Multiple sequence alignment - TraesCS3D01G413800

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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 TraesCS3D01G413800 chr3D 100.000 5536 0 0 1 5536 526042902 526048437 0.000000e+00 10224
1 TraesCS3D01G413800 chr3D 89.547 287 26 3 11 297 525824964 525824682 1.470000e-95 361
2 TraesCS3D01G413800 chr3D 86.517 178 18 4 446 620 525823948 525823774 2.040000e-44 191
3 TraesCS3D01G413800 chr3D 92.105 114 8 1 342 455 525824115 525824003 5.740000e-35 159
4 TraesCS3D01G413800 chr3A 88.494 2451 175 36 2177 4569 660233211 660235612 0.000000e+00 2865
5 TraesCS3D01G413800 chr3A 85.366 1763 105 49 446 2077 660231479 660233219 0.000000e+00 1685
6 TraesCS3D01G413800 chr3A 90.328 641 47 6 4908 5536 660235965 660236602 0.000000e+00 826
7 TraesCS3D01G413800 chr3A 88.070 285 25 2 8 284 660230457 660230740 4.130000e-86 329
8 TraesCS3D01G413800 chr3B 91.667 1860 117 29 2859 4710 694321681 694323510 0.000000e+00 2542
9 TraesCS3D01G413800 chr3B 91.115 1148 52 25 838 1956 694320092 694321218 0.000000e+00 1509
10 TraesCS3D01G413800 chr3B 91.451 772 58 8 4770 5536 694323515 694324283 0.000000e+00 1053
11 TraesCS3D01G413800 chr3B 86.453 406 39 10 446 842 694318212 694318610 1.100000e-116 431
12 TraesCS3D01G413800 chr3B 89.781 274 24 3 17 287 694317113 694317385 1.140000e-91 348
13 TraesCS3D01G413800 chr3B 94.048 168 10 0 1684 1851 694321477 694321644 7.120000e-64 255
14 TraesCS3D01G413800 chr3B 93.043 115 6 2 342 455 694318048 694318161 3.430000e-37 167
15 TraesCS3D01G413800 chr3B 82.540 189 12 7 1954 2142 694321318 694321485 4.470000e-31 147
16 TraesCS3D01G413800 chr3B 96.429 84 3 0 3115 3198 694321885 694321968 7.480000e-29 139


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 TraesCS3D01G413800 chr3D 526042902 526048437 5535 False 10224.000000 10224 100.000000 1 5536 1 chr3D.!!$F1 5535
1 TraesCS3D01G413800 chr3D 525823774 525824964 1190 True 237.000000 361 89.389667 11 620 3 chr3D.!!$R1 609
2 TraesCS3D01G413800 chr3A 660230457 660236602 6145 False 1426.250000 2865 88.064500 8 5536 4 chr3A.!!$F1 5528
3 TraesCS3D01G413800 chr3B 694317113 694324283 7170 False 732.333333 2542 90.725222 17 5536 9 chr3B.!!$F1 5519

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
344 1000 0.041312 GGTGCGTAGTGTGTGCTTTG 60.041 55.000 0.00 0.0 0.00 2.77 F
1251 3492 0.452987 GACCACGTACGTGCTGGATA 59.547 55.000 36.76 0.0 44.16 2.59 F
1252 3493 0.889994 ACCACGTACGTGCTGGATAA 59.110 50.000 36.76 0.0 44.16 1.75 F
2181 4624 1.129437 GCTGTCTTCGCTGTTGGATTC 59.871 52.381 0.00 0.0 0.00 2.52 F
2751 5201 0.242017 GGAGCTGTCACATGGCAAAC 59.758 55.000 0.00 0.0 0.00 2.93 F
3254 5754 0.994247 ATGACATGACAGCCCCTTCA 59.006 50.000 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 4257 0.035820 TGGGCTACTTAACGGGCTTG 60.036 55.0 0.0 0.0 0.00 4.01 R
2160 4603 0.674895 ATCCAACAGCGAAGACAGCC 60.675 55.0 0.0 0.0 34.64 4.85 R
2731 5181 0.895100 TTTGCCATGTGACAGCTCCC 60.895 55.0 0.0 0.0 0.00 4.30 R
3703 6219 0.242825 TCTTGTACTTCTCACGCCCG 59.757 55.0 0.0 0.0 0.00 6.13 R
4463 6993 0.321653 GCCCAATCTGAACCACGTCT 60.322 55.0 0.0 0.0 0.00 4.18 R
4795 7373 0.401738 TGCTAAGAGTTTGCTGGGCT 59.598 50.0 0.0 0.0 0.00 5.19 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
30 31 4.467084 CCCCATGGTCGTGTCCCG 62.467 72.222 11.73 0.00 38.13 5.14
64 65 1.541147 CCAATGGCAATTCAGACGTGT 59.459 47.619 0.00 0.00 0.00 4.49
65 66 2.030007 CCAATGGCAATTCAGACGTGTT 60.030 45.455 0.00 0.00 0.00 3.32
83 85 0.944999 TTGATAGAGGGGGAGGCTCT 59.055 55.000 15.23 0.00 0.00 4.09
97 99 2.234908 GAGGCTCTGGTGAAAGCTTCTA 59.765 50.000 7.40 0.00 40.39 2.10
103 105 3.259374 TCTGGTGAAAGCTTCTACCTCTG 59.741 47.826 24.31 17.00 34.24 3.35
183 193 3.054361 TGGGGAATAGCTTTGAGGAAGAC 60.054 47.826 0.00 0.00 37.57 3.01
262 272 2.739132 GTGGAAAGACCCGGTCGT 59.261 61.111 12.04 6.01 37.67 4.34
267 277 2.428171 TGGAAAGACCCGGTCGTATAAG 59.572 50.000 12.04 0.00 37.67 1.73
301 728 4.340894 AAATCACATGATACGTGTGTGC 57.659 40.909 19.02 0.00 45.45 4.57
302 729 1.345410 TCACATGATACGTGTGTGCG 58.655 50.000 19.02 0.00 45.45 5.34
308 735 0.160813 GATACGTGTGTGCGTGTGTG 59.839 55.000 0.00 0.00 45.33 3.82
329 985 3.194861 GGTTTGTCTTTCCTTTTGGTGC 58.805 45.455 0.00 0.00 41.38 5.01
330 986 2.857748 GTTTGTCTTTCCTTTTGGTGCG 59.142 45.455 0.00 0.00 41.38 5.34
331 987 1.757682 TGTCTTTCCTTTTGGTGCGT 58.242 45.000 0.00 0.00 41.38 5.24
332 988 2.920524 TGTCTTTCCTTTTGGTGCGTA 58.079 42.857 0.00 0.00 41.38 4.42
333 989 2.875933 TGTCTTTCCTTTTGGTGCGTAG 59.124 45.455 0.00 0.00 41.38 3.51
334 990 2.876550 GTCTTTCCTTTTGGTGCGTAGT 59.123 45.455 0.00 0.00 41.38 2.73
335 991 2.875933 TCTTTCCTTTTGGTGCGTAGTG 59.124 45.455 0.00 0.00 41.38 2.74
336 992 2.335316 TTCCTTTTGGTGCGTAGTGT 57.665 45.000 0.00 0.00 41.38 3.55
