Multiple sequence alignment - TraesCS2B01G586600

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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 TraesCS2B01G586600 chr2B 100.000 4010 0 0 1 4010 773167809 773171818 0.000000e+00 7406.0
1 TraesCS2B01G586600 chr2B 92.675 314 23 0 3230 3543 773228040 773228353 1.700000e-123 453.0
2 TraesCS2B01G586600 chr2B 95.392 217 10 0 3794 4010 773340953 773341169 2.970000e-91 346.0
3 TraesCS2B01G586600 chr2B 95.545 202 9 0 3600 3801 773228552 773228753 1.390000e-84 324.0
4 TraesCS2B01G586600 chr2A 92.986 2937 140 36 281 3196 760597287 760600178 0.000000e+00 4222.0
5 TraesCS2B01G586600 chr2A 88.806 268 24 3 3 266 760596916 760597181 1.390000e-84 324.0
6 TraesCS2B01G586600 chr2A 92.157 102 8 0 3204 3305 760600535 760600636 1.160000e-30 145.0
7 TraesCS2B01G586600 chr2D 89.762 3067 204 53 281 3286 630423665 630426682 0.000000e+00 3823.0
8 TraesCS2B01G586600 chr2D 89.850 266 23 4 3 267 630423298 630423560 4.960000e-89 339.0
9 TraesCS2B01G586600 chr2D 91.463 82 6 1 3348 3428 580260052 580260133 1.180000e-20 111.0
10 TraesCS2B01G586600 chr5B 95.480 354 13 3 1803 2155 473774424 473774775 2.710000e-156 562.0
11 TraesCS2B01G586600 chr6B 91.688 397 25 2 3615 4010 4825547 4825158 9.800000e-151 544.0
12 TraesCS2B01G586600 chr6B 77.419 217 47 2 1299 1514 151372668 151372883 1.170000e-25 128.0
13 TraesCS2B01G586600 chr6B 100.000 39 0 0 3509 3547 4825749 4825711 5.560000e-09 73.1
14 TraesCS2B01G586600 chr6A 87.200 375 34 7 3600 3967 914726 914359 8.020000e-112 414.0
15 TraesCS2B01G586600 chr6A 76.389 216 51 0 1299 1514 94227128 94227343 2.530000e-22 117.0
16 TraesCS2B01G586600 chr6A 82.443 131 19 4 3667 3793 909775 909645 1.180000e-20 111.0
17 TraesCS2B01G586600 chr6D 83.947 380 40 11 3600 3971 1979570 1979936 1.070000e-90 344.0
18 TraesCS2B01G586600 chr6D 84.677 124 8 6 3433 3547 1979264 1979385 3.280000e-21 113.0
19 TraesCS2B01G586600 chr6D 76.126 222 45 7 1299 1516 402353142 402352925 4.240000e-20 110.0
20 TraesCS2B01G586600 chr1A 92.771 83 5 1 3346 3427 366546991 366547073 7.040000e-23 119.0
21 TraesCS2B01G586600 chr7B 95.775 71 3 0 3367 3437 740159915 740159845 9.110000e-22 115.0
22 TraesCS2B01G586600 chr7B 95.775 71 3 0 3367 3437 740520177 740520107 9.110000e-22 115.0
23 TraesCS2B01G586600 chr7B 76.804 194 37 7 1297 1489 409712036 409711850 7.090000e-18 102.0
24 TraesCS2B01G586600 chr5D 76.923 195 45 0 1300 1494 315485372 315485178 1.180000e-20 111.0
25 TraesCS2B01G586600 chr5A 75.893 224 50 3 1300 1521 410203484 410203263 1.180000e-20 111.0
26 TraesCS2B01G586600 chr7A 90.476 84 7 1 3349 3431 729144439 729144356 4.240000e-20 110.0
27 TraesCS2B01G586600 chrUn 90.361 83 6 2 3348 3428 328115672 328115754 1.520000e-19 108.0
28 TraesCS2B01G586600 chr1B 88.043 92 8 3 3340 3431 148403959 148404047 5.480000e-19 106.0
29 TraesCS2B01G586600 chr4B 92.958 71 5 0 3367 3437 599824058 599823988 1.970000e-18 104.0
30 TraesCS2B01G586600 chr7D 76.289 194 38 7 1297 1489 400171045 400170859 3.300000e-16 97.1


