Multiple sequence alignment - TraesCS3D01G226100

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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 TraesCS3D01G226100 chr3D 100.000 4526 0 0 1 4526 307878998 307883523 0.000000e+00 8359
1 TraesCS3D01G226100 chr3A 95.524 3195 126 6 625 3811 427191156 427194341 0.000000e+00 5092
2 TraesCS3D01G226100 chr3A 94.311 457 23 1 3803 4256 427197818 427198274 0.000000e+00 697
3 TraesCS3D01G226100 chr3A 87.526 489 35 6 1 474 427183805 427184282 3.980000e-150 542
4 TraesCS3D01G226100 chr3B 93.159 1871 78 19 603 2437 413866441 413864585 0.000000e+00 2700
5 TraesCS3D01G226100 chr3B 94.161 1781 70 12 2483 4256 413864206 413862453 0.000000e+00 2682
6 TraesCS3D01G226100 chr3B 94.051 353 18 2 253 604 413873009 413872659 2.400000e-147 532
7 TraesCS3D01G226100 chr3B 93.333 240 9 3 24 263 413874638 413874406 9.320000e-92 348
8 TraesCS3D01G226100 chr3B 77.000 400 86 6 2623 3019 413970527 413970923 1.640000e-54 224
9 TraesCS3D01G226100 chr2D 83.013 936 148 9 2623 3552 174324527 174325457 0.000000e+00 837
10 TraesCS3D01G226100 chr2D 81.959 776 129 8 2601 3370 174383078 174383848 0.000000e+00 647
11 TraesCS3D01G226100 chr2D 82.923 568 84 9 971 1531 174322127 174322688 2.430000e-137 499
12 TraesCS3D01G226100 chr2D 83.377 385 61 3 1148 1531 174382071 174382453 2.000000e-93 353
13 TraesCS3D01G226100 chr2A 82.924 937 148 10 2623 3552 174027289 174028220 0.000000e+00 833
14 TraesCS3D01G226100 chr2A 83.392 849 131 8 2601 3444 174245655 174246498 0.000000e+00 778
15 TraesCS3D01G226100 chr2A 81.550 542 95 5 992 1531 174039101 174039639 4.160000e-120 442
16 TraesCS3D01G226100 chr2A 80.443 542 101 5 992 1531 174244492 174245030 4.210000e-110 409
17 TraesCS3D01G226100 chr2A 87.273 275 30 5 4256 4526 170608344 170608617 4.400000e-80 309
18 TraesCS3D01G226100 chr2B 81.925 935 159 7 2623 3552 222143177 222144106 0.000000e+00 782
19 TraesCS3D01G226100 chr2B 85.145 276 33 5 4257 4526 741112720 741112447 4.460000e-70 276
20 TraesCS3D01G226100 chr6B 78.333 900 186 9 2624 3522 688470551 688471442 1.410000e-159 573
21 TraesCS3D01G226100 chr6B 77.298 903 189 12 2623 3522 689032363 689031474 6.710000e-143 518
22 TraesCS3D01G226100 chr6B 80.615 423 78 4 1111 1531 688469653 688470073 1.570000e-84 324
23 TraesCS3D01G226100 chr6A 77.913 901 190 9 2623 3522 599830951 599830059 1.840000e-153 553
24 TraesCS3D01G226100 chr6A 81.882 425 69 7 1111 1531 599831943 599831523 7.200000e-93 351
25 TraesCS3D01G226100 chr6D 77.469 901 194 9 2623 3522 453651418 453650526 8.620000e-147 531
26 TraesCS3D01G226100 chr6D 76.413 814 160 25 1111 1909 453652382 453651586 1.170000e-110 411
27 TraesCS3D01G226100 chr5A 92.937 269 18 1 4258 4526 454196387 454196120 1.530000e-104 390
28 TraesCS3D01G226100 chr5A 89.219 269 26 3 4260 4526 24193214 24193481 2.610000e-87 333
29 TraesCS3D01G226100 chr4B 90.385 260 24 1 4267 4526 659129975 659129717 1.560000e-89 340
30 TraesCS3D01G226100 chr4B 79.791 287 36 14 2179 2450 614053107 614052828 5.980000e-44 189
31 TraesCS3D01G226100 chr1D 88.768 276 25 6 4253 4526 342499079 342498808 2.610000e-87 333
32 TraesCS3D01G226100 chr1D 86.667 270 32 4 4259 4526 455550277 455550544 3.420000e-76 296
33 TraesCS3D01G226100 chr7A 88.930 271 25 5 4258 4526 29450306 29450039 3.380000e-86 329
34 TraesCS3D01G226100 chr7B 88.519 270 28 3 4258 4526 589367498 589367765 1.570000e-84 324


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 TraesCS3D01G226100 chr3D 307878998 307883523 4525 False 8359.0 8359 100.0000 1 4526 1 chr3D.!!$F1 4525
1 TraesCS3D01G226100 chr3A 427191156 427198274 7118 False 2894.5 5092 94.9175 625 4256 2 chr3A.!!$F2 3631
2 TraesCS3D01G226100 chr3B 413862453 413866441 3988 True 2691.0 2700 93.6600 603 4256 2 chr3B.!!$R1 3653
3 TraesCS3D01G226100 chr3B 413872659 413874638 1979 True 440.0 532 93.6920 24 604 2 chr3B.!!$R2 580
4 TraesCS3D01G226100 chr2D 174322127 174325457 3330 False 668.0 837 82.9680 971 3552 2 chr2D.!!$F1 2581
5 TraesCS3D01G226100 chr2D 174382071 174383848 1777 False 500.0 647 82.6680 1148 3370 2 chr2D.!!$F2 2222
6 TraesCS3D01G226100 chr2A 174027289 174028220 931 False 833.0 833 82.9240 2623 3552 1 chr2A.!!$F2 929
7 TraesCS3D01G226100 chr2A 174244492 174246498 2006 False 593.5 778 81.9175 992 3444 2 chr2A.!!$F4 2452
8 TraesCS3D01G226100 chr2A 174039101 174039639 538 False 442.0 442 81.5500 992 1531 1 chr2A.!!$F3 539
9 TraesCS3D01G226100 chr2B 222143177 222144106 929 False 782.0 782 81.9250 2623 3552 1 chr2B.!!$F1 929
10 TraesCS3D01G226100 chr6B 689031474 689032363 889 True 518.0 518 77.2980 2623 3522 1 chr6B.!!$R1 899
11 TraesCS3D01G226100 chr6B 688469653 688471442 1789 False 448.5 573 79.4740 1111 3522 2 chr6B.!!$F1 2411
