Multiple sequence alignment - TraesCS1A01G193200

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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 TraesCS1A01G193200 chr1A 100.000 2929 0 0 1459 4387 349358923 349361851 0.000000e+00 5409.0
1 TraesCS1A01G193200 chr1A 100.000 1050 0 0 1 1050 349357465 349358514 0.000000e+00 1940.0
2 TraesCS1A01G193200 chr1D 95.984 2938 53 17 1459 4387 277093044 277095925 0.000000e+00 4711.0
3 TraesCS1A01G193200 chr1D 92.188 640 25 11 424 1050 277092313 277092940 0.000000e+00 881.0
4 TraesCS1A01G193200 chr1B 95.366 2935 69 23 1459 4382 376071284 376074162 0.000000e+00 4604.0
5 TraesCS1A01G193200 chr1B 89.248 1051 83 15 2 1050 376070158 376071180 0.000000e+00 1288.0
6 TraesCS1A01G193200 chr3D 90.355 197 19 0 2791 2987 355319164 355318968 4.350000e-65 259.0
7 TraesCS1A01G193200 chr3B 90.355 197 19 0 2791 2987 456323865 456323669 4.350000e-65 259.0
8 TraesCS1A01G193200 chr3B 91.005 189 17 0 2791 2979 463204071 463204259 5.630000e-64 255.0
9 TraesCS1A01G193200 chr3B 84.337 166 21 3 286 449 795346357 795346519 1.630000e-34 158.0
10 TraesCS1A01G193200 chr3A 90.374 187 18 0 2801 2987 474209620 474209434 3.390000e-61 246.0
11 TraesCS1A01G193200 chr4D 86.364 154 16 4 298 448 421404962 421405113 3.510000e-36 163.0
12 TraesCS1A01G193200 chr4D 83.529 170 22 6 286 451 283060263 283060096 2.110000e-33 154.0
13 TraesCS1A01G193200 chr2D 84.848 165 20 4 286 448 336511134 336511295 1.260000e-35 161.0
14 TraesCS1A01G193200 chr5B 83.815 173 22 5 286 455 316708985 316709154 4.540000e-35 159.0
15 TraesCS1A01G193200 chr2A 83.721 172 23 4 285 453 670457898 670457729 1.630000e-34 158.0
16 TraesCS1A01G193200 chr7A 84.242 165 21 4 286 448 524701256 524701417 5.870000e-34 156.0
17 TraesCS1A01G193200 chr5A 83.333 174 24 4 286 455 369636209 369636037 5.870000e-34 156.0
18 TraesCS1A01G193200 chr2B 94.231 52 3 0 1975 2026 788803903 788803852 3.640000e-11 80.5


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 TraesCS1A01G193200 chr1A 349357465 349361851 4386 False 3674.5 5409 100.000 1 4387 2 chr1A.!!$F1 4386
1 TraesCS1A01G193200 chr1D 277092313 277095925 3612 False 2796.0 4711 94.086 424 4387 2 chr1D.!!$F1 3963
2 TraesCS1A01G193200 chr1B 376070158 376074162 4004 False 2946.0 4604 92.307 2 4382 2 chr1B.!!$F1 4380

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
585 589 0.036875 GGGGAGGCTAAATCCGATGG 59.963 60.000 0.00 0.00 37.75 3.51 F
675 679 0.390209 CCAAAATTCGGGCAGCCAAG 60.390 55.000 15.19 6.81 0.00 3.61 F
766 771 1.224436 TTCCCCTATTTTACCCCGGG 58.776 55.000 15.80 15.80 34.62 5.73 F
2417 2436 1.303643 CCCGCCTTTCTTCAAGCCT 60.304 57.895 0.00 0.00 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 2190 1.737008 GGTGCTCCCGTTCTCGAAC 60.737 63.158 0.0 0.0 39.71 3.95 R
2639 2658 1.450312 CATCCCCTCGTTGGCTGTC 60.450 63.158 0.0 0.0 0.00 3.51 R
