Multiple sequence alignment - TraesCS7A01G398400

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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 TraesCS7A01G398400 chr7A 100.000 3907 0 0 1 3907 577446023 577442117 0.000000e+00 7215.0
1 TraesCS7A01G398400 chr7A 98.765 729 8 1 1 728 719988612 719989340 0.000000e+00 1295.0
2 TraesCS7A01G398400 chr7A 98.438 64 0 1 3122 3184 577442840 577442777 1.150000e-20 111.0
3 TraesCS7A01G398400 chr7A 98.438 64 0 1 3184 3247 577442902 577442840 1.150000e-20 111.0
4 TraesCS7A01G398400 chr7D 95.203 2314 71 16 727 3027 507820095 507817809 0.000000e+00 3622.0
5 TraesCS7A01G398400 chr7D 92.614 352 22 2 3556 3907 507817357 507817010 1.620000e-138 503.0
6 TraesCS7A01G398400 chr7D 90.333 300 15 7 3184 3472 507817681 507817385 7.920000e-102 381.0
7 TraesCS7A01G398400 chr7D 95.625 160 3 1 3025 3184 507817774 507817619 1.800000e-63 254.0
8 TraesCS7A01G398400 chr7D 97.059 34 1 0 3490 3523 507817385 507817352 1.520000e-04 58.4
9 TraesCS7A01G398400 chr7B 91.806 1379 63 27 1811 3184 536006213 536004880 0.000000e+00 1875.0
10 TraesCS7A01G398400 chr7B 92.196 1102 51 13 727 1814 536007415 536006335 0.000000e+00 1526.0
11 TraesCS7A01G398400 chr7B 98.760 726 9 0 1 726 733805857 733805132 0.000000e+00 1291.0
12 TraesCS7A01G398400 chr7B 98.356 730 11 1 1 729 189385332 189384603 0.000000e+00 1280.0
13 TraesCS7A01G398400 chr7B 92.531 723 35 9 3188 3907 536004934 536004228 0.000000e+00 1018.0
14 TraesCS7A01G398400 chr6A 98.628 729 8 1 1 729 111537306 111536580 0.000000e+00 1290.0
15 TraesCS7A01G398400 chr6A 98.226 733 11 2 1 731 15225804 15225072 0.000000e+00 1280.0
16 TraesCS7A01G398400 chr2A 98.624 727 10 0 1 727 562641453 562642179 0.000000e+00 1288.0
17 TraesCS7A01G398400 chr2A 98.491 729 11 0 1 729 7682313 7683041 0.000000e+00 1286.0
18 TraesCS7A01G398400 chr4B 98.621 725 10 0 1 725 516361890 516362614 0.000000e+00 1284.0
19 TraesCS7A01G398400 chr3A 98.621 725 10 0 1 725 446473445 446474169 0.000000e+00 1284.0


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 TraesCS7A01G398400 chr7A 577442117 577446023 3906 True 2479.00 7215 98.958667 1 3907 3 chr7A.!!$R1 3906
1 TraesCS7A01G398400 chr7A 719988612 719989340 728 False 1295.00 1295 98.765000 1 728 1 chr7A.!!$F1 727
2 TraesCS7A01G398400 chr7D 507817010 507820095 3085 True 963.68 3622 94.166800 727 3907 5 chr7D.!!$R1 3180
3 TraesCS7A01G398400 chr7B 536004228 536007415 3187 True 1473.00 1875 92.177667 727 3907 3 chr7B.!!$R3 3180
4 TraesCS7A01G398400 chr7B 733805132 733805857 725 True 1291.00 1291 98.760000 1 726 1 chr7B.!!$R2 725
5 TraesCS7A01G398400 chr7B 189384603 189385332 729 True 1280.00 1280 98.356000 1 729 1 chr7B.!!$R1 728
6 TraesCS7A01G398400 chr6A 111536580 111537306 726 True 1290.00 1290 98.628000 1 729 1 chr6A.!!$R2 728
7 TraesCS7A01G398400 chr6A 15225072 15225804 732 True 1280.00 1280 98.226000 1 731 1 chr6A.!!$R1 730
8 TraesCS7A01G398400 chr2A 562641453 562642179 726 False 1288.00 1288 98.624000 1 727 1 chr2A.!!$F2 726
9 TraesCS7A01G398400 chr2A 7682313 7683041 728 False 1286.00 1286 98.491000 1 729 1 chr2A.!!$F1 728
