Multiple sequence alignment - TraesCS4D01G261500

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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 TraesCS4D01G261500 chr4D 100.000 4520 0 0 1 4520 432742669 432747188 0.000000e+00 8347.0
1 TraesCS4D01G261500 chr4A 93.355 3010 120 31 3 2974 34021200 34024167 0.000000e+00 4377.0
2 TraesCS4D01G261500 chr4A 89.316 1301 58 40 3252 4520 34024360 34025611 0.000000e+00 1557.0
3 TraesCS4D01G261500 chr4A 83.111 225 22 10 3011 3229 34024166 34024380 1.660000e-44 191.0
4 TraesCS4D01G261500 chr4B 90.314 1084 60 27 943 1989 530525445 530524370 0.000000e+00 1378.0
5 TraesCS4D01G261500 chr4B 86.029 1224 114 27 2053 3229 530524342 530523129 0.000000e+00 1260.0
6 TraesCS4D01G261500 chr4B 84.330 1053 67 53 3253 4249 530523147 530522137 0.000000e+00 941.0
7 TraesCS4D01G261500 chr4B 90.991 222 15 3 1483 1704 14582963 14583179 1.230000e-75 294.0
8 TraesCS4D01G261500 chr4B 93.506 77 5 0 4442 4518 530522012 530521936 1.030000e-21 115.0
9 TraesCS4D01G261500 chr4B 95.000 60 1 1 4318 4375 530522127 530522068 4.810000e-15 93.5
10 TraesCS4D01G261500 chr2A 91.441 222 18 1 1483 1704 686222783 686222563 2.040000e-78 303.0
11 TraesCS4D01G261500 chr1D 84.821 112 8 3 3739 3842 17648568 17648458 2.220000e-18 104.0


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 TraesCS4D01G261500 chr4D 432742669 432747188 4519 False 8347.000000 8347 100.0000 1 4520 1 chr4D.!!$F1 4519
1 TraesCS4D01G261500 chr4A 34021200 34025611 4411 False 2041.666667 4377 88.5940 3 4520 3 chr4A.!!$F1 4517
2 TraesCS4D01G261500 chr4B 530521936 530525445 3509 True 757.500000 1378 89.8358 943 4518 5 chr4B.!!$R1 3575

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
466 475 0.037232 GGTGGGACCGAGAGAAACTG 60.037 60.000 0.00 0.00 0.00 3.16 F
467 476 0.966920 GTGGGACCGAGAGAAACTGA 59.033 55.000 0.00 0.00 0.00 3.41 F
1038 1050 1.290134 GACCTGGATGGAAGTCCCTT 58.710 55.000 0.00 0.00 37.48 3.95 F
2440 2489 2.012673 GTTAGGCAGTTCATGGAGCTG 58.987 52.381 0.00 5.81 42.41 4.24 F
3047 3136 0.899720 ATTCAGCATGGGCCAACTTG 59.100 50.000 11.89 5.62 42.56 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2042 1.272490 CAGCGGACACTGGACTAAAGA 59.728 52.381 0.00 0.0 33.85 2.52 R
2174 2220 4.759693 TGATTTGCACGAGGACAGTAAAAT 59.240 37.500 0.00 0.0 0.00 1.82 R
2542 2591 0.657840 CGAGCCGATTCACCCATTTC 59.342 55.000 0.00 0.0 0.00 2.17 R
3348 3442 0.108329 GGCGTTTCTCCGAATCCTCA 60.108 55.000 0.00 0.0 0.00 3.86 R
4409 4583 0.109412 GACGTACGCAGGTTAGCAGT 60.109 55.000 16.72 0.0 0.00 4.40 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
23 24 2.105821 TCGTTCATTTCCCCTCAGTTGT 59.894 45.455 0.00 0.00 0.00 3.32
27 28 2.642311 TCATTTCCCCTCAGTTGTAGCA 59.358 45.455 0.00 0.00 0.00 3.49
41 42 1.137282 TGTAGCAAGTGTCACCGTTGA 59.863 47.619 8.69 0.00 0.00 3.18
43 44 1.967319 AGCAAGTGTCACCGTTGAAT 58.033 45.000 8.69 0.00 31.90 2.57
44 45 2.297701 AGCAAGTGTCACCGTTGAATT 58.702 42.857 8.69 0.00 31.90 2.17
45 46 2.687935 AGCAAGTGTCACCGTTGAATTT 59.312 40.909 8.69 0.00 31.90 1.82
91 100 3.365820 GGTAGTACCAATCGTTGTGTTCG 59.634 47.826 14.82 0.00 38.42 3.95
99 108 0.935831 TCGTTGTGTTCGTAGCACCG 60.936 55.000 0.00 0.00 36.11 4.94
115 124 2.350102 GCACCGTAGCAGTTTGTTTACC 60.350 50.000 0.00 0.00 0.00 2.85
210 219 3.804036 CAGTAATGGAATGGAGCGGTAA 58.196 45.455 0.00 0.00 0.00 2.85
223 232 2.163613 GAGCGGTAAATGGAACCAAAGG 59.836 50.000 0.00 0.00 36.78 3.11
241 250 0.180406 GGTGGTACCTACATGGCTGG 59.820 60.000 14.36 0.00 40.22 4.85
271 280 5.871524 TGTTGAATTTTTGTTGCTGCTGTTA 59.128 32.000 0.00 0.00 0.00 2.41
298 307 2.591923 TGCCCTGAAGTAATTGTTGCA 58.408 42.857 0.00 0.00 0.00 4.08
299 308 2.557924 TGCCCTGAAGTAATTGTTGCAG 59.442 45.455 0.00 0.00 0.00 4.41
404 413 7.382218 CACCAACAAAATGTGGAAGAACTAATC 59.618 37.037 0.00 0.00 0.00 1.75
421 430 9.362151 AGAACTAATCTTTGATAGAGGGTAGAG 57.638 37.037 0.00 0.00 36.02 2.43
