Multiple sequence alignment - TraesCS5D01G461300

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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 TraesCS5D01G461300 chr5D 100.000 3528 0 0 1 3528 505419583 505423110 0.000000e+00 6516
1 TraesCS5D01G461300 chr5D 83.735 1328 161 29 1076 2388 505429029 505430316 0.000000e+00 1205
2 TraesCS5D01G461300 chr5D 86.082 776 76 15 1081 1849 505410041 505410791 0.000000e+00 806
3 TraesCS5D01G461300 chr5D 78.203 1124 163 49 1541 2631 505456337 505457411 0.000000e+00 643
4 TraesCS5D01G461300 chr5D 81.506 757 101 25 1526 2254 505405709 505406454 1.410000e-163 586
5 TraesCS5D01G461300 chr5D 79.258 863 138 23 1360 2209 505347809 505348643 6.610000e-157 564
6 TraesCS5D01G461300 chr5D 89.552 268 27 1 1038 1305 505405206 505405472 4.360000e-89 339
7 TraesCS5D01G461300 chr5D 86.195 297 21 7 2381 2658 505430372 505430667 1.590000e-78 303
8 TraesCS5D01G461300 chr5B 93.034 2139 112 13 956 3068 635515065 635517192 0.000000e+00 3090
9 TraesCS5D01G461300 chr5B 94.241 955 55 0 1 955 9842354 9843308 0.000000e+00 1459
10 TraesCS5D01G461300 chr5B 84.778 1327 143 31 1039 2347 635533316 635534601 0.000000e+00 1277
11 TraesCS5D01G461300 chr5B 86.615 777 70 20 1081 1849 635510516 635511266 0.000000e+00 828
12 TraesCS5D01G461300 chr5B 78.545 1072 172 28 1142 2199 635346288 635347315 0.000000e+00 652
13 TraesCS5D01G461300 chr5B 80.780 744 105 19 1541 2254 635467341 635468076 6.660000e-152 547
14 TraesCS5D01G461300 chr5B 77.764 805 141 26 1541 2331 635573720 635574500 8.920000e-126 460
15 TraesCS5D01G461300 chr5B 87.456 287 26 4 3248 3526 635517429 635517713 4.390000e-84 322
16 TraesCS5D01G461300 chr5B 88.571 245 22 3 2387 2631 635560994 635561232 3.440000e-75 292
17 TraesCS5D01G461300 chr5B 75.158 632 108 35 2058 2647 635508282 635508906 5.850000e-63 252
18 TraesCS5D01G461300 chr5B 89.759 166 17 0 2392 2557 635534677 635534842 2.760000e-51 213
19 TraesCS5D01G461300 chr5A 90.352 1337 70 34 1047 2371 632903710 632904999 0.000000e+00 1700
20 TraesCS5D01G461300 chr5A 84.173 1390 154 34 1020 2388 632992910 632994254 0.000000e+00 1288
21 TraesCS5D01G461300 chr5A 96.372 441 16 0 2439 2879 632905030 632905470 0.000000e+00 726
22 TraesCS5D01G461300 chr5A 79.289 816 120 25 1559 2333 632886581 632887388 3.120000e-145 525
23 TraesCS5D01G461300 chr5A 77.491 813 136 30 1541 2331 633022509 633023296 8.990000e-121 444
24 TraesCS5D01G461300 chr5A 89.818 275 23 2 2391 2660 632994609 632994883 7.250000e-92 348
25 TraesCS5D01G461300 chr5A 88.060 268 30 1 1038 1305 632886078 632886343 2.040000e-82 316
26 TraesCS5D01G461300 chr5A 85.616 292 29 9 3248 3528 632905708 632905997 9.580000e-76 294
27 TraesCS5D01G461300 chr5A 86.755 151 18 1 3065 3213 632905555 632905705 2.180000e-37 167
28 TraesCS5D01G461300 chr1D 97.390 958 25 0 1 958 253187773 253186816 0.000000e+00 1631
