Multiple sequence alignment - TraesCS4B01G214500

Loading Multiple Alignment...

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 TraesCS4B01G214500 chr4B 100.000 5908 0 0 1 5908 454032239 454038146 0.000000e+00 10911.0
1 TraesCS4B01G214500 chr4D 92.081 3018 167 39 624 3596 368864127 368867117 0.000000e+00 4183.0
2 TraesCS4B01G214500 chr4D 93.643 1054 49 9 4430 5468 368867874 368868924 0.000000e+00 1559.0
3 TraesCS4B01G214500 chr4D 90.444 450 32 4 3907 4348 368867393 368867839 3.070000e-162 582.0
4 TraesCS4B01G214500 chr4D 88.154 363 38 3 2 364 368863310 368863667 1.520000e-115 427.0
5 TraesCS4B01G214500 chr4D 93.066 274 14 2 368 636 368863838 368864111 4.290000e-106 396.0
6 TraesCS4B01G214500 chr4D 82.232 439 39 21 5502 5908 368869768 368870199 5.670000e-90 342.0
7 TraesCS4B01G214500 chr4D 86.740 181 14 6 3614 3787 368867172 368867349 6.040000e-45 193.0
8 TraesCS4B01G214500 chr4A 93.865 2282 83 22 2117 4352 96022484 96020214 0.000000e+00 3386.0
9 TraesCS4B01G214500 chr4A 94.534 1299 51 14 861 2145 96023778 96022486 0.000000e+00 1988.0
10 TraesCS4B01G214500 chr4A 92.595 1310 65 19 4433 5723 96020177 96018881 0.000000e+00 1853.0
11 TraesCS4B01G214500 chr4A 90.377 239 13 7 5679 5908 96018880 96018643 7.440000e-79 305.0
12 TraesCS4B01G214500 chr4A 83.562 73 10 2 4363 4434 541357029 541356958 3.820000e-07 67.6
13 TraesCS4B01G214500 chr7B 91.406 128 7 2 3785 3909 428829537 428829411 7.870000e-39 172.0
14 TraesCS4B01G214500 chr7B 96.364 55 2 0 4351 4405 91569203 91569257 2.270000e-14 91.6
15 TraesCS4B01G214500 chr7B 96.364 55 2 0 4351 4405 697074774 697074720 2.270000e-14 91.6
16 TraesCS4B01G214500 chr7B 93.548 62 1 2 4347 4406 750584056 750583996 8.150000e-14 89.8
17 TraesCS4B01G214500 chr3A 89.781 137 10 2 3776 3909 727233912 727233777 7.870000e-39 172.0
18 TraesCS4B01G214500 chr3A 85.135 148 16 5 5736 5877 582283366 582283219 4.770000e-31 147.0
19 TraesCS4B01G214500 chr3A 83.673 147 19 3 5736 5877 498230085 498229939 3.710000e-27 134.0
20 TraesCS4B01G214500 chr1B 91.406 128 8 1 3785 3909 334894668 334894541 7.870000e-39 172.0
21 TraesCS4B01G214500 chr1B 96.364 55 2 0 4351 4405 89795737 89795791 2.270000e-14 91.6
22 TraesCS4B01G214500 chr7D 91.736 121 7 1 3786 3903 182349978 182350098 1.320000e-36 165.0
23 TraesCS4B01G214500 chr7D 95.522 67 0 2 4345 4409 597043672 597043607 2.910000e-18 104.0
24 TraesCS4B01G214500 chr6D 89.764 127 10 1 3786 3909 16509841 16509967 6.130000e-35 159.0
25 TraesCS4B01G214500 chr7A 89.147 129 11 1 3784 3909 451519975 451519847 2.200000e-34 158.0
26 TraesCS4B01G214500 chr7A 89.147 129 10 2 3785 3909 476915813 476915685 2.200000e-34 158.0
27 TraesCS4B01G214500 chr5A 89.147 129 10 2 3785 3909 371028324 371028452 2.200000e-34 158.0
28 TraesCS4B01G214500 chr5A 83.108 148 19 2 5736 5877 329991951 329991804 4.800000e-26 130.0
29 TraesCS4B01G214500 chr5A 83.942 137 17 3 1268 1403 658677355 658677223 6.220000e-25 126.0
30 TraesCS4B01G214500 chr3D 84.459 148 17 5 5736 5877 441388818 441388671 2.220000e-29 141.0
31 TraesCS4B01G214500 chr3D 82.432 148 19 6 5736 5877 375193909 375193763 8.040000e-24 122.0
32 TraesCS4B01G214500 chr3D 81.457 151 18 8 5735 5877 170537951 170537803 1.350000e-21 115.0
33 TraesCS4B01G214500 chr2A 86.325 117 12 2 5761 5877 133345617 133345505 2.240000e-24 124.0
34 TraesCS4B01G214500 chr3B 82.313 147 21 3 5736 5877 489352875 489352729 8.040000e-24 122.0
35 TraesCS4B01G214500 chr3B 98.182 55 1 0 4351 4405 615336837 615336891 4.870000e-16 97.1
36 TraesCS4B01G214500 chr1D 96.429 56 2 0 4351 4406 466973436 466973491 6.300000e-15 93.5
37 TraesCS4B01G214500 chr6B 96.364 55 2 0 4351 4405 453857393 453857339 2.270000e-14 91.6
38 TraesCS4B01G214500 chr5B 96.364 55 2 0 4351 4405 464479764 464479818 2.270000e-14 91.6


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 TraesCS4B01G214500 chr4B 454032239 454038146 5907 False 10911.000000 10911 100.00000 1 5908 1 chr4B.!!$F1 5907
1 TraesCS4B01G214500 chr4D 368863310 368870199 6889 False 1097.428571 4183 89.48000 2 5908 7 chr4D.!!$F1 5906
2 TraesCS4B01G214500 chr4A 96018643 96023778 5135 True 1883.000000 3386 92.84275 861 5908 4 chr4A.!!$R2 5047

