Multiple sequence alignment - TraesCS6B01G021200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G021200 chr6B 100.000 3944 0 0 1 3944 12885585 12889528 0.000000e+00 7284.0
1 TraesCS6B01G021200 chr6B 92.183 2597 171 16 1027 3608 13441356 13438777 0.000000e+00 3642.0
2 TraesCS6B01G021200 chr6B 90.950 2210 189 8 973 3174 13653949 13651743 0.000000e+00 2963.0
3 TraesCS6B01G021200 chr6B 89.868 2270 212 14 999 3255 26861804 26864068 0.000000e+00 2902.0
4 TraesCS6B01G021200 chr6B 91.113 1204 85 14 955 2144 13704897 13703702 0.000000e+00 1611.0
5 TraesCS6B01G021200 chr6B 80.000 160 9 9 723 867 13654207 13654056 3.240000e-16 97.1
6 TraesCS6B01G021200 chr6B 84.615 65 6 3 3649 3711 12889131 12889193 1.180000e-05 62.1
7 TraesCS6B01G021200 chr6B 84.615 65 6 3 3547 3609 12889233 12889295 1.180000e-05 62.1
8 TraesCS6B01G021200 chr6B 91.111 45 2 2 3649 3693 13438838 13438796 4.260000e-05 60.2
9 TraesCS6B01G021200 chr5B 92.790 2871 134 26 413 3246 432982103 432984937 0.000000e+00 4087.0
10 TraesCS6B01G021200 chr5B 90.993 433 21 7 1 416 432981591 432982022 5.720000e-158 568.0
11 TraesCS6B01G021200 chrUn 92.302 2650 188 9 973 3608 79937079 79939726 0.000000e+00 3749.0
12 TraesCS6B01G021200 chrUn 90.049 2653 246 12 973 3608 80037167 80034516 0.000000e+00 3421.0
13 TraesCS6B01G021200 chrUn 92.857 42 1 2 3649 3690 79939665 79939704 4.260000e-05 60.2
14 TraesCS6B01G021200 chrUn 91.111 45 2 2 3649 3693 80034577 80034535 4.260000e-05 60.2
15 TraesCS6B01G021200 chr7D 90.618 2718 232 15 942 3641 597677191 597674479 0.000000e+00 3585.0
16 TraesCS6B01G021200 chr7D 90.688 247 16 5 3701 3944 597674320 597674078 4.920000e-84 322.0
17 TraesCS6B01G021200 chr7D 91.111 45 2 2 3649 3693 597674572 597674530 4.260000e-05 60.2
18 TraesCS6B01G021200 chr6A 90.084 2753 232 24 877 3597 7176097 7173354 0.000000e+00 3533.0
19 TraesCS6B01G021200 chr6A 88.950 2534 235 27 746 3246 7079346 7081867 0.000000e+00 3086.0
20 TraesCS6B01G021200 chr6A 91.222 2210 172 16 949 3147 7186852 7184654 0.000000e+00 2987.0
21 TraesCS6B01G021200 chr6A 93.393 333 14 4 3317 3641 7120250 7120582 1.650000e-133 486.0
22 TraesCS6B01G021200 chr6A 90.873 252 21 2 3694 3944 7120774 7121024 1.760000e-88 337.0
23 TraesCS6B01G021200 chr6A 94.231 208 12 0 1 208 7063689 7063896 6.360000e-83 318.0
24 TraesCS6B01G021200 chr6A 91.489 235 10 5 207 431 7063943 7064177 8.230000e-82 315.0
25 TraesCS6B01G021200 chr6D 88.889 90 8 2 3381 3468 7698220 7698309 4.170000e-20 110.0
26 TraesCS6B01G021200 chr6D 85.484 62 4 4 748 807 7359614 7359556 4.260000e-05 60.2
27 TraesCS6B01G021200 chr6D 100.000 30 0 0 754 783 7346201 7346172 5.510000e-04 56.5