10 TraesCS7A01G398400 chr4B 516361890 516362614 724 False 1284.00 1284 98.621000 1 725 1 chr4B.!!$F1 724
11 TraesCS7A01G398400 chr3A 446473445 446474169 724 False 1284.00 1284 98.621000 1 725 1 chr3A.!!$F1 724

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
985 988 1.336148 CCGCTATATAACAACCGGCGA 60.336 52.381 9.3 0.0 43.05 5.54 F
1964 2107 0.480252 GGCTATTTGGGAGCTGGGAT 59.520 55.000 0.0 0.0 39.98 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 2491 0.311790 ATGAGCACAAGCCAACGTTG 59.688 50.0 21.47 21.47 43.56 4.10 R
3180 3367 0.544697 ACTTGTGACTTCAACCCCGT 59.455 50.0 0.00 0.00 0.00 5.28 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
130 131 4.206843 GCATCGTCGCTCTTGAATAATTG 58.793 43.478 0.00 0.00 0.00 2.32
223 224 8.186821 GGATTGACAACAAATAATCAGAGAAGG 58.813 37.037 0.00 0.00 39.54 3.46
864 866 4.720902 CCAGGCCACGGCATCACA 62.721 66.667 10.83 0.00 44.11 3.58
865 867 3.129502 CAGGCCACGGCATCACAG 61.130 66.667 10.83 0.00 44.11 3.66
883 885 2.124736 CGCGTGGGTCCCATTCAT 60.125 61.111 15.49 0.00 35.28 2.57
942 944 1.535444 TCTCCTTCCCCACGAAGCA 60.535 57.895 0.00 0.00 45.83 3.91
985 988 1.336148 CCGCTATATAACAACCGGCGA 60.336 52.381 9.30 0.00 43.05 5.54
1011 1014 3.798202 AGACCGAGACAAAATAGCATCC 58.202 45.455 0.00 0.00 0.00 3.51
1051 1054 4.135153 CTCGACCTGGACGCCCTG 62.135 72.222 13.62 0.00 0.00 4.45
1398 1401 3.063084 GACGCCGGAGACAGAGGT 61.063 66.667 13.83 0.00 0.00 3.85
1435 1438 1.883084 GACGGATGTGGATGGCGAC 60.883 63.158 0.00 0.00 0.00 5.19
1458 1461 4.716794 GATCCCATCAGCAAGAAGAAGAT 58.283 43.478 0.00 0.00 0.00 2.40
1477 1480 7.118723 AGAAGATGAGGTATGCCAATTTTGTA 58.881 34.615 1.54 0.00 37.19 2.41
1519 1524 4.437390 CGTCTGTCATCTAAAATTGGGCAC 60.437 45.833 0.00 0.00 0.00 5.01
1524 1529 5.538053 TGTCATCTAAAATTGGGCACTTTCA 59.462 36.000 0.00 0.00 0.00 2.69
1548 1553 2.623878 TCTTGTTTGCCCGTAGAACA 57.376 45.000 0.00 0.00 0.00 3.18
1579 1584 7.572523 TTACATCCAGCTTAAGGATCAATTG 57.427 36.000 4.29 0.00 43.90 2.32
1584 1589 5.045651 TCCAGCTTAAGGATCAATTGTCTGA 60.046 40.000 5.13 0.00 0.00 3.27
1611 1622 6.820152 GGGTCGTTGTCATACTTAACCTAATT 59.180 38.462 0.00 0.00 0.00 1.40
1616 1627 8.526681 CGTTGTCATACTTAACCTAATTCGTAC 58.473 37.037 0.00 0.00 0.00 3.67
1644 1655 9.677567 ACTACTAAAATGCACAAAATTGTACTG 57.322 29.630 0.00 0.00 39.91 2.74
1645 1656 9.677567 CTACTAAAATGCACAAAATTGTACTGT 57.322 29.630 0.00 0.00 39.91 3.55
1647 1658 9.458374 ACTAAAATGCACAAAATTGTACTGTAC 57.542 29.630 10.98 10.98 39.91 2.90
1676 1687 7.041508 ACAAACTCTTAAGCTTTCAGAGATGTG 60.042 37.037 29.14 24.31 37.12 3.21
1677 1688 6.107901 ACTCTTAAGCTTTCAGAGATGTGT 57.892 37.500 29.14 13.48 37.97 3.72
1703 1714 5.408880 TCCGTATGGTGAATGTTACTCAA 57.591 39.130 0.00 0.00 36.30 3.02
1704 1715 5.172934 TCCGTATGGTGAATGTTACTCAAC 58.827 41.667 0.00 0.00 36.30 3.18
1736 1752 8.823220 AAATTTTAAGTACATGAGGGCACTAT 57.177 30.769 0.00 0.00 0.00 2.12
1737 1753 8.823220 AATTTTAAGTACATGAGGGCACTATT 57.177 30.769 0.00 0.00 0.00 1.73
1738 1754 8.823220 ATTTTAAGTACATGAGGGCACTATTT 57.177 30.769 0.00 0.00 0.00 1.40