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 TraesCS2B01G586600 chr2B 773167809 773171818 4009 False 7406.000000 7406 100.000000 1 4010 1 chr2B.!!$F1 4009
1 TraesCS2B01G586600 chr2B 773228040 773228753 713 False 388.500000 453 94.110000 3230 3801 2 chr2B.!!$F3 571
2 TraesCS2B01G586600 chr2A 760596916 760600636 3720 False 1563.666667 4222 91.316333 3 3305 3 chr2A.!!$F1 3302
3 TraesCS2B01G586600 chr2D 630423298 630426682 3384 False 2081.000000 3823 89.806000 3 3286 2 chr2D.!!$F2 3283
4 TraesCS2B01G586600 chr6B 4825158 4825749 591 True 308.550000 544 95.844000 3509 4010 2 chr6B.!!$R1 501
5 TraesCS2B01G586600 chr6D 1979264 1979936 672 False 228.500000 344 84.312000 3433 3971 2 chr6D.!!$F1 538

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
996 1149 0.791238 CTGCAGAGACGAACGAGACG 60.791 60.0 8.42 0.0 0.00 4.18 F
1573 1733 0.389166 CCCAGTCTGACTCGCTGTTC 60.389 60.0 7.49 0.0 0.00 3.18 F
2952 3117 0.388649 ACGACAAGCTCACCATCGTC 60.389 55.0 0.00 0.0 41.96 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2930 3095 0.109272 GATGGTGAGCTTGTCGTCGA 60.109 55.0 0.0 0.0 0.0 4.20 R
2983 3151 0.240411 GTCTTGTACTCTGCGACGGT 59.760 55.0 0.0 0.0 0.0 4.83 R
3878 4593 2.354003 GCATGGTTGGACAAAAGGGATG 60.354 50.0 0.0 0.0 0.0 3.51 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
54 55 6.183360 TGTTTTAGGGGTCTTGTTTCATGTTC 60.183 38.462 0.00 0.00 0.00 3.18
90 91 5.529060 GGGATTTGATCTGTTGTACCATCTC 59.471 44.000 0.00 0.00 0.00 2.75
118 119 7.178274 ACTCTACCTATATGCATCTCCTCAAAG 59.822 40.741 0.19 0.00 0.00 2.77
158 159 6.294120 CCTGTTTGTGCAACTATCATCTTTCA 60.294 38.462 0.00 0.00 38.04 2.69
161 162 7.978414 TGTTTGTGCAACTATCATCTTTCAAAA 59.022 29.630 0.00 0.00 38.04 2.44
162 163 8.816144 GTTTGTGCAACTATCATCTTTCAAAAA 58.184 29.630 0.00 0.00 38.04 1.94
215 219 9.362539 GATGCAAGAATGTCAACTTTGATAAAT 57.637 29.630 0.00 0.00 39.73 1.40
216 220 9.715121 ATGCAAGAATGTCAACTTTGATAAATT 57.285 25.926 0.00 0.00 39.73 1.82
272 276 8.531622 AAAACAATGCGACATAATTTGAATGA 57.468 26.923 0.00 0.00 0.00 2.57
275 279 8.706492 ACAATGCGACATAATTTGAATGATTT 57.294 26.923 0.00 0.00 0.00 2.17
276 280 8.597227 ACAATGCGACATAATTTGAATGATTTG 58.403 29.630 0.00 0.00 0.00 2.32
279 283 7.766283 TGCGACATAATTTGAATGATTTGGTA 58.234 30.769 0.00 0.00 0.00 3.25
339 436 5.244755 TGATTTGAAGATTGATCACCACGA 58.755 37.500 0.00 0.00 0.00 4.35
342 439 3.588955 TGAAGATTGATCACCACGACTG 58.411 45.455 0.00 0.00 0.00 3.51
362 459 4.868734 ACTGCCACGCTTAATTCTACTAAC 59.131 41.667 0.00 0.00 0.00 2.34
366 463 5.579511 GCCACGCTTAATTCTACTAACTGAA 59.420 40.000 0.00 0.00 0.00 3.02
369 466 7.164858 CACGCTTAATTCTACTAACTGAAACG 58.835 38.462 0.00 0.00 0.00 3.60
393 490 9.658799 ACGAATAAGATAATTGATCCACTATGG 57.341 33.333 0.00 0.00 39.43 2.74
412 509 3.219281 TGGCAACCATCATGATGAGATG 58.781 45.455 32.71 26.03 41.20 2.90
425 522 4.640364 TGATGAGATGTAGCACAACACAA 58.360 39.130 0.00 0.00 27.33 3.33
471 570 4.298103 TCCTCTAGAAAGGACACGTACT 57.702 45.455 0.00 0.00 40.60 2.73