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 TraesCS6B01G021200 chr6B 12885585 12889528 3943 False 2469.40 7284 89.743333 1 3944 3 chr6B.!!$F2 3943
1 TraesCS6B01G021200 chr6B 26861804 26864068 2264 False 2902.00 2902 89.868000 999 3255 1 chr6B.!!$F1 2256
2 TraesCS6B01G021200 chr6B 13438777 13441356 2579 True 1851.10 3642 91.647000 1027 3693 2 chr6B.!!$R2 2666
3 TraesCS6B01G021200 chr6B 13703702 13704897 1195 True 1611.00 1611 91.113000 955 2144 1 chr6B.!!$R1 1189
4 TraesCS6B01G021200 chr6B 13651743 13654207 2464 True 1530.05 2963 85.475000 723 3174 2 chr6B.!!$R3 2451
5 TraesCS6B01G021200 chr5B 432981591 432984937 3346 False 2327.50 4087 91.891500 1 3246 2 chr5B.!!$F1 3245
6 TraesCS6B01G021200 chrUn 79937079 79939726 2647 False 1904.60 3749 92.579500 973 3690 2 chrUn.!!$F1 2717
7 TraesCS6B01G021200 chrUn 80034516 80037167 2651 True 1740.60 3421 90.580000 973 3693 2 chrUn.!!$R1 2720
8 TraesCS6B01G021200 chr7D 597674078 597677191 3113 True 1322.40 3585 90.805667 942 3944 3 chr7D.!!$R1 3002
9 TraesCS6B01G021200 chr6A 7173354 7176097 2743 True 3533.00 3533 90.084000 877 3597 1 chr6A.!!$R1 2720
10 TraesCS6B01G021200 chr6A 7079346 7081867 2521 False 3086.00 3086 88.950000 746 3246 1 chr6A.!!$F1 2500
11 TraesCS6B01G021200 chr6A 7184654 7186852 2198 True 2987.00 2987 91.222000 949 3147 1 chr6A.!!$R2 2198
12 TraesCS6B01G021200 chr6A 7120250 7121024 774 False 411.50 486 92.133000 3317 3944 2 chr6A.!!$F3 627

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
335 346 0.036010 AGATGTTGCCTCCTTCGTGG 60.036 55.0 0.0 0.0 37.10 4.94 F
832 979 0.317479 ATCGCATTACCTCCTACGGC 59.683 55.0 0.0 0.0 0.00 5.68 F
835 982 0.464452 GCATTACCTCCTACGGCAGT 59.536 55.0 0.0 0.0 0.00 4.40 F
1632 1822 0.693049 AGGTGGACCAAGCTTACAGG 59.307 55.0 0.0 0.0 38.89 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2250 2440 2.602257 TGAACTGGGACATAGCATCG 57.398 50.000 0.00 0.00 38.20 3.84 R
2434 2627 2.553602 CCCTTTCATTTTTGCAAAGGCC 59.446 45.455 12.41 0.00 43.39 5.19 R
2774 2967 4.442073 CGTCAAACAAATCTTTGGCTTCTG 59.558 41.667 7.51 0.00 42.34 3.02 R
3022 3216 1.214175 TGGAAGCTTCAAGGGTGAACA 59.786 47.619 27.02 10.13 38.88 3.18 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
55 56 2.202878 GGCGTGCCTATTCTGCGA 60.203 61.111 2.98 0.00 0.00 5.10
56 57 2.526120 GGCGTGCCTATTCTGCGAC 61.526 63.158 2.98 0.00 0.00 5.19
70 71 3.066233 GCGACCGGGAAGAGGAGAC 62.066 68.421 6.32 0.00 0.00 3.36
125 126 0.390735 GCGAGGTATGGACGGTTGTT 60.391 55.000 0.00 0.00 0.00 2.83
136 137 2.542907 CGGTTGTTTGCCACGCTCT 61.543 57.895 0.00 0.00 0.00 4.09
149 150 2.821810 GCTCTCGGGAAGCAAGGC 60.822 66.667 2.36 0.00 0.00 4.35