423 432 7.302184 ACTAATCTTTGATAGAGGGTAGAGCT 58.698 38.462 0.00 0.00 36.02 4.09
446 455 3.264450 AGCCAGCTAGGTTGAGTACATTT 59.736 43.478 0.00 0.00 40.61 2.32
451 460 3.689649 GCTAGGTTGAGTACATTTGGTGG 59.310 47.826 0.00 0.00 0.00 4.61
452 461 3.154827 AGGTTGAGTACATTTGGTGGG 57.845 47.619 0.00 0.00 0.00 4.61
453 462 2.714250 AGGTTGAGTACATTTGGTGGGA 59.286 45.455 0.00 0.00 0.00 4.37
454 463 2.817844 GGTTGAGTACATTTGGTGGGAC 59.182 50.000 0.00 0.00 0.00 4.46
455 464 2.817844 GTTGAGTACATTTGGTGGGACC 59.182 50.000 0.00 0.00 39.22 4.46
456 465 1.002659 TGAGTACATTTGGTGGGACCG 59.997 52.381 0.00 0.00 42.58 4.79
457 466 1.276989 GAGTACATTTGGTGGGACCGA 59.723 52.381 0.00 0.00 42.58 4.69
458 467 1.278127 AGTACATTTGGTGGGACCGAG 59.722 52.381 0.00 0.00 42.58 4.63
459 468 1.276989 GTACATTTGGTGGGACCGAGA 59.723 52.381 0.00 0.00 42.58 4.04
460 469 0.324943 ACATTTGGTGGGACCGAGAG 59.675 55.000 0.00 0.00 42.58 3.20
461 470 0.613260 CATTTGGTGGGACCGAGAGA 59.387 55.000 0.00 0.00 42.58 3.10
462 471 1.003118 CATTTGGTGGGACCGAGAGAA 59.997 52.381 0.00 0.00 42.58 2.87
463 472 1.133363 TTTGGTGGGACCGAGAGAAA 58.867 50.000 0.00 0.00 42.58 2.52
464 473 0.395312 TTGGTGGGACCGAGAGAAAC 59.605 55.000 0.00 0.00 42.58 2.78
465 474 0.471211 TGGTGGGACCGAGAGAAACT 60.471 55.000 0.00 0.00 42.58 2.66
466 475 0.037232 GGTGGGACCGAGAGAAACTG 60.037 60.000 0.00 0.00 0.00 3.16
467 476 0.966920 GTGGGACCGAGAGAAACTGA 59.033 55.000 0.00 0.00 0.00 3.41
468 477 1.550976 GTGGGACCGAGAGAAACTGAT 59.449 52.381 0.00 0.00 0.00 2.90
469 478 2.028020 GTGGGACCGAGAGAAACTGATT 60.028 50.000 0.00 0.00 0.00 2.57
501 510 8.318412 TGTTTGCTCTTTCATATAGTCTTACCA 58.682 33.333 0.00 0.00 0.00 3.25
547 557 1.672356 GTGTGGTAGCAGCCTGTGG 60.672 63.158 0.00 0.00 0.00 4.17
601 611 2.191128 ATTCTGTTCTGTGGGAGCAC 57.809 50.000 0.00 0.00 31.96 4.40
609 619 1.618837 TCTGTGGGAGCACACTAAGAC 59.381 52.381 4.33 0.00 41.84 3.01
614 624 1.402984 GGGAGCACACTAAGACACTCG 60.403 57.143 0.00 0.00 0.00 4.18
620 630 3.235195 CACACTAAGACACTCGTAGCAC 58.765 50.000 0.00 0.00 32.77 4.40
627 637 3.381949 AGACACTCGTAGCACTTTCAAC 58.618 45.455 0.00 0.00 0.00 3.18
658 668 5.369110 AGAGATTTCAGATTCCTACCATGCT 59.631 40.000 0.00 0.00 0.00 3.79
748 758 6.074648 TCTTTCATATTTCACAAAGGTGGGT 58.925 36.000 0.00 0.00 45.32 4.51
780 790 6.092533 ACACATTTTTCAGTTTCCTGCTTTTG 59.907 34.615 0.00 0.00 38.66 2.44
800 810 8.328146 GCTTTTGTTTTACAAGTCCTTGAAATC 58.672 33.333 13.69 8.99 42.93 2.17
820 830 9.028284 TGAAATCAGATTTAGCCTCTTCAAAAT 57.972 29.630 8.45 0.00 31.47 1.82
826 836 9.741647 CAGATTTAGCCTCTTCAAAATAAATCC 57.258 33.333 10.34 0.00 39.06 3.01
827 837 9.706529 AGATTTAGCCTCTTCAAAATAAATCCT 57.293 29.630 10.34 0.00 39.06 3.24
830 840 6.442513 AGCCTCTTCAAAATAAATCCTTCG 57.557 37.500 0.00 0.00 0.00 3.79
928 940 7.436933 GGAAAACCATTTCAGAGAAAGTTGAT 58.563 34.615 3.97 0.00 45.53 2.57
967 979 8.202811 TGATCTTTCTGAACTAGATCCTTCATG 58.797 37.037 21.01 0.00 42.21 3.07
1038 1050 1.290134 GACCTGGATGGAAGTCCCTT 58.710 55.000 0.00 0.00 37.48 3.95
1125 1137 2.884639 CGGTCAATCCCCAAATGATACC 59.115 50.000 0.00 0.00 0.00 2.73
1267 1279 4.033587 AGCAAACGTACTATTTATGCACCG 59.966 41.667 0.00 0.00 34.89 4.94
1276 1288 6.584185 ACTATTTATGCACCGGTTCTTTTT 57.416 33.333 2.97 0.00 0.00 1.94
1277 1289 6.386654 ACTATTTATGCACCGGTTCTTTTTG 58.613 36.000 2.97 0.00 0.00 2.44
1321 1333 6.311935 TGTTCGGTTTCGAGTTATAAATCCAG 59.688 38.462 7.31 0.00 46.75 3.86
1408 1420 5.804173 GCTCATCACAGCTAATGTTAACTG 58.196 41.667 7.22 0.00 41.41 3.16
1563 1578 3.482156 AGCGCTTATTCTGACCATCAT 57.518 42.857 2.64 0.00 0.00 2.45
1596 1612 3.976339 ATGCGACTACAGGCATCTC 57.024 52.632 0.00 0.00 46.31 2.75
1622 1638 5.765182 GCCACCAGTATCATAGCAATTTAGT 59.235 40.000 0.00 0.00 0.00 2.24
1627 1643 7.931948 ACCAGTATCATAGCAATTTAGTACACC 59.068 37.037 0.00 0.00 0.00 4.16
1662 1678 4.826274 TCAGCTAGTACAGATTTTGGCT 57.174 40.909 0.00 0.00 0.00 4.75
1880 1926 3.371965 AGGGACCGCTCTAACTTCAATA 58.628 45.455 0.00 0.00 0.00 1.90
