Multiple sequence alignment - TraesCS4D01G203300

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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 TraesCS4D01G203300 chr4D 100.000 4756 0 0 1 4756 350250774 350246019 0.000000e+00 8783
1 TraesCS4D01G203300 chr4A 92.996 3869 147 41 31 3865 114740883 114744661 0.000000e+00 5529
2 TraesCS4D01G203300 chr4A 94.568 718 25 6 4050 4756 114744678 114745392 0.000000e+00 1098
3 TraesCS4D01G203300 chr4A 86.797 462 57 2 31 492 114738566 114739023 3.280000e-141 512
4 TraesCS4D01G203300 chr4A 84.532 278 19 14 347 624 114739208 114739461 2.200000e-63 254
5 TraesCS4D01G203300 chr4A 79.275 193 28 9 1330 1512 114742059 114742249 1.800000e-24 124
6 TraesCS4D01G203300 chr4B 93.064 3835 129 43 31 3807 433336805 433333050 0.000000e+00 5481
7 TraesCS4D01G203300 chr4B 88.687 716 32 17 4050 4756 433332940 433332265 0.000000e+00 828
8 TraesCS4D01G203300 chr4B 79.793 193 27 9 1330 1512 433335603 433335413 3.860000e-26 130
9 TraesCS4D01G203300 chr4B 91.111 90 7 1 3784 3872 433333039 433332950 2.320000e-23 121
10 TraesCS4D01G203300 chr3D 91.578 748 20 10 933 1679 63767189 63767894 0.000000e+00 992
11 TraesCS4D01G203300 chr3D 86.184 456 41 10 1754 2205 5451462 5451025 1.550000e-129 473
12 TraesCS4D01G203300 chr3D 84.648 469 49 12 1736 2200 226702770 226702321 3.380000e-121 446
13 TraesCS4D01G203300 chr3D 92.893 197 13 1 2405 2600 5450920 5450724 7.790000e-73 285
14 TraesCS4D01G203300 chr3D 92.386 197 14 1 2405 2600 226702070 226701874 3.620000e-71 279
15 TraesCS4D01G203300 chr3D 95.732 164 7 0 3888 4051 486424786 486424949 1.010000e-66 265
16 TraesCS4D01G203300 chr3A 87.727 440 32 12 2163 2600 198163496 198163915 1.190000e-135 494
17 TraesCS4D01G203300 chr3A 88.917 397 31 10 2163 2558 390143610 390143994 1.200000e-130 477
18 TraesCS4D01G203300 chr3A 88.917 397 31 8 2163 2558 619531278 619531662 1.200000e-130 477
19 TraesCS4D01G203300 chr3B 87.075 441 35 10 1769 2205 817853675 817853253 3.330000e-131 479
20 TraesCS4D01G203300 chr5A 85.745 470 44 9 1740 2205 399311323 399310873 4.310000e-130 475
21 TraesCS4D01G203300 chr5B 86.105 439 42 8 2163 2600 669600243 669599823 5.610000e-124 455
22 TraesCS4D01G203300 chr5D 85.973 442 40 9 2163 2600 47734026 47734449 2.020000e-123 453
23 TraesCS4D01G203300 chr5D 84.430 456 48 11 1754 2205 106891539 106891103 1.220000e-115 427
24 TraesCS4D01G203300 chr5D 94.643 168 9 0 3885 4052 431780422 431780589 1.310000e-65 261
25 TraesCS4D01G203300 chr5D 93.805 113 6 1 2235 2347 106891105 106890994 8.190000e-38 169
26 TraesCS4D01G203300 chr6A 85.941 441 39 10 1769 2205 464136646 464136225 2.610000e-122 449
27 TraesCS4D01G203300 chr6A 91.878 197 14 2 2405 2600 464136120 464135925 1.690000e-69 274
28 TraesCS4D01G203300 chr6A 92.920 113 7 1 2235 2347 464136227 464136116 3.810000e-36 163
29 TraesCS4D01G203300 chr1A 85.372 417 36 12 1796 2205 488634664 488635062 4.430000e-110 409
30 TraesCS4D01G203300 chr2D 98.160 163 1 1 3889 4051 143302829 143302989 2.800000e-72 283
31 TraesCS4D01G203300 chr2D 95.808 167 7 0 3889 4055 425155681 425155515 2.180000e-68 270
32 TraesCS4D01G203300 chr7D 94.152 171 10 0 3889 4059 88055090 88055260 1.310000e-65 261
33 TraesCS4D01G203300 chr1D 94.118 170 10 0 3889 4058 311986774 311986605 4.720000e-65 259
34 TraesCS4D01G203300 chr1D 93.182 176 9 2 3887 4062 160451493 160451665 6.110000e-64 255
35 TraesCS4D01G203300 chr1B 93.143 175 11 1 3889 4063 370161653 370161826 6.110000e-64 255
36 TraesCS4D01G203300 chr7B 89.447 199 15 5 3886 4081 741942700 741942505 3.680000e-61 246
37 TraesCS4D01G203300 chr7B 93.103 116 7 1 2235 2350 703151201 703151087 8.190000e-38 169


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 TraesCS4D01G203300 chr4D 350246019 350250774 4755 True 8783.000000 8783 100.000000 1 4756 1 chr4D.!!$R1 4755
1 TraesCS4D01G203300 chr4A 114738566 114745392 6826 False 1503.400000 5529 87.633600 31 4756 5 chr4A.!!$F1 4725
2 TraesCS4D01G203300 chr4B 433332265 433336805 4540 True 1640.000000 5481 88.163750 31 4756 4 chr4B.!!$R1 4725
3 TraesCS4D01G203300 chr3D 63767189 63767894 705 False 992.000000 992 91.578000 933 1679 1 chr3D.!!$F1 746
4 TraesCS4D01G203300 chr3D 5450724 5451462 738 True 379.000000 473 89.538500 1754 2600 2 chr3D.!!$R1 846
5 TraesCS4D01G203300 chr3D 226701874 226702770 896 True 362.500000 446 88.517000 1736 2600 2 chr3D.!!$R2 864
6 TraesCS4D01G203300 chr5D 106890994 106891539 545 True 298.000000 427 89.117500 1754 2347 2 chr5D.!!$R1 593
7 TraesCS4D01G203300 chr6A 464135925 464136646 721 True 295.333333 449 90.246333 1769 2600 3 chr6A.!!$R1 831

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
480 813 0.382158 TCTAGCGCGTGGAGAAGATG 59.618 55.0 8.43 0.0 0.00 2.90 F