164 165 2.684927 GCAAGGCTGGATACCATCAAGT 60.685 50.000 0.00 0.00 32.68 3.16
165 166 3.624777 CAAGGCTGGATACCATCAAGTT 58.375 45.455 0.00 0.00 32.68 2.66
183 184 3.238597 AGTTGAGAGAAGCTTCAGGAGT 58.761 45.455 27.57 7.06 0.00 3.85
186 187 1.899142 GAGAGAAGCTTCAGGAGTGGT 59.101 52.381 27.57 4.70 0.00 4.16
228 229 4.282068 CGAAATATGGAAGCACCGAAATG 58.718 43.478 0.00 0.00 42.61 2.32
273 274 4.450757 TGCCATCGATAAACCATGTATTCG 59.549 41.667 0.00 0.00 0.00 3.34
282 283 7.973944 CGATAAACCATGTATTCGATAGGATCA 59.026 37.037 0.00 0.00 34.75 2.92
297 308 1.004745 GGATCAAAGGAGGTGGAAGCA 59.995 52.381 0.00 0.00 36.26 3.91
332 343 3.071580 GGAGATGTTGCCTCCTTCG 57.928 57.895 0.00 0.00 45.18 3.79
335 346 0.036010 AGATGTTGCCTCCTTCGTGG 60.036 55.000 0.00 0.00 37.10 4.94
348 359 2.550978 CTTCGTGGGAGCGTTATCATT 58.449 47.619 0.00 0.00 0.00 2.57
372 390 0.953003 GCTACGGCGAGGAGTTAGAT 59.047 55.000 16.62 0.00 31.77 1.98
391 409 1.252175 TTAGCCAACGTACACGGGTA 58.748 50.000 6.72 0.00 44.95 3.69
431 533 7.786178 AATATGTACACACTCATGCGTATTT 57.214 32.000 0.00 0.00 0.00 1.40
433 535 4.561105 TGTACACACTCATGCGTATTTGA 58.439 39.130 0.00 0.00 0.00 2.69
500 617 8.307582 TCCTACCCAAAAATAAAACAAAGACA 57.692 30.769 0.00 0.00 0.00 3.41
556 674 7.694886 TCAGTTAGTTCACGATACAGATACAG 58.305 38.462 0.00 0.00 0.00 2.74
557 675 6.913132 CAGTTAGTTCACGATACAGATACAGG 59.087 42.308 0.00 0.00 0.00 4.00
559 677 5.250235 AGTTCACGATACAGATACAGGTG 57.750 43.478 0.00 0.00 0.00 4.00
560 678 4.705507 AGTTCACGATACAGATACAGGTGT 59.294 41.667 0.00 0.00 0.00 4.16
561 679 4.632538 TCACGATACAGATACAGGTGTG 57.367 45.455 0.00 0.00 0.00 3.82
562 680 3.116300 CACGATACAGATACAGGTGTGC 58.884 50.000 0.00 0.00 0.00 4.57
563 681 2.223502 ACGATACAGATACAGGTGTGCG 60.224 50.000 0.00 0.00 34.19 5.34
564 682 2.032924 CGATACAGATACAGGTGTGCGA 59.967 50.000 0.00 0.00 31.47 5.10
565 683 3.488553 CGATACAGATACAGGTGTGCGAA 60.489 47.826 0.00 0.00 31.47 4.70
579 697 4.578913 CGAAGCCGCTTCTTCAGA 57.421 55.556 26.53 0.00 41.84 3.27
580 698 3.056628 CGAAGCCGCTTCTTCAGAT 57.943 52.632 26.53 0.00 41.84 2.90
581 699 2.209838 CGAAGCCGCTTCTTCAGATA 57.790 50.000 26.53 0.00 41.84 1.98
582 700 1.855360 CGAAGCCGCTTCTTCAGATAC 59.145 52.381 26.53 2.57 41.84 2.24
583 701 2.735444 CGAAGCCGCTTCTTCAGATACA 60.735 50.000 26.53 0.00 41.84 2.29
584 702 2.593346 AGCCGCTTCTTCAGATACAG 57.407 50.000 0.00 0.00 0.00 2.74
654 784 3.394836 GCGTTGAGGCCCTCTCCT 61.395 66.667 12.94 0.00 41.76 3.69
662 792 3.145551 GCCCTCTCCTCCGCGTTA 61.146 66.667 4.92 0.00 0.00 3.18
733 864 3.847602 CTCTCCTCAGGGCCGCTG 61.848 72.222 13.43 13.43 0.00 5.18
829 976 4.547532 CAGTACATCGCATTACCTCCTAC 58.452 47.826 0.00 0.00 0.00 3.18
