Multiple sequence alignment - TraesCS7D01G229900

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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 TraesCS7D01G229900 chr7D 100.000 3393 0 0 1 3393 190446108 190449500 0.000000e+00 6266
1 TraesCS7D01G229900 chr7D 97.517 725 17 1 1 724 190402445 190403169 0.000000e+00 1238
2 TraesCS7D01G229900 chr7B 92.005 3252 224 16 24 3262 335443572 335446800 0.000000e+00 4532
3 TraesCS7D01G229900 chr7A 93.629 2684 154 13 584 3256 199237022 199239699 0.000000e+00 3993
4 TraesCS7D01G229900 chr7A 90.792 543 45 3 1 539 199220434 199220975 0.000000e+00 721
5 TraesCS7D01G229900 chr7A 95.455 132 5 1 3262 3393 432247046 432247176 3.430000e-50 209
6 TraesCS7D01G229900 chr3D 95.556 135 6 0 3259 3393 436492212 436492346 2.050000e-52 217
7 TraesCS7D01G229900 chr3D 96.183 131 5 0 3263 3393 145765083 145765213 7.370000e-52 215
8 TraesCS7D01G229900 chr3D 96.154 130 5 0 3263 3392 309389957 309389828 2.650000e-51 213
9 TraesCS7D01G229900 chr1D 96.183 131 5 0 3263 3393 122286693 122286563 7.370000e-52 215
10 TraesCS7D01G229900 chr5D 95.489 133 6 0 3261 3393 36260907 36261039 2.650000e-51 213
11 TraesCS7D01G229900 chr2D 96.154 130 5 0 3263 3392 334869044 334868915 2.650000e-51 213
12 TraesCS7D01G229900 chr2D 96.154 130 5 0 3263 3392 367209462 367209591 2.650000e-51 213
13 TraesCS7D01G229900 chr2D 94.815 135 6 1 3260 3393 355533303 355533437 3.430000e-50 209


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 TraesCS7D01G229900 chr7D 190446108 190449500 3392 False 6266 6266 100.000 1 3393 1 chr7D.!!$F2 3392
1 TraesCS7D01G229900 chr7D 190402445 190403169 724 False 1238 1238 97.517 1 724 1 chr7D.!!$F1 723
2 TraesCS7D01G229900 chr7B 335443572 335446800 3228 False 4532 4532 92.005 24 3262 1 chr7B.!!$F1 3238
3 TraesCS7D01G229900 chr7A 199237022 199239699 2677 False 3993 3993 93.629 584 3256 1 chr7A.!!$F2 2672
4 TraesCS7D01G229900 chr7A 199220434 199220975 541 False 721 721 90.792 1 539 1 chr7A.!!$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
320 322 1.203001 TGGGCCGTCCAATTTCTTCTT 60.203 47.619 0.0 0.0 43.84 2.52 F
2117 2126 0.251209 GCCTCCTTTTCCGTCCCTTT 60.251 55.000 0.0 0.0 0.00 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 2128 0.179020 CGGTGGTCATGGGCATGTAT 60.179 55.0 0.00 0.00 39.72 2.29 R
3268 3283 0.106015 GGACCCCCATTCCCAGAATG 60.106 60.0 9.82 9.82 0.00 2.67 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
240 241 5.936187 AAATGGACATATCACCATGCAAA 57.064 34.783 9.96 0.00 44.79 3.68
265 266 6.620877 TTCCATACATCTCAAACCAGTAGT 57.379 37.500 0.00 0.00 0.00 2.73
320 322 1.203001 TGGGCCGTCCAATTTCTTCTT 60.203 47.619 0.00 0.00 43.84 2.52
333 335 6.310197 CAATTTCTTCTTGATCTCGTTGGAC 58.690 40.000 0.00 0.00 0.00 4.02
344 346 2.425668 TCTCGTTGGACGCTTCATATCA 59.574 45.455 0.00 0.00 42.21 2.15