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
493 661 0.248866 GCCGGATTTTAACCATGGCG 60.249 55.000 13.04 4.26 0.00 5.69 F
975 1199 0.249868 CAGACCGTTGTTGAGCAGGA 60.250 55.000 0.00 0.00 0.00 3.86 F
1215 1461 1.003233 GGACAGGAGGCGCTTCTTT 60.003 57.895 19.65 5.39 0.00 2.52 F
2386 2668 0.976641 ACAAAGATGGCAGGTCTCGA 59.023 50.000 0.00 0.00 0.00 4.04 F
3064 3364 1.374947 GCCACTTGCTGGGACTACA 59.625 57.895 0.00 0.00 41.02 2.74 F
4145 4520 1.611977 GGCGCCAAAGGTTAACTCTTT 59.388 47.619 24.80 13.23 35.09 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1661 1907 0.825425 TTGATTTTGGCCGCTCACCA 60.825 50.000 0.0 0.0 34.65 4.17 R
1858 2104 0.967380 GCCCCAAGTGAACATCAGGG 60.967 60.000 0.0 0.0 32.84 4.45 R
2609 2891 1.672881 CTTAGCCTGCATAACAGCACC 59.327 52.381 0.0 0.0 45.78 5.01 R
4351 4733 0.034283 GACACTAGGACGGAGGGAGT 60.034 60.000 0.0 0.0 0.00 3.85 R
4352 4734 0.034380 TGACACTAGGACGGAGGGAG 60.034 60.000 0.0 0.0 0.00 4.30 R
5588 6809 0.592637 ATCCAATGCGTGTGTGTGTG 59.407 50.000 0.0 0.0 0.00 3.82 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 8.611654 TTTTACCTCGTCTACATTTAGCTTTT 57.388 30.769 0.00 0.00 0.00 2.27
50 51 7.229506 AGCTTTTGTCTTATGACTTTGCTAGTT 59.770 33.333 9.87 0.00 43.29 2.24
55 56 7.097192 TGTCTTATGACTTTGCTAGTTACCAG 58.903 38.462 9.87 0.00 43.29 4.00
59 60 3.256383 TGACTTTGCTAGTTACCAGCGTA 59.744 43.478 0.00 0.00 42.13 4.42
80 81 1.911057 TTGTGTGTGTTGGTGTTGGA 58.089 45.000 0.00 0.00 0.00 3.53
83 84 0.743688 TGTGTGTTGGTGTTGGATGC 59.256 50.000 0.00 0.00 0.00 3.91
96 97 1.745115 GGATGCGTGCACCTTAGCA 60.745 57.895 17.56 17.56 44.13 3.49
107 108 0.622665 ACCTTAGCAATGCAGAGGCT 59.377 50.000 21.50 13.18 41.91 4.58
117 118 3.252284 CAGAGGCTGGGTGTGGGT 61.252 66.667 0.00 0.00 0.00 4.51
119 120 2.084930 AGAGGCTGGGTGTGGGTTT 61.085 57.895 0.00 0.00 0.00 3.27
130 131 3.551250 GGGTGTGGGTTTATCGTGTTTTG 60.551 47.826 0.00 0.00 0.00 2.44
131 132 3.315749 GGTGTGGGTTTATCGTGTTTTGA 59.684 43.478 0.00 0.00 0.00 2.69
145 146 4.320421 CGTGTTTTGAATCCTCTTGATGCA 60.320 41.667 0.00 0.00 37.23 3.96
157 158 5.356190 TCCTCTTGATGCATCATTTTGAGTC 59.644 40.000 29.13 0.00 36.56 3.36
160 161 6.384224 TCTTGATGCATCATTTTGAGTCAAC 58.616 36.000 29.13 0.00 36.56 3.18
178 179 4.502645 GTCAACAAAATTCACCCTTTGTCG 59.497 41.667 1.05 0.00 43.25 4.35
179 180 4.399618 TCAACAAAATTCACCCTTTGTCGA 59.600 37.500 1.05 0.00 43.25 4.20
219 220 9.852091 ATGCTCACATATGCATATATATAGTCG 57.148 33.333 18.70 6.85 46.53 4.18
238 239 6.360370 AGTCGTCCCTATAAATGTATGCAT 57.640 37.500 3.79 3.79 36.80 3.96
242 243 7.063074 GTCGTCCCTATAAATGTATGCATACAC 59.937 40.741 35.53 20.04 45.11 2.90
252 253 7.969536 AATGTATGCATACACATCCTACTTC 57.030 36.000 35.53 8.23 45.11 3.01
283 284 1.087501 TCGAGTGACTGAGACGATGG 58.912 55.000 0.00 0.00 0.00 3.51
309 310 3.759418 TGAGATCGATGAACTCAACGTC 58.241 45.455 0.54 6.57 38.25 4.34
310 311 3.109619 GAGATCGATGAACTCAACGTCC 58.890 50.000 0.54 3.44 41.83 4.79
314 315 1.664874 CGATGAACTCAACGTCCACGA 60.665 52.381 6.03 0.00 43.02 4.35
323 324 0.672401 AACGTCCACGATTTGCCGAT 60.672 50.000 6.03 0.00 43.02 4.18
379 546 6.787085 AATACTTCGCATAGATAACAAGGC 57.213 37.500 0.00 0.00 0.00 4.35
394 561 5.806654 AACAAGGCCTAAACATTTGTGAT 57.193 34.783 5.16 0.00 32.75 3.06
424 591 6.377996 TCATGGAAATAACATTTCCTCCACTG 59.622 38.462 24.05 15.72 46.16 3.66
446 613 6.096846 ACTGGAGAAAATATTGCCATGGTAAC 59.903 38.462 18.22 3.98 0.00 2.50
461 628 6.683715 CCATGGTAACGTTTTAGGATTTTGT 58.316 36.000 5.91 0.00 42.51 2.83
493 661 0.248866 GCCGGATTTTAACCATGGCG 60.249 55.000 13.04 4.26 0.00 5.69
497 665 3.550030 CCGGATTTTAACCATGGCGAATC 60.550 47.826 13.04 15.00 0.00 2.52
499 667 3.314080 GGATTTTAACCATGGCGAATCGA 59.686 43.478 13.04 0.00 0.00 3.59
504 672 3.401033 AACCATGGCGAATCGATCATA 57.599 42.857 13.04 0.00 0.00 2.15
505 673 3.401033 ACCATGGCGAATCGATCATAA 57.599 42.857 13.04 0.00 0.00 1.90
583 755 3.992427 GACGTTCCCGAAGTTTTATCTGT 59.008 43.478 0.00 0.00 37.88 3.41
584 756 4.383173 ACGTTCCCGAAGTTTTATCTGTT 58.617 39.130 0.00 0.00 37.88 3.16
588 760 6.312487 GTTCCCGAAGTTTTATCTGTTTAGC 58.688 40.000 0.00 0.00 0.00 3.09