830 977 2.795175 ACATCGCATTACCTCCTACG 57.205 50.000 0.00 0.00 0.00 3.51
831 978 1.340248 ACATCGCATTACCTCCTACGG 59.660 52.381 0.00 0.00 0.00 4.02
832 979 0.317479 ATCGCATTACCTCCTACGGC 59.683 55.000 0.00 0.00 0.00 5.68
833 980 1.038681 TCGCATTACCTCCTACGGCA 61.039 55.000 0.00 0.00 0.00 5.69
834 981 0.597637 CGCATTACCTCCTACGGCAG 60.598 60.000 0.00 0.00 0.00 4.85
835 982 0.464452 GCATTACCTCCTACGGCAGT 59.536 55.000 0.00 0.00 0.00 4.40
1243 1430 1.077265 AAGGTGCCTCCCCACAATG 59.923 57.895 0.00 0.00 37.46 2.82
1464 1651 3.247648 ACTGTGTTCCGAACATTTTCTCG 59.752 43.478 16.80 4.20 44.35 4.04
1632 1822 0.693049 AGGTGGACCAAGCTTACAGG 59.307 55.000 0.00 0.00 38.89 4.00
1858 2048 3.926527 GGATCGGGTTTTCAAAGAAATGC 59.073 43.478 0.00 0.00 0.00 3.56
1975 2165 2.905415 TTCCATGATCAGTTTGGGCT 57.095 45.000 12.80 0.00 0.00 5.19
2232 2422 7.025963 ACGGAACAGTAATAGACTTACTTTCG 58.974 38.462 0.00 0.00 35.64 3.46
2250 2440 3.526931 TCGAGGATTGACTGAATGGAC 57.473 47.619 0.00 0.00 0.00 4.02
2434 2627 5.996219 TGTTCTTCAACACAATTATGGACG 58.004 37.500 0.00 0.00 37.61 4.79
2774 2967 1.134995 GCTTAAATGTGGCAGGAAGGC 60.135 52.381 0.00 0.00 44.50 4.35
2811 3004 0.035820 TTGACGGTATCTGGGCCAAC 60.036 55.000 8.04 2.33 0.00 3.77
3085 3280 1.464722 CTTCAGGGGGAAAGGCCAA 59.535 57.895 5.01 0.00 38.95 4.52
3177 3377 3.960571 ACAGATTTTGCCTAGATGCTGT 58.039 40.909 0.00 0.00 0.00 4.40
3313 3518 8.841300 ACTGTCAACCTTTTCTAGAGATTTTTC 58.159 33.333 0.00 0.00 0.00 2.29
3356 3569 9.067986 AGCTAGTAGTAAACTTTCTGCATTTTT 57.932 29.630 0.00 0.00 39.80 1.94
3491 3704 7.149202 TGTCCTAATAAGTTATCCTTGGCAT 57.851 36.000 0.00 0.00 34.46 4.40
3620 3833 4.379499 GCACTCCTTTAACCATGCTGTTAC 60.379 45.833 0.00 0.00 30.73 2.50
3656 4043 6.656902 ACCATTGTACTGATCATCATGACTT 58.343 36.000 0.00 0.00 0.00 3.01
3658 4045 7.066645 ACCATTGTACTGATCATCATGACTTTG 59.933 37.037 0.00 0.00 0.00 2.77
3659 4046 6.990341 TTGTACTGATCATCATGACTTTGG 57.010 37.500 0.00 0.00 0.00 3.28
3660 4047 6.298441 TGTACTGATCATCATGACTTTGGA 57.702 37.500 0.00 0.00 0.00 3.53
3661 4048 6.343703 TGTACTGATCATCATGACTTTGGAG 58.656 40.000 0.00 0.00 0.00 3.86
3662 4049 5.432680 ACTGATCATCATGACTTTGGAGT 57.567 39.130 0.00 0.00 39.32 3.85
3663 4050 6.550938 ACTGATCATCATGACTTTGGAGTA 57.449 37.500 0.00 0.00 35.88 2.59
3664 4051 6.950842 ACTGATCATCATGACTTTGGAGTAA 58.049 36.000 0.00 0.00 35.88 2.24
3665 4052 7.397221 ACTGATCATCATGACTTTGGAGTAAA 58.603 34.615 0.00 0.00 35.88 2.01
3666 4053 7.335422 ACTGATCATCATGACTTTGGAGTAAAC 59.665 37.037 0.00 0.00 35.88 2.01
3667 4054 7.397221 TGATCATCATGACTTTGGAGTAAACT 58.603 34.615 0.00 0.00 35.88 2.66
3668 4055 7.884877 TGATCATCATGACTTTGGAGTAAACTT 59.115 33.333 0.00 0.00 35.88 2.66
