Multiple sequence alignment - TraesCS2B01G300200

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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 TraesCS2B01G300200 chr2B 100.000 5944 0 0 1 5944 421713718 421707775 0.000000e+00 10977.0
1 TraesCS2B01G300200 chr2B 90.969 764 56 8 97 847 110430231 110429468 0.000000e+00 1016.0
2 TraesCS2B01G300200 chr2B 88.684 813 76 9 87 885 374023466 374022656 0.000000e+00 977.0
3 TraesCS2B01G300200 chr2B 88.752 809 75 10 97 891 747813424 747814230 0.000000e+00 976.0
4 TraesCS2B01G300200 chr2B 86.164 318 38 5 3084 3397 541094882 541095197 7.380000e-89 339.0
5 TraesCS2B01G300200 chr2B 82.667 150 26 0 4042 4191 541095272 541095421 3.740000e-27 134.0
6 TraesCS2B01G300200 chr2D 93.815 2603 101 27 926 3499 354748137 354745566 0.000000e+00 3860.0
7 TraesCS2B01G300200 chr2D 96.361 1209 38 6 3660 4864 354745567 354744361 0.000000e+00 1984.0
8 TraesCS2B01G300200 chr2D 93.286 566 28 5 5387 5944 354743865 354743302 0.000000e+00 826.0
9 TraesCS2B01G300200 chr2D 90.612 490 35 6 4856 5344 354744342 354743863 1.810000e-179 640.0
10 TraesCS2B01G300200 chr2D 88.498 313 23 3 592 891 632474648 632474960 3.380000e-97 366.0
11 TraesCS2B01G300200 chr2D 86.478 318 37 5 3084 3397 459825796 459826111 1.590000e-90 344.0
12 TraesCS2B01G300200 chr2D 86.636 217 18 9 3519 3727 47251472 47251685 4.630000e-56 230.0
13 TraesCS2B01G300200 chr2D 82.000 150 27 0 4042 4191 459826182 459826331 1.740000e-25 128.0
14 TraesCS2B01G300200 chr2A 92.208 2464 102 34 3539 5944 474312383 474309952 0.000000e+00 3404.0
15 TraesCS2B01G300200 chr2A 92.358 1819 87 29 1053 2841 474315394 474313598 0.000000e+00 2542.0
16 TraesCS2B01G300200 chr2A 97.073 615 17 1 2827 3440 474313273 474312659 0.000000e+00 1035.0
17 TraesCS2B01G300200 chr2A 86.478 318 37 5 3084 3397 602800094 602800409 1.590000e-90 344.0
18 TraesCS2B01G300200 chr2A 96.000 150 4 2 2392 2539 474313597 474313448 5.950000e-60 243.0
19 TraesCS2B01G300200 chr2A 98.020 101 0 1 2690 2790 474313450 474313352 2.200000e-39 174.0
20 TraesCS2B01G300200 chr2A 82.667 150 26 0 4042 4191 602800484 602800633 3.740000e-27 134.0
21 TraesCS2B01G300200 chr2A 100.000 36 0 0 3477 3512 474312658 474312623 3.840000e-07 67.6
22 TraesCS2B01G300200 chr2A 94.444 36 2 0 2823 2858 474313343 474313308 8.320000e-04 56.5
23 TraesCS2B01G300200 chr7D 89.744 819 70 6 87 891 562820282 562819464 0.000000e+00 1035.0
24 TraesCS2B01G300200 chr7D 88.139 548 48 9 353 885 550995852 550996397 2.340000e-178 636.0
25 TraesCS2B01G300200 chr7D 87.638 542 61 5 353 891 580229018 580228480 5.060000e-175 625.0
26 TraesCS2B01G300200 chr7D 86.667 75 8 2 3628 3701 75053429 75053502 1.370000e-11 82.4
27 TraesCS2B01G300200 chr7B 89.740 809 67 11 97 891 337644302 337643496 0.000000e+00 1020.0
28 TraesCS2B01G300200 chr3D 89.448 815 71 5 87 887 8512463 8513276 0.000000e+00 1014.0
29 TraesCS2B01G300200 chr3D 88.425 838 66 15 87 894 36634240 36633404 0.000000e+00 981.0
30 TraesCS2B01G300200 chr5D 89.082 806 66 9 95 885 510061030 510060232 0.000000e+00 981.0
31 TraesCS2B01G300200 chr5D 95.699 93 4 0 1 93 497928944 497929036 3.710000e-32 150.0
32 TraesCS2B01G300200 chr5D 83.444 151 18 6 3529 3672 487506678 487506828 3.740000e-27 134.0
33 TraesCS2B01G300200 chr1B 88.684 813 76 6 87 885 532489542 532490352 0.000000e+00 977.0
34 TraesCS2B01G300200 chr1B 81.938 227 27 10 3491 3710 548619270 548619051 4.730000e-41 180.0
35 TraesCS2B01G300200 chr1B 92.857 70 5 0 3629 3698 375802391 375802460 1.050000e-17 102.0
36 TraesCS2B01G300200 chr1B 89.189 74 6 2 3528 3599 488397391 488397464 2.280000e-14 91.6
37 TraesCS2B01G300200 chr3B 88.765 810 74 11 87 881 203703936 203704743 0.000000e+00 976.0
38 TraesCS2B01G300200 chr3B 96.667 90 3 0 7 96 98994990 98994901 3.710000e-32 150.0
39 TraesCS2B01G300200 chr1A 89.053 676 61 5 87 749 418611422 418610747 0.000000e+00 826.0
40 TraesCS2B01G300200 chr1D 89.251 521 42 4 379 885 246950984 246951504 1.810000e-179 640.0
41 TraesCS2B01G300200 chr1D 95.833 96 4 0 1 96 126606286 126606381 7.980000e-34 156.0
42 TraesCS2B01G300200 chr1D 94.792 96 5 0 1 96 246950588 246950683 3.710000e-32 150.0
43 TraesCS2B01G300200 chr1D 86.957 92 9 3 3608 3698 276500800 276500889 3.790000e-17 100.0
44 TraesCS2B01G300200 chr6D 88.160 549 47 9 353 885 54233378 54232832 6.500000e-179 638.0
45 TraesCS2B01G300200 chr6D 88.038 209 16 6 3530 3731 303623279 303623073 7.700000e-59 239.0
46 TraesCS2B01G300200 chr6D 91.429 105 9 0 1 105 411784823 411784719 1.730000e-30 145.0
47 TraesCS2B01G300200 chr6D 93.750 96 6 0 1 96 462396842 462396747 1.730000e-30 145.0
48 TraesCS2B01G300200 chr7A 89.062 512 40 5 388 885 8806544 8807053 6.540000e-174 621.0
49 TraesCS2B01G300200 chr4D 86.813 546 46 9 353 884 19148975 19148442 2.390000e-163 586.0
50 TraesCS2B01G300200 chr4D 94.792 96 5 0 1 96 484628837 484628932 3.710000e-32 150.0
51 TraesCS2B01G300200 chr4D 93.750 96 6 0 1 96 19149468 19149373 1.730000e-30 145.0
52 TraesCS2B01G300200 chr6A 87.619 210 16 8 3530 3731 412366259 412366052 9.960000e-58 235.0
