Multiple sequence alignment - TraesCS3D01G495300

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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 TraesCS3D01G495300 chr3D 100.000 3723 0 0 1 3723 587587580 587583858 0.000000e+00 6876.0
1 TraesCS3D01G495300 chr3D 83.213 828 88 29 931 1731 587596586 587595783 0.000000e+00 712.0
2 TraesCS3D01G495300 chr3D 80.130 770 100 27 1008 1731 587648487 587647725 3.290000e-145 525.0
3 TraesCS3D01G495300 chr3D 81.789 615 71 25 1171 1764 587745875 587746469 9.350000e-131 477.0
4 TraesCS3D01G495300 chr3D 91.111 45 3 1 1795 1838 587595770 587595726 4.020000e-05 60.2
5 TraesCS3D01G495300 chr3A 90.122 1802 117 22 1 1759 716949280 716947497 0.000000e+00 2285.0
6 TraesCS3D01G495300 chr3A 87.900 719 59 10 2093 2801 716946992 716946292 0.000000e+00 821.0
7 TraesCS3D01G495300 chr3A 82.888 824 92 28 933 1731 716967019 716966220 0.000000e+00 695.0
8 TraesCS3D01G495300 chr3A 89.228 492 47 3 1 488 716949928 716949439 8.840000e-171 610.0
9 TraesCS3D01G495300 chr3A 90.043 462 36 6 2803 3259 716946227 716945771 1.150000e-164 590.0
10 TraesCS3D01G495300 chr3A 88.073 327 22 10 1868 2186 716947306 716946989 4.540000e-99 372.0
11 TraesCS3D01G495300 chr3A 87.083 240 26 2 3291 3526 716945522 716945284 2.200000e-67 267.0
12 TraesCS3D01G495300 chr3A 91.111 45 3 1 1795 1838 716966207 716966163 4.020000e-05 60.2
13 TraesCS3D01G495300 chr3B 94.109 1290 50 7 496 1759 784871115 784869826 0.000000e+00 1938.0
14 TraesCS3D01G495300 chr3B 89.091 495 47 5 5 494 784871643 784871151 3.180000e-170 608.0
15 TraesCS3D01G495300 chr3B 80.970 825 89 35 931 1730 784900948 784900167 3.200000e-165 592.0
16 TraesCS3D01G495300 chr3B 84.538 498 32 18 1868 2341 784869677 784869201 5.670000e-123 451.0
17 TraesCS3D01G495300 chr3B 91.111 45 3 1 1795 1838 784900153 784900109 4.020000e-05 60.2


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 TraesCS3D01G495300 chr3D 587583858 587587580 3722 True 6876.000000 6876 100.0000 1 3723 1 chr3D.!!$R1 3722
1 TraesCS3D01G495300 chr3D 587647725 587648487 762 True 525.000000 525 80.1300 1008 1731 1 chr3D.!!$R2 723
2 TraesCS3D01G495300 chr3D 587745875 587746469 594 False 477.000000 477 81.7890 1171 1764 1 chr3D.!!$F1 593
3 TraesCS3D01G495300 chr3D 587595726 587596586 860 True 386.100000 712 87.1620 931 1838 2 chr3D.!!$R3 907
4 TraesCS3D01G495300 chr3A 716945284 716949928 4644 True 824.166667 2285 88.7415 1 3526 6 chr3A.!!$R1 3525
5 TraesCS3D01G495300 chr3A 716966163 716967019 856 True 377.600000 695 86.9995 933 1838 2 chr3A.!!$R2 905
6 TraesCS3D01G495300 chr3B 784869201 784871643 2442 True 999.000000 1938 89.2460 5 2341 3 chr3B.!!$R1 2336
7 TraesCS3D01G495300 chr3B 784900109 784900948 839 True 326.100000 592 86.0405 931 1838 2 chr3B.!!$R2 907

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
967 1664 2.045561 TCTCTAGAACCTCTCCGCAG 57.954 55.0 0.0 0.0 0.00 5.18 F
1069 1779 0.541863 GGAGGCGGAAATCTTCTCCA 59.458 55.0 0.0 0.0 42.49 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 3248 0.036388 TGTCCTGATCCGTTTGAGGC 60.036 55.0 0.0 0.0 0.00 4.70 R
2997 4096 0.318955 GAATGCACGCCACTGCTTTT 60.319 50.0 0.0 0.0 38.07 2.27 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
26 27 8.406730 AGAGCTTTGAAAGAAGATCAATCTTT 57.593 30.769 20.25 20.25 46.47 2.52
81 82 7.252612 TCTGAAACATATGGTGGAACTCTAA 57.747 36.000 7.80 0.00 36.74 2.10
111 112 8.972127 ACATAGTGATACACTCTAGAACACAAT 58.028 33.333 7.68 0.00 41.21 2.71
112 113 9.809096 CATAGTGATACACTCTAGAACACAATT 57.191 33.333 7.68 0.00 41.21 2.32
139 788 6.171213 ACCTAGTAAAACCTGATAAGCACAC 58.829 40.000 0.00 0.00 0.00 3.82
141 790 5.941948 AGTAAAACCTGATAAGCACACAC 57.058 39.130 0.00 0.00 0.00 3.82
204 853 7.907563 CCACAAAAACAAACATATTGTTTCACC 59.092 33.333 16.82 0.00 46.61 4.02
205 854 8.446273 CACAAAAACAAACATATTGTTTCACCA 58.554 29.630 16.82 0.00 46.61 4.17
221 870 2.169144 TCACCATGCTTCATCGTGATCT 59.831 45.455 3.70 0.00 37.14 2.75
252 901 9.943465 CATATCATAATGTTTCATTACGTCTCG 57.057 33.333 0.00 0.00 0.00 4.04
260 909 2.797491 TCATTACGTCTCGACATGCTG 58.203 47.619 0.00 0.00 0.00 4.41
277 926 6.785191 ACATGCTGCAAACATAATACTACAC 58.215 36.000 6.36 0.00 0.00 2.90
278 927 6.374053 ACATGCTGCAAACATAATACTACACA 59.626 34.615 6.36 0.00 0.00 3.72
366 1017 8.993121 CACTATGTTTGATATAGTTCCCATCAC 58.007 37.037 0.00 0.00 38.85 3.06
448 1099 5.045578 AGTGTCCTAGTTGCAAGGAACATAT 60.046 40.000 7.20 0.74 44.67 1.78
452 1103 6.037610 GTCCTAGTTGCAAGGAACATATCAAG 59.962 42.308 7.20 0.00 44.67 3.02
530 1215 2.894126 TGGAGTGTGAGAGAGAAAGGAC 59.106 50.000 0.00 0.00 0.00 3.85
579 1264 5.001232 ACTGCATGACATAAAGGTAACGTT 58.999 37.500 5.88 5.88 46.39 3.99
582 1267 5.106869 TGCATGACATAAAGGTAACGTTGAC 60.107 40.000 11.99 3.31 46.39 3.18
736 1424 7.414098 CCCTTTACCTCACTTTCATAATGTTCG 60.414 40.741 0.00 0.00 0.00 3.95
761 1449 4.473196 TGGAGTATGCCTTTTAGACATCCA 59.527 41.667 0.00 0.00 0.00 3.41
820 1510 4.291513 TCTCTCGCCCTATATAAAGGAGGA 59.708 45.833 3.16 0.00 39.15 3.71
839 1529 3.423154 GCCACTCCGGAACTTGCG 61.423 66.667 5.23 0.00 36.56 4.85
