Multiple sequence alignment - TraesCS5B01G153700

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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 TraesCS5B01G153700 chr5B 100.000 5194 0 0 1 5194 283024472 283019279 0.000000e+00 9592.0
1 TraesCS5B01G153700 chr5B 85.018 821 119 4 2777 3595 283204942 283204124 0.000000e+00 832.0
2 TraesCS5B01G153700 chr5B 83.559 517 81 4 1256 1770 283206459 283205945 1.010000e-131 481.0
3 TraesCS5B01G153700 chr5B 86.614 127 13 2 3790 3915 283204019 283203896 2.520000e-28 137.0
4 TraesCS5B01G153700 chr5B 98.148 54 0 1 3666 3718 283020754 283020701 5.540000e-15 93.5
5 TraesCS5B01G153700 chr5B 98.148 54 0 1 3719 3772 283020807 283020755 5.540000e-15 93.5
6 TraesCS5B01G153700 chr5D 96.656 1794 41 3 1928 3718 250074845 250073068 0.000000e+00 2963.0
7 TraesCS5B01G153700 chr5D 94.129 1005 34 7 925 1925 250075949 250074966 0.000000e+00 1506.0
8 TraesCS5B01G153700 chr5D 96.347 657 11 3 4548 5194 250072254 250071601 0.000000e+00 1068.0
9 TraesCS5B01G153700 chr5D 83.942 822 128 4 2776 3595 250407808 250406989 0.000000e+00 784.0
10 TraesCS5B01G153700 chr5D 79.772 791 121 18 982 1770 250409554 250408801 5.920000e-149 538.0
11 TraesCS5B01G153700 chr5D 90.033 301 27 1 3719 4019 250073121 250072824 2.270000e-103 387.0
12 TraesCS5B01G153700 chr5D 82.162 185 26 4 3753 3934 250406904 250406724 9.010000e-33 152.0
13 TraesCS5B01G153700 chr5A 97.824 1011 20 2 2709 3718 333420796 333419787 0.000000e+00 1744.0
14 TraesCS5B01G153700 chr5A 95.704 1001 34 1 925 1925 333422400 333421409 0.000000e+00 1602.0
15 TraesCS5B01G153700 chr5A 96.195 657 10 5 4548 5194 333419091 333418440 0.000000e+00 1061.0
16 TraesCS5B01G153700 chr5A 84.933 823 120 4 2776 3596 333441237 333440417 0.000000e+00 830.0
17 TraesCS5B01G153700 chr5A 95.902 488 19 1 1928 2415 333421286 333420800 0.000000e+00 789.0
18 TraesCS5B01G153700 chr5A 79.794 777 119 18 995 1770 333442875 333442136 9.900000e-147 531.0
19 TraesCS5B01G153700 chr5A 83.579 475 39 17 3719 4190 333419840 333419402 4.840000e-110 409.0
20 TraesCS5B01G153700 chr5A 90.090 111 8 1 3805 3915 333440358 333440251 1.950000e-29 141.0
21 TraesCS5B01G153700 chr3B 98.375 923 14 1 1 922 821079529 821078607 0.000000e+00 1620.0
22 TraesCS5B01G153700 chr7B 91.572 617 40 2 39 651 340518976 340519584 0.000000e+00 841.0
23 TraesCS5B01G153700 chr7B 78.748 607 95 14 3005 3610 87148498 87147925 4.910000e-100 375.0
24 TraesCS5B01G153700 chr7B 89.216 102 11 0 3831 3932 87147838 87147737 1.520000e-25 128.0
25 TraesCS5B01G153700 chr7B 76.804 194 40 5 734 924 614613736 614613927 2.560000e-18 104.0
26 TraesCS5B01G153700 chr7B 100.000 36 0 0 1 36 340518921 340518956 3.360000e-07 67.6
27 TraesCS5B01G153700 chr7D 82.215 641 104 4 3000 3640 126647958 126647328 1.270000e-150 544.0
28 TraesCS5B01G153700 chr7D 78.878 606 95 13 3005 3610 126477518 126476946 3.800000e-101 379.0
29 TraesCS5B01G153700 chr7D 83.696 184 18 11 3772 3953 126647279 126647106 4.160000e-36 163.0
30 TraesCS5B01G153700 chr7D 86.179 123 15 2 3831 3953 126476861 126476741 1.170000e-26 132.0
31 TraesCS5B01G153700 chr7A 80.997 642 103 9 3000 3640 127582002 127581379 4.670000e-135 492.0
32 TraesCS5B01G153700 chr7A 83.243 185 19 11 3771 3953 127581337 127581163 5.380000e-35 159.0
33 TraesCS5B01G153700 chr3D 83.784 74 12 0 853 926 574513029 574512956 2.590000e-08 71.3


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 TraesCS5B01G153700 chr5B 283019279 283024472 5193 True 3259.666667 9592 98.765333 1 5194 3 chr5B.!!$R1 5193
1 TraesCS5B01G153700 chr5B 283203896 283206459 2563 True 483.333333 832 85.063667 1256 3915 3 chr5B.!!$R2 2659
2 TraesCS5B01G153700 chr5D 250071601 250075949 4348 True 1481.000000 2963 94.291250 925 5194 4 chr5D.!!$R1 4269
3 TraesCS5B01G153700 chr5D 250406724 250409554 2830 True 491.333333 784 81.958667 982 3934 3 chr5D.!!$R2 2952
4 TraesCS5B01G153700 chr5A 333418440 333422400 3960 True 1121.000000 1744 93.840800 925 5194 5 chr5A.!!$R1 4269
5 TraesCS5B01G153700 chr5A 333440251 333442875 2624 True 500.666667 830 84.939000 995 3915 3 chr5A.!!$R2 2920
6 TraesCS5B01G153700 chr3B 821078607 821079529 922 True 1620.000000 1620 98.375000 1 922 1 chr3B.!!$R1 921
7 TraesCS5B01G153700 chr7B 340518921 340519584 663 False 454.300000 841 95.786000 1 651 2 chr7B.!!$F2 650
8 TraesCS5B01G153700 chr7B 87147737 87148498 761 True 251.500000 375 83.982000 3005 3932 2 chr7B.!!$R1 927
9 TraesCS5B01G153700 chr7D 126647106 126647958 852 True 353.500000 544 82.955500 3000 3953 2 chr7D.!!$R2 953
10 TraesCS5B01G153700 chr7D 126476741 126477518 777 True 255.500000 379 82.528500 3005 3953 2 chr7D.!!$R1 948
