Multiple sequence alignment - TraesCS2B01G193200

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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 TraesCS2B01G193200 chr2B 100.000 5478 0 0 1 5478 168831968 168826491 0.000000e+00 10117.0
1 TraesCS2B01G193200 chr2B 93.216 737 44 3 4743 5473 169374304 169375040 0.000000e+00 1079.0
2 TraesCS2B01G193200 chr2B 93.216 737 44 3 4743 5473 169388233 169388969 0.000000e+00 1079.0
3 TraesCS2B01G193200 chr2B 93.080 737 45 3 4743 5473 169402411 169403147 0.000000e+00 1074.0
4 TraesCS2B01G193200 chr2B 93.427 639 35 3 4743 5375 169545969 169546606 0.000000e+00 941.0
5 TraesCS2B01G193200 chr2B 81.967 366 60 5 5114 5475 380242828 380243191 6.890000e-79 305.0
6 TraesCS2B01G193200 chr2B 79.545 132 18 6 4981 5110 265450478 265450354 9.780000e-13 86.1
7 TraesCS2B01G193200 chr2D 92.891 3840 136 43 849 4606 118050483 118046699 0.000000e+00 5452.0
8 TraesCS2B01G193200 chr2A 95.484 2436 89 14 2003 4435 119305676 119303259 0.000000e+00 3869.0
9 TraesCS2B01G193200 chr2A 93.294 2058 65 28 1 2011 119307893 119305862 0.000000e+00 2968.0
10 TraesCS2B01G193200 chr2A 91.954 174 12 2 4435 4606 119302975 119302802 5.480000e-60 243.0
11 TraesCS2B01G193200 chr5D 88.424 311 27 2 3256 3557 243092075 243092385 3.120000e-97 366.0
12 TraesCS2B01G193200 chr5D 82.632 380 61 4 5103 5478 129884753 129884375 1.140000e-86 331.0
13 TraesCS2B01G193200 chr5D 81.842 380 64 4 5103 5478 129595301 129594923 1.150000e-81 315.0
14 TraesCS2B01G193200 chr5B 87.619 315 30 3 3256 3563 255227976 255227664 1.880000e-94 357.0
15 TraesCS2B01G193200 chr5A 87.107 318 31 4 3256 3563 308460454 308460137 8.730000e-93 351.0
16 TraesCS2B01G193200 chr5A 83.465 381 56 5 5103 5478 45003969 45003591 1.130000e-91 348.0
17 TraesCS2B01G193200 chr5A 91.772 158 10 3 4601 4757 396486671 396486516 3.320000e-52 217.0
18 TraesCS2B01G193200 chr6B 88.561 271 27 4 4743 5011 317094185 317093917 5.290000e-85 326.0
19 TraesCS2B01G193200 chr4A 83.379 367 44 15 4743 5102 238514396 238514752 1.900000e-84 324.0
20 TraesCS2B01G193200 chr6A 82.597 362 54 8 5112 5468 454062383 454062026 1.480000e-80 311.0
21 TraesCS2B01G193200 chr3A 82.597 362 46 15 4743 5095 401493737 401494090 2.480000e-78 303.0
22 TraesCS2B01G193200 chr3A 81.941 371 49 16 4743 5102 401435023 401435386 1.150000e-76 298.0
23 TraesCS2B01G193200 chr3A 81.994 361 50 14 4743 5095 401452674 401453027 5.370000e-75 292.0
24 TraesCS2B01G193200 chr3A 90.506 158 13 2 4601 4757 732088556 732088400 2.000000e-49 207.0
25 TraesCS2B01G193200 chr7A 91.503 153 11 2 4606 4757 321656830 321656981 5.560000e-50 209.0


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 TraesCS2B01G193200 chr2B 168826491 168831968 5477 True 10117 10117 100.000000 1 5478 1 chr2B.!!$R1 5477
1 TraesCS2B01G193200 chr2B 169374304 169375040 736 False 1079 1079 93.216000 4743 5473 1 chr2B.!!$F1 730
2 TraesCS2B01G193200 chr2B 169388233 169388969 736 False 1079 1079 93.216000 4743 5473 1 chr2B.!!$F2 730
3 TraesCS2B01G193200 chr2B 169402411 169403147 736 False 1074 1074 93.080000 4743 5473 1 chr2B.!!$F3 730
4 TraesCS2B01G193200 chr2B 169545969 169546606 637 False 941 941 93.427000 4743 5375 1 chr2B.!!$F4 632
5 TraesCS2B01G193200 chr2D 118046699 118050483 3784 True 5452 5452 92.891000 849 4606 1 chr2D.!!$R1 3757
6 TraesCS2B01G193200 chr2A 119302802 119307893 5091 True 2360 3869 93.577333 1 4606 3 chr2A.!!$R1 4605

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
815 837 0.795085 CCGCTGCTCTCTTTGTTCAG 59.205 55.0 0.00 0.0 0.00 3.02 F
1742 1837 0.617413 ACATCAAGTCTGCCTCTGGG 59.383 55.0 0.00 0.0 0.00 4.45 F
3377 3674 0.861837 GCGAGGAGGTATTTCATGCG 59.138 55.0 0.00 0.0 0.00 4.73 F
3745 4043 0.391528 TCTTATCGCAGCTTGCAGCA 60.392 50.0 10.37 0.0 45.36 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 2519 2.040278 TCATGGCTGGCAGTTTCTAACT 59.960 45.455 17.16 0.0 44.06 2.24 R
3722 4020 0.659427 GCAAGCTGCGATAAGATGCA 59.341 50.000 0.00 0.0 39.13 3.96 R
4357 4655 0.172803 CAGGCTTGATTTCCAGCAGC 59.827 55.000 6.05 0.0 0.00 5.25 R
4713 5297 0.175760 GTGCATCGCCCTCTTCTACA 59.824 55.000 0.00 0.0 0.00 2.74 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
92 93 8.010733 TGGATTTAAAGCTTCATTTAGATGGG 57.989 34.615 0.00 0.00 33.93 4.00
134 136 3.415212 CATTCAGGTGCTTTCTGAGGAA 58.585 45.455 0.00 0.00 41.57 3.36
146 148 2.631384 TCTGAGGAAGGTGGATTTGGA 58.369 47.619 0.00 0.00 0.00 3.53
240 242 0.826715 AGGCTCACGAGTATGCATGT 59.173 50.000 10.16 0.00 0.00 3.21
241 243 2.031870 AGGCTCACGAGTATGCATGTA 58.968 47.619 10.16 0.00 0.00 2.29
242 244 2.035193 AGGCTCACGAGTATGCATGTAG 59.965 50.000 10.16 0.00 0.00 2.74