2708 2727 2.584391 GGACTCCGACTTGGCTGGT 61.584 63.158 0.0 0.0 37.80 4.00 R
4071 4099 0.032615 TTGCCTCTCCTCTCCTCTCC 60.033 60.000 0.0 0.0 0.00 3.71 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
43 44 1.838112 TTGGGAAGTGCATGATCACC 58.162 50.000 0.00 0.00 37.68 4.02
61 62 8.993404 TGATCACCACCAAATAATATGATGAA 57.007 30.769 0.00 0.00 0.00 2.57
66 67 9.820725 CACCACCAAATAATATGATGAAAATGT 57.179 29.630 0.00 0.00 0.00 2.71
101 102 8.506168 TTTTTGTAAGAGAAGTGAATCACTGT 57.494 30.769 17.46 7.45 44.62 3.55
131 132 7.234384 CAGTTAAGGACGTCATAAATGTGAAC 58.766 38.462 22.22 12.06 0.00 3.18
137 138 6.367969 AGGACGTCATAAATGTGAACTAACAC 59.632 38.462 18.91 0.00 40.68 3.32
155 156 0.616891 ACGACCCAAAGATACCACCC 59.383 55.000 0.00 0.00 0.00 4.61
163 164 4.887655 CCCAAAGATACCACCCTCATTTAC 59.112 45.833 0.00 0.00 0.00 2.01
189 191 5.796350 AAAGTAATCTAACGGTCACATGC 57.204 39.130 0.00 0.00 0.00 4.06
191 193 5.086104 AGTAATCTAACGGTCACATGCTT 57.914 39.130 0.00 0.00 0.00 3.91
200 202 2.096496 CGGTCACATGCTTTGGATCTTC 59.904 50.000 0.00 0.00 0.00 2.87
227 229 1.284785 CCCCCTATGCTTCCAGTGAAA 59.715 52.381 0.00 0.00 0.00 2.69
228 230 2.091665 CCCCCTATGCTTCCAGTGAAAT 60.092 50.000 0.00 0.00 0.00 2.17
243 245 5.236263 CCAGTGAAATTTTGCTTGTTTACCC 59.764 40.000 0.00 0.00 0.00 3.69
244 246 5.814705 CAGTGAAATTTTGCTTGTTTACCCA 59.185 36.000 0.00 0.00 0.00 4.51
247 249 6.019075 GTGAAATTTTGCTTGTTTACCCAGTC 60.019 38.462 0.00 0.00 0.00 3.51
249 251 3.306472 TTTGCTTGTTTACCCAGTCCT 57.694 42.857 0.00 0.00 0.00 3.85
253 255 1.985895 CTTGTTTACCCAGTCCTCCCT 59.014 52.381 0.00 0.00 0.00 4.20
255 257 1.702957 TGTTTACCCAGTCCTCCCTTG 59.297 52.381 0.00 0.00 0.00 3.61
258 260 2.449967 TACCCAGTCCTCCCTTGCGA 62.450 60.000 0.00 0.00 0.00 5.10
267 269 1.807142 CCTCCCTTGCGACTCTTTTTC 59.193 52.381 0.00 0.00 0.00 2.29
269 271 1.202604 TCCCTTGCGACTCTTTTTCGT 60.203 47.619 0.00 0.00 38.77 3.85
271 273 1.660333 CCTTGCGACTCTTTTTCGTGC 60.660 52.381 0.00 0.00 38.77 5.34
280 282 1.265635 TCTTTTTCGTGCCGTGATTGG 59.734 47.619 0.00 0.00 0.00 3.16
287 289 2.417239 TCGTGCCGTGATTGGAAAATAC 59.583 45.455 0.00 0.00 0.00 1.89
288 290 2.477189 CGTGCCGTGATTGGAAAATACC 60.477 50.000 0.00 0.00 0.00 2.73
289 291 2.096248 TGCCGTGATTGGAAAATACCC 58.904 47.619 0.00 0.00 0.00 3.69
293 295 3.361786 CGTGATTGGAAAATACCCCCTT 58.638 45.455 0.00 0.00 0.00 3.95
312 314 9.601810 ACCCCCTTCATTTCTAAATATAAATCC 57.398 33.333 0.00 0.00 0.00 3.01
388 390 9.534565 TGTAGAGTATAGATTCACTCATTTTGC 57.465 33.333 4.70 0.00 42.99 3.68
389 391 9.757227 GTAGAGTATAGATTCACTCATTTTGCT 57.243 33.333 4.70 0.00 42.99 3.91
391 393 9.678260 AGAGTATAGATTCACTCATTTTGCTTT 57.322 29.630 4.70 0.00 42.99 3.51
402 404 7.023575 CACTCATTTTGCTTTGTATGTAGTCC 58.976 38.462 0.00 0.00 0.00 3.85
403 405 6.151144 ACTCATTTTGCTTTGTATGTAGTCCC 59.849 38.462 0.00 0.00 0.00 4.46
410 412 6.953101 TGCTTTGTATGTAGTCCCTTATTGA 58.047 36.000 0.00 0.00 0.00 2.57
