71 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
20 22 1.509923 CGGTCCACCTAGACGGTTC 59.490 63.158 0.00 0.00 46.37 3.62
24 26 1.679977 CCACCTAGACGGTTCGGGA 60.680 63.158 0.00 0.00 46.37 5.14
37 39 1.131303 TTCGGGACACAGGGGTTGAT 61.131 55.000 0.00 0.00 0.00 2.57
39 41 1.000896 GGGACACAGGGGTTGATGG 60.001 63.158 0.00 0.00 0.00 3.51
47 49 1.633432 CAGGGGTTGATGGTTCCTACA 59.367 52.381 0.00 0.00 0.00 2.74
122 125 0.322975 GACTTCTGCTCTTCCTGCCA 59.677 55.000 0.00 0.00 0.00 4.92
293 296 3.053896 GTGTAGCGGTGGGTTGCC 61.054 66.667 0.00 0.00 0.00 4.52
300 303 2.520968 GGTGGGTTGCCTGGTCTT 59.479 61.111 0.00 0.00 0.00 3.01
315 318 4.580167 CCTGGTCTTGTTCTTTGTCATTGA 59.420 41.667 0.00 0.00 0.00 2.57
320 323 5.916883 GTCTTGTTCTTTGTCATTGACATGG 59.083 40.000 19.63 14.66 42.40 3.66
393 396 2.187958 TCGATTCCTCCCTGACAATGT 58.812 47.619 0.00 0.00 0.00 2.71
396 399 2.879103 TTCCTCCCTGACAATGTTCC 57.121 50.000 0.00 0.00 0.00 3.62
399 402 0.321564 CTCCCTGACAATGTTCCGCA 60.322 55.000 0.00 0.00 0.00 5.69
448 451 2.103934 CGCGGCTCTCCTCTTGAG 59.896 66.667 0.00 0.00 42.90 3.02
478 481 1.241990 TGGTTCTCCTCTCCGTGTCG 61.242 60.000 0.00 0.00 34.23 4.35
488 491 3.045492 CCGTGTCGGGTTTTCGGG 61.045 66.667 0.00 0.00 44.15 5.14
619 622 6.613755 TTGTGTTTCAACTTAGCTTCCTAC 57.386 37.500 0.00 0.00 0.00 3.18
620 623 5.925509 TGTGTTTCAACTTAGCTTCCTACT 58.074 37.500 0.00 0.00 0.00 2.57
621 624 7.058023 TGTGTTTCAACTTAGCTTCCTACTA 57.942 36.000 0.00 0.00 0.00 1.82
765 770 0.677288 GTTTTCCTTTTCCCCCACGG 59.323 55.000 0.00 0.00 0.00 4.94
840 865 1.009900 CGTCTACTCCATCGTCGGC 60.010 63.158 0.00 0.00 0.00 5.54
852 877 1.136774 CGTCGGCTGAGAATCGTCA 59.863 57.895 0.00 0.00 38.61 4.35
867 892 6.292150 AGAATCGTCAAAGAAAAGAACTCCT 58.708 36.000 0.00 0.00 0.00 3.69
868 893 7.442656 AGAATCGTCAAAGAAAAGAACTCCTA 58.557 34.615 0.00 0.00 0.00 2.94
869 894 8.097662 AGAATCGTCAAAGAAAAGAACTCCTAT 58.902 33.333 0.00 0.00 0.00 2.57
870 895 7.835634 ATCGTCAAAGAAAAGAACTCCTATC 57.164 36.000 0.00 0.00 0.00 2.08
871 896 6.164176 TCGTCAAAGAAAAGAACTCCTATCC 58.836 40.000 0.00 0.00 0.00 2.59
932 958 3.447918 TCGCTATAAATATAGGCCGGC 57.552 47.619 21.18 21.18 36.90 6.13
933 959 3.028850 TCGCTATAAATATAGGCCGGCT 58.971 45.455 28.56 15.07 36.90 5.52
947 983 1.716826 CCGGCTAGAGGAGACACGAC 61.717 65.000 0.00 0.00 28.99 4.34
950 986 0.452585 GCTAGAGGAGACACGACCAC 59.547 60.000 0.00 0.00 0.00 4.16
951 987 0.727970 CTAGAGGAGACACGACCACG 59.272 60.000 0.00 0.00 45.75 4.94
955 991 0.536687 AGGAGACACGACCACGAGAA 60.537 55.000 0.00 0.00 42.66 2.87
959 995 0.725118 GACACGACCACGAGAACGAG 60.725 60.000 0.00 0.00 42.66 4.18
965 1001 2.383527 CCACGAGAACGAGCAAGCC 61.384 63.158 0.00 0.00 42.66 4.35
988 1024 1.153086 AGCAGTTGATCCATCGGCC 60.153 57.895 0.00 0.00 0.00 6.13
991 1027 0.734889 CAGTTGATCCATCGGCCAAC 59.265 55.000 2.24 0.00 36.76 3.77
995 1033 1.031571 TGATCCATCGGCCAACAAGC 61.032 55.000 2.24 0.00 0.00 4.01
1050 1088 1.297745 GACGATCACGCTCGAGGTC 60.298 63.158 15.58 7.25 43.96 3.85
1174 1288 2.604046 ATCGACCATGCTGAACCTAC 57.396 50.000 0.00 0.00 0.00 3.18
1216 1334 4.598894 CCTCCGGATCAGCAGCGG 62.599 72.222 3.57 0.00 0.00 5.52
1300 1418 3.923864 TCGACGCTGCACCTGGTT 61.924 61.111 0.00 0.00 0.00 3.67
1576 1697 3.260884 ACCGCCGTCCAATATGATAGATT 59.739 43.478 0.00 0.00 0.00 2.40
1577 1698 4.253685 CCGCCGTCCAATATGATAGATTT 58.746 43.478 0.00 0.00 0.00 2.17
1661 2152 8.771920 AGGTTTTAACTTTTATTAAGCCATGC 57.228 30.769 0.00 0.00 0.00 4.06
1662 2153 7.544217 AGGTTTTAACTTTTATTAAGCCATGCG 59.456 33.333 0.00 0.00 0.00 4.73
1664 2155 8.917655 GTTTTAACTTTTATTAAGCCATGCGAA 58.082 29.630 0.00 0.00 0.00 4.70
1730 2253 7.598869 TGCGAGTTATTATGGATGTCTAATGAC 59.401 37.037 0.00 0.00 43.20 3.06
1731 2254 7.815068 GCGAGTTATTATGGATGTCTAATGACT 59.185 37.037 0.00 0.00 43.29 3.41
1738 2261 9.935241 ATTATGGATGTCTAATGACTACACATC 57.065 33.333 0.00 0.00 43.29 3.06
1746 2269 7.172480 GTCTAATGACTACACATCTCTGTGCC 61.172 46.154 5.68 0.00 45.97 5.01
1768 2291 5.353956 GCCCAGATTTTGTTTGTCTGTTTTT 59.646 36.000 0.00 0.00 38.10 1.94
1769 2292 6.456853 GCCCAGATTTTGTTTGTCTGTTTTTC 60.457 38.462 0.00 0.00 38.10 2.29
1770 2293 6.237808 CCCAGATTTTGTTTGTCTGTTTTTCG 60.238 38.462 0.00 0.00 38.10 3.46
1783 2306 5.398416 GTCTGTTTTTCGTTCATTAGCCAAC 59.602 40.000 0.00 0.00 0.00 3.77
1811 2334 0.736053 TTTCTGAACGCCACAACCAC 59.264 50.000 0.00 0.00 0.00 4.16