926 1616 4.794278 TCAACTACCGTAGATCAAGCAA 57.206 40.909 12.66 0.00 0.00 3.91
954 1651 4.463539 CCTCTCATCCACCATCATCTCTAG 59.536 50.000 0.00 0.00 0.00 2.43
964 1661 3.505680 CCATCATCTCTAGAACCTCTCCG 59.494 52.174 0.00 0.00 0.00 4.63
967 1664 2.045561 TCTCTAGAACCTCTCCGCAG 57.954 55.000 0.00 0.00 0.00 5.18
1069 1779 0.541863 GGAGGCGGAAATCTTCTCCA 59.458 55.000 0.00 0.00 42.49 3.86
1077 1793 2.357569 GGAAATCTTCTCCAGTGGCCAT 60.358 50.000 9.72 0.00 32.77 4.40
1386 2158 5.181009 ACTGAGCATCTGATCGATTTTTCA 58.819 37.500 0.00 0.00 37.51 2.69
1507 2288 3.633094 GAAGGAGCAGCTGACGCGA 62.633 63.158 20.43 0.00 42.32 5.87
1720 2516 5.047377 CAGGACCTTCTATAGCCTTCATCTC 60.047 48.000 0.00 0.00 0.00 2.75
1751 2550 4.348168 ACACATGGGTCTTCTGACTTAAGT 59.652 41.667 8.13 8.13 42.54 2.24
1759 2558 6.056236 GGTCTTCTGACTTAAGTTCCTGTTT 58.944 40.000 10.02 0.00 42.54 2.83
1807 2606 5.300792 TGAACTTAAATTCCTGTTGGTGTCC 59.699 40.000 0.00 0.00 34.23 4.02
1838 2637 8.893219 TCGATGCTTATGATTTGATCTTAACT 57.107 30.769 0.00 0.00 0.00 2.24
1937 2861 6.260936 CGTTGATTGAGGTGGATTTAGCTAAT 59.739 38.462 7.08 0.00 0.00 1.73
1995 2930 5.303845 CCCTACTCTGGGTTATACACTAACC 59.696 48.000 5.74 5.74 44.64 2.85
2033 2968 6.192234 TCACTCTATCAAGGTAAACGACTC 57.808 41.667 0.00 0.00 0.00 3.36
2091 3027 5.991568 TGTGCATTTGAATGAATTTTGCTG 58.008 33.333 7.86 0.00 38.70 4.41
2151 3174 4.398988 TGGTAACATAGTACGATGAACGGT 59.601 41.667 21.06 5.00 46.17 4.83
2152 3175 5.676837 TGGTAACATAGTACGATGAACGGTG 60.677 44.000 21.06 0.00 46.17 4.94
2153 3176 7.792594 TGGTAACATAGTACGATGAACGGTGA 61.793 42.308 21.06 3.59 46.17 4.02
2154 3177 9.179590 TGGTAACATAGTACGATGAACGGTGAA 62.180 40.741 21.06 0.00 46.17 3.18
2165 3188 2.160615 TGAACGGTGAATTAATGGTGCG 59.839 45.455 0.00 0.00 0.00 5.34
2166 3189 1.816074 ACGGTGAATTAATGGTGCGT 58.184 45.000 0.00 0.00 0.00 5.24
2203 3226 8.795842 TGACCGATAACATGTAATTAAGGTTT 57.204 30.769 0.00 0.00 31.10 3.27
2214 3237 7.296628 TGTAATTAAGGTTTTGATGCAAGGT 57.703 32.000 0.00 0.00 0.00 3.50
2221 3244 4.460382 AGGTTTTGATGCAAGGTATCTGTG 59.540 41.667 0.00 0.00 0.00 3.66
2223 3246 5.156355 GTTTTGATGCAAGGTATCTGTGTG 58.844 41.667 0.00 0.00 0.00 3.82
2225 3248 3.865446 TGATGCAAGGTATCTGTGTGAG 58.135 45.455 0.00 0.00 0.00 3.51
2226 3249 2.099141 TGCAAGGTATCTGTGTGAGC 57.901 50.000 0.00 0.00 0.00 4.26
2227 3250 1.339055 TGCAAGGTATCTGTGTGAGCC 60.339 52.381 0.00 0.00 0.00 4.70
2240 3273 3.840831 TGAGCCTCAAACGGATCAG 57.159 52.632 0.00 0.00 43.96 2.90
2260 3293 2.028930 AGGACAAGTTTCTCCTACTGCG 60.029 50.000 0.00 0.00 34.93 5.18
2266 3299 3.600388 AGTTTCTCCTACTGCGAAATGG 58.400 45.455 0.00 0.00 0.00 3.16
2343 3376 3.441572 GCCATATGTAGCATGGATTCCAC 59.558 47.826 7.76 0.00 44.95 4.02
2353 3386 1.060729 TGGATTCCACGAAACCCTCA 58.939 50.000 0.00 0.00 34.24 3.86
2363 3396 3.557595 CACGAAACCCTCATCATTCTAGC 59.442 47.826 0.00 0.00 0.00 3.42
2364 3397 3.452627 ACGAAACCCTCATCATTCTAGCT 59.547 43.478 0.00 0.00 0.00 3.32
2365 3398 4.649674 ACGAAACCCTCATCATTCTAGCTA 59.350 41.667 0.00 0.00 0.00 3.32
2366 3399 5.221342 ACGAAACCCTCATCATTCTAGCTAG 60.221 44.000 15.01 15.01 0.00 3.42
2367 3400 5.546526 GAAACCCTCATCATTCTAGCTAGG 58.453 45.833 20.58 5.07 0.00 3.02
2368 3401 2.903135 ACCCTCATCATTCTAGCTAGGC 59.097 50.000 20.58 0.00 0.00 3.93
2387 3420 2.437413 GCTTTTCGGGTTCCATCTTCT 58.563 47.619 0.00 0.00 0.00 2.85
2391 3424 1.452108 CGGGTTCCATCTTCTGGGC 60.452 63.158 0.00 0.00 45.98 5.36
2404 3437 1.304464 CTGGGCTTTGGAGGGTTCC 60.304 63.158 0.00 0.00 44.31 3.62
2446 3479 7.394077 ACACTCATTGTTGGTGATCAATTATCA 59.606 33.333 0.00 0.00 37.43 2.15
2453 3486 5.518848 TGGTGATCAATTATCATGCAACC 57.481 39.130 0.00 0.00 46.21 3.77
2454 3487 4.036616 TGGTGATCAATTATCATGCAACCG 59.963 41.667 0.00 0.00 46.21 4.44
2540 3573 7.930513 TTGTAATATTGACTAGATGTCTGCG 57.069 36.000 0.00 0.00 45.54 5.18
2544 3577 7.511959 AATATTGACTAGATGTCTGCGACTA 57.488 36.000 0.00 0.00 45.54 2.59
2554 3587 4.983671 TGTCTGCGACTATGTCTTATGT 57.016 40.909 9.49 0.00 33.15 2.29
2563 3596 6.755141 GCGACTATGTCTTATGTTCCAACTTA 59.245 38.462 0.00 0.00 0.00 2.24
2579 3612 4.217550 CCAACTTACATTTGTCGGAATGGT 59.782 41.667 10.37 0.00 40.50 3.55
2585 3618 5.622770 ACATTTGTCGGAATGGTAACTTC 57.377 39.130 10.37 0.00 40.50 3.01
2650 3683 1.608590 ACCCAACGAACAATGAGCAAG 59.391 47.619 0.00 0.00 0.00 4.01
2674 3707 3.002656 AGTGCTCAACATTTTGTGACGAG 59.997 43.478 0.00 0.00 34.02 4.18
2732 3765 8.362464 ACATCCACATTACTAGTAGAAGACAA 57.638 34.615 3.59 0.00 0.00 3.18
2767 3800 6.874134 GGTGGATGCGATCATATTTAAGTACT 59.126 38.462 0.00 0.00 31.96 2.73
2768 3801 8.033038 GGTGGATGCGATCATATTTAAGTACTA 58.967 37.037 0.00 0.00 31.96 1.82
2769 3802 8.861101 GTGGATGCGATCATATTTAAGTACTAC 58.139 37.037 0.00 0.00 31.96 2.73
2772 3805 9.419297 GATGCGATCATATTTAAGTACTACCAA 57.581 33.333 0.00 0.00 31.96 3.67
2801 3834 8.510243 TCAAAATGCATGCCATACCTATATAG 57.490 34.615 16.68 2.46 32.67 1.31
2842 3941 4.006780 AGTACCGATGCATGCATGATAA 57.993 40.909 36.73 16.83 36.70 1.75
2929 4028 5.452077 CCTCTTGATGTACCCTAGCTTGTAC 60.452 48.000 11.75 11.75 38.22 2.90