243 245 2.398498 GCTCACGAGTATGCATGTAGG 58.602 52.381 10.16 0.00 0.00 3.18
244 246 2.034685 GCTCACGAGTATGCATGTAGGA 59.965 50.000 10.16 0.00 0.00 2.94
245 247 3.855154 GCTCACGAGTATGCATGTAGGAG 60.855 52.174 10.16 9.58 0.00 3.69
246 248 3.288092 TCACGAGTATGCATGTAGGAGT 58.712 45.455 10.16 0.00 0.00 3.85
256 258 9.113838 AGTATGCATGTAGGAGTAATCTTTTTG 57.886 33.333 10.16 0.00 0.00 2.44
317 319 4.061596 GTTCTCAGGTGAAAGAGTTCCTG 58.938 47.826 0.00 0.00 46.00 3.86
480 492 2.289945 GCTGGTGATGGAGAAGTTGACT 60.290 50.000 0.00 0.00 0.00 3.41
481 493 3.055819 GCTGGTGATGGAGAAGTTGACTA 60.056 47.826 0.00 0.00 0.00 2.59
487 499 9.159254 TGGTGATGGAGAAGTTGACTATATATT 57.841 33.333 0.00 0.00 0.00 1.28
581 593 2.127003 GTTACAAAGCGCCGTGGC 60.127 61.111 2.29 0.00 37.85 5.01
634 646 1.825090 ACTGGATTGCTTCATGCGAA 58.175 45.000 0.00 0.00 46.63 4.70
765 787 2.060275 ACGGAGTTTTTAGGGGAAGGT 58.940 47.619 0.00 0.00 37.78 3.50
810 832 3.494336 CCGCCGCTGCTCTCTTTG 61.494 66.667 0.00 0.00 34.43 2.77
811 833 2.740055 CGCCGCTGCTCTCTTTGT 60.740 61.111 0.00 0.00 34.43 2.83
812 834 2.320587 CGCCGCTGCTCTCTTTGTT 61.321 57.895 0.00 0.00 34.43 2.83
813 835 1.499502 GCCGCTGCTCTCTTTGTTC 59.500 57.895 0.00 0.00 33.53 3.18
815 837 0.795085 CCGCTGCTCTCTTTGTTCAG 59.205 55.000 0.00 0.00 0.00 3.02
816 838 1.506493 CGCTGCTCTCTTTGTTCAGT 58.494 50.000 0.00 0.00 0.00 3.41
818 840 1.069364 GCTGCTCTCTTTGTTCAGTGC 60.069 52.381 0.00 0.00 0.00 4.40
821 843 1.458827 GCTCTCTTTGTTCAGTGCTCG 59.541 52.381 0.00 0.00 0.00 5.03
822 844 2.864097 GCTCTCTTTGTTCAGTGCTCGA 60.864 50.000 0.00 0.00 0.00 4.04
968 1015 6.771573 TCCGTTTGGAAGTAATTTTCCTAGA 58.228 36.000 9.74 0.00 45.59 2.43
969 1016 6.877322 TCCGTTTGGAAGTAATTTTCCTAGAG 59.123 38.462 9.74 2.10 45.59 2.43
970 1017 6.653740 CCGTTTGGAAGTAATTTTCCTAGAGT 59.346 38.462 9.74 0.00 45.59 3.24
971 1018 7.820872 CCGTTTGGAAGTAATTTTCCTAGAGTA 59.179 37.037 9.74 0.00 45.59 2.59
972 1019 9.379791 CGTTTGGAAGTAATTTTCCTAGAGTAT 57.620 33.333 9.74 0.00 45.59 2.12
1280 1357 5.231568 CGTATTGACTCTGTTATTTCGTCCC 59.768 44.000 0.00 0.00 0.00 4.46
1312 1389 5.710567 TCTCATGTATTATCTACCGACCCAG 59.289 44.000 0.00 0.00 0.00 4.45
1320 1397 0.673644 CTACCGACCCAGTTTGCCTG 60.674 60.000 0.00 0.00 41.15 4.85
1527 1613 7.364522 TCACATGCTTAGTTAACAGATTGAC 57.635 36.000 8.61 0.00 0.00 3.18
1643 1736 6.702329 AGCATCGTATTTCTTTAGGATAGGG 58.298 40.000 0.00 0.00 0.00 3.53
1644 1737 5.875359 GCATCGTATTTCTTTAGGATAGGGG 59.125 44.000 0.00 0.00 0.00 4.79
1696 1789 9.922305 CTTACTTATCGGATGAATTTTGACTTC 57.078 33.333 0.00 0.00 0.00 3.01
1697 1790 7.005062 ACTTATCGGATGAATTTTGACTTCG 57.995 36.000 0.00 0.00 0.00 3.79
1703 1796 4.494199 GGATGAATTTTGACTTCGGCGTAG 60.494 45.833 12.16 12.16 0.00 3.51
1742 1837 0.617413 ACATCAAGTCTGCCTCTGGG 59.383 55.000 0.00 0.00 0.00 4.45
1755 1850 1.202806 CCTCTGGGTGACTGCTTCAAA 60.203 52.381 0.00 0.00 35.39 2.69
1772 1867 5.482006 CTTCAAATTTGGGGATTCCTTCAC 58.518 41.667 17.90 0.00 36.20 3.18
1802 1897 1.890489 TGCTGATTTTGCTGCATCACT 59.110 42.857 1.84 0.00 37.73 3.41
1803 1898 3.083293 TGCTGATTTTGCTGCATCACTA 58.917 40.909 1.84 0.00 37.73 2.74
1804 1899 3.506844 TGCTGATTTTGCTGCATCACTAA 59.493 39.130 1.84 0.00 37.73 2.24
1805 1900 4.158949 TGCTGATTTTGCTGCATCACTAAT 59.841 37.500 1.84 0.00 37.73 1.73
1839 1938 1.816835 CACCTTGCATTGCATCTGTCT 59.183 47.619 12.95 0.00 38.76 3.41
1876 1975 3.777465 AACTGCATCTTGATCACATGC 57.223 42.857 23.55 23.55 38.60 4.06
1924 2023 5.376854 AACATCCTCAAACACTTGCATAC 57.623 39.130 0.00 0.00 32.14 2.39
1927 2026 5.124457 ACATCCTCAAACACTTGCATACATC 59.876 40.000 0.00 0.00 32.14 3.06
1974 2073 9.278734 GCTTTTTATGAGCTAAAATCACTGTAC 57.721 33.333 0.00 0.00 38.70 2.90
2016 2311 6.072618 CCATCTCCTATGCTCATTTGAATGTC 60.073 42.308 3.85 0.00 37.65 3.06
2082 2377 2.568546 ACTGGATACTGGGTCCATCA 57.431 50.000 4.13 0.00 44.34 3.07
2149 2445 7.776933 ATGTTGTACAGTATAGCACATTCAG 57.223 36.000 0.00 0.00 0.00 3.02
2223 2519 5.359576 ACAACAAAGTCACAGGATTGCTAAA 59.640 36.000 0.00 0.00 0.00 1.85
2224 2520 5.695851 ACAAAGTCACAGGATTGCTAAAG 57.304 39.130 0.00 0.00 0.00 1.85
2237 2533 5.183140 GGATTGCTAAAGTTAGAAACTGCCA 59.817 40.000 2.18 0.00 41.91 4.92
2244 2540 2.040278 AGTTAGAAACTGCCAGCCATGA 59.960 45.455 0.00 0.00 41.01 3.07
2310 2606 6.506500 AAGAGCTCAACTACCAATTCATTG 57.493 37.500 17.77 0.00 37.52 2.82
2324 2620 6.425721 ACCAATTCATTGCTTGAGTGAAATTG 59.574 34.615 0.00 0.00 35.70 2.32
2338 2634 4.101430 AGTGAAATTGCCAATTGGTTGACT 59.899 37.500 25.19 17.06 37.53 3.41
2485 2781 7.988937 TGTTGGATCTGAATATAAATAGGGCT 58.011 34.615 0.00 0.00 0.00 5.19
