Multiple sequence alignment - TraesCS1D01G271000

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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 TraesCS1D01G271000 chr1D 100.000 5394 0 0 1 5394 365732206 365726813 0.000000e+00 9961.0
1 TraesCS1D01G271000 chr1D 97.561 41 1 0 5204 5244 279100748 279100788 2.700000e-08 71.3
2 TraesCS1D01G271000 chr1D 95.455 44 2 0 5204 5247 436612057 436612014 2.700000e-08 71.3
3 TraesCS1D01G271000 chr1B 94.418 4174 163 31 731 4880 489253244 489249117 0.000000e+00 6353.0
4 TraesCS1D01G271000 chr1B 88.920 352 20 5 5041 5392 489249119 489248787 3.010000e-112 416.0
5 TraesCS1D01G271000 chr1B 96.087 230 8 1 1 230 489254425 489254197 1.830000e-99 374.0
6 TraesCS1D01G271000 chr1B 91.250 240 20 1 278 517 489254043 489253805 5.210000e-85 326.0
7 TraesCS1D01G271000 chr1B 85.075 268 31 7 4831 5096 329485000 329484740 1.150000e-66 265.0
8 TraesCS1D01G271000 chr1A 93.506 2926 116 38 640 3517 464840821 464837922 0.000000e+00 4283.0
9 TraesCS1D01G271000 chr1A 96.251 1387 43 5 3502 4880 464837904 464836519 0.000000e+00 2265.0
10 TraesCS1D01G271000 chr1A 87.261 628 62 15 1 614 464841525 464840902 0.000000e+00 701.0
11 TraesCS1D01G271000 chr1A 92.978 356 20 4 5037 5392 464836525 464836175 1.040000e-141 514.0
12 TraesCS1D01G271000 chr5A 92.694 219 14 2 4828 5046 670399109 670399325 1.130000e-81 315.0
13 TraesCS1D01G271000 chr5A 84.932 73 3 5 3331 3402 534904728 534904663 3.490000e-07 67.6
14 TraesCS1D01G271000 chr5A 100.000 34 0 0 3319 3352 33108186 33108219 4.510000e-06 63.9
15 TraesCS1D01G271000 chr5A 100.000 31 0 0 3367 3397 385932706 385932736 2.100000e-04 58.4
16 TraesCS1D01G271000 chr4B 87.085 271 33 2 4827 5096 188648786 188648517 6.790000e-79 305.0
17 TraesCS1D01G271000 chr4B 92.821 195 10 4 4875 5066 99432912 99433105 4.110000e-71 279.0
18 TraesCS1D01G271000 chr4B 94.595 37 2 0 3366 3402 112038685 112038721 2.100000e-04 58.4
19 TraesCS1D01G271000 chr7A 85.567 291 35 6 4818 5105 581843878 581844164 1.140000e-76 298.0
20 TraesCS1D01G271000 chr7A 90.196 51 5 0 5194 5244 38731870 38731920 3.490000e-07 67.6
21 TraesCS1D01G271000 chr3A 85.874 269 37 1 4828 5096 10301594 10301861 8.840000e-73 285.0
22 TraesCS1D01G271000 chr3A 89.109 101 11 0 2057 2157 631577020 631577120 5.670000e-25 126.0
23 TraesCS1D01G271000 chr5B 85.240 271 37 3 4827 5096 363261447 363261179 5.320000e-70 276.0
24 TraesCS1D01G271000 chr2B 88.546 227 22 3 4817 5043 550974891 550975113 6.880000e-69 272.0
25 TraesCS1D01G271000 chr2B 86.885 244 22 8 4856 5094 75846373 75846611 1.150000e-66 265.0
26 TraesCS1D01G271000 chr7D 85.075 268 37 2 4834 5100 458952948 458952683 2.480000e-68 270.0
27 TraesCS1D01G271000 chr5D 89.202 213 21 2 4831 5042 542970901 542971112 1.150000e-66 265.0
28 TraesCS1D01G271000 chr5D 83.951 81 5 3 3319 3399 43256559 43256631 2.700000e-08 71.3
29 TraesCS1D01G271000 chr5D 84.058 69 5 6 3334 3402 325428579 325428517 1.620000e-05 62.1
30 TraesCS1D01G271000 chr3B 90.291 103 10 0 2055 2157 650798574 650798676 9.420000e-28 135.0
31 TraesCS1D01G271000 chr3B 97.619 42 1 0 5204 5245 686338174 686338133 7.490000e-09 73.1
32 TraesCS1D01G271000 chr3D 90.099 101 10 0 2057 2157 487808646 487808746 1.220000e-26 132.0
33 TraesCS1D01G271000 chr4A 88.571 70 4 1 3334 3403 681925241 681925176 1.250000e-11 82.4
34 TraesCS1D01G271000 chr6D 92.453 53 3 1 5193 5244 302639690 302639638 2.080000e-09 75.0
35 TraesCS1D01G271000 chr4D 97.619 42 1 0 5204 5245 139044983 139044942 7.490000e-09 73.1
36 TraesCS1D01G271000 chr4D 85.075 67 5 2 3335 3401 416417182 416417243 4.510000e-06 63.9
37 TraesCS1D01G271000 chr6B 90.385 52 3 2 5204 5255 120677349 120677300 3.490000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G271000 chr1D 365726813 365732206 5393 True 9961.00 9961 100.00000 1 5394 1 chr1D.!!$R1 5393
1 TraesCS1D01G271000 chr1B 489248787 489254425 5638 True 1867.25 6353 92.66875 1 5392 4 chr1B.!!$R2 5391
2 TraesCS1D01G271000 chr1A 464836175 464841525 5350 True 1940.75 4283 92.49900 1 5392 4 chr1A.!!$R1 5391

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
723 1229 0.600057 GAAGCCTTTTGTGGAGCTGG 59.400 55.0 0.0 0.0 35.30 4.85 F
1650 2197 0.821517 TGATCCTAACACCGACGCAT 59.178 50.0 0.0 0.0 0.00 4.73 F
2137 2688 0.946221 CCCGGCTCAAGATATGCGAC 60.946 60.0 0.0 0.0 0.00 5.19 F
2955 3513 0.178992 TCAGACTTTGGCACCCCTTG 60.179 55.0 0.0 0.0 0.00 3.61 F
4225 4817 0.951040 AAGACGCAAGGAAGAAGCCG 60.951 55.0 0.0 0.0 46.39 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2450 3006 0.108992 TAAGTGGCGTGCTCTTACCG 60.109 55.000 0.00 0.0 0.00 4.02 R
