Multiple sequence alignment - TraesCS2D01G131100

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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 TraesCS2D01G131100 chr2D 100.000 2195 0 0 1 2195 76633429 76635623 0.000000e+00 4054.0
1 TraesCS2D01G131100 chr2D 81.096 365 51 13 1 357 580532232 580532586 2.150000e-70 276.0
2 TraesCS2D01G131100 chr2A 88.811 572 37 7 619 1188 77162520 77163066 0.000000e+00 676.0
3 TraesCS2D01G131100 chr2A 89.297 327 14 10 1233 1552 77163159 77163471 7.350000e-105 390.0
4 TraesCS2D01G131100 chr2A 90.136 294 26 2 1904 2195 77163747 77164039 1.590000e-101 379.0
5 TraesCS2D01G131100 chr2A 94.444 90 5 0 364 453 77162429 77162518 2.940000e-29 139.0
6 TraesCS2D01G131100 chr2B 88.710 558 42 5 618 1173 117875642 117876180 0.000000e+00 662.0
7 TraesCS2D01G131100 chr2B 89.256 363 33 5 1 361 117871581 117871939 1.200000e-122 449.0
8 TraesCS2D01G131100 chr2B 87.419 310 27 8 1894 2195 117877295 117877600 1.610000e-91 346.0
9 TraesCS2D01G131100 chr2B 89.600 250 10 5 1233 1479 117876676 117876912 9.850000e-79 303.0
10 TraesCS2D01G131100 chr2B 92.169 166 12 1 454 619 472909784 472909620 1.310000e-57 233.0
11 TraesCS2D01G131100 chr2B 95.960 99 3 1 358 455 117875545 117875643 2.260000e-35 159.0
12 TraesCS2D01G131100 chr2B 92.391 92 7 0 1817 1908 791706717 791706808 4.920000e-27 132.0
13 TraesCS2D01G131100 chr2B 95.556 45 2 0 1508 1552 117876914 117876958 3.020000e-09 73.1
14 TraesCS2D01G131100 chr6D 82.703 370 46 16 1 361 148083847 148084207 1.640000e-81 313.0
15 TraesCS2D01G131100 chr6D 80.886 361 47 20 2 353 329365414 329365761 4.650000e-67 265.0
16 TraesCS2D01G131100 chr5A 83.232 328 48 7 1 327 606850696 606851017 5.930000e-76 294.0
17 TraesCS2D01G131100 chr5A 81.918 365 47 15 1 357 667928115 667928468 7.670000e-75 291.0
18 TraesCS2D01G131100 chr4B 83.129 326 40 13 1 324 105954045 105953733 1.280000e-72 283.0
19 TraesCS2D01G131100 chr4B 91.566 166 13 1 454 619 429241920 429242084 6.100000e-56 228.0
20 TraesCS2D01G131100 chr1D 81.301 369 42 20 1 360 195159841 195159491 7.720000e-70 274.0
21 TraesCS2D01G131100 chr4D 82.229 332 43 15 2 327 391426217 391425896 2.780000e-69 272.0
22 TraesCS2D01G131100 chr4A 91.566 166 13 1 454 619 665604122 665604286 6.100000e-56 228.0
23 TraesCS2D01G131100 chrUn 90.964 166 14 1 454 619 321005421 321005257 2.840000e-54 222.0
24 TraesCS2D01G131100 chr5B 90.058 171 17 0 450 620 424161204 424161374 2.840000e-54 222.0
25 TraesCS2D01G131100 chr5B 87.736 106 11 2 986 1090 150777161 150777265 2.960000e-24 122.0
26 TraesCS2D01G131100 chr5B 83.871 124 20 0 1781 1904 458904921 458905044 3.830000e-23 119.0
27 TraesCS2D01G131100 chr3B 89.385 179 14 5 444 620 51929312 51929487 1.020000e-53 220.0
28 TraesCS2D01G131100 chr3B 90.625 64 6 0 1773 1836 43826457 43826394 3.880000e-13 86.1
29 TraesCS2D01G131100 chr1B 88.043 184 19 3 450 633 593011327 593011507 4.750000e-52 215.0
30 TraesCS2D01G131100 chr7D 89.412 170 17 1 454 623 5492209 5492041 1.710000e-51 213.0
31 TraesCS2D01G131100 chr5D 89.349 169 17 1 454 622 553671659 553671492 6.140000e-51 211.0
32 TraesCS2D01G131100 chr5D 86.290 124 17 0 1781 1904 382495081 382495204 3.800000e-28 135.0
33 TraesCS2D01G131100 chr7A 87.302 126 16 0 1781 1906 6627354 6627229 6.320000e-31 145.0
34 TraesCS2D01G131100 chr3A 82.222 135 23 1 1774 1908 36790395 36790262 4.950000e-22 115.0
35 TraesCS2D01G131100 chr3A 81.890 127 23 0 1781 1907 724539877 724540003 8.290000e-20 108.0
36 TraesCS2D01G131100 chr3A 82.203 118 21 0 1781 1898 724540132 724540249 3.860000e-18 102.0
37 TraesCS2D01G131100 chr6A 83.471 121 20 0 1787 1907 107800936 107800816 1.780000e-21 113.0


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 TraesCS2D01G131100 chr2D 76633429 76635623 2194 False 4054.000000 4054 100.0000 1 2195 1 chr2D.!!$F1 2194
1 TraesCS2D01G131100 chr2A 77162429 77164039 1610 False 396.000000 676 90.6720 364 2195 4 chr2A.!!$F1 1831
2 TraesCS2D01G131100 chr2B 117871581 117877600 6019 False 332.016667 662 91.0835 1 2195 6 chr2B.!!$F2 2194

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
996 4617 0.180406 AAGCGAGGTTGTGGTGTTCT 59.82 50.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 5996 0.251341 GGGAACTGCAACTCCACCAT 60.251 55.0 14.15 0.0 32.95 3.55 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
54 55 1.895798 TGTGTGTTCAAAAGTGCCCAA 59.104 42.857 0.00 0.00 0.00 4.12
56 57 3.244215 TGTGTGTTCAAAAGTGCCCAAAA 60.244 39.130 0.00 0.00 0.00 2.44
57 58 3.124466 GTGTGTTCAAAAGTGCCCAAAAC 59.876 43.478 0.00 0.00 0.00 2.43
60 61 3.008485 TGTTCAAAAGTGCCCAAAACCTT 59.992 39.130 0.00 0.00 0.00 3.50
62 63 4.293662 TCAAAAGTGCCCAAAACCTTTT 57.706 36.364 0.00 0.00 37.55 2.27
83 84 9.101325 CCTTTTGTATATATAGGTTGGAGAGGA 57.899 37.037 0.00 0.00 0.00 3.71
90 91 0.338120 AGGTTGGAGAGGAGAGAGGG 59.662 60.000 0.00 0.00 0.00 4.30
131 132 1.261238 AAGTCTCTCTCCCTTGGCCG 61.261 60.000 0.00 0.00 0.00 6.13
148 149 2.368878 GGCCAAGAGGAGGGGGAT 60.369 66.667 0.00 0.00 36.89 3.85
166 167 2.505405 GATTTCCCCTCTAATTCGGCC 58.495 52.381 0.00 0.00 0.00 6.13
175 178 1.132500 CTAATTCGGCCTCCCCTTCT 58.868 55.000 0.00 0.00 0.00 2.85
185 188 1.425448 CCTCCCCTTCTTTCCACAAGT 59.575 52.381 0.00 0.00 0.00 3.16
196 199 1.228862 CCACAAGTGGGGGAAAGGG 60.229 63.158 11.43 0.00 46.81 3.95