29 TraesCS5D01G461300 chr1D 95.278 953 45 0 3 955 301221591 301222543 0.000000e+00 1511
30 TraesCS5D01G461300 chr3D 97.487 955 19 1 1 955 40777892 40778841 0.000000e+00 1626
31 TraesCS5D01G461300 chr3B 96.545 955 32 1 1 955 357730725 357731678 0.000000e+00 1580
32 TraesCS5D01G461300 chr2B 96.033 958 37 1 1 958 777195009 777194053 0.000000e+00 1557
33 TraesCS5D01G461300 chrUn 94.874 956 48 1 1 955 26248367 26249322 0.000000e+00 1493
34 TraesCS5D01G461300 chrUn 94.346 955 54 0 1 955 296439080 296440034 0.000000e+00 1465
35 TraesCS5D01G461300 chr7B 94.259 958 55 0 1 958 483803581 483802624 0.000000e+00 1465


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 TraesCS5D01G461300 chr5D 505419583 505423110 3527 False 6516.00 6516 100.000000 1 3528 1 chr5D.!!$F2 3527
1 TraesCS5D01G461300 chr5D 505429029 505430667 1638 False 754.00 1205 84.965000 1076 2658 2 chr5D.!!$F5 1582
2 TraesCS5D01G461300 chr5D 505456337 505457411 1074 False 643.00 643 78.203000 1541 2631 1 chr5D.!!$F3 1090
3 TraesCS5D01G461300 chr5D 505405206 505410791 5585 False 577.00 806 85.713333 1038 2254 3 chr5D.!!$F4 1216
4 TraesCS5D01G461300 chr5D 505347809 505348643 834 False 564.00 564 79.258000 1360 2209 1 chr5D.!!$F1 849
5 TraesCS5D01G461300 chr5B 9842354 9843308 954 False 1459.00 1459 94.241000 1 955 1 chr5B.!!$F1 954
6 TraesCS5D01G461300 chr5B 635508282 635517713 9431 False 1123.00 3090 85.565750 956 3526 4 chr5B.!!$F6 2570
7 TraesCS5D01G461300 chr5B 635533316 635534842 1526 False 745.00 1277 87.268500 1039 2557 2 chr5B.!!$F7 1518
8 TraesCS5D01G461300 chr5B 635346288 635347315 1027 False 652.00 652 78.545000 1142 2199 1 chr5B.!!$F2 1057
9 TraesCS5D01G461300 chr5B 635467341 635468076 735 False 547.00 547 80.780000 1541 2254 1 chr5B.!!$F3 713
10 TraesCS5D01G461300 chr5B 635573720 635574500 780 False 460.00 460 77.764000 1541 2331 1 chr5B.!!$F5 790
11 TraesCS5D01G461300 chr5A 632992910 632994883 1973 False 818.00 1288 86.995500 1020 2660 2 chr5A.!!$F4 1640
12 TraesCS5D01G461300 chr5A 632903710 632905997 2287 False 721.75 1700 89.773750 1047 3528 4 chr5A.!!$F3 2481
13 TraesCS5D01G461300 chr5A 633022509 633023296 787 False 444.00 444 77.491000 1541 2331 1 chr5A.!!$F1 790
14 TraesCS5D01G461300 chr5A 632886078 632887388 1310 False 420.50 525 83.674500 1038 2333 2 chr5A.!!$F2 1295
15 TraesCS5D01G461300 chr1D 253186816 253187773 957 True 1631.00 1631 97.390000 1 958 1 chr1D.!!$R1 957
16 TraesCS5D01G461300 chr1D 301221591 301222543 952 False 1511.00 1511 95.278000 3 955 1 chr1D.!!$F1 952
17 TraesCS5D01G461300 chr3D 40777892 40778841 949 False 1626.00 1626 97.487000 1 955 1 chr3D.!!$F1 954
18 TraesCS5D01G461300 chr3B 357730725 357731678 953 False 1580.00 1580 96.545000 1 955 1 chr3B.!!$F1 954
19 TraesCS5D01G461300 chr2B 777194053 777195009 956 True 1557.00 1557 96.033000 1 958 1 chr2B.!!$R1 957
20 TraesCS5D01G461300 chrUn 26248367 26249322 955 False 1493.00 1493 94.874000 1 955 1 chrUn.!!$F1 954