472 571 5.426689 TCCTCTAGAAAGGACACGTACTA 57.573 43.478 0.00 0.00 40.60 1.82
473 572 5.999044 TCCTCTAGAAAGGACACGTACTAT 58.001 41.667 0.00 0.00 40.60 2.12
474 573 7.129457 TCCTCTAGAAAGGACACGTACTATA 57.871 40.000 0.00 0.00 40.60 1.31
484 583 5.468072 AGGACACGTACTATATAGTTGACCG 59.532 44.000 20.21 17.63 37.73 4.79
583 682 2.232208 TGATCACACATCTTCAGCGACT 59.768 45.455 0.00 0.00 0.00 4.18
851 994 1.380785 CTCTACCCCCTACGTGCCA 60.381 63.158 0.00 0.00 0.00 4.92
967 1113 2.049802 ACGACGACGGCGACATTT 60.050 55.556 32.70 3.00 44.46 2.32
979 1125 1.737793 GCGACATTTCCCACTTACCTG 59.262 52.381 0.00 0.00 0.00 4.00
996 1149 0.791238 CTGCAGAGACGAACGAGACG 60.791 60.000 8.42 0.00 0.00 4.18
1210 1369 2.376165 GGCTTCTCCCAGGGGGTAC 61.376 68.421 4.81 0.00 44.74 3.34
1211 1370 2.732619 GCTTCTCCCAGGGGGTACG 61.733 68.421 4.81 0.00 44.74 3.67
1536 1696 2.038329 CCACTCCCGTCCCACCTA 59.962 66.667 0.00 0.00 0.00 3.08
1544 1704 1.987855 CGTCCCACCTAAGCCCAGA 60.988 63.158 0.00 0.00 0.00 3.86
1568 1728 4.803426 CGGCCCAGTCTGACTCGC 62.803 72.222 7.49 12.09 0.00 5.03
1569 1729 3.386237 GGCCCAGTCTGACTCGCT 61.386 66.667 20.00 0.00 0.00 4.93
1572 1732 1.668294 CCCAGTCTGACTCGCTGTT 59.332 57.895 7.49 0.00 0.00 3.16
1573 1733 0.389166 CCCAGTCTGACTCGCTGTTC 60.389 60.000 7.49 0.00 0.00 3.18
1576 1736 1.000827 CAGTCTGACTCGCTGTTCTGT 60.001 52.381 7.49 0.00 0.00 3.41
1577 1737 1.683917 AGTCTGACTCGCTGTTCTGTT 59.316 47.619 4.06 0.00 0.00 3.16
1578 1738 2.101582 AGTCTGACTCGCTGTTCTGTTT 59.898 45.455 4.06 0.00 0.00 2.83
1580 1740 1.453524 CTGACTCGCTGTTCTGTTTCG 59.546 52.381 0.00 0.00 0.00 3.46
1590 1755 0.841289 TTCTGTTTCGGAAGGTGGGT 59.159 50.000 0.00 0.00 0.00 4.51
1596 1761 4.388499 CGGAAGGTGGGTGACGGG 62.388 72.222 0.00 0.00 0.00 5.28
2073 2238 2.421739 GGCGGCGATGGTGACTAT 59.578 61.111 12.98 0.00 0.00 2.12
2124 2289 1.291184 CCGAGTTCTTCATGTGCGCA 61.291 55.000 5.66 5.66 0.00 6.09
2166 2331 3.622826 AACGTCAGGACCACCCCG 61.623 66.667 0.00 0.00 36.73 5.73
2253 2418 1.351012 CGTCTACGCCGACTACCTG 59.649 63.158 0.00 0.00 0.00 4.00
2260 2425 2.439701 CCGACTACCTGGCCGAGA 60.440 66.667 0.00 0.00 0.00 4.04
2737 2902 2.661537 CGCTGGAGTTCGTGCACA 60.662 61.111 18.64 0.81 0.00 4.57
2749 2914 3.787001 TGCACACGGTCACCCACA 61.787 61.111 0.00 0.00 0.00 4.17
2773 2938 2.710724 GAAGACCAACGGCGTGGACT 62.711 60.000 27.18 23.67 44.15 3.85
2829 2994 1.345715 CCCACCCCATCACCTACCTC 61.346 65.000 0.00 0.00 0.00 3.85
2831 2996 0.833287 CACCCCATCACCTACCTCAG 59.167 60.000 0.00 0.00 0.00 3.35
2842 3007 2.093537 CTACCTCAGGCTGCGGATCC 62.094 65.000 29.19 0.00 0.00 3.36
2874 3039 2.728817 CCCATCTACGGCGTCTCC 59.271 66.667 19.21 0.00 0.00 3.71
2930 3095 4.057428 GCTCACCAGGCTCGACGT 62.057 66.667 0.00 0.00 0.00 4.34
2937 3102 3.786586 AGGCTCGACGTCGACGAC 61.787 66.667 41.52 33.70 44.22 4.34
2952 3117 0.388649 ACGACAAGCTCACCATCGTC 60.389 55.000 0.00 0.00 41.96 4.20
2991 3159 2.434185 GCCAAGATCACCGTCGCA 60.434 61.111 0.00 0.00 0.00 5.10
3011 3179 1.174783 GAGTACAAGACGGGCTGAGA 58.825 55.000 0.00 0.00 0.00 3.27