470 475 3.943381 TGATGAACATCTCCACTTGATGC 59.057 43.478 14.50 0.00 43.53 3.91
491 496 5.454966 TGCCATCCTCACATAGTCTACTTA 58.545 41.667 0.00 0.00 0.00 2.24
664 670 1.500474 ATCACTAGCTGGCTAAGGCA 58.500 50.000 0.00 0.00 40.87 4.75
727 733 9.158233 CTCGTTATCCATAACAAAAACCTAAGA 57.842 33.333 9.57 0.00 42.02 2.10
830 836 2.771943 CACACACATACCACCCTCCTAT 59.228 50.000 0.00 0.00 0.00 2.57
840 846 4.566837 ACCACCCTCCTATGATTGTATGA 58.433 43.478 0.00 0.00 0.00 2.15
875 881 1.267806 CATCCCTTGCTTGTGTGTGTC 59.732 52.381 0.00 0.00 0.00 3.67
889 895 7.094975 GCTTGTGTGTGTCTACATACCATAAAA 60.095 37.037 7.42 0.00 45.20 1.52
933 939 8.299990 TCCCTCTCTCTTCTAGACATTTTAAG 57.700 38.462 0.00 0.00 0.00 1.85
940 946 6.565234 TCTTCTAGACATTTTAAGCCTCTCG 58.435 40.000 0.00 0.00 0.00 4.04
971 977 7.556996 TCGAAAAGCTAGGATAGTCTAGAAACT 59.443 37.037 0.00 0.00 41.93 2.66
1239 1245 1.444895 CCACAAGCGCTTTGATGCC 60.445 57.895 22.51 0.00 39.21 4.40
1362 1368 9.871175 TGAACACCCTGAATACTATGTATACTA 57.129 33.333 4.17 0.00 0.00 1.82
1365 1371 9.175312 ACACCCTGAATACTATGTATACTATCG 57.825 37.037 4.17 0.00 0.00 2.92
1457 1463 8.383619 GCACTTTGATGTGATACTACTTTAGTG 58.616 37.037 0.00 0.00 38.62 2.74
1470 1476 6.472887 ACTACTTTAGTGCTGATTTTGCCTA 58.527 36.000 0.00 0.00 37.69 3.93
1499 1505 2.031870 GTTTGTGCCTTCTTCCAAGGT 58.968 47.619 2.42 0.00 39.60 3.50
1531 1537 4.500035 GGCCTCCATTTGTAACACGAAAAA 60.500 41.667 0.00 0.00 0.00 1.94
1602 1608 3.703286 ATTTGATGCACATCCACATCG 57.297 42.857 8.11 0.00 44.57 3.84
1610 1616 1.207089 CACATCCACATCGTACCACCT 59.793 52.381 0.00 0.00 0.00 4.00
1684 1690 6.881602 TGCATGATATGTAGTTTGTTGGTACA 59.118 34.615 0.00 0.00 0.00 2.90
1690 1696 5.369685 TGTAGTTTGTTGGTACATGCATG 57.630 39.130 25.09 25.09 39.30 4.06
1819 1826 8.624776 GCTAATGCAAATCTTAAAGTGGTAGAT 58.375 33.333 0.00 0.00 39.41 1.98
1943 1952 4.868171 TGTTGTTATGTAGGAAGATGCGAC 59.132 41.667 0.00 0.00 0.00 5.19
2047 2056 2.359967 GGTAGCGAACCTCCAGGCT 61.360 63.158 4.19 0.00 45.75 4.58
2115 2124 2.955881 CGCCTCCTTTTCCGTCCCT 61.956 63.158 0.00 0.00 0.00 4.20
2116 2125 1.379146 GCCTCCTTTTCCGTCCCTT 59.621 57.895 0.00 0.00 0.00 3.95
2117 2126 0.251209 GCCTCCTTTTCCGTCCCTTT 60.251 55.000 0.00 0.00 0.00 3.11
2119 2128 1.073284 CCTCCTTTTCCGTCCCTTTCA 59.927 52.381 0.00 0.00 0.00 2.69
2137 2146 1.133823 TCATACATGCCCATGACCACC 60.134 52.381 14.69 0.00 41.20 4.61
2188 2197 1.296056 CCAATGTCCCGAACACCGTC 61.296 60.000 0.00 0.00 41.75 4.79
2200 2209 3.668757 CGAACACCGTCGAACTATCTTCA 60.669 47.826 0.00 0.00 43.86 3.02
2263 2272 1.401552 CAACAACCATATGGCCAGACG 59.598 52.381 22.18 0.00 39.32 4.18
2276 2285 1.381327 CAGACGGGGGAAGGCTCTA 60.381 63.158 0.00 0.00 0.00 2.43
2277 2286 1.075896 AGACGGGGGAAGGCTCTAG 60.076 63.158 0.00 0.00 0.00 2.43
2376 2385 2.604382 GGCACCCCAGCAACCATT 60.604 61.111 0.00 0.00 35.83 3.16