1799 1815 2.288825 GGGTTTGACCTTGGCTAAAAGC 60.289 50.000 0.00 0.00 38.64 3.51
1958 2101 1.185315 TTGCAAGGCTATTTGGGAGC 58.815 50.000 0.00 0.00 39.33 4.70
1964 2107 0.480252 GGCTATTTGGGAGCTGGGAT 59.520 55.000 0.00 0.00 39.98 3.85
1974 2117 2.559931 GGGAGCTGGGATGTATAGCCTA 60.560 54.545 0.00 0.00 38.18 3.93
2079 2224 9.952124 GTCATATGTGAAGGACTTGGAGACGAG 62.952 48.148 1.90 0.00 41.09 4.18
2240 2385 3.197766 ACTTTCGGGTAAGATGCTGATGA 59.802 43.478 0.00 0.00 0.00 2.92
2250 2395 4.978083 AGATGCTGATGATTTTCACCAC 57.022 40.909 0.00 0.00 0.00 4.16
2254 2399 3.890756 TGCTGATGATTTTCACCACAAGT 59.109 39.130 0.00 0.00 0.00 3.16
2299 2444 2.791383 TGGTTTTCATTGCTCAACCG 57.209 45.000 0.00 0.00 41.51 4.44
2382 2527 7.935520 TGTGCTCATGTAACTTGAAATTGTTA 58.064 30.769 0.00 0.00 0.00 2.41
2503 2649 2.606725 CAGAACTTAGCGAGCTTGATGG 59.393 50.000 4.70 0.00 0.00 3.51
2511 2657 4.315588 AGCTTGATGGCTCACAGC 57.684 55.556 0.00 10.20 38.24 4.40
2512 2658 1.684035 AGCTTGATGGCTCACAGCT 59.316 52.632 12.76 12.76 41.99 4.24
2513 2659 0.392729 AGCTTGATGGCTCACAGCTC 60.393 55.000 12.76 0.00 39.51 4.09
2514 2660 1.703438 GCTTGATGGCTCACAGCTCG 61.703 60.000 0.00 0.00 41.99 5.03
2515 2661 0.390866 CTTGATGGCTCACAGCTCGT 60.391 55.000 0.00 0.00 41.99 4.18
2516 2662 0.390340 TTGATGGCTCACAGCTCGTC 60.390 55.000 0.00 0.00 41.99 4.20
2517 2663 1.216444 GATGGCTCACAGCTCGTCA 59.784 57.895 0.00 0.00 41.99 4.35
2518 2664 0.179089 GATGGCTCACAGCTCGTCAT 60.179 55.000 0.00 0.00 41.99 3.06
2519 2665 0.251354 ATGGCTCACAGCTCGTCATT 59.749 50.000 0.00 0.00 41.99 2.57
2520 2666 0.390340 TGGCTCACAGCTCGTCATTC 60.390 55.000 0.00 0.00 41.99 2.67
2523 2669 1.936656 GCTCACAGCTCGTCATTCACA 60.937 52.381 0.00 0.00 38.45 3.58
3022 3170 2.944129 TGCTAGTTTTGAAACCTGGCT 58.056 42.857 11.60 0.00 39.71 4.75
3150 3337 3.821033 GTCACAAGTGAAAGGCCACTAAT 59.179 43.478 5.01 0.00 45.82 1.73
3151 3338 5.001232 GTCACAAGTGAAAGGCCACTAATA 58.999 41.667 5.01 0.00 45.82 0.98
3154 3341 5.122396 CACAAGTGAAAGGCCACTAATACTC 59.878 44.000 5.01 0.00 45.82 2.59
3155 3342 4.489306 AGTGAAAGGCCACTAATACTCC 57.511 45.455 5.01 0.00 44.82 3.85
3156 3343 3.844211 AGTGAAAGGCCACTAATACTCCA 59.156 43.478 5.01 0.00 44.82 3.86
3157 3344 4.080863 AGTGAAAGGCCACTAATACTCCAG 60.081 45.833 5.01 0.00 44.82 3.86
3158 3345 3.844211 TGAAAGGCCACTAATACTCCAGT 59.156 43.478 5.01 0.00 0.00 4.00
3159 3346 3.914426 AAGGCCACTAATACTCCAGTG 57.086 47.619 5.01 0.00 41.51 3.66
3160 3347 2.834113 AGGCCACTAATACTCCAGTGT 58.166 47.619 5.01 0.00 40.47 3.55
3161 3348 3.990369 AGGCCACTAATACTCCAGTGTA 58.010 45.455 5.01 0.00 40.47 2.90
3162 3349 3.961408 AGGCCACTAATACTCCAGTGTAG 59.039 47.826 5.01 0.00 40.47 2.74
3163 3350 3.705072 GGCCACTAATACTCCAGTGTAGT 59.295 47.826 0.00 0.00 40.47 2.73
3164 3351 4.161754 GGCCACTAATACTCCAGTGTAGTT 59.838 45.833 0.00 0.00 40.47 2.24
3165 3352 5.109903 GCCACTAATACTCCAGTGTAGTTG 58.890 45.833 0.00 0.00 40.47 3.16
3166 3353 5.337330 GCCACTAATACTCCAGTGTAGTTGT 60.337 44.000 0.00 0.00 40.47 3.32
3167 3354 6.331061 CCACTAATACTCCAGTGTAGTTGTC 58.669 44.000 0.00 0.00 40.47 3.18
3168 3355 6.071560 CCACTAATACTCCAGTGTAGTTGTCA 60.072 42.308 0.00 0.00 40.47 3.58