11 TraesCS5B01G153700 chr7A 127581163 127582002 839 True 325.500000 492 82.120000 3000 3953 2 chr7A.!!$R1 953

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
968 995 0.322008 CCCCTTCCTCTTGTCTGTGC 60.322 60.000 0.00 0.00 0.00 4.57 F
2609 2952 1.071471 CCAGTTCGGTGCAGGTCTT 59.929 57.895 0.00 0.00 0.00 3.01 F
3572 3949 0.108233 GAACTCTCAGAGGGCTGCTG 60.108 60.000 6.64 1.54 42.01 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2672 3015 3.913548 TGCATGTAAGCAAAACGTGAT 57.086 38.095 8.88 0.0 42.46 3.06 R
3941 4395 0.748729 AGTCGTCGTCATCCTCCTCC 60.749 60.000 0.00 0.0 0.00 4.30 R
4902 5556 0.805614 TCGAAGCTGAGAAGGAGACG 59.194 55.000 0.00 0.0 0.00 4.18 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
191 209 1.078143 GGCTGAATCTCCGCCTGTT 60.078 57.895 2.19 0.00 40.62 3.16
242 260 4.043100 TCCGCTGGAGAGGACCGA 62.043 66.667 0.00 0.00 39.12 4.69
245 263 2.636412 CGCTGGAGAGGACCGAACA 61.636 63.158 0.00 0.00 0.00 3.18
407 425 2.354729 CCGGATTGGGAGTGGCAA 59.645 61.111 0.00 0.00 0.00 4.52
480 498 2.095364 CGCACTTGTAGTACCGAGTTCT 60.095 50.000 0.00 0.00 0.00 3.01
873 896 1.323534 GCGAATCTTAGCGCGAAAGAA 59.676 47.619 25.25 13.34 43.96 2.52
922 945 3.775202 TCGAGCTCAGAATAGCACTTTC 58.225 45.455 15.40 0.00 45.30 2.62
923 946 2.533535 CGAGCTCAGAATAGCACTTTCG 59.466 50.000 15.40 0.00 45.30 3.46
968 995 0.322008 CCCCTTCCTCTTGTCTGTGC 60.322 60.000 0.00 0.00 0.00 4.57
976 1003 4.539083 TTGTCTGTGCCGCACCGT 62.539 61.111 20.67 0.00 32.73 4.83
1131 1158 1.117749 CCATCCAGGCATCTCTCCGA 61.118 60.000 0.00 0.00 0.00 4.55
1210 1237 4.150454 CCGCCTCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
1211 1238 2.520741 CGCCTCCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
1212 1239 2.520741 GCCTCCTCCTCCTCCTCG 60.521 72.222 0.00 0.00 0.00 4.63
1635 1662 2.114411 GAAGGGTTTGTGGGCGGA 59.886 61.111 0.00 0.00 0.00 5.54
2035 2323 9.830975 TCCATTTTACCATACATCGGATATATG 57.169 33.333 8.91 8.91 0.00 1.78
2049 2337 7.236674 TCGGATATATGGTGTTTTTACAACG 57.763 36.000 0.00 0.00 0.00 4.10
2075 2363 8.148999 GGGGATATACAGTTAACGAATCTCTTT 58.851 37.037 0.00 0.00 0.00 2.52
2227 2515 4.292186 TGCTGTTAGAAAAGCAGAGGAT 57.708 40.909 2.88 0.00 44.26 3.24
2466 2806 3.912496 ATGTGACTAGTATGGCAGCAA 57.088 42.857 0.00 0.00 0.00 3.91
2564 2907 5.645056 TCCTATTTGTCTGGCATAATGGA 57.355 39.130 0.00 0.00 0.00 3.41
2609 2952 1.071471 CCAGTTCGGTGCAGGTCTT 59.929 57.895 0.00 0.00 0.00 3.01
2644 2987 4.332819 CAGTAGAAGTATTTTCCCTTGCCG 59.667 45.833 0.00 0.00 0.00 5.69
2648 2991 3.434940 AGTATTTTCCCTTGCCGAAGT 57.565 42.857 0.00 0.00 0.00 3.01
2666 3009 6.915843 GCCGAAGTGAAAATTGAGTAAAGAAA 59.084 34.615 0.00 0.00 0.00 2.52
2695 3038 5.559427 TCACGTTTTGCTTACATGCATAT 57.441 34.783 0.00 0.00 42.96 1.78
3135 3510 6.195700 AGTTAAGCTACTCCATGGAACTCTA 58.804 40.000 17.00 2.23 0.00 2.43
3231 3607 4.126437 TGTTAGATATCATGGTGCAACGG 58.874 43.478 5.32 0.00 38.12 4.44
3572 3949 0.108233 GAACTCTCAGAGGGCTGCTG 60.108 60.000 6.64 1.54 42.01 4.41
3686 4097 8.766000 TGATTTTTCATGTCAATCAATTCCTG 57.234 30.769 11.89 0.00 34.66 3.86
3687 4098 8.369424 TGATTTTTCATGTCAATCAATTCCTGT 58.631 29.630 11.89 0.00 34.66 4.00
3689 4100 7.949903 TTTTCATGTCAATCAATTCCTGTTG 57.050 32.000 0.00 0.00 0.00 3.33
3690 4101 6.897706 TTCATGTCAATCAATTCCTGTTGA 57.102 33.333 0.00 0.00 41.88 3.18
3692 4103 6.859017 TCATGTCAATCAATTCCTGTTGATG 58.141 36.000 3.18 0.00 45.49 3.07
3693 4104 6.434965 TCATGTCAATCAATTCCTGTTGATGT 59.565 34.615 3.18 0.00 45.49 3.06
3694 4105 6.016213 TGTCAATCAATTCCTGTTGATGTG 57.984 37.500 3.18 4.85 45.49 3.21
3696 4107 6.040729 TGTCAATCAATTCCTGTTGATGTGTT 59.959 34.615 3.18 0.00 45.49 3.32
3697 4108 6.925165 GTCAATCAATTCCTGTTGATGTGTTT 59.075 34.615 3.18 0.00 45.49 2.83
3698 4109 7.439056 GTCAATCAATTCCTGTTGATGTGTTTT 59.561 33.333 3.18 0.00 45.49 2.43
3699 4110 7.986320 TCAATCAATTCCTGTTGATGTGTTTTT 59.014 29.630 3.18 0.00 45.49 1.94
3700 4111 7.951530 ATCAATTCCTGTTGATGTGTTTTTC 57.048 32.000 1.66 0.00 44.75 2.29
3701 4112 6.871844 TCAATTCCTGTTGATGTGTTTTTCA 58.128 32.000 0.00 0.00 33.41 2.69
3702 4113 7.499292 TCAATTCCTGTTGATGTGTTTTTCAT 58.501 30.769 0.00 0.00 33.41 2.57
3703 4114 7.438757 TCAATTCCTGTTGATGTGTTTTTCATG 59.561 33.333 0.00 0.00 33.41 3.07
3704 4115 5.850557 TCCTGTTGATGTGTTTTTCATGT 57.149 34.783 0.00 0.00 0.00 3.21
3705 4116 5.830912 TCCTGTTGATGTGTTTTTCATGTC 58.169 37.500 0.00 0.00 0.00 3.06
3706 4117 4.984161 CCTGTTGATGTGTTTTTCATGTCC 59.016 41.667 0.00 0.00 0.00 4.02
3707 4118 5.221303 CCTGTTGATGTGTTTTTCATGTCCT 60.221 40.000 0.00 0.00 0.00 3.85