2933 4032 1.475280 TGTACCCTAGCTTGTACGCAG 59.525 52.381 13.08 0.00 40.12 5.18
2960 4059 5.929992 GCGGGTTGAGTATAATTAGTATGCA 59.070 40.000 0.00 0.00 0.00 3.96
2997 4096 2.411628 TAAATTTAGAGCTGGCCGCA 57.588 45.000 19.30 1.45 42.61 5.69
3101 4202 8.147704 ACCATGTCGTGTAATGTTCATATATGA 58.852 33.333 11.49 11.49 34.44 2.15
3143 4244 6.372937 TGATTAATTTGCCTCAACACATCGTA 59.627 34.615 0.00 0.00 0.00 3.43
3147 4248 5.446143 TTTGCCTCAACACATCGTATTTT 57.554 34.783 0.00 0.00 0.00 1.82
3154 4255 7.638683 GCCTCAACACATCGTATTTTTACATAC 59.361 37.037 0.00 0.00 0.00 2.39
3181 4282 2.522836 ATTCAGACTCCTAGCATGCG 57.477 50.000 13.01 0.00 0.00 4.73
3182 4283 0.179100 TTCAGACTCCTAGCATGCGC 60.179 55.000 13.01 0.00 38.99 6.09
3191 4292 2.813754 TCCTAGCATGCGCAAATAATCC 59.186 45.455 17.11 0.00 42.27 3.01
3207 4308 7.605449 CAAATAATCCATCACTTGGTTTCAGT 58.395 34.615 0.00 0.00 46.52 3.41
3218 4319 2.862541 TGGTTTCAGTGAGGACCATTG 58.137 47.619 20.52 0.00 37.26 2.82
3221 4322 3.476552 GTTTCAGTGAGGACCATTGACA 58.523 45.455 0.00 0.00 40.57 3.58
3229 4330 1.559682 AGGACCATTGACAATACGGCT 59.440 47.619 0.00 0.00 0.00 5.52
3231 4332 1.940613 GACCATTGACAATACGGCTCC 59.059 52.381 0.00 0.00 0.00 4.70
3237 4338 2.730382 TGACAATACGGCTCCTCAGTA 58.270 47.619 0.00 0.00 0.00 2.74
3256 4357 4.148348 CAGTAACTCTTCTTGTTTCGGACG 59.852 45.833 0.00 0.00 0.00 4.79
3259 4360 2.059541 CTCTTCTTGTTTCGGACGACC 58.940 52.381 0.00 0.00 0.00 4.79
3261 4362 2.036733 TCTTCTTGTTTCGGACGACCAT 59.963 45.455 4.48 0.00 35.59 3.55
3262 4363 1.790755 TCTTGTTTCGGACGACCATG 58.209 50.000 4.48 0.00 35.59 3.66
3263 4364 1.341852 TCTTGTTTCGGACGACCATGA 59.658 47.619 4.48 0.17 35.59 3.07
3264 4365 2.139917 CTTGTTTCGGACGACCATGAA 58.860 47.619 4.48 0.00 35.59 2.57
3266 4367 2.073056 TGTTTCGGACGACCATGAATG 58.927 47.619 4.48 0.00 35.59 2.67
3269 4370 3.596310 TTCGGACGACCATGAATGTTA 57.404 42.857 4.48 0.00 35.59 2.41
3270 4371 2.883574 TCGGACGACCATGAATGTTAC 58.116 47.619 4.48 0.00 35.59 2.50
3271 4372 2.494471 TCGGACGACCATGAATGTTACT 59.506 45.455 4.48 0.00 35.59 2.24
3273 4374 4.340097 TCGGACGACCATGAATGTTACTAT 59.660 41.667 4.48 0.00 35.59 2.12
3274 4375 5.532032 TCGGACGACCATGAATGTTACTATA 59.468 40.000 4.48 0.00 35.59 1.31
3275 4376 6.039605 TCGGACGACCATGAATGTTACTATAA 59.960 38.462 4.48 0.00 35.59 0.98
3278 4379 9.701098 GGACGACCATGAATGTTACTATAATTA 57.299 33.333 0.00 0.00 35.97 1.40
3327 4645 7.599630 ATTTGGTAATCATTTGTTGATGTGC 57.400 32.000 0.00 0.00 44.51 4.57
3349 4667 7.065683 TGTGCTATATCATTTTGTGTCGTCATT 59.934 33.333 0.00 0.00 0.00 2.57
3354 4672 5.242069 TCATTTTGTGTCGTCATTGTGTT 57.758 34.783 0.00 0.00 0.00 3.32
3371 4689 2.549754 GTGTTCTCATCTTGTGGTGTGG 59.450 50.000 0.00 0.00 0.00 4.17
3402 4720 0.518636 CGTTGGTGCATGTCTCCAAG 59.481 55.000 17.98 11.56 45.76 3.61
3405 4723 2.408271 TGGTGCATGTCTCCAAGATC 57.592 50.000 8.01 0.00 35.56 2.75
3407 4725 2.286872 GGTGCATGTCTCCAAGATCTG 58.713 52.381 0.00 0.00 0.00 2.90
3408 4726 1.669779 GTGCATGTCTCCAAGATCTGC 59.330 52.381 0.00 0.00 36.00 4.26
3429 4747 3.666334 GCTCGTATCGCTTGTCTTAGATG 59.334 47.826 0.00 0.00 0.00 2.90
3430 4748 3.629058 TCGTATCGCTTGTCTTAGATGC 58.371 45.455 0.00 0.00 0.00 3.91
3431 4749 3.315470 TCGTATCGCTTGTCTTAGATGCT 59.685 43.478 0.00 0.00 0.00 3.79
3432 4750 4.514066 TCGTATCGCTTGTCTTAGATGCTA 59.486 41.667 0.00 0.00 0.00 3.49
3435 4753 2.690497 TCGCTTGTCTTAGATGCTAGCT 59.310 45.455 17.23 0.83 0.00 3.32
3436 4754 3.131223 TCGCTTGTCTTAGATGCTAGCTT 59.869 43.478 17.23 9.95 0.00 3.74
3437 4755 3.868077 CGCTTGTCTTAGATGCTAGCTTT 59.132 43.478 17.23 3.07 0.00 3.51
3438 4756 4.331168 CGCTTGTCTTAGATGCTAGCTTTT 59.669 41.667 17.23 7.60 0.00 2.27
3466 4787 6.530120 TGAGAAACTTTAGATGCCAGTTGTA 58.470 36.000 0.00 0.00 31.00 2.41
3475 4796 2.691409 TGCCAGTTGTAGTATCCTGC 57.309 50.000 0.00 0.00 0.00 4.85
3485 4806 6.041069 AGTTGTAGTATCCTGCTGTATTCCTC 59.959 42.308 0.00 0.00 0.00 3.71
3498 4819 5.654497 CTGTATTCCTCCTTTGGCATTTTC 58.346 41.667 0.00 0.00 0.00 2.29
3505 4826 0.532115 CTTTGGCATTTTCGGAGGGG 59.468 55.000 0.00 0.00 0.00 4.79
3511 4832 2.017113 GCATTTTCGGAGGGGAACGAT 61.017 52.381 0.00 0.00 39.06 3.73
3515 4836 1.550130 TTCGGAGGGGAACGATTGCT 61.550 55.000 0.00 0.00 39.06 3.91
3517 4838 1.602237 GGAGGGGAACGATTGCTGA 59.398 57.895 0.00 0.00 0.00 4.26
3526 4847 2.743752 CGATTGCTGAGGTGGTGCG 61.744 63.158 0.00 0.00 0.00 5.34
3527 4848 3.044059 GATTGCTGAGGTGGTGCGC 62.044 63.158 0.00 0.00 0.00 6.09
3543 4864 4.785453 GCCGGGTGAGAAGGCCAG 62.785 72.222 5.01 0.00 44.80 4.85
3544 4865 4.101448 CCGGGTGAGAAGGCCAGG 62.101 72.222 5.01 0.00 34.04 4.45
3545 4866 3.322466 CGGGTGAGAAGGCCAGGT 61.322 66.667 5.01 0.00 0.00 4.00
3546 4867 2.895424 CGGGTGAGAAGGCCAGGTT 61.895 63.158 5.01 0.00 0.00 3.50
3547 4868 1.002011 GGGTGAGAAGGCCAGGTTC 60.002 63.158 5.01 0.00 0.00 3.62
3548 4869 1.761174 GGTGAGAAGGCCAGGTTCA 59.239 57.895 5.01 0.00 0.00 3.18
3549 4870 0.322008 GGTGAGAAGGCCAGGTTCAG 60.322 60.000 5.01 0.00 0.00 3.02
3550 4871 0.687354 GTGAGAAGGCCAGGTTCAGA 59.313 55.000 5.01 0.00 0.00 3.27