12 TraesCS3D01G226100 chr6A 599830059 599831943 1884 True 452.0 553 79.8975 1111 3522 2 chr6A.!!$R1 2411
13 TraesCS3D01G226100 chr6D 453650526 453652382 1856 True 471.0 531 76.9410 1111 3522 2 chr6D.!!$R1 2411

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
84 85 0.388134 AGTAGTACTTGTGCACCGCG 60.388 55.0 15.69 0.00 0.00 6.46 F
112 113 0.586319 CAGTTCCGCGTCATTGTTGT 59.414 50.0 4.92 0.00 0.00 3.32 F
1689 3270 0.390866 CTTGTGAGCAGATGGACGCT 60.391 55.0 0.00 0.00 42.42 5.07 F
3000 5877 0.242017 ATTGAGCACGAAGGCTTTGC 59.758 50.0 14.50 14.54 45.99 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 2930 0.252881 TGCAGGGTTGAGGATCCTCT 60.253 55.000 35.84 17.62 43.12 3.69 R
1749 3330 0.579156 GCGAGAAATGACATCTCCGC 59.421 55.000 8.27 8.27 40.16 5.54 R
3400 6295 3.760151 TGAAGGATCATGCACAAGGAAAG 59.240 43.478 0.00 0.00 0.00 2.62 R
4476 10866 0.107848 CGGGCTATCTTCAACCGGTT 60.108 55.000 15.86 15.86 40.79 4.44 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
48 49 6.624861 GCCGATGATGAAAAGTTGATAACCAA 60.625 38.462 0.00 0.00 0.00 3.67
84 85 0.388134 AGTAGTACTTGTGCACCGCG 60.388 55.000 15.69 0.00 0.00 6.46
86 87 1.525718 TAGTACTTGTGCACCGCGGA 61.526 55.000 35.90 6.51 0.00 5.54
87 88 2.356553 TACTTGTGCACCGCGGAC 60.357 61.111 35.90 23.77 36.27 4.79
101 102 3.134127 GGACATGGGCAGTTCCGC 61.134 66.667 0.00 0.00 34.94 5.54
111 112 0.725784 GCAGTTCCGCGTCATTGTTG 60.726 55.000 4.92 0.00 0.00 3.33
112 113 0.586319 CAGTTCCGCGTCATTGTTGT 59.414 50.000 4.92 0.00 0.00 3.32
113 114 0.586319 AGTTCCGCGTCATTGTTGTG 59.414 50.000 4.92 0.00 0.00 3.33
194 195 4.882842 ATAGGCCGGTTTCAAACAATTT 57.117 36.364 1.90 0.00 0.00 1.82
201 202 3.301515 CGGTTTCAAACAATTTGCACGAC 60.302 43.478 1.93 0.00 40.43 4.34
224 225 4.511527 TCATCAGTGGCTCTTCATTCTTC 58.488 43.478 0.00 0.00 0.00 2.87
234 235 8.772705 GTGGCTCTTCATTCTTCTAAATATGAG 58.227 37.037 0.00 0.00 0.00 2.90
292 1700 8.816894 TGTTTAGAAGAACCATGAGTCTCTTAT 58.183 33.333 0.65 3.74 30.72 1.73
311 1719 4.498520 ATCCGAGCGACTGTGGCG 62.499 66.667 9.15 0.00 35.00 5.69
320 1728 4.988598 ACTGTGGCGACGGCAAGG 62.989 66.667 26.69 21.74 40.46 3.61
373 1781 3.557595 GCTGAGCAAATATAGTTCGCAGT 59.442 43.478 0.00 0.00 0.00 4.40
462 1870 0.947960 TTTTTCTGAACCGCGCATCA 59.052 45.000 8.75 7.82 0.00 3.07
476 1884 2.223572 GCGCATCACCCCTTTTCATTAG 60.224 50.000 0.30 0.00 0.00 1.73
485 1893 6.071616 TCACCCCTTTTCATTAGTTGCATAAC 60.072 38.462 0.00 0.00 37.06 1.89
498 1906 6.751514 AGTTGCATAACGGAAATACATCAA 57.248 33.333 0.00 0.00 41.71 2.57
554 1963 0.823460 ACCCAGCACAACAACAAAGG 59.177 50.000 0.00 0.00 0.00 3.11
558 1967 3.189285 CCAGCACAACAACAAAGGAAAG 58.811 45.455 0.00 0.00 0.00 2.62
568 1977 3.244887 ACAAAGGAAAGGGGAAAGAGG 57.755 47.619 0.00 0.00 0.00 3.69
577 1986 0.973496 GGGGAAAGAGGAGAGCGAGT 60.973 60.000 0.00 0.00 0.00 4.18
753 2178 3.081804 GTGGTATTGTCCTTGTCTTGGG 58.918 50.000 0.00 0.00 0.00 4.12
769 2194 2.584391 GGGAGACCGTTGACTGGCT 61.584 63.158 0.00 0.00 43.64 4.75
934 2359 9.828039 TTCTCTCCATATATATTGTGATGCATC 57.172 33.333 20.14 20.14 0.00 3.91
936 2361 7.512130 TCTCCATATATATTGTGATGCATCCC 58.488 38.462 23.67 13.46 0.00 3.85
937 2362 6.604171 TCCATATATATTGTGATGCATCCCC 58.396 40.000 23.67 14.44 0.00 4.81
961 2390 6.260714 CCACCATACTCATTCAATCGAATCAA 59.739 38.462 0.00 0.00 39.96 2.57
990 2419 2.383338 ACCATTCTTCCCCCAATCAAGT 59.617 45.455 0.00 0.00 0.00 3.16
1009 2452 4.533919 AGTGAGAGAGACATGGTTCTTG 57.466 45.455 0.00 0.00 0.00 3.02
1341 2784 1.486145 CCTGGTTTGGTCCGTACCCT 61.486 60.000 9.17 0.00 46.16 4.34
1487 2930 0.961019 GAGCAATGGGTCAAGCACAA 59.039 50.000 0.00 0.00 41.19 3.33
1600 3113 5.978919 TCAATCAAATGCTGGCGAAATTATC 59.021 36.000 0.00 0.00 0.00 1.75
1689 3270 0.390866 CTTGTGAGCAGATGGACGCT 60.391 55.000 0.00 0.00 42.42 5.07
1725 3306 3.769739 TGGTACATATGAGGTGGATGC 57.230 47.619 10.38 0.00 0.00 3.91
1749 3330 3.070159 TGTCCAGAGTTCCAAAGACTCAG 59.930 47.826 6.98 0.00 44.65 3.35
1936 3523 6.594159 GGCTAATATTTGTGTCTACGGCATAT 59.406 38.462 0.00 0.00 0.00 1.78
2105 3725 5.648092 GCATAGCCGGTCCTGATTAATAAAT 59.352 40.000 1.90 0.00 0.00 1.40
2233 3853 4.776837 TGCATGAAAATGACCCACCTTAAT 59.223 37.500 0.00 0.00 0.00 1.40
2987 5864 8.820933 GCCTATTTGGAAAGAATAAAATTGAGC 58.179 33.333 0.00 0.00 38.35 4.26
3000 5877 0.242017 ATTGAGCACGAAGGCTTTGC 59.758 50.000 14.50 14.54 45.99 3.68
3513 6408 3.108144 GCATGGTGCGTAAATTAAGCTG 58.892 45.455 11.76 3.59 31.71 4.24
3564 6459 7.464830 AGTATGCATGTTCACTATACGAAAC 57.535 36.000 10.16 0.00 31.36 2.78
3654 6549 3.373110 GGGCCTTTTCATATGACCCTTCT 60.373 47.826 17.31 0.00 32.88 2.85
3791 6693 5.356190 TGAGCTCCAATGCTTTATTCTCAAG 59.644 40.000 12.15 0.00 44.17 3.02