3169 3356 7.375834 CACTAATACTCCAGTGTAGTTGTCAA 58.624 38.462 0.00 0.00 37.87 3.18
3170 3357 7.870954 CACTAATACTCCAGTGTAGTTGTCAAA 59.129 37.037 0.00 0.00 37.87 2.69
3171 3358 8.426489 ACTAATACTCCAGTGTAGTTGTCAAAA 58.574 33.333 0.00 0.00 30.75 2.44
3172 3359 9.436957 CTAATACTCCAGTGTAGTTGTCAAAAT 57.563 33.333 0.00 0.00 0.00 1.82
3173 3360 8.691661 AATACTCCAGTGTAGTTGTCAAAATT 57.308 30.769 0.00 0.00 0.00 1.82
3174 3361 9.787435 AATACTCCAGTGTAGTTGTCAAAATTA 57.213 29.630 0.00 0.00 0.00 1.40
3175 3362 7.492352 ACTCCAGTGTAGTTGTCAAAATTAC 57.508 36.000 0.00 0.00 0.00 1.89
3176 3363 7.051623 ACTCCAGTGTAGTTGTCAAAATTACA 58.948 34.615 0.00 0.00 0.00 2.41
3177 3364 7.226720 ACTCCAGTGTAGTTGTCAAAATTACAG 59.773 37.037 6.24 0.27 0.00 2.74
3178 3365 7.051623 TCCAGTGTAGTTGTCAAAATTACAGT 58.948 34.615 6.24 6.79 0.00 3.55
3179 3366 8.205512 TCCAGTGTAGTTGTCAAAATTACAGTA 58.794 33.333 10.68 0.00 0.00 2.74
3180 3367 8.832521 CCAGTGTAGTTGTCAAAATTACAGTAA 58.167 33.333 0.00 0.00 0.00 2.24
3181 3368 9.646336 CAGTGTAGTTGTCAAAATTACAGTAAC 57.354 33.333 0.00 0.00 0.00 2.50
3182 3369 8.545420 AGTGTAGTTGTCAAAATTACAGTAACG 58.455 33.333 0.00 0.00 0.00 3.18
3183 3370 7.795272 GTGTAGTTGTCAAAATTACAGTAACGG 59.205 37.037 0.00 0.00 0.00 4.44
3184 3371 6.308371 AGTTGTCAAAATTACAGTAACGGG 57.692 37.500 0.00 0.00 0.00 5.28
3185 3372 5.239963 AGTTGTCAAAATTACAGTAACGGGG 59.760 40.000 0.00 0.00 0.00 5.73
3186 3373 4.716794 TGTCAAAATTACAGTAACGGGGT 58.283 39.130 0.00 0.00 0.00 4.95
3187 3374 5.131784 TGTCAAAATTACAGTAACGGGGTT 58.868 37.500 0.00 0.00 0.00 4.11
3188 3375 5.008811 TGTCAAAATTACAGTAACGGGGTTG 59.991 40.000 0.00 0.00 0.00 3.77
3189 3376 5.239087 GTCAAAATTACAGTAACGGGGTTGA 59.761 40.000 0.00 0.00 0.00 3.18
3190 3377 5.826737 TCAAAATTACAGTAACGGGGTTGAA 59.173 36.000 0.00 0.00 0.00 2.69
3191 3378 5.952526 AAATTACAGTAACGGGGTTGAAG 57.047 39.130 0.00 0.00 0.00 3.02
3192 3379 4.628963 ATTACAGTAACGGGGTTGAAGT 57.371 40.909 0.00 0.00 0.00 3.01
3193 3380 2.538512 ACAGTAACGGGGTTGAAGTC 57.461 50.000 0.00 0.00 0.00 3.01
3194 3381 1.764134 ACAGTAACGGGGTTGAAGTCA 59.236 47.619 0.00 0.00 0.00 3.41
3195 3382 2.140717 CAGTAACGGGGTTGAAGTCAC 58.859 52.381 0.00 0.00 0.00 3.67
3196 3383 1.764134 AGTAACGGGGTTGAAGTCACA 59.236 47.619 0.00 0.00 0.00 3.58
3197 3384 2.171027 AGTAACGGGGTTGAAGTCACAA 59.829 45.455 0.00 0.00 0.00 3.33
3198 3385 1.675552 AACGGGGTTGAAGTCACAAG 58.324 50.000 0.00 0.00 0.00 3.16
3199 3386 0.544697 ACGGGGTTGAAGTCACAAGT 59.455 50.000 0.00 0.00 0.00 3.16
3200 3387 0.944386 CGGGGTTGAAGTCACAAGTG 59.056 55.000 0.00 0.00 0.00 3.16
3201 3388 1.474320 CGGGGTTGAAGTCACAAGTGA 60.474 52.381 0.00 0.00 37.24 3.41
3202 3389 2.650322 GGGGTTGAAGTCACAAGTGAA 58.350 47.619 4.20 0.00 41.85 3.18
3203 3390 3.020984 GGGGTTGAAGTCACAAGTGAAA 58.979 45.455 4.20 0.00 41.85 2.69
3204 3391 3.066760 GGGGTTGAAGTCACAAGTGAAAG 59.933 47.826 4.20 0.00 41.85 2.62
3205 3392 3.066760 GGGTTGAAGTCACAAGTGAAAGG 59.933 47.826 4.20 0.00 41.85 3.11
3206 3393 3.489229 GGTTGAAGTCACAAGTGAAAGGC 60.489 47.826 4.20 0.00 41.85 4.35
