Multiple sequence alignment - TraesCS2A01G236600

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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 TraesCS2A01G236600 chr2A 100.000 5222 0 0 1 5222 304983589 304978368 0.000000e+00 9644.0
1 TraesCS2A01G236600 chr2B 95.821 1675 50 8 684 2340 332331498 332333170 0.000000e+00 2687.0
2 TraesCS2A01G236600 chr2B 93.857 1221 49 14 3476 4686 332334628 332335832 0.000000e+00 1816.0
3 TraesCS2A01G236600 chr2B 91.342 693 27 18 2326 3018 332333200 332333859 0.000000e+00 917.0
4 TraesCS2A01G236600 chr2B 82.238 411 52 7 6 414 332330491 332330882 8.380000e-88 335.0
5 TraesCS2A01G236600 chr2B 83.742 326 20 12 4928 5222 332335919 332336242 1.430000e-70 278.0
6 TraesCS2A01G236600 chr2B 98.969 97 1 0 3331 3427 332333859 332333955 1.930000e-39 174.0
7 TraesCS2A01G236600 chr2B 94.118 85 4 1 4713 4796 332335828 332335912 1.530000e-25 128.0
8 TraesCS2A01G236600 chr2B 94.915 59 3 0 1 59 398163614 398163556 5.570000e-15 93.5
9 TraesCS2A01G236600 chr2B 90.909 44 3 1 593 636 26402934 26402892 2.030000e-04 58.4
10 TraesCS2A01G236600 chr2D 95.565 1443 39 11 1589 3018 216327951 216329381 0.000000e+00 2287.0
11 TraesCS2A01G236600 chr2D 91.941 1365 68 25 3484 4837 216329872 216331205 0.000000e+00 1873.0
12 TraesCS2A01G236600 chr2D 96.467 1019 26 5 661 1670 216326933 216327950 0.000000e+00 1674.0
13 TraesCS2A01G236600 chr2D 88.259 494 48 8 177 669 216325367 216325851 2.710000e-162 582.0
14 TraesCS2A01G236600 chr2D 90.719 334 25 4 3005 3334 502561752 502561421 1.730000e-119 440.0
15 TraesCS2A01G236600 chr2D 91.318 311 20 5 3005 3311 502562274 502561967 8.090000e-113 418.0
16 TraesCS2A01G236600 chr2D 85.000 360 21 15 4893 5220 216331213 216331571 8.380000e-88 335.0
17 TraesCS2A01G236600 chr2D 91.803 183 15 0 1 183 216218803 216218985 6.710000e-64 255.0
18 TraesCS2A01G236600 chr2D 97.600 125 3 0 3331 3455 216329381 216329505 1.140000e-51 215.0
19 TraesCS2A01G236600 chr2D 80.351 285 47 5 71 348 326239203 326238921 1.910000e-49 207.0
20 TraesCS2A01G236600 chr2D 90.909 44 3 1 593 636 2999272 2999314 2.030000e-04 58.4
21 TraesCS2A01G236600 chr7A 98.423 317 4 1 3018 3333 671456855 671456539 1.640000e-154 556.0
22 TraesCS2A01G236600 chr7A 91.562 320 24 2 3016 3334 721994299 721993982 6.210000e-119 438.0
23 TraesCS2A01G236600 chr7A 80.137 146 24 4 493 635 61806763 61806620 2.570000e-18 104.0
24 TraesCS2A01G236600 chr7A 82.796 93 12 3 530 622 9861128 9861040 4.330000e-11 80.5
25 TraesCS2A01G236600 chr7A 100.000 28 0 0 4971 4998 38030688 38030715 9.000000e-03 52.8
26 TraesCS2A01G236600 chr1A 97.476 317 6 2 3018 3333 421798651 421798966 1.650000e-149 540.0
27 TraesCS2A01G236600 chr1A 90.190 316 25 3 3018 3332 532232524 532232214 1.750000e-109 407.0
28 TraesCS2A01G236600 chr1A 81.148 122 18 4 503 623 554221428 554221545 5.570000e-15 93.5
29 TraesCS2A01G236600 chr6D 91.483 317 19 5 3017 3332 78705727 78706036 3.740000e-116 429.0
30 TraesCS2A01G236600 chr6D 80.132 302 56 4 71 371 452838140 452838438 6.810000e-54 222.0
31 TraesCS2A01G236600 chr6A 90.852 317 23 3 3017 3332 32888283 32887972 2.250000e-113 420.0
32 TraesCS2A01G236600 chr6A 90.909 44 3 1 593 636 41191045 41191087 2.030000e-04 58.4
33 TraesCS2A01G236600 chr3A 89.623 318 30 2 3017 3333 359060176 359059861 8.150000e-108 401.0
34 TraesCS2A01G236600 chr3A 79.321 324 57 6 71 384 724070596 724070919 8.800000e-53 219.0
35 TraesCS2A01G236600 chr3D 81.322 348 53 6 71 407 123565249 123564903 6.660000e-69 272.0
36 TraesCS2A01G236600 chr3D 79.167 312 53 9 71 372 84920695 84920386 6.850000e-49 206.0
37 TraesCS2A01G236600 chr7D 79.375 320 57 7 71 385 17116257 17115942 3.170000e-52 217.0
38 TraesCS2A01G236600 chr4D 91.743 109 9 0 1010 1118 473809695 473809803 9.060000e-33 152.0
39 TraesCS2A01G236600 chr4B 91.743 109 9 0 1010 1118 596372806 596372914 9.060000e-33 152.0
40 TraesCS2A01G236600 chr4A 91.743 109 9 0 1010 1118 680370195 680370303 9.060000e-33 152.0