3708 4119 6.016360 CCTGTTGATGTGTTTTTCATGTCCTA 60.016 38.462 0.00 0.00 0.00 2.94
3709 4120 7.340122 TGTTGATGTGTTTTTCATGTCCTAA 57.660 32.000 0.00 0.00 0.00 2.69
3710 4121 7.950512 TGTTGATGTGTTTTTCATGTCCTAAT 58.049 30.769 0.00 0.00 0.00 1.73
3711 4122 7.866898 TGTTGATGTGTTTTTCATGTCCTAATG 59.133 33.333 0.00 0.00 0.00 1.90
3712 4123 6.389091 TGATGTGTTTTTCATGTCCTAATGC 58.611 36.000 0.00 0.00 0.00 3.56
3713 4124 6.209192 TGATGTGTTTTTCATGTCCTAATGCT 59.791 34.615 0.00 0.00 0.00 3.79
3714 4125 6.012658 TGTGTTTTTCATGTCCTAATGCTC 57.987 37.500 0.00 0.00 0.00 4.26
3715 4126 5.534278 TGTGTTTTTCATGTCCTAATGCTCA 59.466 36.000 0.00 0.00 0.00 4.26
3716 4127 5.858581 GTGTTTTTCATGTCCTAATGCTCAC 59.141 40.000 0.00 0.00 0.00 3.51
3717 4128 5.534278 TGTTTTTCATGTCCTAATGCTCACA 59.466 36.000 0.00 0.00 0.00 3.58
3718 4129 6.209192 TGTTTTTCATGTCCTAATGCTCACAT 59.791 34.615 0.00 0.00 38.49 3.21
3720 4131 6.839124 TTTCATGTCCTAATGCTCACATTT 57.161 33.333 0.00 0.00 44.21 2.32
3721 4132 6.839124 TTCATGTCCTAATGCTCACATTTT 57.161 33.333 0.00 0.00 44.21 1.82
3722 4133 6.441093 TCATGTCCTAATGCTCACATTTTC 57.559 37.500 0.00 0.00 44.21 2.29
3723 4134 5.945191 TCATGTCCTAATGCTCACATTTTCA 59.055 36.000 0.00 0.00 44.21 2.69
3724 4135 6.604396 TCATGTCCTAATGCTCACATTTTCAT 59.396 34.615 0.00 0.00 44.21 2.57
3725 4136 6.198650 TGTCCTAATGCTCACATTTTCATG 57.801 37.500 0.00 0.00 44.21 3.07
3726 4137 5.711506 TGTCCTAATGCTCACATTTTCATGT 59.288 36.000 0.00 0.00 44.21 3.21
3727 4138 6.127925 TGTCCTAATGCTCACATTTTCATGTC 60.128 38.462 0.00 0.00 44.21 3.06
3728 4139 5.945191 TCCTAATGCTCACATTTTCATGTCA 59.055 36.000 0.00 0.00 44.21 3.58
3729 4140 6.433716 TCCTAATGCTCACATTTTCATGTCAA 59.566 34.615 0.00 0.00 44.21 3.18
3730 4141 7.123098 TCCTAATGCTCACATTTTCATGTCAAT 59.877 33.333 0.00 0.00 44.21 2.57
3731 4142 7.434307 CCTAATGCTCACATTTTCATGTCAATC 59.566 37.037 0.00 0.00 44.21 2.67
3732 4143 5.708877 TGCTCACATTTTCATGTCAATCA 57.291 34.783 0.00 0.00 42.14 2.57
3733 4144 6.086785 TGCTCACATTTTCATGTCAATCAA 57.913 33.333 0.00 0.00 42.14 2.57
3734 4145 6.693466 TGCTCACATTTTCATGTCAATCAAT 58.307 32.000 0.00 0.00 42.14 2.57
3735 4146 7.156000 TGCTCACATTTTCATGTCAATCAATT 58.844 30.769 0.00 0.00 42.14 2.32
3736 4147 7.329962 TGCTCACATTTTCATGTCAATCAATTC 59.670 33.333 0.00 0.00 42.14 2.17
3737 4148 7.201496 GCTCACATTTTCATGTCAATCAATTCC 60.201 37.037 0.00 0.00 42.14 3.01
3738 4149 7.668492 TCACATTTTCATGTCAATCAATTCCA 58.332 30.769 0.00 0.00 42.14 3.53
3741 4152 8.098286 ACATTTTCATGTCAATCAATTCCATGT 58.902 29.630 0.00 0.00 39.69 3.21
3817 4228 3.251004 ACCTTTTCGTGCATCTTGTTCTC 59.749 43.478 0.00 0.00 0.00 2.87
3821 4232 0.368227 CGTGCATCTTGTTCTCGCTC 59.632 55.000 0.00 0.00 0.00 5.03
3956 4410 0.395862 TGGAGGAGGAGGATGACGAC 60.396 60.000 0.00 0.00 0.00 4.34
3959 4413 0.748729 AGGAGGAGGATGACGACGAC 60.749 60.000 0.00 0.00 0.00 4.34
3960 4414 0.748729 GGAGGAGGATGACGACGACT 60.749 60.000 0.00 0.00 0.00 4.18
3968 4422 4.643463 AGGATGACGACGACTATGACTAT 58.357 43.478 0.00 0.00 0.00 2.12
3971 4425 4.790810 TGACGACGACTATGACTATGAC 57.209 45.455 0.00 0.00 0.00 3.06
3972 4426 4.439968 TGACGACGACTATGACTATGACT 58.560 43.478 0.00 0.00 0.00 3.41
3974 4428 6.221659 TGACGACGACTATGACTATGACTAT 58.778 40.000 0.00 0.00 0.00 2.12
3977 4431 6.145858 ACGACGACTATGACTATGACTATGAC 59.854 42.308 0.00 0.00 0.00 3.06
3978 4432 6.366604 CGACGACTATGACTATGACTATGACT 59.633 42.308 0.00 0.00 0.00 3.41
3980 4434 9.373603 GACGACTATGACTATGACTATGACTAT 57.626 37.037 0.00 0.00 0.00 2.12
4008 4462 9.679661 ACTATGACTATGACTATGACTATGAGG 57.320 37.037 0.00 0.00 0.00 3.86
4009 4463 9.898152 CTATGACTATGACTATGACTATGAGGA 57.102 37.037 0.00 0.00 0.00 3.71
4011 4465 8.572855 TGACTATGACTATGACTATGAGGATG 57.427 38.462 0.00 0.00 0.00 3.51
4012 4466 8.386264 TGACTATGACTATGACTATGAGGATGA 58.614 37.037 0.00 0.00 0.00 2.92
4013 4467 8.806429 ACTATGACTATGACTATGAGGATGAG 57.194 38.462 0.00 0.00 0.00 2.90
4025 4479 4.143406 TGAGGATGAGGATGAGGATGAT 57.857 45.455 0.00 0.00 0.00 2.45
4035 4489 6.499350 TGAGGATGAGGATGATGATGATTACA 59.501 38.462 0.00 0.00 0.00 2.41
4058 4586 7.675062 ACAATGATTACTATGCTAGAGAAGGG 58.325 38.462 0.00 0.00 0.00 3.95
4071 4599 2.906389 AGAGAAGGGCAACACTATGACA 59.094 45.455 0.00 0.00 39.74 3.58
4079 4607 3.885297 GGCAACACTATGACAGGCATAAT 59.115 43.478 0.00 0.00 38.92 1.28
4085 4613 1.325355 ATGACAGGCATAATGCTGGC 58.675 50.000 0.00 0.00 44.28 4.85
4091 4619 1.329171 GGCATAATGCTGGCCACCAA 61.329 55.000 0.00 0.00 46.92 3.67
4105 4633 4.326255 CCAACATGGTGGAGGAGC 57.674 61.111 26.58 0.00 41.65 4.70
4106 4634 1.746615 CCAACATGGTGGAGGAGCG 60.747 63.158 26.58 0.00 41.65 5.03
4107 4635 1.296392 CAACATGGTGGAGGAGCGA 59.704 57.895 1.63 0.00 0.00 4.93
