Multiple sequence alignment - TraesCS6B01G087900

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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 TraesCS6B01G087900 chr6B 100.000 3861 0 0 1 3861 63712555 63716415 0.000000e+00 7131
1 TraesCS6B01G087900 chr6B 88.023 1027 47 17 1 952 164572363 164573388 0.000000e+00 1146
2 TraesCS6B01G087900 chr6B 76.391 1186 221 38 973 2113 63214000 63215171 5.560000e-163 584
3 TraesCS6B01G087900 chr6B 76.391 1186 221 38 973 2113 63245022 63246193 5.560000e-163 584
4 TraesCS6B01G087900 chr6B 77.833 803 117 32 1141 1917 77738647 77737880 1.270000e-119 440
5 TraesCS6B01G087900 chr6B 75.503 596 126 17 1019 1601 60593847 60594435 1.370000e-69 274
6 TraesCS6B01G087900 chr6B 75.395 569 105 25 1024 1576 81008065 81008614 3.850000e-60 243
7 TraesCS6B01G087900 chr6B 74.752 606 106 25 1019 1590 77841566 77840974 1.080000e-55 228
8 TraesCS6B01G087900 chr6B 72.711 568 103 38 1059 1606 57910696 57910161 4.020000e-30 143
9 TraesCS6B01G087900 chr6B 77.032 283 39 19 1325 1591 62119438 62119710 5.200000e-29 139
10 TraesCS6B01G087900 chr6B 79.470 151 27 4 1360 1508 60623285 60623433 1.900000e-18 104
11 TraesCS6B01G087900 chr2B 92.004 988 42 12 1 953 500278745 500279730 0.000000e+00 1352
12 TraesCS6B01G087900 chr2B 93.553 698 37 8 2878 3570 744771777 744772471 0.000000e+00 1033
13 TraesCS6B01G087900 chr2B 85.987 785 66 23 3081 3861 205065141 205064397 0.000000e+00 800
14 TraesCS6B01G087900 chr2B 85.478 785 71 17 3081 3861 68641902 68642647 0.000000e+00 778
15 TraesCS6B01G087900 chr1A 92.789 943 50 10 2931 3861 592522497 592523433 0.000000e+00 1349
16 TraesCS6B01G087900 chr1A 93.147 715 44 5 2871 3582 534516545 534517257 0.000000e+00 1044
17 TraesCS6B01G087900 chr1A 82.808 698 73 27 3169 3861 309454515 309453860 7.190000e-162 580
18 TraesCS6B01G087900 chr7B 91.405 989 44 13 1 952 477373102 477372118 0.000000e+00 1317
19 TraesCS6B01G087900 chr7B 91.800 939 44 10 34 953 633321824 633322748 0.000000e+00 1277
20 TraesCS6B01G087900 chr1B 90.653 995 47 15 1 953 473219078 473220068 0.000000e+00 1280
21 TraesCS6B01G087900 chr1B 90.423 992 41 11 1 953 595461141 595462117 0.000000e+00 1256
22 TraesCS6B01G087900 chr1B 94.774 708 33 4 2878 3581 522705705 522704998 0.000000e+00 1099
23 TraesCS6B01G087900 chr1B 93.931 692 37 4 2878 3565 314085379 314086069 0.000000e+00 1040
24 TraesCS6B01G087900 chr1B 87.896 694 62 15 158 843 567683381 567682702 0.000000e+00 797
25 TraesCS6B01G087900 chr1B 81.560 141 14 8 809 947 35638162 35638032 5.280000e-19 106
26 TraesCS6B01G087900 chr5B 90.287 1009 44 17 1 955 511314515 511315523 0.000000e+00 1271
27 TraesCS6B01G087900 chr5B 87.725 1002 87 20 2875 3861 38934438 38935418 0.000000e+00 1136
28 TraesCS6B01G087900 chr5B 90.883 702 40 14 3162 3859 190543095 190542414 0.000000e+00 920
29 TraesCS6B01G087900 chr5B 88.554 332 11 7 648 953 641398207 641397877 1.010000e-100 377
30 TraesCS6B01G087900 chr4B 94.901 706 33 3 2877 3579 515442758 515443463 0.000000e+00 1101
31 TraesCS6B01G087900 chr4B 85.864 382 11 6 616 954 578035545 578035926 2.190000e-97 366
32 TraesCS6B01G087900 chr3A 94.618 706 37 1 2878 3582 418683974 418683269 0.000000e+00 1092
33 TraesCS6B01G087900 chr3A 88.018 651 61 15 158 797 580810088 580809444 0.000000e+00 754
34 TraesCS6B01G087900 chr3B 94.484 707 37 2 2878 3582 815754836 815754130 0.000000e+00 1088
35 TraesCS6B01G087900 chr3B 94.469 687 36 2 2878 3562 524256865 524257551 0.000000e+00 1057
36 TraesCS6B01G087900 chr3B 92.857 252 18 0 3610 3861 697515047 697515298 2.190000e-97 366
37 TraesCS6B01G087900 chr5D 89.635 849 68 16 1 841 493410221 493411057 0.000000e+00 1062
38 TraesCS6B01G087900 chr7A 92.655 708 48 4 2878 3582 514265369 514266075 0.000000e+00 1016
39 TraesCS6B01G087900 chr5A 88.848 807 72 15 44 841 85170954 85171751 0.000000e+00 976
40 TraesCS6B01G087900 chr5A 85.265 699 74 25 158 841 123285911 123286595 0.000000e+00 693
41 TraesCS6B01G087900 chr2D 85.924 952 87 21 2922 3861 123706362 123707278 0.000000e+00 972
42 TraesCS6B01G087900 chr2D 88.906 640 56 14 157 786 394652949 394652315 0.000000e+00 774
43 TraesCS6B01G087900 chrUn 81.144 1119 169 23 1005 2093 112931938 112933044 0.000000e+00 859
44 TraesCS6B01G087900 chrUn 80.060 993 142 33 1137 2113 112855381 112856333 0.000000e+00 686
45 TraesCS6B01G087900 chrUn 76.686 1201 206 51 973 2113 102522669 102521483 1.990000e-167 599
46 TraesCS6B01G087900 chrUn 81.908 608 76 19 2301 2877 112933256 112933860 2.090000e-132 483
47 TraesCS6B01G087900 chrUn 78.892 668 73 33 2132 2747 112856413 112857064 1.300000e-104 390
48 TraesCS6B01G087900 chrUn 75.336 596 124 15 1019 1601 26705193 26704608 8.220000e-67 265
