Multiple sequence alignment - TraesCS4D01G245300

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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 TraesCS4D01G245300 chr4D 100.000 5782 0 0 1 5782 412718734 412712953 0.000000e+00 10678
1 TraesCS4D01G245300 chr4A 94.819 3590 111 32 1 3537 51136937 51140504 0.000000e+00 5529
2 TraesCS4D01G245300 chr4A 94.421 1685 66 12 3514 5178 51140687 51142363 0.000000e+00 2566
3 TraesCS4D01G245300 chr4A 93.952 248 12 3 5533 5778 51142403 51142649 7.080000e-99 372
4 TraesCS4D01G245300 chr4B 95.331 2163 72 17 1 2149 509038335 509036188 0.000000e+00 3408
5 TraesCS4D01G245300 chr4B 90.324 1788 119 18 3364 5133 509034822 509033071 0.000000e+00 2294
6 TraesCS4D01G245300 chr4B 92.857 896 45 9 2109 2999 509036178 509035297 0.000000e+00 1282
7 TraesCS4D01G245300 chr4B 93.386 378 23 2 2992 3369 509035238 509034863 5.060000e-155 558
8 TraesCS4D01G245300 chr4B 87.773 229 23 3 5554 5781 509008268 509008044 4.440000e-66 263
9 TraesCS4D01G245300 chr3D 90.836 371 29 5 5177 5544 6302294 6302662 5.210000e-135 492
10 TraesCS4D01G245300 chr3D 90.541 370 26 6 5180 5544 545256791 545256426 1.130000e-131 481
11 TraesCS4D01G245300 chr3D 89.577 355 30 6 5186 5537 418215947 418216297 1.480000e-120 444
12 TraesCS4D01G245300 chr2D 90.054 372 28 7 5177 5544 564703807 564704173 1.890000e-129 473
13 TraesCS4D01G245300 chr5B 90.251 359 27 6 5180 5535 521138081 521137728 4.080000e-126 462
14 TraesCS4D01G245300 chr6D 90.671 343 26 5 5180 5518 392524772 392525112 8.830000e-123 451
15 TraesCS4D01G245300 chr1D 88.705 363 31 7 5178 5537 491403664 491404019 8.900000e-118 435
16 TraesCS4D01G245300 chr1D 88.378 370 30 7 5185 5544 33857249 33857615 3.200000e-117 433
17 TraesCS4D01G245300 chr5A 88.366 361 35 5 5180 5537 564772676 564772320 1.490000e-115 427


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 TraesCS4D01G245300 chr4D 412712953 412718734 5781 True 10678.000000 10678 100.000000 1 5782 1 chr4D.!!$R1 5781
1 TraesCS4D01G245300 chr4A 51136937 51142649 5712 False 2822.333333 5529 94.397333 1 5778 3 chr4A.!!$F1 5777
2 TraesCS4D01G245300 chr4B 509033071 509038335 5264 True 1885.500000 3408 92.974500 1 5133 4 chr4B.!!$R2 5132


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
729 737 0.455633 GTGTCCGTCTAACGATGCGT 60.456 55.000 0.24 0.0 46.05 5.24 F
891 916 0.760945 CTCCTACCCTCCGCATCCTT 60.761 60.000 0.00 0.0 0.00 3.36 F
2326 2427 0.754217 CTCCTGTGCATTCATGGGGG 60.754 60.000 0.00 0.0 0.00 5.40 F
2828 2941 1.151668 CAGAGAAGAAACACCGCCTG 58.848 55.000 0.00 0.0 0.00 4.85 F
3639 4073 1.334059 GCACACCACACGAATTGACTG 60.334 52.381 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 1978 0.032267 GCTACCTATCCTGCACCGTC 59.968 60.000 0.0 0.0 0.00 4.79 R
2337 2444 0.331278 AAGAACCATGAATGCCCCGA 59.669 50.000 0.0 0.0 0.00 5.14 R
3736 4171 0.988832 CCTAGGCAACAACCCCACTA 59.011 55.000 0.0 0.0 41.41 2.74 R
4419 4870 1.070758 CATGTAGGGGGAGAATGGACG 59.929 57.143 0.0 0.0 0.00 4.79 R
5205 5669 0.031721 GTTCGTATAGGGGTGCGGAG 59.968 60.000 0.0 0.0 0.00 4.63 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
77 78 4.657504 TGATAGAGCATCAGATGGGAACTT 59.342 41.667 12.54 0.00 38.79 2.66
129 130 1.899534 CCCCTCGGAGATCGACCTC 60.900 68.421 6.58 0.00 43.74 3.85
130 131 1.149627 CCCTCGGAGATCGACCTCT 59.850 63.158 6.78 0.00 43.74 3.69
196 197 3.256879 ACATCGCAGTACATAGGATCCTG 59.743 47.826 25.28 12.09 0.00 3.86
286 288 2.295349 TCCTCACAGTACTCGACCAAAC 59.705 50.000 0.00 0.00 0.00 2.93
330 332 5.125097 TCAAACTACTCAAGTCGATCTACCC 59.875 44.000 0.00 0.00 37.50 3.69
556 564 0.489567 CTAGGATGGAGGGGCTAGGT 59.510 60.000 0.00 0.00 0.00 3.08
575 583 3.791586 GGAGGAGGTGGAGCAGGC 61.792 72.222 0.00 0.00 0.00 4.85
576 584 3.791586 GAGGAGGTGGAGCAGGCC 61.792 72.222 0.00 0.00 0.00 5.19
654 662 4.089239 TGCGAGTATGCGGGGCAA 62.089 61.111 0.00 0.00 43.62 4.52
721 729 4.571919 CAACTTTATGGGTGTCCGTCTAA 58.428 43.478 0.00 0.00 35.24 2.10
729 737 0.455633 GTGTCCGTCTAACGATGCGT 60.456 55.000 0.24 0.00 46.05 5.24
884 909 2.444140 CCACCCTCCTACCCTCCG 60.444 72.222 0.00 0.00 0.00 4.63
891 916 0.760945 CTCCTACCCTCCGCATCCTT 60.761 60.000 0.00 0.00 0.00 3.36
913 938 1.630244 CTTCTGTTGGCTCTTCGCGG 61.630 60.000 6.13 0.00 40.44 6.46
1099 1125 1.046204 AAACTCCTCGAGAAACCGGT 58.954 50.000 15.71 0.00 33.32 5.28
1217 1244 1.078143 GCCAGATCAGTCCGGCTTT 60.078 57.895 0.00 0.00 41.50 3.51
1263 1290 6.612741 AGGAGGGGACACTTACTAGTATTAG 58.387 44.000 2.79 1.65 31.96 1.73
1374 1401 4.292186 AGCTAGTGTGTCATGTTCCATT 57.708 40.909 0.00 0.00 0.00 3.16
1429 1456 7.829211 CCAGACCTCCATACTCTTTATTTTTCA 59.171 37.037 0.00 0.00 0.00 2.69
1568 1595 2.430546 TGCACAAATTAACAAGGGCG 57.569 45.000 0.00 0.00 0.00 6.13
1883 1917 8.887264 TTAATTTGGGGTTTATCTTCTTGCTA 57.113 30.769 0.00 0.00 0.00 3.49