3831 10218 4.803613 AGAAAACCAAAGCGTGAACAAATC 59.196 37.500 0.00 0.00 0.00 2.17
3872 10259 6.985188 TGTTACTGCTATGGTTCAGAATTC 57.015 37.500 0.00 0.00 34.57 2.17
3992 10379 2.335712 GGGAACTCAGCAAAGCCCG 61.336 63.158 0.00 0.00 0.00 6.13
4102 10492 5.542779 GAGTTTCTATTATCGGGCACTCAT 58.457 41.667 0.00 0.00 31.56 2.90
4118 10508 7.095271 CGGGCACTCATCAAACATTTAAAAATT 60.095 33.333 0.00 0.00 0.00 1.82
4173 10563 3.934068 AGTACCATGTTAGGTGAAACGG 58.066 45.455 0.00 0.00 43.14 4.44
4256 10646 3.705051 TGACGACTAGGGGTAAGATGTT 58.295 45.455 0.00 0.00 0.00 2.71
4257 10647 4.858850 TGACGACTAGGGGTAAGATGTTA 58.141 43.478 0.00 0.00 0.00 2.41
4258 10648 5.452255 TGACGACTAGGGGTAAGATGTTAT 58.548 41.667 0.00 0.00 0.00 1.89
4259 10649 5.895534 TGACGACTAGGGGTAAGATGTTATT 59.104 40.000 0.00 0.00 0.00 1.40
4260 10650 6.381994 TGACGACTAGGGGTAAGATGTTATTT 59.618 38.462 0.00 0.00 0.00 1.40
4261 10651 7.093201 TGACGACTAGGGGTAAGATGTTATTTT 60.093 37.037 0.00 0.00 0.00 1.82
4262 10652 7.627311 ACGACTAGGGGTAAGATGTTATTTTT 58.373 34.615 0.00 0.00 0.00 1.94
4282 10672 4.698201 TTTTGAAAAGGGGGTTGAATCC 57.302 40.909 0.00 0.00 0.00 3.01
4283 10673 2.319025 TGAAAAGGGGGTTGAATCCC 57.681 50.000 4.49 4.49 46.31 3.85
4289 10679 3.739613 GGGTTGAATCCCCGGCCT 61.740 66.667 0.00 0.00 41.54 5.19
4290 10680 2.124278 GGTTGAATCCCCGGCCTC 60.124 66.667 0.00 0.00 0.00 4.70
4291 10681 2.680370 GGTTGAATCCCCGGCCTCT 61.680 63.158 0.00 0.00 0.00 3.69
4292 10682 1.452108 GTTGAATCCCCGGCCTCTG 60.452 63.158 0.00 0.00 0.00 3.35
4293 10683 3.344137 TTGAATCCCCGGCCTCTGC 62.344 63.158 0.00 0.00 0.00 4.26
4294 10684 3.797353 GAATCCCCGGCCTCTGCA 61.797 66.667 0.00 0.00 40.13 4.41
4295 10685 3.099170 AATCCCCGGCCTCTGCAT 61.099 61.111 0.00 0.00 40.13 3.96
4296 10686 3.125376 AATCCCCGGCCTCTGCATC 62.125 63.158 0.00 0.00 40.13 3.91
4298 10688 4.559063 CCCCGGCCTCTGCATCAG 62.559 72.222 0.00 0.00 40.13 2.90
4299 10689 3.473647 CCCGGCCTCTGCATCAGA 61.474 66.667 0.00 0.00 38.25 3.27
4300 10690 2.586245 CCGGCCTCTGCATCAGAA 59.414 61.111 0.00 0.00 40.18 3.02
4301 10691 1.147824 CCGGCCTCTGCATCAGAAT 59.852 57.895 0.00 0.00 40.18 2.40
4302 10692 1.164662 CCGGCCTCTGCATCAGAATG 61.165 60.000 0.00 0.00 40.18 2.67
4315 10705 3.581265 TCAGAATGATGCATAAGGCCA 57.419 42.857 5.01 0.00 42.56 5.36
4316 10706 4.108501 TCAGAATGATGCATAAGGCCAT 57.891 40.909 5.01 0.00 42.56 4.40
4317 10707 5.245584 TCAGAATGATGCATAAGGCCATA 57.754 39.130 5.01 0.00 42.56 2.74
4318 10708 5.823312 TCAGAATGATGCATAAGGCCATAT 58.177 37.500 5.01 0.00 42.56 1.78
4319 10709 6.250711 TCAGAATGATGCATAAGGCCATATT 58.749 36.000 5.01 0.00 42.56 1.28
4320 10710 7.404481 TCAGAATGATGCATAAGGCCATATTA 58.596 34.615 5.01 0.00 42.56 0.98
4321 10711 8.057011 TCAGAATGATGCATAAGGCCATATTAT 58.943 33.333 5.01 0.00 42.56 1.28
4322 10712 8.692710 CAGAATGATGCATAAGGCCATATTATT 58.307 33.333 5.01 0.00 39.87 1.40
4323 10713 9.925545 AGAATGATGCATAAGGCCATATTATTA 57.074 29.630 5.01 0.00 43.89 0.98
4349 10739 6.855763 AATCCAAAGGTTCAGCAATATTCA 57.144 33.333 0.00 0.00 0.00 2.57
4350 10740 7.427989 AATCCAAAGGTTCAGCAATATTCAT 57.572 32.000 0.00 0.00 0.00 2.57
4351 10741 6.455360 TCCAAAGGTTCAGCAATATTCATC 57.545 37.500 0.00 0.00 0.00 2.92
4352 10742 5.951148 TCCAAAGGTTCAGCAATATTCATCA 59.049 36.000 0.00 0.00 0.00 3.07
4353 10743 6.608405 TCCAAAGGTTCAGCAATATTCATCAT 59.392 34.615 0.00 0.00 0.00 2.45
4354 10744 6.700081 CCAAAGGTTCAGCAATATTCATCATG 59.300 38.462 0.00 0.00 0.00 3.07
4355 10745 7.262772 CAAAGGTTCAGCAATATTCATCATGT 58.737 34.615 0.00 0.00 0.00 3.21
4356 10746 6.630444 AGGTTCAGCAATATTCATCATGTC 57.370 37.500 0.00 0.00 0.00 3.06
4357 10747 6.363065 AGGTTCAGCAATATTCATCATGTCT 58.637 36.000 0.00 0.00 0.00 3.41
4358 10748 6.485984 AGGTTCAGCAATATTCATCATGTCTC 59.514 38.462 0.00 0.00 0.00 3.36
4359 10749 6.261603 GGTTCAGCAATATTCATCATGTCTCA 59.738 38.462 0.00 0.00 0.00 3.27
4360 10750 7.201758 GGTTCAGCAATATTCATCATGTCTCAA 60.202 37.037 0.00 0.00 0.00 3.02
4361 10751 7.868906 TCAGCAATATTCATCATGTCTCAAA 57.131 32.000 0.00 0.00 0.00 2.69
4362 10752 8.283699 TCAGCAATATTCATCATGTCTCAAAA 57.716 30.769 0.00 0.00 0.00 2.44
4363 10753 8.186163 TCAGCAATATTCATCATGTCTCAAAAC 58.814 33.333 0.00 0.00 0.00 2.43
4364 10754 7.971722 CAGCAATATTCATCATGTCTCAAAACA 59.028 33.333 0.00 0.00 0.00 2.83
4365 10755 8.525316 AGCAATATTCATCATGTCTCAAAACAA 58.475 29.630 0.00 0.00 31.81 2.83
4366 10756 9.142515 GCAATATTCATCATGTCTCAAAACAAA 57.857 29.630 0.00 0.00 31.81 2.83
4368 10758 8.922058 ATATTCATCATGTCTCAAAACAAAGC 57.078 30.769 0.00 0.00 31.81 3.51
4369 10759 4.786507 TCATCATGTCTCAAAACAAAGCG 58.213 39.130 0.00 0.00 31.81 4.68
4370 10760 3.624326 TCATGTCTCAAAACAAAGCGG 57.376 42.857 0.00 0.00 31.81 5.52
4371 10761 3.210227 TCATGTCTCAAAACAAAGCGGA 58.790 40.909 0.00 0.00 31.81 5.54