413 415 8.736244 GCTTTGTATGTAGTCCCTTATTGAAAA 58.264 33.333 0.00 0.00 0.00 2.29
470 472 8.522830 AGTATTTGTTTGAGGGACACATAATTG 58.477 33.333 0.00 0.00 0.00 2.32
477 479 8.306761 GTTTGAGGGACACATAATTGAAAAGAT 58.693 33.333 0.00 0.00 0.00 2.40
478 480 9.527157 TTTGAGGGACACATAATTGAAAAGATA 57.473 29.630 0.00 0.00 0.00 1.98
584 588 1.059913 AGGGGAGGCTAAATCCGATG 58.940 55.000 0.00 0.00 37.75 3.84
585 589 0.036875 GGGGAGGCTAAATCCGATGG 59.963 60.000 0.00 0.00 37.75 3.51
642 646 0.462225 TCGAGACAGGAGGCTACGAG 60.462 60.000 0.00 0.00 0.00 4.18
675 679 0.390209 CCAAAATTCGGGCAGCCAAG 60.390 55.000 15.19 6.81 0.00 3.61
678 682 1.470996 AAATTCGGGCAGCCAAGCAA 61.471 50.000 15.19 0.00 35.83 3.91
683 687 3.756727 GGCAGCCAAGCAAGGAGC 61.757 66.667 6.55 1.76 46.19 4.70
766 771 1.224436 TTCCCCTATTTTACCCCGGG 58.776 55.000 15.80 15.80 34.62 5.73
940 953 3.804193 CCCCGCGCTTGCTTTCTC 61.804 66.667 5.56 0.00 36.08 2.87
941 954 2.743928 CCCGCGCTTGCTTTCTCT 60.744 61.111 5.56 0.00 36.08 3.10
942 955 2.744768 CCCGCGCTTGCTTTCTCTC 61.745 63.158 5.56 0.00 36.08 3.20
2177 2190 2.664185 CCGCCGCAGATCCATCAG 60.664 66.667 0.00 0.00 0.00 2.90
2333 2352 1.975407 GCTCCAGCACCAGCACAAT 60.975 57.895 0.00 0.00 45.49 2.71
2417 2436 1.303643 CCCGCCTTTCTTCAAGCCT 60.304 57.895 0.00 0.00 0.00 4.58
2639 2658 4.619227 AACCACCACCAGACCGCG 62.619 66.667 0.00 0.00 0.00 6.46
2987 3006 3.181471 CCATCTCCTACATCAACGAGCTT 60.181 47.826 0.00 0.00 0.00 3.74
3525 3545 0.640768 GAAAGAAGGCGACGATCGTG 59.359 55.000 28.12 18.27 42.81 4.35
3575 3595 1.340795 GGAGGATGGATGGATGGATGC 60.341 57.143 0.00 0.00 0.00 3.91
3579 3599 2.556782 GGATGGATGGATGGATGCATGT 60.557 50.000 2.46 0.00 39.04 3.21
3580 3600 1.989706 TGGATGGATGGATGCATGTG 58.010 50.000 2.46 0.00 39.04 3.21
3582 3602 2.442502 TGGATGGATGGATGCATGTGTA 59.557 45.455 2.46 0.00 39.04 2.90
3583 3603 2.816087 GGATGGATGGATGCATGTGTAC 59.184 50.000 2.46 0.00 39.04 2.90
3584 3604 3.479489 GATGGATGGATGCATGTGTACA 58.521 45.455 2.46 0.00 39.04 2.90
3586 3606 3.479489 TGGATGGATGCATGTGTACATC 58.521 45.455 2.46 13.32 41.60 3.06
3587 3607 3.117963 TGGATGGATGCATGTGTACATCA 60.118 43.478 19.69 0.00 43.64 3.07
3588 3608 4.077108 GGATGGATGCATGTGTACATCAT 58.923 43.478 19.69 1.91 43.64 2.45
3589 3609 4.155462 GGATGGATGCATGTGTACATCATC 59.845 45.833 19.69 18.61 43.64 2.92
3590 3610 4.153673 TGGATGCATGTGTACATCATCA 57.846 40.909 23.22 15.51 43.64 3.07
3591 3611 4.721132 TGGATGCATGTGTACATCATCAT 58.279 39.130 23.22 17.87 43.64 2.45
3592 3612 4.758165 TGGATGCATGTGTACATCATCATC 59.242 41.667 23.22 21.64 43.64 2.92
3593 3613 4.758165 GGATGCATGTGTACATCATCATCA 59.242 41.667 25.62 17.68 43.64 3.07
3594 3614 5.414765 GGATGCATGTGTACATCATCATCAT 59.585 40.000 25.62 19.65 43.64 2.45
3595 3615 5.934935 TGCATGTGTACATCATCATCATC 57.065 39.130 0.00 0.00 33.61 2.92
3596 3616 5.369833 TGCATGTGTACATCATCATCATCA 58.630 37.500 0.00 0.00 33.61 3.07
