Multiple sequence alignment - TraesCS4B01G095900

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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 TraesCS4B01G095900 chr4B 100.000 4290 0 0 1 4290 99434476 99438765 0.000000e+00 7923.0
1 TraesCS4B01G095900 chr4B 79.392 592 91 20 2 584 291846742 291847311 5.200000e-104 388.0
2 TraesCS4B01G095900 chr4D 97.527 1496 37 0 948 2443 67334978 67333483 0.000000e+00 2558.0
3 TraesCS4B01G095900 chr4D 96.051 1266 30 5 3026 4290 67333106 67331860 0.000000e+00 2043.0
4 TraesCS4B01G095900 chr4D 94.465 813 37 3 75 881 67336529 67335719 0.000000e+00 1245.0
5 TraesCS4B01G095900 chr4D 95.288 382 15 2 2566 2945 67333485 67333105 1.710000e-168 603.0
6 TraesCS4B01G095900 chr4D 97.414 116 3 0 766 881 67335717 67335602 9.410000e-47 198.0
7 TraesCS4B01G095900 chr4D 92.233 103 4 4 2932 3032 3719271 3719371 4.470000e-30 143.0
8 TraesCS4B01G095900 chr1A 89.402 585 47 5 2 585 171022716 171022146 0.000000e+00 723.0
9 TraesCS4B01G095900 chr1A 97.761 134 3 0 2434 2567 208592275 208592408 9.280000e-57 231.0
10 TraesCS4B01G095900 chr3B 75.510 980 191 24 1027 1982 14046530 14045576 6.590000e-118 435.0
11 TraesCS4B01G095900 chr3B 89.527 296 24 6 293 585 640536687 640536978 6.780000e-98 368.0
12 TraesCS4B01G095900 chr3B 74.390 902 179 33 1002 1890 14053312 14052450 5.310000e-89 339.0
13 TraesCS4B01G095900 chr3B 99.231 130 1 0 2441 2570 709011864 709011735 7.170000e-58 235.0
14 TraesCS4B01G095900 chr3B 83.168 202 27 5 3167 3366 13803607 13803411 1.230000e-40 178.0
15 TraesCS4B01G095900 chr3B 85.235 149 9 1 116 264 640536561 640536696 1.610000e-29 141.0
16 TraesCS4B01G095900 chr3B 80.240 167 31 2 1328 1493 47262331 47262496 1.620000e-24 124.0
17 TraesCS4B01G095900 chr3B 76.166 193 29 4 1802 1977 28370836 28370644 7.640000e-13 86.1
18 TraesCS4B01G095900 chr3A 77.341 534 99 13 1808 2331 11536418 11536939 3.240000e-76 296.0
19 TraesCS4B01G095900 chr3A 74.265 680 138 23 1764 2428 11528104 11528761 7.120000e-63 252.0
20 TraesCS4B01G095900 chr3A 96.992 133 4 0 2441 2573 287820925 287820793 1.550000e-54 224.0
21 TraesCS4B01G095900 chr3A 81.928 83 14 1 2621 2703 10874334 10874415 7.700000e-08 69.4
22 TraesCS4B01G095900 chr3D 74.889 677 143 18 1766 2435 4844185 4844841 2.530000e-72 283.0
23 TraesCS4B01G095900 chr3D 76.686 519 102 13 1823 2331 5052510 5053019 1.970000e-68 270.0
24 TraesCS4B01G095900 chr3D 96.377 138 5 0 2434 2571 370481327 370481464 1.200000e-55 228.0
25 TraesCS4B01G095900 chr3D 95.714 140 6 0 2434 2573 112489136 112488997 4.320000e-55 226.0
26 TraesCS4B01G095900 chr3D 81.592 201 35 2 3159 3357 9762777 9762577 9.540000e-37 165.0
27 TraesCS4B01G095900 chr3D 80.100 201 37 3 3159 3357 4812497 4812696 3.460000e-31 147.0
28 TraesCS4B01G095900 chr3D 80.838 167 30 2 1328 1493 28242885 28243050 3.480000e-26 130.0
29 TraesCS4B01G095900 chr3D 78.488 172 28 9 1978 2145 4872615 4872449 2.110000e-18 104.0
30 TraesCS4B01G095900 chrUn 74.381 687 139 23 1764 2435 290169090 290169754 4.260000e-65 259.0
31 TraesCS4B01G095900 chrUn 81.768 181 32 1 3159 3338 225566417 225566237 2.670000e-32 150.0
32 TraesCS4B01G095900 chrUn 81.768 181 32 1 3159 3338 237457953 237458133 2.670000e-32 150.0
33 TraesCS4B01G095900 chrUn 81.768 181 32 1 3159 3338 257669669 257669849 2.670000e-32 150.0
34 TraesCS4B01G095900 chrUn 79.104 201 40 2 3159 3357 36001966 36002166 2.080000e-28 137.0
35 TraesCS4B01G095900 chrUn 73.735 415 78 26 1907 2313 35360227 35359836 2.690000e-27 134.0
36 TraesCS4B01G095900 chrUn 73.735 415 78 26 1907 2313 263318466 263318075 2.690000e-27 134.0
37 TraesCS4B01G095900 chr2D 97.059 136 4 0 2434 2569 622315651 622315786 3.340000e-56 230.0
38 TraesCS4B01G095900 chr4A 96.403 139 4 1 2436 2573 95379503 95379641 1.200000e-55 228.0
39 TraesCS4B01G095900 chr2B 95.139 144 7 0 2428 2571 678011633 678011490 1.200000e-55 228.0
40 TraesCS4B01G095900 chr2B 97.826 92 1 1 2944 3034 63783810 63783719 1.600000e-34 158.0
41 TraesCS4B01G095900 chr7D 92.208 154 10 2 2421 2574 617211620 617211469 2.600000e-52 217.0
42 TraesCS4B01G095900 chr7D 95.876 97 2 2 2942 3037 426558985 426558890 5.740000e-34 156.0
43 TraesCS4B01G095900 chr7D 93.069 101 5 2 2944 3043 22959750 22959651 3.460000e-31 147.0
44 TraesCS4B01G095900 chr7D 92.079 101 6 2 2944 3043 226690430 226690331 1.610000e-29 141.0
45 TraesCS4B01G095900 chr6D 97.753 89 1 1 2942 3029 78083165 78083077 7.430000e-33 152.0
46 TraesCS4B01G095900 chr6D 89.908 109 9 2 2944 3051 95294989 95294882 5.780000e-29 139.0
47 TraesCS4B01G095900 chr5D 92.157 102 6 2 2930 3030 554927656 554927756 4.470000e-30 143.0
48 TraesCS4B01G095900 chr1D 92.233 103 5 3 2943 3043 232558457 232558558 4.470000e-30 143.0
49 TraesCS4B01G095900 chr7B 77.647 170 34 4 1325 1492 747839756 747839589 2.730000e-17 100.0
50 TraesCS4B01G095900 chr6B 85.938 64 8 1 3217 3280 66498769 66498707 2.770000e-07 67.6


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 TraesCS4B01G095900 chr4B 99434476 99438765 4289 False 7923.0 7923 100.000 1 4290 1 chr4B.!!$F1 4289
1 TraesCS4B01G095900 chr4B 291846742 291847311 569 False 388.0 388 79.392 2 584 1 chr4B.!!$F2 582
2 TraesCS4B01G095900 chr4D 67331860 67336529 4669 True 1329.4 2558 96.149 75 4290 5 chr4D.!!$R1 4215