53 TraesCS2B01G300200 chr6A 88.660 97 10 1 3629 3724 340097882 340097786 3.760000e-22 117.0
54 TraesCS2B01G300200 chr6B 85.167 209 22 6 3530 3731 469288134 469287928 7.810000e-49 206.0
55 TraesCS2B01G300200 chr6B 89.899 99 9 1 3629 3726 345580106 345580008 6.250000e-25 126.0
56 TraesCS2B01G300200 chr6B 88.636 88 10 0 3526 3613 633540689 633540602 2.270000e-19 108.0
57 TraesCS2B01G300200 chr5A 85.427 199 22 6 3533 3726 607717989 607718185 3.630000e-47 200.0
58 TraesCS2B01G300200 chr5A 85.000 140 13 7 3528 3659 608313597 608313736 1.040000e-27 135.0
59 TraesCS2B01G300200 chr3A 94.792 96 5 0 1 96 642718562 642718467 3.710000e-32 150.0
60 TraesCS2B01G300200 chr5B 84.868 152 16 6 3528 3672 600083534 600083685 4.800000e-31 147.0


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 TraesCS2B01G300200 chr2B 421707775 421713718 5943 True 10977.000000 10977 100.0000 1 5944 1 chr2B.!!$R3 5943
1 TraesCS2B01G300200 chr2B 110429468 110430231 763 True 1016.000000 1016 90.9690 97 847 1 chr2B.!!$R1 750
2 TraesCS2B01G300200 chr2B 374022656 374023466 810 True 977.000000 977 88.6840 87 885 1 chr2B.!!$R2 798
3 TraesCS2B01G300200 chr2B 747813424 747814230 806 False 976.000000 976 88.7520 97 891 1 chr2B.!!$F1 794
4 TraesCS2B01G300200 chr2B 541094882 541095421 539 False 236.500000 339 84.4155 3084 4191 2 chr2B.!!$F2 1107
5 TraesCS2B01G300200 chr2D 354743302 354748137 4835 True 1827.500000 3860 93.5185 926 5944 4 chr2D.!!$R1 5018
6 TraesCS2B01G300200 chr2D 459825796 459826331 535 False 236.000000 344 84.2390 3084 4191 2 chr2D.!!$F3 1107
7 TraesCS2B01G300200 chr2A 474309952 474315394 5442 True 1074.585714 3404 95.7290 1053 5944 7 chr2A.!!$R1 4891
8 TraesCS2B01G300200 chr2A 602800094 602800633 539 False 239.000000 344 84.5725 3084 4191 2 chr2A.!!$F1 1107
9 TraesCS2B01G300200 chr7D 562819464 562820282 818 True 1035.000000 1035 89.7440 87 891 1 chr7D.!!$R1 804
10 TraesCS2B01G300200 chr7D 550995852 550996397 545 False 636.000000 636 88.1390 353 885 1 chr7D.!!$F2 532
11 TraesCS2B01G300200 chr7D 580228480 580229018 538 True 625.000000 625 87.6380 353 891 1 chr7D.!!$R2 538
12 TraesCS2B01G300200 chr7B 337643496 337644302 806 True 1020.000000 1020 89.7400 97 891 1 chr7B.!!$R1 794
13 TraesCS2B01G300200 chr3D 8512463 8513276 813 False 1014.000000 1014 89.4480 87 887 1 chr3D.!!$F1 800
14 TraesCS2B01G300200 chr3D 36633404 36634240 836 True 981.000000 981 88.4250 87 894 1 chr3D.!!$R1 807
15 TraesCS2B01G300200 chr5D 510060232 510061030 798 True 981.000000 981 89.0820 95 885 1 chr5D.!!$R1 790
16 TraesCS2B01G300200 chr1B 532489542 532490352 810 False 977.000000 977 88.6840 87 885 1 chr1B.!!$F3 798
17 TraesCS2B01G300200 chr3B 203703936 203704743 807 False 976.000000 976 88.7650 87 881 1 chr3B.!!$F1 794
18 TraesCS2B01G300200 chr1A 418610747 418611422 675 True 826.000000 826 89.0530 87 749 1 chr1A.!!$R1 662
19 TraesCS2B01G300200 chr1D 246950588 246951504 916 False 395.000000 640 92.0215 1 885 2 chr1D.!!$F3 884
20 TraesCS2B01G300200 chr6D 54232832 54233378 546 True 638.000000 638 88.1600 353 885 1 chr6D.!!$R1 532
21 TraesCS2B01G300200 chr7A 8806544 8807053 509 False 621.000000 621 89.0620 388 885 1 chr7A.!!$F1 497
22 TraesCS2B01G300200 chr4D 19148442 19149468 1026 True 365.500000 586 90.2815 1 884 2 chr4D.!!$R1 883

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
897 1072 0.031449 GAGCCAGACGGAGATACTGC 59.969 60.000 0.00 0.0 0.00 4.40 F
924 1099 0.036590 GGTAACCAAACACGCCCCTA 59.963 55.000 0.00 0.0 0.00 3.53 F
1034 1209 0.037303 ACTAGGTTGACTCGGACGGA 59.963 55.000 0.00 0.0 0.00 4.69 F
1055 1230 0.679640 CCACACCAACCACACACACT 60.680 55.000 0.00 0.0 0.00 3.55 F
1056 1231 1.173043 CACACCAACCACACACACTT 58.827 50.000 0.00 0.0 0.00 3.16 F
1085 1274 1.681486 CTTCCTTCTCCTCCGCCTCC 61.681 65.000 0.00 0.0 0.00 4.30 F
1496 1692 2.000447 GATCTAACCAACCGTGCACTC 59.000 52.381 16.19 0.0 0.00 3.51 F
2081 2306 2.092429 TCAGGTTTCTGTGTTTCTGCCT 60.092 45.455 0.00 0.0 41.59 4.75 F
3524 4088 0.035725 CTTCGGTAACAACCCCCTCC 60.036 60.000 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2306 0.684535 TCTGGCAATCCAAGTCGTGA 59.315 50.000 0.00 0.00 42.91 4.35 R
2676 2904 3.386726 TGGATCCTACAAGTACATTCCCG 59.613 47.826 14.23 0.00 0.00 5.14 R
2825 3320 4.758688 TCTGCCCTGCATTATGATATACG 58.241 43.478 0.00 0.00 38.13 3.06 R
3399 3963 1.066071 TGACGAACAAACACAGGTGGA 60.066 47.619 4.24 0.00 34.19 4.02 R
3458 4022 5.758790 ATCCTAGGTGATCTCAATGGATG 57.241 43.478 9.08 0.00 32.55 3.51 R
3512 4076 1.541620 GAGGAGGGAGGGGGTTGTT 60.542 63.158 0.00 0.00 0.00 2.83 R
3517 4081 0.045778 TTTAAGGAGGAGGGAGGGGG 59.954 60.000 0.00 0.00 0.00 5.40 R
4434 5219 1.014352 CCCTTTGCGGTGCAGTATAC 58.986 55.000 0.00 0.00 40.61 1.47 R
5740 6581 0.032416 AGGTCCAGGCTGTATACCGT 60.032 55.000 14.43 5.63 35.32 4.83 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
76 77 2.167693 AGGCGATCGGTTCATAGTTTCA 59.832 45.455 18.30 0.00 0.00 2.69
93 203 0.323629 TCATCGGCCGGAAGTTCTTT 59.676 50.000 27.83 0.00 0.00 2.52
