Multiple sequence alignment - TraesCS5D01G309300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G309300 chr5D 100.000 4100 0 0 1 4100 406414460 406418559 0.000000e+00 7572.0
1 TraesCS5D01G309300 chr5B 91.854 3474 164 56 452 3873 487437123 487440529 0.000000e+00 4737.0
2 TraesCS5D01G309300 chr5B 87.190 1413 156 19 1728 3127 505276215 505277615 0.000000e+00 1583.0
3 TraesCS5D01G309300 chr5B 87.152 1401 153 18 1728 3119 505379199 505380581 0.000000e+00 1565.0
4 TraesCS5D01G309300 chr5B 85.452 818 85 21 999 1793 505378335 505379141 0.000000e+00 821.0
5 TraesCS5D01G309300 chr5B 90.890 472 27 7 3602 4064 487481401 487481865 1.620000e-173 619.0
6 TraesCS5D01G309300 chr5B 83.929 448 52 10 10 453 487436654 487437085 1.060000e-110 411.0
7 TraesCS5D01G309300 chr5B 88.571 70 5 1 4031 4100 487440550 487440616 9.450000e-12 82.4
8 TraesCS5D01G309300 chr5A 93.943 2922 116 29 452 3345 512059024 512061912 0.000000e+00 4359.0
9 TraesCS5D01G309300 chr5A 88.052 1314 137 17 1822 3127 532740690 532741991 0.000000e+00 1539.0
10 TraesCS5D01G309300 chr5A 94.857 175 6 1 3703 3877 512062166 512062337 1.880000e-68 270.0
11 TraesCS5D01G309300 chr5A 85.145 276 15 9 3404 3673 512061908 512062163 4.070000e-65 259.0
12 TraesCS5D01G309300 chr6D 88.230 2209 202 30 968 3129 36252638 36254835 0.000000e+00 2586.0
13 TraesCS5D01G309300 chr6B 87.641 2209 215 33 968 3129 75941512 75943709 0.000000e+00 2514.0
14 TraesCS5D01G309300 chr1B 87.414 2169 231 27 992 3131 598190650 598192805 0.000000e+00 2455.0
15 TraesCS5D01G309300 chr1D 87.506 2161 223 24 992 3119 440718422 440720568 0.000000e+00 2451.0
16 TraesCS5D01G309300 chr6A 86.953 2215 219 37 968 3129 40297943 40300140 0.000000e+00 2425.0
17 TraesCS5D01G309300 chr6A 80.804 224 28 12 3296 3505 139424321 139424099 1.180000e-35 161.0
18 TraesCS5D01G309300 chr1A 87.407 2160 209 33 998 3119 537347813 537345679 0.000000e+00 2423.0
19 TraesCS5D01G309300 chr7B 88.430 1815 160 23 1000 2804 538053825 538052051 0.000000e+00 2143.0
20 TraesCS5D01G309300 chr7D 89.040 1761 145 25 1060 2804 509632461 509630733 0.000000e+00 2139.0
21 TraesCS5D01G309300 chr3A 88.800 125 13 1 1580 1704 146763727 146763604 7.100000e-33 152.0
22 TraesCS5D01G309300 chr4B 87.931 58 5 2 4043 4099 11742283 11742339 2.640000e-07 67.6
23 TraesCS5D01G309300 chr3B 91.304 46 4 0 4043 4088 550797259 550797304 3.420000e-06 63.9
24 TraesCS5D01G309300 chr4D 86.207 58 6 2 4043 4099 6586185 6586241 1.230000e-05 62.1
25 TraesCS5D01G309300 chr4A 91.304 46 2 2 4055 4099 596820761 596820717 1.230000e-05 62.1


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 TraesCS5D01G309300 chr5D 406414460 406418559 4099 False 7572.000000 7572 100.000 1 4100 1 chr5D.!!$F1 4099
1 TraesCS5D01G309300 chr5B 487436654 487440616 3962 False 1743.466667 4737 88.118 10 4100 3 chr5B.!!$F3 4090
2 TraesCS5D01G309300 chr5B 505276215 505277615 1400 False 1583.000000 1583 87.190 1728 3127 1 chr5B.!!$F2 1399
3 TraesCS5D01G309300 chr5B 505378335 505380581 2246 False 1193.000000 1565 86.302 999 3119 2 chr5B.!!$F4 2120
4 TraesCS5D01G309300 chr5A 512059024 512062337 3313 False 1629.333333 4359 91.315 452 3877 3 chr5A.!!$F2 3425
5 TraesCS5D01G309300 chr5A 532740690 532741991 1301 False 1539.000000 1539 88.052 1822 3127 1 chr5A.!!$F1 1305
6 TraesCS5D01G309300 chr6D 36252638 36254835 2197 False 2586.000000 2586 88.230 968 3129 1 chr6D.!!$F1 2161
7 TraesCS5D01G309300 chr6B 75941512 75943709 2197 False 2514.000000 2514 87.641 968 3129 1 chr6B.!!$F1 2161
8 TraesCS5D01G309300 chr1B 598190650 598192805 2155 False 2455.000000 2455 87.414 992 3131 1 chr1B.!!$F1 2139
9 TraesCS5D01G309300 chr1D 440718422 440720568 2146 False 2451.000000 2451 87.506 992 3119 1 chr1D.!!$F1 2127
10 TraesCS5D01G309300 chr6A 40297943 40300140 2197 False 2425.000000 2425 86.953 968 3129 1 chr6A.!!$F1 2161
11 TraesCS5D01G309300 chr1A 537345679 537347813 2134 True 2423.000000 2423 87.407 998 3119 1 chr1A.!!$R1 2121
12 TraesCS5D01G309300 chr7B 538052051 538053825 1774 True 2143.000000 2143 88.430 1000 2804 1 chr7B.!!$R1 1804
13 TraesCS5D01G309300 chr7D 509630733 509632461 1728 True 2139.000000 2139 89.040 1060 2804 1 chr7D.!!$R1 1744

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
204 206 0.175531 GAAATGCAACGGGGGATTGG 59.824 55.0 0.0 0.0 0.00 3.16 F
804 857 0.252197 GGCTCCCACTATGTCGGTTT 59.748 55.0 0.0 0.0 0.00 3.27 F
883 939 0.903454 GTCGGTTCCTCCTTCCTCCA 60.903 60.0 0.0 0.0 0.00 3.86 F
2622 2909 1.649271 GGCCCCAGATCCACCTGATT 61.649 60.0 0.0 0.0 36.29 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2550 2835 2.187992 CTCCTCGCTGAGCTCTGAA 58.812 57.895 23.35 9.84 0.00 3.02 R
2835 3149 1.035932 CCTCGTAGTCCGTGTCCCAT 61.036 60.000 0.00 0.00 37.94 4.00 R
2931 3245 1.208358 CGTCACTGGCGTCGACTTA 59.792 57.895 14.70 0.00 0.00 2.24 R
4037 4419 0.108756 GCGGTTAGCGGAGAAGAAGT 60.109 55.000 5.84 0.00 35.41 3.01 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 3.158676 AGGTAGGAGATGGCTATCGAAC 58.841 50.000 4.21 2.12 38.38 3.95
49 50 1.982660 AGGAGATGGCTATCGAACGA 58.017 50.000 4.21 0.00 38.38 3.85
56 57 2.876091 TGGCTATCGAACGACAGAAAG 58.124 47.619 6.69 0.00 0.00 2.62
123 125 2.542595 GGTTGCCCGACGACTATTATTG 59.457 50.000 0.00 0.00 32.66 1.90
126 128 2.223876 TGCCCGACGACTATTATTGTCC 60.224 50.000 0.00 0.00 30.17 4.02