2421 2430 3.437213 TGCCTAGCTAGGTGAACTAACA 58.563 45.455 34.85 21.31 45.42 2.41
2546 2556 2.625790 ACCACCGCTTTTTGCTTATCAA 59.374 40.909 0.00 0.00 40.11 2.57
2550 2560 5.866633 CCACCGCTTTTTGCTTATCAATTTA 59.133 36.000 0.00 0.00 40.11 1.40
2818 2833 5.999044 AGTGTGAGCTCCATATCTTGATTT 58.001 37.500 12.15 0.00 0.00 2.17
2819 2834 5.821470 AGTGTGAGCTCCATATCTTGATTTG 59.179 40.000 12.15 0.00 0.00 2.32
2854 2869 7.250569 ACATTTTGAGTCAATAAAGTATGCCG 58.749 34.615 6.36 0.00 0.00 5.69
2861 2876 7.766738 TGAGTCAATAAAGTATGCCGTTTATCA 59.233 33.333 0.00 0.00 30.22 2.15
2872 2887 9.120538 AGTATGCCGTTTATCAAAACATAGATT 57.879 29.630 2.33 0.00 44.37 2.40
2966 2981 5.930837 AAACAACAACAGAAAATCCTGGA 57.069 34.783 0.00 0.00 38.44 3.86
2967 2982 5.520376 AACAACAACAGAAAATCCTGGAG 57.480 39.130 1.52 0.00 38.44 3.86
3025 3040 4.986659 CCTTCTTCAAAAGATTTGCACCAG 59.013 41.667 0.00 0.00 37.38 4.00
3081 3096 6.366061 TCAATACTCATCACAACAAGTCTTCG 59.634 38.462 0.00 0.00 0.00 3.79
3114 3129 6.213600 ACAACCACATAAGTAGGAGAGACAAT 59.786 38.462 0.00 0.00 0.00 2.71
3130 3145 5.544176 AGAGACAATTACACTTTCAGGGAGA 59.456 40.000 0.00 0.00 0.00 3.71
3148 3163 1.073964 GACGCCCGTAAAAGAAGGAC 58.926 55.000 0.00 0.00 0.00 3.85
3169 3184 5.454897 GGACAAGTTTGGTCTCCTCTTACTT 60.455 44.000 0.00 0.00 35.61 2.24
3206 3221 3.754965 TCAATGGTTGAAGGTCAGGAAG 58.245 45.455 0.00 0.00 36.59 3.46
3243 3258 1.147824 CGCATCTCCAATGGGCTCT 59.852 57.895 0.00 0.00 0.00 4.09
3258 3273 3.740128 CTCTCCCATTCCGCACCCG 62.740 68.421 0.00 0.00 0.00 5.28
3262 3277 2.671619 CCATTCCGCACCCGTGTT 60.672 61.111 0.00 0.00 0.00 3.32
3263 3278 2.560861 CATTCCGCACCCGTGTTG 59.439 61.111 0.00 0.00 0.00 3.33
3264 3279 2.112297 ATTCCGCACCCGTGTTGT 59.888 55.556 0.00 0.00 0.00 3.32
3265 3280 1.964373 ATTCCGCACCCGTGTTGTC 60.964 57.895 0.00 0.00 0.00 3.18
3266 3281 4.953868 TCCGCACCCGTGTTGTCG 62.954 66.667 0.00 0.00 0.00 4.35
3273 3288 3.966215 CCGTGTTGTCGGCATTCT 58.034 55.556 0.00 0.00 43.96 2.40
3274 3289 1.497278 CCGTGTTGTCGGCATTCTG 59.503 57.895 0.00 0.00 43.96 3.02
3275 3290 1.497278 CGTGTTGTCGGCATTCTGG 59.503 57.895 0.00 0.00 0.00 3.86
3276 3291 1.875963 GTGTTGTCGGCATTCTGGG 59.124 57.895 0.00 0.00 0.00 4.45
3277 3292 0.605319 GTGTTGTCGGCATTCTGGGA 60.605 55.000 0.00 0.00 0.00 4.37
3278 3293 0.109532 TGTTGTCGGCATTCTGGGAA 59.890 50.000 0.00 0.00 0.00 3.97
3279 3294 1.271871 TGTTGTCGGCATTCTGGGAAT 60.272 47.619 0.00 0.00 0.00 3.01
3280 3295 1.133025 GTTGTCGGCATTCTGGGAATG 59.867 52.381 13.86 13.86 0.00 2.67
3281 3296 0.394216 TGTCGGCATTCTGGGAATGG 60.394 55.000 18.08 6.37 0.00 3.16
3282 3297 1.103398 GTCGGCATTCTGGGAATGGG 61.103 60.000 18.08 0.00 0.00 4.00
3283 3298 1.829533 CGGCATTCTGGGAATGGGG 60.830 63.158 18.08 0.00 0.00 4.96
3284 3299 1.458209 GGCATTCTGGGAATGGGGG 60.458 63.158 18.08 0.00 0.00 5.40
