Multiple sequence alignment - TraesCS6B01G276300

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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 TraesCS6B01G276300 chr6B 100.000 4069 0 0 1 4069 500213162 500209094 0.000000e+00 7515.0
1 TraesCS6B01G276300 chr6B 97.222 828 23 0 3242 4069 678347348 678348175 0.000000e+00 1402.0
2 TraesCS6B01G276300 chr6B 96.014 577 22 1 3242 3818 678353134 678353709 0.000000e+00 937.0
3 TraesCS6B01G276300 chr6B 82.412 398 54 14 3674 4063 707804985 707805374 2.340000e-87 333.0
4 TraesCS6B01G276300 chr6D 92.853 3260 166 31 1 3241 323712676 323715887 0.000000e+00 4667.0
5 TraesCS6B01G276300 chr6D 84.783 368 44 10 3707 4069 460240205 460239845 3.870000e-95 359.0
6 TraesCS6B01G276300 chr6A 91.858 3218 161 43 56 3241 461144430 461147578 0.000000e+00 4397.0
7 TraesCS6B01G276300 chr6A 95.516 223 10 0 3242 3464 599635596 599635374 1.390000e-94 357.0
8 TraesCS6B01G276300 chr6A 94.444 126 7 0 847 972 4929203 4929078 1.150000e-45 195.0
9 TraesCS6B01G276300 chr6A 100.000 38 0 0 1 38 461144395 461144432 2.030000e-08 71.3
10 TraesCS6B01G276300 chr4A 94.832 832 42 1 3239 4069 493700936 493701767 0.000000e+00 1297.0
11 TraesCS6B01G276300 chr4A 94.983 578 28 1 3242 3818 493706772 493707349 0.000000e+00 905.0
12 TraesCS6B01G276300 chr3A 95.156 578 28 0 3241 3818 728740270 728740847 0.000000e+00 913.0
13 TraesCS6B01G276300 chr3A 94.983 578 29 0 3241 3818 728741852 728742429 0.000000e+00 907.0
14 TraesCS6B01G276300 chr3A 94.810 578 30 0 3241 3818 728743433 728744010 0.000000e+00 902.0
15 TraesCS6B01G276300 chr2A 86.767 529 65 5 3529 4054 700084407 700084933 5.860000e-163 584.0
16 TraesCS6B01G276300 chr2A 85.286 367 43 9 3707 4069 747443287 747442928 6.430000e-98 368.0
17 TraesCS6B01G276300 chr2A 93.600 125 8 0 848 972 774084097 774083973 1.930000e-43 187.0
18 TraesCS6B01G276300 chr2A 87.162 148 13 5 2601 2745 669752489 669752633 3.250000e-36 163.0
19 TraesCS6B01G276300 chr2A 84.848 132 12 5 1248 1372 774083971 774083841 4.270000e-25 126.0
20 TraesCS6B01G276300 chr7D 79.817 545 80 21 3539 4069 464266423 464266951 1.790000e-98 370.0
21 TraesCS6B01G276300 chr7D 85.890 326 40 5 3242 3563 24028277 24028600 3.890000e-90 342.0
22 TraesCS6B01G276300 chr7D 93.651 126 7 1 848 972 139228840 139228715 1.930000e-43 187.0
23 TraesCS6B01G276300 chr7D 84.848 132 12 5 1248 1372 139228713 139228583 4.270000e-25 126.0
24 TraesCS6B01G276300 chr7B 84.153 366 48 10 3707 4069 112008156 112007798 3.010000e-91 346.0
25 TraesCS6B01G276300 chr7B 92.308 130 10 0 843 972 616912392 616912521 6.950000e-43 185.0
26 TraesCS6B01G276300 chr3B 78.727 550 87 23 3539 4069 283197 282659 1.400000e-89 340.0
27 TraesCS6B01G276300 chr3B 82.222 135 16 5 1245 1372 210688166 210688299 4.300000e-20 110.0