840 3158 0.958382 ACACCCACACACACACACAC 60.958 55.0 0.00 0.0 0.00 3.82 F
2104 4481 1.065410 TGGGAACAGGGGAGCTTTGA 61.065 55.0 0.00 0.0 35.01 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2102 4479 4.277476 AGACACAAACAAGGTCCAAATCA 58.723 39.130 0.00 0.0 31.99 2.57 R
2757 5255 1.451927 GGCCGGATCAGCATTCACA 60.452 57.895 5.05 0.0 0.00 3.58 R
3774 6273 0.241213 GCCAAAAAGACCGAGGCTTC 59.759 55.000 0.00 0.0 42.01 3.86 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
27 28 7.948278 ATACAAGTAGTTCGGAATTATGAGC 57.052 36.000 0.00 0.00 0.00 4.26
28 29 5.978814 ACAAGTAGTTCGGAATTATGAGCT 58.021 37.500 0.00 0.00 0.00 4.09
29 30 6.043411 ACAAGTAGTTCGGAATTATGAGCTC 58.957 40.000 6.82 6.82 0.00 4.09
30 31 6.127310 ACAAGTAGTTCGGAATTATGAGCTCT 60.127 38.462 16.19 3.04 0.00 4.09
31 32 5.837437 AGTAGTTCGGAATTATGAGCTCTG 58.163 41.667 16.19 0.00 0.00 3.35
32 33 3.462021 AGTTCGGAATTATGAGCTCTGC 58.538 45.455 16.19 0.00 0.00 4.26
56 57 1.155390 AGAAGGACCAGGGACGACA 59.845 57.895 0.00 0.00 0.00 4.35
60 61 0.397254 AGGACCAGGGACGACATAGG 60.397 60.000 0.00 0.00 0.00 2.57
136 137 8.508875 TGGAAAATCCGAAGAAAACTTATACAC 58.491 33.333 0.00 0.00 40.17 2.90
137 138 7.966753 GGAAAATCCGAAGAAAACTTATACACC 59.033 37.037 0.00 0.00 0.00 4.16
151 152 5.183331 ACTTATACACCATCGTCATCGCTAT 59.817 40.000 0.00 0.00 36.96 2.97
163 164 2.152297 ATCGCTATCGCCAGAGCCAG 62.152 60.000 0.00 0.00 35.13 4.85
164 165 2.030262 GCTATCGCCAGAGCCAGG 59.970 66.667 0.00 0.00 34.57 4.45
210 211 4.404715 GCCCAACTAAGATACCAGACTACA 59.595 45.833 0.00 0.00 0.00 2.74
255 256 2.045242 GTTCCCTTCCTTCCCGCC 60.045 66.667 0.00 0.00 0.00 6.13
276 277 2.434359 GCCACGGTAGCTGGTGAC 60.434 66.667 13.86 1.39 36.25 3.67
303 304 2.093869 GGAACCATAGTGGCACGAAGTA 60.094 50.000 12.71 0.00 42.67 2.24
309 310 1.177256 AGTGGCACGAAGTACGAGGT 61.177 55.000 12.71 0.00 41.61 3.85
310 311 0.523072 GTGGCACGAAGTACGAGGTA 59.477 55.000 0.00 0.00 41.61 3.08
392 396 5.478679 TGGTTGTTAATGGGGTCTACATTTG 59.521 40.000 0.00 0.00 39.18 2.32
480 813 0.382158 TCTAGCGCGTGGAGAAGATG 59.618 55.000 8.43 0.00 0.00 2.90
500 833 8.599624 AAGATGAGTGGATTTAATCATTGGTT 57.400 30.769 7.29 0.00 35.72 3.67
501 834 8.230472 AGATGAGTGGATTTAATCATTGGTTC 57.770 34.615 7.29 0.00 35.72 3.62
502 835 6.773976 TGAGTGGATTTAATCATTGGTTCC 57.226 37.500 7.29 0.00 0.00 3.62
541 874 6.977213 TCTCCATGCAATCACATAAATCATG 58.023 36.000 0.00 0.00 40.78 3.07
543 876 7.720515 TCTCCATGCAATCACATAAATCATGTA 59.279 33.333 0.00 0.00 46.47 2.29
545 878 8.693625 TCCATGCAATCACATAAATCATGTAAA 58.306 29.630 0.00 0.00 46.47 2.01
561 894 7.250445 TCATGTAAAATTCCATGACGATGAG 57.750 36.000 9.93 0.00 41.77 2.90
562 895 6.260714 TCATGTAAAATTCCATGACGATGAGG 59.739 38.462 9.93 0.00 41.77 3.86
563 896 4.335315 TGTAAAATTCCATGACGATGAGGC 59.665 41.667 0.00 0.00 0.00 4.70
564 897 3.287867 AAATTCCATGACGATGAGGCT 57.712 42.857 0.00 0.00 0.00 4.58
565 898 3.287867 AATTCCATGACGATGAGGCTT 57.712 42.857 0.00 0.00 0.00 4.35
566 899 2.787473 TTCCATGACGATGAGGCTTT 57.213 45.000 0.00 0.00 0.00 3.51
567 900 2.787473 TCCATGACGATGAGGCTTTT 57.213 45.000 0.00 0.00 0.00 2.27
568 901 3.071874 TCCATGACGATGAGGCTTTTT 57.928 42.857 0.00 0.00 0.00 1.94
569 902 4.214986 TCCATGACGATGAGGCTTTTTA 57.785 40.909 0.00 0.00 0.00 1.52
570 903 4.584874 TCCATGACGATGAGGCTTTTTAA 58.415 39.130 0.00 0.00 0.00 1.52
571 904 5.192927 TCCATGACGATGAGGCTTTTTAAT 58.807 37.500 0.00 0.00 0.00 1.40
572 905 6.353323 TCCATGACGATGAGGCTTTTTAATA 58.647 36.000 0.00 0.00 0.00 0.98
573 906 6.998074 TCCATGACGATGAGGCTTTTTAATAT 59.002 34.615 0.00 0.00 0.00 1.28
574 907 7.041167 TCCATGACGATGAGGCTTTTTAATATG 60.041 37.037 0.00 0.00 0.00 1.78
575 908 7.255242 CCATGACGATGAGGCTTTTTAATATGT 60.255 37.037 0.00 0.00 0.00 2.29
576 909 7.624360 TGACGATGAGGCTTTTTAATATGTT 57.376 32.000 0.00 0.00 0.00 2.71
577 910 8.050778 TGACGATGAGGCTTTTTAATATGTTT 57.949 30.769 0.00 0.00 0.00 2.83
578 911 8.519526 TGACGATGAGGCTTTTTAATATGTTTT 58.480 29.630 0.00 0.00 0.00 2.43
579 912 8.911247 ACGATGAGGCTTTTTAATATGTTTTC 57.089 30.769 0.00 0.00 0.00 2.29
580 913 8.739972 ACGATGAGGCTTTTTAATATGTTTTCT 58.260 29.630 0.00 0.00 0.00 2.52
649 2962 9.840427 TTTTTCATAGCTGCAATACTAGTTTTC 57.160 29.630 0.00 0.00 0.00 2.29
650 2963 8.560355 TTTCATAGCTGCAATACTAGTTTTCA 57.440 30.769 0.00 0.00 0.00 2.69
651 2964 7.776933 TCATAGCTGCAATACTAGTTTTCAG 57.223 36.000 0.00 10.16 0.00 3.02
712 3025 9.265901 CACAGAAGGAGATAATAATTCGTGATT 57.734 33.333 0.00 0.00 31.90 2.57
826 3144 2.518349 CCACACACCCACACACCC 60.518 66.667 0.00 0.00 0.00 4.61
827 3145 2.273776 CACACACCCACACACCCA 59.726 61.111 0.00 0.00 0.00 4.51
828 3146 2.118404 CACACACCCACACACCCAC 61.118 63.158 0.00 0.00 0.00 4.61
829 3147 2.273776 CACACCCACACACCCACA 59.726 61.111 0.00 0.00 0.00 4.17