3012 3180 0.889306 AGTACAAGACGGGCTGAGAC 59.111 55.000 0.00 0.00 0.00 3.36
3039 3207 3.303725 CCACACCAAACACTATTGACACG 60.304 47.826 0.00 0.00 31.84 4.49
3042 3210 2.806244 ACCAAACACTATTGACACGCTC 59.194 45.455 0.00 0.00 31.84 5.03
3043 3211 3.067106 CCAAACACTATTGACACGCTCT 58.933 45.455 0.00 0.00 31.84 4.09
3044 3212 3.498397 CCAAACACTATTGACACGCTCTT 59.502 43.478 0.00 0.00 31.84 2.85
3045 3213 4.377431 CCAAACACTATTGACACGCTCTTC 60.377 45.833 0.00 0.00 31.84 2.87
3048 3216 4.238514 ACACTATTGACACGCTCTTCTTC 58.761 43.478 0.00 0.00 0.00 2.87
3113 3281 9.974980 TTTTTAGTTTCTCTCTCTTTCTCTCTC 57.025 33.333 0.00 0.00 0.00 3.20
3114 3282 8.934023 TTTAGTTTCTCTCTCTTTCTCTCTCT 57.066 34.615 0.00 0.00 0.00 3.10
3115 3283 8.561738 TTAGTTTCTCTCTCTTTCTCTCTCTC 57.438 38.462 0.00 0.00 0.00 3.20
3116 3284 6.784031 AGTTTCTCTCTCTTTCTCTCTCTCT 58.216 40.000 0.00 0.00 0.00 3.10
3117 3285 6.881602 AGTTTCTCTCTCTTTCTCTCTCTCTC 59.118 42.308 0.00 0.00 0.00 3.20
3118 3286 6.627087 TTCTCTCTCTTTCTCTCTCTCTCT 57.373 41.667 0.00 0.00 0.00 3.10
3119 3287 6.227298 TCTCTCTCTTTCTCTCTCTCTCTC 57.773 45.833 0.00 0.00 0.00 3.20
3120 3288 5.960811 TCTCTCTCTTTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
3121 3289 6.097554 TCTCTCTCTTTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
3122 3290 5.960811 TCTCTCTTTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
3123 3291 6.097554 TCTCTCTTTCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
3127 3295 5.762179 TTCTCTCTCTCTCTCTCTCTGTT 57.238 43.478 0.00 0.00 0.00 3.16
3137 3305 5.575157 TCTCTCTCTCTGTTTGTGGTATCT 58.425 41.667 0.00 0.00 0.00 1.98
3196 3364 9.995957 GTTTGCTTTTGTTGTTTGGTTTATTAT 57.004 25.926 0.00 0.00 0.00 1.28
3311 3828 2.826725 CGGGACCTCCTAATCTATGTCC 59.173 54.545 0.00 0.00 41.17 4.02
3312 3829 2.826725 GGGACCTCCTAATCTATGTCCG 59.173 54.545 0.00 0.00 42.48 4.79
3406 3923 9.650371 CATAACAATTACAGGTACATTGATTCG 57.350 33.333 9.21 0.00 33.02 3.34
3547 4071 6.454795 TCTTCAATCAAGTTAACCAAATGCC 58.545 36.000 0.88 0.00 33.27 4.40
3548 4072 5.146010 TCAATCAAGTTAACCAAATGCCC 57.854 39.130 0.88 0.00 0.00 5.36
3549 4073 4.020662 TCAATCAAGTTAACCAAATGCCCC 60.021 41.667 0.88 0.00 0.00 5.80
3550 4074 1.889829 TCAAGTTAACCAAATGCCCCG 59.110 47.619 0.88 0.00 0.00 5.73
3551 4075 0.606096 AAGTTAACCAAATGCCCCGC 59.394 50.000 0.88 0.00 0.00 6.13
3552 4076 0.540830 AGTTAACCAAATGCCCCGCA 60.541 50.000 0.88 0.00 44.86 5.69
3553 4077 0.318762 GTTAACCAAATGCCCCGCAA 59.681 50.000 0.00 0.00 43.62 4.85
3554 4078 1.048601 TTAACCAAATGCCCCGCAAA 58.951 45.000 0.00 0.00 43.62 3.68
3555 4079 1.048601 TAACCAAATGCCCCGCAAAA 58.951 45.000 0.00 0.00 43.62 2.44
3556 4080 0.181350 AACCAAATGCCCCGCAAAAA 59.819 45.000 0.00 0.00 43.62 1.94
3591 4115 5.068987 TCAAGTTAACCAAATGCTGCTCTTT 59.931 36.000 0.88 0.00 0.00 2.52
3594 4118 5.068987 AGTTAACCAAATGCTGCTCTTTCAA 59.931 36.000 0.88 0.00 0.00 2.69
3598 4122 4.584325 ACCAAATGCTGCTCTTTCAAGTTA 59.416 37.500 0.00 0.00 0.00 2.24
3677 4382 5.957798 TCATCGGTAACTTGTAGGTGTTAG 58.042 41.667 0.00 0.00 30.50 2.34
