Multiple sequence alignment - TraesCS6D01G194400

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 TraesCS6D01G194400 chr6D 100.000 3487 0 0 1 3487 269804285 269807771 0.000000e+00 6440
1 TraesCS6D01G194400 chr6D 73.881 536 118 19 2963 3487 73644470 73644994 9.880000e-46 195
2 TraesCS6D01G194400 chr6D 91.398 93 8 0 160 252 104145380 104145472 1.020000e-25 128
3 TraesCS6D01G194400 chr6B 93.050 1669 85 14 235 1891 422565035 422566684 0.000000e+00 2410
4 TraesCS6D01G194400 chr6B 95.582 747 23 2 2189 2926 422567339 422568084 0.000000e+00 1188
5 TraesCS6D01G194400 chr6B 88.746 311 7 10 1884 2166 422566867 422567177 4.280000e-94 355
6 TraesCS6D01G194400 chr6A 92.195 1499 53 18 576 2025 384314282 384315765 0.000000e+00 2061
7 TraesCS6D01G194400 chr6A 92.325 886 33 7 2075 2926 384315769 384316653 0.000000e+00 1227
8 TraesCS6D01G194400 chr6A 92.931 580 39 2 1 580 384304886 384305463 0.000000e+00 843
9 TraesCS6D01G194400 chr3D 84.181 531 58 11 2963 3486 108203438 108202927 3.130000e-135 492
10 TraesCS6D01G194400 chr7A 86.111 252 34 1 1 252 672645678 672645428 1.600000e-68 270
11 TraesCS6D01G194400 chr5A 84.921 252 37 1 1 252 342441976 342442226 1.610000e-63 254
12 TraesCS6D01G194400 chr2A 84.921 252 37 1 1 252 709250269 709250019 1.610000e-63 254
13 TraesCS6D01G194400 chr2A 90.811 185 15 2 2256 2439 551481415 551481232 2.690000e-61 246
14 TraesCS6D01G194400 chr2A 84.454 238 26 7 2258 2488 551372303 551372070 1.260000e-54 224
15 TraesCS6D01G194400 chr2A 89.011 182 16 3 2256 2435 551462059 551461880 4.530000e-54 222
16 TraesCS6D01G194400 chr2A 88.172 186 18 3 2256 2439 551446875 551446692 5.860000e-53 219
17 TraesCS6D01G194400 chr2A 88.172 186 18 3 2256 2439 551467947 551467764 5.860000e-53 219
18 TraesCS6D01G194400 chr5D 84.921 252 35 3 1 252 482387455 482387703 5.780000e-63 252
19 TraesCS6D01G194400 chr2B 84.583 240 26 7 2256 2488 513696572 513696807 9.740000e-56 228
20 TraesCS6D01G194400 chr2D 89.888 178 14 3 2256 2431 435197482 435197657 3.500000e-55 226


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 TraesCS6D01G194400 chr6D 269804285 269807771 3486 False 6440.000000 6440 100.000000 1 3487 1 chr6D.!!$F3 3486
1 TraesCS6D01G194400 chr6B 422565035 422568084 3049 False 1317.666667 2410 92.459333 235 2926 3 chr6B.!!$F1 2691
2 TraesCS6D01G194400 chr6A 384314282 384316653 2371 False 1644.000000 2061 92.260000 576 2926 2 chr6A.!!$F2 2350
3 TraesCS6D01G194400 chr6A 384304886 384305463 577 False 843.000000 843 92.931000 1 580 1 chr6A.!!$F1 579
4 TraesCS6D01G194400 chr3D 108202927 108203438 511 True 492.000000 492 84.181000 2963 3486 1 chr3D.!!$R1 523


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
814 816 0.108138 CTGTTCATCGGGTCCCACTC 60.108 60.0 9.12 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2587 3037 0.833287 CCACTCGGACCATTCCAGAT 59.167 55.0 0.0 0.0 43.0 2.9 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
23 24 2.429250 TCTTCTGTCGTGACTTGTGGAA 59.571 45.455 1.23 0.00 0.00 3.53
27 28 5.147330 TCTGTCGTGACTTGTGGAATATT 57.853 39.130 1.23 0.00 0.00 1.28
30 31 7.327975 TCTGTCGTGACTTGTGGAATATTATT 58.672 34.615 1.23 0.00 0.00 1.40
35 36 8.447833 TCGTGACTTGTGGAATATTATTTGTTC 58.552 33.333 0.00 0.00 0.00 3.18
60 61 3.696548 GTCTCATCAAGGGTGAAATTCCC 59.303 47.826 0.00 0.00 44.90 3.97