337 993 1.588674 TCCTTTTGGTGCGTAGTGTG 58.411 50.000 0.00 0.00 41.38 3.82
338 994 1.134340 TCCTTTTGGTGCGTAGTGTGT 60.134 47.619 0.00 0.00 41.38 3.72
339 995 1.002900 CCTTTTGGTGCGTAGTGTGTG 60.003 52.381 0.00 0.00 34.07 3.82
340 996 0.378962 TTTTGGTGCGTAGTGTGTGC 59.621 50.000 0.00 0.00 0.00 4.57
341 997 0.462937 TTTGGTGCGTAGTGTGTGCT 60.463 50.000 0.00 0.00 0.00 4.40
342 998 0.462937 TTGGTGCGTAGTGTGTGCTT 60.463 50.000 0.00 0.00 0.00 3.91
343 999 0.462937 TGGTGCGTAGTGTGTGCTTT 60.463 50.000 0.00 0.00 0.00 3.51
344 1000 0.041312 GGTGCGTAGTGTGTGCTTTG 60.041 55.000 0.00 0.00 0.00 2.77
345 1001 0.655733 GTGCGTAGTGTGTGCTTTGT 59.344 50.000 0.00 0.00 0.00 2.83
346 1002 0.934496 TGCGTAGTGTGTGCTTTGTC 59.066 50.000 0.00 0.00 0.00 3.18
347 1003 1.217882 GCGTAGTGTGTGCTTTGTCT 58.782 50.000 0.00 0.00 0.00 3.41
348 1004 1.597663 GCGTAGTGTGTGCTTTGTCTT 59.402 47.619 0.00 0.00 0.00 3.01
349 1005 2.031683 GCGTAGTGTGTGCTTTGTCTTT 59.968 45.455 0.00 0.00 0.00 2.52
350 1006 3.844943 GCGTAGTGTGTGCTTTGTCTTTC 60.845 47.826 0.00 0.00 0.00 2.62
351 1007 3.303132 CGTAGTGTGTGCTTTGTCTTTCC 60.303 47.826 0.00 0.00 0.00 3.13
352 1008 3.004752 AGTGTGTGCTTTGTCTTTCCT 57.995 42.857 0.00 0.00 0.00 3.36
353 1009 3.356290 AGTGTGTGCTTTGTCTTTCCTT 58.644 40.909 0.00 0.00 0.00 3.36
354 1010 3.763897 AGTGTGTGCTTTGTCTTTCCTTT 59.236 39.130 0.00 0.00 0.00 3.11
355 1011 4.220602 AGTGTGTGCTTTGTCTTTCCTTTT 59.779 37.500 0.00 0.00 0.00 2.27
356 1012 4.327087 GTGTGTGCTTTGTCTTTCCTTTTG 59.673 41.667 0.00 0.00 0.00 2.44
357 1013 4.219507 TGTGTGCTTTGTCTTTCCTTTTGA 59.780 37.500 0.00 0.00 0.00 2.69
358 1014 5.105392 TGTGTGCTTTGTCTTTCCTTTTGAT 60.105 36.000 0.00 0.00 0.00 2.57
359 1015 5.232838 GTGTGCTTTGTCTTTCCTTTTGATG 59.767 40.000 0.00 0.00 0.00 3.07
407 1064 2.173143 TCAGACCAGGCAATGCATATGA 59.827 45.455 7.79 0.00 0.00 2.15
429 1086 5.547666 TGAAGTACTCATGCATATGGGGTAT 59.452 40.000 0.00 0.00 39.20 2.73
449 1106 2.703190 GCATCGAGCAACTCTTAACG 57.297 50.000 0.00 0.00 44.79 3.18
450 1107 1.267087 GCATCGAGCAACTCTTAACGC 60.267 52.381 0.00 0.00 44.79 4.84
451 1108 1.992667 CATCGAGCAACTCTTAACGCA 59.007 47.619 0.00 0.00 0.00 5.24
480 1200 8.402798 TCAAAGACTTGCTTATTTCCATGTTA 57.597 30.769 0.00 0.00 35.24 2.41
490 1210 6.511767 GCTTATTTCCATGTTATGAGTGACCG 60.512 42.308 0.00 0.00 0.00 4.79
496 1216 3.159353 TGTTATGAGTGACCGGAATCG 57.841 47.619 9.46 0.00 0.00 3.34
504 1224 3.408634 AGTGACCGGAATCGATTGTTTT 58.591 40.909 16.96 0.00 39.00 2.43
539 1259 6.689669 AGTTATTGTTTTCTTTTTCGTCACCG 59.310 34.615 0.00 0.00 0.00 4.94
552 1272 5.409643 TTCGTCACCGTAGCTATTACTAC 57.590 43.478 0.00 0.00 39.35 2.73
576 1296 7.539436 ACGGCTAGTAGATATACATGACAATG 58.461 38.462 0.00 0.00 39.89 2.82
614 1334 7.330946 ACTTCAAACTGATCAATGAATTGCATG 59.669 33.333 14.90 7.95 37.28 4.06
629 1353 4.829064 TTGCATGGTGTACAAAGAACTC 57.171 40.909 0.00 0.00 0.00 3.01
646 1370 8.788813 CAAAGAACTCGTAATATGATTGCAAAC 58.211 33.333 1.71 0.04 0.00 2.93
680 1411 8.545420 GCTTCATGTTCAAATAGCCATATTTTG 58.455 33.333 0.00 0.00 39.15 2.44
696 1428 8.243289 CCATATTTTGGTAGAAAACTTTGCTG 57.757 34.615 0.00 0.00 40.99 4.41
736 1469 8.576442 CACTGTTAGGGATTTTTACAACTTGAT 58.424 33.333 0.00 0.00 0.00 2.57
796 1529 6.879458 GGGCTATTAAGAGAAGAAAACAGTCA 59.121 38.462 0.11 0.00 0.00 3.41
825 1558 2.376032 GACTGCTCGTTTTCTTTGTGC 58.624 47.619 0.00 0.00 0.00 4.57
857 3078 6.995686 TGCTGAAAAACAATACTCCTACTTCA 59.004 34.615 0.00 0.00 0.00 3.02
1069 3299 2.363018 CCTCCACGCTCCTCCTCA 60.363 66.667 0.00 0.00 0.00 3.86
1185 3415 2.427245 CCCCGCCGTCATCTCTCTT 61.427 63.158 0.00 0.00 0.00 2.85
1218 3453 1.784856 CATACTGCACGTACGTATGCC 59.215 52.381 22.34 10.26 41.33 4.40
1225 3460 0.743097 ACGTACGTATGCCCCTCTTC 59.257 55.000 21.41 0.00 0.00 2.87
1226 3461 1.030457 CGTACGTATGCCCCTCTTCT 58.970 55.000 7.22 0.00 0.00 2.85
1227 3462 1.001597 CGTACGTATGCCCCTCTTCTC 60.002 57.143 7.22 0.00 0.00 2.87
1236 3477 1.944177 CCCCTCTTCTCTTCTGACCA 58.056 55.000 0.00 0.00 0.00 4.02
1240 3481 3.082548 CCTCTTCTCTTCTGACCACGTA 58.917 50.000 0.00 0.00 0.00 3.57
1249 3490 2.137425 CTGACCACGTACGTGCTGGA 62.137 60.000 36.76 20.88 44.16 3.86
1251 3492 0.452987 GACCACGTACGTGCTGGATA 59.547 55.000 36.76 0.00 44.16 2.59
1252 3493 0.889994 ACCACGTACGTGCTGGATAA 59.110 50.000 36.76 0.00 44.16 1.75
1254 3495 2.689471 ACCACGTACGTGCTGGATAATA 59.311 45.455 36.76 0.00 44.16 0.98
1595 3872 2.560542 TGCACAGAACCAAAACAAGTGT 59.439 40.909 0.00 0.00 0.00 3.55
1602 3879 5.925969 CAGAACCAAAACAAGTGTGAAAGTT 59.074 36.000 0.00 0.00 0.00 2.66
1640 3935 5.240623 ACGAAAAACAATGAAGTGCCTATCA 59.759 36.000 0.00 0.00 0.00 2.15
1641 3936 6.071952 ACGAAAAACAATGAAGTGCCTATCAT 60.072 34.615 0.00 0.00 37.88 2.45
1839 4170 2.741517 GCCACAATGCCAACAAAATACC 59.258 45.455 0.00 0.00 0.00 2.73
1854 4185 1.750193 ATACCGCCATGACAAACAGG 58.250 50.000 0.00 0.00 0.00 4.00