3597 3617 6.001460 TGCATGTGTACATCATCATCATCAT 58.999 36.000 0.00 0.00 33.61 2.45
3598 3618 6.148811 TGCATGTGTACATCATCATCATCATC 59.851 38.462 0.00 0.00 33.61 2.92
3599 3619 6.148811 GCATGTGTACATCATCATCATCATCA 59.851 38.462 0.00 0.00 33.61 3.07
3600 3620 7.148239 GCATGTGTACATCATCATCATCATCAT 60.148 37.037 0.00 0.00 33.61 2.45
3680 3700 3.243643 CCGGATCCGTCGTTGTTAATTAC 59.756 47.826 31.22 0.00 37.81 1.89
3681 3701 4.107622 CGGATCCGTCGTTGTTAATTACT 58.892 43.478 26.35 0.00 34.35 2.24
3682 3702 4.027132 CGGATCCGTCGTTGTTAATTACTG 60.027 45.833 26.35 0.00 34.35 2.74
3683 3703 4.866486 GGATCCGTCGTTGTTAATTACTGT 59.134 41.667 0.00 0.00 0.00 3.55
3684 3704 6.035843 GGATCCGTCGTTGTTAATTACTGTA 58.964 40.000 0.00 0.00 0.00 2.74
3713 3734 1.209383 CTGTGATCGACGACGGTGT 59.791 57.895 7.55 0.00 40.21 4.16
3714 3735 0.445043 CTGTGATCGACGACGGTGTA 59.555 55.000 7.55 0.00 40.21 2.90
3715 3736 1.063616 CTGTGATCGACGACGGTGTAT 59.936 52.381 7.55 0.00 40.21 2.29
3716 3737 1.063027 TGTGATCGACGACGGTGTATC 59.937 52.381 7.55 3.76 40.21 2.24
3717 3738 0.302589 TGATCGACGACGGTGTATCG 59.697 55.000 7.55 0.00 45.17 2.92
3727 3748 1.723870 GGTGTATCGTCGGCGTAGT 59.276 57.895 10.18 0.00 39.49 2.73
3797 3818 3.243771 CCGTTCTCCTCTAGTGTTGTTGT 60.244 47.826 0.00 0.00 0.00 3.32
3798 3819 4.369182 CGTTCTCCTCTAGTGTTGTTGTT 58.631 43.478 0.00 0.00 0.00 2.83
3799 3820 4.209288 CGTTCTCCTCTAGTGTTGTTGTTG 59.791 45.833 0.00 0.00 0.00 3.33
3841 3862 1.357991 GCTTCTCGTCTTGGCAGAGC 61.358 60.000 0.00 0.00 32.42 4.09
3842 3863 1.075425 CTTCTCGTCTTGGCAGAGCG 61.075 60.000 0.00 0.00 32.42 5.03
3843 3864 1.524008 TTCTCGTCTTGGCAGAGCGA 61.524 55.000 8.55 8.55 33.96 4.93
3844 3865 1.515952 CTCGTCTTGGCAGAGCGAG 60.516 63.158 17.33 17.33 40.76 5.03
3933 3961 4.493220 GCTCGTATGCTTCTTGATTGTGTC 60.493 45.833 0.00 0.00 0.00 3.67
3996 4024 0.909133 GGGGGCATGTGATTTGGGTT 60.909 55.000 0.00 0.00 0.00 4.11
4065 4093 3.576550 GAGAAGGATTAGCGAGGAAGGAT 59.423 47.826 0.00 0.00 0.00 3.24
4066 4094 3.323403 AGAAGGATTAGCGAGGAAGGATG 59.677 47.826 0.00 0.00 0.00 3.51
4067 4095 1.974236 AGGATTAGCGAGGAAGGATGG 59.026 52.381 0.00 0.00 0.00 3.51
4068 4096 1.971357 GGATTAGCGAGGAAGGATGGA 59.029 52.381 0.00 0.00 0.00 3.41
4069 4097 2.028567 GGATTAGCGAGGAAGGATGGAG 60.029 54.545 0.00 0.00 0.00 3.86
4070 4098 2.454336 TTAGCGAGGAAGGATGGAGA 57.546 50.000 0.00 0.00 0.00 3.71
4071 4099 1.988293 TAGCGAGGAAGGATGGAGAG 58.012 55.000 0.00 0.00 0.00 3.20
4072 4100 0.758685 AGCGAGGAAGGATGGAGAGG 60.759 60.000 0.00 0.00 0.00 3.69
4073 4101 0.757188 GCGAGGAAGGATGGAGAGGA 60.757 60.000 0.00 0.00 0.00 3.71
4074 4102 1.327303 CGAGGAAGGATGGAGAGGAG 58.673 60.000 0.00 0.00 0.00 3.69
4130 4158 4.274147 TCTTGGCAGAACAAAAGGTAACA 58.726 39.130 0.00 0.00 41.41 2.41
4140 4168 3.720002 ACAAAAGGTAACAAGGAGAGGGA 59.280 43.478 0.00 0.00 41.41 4.20
4170 4199 1.228429 CCCGTCCTTCCTTGGCAAA 60.228 57.895 0.00 0.00 0.00 3.68
