Multiple sequence alignment - TraesCS4B01G074500

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 TraesCS4B01G074500 chr4B 100.000 3389 0 0 1 3389 70057994 70054606 0.000000e+00 6259.0
1 TraesCS4B01G074500 chr4B 88.235 85 8 2 392 476 617384386 617384468 2.150000e-17 100.0
2 TraesCS4B01G074500 chr4B 88.235 85 8 2 392 476 648518011 648517929 2.150000e-17 100.0
3 TraesCS4B01G074500 chr4D 92.933 2434 108 29 8 2389 47749077 47746656 0.000000e+00 3483.0
4 TraesCS4B01G074500 chr4D 94.037 218 8 2 2461 2674 47746639 47746423 3.260000e-85 326.0
5 TraesCS4B01G074500 chr4D 87.132 272 34 1 3119 3389 47745176 47744905 1.180000e-79 307.0
6 TraesCS4B01G074500 chr4A 94.481 1830 85 7 585 2405 549922278 549924100 0.000000e+00 2806.0
7 TraesCS4B01G074500 chr4A 84.790 572 40 13 1 532 549921705 549922269 6.440000e-147 531.0
8 TraesCS4B01G074500 chr4A 93.197 294 15 3 2457 2749 549924096 549924385 8.690000e-116 427.0
9 TraesCS4B01G074500 chr4A 88.148 270 32 0 3120 3389 549925210 549925479 4.220000e-84 322.0
10 TraesCS4B01G074500 chr4A 95.556 45 2 0 474 518 689629100 689629144 4.690000e-09 73.1
11 TraesCS4B01G074500 chr5D 88.211 246 28 1 3119 3364 410848253 410848497 3.310000e-75 292.0
12 TraesCS4B01G074500 chr3B 84.553 246 37 1 3119 3364 630369201 630368957 3.380000e-60 243.0
13 TraesCS4B01G074500 chr1B 85.398 226 30 1 3139 3364 311424872 311424650 7.310000e-57 231.0
14 TraesCS4B01G074500 chr1B 83.607 244 36 1 3119 3362 328644628 328644867 3.400000e-55 226.0
15 TraesCS4B01G074500 chr3D 85.068 221 33 0 3144 3364 384438160 384438380 3.400000e-55 226.0
16 TraesCS4B01G074500 chr3D 83.471 121 15 5 402 518 397109300 397109181 1.290000e-19 108.0
17 TraesCS4B01G074500 chr6B 83.200 250 35 5 3119 3364 164612985 164612739 4.400000e-54 222.0
18 TraesCS4B01G074500 chr7B 83.761 234 36 2 3132 3364 716372660 716372428 1.580000e-53 220.0
19 TraesCS4B01G074500 chr6D 89.189 111 12 0 2895 3005 7165136 7165246 4.560000e-29 139.0
20 TraesCS4B01G074500 chr6A 79.235 183 23 8 2895 3063 6827705 6827886 2.760000e-21 113.0
21 TraesCS4B01G074500 chr5A 89.412 85 7 2 392 476 67524884 67524966 4.620000e-19 106.0
22 TraesCS4B01G074500 chr5A 86.813 91 10 2 392 482 60443885 60443797 2.150000e-17 100.0
23 TraesCS4B01G074500 chr3A 86.813 91 10 2 392 482 589603107 589603019 2.150000e-17 100.0
24 TraesCS4B01G074500 chr3A 86.813 91 10 2 392 482 589604306 589604218 2.150000e-17 100.0