637 837 5.120830 CAGTGCTTGTAAGTAGTTTAGGCAG 59.879 44.000 4.87 0.00 0.00 4.85
705 910 4.402155 TCATTACCTGCCAATCCAATCAAC 59.598 41.667 0.00 0.00 0.00 3.18
711 916 4.378774 CTGCCAATCCAATCAACAAACAA 58.621 39.130 0.00 0.00 0.00 2.83
725 931 9.598517 AATCAACAAACAAAACTTATCACATGT 57.401 25.926 0.00 0.00 0.00 3.21
759 965 2.435693 CGTGGTCATCCTCTCCCCC 61.436 68.421 0.00 0.00 34.23 5.40
890 1111 0.942962 CGGATTGCAGCTTCTCATCC 59.057 55.000 1.82 1.82 0.00 3.51
955 1179 2.681706 CGAAATCTGACAGAGCAGTGT 58.318 47.619 11.52 0.00 37.20 3.55
975 1199 0.249868 CAGACCGTTGTTGAGCAGGA 60.250 55.000 0.00 0.00 0.00 3.86
978 1202 1.166531 ACCGTTGTTGAGCAGGAAGC 61.167 55.000 0.00 0.00 46.19 3.86
987 1211 2.347490 GCAGGAAGCGGAAGGACA 59.653 61.111 0.00 0.00 0.00 4.02
988 1212 1.743252 GCAGGAAGCGGAAGGACAG 60.743 63.158 0.00 0.00 0.00 3.51
1201 1447 3.239627 AAGGCGGAGGAGGAGGACA 62.240 63.158 0.00 0.00 0.00 4.02
1215 1461 1.003233 GGACAGGAGGCGCTTCTTT 60.003 57.895 19.65 5.39 0.00 2.52
1227 1473 4.634703 TTCTTTGAGGCGGCGGCA 62.635 61.111 34.87 13.35 42.47 5.69
1281 1527 1.141881 GGAGTGCATCGTGTCGGAT 59.858 57.895 0.00 0.00 0.00 4.18
1407 1653 2.260247 CGTTGTACGTCCCTCCTCA 58.740 57.895 0.00 0.00 36.74 3.86
1417 1663 2.885894 CGTCCCTCCTCACTAATCTACC 59.114 54.545 0.00 0.00 0.00 3.18
1420 1666 2.180308 CCCTCCTCACTAATCTACCCCT 59.820 54.545 0.00 0.00 0.00 4.79
1426 1672 5.858408 TCCTCACTAATCTACCCCTCTATCT 59.142 44.000 0.00 0.00 0.00 1.98
1440 1686 6.962902 ACCCCTCTATCTATTCTTATCCTTGG 59.037 42.308 0.00 0.00 0.00 3.61
1559 1805 1.588239 TCATGGACCATGAGAAGGCT 58.412 50.000 29.67 0.00 44.60 4.58
1670 1916 2.743928 GCCTTCAGTGGTGAGCGG 60.744 66.667 0.00 0.00 32.98 5.52
1729 1975 3.233507 AGTTGCCTGATGTTGAAATGGT 58.766 40.909 0.00 0.00 0.00 3.55
1858 2104 1.344763 CCCCACGATGATAGGAACCTC 59.655 57.143 0.00 0.00 0.00 3.85
1988 2234 1.686052 GATTTGTTGTTGCCAGGGACA 59.314 47.619 0.00 0.00 0.00 4.02
2131 2407 6.882678 TGGCCATAGGAAGAACTAAACTAAAC 59.117 38.462 0.00 0.00 0.00 2.01
2218 2497 3.058016 CCATGTTCAGTAGGTTGCAACTG 60.058 47.826 27.64 18.45 43.63 3.16
2301 2583 2.283145 AATTCTGTGGCTCTGTGCTT 57.717 45.000 1.44 0.00 42.39 3.91
2383 2665 2.240667 AGCATACAAAGATGGCAGGTCT 59.759 45.455 0.00 0.00 0.00 3.85
2386 2668 0.976641 ACAAAGATGGCAGGTCTCGA 59.023 50.000 0.00 0.00 0.00 4.04
2609 2891 4.633126 CCATGACAAGTGATGAGTACAAGG 59.367 45.833 1.09 0.00 0.00 3.61
2969 3269 4.600062 GAGAAGGTATGTGGACCCATTTT 58.400 43.478 1.40 0.00 40.74 1.82
3064 3364 1.374947 GCCACTTGCTGGGACTACA 59.625 57.895 0.00 0.00 41.02 2.74
3136 3436 3.308438 AGTGATCAAAAGCAATGTGCC 57.692 42.857 0.00 0.00 46.52 5.01
3198 3498 5.329399 TGGCAAGGTATGTATTCCTTTTGT 58.671 37.500 0.58 0.00 41.44 2.83
3238 3538 8.478877 TGAGGCAATCTTTTTAACTTTTTACCA 58.521 29.630 0.00 0.00 0.00 3.25
3461 3761 2.038557 ACATCAGCTCCACGGTAAACTT 59.961 45.455 0.00 0.00 0.00 2.66
3516 3817 3.125658 CCATTTTACACCGGGAGTTTACG 59.874 47.826 6.32 0.00 0.00 3.18
3614 3926 7.433425 GCAACTATCTGCCAGATTACATTTTTC 59.567 37.037 13.32 0.00 36.20 2.29
3621 3933 8.970020 TCTGCCAGATTACATTTTTCATGTTAT 58.030 29.630 0.00 0.00 33.76 1.89
3833 4204 4.800471 GGCTTTTTAGAGATTTCAATGCGG 59.200 41.667 0.00 0.00 0.00 5.69
3838 4209 6.903883 TTTAGAGATTTCAATGCGGACTAC 57.096 37.500 0.00 0.00 0.00 2.73
3839 4210 4.471904 AGAGATTTCAATGCGGACTACA 57.528 40.909 0.00 0.00 0.00 2.74
3904 4278 5.955959 AGACATCCGTATGTAGCCCATATTA 59.044 40.000 0.00 0.00 46.49 0.98
3944 4319 6.635030 AGGACTTGGTTTGTCATTTAGAAC 57.365 37.500 0.00 0.00 36.26 3.01
4071 4446 3.316588 TCAGTGGAGAGTTAGATGATCGC 59.683 47.826 0.00 0.00 0.00 4.58
4074 4449 3.068873 GTGGAGAGTTAGATGATCGCCTT 59.931 47.826 0.00 0.00 34.39 4.35
4128 4503 2.358737 GGAACAGTCAGTGGGGCG 60.359 66.667 0.00 0.00 0.00 6.13
4145 4520 1.611977 GGCGCCAAAGGTTAACTCTTT 59.388 47.619 24.80 13.23 35.09 2.52
4226 4601 7.275341 TCAAGCACTTGTTTGACAACTTTATTG 59.725 33.333 10.05 0.00 39.71 1.90
4251 4626 4.358851 TCTTTGCACCGTGAAGAATTTTG 58.641 39.130 1.65 0.00 0.00 2.44
4282 4664 7.411264 CGATGTATATCATTTTGCCTCTTCTCG 60.411 40.741 0.11 0.00 36.83 4.04
4348 4730 6.375174 TGGTTTGTCTGGATTCTTGATACATG 59.625 38.462 0.00 0.00 0.00 3.21