4108 4636 0.742281 CAACATGGTGGAGGAGCGAG 60.742 60.000 1.63 0.00 0.00 5.03
4130 4661 7.968405 GCGAGGAATTTTTATGACTACAACAAT 59.032 33.333 0.00 0.00 0.00 2.71
4144 4675 2.305928 CAACAATAATCCCGGGCATCA 58.694 47.619 18.49 0.00 0.00 3.07
4150 4681 1.061905 AATCCCGGGCATCATCCTCA 61.062 55.000 18.49 0.00 0.00 3.86
4151 4682 1.772819 ATCCCGGGCATCATCCTCAC 61.773 60.000 18.49 0.00 0.00 3.51
4190 4784 6.349033 GGGCACGAAATTTCTACAACTACAAT 60.349 38.462 15.92 0.00 0.00 2.71
4242 4876 3.791175 CGTTTGCGTTTAGTGTCTAACC 58.209 45.455 0.00 0.00 0.00 2.85
4244 4878 4.607557 CGTTTGCGTTTAGTGTCTAACCAG 60.608 45.833 0.00 0.00 0.00 4.00
4245 4879 3.738830 TGCGTTTAGTGTCTAACCAGT 57.261 42.857 0.00 0.00 0.00 4.00
4246 4880 4.062677 TGCGTTTAGTGTCTAACCAGTT 57.937 40.909 0.00 0.00 0.00 3.16
4247 4881 3.805422 TGCGTTTAGTGTCTAACCAGTTG 59.195 43.478 0.00 0.00 0.00 3.16
4248 4882 4.053295 GCGTTTAGTGTCTAACCAGTTGA 58.947 43.478 0.00 0.00 0.00 3.18
4249 4883 4.084693 GCGTTTAGTGTCTAACCAGTTGAC 60.085 45.833 0.00 0.61 0.00 3.18
4250 4884 5.287226 CGTTTAGTGTCTAACCAGTTGACT 58.713 41.667 11.61 0.00 0.00 3.41
4251 4885 5.175126 CGTTTAGTGTCTAACCAGTTGACTG 59.825 44.000 4.15 4.15 43.40 3.51
4269 4904 3.031736 ACTGCTGATGGTACTATCCGTT 58.968 45.455 15.79 0.00 0.00 4.44
4274 4909 2.895404 TGATGGTACTATCCGTTAGGCC 59.105 50.000 15.79 0.00 37.47 5.19
4285 4920 1.369625 CGTTAGGCCCACATGAACTC 58.630 55.000 0.00 0.00 0.00 3.01
4297 4932 1.614903 CATGAACTCAGGCAAGGCAAA 59.385 47.619 0.00 0.00 0.00 3.68
4298 4933 1.999648 TGAACTCAGGCAAGGCAAAT 58.000 45.000 0.00 0.00 0.00 2.32
4322 4965 2.490115 TGAGTGAACGTTGGTTTTTGCT 59.510 40.909 5.00 0.00 36.24 3.91
4329 4972 5.545093 AACGTTGGTTTTTGCTCATGGCA 62.545 43.478 0.00 4.93 40.64 4.92
4342 4985 5.044428 GCTCATGGCATATGTTCTTGATC 57.956 43.478 0.00 4.05 41.35 2.92
4343 4986 4.760715 GCTCATGGCATATGTTCTTGATCT 59.239 41.667 0.00 0.00 41.35 2.75
4344 4987 5.334957 GCTCATGGCATATGTTCTTGATCTG 60.335 44.000 0.00 2.42 41.35 2.90
4345 4988 5.932455 TCATGGCATATGTTCTTGATCTGA 58.068 37.500 0.00 0.00 0.00 3.27
4346 4989 6.540083 TCATGGCATATGTTCTTGATCTGAT 58.460 36.000 0.00 0.00 0.00 2.90
4347 4990 7.682628 TCATGGCATATGTTCTTGATCTGATA 58.317 34.615 0.00 0.00 0.00 2.15
4348 4991 8.326529 TCATGGCATATGTTCTTGATCTGATAT 58.673 33.333 0.00 0.00 0.00 1.63
4349 4992 8.957466 CATGGCATATGTTCTTGATCTGATATT 58.043 33.333 0.00 0.00 0.00 1.28
4373 5016 9.643693 ATTAATCAGCAGTGGTATTTTCTTTTG 57.356 29.630 0.00 0.00 0.00 2.44
4376 5019 5.592282 TCAGCAGTGGTATTTTCTTTTGTGA 59.408 36.000 0.00 0.00 0.00 3.58
4377 5020 6.265196 TCAGCAGTGGTATTTTCTTTTGTGAT 59.735 34.615 0.00 0.00 0.00 3.06
4378 5021 7.446931 TCAGCAGTGGTATTTTCTTTTGTGATA 59.553 33.333 0.00 0.00 0.00 2.15
4379 5022 8.081633 CAGCAGTGGTATTTTCTTTTGTGATAA 58.918 33.333 0.00 0.00 0.00 1.75
4380 5023 8.806146 AGCAGTGGTATTTTCTTTTGTGATAAT 58.194 29.630 0.00 0.00 0.00 1.28
4381 5024 8.863049 GCAGTGGTATTTTCTTTTGTGATAATG 58.137 33.333 0.00 0.00 0.00 1.90
4410 5053 5.777223 TCTCTAGGATAGTATGCACATGCTT 59.223 40.000 6.55 1.27 40.38 3.91
4411 5054 6.030548 TCTAGGATAGTATGCACATGCTTC 57.969 41.667 6.55 4.93 40.38 3.86
4412 5055 4.970860 AGGATAGTATGCACATGCTTCT 57.029 40.909 6.55 3.80 42.66 2.85
4426 5069 1.966354 TGCTTCTCAGAACAGAGCTGA 59.034 47.619 4.21 0.00 39.90 4.26
4475 5118 6.340962 TCGTCTCTTCACTTCCATCTTAAA 57.659 37.500 0.00 0.00 0.00 1.52
4482 5125 7.461749 TCTTCACTTCCATCTTAAACCTCAAT 58.538 34.615 0.00 0.00 0.00 2.57
4485 5128 6.881065 TCACTTCCATCTTAAACCTCAATCAG 59.119 38.462 0.00 0.00 0.00 2.90
4501 5144 5.748402 TCAATCAGGAAACATATCACAGCT 58.252 37.500 0.00 0.00 0.00 4.24
4502 5145 5.587443 TCAATCAGGAAACATATCACAGCTG 59.413 40.000 13.48 13.48 0.00 4.24
4504 5147 5.363562 TCAGGAAACATATCACAGCTGAT 57.636 39.130 23.35 7.26 40.47 2.90
4505 5148 5.748402 TCAGGAAACATATCACAGCTGATT 58.252 37.500 23.35 6.89 38.21 2.57
4506 5149 6.888105 TCAGGAAACATATCACAGCTGATTA 58.112 36.000 23.35 9.02 38.21 1.75
4507 5150 7.337938 TCAGGAAACATATCACAGCTGATTAA 58.662 34.615 23.35 3.20 38.21 1.40
4508 5151 7.994911 TCAGGAAACATATCACAGCTGATTAAT 59.005 33.333 23.35 10.09 38.21 1.40
4509 5152 8.627403 CAGGAAACATATCACAGCTGATTAATT 58.373 33.333 23.35 4.66 38.21 1.40
4510 5153 9.851686 AGGAAACATATCACAGCTGATTAATTA 57.148 29.630 23.35 3.54 38.21 1.40
4515 5158 9.224267 ACATATCACAGCTGATTAATTATGACC 57.776 33.333 23.35 0.00 38.21 4.02
4516 5159 6.791887 ATCACAGCTGATTAATTATGACCG 57.208 37.500 23.35 0.00 32.79 4.79
4517 5160 5.056480 TCACAGCTGATTAATTATGACCGG 58.944 41.667 23.35 0.00 0.00 5.28
4518 5161 4.214119 CACAGCTGATTAATTATGACCGGG 59.786 45.833 23.35 0.00 0.00 5.73