3551 4872 0.979665 TGAGAAGGCCAGGTTCAGAG 59.020 55.000 5.01 0.00 0.00 3.35
3552 4873 0.392327 GAGAAGGCCAGGTTCAGAGC 60.392 60.000 5.01 0.00 0.00 4.09
3553 4874 1.130054 AGAAGGCCAGGTTCAGAGCA 61.130 55.000 5.01 0.00 0.00 4.26
3554 4875 0.957888 GAAGGCCAGGTTCAGAGCAC 60.958 60.000 5.01 0.00 0.00 4.40
3555 4876 2.360475 GGCCAGGTTCAGAGCACC 60.360 66.667 0.00 0.00 34.06 5.01
3556 4877 2.360475 GCCAGGTTCAGAGCACCC 60.360 66.667 0.00 0.00 34.44 4.61
3557 4878 3.160585 CCAGGTTCAGAGCACCCA 58.839 61.111 0.00 0.00 34.44 4.51
3558 4879 1.687612 CCAGGTTCAGAGCACCCAT 59.312 57.895 0.00 0.00 34.44 4.00
3559 4880 0.679002 CCAGGTTCAGAGCACCCATG 60.679 60.000 0.00 0.00 34.44 3.66
3560 4881 0.037303 CAGGTTCAGAGCACCCATGT 59.963 55.000 0.00 0.00 34.44 3.21
3561 4882 1.278985 CAGGTTCAGAGCACCCATGTA 59.721 52.381 0.00 0.00 34.44 2.29
3562 4883 2.092753 CAGGTTCAGAGCACCCATGTAT 60.093 50.000 0.00 0.00 34.44 2.29
3563 4884 3.134623 CAGGTTCAGAGCACCCATGTATA 59.865 47.826 0.00 0.00 34.44 1.47
3564 4885 3.134804 AGGTTCAGAGCACCCATGTATAC 59.865 47.826 0.00 0.00 34.44 1.47
3565 4886 3.123804 GTTCAGAGCACCCATGTATACG 58.876 50.000 0.00 0.00 0.00 3.06
3566 4887 1.686587 TCAGAGCACCCATGTATACGG 59.313 52.381 0.00 0.00 0.00 4.02
3567 4888 0.393077 AGAGCACCCATGTATACGGC 59.607 55.000 0.00 0.00 0.00 5.68
3568 4889 0.602905 GAGCACCCATGTATACGGCC 60.603 60.000 0.00 0.00 0.00 6.13
3569 4890 1.054406 AGCACCCATGTATACGGCCT 61.054 55.000 0.00 0.00 0.00 5.19
3570 4891 0.682852 GCACCCATGTATACGGCCTA 59.317 55.000 0.00 0.00 0.00 3.93
3571 4892 1.278127 GCACCCATGTATACGGCCTAT 59.722 52.381 0.00 0.29 0.00 2.57
3572 4893 2.498481 GCACCCATGTATACGGCCTATA 59.502 50.000 0.00 0.00 0.00 1.31
3573 4894 3.430374 GCACCCATGTATACGGCCTATAG 60.430 52.174 0.00 0.00 0.00 1.31
3574 4895 3.132289 CACCCATGTATACGGCCTATAGG 59.868 52.174 15.01 15.01 38.53 2.57
3575 4896 3.245875 ACCCATGTATACGGCCTATAGGT 60.246 47.826 20.10 3.12 37.57 3.08
3576 4897 3.132289 CCCATGTATACGGCCTATAGGTG 59.868 52.174 20.10 14.86 37.57 4.00
3577 4898 4.021229 CCATGTATACGGCCTATAGGTGA 58.979 47.826 20.10 3.82 37.57 4.02
3578 4899 4.464951 CCATGTATACGGCCTATAGGTGAA 59.535 45.833 20.10 4.39 37.57 3.18
3579 4900 5.408356 CATGTATACGGCCTATAGGTGAAC 58.592 45.833 20.10 13.13 37.57 3.18
3580 4901 4.472496 TGTATACGGCCTATAGGTGAACA 58.528 43.478 20.10 15.02 37.57 3.18
3581 4902 4.521639 TGTATACGGCCTATAGGTGAACAG 59.478 45.833 20.10 6.68 37.57 3.16
3582 4903 2.154567 ACGGCCTATAGGTGAACAGA 57.845 50.000 20.10 0.00 37.57 3.41
3583 4904 2.032620 ACGGCCTATAGGTGAACAGAG 58.967 52.381 20.10 5.72 37.57 3.35
3584 4905 2.032620 CGGCCTATAGGTGAACAGAGT 58.967 52.381 20.10 0.00 37.57 3.24
3585 4906 2.431057 CGGCCTATAGGTGAACAGAGTT 59.569 50.000 20.10 0.00 37.57 3.01
3586 4907 3.118738 CGGCCTATAGGTGAACAGAGTTT 60.119 47.826 20.10 0.00 37.57 2.66
3587 4908 4.623171 CGGCCTATAGGTGAACAGAGTTTT 60.623 45.833 20.10 0.00 37.57 2.43
3588 4909 5.254115 GGCCTATAGGTGAACAGAGTTTTT 58.746 41.667 20.10 0.00 37.57 1.94
3589 4910 5.354513 GGCCTATAGGTGAACAGAGTTTTTC 59.645 44.000 20.10 0.00 37.57 2.29
3590 4911 5.938125 GCCTATAGGTGAACAGAGTTTTTCA 59.062 40.000 20.10 0.00 37.57 2.69
3598 4919 6.507958 TGAACAGAGTTTTTCACACATGAA 57.492 33.333 0.00 0.00 43.28 2.57
3599 4920 7.099266 TGAACAGAGTTTTTCACACATGAAT 57.901 32.000 0.00 0.00 44.36 2.57
3600 4921 7.546358 TGAACAGAGTTTTTCACACATGAATT 58.454 30.769 0.00 0.00 44.36 2.17
3601 4922 8.681806 TGAACAGAGTTTTTCACACATGAATTA 58.318 29.630 0.00 0.00 44.36 1.40
3602 4923 9.173939 GAACAGAGTTTTTCACACATGAATTAG 57.826 33.333 0.00 0.00 44.36 1.73
3603 4924 8.225603 ACAGAGTTTTTCACACATGAATTAGT 57.774 30.769 0.00 0.00 44.36 2.24
3604 4925 9.337396 ACAGAGTTTTTCACACATGAATTAGTA 57.663 29.630 0.00 0.00 44.36 1.82
3605 4926 9.817365 CAGAGTTTTTCACACATGAATTAGTAG 57.183 33.333 0.00 0.00 44.36 2.57
3606 4927 9.561069 AGAGTTTTTCACACATGAATTAGTAGT 57.439 29.630 0.00 0.00 44.36 2.73
3609 4930 9.394477 GTTTTTCACACATGAATTAGTAGTTCC 57.606 33.333 0.00 0.00 44.36 3.62
3610 4931 8.684386 TTTTCACACATGAATTAGTAGTTCCA 57.316 30.769 0.00 0.00 44.36 3.53
3611 4932 8.862325 TTTCACACATGAATTAGTAGTTCCAT 57.138 30.769 0.00 0.00 44.36 3.41
3612 4933 7.848223 TCACACATGAATTAGTAGTTCCATG 57.152 36.000 0.00 8.74 0.00 3.66
3613 4934 6.316140 TCACACATGAATTAGTAGTTCCATGC 59.684 38.462 0.00 0.00 0.00 4.06
3614 4935 5.590259 ACACATGAATTAGTAGTTCCATGCC 59.410 40.000 0.00 0.00 0.00 4.40
3615 4936 5.009010 CACATGAATTAGTAGTTCCATGCCC 59.991 44.000 0.00 0.00 0.00 5.36
3616 4937 5.103940 ACATGAATTAGTAGTTCCATGCCCT 60.104 40.000 0.00 0.00 0.00 5.19
3617 4938 6.101150 ACATGAATTAGTAGTTCCATGCCCTA 59.899 38.462 0.00 0.00 0.00 3.53
3618 4939 6.569127 TGAATTAGTAGTTCCATGCCCTAA 57.431 37.500 3.22 0.00 0.00 2.69
3619 4940 6.964464 TGAATTAGTAGTTCCATGCCCTAAA 58.036 36.000 3.22 0.00 0.00 1.85
3620 4941 7.406916 TGAATTAGTAGTTCCATGCCCTAAAA 58.593 34.615 3.22 0.00 0.00 1.52
3621 4942 7.891183 TGAATTAGTAGTTCCATGCCCTAAAAA 59.109 33.333 3.22 0.00 0.00 1.94
3641 4962 5.876612 AAAAACAAACATGCAGCAAAAGA 57.123 30.435 0.00 0.00 0.00 2.52