3 TraesCS4B01G095900 chr1A 171022146 171022716 570 True 723.0 723 89.402 2 585 1 chr1A.!!$R1 583
4 TraesCS4B01G095900 chr3B 14045576 14046530 954 True 435.0 435 75.510 1027 1982 1 chr3B.!!$R2 955
5 TraesCS4B01G095900 chr3B 14052450 14053312 862 True 339.0 339 74.390 1002 1890 1 chr3B.!!$R3 888
6 TraesCS4B01G095900 chr3A 11536418 11536939 521 False 296.0 296 77.341 1808 2331 1 chr3A.!!$F3 523
7 TraesCS4B01G095900 chr3A 11528104 11528761 657 False 252.0 252 74.265 1764 2428 1 chr3A.!!$F2 664
8 TraesCS4B01G095900 chr3D 4844185 4844841 656 False 283.0 283 74.889 1766 2435 1 chr3D.!!$F2 669
9 TraesCS4B01G095900 chr3D 5052510 5053019 509 False 270.0 270 76.686 1823 2331 1 chr3D.!!$F3 508
10 TraesCS4B01G095900 chrUn 290169090 290169754 664 False 259.0 259 74.381 1764 2435 1 chrUn.!!$F4 671

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
693 703 0.033894 ACGAAACAAACCACACCCCT 60.034 50.0 0.00 0.00 0.00 4.79 F
699 709 0.036875 CAAACCACACCCCTCTCTCC 59.963 60.0 0.00 0.00 0.00 3.71 F
800 927 0.110486 ACCATTGAAGAGGGCAACGT 59.890 50.0 0.00 0.00 30.38 3.99 F
919 1046 0.178767 CCAGATCCATGCCGTTGAGA 59.821 55.0 0.00 0.00 0.00 3.27 F
1132 1829 0.322816 TGAGGAGGTTGCTGGAATGC 60.323 55.0 0.00 0.00 0.00 3.56 F
2563 3299 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2544 3280 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 R
2547 3283 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.0 44.66 2.17 R
2552 3288 0.750546 TCATGTACTCCCTCCGTCCG 60.751 60.000 0.00 0.0 0.00 4.79 R
2555 3291 1.139058 GCAATCATGTACTCCCTCCGT 59.861 52.381 0.00 0.0 0.00 4.69 R
3006 3744 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.0 0.00 1.90 R
4206 4945 0.831966 AGCTGAGAATCCAGGCAGAG 59.168 55.000 0.00 0.0 34.82 3.35 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
71 73 1.842381 CTCGTCCCCTTTTCTGGGCT 61.842 60.000 0.00 0.00 45.78 5.19
72 74 1.675641 CGTCCCCTTTTCTGGGCTG 60.676 63.158 0.00 0.00 45.78 4.85
99 101 6.553100 AGTGTTTCCAAAAGGAAATCCATACA 59.447 34.615 12.32 3.54 39.57 2.29
354 363 0.974383 ACGACGAGGAATTTGGGAGT 59.026 50.000 0.00 0.00 0.00 3.85
361 370 3.767711 GAGGAATTTGGGAGTGGTTCTT 58.232 45.455 0.00 0.00 0.00 2.52
437 446 4.099419 GTGTTTTGGGTGTCTTCTCCAAAT 59.901 41.667 7.46 0.00 46.08 2.32
449 459 3.848272 TCTCCAAATTTTGTCCGATGC 57.152 42.857 8.26 0.00 0.00 3.91
556 566 1.562942 AGGCAGACACACCATCATCAT 59.437 47.619 0.00 0.00 0.00 2.45
563 573 5.645067 CAGACACACCATCATCATAAACTGT 59.355 40.000 0.00 0.00 0.00 3.55
594 604 8.508883 TTATAGGAGTAGAGATTTAGATCGGC 57.491 38.462 0.00 0.00 37.37 5.54
599 609 1.341531 AGAGATTTAGATCGGCCGTGG 59.658 52.381 27.15 0.00 37.37 4.94
690 700 1.469308 TGTCACGAAACAAACCACACC 59.531 47.619 0.00 0.00 0.00 4.16
692 702 0.101579 CACGAAACAAACCACACCCC 59.898 55.000 0.00 0.00 0.00 4.95
693 703 0.033894 ACGAAACAAACCACACCCCT 60.034 50.000 0.00 0.00 0.00 4.79
698 708 0.765510 ACAAACCACACCCCTCTCTC 59.234 55.000 0.00 0.00 0.00 3.20
699 709 0.036875 CAAACCACACCCCTCTCTCC 59.963 60.000 0.00 0.00 0.00 3.71
780 907 2.617532 GCAATGTGCTCCTCCTTTCTCT 60.618 50.000 0.00 0.00 40.96 3.10
800 927 0.110486 ACCATTGAAGAGGGCAACGT 59.890 50.000 0.00 0.00 30.38 3.99
897 1024 3.685435 CGCAGGGTGCAATTCCTT 58.315 55.556 2.15 0.00 45.36 3.36
899 1026 0.451783 CGCAGGGTGCAATTCCTTAC 59.548 55.000 2.15 0.00 45.36 2.34
900 1027 0.817654 GCAGGGTGCAATTCCTTACC 59.182 55.000 2.15 0.00 44.26 2.85
904 1031 2.507407 GGTGCAATTCCTTACCCAGA 57.493 50.000 0.00 0.00 0.00 3.86
905 1032 3.018423 GGTGCAATTCCTTACCCAGAT 57.982 47.619 0.00 0.00 0.00 2.90
906 1033 2.952310 GGTGCAATTCCTTACCCAGATC 59.048 50.000 0.00 0.00 0.00 2.75
907 1034 2.952310 GTGCAATTCCTTACCCAGATCC 59.048 50.000 0.00 0.00 0.00 3.36
908 1035 2.580322 TGCAATTCCTTACCCAGATCCA 59.420 45.455 0.00 0.00 0.00 3.41
909 1036 3.205056 TGCAATTCCTTACCCAGATCCAT 59.795 43.478 0.00 0.00 0.00 3.41
910 1037 3.571401 GCAATTCCTTACCCAGATCCATG 59.429 47.826 0.00 0.00 0.00 3.66
913 1040 0.250467 CCTTACCCAGATCCATGCCG 60.250 60.000 0.00 0.00 0.00 5.69
918 1045 0.816825 CCCAGATCCATGCCGTTGAG 60.817 60.000 0.00 0.00 0.00 3.02
919 1046 0.178767 CCAGATCCATGCCGTTGAGA 59.821 55.000 0.00 0.00 0.00 3.27
924 1051 1.002134 CCATGCCGTTGAGAAGGGT 60.002 57.895 0.00 0.00 38.66 4.34
925 1052 1.308069 CCATGCCGTTGAGAAGGGTG 61.308 60.000 0.00 0.00 38.66 4.61
931 1058 0.666577 CGTTGAGAAGGGTGACGGAC 60.667 60.000 0.00 0.00 0.00 4.79
933 1060 1.070289 GTTGAGAAGGGTGACGGACTT 59.930 52.381 0.00 0.00 0.00 3.01
945 1072 4.740822 GGACTTGCCCACCCGCAT 62.741 66.667 0.00 0.00 38.87 4.73
946 1073 3.443045 GACTTGCCCACCCGCATG 61.443 66.667 0.00 0.00 38.87 4.06
959 1655 1.512522 CGCATGGCATGTGTGTTCG 60.513 57.895 28.34 18.18 36.09 3.95
964 1660 1.302511 GGCATGTGTGTTCGTCCCT 60.303 57.895 0.00 0.00 0.00 4.20
992 1688 2.347490 CGGTGAGGAGGTTGGTGG 59.653 66.667 0.00 0.00 0.00 4.61
1001 1697 2.359478 GGTTGGTGGCGTCGGAAT 60.359 61.111 0.00 0.00 0.00 3.01
1132 1829 0.322816 TGAGGAGGTTGCTGGAATGC 60.323 55.000 0.00 0.00 0.00 3.56
1222 1919 2.486504 CATGTGGCATGTGCGTCC 59.513 61.111 0.00 0.00 43.26 4.79
1453 2150 2.609747 AGTTCCTCTGCCAGTTCTACA 58.390 47.619 0.00 0.00 0.00 2.74
1462 2159 1.202651 GCCAGTTCTACACACACCACT 60.203 52.381 0.00 0.00 0.00 4.00
1533 2232 2.938798 TTCACCCCCATTCCGGCT 60.939 61.111 0.00 0.00 0.00 5.52