3711 4416 9.826574 TCCCATTCTTTGTACTATGTATGTTAC 57.173 33.333 0.00 0.00 0.00 2.50
3777 4487 2.301870 AGCTGACCCTGTTCGTTCATTA 59.698 45.455 0.00 0.00 0.00 1.90
3814 4524 6.767456 ACTTATGACTGATGGATGGAGATTC 58.233 40.000 0.00 0.00 0.00 2.52
3878 4593 8.511604 TTTAAGTTCATCCTGATTCCTGAATC 57.488 34.615 11.99 11.99 45.55 2.52
3893 4610 4.088634 CCTGAATCATCCCTTTTGTCCAA 58.911 43.478 0.00 0.00 0.00 3.53
3910 4627 4.158209 TGTCCAACCATGCTGTAAATGATG 59.842 41.667 0.00 0.00 0.00 3.07
3944 4661 9.169592 CATGCATTCACCTGATTATGACATATA 57.830 33.333 0.00 0.00 0.00 0.86
3948 4665 9.492973 CATTCACCTGATTATGACATATACACA 57.507 33.333 0.00 0.00 0.00 3.72
3980 4697 5.360999 TGGATACATCAGTGACCACTCTTAG 59.639 44.000 0.00 0.00 46.17 2.18
3983 4700 4.667573 ACATCAGTGACCACTCTTAGAGA 58.332 43.478 16.95 0.00 40.20 3.10
3993 4710 6.600032 TGACCACTCTTAGAGAAGTCTGATAC 59.400 42.308 24.71 9.22 36.75 2.24
3999 4716 7.931948 ACTCTTAGAGAAGTCTGATACTAGCTC 59.068 40.741 16.95 0.00 38.83 4.09
4007 4724 2.879026 TCTGATACTAGCTCGCAACGAT 59.121 45.455 0.00 0.00 34.61 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 7.721409 AACAAGACCCCTAAAACACTAAAAA 57.279 32.000 0.00 0.00 0.00 1.94
36 37 2.876581 AGGAACATGAAACAAGACCCC 58.123 47.619 0.00 0.00 0.00 4.95
54 55 6.103997 CAGATCAAATCCCATTGAAACAAGG 58.896 40.000 0.00 0.00 42.22 3.61
90 91 7.342581 TGAGGAGATGCATATAGGTAGAGTAG 58.657 42.308 0.00 0.00 0.00 2.57
188 192 5.771153 TCAAAGTTGACATTCTTGCATCA 57.229 34.783 0.00 0.00 31.01 3.07
215 219 6.301108 GCGACGACTTGTGAAAACATAATAA 58.699 36.000 0.00 0.00 0.00 1.40
216 220 5.163933 GGCGACGACTTGTGAAAACATAATA 60.164 40.000 0.00 0.00 0.00 0.98
339 436 3.611766 AGTAGAATTAAGCGTGGCAGT 57.388 42.857 0.00 0.00 0.00 4.40
342 439 5.107133 TCAGTTAGTAGAATTAAGCGTGGC 58.893 41.667 0.00 0.00 0.00 5.01
362 459 9.869844 GTGGATCAATTATCTTATTCGTTTCAG 57.130 33.333 0.00 0.00 34.75 3.02
369 466 9.453572 TGCCATAGTGGATCAATTATCTTATTC 57.546 33.333 0.00 0.00 40.96 1.75
393 490 4.083431 GCTACATCTCATCATGATGGTTGC 60.083 45.833 30.54 25.90 43.88 4.17
412 509 8.180317 ACAAATTAACTTTTGTGTTGTGCTAC 57.820 30.769 6.42 0.00 45.55 3.58
425 522 9.093970 GAAGTGTTTAAGCCACAAATTAACTTT 57.906 29.630 9.26 0.00 35.24 2.66
446 543 3.256136 ACGTGTCCTTTCTAGAGGAAGTG 59.744 47.826 2.39 0.00 46.95 3.16
471 570 4.708421 GGCCTATGGTCGGTCAACTATATA 59.292 45.833 0.00 0.00 0.00 0.86
472 571 3.514309 GGCCTATGGTCGGTCAACTATAT 59.486 47.826 0.00 0.00 0.00 0.86
473 572 2.895404 GGCCTATGGTCGGTCAACTATA 59.105 50.000 0.00 0.00 0.00 1.31
474 573 1.692519 GGCCTATGGTCGGTCAACTAT 59.307 52.381 0.00 0.00 0.00 2.12
484 583 4.497507 GCTTTATTTTGTCGGCCTATGGTC 60.498 45.833 0.00 0.00 0.00 4.02
552 651 0.666374 TGTGTGATCACGTCGTGAGT 59.334 50.000 29.78 18.97 46.04 3.41
583 682 2.335316 AGTTCTGCCCGTACACAAAA 57.665 45.000 0.00 0.00 0.00 2.44
714 857 8.833231 TTCGACATTAGACATTTCTTCTTCTT 57.167 30.769 0.00 0.00 32.75 2.52
715 858 8.833231 TTTCGACATTAGACATTTCTTCTTCT 57.167 30.769 0.00 0.00 32.75 2.85
967 1113 1.267121 GTCTCTGCAGGTAAGTGGGA 58.733 55.000 15.13 0.00 0.00 4.37