1969 2015 4.100808 AGACCCATCTCTTAGACATGAAGC 59.899 45.833 0.00 0.00 0.00 3.86
2047 2093 3.772025 AGAGGATGGATATTTAGGGCTCG 59.228 47.826 0.00 0.00 0.00 5.03
2118 2164 7.841956 TGTGAAAAGGTGGAACAAGAATTAAA 58.158 30.769 0.00 0.00 44.16 1.52
2167 2213 3.117284 ACAACACCAAAATCCTACCTGGT 60.117 43.478 4.05 4.05 43.01 4.00
2174 2220 5.550403 ACCAAAATCCTACCTGGTTCTTCTA 59.450 40.000 3.84 0.00 39.14 2.10
2226 2273 8.698973 TGGACAATTTTTGTGGAGTAAGATTA 57.301 30.769 0.00 0.00 45.52 1.75
2440 2489 2.012673 GTTAGGCAGTTCATGGAGCTG 58.987 52.381 0.00 5.81 42.41 4.24
2542 2591 1.154035 GACCGGCAGCAAAATTCCG 60.154 57.895 0.00 0.00 41.41 4.30
2623 2672 9.688091 TGCTTATTATTATTAGTTGGTCAACCA 57.312 29.630 9.90 0.00 45.94 3.67
2724 2785 7.436118 GGCCATCATTCTTGCTGATTAAATTA 58.564 34.615 0.00 0.00 31.00 1.40
2725 2786 8.092687 GGCCATCATTCTTGCTGATTAAATTAT 58.907 33.333 0.00 0.00 31.00 1.28
2834 2895 8.552034 GCAATTCTATAGTCTTTACAGCGATTT 58.448 33.333 0.00 0.00 0.00 2.17
2887 2949 6.659242 AGAATATAACCCTCAACCACACAAAG 59.341 38.462 0.00 0.00 0.00 2.77
2896 2958 3.119173 TCAACCACACAAAGAAAAGGCAG 60.119 43.478 0.00 0.00 0.00 4.85
2909 2971 5.431765 AGAAAAGGCAGTATATGACAGTGG 58.568 41.667 0.00 0.00 40.68 4.00
2910 2972 4.844349 AAAGGCAGTATATGACAGTGGT 57.156 40.909 0.00 0.00 40.68 4.16
2943 3005 4.337274 TGATCTTGTTGCAGCCTAATCATG 59.663 41.667 0.00 0.00 0.00 3.07
2945 3007 4.842574 TCTTGTTGCAGCCTAATCATGTA 58.157 39.130 0.00 0.00 0.00 2.29
2956 3018 8.307483 GCAGCCTAATCATGTACTAGAGATTTA 58.693 37.037 0.00 0.00 33.22 1.40
2976 3040 7.875554 AGATTTAAGAAGTCTGTTTCCAGTCTC 59.124 37.037 0.00 0.00 36.28 3.36
2985 3049 2.172505 TGTTTCCAGTCTCAAAGGAGCA 59.827 45.455 0.00 0.00 41.13 4.26
2986 3050 2.550180 GTTTCCAGTCTCAAAGGAGCAC 59.450 50.000 0.00 0.00 41.13 4.40
2987 3051 1.722034 TCCAGTCTCAAAGGAGCACT 58.278 50.000 0.00 0.00 41.13 4.40
2988 3052 2.050144 TCCAGTCTCAAAGGAGCACTT 58.950 47.619 0.00 0.00 41.13 3.16
3004 3068 7.721402 AGGAGCACTTTAGATGTAGTATTGAG 58.279 38.462 0.00 0.00 0.00 3.02
3006 3070 8.364142 GGAGCACTTTAGATGTAGTATTGAGAT 58.636 37.037 0.00 0.00 0.00 2.75
3047 3136 0.899720 ATTCAGCATGGGCCAACTTG 59.100 50.000 11.89 5.62 42.56 3.16
3080 3169 6.603237 TGAAACTCTGAACATGTAGTTGTG 57.397 37.500 11.52 1.85 41.51 3.33
3101 3191 1.977854 AGTCCATGGTCTGTGCAGTTA 59.022 47.619 12.58 0.00 0.00 2.24
3160 3252 9.681692 TGAGATTCTTGTTACACATCAAATTTG 57.318 29.630 12.15 12.15 0.00 2.32
3174 3266 8.853345 CACATCAAATTTGTTACTTGTCATAGC 58.147 33.333 17.47 0.00 0.00 2.97
3176 3268 9.577110 CATCAAATTTGTTACTTGTCATAGCAT 57.423 29.630 17.47 0.00 0.00 3.79
3181 3273 8.761575 ATTTGTTACTTGTCATAGCATTTTGG 57.238 30.769 0.00 0.00 0.00 3.28
3188 3280 7.047271 ACTTGTCATAGCATTTTGGTGTTTTT 58.953 30.769 0.00 0.00 0.00 1.94
3195 3289 3.248363 GCATTTTGGTGTTTTTCTGAGGC 59.752 43.478 0.00 0.00 0.00 4.70
3200 3294 2.039418 GGTGTTTTTCTGAGGCCCTTT 58.961 47.619 0.00 0.00 0.00 3.11
3208 3302 3.876309 TCTGAGGCCCTTTAAAACTGT 57.124 42.857 0.00 0.00 0.00 3.55
3209 3303 4.178956 TCTGAGGCCCTTTAAAACTGTT 57.821 40.909 0.00 0.00 0.00 3.16
3210 3304 4.542697 TCTGAGGCCCTTTAAAACTGTTT 58.457 39.130 0.00 0.00 0.00 2.83
3211 3305 4.959839 TCTGAGGCCCTTTAAAACTGTTTT 59.040 37.500 20.87 20.87 36.67 2.43
3212 3306 5.423931 TCTGAGGCCCTTTAAAACTGTTTTT 59.576 36.000 22.07 8.18 38.51 1.94
3213 3307 6.608002 TCTGAGGCCCTTTAAAACTGTTTTTA 59.392 34.615 22.07 11.77 36.32 1.52
3214 3308 7.289084 TCTGAGGCCCTTTAAAACTGTTTTTAT 59.711 33.333 22.07 2.69 37.10 1.40
3215 3309 7.438564 TGAGGCCCTTTAAAACTGTTTTTATC 58.561 34.615 22.07 8.47 37.10 1.75
3216 3310 6.765403 AGGCCCTTTAAAACTGTTTTTATCC 58.235 36.000 22.07 14.39 37.10 2.59
3217 3311 5.935789 GGCCCTTTAAAACTGTTTTTATCCC 59.064 40.000 22.07 12.15 37.10 3.85
3218 3312 6.239772 GGCCCTTTAAAACTGTTTTTATCCCT 60.240 38.462 22.07 0.56 37.10 4.20
3219 3313 7.221450 GCCCTTTAAAACTGTTTTTATCCCTT 58.779 34.615 22.07 0.00 37.10 3.95