2100 2835 6.549364 TGTTGTCCTGTCATAACCTTCAAATT 59.451 34.615 0.00 0.00 0.00 1.82
2213 2948 4.129380 GGCAATAAAAGGATCAAATGGCC 58.871 43.478 0.00 0.00 0.00 5.36
2440 3176 6.777580 AGTAACCCAATCTTGTGATGTTTTCT 59.222 34.615 0.00 0.00 32.44 2.52
2441 3177 7.942341 AGTAACCCAATCTTGTGATGTTTTCTA 59.058 33.333 0.00 0.00 32.44 2.10
2442 3178 6.575162 ACCCAATCTTGTGATGTTTTCTAC 57.425 37.500 0.00 0.00 32.44 2.59
2443 3179 6.306987 ACCCAATCTTGTGATGTTTTCTACT 58.693 36.000 0.00 0.00 32.44 2.57
2444 3180 6.431234 ACCCAATCTTGTGATGTTTTCTACTC 59.569 38.462 0.00 0.00 32.44 2.59
2445 3181 6.127897 CCCAATCTTGTGATGTTTTCTACTCC 60.128 42.308 0.00 0.00 32.44 3.85
2446 3182 6.127897 CCAATCTTGTGATGTTTTCTACTCCC 60.128 42.308 0.00 0.00 32.44 4.30
2447 3183 5.825593 TCTTGTGATGTTTTCTACTCCCT 57.174 39.130 0.00 0.00 0.00 4.20
2448 3184 5.794894 TCTTGTGATGTTTTCTACTCCCTC 58.205 41.667 0.00 0.00 0.00 4.30
2449 3185 4.553330 TGTGATGTTTTCTACTCCCTCC 57.447 45.455 0.00 0.00 0.00 4.30
2450 3186 3.056107 TGTGATGTTTTCTACTCCCTCCG 60.056 47.826 0.00 0.00 0.00 4.63
2451 3187 3.056035 GTGATGTTTTCTACTCCCTCCGT 60.056 47.826 0.00 0.00 0.00 4.69
2452 3188 3.194968 TGATGTTTTCTACTCCCTCCGTC 59.805 47.826 0.00 0.00 0.00 4.79
2453 3189 1.897802 TGTTTTCTACTCCCTCCGTCC 59.102 52.381 0.00 0.00 0.00 4.79
2454 3190 1.135170 GTTTTCTACTCCCTCCGTCCG 60.135 57.143 0.00 0.00 0.00 4.79
2455 3191 0.329261 TTTCTACTCCCTCCGTCCGA 59.671 55.000 0.00 0.00 0.00 4.55
2456 3192 0.329261 TTCTACTCCCTCCGTCCGAA 59.671 55.000 0.00 0.00 0.00 4.30
2457 3193 0.329261 TCTACTCCCTCCGTCCGAAA 59.671 55.000 0.00 0.00 0.00 3.46
2458 3194 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
2459 3195 1.755380 CTACTCCCTCCGTCCGAAAAT 59.245 52.381 0.00 0.00 0.00 1.82
2460 3196 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2461 3197 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2462 3198 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2463 3199 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2464 3200 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2465 3201 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2466 3202 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2467 3203 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2468 3204 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2469 3205 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2470 3206 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2471 3207 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2472 3208 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2473 3209 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2474 3210 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2475 3211 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2476 3212 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
2477 3213 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
2478 3214 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
2486 3222 9.918630 ACTTGTCATCAAAATGGATAAAAAGAG 57.081 29.630 0.00 0.00 33.42 2.85
2518 3254 9.117183 TCTAGAACTAAAATACGTCTAGATGCA 57.883 33.333 12.04 0.00 32.48 3.96
2519 3255 9.900710 CTAGAACTAAAATACGTCTAGATGCAT 57.099 33.333 12.04 0.00 0.00 3.96
2520 3256 8.804688 AGAACTAAAATACGTCTAGATGCATC 57.195 34.615 19.37 19.37 0.00 3.91
2521 3257 7.868415 AGAACTAAAATACGTCTAGATGCATCC 59.132 37.037 23.06 6.84 0.00 3.51
2522 3258 6.456501 ACTAAAATACGTCTAGATGCATCCC 58.543 40.000 23.06 7.99 0.00 3.85
2523 3259 3.963428 AATACGTCTAGATGCATCCCC 57.037 47.619 23.06 7.64 0.00 4.81
2524 3260 2.677542 TACGTCTAGATGCATCCCCT 57.322 50.000 23.06 7.62 0.00 4.79
2525 3261 1.794714 ACGTCTAGATGCATCCCCTT 58.205 50.000 23.06 7.24 0.00 3.95
2526 3262 2.119495 ACGTCTAGATGCATCCCCTTT 58.881 47.619 23.06 6.85 0.00 3.11
2527 3263 2.505819 ACGTCTAGATGCATCCCCTTTT 59.494 45.455 23.06 6.10 0.00 2.27
2528 3264 3.709653 ACGTCTAGATGCATCCCCTTTTA 59.290 43.478 23.06 6.97 0.00 1.52
2529 3265 4.348168 ACGTCTAGATGCATCCCCTTTTAT 59.652 41.667 23.06 4.58 0.00 1.40
2530 3266 4.932200 CGTCTAGATGCATCCCCTTTTATC 59.068 45.833 23.06 0.00 0.00 1.75
2531 3267 5.249420 GTCTAGATGCATCCCCTTTTATCC 58.751 45.833 23.06 0.00 0.00 2.59
2532 3268 4.913355 TCTAGATGCATCCCCTTTTATCCA 59.087 41.667 23.06 0.00 0.00 3.41
2533 3269 4.754411 AGATGCATCCCCTTTTATCCAT 57.246 40.909 23.06 0.00 0.00 3.41
2534 3270 5.083953 AGATGCATCCCCTTTTATCCATT 57.916 39.130 23.06 0.00 0.00 3.16
2535 3271 5.470501 AGATGCATCCCCTTTTATCCATTT 58.529 37.500 23.06 0.00 0.00 2.32
2536 3272 5.907079 AGATGCATCCCCTTTTATCCATTTT 59.093 36.000 23.06 0.00 0.00 1.82
2537 3273 5.356291 TGCATCCCCTTTTATCCATTTTG 57.644 39.130 0.00 0.00 0.00 2.44
2538 3274 5.028802 TGCATCCCCTTTTATCCATTTTGA 58.971 37.500 0.00 0.00 0.00 2.69
2539 3275 5.666718 TGCATCCCCTTTTATCCATTTTGAT 59.333 36.000 0.00 0.00 0.00 2.57
2540 3276 5.993441 GCATCCCCTTTTATCCATTTTGATG 59.007 40.000 0.00 0.00 0.00 3.07
2541 3277 6.183360 GCATCCCCTTTTATCCATTTTGATGA 60.183 38.462 0.00 0.00 0.00 2.92
2542 3278 6.790232 TCCCCTTTTATCCATTTTGATGAC 57.210 37.500 0.00 0.00 0.00 3.06
2543 3279 6.259893 TCCCCTTTTATCCATTTTGATGACA 58.740 36.000 0.00 0.00 0.00 3.58
2544 3280 6.728164 TCCCCTTTTATCCATTTTGATGACAA 59.272 34.615 0.00 0.00 0.00 3.18