4372 10762 3.629855 TCATGTCTCAAAACAAAGCGGAA 59.370 39.130 0.00 0.00 31.81 4.30
4373 10763 4.097135 TCATGTCTCAAAACAAAGCGGAAA 59.903 37.500 0.00 0.00 31.81 3.13
4374 10764 4.442375 TGTCTCAAAACAAAGCGGAAAA 57.558 36.364 0.00 0.00 0.00 2.29
4375 10765 4.810790 TGTCTCAAAACAAAGCGGAAAAA 58.189 34.783 0.00 0.00 0.00 1.94
4404 10794 8.719478 CTCACTAAGAGCAAACAAAATACAAG 57.281 34.615 0.00 0.00 37.59 3.16
4405 10795 7.648142 TCACTAAGAGCAAACAAAATACAAGG 58.352 34.615 0.00 0.00 0.00 3.61
4406 10796 7.500892 TCACTAAGAGCAAACAAAATACAAGGA 59.499 33.333 0.00 0.00 0.00 3.36
4407 10797 7.591426 CACTAAGAGCAAACAAAATACAAGGAC 59.409 37.037 0.00 0.00 0.00 3.85
4408 10798 5.108385 AGAGCAAACAAAATACAAGGACG 57.892 39.130 0.00 0.00 0.00 4.79
4409 10799 3.638484 AGCAAACAAAATACAAGGACGC 58.362 40.909 0.00 0.00 0.00 5.19
4410 10800 2.729360 GCAAACAAAATACAAGGACGCC 59.271 45.455 0.00 0.00 0.00 5.68
4411 10801 3.797184 GCAAACAAAATACAAGGACGCCA 60.797 43.478 0.00 0.00 0.00 5.69
4412 10802 3.636282 AACAAAATACAAGGACGCCAC 57.364 42.857 0.00 0.00 0.00 5.01
4413 10803 2.577700 ACAAAATACAAGGACGCCACA 58.422 42.857 0.00 0.00 0.00 4.17
4414 10804 2.952978 ACAAAATACAAGGACGCCACAA 59.047 40.909 0.00 0.00 0.00 3.33
4415 10805 3.243267 ACAAAATACAAGGACGCCACAAC 60.243 43.478 0.00 0.00 0.00 3.32
4416 10806 1.530323 AATACAAGGACGCCACAACC 58.470 50.000 0.00 0.00 0.00 3.77
4417 10807 0.672401 ATACAAGGACGCCACAACCG 60.672 55.000 0.00 0.00 0.00 4.44
4418 10808 2.718747 TACAAGGACGCCACAACCGG 62.719 60.000 0.00 0.00 0.00 5.28
4426 10816 2.045438 CCACAACCGGCTGGCATA 60.045 61.111 12.89 0.00 39.70 3.14
4427 10817 1.677300 CCACAACCGGCTGGCATAA 60.677 57.895 12.89 0.00 39.70 1.90
4428 10818 1.247419 CCACAACCGGCTGGCATAAA 61.247 55.000 12.89 0.00 39.70 1.40
4429 10819 0.600557 CACAACCGGCTGGCATAAAA 59.399 50.000 12.89 0.00 39.70 1.52
4430 10820 1.000283 CACAACCGGCTGGCATAAAAA 60.000 47.619 12.89 0.00 39.70 1.94
4456 10846 9.440761 AAGATAGGAACACTAAATGTCTATCCT 57.559 33.333 10.10 7.62 44.76 3.24
4457 10847 8.865090 AGATAGGAACACTAAATGTCTATCCTG 58.135 37.037 8.42 0.00 43.25 3.86
4458 10848 6.875972 AGGAACACTAAATGTCTATCCTGT 57.124 37.500 0.00 0.00 42.27 4.00
4459 10849 7.259088 AGGAACACTAAATGTCTATCCTGTT 57.741 36.000 0.00 0.00 42.27 3.16
4460 10850 8.375493 AGGAACACTAAATGTCTATCCTGTTA 57.625 34.615 0.00 0.00 42.27 2.41
4461 10851 8.258708 AGGAACACTAAATGTCTATCCTGTTAC 58.741 37.037 0.00 0.00 42.27 2.50
4462 10852 8.038944 GGAACACTAAATGTCTATCCTGTTACA 58.961 37.037 0.00 0.00 42.31 2.41
4463 10853 9.601217 GAACACTAAATGTCTATCCTGTTACAT 57.399 33.333 0.00 0.00 42.31 2.29
4464 10854 8.948631 ACACTAAATGTCTATCCTGTTACATG 57.051 34.615 0.00 0.00 36.54 3.21
4465 10855 8.758829 ACACTAAATGTCTATCCTGTTACATGA 58.241 33.333 0.00 0.00 36.54 3.07
4466 10856 9.035607 CACTAAATGTCTATCCTGTTACATGAC 57.964 37.037 0.00 0.00 33.04 3.06
4467 10857 8.204836 ACTAAATGTCTATCCTGTTACATGACC 58.795 37.037 0.00 0.00 33.04 4.02
4468 10858 4.649088 TGTCTATCCTGTTACATGACCG 57.351 45.455 0.00 0.00 0.00 4.79
4469 10859 3.181479 TGTCTATCCTGTTACATGACCGC 60.181 47.826 0.00 0.00 0.00 5.68
4470 10860 2.364324 TCTATCCTGTTACATGACCGCC 59.636 50.000 0.00 0.00 0.00 6.13
4471 10861 0.908910 ATCCTGTTACATGACCGCCA 59.091 50.000 0.00 0.00 0.00 5.69
4472 10862 0.908910 TCCTGTTACATGACCGCCAT 59.091 50.000 0.00 0.00 35.44 4.40
4473 10863 1.134521 TCCTGTTACATGACCGCCATC 60.135 52.381 0.00 0.00 31.94 3.51
4474 10864 1.299541 CTGTTACATGACCGCCATCC 58.700 55.000 0.00 0.00 31.94 3.51
4475 10865 0.615850 TGTTACATGACCGCCATCCA 59.384 50.000 0.00 0.00 31.94 3.41
4476 10866 1.003696 TGTTACATGACCGCCATCCAA 59.996 47.619 0.00 0.00 31.94 3.53
4477 10867 2.088423 GTTACATGACCGCCATCCAAA 58.912 47.619 0.00 0.00 31.94 3.28
4478 10868 1.745232 TACATGACCGCCATCCAAAC 58.255 50.000 0.00 0.00 31.94 2.93
4479 10869 0.965363 ACATGACCGCCATCCAAACC 60.965 55.000 0.00 0.00 31.94 3.27
4480 10870 1.748879 ATGACCGCCATCCAAACCG 60.749 57.895 0.00 0.00 0.00 4.44
4481 10871 3.131478 GACCGCCATCCAAACCGG 61.131 66.667 0.00 0.00 45.80 5.28
4483 10873 2.675075 CCGCCATCCAAACCGGTT 60.675 61.111 15.86 15.86 36.18 4.44
4484 10874 2.566010 CGCCATCCAAACCGGTTG 59.434 61.111 23.08 14.70 36.94 3.77
4485 10875 1.969064 CGCCATCCAAACCGGTTGA 60.969 57.895 23.08 15.50 39.87 3.18
4486 10876 1.519751 CGCCATCCAAACCGGTTGAA 61.520 55.000 23.08 9.90 39.87 2.69
4487 10877 0.243636 GCCATCCAAACCGGTTGAAG 59.756 55.000 23.08 13.88 39.87 3.02
4488 10878 1.904287 CCATCCAAACCGGTTGAAGA 58.096 50.000 23.08 17.89 39.87 2.87
4489 10879 2.446435 CCATCCAAACCGGTTGAAGAT 58.554 47.619 23.08 19.33 39.87 2.40
4490 10880 3.616219 CCATCCAAACCGGTTGAAGATA 58.384 45.455 23.08 4.03 39.87 1.98