1812 2335 0.393132 TTCTGAACGCCACAACCACA 60.393 50.000 0.00 0.00 0.00 4.17
1830 2357 3.122948 CCACAACCGTAATCTCTTGAACG 59.877 47.826 0.00 0.00 35.20 3.95
1835 2362 3.255149 ACCGTAATCTCTTGAACGACAGT 59.745 43.478 0.00 0.00 37.53 3.55
1838 2365 5.860182 CCGTAATCTCTTGAACGACAGTAAA 59.140 40.000 0.00 0.00 37.53 2.01
1860 2391 4.582701 AATGACGCAAAGGAACAAATCA 57.417 36.364 0.00 0.00 0.00 2.57
1908 2446 1.178534 ACGTTTTGTCCATGGGCAGG 61.179 55.000 20.30 12.55 0.00 4.85
1980 2518 2.557924 TGGGTGATGTTTTGCAGATCAC 59.442 45.455 16.18 16.18 36.74 3.06
1996 2538 1.452651 CACGGGAGCATGCTGGATT 60.453 57.895 28.27 0.00 36.98 3.01
2001 2543 1.410083 GGGAGCATGCTGGATTGGTTA 60.410 52.381 28.27 0.00 0.00 2.85
2016 2558 1.310904 GGTTAAACACCTGAACGGCA 58.689 50.000 0.00 0.00 43.29 5.69
2018 2560 2.095415 GGTTAAACACCTGAACGGCATC 60.095 50.000 0.00 0.00 43.29 3.91
2019 2561 1.434555 TAAACACCTGAACGGCATCG 58.565 50.000 0.00 0.00 43.02 3.84
2032 2640 1.793714 CGGCATCGTGTATTGTTTGCC 60.794 52.381 1.70 1.70 44.78 4.52
2132 2748 2.974148 CAGCGGTGCTTGCACTGA 60.974 61.111 31.29 0.00 36.40 3.41
2134 2750 2.177531 GCGGTGCTTGCACTGATG 59.822 61.111 31.29 17.06 33.45 3.07
2135 2751 2.327343 GCGGTGCTTGCACTGATGA 61.327 57.895 31.29 0.00 33.45 2.92
2136 2752 1.792301 CGGTGCTTGCACTGATGAG 59.208 57.895 25.29 7.75 33.45 2.90
2137 2753 0.671472 CGGTGCTTGCACTGATGAGA 60.671 55.000 25.29 0.00 33.45 3.27
2138 2754 1.527034 GGTGCTTGCACTGATGAGAA 58.473 50.000 22.55 0.00 0.00 2.87
2139 2755 1.881973 GGTGCTTGCACTGATGAGAAA 59.118 47.619 22.55 0.00 0.00 2.52
2140 2756 2.294233 GGTGCTTGCACTGATGAGAAAA 59.706 45.455 22.55 0.00 0.00 2.29
2142 2758 4.156556 GGTGCTTGCACTGATGAGAAAATA 59.843 41.667 22.55 0.00 0.00 1.40
2143 2759 5.330295 GTGCTTGCACTGATGAGAAAATAG 58.670 41.667 17.36 0.00 0.00 1.73
2144 2760 4.397103 TGCTTGCACTGATGAGAAAATAGG 59.603 41.667 0.00 0.00 0.00 2.57
2145 2761 4.732938 GCTTGCACTGATGAGAAAATAGGC 60.733 45.833 0.00 0.00 0.00 3.93
2146 2762 3.954200 TGCACTGATGAGAAAATAGGCA 58.046 40.909 0.00 0.00 0.00 4.75
2148 2764 3.944015 GCACTGATGAGAAAATAGGCAGT 59.056 43.478 0.00 0.00 35.70 4.40
2149 2765 4.397417 GCACTGATGAGAAAATAGGCAGTT 59.603 41.667 0.00 0.00 33.29 3.16
2150 2766 5.105997 GCACTGATGAGAAAATAGGCAGTTT 60.106 40.000 0.00 0.00 33.29 2.66
2151 2767 6.571150 GCACTGATGAGAAAATAGGCAGTTTT 60.571 38.462 0.00 0.34 33.29 2.43
2154 2770 6.611381 TGATGAGAAAATAGGCAGTTTTTCG 58.389 36.000 11.38 0.00 43.37 3.46
2155 2771 6.429692 TGATGAGAAAATAGGCAGTTTTTCGA 59.570 34.615 11.38 0.00 43.37 3.71
2156 2772 6.817765 TGAGAAAATAGGCAGTTTTTCGAT 57.182 33.333 11.38 0.24 43.37 3.59
2157 2773 7.214467 TGAGAAAATAGGCAGTTTTTCGATT 57.786 32.000 11.38 0.00 43.37 3.34
2158 2774 8.330466 TGAGAAAATAGGCAGTTTTTCGATTA 57.670 30.769 11.38 1.81 43.37 1.75
2159 2775 8.788806 TGAGAAAATAGGCAGTTTTTCGATTAA 58.211 29.630 11.38 0.00 43.37 1.40
2160 2776 9.620660 GAGAAAATAGGCAGTTTTTCGATTAAA 57.379 29.630 11.38 0.00 43.37 1.52
2168 2784 8.527810 AGGCAGTTTTTCGATTAAATTAATCCA 58.472 29.630 17.23 4.78 41.10 3.41
2169 2785 9.313118 GGCAGTTTTTCGATTAAATTAATCCAT 57.687 29.630 17.23 0.00 41.10 3.41
2194 2810 6.773685 TGAATGAATCATAAGCATGACATGGA 59.226 34.615 17.03 5.76 43.89 3.41
2195 2811 6.570672 ATGAATCATAAGCATGACATGGAC 57.429 37.500 17.03 1.41 43.89 4.02
2196 2812 5.438833 TGAATCATAAGCATGACATGGACA 58.561 37.500 17.03 0.00 43.89 4.02
2197 2813 5.529800 TGAATCATAAGCATGACATGGACAG 59.470 40.000 17.03 0.00 43.89 3.51
2199 2815 2.785540 TAAGCATGACATGGACAGCA 57.214 45.000 17.03 0.00 0.00 4.41
2200 2816 2.139323 AAGCATGACATGGACAGCAT 57.861 45.000 17.03 0.00 0.00 3.79
2201 2817 2.139323 AGCATGACATGGACAGCATT 57.861 45.000 17.03 0.00 0.00 3.56
2202 2818 1.749063 AGCATGACATGGACAGCATTG 59.251 47.619 17.03 0.00 0.00 2.82
2203 2819 1.746787 GCATGACATGGACAGCATTGA 59.253 47.619 17.03 0.00 0.00 2.57
2206 2822 4.037089 GCATGACATGGACAGCATTGATAA 59.963 41.667 17.03 0.00 0.00 1.75
2207 2823 5.516996 CATGACATGGACAGCATTGATAAC 58.483 41.667 7.60 0.00 0.00 1.89
2209 2825 4.395854 TGACATGGACAGCATTGATAACAC 59.604 41.667 0.00 0.00 0.00 3.32
2210 2826 4.334552 ACATGGACAGCATTGATAACACA 58.665 39.130 0.00 0.00 0.00 3.72
2211 2827 4.156556 ACATGGACAGCATTGATAACACAC 59.843 41.667 0.00 0.00 0.00 3.82
2212 2828 4.019792 TGGACAGCATTGATAACACACT 57.980 40.909 0.00 0.00 0.00 3.55
2213 2829 3.752747 TGGACAGCATTGATAACACACTG 59.247 43.478 0.00 0.00 0.00 3.66