41 TraesCS2A01G236600 chr6B 80.000 155 23 8 488 639 298824934 298824785 1.990000e-19 108.0
42 TraesCS2A01G236600 chr5A 97.500 40 1 0 4963 5002 581297506 581297545 9.380000e-08 69.4
43 TraesCS2A01G236600 chr7B 90.909 44 3 1 593 636 121027152 121027110 2.030000e-04 58.4
44 TraesCS2A01G236600 chr7B 100.000 30 0 0 4971 5000 711450348 711450377 7.310000e-04 56.5
45 TraesCS2A01G236600 chr1D 100.000 28 0 0 4973 5000 27880482 27880509 9.000000e-03 52.8
46 TraesCS2A01G236600 chr1B 96.774 31 1 0 4970 5000 26363069 26363099 9.000000e-03 52.8


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 TraesCS2A01G236600 chr2A 304978368 304983589 5221 True 9644 9644 100.0000 1 5222 1 chr2A.!!$R1 5221
1 TraesCS2A01G236600 chr2B 332330491 332336242 5751 False 905 2687 91.4410 6 5222 7 chr2B.!!$F1 5216
2 TraesCS2A01G236600 chr2D 216325367 216331571 6204 False 1161 2287 92.4720 177 5220 6 chr2D.!!$F3 5043
3 TraesCS2A01G236600 chr2D 502561421 502562274 853 True 429 440 91.0185 3005 3334 2 chr2D.!!$R2 329


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
214 215 0.108992 TAAGATCGGTTTGCGTCGCT 60.109 50.0 19.50 0.0 0.00 4.93 F
801 2013 0.304705 CGCTAATAAACGGCAGGCAG 59.695 55.0 0.00 0.0 0.00 4.85 F
1280 2496 0.544357 ATCTGACCCTGTGAACGGGA 60.544 55.0 10.02 0.0 45.36 5.14 F
1711 3024 0.614979 AGAGGTACCATGACGCCTGT 60.615 55.0 15.94 0.0 0.00 4.00 F
3043 4405 0.952010 GATACCCCGCACGTTGTTGT 60.952 55.0 0.00 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 3028 0.472471 AGCAAAAGGTTCCGTCTGGA 59.528 50.000 0.00 0.0 44.61 3.86 R
2468 3828 1.270826 CTCTCAGTGCGAACTTCCTCA 59.729 52.381 0.00 0.0 0.00 3.86 R
3240 4605 1.608542 GCAACATGCATGGCAAAAGGA 60.609 47.619 29.41 0.0 43.62 3.36 R
3465 5353 0.247655 GTGCGTGTGTCTGTGTGTTG 60.248 55.000 0.00 0.0 0.00 3.33 R
4801 7339 0.034756 ACGTGCCAGTGTGATGCTTA 59.965 50.000 0.00 0.0 0.00 3.09 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
47 48 2.359169 TGATGCAGGAGTCCCGGTC 61.359 63.158 5.25 0.00 37.58 4.79
48 49 3.083997 ATGCAGGAGTCCCGGTCC 61.084 66.667 5.25 0.00 37.58 4.46
49 50 3.924013 ATGCAGGAGTCCCGGTCCA 62.924 63.158 11.86 0.00 36.43 4.02
60 61 4.473520 CGGTCCAAGCAGGGCGAT 62.474 66.667 0.00 0.00 45.54 4.58
83 84 1.804601 GACCAACTAGGGTTTGTCCG 58.195 55.000 0.00 0.00 42.53 4.79
84 85 0.250597 ACCAACTAGGGTTTGTCCGC 60.251 55.000 0.00 0.00 43.89 5.54
86 87 1.004200 AACTAGGGTTTGTCCGCCG 60.004 57.895 0.00 0.00 37.00 6.46
90 91 4.629523 GGGTTTGTCCGCCGGTCA 62.630 66.667 1.63 0.00 37.00 4.02
114 115 0.324830 GACCACCTGCCCTAGAGAGT 60.325 60.000 0.00 0.00 0.00 3.24
140 141 2.203070 CGATCCTTTGCTCGGGGG 60.203 66.667 0.00 0.00 0.00 5.40
155 156 1.893210 CGGGGGTTTCTCTCTCTCACT 60.893 57.143 0.00 0.00 0.00 3.41
165 166 3.571828 TCTCTCTCTCACTGGTCACTTTG 59.428 47.826 0.00 0.00 0.00 2.77
168 169 4.590647 TCTCTCTCACTGGTCACTTTGATT 59.409 41.667 0.00 0.00 0.00 2.57
183 184 8.706035 GTCACTTTGATTAGCGTTTACTCTTTA 58.294 33.333 0.00 0.00 0.00 1.85
214 215 0.108992 TAAGATCGGTTTGCGTCGCT 60.109 50.000 19.50 0.00 0.00 4.93
217 218 3.909258 ATCGGTTTGCGTCGCTCGT 62.909 57.895 19.50 5.69 42.13 4.18
286 287 2.346365 GCCTTTTCTCCGACCCGT 59.654 61.111 0.00 0.00 0.00 5.28
336 337 2.050351 CGTCGTTCACGCCTCTGT 60.050 61.111 0.00 0.00 42.87 3.41
390 391 1.664321 GCTACGACCGGGACTCATGT 61.664 60.000 6.32 0.00 0.00 3.21
440 443 4.331717 ACAAGGTGGAATAAATCTAACGCG 59.668 41.667 3.53 3.53 30.12 6.01
456 459 7.909777 TCTAACGCGATCTTATGTTTTCTAG 57.090 36.000 15.93 0.00 0.00 2.43
487 490 8.521176 ACATTATACTCGACAACAAGTACTCTT 58.479 33.333 0.00 0.00 31.15 2.85
490 493 3.635373 ACTCGACAACAAGTACTCTTCCA 59.365 43.478 0.00 0.00 0.00 3.53
493 496 3.608506 CGACAACAAGTACTCTTCCATCG 59.391 47.826 0.00 0.00 0.00 3.84
513 516 9.559732 TCCATCGTTCATGAATATAAGATGTTT 57.440 29.630 23.26 4.42 33.80 2.83
563 566 5.751243 AGACATGGTTTAGTGTGTTTGTC 57.249 39.130 0.00 0.00 34.02 3.18
569 572 4.156922 TGGTTTAGTGTGTTTGTCCACTTG 59.843 41.667 0.00 0.00 41.85 3.16