28 TraesCS6B01G276300 chr4D 95.200 125 6 0 848 972 493213131 493213255 8.920000e-47 198.0
29 TraesCS6B01G276300 chr4D 83.099 142 15 6 1244 1378 251093237 251093098 1.990000e-23 121.0
30 TraesCS6B01G276300 chr4D 83.704 135 14 5 1245 1372 493213254 493213387 1.990000e-23 121.0
31 TraesCS6B01G276300 chr3D 93.600 125 8 0 848 972 77840481 77840605 1.930000e-43 187.0
32 TraesCS6B01G276300 chr4B 91.538 130 11 0 843 972 548863072 548862943 3.230000e-41 180.0
33 TraesCS6B01G276300 chr5A 84.615 117 16 2 2629 2744 394181693 394181578 9.240000e-22 115.0
34 TraesCS6B01G276300 chr5D 83.761 117 17 2 2629 2744 303759462 303759347 4.300000e-20 110.0
35 TraesCS6B01G276300 chr5B 83.761 117 17 2 2629 2744 348448605 348448490 4.300000e-20 110.0


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 TraesCS6B01G276300 chr6B 500209094 500213162 4068 True 7515.000000 7515 100.000 1 4069 1 chr6B.!!$R1 4068
1 TraesCS6B01G276300 chr6B 678347348 678348175 827 False 1402.000000 1402 97.222 3242 4069 1 chr6B.!!$F1 827
2 TraesCS6B01G276300 chr6B 678353134 678353709 575 False 937.000000 937 96.014 3242 3818 1 chr6B.!!$F2 576
3 TraesCS6B01G276300 chr6D 323712676 323715887 3211 False 4667.000000 4667 92.853 1 3241 1 chr6D.!!$F1 3240
4 TraesCS6B01G276300 chr6A 461144395 461147578 3183 False 2234.150000 4397 95.929 1 3241 2 chr6A.!!$F1 3240
5 TraesCS6B01G276300 chr4A 493700936 493701767 831 False 1297.000000 1297 94.832 3239 4069 1 chr4A.!!$F1 830
6 TraesCS6B01G276300 chr4A 493706772 493707349 577 False 905.000000 905 94.983 3242 3818 1 chr4A.!!$F2 576
7 TraesCS6B01G276300 chr3A 728740270 728744010 3740 False 907.333333 913 94.983 3241 3818 3 chr3A.!!$F1 577
8 TraesCS6B01G276300 chr2A 700084407 700084933 526 False 584.000000 584 86.767 3529 4054 1 chr2A.!!$F2 525
9 TraesCS6B01G276300 chr7D 464266423 464266951 528 False 370.000000 370 79.817 3539 4069 1 chr7D.!!$F2 530
10 TraesCS6B01G276300 chr3B 282659 283197 538 True 340.000000 340 78.727 3539 4069 1 chr3B.!!$R1 530

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
388 393 1.068948 TAGTTAAGGCCAACCCAGCA 58.931 50.0 5.01 0.0 36.11 4.41 F
2155 2166 0.108186 TGATCGATGAGGTGCGCTTT 60.108 50.0 9.73 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 2332 0.603569 GCTCGTGACTTCCAAGAGGA 59.396 55.0 9.33 0.0 46.84 3.71 R
3086 3129 0.243095 ACTGTCGCCTCGGAAACTAC 59.757 55.0 0.00 0.0 0.00 2.73 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 2.781945 CCTCTGGCAATTTAATCGCC 57.218 50.000 0.00 0.00 46.43 5.54
150 151 3.439129 GCCCTAAACTTGCGTACAGAATT 59.561 43.478 0.00 0.00 0.00 2.17
191 192 4.626172 CCTACCGTTCTTAAGTTCAGAAGC 59.374 45.833 1.63 0.00 30.72 3.86
192 193 4.067972 ACCGTTCTTAAGTTCAGAAGCA 57.932 40.909 1.63 0.00 30.72 3.91
257 258 1.674441 CACACATGGCATCAGACATCC 59.326 52.381 0.00 0.00 40.24 3.51
388 393 1.068948 TAGTTAAGGCCAACCCAGCA 58.931 50.000 5.01 0.00 36.11 4.41