3642 4963 6.439675 AAAAACAAACATGCAGCAAAAGAT 57.560 29.167 0.00 0.00 0.00 2.40
3643 4964 5.412526 AAACAAACATGCAGCAAAAGATG 57.587 34.783 0.00 0.00 0.00 2.90
3644 4965 4.062677 ACAAACATGCAGCAAAAGATGT 57.937 36.364 0.00 0.00 0.00 3.06
3645 4966 4.053295 ACAAACATGCAGCAAAAGATGTC 58.947 39.130 0.00 0.00 0.00 3.06
3646 4967 4.052608 CAAACATGCAGCAAAAGATGTCA 58.947 39.130 0.00 0.00 0.00 3.58
3647 4968 4.325028 AACATGCAGCAAAAGATGTCAA 57.675 36.364 0.00 0.00 0.00 3.18
3648 4969 4.325028 ACATGCAGCAAAAGATGTCAAA 57.675 36.364 0.00 0.00 0.00 2.69
3649 4970 4.695396 ACATGCAGCAAAAGATGTCAAAA 58.305 34.783 0.00 0.00 0.00 2.44
3650 4971 5.117584 ACATGCAGCAAAAGATGTCAAAAA 58.882 33.333 0.00 0.00 0.00 1.94
3671 4992 7.482169 AAAAAGTTCAGACCTTCCTTTTCTT 57.518 32.000 0.00 0.00 35.05 2.52
3672 4993 6.456795 AAAGTTCAGACCTTCCTTTTCTTG 57.543 37.500 0.00 0.00 0.00 3.02
3673 4994 5.117406 AGTTCAGACCTTCCTTTTCTTGT 57.883 39.130 0.00 0.00 0.00 3.16
3674 4995 6.248569 AGTTCAGACCTTCCTTTTCTTGTA 57.751 37.500 0.00 0.00 0.00 2.41
3675 4996 6.659824 AGTTCAGACCTTCCTTTTCTTGTAA 58.340 36.000 0.00 0.00 0.00 2.41
3676 4997 7.290813 AGTTCAGACCTTCCTTTTCTTGTAAT 58.709 34.615 0.00 0.00 0.00 1.89
3677 4998 8.437575 AGTTCAGACCTTCCTTTTCTTGTAATA 58.562 33.333 0.00 0.00 0.00 0.98
3678 4999 9.063615 GTTCAGACCTTCCTTTTCTTGTAATAA 57.936 33.333 0.00 0.00 0.00 1.40
3679 5000 9.635404 TTCAGACCTTCCTTTTCTTGTAATAAA 57.365 29.630 0.00 0.00 0.00 1.40
3680 5001 9.635404 TCAGACCTTCCTTTTCTTGTAATAAAA 57.365 29.630 0.00 0.00 0.00 1.52
3700 5021 9.906660 AATAAAATAAAAATCAGACGTTGCAGA 57.093 25.926 0.00 0.00 0.00 4.26
3701 5022 7.623268 AAAATAAAAATCAGACGTTGCAGAC 57.377 32.000 0.00 0.00 0.00 3.51
3715 5036 3.853831 TGCAGACGAAAAATGCATCAT 57.146 38.095 0.00 0.00 44.56 2.45
3716 5037 4.961435 TGCAGACGAAAAATGCATCATA 57.039 36.364 0.00 0.00 44.56 2.15
3717 5038 5.503662 TGCAGACGAAAAATGCATCATAT 57.496 34.783 0.00 0.00 44.56 1.78
3718 5039 5.893687 TGCAGACGAAAAATGCATCATATT 58.106 33.333 0.00 0.00 44.56 1.28
3719 5040 7.025485 TGCAGACGAAAAATGCATCATATTA 57.975 32.000 0.00 0.00 44.56 0.98
3720 5041 7.479150 TGCAGACGAAAAATGCATCATATTAA 58.521 30.769 0.00 0.00 44.56 1.40
3721 5042 7.431960 TGCAGACGAAAAATGCATCATATTAAC 59.568 33.333 0.00 0.00 44.56 2.01
3722 5043 7.645340 GCAGACGAAAAATGCATCATATTAACT 59.355 33.333 0.00 0.00 39.75 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 7.331026 TCTTAGAGTTCCACCATATGTTTCAG 58.669 38.462 1.24 0.00 0.00 3.02
81 82 9.244292 TGTTCTAGAGTGTATCACTATGTTTCT 57.756 33.333 7.20 1.17 45.44 2.52
111 112 9.223099 GTGCTTATCAGGTTTTACTAGGTTTAA 57.777 33.333 0.00 0.00 0.00 1.52
112 113 8.377034 TGTGCTTATCAGGTTTTACTAGGTTTA 58.623 33.333 0.00 0.00 0.00 2.01
204 853 4.567959 TGTTGTAGATCACGATGAAGCATG 59.432 41.667 0.00 0.00 0.00 4.06
205 854 4.758688 TGTTGTAGATCACGATGAAGCAT 58.241 39.130 0.00 0.00 0.00 3.79
252 901 6.907212 GTGTAGTATTATGTTTGCAGCATGTC 59.093 38.462 13.85 0.00 39.31 3.06
298 947 8.028938 CGGAAAAACATAGGAAAACTTGATGAT 58.971 33.333 0.00 0.00 0.00 2.45
322 971 1.257936 GTGATGCATTGTAGTACGCGG 59.742 52.381 12.47 0.00 0.00 6.46
359 1010 2.226330 TGAGTTCCAAAACGTGATGGG 58.774 47.619 17.19 4.57 40.48 4.00
448 1099 9.752961 CACAAATCCAATTTATGATATGCTTGA 57.247 29.630 0.00 0.00 28.30 3.02
452 1103 8.891671 AACCACAAATCCAATTTATGATATGC 57.108 30.769 0.00 0.00 28.30 3.14
509 1194 2.894126 GTCCTTTCTCTCTCACACTCCA 59.106 50.000 0.00 0.00 0.00 3.86
530 1215 1.472376 GGATTCCTGCAACCTCTCTCG 60.472 57.143 0.00 0.00 0.00 4.04
736 1424 3.873910 TGTCTAAAAGGCATACTCCAGC 58.126 45.455 0.00 0.00 0.00 4.85
761 1449 1.988107 TCCAGAGAACTGATTTGGCCT 59.012 47.619 3.32 0.00 46.03 5.19
820 1510 2.030562 CAAGTTCCGGAGTGGCGT 59.969 61.111 3.34 0.00 37.80 5.68
912 1602 2.093447 AGGGAACTTGCTTGATCTACGG 60.093 50.000 0.00 0.00 37.44 4.02
954 1651 1.446272 CGTTCCTGCGGAGAGGTTC 60.446 63.158 5.10 0.00 34.36 3.62
964 1661 1.294659 CTGCTTGGTCTCGTTCCTGC 61.295 60.000 0.00 0.00 0.00 4.85
967 1664 1.433534 CTTCTGCTTGGTCTCGTTCC 58.566 55.000 0.00 0.00 0.00 3.62
1386 2158 1.515088 CTCTGCGACGTCAGCGAAT 60.515 57.895 17.16 0.00 42.00 3.34
1720 2516 0.984230 AGACCCATGTGTGTACCTGG 59.016 55.000 0.00 0.00 40.92 4.45
1736 2532 7.555306 AAAACAGGAACTTAAGTCAGAAGAC 57.445 36.000 8.95 0.00 40.79 3.01
1774 2573 7.206687 ACAGGAATTTAAGTTCATCGCAAAAA 58.793 30.769 12.19 0.00 0.00 1.94
1775 2574 6.744112 ACAGGAATTTAAGTTCATCGCAAAA 58.256 32.000 12.19 0.00 0.00 2.44
1776 2575 6.325919 ACAGGAATTTAAGTTCATCGCAAA 57.674 33.333 12.19 0.00 0.00 3.68
1777 2576 5.957842 ACAGGAATTTAAGTTCATCGCAA 57.042 34.783 12.19 0.00 0.00 4.85
1778 2577 5.335583 CCAACAGGAATTTAAGTTCATCGCA 60.336 40.000 12.19 0.00 0.00 5.10
1779 2578 5.095490 CCAACAGGAATTTAAGTTCATCGC 58.905 41.667 12.19 0.00 0.00 4.58
1780 2579 6.086222 CACCAACAGGAATTTAAGTTCATCG 58.914 40.000 12.19 3.92 0.00 3.84
1781 2580 6.981722 ACACCAACAGGAATTTAAGTTCATC 58.018 36.000 12.19 0.00 0.00 2.92
1782 2581 6.015434 GGACACCAACAGGAATTTAAGTTCAT 60.015 38.462 12.19 2.66 0.00 2.57
1783 2582 5.300792 GGACACCAACAGGAATTTAAGTTCA 59.699 40.000 12.19 0.00 0.00 3.18