4349 4731 6.261118 GTTTGTCTGGATTCTTGATACATGC 58.739 40.000 0.00 0.00 0.00 4.06
4350 4732 5.363562 TGTCTGGATTCTTGATACATGCT 57.636 39.130 0.00 0.00 0.00 3.79
4351 4733 6.484364 TGTCTGGATTCTTGATACATGCTA 57.516 37.500 0.00 0.00 0.00 3.49
4352 4734 6.283694 TGTCTGGATTCTTGATACATGCTAC 58.716 40.000 0.00 0.00 0.00 3.58
4353 4735 6.098838 TGTCTGGATTCTTGATACATGCTACT 59.901 38.462 0.00 0.00 0.00 2.57
4354 4736 6.644592 GTCTGGATTCTTGATACATGCTACTC 59.355 42.308 0.00 0.00 0.00 2.59
4355 4737 5.858381 TGGATTCTTGATACATGCTACTCC 58.142 41.667 0.00 0.00 0.00 3.85
4356 4738 5.221722 TGGATTCTTGATACATGCTACTCCC 60.222 44.000 0.00 0.00 0.00 4.30
4357 4739 5.012561 GGATTCTTGATACATGCTACTCCCT 59.987 44.000 0.00 0.00 0.00 4.20
4358 4740 5.537300 TTCTTGATACATGCTACTCCCTC 57.463 43.478 0.00 0.00 0.00 4.30
4359 4741 3.898123 TCTTGATACATGCTACTCCCTCC 59.102 47.826 0.00 0.00 0.00 4.30
4360 4742 2.239400 TGATACATGCTACTCCCTCCG 58.761 52.381 0.00 0.00 0.00 4.63
4361 4743 2.240279 GATACATGCTACTCCCTCCGT 58.760 52.381 0.00 0.00 0.00 4.69
4362 4744 1.688772 TACATGCTACTCCCTCCGTC 58.311 55.000 0.00 0.00 0.00 4.79
4363 4745 1.043673 ACATGCTACTCCCTCCGTCC 61.044 60.000 0.00 0.00 0.00 4.79
4364 4746 0.757188 CATGCTACTCCCTCCGTCCT 60.757 60.000 0.00 0.00 0.00 3.85
4365 4747 0.851469 ATGCTACTCCCTCCGTCCTA 59.149 55.000 0.00 0.00 0.00 2.94
4366 4748 0.183014 TGCTACTCCCTCCGTCCTAG 59.817 60.000 0.00 0.00 0.00 3.02
4367 4749 0.183252 GCTACTCCCTCCGTCCTAGT 59.817 60.000 0.00 0.00 0.00 2.57
4368 4750 1.970092 CTACTCCCTCCGTCCTAGTG 58.030 60.000 0.00 0.00 0.00 2.74
4369 4751 1.212441 CTACTCCCTCCGTCCTAGTGT 59.788 57.143 0.00 0.00 0.00 3.55
4370 4752 0.034283 ACTCCCTCCGTCCTAGTGTC 60.034 60.000 0.00 0.00 0.00 3.67
4371 4753 0.034380 CTCCCTCCGTCCTAGTGTCA 60.034 60.000 0.00 0.00 0.00 3.58
4372 4754 0.406750 TCCCTCCGTCCTAGTGTCAA 59.593 55.000 0.00 0.00 0.00 3.18
4373 4755 1.203087 TCCCTCCGTCCTAGTGTCAAA 60.203 52.381 0.00 0.00 0.00 2.69
4374 4756 1.621814 CCCTCCGTCCTAGTGTCAAAA 59.378 52.381 0.00 0.00 0.00 2.44
4375 4757 2.038033 CCCTCCGTCCTAGTGTCAAAAA 59.962 50.000 0.00 0.00 0.00 1.94
4376 4758 3.064931 CCTCCGTCCTAGTGTCAAAAAC 58.935 50.000 0.00 0.00 0.00 2.43
4377 4759 2.729882 CTCCGTCCTAGTGTCAAAAACG 59.270 50.000 0.00 0.00 0.00 3.60
4378 4760 2.101249 TCCGTCCTAGTGTCAAAAACGT 59.899 45.455 0.00 0.00 0.00 3.99
4379 4761 2.867975 CCGTCCTAGTGTCAAAAACGTT 59.132 45.455 0.00 0.00 0.00 3.99
4380 4762 3.060070 CCGTCCTAGTGTCAAAAACGTTC 60.060 47.826 0.00 0.00 0.00 3.95
4381 4763 3.800506 CGTCCTAGTGTCAAAAACGTTCT 59.199 43.478 0.00 0.00 0.00 3.01
4382 4764 4.269363 CGTCCTAGTGTCAAAAACGTTCTT 59.731 41.667 0.00 0.00 0.00 2.52
4383 4765 5.459762 CGTCCTAGTGTCAAAAACGTTCTTA 59.540 40.000 0.00 0.00 0.00 2.10
4384 4766 6.145048 CGTCCTAGTGTCAAAAACGTTCTTAT 59.855 38.462 0.00 0.00 0.00 1.73
4385 4767 7.326789 CGTCCTAGTGTCAAAAACGTTCTTATA 59.673 37.037 0.00 0.00 0.00 0.98
4386 4768 9.148104 GTCCTAGTGTCAAAAACGTTCTTATAT 57.852 33.333 0.00 0.00 0.00 0.86
4387 4769 9.715121 TCCTAGTGTCAAAAACGTTCTTATATT 57.285 29.630 0.00 0.00 0.00 1.28
4392 4774 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
4393 4775 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
4394 4776 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
4413 4798 2.955660 GACAGAGGGAGTAGATCACTGG 59.044 54.545 0.00 0.00 43.76 4.00
4444 4838 6.734104 AAATTCAGATTGTACTCTGTGCTC 57.266 37.500 10.86 0.00 42.68 4.26
4730 5124 1.073763 ACAGCTCCAAGCCACAATACA 59.926 47.619 0.00 0.00 43.77 2.29
4757 5151 8.293699 TGTACTCATACAAAAGCTCAGATAGA 57.706 34.615 0.00 0.00 38.40 1.98
4850 5244 6.015180 AGCAAAAAGAATGTGAGAATAAGGCA 60.015 34.615 0.00 0.00 0.00 4.75
4914 5308 5.738619 TGTAGACAAAGAATAGAGTGCCA 57.261 39.130 0.00 0.00 0.00 4.92
4916 5310 6.166279 TGTAGACAAAGAATAGAGTGCCAAG 58.834 40.000 0.00 0.00 0.00 3.61
4918 5312 5.625150 AGACAAAGAATAGAGTGCCAAGTT 58.375 37.500 0.00 0.00 0.00 2.66
4919 5313 5.471456 AGACAAAGAATAGAGTGCCAAGTTG 59.529 40.000 0.00 0.00 0.00 3.16
4924 5323 6.715347 AGAATAGAGTGCCAAGTTGTTTTT 57.285 33.333 1.45 0.00 0.00 1.94
4949 5348 4.870363 AGTTGTTCATCATTTTTCACCCG 58.130 39.130 0.00 0.00 0.00 5.28