2736 3293 0.107410 AGACACAAAACTGTGGGCGA 60.107 50.000 9.85 0.0 43.59 5.54 R
3979 4570 1.865970 CGATCTTGCAATCTGGAGAGC 59.134 52.381 0.00 0.0 0.00 4.09 R
4330 4922 1.900486 ACCTCCCTAACCTTCTTGTCG 59.100 52.381 0.00 0.0 0.00 4.35 R
5026 5625 2.077687 TATGTACTCCCTCCGTTCCC 57.922 55.000 0.00 0.0 0.00 3.97 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
68 69 5.650266 GGGTTTTGAAAATTTGAGGGTTTGT 59.350 36.000 0.00 0.00 0.00 2.83
96 97 6.645827 CAGACAATTGCACATTTCCAATGTTA 59.354 34.615 5.05 0.00 32.40 2.41
105 106 6.033831 GCACATTTCCAATGTTAAAGTCATCG 59.966 38.462 0.00 0.00 0.00 3.84
107 108 7.482743 CACATTTCCAATGTTAAAGTCATCGAG 59.517 37.037 0.00 0.00 0.00 4.04
239 241 8.943909 ATTATACTTTAGAAAAGTCGGTGAGG 57.056 34.615 8.24 0.00 0.00 3.86
241 243 3.644738 ACTTTAGAAAAGTCGGTGAGGGA 59.355 43.478 0.00 0.00 0.00 4.20
242 244 4.102054 ACTTTAGAAAAGTCGGTGAGGGAA 59.898 41.667 0.00 0.00 0.00 3.97
244 246 3.570912 AGAAAAGTCGGTGAGGGAAAA 57.429 42.857 0.00 0.00 0.00 2.29
245 247 3.211865 AGAAAAGTCGGTGAGGGAAAAC 58.788 45.455 0.00 0.00 0.00 2.43
253 262 3.056107 TCGGTGAGGGAAAACATAGAGTG 60.056 47.826 0.00 0.00 0.00 3.51
326 438 4.081365 TGGATCGCCTAAACATCAGTTGTA 60.081 41.667 0.00 0.00 34.12 2.41
385 497 2.622436 GTTCATCTTCTTCCTCCCACG 58.378 52.381 0.00 0.00 0.00 4.94
391 503 2.561419 TCTTCTTCCTCCCACGTACTTG 59.439 50.000 0.00 0.00 0.00 3.16
423 535 2.489329 CCTACAACCTAGTTCGAACCGA 59.511 50.000 24.22 12.10 0.00 4.69
481 594 2.048222 CGCTCCGTCTTGCCTGAA 60.048 61.111 0.00 0.00 0.00 3.02
507 620 3.519973 CTCCGCCATGCTATCGCCA 62.520 63.158 0.00 0.00 34.43 5.69
544 657 4.144703 GCCCCCTTCTCCGACGTC 62.145 72.222 5.18 5.18 0.00 4.34
546 659 2.749044 CCCCTTCTCCGACGTCGA 60.749 66.667 37.65 22.12 43.02 4.20
551 664 1.066114 CTTCTCCGACGTCGACAAGC 61.066 60.000 37.65 0.00 43.02 4.01
560 673 3.948719 TCGACAAGCCACCCCCAC 61.949 66.667 0.00 0.00 0.00 4.61
568 681 3.650950 CCACCCCCACCCACAGAG 61.651 72.222 0.00 0.00 0.00 3.35
628 1124 2.350522 CTCACACGCAGCTTAGGATTT 58.649 47.619 0.00 0.00 0.00 2.17
629 1125 3.521560 CTCACACGCAGCTTAGGATTTA 58.478 45.455 0.00 0.00 0.00 1.40
630 1126 3.932710 CTCACACGCAGCTTAGGATTTAA 59.067 43.478 0.00 0.00 0.00 1.52
631 1127 4.513442 TCACACGCAGCTTAGGATTTAAT 58.487 39.130 0.00 0.00 0.00 1.40
632 1128 4.941263 TCACACGCAGCTTAGGATTTAATT 59.059 37.500 0.00 0.00 0.00 1.40
633 1129 6.110033 TCACACGCAGCTTAGGATTTAATTA 58.890 36.000 0.00 0.00 0.00 1.40
634 1130 6.596106 TCACACGCAGCTTAGGATTTAATTAA 59.404 34.615 0.00 0.00 0.00 1.40
635 1131 7.119992 TCACACGCAGCTTAGGATTTAATTAAA 59.880 33.333 12.85 12.85 0.00 1.52
662 1167 5.945144 AATAAAGACTACTAAGCCGGGAA 57.055 39.130 2.18 0.00 0.00 3.97
714 1219 4.555511 GCAGTCTACTGTTGAAGCCTTTTG 60.556 45.833 11.54 0.00 45.45 2.44
715 1220 4.576463 CAGTCTACTGTTGAAGCCTTTTGT 59.424 41.667 1.81 0.00 39.09 2.83
723 1229 0.600057 GAAGCCTTTTGTGGAGCTGG 59.400 55.000 0.00 0.00 35.30 4.85
1184 1711 1.541452 GGCTCCTCCGCTCCTTAAATC 60.541 57.143 0.00 0.00 0.00 2.17
1185 1712 1.139058 GCTCCTCCGCTCCTTAAATCA 59.861 52.381 0.00 0.00 0.00 2.57
1187 1714 3.745797 GCTCCTCCGCTCCTTAAATCAAT 60.746 47.826 0.00 0.00 0.00 2.57
1189 1716 4.451900 TCCTCCGCTCCTTAAATCAATTC 58.548 43.478 0.00 0.00 0.00 2.17
1190 1717 4.080582 TCCTCCGCTCCTTAAATCAATTCA 60.081 41.667 0.00 0.00 0.00 2.57
1233 1762 2.142104 TTCCGGGGGTTCGTTCTGT 61.142 57.895 0.00 0.00 0.00 3.41
1318 1848 2.665185 GTCAACCACCGCTCGCTT 60.665 61.111 0.00 0.00 0.00 4.68
1364 1894 3.719121 AGGTGCGCCTTCTCATCT 58.281 55.556 14.67 0.00 44.18 2.90
1393 1925 2.544480 GCGACCAGCTGTAAAAATCC 57.456 50.000 13.81 0.00 44.04 3.01
1405 1937 7.223387 CAGCTGTAAAAATCCCTTATTCATTGC 59.777 37.037 5.25 0.00 0.00 3.56
1570 2111 1.180907 TTCTGCACTTGTTTGGCACA 58.819 45.000 0.00 0.00 33.34 4.57
1581 2128 2.909965 TGGCACAAGGCGTTTCCC 60.910 61.111 0.00 0.00 46.16 3.97
1590 2137 2.799978 CAAGGCGTTTCCCATTTCAAAC 59.200 45.455 0.00 0.00 34.51 2.93
1623 2170 5.546526 TGGGTGCTTACATTGGAAATTTTC 58.453 37.500 0.24 0.24 0.00 2.29
1647 2194 3.340727 GGTGATCCTAACACCGACG 57.659 57.895 0.00 0.00 46.15 5.12
1650 2197 0.821517 TGATCCTAACACCGACGCAT 59.178 50.000 0.00 0.00 0.00 4.73
1671 2218 4.406648 TCTTGCAATCGTGATGGAGTAT 57.593 40.909 0.00 0.00 0.00 2.12
1742 2289 1.726791 CGAGGACGAGGTCACAATTTG 59.273 52.381 0.00 0.00 42.66 2.32
1767 2314 3.578716 ACCCTCGTCTTGATCTTCTTTCA 59.421 43.478 0.00 0.00 0.00 2.69
1776 2324 6.370994 GTCTTGATCTTCTTTCATCAGCAGAA 59.629 38.462 0.00 0.00 30.68 3.02