830 3148 2.118404 CACACCCACACACCCACAC 61.118 63.158 0.00 0.00 0.00 3.82
831 3149 2.273776 CACCCACACACCCACACA 59.726 61.111 0.00 0.00 0.00 3.72
840 3158 0.958382 ACACCCACACACACACACAC 60.958 55.000 0.00 0.00 0.00 3.82
901 3228 4.513442 TCTCCGATTGATTTCGTTCCATT 58.487 39.130 0.00 0.00 37.42 3.16
902 3229 4.570772 TCTCCGATTGATTTCGTTCCATTC 59.429 41.667 0.00 0.00 37.42 2.67
903 3230 3.625764 TCCGATTGATTTCGTTCCATTCC 59.374 43.478 0.00 0.00 37.42 3.01
904 3231 3.376859 CCGATTGATTTCGTTCCATTCCA 59.623 43.478 0.00 0.00 37.42 3.53
905 3232 4.036734 CCGATTGATTTCGTTCCATTCCAT 59.963 41.667 0.00 0.00 37.42 3.41
906 3233 5.207768 CGATTGATTTCGTTCCATTCCATC 58.792 41.667 0.00 0.00 34.46 3.51
907 3234 5.220835 CGATTGATTTCGTTCCATTCCATCA 60.221 40.000 0.00 0.00 34.46 3.07
1175 3536 3.502211 GTGGTGATCCTTACTTGTGTTGG 59.498 47.826 0.00 0.00 34.23 3.77
1176 3537 2.488153 GGTGATCCTTACTTGTGTTGGC 59.512 50.000 0.00 0.00 0.00 4.52
2055 4424 8.612619 CACTCACAAACACTTCAATACTAAACT 58.387 33.333 0.00 0.00 0.00 2.66
2102 4479 4.018195 TGGGAACAGGGGAGCTTT 57.982 55.556 0.00 0.00 35.01 3.51
2103 4480 1.460255 TGGGAACAGGGGAGCTTTG 59.540 57.895 0.00 0.00 35.01 2.77
2104 4481 1.065410 TGGGAACAGGGGAGCTTTGA 61.065 55.000 0.00 0.00 35.01 2.69
2176 4553 6.607600 AGAAAGGGTTTTATGGATTCCTAAGC 59.392 38.462 3.95 3.31 0.00 3.09
2757 5255 1.512926 CTGCGGTTGTTAGAGCACTT 58.487 50.000 0.00 0.00 35.59 3.16
2785 5283 2.289694 GCTGATCCGGCCATAGTTATGT 60.290 50.000 2.24 0.00 31.82 2.29
2873 5371 5.769662 TCTTCTGCCATGTTAAATCTTGTGT 59.230 36.000 0.00 0.00 0.00 3.72
3230 5729 1.002069 TCCACAGGGAAGGCATCAAT 58.998 50.000 0.00 0.00 41.32 2.57
3269 5768 1.027357 CAGTTGTGGCTGTGCTCTTT 58.973 50.000 0.00 0.00 0.00 2.52
3611 6110 1.750399 GATCATGGCCGGTGTGCTT 60.750 57.895 1.90 0.00 0.00 3.91
3689 6188 0.468226 TGAAGTCAACAAGGCGGAGT 59.532 50.000 0.00 0.00 0.00 3.85
3769 6268 1.066573 CATATGAGGGTGATCTCCGGC 60.067 57.143 7.70 3.12 33.04 6.13
3772 6271 1.152525 GAGGGTGATCTCCGGCCTA 60.153 63.158 0.00 0.00 0.00 3.93
3773 6272 0.543174 GAGGGTGATCTCCGGCCTAT 60.543 60.000 0.00 0.00 0.00 2.57
3774 6273 0.833834 AGGGTGATCTCCGGCCTATG 60.834 60.000 0.00 0.00 0.00 2.23
3776 6275 1.048601 GGTGATCTCCGGCCTATGAA 58.951 55.000 0.00 0.00 0.00 2.57
3778 6277 0.681733 TGATCTCCGGCCTATGAAGC 59.318 55.000 0.00 0.00 0.00 3.86
3816 6352 1.349259 GCCACACGACACGGATGTAC 61.349 60.000 0.00 0.00 39.95 2.90
3835 6374 3.306472 ACAAAGAAAGGGTTGGCACTA 57.694 42.857 0.00 0.00 0.00 2.74
3870 6409 4.039092 CCCTCCAGGTGCTGTGGG 62.039 72.222 0.00 0.00 37.15 4.61
3871 6410 3.252284 CCTCCAGGTGCTGTGGGT 61.252 66.667 0.50 0.00 35.58 4.51
3872 6411 1.918293 CCTCCAGGTGCTGTGGGTA 60.918 63.158 0.50 0.00 35.58 3.69
3873 6412 1.274703 CCTCCAGGTGCTGTGGGTAT 61.275 60.000 0.50 0.00 35.58 2.73
3874 6413 0.107508 CTCCAGGTGCTGTGGGTATG 60.108 60.000 0.50 0.00 35.58 2.39
3891 6430 4.347876 GGGTATGGGGTTTTACCGTATACT 59.652 45.833 14.93 0.00 39.83 2.12
3892 6431 5.511373 GGGTATGGGGTTTTACCGTATACTC 60.511 48.000 14.93 10.65 39.83 2.59
3893 6432 4.694760 ATGGGGTTTTACCGTATACTCC 57.305 45.455 0.56 4.10 39.83 3.85
3894 6433 2.771372 TGGGGTTTTACCGTATACTCCC 59.229 50.000 0.56 0.00 39.83 4.30
3895 6434 3.041211 GGGGTTTTACCGTATACTCCCT 58.959 50.000 0.56 0.00 39.83 4.20
3896 6435 3.070159 GGGGTTTTACCGTATACTCCCTC 59.930 52.174 0.56 0.00 39.83 4.30
3897 6436 3.070159 GGGTTTTACCGTATACTCCCTCC 59.930 52.174 0.56 0.00 39.83 4.30
3898 6437 3.243535 GGTTTTACCGTATACTCCCTCCG 60.244 52.174 0.56 0.00 0.00 4.63
3899 6438 3.297134 TTTACCGTATACTCCCTCCGT 57.703 47.619 0.56 0.00 0.00 4.69
3900 6439 3.297134 TTACCGTATACTCCCTCCGTT 57.703 47.619 0.56 0.00 0.00 4.44
3901 6440 1.685148 ACCGTATACTCCCTCCGTTC 58.315 55.000 0.56 0.00 0.00 3.95
3902 6441 0.957362 CCGTATACTCCCTCCGTTCC 59.043 60.000 0.56 0.00 0.00 3.62
3903 6442 1.478288 CCGTATACTCCCTCCGTTCCT 60.478 57.143 0.56 0.00 0.00 3.36
3904 6443 2.224621 CCGTATACTCCCTCCGTTCCTA 60.225 54.545 0.56 0.00 0.00 2.94
3905 6444 3.480470 CGTATACTCCCTCCGTTCCTAA 58.520 50.000 0.56 0.00 0.00 2.69
3906 6445 3.885297 CGTATACTCCCTCCGTTCCTAAA 59.115 47.826 0.56 0.00 0.00 1.85
3907 6446 4.522022 CGTATACTCCCTCCGTTCCTAAAT 59.478 45.833 0.56 0.00 0.00 1.40
3908 6447 5.707298 CGTATACTCCCTCCGTTCCTAAATA 59.293 44.000 0.56 0.00 0.00 1.40
3909 6448 6.376581 CGTATACTCCCTCCGTTCCTAAATAT 59.623 42.308 0.56 0.00 0.00 1.28
3910 6449 7.554118 CGTATACTCCCTCCGTTCCTAAATATA 59.446 40.741 0.56 0.00 0.00 0.86
3911 6450 9.247861 GTATACTCCCTCCGTTCCTAAATATAA 57.752 37.037 0.00 0.00 0.00 0.98
3912 6451 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3913 6452 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3914 6453 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3915 6454 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3916 6455 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3917 6456 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3918 6457 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