1784 2583 5.535030 AGGACACCAACAGGAATTTAAGTTC 59.465 40.000 2.22 2.22 0.00 3.01
1785 2584 5.301805 CAGGACACCAACAGGAATTTAAGTT 59.698 40.000 0.00 0.00 0.00 2.66
1807 2606 6.535274 TCAAATCATAAGCATCGATGACAG 57.465 37.500 29.20 12.57 34.98 3.51
1908 2832 0.037697 TCCACCTCAATCAACGTCGG 60.038 55.000 0.00 0.00 0.00 4.79
1937 2861 6.236558 TGTCCACAAATTCGTATATACCCA 57.763 37.500 7.30 0.00 0.00 4.51
1987 2918 8.413229 GTGAATAAATATTGCATGGGTTAGTGT 58.587 33.333 0.00 0.00 0.00 3.55
2077 3013 3.118542 GGGATCGCAGCAAAATTCATTC 58.881 45.455 4.64 0.00 0.00 2.67
2087 3023 4.408821 GGTGGTGGGATCGCAGCA 62.409 66.667 32.99 32.99 0.00 4.41
2091 3027 4.796495 GTGGGGTGGTGGGATCGC 62.796 72.222 2.14 2.14 0.00 4.58
2128 3064 4.398988 ACCGTTCATCGTACTATGTTACCA 59.601 41.667 7.21 0.00 37.94 3.25
2148 3171 2.911819 AACGCACCATTAATTCACCG 57.088 45.000 0.00 0.00 0.00 4.94
2149 3172 3.122780 GCAAAACGCACCATTAATTCACC 59.877 43.478 0.00 0.00 41.79 4.02
2151 3174 4.250116 AGCAAAACGCACCATTAATTCA 57.750 36.364 0.00 0.00 46.13 2.57
2152 3175 5.061684 GGTAAGCAAAACGCACCATTAATTC 59.938 40.000 0.00 0.00 46.13 2.17
2153 3176 4.926832 GGTAAGCAAAACGCACCATTAATT 59.073 37.500 0.00 0.00 46.13 1.40
2154 3177 4.219725 AGGTAAGCAAAACGCACCATTAAT 59.780 37.500 0.00 0.00 46.13 1.40
2155 3178 3.570550 AGGTAAGCAAAACGCACCATTAA 59.429 39.130 0.00 0.00 46.13 1.40
2156 3179 3.150767 AGGTAAGCAAAACGCACCATTA 58.849 40.909 0.00 0.00 46.13 1.90
2165 3188 5.049267 TGTTATCGGTCAAGGTAAGCAAAAC 60.049 40.000 0.00 0.00 0.00 2.43
2166 3189 5.064558 TGTTATCGGTCAAGGTAAGCAAAA 58.935 37.500 0.00 0.00 0.00 2.44
2203 3226 4.256110 CTCACACAGATACCTTGCATCAA 58.744 43.478 0.00 0.00 0.00 2.57
2214 3237 2.353704 CCGTTTGAGGCTCACACAGATA 60.354 50.000 27.76 6.65 28.15 1.98
2221 3244 1.363744 CTGATCCGTTTGAGGCTCAC 58.636 55.000 18.55 5.82 33.41 3.51
2223 3246 0.537188 TCCTGATCCGTTTGAGGCTC 59.463 55.000 7.79 7.79 0.00 4.70
2225 3248 0.036388 TGTCCTGATCCGTTTGAGGC 60.036 55.000 0.00 0.00 0.00 4.70
2226 3249 2.289694 ACTTGTCCTGATCCGTTTGAGG 60.290 50.000 0.00 0.00 0.00 3.86
2227 3250 3.045601 ACTTGTCCTGATCCGTTTGAG 57.954 47.619 0.00 0.00 0.00 3.02
2240 3273 2.029290 TCGCAGTAGGAGAAACTTGTCC 60.029 50.000 0.00 0.00 40.72 4.02
2260 3293 6.430451 CAATGCTATAACCGAGAACCATTTC 58.570 40.000 0.00 0.00 0.00 2.17
2266 3299 4.694339 ACTCCAATGCTATAACCGAGAAC 58.306 43.478 0.00 0.00 0.00 3.01
2343 3376 4.065321 AGCTAGAATGATGAGGGTTTCG 57.935 45.455 0.00 0.00 0.00 3.46
2353 3386 4.503991 CCCGAAAAGCCTAGCTAGAATGAT 60.504 45.833 22.70 1.04 38.25 2.45
2363 3396 2.092914 AGATGGAACCCGAAAAGCCTAG 60.093 50.000 0.00 0.00 0.00 3.02
2364 3397 1.913419 AGATGGAACCCGAAAAGCCTA 59.087 47.619 0.00 0.00 0.00 3.93
2365 3398 0.698818 AGATGGAACCCGAAAAGCCT 59.301 50.000 0.00 0.00 0.00 4.58
2366 3399 1.472878 GAAGATGGAACCCGAAAAGCC 59.527 52.381 0.00 0.00 0.00 4.35
2367 3400 2.162408 CAGAAGATGGAACCCGAAAAGC 59.838 50.000 0.00 0.00 0.00 3.51
2387 3420 2.851045 GGAACCCTCCAAAGCCCA 59.149 61.111 0.00 0.00 41.96 5.36
2391 3424 0.955919 GCTGTCGGAACCCTCCAAAG 60.956 60.000 0.00 0.00 42.58 2.77
2404 3437 2.022808 GTGTTGACACATTGCTGTCG 57.977 50.000 9.28 0.00 45.75 4.35
2443 3476 3.724508 TTTTTGACACGGTTGCATGAT 57.275 38.095 0.00 0.00 0.00 2.45
2446 3479 5.777802 TGATAATTTTTGACACGGTTGCAT 58.222 33.333 0.00 0.00 0.00 3.96
2479 3512 9.823647 CATCCATAGAACTATTGTGTTACTTCT 57.176 33.333 0.00 0.00 0.00 2.85
2480 3513 9.601217 ACATCCATAGAACTATTGTGTTACTTC 57.399 33.333 0.00 0.00 0.00 3.01
2536 3569 4.682787 TGGAACATAAGACATAGTCGCAG 58.317 43.478 0.00 0.00 37.67 5.18
2540 3573 8.997621 TGTAAGTTGGAACATAAGACATAGTC 57.002 34.615 0.00 0.00 39.30 2.59
2563 3596 5.048991 GTGAAGTTACCATTCCGACAAATGT 60.049 40.000 0.00 0.00 35.31 2.71
2568 3601 3.181464 TGTGTGAAGTTACCATTCCGACA 60.181 43.478 0.00 0.00 0.00 4.35
2617 3650 4.785511 TCGTTGGGTTTTCTGTTTCAAA 57.214 36.364 0.00 0.00 0.00 2.69
2618 3651 4.022242 TGTTCGTTGGGTTTTCTGTTTCAA 60.022 37.500 0.00 0.00 0.00 2.69
2628 3661 2.028130 TGCTCATTGTTCGTTGGGTTT 58.972 42.857 0.00 0.00 0.00 3.27
2650 3683 3.632189 GTCACAAAATGTTGAGCACTCC 58.368 45.455 1.62 0.00 38.20 3.85
2660 3693 2.146342 CTCCAGCTCGTCACAAAATGT 58.854 47.619 0.00 0.00 0.00 2.71
2674 3707 2.357034 TTCACGGCGTTCTCCAGC 60.357 61.111 11.19 0.00 0.00 4.85
2732 3765 5.559770 TGATCGCATCCACCATTATTATGT 58.440 37.500 0.00 0.00 0.00 2.29
2767 3800 4.222366 TGGCATGCATTTTGATTCTTGGTA 59.778 37.500 21.36 0.00 0.00 3.25
2768 3801 3.008157 TGGCATGCATTTTGATTCTTGGT 59.992 39.130 21.36 0.00 0.00 3.67
2769 3802 3.601435 TGGCATGCATTTTGATTCTTGG 58.399 40.909 21.36 0.00 0.00 3.61
2772 3805 4.652421 AGGTATGGCATGCATTTTGATTCT 59.348 37.500 21.36 1.91 0.00 2.40
2813 3909 5.793817 TGCATGCATCGGTACTATTTATCT 58.206 37.500 18.46 0.00 0.00 1.98
2817 3913 4.388485 TCATGCATGCATCGGTACTATTT 58.612 39.130 30.07 2.89 33.90 1.40
2883 3982 4.953579 GGAAAATGTAGGGCCTGAATGTAA 59.046 41.667 18.53 0.00 0.00 2.41
2891 3990 2.919602 TCAAGAGGAAAATGTAGGGCCT 59.080 45.455 12.58 12.58 0.00 5.19
2933 4032 7.201530 GCATACTAATTATACTCAACCCGCATC 60.202 40.741 0.00 0.00 0.00 3.91