149 259 4.261405 CGATCGTAGCTTCATCTCTCCTTT 60.261 45.833 7.03 0.00 0.00 3.11
151 261 6.348950 CGATCGTAGCTTCATCTCTCCTTTAT 60.349 42.308 7.03 0.00 0.00 1.40
288 398 5.874261 GTCCTACTACACTAGAGTCGTTTCT 59.126 44.000 2.95 0.00 0.00 2.52
371 513 1.813753 ACACTGCAGTTTGTCGCGT 60.814 52.632 18.94 7.32 0.00 6.01
412 554 2.441164 GCCTCCTCTCTCTCGCCA 60.441 66.667 0.00 0.00 0.00 5.69
469 629 3.008157 CGGCCTACTCTCTCATCCTACTA 59.992 52.174 0.00 0.00 0.00 1.82
528 688 0.464036 TCTGTCCACTGTCTTTGCGT 59.536 50.000 0.00 0.00 0.00 5.24
549 710 0.034059 AGCACTGCAACTAGTTCGCT 59.966 50.000 22.16 15.11 0.00 4.93
564 725 4.400109 GCTGACGGTGTCGCTCGA 62.400 66.667 0.00 0.00 40.63 4.04
667 840 1.802960 CGCACACTGCATTTCTTCTCT 59.197 47.619 0.00 0.00 45.36 3.10
786 959 0.957395 CGAGACAATGCAGGCAACCT 60.957 55.000 0.00 0.00 37.17 3.50
833 1007 2.042686 TGCAGGAAGTCCATATGCAC 57.957 50.000 8.29 0.00 39.03 4.57
867 1041 4.948847 ACTTGCAGATGTCGCATATAAGA 58.051 39.130 0.00 0.00 39.58 2.10
887 1062 3.499918 AGATTGTTTTTCAGAGCCAGACG 59.500 43.478 0.00 0.00 0.00 4.18
891 1066 1.338107 TTTTCAGAGCCAGACGGAGA 58.662 50.000 0.00 0.00 0.00 3.71
892 1067 1.561643 TTTCAGAGCCAGACGGAGAT 58.438 50.000 0.00 0.00 0.00 2.75
893 1068 2.437085 TTCAGAGCCAGACGGAGATA 57.563 50.000 0.00 0.00 0.00 1.98
894 1069 1.681538 TCAGAGCCAGACGGAGATAC 58.318 55.000 0.00 0.00 0.00 2.24
895 1070 1.213182 TCAGAGCCAGACGGAGATACT 59.787 52.381 0.00 0.00 0.00 2.12
896 1071 1.336440 CAGAGCCAGACGGAGATACTG 59.664 57.143 0.00 0.00 0.00 2.74
897 1072 0.031449 GAGCCAGACGGAGATACTGC 59.969 60.000 0.00 0.00 0.00 4.40
898 1073 0.684479 AGCCAGACGGAGATACTGCA 60.684 55.000 0.00 0.00 0.00 4.41
899 1074 0.249238 GCCAGACGGAGATACTGCAG 60.249 60.000 13.48 13.48 0.00 4.41
900 1075 0.387202 CCAGACGGAGATACTGCAGG 59.613 60.000 19.93 0.00 0.00 4.85
901 1076 0.249238 CAGACGGAGATACTGCAGGC 60.249 60.000 19.93 7.03 0.00 4.85
902 1077 1.299468 GACGGAGATACTGCAGGCG 60.299 63.158 19.93 0.00 0.00 5.52
903 1078 1.725557 GACGGAGATACTGCAGGCGA 61.726 60.000 19.93 2.87 0.00 5.54
904 1079 1.299468 CGGAGATACTGCAGGCGAC 60.299 63.158 19.93 6.51 0.00 5.19
905 1080 1.299468 GGAGATACTGCAGGCGACG 60.299 63.158 19.93 0.00 0.00 5.12
906 1081 1.299468 GAGATACTGCAGGCGACGG 60.299 63.158 19.93 0.00 0.00 4.79
907 1082 2.005960 GAGATACTGCAGGCGACGGT 62.006 60.000 19.93 0.00 0.00 4.83
908 1083 0.750546 AGATACTGCAGGCGACGGTA 60.751 55.000 19.93 0.00 0.00 4.02
909 1084 0.101759 GATACTGCAGGCGACGGTAA 59.898 55.000 19.93 0.00 0.00 2.85
910 1085 0.179119 ATACTGCAGGCGACGGTAAC 60.179 55.000 19.93 0.00 0.00 2.50
911 1086 2.216750 TACTGCAGGCGACGGTAACC 62.217 60.000 19.93 0.00 0.00 2.85
912 1087 3.583276 CTGCAGGCGACGGTAACCA 62.583 63.158 5.57 0.00 0.00 3.67
913 1088 2.357760 GCAGGCGACGGTAACCAA 60.358 61.111 0.00 0.00 0.00 3.67
914 1089 1.962306 GCAGGCGACGGTAACCAAA 60.962 57.895 0.00 0.00 0.00 3.28
915 1090 1.864176 CAGGCGACGGTAACCAAAC 59.136 57.895 0.00 0.00 0.00 2.93
916 1091 0.881159 CAGGCGACGGTAACCAAACA 60.881 55.000 0.00 0.00 0.00 2.83
917 1092 0.881600 AGGCGACGGTAACCAAACAC 60.882 55.000 0.00 0.00 0.00 3.32
918 1093 1.202320 GCGACGGTAACCAAACACG 59.798 57.895 0.00 0.00 0.00 4.49
919 1094 1.202320 CGACGGTAACCAAACACGC 59.798 57.895 0.00 0.00 0.00 5.34
920 1095 1.570967 GACGGTAACCAAACACGCC 59.429 57.895 0.00 0.00 0.00 5.68
921 1096 1.844771 GACGGTAACCAAACACGCCC 61.845 60.000 0.00 0.00 0.00 6.13
922 1097 2.619165 CGGTAACCAAACACGCCCC 61.619 63.158 0.00 0.00 0.00 5.80
923 1098 1.228337 GGTAACCAAACACGCCCCT 60.228 57.895 0.00 0.00 0.00 4.79
924 1099 0.036590 GGTAACCAAACACGCCCCTA 59.963 55.000 0.00 0.00 0.00 3.53
929 1104 0.463833 CCAAACACGCCCCTAGGATC 60.464 60.000 11.48 0.00 33.47 3.36
935 1110 2.735237 GCCCCTAGGATCGGTTCG 59.265 66.667 11.48 0.00 33.47 3.95
949 1124 4.569761 TCGGTTCGATCCTTTCATCTAG 57.430 45.455 10.71 0.00 0.00 2.43
950 1125 4.204799 TCGGTTCGATCCTTTCATCTAGA 58.795 43.478 10.71 0.00 0.00 2.43
1005 1180 2.427320 CGGGATCCATGGATGCGT 59.573 61.111 32.40 12.53 42.71 5.24
1027 1202 4.945246 TCACTTGTTGACTAGGTTGACTC 58.055 43.478 0.00 0.00 0.00 3.36
1028 1203 3.736252 CACTTGTTGACTAGGTTGACTCG 59.264 47.826 0.00 0.00 0.00 4.18
1029 1204 3.243771 ACTTGTTGACTAGGTTGACTCGG 60.244 47.826 0.00 0.00 0.00 4.63
1030 1205 2.589720 TGTTGACTAGGTTGACTCGGA 58.410 47.619 0.00 0.00 0.00 4.55
1032 1207 1.162698 TGACTAGGTTGACTCGGACG 58.837 55.000 0.00 0.00 0.00 4.79
1033 1208 0.450983 GACTAGGTTGACTCGGACGG 59.549 60.000 0.00 0.00 0.00 4.79
1034 1209 0.037303 ACTAGGTTGACTCGGACGGA 59.963 55.000 0.00 0.00 0.00 4.69
1044 1219 4.308458 CGGACGGAGCCACACCAA 62.308 66.667 0.00 0.00 0.00 3.67
1046 1221 2.668550 GACGGAGCCACACCAACC 60.669 66.667 0.00 0.00 0.00 3.77
1047 1222 3.469863 GACGGAGCCACACCAACCA 62.470 63.158 0.00 0.00 0.00 3.67
1048 1223 2.978010 CGGAGCCACACCAACCAC 60.978 66.667 0.00 0.00 0.00 4.16
1049 1224 2.194597 GGAGCCACACCAACCACA 59.805 61.111 0.00 0.00 0.00 4.17
1052 1227 1.724582 GAGCCACACCAACCACACAC 61.725 60.000 0.00 0.00 0.00 3.82
1053 1228 2.049185 GCCACACCAACCACACACA 61.049 57.895 0.00 0.00 0.00 3.72