197 200 1.541672 CACAAGTGGGGGAAAGGGT 59.458 57.895 0.00 0.00 0.00 4.34
212 215 1.668826 AGGGTGCCACCTCTATTTGA 58.331 50.000 14.71 0.00 38.64 2.69
214 217 1.383523 GGTGCCACCTCTATTTGAGC 58.616 55.000 6.63 0.00 41.35 4.26
236 239 1.068121 AAGTGGCCCAAGTAGCTCTT 58.932 50.000 0.00 0.00 36.75 2.85
243 246 1.625818 CCCAAGTAGCTCTTCACCACT 59.374 52.381 0.00 0.00 33.63 4.00
246 249 3.070018 CAAGTAGCTCTTCACCACTTGG 58.930 50.000 13.25 0.00 41.40 3.61
307 310 7.451501 AGTCTCGTAACTATTATTAGAGCCC 57.548 40.000 0.00 0.00 0.00 5.19
382 3995 2.031012 CACTTGCGAGGCCACTCA 59.969 61.111 5.01 0.00 44.17 3.41
455 4068 6.421202 GCCAGTATACAGTGCATAGAACTTAC 59.579 42.308 5.50 0.00 0.00 2.34
456 4069 7.684670 GCCAGTATACAGTGCATAGAACTTACT 60.685 40.741 5.50 0.00 0.00 2.24
457 4070 7.863375 CCAGTATACAGTGCATAGAACTTACTC 59.137 40.741 5.50 0.00 0.00 2.59
458 4071 7.863375 CAGTATACAGTGCATAGAACTTACTCC 59.137 40.741 5.50 0.00 0.00 3.85
459 4072 4.473477 ACAGTGCATAGAACTTACTCCC 57.527 45.455 0.00 0.00 0.00 4.30
460 4073 4.097418 ACAGTGCATAGAACTTACTCCCT 58.903 43.478 0.00 0.00 0.00 4.20
461 4074 4.160626 ACAGTGCATAGAACTTACTCCCTC 59.839 45.833 0.00 0.00 0.00 4.30
462 4075 3.707102 AGTGCATAGAACTTACTCCCTCC 59.293 47.826 0.00 0.00 0.00 4.30
463 4076 2.693591 TGCATAGAACTTACTCCCTCCG 59.306 50.000 0.00 0.00 0.00 4.63
464 4077 2.694109 GCATAGAACTTACTCCCTCCGT 59.306 50.000 0.00 0.00 0.00 4.69
465 4078 3.132467 GCATAGAACTTACTCCCTCCGTT 59.868 47.826 0.00 0.00 0.00 4.44
466 4079 4.737055 GCATAGAACTTACTCCCTCCGTTC 60.737 50.000 0.00 0.00 35.44 3.95
467 4080 2.177734 AGAACTTACTCCCTCCGTTCC 58.822 52.381 0.00 0.00 35.73 3.62
468 4081 2.177734 GAACTTACTCCCTCCGTTCCT 58.822 52.381 0.00 0.00 0.00 3.36
469 4082 3.011032 AGAACTTACTCCCTCCGTTCCTA 59.989 47.826 0.00 0.00 35.73 2.94
470 4083 3.463048 ACTTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
471 4084 3.782992 ACTTACTCCCTCCGTTCCTAAA 58.217 45.455 0.00 0.00 0.00 1.85
472 4085 4.359996 ACTTACTCCCTCCGTTCCTAAAT 58.640 43.478 0.00 0.00 0.00 1.40
473 4086 5.522641 ACTTACTCCCTCCGTTCCTAAATA 58.477 41.667 0.00 0.00 0.00 1.40
474 4087 6.141790 ACTTACTCCCTCCGTTCCTAAATAT 58.858 40.000 0.00 0.00 0.00 1.28
475 4088 7.300658 ACTTACTCCCTCCGTTCCTAAATATA 58.699 38.462 0.00 0.00 0.00 0.86
476 4089 7.786464 ACTTACTCCCTCCGTTCCTAAATATAA 59.214 37.037 0.00 0.00 0.00 0.98
477 4090 8.731591 TTACTCCCTCCGTTCCTAAATATAAT 57.268 34.615 0.00 0.00 0.00 1.28
478 4091 7.628501 ACTCCCTCCGTTCCTAAATATAATT 57.371 36.000 0.00 0.00 0.00 1.40
479 4092 8.042286 ACTCCCTCCGTTCCTAAATATAATTT 57.958 34.615 0.00 0.00 0.00 1.82
480 4093 8.500238 ACTCCCTCCGTTCCTAAATATAATTTT 58.500 33.333 0.00 0.00 0.00 1.82
481 4094 9.350951 CTCCCTCCGTTCCTAAATATAATTTTT 57.649 33.333 0.00 0.00 0.00 1.94
506 4119 9.877178 TTTTTAAAGGTTTCAAATGAGCTACAA 57.123 25.926 0.00 0.00 0.00 2.41
507 4120 8.865590 TTTAAAGGTTTCAAATGAGCTACAAC 57.134 30.769 0.00 0.00 0.00 3.32
508 4121 6.463995 AAAGGTTTCAAATGAGCTACAACA 57.536 33.333 0.00 0.00 0.00 3.33
509 4122 6.655078 AAGGTTTCAAATGAGCTACAACAT 57.345 33.333 0.00 0.00 0.00 2.71
510 4123 7.759489 AAGGTTTCAAATGAGCTACAACATA 57.241 32.000 0.00 0.00 0.00 2.29
511 4124 7.145932 AGGTTTCAAATGAGCTACAACATAC 57.854 36.000 0.00 0.00 0.00 2.39
512 4125 6.021596 GGTTTCAAATGAGCTACAACATACG 58.978 40.000 0.00 0.00 0.00 3.06
513 4126 5.794687 TTCAAATGAGCTACAACATACGG 57.205 39.130 0.00 0.00 0.00 4.02
514 4127 5.079689 TCAAATGAGCTACAACATACGGA 57.920 39.130 0.00 0.00 0.00 4.69
515 4128 5.670485 TCAAATGAGCTACAACATACGGAT 58.330 37.500 0.00 0.00 0.00 4.18
516 4129 5.523552 TCAAATGAGCTACAACATACGGATG 59.476 40.000 5.94 5.94 39.16 3.51
518 4131 5.784578 ATGAGCTACAACATACGGATGTA 57.215 39.130 15.10 0.00 45.93 2.29
519 4132 5.784578 TGAGCTACAACATACGGATGTAT 57.215 39.130 15.10 8.21 45.93 2.29
520 4133 6.887626 TGAGCTACAACATACGGATGTATA 57.112 37.500 15.10 8.98 45.93 1.47
521 4134 7.462571 TGAGCTACAACATACGGATGTATAT 57.537 36.000 15.10 5.13 45.93 0.86
522 4135 8.570068 TGAGCTACAACATACGGATGTATATA 57.430 34.615 15.10 6.07 45.93 0.86
523 4136 8.674607 TGAGCTACAACATACGGATGTATATAG 58.325 37.037 15.10 15.87 45.93 1.31
524 4137 8.803397 AGCTACAACATACGGATGTATATAGA 57.197 34.615 15.10 0.00 45.93 1.98
525 4138 8.675504 AGCTACAACATACGGATGTATATAGAC 58.324 37.037 15.10 11.37 45.93 2.59
526 4139 8.456471 GCTACAACATACGGATGTATATAGACA 58.544 37.037 15.10 2.07 45.93 3.41
560 4173 9.214953 GAGTGTAGATTCATTTATTTTGCTTCG 57.785 33.333 0.00 0.00 0.00 3.79
561 4174 7.698130 AGTGTAGATTCATTTATTTTGCTTCGC 59.302 33.333 0.00 0.00 0.00 4.70
562 4175 7.484641 GTGTAGATTCATTTATTTTGCTTCGCA 59.515 33.333 0.00 0.00 36.47 5.10
563 4176 8.190122 TGTAGATTCATTTATTTTGCTTCGCAT 58.810 29.630 0.00 0.00 38.76 4.73
564 4177 7.459394 AGATTCATTTATTTTGCTTCGCATG 57.541 32.000 0.00 0.00 38.76 4.06
565 4178 7.037438 AGATTCATTTATTTTGCTTCGCATGT 58.963 30.769 0.00 0.00 38.76 3.21
566 4179 8.190122 AGATTCATTTATTTTGCTTCGCATGTA 58.810 29.630 0.00 0.00 38.76 2.29
567 4180 7.739022 TTCATTTATTTTGCTTCGCATGTAG 57.261 32.000 0.00 0.00 38.76 2.74
568 4181 6.851609 TCATTTATTTTGCTTCGCATGTAGT 58.148 32.000 0.00 0.00 38.76 2.73
569 4182 6.966632 TCATTTATTTTGCTTCGCATGTAGTC 59.033 34.615 0.00 0.00 38.76 2.59
570 4183 3.764885 ATTTTGCTTCGCATGTAGTCC 57.235 42.857 0.00 0.00 38.76 3.85
571 4184 1.448985 TTTGCTTCGCATGTAGTCCC 58.551 50.000 0.00 0.00 38.76 4.46