4192 4224 4.882559 AGAGAAGAGAAGTGGATGAGGAT 58.117 43.478 0.00 0.00 0.00 3.24
4193 4225 5.279685 AGAGAAGAGAAGTGGATGAGGATT 58.720 41.667 0.00 0.00 0.00 3.01
4194 4226 5.129155 AGAGAAGAGAAGTGGATGAGGATTG 59.871 44.000 0.00 0.00 0.00 2.67
4195 4227 5.028802 AGAAGAGAAGTGGATGAGGATTGA 58.971 41.667 0.00 0.00 0.00 2.57
4196 4228 5.129155 AGAAGAGAAGTGGATGAGGATTGAG 59.871 44.000 0.00 0.00 0.00 3.02
4197 4229 3.710677 AGAGAAGTGGATGAGGATTGAGG 59.289 47.826 0.00 0.00 0.00 3.86
4198 4230 3.708631 GAGAAGTGGATGAGGATTGAGGA 59.291 47.826 0.00 0.00 0.00 3.71
4199 4231 3.710677 AGAAGTGGATGAGGATTGAGGAG 59.289 47.826 0.00 0.00 0.00 3.69
4224 4256 1.000107 GGGAGGGGACACGAGTAGT 60.000 63.158 0.00 0.00 0.00 2.73
4329 4361 2.267006 CGCTGCCTCTCCACATGT 59.733 61.111 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.975410 TTTTTGGGAGCAAATTAAACACG 57.025 34.783 0.00 0.00 0.00 4.49
19 20 5.240121 GTGATCATGCACTTCCCAAATTTT 58.760 37.500 0.00 0.00 35.91 1.82
28 29 1.825090 TGGTGGTGATCATGCACTTC 58.175 50.000 0.00 0.00 38.78 3.01
77 78 7.552687 ACACAGTGATTCACTTCTCTTACAAAA 59.447 33.333 16.64 0.00 42.59 2.44
101 102 5.981088 TTATGACGTCCTTAACTGGTACA 57.019 39.130 14.12 0.00 0.00 2.90
109 110 8.928733 GTTAGTTCACATTTATGACGTCCTTAA 58.071 33.333 14.12 8.44 0.00 1.85
131 132 3.930848 GTGGTATCTTTGGGTCGTGTTAG 59.069 47.826 0.00 0.00 0.00 2.34
137 138 0.909623 AGGGTGGTATCTTTGGGTCG 59.090 55.000 0.00 0.00 0.00 4.79
170 172 5.447279 CCAAAGCATGTGACCGTTAGATTAC 60.447 44.000 0.00 0.00 0.00 1.89
171 173 4.634004 CCAAAGCATGTGACCGTTAGATTA 59.366 41.667 0.00 0.00 0.00 1.75
189 191 1.090052 GGGCGACCGAAGATCCAAAG 61.090 60.000 0.00 0.00 43.64 2.77
191 193 2.582436 GGGCGACCGAAGATCCAA 59.418 61.111 0.00 0.00 43.64 3.53
219 221 5.236263 GGGTAAACAAGCAAAATTTCACTGG 59.764 40.000 0.00 0.00 0.00 4.00
227 229 4.223144 AGGACTGGGTAAACAAGCAAAAT 58.777 39.130 0.00 0.00 0.00 1.82
228 230 3.634910 GAGGACTGGGTAAACAAGCAAAA 59.365 43.478 0.00 0.00 0.00 2.44
243 245 1.216710 GAGTCGCAAGGGAGGACTG 59.783 63.158 0.00 0.00 40.88 3.51
244 246 0.543174 AAGAGTCGCAAGGGAGGACT 60.543 55.000 0.00 0.00 43.32 3.85
247 249 1.807142 GAAAAAGAGTCGCAAGGGAGG 59.193 52.381 0.00 0.00 38.47 4.30
249 251 1.202604 ACGAAAAAGAGTCGCAAGGGA 60.203 47.619 0.00 0.00 42.27 4.20
253 255 0.306533 GGCACGAAAAAGAGTCGCAA 59.693 50.000 0.00 0.00 42.27 4.85
255 257 4.820458 GGCACGAAAAAGAGTCGC 57.180 55.556 0.00 0.00 42.27 5.19
269 271 2.096248 GGGTATTTTCCAATCACGGCA 58.904 47.619 0.00 0.00 0.00 5.69
271 273 2.028876 GGGGGTATTTTCCAATCACGG 58.971 52.381 0.00 0.00 0.00 4.94
287 289 9.828691 AGGATTTATATTTAGAAATGAAGGGGG 57.171 33.333 0.00 0.00 28.28 5.40
354 356 9.860650 AGTGAATCTATACTCTACAATCTGTCT 57.139 33.333 0.00 0.00 0.00 3.41
363 365 9.757227 AGCAAAATGAGTGAATCTATACTCTAC 57.243 33.333 0.00 0.00 42.86 2.59
373 375 9.282247 CTACATACAAAGCAAAATGAGTGAATC 57.718 33.333 0.00 0.00 0.00 2.52
389 391 9.802039 AGTTTTCAATAAGGGACTACATACAAA 57.198 29.630 0.00 0.00 38.49 2.83