127 129 2.658285 CCCGACGACTATTATTGTCCG 58.342 52.381 0.00 1.01 30.17 4.79
145 147 4.705110 TCCGGATGATAATGGACATGTT 57.295 40.909 0.00 0.00 0.00 2.71
147 149 3.503363 CCGGATGATAATGGACATGTTGG 59.497 47.826 0.00 0.00 0.00 3.77
168 170 2.365293 GCATGGGCAAGTTTATTAGGGG 59.635 50.000 0.00 0.00 40.72 4.79
174 176 4.387550 GGGCAAGTTTATTAGGGGGAAGAT 60.388 45.833 0.00 0.00 0.00 2.40
194 196 4.994744 GGCACCCTGAAATGCAAC 57.005 55.556 0.00 0.00 43.93 4.17
200 202 1.304052 CCTGAAATGCAACGGGGGA 60.304 57.895 0.00 0.00 0.00 4.81
201 203 0.684153 CCTGAAATGCAACGGGGGAT 60.684 55.000 0.00 0.00 0.00 3.85
202 204 1.185315 CTGAAATGCAACGGGGGATT 58.815 50.000 0.00 0.00 0.00 3.01
203 205 0.894141 TGAAATGCAACGGGGGATTG 59.106 50.000 0.00 0.00 0.00 2.67
204 206 0.175531 GAAATGCAACGGGGGATTGG 59.824 55.000 0.00 0.00 0.00 3.16
205 207 1.264045 AAATGCAACGGGGGATTGGG 61.264 55.000 0.00 0.00 0.00 4.12
206 208 3.677480 ATGCAACGGGGGATTGGGG 62.677 63.158 0.00 0.00 0.00 4.96
207 209 4.055227 GCAACGGGGGATTGGGGA 62.055 66.667 0.00 0.00 0.00 4.81
208 210 3.015383 CAACGGGGGATTGGGGAT 58.985 61.111 0.00 0.00 0.00 3.85
209 211 1.455587 CAACGGGGGATTGGGGATG 60.456 63.158 0.00 0.00 0.00 3.51
218 220 2.011617 GATTGGGGATGTGGGGAGGG 62.012 65.000 0.00 0.00 0.00 4.30
222 224 1.720077 GGGGATGTGGGGAGGGATTC 61.720 65.000 0.00 0.00 0.00 2.52
223 225 0.993509 GGGATGTGGGGAGGGATTCA 60.994 60.000 0.00 0.00 0.00 2.57
291 293 2.046892 CCACCAGGGCTCAAGTCG 60.047 66.667 0.00 0.00 0.00 4.18
294 296 0.320374 CACCAGGGCTCAAGTCGTAA 59.680 55.000 0.00 0.00 0.00 3.18
325 328 4.662468 TGGTGCTTGCATTTTACTTTCA 57.338 36.364 0.00 0.00 0.00 2.69
327 330 4.340666 TGGTGCTTGCATTTTACTTTCAGA 59.659 37.500 0.00 0.00 0.00 3.27
336 340 4.823790 TTTTACTTTCAGACTTTCCGCC 57.176 40.909 0.00 0.00 0.00 6.13
348 352 0.871722 TTTCCGCCATGTTCGTTCAG 59.128 50.000 0.00 0.00 0.00 3.02
354 358 2.650608 GCCATGTTCGTTCAGTGAAAC 58.349 47.619 7.25 3.11 0.00 2.78
380 384 3.179048 CGTTCTCGTCAACTATGATGCA 58.821 45.455 0.00 0.00 41.50 3.96
381 385 3.000674 CGTTCTCGTCAACTATGATGCAC 60.001 47.826 0.00 0.00 41.50 4.57
382 386 3.866883 TCTCGTCAACTATGATGCACA 57.133 42.857 0.00 0.00 41.50 4.57
387 391 3.242511 CGTCAACTATGATGCACATGTGG 60.243 47.826 26.55 10.84 39.77 4.17
391 395 8.315906 GTCAACTATGATGCACATGTGGTGAG 62.316 46.154 26.55 10.61 43.29 3.51
403 407 3.026630 TGTGGTGAGTTCGACAATCTC 57.973 47.619 0.00 0.00 0.00 2.75
404 408 2.364002 TGTGGTGAGTTCGACAATCTCA 59.636 45.455 0.00 0.00 36.12 3.27
416 420 4.686091 TCGACAATCTCAAGATGTTGTGTC 59.314 41.667 11.75 11.75 36.21 3.67
417 421 4.448732 CGACAATCTCAAGATGTTGTGTCA 59.551 41.667 18.20 0.00 37.95 3.58
429 433 4.471904 TGTTGTGTCAGTTCAGTCTCTT 57.528 40.909 0.00 0.00 0.00 2.85
433 437 5.282055 TGTGTCAGTTCAGTCTCTTGAAT 57.718 39.130 0.00 0.00 39.13 2.57
436 440 6.183360 TGTGTCAGTTCAGTCTCTTGAATGTA 60.183 38.462 0.00 0.00 39.13 2.29
456 460 5.535029 TGTACTCATAGGGGTATGGTCTTT 58.465 41.667 0.00 0.00 0.00 2.52
462 504 3.669939 AGGGGTATGGTCTTTGATTGG 57.330 47.619 0.00 0.00 0.00 3.16
468 510 5.338871 GGGTATGGTCTTTGATTGGAGTGTA 60.339 44.000 0.00 0.00 0.00 2.90
474 516 8.335532 TGGTCTTTGATTGGAGTGTATTAAAG 57.664 34.615 0.00 0.00 31.99 1.85
476 518 9.010029 GGTCTTTGATTGGAGTGTATTAAAGAA 57.990 33.333 0.00 0.00 37.79 2.52
528 570 5.643379 TTTTAGACATGGCAGATCAAACC 57.357 39.130 0.00 0.00 0.00 3.27
539 581 2.507058 CAGATCAAACCCCTGAGATGGA 59.493 50.000 0.00 0.00 0.00 3.41
552 595 5.124457 CCCTGAGATGGAAATTATATTGCCG 59.876 44.000 0.00 0.00 0.00 5.69
553 596 5.707298 CCTGAGATGGAAATTATATTGCCGT 59.293 40.000 0.00 0.00 0.00 5.68
557 600 6.533730 AGATGGAAATTATATTGCCGTGAGA 58.466 36.000 0.00 0.00 0.00 3.27
561 604 5.858581 GGAAATTATATTGCCGTGAGAATGC 59.141 40.000 0.00 0.00 0.00 3.56
562 605 5.376854 AATTATATTGCCGTGAGAATGCC 57.623 39.130 0.00 0.00 0.00 4.40
565 608 1.477553 ATTGCCGTGAGAATGCCAAT 58.522 45.000 0.00 0.00 0.00 3.16
569 612 2.262211 GCCGTGAGAATGCCAATTTTC 58.738 47.619 0.00 0.00 0.00 2.29
570 613 2.094545 GCCGTGAGAATGCCAATTTTCT 60.095 45.455 0.00 0.00 34.95 2.52
596 640 3.367703 GCAAGCACATGCAAATCCTTACT 60.368 43.478 6.64 0.00 45.70 2.24
628 672 3.685139 TTTTTGCCGGAAATTGCCATA 57.315 38.095 5.05 0.00 0.00 2.74
634 678 2.482864 CCGGAAATTGCCATAATTGCC 58.517 47.619 2.58 0.00 32.92 4.52
640 684 5.295045 GGAAATTGCCATAATTGCCAAAGAG 59.705 40.000 0.00 0.00 35.74 2.85
644 688 6.788598 TTGCCATAATTGCCAAAGAGAATA 57.211 33.333 0.00 0.00 0.00 1.75
655 699 4.442192 GCCAAAGAGAATAGTCATCCTCGT 60.442 45.833 0.00 0.00 0.00 4.18
669 713 7.534085 GTCATCCTCGTGACAACATAATTTA 57.466 36.000 2.40 0.00 46.04 1.40
705 751 5.471797 TCCGATTTGCTGTGTCTAAAAATCA 59.528 36.000 0.00 0.00 37.17 2.57
789 839 4.568152 AATTAACCACGCATAATGGCTC 57.432 40.909 0.00 0.00 41.31 4.70
791 841 0.751643 AACCACGCATAATGGCTCCC 60.752 55.000 0.00 0.00 41.31 4.30
804 857 0.252197 GGCTCCCACTATGTCGGTTT 59.748 55.000 0.00 0.00 0.00 3.27
840 894 3.254654 CACGCGACGCCGATCAAT 61.255 61.111 15.93 0.00 38.22 2.57
883 939 0.903454 GTCGGTTCCTCCTTCCTCCA 60.903 60.000 0.00 0.00 0.00 3.86
960 1022 1.690633 CTTCTCCCCAGCCTAGCCA 60.691 63.158 0.00 0.00 0.00 4.75
1761 2025 3.371063 TCTGTCGCGGTCCAGGAC 61.371 66.667 11.70 11.70 0.00 3.85
2454 2739 4.477975 GTGGACGACCTCCGCTCG 62.478 72.222 5.33 0.00 45.20 5.03
2608 2893 4.168291 CCTTCAGCGAGAGGCCCC 62.168 72.222 0.00 0.00 45.17 5.80
