Multiple sequence alignment - TraesCS7D01G506400

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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 TraesCS7D01G506400 chr7D 100.000 5543 0 0 1 5543 611264662 611259120 0.000000e+00 10237.0
1 TraesCS7D01G506400 chr7D 85.821 268 26 2 2 257 611265769 611266036 1.970000e-69 274.0
2 TraesCS7D01G506400 chr7D 83.333 210 26 6 3079 3285 600885371 600885574 9.480000e-43 185.0
3 TraesCS7D01G506400 chr7B 95.080 2927 77 18 1 2911 700423993 700421118 0.000000e+00 4545.0
4 TraesCS7D01G506400 chr7B 91.142 779 54 8 3343 4106 700420664 700419886 0.000000e+00 1042.0
5 TraesCS7D01G506400 chr7B 87.387 444 38 8 4128 4554 700419517 700419075 1.390000e-135 494.0
6 TraesCS7D01G506400 chr7B 93.056 216 12 3 2932 3146 700420883 700420670 4.170000e-81 313.0
7 TraesCS7D01G506400 chr7B 85.185 270 25 5 2 257 700425088 700425356 4.260000e-66 263.0
8 TraesCS7D01G506400 chr7B 79.787 282 39 10 678 944 687546178 687546456 7.330000e-44 189.0
9 TraesCS7D01G506400 chr7A 91.312 2210 122 30 736 2911 701311683 701309510 0.000000e+00 2953.0
10 TraesCS7D01G506400 chr7A 90.268 1007 63 18 4551 5543 701307329 701306344 0.000000e+00 1284.0
11 TraesCS7D01G506400 chr7A 92.121 825 60 4 3284 4105 701308905 701308083 0.000000e+00 1158.0
12 TraesCS7D01G506400 chr7A 91.542 201 14 3 2969 3167 701309113 701308914 1.970000e-69 274.0
13 TraesCS7D01G506400 chr7A 85.766 274 18 8 4129 4388 701307707 701307441 2.540000e-68 270.0
14 TraesCS7D01G506400 chr7A 86.800 250 18 5 1 239 701311923 701311678 1.180000e-66 265.0
15 TraesCS7D01G506400 chr7A 83.516 273 27 13 2 257 701313091 701313362 7.180000e-59 239.0
16 TraesCS7D01G506400 chr7A 100.000 28 0 0 5115 5142 540201720 540201747 1.000000e-02 52.8
17 TraesCS7D01G506400 chr6A 85.848 749 70 18 2193 2911 427452232 427451490 0.000000e+00 763.0
18 TraesCS7D01G506400 chr6A 88.843 484 42 8 3287 3767 427451075 427450601 8.000000e-163 584.0
19 TraesCS7D01G506400 chr6A 85.686 503 52 8 995 1496 427453184 427452701 3.830000e-141 512.0
20 TraesCS7D01G506400 chr6A 83.796 432 44 9 4129 4554 427450129 427449718 2.420000e-103 387.0
21 TraesCS7D01G506400 chr6A 81.308 214 29 5 742 944 567344765 567344552 4.440000e-36 163.0
22 TraesCS7D01G506400 chr6B 84.605 747 77 15 2193 2911 457873786 457874522 0.000000e+00 708.0
23 TraesCS7D01G506400 chr6B 89.278 485 38 10 3287 3767 457874941 457875415 3.700000e-166 595.0
24 TraesCS7D01G506400 chr6B 87.327 505 60 4 995 1496 457872817 457873320 4.820000e-160 575.0
25 TraesCS7D01G506400 chr6B 83.945 436 43 11 4126 4554 457876121 457876536 5.210000e-105 392.0
26 TraesCS7D01G506400 chr6D 84.986 706 76 12 2232 2911 293315608 293316309 0.000000e+00 689.0
27 TraesCS7D01G506400 chr6D 89.050 484 41 8 3287 3767 293316823 293317297 1.720000e-164 590.0
28 TraesCS7D01G506400 chr6D 89.315 365 38 1 995 1358 293314879 293315243 1.820000e-124 457.0
29 TraesCS7D01G506400 chr6D 83.486 436 46 9 4126 4554 293317768 293318184 3.130000e-102 383.0
30 TraesCS7D01G506400 chr5B 81.004 279 31 14 648 906 19589225 19588949 9.420000e-48 202.0
31 TraesCS7D01G506400 chr5B 82.857 140 15 5 795 925 19589422 19589561 3.510000e-22 117.0
32 TraesCS7D01G506400 chr5B 84.946 93 14 0 3079 3171 655703192 655703284 1.640000e-15 95.3
33 TraesCS7D01G506400 chr5B 83.838 99 7 3 3063 3160 347700906 347700996 9.890000e-13 86.1
34 TraesCS7D01G506400 chr1D 80.727 275 32 9 3 257 472422485 472422758 1.580000e-45 195.0
35 TraesCS7D01G506400 chr1D 78.512 242 28 16 680 898 369912313 369912553 2.690000e-28 137.0
36 TraesCS7D01G506400 chr5D 83.333 216 25 6 3081 3289 278634168 278633957 7.330000e-44 189.0
37 TraesCS7D01G506400 chr5D 96.154 52 1 1 874 925 529749300 529749350 3.560000e-12 84.2
38 TraesCS7D01G506400 chr1B 80.132 151 21 7 3101 3251 510200982 510201123 2.730000e-18 104.0
39 TraesCS7D01G506400 chr3A 84.416 77 11 1 870 945 64319302 64319226 2.140000e-09 75.0
40 TraesCS7D01G506400 chr3A 100.000 29 0 0 3139 3167 627255088 627255060 3.000000e-03 54.7
41 TraesCS7D01G506400 chr3B 88.333 60 3 4 3064 3121 263785121 263785064 9.960000e-08 69.4
42 TraesCS7D01G506400 chr3D 95.238 42 0 2 3079 3119 185065294 185065334 1.290000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G506400 chr7D 611259120 611264662 5542 True 10237.00 10237 100.000000 1 5543 1 chr7D.!!$R1 5542
1 TraesCS7D01G506400 chr7B 700419075 700423993 4918 True 1598.50 4545 91.666250 1 4554 4 chr7B.!!$R1 4553
2 TraesCS7D01G506400 chr7A 701306344 701311923 5579 True 1034.00 2953 89.634833 1 5543 6 chr7A.!!$R1 5542
3 TraesCS7D01G506400 chr6A 427449718 427453184 3466 True 561.50 763 86.043250 995 4554 4 chr6A.!!$R2 3559
4 TraesCS7D01G506400 chr6B 457872817 457876536 3719 False 567.50 708 86.288750 995 4554 4 chr6B.!!$F1 3559
5 TraesCS7D01G506400 chr6D 293314879 293318184 3305 False 529.75 689 86.709250 995 4554 4 chr6D.!!$F1 3559

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
296 310 0.165511 AGCGTGAGACGTCGTACTTC 59.834 55.000 10.46 2.11 44.73 3.01 F
664 678 1.072159 GCTGGTGACCTGACTTGCT 59.928 57.895 13.05 0.00 0.00 3.91 F
712 726 1.153349 CTAGGGTTGAAGAGGCGCC 60.153 63.158 21.89 21.89 0.00 6.53 F