3220 3314 7.386848 GCCCTTTAAAACTGTTTTTATCCCTTC 59.613 37.037 22.07 4.15 37.10 3.46
3221 3315 8.647796 CCCTTTAAAACTGTTTTTATCCCTTCT 58.352 33.333 22.07 0.00 37.10 2.85
3222 3316 9.692749 CCTTTAAAACTGTTTTTATCCCTTCTC 57.307 33.333 22.07 0.00 37.10 2.87
3223 3317 9.692749 CTTTAAAACTGTTTTTATCCCTTCTCC 57.307 33.333 22.07 0.00 37.10 3.71
3224 3318 9.429109 TTTAAAACTGTTTTTATCCCTTCTCCT 57.571 29.630 22.07 0.00 37.10 3.69
3226 3320 7.997773 AAACTGTTTTTATCCCTTCTCCTAC 57.002 36.000 0.00 0.00 0.00 3.18
3227 3321 6.697641 ACTGTTTTTATCCCTTCTCCTACA 57.302 37.500 0.00 0.00 0.00 2.74
3228 3322 6.712276 ACTGTTTTTATCCCTTCTCCTACAG 58.288 40.000 0.00 0.00 36.32 2.74
3229 3323 6.272558 ACTGTTTTTATCCCTTCTCCTACAGT 59.727 38.462 0.00 0.00 38.05 3.55
3230 3324 7.086685 TGTTTTTATCCCTTCTCCTACAGTT 57.913 36.000 0.00 0.00 0.00 3.16
3231 3325 7.523415 TGTTTTTATCCCTTCTCCTACAGTTT 58.477 34.615 0.00 0.00 0.00 2.66
3232 3326 7.447238 TGTTTTTATCCCTTCTCCTACAGTTTG 59.553 37.037 0.00 0.00 0.00 2.93
3233 3327 3.636153 ATCCCTTCTCCTACAGTTTGC 57.364 47.619 0.00 0.00 0.00 3.68
3234 3328 2.334977 TCCCTTCTCCTACAGTTTGCA 58.665 47.619 0.00 0.00 0.00 4.08
3235 3329 2.303022 TCCCTTCTCCTACAGTTTGCAG 59.697 50.000 0.00 0.00 0.00 4.41
3236 3330 2.303022 CCCTTCTCCTACAGTTTGCAGA 59.697 50.000 0.00 0.00 0.00 4.26
3237 3331 3.054802 CCCTTCTCCTACAGTTTGCAGAT 60.055 47.826 0.00 0.00 0.00 2.90
3238 3332 4.566488 CCCTTCTCCTACAGTTTGCAGATT 60.566 45.833 0.00 0.00 0.00 2.40
3239 3333 5.338381 CCCTTCTCCTACAGTTTGCAGATTA 60.338 44.000 0.00 0.00 0.00 1.75
3240 3334 6.173339 CCTTCTCCTACAGTTTGCAGATTAA 58.827 40.000 0.00 0.00 0.00 1.40
3241 3335 6.655003 CCTTCTCCTACAGTTTGCAGATTAAA 59.345 38.462 0.00 0.00 0.00 1.52
3242 3336 7.174946 CCTTCTCCTACAGTTTGCAGATTAAAA 59.825 37.037 0.00 0.00 0.00 1.52
3243 3337 8.458573 TTCTCCTACAGTTTGCAGATTAAAAA 57.541 30.769 0.00 0.00 0.00 1.94
3244 3338 7.871853 TCTCCTACAGTTTGCAGATTAAAAAC 58.128 34.615 0.00 0.00 34.68 2.43
3245 3339 7.719633 TCTCCTACAGTTTGCAGATTAAAAACT 59.280 33.333 0.00 0.00 43.18 2.66
3246 3340 8.911918 TCCTACAGTTTGCAGATTAAAAACTA 57.088 30.769 2.69 0.00 41.08 2.24
3247 3341 9.515226 TCCTACAGTTTGCAGATTAAAAACTAT 57.485 29.630 2.69 0.00 41.08 2.12
3348 3442 0.333993 ATGATCCAAACAGCCAGCCT 59.666 50.000 0.00 0.00 0.00 4.58
3357 3451 1.523258 CAGCCAGCCTGAGGATTCG 60.523 63.158 0.65 0.00 44.64 3.34
3363 3457 1.208052 CAGCCTGAGGATTCGGAGAAA 59.792 52.381 0.65 0.00 45.90 2.52
3441 3535 0.404426 CCCCGTCTTCTTCCCCTTTT 59.596 55.000 0.00 0.00 0.00 2.27
3444 3538 1.613520 CCGTCTTCTTCCCCTTTTCCC 60.614 57.143 0.00 0.00 0.00 3.97
3505 3599 3.876589 AAATCCAGCACCGCGTCGT 62.877 57.895 4.92 0.00 0.00 4.34
3537 3631 3.058708 GGTAGCCCGTGTAACTTTTGAAC 60.059 47.826 0.00 0.00 31.75 3.18
3541 3637 2.287368 CCCGTGTAACTTTTGAACCAGC 60.287 50.000 0.00 0.00 31.75 4.85
3592 3699 3.254903 ACGGTGCCAGTTAATTTTTCTCC 59.745 43.478 0.00 0.00 0.00 3.71
3599 3706 6.431234 TGCCAGTTAATTTTTCTCCTTCTCTC 59.569 38.462 0.00 0.00 0.00 3.20
3600 3707 6.657117 GCCAGTTAATTTTTCTCCTTCTCTCT 59.343 38.462 0.00 0.00 0.00 3.10
3641 3750 4.492895 GCTTGCTTGTTGATGTTGTTGTTG 60.493 41.667 0.00 0.00 0.00 3.33
3642 3751 4.185467 TGCTTGTTGATGTTGTTGTTGT 57.815 36.364 0.00 0.00 0.00 3.32
3692 3803 3.669251 AAAGAGTGGCTACAGACAGAC 57.331 47.619 2.02 0.00 30.83 3.51
3706 3817 2.069273 GACAGACGTGATTTGGGTGAG 58.931 52.381 0.00 0.00 0.00 3.51
3822 3941 1.359130 TCAGTCTCCCCTGTCTCATCA 59.641 52.381 0.00 0.00 34.02 3.07
3826 3945 2.294791 GTCTCCCCTGTCTCATCATACG 59.705 54.545 0.00 0.00 0.00 3.06
3827 3946 2.091830 TCTCCCCTGTCTCATCATACGT 60.092 50.000 0.00 0.00 0.00 3.57
3828 3947 3.137728 TCTCCCCTGTCTCATCATACGTA 59.862 47.826 0.00 0.00 0.00 3.57
3829 3948 3.220110 TCCCCTGTCTCATCATACGTAC 58.780 50.000 0.00 0.00 0.00 3.67
3842 3961 6.377429 TCATCATACGTACCTGATATCTTCCC 59.623 42.308 10.54 0.00 31.05 3.97
3872 3992 5.008911 GTCATATCCATGCATGCTTGTGTTA 59.991 40.000 26.41 17.97 31.73 2.41