21 TraesCS5D01G461300 chrUn 296439080 296440034 954 False 1465.00 1465 94.346000 1 955 1 chrUn.!!$F2 954
22 TraesCS5D01G461300 chr7B 483802624 483803581 957 True 1465.00 1465 94.259000 1 958 1 chr7B.!!$R1 957

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
960 963 0.108898 CTGACTCCCTTCTCAGCGTG 60.109 60.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2911 9439 0.669318 TGCGAGGGTCAATTGTCGAC 60.669 55.0 17.4 9.11 34.28 4.2 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
125 126 3.386486 CAAGCTGTACGTACAACTTCCA 58.614 45.455 31.47 9.89 39.74 3.53
261 262 6.639686 TCTGAGTGTACATGTTCTTCGTTTAC 59.360 38.462 2.30 0.00 0.00 2.01
281 282 3.264897 CCGCCGCTCGAGGAAATG 61.265 66.667 15.58 0.00 41.67 2.32
456 457 1.958288 TTCCCTCCCTCTTTCTCTGG 58.042 55.000 0.00 0.00 0.00 3.86
754 756 4.563524 ATTTAAAACTCGACGAAGCTCG 57.436 40.909 0.00 4.36 46.93 5.03
825 827 3.679083 GCTTTGGTACGCTCCTGTAGATT 60.679 47.826 0.00 0.00 0.00 2.40
912 915 2.050350 CCGGCGTACCTCCTCTTCA 61.050 63.158 6.01 0.00 0.00 3.02
937 940 2.256591 GCCGATGCGCCATCATCTT 61.257 57.895 4.18 0.00 40.54 2.40
960 963 0.108898 CTGACTCCCTTCTCAGCGTG 60.109 60.000 0.00 0.00 0.00 5.34
962 965 0.603569 GACTCCCTTCTCAGCGTGAA 59.396 55.000 0.00 0.00 0.00 3.18
964 967 1.625818 ACTCCCTTCTCAGCGTGAAAT 59.374 47.619 0.00 0.00 0.00 2.17
965 968 2.005451 CTCCCTTCTCAGCGTGAAATG 58.995 52.381 0.00 0.00 0.00 2.32
980 1342 6.164408 CGTGAAATGCACTTAGTGAATGTA 57.836 37.500 17.40 0.00 45.49 2.29
985 1347 9.243637 TGAAATGCACTTAGTGAATGTAAAAAC 57.756 29.630 17.40 0.00 31.26 2.43
990 1352 8.894731 TGCACTTAGTGAATGTAAAAACTGTAA 58.105 29.630 17.40 0.00 35.23 2.41
991 1353 9.724839 GCACTTAGTGAATGTAAAAACTGTAAA 57.275 29.630 17.40 0.00 35.23 2.01
1025 2203 1.439679 GGTGAAAACTGTAGCTCCGG 58.560 55.000 0.00 0.00 0.00 5.14
1030 2208 1.187087 AAACTGTAGCTCCGGAGAGG 58.813 55.000 35.69 19.31 40.79 3.69
1031 2209 1.324005 AACTGTAGCTCCGGAGAGGC 61.324 60.000 35.69 20.92 40.79 4.70
1051 2229 2.431942 CGGTCCACTCGTTTCCCG 60.432 66.667 0.00 0.00 38.13 5.14
1356 2534 4.796231 CTCGTTCCCACCTCCGCG 62.796 72.222 0.00 0.00 0.00 6.46
1505 2746 1.077334 CCTCGTGTCCTCCCCCTATAT 59.923 57.143 0.00 0.00 0.00 0.86
1510 2751 2.638363 GTGTCCTCCCCCTATATTCACC 59.362 54.545 0.00 0.00 0.00 4.02
1511 2752 2.267192 GTCCTCCCCCTATATTCACCC 58.733 57.143 0.00 0.00 0.00 4.61
1512 2753 1.203262 TCCTCCCCCTATATTCACCCG 60.203 57.143 0.00 0.00 0.00 5.28
1513 2754 1.276622 CTCCCCCTATATTCACCCGG 58.723 60.000 0.00 0.00 0.00 5.73
1514 2755 0.569204 TCCCCCTATATTCACCCGGT 59.431 55.000 0.00 0.00 0.00 5.28
1515 2756 0.981943 CCCCCTATATTCACCCGGTC 59.018 60.000 0.00 0.00 0.00 4.79
1516 2757 1.724545 CCCCTATATTCACCCGGTCA 58.275 55.000 0.00 0.00 0.00 4.02
1517 2758 1.623811 CCCCTATATTCACCCGGTCAG 59.376 57.143 0.00 0.00 0.00 3.51
1518 2759 1.002087 CCCTATATTCACCCGGTCAGC 59.998 57.143 0.00 0.00 0.00 4.26