1926 4257 6.652481 TCTTCATCTGAGAGGTGAACATTTTC 59.348 38.462 0.00 0.00 0.00 2.29
1927 4258 5.868454 TCATCTGAGAGGTGAACATTTTCA 58.132 37.500 0.00 0.00 39.55 2.69
2061 4504 1.336795 GCCATTTGTCCTCCCAAAACG 60.337 52.381 0.00 0.00 37.81 3.60
2104 4547 4.066139 GCCAGGATTGGGCCAGGT 62.066 66.667 6.23 0.00 45.87 4.00
2107 4550 2.128226 AGGATTGGGCCAGGTCCT 59.872 61.111 27.61 27.61 36.29 3.85
2108 4551 2.276740 GGATTGGGCCAGGTCCTG 59.723 66.667 24.84 12.40 0.00 3.86
2109 4552 2.308722 GGATTGGGCCAGGTCCTGA 61.309 63.158 24.84 0.00 32.44 3.86
2119 4562 4.821589 GGTCCTGAGCCGCCTTCG 62.822 72.222 0.00 0.00 0.00 3.79
2123 4566 4.441695 CTGAGCCGCCTTCGAGCA 62.442 66.667 0.00 0.00 38.10 4.26
2132 4575 2.202492 CTTCGAGCACCGTCTCCG 60.202 66.667 0.00 0.00 39.75 4.63
2172 4615 3.710722 CCTGGGGCTGTCTTCGCT 61.711 66.667 0.00 0.00 0.00 4.93
2173 4616 2.435586 CTGGGGCTGTCTTCGCTG 60.436 66.667 0.00 0.00 0.00 5.18
2174 4617 3.241530 TGGGGCTGTCTTCGCTGT 61.242 61.111 0.00 0.00 0.00 4.40
2175 4618 2.032681 GGGGCTGTCTTCGCTGTT 59.967 61.111 0.00 0.00 0.00 3.16
2176 4619 2.328099 GGGGCTGTCTTCGCTGTTG 61.328 63.158 0.00 0.00 0.00 3.33
2177 4620 2.328099 GGGCTGTCTTCGCTGTTGG 61.328 63.158 0.00 0.00 0.00 3.77
2178 4621 1.301716 GGCTGTCTTCGCTGTTGGA 60.302 57.895 0.00 0.00 0.00 3.53
2181 4624 1.129437 GCTGTCTTCGCTGTTGGATTC 59.871 52.381 0.00 0.00 0.00 2.52
2183 4626 3.005554 CTGTCTTCGCTGTTGGATTCAT 58.994 45.455 0.00 0.00 0.00 2.57
2184 4627 3.002791 TGTCTTCGCTGTTGGATTCATC 58.997 45.455 0.00 0.00 0.00 2.92
2209 4652 9.042450 TCCTTGTTTAAATAGTCATAGAGGTGA 57.958 33.333 0.00 0.00 0.00 4.02
2225 4668 4.898861 AGAGGTGAAAACAAATGGCCTTTA 59.101 37.500 3.32 0.00 0.00 1.85
2242 4685 3.007831 CCTTTATCAAGCCAGCCCAAAAA 59.992 43.478 0.00 0.00 0.00 1.94
2251 4694 1.470098 CCAGCCCAAAAATGAGAGTCG 59.530 52.381 0.00 0.00 0.00 4.18
2266 4709 1.999735 GAGTCGCGATGTTTCCATTCA 59.000 47.619 14.06 0.00 0.00 2.57
2269 4712 2.159627 GTCGCGATGTTTCCATTCAACT 59.840 45.455 14.06 0.00 0.00 3.16
2285 4728 2.886523 TCAACTCAAGACATGGCTTTGG 59.113 45.455 12.33 9.85 0.00 3.28
2331 4774 7.283329 ACTAATTCCTACCAAATGTCATCCTC 58.717 38.462 0.00 0.00 0.00 3.71
2336 4779 5.724370 TCCTACCAAATGTCATCCTCTGTTA 59.276 40.000 0.00 0.00 0.00 2.41
2360 4804 7.597288 AAGAGCTTAAAAACCCATTTAGTGT 57.403 32.000 0.00 0.00 0.00 3.55
2372 4816 7.916914 ACCCATTTAGTGTGTAAGACAATAC 57.083 36.000 0.00 0.00 34.91 1.89
2404 4849 4.982241 TGAATCATGGATTCCTAGTCCC 57.018 45.455 14.45 0.00 45.37 4.46
2405 4850 3.652869 TGAATCATGGATTCCTAGTCCCC 59.347 47.826 14.45 0.00 45.37 4.81
2416 4861 7.091537 TGGATTCCTAGTCCCCTTTGATATTTT 60.092 37.037 3.95 0.00 34.76 1.82
2441 4887 5.120674 GGCAACAAAGAATACTTCATTTGGC 59.879 40.000 0.00 0.00 37.39 4.52
2446 4892 3.026694 AGAATACTTCATTTGGCCAGCC 58.973 45.455 5.11 0.38 0.00 4.85
2454 4900 2.361757 TCATTTGGCCAGCCGATATTTG 59.638 45.455 5.11 0.00 39.42 2.32
2457 4903 1.846007 TGGCCAGCCGATATTTGTTT 58.154 45.000 0.00 0.00 39.42 2.83
2475 4921 5.921004 TGTTTTGTTGGCTATCATTTTGC 57.079 34.783 0.00 0.00 0.00 3.68
2491 4937 5.697633 TCATTTTGCCAAAAGAATCTTGAGC 59.302 36.000 8.75 0.79 33.22 4.26
2500 4946 3.951775 AGAATCTTGAGCGAACAGTCT 57.048 42.857 0.00 0.00 0.00 3.24
2502 4948 5.590530 AGAATCTTGAGCGAACAGTCTAT 57.409 39.130 0.00 0.00 0.00 1.98
2503 4949 5.587289 AGAATCTTGAGCGAACAGTCTATC 58.413 41.667 0.00 0.00 0.00 2.08
2504 4950 3.784701 TCTTGAGCGAACAGTCTATCC 57.215 47.619 0.00 0.00 0.00 2.59
2505 4951 3.089284 TCTTGAGCGAACAGTCTATCCA 58.911 45.455 0.00 0.00 0.00 3.41
2506 4952 3.701542 TCTTGAGCGAACAGTCTATCCAT 59.298 43.478 0.00 0.00 0.00 3.41
2507 4953 4.160439 TCTTGAGCGAACAGTCTATCCATT 59.840 41.667 0.00 0.00 0.00 3.16
2508 4954 3.785486 TGAGCGAACAGTCTATCCATTG 58.215 45.455 0.00 0.00 0.00 2.82
2514 4960 5.118990 CGAACAGTCTATCCATTGTCCATT 58.881 41.667 0.00 0.00 0.00 3.16
2524 4970 9.473007 TCTATCCATTGTCCATTGTAAAATTCA 57.527 29.630 0.00 0.00 0.00 2.57
2525 4971 9.520204 CTATCCATTGTCCATTGTAAAATTCAC 57.480 33.333 0.00 0.00 0.00 3.18
2526 4972 7.295322 TCCATTGTCCATTGTAAAATTCACA 57.705 32.000 0.00 0.00 0.00 3.58
2528 4974 7.871973 TCCATTGTCCATTGTAAAATTCACAAG 59.128 33.333 10.33 4.59 39.15 3.16
2573 5023 9.807921 TGATATACATGACCATACTACTCAAGA 57.192 33.333 0.00 0.00 0.00 3.02
2575 5025 9.815306 ATATACATGACCATACTACTCAAGAGT 57.185 33.333 7.96 7.96 45.02 3.24
2576 5026 6.458232 ACATGACCATACTACTCAAGAGTC 57.542 41.667 5.91 0.00 42.54 3.36
2577 5027 5.952347 ACATGACCATACTACTCAAGAGTCA 59.048 40.000 5.91 0.00 42.54 3.41
2613 5063 5.881923 AAGTACAAGACTCTTAACCACCA 57.118 39.130 0.00 0.00 37.44 4.17
2616 5066 4.772886 ACAAGACTCTTAACCACCAGTT 57.227 40.909 0.00 0.00 42.83 3.16
2630 5080 7.750947 AACCACCAGTTAAGAGGATATTACT 57.249 36.000 0.30 0.00 36.74 2.24
2632 5082 6.040616 ACCACCAGTTAAGAGGATATTACTCG 59.959 42.308 0.30 0.00 39.90 4.18