3919 6458 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
3922 6461 9.257651 CCGTTCCTAAATATAAGTCTTTGTAGG 57.742 37.037 0.00 0.00 0.00 3.18
3923 6462 9.257651 CGTTCCTAAATATAAGTCTTTGTAGGG 57.742 37.037 0.00 0.00 0.00 3.53
3936 6475 9.892130 AAGTCTTTGTAGGGATTTTACTAGATG 57.108 33.333 0.00 0.00 0.00 2.90
3937 6476 8.487028 AGTCTTTGTAGGGATTTTACTAGATGG 58.513 37.037 0.00 0.00 0.00 3.51
3938 6477 8.483758 GTCTTTGTAGGGATTTTACTAGATGGA 58.516 37.037 0.00 0.00 0.00 3.41
3939 6478 8.483758 TCTTTGTAGGGATTTTACTAGATGGAC 58.516 37.037 0.00 0.00 0.00 4.02
3940 6479 7.989947 TTGTAGGGATTTTACTAGATGGACT 57.010 36.000 0.00 0.00 0.00 3.85
3941 6480 9.496710 TTTGTAGGGATTTTACTAGATGGACTA 57.503 33.333 0.00 0.00 0.00 2.59
3942 6481 8.474710 TGTAGGGATTTTACTAGATGGACTAC 57.525 38.462 0.00 0.00 0.00 2.73
3943 6482 8.063153 TGTAGGGATTTTACTAGATGGACTACA 58.937 37.037 0.00 0.00 35.09 2.74
3944 6483 9.091220 GTAGGGATTTTACTAGATGGACTACAT 57.909 37.037 0.00 0.00 44.18 2.29
3946 6485 9.091220 AGGGATTTTACTAGATGGACTACATAC 57.909 37.037 0.00 0.00 40.72 2.39
3947 6486 8.027771 GGGATTTTACTAGATGGACTACATACG 58.972 40.741 0.00 0.00 40.72 3.06
3948 6487 8.027771 GGATTTTACTAGATGGACTACATACGG 58.972 40.741 0.00 0.00 40.72 4.02
3949 6488 8.701908 ATTTTACTAGATGGACTACATACGGA 57.298 34.615 0.00 0.00 40.72 4.69
3950 6489 7.741027 TTTACTAGATGGACTACATACGGAG 57.259 40.000 0.00 0.00 40.72 4.63
3951 6490 4.073549 ACTAGATGGACTACATACGGAGC 58.926 47.826 0.00 0.00 40.72 4.70
3952 6491 2.945456 AGATGGACTACATACGGAGCA 58.055 47.619 0.00 0.00 40.72 4.26
3953 6492 3.296854 AGATGGACTACATACGGAGCAA 58.703 45.455 0.00 0.00 40.72 3.91
3954 6493 3.704566 AGATGGACTACATACGGAGCAAA 59.295 43.478 0.00 0.00 40.72 3.68
3955 6494 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
3956 6495 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
3957 6496 4.839121 TGGACTACATACGGAGCAAAATT 58.161 39.130 0.00 0.00 0.00 1.82
3958 6497 5.979993 TGGACTACATACGGAGCAAAATTA 58.020 37.500 0.00 0.00 0.00 1.40
3959 6498 6.408035 TGGACTACATACGGAGCAAAATTAA 58.592 36.000 0.00 0.00 0.00 1.40
3960 6499 7.051623 TGGACTACATACGGAGCAAAATTAAT 58.948 34.615 0.00 0.00 0.00 1.40
3961 6500 7.011950 TGGACTACATACGGAGCAAAATTAATG 59.988 37.037 0.00 0.00 0.00 1.90
3962 6501 7.225931 GGACTACATACGGAGCAAAATTAATGA 59.774 37.037 0.00 0.00 0.00 2.57
3963 6502 8.500753 ACTACATACGGAGCAAAATTAATGAA 57.499 30.769 0.00 0.00 0.00 2.57
3964 6503 9.120538 ACTACATACGGAGCAAAATTAATGAAT 57.879 29.630 0.00 0.00 0.00 2.57
3965 6504 9.385902 CTACATACGGAGCAAAATTAATGAATG 57.614 33.333 0.00 0.00 0.00 2.67
3966 6505 7.771183 ACATACGGAGCAAAATTAATGAATGT 58.229 30.769 0.00 0.00 0.00 2.71
3967 6506 8.898761 ACATACGGAGCAAAATTAATGAATGTA 58.101 29.630 0.00 0.00 0.00 2.29
3968 6507 9.169468 CATACGGAGCAAAATTAATGAATGTAC 57.831 33.333 0.00 0.00 0.00 2.90
3969 6508 7.151999 ACGGAGCAAAATTAATGAATGTACA 57.848 32.000 0.00 0.00 0.00 2.90
3970 6509 7.027161 ACGGAGCAAAATTAATGAATGTACAC 58.973 34.615 0.00 0.00 0.00 2.90
3971 6510 7.094377 ACGGAGCAAAATTAATGAATGTACACT 60.094 33.333 0.00 0.00 0.00 3.55
3972 6511 7.754924 CGGAGCAAAATTAATGAATGTACACTT 59.245 33.333 0.00 0.00 0.00 3.16
3995 6534 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
4000 6539 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
4001 6540 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
4002 6541 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
4003 6542 7.093509 TGCATCTATATACATCCGTATGTGGTT 60.094 37.037 3.56 0.00 45.99 3.67
4004 6543 7.435488 GCATCTATATACATCCGTATGTGGTTC 59.565 40.741 3.56 0.00 45.99 3.62
4005 6544 8.466798 CATCTATATACATCCGTATGTGGTTCA 58.533 37.037 3.56 0.00 45.99 3.18
4006 6545 8.589701 TCTATATACATCCGTATGTGGTTCAT 57.410 34.615 3.56 0.00 45.99 2.57
4007 6546 9.689501 TCTATATACATCCGTATGTGGTTCATA 57.310 33.333 3.56 0.00 45.99 2.15
4008 6547 9.952188 CTATATACATCCGTATGTGGTTCATAG 57.048 37.037 3.56 0.80 45.99 2.23
4009 6548 6.665992 ATACATCCGTATGTGGTTCATAGT 57.334 37.500 3.56 0.00 45.99 2.12
4010 6549 4.693283 ACATCCGTATGTGGTTCATAGTG 58.307 43.478 0.00 0.00 44.79 2.74
4011 6550 4.404394 ACATCCGTATGTGGTTCATAGTGA 59.596 41.667 0.00 0.00 44.79 3.41
4012 6551 5.105106 ACATCCGTATGTGGTTCATAGTGAA 60.105 40.000 0.00 0.00 44.79 3.18
4013 6552 5.408880 TCCGTATGTGGTTCATAGTGAAA 57.591 39.130 0.00 0.00 38.22 2.69
4014 6553 5.984725 TCCGTATGTGGTTCATAGTGAAAT 58.015 37.500 0.00 0.00 38.22 2.17
4015 6554 6.411376 TCCGTATGTGGTTCATAGTGAAATT 58.589 36.000 0.00 0.00 38.22 1.82
4016 6555 6.882140 TCCGTATGTGGTTCATAGTGAAATTT 59.118 34.615 0.00 0.00 38.22 1.82