3070 3636 1.002857 AGCTTAAGGTCAAGGGCCAT 58.997 50.000 6.18 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1107 1121 1.629043 ACTGGAGGCAGTACTCGAAA 58.371 50.000 0.00 0.0 38.39 3.46 R
2220 2260 1.981256 TCCAGCAGAAGTTTTGACCC 58.019 50.000 0.00 0.0 0.00 4.46 R
3077 3643 3.825623 AGCCAGCCATAAGCCCCC 61.826 66.667 0.00 0.0 45.47 5.40 R
5288 6566 0.038892 CATTCCAGCTGTGGTGTTGC 60.039 55.000 13.81 0.0 45.28 4.17 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
25 26 7.797121 AGTTAAGGAATTCCATGGTGAAATT 57.203 32.000 26.22 10.55 38.89 1.82
28 29 9.936759 GTTAAGGAATTCCATGGTGAAATTTTA 57.063 29.630 26.22 8.53 38.89 1.52
40 41 5.534278 TGGTGAAATTTTAGTCAGCATGTGA 59.466 36.000 5.80 0.00 44.84 3.58
110 122 0.615850 AAGAGCCTAAGGTGCAGGAC 59.384 55.000 0.00 0.00 34.91 3.85
221 234 5.534207 TCTTGCCATTTGTTCTCATTGTT 57.466 34.783 0.00 0.00 0.00 2.83
250 263 7.816640 TCTCTTATTTTAGGTGCATGTTCAAC 58.183 34.615 0.00 0.00 0.00 3.18
280 293 2.032528 TCTTTCAGCCACCCAGCG 59.967 61.111 0.00 0.00 38.01 5.18
296 310 0.165511 AGCGTGAGACGTCGTACTTC 59.834 55.000 10.46 2.11 44.73 3.01
319 333 3.784701 TTCTTTCTGCTAGTAGAGGCG 57.215 47.619 10.59 4.13 0.00 5.52
322 336 1.182667 TTCTGCTAGTAGAGGCGCAA 58.817 50.000 10.83 0.00 31.24 4.85
347 361 1.613925 TCTTGTCCTCCAACTCAGTCG 59.386 52.381 0.00 0.00 0.00 4.18
370 384 8.223769 GTCGCCTTCATACTAATATTCAACATG 58.776 37.037 0.00 0.00 0.00 3.21
443 457 2.360165 GCTGTAATCTTCCAAGGGCATG 59.640 50.000 0.00 0.00 0.00 4.06
459 473 1.526887 GCATGCATACGTACGCAAGAT 59.473 47.619 21.09 0.85 42.37 2.40
515 529 4.040461 TGGAAGAATACACTAGCTATGGCC 59.960 45.833 0.00 0.00 39.73 5.36
526 540 2.412591 AGCTATGGCCTGTGGACTATT 58.587 47.619 3.32 0.00 39.73 1.73
611 625 7.467557 ACGAGAGTACTACTTAAATCGAGAG 57.532 40.000 15.31 0.00 46.88 3.20
612 626 7.264221 ACGAGAGTACTACTTAAATCGAGAGA 58.736 38.462 15.31 0.00 46.88 3.10
613 627 7.436080 ACGAGAGTACTACTTAAATCGAGAGAG 59.564 40.741 15.31 0.00 44.93 3.20
664 678 1.072159 GCTGGTGACCTGACTTGCT 59.928 57.895 13.05 0.00 0.00 3.91
691 705 3.310774 CCACAACGGATGATGAGTTGATC 59.689 47.826 13.48 0.00 45.66 2.92
712 726 1.153349 CTAGGGTTGAAGAGGCGCC 60.153 63.158 21.89 21.89 0.00 6.53
714 728 2.180159 TAGGGTTGAAGAGGCGCCAC 62.180 60.000 31.54 24.27 0.00 5.01
715 729 3.056328 GGTTGAAGAGGCGCCACC 61.056 66.667 31.54 22.40 39.61 4.61
731 745 2.513204 CCTGATGAGGTGCGGCTG 60.513 66.667 0.00 0.00 34.16 4.85
732 746 3.200593 CTGATGAGGTGCGGCTGC 61.201 66.667 11.65 11.65 43.20 5.25
733 747 3.677284 CTGATGAGGTGCGGCTGCT 62.677 63.158 20.27 0.00 43.34 4.24
947 961 5.574188 AGCAATTAGTGAAATTCCTCCTGT 58.426 37.500 0.00 0.00 35.54 4.00
1011 1025 1.428869 CAGGAGGTATGGAAGGGGAG 58.571 60.000 0.00 0.00 0.00 4.30
1107 1121 2.586792 GATGTCCGCTTCCAGGCT 59.413 61.111 0.00 0.00 0.00 4.58
1203 1219 3.118555 ACTGGTTTTGTTAACTTTGCCCC 60.119 43.478 7.22 0.57 0.00 5.80
1326 1342 6.823286 TCAGGATCCAATATAACTGAACCA 57.177 37.500 15.82 0.00 32.60 3.67
1376 1392 5.428253 GCACTACCAGATTCTAAATGGTCA 58.572 41.667 0.00 0.00 43.94 4.02
1426 1442 9.193133 ACATGCTAATAATGTTACGTCATCTAC 57.807 33.333 0.00 0.00 34.60 2.59
1521 1544 3.274393 CTGACTGCAGTATACGGCC 57.726 57.895 21.73 5.88 37.37 6.13
2911 2986 3.582208 AGCAAGACCTTCTGATTCTCAGT 59.418 43.478 4.21 0.00 44.58 3.41
2912 2987 4.041444 AGCAAGACCTTCTGATTCTCAGTT 59.959 41.667 4.21 0.00 44.58 3.16
2916 2991 6.371595 AGACCTTCTGATTCTCAGTTCAAT 57.628 37.500 4.21 0.00 44.58 2.57
2919 2994 8.547173 AGACCTTCTGATTCTCAGTTCAATATT 58.453 33.333 4.21 0.00 44.58 1.28
2920 2995 9.823647 GACCTTCTGATTCTCAGTTCAATATTA 57.176 33.333 4.21 0.00 44.58 0.98
3070 3636 1.002857 AGCTTAAGGTCAAGGGCCAT 58.997 50.000 6.18 0.00 0.00 4.40
3073 3639 2.567169 GCTTAAGGTCAAGGGCCATTTT 59.433 45.455 6.18 0.00 0.00 1.82
3109 3675 1.747355 CTGGCTGTGGAAATAAGCTGG 59.253 52.381 0.00 0.00 37.12 4.85
3127 3693 0.032117 GGCCCTTCCCCAGCTTATTT 60.032 55.000 0.00 0.00 0.00 1.40
3191 3757 8.376803 AGTTAACCATTACTTAGTAGGCTTCT 57.623 34.615 0.88 0.00 0.00 2.85
3192 3758 9.484806 AGTTAACCATTACTTAGTAGGCTTCTA 57.515 33.333 0.88 0.00 0.00 2.10
3223 3789 8.791327 AATAAATAAATTGGTTGGGCTTCTTG 57.209 30.769 0.00 0.00 0.00 3.02
3224 3790 6.432403 AAATAAATTGGTTGGGCTTCTTGA 57.568 33.333 0.00 0.00 0.00 3.02
3225 3791 6.432403 AATAAATTGGTTGGGCTTCTTGAA 57.568 33.333 0.00 0.00 0.00 2.69
3226 3792 4.980339 AAATTGGTTGGGCTTCTTGAAT 57.020 36.364 0.00 0.00 0.00 2.57
3227 3793 7.732222 ATAAATTGGTTGGGCTTCTTGAATA 57.268 32.000 0.00 0.00 0.00 1.75
3228 3794 6.432403 AAATTGGTTGGGCTTCTTGAATAA 57.568 33.333 0.00 0.00 0.00 1.40
3229 3795 5.665916 ATTGGTTGGGCTTCTTGAATAAG 57.334 39.130 0.00 0.00 35.16 1.73
3230 3796 2.825532 TGGTTGGGCTTCTTGAATAAGC 59.174 45.455 6.74 6.74 46.90 3.09
3231 3797 3.092301 GGTTGGGCTTCTTGAATAAGCT 58.908 45.455 13.79 0.00 46.81 3.74
3232 3798 4.263727 TGGTTGGGCTTCTTGAATAAGCTA 60.264 41.667 13.79 2.87 46.81 3.32
3233 3799 4.336713 GGTTGGGCTTCTTGAATAAGCTAG 59.663 45.833 13.79 0.00 46.81 3.42
3234 3800 4.844349 TGGGCTTCTTGAATAAGCTAGT 57.156 40.909 13.79 0.00 46.81 2.57
3235 3801 4.517285 TGGGCTTCTTGAATAAGCTAGTG 58.483 43.478 13.79 0.00 46.81 2.74
3236 3802 4.225042 TGGGCTTCTTGAATAAGCTAGTGA 59.775 41.667 13.79 0.00 46.81 3.41