1777 2325 6.594547 TCTTGATCTTCTTTCATCAGCAGAAG 59.405 38.462 2.32 2.32 43.38 2.85
1778 2326 5.802465 TGATCTTCTTTCATCAGCAGAAGT 58.198 37.500 7.78 0.00 42.82 3.01
1992 2543 1.070134 AGTAGAAAGTGCCAGCGTGAA 59.930 47.619 0.00 0.00 0.00 3.18
2137 2688 0.946221 CCCGGCTCAAGATATGCGAC 60.946 60.000 0.00 0.00 0.00 5.19
2222 2776 7.667043 TGTAAATCCTGTCATGTTTCTGTAC 57.333 36.000 0.00 0.00 0.00 2.90
2445 3001 4.749245 ATGTTTCTGACCTTTGTAAGCG 57.251 40.909 0.00 0.00 0.00 4.68
2450 3006 1.398390 CTGACCTTTGTAAGCGCATCC 59.602 52.381 11.47 0.00 0.00 3.51
2505 3061 6.285790 TCACGATGACATGCACATAAATAC 57.714 37.500 6.06 0.00 0.00 1.89
2506 3062 6.048509 TCACGATGACATGCACATAAATACT 58.951 36.000 6.06 0.00 0.00 2.12
2507 3063 6.200854 TCACGATGACATGCACATAAATACTC 59.799 38.462 6.06 0.00 0.00 2.59
2554 3111 2.642139 AAGAATGATTTGCCACGCAG 57.358 45.000 0.00 0.00 40.61 5.18
2600 3157 4.274459 GCTGAGCACCATAATTTAGGAGTG 59.726 45.833 0.00 5.75 0.00 3.51
2679 3236 5.784578 TGTACAACACTGCGATAGGATAT 57.215 39.130 0.00 0.00 34.18 1.63
2684 3241 5.246203 ACAACACTGCGATAGGATATGGTAT 59.754 40.000 0.00 0.00 34.18 2.73
2698 3255 3.862877 ATGGTATAGGATGTGCTTGCA 57.137 42.857 0.00 0.00 0.00 4.08
2736 3293 8.242729 AGTTTTTGAAGGAAGTTGAATCTGAT 57.757 30.769 0.00 0.00 0.00 2.90
2737 3294 8.355913 AGTTTTTGAAGGAAGTTGAATCTGATC 58.644 33.333 0.00 0.00 0.00 2.92
2818 3375 0.329596 GGGACTTGGCTCATGGAAGT 59.670 55.000 0.00 0.00 32.57 3.01
2955 3513 0.178992 TCAGACTTTGGCACCCCTTG 60.179 55.000 0.00 0.00 0.00 3.61
2971 3529 3.119352 CCCCTTGTGAAAGCAGAATTAGC 60.119 47.826 0.00 0.00 0.00 3.09
2999 3557 3.724732 ATTGGCATTCCCTTTGCAAAT 57.275 38.095 13.23 0.00 41.95 2.32
3079 3637 8.336801 AGTTATTTGATTGAACACCCTCTTAC 57.663 34.615 0.00 0.00 0.00 2.34
3161 3719 9.520515 AGGAATTATCTTGCTAAGTTCTTTTGA 57.479 29.630 0.00 0.00 0.00 2.69
3213 3771 3.275617 TTTATCCAACACCCTCCATCG 57.724 47.619 0.00 0.00 0.00 3.84
3247 3805 2.972625 TGGCCTGATTTTCGTACAGAG 58.027 47.619 3.32 0.00 34.07 3.35
3250 3808 4.000988 GGCCTGATTTTCGTACAGAGAAA 58.999 43.478 0.00 0.00 36.00 2.52
3390 3948 4.794248 GCAAATCTTTTGCCTTCGTTTT 57.206 36.364 12.74 0.00 39.38 2.43
3602 4193 4.849518 AGAATAAGAAGAGGGAAGTTGGC 58.150 43.478 0.00 0.00 0.00 4.52
3963 4554 6.003326 TCTTATCTTTGTGAGCAATCCAACA 58.997 36.000 0.00 0.00 34.18 3.33
3979 4570 3.071023 TCCAACAAAGGTACTGGTCTCAG 59.929 47.826 0.00 0.00 46.10 3.35
4015 4606 2.753452 AGATCGACGTGTCCATAAGTGT 59.247 45.455 0.00 0.00 0.00 3.55
4019 4610 2.163010 CGACGTGTCCATAAGTGTACCT 59.837 50.000 0.00 0.00 0.00 3.08
4126 4718 1.264045 GGGAGCTCACAGAGGAAGCT 61.264 60.000 17.19 0.00 38.68 3.74
4225 4817 0.951040 AAGACGCAAGGAAGAAGCCG 60.951 55.000 0.00 0.00 46.39 5.52
4330 4922 4.032672 CAGAATGACGAAGAAGATGAGTGC 59.967 45.833 0.00 0.00 39.69 4.40
4415 5007 1.589716 GCTGCTTGTGATGTGGGACC 61.590 60.000 0.00 0.00 0.00 4.46
4450 5045 9.971922 GTAGATAATTGGCTATTTTGATTTGCT 57.028 29.630 0.00 0.00 0.00 3.91
4643 5242 2.041922 ATCTGGGAGGGCTGCGTA 60.042 61.111 0.00 0.00 0.00 4.42
4644 5243 2.093537 GATCTGGGAGGGCTGCGTAG 62.094 65.000 0.00 0.00 0.00 3.51
4659 5258 4.801891 CTGCGTAGTTACTACAGGTTTGA 58.198 43.478 20.62 0.00 36.83 2.69
4666 5265 7.222224 CGTAGTTACTACAGGTTTGATGAATCC 59.778 40.741 20.62 0.00 36.83 3.01
4708 5307 6.250819 CGTGTTGTTGACTGAAATGGATATC 58.749 40.000 0.00 0.00 0.00 1.63
4731 5330 3.631686 ACCGCTTTCAGCATATGCAAATA 59.368 39.130 28.62 10.82 42.58 1.40
4764 5363 6.205658 ACTTCAGATTTTGTTGCTAGGACTTC 59.794 38.462 0.00 0.00 0.00 3.01
4807 5406 4.037923 GCCAGGATTTGTCAGTTCTTTTGA 59.962 41.667 0.00 0.00 0.00 2.69
4817 5416 4.881850 GTCAGTTCTTTTGACTGAAAGGGA 59.118 41.667 8.37 0.00 41.29 4.20
4829 5428 6.074648 TGACTGAAAGGGAAAAATGTGGTAT 58.925 36.000 0.00 0.00 39.30 2.73
4883 5482 9.793259 TTGGATATTTCAATATGAACTACTCCC 57.207 33.333 0.00 0.00 35.89 4.30
4884 5483 9.170890 TGGATATTTCAATATGAACTACTCCCT 57.829 33.333 0.00 0.00 35.89 4.20
4885 5484 9.660180 GGATATTTCAATATGAACTACTCCCTC 57.340 37.037 0.00 0.00 35.89 4.30
4886 5485 9.660180 GATATTTCAATATGAACTACTCCCTCC 57.340 37.037 0.00 0.00 35.89 4.30
4887 5486 5.531122 TTCAATATGAACTACTCCCTCCG 57.469 43.478 0.00 0.00 30.26 4.63
4888 5487 4.543689 TCAATATGAACTACTCCCTCCGT 58.456 43.478 0.00 0.00 0.00 4.69
4889 5488 4.960469 TCAATATGAACTACTCCCTCCGTT 59.040 41.667 0.00 0.00 0.00 4.44
4890 5489 5.068723 TCAATATGAACTACTCCCTCCGTTC 59.931 44.000 0.00 0.00 37.02 3.95
4891 5490 1.553706 TGAACTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 35.97 3.62