572 4185 0.613260 TTGCTTCGCATGTAGTCCCT 59.387 50.000 0.00 0.00 38.76 4.20
573 4186 0.613260 TGCTTCGCATGTAGTCCCTT 59.387 50.000 0.00 0.00 31.71 3.95
574 4187 1.009829 GCTTCGCATGTAGTCCCTTG 58.990 55.000 0.00 0.00 0.00 3.61
575 4188 1.676014 GCTTCGCATGTAGTCCCTTGT 60.676 52.381 0.00 0.00 0.00 3.16
576 4189 2.699954 CTTCGCATGTAGTCCCTTGTT 58.300 47.619 0.00 0.00 0.00 2.83
577 4190 3.857052 CTTCGCATGTAGTCCCTTGTTA 58.143 45.455 0.00 0.00 0.00 2.41
578 4191 3.965379 TCGCATGTAGTCCCTTGTTAA 57.035 42.857 0.00 0.00 0.00 2.01
579 4192 4.274602 TCGCATGTAGTCCCTTGTTAAA 57.725 40.909 0.00 0.00 0.00 1.52
580 4193 4.643463 TCGCATGTAGTCCCTTGTTAAAA 58.357 39.130 0.00 0.00 0.00 1.52
581 4194 5.250200 TCGCATGTAGTCCCTTGTTAAAAT 58.750 37.500 0.00 0.00 0.00 1.82
582 4195 5.353123 TCGCATGTAGTCCCTTGTTAAAATC 59.647 40.000 0.00 0.00 0.00 2.17
583 4196 5.354234 CGCATGTAGTCCCTTGTTAAAATCT 59.646 40.000 0.00 0.00 0.00 2.40
584 4197 6.456988 CGCATGTAGTCCCTTGTTAAAATCTC 60.457 42.308 0.00 0.00 0.00 2.75
585 4198 6.599638 GCATGTAGTCCCTTGTTAAAATCTCT 59.400 38.462 0.00 0.00 0.00 3.10
586 4199 7.769044 GCATGTAGTCCCTTGTTAAAATCTCTA 59.231 37.037 0.00 0.00 0.00 2.43
587 4200 9.667107 CATGTAGTCCCTTGTTAAAATCTCTAA 57.333 33.333 0.00 0.00 0.00 2.10
613 4226 6.803154 AAGACTTAAATTTGAGAACGGAGG 57.197 37.500 16.20 0.00 0.00 4.30
614 4227 5.246307 AGACTTAAATTTGAGAACGGAGGG 58.754 41.667 16.20 0.00 0.00 4.30
615 4228 5.012768 AGACTTAAATTTGAGAACGGAGGGA 59.987 40.000 16.20 0.00 0.00 4.20
616 4229 5.246307 ACTTAAATTTGAGAACGGAGGGAG 58.754 41.667 16.20 0.00 0.00 4.30
617 4230 3.790089 AAATTTGAGAACGGAGGGAGT 57.210 42.857 0.00 0.00 0.00 3.85
661 4274 5.106791 CGAGAGATATTTGTTGCCATGGATC 60.107 44.000 18.40 6.81 0.00 3.36
763 4376 3.826157 CCTGCAACACCAATTCCTTTAGA 59.174 43.478 0.00 0.00 0.00 2.10
770 4383 5.640147 ACACCAATTCCTTTAGATTCCACA 58.360 37.500 0.00 0.00 0.00 4.17
781 4394 6.371548 CCTTTAGATTCCACATTCGTCTTTCA 59.628 38.462 0.00 0.00 0.00 2.69
783 4396 5.613358 AGATTCCACATTCGTCTTTCAAC 57.387 39.130 0.00 0.00 0.00 3.18
787 4400 2.504367 CACATTCGTCTTTCAACCCCT 58.496 47.619 0.00 0.00 0.00 4.79
788 4401 3.558321 CCACATTCGTCTTTCAACCCCTA 60.558 47.826 0.00 0.00 0.00 3.53
790 4403 4.070009 ACATTCGTCTTTCAACCCCTAAC 58.930 43.478 0.00 0.00 0.00 2.34
798 4411 0.318120 TCAACCCCTAACGACGTTCC 59.682 55.000 17.94 0.00 0.00 3.62
806 4419 0.447801 TAACGACGTTCCGCTACTCC 59.552 55.000 17.94 0.00 0.00 3.85
807 4420 1.518056 AACGACGTTCCGCTACTCCA 61.518 55.000 7.57 0.00 0.00 3.86
808 4421 1.210931 CGACGTTCCGCTACTCCAA 59.789 57.895 0.00 0.00 0.00 3.53
809 4422 0.797249 CGACGTTCCGCTACTCCAAG 60.797 60.000 0.00 0.00 0.00 3.61
810 4423 0.524862 GACGTTCCGCTACTCCAAGA 59.475 55.000 0.00 0.00 0.00 3.02
811 4424 1.134560 GACGTTCCGCTACTCCAAGAT 59.865 52.381 0.00 0.00 0.00 2.40
836 4457 3.458857 AGAGGATGGTGAAGATTCATGCT 59.541 43.478 0.00 0.00 41.17 3.79
843 4464 5.569355 TGGTGAAGATTCATGCTCCTTAAA 58.431 37.500 0.00 0.00 39.73 1.52
866 4487 2.873649 GCAGACAGGAAGAAGGTTCTGG 60.874 54.545 0.00 0.00 37.65 3.86
871 4492 2.026449 CAGGAAGAAGGTTCTGGCTCAT 60.026 50.000 0.00 0.00 37.65 2.90
882 4503 1.134699 TCTGGCTCATCAAGGTAAGCG 60.135 52.381 0.00 0.00 35.58 4.68
883 4504 0.744414 TGGCTCATCAAGGTAAGCGC 60.744 55.000 0.00 0.00 35.58 5.92
884 4505 0.462759 GGCTCATCAAGGTAAGCGCT 60.463 55.000 2.64 2.64 35.58 5.92
885 4506 0.933796 GCTCATCAAGGTAAGCGCTC 59.066 55.000 12.06 0.00 0.00 5.03
886 4507 1.472376 GCTCATCAAGGTAAGCGCTCT 60.472 52.381 12.06 0.00 0.00 4.09
887 4508 2.468831 CTCATCAAGGTAAGCGCTCTC 58.531 52.381 12.06 6.83 0.00 3.20
888 4509 2.100584 CTCATCAAGGTAAGCGCTCTCT 59.899 50.000 12.06 5.76 0.00 3.10
889 4510 2.099921 TCATCAAGGTAAGCGCTCTCTC 59.900 50.000 12.06 0.53 0.00 3.20
890 4511 1.840737 TCAAGGTAAGCGCTCTCTCT 58.159 50.000 12.06 3.27 0.00 3.10
891 4512 1.746220 TCAAGGTAAGCGCTCTCTCTC 59.254 52.381 12.06 0.00 0.00 3.20
892 4513 1.748493 CAAGGTAAGCGCTCTCTCTCT 59.252 52.381 12.06 0.00 0.00 3.10
893 4514 1.675552 AGGTAAGCGCTCTCTCTCTC 58.324 55.000 12.06 0.00 0.00 3.20
894 4515 1.211949 AGGTAAGCGCTCTCTCTCTCT 59.788 52.381 12.06 0.00 0.00 3.10
895 4516 1.602377 GGTAAGCGCTCTCTCTCTCTC 59.398 57.143 12.06 0.00 0.00 3.20
896 4517 2.561569 GTAAGCGCTCTCTCTCTCTCT 58.438 52.381 12.06 0.00 0.00 3.10
897 4518 1.668419 AAGCGCTCTCTCTCTCTCTC 58.332 55.000 12.06 0.00 0.00 3.20
898 4519 0.833287 AGCGCTCTCTCTCTCTCTCT 59.167 55.000 2.64 0.00 0.00 3.10
899 4520 1.202580 AGCGCTCTCTCTCTCTCTCTC 60.203 57.143 2.64 0.00 0.00 3.20
904 4525 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
905 4526 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
935 4556 3.408634 TCTTCATGTTCTTTTCCCCGTC 58.591 45.455 0.00 0.00 0.00 4.79
937 4558 3.433306 TCATGTTCTTTTCCCCGTCAT 57.567 42.857 0.00 0.00 0.00 3.06
940 4561 0.526211 GTTCTTTTCCCCGTCATGGC 59.474 55.000 0.00 0.00 35.87 4.40
995 4616 0.586802 GAAGCGAGGTTGTGGTGTTC 59.413 55.000 0.00 0.00 0.00 3.18
996 4617 0.180406 AAGCGAGGTTGTGGTGTTCT 59.820 50.000 0.00 0.00 0.00 3.01
1142 4763 0.183014 ATCTCTCCGTCTAAGGCCGA 59.817 55.000 0.00 0.00 0.00 5.54
1202 4854 5.109210 TGCGTCTACAGATTGATTTACAGG 58.891 41.667 0.00 0.00 0.00 4.00
1228 4880 4.082463 GGTAACCAGATGCGATTTTCCAAA 60.082 41.667 0.00 0.00 0.00 3.28
1265 5328 2.494073 AGAAGACGGCTGTCCTTAAGAG 59.506 50.000 22.17 0.00 46.74 2.85
1266 5329 1.926108 AGACGGCTGTCCTTAAGAGT 58.074 50.000 22.17 0.00 46.74 3.24