4519 5162 3.753272 CAGCTGATTAATTATGACCGGGG 59.247 47.826 8.42 0.00 0.00 5.73
4520 5163 2.488153 GCTGATTAATTATGACCGGGGC 59.512 50.000 6.32 0.00 0.00 5.80
4521 5164 3.750371 CTGATTAATTATGACCGGGGCA 58.250 45.455 4.28 4.28 0.00 5.36
4522 5165 4.141287 CTGATTAATTATGACCGGGGCAA 58.859 43.478 6.69 0.00 0.00 4.52
4523 5166 4.735369 TGATTAATTATGACCGGGGCAAT 58.265 39.130 6.69 0.00 0.00 3.56
4524 5167 5.882040 TGATTAATTATGACCGGGGCAATA 58.118 37.500 6.69 0.00 0.00 1.90
4525 5168 6.307776 TGATTAATTATGACCGGGGCAATAA 58.692 36.000 6.69 6.94 0.00 1.40
4526 5169 6.778069 TGATTAATTATGACCGGGGCAATAAA 59.222 34.615 6.69 1.91 0.00 1.40
4527 5170 7.287927 TGATTAATTATGACCGGGGCAATAAAA 59.712 33.333 6.69 0.00 0.00 1.52
4528 5171 5.941555 AATTATGACCGGGGCAATAAAAA 57.058 34.783 6.69 0.00 0.00 1.94
4529 5172 6.493189 AATTATGACCGGGGCAATAAAAAT 57.507 33.333 6.69 0.00 0.00 1.82
4530 5173 7.604657 AATTATGACCGGGGCAATAAAAATA 57.395 32.000 6.69 0.00 0.00 1.40
4531 5174 7.604657 ATTATGACCGGGGCAATAAAAATAA 57.395 32.000 6.69 0.00 0.00 1.40
4532 5175 5.941555 ATGACCGGGGCAATAAAAATAAA 57.058 34.783 6.69 0.00 0.00 1.40
4533 5176 5.331876 TGACCGGGGCAATAAAAATAAAG 57.668 39.130 6.32 0.00 0.00 1.85
4534 5177 4.160626 TGACCGGGGCAATAAAAATAAAGG 59.839 41.667 6.32 0.00 0.00 3.11
4535 5178 3.452990 ACCGGGGCAATAAAAATAAAGGG 59.547 43.478 6.32 0.00 0.00 3.95
4536 5179 3.707102 CCGGGGCAATAAAAATAAAGGGA 59.293 43.478 0.00 0.00 0.00 4.20
4537 5180 4.202212 CCGGGGCAATAAAAATAAAGGGAG 60.202 45.833 0.00 0.00 0.00 4.30
4538 5181 4.647399 CGGGGCAATAAAAATAAAGGGAGA 59.353 41.667 0.00 0.00 0.00 3.71
4539 5182 5.128008 CGGGGCAATAAAAATAAAGGGAGAA 59.872 40.000 0.00 0.00 0.00 2.87
4540 5183 6.582636 GGGGCAATAAAAATAAAGGGAGAAG 58.417 40.000 0.00 0.00 0.00 2.85
4541 5184 6.408092 GGGGCAATAAAAATAAAGGGAGAAGG 60.408 42.308 0.00 0.00 0.00 3.46
4542 5185 6.408092 GGGCAATAAAAATAAAGGGAGAAGGG 60.408 42.308 0.00 0.00 0.00 3.95
4543 5186 6.408092 GGCAATAAAAATAAAGGGAGAAGGGG 60.408 42.308 0.00 0.00 0.00 4.79
4544 5187 6.382859 GCAATAAAAATAAAGGGAGAAGGGGA 59.617 38.462 0.00 0.00 0.00 4.81
4545 5188 7.093068 GCAATAAAAATAAAGGGAGAAGGGGAA 60.093 37.037 0.00 0.00 0.00 3.97
4546 5189 7.973048 ATAAAAATAAAGGGAGAAGGGGAAC 57.027 36.000 0.00 0.00 0.00 3.62
4561 5204 2.365293 GGGGAACACAAGAAAAGCACAT 59.635 45.455 0.00 0.00 0.00 3.21
4563 5206 3.383761 GGAACACAAGAAAAGCACATGG 58.616 45.455 0.00 0.00 0.00 3.66
4564 5207 2.514205 ACACAAGAAAAGCACATGGC 57.486 45.000 0.00 0.00 45.30 4.40
5112 5766 0.896479 TCCGGGTCTTCATCACGTCA 60.896 55.000 0.00 0.00 0.00 4.35
5139 5793 0.394216 TGGTGACAACTGCTGCAAGT 60.394 50.000 3.02 2.58 37.44 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 209 2.427905 CAACTTCGACGACGGCGA 60.428 61.111 24.20 24.20 41.64 5.54
480 498 4.116328 CCTTCGTCTCTCGCGGCA 62.116 66.667 6.13 0.00 39.67 5.69
688 710 4.137543 GCTCATCCGTTATCTTCCCAAAT 58.862 43.478 0.00 0.00 0.00 2.32
873 896 1.484653 TGCACCTGTTATCATAGCCGT 59.515 47.619 0.00 0.00 0.00 5.68
922 945 1.333791 GGAGTTTGGAAACAGAACGCG 60.334 52.381 3.53 3.53 44.54 6.01
923 946 1.673920 TGGAGTTTGGAAACAGAACGC 59.326 47.619 5.11 0.00 44.54 4.84
1131 1158 2.194388 TACTGGAGAGGGCGTCGAGT 62.194 60.000 0.00 12.11 36.93 4.18
1204 1231 2.271497 GGACGAGGACGAGGAGGA 59.729 66.667 0.00 0.00 42.66 3.71
1205 1232 2.829458 GGGACGAGGACGAGGAGG 60.829 72.222 0.00 0.00 42.66 4.30
1659 1686 1.984570 CTGGAGGCCTTCGGTGAGA 60.985 63.158 12.36 0.00 0.00 3.27
1863 1910 4.871993 ACAATGAGATCAATTCTGCGAC 57.128 40.909 0.00 0.00 33.74 5.19
2035 2323 5.647225 TGTATATCCCCGTTGTAAAAACACC 59.353 40.000 0.00 0.00 0.00 4.16
2049 2337 7.229581 AGAGATTCGTTAACTGTATATCCCC 57.770 40.000 3.71 0.00 0.00 4.81
2075 2363 4.897509 AGACAGTGATCTCATTTCACCA 57.102 40.909 0.00 0.00 43.62 4.17
2609 2952 8.974060 AAATACTTCTACTGAACTCAAAACCA 57.026 30.769 0.00 0.00 0.00 3.67
2671 3014 4.235939 TGCATGTAAGCAAAACGTGATT 57.764 36.364 8.88 0.00 42.46 2.57
2672 3015 3.913548 TGCATGTAAGCAAAACGTGAT 57.086 38.095 8.88 0.00 42.46 3.06
2976 3351 2.189594 TGCTAGCATTCACAGCAACT 57.810 45.000 14.93 0.00 42.09 3.16
3231 3607 1.696884 GGGATCTGTCCTTCCCTGATC 59.303 57.143 0.63 0.00 46.91 2.92
3572 3949 3.873910 ACTTACACACAGGTCATATGGC 58.126 45.455 2.13 0.00 0.00 4.40
3642 4025 9.991906 AAAAATCATAAGAATAGGCCATTCATG 57.008 29.630 22.09 18.25 44.81 3.07
3686 4097 7.148755 GCATTAGGACATGAAAAACACATCAAC 60.149 37.037 0.00 0.00 0.00 3.18
3687 4098 6.867816 GCATTAGGACATGAAAAACACATCAA 59.132 34.615 0.00 0.00 0.00 2.57
3689 4100 6.624423 AGCATTAGGACATGAAAAACACATC 58.376 36.000 0.00 0.00 0.00 3.06
3690 4101 6.209192 TGAGCATTAGGACATGAAAAACACAT 59.791 34.615 0.00 0.00 0.00 3.21