3237 3803 4.813697 GGGCTTCTTGAATAAGCTAGTGAG 59.186 45.833 13.79 0.00 46.81 3.51
3238 3804 5.395768 GGGCTTCTTGAATAAGCTAGTGAGA 60.396 44.000 13.79 0.00 46.81 3.27
3239 3805 5.752955 GGCTTCTTGAATAAGCTAGTGAGAG 59.247 44.000 13.79 0.00 46.81 3.20
3240 3806 5.752955 GCTTCTTGAATAAGCTAGTGAGAGG 59.247 44.000 7.90 0.00 44.75 3.69
3241 3807 5.860941 TCTTGAATAAGCTAGTGAGAGGG 57.139 43.478 0.00 0.00 33.82 4.30
3242 3808 5.273208 TCTTGAATAAGCTAGTGAGAGGGT 58.727 41.667 0.00 0.00 33.82 4.34
3243 3809 6.432581 TCTTGAATAAGCTAGTGAGAGGGTA 58.567 40.000 0.00 0.00 33.82 3.69
3244 3810 6.547880 TCTTGAATAAGCTAGTGAGAGGGTAG 59.452 42.308 0.00 0.00 33.82 3.18
3245 3811 4.585162 TGAATAAGCTAGTGAGAGGGTAGC 59.415 45.833 0.00 0.00 39.64 3.58
3247 3813 2.838637 AGCTAGTGAGAGGGTAGCTT 57.161 50.000 0.00 0.00 45.82 3.74
3248 3814 3.955524 AGCTAGTGAGAGGGTAGCTTA 57.044 47.619 0.00 0.00 45.82 3.09
3249 3815 4.463050 AGCTAGTGAGAGGGTAGCTTAT 57.537 45.455 0.00 0.00 45.82 1.73
3250 3816 4.810345 AGCTAGTGAGAGGGTAGCTTATT 58.190 43.478 0.00 0.00 45.82 1.40
3251 3817 5.212745 AGCTAGTGAGAGGGTAGCTTATTT 58.787 41.667 0.00 0.00 45.82 1.40
3252 3818 5.303333 AGCTAGTGAGAGGGTAGCTTATTTC 59.697 44.000 0.00 0.00 45.82 2.17
3253 3819 5.510009 GCTAGTGAGAGGGTAGCTTATTTCC 60.510 48.000 0.00 0.00 36.93 3.13
3254 3820 3.385111 AGTGAGAGGGTAGCTTATTTCCG 59.615 47.826 0.00 0.00 0.00 4.30
3255 3821 2.102588 TGAGAGGGTAGCTTATTTCCGC 59.897 50.000 0.00 0.00 0.00 5.54
3256 3822 2.102588 GAGAGGGTAGCTTATTTCCGCA 59.897 50.000 0.00 0.00 0.00 5.69
3257 3823 2.103263 AGAGGGTAGCTTATTTCCGCAG 59.897 50.000 0.00 0.00 0.00 5.18
3258 3824 0.945099 GGGTAGCTTATTTCCGCAGC 59.055 55.000 0.00 0.00 0.00 5.25
3259 3825 0.945099 GGTAGCTTATTTCCGCAGCC 59.055 55.000 0.00 0.00 33.73 4.85
3260 3826 1.663695 GTAGCTTATTTCCGCAGCCA 58.336 50.000 0.00 0.00 33.73 4.75
3261 3827 1.599542 GTAGCTTATTTCCGCAGCCAG 59.400 52.381 0.00 0.00 33.73 4.85
3262 3828 1.064783 GCTTATTTCCGCAGCCAGC 59.935 57.895 0.00 0.00 40.87 4.85
3263 3829 1.729881 CTTATTTCCGCAGCCAGCC 59.270 57.895 0.00 0.00 41.38 4.85
3264 3830 1.001517 TTATTTCCGCAGCCAGCCA 60.002 52.632 0.00 0.00 41.38 4.75
3265 3831 0.395586 TTATTTCCGCAGCCAGCCAT 60.396 50.000 0.00 0.00 41.38 4.40
3266 3832 0.472044 TATTTCCGCAGCCAGCCATA 59.528 50.000 0.00 0.00 41.38 2.74
3267 3833 0.395586 ATTTCCGCAGCCAGCCATAA 60.396 50.000 0.00 0.00 41.38 1.90
3268 3834 1.312371 TTTCCGCAGCCAGCCATAAC 61.312 55.000 0.00 0.00 41.38 1.89
3269 3835 3.211963 CCGCAGCCAGCCATAACC 61.212 66.667 0.00 0.00 41.38 2.85
3270 3836 3.211963 CGCAGCCAGCCATAACCC 61.212 66.667 0.00 0.00 41.38 4.11
3271 3837 2.834968 GCAGCCAGCCATAACCCC 60.835 66.667 0.00 0.00 37.23 4.95
3272 3838 2.682846 CAGCCAGCCATAACCCCA 59.317 61.111 0.00 0.00 0.00 4.96
3273 3839 1.000233 CAGCCAGCCATAACCCCAA 60.000 57.895 0.00 0.00 0.00 4.12
3274 3840 0.614415 CAGCCAGCCATAACCCCAAA 60.614 55.000 0.00 0.00 0.00 3.28
3275 3841 0.116143 AGCCAGCCATAACCCCAAAA 59.884 50.000 0.00 0.00 0.00 2.44
3276 3842 0.536724 GCCAGCCATAACCCCAAAAG 59.463 55.000 0.00 0.00 0.00 2.27
3277 3843 1.894978 GCCAGCCATAACCCCAAAAGA 60.895 52.381 0.00 0.00 0.00 2.52
3278 3844 2.534990 CCAGCCATAACCCCAAAAGAA 58.465 47.619 0.00 0.00 0.00 2.52
3279 3845 2.233676 CCAGCCATAACCCCAAAAGAAC 59.766 50.000 0.00 0.00 0.00 3.01
3280 3846 3.165071 CAGCCATAACCCCAAAAGAACT 58.835 45.455 0.00 0.00 0.00 3.01
3281 3847 3.056607 CAGCCATAACCCCAAAAGAACTG 60.057 47.826 0.00 0.00 0.00 3.16
3282 3848 2.233676 GCCATAACCCCAAAAGAACTGG 59.766 50.000 0.00 0.00 0.00 4.00
3313 3879 5.182001 AGCTTGTTTGCAATAAGGTACTCAG 59.818 40.000 20.43 8.61 38.33 3.35
3337 3903 7.842721 CAGTAAATCATACGTTTACGGCTTTAC 59.157 37.037 7.24 11.26 43.41 2.01
3338 3904 6.724694 AAATCATACGTTTACGGCTTTACA 57.275 33.333 7.24 0.00 44.95 2.41
3342 3908 2.548875 ACGTTTACGGCTTTACACACA 58.451 42.857 7.24 0.00 44.95 3.72
3357 3925 6.516739 TTACACACATTTGGTTCACTGAAA 57.483 33.333 0.00 0.00 0.00 2.69
3405 3974 4.333372 ACAACCTGCATTTTCAAAAAGCAG 59.667 37.500 26.24 26.24 42.73 4.24
3406 3975 4.141233 ACCTGCATTTTCAAAAAGCAGT 57.859 36.364 29.01 18.63 42.21 4.40
3692 4270 5.269505 AGGCAAGCTACATACAAGAGTAG 57.730 43.478 0.00 0.00 40.45 2.57
3769 4347 7.754624 TCAGGATAATATTGAAGGTATGCCAA 58.245 34.615 1.54 0.00 37.19 4.52
3795 4373 9.717942 ATAGATTCAGTAATGAATACCTCAAGC 57.282 33.333 17.72 3.99 38.50 4.01
3806 4384 5.600484 TGAATACCTCAAGCAAAGGGAAAAA 59.400 36.000 4.35 0.00 38.29 1.94
3886 4464 6.862209 TCTGCATATCCAAATTACGCTTTTT 58.138 32.000 0.00 0.00 0.00 1.94
3938 4516 5.941058 TCAGGTTGTAGTTTTGACTTCAACA 59.059 36.000 21.93 7.16 44.44 3.33
3993 4575 7.076842 TGCTTTCTGAATATCACAAGCTTAC 57.923 36.000 0.00 0.00 37.96 2.34
4106 4762 5.583854 CAGTTGAGATGATTAGTGAAGGGTG 59.416 44.000 0.00 0.00 0.00 4.61
4107 4763 5.249393 AGTTGAGATGATTAGTGAAGGGTGT 59.751 40.000 0.00 0.00 0.00 4.16
4108 4764 5.344743 TGAGATGATTAGTGAAGGGTGTC 57.655 43.478 0.00 0.00 0.00 3.67
4109 4765 4.777366 TGAGATGATTAGTGAAGGGTGTCA 59.223 41.667 0.00 0.00 0.00 3.58
4110 4766 5.248248 TGAGATGATTAGTGAAGGGTGTCAA 59.752 40.000 0.00 0.00 0.00 3.18
4112 4768 6.725364 AGATGATTAGTGAAGGGTGTCAATT 58.275 36.000 0.00 0.00 0.00 2.32
4114 4770 7.671398 AGATGATTAGTGAAGGGTGTCAATTTT 59.329 33.333 0.00 0.00 0.00 1.82