2637 5087 8.361139 CCAGTTAAGAGGATATTACTCGTGAAT 58.639 37.037 6.94 0.00 39.90 2.57
2645 5095 8.019656 AGGATATTACTCGTGAATTACCAAGT 57.980 34.615 0.00 0.00 0.00 3.16
2656 5106 6.090088 CGTGAATTACCAAGTCTCTTCTGAAG 59.910 42.308 11.18 11.18 0.00 3.02
2679 5129 3.558109 CCTTTCTCCAACCTCTTCCAGTC 60.558 52.174 0.00 0.00 0.00 3.51
2691 5141 5.072741 CCTCTTCCAGTCTGAATTCCAAAA 58.927 41.667 0.00 0.00 0.00 2.44
2697 5147 4.095483 CCAGTCTGAATTCCAAAATCTCCG 59.905 45.833 0.00 0.00 0.00 4.63
2701 5151 6.660949 AGTCTGAATTCCAAAATCTCCGAAAT 59.339 34.615 2.27 0.00 0.00 2.17
2726 5176 7.114866 TGAATATGAATACCGAGGTAACACA 57.885 36.000 6.04 7.33 41.41 3.72
2729 5179 4.445452 TGAATACCGAGGTAACACAGAC 57.555 45.455 6.04 0.00 41.41 3.51
2731 5181 1.167851 TACCGAGGTAACACAGACGG 58.832 55.000 0.00 0.00 44.77 4.79
2736 5186 1.079336 GGTAACACAGACGGGGAGC 60.079 63.158 0.00 0.00 0.00 4.70
2749 5199 1.303561 GGGAGCTGTCACATGGCAA 60.304 57.895 0.00 0.00 0.00 4.52
2751 5201 0.242017 GGAGCTGTCACATGGCAAAC 59.758 55.000 0.00 0.00 0.00 2.93
2777 5227 6.318144 CCAATCAACTCAGAATATTGCTCAGT 59.682 38.462 0.00 0.00 0.00 3.41
2789 5239 2.099141 TGCTCAGTGGCATCTACAAC 57.901 50.000 0.00 0.00 37.29 3.32
2790 5240 1.625315 TGCTCAGTGGCATCTACAACT 59.375 47.619 0.00 0.00 37.29 3.16
2791 5241 2.038952 TGCTCAGTGGCATCTACAACTT 59.961 45.455 0.00 0.00 37.29 2.66
2799 5268 7.333423 TCAGTGGCATCTACAACTTAATAACAC 59.667 37.037 0.00 0.00 0.00 3.32
2853 5322 2.100584 GGTTCCACAAATTCACACAGCA 59.899 45.455 0.00 0.00 0.00 4.41
2869 5338 1.601759 GCAGGAGCTTGAGGTTGCA 60.602 57.895 0.00 0.00 37.91 4.08
2890 5359 4.245660 CAAGCTTTCTCGAGGTCATGTTA 58.754 43.478 13.56 0.00 0.00 2.41
2985 5454 6.888105 TCAATTAGGATGACAAGCATGTAGA 58.112 36.000 0.00 0.00 40.74 2.59
3002 5471 6.632834 GCATGTAGACAACTGTGTTAAAACTG 59.367 38.462 1.33 1.33 38.41 3.16
3014 5483 7.700656 ACTGTGTTAAAACTGAAAAAGAATCCG 59.299 33.333 9.46 0.00 0.00 4.18
3024 5493 2.951229 AAAGAATCCGGGACACTGTT 57.049 45.000 0.00 0.00 0.00 3.16
3026 5495 1.645710 AGAATCCGGGACACTGTTCT 58.354 50.000 0.00 0.94 0.00 3.01
3040 5509 4.841246 ACACTGTTCTCCTCTACCTCAAAT 59.159 41.667 0.00 0.00 0.00 2.32
3102 5573 3.300388 TCAATAGCCACACTCCCTCTAG 58.700 50.000 0.00 0.00 0.00 2.43
3112 5583 5.892119 CCACACTCCCTCTAGATACAAAGTA 59.108 44.000 0.00 0.00 0.00 2.24
3120 5591 6.608002 CCCTCTAGATACAAAGTACTCAACCT 59.392 42.308 0.00 0.00 0.00 3.50
3161 5632 7.859875 GGAGAGAAAAAGACAATTTGACTTCAG 59.140 37.037 13.18 0.00 31.62 3.02
3162 5633 8.286191 AGAGAAAAAGACAATTTGACTTCAGT 57.714 30.769 13.18 3.81 31.62 3.41
3254 5754 0.994247 ATGACATGACAGCCCCTTCA 59.006 50.000 0.00 0.00 0.00 3.02
3282 5782 2.421388 CCCTCCCTTGCATAAATGTCGA 60.421 50.000 0.00 0.00 0.00 4.20
3503 6010 3.064271 TGTTAAGGTGTTGTTCAGAACGC 59.936 43.478 8.80 4.96 35.91 4.84
3702 6218 2.172293 AGGATCCTCTCAGGTCATTTGC 59.828 50.000 9.02 0.00 36.53 3.68
3703 6219 2.570135 GATCCTCTCAGGTCATTTGCC 58.430 52.381 0.00 0.00 36.53 4.52
3739 6255 1.293062 AGAGGCCATTGTGGATCACT 58.707 50.000 5.01 0.00 40.96 3.41
3777 6293 3.641906 CCTACGGTGGTAAGGATTGATCT 59.358 47.826 0.00 0.00 0.00 2.75
3787 6303 6.100279 TGGTAAGGATTGATCTAGCTTCATGT 59.900 38.462 0.00 0.00 0.00 3.21
3796 6312 8.429493 TTGATCTAGCTTCATGTCATTACTTG 57.571 34.615 0.00 0.00 33.22 3.16
3828 6349 8.039603 TCATATATGTTCACCACAAACAACTC 57.960 34.615 12.42 0.00 39.84 3.01
3911 6433 1.743394 CTCCATAAAACTTCCCGCACC 59.257 52.381 0.00 0.00 0.00 5.01
3932 6454 2.418628 CGCACATCATTTTTCGGTACCT 59.581 45.455 10.90 0.00 0.00 3.08
3945 6467 1.468520 CGGTACCTGTTTCAAGCATGG 59.531 52.381 10.90 0.00 0.00 3.66
4009 6531 3.119388 AGGAAATGTCAATGCAATCCACG 60.119 43.478 0.00 0.00 33.50 4.94
4094 6616 4.329545 GGGAGCTGGTTGTCCGCA 62.330 66.667 0.00 0.00 36.34 5.69
4126 6648 1.924731 TCGTCCTGAACCAGATCAGT 58.075 50.000 0.00 0.00 44.32 3.41
4463 6993 0.107214 GGCCGGATGATCTGAACCAA 60.107 55.000 5.05 0.00 0.00 3.67
4547 7077 4.142578 ACGACTCTGTGATGATGACTGTAC 60.143 45.833 0.00 0.00 0.00 2.90
4579 7137 1.993370 CGTGACTGAATTCTCCGGAAC 59.007 52.381 5.23 0.00 33.96 3.62
4680 7242 7.275920 AGTTTTTGAGACTAGTCACTTGATGT 58.724 34.615 24.44 0.95 0.00 3.06
4683 7245 6.656632 TTGAGACTAGTCACTTGATGTTCT 57.343 37.500 24.44 0.00 0.00 3.01
4712 7288 1.541588 GGCACTGATCACTTGGTTTCC 59.458 52.381 0.00 0.00 0.00 3.13
4715 7291 3.743521 CACTGATCACTTGGTTTCCTCA 58.256 45.455 0.00 0.00 0.00 3.86
4717 7293 3.077359 CTGATCACTTGGTTTCCTCACC 58.923 50.000 0.00 0.00 37.34 4.02
4718 7294 2.441375 TGATCACTTGGTTTCCTCACCA 59.559 45.455 0.00 0.00 45.68 4.17
4725 7301 0.606673 GGTTTCCTCACCAGTCAGCC 60.607 60.000 0.00 0.00 36.73 4.85
4730 7306 1.153745 CTCACCAGTCAGCCGTAGC 60.154 63.158 0.00 0.00 40.32 3.58
4754 7330 1.088340 CGAGCAGCAGTTGATCAGGG 61.088 60.000 3.27 0.00 42.35 4.45
4807 7385 2.914097 GGCACAGCCCAGCAAACT 60.914 61.111 0.00 0.00 44.06 2.66