25 TraesCS4B01G074500 chr3A 81.651 109 14 5 277 384 567569235 567569132 6.030000e-13 86.1
26 TraesCS4B01G074500 chr2A 88.235 85 8 2 392 476 139921898 139921980 2.150000e-17 100.0
27 TraesCS4B01G074500 chr2A 97.500 40 1 0 277 316 61819948 61819909 6.070000e-08 69.4
28 TraesCS4B01G074500 chr5B 80.734 109 15 6 277 384 544776835 544776732 2.800000e-11 80.5
29 TraesCS4B01G074500 chr5B 80.556 108 17 4 277 384 544795655 544795552 2.800000e-11 80.5
30 TraesCS4B01G074500 chr7A 97.778 45 1 0 474 518 35361718 35361762 1.010000e-10 78.7
31 TraesCS4B01G074500 chr7A 88.000 50 6 0 278 327 507138182 507138133 3.650000e-05 60.2
32 TraesCS4B01G074500 chr7D 95.122 41 2 0 2739 2779 123492622 123492582 7.850000e-07 65.8
33 TraesCS4B01G074500 chrUn 82.857 70 8 3 277 346 34358847 34358782 3.650000e-05 60.2
34 TraesCS4B01G074500 chrUn 82.857 70 8 3 277 346 269479965 269480030 3.650000e-05 60.2


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 TraesCS4B01G074500 chr4B 70054606 70057994 3388 True 6259.0 6259 100.000000 1 3389 1 chr4B.!!$R1 3388
1 TraesCS4B01G074500 chr4D 47744905 47749077 4172 True 1372.0 3483 91.367333 8 3389 3 chr4D.!!$R1 3381
2 TraesCS4B01G074500 chr4A 549921705 549925479 3774 False 1021.5 2806 90.154000 1 3389 4 chr4A.!!$F2 3388

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
372 381 0.036732 AGCCTTTCCTGCGATGTTCA 59.963 50.0 0.00 0.0 0.00 3.18 F
991 1050 0.038251 CGAGCACACCAGCTAGTTGA 60.038 55.0 8.34 0.0 46.75 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2184 0.252479 CACAGCTCCATGGAAGCTCT 59.748 55.0 26.37 17.4 36.69 4.09 R
2786 3050 0.179018 GGGAGGTTGCGGCATAGATT 60.179 55.0 2.28 0.0 0.00 2.40 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
46 47 6.792326 AGTTAAACTAGTGTCCAAAGTTTGC 58.208 36.000 10.25 0.00 42.01 3.68
92 93 1.454201 CGGAGCAGAGAGAGTACACA 58.546 55.000 0.00 0.00 0.00 3.72
105 106 9.614792 AGAGAGAGTACACACTTTTTATTTTGT 57.385 29.630 0.00 0.00 34.21 2.83
128 137 3.697542 GAGGGAGAAGAAGAGTACACTCC 59.302 52.174 5.76 0.00 43.88 3.85
130 139 3.445805 GGGAGAAGAAGAGTACACTCCAG 59.554 52.174 0.00 0.00 43.88 3.86
157 166 4.556699 GCTAGTGTTGTTGGTTGGACAATC 60.557 45.833 0.00 0.00 39.03 2.67
158 167 3.360867 AGTGTTGTTGGTTGGACAATCA 58.639 40.909 0.00 0.00 39.03 2.57
166 175 5.175127 GTTGGTTGGACAATCAGTTTTTGT 58.825 37.500 0.00 0.00 39.91 2.83
214 223 5.278561 CCCGTTTGACCAACTAATTTTAGCA 60.279 40.000 0.00 0.00 34.09 3.49