1519 2760 1.971357 CCTATATTCACCCGGTCAGCT 59.029 52.381 0.00 0.00 0.00 4.24
1520 2761 2.368875 CCTATATTCACCCGGTCAGCTT 59.631 50.000 0.00 0.00 0.00 3.74
1521 2762 2.622064 ATATTCACCCGGTCAGCTTC 57.378 50.000 0.00 0.00 0.00 3.86
1522 2763 1.271856 TATTCACCCGGTCAGCTTCA 58.728 50.000 0.00 0.00 0.00 3.02
1523 2764 0.400213 ATTCACCCGGTCAGCTTCAA 59.600 50.000 0.00 0.00 0.00 2.69
1524 2765 0.400213 TTCACCCGGTCAGCTTCAAT 59.600 50.000 0.00 0.00 0.00 2.57
1525 2766 0.321564 TCACCCGGTCAGCTTCAATG 60.322 55.000 0.00 0.00 0.00 2.82
1526 2767 1.675641 ACCCGGTCAGCTTCAATGC 60.676 57.895 0.00 0.00 0.00 3.56
1527 2768 2.753966 CCCGGTCAGCTTCAATGCG 61.754 63.158 0.00 0.00 38.13 4.73
1528 2769 2.753966 CCGGTCAGCTTCAATGCGG 61.754 63.158 0.00 0.00 38.13 5.69
1529 2770 2.486966 GGTCAGCTTCAATGCGGC 59.513 61.111 0.00 0.00 38.13 6.53
1530 2771 2.099062 GTCAGCTTCAATGCGGCG 59.901 61.111 0.51 0.51 38.13 6.46
1782 7746 4.804261 GCACTCTACTTCAACTTGGATGGT 60.804 45.833 0.00 0.00 0.00 3.55
1818 7782 2.061773 CTTGGTACACTCTGCTTGTCG 58.938 52.381 0.00 0.00 39.29 4.35
2032 8011 4.079787 CCCTAACATTGGAATTCAGGAGGA 60.080 45.833 7.93 0.00 0.00 3.71
2056 8053 4.450976 GGTACATGCATTGGTGATCAGTA 58.549 43.478 0.00 0.00 0.00 2.74
2394 8796 3.994392 TCTTAAACGTCTGGATGACTTGC 59.006 43.478 0.00 0.00 43.25 4.01
2580 8997 0.886563 AATGGAGCAAGCTCTTGTGC 59.113 50.000 20.26 0.00 42.31 4.57
2663 9093 3.568430 ACCTGTAACTTTGTTTAGGCTGC 59.432 43.478 0.00 0.00 0.00 5.25
2666 9096 3.249080 TGTAACTTTGTTTAGGCTGCGTC 59.751 43.478 0.00 0.00 0.00 5.19
2766 9196 2.276732 AGTTGCTGCTCCTTTGCTTA 57.723 45.000 0.00 0.00 0.00 3.09
2785 9215 8.500837 TTGCTTACAATAATTTTCAGTCGTTG 57.499 30.769 0.00 0.00 0.00 4.10
2844 9366 4.002906 TGATTGACTGGTACTCCACAAC 57.997 45.455 0.00 0.00 39.03 3.32
2882 9404 0.896923 TTTTTAGCTCGCCTACCCGA 59.103 50.000 0.00 0.00 35.68 5.14
2883 9405 0.174162 TTTTAGCTCGCCTACCCGAC 59.826 55.000 0.00 0.00 33.12 4.79
2890 9412 3.766691 GCCTACCCGACTCCGCAA 61.767 66.667 0.00 0.00 0.00 4.85
2891 9413 2.494918 CCTACCCGACTCCGCAAG 59.505 66.667 0.00 0.00 0.00 4.01
2896 9418 1.004918 CCCGACTCCGCAAGAAGTT 60.005 57.895 0.00 0.00 43.02 2.66
2898 9420 0.600255 CCGACTCCGCAAGAAGTTGT 60.600 55.000 0.00 0.00 43.02 3.32
2911 9439 5.738370 CAAGAAGTTGTTGTCTTCCGTTAG 58.262 41.667 4.61 0.00 41.27 2.34
2918 9446 3.181488 TGTTGTCTTCCGTTAGTCGACAA 60.181 43.478 19.50 7.32 42.86 3.18
3069 9599 4.700692 GGAGTTGGACAGATTAAACCCTTC 59.299 45.833 0.00 0.00 0.00 3.46
3070 9600 4.324267 AGTTGGACAGATTAAACCCTTCG 58.676 43.478 0.00 0.00 0.00 3.79
3071 9601 4.041198 AGTTGGACAGATTAAACCCTTCGA 59.959 41.667 0.00 0.00 0.00 3.71
3073 9603 3.325425 TGGACAGATTAAACCCTTCGACA 59.675 43.478 0.00 0.00 0.00 4.35
3075 9605 4.941873 GGACAGATTAAACCCTTCGACAAT 59.058 41.667 0.00 0.00 0.00 2.71
3076 9606 5.163754 GGACAGATTAAACCCTTCGACAATG 60.164 44.000 0.00 0.00 0.00 2.82