1944 1978 4.202070 GGAGAGAGAAAGTAATGAGGACGG 60.202 50.000 0.00 0.00 0.00 4.79
1958 1992 1.065928 GACGGACGGTGCAGGATAG 59.934 63.158 0.00 0.00 0.00 2.08
1960 1994 2.423898 CGGACGGTGCAGGATAGGT 61.424 63.158 0.00 0.00 0.00 3.08
2106 2148 6.479990 GCCTTTTCTTTGCTATCTTTGTTTGT 59.520 34.615 0.00 0.00 0.00 2.83
2118 2218 4.626042 TCTTTGTTTGTGCTCTCTCTCTC 58.374 43.478 0.00 0.00 0.00 3.20
2119 2219 4.343526 TCTTTGTTTGTGCTCTCTCTCTCT 59.656 41.667 0.00 0.00 0.00 3.10
2120 2220 3.932545 TGTTTGTGCTCTCTCTCTCTC 57.067 47.619 0.00 0.00 0.00 3.20
2121 2221 3.495331 TGTTTGTGCTCTCTCTCTCTCT 58.505 45.455 0.00 0.00 0.00 3.10
2122 2222 3.505680 TGTTTGTGCTCTCTCTCTCTCTC 59.494 47.826 0.00 0.00 0.00 3.20
2123 2223 3.719268 TTGTGCTCTCTCTCTCTCTCT 57.281 47.619 0.00 0.00 0.00 3.10
2124 2224 3.266510 TGTGCTCTCTCTCTCTCTCTC 57.733 52.381 0.00 0.00 0.00 3.20
2125 2225 2.840038 TGTGCTCTCTCTCTCTCTCTCT 59.160 50.000 0.00 0.00 0.00 3.10
2326 2427 0.754217 CTCCTGTGCATTCATGGGGG 60.754 60.000 0.00 0.00 0.00 5.40
2525 2636 2.158667 ACATATTTCCGGCTGTTAGGGG 60.159 50.000 0.00 0.00 0.00 4.79
2828 2941 1.151668 CAGAGAAGAAACACCGCCTG 58.848 55.000 0.00 0.00 0.00 4.85
2912 3025 5.300034 TGTTCAAATGCATCATACATCCCTC 59.700 40.000 0.00 0.00 0.00 4.30
2921 3034 6.014584 TGCATCATACATCCCTCGTACTATTT 60.015 38.462 0.00 0.00 0.00 1.40
3000 3178 5.753921 CGGCCCTTATTTAACTGAGTCTTAG 59.246 44.000 0.00 0.00 0.00 2.18
3117 3295 6.545666 CCAGTGGTACAATATATTGAAGCCAA 59.454 38.462 28.13 14.68 44.16 4.52
3132 3310 4.891168 TGAAGCCAACATATAGGTAGTCGA 59.109 41.667 0.00 0.00 0.00 4.20
3300 3478 7.827701 TGCACAAACCATATTTTCCGTATAAA 58.172 30.769 0.00 0.00 0.00 1.40
3342 3520 5.131067 TCTAACATGCTACCACGAGATACT 58.869 41.667 0.00 0.00 0.00 2.12
3381 3605 9.688592 GGCTTATTAATTAGTAAACGAGCTAGA 57.311 33.333 0.00 0.00 31.12 2.43
3439 3664 1.345415 CTTGCCTTGCCAGTTTGGAAT 59.655 47.619 0.00 0.00 40.96 3.01
3448 3673 4.415596 TGCCAGTTTGGAATCAAGGTAAT 58.584 39.130 0.00 0.00 40.96 1.89
3571 4005 8.421002 ACCACATTATAAATTAAATCAGTGGGC 58.579 33.333 16.44 0.00 45.19 5.36
3572 4006 7.872483 CCACATTATAAATTAAATCAGTGGGCC 59.128 37.037 0.00 0.00 39.18 5.80
3581 4015 2.457813 ATCAGTGGGCCAAATGCATA 57.542 45.000 8.40 0.00 43.89 3.14
3639 4073 1.334059 GCACACCACACGAATTGACTG 60.334 52.381 0.00 0.00 0.00 3.51
3781 4216 7.610580 ACCCAACAATTTTCTCAAATCCTTA 57.389 32.000 0.00 0.00 30.80 2.69
3984 4425 6.404293 GGCACATGTCGAACTAACCATTAATT 60.404 38.462 0.00 0.00 0.00 1.40
3985 4426 7.201661 GGCACATGTCGAACTAACCATTAATTA 60.202 37.037 0.00 0.00 0.00 1.40
3986 4427 8.178964 GCACATGTCGAACTAACCATTAATTAA 58.821 33.333 0.00 0.00 0.00 1.40
4068 4509 7.121315 GTGCCTTGAGGTCAGTTTTAATTAGAT 59.879 37.037 0.00 0.00 37.57 1.98
4073 4514 8.380742 TGAGGTCAGTTTTAATTAGATCTCCT 57.619 34.615 0.00 0.00 36.00 3.69
4151 4596 2.092968 AGTCCTTCACAACACTGCTTGA 60.093 45.455 0.00 0.00 0.00 3.02
4187 4634 2.300152 TGAGATATAGCAGGGCCGAAAG 59.700 50.000 0.00 0.00 0.00 2.62
4419 4870 5.340138 GCTGCTAAGAACGTAAGATCGATAC 59.660 44.000 0.00 0.00 44.80 2.24
4462 4914 3.214328 TGTTCAGCTTTTCCTCCAGTTC 58.786 45.455 0.00 0.00 0.00 3.01
4478 4930 9.231297 TCCTCCAGTTCAATTATTTACTGAAAG 57.769 33.333 14.73 11.86 40.24 2.62
4479 4931 8.462016 CCTCCAGTTCAATTATTTACTGAAAGG 58.538 37.037 14.73 15.14 40.24 3.11
4503 4955 6.258160 GTCTAAAACAATCCCATTGATCACG 58.742 40.000 0.00 0.00 42.83 4.35
4594 5046 2.752807 GCCCCGGAGCCCAGAATAA 61.753 63.158 0.73 0.00 0.00 1.40
4724 5176 2.063378 GTAGCTGCAGGAGAGGGCT 61.063 63.158 17.12 7.77 37.08 5.19
4797 5249 3.438087 CGCCTAAGGAATCATAAGCATGG 59.562 47.826 0.00 0.00 32.61 3.66
4902 5354 3.708930 ATGCATAAGCGCACGCGTTTT 62.709 47.619 18.29 12.53 46.56 2.43
4991 5443 1.337703 TGTTGTTGGAGCGTACGTACT 59.662 47.619 22.55 6.08 0.00 2.73
4995 5447 1.069022 GTTGGAGCGTACGTACTCACA 60.069 52.381 22.55 14.88 34.48 3.58
5062 5515 7.800380 CGAAATTGTTCTTGGCTGTATATCATC 59.200 37.037 0.00 0.00 0.00 2.92
5179 5643 8.827177 TTTATTATGTACCTAGCCTTTGATCG 57.173 34.615 0.00 0.00 0.00 3.69
5180 5644 3.753294 ATGTACCTAGCCTTTGATCGG 57.247 47.619 0.00 0.00 0.00 4.18
5181 5645 2.742348 TGTACCTAGCCTTTGATCGGA 58.258 47.619 0.00 0.00 0.00 4.55
5182 5646 2.429610 TGTACCTAGCCTTTGATCGGAC 59.570 50.000 0.00 0.00 0.00 4.79
5183 5647 0.831307 ACCTAGCCTTTGATCGGACC 59.169 55.000 0.00 0.00 0.00 4.46
5184 5648 0.830648 CCTAGCCTTTGATCGGACCA 59.169 55.000 0.00 0.00 0.00 4.02
5185 5649 1.202580 CCTAGCCTTTGATCGGACCAG 60.203 57.143 0.00 0.00 0.00 4.00
5186 5650 0.830648 TAGCCTTTGATCGGACCAGG 59.169 55.000 0.00 0.00 0.00 4.45
5187 5651 0.909610 AGCCTTTGATCGGACCAGGA 60.910 55.000 0.00 0.00 0.00 3.86
5189 5653 1.408822 GCCTTTGATCGGACCAGGATT 60.409 52.381 0.00 0.00 0.00 3.01
5190 5654 2.945890 GCCTTTGATCGGACCAGGATTT 60.946 50.000 0.00 0.00 0.00 2.17
5201 5665 2.772739 CAGGATTTGGAGCACTCGG 58.227 57.895 0.00 0.00 0.00 4.63
5202 5666 0.745845 CAGGATTTGGAGCACTCGGG 60.746 60.000 0.00 0.00 0.00 5.14
