Multiple sequence alignment - TraesCS1A01G227200

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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 TraesCS1A01G227200 chr1A 100.000 5669 0 0 1 5669 397777081 397771413 0.000000e+00 10469.0
1 TraesCS1A01G227200 chr1B 93.020 2407 123 19 3289 5669 428810725 428808338 0.000000e+00 3472.0
2 TraesCS1A01G227200 chr1B 89.313 1806 88 30 628 2339 428813635 428811841 0.000000e+00 2169.0
3 TraesCS1A01G227200 chr1B 89.378 932 60 11 2384 3284 428811765 428810842 0.000000e+00 1136.0
4 TraesCS1A01G227200 chr1B 91.681 589 44 3 1 585 428816508 428815921 0.000000e+00 811.0
5 TraesCS1A01G227200 chr1B 100.000 39 0 0 3285 3323 370044470 370044508 7.880000e-09 73.1
6 TraesCS1A01G227200 chr1D 92.344 1933 116 19 3319 5241 316682793 316680883 0.000000e+00 2721.0
7 TraesCS1A01G227200 chr1D 89.731 2084 119 38 345 2339 316686170 316684093 0.000000e+00 2575.0
8 TraesCS1A01G227200 chr1D 90.670 911 55 9 2369 3256 316684032 316683129 0.000000e+00 1184.0
9 TraesCS1A01G227200 chr1D 94.218 294 16 1 3 295 316686456 316686163 1.120000e-121 448.0
10 TraesCS1A01G227200 chr1D 91.586 309 19 5 2967 3271 316683097 316682792 2.440000e-113 420.0
11 TraesCS1A01G227200 chr1D 90.800 250 14 5 5427 5669 316680703 316680456 5.480000e-85 326.0
12 TraesCS1A01G227200 chr1D 92.632 190 10 2 5276 5462 316680893 316680705 2.600000e-68 270.0
13 TraesCS1A01G227200 chrUn 97.619 42 0 1 3287 3327 378270618 378270659 2.830000e-08 71.3
14 TraesCS1A01G227200 chrUn 97.619 42 0 1 3287 3327 447954296 447954255 2.830000e-08 71.3
15 TraesCS1A01G227200 chrUn 95.455 44 0 2 3285 3327 94223237 94223195 1.020000e-07 69.4
16 TraesCS1A01G227200 chr2A 90.909 55 1 3 3269 3320 747263465 747263412 2.830000e-08 71.3
17 TraesCS1A01G227200 chr7D 87.931 58 3 2 3266 3320 102542967 102542911 1.320000e-06 65.8
18 TraesCS1A01G227200 chr7D 87.500 56 3 2 3269 3322 52267949 52267896 1.710000e-05 62.1
19 TraesCS1A01G227200 chr4A 88.136 59 2 4 3269 3322 88012064 88012122 1.320000e-06 65.8
20 TraesCS1A01G227200 chr4A 100.000 28 0 0 12 39 646975252 646975225 1.000000e-02 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 TraesCS1A01G227200 chr1A 397771413 397777081 5668 True 10469.000000 10469 100.000000 1 5669 1 chr1A.!!$R1 5668
1 TraesCS1A01G227200 chr1B 428808338 428816508 8170 True 1897.000000 3472 90.848000 1 5669 4 chr1B.!!$R1 5668
2 TraesCS1A01G227200 chr1D 316680456 316686456 6000 True 1134.857143 2721 91.711571 3 5669 7 chr1D.!!$R1 5666

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
633 2882 0.551624 TTTGTAGCCCTAAGCCCCCT 60.552 55.000 0.00 0.0 45.47 4.79 F
1144 3426 0.611618 TTGGGGCTGATGCGTGATTT 60.612 50.000 0.00 0.0 40.82 2.17 F
1156 3438 1.132640 GTGATTTCGCTGTGGTCGC 59.867 57.895 0.00 0.0 0.00 5.19 F
1693 3990 1.265236 CTGCTCCCTTGACAGAGAGT 58.735 55.000 0.00 0.0 33.10 3.24 F
2593 4976 0.250727 GCCCAGAACTGTGTAGGCAA 60.251 55.000 12.48 0.0 40.20 4.52 F
2805 5188 0.837272 GCCCTCTTAGGTGCCATGTA 59.163 55.000 0.00 0.0 31.93 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2510 4893 0.036875 AGCTAGCCTGTGTTGAACCC 59.963 55.000 12.13 0.00 0.00 4.11 R
2571 4954 1.614317 GCCTACACAGTTCTGGGCAAT 60.614 52.381 11.10 0.00 39.38 3.56 R
2575 4958 2.086869 CATTGCCTACACAGTTCTGGG 58.913 52.381 0.09 0.09 0.00 4.45 R
3577 6428 0.467804 TGGCAGCAGTACAGTGTGAA 59.532 50.000 5.88 0.00 0.00 3.18 R
4203 7054 0.099791 ACGTCAAAAAGGCAACCACG 59.900 50.000 0.00 0.00 37.17 4.94 R
4740 7613 0.032403 TGCATGAACAAGGTTGCAGC 59.968 50.000 0.00 0.00 39.98 5.25 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
119 120 6.729187 ACTTTGCACTCTATTTTGTGACTTC 58.271 36.000 0.00 0.00 36.38 3.01
134 135 3.683822 GTGACTTCAAGGCATCTTCTGAG 59.316 47.826 0.00 0.00 34.53 3.35
259 260 2.349590 CATCCGTGCAAGTTCATGAGA 58.650 47.619 0.00 0.00 0.00 3.27
263 264 2.079158 CGTGCAAGTTCATGAGATGGT 58.921 47.619 0.00 0.00 0.00 3.55
316 317 1.306654 TCCCGGGCCTGTGATAAGT 60.307 57.895 18.49 0.00 0.00 2.24
326 327 4.222124 CCTGTGATAAGTAAGGCTTGGT 57.778 45.455 10.69 0.00 38.05 3.67
358 359 2.615493 CCATGTCTGGCTAAGTCGGTTT 60.615 50.000 0.00 0.00 35.23 3.27
413 414 1.231958 GCCATCCGTCACCGTTTGAA 61.232 55.000 0.00 0.00 35.39 2.69
421 423 2.599848 CGTCACCGTTTGAAGCTTCTTG 60.600 50.000 26.09 13.06 35.39 3.02
424 426 2.097466 CACCGTTTGAAGCTTCTTGTGT 59.903 45.455 26.09 14.04 0.00 3.72
448 450 7.885922 TGTCTTCTGTATCTAGTCACTTCTTCT 59.114 37.037 0.00 0.00 0.00 2.85