317 326 3.336138 GGTTCAAGACCTAGACTTGGG 57.664 52.381 20.88 0.60 45.55 4.12
320 329 2.537143 TCAAGACCTAGACTTGGGACC 58.463 52.381 20.88 0.00 43.11 4.46
322 331 0.702902 AGACCTAGACTTGGGACCGA 59.297 55.000 7.88 0.00 0.00 4.69
330 339 2.745884 TTGGGACCGATGCTTGCG 60.746 61.111 0.00 0.00 0.00 4.85
333 342 1.448893 GGGACCGATGCTTGCGTTA 60.449 57.895 0.00 0.00 0.00 3.18
334 343 0.814010 GGGACCGATGCTTGCGTTAT 60.814 55.000 0.00 0.00 0.00 1.89
335 344 1.014352 GGACCGATGCTTGCGTTATT 58.986 50.000 0.00 0.00 0.00 1.40
336 345 1.400494 GGACCGATGCTTGCGTTATTT 59.600 47.619 0.00 0.00 0.00 1.40
372 381 0.036732 AGCCTTTCCTGCGATGTTCA 59.963 50.000 0.00 0.00 0.00 3.18
377 386 3.191162 CCTTTCCTGCGATGTTCATTCAA 59.809 43.478 0.00 0.00 0.00 2.69
379 388 5.066375 CCTTTCCTGCGATGTTCATTCAATA 59.934 40.000 0.00 0.00 0.00 1.90
387 403 5.605534 CGATGTTCATTCAATAGGAGACCT 58.394 41.667 0.00 0.00 37.71 3.85
449 485 0.471617 CTTGGAGGTGCTCATAGGGG 59.528 60.000 0.00 0.00 31.08 4.79
453 489 1.343069 GAGGTGCTCATAGGGGTAGG 58.657 60.000 0.00 0.00 0.00 3.18
533 585 3.710326 AAAAACTCCTCGCAAAAGGTC 57.290 42.857 0.00 0.00 37.69 3.85
535 587 1.884235 AACTCCTCGCAAAAGGTCAG 58.116 50.000 0.00 0.00 37.69 3.51
541 593 4.647611 TCCTCGCAAAAGGTCAGAAAATA 58.352 39.130 0.00 0.00 37.69 1.40
542 594 4.454504 TCCTCGCAAAAGGTCAGAAAATAC 59.545 41.667 0.00 0.00 37.69 1.89
663 716 5.963586 CGAAGAACAAGGACTTAAACACAAC 59.036 40.000 0.00 0.00 0.00 3.32
699 752 3.756117 AGGAGCGAAAAGGAAACTGAAT 58.244 40.909 0.00 0.00 42.68 2.57
709 762 6.581171 AAAGGAAACTGAATCATCACTTCC 57.419 37.500 6.76 6.76 42.68 3.46
775 828 4.785453 CGCCTCAACTGCCCCTCC 62.785 72.222 0.00 0.00 0.00 4.30
791 844 0.331616 CTCCCCGTCCCTTTCCAATT 59.668 55.000 0.00 0.00 0.00 2.32
982 1041 3.279116 GCAAGCACGAGCACACCA 61.279 61.111 7.77 0.00 45.49 4.17
983 1042 2.941333 CAAGCACGAGCACACCAG 59.059 61.111 7.77 0.00 45.49 4.00
984 1043 2.974698 AAGCACGAGCACACCAGC 60.975 61.111 7.77 0.00 45.49 4.85
986 1045 2.048222 GCACGAGCACACCAGCTA 60.048 61.111 0.00 0.00 46.75 3.32
987 1046 2.097038 GCACGAGCACACCAGCTAG 61.097 63.158 0.00 0.00 46.75 3.42
988 1047 3.778955 ACGAGCACACCAGCTAGT 58.221 55.556 0.00 0.00 46.75 2.57
989 1048 0.319900 CACGAGCACACCAGCTAGTT 60.320 55.000 0.00 0.00 46.17 2.24
990 1049 0.319900 ACGAGCACACCAGCTAGTTG 60.320 55.000 0.00 0.00 46.17 3.16
991 1050 0.038251 CGAGCACACCAGCTAGTTGA 60.038 55.000 8.34 0.00 46.75 3.18