1055 1230 0.679640 CCACACCAACCACACACACT 60.680 55.000 0.00 0.00 0.00 3.55
1056 1231 1.173043 CACACCAACCACACACACTT 58.827 50.000 0.00 0.00 0.00 3.16
1072 1261 3.316573 CTTCCCCTCGCGCTTCCTT 62.317 63.158 5.56 0.00 0.00 3.36
1077 1266 2.716017 CCTCGCGCTTCCTTCTCCT 61.716 63.158 5.56 0.00 0.00 3.69
1080 1269 2.202810 GCGCTTCCTTCTCCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
1082 1271 2.188207 GCTTCCTTCTCCTCCGCC 59.812 66.667 0.00 0.00 0.00 6.13
1083 1272 2.363172 GCTTCCTTCTCCTCCGCCT 61.363 63.158 0.00 0.00 0.00 5.52
1084 1273 1.819905 CTTCCTTCTCCTCCGCCTC 59.180 63.158 0.00 0.00 0.00 4.70
1085 1274 1.681486 CTTCCTTCTCCTCCGCCTCC 61.681 65.000 0.00 0.00 0.00 4.30
1366 1561 2.151202 TCTCGCATGTTCTTTGTTCCC 58.849 47.619 0.00 0.00 0.00 3.97
1494 1690 2.094762 AGATCTAACCAACCGTGCAC 57.905 50.000 6.82 6.82 0.00 4.57
1496 1692 2.000447 GATCTAACCAACCGTGCACTC 59.000 52.381 16.19 0.00 0.00 3.51
1511 1707 2.348411 CACTCCCAAGTGTTCCAGTT 57.652 50.000 0.00 0.00 46.52 3.16
1535 1731 3.118738 ACTCACGGTTTGACATATCCTCC 60.119 47.826 0.00 0.00 0.00 4.30
1639 1835 9.625747 TGATTACCAGCATAATAAAGATGTGAA 57.374 29.630 0.00 0.00 0.00 3.18
1810 2034 9.818796 GAACAATTCTAGCTCAGAAAGTTAAAG 57.181 33.333 17.06 0.00 46.29 1.85
1826 2050 7.913674 AAGTTAAAGTGCAAATGTTTTTCCA 57.086 28.000 0.00 0.00 0.00 3.53
1935 2160 6.585702 TGCTGATTTGTTGATGAAATAAACCG 59.414 34.615 0.00 0.00 36.82 4.44
2042 2267 3.259123 AGGTTTTTCATGCATTGGAGTCC 59.741 43.478 0.73 0.73 0.00 3.85
2081 2306 2.092429 TCAGGTTTCTGTGTTTCTGCCT 60.092 45.455 0.00 0.00 41.59 4.75
2386 2611 9.520515 AATGTTTTGGTGAGTAATCTTATGAGT 57.479 29.630 0.00 0.00 0.00 3.41
2389 2614 9.871238 GTTTTGGTGAGTAATCTTATGAGTCTA 57.129 33.333 0.00 0.00 0.00 2.59
2467 2692 7.005709 TCTTTCTACTAAAAGTTGCTAGGCT 57.994 36.000 0.00 0.00 37.49 4.58
2480 2705 5.714806 AGTTGCTAGGCTTAAGGCATTAAAA 59.285 36.000 28.60 14.11 44.01 1.52
2676 2904 2.684881 CCACTCCATGGTGCTCAATTAC 59.315 50.000 12.58 0.00 44.46 1.89
2792 3023 3.256631 GGGCATATTTGGATAGTGCAAGG 59.743 47.826 0.00 0.00 37.53 3.61
2808 3039 6.296026 AGTGCAAGGTAAGATAGTTTTCACA 58.704 36.000 0.00 0.00 0.00 3.58
2809 3040 6.770785 AGTGCAAGGTAAGATAGTTTTCACAA 59.229 34.615 0.00 0.00 0.00 3.33
2810 3041 7.284489 AGTGCAAGGTAAGATAGTTTTCACAAA 59.716 33.333 0.00 0.00 0.00 2.83
2812 3043 8.470805 TGCAAGGTAAGATAGTTTTCACAAAAA 58.529 29.630 0.00 0.00 31.13 1.94
2825 3320 8.406297 AGTTTTCACAAAAATCTCTTCAGTACC 58.594 33.333 0.00 0.00 36.77 3.34
3195 3759 5.427378 TGCACATAAAAGCTGCTATAGACA 58.573 37.500 0.90 0.30 0.00 3.41
3458 4022 9.371136 TCATTCAAGAGTTATGATTGTACTCAC 57.629 33.333 0.00 0.00 40.53 3.51
3471 4035 6.988580 TGATTGTACTCACATCCATTGAGATC 59.011 38.462 6.37 0.31 42.81 2.75
3518 4082 3.703286 AGTTTTGCTTCGGTAACAACC 57.297 42.857 0.00 0.00 0.00 3.77
3519 4083 2.359848 AGTTTTGCTTCGGTAACAACCC 59.640 45.455 0.00 0.00 0.00 4.11
3520 4084 1.320507 TTTGCTTCGGTAACAACCCC 58.679 50.000 0.00 0.00 0.00 4.95
3521 4085 0.537828 TTGCTTCGGTAACAACCCCC 60.538 55.000 0.00 0.00 0.00 5.40
3522 4086 1.377612 GCTTCGGTAACAACCCCCT 59.622 57.895 0.00 0.00 0.00 4.79
3523 4087 0.675837 GCTTCGGTAACAACCCCCTC 60.676 60.000 0.00 0.00 0.00 4.30
3524 4088 0.035725 CTTCGGTAACAACCCCCTCC 60.036 60.000 0.00 0.00 0.00 4.30
3525 4089 1.491274 TTCGGTAACAACCCCCTCCC 61.491 60.000 0.00 0.00 0.00 4.30
3526 4090 1.921857 CGGTAACAACCCCCTCCCT 60.922 63.158 0.00 0.00 0.00 4.20
3527 4091 1.907222 CGGTAACAACCCCCTCCCTC 61.907 65.000 0.00 0.00 0.00 4.30
3528 4092 1.569030 GGTAACAACCCCCTCCCTCC 61.569 65.000 0.00 0.00 0.00 4.30
3529 4093 0.549413 GTAACAACCCCCTCCCTCCT 60.549 60.000 0.00 0.00 0.00 3.69
3530 4094 0.253020 TAACAACCCCCTCCCTCCTC 60.253 60.000 0.00 0.00 0.00 3.71
3531 4095 2.692741 CAACCCCCTCCCTCCTCC 60.693 72.222 0.00 0.00 0.00 4.30
3532 4096 2.882143 AACCCCCTCCCTCCTCCT 60.882 66.667 0.00 0.00 0.00 3.69
3533 4097 2.511458 AACCCCCTCCCTCCTCCTT 61.511 63.158 0.00 0.00 0.00 3.36
3534 4098 1.166973 AACCCCCTCCCTCCTCCTTA 61.167 60.000 0.00 0.00 0.00 2.69
3535 4099 1.166973 ACCCCCTCCCTCCTCCTTAA 61.167 60.000 0.00 0.00 0.00 1.85
3536 4100 0.045778 CCCCCTCCCTCCTCCTTAAA 59.954 60.000 0.00 0.00 0.00 1.52
3537 4101 1.559584 CCCCCTCCCTCCTCCTTAAAA 60.560 57.143 0.00 0.00 0.00 1.52
3595 4372 2.299013 CGCCATATTAGCCTACAGGTCA 59.701 50.000 0.00 0.00 37.57 4.02
3856 4638 8.804688 TTACCAAGTATGCAAATGTTTACAAC 57.195 30.769 0.00 0.00 0.00 3.32
3857 4639 7.049799 ACCAAGTATGCAAATGTTTACAACT 57.950 32.000 0.00 0.00 0.00 3.16
3858 4640 8.172352 ACCAAGTATGCAAATGTTTACAACTA 57.828 30.769 0.00 0.00 0.00 2.24
3859 4641 8.296713 ACCAAGTATGCAAATGTTTACAACTAG 58.703 33.333 0.00 0.00 0.00 2.57
3860 4642 8.511321 CCAAGTATGCAAATGTTTACAACTAGA 58.489 33.333 0.00 0.00 0.00 2.43
3861 4643 9.546909 CAAGTATGCAAATGTTTACAACTAGAG 57.453 33.333 0.00 0.00 0.00 2.43
3863 4645 8.100791 AGTATGCAAATGTTTACAACTAGAGGA 58.899 33.333 0.00 0.00 0.00 3.71
3864 4646 6.801539 TGCAAATGTTTACAACTAGAGGAG 57.198 37.500 0.00 0.00 0.00 3.69
3875 4659 4.148838 CAACTAGAGGAGTAGGAGGGATG 58.851 52.174 0.00 0.00 37.44 3.51