450 452 8.735315 TCTTCTGTATCTAGTCACTTCTTCTTG 58.265 37.037 0.00 0.00 0.00 3.02
486 488 3.539604 CAATCCTTTTTGTTGGGTTGCA 58.460 40.909 0.00 0.00 37.59 4.08
500 502 3.004171 GGGTTGCATGTACGTGAATGTA 58.996 45.455 19.38 0.00 0.00 2.29
504 506 6.647481 GGGTTGCATGTACGTGAATGTATATA 59.353 38.462 19.38 0.00 0.00 0.86
620 2854 5.835113 ATTCCGATTTCCCACATTTGTAG 57.165 39.130 0.00 0.00 0.00 2.74
625 2859 4.532834 GATTTCCCACATTTGTAGCCCTA 58.467 43.478 0.00 0.00 0.00 3.53
626 2860 4.390129 TTTCCCACATTTGTAGCCCTAA 57.610 40.909 0.00 0.00 0.00 2.69
633 2882 0.551624 TTTGTAGCCCTAAGCCCCCT 60.552 55.000 0.00 0.00 45.47 4.79
860 3118 2.279186 GGCCAACAAACACCGCAC 60.279 61.111 0.00 0.00 0.00 5.34
861 3119 2.653766 GCCAACAAACACCGCACG 60.654 61.111 0.00 0.00 0.00 5.34
862 3120 2.653766 CCAACAAACACCGCACGC 60.654 61.111 0.00 0.00 0.00 5.34
863 3121 2.407210 CAACAAACACCGCACGCT 59.593 55.556 0.00 0.00 0.00 5.07
963 3221 2.909662 ACAAAGGGGAAAGGAGAGAGAG 59.090 50.000 0.00 0.00 0.00 3.20
964 3222 3.177228 CAAAGGGGAAAGGAGAGAGAGA 58.823 50.000 0.00 0.00 0.00 3.10
1011 3269 3.087253 TCCGCCATGGATTCCGGT 61.087 61.111 22.82 0.00 43.74 5.28
1144 3426 0.611618 TTGGGGCTGATGCGTGATTT 60.612 50.000 0.00 0.00 40.82 2.17
1156 3438 1.132640 GTGATTTCGCTGTGGTCGC 59.867 57.895 0.00 0.00 0.00 5.19
1354 3651 2.019984 GCCCTTTCTGATGATTCGCTT 58.980 47.619 0.00 0.00 0.00 4.68
1419 3716 4.337145 TGGGACATTTTACGCCAAGTATT 58.663 39.130 0.00 0.00 34.88 1.89
1478 3775 2.685106 TGGTGCAATTAAGGAACCCA 57.315 45.000 4.94 0.00 0.00 4.51
1567 3864 8.571461 TTTGTAGATTGCTGAAAAGATGAGAT 57.429 30.769 0.00 0.00 0.00 2.75
1664 3961 2.331451 GTGGCTGCGTTGGAACAC 59.669 61.111 0.00 0.00 39.29 3.32
1675 3972 3.473625 CGTTGGAACACTTTAGGAACCT 58.526 45.455 0.00 0.00 39.29 3.50
1676 3973 3.250040 CGTTGGAACACTTTAGGAACCTG 59.750 47.826 3.36 0.00 39.29 4.00
1681 3978 1.351350 ACACTTTAGGAACCTGCTCCC 59.649 52.381 3.36 0.00 35.95 4.30
1693 3990 1.265236 CTGCTCCCTTGACAGAGAGT 58.735 55.000 0.00 0.00 33.10 3.24
1696 3993 2.037772 TGCTCCCTTGACAGAGAGTTTC 59.962 50.000 0.00 0.00 31.43 2.78
1765 4062 4.683832 CGTTCCTACAGGAGTCTTTATGG 58.316 47.826 0.00 0.00 46.36 2.74
1766 4063 4.443621 GTTCCTACAGGAGTCTTTATGGC 58.556 47.826 0.00 0.00 46.36 4.40
1781 4094 6.813649 GTCTTTATGGCTCTTGGGAATTTTTC 59.186 38.462 0.00 0.00 0.00 2.29
1799 4112 5.491323 TTTTCCTTTGGTCAGTTTGGTTT 57.509 34.783 0.00 0.00 0.00 3.27
1849 4162 7.793036 AGGAGTATTAGGTATTGTTGGTTCTC 58.207 38.462 0.00 0.00 0.00 2.87
1854 4167 4.618920 AGGTATTGTTGGTTCTCGAGTT 57.381 40.909 13.13 0.00 0.00 3.01
1855 4168 4.315803 AGGTATTGTTGGTTCTCGAGTTG 58.684 43.478 13.13 0.00 0.00 3.16
1857 4170 4.389077 GGTATTGTTGGTTCTCGAGTTGAG 59.611 45.833 13.13 0.29 46.72 3.02
1858 4171 3.536956 TTGTTGGTTCTCGAGTTGAGT 57.463 42.857 13.13 0.00 45.46 3.41
1859 4172 3.536956 TGTTGGTTCTCGAGTTGAGTT 57.463 42.857 13.13 0.00 45.46 3.01
1860 4173 4.659111 TGTTGGTTCTCGAGTTGAGTTA 57.341 40.909 13.13 0.00 45.46 2.24
1863 4176 3.585862 TGGTTCTCGAGTTGAGTTATGC 58.414 45.455 13.13 0.00 45.46 3.14
1864 4177 3.006430 TGGTTCTCGAGTTGAGTTATGCA 59.994 43.478 13.13 0.00 45.46 3.96
1865 4178 3.994392 GGTTCTCGAGTTGAGTTATGCAA 59.006 43.478 13.13 0.00 45.46 4.08
1890 4214 7.417612 ACTAGCTGAAACAGTTTTGTGTTATG 58.582 34.615 0.00 0.00 39.82 1.90
1908 4232 2.530460 TGGCTGGCCAATAAGATTGT 57.470 45.000 12.27 0.00 44.12 2.71
1910 4234 2.291475 TGGCTGGCCAATAAGATTGTCA 60.291 45.455 12.27 0.00 44.12 3.58
1924 4268 4.152647 AGATTGTCAGTACACAGTGGAGA 58.847 43.478 5.31 0.00 34.61 3.71
1952 4296 7.553881 TGCTCAAAGCTTAATACACTAATCC 57.446 36.000 0.00 0.00 42.97 3.01
1960 4304 7.431249 AGCTTAATACACTAATCCGAATCGAA 58.569 34.615 3.36 0.00 0.00 3.71
2033 4383 5.505173 AATCATGACATCACCGAAATTCC 57.495 39.130 0.00 0.00 0.00 3.01
2040 4390 4.398319 ACATCACCGAAATTCCTCACTTT 58.602 39.130 0.00 0.00 0.00 2.66
2054 4404 9.785982 AATTCCTCACTTTCTCCTAATATTAGC 57.214 33.333 15.86 0.00 0.00 3.09
2114 4464 9.758651 AACCATCAACTTTGGTAAAATTCTTAC 57.241 29.630 0.00 3.37 46.75 2.34
2134 4484 3.150767 ACCATATAGCTGACTCGGTCTC 58.849 50.000 0.00 0.00 33.15 3.36
2145 4495 5.452077 GCTGACTCGGTCTCAAATATAAGGT 60.452 44.000 5.77 0.00 33.15 3.50
2147 4497 5.421056 TGACTCGGTCTCAAATATAAGGTGT 59.579 40.000 5.77 0.00 33.15 4.16
2148 4498 5.661458 ACTCGGTCTCAAATATAAGGTGTG 58.339 41.667 0.00 0.00 0.00 3.82
2252 4604 8.437742 GTTCATTTCAACATGATTCCAACAATC 58.562 33.333 0.00 0.00 33.07 2.67