4115 4771 7.214467 TGATTAGTGAAGGGTGTCAATTTTC 57.786 36.000 0.00 0.00 0.00 2.29
4116 4772 7.004086 TGATTAGTGAAGGGTGTCAATTTTCT 58.996 34.615 0.00 0.00 0.00 2.52
4122 5309 3.500343 AGGGTGTCAATTTTCTTCCCTG 58.500 45.455 0.00 0.00 41.67 4.45
4123 5310 3.117131 AGGGTGTCAATTTTCTTCCCTGT 60.117 43.478 0.00 0.00 41.67 4.00
4124 5311 3.255888 GGGTGTCAATTTTCTTCCCTGTC 59.744 47.826 0.00 0.00 0.00 3.51
4139 5326 5.772825 TCCCTGTCTCAAAATTTTGTCTG 57.227 39.130 25.98 19.61 39.18 3.51
4154 5341 3.018423 TGTCTGGATAGTGCTGCTAGA 57.982 47.619 0.00 0.00 32.45 2.43
4155 5342 3.570540 TGTCTGGATAGTGCTGCTAGAT 58.429 45.455 0.00 0.00 32.45 1.98
4218 5405 5.594317 GGTTTGGTTCAGAATGTATGCCTAT 59.406 40.000 0.00 0.00 37.40 2.57
4234 5424 3.072330 TGCCTATTCAACTGTCCTGAACA 59.928 43.478 0.00 0.00 35.70 3.18
4376 5586 2.292559 TTTAGCGCCGGGTAAGGGT 61.293 57.895 2.29 0.00 37.42 4.34
4377 5587 2.524951 TTTAGCGCCGGGTAAGGGTG 62.525 60.000 2.29 0.00 37.42 4.61
4382 5592 2.300197 GCCGGGTAAGGGTGGGTTA 61.300 63.158 2.18 0.00 0.00 2.85
4406 5616 4.030913 ACCGTCATTTTCCTCTGGATCTA 58.969 43.478 0.00 0.00 0.00 1.98
4456 5667 2.746472 GCCACACACTTTTCTCTCACCT 60.746 50.000 0.00 0.00 0.00 4.00
4458 5669 3.181461 CCACACACTTTTCTCTCACCTCT 60.181 47.826 0.00 0.00 0.00 3.69
4469 5680 3.960755 TCTCTCACCTCTCTGTTTCACAA 59.039 43.478 0.00 0.00 0.00 3.33
4470 5681 4.405680 TCTCTCACCTCTCTGTTTCACAAA 59.594 41.667 0.00 0.00 0.00 2.83
4534 5745 4.404654 CCGTGAAAGGCTTGCGGC 62.405 66.667 19.82 7.23 35.90 6.53
4554 5766 3.202906 GCAGGAGTAACTTGTGTTGTGA 58.797 45.455 0.00 0.00 37.59 3.58
4555 5767 3.625764 GCAGGAGTAACTTGTGTTGTGAA 59.374 43.478 0.00 0.00 37.59 3.18
4557 5769 5.560953 GCAGGAGTAACTTGTGTTGTGAATC 60.561 44.000 0.00 0.00 37.59 2.52
4559 5771 5.992217 AGGAGTAACTTGTGTTGTGAATCTC 59.008 40.000 0.00 0.00 37.59 2.75
4569 5835 4.627467 GTGTTGTGAATCTCGTCAAGCTAT 59.373 41.667 0.00 0.00 0.00 2.97
4652 5918 4.573607 TGCATGATCAGCAGAGTCATAAAC 59.426 41.667 13.62 0.90 37.02 2.01
4732 5998 1.552792 GAGCATATACTGAGGGAGGGC 59.447 57.143 0.00 0.00 0.00 5.19
4756 6022 3.739300 CCCGGCGTATTCTAACTTGTATG 59.261 47.826 6.01 0.00 0.00 2.39
4759 6025 5.694910 CCGGCGTATTCTAACTTGTATGATT 59.305 40.000 6.01 0.00 0.00 2.57
4813 6079 1.040646 AGGAGTTGAGCACACGAAGA 58.959 50.000 0.00 0.00 0.00 2.87
4837 6114 2.502295 AGCTCTTTCTTCAGCAACAGG 58.498 47.619 0.00 0.00 38.18 4.00
4843 6120 2.669569 TTCAGCAACAGGCCGCTC 60.670 61.111 0.00 0.00 46.50 5.03
4870 6147 7.179076 TCCTCTATAACTTCAACTGGGTAAC 57.821 40.000 0.00 0.00 0.00 2.50
4892 6169 1.577328 CCTGGTGCTTGTGCTTACCG 61.577 60.000 0.00 0.00 37.88 4.02
4906 6183 2.797439 GCTTACCGTCGACAATACCCTC 60.797 54.545 17.16 0.00 0.00 4.30
4910 6187 1.378882 CGTCGACAATACCCTCGGGA 61.379 60.000 17.16 0.00 38.96 5.14
4960 6237 1.101331 GCCTCCAGAATTCTGCAAGG 58.899 55.000 31.66 31.66 43.00 3.61
4988 6265 7.974501 CACTATAGGGTTACTAACACTGTTGAG 59.025 40.741 13.20 5.37 46.63 3.02
5047 6325 1.131883 CTCATTTGAGCTGGGCTTTCG 59.868 52.381 0.00 0.00 39.88 3.46
5075 6353 1.402259 TCAACCATTGTCGCGTTTTGT 59.598 42.857 5.77 0.00 0.00 2.83
5083 6361 2.024588 CGCGTTTTGTGCTGCTGT 59.975 55.556 0.00 0.00 0.00 4.40
5091 6369 4.222114 GTTTTGTGCTGCTGTAGATTCAC 58.778 43.478 0.00 0.00 0.00 3.18
5134 6412 4.399483 TCTTACTACTCCCTGTGTTCCT 57.601 45.455 0.00 0.00 0.00 3.36
5145 6423 7.736893 ACTCCCTGTGTTCCTAAATATATGAC 58.263 38.462 0.00 0.00 0.00 3.06
5171 6449 0.592637 TGAAGTGCCAAAGCGTCATG 59.407 50.000 0.00 0.00 44.31 3.07
5172 6450 0.593128 GAAGTGCCAAAGCGTCATGT 59.407 50.000 0.00 0.00 44.31 3.21
5188 6466 4.202080 CGTCATGTATTTAGGAACGGAGGA 60.202 45.833 0.00 0.00 0.00 3.71
5189 6467 5.290386 GTCATGTATTTAGGAACGGAGGAG 58.710 45.833 0.00 0.00 0.00 3.69
5192 6470 3.449737 TGTATTTAGGAACGGAGGAGGTG 59.550 47.826 0.00 0.00 0.00 4.00
5208 6486 6.456795 AGGAGGTGTCTTTTCTTTTTCAAG 57.543 37.500 0.00 0.00 0.00 3.02
5224 6502 6.588719 TTTTCAAGGATACACCATGGAAAG 57.411 37.500 21.47 10.40 39.15 2.62
5231 6509 4.519610 ACCATGGAAAGGGTGCAC 57.480 55.556 21.47 8.80 35.67 4.57
5254 6532 5.188434 CCAGTATCATTGAAGAAGAGCCAA 58.812 41.667 0.00 0.00 0.00 4.52
5288 6566 3.967734 CCTTTCGGCATACAACACG 57.032 52.632 0.00 0.00 0.00 4.49
5296 6574 0.309302 GCATACAACACGCAACACCA 59.691 50.000 0.00 0.00 0.00 4.17
5302 6580 1.992233 AACACGCAACACCACAGCTG 61.992 55.000 13.48 13.48 0.00 4.24
5303 6581 2.901840 ACGCAACACCACAGCTGG 60.902 61.111 19.93 4.24 44.26 4.85
5310 6588 0.473755 ACACCACAGCTGGAATGACA 59.526 50.000 19.93 0.00 40.55 3.58
5328 6606 2.132762 ACAAAACAACTCGCCTAGTCG 58.867 47.619 0.00 0.00 37.50 4.18
5335 6613 0.322277 ACTCGCCTAGTCGAACCTCA 60.322 55.000 0.00 0.00 38.08 3.86
5358 6636 3.153919 GACACAAAATGGCAAGGAGGTA 58.846 45.455 0.00 0.00 35.73 3.08
5359 6637 3.157087 ACACAAAATGGCAAGGAGGTAG 58.843 45.455 0.00 0.00 0.00 3.18
5360 6638 3.157087 CACAAAATGGCAAGGAGGTAGT 58.843 45.455 0.00 0.00 0.00 2.73
5361 6639 4.202524 ACACAAAATGGCAAGGAGGTAGTA 60.203 41.667 0.00 0.00 0.00 1.82
5384 6662 2.537625 GACTCAAAGATCAAGGATCGCG 59.462 50.000 0.00 0.00 43.17 5.87
5400 6678 1.803943 GCGTCACAACCAACACCAA 59.196 52.632 0.00 0.00 0.00 3.67
5408 6686 1.682854 CAACCAACACCAAGACAGCAT 59.317 47.619 0.00 0.00 0.00 3.79