3691 4102 5.534278 TGAGCATTAGGACATGAAAAACACA 59.466 36.000 0.00 0.00 0.00 3.72
3692 4103 5.858581 GTGAGCATTAGGACATGAAAAACAC 59.141 40.000 0.00 0.00 0.00 3.32
3693 4104 5.534278 TGTGAGCATTAGGACATGAAAAACA 59.466 36.000 0.00 0.00 0.00 2.83
3694 4105 6.012658 TGTGAGCATTAGGACATGAAAAAC 57.987 37.500 0.00 0.00 0.00 2.43
3696 4107 6.839124 AATGTGAGCATTAGGACATGAAAA 57.161 33.333 0.00 0.00 42.96 2.29
3697 4108 6.839124 AAATGTGAGCATTAGGACATGAAA 57.161 33.333 0.00 0.00 43.89 2.69
3698 4109 6.433716 TGAAAATGTGAGCATTAGGACATGAA 59.566 34.615 0.00 0.00 43.89 2.57
3699 4110 5.945191 TGAAAATGTGAGCATTAGGACATGA 59.055 36.000 0.00 0.00 43.89 3.07
3700 4111 6.198650 TGAAAATGTGAGCATTAGGACATG 57.801 37.500 0.00 0.00 43.89 3.21
3701 4112 6.379133 ACATGAAAATGTGAGCATTAGGACAT 59.621 34.615 0.00 0.00 43.89 3.06
3702 4113 5.711506 ACATGAAAATGTGAGCATTAGGACA 59.288 36.000 0.00 0.00 43.89 4.02
3703 4114 6.127925 TGACATGAAAATGTGAGCATTAGGAC 60.128 38.462 0.00 0.00 43.89 3.85
3704 4115 5.945191 TGACATGAAAATGTGAGCATTAGGA 59.055 36.000 0.00 0.00 43.89 2.94
3705 4116 6.198650 TGACATGAAAATGTGAGCATTAGG 57.801 37.500 0.00 0.00 43.89 2.69
3706 4117 7.971722 TGATTGACATGAAAATGTGAGCATTAG 59.028 33.333 0.00 0.00 43.89 1.73
3707 4118 7.828712 TGATTGACATGAAAATGTGAGCATTA 58.171 30.769 0.00 0.00 43.89 1.90
3708 4119 6.693466 TGATTGACATGAAAATGTGAGCATT 58.307 32.000 0.00 0.00 46.38 3.56
3709 4120 6.275494 TGATTGACATGAAAATGTGAGCAT 57.725 33.333 0.00 0.00 34.45 3.79
3710 4121 5.708877 TGATTGACATGAAAATGTGAGCA 57.291 34.783 0.00 0.00 34.45 4.26
3711 4122 7.201496 GGAATTGATTGACATGAAAATGTGAGC 60.201 37.037 0.00 0.00 34.45 4.26
3712 4123 7.815549 TGGAATTGATTGACATGAAAATGTGAG 59.184 33.333 0.00 0.00 34.45 3.51
3713 4124 7.668492 TGGAATTGATTGACATGAAAATGTGA 58.332 30.769 0.00 0.00 34.45 3.58
3714 4125 7.892778 TGGAATTGATTGACATGAAAATGTG 57.107 32.000 0.00 0.00 34.45 3.21
3715 4126 8.098286 ACATGGAATTGATTGACATGAAAATGT 58.902 29.630 17.70 0.00 40.92 2.71
3716 4127 8.487313 ACATGGAATTGATTGACATGAAAATG 57.513 30.769 17.70 0.00 40.92 2.32
3717 4128 8.941977 CAACATGGAATTGATTGACATGAAAAT 58.058 29.630 17.70 0.00 40.92 1.82
3718 4129 8.148999 TCAACATGGAATTGATTGACATGAAAA 58.851 29.630 17.70 0.00 40.92 2.29
3719 4130 7.668492 TCAACATGGAATTGATTGACATGAAA 58.332 30.769 17.70 0.00 40.92 2.69
3720 4131 7.229581 TCAACATGGAATTGATTGACATGAA 57.770 32.000 17.70 0.00 40.92 2.57
3721 4132 6.837471 TCAACATGGAATTGATTGACATGA 57.163 33.333 17.70 2.52 40.92 3.07
3722 4133 7.010091 CACATCAACATGGAATTGATTGACATG 59.990 37.037 7.18 12.66 42.81 3.21
3723 4134 7.039270 CACATCAACATGGAATTGATTGACAT 58.961 34.615 7.18 0.00 42.81 3.06
3724 4135 6.015265 ACACATCAACATGGAATTGATTGACA 60.015 34.615 16.97 0.00 42.81 3.58
3725 4136 6.392354 ACACATCAACATGGAATTGATTGAC 58.608 36.000 16.97 0.00 42.81 3.18
3726 4137 6.593268 ACACATCAACATGGAATTGATTGA 57.407 33.333 16.97 9.44 42.81 2.57
3727 4138 7.661127 AAACACATCAACATGGAATTGATTG 57.339 32.000 7.18 10.53 42.81 2.67
3728 4139 8.680039 AAAAACACATCAACATGGAATTGATT 57.320 26.923 7.18 0.00 42.81 2.57
3729 4140 7.932491 TGAAAAACACATCAACATGGAATTGAT 59.068 29.630 4.61 4.61 45.57 2.57
3730 4141 7.270779 TGAAAAACACATCAACATGGAATTGA 58.729 30.769 0.00 0.00 40.25 2.57
3731 4142 7.479897 TGAAAAACACATCAACATGGAATTG 57.520 32.000 0.00 0.00 33.82 2.32
3732 4143 7.716123 ACATGAAAAACACATCAACATGGAATT 59.284 29.630 0.00 0.00 38.19 2.17
3733 4144 7.218614 ACATGAAAAACACATCAACATGGAAT 58.781 30.769 0.00 0.00 38.19 3.01
3734 4145 6.580788 ACATGAAAAACACATCAACATGGAA 58.419 32.000 0.00 0.00 38.19 3.53
3735 4146 6.159299 ACATGAAAAACACATCAACATGGA 57.841 33.333 0.00 0.00 38.19 3.41
3736 4147 5.406175 GGACATGAAAAACACATCAACATGG 59.594 40.000 0.00 0.00 38.19 3.66
3737 4148 6.218019 AGGACATGAAAAACACATCAACATG 58.782 36.000 0.00 0.00 39.27 3.21
3738 4149 6.409524 AGGACATGAAAAACACATCAACAT 57.590 33.333 0.00 0.00 0.00 2.71
3741 4152 6.867816 GCATTAGGACATGAAAAACACATCAA 59.132 34.615 0.00 0.00 0.00 2.57
3941 4395 0.748729 AGTCGTCGTCATCCTCCTCC 60.749 60.000 0.00 0.00 0.00 4.30
3956 4410 9.372369 TCATAGTCATAGTCATAGTCATAGTCG 57.628 37.037 0.00 0.00 0.00 4.18
3983 4437 9.898152 TCCTCATAGTCATAGTCATAGTCATAG 57.102 37.037 0.00 0.00 0.00 2.23
3998 4452 4.106987 TCCTCATCCTCATCCTCATAGTCA 59.893 45.833 0.00 0.00 0.00 3.41
3999 4453 4.671831 TCCTCATCCTCATCCTCATAGTC 58.328 47.826 0.00 0.00 0.00 2.59
4000 4454 4.756203 TCCTCATCCTCATCCTCATAGT 57.244 45.455 0.00 0.00 0.00 2.12
4001 4455 5.270794 TCATCCTCATCCTCATCCTCATAG 58.729 45.833 0.00 0.00 0.00 2.23
4002 4456 5.280998 TCATCCTCATCCTCATCCTCATA 57.719 43.478 0.00 0.00 0.00 2.15