2622 2909 1.649271 GGCCCCAGATCCACCTGATT 61.649 60.000 0.00 0.00 36.29 2.57
2931 3245 0.827925 TCTGGAACCTGCGTGACTCT 60.828 55.000 0.00 0.00 0.00 3.24
3145 3471 8.401490 AGCTTAGTTTGATCAGTTCTTTTCAT 57.599 30.769 0.00 0.00 0.00 2.57
3191 3519 4.582656 TCAGAATTCGAACCAAAACCATGT 59.417 37.500 0.00 0.00 0.00 3.21
3324 3653 5.105635 TGCATGAATGAACTTCTGAATTCCC 60.106 40.000 2.27 0.00 34.75 3.97
3376 3705 7.966246 TTTCTGAATCCAAACCAAAATCATG 57.034 32.000 0.00 0.00 0.00 3.07
3401 3731 7.015292 TGCTTGTAACCTTTTTCTCTCTCTCTA 59.985 37.037 0.00 0.00 0.00 2.43
3463 3793 4.110482 GCTTAATACTGTACGTCCACTGG 58.890 47.826 0.00 0.00 0.00 4.00
3468 3800 2.108168 ACTGTACGTCCACTGGCATAT 58.892 47.619 0.00 0.00 0.00 1.78
3512 3844 5.843673 TCCAACAACATGCTTCTTTGTTA 57.156 34.783 10.10 0.00 40.62 2.41
3564 3896 5.466393 GCTGTTAATTTGCCAGTTCATTTGT 59.534 36.000 0.00 0.00 0.00 2.83
3595 3931 3.189285 ACTGCTGAAACACAATTGTTGC 58.811 40.909 8.77 7.31 45.69 4.17
3598 3934 1.522258 CTGAAACACAATTGTTGCGGC 59.478 47.619 8.77 0.00 45.69 6.53
3600 3936 1.486644 AAACACAATTGTTGCGGCGC 61.487 50.000 27.44 27.44 45.69 6.53
3612 3948 3.853330 CGGCGCTTGTCATGGTCG 61.853 66.667 7.64 0.00 0.00 4.79
3618 3954 0.163788 GCTTGTCATGGTCGTGTTCG 59.836 55.000 0.00 0.00 38.55 3.95
3629 3965 1.802365 GTCGTGTTCGTGCCCTTTATT 59.198 47.619 0.00 0.00 38.33 1.40
3630 3966 1.801771 TCGTGTTCGTGCCCTTTATTG 59.198 47.619 0.00 0.00 38.33 1.90
3634 3970 2.554893 TGTTCGTGCCCTTTATTGGTTC 59.445 45.455 0.00 0.00 0.00 3.62
3644 3980 4.765339 CCCTTTATTGGTTCTCTCGGTTTT 59.235 41.667 0.00 0.00 0.00 2.43
3673 4055 4.819630 TCGTGGTGTTTTGATTAGCTTCTT 59.180 37.500 0.00 0.00 0.00 2.52
3674 4056 5.992829 TCGTGGTGTTTTGATTAGCTTCTTA 59.007 36.000 0.00 0.00 0.00 2.10
3675 4057 6.653320 TCGTGGTGTTTTGATTAGCTTCTTAT 59.347 34.615 0.00 0.00 0.00 1.73
3676 4058 7.174253 TCGTGGTGTTTTGATTAGCTTCTTATT 59.826 33.333 0.00 0.00 0.00 1.40
3677 4059 7.807907 CGTGGTGTTTTGATTAGCTTCTTATTT 59.192 33.333 0.00 0.00 0.00 1.40
3678 4060 9.129209 GTGGTGTTTTGATTAGCTTCTTATTTC 57.871 33.333 0.00 0.00 0.00 2.17
3679 4061 8.303876 TGGTGTTTTGATTAGCTTCTTATTTCC 58.696 33.333 0.00 0.00 0.00 3.13
3680 4062 8.303876 GGTGTTTTGATTAGCTTCTTATTTCCA 58.696 33.333 0.00 0.00 0.00 3.53
3681 4063 9.346725 GTGTTTTGATTAGCTTCTTATTTCCAG 57.653 33.333 0.00 0.00 0.00 3.86
3682 4064 9.295825 TGTTTTGATTAGCTTCTTATTTCCAGA 57.704 29.630 0.00 0.00 0.00 3.86
3758 4140 8.986991 AGGAATGTAGTGAGTCTCTTTGATTAT 58.013 33.333 0.00 0.00 0.00 1.28
3759 4141 9.606631 GGAATGTAGTGAGTCTCTTTGATTATT 57.393 33.333 0.00 0.00 0.00 1.40
3777 4159 9.961265 TTGATTATTACTGTCGTAGGTATGAAG 57.039 33.333 0.00 0.00 0.00 3.02
3802 4184 2.859165 TCAGTTCAGGGCCAGTTTAG 57.141 50.000 6.18 0.00 0.00 1.85
3878 4260 5.357742 AAATGGCTTTGAATGGGGAATAC 57.642 39.130 0.00 0.00 0.00 1.89
3879 4261 3.464720 TGGCTTTGAATGGGGAATACA 57.535 42.857 0.00 0.00 0.00 2.29
3880 4262 3.992999 TGGCTTTGAATGGGGAATACAT 58.007 40.909 0.00 0.00 0.00 2.29
3881 4263 4.360889 TGGCTTTGAATGGGGAATACATT 58.639 39.130 0.00 0.00 40.98 2.71
3883 4265 4.122046 GCTTTGAATGGGGAATACATTGC 58.878 43.478 0.00 0.00 38.57 3.56
3884 4266 4.141869 GCTTTGAATGGGGAATACATTGCT 60.142 41.667 0.00 0.00 38.57 3.91
3887 4269 3.953612 TGAATGGGGAATACATTGCTGTC 59.046 43.478 0.00 0.00 38.57 3.51
3888 4270 3.668141 ATGGGGAATACATTGCTGTCA 57.332 42.857 0.00 0.00 36.79 3.58
3889 4271 3.448093 TGGGGAATACATTGCTGTCAA 57.552 42.857 0.00 0.00 36.79 3.18
3890 4272 3.088532 TGGGGAATACATTGCTGTCAAC 58.911 45.455 0.00 0.00 36.79 3.18
3891 4273 3.088532 GGGGAATACATTGCTGTCAACA 58.911 45.455 0.00 0.00 36.79 3.33
3893 4275 4.380867 GGGGAATACATTGCTGTCAACAAG 60.381 45.833 0.00 0.00 36.79 3.16
3894 4276 4.218417 GGGAATACATTGCTGTCAACAAGT 59.782 41.667 0.00 0.00 36.79 3.16
3896 4278 6.215845 GGAATACATTGCTGTCAACAAGTTT 58.784 36.000 0.00 0.00 36.79 2.66
3898 4280 4.717233 ACATTGCTGTCAACAAGTTTGA 57.283 36.364 0.00 0.00 34.60 2.69
3901 4283 5.348451 ACATTGCTGTCAACAAGTTTGAAAC 59.652 36.000 0.00 0.00 34.60 2.78
3902 4284 4.511617 TGCTGTCAACAAGTTTGAAACA 57.488 36.364 11.02 0.00 0.00 2.83
3903 4285 4.876125 TGCTGTCAACAAGTTTGAAACAA 58.124 34.783 11.02 0.00 0.00 2.83
3904 4286 4.922692 TGCTGTCAACAAGTTTGAAACAAG 59.077 37.500 11.02 4.64 0.00 3.16
3905 4287 5.160641 GCTGTCAACAAGTTTGAAACAAGA 58.839 37.500 11.02 0.00 0.00 3.02
3906 4288 5.633182 GCTGTCAACAAGTTTGAAACAAGAA 59.367 36.000 11.02 0.00 0.00 2.52
3907 4289 6.145371 GCTGTCAACAAGTTTGAAACAAGAAA 59.855 34.615 11.02 0.00 0.00 2.52
3908 4290 7.148590 GCTGTCAACAAGTTTGAAACAAGAAAT 60.149 33.333 11.02 0.00 0.00 2.17
3909 4291 9.352784 CTGTCAACAAGTTTGAAACAAGAAATA 57.647 29.630 11.02 0.00 0.00 1.40
3910 4292 9.134734 TGTCAACAAGTTTGAAACAAGAAATAC 57.865 29.630 11.02 1.41 0.00 1.89
3911 4293 9.353999 GTCAACAAGTTTGAAACAAGAAATACT 57.646 29.630 11.02 0.00 0.00 2.12
3912 4294 9.352784 TCAACAAGTTTGAAACAAGAAATACTG 57.647 29.630 11.02 0.00 0.00 2.74
3913 4295 9.352784 CAACAAGTTTGAAACAAGAAATACTGA 57.647 29.630 11.02 0.00 0.00 3.41
3914 4296 9.573133 AACAAGTTTGAAACAAGAAATACTGAG 57.427 29.630 11.02 0.00 0.00 3.35
3915 4297 8.956426 ACAAGTTTGAAACAAGAAATACTGAGA 58.044 29.630 11.02 0.00 0.00 3.27
3916 4298 9.956720 CAAGTTTGAAACAAGAAATACTGAGAT 57.043 29.630 11.02 0.00 0.00 2.75