2545 3281 7.043565 CCCCTTTTATCCATTTTGATGACAAG 58.956 38.462 0.00 0.00 37.32 3.16
2546 3282 7.310609 CCCCTTTTATCCATTTTGATGACAAGT 60.311 37.037 0.00 0.00 37.32 3.16
2547 3283 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
2553 3289 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
2554 3290 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
2555 3291 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
2556 3292 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2557 3293 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2558 3294 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2559 3295 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
2560 3296 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
2561 3297 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2562 3298 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2563 3299 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2564 3300 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2581 3317 2.487934 GGAGTACATGATTGCTCGCAT 58.512 47.619 0.00 0.00 0.00 4.73
2582 3318 3.554960 GGGAGTACATGATTGCTCGCATA 60.555 47.826 0.00 0.00 39.64 3.14
2583 3319 3.677121 GGAGTACATGATTGCTCGCATAG 59.323 47.826 0.00 0.00 0.00 2.23
2586 3322 2.910199 ACATGATTGCTCGCATAGTGT 58.090 42.857 0.00 0.00 0.00 3.55
2594 3332 2.935849 TGCTCGCATAGTGTTATTGTGG 59.064 45.455 0.00 0.00 0.00 4.17
2634 3372 8.276325 CACTTACAACTTGAACTTAGTTAGCAG 58.724 37.037 0.00 0.00 34.22 4.24
2787 3525 5.250543 TCTCATTTGTTCATGACCCCTTCTA 59.749 40.000 0.00 0.00 0.00 2.10
2892 3630 5.923204 ACTTCCATCGAATCTATGCTTTCT 58.077 37.500 0.00 0.00 0.00 2.52
2931 3669 0.038166 TCACTTGCCAATGACCCCTC 59.962 55.000 0.00 0.00 0.00 4.30
2944 3682 1.080354 CCCCTCCACCTGGTGACTA 59.920 63.158 27.94 11.73 35.23 2.59
2945 3683 1.265454 CCCCTCCACCTGGTGACTAC 61.265 65.000 27.94 0.00 35.23 2.73
2946 3684 0.252284 CCCTCCACCTGGTGACTACT 60.252 60.000 27.94 0.00 35.23 2.57
2947 3685 1.187087 CCTCCACCTGGTGACTACTC 58.813 60.000 27.94 0.00 35.23 2.59
2948 3686 1.187087 CTCCACCTGGTGACTACTCC 58.813 60.000 27.94 0.00 35.23 3.85
2949 3687 0.252103 TCCACCTGGTGACTACTCCC 60.252 60.000 27.94 0.00 35.23 4.30
2950 3688 0.252284 CCACCTGGTGACTACTCCCT 60.252 60.000 27.94 0.00 35.23 4.20
2951 3689 1.187087 CACCTGGTGACTACTCCCTC 58.813 60.000 22.33 0.00 35.23 4.30
2952 3690 0.041386 ACCTGGTGACTACTCCCTCC 59.959 60.000 0.00 0.00 0.00 4.30
2953 3691 1.038130 CCTGGTGACTACTCCCTCCG 61.038 65.000 0.00 0.00 0.00 4.63
2954 3692 0.323542 CTGGTGACTACTCCCTCCGT 60.324 60.000 0.00 0.00 0.00 4.69
2955 3693 0.323178 TGGTGACTACTCCCTCCGTC 60.323 60.000 0.00 0.00 0.00 4.79
2956 3694 1.036481 GGTGACTACTCCCTCCGTCC 61.036 65.000 0.00 0.00 0.00 4.79
2957 3695 1.036481 GTGACTACTCCCTCCGTCCC 61.036 65.000 0.00 0.00 0.00 4.46
2958 3696 1.305623 GACTACTCCCTCCGTCCCA 59.694 63.158 0.00 0.00 0.00 4.37
2959 3697 0.106116 GACTACTCCCTCCGTCCCAT 60.106 60.000 0.00 0.00 0.00 4.00
2960 3698 1.144503 GACTACTCCCTCCGTCCCATA 59.855 57.143 0.00 0.00 0.00 2.74
2961 3699 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2962 3700 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2963 3701 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2964 3702 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2965 3703 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2966 3704 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2967 3705 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2968 3706 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2969 3707 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2970 3708 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2971 3709 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2972 3710 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2973 3711 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2974 3712 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2975 3713 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2976 3714 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2977 3715 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
2978 3716 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
2979 3717 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
2980 3718 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
2981 3719 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
2982 3720 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
2985 3723 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
2986 3724 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
2987 3725 3.793559 AGAGCGTTTTTGACACTACACT 58.206 40.909 0.00 0.00 0.00 3.55
2988 3726 4.940463 AGAGCGTTTTTGACACTACACTA 58.060 39.130 0.00 0.00 0.00 2.74
2989 3727 4.982916 AGAGCGTTTTTGACACTACACTAG 59.017 41.667 0.00 0.00 0.00 2.57
2990 3728 4.690122 AGCGTTTTTGACACTACACTAGT 58.310 39.130 0.00 0.00 40.28 2.57
3016 3754 4.976224 AAAACGCCTTATATTGTGGGAC 57.024 40.909 0.00 0.00 0.00 4.46
3017 3755 2.234300 ACGCCTTATATTGTGGGACG 57.766 50.000 0.00 0.00 0.00 4.79
3018 3756 1.202604 ACGCCTTATATTGTGGGACGG 60.203 52.381 0.00 0.00 0.00 4.79
3019 3757 1.069513 CGCCTTATATTGTGGGACGGA 59.930 52.381 0.00 0.00 0.00 4.69
3020 3758 2.767505 GCCTTATATTGTGGGACGGAG 58.232 52.381 0.00 0.00 0.00 4.63