68 69 3.458044 GGGTGAAATTCCCTTCTTCCT 57.542 47.619 0.00 0.00 41.58 3.36
89 90 0.960364 TGCCCCGAACAGAGATTTGC 60.960 55.000 0.00 0.00 0.00 3.68
100 101 6.092122 CGAACAGAGATTTGCAGTATTTGGTA 59.908 38.462 0.00 0.00 0.00 3.25
122 123 7.156000 GGTAATATAACTCTTGAGCTCTTCCC 58.844 42.308 16.19 0.00 0.00 3.97
129 130 0.608640 TTGAGCTCTTCCCGACCTTC 59.391 55.000 16.19 0.00 0.00 3.46
136 137 1.664321 CTTCCCGACCTTCGATCCGT 61.664 60.000 0.00 0.00 43.74 4.69
156 157 3.339141 GTCCTTCATCTTGTTGGAGACC 58.661 50.000 0.00 0.00 0.00 3.85
157 158 2.978978 TCCTTCATCTTGTTGGAGACCA 59.021 45.455 0.00 0.00 0.00 4.02
190 191 0.916086 TTCCTATGCCGACCATTGGT 59.084 50.000 8.42 8.42 44.23 3.67
212 213 4.092968 GTGACCAATTGGAAGTATCGTGTC 59.907 45.833 31.22 13.70 38.94 3.67
300 301 4.640647 GCGAGGGTTTCATCCTTCTTTTAT 59.359 41.667 0.00 0.00 34.21 1.40
332 334 5.591877 ACTGTGCTCTGAAATCTTTGACTTT 59.408 36.000 0.00 0.00 0.00 2.66
356 358 5.007430 TCTCGTCTAGATACATCCGTTTGAC 59.993 44.000 0.00 0.00 0.00 3.18
358 360 4.618965 GTCTAGATACATCCGTTTGACCC 58.381 47.826 0.00 0.00 0.00 4.46
395 397 6.428159 CCGATGGAGAAAGTATATCCCAAAAG 59.572 42.308 0.00 0.00 31.73 2.27
403 405 7.615757 AGAAAGTATATCCCAAAAGGGTTCAAG 59.384 37.037 0.00 0.00 35.67 3.02
444 446 0.763035 ACAACCCCTAAAGCGTCACT 59.237 50.000 0.00 0.00 0.00 3.41
449 451 2.496470 ACCCCTAAAGCGTCACTAGAAG 59.504 50.000 0.00 0.00 0.00 2.85
795 797 0.251787 AACATGGGTCCTCCTTTGCC 60.252 55.000 0.00 0.00 36.20 4.52
814 816 0.108138 CTGTTCATCGGGTCCCACTC 60.108 60.000 9.12 0.00 0.00 3.51
851 853 1.599047 CCTGCATCCTCCTCGTTGT 59.401 57.895 0.00 0.00 0.00 3.32
925 933 2.363018 CCTGGCTCCTCGTCCTCA 60.363 66.667 0.00 0.00 0.00 3.86
935 945 5.381757 GCTCCTCGTCCTCATCCTATATAT 58.618 45.833 0.00 0.00 0.00 0.86
1495 1537 1.852067 ATCAAACAACGTCGCAGCCC 61.852 55.000 0.00 0.00 0.00 5.19
1496 1538 2.203153 AAACAACGTCGCAGCCCT 60.203 55.556 0.00 0.00 0.00 5.19
1497 1539 1.822186 AAACAACGTCGCAGCCCTT 60.822 52.632 0.00 0.00 0.00 3.95
1498 1540 1.381165 AAACAACGTCGCAGCCCTTT 61.381 50.000 0.00 0.00 0.00 3.11
1499 1541 1.381165 AACAACGTCGCAGCCCTTTT 61.381 50.000 0.00 0.00 0.00 2.27
1500 1542 1.358759 CAACGTCGCAGCCCTTTTT 59.641 52.632 0.00 0.00 0.00 1.94
1579 1637 3.459828 TGAGAAGAACCCATCACCCATA 58.540 45.455 0.00 0.00 0.00 2.74
1585 1643 5.994416 AGAACCCATCACCCATAAATAGT 57.006 39.130 0.00 0.00 0.00 2.12
1632 1691 2.290514 ACAGTAGCATGCACCACTCAAT 60.291 45.455 21.98 5.09 0.00 2.57
1745 1805 1.135139 GAATACGCTGCAGAGTCCTGA 59.865 52.381 26.96 9.91 43.02 3.86
1755 1815 2.679349 GCAGAGTCCTGATGTTTCCCTC 60.679 54.545 0.00 0.00 43.02 4.30
1813 1873 5.636543 CGAAACTCATAACGTTACCTTTCCT 59.363 40.000 10.81 0.00 0.00 3.36
1853 1913 8.691661 ACTCTAAAAATACCAACAGTTGACAT 57.308 30.769 15.36 4.46 0.00 3.06
1903 2154 8.494433 TCTAGATAATAAAAGGACACTTGCCAT 58.506 33.333 0.00 0.00 36.93 4.40
1942 2208 5.706369 TCTTCAGAAGTCAGGACTAGTACAC 59.294 44.000 8.10 0.00 41.58 2.90
2247 2688 5.008613 TCACAATGTAACAGGAAGCTTGTTC 59.991 40.000 2.10 0.00 39.36 3.18
2539 2989 4.844884 AGTAGAGCAGGAATGGTTTTACC 58.155 43.478 0.00 0.00 39.22 2.85
2618 3068 0.753848 CCGAGTGGGGGTGTGTTTTT 60.754 55.000 0.00 0.00 0.00 1.94
2705 3155 5.509498 AGTATGAGAGTGAGAGAGCTTTCT 58.491 41.667 6.45 6.45 0.00 2.52
2769 3220 3.262420 ACGATGTGATGTTAAGCCTGAC 58.738 45.455 0.00 0.00 0.00 3.51
2955 3406 9.996554 ATATGAAATACATACAGACCGAAATGA 57.003 29.630 0.00 0.00 43.12 2.57