49 TraesCS6B01G087900 chrUn 75.923 569 104 23 1023 1576 27038636 27039186 1.060000e-65 261
50 TraesCS6B01G087900 chrUn 75.084 594 101 25 1019 1578 265564642 265565222 2.320000e-57 233
51 TraesCS6B01G087900 chrUn 74.746 590 104 23 1034 1590 328345535 328344958 5.020000e-54 222
52 TraesCS6B01G087900 chrUn 85.401 137 19 1 2742 2877 112857190 112857326 1.450000e-29 141
53 TraesCS6B01G087900 chr3D 91.456 632 41 13 158 780 172620480 172619853 0.000000e+00 856
54 TraesCS6B01G087900 chr6D 86.107 727 57 19 3139 3861 436156868 436157554 0.000000e+00 743
55 TraesCS6B01G087900 chr6D 76.717 597 109 26 1018 1601 27711114 27711693 4.850000e-79 305
56 TraesCS6B01G087900 chr6D 76.382 597 119 18 1018 1600 27683719 27683131 6.270000e-78 302
57 TraesCS6B01G087900 chr6D 75.889 506 101 18 1015 1508 29094585 29094089 4.990000e-59 239
58 TraesCS6B01G087900 chr6D 74.118 595 114 29 1026 1606 29875223 29875791 3.910000e-50 209
59 TraesCS6B01G087900 chr6A 78.571 504 91 16 1016 1511 30422631 30423125 2.240000e-82 316
60 TraesCS6B01G087900 chr6A 80.495 364 61 9 2522 2877 34526181 34526542 1.770000e-68 270
61 TraesCS6B01G087900 chr6A 75.747 569 103 26 1023 1575 47139837 47140386 1.780000e-63 254
62 TraesCS6B01G087900 chr6A 75.299 502 106 16 1016 1508 33529921 33530413 1.400000e-54 224


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 TraesCS6B01G087900 chr6B 63712555 63716415 3860 False 7131.000000 7131 100.000 1 3861 1 chr6B.!!$F6 3860
1 TraesCS6B01G087900 chr6B 164572363 164573388 1025 False 1146.000000 1146 88.023 1 952 1 chr6B.!!$F8 951
2 TraesCS6B01G087900 chr6B 63214000 63215171 1171 False 584.000000 584 76.391 973 2113 1 chr6B.!!$F4 1140
3 TraesCS6B01G087900 chr6B 63245022 63246193 1171 False 584.000000 584 76.391 973 2113 1 chr6B.!!$F5 1140
4 TraesCS6B01G087900 chr6B 77737880 77738647 767 True 440.000000 440 77.833 1141 1917 1 chr6B.!!$R2 776
5 TraesCS6B01G087900 chr6B 60593847 60594435 588 False 274.000000 274 75.503 1019 1601 1 chr6B.!!$F1 582
6 TraesCS6B01G087900 chr6B 81008065 81008614 549 False 243.000000 243 75.395 1024 1576 1 chr6B.!!$F7 552
7 TraesCS6B01G087900 chr6B 77840974 77841566 592 True 228.000000 228 74.752 1019 1590 1 chr6B.!!$R3 571
8 TraesCS6B01G087900 chr2B 500278745 500279730 985 False 1352.000000 1352 92.004 1 953 1 chr2B.!!$F2 952
9 TraesCS6B01G087900 chr2B 744771777 744772471 694 False 1033.000000 1033 93.553 2878 3570 1 chr2B.!!$F3 692
10 TraesCS6B01G087900 chr2B 205064397 205065141 744 True 800.000000 800 85.987 3081 3861 1 chr2B.!!$R1 780
11 TraesCS6B01G087900 chr2B 68641902 68642647 745 False 778.000000 778 85.478 3081 3861 1 chr2B.!!$F1 780
12 TraesCS6B01G087900 chr1A 592522497 592523433 936 False 1349.000000 1349 92.789 2931 3861 1 chr1A.!!$F2 930
13 TraesCS6B01G087900 chr1A 534516545 534517257 712 False 1044.000000 1044 93.147 2871 3582 1 chr1A.!!$F1 711
14 TraesCS6B01G087900 chr1A 309453860 309454515 655 True 580.000000 580 82.808 3169 3861 1 chr1A.!!$R1 692
15 TraesCS6B01G087900 chr7B 477372118 477373102 984 True 1317.000000 1317 91.405 1 952 1 chr7B.!!$R1 951
16 TraesCS6B01G087900 chr7B 633321824 633322748 924 False 1277.000000 1277 91.800 34 953 1 chr7B.!!$F1 919
17 TraesCS6B01G087900 chr1B 473219078 473220068 990 False 1280.000000 1280 90.653 1 953 1 chr1B.!!$F2 952
18 TraesCS6B01G087900 chr1B 595461141 595462117 976 False 1256.000000 1256 90.423 1 953 1 chr1B.!!$F3 952
19 TraesCS6B01G087900 chr1B 522704998 522705705 707 True 1099.000000 1099 94.774 2878 3581 1 chr1B.!!$R2 703
20 TraesCS6B01G087900 chr1B 314085379 314086069 690 False 1040.000000 1040 93.931 2878 3565 1 chr1B.!!$F1 687
21 TraesCS6B01G087900 chr1B 567682702 567683381 679 True 797.000000 797 87.896 158 843 1 chr1B.!!$R3 685
22 TraesCS6B01G087900 chr5B 511314515 511315523 1008 False 1271.000000 1271 90.287 1 955 1 chr5B.!!$F2 954
23 TraesCS6B01G087900 chr5B 38934438 38935418 980 False 1136.000000 1136 87.725 2875 3861 1 chr5B.!!$F1 986
24 TraesCS6B01G087900 chr5B 190542414 190543095 681 True 920.000000 920 90.883 3162 3859 1 chr5B.!!$R1 697
25 TraesCS6B01G087900 chr4B 515442758 515443463 705 False 1101.000000 1101 94.901 2877 3579 1 chr4B.!!$F1 702
26 TraesCS6B01G087900 chr3A 418683269 418683974 705 True 1092.000000 1092 94.618 2878 3582 1 chr3A.!!$R1 704
27 TraesCS6B01G087900 chr3A 580809444 580810088 644 True 754.000000 754 88.018 158 797 1 chr3A.!!$R2 639
28 TraesCS6B01G087900 chr3B 815754130 815754836 706 True 1088.000000 1088 94.484 2878 3582 1 chr3B.!!$R1 704
29 TraesCS6B01G087900 chr3B 524256865 524257551 686 False 1057.000000 1057 94.469 2878 3562 1 chr3B.!!$F1 684