3940 4074 4.284490 TCAGTCCAGTTCAGCAGTAAATCT 59.716 41.667 0.00 0.00 0.00 2.40
3971 4121 5.043903 CGCTATGTCTACATGCAGTTTACT 58.956 41.667 5.85 0.00 37.15 2.24
3993 4147 6.228258 ACTACGTACATGTGGTTTTCTGAAT 58.772 36.000 9.11 0.00 28.06 2.57
3994 4148 7.380536 ACTACGTACATGTGGTTTTCTGAATA 58.619 34.615 9.11 0.00 28.06 1.75
3995 4149 8.038944 ACTACGTACATGTGGTTTTCTGAATAT 58.961 33.333 9.11 0.00 28.06 1.28
3996 4150 7.072177 ACGTACATGTGGTTTTCTGAATATG 57.928 36.000 9.11 0.00 0.00 1.78
3997 4151 6.093495 ACGTACATGTGGTTTTCTGAATATGG 59.907 38.462 9.11 0.00 0.00 2.74
3998 4152 6.315144 CGTACATGTGGTTTTCTGAATATGGA 59.685 38.462 9.11 0.00 0.00 3.41
4047 4201 0.322277 ATGGCAGTGCTCAGTTGAGG 60.322 55.000 16.11 0.00 42.29 3.86
4074 4234 1.439679 GGAAGTCAGTAAAGGTGGCG 58.560 55.000 0.00 0.00 0.00 5.69
4075 4235 1.439679 GAAGTCAGTAAAGGTGGCGG 58.560 55.000 0.00 0.00 0.00 6.13
4076 4236 0.605589 AAGTCAGTAAAGGTGGCGGC 60.606 55.000 0.00 0.00 0.00 6.53
4077 4237 1.003718 GTCAGTAAAGGTGGCGGCT 60.004 57.895 11.43 0.00 0.00 5.52
4078 4238 1.003839 TCAGTAAAGGTGGCGGCTG 60.004 57.895 11.43 0.00 0.00 4.85
4141 4305 0.179000 GCCATACAGGTGTAGCAGCT 59.821 55.000 0.00 0.00 43.33 4.24
4261 4433 4.828409 CTGAAAGCTCTGCCCCAA 57.172 55.556 0.00 0.00 0.00 4.12
4273 4445 1.213678 CTGCCCCAATCTCCAATCTCA 59.786 52.381 0.00 0.00 0.00 3.27
4280 4452 4.039730 CCCAATCTCCAATCTCATCGTACT 59.960 45.833 0.00 0.00 0.00 2.73
4376 4550 1.227205 CAACGCCAAAGCCAAAGCA 60.227 52.632 0.00 0.00 43.56 3.91
4377 4551 0.600782 CAACGCCAAAGCCAAAGCAT 60.601 50.000 0.00 0.00 43.56 3.79
4378 4552 0.600782 AACGCCAAAGCCAAAGCATG 60.601 50.000 0.00 0.00 43.56 4.06
4386 4560 2.577059 CCAAAGCATGGCCAGCAG 59.423 61.111 23.46 12.80 43.80 4.24
4388 4562 2.602267 AAAGCATGGCCAGCAGCA 60.602 55.556 24.17 0.00 46.50 4.41
4389 4563 2.211410 AAAGCATGGCCAGCAGCAA 61.211 52.632 24.17 0.00 46.50 3.91
4390 4564 1.760479 AAAGCATGGCCAGCAGCAAA 61.760 50.000 24.17 0.00 46.50 3.68
4391 4565 2.125673 GCATGGCCAGCAGCAAAG 60.126 61.111 13.05 0.00 46.50 2.77
4392 4566 2.577059 CATGGCCAGCAGCAAAGG 59.423 61.111 13.05 0.00 46.50 3.11
4393 4567 3.387947 ATGGCCAGCAGCAAAGGC 61.388 61.111 13.05 13.54 46.50 4.35
4428 4602 0.109412 ACTGCTAACCTGCGTACGTC 60.109 55.000 17.90 9.82 35.36 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.991250 ACTGAGGGGAAATGAACGATG 58.009 47.619 0.00 0.00 0.00 3.84
1 2 3.244911 ACAACTGAGGGGAAATGAACGAT 60.245 43.478 0.00 0.00 0.00 3.73
2 3 2.105821 ACAACTGAGGGGAAATGAACGA 59.894 45.455 0.00 0.00 0.00 3.85
3 4 2.504367 ACAACTGAGGGGAAATGAACG 58.496 47.619 0.00 0.00 0.00 3.95
4 5 3.440522 GCTACAACTGAGGGGAAATGAAC 59.559 47.826 0.00 0.00 0.00 3.18
6 7 2.642311 TGCTACAACTGAGGGGAAATGA 59.358 45.455 0.00 0.00 0.00 2.57
23 24 2.605837 TTCAACGGTGACACTTGCTA 57.394 45.000 0.44 0.00 31.90 3.49
45 46 6.098552 CCAAACTGAACTAAACCCCCTAAAAA 59.901 38.462 0.00 0.00 0.00 1.94
91 100 1.792006 ACAAACTGCTACGGTGCTAC 58.208 50.000 3.74 0.00 0.00 3.58
99 108 5.058490 TGGTACAGGTAAACAAACTGCTAC 58.942 41.667 0.00 0.00 35.70 3.58
223 232 0.909623 ACCAGCCATGTAGGTACCAC 59.090 55.000 15.94 10.84 40.61 4.16
241 250 5.452944 CAGCAACAAAAATTCAACAATGCAC 59.547 36.000 0.00 0.00 33.89 4.57
271 280 2.335316 TTACTTCAGGGCAAACACGT 57.665 45.000 0.00 0.00 0.00 4.49
298 307 4.993584 CGCATAATCCTTCAATCTACAGCT 59.006 41.667 0.00 0.00 0.00 4.24
299 308 4.153117 CCGCATAATCCTTCAATCTACAGC 59.847 45.833 0.00 0.00 0.00 4.40
371 380 6.325919 TCCACATTTTGTTGGTGAGAATAC 57.674 37.500 0.00 0.00 34.52 1.89
383 392 8.912988 TCAAAGATTAGTTCTTCCACATTTTGT 58.087 29.630 0.00 0.00 44.09 2.83
404 413 4.219725 GGCTAGCTCTACCCTCTATCAAAG 59.780 50.000 15.72 0.00 0.00 2.77
423 432 3.095912 TGTACTCAACCTAGCTGGCTA 57.904 47.619 0.00 2.23 40.22 3.93
446 455 0.471211 AGTTTCTCTCGGTCCCACCA 60.471 55.000 0.00 0.00 38.47 4.17
451 460 2.233922 TGGAATCAGTTTCTCTCGGTCC 59.766 50.000 0.00 0.00 34.56 4.46
452 461 3.594603 TGGAATCAGTTTCTCTCGGTC 57.405 47.619 0.00 0.00 34.56 4.79