5459 6742 2.061773 CATAGCGCCTAAGAATCACCG 58.938 52.381 2.29 0.00 0.00 4.94
5460 6743 1.395635 TAGCGCCTAAGAATCACCGA 58.604 50.000 2.29 0.00 0.00 4.69
5461 6744 0.103208 AGCGCCTAAGAATCACCGAG 59.897 55.000 2.29 0.00 0.00 4.63
5462 6745 0.179108 GCGCCTAAGAATCACCGAGT 60.179 55.000 0.00 0.00 0.00 4.18
5463 6746 1.560923 CGCCTAAGAATCACCGAGTG 58.439 55.000 0.00 0.00 34.45 3.51
5464 6747 1.134367 CGCCTAAGAATCACCGAGTGA 59.866 52.381 8.81 8.81 46.90 3.41
5465 6748 2.416836 CGCCTAAGAATCACCGAGTGAA 60.417 50.000 10.17 0.00 45.96 3.18
5466 6749 2.930682 GCCTAAGAATCACCGAGTGAAC 59.069 50.000 10.17 8.07 45.96 3.18
5467 6750 3.616560 GCCTAAGAATCACCGAGTGAACA 60.617 47.826 10.17 0.00 45.96 3.18
5468 6751 4.177026 CCTAAGAATCACCGAGTGAACAG 58.823 47.826 10.17 4.66 45.96 3.16
5469 6752 2.086054 AGAATCACCGAGTGAACAGC 57.914 50.000 10.17 2.33 45.96 4.40
5470 6753 0.716108 GAATCACCGAGTGAACAGCG 59.284 55.000 10.17 0.00 45.96 5.18
5471 6754 0.670546 AATCACCGAGTGAACAGCGG 60.671 55.000 10.17 11.64 45.96 5.52
5472 6755 1.532604 ATCACCGAGTGAACAGCGGA 61.533 55.000 17.85 1.58 45.96 5.54
5473 6756 3.036427 ATCACCGAGTGAACAGCGGAA 62.036 52.381 17.85 8.56 45.96 4.30
5475 6758 3.550656 CGAGTGAACAGCGGAACC 58.449 61.111 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 89 2.367567 AGGCTCTTCGGTTGTTACAAGA 59.632 45.455 0.00 0.00 0.00 3.02
85 97 1.726853 CACCTTAGGCTCTTCGGTTG 58.273 55.000 0.00 0.00 0.00 3.77
110 122 6.708949 ACAAATTGTGGTACTGTTGTAGGTAG 59.291 38.462 0.00 0.00 0.00 3.18
186 199 6.265196 ACAAATGGCAAGAAGAACAGATTGTA 59.735 34.615 0.00 0.00 30.24 2.41
194 207 5.186996 TGAGAACAAATGGCAAGAAGAAC 57.813 39.130 0.00 0.00 0.00 3.01
221 234 6.711277 ACATGCACCTAAAATAAGAGAGTGA 58.289 36.000 0.00 0.00 0.00 3.41
280 293 2.985406 AAGGAAGTACGACGTCTCAC 57.015 50.000 14.70 10.88 0.00 3.51
296 310 4.438148 GCCTCTACTAGCAGAAAGAAAGG 58.562 47.826 0.00 0.00 0.00 3.11
319 333 5.415701 TGAGTTGGAGGACAAGAATATTTGC 59.584 40.000 0.00 0.00 40.38 3.68
322 336 6.380079 ACTGAGTTGGAGGACAAGAATATT 57.620 37.500 0.00 0.00 40.38 1.28
347 361 8.507249 GGACATGTTGAATATTAGTATGAAGGC 58.493 37.037 0.00 0.00 0.00 4.35
389 403 4.142609 ACGACTGGACATGCTGAATATT 57.857 40.909 0.00 0.00 0.00 1.28
392 406 2.079158 CAACGACTGGACATGCTGAAT 58.921 47.619 0.00 0.00 0.00 2.57
393 407 1.511850 CAACGACTGGACATGCTGAA 58.488 50.000 0.00 0.00 0.00 3.02
394 408 0.950555 GCAACGACTGGACATGCTGA 60.951 55.000 0.00 0.00 34.29 4.26
443 457 2.845764 GCAACATCTTGCGTACGTATGC 60.846 50.000 28.80 28.80 43.42 3.14
459 473 7.894753 TTATAGGATTTGGATTCATGCAACA 57.105 32.000 0.00 0.00 37.85 3.33
472 486 9.342308 TCTTCCAGCAAGTAATTATAGGATTTG 57.658 33.333 0.00 0.00 33.27 2.32
515 529 5.647658 TGTTAGGATGCAAAATAGTCCACAG 59.352 40.000 4.66 0.00 33.12 3.66
526 540 9.801873 GCTTAGAATATTTTGTTAGGATGCAAA 57.198 29.630 0.00 0.00 33.40 3.68
596 610 8.572828 TCGTAGTACTCTCTCGATTTAAGTAG 57.427 38.462 0.00 0.00 0.00 2.57
597 611 8.812329 GTTCGTAGTACTCTCTCGATTTAAGTA 58.188 37.037 0.00 0.00 33.27 2.24
598 612 7.463913 CGTTCGTAGTACTCTCTCGATTTAAGT 60.464 40.741 0.00 0.00 33.27 2.24
599 613 6.840292 CGTTCGTAGTACTCTCTCGATTTAAG 59.160 42.308 0.00 0.00 33.27 1.85
600 614 6.311445 ACGTTCGTAGTACTCTCTCGATTTAA 59.689 38.462 0.00 0.00 33.27 1.52
601 615 5.807520 ACGTTCGTAGTACTCTCTCGATTTA 59.192 40.000 0.00 0.00 33.27 1.40
602 616 4.629200 ACGTTCGTAGTACTCTCTCGATTT 59.371 41.667 0.00 0.00 33.27 2.17
603 617 4.180057 ACGTTCGTAGTACTCTCTCGATT 58.820 43.478 0.00 0.00 33.27 3.34
604 618 3.779759 ACGTTCGTAGTACTCTCTCGAT 58.220 45.455 0.00 0.00 33.27 3.59
605 619 3.223423 ACGTTCGTAGTACTCTCTCGA 57.777 47.619 0.00 3.51 0.00 4.04
606 620 3.539210 CGAACGTTCGTAGTACTCTCTCG 60.539 52.174 35.92 11.90 45.09 4.04
607 621 3.910328 CGAACGTTCGTAGTACTCTCTC 58.090 50.000 35.92 3.33 45.09 3.20
608 622 3.987807 CGAACGTTCGTAGTACTCTCT 57.012 47.619 35.92 0.00 45.09 3.10
664 678 3.620419 ATCATCCGTTGTGGCGCCA 62.620 57.895 29.03 29.03 37.80 5.69
691 705 1.153349 GCCTCTTCAACCCTAGGCG 60.153 63.158 2.05 0.00 44.63 5.52
714 728 2.513204 CAGCCGCACCTCATCAGG 60.513 66.667 0.00 0.00 46.87 3.86
715 729 3.200593 GCAGCCGCACCTCATCAG 61.201 66.667 0.00 0.00 38.36 2.90
716 730 3.709633 AGCAGCCGCACCTCATCA 61.710 61.111 0.00 0.00 42.27 3.07
717 731 3.200593 CAGCAGCCGCACCTCATC 61.201 66.667 0.00 0.00 42.27 2.92
718 732 3.557903 AACAGCAGCCGCACCTCAT 62.558 57.895 0.00 0.00 42.27 2.90
719 733 3.772853 AAACAGCAGCCGCACCTCA 62.773 57.895 0.00 0.00 42.27 3.86
720 734 2.980233 AAACAGCAGCCGCACCTC 60.980 61.111 0.00 0.00 42.27 3.85
721 735 3.289834 CAAACAGCAGCCGCACCT 61.290 61.111 0.00 0.00 42.27 4.00
722 736 4.347453 CCAAACAGCAGCCGCACC 62.347 66.667 0.00 0.00 42.27 5.01
723 737 4.347453 CCCAAACAGCAGCCGCAC 62.347 66.667 0.00 0.00 42.27 5.34
724 738 4.892965 ACCCAAACAGCAGCCGCA 62.893 61.111 0.00 0.00 42.27 5.69
725 739 4.347453 CACCCAAACAGCAGCCGC 62.347 66.667 0.00 0.00 38.99 6.53
726 740 3.673484 CCACCCAAACAGCAGCCG 61.673 66.667 0.00 0.00 0.00 5.52
727 741 2.203480 TCCACCCAAACAGCAGCC 60.203 61.111 0.00 0.00 0.00 4.85
728 742 2.270986 CCTCCACCCAAACAGCAGC 61.271 63.158 0.00 0.00 0.00 5.25
729 743 2.270986 GCCTCCACCCAAACAGCAG 61.271 63.158 0.00 0.00 0.00 4.24
730 744 2.203480 GCCTCCACCCAAACAGCA 60.203 61.111 0.00 0.00 0.00 4.41