3917 4299 9.956720 AAGTTTGAAACAAGAAATACTGAGATG 57.043 29.630 11.02 0.00 0.00 2.90
3918 4300 9.125026 AGTTTGAAACAAGAAATACTGAGATGT 57.875 29.630 11.02 0.00 0.00 3.06
3919 4301 9.736023 GTTTGAAACAAGAAATACTGAGATGTT 57.264 29.630 2.68 0.00 30.23 2.71
3954 4336 9.851686 TTATTATTATCATGAGACTTTGGCAGT 57.148 29.630 0.09 0.00 39.07 4.40
3955 4337 8.757982 ATTATTATCATGAGACTTTGGCAGTT 57.242 30.769 0.09 0.00 35.01 3.16
3956 4338 8.579850 TTATTATCATGAGACTTTGGCAGTTT 57.420 30.769 0.09 0.00 35.01 2.66
3957 4339 6.500684 TTATCATGAGACTTTGGCAGTTTC 57.499 37.500 0.09 0.00 37.18 2.78
3962 4344 5.596836 TGAGACTTTGGCAGTTTCATTTT 57.403 34.783 0.00 0.00 40.81 1.82
3963 4345 6.707440 TGAGACTTTGGCAGTTTCATTTTA 57.293 33.333 0.00 0.00 40.81 1.52
3964 4346 6.738114 TGAGACTTTGGCAGTTTCATTTTAG 58.262 36.000 0.00 0.00 40.81 1.85
3965 4347 6.545666 TGAGACTTTGGCAGTTTCATTTTAGA 59.454 34.615 0.00 0.00 40.81 2.10
3966 4348 6.974965 AGACTTTGGCAGTTTCATTTTAGAG 58.025 36.000 0.00 0.00 35.01 2.43
3967 4349 6.772716 AGACTTTGGCAGTTTCATTTTAGAGA 59.227 34.615 0.00 0.00 35.01 3.10
3968 4350 7.285401 AGACTTTGGCAGTTTCATTTTAGAGAA 59.715 33.333 0.00 0.00 35.01 2.87
3969 4351 7.428826 ACTTTGGCAGTTTCATTTTAGAGAAG 58.571 34.615 0.00 0.00 27.32 2.85
3970 4352 5.376854 TGGCAGTTTCATTTTAGAGAAGC 57.623 39.130 0.00 0.00 0.00 3.86
3971 4353 4.826733 TGGCAGTTTCATTTTAGAGAAGCA 59.173 37.500 0.00 0.00 0.00 3.91
3972 4354 5.157067 GGCAGTTTCATTTTAGAGAAGCAC 58.843 41.667 0.00 0.00 0.00 4.40
3973 4355 5.048434 GGCAGTTTCATTTTAGAGAAGCACT 60.048 40.000 0.00 0.00 0.00 4.40
3974 4356 6.442112 GCAGTTTCATTTTAGAGAAGCACTT 58.558 36.000 0.00 0.00 0.00 3.16
3975 4357 6.580416 GCAGTTTCATTTTAGAGAAGCACTTC 59.420 38.462 2.04 2.04 39.78 3.01
3986 4368 3.978718 GAAGCACTTCTGCAAAGTCTT 57.021 42.857 10.19 13.96 46.97 3.01
3987 4369 4.298744 GAAGCACTTCTGCAAAGTCTTT 57.701 40.909 10.19 0.00 46.97 2.52
3988 4370 5.424121 GAAGCACTTCTGCAAAGTCTTTA 57.576 39.130 10.19 0.00 46.97 1.85
3989 4371 5.429957 AAGCACTTCTGCAAAGTCTTTAG 57.570 39.130 10.19 0.00 46.97 1.85
3990 4372 4.708177 AGCACTTCTGCAAAGTCTTTAGA 58.292 39.130 10.19 0.00 46.97 2.10
3991 4373 5.312079 AGCACTTCTGCAAAGTCTTTAGAT 58.688 37.500 10.19 0.00 46.97 1.98
3992 4374 5.180868 AGCACTTCTGCAAAGTCTTTAGATG 59.819 40.000 10.19 3.95 46.97 2.90
3993 4375 5.180117 GCACTTCTGCAAAGTCTTTAGATGA 59.820 40.000 13.83 3.18 43.62 2.92
3994 4376 6.620303 GCACTTCTGCAAAGTCTTTAGATGAG 60.620 42.308 13.83 9.36 43.62 2.90
3995 4377 6.426328 CACTTCTGCAAAGTCTTTAGATGAGT 59.574 38.462 13.83 7.07 0.00 3.41
3996 4378 6.648725 ACTTCTGCAAAGTCTTTAGATGAGTC 59.351 38.462 13.83 0.00 0.00 3.36
3997 4379 6.352016 TCTGCAAAGTCTTTAGATGAGTCT 57.648 37.500 0.00 0.00 38.52 3.24
3998 4380 6.162079 TCTGCAAAGTCTTTAGATGAGTCTG 58.838 40.000 0.00 0.00 35.87 3.51
3999 4381 4.692625 TGCAAAGTCTTTAGATGAGTCTGC 59.307 41.667 0.00 0.00 35.87 4.26
4000 4382 4.094146 GCAAAGTCTTTAGATGAGTCTGCC 59.906 45.833 0.00 0.00 35.87 4.85
4001 4383 5.486526 CAAAGTCTTTAGATGAGTCTGCCT 58.513 41.667 0.00 0.00 35.87 4.75
4002 4384 5.753721 AAGTCTTTAGATGAGTCTGCCTT 57.246 39.130 0.00 0.00 35.87 4.35
4003 4385 5.337578 AGTCTTTAGATGAGTCTGCCTTC 57.662 43.478 0.00 0.00 35.87 3.46
4004 4386 5.022787 AGTCTTTAGATGAGTCTGCCTTCT 58.977 41.667 0.00 0.00 35.87 2.85
4005 4387 5.483583 AGTCTTTAGATGAGTCTGCCTTCTT 59.516 40.000 0.00 0.00 35.87 2.52
4006 4388 6.013812 AGTCTTTAGATGAGTCTGCCTTCTTT 60.014 38.462 0.00 0.00 35.87 2.52
4007 4389 7.179338 AGTCTTTAGATGAGTCTGCCTTCTTTA 59.821 37.037 0.00 0.00 35.87 1.85
4008 4390 7.491048 GTCTTTAGATGAGTCTGCCTTCTTTAG 59.509 40.741 0.00 0.00 35.87 1.85
4009 4391 4.135747 AGATGAGTCTGCCTTCTTTAGC 57.864 45.455 0.00 0.00 32.13 3.09
4010 4392 3.774216 AGATGAGTCTGCCTTCTTTAGCT 59.226 43.478 0.00 0.00 32.13 3.32
4011 4393 4.224818 AGATGAGTCTGCCTTCTTTAGCTT 59.775 41.667 0.00 0.00 32.13 3.74
4012 4394 3.931578 TGAGTCTGCCTTCTTTAGCTTC 58.068 45.455 0.00 0.00 0.00 3.86
4013 4395 3.580458 TGAGTCTGCCTTCTTTAGCTTCT 59.420 43.478 0.00 0.00 0.00 2.85
4014 4396 4.040952 TGAGTCTGCCTTCTTTAGCTTCTT 59.959 41.667 0.00 0.00 0.00 2.52
4015 4397 4.574892 AGTCTGCCTTCTTTAGCTTCTTC 58.425 43.478 0.00 0.00 0.00 2.87
4016 4398 4.285775 AGTCTGCCTTCTTTAGCTTCTTCT 59.714 41.667 0.00 0.00 0.00 2.85
4017 4399 4.629634 GTCTGCCTTCTTTAGCTTCTTCTC 59.370 45.833 0.00 0.00 0.00 2.87
4018 4400 3.938334 CTGCCTTCTTTAGCTTCTTCTCC 59.062 47.826 0.00 0.00 0.00 3.71
4019 4401 3.327757 TGCCTTCTTTAGCTTCTTCTCCA 59.672 43.478 0.00 0.00 0.00 3.86
4020 4402 4.202461 TGCCTTCTTTAGCTTCTTCTCCAA 60.202 41.667 0.00 0.00 0.00 3.53
4021 4403 4.155099 GCCTTCTTTAGCTTCTTCTCCAAC 59.845 45.833 0.00 0.00 0.00 3.77
4022 4404 5.555966 CCTTCTTTAGCTTCTTCTCCAACT 58.444 41.667 0.00 0.00 0.00 3.16
4023 4405 5.411053 CCTTCTTTAGCTTCTTCTCCAACTG 59.589 44.000 0.00 0.00 0.00 3.16
4024 4406 5.808366 TCTTTAGCTTCTTCTCCAACTGA 57.192 39.130 0.00 0.00 0.00 3.41
4025 4407 6.365970 TCTTTAGCTTCTTCTCCAACTGAT 57.634 37.500 0.00 0.00 0.00 2.90
4026 4408 6.402222 TCTTTAGCTTCTTCTCCAACTGATC 58.598 40.000 0.00 0.00 0.00 2.92
4027 4409 5.745312 TTAGCTTCTTCTCCAACTGATCA 57.255 39.130 0.00 0.00 0.00 2.92
4028 4410 4.205065 AGCTTCTTCTCCAACTGATCAG 57.795 45.455 21.37 21.37 0.00 2.90
4029 4411 3.582208 AGCTTCTTCTCCAACTGATCAGT 59.418 43.478 22.89 22.89 44.94 3.41
4030 4412 3.932089 GCTTCTTCTCCAACTGATCAGTC 59.068 47.826 28.01 7.83 41.58 3.51