575 578 4.279671 AGTGTGTTTGTCCACTTGTTTCAA 59.720 37.500 0.00 0.00 38.76 2.69
588 591 7.390440 TCCACTTGTTTCAATCCTTATGTAGTG 59.610 37.037 0.00 0.00 0.00 2.74
647 650 4.829872 AACGGAGGGAATACATAACACA 57.170 40.909 0.00 0.00 0.00 3.72
739 1950 2.228822 TGAAAAAGGAAATCAGCGAGGC 59.771 45.455 0.00 0.00 0.00 4.70
742 1953 1.743996 AAGGAAATCAGCGAGGCTTC 58.256 50.000 0.00 0.00 36.40 3.86
801 2013 0.304705 CGCTAATAAACGGCAGGCAG 59.695 55.000 0.00 0.00 0.00 4.85
1186 2402 0.951558 TCTTTCCTCTGTTTTGCCGC 59.048 50.000 0.00 0.00 0.00 6.53
1280 2496 0.544357 ATCTGACCCTGTGAACGGGA 60.544 55.000 10.02 0.00 45.36 5.14
1343 2559 2.109834 TCTTCTTGATTTGGGGCTTGGA 59.890 45.455 0.00 0.00 0.00 3.53
1374 2590 6.655003 CCATGGTTACAGTATTTGAGACTTGT 59.345 38.462 2.57 0.00 0.00 3.16
1509 2740 6.990798 TCTGTGTGATTTGGAATTTAATGCA 58.009 32.000 0.00 0.00 0.00 3.96
1627 2940 2.872858 GGAGAATTCTGGCGGATGTAAC 59.127 50.000 14.00 0.00 0.00 2.50
1637 2950 2.484241 GGCGGATGTAACGTAGGGAATT 60.484 50.000 0.00 0.00 0.00 2.17
1638 2951 2.798847 GCGGATGTAACGTAGGGAATTC 59.201 50.000 0.00 0.00 0.00 2.17
1676 2989 3.118665 AGTTGTTTCAATGCCACTTTGCT 60.119 39.130 0.00 0.00 0.00 3.91
1711 3024 0.614979 AGAGGTACCATGACGCCTGT 60.615 55.000 15.94 0.00 0.00 4.00
1715 3028 1.406887 GGTACCATGACGCCTGTGATT 60.407 52.381 7.15 0.00 0.00 2.57
1765 3078 4.541779 GAGTTCACTATGATACCTGCGAG 58.458 47.826 0.00 0.00 0.00 5.03
1783 3096 4.263462 TGCGAGCCCAATTAGATATGGAAT 60.263 41.667 0.00 0.00 39.12 3.01
1886 3201 7.120051 AGCCTCTTCATATGTATATCGGTACT 58.880 38.462 1.90 0.00 0.00 2.73
1900 3215 4.247267 TCGGTACTTACAACAGACTTGG 57.753 45.455 0.00 0.00 0.00 3.61
1922 3237 4.039124 GGTTTTCCTGGTGAACAATGATGT 59.961 41.667 13.83 0.00 38.05 3.06
1986 3301 8.327941 TCAGTTGTTCTGATTCTATTTTCCTG 57.672 34.615 0.00 0.00 46.77 3.86
2404 3763 7.859598 CAAAGTTGCAAATTTTACTGGCATTA 58.140 30.769 21.27 0.00 33.16 1.90
2468 3828 4.624015 TCTTAAACACGTCGAAGTGGATT 58.376 39.130 30.30 25.31 45.80 3.01
2646 4006 8.026026 GTCACATGTGATATCCTATGTACTCTG 58.974 40.741 30.10 8.53 42.18 3.35
2819 4179 2.489722 CTCAGTCTGATCCACTTGTCGA 59.510 50.000 2.22 0.00 0.00 4.20
2822 4182 4.021104 TCAGTCTGATCCACTTGTCGATTT 60.021 41.667 0.00 0.00 0.00 2.17
2823 4183 5.185056 TCAGTCTGATCCACTTGTCGATTTA 59.815 40.000 0.00 0.00 0.00 1.40
2930 4292 3.967332 ACCTCAATTTTCATGGCCTTG 57.033 42.857 12.41 12.41 0.00 3.61
2938 4300 6.654161 TCAATTTTCATGGCCTTGTTAATTGG 59.346 34.615 31.53 23.04 33.88 3.16
2959 4321 7.572523 TTGGAGATATACAATTCTTTGCAGG 57.427 36.000 0.00 0.00 36.22 4.85
3043 4405 0.952010 GATACCCCGCACGTTGTTGT 60.952 55.000 0.00 0.00 0.00 3.32
3057 4419 4.021544 ACGTTGTTGTGGGAATATTTGCAT 60.022 37.500 0.00 0.00 0.00 3.96
3202 4565 7.451501 TCTCATTTATGTTTGCATGTTGAGA 57.548 32.000 0.00 11.36 39.93 3.27
3214 4577 4.768448 TGCATGTTGAGATGGACATTTTCT 59.232 37.500 0.00 0.00 34.42 2.52
3216 4579 6.433716 TGCATGTTGAGATGGACATTTTCTTA 59.566 34.615 0.00 0.00 34.42 2.10
3225 4588 8.246430 AGATGGACATTTTCTTATGCATGAAT 57.754 30.769 10.16 0.00 0.00 2.57
3226 4589 9.358406 AGATGGACATTTTCTTATGCATGAATA 57.642 29.630 10.16 0.89 0.00 1.75
3434 5322 5.835280 AGAGAAGTCCAAATTGAACCATGTT 59.165 36.000 0.00 0.00 0.00 2.71
3455 5343 5.659079 TGTTCCATAAAACATGTTATCCCCC 59.341 40.000 12.39 0.00 34.31 5.40
3604 6121 3.841255 AGGGAGACAAGAAGTTAAGGGAG 59.159 47.826 0.00 0.00 0.00 4.30
3650 6167 0.603707 CATGGGGTCGATTCGGATGG 60.604 60.000 6.18 0.00 0.00 3.51
3723 6241 5.812127 GCTAAATCACCAATGGTTTTGGATC 59.188 40.000 14.53 0.00 39.86 3.36
3740 6258 5.705609 TGGATCTCCTTTGTTTGTAAAGC 57.294 39.130 0.00 0.00 36.55 3.51
4007 6525 3.067833 GCAGCGGAATAGGGTTATTCTC 58.932 50.000 7.10 1.65 43.07 2.87
4008 6526 3.494398 GCAGCGGAATAGGGTTATTCTCA 60.494 47.826 7.10 0.00 43.07 3.27
4489 7008 2.806818 CGCTCGGCTGAGTATTAGAGTA 59.193 50.000 23.36 0.00 44.48 2.59
4639 7177 8.130671 TGTAAGCTAATAAGTCCTGTGTTACT 57.869 34.615 0.00 0.00 0.00 2.24
4658 7196 6.156256 TGTTACTCCAGGTATTTGAGCACTAT 59.844 38.462 0.00 0.00 0.00 2.12