2261 4613 8.542497 ACATGATTCCAACAATCTCATTTTTG 57.458 30.769 0.00 0.00 31.50 2.44
2281 4633 8.760103 TTTTTGAATCACACAATCCACATATG 57.240 30.769 0.00 0.00 0.00 1.78
2340 4692 9.941664 CTTGAGAAACATGTGCTATATTTTAGG 57.058 33.333 0.00 0.00 0.00 2.69
2341 4693 9.679661 TTGAGAAACATGTGCTATATTTTAGGA 57.320 29.630 0.00 0.00 0.00 2.94
2345 4697 6.169557 ACATGTGCTATATTTTAGGACCGA 57.830 37.500 0.00 0.00 35.41 4.69
2346 4698 6.588204 ACATGTGCTATATTTTAGGACCGAA 58.412 36.000 0.00 0.00 35.41 4.30
2347 4699 6.706270 ACATGTGCTATATTTTAGGACCGAAG 59.294 38.462 0.00 0.00 35.41 3.79
2348 4700 6.474140 TGTGCTATATTTTAGGACCGAAGA 57.526 37.500 3.96 0.00 35.41 2.87
2350 4702 6.984474 TGTGCTATATTTTAGGACCGAAGAAG 59.016 38.462 3.96 0.00 35.41 2.85
2351 4703 6.985059 GTGCTATATTTTAGGACCGAAGAAGT 59.015 38.462 0.00 0.00 30.94 3.01
2352 4704 8.139989 GTGCTATATTTTAGGACCGAAGAAGTA 58.860 37.037 0.00 0.00 30.94 2.24
2354 4706 9.356433 GCTATATTTTAGGACCGAAGAAGTATC 57.644 37.037 0.00 0.00 0.00 2.24
2357 4709 6.845758 TTTTAGGACCGAAGAAGTATCTCA 57.154 37.500 0.00 0.00 33.77 3.27
2359 4711 2.691011 AGGACCGAAGAAGTATCTCAGC 59.309 50.000 0.00 0.00 33.77 4.26
2360 4712 2.691011 GGACCGAAGAAGTATCTCAGCT 59.309 50.000 0.00 0.00 33.77 4.24
2361 4713 3.884091 GGACCGAAGAAGTATCTCAGCTA 59.116 47.826 0.00 0.00 33.77 3.32
2362 4714 4.023536 GGACCGAAGAAGTATCTCAGCTAG 60.024 50.000 0.00 0.00 33.77 3.42
2363 4715 4.528920 ACCGAAGAAGTATCTCAGCTAGT 58.471 43.478 0.00 0.00 33.77 2.57
2364 4716 4.577283 ACCGAAGAAGTATCTCAGCTAGTC 59.423 45.833 0.00 0.00 33.77 2.59
2366 4718 5.066634 CCGAAGAAGTATCTCAGCTAGTCAA 59.933 44.000 0.00 0.00 33.77 3.18
2367 4719 6.404844 CCGAAGAAGTATCTCAGCTAGTCAAA 60.405 42.308 0.00 0.00 33.77 2.69
2369 4721 8.346300 CGAAGAAGTATCTCAGCTAGTCAAATA 58.654 37.037 0.00 0.00 33.77 1.40
2466 4849 4.162690 CCTCCCCTGCTACACGGC 62.163 72.222 0.00 0.00 0.00 5.68
2473 4856 2.283604 TGCTACACGGCCTCTGGA 60.284 61.111 0.00 0.00 0.00 3.86
2491 4874 3.192954 ATGCCAACGTGTTGTGCGG 62.193 57.895 11.45 0.00 38.61 5.69
2510 4893 1.297967 CACGCGATGACGAGAGAGG 60.298 63.158 15.93 0.00 41.48 3.69
2583 4966 1.870055 CGCTTGCATTGCCCAGAACT 61.870 55.000 6.12 0.00 0.00 3.01
2593 4976 0.250727 GCCCAGAACTGTGTAGGCAA 60.251 55.000 12.48 0.00 40.20 4.52
2596 4979 1.470098 CCAGAACTGTGTAGGCAATGC 59.530 52.381 0.00 0.00 0.00 3.56
2612 4995 3.790820 GCAATGCCACACGTATTAACATG 59.209 43.478 0.00 0.00 0.00 3.21
2616 4999 3.874543 TGCCACACGTATTAACATGATCC 59.125 43.478 0.00 0.00 0.00 3.36
2632 5015 7.814264 ACATGATCCCTTTTGTGATTATCTC 57.186 36.000 0.00 0.00 0.00 2.75
2639 5022 6.073314 CCCTTTTGTGATTATCTCCCATGAT 58.927 40.000 0.00 0.00 0.00 2.45
2640 5023 6.552350 CCCTTTTGTGATTATCTCCCATGATT 59.448 38.462 0.00 0.00 0.00 2.57
2641 5024 7.431249 CCTTTTGTGATTATCTCCCATGATTG 58.569 38.462 0.00 0.00 0.00 2.67
2642 5025 6.395426 TTTGTGATTATCTCCCATGATTGC 57.605 37.500 0.00 0.00 0.00 3.56
2643 5026 5.314718 TGTGATTATCTCCCATGATTGCT 57.685 39.130 0.00 0.00 0.00 3.91
2725 5108 3.759086 CCTGATAGATTCGCTACTGGCTA 59.241 47.826 0.00 0.00 39.13 3.93
2734 5117 4.303086 TCGCTACTGGCTATACAAGTTC 57.697 45.455 0.00 0.00 39.13 3.01
2784 5167 7.941795 TTTTAGTTTCCTGTTCTTAGTCTCG 57.058 36.000 0.00 0.00 0.00 4.04
2799 5182 3.081409 TCGGGCCCTCTTAGGTGC 61.081 66.667 22.43 0.00 31.93 5.01
2805 5188 0.837272 GCCCTCTTAGGTGCCATGTA 59.163 55.000 0.00 0.00 31.93 2.29
2813 5196 6.240002 CCTCTTAGGTGCCATGTATTATTCCT 60.240 42.308 0.00 0.00 0.00 3.36
2881 5281 7.946381 TCTAAGCTCTCTGAATTGTAGAAGA 57.054 36.000 0.00 0.00 0.00 2.87
2919 5319 5.648526 TCAAAGTAGGGCGTGCATTATTAAA 59.351 36.000 0.00 0.00 0.00 1.52
2921 5321 7.499563 TCAAAGTAGGGCGTGCATTATTAAATA 59.500 33.333 0.00 0.00 0.00 1.40
2971 5380 4.683832 AGGCTAGCTATGTTCGTTAGTTG 58.316 43.478 15.72 0.00 0.00 3.16
2983 5717 6.751157 TGTTCGTTAGTTGAGAGTTTGGATA 58.249 36.000 0.00 0.00 0.00 2.59
2984 5718 6.643770 TGTTCGTTAGTTGAGAGTTTGGATAC 59.356 38.462 0.00 0.00 0.00 2.24
3011 5745 6.040278 TGGTTCTTGCACATTTCATTGAGTAA 59.960 34.615 0.00 0.00 0.00 2.24
3016 5750 8.196771 TCTTGCACATTTCATTGAGTAAAAGTT 58.803 29.630 0.00 0.00 0.00 2.66
3068 5803 9.381033 GTGCGGAGTAGAGTTATCTATAGAATA 57.619 37.037 6.52 0.00 40.16 1.75
3125 5860 5.957842 TTGCTACCTGGTTTTCTACATTG 57.042 39.130 3.84 0.00 0.00 2.82
3134 5872 4.141367 TGGTTTTCTACATTGGGACTCACA 60.141 41.667 0.00 0.00 0.00 3.58
3146 5884 7.174946 ACATTGGGACTCACATTTACTGTTTAG 59.825 37.037 0.00 0.00 35.29 1.85