3285 3300 1.311059 GCATTCTGGGAATGGGGGT 59.689 57.895 18.08 0.00 0.00 4.95
3286 3301 0.756815 GCATTCTGGGAATGGGGGTC 60.757 60.000 18.08 2.15 0.00 4.46
3287 3302 0.106015 CATTCTGGGAATGGGGGTCC 60.106 60.000 11.18 0.00 0.00 4.46
3298 3313 4.678743 GGGGTCCCCACACTTGCC 62.679 72.222 23.53 0.00 44.65 4.52
3299 3314 3.580319 GGGTCCCCACACTTGCCT 61.580 66.667 0.00 0.00 35.81 4.75
3300 3315 2.282462 GGTCCCCACACTTGCCTG 60.282 66.667 0.00 0.00 0.00 4.85
3301 3316 2.985847 GTCCCCACACTTGCCTGC 60.986 66.667 0.00 0.00 0.00 4.85
3302 3317 4.284550 TCCCCACACTTGCCTGCC 62.285 66.667 0.00 0.00 0.00 4.85
3303 3318 4.290622 CCCCACACTTGCCTGCCT 62.291 66.667 0.00 0.00 0.00 4.75
3304 3319 2.987547 CCCACACTTGCCTGCCTG 60.988 66.667 0.00 0.00 0.00 4.85
3305 3320 3.677648 CCACACTTGCCTGCCTGC 61.678 66.667 0.00 0.00 0.00 4.85
3306 3321 4.034258 CACACTTGCCTGCCTGCG 62.034 66.667 0.00 0.00 0.00 5.18
3337 3352 3.465403 CTCCGCTAGCAGGCCTGT 61.465 66.667 32.81 21.44 0.00 4.00
3338 3353 2.043349 TCCGCTAGCAGGCCTGTA 60.043 61.111 32.81 21.41 0.00 2.74
3339 3354 2.107141 CCGCTAGCAGGCCTGTAC 59.893 66.667 32.81 18.00 0.00 2.90
3340 3355 2.278857 CGCTAGCAGGCCTGTACG 60.279 66.667 32.81 25.07 0.00 3.67
3341 3356 2.771639 CGCTAGCAGGCCTGTACGA 61.772 63.158 32.81 13.29 0.00 3.43
3342 3357 1.227002 GCTAGCAGGCCTGTACGAC 60.227 63.158 32.81 16.47 0.00 4.34
3343 3358 1.437986 CTAGCAGGCCTGTACGACC 59.562 63.158 32.81 15.72 0.00 4.79
3344 3359 2.017559 CTAGCAGGCCTGTACGACCC 62.018 65.000 32.81 14.98 0.00 4.46
3345 3360 2.791613 TAGCAGGCCTGTACGACCCA 62.792 60.000 32.81 1.98 0.00 4.51
3346 3361 3.031417 GCAGGCCTGTACGACCCAT 62.031 63.158 32.81 0.00 0.00 4.00
3347 3362 1.144057 CAGGCCTGTACGACCCATC 59.856 63.158 25.53 0.00 0.00 3.51
3348 3363 1.001760 AGGCCTGTACGACCCATCT 59.998 57.895 3.11 0.00 0.00 2.90
3349 3364 0.617820 AGGCCTGTACGACCCATCTT 60.618 55.000 3.11 0.00 0.00 2.40
3350 3365 0.179081 GGCCTGTACGACCCATCTTC 60.179 60.000 0.00 0.00 0.00 2.87
3351 3366 0.535335 GCCTGTACGACCCATCTTCA 59.465 55.000 0.00 0.00 0.00 3.02
3352 3367 1.139058 GCCTGTACGACCCATCTTCAT 59.861 52.381 0.00 0.00 0.00 2.57
3353 3368 2.803492 GCCTGTACGACCCATCTTCATC 60.803 54.545 0.00 0.00 0.00 2.92
3354 3369 2.430694 CCTGTACGACCCATCTTCATCA 59.569 50.000 0.00 0.00 0.00 3.07
3355 3370 3.118775 CCTGTACGACCCATCTTCATCAA 60.119 47.826 0.00 0.00 0.00 2.57
3356 3371 3.857052 TGTACGACCCATCTTCATCAAC 58.143 45.455 0.00 0.00 0.00 3.18
3357 3372 3.259625 TGTACGACCCATCTTCATCAACA 59.740 43.478 0.00 0.00 0.00 3.33
3358 3373 3.417069 ACGACCCATCTTCATCAACAA 57.583 42.857 0.00 0.00 0.00 2.83
3359 3374 3.338249 ACGACCCATCTTCATCAACAAG 58.662 45.455 0.00 0.00 0.00 3.16
3360 3375 2.679837 CGACCCATCTTCATCAACAAGG 59.320 50.000 0.00 0.00 0.00 3.61
3361 3376 2.424956 GACCCATCTTCATCAACAAGGC 59.575 50.000 0.00 0.00 0.00 4.35
3362 3377 2.225091 ACCCATCTTCATCAACAAGGCA 60.225 45.455 0.00 0.00 0.00 4.75