2487 2783 9.384764 GTTGGATCTGAATATAAATAGGGCTAC 57.615 37.037 0.00 0.00 0.00 3.58
2626 2922 7.717436 TCCTTTTTGGTTTATTGGACATTTTCC 59.283 33.333 0.00 0.00 40.08 3.13
2648 2944 8.421249 TTCCTAAATCAAATCATCACCTTTGT 57.579 30.769 0.00 0.00 34.66 2.83
2650 2946 6.532657 CCTAAATCAAATCATCACCTTTGTGC 59.467 38.462 0.00 0.00 42.46 4.57
2684 2980 4.348168 GCAGATAGAAAGTATGGGAAGGGA 59.652 45.833 0.00 0.00 0.00 4.20
2936 3233 4.664688 ATGAGGGTCATGGAAAGAAAGT 57.335 40.909 0.00 0.00 35.43 2.66
2971 3268 3.003275 AGTTTTGACACGGTATTGTGCTG 59.997 43.478 0.00 0.00 43.74 4.41
3038 3335 4.952335 ACCAATGAGCTTAAATTCAGGGAG 59.048 41.667 12.51 0.00 0.00 4.30
3047 3344 9.227777 GAGCTTAAATTCAGGGAGTTTACTTTA 57.772 33.333 0.00 0.00 0.00 1.85
3095 3392 3.822735 TCAGGAAAAAGATCAAGGCTGTG 59.177 43.478 0.00 0.00 0.00 3.66
3127 3424 6.035368 AGGTAGCATACATTATCTGCTCTG 57.965 41.667 0.00 0.00 45.43 3.35
3145 3442 2.364002 TCTGATCAGTGTTGTGTTCGGA 59.636 45.455 21.92 0.00 0.00 4.55
3153 3450 4.056050 AGTGTTGTGTTCGGAACAGTATC 58.944 43.478 22.99 12.22 43.10 2.24
3164 3461 4.219944 TCGGAACAGTATCTAACTTGCTGT 59.780 41.667 0.00 0.00 41.51 4.40
3232 3529 4.908601 TTGATCCCATTACTCAGTGTGT 57.091 40.909 2.99 2.99 0.00 3.72
3377 3674 0.861837 GCGAGGAGGTATTTCATGCG 59.138 55.000 0.00 0.00 0.00 4.73
3425 3722 6.183360 GGCTCCTTGTTAACCTTGTTTACTTT 60.183 38.462 2.48 0.00 0.00 2.66
3563 3860 8.102047 CCTTTAAGATATCCTCTCTTGCATGAT 58.898 37.037 2.33 0.00 34.81 2.45
3588 3885 3.995199 ACATTATAGCATCTCCCACACG 58.005 45.455 0.00 0.00 0.00 4.49
3599 3896 3.460103 TCTCCCACACGTTTTACAAGAC 58.540 45.455 0.00 0.00 0.00 3.01
3626 3923 8.819643 ATCTTTAGTATAATCCAAGCGTTCTC 57.180 34.615 0.00 0.00 0.00 2.87
3722 4020 2.916934 TCACATGCCTAGGGGTAGTTTT 59.083 45.455 11.72 0.00 34.45 2.43
3745 4043 0.391528 TCTTATCGCAGCTTGCAGCA 60.392 50.000 10.37 0.00 45.36 4.41
3843 4141 3.387962 TGATTCTGCACCTCCTATTCCT 58.612 45.455 0.00 0.00 0.00 3.36
3994 4292 6.226787 ACGTGATCTCTTGAAGAAGATTGTT 58.773 36.000 0.00 0.00 37.58 2.83
4116 4414 3.303881 GCCTGAAGGTGAAAATGAACC 57.696 47.619 0.00 0.00 37.57 3.62
4127 4425 1.534729 AAATGAACCGTCTCAAGGGC 58.465 50.000 0.00 0.00 33.52 5.19
4261 4559 1.883021 GGTGGCGTGGAGAAATTGG 59.117 57.895 0.00 0.00 0.00 3.16
4344 4642 3.821033 GGATAAAGAACTTATGCCGGCAT 59.179 43.478 41.28 41.28 40.19 4.40
4357 4655 0.937304 CCGGCATTGATTAGGTGTCG 59.063 55.000 0.00 0.00 40.36 4.35
4384 4682 4.326826 TGGAAATCAAGCCTGAGTTACTG 58.673 43.478 9.03 0.00 40.47 2.74
4400 4698 9.132923 CTGAGTTACTGATTGGGTAGACTATAA 57.867 37.037 0.00 0.00 0.00 0.98
4545 5129 9.343539 GTATCAGGTTGAAGAGGCTTTATAAAT 57.656 33.333 0.00 0.00 0.00 1.40
4569 5153 5.348986 TCGTTATCTACTTGAATGGTCAGC 58.651 41.667 0.00 0.00 34.49 4.26
4593 5177 6.363357 GCAACATTTGGATTCACTAAACTCAC 59.637 38.462 0.00 0.00 32.18 3.51
4606 5190 6.586463 TCACTAAACTCACTGCTTTTATCTCG 59.414 38.462 0.00 0.00 0.00 4.04
4607 5191 6.586463 CACTAAACTCACTGCTTTTATCTCGA 59.414 38.462 0.00 0.00 0.00 4.04
4608 5192 7.116376 CACTAAACTCACTGCTTTTATCTCGAA 59.884 37.037 0.00 0.00 0.00 3.71
4609 5193 6.861065 AAACTCACTGCTTTTATCTCGAAA 57.139 33.333 0.00 0.00 0.00 3.46
4610 5194 6.861065 AACTCACTGCTTTTATCTCGAAAA 57.139 33.333 0.00 0.00 0.00 2.29
4611 5195 7.440523 AACTCACTGCTTTTATCTCGAAAAT 57.559 32.000 0.00 0.00 0.00 1.82
4612 5196 6.835914 ACTCACTGCTTTTATCTCGAAAATG 58.164 36.000 0.00 0.00 0.00 2.32
4613 5197 6.128172 ACTCACTGCTTTTATCTCGAAAATGG 60.128 38.462 0.00 0.00 0.00 3.16
4614 5198 4.795278 CACTGCTTTTATCTCGAAAATGGC 59.205 41.667 0.00 0.00 0.00 4.40
4615 5199 4.142381 ACTGCTTTTATCTCGAAAATGGCC 60.142 41.667 0.00 0.00 0.00 5.36
4616 5200 4.016444 TGCTTTTATCTCGAAAATGGCCT 58.984 39.130 3.32 0.00 0.00 5.19
4617 5201 4.462483 TGCTTTTATCTCGAAAATGGCCTT 59.538 37.500 3.32 0.00 0.00 4.35
4618 5202 5.047377 TGCTTTTATCTCGAAAATGGCCTTT 60.047 36.000 3.32 0.00 0.00 3.11
4619 5203 5.289434 GCTTTTATCTCGAAAATGGCCTTTG 59.711 40.000 3.32 0.00 0.00 2.77
4620 5204 4.981806 TTATCTCGAAAATGGCCTTTGG 57.018 40.909 3.32 0.00 0.00 3.28
4621 5205 2.286365 TCTCGAAAATGGCCTTTGGT 57.714 45.000 3.32 0.00 0.00 3.67
4622 5206 1.885887 TCTCGAAAATGGCCTTTGGTG 59.114 47.619 3.32 0.00 0.00 4.17
4623 5207 0.965439 TCGAAAATGGCCTTTGGTGG 59.035 50.000 3.32 0.00 0.00 4.61
4631 5215 4.041762 CCTTTGGTGGCCGGGCTA 62.042 66.667 29.87 10.71 0.00 3.93
4632 5216 2.438434 CTTTGGTGGCCGGGCTAG 60.438 66.667 29.87 13.86 0.00 3.42
4633 5217 4.733542 TTTGGTGGCCGGGCTAGC 62.734 66.667 29.87 25.35 38.00 3.42
4644 5228 2.838225 GGCTAGCTGGAGGCCGTA 60.838 66.667 15.72 0.00 43.05 4.02
4645 5229 2.432300 GGCTAGCTGGAGGCCGTAA 61.432 63.158 15.72 0.00 43.05 3.18