4017 6556 7.065324 TCCGTATGTGGTTCATAGTGAAATTTC 59.935 37.037 11.41 11.41 38.22 2.17
4018 6557 7.065803 CCGTATGTGGTTCATAGTGAAATTTCT 59.934 37.037 18.64 2.61 38.22 2.52
4019 6558 9.093970 CGTATGTGGTTCATAGTGAAATTTCTA 57.906 33.333 18.64 4.82 38.22 2.10
4021 6560 8.862325 ATGTGGTTCATAGTGAAATTTCTACA 57.138 30.769 18.64 4.82 38.22 2.74
4022 6561 8.684386 TGTGGTTCATAGTGAAATTTCTACAA 57.316 30.769 18.64 3.14 38.22 2.41
4023 6562 9.126151 TGTGGTTCATAGTGAAATTTCTACAAA 57.874 29.630 18.64 8.40 38.22 2.83
4024 6563 9.612620 GTGGTTCATAGTGAAATTTCTACAAAG 57.387 33.333 18.64 5.49 38.22 2.77
4025 6564 9.567776 TGGTTCATAGTGAAATTTCTACAAAGA 57.432 29.630 18.64 7.52 38.22 2.52
4026 6565 9.827411 GGTTCATAGTGAAATTTCTACAAAGAC 57.173 33.333 18.64 7.04 38.22 3.01
4041 6580 8.752766 TCTACAAAGACTTGTATTTAGGAACG 57.247 34.615 0.00 0.00 44.95 3.95
4042 6581 6.796705 ACAAAGACTTGTATTTAGGAACGG 57.203 37.500 0.00 0.00 44.14 4.44
4043 6582 6.527423 ACAAAGACTTGTATTTAGGAACGGA 58.473 36.000 0.00 0.00 44.14 4.69
4044 6583 6.649557 ACAAAGACTTGTATTTAGGAACGGAG 59.350 38.462 0.00 0.00 44.14 4.63
4045 6584 5.340439 AGACTTGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
4046 6585 4.161754 AGACTTGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
4047 6586 4.098894 ACTTGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
4048 6587 4.161754 ACTTGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
4049 6588 3.716431 TGTATTTAGGAACGGAGGGAGT 58.284 45.455 0.00 0.00 0.00 3.85
4050 6589 4.870636 TGTATTTAGGAACGGAGGGAGTA 58.129 43.478 0.00 0.00 0.00 2.59
4051 6590 4.646492 TGTATTTAGGAACGGAGGGAGTAC 59.354 45.833 0.00 0.00 0.00 2.73
4078 6617 2.787473 TAAGCTGGTGTTCCTGGATG 57.213 50.000 0.00 0.00 33.97 3.51
4246 6792 6.616947 TGTACCTTTTGTTAATATGCTGTGC 58.383 36.000 0.00 0.00 0.00 4.57
4275 6825 6.477033 CAGAATGGTATGTGTACTTAGCACTC 59.523 42.308 10.66 9.91 37.00 3.51
4338 6888 3.129638 AGCTTCTAGTTAAGTCTGGCGAG 59.870 47.826 0.00 0.00 0.00 5.03
4480 7030 1.591863 GCAATAGAGACGGGGCGAC 60.592 63.158 0.00 0.00 0.00 5.19
4570 7124 1.006571 TGGAGGAGAAACGTCACGC 60.007 57.895 0.00 0.00 35.40 5.34
4587 7141 1.488812 ACGCAGGCAATATTAGGTGGA 59.511 47.619 0.00 0.00 0.00 4.02
4613 7167 1.141881 CGAGCAGATAACCGTGGCT 59.858 57.895 0.00 0.00 37.56 4.75
4666 7220 1.080434 GTCGTCTGCTCAGGTCACC 60.080 63.158 0.00 0.00 0.00 4.02
4685 7239 0.615544 CCCCTGCCACCACATGATTT 60.616 55.000 0.00 0.00 0.00 2.17
4720 7274 1.338020 GGCAAGTTGAAGGGTCACTTG 59.662 52.381 7.16 6.87 40.21 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.472361 GCTCATAATTCCGAACTACTTGTATAA 57.528 33.333 0.00 0.00 0.00 0.98
3 4 7.727181 AGCTCATAATTCCGAACTACTTGTAT 58.273 34.615 0.00 0.00 0.00 2.29
4 5 7.068348 AGAGCTCATAATTCCGAACTACTTGTA 59.932 37.037 17.77 0.00 0.00 2.41
5 6 5.978814 AGCTCATAATTCCGAACTACTTGT 58.021 37.500 0.00 0.00 0.00 3.16
6 7 6.199908 CAGAGCTCATAATTCCGAACTACTTG 59.800 42.308 17.77 0.00 0.00 3.16
7 8 6.276847 CAGAGCTCATAATTCCGAACTACTT 58.723 40.000 17.77 0.00 0.00 2.24
8 9 5.737635 GCAGAGCTCATAATTCCGAACTACT 60.738 44.000 17.77 0.00 0.00 2.57
9 10 4.446051 GCAGAGCTCATAATTCCGAACTAC 59.554 45.833 17.77 0.00 0.00 2.73
10 11 4.099419 TGCAGAGCTCATAATTCCGAACTA 59.901 41.667 17.77 0.00 0.00 2.24
11 12 3.118629 TGCAGAGCTCATAATTCCGAACT 60.119 43.478 17.77 0.00 0.00 3.01
12 13 3.198068 TGCAGAGCTCATAATTCCGAAC 58.802 45.455 17.77 0.00 0.00 3.95
13 14 3.541996 TGCAGAGCTCATAATTCCGAA 57.458 42.857 17.77 0.00 0.00 4.30
14 15 3.758755 ATGCAGAGCTCATAATTCCGA 57.241 42.857 17.77 0.00 0.00 4.55
15 16 5.173664 TGATATGCAGAGCTCATAATTCCG 58.826 41.667 17.77 0.00 31.08 4.30
29 30 2.224475 CCCTGGTCCTTCTGATATGCAG 60.224 54.545 0.00 0.00 46.31 4.41
30 31 1.770658 CCCTGGTCCTTCTGATATGCA 59.229 52.381 0.00 0.00 0.00 3.96
31 32 2.050144 TCCCTGGTCCTTCTGATATGC 58.950 52.381 0.00 0.00 0.00 3.14
32 33 2.036475 CGTCCCTGGTCCTTCTGATATG 59.964 54.545 0.00 0.00 0.00 1.78
60 61 0.899717 TTGGATTTGGGAGGCAGTGC 60.900 55.000 6.55 6.55 0.00 4.40
113 114 8.398878 TGGTGTATAAGTTTTCTTCGGATTTT 57.601 30.769 0.00 0.00 40.91 1.82
210 211 4.142271 TGACTTTGTTTCCGTCTGCATTTT 60.142 37.500 0.00 0.00 0.00 1.82
260 261 2.126071 CGTCACCAGCTACCGTGG 60.126 66.667 7.65 0.00 41.30 4.94
264 265 0.389948 CCTTCACGTCACCAGCTACC 60.390 60.000 0.00 0.00 0.00 3.18
270 271 0.762418 ATGGTTCCTTCACGTCACCA 59.238 50.000 0.00 0.00 41.74 4.17
276 277 1.338674 TGCCACTATGGTTCCTTCACG 60.339 52.381 0.00 0.00 40.46 4.35
373 377 5.891551 ACATCCAAATGTAGACCCCATTAAC 59.108 40.000 0.00 0.00 44.38 2.01
392 396 4.794655 GCTCGATTGACCTTCTCTACATCC 60.795 50.000 0.00 0.00 0.00 3.51
502 835 1.450312 GAGAAGATGCACACGGGGG 60.450 63.158 0.00 0.00 0.00 5.40
541 874 4.576463 AGCCTCATCGTCATGGAATTTTAC 59.424 41.667 0.00 0.00 0.00 2.01