1031 1094 0.458025 CTCCCGGTGTCTAACGCTTC 60.458 60.000 0.00 0.00 0.00 3.86
1037 1100 0.391263 GTGTCTAACGCTTCCCCAGG 60.391 60.000 0.00 0.00 0.00 4.45
1053 1116 3.244700 CCCCAGGTGGAATCTATGCTAAG 60.245 52.174 0.00 0.00 37.39 2.18
1140 1203 4.436998 CCGCCTTCGACCTTCGCT 62.437 66.667 0.00 0.00 40.21 4.93
1341 1404 2.490217 CTCCGTGCCGAGATCGTT 59.510 61.111 1.09 0.00 37.74 3.85
1381 1444 2.017783 GCGACGTACAAGGCGTTCA 61.018 57.895 0.00 0.00 43.04 3.18
1398 1461 3.823330 AACCTAGACGCCGGCTCG 61.823 66.667 26.68 12.89 0.00 5.03
1500 1563 2.169146 GTACATTTACGCCGCGCCT 61.169 57.895 13.88 0.00 0.00 5.52
1569 1635 3.696676 TACGTGGCGGTGGCATCA 61.697 61.111 0.00 0.00 40.92 3.07
1575 1641 2.202932 GCGGTGGCATCAGACGAT 60.203 61.111 0.00 0.00 39.62 3.73
1627 1693 3.384532 TGTCCTTCCGGGGTACGC 61.385 66.667 0.00 0.29 42.52 4.42
1926 1992 2.290122 CTGAGCTCGGCCTGAATCGT 62.290 60.000 10.21 0.00 0.00 3.73
2031 2097 1.122019 ACGAGCTGGGAGTGAAGGTT 61.122 55.000 0.00 0.00 0.00 3.50
2037 2103 1.277557 CTGGGAGTGAAGGTTCTGAGG 59.722 57.143 0.00 0.00 0.00 3.86
2073 2139 0.813184 ATCCAATCACAAAGCTGCCG 59.187 50.000 0.00 0.00 0.00 5.69
2118 2184 2.062636 AGAGTTTTGGGAGGCAGGTTA 58.937 47.619 0.00 0.00 0.00 2.85
2148 2214 0.674581 GGAGCTGTGCATGCTACACA 60.675 55.000 20.33 13.93 45.42 3.72
2151 2217 0.110056 GCTGTGCATGCTACACACAC 60.110 55.000 20.33 7.20 42.88 3.82
2285 2351 4.990910 AGGGGTGGAGCTGGCAGT 62.991 66.667 17.16 2.59 0.00 4.40
2313 2379 3.753294 AGGAAATTCGATCTACGGCAT 57.247 42.857 0.00 0.00 42.82 4.40
2320 2386 7.170320 GGAAATTCGATCTACGGCATAGTTTTA 59.830 37.037 0.00 0.00 42.82 1.52
2363 2429 3.411446 TGACTGCCATTCAAGTTAGTGG 58.589 45.455 0.00 0.00 34.84 4.00
2370 2436 4.331968 CCATTCAAGTTAGTGGCTTGGTA 58.668 43.478 5.39 0.00 42.44 3.25
2573 2643 6.005583 ACACAATGAAGAGTGCAAATACAG 57.994 37.500 0.00 0.00 39.30 2.74
2597 2667 9.360093 CAGGTTAACTAGAAATACAAGAGACTG 57.640 37.037 5.42 0.00 0.00 3.51
2725 2989 6.420903 TCATAGTGCGACTTATTGATTAGTGC 59.579 38.462 0.00 0.00 0.00 4.40
2754 3018 0.034960 TGTGACCCTCTCTCCTCTCG 60.035 60.000 0.00 0.00 0.00 4.04
2798 3062 1.526686 CCTGCCAATCTATGCCGCA 60.527 57.895 0.00 0.00 0.00 5.69
2812 3077 2.685380 CGCAACCTCCCTCCTCCT 60.685 66.667 0.00 0.00 0.00 3.69
2817 3082 1.465189 AACCTCCCTCCTCCTCCCTT 61.465 60.000 0.00 0.00 0.00 3.95
2832 3101 2.033757 CTTGCTGCTGCCAGAGGT 59.966 61.111 13.47 0.00 41.77 3.85