3991 4775 2.811431 TCAATTCGCCTGTGAATTCGTT 59.189 40.909 14.07 0.00 44.55 3.85
4298 5083 9.866655 AACATCCTCTAATATTGCCTTGAATTA 57.133 29.630 0.00 0.00 0.00 1.40
4556 5341 4.402155 AGCTGTTCAATTTGGAGTGTGAAA 59.598 37.500 0.00 0.00 32.12 2.69
4628 5413 0.402504 TCGCCATAAAAGGTGGTGGT 59.597 50.000 5.94 0.00 45.18 4.16
4649 5434 4.106925 CCCTCACCTGCCAGCCTC 62.107 72.222 0.00 0.00 0.00 4.70
4731 5516 0.036294 GTACACTGTCCCTCAAGCCC 60.036 60.000 0.00 0.00 0.00 5.19
4733 5518 1.352622 ACACTGTCCCTCAAGCCCAA 61.353 55.000 0.00 0.00 0.00 4.12
4738 5523 0.251787 GTCCCTCAAGCCCAACCATT 60.252 55.000 0.00 0.00 0.00 3.16
4739 5524 0.251742 TCCCTCAAGCCCAACCATTG 60.252 55.000 0.00 0.00 0.00 2.82
4776 5561 7.392673 GTGAGCCATGATGATTTCTACCATTAT 59.607 37.037 0.00 0.00 0.00 1.28
4777 5562 7.609146 TGAGCCATGATGATTTCTACCATTATC 59.391 37.037 0.00 0.00 0.00 1.75
4825 5610 5.139727 CAAGCCCTGATGGTTTATTCCATA 58.860 41.667 0.00 0.00 46.72 2.74
4836 5621 6.423182 TGGTTTATTCCATAACCCTCTTCAG 58.577 40.000 0.00 0.00 29.52 3.02
4838 5623 6.318900 GGTTTATTCCATAACCCTCTTCAGTG 59.681 42.308 0.00 0.00 0.00 3.66
4894 5707 5.360649 TGGACATGGAAATACGTTATCCA 57.639 39.130 16.03 16.03 46.60 3.41
4953 5766 0.819582 TAACCCGTAGAAAGGAGCGG 59.180 55.000 0.00 0.00 43.40 5.52
5046 5859 7.433708 TGCTTTCGAGAATTTGAGATTTGTA 57.566 32.000 0.00 0.00 0.00 2.41
5051 5864 6.936279 TCGAGAATTTGAGATTTGTACCTCT 58.064 36.000 0.00 0.00 0.00 3.69
5104 5917 2.742053 TGAGGCAGACGATTTTAGCAAC 59.258 45.455 0.00 0.00 0.00 4.17
5120 5933 1.732405 GCAACTTGTAAATGAGGCGGC 60.732 52.381 0.00 0.00 0.00 6.53
5126 5939 1.017177 GTAAATGAGGCGGCGTGACA 61.017 55.000 9.37 6.63 0.00 3.58
5140 5953 4.442733 CGGCGTGACAAAATGTTTGTAAAT 59.557 37.500 6.36 0.00 31.96 1.40
5142 5955 5.233263 GGCGTGACAAAATGTTTGTAAATGT 59.767 36.000 6.36 0.00 31.96 2.71
5143 5956 6.418226 GGCGTGACAAAATGTTTGTAAATGTA 59.582 34.615 6.36 0.00 31.96 2.29
5144 5957 7.115663 GGCGTGACAAAATGTTTGTAAATGTAT 59.884 33.333 6.36 0.00 31.96 2.29
5145 5958 7.944120 GCGTGACAAAATGTTTGTAAATGTATG 59.056 33.333 6.36 0.00 31.96 2.39
5146 5959 7.944120 CGTGACAAAATGTTTGTAAATGTATGC 59.056 33.333 6.36 0.00 31.96 3.14
5147 5960 8.977505 GTGACAAAATGTTTGTAAATGTATGCT 58.022 29.630 6.36 0.00 31.96 3.79
5148 5961 8.976471 TGACAAAATGTTTGTAAATGTATGCTG 58.024 29.630 6.36 0.00 31.96 4.41
5149 5962 7.795859 ACAAAATGTTTGTAAATGTATGCTGC 58.204 30.769 4.59 0.00 0.00 5.25
5176 5989 2.158475 TGTCAGCAAACCTGGATTCCTT 60.158 45.455 0.00 0.00 42.05 3.36
5183 5996 3.593442 AACCTGGATTCCTTGTGTCAA 57.407 42.857 0.00 0.00 0.00 3.18
5184 5997 3.814504 ACCTGGATTCCTTGTGTCAAT 57.185 42.857 0.00 0.00 0.00 2.57
5185 5998 4.118168 ACCTGGATTCCTTGTGTCAATT 57.882 40.909 0.00 0.00 0.00 2.32
5186 5999 4.482990 ACCTGGATTCCTTGTGTCAATTT 58.517 39.130 0.00 0.00 0.00 1.82
5187 6000 4.901250 ACCTGGATTCCTTGTGTCAATTTT 59.099 37.500 0.00 0.00 0.00 1.82
5188 6001 5.011023 ACCTGGATTCCTTGTGTCAATTTTC 59.989 40.000 0.00 0.00 0.00 2.29
5189 6002 5.010922 CCTGGATTCCTTGTGTCAATTTTCA 59.989 40.000 3.95 0.00 0.00 2.69
5190 6003 6.462768 CCTGGATTCCTTGTGTCAATTTTCAA 60.463 38.462 3.95 0.00 0.00 2.69
5219 6032 8.852135 TCAATAAAATAAACCACCTTCGAAGTT 58.148 29.630 23.03 12.89 0.00 2.66
5256 6076 8.870879 GTTTCTCACCAATGTATGTAGTAAGTC 58.129 37.037 0.00 0.00 0.00 3.01
5261 6081 7.121611 TCACCAATGTATGTAGTAAGTCGAAGA 59.878 37.037 0.00 0.00 0.00 2.87
5312 6132 2.877097 TTATTTGGCAGCAGGACTCA 57.123 45.000 0.00 0.00 0.00 3.41
5316 6136 0.250467 TTGGCAGCAGGACTCAAGAC 60.250 55.000 0.00 0.00 0.00 3.01
5326 6146 0.723981 GACTCAAGACTTGCATCGGC 59.276 55.000 10.50 0.00 41.68 5.54
5375 6196 8.867112 TGTATACAGATTTCATAGACGTTTCC 57.133 34.615 0.08 0.00 0.00 3.13
5377 6198 7.772332 ATACAGATTTCATAGACGTTTCCAC 57.228 36.000 0.00 0.00 0.00 4.02
5383 6204 5.873179 TTCATAGACGTTTCCACAAATCC 57.127 39.130 0.00 0.00 0.00 3.01
5385 6206 2.649531 AGACGTTTCCACAAATCCCA 57.350 45.000 0.00 0.00 0.00 4.37
5407 6228 6.362283 CCCAAAACTACAAGCATCTTTAAACG 59.638 38.462 0.00 0.00 0.00 3.60
5509 6336 3.744238 ATTTGGGCCAAAGTAACACAC 57.256 42.857 32.84 0.00 36.76 3.82
5577 6418 0.583438 CTTTATGTCGCATGGAGCCG 59.417 55.000 0.00 0.00 41.38 5.52
5584 6425 2.537560 CGCATGGAGCCGATGAACC 61.538 63.158 0.00 0.00 41.38 3.62
5619 6460 6.624423 ACACAATATTTCCATTTGAGACAGC 58.376 36.000 0.00 0.00 0.00 4.40
5640 6481 4.638421 AGCACTTACAAGTACAGCAAAACA 59.362 37.500 0.00 0.00 37.08 2.83
5740 6581 4.033009 TCCTGTTATCTCTTCTCATGGCA 58.967 43.478 0.00 0.00 0.00 4.92
5769 6610 0.668535 GCCTGGACCTGAACAACAAC 59.331 55.000 0.00 0.00 0.00 3.32
5830 6671 7.278461 TCTAGGTTGCAGACTAGAATACATC 57.722 40.000 20.63 0.00 41.84 3.06
5850 6691 4.156455 TCTGATCATAGGAAAACAGGGC 57.844 45.455 0.00 0.00 0.00 5.19
5913 6754 9.942850 ATTTTTACAGAAACATATTTTCCCCTG 57.057 29.630 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.360607 GCATCTTTTTCGTGTAAAGCTTACCTA 60.361 37.037 0.00 0.00 33.61 3.08
15 16 3.185594 CGAGGTGCATCTTTTTCGTGTAA 59.814 43.478 0.00 0.00 0.00 2.41
76 77 4.124970 GTTATAAAGAACTTCCGGCCGAT 58.875 43.478 30.73 10.53 0.00 4.18