4646 5230 1.749033 GCTAGCTGGAGGCCGTAAT 59.251 57.895 7.70 0.00 43.05 1.89
4647 5231 0.319986 GCTAGCTGGAGGCCGTAATC 60.320 60.000 7.70 0.00 43.05 1.75
4648 5232 1.040646 CTAGCTGGAGGCCGTAATCA 58.959 55.000 0.00 0.00 43.05 2.57
4649 5233 1.000283 CTAGCTGGAGGCCGTAATCAG 60.000 57.143 0.00 3.31 43.05 2.90
4650 5234 1.889573 GCTGGAGGCCGTAATCAGC 60.890 63.158 17.78 17.78 42.89 4.26
4651 5235 1.826024 CTGGAGGCCGTAATCAGCT 59.174 57.895 0.00 0.00 0.00 4.24
4652 5236 0.249657 CTGGAGGCCGTAATCAGCTC 60.250 60.000 0.00 0.00 0.00 4.09
4653 5237 1.069935 GGAGGCCGTAATCAGCTCC 59.930 63.158 0.00 0.00 0.00 4.70
4654 5238 1.300233 GAGGCCGTAATCAGCTCCG 60.300 63.158 0.00 0.00 0.00 4.63
4655 5239 2.017559 GAGGCCGTAATCAGCTCCGT 62.018 60.000 0.00 0.00 0.00 4.69
4656 5240 1.591863 GGCCGTAATCAGCTCCGTC 60.592 63.158 0.00 0.00 0.00 4.79
4657 5241 1.141019 GCCGTAATCAGCTCCGTCA 59.859 57.895 0.00 0.00 0.00 4.35
4658 5242 0.872021 GCCGTAATCAGCTCCGTCAG 60.872 60.000 0.00 0.00 0.00 3.51
4659 5243 0.456221 CCGTAATCAGCTCCGTCAGT 59.544 55.000 0.00 0.00 0.00 3.41
4660 5244 1.674441 CCGTAATCAGCTCCGTCAGTA 59.326 52.381 0.00 0.00 0.00 2.74
4661 5245 2.541178 CCGTAATCAGCTCCGTCAGTAC 60.541 54.545 0.00 0.00 0.00 2.73
4662 5246 2.541178 CGTAATCAGCTCCGTCAGTACC 60.541 54.545 0.00 0.00 0.00 3.34
4663 5247 0.824759 AATCAGCTCCGTCAGTACCC 59.175 55.000 0.00 0.00 0.00 3.69
4664 5248 1.384989 ATCAGCTCCGTCAGTACCCG 61.385 60.000 0.00 0.00 0.00 5.28
4665 5249 2.035312 AGCTCCGTCAGTACCCGT 59.965 61.111 0.00 0.00 0.00 5.28
4666 5250 2.045131 AGCTCCGTCAGTACCCGTC 61.045 63.158 0.00 0.00 0.00 4.79
4667 5251 2.789917 CTCCGTCAGTACCCGTCG 59.210 66.667 0.00 0.00 0.00 5.12
4668 5252 3.392595 CTCCGTCAGTACCCGTCGC 62.393 68.421 0.00 0.00 0.00 5.19
4669 5253 4.824166 CCGTCAGTACCCGTCGCG 62.824 72.222 0.00 0.00 0.00 5.87
4670 5254 3.792047 CGTCAGTACCCGTCGCGA 61.792 66.667 3.71 3.71 0.00 5.87
4671 5255 2.796651 GTCAGTACCCGTCGCGAT 59.203 61.111 14.06 0.00 0.00 4.58
4672 5256 1.298190 GTCAGTACCCGTCGCGATC 60.298 63.158 14.06 5.25 0.00 3.69
4673 5257 2.352001 CAGTACCCGTCGCGATCG 60.352 66.667 14.06 17.58 0.00 3.69
4674 5258 3.580193 AGTACCCGTCGCGATCGG 61.580 66.667 30.41 30.41 46.49 4.18
4675 5259 3.880846 GTACCCGTCGCGATCGGT 61.881 66.667 32.59 29.91 45.63 4.69
4676 5260 3.879682 TACCCGTCGCGATCGGTG 61.880 66.667 32.59 27.51 45.63 4.94
4681 5265 3.554692 GTCGCGATCGGTGCCAAG 61.555 66.667 14.06 0.00 36.13 3.61
4682 5266 4.812476 TCGCGATCGGTGCCAAGG 62.812 66.667 18.30 0.00 36.13 3.61
4685 5269 4.096003 CGATCGGTGCCAAGGGGT 62.096 66.667 7.38 0.00 36.17 4.95
4686 5270 2.727392 CGATCGGTGCCAAGGGGTA 61.727 63.158 7.38 0.00 36.17 3.69
4687 5271 1.837090 GATCGGTGCCAAGGGGTAT 59.163 57.895 0.00 0.00 36.17 2.73
4688 5272 0.535102 GATCGGTGCCAAGGGGTATG 60.535 60.000 0.00 0.00 36.17 2.39
4689 5273 0.986019 ATCGGTGCCAAGGGGTATGA 60.986 55.000 0.00 0.00 36.17 2.15
4690 5274 1.451387 CGGTGCCAAGGGGTATGAC 60.451 63.158 0.00 0.00 36.17 3.06
4691 5275 1.451387 GGTGCCAAGGGGTATGACG 60.451 63.158 0.00 0.00 36.17 4.35
4692 5276 2.112815 GTGCCAAGGGGTATGACGC 61.113 63.158 0.00 0.00 36.17 5.19
4693 5277 2.297895 TGCCAAGGGGTATGACGCT 61.298 57.895 0.00 0.00 36.17 5.07
4694 5278 0.978667 TGCCAAGGGGTATGACGCTA 60.979 55.000 0.00 0.00 36.17 4.26
4695 5279 0.532196 GCCAAGGGGTATGACGCTAC 60.532 60.000 0.00 0.00 36.17 3.58
4696 5280 1.120530 CCAAGGGGTATGACGCTACT 58.879 55.000 0.00 0.00 32.86 2.57
4697 5281 1.202533 CCAAGGGGTATGACGCTACTG 60.203 57.143 0.00 0.00 32.86 2.74
4698 5282 1.480954 CAAGGGGTATGACGCTACTGT 59.519 52.381 0.00 0.00 32.86 3.55
4699 5283 2.691526 CAAGGGGTATGACGCTACTGTA 59.308 50.000 0.00 0.00 32.86 2.74
4700 5284 3.240310 AGGGGTATGACGCTACTGTAT 57.760 47.619 0.00 0.00 0.00 2.29
4701 5285 3.573695 AGGGGTATGACGCTACTGTATT 58.426 45.455 0.00 0.00 0.00 1.89
4702 5286 3.573110 AGGGGTATGACGCTACTGTATTC 59.427 47.826 0.00 0.00 0.00 1.75
4703 5287 3.573110 GGGGTATGACGCTACTGTATTCT 59.427 47.826 0.00 0.00 0.00 2.40
4704 5288 4.547532 GGGTATGACGCTACTGTATTCTG 58.452 47.826 0.00 0.00 0.00 3.02
4705 5289 3.982058 GGTATGACGCTACTGTATTCTGC 59.018 47.826 0.00 0.00 0.00 4.26
4706 5290 3.801114 ATGACGCTACTGTATTCTGCA 57.199 42.857 0.00 0.00 0.00 4.41
4707 5291 3.801114 TGACGCTACTGTATTCTGCAT 57.199 42.857 0.00 0.00 0.00 3.96
4708 5292 3.447742 TGACGCTACTGTATTCTGCATG 58.552 45.455 0.00 0.00 0.00 4.06
4709 5293 3.119137 TGACGCTACTGTATTCTGCATGT 60.119 43.478 0.00 0.00 0.00 3.21
4710 5294 4.097286 TGACGCTACTGTATTCTGCATGTA 59.903 41.667 0.00 0.00 0.00 2.29
4711 5295 5.201713 ACGCTACTGTATTCTGCATGTAT 57.798 39.130 0.00 0.00 0.00 2.29
4712 5296 5.601662 ACGCTACTGTATTCTGCATGTATT 58.398 37.500 0.00 0.00 0.00 1.89