3669 4056 8.641498 ATCATCATGACTTTGGAGTAAACTTT 57.359 30.769 0.00 0.00 35.88 2.66
3670 4057 7.874940 TCATCATGACTTTGGAGTAAACTTTG 58.125 34.615 0.00 0.00 35.88 2.77
3671 4058 6.633500 TCATGACTTTGGAGTAAACTTTGG 57.367 37.500 0.00 0.00 35.88 3.28
3672 4059 6.361433 TCATGACTTTGGAGTAAACTTTGGA 58.639 36.000 0.00 0.00 35.88 3.53
3673 4060 6.486657 TCATGACTTTGGAGTAAACTTTGGAG 59.513 38.462 0.00 0.00 35.88 3.86
3674 4061 5.751586 TGACTTTGGAGTAAACTTTGGAGT 58.248 37.500 0.00 0.00 35.88 3.85
3675 4062 6.891388 TGACTTTGGAGTAAACTTTGGAGTA 58.109 36.000 0.00 0.00 35.88 2.59
3676 4063 7.340256 TGACTTTGGAGTAAACTTTGGAGTAA 58.660 34.615 0.00 0.00 35.88 2.24
3677 4064 7.830201 TGACTTTGGAGTAAACTTTGGAGTAAA 59.170 33.333 0.00 0.00 35.88 2.01
3678 4065 8.221965 ACTTTGGAGTAAACTTTGGAGTAAAG 57.778 34.615 0.00 0.00 41.94 1.85
3679 4066 7.201794 ACTTTGGAGTAAACTTTGGAGTAAAGC 60.202 37.037 0.00 0.00 40.92 3.51
3688 4075 5.240713 CTTTGGAGTAAAGCTATGGCAAG 57.759 43.478 3.10 0.00 39.36 4.01
3690 4077 5.429681 TTGGAGTAAAGCTATGGCAAGTA 57.570 39.130 3.10 0.00 41.70 2.24
3692 4079 4.141711 TGGAGTAAAGCTATGGCAAGTAGG 60.142 45.833 3.10 0.00 41.70 3.18
3698 4085 0.178068 CTATGGCAAGTAGGGCACGT 59.822 55.000 0.00 0.00 46.76 4.49
3699 4086 0.107897 TATGGCAAGTAGGGCACGTG 60.108 55.000 12.28 12.28 46.76 4.49
3708 4095 3.276846 GGGCACGTGCACTCGTTT 61.277 61.111 38.60 0.00 42.27 3.60
3735 4123 5.401531 TGTAGCAGTAAGTTAGTTCCTGG 57.598 43.478 0.00 0.00 0.00 4.45
3770 4158 9.866655 TCTCTTTTACATTATATGGGAAGCATT 57.133 29.630 0.00 0.00 33.60 3.56
3780 4168 4.524802 ATGGGAAGCATTATGTCCTCAA 57.475 40.909 2.55 0.00 0.00 3.02
3784 4172 5.045213 TGGGAAGCATTATGTCCTCAACTAA 60.045 40.000 2.55 0.00 0.00 2.24
3860 4248 3.558931 TGGTGCCCTACATGATTACAG 57.441 47.619 0.00 0.00 0.00 2.74
3866 4254 3.393800 CCCTACATGATTACAGCGAAGG 58.606 50.000 0.00 0.00 0.00 3.46
3868 4256 4.038763 CCCTACATGATTACAGCGAAGGTA 59.961 45.833 0.00 0.00 35.08 3.08
3887 4275 7.380423 AAGGTATTAGGTGCTATTGACTGAT 57.620 36.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.042843 CCCTCCGAGCTAGGTGGT 60.043 66.667 26.24 0.00 41.96 4.16
5 6 2.840102 CCCCTCCGAGCTAGGTGG 60.840 72.222 22.99 22.99 42.87 4.61
46 47 0.744874 CTCTTCCCGGTCGCAGAATA 59.255 55.000 0.00 0.00 39.69 1.75
55 56 0.549950 TATCGTCTCCTCTTCCCGGT 59.450 55.000 0.00 0.00 0.00 5.28
56 57 1.688772 TTATCGTCTCCTCTTCCCGG 58.311 55.000 0.00 0.00 0.00 5.73
70 71 4.855715 TCTAGCAGGAGATGGTTTATCG 57.144 45.455 0.00 0.00 40.89 2.92
125 126 3.589654 CTTCCCGAGAGCGTGGCAA 62.590 63.158 0.00 0.00 35.23 4.52
136 137 0.980754 TATCCAGCCTTGCTTCCCGA 60.981 55.000 0.00 0.00 36.40 5.14
149 150 5.604758 TCTCTCAACTTGATGGTATCCAG 57.395 43.478 0.00 0.00 36.75 3.86