149 259 4.571176 CGTGAGTACACTAGACTGCTGATA 59.429 45.833 0.00 0.00 43.99 2.15
151 261 2.742589 CGTGAGTACACTAGACTGCTGA 59.257 50.000 0.00 0.00 43.99 4.26
288 398 2.885113 CCGAGATGAGTGACGCCA 59.115 61.111 0.00 0.00 0.00 5.69
412 554 3.378339 CGAAAACGACTCCAGTGTAGTT 58.622 45.455 0.00 0.00 37.37 2.24
469 629 1.143183 GCCATGGTATCGTCCGTGT 59.857 57.895 14.67 0.00 41.44 4.49
528 688 1.783284 CGAACTAGTTGCAGTGCTCA 58.217 50.000 14.14 0.00 0.00 4.26
549 710 4.379143 CGTCGAGCGACACCGTCA 62.379 66.667 21.09 0.00 44.77 4.35
622 784 1.940883 GCGGTGGATAGTGGTCGTGA 61.941 60.000 0.00 0.00 0.00 4.35
667 840 0.633921 AGAGCTAGCAGAGGAAGGGA 59.366 55.000 18.83 0.00 0.00 4.20
710 883 5.339008 TGGGGTATGATTAATAGCTAGCG 57.661 43.478 9.55 0.00 38.94 4.26
786 959 4.985409 GGAATCAATTTTGGCACGTTGTTA 59.015 37.500 0.00 0.00 0.00 2.41
833 1007 3.229276 TCTGCAAGTTGTTTGGTTGTG 57.771 42.857 4.48 0.00 37.26 3.33
867 1041 2.554032 CCGTCTGGCTCTGAAAAACAAT 59.446 45.455 0.00 0.00 0.00 2.71
887 1062 1.299468 CGTCGCCTGCAGTATCTCC 60.299 63.158 13.81 0.00 0.00 3.71
891 1066 0.179119 GTTACCGTCGCCTGCAGTAT 60.179 55.000 13.81 0.00 0.00 2.12
892 1067 1.213537 GTTACCGTCGCCTGCAGTA 59.786 57.895 13.81 0.00 0.00 2.74
893 1068 2.048503 GTTACCGTCGCCTGCAGT 60.049 61.111 13.81 0.00 0.00 4.40
894 1069 2.813908 GGTTACCGTCGCCTGCAG 60.814 66.667 6.78 6.78 0.00 4.41
895 1070 2.661840 TTTGGTTACCGTCGCCTGCA 62.662 55.000 0.00 0.00 0.00 4.41
896 1071 1.962306 TTTGGTTACCGTCGCCTGC 60.962 57.895 0.00 0.00 0.00 4.85
897 1072 0.881159 TGTTTGGTTACCGTCGCCTG 60.881 55.000 0.00 0.00 0.00 4.85
898 1073 0.881600 GTGTTTGGTTACCGTCGCCT 60.882 55.000 0.00 0.00 0.00 5.52
899 1074 1.570967 GTGTTTGGTTACCGTCGCC 59.429 57.895 0.00 0.00 0.00 5.54
900 1075 1.202320 CGTGTTTGGTTACCGTCGC 59.798 57.895 0.00 0.00 0.00 5.19
901 1076 1.202320 GCGTGTTTGGTTACCGTCG 59.798 57.895 0.00 0.00 0.00 5.12
902 1077 1.570967 GGCGTGTTTGGTTACCGTC 59.429 57.895 0.00 0.00 0.00 4.79
903 1078 1.893335 GGGCGTGTTTGGTTACCGT 60.893 57.895 0.00 0.00 0.00 4.83
904 1079 2.619165 GGGGCGTGTTTGGTTACCG 61.619 63.158 0.00 0.00 0.00 4.02
905 1080 0.036590 TAGGGGCGTGTTTGGTTACC 59.963 55.000 0.00 0.00 0.00 2.85
906 1081 1.445871 CTAGGGGCGTGTTTGGTTAC 58.554 55.000 0.00 0.00 0.00 2.50
907 1082 0.325602 CCTAGGGGCGTGTTTGGTTA 59.674 55.000 0.00 0.00 0.00 2.85
908 1083 1.074248 CCTAGGGGCGTGTTTGGTT 59.926 57.895 0.00 0.00 0.00 3.67
909 1084 1.205460 ATCCTAGGGGCGTGTTTGGT 61.205 55.000 9.46 0.00 0.00 3.67
910 1085 0.463833 GATCCTAGGGGCGTGTTTGG 60.464 60.000 9.46 0.00 0.00 3.28
911 1086 0.810031 CGATCCTAGGGGCGTGTTTG 60.810 60.000 9.46 0.00 0.00 2.93
912 1087 1.520666 CGATCCTAGGGGCGTGTTT 59.479 57.895 9.46 0.00 0.00 2.83
913 1088 2.432300 CCGATCCTAGGGGCGTGTT 61.432 63.158 9.46 0.00 0.00 3.32
914 1089 2.838225 CCGATCCTAGGGGCGTGT 60.838 66.667 9.46 0.00 0.00 4.49
915 1090 2.365095 GAACCGATCCTAGGGGCGTG 62.365 65.000 9.46 9.41 0.00 5.34
916 1091 2.042230 AACCGATCCTAGGGGCGT 60.042 61.111 9.46 0.00 0.00 5.68
917 1092 2.735237 GAACCGATCCTAGGGGCG 59.265 66.667 9.46 12.71 0.00 6.13
918 1093 1.186267 ATCGAACCGATCCTAGGGGC 61.186 60.000 9.46 0.00 43.45 5.80
919 1094 3.053146 ATCGAACCGATCCTAGGGG 57.947 57.895 9.46 4.84 43.45 4.79
929 1104 4.569761 TCTAGATGAAAGGATCGAACCG 57.430 45.455 6.02 0.00 34.73 4.44
946 1121 6.771188 ATAATCCGCGACATTTCTTTCTAG 57.229 37.500 8.23 0.00 0.00 2.43
947 1122 8.827177 ATAATAATCCGCGACATTTCTTTCTA 57.173 30.769 8.23 0.00 0.00 2.10
948 1123 7.730364 ATAATAATCCGCGACATTTCTTTCT 57.270 32.000 8.23 0.00 0.00 2.52
949 1124 9.872757 TTTATAATAATCCGCGACATTTCTTTC 57.127 29.630 8.23 0.00 0.00 2.62
953 1128 9.113876 CCTTTTTATAATAATCCGCGACATTTC 57.886 33.333 8.23 0.00 0.00 2.17
957 1132 7.789273 TTCCTTTTTATAATAATCCGCGACA 57.211 32.000 8.23 0.00 0.00 4.35
989 1164 0.886490 GTGACGCATCCATGGATCCC 60.886 60.000 24.93 16.66 31.62 3.85
1005 1180 4.499188 CGAGTCAACCTAGTCAACAAGTGA 60.499 45.833 0.00 0.00 0.00 3.41
1017 1192 1.310933 GCTCCGTCCGAGTCAACCTA 61.311 60.000 0.00 0.00 41.10 3.08
1018 1193 2.637383 GCTCCGTCCGAGTCAACCT 61.637 63.158 0.00 0.00 41.10 3.50
1019 1194 2.126031 GCTCCGTCCGAGTCAACC 60.126 66.667 0.00 0.00 41.10 3.77
1020 1195 2.126031 GGCTCCGTCCGAGTCAAC 60.126 66.667 0.00 0.00 43.22 3.18
1023 1198 3.371063 TGTGGCTCCGTCCGAGTC 61.371 66.667 0.00 0.00 44.07 3.36
1024 1199 3.681835 GTGTGGCTCCGTCCGAGT 61.682 66.667 0.00 0.00 41.10 4.18
1025 1200 4.436998 GGTGTGGCTCCGTCCGAG 62.437 72.222 0.00 0.00 42.04 4.63
1027 1202 4.308458 TTGGTGTGGCTCCGTCCG 62.308 66.667 0.00 0.00 0.00 4.79
1028 1203 2.668550 GTTGGTGTGGCTCCGTCC 60.669 66.667 0.00 0.00 0.00 4.79
1029 1204 2.668550 GGTTGGTGTGGCTCCGTC 60.669 66.667 0.00 0.00 0.00 4.79
1030 1205 3.484806 TGGTTGGTGTGGCTCCGT 61.485 61.111 0.00 0.00 0.00 4.69
1032 1207 2.193536 GTGTGGTTGGTGTGGCTCC 61.194 63.158 0.00 0.00 0.00 4.70
1033 1208 1.453015 TGTGTGGTTGGTGTGGCTC 60.453 57.895 0.00 0.00 0.00 4.70
1034 1209 1.752694 GTGTGTGGTTGGTGTGGCT 60.753 57.895 0.00 0.00 0.00 4.75
1035 1210 2.049185 TGTGTGTGGTTGGTGTGGC 61.049 57.895 0.00 0.00 0.00 5.01