1267 5330 2.249139 AGACGGCTGTCCTTAAGAGTT 58.751 47.619 22.17 0.00 46.74 3.01
1268 5331 3.428532 AGACGGCTGTCCTTAAGAGTTA 58.571 45.455 22.17 0.00 46.74 2.24
1269 5332 3.830755 AGACGGCTGTCCTTAAGAGTTAA 59.169 43.478 22.17 0.00 46.74 2.01
1270 5333 4.082136 AGACGGCTGTCCTTAAGAGTTAAG 60.082 45.833 22.17 0.23 46.74 1.85
1271 5334 3.830755 ACGGCTGTCCTTAAGAGTTAAGA 59.169 43.478 3.36 0.00 44.19 2.10
1324 5387 4.396790 TCAACTAAAGCGTGTTGTTCCTTT 59.603 37.500 11.60 0.00 42.71 3.11
1352 5415 4.657952 GGGGGTCAGCATGGTTAC 57.342 61.111 0.00 0.00 36.16 2.50
1355 5418 1.682087 GGGGGTCAGCATGGTTACTTC 60.682 57.143 8.96 2.75 36.16 3.01
1388 5451 5.970317 TCACTGACTACGACCTGAAATAA 57.030 39.130 0.00 0.00 0.00 1.40
1390 5453 5.475909 TCACTGACTACGACCTGAAATAACT 59.524 40.000 0.00 0.00 0.00 2.24
1391 5454 6.015688 TCACTGACTACGACCTGAAATAACTT 60.016 38.462 0.00 0.00 0.00 2.66
1422 5485 4.638865 GGCGAAATTACCACCTGAAATACT 59.361 41.667 0.00 0.00 0.00 2.12
1423 5486 5.124936 GGCGAAATTACCACCTGAAATACTT 59.875 40.000 0.00 0.00 0.00 2.24
1424 5487 6.027749 GCGAAATTACCACCTGAAATACTTG 58.972 40.000 0.00 0.00 0.00 3.16
1425 5488 6.128117 GCGAAATTACCACCTGAAATACTTGA 60.128 38.462 0.00 0.00 0.00 3.02
1502 5572 6.536941 GGTCTAGCTCCACTTTTAATCTGAAG 59.463 42.308 0.00 0.00 0.00 3.02
1543 5613 7.725397 TGAGATGGCCTAGCAAATAATTATTGT 59.275 33.333 11.42 2.93 0.00 2.71
1564 5662 1.016130 GTCGGTCACCTCACATGCTG 61.016 60.000 0.00 0.00 0.00 4.41
1582 5680 1.679305 GTCAGGAGTCAGGAGCCGA 60.679 63.158 0.00 0.00 0.00 5.54
1595 5693 6.828785 AGTCAGGAGCCGAATTATTTTAATGT 59.171 34.615 0.00 0.00 0.00 2.71
1675 5831 2.799126 TGACTTTGGCATACCGGATT 57.201 45.000 9.46 0.00 39.70 3.01
1694 5850 6.922957 CCGGATTGAAGAGAACAAATTTGAAA 59.077 34.615 24.64 6.11 0.00 2.69
1760 5916 7.745022 AAAAATGTATGATGTCAATGCTTCG 57.255 32.000 0.00 0.00 0.00 3.79
1777 5933 3.796717 GCTTCGGCATAACAAATTTAGGC 59.203 43.478 0.00 0.00 41.33 3.93
1779 5935 3.011119 TCGGCATAACAAATTTAGGCGT 58.989 40.909 16.21 0.00 44.00 5.68
1780 5936 3.440872 TCGGCATAACAAATTTAGGCGTT 59.559 39.130 16.21 8.80 44.00 4.84
1781 5937 3.545873 CGGCATAACAAATTTAGGCGTTG 59.454 43.478 0.00 0.00 39.69 4.10
1782 5938 4.490743 GGCATAACAAATTTAGGCGTTGT 58.509 39.130 0.00 0.00 37.07 3.32
1783 5939 4.926832 GGCATAACAAATTTAGGCGTTGTT 59.073 37.500 6.30 6.30 45.08 2.83
1784 5940 5.061684 GGCATAACAAATTTAGGCGTTGTTC 59.938 40.000 4.41 0.00 42.79 3.18
1785 5941 5.219951 GCATAACAAATTTAGGCGTTGTTCG 60.220 40.000 4.41 0.33 42.79 3.95
1786 5942 3.276882 ACAAATTTAGGCGTTGTTCGG 57.723 42.857 0.00 0.00 40.26 4.30
1787 5943 2.619646 ACAAATTTAGGCGTTGTTCGGT 59.380 40.909 0.00 0.00 40.26 4.69
1789 5945 4.456566 ACAAATTTAGGCGTTGTTCGGTAT 59.543 37.500 0.00 0.00 40.26 2.73
1791 5947 2.298411 TTAGGCGTTGTTCGGTATCC 57.702 50.000 0.00 0.00 40.26 2.59
1792 5948 0.461135 TAGGCGTTGTTCGGTATCCC 59.539 55.000 0.00 0.00 40.26 3.85
1795 5951 0.808847 GCGTTGTTCGGTATCCCTCC 60.809 60.000 0.00 0.00 40.26 4.30
1797 5953 0.808847 GTTGTTCGGTATCCCTCCGC 60.809 60.000 0.00 0.00 46.49 5.54
1798 5954 0.974010 TTGTTCGGTATCCCTCCGCT 60.974 55.000 0.00 0.00 46.49 5.52
1799 5955 1.363080 GTTCGGTATCCCTCCGCTC 59.637 63.158 0.00 0.00 46.49 5.03
1800 5956 1.831286 TTCGGTATCCCTCCGCTCC 60.831 63.158 0.00 0.00 46.49 4.70
1802 5958 2.857744 CGGTATCCCTCCGCTCCAC 61.858 68.421 0.00 0.00 41.48 4.02
1803 5959 1.760875 GGTATCCCTCCGCTCCACA 60.761 63.158 0.00 0.00 0.00 4.17
1804 5960 1.335132 GGTATCCCTCCGCTCCACAA 61.335 60.000 0.00 0.00 0.00 3.33
1805 5961 0.179081 GTATCCCTCCGCTCCACAAC 60.179 60.000 0.00 0.00 0.00 3.32
1806 5962 0.325296 TATCCCTCCGCTCCACAACT 60.325 55.000 0.00 0.00 0.00 3.16
1807 5963 1.617947 ATCCCTCCGCTCCACAACTC 61.618 60.000 0.00 0.00 0.00 3.01
1808 5964 2.266055 CCTCCGCTCCACAACTCC 59.734 66.667 0.00 0.00 0.00 3.85
1811 5967 4.760047 CCGCTCCACAACTCCGGG 62.760 72.222 0.00 0.00 35.54 5.73
1812 5968 3.691342 CGCTCCACAACTCCGGGA 61.691 66.667 0.00 0.00 0.00 5.14
1814 5970 2.266055 CTCCACAACTCCGGGAGC 59.734 66.667 23.84 0.00 41.53 4.70
1815 5971 2.525629 TCCACAACTCCGGGAGCA 60.526 61.111 23.84 0.00 32.04 4.26
1816 5972 2.046892 CCACAACTCCGGGAGCAG 60.047 66.667 23.84 17.86 32.04 4.24
1817 5973 2.583441 CCACAACTCCGGGAGCAGA 61.583 63.158 23.84 0.00 32.04 4.26
1818 5974 1.079543 CACAACTCCGGGAGCAGAG 60.080 63.158 23.84 13.03 36.16 3.35
1819 5975 1.534235 ACAACTCCGGGAGCAGAGT 60.534 57.895 23.84 13.65 45.18 3.24
1820 5976 4.217112 AACTCCGGGAGCAGAGTT 57.783 55.556 23.84 8.33 46.05 3.01
1821 5977 3.382111 ACTCCGGGAGCAGAGTTG 58.618 61.111 23.84 0.00 40.43 3.16
1822 5978 2.286523 ACTCCGGGAGCAGAGTTGG 61.287 63.158 23.84 0.00 40.43 3.77
1823 5979 3.672295 CTCCGGGAGCAGAGTTGGC 62.672 68.421 11.83 0.00 0.00 4.52
1824 5980 4.020617 CCGGGAGCAGAGTTGGCA 62.021 66.667 0.00 0.00 0.00 4.92
1825 5981 2.435586 CGGGAGCAGAGTTGGCAG 60.436 66.667 0.00 0.00 0.00 4.85
1826 5982 2.947532 CGGGAGCAGAGTTGGCAGA 61.948 63.158 0.00 0.00 0.00 4.26
1827 5983 1.078567 GGGAGCAGAGTTGGCAGAG 60.079 63.158 0.00 0.00 0.00 3.35
1828 5984 1.744741 GGAGCAGAGTTGGCAGAGC 60.745 63.158 0.00 0.00 0.00 4.09
1829 5985 1.296068 GAGCAGAGTTGGCAGAGCT 59.704 57.895 0.00 0.00 34.61 4.09
1830 5986 1.003597 AGCAGAGTTGGCAGAGCTG 60.004 57.895 0.00 7.82 0.00 4.24
1843 5999 2.942710 CAGAGCTGCAGTTCAAAATGG 58.057 47.619 29.15 9.86 0.00 3.16