4892 5491 1.076677 TGAACTACTCCCTCCGTTCCT 59.923 52.381 0.00 0.00 35.97 3.36
4893 5492 2.309755 TGAACTACTCCCTCCGTTCCTA 59.690 50.000 0.00 0.00 35.97 2.94
4894 5493 3.245371 TGAACTACTCCCTCCGTTCCTAA 60.245 47.826 0.00 0.00 35.97 2.69
4895 5494 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
4896 5495 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
4897 5496 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
4898 5497 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
4899 5498 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
4900 5499 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4901 5500 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4902 5501 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4903 5502 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4904 5503 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4905 5504 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4906 5505 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4907 5506 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
4908 5507 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
4909 5508 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
4910 5509 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
4911 5510 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
4928 5527 9.436957 TCTTTCTAGACATTTCAAATGGACTAC 57.563 33.333 14.70 1.26 0.00 2.73
4929 5528 9.219603 CTTTCTAGACATTTCAAATGGACTACA 57.780 33.333 14.70 3.48 0.00 2.74
4930 5529 9.567776 TTTCTAGACATTTCAAATGGACTACAA 57.432 29.630 14.70 8.52 0.00 2.41
4931 5530 8.547967 TCTAGACATTTCAAATGGACTACAAC 57.452 34.615 14.70 0.00 0.00 3.32
4932 5531 8.154203 TCTAGACATTTCAAATGGACTACAACA 58.846 33.333 14.70 0.00 0.00 3.33
4933 5532 7.765695 AGACATTTCAAATGGACTACAACAT 57.234 32.000 14.70 0.00 0.00 2.71
4934 5533 8.862325 AGACATTTCAAATGGACTACAACATA 57.138 30.769 14.70 0.00 0.00 2.29
4935 5534 8.730680 AGACATTTCAAATGGACTACAACATAC 58.269 33.333 14.70 0.00 0.00 2.39
4936 5535 7.526608 ACATTTCAAATGGACTACAACATACG 58.473 34.615 14.70 0.00 0.00 3.06
4937 5536 6.489127 TTTCAAATGGACTACAACATACGG 57.511 37.500 0.00 0.00 0.00 4.02
4938 5537 5.408880 TCAAATGGACTACAACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
4939 5538 5.984725 TCAAATGGACTACAACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
4940 5539 5.815222 TCAAATGGACTACAACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
4942 5541 6.474140 AATGGACTACAACATACGGATGTA 57.526 37.500 15.10 0.00 45.93 2.29
4943 5542 6.665992 ATGGACTACAACATACGGATGTAT 57.334 37.500 15.10 8.21 45.93 2.29
4980 5579 6.259550 AGAATGTAGGTTCACTCATTTTGC 57.740 37.500 0.00 0.00 31.53 3.68
4981 5580 6.006449 AGAATGTAGGTTCACTCATTTTGCT 58.994 36.000 0.00 0.00 31.53 3.91
4982 5581 6.491403 AGAATGTAGGTTCACTCATTTTGCTT 59.509 34.615 0.00 0.00 31.53 3.91
4983 5582 5.689383 TGTAGGTTCACTCATTTTGCTTC 57.311 39.130 0.00 0.00 0.00 3.86
4984 5583 3.904136 AGGTTCACTCATTTTGCTTCG 57.096 42.857 0.00 0.00 0.00 3.79
4985 5584 3.214328 AGGTTCACTCATTTTGCTTCGT 58.786 40.909 0.00 0.00 0.00 3.85
4986 5585 4.385825 AGGTTCACTCATTTTGCTTCGTA 58.614 39.130 0.00 0.00 0.00 3.43
4987 5586 5.003804 AGGTTCACTCATTTTGCTTCGTAT 58.996 37.500 0.00 0.00 0.00 3.06
4988 5587 5.088739 GGTTCACTCATTTTGCTTCGTATG 58.911 41.667 0.00 0.00 0.00 2.39
4989 5588 5.334879 GGTTCACTCATTTTGCTTCGTATGT 60.335 40.000 0.00 0.00 0.00 2.29
4990 5589 6.128391 GGTTCACTCATTTTGCTTCGTATGTA 60.128 38.462 0.00 0.00 0.00 2.29
4991 5590 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
4992 5591 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
4993 5592 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
4994 5593 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
4995 5594 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
4996 5595 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
4997 5596 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
4998 5597 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
4999 5598 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
5000 5599 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
5001 5600 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
5002 5601 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
5003 5602 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
5004 5603 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
5005 5604 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
5006 5605 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