4031 4413 4.502962 CTTCTTCTCCAACTGATCAGTCC 58.497 47.826 28.01 0.00 41.58 3.85
4032 4414 3.784178 TCTTCTCCAACTGATCAGTCCT 58.216 45.455 28.01 11.57 41.58 3.85
4033 4415 4.935578 TCTTCTCCAACTGATCAGTCCTA 58.064 43.478 28.01 14.82 41.58 2.94
4034 4416 4.952957 TCTTCTCCAACTGATCAGTCCTAG 59.047 45.833 28.01 22.27 41.58 3.02
4035 4417 3.027412 TCTCCAACTGATCAGTCCTAGC 58.973 50.000 28.01 0.00 41.58 3.42
4036 4418 2.762887 CTCCAACTGATCAGTCCTAGCA 59.237 50.000 28.01 8.86 41.58 3.49
4037 4419 3.173151 TCCAACTGATCAGTCCTAGCAA 58.827 45.455 28.01 7.71 41.58 3.91
4038 4420 3.055819 TCCAACTGATCAGTCCTAGCAAC 60.056 47.826 28.01 0.00 41.58 4.17
4039 4421 3.055530 CCAACTGATCAGTCCTAGCAACT 60.056 47.826 28.01 6.95 41.58 3.16
4040 4422 4.564406 CCAACTGATCAGTCCTAGCAACTT 60.564 45.833 28.01 6.19 41.58 2.66
4051 4433 2.427453 CCTAGCAACTTCTTCTCCGCTA 59.573 50.000 0.00 0.00 0.00 4.26
4083 4465 1.803555 GAGCCTTCAGTGTTGCTCTTC 59.196 52.381 17.89 0.96 45.21 2.87
4084 4466 0.877743 GCCTTCAGTGTTGCTCTTCC 59.122 55.000 0.00 0.00 0.00 3.46
4088 4470 2.839486 TCAGTGTTGCTCTTCCGATT 57.161 45.000 0.00 0.00 0.00 3.34
4093 4475 3.882888 AGTGTTGCTCTTCCGATTCAAAA 59.117 39.130 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.107643 TTCACCCTCGCAATGTCACA 59.892 50.000 0.00 0.00 0.00 3.58
1 2 1.234821 TTTCACCCTCGCAATGTCAC 58.765 50.000 0.00 0.00 0.00 3.67
2 3 1.974265 TTTTCACCCTCGCAATGTCA 58.026 45.000 0.00 0.00 0.00 3.58
3 4 2.415893 CCATTTTCACCCTCGCAATGTC 60.416 50.000 0.00 0.00 0.00 3.06
4 5 1.545582 CCATTTTCACCCTCGCAATGT 59.454 47.619 0.00 0.00 0.00 2.71
5 6 1.135024 CCCATTTTCACCCTCGCAATG 60.135 52.381 0.00 0.00 0.00 2.82
6 7 1.185315 CCCATTTTCACCCTCGCAAT 58.815 50.000 0.00 0.00 0.00 3.56
7 8 0.111446 TCCCATTTTCACCCTCGCAA 59.889 50.000 0.00 0.00 0.00 4.85
8 9 0.322456 CTCCCATTTTCACCCTCGCA 60.322 55.000 0.00 0.00 0.00 5.10
47 48 1.007336 CCGTCGGGTTCTTTCTGTCG 61.007 60.000 2.34 0.00 0.00 4.35
49 50 0.754472 TTCCGTCGGGTTCTTTCTGT 59.246 50.000 12.29 0.00 33.83 3.41
74 76 0.249398 GCTAGAACGGTCACCCACAT 59.751 55.000 1.87 0.00 0.00 3.21
75 77 1.669440 GCTAGAACGGTCACCCACA 59.331 57.895 1.87 0.00 0.00 4.17
77 79 2.288025 GGGCTAGAACGGTCACCCA 61.288 63.158 18.44 0.00 35.02 4.51
109 111 3.614159 TCCGGACAATAATAGTCGTCG 57.386 47.619 0.00 0.00 36.87 5.12
110 112 5.117355 TCATCCGGACAATAATAGTCGTC 57.883 43.478 6.12 0.00 36.87 4.20
112 114 7.222805 CCATTATCATCCGGACAATAATAGTCG 59.777 40.741 23.13 15.13 36.87 4.18
123 125 4.008074 ACATGTCCATTATCATCCGGAC 57.992 45.455 6.12 0.00 46.69 4.79
126 128 3.058016 GCCAACATGTCCATTATCATCCG 60.058 47.826 0.00 0.00 0.00 4.18
127 129 3.890756 TGCCAACATGTCCATTATCATCC 59.109 43.478 0.00 0.00 0.00 3.51
144 146 3.450457 CCTAATAAACTTGCCCATGCCAA 59.550 43.478 0.00 0.00 36.33 4.52
145 147 3.030291 CCTAATAAACTTGCCCATGCCA 58.970 45.455 0.00 0.00 36.33 4.92
147 149 2.365293 CCCCTAATAAACTTGCCCATGC 59.635 50.000 0.00 0.00 38.26 4.06
185 187 0.175531 CCAATCCCCCGTTGCATTTC 59.824 55.000 0.00 0.00 0.00 2.17
194 196 2.195683 CACATCCCCAATCCCCCG 59.804 66.667 0.00 0.00 0.00 5.73
200 202 2.014550 CCCTCCCCACATCCCCAAT 61.015 63.158 0.00 0.00 0.00 3.16
201 203 2.522453 ATCCCTCCCCACATCCCCAA 62.522 60.000 0.00 0.00 0.00 4.12
202 204 2.522453 AATCCCTCCCCACATCCCCA 62.522 60.000 0.00 0.00 0.00 4.96
203 205 1.701390 AATCCCTCCCCACATCCCC 60.701 63.158 0.00 0.00 0.00 4.81
204 206 0.993509 TGAATCCCTCCCCACATCCC 60.994 60.000 0.00 0.00 0.00 3.85
205 207 1.152649 ATGAATCCCTCCCCACATCC 58.847 55.000 0.00 0.00 0.00 3.51
206 208 2.307098 CCTATGAATCCCTCCCCACATC 59.693 54.545 0.00 0.00 0.00 3.06
207 209 2.352371 CCTATGAATCCCTCCCCACAT 58.648 52.381 0.00 0.00 0.00 3.21
208 210 1.010793 ACCTATGAATCCCTCCCCACA 59.989 52.381 0.00 0.00 0.00 4.17
209 211 1.821088 ACCTATGAATCCCTCCCCAC 58.179 55.000 0.00 0.00 0.00 4.61
288 290 2.920647 GCACCAATGCCAAGTTTACGAC 60.921 50.000 0.00 0.00 46.97 4.34
320 323 2.154462 ACATGGCGGAAAGTCTGAAAG 58.846 47.619 0.00 0.00 0.00 2.62
325 328 0.034896 ACGAACATGGCGGAAAGTCT 59.965 50.000 13.57 0.00 0.00 3.24
327 330 0.872388 GAACGAACATGGCGGAAAGT 59.128 50.000 13.57 0.00 0.00 2.66
358 362 8.985866 ATGTGCATCATAGTTGACGAGAACGT 62.986 42.308 0.00 0.00 44.40 3.99
360 364 3.926527 TGTGCATCATAGTTGACGAGAAC 59.073 43.478 0.00 0.00 33.85 3.01
363 367 3.867493 ACATGTGCATCATAGTTGACGAG 59.133 43.478 0.00 0.00 33.85 4.18
364 368 3.618150 CACATGTGCATCATAGTTGACGA 59.382 43.478 13.94 0.00 33.85 4.20
365 369 3.242511 CCACATGTGCATCATAGTTGACG 60.243 47.826 20.81 0.00 33.85 4.35
367 371 3.690628 CACCACATGTGCATCATAGTTGA 59.309 43.478 20.81 0.00 38.34 3.18
374 378 2.153645 GAACTCACCACATGTGCATCA 58.846 47.619 20.81 2.80 45.03 3.07
380 384 2.613026 TTGTCGAACTCACCACATGT 57.387 45.000 0.00 0.00 0.00 3.21
381 385 3.329386 AGATTGTCGAACTCACCACATG 58.671 45.455 0.00 0.00 0.00 3.21
382 386 3.006859 TGAGATTGTCGAACTCACCACAT 59.993 43.478 8.19 0.00 36.04 3.21
387 391 4.926238 ACATCTTGAGATTGTCGAACTCAC 59.074 41.667 10.76 0.00 39.80 3.51
391 395 5.050091 ACACAACATCTTGAGATTGTCGAAC 60.050 40.000 0.00 0.00 31.21 3.95
395 399 5.468072 ACTGACACAACATCTTGAGATTGTC 59.532 40.000 13.06 13.06 38.28 3.18
396 400 5.371526 ACTGACACAACATCTTGAGATTGT 58.628 37.500 0.00 0.00 31.21 2.71
403 407 4.813161 AGACTGAACTGACACAACATCTTG 59.187 41.667 0.00 0.00 0.00 3.02