3162 5900 6.550163 ACTGTTTAGGGACACTAGAGAGTTA 58.450 40.000 0.00 0.00 37.16 2.24
3171 5909 6.869388 GGGACACTAGAGAGTTAAGTTTCTTG 59.131 42.308 8.52 9.17 31.73 3.02
3258 5996 5.045066 TGGACTGTAAGCCTAGAGAGAGTTA 60.045 44.000 0.00 0.00 37.60 2.24
3268 6006 7.314393 AGCCTAGAGAGAGTTAAACTAAAACG 58.686 38.462 0.00 0.00 32.00 3.60
3278 6016 7.232330 AGAGTTAAACTAAAACGTACTCCCTCT 59.768 37.037 5.87 0.00 32.92 3.69
3281 6019 4.780275 ACTAAAACGTACTCCCTCTGTC 57.220 45.455 0.00 0.00 0.00 3.51
3283 6021 2.305858 AAACGTACTCCCTCTGTCCT 57.694 50.000 0.00 0.00 0.00 3.85
3285 6023 1.836802 ACGTACTCCCTCTGTCCTTC 58.163 55.000 0.00 0.00 0.00 3.46
3288 6026 2.561419 CGTACTCCCTCTGTCCTTCAAA 59.439 50.000 0.00 0.00 0.00 2.69
3290 6028 4.502604 CGTACTCCCTCTGTCCTTCAAAAA 60.503 45.833 0.00 0.00 0.00 1.94
3323 6173 2.233305 TGGGACAGAGGGAGTAGTTC 57.767 55.000 0.00 0.00 0.00 3.01
3339 6189 9.895138 GGGAGTAGTTCATTTTTACCTGTATTA 57.105 33.333 0.00 0.00 0.00 0.98
3386 6237 7.496529 TCTTTTCTTGTAGGACTTCATTGTG 57.503 36.000 0.00 0.00 0.00 3.33
3391 6242 4.002906 TGTAGGACTTCATTGTGACACC 57.997 45.455 2.45 0.00 0.00 4.16
3397 6248 1.195448 CTTCATTGTGACACCGTGCTC 59.805 52.381 2.45 0.00 0.00 4.26
3404 6255 1.227556 GACACCGTGCTCACCTTGT 60.228 57.895 0.00 2.00 0.00 3.16
3515 6366 1.357272 TGTGCTACAAGGGTTGGGGT 61.357 55.000 0.00 0.00 34.12 4.95
3572 6423 9.449719 TGGAAGTTACTTCAAGATATCCTTTTC 57.550 33.333 24.09 4.74 41.77 2.29
3603 6454 2.567169 ACTGTACTGCTGCCAATGAGTA 59.433 45.455 0.00 0.00 0.00 2.59
3733 6584 3.866327 GCAGAGTCCGAAAAGTATCTTCC 59.134 47.826 0.00 0.00 0.00 3.46
3835 6686 1.618837 GTATCTAATCCTCCCGCTGCA 59.381 52.381 0.00 0.00 0.00 4.41
3956 6807 8.477256 TGCTAAATAAATTCCCAGATGAAAAGG 58.523 33.333 0.00 0.00 0.00 3.11
3997 6848 3.317430 CCTCAAGCTTTGTTCTTTCTGCT 59.683 43.478 0.00 0.00 0.00 4.24
4011 6862 4.074526 TGCTGCCTCACTCCGCTC 62.075 66.667 0.00 0.00 0.00 5.03
4013 6864 3.073735 CTGCCTCACTCCGCTCCT 61.074 66.667 0.00 0.00 0.00 3.69
4027 6878 1.739035 CGCTCCTTCTTTGCCACGATA 60.739 52.381 0.00 0.00 0.00 2.92
4033 6884 4.951715 TCCTTCTTTGCCACGATACTACTA 59.048 41.667 0.00 0.00 0.00 1.82
4035 6886 5.921408 CCTTCTTTGCCACGATACTACTATC 59.079 44.000 0.00 0.00 0.00 2.08
4042 6893 4.142773 GCCACGATACTACTATCTCTGCTC 60.143 50.000 0.00 0.00 0.00 4.26
4101 6952 1.209504 TCCTTGTGCATAGCCAGTACC 59.790 52.381 0.00 0.00 0.00 3.34
4107 6958 1.339631 TGCATAGCCAGTACCGCTTTT 60.340 47.619 10.09 0.00 37.79 2.27
4121 6972 2.033424 CCGCTTTTTATGCCCTCTAAGC 59.967 50.000 0.00 0.00 35.77 3.09
4133 6984 4.038282 TGCCCTCTAAGCATGCATAAAATG 59.962 41.667 21.98 4.41 34.69 2.32
4155 7006 3.192466 GCAAAGCCTTGATGCCAATTAG 58.808 45.455 0.00 0.00 34.14 1.73
4156 7007 3.368739 GCAAAGCCTTGATGCCAATTAGT 60.369 43.478 0.00 0.00 34.14 2.24
4210 7061 4.059511 TGTCTGTTATGGTTACGTGGTTG 58.940 43.478 0.00 0.00 0.00 3.77
4227 7078 4.913345 GTGGTTGCCTTTTTGACGTATTAC 59.087 41.667 0.00 0.00 0.00 1.89
4230 7081 5.627780 GGTTGCCTTTTTGACGTATTACTTG 59.372 40.000 0.00 0.00 0.00 3.16
4239 7090 8.674263 TTTTGACGTATTACTTGTCCCTTTTA 57.326 30.769 0.00 0.00 0.00 1.52
4240 7091 7.656707 TTGACGTATTACTTGTCCCTTTTAC 57.343 36.000 0.00 0.00 0.00 2.01
4253 7104 5.047164 TGTCCCTTTTACGCTGTTAGTATGA 60.047 40.000 0.00 0.00 0.00 2.15
4256 7107 4.868171 CCTTTTACGCTGTTAGTATGAGCA 59.132 41.667 0.00 0.00 32.70 4.26
4267 7118 8.997323 GCTGTTAGTATGAGCATGATTTATTCT 58.003 33.333 0.00 0.00 32.70 2.40
4280 7131 8.975439 GCATGATTTATTCTTTAATCTGCTTGG 58.025 33.333 0.00 0.00 35.04 3.61
4294 7145 5.155278 TCTGCTTGGCATCATTTGATTTT 57.845 34.783 0.00 0.00 38.13 1.82
4322 7173 8.045176 AGATATTTGTCCAAGAAAACACTAGC 57.955 34.615 0.00 0.00 0.00 3.42
4325 7176 6.524101 TTTGTCCAAGAAAACACTAGCTTT 57.476 33.333 0.00 0.00 0.00 3.51
4332 7183 9.398538 TCCAAGAAAACACTAGCTTTAACTTAA 57.601 29.630 0.00 0.00 0.00 1.85
4341 7192 7.148239 ACACTAGCTTTAACTTAATCATGTGCC 60.148 37.037 0.00 0.00 0.00 5.01
4352 7203 9.719355 AACTTAATCATGTGCCGTATATCATAA 57.281 29.630 0.00 0.00 0.00 1.90
4379 7230 5.924825 GTCTACCCATCCGTATGTTTCATAC 59.075 44.000 9.13 9.13 0.00 2.39
4387 7238 7.388776 CCATCCGTATGTTTCATACTGATGATT 59.611 37.037 31.45 13.14 43.08 2.57
4417 7268 5.999205 TGTGCCTTATGGTTTTTGATGAT 57.001 34.783 0.00 0.00 35.27 2.45
4428 7279 6.289834 TGGTTTTTGATGATTTGTTGCTCAT 58.710 32.000 0.00 0.00 34.86 2.90
4468 7341 4.901197 TCTCAGTACCAAATGTAGGCAA 57.099 40.909 0.00 0.00 0.00 4.52