2956 3407 8.731275 ATGAAATACATACAGACCGAAATGAA 57.269 30.769 0.00 0.00 37.46 2.57
2957 3408 8.554835 TGAAATACATACAGACCGAAATGAAA 57.445 30.769 0.00 0.00 0.00 2.69
2958 3409 8.447833 TGAAATACATACAGACCGAAATGAAAC 58.552 33.333 0.00 0.00 0.00 2.78
2959 3410 6.920569 ATACATACAGACCGAAATGAAACC 57.079 37.500 0.00 0.00 0.00 3.27
2960 3411 4.007659 ACATACAGACCGAAATGAAACCC 58.992 43.478 0.00 0.00 0.00 4.11
2961 3412 2.649531 ACAGACCGAAATGAAACCCA 57.350 45.000 0.00 0.00 0.00 4.51
2962 3413 2.227194 ACAGACCGAAATGAAACCCAC 58.773 47.619 0.00 0.00 0.00 4.61
2963 3414 2.226330 CAGACCGAAATGAAACCCACA 58.774 47.619 0.00 0.00 0.00 4.17
2964 3415 2.621055 CAGACCGAAATGAAACCCACAA 59.379 45.455 0.00 0.00 0.00 3.33
2965 3416 2.884639 AGACCGAAATGAAACCCACAAG 59.115 45.455 0.00 0.00 0.00 3.16
2966 3417 1.960689 ACCGAAATGAAACCCACAAGG 59.039 47.619 0.00 0.00 43.78 3.61
2973 3424 1.133199 TGAAACCCACAAGGAGGCAAT 60.133 47.619 0.00 0.00 39.89 3.56
3009 3460 9.018582 CCTCTTCTCAATGTTAATTTCCTTCTT 57.981 33.333 0.00 0.00 0.00 2.52
3015 3466 4.882842 TGTTAATTTCCTTCTTTGGGGC 57.117 40.909 0.00 0.00 0.00 5.80
3024 3475 0.252193 TTCTTTGGGGCAATGGAGGG 60.252 55.000 0.00 0.00 0.00 4.30
3025 3476 1.145900 TCTTTGGGGCAATGGAGGGA 61.146 55.000 0.00 0.00 0.00 4.20
3032 3483 1.632589 GGCAATGGAGGGACAAACTT 58.367 50.000 0.00 0.00 0.00 2.66
3054 3505 4.858850 TGTGTTGGGAGCTTGATCAATAT 58.141 39.130 8.96 0.00 0.00 1.28
3058 3509 6.203723 GTGTTGGGAGCTTGATCAATATCTAC 59.796 42.308 8.96 7.31 32.93 2.59
3060 3511 6.692849 TGGGAGCTTGATCAATATCTACAT 57.307 37.500 8.96 0.00 32.93 2.29
3066 3517 9.486497 GAGCTTGATCAATATCTACATGAGAAA 57.514 33.333 8.96 0.00 37.85 2.52
3079 3530 2.795231 TGAGAAAGAGGATGCTTGGG 57.205 50.000 0.00 0.00 0.00 4.12
3091 3544 1.927487 TGCTTGGGCACATCTTCAAT 58.073 45.000 0.00 0.00 44.28 2.57
3125 3578 6.591001 AGAAAATCCTATCTCCAAGCTCTTC 58.409 40.000 0.00 0.00 0.00 2.87
3139 3592 2.170187 AGCTCTTCGATCTCCTGCAATT 59.830 45.455 0.00 0.00 0.00 2.32
3144 3597 5.188434 TCTTCGATCTCCTGCAATTTTCAT 58.812 37.500 0.00 0.00 0.00 2.57
3151 3604 3.881688 CTCCTGCAATTTTCATCGATCCT 59.118 43.478 0.00 0.00 0.00 3.24
3157 3610 4.790766 GCAATTTTCATCGATCCTCGCAAT 60.791 41.667 0.00 0.00 40.21 3.56
3163 3616 3.006217 TCATCGATCCTCGCAATTCTGAT 59.994 43.478 0.00 0.00 40.21 2.90
3166 3619 2.288702 CGATCCTCGCAATTCTGATCCT 60.289 50.000 0.00 0.00 31.14 3.24
3167 3620 3.057245 CGATCCTCGCAATTCTGATCCTA 60.057 47.826 0.00 0.00 31.14 2.94
3172 3625 4.220382 CCTCGCAATTCTGATCCTAGATCT 59.780 45.833 0.00 0.00 0.00 2.75
3175 3628 4.620609 CGCAATTCTGATCCTAGATCTTCG 59.379 45.833 0.00 0.00 0.00 3.79
3176 3629 4.388469 GCAATTCTGATCCTAGATCTTCGC 59.612 45.833 0.00 0.00 0.00 4.70
3194 3647 4.295857 TCGCAAAATCACCATGATCATG 57.704 40.909 25.97 25.97 35.76 3.07
3196 3649 3.490249 CGCAAAATCACCATGATCATGCT 60.490 43.478 27.24 13.63 41.86 3.79
3204 3657 2.105477 ACCATGATCATGCTACCAGGAC 59.895 50.000 27.24 0.00 34.21 3.85
3209 3662 1.583556 TCATGCTACCAGGACACCAT 58.416 50.000 0.00 0.00 0.00 3.55
3210 3663 1.486310 TCATGCTACCAGGACACCATC 59.514 52.381 0.00 0.00 0.00 3.51
3211 3664 1.210234 CATGCTACCAGGACACCATCA 59.790 52.381 0.00 0.00 0.00 3.07
3212 3665 1.357137 TGCTACCAGGACACCATCAA 58.643 50.000 0.00 0.00 0.00 2.57
3213 3666 1.003118 TGCTACCAGGACACCATCAAC 59.997 52.381 0.00 0.00 0.00 3.18