4491 10881 3.627577 CCATCCAAACCGGTTGAAGATAG 59.372 47.826 23.08 12.36 39.87 2.08
4492 10882 2.706890 TCCAAACCGGTTGAAGATAGC 58.293 47.619 23.08 0.00 39.87 2.97
4493 10883 1.743394 CCAAACCGGTTGAAGATAGCC 59.257 52.381 23.08 0.00 39.87 3.93
4494 10884 1.743394 CAAACCGGTTGAAGATAGCCC 59.257 52.381 23.08 0.00 39.87 5.19
4495 10885 0.107848 AACCGGTTGAAGATAGCCCG 60.108 55.000 21.56 0.00 38.39 6.13
4496 10886 1.262640 ACCGGTTGAAGATAGCCCGT 61.263 55.000 0.00 0.00 36.98 5.28
4497 10887 0.810031 CCGGTTGAAGATAGCCCGTG 60.810 60.000 0.00 0.00 36.98 4.94
4498 10888 1.429148 CGGTTGAAGATAGCCCGTGC 61.429 60.000 0.00 0.00 34.10 5.34
4508 10898 2.508663 GCCCGTGCTACCGTCTTC 60.509 66.667 0.00 0.00 33.53 2.87
4509 10899 2.183555 CCCGTGCTACCGTCTTCC 59.816 66.667 0.00 0.00 0.00 3.46
4510 10900 2.642254 CCCGTGCTACCGTCTTCCA 61.642 63.158 0.00 0.00 0.00 3.53
4511 10901 1.515954 CCGTGCTACCGTCTTCCAT 59.484 57.895 0.00 0.00 0.00 3.41
4512 10902 0.527817 CCGTGCTACCGTCTTCCATC 60.528 60.000 0.00 0.00 0.00 3.51
4513 10903 0.866061 CGTGCTACCGTCTTCCATCG 60.866 60.000 0.00 0.00 0.00 3.84
4522 10912 3.495670 CGTCTTCCATCGGATAGATCC 57.504 52.381 0.00 0.00 43.65 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.337554 CCGTCAACATATAGTCAAGTCGAA 58.662 41.667 0.00 0.00 0.00 3.71
1 2 4.732647 GCCGTCAACATATAGTCAAGTCGA 60.733 45.833 0.00 0.00 0.00 4.20
2 3 3.486108 GCCGTCAACATATAGTCAAGTCG 59.514 47.826 0.00 0.00 0.00 4.18
3 4 3.802685 GGCCGTCAACATATAGTCAAGTC 59.197 47.826 0.00 0.00 0.00 3.01
4 5 3.737047 CGGCCGTCAACATATAGTCAAGT 60.737 47.826 19.50 0.00 0.00 3.16
5 6 2.794910 CGGCCGTCAACATATAGTCAAG 59.205 50.000 19.50 0.00 0.00 3.02
6 7 2.427812 TCGGCCGTCAACATATAGTCAA 59.572 45.455 27.15 0.00 0.00 3.18
7 8 2.025898 TCGGCCGTCAACATATAGTCA 58.974 47.619 27.15 0.00 0.00 3.41
8 9 2.787601 TCGGCCGTCAACATATAGTC 57.212 50.000 27.15 0.00 0.00 2.59
9 10 2.626266 TCATCGGCCGTCAACATATAGT 59.374 45.455 27.15 0.00 0.00 2.12
10 11 3.297830 TCATCGGCCGTCAACATATAG 57.702 47.619 27.15 4.65 0.00 1.31
11 12 3.257127 TCATCATCGGCCGTCAACATATA 59.743 43.478 27.15 1.58 0.00 0.86
12 13 2.037121 TCATCATCGGCCGTCAACATAT 59.963 45.455 27.15 6.18 0.00 1.78
13 14 1.410882 TCATCATCGGCCGTCAACATA 59.589 47.619 27.15 3.40 0.00 2.29
14 15 0.177836 TCATCATCGGCCGTCAACAT 59.822 50.000 27.15 7.91 0.00 2.71
15 16 0.036858 TTCATCATCGGCCGTCAACA 60.037 50.000 27.15 5.24 0.00 3.33
16 17 1.083489 TTTCATCATCGGCCGTCAAC 58.917 50.000 27.15 0.00 0.00 3.18
17 18 1.737236 CTTTTCATCATCGGCCGTCAA 59.263 47.619 27.15 11.90 0.00 3.18
18 19 1.338674 ACTTTTCATCATCGGCCGTCA 60.339 47.619 27.15 7.11 0.00 4.35
19 20 1.369625 ACTTTTCATCATCGGCCGTC 58.630 50.000 27.15 0.00 0.00 4.79
20 21 1.468520 CAACTTTTCATCATCGGCCGT 59.531 47.619 27.15 10.00 0.00 5.68
21 22 1.737236 TCAACTTTTCATCATCGGCCG 59.263 47.619 22.12 22.12 0.00 6.13
22 23 5.273944 GTTATCAACTTTTCATCATCGGCC 58.726 41.667 0.00 0.00 0.00 6.13
64 65 1.792006 GCGGTGCACAAGTACTACTT 58.208 50.000 20.43 0.00 39.39 2.24
65 66 0.388134 CGCGGTGCACAAGTACTACT 60.388 55.000 20.43 0.00 0.00 2.57
66 67 1.349259 CCGCGGTGCACAAGTACTAC 61.349 60.000 19.50 0.00 0.00 2.73
67 68 1.080366 CCGCGGTGCACAAGTACTA 60.080 57.895 19.50 0.00 0.00 1.82
72 73 3.049674 ATGTCCGCGGTGCACAAG 61.050 61.111 27.15 13.12 0.00 3.16
84 85 3.134127 GCGGAACTGCCCATGTCC 61.134 66.667 0.00 0.00 0.00 4.02
86 87 4.329545 ACGCGGAACTGCCCATGT 62.330 61.111 12.47 0.00 0.00 3.21
87 88 3.499737 GACGCGGAACTGCCCATG 61.500 66.667 12.47 0.00 0.00 3.66
101 102 4.775440 ACAAAAATGCACAACAATGACG 57.225 36.364 0.00 0.00 0.00 4.35
194 195 1.374631 GCCACTGATGAGTCGTGCA 60.375 57.895 0.00 0.00 31.80 4.57
201 202 4.139859 AGAATGAAGAGCCACTGATGAG 57.860 45.455 0.00 0.00 0.00 2.90
263 264 6.226787 AGACTCATGGTTCTTCTAAACACAG 58.773 40.000 0.00 0.00 0.00 3.66
264 265 6.042093 AGAGACTCATGGTTCTTCTAAACACA 59.958 38.462 5.02 0.00 0.00 3.72
292 1700 2.885113 CCACAGTCGCTCGGATCA 59.115 61.111 0.00 0.00 0.00 2.92
311 1719 2.358737 CCACCTGACCTTGCCGTC 60.359 66.667 0.00 0.00 0.00 4.79
320 1728 4.314440 TCGCTGCACCCACCTGAC 62.314 66.667 0.00 0.00 0.00 3.51
339 1747 1.376037 GCTCAGCCACTGTACCCAC 60.376 63.158 0.00 0.00 32.61 4.61
382 1790 4.878439 TCATTCGGACCAAATATAGTCGG 58.122 43.478 0.00 0.00 35.36 4.79
443 1851 0.947960 TGATGCGCGGTTCAGAAAAA 59.052 45.000 8.83 0.00 0.00 1.94
455 1863 0.532115 AATGAAAAGGGGTGATGCGC 59.468 50.000 0.00 0.00 0.00 6.09
462 1870 5.105917 CGTTATGCAACTAATGAAAAGGGGT 60.106 40.000 0.00 0.00 32.09 4.95
476 1884 7.915397 AGAATTGATGTATTTCCGTTATGCAAC 59.085 33.333 0.00 0.00 0.00 4.17
485 1893 5.063204 TGGGCTAGAATTGATGTATTTCCG 58.937 41.667 0.00 0.00 0.00 4.30
498 1906 0.962489 CGAGACGGATGGGCTAGAAT 59.038 55.000 0.00 0.00 0.00 2.40
528 1937 0.546122 TGTTGTGCTGGGTCAGAACT 59.454 50.000 7.47 0.00 40.51 3.01