3207 3394 2.297701 TGAAGTCACAAGTGAAAGGCC 58.702 47.619 4.20 0.00 41.85 5.19
3208 3395 2.297701 GAAGTCACAAGTGAAAGGCCA 58.702 47.619 5.01 0.00 41.85 5.36
3209 3396 1.680338 AGTCACAAGTGAAAGGCCAC 58.320 50.000 5.01 0.00 41.85 5.01
3211 3398 2.438021 AGTCACAAGTGAAAGGCCACTA 59.562 45.455 5.01 0.00 45.82 2.74
3212 3399 3.118038 AGTCACAAGTGAAAGGCCACTAA 60.118 43.478 5.01 0.00 45.82 2.24
3213 3400 3.821033 GTCACAAGTGAAAGGCCACTAAT 59.179 43.478 5.01 0.00 45.82 1.73
3214 3401 5.001232 GTCACAAGTGAAAGGCCACTAATA 58.999 41.667 5.01 0.00 45.82 0.98
3215 3402 5.001232 TCACAAGTGAAAGGCCACTAATAC 58.999 41.667 5.01 0.00 45.82 1.89
3216 3403 5.003804 CACAAGTGAAAGGCCACTAATACT 58.996 41.667 5.01 0.00 45.82 2.12
3217 3404 5.122396 CACAAGTGAAAGGCCACTAATACTC 59.878 44.000 5.01 0.00 45.82 2.59
3287 3474 4.141801 TGCAGTACTGTAGTGTTTTCCTGT 60.142 41.667 23.44 0.00 0.00 4.00
3291 3478 7.186804 CAGTACTGTAGTGTTTTCCTGTTTTG 58.813 38.462 15.06 0.00 0.00 2.44
3488 3687 6.183360 CCCCTGTCTCTTATGACGAAAGATTA 60.183 42.308 0.00 0.00 39.64 1.75
3548 3747 4.418863 AGAAAGCCTAGTCCCTCTCTCTAT 59.581 45.833 0.00 0.00 0.00 1.98
3561 3760 9.705290 GTCCCTCTCTCTATATTTCATTTTCTC 57.295 37.037 0.00 0.00 0.00 2.87
3658 3857 4.546829 TCCTACCCAACACAATACAGAC 57.453 45.455 0.00 0.00 0.00 3.51
3692 3891 7.523293 TTTTCTGAACCATGCAAGAGAATTA 57.477 32.000 0.00 0.00 0.00 1.40
3731 3930 7.628234 AGATGAGGAAAATGAGTACATCACTT 58.372 34.615 0.00 0.00 41.91 3.16
3838 4037 6.474751 ACTTGTAGAAGTCAAACACTAACGAC 59.525 38.462 0.00 0.00 38.01 4.34
3892 4091 5.123227 ACATACTACCCCAACAATGAATCG 58.877 41.667 0.00 0.00 0.00 3.34
3896 4095 3.085952 ACCCCAACAATGAATCGTCAT 57.914 42.857 0.00 0.00 46.91 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 224 0.747255 TCCTCATCTCGTTGGCTAGC 59.253 55.000 6.04 6.04 0.00 3.42
830 832 2.670148 GGCCAATGGGAGAGACCGT 61.670 63.158 0.00 0.00 40.11 4.83
864 866 4.778143 GAATGGGACCCACGCGCT 62.778 66.667 17.78 0.00 35.80 5.92
883 885 1.390926 GTGAGGGGTACAGAGGGGA 59.609 63.158 0.00 0.00 0.00 4.81
985 988 3.368531 GCTATTTTGTCTCGGTCTCTGGT 60.369 47.826 0.00 0.00 0.00 4.00
1011 1014 3.264052 TGTCCATGGGTGGGGTGG 61.264 66.667 13.02 0.00 46.06 4.61
1339 1342 0.563173 CCCTCCTAGAGTCCCCATCA 59.437 60.000 0.00 0.00 0.00 3.07
1366 1369 3.647771 GTCACCACCTCCACCCCC 61.648 72.222 0.00 0.00 0.00 5.40
1423 1426 2.499205 GGATCGTCGCCATCCACA 59.501 61.111 7.84 0.00 39.88 4.17
1426 1429 1.374758 GATGGGATCGTCGCCATCC 60.375 63.158 15.63 10.67 37.82 3.51
1435 1438 2.609427 TCTTCTTGCTGATGGGATCG 57.391 50.000 0.00 0.00 0.00 3.69
1458 1461 7.675062 ACAAATTACAAAATTGGCATACCTCA 58.325 30.769 0.00 0.00 35.46 3.86
1477 1480 5.635280 CAGACGATATATCCTGCGACAAATT 59.365 40.000 7.15 0.00 0.00 1.82
1519 1524 5.469479 ACGGGCAAACAAGATAAATGAAAG 58.531 37.500 0.00 0.00 0.00 2.62
1524 1529 5.708230 TGTTCTACGGGCAAACAAGATAAAT 59.292 36.000 0.00 0.00 30.39 1.40
1548 1553 9.732130 GATCCTTAAGCTGGATGTAAATTCTAT 57.268 33.333 8.73 0.00 43.68 1.98
1579 1584 2.457366 ATGACAACGACCCTTCAGAC 57.543 50.000 0.00 0.00 0.00 3.51
1584 1589 4.285260 AGGTTAAGTATGACAACGACCCTT 59.715 41.667 0.00 0.00 0.00 3.95