3214 3667 2.007049 GCTACCAGGACACCATCAACG 61.007 57.143 0.00 0.00 0.00 4.10
3215 3668 0.611200 TACCAGGACACCATCAACGG 59.389 55.000 0.00 0.00 0.00 4.44
3216 3669 1.377202 CCAGGACACCATCAACGGG 60.377 63.158 0.00 0.00 0.00 5.28
3217 3670 1.676968 CAGGACACCATCAACGGGA 59.323 57.895 0.00 0.00 0.00 5.14
3218 3671 0.391661 CAGGACACCATCAACGGGAG 60.392 60.000 0.00 0.00 0.00 4.30
3219 3672 1.745489 GGACACCATCAACGGGAGC 60.745 63.158 0.00 0.00 0.00 4.70
3220 3673 1.003839 GACACCATCAACGGGAGCA 60.004 57.895 0.00 0.00 0.00 4.26
3221 3674 1.003355 ACACCATCAACGGGAGCAG 60.003 57.895 0.00 0.00 0.00 4.24
3222 3675 1.296392 CACCATCAACGGGAGCAGA 59.704 57.895 0.00 0.00 0.00 4.26
3223 3676 1.021390 CACCATCAACGGGAGCAGAC 61.021 60.000 0.00 0.00 0.00 3.51
3224 3677 1.450312 CCATCAACGGGAGCAGACC 60.450 63.158 0.00 0.00 0.00 3.85
3225 3678 1.599047 CATCAACGGGAGCAGACCT 59.401 57.895 0.00 0.00 0.00 3.85
3260 3713 1.107114 TGCCCACAATGTTGTCGTTT 58.893 45.000 0.00 0.00 39.91 3.60
3266 3719 4.466828 CCACAATGTTGTCGTTTCTGATC 58.533 43.478 0.00 0.00 39.91 2.92
3273 3726 0.806492 GTCGTTTCTGATCGGAGGGC 60.806 60.000 4.04 0.00 0.00 5.19
3277 3730 3.672338 TTCTGATCGGAGGGCGGGA 62.672 63.158 4.04 0.00 0.00 5.14
3278 3731 2.919856 CTGATCGGAGGGCGGGAT 60.920 66.667 0.00 0.00 0.00 3.85
3279 3732 2.917751 TGATCGGAGGGCGGGATC 60.918 66.667 0.00 0.00 37.63 3.36
3281 3734 1.304217 GATCGGAGGGCGGGATCTA 60.304 63.158 0.00 0.00 34.99 1.98
3282 3735 1.596895 GATCGGAGGGCGGGATCTAC 61.597 65.000 0.00 0.00 34.99 2.59
3283 3736 3.671411 CGGAGGGCGGGATCTACG 61.671 72.222 6.08 6.08 0.00 3.51
3315 3770 3.202818 ACAGGCCCACATGAATCATTCTA 59.797 43.478 0.00 0.00 0.00 2.10
3322 3777 4.512571 CCACATGAATCATTCTATGTGCGA 59.487 41.667 23.81 0.00 41.91 5.10
3324 3779 6.077838 CACATGAATCATTCTATGTGCGATG 58.922 40.000 20.50 8.46 39.67 3.84
3333 3788 3.225940 TCTATGTGCGATGTCTCCTCAT 58.774 45.455 0.00 0.00 0.00 2.90
3361 3816 1.892338 CAGGCCCAATTGCACGAAT 59.108 52.632 0.00 0.00 0.00 3.34
3374 3829 2.351418 TGCACGAATCGGATCAAATGTC 59.649 45.455 7.80 0.00 0.00 3.06
3375 3830 2.597505 GCACGAATCGGATCAAATGTCG 60.598 50.000 7.80 6.08 0.00 4.35
3384 3839 6.102006 TCGGATCAAATGTCGAAAATGTAC 57.898 37.500 0.00 0.00 0.00 2.90
3397 3852 1.140312 AATGTACGAGATGGGGCCAT 58.860 50.000 4.39 0.00 39.69 4.40
3408 3863 1.229076 GGGGCCATATTGAACGGGT 59.771 57.895 4.39 0.00 0.00 5.28
3412 3867 1.408266 GGCCATATTGAACGGGTCTGT 60.408 52.381 0.00 0.00 0.00 3.41
3416 3871 3.377172 CCATATTGAACGGGTCTGTTTCC 59.623 47.826 0.00 0.00 30.75 3.13
3418 3873 0.547075 TTGAACGGGTCTGTTTCCCA 59.453 50.000 0.00 0.00 44.81 4.37
3420 3875 1.226030 GAACGGGTCTGTTTCCCACG 61.226 60.000 1.91 0.00 44.81 4.94
3427 3882 3.801068 CTGTTTCCCACGGGCCCAA 62.801 63.158 24.92 4.68 34.68 4.12
3428 3883 2.283604 GTTTCCCACGGGCCCAAT 60.284 61.111 24.92 6.05 34.68 3.16
3438 3893 4.066139 GGCCCAATCCAGCCCAGT 62.066 66.667 0.00 0.00 43.76 4.00
3446 3901 0.106819 ATCCAGCCCAGTCAATGAGC 60.107 55.000 0.00 0.00 0.00 4.26
3455 3910 3.209410 CCAGTCAATGAGCCCAATCTAC 58.791 50.000 0.00 0.00 0.00 2.59
3480 3935 2.499685 CCCGAGGGTCGACATTCC 59.500 66.667 18.91 9.63 43.74 3.01
3486 3941 2.577059 GGTCGACATTCCGAGGCA 59.423 61.111 18.91 0.00 39.43 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.509052 TCCACAAGTCACGACAGAAG 57.491 50.000 0.00 0.00 0.00 2.85