30 TraesCS6B01G087900 chr5D 493410221 493411057 836 False 1062.000000 1062 89.635 1 841 1 chr5D.!!$F1 840
31 TraesCS6B01G087900 chr7A 514265369 514266075 706 False 1016.000000 1016 92.655 2878 3582 1 chr7A.!!$F1 704
32 TraesCS6B01G087900 chr5A 85170954 85171751 797 False 976.000000 976 88.848 44 841 1 chr5A.!!$F1 797
33 TraesCS6B01G087900 chr5A 123285911 123286595 684 False 693.000000 693 85.265 158 841 1 chr5A.!!$F2 683
34 TraesCS6B01G087900 chr2D 123706362 123707278 916 False 972.000000 972 85.924 2922 3861 1 chr2D.!!$F1 939
35 TraesCS6B01G087900 chr2D 394652315 394652949 634 True 774.000000 774 88.906 157 786 1 chr2D.!!$R1 629
36 TraesCS6B01G087900 chrUn 112931938 112933860 1922 False 671.000000 859 81.526 1005 2877 2 chrUn.!!$F4 1872
37 TraesCS6B01G087900 chrUn 102521483 102522669 1186 True 599.000000 599 76.686 973 2113 1 chrUn.!!$R2 1140
38 TraesCS6B01G087900 chrUn 112855381 112857326 1945 False 405.666667 686 81.451 1137 2877 3 chrUn.!!$F3 1740
39 TraesCS6B01G087900 chrUn 26704608 26705193 585 True 265.000000 265 75.336 1019 1601 1 chrUn.!!$R1 582
40 TraesCS6B01G087900 chrUn 27038636 27039186 550 False 261.000000 261 75.923 1023 1576 1 chrUn.!!$F1 553
41 TraesCS6B01G087900 chrUn 265564642 265565222 580 False 233.000000 233 75.084 1019 1578 1 chrUn.!!$F2 559
42 TraesCS6B01G087900 chrUn 328344958 328345535 577 True 222.000000 222 74.746 1034 1590 1 chrUn.!!$R3 556
43 TraesCS6B01G087900 chr3D 172619853 172620480 627 True 856.000000 856 91.456 158 780 1 chr3D.!!$R1 622
44 TraesCS6B01G087900 chr6D 436156868 436157554 686 False 743.000000 743 86.107 3139 3861 1 chr6D.!!$F3 722
45 TraesCS6B01G087900 chr6D 27711114 27711693 579 False 305.000000 305 76.717 1018 1601 1 chr6D.!!$F1 583
46 TraesCS6B01G087900 chr6D 27683131 27683719 588 True 302.000000 302 76.382 1018 1600 1 chr6D.!!$R1 582
47 TraesCS6B01G087900 chr6D 29875223 29875791 568 False 209.000000 209 74.118 1026 1606 1 chr6D.!!$F2 580
48 TraesCS6B01G087900 chr6A 47139837 47140386 549 False 254.000000 254 75.747 1023 1575 1 chr6A.!!$F4 552

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
969 1214 0.035820 TCCCACTAAACACATCCCGC 60.036 55.0 0.00 0.00 0.00 6.13 F
2004 2348 0.036164 TCCTGTGGACATTGAACGGG 59.964 55.0 9.21 9.21 41.03 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2769 0.249911 AGAGAAACCACGCCACAGTC 60.250 55.0 0.00 0.0 0.00 3.51 R
3435 4063 1.093972 CCAACGCATCTATGTGGCAA 58.906 50.0 8.28 0.0 42.35 4.52 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
148 149 4.047822 CCAAGAACAAATTTGTAAGCGCA 58.952 39.130 23.53 0.00 41.31 6.09
232 341 7.489113 TCTTGAGAACAAAATTTGAAACAGAGC 59.511 33.333 13.19 0.00 35.49 4.09
328 443 1.978782 GAACAAATTTGGAAGCGCGAG 59.021 47.619 21.74 0.00 0.00 5.03
853 1097 0.178975 AAACCGGATTGGGCAGTTGA 60.179 50.000 9.46 0.00 44.64 3.18
955 1200 1.681264 CGGCCAATAGGAAATTCCCAC 59.319 52.381 8.66 0.00 37.19 4.61
956 1201 2.686715 CGGCCAATAGGAAATTCCCACT 60.687 50.000 8.66 0.00 37.19 4.00
957 1202 3.434453 CGGCCAATAGGAAATTCCCACTA 60.434 47.826 8.66 0.00 37.19 2.74
958 1203 4.542697 GGCCAATAGGAAATTCCCACTAA 58.457 43.478 8.66 0.00 37.19 2.24
959 1204 4.959839 GGCCAATAGGAAATTCCCACTAAA 59.040 41.667 8.66 0.00 37.19 1.85
960 1205 5.163447 GGCCAATAGGAAATTCCCACTAAAC 60.163 44.000 8.66 0.00 37.19 2.01
961 1206 5.420739 GCCAATAGGAAATTCCCACTAAACA 59.579 40.000 8.66 0.00 37.19 2.83
962 1207 6.627287 GCCAATAGGAAATTCCCACTAAACAC 60.627 42.308 8.66 0.00 37.19 3.32
963 1208 6.435904 CCAATAGGAAATTCCCACTAAACACA 59.564 38.462 8.66 0.00 37.19 3.72
964 1209 7.124147 CCAATAGGAAATTCCCACTAAACACAT 59.876 37.037 8.66 0.00 37.19 3.21
965 1210 7.881775 ATAGGAAATTCCCACTAAACACATC 57.118 36.000 8.66 0.00 37.19 3.06
966 1211 5.016831 AGGAAATTCCCACTAAACACATCC 58.983 41.667 8.66 0.00 37.19 3.51
967 1212 4.159693 GGAAATTCCCACTAAACACATCCC 59.840 45.833 0.00 0.00 0.00 3.85
968 1213 2.483014 TTCCCACTAAACACATCCCG 57.517 50.000 0.00 0.00 0.00 5.14
969 1214 0.035820 TCCCACTAAACACATCCCGC 60.036 55.000 0.00 0.00 0.00 6.13
970 1215 0.322098 CCCACTAAACACATCCCGCA 60.322 55.000 0.00 0.00 0.00 5.69
971 1216 1.681780 CCCACTAAACACATCCCGCAT 60.682 52.381 0.00 0.00 0.00 4.73
991 1236 2.571528 GCATCGCGTCAGTGAGTAG 58.428 57.895 5.77 0.00 40.58 2.57
992 1237 0.867753 GCATCGCGTCAGTGAGTAGG 60.868 60.000 5.77 0.00 40.58 3.18
1054 1302 1.134788 CGCTGGAGGACGAAAACCTAT 60.135 52.381 0.00 0.00 37.93 2.57
1068 1316 3.917324 AACCTATTCCCCGAGATCCTA 57.083 47.619 0.00 0.00 0.00 2.94
1129 1377 4.299547 TCGTCTGCAAGCGCTGGT 62.300 61.111 12.58 0.00 39.64 4.00
1218 1469 2.586792 GGCTGCCTCGTCCAAGAT 59.413 61.111 12.43 0.00 0.00 2.40
1245 1496 2.679082 GGCATCTCCTTCCTACCTACA 58.321 52.381 0.00 0.00 0.00 2.74