4689 7227 6.726379 TGGTTTATGGTTCCAATCACAGATA 58.274 36.000 0.00 0.00 0.00 1.98
4707 7245 1.209621 TAGCCAGGCCTACCGAAAAT 58.790 50.000 3.98 0.00 42.76 1.82
4711 7249 2.654863 CCAGGCCTACCGAAAATGAAT 58.345 47.619 3.98 0.00 42.76 2.57
4715 7253 3.694566 AGGCCTACCGAAAATGAATTCAC 59.305 43.478 11.07 0.00 42.76 3.18
4716 7254 3.442273 GGCCTACCGAAAATGAATTCACA 59.558 43.478 11.07 0.00 0.00 3.58
4718 7256 5.036737 GCCTACCGAAAATGAATTCACATG 58.963 41.667 11.07 0.00 0.00 3.21
4720 7258 6.624861 GCCTACCGAAAATGAATTCACATGAA 60.625 38.462 11.07 0.00 38.56 2.57
4721 7259 7.312154 CCTACCGAAAATGAATTCACATGAAA 58.688 34.615 11.07 0.00 37.61 2.69
4722 7260 7.975616 CCTACCGAAAATGAATTCACATGAAAT 59.024 33.333 11.07 0.00 37.61 2.17
4723 7261 9.357652 CTACCGAAAATGAATTCACATGAAATT 57.642 29.630 11.07 5.10 37.61 1.82
4724 7262 8.243289 ACCGAAAATGAATTCACATGAAATTC 57.757 30.769 11.07 21.24 37.61 2.17
4725 7263 7.871973 ACCGAAAATGAATTCACATGAAATTCA 59.128 29.630 27.33 27.33 37.61 2.57
4726 7264 8.875803 CCGAAAATGAATTCACATGAAATTCAT 58.124 29.630 28.46 28.46 40.14 2.57
4778 7316 0.240678 CAACAATTGCTACGCCTGCA 59.759 50.000 5.05 0.00 38.80 4.41
4796 7334 6.581712 GCCTGCAGATAAATTTTCCCAAATA 58.418 36.000 17.39 0.00 31.89 1.40
4799 7337 9.048446 CCTGCAGATAAATTTTCCCAAATAATG 57.952 33.333 17.39 0.00 31.89 1.90
4810 7348 9.768662 ATTTTCCCAAATAATGATAAGCATCAC 57.231 29.630 0.00 0.00 36.09 3.06
4811 7349 7.894753 TTCCCAAATAATGATAAGCATCACA 57.105 32.000 0.00 0.00 43.89 3.58
4812 7350 7.275888 TCCCAAATAATGATAAGCATCACAC 57.724 36.000 0.00 0.00 43.89 3.82
4818 7356 2.358957 TGATAAGCATCACACTGGCAC 58.641 47.619 0.00 0.00 36.22 5.01
4826 7364 3.521560 CATCACACTGGCACGTAGTAAT 58.478 45.455 0.00 0.00 41.61 1.89
4830 7368 2.827322 ACACTGGCACGTAGTAATACCA 59.173 45.455 0.00 0.00 41.61 3.25
4832 7370 2.167075 ACTGGCACGTAGTAATACCACC 59.833 50.000 0.00 0.00 41.61 4.61
4837 7375 3.119029 GCACGTAGTAATACCACCCTGAA 60.119 47.826 0.00 0.00 41.61 3.02
4838 7376 4.679662 CACGTAGTAATACCACCCTGAAG 58.320 47.826 0.00 0.00 41.61 3.02
4839 7377 4.159135 CACGTAGTAATACCACCCTGAAGT 59.841 45.833 0.00 0.00 41.61 3.01
4840 7378 4.774200 ACGTAGTAATACCACCCTGAAGTT 59.226 41.667 0.00 0.00 41.94 2.66
4853 7437 9.423964 ACCACCCTGAAGTTTTTATAACTAAAA 57.576 29.630 0.00 0.00 35.53 1.52
4884 7468 2.519771 AAATAAAACGACCCTCCCCC 57.480 50.000 0.00 0.00 0.00 5.40
4922 7506 9.558396 AAATTTGAAAATTGCCATCTAAACAGA 57.442 25.926 1.91 0.00 38.53 3.41
4923 7507 9.558396 AATTTGAAAATTGCCATCTAAACAGAA 57.442 25.926 0.28 0.00 37.24 3.02
4924 7508 8.954950 TTTGAAAATTGCCATCTAAACAGAAA 57.045 26.923 0.00 0.00 0.00 2.52
4925 7509 8.592105 TTGAAAATTGCCATCTAAACAGAAAG 57.408 30.769 0.00 0.00 0.00 2.62
4926 7510 7.725251 TGAAAATTGCCATCTAAACAGAAAGT 58.275 30.769 0.00 0.00 0.00 2.66
4927 7511 8.203485 TGAAAATTGCCATCTAAACAGAAAGTT 58.797 29.630 0.00 0.00 43.89 2.66
4928 7512 7.951530 AAATTGCCATCTAAACAGAAAGTTG 57.048 32.000 0.00 0.00 41.19 3.16
4929 7513 4.503741 TGCCATCTAAACAGAAAGTTGC 57.496 40.909 0.00 0.00 41.19 4.17
4930 7514 3.255642 TGCCATCTAAACAGAAAGTTGCC 59.744 43.478 0.00 0.00 41.19 4.52
4931 7515 3.255642 GCCATCTAAACAGAAAGTTGCCA 59.744 43.478 0.00 0.00 41.19 4.92
4932 7516 4.082026 GCCATCTAAACAGAAAGTTGCCAT 60.082 41.667 0.00 0.00 41.19 4.40
4933 7517 5.404946 CCATCTAAACAGAAAGTTGCCATG 58.595 41.667 0.00 0.00 41.19 3.66
4934 7518 4.503741 TCTAAACAGAAAGTTGCCATGC 57.496 40.909 0.00 0.00 41.19 4.06
4935 7519 4.144297 TCTAAACAGAAAGTTGCCATGCT 58.856 39.130 0.00 0.00 41.19 3.79
4936 7520 3.825143 AAACAGAAAGTTGCCATGCTT 57.175 38.095 0.00 0.00 41.19 3.91
4937 7521 3.825143 AACAGAAAGTTGCCATGCTTT 57.175 38.095 0.00 0.00 39.49 3.51
4938 7522 4.935352 AACAGAAAGTTGCCATGCTTTA 57.065 36.364 0.00 0.00 39.49 1.85
4939 7523 5.473066 AACAGAAAGTTGCCATGCTTTAT 57.527 34.783 0.00 0.00 39.49 1.40
4940 7524 6.588719 AACAGAAAGTTGCCATGCTTTATA 57.411 33.333 0.00 0.00 39.49 0.98
4941 7525 6.588719 ACAGAAAGTTGCCATGCTTTATAA 57.411 33.333 0.00 0.00 35.35 0.98