6 7 7.539712 AATAATATTCCACAAGTCACGACAG 57.460 36.000 0.00 0.00 0.00 3.51
10 11 8.450964 AGAACAAATAATATTCCACAAGTCACG 58.549 33.333 0.00 0.00 0.00 4.35
27 28 7.180229 TCACCCTTGATGAGACTAGAACAAATA 59.820 37.037 0.00 0.00 0.00 1.40
30 31 4.838423 TCACCCTTGATGAGACTAGAACAA 59.162 41.667 0.00 0.00 0.00 2.83
35 36 5.819901 GGAATTTCACCCTTGATGAGACTAG 59.180 44.000 0.00 0.00 0.00 2.57
37 38 4.568592 GGGAATTTCACCCTTGATGAGACT 60.569 45.833 0.00 0.00 43.65 3.24
60 61 1.209504 TGTTCGGGGCATAGGAAGAAG 59.790 52.381 0.00 0.00 0.00 2.85
68 69 2.917933 CAAATCTCTGTTCGGGGCATA 58.082 47.619 0.00 0.00 0.00 3.14
100 101 5.598830 TCGGGAAGAGCTCAAGAGTTATATT 59.401 40.000 17.77 0.00 0.00 1.28
115 116 0.386113 GGATCGAAGGTCGGGAAGAG 59.614 60.000 0.00 0.00 40.88 2.85
122 123 0.248539 GAAGGACGGATCGAAGGTCG 60.249 60.000 0.00 0.00 42.10 4.79
129 130 2.586258 ACAAGATGAAGGACGGATCG 57.414 50.000 0.00 0.00 0.00 3.69
136 137 2.978978 TGGTCTCCAACAAGATGAAGGA 59.021 45.455 0.00 0.00 0.00 3.36
168 169 2.213499 CAATGGTCGGCATAGGAAGAC 58.787 52.381 0.00 0.00 0.00 3.01
190 191 4.020573 AGACACGATACTTCCAATTGGTCA 60.021 41.667 23.76 11.18 36.34 4.02
200 201 5.448904 GGGAGACAGTAAGACACGATACTTC 60.449 48.000 0.00 0.00 30.09 3.01
212 213 5.667539 TCATCTTGAAGGGAGACAGTAAG 57.332 43.478 0.00 0.00 0.00 2.34
239 240 4.042187 AGGTGAAGTACAAGATCCAAAGCT 59.958 41.667 0.00 0.00 0.00 3.74
332 334 5.007430 GTCAAACGGATGTATCTAGACGAGA 59.993 44.000 0.00 0.00 39.01 4.04
356 358 4.347000 TCTCCATCGGGAATTAGTTAAGGG 59.653 45.833 0.00 0.00 44.38 3.95
358 360 7.048512 ACTTTCTCCATCGGGAATTAGTTAAG 58.951 38.462 0.00 0.00 44.38 1.85
395 397 2.193087 TTAGCGAGGCCCTTGAACCC 62.193 60.000 0.80 0.00 0.00 4.11
403 405 2.044555 GGTGGTTTTAGCGAGGCCC 61.045 63.158 0.00 0.00 0.00 5.80
444 446 5.204292 AGGTATGTGTGATCTCAGCTTCTA 58.796 41.667 0.00 0.00 0.00 2.10
449 451 3.624861 CCAAAGGTATGTGTGATCTCAGC 59.375 47.826 0.00 0.00 0.00 4.26
550 552 4.389576 CGTGCTCGCTTGGTTGCC 62.390 66.667 0.00 0.00 0.00 4.52
795 797 0.108138 GAGTGGGACCCGATGAACAG 60.108 60.000 5.91 0.00 0.00 3.16
925 933 7.739995 AGGCATGTGTGTGTATATATAGGAT 57.260 36.000 0.00 0.00 0.00 3.24
935 945 2.639970 GCCAAGGCATGTGTGTGTA 58.360 52.632 6.14 0.00 41.49 2.90
1338 1363 5.120830 AGCTACTCGCATAACAAGAAAACAG 59.879 40.000 0.00 0.00 42.61 3.16
1339 1364 4.994852 AGCTACTCGCATAACAAGAAAACA 59.005 37.500 0.00 0.00 42.61 2.83
1340 1365 5.446073 GGAGCTACTCGCATAACAAGAAAAC 60.446 44.000 0.00 0.00 42.61 2.43
1341 1366 4.630069 GGAGCTACTCGCATAACAAGAAAA 59.370 41.667 0.00 0.00 42.61 2.29
1342 1367 4.081642 AGGAGCTACTCGCATAACAAGAAA 60.082 41.667 0.00 0.00 42.61 2.52
1343 1368 3.447586 AGGAGCTACTCGCATAACAAGAA 59.552 43.478 0.00 0.00 42.61 2.52
1344 1369 3.024547 AGGAGCTACTCGCATAACAAGA 58.975 45.455 0.00 0.00 42.61 3.02
1345 1370 3.444703 AGGAGCTACTCGCATAACAAG 57.555 47.619 0.00 0.00 42.61 3.16
1346 1371 6.264744 AGTTATAGGAGCTACTCGCATAACAA 59.735 38.462 23.28 0.00 38.63 2.83
1347 1372 5.768662 AGTTATAGGAGCTACTCGCATAACA 59.231 40.000 23.28 0.00 38.63 2.41
1498 1540 6.487668 TCACTGATGCAAGAGAATGAGAAAAA 59.512 34.615 0.00 0.00 0.00 1.94
1499 1541 5.999600 TCACTGATGCAAGAGAATGAGAAAA 59.000 36.000 0.00 0.00 0.00 2.29
1500 1542 5.554070 TCACTGATGCAAGAGAATGAGAAA 58.446 37.500 0.00 0.00 0.00 2.52
1501 1543 5.156608 TCACTGATGCAAGAGAATGAGAA 57.843 39.130 0.00 0.00 0.00 2.87