4834 7415 0.109597 CTTGATGGTGGCAACGAAGC 60.110 55.000 0.00 0.00 42.51 3.86
4864 7445 4.399395 TGGCTCGCCCAAGCTCAG 62.399 66.667 5.33 0.00 41.82 3.35
4867 7448 2.359107 CTCGCCCAAGCTCAGCAA 60.359 61.111 0.00 0.00 36.60 3.91
4904 7485 0.387202 CTGCCGGACCTATCAGTGAG 59.613 60.000 5.05 0.00 0.00 3.51
4905 7486 1.043116 TGCCGGACCTATCAGTGAGG 61.043 60.000 5.05 0.00 40.22 3.86
4912 7493 2.035632 ACCTATCAGTGAGGTAGCTGC 58.964 52.381 0.00 0.00 45.82 5.25
4916 7497 1.449246 CAGTGAGGTAGCTGCTGCC 60.449 63.158 26.79 26.79 40.80 4.85
4917 7498 1.915266 AGTGAGGTAGCTGCTGCCA 60.915 57.895 33.32 15.23 38.73 4.92
4918 7499 1.449246 GTGAGGTAGCTGCTGCCAG 60.449 63.158 33.32 0.00 38.73 4.85
4951 7536 1.005347 GCGATGGATACGTGGTTTTCG 60.005 52.381 0.00 2.91 42.51 3.46
4971 7557 1.870458 CCTTGCGTCGCGATCGTAA 60.870 57.895 23.75 23.75 36.96 3.18
4980 7566 3.758035 CGATCGTAACCGCACGTT 58.242 55.556 7.03 0.00 42.51 3.99
4994 7580 0.036952 CACGTTGCAGGATCTCTGGT 60.037 55.000 11.63 1.09 43.54 4.00
5085 7671 3.635373 ACATTGCCATCCAAGCTAGATTG 59.365 43.478 13.85 13.85 36.76 2.67
5159 7745 2.048970 ACGCGCACGGTACAATCA 60.049 55.556 5.73 0.00 46.04 2.57
5172 7758 6.916387 CACGGTACAATCACGATCTATACTTT 59.084 38.462 0.00 0.00 0.00 2.66
5173 7759 7.113124 CACGGTACAATCACGATCTATACTTTC 59.887 40.741 0.00 0.00 0.00 2.62
5175 7761 6.581542 GGTACAATCACGATCTATACTTTCGG 59.418 42.308 0.00 0.00 37.20 4.30
5281 7874 1.305219 TGCCCTGAATTACGCTGCAC 61.305 55.000 0.00 0.00 0.00 4.57
5292 7885 2.113860 ACGCTGCACCATGAAAGTAT 57.886 45.000 0.00 0.00 0.00 2.12
5293 7886 3.260475 ACGCTGCACCATGAAAGTATA 57.740 42.857 0.00 0.00 0.00 1.47
5296 7889 4.273480 ACGCTGCACCATGAAAGTATATTC 59.727 41.667 0.00 0.00 0.00 1.75
5332 7928 5.899299 AGCATCATGAAAGTAATTGAAGCC 58.101 37.500 0.00 0.00 34.34 4.35
5362 7958 0.179179 GATGAAGACAAAGCAGGCGC 60.179 55.000 0.00 0.00 38.99 6.53
5363 7959 0.890542 ATGAAGACAAAGCAGGCGCA 60.891 50.000 10.83 0.00 42.27 6.09
5368 7964 0.591170 GACAAAGCAGGCGCAGTAAA 59.409 50.000 10.83 0.00 42.27 2.01
5441 8037 7.496346 TTCCATGTACTCCTAATATCCATCC 57.504 40.000 0.00 0.00 0.00 3.51
5452 8048 7.487338 TCCTAATATCCATCCTGATACCTCAA 58.513 38.462 0.00 0.00 30.36 3.02
5531 8127 0.106149 CATAAGGTCCGTAGCCCACC 59.894 60.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 0.944999 AGAGCCTCCCCCTCTATCAA 59.055 55.000 0.00 0.00 37.88 2.57
65 66 0.189574 CAGAGCCTCCCCCTCTATCA 59.810 60.000 0.00 0.00 37.57 2.15
83 85 2.289694 GCAGAGGTAGAAGCTTTCACCA 60.290 50.000 24.42 0.00 35.01 4.17
97 99 1.186200 TGATAGTTCGCTGCAGAGGT 58.814 50.000 20.43 5.51 0.00 3.85
103 105 4.272018 ACATCTTTCATGATAGTTCGCTGC 59.728 41.667 12.19 0.00 0.00 5.25
183 193 4.637534 ACCACCAATCTCAAATCATCTTCG 59.362 41.667 0.00 0.00 0.00 3.79
289 716 0.160813 CACACACGCACACACGTATC 59.839 55.000 0.00 0.00 46.34 2.24
293 720 2.246993 AAACCACACACGCACACACG 62.247 55.000 0.00 0.00 39.50 4.49
294 721 0.796491 CAAACCACACACGCACACAC 60.796 55.000 0.00 0.00 0.00 3.82
301 728 2.014128 AGGAAAGACAAACCACACACG 58.986 47.619 0.00 0.00 0.00 4.49
302 729 4.450082 AAAGGAAAGACAAACCACACAC 57.550 40.909 0.00 0.00 0.00 3.82
308 735 3.194861 GCACCAAAAGGAAAGACAAACC 58.805 45.455 0.00 0.00 0.00 3.27
329 985 3.303132 GGAAAGACAAAGCACACACTACG 60.303 47.826 0.00 0.00 0.00 3.51
330 986 3.877508 AGGAAAGACAAAGCACACACTAC 59.122 43.478 0.00 0.00 0.00 2.73
331 987 4.150897 AGGAAAGACAAAGCACACACTA 57.849 40.909 0.00 0.00 0.00 2.74
332 988 3.004752 AGGAAAGACAAAGCACACACT 57.995 42.857 0.00 0.00 0.00 3.55
333 989 3.782889 AAGGAAAGACAAAGCACACAC 57.217 42.857 0.00 0.00 0.00 3.82
334 990 4.219507 TCAAAAGGAAAGACAAAGCACACA 59.780 37.500 0.00 0.00 0.00 3.72
335 991 4.743493 TCAAAAGGAAAGACAAAGCACAC 58.257 39.130 0.00 0.00 0.00 3.82
336 992 5.350633 CATCAAAAGGAAAGACAAAGCACA 58.649 37.500 0.00 0.00 0.00 4.57
337 993 4.209911 GCATCAAAAGGAAAGACAAAGCAC 59.790 41.667 0.00 0.00 0.00 4.40
338 994 4.370917 GCATCAAAAGGAAAGACAAAGCA 58.629 39.130 0.00 0.00 0.00 3.91
339 995 3.426525 CGCATCAAAAGGAAAGACAAAGC 59.573 43.478 0.00 0.00 0.00 3.51
340 996 4.610945 ACGCATCAAAAGGAAAGACAAAG 58.389 39.130 0.00 0.00 0.00 2.77
341 997 4.647424 ACGCATCAAAAGGAAAGACAAA 57.353 36.364 0.00 0.00 0.00 2.83
342 998 5.060506 TCTACGCATCAAAAGGAAAGACAA 58.939 37.500 0.00 0.00 0.00 3.18
343 999 4.637276 TCTACGCATCAAAAGGAAAGACA 58.363 39.130 0.00 0.00 0.00 3.41
344 1000 5.351465 TGATCTACGCATCAAAAGGAAAGAC 59.649 40.000 0.00 0.00 29.41 3.01
345 1001 5.487433 TGATCTACGCATCAAAAGGAAAGA 58.513 37.500 0.00 0.00 29.41 2.52
346 1002 5.801350 TGATCTACGCATCAAAAGGAAAG 57.199 39.130 0.00 0.00 29.41 2.62
347 1003 5.123820 CCTTGATCTACGCATCAAAAGGAAA 59.876 40.000 6.52 0.00 41.28 3.13
348 1004 4.635765 CCTTGATCTACGCATCAAAAGGAA 59.364 41.667 6.52 0.00 41.28 3.36
349 1005 4.191544 CCTTGATCTACGCATCAAAAGGA 58.808 43.478 6.52 0.00 41.28 3.36