1256 1507 0.178958 CTACCTACATCGGAGCCCCT 60.179 60.000 0.00 0.00 0.00 4.79
1294 1547 2.484889 GTCGTTTCTCCTTGCAGTTCT 58.515 47.619 0.00 0.00 0.00 3.01
1295 1548 2.872858 GTCGTTTCTCCTTGCAGTTCTT 59.127 45.455 0.00 0.00 0.00 2.52
1296 1549 4.056050 GTCGTTTCTCCTTGCAGTTCTTA 58.944 43.478 0.00 0.00 0.00 2.10
1298 1551 4.058817 CGTTTCTCCTTGCAGTTCTTACT 58.941 43.478 0.00 0.00 34.00 2.24
1308 1564 2.866460 GCAGTTCTTACTCAGCAACGGA 60.866 50.000 0.00 0.00 30.26 4.69
1335 1598 4.758251 CACGACTGCCGCCATGGA 62.758 66.667 18.40 0.00 43.32 3.41
1344 1607 1.515954 CCGCCATGGACTCGTACTT 59.484 57.895 18.40 0.00 42.00 2.24
1347 1610 2.394708 CGCCATGGACTCGTACTTATG 58.605 52.381 18.40 0.00 0.00 1.90
1413 1694 4.814294 GACCAGCACCGCCTACCG 62.814 72.222 0.00 0.00 0.00 4.02
1446 1739 2.515523 GATCCGAGGACGACCCGA 60.516 66.667 14.12 3.03 42.66 5.14
1495 1788 0.586802 GGACGTCAAACACTTCCAGC 59.413 55.000 18.91 0.00 42.11 4.85
1517 1810 4.002982 CTGGTCTTTGTAGCAGCATACAA 58.997 43.478 11.30 11.30 42.42 2.41
1579 1881 1.958902 GACCGGCGTATGGGGTAACA 61.959 60.000 6.01 0.00 33.28 2.41
1601 1903 3.750371 TCGTCTCAACACCAATTCCATT 58.250 40.909 0.00 0.00 0.00 3.16
1614 1916 0.961857 TTCCATTCGAGTCCGACCGA 60.962 55.000 7.70 7.70 45.50 4.69
1615 1917 1.064296 CCATTCGAGTCCGACCGAG 59.936 63.158 10.61 3.37 45.50 4.63
1616 1918 1.064296 CATTCGAGTCCGACCGAGG 59.936 63.158 10.61 5.86 45.50 4.63
1617 1919 2.119655 ATTCGAGTCCGACCGAGGG 61.120 63.158 10.61 0.00 45.50 4.30
1618 1920 2.833604 ATTCGAGTCCGACCGAGGGT 62.834 60.000 10.61 0.00 45.50 4.34
1631 1933 1.254026 CGAGGGTCCGCCTTATATCA 58.746 55.000 0.00 0.00 34.45 2.15
1638 1940 4.505039 GGGTCCGCCTTATATCAGATGTTT 60.505 45.833 0.00 0.00 34.45 2.83
1639 1941 5.279809 GGGTCCGCCTTATATCAGATGTTTA 60.280 44.000 0.00 0.00 34.45 2.01
1645 1947 7.359264 CCGCCTTATATCAGATGTTTACTTTCG 60.359 40.741 0.00 0.00 0.00 3.46
1717 2025 5.107133 GGATTCTTGCCAATTGTTCATCAG 58.893 41.667 4.43 0.00 0.00 2.90
1728 2036 2.995283 TGTTCATCAGGCATCCTTGAG 58.005 47.619 0.00 0.00 0.00 3.02
1749 2057 7.984422 TGAGTTTAATTTTGAGATGCAGAGA 57.016 32.000 0.00 0.00 0.00 3.10
1764 2090 3.822594 CAGAGACTAGCTGCTATACGG 57.177 52.381 10.23 0.87 0.00 4.02
1765 2091 2.486203 CAGAGACTAGCTGCTATACGGG 59.514 54.545 10.23 0.48 0.00 5.28
1766 2092 2.106857 AGAGACTAGCTGCTATACGGGT 59.893 50.000 10.23 3.99 39.25 5.28
1768 2094 0.674534 ACTAGCTGCTATACGGGTGC 59.325 55.000 10.23 0.00 36.55 5.01
1769 2095 0.038159 CTAGCTGCTATACGGGTGCC 60.038 60.000 10.23 0.00 36.55 5.01
1770 2096 0.757561 TAGCTGCTATACGGGTGCCA 60.758 55.000 5.02 0.00 36.55 4.92
1771 2097 1.887707 GCTGCTATACGGGTGCCAC 60.888 63.158 0.00 0.00 0.00 5.01
1773 2099 0.106708 CTGCTATACGGGTGCCACAT 59.893 55.000 0.00 0.00 0.00 3.21
1774 2100 0.105964 TGCTATACGGGTGCCACATC 59.894 55.000 0.00 0.00 0.00 3.06
1775 2101 0.393077 GCTATACGGGTGCCACATCT 59.607 55.000 0.00 0.00 0.00 2.90
1776 2102 1.873903 GCTATACGGGTGCCACATCTG 60.874 57.143 0.00 0.00 0.00 2.90
1777 2103 1.412710 CTATACGGGTGCCACATCTGT 59.587 52.381 0.00 0.00 37.82 3.41
1778 2104 1.491668 ATACGGGTGCCACATCTGTA 58.508 50.000 2.19 2.19 40.10 2.74
1781 2107 1.412710 ACGGGTGCCACATCTGTATAG 59.587 52.381 0.00 0.00 31.63 1.31
1795 2121 7.381948 CACATCTGTATAGAGATCACTTCAAGC 59.618 40.741 9.37 0.00 36.14 4.01
1806 2132 5.525378 AGATCACTTCAAGCTTATAAAGGCG 59.475 40.000 15.73 9.15 0.00 5.52
1825 2151 1.527370 GATAGTGGTGGGCTGGGTC 59.473 63.158 0.00 0.00 0.00 4.46
1827 2153 1.274703 ATAGTGGTGGGCTGGGTCTG 61.275 60.000 0.00 0.00 0.00 3.51
1831 2157 4.416738 GTGGGCTGGGTCTGCTCC 62.417 72.222 0.00 0.00 0.00 4.70
1836 2162 1.626356 GGCTGGGTCTGCTCCACATA 61.626 60.000 0.00 0.00 0.00 2.29
1845 2171 4.662468 TCTGCTCCACATATCAGACTTC 57.338 45.455 0.00 0.00 31.35 3.01
1846 2172 4.026052 TCTGCTCCACATATCAGACTTCA 58.974 43.478 0.00 0.00 31.35 3.02
1847 2173 4.118410 CTGCTCCACATATCAGACTTCAC 58.882 47.826 0.00 0.00 0.00 3.18
1850 2194 4.444022 GCTCCACATATCAGACTTCACCAT 60.444 45.833 0.00 0.00 0.00 3.55
1853 2197 4.193865 CACATATCAGACTTCACCATGCA 58.806 43.478 0.00 0.00 0.00 3.96
1854 2198 4.637091 CACATATCAGACTTCACCATGCAA 59.363 41.667 0.00 0.00 0.00 4.08
1856 2200 2.936919 TCAGACTTCACCATGCAAGT 57.063 45.000 0.00 3.33 35.48 3.16
1858 2202 2.158769 TCAGACTTCACCATGCAAGTGT 60.159 45.455 17.04 0.00 36.58 3.55
1859 2203 2.031420 CAGACTTCACCATGCAAGTGTG 60.031 50.000 17.04 12.24 37.50 3.82
1933 2277 5.842339 ACAAATTACTTCCCCTGAATCCAT 58.158 37.500 0.00 0.00 0.00 3.41
1935 2279 6.833933 ACAAATTACTTCCCCTGAATCCATAC 59.166 38.462 0.00 0.00 0.00 2.39
1951 2295 7.833682 TGAATCCATACAAGGACAACATAATGT 59.166 33.333 0.00 0.00 41.30 2.71
1955 2299 7.773224 TCCATACAAGGACAACATAATGTTAGG 59.227 37.037 0.00 0.00 33.79 2.69