4713 5297 6.049149 ACGCTACTGTATTCTGCATGTATTT 58.951 36.000 0.00 0.00 0.00 1.40
4714 5298 6.018751 ACGCTACTGTATTCTGCATGTATTTG 60.019 38.462 0.00 0.00 0.00 2.32
4715 5299 6.018751 CGCTACTGTATTCTGCATGTATTTGT 60.019 38.462 0.00 0.00 0.00 2.83
4716 5300 7.169140 CGCTACTGTATTCTGCATGTATTTGTA 59.831 37.037 0.00 0.00 0.00 2.41
4717 5301 8.491152 GCTACTGTATTCTGCATGTATTTGTAG 58.509 37.037 0.00 0.00 0.00 2.74
4718 5302 9.750125 CTACTGTATTCTGCATGTATTTGTAGA 57.250 33.333 0.00 0.00 36.69 2.59
4720 5304 9.102757 ACTGTATTCTGCATGTATTTGTAGAAG 57.897 33.333 10.04 1.03 46.67 2.85
4721 5305 9.317936 CTGTATTCTGCATGTATTTGTAGAAGA 57.682 33.333 10.04 3.95 46.67 2.87
4722 5306 9.317936 TGTATTCTGCATGTATTTGTAGAAGAG 57.682 33.333 10.04 0.00 46.67 2.85
4723 5307 7.798596 ATTCTGCATGTATTTGTAGAAGAGG 57.201 36.000 10.04 0.00 46.67 3.69
4724 5308 5.674525 TCTGCATGTATTTGTAGAAGAGGG 58.325 41.667 0.00 0.00 35.73 4.30
4725 5309 4.199310 TGCATGTATTTGTAGAAGAGGGC 58.801 43.478 0.00 0.00 0.00 5.19
4726 5310 3.248602 GCATGTATTTGTAGAAGAGGGCG 59.751 47.826 0.00 0.00 0.00 6.13
4727 5311 4.693283 CATGTATTTGTAGAAGAGGGCGA 58.307 43.478 0.00 0.00 0.00 5.54
4728 5312 5.300752 CATGTATTTGTAGAAGAGGGCGAT 58.699 41.667 0.00 0.00 0.00 4.58
4729 5313 4.693283 TGTATTTGTAGAAGAGGGCGATG 58.307 43.478 0.00 0.00 0.00 3.84
4730 5314 2.024176 TTTGTAGAAGAGGGCGATGC 57.976 50.000 0.00 0.00 0.00 3.91
4731 5315 0.901827 TTGTAGAAGAGGGCGATGCA 59.098 50.000 0.00 0.00 0.00 3.96
4732 5316 0.175760 TGTAGAAGAGGGCGATGCAC 59.824 55.000 0.00 0.00 0.00 4.57
4733 5317 0.175760 GTAGAAGAGGGCGATGCACA 59.824 55.000 0.00 0.00 32.33 4.57
4734 5318 0.901827 TAGAAGAGGGCGATGCACAA 59.098 50.000 0.00 0.00 32.33 3.33
4735 5319 0.674895 AGAAGAGGGCGATGCACAAC 60.675 55.000 0.00 0.00 32.33 3.32
4736 5320 1.970917 GAAGAGGGCGATGCACAACG 61.971 60.000 0.00 0.00 32.33 4.10
5065 5652 0.107831 GGGATGGCGTGGCATTAGTA 59.892 55.000 10.44 0.00 0.00 1.82
5133 5720 1.152756 GGCCATAATTGGGTCGGCT 60.153 57.895 0.00 0.00 43.84 5.52
5143 5730 2.665185 GGTCGGCTCGCAACAAGT 60.665 61.111 0.00 0.00 0.00 3.16
5148 5735 0.796312 CGGCTCGCAACAAGTTGTAT 59.204 50.000 9.37 0.00 42.31 2.29
5150 5737 2.584791 GGCTCGCAACAAGTTGTATTG 58.415 47.619 9.37 6.13 42.31 1.90
5257 5847 0.107654 AGTTCGGCCCATGTAGCTTC 60.108 55.000 0.00 0.00 0.00 3.86
5381 5971 3.130734 AGTCCATGGGCCTTTAGTAGA 57.869 47.619 14.18 0.00 0.00 2.59
5382 5972 3.669949 AGTCCATGGGCCTTTAGTAGAT 58.330 45.455 14.18 0.00 0.00 1.98
5393 5983 7.066525 TGGGCCTTTAGTAGATTGAAATAAACG 59.933 37.037 4.53 0.00 0.00 3.60
5402 5992 4.876107 AGATTGAAATAAACGTCGAGCCAT 59.124 37.500 0.00 0.00 0.00 4.40
5404 5994 4.593597 TGAAATAAACGTCGAGCCATTC 57.406 40.909 0.00 0.00 0.00 2.67
5463 6053 0.034477 ATACCTCGGGCCTTGGTTTG 60.034 55.000 19.77 0.00 35.48 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.499321 TTTTACCTTAAAAGCGTCTTCATCA 57.501 32.000 0.00 0.00 33.08 3.07
134 136 0.748005 CGCGGATTCCAAATCCACCT 60.748 55.000 16.69 0.00 38.08 4.00
146 148 2.034879 CCACTTGCAGACGCGGATT 61.035 57.895 12.47 0.00 42.97 3.01
240 242 7.092623 TGGATACAGCCAAAAAGATTACTCCTA 60.093 37.037 0.00 0.00 46.17 2.94
241 243 6.122964 GGATACAGCCAAAAAGATTACTCCT 58.877 40.000 0.00 0.00 0.00 3.69
242 244 5.885912 TGGATACAGCCAAAAAGATTACTCC 59.114 40.000 0.00 0.00 46.17 3.85
317 319 3.123620 CAGCGCACCAGCTTCTCC 61.124 66.667 11.47 0.00 46.80 3.71
487 499 9.701098 CAGGTATGTGTACTTACTACAGAAAAA 57.299 33.333 0.00 0.00 35.93 1.94
506 518 2.768527 AGTCACTCCATCACCAGGTATG 59.231 50.000 0.00 0.00 0.00 2.39
507 519 3.121929 AGTCACTCCATCACCAGGTAT 57.878 47.619 0.00 0.00 0.00 2.73
600 612 1.146263 CAGTACTCCGAATGCCCCC 59.854 63.158 0.00 0.00 0.00 5.40
672 686 0.249120 CACCCTTGTGCGACATCCTA 59.751 55.000 0.00 0.00 35.31 2.94
678 692 1.961277 CTGACCACCCTTGTGCGAC 60.961 63.158 0.00 0.00 41.35 5.19
705 727 0.744874 TCTCCCGCTTTCCTACATCG 59.255 55.000 0.00 0.00 0.00 3.84
765 787 1.682451 CCCCATCCGGCGTTTCTCTA 61.682 60.000 6.01 0.00 0.00 2.43
800 822 2.487934 GAGCACTGAACAAAGAGAGCA 58.512 47.619 0.00 0.00 0.00 4.26
804 826 2.748605 ACTCGAGCACTGAACAAAGAG 58.251 47.619 13.61 0.00 0.00 2.85
808 830 1.605232 TCGTACTCGAGCACTGAACAA 59.395 47.619 13.61 0.00 41.35 2.83
809 831 1.232119 TCGTACTCGAGCACTGAACA 58.768 50.000 13.61 0.00 41.35 3.18
821 843 0.520827 CGCCTCGTTGACTCGTACTC 60.521 60.000 0.00 0.00 0.00 2.59
822 844 0.952497 TCGCCTCGTTGACTCGTACT 60.952 55.000 0.00 0.00 0.00 2.73
970 1017 9.327731 GGGAGGAGAGGAAAATAATAGAAGATA 57.672 37.037 0.00 0.00 0.00 1.98
971 1018 8.022062 AGGGAGGAGAGGAAAATAATAGAAGAT 58.978 37.037 0.00 0.00 0.00 2.40