5204 5668 1.026718 GGATTTGGAGCACTCGGGTG 61.027 60.000 12.23 12.23 45.53 4.61
5220 5684 3.546009 TGCTCCGCACCCCTATAC 58.454 61.111 0.00 0.00 31.71 1.47
5221 5685 2.338984 GCTCCGCACCCCTATACG 59.661 66.667 0.00 0.00 0.00 3.06
5222 5686 2.198287 GCTCCGCACCCCTATACGA 61.198 63.158 0.00 0.00 0.00 3.43
5223 5687 1.741327 GCTCCGCACCCCTATACGAA 61.741 60.000 0.00 0.00 0.00 3.85
5224 5688 0.031721 CTCCGCACCCCTATACGAAC 59.968 60.000 0.00 0.00 0.00 3.95
5225 5689 0.683828 TCCGCACCCCTATACGAACA 60.684 55.000 0.00 0.00 0.00 3.18
5226 5690 0.176219 CCGCACCCCTATACGAACAA 59.824 55.000 0.00 0.00 0.00 2.83
5227 5691 1.202604 CCGCACCCCTATACGAACAAT 60.203 52.381 0.00 0.00 0.00 2.71
5228 5692 2.557317 CGCACCCCTATACGAACAATT 58.443 47.619 0.00 0.00 0.00 2.32
5229 5693 2.542595 CGCACCCCTATACGAACAATTC 59.457 50.000 0.00 0.00 0.00 2.17
5230 5694 3.537580 GCACCCCTATACGAACAATTCA 58.462 45.455 0.00 0.00 0.00 2.57
5231 5695 4.134563 GCACCCCTATACGAACAATTCAT 58.865 43.478 0.00 0.00 0.00 2.57
5232 5696 4.578928 GCACCCCTATACGAACAATTCATT 59.421 41.667 0.00 0.00 0.00 2.57
5233 5697 5.067283 GCACCCCTATACGAACAATTCATTT 59.933 40.000 0.00 0.00 0.00 2.32
5234 5698 6.261381 GCACCCCTATACGAACAATTCATTTA 59.739 38.462 0.00 0.00 0.00 1.40
5235 5699 7.201750 GCACCCCTATACGAACAATTCATTTAA 60.202 37.037 0.00 0.00 0.00 1.52
5236 5700 8.679100 CACCCCTATACGAACAATTCATTTAAA 58.321 33.333 0.00 0.00 0.00 1.52
5237 5701 9.245481 ACCCCTATACGAACAATTCATTTAAAA 57.755 29.630 0.00 0.00 0.00 1.52
5283 5747 6.710499 AAAAATGGGATTTTGGGGTATCAA 57.290 33.333 0.00 0.00 41.30 2.57
5284 5748 6.710499 AAAATGGGATTTTGGGGTATCAAA 57.290 33.333 0.00 0.00 40.69 2.69
5285 5749 5.692115 AATGGGATTTTGGGGTATCAAAC 57.308 39.130 0.00 0.00 36.49 2.93
5286 5750 3.093057 TGGGATTTTGGGGTATCAAACG 58.907 45.455 0.00 0.00 36.49 3.60
5287 5751 3.093814 GGGATTTTGGGGTATCAAACGT 58.906 45.455 0.00 0.00 36.49 3.99
5288 5752 3.119280 GGGATTTTGGGGTATCAAACGTG 60.119 47.826 0.00 0.00 36.49 4.49
5289 5753 3.119280 GGATTTTGGGGTATCAAACGTGG 60.119 47.826 0.00 0.00 36.49 4.94
5290 5754 1.912417 TTTGGGGTATCAAACGTGGG 58.088 50.000 0.00 0.00 32.39 4.61
5291 5755 0.772384 TTGGGGTATCAAACGTGGGT 59.228 50.000 0.00 0.00 0.00 4.51
5292 5756 0.772384 TGGGGTATCAAACGTGGGTT 59.228 50.000 0.00 0.00 38.22 4.11
5293 5757 1.271488 TGGGGTATCAAACGTGGGTTC 60.271 52.381 0.00 0.00 34.62 3.62
5294 5758 1.456296 GGGTATCAAACGTGGGTTCC 58.544 55.000 0.00 0.00 34.62 3.62
5295 5759 1.456296 GGTATCAAACGTGGGTTCCC 58.544 55.000 0.12 0.12 34.62 3.97
5296 5760 1.081094 GTATCAAACGTGGGTTCCCG 58.919 55.000 3.27 0.00 34.62 5.14
5297 5761 0.975135 TATCAAACGTGGGTTCCCGA 59.025 50.000 3.27 0.00 34.62 5.14
5298 5762 0.326927 ATCAAACGTGGGTTCCCGAT 59.673 50.000 3.27 0.00 34.62 4.18
5299 5763 0.320946 TCAAACGTGGGTTCCCGATC 60.321 55.000 3.27 0.00 34.62 3.69
5300 5764 0.321298 CAAACGTGGGTTCCCGATCT 60.321 55.000 3.27 0.00 34.62 2.75
5301 5765 1.066716 CAAACGTGGGTTCCCGATCTA 60.067 52.381 3.27 0.00 34.62 1.98
5302 5766 0.822164 AACGTGGGTTCCCGATCTAG 59.178 55.000 3.27 0.00 0.00 2.43
5303 5767 0.324091 ACGTGGGTTCCCGATCTAGT 60.324 55.000 3.27 0.00 0.00 2.57
5304 5768 0.384669 CGTGGGTTCCCGATCTAGTC 59.615 60.000 3.27 0.00 0.00 2.59
5305 5769 0.751452 GTGGGTTCCCGATCTAGTCC 59.249 60.000 3.27 0.00 0.00 3.85
5306 5770 0.398098 TGGGTTCCCGATCTAGTCCC 60.398 60.000 3.27 0.00 0.00 4.46
5307 5771 1.461911 GGGTTCCCGATCTAGTCCCG 61.462 65.000 0.00 0.00 0.00 5.14
5308 5772 1.461911 GGTTCCCGATCTAGTCCCGG 61.462 65.000 0.00 0.00 42.64 5.73
5309 5773 0.754587 GTTCCCGATCTAGTCCCGGT 60.755 60.000 0.00 0.00 41.53 5.28
5310 5774 0.754217 TTCCCGATCTAGTCCCGGTG 60.754 60.000 0.00 0.00 41.53 4.94
5311 5775 1.152819 CCCGATCTAGTCCCGGTGA 60.153 63.158 0.00 0.00 41.53 4.02
5312 5776 0.754217 CCCGATCTAGTCCCGGTGAA 60.754 60.000 0.00 0.00 41.53 3.18
5313 5777 1.108776 CCGATCTAGTCCCGGTGAAA 58.891 55.000 0.00 0.00 38.55 2.69
5314 5778 1.687123 CCGATCTAGTCCCGGTGAAAT 59.313 52.381 0.00 0.00 38.55 2.17
5315 5779 2.102588 CCGATCTAGTCCCGGTGAAATT 59.897 50.000 0.00 0.00 38.55 1.82
5316 5780 3.431766 CCGATCTAGTCCCGGTGAAATTT 60.432 47.826 0.00 0.00 38.55 1.82
5317 5781 3.802685 CGATCTAGTCCCGGTGAAATTTC 59.197 47.826 11.41 11.41 0.00 2.17
5318 5782 3.241067 TCTAGTCCCGGTGAAATTTCG 57.759 47.619 13.34 2.41 0.00 3.46
5319 5783 2.564062 TCTAGTCCCGGTGAAATTTCGT 59.436 45.455 13.34 0.00 0.00 3.85
5320 5784 1.519408 AGTCCCGGTGAAATTTCGTG 58.481 50.000 13.34 5.57 0.00 4.35
5321 5785 1.071071 AGTCCCGGTGAAATTTCGTGA 59.929 47.619 13.34 2.89 0.00 4.35
5322 5786 1.874872 GTCCCGGTGAAATTTCGTGAA 59.125 47.619 13.34 0.00 0.00 3.18
5323 5787 2.291190 GTCCCGGTGAAATTTCGTGAAA 59.709 45.455 13.34 0.00 34.46 2.69
5324 5788 2.950309 TCCCGGTGAAATTTCGTGAAAA 59.050 40.909 13.34 0.00 33.56 2.29
5325 5789 3.380637 TCCCGGTGAAATTTCGTGAAAAA 59.619 39.130 13.34 0.00 33.56 1.94