542 875 4.780815 AGCCTCATCGTCATGGAATTTTA 58.219 39.130 0.00 0.00 0.00 1.52
543 876 3.624777 AGCCTCATCGTCATGGAATTTT 58.375 40.909 0.00 0.00 0.00 1.82
545 878 3.287867 AAGCCTCATCGTCATGGAATT 57.712 42.857 0.00 0.00 0.00 2.17
549 882 4.963276 TTAAAAAGCCTCATCGTCATGG 57.037 40.909 0.00 0.00 0.00 3.66
550 883 7.642669 ACATATTAAAAAGCCTCATCGTCATG 58.357 34.615 0.00 0.00 0.00 3.07
551 884 7.807977 ACATATTAAAAAGCCTCATCGTCAT 57.192 32.000 0.00 0.00 0.00 3.06
553 886 8.911247 AAAACATATTAAAAAGCCTCATCGTC 57.089 30.769 0.00 0.00 0.00 4.20
593 926 3.338249 TGAGCAGATACTCTTGTTTGCC 58.662 45.455 0.00 0.00 37.58 4.52
646 2959 3.576550 GCCCCCAATAACTGAAACTGAAA 59.423 43.478 0.00 0.00 0.00 2.69
647 2960 3.161866 GCCCCCAATAACTGAAACTGAA 58.838 45.455 0.00 0.00 0.00 3.02
648 2961 2.802719 GCCCCCAATAACTGAAACTGA 58.197 47.619 0.00 0.00 0.00 3.41
649 2962 1.472480 CGCCCCCAATAACTGAAACTG 59.528 52.381 0.00 0.00 0.00 3.16
650 2963 1.353022 TCGCCCCCAATAACTGAAACT 59.647 47.619 0.00 0.00 0.00 2.66
651 2964 1.471287 GTCGCCCCCAATAACTGAAAC 59.529 52.381 0.00 0.00 0.00 2.78
712 3025 1.460273 GGGGCTTTTGTCGCTTTCCA 61.460 55.000 0.00 0.00 33.90 3.53
826 3144 0.447406 CTGGTGTGTGTGTGTGTGTG 59.553 55.000 0.00 0.00 0.00 3.82
827 3145 0.323302 TCTGGTGTGTGTGTGTGTGT 59.677 50.000 0.00 0.00 0.00 3.72
828 3146 0.726827 GTCTGGTGTGTGTGTGTGTG 59.273 55.000 0.00 0.00 0.00 3.82
829 3147 0.739462 CGTCTGGTGTGTGTGTGTGT 60.739 55.000 0.00 0.00 0.00 3.72
830 3148 1.428370 CCGTCTGGTGTGTGTGTGTG 61.428 60.000 0.00 0.00 0.00 3.82
831 3149 1.153449 CCGTCTGGTGTGTGTGTGT 60.153 57.895 0.00 0.00 0.00 3.72
855 3173 1.518903 GCCTCCGCTTGCTTTCAGTT 61.519 55.000 0.00 0.00 0.00 3.16
901 3228 2.583024 TTTGGCTGTGTGATGATGGA 57.417 45.000 0.00 0.00 0.00 3.41
902 3229 2.821378 TCTTTTGGCTGTGTGATGATGG 59.179 45.455 0.00 0.00 0.00 3.51
903 3230 3.366679 GGTCTTTTGGCTGTGTGATGATG 60.367 47.826 0.00 0.00 0.00 3.07
904 3231 2.821969 GGTCTTTTGGCTGTGTGATGAT 59.178 45.455 0.00 0.00 0.00 2.45
905 3232 2.229792 GGTCTTTTGGCTGTGTGATGA 58.770 47.619 0.00 0.00 0.00 2.92
906 3233 1.069022 CGGTCTTTTGGCTGTGTGATG 60.069 52.381 0.00 0.00 0.00 3.07
907 3234 1.238439 CGGTCTTTTGGCTGTGTGAT 58.762 50.000 0.00 0.00 0.00 3.06
1082 3427 3.279875 GGAATCGACGGCCATGGC 61.280 66.667 29.47 29.47 41.06 4.40
1226 3588 1.916777 GAAACCCCTCCCTCCGACA 60.917 63.158 0.00 0.00 0.00 4.35
2100 4477 5.186797 AGACACAAACAAGGTCCAAATCAAA 59.813 36.000 0.00 0.00 31.99 2.69
2101 4478 4.709397 AGACACAAACAAGGTCCAAATCAA 59.291 37.500 0.00 0.00 31.99 2.57
2102 4479 4.277476 AGACACAAACAAGGTCCAAATCA 58.723 39.130 0.00 0.00 31.99 2.57
2103 4480 4.918810 AGACACAAACAAGGTCCAAATC 57.081 40.909 0.00 0.00 31.99 2.17
2104 4481 5.531287 GTCTAGACACAAACAAGGTCCAAAT 59.469 40.000 18.20 0.00 31.99 2.32
2176 4553 6.151691 CCATAAAACCATGGCGATCAATTAG 58.848 40.000 13.04 0.00 39.18 1.73
2355 4852 7.148188 GGAGTAAAGATGAAACAGCATGAATGA 60.148 37.037 0.00 0.00 39.69 2.57
2664 5162 2.451167 CCGAGCAAGCTGAGCTTCG 61.451 63.158 18.16 17.75 46.77 3.79
2757 5255 1.451927 GGCCGGATCAGCATTCACA 60.452 57.895 5.05 0.00 0.00 3.58
2785 5283 5.606348 AAGTTGCCATTTTTGTCAGGTAA 57.394 34.783 0.00 0.00 0.00 2.85
2914 5413 4.672024 GCTCATTCACAATCTGCAACAGAG 60.672 45.833 3.42 0.00 44.08 3.35
3059 5558 3.117171 GCTCTCACTGCACCAGCG 61.117 66.667 0.00 0.00 46.23 5.18
3230 5729 4.881273 ACTGTGACAGAGTTTGTTGCATTA 59.119 37.500 20.97 0.00 41.05 1.90
3269 5768 0.249531 CAGCAAATGCAACTGTGGCA 60.250 50.000 13.04 13.04 46.66 4.92
3314 5813 0.682292 TTGCTACACCATGGTCGTCA 59.318 50.000 16.53 7.96 0.00 4.35
3611 6110 3.492482 CCACATAGTATGTCATCGTGCCA 60.492 47.826 13.00 0.00 42.70 4.92
3689 6188 1.144708 TGGTTCCATGAGTTTGAGCCA 59.855 47.619 0.00 0.00 37.09 4.75
3769 6268 2.990066 AAAGACCGAGGCTTCATAGG 57.010 50.000 0.00 0.00 0.00 2.57
3772 6271 2.162681 CCAAAAAGACCGAGGCTTCAT 58.837 47.619 0.00 0.00 0.00 2.57
3773 6272 1.604604 CCAAAAAGACCGAGGCTTCA 58.395 50.000 0.00 0.00 0.00 3.02
3774 6273 0.241213 GCCAAAAAGACCGAGGCTTC 59.759 55.000 0.00 0.00 42.01 3.86
3776 6275 1.966451 CGCCAAAAAGACCGAGGCT 60.966 57.895 0.00 0.00 43.07 4.58
3778 6277 2.978018 GCCGCCAAAAAGACCGAGG 61.978 63.158 0.00 0.00 0.00 4.63
3779 6278 2.561373 GCCGCCAAAAAGACCGAG 59.439 61.111 0.00 0.00 0.00 4.63
3816 6352 3.636764 ACTTAGTGCCAACCCTTTCTTTG 59.363 43.478 0.00 0.00 0.00 2.77
3835 6374 5.222048 TGGAGGGTCAAAGCTGTTTATACTT 60.222 40.000 0.00 0.00 0.00 2.24
3866 6405 1.004628 ACGGTAAAACCCCATACCCAC 59.995 52.381 0.00 0.00 38.68 4.61
3868 6407 3.862877 ATACGGTAAAACCCCATACCC 57.137 47.619 0.00 0.00 38.68 3.69
3869 6408 5.511373 GGAGTATACGGTAAAACCCCATACC 60.511 48.000 0.00 0.00 34.44 2.73
3870 6409 5.511373 GGGAGTATACGGTAAAACCCCATAC 60.511 48.000 16.76 6.62 33.75 2.39
3871 6410 4.592778 GGGAGTATACGGTAAAACCCCATA 59.407 45.833 16.76 0.00 33.75 2.74