3077 9607 5.313712 ACAGATTAAACCCTTCGACAATGT 58.686 37.500 0.00 0.00 0.00 2.71
3099 9716 1.157870 GGACTGTTGTCACACCACCG 61.158 60.000 0.00 0.00 44.61 4.94
3154 9860 5.413309 TCTGACTCTCCTCTGGAAAATTC 57.587 43.478 0.00 0.00 0.00 2.17
3217 9923 2.670934 CAGGCCTGCTGTGGTGTC 60.671 66.667 22.33 0.00 0.00 3.67
3218 9924 3.170672 AGGCCTGCTGTGGTGTCA 61.171 61.111 3.11 0.00 0.00 3.58
3219 9925 2.203337 GGCCTGCTGTGGTGTCAA 60.203 61.111 0.00 0.00 0.00 3.18
3221 9927 1.181098 GGCCTGCTGTGGTGTCAAAT 61.181 55.000 0.00 0.00 0.00 2.32
3223 9929 1.321474 CCTGCTGTGGTGTCAAATGT 58.679 50.000 0.00 0.00 0.00 2.71
3224 9930 1.267806 CCTGCTGTGGTGTCAAATGTC 59.732 52.381 0.00 0.00 0.00 3.06
3225 9931 1.948834 CTGCTGTGGTGTCAAATGTCA 59.051 47.619 0.00 0.00 0.00 3.58
3226 9932 2.555325 CTGCTGTGGTGTCAAATGTCAT 59.445 45.455 0.00 0.00 0.00 3.06
3227 9933 2.553602 TGCTGTGGTGTCAAATGTCATC 59.446 45.455 0.00 0.00 0.00 2.92
3228 9934 2.816087 GCTGTGGTGTCAAATGTCATCT 59.184 45.455 0.00 0.00 0.00 2.90
3230 9936 4.637534 GCTGTGGTGTCAAATGTCATCTAT 59.362 41.667 0.00 0.00 0.00 1.98
3231 9937 5.448225 GCTGTGGTGTCAAATGTCATCTATG 60.448 44.000 0.00 0.00 0.00 2.23
3232 9938 5.803552 TGTGGTGTCAAATGTCATCTATGA 58.196 37.500 0.00 0.00 0.00 2.15
3235 9941 6.765036 GTGGTGTCAAATGTCATCTATGATCT 59.235 38.462 0.00 0.00 39.30 2.75
3236 9942 6.988580 TGGTGTCAAATGTCATCTATGATCTC 59.011 38.462 0.00 0.00 39.30 2.75
3237 9943 6.988580 GGTGTCAAATGTCATCTATGATCTCA 59.011 38.462 0.00 0.00 39.30 3.27
3238 9944 7.042187 GGTGTCAAATGTCATCTATGATCTCAC 60.042 40.741 0.00 0.00 39.30 3.51
3239 9945 6.988580 TGTCAAATGTCATCTATGATCTCACC 59.011 38.462 0.00 0.00 39.30 4.02
3240 9946 6.426328 GTCAAATGTCATCTATGATCTCACCC 59.574 42.308 0.00 0.00 39.30 4.61
3241 9947 5.495926 AATGTCATCTATGATCTCACCCC 57.504 43.478 0.00 0.00 39.30 4.95
3242 9948 3.242867 TGTCATCTATGATCTCACCCCC 58.757 50.000 0.00 0.00 39.30 5.40
3244 9950 3.260380 GTCATCTATGATCTCACCCCCTG 59.740 52.174 0.00 0.00 39.30 4.45
3245 9951 3.142787 TCATCTATGATCTCACCCCCTGA 59.857 47.826 0.00 0.00 0.00 3.86
3262 9968 4.521146 CCCTGAACTCATACAAGCTGAAT 58.479 43.478 0.00 0.00 0.00 2.57
3281 9987 5.181009 TGAATGTGTGCAAAAACATTTCCA 58.819 33.333 19.13 13.18 44.83 3.53
3282 9988 5.645067 TGAATGTGTGCAAAAACATTTCCAA 59.355 32.000 19.13 8.07 44.83 3.53
3286 11745 3.314635 TGTGCAAAAACATTTCCAATGGC 59.685 39.130 0.00 0.00 0.00 4.40
3288 11747 2.805099 GCAAAAACATTTCCAATGGCGA 59.195 40.909 0.00 0.00 0.00 5.54
3371 11839 7.279981 CACTACGAAATCCATGGAGTGAAAATA 59.720 37.037 21.33 6.22 35.87 1.40
3410 11879 3.711704 AGATCGTGGGAAATGGTGACTAT 59.288 43.478 0.00 0.00 0.00 2.12
3440 11909 0.817013 TTGAATGATTTGGCTCGCCC 59.183 50.000 5.33 0.00 34.56 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 3.260884 TGGCTGAAAGAAGAGACGGTTAT 59.739 43.478 0.00 0.00 34.07 1.89
261 262 4.735132 TTCCTCGAGCGGCGGTTG 62.735 66.667 19.83 19.83 41.33 3.77