390 392 9.444600 GAGTTTTCAATAAGGGACTACATACAA 57.555 33.333 0.00 0.00 38.49 2.41
391 393 8.822805 AGAGTTTTCAATAAGGGACTACATACA 58.177 33.333 0.00 0.00 38.49 2.29
419 421 7.574607 TCCCTCCATTCCTAAATAAGTCTTTC 58.425 38.462 0.00 0.00 0.00 2.62
429 431 6.652205 ACAAATACTCCCTCCATTCCTAAA 57.348 37.500 0.00 0.00 0.00 1.85
430 432 6.652205 AACAAATACTCCCTCCATTCCTAA 57.348 37.500 0.00 0.00 0.00 2.69
431 433 6.216662 TCAAACAAATACTCCCTCCATTCCTA 59.783 38.462 0.00 0.00 0.00 2.94
433 435 5.261216 TCAAACAAATACTCCCTCCATTCC 58.739 41.667 0.00 0.00 0.00 3.01
434 436 5.358160 CCTCAAACAAATACTCCCTCCATTC 59.642 44.000 0.00 0.00 0.00 2.67
435 437 5.264395 CCTCAAACAAATACTCCCTCCATT 58.736 41.667 0.00 0.00 0.00 3.16
436 438 4.325344 CCCTCAAACAAATACTCCCTCCAT 60.325 45.833 0.00 0.00 0.00 3.41
437 439 3.010138 CCCTCAAACAAATACTCCCTCCA 59.990 47.826 0.00 0.00 0.00 3.86
477 479 9.391006 GGGTTTTATCTGTGTGAATGAGTTATA 57.609 33.333 0.00 0.00 0.00 0.98
478 480 7.888021 TGGGTTTTATCTGTGTGAATGAGTTAT 59.112 33.333 0.00 0.00 0.00 1.89
488 492 7.447374 TTCTATTGTGGGTTTTATCTGTGTG 57.553 36.000 0.00 0.00 0.00 3.82
500 504 5.250774 ACCAGTGACTTATTCTATTGTGGGT 59.749 40.000 0.00 0.00 0.00 4.51
516 520 1.302033 CCTGTCAGCCACCAGTGAC 60.302 63.158 0.00 0.00 42.93 3.67
584 588 2.943033 CAGTGACCGATTTAACCCATCC 59.057 50.000 0.00 0.00 0.00 3.51
585 589 3.621715 GTCAGTGACCGATTTAACCCATC 59.378 47.826 12.54 0.00 0.00 3.51
652 656 1.591183 CTGCCCGAATTTTGGGGTG 59.409 57.895 21.25 5.18 46.84 4.61
675 679 1.277557 TCTCTCTTTCCTGCTCCTTGC 59.722 52.381 0.00 0.00 43.25 4.01
678 682 3.182887 TCTTCTCTCTTTCCTGCTCCT 57.817 47.619 0.00 0.00 0.00 3.69
680 684 3.677596 CGTTTCTTCTCTCTTTCCTGCTC 59.322 47.826 0.00 0.00 0.00 4.26
681 685 3.556004 CCGTTTCTTCTCTCTTTCCTGCT 60.556 47.826 0.00 0.00 0.00 4.24
683 687 2.739379 GCCGTTTCTTCTCTCTTTCCTG 59.261 50.000 0.00 0.00 0.00 3.86
862 867 1.003718 GTGGTGAGGAAAGACGGGG 60.004 63.158 0.00 0.00 0.00 5.73
866 871 2.224769 TGGATTGGTGGTGAGGAAAGAC 60.225 50.000 0.00 0.00 0.00 3.01
939 952 0.401979 GGGAATGGATGGGAGGGAGA 60.402 60.000 0.00 0.00 0.00 3.71
940 953 1.430369 GGGGAATGGATGGGAGGGAG 61.430 65.000 0.00 0.00 0.00 4.30
941 954 1.387347 GGGGAATGGATGGGAGGGA 60.387 63.158 0.00 0.00 0.00 4.20
942 955 1.001140 AAGGGGAATGGATGGGAGGG 61.001 60.000 0.00 0.00 0.00 4.30
2177 2190 1.737008 GGTGCTCCCGTTCTCGAAC 60.737 63.158 0.00 0.00 39.71 3.95
2333 2352 3.702048 CGGCGGAAAGGACCCTGA 61.702 66.667 0.00 0.00 0.00 3.86
2392 2411 2.125766 GAAGAAAGGCGGGGTCACCT 62.126 60.000 0.00 0.00 38.14 4.00
2417 2436 4.678256 AGTTTAGGATCTCACCAGACTCA 58.322 43.478 0.00 0.00 0.00 3.41
2639 2658 1.450312 CATCCCCTCGTTGGCTGTC 60.450 63.158 0.00 0.00 0.00 3.51
2708 2727 2.584391 GGACTCCGACTTGGCTGGT 61.584 63.158 0.00 0.00 37.80 4.00
2735 2754 4.680537 ACCGACGCCTCCAGGTCT 62.681 66.667 0.00 0.00 37.57 3.85