164 165 2.301296 CCACTCCTGAAGCTTCTCTCAA 59.699 50.000 26.09 5.66 0.00 3.02
165 166 1.898472 CCACTCCTGAAGCTTCTCTCA 59.102 52.381 26.09 6.84 0.00 3.27
200 201 2.016318 TGCTTCCATATTTCGGTGCAG 58.984 47.619 0.00 0.00 33.04 4.41
205 206 1.948104 TCGGTGCTTCCATATTTCGG 58.052 50.000 0.00 0.00 35.57 4.30
228 229 5.501715 CACTACACCATCAAATACAATCGC 58.498 41.667 0.00 0.00 0.00 4.58
273 274 4.745172 GCTTCCACCTCCTTTGATCCTATC 60.745 50.000 0.00 0.00 0.00 2.08
282 283 1.075659 GCCTGCTTCCACCTCCTTT 59.924 57.895 0.00 0.00 0.00 3.11
297 308 2.273449 CTTTGATGAGCCCGGCCT 59.727 61.111 5.55 0.00 0.00 5.19
332 343 1.670811 CCACAATGATAACGCTCCCAC 59.329 52.381 0.00 0.00 0.00 4.61
335 346 0.663153 GCCCACAATGATAACGCTCC 59.337 55.000 0.00 0.00 0.00 4.70
372 390 1.202114 CTACCCGTGTACGTTGGCTAA 59.798 52.381 0.00 0.00 37.74 3.09
391 409 5.416271 ACATATTACACGAACCCAACTCT 57.584 39.130 0.00 0.00 0.00 3.24
444 546 6.512297 AGCACCCACTTACAACTTAATTTTG 58.488 36.000 0.00 0.00 0.00 2.44
446 548 5.243060 GGAGCACCCACTTACAACTTAATTT 59.757 40.000 0.00 0.00 34.14 1.82
449 551 3.746940 GGAGCACCCACTTACAACTTAA 58.253 45.455 0.00 0.00 34.14 1.85
472 574 9.990360 TCTTTGTTTTATTTTTGGGTAGGAATC 57.010 29.630 0.00 0.00 0.00 2.52
562 680 1.855360 GTATCTGAAGAAGCGGCTTCG 59.145 52.381 30.68 19.53 45.62 3.79
563 681 2.863137 CTGTATCTGAAGAAGCGGCTTC 59.137 50.000 30.39 30.39 43.53 3.86
564 682 2.234908 ACTGTATCTGAAGAAGCGGCTT 59.765 45.455 16.36 16.36 0.00 4.35
565 683 1.827969 ACTGTATCTGAAGAAGCGGCT 59.172 47.619 0.00 0.00 0.00 5.52
567 685 2.159366 ACGACTGTATCTGAAGAAGCGG 60.159 50.000 0.00 0.00 0.00 5.52
568 686 3.102276 GACGACTGTATCTGAAGAAGCG 58.898 50.000 0.00 0.00 0.00 4.68
569 687 4.142578 TGAGACGACTGTATCTGAAGAAGC 60.143 45.833 0.00 0.00 37.24 3.86
570 688 5.448496 CCTGAGACGACTGTATCTGAAGAAG 60.448 48.000 0.00 0.00 37.43 2.85
571 689 4.396478 CCTGAGACGACTGTATCTGAAGAA 59.604 45.833 0.00 0.00 37.43 2.52
572 690 3.942115 CCTGAGACGACTGTATCTGAAGA 59.058 47.826 0.00 0.00 37.43 2.87
574 692 2.423892 GCCTGAGACGACTGTATCTGAA 59.576 50.000 0.00 0.00 37.43 3.02
575 693 2.017782 GCCTGAGACGACTGTATCTGA 58.982 52.381 0.00 0.00 37.43 3.27
576 694 1.066303 GGCCTGAGACGACTGTATCTG 59.934 57.143 0.00 0.00 37.24 2.90
577 695 1.394618 GGCCTGAGACGACTGTATCT 58.605 55.000 0.00 0.00 37.24 1.98
579 697 1.384989 CCGGCCTGAGACGACTGTAT 61.385 60.000 0.00 0.00 0.00 2.29
580 698 2.044555 CCGGCCTGAGACGACTGTA 61.045 63.158 0.00 0.00 0.00 2.74
581 699 3.374402 CCGGCCTGAGACGACTGT 61.374 66.667 0.00 0.00 0.00 3.55
582 700 4.803426 GCCGGCCTGAGACGACTG 62.803 72.222 18.11 0.00 0.00 3.51
654 784 0.106066 TTCCCCTATCCTAACGCGGA 60.106 55.000 12.47 0.00 37.50 5.54