4003 4457 4.143406 TCATCCTCATCCTCATCCTCAT 57.857 45.455 0.00 0.00 0.00 2.90
4004 4458 3.625252 TCATCCTCATCCTCATCCTCA 57.375 47.619 0.00 0.00 0.00 3.86
4005 4459 4.095211 TCATCATCCTCATCCTCATCCTC 58.905 47.826 0.00 0.00 0.00 3.71
4006 4460 4.143406 TCATCATCCTCATCCTCATCCT 57.857 45.455 0.00 0.00 0.00 3.24
4007 4461 4.470304 TCATCATCATCCTCATCCTCATCC 59.530 45.833 0.00 0.00 0.00 3.51
4008 4462 5.678955 TCATCATCATCCTCATCCTCATC 57.321 43.478 0.00 0.00 0.00 2.92
4009 4463 6.644308 AATCATCATCATCCTCATCCTCAT 57.356 37.500 0.00 0.00 0.00 2.90
4010 4464 6.499350 TGTAATCATCATCATCCTCATCCTCA 59.501 38.462 0.00 0.00 0.00 3.86
4011 4465 6.944096 TGTAATCATCATCATCCTCATCCTC 58.056 40.000 0.00 0.00 0.00 3.71
4012 4466 6.947376 TGTAATCATCATCATCCTCATCCT 57.053 37.500 0.00 0.00 0.00 3.24
4013 4467 7.827729 TCATTGTAATCATCATCATCCTCATCC 59.172 37.037 0.00 0.00 0.00 3.51
4035 4489 6.270927 TGCCCTTCTCTAGCATAGTAATCATT 59.729 38.462 0.00 0.00 40.38 2.57
4058 4586 4.790766 GCATTATGCCTGTCATAGTGTTGC 60.791 45.833 5.80 0.00 43.36 4.17
4071 4599 1.456331 GGTGGCCAGCATTATGCCT 60.456 57.895 29.70 0.00 46.52 4.75
4091 4619 2.362369 CCTCGCTCCTCCACCATGT 61.362 63.158 0.00 0.00 0.00 3.21
4100 4628 5.104259 AGTCATAAAAATTCCTCGCTCCT 57.896 39.130 0.00 0.00 0.00 3.69
4130 4661 0.984230 GAGGATGATGCCCGGGATTA 59.016 55.000 29.31 12.29 0.00 1.75
4190 4784 6.697395 TCAGTTGTAGCTGCAAATAGACTAA 58.303 36.000 19.29 0.00 36.49 2.24
4196 4790 7.195646 GCAAATATCAGTTGTAGCTGCAAATA 58.804 34.615 19.29 13.37 36.49 1.40
4198 4792 5.401550 GCAAATATCAGTTGTAGCTGCAAA 58.598 37.500 19.29 4.25 36.49 3.68
4242 4876 3.325293 AGTACCATCAGCAGTCAACTG 57.675 47.619 5.77 5.77 46.40 3.16
4244 4878 4.372656 GGATAGTACCATCAGCAGTCAAC 58.627 47.826 3.66 0.00 0.00 3.18
4245 4879 3.068165 CGGATAGTACCATCAGCAGTCAA 59.932 47.826 3.66 0.00 0.00 3.18
4246 4880 2.623416 CGGATAGTACCATCAGCAGTCA 59.377 50.000 3.66 0.00 0.00 3.41
4247 4881 2.623889 ACGGATAGTACCATCAGCAGTC 59.376 50.000 3.66 0.00 0.00 3.51
4248 4882 2.667470 ACGGATAGTACCATCAGCAGT 58.333 47.619 3.66 0.00 0.00 4.40
4249 4883 3.735237 AACGGATAGTACCATCAGCAG 57.265 47.619 3.66 0.00 0.00 4.24
4250 4884 3.572682 CCTAACGGATAGTACCATCAGCA 59.427 47.826 3.66 0.00 0.00 4.41
4251 4885 3.614390 GCCTAACGGATAGTACCATCAGC 60.614 52.174 3.66 0.00 0.00 4.26
4269 4904 0.911769 CCTGAGTTCATGTGGGCCTA 59.088 55.000 4.53 0.00 0.00 3.93
4274 4909 1.171308 CCTTGCCTGAGTTCATGTGG 58.829 55.000 0.00 0.00 0.00 4.17
4285 4920 3.444742 TCACTCATAATTTGCCTTGCCTG 59.555 43.478 0.00 0.00 0.00 4.85
4297 4932 5.689961 GCAAAAACCAACGTTCACTCATAAT 59.310 36.000 0.00 0.00 0.00 1.28
4298 4933 5.038033 GCAAAAACCAACGTTCACTCATAA 58.962 37.500 0.00 0.00 0.00 1.90
4322 4965 5.932455 TCAGATCAAGAACATATGCCATGA 58.068 37.500 1.58 4.51 0.00 3.07
4343 4986 9.851686 AGAAAATACCACTGCTGATTAATATCA 57.148 29.630 0.00 0.00 38.45 2.15
4347 4990 9.643693 CAAAAGAAAATACCACTGCTGATTAAT 57.356 29.630 0.00 0.00 0.00 1.40
4348 4991 8.637986 ACAAAAGAAAATACCACTGCTGATTAA 58.362 29.630 0.00 0.00 0.00 1.40
4349 4992 8.081633 CACAAAAGAAAATACCACTGCTGATTA 58.918 33.333 0.00 0.00 0.00 1.75
4350 4993 6.925165 CACAAAAGAAAATACCACTGCTGATT 59.075 34.615 0.00 0.00 0.00 2.57
4351 4994 6.265196 TCACAAAAGAAAATACCACTGCTGAT 59.735 34.615 0.00 0.00 0.00 2.90
4352 4995 5.592282 TCACAAAAGAAAATACCACTGCTGA 59.408 36.000 0.00 0.00 0.00 4.26
4353 4996 5.830912 TCACAAAAGAAAATACCACTGCTG 58.169 37.500 0.00 0.00 0.00 4.41
4354 4997 6.655078 ATCACAAAAGAAAATACCACTGCT 57.345 33.333 0.00 0.00 0.00 4.24
4355 4998 8.863049 CATTATCACAAAAGAAAATACCACTGC 58.137 33.333 0.00 0.00 0.00 4.40
4378 5021 9.184523 GTGCATACTATCCTAGAGAGTATCATT 57.815 37.037 8.53 0.00 42.71 2.57
4379 5022 8.332487 TGTGCATACTATCCTAGAGAGTATCAT 58.668 37.037 8.53 0.00 42.71 2.45
4380 5023 7.690256 TGTGCATACTATCCTAGAGAGTATCA 58.310 38.462 8.53 7.69 42.71 2.15
4381 5024 8.620416 CATGTGCATACTATCCTAGAGAGTATC 58.380 40.741 8.53 5.77 42.71 2.24
4382 5025 7.068103 GCATGTGCATACTATCCTAGAGAGTAT 59.932 40.741 6.16 6.16 44.57 2.12
4383 5026 6.375736 GCATGTGCATACTATCCTAGAGAGTA 59.624 42.308 1.91 1.91 40.01 2.59
4386 5029 5.328565 AGCATGTGCATACTATCCTAGAGA 58.671 41.667 7.83 0.00 45.16 3.10
4391 5034 4.346127 TGAGAAGCATGTGCATACTATCCT 59.654 41.667 7.83 0.00 45.16 3.24
4410 5053 2.166829 GGAGTCAGCTCTGTTCTGAGA 58.833 52.381 10.14 0.00 40.82 3.27
4411 5054 1.135431 CGGAGTCAGCTCTGTTCTGAG 60.135 57.143 0.00 2.99 41.91 3.35
4412 5055 0.884514 CGGAGTCAGCTCTGTTCTGA 59.115 55.000 0.00 0.00 41.91 3.27
4454 5097 6.468543 AGGTTTAAGATGGAAGTGAAGAGAC 58.531 40.000 0.00 0.00 0.00 3.36
4461 5104 6.094603 CCTGATTGAGGTTTAAGATGGAAGTG 59.905 42.308 0.00 0.00 37.02 3.16