1502 1544 4.222366 ACTCACTGATGCAAGAGAATGAGA 59.778 41.667 17.66 0.00 36.63 3.27
1503 1545 4.330347 CACTCACTGATGCAAGAGAATGAG 59.670 45.833 12.04 12.04 38.60 2.90
1504 1546 4.251268 CACTCACTGATGCAAGAGAATGA 58.749 43.478 0.00 0.00 32.59 2.57
1505 1547 4.001652 ACACTCACTGATGCAAGAGAATG 58.998 43.478 0.00 0.00 32.59 2.67
1506 1548 4.283363 ACACTCACTGATGCAAGAGAAT 57.717 40.909 0.00 0.00 32.59 2.40
1507 1549 3.758755 ACACTCACTGATGCAAGAGAA 57.241 42.857 0.00 0.00 32.59 2.87
1508 1550 3.181462 ACAACACTCACTGATGCAAGAGA 60.181 43.478 0.00 0.00 32.59 3.10
1509 1551 3.136763 ACAACACTCACTGATGCAAGAG 58.863 45.455 0.00 0.00 0.00 2.85
1585 1643 7.867305 TTGACATTTACTTCACACCAAACTA 57.133 32.000 0.00 0.00 0.00 2.24
1632 1691 7.094508 TGCAAGTGAAGATGTGAAGTAAAAA 57.905 32.000 0.00 0.00 0.00 1.94
1694 1754 4.223032 ACACATCTGGGAGTAAAACGATCT 59.777 41.667 0.00 0.00 0.00 2.75
1871 1931 6.931840 GTGTCCTTTTATTATCTAGAGCAGGG 59.068 42.308 0.00 0.00 0.00 4.45
1903 2154 1.874345 GAAGAAGACGGACTGGGCGA 61.874 60.000 0.00 0.00 0.00 5.54
2014 2282 4.629634 TCAGTATGGTGAACTAAATGTGCG 59.370 41.667 0.00 0.00 36.16 5.34
2247 2688 2.827322 TCAGTTCCCCTGCAATTTGATG 59.173 45.455 0.00 0.00 41.25 3.07
2273 2714 1.065782 CCGGTCACCATGGACAACATA 60.066 52.381 21.47 0.00 37.84 2.29
2277 2718 2.753701 CCCGGTCACCATGGACAA 59.246 61.111 21.47 0.00 39.59 3.18
2539 2989 6.086502 TGTTCCGCAACGAAAATTAATAAACG 59.913 34.615 0.00 0.00 34.95 3.60
2587 3037 0.833287 CCACTCGGACCATTCCAGAT 59.167 55.000 0.00 0.00 43.00 2.90
2659 3109 1.007118 AGGGACCCTTATTTTGCCCTG 59.993 52.381 7.44 0.00 43.97 4.45
2705 3155 7.611770 ACACTAGCAACTACTAACATGATCAA 58.388 34.615 0.00 0.00 0.00 2.57
2769 3220 1.586154 GGGACAACATGAGCCCAACG 61.586 60.000 0.00 0.00 36.20 4.10
2929 3380 9.996554 TCATTTCGGTCTGTATGTATTTCATAT 57.003 29.630 0.00 0.00 40.54 1.78
2930 3381 9.825109 TTCATTTCGGTCTGTATGTATTTCATA 57.175 29.630 0.00 0.00 37.91 2.15
2931 3382 8.731275 TTCATTTCGGTCTGTATGTATTTCAT 57.269 30.769 0.00 0.00 40.25 2.57
2932 3383 8.447833 GTTTCATTTCGGTCTGTATGTATTTCA 58.552 33.333 0.00 0.00 0.00 2.69
2933 3384 7.908601 GGTTTCATTTCGGTCTGTATGTATTTC 59.091 37.037 0.00 0.00 0.00 2.17
2934 3385 7.148137 GGGTTTCATTTCGGTCTGTATGTATTT 60.148 37.037 0.00 0.00 0.00 1.40
2935 3386 6.317893 GGGTTTCATTTCGGTCTGTATGTATT 59.682 38.462 0.00 0.00 0.00 1.89
2936 3387 5.820947 GGGTTTCATTTCGGTCTGTATGTAT 59.179 40.000 0.00 0.00 0.00 2.29
2937 3388 5.180271 GGGTTTCATTTCGGTCTGTATGTA 58.820 41.667 0.00 0.00 0.00 2.29
2938 3389 4.007659 GGGTTTCATTTCGGTCTGTATGT 58.992 43.478 0.00 0.00 0.00 2.29
2939 3390 4.006989 TGGGTTTCATTTCGGTCTGTATG 58.993 43.478 0.00 0.00 0.00 2.39
2940 3391 4.007659 GTGGGTTTCATTTCGGTCTGTAT 58.992 43.478 0.00 0.00 0.00 2.29
2941 3392 3.181453 TGTGGGTTTCATTTCGGTCTGTA 60.181 43.478 0.00 0.00 0.00 2.74
2942 3393 2.227194 GTGGGTTTCATTTCGGTCTGT 58.773 47.619 0.00 0.00 0.00 3.41
2943 3394 2.226330 TGTGGGTTTCATTTCGGTCTG 58.774 47.619 0.00 0.00 0.00 3.51
2944 3395 2.649531 TGTGGGTTTCATTTCGGTCT 57.350 45.000 0.00 0.00 0.00 3.85
2945 3396 2.030274 CCTTGTGGGTTTCATTTCGGTC 60.030 50.000 0.00 0.00 0.00 4.79
2946 3397 1.960689 CCTTGTGGGTTTCATTTCGGT 59.039 47.619 0.00 0.00 0.00 4.69
2947 3398 2.228822 CTCCTTGTGGGTTTCATTTCGG 59.771 50.000 0.00 0.00 36.25 4.30
2948 3399 2.228822 CCTCCTTGTGGGTTTCATTTCG 59.771 50.000 0.00 0.00 36.25 3.46
2949 3400 2.029020 GCCTCCTTGTGGGTTTCATTTC 60.029 50.000 0.00 0.00 36.25 2.17