4488 7361 5.290885 GGCAAGTTGTACCTTTTGAGTTTTG 59.709 40.000 4.48 0.00 0.00 2.44
4600 7473 2.242452 TCCGAGAAGGATCAGAAGGAGA 59.758 50.000 0.00 0.00 45.98 3.71
4608 7481 1.688197 GATCAGAAGGAGAGGGCTCAG 59.312 57.143 0.00 0.00 43.14 3.35
4685 7558 5.453903 CCATGTAAGGGAGATCGACTTTGAT 60.454 44.000 5.20 0.00 43.46 2.57
4706 7579 2.991250 AGTGGTTGCATGACATAGTCC 58.009 47.619 0.00 0.00 0.00 3.85
4712 7585 0.882042 GCATGACATAGTCCAGGGCG 60.882 60.000 0.00 0.00 0.00 6.13
4717 7590 1.068753 CATAGTCCAGGGCGCTCAG 59.931 63.158 11.40 0.00 0.00 3.35
4740 7613 5.982516 AGCACAAGAGAATTTATCTAGAGCG 59.017 40.000 0.00 0.00 38.96 5.03
4752 7625 0.671781 CTAGAGCGCTGCAACCTTGT 60.672 55.000 18.48 0.00 0.00 3.16
5046 7919 5.496133 AGTATGTGAGATTGCTTTGATGC 57.504 39.130 0.00 0.00 0.00 3.91
5192 8065 7.904558 ATCTCTTGATGGTTAGTACATCTCA 57.095 36.000 6.92 0.00 43.88 3.27
5217 8090 0.378962 TTTCACCGCTTGGTTTCACG 59.621 50.000 0.00 0.00 46.51 4.35
5307 8180 5.698089 GCAGCTTCTCTGTTATATATGCACA 59.302 40.000 0.00 0.00 44.66 4.57
5329 8202 2.924290 GGAACGAAATTCAGAGACTCGG 59.076 50.000 0.00 0.00 39.30 4.63
5350 8223 2.530700 GCGACGAAGCTGTACATCTAAC 59.469 50.000 0.00 0.00 0.00 2.34
5402 8275 4.917906 ACCTAGAAAAGCTGAACCTGAT 57.082 40.909 0.00 0.00 0.00 2.90
5417 8290 7.773690 GCTGAACCTGATATTTACTAAAAGGGA 59.226 37.037 0.00 0.00 0.00 4.20
5432 8305 0.966920 AGGGACGTGTTCACTACCAG 59.033 55.000 0.00 0.00 35.53 4.00
5468 8384 1.325355 GAGAATGATGTGCATGGGGG 58.675 55.000 0.00 0.00 37.28 5.40
5622 8541 3.423515 CGTTTTGTGATCACCATGAGTCG 60.424 47.826 22.85 13.55 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 1.732809 GAGAAAGTCTAGGGTTTGCGC 59.267 52.381 0.00 0.00 0.00 6.09
119 120 4.260170 ACTAAAGCTCAGAAGATGCCTTG 58.740 43.478 2.46 0.00 31.62 3.61
134 135 5.049612 GTGTTAGACCCTGACAAACTAAAGC 60.050 44.000 0.00 0.00 32.02 3.51
259 260 3.450904 TGCCAGAGTCTACCTAAACCAT 58.549 45.455 0.00 0.00 0.00 3.55
263 264 3.260884 CCAGTTGCCAGAGTCTACCTAAA 59.739 47.826 0.00 0.00 0.00 1.85
297 298 1.146263 CTTATCACAGGCCCGGGAC 59.854 63.158 29.31 26.25 0.00 4.46
316 317 3.508402 GGGAAAATTCGAACCAAGCCTTA 59.492 43.478 0.00 0.00 0.00 2.69
413 414 5.736951 AGATACAGAAGACACAAGAAGCT 57.263 39.130 0.00 0.00 0.00 3.74
421 423 7.385778 AGAAGTGACTAGATACAGAAGACAC 57.614 40.000 0.00 0.00 36.56 3.67
424 426 8.735315 CAAGAAGAAGTGACTAGATACAGAAGA 58.265 37.037 0.00 0.00 0.00 2.87
448 450 0.260230 TTGGGGTTGTGAAGGAGCAA 59.740 50.000 0.00 0.00 0.00 3.91
450 452 1.177401 GATTGGGGTTGTGAAGGAGC 58.823 55.000 0.00 0.00 0.00 4.70
565 571 9.534565 CGATTTGAGAAGTATTTCCTCATTCTA 57.465 33.333 0.00 0.00 33.64 2.10
571 577 7.203910 TCTAGCGATTTGAGAAGTATTTCCTC 58.796 38.462 0.00 0.00 33.64 3.71
585 2810 5.909610 GGAAATCGGAATTTCTAGCGATTTG 59.090 40.000 25.46 7.41 46.65 2.32
586 2811 5.008712 GGGAAATCGGAATTTCTAGCGATTT 59.991 40.000 22.84 22.84 46.65 2.17
587 2812 4.515567 GGGAAATCGGAATTTCTAGCGATT 59.484 41.667 12.87 12.87 46.65 3.34
588 2813 4.065789 GGGAAATCGGAATTTCTAGCGAT 58.934 43.478 9.90 4.00 46.65 4.58
589 2814 3.118555 TGGGAAATCGGAATTTCTAGCGA 60.119 43.478 9.90 0.00 46.65 4.93
590 2815 3.002348 GTGGGAAATCGGAATTTCTAGCG 59.998 47.826 9.90 0.00 46.65 4.26
613 2847 0.556258 GGGGGCTTAGGGCTACAAAT 59.444 55.000 0.00 0.00 41.46 2.32
614 2848 0.551624 AGGGGGCTTAGGGCTACAAA 60.552 55.000 0.00 0.00 41.46 2.83
617 2851 1.532238 CAAGGGGGCTTAGGGCTAC 59.468 63.158 0.00 0.00 41.46 3.58
620 2854 2.383601 TAGCAAGGGGGCTTAGGGC 61.384 63.158 0.00 0.00 42.71 5.19
709 2963 4.338710 TAACTGCACGGTGGGGCC 62.339 66.667 10.60 0.00 0.00 5.80
963 3221 3.972276 CTAGCCTCGCCTCGCCTC 61.972 72.222 0.00 0.00 0.00 4.70
1144 3426 4.994201 GACGTGCGACCACAGCGA 62.994 66.667 0.00 0.00 42.17 4.93
1156 3438 2.481969 CCCCATGTACAGATCTGACGTG 60.482 54.545 29.27 26.69 32.53 4.49
1231 3513 0.240945 CGCAAAAGGGGCAGTTGTAG 59.759 55.000 0.00 0.00 0.00 2.74
1478 3775 6.128200 GGATTTTCCGAACCACTAAAACGTAT 60.128 38.462 0.00 0.00 0.00 3.06
1538 3835 6.005583 TCTTTTCAGCAATCTACAAAGCAG 57.994 37.500 0.00 0.00 0.00 4.24
1567 3864 4.356405 TCTCCAGCAGAACATTCAAGAA 57.644 40.909 0.00 0.00 0.00 2.52
1664 3961 2.305927 TCAAGGGAGCAGGTTCCTAAAG 59.694 50.000 0.00 0.00 37.40 1.85
1681 3978 6.708054 ACACCATAAAGAAACTCTCTGTCAAG 59.292 38.462 0.00 0.00 33.37 3.02
1693 3990 4.202202 CCAACCAGCAACACCATAAAGAAA 60.202 41.667 0.00 0.00 0.00 2.52
1696 3993 2.890311 TCCAACCAGCAACACCATAAAG 59.110 45.455 0.00 0.00 0.00 1.85