1036 1211 0.679640 AGTGTGTGTGGTTGGTGTGG 60.680 55.000 0.00 0.00 0.00 4.17
1038 1213 1.459450 GAAGTGTGTGTGGTTGGTGT 58.541 50.000 0.00 0.00 0.00 4.16
1039 1214 0.738389 GGAAGTGTGTGTGGTTGGTG 59.262 55.000 0.00 0.00 0.00 4.17
1040 1215 0.395173 GGGAAGTGTGTGTGGTTGGT 60.395 55.000 0.00 0.00 0.00 3.67
1041 1216 1.106944 GGGGAAGTGTGTGTGGTTGG 61.107 60.000 0.00 0.00 0.00 3.77
1043 1218 0.182775 GAGGGGAAGTGTGTGTGGTT 59.817 55.000 0.00 0.00 0.00 3.67
1044 1219 1.837090 GAGGGGAAGTGTGTGTGGT 59.163 57.895 0.00 0.00 0.00 4.16
1046 1221 1.961277 GCGAGGGGAAGTGTGTGTG 60.961 63.158 0.00 0.00 0.00 3.82
1047 1222 2.426023 GCGAGGGGAAGTGTGTGT 59.574 61.111 0.00 0.00 0.00 3.72
1048 1223 2.738521 CGCGAGGGGAAGTGTGTG 60.739 66.667 0.00 0.00 0.00 3.82
1049 1224 4.681978 GCGCGAGGGGAAGTGTGT 62.682 66.667 12.10 0.00 0.00 3.72
1052 1227 2.815647 GAAGCGCGAGGGGAAGTG 60.816 66.667 12.10 0.00 0.00 3.16
1053 1228 4.083862 GGAAGCGCGAGGGGAAGT 62.084 66.667 12.10 0.00 0.00 3.01
1055 1230 3.310860 GAAGGAAGCGCGAGGGGAA 62.311 63.158 12.10 0.00 0.00 3.97
1056 1231 3.771160 GAAGGAAGCGCGAGGGGA 61.771 66.667 12.10 0.00 0.00 4.81
1072 1261 3.408853 TCGAGGAGGCGGAGGAGA 61.409 66.667 0.00 0.00 0.00 3.71
1080 1269 3.607661 GGATCGGGTCGAGGAGGC 61.608 72.222 0.00 0.00 39.91 4.70
1082 1271 2.123854 TGGGATCGGGTCGAGGAG 60.124 66.667 0.00 0.00 39.91 3.69
1083 1272 2.441532 GTGGGATCGGGTCGAGGA 60.442 66.667 0.00 0.00 39.91 3.71
1084 1273 2.442272 AGTGGGATCGGGTCGAGG 60.442 66.667 0.00 0.00 39.91 4.63
1085 1274 2.835705 CGAGTGGGATCGGGTCGAG 61.836 68.421 0.00 0.00 39.91 4.04
1094 1283 4.241555 GGATGCCGCGAGTGGGAT 62.242 66.667 8.23 9.43 43.52 3.85
1141 1336 2.689771 GGGGGCGAAGTAAGGGGA 60.690 66.667 0.00 0.00 0.00 4.81
1333 1528 2.701780 GCGAGAAGCGTGAGAGGGA 61.702 63.158 0.00 0.00 43.41 4.20
1494 1690 4.065789 GAGTTAACTGGAACACTTGGGAG 58.934 47.826 14.14 0.00 0.00 4.30
1496 1692 3.564225 GTGAGTTAACTGGAACACTTGGG 59.436 47.826 14.14 0.00 0.00 4.12
1511 1707 5.394883 GGAGGATATGTCAAACCGTGAGTTA 60.395 44.000 0.00 0.00 37.88 2.24
1535 1731 6.296145 GGATAGGGTAATTCTCATCTTCCCAG 60.296 46.154 0.00 0.00 36.24 4.45
1639 1835 7.360946 GCAAGTTACGTCCAGATGAACTTTAAT 60.361 37.037 7.46 0.00 38.06 1.40
1648 1844 4.685169 AAATGCAAGTTACGTCCAGATG 57.315 40.909 0.00 0.00 0.00 2.90
1810 2034 7.693020 ACAAATACTTGGAAAAACATTTGCAC 58.307 30.769 0.00 0.00 34.37 4.57
1826 2050 6.622896 GCAGCATTTACCGAGAACAAATACTT 60.623 38.462 0.00 0.00 0.00 2.24
1977 2202 3.943671 TTCACAGAACCCTGGAAAAGA 57.056 42.857 0.00 0.00 44.60 2.52
2081 2306 0.684535 TCTGGCAATCCAAGTCGTGA 59.315 50.000 0.00 0.00 42.91 4.35
2386 2611 8.958060 AAGGAGTTACAGCCTATTATGATAGA 57.042 34.615 6.09 0.00 37.97 1.98
2676 2904 3.386726 TGGATCCTACAAGTACATTCCCG 59.613 47.826 14.23 0.00 0.00 5.14
2738 2966 6.209192 ACTTGCATTGTAAGAATCATGTCCAA 59.791 34.615 19.57 0.00 0.00 3.53
2814 3045 8.244113 TGCATTATGATATACGGTACTGAAGAG 58.756 37.037 9.17 0.00 0.00 2.85
2815 3046 8.117813 TGCATTATGATATACGGTACTGAAGA 57.882 34.615 9.17 0.00 0.00 2.87
2816 3047 7.489435 CCTGCATTATGATATACGGTACTGAAG 59.511 40.741 9.17 0.00 0.00 3.02
2817 3048 7.320399 CCTGCATTATGATATACGGTACTGAA 58.680 38.462 9.17 0.00 0.00 3.02
2819 3050 6.042777 CCCTGCATTATGATATACGGTACTG 58.957 44.000 0.00 0.00 0.00 2.74
2820 3051 5.395324 GCCCTGCATTATGATATACGGTACT 60.395 44.000 0.00 0.00 0.00 2.73
2821 3052 4.809426 GCCCTGCATTATGATATACGGTAC 59.191 45.833 0.00 0.00 0.00 3.34
2825 3320 4.758688 TCTGCCCTGCATTATGATATACG 58.241 43.478 0.00 0.00 38.13 3.06
3398 3962 2.218603 GACGAACAAACACAGGTGGAT 58.781 47.619 4.24 0.00 34.19 3.41
3399 3963 1.066071 TGACGAACAAACACAGGTGGA 60.066 47.619 4.24 0.00 34.19 4.02
3458 4022 5.758790 ATCCTAGGTGATCTCAATGGATG 57.241 43.478 9.08 0.00 32.55 3.51
3512 4076 1.541620 GAGGAGGGAGGGGGTTGTT 60.542 63.158 0.00 0.00 0.00 2.83
3513 4077 2.125225 GAGGAGGGAGGGGGTTGT 59.875 66.667 0.00 0.00 0.00 3.32
3514 4078 2.692741 GGAGGAGGGAGGGGGTTG 60.693 72.222 0.00 0.00 0.00 3.77
3515 4079 1.166973 TAAGGAGGAGGGAGGGGGTT 61.167 60.000 0.00 0.00 0.00 4.11
3516 4080 1.166973 TTAAGGAGGAGGGAGGGGGT 61.167 60.000 0.00 0.00 0.00 4.95
3517 4081 0.045778 TTTAAGGAGGAGGGAGGGGG 59.954 60.000 0.00 0.00 0.00 5.40
3518 4082 1.847088 CTTTTAAGGAGGAGGGAGGGG 59.153 57.143 0.00 0.00 0.00 4.79
3519 4083 2.563406 ACTTTTAAGGAGGAGGGAGGG 58.437 52.381 0.00 0.00 0.00 4.30
3520 4084 4.336280 CAAACTTTTAAGGAGGAGGGAGG 58.664 47.826 0.00 0.00 0.00 4.30
3521 4085 3.759086 GCAAACTTTTAAGGAGGAGGGAG 59.241 47.826 0.00 0.00 0.00 4.30
3522 4086 3.139397 TGCAAACTTTTAAGGAGGAGGGA 59.861 43.478 0.00 0.00 0.00 4.20
3523 4087 3.496331 TGCAAACTTTTAAGGAGGAGGG 58.504 45.455 0.00 0.00 0.00 4.30
3524 4088 4.766891 TCATGCAAACTTTTAAGGAGGAGG 59.233 41.667 0.00 0.00 0.00 4.30
3525 4089 5.964958 TCATGCAAACTTTTAAGGAGGAG 57.035 39.130 0.00 0.00 0.00 3.69
3526 4090 6.721208 AGATTCATGCAAACTTTTAAGGAGGA 59.279 34.615 0.00 0.00 0.00 3.71
3527 4091 6.928520 AGATTCATGCAAACTTTTAAGGAGG 58.071 36.000 0.00 0.00 0.00 4.30
3528 4092 9.912634 TTAAGATTCATGCAAACTTTTAAGGAG 57.087 29.630 0.00 0.00 0.00 3.69