2838 3107 2.194388 CTGCTGCCAGAGGTCATGGT 62.194 60.000 0.00 0.00 41.77 3.55
2844 3113 3.461773 AGAGGTCATGGTCGGGCG 61.462 66.667 0.00 0.00 0.00 6.13
2895 3211 4.452733 GGGTCAGGGCGAGGAACG 62.453 72.222 0.00 0.00 45.66 3.95
2929 3246 4.694233 CTGCTGCTGCACGAGGGT 62.694 66.667 14.93 0.00 45.31 4.34
3036 3353 1.725803 ACTACTCCCTTTTCGGTGGT 58.274 50.000 0.00 0.00 0.00 4.16
3042 3359 0.399075 CCCTTTTCGGTGGTAGTGGT 59.601 55.000 0.00 0.00 0.00 4.16
3048 3365 0.178955 TCGGTGGTAGTGGTTGAGGA 60.179 55.000 0.00 0.00 0.00 3.71
3063 3380 4.083862 GGACGGTGGTGGAGCTCC 62.084 72.222 26.78 26.78 0.00 4.70
3117 3434 3.448194 CGGCAGATCGGATCTCCA 58.552 61.111 17.41 0.00 37.58 3.86
3147 4037 0.318107 ACATGCTGAACAGTTTGCGC 60.318 50.000 0.00 0.00 0.00 6.09
3177 4067 4.676951 CCCCATTGTGCCCCGTGT 62.677 66.667 0.00 0.00 0.00 4.49
3178 4068 2.600173 CCCATTGTGCCCCGTGTT 60.600 61.111 0.00 0.00 0.00 3.32
3188 4078 4.953868 CCCGTGTTGGCGTCGACA 62.954 66.667 17.16 5.84 35.05 4.35
3194 4084 2.915659 TTGGCGTCGACAGAGGGT 60.916 61.111 17.16 0.00 33.21 4.34
3203 4093 3.573626 GACAGAGGGTCGGACTAGT 57.426 57.895 8.23 0.00 36.65 2.57
3224 4114 3.399440 AAGGATGATGCGGATCTCTTC 57.601 47.619 18.23 11.52 0.00 2.87
3247 4138 0.036388 GAAGATGGGTCAGCGGTTCA 60.036 55.000 0.00 0.00 0.00 3.18
3260 4151 1.298602 CGGTTCAATGATGATGGCGA 58.701 50.000 0.00 0.00 34.96 5.54
3294 4185 2.224549 GTGCATGTGGTGTACGCTTTAA 59.775 45.455 6.35 0.00 33.74 1.52
3306 4197 1.269051 ACGCTTTAAGTTTGCTGCACC 60.269 47.619 0.00 0.00 0.00 5.01
3307 4198 1.268999 CGCTTTAAGTTTGCTGCACCA 60.269 47.619 0.00 0.00 0.00 4.17
3308 4199 2.797792 CGCTTTAAGTTTGCTGCACCAA 60.798 45.455 0.00 0.00 0.00 3.67
3311 4202 4.499019 GCTTTAAGTTTGCTGCACCAACTA 60.499 41.667 17.35 3.53 0.00 2.24
3324 4215 3.305881 GCACCAACTATAGGTCCCGATAC 60.306 52.174 4.43 0.00 37.23 2.24
3366 4257 4.497006 CGACGACACCGGTTTTAGATAGAT 60.497 45.833 2.97 0.00 40.78 1.98
3374 4265 5.602978 ACCGGTTTTAGATAGATCACTCCAT 59.397 40.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 8.533569 TTCTTCTCCCTCACAAAATAAAAAGT 57.466 30.769 0.00 0.00 0.00 2.66
105 106 4.337145 GAGTGTACTCTTCTTCTCCCTCA 58.663 47.826 4.81 0.00 39.81 3.86
128 137 1.949525 ACCAACAACACTAGCTTGCTG 59.050 47.619 5.26 0.00 0.00 4.41
130 139 2.543653 CCAACCAACAACACTAGCTTGC 60.544 50.000 0.00 0.00 0.00 4.01
157 166 7.704472 TGTAATGCCAACTAGAAACAAAAACTG 59.296 33.333 0.00 0.00 0.00 3.16