3021 3759 2.550208 GCCTTATATTGTGGGACGGAGG 60.550 54.545 0.00 0.00 0.00 4.30
3022 3760 2.038557 CCTTATATTGTGGGACGGAGGG 59.961 54.545 0.00 0.00 0.00 4.30
3023 3761 2.779429 TATATTGTGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3024 3762 1.424638 ATATTGTGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3025 3763 0.042131 TATTGTGGGACGGAGGGAGT 59.958 55.000 0.00 0.00 0.00 3.85
3037 3775 5.278858 GGACGGAGGGAGTAGTATATTTGTG 60.279 48.000 0.00 0.00 0.00 3.33
3081 3819 3.505386 TCTTGTCTCTTGAGCTCCTCTT 58.495 45.455 12.15 0.00 0.00 2.85
3088 3826 7.054124 TGTCTCTTGAGCTCCTCTTTTTAAAA 58.946 34.615 12.15 0.00 0.00 1.52
3091 3829 7.227512 TCTCTTGAGCTCCTCTTTTTAAAACAG 59.772 37.037 12.15 0.00 0.00 3.16
3094 3832 5.531287 TGAGCTCCTCTTTTTAAAACAGGAC 59.469 40.000 18.24 15.49 0.00 3.85
3154 3893 9.823647 TTTGGCATAATTTTCACTTTGTTTCTA 57.176 25.926 0.00 0.00 0.00 2.10
3308 4047 3.531538 TGACTGCCTGGTTCGATATTTC 58.468 45.455 0.00 0.00 0.00 2.17
3471 4210 6.159988 GTCAATCGGTAATTCCTAGGAGATG 58.840 44.000 12.26 5.77 0.00 2.90
3677 4416 0.892814 GAAGAAAGGGCTGCTGCAGT 60.893 55.000 28.50 10.39 41.91 4.40
3837 4576 7.862372 GTCAGATTTCAAGATGTTTTTACTGCA 59.138 33.333 0.00 0.00 0.00 4.41
3863 4602 0.399454 TGCTTGGCTGCTCTTCTCTT 59.601 50.000 0.00 0.00 0.00 2.85
3886 4625 4.202010 TGAGCCAAAAGAGTTTTGTGTAGC 60.202 41.667 10.41 7.04 46.53 3.58
3888 4627 3.488553 GCCAAAAGAGTTTTGTGTAGCGT 60.489 43.478 10.41 0.00 46.53 5.07
3907 4646 4.576463 AGCGTTGAGAGTTTTTGAGATGTT 59.424 37.500 0.00 0.00 0.00 2.71
3949 4688 4.625607 AGGAACTAGAACCCTGAAACTG 57.374 45.455 0.00 0.00 36.02 3.16
3953 4692 5.221661 GGAACTAGAACCCTGAAACTGAGAA 60.222 44.000 0.00 0.00 0.00 2.87
3957 4696 4.646572 AGAACCCTGAAACTGAGAATGTC 58.353 43.478 0.00 0.00 0.00 3.06
3968 4707 3.005554 CTGAGAATGTCGATGTTGGCTT 58.994 45.455 0.00 0.00 0.00 4.35
4079 4818 4.938080 TGGTTTCGTTTGCATGTTTGTAT 58.062 34.783 0.00 0.00 0.00 2.29
4119 4858 1.813513 AGCTGAAACCAGGAATGTCG 58.186 50.000 0.00 0.00 32.40 4.35
4120 4859 1.072331 AGCTGAAACCAGGAATGTCGT 59.928 47.619 0.00 0.00 32.40 4.34
4121 4860 1.197721 GCTGAAACCAGGAATGTCGTG 59.802 52.381 0.00 0.00 32.40 4.35
4122 4861 2.766313 CTGAAACCAGGAATGTCGTGA 58.234 47.619 0.00 0.00 34.44 4.35
4123 4862 2.480419 CTGAAACCAGGAATGTCGTGAC 59.520 50.000 0.00 0.00 34.44 3.67
4124 4863 2.158885 TGAAACCAGGAATGTCGTGACA 60.159 45.455 4.99 4.99 46.44 3.58
4138 4877 4.202233 TGTCGTGACATAGGGTGTAAAACA 60.202 41.667 0.00 0.00 42.36 2.83
4206 4945 6.831769 TCTGACTGAAAATTCGCAGTAATTC 58.168 36.000 11.73 2.95 44.77 2.17
4232 4971 3.008330 CCTGGATTCTCAGCTGAAACAG 58.992 50.000 18.85 18.54 36.08 3.16
4243 4982 2.965477 CTGAAACAGCAAGTCAGCTC 57.035 50.000 0.00 0.00 44.54 4.09
4272 5011 1.576421 CGCCAAAGCACAGAGGAAC 59.424 57.895 0.00 0.00 39.83 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 67 2.270352 TTGGAAACACTACAGCCCAG 57.730 50.000 0.00 0.00 42.67 4.45
99 101 2.936032 GTCCTGCCACCCCTCCTT 60.936 66.667 0.00 0.00 0.00 3.36
187 194 1.678627 TCTGCTTCTAGATCTCACCGC 59.321 52.381 0.00 0.00 0.00 5.68
191 198 5.000591 CCGTATCTCTGCTTCTAGATCTCA 58.999 45.833 0.00 0.00 34.36 3.27
288 297 2.357034 GCCGGAGTTGAGTTGCGA 60.357 61.111 5.05 0.00 0.00 5.10
314 323 1.355718 GGCCCTTCCCATCTCATCCA 61.356 60.000 0.00 0.00 0.00 3.41
354 363 1.946768 CAAACGAGCCTTCAAGAACCA 59.053 47.619 0.00 0.00 0.00 3.67
361 370 0.306533 GCGAAACAAACGAGCCTTCA 59.693 50.000 0.00 0.00 0.00 3.02
437 446 1.969064 CCCCACGCATCGGACAAAA 60.969 57.895 0.00 0.00 0.00 2.44
449 459 0.457851 TTTTGCAGAAACACCCCACG 59.542 50.000 0.00 0.00 0.00 4.94
594 604 5.959618 ACTTTTTCTTCCTTATTCCACGG 57.040 39.130 0.00 0.00 0.00 4.94
690 700 3.174265 GGCATGGGGGAGAGAGGG 61.174 72.222 0.00 0.00 0.00 4.30
692 702 1.704007 GGAAGGCATGGGGGAGAGAG 61.704 65.000 0.00 0.00 0.00 3.20
693 703 1.694169 GGAAGGCATGGGGGAGAGA 60.694 63.158 0.00 0.00 0.00 3.10
698 708 3.307089 AAGCAGGAAGGCATGGGGG 62.307 63.158 0.00 0.00 35.83 5.40
699 709 1.755783 GAAGCAGGAAGGCATGGGG 60.756 63.158 0.00 0.00 35.83 4.96
763 773 2.180276 GGTAGAGAAAGGAGGAGCACA 58.820 52.381 0.00 0.00 0.00 4.57
780 907 1.349688 ACGTTGCCCTCTTCAATGGTA 59.650 47.619 0.00 0.00 35.38 3.25
800 927 2.044451 CGCTTGGGTGGGCCAATA 60.044 61.111 8.40 0.00 36.17 1.90
881 1008 0.817654 GGTAAGGAATTGCACCCTGC 59.182 55.000 0.00 0.00 45.29 4.85
882 1009 1.474330 GGGTAAGGAATTGCACCCTG 58.526 55.000 15.80 0.00 46.08 4.45
885 1012 2.507407 TCTGGGTAAGGAATTGCACC 57.493 50.000 0.00 0.00 0.00 5.01
886 1013 2.952310 GGATCTGGGTAAGGAATTGCAC 59.048 50.000 0.00 0.00 0.00 4.57
887 1014 2.580322 TGGATCTGGGTAAGGAATTGCA 59.420 45.455 0.00 0.00 0.00 4.08
888 1015 3.297134 TGGATCTGGGTAAGGAATTGC 57.703 47.619 0.00 0.00 0.00 3.56
890 1017 3.437052 GGCATGGATCTGGGTAAGGAATT 60.437 47.826 0.00 0.00 0.00 2.17
891 1018 2.108952 GGCATGGATCTGGGTAAGGAAT 59.891 50.000 0.00 0.00 0.00 3.01
895 1022 0.469917 ACGGCATGGATCTGGGTAAG 59.530 55.000 0.00 0.00 0.00 2.34
896 1023 0.916086 AACGGCATGGATCTGGGTAA 59.084 50.000 0.00 0.00 0.00 2.85
897 1024 0.180171 CAACGGCATGGATCTGGGTA 59.820 55.000 0.00 0.00 0.00 3.69
899 1026 0.816825 CTCAACGGCATGGATCTGGG 60.817 60.000 0.00 0.00 0.00 4.45
900 1027 0.178767 TCTCAACGGCATGGATCTGG 59.821 55.000 0.00 0.00 0.00 3.86
901 1028 1.938577 CTTCTCAACGGCATGGATCTG 59.061 52.381 0.00 0.00 0.00 2.90