3257 3276 2.787473 TCATGATGTCCTTCACCACC 57.213 50.000 0.00 0.00 0.00 4.61
3395 3414 1.689273 GCTACTACCTGGTGGATGGAG 59.311 57.143 17.76 3.77 37.04 3.86
3396 3415 1.007842 TGCTACTACCTGGTGGATGGA 59.992 52.381 17.76 7.19 37.04 3.41
3473 3492 0.388134 CCATCGGGCTATAACGACGG 60.388 60.000 0.00 0.00 42.39 4.79
3477 3496 2.607187 GATGTCCATCGGGCTATAACG 58.393 52.381 0.00 0.00 0.00 3.18
3525 3545 6.215845 AGAGATTTTACAACAACAACATGGC 58.784 36.000 0.00 0.00 0.00 4.40
3575 3595 7.667043 TGATGATGATGATGATGTACACATG 57.333 36.000 13.42 0.00 36.57 3.21
3579 3599 8.318412 TGATGATGATGATGATGATGATGTACA 58.682 33.333 0.00 0.00 0.00 2.90
3580 3600 8.718102 TGATGATGATGATGATGATGATGTAC 57.282 34.615 0.00 0.00 0.00 2.90
3582 3602 8.049117 TGATGATGATGATGATGATGATGATGT 58.951 33.333 0.00 0.00 0.00 3.06
3583 3603 8.442632 TGATGATGATGATGATGATGATGATG 57.557 34.615 0.00 0.00 0.00 3.07
3584 3604 9.282569 GATGATGATGATGATGATGATGATGAT 57.717 33.333 0.00 0.00 0.00 2.45
3586 3606 8.442632 TGATGATGATGATGATGATGATGATG 57.557 34.615 0.00 0.00 0.00 3.07
3587 3607 9.282569 GATGATGATGATGATGATGATGATGAT 57.717 33.333 0.00 0.00 0.00 2.45
3588 3608 8.267183 TGATGATGATGATGATGATGATGATGA 58.733 33.333 0.00 0.00 0.00 2.92
3589 3609 8.442632 TGATGATGATGATGATGATGATGATG 57.557 34.615 0.00 0.00 0.00 3.07
3590 3610 9.282569 GATGATGATGATGATGATGATGATGAT 57.717 33.333 0.00 0.00 0.00 2.45
3591 3611 8.489489 AGATGATGATGATGATGATGATGATGA 58.511 33.333 0.00 0.00 0.00 2.92
3592 3612 8.674263 AGATGATGATGATGATGATGATGATG 57.326 34.615 0.00 0.00 0.00 3.07
3593 3613 9.118300 CAAGATGATGATGATGATGATGATGAT 57.882 33.333 0.00 0.00 0.00 2.45
3594 3614 8.103305 ACAAGATGATGATGATGATGATGATGA 58.897 33.333 0.00 0.00 0.00 2.92
3595 3615 8.273780 ACAAGATGATGATGATGATGATGATG 57.726 34.615 0.00 0.00 0.00 3.07
3596 3616 8.734386 CAACAAGATGATGATGATGATGATGAT 58.266 33.333 0.00 0.00 0.00 2.45
3597 3617 7.719633 ACAACAAGATGATGATGATGATGATGA 59.280 33.333 0.00 0.00 0.00 2.92
3598 3618 7.805071 CACAACAAGATGATGATGATGATGATG 59.195 37.037 0.00 0.00 0.00 3.07
3599 3619 7.502561 ACACAACAAGATGATGATGATGATGAT 59.497 33.333 0.00 0.00 0.00 2.45
3600 3620 6.826741 ACACAACAAGATGATGATGATGATGA 59.173 34.615 0.00 0.00 0.00 2.92
3666 3686 9.297586 TCATGAGATACAGTAATTAACAACGAC 57.702 33.333 0.00 0.00 0.00 4.34
3680 3700 4.558296 CGATCACAGGGTCATGAGATACAG 60.558 50.000 0.00 0.00 31.71 2.74
3681 3701 3.319122 CGATCACAGGGTCATGAGATACA 59.681 47.826 0.00 0.00 31.71 2.29
3682 3702 3.570125 TCGATCACAGGGTCATGAGATAC 59.430 47.826 0.00 0.00 31.71 2.24
3683 3703 3.570125 GTCGATCACAGGGTCATGAGATA 59.430 47.826 0.00 0.00 31.71 1.98
3684 3704 2.363680 GTCGATCACAGGGTCATGAGAT 59.636 50.000 0.00 0.00 33.85 2.75
3713 3734 1.354155 CAGCACTACGCCGACGATA 59.646 57.895 0.00 0.00 44.04 2.92
3714 3735 2.102357 CAGCACTACGCCGACGAT 59.898 61.111 0.00 0.00 44.04 3.73
3715 3736 2.911484 AACAGCACTACGCCGACGA 61.911 57.895 0.00 0.00 44.04 4.20