979 1125 1.512310 CCGTCTCGTTCGTCTCTGC 60.512 63.158 0.00 0.00 0.00 4.26
996 1149 4.256090 GTCAATCGCGCCATGGCC 62.256 66.667 30.79 21.30 37.98 5.36
1266 1425 6.515272 TCCATTCTTTCTCCATAAGCAAAC 57.485 37.500 0.00 0.00 0.00 2.93
1557 1717 1.323412 ACAGAACAGCGAGTCAGACT 58.677 50.000 1.46 1.46 0.00 3.24
1559 1719 2.743938 GAAACAGAACAGCGAGTCAGA 58.256 47.619 0.00 0.00 0.00 3.27
1568 1728 1.873591 CCACCTTCCGAAACAGAACAG 59.126 52.381 0.00 0.00 0.00 3.16
1569 1729 1.476110 CCCACCTTCCGAAACAGAACA 60.476 52.381 0.00 0.00 0.00 3.18
1572 1732 0.107831 CACCCACCTTCCGAAACAGA 59.892 55.000 0.00 0.00 0.00 3.41
1573 1733 0.107831 TCACCCACCTTCCGAAACAG 59.892 55.000 0.00 0.00 0.00 3.16
1576 1736 1.070105 CGTCACCCACCTTCCGAAA 59.930 57.895 0.00 0.00 0.00 3.46
1577 1737 2.738480 CGTCACCCACCTTCCGAA 59.262 61.111 0.00 0.00 0.00 4.30
1578 1738 3.307906 CCGTCACCCACCTTCCGA 61.308 66.667 0.00 0.00 0.00 4.55
1580 1740 4.029809 CCCCGTCACCCACCTTCC 62.030 72.222 0.00 0.00 0.00 3.46
1596 1761 2.357517 CACAGGTGGTCGCTGTCC 60.358 66.667 0.00 0.00 0.00 4.02
1725 1890 0.244450 CGTAGTGCCGGAACACCTTA 59.756 55.000 16.99 0.00 41.67 2.69
2073 2238 4.600576 TGCTTGAGCGTGTCGGCA 62.601 61.111 0.00 0.00 45.83 5.69
2124 2289 1.091771 CGCCGTTCTTCTGGATGCAT 61.092 55.000 0.00 0.00 0.00 3.96
2436 2601 1.799121 GTCGTTGACGGCGTAGACC 60.799 63.158 14.74 0.00 40.29 3.85
2475 2640 2.516923 CTGTTGTAGTAGGCGTCGAAG 58.483 52.381 0.00 0.00 0.00 3.79
2746 2911 1.495584 CCGTTGGTCTTCCACGTGTG 61.496 60.000 15.65 6.24 44.22 3.82
2749 2914 2.280592 GCCGTTGGTCTTCCACGT 60.281 61.111 0.00 0.00 44.22 4.49
2755 2920 1.466025 TAGTCCACGCCGTTGGTCTT 61.466 55.000 9.66 0.42 36.55 3.01
2758 2923 0.895100 TAGTAGTCCACGCCGTTGGT 60.895 55.000 0.00 0.00 37.93 3.67
2759 2924 0.457337 GTAGTAGTCCACGCCGTTGG 60.457 60.000 0.00 0.00 38.10 3.77
2773 2938 1.670730 TCACGACGTGCCGGTAGTA 60.671 57.895 22.99 0.04 32.98 1.82
2810 2975 1.307866 AGGTAGGTGATGGGGTGGG 60.308 63.158 0.00 0.00 0.00 4.61
2823 2988 1.365633 GATCCGCAGCCTGAGGTAG 59.634 63.158 14.46 0.00 38.55 3.18
2829 2994 4.559063 CCCTGGATCCGCAGCCTG 62.559 72.222 7.39 0.00 0.00 4.85
2914 3079 2.179517 GACGTCGAGCCTGGTGAG 59.820 66.667 0.00 0.00 0.00 3.51
2925 3090 2.127345 AGCTTGTCGTCGACGTCG 60.127 61.111 34.40 31.30 40.80 5.12
2930 3095 0.109272 GATGGTGAGCTTGTCGTCGA 60.109 55.000 0.00 0.00 0.00 4.20
2933 3098 0.388649 GACGATGGTGAGCTTGTCGT 60.389 55.000 10.93 10.93 46.78 4.34
2937 3102 2.654749 TGTAGACGATGGTGAGCTTG 57.345 50.000 0.00 0.00 0.00 4.01
2952 3117 2.150051 GGGGCCCTCCTGGATGTAG 61.150 68.421 24.38 0.00 35.39 2.74
2973 3141 3.554692 GCGACGGTGATCTTGGCG 61.555 66.667 0.00 3.72 0.00 5.69
2983 3151 0.240411 GTCTTGTACTCTGCGACGGT 59.760 55.000 0.00 0.00 0.00 4.83
2991 3159 1.178276 CTCAGCCCGTCTTGTACTCT 58.822 55.000 0.00 0.00 0.00 3.24
3011 3179 6.038936 GTCAATAGTGTTTGGTGTGGTTAAGT 59.961 38.462 0.00 0.00 0.00 2.24
3012 3180 6.038825 TGTCAATAGTGTTTGGTGTGGTTAAG 59.961 38.462 0.00 0.00 0.00 1.85