902 1029 1.134280 CCTTCTCAACGGCATGGATCT 60.134 52.381 0.00 0.00 0.00 2.75
903 1030 1.303309 CCTTCTCAACGGCATGGATC 58.697 55.000 0.00 0.00 0.00 3.36
904 1031 0.107017 CCCTTCTCAACGGCATGGAT 60.107 55.000 0.00 0.00 0.00 3.41
905 1032 1.299648 CCCTTCTCAACGGCATGGA 59.700 57.895 0.00 0.00 0.00 3.41
906 1033 1.002134 ACCCTTCTCAACGGCATGG 60.002 57.895 0.00 0.00 0.00 3.66
907 1034 0.321564 TCACCCTTCTCAACGGCATG 60.322 55.000 0.00 0.00 0.00 4.06
908 1035 0.321653 GTCACCCTTCTCAACGGCAT 60.322 55.000 0.00 0.00 0.00 4.40
909 1036 1.070786 GTCACCCTTCTCAACGGCA 59.929 57.895 0.00 0.00 0.00 5.69
910 1037 2.027625 CGTCACCCTTCTCAACGGC 61.028 63.158 0.00 0.00 0.00 5.68
913 1040 0.680061 AGTCCGTCACCCTTCTCAAC 59.320 55.000 0.00 0.00 0.00 3.18
918 1045 1.671379 GGCAAGTCCGTCACCCTTC 60.671 63.158 0.00 0.00 0.00 3.46
919 1046 2.430367 GGCAAGTCCGTCACCCTT 59.570 61.111 0.00 0.00 0.00 3.95
924 1051 3.948719 GGGTGGGCAAGTCCGTCA 61.949 66.667 0.00 0.00 34.94 4.35
942 1069 0.454957 GACGAACACACATGCCATGC 60.455 55.000 4.17 0.00 0.00 4.06
943 1070 0.168788 GGACGAACACACATGCCATG 59.831 55.000 2.40 2.40 0.00 3.66
945 1072 1.599518 GGGACGAACACACATGCCA 60.600 57.895 0.00 0.00 0.00 4.92
946 1073 0.036765 TAGGGACGAACACACATGCC 60.037 55.000 0.00 0.00 0.00 4.40
959 1655 2.210711 CCGGCCTGGATCTAGGGAC 61.211 68.421 25.05 10.35 42.00 4.46
964 1660 1.457643 CCTCACCGGCCTGGATCTA 60.458 63.158 18.74 0.00 42.00 1.98
1019 1715 1.070758 TCTCAGAAAGGAGGTGTGTGC 59.929 52.381 0.00 0.00 35.58 4.57
1092 1788 1.142465 CTTGGGTGGATCTGAGGATGG 59.858 57.143 0.00 0.00 31.46 3.51
1094 1790 1.842562 CACTTGGGTGGATCTGAGGAT 59.157 52.381 0.00 0.00 39.59 3.24
1149 1846 0.473694 TCTGGGAAAGGAGGAGTGCA 60.474 55.000 0.00 0.00 0.00 4.57
1153 1850 1.488393 GTGGATCTGGGAAAGGAGGAG 59.512 57.143 0.00 0.00 0.00 3.69
1154 1851 1.203428 TGTGGATCTGGGAAAGGAGGA 60.203 52.381 0.00 0.00 0.00 3.71
1222 1919 2.765807 AGCCTGGATCTGGGGACG 60.766 66.667 0.00 0.00 0.00 4.79
1329 2026 7.083875 GAGAAAGATCTCCCTGAGTATATCG 57.916 44.000 0.00 0.00 45.35 2.92
1453 2150 2.901840 CGGCTTGCAGTGGTGTGT 60.902 61.111 0.00 0.00 0.00 3.72
1533 2232 2.029623 GGGATGTAGTCGGCAACTAGA 58.970 52.381 0.00 0.00 41.17 2.43
2100 2835 2.158475 ACAATTGACCTTCCTCTGCCAA 60.158 45.455 13.59 0.00 0.00 4.52
2213 2948 3.278574 TCATAGCCCAGAAATTTGTCCG 58.721 45.455 0.00 0.00 0.00 4.79
2440 3176 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
2441 3177 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
2442 3178 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2443 3179 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2444 3180 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2445 3181 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2446 3182 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2447 3183 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2448 3184 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2449 3185 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2450 3186 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
2451 3187 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
2452 3188 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
2453 3189 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
2460 3196 9.918630 CTCTTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
2492 3228 9.117183 TGCATCTAGACGTATTTTAGTTCTAGA 57.883 33.333 8.64 8.64 38.94 2.43
2493 3229 9.900710 ATGCATCTAGACGTATTTTAGTTCTAG 57.099 33.333 0.00 0.00 0.00 2.43
2494 3230 9.894783 GATGCATCTAGACGTATTTTAGTTCTA 57.105 33.333 19.70 0.00 0.00 2.10
2495 3231 7.868415 GGATGCATCTAGACGTATTTTAGTTCT 59.132 37.037 25.28 0.00 0.00 3.01
2496 3232 7.116519 GGGATGCATCTAGACGTATTTTAGTTC 59.883 40.741 25.28 2.81 0.00 3.01
2497 3233 6.929606 GGGATGCATCTAGACGTATTTTAGTT 59.070 38.462 25.28 0.00 0.00 2.24
2498 3234 6.456501 GGGATGCATCTAGACGTATTTTAGT 58.543 40.000 25.28 0.00 0.00 2.24
2499 3235 5.869888 GGGGATGCATCTAGACGTATTTTAG 59.130 44.000 25.28 0.00 0.00 1.85
2500 3236 5.542635 AGGGGATGCATCTAGACGTATTTTA 59.457 40.000 25.28 0.00 0.00 1.52
2501 3237 4.348168 AGGGGATGCATCTAGACGTATTTT 59.652 41.667 25.28 0.00 0.00 1.82
2502 3238 3.904339 AGGGGATGCATCTAGACGTATTT 59.096 43.478 25.28 0.00 0.00 1.40
2503 3239 3.511477 AGGGGATGCATCTAGACGTATT 58.489 45.455 25.28 0.13 0.00 1.89
2504 3240 3.176924 AGGGGATGCATCTAGACGTAT 57.823 47.619 25.28 0.00 0.00 3.06
2505 3241 2.677542 AGGGGATGCATCTAGACGTA 57.322 50.000 25.28 0.00 0.00 3.57
2506 3242 1.794714 AAGGGGATGCATCTAGACGT 58.205 50.000 25.28 12.28 0.00 4.34
2507 3243 2.918712 AAAGGGGATGCATCTAGACG 57.081 50.000 25.28 0.00 0.00 4.18
2508 3244 5.221925 TGGATAAAAGGGGATGCATCTAGAC 60.222 44.000 25.28 13.29 0.00 2.59
2509 3245 4.913355 TGGATAAAAGGGGATGCATCTAGA 59.087 41.667 25.28 0.00 0.00 2.43
2510 3246 5.246981 TGGATAAAAGGGGATGCATCTAG 57.753 43.478 25.28 0.00 0.00 2.43
2511 3247 5.865977 ATGGATAAAAGGGGATGCATCTA 57.134 39.130 25.28 9.84 29.02 1.98
2512 3248 4.754411 ATGGATAAAAGGGGATGCATCT 57.246 40.909 25.28 7.83 29.02 2.90
2513 3249 5.813513 AAATGGATAAAAGGGGATGCATC 57.186 39.130 18.81 18.81 33.50 3.91
2514 3250 5.666718 TCAAAATGGATAAAAGGGGATGCAT 59.333 36.000 0.00 0.00 35.84 3.96