972 1019 7.374271 AGGGAGGAGAGGAAAATAATAGAAGA 58.626 38.462 0.00 0.00 0.00 2.87
973 1020 7.512402 AGAGGGAGGAGAGGAAAATAATAGAAG 59.488 40.741 0.00 0.00 0.00 2.85
974 1021 7.374271 AGAGGGAGGAGAGGAAAATAATAGAA 58.626 38.462 0.00 0.00 0.00 2.10
976 1023 7.016296 AGAGAGGGAGGAGAGGAAAATAATAG 58.984 42.308 0.00 0.00 0.00 1.73
977 1024 6.939617 AGAGAGGGAGGAGAGGAAAATAATA 58.060 40.000 0.00 0.00 0.00 0.98
978 1025 5.798419 AGAGAGGGAGGAGAGGAAAATAAT 58.202 41.667 0.00 0.00 0.00 1.28
1280 1357 9.958234 CGGTAGATAATACATGAGATAATGAGG 57.042 37.037 0.00 0.00 0.00 3.86
1320 1397 2.036604 GGATACTCAACCCTAGCTGCTC 59.963 54.545 4.91 0.00 0.00 4.26
1643 1736 2.492088 GGGCCAACAATTTGAGTAGTCC 59.508 50.000 4.39 0.00 34.24 3.85
1644 1737 3.153919 TGGGCCAACAATTTGAGTAGTC 58.846 45.455 2.13 0.00 34.24 2.59
1742 1837 2.627699 TCCCCAAATTTGAAGCAGTCAC 59.372 45.455 19.86 0.00 35.39 3.67
1755 1850 3.173151 GTTGGTGAAGGAATCCCCAAAT 58.827 45.455 8.91 0.00 45.56 2.32
1772 1867 2.997986 GCAAAATCAGCATCAAGGTTGG 59.002 45.455 0.00 0.00 0.00 3.77
1798 1893 5.414454 GGTGCAAACAGGACATAATTAGTGA 59.586 40.000 0.00 0.00 40.89 3.41
1802 1897 5.336372 GCAAGGTGCAAACAGGACATAATTA 60.336 40.000 0.00 0.00 44.26 1.40
1803 1898 4.561326 GCAAGGTGCAAACAGGACATAATT 60.561 41.667 0.00 0.00 44.26 1.40
1804 1899 3.056607 GCAAGGTGCAAACAGGACATAAT 60.057 43.478 0.00 0.00 44.26 1.28
1805 1900 2.295909 GCAAGGTGCAAACAGGACATAA 59.704 45.455 0.00 0.00 44.26 1.90
1839 1938 3.411446 CAGTTTCAGGTGTGGCTGATAA 58.589 45.455 0.00 0.00 0.00 1.75
1924 2023 6.678878 CAGAATAATTTGGCAGGAGATGATG 58.321 40.000 0.00 0.00 0.00 3.07
1927 2026 4.583489 AGCAGAATAATTTGGCAGGAGATG 59.417 41.667 0.00 0.00 0.00 2.90
1974 2073 3.649981 AGATGGATCCAATACACTCCTGG 59.350 47.826 20.67 0.00 0.00 4.45
2016 2311 5.906113 TCTCTGAGCTCTTACAGTAAAGG 57.094 43.478 16.19 0.00 35.84 3.11
2110 2406 4.877378 ACAACATTTGCAATCTGGACAT 57.123 36.364 0.00 0.00 0.00 3.06
2149 2445 5.124457 ACTTGACATCTCAATACATGGCAAC 59.876 40.000 0.00 0.00 42.08 4.17
2223 2519 2.040278 TCATGGCTGGCAGTTTCTAACT 59.960 45.455 17.16 0.00 44.06 2.24
2224 2520 2.162408 GTCATGGCTGGCAGTTTCTAAC 59.838 50.000 17.16 4.51 0.00 2.34
2237 2533 3.222173 TGGTGTTAACTTGTCATGGCT 57.778 42.857 7.22 0.00 0.00 4.75
2310 2606 3.434299 CCAATTGGCAATTTCACTCAAGC 59.566 43.478 22.26 0.00 0.00 4.01
2324 2620 2.622942 TCAACTGAGTCAACCAATTGGC 59.377 45.455 24.79 8.06 41.01 4.52
2338 2634 6.611613 AGAGAAATGGTATGACTCAACTGA 57.388 37.500 0.00 0.00 0.00 3.41
2367 2663 9.816787 TGGTATAGGAAAAACAATAAAGAACCT 57.183 29.630 0.00 0.00 0.00 3.50
2626 2922 7.816031 AAGCACAAAGGTGATGATTTGATTTAG 59.184 33.333 4.79 0.00 44.20 1.85
2684 2980 3.429547 CCTCATCGTCGATCTTGTCCTTT 60.430 47.826 4.34 0.00 0.00 3.11
2835 3131 4.040936 TGGCAGCTAAACTAATTTCCCA 57.959 40.909 0.00 0.00 0.00 4.37
2838 3134 9.855021 TTAGATTTTGGCAGCTAAACTAATTTC 57.145 29.630 2.91 0.00 0.00 2.17
2841 3137 8.581253 ACTTAGATTTTGGCAGCTAAACTAAT 57.419 30.769 2.91 0.00 0.00 1.73
2936 3233 5.465935 GTGTCAAAACTCAAAAACAGACCA 58.534 37.500 0.00 0.00 0.00 4.02
2971 3268 7.704578 TCTGCACTTATCTATATCTGTACCC 57.295 40.000 0.00 0.00 0.00 3.69
3047 3344 6.820152 TCACATCGAATGATTTCTCACAATCT 59.180 34.615 0.00 0.00 34.66 2.40
3066 3363 6.679884 GCCTTGATCTTTTTCCTGATCACATC 60.680 42.308 5.32 0.00 45.72 3.06
3122 3419 2.156504 CGAACACAACACTGATCAGAGC 59.843 50.000 29.27 5.75 0.00 4.09
3127 3424 2.869801 TGTTCCGAACACAACACTGATC 59.130 45.455 9.99 0.00 36.25 2.92
3145 3442 6.102897 ACTGACAGCAAGTTAGATACTGTT 57.897 37.500 1.25 0.00 41.45 3.16
3153 3450 2.549754 CCCACAACTGACAGCAAGTTAG 59.450 50.000 1.25 0.50 39.59 2.34
3164 3461 1.827789 GCCACAAGCCCACAACTGA 60.828 57.895 0.00 0.00 34.35 3.41
3377 3674 6.024049 CCAGCACGAATTCTTCATTAAAGAC 58.976 40.000 3.52 0.00 43.75 3.01
3395 3692 0.881796 GGTTAACAAGGAGCCAGCAC 59.118 55.000 8.10 0.00 0.00 4.40
3425 3722 3.220940 TGTCCAATGCTGAACAACATCA 58.779 40.909 0.00 0.00 0.00 3.07
3563 3860 6.072119 CGTGTGGGAGATGCTATAATGTACTA 60.072 42.308 0.00 0.00 0.00 1.82
3564 3861 5.279006 CGTGTGGGAGATGCTATAATGTACT 60.279 44.000 0.00 0.00 0.00 2.73
3565 3862 4.923871 CGTGTGGGAGATGCTATAATGTAC 59.076 45.833 0.00 0.00 0.00 2.90
3599 3896 9.046296 AGAACGCTTGGATTATACTAAAGATTG 57.954 33.333 0.00 0.00 0.00 2.67
3722 4020 0.659427 GCAAGCTGCGATAAGATGCA 59.341 50.000 0.00 0.00 39.13 3.96
3745 4043 6.406370 TGACAGAGTTATCGAAATGTGGAAT 58.594 36.000 0.00 0.00 28.81 3.01
3994 4292 1.806542 GCTCGCTTTGGTTTGATCTCA 59.193 47.619 0.00 0.00 0.00 3.27
4116 4414 1.079543 CTGACTGGCCCTTGAGACG 60.080 63.158 0.00 0.00 0.00 4.18
4127 4425 0.031178 GGTTGCACAAAGCTGACTGG 59.969 55.000 0.00 0.00 45.94 4.00