4942 7526 6.389906 ACAGAAAGTTGCCATGCTTTATAAC 58.610 36.000 0.00 0.00 35.35 1.89
4943 7527 6.209391 ACAGAAAGTTGCCATGCTTTATAACT 59.791 34.615 0.00 0.00 35.35 2.24
4944 7528 7.393234 ACAGAAAGTTGCCATGCTTTATAACTA 59.607 33.333 0.00 0.00 35.35 2.24
4945 7529 8.408601 CAGAAAGTTGCCATGCTTTATAACTAT 58.591 33.333 0.00 0.00 35.35 2.12
4946 7530 8.971073 AGAAAGTTGCCATGCTTTATAACTATT 58.029 29.630 0.00 0.00 35.35 1.73
4947 7531 8.931385 AAAGTTGCCATGCTTTATAACTATTG 57.069 30.769 0.00 0.00 33.68 1.90
4948 7532 7.645058 AGTTGCCATGCTTTATAACTATTGT 57.355 32.000 0.00 0.00 0.00 2.71
4949 7533 7.707104 AGTTGCCATGCTTTATAACTATTGTC 58.293 34.615 0.00 0.00 0.00 3.18
4950 7534 7.339212 AGTTGCCATGCTTTATAACTATTGTCA 59.661 33.333 0.00 0.00 0.00 3.58
4951 7535 7.822161 TGCCATGCTTTATAACTATTGTCAT 57.178 32.000 0.00 0.00 0.00 3.06
4952 7536 7.874940 TGCCATGCTTTATAACTATTGTCATC 58.125 34.615 0.00 0.00 0.00 2.92
4953 7537 7.501892 TGCCATGCTTTATAACTATTGTCATCA 59.498 33.333 0.00 0.00 0.00 3.07
4954 7538 8.352201 GCCATGCTTTATAACTATTGTCATCAA 58.648 33.333 0.00 0.00 37.98 2.57
4976 7560 4.582701 AAAATGTGACGGAATTGCTTCA 57.417 36.364 1.85 1.85 32.70 3.02
4979 7563 2.503331 TGTGACGGAATTGCTTCATGT 58.497 42.857 9.32 0.00 32.70 3.21
5082 7676 4.693420 AGAAATTCAGGAGGGAGAGAGAA 58.307 43.478 0.00 0.00 0.00 2.87
5091 7685 3.386402 GGAGGGAGAGAGAATACTGGTTG 59.614 52.174 0.00 0.00 0.00 3.77
5119 7713 9.846248 AGTTGCTCAGTGATCAATATTTAAAAC 57.154 29.630 12.24 0.00 0.00 2.43
5120 7714 8.788813 GTTGCTCAGTGATCAATATTTAAAACG 58.211 33.333 12.24 0.00 0.00 3.60
5122 7716 8.726068 TGCTCAGTGATCAATATTTAAAACGAA 58.274 29.630 0.00 0.00 0.00 3.85
5123 7717 9.722056 GCTCAGTGATCAATATTTAAAACGAAT 57.278 29.630 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.590792 GCCTCCGCCGTGTATGTAC 60.591 63.158 0.00 0.00 0.00 2.90
18 19 3.746949 CTGCATCACCTCCCGCCTC 62.747 68.421 0.00 0.00 0.00 4.70
47 48 3.197790 CGTCATCGCCCTGCTTGG 61.198 66.667 0.00 0.00 0.00 3.61
48 49 2.125552 TCGTCATCGCCCTGCTTG 60.126 61.111 0.00 0.00 36.96 4.01
49 50 2.125512 GTCGTCATCGCCCTGCTT 60.126 61.111 0.00 0.00 36.96 3.91
59 60 2.370849 ACAAACCCTAGTTGGTCGTCAT 59.629 45.455 0.00 0.00 34.96 3.06
60 61 1.764134 ACAAACCCTAGTTGGTCGTCA 59.236 47.619 0.00 0.00 34.96 4.35
69 70 2.660802 CGGCGGACAAACCCTAGT 59.339 61.111 0.00 0.00 34.64 2.57
90 91 0.620556 CTAGGGCAGGTGGTCAACAT 59.379 55.000 0.00 0.00 0.00 2.71
99 100 2.632763 AAAGACTCTCTAGGGCAGGT 57.367 50.000 0.00 0.00 0.00 4.00
133 134 1.107945 GAGAGAGAGAAACCCCCGAG 58.892 60.000 0.00 0.00 0.00 4.63
136 137 1.552792 CAGTGAGAGAGAGAAACCCCC 59.447 57.143 0.00 0.00 0.00 5.40
140 141 3.572255 AGTGACCAGTGAGAGAGAGAAAC 59.428 47.826 0.00 0.00 0.00 2.78
155 156 5.302360 AGTAAACGCTAATCAAAGTGACCA 58.698 37.500 0.00 0.00 0.00 4.02
183 184 7.084486 GCAAACCGATCTTAGATTGAAAAACT 58.916 34.615 10.87 0.00 32.08 2.66
191 192 2.858344 CGACGCAAACCGATCTTAGATT 59.142 45.455 0.00 0.00 41.02 2.40
269 270 1.740664 GACGGGTCGGAGAAAAGGC 60.741 63.158 0.00 0.00 39.69 4.35
472 475 4.557205 ACGATGGAAGAGTACTTGTTGTC 58.443 43.478 0.00 0.00 36.39 3.18
474 477 4.988540 TGAACGATGGAAGAGTACTTGTTG 59.011 41.667 0.00 0.00 36.39 3.33
487 490 9.559732 AAACATCTTATATTCATGAACGATGGA 57.440 29.630 23.00 15.62 33.27 3.41
513 516 6.627395 ACATCCGATTCACACAAAAACTAA 57.373 33.333 0.00 0.00 0.00 2.24
516 519 9.864034 CTATATACATCCGATTCACACAAAAAC 57.136 33.333 0.00 0.00 0.00 2.43
517 520 9.825109 TCTATATACATCCGATTCACACAAAAA 57.175 29.630 0.00 0.00 0.00 1.94
524 527 7.548097 ACCATGTCTATATACATCCGATTCAC 58.452 38.462 0.94 0.00 38.01 3.18
553 556 4.167554 TGAAACAAGTGGACAAACACAC 57.832 40.909 0.00 0.00 43.72 3.82
563 566 7.174946 ACACTACATAAGGATTGAAACAAGTGG 59.825 37.037 0.00 0.00 35.06 4.00
624 627 4.938832 TGTGTTATGTATTCCCTCCGTTTG 59.061 41.667 0.00 0.00 0.00 2.93
625 628 5.168647 TGTGTTATGTATTCCCTCCGTTT 57.831 39.130 0.00 0.00 0.00 3.60
739 1950 2.923020 CCGGAAATGAAAAATGGCGAAG 59.077 45.455 0.00 0.00 0.00 3.79