5007 5606 7.375834 TCGTATGTAGTCACTTGTTGAAATCT 58.624 34.615 0.00 0.00 35.39 2.40
5008 5607 7.541091 TCGTATGTAGTCACTTGTTGAAATCTC 59.459 37.037 0.00 0.00 35.39 2.75
5009 5608 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
5010 5609 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
5011 5610 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
5012 5611 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
5013 5612 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
5014 5613 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
5015 5614 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
5016 5615 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
5017 5616 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
5018 5617 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
5019 5618 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
5020 5619 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
5031 5630 9.449719 TCTCTAGAAAGACAAATATTTGGGAAC 57.550 33.333 27.43 16.80 42.34 3.62
5032 5631 8.263940 TCTAGAAAGACAAATATTTGGGAACG 57.736 34.615 27.43 11.14 42.34 3.95
5033 5632 6.267496 AGAAAGACAAATATTTGGGAACGG 57.733 37.500 27.43 5.66 42.34 4.44
5034 5633 6.007703 AGAAAGACAAATATTTGGGAACGGA 58.992 36.000 27.43 0.00 42.34 4.69
5035 5634 5.897377 AAGACAAATATTTGGGAACGGAG 57.103 39.130 27.43 4.34 42.34 4.63
5036 5635 4.270008 AGACAAATATTTGGGAACGGAGG 58.730 43.478 27.43 3.68 42.34 4.30
5037 5636 3.361786 ACAAATATTTGGGAACGGAGGG 58.638 45.455 27.43 3.22 42.34 4.30
5038 5637 3.010808 ACAAATATTTGGGAACGGAGGGA 59.989 43.478 27.43 0.00 42.34 4.20
5039 5638 3.577805 AATATTTGGGAACGGAGGGAG 57.422 47.619 0.00 0.00 0.00 4.30
5065 5664 6.484288 ACATATGAACTGAAATGAGGGAACA 58.516 36.000 10.38 0.00 0.00 3.18
5075 5674 4.654091 AATGAGGGAACAAAACACACTG 57.346 40.909 0.00 0.00 0.00 3.66
5233 5832 6.834168 AAACCACGACAAGAATTATGGAAT 57.166 33.333 0.00 0.00 0.00 3.01
5260 5859 4.385310 GGGAGTACATGCATTTTCCCTACT 60.385 45.833 19.92 6.22 40.86 2.57
5327 5926 9.901172 AGTACTTAATTAGAGTAATTTGGTGGG 57.099 33.333 0.00 0.00 39.06 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 5.781210 TGGAAATGTGCAATTGTCTGTAA 57.219 34.783 7.40 0.00 0.00 2.41
105 106 3.131046 CCCAAAACTATGGTCATTGGCTC 59.869 47.826 16.68 0.00 39.22 4.70
107 108 2.168313 CCCCAAAACTATGGTCATTGGC 59.832 50.000 16.68 0.00 39.22 4.52
159 160 9.311916 CACAGATTGTTTCTTCAAATAACCAAA 57.688 29.630 0.00 0.00 29.93 3.28
230 232 3.056035 ACTCTATGTTTTCCCTCACCGAC 60.056 47.826 0.00 0.00 0.00 4.79
232 234 3.262420 CACTCTATGTTTTCCCTCACCG 58.738 50.000 0.00 0.00 0.00 4.94
233 235 3.009143 ACCACTCTATGTTTTCCCTCACC 59.991 47.826 0.00 0.00 0.00 4.02
238 240 2.092323 GGCACCACTCTATGTTTTCCC 58.908 52.381 0.00 0.00 0.00 3.97
239 241 3.073274 AGGCACCACTCTATGTTTTCC 57.927 47.619 0.00 0.00 0.00 3.13
241 243 4.373156 AGAAGGCACCACTCTATGTTTT 57.627 40.909 0.00 0.00 0.00 2.43
242 244 4.532521 AGTAGAAGGCACCACTCTATGTTT 59.467 41.667 2.84 0.00 0.00 2.83
244 246 3.714144 AGTAGAAGGCACCACTCTATGT 58.286 45.455 2.84 0.00 0.00 2.29
245 247 4.744795 AAGTAGAAGGCACCACTCTATG 57.255 45.455 2.84 0.00 0.00 2.23
341 453 4.815846 GGTGTGGCAAACAAAATCAATTCT 59.184 37.500 10.52 0.00 41.57 2.40
344 456 3.129871 CGGTGTGGCAAACAAAATCAAT 58.870 40.909 10.52 0.00 41.57 2.57
353 465 0.951558 AGATGAACGGTGTGGCAAAC 59.048 50.000 0.00 0.00 0.00 2.93
385 497 0.400594 AGGGTGGTTGGAGCAAGTAC 59.599 55.000 0.00 0.00 0.00 2.73
391 503 0.608308 GGTTGTAGGGTGGTTGGAGC 60.608 60.000 0.00 0.00 0.00 4.70
462 575 4.379243 CAGGCAAGACGGAGCGGT 62.379 66.667 0.00 0.00 0.00 5.68
507 620 1.421646 CTTTAGAGGGATGGCCGGAAT 59.578 52.381 5.05 0.00 33.83 3.01
551 664 3.650950 CTCTGTGGGTGGGGGTGG 61.651 72.222 0.00 0.00 0.00 4.61
568 681 1.379146 GGGAGGTGGAGGTTTGACC 59.621 63.158 0.00 0.00 38.99 4.02
634 1130 9.117183 CCCGGCTTAGTAGTCTTTATTTATTTT 57.883 33.333 0.00 0.00 0.00 1.82
635 1131 8.488668 TCCCGGCTTAGTAGTCTTTATTTATTT 58.511 33.333 0.00 0.00 0.00 1.40
714 1219 0.250901 TTTTCCTGCTCCAGCTCCAC 60.251 55.000 0.00 0.00 42.66 4.02
715 1220 0.037303 CTTTTCCTGCTCCAGCTCCA 59.963 55.000 0.00 0.00 42.66 3.86
723 1229 4.853924 TTCAACAATCCTTTTCCTGCTC 57.146 40.909 0.00 0.00 0.00 4.26
755 1261 7.480542 CGTACCGTATTCCTTTCAAGATTTTTG 59.519 37.037 0.00 0.00 0.00 2.44
902 1419 2.920384 TGTGGTCTGTGGCGCCTA 60.920 61.111 29.70 15.92 0.00 3.93
1184 1711 8.624701 AGCAACAGAAATCGATAAATGAATTG 57.375 30.769 0.00 0.00 0.00 2.32
1185 1712 8.680903 AGAGCAACAGAAATCGATAAATGAATT 58.319 29.630 0.00 0.00 0.00 2.17