731 745 3.365265 CGCCTCCACCCAAACAGC 61.365 66.667 0.00 0.00 0.00 4.40
732 746 2.113139 ACGCCTCCACCCAAACAG 59.887 61.111 0.00 0.00 0.00 3.16
733 747 2.203280 CACGCCTCCACCCAAACA 60.203 61.111 0.00 0.00 0.00 2.83
925 939 5.904362 ACAGGAGGAATTTCACTAATTGC 57.096 39.130 0.00 0.00 42.87 3.56
947 961 4.168479 AGAAACAAAGGTAAACCCCAGGTA 59.832 41.667 0.00 0.00 33.12 3.08
1107 1121 1.629043 ACTGGAGGCAGTACTCGAAA 58.371 50.000 0.00 0.00 38.39 3.46
1176 1192 5.680151 GCAAAGTTAACAAAACCAGTAGGCA 60.680 40.000 8.61 0.00 39.06 4.75
1203 1219 2.166459 TCCCTGTAGAATGACAGCGAAG 59.834 50.000 0.00 0.00 44.65 3.79
1326 1342 5.248934 TGAATGCTCCAAAATTCCAAAGGAT 59.751 36.000 0.00 0.00 32.81 3.24
1376 1392 2.625282 AGTAACTACTCTGGCCAGGT 57.375 50.000 32.23 27.70 0.00 4.00
1426 1442 5.707298 ACAATTTCCCTGTGTAATCACTGAG 59.293 40.000 6.78 0.00 43.16 3.35
1521 1544 7.152645 ACTAGGAAAACTACACACATACACTG 58.847 38.462 0.00 0.00 0.00 3.66
2220 2260 1.981256 TCCAGCAGAAGTTTTGACCC 58.019 50.000 0.00 0.00 0.00 4.46
3077 3643 3.825623 AGCCAGCCATAAGCCCCC 61.826 66.667 0.00 0.00 45.47 5.40
3109 3675 1.866015 AAAATAAGCTGGGGAAGGGC 58.134 50.000 0.00 0.00 0.00 5.19
3127 3693 8.673456 AATAAAATTTTAGGTGGGGCTTCTAA 57.327 30.769 15.45 0.00 0.00 2.10
3197 3763 9.230122 CAAGAAGCCCAACCAATTTATTTATTT 57.770 29.630 0.00 0.00 0.00 1.40
3198 3764 8.601546 TCAAGAAGCCCAACCAATTTATTTATT 58.398 29.630 0.00 0.00 0.00 1.40
3199 3765 8.144862 TCAAGAAGCCCAACCAATTTATTTAT 57.855 30.769 0.00 0.00 0.00 1.40
3200 3766 7.546250 TCAAGAAGCCCAACCAATTTATTTA 57.454 32.000 0.00 0.00 0.00 1.40
3201 3767 6.432403 TCAAGAAGCCCAACCAATTTATTT 57.568 33.333 0.00 0.00 0.00 1.40
3202 3768 6.432403 TTCAAGAAGCCCAACCAATTTATT 57.568 33.333 0.00 0.00 0.00 1.40
3203 3769 6.625532 ATTCAAGAAGCCCAACCAATTTAT 57.374 33.333 0.00 0.00 0.00 1.40
3204 3770 7.546250 TTATTCAAGAAGCCCAACCAATTTA 57.454 32.000 0.00 0.00 0.00 1.40
3205 3771 4.980339 ATTCAAGAAGCCCAACCAATTT 57.020 36.364 0.00 0.00 0.00 1.82
3206 3772 5.569428 GCTTATTCAAGAAGCCCAACCAATT 60.569 40.000 5.38 0.00 42.90 2.32
3207 3773 4.081476 GCTTATTCAAGAAGCCCAACCAAT 60.081 41.667 5.38 0.00 42.90 3.16
3208 3774 3.258123 GCTTATTCAAGAAGCCCAACCAA 59.742 43.478 5.38 0.00 42.90 3.67
3209 3775 2.825532 GCTTATTCAAGAAGCCCAACCA 59.174 45.455 5.38 0.00 42.90 3.67
3210 3776 3.510388 GCTTATTCAAGAAGCCCAACC 57.490 47.619 5.38 0.00 42.90 3.77
3217 3783 6.127196 ACCCTCTCACTAGCTTATTCAAGAAG 60.127 42.308 0.00 0.00 33.20 2.85
3218 3784 5.721960 ACCCTCTCACTAGCTTATTCAAGAA 59.278 40.000 0.00 0.00 33.20 2.52
3219 3785 5.273208 ACCCTCTCACTAGCTTATTCAAGA 58.727 41.667 0.00 0.00 33.20 3.02
3220 3786 5.606348 ACCCTCTCACTAGCTTATTCAAG 57.394 43.478 0.00 0.00 34.66 3.02
3221 3787 5.069251 GCTACCCTCTCACTAGCTTATTCAA 59.931 44.000 0.00 0.00 31.82 2.69
3222 3788 4.585162 GCTACCCTCTCACTAGCTTATTCA 59.415 45.833 0.00 0.00 31.82 2.57
3223 3789 4.830600 AGCTACCCTCTCACTAGCTTATTC 59.169 45.833 0.00 0.00 40.26 1.75
3224 3790 4.810345 AGCTACCCTCTCACTAGCTTATT 58.190 43.478 0.00 0.00 40.26 1.40
3225 3791 4.463050 AGCTACCCTCTCACTAGCTTAT 57.537 45.455 0.00 0.00 40.26 1.73
3226 3792 3.955524 AGCTACCCTCTCACTAGCTTA 57.044 47.619 0.00 0.00 40.26 3.09
3227 3793 2.838637 AGCTACCCTCTCACTAGCTT 57.161 50.000 0.00 0.00 40.26 3.74
3228 3794 2.838637 AAGCTACCCTCTCACTAGCT 57.161 50.000 0.00 0.00 44.14 3.32
3229 3795 5.510009 GGAAATAAGCTACCCTCTCACTAGC 60.510 48.000 0.00 0.00 34.27 3.42
3230 3796 5.278561 CGGAAATAAGCTACCCTCTCACTAG 60.279 48.000 0.00 0.00 0.00 2.57
3231 3797 4.583489 CGGAAATAAGCTACCCTCTCACTA 59.417 45.833 0.00 0.00 0.00 2.74
3232 3798 3.385111 CGGAAATAAGCTACCCTCTCACT 59.615 47.826 0.00 0.00 0.00 3.41
3233 3799 3.718815 CGGAAATAAGCTACCCTCTCAC 58.281 50.000 0.00 0.00 0.00 3.51
3234 3800 2.102588 GCGGAAATAAGCTACCCTCTCA 59.897 50.000 0.00 0.00 0.00 3.27
3235 3801 2.102588 TGCGGAAATAAGCTACCCTCTC 59.897 50.000 0.00 0.00 0.00 3.20
3236 3802 2.103263 CTGCGGAAATAAGCTACCCTCT 59.897 50.000 0.00 0.00 0.00 3.69
3237 3803 2.484889 CTGCGGAAATAAGCTACCCTC 58.515 52.381 0.00 0.00 0.00 4.30
3238 3804 1.475213 GCTGCGGAAATAAGCTACCCT 60.475 52.381 0.00 0.00 34.05 4.34
3239 3805 0.945099 GCTGCGGAAATAAGCTACCC 59.055 55.000 0.00 0.00 34.05 3.69
3240 3806 0.945099 GGCTGCGGAAATAAGCTACC 59.055 55.000 0.00 0.00 37.12 3.18
3241 3807 1.599542 CTGGCTGCGGAAATAAGCTAC 59.400 52.381 0.00 0.00 37.12 3.58
3242 3808 1.953559 CTGGCTGCGGAAATAAGCTA 58.046 50.000 0.00 0.00 37.12 3.32
3243 3809 1.379642 GCTGGCTGCGGAAATAAGCT 61.380 55.000 0.00 0.00 37.12 3.74
3244 3810 1.064783 GCTGGCTGCGGAAATAAGC 59.935 57.895 0.00 0.00 36.17 3.09
3245 3811 1.031571 TGGCTGGCTGCGGAAATAAG 61.032 55.000 10.35 0.00 44.05 1.73
3246 3812 0.395586 ATGGCTGGCTGCGGAAATAA 60.396 50.000 10.35 0.00 44.05 1.40
3247 3813 0.472044 TATGGCTGGCTGCGGAAATA 59.528 50.000 10.35 3.49 44.05 1.40
3248 3814 0.395586 TTATGGCTGGCTGCGGAAAT 60.396 50.000 10.35 4.37 44.05 2.17
3249 3815 1.001517 TTATGGCTGGCTGCGGAAA 60.002 52.632 10.35 1.49 44.05 3.13
3250 3816 1.748879 GTTATGGCTGGCTGCGGAA 60.749 57.895 10.35 1.60 44.05 4.30
3251 3817 2.124736 GTTATGGCTGGCTGCGGA 60.125 61.111 10.35 0.00 44.05 5.54
3252 3818 3.211963 GGTTATGGCTGGCTGCGG 61.212 66.667 10.35 0.00 44.05 5.69