453 462 4.559862 AATGGAATCAGTTTCTCTCGGT 57.440 40.909 0.00 0.00 34.56 4.69
454 463 4.697352 ACAAATGGAATCAGTTTCTCTCGG 59.303 41.667 0.00 0.00 34.56 4.63
455 464 5.869753 ACAAATGGAATCAGTTTCTCTCG 57.130 39.130 0.00 0.00 34.56 4.04
456 465 6.364435 GCAAACAAATGGAATCAGTTTCTCTC 59.636 38.462 0.00 0.00 32.97 3.20
457 466 6.041296 AGCAAACAAATGGAATCAGTTTCTCT 59.959 34.615 0.00 0.00 32.97 3.10
458 467 6.218746 AGCAAACAAATGGAATCAGTTTCTC 58.781 36.000 0.00 0.00 32.97 2.87
459 468 6.041296 AGAGCAAACAAATGGAATCAGTTTCT 59.959 34.615 0.00 0.00 32.97 2.52
460 469 6.218746 AGAGCAAACAAATGGAATCAGTTTC 58.781 36.000 0.00 0.00 32.97 2.78
461 470 6.165700 AGAGCAAACAAATGGAATCAGTTT 57.834 33.333 0.00 0.00 34.77 2.66
462 471 5.796424 AGAGCAAACAAATGGAATCAGTT 57.204 34.783 0.00 0.00 0.00 3.16
463 472 5.796424 AAGAGCAAACAAATGGAATCAGT 57.204 34.783 0.00 0.00 0.00 3.41
464 473 6.218019 TGAAAGAGCAAACAAATGGAATCAG 58.782 36.000 0.00 0.00 0.00 2.90
465 474 6.159299 TGAAAGAGCAAACAAATGGAATCA 57.841 33.333 0.00 0.00 0.00 2.57
466 475 8.937634 ATATGAAAGAGCAAACAAATGGAATC 57.062 30.769 0.00 0.00 0.00 2.52
468 477 9.023962 ACTATATGAAAGAGCAAACAAATGGAA 57.976 29.630 0.00 0.00 0.00 3.53
469 478 8.579850 ACTATATGAAAGAGCAAACAAATGGA 57.420 30.769 0.00 0.00 0.00 3.41
498 507 4.917906 AGAGGCTCTAATTTGAAGTGGT 57.082 40.909 17.09 0.00 0.00 4.16
499 508 7.687941 TTTAAGAGGCTCTAATTTGAAGTGG 57.312 36.000 19.07 0.00 0.00 4.00
501 510 7.361286 CGCTTTTAAGAGGCTCTAATTTGAAGT 60.361 37.037 19.07 0.70 0.00 3.01
583 593 0.836606 TGTGCTCCCACAGAACAGAA 59.163 50.000 0.00 0.00 46.51 3.02
601 611 3.833545 AGTGCTACGAGTGTCTTAGTG 57.166 47.619 0.00 0.00 0.00 2.74
609 619 4.547532 ACTAGTTGAAAGTGCTACGAGTG 58.452 43.478 0.00 0.00 31.15 3.51
614 624 5.047943 TCTCTGGACTAGTTGAAAGTGCTAC 60.048 44.000 0.00 0.00 36.38 3.58
620 630 7.382110 TCTGAAATCTCTGGACTAGTTGAAAG 58.618 38.462 0.00 0.00 0.00 2.62
627 637 6.729690 AGGAATCTGAAATCTCTGGACTAG 57.270 41.667 0.00 0.00 0.00 2.57
658 668 5.003160 ACAACATGTGCACTAGATTTAGCA 58.997 37.500 19.41 0.00 34.10 3.49
724 734 6.015519 CACCCACCTTTGTGAAATATGAAAGA 60.016 38.462 0.00 0.00 45.76 2.52
748 758 7.616313 AGGAAACTGAAAAATGTGTTAAACCA 58.384 30.769 0.00 0.00 41.13 3.67
780 790 9.750125 AAATCTGATTTCAAGGACTTGTAAAAC 57.250 29.630 9.76 9.74 41.16 2.43
800 810 9.741647 GGATTTATTTTGAAGAGGCTAAATCTG 57.258 33.333 11.31 0.00 36.51 2.90
899 911 4.093472 TCTCTGAAATGGTTTTCCCGAA 57.907 40.909 0.00 0.00 40.49 4.30
928 940 7.806409 TCAGAAAGATCAACAATTGAGAACA 57.194 32.000 13.59 0.00 43.98 3.18
1125 1137 7.979444 ATCATACACATTAAGATAAACCGGG 57.021 36.000 6.32 0.00 0.00 5.73
1267 1279 8.932945 ATGAGAAAAGAAGAACAAAAAGAACC 57.067 30.769 0.00 0.00 0.00 3.62
1276 1288 7.409697 CGAACAGAAATGAGAAAAGAAGAACA 58.590 34.615 0.00 0.00 0.00 3.18
1277 1289 6.853362 CCGAACAGAAATGAGAAAAGAAGAAC 59.147 38.462 0.00 0.00 0.00 3.01
1321 1333 1.996292 TAGCATCAGTGAAGTCGTGC 58.004 50.000 7.44 7.44 0.00 5.34
1596 1612 2.916702 TGCTATGATACTGGTGGCAG 57.083 50.000 0.00 0.00 0.00 4.85
1627 1643 1.531423 AGCTGAACACCTGAAGCATG 58.469 50.000 0.00 0.00 38.14 4.06
1662 1678 5.307976 ACATGATGGAGCTTACATAGGCTAA 59.692 40.000 0.00 0.00 38.86 3.09
1843 1871 4.512484 GGTCCCTCAAAATCAAGAGAGAG 58.488 47.826 0.00 0.00 33.74 3.20
1969 2015 4.978438 ATGAGATCCAGGAAGATCCTTG 57.022 45.455 0.00 0.00 46.91 3.61
1988 2034 7.464358 CGGACACTGGACTAAAGAATTAAATG 58.536 38.462 0.00 0.00 0.00 2.32
1989 2035 6.093633 GCGGACACTGGACTAAAGAATTAAAT 59.906 38.462 0.00 0.00 0.00 1.40
1990 2036 5.410439 GCGGACACTGGACTAAAGAATTAAA 59.590 40.000 0.00 0.00 0.00 1.52
1991 2037 4.933400 GCGGACACTGGACTAAAGAATTAA 59.067 41.667 0.00 0.00 0.00 1.40
1992 2038 4.222145 AGCGGACACTGGACTAAAGAATTA 59.778 41.667 0.00 0.00 0.00 1.40
1993 2039 3.008049 AGCGGACACTGGACTAAAGAATT 59.992 43.478 0.00 0.00 0.00 2.17
1994 2040 2.567615 AGCGGACACTGGACTAAAGAAT 59.432 45.455 0.00 0.00 0.00 2.40