404 408 5.028549 AGACTGAACTGACACAACATCTT 57.971 39.130 0.00 0.00 0.00 2.40
416 420 6.450545 TGAGTACATTCAAGAGACTGAACTG 58.549 40.000 0.00 0.00 38.12 3.16
417 421 6.656632 TGAGTACATTCAAGAGACTGAACT 57.343 37.500 0.00 0.00 38.12 3.01
429 433 5.473273 ACCATACCCCTATGAGTACATTCA 58.527 41.667 0.00 0.00 37.87 2.57
433 437 4.827036 AGACCATACCCCTATGAGTACA 57.173 45.455 0.00 0.00 32.66 2.90
436 440 4.631234 TCAAAGACCATACCCCTATGAGT 58.369 43.478 0.00 0.00 32.66 3.41
476 518 9.378551 TGACGTCAAATTTATAGCAGAATACTT 57.621 29.630 17.62 0.00 0.00 2.24
478 520 9.031360 TCTGACGTCAAATTTATAGCAGAATAC 57.969 33.333 20.49 0.00 0.00 1.89
479 521 9.764363 ATCTGACGTCAAATTTATAGCAGAATA 57.236 29.630 20.49 0.00 34.09 1.75
501 543 6.688637 TGATCTGCCATGTCTAAAAATCTG 57.311 37.500 0.00 0.00 0.00 2.90
528 570 5.124457 CGGCAATATAATTTCCATCTCAGGG 59.876 44.000 0.00 0.00 0.00 4.45
539 581 5.301551 TGGCATTCTCACGGCAATATAATTT 59.698 36.000 0.00 0.00 34.36 1.82
552 595 6.158598 TGCTAAAGAAAATTGGCATTCTCAC 58.841 36.000 2.53 0.00 41.14 3.51
553 596 6.343716 TGCTAAAGAAAATTGGCATTCTCA 57.656 33.333 2.53 0.00 41.14 3.27
557 600 5.179929 GTGCTTGCTAAAGAAAATTGGCATT 59.820 36.000 0.00 0.00 44.64 3.56
561 604 5.390145 GCATGTGCTTGCTAAAGAAAATTGG 60.390 40.000 0.00 0.00 39.57 3.16
562 605 5.177881 TGCATGTGCTTGCTAAAGAAAATTG 59.822 36.000 6.55 0.00 43.18 2.32
565 608 4.319139 TGCATGTGCTTGCTAAAGAAAA 57.681 36.364 6.55 0.00 43.18 2.29
569 612 3.615496 GGATTTGCATGTGCTTGCTAAAG 59.385 43.478 6.55 0.00 43.18 1.85
570 613 3.258872 AGGATTTGCATGTGCTTGCTAAA 59.741 39.130 6.55 9.49 43.18 1.85
612 656 2.741228 GCAATTATGGCAATTTCCGGCA 60.741 45.455 0.00 0.00 43.74 5.69
628 672 6.430007 AGGATGACTATTCTCTTTGGCAATT 58.570 36.000 0.00 0.00 0.00 2.32
634 678 5.746245 GTCACGAGGATGACTATTCTCTTTG 59.254 44.000 0.00 0.00 44.71 2.77
682 728 5.698832 TGATTTTTAGACACAGCAAATCGG 58.301 37.500 0.00 0.00 36.87 4.18
752 802 9.061610 CGTGGTTAATTTTGCTTAATTACTCTG 57.938 33.333 4.10 0.00 31.54 3.35
753 803 7.753580 GCGTGGTTAATTTTGCTTAATTACTCT 59.246 33.333 4.10 0.00 31.54 3.24
754 804 7.539366 TGCGTGGTTAATTTTGCTTAATTACTC 59.461 33.333 4.10 2.38 31.54 2.59
755 805 7.371936 TGCGTGGTTAATTTTGCTTAATTACT 58.628 30.769 4.10 0.00 31.54 2.24
756 806 7.569677 TGCGTGGTTAATTTTGCTTAATTAC 57.430 32.000 4.10 0.00 31.54 1.89
757 807 9.856488 TTATGCGTGGTTAATTTTGCTTAATTA 57.144 25.926 0.00 0.00 0.00 1.40
758 808 8.764524 TTATGCGTGGTTAATTTTGCTTAATT 57.235 26.923 0.00 2.89 0.00 1.40
759 809 8.816144 CATTATGCGTGGTTAATTTTGCTTAAT 58.184 29.630 0.00 0.00 34.81 1.40
760 810 7.276658 CCATTATGCGTGGTTAATTTTGCTTAA 59.723 33.333 0.00 0.00 31.96 1.85
761 811 6.754209 CCATTATGCGTGGTTAATTTTGCTTA 59.246 34.615 0.00 0.00 31.96 3.09
762 812 5.580297 CCATTATGCGTGGTTAATTTTGCTT 59.420 36.000 0.00 0.00 31.96 3.91
763 813 5.108517 CCATTATGCGTGGTTAATTTTGCT 58.891 37.500 0.00 0.00 31.96 3.91
764 814 4.260172 GCCATTATGCGTGGTTAATTTTGC 60.260 41.667 0.00 0.00 39.01 3.68
765 815 5.108517 AGCCATTATGCGTGGTTAATTTTG 58.891 37.500 0.00 0.00 39.01 2.44
769 819 2.884639 GGAGCCATTATGCGTGGTTAAT 59.115 45.455 0.00 0.00 39.01 1.40
771 821 1.476110 GGGAGCCATTATGCGTGGTTA 60.476 52.381 0.00 0.00 39.01 2.85
789 839 1.737793 GCTTCAAACCGACATAGTGGG 59.262 52.381 0.00 0.00 37.44 4.61
791 841 2.159841 CGTGCTTCAAACCGACATAGTG 60.160 50.000 0.00 0.00 0.00 2.74
804 857 3.706373 GCCCTCCCTCGTGCTTCA 61.706 66.667 0.00 0.00 0.00 3.02
883 939 4.098807 GGCGTTGGTTGGTTATATGGATTT 59.901 41.667 0.00 0.00 0.00 2.17
960 1022 2.840203 TTTGGGGGATCGAGGGAGCT 62.840 60.000 0.00 0.00 0.00 4.09
2550 2835 2.187992 CTCCTCGCTGAGCTCTGAA 58.812 57.895 23.35 9.84 0.00 3.02
2608 2893 2.173356 TGCCCTTAATCAGGTGGATCTG 59.827 50.000 0.00 0.00 42.02 2.90
2809 3096 2.729862 GCGAGCATAGTACCCGCG 60.730 66.667 0.00 0.00 36.53 6.46
2835 3149 1.035932 CCTCGTAGTCCGTGTCCCAT 61.036 60.000 0.00 0.00 37.94 4.00
2931 3245 1.208358 CGTCACTGGCGTCGACTTA 59.792 57.895 14.70 0.00 0.00 2.24
3145 3471 5.500234 AGAATCAACACTAGCTGCCAATTA 58.500 37.500 0.00 0.00 0.00 1.40
3376 3705 6.227522 AGAGAGAGAGAAAAAGGTTACAAGC 58.772 40.000 0.00 0.00 0.00 4.01
3401 3731 3.371917 CCAGTCCAATCACCATACCACAT 60.372 47.826 0.00 0.00 0.00 3.21
3463 3793 9.104965 TCAACAATACAACTACCTACAATATGC 57.895 33.333 0.00 0.00 0.00 3.14
3468 3800 7.681679 TGGATCAACAATACAACTACCTACAA 58.318 34.615 0.00 0.00 0.00 2.41
3537 3869 3.382865 TGAACTGGCAAATTAACAGCACA 59.617 39.130 0.00 3.20 35.70 4.57
3538 3870 3.976169 TGAACTGGCAAATTAACAGCAC 58.024 40.909 0.00 1.23 35.70 4.40
3539 3871 4.870123 ATGAACTGGCAAATTAACAGCA 57.130 36.364 0.00 0.00 35.70 4.41
3540 3872 5.466393 ACAAATGAACTGGCAAATTAACAGC 59.534 36.000 0.00 0.00 35.70 4.40
3541 3873 8.761575 ATACAAATGAACTGGCAAATTAACAG 57.238 30.769 0.00 0.00 38.19 3.16
3569 3901 7.362662 CAACAATTGTGTTTCAGCAGTATACT 58.637 34.615 12.82 0.00 46.01 2.12
3584 3920 1.661197 AAGCGCCGCAACAATTGTG 60.661 52.632 13.36 7.69 40.74 3.33
3595 3931 3.853330 CGACCATGACAAGCGCCG 61.853 66.667 2.29 0.00 0.00 6.46
3598 3934 0.163788 GAACACGACCATGACAAGCG 59.836 55.000 0.00 0.00 0.00 4.68
3600 3936 1.192312 CACGAACACGACCATGACAAG 59.808 52.381 0.00 0.00 0.00 3.16
3612 3948 1.883926 ACCAATAAAGGGCACGAACAC 59.116 47.619 0.00 0.00 0.00 3.32
3618 3954 2.678336 CGAGAGAACCAATAAAGGGCAC 59.322 50.000 0.00 0.00 0.00 5.01
3629 3965 3.349022 ACAAACAAAACCGAGAGAACCA 58.651 40.909 0.00 0.00 0.00 3.67