158 167 7.777095 TGTAATGCCAACTAGAAACAAAAACT 58.223 30.769 0.00 0.00 0.00 2.66
317 326 2.825086 AAATAACGCAAGCATCGGTC 57.175 45.000 0.00 0.00 45.62 4.79
335 344 9.719355 GGAAAGGCTAAAATAAATCCAGAAAAA 57.281 29.630 0.00 0.00 0.00 1.94
336 345 9.100197 AGGAAAGGCTAAAATAAATCCAGAAAA 57.900 29.630 0.00 0.00 0.00 2.29
340 349 6.276091 GCAGGAAAGGCTAAAATAAATCCAG 58.724 40.000 0.00 0.00 0.00 3.86
372 381 4.282496 AGTCGACAGGTCTCCTATTGAAT 58.718 43.478 19.50 0.00 29.64 2.57
377 386 2.485124 CCGTAGTCGACAGGTCTCCTAT 60.485 54.545 19.50 0.00 39.71 2.57
379 388 0.392729 CCGTAGTCGACAGGTCTCCT 60.393 60.000 19.50 0.00 39.71 3.69
387 403 2.429478 TGAGATTGACCGTAGTCGACA 58.571 47.619 19.50 0.48 46.74 4.35
449 485 2.046314 ATGCACGCACACCCCTAC 60.046 61.111 0.00 0.00 0.00 3.18
453 489 3.285523 AATGCATGCACGCACACCC 62.286 57.895 25.37 0.00 46.56 4.61
469 505 6.533012 GCAGACGCTCATACATACATATGAAT 59.467 38.462 10.38 0.00 40.28 2.57
476 512 1.404035 ACGCAGACGCTCATACATACA 59.596 47.619 0.00 0.00 45.53 2.29
517 569 1.048601 TCTGACCTTTTGCGAGGAGT 58.951 50.000 7.51 0.00 39.25 3.85
533 585 4.928661 ACGCTGCACTTAGTATTTTCTG 57.071 40.909 0.00 0.00 0.00 3.02
535 587 5.086727 GGAAACGCTGCACTTAGTATTTTC 58.913 41.667 0.00 0.00 0.00 2.29
541 593 2.256117 AAGGAAACGCTGCACTTAGT 57.744 45.000 0.00 0.00 0.00 2.24
542 594 4.742438 TTTAAGGAAACGCTGCACTTAG 57.258 40.909 0.00 0.00 0.00 2.18
579 632 6.483307 CGACCTTAATCATTTGAAGGATGCTA 59.517 38.462 6.01 0.00 42.05 3.49
581 634 5.506317 CCGACCTTAATCATTTGAAGGATGC 60.506 44.000 6.01 0.00 42.05 3.91
663 716 1.003355 TCCTTCTTTGCTCGCCCTG 60.003 57.895 0.00 0.00 0.00 4.45
699 752 1.003839 GTGGGCGTGGAAGTGATGA 60.004 57.895 0.00 0.00 0.00 2.92
709 762 2.202797 CTGGATCGAGTGGGCGTG 60.203 66.667 0.00 0.00 0.00 5.34
775 828 1.389555 GCTAATTGGAAAGGGACGGG 58.610 55.000 0.00 0.00 0.00 5.28
791 844 2.126618 CGCGAGACGTGTTGGCTA 60.127 61.111 0.00 0.00 36.87 3.93
828 881 2.682876 GGGAAAAATGACGCGGCGA 61.683 57.895 30.94 8.00 0.00 5.54
983 1042 4.139302 GCCATTGCTGAGCTCAACTAGC 62.139 54.545 18.85 17.52 42.60 3.42
984 1043 1.669779 GCCATTGCTGAGCTCAACTAG 59.330 52.381 18.85 7.12 33.53 2.57
985 1044 1.742761 GCCATTGCTGAGCTCAACTA 58.257 50.000 18.85 10.93 33.53 2.24
986 1045 1.303799 CGCCATTGCTGAGCTCAACT 61.304 55.000 18.85 0.00 34.43 3.16
987 1046 1.136147 CGCCATTGCTGAGCTCAAC 59.864 57.895 18.85 14.43 34.43 3.18
988 1047 0.393402 ATCGCCATTGCTGAGCTCAA 60.393 50.000 18.85 3.02 34.43 3.02