1844 6000 2.295349 CAGAGCTGCAGTTCAAAATGGT 59.705 45.455 29.15 6.85 0.00 3.55
1845 6001 2.295349 AGAGCTGCAGTTCAAAATGGTG 59.705 45.455 29.15 0.00 0.00 4.17
1846 6002 1.342174 AGCTGCAGTTCAAAATGGTGG 59.658 47.619 16.64 0.00 0.00 4.61
1847 6003 1.340889 GCTGCAGTTCAAAATGGTGGA 59.659 47.619 16.64 0.00 0.00 4.02
1848 6004 2.608752 GCTGCAGTTCAAAATGGTGGAG 60.609 50.000 16.64 0.00 0.00 3.86
1849 6005 2.624838 CTGCAGTTCAAAATGGTGGAGT 59.375 45.455 5.25 0.00 0.00 3.85
1850 6006 3.030291 TGCAGTTCAAAATGGTGGAGTT 58.970 40.909 0.00 0.00 0.00 3.01
1851 6007 3.181477 TGCAGTTCAAAATGGTGGAGTTG 60.181 43.478 0.00 0.00 0.00 3.16
1852 6008 3.383761 CAGTTCAAAATGGTGGAGTTGC 58.616 45.455 0.00 0.00 0.00 4.17
1853 6009 3.030291 AGTTCAAAATGGTGGAGTTGCA 58.970 40.909 0.00 0.00 0.00 4.08
1854 6010 3.068590 AGTTCAAAATGGTGGAGTTGCAG 59.931 43.478 0.00 0.00 0.00 4.41
1855 6011 2.665165 TCAAAATGGTGGAGTTGCAGT 58.335 42.857 0.00 0.00 0.00 4.40
1856 6012 3.030291 TCAAAATGGTGGAGTTGCAGTT 58.970 40.909 0.00 0.00 0.00 3.16
1857 6013 3.068024 TCAAAATGGTGGAGTTGCAGTTC 59.932 43.478 0.00 0.00 0.00 3.01
1858 6014 1.620822 AATGGTGGAGTTGCAGTTCC 58.379 50.000 10.72 10.72 0.00 3.62
1859 6015 0.251341 ATGGTGGAGTTGCAGTTCCC 60.251 55.000 14.03 7.11 32.29 3.97
1860 6016 1.603739 GGTGGAGTTGCAGTTCCCC 60.604 63.158 14.03 11.26 32.29 4.81
1861 6017 1.603739 GTGGAGTTGCAGTTCCCCC 60.604 63.158 14.03 3.73 32.29 5.40
1862 6018 2.359975 GGAGTTGCAGTTCCCCCG 60.360 66.667 7.20 0.00 0.00 5.73
1863 6019 3.056328 GAGTTGCAGTTCCCCCGC 61.056 66.667 0.00 0.00 0.00 6.13
1864 6020 3.553095 GAGTTGCAGTTCCCCCGCT 62.553 63.158 0.00 0.00 0.00 5.52
1865 6021 3.056328 GTTGCAGTTCCCCCGCTC 61.056 66.667 0.00 0.00 0.00 5.03
1866 6022 4.344865 TTGCAGTTCCCCCGCTCC 62.345 66.667 0.00 0.00 0.00 4.70
1884 6040 2.513897 GCGAATTCCGGGAGTGGG 60.514 66.667 0.00 0.00 39.04 4.61
1885 6041 2.987125 CGAATTCCGGGAGTGGGT 59.013 61.111 0.00 0.00 33.91 4.51
1886 6042 1.449601 CGAATTCCGGGAGTGGGTG 60.450 63.158 0.00 0.00 33.91 4.61
1887 6043 1.895020 CGAATTCCGGGAGTGGGTGA 61.895 60.000 0.00 0.00 33.91 4.02
1888 6044 0.546598 GAATTCCGGGAGTGGGTGAT 59.453 55.000 0.00 0.00 0.00 3.06
1889 6045 1.766496 GAATTCCGGGAGTGGGTGATA 59.234 52.381 0.00 0.00 0.00 2.15
1890 6046 1.887797 ATTCCGGGAGTGGGTGATAA 58.112 50.000 0.00 0.00 0.00 1.75
1891 6047 0.906775 TTCCGGGAGTGGGTGATAAC 59.093 55.000 0.00 0.00 0.00 1.89
1892 6048 0.979187 TCCGGGAGTGGGTGATAACC 60.979 60.000 0.00 0.00 0.00 2.85
1893 6049 1.143183 CGGGAGTGGGTGATAACCG 59.857 63.158 0.00 0.00 0.00 4.44
1894 6050 1.324740 CGGGAGTGGGTGATAACCGA 61.325 60.000 0.00 0.00 42.19 4.69
1895 6051 0.906775 GGGAGTGGGTGATAACCGAA 59.093 55.000 0.00 0.00 0.00 4.30
1896 6052 1.406477 GGGAGTGGGTGATAACCGAAC 60.406 57.143 0.00 0.00 0.00 3.95
1897 6053 1.276989 GGAGTGGGTGATAACCGAACA 59.723 52.381 6.49 0.00 0.00 3.18
1898 6054 2.618053 GAGTGGGTGATAACCGAACAG 58.382 52.381 6.49 0.00 0.00 3.16
1900 6056 0.616371 TGGGTGATAACCGAACAGGG 59.384 55.000 0.00 0.00 46.96 4.45
1901 6057 0.746923 GGGTGATAACCGAACAGGGC 60.747 60.000 0.00 0.00 46.96 5.19
1902 6058 0.746923 GGTGATAACCGAACAGGGCC 60.747 60.000 0.00 0.00 46.96 5.80
1913 6069 2.675317 CGAACAGGGCCTTAGTTCTCAG 60.675 54.545 25.55 12.76 39.48 3.35
1915 6071 3.185880 ACAGGGCCTTAGTTCTCAGTA 57.814 47.619 1.32 0.00 0.00 2.74
2013 6173 5.283717 GCGTTCTTACAAACTGTTATGCATG 59.716 40.000 10.16 0.00 0.00 4.06
2021 6181 6.208644 ACAAACTGTTATGCATGACTTTGAC 58.791 36.000 28.08 6.93 0.00 3.18
2024 6184 5.762045 ACTGTTATGCATGACTTTGACAAC 58.238 37.500 20.83 9.26 0.00 3.32
2075 6236 9.716507 CTTATATTTGTTCACTTATTTCCGTGG 57.283 33.333 0.00 0.00 0.00 4.94
2123 6284 7.859377 TCGGTCTTCTAAATATGAACGATACAC 59.141 37.037 0.00 0.00 42.56 2.90
2125 6286 9.477484 GGTCTTCTAAATATGAACGATACACAT 57.523 33.333 0.00 0.00 0.00 3.21
2128 6289 9.698309 CTTCTAAATATGAACGATACACATCCT 57.302 33.333 0.00 0.00 0.00 3.24
2159 6320 4.600012 GGCCATATTGGTCGATATTTCG 57.400 45.455 0.00 0.00 41.55 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.782889 ACACACAAGTTTTGAAGCCTC 57.217 42.857 0.00 0.00 0.00 4.70
23 24 5.837586 TTTGAACACACAAGTTTTGAAGC 57.162 34.783 0.00 0.00 0.00 3.86
56 57 8.881262 CCTCTCCAACCTATATATACAAAAGGT 58.119 37.037 0.00 0.00 42.35 3.50
57 58 9.101325 TCCTCTCCAACCTATATATACAAAAGG 57.899 37.037 0.00 0.00 0.00 3.11
60 61 9.535170 CTCTCCTCTCCAACCTATATATACAAA 57.465 37.037 0.00 0.00 0.00 2.83
62 63 8.464426 TCTCTCCTCTCCAACCTATATATACA 57.536 38.462 0.00 0.00 0.00 2.29
131 132 1.584717 AAATCCCCCTCCTCTTGGCC 61.585 60.000 0.00 0.00 0.00 5.36
148 149 1.489230 GAGGCCGAATTAGAGGGGAAA 59.511 52.381 0.00 0.00 0.00 3.13
157 158 1.591768 AAGAAGGGGAGGCCGAATTA 58.408 50.000 0.00 0.00 0.00 1.40
166 167 2.508526 CACTTGTGGAAAGAAGGGGAG 58.491 52.381 0.00 0.00 0.00 4.30
175 178 1.412361 CCTTTCCCCCACTTGTGGAAA 60.412 52.381 20.27 11.88 43.86 3.13
185 188 3.909651 GTGGCACCCTTTCCCCCA 61.910 66.667 6.29 0.00 0.00 4.96
187 190 3.585525 GAGGTGGCACCCTTTCCCC 62.586 68.421 32.30 5.65 39.75 4.81
190 193 2.755103 CAAATAGAGGTGGCACCCTTTC 59.245 50.000 32.30 22.87 39.75 2.62
192 195 1.992557 TCAAATAGAGGTGGCACCCTT 59.007 47.619 32.30 22.42 39.75 3.95
193 196 1.561542 CTCAAATAGAGGTGGCACCCT 59.438 52.381 32.30 27.79 39.75 4.34
196 199 1.383523 GGCTCAAATAGAGGTGGCAC 58.616 55.000 9.70 9.70 44.86 5.01
197 200 0.255890 GGGCTCAAATAGAGGTGGCA 59.744 55.000 0.00 0.00 44.86 4.92