3595 4372 9.661563 TGTATCCAAAATCTACTCAATACGTTT 57.338 29.630 0.00 0.00 0.00 3.60
3666 4443 5.622914 CGGATTTTGATGCAGATTGAAGGTT 60.623 40.000 0.00 0.00 0.00 3.50
3856 4638 2.719705 ACCATCCCTCCTACTCCTCTAG 59.280 54.545 0.00 0.00 0.00 2.43
3857 4639 2.447429 CACCATCCCTCCTACTCCTCTA 59.553 54.545 0.00 0.00 0.00 2.43
3858 4640 1.219213 CACCATCCCTCCTACTCCTCT 59.781 57.143 0.00 0.00 0.00 3.69
3859 4641 1.062810 ACACCATCCCTCCTACTCCTC 60.063 57.143 0.00 0.00 0.00 3.71
3860 4642 1.019650 ACACCATCCCTCCTACTCCT 58.980 55.000 0.00 0.00 0.00 3.69
3861 4643 1.343075 TGACACCATCCCTCCTACTCC 60.343 57.143 0.00 0.00 0.00 3.85
3863 4645 2.683768 GATGACACCATCCCTCCTACT 58.316 52.381 0.00 0.00 42.55 2.57
3875 4659 2.234908 AGTTAGAGCCACAGATGACACC 59.765 50.000 0.00 0.00 0.00 4.16
3991 4775 6.808357 TCTAAGTACTAGAGAGGGGGAAAAA 58.192 40.000 0.00 0.00 32.56 1.94
3996 4780 5.515886 CCTCATCTAAGTACTAGAGAGGGGG 60.516 52.000 18.74 18.74 41.97 5.40
3997 4781 5.311121 TCCTCATCTAAGTACTAGAGAGGGG 59.689 48.000 24.20 19.29 43.59 4.79
3998 4782 6.183361 TGTCCTCATCTAAGTACTAGAGAGGG 60.183 46.154 24.20 19.23 43.59 4.30
4321 5106 7.342284 TCTCTTAAGTTACTGGATAGAACTGGG 59.658 40.741 1.63 0.00 33.75 4.45
4403 5188 5.772825 TGCAGCTTCTCAATAAACAAGTT 57.227 34.783 0.00 0.00 0.00 2.66
4433 5218 1.677518 CCCTTTGCGGTGCAGTATACA 60.678 52.381 5.50 0.00 40.61 2.29
4434 5219 1.014352 CCCTTTGCGGTGCAGTATAC 58.986 55.000 0.00 0.00 40.61 1.47
4574 5359 7.231925 TCCTGCATATCAAATATTCATGTGCTT 59.768 33.333 20.44 0.75 36.08 3.91
4628 5413 2.592993 GCTGGCAGGTGAGGGTACA 61.593 63.158 17.64 0.00 0.00 2.90
4635 5420 4.980592 TGGGAGGCTGGCAGGTGA 62.981 66.667 17.64 0.00 0.00 4.02
4649 5434 4.080129 TCCTTGATCTCCTGAAAAGATGGG 60.080 45.833 0.00 0.00 33.64 4.00
4724 5509 0.896923 GCATCAATGGTTGGGCTTGA 59.103 50.000 0.00 0.00 33.75 3.02
4731 5516 1.619827 ACCACTTGGCATCAATGGTTG 59.380 47.619 6.65 0.00 40.86 3.77
4733 5518 1.203038 TCACCACTTGGCATCAATGGT 60.203 47.619 6.65 6.65 44.58 3.55
4738 5523 1.303561 GGCTCACCACTTGGCATCA 60.304 57.895 0.00 0.00 39.32 3.07
4739 5524 1.303561 TGGCTCACCACTTGGCATC 60.304 57.895 0.00 0.00 42.67 3.91
4776 5561 5.745312 AGTCATGTCTACATTGAACAGGA 57.255 39.130 0.00 0.00 33.61 3.86
4777 5562 5.122869 CCAAGTCATGTCTACATTGAACAGG 59.877 44.000 0.00 0.00 33.61 4.00
4825 5610 3.904339 ACATGTCTACACTGAAGAGGGTT 59.096 43.478 0.00 0.00 37.01 4.11
4836 5621 4.454504 CACTTGGGGTTAACATGTCTACAC 59.545 45.833 8.10 0.97 0.00 2.90
4838 5623 4.007659 CCACTTGGGGTTAACATGTCTAC 58.992 47.826 8.10 0.00 0.00 2.59
4974 5787 3.094572 CCTGGATCCCATTTCCATATGC 58.905 50.000 9.90 0.00 42.26 3.14
4975 5788 4.084287 CACCTGGATCCCATTTCCATATG 58.916 47.826 9.90 0.00 42.26 1.78
5051 5864 2.044650 GCTCTGCCTCATTGCCCA 60.045 61.111 0.00 0.00 0.00 5.36
5104 5917 0.096976 CACGCCGCCTCATTTACAAG 59.903 55.000 0.00 0.00 0.00 3.16
5120 5933 7.944120 GCATACATTTACAAACATTTTGTCACG 59.056 33.333 7.54 0.00 34.11 4.35
5126 5939 8.606040 AAGCAGCATACATTTACAAACATTTT 57.394 26.923 0.00 0.00 0.00 1.82
5140 5953 2.153645 CTGACACCAAAGCAGCATACA 58.846 47.619 0.00 0.00 0.00 2.29
5148 5961 0.746659 AGGTTTGCTGACACCAAAGC 59.253 50.000 14.72 14.72 45.82 3.51
5149 5962 1.067516 CCAGGTTTGCTGACACCAAAG 59.932 52.381 0.00 0.00 35.25 2.77
5209 6022 5.424121 ACATTTCTCAACAACTTCGAAGG 57.576 39.130 27.86 14.23 0.00 3.46
5295 6115 1.074405 TCTTGAGTCCTGCTGCCAAAT 59.926 47.619 0.00 0.00 0.00 2.32
5326 6146 8.776470 ACATTTCAGTTTAATGCTCCAAAATTG 58.224 29.630 0.00 0.00 36.65 2.32
5365 6186 3.773418 TGGGATTTGTGGAAACGTCTA 57.227 42.857 0.00 0.00 0.00 2.59
5369 6190 4.053469 AGTTTTGGGATTTGTGGAAACG 57.947 40.909 0.00 0.00 33.52 3.60
5375 6196 4.942852 TGCTTGTAGTTTTGGGATTTGTG 58.057 39.130 0.00 0.00 0.00 3.33
5377 6198 6.029346 AGATGCTTGTAGTTTTGGGATTTG 57.971 37.500 0.00 0.00 0.00 2.32
5383 6204 6.915843 ACGTTTAAAGATGCTTGTAGTTTTGG 59.084 34.615 0.00 0.00 0.00 3.28
5407 6228 8.814235 ACACTATAGCGAACATGTTTACATAAC 58.186 33.333 13.36 0.00 34.26 1.89
5434 6261 4.846779 ATGTAACAGCACGGTTTTCATT 57.153 36.364 0.00 0.00 32.29 2.57
5509 6336 5.471116 TGTGAACTGATGAGGAAGAACATTG 59.529 40.000 0.00 0.00 0.00 2.82
5562 6403 1.596203 CATCGGCTCCATGCGACAT 60.596 57.895 0.00 0.00 44.05 3.06
5577 6418 3.181485 TGTGTTTGGTTTTCCGGTTCATC 60.181 43.478 0.00 0.00 44.36 2.92
5584 6425 5.986135 TGGAAATATTGTGTTTGGTTTTCCG 59.014 36.000 0.00 0.00 42.13 4.30
5593 6434 7.599998 GCTGTCTCAAATGGAAATATTGTGTTT 59.400 33.333 0.00 0.00 0.00 2.83
5640 6481 1.117150 ACACCGGCGTCCTGTTATAT 58.883 50.000 6.01 0.00 0.00 0.86
5740 6581 0.032416 AGGTCCAGGCTGTATACCGT 60.032 55.000 14.43 5.63 35.32 4.83
5769 6610 9.708222 CAGATATTTTGTTTAATGAGACTTCGG 57.292 33.333 0.00 0.00 0.00 4.30
5830 6671 2.874701 CGCCCTGTTTTCCTATGATCAG 59.125 50.000 0.09 0.00 0.00 2.90
5850 6691 1.461127 GCTTCAAGTGAGCAGGTAACG 59.539 52.381 0.00 0.00 46.39 3.18
5913 6754 7.201741 GGCCAAGTAAGTCAGAAAATATCTTCC 60.202 40.741 0.00 0.00 35.73 3.46


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

AutoCloner maintained by Alex Coulton.