3630 3966 3.545426 CGACAAACAAAACCGAGAGAACC 60.545 47.826 0.00 0.00 0.00 3.62
3634 3970 2.286184 CCACGACAAACAAAACCGAGAG 60.286 50.000 0.00 0.00 0.00 3.20
3644 3980 4.442375 AATCAAAACACCACGACAAACA 57.558 36.364 0.00 0.00 0.00 2.83
3690 4072 9.768662 AAAGCAACATGTTCAGATATTCTTTTT 57.231 25.926 8.48 0.00 0.00 1.94
3693 4075 9.236006 ACTAAAGCAACATGTTCAGATATTCTT 57.764 29.630 8.48 0.07 0.00 2.52
3694 4076 8.798859 ACTAAAGCAACATGTTCAGATATTCT 57.201 30.769 8.48 0.00 0.00 2.40
3695 4077 9.282247 CAACTAAAGCAACATGTTCAGATATTC 57.718 33.333 8.48 0.00 0.00 1.75
3696 4078 8.246180 CCAACTAAAGCAACATGTTCAGATATT 58.754 33.333 8.48 1.49 0.00 1.28
3697 4079 7.394359 ACCAACTAAAGCAACATGTTCAGATAT 59.606 33.333 8.48 0.00 0.00 1.63
3698 4080 6.714810 ACCAACTAAAGCAACATGTTCAGATA 59.285 34.615 8.48 0.00 0.00 1.98
3699 4081 5.536161 ACCAACTAAAGCAACATGTTCAGAT 59.464 36.000 8.48 0.00 0.00 2.90
3700 4082 4.887071 ACCAACTAAAGCAACATGTTCAGA 59.113 37.500 8.48 0.00 0.00 3.27
3701 4083 5.186996 ACCAACTAAAGCAACATGTTCAG 57.813 39.130 8.48 0.00 0.00 3.02
3758 4140 6.822667 TTCACTTCATACCTACGACAGTAA 57.177 37.500 0.00 0.00 31.59 2.24
3759 4141 7.121611 TGAATTCACTTCATACCTACGACAGTA 59.878 37.037 3.38 0.00 38.97 2.74
3760 4142 5.916661 ATTCACTTCATACCTACGACAGT 57.083 39.130 0.00 0.00 0.00 3.55
3761 4143 6.330278 TGAATTCACTTCATACCTACGACAG 58.670 40.000 3.38 0.00 38.97 3.51
3777 4159 1.815003 CTGGCCCTGAACTGAATTCAC 59.185 52.381 3.38 0.00 42.62 3.18
3802 4184 4.863491 TGCAGAAACAGAGAATTTCAAGC 58.137 39.130 0.00 4.66 38.32 4.01
3878 4260 5.348179 TGTTTCAAACTTGTTGACAGCAATG 59.652 36.000 5.11 1.88 36.22 2.82
3879 4261 5.477510 TGTTTCAAACTTGTTGACAGCAAT 58.522 33.333 5.11 0.00 36.22 3.56
3880 4262 4.876125 TGTTTCAAACTTGTTGACAGCAA 58.124 34.783 4.57 4.57 0.00 3.91
3881 4263 4.511617 TGTTTCAAACTTGTTGACAGCA 57.488 36.364 1.10 0.00 0.00 4.41
3883 4265 7.636259 TTTCTTGTTTCAAACTTGTTGACAG 57.364 32.000 1.10 0.00 0.00 3.51
3884 4266 9.134734 GTATTTCTTGTTTCAAACTTGTTGACA 57.865 29.630 1.10 0.00 0.00 3.58
3887 4269 9.352784 TCAGTATTTCTTGTTTCAAACTTGTTG 57.647 29.630 1.10 0.00 0.00 3.33
3888 4270 9.573133 CTCAGTATTTCTTGTTTCAAACTTGTT 57.427 29.630 1.10 0.00 0.00 2.83
3889 4271 8.956426 TCTCAGTATTTCTTGTTTCAAACTTGT 58.044 29.630 1.10 0.00 0.00 3.16
3890 4272 9.956720 ATCTCAGTATTTCTTGTTTCAAACTTG 57.043 29.630 1.10 0.00 0.00 3.16
3891 4273 9.956720 CATCTCAGTATTTCTTGTTTCAAACTT 57.043 29.630 1.10 0.00 0.00 2.66
3893 4275 9.736023 AACATCTCAGTATTTCTTGTTTCAAAC 57.264 29.630 0.00 0.00 0.00 2.93
3928 4310 9.851686 ACTGCCAAAGTCTCATGATAATAATAA 57.148 29.630 0.00 0.00 31.64 1.40
3929 4311 9.851686 AACTGCCAAAGTCTCATGATAATAATA 57.148 29.630 0.00 0.00 38.56 0.98
3930 4312 8.757982 AACTGCCAAAGTCTCATGATAATAAT 57.242 30.769 0.00 0.00 38.56 1.28
3931 4313 8.579850 AAACTGCCAAAGTCTCATGATAATAA 57.420 30.769 0.00 0.00 38.56 1.40
3932 4314 7.828717 TGAAACTGCCAAAGTCTCATGATAATA 59.171 33.333 0.00 0.00 38.56 0.98
3933 4315 6.660521 TGAAACTGCCAAAGTCTCATGATAAT 59.339 34.615 0.00 0.00 38.56 1.28
3934 4316 6.003326 TGAAACTGCCAAAGTCTCATGATAA 58.997 36.000 0.00 0.00 38.56 1.75
3935 4317 5.559770 TGAAACTGCCAAAGTCTCATGATA 58.440 37.500 0.00 0.00 38.56 2.15
3936 4318 4.401022 TGAAACTGCCAAAGTCTCATGAT 58.599 39.130 0.00 0.00 38.56 2.45
3937 4319 3.819368 TGAAACTGCCAAAGTCTCATGA 58.181 40.909 0.00 0.00 38.56 3.07
3938 4320 4.778534 ATGAAACTGCCAAAGTCTCATG 57.221 40.909 0.00 0.00 43.58 3.07
3939 4321 5.796424 AAATGAAACTGCCAAAGTCTCAT 57.204 34.783 0.00 0.00 46.53 2.90
3940 4322 5.596836 AAAATGAAACTGCCAAAGTCTCA 57.403 34.783 0.00 0.00 40.17 3.27
3941 4323 6.970484 TCTAAAATGAAACTGCCAAAGTCTC 58.030 36.000 0.00 0.00 38.56 3.36
3942 4324 6.772716 TCTCTAAAATGAAACTGCCAAAGTCT 59.227 34.615 0.00 0.00 38.56 3.24
3943 4325 6.970484 TCTCTAAAATGAAACTGCCAAAGTC 58.030 36.000 0.00 0.00 38.56 3.01
3944 4326 6.959639 TCTCTAAAATGAAACTGCCAAAGT 57.040 33.333 0.00 0.00 42.60 2.66
3945 4327 6.364435 GCTTCTCTAAAATGAAACTGCCAAAG 59.636 38.462 0.00 0.00 0.00 2.77
3946 4328 6.183360 TGCTTCTCTAAAATGAAACTGCCAAA 60.183 34.615 0.00 0.00 0.00 3.28
3947 4329 5.301551 TGCTTCTCTAAAATGAAACTGCCAA 59.698 36.000 0.00 0.00 0.00 4.52
3948 4330 4.826733 TGCTTCTCTAAAATGAAACTGCCA 59.173 37.500 0.00 0.00 0.00 4.92
3949 4331 5.048434 AGTGCTTCTCTAAAATGAAACTGCC 60.048 40.000 0.00 0.00 0.00 4.85
3950 4332 6.006759 AGTGCTTCTCTAAAATGAAACTGC 57.993 37.500 0.00 0.00 0.00 4.40
3951 4333 7.802251 CAGAAGTGCTTCTCTAAAATGAAACTG 59.198 37.037 11.15 0.00 46.13 3.16
3952 4334 7.521261 GCAGAAGTGCTTCTCTAAAATGAAACT 60.521 37.037 11.15 0.00 46.13 2.66
3953 4335 6.580416 GCAGAAGTGCTTCTCTAAAATGAAAC 59.420 38.462 11.15 0.00 46.13 2.78
3954 4336 6.672147 GCAGAAGTGCTTCTCTAAAATGAAA 58.328 36.000 11.15 0.00 46.13 2.69
3955 4337 6.246420 GCAGAAGTGCTTCTCTAAAATGAA 57.754 37.500 11.15 0.00 46.13 2.57
3956 4338 5.869753 GCAGAAGTGCTTCTCTAAAATGA 57.130 39.130 11.15 0.00 46.13 2.57
3970 4352 6.426328 ACTCATCTAAAGACTTTGCAGAAGTG 59.574 38.462 15.84 6.98 0.00 3.16
3971 4353 6.529220 ACTCATCTAAAGACTTTGCAGAAGT 58.471 36.000 10.80 12.23 0.00 3.01
3972 4354 6.873076 AGACTCATCTAAAGACTTTGCAGAAG 59.127 38.462 10.80 4.01 31.46 2.85
3973 4355 6.648310 CAGACTCATCTAAAGACTTTGCAGAA 59.352 38.462 10.80 0.00 32.25 3.02
3974 4356 6.162079 CAGACTCATCTAAAGACTTTGCAGA 58.838 40.000 10.80 6.77 32.25 4.26