5359 5823 5.797909 CGTATTCGTGCAAAAATGACAAA 57.202 34.783 0.00 0.00 0.00 2.83
5360 5824 6.191534 CGTATTCGTGCAAAAATGACAAAA 57.808 33.333 0.00 0.00 0.00 2.44
5361 5825 6.281056 CGTATTCGTGCAAAAATGACAAAAG 58.719 36.000 0.00 0.00 0.00 2.27
5362 5826 6.075099 CGTATTCGTGCAAAAATGACAAAAGT 60.075 34.615 0.00 0.00 0.00 2.66
5363 5827 6.660887 ATTCGTGCAAAAATGACAAAAGTT 57.339 29.167 0.00 0.00 0.00 2.66
5364 5828 6.473397 TTCGTGCAAAAATGACAAAAGTTT 57.527 29.167 0.00 0.00 0.00 2.66
5365 5829 6.088719 TCGTGCAAAAATGACAAAAGTTTC 57.911 33.333 0.00 0.00 0.00 2.78
5366 5830 5.062809 TCGTGCAAAAATGACAAAAGTTTCC 59.937 36.000 0.00 0.00 0.00 3.13
5367 5831 5.063312 CGTGCAAAAATGACAAAAGTTTCCT 59.937 36.000 0.00 0.00 0.00 3.36
5368 5832 6.254589 CGTGCAAAAATGACAAAAGTTTCCTA 59.745 34.615 0.00 0.00 0.00 2.94
5369 5833 7.042791 CGTGCAAAAATGACAAAAGTTTCCTAT 60.043 33.333 0.00 0.00 0.00 2.57
5370 5834 8.063630 GTGCAAAAATGACAAAAGTTTCCTATG 58.936 33.333 0.00 0.00 0.00 2.23
5371 5835 7.768120 TGCAAAAATGACAAAAGTTTCCTATGT 59.232 29.630 0.00 0.00 0.00 2.29
5372 5836 9.255304 GCAAAAATGACAAAAGTTTCCTATGTA 57.745 29.630 0.00 0.00 0.00 2.29
5405 5869 8.856153 AAAAACTGTTTGGGTAGATTTTTGTT 57.144 26.923 6.53 0.00 28.49 2.83
5406 5870 8.487313 AAAACTGTTTGGGTAGATTTTTGTTC 57.513 30.769 6.53 0.00 0.00 3.18
5407 5871 5.827666 ACTGTTTGGGTAGATTTTTGTTCG 58.172 37.500 0.00 0.00 0.00 3.95
5408 5872 5.189659 TGTTTGGGTAGATTTTTGTTCGG 57.810 39.130 0.00 0.00 0.00 4.30
5409 5873 4.888239 TGTTTGGGTAGATTTTTGTTCGGA 59.112 37.500 0.00 0.00 0.00 4.55
5410 5874 5.217393 GTTTGGGTAGATTTTTGTTCGGAC 58.783 41.667 0.00 0.00 0.00 4.79
5411 5875 4.088056 TGGGTAGATTTTTGTTCGGACA 57.912 40.909 0.00 0.00 0.00 4.02
5412 5876 4.069304 TGGGTAGATTTTTGTTCGGACAG 58.931 43.478 0.00 0.00 37.04 3.51
5413 5877 4.070009 GGGTAGATTTTTGTTCGGACAGT 58.930 43.478 0.00 0.00 37.04 3.55
5414 5878 5.221682 TGGGTAGATTTTTGTTCGGACAGTA 60.222 40.000 0.00 0.00 37.04 2.74
5415 5879 5.878669 GGGTAGATTTTTGTTCGGACAGTAT 59.121 40.000 0.00 0.00 37.04 2.12
5416 5880 6.373495 GGGTAGATTTTTGTTCGGACAGTATT 59.627 38.462 0.00 0.00 37.04 1.89
5417 5881 7.094506 GGGTAGATTTTTGTTCGGACAGTATTT 60.095 37.037 0.00 0.00 37.04 1.40
5418 5882 7.961283 GGTAGATTTTTGTTCGGACAGTATTTC 59.039 37.037 0.00 0.00 37.04 2.17
5419 5883 6.909909 AGATTTTTGTTCGGACAGTATTTCC 58.090 36.000 0.00 0.00 37.04 3.13
5420 5884 6.715264 AGATTTTTGTTCGGACAGTATTTCCT 59.285 34.615 0.00 0.00 37.04 3.36
5421 5885 6.702716 TTTTTGTTCGGACAGTATTTCCTT 57.297 33.333 0.00 0.00 37.04 3.36
5422 5886 5.934935 TTTGTTCGGACAGTATTTCCTTC 57.065 39.130 0.00 0.00 37.04 3.46
5423 5887 3.581755 TGTTCGGACAGTATTTCCTTCG 58.418 45.455 0.00 0.00 0.00 3.79
5424 5888 2.288961 TCGGACAGTATTTCCTTCGC 57.711 50.000 0.00 0.00 0.00 4.70
5425 5889 1.134907 TCGGACAGTATTTCCTTCGCC 60.135 52.381 0.00 0.00 0.00 5.54
5426 5890 1.404986 CGGACAGTATTTCCTTCGCCA 60.405 52.381 0.00 0.00 0.00 5.69
5427 5891 2.007608 GGACAGTATTTCCTTCGCCAC 58.992 52.381 0.00 0.00 0.00 5.01
5428 5892 1.659098 GACAGTATTTCCTTCGCCACG 59.341 52.381 0.00 0.00 0.00 4.94
5429 5893 1.006832 CAGTATTTCCTTCGCCACGG 58.993 55.000 0.00 0.00 0.00 4.94
5430 5894 0.899720 AGTATTTCCTTCGCCACGGA 59.100 50.000 0.00 0.00 0.00 4.69
5431 5895 1.485066 AGTATTTCCTTCGCCACGGAT 59.515 47.619 0.00 0.00 0.00 4.18
5432 5896 2.696707 AGTATTTCCTTCGCCACGGATA 59.303 45.455 0.00 0.00 0.00 2.59
5433 5897 1.949465 ATTTCCTTCGCCACGGATAC 58.051 50.000 0.00 0.00 0.00 2.24
5473 5937 9.672086 TTTTTATGAAATTTCACACGGAACTAG 57.328 29.630 22.71 0.00 40.49 2.57
5474 5938 8.610248 TTTATGAAATTTCACACGGAACTAGA 57.390 30.769 22.71 2.18 40.49 2.43
5475 5939 8.786826 TTATGAAATTTCACACGGAACTAGAT 57.213 30.769 22.71 5.30 40.49 1.98
5476 5940 7.687941 ATGAAATTTCACACGGAACTAGATT 57.312 32.000 22.71 0.00 40.49 2.40
5477 5941 6.898041 TGAAATTTCACACGGAACTAGATTG 58.102 36.000 16.91 0.00 34.56 2.67
5478 5942 5.880054 AATTTCACACGGAACTAGATTGG 57.120 39.130 0.00 0.00 34.56 3.16
5479 5943 3.328382 TTCACACGGAACTAGATTGGG 57.672 47.619 0.00 0.00 0.00 4.12
5480 5944 2.531771 TCACACGGAACTAGATTGGGA 58.468 47.619 0.00 0.00 0.00 4.37
5481 5945 2.901192 TCACACGGAACTAGATTGGGAA 59.099 45.455 0.00 0.00 0.00 3.97
5482 5946 3.517901 TCACACGGAACTAGATTGGGAAT 59.482 43.478 0.00 0.00 0.00 3.01
5483 5947 3.623060 CACACGGAACTAGATTGGGAATG 59.377 47.826 0.00 0.00 0.00 2.67
5484 5948 2.614057 CACGGAACTAGATTGGGAATGC 59.386 50.000 0.00 0.00 0.00 3.56
5485 5949 2.238646 ACGGAACTAGATTGGGAATGCA 59.761 45.455 0.00 0.00 0.00 3.96
5486 5950 2.874701 CGGAACTAGATTGGGAATGCAG 59.125 50.000 0.00 0.00 0.00 4.41
5487 5951 3.217626 GGAACTAGATTGGGAATGCAGG 58.782 50.000 0.00 0.00 0.00 4.85
5488 5952 3.372025 GGAACTAGATTGGGAATGCAGGT 60.372 47.826 0.00 0.00 0.00 4.00
5489 5953 4.273318 GAACTAGATTGGGAATGCAGGTT 58.727 43.478 0.00 0.00 0.00 3.50