989 1048 0.393402 AATCGCCATTGCTGAGCTCA 60.393 50.000 17.19 17.19 34.43 4.26
990 1049 0.307146 GAATCGCCATTGCTGAGCTC 59.693 55.000 6.82 6.82 34.43 4.09
991 1050 1.434622 CGAATCGCCATTGCTGAGCT 61.435 55.000 5.83 0.00 34.43 4.09
1031 1094 1.143813 AGCATAGATTCCACCTGGGG 58.856 55.000 0.00 0.00 37.22 4.96
1037 1100 1.801178 GCGGCTTAGCATAGATTCCAC 59.199 52.381 6.53 0.00 37.05 4.02
1155 1218 2.415608 GGTCGATGGTGCCGAGAGA 61.416 63.158 0.00 0.00 36.66 3.10
1329 1392 1.063649 GTAGCGAACGATCTCGGCA 59.936 57.895 6.51 0.00 44.95 5.69
1381 1444 3.823330 CGAGCCGGCGTCTAGGTT 61.823 66.667 23.20 0.00 0.00 3.50
1398 1461 3.251571 CTTACAGTTGAGGTACCGCTTC 58.748 50.000 17.09 9.46 0.00 3.86
1500 1563 3.062466 CCAGGGAGCGAGACGTCA 61.062 66.667 19.50 0.00 0.00 4.35
1627 1693 0.833834 ACCCACTCAGACCCTGTCAG 60.834 60.000 0.00 0.00 34.60 3.51
1809 1875 5.625311 GTGCTTATATTGTTTAATGAGCCGC 59.375 40.000 0.00 0.00 32.12 6.53
1926 1992 2.534396 ATGGTTGCCCCTTCCGTCA 61.534 57.895 0.00 0.00 0.00 4.35
2022 2088 1.059913 CCACCCTCAGAACCTTCACT 58.940 55.000 0.00 0.00 0.00 3.41
2031 2097 0.757561 TCACGTTCACCACCCTCAGA 60.758 55.000 0.00 0.00 0.00 3.27
2037 2103 0.788391 GATCGTTCACGTTCACCACC 59.212 55.000 5.70 0.00 40.80 4.61
2073 2139 5.593502 AGATTTCTCATTGAAGAAGATGCCC 59.406 40.000 0.00 0.00 36.66 5.36
2118 2184 0.252479 CACAGCTCCATGGAAGCTCT 59.748 55.000 26.37 17.40 36.69 4.09
2148 2214 1.301716 AAGCTCAACGCCGATGTGT 60.302 52.632 0.00 0.00 40.39 3.72
2151 2217 2.099062 GCAAGCTCAACGCCGATG 59.901 61.111 0.00 0.00 40.39 3.84
2273 2339 1.601759 GCTTTGACTGCCAGCTCCA 60.602 57.895 0.00 0.00 0.00 3.86
2285 2351 5.063438 CGTAGATCGAATTTCCTTGCTTTGA 59.937 40.000 0.00 0.00 42.86 2.69
2313 2379 4.458989 CACCTCCAAGCAGCATTAAAACTA 59.541 41.667 0.00 0.00 0.00 2.24
2320 2386 1.980772 GCCACCTCCAAGCAGCATT 60.981 57.895 0.00 0.00 0.00 3.56
2349 2415 4.759693 TGTACCAAGCCACTAACTTGAATG 59.240 41.667 5.12 0.00 45.99 2.67
2363 2429 3.926058 TCCCTAAGGATTGTACCAAGC 57.074 47.619 0.00 0.00 37.19 4.01
2457 2523 6.043938 GGGAATGGAAACTGACCCTGTATATA 59.956 42.308 0.00 0.00 34.99 0.86
2459 2525 4.165372 GGGAATGGAAACTGACCCTGTATA 59.835 45.833 0.00 0.00 34.99 1.47
2687 2951 4.067896 CGCACTATGAGCCATCCTTTTAT 58.932 43.478 0.00 0.00 0.00 1.40
2691 2955 1.123077 TCGCACTATGAGCCATCCTT 58.877 50.000 0.00 0.00 0.00 3.36
2786 3050 0.179018 GGGAGGTTGCGGCATAGATT 60.179 55.000 2.28 0.00 0.00 2.40