3363 3378 2.827322 CCCATCTTCATCAACAAGGCAA 59.173 45.455 0.00 0.00 0.00 4.52
3364 3379 3.449737 CCCATCTTCATCAACAAGGCAAT 59.550 43.478 0.00 0.00 0.00 3.56
3365 3380 4.441079 CCCATCTTCATCAACAAGGCAATC 60.441 45.833 0.00 0.00 0.00 2.67
3366 3381 4.158949 CCATCTTCATCAACAAGGCAATCA 59.841 41.667 0.00 0.00 0.00 2.57
3367 3382 5.336929 CCATCTTCATCAACAAGGCAATCAA 60.337 40.000 0.00 0.00 0.00 2.57
3368 3383 5.381174 TCTTCATCAACAAGGCAATCAAG 57.619 39.130 0.00 0.00 0.00 3.02
3369 3384 5.072055 TCTTCATCAACAAGGCAATCAAGA 58.928 37.500 0.00 0.00 0.00 3.02
3370 3385 4.771590 TCATCAACAAGGCAATCAAGAC 57.228 40.909 0.00 0.00 0.00 3.01
3371 3386 3.507233 TCATCAACAAGGCAATCAAGACC 59.493 43.478 0.00 0.00 0.00 3.85
3372 3387 2.238521 TCAACAAGGCAATCAAGACCC 58.761 47.619 0.00 0.00 0.00 4.46
3373 3388 2.158475 TCAACAAGGCAATCAAGACCCT 60.158 45.455 0.00 0.00 0.00 4.34
3374 3389 2.206576 ACAAGGCAATCAAGACCCTC 57.793 50.000 0.00 0.00 0.00 4.30
3375 3390 1.089920 CAAGGCAATCAAGACCCTCG 58.910 55.000 0.00 0.00 0.00 4.63
3376 3391 0.678048 AAGGCAATCAAGACCCTCGC 60.678 55.000 0.00 0.00 0.00 5.03
3377 3392 2.464459 GGCAATCAAGACCCTCGCG 61.464 63.158 0.00 0.00 0.00 5.87
3378 3393 1.447838 GCAATCAAGACCCTCGCGA 60.448 57.895 9.26 9.26 0.00 5.87
3379 3394 1.424493 GCAATCAAGACCCTCGCGAG 61.424 60.000 29.06 29.06 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
240 241 7.554118 CACTACTGGTTTGAGATGTATGGAAAT 59.446 37.037 0.00 0.00 0.00 2.17
320 322 0.601057 TGAAGCGTCCAACGAGATCA 59.399 50.000 3.28 1.52 46.05 2.92
333 335 2.998670 CAGTAGCCCATGATATGAAGCG 59.001 50.000 0.00 0.00 35.40 4.68
344 346 4.778213 TTTGATTAGAGCAGTAGCCCAT 57.222 40.909 0.00 0.00 43.56 4.00
470 475 9.482627 GATTTTAAGTAGACTATGTGAGGATGG 57.517 37.037 0.00 0.00 0.00 3.51
491 496 7.715657 TGTTCTTGCATGACAGTAAAGATTTT 58.284 30.769 1.02 0.00 0.00 1.82
830 836 5.584251 TGCGAGCAATTAGTTCATACAATCA 59.416 36.000 0.00 0.00 0.00 2.57
840 846 2.017049 GGGATGTGCGAGCAATTAGTT 58.983 47.619 0.00 0.00 0.00 2.24
889 895 2.305635 GGAAGGGAATTTGTGGGCATTT 59.694 45.455 0.00 0.00 0.00 2.32
901 907 3.793842 AGAAGAGAGAGGGAAGGGAAT 57.206 47.619 0.00 0.00 0.00 3.01
940 946 6.566141 AGACTATCCTAGCTTTTCGAACTTC 58.434 40.000 0.00 0.00 0.00 3.01
949 955 7.286775 CCTCAGTTTCTAGACTATCCTAGCTTT 59.713 40.741 0.00 0.00 36.84 3.51
971 977 2.679082 GGAATGGTACCTAGCTCCTCA 58.321 52.381 14.36 0.00 0.00 3.86
1048 1054 1.335882 GGCCCTCCACTACTACCACC 61.336 65.000 0.00 0.00 0.00 4.61
1231 1237 0.608856 ACAGTGATGGCGGCATCAAA 60.609 50.000 44.32 27.62 42.46 2.69
1239 1245 3.742882 CCTCATAACATACAGTGATGGCG 59.257 47.826 0.00 0.00 39.28 5.69
1362 1368 9.149225 GCAATTATATGACAAAGAGAGATCGAT 57.851 33.333 0.00 0.00 0.00 3.59
1394 1400 5.771666 ACCAATTCAATATCCGCTGATCATT 59.228 36.000 0.00 0.00 32.18 2.57