1781 4094 3.196685 TCCAAAACCAAACTGACCAAAGG 59.803 43.478 0.00 0.00 0.00 3.11
1788 4101 6.783708 AACTACATTCCAAAACCAAACTGA 57.216 33.333 0.00 0.00 0.00 3.41
1854 4167 5.304778 TGTTTCAGCTAGTTGCATAACTCA 58.695 37.500 0.97 0.00 43.53 3.41
1855 4168 5.409826 ACTGTTTCAGCTAGTTGCATAACTC 59.590 40.000 0.97 0.00 45.94 3.01
1857 4170 5.613358 ACTGTTTCAGCTAGTTGCATAAC 57.387 39.130 0.97 6.85 45.94 1.89
1858 4171 6.633500 AAACTGTTTCAGCTAGTTGCATAA 57.367 33.333 0.97 0.00 45.94 1.90
1859 4172 6.039270 ACAAAACTGTTTCAGCTAGTTGCATA 59.961 34.615 6.20 0.00 45.94 3.14
1860 4173 5.163519 ACAAAACTGTTTCAGCTAGTTGCAT 60.164 36.000 6.20 0.00 45.94 3.96
1863 4176 5.640732 ACACAAAACTGTTTCAGCTAGTTG 58.359 37.500 6.20 0.00 35.06 3.16
1864 4177 5.897377 ACACAAAACTGTTTCAGCTAGTT 57.103 34.783 6.20 0.00 36.29 2.24
1865 4178 5.897377 AACACAAAACTGTTTCAGCTAGT 57.103 34.783 6.20 0.99 34.37 2.57
1867 4180 6.734137 CCATAACACAAAACTGTTTCAGCTA 58.266 36.000 6.20 0.00 35.87 3.32
1869 4182 4.209080 GCCATAACACAAAACTGTTTCAGC 59.791 41.667 6.20 0.00 35.87 4.26
1890 4214 2.360165 CTGACAATCTTATTGGCCAGCC 59.640 50.000 5.11 0.38 0.00 4.85
1908 4232 4.711846 AGCATATTCTCCACTGTGTACTGA 59.288 41.667 7.08 0.00 0.00 3.41
1910 4234 4.711846 TGAGCATATTCTCCACTGTGTACT 59.288 41.667 7.08 0.00 32.22 2.73
1952 4296 9.277565 ACATTTGATGTTTATTTCTTCGATTCG 57.722 29.630 0.00 0.00 41.63 3.34
2002 4346 6.991531 TCGGTGATGTCATGATTATTTGATGA 59.008 34.615 0.00 0.00 0.00 2.92
2024 4374 3.944087 AGGAGAAAGTGAGGAATTTCGG 58.056 45.455 0.00 0.00 39.78 4.30
2025 4375 8.894768 ATATTAGGAGAAAGTGAGGAATTTCG 57.105 34.615 0.00 0.00 39.78 3.46
2033 4383 9.770097 TCATTGCTAATATTAGGAGAAAGTGAG 57.230 33.333 21.30 6.30 32.59 3.51
2040 4390 9.330063 CACACTTTCATTGCTAATATTAGGAGA 57.670 33.333 21.30 11.89 32.59 3.71
2052 4402 3.290710 ACCACTTCACACTTTCATTGCT 58.709 40.909 0.00 0.00 0.00 3.91
2054 4404 6.377327 AGTTACCACTTCACACTTTCATTG 57.623 37.500 0.00 0.00 0.00 2.82
2114 4464 3.149981 TGAGACCGAGTCAGCTATATGG 58.850 50.000 6.78 0.00 34.60 2.74
2124 4474 5.749109 CACACCTTATATTTGAGACCGAGTC 59.251 44.000 0.00 0.00 0.00 3.36
2187 4539 9.991388 CCGATTTCGTATAAGTTAATCCAAAAA 57.009 29.630 0.00 0.00 37.74 1.94
2188 4540 9.165035 ACCGATTTCGTATAAGTTAATCCAAAA 57.835 29.630 0.00 0.00 37.74 2.44
2190 4542 9.985730 ATACCGATTTCGTATAAGTTAATCCAA 57.014 29.630 0.00 0.00 37.74 3.53
2233 4585 7.470935 AATGAGATTGTTGGAATCATGTTGA 57.529 32.000 0.00 0.00 31.24 3.18
2239 4591 9.426837 GATTCAAAAATGAGATTGTTGGAATCA 57.573 29.630 0.00 0.00 37.91 2.57
2242 4594 8.202811 TGTGATTCAAAAATGAGATTGTTGGAA 58.797 29.630 0.00 0.00 37.91 3.53
2252 4604 6.924612 TGTGGATTGTGTGATTCAAAAATGAG 59.075 34.615 0.00 0.00 0.00 2.90
2281 4633 7.630242 TGATCAAGAATCTAATTGGTCAACC 57.370 36.000 0.00 0.00 42.12 3.77
2339 4691 2.691011 AGCTGAGATACTTCTTCGGTCC 59.309 50.000 0.00 0.00 30.30 4.46
2340 4692 4.577283 ACTAGCTGAGATACTTCTTCGGTC 59.423 45.833 0.00 0.00 30.30 4.79
2341 4693 4.528920 ACTAGCTGAGATACTTCTTCGGT 58.471 43.478 0.00 0.00 30.30 4.69
2380 4732 9.801873 CAACTTCTTTTCTTTCCAAATTCAGTA 57.198 29.630 0.00 0.00 0.00 2.74
2382 4734 7.493645 AGCAACTTCTTTTCTTTCCAAATTCAG 59.506 33.333 0.00 0.00 0.00 3.02
2466 4849 0.606401 AACACGTTGGCATCCAGAGG 60.606 55.000 0.00 0.00 33.81 3.69
2473 4856 2.331098 CGCACAACACGTTGGCAT 59.669 55.556 14.07 0.00 44.45 4.40
2491 4874 1.936880 CTCTCTCGTCATCGCGTGC 60.937 63.158 5.77 0.07 36.96 5.34
2496 4879 0.382515 GAACCCCTCTCTCGTCATCG 59.617 60.000 0.00 0.00 38.55 3.84
2499 4882 0.966920 GTTGAACCCCTCTCTCGTCA 59.033 55.000 0.00 0.00 0.00 4.35
2510 4893 0.036875 AGCTAGCCTGTGTTGAACCC 59.963 55.000 12.13 0.00 0.00 4.11
2571 4954 1.614317 GCCTACACAGTTCTGGGCAAT 60.614 52.381 11.10 0.00 39.38 3.56
2575 4958 2.086869 CATTGCCTACACAGTTCTGGG 58.913 52.381 0.09 0.09 0.00 4.45
2593 4976 4.515191 GGATCATGTTAATACGTGTGGCAT 59.485 41.667 0.00 0.00 41.20 4.40
2596 4979 4.703897 AGGGATCATGTTAATACGTGTGG 58.296 43.478 0.00 0.00 41.20 4.17
2612 4995 5.694995 TGGGAGATAATCACAAAAGGGATC 58.305 41.667 0.00 0.00 38.82 3.36
2616 4999 7.431249 CAATCATGGGAGATAATCACAAAAGG 58.569 38.462 0.00 0.00 46.85 3.11
2632 5015 3.128349 GCATAAGCAAAGCAATCATGGG 58.872 45.455 0.00 0.00 41.58 4.00
2673 5056 3.615155 GACAGCCTAGCCTCTGATTTTT 58.385 45.455 10.55 0.00 34.57 1.94
2762 5145 5.047519 CCCGAGACTAAGAACAGGAAACTAA 60.048 44.000 0.00 0.00 40.21 2.24
2784 5167 2.386935 ATGGCACCTAAGAGGGCCC 61.387 63.158 16.46 16.46 45.48 5.80