5490 5954 4.322057 ACTAGATTGGGAATGCAGGTTT 57.678 40.909 0.00 0.00 0.00 3.27
5491 5955 4.019174 ACTAGATTGGGAATGCAGGTTTG 58.981 43.478 0.00 0.00 0.00 2.93
5492 5956 3.173953 AGATTGGGAATGCAGGTTTGA 57.826 42.857 0.00 0.00 0.00 2.69
5493 5957 3.716431 AGATTGGGAATGCAGGTTTGAT 58.284 40.909 0.00 0.00 0.00 2.57
5494 5958 4.870636 AGATTGGGAATGCAGGTTTGATA 58.129 39.130 0.00 0.00 0.00 2.15
5495 5959 5.461327 AGATTGGGAATGCAGGTTTGATAT 58.539 37.500 0.00 0.00 0.00 1.63
5496 5960 5.537674 AGATTGGGAATGCAGGTTTGATATC 59.462 40.000 0.00 0.00 0.00 1.63
5497 5961 3.565307 TGGGAATGCAGGTTTGATATCC 58.435 45.455 0.00 0.00 0.00 2.59
5498 5962 2.893489 GGGAATGCAGGTTTGATATCCC 59.107 50.000 0.00 0.00 0.00 3.85
5499 5963 2.893489 GGAATGCAGGTTTGATATCCCC 59.107 50.000 0.00 0.00 0.00 4.81
5500 5964 3.565307 GAATGCAGGTTTGATATCCCCA 58.435 45.455 0.00 0.00 0.00 4.96
5501 5965 3.686227 ATGCAGGTTTGATATCCCCAA 57.314 42.857 0.00 0.00 0.00 4.12
5502 5966 3.464720 TGCAGGTTTGATATCCCCAAA 57.535 42.857 0.00 0.00 0.00 3.28
5503 5967 3.992999 TGCAGGTTTGATATCCCCAAAT 58.007 40.909 0.00 0.00 36.14 2.32
5504 5968 4.360889 TGCAGGTTTGATATCCCCAAATT 58.639 39.130 0.00 0.00 36.14 1.82
5505 5969 4.782156 TGCAGGTTTGATATCCCCAAATTT 59.218 37.500 0.00 0.00 36.14 1.82
5506 5970 5.250313 TGCAGGTTTGATATCCCCAAATTTT 59.750 36.000 0.00 0.00 36.14 1.82
5507 5971 6.441924 TGCAGGTTTGATATCCCCAAATTTTA 59.558 34.615 0.00 0.00 36.14 1.52
5508 5972 6.986231 GCAGGTTTGATATCCCCAAATTTTAG 59.014 38.462 0.00 0.00 36.14 1.85
5509 5973 7.147742 GCAGGTTTGATATCCCCAAATTTTAGA 60.148 37.037 0.00 0.00 36.14 2.10
5510 5974 8.927411 CAGGTTTGATATCCCCAAATTTTAGAT 58.073 33.333 0.00 0.00 36.14 1.98
5511 5975 9.506042 AGGTTTGATATCCCCAAATTTTAGATT 57.494 29.630 0.00 0.00 36.14 2.40
5618 6082 6.588756 TGAGAAATAAGGTTACTAGTTGCACG 59.411 38.462 0.00 0.00 0.00 5.34
5667 6131 5.171339 AGTTGTCAAAGATAGTGCTCCAT 57.829 39.130 0.00 0.00 0.00 3.41
5744 6210 6.605594 CCTAAATACAAGGCCATTTGTTAGGA 59.394 38.462 19.96 4.95 39.35 2.94
5753 6219 5.543790 AGGCCATTTGTTAGGAATTTTCTGT 59.456 36.000 5.01 0.00 0.00 3.41
5769 6235 9.696917 GAATTTTCTGTTTTCTGTTATGGACAT 57.303 29.630 0.00 0.00 37.69 3.06
5779 6245 9.559732 TTTTCTGTTATGGACATACTGATATGG 57.440 33.333 0.00 0.00 42.32 2.74
5780 6246 8.491045 TTCTGTTATGGACATACTGATATGGA 57.509 34.615 0.00 0.00 42.32 3.41
5781 6247 7.896811 TCTGTTATGGACATACTGATATGGAC 58.103 38.462 0.00 0.00 42.32 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 2.895680 GCTGATGGCGACCTCTCA 59.104 61.111 0.00 0.00 0.00 3.27
196 197 2.808543 GGTGTCCTGTGAATTCACTCAC 59.191 50.000 32.57 29.47 46.55 3.51
286 288 2.094539 CGACATGTGCGCGTTCAG 59.905 61.111 1.15 4.60 0.00 3.02
352 354 2.440517 TCGGTGTAGGCCTATGTACA 57.559 50.000 17.38 9.12 0.00 2.90
556 564 2.284921 CTGCTCCACCTCCTCCCA 60.285 66.667 0.00 0.00 0.00 4.37
590 598 2.135933 GAAAGAGGAACTGTCACACCG 58.864 52.381 0.00 0.00 41.55 4.94
762 770 6.273825 GGTTTCTACTCTCGCAATAATGAGA 58.726 40.000 0.00 0.00 38.85 3.27
884 909 1.200948 GCCAACAGAAGACAAGGATGC 59.799 52.381 0.00 0.00 0.00 3.91
891 916 1.873903 GCGAAGAGCCAACAGAAGACA 60.874 52.381 0.00 0.00 40.81 3.41
913 938 1.968540 AAGAGTGAGCTTTGGCGCC 60.969 57.895 22.73 22.73 44.37 6.53
978 1004 2.508663 GCTAGCCAACGGACGACC 60.509 66.667 2.29 0.00 0.00 4.79
1099 1125 5.288699 TACTAGCCCAGTAGCCAGTAGCA 62.289 52.174 0.00 0.00 40.72 3.49
1217 1244 2.092753 CCAATCAGGGAGAGCTAGCAAA 60.093 50.000 18.83 0.00 0.00 3.68
1263 1290 3.745332 TCAATCATGTCGCATGAACAC 57.255 42.857 20.89 0.00 0.00 3.32
1429 1456 5.376625 TGCATGTTACAAGAAAGAAGAGGT 58.623 37.500 0.00 0.00 0.00 3.85
1568 1595 3.211963 CCCTTGCATGGCGCTACC 61.212 66.667 13.15 0.00 43.06 3.18
1910 1944 5.729510 ACTTTCTCTCTCCTCATAACAAGC 58.270 41.667 0.00 0.00 0.00 4.01
1944 1978 0.032267 GCTACCTATCCTGCACCGTC 59.968 60.000 0.00 0.00 0.00 4.79
1958 1992 1.508632 TTTTCGTCAGTGCAGCTACC 58.491 50.000 0.00 0.00 0.00 3.18
2106 2148 3.378512 AGAGAGAGAGAGAGAGAGAGCA 58.621 50.000 0.00 0.00 0.00 4.26
2118 2218 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2119 2219 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2120 2220 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2121 2221 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2122 2222 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2123 2223 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2124 2224 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2125 2225 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2337 2444 0.331278 AAGAACCATGAATGCCCCGA 59.669 50.000 0.00 0.00 0.00 5.14
2398 2509 4.245660 TCTTCACGAGCCATCAAAACTAG 58.754 43.478 0.00 0.00 0.00 2.57
2457 2568 1.758936 TGACATGTACGGATCGAGGT 58.241 50.000 0.00 0.00 0.00 3.85
2467 2578 9.713740 GAATCAAGATCTCAAAATGACATGTAC 57.286 33.333 0.00 0.00 0.00 2.90
2828 2941 0.533755 AGCGATTGTAGGCAGATGGC 60.534 55.000 0.00 0.00 43.74 4.40