660 790 3.053170 GCCTTTGGTTTCCCCTATCCTAA 60.053 47.826 0.00 0.00 0.00 2.69
662 792 1.288037 GCCTTTGGTTTCCCCTATCCT 59.712 52.381 0.00 0.00 0.00 3.24
913 1060 4.769345 AGGAAGGAAAGCAGAGGAATAG 57.231 45.455 0.00 0.00 0.00 1.73
915 1062 4.394797 AAAGGAAGGAAAGCAGAGGAAT 57.605 40.909 0.00 0.00 0.00 3.01
1222 1409 3.580319 GTGGGGAGGCACCTTGGT 61.580 66.667 0.00 0.00 38.98 3.67
1243 1430 5.023533 TCAACTAGAATGCCATAGGTGAC 57.976 43.478 0.00 0.00 40.06 3.67
1632 1822 3.762779 ACGCAGCATTTCAGAAAATAGC 58.237 40.909 0.00 5.09 33.27 2.97
1975 2165 7.283625 TGTAGGTAGTAACAGTCGGTTTTTA 57.716 36.000 0.00 0.00 40.96 1.52
2232 2422 3.526931 TCGTCCATTCAGTCAATCCTC 57.473 47.619 0.00 0.00 0.00 3.71
2250 2440 2.602257 TGAACTGGGACATAGCATCG 57.398 50.000 0.00 0.00 38.20 3.84
2434 2627 2.553602 CCCTTTCATTTTTGCAAAGGCC 59.446 45.455 12.41 0.00 43.39 5.19
2774 2967 4.442073 CGTCAAACAAATCTTTGGCTTCTG 59.558 41.667 7.51 0.00 42.34 3.02
2811 3004 5.529430 TGTAATAACATTGGGCACTAATCCG 59.471 40.000 0.00 0.00 37.45 4.18
3022 3216 1.214175 TGGAAGCTTCAAGGGTGAACA 59.786 47.619 27.02 10.13 38.88 3.18
3112 3307 4.040461 TCCTGTTCCAGAAAAGAGTGGTAG 59.960 45.833 0.00 0.00 35.14 3.18
3157 3352 5.007430 CACTACAGCATCTAGGCAAAATCTG 59.993 44.000 0.00 0.00 35.83 2.90
3177 3377 2.067365 TCAGCCCTCGATTAGCACTA 57.933 50.000 4.55 0.00 0.00 2.74
3260 3464 9.057089 CAGAAAGTTTACTACAGTTTCTCCAAT 57.943 33.333 3.08 0.00 35.72 3.16
3313 3518 5.542779 ACTAGCTTGTTGGAAGAAGTACTG 58.457 41.667 0.00 0.00 32.36 2.74
3438 3651 8.846211 TCCAGGACTGACAAAACTAATTAAAAG 58.154 33.333 0.00 0.00 0.00 2.27
3491 3704 4.644685 ACAGCAGAAAAGTAAGGCAAAAGA 59.355 37.500 0.00 0.00 0.00 2.52
3604 3817 4.261825 GCCAACTGTAACAGCATGGTTAAA 60.262 41.667 2.38 0.00 43.62 1.52
3656 4043 6.362248 AGCTTTACTCCAAAGTTTACTCCAA 58.638 36.000 0.00 0.00 44.73 3.53
3658 4045 7.065923 CCATAGCTTTACTCCAAAGTTTACTCC 59.934 40.741 0.00 0.00 44.73 3.85
3659 4046 7.414208 GCCATAGCTTTACTCCAAAGTTTACTC 60.414 40.741 0.00 0.00 44.73 2.59
3660 4047 6.374613 GCCATAGCTTTACTCCAAAGTTTACT 59.625 38.462 0.00 0.00 44.73 2.24
3661 4048 6.150474 TGCCATAGCTTTACTCCAAAGTTTAC 59.850 38.462 0.00 0.00 44.73 2.01
3662 4049 6.242396 TGCCATAGCTTTACTCCAAAGTTTA 58.758 36.000 0.00 0.00 44.73 2.01
3663 4050 5.076873 TGCCATAGCTTTACTCCAAAGTTT 58.923 37.500 0.00 0.00 44.73 2.66
3664 4051 4.662278 TGCCATAGCTTTACTCCAAAGTT 58.338 39.130 0.00 0.00 44.73 2.66
3665 4052 4.301072 TGCCATAGCTTTACTCCAAAGT 57.699 40.909 0.00 0.00 44.73 2.66
3666 4053 4.702131 ACTTGCCATAGCTTTACTCCAAAG 59.298 41.667 0.00 0.00 45.55 2.77
3667 4054 4.662278 ACTTGCCATAGCTTTACTCCAAA 58.338 39.130 0.00 0.00 40.80 3.28