1457 1463 4.082026 ACAACTCCAATAGGCAAAATCAGC 60.082 41.667 0.00 0.00 33.74 4.26
1470 1476 3.299503 AGAAGGCACAAACAACTCCAAT 58.700 40.909 0.00 0.00 0.00 3.16
1531 1537 6.048509 CCTTTAATTTGCTTGACTTGTTGGT 58.951 36.000 0.00 0.00 0.00 3.67
1577 1583 6.798476 CGATGTGGATGTGCATCAAATTATAC 59.202 38.462 13.37 2.81 40.93 1.47
1602 1608 8.358895 GGTAGATGAGAGTATTAAAGGTGGTAC 58.641 40.741 0.00 0.00 0.00 3.34
1684 1690 6.039717 GGAGTATGGTGATTTAACACATGCAT 59.960 38.462 0.00 0.00 41.88 3.96
1690 1696 7.280205 CCAACTAGGAGTATGGTGATTTAACAC 59.720 40.741 0.00 0.00 41.22 3.32
1731 1738 4.278310 GCCTATGTCCCTTGTTGGTTTAT 58.722 43.478 0.00 0.00 0.00 1.40
1732 1739 3.562609 GGCCTATGTCCCTTGTTGGTTTA 60.563 47.826 0.00 0.00 0.00 2.01
1808 1815 4.906060 GGGTGGGTATCTATCTACCACTTT 59.094 45.833 11.40 0.00 42.57 2.66
1819 1826 0.542805 GTTTGGCGGGTGGGTATCTA 59.457 55.000 0.00 0.00 0.00 1.98
2047 2056 0.970937 CCTGTAGGGAGGCGACTTCA 60.971 60.000 0.00 0.00 44.43 3.02
2068 2077 0.529773 GTTGCAGTGTCGTGAGGTGA 60.530 55.000 0.00 0.00 0.00 4.02
2115 2124 3.023119 GTGGTCATGGGCATGTATGAAA 58.977 45.455 9.85 2.10 39.72 2.69
2116 2125 2.653726 GTGGTCATGGGCATGTATGAA 58.346 47.619 9.85 0.00 39.72 2.57
2117 2126 1.133823 GGTGGTCATGGGCATGTATGA 60.134 52.381 0.00 0.01 39.72 2.15
2119 2128 0.179020 CGGTGGTCATGGGCATGTAT 60.179 55.000 0.00 0.00 39.72 2.29
2137 2146 3.681897 CCAGTTCAGAAATGGAGAACTCG 59.318 47.826 22.93 0.00 46.47 4.18
2237 2246 2.094234 GGCCATATGGTTGTTGGTGTTC 60.094 50.000 22.79 1.56 37.57 3.18
2263 2272 2.941563 TACCGCTAGAGCCTTCCCCC 62.942 65.000 0.00 0.00 37.91 5.40
2276 2285 1.764571 TTGGTGTTGCCTCTACCGCT 61.765 55.000 0.00 0.00 37.29 5.52
2277 2286 1.302192 TTGGTGTTGCCTCTACCGC 60.302 57.895 0.00 0.00 37.29 5.68
2305 2314 0.609957 CCAGGGCTTGCAAGTCATCA 60.610 55.000 30.67 0.00 30.55 3.07
2360 2369 1.470996 TTCAATGGTTGCTGGGGTGC 61.471 55.000 0.00 0.00 0.00 5.01
2376 2385 5.895636 ACAATCTCAAAACTGTGTGTTCA 57.104 34.783 0.00 0.00 38.03 3.18
2501 2510 7.228108 GGTGCCTATTAACTACCTTCCATAAAC 59.772 40.741 0.00 0.00 0.00 2.01
2510 2519 2.433239 CGGTGGTGCCTATTAACTACCT 59.567 50.000 6.75 0.00 43.65 3.08
2546 2556 8.218488 CCCTGCTACCCTAGTAAAGAATTAAAT 58.782 37.037 0.00 0.00 0.00 1.40
2550 2560 4.412528 CCCCTGCTACCCTAGTAAAGAATT 59.587 45.833 0.00 0.00 0.00 2.17
2619 2629 6.642733 ATAAACTCCCTCCAATCTTCTTCA 57.357 37.500 0.00 0.00 0.00 3.02
2717 2732 1.264826 CACAATGGCCAAAAGCAAAGC 59.735 47.619 10.96 0.00 46.50 3.51
2818 2833 6.880942 TGACTCAAAATGTCACATCAATCA 57.119 33.333 0.00 0.00 39.23 2.57
2819 2834 9.844790 TTATTGACTCAAAATGTCACATCAATC 57.155 29.630 4.22 0.00 43.13 2.67
2872 2887 9.214957 GGTATTGTATCGTCATAAATGGATGAA 57.785 33.333 0.00 0.00 37.58 2.57
2885 2900 6.979238 GCAGGGATATTAGGTATTGTATCGTC 59.021 42.308 0.00 0.00 0.00 4.20
2887 2902 7.113658 AGCAGGGATATTAGGTATTGTATCG 57.886 40.000 0.00 0.00 0.00 2.92