214 217 1.678970 GCTACTTGGGCCACTTGGG 60.679 63.158 5.23 0.00 40.85 4.12
236 239 2.593026 CCTTAAAAGGCCAAGTGGTGA 58.407 47.619 5.01 0.00 39.76 4.02
285 288 8.474710 AAAGGGCTCTAATAATAGTTACGAGA 57.525 34.615 0.00 0.00 0.00 4.04
357 360 1.364626 GCCTCGCAAGTGTCTGGATG 61.365 60.000 0.00 0.00 39.48 3.51
361 364 2.031012 TGGCCTCGCAAGTGTCTG 59.969 61.111 3.32 0.00 39.48 3.51
362 365 2.031163 GTGGCCTCGCAAGTGTCT 59.969 61.111 3.32 0.00 39.48 3.41
455 4068 8.919777 AAAATTATATTTAGGAACGGAGGGAG 57.080 34.615 0.00 0.00 0.00 4.30
480 4093 9.877178 TTGTAGCTCATTTGAAACCTTTAAAAA 57.123 25.926 0.00 0.00 0.00 1.94
481 4094 9.308318 GTTGTAGCTCATTTGAAACCTTTAAAA 57.692 29.630 0.00 0.00 0.00 1.52
482 4095 8.470805 TGTTGTAGCTCATTTGAAACCTTTAAA 58.529 29.630 0.00 0.00 0.00 1.52
483 4096 8.001881 TGTTGTAGCTCATTTGAAACCTTTAA 57.998 30.769 0.00 0.00 0.00 1.52
484 4097 7.575414 TGTTGTAGCTCATTTGAAACCTTTA 57.425 32.000 0.00 0.00 0.00 1.85
485 4098 6.463995 TGTTGTAGCTCATTTGAAACCTTT 57.536 33.333 0.00 0.00 0.00 3.11
486 4099 6.655078 ATGTTGTAGCTCATTTGAAACCTT 57.345 33.333 0.00 0.00 0.00 3.50
487 4100 6.128282 CGTATGTTGTAGCTCATTTGAAACCT 60.128 38.462 0.00 0.00 0.00 3.50
488 4101 6.021596 CGTATGTTGTAGCTCATTTGAAACC 58.978 40.000 0.00 0.00 0.00 3.27
489 4102 6.021596 CCGTATGTTGTAGCTCATTTGAAAC 58.978 40.000 0.00 0.00 0.00 2.78
490 4103 5.935206 TCCGTATGTTGTAGCTCATTTGAAA 59.065 36.000 0.00 0.00 0.00 2.69
491 4104 5.483811 TCCGTATGTTGTAGCTCATTTGAA 58.516 37.500 0.00 0.00 0.00 2.69
492 4105 5.079689 TCCGTATGTTGTAGCTCATTTGA 57.920 39.130 0.00 0.00 0.00 2.69
493 4106 5.294306 ACATCCGTATGTTGTAGCTCATTTG 59.706 40.000 0.00 0.00 44.07 2.32
494 4107 5.428253 ACATCCGTATGTTGTAGCTCATTT 58.572 37.500 0.00 0.00 44.07 2.32
495 4108 5.023533 ACATCCGTATGTTGTAGCTCATT 57.976 39.130 0.00 0.00 44.07 2.57
496 4109 4.672587 ACATCCGTATGTTGTAGCTCAT 57.327 40.909 0.00 0.00 44.07 2.90
497 4110 5.784578 ATACATCCGTATGTTGTAGCTCA 57.215 39.130 0.00 0.00 44.07 4.26
498 4111 8.890718 TCTATATACATCCGTATGTTGTAGCTC 58.109 37.037 0.00 0.00 44.07 4.09
499 4112 8.675504 GTCTATATACATCCGTATGTTGTAGCT 58.324 37.037 0.00 0.00 44.07 3.32
500 4113 8.456471 TGTCTATATACATCCGTATGTTGTAGC 58.544 37.037 0.00 0.00 44.07 3.58
534 4147 9.214953 CGAAGCAAAATAAATGAATCTACACTC 57.785 33.333 0.00 0.00 0.00 3.51
556 4169 2.386661 ACAAGGGACTACATGCGAAG 57.613 50.000 0.00 0.00 38.49 3.79
557 4170 2.851263 AACAAGGGACTACATGCGAA 57.149 45.000 0.00 0.00 38.49 4.70
558 4171 3.965379 TTAACAAGGGACTACATGCGA 57.035 42.857 0.00 0.00 38.49 5.10
559 4172 5.354234 AGATTTTAACAAGGGACTACATGCG 59.646 40.000 0.00 0.00 38.49 4.73
560 4173 6.599638 AGAGATTTTAACAAGGGACTACATGC 59.400 38.462 0.00 0.00 38.49 4.06
561 4174 9.667107 TTAGAGATTTTAACAAGGGACTACATG 57.333 33.333 0.00 0.00 38.49 3.21
587 4200 8.135529 CCTCCGTTCTCAAATTTAAGTCTTTTT 58.864 33.333 0.00 0.00 0.00 1.94
588 4201 7.255486 CCCTCCGTTCTCAAATTTAAGTCTTTT 60.255 37.037 0.00 0.00 0.00 2.27
589 4202 6.206829 CCCTCCGTTCTCAAATTTAAGTCTTT 59.793 38.462 0.00 0.00 0.00 2.52
590 4203 5.705905 CCCTCCGTTCTCAAATTTAAGTCTT 59.294 40.000 0.00 0.00 0.00 3.01
591 4204 5.012768 TCCCTCCGTTCTCAAATTTAAGTCT 59.987 40.000 0.00 0.00 0.00 3.24
592 4205 5.243207 TCCCTCCGTTCTCAAATTTAAGTC 58.757 41.667 0.00 0.00 0.00 3.01
593 4206 5.221864 ACTCCCTCCGTTCTCAAATTTAAGT 60.222 40.000 0.00 0.00 0.00 2.24
594 4207 5.246307 ACTCCCTCCGTTCTCAAATTTAAG 58.754 41.667 0.00 0.00 0.00 1.85
595 4208 5.237236 ACTCCCTCCGTTCTCAAATTTAA 57.763 39.130 0.00 0.00 0.00 1.52
596 4209 4.903045 ACTCCCTCCGTTCTCAAATTTA 57.097 40.909 0.00 0.00 0.00 1.40
597 4210 3.790089 ACTCCCTCCGTTCTCAAATTT 57.210 42.857 0.00 0.00 0.00 1.82
598 4211 4.094476 TCTACTCCCTCCGTTCTCAAATT 58.906 43.478 0.00 0.00 0.00 1.82
599 4212 3.709587 TCTACTCCCTCCGTTCTCAAAT 58.290 45.455 0.00 0.00 0.00 2.32
600 4213 3.165087 TCTACTCCCTCCGTTCTCAAA 57.835 47.619 0.00 0.00 0.00 2.69
601 4214 2.893215 TCTACTCCCTCCGTTCTCAA 57.107 50.000 0.00 0.00 0.00 3.02
602 4215 3.383698 AATCTACTCCCTCCGTTCTCA 57.616 47.619 0.00 0.00 0.00 3.27
603 4216 4.739587 AAAATCTACTCCCTCCGTTCTC 57.260 45.455 0.00 0.00 0.00 2.87
604 4217 5.395435 GCTAAAAATCTACTCCCTCCGTTCT 60.395 44.000 0.00 0.00 0.00 3.01
605 4218 4.809958 GCTAAAAATCTACTCCCTCCGTTC 59.190 45.833 0.00 0.00 0.00 3.95
606 4219 4.224370 TGCTAAAAATCTACTCCCTCCGTT 59.776 41.667 0.00 0.00 0.00 4.44
607 4220 3.773119 TGCTAAAAATCTACTCCCTCCGT 59.227 43.478 0.00 0.00 0.00 4.69
608 4221 4.402056 TGCTAAAAATCTACTCCCTCCG 57.598 45.455 0.00 0.00 0.00 4.63
609 4222 8.747538 TTTTATGCTAAAAATCTACTCCCTCC 57.252 34.615 0.00 0.00 0.00 4.30
612 4225 9.665264 CGATTTTTATGCTAAAAATCTACTCCC 57.335 33.333 28.10 15.60 46.49 4.30
661 4274 0.394352 CCCATCCCTTTCACCTTCCG 60.394 60.000 0.00 0.00 0.00 4.30
763 4376 3.506067 GGGTTGAAAGACGAATGTGGAAT 59.494 43.478 0.00 0.00 0.00 3.01
770 4383 3.007182 TCGTTAGGGGTTGAAAGACGAAT 59.993 43.478 0.00 0.00 35.45 3.34
798 4411 2.690497 TCCTCTTGATCTTGGAGTAGCG 59.310 50.000 0.00 0.00 0.00 4.26
806 4419 5.095145 TCTTCACCATCCTCTTGATCTTG 57.905 43.478 0.00 0.00 0.00 3.02
807 4420 5.972327 ATCTTCACCATCCTCTTGATCTT 57.028 39.130 0.00 0.00 0.00 2.40
808 4421 5.427806 TGAATCTTCACCATCCTCTTGATCT 59.572 40.000 0.00 0.00 31.01 2.75
809 4422 5.678583 TGAATCTTCACCATCCTCTTGATC 58.321 41.667 0.00 0.00 31.01 2.92