2515 3251 5.028802 TCAAAATGGATAAAAGGGGATGCA 58.971 37.500 0.00 0.00 0.00 3.96
2516 3252 5.612725 TCAAAATGGATAAAAGGGGATGC 57.387 39.130 0.00 0.00 0.00 3.91
2517 3253 7.147689 TGTCATCAAAATGGATAAAAGGGGATG 60.148 37.037 0.00 0.00 33.42 3.51
2518 3254 6.902416 TGTCATCAAAATGGATAAAAGGGGAT 59.098 34.615 0.00 0.00 33.42 3.85
2519 3255 6.259893 TGTCATCAAAATGGATAAAAGGGGA 58.740 36.000 0.00 0.00 33.42 4.81
2520 3256 6.543430 TGTCATCAAAATGGATAAAAGGGG 57.457 37.500 0.00 0.00 33.42 4.79
2521 3257 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
2527 3263 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
2528 3264 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
2529 3265 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
2530 3266 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
2531 3267 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2532 3268 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2533 3269 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2534 3270 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2535 3271 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2536 3272 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
2537 3273 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
2538 3274 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2539 3275 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2540 3276 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2541 3277 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2542 3278 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2543 3279 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2544 3280 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2545 3281 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2546 3282 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2547 3283 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2548 3284 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2549 3285 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2550 3286 1.929860 ATGTACTCCCTCCGTCCGGA 61.930 60.000 0.00 0.00 42.90 5.14
2551 3287 1.455217 ATGTACTCCCTCCGTCCGG 60.455 63.158 0.00 0.00 0.00 5.14
2552 3288 0.750546 TCATGTACTCCCTCCGTCCG 60.751 60.000 0.00 0.00 0.00 4.79
2553 3289 1.705873 ATCATGTACTCCCTCCGTCC 58.294 55.000 0.00 0.00 0.00 4.79
2554 3290 2.803492 GCAATCATGTACTCCCTCCGTC 60.803 54.545 0.00 0.00 0.00 4.79
2555 3291 1.139058 GCAATCATGTACTCCCTCCGT 59.861 52.381 0.00 0.00 0.00 4.69
2556 3292 1.414181 AGCAATCATGTACTCCCTCCG 59.586 52.381 0.00 0.00 0.00 4.63
2557 3293 2.546795 CGAGCAATCATGTACTCCCTCC 60.547 54.545 0.00 0.00 0.00 4.30
2558 3294 2.748605 CGAGCAATCATGTACTCCCTC 58.251 52.381 0.00 0.00 0.00 4.30
2559 3295 1.202580 GCGAGCAATCATGTACTCCCT 60.203 52.381 0.00 0.00 0.00 4.20
2560 3296 1.221414 GCGAGCAATCATGTACTCCC 58.779 55.000 0.00 0.00 0.00 4.30
2561 3297 1.939974 TGCGAGCAATCATGTACTCC 58.060 50.000 0.00 0.00 0.00 3.85
2562 3298 4.149571 CACTATGCGAGCAATCATGTACTC 59.850 45.833 0.57 0.00 0.00 2.59
2563 3299 4.053983 CACTATGCGAGCAATCATGTACT 58.946 43.478 0.57 0.00 0.00 2.73
2564 3300 3.804325 ACACTATGCGAGCAATCATGTAC 59.196 43.478 0.57 0.00 0.00 2.90
2583 3319 9.953697 TGTAACATTTAAGAACCACAATAACAC 57.046 29.630 0.00 0.00 0.00 3.32
2613 3351 6.458342 GCAACTGCTAACTAAGTTCAAGTTGT 60.458 38.462 18.91 0.00 39.58 3.32
2787 3525 6.986817 GTGCTATGACTGTAACAATCACCTAT 59.013 38.462 0.00 0.00 0.00 2.57
2863 3601 7.220030 AGCATAGATTCGATGGAAGTTGTAAT 58.780 34.615 8.57 0.00 35.19 1.89
2931 3669 0.252284 AGGGAGTAGTCACCAGGTGG 60.252 60.000 20.14 0.00 42.17 4.61
2944 3682 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2945 3683 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2946 3684 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2947 3685 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2948 3686 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2949 3687 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2950 3688 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2951 3689 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2952 3690 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2953 3691 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
2954 3692 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
2955 3693 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
2956 3694 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
2959 3697 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
2960 3698 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
2961 3699 7.817962 AGTGTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 0.00 0.00 45.69 0.86
2962 3700 7.149973 AGTGTAGTGTCAAAAACGCTCTTATA 58.850 34.615 0.00 0.00 45.69 0.98
2963 3701 5.989777 AGTGTAGTGTCAAAAACGCTCTTAT 59.010 36.000 0.00 0.00 45.69 1.73
2964 3702 5.353938 AGTGTAGTGTCAAAAACGCTCTTA 58.646 37.500 0.00 0.00 45.69 2.10
2965 3703 4.189231 AGTGTAGTGTCAAAAACGCTCTT 58.811 39.130 0.00 0.00 45.69 2.85
2966 3704 3.793559 AGTGTAGTGTCAAAAACGCTCT 58.206 40.909 0.00 0.00 45.69 4.09
2967 3705 4.743644 ACTAGTGTAGTGTCAAAAACGCTC 59.256 41.667 0.00 0.00 45.69 5.03
2994 3732 4.142556 CGTCCCACAATATAAGGCGTTTTT 60.143 41.667 0.00 0.00 0.00 1.94
2995 3733 3.375922 CGTCCCACAATATAAGGCGTTTT 59.624 43.478 0.00 0.00 0.00 2.43