3716 3737 2.430244 AACAGCACTACGCCGACG 60.430 61.111 0.00 0.00 44.04 5.12
3717 3738 0.942410 TTCAACAGCACTACGCCGAC 60.942 55.000 0.00 0.00 44.04 4.79
3727 3748 7.549134 CCTATATACAGTTTCAGTTCAACAGCA 59.451 37.037 0.00 0.00 0.00 4.41
3797 3818 2.607526 GCATGCATACACACAACAGCAA 60.608 45.455 14.21 0.00 35.45 3.91
3798 3819 1.068402 GCATGCATACACACAACAGCA 60.068 47.619 14.21 0.00 36.34 4.41
3799 3820 1.068402 TGCATGCATACACACAACAGC 60.068 47.619 18.46 0.00 0.00 4.40
3841 3862 0.511653 CAATCATCCATGCTCGCTCG 59.488 55.000 0.00 0.00 0.00 5.03
3842 3863 1.875009 TCAATCATCCATGCTCGCTC 58.125 50.000 0.00 0.00 0.00 5.03
3843 3864 2.563261 ATCAATCATCCATGCTCGCT 57.437 45.000 0.00 0.00 0.00 4.93
3844 3865 3.064958 CCATATCAATCATCCATGCTCGC 59.935 47.826 0.00 0.00 0.00 5.03
3933 3961 1.068055 GCCAAGTTGCACAAGATGAGG 60.068 52.381 0.00 0.00 0.00 3.86
3996 4024 3.487372 CCTATGATGTCGAGGTCTACCA 58.513 50.000 1.26 0.00 38.89 3.25
4035 4063 5.255710 TCGCTAATCCTTCTCTTCTTCTG 57.744 43.478 0.00 0.00 0.00 3.02
4036 4064 4.340950 CCTCGCTAATCCTTCTCTTCTTCT 59.659 45.833 0.00 0.00 0.00 2.85
4065 4093 1.221635 CTCCTCTCCTCTCCTCTCCA 58.778 60.000 0.00 0.00 0.00 3.86
4066 4094 1.421646 CTCTCCTCTCCTCTCCTCTCC 59.578 61.905 0.00 0.00 0.00 3.71
4067 4095 1.421646 CCTCTCCTCTCCTCTCCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
4068 4096 1.522900 CCTCTCCTCTCCTCTCCTCT 58.477 60.000 0.00 0.00 0.00 3.69
4069 4097 0.178990 GCCTCTCCTCTCCTCTCCTC 60.179 65.000 0.00 0.00 0.00 3.71
4070 4098 0.923729 TGCCTCTCCTCTCCTCTCCT 60.924 60.000 0.00 0.00 0.00 3.69
4071 4099 0.032615 TTGCCTCTCCTCTCCTCTCC 60.033 60.000 0.00 0.00 0.00 3.71
4072 4100 1.756538 CTTTGCCTCTCCTCTCCTCTC 59.243 57.143 0.00 0.00 0.00 3.20
4073 4101 1.864669 CTTTGCCTCTCCTCTCCTCT 58.135 55.000 0.00 0.00 0.00 3.69
4074 4102 0.177836 GCTTTGCCTCTCCTCTCCTC 59.822 60.000 0.00 0.00 0.00 3.71
4116 4144 4.519350 CCCTCTCCTTGTTACCTTTTGTTC 59.481 45.833 0.00 0.00 0.00 3.18
4130 4158 1.489560 CCACGGGTTTCCCTCTCCTT 61.490 60.000 3.25 0.00 42.67 3.36
4170 4199 4.329638 TCCTCATCCACTTCTCTTCTCT 57.670 45.455 0.00 0.00 0.00 3.10
4192 4224 1.706575 CTCCCTCCCTCCTCCTCAA 59.293 63.158 0.00 0.00 0.00 3.02
4193 4225 2.328589 CCTCCCTCCCTCCTCCTCA 61.329 68.421 0.00 0.00 0.00 3.86
4194 4226 2.612251 CCTCCCTCCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
4195 4227 3.039526 CCCTCCCTCCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
4196 4228 4.179599 CCCCTCCCTCCCTCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
4197 4229 3.036959 TCCCCTCCCTCCCTCCTC 61.037 72.222 0.00 0.00 0.00 3.71
4198 4230 3.369388 GTCCCCTCCCTCCCTCCT 61.369 72.222 0.00 0.00 0.00 3.69
4199 4231 3.695825 TGTCCCCTCCCTCCCTCC 61.696 72.222 0.00 0.00 0.00 4.30
4224 4256 1.967319 AGAAGAAGAAAAGCCGCACA 58.033 45.000 0.00 0.00 0.00 4.57
4329 4361 1.522092 GATCAGGTGGTGGCATCGA 59.478 57.895 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.