2215 2831 4.637534 GGACAGCATTGATAACACACTGAT 59.362 41.667 0.00 0.00 0.00 2.90
2216 2832 5.124457 GGACAGCATTGATAACACACTGATT 59.876 40.000 0.00 0.00 0.00 2.57
2217 2833 6.316140 GGACAGCATTGATAACACACTGATTA 59.684 38.462 0.00 0.00 0.00 1.75
2219 2835 6.654582 ACAGCATTGATAACACACTGATTACA 59.345 34.615 0.00 0.00 0.00 2.41
2220 2836 7.174772 ACAGCATTGATAACACACTGATTACAA 59.825 33.333 0.00 0.00 0.00 2.41
2221 2837 8.186163 CAGCATTGATAACACACTGATTACAAT 58.814 33.333 0.00 0.00 0.00 2.71
2222 2838 8.400947 AGCATTGATAACACACTGATTACAATC 58.599 33.333 0.00 0.00 35.97 2.67
2223 2839 8.400947 GCATTGATAACACACTGATTACAATCT 58.599 33.333 3.76 0.00 36.39 2.40
2227 2843 9.936759 TGATAACACACTGATTACAATCTAACA 57.063 29.630 3.76 0.00 36.39 2.41
2229 2845 6.727824 ACACACTGATTACAATCTAACAGC 57.272 37.500 3.76 0.00 36.39 4.40
2230 2846 5.643777 ACACACTGATTACAATCTAACAGCC 59.356 40.000 3.76 0.00 36.39 4.85
2231 2847 5.065218 CACACTGATTACAATCTAACAGCCC 59.935 44.000 3.76 0.00 36.39 5.19
2232 2848 4.576463 CACTGATTACAATCTAACAGCCCC 59.424 45.833 3.76 0.00 36.39 5.80
2233 2849 3.804036 TGATTACAATCTAACAGCCCCG 58.196 45.455 3.76 0.00 36.39 5.73
2234 2850 2.032680 TTACAATCTAACAGCCCCGC 57.967 50.000 0.00 0.00 0.00 6.13
2235 2851 0.906066 TACAATCTAACAGCCCCGCA 59.094 50.000 0.00 0.00 0.00 5.69
2236 2852 0.037590 ACAATCTAACAGCCCCGCAA 59.962 50.000 0.00 0.00 0.00 4.85
2237 2853 1.173043 CAATCTAACAGCCCCGCAAA 58.827 50.000 0.00 0.00 0.00 3.68
2238 2854 1.543802 CAATCTAACAGCCCCGCAAAA 59.456 47.619 0.00 0.00 0.00 2.44
2239 2855 1.917872 ATCTAACAGCCCCGCAAAAA 58.082 45.000 0.00 0.00 0.00 1.94
2265 2881 6.857777 AGATTACAATCTAACAGAGCATGC 57.142 37.500 10.51 10.51 43.66 4.06
2266 2882 6.590068 AGATTACAATCTAACAGAGCATGCT 58.410 36.000 22.92 22.92 43.66 3.79
2267 2883 6.482641 AGATTACAATCTAACAGAGCATGCTG 59.517 38.462 28.27 15.65 43.66 4.41
2268 2884 6.259608 GATTACAATCTAACAGAGCATGCTGT 59.740 38.462 28.27 20.25 40.18 4.40
2269 2885 7.439356 GATTACAATCTAACAGAGCATGCTGTA 59.561 37.037 28.27 14.54 38.93 2.74
2274 2890 2.568696 ACAGAGCATGCTGTACTACG 57.431 50.000 28.27 11.39 46.67 3.51
2275 2891 1.203928 CAGAGCATGCTGTACTACGC 58.796 55.000 28.27 7.90 0.00 4.42
2276 2892 0.817654 AGAGCATGCTGTACTACGCA 59.182 50.000 28.27 7.35 40.87 5.24
2277 2893 0.924090 GAGCATGCTGTACTACGCAC 59.076 55.000 28.27 1.91 39.21 5.34
2278 2894 0.246360 AGCATGCTGTACTACGCACA 59.754 50.000 21.98 0.00 39.21 4.57
2279 2895 1.134699 AGCATGCTGTACTACGCACAT 60.135 47.619 21.98 0.00 39.21 3.21
2280 2896 2.100749 AGCATGCTGTACTACGCACATA 59.899 45.455 21.98 0.00 39.21 2.29
2281 2897 2.472861 GCATGCTGTACTACGCACATAG 59.527 50.000 11.37 1.48 39.21 2.23
2282 2898 3.706698 CATGCTGTACTACGCACATAGT 58.293 45.455 7.11 0.00 39.21 2.12
2283 2899 4.791734 GCATGCTGTACTACGCACATAGTA 60.792 45.833 11.37 0.00 39.21 1.82
2284 2900 4.547406 TGCTGTACTACGCACATAGTAG 57.453 45.455 0.00 2.25 45.11 2.57
2285 2901 4.193865 TGCTGTACTACGCACATAGTAGA 58.806 43.478 9.96 0.93 43.00 2.59
2286 2902 4.637091 TGCTGTACTACGCACATAGTAGAA 59.363 41.667 9.96 0.00 43.00 2.10
2287 2903 5.124297 TGCTGTACTACGCACATAGTAGAAA 59.876 40.000 9.96 0.00 43.00 2.52
2288 2904 5.454877 GCTGTACTACGCACATAGTAGAAAC 59.545 44.000 9.96 8.02 43.00 2.78
2289 2905 6.499234 TGTACTACGCACATAGTAGAAACA 57.501 37.500 9.96 10.01 43.00 2.83
2290 2906 7.092137 TGTACTACGCACATAGTAGAAACAT 57.908 36.000 9.96 0.00 43.00 2.71
2291 2907 7.191551 TGTACTACGCACATAGTAGAAACATC 58.808 38.462 9.96 0.00 43.00 3.06
2292 2908 6.452494 ACTACGCACATAGTAGAAACATCT 57.548 37.500 9.96 0.00 43.00 2.90
2293 2909 7.563888 ACTACGCACATAGTAGAAACATCTA 57.436 36.000 9.96 0.00 43.00 1.98
2294 2910 7.416022 ACTACGCACATAGTAGAAACATCTAC 58.584 38.462 9.96 7.72 43.00 2.59
2295 2911 5.271625 ACGCACATAGTAGAAACATCTACG 58.728 41.667 9.62 0.87 45.23 3.51
2296 2912 5.163683 ACGCACATAGTAGAAACATCTACGT 60.164 40.000 9.62 0.00 45.23 3.57
2297 2913 6.037500 ACGCACATAGTAGAAACATCTACGTA 59.962 38.462 9.62 0.00 45.23 3.57
2298 2914 7.076362 CGCACATAGTAGAAACATCTACGTAT 58.924 38.462 9.62 6.36 45.23 3.06
2299 2915 8.225777 CGCACATAGTAGAAACATCTACGTATA 58.774 37.037 9.62 0.00 45.23 1.47
2312 2928 7.528307 ACATCTACGTATATTGCTAGTACTGC 58.472 38.462 5.39 7.95 0.00 4.40
2321 2937 5.661056 ATTGCTAGTACTGCTACAACAGA 57.339 39.130 5.39 0.00 40.25 3.41
2322 2938 5.462530 TTGCTAGTACTGCTACAACAGAA 57.537 39.130 5.39 0.00 40.25 3.02