3872 6411 3.392285 GGGAGTATACGGTAAAACCCCAT 59.608 47.826 16.76 0.00 33.75 4.00
3873 6412 2.771372 GGGAGTATACGGTAAAACCCCA 59.229 50.000 16.76 0.00 33.75 4.96
3874 6413 3.041211 AGGGAGTATACGGTAAAACCCC 58.959 50.000 14.72 15.03 37.06 4.95
3891 6430 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3892 6431 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3893 6432 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
3894 6433 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
3896 6435 9.257651 CCTACAAAGACTTATATTTAGGAACGG 57.742 37.037 0.00 0.00 0.00 4.44
3897 6436 9.257651 CCCTACAAAGACTTATATTTAGGAACG 57.742 37.037 0.00 0.00 0.00 3.95
3910 6449 9.892130 CATCTAGTAAAATCCCTACAAAGACTT 57.108 33.333 0.00 0.00 0.00 3.01
3911 6450 8.487028 CCATCTAGTAAAATCCCTACAAAGACT 58.513 37.037 0.00 0.00 0.00 3.24
3912 6451 8.483758 TCCATCTAGTAAAATCCCTACAAAGAC 58.516 37.037 0.00 0.00 0.00 3.01
3913 6452 8.483758 GTCCATCTAGTAAAATCCCTACAAAGA 58.516 37.037 0.00 0.00 0.00 2.52
3914 6453 8.487028 AGTCCATCTAGTAAAATCCCTACAAAG 58.513 37.037 0.00 0.00 0.00 2.77
3915 6454 8.388656 AGTCCATCTAGTAAAATCCCTACAAA 57.611 34.615 0.00 0.00 0.00 2.83
3916 6455 7.989947 AGTCCATCTAGTAAAATCCCTACAA 57.010 36.000 0.00 0.00 0.00 2.41
3917 6456 8.063153 TGTAGTCCATCTAGTAAAATCCCTACA 58.937 37.037 0.00 0.00 0.00 2.74
3918 6457 8.474710 TGTAGTCCATCTAGTAAAATCCCTAC 57.525 38.462 0.00 0.00 0.00 3.18
3920 6459 9.091220 GTATGTAGTCCATCTAGTAAAATCCCT 57.909 37.037 0.00 0.00 34.86 4.20
3921 6460 8.027771 CGTATGTAGTCCATCTAGTAAAATCCC 58.972 40.741 0.00 0.00 34.86 3.85
3922 6461 8.027771 CCGTATGTAGTCCATCTAGTAAAATCC 58.972 40.741 0.00 0.00 34.86 3.01
3923 6462 8.790718 TCCGTATGTAGTCCATCTAGTAAAATC 58.209 37.037 0.00 0.00 34.86 2.17
3924 6463 8.701908 TCCGTATGTAGTCCATCTAGTAAAAT 57.298 34.615 0.00 0.00 34.86 1.82
3925 6464 7.255381 GCTCCGTATGTAGTCCATCTAGTAAAA 60.255 40.741 0.00 0.00 34.86 1.52
3926 6465 6.206243 GCTCCGTATGTAGTCCATCTAGTAAA 59.794 42.308 0.00 0.00 34.86 2.01
3927 6466 5.704515 GCTCCGTATGTAGTCCATCTAGTAA 59.295 44.000 0.00 0.00 34.86 2.24
3928 6467 5.221783 TGCTCCGTATGTAGTCCATCTAGTA 60.222 44.000 0.00 0.00 34.86 1.82
3929 6468 4.073549 GCTCCGTATGTAGTCCATCTAGT 58.926 47.826 0.00 0.00 34.86 2.57
3930 6469 4.072839 TGCTCCGTATGTAGTCCATCTAG 58.927 47.826 0.00 0.00 34.86 2.43
3931 6470 4.094830 TGCTCCGTATGTAGTCCATCTA 57.905 45.455 0.00 0.00 34.86 1.98
3932 6471 2.945456 TGCTCCGTATGTAGTCCATCT 58.055 47.619 0.00 0.00 34.86 2.90
3933 6472 3.728076 TTGCTCCGTATGTAGTCCATC 57.272 47.619 0.00 0.00 34.86 3.51
3934 6473 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
3935 6474 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
3936 6475 6.913873 TTAATTTTGCTCCGTATGTAGTCC 57.086 37.500 0.00 0.00 0.00 3.85
3937 6476 8.138365 TCATTAATTTTGCTCCGTATGTAGTC 57.862 34.615 0.00 0.00 0.00 2.59
3938 6477 8.500753 TTCATTAATTTTGCTCCGTATGTAGT 57.499 30.769 0.00 0.00 0.00 2.73
3939 6478 9.385902 CATTCATTAATTTTGCTCCGTATGTAG 57.614 33.333 0.00 0.00 0.00 2.74
3940 6479 8.898761 ACATTCATTAATTTTGCTCCGTATGTA 58.101 29.630 0.00 0.00 0.00 2.29
3941 6480 7.771183 ACATTCATTAATTTTGCTCCGTATGT 58.229 30.769 0.00 0.00 0.00 2.29
3942 6481 9.169468 GTACATTCATTAATTTTGCTCCGTATG 57.831 33.333 0.00 0.00 0.00 2.39
3943 6482 8.898761 TGTACATTCATTAATTTTGCTCCGTAT 58.101 29.630 0.00 0.00 0.00 3.06
3944 6483 8.178964 GTGTACATTCATTAATTTTGCTCCGTA 58.821 33.333 0.00 0.00 0.00 4.02
3945 6484 7.027161 GTGTACATTCATTAATTTTGCTCCGT 58.973 34.615 0.00 0.00 0.00 4.69
3946 6485 7.250569 AGTGTACATTCATTAATTTTGCTCCG 58.749 34.615 0.00 0.00 0.00 4.63
3947 6486 8.986477 AAGTGTACATTCATTAATTTTGCTCC 57.014 30.769 0.00 0.00 0.00 4.70
3969 6508 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
3973 6512 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
3974 6513 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
3975 6514 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
3976 6515 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
3977 6516 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
3978 6517 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
3979 6518 8.466798 TGAACCACATACGGATGTATATAGATG 58.533 37.037 14.23 0.00 44.82 2.90
3980 6519 8.589701 TGAACCACATACGGATGTATATAGAT 57.410 34.615 14.23 0.00 44.82 1.98
3981 6520 8.589701 ATGAACCACATACGGATGTATATAGA 57.410 34.615 14.23 0.00 44.82 1.98
3982 6521 9.952188 CTATGAACCACATACGGATGTATATAG 57.048 37.037 14.23 12.28 44.82 1.31
3983 6522 9.470399 ACTATGAACCACATACGGATGTATATA 57.530 33.333 14.23 7.10 44.82 0.86
3984 6523 8.251026 CACTATGAACCACATACGGATGTATAT 58.749 37.037 14.23 1.68 44.82 0.86
3985 6524 7.449086 TCACTATGAACCACATACGGATGTATA 59.551 37.037 14.23 6.48 44.82 1.47