4463 5106 6.418101 TCCTGATTGAGGTTTAAGATGGAAG 58.582 40.000 0.00 0.00 43.37 3.46
4466 5109 6.434028 TGTTTCCTGATTGAGGTTTAAGATGG 59.566 38.462 0.00 0.00 43.37 3.51
4475 5118 6.065976 TGTGATATGTTTCCTGATTGAGGT 57.934 37.500 0.00 0.00 43.37 3.85
4482 5125 4.824479 TCAGCTGTGATATGTTTCCTGA 57.176 40.909 14.67 0.00 0.00 3.86
4492 5135 6.873605 CCGGTCATAATTAATCAGCTGTGATA 59.126 38.462 14.67 2.75 43.04 2.15
4497 5140 3.753272 CCCCGGTCATAATTAATCAGCTG 59.247 47.826 7.63 7.63 0.00 4.24
4501 5144 3.866703 TGCCCCGGTCATAATTAATCA 57.133 42.857 0.00 0.00 0.00 2.57
4502 5145 6.827586 TTATTGCCCCGGTCATAATTAATC 57.172 37.500 0.00 0.00 0.00 1.75
4504 5147 7.419711 TTTTTATTGCCCCGGTCATAATTAA 57.580 32.000 0.00 0.00 0.00 1.40
4505 5148 7.604657 ATTTTTATTGCCCCGGTCATAATTA 57.395 32.000 0.00 0.00 0.00 1.40
4506 5149 5.941555 TTTTTATTGCCCCGGTCATAATT 57.058 34.783 0.00 0.00 0.00 1.40
4507 5150 7.604657 TTATTTTTATTGCCCCGGTCATAAT 57.395 32.000 0.00 0.00 0.00 1.28
4508 5151 7.418025 CCTTTATTTTTATTGCCCCGGTCATAA 60.418 37.037 0.00 0.00 0.00 1.90
4509 5152 6.041069 CCTTTATTTTTATTGCCCCGGTCATA 59.959 38.462 0.00 0.00 0.00 2.15
4510 5153 5.163353 CCTTTATTTTTATTGCCCCGGTCAT 60.163 40.000 0.00 0.00 0.00 3.06
4511 5154 4.160626 CCTTTATTTTTATTGCCCCGGTCA 59.839 41.667 0.00 0.00 0.00 4.02
4512 5155 4.442332 CCCTTTATTTTTATTGCCCCGGTC 60.442 45.833 0.00 0.00 0.00 4.79
4513 5156 3.452990 CCCTTTATTTTTATTGCCCCGGT 59.547 43.478 0.00 0.00 0.00 5.28
4514 5157 3.707102 TCCCTTTATTTTTATTGCCCCGG 59.293 43.478 0.00 0.00 0.00 5.73
4515 5158 4.647399 TCTCCCTTTATTTTTATTGCCCCG 59.353 41.667 0.00 0.00 0.00 5.73
4516 5159 6.408092 CCTTCTCCCTTTATTTTTATTGCCCC 60.408 42.308 0.00 0.00 0.00 5.80
4517 5160 6.408092 CCCTTCTCCCTTTATTTTTATTGCCC 60.408 42.308 0.00 0.00 0.00 5.36
4518 5161 6.408092 CCCCTTCTCCCTTTATTTTTATTGCC 60.408 42.308 0.00 0.00 0.00 4.52
4519 5162 6.382859 TCCCCTTCTCCCTTTATTTTTATTGC 59.617 38.462 0.00 0.00 0.00 3.56
4520 5163 7.971368 TCCCCTTCTCCCTTTATTTTTATTG 57.029 36.000 0.00 0.00 0.00 1.90
4521 5164 7.959152 TGTTCCCCTTCTCCCTTTATTTTTATT 59.041 33.333 0.00 0.00 0.00 1.40
4522 5165 7.399191 GTGTTCCCCTTCTCCCTTTATTTTTAT 59.601 37.037 0.00 0.00 0.00 1.40
4523 5166 6.722590 GTGTTCCCCTTCTCCCTTTATTTTTA 59.277 38.462 0.00 0.00 0.00 1.52
4524 5167 5.542635 GTGTTCCCCTTCTCCCTTTATTTTT 59.457 40.000 0.00 0.00 0.00 1.94
4525 5168 5.084519 GTGTTCCCCTTCTCCCTTTATTTT 58.915 41.667 0.00 0.00 0.00 1.82
4526 5169 4.107311 TGTGTTCCCCTTCTCCCTTTATTT 59.893 41.667 0.00 0.00 0.00 1.40
4527 5170 3.660669 TGTGTTCCCCTTCTCCCTTTATT 59.339 43.478 0.00 0.00 0.00 1.40
4528 5171 3.265489 TGTGTTCCCCTTCTCCCTTTAT 58.735 45.455 0.00 0.00 0.00 1.40
4529 5172 2.708759 TGTGTTCCCCTTCTCCCTTTA 58.291 47.619 0.00 0.00 0.00 1.85
4530 5173 1.529744 TGTGTTCCCCTTCTCCCTTT 58.470 50.000 0.00 0.00 0.00 3.11
4531 5174 1.425448 CTTGTGTTCCCCTTCTCCCTT 59.575 52.381 0.00 0.00 0.00 3.95
4532 5175 1.068121 CTTGTGTTCCCCTTCTCCCT 58.932 55.000 0.00 0.00 0.00 4.20
4533 5176 1.064825 TCTTGTGTTCCCCTTCTCCC 58.935 55.000 0.00 0.00 0.00 4.30
4534 5177 2.951229 TTCTTGTGTTCCCCTTCTCC 57.049 50.000 0.00 0.00 0.00 3.71
4535 5178 3.004839 GCTTTTCTTGTGTTCCCCTTCTC 59.995 47.826 0.00 0.00 0.00 2.87
4536 5179 2.959030 GCTTTTCTTGTGTTCCCCTTCT 59.041 45.455 0.00 0.00 0.00 2.85
4537 5180 2.693074 TGCTTTTCTTGTGTTCCCCTTC 59.307 45.455 0.00 0.00 0.00 3.46
4538 5181 2.430694 GTGCTTTTCTTGTGTTCCCCTT 59.569 45.455 0.00 0.00 0.00 3.95
4539 5182 2.031870 GTGCTTTTCTTGTGTTCCCCT 58.968 47.619 0.00 0.00 0.00 4.79
4540 5183 1.754226 TGTGCTTTTCTTGTGTTCCCC 59.246 47.619 0.00 0.00 0.00 4.81
4541 5184 3.383761 CATGTGCTTTTCTTGTGTTCCC 58.616 45.455 0.00 0.00 0.00 3.97
4542 5185 3.383761 CCATGTGCTTTTCTTGTGTTCC 58.616 45.455 0.00 0.00 0.00 3.62
4543 5186 2.796593 GCCATGTGCTTTTCTTGTGTTC 59.203 45.455 0.00 0.00 36.87 3.18
4544 5187 2.168106 TGCCATGTGCTTTTCTTGTGTT 59.832 40.909 7.54 0.00 42.00 3.32
4545 5188 1.755959 TGCCATGTGCTTTTCTTGTGT 59.244 42.857 7.54 0.00 42.00 3.72
4546 5189 2.034939 TCTGCCATGTGCTTTTCTTGTG 59.965 45.455 7.54 0.00 42.00 3.33
4561 5204 3.603532 CAGAGCTTACTTTCATCTGCCA 58.396 45.455 0.00 0.00 31.83 4.92
4564 5207 3.622163 CCTGCAGAGCTTACTTTCATCTG 59.378 47.826 17.39 0.00 40.26 2.90
4566 5209 3.866651 TCCTGCAGAGCTTACTTTCATC 58.133 45.455 17.39 0.00 0.00 2.92
4567 5210 3.988976 TCCTGCAGAGCTTACTTTCAT 57.011 42.857 17.39 0.00 0.00 2.57
4902 5556 0.805614 TCGAAGCTGAGAAGGAGACG 59.194 55.000 0.00 0.00 0.00 4.18
5112 5766 1.750682 GCAGTTGTCACCACTCCCTTT 60.751 52.381 0.00 0.00 0.00 3.11
5139 5793 1.003580 GTTGGAGCATTGTCTGGAGGA 59.996 52.381 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.