2323 2939 5.462530 TGCTAGTACTGCTACAACAGAAA 57.537 39.130 5.39 0.00 40.25 2.52
2325 2941 6.285224 TGCTAGTACTGCTACAACAGAAAAA 58.715 36.000 5.39 0.00 40.25 1.94
2344 2960 3.947910 AAACACGAGAGGGATAAACGA 57.052 42.857 0.00 0.00 38.45 3.85
2345 2961 4.467198 AAACACGAGAGGGATAAACGAT 57.533 40.909 0.00 0.00 38.45 3.73
2346 2962 3.438297 ACACGAGAGGGATAAACGATG 57.562 47.619 0.00 0.00 38.45 3.84
2347 2963 2.758979 ACACGAGAGGGATAAACGATGT 59.241 45.455 0.00 0.00 38.45 3.06
2348 2964 3.949754 ACACGAGAGGGATAAACGATGTA 59.050 43.478 0.00 0.00 38.45 2.29
2349 2965 4.583489 ACACGAGAGGGATAAACGATGTAT 59.417 41.667 0.00 0.00 38.45 2.29
2350 2966 5.766670 ACACGAGAGGGATAAACGATGTATA 59.233 40.000 0.00 0.00 38.45 1.47
2351 2967 6.084925 CACGAGAGGGATAAACGATGTATAC 58.915 44.000 0.00 0.00 35.60 1.47
2355 2971 5.997384 AGGGATAAACGATGTATACCCTC 57.003 43.478 0.00 0.00 42.10 4.30
2358 2974 5.012354 GGGATAAACGATGTATACCCTCCAA 59.988 44.000 0.00 0.00 33.99 3.53
2359 2975 6.296259 GGGATAAACGATGTATACCCTCCAAT 60.296 42.308 0.00 0.00 33.99 3.16
2360 2976 6.817140 GGATAAACGATGTATACCCTCCAATC 59.183 42.308 0.00 0.00 0.00 2.67
2361 2977 3.936372 ACGATGTATACCCTCCAATCG 57.064 47.619 15.52 15.52 36.50 3.34
2363 2979 2.674177 CGATGTATACCCTCCAATCGGC 60.674 54.545 11.28 0.00 0.00 5.54
2364 2980 1.053424 TGTATACCCTCCAATCGGCC 58.947 55.000 0.00 0.00 0.00 6.13
2367 2983 2.040009 ATACCCTCCAATCGGCCACG 62.040 60.000 2.24 0.00 42.74 4.94
2404 3412 4.521062 AGCAGCCGCGACATCCTC 62.521 66.667 8.23 0.00 45.49 3.71
2408 3416 4.819761 GCCGCGACATCCTCAGCA 62.820 66.667 8.23 0.00 0.00 4.41
2409 3417 2.584418 CCGCGACATCCTCAGCAG 60.584 66.667 8.23 0.00 0.00 4.24
2411 3419 2.894387 GCGACATCCTCAGCAGCC 60.894 66.667 0.00 0.00 0.00 4.85
2412 3420 2.898738 CGACATCCTCAGCAGCCT 59.101 61.111 0.00 0.00 0.00 4.58
2413 3421 1.220206 CGACATCCTCAGCAGCCTT 59.780 57.895 0.00 0.00 0.00 4.35
2415 3423 0.540923 GACATCCTCAGCAGCCTTCT 59.459 55.000 0.00 0.00 0.00 2.85
2416 3424 0.990374 ACATCCTCAGCAGCCTTCTT 59.010 50.000 0.00 0.00 0.00 2.52
2417 3425 1.339824 ACATCCTCAGCAGCCTTCTTG 60.340 52.381 0.00 0.00 0.00 3.02
2418 3426 0.990374 ATCCTCAGCAGCCTTCTTGT 59.010 50.000 0.00 0.00 0.00 3.16
2419 3427 0.322975 TCCTCAGCAGCCTTCTTGTC 59.677 55.000 0.00 0.00 0.00 3.18
2420 3428 1.018226 CCTCAGCAGCCTTCTTGTCG 61.018 60.000 0.00 0.00 0.00 4.35
2421 3429 0.037882 CTCAGCAGCCTTCTTGTCGA 60.038 55.000 0.00 0.00 0.00 4.20
2422 3430 0.319900 TCAGCAGCCTTCTTGTCGAC 60.320 55.000 9.11 9.11 0.00 4.20
2423 3431 1.004440 AGCAGCCTTCTTGTCGACC 60.004 57.895 14.12 0.00 0.00 4.79
2424 3432 1.004440 GCAGCCTTCTTGTCGACCT 60.004 57.895 14.12 0.00 0.00 3.85
2425 3433 1.016653 GCAGCCTTCTTGTCGACCTC 61.017 60.000 14.12 0.00 0.00 3.85
2426 3434 0.318441 CAGCCTTCTTGTCGACCTCA 59.682 55.000 14.12 0.00 0.00 3.86
2427 3435 0.605589 AGCCTTCTTGTCGACCTCAG 59.394 55.000 14.12 6.63 0.00 3.35
2428 3436 1.016653 GCCTTCTTGTCGACCTCAGC 61.017 60.000 14.12 4.90 0.00 4.26
2429 3437 0.390472 CCTTCTTGTCGACCTCAGCC 60.390 60.000 14.12 0.00 0.00 4.85
2430 3438 0.605589 CTTCTTGTCGACCTCAGCCT 59.394 55.000 14.12 0.00 0.00 4.58
2431 3439 1.001406 CTTCTTGTCGACCTCAGCCTT 59.999 52.381 14.12 0.00 0.00 4.35
2432 3440 0.603569 TCTTGTCGACCTCAGCCTTC 59.396 55.000 14.12 0.00 0.00 3.46
2433 3441 0.605589 CTTGTCGACCTCAGCCTTCT 59.394 55.000 14.12 0.00 0.00 2.85
2434 3442 0.603569 TTGTCGACCTCAGCCTTCTC 59.396 55.000 14.12 0.00 0.00 2.87
2435 3443 0.539669 TGTCGACCTCAGCCTTCTCA 60.540 55.000 14.12 0.00 0.00 3.27
2436 3444 0.172352 GTCGACCTCAGCCTTCTCAG 59.828 60.000 3.51 0.00 0.00 3.35
2437 3445 1.153667 CGACCTCAGCCTTCTCAGC 60.154 63.158 0.00 0.00 0.00 4.26
2438 3446 1.153667 GACCTCAGCCTTCTCAGCG 60.154 63.158 0.00 0.00 34.64 5.18
2439 3447 2.186384 CCTCAGCCTTCTCAGCGG 59.814 66.667 0.00 0.00 34.64 5.52
2440 3448 2.511145 CTCAGCCTTCTCAGCGGC 60.511 66.667 0.00 0.00 46.65 6.53
2467 3475 4.771356 CGCGTCGGTCGACATGGT 62.771 66.667 18.91 0.00 44.77 3.55
2470 3478 1.138883 CGTCGGTCGACATGGTGAT 59.861 57.895 18.91 0.00 44.77 3.06
2471 3479 1.139816 CGTCGGTCGACATGGTGATG 61.140 60.000 18.91 8.13 44.77 3.07
2479 3487 1.404181 CGACATGGTGATGACGAAGGT 60.404 52.381 0.00 0.00 46.47 3.50
2483 3491 2.385013 TGGTGATGACGAAGGTGATG 57.615 50.000 0.00 0.00 0.00 3.07
2485 3493 0.647410 GTGATGACGAAGGTGATGCG 59.353 55.000 0.00 0.00 0.00 4.73
2486 3494 0.460109 TGATGACGAAGGTGATGCGG 60.460 55.000 0.00 0.00 0.00 5.69