529 1938 1.065551 GTTGTTGTGCTGGGTCAGAAC 59.934 52.381 0.00 0.00 40.30 3.01
554 1963 1.406205 CGCTCTCCTCTTTCCCCTTTC 60.406 57.143 0.00 0.00 0.00 2.62
558 1967 0.973496 ACTCGCTCTCCTCTTTCCCC 60.973 60.000 0.00 0.00 0.00 4.81
568 1977 1.011451 GTGGTGCTGAACTCGCTCTC 61.011 60.000 0.00 0.00 0.00 3.20
753 2178 0.247736 ATGAGCCAGTCAACGGTCTC 59.752 55.000 0.00 0.00 39.19 3.36
934 2359 3.141398 CGATTGAATGAGTATGGTGGGG 58.859 50.000 0.00 0.00 0.00 4.96
936 2361 5.759763 TGATTCGATTGAATGAGTATGGTGG 59.240 40.000 13.12 0.00 44.79 4.61
937 2362 6.849588 TGATTCGATTGAATGAGTATGGTG 57.150 37.500 13.12 0.00 44.79 4.17
961 2390 2.091111 GGGGGAAGAATGGTTGGATGAT 60.091 50.000 0.00 0.00 0.00 2.45
990 2419 3.510459 TCCAAGAACCATGTCTCTCTCA 58.490 45.455 0.00 0.00 0.00 3.27
1009 2452 1.134670 AGCTGGACTAATCAACGCTCC 60.135 52.381 0.00 0.00 0.00 4.70
1341 2784 0.535335 GGTCGCTGATGGTCACCTTA 59.465 55.000 0.00 0.00 0.00 2.69
1487 2930 0.252881 TGCAGGGTTGAGGATCCTCT 60.253 55.000 35.84 17.62 43.12 3.69
1689 3270 8.588472 CATATGTACCATCAGAACCAAGAGATA 58.412 37.037 0.00 0.00 0.00 1.98
1725 3306 2.370189 AGTCTTTGGAACTCTGGACAGG 59.630 50.000 0.00 0.00 0.00 4.00
1749 3330 0.579156 GCGAGAAATGACATCTCCGC 59.421 55.000 8.27 8.27 40.16 5.54
1936 3523 9.349713 ACCATAACACAAAGAAAACAGATAGAA 57.650 29.630 0.00 0.00 0.00 2.10
2105 3725 5.700832 GCACGATCCCTATAATTGATGTTGA 59.299 40.000 0.00 0.00 0.00 3.18
2168 3788 6.646240 GTCATGCTGGTATGTTGAAACAAATT 59.354 34.615 0.00 0.00 43.03 1.82
2233 3853 6.767456 ACCTTTTGATTTGAATGGTTGCATA 58.233 32.000 0.00 0.00 32.45 3.14
2389 4010 3.940209 TGGGACATGAACATTTGAAGC 57.060 42.857 0.00 0.00 0.00 3.86
2488 4541 2.229792 TGACAAAACATGGTCTCTGGC 58.770 47.619 0.00 0.00 35.11 4.85
3400 6295 3.760151 TGAAGGATCATGCACAAGGAAAG 59.240 43.478 0.00 0.00 0.00 2.62
3502 6397 8.134895 CGATTAAATTGCCCTCAGCTTAATTTA 58.865 33.333 0.00 0.00 44.23 1.40
3513 6408 4.900635 ATGTGACGATTAAATTGCCCTC 57.099 40.909 0.00 0.00 0.00 4.30
3564 6459 6.478673 TGACGGTAAATAGTGAACATGCATAG 59.521 38.462 0.00 0.00 0.00 2.23
3654 6549 8.129840 GCAGTCTCTGTCTACGAGAATAAAATA 58.870 37.037 0.00 0.00 39.08 1.40
3791 6693 7.727181 TGGTTTTCTGTAGAGAGCCTATTATC 58.273 38.462 6.81 0.00 0.00 1.75
3807 6709 3.143807 TGTTCACGCTTTGGTTTTCTG 57.856 42.857 0.00 0.00 0.00 3.02
3850 10237 6.985188 TGAATTCTGAACCATAGCAGTAAC 57.015 37.500 7.05 0.00 33.90 2.50
4046 10433 1.779061 ATTGCCGACCCTTGTCCAGT 61.779 55.000 0.00 0.00 38.32 4.00
4102 10492 8.370493 TCGGCAATGAATTTTTAAATGTTTGA 57.630 26.923 0.00 0.00 0.00 2.69
4118 10508 3.065510 TCGTTTTTGAAACTCGGCAATGA 59.934 39.130 2.53 0.00 0.00 2.57
4260 10650 4.141367 GGGATTCAACCCCCTTTTCAAAAA 60.141 41.667 0.00 0.00 43.81 1.94
4261 10651 3.392947 GGGATTCAACCCCCTTTTCAAAA 59.607 43.478 0.00 0.00 43.81 2.44
4262 10652 2.976185 GGGATTCAACCCCCTTTTCAAA 59.024 45.455 0.00 0.00 43.81 2.69
4263 10653 2.615391 GGGATTCAACCCCCTTTTCAA 58.385 47.619 0.00 0.00 43.81 2.69
4264 10654 2.319025 GGGATTCAACCCCCTTTTCA 57.681 50.000 0.00 0.00 43.81 2.69
4273 10663 2.124278 GAGGCCGGGGATTCAACC 60.124 66.667 2.18 0.00 0.00 3.77
4274 10664 1.452108 CAGAGGCCGGGGATTCAAC 60.452 63.158 2.18 0.00 0.00 3.18
4275 10665 2.998097 CAGAGGCCGGGGATTCAA 59.002 61.111 2.18 0.00 0.00 2.69
4276 10666 3.797353 GCAGAGGCCGGGGATTCA 61.797 66.667 2.18 0.00 0.00 2.57
4277 10667 3.125376 ATGCAGAGGCCGGGGATTC 62.125 63.158 2.18 0.00 40.13 2.52
4278 10668 3.099170 ATGCAGAGGCCGGGGATT 61.099 61.111 2.18 0.00 40.13 3.01
4279 10669 3.564218 GATGCAGAGGCCGGGGAT 61.564 66.667 2.18 0.00 40.13 3.85
4281 10671 4.559063 CTGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
4282 10672 2.335092 ATTCTGATGCAGAGGCCGGG 62.335 60.000 2.18 0.00 41.75 5.73
4283 10673 1.147824 ATTCTGATGCAGAGGCCGG 59.852 57.895 0.00 0.00 41.75 6.13
4284 10674 0.179065 TCATTCTGATGCAGAGGCCG 60.179 55.000 0.00 0.00 41.75 6.13
4285 10675 1.880675 CATCATTCTGATGCAGAGGCC 59.119 52.381 0.00 0.00 46.37 5.19
4294 10684 4.108501 TGGCCTTATGCATCATTCTGAT 57.891 40.909 0.19 0.00 43.89 2.90
4295 10685 3.581265 TGGCCTTATGCATCATTCTGA 57.419 42.857 0.19 0.00 43.89 3.27
4296 10686 6.525578 AATATGGCCTTATGCATCATTCTG 57.474 37.500 11.69 0.00 43.89 3.02
4297 10687 8.834004 AATAATATGGCCTTATGCATCATTCT 57.166 30.769 11.69 0.00 43.89 2.40
4323 10713 8.980596 TGAATATTGCTGAACCTTTGGATTATT 58.019 29.630 0.00 0.00 0.00 1.40
4324 10714 8.537728 TGAATATTGCTGAACCTTTGGATTAT 57.462 30.769 0.00 0.00 0.00 1.28
4325 10715 7.953005 TGAATATTGCTGAACCTTTGGATTA 57.047 32.000 0.00 0.00 0.00 1.75
4326 10716 6.855763 TGAATATTGCTGAACCTTTGGATT 57.144 33.333 0.00 0.00 0.00 3.01
4327 10717 6.608405 TGATGAATATTGCTGAACCTTTGGAT 59.392 34.615 0.00 0.00 0.00 3.41