2950 3401 1.970640 GCCTCCTTGTGGGTTTCATTT 59.029 47.619 0.00 0.00 36.25 2.32
2951 3402 1.133199 TGCCTCCTTGTGGGTTTCATT 60.133 47.619 0.00 0.00 36.25 2.57
2952 3403 0.482446 TGCCTCCTTGTGGGTTTCAT 59.518 50.000 0.00 0.00 36.25 2.57
2953 3404 0.260230 TTGCCTCCTTGTGGGTTTCA 59.740 50.000 0.00 0.00 36.25 2.69
2954 3405 1.632589 ATTGCCTCCTTGTGGGTTTC 58.367 50.000 0.00 0.00 36.25 2.78
2955 3406 2.990740 TATTGCCTCCTTGTGGGTTT 57.009 45.000 0.00 0.00 36.25 3.27
2956 3407 2.582636 AGATATTGCCTCCTTGTGGGTT 59.417 45.455 0.00 0.00 36.25 4.11
2957 3408 2.173569 GAGATATTGCCTCCTTGTGGGT 59.826 50.000 0.00 0.00 36.25 4.51
2958 3409 2.441001 AGAGATATTGCCTCCTTGTGGG 59.559 50.000 0.00 0.00 0.00 4.61
2959 3410 3.390639 AGAGAGATATTGCCTCCTTGTGG 59.609 47.826 0.00 0.00 0.00 4.17
2960 3411 4.502950 GGAGAGAGATATTGCCTCCTTGTG 60.503 50.000 0.00 0.00 40.07 3.33
2961 3412 3.645687 GGAGAGAGATATTGCCTCCTTGT 59.354 47.826 0.00 0.00 40.07 3.16
2962 3413 3.007831 GGGAGAGAGATATTGCCTCCTTG 59.992 52.174 0.00 0.00 42.21 3.61
2963 3414 3.116395 AGGGAGAGAGATATTGCCTCCTT 60.116 47.826 0.00 0.00 42.21 3.36
2964 3415 2.454381 AGGGAGAGAGATATTGCCTCCT 59.546 50.000 0.00 0.00 42.21 3.69
2965 3416 2.831526 GAGGGAGAGAGATATTGCCTCC 59.168 54.545 0.00 0.00 41.88 4.30
2966 3417 3.778265 AGAGGGAGAGAGATATTGCCTC 58.222 50.000 4.21 4.21 46.32 4.70
2973 3424 6.024563 ACATTGAGAAGAGGGAGAGAGATA 57.975 41.667 0.00 0.00 0.00 1.98
3009 3460 1.734420 TTGTCCCTCCATTGCCCCAA 61.734 55.000 0.00 0.00 0.00 4.12
3015 3466 2.958355 ACACAAGTTTGTCCCTCCATTG 59.042 45.455 0.00 0.00 39.91 2.82
3024 3475 2.024414 AGCTCCCAACACAAGTTTGTC 58.976 47.619 0.00 0.00 39.91 3.18
3025 3476 2.143876 AGCTCCCAACACAAGTTTGT 57.856 45.000 0.00 0.00 43.36 2.83
3032 3483 2.655090 TTGATCAAGCTCCCAACACA 57.345 45.000 3.38 0.00 0.00 3.72
3054 3505 5.396101 CCAAGCATCCTCTTTCTCATGTAGA 60.396 44.000 0.00 0.00 0.00 2.59
3058 3509 2.950309 CCCAAGCATCCTCTTTCTCATG 59.050 50.000 0.00 0.00 0.00 3.07
3060 3511 1.340405 GCCCAAGCATCCTCTTTCTCA 60.340 52.381 0.00 0.00 39.53 3.27
3079 3530 1.002033 GGATGGCGATTGAAGATGTGC 60.002 52.381 0.00 0.00 0.00 4.57
3081 3532 3.643320 TCTAGGATGGCGATTGAAGATGT 59.357 43.478 0.00 0.00 0.00 3.06
3091 3544 5.087323 AGATAGGATTTTCTAGGATGGCGA 58.913 41.667 0.00 0.00 0.00 5.54
3125 3578 3.557185 TCGATGAAAATTGCAGGAGATCG 59.443 43.478 0.00 0.00 34.25 3.69
3151 3604 5.563671 CGAAGATCTAGGATCAGAATTGCGA 60.564 44.000 0.00 0.00 0.00 5.10
3157 3610 5.598416 TTTGCGAAGATCTAGGATCAGAA 57.402 39.130 0.00 0.00 0.00 3.02
3163 3616 4.081142 TGGTGATTTTGCGAAGATCTAGGA 60.081 41.667 0.00 0.00 0.00 2.94
3166 3619 5.427378 TCATGGTGATTTTGCGAAGATCTA 58.573 37.500 0.00 0.00 0.00 1.98
3167 3620 4.264253 TCATGGTGATTTTGCGAAGATCT 58.736 39.130 0.00 0.00 0.00 2.75
3172 3625 4.674475 CATGATCATGGTGATTTTGCGAA 58.326 39.130 25.37 0.00 37.20 4.70
3175 3628 4.054780 AGCATGATCATGGTGATTTTGC 57.945 40.909 33.50 19.38 46.50 3.68
3194 3647 1.739067 GTTGATGGTGTCCTGGTAGC 58.261 55.000 0.00 0.00 0.00 3.58
3196 3649 0.611200 CCGTTGATGGTGTCCTGGTA 59.389 55.000 0.00 0.00 0.00 3.25
3204 3657 1.021390 GTCTGCTCCCGTTGATGGTG 61.021 60.000 0.00 0.00 0.00 4.17
3209 3662 1.118965 TGAAGGTCTGCTCCCGTTGA 61.119 55.000 0.00 0.00 0.00 3.18
3210 3663 0.951040 GTGAAGGTCTGCTCCCGTTG 60.951 60.000 0.00 0.00 0.00 4.10