2921 3034 8.504812 ACAGCATAAATTATGTCACATGTACA 57.495 30.769 13.77 0.00 38.43 2.90
3373 3597 9.425893 CAATATATTTTGTTTGTGTCTAGCTCG 57.574 33.333 0.00 0.00 0.00 5.03
3401 3625 6.447162 AGGCAAGATTGTACAAAAGTTTAGC 58.553 36.000 13.23 10.14 0.00 3.09
3407 3631 3.989817 GGCAAGGCAAGATTGTACAAAAG 59.010 43.478 13.23 4.17 0.00 2.27
3568 4002 2.757868 TGTTACTGTATGCATTTGGCCC 59.242 45.455 3.54 0.00 43.89 5.80
3571 4005 7.887996 AAAATGTGTTACTGTATGCATTTGG 57.112 32.000 3.54 0.00 36.87 3.28
3572 4006 9.624697 AGTAAAATGTGTTACTGTATGCATTTG 57.375 29.630 3.54 0.00 41.67 2.32
3581 4015 6.838382 AGGAGGAAGTAAAATGTGTTACTGT 58.162 36.000 0.00 0.00 42.25 3.55
3639 4073 5.871396 TTTATACTGGATGACTCCCTGAC 57.129 43.478 0.00 0.00 41.29 3.51
3672 4106 9.193133 CTTTATATCGAACTCGGTCATTAACAT 57.807 33.333 0.00 0.00 40.29 2.71
3679 4113 6.543465 TCCTTACTTTATATCGAACTCGGTCA 59.457 38.462 0.00 0.00 40.29 4.02
3681 4115 6.949352 TCCTTACTTTATATCGAACTCGGT 57.051 37.500 0.00 0.00 40.29 4.69
3736 4171 0.988832 CCTAGGCAACAACCCCACTA 59.011 55.000 0.00 0.00 41.41 2.74
3833 4271 9.930693 AAAACTTCGAATAGAGATAGTCACTTT 57.069 29.630 0.00 0.00 0.00 2.66
3843 4281 6.015350 AGACTGGTCAAAACTTCGAATAGAGA 60.015 38.462 0.00 0.00 0.00 3.10
3844 4282 6.159988 AGACTGGTCAAAACTTCGAATAGAG 58.840 40.000 0.00 0.00 0.00 2.43
3851 4289 4.142687 ACACAAAGACTGGTCAAAACTTCG 60.143 41.667 3.51 0.00 0.00 3.79
3937 4378 7.067494 GTGCCACTTCCAACTCTATTCATTAAT 59.933 37.037 0.00 0.00 0.00 1.40
3984 4425 8.674173 TCCATGCCCTATCAACCTATTTTATTA 58.326 33.333 0.00 0.00 0.00 0.98
3985 4426 7.534852 TCCATGCCCTATCAACCTATTTTATT 58.465 34.615 0.00 0.00 0.00 1.40
3986 4427 7.102518 TCCATGCCCTATCAACCTATTTTAT 57.897 36.000 0.00 0.00 0.00 1.40
3987 4428 6.523035 TCCATGCCCTATCAACCTATTTTA 57.477 37.500 0.00 0.00 0.00 1.52
4068 4509 2.381752 TGCGGGATCAGAATAGGAGA 57.618 50.000 0.00 0.00 0.00 3.71
4079 4520 7.729894 TGCTAAGTTATAGCAATTGCGGGATC 61.730 42.308 24.02 15.35 46.29 3.36
4123 4568 4.821805 CAGTGTTGTGAAGGACTTACCAAT 59.178 41.667 0.00 0.00 42.04 3.16
4130 4575 2.092968 TCAAGCAGTGTTGTGAAGGACT 60.093 45.455 0.00 0.00 0.00 3.85
4142 4587 4.255833 AGTTCTCTCTCTTCAAGCAGTG 57.744 45.455 0.00 0.00 0.00 3.66
4151 4596 8.436778 TGCTATATCTCACTAGTTCTCTCTCTT 58.563 37.037 0.00 0.00 0.00 2.85
4187 4634 7.406553 TGCTTATTTATGTCATGCGTTCTTAC 58.593 34.615 0.00 0.00 0.00 2.34
4324 4775 2.802719 GTTGTATTTCCTCCCTGGCAA 58.197 47.619 0.00 0.00 35.26 4.52
4419 4870 1.070758 CATGTAGGGGGAGAATGGACG 59.929 57.143 0.00 0.00 0.00 4.79
4478 4930 6.564328 GTGATCAATGGGATTGTTTTAGACC 58.436 40.000 0.00 0.00 41.02 3.85
4479 4931 6.258160 CGTGATCAATGGGATTGTTTTAGAC 58.742 40.000 0.00 0.00 41.02 2.59
4503 4955 3.198068 CTGCATATGTACATATCCGGGC 58.802 50.000 22.81 21.67 31.98 6.13
4594 5046 1.762460 CCTGAGGACCGGGCACTAT 60.762 63.158 11.00 0.00 33.85 2.12
4650 5102 8.507470 TTCAGTATCGATCATATTTCTGAACG 57.493 34.615 0.00 0.00 41.22 3.95
4724 5176 1.272490 CTCTCAACCACTTGCTCGGTA 59.728 52.381 0.00 0.00 33.17 4.02
4736 5188 2.663826 AGATGTCGAAGCTCTCAACC 57.336 50.000 0.00 0.00 0.00 3.77
4784 5236 7.860649 AATTAATCCCACCATGCTTATGATT 57.139 32.000 0.00 0.00 0.00 2.57
4797 5249 5.924825 CGGTAGCAGTACTAATTAATCCCAC 59.075 44.000 0.00 0.00 30.90 4.61
4902 5354 5.972382 GCAACGAAGTAACCAAACACAAATA 59.028 36.000 0.00 0.00 45.00 1.40
4991 5443 6.430925 AGCAGCTGTTCATAATTAAAGTGTGA 59.569 34.615 16.64 0.00 0.00 3.58
4995 5447 7.112779 AGGTAGCAGCTGTTCATAATTAAAGT 58.887 34.615 16.64 0.00 0.00 2.66
5062 5515 3.976015 ACCAATTACCTGTAACCCATGG 58.024 45.455 4.14 4.14 0.00 3.66
5107 5571 6.481644 CCGGAAGAGGTACTATATATACCGTC 59.518 46.154 0.00 11.12 45.84 4.79
5165 5629 0.830648 TGGTCCGATCAAAGGCTAGG 59.169 55.000 0.00 0.00 0.00 3.02
5169 5633 0.181350 ATCCTGGTCCGATCAAAGGC 59.819 55.000 0.00 0.00 0.00 4.35
5178 5642 1.026718 GTGCTCCAAATCCTGGTCCG 61.027 60.000 0.00 0.00 46.51 4.79
5179 5643 0.329596 AGTGCTCCAAATCCTGGTCC 59.670 55.000 0.00 0.00 46.51 4.46
5180 5644 1.743996 GAGTGCTCCAAATCCTGGTC 58.256 55.000 0.00 0.00 46.51 4.02
5181 5645 0.036010 CGAGTGCTCCAAATCCTGGT 60.036 55.000 0.00 0.00 46.51 4.00
5183 5647 0.745845 CCCGAGTGCTCCAAATCCTG 60.746 60.000 0.00 0.00 0.00 3.86
5184 5648 1.201429 ACCCGAGTGCTCCAAATCCT 61.201 55.000 0.00 0.00 0.00 3.24
5185 5649 1.026718 CACCCGAGTGCTCCAAATCC 61.027 60.000 0.00 0.00 37.14 3.01
5186 5650 2.471255 CACCCGAGTGCTCCAAATC 58.529 57.895 0.00 0.00 37.14 2.17
5187 5651 4.722193 CACCCGAGTGCTCCAAAT 57.278 55.556 0.00 0.00 37.14 2.32
5205 5669 0.031721 GTTCGTATAGGGGTGCGGAG 59.968 60.000 0.00 0.00 0.00 4.63
5206 5670 0.683828 TGTTCGTATAGGGGTGCGGA 60.684 55.000 0.00 0.00 0.00 5.54
5207 5671 0.176219 TTGTTCGTATAGGGGTGCGG 59.824 55.000 0.00 0.00 0.00 5.69
5208 5672 2.234300 ATTGTTCGTATAGGGGTGCG 57.766 50.000 0.00 0.00 0.00 5.34
5209 5673 3.537580 TGAATTGTTCGTATAGGGGTGC 58.462 45.455 0.00 0.00 0.00 5.01