742 1953 2.258755 GACCGGAAATGAAAAATGGCG 58.741 47.619 9.46 0.00 0.00 5.69
801 2013 2.657620 GCGCGTCCCCGAGATTAC 60.658 66.667 8.43 0.00 35.78 1.89
924 2136 2.204090 GGTGGGTGGAGAAGGGGA 60.204 66.667 0.00 0.00 0.00 4.81
1156 2372 6.874288 AACAGAGGAAAGAAACTGAATCAG 57.126 37.500 8.98 8.98 37.52 2.90
1159 2375 6.276091 GCAAAACAGAGGAAAGAAACTGAAT 58.724 36.000 0.00 0.00 34.88 2.57
1186 2402 2.485795 CCGGCTCGAGGAGAGGAAG 61.486 68.421 15.58 0.00 46.91 3.46
1280 2496 4.502259 GCACCCGATCAACAGATCTAATCT 60.502 45.833 0.00 0.00 41.15 2.40
1343 2559 4.689612 AATACTGTAACCATGGATCGCT 57.310 40.909 21.47 0.00 0.00 4.93
1374 2590 6.588719 AAAGGTTGTAAAATAGCAGATGCA 57.411 33.333 7.68 0.00 45.16 3.96
1509 2740 2.290260 TGACGGCAGGACAATTTCTCAT 60.290 45.455 0.00 0.00 0.00 2.90
1627 2940 6.251655 ACGTATTAGCTAGAATTCCCTACG 57.748 41.667 0.65 7.84 0.00 3.51
1637 2950 6.668541 AACAACTCGTACGTATTAGCTAGA 57.331 37.500 16.05 0.00 0.00 2.43
1638 2951 6.963242 TGAAACAACTCGTACGTATTAGCTAG 59.037 38.462 16.05 4.97 0.00 3.42
1676 2989 4.938575 ACCTCTCTCTCTTTCTCAGGTA 57.061 45.455 0.00 0.00 30.76 3.08
1715 3028 0.472471 AGCAAAAGGTTCCGTCTGGA 59.528 50.000 0.00 0.00 44.61 3.86
1765 3078 5.928264 GCAAACATTCCATATCTAATTGGGC 59.072 40.000 0.00 0.00 33.62 5.36
1783 3096 8.296713 GTCTTTAAGTCATAGAAATGGCAAACA 58.703 33.333 0.00 0.00 40.36 2.83
1886 3201 4.642885 CCAGGAAAACCAAGTCTGTTGTAA 59.357 41.667 0.00 0.00 0.00 2.41
1900 3215 5.010012 AGACATCATTGTTCACCAGGAAAAC 59.990 40.000 0.00 0.00 37.23 2.43
1922 3237 9.838975 CAATAATACAGCACAATGTTAACAAGA 57.161 29.630 13.23 0.00 34.56 3.02
2223 3538 3.266772 TGACCAGCTGTATCCCTGAAAAT 59.733 43.478 13.81 0.00 0.00 1.82
2404 3763 9.791801 AAGCATGAAACAAAAATAAATAAGGGT 57.208 25.926 0.00 0.00 0.00 4.34
2468 3828 1.270826 CTCTCAGTGCGAACTTCCTCA 59.729 52.381 0.00 0.00 0.00 3.86
2646 4006 4.559153 ACTGCAAATTTTGGTACATCTGC 58.441 39.130 10.96 0.00 39.30 4.26
2699 4059 5.892160 AACTACGCTAGTATCACTCACAA 57.108 39.130 0.00 0.00 38.26 3.33
2799 4159 2.514803 TCGACAAGTGGATCAGACTGA 58.485 47.619 7.80 7.80 0.00 3.41
2800 4160 3.516981 ATCGACAAGTGGATCAGACTG 57.483 47.619 0.00 0.00 0.00 3.51
2819 4179 9.119418 ACAAAAAGGCAGTTTGCTTAAATAAAT 57.881 25.926 11.47 0.00 44.28 1.40
2822 4182 8.499403 AAACAAAAAGGCAGTTTGCTTAAATA 57.501 26.923 11.47 0.00 44.28 1.40
2823 4183 7.389803 AAACAAAAAGGCAGTTTGCTTAAAT 57.610 28.000 11.47 0.00 44.28 1.40
2938 4300 5.532406 TGGCCTGCAAAGAATTGTATATCTC 59.468 40.000 3.32 0.00 38.85 2.75
2954 4316 2.427812 CACAAATATCATGTGGCCTGCA 59.572 45.455 3.32 3.24 43.45 4.41
3120 4482 9.979578 AACACAATAAAGCATCTGAATTTACAA 57.020 25.926 0.00 0.00 0.00 2.41
3121 4483 9.979578 AAACACAATAAAGCATCTGAATTTACA 57.020 25.926 0.00 0.00 0.00 2.41
3196 4559 6.855836 TGCATAAGAAAATGTCCATCTCAAC 58.144 36.000 0.00 0.00 0.00 3.18
3202 4565 8.916062 TGTATTCATGCATAAGAAAATGTCCAT 58.084 29.630 0.00 0.00 0.00 3.41
3225 4588 3.586470 AAAGGACCACCACAACATGTA 57.414 42.857 0.00 0.00 38.94 2.29
3226 4589 2.430332 CAAAAGGACCACCACAACATGT 59.570 45.455 0.00 0.00 38.94 3.21
3240 4605 1.608542 GCAACATGCATGGCAAAAGGA 60.609 47.619 29.41 0.00 43.62 3.36
3461 5349 1.101049 GTGTGTCTGTGTGTTGGGGG 61.101 60.000 0.00 0.00 0.00 5.40
3462 5350 1.436195 CGTGTGTCTGTGTGTTGGGG 61.436 60.000 0.00 0.00 0.00 4.96
3463 5351 2.013807 CGTGTGTCTGTGTGTTGGG 58.986 57.895 0.00 0.00 0.00 4.12
3464 5352 1.351707 GCGTGTGTCTGTGTGTTGG 59.648 57.895 0.00 0.00 0.00 3.77
3465 5353 0.247655 GTGCGTGTGTCTGTGTGTTG 60.248 55.000 0.00 0.00 0.00 3.33
3466 5354 0.672091 TGTGCGTGTGTCTGTGTGTT 60.672 50.000 0.00 0.00 0.00 3.32
3467 5355 0.672091 TTGTGCGTGTGTCTGTGTGT 60.672 50.000 0.00 0.00 0.00 3.72
3468 5356 0.445829 TTTGTGCGTGTGTCTGTGTG 59.554 50.000 0.00 0.00 0.00 3.82
3469 5357 1.378531 ATTTGTGCGTGTGTCTGTGT 58.621 45.000 0.00 0.00 0.00 3.72
3470 5358 3.600717 TTATTTGTGCGTGTGTCTGTG 57.399 42.857 0.00 0.00 0.00 3.66
3471 5359 3.563808 ACATTATTTGTGCGTGTGTCTGT 59.436 39.130 0.00 0.00 37.11 3.41
3472 5360 4.145876 ACATTATTTGTGCGTGTGTCTG 57.854 40.909 0.00 0.00 37.11 3.51