1958 2302 5.648092 ACAAGGACAACATAATGTTAGGAGC 59.352 40.000 0.00 0.00 38.77 4.70
1965 2309 3.377172 ACATAATGTTAGGAGCGTTTGCC 59.623 43.478 0.00 0.00 44.31 4.52
1990 2334 6.542370 CGAGGAAAATAATATGGTGTTCCTGT 59.458 38.462 14.02 0.00 43.76 4.00
2004 2348 0.036164 TCCTGTGGACATTGAACGGG 59.964 55.000 9.21 9.21 41.03 5.28
2014 2358 0.464036 ATTGAACGGGCTCTATGCGA 59.536 50.000 0.00 0.00 44.05 5.10
2035 2379 3.920231 TCCATCTTCAGTCATTGGAGG 57.080 47.619 0.00 0.00 32.77 4.30
2057 2410 2.619646 TGAAAAAGCTACCCGAAACCAC 59.380 45.455 0.00 0.00 0.00 4.16
2060 2413 0.475044 AAGCTACCCGAAACCACCAA 59.525 50.000 0.00 0.00 0.00 3.67
2079 2432 6.295349 CCACCAACATATCTCACTACTATCCC 60.295 46.154 0.00 0.00 0.00 3.85
2088 2441 5.978814 TCTCACTACTATCCCTTTGAAAGC 58.021 41.667 0.00 0.00 0.00 3.51
2092 2445 3.695830 ACTATCCCTTTGAAAGCGTCA 57.304 42.857 0.00 0.00 0.00 4.35
2113 2466 5.983720 GTCAATACGACAGGTAATAGCATGT 59.016 40.000 0.00 0.00 44.69 3.21
2114 2467 6.479001 GTCAATACGACAGGTAATAGCATGTT 59.521 38.462 0.00 0.00 44.69 2.71
2116 2469 8.198778 TCAATACGACAGGTAATAGCATGTTTA 58.801 33.333 0.00 0.00 34.09 2.01
2121 2474 8.988934 ACGACAGGTAATAGCATGTTTATATTG 58.011 33.333 0.00 0.00 0.00 1.90
2122 2475 7.957484 CGACAGGTAATAGCATGTTTATATTGC 59.043 37.037 0.00 0.00 36.63 3.56
2158 2572 9.640963 ACTAAGCTAACAATTCTAAGTAGTGTG 57.359 33.333 0.00 0.00 0.00 3.82
2159 2573 9.640963 CTAAGCTAACAATTCTAAGTAGTGTGT 57.359 33.333 0.00 0.00 0.00 3.72
2161 2575 8.311650 AGCTAACAATTCTAAGTAGTGTGTTG 57.688 34.615 0.00 0.00 30.98 3.33
2236 2658 0.867746 TTGTGTCGATGCTTCTGTGC 59.132 50.000 0.00 0.00 0.00 4.57
2237 2659 0.950555 TGTGTCGATGCTTCTGTGCC 60.951 55.000 0.00 0.00 0.00 5.01
2248 2670 2.417243 GCTTCTGTGCCGGCATTTTATT 60.417 45.455 35.23 0.00 0.00 1.40
2261 2683 6.697019 CCGGCATTTTATTTAATGGTTCTGAG 59.303 38.462 0.00 0.00 36.30 3.35
2264 2686 8.413229 GGCATTTTATTTAATGGTTCTGAGCTA 58.587 33.333 0.00 0.00 36.30 3.32
2272 2694 8.918202 TTTAATGGTTCTGAGCTAGAAAAAGA 57.082 30.769 0.00 0.00 46.48 2.52
2306 2728 9.453325 GTAGCAGTATCTAGTTCAGTTTATGTC 57.547 37.037 0.00 0.00 0.00 3.06
2350 2787 1.557443 CGACTGTGGCGTGGTTTCTC 61.557 60.000 0.00 0.00 0.00 2.87
2356 2793 1.464997 GTGGCGTGGTTTCTCTGATTC 59.535 52.381 0.00 0.00 0.00 2.52
2358 2795 2.151202 GGCGTGGTTTCTCTGATTCAA 58.849 47.619 0.00 0.00 0.00 2.69
2372 2809 0.779997 ATTCAAGCAGAGGGGGTTGT 59.220 50.000 5.20 0.00 44.40 3.32
2374 2811 1.604593 CAAGCAGAGGGGGTTGTGG 60.605 63.158 0.00 0.00 40.43 4.17
2376 2813 0.770557 AAGCAGAGGGGGTTGTGGTA 60.771 55.000 0.00 0.00 0.00 3.25
2377 2814 0.550147 AGCAGAGGGGGTTGTGGTAT 60.550 55.000 0.00 0.00 0.00 2.73
2378 2815 0.107165 GCAGAGGGGGTTGTGGTATC 60.107 60.000 0.00 0.00 0.00 2.24
2380 2817 1.916181 CAGAGGGGGTTGTGGTATCTT 59.084 52.381 0.00 0.00 0.00 2.40
2381 2818 2.092914 CAGAGGGGGTTGTGGTATCTTC 60.093 54.545 0.00 0.00 0.00 2.87
2382 2819 2.197465 GAGGGGGTTGTGGTATCTTCT 58.803 52.381 0.00 0.00 0.00 2.85
2391 2828 5.237779 GGTTGTGGTATCTTCTTTGTCGAAA 59.762 40.000 0.00 0.00 0.00 3.46
2403 2840 8.443160 TCTTCTTTGTCGAAAATTATGTAGCAG 58.557 33.333 0.00 0.00 0.00 4.24
2405 2842 4.514545 TGTCGAAAATTATGTAGCAGCG 57.485 40.909 0.00 0.00 0.00 5.18
2412 2849 6.087555 CGAAAATTATGTAGCAGCGTTGTTTT 59.912 34.615 0.00 0.00 0.00 2.43
2413 2850 7.358023 CGAAAATTATGTAGCAGCGTTGTTTTT 60.358 33.333 0.00 0.00 0.00 1.94
2414 2851 6.689178 AATTATGTAGCAGCGTTGTTTTTG 57.311 33.333 0.00 0.00 0.00 2.44
2415 2852 3.980646 ATGTAGCAGCGTTGTTTTTGA 57.019 38.095 0.00 0.00 0.00 2.69
2416 2853 3.766676 TGTAGCAGCGTTGTTTTTGAA 57.233 38.095 0.00 0.00 0.00 2.69
2418 2855 5.425577 TGTAGCAGCGTTGTTTTTGAATA 57.574 34.783 0.00 0.00 0.00 1.75
2420 2857 6.442952 TGTAGCAGCGTTGTTTTTGAATATT 58.557 32.000 0.00 0.00 0.00 1.28
2421 2858 6.580791 TGTAGCAGCGTTGTTTTTGAATATTC 59.419 34.615 8.60 8.60 0.00 1.75
2422 2859 5.772521 AGCAGCGTTGTTTTTGAATATTCT 58.227 33.333 16.24 0.00 0.00 2.40
2423 2860 5.630680 AGCAGCGTTGTTTTTGAATATTCTG 59.369 36.000 16.24 3.29 0.00 3.02
2424 2861 5.629020 GCAGCGTTGTTTTTGAATATTCTGA 59.371 36.000 16.24 2.86 0.00 3.27
2425 2862 6.308766 GCAGCGTTGTTTTTGAATATTCTGAT 59.691 34.615 16.24 0.00 0.00 2.90
2426 2863 7.660059 CAGCGTTGTTTTTGAATATTCTGATG 58.340 34.615 16.24 1.51 0.00 3.07
2428 2865 7.867403 AGCGTTGTTTTTGAATATTCTGATGTT 59.133 29.630 16.24 0.00 0.00 2.71
2429 2866 9.123709 GCGTTGTTTTTGAATATTCTGATGTTA 57.876 29.630 16.24 0.00 0.00 2.41
2481 2921 7.418025 GGACTATGTGGTTTAAGTCTAGCAGAT 60.418 40.741 0.00 0.00 38.69 2.90
2482 2922 7.852263 ACTATGTGGTTTAAGTCTAGCAGATT 58.148 34.615 0.00 0.00 29.98 2.40
2485 2925 7.435068 TGTGGTTTAAGTCTAGCAGATTTTC 57.565 36.000 0.00 0.00 0.00 2.29
2504 2944 3.423539 TCTGCCTGTCAAGTTTAGCAT 57.576 42.857 0.00 0.00 0.00 3.79