5210 5674 6.693315 AAATGAATTGTTCGTATAGGGGTG 57.307 37.500 0.00 0.00 0.00 4.61
5211 5675 8.810990 TTTAAATGAATTGTTCGTATAGGGGT 57.189 30.769 0.00 0.00 0.00 4.95
5260 5724 6.710499 TTGATACCCCAAAATCCCATTTTT 57.290 33.333 0.00 0.00 40.27 1.94
5261 5725 6.480763 GTTTGATACCCCAAAATCCCATTTT 58.519 36.000 0.00 0.00 42.81 1.82
5262 5726 5.337975 CGTTTGATACCCCAAAATCCCATTT 60.338 40.000 0.00 0.00 37.72 2.32
5263 5727 4.161377 CGTTTGATACCCCAAAATCCCATT 59.839 41.667 0.00 0.00 37.72 3.16
5264 5728 3.704061 CGTTTGATACCCCAAAATCCCAT 59.296 43.478 0.00 0.00 37.72 4.00
5265 5729 3.093057 CGTTTGATACCCCAAAATCCCA 58.907 45.455 0.00 0.00 37.72 4.37
5266 5730 3.093814 ACGTTTGATACCCCAAAATCCC 58.906 45.455 0.00 0.00 37.72 3.85
5267 5731 3.119280 CCACGTTTGATACCCCAAAATCC 60.119 47.826 0.00 0.00 37.72 3.01
5268 5732 3.119280 CCCACGTTTGATACCCCAAAATC 60.119 47.826 0.00 0.00 37.72 2.17
5269 5733 2.829120 CCCACGTTTGATACCCCAAAAT 59.171 45.455 0.00 0.00 37.72 1.82
5270 5734 2.240279 CCCACGTTTGATACCCCAAAA 58.760 47.619 0.00 0.00 37.72 2.44
5271 5735 1.145325 ACCCACGTTTGATACCCCAAA 59.855 47.619 0.00 0.00 34.03 3.28
5272 5736 0.772384 ACCCACGTTTGATACCCCAA 59.228 50.000 0.00 0.00 0.00 4.12
5273 5737 0.772384 AACCCACGTTTGATACCCCA 59.228 50.000 0.00 0.00 0.00 4.96
5274 5738 1.456296 GAACCCACGTTTGATACCCC 58.544 55.000 0.00 0.00 30.30 4.95
5275 5739 1.456296 GGAACCCACGTTTGATACCC 58.544 55.000 0.00 0.00 30.30 3.69
5290 5754 2.039509 CCGGGACTAGATCGGGAAC 58.960 63.158 12.76 0.00 40.07 3.62
5291 5755 4.593033 CCGGGACTAGATCGGGAA 57.407 61.111 12.76 0.00 40.07 3.97
5295 5759 3.454371 AATTTCACCGGGACTAGATCG 57.546 47.619 6.32 0.00 0.00 3.69
5296 5760 3.802685 CGAAATTTCACCGGGACTAGATC 59.197 47.826 17.99 0.00 0.00 2.75
5297 5761 3.197116 ACGAAATTTCACCGGGACTAGAT 59.803 43.478 17.99 0.00 0.00 1.98
5298 5762 2.564062 ACGAAATTTCACCGGGACTAGA 59.436 45.455 17.99 0.00 0.00 2.43
5299 5763 2.671396 CACGAAATTTCACCGGGACTAG 59.329 50.000 17.99 0.54 0.00 2.57
5300 5764 2.299582 TCACGAAATTTCACCGGGACTA 59.700 45.455 17.99 0.00 30.06 2.59
5301 5765 1.071071 TCACGAAATTTCACCGGGACT 59.929 47.619 17.99 0.00 30.06 3.85
5302 5766 1.515081 TCACGAAATTTCACCGGGAC 58.485 50.000 17.99 0.00 30.06 4.46
5303 5767 2.257691 TTCACGAAATTTCACCGGGA 57.742 45.000 17.99 8.66 33.55 5.14
5304 5768 3.357166 TTTTCACGAAATTTCACCGGG 57.643 42.857 17.99 6.35 0.00 5.73
5337 5801 5.797909 TTTGTCATTTTTGCACGAATACG 57.202 34.783 0.00 0.00 45.75 3.06
5338 5802 7.160633 ACTTTTGTCATTTTTGCACGAATAC 57.839 32.000 0.00 0.00 0.00 1.89
5339 5803 7.763172 AACTTTTGTCATTTTTGCACGAATA 57.237 28.000 0.00 0.00 0.00 1.75
5340 5804 6.660887 AACTTTTGTCATTTTTGCACGAAT 57.339 29.167 0.00 0.00 0.00 3.34
5341 5805 6.401581 GGAAACTTTTGTCATTTTTGCACGAA 60.402 34.615 0.00 0.00 0.00 3.85
5342 5806 5.062809 GGAAACTTTTGTCATTTTTGCACGA 59.937 36.000 0.00 0.00 0.00 4.35
5343 5807 5.063312 AGGAAACTTTTGTCATTTTTGCACG 59.937 36.000 0.00 0.00 37.44 5.34
5344 5808 6.421377 AGGAAACTTTTGTCATTTTTGCAC 57.579 33.333 0.00 0.00 37.44 4.57
5345 5809 7.768120 ACATAGGAAACTTTTGTCATTTTTGCA 59.232 29.630 0.00 0.00 43.67 4.08
5346 5810 8.141835 ACATAGGAAACTTTTGTCATTTTTGC 57.858 30.769 0.00 0.00 43.67 3.68
5380 5844 8.856153 AACAAAAATCTACCCAAACAGTTTTT 57.144 26.923 0.00 0.00 0.00 1.94
5381 5845 7.276878 CGAACAAAAATCTACCCAAACAGTTTT 59.723 33.333 0.00 0.00 0.00 2.43
5382 5846 6.754675 CGAACAAAAATCTACCCAAACAGTTT 59.245 34.615 0.00 0.00 0.00 2.66
5383 5847 6.270064 CGAACAAAAATCTACCCAAACAGTT 58.730 36.000 0.00 0.00 0.00 3.16
5384 5848 5.221165 CCGAACAAAAATCTACCCAAACAGT 60.221 40.000 0.00 0.00 0.00 3.55
5385 5849 5.009210 TCCGAACAAAAATCTACCCAAACAG 59.991 40.000 0.00 0.00 0.00 3.16
5386 5850 4.888239 TCCGAACAAAAATCTACCCAAACA 59.112 37.500 0.00 0.00 0.00 2.83
5387 5851 5.217393 GTCCGAACAAAAATCTACCCAAAC 58.783 41.667 0.00 0.00 0.00 2.93
5388 5852 4.888239 TGTCCGAACAAAAATCTACCCAAA 59.112 37.500 0.00 0.00 30.70 3.28
5389 5853 4.462133 TGTCCGAACAAAAATCTACCCAA 58.538 39.130 0.00 0.00 30.70 4.12
5390 5854 4.069304 CTGTCCGAACAAAAATCTACCCA 58.931 43.478 0.00 0.00 34.24 4.51
5391 5855 4.070009 ACTGTCCGAACAAAAATCTACCC 58.930 43.478 0.00 0.00 34.24 3.69
5392 5856 6.980051 ATACTGTCCGAACAAAAATCTACC 57.020 37.500 0.00 0.00 34.24 3.18
5393 5857 7.961283 GGAAATACTGTCCGAACAAAAATCTAC 59.039 37.037 0.00 0.00 34.24 2.59
5394 5858 7.881232 AGGAAATACTGTCCGAACAAAAATCTA 59.119 33.333 0.00 0.00 40.36 1.98
5395 5859 6.715264 AGGAAATACTGTCCGAACAAAAATCT 59.285 34.615 0.00 0.00 40.36 2.40
5396 5860 6.909909 AGGAAATACTGTCCGAACAAAAATC 58.090 36.000 0.00 0.00 40.36 2.17
5397 5861 6.894339 AGGAAATACTGTCCGAACAAAAAT 57.106 33.333 0.00 0.00 40.36 1.82
5398 5862 6.512091 CGAAGGAAATACTGTCCGAACAAAAA 60.512 38.462 0.00 0.00 40.36 1.94
5399 5863 5.049954 CGAAGGAAATACTGTCCGAACAAAA 60.050 40.000 0.00 0.00 40.36 2.44