2938 4037 9.672673 ATCATGCATACTAATTATACTCAACCC 57.327 33.333 0.00 0.00 0.00 4.11
2997 4096 0.318955 GAATGCACGCCACTGCTTTT 60.319 50.000 0.00 0.00 38.07 2.27
3074 4175 4.944962 ATGAACATTACACGACATGGTG 57.055 40.909 0.00 0.00 43.54 4.17
3103 4204 9.985730 GCAAATTAATCATCCTCATAATTCCAA 57.014 29.630 0.00 0.00 30.01 3.53
3105 4206 8.810041 AGGCAAATTAATCATCCTCATAATTCC 58.190 33.333 0.00 0.00 30.01 3.01
3108 4209 8.945195 TGAGGCAAATTAATCATCCTCATAAT 57.055 30.769 19.97 0.00 43.45 1.28
3110 4211 7.779326 TGTTGAGGCAAATTAATCATCCTCATA 59.221 33.333 22.45 15.96 46.35 2.15
3113 4214 6.127647 TGTGTTGAGGCAAATTAATCATCCTC 60.128 38.462 16.72 16.72 40.24 3.71
3154 4255 7.637229 CATGCTAGGAGTCTGAATTGTTTATG 58.363 38.462 0.00 0.00 0.00 1.90
3161 4262 2.831333 CGCATGCTAGGAGTCTGAATT 58.169 47.619 17.13 0.00 0.00 2.17
3165 4266 0.460811 TTGCGCATGCTAGGAGTCTG 60.461 55.000 12.75 0.00 43.34 3.51
3173 4274 3.819902 TGATGGATTATTTGCGCATGCTA 59.180 39.130 12.75 0.00 43.34 3.49
3200 4301 3.476552 TGTCAATGGTCCTCACTGAAAC 58.523 45.455 0.00 0.00 33.10 2.78
3207 4308 2.679639 GCCGTATTGTCAATGGTCCTCA 60.680 50.000 8.39 0.00 0.00 3.86
3218 4319 3.130693 AGTTACTGAGGAGCCGTATTGTC 59.869 47.826 0.00 0.00 0.00 3.18
3221 4322 3.633418 AGAGTTACTGAGGAGCCGTATT 58.367 45.455 0.00 0.00 0.00 1.89
3229 4330 5.509163 CCGAAACAAGAAGAGTTACTGAGGA 60.509 44.000 0.00 0.00 0.00 3.71
3231 4332 5.402867 GTCCGAAACAAGAAGAGTTACTGAG 59.597 44.000 0.00 0.00 0.00 3.35
3237 4338 3.121544 GTCGTCCGAAACAAGAAGAGTT 58.878 45.455 0.00 0.00 0.00 3.01
3301 4619 9.149225 GCACATCAACAAATGATTACCAAATTA 57.851 29.630 0.00 0.00 46.85 1.40
3315 4633 9.356433 CACAAAATGATATAGCACATCAACAAA 57.644 29.630 0.00 0.00 36.08 2.83
3318 4636 7.374228 CGACACAAAATGATATAGCACATCAAC 59.626 37.037 0.00 0.00 36.08 3.18
3327 4645 8.390354 ACACAATGACGACACAAAATGATATAG 58.610 33.333 0.00 0.00 0.00 1.31
3349 4667 3.205338 CACACCACAAGATGAGAACACA 58.795 45.455 0.00 0.00 0.00 3.72
3354 4672 1.072173 CACCCACACCACAAGATGAGA 59.928 52.381 0.00 0.00 0.00 3.27
3371 4689 2.260869 ACCAACGCATGAGCACACC 61.261 57.895 0.00 0.00 42.27 4.16
3402 4720 2.047769 GACAAGCGATACGAGCAGATC 58.952 52.381 0.00 0.00 37.01 2.75
3405 4723 1.914634 AAGACAAGCGATACGAGCAG 58.085 50.000 0.00 0.00 37.01 4.24
3407 4725 3.335786 TCTAAGACAAGCGATACGAGC 57.664 47.619 0.00 0.00 0.00 5.03
3408 4726 3.666334 GCATCTAAGACAAGCGATACGAG 59.334 47.826 0.00 0.00 0.00 4.18
3438 4756 7.346751 ACTGGCATCTAAAGTTTCTCAAAAA 57.653 32.000 0.00 0.00 0.00 1.94
3475 4796 5.654497 GAAAATGCCAAAGGAGGAATACAG 58.346 41.667 0.00 0.00 0.00 2.74
3485 4806 0.532115 CCCTCCGAAAATGCCAAAGG 59.468 55.000 0.00 0.00 0.00 3.11
3498 4819 1.815421 CAGCAATCGTTCCCCTCCG 60.815 63.158 0.00 0.00 0.00 4.63
3505 4826 0.798776 CACCACCTCAGCAATCGTTC 59.201 55.000 0.00 0.00 0.00 3.95
3526 4847 4.785453 CTGGCCTTCTCACCCGGC 62.785 72.222 3.32 0.00 43.03 6.13
3527 4848 4.101448 CCTGGCCTTCTCACCCGG 62.101 72.222 3.32 0.00 0.00 5.73
3528 4849 2.804828 GAACCTGGCCTTCTCACCCG 62.805 65.000 3.32 0.00 0.00 5.28
3529 4850 1.002011 GAACCTGGCCTTCTCACCC 60.002 63.158 3.32 0.00 0.00 4.61
3530 4851 0.322008 CTGAACCTGGCCTTCTCACC 60.322 60.000 3.32 0.00 0.00 4.02
3531 4852 0.687354 TCTGAACCTGGCCTTCTCAC 59.313 55.000 3.32 0.00 0.00 3.51
3532 4853 0.979665 CTCTGAACCTGGCCTTCTCA 59.020 55.000 3.32 0.52 0.00 3.27
3533 4854 0.392327 GCTCTGAACCTGGCCTTCTC 60.392 60.000 3.32 0.00 0.00 2.87
3534 4855 1.130054 TGCTCTGAACCTGGCCTTCT 61.130 55.000 3.32 0.00 0.00 2.85
3535 4856 0.957888 GTGCTCTGAACCTGGCCTTC 60.958 60.000 3.32 0.00 0.00 3.46
3536 4857 1.073897 GTGCTCTGAACCTGGCCTT 59.926 57.895 3.32 0.00 0.00 4.35
3537 4858 2.753029 GTGCTCTGAACCTGGCCT 59.247 61.111 3.32 0.00 0.00 5.19
3538 4859 2.360475 GGTGCTCTGAACCTGGCC 60.360 66.667 0.00 0.00 34.66 5.36
3539 4860 2.360475 GGGTGCTCTGAACCTGGC 60.360 66.667 0.00 0.00 37.85 4.85
3540 4861 0.679002 CATGGGTGCTCTGAACCTGG 60.679 60.000 0.00 0.00 37.85 4.45
3541 4862 0.037303 ACATGGGTGCTCTGAACCTG 59.963 55.000 0.00 0.00 37.85 4.00
3542 4863 1.656587 TACATGGGTGCTCTGAACCT 58.343 50.000 0.00 0.00 37.85 3.50
3543 4864 2.717639 ATACATGGGTGCTCTGAACC 57.282 50.000 0.00 0.00 36.94 3.62
3544 4865 3.123804 CGTATACATGGGTGCTCTGAAC 58.876 50.000 3.32 0.00 0.00 3.18
3545 4866 2.102420 CCGTATACATGGGTGCTCTGAA 59.898 50.000 3.32 0.00 0.00 3.02
3546 4867 1.686587 CCGTATACATGGGTGCTCTGA 59.313 52.381 3.32 0.00 0.00 3.27
3547 4868 1.873903 GCCGTATACATGGGTGCTCTG 60.874 57.143 3.32 0.00 0.00 3.35
3548 4869 0.393077 GCCGTATACATGGGTGCTCT 59.607 55.000 3.32 0.00 0.00 4.09
3549 4870 0.602905 GGCCGTATACATGGGTGCTC 60.603 60.000 3.32 0.00 0.00 4.26
3550 4871 1.054406 AGGCCGTATACATGGGTGCT 61.054 55.000 3.32 0.00 0.00 4.40
3551 4872 0.682852 TAGGCCGTATACATGGGTGC 59.317 55.000 3.32 0.00 0.00 5.01
3552 4873 3.132289 CCTATAGGCCGTATACATGGGTG 59.868 52.174 5.67 0.00 0.00 4.61
3553 4874 3.245875 ACCTATAGGCCGTATACATGGGT 60.246 47.826 19.25 3.27 39.32 4.51
3554 4875 3.132289 CACCTATAGGCCGTATACATGGG 59.868 52.174 19.25 2.65 39.32 4.00