1611 1622 8.815141 TTTTGTGCATTTTAGTAGTAGTACGA 57.185 30.769 2.04 0.00 33.97 3.43
1641 1652 8.959705 AAAGCTTAAGAGTTTGTTAGTACAGT 57.040 30.769 6.67 0.00 35.28 3.55
1642 1653 9.042008 TGAAAGCTTAAGAGTTTGTTAGTACAG 57.958 33.333 6.67 0.00 35.28 2.74
1643 1654 8.951787 TGAAAGCTTAAGAGTTTGTTAGTACA 57.048 30.769 6.67 0.00 0.00 2.90
1644 1655 9.257651 TCTGAAAGCTTAAGAGTTTGTTAGTAC 57.742 33.333 6.67 0.00 0.00 2.73
1645 1656 9.477484 CTCTGAAAGCTTAAGAGTTTGTTAGTA 57.523 33.333 22.44 0.00 34.09 1.82
1646 1657 8.204836 TCTCTGAAAGCTTAAGAGTTTGTTAGT 58.795 33.333 26.48 0.00 38.84 2.24
1647 1658 8.594881 TCTCTGAAAGCTTAAGAGTTTGTTAG 57.405 34.615 26.48 6.69 38.84 2.34
1676 1687 4.759516 AACATTCACCATACGGAACAAC 57.240 40.909 0.00 0.00 35.59 3.32
1677 1688 5.553123 AGTAACATTCACCATACGGAACAA 58.447 37.500 0.00 0.00 35.59 2.83
1703 1714 9.014297 CCTCATGTACTTAAAATTTCTTCCAGT 57.986 33.333 0.00 0.00 0.00 4.00
1704 1715 8.462016 CCCTCATGTACTTAAAATTTCTTCCAG 58.538 37.037 0.00 0.00 0.00 3.86
1744 1760 9.515020 CAACCGACAAGTTATGCAATTATATTT 57.485 29.630 0.00 0.00 0.00 1.40
1745 1761 8.898761 TCAACCGACAAGTTATGCAATTATATT 58.101 29.630 0.00 0.00 0.00 1.28
1746 1762 8.342634 GTCAACCGACAAGTTATGCAATTATAT 58.657 33.333 0.00 0.00 42.13 0.86
1799 1815 5.296780 ACCAAGAGATGTACAAAATATGGCG 59.703 40.000 16.01 0.00 0.00 5.69
1827 1968 4.858692 CAGCAAGACAAAATAACATTCCGG 59.141 41.667 0.00 0.00 0.00 5.14
1880 2022 5.350504 ACTGGATAGTTCTCATCTGGTTG 57.649 43.478 0.00 0.00 31.66 3.77
1958 2101 7.246171 ACTTGTAATAGGCTATACATCCCAG 57.754 40.000 7.59 8.91 0.00 4.45
1964 2107 8.746052 AAATGCAACTTGTAATAGGCTATACA 57.254 30.769 7.59 9.57 0.00 2.29
1974 2117 8.449251 AAATCACCAAAAATGCAACTTGTAAT 57.551 26.923 0.00 0.00 0.00 1.89
2079 2224 0.747255 TGCCTCGAGATACTTGCTCC 59.253 55.000 15.71 0.00 0.00 4.70
2299 2444 2.354510 TGCACTAGTTGTTTGTCAGCAC 59.645 45.455 0.00 0.00 0.00 4.40
2346 2491 0.311790 ATGAGCACAAGCCAACGTTG 59.688 50.000 21.47 21.47 43.56 4.10
2382 2527 7.917003 ACCCAAAAAGCTTAAATGGACATATT 58.083 30.769 20.77 0.00 32.82 1.28
2387 2532 6.092122 GCATAACCCAAAAAGCTTAAATGGAC 59.908 38.462 20.77 5.25 32.82 4.02
2424 2569 6.936900 CACCAAAGGAAACTAGATTTCTGAGA 59.063 38.462 0.00 0.00 45.32 3.27
2503 2649 0.718343 GTGAATGACGAGCTGTGAGC 59.282 55.000 0.00 0.00 42.84 4.26
2508 2654 4.039151 ACTCTATGTGAATGACGAGCTG 57.961 45.455 0.00 0.00 0.00 4.24
2510 2656 4.493220 GCAAACTCTATGTGAATGACGAGC 60.493 45.833 0.00 0.00 0.00 5.03
2511 2657 4.627035 TGCAAACTCTATGTGAATGACGAG 59.373 41.667 0.00 0.00 0.00 4.18
2512 2658 4.565022 TGCAAACTCTATGTGAATGACGA 58.435 39.130 0.00 0.00 0.00 4.20
2513 2659 4.926860 TGCAAACTCTATGTGAATGACG 57.073 40.909 0.00 0.00 0.00 4.35
2514 2660 6.426980 TCATGCAAACTCTATGTGAATGAC 57.573 37.500 0.00 0.00 0.00 3.06
2515 2661 7.451501 TTTCATGCAAACTCTATGTGAATGA 57.548 32.000 0.00 0.00 0.00 2.57
2516 2662 8.115491 CATTTCATGCAAACTCTATGTGAATG 57.885 34.615 0.00 0.00 0.00 2.67
2543 2690 1.291132 GCGAGCAAGTAATCCAGGTC 58.709 55.000 0.00 0.00 0.00 3.85
3016 3164 3.181467 CCAGAGAGATAGACAAAGCCAGG 60.181 52.174 0.00 0.00 0.00 4.45