1995 2041 1.968493 AGCGGACACTGGACTAAAGAA 59.032 47.619 0.00 0.00 0.00 2.52
1996 2042 1.272490 CAGCGGACACTGGACTAAAGA 59.728 52.381 0.00 0.00 33.85 2.52
2167 2213 5.867716 GCACGAGGACAGTAAAATAGAAGAA 59.132 40.000 0.00 0.00 0.00 2.52
2174 2220 4.759693 TGATTTGCACGAGGACAGTAAAAT 59.240 37.500 0.00 0.00 0.00 1.82
2380 2429 5.723135 GCACGTCGTACCAAGAAATATTGAC 60.723 44.000 0.00 0.00 31.55 3.18
2440 2489 5.479306 TCTCCATTGTAGTTTACTGACTGC 58.521 41.667 0.00 0.00 33.50 4.40
2542 2591 0.657840 CGAGCCGATTCACCCATTTC 59.342 55.000 0.00 0.00 0.00 2.17
2724 2785 9.125026 CATTTCTAGGAACTAAAGTGGCAATAT 57.875 33.333 0.00 0.00 42.17 1.28
2725 2786 8.107095 ACATTTCTAGGAACTAAAGTGGCAATA 58.893 33.333 0.00 0.00 42.17 1.90
2816 2877 7.097192 TCAAGTCAAATCGCTGTAAAGACTAT 58.903 34.615 0.00 0.00 34.10 2.12
2834 2895 7.126061 TCCTAATCTATCAAGGTCTCAAGTCA 58.874 38.462 0.00 0.00 0.00 3.41
2876 2938 2.831526 ACTGCCTTTTCTTTGTGTGGTT 59.168 40.909 0.00 0.00 0.00 3.67
2887 2949 5.186198 ACCACTGTCATATACTGCCTTTTC 58.814 41.667 0.00 0.00 0.00 2.29
2896 2958 5.105310 AGGTGTCAAGACCACTGTCATATAC 60.105 44.000 0.00 0.00 44.33 1.47
2909 2971 3.058639 GCAACAAGATCAGGTGTCAAGAC 60.059 47.826 5.30 0.00 0.00 3.01
2910 2972 3.141398 GCAACAAGATCAGGTGTCAAGA 58.859 45.455 5.30 0.00 0.00 3.02
2945 3007 8.871125 TGGAAACAGACTTCTTAAATCTCTAGT 58.129 33.333 0.00 0.00 35.01 2.57
2969 3033 2.557920 AAGTGCTCCTTTGAGACTGG 57.442 50.000 0.00 0.00 41.42 4.00
2976 3040 8.607459 CAATACTACATCTAAAGTGCTCCTTTG 58.393 37.037 10.89 0.27 43.27 2.77
3006 3070 8.810652 GAATGCAATTCCTGTTTAAAACAGTA 57.189 30.769 0.09 0.00 46.93 2.74
3007 3071 7.713764 GAATGCAATTCCTGTTTAAAACAGT 57.286 32.000 0.09 0.00 46.93 3.55
3047 3136 1.264020 TCAGAGTTTCATGTTGTGCGC 59.736 47.619 0.00 0.00 0.00 6.09
3078 3167 0.035317 TGCACAGACCATGGACTCAC 59.965 55.000 21.47 9.55 0.00 3.51
3080 3169 0.322975 ACTGCACAGACCATGGACTC 59.677 55.000 21.47 6.48 0.00 3.36
3101 3191 6.380079 AGACTTTATCTGGACAAGGAATGT 57.620 37.500 0.00 0.00 40.10 2.71
3148 3238 8.853345 GCTATGACAAGTAACAAATTTGATGTG 58.147 33.333 24.64 14.08 0.00 3.21
3160 3252 6.677913 ACACCAAAATGCTATGACAAGTAAC 58.322 36.000 0.00 0.00 0.00 2.50
3163 3255 5.789643 AACACCAAAATGCTATGACAAGT 57.210 34.783 0.00 0.00 0.00 3.16
3174 3266 3.809279 GGCCTCAGAAAAACACCAAAATG 59.191 43.478 0.00 0.00 0.00 2.32
3176 3268 2.169561 GGGCCTCAGAAAAACACCAAAA 59.830 45.455 0.84 0.00 0.00 2.44
3181 3273 4.929819 TTAAAGGGCCTCAGAAAAACAC 57.070 40.909 6.46 0.00 0.00 3.32
3188 3280 3.876309 ACAGTTTTAAAGGGCCTCAGA 57.124 42.857 6.46 0.00 0.00 3.27
3195 3289 8.647796 AGAAGGGATAAAAACAGTTTTAAAGGG 58.352 33.333 11.76 0.00 41.38 3.95
3200 3294 9.511272 GTAGGAGAAGGGATAAAAACAGTTTTA 57.489 33.333 11.76 2.65 42.06 1.52
3208 3302 6.433093 GCAAACTGTAGGAGAAGGGATAAAAA 59.567 38.462 0.00 0.00 0.00 1.94
3209 3303 5.944007 GCAAACTGTAGGAGAAGGGATAAAA 59.056 40.000 0.00 0.00 0.00 1.52
3210 3304 5.013704 TGCAAACTGTAGGAGAAGGGATAAA 59.986 40.000 0.00 0.00 0.00 1.40
3211 3305 4.534500 TGCAAACTGTAGGAGAAGGGATAA 59.466 41.667 0.00 0.00 0.00 1.75
3212 3306 4.101114 TGCAAACTGTAGGAGAAGGGATA 58.899 43.478 0.00 0.00 0.00 2.59
3213 3307 2.912956 TGCAAACTGTAGGAGAAGGGAT 59.087 45.455 0.00 0.00 0.00 3.85
3214 3308 2.303022 CTGCAAACTGTAGGAGAAGGGA 59.697 50.000 0.00 0.00 0.00 4.20
3215 3309 2.303022 TCTGCAAACTGTAGGAGAAGGG 59.697 50.000 2.67 0.00 30.69 3.95
3216 3310 3.685139 TCTGCAAACTGTAGGAGAAGG 57.315 47.619 2.67 0.00 30.69 3.46
3217 3311 7.672983 TTTAATCTGCAAACTGTAGGAGAAG 57.327 36.000 8.09 0.00 35.82 2.85
3218 3312 8.349983 GTTTTTAATCTGCAAACTGTAGGAGAA 58.650 33.333 8.09 0.00 35.82 2.87
3219 3313 7.719633 AGTTTTTAATCTGCAAACTGTAGGAGA 59.280 33.333 6.80 6.80 38.92 3.71
3220 3314 7.875971 AGTTTTTAATCTGCAAACTGTAGGAG 58.124 34.615 2.22 0.00 38.92 3.69
3221 3315 7.817418 AGTTTTTAATCTGCAAACTGTAGGA 57.183 32.000 2.22 0.00 38.92 2.94
3250 3344 5.071370 TGCGTGTAGGAAAAGGGATAAAAA 58.929 37.500 0.00 0.00 0.00 1.94