3555 4876 4.021229 TCACCTATAGGCCGTATACATGG 58.979 47.826 19.25 0.00 39.32 3.66
3556 4877 5.047590 TGTTCACCTATAGGCCGTATACATG 60.048 44.000 19.25 6.31 39.32 3.21
3557 4878 5.081728 TGTTCACCTATAGGCCGTATACAT 58.918 41.667 19.25 0.00 39.32 2.29
3558 4879 4.472496 TGTTCACCTATAGGCCGTATACA 58.528 43.478 19.25 11.24 39.32 2.29
3559 4880 4.763793 TCTGTTCACCTATAGGCCGTATAC 59.236 45.833 19.25 8.96 39.32 1.47
3560 4881 4.989277 TCTGTTCACCTATAGGCCGTATA 58.011 43.478 19.25 2.16 39.32 1.47
3561 4882 3.827302 CTCTGTTCACCTATAGGCCGTAT 59.173 47.826 19.25 0.00 39.32 3.06
3562 4883 3.220110 CTCTGTTCACCTATAGGCCGTA 58.780 50.000 19.25 1.38 39.32 4.02
3563 4884 2.032620 CTCTGTTCACCTATAGGCCGT 58.967 52.381 19.25 0.00 39.32 5.68
3564 4885 2.032620 ACTCTGTTCACCTATAGGCCG 58.967 52.381 19.25 10.44 39.32 6.13
3565 4886 4.489306 AAACTCTGTTCACCTATAGGCC 57.511 45.455 19.25 0.00 39.32 5.19
3566 4887 5.938125 TGAAAAACTCTGTTCACCTATAGGC 59.062 40.000 19.25 2.89 39.32 3.93
3567 4888 7.365840 GTGAAAAACTCTGTTCACCTATAGG 57.634 40.000 17.73 17.73 45.13 2.57
3575 4896 6.507958 TTCATGTGTGAAAAACTCTGTTCA 57.492 33.333 0.00 0.00 41.22 3.18
3576 4897 7.992180 AATTCATGTGTGAAAAACTCTGTTC 57.008 32.000 0.00 0.00 46.67 3.18
3577 4898 8.686334 ACTAATTCATGTGTGAAAAACTCTGTT 58.314 29.630 0.00 0.00 46.67 3.16
3578 4899 8.225603 ACTAATTCATGTGTGAAAAACTCTGT 57.774 30.769 0.00 0.00 46.67 3.41
3579 4900 9.817365 CTACTAATTCATGTGTGAAAAACTCTG 57.183 33.333 0.00 0.00 46.67 3.35
3580 4901 9.561069 ACTACTAATTCATGTGTGAAAAACTCT 57.439 29.630 0.00 0.00 46.67 3.24
3583 4904 9.394477 GGAACTACTAATTCATGTGTGAAAAAC 57.606 33.333 0.00 0.00 46.67 2.43
3584 4905 9.126151 TGGAACTACTAATTCATGTGTGAAAAA 57.874 29.630 0.00 0.00 46.67 1.94
3585 4906 8.684386 TGGAACTACTAATTCATGTGTGAAAA 57.316 30.769 0.00 0.00 46.67 2.29
3586 4907 8.729756 CATGGAACTACTAATTCATGTGTGAAA 58.270 33.333 0.00 0.00 46.67 2.69
3588 4909 6.316140 GCATGGAACTACTAATTCATGTGTGA 59.684 38.462 0.00 0.00 0.00 3.58
3589 4910 6.458751 GGCATGGAACTACTAATTCATGTGTG 60.459 42.308 0.00 0.00 0.00 3.82
3590 4911 5.590259 GGCATGGAACTACTAATTCATGTGT 59.410 40.000 0.00 0.00 0.00 3.72
3591 4912 5.009010 GGGCATGGAACTACTAATTCATGTG 59.991 44.000 0.00 0.00 0.00 3.21
3592 4913 5.103940 AGGGCATGGAACTACTAATTCATGT 60.104 40.000 0.00 0.00 0.00 3.21
3593 4914 5.380043 AGGGCATGGAACTACTAATTCATG 58.620 41.667 0.00 0.00 0.00 3.07
3594 4915 5.653255 AGGGCATGGAACTACTAATTCAT 57.347 39.130 0.00 0.00 0.00 2.57
3595 4916 6.569127 TTAGGGCATGGAACTACTAATTCA 57.431 37.500 0.00 0.00 0.00 2.57
3596 4917 7.875327 TTTTAGGGCATGGAACTACTAATTC 57.125 36.000 0.00 0.00 0.00 2.17
3619 4940 5.876612 TCTTTTGCTGCATGTTTGTTTTT 57.123 30.435 1.84 0.00 0.00 1.94
3620 4941 5.354792 ACATCTTTTGCTGCATGTTTGTTTT 59.645 32.000 1.84 0.00 0.00 2.43
3621 4942 4.877251 ACATCTTTTGCTGCATGTTTGTTT 59.123 33.333 1.84 0.00 0.00 2.83
3622 4943 4.444536 ACATCTTTTGCTGCATGTTTGTT 58.555 34.783 1.84 0.00 0.00 2.83
3623 4944 4.053295 GACATCTTTTGCTGCATGTTTGT 58.947 39.130 1.84 4.37 29.43 2.83
3624 4945 4.052608 TGACATCTTTTGCTGCATGTTTG 58.947 39.130 1.84 0.99 29.43 2.93
3625 4946 4.325028 TGACATCTTTTGCTGCATGTTT 57.675 36.364 1.84 0.00 29.43 2.83
3626 4947 4.325028 TTGACATCTTTTGCTGCATGTT 57.675 36.364 1.84 0.00 29.43 2.71
3627 4948 4.325028 TTTGACATCTTTTGCTGCATGT 57.675 36.364 1.84 4.06 32.02 3.21
3628 4949 5.660629 TTTTTGACATCTTTTGCTGCATG 57.339 34.783 1.84 0.15 0.00 4.06
3647 4968 7.039011 ACAAGAAAAGGAAGGTCTGAACTTTTT 60.039 33.333 9.69 6.37 40.32 1.94
3648 4969 6.437477 ACAAGAAAAGGAAGGTCTGAACTTTT 59.563 34.615 9.69 0.00 42.20 2.27
3649 4970 5.952347 ACAAGAAAAGGAAGGTCTGAACTTT 59.048 36.000 9.69 0.00 33.19 2.66
3650 4971 5.510430 ACAAGAAAAGGAAGGTCTGAACTT 58.490 37.500 7.87 7.87 0.00 2.66
3651 4972 5.117406 ACAAGAAAAGGAAGGTCTGAACT 57.883 39.130 0.00 0.00 0.00 3.01
3652 4973 6.937436 TTACAAGAAAAGGAAGGTCTGAAC 57.063 37.500 0.00 0.00 0.00 3.18
3653 4974 9.635404 TTTATTACAAGAAAAGGAAGGTCTGAA 57.365 29.630 0.00 0.00 0.00 3.02
3654 4975 9.635404 TTTTATTACAAGAAAAGGAAGGTCTGA 57.365 29.630 0.00 0.00 0.00 3.27
3674 4995 9.906660 TCTGCAACGTCTGATTTTTATTTTATT 57.093 25.926 0.00 0.00 0.00 1.40
3675 4996 9.341899 GTCTGCAACGTCTGATTTTTATTTTAT 57.658 29.630 0.00 0.00 0.00 1.40
3676 4997 7.532546 CGTCTGCAACGTCTGATTTTTATTTTA 59.467 33.333 11.62 0.00 46.42 1.52
3677 4998 6.359617 CGTCTGCAACGTCTGATTTTTATTTT 59.640 34.615 11.62 0.00 46.42 1.82
3678 4999 5.851177 CGTCTGCAACGTCTGATTTTTATTT 59.149 36.000 11.62 0.00 46.42 1.40
3679 5000 5.382303 CGTCTGCAACGTCTGATTTTTATT 58.618 37.500 11.62 0.00 46.42 1.40
3680 5001 4.957971 CGTCTGCAACGTCTGATTTTTAT 58.042 39.130 11.62 0.00 46.42 1.40
3681 5002 4.383774 CGTCTGCAACGTCTGATTTTTA 57.616 40.909 11.62 0.00 46.42 1.52
3682 5003 3.253371 CGTCTGCAACGTCTGATTTTT 57.747 42.857 11.62 0.00 46.42 1.94
3683 5004 2.949714 CGTCTGCAACGTCTGATTTT 57.050 45.000 11.62 0.00 46.42 1.82
3696 5017 7.645340 AGTTAATATGATGCATTTTTCGTCTGC 59.355 33.333 0.00 0.00 36.45 4.26


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

AutoCloner maintained by Alex Coulton.