4973 5372 6.048509 GGTTCATGTTGGAAAGTTGTTCATT 58.951 36.000 0.00 0.00 0.00 2.57
5008 5407 5.068987 CCAGTTCATGTTGGGAAGAAAGAAA 59.931 40.000 0.00 0.00 0.00 2.52
5014 5413 7.657336 TCATGTTGGGAAGAAAGAAACAATAC 58.343 34.615 0.00 0.00 34.67 1.89
5021 5420 7.173032 GGGAAGAAAGAAACAATACCCTTCTA 58.827 38.462 0.00 0.00 32.00 2.10
5027 5426 6.936968 AGAAACAATACCCTTCTACTGTCT 57.063 37.500 0.00 0.00 0.00 3.41
5028 5427 6.937392 AGAAACAATACCCTTCTACTGTCTC 58.063 40.000 0.00 0.00 0.00 3.36
5029 5428 5.678955 AACAATACCCTTCTACTGTCTCC 57.321 43.478 0.00 0.00 0.00 3.71
5030 5429 4.031611 ACAATACCCTTCTACTGTCTCCC 58.968 47.826 0.00 0.00 0.00 4.30
5048 5447 7.561251 TGTCTCCCGTGAATTGAATAAATCTA 58.439 34.615 0.00 0.00 0.00 1.98
5054 5453 7.095439 CCCGTGAATTGAATAAATCTAGAGCTC 60.095 40.741 5.27 5.27 0.00 4.09
5215 5621 3.747529 CCATTGGAAAAACACAAGCATCC 59.252 43.478 0.00 0.00 0.00 3.51
5535 6754 1.271871 TGCACCGAATTCACCCTTCAT 60.272 47.619 6.22 0.00 0.00 2.57
5536 6755 1.818674 GCACCGAATTCACCCTTCATT 59.181 47.619 6.22 0.00 0.00 2.57
5539 6758 4.261197 GCACCGAATTCACCCTTCATTATC 60.261 45.833 6.22 0.00 0.00 1.75
5540 6759 5.126067 CACCGAATTCACCCTTCATTATCT 58.874 41.667 6.22 0.00 0.00 1.98
5552 6773 5.067805 CCCTTCATTATCTTTACTTGCACCC 59.932 44.000 0.00 0.00 0.00 4.61
5800 7088 5.471556 TGGACTACAAACGGATAGAAACA 57.528 39.130 0.00 0.00 0.00 2.83
5828 7116 6.148150 TGAACAAACACACTAAAACGTCTCTT 59.852 34.615 0.00 0.00 0.00 2.85
5899 7195 3.113260 ACTCCGTTTGGAACAGAAGAG 57.887 47.619 0.00 0.00 45.87 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.869897 TCATAAGACAAAAGCTAAATGTAGACG 58.130 33.333 0.00 0.00 0.00 4.18
30 31 6.999950 TGGTAACTAGCAAAGTCATAAGACA 58.000 36.000 0.31 0.00 42.36 3.41
50 51 3.114668 ACACACACAAATACGCTGGTA 57.885 42.857 0.00 0.00 0.00 3.25
55 56 2.223386 ACACCAACACACACAAATACGC 60.223 45.455 0.00 0.00 0.00 4.42
59 60 2.828520 TCCAACACCAACACACACAAAT 59.171 40.909 0.00 0.00 0.00 2.32
80 81 0.452987 CATTGCTAAGGTGCACGCAT 59.547 50.000 16.26 5.55 43.20 4.73
83 84 0.179181 CTGCATTGCTAAGGTGCACG 60.179 55.000 11.45 0.00 43.30 5.34
96 97 1.303888 CACACCCAGCCTCTGCATT 60.304 57.895 0.00 0.00 41.13 3.56
97 98 2.353958 CACACCCAGCCTCTGCAT 59.646 61.111 0.00 0.00 41.13 3.96
107 108 0.766131 ACACGATAAACCCACACCCA 59.234 50.000 0.00 0.00 0.00 4.51
117 118 7.737972 TCAAGAGGATTCAAAACACGATAAA 57.262 32.000 0.00 0.00 0.00 1.40
119 120 6.183360 GCATCAAGAGGATTCAAAACACGATA 60.183 38.462 0.00 0.00 32.57 2.92
130 131 6.802608 TCAAAATGATGCATCAAGAGGATTC 58.197 36.000 31.79 1.21 40.69 2.52
131 132 6.380274 ACTCAAAATGATGCATCAAGAGGATT 59.620 34.615 32.13 22.13 40.69 3.01
157 158 4.677584 TCGACAAAGGGTGAATTTTGTTG 58.322 39.130 9.85 9.85 44.88 3.33
160 161 6.654793 TTTTTCGACAAAGGGTGAATTTTG 57.345 33.333 0.00 0.00 39.55 2.44
214 215 6.904463 TGCATACATTTATAGGGACGACTA 57.096 37.500 0.00 0.00 0.00 2.59
215 216 5.801531 TGCATACATTTATAGGGACGACT 57.198 39.130 0.00 0.00 0.00 4.18
219 220 8.792830 ATGTGTATGCATACATTTATAGGGAC 57.207 34.615 35.33 21.31 44.25 4.46
230 231 6.731292 AGAAGTAGGATGTGTATGCATACA 57.269 37.500 31.03 31.03 40.69 2.29
238 239 8.079211 AGATGCTTAAAGAAGTAGGATGTGTA 57.921 34.615 0.00 0.00 34.90 2.90
242 243 6.980978 TCGAAGATGCTTAAAGAAGTAGGATG 59.019 38.462 0.00 0.00 34.90 3.51
252 253 5.164233 TCAGTCACTCGAAGATGCTTAAAG 58.836 41.667 0.00 0.00 33.89 1.85
283 284 5.172951 CGTTGAGTTCATCGATCTCAAGATC 59.827 44.000 21.78 13.02 44.05 2.75
297 298 2.519377 AATCGTGGACGTTGAGTTCA 57.481 45.000 0.00 0.00 40.80 3.18
298 299 2.661979 GCAAATCGTGGACGTTGAGTTC 60.662 50.000 6.69 0.00 40.80 3.01
305 306 1.079405 ATCGGCAAATCGTGGACGT 60.079 52.632 0.00 0.00 40.80 4.34
309 310 1.262417 CTCATCATCGGCAAATCGTGG 59.738 52.381 0.00 0.00 0.00 4.94
310 311 2.204237 TCTCATCATCGGCAAATCGTG 58.796 47.619 0.00 0.00 0.00 4.35
314 315 2.609459 GACGTTCTCATCATCGGCAAAT 59.391 45.455 0.00 0.00 0.00 2.32
323 324 1.511305 GGAGGCGACGTTCTCATCA 59.489 57.895 17.46 0.00 0.00 3.07
354 355 7.255139 GGCCTTGTTATCTATGCGAAGTATTTT 60.255 37.037 0.00 0.00 32.95 1.82
357 358 5.012148 AGGCCTTGTTATCTATGCGAAGTAT 59.988 40.000 0.00 0.00 36.38 2.12