1187 1714 7.201644 GGAGAGCAACAGAAATCGATAAATGAA 60.202 37.037 0.00 0.00 0.00 2.57
1189 1716 6.425504 GGAGAGCAACAGAAATCGATAAATG 58.574 40.000 0.00 0.00 0.00 2.32
1190 1717 5.235186 CGGAGAGCAACAGAAATCGATAAAT 59.765 40.000 0.00 0.00 0.00 1.40
1223 1752 0.653636 TTGGAACGCACAGAACGAAC 59.346 50.000 0.00 0.00 0.00 3.95
1233 1762 0.109532 TCAGACCCAATTGGAACGCA 59.890 50.000 26.60 3.70 37.39 5.24
1318 1848 1.077787 GATGATGTTGGGGTGCCGA 60.078 57.895 0.00 0.00 0.00 5.54
1364 1894 2.342279 CTGGTCGCTCCGTTTCCA 59.658 61.111 0.00 0.00 39.52 3.53
1393 1925 4.396166 AGAGGACAAACGCAATGAATAAGG 59.604 41.667 0.00 0.00 0.00 2.69
1405 1937 5.219633 CAATTAAACCCAAGAGGACAAACG 58.780 41.667 0.00 0.00 39.89 3.60
1512 2048 7.862372 CGGAAATTTCCCAATCAGTTACATATG 59.138 37.037 27.72 0.00 44.67 1.78
1570 2111 2.698274 AGTTTGAAATGGGAAACGCCTT 59.302 40.909 0.00 0.00 37.19 4.35
1572 2113 2.035321 TCAGTTTGAAATGGGAAACGCC 59.965 45.455 0.00 0.00 37.19 5.68
1581 2128 6.154445 CACCCAAGATTCTCAGTTTGAAATG 58.846 40.000 0.00 0.00 0.00 2.32
1590 2137 3.942829 TGTAAGCACCCAAGATTCTCAG 58.057 45.455 0.00 0.00 0.00 3.35
1647 2194 1.672363 TCCATCACGATTGCAAGATGC 59.328 47.619 16.89 0.00 45.29 3.91
1650 2197 2.768253 ACTCCATCACGATTGCAAGA 57.232 45.000 4.94 0.00 0.00 3.02
1698 2245 2.726180 CGGCCACGATCGACGATC 60.726 66.667 24.76 24.76 45.77 3.69
1742 2289 4.722361 AGAAGATCAAGACGAGGGTTAC 57.278 45.455 0.00 0.00 0.00 2.50
1767 2314 5.127194 TGGATTTCGTACTACTTCTGCTGAT 59.873 40.000 0.00 0.00 0.00 2.90
1776 2324 6.777213 ATTGACTCTGGATTTCGTACTACT 57.223 37.500 0.00 0.00 0.00 2.57
1777 2325 7.829378 AAATTGACTCTGGATTTCGTACTAC 57.171 36.000 0.00 0.00 0.00 2.73
1778 2326 8.746530 AGTAAATTGACTCTGGATTTCGTACTA 58.253 33.333 0.00 0.00 0.00 1.82
1992 2543 7.235399 AGGTCCCACTCACATTTATTTGAAAAT 59.765 33.333 0.00 0.00 0.00 1.82
2445 3001 2.526120 GCGTGCTCTTACCGGATGC 61.526 63.158 9.46 5.16 0.00 3.91
2450 3006 0.108992 TAAGTGGCGTGCTCTTACCG 60.109 55.000 0.00 0.00 0.00 4.02
2505 3061 4.193865 TGCAGTATGTCAACATCATGGAG 58.806 43.478 0.00 0.00 39.31 3.86
2506 3062 4.219264 TGCAGTATGTCAACATCATGGA 57.781 40.909 0.00 0.00 39.31 3.41
2507 3063 5.509716 AATGCAGTATGTCAACATCATGG 57.490 39.130 0.00 0.00 39.31 3.66
2554 3111 3.782889 AACAACACTTCAGGTTTGCTC 57.217 42.857 0.00 0.00 0.00 4.26
2679 3236 3.862877 ATGCAAGCACATCCTATACCA 57.137 42.857 0.00 0.00 0.00 3.25
2684 3241 2.942376 CCGTAAATGCAAGCACATCCTA 59.058 45.455 0.00 0.00 0.00 2.94
2698 3255 6.038492 TCCTTCAAAAACTCGAAACCGTAAAT 59.962 34.615 0.00 0.00 0.00 1.40
2736 3293 0.107410 AGACACAAAACTGTGGGCGA 60.107 50.000 9.85 0.00 43.59 5.54
2737 3294 0.738389 AAGACACAAAACTGTGGGCG 59.262 50.000 9.85 0.00 43.59 6.13
2818 3375 0.688087 ACTTTCCCCAAAACCGGCAA 60.688 50.000 0.00 0.00 0.00 4.52
2959 3517 3.516700 AATTGGCCAAGCTAATTCTGCTT 59.483 39.130 24.94 5.50 44.16 3.91
2984 3542 8.721019 AATACACATTATTTGCAAAGGGAATG 57.279 30.769 26.72 26.72 0.00 2.67
3158 3716 8.914654 CGATCAATTAAATTTTGCAGAACTCAA 58.085 29.630 0.00 0.00 0.00 3.02
3161 3719 8.816640 AACGATCAATTAAATTTTGCAGAACT 57.183 26.923 0.00 0.00 0.00 3.01
3179 3737 7.596995 GGTGTTGGATAAAAATTCAAACGATCA 59.403 33.333 0.00 0.00 30.91 2.92
3213 3771 2.017049 CAGGCCATGCACTACTAAACC 58.983 52.381 5.01 0.00 0.00 3.27
3247 3805 5.632347 CACAATTCACATCTTGAGCCTTTTC 59.368 40.000 0.00 0.00 34.94 2.29
3250 3808 4.401022 TCACAATTCACATCTTGAGCCTT 58.599 39.130 0.00 0.00 34.94 4.35
3359 3917 5.587033 GCAAAAGATTTGCCTCAAAAGAG 57.413 39.130 15.12 0.00 36.90 2.85
3400 3958 9.417561 AGAACAATGATGAAAGAATGGTATCAT 57.582 29.630 0.00 0.00 39.45 2.45
3602 4193 6.344572 TGTTTATCGATTGAATGACCTTCG 57.655 37.500 1.71 0.00 36.60 3.79
3936 4527 6.111382 TGGATTGCTCACAAAGATAAGAGAG 58.889 40.000 0.00 0.00 39.77 3.20
3963 4554 2.829120 GAGAGCTGAGACCAGTACCTTT 59.171 50.000 0.00 0.00 42.35 3.11
3979 4570 1.865970 CGATCTTGCAATCTGGAGAGC 59.134 52.381 0.00 0.00 0.00 4.09
4015 4606 6.265196 AGAAAAATGTCACATCAAAGCAGGTA 59.735 34.615 0.00 0.00 0.00 3.08
4019 4610 8.114331 AGATAGAAAAATGTCACATCAAAGCA 57.886 30.769 0.00 0.00 0.00 3.91
4126 4718 3.055312 TCCTCTCGTAGTAGTCTGCTTGA 60.055 47.826 0.00 0.00 0.00 3.02
4225 4817 2.328819 AGCCTGATGTGCTTGATCTC 57.671 50.000 0.00 0.00 34.87 2.75
4330 4922 1.900486 ACCTCCCTAACCTTCTTGTCG 59.100 52.381 0.00 0.00 0.00 4.35
4415 5007 3.261897 AGCCAATTATCTACATCCTCCCG 59.738 47.826 0.00 0.00 0.00 5.14
4450 5045 3.075884 GCATACGTCCTACCAAAACCAA 58.924 45.455 0.00 0.00 0.00 3.67
4643 5242 6.106673 CGGATTCATCAAACCTGTAGTAACT 58.893 40.000 0.00 0.00 0.00 2.24