2799 5182 8.834465 CAAACTGAAGAGAGGAATAATACATGG 58.166 37.037 0.00 0.00 0.00 3.66
2881 5281 5.131809 CCCTACTTTGAAGGAGAAGGATGAT 59.868 44.000 4.52 0.00 39.45 2.45
2956 5356 6.866770 TCCAAACTCTCAACTAACGAACATAG 59.133 38.462 0.00 0.00 0.00 2.23
2957 5357 6.751157 TCCAAACTCTCAACTAACGAACATA 58.249 36.000 0.00 0.00 0.00 2.29
2958 5358 5.607477 TCCAAACTCTCAACTAACGAACAT 58.393 37.500 0.00 0.00 0.00 2.71
2959 5359 5.013568 TCCAAACTCTCAACTAACGAACA 57.986 39.130 0.00 0.00 0.00 3.18
2960 5360 6.643770 TGTATCCAAACTCTCAACTAACGAAC 59.356 38.462 0.00 0.00 0.00 3.95
2963 5372 6.036083 CCATGTATCCAAACTCTCAACTAACG 59.964 42.308 0.00 0.00 0.00 3.18
2965 5374 7.016153 ACCATGTATCCAAACTCTCAACTAA 57.984 36.000 0.00 0.00 0.00 2.24
2971 5380 5.163713 GCAAGAACCATGTATCCAAACTCTC 60.164 44.000 0.00 0.00 0.00 3.20
2983 5717 4.877378 ATGAAATGTGCAAGAACCATGT 57.123 36.364 0.00 0.00 0.00 3.21
2984 5718 5.231702 TCAATGAAATGTGCAAGAACCATG 58.768 37.500 0.00 0.00 0.00 3.66
3011 5745 9.515020 CACAAATTAATCAGTGTACACAACTTT 57.485 29.630 27.06 16.20 0.00 2.66
3016 5750 7.413644 CACACACAAATTAATCAGTGTACACA 58.586 34.615 27.06 8.66 42.79 3.72
3083 5818 5.090083 GCAATCGCGAACCATAAAAAGTTA 58.910 37.500 15.24 0.00 0.00 2.24
3088 5823 3.064271 GGTAGCAATCGCGAACCATAAAA 59.936 43.478 19.45 0.00 44.22 1.52
3125 5860 4.941873 CCCTAAACAGTAAATGTGAGTCCC 59.058 45.833 0.00 0.00 43.00 4.46
3134 5872 7.674772 ACTCTCTAGTGTCCCTAAACAGTAAAT 59.325 37.037 0.00 0.00 35.27 1.40
3146 5884 6.593268 AGAAACTTAACTCTCTAGTGTCCC 57.407 41.667 0.00 0.00 35.62 4.46
3204 5942 1.314730 AGGTAACCCAGCAAAACACG 58.685 50.000 0.00 0.00 37.17 4.49
3209 5947 3.306472 AACTCAAGGTAACCCAGCAAA 57.694 42.857 0.00 0.00 37.17 3.68
3258 5996 5.510349 GGACAGAGGGAGTACGTTTTAGTTT 60.510 44.000 0.00 0.00 0.00 2.66
3268 6006 4.618920 TTTTGAAGGACAGAGGGAGTAC 57.381 45.455 0.00 0.00 0.00 2.73
3288 6026 7.931948 CCTCTGTCCCATAATATAAGACGTTTT 59.068 37.037 0.00 0.00 0.00 2.43
3290 6028 6.014499 CCCTCTGTCCCATAATATAAGACGTT 60.014 42.308 0.00 0.00 0.00 3.99
3292 6030 5.715279 TCCCTCTGTCCCATAATATAAGACG 59.285 44.000 0.00 0.00 0.00 4.18
3298 6036 6.234404 ACTACTCCCTCTGTCCCATAATAT 57.766 41.667 0.00 0.00 0.00 1.28
3300 6038 4.561254 ACTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
3301 6039 4.264668 TGAACTACTCCCTCTGTCCCATAA 60.265 45.833 0.00 0.00 0.00 1.90
3302 6040 3.271225 TGAACTACTCCCTCTGTCCCATA 59.729 47.826 0.00 0.00 0.00 2.74
3304 6042 1.431633 TGAACTACTCCCTCTGTCCCA 59.568 52.381 0.00 0.00 0.00 4.37
3305 6043 2.233305 TGAACTACTCCCTCTGTCCC 57.767 55.000 0.00 0.00 0.00 4.46
3306 6044 4.828072 AAATGAACTACTCCCTCTGTCC 57.172 45.455 0.00 0.00 0.00 4.02
3307 6045 6.594547 GGTAAAAATGAACTACTCCCTCTGTC 59.405 42.308 0.00 0.00 0.00 3.51
3308 6046 6.272558 AGGTAAAAATGAACTACTCCCTCTGT 59.727 38.462 0.00 0.00 0.00 3.41
3339 6189 6.211384 AGAAAACTAAACTGCCAATTATGCCT 59.789 34.615 0.00 0.00 0.00 4.75
3341 6191 7.889589 AAGAAAACTAAACTGCCAATTATGC 57.110 32.000 0.00 0.00 0.00 3.14
3357 6207 8.753497 ATGAAGTCCTACAAGAAAAGAAAACT 57.247 30.769 0.00 0.00 0.00 2.66
3361 6211 7.773224 TCACAATGAAGTCCTACAAGAAAAGAA 59.227 33.333 0.00 0.00 0.00 2.52
3363 6213 7.012327 TGTCACAATGAAGTCCTACAAGAAAAG 59.988 37.037 0.00 0.00 0.00 2.27
3370 6221 3.554129 CGGTGTCACAATGAAGTCCTACA 60.554 47.826 5.12 0.00 0.00 2.74
3386 6237 1.227556 ACAAGGTGAGCACGGTGTC 60.228 57.895 10.24 6.85 0.00 3.67
3391 6242 0.532862 AAGGACACAAGGTGAGCACG 60.533 55.000 2.98 0.00 36.96 5.34
3397 6248 1.066002 CACAAGCAAGGACACAAGGTG 59.934 52.381 0.00 0.00 39.75 4.00
3404 6255 2.706636 GCTCACACAAGCAAGGACA 58.293 52.632 0.00 0.00 42.05 4.02
3515 6366 2.027192 GTCAAGTGGCCTATCAAGTCCA 60.027 50.000 3.32 0.00 0.00 4.02
3572 6423 4.142816 GGCAGCAGTACAGTGTGAATAAAG 60.143 45.833 5.88 0.00 0.00 1.85
3576 6427 1.072173 TGGCAGCAGTACAGTGTGAAT 59.928 47.619 5.88 0.00 0.00 2.57
3577 6428 0.467804 TGGCAGCAGTACAGTGTGAA 59.532 50.000 5.88 0.00 0.00 3.18
3580 6431 1.072173 TCATTGGCAGCAGTACAGTGT 59.928 47.619 0.00 0.00 0.00 3.55
3626 6477 5.190528 ACCATGTATTCTGAAGAGGACACAT 59.809 40.000 0.00 0.00 0.00 3.21
3692 6543 0.589729 CGCCTGCGTTGCATGTATTC 60.590 55.000 2.83 0.00 38.13 1.75
3733 6584 0.609131 ACAGCAAAGAATGGGACCCG 60.609 55.000 5.91 0.00 0.00 5.28
3835 6686 1.197812 GCAAAAATGGATCAGGGGCT 58.802 50.000 0.00 0.00 0.00 5.19
3956 6807 3.967203 GGTGACATACCTCTCTACGAC 57.033 52.381 0.00 0.00 46.51 4.34