2507 2947 6.233905 TCTGCCTGTCAAGTTTAGCATATA 57.766 37.500 0.00 0.00 0.00 0.86
2586 3049 6.204359 CCTGCTTATTCACATATGCAAGAAC 58.796 40.000 1.58 0.00 42.50 3.01
2607 3070 7.210873 AGAACTTTATATGGTAGTGCTAGTGC 58.789 38.462 0.00 0.00 40.20 4.40
2665 3130 5.236478 ACATAACTGTTGGAAGTTGAAGACG 59.764 40.000 2.69 0.00 40.58 4.18
2666 3131 1.940613 ACTGTTGGAAGTTGAAGACGC 59.059 47.619 0.00 0.00 0.00 5.19
2668 3133 1.305201 GTTGGAAGTTGAAGACGCCA 58.695 50.000 0.00 0.00 36.32 5.69
2684 3149 4.819630 AGACGCCAACATGAAAAACTAGAA 59.180 37.500 0.00 0.00 0.00 2.10
2697 3162 9.825972 ATGAAAAACTAGAATGTCAAATGTACG 57.174 29.630 0.00 0.00 0.00 3.67
2703 3168 6.973474 ACTAGAATGTCAAATGTACGTAGCTC 59.027 38.462 0.00 0.00 0.00 4.09
2707 3172 6.985188 ATGTCAAATGTACGTAGCTCAATT 57.015 33.333 0.00 0.00 0.00 2.32
2709 3174 6.163476 TGTCAAATGTACGTAGCTCAATTCT 58.837 36.000 0.00 0.00 0.00 2.40
2711 3176 6.955963 GTCAAATGTACGTAGCTCAATTCTTG 59.044 38.462 0.00 0.00 0.00 3.02
2712 3177 6.092122 TCAAATGTACGTAGCTCAATTCTTGG 59.908 38.462 0.00 0.00 0.00 3.61
2713 3178 3.857052 TGTACGTAGCTCAATTCTTGGG 58.143 45.455 0.00 0.00 0.00 4.12
2721 3186 2.632512 GCTCAATTCTTGGGGTTGGAAA 59.367 45.455 0.00 0.00 0.00 3.13
2769 3367 5.689383 TCAACTTTGTTATTCCTGCTGAC 57.311 39.130 0.00 0.00 0.00 3.51
2770 3368 4.518970 TCAACTTTGTTATTCCTGCTGACC 59.481 41.667 0.00 0.00 0.00 4.02
2773 3371 4.762251 ACTTTGTTATTCCTGCTGACCTTC 59.238 41.667 0.00 0.00 0.00 3.46
2777 3375 6.313519 TGTTATTCCTGCTGACCTTCTAAT 57.686 37.500 0.00 0.00 0.00 1.73
2787 3385 7.042658 CCTGCTGACCTTCTAATATTCGTAAAC 60.043 40.741 0.00 0.00 0.00 2.01
3016 3616 0.034670 GGCCAGAGGAGCAACAAGAT 60.035 55.000 0.00 0.00 0.00 2.40
3202 3812 5.046591 CGCCCCTTCAACATATATAAGGAGA 60.047 44.000 11.97 0.00 40.85 3.71
3249 3867 6.396829 AGCTACAAGCAAGAAGAAACAATT 57.603 33.333 1.22 0.00 45.56 2.32
3435 4063 1.059913 CCACTCAACCCCTCTCAAGT 58.940 55.000 0.00 0.00 0.00 3.16
3437 4065 2.498167 CACTCAACCCCTCTCAAGTTG 58.502 52.381 0.00 0.00 41.75 3.16
3490 4119 3.057969 CTTACACAAGGACATCTGCCA 57.942 47.619 0.00 0.00 0.00 4.92
3839 4470 3.026630 ACCGGATTGCTACGATGTATG 57.973 47.619 9.46 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 128 4.975502 TCTGCGCTTACAAATTTGTTCTTG 59.024 37.500 27.66 16.46 42.35 3.02
128 129 5.181690 TCTGCGCTTACAAATTTGTTCTT 57.818 34.783 27.66 6.70 42.35 2.52
232 341 2.791383 TCCGTGCTTCCAAATTTGTG 57.209 45.000 16.73 8.58 0.00 3.33
264 375 9.051679 TCTCAAGATTCAAGAAAAATGTTCGTA 57.948 29.630 0.00 0.00 0.00 3.43
266 377 8.685536 GTTCTCAAGATTCAAGAAAAATGTTCG 58.314 33.333 0.00 0.00 31.26 3.95
328 443 7.412137 AAATGTTCATGCTTTAAGAAAGTGC 57.588 32.000 0.00 0.00 40.64 4.40
527 666 8.964476 TTTGTTTGCCTTTCCATAAAATGTTA 57.036 26.923 0.00 0.00 0.00 2.41
805 1012 5.810095 ACTTTCTAGAAGGTTCCCTGATTG 58.190 41.667 14.09 0.00 32.13 2.67
853 1097 2.298163 CCGGCCCACTTAGATACGTTAT 59.702 50.000 0.00 0.00 0.00 1.89
955 1200 0.304705 GCGATGCGGGATGTGTTTAG 59.695 55.000 0.00 0.00 0.00 1.85
956 1201 0.391793 TGCGATGCGGGATGTGTTTA 60.392 50.000 0.00 0.00 0.00 2.01
957 1202 1.031571 ATGCGATGCGGGATGTGTTT 61.032 50.000 0.00 0.00 0.00 2.83
958 1203 1.439353 GATGCGATGCGGGATGTGTT 61.439 55.000 0.00 0.00 0.00 3.32
959 1204 1.889105 GATGCGATGCGGGATGTGT 60.889 57.895 0.00 0.00 0.00 3.72
960 1205 2.941333 GATGCGATGCGGGATGTG 59.059 61.111 0.00 0.00 0.00 3.21
961 1206 2.662857 CGATGCGATGCGGGATGT 60.663 61.111 0.00 0.00 0.00 3.06
962 1207 4.081030 GCGATGCGATGCGGGATG 62.081 66.667 0.00 0.00 0.00 3.51
988 1233 2.093537 CTGCTCATCTCGCCCCCTAC 62.094 65.000 0.00 0.00 0.00 3.18
991 1236 4.925861 GCTGCTCATCTCGCCCCC 62.926 72.222 0.00 0.00 0.00 5.40
992 1237 4.925861 GGCTGCTCATCTCGCCCC 62.926 72.222 0.00 0.00 36.56 5.80
1010 1255 3.574445 CCGCCGACGACGAGAGAT 61.574 66.667 9.28 0.00 43.93 2.75
1054 1302 0.178998 CGGAGTAGGATCTCGGGGAA 60.179 60.000 0.00 0.00 35.52 3.97
1144 1392 4.035102 GCGGAGGAAGCTGGGGTT 62.035 66.667 0.00 0.00 0.00 4.11
1163 1411 2.351276 GGTGGTGGATGCGGAAGT 59.649 61.111 0.00 0.00 0.00 3.01
1218 1469 2.363795 AAGGAGATGCCGTCGGGA 60.364 61.111 14.38 11.53 43.43 5.14
1245 1496 3.470888 CGGTTGAGGGGCTCCGAT 61.471 66.667 0.00 0.00 44.86 4.18
1275 1526 2.910688 AGAACTGCAAGGAGAAACGA 57.089 45.000 0.00 0.00 39.30 3.85
1294 1547 2.333926 CGTGAATCCGTTGCTGAGTAA 58.666 47.619 0.00 0.00 0.00 2.24
1295 1548 1.990799 CGTGAATCCGTTGCTGAGTA 58.009 50.000 0.00 0.00 0.00 2.59
1296 1549 1.291877 GCGTGAATCCGTTGCTGAGT 61.292 55.000 0.00 0.00 0.00 3.41
1298 1551 0.245266 TAGCGTGAATCCGTTGCTGA 59.755 50.000 0.00 0.00 37.12 4.26
1308 1564 0.736325 GGCAGTCGTGTAGCGTGAAT 60.736 55.000 0.00 0.00 42.13 2.57
1436 1717 0.814010 CCCATTGATTCGGGTCGTCC 60.814 60.000 0.00 0.00 37.70 4.79