2488 3496 0.460284 ATGACGAAGGTGATGCGGAC 60.460 55.000 0.00 0.00 0.00 4.79
2491 3499 1.138036 CGAAGGTGATGCGGACGTA 59.862 57.895 0.00 0.00 0.00 3.57
2492 3500 0.866061 CGAAGGTGATGCGGACGTAG 60.866 60.000 0.00 0.00 0.00 3.51
2493 3501 0.454600 GAAGGTGATGCGGACGTAGA 59.545 55.000 0.00 0.00 0.00 2.59
2494 3502 1.067212 GAAGGTGATGCGGACGTAGAT 59.933 52.381 0.00 0.00 0.00 1.98
2495 3503 0.385751 AGGTGATGCGGACGTAGATG 59.614 55.000 0.00 0.00 0.00 2.90
2497 3505 1.202371 GGTGATGCGGACGTAGATGAA 60.202 52.381 0.00 0.00 0.00 2.57
2498 3506 1.852895 GTGATGCGGACGTAGATGAAC 59.147 52.381 0.00 0.00 0.00 3.18
2500 3508 2.120232 GATGCGGACGTAGATGAACAG 58.880 52.381 0.00 0.00 0.00 3.16
2502 3510 1.542472 TGCGGACGTAGATGAACAGAA 59.458 47.619 0.00 0.00 0.00 3.02
2505 3513 2.186076 GGACGTAGATGAACAGAAGCG 58.814 52.381 0.00 0.00 0.00 4.68
2506 3514 2.159421 GGACGTAGATGAACAGAAGCGA 60.159 50.000 0.00 0.00 0.00 4.93
2507 3515 3.102276 GACGTAGATGAACAGAAGCGAG 58.898 50.000 0.00 0.00 0.00 5.03
2508 3516 1.849219 CGTAGATGAACAGAAGCGAGC 59.151 52.381 0.00 0.00 0.00 5.03
2510 3518 2.007360 AGATGAACAGAAGCGAGCAG 57.993 50.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 22 1.377202 CATCAACCCCTGTGTCCCG 60.377 63.158 0.00 0.00 0.00 5.14
24 26 0.112412 GGAACCATCAACCCCTGTGT 59.888 55.000 0.00 0.00 0.00 3.72
37 39 3.355378 CATGCTTCCATTGTAGGAACCA 58.645 45.455 0.00 0.00 42.56 3.67
39 41 3.378427 GTCCATGCTTCCATTGTAGGAAC 59.622 47.826 0.00 0.00 42.56 3.62
47 49 1.002069 TCAGGGTCCATGCTTCCATT 58.998 50.000 0.00 0.00 0.00 3.16
122 125 1.064017 ACATCACAACACACCAACCCT 60.064 47.619 0.00 0.00 0.00 4.34
293 296 5.066375 TGTCAATGACAAAGAACAAGACCAG 59.934 40.000 14.37 0.00 39.78 4.00
300 303 5.008911 CACTCCATGTCAATGACAAAGAACA 59.991 40.000 20.64 0.00 45.96 3.18
399 402 2.906897 CACCACTGGCGCCAAAGT 60.907 61.111 32.09 23.17 0.00 2.66
411 414 2.663852 CGTTCGTGTCCCCACCAC 60.664 66.667 0.00 0.00 38.41 4.16
448 451 1.002087 AGGAGAACCACAATGACGTCC 59.998 52.381 14.12 0.00 38.94 4.79
478 481 2.637521 GGTCTTCACCCGAAAACCC 58.362 57.895 0.00 0.00 36.40 4.11
488 491 1.070289 AGAACGGACAAGGGTCTTCAC 59.930 52.381 0.00 0.00 43.77 3.18
619 622 6.246332 CACTGAAACGTTTTAATCGCATGTAG 59.754 38.462 15.89 0.00 0.00 2.74
620 623 6.074642 CACTGAAACGTTTTAATCGCATGTA 58.925 36.000 15.89 0.00 0.00 2.29
621 624 4.909305 CACTGAAACGTTTTAATCGCATGT 59.091 37.500 15.89 0.48 0.00 3.21
765 770 1.595794 GTCGTGATCTCTCTCGTCTCC 59.404 57.143 0.00 0.00 38.98 3.71
779 784 2.732016 CTTCCACCACCGTCGTGA 59.268 61.111 0.00 0.00 43.14 4.35
840 865 7.183580 AGTTCTTTTCTTTGACGATTCTCAG 57.816 36.000 0.00 0.00 0.00 3.35
852 877 6.376581 CAGCATGGATAGGAGTTCTTTTCTTT 59.623 38.462 0.00 0.00 0.00 2.52
871 896 6.347725 GCTACGAAATTATAGAACCCAGCATG 60.348 42.308 0.00 0.00 0.00 4.06
932 958 0.727970 CGTGGTCGTGTCTCCTCTAG 59.272 60.000 0.00 0.00 0.00 2.43
933 959 0.322648 TCGTGGTCGTGTCTCCTCTA 59.677 55.000 0.00 0.00 38.33 2.43
947 983 2.383527 GGCTTGCTCGTTCTCGTGG 61.384 63.158 0.00 0.00 38.33 4.94
950 986 2.097038 CCTGGCTTGCTCGTTCTCG 61.097 63.158 0.00 0.00 38.55 4.04
951 987 1.743252 CCCTGGCTTGCTCGTTCTC 60.743 63.158 0.00 0.00 0.00 2.87
955 991 4.400961 GCTCCCTGGCTTGCTCGT 62.401 66.667 0.00 0.00 0.00 4.18
959 995 2.282745 AACTGCTCCCTGGCTTGC 60.283 61.111 0.00 0.00 0.00 4.01
965 1001 1.809271 CGATGGATCAACTGCTCCCTG 60.809 57.143 0.00 0.00 29.55 4.45
981 1017 0.597568 TCTTTGCTTGTTGGCCGATG 59.402 50.000 0.00 0.00 0.00 3.84
988 1024 4.806330 AAGATCTGCATCTTTGCTTGTTG 58.194 39.130 0.00 0.00 45.68 3.33
1050 1088 0.655915 CGATAGTGTCGCTGCTCTCG 60.656 60.000 0.00 0.00 44.33 4.04
1174 1288 2.540361 GCCTGCAATCGATAAGCAACAG 60.540 50.000 21.27 15.33 37.89 3.16
1216 1334 4.609995 TTCCCGGCGAAGATCAAC 57.390 55.556 9.30 0.00 0.00 3.18
1255 1373 0.535335 GGATGTTGTAGTCGGCCAGA 59.465 55.000 2.24 0.00 0.00 3.86
1612 1821 9.411189 CCTAGTAAGACTTAAGACTATCTTGGT 57.589 37.037 10.09 2.85 37.29 3.67
1613 1822 9.411189 ACCTAGTAAGACTTAAGACTATCTTGG 57.589 37.037 22.47 22.47 37.29 3.61
1647 2138 5.526111 GGACTAGTTCGCATGGCTTAATAAA 59.474 40.000 0.00 0.00 0.00 1.40
1648 2139 5.054477 GGACTAGTTCGCATGGCTTAATAA 58.946 41.667 0.00 0.00 0.00 1.40
1650 2141 3.467803 GGACTAGTTCGCATGGCTTAAT 58.532 45.455 0.00 0.00 0.00 1.40
1651 2142 2.737359 CGGACTAGTTCGCATGGCTTAA 60.737 50.000 11.35 0.00 0.00 1.85
1652 2143 1.202371 CGGACTAGTTCGCATGGCTTA 60.202 52.381 11.35 0.00 0.00 3.09