2996 3734 2.940410 CGTCCCACAATATAAGGCGTTT 59.060 45.455 0.00 0.00 0.00 3.60
2997 3735 2.557317 CGTCCCACAATATAAGGCGTT 58.443 47.619 0.00 0.00 0.00 4.84
2998 3736 1.202604 CCGTCCCACAATATAAGGCGT 60.203 52.381 0.00 0.00 0.00 5.68
2999 3737 1.069513 TCCGTCCCACAATATAAGGCG 59.930 52.381 0.00 0.00 0.00 5.52
3000 3738 2.550208 CCTCCGTCCCACAATATAAGGC 60.550 54.545 0.00 0.00 0.00 4.35
3001 3739 2.038557 CCCTCCGTCCCACAATATAAGG 59.961 54.545 0.00 0.00 0.00 2.69
3002 3740 2.969950 TCCCTCCGTCCCACAATATAAG 59.030 50.000 0.00 0.00 0.00 1.73
3003 3741 2.969950 CTCCCTCCGTCCCACAATATAA 59.030 50.000 0.00 0.00 0.00 0.98
3004 3742 2.090943 ACTCCCTCCGTCCCACAATATA 60.091 50.000 0.00 0.00 0.00 0.86
3005 3743 1.344087 ACTCCCTCCGTCCCACAATAT 60.344 52.381 0.00 0.00 0.00 1.28
3006 3744 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.00 0.00 1.90
3007 3745 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
3008 3746 0.613853 CTACTCCCTCCGTCCCACAA 60.614 60.000 0.00 0.00 0.00 3.33
3009 3747 1.000019 CTACTCCCTCCGTCCCACA 60.000 63.158 0.00 0.00 0.00 4.17
3010 3748 0.257039 TACTACTCCCTCCGTCCCAC 59.743 60.000 0.00 0.00 0.00 4.61
3011 3749 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
3012 3750 3.735720 ATATACTACTCCCTCCGTCCC 57.264 52.381 0.00 0.00 0.00 4.46
3013 3751 4.831710 ACAAATATACTACTCCCTCCGTCC 59.168 45.833 0.00 0.00 0.00 4.79
3014 3752 5.301298 ACACAAATATACTACTCCCTCCGTC 59.699 44.000 0.00 0.00 0.00 4.79
3015 3753 5.206587 ACACAAATATACTACTCCCTCCGT 58.793 41.667 0.00 0.00 0.00 4.69
3016 3754 5.535406 AGACACAAATATACTACTCCCTCCG 59.465 44.000 0.00 0.00 0.00 4.63
3017 3755 6.778559 AGAGACACAAATATACTACTCCCTCC 59.221 42.308 0.00 0.00 0.00 4.30
3018 3756 7.308109 CGAGAGACACAAATATACTACTCCCTC 60.308 44.444 0.00 0.00 0.00 4.30
3019 3757 6.487331 CGAGAGACACAAATATACTACTCCCT 59.513 42.308 0.00 0.00 0.00 4.20
3020 3758 6.485984 TCGAGAGACACAAATATACTACTCCC 59.514 42.308 0.00 0.00 33.31 4.30
3021 3759 7.493743 TCGAGAGACACAAATATACTACTCC 57.506 40.000 0.00 0.00 33.31 3.85
3022 3760 9.784680 TTTTCGAGAGACACAAATATACTACTC 57.215 33.333 0.00 0.00 41.84 2.59
3081 3819 5.894393 TGAGATTGGGTGTCCTGTTTTAAAA 59.106 36.000 0.00 0.00 0.00 1.52
3088 3826 1.734655 AGTGAGATTGGGTGTCCTGT 58.265 50.000 0.00 0.00 0.00 4.00
3091 3829 2.863809 ACAAAGTGAGATTGGGTGTCC 58.136 47.619 0.00 0.00 32.02 4.02
3094 3832 5.530915 TGTAGAAACAAAGTGAGATTGGGTG 59.469 40.000 0.00 0.00 30.91 4.61
3154 3893 5.751680 CAACATGAGACAATTCGAAACTGT 58.248 37.500 14.20 14.20 0.00 3.55
3308 4047 4.370049 TGTTGAACCATTTCAGCACATTG 58.630 39.130 0.37 0.00 45.09 2.82
3386 4125 2.162681 GTGGGGGAGTTGAAAGATGTG 58.837 52.381 0.00 0.00 0.00 3.21
3677 4416 7.223971 GTGATGTGACAAAGTGACAACTAACTA 59.776 37.037 0.00 0.00 32.93 2.24
3750 4489 5.454045 GGAGCTTAGCTAGACTAAAAGCCAT 60.454 44.000 6.75 0.00 39.75 4.40
3837 4576 2.914097 GCAGCCAAGCACAACCCT 60.914 61.111 0.00 0.00 0.00 4.34
3886 4625 5.810525 ACAACATCTCAAAAACTCTCAACG 58.189 37.500 0.00 0.00 0.00 4.10
3907 4646 6.003326 TCCTTCAGCATCAGTCATTTAAACA 58.997 36.000 0.00 0.00 0.00 2.83
3949 4688 3.063180 CAGAAGCCAACATCGACATTCTC 59.937 47.826 0.00 0.00 0.00 2.87
3953 4692 1.089920 GCAGAAGCCAACATCGACAT 58.910 50.000 0.00 0.00 33.58 3.06
3957 4696 2.015736 AGTAGCAGAAGCCAACATCG 57.984 50.000 0.00 0.00 43.56 3.84
4079 4818 7.013942 TCAGCTATATTTAGTTAAGAGTCGGCA 59.986 37.037 0.00 0.00 0.00 5.69
4119 4858 5.163754 GCATCTGTTTTACACCCTATGTCAC 60.164 44.000 0.00 0.00 42.09 3.67
4120 4859 4.941263 GCATCTGTTTTACACCCTATGTCA 59.059 41.667 0.00 0.00 42.09 3.58
4121 4860 5.065218 CAGCATCTGTTTTACACCCTATGTC 59.935 44.000 0.00 0.00 42.09 3.06
4122 4861 4.943705 CAGCATCTGTTTTACACCCTATGT 59.056 41.667 0.00 0.00 46.06 2.29
4123 4862 4.201950 GCAGCATCTGTTTTACACCCTATG 60.202 45.833 0.00 0.00 33.43 2.23
4124 4863 3.947834 GCAGCATCTGTTTTACACCCTAT 59.052 43.478 0.00 0.00 33.43 2.57
4125 4864 3.009033 AGCAGCATCTGTTTTACACCCTA 59.991 43.478 0.00 0.00 33.43 3.53
4126 4865 2.162681 GCAGCATCTGTTTTACACCCT 58.837 47.619 0.00 0.00 33.43 4.34
4127 4866 2.162681 AGCAGCATCTGTTTTACACCC 58.837 47.619 0.00 0.00 33.43 4.61
4128 4867 4.003648 AGTAGCAGCATCTGTTTTACACC 58.996 43.478 0.00 0.00 33.43 4.16
4129 4868 4.452455 ACAGTAGCAGCATCTGTTTTACAC 59.548 41.667 14.23 0.00 39.00 2.90
4130 4869 4.641396 ACAGTAGCAGCATCTGTTTTACA 58.359 39.130 14.23 0.00 39.00 2.41
4131 4870 4.932200 AGACAGTAGCAGCATCTGTTTTAC 59.068 41.667 18.96 9.72 41.58 2.01
4132 4871 5.152623 AGACAGTAGCAGCATCTGTTTTA 57.847 39.130 18.96 0.00 41.58 1.52
4133 4872 4.013267 AGACAGTAGCAGCATCTGTTTT 57.987 40.909 18.96 10.92 41.58 2.43
4134 4873 3.692257 AGACAGTAGCAGCATCTGTTT 57.308 42.857 18.96 13.09 41.58 2.83
4138 4877 7.888021 AGAGTATTATAGACAGTAGCAGCATCT 59.112 37.037 0.00 0.00 0.00 2.90
4171 4910 7.044706 CGAATTTTCAGTCAGAAACAGAACAAC 60.045 37.037 0.00 0.00 45.48 3.32
4173 4912 6.486248 CGAATTTTCAGTCAGAAACAGAACA 58.514 36.000 0.00 0.00 45.48 3.18
4206 4945 0.831966 AGCTGAGAATCCAGGCAGAG 59.168 55.000 0.00 0.00 34.82 3.35
4243 4982 0.994263 GCTTTGGCGCTTAAGCATTG 59.006 50.000 29.18 11.92 44.70 2.82
4254 4993 0.886490 AGTTCCTCTGTGCTTTGGCG 60.886 55.000 0.00 0.00 42.25 5.69


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

AutoCloner maintained by Alex Coulton.