3253 3819 3.211963 GGGTTATGGCTGGCTGCG 61.212 66.667 10.35 0.00 44.05 5.18
3254 3820 2.834968 GGGGTTATGGCTGGCTGC 60.835 66.667 7.96 7.96 41.94 5.25
3255 3821 0.614415 TTTGGGGTTATGGCTGGCTG 60.614 55.000 2.00 0.00 0.00 4.85
3256 3822 0.116143 TTTTGGGGTTATGGCTGGCT 59.884 50.000 2.00 0.00 0.00 4.75
3257 3823 0.536724 CTTTTGGGGTTATGGCTGGC 59.463 55.000 0.00 0.00 0.00 4.85
3258 3824 2.230130 TCTTTTGGGGTTATGGCTGG 57.770 50.000 0.00 0.00 0.00 4.85
3259 3825 3.056607 CAGTTCTTTTGGGGTTATGGCTG 60.057 47.826 0.00 0.00 0.00 4.85
3260 3826 3.165071 CAGTTCTTTTGGGGTTATGGCT 58.835 45.455 0.00 0.00 0.00 4.75
3261 3827 2.233676 CCAGTTCTTTTGGGGTTATGGC 59.766 50.000 0.00 0.00 31.87 4.40
3262 3828 2.233676 GCCAGTTCTTTTGGGGTTATGG 59.766 50.000 0.00 0.00 36.19 2.74
3263 3829 2.233676 GGCCAGTTCTTTTGGGGTTATG 59.766 50.000 0.00 0.00 36.19 1.90
3264 3830 2.536066 GGCCAGTTCTTTTGGGGTTAT 58.464 47.619 0.00 0.00 36.19 1.89
3265 3831 1.481615 GGGCCAGTTCTTTTGGGGTTA 60.482 52.381 4.39 0.00 36.19 2.85
3266 3832 0.762842 GGGCCAGTTCTTTTGGGGTT 60.763 55.000 4.39 0.00 36.19 4.11
3267 3833 1.152333 GGGCCAGTTCTTTTGGGGT 60.152 57.895 4.39 0.00 36.19 4.95
3268 3834 1.913262 GGGGCCAGTTCTTTTGGGG 60.913 63.158 4.39 0.00 36.19 4.96
3269 3835 0.762461 TTGGGGCCAGTTCTTTTGGG 60.762 55.000 4.39 0.00 36.19 4.12
3270 3836 1.070601 CTTTGGGGCCAGTTCTTTTGG 59.929 52.381 4.39 0.00 38.78 3.28
3271 3837 1.541015 GCTTTGGGGCCAGTTCTTTTG 60.541 52.381 4.39 0.00 0.00 2.44
3272 3838 0.758734 GCTTTGGGGCCAGTTCTTTT 59.241 50.000 4.39 0.00 0.00 2.27
3273 3839 0.105504 AGCTTTGGGGCCAGTTCTTT 60.106 50.000 4.39 0.00 0.00 2.52
3274 3840 0.105504 AAGCTTTGGGGCCAGTTCTT 60.106 50.000 4.39 0.00 0.00 2.52
3275 3841 0.829182 CAAGCTTTGGGGCCAGTTCT 60.829 55.000 4.39 0.00 0.00 3.01
3276 3842 1.115326 ACAAGCTTTGGGGCCAGTTC 61.115 55.000 4.39 0.00 34.12 3.01
3277 3843 0.690744 AACAAGCTTTGGGGCCAGTT 60.691 50.000 4.39 0.00 34.12 3.16
3278 3844 0.690744 AAACAAGCTTTGGGGCCAGT 60.691 50.000 4.39 0.00 34.12 4.00
3279 3845 0.249996 CAAACAAGCTTTGGGGCCAG 60.250 55.000 4.39 0.00 34.12 4.85
3280 3846 1.828768 CAAACAAGCTTTGGGGCCA 59.171 52.632 4.39 0.00 34.12 5.36
3281 3847 1.597854 GCAAACAAGCTTTGGGGCC 60.598 57.895 0.00 0.00 34.12 5.80
3282 3848 0.463474 TTGCAAACAAGCTTTGGGGC 60.463 50.000 0.00 0.00 34.99 5.80
3313 3879 7.632132 GTGTAAAGCCGTAAACGTATGATTTAC 59.368 37.037 16.81 16.81 38.57 2.01
3337 3903 4.111916 GGTTTCAGTGAACCAAATGTGTG 58.888 43.478 4.68 0.00 46.66 3.82
3338 3904 4.385358 GGTTTCAGTGAACCAAATGTGT 57.615 40.909 4.68 0.00 46.66 3.72
3461 4036 4.160065 CCCATCTTTATGCAACACCATTGA 59.840 41.667 0.00 0.00 0.00 2.57
3663 4241 4.402829 TGTATGTAGCTTGCCTTTCCAAA 58.597 39.130 0.00 0.00 0.00 3.28
3692 4270 6.587273 ACTTCAGTGATAGAGGAATTAAGGC 58.413 40.000 0.00 0.00 0.00 4.35
3742 4320 8.393259 TGGCATACCTTCAATATTATCCTGAAT 58.607 33.333 0.00 0.00 36.63 2.57
3757 4335 8.725148 CATTACTGAATCTATTGGCATACCTTC 58.275 37.037 0.00 0.00 36.63 3.46
3769 4347 9.717942 GCTTGAGGTATTCATTACTGAATCTAT 57.282 33.333 11.23 0.07 46.83 1.98
3806 4384 9.709495 TCTAATTGTGCATAATTTTCTTTGCTT 57.291 25.926 23.95 2.18 36.10 3.91
3822 4400 7.029563 CCTTGGAAGTTTACATCTAATTGTGC 58.970 38.462 0.00 0.00 0.00 4.57
3886 4464 9.899661 AGTACTAATACAATATTGGTGAGCAAA 57.100 29.630 19.37 0.00 33.30 3.68
3899 4477 9.476928 ACTACAACCTGAGAGTACTAATACAAT 57.523 33.333 0.00 0.00 33.30 2.71
3938 4516 3.706600 AAACTTTGGCATGCCATCAAT 57.293 38.095 38.78 22.65 46.64 2.57
4106 4762 6.391227 TTTGAGACAGGGAAGAAAATTGAC 57.609 37.500 0.00 0.00 0.00 3.18
4107 4763 7.601705 ATTTTGAGACAGGGAAGAAAATTGA 57.398 32.000 0.00 0.00 0.00 2.57
4108 4764 8.667076 AAATTTTGAGACAGGGAAGAAAATTG 57.333 30.769 0.00 0.00 34.72 2.32
4109 4765 9.112725 CAAAATTTTGAGACAGGGAAGAAAATT 57.887 29.630 23.72 0.00 40.55 1.82
4110 4766 8.267183 ACAAAATTTTGAGACAGGGAAGAAAAT 58.733 29.630 32.20 5.56 40.55 1.82
4112 4768 7.124147 AGACAAAATTTTGAGACAGGGAAGAAA 59.876 33.333 32.20 0.00 40.55 2.52
4114 4770 6.039717 CAGACAAAATTTTGAGACAGGGAAGA 59.960 38.462 32.20 0.00 40.55 2.87
4115 4771 6.211515 CAGACAAAATTTTGAGACAGGGAAG 58.788 40.000 32.20 6.45 40.55 3.46
4116 4772 5.068987 CCAGACAAAATTTTGAGACAGGGAA 59.931 40.000 32.20 0.00 40.55 3.97
4122 5309 6.803807 GCACTATCCAGACAAAATTTTGAGAC 59.196 38.462 32.20 22.06 40.55 3.36
4123 5310 6.716628 AGCACTATCCAGACAAAATTTTGAGA 59.283 34.615 32.20 22.35 40.55 3.27
4124 5311 6.805271 CAGCACTATCCAGACAAAATTTTGAG 59.195 38.462 32.20 20.47 40.55 3.02
4139 5326 6.402766 CGAGTAGTAATCTAGCAGCACTATCC 60.403 46.154 0.00 0.00 0.00 2.59
4155 5342 8.233190 GCAAAACTAGTACTTCTCGAGTAGTAA 58.767 37.037 27.19 15.55 43.05 2.24
4218 5405 2.880268 CTGCATGTTCAGGACAGTTGAA 59.120 45.455 0.00 0.00 42.62 2.69
4234 5424 2.133281 TGCCTTCACAATAGCTGCAT 57.867 45.000 1.02 0.00 0.00 3.96
4364 5560 2.300197 TAACCCACCCTTACCCGGC 61.300 63.158 0.00 0.00 0.00 6.13
4378 5588 8.971827 ATCCAGAGGAAAATGACGGTGTAACC 62.972 46.154 0.00 0.00 45.40 2.85
4379 5589 3.435671 CCAGAGGAAAATGACGGTGTAAC 59.564 47.826 0.00 0.00 0.00 2.50
4382 5592 1.697432 TCCAGAGGAAAATGACGGTGT 59.303 47.619 0.00 0.00 0.00 4.16
4421 5632 6.425210 AGTGTGTGGCATAGATACATACAT 57.575 37.500 0.00 0.00 38.25 2.29