1446 1739 1.305213 AAGCACCGCCCCATTGATT 60.305 52.632 0.00 0.00 0.00 2.57
1483 1776 2.689983 CAAAGACCAGCTGGAAGTGTTT 59.310 45.455 39.19 23.19 38.94 2.83
1495 1788 3.599343 TGTATGCTGCTACAAAGACCAG 58.401 45.455 0.00 0.00 0.00 4.00
1513 1806 1.976898 CTGCTACCCCGTGGTTGTA 59.023 57.895 0.00 0.00 44.75 2.41
1538 1840 1.810030 GACGAGTAAAGGCAGGCGG 60.810 63.158 0.00 0.00 0.00 6.13
1579 1881 3.417069 TGGAATTGGTGTTGAGACGAT 57.583 42.857 0.00 0.00 0.00 3.73
1601 1903 3.965539 GACCCTCGGTCGGACTCGA 62.966 68.421 16.81 16.81 43.14 4.04
1615 1917 2.567615 ACATCTGATATAAGGCGGACCC 59.432 50.000 0.00 0.00 36.11 4.46
1616 1918 3.963428 ACATCTGATATAAGGCGGACC 57.037 47.619 0.00 0.00 0.00 4.46
1617 1919 6.456501 AGTAAACATCTGATATAAGGCGGAC 58.543 40.000 0.00 0.00 0.00 4.79
1618 1920 6.665992 AGTAAACATCTGATATAAGGCGGA 57.334 37.500 0.00 0.00 0.00 5.54
1619 1921 7.359264 CGAAAGTAAACATCTGATATAAGGCGG 60.359 40.741 0.00 0.00 0.00 6.13
1631 1933 8.166422 AGAAATTGTTCCGAAAGTAAACATCT 57.834 30.769 0.00 0.00 35.62 2.90
1638 1940 5.782047 TCCGTAGAAATTGTTCCGAAAGTA 58.218 37.500 0.00 0.00 33.92 2.24
1639 1941 4.634199 TCCGTAGAAATTGTTCCGAAAGT 58.366 39.130 0.00 0.00 33.92 2.66
1645 1947 2.014857 GGGCTCCGTAGAAATTGTTCC 58.985 52.381 0.00 0.00 33.92 3.62
1702 2010 2.482490 GGATGCCTGATGAACAATTGGC 60.482 50.000 10.83 1.07 38.16 4.52
1717 2025 6.924111 TCTCAAAATTAAACTCAAGGATGCC 58.076 36.000 0.00 0.00 0.00 4.40
1728 2036 7.907563 GCTAGTCTCTGCATCTCAAAATTAAAC 59.092 37.037 0.00 0.00 0.00 2.01
1749 2057 0.674534 GCACCCGTATAGCAGCTAGT 59.325 55.000 8.43 0.00 0.00 2.57
1757 2083 1.412710 ACAGATGTGGCACCCGTATAG 59.587 52.381 16.26 1.24 0.00 1.31
1759 2085 1.491668 TACAGATGTGGCACCCGTAT 58.508 50.000 16.26 0.85 0.00 3.06
1761 2087 1.412710 CTATACAGATGTGGCACCCGT 59.587 52.381 16.26 9.16 0.00 5.28
1762 2088 1.686587 TCTATACAGATGTGGCACCCG 59.313 52.381 16.26 3.16 0.00 5.28
1763 2089 2.965831 TCTCTATACAGATGTGGCACCC 59.034 50.000 16.26 7.10 0.00 4.61
1764 2090 4.281941 TGATCTCTATACAGATGTGGCACC 59.718 45.833 16.26 0.00 32.94 5.01
1765 2091 5.010516 AGTGATCTCTATACAGATGTGGCAC 59.989 44.000 11.55 11.55 32.94 5.01
1766 2092 5.143369 AGTGATCTCTATACAGATGTGGCA 58.857 41.667 0.00 0.00 32.94 4.92
1768 2094 7.282332 TGAAGTGATCTCTATACAGATGTGG 57.718 40.000 0.00 0.00 32.94 4.17
1769 2095 7.381948 GCTTGAAGTGATCTCTATACAGATGTG 59.618 40.741 0.00 0.00 32.94 3.21
1770 2096 7.287466 AGCTTGAAGTGATCTCTATACAGATGT 59.713 37.037 0.00 0.00 32.94 3.06
1771 2097 7.660112 AGCTTGAAGTGATCTCTATACAGATG 58.340 38.462 0.00 0.00 32.94 2.90
1773 2099 7.652524 AAGCTTGAAGTGATCTCTATACAGA 57.347 36.000 0.00 0.00 0.00 3.41
1778 2104 9.995003 CCTTTATAAGCTTGAAGTGATCTCTAT 57.005 33.333 9.86 0.00 0.00 1.98
1781 2107 6.292596 CGCCTTTATAAGCTTGAAGTGATCTC 60.293 42.308 9.86 0.00 0.00 2.75
1795 2121 4.315803 CCACCACTATCCGCCTTTATAAG 58.684 47.826 0.00 0.00 0.00 1.73
1802 2128 3.480133 GCCCACCACTATCCGCCT 61.480 66.667 0.00 0.00 0.00 5.52
1806 2132 1.984288 GACCCAGCCCACCACTATCC 61.984 65.000 0.00 0.00 0.00 2.59
1825 2151 4.118410 GTGAAGTCTGATATGTGGAGCAG 58.882 47.826 0.00 0.00 0.00 4.24
1827 2153 3.118629 TGGTGAAGTCTGATATGTGGAGC 60.119 47.826 0.00 0.00 0.00 4.70
1831 2157 4.193865 TGCATGGTGAAGTCTGATATGTG 58.806 43.478 0.00 0.00 0.00 3.21
1836 2162 3.079578 CACTTGCATGGTGAAGTCTGAT 58.920 45.455 13.05 0.00 36.89 2.90
1853 2197 3.146066 ACACCATCGTAATTGCACACTT 58.854 40.909 0.00 0.00 0.00 3.16
1854 2198 2.778299 ACACCATCGTAATTGCACACT 58.222 42.857 0.00 0.00 0.00 3.55
1856 2200 2.351253 GCAACACCATCGTAATTGCACA 60.351 45.455 6.71 0.00 40.51 4.57
1858 2202 2.158559 AGCAACACCATCGTAATTGCA 58.841 42.857 12.16 0.00 42.05 4.08
1859 2203 2.919666 AGCAACACCATCGTAATTGC 57.080 45.000 4.15 4.15 40.85 3.56
1865 2209 1.167851 CCATGAAGCAACACCATCGT 58.832 50.000 0.00 0.00 0.00 3.73
1933 2277 6.821665 GCTCCTAACATTATGTTGTCCTTGTA 59.178 38.462 19.55 0.00 41.30 2.41
1935 2279 5.220662 CGCTCCTAACATTATGTTGTCCTTG 60.221 44.000 19.55 6.96 41.30 3.61
1951 2295 1.079405 CCTCGGCAAACGCTCCTAA 60.079 57.895 0.00 0.00 43.86 2.69
1955 2299 0.521735 ATTTTCCTCGGCAAACGCTC 59.478 50.000 0.00 0.00 43.86 5.03
1958 2302 5.212194 CCATATTATTTTCCTCGGCAAACG 58.788 41.667 0.00 0.00 46.11 3.60
1965 2309 6.542370 ACAGGAACACCATATTATTTTCCTCG 59.458 38.462 0.00 0.00 40.71 4.63
1990 2334 1.271856 TAGAGCCCGTTCAATGTCCA 58.728 50.000 0.00 0.00 0.00 4.02
2004 2348 3.252400 CTGAAGATGGATCGCATAGAGC 58.748 50.000 0.00 0.00 40.87 4.09
2014 2358 3.784763 ACCTCCAATGACTGAAGATGGAT 59.215 43.478 0.00 0.00 39.33 3.41
2035 2379 2.619646 TGGTTTCGGGTAGCTTTTTCAC 59.380 45.455 0.00 0.00 0.00 3.18
2057 2410 7.546250 AAGGGATAGTAGTGAGATATGTTGG 57.454 40.000 0.00 0.00 0.00 3.77