4261 4559 3.366440 ACTTCAACACGGAGTCTACAC 57.634 47.619 0.00 0.00 41.61 2.90
4286 4584 6.265649 ACAACAGAGTCTAGCAAGAGAACTTA 59.734 38.462 0.00 0.00 34.70 2.24
4287 4585 5.069781 ACAACAGAGTCTAGCAAGAGAACTT 59.930 40.000 0.00 0.00 36.73 2.66
4288 4586 4.586841 ACAACAGAGTCTAGCAAGAGAACT 59.413 41.667 0.00 0.00 30.45 3.01
4305 4603 9.605275 TTCTTTATCCTTCTGATGATACAACAG 57.395 33.333 0.00 0.00 35.94 3.16
4344 4642 1.675714 CCAGCAGCGACACCTAATCAA 60.676 52.381 0.00 0.00 0.00 2.57
4357 4655 0.172803 CAGGCTTGATTTCCAGCAGC 59.827 55.000 6.05 0.00 0.00 5.25
4384 4682 7.671302 TCTGCAAGATTATAGTCTACCCAATC 58.329 38.462 0.00 3.87 38.67 2.67
4400 4698 8.944029 GCAATCACATATATAGTTCTGCAAGAT 58.056 33.333 0.00 0.00 46.36 2.40
4500 5082 9.671279 CCTGATACATTTGCTATGGTGAATATA 57.329 33.333 4.75 0.00 0.00 0.86
4545 5129 5.810587 GCTGACCATTCAAGTAGATAACGAA 59.189 40.000 0.00 0.00 0.00 3.85
4569 5153 7.592533 CAGTGAGTTTAGTGAATCCAAATGTTG 59.407 37.037 0.00 0.00 0.00 3.33
4593 5177 4.096984 AGGCCATTTTCGAGATAAAAGCAG 59.903 41.667 5.01 0.00 32.20 4.24
4614 5198 3.995506 CTAGCCCGGCCACCAAAGG 62.996 68.421 5.55 0.00 0.00 3.11
4615 5199 2.438434 CTAGCCCGGCCACCAAAG 60.438 66.667 5.55 0.00 0.00 2.77
4616 5200 4.733542 GCTAGCCCGGCCACCAAA 62.734 66.667 5.55 0.00 0.00 3.28
4627 5211 1.759459 ATTACGGCCTCCAGCTAGCC 61.759 60.000 12.13 6.25 43.05 3.93
4628 5212 0.319986 GATTACGGCCTCCAGCTAGC 60.320 60.000 6.62 6.62 43.05 3.42
4629 5213 1.000283 CTGATTACGGCCTCCAGCTAG 60.000 57.143 0.00 0.00 43.05 3.42
4630 5214 1.040646 CTGATTACGGCCTCCAGCTA 58.959 55.000 0.00 0.00 43.05 3.32
4631 5215 1.826024 CTGATTACGGCCTCCAGCT 59.174 57.895 0.00 0.00 43.05 4.24
4632 5216 1.889573 GCTGATTACGGCCTCCAGC 60.890 63.158 0.00 8.47 42.05 4.85
4633 5217 4.445699 GCTGATTACGGCCTCCAG 57.554 61.111 0.00 1.78 42.05 3.86
4640 5224 0.456221 ACTGACGGAGCTGATTACGG 59.544 55.000 0.00 0.00 0.00 4.02
4641 5225 2.541178 GGTACTGACGGAGCTGATTACG 60.541 54.545 0.00 0.00 0.00 3.18
4642 5226 2.223758 GGGTACTGACGGAGCTGATTAC 60.224 54.545 0.00 0.00 0.00 1.89
4643 5227 2.029623 GGGTACTGACGGAGCTGATTA 58.970 52.381 0.00 0.00 0.00 1.75
4644 5228 0.824759 GGGTACTGACGGAGCTGATT 59.175 55.000 0.00 0.00 0.00 2.57
4645 5229 1.384989 CGGGTACTGACGGAGCTGAT 61.385 60.000 0.00 0.00 36.31 2.90
4646 5230 2.044555 CGGGTACTGACGGAGCTGA 61.045 63.158 0.00 0.00 36.31 4.26
4647 5231 2.267681 GACGGGTACTGACGGAGCTG 62.268 65.000 0.00 0.00 38.67 4.24
4648 5232 2.035312 ACGGGTACTGACGGAGCT 59.965 61.111 9.26 0.00 38.67 4.09
4649 5233 2.488820 GACGGGTACTGACGGAGC 59.511 66.667 9.26 0.00 38.67 4.70
4654 5238 1.298190 GATCGCGACGGGTACTGAC 60.298 63.158 12.93 0.00 38.67 3.51
4655 5239 2.816360 CGATCGCGACGGGTACTGA 61.816 63.158 12.93 0.00 40.82 3.41
4656 5240 2.352001 CGATCGCGACGGGTACTG 60.352 66.667 12.93 0.00 40.82 2.74
4657 5241 3.580193 CCGATCGCGACGGGTACT 61.580 66.667 29.99 8.83 45.65 2.73
4664 5248 3.554692 CTTGGCACCGATCGCGAC 61.555 66.667 12.93 5.55 40.82 5.19
4665 5249 4.812476 CCTTGGCACCGATCGCGA 62.812 66.667 13.09 13.09 40.82 5.87
4668 5252 2.040009 ATACCCCTTGGCACCGATCG 62.040 60.000 8.51 8.51 33.59 3.69
4669 5253 0.535102 CATACCCCTTGGCACCGATC 60.535 60.000 0.00 0.00 33.59 3.69
4670 5254 0.986019 TCATACCCCTTGGCACCGAT 60.986 55.000 0.00 0.00 33.59 4.18
4671 5255 1.613928 TCATACCCCTTGGCACCGA 60.614 57.895 0.00 0.00 33.59 4.69
4672 5256 1.451387 GTCATACCCCTTGGCACCG 60.451 63.158 0.00 0.00 33.59 4.94
4673 5257 1.451387 CGTCATACCCCTTGGCACC 60.451 63.158 0.00 0.00 33.59 5.01
4674 5258 2.112815 GCGTCATACCCCTTGGCAC 61.113 63.158 0.00 0.00 33.59 5.01
4675 5259 0.978667 TAGCGTCATACCCCTTGGCA 60.979 55.000 0.00 0.00 33.59 4.92
4676 5260 0.532196 GTAGCGTCATACCCCTTGGC 60.532 60.000 0.00 0.00 33.59 4.52
4677 5261 1.120530 AGTAGCGTCATACCCCTTGG 58.879 55.000 0.00 0.00 37.80 3.61
4678 5262 1.480954 ACAGTAGCGTCATACCCCTTG 59.519 52.381 0.00 0.00 0.00 3.61
4679 5263 1.861982 ACAGTAGCGTCATACCCCTT 58.138 50.000 0.00 0.00 0.00 3.95
4680 5264 2.742428 TACAGTAGCGTCATACCCCT 57.258 50.000 0.00 0.00 0.00 4.79
4681 5265 3.573110 AGAATACAGTAGCGTCATACCCC 59.427 47.826 0.00 0.00 0.00 4.95
4682 5266 4.547532 CAGAATACAGTAGCGTCATACCC 58.452 47.826 0.00 0.00 0.00 3.69
4683 5267 3.982058 GCAGAATACAGTAGCGTCATACC 59.018 47.826 0.00 0.00 0.00 2.73
4684 5268 4.607955 TGCAGAATACAGTAGCGTCATAC 58.392 43.478 0.00 0.00 0.00 2.39
4685 5269 4.911514 TGCAGAATACAGTAGCGTCATA 57.088 40.909 0.00 0.00 0.00 2.15
4686 5270 3.801114 TGCAGAATACAGTAGCGTCAT 57.199 42.857 0.00 0.00 0.00 3.06
4687 5271 3.119137 ACATGCAGAATACAGTAGCGTCA 60.119 43.478 0.00 0.00 0.00 4.35
4688 5272 3.448686 ACATGCAGAATACAGTAGCGTC 58.551 45.455 0.00 0.00 0.00 5.19