4469 5680 4.538746 GTGCTAGGACTAGAACCTGTTT 57.461 45.455 18.37 1.31 36.01 2.83
4534 5745 5.760253 AGATTCACAACACAAGTTACTCCTG 59.240 40.000 0.00 0.00 35.85 3.86
4554 5766 3.252215 CGAGAGGATAGCTTGACGAGATT 59.748 47.826 0.00 0.00 0.00 2.40
4555 5767 2.811431 CGAGAGGATAGCTTGACGAGAT 59.189 50.000 0.00 0.00 0.00 2.75
4557 5769 1.334599 GCGAGAGGATAGCTTGACGAG 60.335 57.143 0.00 0.00 0.00 4.18
4559 5771 0.665835 AGCGAGAGGATAGCTTGACG 59.334 55.000 0.00 0.00 36.30 4.35
4569 5835 0.837940 TCAGGTAGCTAGCGAGAGGA 59.162 55.000 16.82 8.37 0.00 3.71
4596 5862 5.769662 TGTACATGCAGGTCTTCTGAAAAAT 59.230 36.000 7.56 0.00 46.18 1.82
4600 5866 4.256110 CATGTACATGCAGGTCTTCTGAA 58.744 43.478 22.27 0.00 46.18 3.02
4630 5896 4.573607 TGTTTATGACTCTGCTGATCATGC 59.426 41.667 19.28 2.91 34.86 4.06
4689 5955 7.594015 GCTCTATTTTTCATTGATGCACCTATG 59.406 37.037 0.00 0.00 0.00 2.23
4732 5998 0.466963 AAGTTAGAATACGCCGGGGG 59.533 55.000 23.83 9.88 0.00 5.40
4773 6039 1.619654 CTGGGTCAATTGGTTGCAGA 58.380 50.000 5.42 0.00 35.26 4.26
4813 6079 2.620585 GTTGCTGAAGAAAGAGCTTGGT 59.379 45.455 0.00 0.00 36.11 3.67
4837 6114 1.337387 AGTTATAGAGGAACGAGCGGC 59.663 52.381 0.00 0.00 31.85 6.53
4843 6120 5.109903 CCCAGTTGAAGTTATAGAGGAACG 58.890 45.833 0.00 0.00 31.85 3.95
4874 6151 0.884704 ACGGTAAGCACAAGCACCAG 60.885 55.000 0.00 0.00 45.49 4.00
4884 6161 1.135024 GGGTATTGTCGACGGTAAGCA 60.135 52.381 11.62 0.00 0.00 3.91
4892 6169 0.819582 TTCCCGAGGGTATTGTCGAC 59.180 55.000 9.11 9.11 38.50 4.20
4906 6183 0.674895 CAGGAAGAAGCCAGTTCCCG 60.675 60.000 5.21 0.00 42.97 5.14
4960 6237 5.128335 ACAGTGTTAGTAACCCTATAGTGGC 59.872 44.000 10.51 0.00 0.00 5.01
5066 6344 0.722469 CTACAGCAGCACAAAACGCG 60.722 55.000 3.53 3.53 0.00 6.01
5075 6353 1.713597 CACGTGAATCTACAGCAGCA 58.286 50.000 10.90 0.00 0.00 4.41
5083 6361 4.637276 TCCAAGAAAAGCACGTGAATCTA 58.363 39.130 22.23 0.00 0.00 1.98
5091 6369 0.386478 GCAGCTCCAAGAAAAGCACG 60.386 55.000 0.00 0.00 41.06 5.34
5156 6434 2.919666 AATACATGACGCTTTGGCAC 57.080 45.000 0.00 0.00 38.60 5.01
5164 6442 3.450578 TCCGTTCCTAAATACATGACGC 58.549 45.455 0.00 0.00 0.00 5.19
5171 6449 3.450096 ACACCTCCTCCGTTCCTAAATAC 59.550 47.826 0.00 0.00 0.00 1.89
5172 6450 3.703052 GACACCTCCTCCGTTCCTAAATA 59.297 47.826 0.00 0.00 0.00 1.40
5188 6466 7.559897 TGTATCCTTGAAAAAGAAAAGACACCT 59.440 33.333 0.00 0.00 0.00 4.00
5189 6467 7.648112 GTGTATCCTTGAAAAAGAAAAGACACC 59.352 37.037 0.00 0.00 0.00 4.16
5192 6470 7.712797 TGGTGTATCCTTGAAAAAGAAAAGAC 58.287 34.615 0.00 0.00 37.07 3.01
5208 6486 2.654863 CACCCTTTCCATGGTGTATCC 58.345 52.381 12.58 0.00 45.61 2.59
5224 6502 2.418368 TCAATGATACTGGTGCACCC 57.582 50.000 32.62 17.27 34.29 4.61
5231 6509 4.774124 TGGCTCTTCTTCAATGATACTGG 58.226 43.478 0.00 0.00 0.00 4.00
5288 6566 0.038892 CATTCCAGCTGTGGTGTTGC 60.039 55.000 13.81 0.00 45.28 4.17
5296 6574 3.701040 AGTTGTTTTGTCATTCCAGCTGT 59.299 39.130 13.81 0.00 0.00 4.40
5302 6580 2.293399 AGGCGAGTTGTTTTGTCATTCC 59.707 45.455 0.00 0.00 0.00 3.01
5303 6581 3.626028 AGGCGAGTTGTTTTGTCATTC 57.374 42.857 0.00 0.00 0.00 2.67
5310 6588 2.798847 GTTCGACTAGGCGAGTTGTTTT 59.201 45.455 21.89 0.00 41.79 2.43
5328 6606 3.068024 TGCCATTTTGTGTCTTGAGGTTC 59.932 43.478 0.00 0.00 0.00 3.62
5335 6613 2.629617 CCTCCTTGCCATTTTGTGTCTT 59.370 45.455 0.00 0.00 0.00 3.01
5358 6636 6.568869 CGATCCTTGATCTTTGAGTCTTACT 58.431 40.000 0.00 0.00 36.96 2.24
5359 6637 5.233263 GCGATCCTTGATCTTTGAGTCTTAC 59.767 44.000 0.00 0.00 36.96 2.34
5360 6638 5.352284 GCGATCCTTGATCTTTGAGTCTTA 58.648 41.667 0.00 0.00 36.96 2.10
5361 6639 4.187694 GCGATCCTTGATCTTTGAGTCTT 58.812 43.478 0.00 0.00 36.96 3.01
5384 6662 2.088423 TGTCTTGGTGTTGGTTGTGAC 58.912 47.619 0.00 0.00 0.00 3.67
5408 6686 1.342074 CTGAGGTGAAGACAGGGTCA 58.658 55.000 0.00 0.00 34.60 4.02
5459 6742 1.569479 GCTGGTTCCGCTGTTCACTC 61.569 60.000 0.00 0.00 0.00 3.51
5460 6743 1.598130 GCTGGTTCCGCTGTTCACT 60.598 57.895 0.00 0.00 0.00 3.41
5461 6744 2.617274 GGCTGGTTCCGCTGTTCAC 61.617 63.158 5.89 0.00 0.00 3.18
5462 6745 2.281484 GGCTGGTTCCGCTGTTCA 60.281 61.111 5.89 0.00 0.00 3.18
5463 6746 2.281484 TGGCTGGTTCCGCTGTTC 60.281 61.111 5.89 0.00 0.00 3.18
5464 6747 2.281761 CTGGCTGGTTCCGCTGTT 60.282 61.111 5.89 0.00 0.00 3.16
5465 6748 3.241530 TCTGGCTGGTTCCGCTGT 61.242 61.111 0.00 0.00 0.00 4.40
5466 6749 2.743928 GTCTGGCTGGTTCCGCTG 60.744 66.667 0.00 0.00 0.00 5.18
5467 6750 2.925170 AGTCTGGCTGGTTCCGCT 60.925 61.111 0.00 0.00 0.00 5.52
5468 6751 2.435059 GAGTCTGGCTGGTTCCGC 60.435 66.667 0.00 0.00 0.00 5.54
5469 6752 0.250295 TTTGAGTCTGGCTGGTTCCG 60.250 55.000 0.00 0.00 0.00 4.30
5470 6753 2.206576 ATTTGAGTCTGGCTGGTTCC 57.793 50.000 0.00 0.00 0.00 3.62
5471 6754 4.393371 GTCTTATTTGAGTCTGGCTGGTTC 59.607 45.833 0.00 0.00 0.00 3.62
5472 6755 4.202461 TGTCTTATTTGAGTCTGGCTGGTT 60.202 41.667 0.00 0.00 0.00 3.67
5473 6756 3.327757 TGTCTTATTTGAGTCTGGCTGGT 59.672 43.478 0.00 0.00 0.00 4.00
5474 6757 3.942829 TGTCTTATTTGAGTCTGGCTGG 58.057 45.455 0.00 0.00 0.00 4.85
5475 6758 5.426504 AGATGTCTTATTTGAGTCTGGCTG 58.573 41.667 0.00 0.00 0.00 4.85
5521 6804 2.031163 GCTCTCGGGGCGCAATAT 59.969 61.111 10.83 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.