277 278 3.360867 TGTGGATTGGGCGAATACATTT 58.639 40.909 10.49 0.00 37.23 2.32
281 282 3.880490 TGTAATGTGGATTGGGCGAATAC 59.120 43.478 0.00 0.00 0.00 1.89
456 457 9.122613 GAGATTTTAATGAAGTTTTGCTCTCAC 57.877 33.333 0.00 0.00 0.00 3.51
754 756 8.662141 TCTCACTTAAATAAATGTAAAGCCGAC 58.338 33.333 0.00 0.00 0.00 4.79
783 785 6.655078 AAGCAGAGCTAATTTTCCTTTCAA 57.345 33.333 0.00 0.00 38.25 2.69
825 827 2.126463 CGGTTCGCGAGCTCTTGA 60.126 61.111 22.36 6.41 0.00 3.02
937 940 1.620819 GCTGAGAAGGGAGTCAGTTGA 59.379 52.381 1.61 0.00 41.99 3.18
960 963 9.463443 AGTTTTTACATTCACTAAGTGCATTTC 57.537 29.630 0.00 0.00 32.98 2.17
962 965 8.413229 ACAGTTTTTACATTCACTAAGTGCATT 58.587 29.630 0.00 0.00 32.98 3.56
964 967 7.328277 ACAGTTTTTACATTCACTAAGTGCA 57.672 32.000 0.00 0.00 32.98 4.57
965 968 9.724839 TTTACAGTTTTTACATTCACTAAGTGC 57.275 29.630 0.00 0.00 32.98 4.40
998 1360 6.067217 AGCTACAGTTTTCACCCTTCATAT 57.933 37.500 0.00 0.00 0.00 1.78
999 1361 5.488341 GAGCTACAGTTTTCACCCTTCATA 58.512 41.667 0.00 0.00 0.00 2.15
1001 1363 3.496160 GGAGCTACAGTTTTCACCCTTCA 60.496 47.826 0.00 0.00 0.00 3.02
1002 1364 3.075148 GGAGCTACAGTTTTCACCCTTC 58.925 50.000 0.00 0.00 0.00 3.46
1003 1365 2.550208 CGGAGCTACAGTTTTCACCCTT 60.550 50.000 0.00 0.00 0.00 3.95
1005 1367 1.439679 CGGAGCTACAGTTTTCACCC 58.560 55.000 0.00 0.00 0.00 4.61
1006 1368 1.001633 TCCGGAGCTACAGTTTTCACC 59.998 52.381 0.00 0.00 0.00 4.02
1007 1369 2.029290 TCTCCGGAGCTACAGTTTTCAC 60.029 50.000 27.39 0.00 0.00 3.18
1008 1370 2.231478 CTCTCCGGAGCTACAGTTTTCA 59.769 50.000 27.39 3.64 32.43 2.69
1009 1371 2.417515 CCTCTCCGGAGCTACAGTTTTC 60.418 54.545 27.39 0.00 38.21 2.29
1010 1372 1.550976 CCTCTCCGGAGCTACAGTTTT 59.449 52.381 27.39 0.00 38.21 2.43
1011 1373 1.187087 CCTCTCCGGAGCTACAGTTT 58.813 55.000 27.39 0.00 38.21 2.66
1012 1374 1.324005 GCCTCTCCGGAGCTACAGTT 61.324 60.000 27.39 0.00 38.21 3.16
1013 1375 1.755008 GCCTCTCCGGAGCTACAGT 60.755 63.158 27.39 0.00 38.21 3.55
1031 2209 3.110178 GAAACGAGTGGACCGCGG 61.110 66.667 26.86 26.86 0.00 6.46
1044 2222 0.892358 GAGGGTTTGGGTCGGGAAAC 60.892 60.000 0.00 0.00 0.00 2.78
1051 2229 2.046217 GAGGCGAGGGTTTGGGTC 60.046 66.667 0.00 0.00 0.00 4.46
1287 2465 1.463214 TTGGAAGAGCCCCAGGACA 60.463 57.895 0.00 0.00 34.77 4.02
1356 2534 4.811364 GGCTGGGCAGGGAAGAGC 62.811 72.222 0.00 0.00 0.00 4.09
1505 2746 0.400213 ATTGAAGCTGACCGGGTGAA 59.600 50.000 3.30 0.00 0.00 3.18
1510 2751 2.753966 CCGCATTGAAGCTGACCGG 61.754 63.158 0.00 0.00 0.00 5.28
1511 2752 2.787249 CCGCATTGAAGCTGACCG 59.213 61.111 0.00 0.00 0.00 4.79
1512 2753 2.486966 GCCGCATTGAAGCTGACC 59.513 61.111 0.00 0.00 0.00 4.02
1513 2754 2.099062 CGCCGCATTGAAGCTGAC 59.901 61.111 0.00 0.00 0.00 3.51
1514 2755 3.803082 GCGCCGCATTGAAGCTGA 61.803 61.111 3.15 0.00 0.00 4.26
1515 2756 4.842091 GGCGCCGCATTGAAGCTG 62.842 66.667 12.58 0.00 0.00 4.24
1529 2770 3.114616 CACTGAAGCTGACCGGCG 61.115 66.667 0.00 0.00 37.29 6.46