1655 2146 3.706140 CGGACTAGTTCGCATGGC 58.294 61.111 11.35 0.00 0.00 4.40
1661 2152 0.653897 GATCGACGCGGACTAGTTCG 60.654 60.000 19.64 19.64 0.00 3.95
1662 2153 0.653897 CGATCGACGCGGACTAGTTC 60.654 60.000 10.26 0.00 34.51 3.01
1664 2155 3.012399 CGATCGACGCGGACTAGT 58.988 61.111 10.26 0.00 34.51 2.57
1674 2197 1.328439 GATACACGCATCCGATCGAC 58.672 55.000 18.66 1.89 38.29 4.20
1746 2269 6.310224 ACGAAAAACAGACAAACAAAATCTGG 59.690 34.615 5.54 0.00 43.46 3.86
1783 2306 7.009174 GGTTGTGGCGTTCAGAAAATAATTATG 59.991 37.037 0.00 0.00 30.09 1.90
1811 2334 3.985279 TGTCGTTCAAGAGATTACGGTTG 59.015 43.478 0.00 0.00 34.93 3.77
1812 2335 4.235360 CTGTCGTTCAAGAGATTACGGTT 58.765 43.478 0.00 0.00 34.93 4.44
1830 2357 5.103290 TCCTTTGCGTCATTTTTACTGTC 57.897 39.130 0.00 0.00 0.00 3.51
1835 2362 6.980978 TGATTTGTTCCTTTGCGTCATTTTTA 59.019 30.769 0.00 0.00 0.00 1.52
1838 2365 4.942852 TGATTTGTTCCTTTGCGTCATTT 58.057 34.783 0.00 0.00 0.00 2.32
1860 2391 6.992063 CACAAGAAGAAGGTGTGCTTATAT 57.008 37.500 0.00 0.00 36.55 0.86
1941 2479 2.223340 CCCATACACGATGCTTTGCTTC 60.223 50.000 0.00 0.00 33.79 3.86
1980 2518 2.191513 CCAATCCAGCATGCTCCCG 61.192 63.158 19.68 6.92 31.97 5.14
2001 2543 2.244000 CGATGCCGTTCAGGTGTTT 58.756 52.632 0.00 0.00 43.70 2.83
2016 2558 3.568007 ACACAAGGCAAACAATACACGAT 59.432 39.130 0.00 0.00 0.00 3.73
2018 2560 3.347958 ACACAAGGCAAACAATACACG 57.652 42.857 0.00 0.00 0.00 4.49
2019 2561 4.429108 ACAACACAAGGCAAACAATACAC 58.571 39.130 0.00 0.00 0.00 2.90
2020 2562 4.400884 AGACAACACAAGGCAAACAATACA 59.599 37.500 0.00 0.00 0.00 2.29
2021 2563 4.932146 AGACAACACAAGGCAAACAATAC 58.068 39.130 0.00 0.00 0.00 1.89
2022 2564 4.642437 TGAGACAACACAAGGCAAACAATA 59.358 37.500 0.00 0.00 0.00 1.90
2032 2640 2.905075 TGACCACTGAGACAACACAAG 58.095 47.619 0.00 0.00 0.00 3.16
2132 2748 6.817765 TCGAAAAACTGCCTATTTTCTCAT 57.182 33.333 12.92 0.00 41.26 2.90
2134 2750 9.620660 TTTAATCGAAAAACTGCCTATTTTCTC 57.379 29.630 12.92 4.27 41.26 2.87
2142 2758 8.527810 TGGATTAATTTAATCGAAAAACTGCCT 58.472 29.630 18.38 0.00 44.24 4.75
2143 2759 8.696410 TGGATTAATTTAATCGAAAAACTGCC 57.304 30.769 18.38 6.28 44.24 4.85
2162 2778 9.523168 TCATGCTTATGATTCATTCATGGATTA 57.477 29.630 22.17 10.59 44.90 1.75
2163 2779 8.304596 GTCATGCTTATGATTCATTCATGGATT 58.695 33.333 22.17 0.00 44.90 3.01
2164 2780 7.450323 TGTCATGCTTATGATTCATTCATGGAT 59.550 33.333 22.17 8.70 44.90 3.41
2165 2781 6.773685 TGTCATGCTTATGATTCATTCATGGA 59.226 34.615 22.17 13.88 44.90 3.41
2166 2782 6.977213 TGTCATGCTTATGATTCATTCATGG 58.023 36.000 22.17 12.47 44.90 3.66
2168 2784 7.450323 TCCATGTCATGCTTATGATTCATTCAT 59.550 33.333 7.35 4.11 46.86 2.57
2169 2785 6.773685 TCCATGTCATGCTTATGATTCATTCA 59.226 34.615 7.35 1.95 39.12 2.57
2172 2788 6.066032 TGTCCATGTCATGCTTATGATTCAT 58.934 36.000 7.35 4.28 32.61 2.57
2174 2790 5.562307 GCTGTCCATGTCATGCTTATGATTC 60.562 44.000 7.35 0.00 32.61 2.52
2175 2791 4.277672 GCTGTCCATGTCATGCTTATGATT 59.722 41.667 7.35 0.00 32.61 2.57
2178 2794 2.946990 TGCTGTCCATGTCATGCTTATG 59.053 45.455 7.35 0.00 0.00 1.90
2180 2796 2.785540 TGCTGTCCATGTCATGCTTA 57.214 45.000 7.35 0.00 0.00 3.09
2183 2799 1.746787 TCAATGCTGTCCATGTCATGC 59.253 47.619 7.35 0.00 33.49 4.06
2184 2800 5.066764 TGTTATCAATGCTGTCCATGTCATG 59.933 40.000 5.79 5.79 33.49 3.07
2186 2802 4.395854 GTGTTATCAATGCTGTCCATGTCA 59.604 41.667 0.00 0.00 33.49 3.58
2187 2803 4.395854 TGTGTTATCAATGCTGTCCATGTC 59.604 41.667 0.00 0.00 33.49 3.06
2189 2805 4.397103 AGTGTGTTATCAATGCTGTCCATG 59.603 41.667 0.00 0.00 33.49 3.66
2191 2807 3.752747 CAGTGTGTTATCAATGCTGTCCA 59.247 43.478 0.00 0.00 0.00 4.02
2194 2810 6.654582 TGTAATCAGTGTGTTATCAATGCTGT 59.345 34.615 0.00 0.00 34.12 4.40
2195 2811 7.075674 TGTAATCAGTGTGTTATCAATGCTG 57.924 36.000 0.00 0.00 34.12 4.41
2196 2812 7.686438 TTGTAATCAGTGTGTTATCAATGCT 57.314 32.000 0.00 0.00 34.12 3.79
2197 2813 8.400947 AGATTGTAATCAGTGTGTTATCAATGC 58.599 33.333 7.30 0.00 37.89 3.56
2201 2817 9.936759 TGTTAGATTGTAATCAGTGTGTTATCA 57.063 29.630 7.30 0.00 37.89 2.15
2203 2819 8.883731 GCTGTTAGATTGTAATCAGTGTGTTAT 58.116 33.333 7.30 0.00 37.89 1.89
2206 2822 5.643777 GGCTGTTAGATTGTAATCAGTGTGT 59.356 40.000 7.30 0.00 37.89 3.72
2207 2823 5.065218 GGGCTGTTAGATTGTAATCAGTGTG 59.935 44.000 7.30 0.00 37.89 3.82
2209 2825 4.576463 GGGGCTGTTAGATTGTAATCAGTG 59.424 45.833 7.30 0.00 37.89 3.66