3668 4055 4.301072 ACTTGCCATAGCTTTACTCCAA 57.699 40.909 0.00 0.00 40.80 3.53
3669 4056 4.141711 CCTACTTGCCATAGCTTTACTCCA 60.142 45.833 0.00 0.00 40.80 3.86
3670 4057 4.381411 CCTACTTGCCATAGCTTTACTCC 58.619 47.826 0.00 0.00 40.80 3.85
3671 4058 4.381411 CCCTACTTGCCATAGCTTTACTC 58.619 47.826 0.00 0.00 40.80 2.59
3672 4059 3.433740 GCCCTACTTGCCATAGCTTTACT 60.434 47.826 0.00 0.00 40.80 2.24
3673 4060 2.879026 GCCCTACTTGCCATAGCTTTAC 59.121 50.000 0.00 0.00 40.80 2.01
3674 4061 2.507886 TGCCCTACTTGCCATAGCTTTA 59.492 45.455 0.00 0.00 40.80 1.85
3675 4062 1.284785 TGCCCTACTTGCCATAGCTTT 59.715 47.619 0.00 0.00 40.80 3.51
3676 4063 0.918983 TGCCCTACTTGCCATAGCTT 59.081 50.000 0.00 0.00 40.80 3.74
3677 4064 0.181350 GTGCCCTACTTGCCATAGCT 59.819 55.000 0.00 0.00 40.80 3.32
3678 4065 1.160329 CGTGCCCTACTTGCCATAGC 61.160 60.000 0.00 0.00 40.48 2.97
3679 4066 0.178068 ACGTGCCCTACTTGCCATAG 59.822 55.000 0.00 0.00 0.00 2.23
3680 4067 0.107897 CACGTGCCCTACTTGCCATA 60.108 55.000 0.82 0.00 0.00 2.74
3681 4068 1.377202 CACGTGCCCTACTTGCCAT 60.377 57.895 0.82 0.00 0.00 4.40
3682 4069 2.031919 CACGTGCCCTACTTGCCA 59.968 61.111 0.82 0.00 0.00 4.92
3683 4070 3.431725 GCACGTGCCCTACTTGCC 61.432 66.667 30.12 0.00 45.79 4.52
3685 4072 1.291877 GAGTGCACGTGCCCTACTTG 61.292 60.000 35.72 0.00 41.18 3.16
3686 4073 1.004918 GAGTGCACGTGCCCTACTT 60.005 57.895 35.72 17.20 41.18 2.24
3687 4074 2.657237 GAGTGCACGTGCCCTACT 59.343 61.111 35.72 30.70 41.18 2.57
3688 4075 2.809601 CGAGTGCACGTGCCCTAC 60.810 66.667 35.72 26.77 41.18 3.18
3690 4077 2.372040 TAAACGAGTGCACGTGCCCT 62.372 55.000 35.72 31.04 45.83 5.19
3692 4079 0.110823 CTTAAACGAGTGCACGTGCC 60.111 55.000 35.72 26.08 45.83 5.01
3698 4085 3.459145 TGCTACAACTTAAACGAGTGCA 58.541 40.909 0.00 0.00 0.00 4.57
3699 4086 3.493503 ACTGCTACAACTTAAACGAGTGC 59.506 43.478 0.00 0.00 0.00 4.40
3708 4095 8.086522 CAGGAACTAACTTACTGCTACAACTTA 58.913 37.037 0.00 0.00 33.82 2.24
3770 4158 7.252612 TGGACTGATTTTAGTTGAGGACATA 57.747 36.000 0.00 0.00 0.00 2.29
3774 4162 7.110155 GGTAATGGACTGATTTTAGTTGAGGA 58.890 38.462 0.00 0.00 0.00 3.71
3780 4168 9.227777 GTTAAGTGGTAATGGACTGATTTTAGT 57.772 33.333 0.00 0.00 0.00 2.24
3784 4172 8.650143 AATGTTAAGTGGTAATGGACTGATTT 57.350 30.769 0.00 0.00 0.00 2.17
3826 4214 1.747355 GGCACCATGAATCTGGACTTG 59.253 52.381 0.00 0.00 39.73 3.16
3860 4248 4.448060 GTCAATAGCACCTAATACCTTCGC 59.552 45.833 0.00 0.00 0.00 4.70
3896 4284 3.185330 CTCAGTCAATCTGTGATGTCCG 58.815 50.000 0.00 0.00 43.97 4.79
3897 4285 4.199432 ACTCAGTCAATCTGTGATGTCC 57.801 45.455 4.36 0.00 43.97 4.02


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

AutoCloner maintained by Alex Coulton.