358 359 4.344102 AGGCCTTGTTATCTATGCGAAGTA 59.656 41.667 0.00 0.00 0.00 2.24
359 360 3.134804 AGGCCTTGTTATCTATGCGAAGT 59.865 43.478 0.00 0.00 0.00 3.01
360 361 3.733337 AGGCCTTGTTATCTATGCGAAG 58.267 45.455 0.00 0.00 0.00 3.79
362 363 4.948341 TTAGGCCTTGTTATCTATGCGA 57.052 40.909 12.58 0.00 0.00 5.10
364 365 6.884280 ATGTTTAGGCCTTGTTATCTATGC 57.116 37.500 12.58 0.00 0.00 3.14
379 546 6.591062 CCATGACCAAATCACAAATGTTTAGG 59.409 38.462 0.00 0.00 41.24 2.69
424 591 5.067283 ACGTTACCATGGCAATATTTTCTCC 59.933 40.000 13.04 0.00 0.00 3.71
434 601 3.752665 TCCTAAAACGTTACCATGGCAA 58.247 40.909 13.04 1.21 0.00 4.52
461 628 7.701501 GGTTAAAATCCGGCGTTTGATTTATAA 59.298 33.333 18.38 15.51 39.59 0.98
497 665 8.592998 GTGACAACTTAAGTTACCTTATGATCG 58.407 37.037 20.15 6.47 36.32 3.69
499 667 8.308931 TCGTGACAACTTAAGTTACCTTATGAT 58.691 33.333 20.15 0.00 36.32 2.45
504 672 5.069516 TCCTCGTGACAACTTAAGTTACCTT 59.930 40.000 20.15 5.70 36.32 3.50
505 673 4.586001 TCCTCGTGACAACTTAAGTTACCT 59.414 41.667 20.15 6.33 36.32 3.08
524 696 6.265577 CCAATTCAAACGTATTTCCATCCTC 58.734 40.000 0.00 0.00 0.00 3.71
584 756 4.727507 TGTTTTGGCAGAGTTTTGCTAA 57.272 36.364 0.00 0.00 41.86 3.09
588 760 5.650543 AGTACTTGTTTTGGCAGAGTTTTG 58.349 37.500 0.00 0.00 0.00 2.44
668 869 9.991906 TGGCAGGTAATGAATACTAAGTTATAC 57.008 33.333 0.00 0.00 34.74 1.47
681 882 4.608269 TGATTGGATTGGCAGGTAATGAA 58.392 39.130 0.00 0.00 0.00 2.57
684 885 4.352009 TGTTGATTGGATTGGCAGGTAAT 58.648 39.130 0.00 0.00 0.00 1.89
685 886 3.772387 TGTTGATTGGATTGGCAGGTAA 58.228 40.909 0.00 0.00 0.00 2.85
705 910 7.701924 ACTGTGACATGTGATAAGTTTTGTTTG 59.298 33.333 1.15 0.00 0.00 2.93
711 916 7.360353 CGATTCACTGTGACATGTGATAAGTTT 60.360 37.037 10.56 0.00 41.93 2.66
725 931 1.068541 CCACGAGACGATTCACTGTGA 60.069 52.381 6.36 6.36 0.00 3.58
759 965 4.645535 TCTGGGTTTTGACTCTTCTGATG 58.354 43.478 0.00 0.00 0.00 3.07
850 1056 2.105993 GGTTGAGTTTAGAGGTGGTGGT 59.894 50.000 0.00 0.00 0.00 4.16
955 1179 0.249868 CCTGCTCAACAACGGTCTGA 60.250 55.000 0.00 0.00 0.00 3.27
975 1199 2.427506 GATTGAACTGTCCTTCCGCTT 58.572 47.619 0.00 0.00 0.00 4.68
978 1202 1.359848 CGGATTGAACTGTCCTTCCG 58.640 55.000 6.92 6.92 39.48 4.30
985 1209 2.198827 TCCATTGCGGATTGAACTGT 57.801 45.000 0.00 0.00 39.64 3.55
986 1210 3.489738 GGATTCCATTGCGGATTGAACTG 60.490 47.826 0.00 0.00 45.80 3.16
987 1211 2.689983 GGATTCCATTGCGGATTGAACT 59.310 45.455 0.00 0.00 45.80 3.01
988 1212 2.223805 GGGATTCCATTGCGGATTGAAC 60.224 50.000 4.80 0.00 45.80 3.18
1155 1401 1.526917 GCTCCCATTGATCACCGGG 60.527 63.158 18.98 18.98 40.32 5.73
1201 1447 1.298014 CCTCAAAGAAGCGCCTCCT 59.702 57.895 2.29 0.00 0.00 3.69
1281 1527 4.954118 AGCACGGGGGTGAGGTGA 62.954 66.667 0.00 0.00 33.58 4.02
1417 1663 7.192628 TCCCAAGGATAAGAATAGATAGAGGG 58.807 42.308 0.00 0.00 0.00 4.30
1440 1686 4.569719 TCCAGTTTCAGAGGGTTATTCC 57.430 45.455 0.00 0.00 0.00 3.01
1448 1694 4.592942 TGAATCCATTCCAGTTTCAGAGG 58.407 43.478 0.00 0.00 35.97 3.69
1449 1695 5.125097 CCTTGAATCCATTCCAGTTTCAGAG 59.875 44.000 0.00 0.00 35.97 3.35
1451 1697 4.159135 CCCTTGAATCCATTCCAGTTTCAG 59.841 45.833 0.00 0.00 35.97 3.02
1454 1700 4.089361 GACCCTTGAATCCATTCCAGTTT 58.911 43.478 0.00 0.00 35.97 2.66
1550 1796 1.536073 CCGTCACCTCAGCCTTCTCA 61.536 60.000 0.00 0.00 0.00 3.27
1559 1805 2.215942 TGATCTTCTCCGTCACCTCA 57.784 50.000 0.00 0.00 0.00 3.86
1661 1907 0.825425 TTGATTTTGGCCGCTCACCA 60.825 50.000 0.00 0.00 34.65 4.17
1670 1916 9.691362 TTCTCTTATGTTTTAGTTGATTTTGGC 57.309 29.630 0.00 0.00 0.00 4.52
1858 2104 0.967380 GCCCCAAGTGAACATCAGGG 60.967 60.000 0.00 0.00 32.84 4.45
1988 2234 7.600752 GTGAAAGAAGTATGAAGAACAGTAGCT 59.399 37.037 0.00 0.00 0.00 3.32
2028 2274 7.066163 TGCATAAACTGATAGTGATGAACCAAG 59.934 37.037 7.80 0.00 28.80 3.61
2108 2354 7.606839 ACTGTTTAGTTTAGTTCTTCCTATGGC 59.393 37.037 0.00 0.00 31.66 4.40
2131 2407 2.806608 AAAATGACAGGCTTGCACTG 57.193 45.000 0.00 1.47 41.64 3.66
2253 2535 9.643693 AAATGAATACAAGCTTTCCACTAATTG 57.356 29.630 0.00 0.00 0.00 2.32
2301 2583 6.413892 TGGATGACATATACTTTCTGCAACA 58.586 36.000 0.00 0.00 0.00 3.33
2401 2683 6.697019 ACACATTTGCATTGTGAACTTTAGAC 59.303 34.615 27.60 0.00 45.83 2.59