3022 3170 7.496346 ACATAAACCCAGAGAGATAGACAAA 57.504 36.000 0.00 0.00 0.00 2.83
3064 3251 2.996249 TTCTGGCATTGGCAAACAAA 57.004 40.000 14.35 4.03 43.46 2.83
3065 3252 2.367894 TCATTCTGGCATTGGCAAACAA 59.632 40.909 14.35 7.70 44.54 2.83
3066 3253 1.969208 TCATTCTGGCATTGGCAAACA 59.031 42.857 14.35 3.17 43.71 2.83
3067 3254 2.340337 GTCATTCTGGCATTGGCAAAC 58.660 47.619 14.35 0.00 43.71 2.93
3150 3337 8.205512 TGTAATTTTGACAACTACACTGGAGTA 58.794 33.333 0.00 0.00 0.00 2.59
3151 3338 7.051623 TGTAATTTTGACAACTACACTGGAGT 58.948 34.615 0.00 0.00 0.00 3.85
3154 3341 7.259290 ACTGTAATTTTGACAACTACACTGG 57.741 36.000 0.00 0.00 0.00 4.00
3155 3342 9.646336 GTTACTGTAATTTTGACAACTACACTG 57.354 33.333 3.23 0.00 0.00 3.66
3156 3343 8.545420 CGTTACTGTAATTTTGACAACTACACT 58.455 33.333 3.23 0.00 0.00 3.55
3157 3344 7.795272 CCGTTACTGTAATTTTGACAACTACAC 59.205 37.037 3.23 0.00 0.00 2.90
3158 3345 7.041916 CCCGTTACTGTAATTTTGACAACTACA 60.042 37.037 3.23 0.00 0.00 2.74
3159 3346 7.293018 CCCGTTACTGTAATTTTGACAACTAC 58.707 38.462 3.23 0.00 0.00 2.73
3160 3347 6.427547 CCCCGTTACTGTAATTTTGACAACTA 59.572 38.462 3.23 0.00 0.00 2.24
3161 3348 5.239963 CCCCGTTACTGTAATTTTGACAACT 59.760 40.000 3.23 0.00 0.00 3.16
3162 3349 5.008911 ACCCCGTTACTGTAATTTTGACAAC 59.991 40.000 3.23 0.00 0.00 3.32
3163 3350 5.131784 ACCCCGTTACTGTAATTTTGACAA 58.868 37.500 3.23 0.00 0.00 3.18
3164 3351 4.716794 ACCCCGTTACTGTAATTTTGACA 58.283 39.130 3.23 0.00 0.00 3.58
3165 3352 5.239087 TCAACCCCGTTACTGTAATTTTGAC 59.761 40.000 3.23 0.00 0.00 3.18
3166 3353 5.374921 TCAACCCCGTTACTGTAATTTTGA 58.625 37.500 3.23 6.02 0.00 2.69
3167 3354 5.692613 TCAACCCCGTTACTGTAATTTTG 57.307 39.130 3.23 4.06 0.00 2.44
3168 3355 5.829391 ACTTCAACCCCGTTACTGTAATTTT 59.171 36.000 3.23 0.00 0.00 1.82
3169 3356 5.379187 ACTTCAACCCCGTTACTGTAATTT 58.621 37.500 3.23 0.00 0.00 1.82
3170 3357 4.976864 ACTTCAACCCCGTTACTGTAATT 58.023 39.130 3.23 0.00 0.00 1.40
3171 3358 4.040706 TGACTTCAACCCCGTTACTGTAAT 59.959 41.667 3.23 0.00 0.00 1.89
3172 3359 3.387374 TGACTTCAACCCCGTTACTGTAA 59.613 43.478 0.00 0.00 0.00 2.41
3173 3360 2.964464 TGACTTCAACCCCGTTACTGTA 59.036 45.455 0.00 0.00 0.00 2.74
3174 3361 1.764134 TGACTTCAACCCCGTTACTGT 59.236 47.619 0.00 0.00 0.00 3.55
3175 3362 2.140717 GTGACTTCAACCCCGTTACTG 58.859 52.381 0.00 0.00 0.00 2.74
3176 3363 1.764134 TGTGACTTCAACCCCGTTACT 59.236 47.619 0.00 0.00 0.00 2.24
3177 3364 2.243602 TGTGACTTCAACCCCGTTAC 57.756 50.000 0.00 0.00 0.00 2.50
3178 3365 2.171027 ACTTGTGACTTCAACCCCGTTA 59.829 45.455 0.00 0.00 0.00 3.18
3179 3366 1.064979 ACTTGTGACTTCAACCCCGTT 60.065 47.619 0.00 0.00 0.00 4.44
3180 3367 0.544697 ACTTGTGACTTCAACCCCGT 59.455 50.000 0.00 0.00 0.00 5.28
3181 3368 0.944386 CACTTGTGACTTCAACCCCG 59.056 55.000 0.00 0.00 0.00 5.73
3182 3369 2.341846 TCACTTGTGACTTCAACCCC 57.658 50.000 0.00 0.00 0.00 4.95
3183 3370 3.066760 CCTTTCACTTGTGACTTCAACCC 59.933 47.826 2.62 0.00 0.00 4.11
3184 3371 3.489229 GCCTTTCACTTGTGACTTCAACC 60.489 47.826 2.62 0.00 0.00 3.77
3185 3372 3.489229 GGCCTTTCACTTGTGACTTCAAC 60.489 47.826 2.62 0.00 0.00 3.18
3186 3373 2.687935 GGCCTTTCACTTGTGACTTCAA 59.312 45.455 2.62 0.00 0.00 2.69