4644 5243 5.220605 GCGGATTCATCAAACCTGTAGTAAC 60.221 44.000 0.00 0.00 0.00 2.50
4731 5330 8.345724 AGCAACAAAATCTGAAGTTATCTGAT 57.654 30.769 0.00 0.00 45.51 2.90
4764 5363 2.298163 GCAAATTCTGCCCCATCCATAG 59.702 50.000 2.35 0.00 46.13 2.23
4807 5406 6.014584 GGAATACCACATTTTTCCCTTTCAGT 60.015 38.462 0.00 0.00 33.08 3.41
4817 5416 6.015434 GTGAACAGAGGGAATACCACATTTTT 60.015 38.462 0.00 0.00 43.89 1.94
4829 5428 8.328758 ACATCTTATATTTGTGAACAGAGGGAA 58.671 33.333 0.00 0.00 0.00 3.97
4877 5476 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
4878 5477 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
4879 5478 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4880 5479 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
4881 5480 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
4882 5481 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
4883 5482 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
4884 5483 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
4885 5484 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
4902 5501 9.436957 GTAGTCCATTTGAAATGTCTAGAAAGA 57.563 33.333 15.93 1.84 0.00 2.52
4903 5502 9.219603 TGTAGTCCATTTGAAATGTCTAGAAAG 57.780 33.333 15.93 0.00 0.00 2.62
4904 5503 9.567776 TTGTAGTCCATTTGAAATGTCTAGAAA 57.432 29.630 15.93 11.59 0.00 2.52
4905 5504 8.999431 GTTGTAGTCCATTTGAAATGTCTAGAA 58.001 33.333 15.93 16.70 0.00 2.10
4906 5505 8.154203 TGTTGTAGTCCATTTGAAATGTCTAGA 58.846 33.333 15.93 12.79 0.00 2.43
4907 5506 8.322906 TGTTGTAGTCCATTTGAAATGTCTAG 57.677 34.615 15.93 1.90 0.00 2.43
4908 5507 8.862325 ATGTTGTAGTCCATTTGAAATGTCTA 57.138 30.769 15.93 13.97 0.00 2.59
4909 5508 7.765695 ATGTTGTAGTCCATTTGAAATGTCT 57.234 32.000 15.93 14.81 0.00 3.41
4910 5509 7.692291 CGTATGTTGTAGTCCATTTGAAATGTC 59.308 37.037 15.93 9.10 0.00 3.06
4911 5510 7.361713 CCGTATGTTGTAGTCCATTTGAAATGT 60.362 37.037 15.93 1.43 0.00 2.71
4912 5511 6.966632 CCGTATGTTGTAGTCCATTTGAAATG 59.033 38.462 10.84 10.84 0.00 2.32
4913 5512 6.882140 TCCGTATGTTGTAGTCCATTTGAAAT 59.118 34.615 0.00 0.00 0.00 2.17
4914 5513 6.231951 TCCGTATGTTGTAGTCCATTTGAAA 58.768 36.000 0.00 0.00 0.00 2.69
4915 5514 5.795972 TCCGTATGTTGTAGTCCATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
4916 5515 5.408880 TCCGTATGTTGTAGTCCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
4917 5516 5.584649 ACATCCGTATGTTGTAGTCCATTTG 59.415 40.000 0.00 0.00 44.07 2.32
4918 5517 5.741011 ACATCCGTATGTTGTAGTCCATTT 58.259 37.500 0.00 0.00 44.07 2.32
4919 5518 5.353394 ACATCCGTATGTTGTAGTCCATT 57.647 39.130 0.00 0.00 44.07 3.16
4920 5519 6.455647 CATACATCCGTATGTTGTAGTCCAT 58.544 40.000 0.00 0.00 46.70 3.41
4921 5520 5.838529 CATACATCCGTATGTTGTAGTCCA 58.161 41.667 0.00 0.00 46.70 4.02
4954 5553 8.296713 GCAAAATGAGTGAACCTACATTCTAAA 58.703 33.333 0.00 0.00 32.84 1.85
4955 5554 7.665559 AGCAAAATGAGTGAACCTACATTCTAA 59.334 33.333 0.00 0.00 32.84 2.10
4956 5555 7.168219 AGCAAAATGAGTGAACCTACATTCTA 58.832 34.615 0.00 0.00 32.84 2.10
4957 5556 6.006449 AGCAAAATGAGTGAACCTACATTCT 58.994 36.000 0.00 0.00 32.84 2.40
4958 5557 6.259550 AGCAAAATGAGTGAACCTACATTC 57.740 37.500 0.00 0.00 32.84 2.67
4959 5558 6.568462 CGAAGCAAAATGAGTGAACCTACATT 60.568 38.462 0.00 0.00 34.99 2.71
4960 5559 5.106555 CGAAGCAAAATGAGTGAACCTACAT 60.107 40.000 0.00 0.00 0.00 2.29
4961 5560 4.213270 CGAAGCAAAATGAGTGAACCTACA 59.787 41.667 0.00 0.00 0.00 2.74
4962 5561 4.213482 ACGAAGCAAAATGAGTGAACCTAC 59.787 41.667 0.00 0.00 0.00 3.18
4963 5562 4.385825 ACGAAGCAAAATGAGTGAACCTA 58.614 39.130 0.00 0.00 0.00 3.08
4964 5563 3.214328 ACGAAGCAAAATGAGTGAACCT 58.786 40.909 0.00 0.00 0.00 3.50
4965 5564 3.626028 ACGAAGCAAAATGAGTGAACC 57.374 42.857 0.00 0.00 0.00 3.62
4966 5565 5.689819 ACATACGAAGCAAAATGAGTGAAC 58.310 37.500 0.00 0.00 0.00 3.18
4967 5566 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
4968 5567 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
4969 5568 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
4970 5569 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
4971 5570 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
4972 5571 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
4973 5572 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
4974 5573 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
4975 5574 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
4976 5575 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
4977 5576 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