4328 10718 5.951148 TGATGAATATTGCTGAACCTTTGGA 59.049 36.000 0.00 0.00 0.00 3.53
4329 10719 6.211587 TGATGAATATTGCTGAACCTTTGG 57.788 37.500 0.00 0.00 0.00 3.28
4330 10720 7.262772 ACATGATGAATATTGCTGAACCTTTG 58.737 34.615 0.00 0.00 0.00 2.77
4331 10721 7.341256 AGACATGATGAATATTGCTGAACCTTT 59.659 33.333 0.00 0.00 0.00 3.11
4332 10722 6.832384 AGACATGATGAATATTGCTGAACCTT 59.168 34.615 0.00 0.00 0.00 3.50
4333 10723 6.363065 AGACATGATGAATATTGCTGAACCT 58.637 36.000 0.00 0.00 0.00 3.50
4334 10724 6.261603 TGAGACATGATGAATATTGCTGAACC 59.738 38.462 0.00 0.00 0.00 3.62
4335 10725 7.255491 TGAGACATGATGAATATTGCTGAAC 57.745 36.000 0.00 0.00 0.00 3.18
4336 10726 7.868906 TTGAGACATGATGAATATTGCTGAA 57.131 32.000 0.00 0.00 0.00 3.02
4337 10727 7.868906 TTTGAGACATGATGAATATTGCTGA 57.131 32.000 0.00 0.00 0.00 4.26
4338 10728 7.971722 TGTTTTGAGACATGATGAATATTGCTG 59.028 33.333 0.00 0.00 0.00 4.41
4339 10729 8.058667 TGTTTTGAGACATGATGAATATTGCT 57.941 30.769 0.00 0.00 0.00 3.91
4340 10730 8.692110 TTGTTTTGAGACATGATGAATATTGC 57.308 30.769 0.00 0.00 0.00 3.56
4342 10732 9.362539 GCTTTGTTTTGAGACATGATGAATATT 57.637 29.630 0.00 0.00 0.00 1.28
4343 10733 7.699391 CGCTTTGTTTTGAGACATGATGAATAT 59.301 33.333 0.00 0.00 0.00 1.28
4344 10734 7.022979 CGCTTTGTTTTGAGACATGATGAATA 58.977 34.615 0.00 0.00 0.00 1.75
4345 10735 5.860182 CGCTTTGTTTTGAGACATGATGAAT 59.140 36.000 0.00 0.00 0.00 2.57
4346 10736 5.214417 CGCTTTGTTTTGAGACATGATGAA 58.786 37.500 0.00 0.00 0.00 2.57
4347 10737 4.320421 CCGCTTTGTTTTGAGACATGATGA 60.320 41.667 0.00 0.00 0.00 2.92
4348 10738 3.916172 CCGCTTTGTTTTGAGACATGATG 59.084 43.478 0.00 0.00 0.00 3.07
4349 10739 3.820467 TCCGCTTTGTTTTGAGACATGAT 59.180 39.130 0.00 0.00 0.00 2.45
4350 10740 3.210227 TCCGCTTTGTTTTGAGACATGA 58.790 40.909 0.00 0.00 0.00 3.07
4351 10741 3.624326 TCCGCTTTGTTTTGAGACATG 57.376 42.857 0.00 0.00 0.00 3.21
4352 10742 4.647424 TTTCCGCTTTGTTTTGAGACAT 57.353 36.364 0.00 0.00 0.00 3.06
4353 10743 4.442375 TTTTCCGCTTTGTTTTGAGACA 57.558 36.364 0.00 0.00 0.00 3.41
4372 10762 7.391148 TTGTTTGCTCTTAGTGAGTCTTTTT 57.609 32.000 0.00 0.00 44.41 1.94
4373 10763 7.391148 TTTGTTTGCTCTTAGTGAGTCTTTT 57.609 32.000 0.00 0.00 44.41 2.27
4374 10764 7.391148 TTTTGTTTGCTCTTAGTGAGTCTTT 57.609 32.000 0.00 0.00 44.41 2.52
4375 10765 7.573968 ATTTTGTTTGCTCTTAGTGAGTCTT 57.426 32.000 0.00 0.00 44.41 3.01
4376 10766 7.715249 TGTATTTTGTTTGCTCTTAGTGAGTCT 59.285 33.333 0.00 0.00 44.41 3.24
4377 10767 7.861630 TGTATTTTGTTTGCTCTTAGTGAGTC 58.138 34.615 0.00 0.00 44.41 3.36
4378 10768 7.801716 TGTATTTTGTTTGCTCTTAGTGAGT 57.198 32.000 0.00 0.00 44.41 3.41
4379 10769 7.805071 CCTTGTATTTTGTTTGCTCTTAGTGAG 59.195 37.037 0.00 0.00 45.33 3.51
4380 10770 7.500892 TCCTTGTATTTTGTTTGCTCTTAGTGA 59.499 33.333 0.00 0.00 0.00 3.41
4381 10771 7.591426 GTCCTTGTATTTTGTTTGCTCTTAGTG 59.409 37.037 0.00 0.00 0.00 2.74
4382 10772 7.519970 CGTCCTTGTATTTTGTTTGCTCTTAGT 60.520 37.037 0.00 0.00 0.00 2.24
4383 10773 6.797033 CGTCCTTGTATTTTGTTTGCTCTTAG 59.203 38.462 0.00 0.00 0.00 2.18
4384 10774 6.664515 CGTCCTTGTATTTTGTTTGCTCTTA 58.335 36.000 0.00 0.00 0.00 2.10
4385 10775 5.519722 CGTCCTTGTATTTTGTTTGCTCTT 58.480 37.500 0.00 0.00 0.00 2.85
4386 10776 4.556699 GCGTCCTTGTATTTTGTTTGCTCT 60.557 41.667 0.00 0.00 0.00 4.09
4387 10777 3.668656 GCGTCCTTGTATTTTGTTTGCTC 59.331 43.478 0.00 0.00 0.00 4.26
4388 10778 3.552068 GGCGTCCTTGTATTTTGTTTGCT 60.552 43.478 0.00 0.00 0.00 3.91
4389 10779 2.729360 GGCGTCCTTGTATTTTGTTTGC 59.271 45.455 0.00 0.00 0.00 3.68
4390 10780 3.733727 GTGGCGTCCTTGTATTTTGTTTG 59.266 43.478 0.00 0.00 0.00 2.93
4391 10781 3.381908 TGTGGCGTCCTTGTATTTTGTTT 59.618 39.130 0.00 0.00 0.00 2.83
4392 10782 2.952978 TGTGGCGTCCTTGTATTTTGTT 59.047 40.909 0.00 0.00 0.00 2.83
4393 10783 2.577700 TGTGGCGTCCTTGTATTTTGT 58.422 42.857 0.00 0.00 0.00 2.83
4394 10784 3.305110 GTTGTGGCGTCCTTGTATTTTG 58.695 45.455 0.00 0.00 0.00 2.44
4395 10785 2.295070 GGTTGTGGCGTCCTTGTATTTT 59.705 45.455 0.00 0.00 0.00 1.82
4396 10786 1.883926 GGTTGTGGCGTCCTTGTATTT 59.116 47.619 0.00 0.00 0.00 1.40
4397 10787 1.530323 GGTTGTGGCGTCCTTGTATT 58.470 50.000 0.00 0.00 0.00 1.89
4398 10788 0.672401 CGGTTGTGGCGTCCTTGTAT 60.672 55.000 0.00 0.00 0.00 2.29
4399 10789 1.301087 CGGTTGTGGCGTCCTTGTA 60.301 57.895 0.00 0.00 0.00 2.41
4400 10790 2.590575 CGGTTGTGGCGTCCTTGT 60.591 61.111 0.00 0.00 0.00 3.16
4401 10791 3.353836 CCGGTTGTGGCGTCCTTG 61.354 66.667 0.00 0.00 0.00 3.61
4409 10799 1.247419 TTTATGCCAGCCGGTTGTGG 61.247 55.000 17.69 15.43 36.85 4.17
4410 10800 0.600557 TTTTATGCCAGCCGGTTGTG 59.399 50.000 17.69 9.73 33.28 3.33
4411 10801 1.333177 TTTTTATGCCAGCCGGTTGT 58.667 45.000 17.69 1.06 33.28 3.32