810 4423 5.705397 TGAATCTTCACCATCCTCTTGAT 57.295 39.130 0.00 0.00 31.01 2.57
811 4424 5.434408 CATGAATCTTCACCATCCTCTTGA 58.566 41.667 0.00 0.00 40.49 3.02
836 4457 4.974645 TCTTCCTGTCTGCTTTTAAGGA 57.025 40.909 0.00 0.00 35.24 3.36
843 4464 2.708325 AGAACCTTCTTCCTGTCTGCTT 59.292 45.455 0.00 0.00 32.55 3.91
866 4487 0.933796 GAGCGCTTACCTTGATGAGC 59.066 55.000 13.26 0.00 0.00 4.26
871 4492 1.746220 GAGAGAGAGCGCTTACCTTGA 59.254 52.381 13.26 0.00 0.00 3.02
882 4503 3.640967 AGAGAGAGAGAGAGAGAGAGAGC 59.359 52.174 0.00 0.00 0.00 4.09
883 4504 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
884 4505 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
885 4506 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
886 4507 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
887 4508 5.362143 TGAAGAGAGAGAGAGAGAGAGAGAG 59.638 48.000 0.00 0.00 0.00 3.20
888 4509 5.272402 TGAAGAGAGAGAGAGAGAGAGAGA 58.728 45.833 0.00 0.00 0.00 3.10
889 4510 5.604758 TGAAGAGAGAGAGAGAGAGAGAG 57.395 47.826 0.00 0.00 0.00 3.20
890 4511 6.566079 ATTGAAGAGAGAGAGAGAGAGAGA 57.434 41.667 0.00 0.00 0.00 3.10
891 4512 7.052873 AGAATTGAAGAGAGAGAGAGAGAGAG 58.947 42.308 0.00 0.00 0.00 3.20
892 4513 6.962182 AGAATTGAAGAGAGAGAGAGAGAGA 58.038 40.000 0.00 0.00 0.00 3.10
893 4514 7.337689 TGAAGAATTGAAGAGAGAGAGAGAGAG 59.662 40.741 0.00 0.00 0.00 3.20
894 4515 7.174413 TGAAGAATTGAAGAGAGAGAGAGAGA 58.826 38.462 0.00 0.00 0.00 3.10
895 4516 7.395190 TGAAGAATTGAAGAGAGAGAGAGAG 57.605 40.000 0.00 0.00 0.00 3.20
896 4517 7.396907 ACATGAAGAATTGAAGAGAGAGAGAGA 59.603 37.037 0.00 0.00 0.00 3.10
897 4518 7.549839 ACATGAAGAATTGAAGAGAGAGAGAG 58.450 38.462 0.00 0.00 0.00 3.20
898 4519 7.479352 ACATGAAGAATTGAAGAGAGAGAGA 57.521 36.000 0.00 0.00 0.00 3.10
899 4520 8.036575 AGAACATGAAGAATTGAAGAGAGAGAG 58.963 37.037 0.00 0.00 0.00 3.20
904 4525 8.571336 GGAAAAGAACATGAAGAATTGAAGAGA 58.429 33.333 0.00 0.00 0.00 3.10
905 4526 7.811713 GGGAAAAGAACATGAAGAATTGAAGAG 59.188 37.037 0.00 0.00 0.00 2.85
935 4556 1.064166 AGGACCCAGAAATCAGCCATG 60.064 52.381 0.00 0.00 0.00 3.66
937 4558 1.075601 AAGGACCCAGAAATCAGCCA 58.924 50.000 0.00 0.00 0.00 4.75
995 4616 2.827051 CGGCACCATCGCATCCAAG 61.827 63.158 0.00 0.00 0.00 3.61
996 4617 2.823593 CGGCACCATCGCATCCAA 60.824 61.111 0.00 0.00 0.00 3.53
1055 4676 3.080121 AAGAGCCAGCCGAGGAGG 61.080 66.667 0.00 0.00 44.97 4.30
1166 4787 2.726887 GACGCAGAGTCGGTTCTTC 58.273 57.895 0.00 0.00 40.43 2.87
1202 4854 2.622064 AATCGCATCTGGTTACCCTC 57.378 50.000 0.00 0.00 0.00 4.30
1224 4876 4.806330 TCTAAAGACGAGCACTACTTTGG 58.194 43.478 0.00 0.00 34.93 3.28
1265 5328 5.154215 GCATCTGCTCAATGAGTCTTAAC 57.846 43.478 12.29 0.00 38.21 2.01
1352 5415 4.573900 AGTCAGTGATGCTAGTTTGGAAG 58.426 43.478 0.00 0.00 0.00 3.46
1355 5418 3.859961 CGTAGTCAGTGATGCTAGTTTGG 59.140 47.826 0.00 0.00 0.00 3.28
1401 5464 7.372451 TCAAGTATTTCAGGTGGTAATTTCG 57.628 36.000 0.00 0.00 0.00 3.46
1502 5572 2.787473 TCTCATCATGGGACCAACAC 57.213 50.000 0.00 0.00 0.00 3.32
1506 5576 0.475475 GCCATCTCATCATGGGACCA 59.525 55.000 0.00 0.00 43.42 4.02
1543 5613 1.584495 CATGTGAGGTGACCGACGA 59.416 57.895 0.00 0.00 0.00 4.20
1564 5662 1.251527 TTCGGCTCCTGACTCCTGAC 61.252 60.000 0.00 0.00 0.00 3.51
1649 5778 3.485216 CGGTATGCCAAAGTCAAATCGAC 60.485 47.826 0.00 0.00 38.72 4.20
1662 5791 2.115427 TCTCTTCAATCCGGTATGCCA 58.885 47.619 0.00 0.00 34.09 4.92
1669 5798 6.012658 TCAAATTTGTTCTCTTCAATCCGG 57.987 37.500 17.47 0.00 0.00 5.14
1701 5857 9.912634 AAACATATGTTTGAACAAGAGTAATGG 57.087 29.630 28.59 0.00 45.55 3.16
1743 5899 2.916640 TGCCGAAGCATTGACATCATA 58.083 42.857 0.00 0.00 46.52 2.15
1756 5912 4.035017 CGCCTAAATTTGTTATGCCGAAG 58.965 43.478 0.00 0.00 0.00 3.79
1760 5916 4.490743 ACAACGCCTAAATTTGTTATGCC 58.509 39.130 0.00 0.00 28.92 4.40
1772 5928 2.298411 GGATACCGAACAACGCCTAA 57.702 50.000 0.00 0.00 41.07 2.69
1786 5942 0.179081 GTTGTGGAGCGGAGGGATAC 60.179 60.000 0.00 0.00 0.00 2.24
1787 5943 0.325296 AGTTGTGGAGCGGAGGGATA 60.325 55.000 0.00 0.00 0.00 2.59
1789 5945 2.203788 AGTTGTGGAGCGGAGGGA 60.204 61.111 0.00 0.00 0.00 4.20
1791 5947 2.266055 GGAGTTGTGGAGCGGAGG 59.734 66.667 0.00 0.00 0.00 4.30
1792 5948 2.125912 CGGAGTTGTGGAGCGGAG 60.126 66.667 0.00 0.00 0.00 4.63
1795 5951 3.649277 CTCCCGGAGTTGTGGAGCG 62.649 68.421 0.73 0.00 39.29 5.03
1796 5952 2.266055 CTCCCGGAGTTGTGGAGC 59.734 66.667 0.73 0.00 39.29 4.70
1797 5953 2.266055 GCTCCCGGAGTTGTGGAG 59.734 66.667 16.09 0.00 46.87 3.86
1798 5954 2.525629 TGCTCCCGGAGTTGTGGA 60.526 61.111 16.09 0.00 31.39 4.02
1799 5955 2.046892 CTGCTCCCGGAGTTGTGG 60.047 66.667 16.09 0.00 31.39 4.17
1800 5956 1.079543 CTCTGCTCCCGGAGTTGTG 60.080 63.158 16.09 6.43 39.23 3.33
1806 5962 3.706373 GCCAACTCTGCTCCCGGA 61.706 66.667 0.73 0.00 0.00 5.14
1807 5963 3.965539 CTGCCAACTCTGCTCCCGG 62.966 68.421 0.00 0.00 0.00 5.73
1808 5964 2.435586 CTGCCAACTCTGCTCCCG 60.436 66.667 0.00 0.00 0.00 5.14
1811 5967 1.020333 CAGCTCTGCCAACTCTGCTC 61.020 60.000 0.00 0.00 0.00 4.26
1812 5968 1.003597 CAGCTCTGCCAACTCTGCT 60.004 57.895 0.00 0.00 0.00 4.24
1813 5969 3.576004 CAGCTCTGCCAACTCTGC 58.424 61.111 0.00 0.00 0.00 4.26
1823 5979 2.295349 ACCATTTTGAACTGCAGCTCTG 59.705 45.455 15.27 5.37 0.00 3.35
1824 5980 2.295349 CACCATTTTGAACTGCAGCTCT 59.705 45.455 15.27 0.00 0.00 4.09
1825 5981 2.608752 CCACCATTTTGAACTGCAGCTC 60.609 50.000 15.27 12.53 0.00 4.09