1530 2771 3.426568 GCACTGAAGCTGACCGGC 61.427 66.667 0.00 0.00 0.00 6.13
1782 7746 2.308570 ACCAAGTTGGCACTGGATGATA 59.691 45.455 22.25 0.00 42.67 2.15
1789 7753 1.873591 GAGTGTACCAAGTTGGCACTG 59.126 52.381 29.19 7.12 42.67 3.66
1875 7839 3.706373 ACGGCAGCGAATCCCAGT 61.706 61.111 0.00 0.00 0.00 4.00
1926 7890 2.612115 CCCTTGGGTCCAGCCTCT 60.612 66.667 0.00 0.00 37.43 3.69
2032 8011 2.241941 TGATCACCAATGCATGTACCCT 59.758 45.455 0.00 0.00 0.00 4.34
2100 8097 5.769367 TCGAGATCAACCATATAAGAACCG 58.231 41.667 0.00 0.00 0.00 4.44
2217 8232 4.877378 ACAAGGAATTGCACATGATTGT 57.123 36.364 0.00 0.00 36.15 2.71
2218 8233 6.157904 TGTAACAAGGAATTGCACATGATTG 58.842 36.000 0.00 0.00 0.00 2.67
2227 8256 7.115378 CACTGAAAGATTGTAACAAGGAATTGC 59.885 37.037 0.00 0.00 37.43 3.56
2309 8348 4.883585 TCTCTTTCTTGAGCACATGTGTTT 59.116 37.500 26.01 15.28 34.29 2.83
2310 8349 4.454678 TCTCTTTCTTGAGCACATGTGTT 58.545 39.130 26.01 21.28 34.29 3.32
2394 8796 2.511600 GCCGATCACAAGGACCGG 60.512 66.667 0.00 0.00 42.74 5.28
2481 8885 3.447944 TGCTTCCATTGCTGCATAAATGA 59.552 39.130 18.38 6.40 36.13 2.57
2580 8997 2.100916 CACTACCACCTCCCGACTAATG 59.899 54.545 0.00 0.00 0.00 1.90
2663 9093 2.002586 CAGCAGTATTGGTCCTTGACG 58.997 52.381 0.00 0.00 32.65 4.35
2666 9096 3.149196 ACAACAGCAGTATTGGTCCTTG 58.851 45.455 0.00 0.00 31.36 3.61
2882 9404 1.940613 GACAACAACTTCTTGCGGAGT 59.059 47.619 0.00 0.00 0.00 3.85
2883 9405 2.213499 AGACAACAACTTCTTGCGGAG 58.787 47.619 0.00 0.00 0.00 4.63
2888 9410 4.616181 AACGGAAGACAACAACTTCTTG 57.384 40.909 0.00 0.00 42.07 3.02
2889 9411 5.425630 ACTAACGGAAGACAACAACTTCTT 58.574 37.500 0.00 0.00 42.07 2.52
2890 9412 5.019785 ACTAACGGAAGACAACAACTTCT 57.980 39.130 0.00 0.00 42.07 2.85
2891 9413 4.085210 CGACTAACGGAAGACAACAACTTC 60.085 45.833 0.00 0.00 41.79 3.01
2896 9418 2.358582 TGTCGACTAACGGAAGACAACA 59.641 45.455 17.92 0.00 42.82 3.33
2898 9420 3.713858 TTGTCGACTAACGGAAGACAA 57.286 42.857 17.92 5.37 45.78 3.18
2911 9439 0.669318 TGCGAGGGTCAATTGTCGAC 60.669 55.000 17.40 9.11 34.28 4.20
2918 9446 3.641436 TCAGTATGTATGCGAGGGTCAAT 59.359 43.478 0.00 0.00 37.40 2.57
3069 9599 3.064682 TGACAACAGTCCAAACATTGTCG 59.935 43.478 15.15 0.00 46.47 4.35
3070 9600 4.142491 TGTGACAACAGTCCAAACATTGTC 60.142 41.667 14.10 14.10 45.19 3.18
3071 9601 3.761218 TGTGACAACAGTCCAAACATTGT 59.239 39.130 0.00 0.00 38.78 2.71
3073 9603 3.130340 GGTGTGACAACAGTCCAAACATT 59.870 43.478 0.00 0.00 36.84 2.71
3075 9605 2.088423 GGTGTGACAACAGTCCAAACA 58.912 47.619 0.00 0.00 36.84 2.83
3076 9606 2.088423 TGGTGTGACAACAGTCCAAAC 58.912 47.619 0.00 0.00 36.84 2.93
3077 9607 2.088423 GTGGTGTGACAACAGTCCAAA 58.912 47.619 2.25 0.00 36.84 3.28
3154 9860 1.529826 GCGTTTTAAGCGAGCATCCAG 60.530 52.381 5.22 0.00 0.00 3.86
3202 9908 1.181098 ATTTGACACCACAGCAGGCC 61.181 55.000 0.00 0.00 0.00 5.19
3206 9912 2.049888 TGACATTTGACACCACAGCA 57.950 45.000 0.00 0.00 0.00 4.41