3473 5361 4.274705 TCAACATTATTTGTGCGTGTGTCT 59.725 37.500 0.00 0.00 38.99 3.41
3474 5362 4.532276 TCAACATTATTTGTGCGTGTGTC 58.468 39.130 0.00 0.00 38.99 3.67
3475 5363 4.560136 TCAACATTATTTGTGCGTGTGT 57.440 36.364 0.00 0.00 38.99 3.72
3476 5364 5.879948 TTTCAACATTATTTGTGCGTGTG 57.120 34.783 0.00 0.00 38.99 3.82
3477 5365 6.699204 TGATTTTCAACATTATTTGTGCGTGT 59.301 30.769 0.00 0.00 38.99 4.49
3604 6121 8.391106 CCAGTAATATTACAGTTGCACTCTTTC 58.609 37.037 24.05 0.00 36.12 2.62
3650 6167 7.746475 GCTCATTTACACTCTGTTTACATGTTC 59.254 37.037 2.30 0.00 0.00 3.18
3655 6172 9.502091 AAATAGCTCATTTACACTCTGTTTACA 57.498 29.630 0.00 0.00 34.99 2.41
3714 6232 7.042725 GCTTTACAAACAAAGGAGATCCAAAAC 60.043 37.037 0.92 0.00 36.27 2.43
3723 6241 9.559958 CATATTAGTGCTTTACAAACAAAGGAG 57.440 33.333 0.00 0.00 36.66 3.69
3975 6493 1.674359 TTCCGCTGCTTTTGAGTTCA 58.326 45.000 0.00 0.00 0.00 3.18
4007 6525 5.645067 AGTAATGTCATGTGACCAGTTCATG 59.355 40.000 10.40 9.24 44.15 3.07
4008 6526 5.809001 AGTAATGTCATGTGACCAGTTCAT 58.191 37.500 10.40 0.00 44.15 2.57
4051 6569 3.446873 TGGTCAAGAAATTGTGCTTGTGT 59.553 39.130 12.76 0.00 41.60 3.72
4052 6570 4.044336 TGGTCAAGAAATTGTGCTTGTG 57.956 40.909 12.76 0.00 41.60 3.33
4489 7008 7.360113 AGGTTGAAACATAAACCAATCACTT 57.640 32.000 7.28 0.00 46.91 3.16
4522 7042 1.909700 AACACAACAAGATGGGCGAT 58.090 45.000 0.00 0.00 0.00 4.58
4630 7168 4.631813 GCTCAAATACCTGGAGTAACACAG 59.368 45.833 0.00 0.00 33.70 3.66
4639 7177 6.161855 CACTATAGTGCTCAAATACCTGGA 57.838 41.667 19.55 0.00 39.39 3.86
4658 7196 4.374689 TGGAACCATAAACCAAGCACTA 57.625 40.909 0.00 0.00 0.00 2.74
4689 7227 0.394352 CATTTTCGGTAGGCCTGGCT 60.394 55.000 17.99 5.31 0.00 4.75
4707 7245 7.549839 GGAAGGATGAATTTCATGTGAATTCA 58.450 34.615 26.61 26.61 37.20 2.57
4711 7249 5.009631 ACGGAAGGATGAATTTCATGTGAA 58.990 37.500 16.41 0.00 37.20 3.18
4715 7253 7.645340 GTCAATAACGGAAGGATGAATTTCATG 59.355 37.037 16.41 3.94 37.20 3.07
4716 7254 7.339212 TGTCAATAACGGAAGGATGAATTTCAT 59.661 33.333 11.64 11.64 40.34 2.57
4718 7256 7.083875 TGTCAATAACGGAAGGATGAATTTC 57.916 36.000 0.00 0.00 0.00 2.17
4720 7258 7.645058 ATTGTCAATAACGGAAGGATGAATT 57.355 32.000 0.00 0.00 0.00 2.17
4721 7259 7.122650 ACAATTGTCAATAACGGAAGGATGAAT 59.877 33.333 4.92 0.00 0.00 2.57
4722 7260 6.432783 ACAATTGTCAATAACGGAAGGATGAA 59.567 34.615 4.92 0.00 0.00 2.57
4723 7261 5.943416 ACAATTGTCAATAACGGAAGGATGA 59.057 36.000 4.92 0.00 0.00 2.92
4724 7262 6.194796 ACAATTGTCAATAACGGAAGGATG 57.805 37.500 4.92 0.00 0.00 3.51
4725 7263 5.064707 CGACAATTGTCAATAACGGAAGGAT 59.935 40.000 32.06 0.00 44.99 3.24
4726 7264 4.390603 CGACAATTGTCAATAACGGAAGGA 59.609 41.667 32.06 0.00 44.99 3.36
4772 7310 4.470334 TTGGGAAAATTTATCTGCAGGC 57.530 40.909 15.13 0.00 0.00 4.85
4796 7334 3.379372 GTGCCAGTGTGATGCTTATCATT 59.621 43.478 0.00 0.00 35.05 2.57
4799 7337 1.328680 CGTGCCAGTGTGATGCTTATC 59.671 52.381 0.00 0.00 0.00 1.75
4801 7339 0.034756 ACGTGCCAGTGTGATGCTTA 59.965 50.000 0.00 0.00 0.00 3.09
4802 7340 0.034756 TACGTGCCAGTGTGATGCTT 59.965 50.000 0.00 0.00 0.00 3.91
4803 7341 0.390340 CTACGTGCCAGTGTGATGCT 60.390 55.000 0.00 0.00 0.00 3.79
4804 7342 0.670546 ACTACGTGCCAGTGTGATGC 60.671 55.000 0.00 0.00 0.00 3.91
4807 7345 3.119388 GGTATTACTACGTGCCAGTGTGA 60.119 47.826 0.00 0.00 0.00 3.58
4808 7346 3.184541 GGTATTACTACGTGCCAGTGTG 58.815 50.000 0.00 0.00 0.00 3.82
4809 7347 2.827322 TGGTATTACTACGTGCCAGTGT 59.173 45.455 0.00 0.00 0.00 3.55
4810 7348 3.184541 GTGGTATTACTACGTGCCAGTG 58.815 50.000 0.00 0.00 0.00 3.66
4811 7349 2.167075 GGTGGTATTACTACGTGCCAGT 59.833 50.000 0.00 0.00 29.51 4.00
4812 7350 2.482490 GGGTGGTATTACTACGTGCCAG 60.482 54.545 0.00 0.00 29.51 4.85
4818 7356 4.996788 ACTTCAGGGTGGTATTACTACG 57.003 45.455 4.49 0.00 29.51 3.51
4896 7480 9.558396 TCTGTTTAGATGGCAATTTTCAAATTT 57.442 25.926 0.00 0.00 36.52 1.82
4897 7481 9.558396 TTCTGTTTAGATGGCAATTTTCAAATT 57.442 25.926 0.00 0.00 34.41 1.82