2210 2826 4.683400 CGGGGCTGTTAGATTGTAATCAGT 60.683 45.833 7.30 0.00 37.89 3.41
2211 2827 3.809832 CGGGGCTGTTAGATTGTAATCAG 59.190 47.826 7.30 0.00 37.89 2.90
2212 2828 3.804036 CGGGGCTGTTAGATTGTAATCA 58.196 45.455 7.30 0.00 37.89 2.57
2213 2829 2.548480 GCGGGGCTGTTAGATTGTAATC 59.452 50.000 0.00 0.00 35.64 1.75
2215 2831 1.279558 TGCGGGGCTGTTAGATTGTAA 59.720 47.619 0.00 0.00 0.00 2.41
2216 2832 0.906066 TGCGGGGCTGTTAGATTGTA 59.094 50.000 0.00 0.00 0.00 2.41
2217 2833 0.037590 TTGCGGGGCTGTTAGATTGT 59.962 50.000 0.00 0.00 0.00 2.71
2219 2835 1.917872 TTTTGCGGGGCTGTTAGATT 58.082 45.000 0.00 0.00 0.00 2.40
2220 2836 1.917872 TTTTTGCGGGGCTGTTAGAT 58.082 45.000 0.00 0.00 0.00 1.98
2221 2837 3.423344 TTTTTGCGGGGCTGTTAGA 57.577 47.368 0.00 0.00 0.00 2.10
2239 2855 8.186821 GCATGCTCTGTTAGATTGTAATCTTTT 58.813 33.333 11.37 0.00 42.96 2.27
2240 2856 7.555554 AGCATGCTCTGTTAGATTGTAATCTTT 59.444 33.333 16.30 0.00 42.96 2.52
2241 2857 7.012138 CAGCATGCTCTGTTAGATTGTAATCTT 59.988 37.037 19.68 0.00 42.96 2.40
2242 2858 6.482641 CAGCATGCTCTGTTAGATTGTAATCT 59.517 38.462 19.68 11.48 46.85 2.40
2243 2859 6.259608 ACAGCATGCTCTGTTAGATTGTAATC 59.740 38.462 19.68 0.00 44.26 1.75
2244 2860 6.118170 ACAGCATGCTCTGTTAGATTGTAAT 58.882 36.000 19.68 0.00 44.26 1.89
2245 2861 5.491070 ACAGCATGCTCTGTTAGATTGTAA 58.509 37.500 19.68 0.00 44.26 2.41
2246 2862 5.089970 ACAGCATGCTCTGTTAGATTGTA 57.910 39.130 19.68 0.00 44.26 2.41
2247 2863 3.947868 ACAGCATGCTCTGTTAGATTGT 58.052 40.909 19.68 6.65 44.26 2.71
2248 2864 5.114780 AGTACAGCATGCTCTGTTAGATTG 58.885 41.667 19.68 5.93 44.26 2.67
2249 2865 5.350504 AGTACAGCATGCTCTGTTAGATT 57.649 39.130 19.68 0.00 44.26 2.40
2250 2866 5.506483 CGTAGTACAGCATGCTCTGTTAGAT 60.506 44.000 19.68 4.54 44.26 1.98
2251 2867 4.201920 CGTAGTACAGCATGCTCTGTTAGA 60.202 45.833 19.68 0.00 44.26 2.10
2252 2868 4.038361 CGTAGTACAGCATGCTCTGTTAG 58.962 47.826 19.68 8.18 44.26 2.34
2253 2869 3.733988 GCGTAGTACAGCATGCTCTGTTA 60.734 47.826 19.68 5.83 44.26 2.41
2254 2870 2.881074 CGTAGTACAGCATGCTCTGTT 58.119 47.619 19.68 6.88 44.26 3.16
2256 2872 1.203928 GCGTAGTACAGCATGCTCTG 58.796 55.000 19.68 11.67 42.53 3.35
2257 2873 0.817654 TGCGTAGTACAGCATGCTCT 59.182 50.000 19.68 14.93 42.53 4.09
2258 2874 0.924090 GTGCGTAGTACAGCATGCTC 59.076 55.000 19.68 7.05 45.69 4.26
2259 2875 3.050703 GTGCGTAGTACAGCATGCT 57.949 52.632 16.30 16.30 45.69 3.79
2267 2883 7.416022 AGATGTTTCTACTATGTGCGTAGTAC 58.584 38.462 7.08 0.00 45.46 2.73
2268 2884 7.563888 AGATGTTTCTACTATGTGCGTAGTA 57.436 36.000 9.97 9.97 36.39 1.82
2269 2885 6.452494 AGATGTTTCTACTATGTGCGTAGT 57.548 37.500 8.83 8.83 38.42 2.73
2285 2901 9.894783 CAGTACTAGCAATATACGTAGATGTTT 57.105 33.333 2.98 0.00 0.00 2.83
2286 2902 8.021973 GCAGTACTAGCAATATACGTAGATGTT 58.978 37.037 2.98 1.99 0.00 2.71
2287 2903 7.390996 AGCAGTACTAGCAATATACGTAGATGT 59.609 37.037 16.27 0.00 0.00 3.06
2288 2904 7.753659 AGCAGTACTAGCAATATACGTAGATG 58.246 38.462 16.27 2.28 0.00 2.90
2289 2905 7.925043 AGCAGTACTAGCAATATACGTAGAT 57.075 36.000 16.27 0.00 0.00 1.98
2290 2906 7.874528 TGTAGCAGTACTAGCAATATACGTAGA 59.125 37.037 16.27 0.00 0.00 2.59
2291 2907 8.026341 TGTAGCAGTACTAGCAATATACGTAG 57.974 38.462 16.27 0.00 0.00 3.51
2292 2908 7.967890 TGTAGCAGTACTAGCAATATACGTA 57.032 36.000 16.27 0.00 0.00 3.57
2293 2909 6.872628 TGTAGCAGTACTAGCAATATACGT 57.127 37.500 16.27 0.00 0.00 3.57
2294 2910 7.136772 TGTTGTAGCAGTACTAGCAATATACG 58.863 38.462 16.27 0.00 30.15 3.06
2295 2911 8.350722 TCTGTTGTAGCAGTACTAGCAATATAC 58.649 37.037 16.27 11.24 37.70 1.47
2296 2912 8.459911 TCTGTTGTAGCAGTACTAGCAATATA 57.540 34.615 16.27 1.75 37.70 0.86
2297 2913 7.348080 TCTGTTGTAGCAGTACTAGCAATAT 57.652 36.000 16.27 2.50 37.70 1.28
2298 2914 6.769134 TCTGTTGTAGCAGTACTAGCAATA 57.231 37.500 16.27 7.99 37.70 1.90
2299 2915 5.661056 TCTGTTGTAGCAGTACTAGCAAT 57.339 39.130 16.27 3.33 37.70 3.56
2300 2916 5.462530 TTCTGTTGTAGCAGTACTAGCAA 57.537 39.130 16.27 7.84 37.70 3.91
2301 2917 5.462530 TTTCTGTTGTAGCAGTACTAGCA 57.537 39.130 16.27 0.63 37.70 3.49
2322 2938 4.634199 TCGTTTATCCCTCTCGTGTTTTT 58.366 39.130 0.00 0.00 0.00 1.94
2323 2939 4.261578 TCGTTTATCCCTCTCGTGTTTT 57.738 40.909 0.00 0.00 0.00 2.43
2325 2941 3.194968 ACATCGTTTATCCCTCTCGTGTT 59.805 43.478 0.00 0.00 0.00 3.32
2329 2945 5.392811 GGGTATACATCGTTTATCCCTCTCG 60.393 48.000 5.01 0.00 0.00 4.04
2331 2947 5.652324 AGGGTATACATCGTTTATCCCTCT 58.348 41.667 5.01 0.00 39.68 3.69