3986 6525 6.266786 TCACTATGAACCACATACGGATGTAT 59.733 38.462 14.23 5.54 44.82 2.29
3987 6526 5.595133 TCACTATGAACCACATACGGATGTA 59.405 40.000 14.23 0.00 44.82 2.29
3988 6527 5.105106 TTCACTATGAACCACATACGGATGT 60.105 40.000 7.68 7.68 37.89 3.06
3989 6528 4.944048 TCACTATGAACCACATACGGATG 58.056 43.478 5.94 5.94 40.07 3.51
3990 6529 5.607939 TTCACTATGAACCACATACGGAT 57.392 39.130 0.00 0.00 40.07 4.18
3991 6530 5.408880 TTTCACTATGAACCACATACGGA 57.591 39.130 0.00 0.00 35.89 4.69
3992 6531 6.677781 AATTTCACTATGAACCACATACGG 57.322 37.500 0.00 0.00 35.89 4.02
3993 6532 7.974675 AGAAATTTCACTATGAACCACATACG 58.025 34.615 19.99 0.00 35.89 3.06
3995 6534 9.952030 TGTAGAAATTTCACTATGAACCACATA 57.048 29.630 19.99 0.00 35.89 2.29
3996 6535 8.862325 TGTAGAAATTTCACTATGAACCACAT 57.138 30.769 19.99 0.00 35.89 3.21
3997 6536 8.684386 TTGTAGAAATTTCACTATGAACCACA 57.316 30.769 19.99 5.40 35.89 4.17
3998 6537 9.612620 CTTTGTAGAAATTTCACTATGAACCAC 57.387 33.333 19.99 3.25 35.89 4.16
3999 6538 9.567776 TCTTTGTAGAAATTTCACTATGAACCA 57.432 29.630 19.99 0.96 35.89 3.67
4000 6539 9.827411 GTCTTTGTAGAAATTTCACTATGAACC 57.173 33.333 19.99 6.84 31.84 3.62
4020 6559 6.092259 CCTCCGTTCCTAAATACAAGTCTTTG 59.908 42.308 0.00 0.00 40.24 2.77
4021 6560 6.171213 CCTCCGTTCCTAAATACAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
4022 6561 5.338137 CCCTCCGTTCCTAAATACAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
4023 6562 4.161754 CCCTCCGTTCCTAAATACAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
4024 6563 4.161001 TCCCTCCGTTCCTAAATACAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
4025 6564 4.098894 TCCCTCCGTTCCTAAATACAAGT 58.901 43.478 0.00 0.00 0.00 3.16
4026 6565 4.161754 ACTCCCTCCGTTCCTAAATACAAG 59.838 45.833 0.00 0.00 0.00 3.16
4027 6566 4.098894 ACTCCCTCCGTTCCTAAATACAA 58.901 43.478 0.00 0.00 0.00 2.41
4028 6567 3.716431 ACTCCCTCCGTTCCTAAATACA 58.284 45.455 0.00 0.00 0.00 2.29
4029 6568 4.646492 TGTACTCCCTCCGTTCCTAAATAC 59.354 45.833 0.00 0.00 0.00 1.89
4030 6569 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
4031 6570 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
4032 6571 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
4033 6572 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
4034 6573 3.294214 GAATGTACTCCCTCCGTTCCTA 58.706 50.000 0.00 0.00 0.00 2.94
4035 6574 2.108970 GAATGTACTCCCTCCGTTCCT 58.891 52.381 0.00 0.00 0.00 3.36
4036 6575 1.138464 GGAATGTACTCCCTCCGTTCC 59.862 57.143 0.00 0.00 37.17 3.62
4037 6576 1.829222 TGGAATGTACTCCCTCCGTTC 59.171 52.381 0.00 0.00 34.22 3.95
4038 6577 1.946984 TGGAATGTACTCCCTCCGTT 58.053 50.000 0.00 0.00 34.22 4.44
4039 6578 1.946984 TTGGAATGTACTCCCTCCGT 58.053 50.000 0.00 0.00 34.22 4.69
4040 6579 4.632153 CTTATTGGAATGTACTCCCTCCG 58.368 47.826 0.00 0.00 34.22 4.63
4041 6580 4.103311 AGCTTATTGGAATGTACTCCCTCC 59.897 45.833 0.00 0.00 34.22 4.30
4042 6581 5.059833 CAGCTTATTGGAATGTACTCCCTC 58.940 45.833 0.00 0.00 34.22 4.30
4043 6582 4.141390 CCAGCTTATTGGAATGTACTCCCT 60.141 45.833 0.00 0.00 40.87 4.20
4044 6583 4.137543 CCAGCTTATTGGAATGTACTCCC 58.862 47.826 0.00 0.00 40.87 4.30
4045 6584 4.576463 CACCAGCTTATTGGAATGTACTCC 59.424 45.833 0.00 0.00 40.87 3.85
4046 6585 5.186198 ACACCAGCTTATTGGAATGTACTC 58.814 41.667 0.00 0.00 40.87 2.59
4047 6586 5.179452 ACACCAGCTTATTGGAATGTACT 57.821 39.130 0.00 0.00 40.87 2.73
4048 6587 5.163652 GGAACACCAGCTTATTGGAATGTAC 60.164 44.000 0.00 0.00 40.87 2.90
4049 6588 4.947388 GGAACACCAGCTTATTGGAATGTA 59.053 41.667 0.00 0.00 40.87 2.29
4050 6589 3.763897 GGAACACCAGCTTATTGGAATGT 59.236 43.478 0.00 0.00 40.87 2.71
4051 6590 4.019174 AGGAACACCAGCTTATTGGAATG 58.981 43.478 0.00 0.00 40.87 2.67
4091 6630 2.462255 TACAACACGACCGTCGCCTC 62.462 60.000 20.67 0.00 45.12 4.70
4246 6792 6.642950 GCTAAGTACACATACCATTCTGCTAG 59.357 42.308 0.00 0.00 30.88 3.42
4299 6849 5.329399 AGAAGCTTCTAGAACCTTCTCAGA 58.671 41.667 26.95 0.00 38.35 3.27
4338 6888 1.744741 GAGAGCAGCAAGGAGGCAC 60.745 63.158 0.00 0.00 35.83 5.01
4377 6927 2.877043 ATCATGGAAAATCTTGGCGC 57.123 45.000 0.00 0.00 0.00 6.53
4378 6928 5.002464 AGAAATCATGGAAAATCTTGGCG 57.998 39.130 0.00 0.00 0.00 5.69
4491 7041 1.271379 GCCAGGTCAAGCTTTCCTACA 60.271 52.381 16.62 0.00 0.00 2.74
4570 7124 5.242393 CAGGAAATCCACCTAATATTGCCTG 59.758 44.000 6.86 6.86 45.58 4.85
4587 7141 2.565841 GGTTATCTGCTCGCAGGAAAT 58.434 47.619 17.93 7.75 43.75 2.17
4613 7167 3.071457 TCACAAGTCAAATGAGCTGAGGA 59.929 43.478 0.00 0.00 0.00 3.71
4666 7220 0.615544 AAATCATGTGGTGGCAGGGG 60.616 55.000 0.00 0.00 0.00 4.79
4685 7239 2.028112 ACTTGCCGAGCTGATCAAAGTA 60.028 45.455 5.16 0.00 28.89 2.24
4720 7274 3.968649 TCAACTTTCAATGCAGCAACTC 58.031 40.909 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.