3975 4357 5.163874 GCAGACTCATCTAAAGACTTTGCAG 60.164 44.000 10.80 1.19 32.25 4.41
3976 4358 4.692625 GCAGACTCATCTAAAGACTTTGCA 59.307 41.667 10.80 0.00 32.25 4.08
3977 4359 4.094146 GGCAGACTCATCTAAAGACTTTGC 59.906 45.833 10.80 1.96 32.25 3.68
3978 4360 5.486526 AGGCAGACTCATCTAAAGACTTTG 58.513 41.667 10.80 1.41 32.25 2.77
3979 4361 5.753721 AGGCAGACTCATCTAAAGACTTT 57.246 39.130 5.62 5.62 32.25 2.66
3980 4362 5.483583 AGAAGGCAGACTCATCTAAAGACTT 59.516 40.000 0.00 0.00 32.25 3.01
3981 4363 5.022787 AGAAGGCAGACTCATCTAAAGACT 58.977 41.667 0.00 0.00 32.25 3.24
3982 4364 5.337578 AGAAGGCAGACTCATCTAAAGAC 57.662 43.478 0.00 0.00 32.25 3.01
3983 4365 6.365970 AAAGAAGGCAGACTCATCTAAAGA 57.634 37.500 0.00 0.00 32.25 2.52
3984 4366 6.257630 GCTAAAGAAGGCAGACTCATCTAAAG 59.742 42.308 0.00 0.00 32.25 1.85
3985 4367 6.070538 AGCTAAAGAAGGCAGACTCATCTAAA 60.071 38.462 0.00 0.00 32.25 1.85
3986 4368 5.423610 AGCTAAAGAAGGCAGACTCATCTAA 59.576 40.000 0.00 0.00 32.25 2.10
3987 4369 4.959210 AGCTAAAGAAGGCAGACTCATCTA 59.041 41.667 0.00 0.00 32.25 1.98
3988 4370 3.774216 AGCTAAAGAAGGCAGACTCATCT 59.226 43.478 0.00 0.00 34.57 2.90
3989 4371 4.135747 AGCTAAAGAAGGCAGACTCATC 57.864 45.455 0.00 0.00 0.00 2.92
3990 4372 4.224818 AGAAGCTAAAGAAGGCAGACTCAT 59.775 41.667 0.00 0.00 0.00 2.90
3991 4373 3.580458 AGAAGCTAAAGAAGGCAGACTCA 59.420 43.478 0.00 0.00 0.00 3.41
3992 4374 4.200838 AGAAGCTAAAGAAGGCAGACTC 57.799 45.455 0.00 0.00 0.00 3.36
3993 4375 4.285775 AGAAGAAGCTAAAGAAGGCAGACT 59.714 41.667 0.00 0.00 0.00 3.24
3994 4376 4.574892 AGAAGAAGCTAAAGAAGGCAGAC 58.425 43.478 0.00 0.00 0.00 3.51
3995 4377 4.323104 GGAGAAGAAGCTAAAGAAGGCAGA 60.323 45.833 0.00 0.00 0.00 4.26
3996 4378 3.938334 GGAGAAGAAGCTAAAGAAGGCAG 59.062 47.826 0.00 0.00 0.00 4.85
3997 4379 3.327757 TGGAGAAGAAGCTAAAGAAGGCA 59.672 43.478 0.00 0.00 0.00 4.75
3998 4380 3.944087 TGGAGAAGAAGCTAAAGAAGGC 58.056 45.455 0.00 0.00 0.00 4.35
3999 4381 5.411053 CAGTTGGAGAAGAAGCTAAAGAAGG 59.589 44.000 0.00 0.00 0.00 3.46
4000 4382 6.226787 TCAGTTGGAGAAGAAGCTAAAGAAG 58.773 40.000 0.00 0.00 0.00 2.85
4001 4383 6.174720 TCAGTTGGAGAAGAAGCTAAAGAA 57.825 37.500 0.00 0.00 0.00 2.52
4002 4384 5.808366 TCAGTTGGAGAAGAAGCTAAAGA 57.192 39.130 0.00 0.00 0.00 2.52
4003 4385 6.169094 TGATCAGTTGGAGAAGAAGCTAAAG 58.831 40.000 0.00 0.00 0.00 1.85
4004 4386 6.114187 TGATCAGTTGGAGAAGAAGCTAAA 57.886 37.500 0.00 0.00 0.00 1.85
4005 4387 5.247110 ACTGATCAGTTGGAGAAGAAGCTAA 59.753 40.000 22.89 0.00 38.83 3.09
4006 4388 4.774726 ACTGATCAGTTGGAGAAGAAGCTA 59.225 41.667 22.89 0.00 38.83 3.32
4007 4389 3.582208 ACTGATCAGTTGGAGAAGAAGCT 59.418 43.478 22.89 0.00 38.83 3.74
4008 4390 3.932089 GACTGATCAGTTGGAGAAGAAGC 59.068 47.826 28.46 8.28 42.66 3.86
4009 4391 4.222588 AGGACTGATCAGTTGGAGAAGAAG 59.777 45.833 28.46 0.00 42.66 2.85
4010 4392 4.163427 AGGACTGATCAGTTGGAGAAGAA 58.837 43.478 28.46 0.00 42.66 2.52
4011 4393 3.784178 AGGACTGATCAGTTGGAGAAGA 58.216 45.455 28.46 0.00 42.66 2.87
4012 4394 4.441356 GCTAGGACTGATCAGTTGGAGAAG 60.441 50.000 28.46 19.13 42.66 2.85
4013 4395 3.449018 GCTAGGACTGATCAGTTGGAGAA 59.551 47.826 28.46 10.97 42.66 2.87
4014 4396 3.027412 GCTAGGACTGATCAGTTGGAGA 58.973 50.000 28.46 12.09 42.66 3.71
4015 4397 2.762887 TGCTAGGACTGATCAGTTGGAG 59.237 50.000 28.46 23.24 42.66 3.86
4016 4398 2.820178 TGCTAGGACTGATCAGTTGGA 58.180 47.619 28.46 16.87 42.66 3.53
4017 4399 3.055530 AGTTGCTAGGACTGATCAGTTGG 60.056 47.826 28.46 16.79 42.66 3.77
4018 4400 4.199432 AGTTGCTAGGACTGATCAGTTG 57.801 45.455 28.46 18.74 42.66 3.16
4019 4401 4.530161 AGAAGTTGCTAGGACTGATCAGTT 59.470 41.667 28.46 16.66 42.66 3.16
4020 4402 4.093011 AGAAGTTGCTAGGACTGATCAGT 58.907 43.478 28.23 28.23 45.84 3.41
4021 4403 4.734398 AGAAGTTGCTAGGACTGATCAG 57.266 45.455 21.37 21.37 0.00 2.90
4022 4404 4.774726 AGAAGAAGTTGCTAGGACTGATCA 59.225 41.667 0.00 0.00 0.00 2.92
4023 4405 5.337578 AGAAGAAGTTGCTAGGACTGATC 57.662 43.478 0.00 0.00 0.00 2.92
4024 4406 4.161377 GGAGAAGAAGTTGCTAGGACTGAT 59.839 45.833 0.00 0.00 0.00 2.90
4025 4407 3.511934 GGAGAAGAAGTTGCTAGGACTGA 59.488 47.826 0.00 0.00 0.00 3.41
4026 4408 3.674682 CGGAGAAGAAGTTGCTAGGACTG 60.675 52.174 0.00 0.00 0.00 3.51
4027 4409 2.494073 CGGAGAAGAAGTTGCTAGGACT 59.506 50.000 0.00 0.00 0.00 3.85
4028 4410 2.882324 CGGAGAAGAAGTTGCTAGGAC 58.118 52.381 0.00 0.00 0.00 3.85
4029 4411 1.204941 GCGGAGAAGAAGTTGCTAGGA 59.795 52.381 0.00 0.00 0.00 2.94
4030 4412 1.205893 AGCGGAGAAGAAGTTGCTAGG 59.794 52.381 0.00 0.00 0.00 3.02
4031 4413 2.663826 AGCGGAGAAGAAGTTGCTAG 57.336 50.000 0.00 0.00 0.00 3.42
4032 4414 3.368116 GGTTAGCGGAGAAGAAGTTGCTA 60.368 47.826 0.00 0.00 34.08 3.49
4033 4415 2.613223 GGTTAGCGGAGAAGAAGTTGCT 60.613 50.000 0.00 0.00 36.51 3.91
4034 4416 1.732809 GGTTAGCGGAGAAGAAGTTGC 59.267 52.381 0.00 0.00 0.00 4.17
4035 4417 1.993370 CGGTTAGCGGAGAAGAAGTTG 59.007 52.381 0.00 0.00 0.00 3.16
4036 4418 1.672145 GCGGTTAGCGGAGAAGAAGTT 60.672 52.381 5.84 0.00 35.41 2.66
4037 4419 0.108756 GCGGTTAGCGGAGAAGAAGT 60.109 55.000 5.84 0.00 35.41 3.01
4038 4420 2.666989 GCGGTTAGCGGAGAAGAAG 58.333 57.895 5.84 0.00 35.41 2.85
4039 4421 4.904466 GCGGTTAGCGGAGAAGAA 57.096 55.556 5.84 0.00 35.41 2.52


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

AutoCloner maintained by Alex Coulton.