2798 3062 1.465189 AAGGGAGGAGGAGGGAGGTT 61.465 60.000 0.00 0.00 0.00 3.50
2812 3077 3.251509 TCTGGCAGCAGCAAGGGA 61.252 61.111 10.34 0.00 42.40 4.20
2817 3082 2.599757 ATGACCTCTGGCAGCAGCA 61.600 57.895 10.34 5.66 44.61 4.41
2832 3101 4.467084 GGCTTCGCCCGACCATGA 62.467 66.667 0.00 0.00 44.06 3.07
2925 3241 4.555709 TTCACGCCGCAACACCCT 62.556 61.111 0.00 0.00 0.00 4.34
3005 3322 1.411041 GGAGTAGTAACCTCCGGCAT 58.589 55.000 0.00 0.00 39.22 4.40
3006 3323 2.892025 GGAGTAGTAACCTCCGGCA 58.108 57.895 0.00 0.00 39.22 5.69
3020 3337 1.725803 ACTACCACCGAAAAGGGAGT 58.274 50.000 0.00 0.00 44.34 3.85
3026 3343 2.485835 CCTCAACCACTACCACCGAAAA 60.486 50.000 0.00 0.00 0.00 2.29
3029 3346 0.178955 TCCTCAACCACTACCACCGA 60.179 55.000 0.00 0.00 0.00 4.69
3036 3353 0.470456 ACCACCGTCCTCAACCACTA 60.470 55.000 0.00 0.00 0.00 2.74
3042 3359 2.879233 GCTCCACCACCGTCCTCAA 61.879 63.158 0.00 0.00 0.00 3.02
3077 3394 1.381928 GCCACCATGCCACATGAGAG 61.382 60.000 9.10 0.00 0.00 3.20
3130 4020 1.081906 CGCGCAAACTGTTCAGCAT 60.082 52.632 8.75 0.00 0.00 3.79
3135 4025 2.427410 CCTGCGCGCAAACTGTTC 60.427 61.111 35.50 0.68 0.00 3.18
3160 4050 4.676951 ACACGGGGCACAATGGGG 62.677 66.667 0.00 0.00 0.00 4.96
3161 4051 2.600173 AACACGGGGCACAATGGG 60.600 61.111 0.00 0.00 0.00 4.00
3177 4067 2.915659 ACCCTCTGTCGACGCCAA 60.916 61.111 11.62 0.00 0.00 4.52
3178 4068 3.371063 GACCCTCTGTCGACGCCA 61.371 66.667 11.62 0.00 33.49 5.69
3188 4078 2.203584 TCCTTACTAGTCCGACCCTCT 58.796 52.381 0.00 0.00 0.00 3.69
3194 4084 2.552743 CGCATCATCCTTACTAGTCCGA 59.447 50.000 0.00 0.00 0.00 4.55
3203 4093 3.259374 GGAAGAGATCCGCATCATCCTTA 59.741 47.826 0.00 0.00 38.79 2.69
3247 4138 3.134623 TGTTAGAGGTCGCCATCATCATT 59.865 43.478 0.00 0.00 0.00 2.57
3260 4151 1.070134 ACATGCACACGTGTTAGAGGT 59.930 47.619 20.79 10.53 43.67 3.85
3294 4185 3.244911 ACCTATAGTTGGTGCAGCAAACT 60.245 43.478 31.13 27.82 43.45 2.66
3306 4197 4.843220 AACGTATCGGGACCTATAGTTG 57.157 45.455 0.00 0.00 0.00 3.16
3307 4198 5.105997 GCATAACGTATCGGGACCTATAGTT 60.106 44.000 0.00 0.00 0.00 2.24
3308 4199 4.397417 GCATAACGTATCGGGACCTATAGT 59.603 45.833 0.00 0.00 0.00 2.12
3311 4202 2.163010 CGCATAACGTATCGGGACCTAT 59.837 50.000 0.00 0.00 36.87 2.57
3324 4215 1.626654 GCCGATCCATCCGCATAACG 61.627 60.000 0.00 0.00 43.15 3.18


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

AutoCloner maintained by Alex Coulton.