4978 5577 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
4979 5578 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
4980 5579 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
4981 5580 7.870954 AGATTTCAACAAGTGACTACATACGAA 59.129 33.333 0.00 0.00 35.39 3.85
4982 5581 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
4983 5582 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
4984 5583 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
4986 5585 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
4987 5586 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
4988 5587 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
4989 5588 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
4990 5589 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
4991 5590 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
4992 5591 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
4993 5592 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
4994 5593 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
5005 5604 9.449719 GTTCCCAAATATTTGTCTTTCTAGAGA 57.550 33.333 23.24 5.94 36.45 3.10
5006 5605 8.391106 CGTTCCCAAATATTTGTCTTTCTAGAG 58.609 37.037 23.24 7.00 36.45 2.43
5007 5606 7.335924 CCGTTCCCAAATATTTGTCTTTCTAGA 59.664 37.037 23.24 7.17 36.45 2.43
5008 5607 7.335924 TCCGTTCCCAAATATTTGTCTTTCTAG 59.664 37.037 23.24 8.23 36.45 2.43
5009 5608 7.169591 TCCGTTCCCAAATATTTGTCTTTCTA 58.830 34.615 23.24 5.03 36.45 2.10
5010 5609 6.007703 TCCGTTCCCAAATATTTGTCTTTCT 58.992 36.000 23.24 0.00 36.45 2.52
5011 5610 6.262193 TCCGTTCCCAAATATTTGTCTTTC 57.738 37.500 23.24 10.84 36.45 2.62
5012 5611 5.185056 CCTCCGTTCCCAAATATTTGTCTTT 59.815 40.000 23.24 0.00 36.45 2.52
5013 5612 4.705023 CCTCCGTTCCCAAATATTTGTCTT 59.295 41.667 23.24 0.00 36.45 3.01
5014 5613 4.270008 CCTCCGTTCCCAAATATTTGTCT 58.730 43.478 23.24 0.00 36.45 3.41
5015 5614 3.380320 CCCTCCGTTCCCAAATATTTGTC 59.620 47.826 23.24 11.68 36.45 3.18
5016 5615 3.010808 TCCCTCCGTTCCCAAATATTTGT 59.989 43.478 23.24 0.00 36.45 2.83
5017 5616 3.626930 TCCCTCCGTTCCCAAATATTTG 58.373 45.455 19.40 19.40 37.90 2.32
5018 5617 3.268595 ACTCCCTCCGTTCCCAAATATTT 59.731 43.478 0.00 0.00 0.00 1.40
5019 5618 2.850568 ACTCCCTCCGTTCCCAAATATT 59.149 45.455 0.00 0.00 0.00 1.28
5020 5619 2.488836 ACTCCCTCCGTTCCCAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
5021 5620 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
5022 5621 1.558294 GTACTCCCTCCGTTCCCAAAT 59.442 52.381 0.00 0.00 0.00 2.32
5023 5622 0.978907 GTACTCCCTCCGTTCCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
5024 5623 0.178926 TGTACTCCCTCCGTTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
5025 5624 0.042131 ATGTACTCCCTCCGTTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
5026 5625 2.077687 TATGTACTCCCTCCGTTCCC 57.922 55.000 0.00 0.00 0.00 3.97
5027 5626 3.228453 TCATATGTACTCCCTCCGTTCC 58.772 50.000 1.90 0.00 0.00 3.62
5028 5627 4.341520 AGTTCATATGTACTCCCTCCGTTC 59.658 45.833 9.03 0.00 0.00 3.95
5029 5628 4.099573 CAGTTCATATGTACTCCCTCCGTT 59.900 45.833 11.68 0.00 0.00 4.44
5030 5629 3.637229 CAGTTCATATGTACTCCCTCCGT 59.363 47.826 11.68 0.00 0.00 4.69
5031 5630 3.889538 TCAGTTCATATGTACTCCCTCCG 59.110 47.826 11.68 1.31 0.00 4.63
5032 5631 5.871396 TTCAGTTCATATGTACTCCCTCC 57.129 43.478 11.68 0.00 0.00 4.30
5033 5632 7.500992 TCATTTCAGTTCATATGTACTCCCTC 58.499 38.462 11.68 0.00 0.00 4.30
5034 5633 7.419518 CCTCATTTCAGTTCATATGTACTCCCT 60.420 40.741 11.68 0.00 0.00 4.20
5035 5634 6.708054 CCTCATTTCAGTTCATATGTACTCCC 59.292 42.308 11.68 0.00 0.00 4.30
5036 5635 6.708054 CCCTCATTTCAGTTCATATGTACTCC 59.292 42.308 11.68 0.00 0.00 3.85
5037 5636 7.500992 TCCCTCATTTCAGTTCATATGTACTC 58.499 38.462 11.68 0.00 0.00 2.59
5038 5637 7.437713 TCCCTCATTTCAGTTCATATGTACT 57.562 36.000 9.03 9.03 0.00 2.73
5039 5638 7.552687 TGTTCCCTCATTTCAGTTCATATGTAC 59.447 37.037 4.40 4.40 0.00 2.90
5155 5754 9.995003 TTTCAAGGCAATAAAACACTTTATGAT 57.005 25.926 0.00 0.00 37.70 2.45
5156 5755 9.823647 TTTTCAAGGCAATAAAACACTTTATGA 57.176 25.926 0.00 0.00 37.70 2.15
5202 5801 3.390135 TCTTGTCGTGGTTTTAGCTCAG 58.610 45.455 0.00 0.00 0.00 3.35
5206 5805 6.027749 CCATAATTCTTGTCGTGGTTTTAGC 58.972 40.000 0.00 0.00 0.00 3.09
5233 5832 3.620488 GAAAATGCATGTACTCCCTCCA 58.380 45.455 0.00 0.00 0.00 3.86
5327 5926 2.094906 GGGTAATCACCTTTTTGTCGGC 60.095 50.000 0.00 0.00 45.04 5.54


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

AutoCloner maintained by Alex Coulton.