2609 2891 1.672881 CTTAGCCTGCATAACAGCACC 59.327 52.381 0.00 0.00 45.78 5.01
2847 3134 7.253422 GCAAATCAGTGCTTATACAATGTTCT 58.747 34.615 0.00 0.00 41.51 3.01
2969 3269 3.060736 TGCCGTCTGGTTAATAGCAAA 57.939 42.857 0.00 0.00 37.67 3.68
2985 3285 2.292267 AGCTAAAGGACAATGATGCCG 58.708 47.619 0.00 0.00 0.00 5.69
3064 3364 1.674057 CTCTGTCTTGCCCCTTCGT 59.326 57.895 0.00 0.00 0.00 3.85
3136 3436 6.243551 CAAGTCTACAAGCATAATGTGTTCG 58.756 40.000 0.00 0.00 32.27 3.95
3198 3498 6.132658 AGATTGCCTCAGAATGTAGAGTAGA 58.867 40.000 0.00 0.00 37.40 2.59
3238 3538 6.006449 AGCTGTCAAATTTAGTCCATGACTT 58.994 36.000 1.58 0.00 40.28 3.01
3461 3761 9.048446 CATATGAATCATAGATCACACAACACA 57.952 33.333 9.01 0.00 29.42 3.72
3516 3817 9.800433 GAATAACTAGAGGAACTAACTGTAACC 57.200 37.037 0.00 0.00 41.55 2.85
3520 3821 8.532819 CCAAGAATAACTAGAGGAACTAACTGT 58.467 37.037 0.00 0.00 41.55 3.55
3588 3889 6.382869 AAATGTAATCTGGCAGATAGTTGC 57.617 37.500 29.02 18.33 43.34 4.17
3637 3975 8.878769 AGCAACAAAACGAAATAGAAACAAAAT 58.121 25.926 0.00 0.00 0.00 1.82
3657 3995 7.066887 CCCACATGTGTAGAAATATAAGCAACA 59.933 37.037 23.79 0.00 0.00 3.33
3819 4190 5.107837 CGTATGTAGTCCGCATTGAAATCTC 60.108 44.000 0.00 0.00 0.00 2.75
3821 4192 4.743151 TCGTATGTAGTCCGCATTGAAATC 59.257 41.667 0.00 0.00 0.00 2.17
3825 4196 3.702330 CTTCGTATGTAGTCCGCATTGA 58.298 45.455 0.00 0.00 0.00 2.57
3833 4204 6.470160 CACTCATTTTGCTTCGTATGTAGTC 58.530 40.000 0.00 0.00 0.00 2.59
3904 4278 8.164070 ACCAAGTCCTTATCTAGTGACAATTTT 58.836 33.333 0.00 0.00 30.75 1.82
3957 4332 6.546034 GCCAATCACCATACATACCTACTTTT 59.454 38.462 0.00 0.00 0.00 2.27
3966 4341 3.461458 TCCCTTGCCAATCACCATACATA 59.539 43.478 0.00 0.00 0.00 2.29
3967 4342 2.244510 TCCCTTGCCAATCACCATACAT 59.755 45.455 0.00 0.00 0.00 2.29
4071 4446 0.529378 GTGCATCCCAGCTTTCAAGG 59.471 55.000 0.00 0.00 34.99 3.61
4074 4449 1.246056 GCAGTGCATCCCAGCTTTCA 61.246 55.000 11.09 0.00 34.99 2.69
4128 4503 4.583073 TGGAAGAAAGAGTTAACCTTTGGC 59.417 41.667 20.07 11.01 34.33 4.52
4145 4520 6.884472 TGTCCATATAAGAAGGTTGGAAGA 57.116 37.500 0.00 0.00 38.16 2.87
4226 4601 0.884704 TCTTCACGGTGCAAAGAGGC 60.885 55.000 2.51 0.00 0.00 4.70
4251 4626 9.155975 AGAGGCAAAATGATATACATCGATTAC 57.844 33.333 0.00 0.00 38.38 1.89
4348 4730 0.183252 ACTAGGACGGAGGGAGTAGC 59.817 60.000 0.00 0.00 0.00 3.58
4349 4731 1.212441 ACACTAGGACGGAGGGAGTAG 59.788 57.143 0.00 0.00 0.00 2.57
4350 4732 1.211457 GACACTAGGACGGAGGGAGTA 59.789 57.143 0.00 0.00 0.00 2.59
4351 4733 0.034283 GACACTAGGACGGAGGGAGT 60.034 60.000 0.00 0.00 0.00 3.85
4352 4734 0.034380 TGACACTAGGACGGAGGGAG 60.034 60.000 0.00 0.00 0.00 4.30
4353 4735 0.406750 TTGACACTAGGACGGAGGGA 59.593 55.000 0.00 0.00 0.00 4.20
4354 4736 1.263356 TTTGACACTAGGACGGAGGG 58.737 55.000 0.00 0.00 0.00 4.30
4355 4737 3.064931 GTTTTTGACACTAGGACGGAGG 58.935 50.000 0.00 0.00 0.00 4.30
4356 4738 2.729882 CGTTTTTGACACTAGGACGGAG 59.270 50.000 0.00 0.00 0.00 4.63
4357 4739 2.101249 ACGTTTTTGACACTAGGACGGA 59.899 45.455 0.00 0.00 33.74 4.69
4358 4740 2.476821 ACGTTTTTGACACTAGGACGG 58.523 47.619 0.00 0.00 33.74 4.79
4359 4741 3.800506 AGAACGTTTTTGACACTAGGACG 59.199 43.478 0.46 0.00 35.39 4.79
4360 4742 5.729974 AAGAACGTTTTTGACACTAGGAC 57.270 39.130 0.46 0.00 0.00 3.85
4361 4743 9.715121 AATATAAGAACGTTTTTGACACTAGGA 57.285 29.630 13.87 0.00 0.00 2.94
4366 4748 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
4367 4749 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
4368 4750 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
4369 4751 9.451002 TGTCCCATAATATAAGAACGTTTTTGA 57.549 29.630 13.87 2.81 0.00 2.69
4370 4752 9.716507 CTGTCCCATAATATAAGAACGTTTTTG 57.283 33.333 13.87 0.00 0.00 2.44
4371 4753 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
4372 4754 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
4373 4755 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
4374 4756 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
4375 4757 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
4376 4758 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