350 1006 3.242870 GCCTTGATCTACGCATCAAAAGG 60.243 47.826 6.52 6.34 41.28 3.11
351 1007 3.242870 GGCCTTGATCTACGCATCAAAAG 60.243 47.826 0.00 3.45 41.28 2.27
352 1008 2.682856 GGCCTTGATCTACGCATCAAAA 59.317 45.455 0.00 0.00 41.28 2.44
353 1009 2.092968 AGGCCTTGATCTACGCATCAAA 60.093 45.455 0.00 0.00 41.28 2.69
354 1010 1.486310 AGGCCTTGATCTACGCATCAA 59.514 47.619 0.00 5.27 39.91 2.57
355 1011 1.123077 AGGCCTTGATCTACGCATCA 58.877 50.000 0.00 0.00 0.00 3.07
356 1012 3.386768 TTAGGCCTTGATCTACGCATC 57.613 47.619 12.58 0.00 0.00 3.91
357 1013 4.772624 TCTATTAGGCCTTGATCTACGCAT 59.227 41.667 12.58 0.00 0.00 4.73
358 1014 4.022242 GTCTATTAGGCCTTGATCTACGCA 60.022 45.833 12.58 0.00 0.00 5.24
359 1015 4.022242 TGTCTATTAGGCCTTGATCTACGC 60.022 45.833 12.58 0.00 0.00 4.42
407 1064 5.809001 CATACCCCATATGCATGAGTACTT 58.191 41.667 10.16 0.00 34.50 2.24
432 1089 2.363788 TGCGTTAAGAGTTGCTCGAT 57.636 45.000 0.00 0.00 35.36 3.59
448 1105 6.695292 AATAAGCAAGTCTTTGAAAATGCG 57.305 33.333 0.00 0.00 38.74 4.73
449 1106 7.171337 TGGAAATAAGCAAGTCTTTGAAAATGC 59.829 33.333 0.00 0.00 36.36 3.56
450 1107 8.592105 TGGAAATAAGCAAGTCTTTGAAAATG 57.408 30.769 0.00 0.00 36.36 2.32
451 1108 9.211485 CATGGAAATAAGCAAGTCTTTGAAAAT 57.789 29.630 0.00 0.00 36.36 1.82
480 1200 2.168521 ACAATCGATTCCGGTCACTCAT 59.831 45.455 7.92 0.00 36.24 2.90
539 1259 9.762933 ATATCTACTAGCCGTAGTAATAGCTAC 57.237 37.037 0.00 0.00 44.80 3.58
552 1272 7.762382 TCATTGTCATGTATATCTACTAGCCG 58.238 38.462 0.00 0.00 0.00 5.52
576 1296 6.851222 TCAGTTTGAAGTTGAGTCTGAATC 57.149 37.500 0.00 0.00 0.00 2.52
582 1302 7.194607 TCATTGATCAGTTTGAAGTTGAGTC 57.805 36.000 0.00 0.00 0.00 3.36
614 1334 8.644318 ATCATATTACGAGTTCTTTGTACACC 57.356 34.615 0.00 0.00 0.00 4.16
646 1370 7.148689 GGCTATTTGAACATGAAGCAAAAAGAG 60.149 37.037 0.00 7.27 35.44 2.85
655 1379 9.037737 CCAAAATATGGCTATTTGAACATGAAG 57.962 33.333 0.00 0.00 43.80 3.02
680 1411 4.577283 TGTACACCAGCAAAGTTTTCTACC 59.423 41.667 0.00 0.00 0.00 3.18
696 1428 7.959175 TCCCTAACAGTGATATAATGTACACC 58.041 38.462 0.00 0.00 36.42 4.16
738 1471 8.859090 TCATTCCATTTTGAGACACATAAAAGT 58.141 29.630 0.00 0.00 0.00 2.66
796 1529 3.171987 CGAGCAGTCGCAAGCAAT 58.828 55.556 0.00 0.00 39.88 3.56
825 1558 2.791383 TTGTTTTTCAGCATCCGTGG 57.209 45.000 0.00 0.00 0.00 4.94
875 3096 2.680965 CCAACCCCAACGGCCTAT 59.319 61.111 0.00 0.00 33.26 2.57
1047 3277 3.378399 GAGGAGCGTGGAGGAAGGC 62.378 68.421 0.00 0.00 0.00 4.35
1185 3415 4.550422 GTGCAGTATGATCGAGCATAAGA 58.450 43.478 23.84 2.48 39.69 2.10
1218 3453 1.203523 CGTGGTCAGAAGAGAAGAGGG 59.796 57.143 0.00 0.00 0.00 4.30
1225 3460 1.965083 CACGTACGTGGTCAGAAGAG 58.035 55.000 35.09 10.30 42.00 2.85
1226 3461 0.039798 GCACGTACGTGGTCAGAAGA 60.040 55.000 40.17 0.00 45.49 2.87
1227 3462 2.431539 GCACGTACGTGGTCAGAAG 58.568 57.895 40.17 19.67 45.49 2.85
1236 3477 3.709987 GGTTATTATCCAGCACGTACGT 58.290 45.455 16.72 16.72 0.00 3.57
1240 3481 1.483415 ACCGGTTATTATCCAGCACGT 59.517 47.619 0.00 0.00 0.00 4.49
1249 3490 2.639065 CACCACTGCACCGGTTATTAT 58.361 47.619 2.97 0.00 31.41 1.28
1251 3492 0.608035 CCACCACTGCACCGGTTATT 60.608 55.000 2.97 0.00 31.41 1.40
1252 3493 1.002624 CCACCACTGCACCGGTTAT 60.003 57.895 2.97 0.00 31.41 1.89
1254 3495 3.484806 TCCACCACTGCACCGGTT 61.485 61.111 2.97 0.00 31.41 4.44
1291 3532 4.176851 GTCCGTCTCCGACCTCGC 62.177 72.222 0.00 0.00 38.18 5.03
1580 3857 6.779115 AAACTTTCACACTTGTTTTGGTTC 57.221 33.333 0.00 0.00 29.64 3.62
1612 3889 4.109050 GCACTTCATTGTTTTTCGTTCCA 58.891 39.130 0.00 0.00 0.00 3.53
1614 3891 4.359706 AGGCACTTCATTGTTTTTCGTTC 58.640 39.130 0.00 0.00 27.25 3.95
1616 3893 5.240623 TGATAGGCACTTCATTGTTTTTCGT 59.759 36.000 0.00 0.00 41.75 3.85
1617 3894 5.698832 TGATAGGCACTTCATTGTTTTTCG 58.301 37.500 0.00 0.00 41.75 3.46
1640 3935 2.443255 ACCAATGCCGATTCCCTCTAAT 59.557 45.455 0.00 0.00 0.00 1.73
1641 3936 1.843851 ACCAATGCCGATTCCCTCTAA 59.156 47.619 0.00 0.00 0.00 2.10
1839 4170 3.689161 TCTTATTCCTGTTTGTCATGGCG 59.311 43.478 0.00 0.00 0.00 5.69
1854 4185 2.485657 GGGCCCTAGTGTGCTCTTATTC 60.486 54.545 17.04 0.00 0.00 1.75
1926 4257 0.035820 TGGGCTACTTAACGGGCTTG 60.036 55.000 0.00 0.00 0.00 4.01
1927 4258 0.916809 ATGGGCTACTTAACGGGCTT 59.083 50.000 0.00 0.00 0.00 4.35
1988 4420 4.477536 AGCACCTCTCCTCCTAATATCA 57.522 45.455 0.00 0.00 0.00 2.15
2061 4504 2.748605 CACTAGATGGATCCGAAGTGC 58.251 52.381 17.42 1.36 30.83 4.40
2104 4547 3.452786 CTCGAAGGCGGCTCAGGA 61.453 66.667 13.70 9.16 38.28 3.86
2107 4550 4.742201 GTGCTCGAAGGCGGCTCA 62.742 66.667 13.70 1.83 38.28 4.26
2113 4556 2.507324 GAGACGGTGCTCGAAGGC 60.507 66.667 7.01 0.00 42.43 4.35
2155 4598 3.710722 AGCGAAGACAGCCCCAGG 61.711 66.667 0.00 0.00 34.64 4.45
2156 4599 2.435586 CAGCGAAGACAGCCCCAG 60.436 66.667 0.00 0.00 34.64 4.45
2157 4600 2.818169 AACAGCGAAGACAGCCCCA 61.818 57.895 0.00 0.00 34.64 4.96