1826 5982 1.342174 CCACCATTTTGAACTGCAGCT 59.658 47.619 15.27 0.00 0.00 4.24
1827 5983 1.340889 TCCACCATTTTGAACTGCAGC 59.659 47.619 15.27 0.00 0.00 5.25
1828 5984 2.624838 ACTCCACCATTTTGAACTGCAG 59.375 45.455 13.48 13.48 0.00 4.41
1829 5985 2.665165 ACTCCACCATTTTGAACTGCA 58.335 42.857 0.00 0.00 0.00 4.41
1830 5986 3.383761 CAACTCCACCATTTTGAACTGC 58.616 45.455 0.00 0.00 0.00 4.40
1831 5987 3.181477 TGCAACTCCACCATTTTGAACTG 60.181 43.478 0.00 0.00 0.00 3.16
1832 5988 3.030291 TGCAACTCCACCATTTTGAACT 58.970 40.909 0.00 0.00 0.00 3.01
1833 5989 3.181476 ACTGCAACTCCACCATTTTGAAC 60.181 43.478 0.00 0.00 0.00 3.18
1834 5990 3.030291 ACTGCAACTCCACCATTTTGAA 58.970 40.909 0.00 0.00 0.00 2.69
1835 5991 2.665165 ACTGCAACTCCACCATTTTGA 58.335 42.857 0.00 0.00 0.00 2.69
1836 5992 3.383761 GAACTGCAACTCCACCATTTTG 58.616 45.455 0.00 0.00 0.00 2.44
1837 5993 2.365293 GGAACTGCAACTCCACCATTTT 59.635 45.455 8.55 0.00 0.00 1.82
1838 5994 1.963515 GGAACTGCAACTCCACCATTT 59.036 47.619 8.55 0.00 0.00 2.32
1839 5995 1.620822 GGAACTGCAACTCCACCATT 58.379 50.000 8.55 0.00 0.00 3.16
1840 5996 0.251341 GGGAACTGCAACTCCACCAT 60.251 55.000 14.15 0.00 32.95 3.55
1841 5997 1.150536 GGGAACTGCAACTCCACCA 59.849 57.895 14.15 0.00 32.95 4.17
1842 5998 1.603739 GGGGAACTGCAACTCCACC 60.604 63.158 14.15 9.66 32.95 4.61
1843 5999 1.603739 GGGGGAACTGCAACTCCAC 60.604 63.158 14.15 10.96 34.04 4.02
1844 6000 2.843545 GGGGGAACTGCAACTCCA 59.156 61.111 14.15 0.00 32.95 3.86
1845 6001 2.359975 CGGGGGAACTGCAACTCC 60.360 66.667 5.33 5.33 0.00 3.85
1863 6019 2.279517 CTCCCGGAATTCGCGGAG 60.280 66.667 26.99 23.31 44.00 4.63
1864 6020 3.072468 ACTCCCGGAATTCGCGGA 61.072 61.111 26.99 19.40 36.96 5.54
1865 6021 2.890474 CACTCCCGGAATTCGCGG 60.890 66.667 21.58 21.58 37.59 6.46
1866 6022 2.890474 CCACTCCCGGAATTCGCG 60.890 66.667 0.73 0.00 37.59 5.87
1867 6023 2.513897 CCCACTCCCGGAATTCGC 60.514 66.667 0.73 0.00 37.59 4.70
1868 6024 1.449601 CACCCACTCCCGGAATTCG 60.450 63.158 0.73 0.00 38.88 3.34
1869 6025 0.546598 ATCACCCACTCCCGGAATTC 59.453 55.000 0.73 0.00 0.00 2.17
1870 6026 1.887797 TATCACCCACTCCCGGAATT 58.112 50.000 0.73 0.00 0.00 2.17
1871 6027 1.489230 GTTATCACCCACTCCCGGAAT 59.511 52.381 0.73 0.00 0.00 3.01
1872 6028 0.906775 GTTATCACCCACTCCCGGAA 59.093 55.000 0.73 0.00 0.00 4.30
1873 6029 0.979187 GGTTATCACCCACTCCCGGA 60.979 60.000 0.73 0.00 37.03 5.14
1874 6030 1.525442 GGTTATCACCCACTCCCGG 59.475 63.158 0.00 0.00 37.03 5.73
1875 6031 1.143183 CGGTTATCACCCACTCCCG 59.857 63.158 0.00 0.00 40.52 5.14
1876 6032 0.906775 TTCGGTTATCACCCACTCCC 59.093 55.000 0.00 0.00 40.52 4.30
1877 6033 1.276989 TGTTCGGTTATCACCCACTCC 59.723 52.381 0.00 0.00 40.52 3.85
1878 6034 2.618053 CTGTTCGGTTATCACCCACTC 58.382 52.381 0.00 0.00 40.52 3.51
1879 6035 1.278127 CCTGTTCGGTTATCACCCACT 59.722 52.381 0.00 0.00 40.52 4.00
1880 6036 1.677820 CCCTGTTCGGTTATCACCCAC 60.678 57.143 0.00 0.00 40.52 4.61
1881 6037 0.616371 CCCTGTTCGGTTATCACCCA 59.384 55.000 0.00 0.00 40.52 4.51
1882 6038 0.746923 GCCCTGTTCGGTTATCACCC 60.747 60.000 0.00 0.00 40.52 4.61
1883 6039 0.746923 GGCCCTGTTCGGTTATCACC 60.747 60.000 0.00 0.00 40.16 4.02
1884 6040 0.252197 AGGCCCTGTTCGGTTATCAC 59.748 55.000 0.00 0.00 0.00 3.06
1885 6041 0.988832 AAGGCCCTGTTCGGTTATCA 59.011 50.000 0.00 0.00 0.00 2.15
1886 6042 2.169978 ACTAAGGCCCTGTTCGGTTATC 59.830 50.000 0.00 0.00 0.00 1.75
1887 6043 2.193993 ACTAAGGCCCTGTTCGGTTAT 58.806 47.619 0.00 0.00 0.00 1.89
1888 6044 1.648116 ACTAAGGCCCTGTTCGGTTA 58.352 50.000 0.00 0.00 0.00 2.85
1889 6045 0.769247 AACTAAGGCCCTGTTCGGTT 59.231 50.000 0.00 0.00 0.00 4.44
1890 6046 0.323957 GAACTAAGGCCCTGTTCGGT 59.676 55.000 14.53 0.00 32.25 4.69
1891 6047 0.613777 AGAACTAAGGCCCTGTTCGG 59.386 55.000 20.24 2.42 43.19 4.30
1892 6048 1.275291 TGAGAACTAAGGCCCTGTTCG 59.725 52.381 20.24 1.40 43.19 3.95
1893 6049 2.303311 ACTGAGAACTAAGGCCCTGTTC 59.697 50.000 19.36 19.36 40.00 3.18
1894 6050 2.339769 ACTGAGAACTAAGGCCCTGTT 58.660 47.619 0.00 1.52 0.00 3.16
1895 6051 2.031495 ACTGAGAACTAAGGCCCTGT 57.969 50.000 0.00 0.00 0.00 4.00
1896 6052 6.042093 TCAATATACTGAGAACTAAGGCCCTG 59.958 42.308 0.00 0.00 0.00 4.45
1897 6053 6.042208 GTCAATATACTGAGAACTAAGGCCCT 59.958 42.308 0.00 0.00 0.00 5.19
1898 6054 6.042208 AGTCAATATACTGAGAACTAAGGCCC 59.958 42.308 0.00 0.00 0.00 5.80
1899 6055 7.056844 AGTCAATATACTGAGAACTAAGGCC 57.943 40.000 0.00 0.00 0.00 5.19
1900 6056 7.982354 ACAAGTCAATATACTGAGAACTAAGGC 59.018 37.037 0.00 0.00 0.00 4.35
1901 6057 9.877178 AACAAGTCAATATACTGAGAACTAAGG 57.123 33.333 0.00 0.00 0.00 2.69
2003 6163 5.764487 TGTTGTCAAAGTCATGCATAACA 57.236 34.783 2.05 2.35 0.00 2.41
2054 6214 6.488683 TCTTCCACGGAAATAAGTGAACAAAT 59.511 34.615 0.00 0.00 40.56 2.32
2058 6219 5.934935 TTCTTCCACGGAAATAAGTGAAC 57.065 39.130 0.00 0.00 40.56 3.18
2073 6234 7.225341 CGATCATAGATGACAACAATTCTTCCA 59.775 37.037 0.00 0.00 40.03 3.53
2075 6236 7.225538 ACCGATCATAGATGACAACAATTCTTC 59.774 37.037 0.00 0.00 40.03 2.87
2123 6284 2.620251 TGGCCGTTATCTGAAGGATG 57.380 50.000 0.00 0.00 35.98 3.51
2125 6286 4.504864 CCAATATGGCCGTTATCTGAAGGA 60.505 45.833 0.77 0.00 0.00 3.36
2128 6289 4.385825 GACCAATATGGCCGTTATCTGAA 58.614 43.478 0.77 0.00 42.67 3.02


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

AutoCloner maintained by Alex Coulton.