2966 2981 5.584649 GCCAAAAACTTAAAAGCTGGTTTCT 59.415 36.000 5.19 0.00 32.43 2.52
2967 2982 5.352846 TGCCAAAAACTTAAAAGCTGGTTTC 59.647 36.000 5.19 0.00 32.43 2.78
2976 2991 6.431234 ACACAACCATTGCCAAAAACTTAAAA 59.569 30.769 0.00 0.00 0.00 1.52
2977 2992 5.940470 ACACAACCATTGCCAAAAACTTAAA 59.060 32.000 0.00 0.00 0.00 1.52
2978 2993 5.491982 ACACAACCATTGCCAAAAACTTAA 58.508 33.333 0.00 0.00 0.00 1.85
3081 3096 5.410439 CCTACTTATGTGGTTGTGTGGTTAC 59.590 44.000 0.00 0.00 0.00 2.50
3114 3129 1.001633 GGCGTCTCCCTGAAAGTGTAA 59.998 52.381 0.00 0.00 0.00 2.41
3130 3145 0.393820 TGTCCTTCTTTTACGGGCGT 59.606 50.000 0.00 0.00 0.00 5.68
3148 3163 6.760291 ACTAAGTAAGAGGAGACCAAACTTG 58.240 40.000 0.00 0.00 0.00 3.16
3169 3184 5.575157 ACCATTGAGACAGAGAAGAGACTA 58.425 41.667 0.00 0.00 0.00 2.59
3206 3221 3.374988 TGCGTCTTCATCCAAATCATGTC 59.625 43.478 0.00 0.00 0.00 3.06
3243 3258 4.402528 CACGGGTGCGGAATGGGA 62.403 66.667 0.00 0.00 0.00 4.37
3258 3273 0.605319 TCCCAGAATGCCGACAACAC 60.605 55.000 0.00 0.00 31.97 3.32
3262 3277 0.394216 CCATTCCCAGAATGCCGACA 60.394 55.000 11.07 0.00 31.97 4.35
3263 3278 1.103398 CCCATTCCCAGAATGCCGAC 61.103 60.000 11.07 0.00 31.97 4.79
3264 3279 1.227102 CCCATTCCCAGAATGCCGA 59.773 57.895 11.07 0.00 31.97 5.54
3265 3280 1.829533 CCCCATTCCCAGAATGCCG 60.830 63.158 11.07 4.36 31.97 5.69
3266 3281 1.458209 CCCCCATTCCCAGAATGCC 60.458 63.158 11.07 0.00 31.97 4.40
3267 3282 0.756815 GACCCCCATTCCCAGAATGC 60.757 60.000 11.07 0.00 31.97 3.56
3268 3283 0.106015 GGACCCCCATTCCCAGAATG 60.106 60.000 9.82 9.82 0.00 2.67
3269 3284 2.332301 GGACCCCCATTCCCAGAAT 58.668 57.895 0.00 0.00 0.00 2.40
3270 3285 3.850061 GGACCCCCATTCCCAGAA 58.150 61.111 0.00 0.00 0.00 3.02
3284 3299 2.985847 GCAGGCAAGTGTGGGGAC 60.986 66.667 0.00 0.00 0.00 4.46
3285 3300 4.284550 GGCAGGCAAGTGTGGGGA 62.285 66.667 0.00 0.00 0.00 4.81
3286 3301 4.290622 AGGCAGGCAAGTGTGGGG 62.291 66.667 0.00 0.00 0.00 4.96
3287 3302 2.987547 CAGGCAGGCAAGTGTGGG 60.988 66.667 0.00 0.00 0.00 4.61
3288 3303 3.677648 GCAGGCAGGCAAGTGTGG 61.678 66.667 0.00 0.00 0.00 4.17
3289 3304 4.034258 CGCAGGCAGGCAAGTGTG 62.034 66.667 0.00 0.00 0.00 3.82
3320 3335 2.127869 TACAGGCCTGCTAGCGGAG 61.128 63.158 33.06 15.42 0.00 4.63
3321 3336 2.043349 TACAGGCCTGCTAGCGGA 60.043 61.111 33.06 0.00 0.00 5.54
3322 3337 2.107141 GTACAGGCCTGCTAGCGG 59.893 66.667 33.06 17.14 0.00 5.52
3323 3338 2.278857 CGTACAGGCCTGCTAGCG 60.279 66.667 33.06 24.91 0.00 4.26
3324 3339 1.227002 GTCGTACAGGCCTGCTAGC 60.227 63.158 33.06 18.02 0.00 3.42
3325 3340 1.437986 GGTCGTACAGGCCTGCTAG 59.562 63.158 33.06 22.30 42.70 3.42
3326 3341 2.056223 GGGTCGTACAGGCCTGCTA 61.056 63.158 33.06 20.08 46.10 3.49
3327 3342 3.391382 GGGTCGTACAGGCCTGCT 61.391 66.667 33.06 21.13 46.10 4.24
3328 3343 2.925162 GATGGGTCGTACAGGCCTGC 62.925 65.000 33.06 16.43 46.10 4.85