2159 4602 2.328099 CCAACAGCGAAGACAGCCC 61.328 63.158 0.00 0.00 34.64 5.19
2160 4603 0.674895 ATCCAACAGCGAAGACAGCC 60.675 55.000 0.00 0.00 34.64 4.85
2161 4604 1.129437 GAATCCAACAGCGAAGACAGC 59.871 52.381 0.00 0.00 0.00 4.40
2162 4605 2.416747 TGAATCCAACAGCGAAGACAG 58.583 47.619 0.00 0.00 0.00 3.51
2163 4606 2.542020 TGAATCCAACAGCGAAGACA 57.458 45.000 0.00 0.00 0.00 3.41
2164 4607 2.352960 GGATGAATCCAACAGCGAAGAC 59.647 50.000 4.38 0.00 46.38 3.01
2165 4608 2.632377 GGATGAATCCAACAGCGAAGA 58.368 47.619 4.38 0.00 46.38 2.87
2181 4624 9.838339 ACCTCTATGACTATTTAAACAAGGATG 57.162 33.333 0.00 0.00 0.00 3.51
2183 4626 9.042450 TCACCTCTATGACTATTTAAACAAGGA 57.958 33.333 0.00 0.00 0.00 3.36
2184 4627 9.667107 TTCACCTCTATGACTATTTAAACAAGG 57.333 33.333 0.00 0.00 0.00 3.61
2198 4641 4.462483 GGCCATTTGTTTTCACCTCTATGA 59.538 41.667 0.00 0.00 0.00 2.15
2209 4652 5.003160 GGCTTGATAAAGGCCATTTGTTTT 58.997 37.500 5.01 0.00 44.69 2.43
2218 4661 1.395045 GGGCTGGCTTGATAAAGGCC 61.395 60.000 13.67 6.94 46.56 5.19
2225 4668 2.235402 CTCATTTTTGGGCTGGCTTGAT 59.765 45.455 0.00 0.00 0.00 2.57
2242 4685 1.204704 TGGAAACATCGCGACTCTCAT 59.795 47.619 12.93 0.00 33.40 2.90
2266 4709 3.152341 CTCCAAAGCCATGTCTTGAGTT 58.848 45.455 0.00 0.00 0.00 3.01
2269 4712 1.538047 GCTCCAAAGCCATGTCTTGA 58.462 50.000 0.00 0.00 43.10 3.02
2331 4774 9.626045 CTAAATGGGTTTTTAAGCTCTTAACAG 57.374 33.333 1.85 0.00 35.05 3.16
2336 4779 7.069455 ACACACTAAATGGGTTTTTAAGCTCTT 59.931 33.333 0.00 0.00 45.28 2.85
2349 4792 8.561738 AAGTATTGTCTTACACACTAAATGGG 57.438 34.615 0.00 0.00 37.93 4.00
2384 4829 3.913163 AGGGGACTAGGAATCCATGATTC 59.087 47.826 0.61 8.04 42.66 2.52
2385 4830 3.959920 AGGGGACTAGGAATCCATGATT 58.040 45.455 0.61 0.00 40.61 2.57
2404 4849 7.727331 TTCTTTGTTGCCAAAATATCAAAGG 57.273 32.000 14.00 0.00 39.95 3.11
2441 4887 3.925913 CCAACAAAACAAATATCGGCTGG 59.074 43.478 0.00 0.00 0.00 4.85
2446 4892 8.633075 AATGATAGCCAACAAAACAAATATCG 57.367 30.769 0.00 0.00 0.00 2.92
2475 4921 4.023707 ACTGTTCGCTCAAGATTCTTTTGG 60.024 41.667 0.00 0.00 0.00 3.28
2491 4937 4.123497 TGGACAATGGATAGACTGTTCG 57.877 45.455 0.00 0.00 0.00 3.95
2500 4946 9.029368 TGTGAATTTTACAATGGACAATGGATA 57.971 29.630 0.00 0.00 0.00 2.59
2502 4948 7.295322 TGTGAATTTTACAATGGACAATGGA 57.705 32.000 0.00 0.00 0.00 3.41
2503 4949 7.118101 CCTTGTGAATTTTACAATGGACAATGG 59.882 37.037 7.14 0.22 37.41 3.16
2504 4950 7.871973 TCCTTGTGAATTTTACAATGGACAATG 59.128 33.333 15.06 0.00 37.41 2.82
2505 4951 7.961351 TCCTTGTGAATTTTACAATGGACAAT 58.039 30.769 15.06 0.00 37.41 2.71
2506 4952 7.353414 TCCTTGTGAATTTTACAATGGACAA 57.647 32.000 15.06 0.00 37.41 3.18
2507 4953 6.968263 TCCTTGTGAATTTTACAATGGACA 57.032 33.333 15.06 0.00 37.41 4.02
2508 4954 8.306761 AGATTCCTTGTGAATTTTACAATGGAC 58.693 33.333 17.06 11.18 43.81 4.02
2526 4972 9.917887 ATATCATGTCTTTCTTCAAGATTCCTT 57.082 29.630 0.00 0.00 43.72 3.36
2594 5044 5.881923 AACTGGTGGTTAAGAGTCTTGTA 57.118 39.130 15.90 0.57 36.23 2.41
2604 5054 9.275572 AGTAATATCCTCTTAACTGGTGGTTAA 57.724 33.333 0.00 0.00 44.97 2.01
2605 5055 8.849543 AGTAATATCCTCTTAACTGGTGGTTA 57.150 34.615 0.00 0.00 39.17 2.85
2610 5060 6.832384 TCACGAGTAATATCCTCTTAACTGGT 59.168 38.462 0.00 0.00 0.00 4.00
2616 5066 9.358406 TGGTAATTCACGAGTAATATCCTCTTA 57.642 33.333 0.00 0.00 0.00 2.10
2625 5075 7.171630 AGAGACTTGGTAATTCACGAGTAAT 57.828 36.000 0.00 0.00 0.00 1.89
2630 5080 5.243060 TCAGAAGAGACTTGGTAATTCACGA 59.757 40.000 0.00 0.00 0.00 4.35
2632 5082 6.128418 GCTTCAGAAGAGACTTGGTAATTCAC 60.128 42.308 14.86 0.00 0.00 3.18
2637 5087 3.904339 AGGCTTCAGAAGAGACTTGGTAA 59.096 43.478 14.86 0.00 0.00 2.85
2641 5091 4.640364 AGAAAGGCTTCAGAAGAGACTTG 58.360 43.478 14.86 0.00 33.64 3.16
2645 5095 3.242867 TGGAGAAAGGCTTCAGAAGAGA 58.757 45.455 14.86 0.00 33.64 3.10
2656 5106 1.073923 TGGAAGAGGTTGGAGAAAGGC 59.926 52.381 0.00 0.00 0.00 4.35
2679 5129 7.315142 TCAATTTCGGAGATTTTGGAATTCAG 58.685 34.615 7.93 0.00 35.04 3.02
2691 5141 8.094548 TCGGTATTCATATTCAATTTCGGAGAT 58.905 33.333 0.00 0.00 35.04 2.75
2701 5151 7.557724 TGTGTTACCTCGGTATTCATATTCAA 58.442 34.615 0.00 0.00 0.00 2.69
2726 5176 1.610673 ATGTGACAGCTCCCCGTCT 60.611 57.895 3.85 0.00 33.18 4.18
2729 5179 2.124983 CCATGTGACAGCTCCCCG 60.125 66.667 0.00 0.00 0.00 5.73
2731 5181 0.895100 TTTGCCATGTGACAGCTCCC 60.895 55.000 0.00 0.00 0.00 4.30
2736 5186 1.039068 TTGGGTTTGCCATGTGACAG 58.961 50.000 0.00 0.00 36.17 3.51
2749 5199 5.954150 AGCAATATTCTGAGTTGATTGGGTT 59.046 36.000 0.00 0.00 0.00 4.11
2751 5201 5.591472 TGAGCAATATTCTGAGTTGATTGGG 59.409 40.000 0.00 0.00 0.00 4.12
2754 5204 6.318144 CCACTGAGCAATATTCTGAGTTGATT 59.682 38.462 4.96 0.00 0.00 2.57
2777 5227 5.064198 GCGTGTTATTAAGTTGTAGATGCCA 59.936 40.000 0.00 0.00 0.00 4.92
2853 5322 3.336122 CTTGCAACCTCAAGCTCCT 57.664 52.632 0.00 0.00 37.27 3.69