4430 10820 9.440761 AGGATAGACATTTAGTGTTCCTATCTT 57.559 33.333 12.65 6.19 41.59 2.40
4431 10821 8.865090 CAGGATAGACATTTAGTGTTCCTATCT 58.135 37.037 12.65 0.00 41.51 1.98
4432 10822 8.643324 ACAGGATAGACATTTAGTGTTCCTATC 58.357 37.037 7.55 7.55 41.51 2.08
4433 10823 8.554490 ACAGGATAGACATTTAGTGTTCCTAT 57.446 34.615 0.34 0.00 41.51 2.57
4434 10824 7.973048 ACAGGATAGACATTTAGTGTTCCTA 57.027 36.000 0.34 0.00 41.51 2.94
4435 10825 6.875972 ACAGGATAGACATTTAGTGTTCCT 57.124 37.500 0.00 0.00 43.29 3.36
4436 10826 8.038944 TGTAACAGGATAGACATTTAGTGTTCC 58.961 37.037 0.00 0.00 42.36 3.62
4437 10827 8.997621 TGTAACAGGATAGACATTTAGTGTTC 57.002 34.615 0.00 0.00 42.36 3.18
4438 10828 9.383519 CATGTAACAGGATAGACATTTAGTGTT 57.616 33.333 0.00 0.00 42.36 3.32
4439 10829 8.758829 TCATGTAACAGGATAGACATTTAGTGT 58.241 33.333 0.00 0.00 45.83 3.55
4440 10830 9.035607 GTCATGTAACAGGATAGACATTTAGTG 57.964 37.037 0.00 0.00 30.13 2.74
4441 10831 8.204836 GGTCATGTAACAGGATAGACATTTAGT 58.795 37.037 0.00 0.00 30.13 2.24
4442 10832 7.382488 CGGTCATGTAACAGGATAGACATTTAG 59.618 40.741 0.00 0.00 30.13 1.85
4443 10833 7.207383 CGGTCATGTAACAGGATAGACATTTA 58.793 38.462 0.00 0.00 30.13 1.40
4444 10834 6.049149 CGGTCATGTAACAGGATAGACATTT 58.951 40.000 0.00 0.00 30.13 2.32
4445 10835 5.601662 CGGTCATGTAACAGGATAGACATT 58.398 41.667 0.00 0.00 30.13 2.71
4446 10836 4.501571 GCGGTCATGTAACAGGATAGACAT 60.502 45.833 0.00 0.00 32.78 3.06
4447 10837 3.181479 GCGGTCATGTAACAGGATAGACA 60.181 47.826 0.00 0.00 0.00 3.41
4448 10838 3.381949 GCGGTCATGTAACAGGATAGAC 58.618 50.000 0.00 0.00 0.00 2.59
4449 10839 2.364324 GGCGGTCATGTAACAGGATAGA 59.636 50.000 0.00 0.00 0.00 1.98
4450 10840 2.102420 TGGCGGTCATGTAACAGGATAG 59.898 50.000 0.00 0.00 0.00 2.08
4451 10841 2.112190 TGGCGGTCATGTAACAGGATA 58.888 47.619 0.00 0.00 0.00 2.59
4452 10842 0.908910 TGGCGGTCATGTAACAGGAT 59.091 50.000 0.00 0.00 0.00 3.24
4453 10843 0.908910 ATGGCGGTCATGTAACAGGA 59.091 50.000 0.00 0.00 34.22 3.86
4454 10844 1.299541 GATGGCGGTCATGTAACAGG 58.700 55.000 0.00 0.00 35.97 4.00
4455 10845 1.299541 GGATGGCGGTCATGTAACAG 58.700 55.000 0.00 0.00 35.97 3.16
4456 10846 0.615850 TGGATGGCGGTCATGTAACA 59.384 50.000 0.00 0.00 35.97 2.41
4457 10847 1.745232 TTGGATGGCGGTCATGTAAC 58.255 50.000 0.00 0.00 35.97 2.50
4458 10848 2.088423 GTTTGGATGGCGGTCATGTAA 58.912 47.619 0.00 0.00 35.97 2.41
4459 10849 1.680555 GGTTTGGATGGCGGTCATGTA 60.681 52.381 0.00 0.00 35.97 2.29
4460 10850 0.965363 GGTTTGGATGGCGGTCATGT 60.965 55.000 0.00 0.00 35.97 3.21
4461 10851 1.809207 GGTTTGGATGGCGGTCATG 59.191 57.895 0.00 0.00 35.97 3.07
4462 10852 1.748879 CGGTTTGGATGGCGGTCAT 60.749 57.895 0.00 0.00 39.13 3.06
4463 10853 2.359354 CGGTTTGGATGGCGGTCA 60.359 61.111 0.00 0.00 0.00 4.02
4464 10854 3.131478 CCGGTTTGGATGGCGGTC 61.131 66.667 0.00 0.00 42.00 4.79
4465 10855 3.501040 AACCGGTTTGGATGGCGGT 62.501 57.895 15.86 0.00 42.00 5.68
4466 10856 2.675075 AACCGGTTTGGATGGCGG 60.675 61.111 15.86 0.00 42.00 6.13
4467 10857 1.519751 TTCAACCGGTTTGGATGGCG 61.520 55.000 19.55 3.62 40.78 5.69
4468 10858 0.243636 CTTCAACCGGTTTGGATGGC 59.756 55.000 19.55 0.00 40.78 4.40
4469 10859 1.904287 TCTTCAACCGGTTTGGATGG 58.096 50.000 19.55 5.30 40.78 3.51
4470 10860 3.065371 GCTATCTTCAACCGGTTTGGATG 59.935 47.826 19.55 14.79 41.73 3.51
4471 10861 3.279434 GCTATCTTCAACCGGTTTGGAT 58.721 45.455 19.55 21.16 42.00 3.41
4472 10862 2.617021 GGCTATCTTCAACCGGTTTGGA 60.617 50.000 19.55 15.86 42.00 3.53
4473 10863 1.743394 GGCTATCTTCAACCGGTTTGG 59.257 52.381 19.55 7.84 46.41 3.28
4474 10864 1.743394 GGGCTATCTTCAACCGGTTTG 59.257 52.381 19.55 13.53 36.42 2.93
4475 10865 1.677820 CGGGCTATCTTCAACCGGTTT 60.678 52.381 19.55 5.23 40.79 3.27
4476 10866 0.107848 CGGGCTATCTTCAACCGGTT 60.108 55.000 15.86 15.86 40.79 4.44
4477 10867 1.520666 CGGGCTATCTTCAACCGGT 59.479 57.895 0.00 0.00 40.79 5.28
4478 10868 4.438346 CGGGCTATCTTCAACCGG 57.562 61.111 0.00 0.00 40.79 5.28
4480 10870 2.394604 GCACGGGCTATCTTCAACC 58.605 57.895 0.00 0.00 36.96 3.77
4491 10881 2.508663 GAAGACGGTAGCACGGGC 60.509 66.667 0.00 0.00 38.39 6.13
4492 10882 1.956629 ATGGAAGACGGTAGCACGGG 61.957 60.000 0.00 0.00 38.39 5.28
4493 10883 0.527817 GATGGAAGACGGTAGCACGG 60.528 60.000 0.00 0.00 38.39 4.94
4494 10884 0.866061 CGATGGAAGACGGTAGCACG 60.866 60.000 0.00 0.00 40.31 5.34
4495 10885 0.527817 CCGATGGAAGACGGTAGCAC 60.528 60.000 0.00 0.00 43.53 4.40
4496 10886 1.813859 CCGATGGAAGACGGTAGCA 59.186 57.895 0.00 0.00 43.53 3.49
4497 10887 4.732106 CCGATGGAAGACGGTAGC 57.268 61.111 0.00 0.00 43.53 3.58
4502 10892 3.495670 GGATCTATCCGATGGAAGACG 57.504 52.381 0.00 0.00 37.19 4.18


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

AutoCloner maintained by Alex Coulton.