4377 4759 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
4378 4760 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
4379 4761 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
4380 4762 8.116669 TCTACTCCCTCTGTCCCATAATATAAG 58.883 40.741 0.00 0.00 0.00 1.73
4381 4763 8.008104 TCTACTCCCTCTGTCCCATAATATAA 57.992 38.462 0.00 0.00 0.00 0.98
4382 4764 7.599353 TCTACTCCCTCTGTCCCATAATATA 57.401 40.000 0.00 0.00 0.00 0.86
4383 4765 6.485388 TCTACTCCCTCTGTCCCATAATAT 57.515 41.667 0.00 0.00 0.00 1.28
4384 4766 5.942977 TCTACTCCCTCTGTCCCATAATA 57.057 43.478 0.00 0.00 0.00 0.98
4385 4767 4.834406 TCTACTCCCTCTGTCCCATAAT 57.166 45.455 0.00 0.00 0.00 1.28
4386 4768 4.170053 TGATCTACTCCCTCTGTCCCATAA 59.830 45.833 0.00 0.00 0.00 1.90
4387 4769 3.727391 TGATCTACTCCCTCTGTCCCATA 59.273 47.826 0.00 0.00 0.00 2.74
4388 4770 2.520120 TGATCTACTCCCTCTGTCCCAT 59.480 50.000 0.00 0.00 0.00 4.00
4389 4771 1.930204 TGATCTACTCCCTCTGTCCCA 59.070 52.381 0.00 0.00 0.00 4.37
4390 4772 2.091555 AGTGATCTACTCCCTCTGTCCC 60.092 54.545 0.00 0.00 33.17 4.46
4391 4773 2.955660 CAGTGATCTACTCCCTCTGTCC 59.044 54.545 0.00 0.00 37.60 4.02
4392 4774 2.955660 CCAGTGATCTACTCCCTCTGTC 59.044 54.545 0.00 0.00 37.60 3.51
4393 4775 2.583101 TCCAGTGATCTACTCCCTCTGT 59.417 50.000 0.00 0.00 37.60 3.41
4394 4776 3.304911 TCCAGTGATCTACTCCCTCTG 57.695 52.381 0.00 0.00 37.60 3.35
4395 4777 5.671463 TTATCCAGTGATCTACTCCCTCT 57.329 43.478 0.00 0.00 37.60 3.69
4396 4778 6.732896 TTTTATCCAGTGATCTACTCCCTC 57.267 41.667 0.00 0.00 37.60 4.30
4439 4833 5.574443 GCAATTCAATTGGAGTTTAGAGCAC 59.426 40.000 12.14 0.00 40.57 4.40
4444 4838 9.727627 GATCTAAGCAATTCAATTGGAGTTTAG 57.272 33.333 12.14 10.42 40.57 1.85
4508 4902 7.163441 AGAAAGGCACATTGATTGCTAAAAAT 58.837 30.769 0.00 0.00 40.07 1.82
4730 5124 9.539825 CTATCTGAGCTTTTGTATGAGTACATT 57.460 33.333 0.00 0.00 40.35 2.71
4757 5151 4.681978 GCAACCCACTCTCGGCGT 62.682 66.667 6.85 0.00 0.00 5.68
4924 5323 6.920758 CGGGTGAAAAATGATGAACAACTAAA 59.079 34.615 0.00 0.00 0.00 1.85
4949 5348 5.004922 TGAACAACTTTCCAACATGAACC 57.995 39.130 0.00 0.00 0.00 3.62
4973 5372 3.897239 ACATGAACTGGGTGAAGAAACA 58.103 40.909 0.00 0.00 0.00 2.83
5008 5407 4.031611 GGGAGACAGTAGAAGGGTATTGT 58.968 47.826 0.00 0.00 0.00 2.71
5014 5413 0.818296 CACGGGAGACAGTAGAAGGG 59.182 60.000 0.00 0.00 36.26 3.95
5021 5420 3.703001 ATTCAATTCACGGGAGACAGT 57.297 42.857 0.00 0.00 40.29 3.55
5027 5426 6.706270 GCTCTAGATTTATTCAATTCACGGGA 59.294 38.462 0.00 0.00 0.00 5.14
5028 5427 6.708054 AGCTCTAGATTTATTCAATTCACGGG 59.292 38.462 0.00 0.00 0.00 5.28
5029 5428 7.655328 AGAGCTCTAGATTTATTCAATTCACGG 59.345 37.037 16.50 0.00 0.00 4.94
5030 5429 8.586570 AGAGCTCTAGATTTATTCAATTCACG 57.413 34.615 16.50 0.00 0.00 4.35
5048 5447 9.487790 GAGCAAAATACATCTTATTAGAGCTCT 57.512 33.333 22.17 22.17 35.17 4.09
5054 5453 9.208022 TCCGATGAGCAAAATACATCTTATTAG 57.792 33.333 0.00 0.00 38.43 1.73
5200 5606 5.343307 AAGAACAGGATGCTTGTGTTTTT 57.657 34.783 0.00 0.00 42.53 1.94
5215 5621 9.399403 GCTAAAGTGAAAATCCTTTAAGAACAG 57.601 33.333 0.00 0.00 33.91 3.16
5378 5788 9.577110 CAAAATGTAGTAGGAATACGTGTAAGA 57.423 33.333 0.00 0.00 0.00 2.10
5491 5901 2.928334 AGAATGAATGTGCTAGGCTGG 58.072 47.619 0.00 0.00 0.00 4.85
5494 5904 4.260948 GCAAGTAGAATGAATGTGCTAGGC 60.261 45.833 0.00 0.00 0.00 3.93
5535 6754 7.531857 TTGAATTGGGTGCAAGTAAAGATAA 57.468 32.000 0.00 0.00 0.00 1.75
5536 6755 7.531857 TTTGAATTGGGTGCAAGTAAAGATA 57.468 32.000 0.00 0.00 0.00 1.98
5588 6809 0.592637 ATCCAATGCGTGTGTGTGTG 59.407 50.000 0.00 0.00 0.00 3.82
5598 6819 8.856247 CAAATGTCAATATATGAATCCAATGCG 58.144 33.333 0.00 0.00 40.50 4.73
5651 6899 6.293735 CCAAATGATTTTGACATTGCAAGCTT 60.294 34.615 4.94 0.00 44.11 3.74
5726 7014 1.205893 GACGAAGGGAGTGCTGAGAAT 59.794 52.381 0.00 0.00 0.00 2.40
5734 7022 6.338146 TCTTATATTTGTGACGAAGGGAGTG 58.662 40.000 0.00 0.00 0.00 3.51
5771 7059 9.976511 TTCTATCCGTTTGTAGTCCATATTAAG 57.023 33.333 0.00 0.00 0.00 1.85
5800 7088 6.004408 ACGTTTTAGTGTGTTTGTTCACTT 57.996 33.333 3.25 0.00 43.39 3.16
5850 7143 7.067008 CCCTCCGTTCACAAATATAAGATGTTT 59.933 37.037 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.