4898 7482 9.558396 TTTCTGTTTAGATGGCAATTTTCAAAT 57.442 25.926 0.00 0.00 31.81 2.32
4899 7483 8.954950 TTTCTGTTTAGATGGCAATTTTCAAA 57.045 26.923 0.00 0.00 31.81 2.69
4900 7484 8.203485 ACTTTCTGTTTAGATGGCAATTTTCAA 58.797 29.630 0.00 0.00 31.81 2.69
4901 7485 7.725251 ACTTTCTGTTTAGATGGCAATTTTCA 58.275 30.769 0.00 0.00 31.81 2.69
4902 7486 8.490355 CAACTTTCTGTTTAGATGGCAATTTTC 58.510 33.333 0.00 0.00 36.63 2.29
4903 7487 7.041848 GCAACTTTCTGTTTAGATGGCAATTTT 60.042 33.333 0.00 0.00 36.63 1.82
4904 7488 6.424812 GCAACTTTCTGTTTAGATGGCAATTT 59.575 34.615 0.00 0.00 36.63 1.82
4905 7489 5.928264 GCAACTTTCTGTTTAGATGGCAATT 59.072 36.000 0.00 0.00 36.63 2.32
4906 7490 5.473039 GCAACTTTCTGTTTAGATGGCAAT 58.527 37.500 0.00 0.00 36.63 3.56
4907 7491 4.261994 GGCAACTTTCTGTTTAGATGGCAA 60.262 41.667 0.00 0.00 35.81 4.52
4908 7492 3.255642 GGCAACTTTCTGTTTAGATGGCA 59.744 43.478 0.00 0.00 35.81 4.92
4909 7493 3.255642 TGGCAACTTTCTGTTTAGATGGC 59.744 43.478 0.00 0.00 36.63 4.40
4910 7494 5.404946 CATGGCAACTTTCTGTTTAGATGG 58.595 41.667 0.00 0.00 36.63 3.51
4911 7495 4.860907 GCATGGCAACTTTCTGTTTAGATG 59.139 41.667 0.00 0.00 36.63 2.90
4912 7496 4.768968 AGCATGGCAACTTTCTGTTTAGAT 59.231 37.500 0.00 0.00 36.63 1.98
4913 7497 4.144297 AGCATGGCAACTTTCTGTTTAGA 58.856 39.130 0.00 0.00 36.63 2.10
4914 7498 4.510038 AGCATGGCAACTTTCTGTTTAG 57.490 40.909 0.00 0.00 36.63 1.85
4915 7499 4.935352 AAGCATGGCAACTTTCTGTTTA 57.065 36.364 0.00 0.00 36.63 2.01
4916 7500 3.825143 AAGCATGGCAACTTTCTGTTT 57.175 38.095 0.00 0.00 36.63 2.83
4917 7501 3.825143 AAAGCATGGCAACTTTCTGTT 57.175 38.095 11.75 0.00 39.92 3.16
4918 7502 6.209391 AGTTATAAAGCATGGCAACTTTCTGT 59.791 34.615 18.60 10.98 37.33 3.41
4919 7503 6.624423 AGTTATAAAGCATGGCAACTTTCTG 58.376 36.000 18.60 0.95 37.33 3.02
4920 7504 6.840780 AGTTATAAAGCATGGCAACTTTCT 57.159 33.333 18.60 13.26 37.33 2.52
4921 7505 9.023967 CAATAGTTATAAAGCATGGCAACTTTC 57.976 33.333 18.60 7.93 37.33 2.62
4922 7506 8.531146 ACAATAGTTATAAAGCATGGCAACTTT 58.469 29.630 18.92 18.92 39.38 2.66
4923 7507 8.066612 ACAATAGTTATAAAGCATGGCAACTT 57.933 30.769 0.00 0.00 37.61 2.66
4924 7508 7.339212 TGACAATAGTTATAAAGCATGGCAACT 59.661 33.333 0.00 0.00 37.61 3.16
4925 7509 7.479980 TGACAATAGTTATAAAGCATGGCAAC 58.520 34.615 0.00 0.00 0.00 4.17
4926 7510 7.637631 TGACAATAGTTATAAAGCATGGCAA 57.362 32.000 0.00 0.00 0.00 4.52
4927 7511 7.501892 TGATGACAATAGTTATAAAGCATGGCA 59.498 33.333 0.00 0.00 0.00 4.92
4928 7512 7.874940 TGATGACAATAGTTATAAAGCATGGC 58.125 34.615 0.00 0.00 0.00 4.40
4954 7538 4.942852 TGAAGCAATTCCGTCACATTTTT 58.057 34.783 0.00 0.00 0.00 1.94
4955 7539 4.582701 TGAAGCAATTCCGTCACATTTT 57.417 36.364 0.00 0.00 0.00 1.82
4956 7540 4.022068 ACATGAAGCAATTCCGTCACATTT 60.022 37.500 0.00 0.00 0.00 2.32
4957 7541 3.507233 ACATGAAGCAATTCCGTCACATT 59.493 39.130 0.00 0.00 0.00 2.71
4958 7542 3.084039 ACATGAAGCAATTCCGTCACAT 58.916 40.909 0.00 0.00 0.00 3.21
4959 7543 2.483877 GACATGAAGCAATTCCGTCACA 59.516 45.455 0.00 0.00 0.00 3.58
4960 7544 2.483877 TGACATGAAGCAATTCCGTCAC 59.516 45.455 0.00 0.00 31.59 3.67
4961 7545 2.483877 GTGACATGAAGCAATTCCGTCA 59.516 45.455 0.00 6.35 33.07 4.35
4965 7549 2.226437 ACGTGTGACATGAAGCAATTCC 59.774 45.455 12.40 0.00 0.00 3.01
5016 7601 6.231211 CCACACCAGATTGTAAGTTAGTTCT 58.769 40.000 0.00 0.00 0.00 3.01
5031 7616 1.497286 ACTAAAAAGGGCCACACCAGA 59.503 47.619 6.18 0.00 42.05 3.86
5082 7676 4.283467 TCACTGAGCAACTACAACCAGTAT 59.717 41.667 0.00 0.00 34.01 2.12
5118 7712 5.212194 CGGACATTTTGAGTTTTGATTCGT 58.788 37.500 0.00 0.00 0.00 3.85
5119 7713 5.212194 ACGGACATTTTGAGTTTTGATTCG 58.788 37.500 0.00 0.00 0.00 3.34
5120 7714 6.918022 AGAACGGACATTTTGAGTTTTGATTC 59.082 34.615 0.00 0.00 0.00 2.52
5122 7716 6.183360 ACAGAACGGACATTTTGAGTTTTGAT 60.183 34.615 4.58 0.00 33.15 2.57
5123 7717 5.124776 ACAGAACGGACATTTTGAGTTTTGA 59.875 36.000 4.58 0.00 33.15 2.69



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

AutoCloner maintained by Alex Coulton.