3067 3235 1.941377 AGCAGGGGCAAAAATCATCA 58.059 45.000 0.00 0.00 44.61 3.07
3068 3236 3.339253 AAAGCAGGGGCAAAAATCATC 57.661 42.857 0.00 0.00 44.61 2.92
3103 3271 5.738909 ACAGAGAGAGAGAGAGAGAGAAAG 58.261 45.833 0.00 0.00 0.00 2.62
3104 3272 5.762179 ACAGAGAGAGAGAGAGAGAGAAA 57.238 43.478 0.00 0.00 0.00 2.52
3105 3273 5.762179 AACAGAGAGAGAGAGAGAGAGAA 57.238 43.478 0.00 0.00 0.00 2.87
3106 3274 5.013079 ACAAACAGAGAGAGAGAGAGAGAGA 59.987 44.000 0.00 0.00 0.00 3.10
3107 3275 5.122869 CACAAACAGAGAGAGAGAGAGAGAG 59.877 48.000 0.00 0.00 0.00 3.20
3108 3276 5.003160 CACAAACAGAGAGAGAGAGAGAGA 58.997 45.833 0.00 0.00 0.00 3.10
3109 3277 4.156556 CCACAAACAGAGAGAGAGAGAGAG 59.843 50.000 0.00 0.00 0.00 3.20
3110 3278 4.078537 CCACAAACAGAGAGAGAGAGAGA 58.921 47.826 0.00 0.00 0.00 3.10
3111 3279 3.826157 ACCACAAACAGAGAGAGAGAGAG 59.174 47.826 0.00 0.00 0.00 3.20
3112 3280 3.838565 ACCACAAACAGAGAGAGAGAGA 58.161 45.455 0.00 0.00 0.00 3.10
3113 3281 5.652014 AGATACCACAAACAGAGAGAGAGAG 59.348 44.000 0.00 0.00 0.00 3.20
3114 3282 5.417266 CAGATACCACAAACAGAGAGAGAGA 59.583 44.000 0.00 0.00 0.00 3.10
3115 3283 5.417266 TCAGATACCACAAACAGAGAGAGAG 59.583 44.000 0.00 0.00 0.00 3.20
3116 3284 5.325239 TCAGATACCACAAACAGAGAGAGA 58.675 41.667 0.00 0.00 0.00 3.10
3117 3285 5.394005 CCTCAGATACCACAAACAGAGAGAG 60.394 48.000 0.00 0.00 0.00 3.20
3118 3286 4.464244 CCTCAGATACCACAAACAGAGAGA 59.536 45.833 0.00 0.00 0.00 3.10
3119 3287 4.221703 ACCTCAGATACCACAAACAGAGAG 59.778 45.833 0.00 0.00 0.00 3.20
3120 3288 4.160329 ACCTCAGATACCACAAACAGAGA 58.840 43.478 0.00 0.00 0.00 3.10
3121 3289 4.499183 GACCTCAGATACCACAAACAGAG 58.501 47.826 0.00 0.00 0.00 3.35
3122 3290 3.260884 GGACCTCAGATACCACAAACAGA 59.739 47.826 0.00 0.00 0.00 3.41
3123 3291 3.600388 GGACCTCAGATACCACAAACAG 58.400 50.000 0.00 0.00 0.00 3.16
3127 3295 2.335681 TGGGACCTCAGATACCACAA 57.664 50.000 0.00 0.00 0.00 3.33
3137 3305 3.117701 TGTTGTTCTCAATTGGGACCTCA 60.118 43.478 7.75 5.28 35.92 3.86
3196 3364 9.663904 CAGAATGTTCGAATTTGTTTCTCTTAA 57.336 29.630 0.00 0.00 31.73 1.85
3197 3365 9.051679 TCAGAATGTTCGAATTTGTTTCTCTTA 57.948 29.630 0.00 0.00 37.40 2.10
3199 3367 7.496529 TCAGAATGTTCGAATTTGTTTCTCT 57.503 32.000 0.00 0.00 37.40 3.10
3200 3368 6.304208 GCTCAGAATGTTCGAATTTGTTTCTC 59.696 38.462 0.00 0.00 37.40 2.87
3202 3370 5.343325 GGCTCAGAATGTTCGAATTTGTTTC 59.657 40.000 0.00 1.17 37.40 2.78
3220 3737 1.817099 GCATCAAGGTCCGGCTCAG 60.817 63.158 0.00 0.00 0.00 3.35
3329 3846 5.767816 AAAAAGATTGACACACAGGTACC 57.232 39.130 2.73 2.73 0.00 3.34
3391 3908 7.786178 TTTTAGATCCGAATCAATGTACCTG 57.214 36.000 0.00 0.00 34.07 4.00
3428 3945 6.071896 TGTTGTTGTTGATGTTTGTGACCTTA 60.072 34.615 0.00 0.00 0.00 2.69
3438 3955 5.528043 TGGCTAATGTTGTTGTTGATGTT 57.472 34.783 0.00 0.00 0.00 2.71
3559 4083 8.397148 CAGCATTTGGTTAACTTGATTGTTTTT 58.603 29.630 5.42 0.00 0.00 1.94
3560 4084 7.467131 GCAGCATTTGGTTAACTTGATTGTTTT 60.467 33.333 5.42 0.00 0.00 2.43
3561 4085 6.018016 GCAGCATTTGGTTAACTTGATTGTTT 60.018 34.615 5.42 0.00 0.00 2.83