3211 3664 1.122019 AGTGAAGGTCTGCTCCCGTT 61.122 55.000 0.00 0.00 0.00 4.44
3212 3665 1.534235 AGTGAAGGTCTGCTCCCGT 60.534 57.895 0.00 0.00 0.00 5.28
3213 3666 1.216710 GAGTGAAGGTCTGCTCCCG 59.783 63.158 0.00 0.00 0.00 5.14
3214 3667 1.216710 CGAGTGAAGGTCTGCTCCC 59.783 63.158 0.00 0.00 0.00 4.30
3215 3668 1.216710 CCGAGTGAAGGTCTGCTCC 59.783 63.158 0.00 0.00 0.00 4.70
3216 3669 1.216710 CCCGAGTGAAGGTCTGCTC 59.783 63.158 0.00 0.00 0.00 4.26
3217 3670 2.948720 GCCCGAGTGAAGGTCTGCT 61.949 63.158 0.00 0.00 0.00 4.24
3218 3671 2.435059 GCCCGAGTGAAGGTCTGC 60.435 66.667 0.00 0.00 0.00 4.26
3219 3672 0.036010 AATGCCCGAGTGAAGGTCTG 60.036 55.000 0.00 0.00 0.00 3.51
3220 3673 1.568504 TAATGCCCGAGTGAAGGTCT 58.431 50.000 0.00 0.00 0.00 3.85
3221 3674 2.396590 TTAATGCCCGAGTGAAGGTC 57.603 50.000 0.00 0.00 0.00 3.85
3222 3675 2.643551 CATTAATGCCCGAGTGAAGGT 58.356 47.619 1.74 0.00 0.00 3.50
3247 3700 3.431912 TCCGATCAGAAACGACAACATTG 59.568 43.478 0.00 0.00 0.00 2.82
3252 3705 1.067142 CCCTCCGATCAGAAACGACAA 60.067 52.381 0.00 0.00 0.00 3.18
3253 3706 0.530744 CCCTCCGATCAGAAACGACA 59.469 55.000 0.00 0.00 0.00 4.35
3255 3708 1.515954 GCCCTCCGATCAGAAACGA 59.484 57.895 0.00 0.00 0.00 3.85
3260 3713 3.452621 ATCCCGCCCTCCGATCAGA 62.453 63.158 0.00 0.00 40.02 3.27
3266 3719 3.671411 CGTAGATCCCGCCCTCCG 61.671 72.222 0.00 0.00 0.00 4.63
3273 3726 1.847818 TTGAATTCGCGTAGATCCCG 58.152 50.000 5.77 0.00 0.00 5.14
3277 3730 2.351726 GCCTGTTTGAATTCGCGTAGAT 59.648 45.455 5.77 0.00 0.00 1.98
3278 3731 1.730064 GCCTGTTTGAATTCGCGTAGA 59.270 47.619 5.77 0.00 0.00 2.59
3279 3732 1.202031 GGCCTGTTTGAATTCGCGTAG 60.202 52.381 5.77 0.00 0.00 3.51
3281 3734 1.579429 GGCCTGTTTGAATTCGCGT 59.421 52.632 5.77 0.00 0.00 6.01
3282 3735 1.154035 GGGCCTGTTTGAATTCGCG 60.154 57.895 0.84 0.00 0.00 5.87
3283 3736 0.388520 GTGGGCCTGTTTGAATTCGC 60.389 55.000 4.53 0.00 0.00 4.70
3285 3738 2.562298 TCATGTGGGCCTGTTTGAATTC 59.438 45.455 4.53 0.00 0.00 2.17
3286 3739 2.607499 TCATGTGGGCCTGTTTGAATT 58.393 42.857 4.53 0.00 0.00 2.17
3287 3740 2.307496 TCATGTGGGCCTGTTTGAAT 57.693 45.000 4.53 0.00 0.00 2.57
3315 3770 1.202615 CCATGAGGAGACATCGCACAT 60.203 52.381 0.00 0.00 36.89 3.21
3322 3777 1.983691 CTATGGCCCATGAGGAGACAT 59.016 52.381 6.46 0.00 37.51 3.06
3324 3779 0.036022 GCTATGGCCCATGAGGAGAC 59.964 60.000 6.46 0.00 38.24 3.36
3352 3807 2.746904 ACATTTGATCCGATTCGTGCAA 59.253 40.909 5.20 3.70 0.00 4.08
3361 3816 5.220322 CGTACATTTTCGACATTTGATCCGA 60.220 40.000 0.00 0.00 0.00 4.55
3374 3829 1.597663 GCCCCATCTCGTACATTTTCG 59.402 52.381 0.00 0.00 0.00 3.46
3375 3830 1.947456 GGCCCCATCTCGTACATTTTC 59.053 52.381 0.00 0.00 0.00 2.29
3384 3839 2.154462 GTTCAATATGGCCCCATCTCG 58.846 52.381 0.00 0.00 37.82 4.04
3397 3852 3.062122 GGGAAACAGACCCGTTCAATA 57.938 47.619 0.00 0.00 37.85 1.90
3408 3863 3.961414 GGGCCCGTGGGAAACAGA 61.961 66.667 5.69 0.00 37.50 3.41
3412 3867 2.036572 GATTGGGCCCGTGGGAAA 59.963 61.111 19.37 4.57 37.50 3.13
3436 3891 3.683847 GCTGTAGATTGGGCTCATTGACT 60.684 47.826 0.00 0.00 0.00 3.41
3438 3893 2.742856 CGCTGTAGATTGGGCTCATTGA 60.743 50.000 0.00 0.00 0.00 2.57
3446 3901 3.272334 GCGGCGCTGTAGATTGGG 61.272 66.667 26.86 0.00 0.00 4.12
3468 3923 2.202892 GCCTCGGAATGTCGACCC 60.203 66.667 14.12 6.16 35.18 4.46



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

AutoCloner maintained by Alex Coulton.