3329 3344 1.144057 GATGGGTCGTACAGGCCTG 59.856 63.158 31.60 31.60 46.10 4.85
3330 3345 0.617820 AAGATGGGTCGTACAGGCCT 60.618 55.000 0.00 0.00 46.10 5.19
3331 3346 0.179081 GAAGATGGGTCGTACAGGCC 60.179 60.000 0.00 0.00 46.15 5.19
3332 3347 0.535335 TGAAGATGGGTCGTACAGGC 59.465 55.000 0.00 0.00 0.00 4.85
3333 3348 2.430694 TGATGAAGATGGGTCGTACAGG 59.569 50.000 0.00 0.00 0.00 4.00
3334 3349 3.801114 TGATGAAGATGGGTCGTACAG 57.199 47.619 0.00 0.00 0.00 2.74
3335 3350 3.259625 TGTTGATGAAGATGGGTCGTACA 59.740 43.478 0.00 0.00 0.00 2.90
3336 3351 3.857052 TGTTGATGAAGATGGGTCGTAC 58.143 45.455 0.00 0.00 0.00 3.67
3337 3352 4.503910 CTTGTTGATGAAGATGGGTCGTA 58.496 43.478 0.00 0.00 0.00 3.43
3338 3353 3.338249 CTTGTTGATGAAGATGGGTCGT 58.662 45.455 0.00 0.00 0.00 4.34
3339 3354 2.679837 CCTTGTTGATGAAGATGGGTCG 59.320 50.000 0.00 0.00 0.00 4.79
3340 3355 2.424956 GCCTTGTTGATGAAGATGGGTC 59.575 50.000 0.00 0.00 0.00 4.46
3341 3356 2.225091 TGCCTTGTTGATGAAGATGGGT 60.225 45.455 0.00 0.00 0.00 4.51
3342 3357 2.449464 TGCCTTGTTGATGAAGATGGG 58.551 47.619 0.00 0.00 0.00 4.00
3343 3358 4.158949 TGATTGCCTTGTTGATGAAGATGG 59.841 41.667 0.00 0.00 0.00 3.51
3344 3359 5.319140 TGATTGCCTTGTTGATGAAGATG 57.681 39.130 0.00 0.00 0.00 2.90
3345 3360 5.713389 TCTTGATTGCCTTGTTGATGAAGAT 59.287 36.000 0.00 0.00 0.00 2.40
3346 3361 5.048504 GTCTTGATTGCCTTGTTGATGAAGA 60.049 40.000 0.00 0.00 0.00 2.87
3347 3362 5.159209 GTCTTGATTGCCTTGTTGATGAAG 58.841 41.667 0.00 0.00 0.00 3.02
3348 3363 4.022068 GGTCTTGATTGCCTTGTTGATGAA 60.022 41.667 0.00 0.00 0.00 2.57
3349 3364 3.507233 GGTCTTGATTGCCTTGTTGATGA 59.493 43.478 0.00 0.00 0.00 2.92
3350 3365 3.367703 GGGTCTTGATTGCCTTGTTGATG 60.368 47.826 0.00 0.00 0.00 3.07
3351 3366 2.827921 GGGTCTTGATTGCCTTGTTGAT 59.172 45.455 0.00 0.00 0.00 2.57
3352 3367 2.158475 AGGGTCTTGATTGCCTTGTTGA 60.158 45.455 0.00 0.00 0.00 3.18
3353 3368 2.229784 GAGGGTCTTGATTGCCTTGTTG 59.770 50.000 0.00 0.00 0.00 3.33
3354 3369 2.519013 GAGGGTCTTGATTGCCTTGTT 58.481 47.619 0.00 0.00 0.00 2.83
3355 3370 1.611673 CGAGGGTCTTGATTGCCTTGT 60.612 52.381 0.00 0.00 0.00 3.16
3356 3371 1.089920 CGAGGGTCTTGATTGCCTTG 58.910 55.000 0.00 0.00 0.00 3.61
3357 3372 0.678048 GCGAGGGTCTTGATTGCCTT 60.678 55.000 0.00 0.00 0.00 4.35
3358 3373 1.078143 GCGAGGGTCTTGATTGCCT 60.078 57.895 0.00 0.00 0.00 4.75
3359 3374 2.464459 CGCGAGGGTCTTGATTGCC 61.464 63.158 0.00 0.00 0.00 4.52
3360 3375 1.424493 CTCGCGAGGGTCTTGATTGC 61.424 60.000 28.40 0.00 0.00 3.56
3361 3376 0.807667 CCTCGCGAGGGTCTTGATTG 60.808 60.000 41.47 16.37 44.87 2.67
3362 3377 1.517832 CCTCGCGAGGGTCTTGATT 59.482 57.895 41.47 0.00 44.87 2.57
3363 3378 3.211288 CCTCGCGAGGGTCTTGAT 58.789 61.111 41.47 0.00 44.87 2.57


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

AutoCloner maintained by Alex Coulton.