3562 4086 5.466393 GCAGCATTTGGTTAACTTGATTGTT 59.534 36.000 5.42 0.00 0.00 2.83
3563 4087 4.990426 GCAGCATTTGGTTAACTTGATTGT 59.010 37.500 5.42 0.00 0.00 2.71
3564 4088 5.232463 AGCAGCATTTGGTTAACTTGATTG 58.768 37.500 5.42 0.00 32.47 2.67
3565 4089 5.244626 AGAGCAGCATTTGGTTAACTTGATT 59.755 36.000 5.42 0.00 37.72 2.57
3566 4090 4.768968 AGAGCAGCATTTGGTTAACTTGAT 59.231 37.500 5.42 0.00 37.72 2.57
3567 4091 4.144297 AGAGCAGCATTTGGTTAACTTGA 58.856 39.130 5.42 0.00 37.72 3.02
3568 4092 4.510038 AGAGCAGCATTTGGTTAACTTG 57.490 40.909 5.42 0.44 37.72 3.16
3569 4093 5.068987 TGAAAGAGCAGCATTTGGTTAACTT 59.931 36.000 5.42 0.00 37.72 2.66
3570 4094 4.584325 TGAAAGAGCAGCATTTGGTTAACT 59.416 37.500 5.42 0.00 37.72 2.24
3571 4095 4.870363 TGAAAGAGCAGCATTTGGTTAAC 58.130 39.130 0.00 0.00 37.72 2.01
3572 4096 5.068987 ACTTGAAAGAGCAGCATTTGGTTAA 59.931 36.000 0.00 0.00 37.72 2.01
3573 4097 4.584325 ACTTGAAAGAGCAGCATTTGGTTA 59.416 37.500 0.00 0.00 37.72 2.85
3574 4098 3.385755 ACTTGAAAGAGCAGCATTTGGTT 59.614 39.130 0.00 0.00 37.72 3.67
3575 4099 2.961062 ACTTGAAAGAGCAGCATTTGGT 59.039 40.909 0.00 0.00 41.02 3.67
3576 4100 3.655276 ACTTGAAAGAGCAGCATTTGG 57.345 42.857 0.00 0.00 0.00 3.28
3577 4101 5.978919 TGTTAACTTGAAAGAGCAGCATTTG 59.021 36.000 7.22 0.00 0.00 2.32
3578 4102 6.147864 TGTTAACTTGAAAGAGCAGCATTT 57.852 33.333 7.22 0.00 0.00 2.32
3579 4103 5.772825 TGTTAACTTGAAAGAGCAGCATT 57.227 34.783 7.22 0.00 0.00 3.56
3580 4104 5.067674 TGTTGTTAACTTGAAAGAGCAGCAT 59.932 36.000 7.22 0.00 0.00 3.79
3581 4105 4.397730 TGTTGTTAACTTGAAAGAGCAGCA 59.602 37.500 7.22 0.00 0.00 4.41
3582 4106 4.920376 TGTTGTTAACTTGAAAGAGCAGC 58.080 39.130 7.22 0.00 0.00 5.25
3583 4107 5.848036 CGATGTTGTTAACTTGAAAGAGCAG 59.152 40.000 7.22 0.00 0.00 4.24
3591 4115 2.477375 GGTCGCGATGTTGTTAACTTGA 59.523 45.455 14.06 0.00 0.00 3.02
3594 4118 1.065358 CGGTCGCGATGTTGTTAACT 58.935 50.000 14.06 0.00 0.00 2.24
3598 4122 2.369629 CGTCGGTCGCGATGTTGTT 61.370 57.895 14.06 0.00 0.00 2.83
3677 4382 6.980051 AGTACAAAGAATGGGACGAATTAC 57.020 37.500 0.00 0.00 0.00 1.89
3711 4416 5.885230 TCTGAATCCAGCAGTTTATTGTG 57.115 39.130 0.00 0.00 40.20 3.33
3801 4511 3.458857 ACAGCAGAAGAATCTCCATCCAT 59.541 43.478 0.00 0.00 32.03 3.41
3802 4512 2.842496 ACAGCAGAAGAATCTCCATCCA 59.158 45.455 0.00 0.00 32.03 3.41
3803 4513 3.557228 ACAGCAGAAGAATCTCCATCC 57.443 47.619 0.00 0.00 32.03 3.51
3830 4540 3.569701 GCAGAGAAAGAAACCATCCACAA 59.430 43.478 0.00 0.00 0.00 3.33
3878 4593 2.354003 GCATGGTTGGACAAAAGGGATG 60.354 50.000 0.00 0.00 0.00 3.51
3893 4610 6.534475 AATGTTCATCATTTACAGCATGGT 57.466 33.333 0.00 0.00 43.33 3.55
3944 4661 5.769662 ACTGATGTATCCAACAAACATGTGT 59.230 36.000 0.00 0.00 42.70 3.72
3948 4665 5.415701 GGTCACTGATGTATCCAACAAACAT 59.584 40.000 0.00 0.00 42.70 2.71
3980 4697 3.562141 TGCGAGCTAGTATCAGACTTCTC 59.438 47.826 0.00 0.00 39.81 2.87
3983 4700 3.487711 CGTTGCGAGCTAGTATCAGACTT 60.488 47.826 0.00 0.00 39.81 3.01


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

AutoCloner maintained by Alex Coulton.