2869 5338 3.409026 AACATGACCTCGAGAAAGCTT 57.591 42.857 15.71 0.00 0.00 3.74
2985 5454 9.705290 ATTCTTTTTCAGTTTTAACACAGTTGT 57.295 25.926 0.00 0.00 37.67 3.32
3002 5471 3.146847 ACAGTGTCCCGGATTCTTTTTC 58.853 45.455 0.73 0.00 0.00 2.29
3014 5483 1.826096 GGTAGAGGAGAACAGTGTCCC 59.174 57.143 0.00 0.00 37.97 4.46
3024 5493 8.437274 ACTAAAAAGATTTGAGGTAGAGGAGA 57.563 34.615 0.00 0.00 0.00 3.71
3026 5495 9.284968 CAAACTAAAAAGATTTGAGGTAGAGGA 57.715 33.333 0.00 0.00 35.73 3.71
3040 5509 8.287439 TGACATTCTTCACCAAACTAAAAAGA 57.713 30.769 0.00 0.00 0.00 2.52
3083 5554 3.689872 TCTAGAGGGAGTGTGGCTATT 57.310 47.619 0.00 0.00 0.00 1.73
3086 5557 2.245028 TGTATCTAGAGGGAGTGTGGCT 59.755 50.000 0.00 0.00 0.00 4.75
3102 5573 6.872020 TGTGCTTAGGTTGAGTACTTTGTATC 59.128 38.462 0.00 0.00 31.96 2.24
3112 5583 1.202770 GGTGGTGTGCTTAGGTTGAGT 60.203 52.381 0.00 0.00 0.00 3.41
3120 5591 1.347707 CTCTCCAAGGTGGTGTGCTTA 59.652 52.381 0.00 0.00 39.03 3.09
3282 5782 2.192664 TGTGGTTCGGCATACACAAT 57.807 45.000 0.00 0.00 40.50 2.71
3503 6010 1.732259 ACGAACTTTATCCGCAGCAAG 59.268 47.619 0.00 0.00 0.00 4.01
3702 6218 0.736325 CTTGTACTTCTCACGCCCGG 60.736 60.000 0.00 0.00 0.00 5.73
3703 6219 0.242825 TCTTGTACTTCTCACGCCCG 59.757 55.000 0.00 0.00 0.00 6.13
3739 6255 1.074889 GTAGGTTTTTCCAGGGCCTCA 59.925 52.381 0.95 0.00 39.02 3.86
3777 6293 6.371548 GTGGAACAAGTAATGACATGAAGCTA 59.628 38.462 0.00 0.00 44.16 3.32
3796 6312 6.112734 TGTGGTGAACATATATGAGTGGAAC 58.887 40.000 19.63 10.50 32.36 3.62
3828 6349 5.651172 TCGACATGCATAATTAAACCGAG 57.349 39.130 0.00 0.00 0.00 4.63
3911 6433 2.418628 AGGTACCGAAAAATGATGTGCG 59.581 45.455 6.18 0.00 0.00 5.34
3932 6454 1.273048 GATGGCACCATGCTTGAAACA 59.727 47.619 6.96 0.00 44.28 2.83
3945 6467 3.624861 CCAGAGTGTTGATTAGATGGCAC 59.375 47.826 0.00 0.00 0.00 5.01
4009 6531 2.344950 CACTTGATGGTCAGACTGCTC 58.655 52.381 0.00 0.00 0.00 4.26
4087 6609 3.683587 CTGCGAGTCGATGCGGACA 62.684 63.158 18.61 1.36 39.91 4.02
4094 6616 1.136984 GGACGAACTGCGAGTCGAT 59.863 57.895 18.61 0.00 44.57 3.59
4145 6667 1.646624 GAGAGGTCCCACGACTCGAC 61.647 65.000 5.20 0.00 39.15 4.20
4306 6828 2.372688 GGATCTCCCAGGGGGTCA 59.627 66.667 4.81 0.00 44.74 4.02
4463 6993 0.321653 GCCCAATCTGAACCACGTCT 60.322 55.000 0.00 0.00 0.00 4.18
4547 7077 2.269172 TCAGTCACGAGTCGTAGCTAG 58.731 52.381 19.43 5.69 38.32 3.42
4579 7137 6.422701 CGGGTATGTATATACACACAACCTTG 59.577 42.308 22.36 16.00 42.21 3.61
4696 7272 3.077359 GGTGAGGAAACCAAGTGATCAG 58.923 50.000 0.00 0.00 40.22 2.90
4712 7288 1.153745 GCTACGGCTGACTGGTGAG 60.154 63.158 0.00 0.00 35.22 3.51
4715 7291 0.747255 CTATGCTACGGCTGACTGGT 59.253 55.000 0.00 0.00 39.59 4.00
4717 7293 0.936764 CGCTATGCTACGGCTGACTG 60.937 60.000 0.00 0.00 39.59 3.51
4718 7294 1.101635 TCGCTATGCTACGGCTGACT 61.102 55.000 0.00 0.00 39.59 3.41
4722 7298 2.336809 GCTCGCTATGCTACGGCT 59.663 61.111 0.00 0.00 39.59 5.52
4725 7301 1.274126 CTGCTGCTCGCTATGCTACG 61.274 60.000 0.00 0.00 40.11 3.51
4730 7306 1.526041 GATCAACTGCTGCTCGCTATG 59.474 52.381 0.00 0.00 40.11 2.23
4795 7373 0.401738 TGCTAAGAGTTTGCTGGGCT 59.598 50.000 0.00 0.00 0.00 5.19
4799 7377 4.379186 CCATCAAGTGCTAAGAGTTTGCTG 60.379 45.833 0.00 0.00 0.00 4.41
4807 7385 1.350684 TGCCACCATCAAGTGCTAAGA 59.649 47.619 0.00 0.00 36.38 2.10
4889 7470 1.609555 GCTACCTCACTGATAGGTCCG 59.390 57.143 8.58 4.38 44.20 4.79
4890 7471 2.625790 CAGCTACCTCACTGATAGGTCC 59.374 54.545 8.58 3.48 44.20 4.46
4899 7480 1.897225 CTGGCAGCAGCTACCTCACT 61.897 60.000 13.23 0.00 41.70 3.41
4951 7536 2.908088 TACGATCGCGACGCAAGGTC 62.908 60.000 24.04 9.24 41.38 3.85
4980 7566 1.189752 GAGACACCAGAGATCCTGCA 58.810 55.000 5.86 0.00 41.57 4.41
4994 7580 3.319972 CGGAGATATTTTACCGGGAGACA 59.680 47.826 6.32 0.00 41.41 3.41
5085 7671 1.884235 AACCTCTACAGCTTGCACAC 58.116 50.000 0.00 0.00 0.00 3.82
5148 7734 6.630444 AAGTATAGATCGTGATTGTACCGT 57.370 37.500 0.00 0.00 0.00 4.83
5159 7745 6.757237 TCTCTCTACCGAAAGTATAGATCGT 58.243 40.000 0.00 0.00 34.63 3.73
5172 7758 1.282447 ACTGGCTTCTCTCTCTACCGA 59.718 52.381 0.00 0.00 0.00 4.69
5173 7759 1.403679 CACTGGCTTCTCTCTCTACCG 59.596 57.143 0.00 0.00 0.00 4.02
5175 7761 2.452505 ACCACTGGCTTCTCTCTCTAC 58.547 52.381 0.00 0.00 0.00 2.59
5332 7928 5.003590 GCTTTGTCTTCATCTAGTACGTTCG 59.996 44.000 0.00 0.00 0.00 3.95
5362 7958 8.294341 TCTGACTGAAACGAGTAAATTTACTG 57.706 34.615 30.66 23.52 43.64 2.74
5363 7959 8.882415 TTCTGACTGAAACGAGTAAATTTACT 57.118 30.769 27.01 27.01 46.11 2.24
5368 7964 6.934645 TCCATTTCTGACTGAAACGAGTAAAT 59.065 34.615 9.40 0.00 46.08 1.40
5441 8037 6.219417 AGTTGATGACTCTTGAGGTATCAG 57.781 41.667 14.15 0.00 32.58 2.90
5452 8048 3.422796 ACCGTGACTAGTTGATGACTCT 58.577 45.455 0.00 0.00 39.86 3.24


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

AutoCloner maintained by Alex Coulton.