3187 3374 2.297701 GGCCTTTCACTTGTGACTTCA 58.702 47.619 2.62 0.00 0.00 3.02
3188 3375 2.033424 GTGGCCTTTCACTTGTGACTTC 59.967 50.000 3.32 0.00 34.98 3.01
3189 3376 2.024414 GTGGCCTTTCACTTGTGACTT 58.976 47.619 3.32 0.00 34.98 3.01
3190 3377 1.212935 AGTGGCCTTTCACTTGTGACT 59.787 47.619 3.32 0.00 44.74 3.41
3191 3378 1.680338 AGTGGCCTTTCACTTGTGAC 58.320 50.000 3.32 0.00 44.74 3.67
3192 3379 3.569194 TTAGTGGCCTTTCACTTGTGA 57.431 42.857 3.32 0.00 44.74 3.58
3193 3380 5.003804 AGTATTAGTGGCCTTTCACTTGTG 58.996 41.667 3.32 0.00 44.74 3.33
3194 3381 5.242795 AGTATTAGTGGCCTTTCACTTGT 57.757 39.130 3.32 0.00 44.74 3.16
3195 3382 4.636206 GGAGTATTAGTGGCCTTTCACTTG 59.364 45.833 3.32 0.00 44.74 3.16
3196 3383 4.288626 TGGAGTATTAGTGGCCTTTCACTT 59.711 41.667 3.32 0.00 44.74 3.16
3198 3385 4.192317 CTGGAGTATTAGTGGCCTTTCAC 58.808 47.826 3.32 0.00 37.89 3.18
3199 3386 3.844211 ACTGGAGTATTAGTGGCCTTTCA 59.156 43.478 3.32 0.00 0.00 2.69
3200 3387 4.192317 CACTGGAGTATTAGTGGCCTTTC 58.808 47.826 3.32 0.00 40.38 2.62
3201 3388 3.587506 ACACTGGAGTATTAGTGGCCTTT 59.412 43.478 3.32 0.00 46.52 3.11
3202 3389 3.182152 ACACTGGAGTATTAGTGGCCTT 58.818 45.455 3.32 0.00 46.52 4.35
3203 3390 2.834113 ACACTGGAGTATTAGTGGCCT 58.166 47.619 3.32 0.00 46.52 5.19
3204 3391 3.705072 ACTACACTGGAGTATTAGTGGCC 59.295 47.826 0.00 0.00 46.52 5.36
3205 3392 5.109903 CAACTACACTGGAGTATTAGTGGC 58.890 45.833 8.95 0.00 46.52 5.01
3206 3393 6.071560 TGACAACTACACTGGAGTATTAGTGG 60.072 42.308 8.95 0.00 46.52 4.00
3208 3395 7.534723 TTGACAACTACACTGGAGTATTAGT 57.465 36.000 0.00 0.00 31.22 2.24
3209 3396 8.827177 TTTTGACAACTACACTGGAGTATTAG 57.173 34.615 0.00 0.00 0.00 1.73
3210 3397 9.787435 AATTTTGACAACTACACTGGAGTATTA 57.213 29.630 0.00 0.00 0.00 0.98
3211 3398 8.691661 AATTTTGACAACTACACTGGAGTATT 57.308 30.769 0.00 0.00 0.00 1.89
3212 3399 9.216117 GTAATTTTGACAACTACACTGGAGTAT 57.784 33.333 0.00 0.00 0.00 2.12
3213 3400 8.205512 TGTAATTTTGACAACTACACTGGAGTA 58.794 33.333 0.00 0.00 0.00 2.59
3214 3401 7.051623 TGTAATTTTGACAACTACACTGGAGT 58.948 34.615 0.00 0.00 0.00 3.85
3215 3402 7.226720 ACTGTAATTTTGACAACTACACTGGAG 59.773 37.037 0.00 0.00 0.00 3.86
3216 3403 7.051623 ACTGTAATTTTGACAACTACACTGGA 58.948 34.615 0.00 0.00 0.00 3.86
3217 3404 7.259290 ACTGTAATTTTGACAACTACACTGG 57.741 36.000 0.00 0.00 0.00 4.00
3369 3565 4.215613 GGTTGGAACTGGTGATCAACTAAC 59.784 45.833 12.94 7.47 38.13 2.34
3372 3568 2.443255 AGGTTGGAACTGGTGATCAACT 59.557 45.455 12.94 0.00 38.13 3.16
3488 3687 4.322198 GCAAACAAATCAGTCCATCCACAT 60.322 41.667 0.00 0.00 0.00 3.21
3561 3760 8.773645 TCGTGTGCATAAATAGAAGATAAATGG 58.226 33.333 0.00 0.00 0.00 3.16
3692 3891 9.832445 ATTTTCCTCATCTAATATAACACGTGT 57.168 29.630 17.22 17.22 0.00 4.49
3731 3930 6.292381 CGTTTTCTGTTTTGTTGGTTGTGAAA 60.292 34.615 0.00 0.00 0.00 2.69
3817 4016 5.207768 TCGTCGTTAGTGTTTGACTTCTAC 58.792 41.667 0.00 0.00 35.96 2.59
3820 4019 5.571778 ATTCGTCGTTAGTGTTTGACTTC 57.428 39.130 0.00 0.00 35.96 3.01


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

AutoCloner maintained by Alex Coulton.