3264 3358 1.815421 GATGGCACCTGCGTGTAGG 60.815 63.158 2.15 2.15 42.39 3.18
3266 3360 1.079197 CAGATGGCACCTGCGTGTA 60.079 57.895 0.00 0.00 42.39 2.90
3267 3361 2.359107 CAGATGGCACCTGCGTGT 60.359 61.111 0.00 0.00 42.39 4.49
3268 3362 3.807538 GCAGATGGCACCTGCGTG 61.808 66.667 19.84 0.00 46.03 5.34
3348 3442 0.108329 GGCGTTTCTCCGAATCCTCA 60.108 55.000 0.00 0.00 0.00 3.86
3444 3538 1.815421 CTCTTTCACGGGCGATGGG 60.815 63.158 0.00 0.00 0.00 4.00
3505 3599 1.822990 CACGGGCTACCTACTCTTGAA 59.177 52.381 0.00 0.00 33.28 2.69
3537 3631 2.189499 GCCCGAATTAGCCAGCTGG 61.189 63.158 29.34 29.34 38.53 4.85
3541 3637 2.537560 CGCTGCCCGAATTAGCCAG 61.538 63.158 0.00 0.00 40.02 4.85
3592 3699 1.132262 GCTGACACCGAGAGAGAGAAG 59.868 57.143 0.00 0.00 0.00 2.85
3599 3706 1.804372 GCATTAGGCTGACACCGAGAG 60.804 57.143 0.00 0.00 40.25 3.20
3600 3707 0.175760 GCATTAGGCTGACACCGAGA 59.824 55.000 0.00 0.00 40.25 4.04
3641 3750 7.417612 GGGATTACATCACATGATACAACAAC 58.582 38.462 0.00 0.00 32.63 3.32
3642 3751 6.545666 GGGGATTACATCACATGATACAACAA 59.454 38.462 0.00 0.00 33.20 2.83
3692 3803 1.086696 ATTCGCTCACCCAAATCACG 58.913 50.000 0.00 0.00 0.00 4.35
3706 3817 1.327764 GTGGAATCGAGGTGAATTCGC 59.672 52.381 10.64 10.64 37.94 4.70
3795 3907 2.569404 GACAGGGGAGACTGAACTGAAT 59.431 50.000 0.00 0.00 40.97 2.57
3822 3941 4.045590 AGGGGGAAGATATCAGGTACGTAT 59.954 45.833 5.32 0.00 0.00 3.06
3826 3945 2.907042 CCAGGGGGAAGATATCAGGTAC 59.093 54.545 5.32 0.00 35.59 3.34
3827 3946 3.275848 CCAGGGGGAAGATATCAGGTA 57.724 52.381 5.32 0.00 35.59 3.08
3828 3947 2.124560 CCAGGGGGAAGATATCAGGT 57.875 55.000 5.32 0.00 35.59 4.00
3842 3961 0.773014 TGCATGGATATGACCCAGGG 59.227 55.000 2.85 2.85 36.12 4.45
3888 4010 7.553402 TGTGCTTTTACAGTTGACTAGGTAAAA 59.447 33.333 13.98 13.98 41.04 1.52
3889 4011 7.049133 TGTGCTTTTACAGTTGACTAGGTAAA 58.951 34.615 0.00 0.00 34.82 2.01
3890 4012 6.584488 TGTGCTTTTACAGTTGACTAGGTAA 58.416 36.000 0.00 0.00 0.00 2.85
3891 4013 6.041182 TCTGTGCTTTTACAGTTGACTAGGTA 59.959 38.462 5.89 0.00 46.32 3.08
3940 4074 0.959553 GTAGACATAGCGGGCTAGCA 59.040 55.000 18.24 0.00 40.15 3.49
3948 4082 5.043903 AGTAAACTGCATGTAGACATAGCG 58.956 41.667 18.40 2.51 35.01 4.26
3971 4121 7.279090 CCATATTCAGAAAACCACATGTACGTA 59.721 37.037 0.00 0.00 0.00 3.57
3993 4147 1.062886 AGCCTACACTGCTCCTCCATA 60.063 52.381 0.00 0.00 32.41 2.74
3994 4148 0.326048 AGCCTACACTGCTCCTCCAT 60.326 55.000 0.00 0.00 32.41 3.41
3995 4149 1.079256 AGCCTACACTGCTCCTCCA 59.921 57.895 0.00 0.00 32.41 3.86
3996 4150 4.042251 AGCCTACACTGCTCCTCC 57.958 61.111 0.00 0.00 32.41 4.30
4047 4201 3.576648 CTTTACTGACTTCCGACCTCAC 58.423 50.000 0.00 0.00 0.00 3.51
4141 4305 1.561717 AATTGTACGCTCGCAACGCA 61.562 50.000 0.00 0.00 0.00 5.24
4145 4309 2.074942 CGGAATTGTACGCTCGCAA 58.925 52.632 0.00 0.00 0.00 4.85
4261 4433 5.064558 ACGTAGTACGATGAGATTGGAGAT 58.935 41.667 28.47 0.00 46.05 2.75
4280 4452 1.409241 CCCCTGGAGCTGTACTACGTA 60.409 57.143 0.00 0.00 27.93 3.57
4376 4550 3.387947 GCCTTTGCTGCTGGCCAT 61.388 61.111 5.51 0.00 40.71 4.40
4399 4573 0.831307 GGTTAGCAGTACCAGAGGGG 59.169 60.000 0.00 0.00 44.81 4.79
4400 4574 1.482593 CAGGTTAGCAGTACCAGAGGG 59.517 57.143 4.95 0.00 38.16 4.30
4401 4575 1.134670 GCAGGTTAGCAGTACCAGAGG 60.135 57.143 4.95 0.00 38.16 3.69
4402 4576 1.469940 CGCAGGTTAGCAGTACCAGAG 60.470 57.143 4.95 0.00 38.16 3.35
4403 4577 0.530744 CGCAGGTTAGCAGTACCAGA 59.469 55.000 4.95 0.00 38.16 3.86
4404 4578 0.246635 ACGCAGGTTAGCAGTACCAG 59.753 55.000 4.95 0.00 38.16 4.00
4405 4579 1.203052 GTACGCAGGTTAGCAGTACCA 59.797 52.381 4.95 0.00 37.93 3.25
4406 4580 1.796617 CGTACGCAGGTTAGCAGTACC 60.797 57.143 0.52 0.00 39.26 3.34
4407 4581 1.135575 ACGTACGCAGGTTAGCAGTAC 60.136 52.381 16.72 0.00 39.16 2.73
4408 4582 1.131126 GACGTACGCAGGTTAGCAGTA 59.869 52.381 16.72 0.00 0.00 2.74
4409 4583 0.109412 GACGTACGCAGGTTAGCAGT 60.109 55.000 16.72 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.