3207 9913 2.816087 AGATGACATTTGACACCACAGC 59.184 45.455 0.00 0.00 0.00 4.40
3208 9914 5.876460 TCATAGATGACATTTGACACCACAG 59.124 40.000 0.00 0.00 0.00 3.66
3209 9915 5.803552 TCATAGATGACATTTGACACCACA 58.196 37.500 0.00 0.00 0.00 4.17
3213 9919 7.042187 GGTGAGATCATAGATGACATTTGACAC 60.042 40.741 0.00 0.00 40.03 3.67
3215 9921 6.426328 GGGTGAGATCATAGATGACATTTGAC 59.574 42.308 0.00 0.00 40.03 3.18
3217 9923 5.704515 GGGGTGAGATCATAGATGACATTTG 59.295 44.000 0.00 0.00 40.03 2.32
3218 9924 5.222007 GGGGGTGAGATCATAGATGACATTT 60.222 44.000 0.00 0.00 40.03 2.32
3219 9925 4.288105 GGGGGTGAGATCATAGATGACATT 59.712 45.833 0.00 0.00 40.03 2.71
3221 9927 3.116590 AGGGGGTGAGATCATAGATGACA 60.117 47.826 0.00 0.00 40.03 3.58
3223 9929 3.142787 TCAGGGGGTGAGATCATAGATGA 59.857 47.826 0.00 0.00 41.70 2.92
3224 9930 3.514539 TCAGGGGGTGAGATCATAGATG 58.485 50.000 0.00 0.00 0.00 2.90
3225 9931 3.906846 GTTCAGGGGGTGAGATCATAGAT 59.093 47.826 0.00 0.00 36.21 1.98
3226 9932 3.051803 AGTTCAGGGGGTGAGATCATAGA 60.052 47.826 0.00 0.00 36.21 1.98
3227 9933 3.312890 AGTTCAGGGGGTGAGATCATAG 58.687 50.000 0.00 0.00 36.21 2.23
3228 9934 3.309296 GAGTTCAGGGGGTGAGATCATA 58.691 50.000 0.00 0.00 36.21 2.15
3230 9936 1.203300 TGAGTTCAGGGGGTGAGATCA 60.203 52.381 0.00 0.00 36.21 2.92
3231 9937 1.573108 TGAGTTCAGGGGGTGAGATC 58.427 55.000 0.00 0.00 36.21 2.75
3232 9938 2.277008 ATGAGTTCAGGGGGTGAGAT 57.723 50.000 0.00 0.00 36.21 2.75
3235 9941 2.335681 TGTATGAGTTCAGGGGGTGA 57.664 50.000 0.00 0.00 0.00 4.02
3236 9942 2.941415 GCTTGTATGAGTTCAGGGGGTG 60.941 54.545 0.00 0.00 0.00 4.61
3237 9943 1.282157 GCTTGTATGAGTTCAGGGGGT 59.718 52.381 0.00 0.00 0.00 4.95
3238 9944 1.561542 AGCTTGTATGAGTTCAGGGGG 59.438 52.381 0.00 0.00 0.00 5.40
3239 9945 2.237143 TCAGCTTGTATGAGTTCAGGGG 59.763 50.000 0.00 0.00 0.00 4.79
3240 9946 3.616956 TCAGCTTGTATGAGTTCAGGG 57.383 47.619 0.00 0.00 0.00 4.45
3241 9947 4.940046 ACATTCAGCTTGTATGAGTTCAGG 59.060 41.667 6.50 0.00 30.91 3.86
3242 9948 5.410746 ACACATTCAGCTTGTATGAGTTCAG 59.589 40.000 6.50 0.00 28.28 3.02
3244 9950 5.625251 CACACATTCAGCTTGTATGAGTTC 58.375 41.667 6.50 0.00 29.73 3.01
3245 9951 4.083110 GCACACATTCAGCTTGTATGAGTT 60.083 41.667 0.00 0.00 29.73 3.01
3262 9968 4.334759 CCATTGGAAATGTTTTTGCACACA 59.665 37.500 0.00 0.00 42.05 3.72
3297 11756 7.837202 ACATTTTTGCATACATTGGAATGAG 57.163 32.000 6.37 0.00 39.67 2.90
3300 11759 8.320617 AGGTAACATTTTTGCATACATTGGAAT 58.679 29.630 0.00 0.00 35.36 3.01
3303 11762 6.253298 CGAGGTAACATTTTTGCATACATTGG 59.747 38.462 0.00 0.00 41.41 3.16
3311 11770 5.697473 TGATTCGAGGTAACATTTTTGCA 57.303 34.783 0.00 0.00 41.41 4.08
3371 11839 4.937620 ACGATCTGTGCAATAGTGAACAAT 59.062 37.500 5.34 2.49 43.08 2.71
3387 11855 2.009774 GTCACCATTTCCCACGATCTG 58.990 52.381 0.00 0.00 0.00 2.90
3410 11879 5.299148 CCAAATCATTCAAAGGACTGCAAA 58.701 37.500 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.