4689 5273 3.526931 ACATGCAGAATACAGTAGCGT 57.473 42.857 0.00 0.00 0.00 5.07
4690 5274 6.018751 ACAAATACATGCAGAATACAGTAGCG 60.019 38.462 0.00 0.00 0.00 4.26
4691 5275 7.251704 ACAAATACATGCAGAATACAGTAGC 57.748 36.000 0.00 0.00 0.00 3.58
4692 5276 9.750125 TCTACAAATACATGCAGAATACAGTAG 57.250 33.333 0.00 0.49 0.00 2.57
4694 5278 9.102757 CTTCTACAAATACATGCAGAATACAGT 57.897 33.333 0.00 0.00 33.41 3.55
4695 5279 9.317936 TCTTCTACAAATACATGCAGAATACAG 57.682 33.333 0.00 0.00 33.41 2.74
4696 5280 9.317936 CTCTTCTACAAATACATGCAGAATACA 57.682 33.333 0.00 0.00 33.41 2.29
4697 5281 8.768955 CCTCTTCTACAAATACATGCAGAATAC 58.231 37.037 0.00 0.00 33.41 1.89
4698 5282 7.933577 CCCTCTTCTACAAATACATGCAGAATA 59.066 37.037 0.00 0.00 33.41 1.75
4699 5283 6.769822 CCCTCTTCTACAAATACATGCAGAAT 59.230 38.462 0.00 0.00 33.41 2.40
4700 5284 6.115446 CCCTCTTCTACAAATACATGCAGAA 58.885 40.000 0.00 0.00 32.97 3.02
4701 5285 5.674525 CCCTCTTCTACAAATACATGCAGA 58.325 41.667 0.00 0.00 0.00 4.26
4702 5286 4.274459 GCCCTCTTCTACAAATACATGCAG 59.726 45.833 0.00 0.00 0.00 4.41
4703 5287 4.199310 GCCCTCTTCTACAAATACATGCA 58.801 43.478 0.00 0.00 0.00 3.96
4704 5288 3.248602 CGCCCTCTTCTACAAATACATGC 59.751 47.826 0.00 0.00 0.00 4.06
4705 5289 4.693283 TCGCCCTCTTCTACAAATACATG 58.307 43.478 0.00 0.00 0.00 3.21
4706 5290 5.300752 CATCGCCCTCTTCTACAAATACAT 58.699 41.667 0.00 0.00 0.00 2.29
4707 5291 4.693283 CATCGCCCTCTTCTACAAATACA 58.307 43.478 0.00 0.00 0.00 2.29
4708 5292 3.495001 GCATCGCCCTCTTCTACAAATAC 59.505 47.826 0.00 0.00 0.00 1.89
4709 5293 3.133901 TGCATCGCCCTCTTCTACAAATA 59.866 43.478 0.00 0.00 0.00 1.40
4710 5294 2.092968 TGCATCGCCCTCTTCTACAAAT 60.093 45.455 0.00 0.00 0.00 2.32
4711 5295 1.277842 TGCATCGCCCTCTTCTACAAA 59.722 47.619 0.00 0.00 0.00 2.83
4712 5296 0.901827 TGCATCGCCCTCTTCTACAA 59.098 50.000 0.00 0.00 0.00 2.41
4713 5297 0.175760 GTGCATCGCCCTCTTCTACA 59.824 55.000 0.00 0.00 0.00 2.74
4714 5298 0.175760 TGTGCATCGCCCTCTTCTAC 59.824 55.000 0.00 0.00 0.00 2.59
4715 5299 0.901827 TTGTGCATCGCCCTCTTCTA 59.098 50.000 0.00 0.00 0.00 2.10
4716 5300 0.674895 GTTGTGCATCGCCCTCTTCT 60.675 55.000 0.00 0.00 0.00 2.85
4717 5301 1.796796 GTTGTGCATCGCCCTCTTC 59.203 57.895 0.00 0.00 0.00 2.87
4718 5302 2.034879 CGTTGTGCATCGCCCTCTT 61.035 57.895 0.00 0.00 0.00 2.85
4719 5303 2.434884 CGTTGTGCATCGCCCTCT 60.435 61.111 0.00 0.00 0.00 3.69
4720 5304 4.166011 GCGTTGTGCATCGCCCTC 62.166 66.667 18.28 0.00 45.54 4.30
4729 5313 1.226018 GCCAATACGAGCGTTGTGC 60.226 57.895 0.00 0.00 46.98 4.57
4730 5314 0.179225 GTGCCAATACGAGCGTTGTG 60.179 55.000 0.00 0.00 0.00 3.33
4731 5315 0.601576 TGTGCCAATACGAGCGTTGT 60.602 50.000 0.00 0.00 0.00 3.32
4732 5316 0.726827 ATGTGCCAATACGAGCGTTG 59.273 50.000 0.00 0.00 0.00 4.10
4733 5317 2.303163 TATGTGCCAATACGAGCGTT 57.697 45.000 0.00 0.00 0.00 4.84
4734 5318 2.303163 TTATGTGCCAATACGAGCGT 57.697 45.000 0.00 0.00 0.00 5.07
4735 5319 3.878086 ATTTATGTGCCAATACGAGCG 57.122 42.857 0.00 0.00 0.00 5.03
4736 5320 6.368791 TCTCATATTTATGTGCCAATACGAGC 59.631 38.462 0.00 0.00 35.26 5.03
4737 5321 7.384932 TGTCTCATATTTATGTGCCAATACGAG 59.615 37.037 0.00 0.00 35.26 4.18
4738 5322 7.213678 TGTCTCATATTTATGTGCCAATACGA 58.786 34.615 0.00 0.00 35.26 3.43
4739 5323 7.420184 TGTCTCATATTTATGTGCCAATACG 57.580 36.000 0.00 0.00 35.26 3.06
4740 5324 8.620416 TGTTGTCTCATATTTATGTGCCAATAC 58.380 33.333 1.12 0.00 35.26 1.89
4741 5325 8.744568 TGTTGTCTCATATTTATGTGCCAATA 57.255 30.769 1.12 0.00 35.26 1.90
4844 5428 5.583495 TCATTTAAAACAGAACCAACACCG 58.417 37.500 0.00 0.00 0.00 4.94
4932 5516 8.943909 ATTTAAAATGTTCGTTGGGTTGTAAA 57.056 26.923 0.00 0.00 0.00 2.01
4935 5519 7.851387 AAATTTAAAATGTTCGTTGGGTTGT 57.149 28.000 0.00 0.00 0.00 3.32
5021 5605 6.992063 TTTTGCTAAGCTTAATCTCTCCTG 57.008 37.500 7.74 0.00 0.00 3.86
5065 5652 8.950210 CGATAATTATGCTACAATGAATCCCTT 58.050 33.333 1.78 0.00 0.00 3.95
5133 5720 1.883275 CCCCAATACAACTTGTTGCGA 59.117 47.619 12.76 2.80 0.00 5.10
5143 5730 2.044451 CCGCAGGCCCCAATACAA 60.044 61.111 0.00 0.00 46.14 2.41
5257 5847 1.102154 TTCAGCATGTTAATGGCCCG 58.898 50.000 0.00 0.00 37.40 6.13
5302 5892 2.369394 CTAAAGGCCCATGGTGTCTTC 58.631 52.381 17.15 0.00 0.00 2.87
5381 5971 5.354234 AGAATGGCTCGACGTTTATTTCAAT 59.646 36.000 0.00 0.00 0.00 2.57
5382 5972 4.693566 AGAATGGCTCGACGTTTATTTCAA 59.306 37.500 0.00 0.00 0.00 2.69
5402 5992 6.148186 ACCCATAATGTAACTAGGCCTAGAA 58.852 40.000 40.40 26.34 36.97 2.10
5404 5994 5.542635 TGACCCATAATGTAACTAGGCCTAG 59.457 44.000 33.98 33.98 39.04 3.02
5422 6012 1.208706 TTCGGCCTGATAATGACCCA 58.791 50.000 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.