2332 2948 5.997384 AGGGTATACATCGTTTATCCCTC 57.003 43.478 5.01 0.00 39.68 4.30
2334 2950 4.529377 TGGAGGGTATACATCGTTTATCCC 59.471 45.833 5.01 0.00 0.00 3.85
2335 2951 5.733620 TGGAGGGTATACATCGTTTATCC 57.266 43.478 5.01 1.02 0.00 2.59
2336 2952 6.530534 CGATTGGAGGGTATACATCGTTTATC 59.469 42.308 5.01 0.00 0.00 1.75
2337 2953 6.395629 CGATTGGAGGGTATACATCGTTTAT 58.604 40.000 5.01 0.00 0.00 1.40
2338 2954 5.279106 CCGATTGGAGGGTATACATCGTTTA 60.279 44.000 15.62 0.00 37.49 2.01
2339 2955 4.502604 CCGATTGGAGGGTATACATCGTTT 60.503 45.833 15.62 0.00 37.49 3.60
2340 2956 3.006537 CCGATTGGAGGGTATACATCGTT 59.993 47.826 15.62 0.21 37.49 3.85
2341 2957 2.561419 CCGATTGGAGGGTATACATCGT 59.439 50.000 15.62 0.00 37.49 3.73
2342 2958 2.674177 GCCGATTGGAGGGTATACATCG 60.674 54.545 1.98 9.25 37.49 3.84
2343 2959 2.354805 GGCCGATTGGAGGGTATACATC 60.355 54.545 1.98 2.10 37.49 3.06
2344 2960 1.628846 GGCCGATTGGAGGGTATACAT 59.371 52.381 1.98 0.00 37.49 2.29
2345 2961 1.053424 GGCCGATTGGAGGGTATACA 58.947 55.000 1.98 0.00 37.49 2.29
2346 2962 1.053424 TGGCCGATTGGAGGGTATAC 58.947 55.000 1.98 0.00 37.49 1.47
2347 2963 1.053424 GTGGCCGATTGGAGGGTATA 58.947 55.000 1.98 0.00 37.49 1.47
2348 2964 1.837090 GTGGCCGATTGGAGGGTAT 59.163 57.895 1.98 0.00 37.49 2.73
2349 2965 2.727392 CGTGGCCGATTGGAGGGTA 61.727 63.158 1.98 0.00 37.49 3.69
2350 2966 4.096003 CGTGGCCGATTGGAGGGT 62.096 66.667 1.98 0.00 37.49 4.34
2386 3002 4.827087 AGGATGTCGCGGCTGCTG 62.827 66.667 17.03 9.49 39.65 4.41
2387 3003 4.521062 GAGGATGTCGCGGCTGCT 62.521 66.667 17.03 8.19 39.65 4.24
2388 3004 4.819761 TGAGGATGTCGCGGCTGC 62.820 66.667 13.81 7.70 37.91 5.25
2391 3399 4.819761 TGCTGAGGATGTCGCGGC 62.820 66.667 2.29 2.29 45.94 6.53
2396 3404 0.540923 AGAAGGCTGCTGAGGATGTC 59.459 55.000 0.00 0.00 0.00 3.06
2402 3410 0.037882 TCGACAAGAAGGCTGCTGAG 60.038 55.000 0.00 0.00 0.00 3.35
2404 3412 1.294659 GGTCGACAAGAAGGCTGCTG 61.295 60.000 18.91 0.00 0.00 4.41
2408 3416 0.605589 CTGAGGTCGACAAGAAGGCT 59.394 55.000 18.91 2.61 0.00 4.58
2409 3417 1.016653 GCTGAGGTCGACAAGAAGGC 61.017 60.000 18.91 9.50 0.00 4.35
2411 3419 0.605589 AGGCTGAGGTCGACAAGAAG 59.394 55.000 18.91 9.87 0.00 2.85
2412 3420 1.000955 GAAGGCTGAGGTCGACAAGAA 59.999 52.381 18.91 0.00 0.00 2.52
2413 3421 0.603569 GAAGGCTGAGGTCGACAAGA 59.396 55.000 18.91 0.00 0.00 3.02
2415 3423 0.603569 GAGAAGGCTGAGGTCGACAA 59.396 55.000 18.91 1.00 0.00 3.18
2416 3424 0.539669 TGAGAAGGCTGAGGTCGACA 60.540 55.000 18.91 0.00 0.00 4.35
2417 3425 0.172352 CTGAGAAGGCTGAGGTCGAC 59.828 60.000 7.13 7.13 0.00 4.20
2418 3426 1.599606 GCTGAGAAGGCTGAGGTCGA 61.600 60.000 0.00 0.00 0.00 4.20
2419 3427 1.153667 GCTGAGAAGGCTGAGGTCG 60.154 63.158 0.00 0.00 0.00 4.79
2420 3428 1.153667 CGCTGAGAAGGCTGAGGTC 60.154 63.158 0.00 0.00 0.00 3.85
2421 3429 2.654079 CCGCTGAGAAGGCTGAGGT 61.654 63.158 0.00 0.00 0.00 3.85
2422 3430 2.186384 CCGCTGAGAAGGCTGAGG 59.814 66.667 0.00 0.00 0.00 3.86
2453 3461 0.172578 TCATCACCATGTCGACCGAC 59.827 55.000 14.12 14.88 44.77 4.79
2454 3462 0.172578 GTCATCACCATGTCGACCGA 59.827 55.000 14.12 2.20 0.00 4.69
2455 3463 1.139816 CGTCATCACCATGTCGACCG 61.140 60.000 14.12 3.93 42.17 4.79
2456 3464 0.172578 TCGTCATCACCATGTCGACC 59.827 55.000 14.12 0.00 42.97 4.79
2457 3465 1.920574 CTTCGTCATCACCATGTCGAC 59.079 52.381 9.11 9.11 45.99 4.20
2458 3466 1.135112 CCTTCGTCATCACCATGTCGA 60.135 52.381 1.06 1.06 45.11 4.20
2459 3467 1.280982 CCTTCGTCATCACCATGTCG 58.719 55.000 0.00 0.00 41.30 4.35
2460 3468 2.002586 CACCTTCGTCATCACCATGTC 58.997 52.381 0.00 0.00 0.00 3.06
2467 3475 0.460109 CCGCATCACCTTCGTCATCA 60.460 55.000 0.00 0.00 0.00 3.07
2470 3478 1.080093 GTCCGCATCACCTTCGTCA 60.080 57.895 0.00 0.00 0.00 4.35
2471 3479 2.158959 CGTCCGCATCACCTTCGTC 61.159 63.158 0.00 0.00 0.00 4.20
2477 3485 0.384309 TCATCTACGTCCGCATCACC 59.616 55.000 0.00 0.00 0.00 4.02
2479 3487 1.474879 TGTTCATCTACGTCCGCATCA 59.525 47.619 0.00 0.00 0.00 3.07
2483 3491 2.186076 CTTCTGTTCATCTACGTCCGC 58.814 52.381 0.00 0.00 0.00 5.54
2485 3493 2.159421 TCGCTTCTGTTCATCTACGTCC 60.159 50.000 0.00 0.00 0.00 4.79
2486 3494 3.102276 CTCGCTTCTGTTCATCTACGTC 58.898 50.000 0.00 0.00 0.00 4.34
2488 3496 1.849219 GCTCGCTTCTGTTCATCTACG 59.151 52.381 0.00 0.00 0.00 3.51
2491 3499 2.007360 CTGCTCGCTTCTGTTCATCT 57.993 50.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.