3997 6848 2.604686 AAGGAGCGGAGTGAGGCA 60.605 61.111 0.00 0.00 0.00 4.75
4011 6862 4.124851 AGTAGTATCGTGGCAAAGAAGG 57.875 45.455 0.00 0.00 0.00 3.46
4013 6864 6.546403 AGAGATAGTAGTATCGTGGCAAAGAA 59.454 38.462 11.16 0.00 40.22 2.52
4027 6878 4.511786 TCCACTGAGCAGAGATAGTAGT 57.488 45.455 4.21 0.00 0.00 2.73
4033 6884 4.738685 TCTATCATCCACTGAGCAGAGAT 58.261 43.478 4.21 3.60 37.28 2.75
4035 6886 5.471556 AATCTATCATCCACTGAGCAGAG 57.528 43.478 4.21 0.00 37.28 3.35
4069 6920 0.386352 CACAAGGACAGCGCACAATG 60.386 55.000 11.47 0.29 0.00 2.82
4101 6952 2.682856 TGCTTAGAGGGCATAAAAAGCG 59.317 45.455 7.70 0.00 41.65 4.68
4107 6958 3.513909 ATGCATGCTTAGAGGGCATAA 57.486 42.857 20.33 0.00 46.94 1.90
4203 7054 0.099791 ACGTCAAAAAGGCAACCACG 59.900 50.000 0.00 0.00 37.17 4.94
4210 7061 5.388111 GGACAAGTAATACGTCAAAAAGGC 58.612 41.667 0.00 0.00 0.00 4.35
4227 7078 4.062991 ACTAACAGCGTAAAAGGGACAAG 58.937 43.478 0.00 0.00 0.00 3.16
4230 7081 5.413499 TCATACTAACAGCGTAAAAGGGAC 58.587 41.667 0.00 0.00 0.00 4.46
4239 7090 3.801114 TCATGCTCATACTAACAGCGT 57.199 42.857 0.00 0.00 35.81 5.07
4240 7091 5.663795 AAATCATGCTCATACTAACAGCG 57.336 39.130 0.00 0.00 35.81 5.18
4253 7104 9.745880 CAAGCAGATTAAAGAATAAATCATGCT 57.254 29.630 12.23 12.23 42.13 3.79
4256 7107 8.698210 TGCCAAGCAGATTAAAGAATAAATCAT 58.302 29.630 0.00 0.00 35.07 2.45
4267 7118 6.283544 TCAAATGATGCCAAGCAGATTAAA 57.716 33.333 0.00 0.00 43.65 1.52
4294 7145 8.463930 AGTGTTTTCTTGGACAAATATCTTCA 57.536 30.769 0.00 0.00 0.00 3.02
4305 7156 7.260558 AGTTAAAGCTAGTGTTTTCTTGGAC 57.739 36.000 0.00 0.00 0.00 4.02
4332 7183 8.918116 AGACTATTATGATATACGGCACATGAT 58.082 33.333 0.00 0.00 0.00 2.45
4333 7184 8.293699 AGACTATTATGATATACGGCACATGA 57.706 34.615 0.00 0.00 0.00 3.07
4341 7192 8.504815 CGGATGGGTAGACTATTATGATATACG 58.495 40.741 0.00 0.00 0.00 3.06
4352 7203 5.836898 TGAAACATACGGATGGGTAGACTAT 59.163 40.000 13.36 0.00 37.39 2.12
4379 7230 9.836076 CATAAGGCACATAACATTAATCATCAG 57.164 33.333 0.00 0.00 0.00 2.90
4387 7238 8.807118 TCAAAAACCATAAGGCACATAACATTA 58.193 29.630 0.00 0.00 39.06 1.90
4397 7248 6.767456 ACAAATCATCAAAAACCATAAGGCA 58.233 32.000 0.00 0.00 39.06 4.75
4443 7295 5.647658 TGCCTACATTTGGTACTGAGAAATG 59.352 40.000 13.71 13.71 41.07 2.32
4451 7303 4.725490 ACAACTTGCCTACATTTGGTACT 58.275 39.130 0.00 0.00 0.00 2.73
4452 7304 5.106436 GGTACAACTTGCCTACATTTGGTAC 60.106 44.000 0.00 0.00 0.00 3.34
4454 7306 3.824443 GGTACAACTTGCCTACATTTGGT 59.176 43.478 0.00 0.00 0.00 3.67
4461 7313 4.820173 ACTCAAAAGGTACAACTTGCCTAC 59.180 41.667 0.00 0.00 39.99 3.18
4468 7341 8.311109 ACATTTCAAAACTCAAAAGGTACAACT 58.689 29.630 0.00 0.00 0.00 3.16
4496 7369 9.944663 CAAGAACTATTAAACTACAGCAAAACA 57.055 29.630 0.00 0.00 0.00 2.83
4547 7420 4.350368 TCAGCTCTGTAAATTCACCACA 57.650 40.909 0.00 0.00 0.00 4.17
4548 7421 5.008613 TGTTTCAGCTCTGTAAATTCACCAC 59.991 40.000 0.00 0.00 0.00 4.16
4600 7473 0.913451 AATGCACTCCTCTGAGCCCT 60.913 55.000 0.00 0.00 42.74 5.19
4608 7481 1.675641 ACGGGCAAATGCACTCCTC 60.676 57.895 6.04 0.00 43.67 3.71
4685 7558 3.517500 TGGACTATGTCATGCAACCACTA 59.482 43.478 0.00 0.00 33.68 2.74
4706 7579 3.429141 CTTGTGCTGAGCGCCCTG 61.429 66.667 16.16 0.00 38.39 4.45
4712 7585 6.983307 TCTAGATAAATTCTCTTGTGCTGAGC 59.017 38.462 0.00 0.00 35.79 4.26
4717 7590 5.332959 GCGCTCTAGATAAATTCTCTTGTGC 60.333 44.000 0.00 12.28 35.79 4.57
4740 7613 0.032403 TGCATGAACAAGGTTGCAGC 59.968 50.000 0.00 0.00 39.98 5.25
5183 8056 4.740695 GCGGTGAAAGAGTATGAGATGTAC 59.259 45.833 0.00 0.00 0.00 2.90
5184 8057 4.645136 AGCGGTGAAAGAGTATGAGATGTA 59.355 41.667 0.00 0.00 0.00 2.29
5185 8058 3.449018 AGCGGTGAAAGAGTATGAGATGT 59.551 43.478 0.00 0.00 0.00 3.06
5307 8180 3.367498 CCGAGTCTCTGAATTTCGTTCCT 60.367 47.826 0.00 0.00 35.91 3.36
5329 8202 2.470196 TAGATGTACAGCTTCGTCGC 57.530 50.000 20.26 0.00 0.00 5.19
5350 8223 3.309961 TCTACAGCAGAGAAGTTGCAG 57.690 47.619 0.00 0.00 43.92 4.41
5402 8275 7.444299 AGTGAACACGTCCCTTTTAGTAAATA 58.556 34.615 0.00 0.00 36.20 1.40
5417 8290 1.700955 AGACCTGGTAGTGAACACGT 58.299 50.000 0.00 0.00 36.20 4.49
5432 8305 2.042464 TCTCCATCTGGTGCATAGACC 58.958 52.381 5.86 0.00 36.34 3.85
5518 8434 2.328319 TGAAAGGGCTGCCAAAGAAAT 58.672 42.857 22.05 0.00 0.00 2.17
5637 8557 2.377810 TGGCTACAGGGCATGGGAG 61.378 63.158 3.46 1.25 45.79 4.30


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

AutoCloner maintained by Alex Coulton.