2060 2413 8.783660 TTCAAAGGGATAGTAGTGAGATATGT 57.216 34.615 0.00 0.00 0.00 2.29
2174 2588 9.658799 ACGCTATATAATGAAGAAGCAACATAT 57.341 29.630 0.00 0.00 0.00 1.78
2176 2590 7.969536 ACGCTATATAATGAAGAAGCAACAT 57.030 32.000 0.00 0.00 0.00 2.71
2178 2592 9.746711 CAATACGCTATATAATGAAGAAGCAAC 57.253 33.333 0.00 0.00 0.00 4.17
2180 2594 9.489084 AACAATACGCTATATAATGAAGAAGCA 57.511 29.630 0.00 0.00 0.00 3.91
2181 2595 9.959775 GAACAATACGCTATATAATGAAGAAGC 57.040 33.333 0.00 0.00 0.00 3.86
2236 2658 6.568869 TCAGAACCATTAAATAAAATGCCGG 58.431 36.000 0.00 0.00 35.85 6.13
2237 2659 6.198966 GCTCAGAACCATTAAATAAAATGCCG 59.801 38.462 0.00 0.00 35.85 5.69
2248 2670 9.520515 AATCTTTTTCTAGCTCAGAACCATTAA 57.479 29.630 0.00 0.00 43.09 1.40
2275 2697 9.726438 AAACTGAACTAGATACTGCTACAAAAT 57.274 29.630 0.00 0.00 0.00 1.82
2279 2701 8.967918 ACATAAACTGAACTAGATACTGCTACA 58.032 33.333 0.00 0.00 0.00 2.74
2280 2702 9.453325 GACATAAACTGAACTAGATACTGCTAC 57.547 37.037 0.00 0.00 0.00 3.58
2317 2754 1.202639 ACAGTCGAACAATGACAGCCA 60.203 47.619 0.00 0.00 38.83 4.75
2320 2757 1.195448 GCCACAGTCGAACAATGACAG 59.805 52.381 0.00 0.00 38.83 3.51
2332 2769 0.249911 AGAGAAACCACGCCACAGTC 60.250 55.000 0.00 0.00 0.00 3.51
2350 2787 0.622665 ACCCCCTCTGCTTGAATCAG 59.377 55.000 0.00 0.00 0.00 2.90
2356 2793 1.604593 CCACAACCCCCTCTGCTTG 60.605 63.158 0.00 0.00 0.00 4.01
2358 2795 0.550147 ATACCACAACCCCCTCTGCT 60.550 55.000 0.00 0.00 0.00 4.24
2372 2809 9.226606 ACATAATTTTCGACAAAGAAGATACCA 57.773 29.630 0.00 0.00 0.00 3.25
2376 2813 8.946085 TGCTACATAATTTTCGACAAAGAAGAT 58.054 29.630 0.00 0.00 0.00 2.40
2377 2814 8.317891 TGCTACATAATTTTCGACAAAGAAGA 57.682 30.769 0.00 0.00 0.00 2.87
2378 2815 7.217070 GCTGCTACATAATTTTCGACAAAGAAG 59.783 37.037 0.00 0.00 0.00 2.85
2380 2817 6.542852 GCTGCTACATAATTTTCGACAAAGA 58.457 36.000 0.00 0.00 0.00 2.52
2381 2818 5.449113 CGCTGCTACATAATTTTCGACAAAG 59.551 40.000 0.00 0.00 0.00 2.77
2382 2819 5.106869 ACGCTGCTACATAATTTTCGACAAA 60.107 36.000 0.00 0.00 0.00 2.83
2391 2828 6.442952 TCAAAAACAACGCTGCTACATAATT 58.557 32.000 0.00 0.00 0.00 1.40
2403 2840 7.566858 ACATCAGAATATTCAAAAACAACGC 57.433 32.000 17.56 0.00 0.00 4.84
2481 2921 3.951037 TGCTAAACTTGACAGGCAGAAAA 59.049 39.130 0.00 0.00 0.00 2.29
2482 2922 3.550820 TGCTAAACTTGACAGGCAGAAA 58.449 40.909 0.00 0.00 0.00 2.52
2485 2925 6.925610 TTATATGCTAAACTTGACAGGCAG 57.074 37.500 0.00 0.00 33.23 4.85
2636 3101 8.918202 TTCAACTTCCAACAGTTATGTATCTT 57.082 30.769 0.00 0.00 39.29 2.40
2648 3113 1.305201 GGCGTCTTCAACTTCCAACA 58.695 50.000 0.00 0.00 0.00 3.33
2665 3130 6.446318 TGACATTCTAGTTTTTCATGTTGGC 58.554 36.000 0.00 0.00 0.00 4.52
2666 3131 8.870160 TTTGACATTCTAGTTTTTCATGTTGG 57.130 30.769 0.00 0.00 0.00 3.77
2684 3149 6.818644 AGAATTGAGCTACGTACATTTGACAT 59.181 34.615 0.00 0.00 0.00 3.06
2707 3172 4.810345 ACATTAAGTTTCCAACCCCAAGA 58.190 39.130 0.00 0.00 0.00 3.02
2709 3174 5.707495 ACTACATTAAGTTTCCAACCCCAA 58.293 37.500 0.00 0.00 0.00 4.12
2711 3176 6.716173 TGTAACTACATTAAGTTTCCAACCCC 59.284 38.462 0.00 0.00 40.20 4.95
2712 3177 7.748691 TGTAACTACATTAAGTTTCCAACCC 57.251 36.000 0.00 0.00 40.20 4.11
2740 3338 6.583806 GCAGGAATAACAAAGTTGAATGACAG 59.416 38.462 0.00 0.00 0.00 3.51
2745 3343 6.294731 GGTCAGCAGGAATAACAAAGTTGAAT 60.295 38.462 0.00 0.00 0.00 2.57
2751 3349 5.006386 AGAAGGTCAGCAGGAATAACAAAG 58.994 41.667 0.00 0.00 0.00 2.77
2760 3358 4.649674 ACGAATATTAGAAGGTCAGCAGGA 59.350 41.667 2.28 0.00 0.00 3.86
2777 3375 9.537192 CAAGTCACTATTATGGGTTTACGAATA 57.463 33.333 0.00 0.00 0.00 1.75
2795 3393 9.292846 GTTTCGTAAATTTTAAACCAAGTCACT 57.707 29.630 0.00 0.00 0.00 3.41
2796 3394 9.074443 TGTTTCGTAAATTTTAAACCAAGTCAC 57.926 29.630 15.26 0.00 32.18 3.67
2828 3426 7.934120 CAGGACTCTCCCTAAGTTATAAAATGG 59.066 40.741 0.00 0.00 37.19 3.16
2837 3435 2.632763 AGCAGGACTCTCCCTAAGTT 57.367 50.000 0.00 0.00 37.19 2.66
2842 3440 1.573376 ACTCATAGCAGGACTCTCCCT 59.427 52.381 0.00 0.00 37.19 4.20
3105 3714 1.409427 CCGGATACAAGTCCTGGTCTC 59.591 57.143 0.00 0.00 36.07 3.36
3202 3812 2.044450 TATTGGGGAGCCCTGCCT 59.956 61.111 5.38 0.00 45.70 4.75
3218 3829 2.903784 TCTTGCTTGTAGCTTGTCCCTA 59.096 45.455 0.00 0.00 42.97 3.53
3249 3867 2.832129 CCTCTTTGTGTCTAGCCCTACA 59.168 50.000 0.00 0.00 0.00 2.74
3435 4063 1.093972 CCAACGCATCTATGTGGCAA 58.906 50.000 8.28 0.00 42.35 4.52
3437 4065 1.356624 GCCAACGCATCTATGTGGC 59.643 57.895 8.28 7.68 42.35 5.01
3490 4119 3.627577 GCCAACTATCGTGGATTTGTCAT 59.372 43.478 0.00 0.00 0.00 3.06
3839 4470 1.586154 CCGGTTGGACCATTGACTGC 61.586 60.000 0.00 0.00 38.47 4.40


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

AutoCloner maintained by Alex Coulton.