5400 5864 4.449743 CGAAGGAAATACTGTCCGAACAAA 59.550 41.667 0.00 0.00 40.36 2.83
5401 5865 3.991773 CGAAGGAAATACTGTCCGAACAA 59.008 43.478 0.00 0.00 40.36 2.83
5402 5866 3.581755 CGAAGGAAATACTGTCCGAACA 58.418 45.455 0.00 0.00 40.36 3.18
5403 5867 2.347755 GCGAAGGAAATACTGTCCGAAC 59.652 50.000 0.00 0.00 40.36 3.95
5404 5868 2.613691 GCGAAGGAAATACTGTCCGAA 58.386 47.619 0.00 0.00 40.36 4.30
5405 5869 1.134907 GGCGAAGGAAATACTGTCCGA 60.135 52.381 0.00 0.00 40.36 4.55
5406 5870 1.287425 GGCGAAGGAAATACTGTCCG 58.713 55.000 0.00 0.00 40.36 4.79
5407 5871 2.007608 GTGGCGAAGGAAATACTGTCC 58.992 52.381 0.00 0.00 35.17 4.02
5408 5872 1.659098 CGTGGCGAAGGAAATACTGTC 59.341 52.381 0.00 0.00 0.00 3.51
5409 5873 1.674817 CCGTGGCGAAGGAAATACTGT 60.675 52.381 0.00 0.00 0.00 3.55
5410 5874 1.006832 CCGTGGCGAAGGAAATACTG 58.993 55.000 0.00 0.00 0.00 2.74
5411 5875 0.899720 TCCGTGGCGAAGGAAATACT 59.100 50.000 0.00 0.00 32.86 2.12
5412 5876 1.949465 ATCCGTGGCGAAGGAAATAC 58.051 50.000 7.56 0.00 40.32 1.89
5413 5877 2.544277 CGTATCCGTGGCGAAGGAAATA 60.544 50.000 7.56 0.00 40.32 1.40
5414 5878 1.805120 CGTATCCGTGGCGAAGGAAAT 60.805 52.381 7.56 0.00 40.32 2.17
5415 5879 0.458889 CGTATCCGTGGCGAAGGAAA 60.459 55.000 7.56 0.00 40.32 3.13
5416 5880 1.140161 CGTATCCGTGGCGAAGGAA 59.860 57.895 7.56 0.00 40.32 3.36
5417 5881 2.802792 CGTATCCGTGGCGAAGGA 59.197 61.111 5.76 5.76 41.30 3.36
5447 5911 9.672086 CTAGTTCCGTGTGAAATTTCATAAAAA 57.328 29.630 23.05 12.37 39.73 1.94
5448 5912 9.058174 TCTAGTTCCGTGTGAAATTTCATAAAA 57.942 29.630 23.05 12.67 39.73 1.52
5449 5913 8.610248 TCTAGTTCCGTGTGAAATTTCATAAA 57.390 30.769 23.05 9.80 39.73 1.40
5450 5914 8.786826 ATCTAGTTCCGTGTGAAATTTCATAA 57.213 30.769 23.05 12.46 39.73 1.90
5451 5915 8.664798 CAATCTAGTTCCGTGTGAAATTTCATA 58.335 33.333 23.05 18.02 39.73 2.15
5452 5916 7.362056 CCAATCTAGTTCCGTGTGAAATTTCAT 60.362 37.037 23.05 7.89 39.73 2.57
5453 5917 6.072728 CCAATCTAGTTCCGTGTGAAATTTCA 60.073 38.462 16.91 16.91 33.94 2.69
5454 5918 6.314784 CCAATCTAGTTCCGTGTGAAATTTC 58.685 40.000 11.41 11.41 33.94 2.17
5455 5919 5.183140 CCCAATCTAGTTCCGTGTGAAATTT 59.817 40.000 0.00 0.00 33.94 1.82
5456 5920 4.700213 CCCAATCTAGTTCCGTGTGAAATT 59.300 41.667 0.00 0.00 33.94 1.82
5457 5921 4.019681 TCCCAATCTAGTTCCGTGTGAAAT 60.020 41.667 0.00 0.00 33.94 2.17
5458 5922 3.325425 TCCCAATCTAGTTCCGTGTGAAA 59.675 43.478 0.00 0.00 33.94 2.69
5459 5923 2.901192 TCCCAATCTAGTTCCGTGTGAA 59.099 45.455 0.00 0.00 0.00 3.18
5460 5924 2.531771 TCCCAATCTAGTTCCGTGTGA 58.468 47.619 0.00 0.00 0.00 3.58
5461 5925 3.328382 TTCCCAATCTAGTTCCGTGTG 57.672 47.619 0.00 0.00 0.00 3.82
5462 5926 3.873910 CATTCCCAATCTAGTTCCGTGT 58.126 45.455 0.00 0.00 0.00 4.49
5463 5927 2.614057 GCATTCCCAATCTAGTTCCGTG 59.386 50.000 0.00 0.00 0.00 4.94
5464 5928 2.238646 TGCATTCCCAATCTAGTTCCGT 59.761 45.455 0.00 0.00 0.00 4.69
5465 5929 2.874701 CTGCATTCCCAATCTAGTTCCG 59.125 50.000 0.00 0.00 0.00 4.30
5466 5930 3.217626 CCTGCATTCCCAATCTAGTTCC 58.782 50.000 0.00 0.00 0.00 3.62
5467 5931 3.891049 ACCTGCATTCCCAATCTAGTTC 58.109 45.455 0.00 0.00 0.00 3.01
5468 5932 4.322057 AACCTGCATTCCCAATCTAGTT 57.678 40.909 0.00 0.00 0.00 2.24
5469 5933 4.019174 CAAACCTGCATTCCCAATCTAGT 58.981 43.478 0.00 0.00 0.00 2.57
5470 5934 4.272489 TCAAACCTGCATTCCCAATCTAG 58.728 43.478 0.00 0.00 0.00 2.43
5471 5935 4.314522 TCAAACCTGCATTCCCAATCTA 57.685 40.909 0.00 0.00 0.00 1.98
5472 5936 3.173953 TCAAACCTGCATTCCCAATCT 57.826 42.857 0.00 0.00 0.00 2.40
5473 5937 5.279156 GGATATCAAACCTGCATTCCCAATC 60.279 44.000 4.83 0.00 0.00 2.67
5474 5938 4.590222 GGATATCAAACCTGCATTCCCAAT 59.410 41.667 4.83 0.00 0.00 3.16
5475 5939 3.960102 GGATATCAAACCTGCATTCCCAA 59.040 43.478 4.83 0.00 0.00 4.12
5476 5940 3.565307 GGATATCAAACCTGCATTCCCA 58.435 45.455 4.83 0.00 0.00 4.37
5477 5941 2.893489 GGGATATCAAACCTGCATTCCC 59.107 50.000 4.83 0.00 0.00 3.97
5478 5942 2.893489 GGGGATATCAAACCTGCATTCC 59.107 50.000 4.83 0.00 0.00 3.01
5479 5943 3.565307 TGGGGATATCAAACCTGCATTC 58.435 45.455 4.83 0.00 0.00 2.67
5480 5944 3.686227 TGGGGATATCAAACCTGCATT 57.314 42.857 4.83 0.00 0.00 3.56
5481 5945 3.686227 TTGGGGATATCAAACCTGCAT 57.314 42.857 4.83 0.00 0.00 3.96
5482 5946 3.464720 TTTGGGGATATCAAACCTGCA 57.535 42.857 4.83 0.00 0.00 4.41
5483 5947 5.357742 AAATTTGGGGATATCAAACCTGC 57.642 39.130 4.83 0.00 37.00 4.85
5484 5948 8.305046 TCTAAAATTTGGGGATATCAAACCTG 57.695 34.615 4.83 0.00 37.00 4.00
5485 5949 9.506042 AATCTAAAATTTGGGGATATCAAACCT 57.494 29.630 4.83 0.00 37.00 3.50
5646 6110 5.886960 AATGGAGCACTATCTTTGACAAC 57.113 39.130 0.00 0.00 0.00 3.32
5719 6184 6.605594 TCCTAACAAATGGCCTTGTATTTAGG 59.394 38.462 19.20 19.20 38.59 2.69
5753 6219 9.559732 CCATATCAGTATGTCCATAACAGAAAA 57.440 33.333 0.00 0.00 42.37 2.29



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

AutoCloner maintained by Alex Coulton.