422 427 9.378551 AGTTTTTACTTTGACATTTTCCCTTTC 57.621 29.630 0.00 0.00 0.00 2.62
507 512 2.415090 GCTTGACACTTGATCCATGTGC 60.415 50.000 11.35 6.65 41.29 4.57
580 585 4.550076 ACTGAGAAGATCCTCTTGTTGG 57.450 45.455 0.00 0.00 36.73 3.77
608 613 2.498167 GTGCAGTGACACCTTCTGAAT 58.502 47.619 0.84 0.00 34.35 2.57
648 653 2.203582 GGTTGAAACCCCGGCCTT 60.204 61.111 0.00 0.00 43.43 4.35
690 695 1.607148 GTTAAACGGAGCTGGCTTTGT 59.393 47.619 0.00 0.00 0.00 2.83
836 846 4.216687 CCTAACGCTATCCTACCTTCTCTG 59.783 50.000 0.00 0.00 0.00 3.35
852 862 3.435275 TCTCTGCTCAGTTCACAGGTAT 58.565 45.455 0.00 0.00 32.19 2.73
946 956 3.589288 AGACAGTGGGCTAAGAAAATCCT 59.411 43.478 0.00 0.00 0.00 3.24
965 975 1.270826 CTGCTGAAAGAGAGACGACCA 59.729 52.381 0.00 0.00 34.07 4.02
1146 1156 2.735857 GCCGGCGTAAACGTCAGT 60.736 61.111 12.58 0.00 45.47 3.41
1237 1247 2.660552 ACAACGTGGTCTTCGGCG 60.661 61.111 0.00 0.00 0.00 6.46
1246 1256 0.320508 GGTCTTCGGCGAGGAAAACT 60.321 55.000 23.59 0.00 0.00 2.66
1273 1283 4.610333 TGAAGAAGATCCTGCCTACAGTA 58.390 43.478 0.00 0.00 42.81 2.74
1288 1298 5.012148 GCCTACAGTACATGGATGGTAAGAT 59.988 44.000 0.00 0.00 0.00 2.40
1289 1299 6.464465 GCCTACAGTACATGGATGGTAAGATT 60.464 42.308 0.00 0.00 0.00 2.40
1290 1300 7.509546 CCTACAGTACATGGATGGTAAGATTT 58.490 38.462 0.00 0.00 0.00 2.17
1293 1303 8.281212 ACAGTACATGGATGGTAAGATTTTTC 57.719 34.615 0.00 0.00 0.00 2.29
1295 1305 8.906867 CAGTACATGGATGGTAAGATTTTTCAT 58.093 33.333 0.00 0.00 0.00 2.57
1296 1306 8.906867 AGTACATGGATGGTAAGATTTTTCATG 58.093 33.333 0.00 0.00 36.51 3.07
1297 1307 7.959658 ACATGGATGGTAAGATTTTTCATGA 57.040 32.000 0.00 0.00 35.06 3.07
1298 1308 8.543293 ACATGGATGGTAAGATTTTTCATGAT 57.457 30.769 0.00 0.00 35.06 2.45
1300 1310 9.472361 CATGGATGGTAAGATTTTTCATGATTC 57.528 33.333 0.00 0.00 33.46 2.52
1301 1311 8.010733 TGGATGGTAAGATTTTTCATGATTCC 57.989 34.615 0.00 0.00 0.00 3.01
1302 1312 7.840716 TGGATGGTAAGATTTTTCATGATTCCT 59.159 33.333 0.00 0.00 0.00 3.36
1303 1313 8.699130 GGATGGTAAGATTTTTCATGATTCCTT 58.301 33.333 0.00 0.00 0.00 3.36
1311 1321 7.662669 AGATTTTTCATGATTCCTTTTTGGGTG 59.337 33.333 0.00 0.00 36.20 4.61
1312 1322 6.491714 TTTTCATGATTCCTTTTTGGGTGA 57.508 33.333 0.00 0.00 36.20 4.02
1313 1323 5.467035 TTCATGATTCCTTTTTGGGTGAC 57.533 39.130 0.00 0.00 36.20 3.67
1316 1326 4.088056 TGATTCCTTTTTGGGTGACGTA 57.912 40.909 0.00 0.00 36.20 3.57
1317 1327 3.816523 TGATTCCTTTTTGGGTGACGTAC 59.183 43.478 0.00 0.00 36.20 3.67
1318 1328 3.564053 TTCCTTTTTGGGTGACGTACT 57.436 42.857 0.00 0.00 36.20 2.73
1320 1330 3.993920 TCCTTTTTGGGTGACGTACTAC 58.006 45.455 0.00 0.00 36.20 2.73
1321 1331 3.642848 TCCTTTTTGGGTGACGTACTACT 59.357 43.478 0.00 0.00 36.20 2.57
1322 1332 4.832266 TCCTTTTTGGGTGACGTACTACTA 59.168 41.667 0.00 0.00 36.20 1.82
1323 1333 5.047802 TCCTTTTTGGGTGACGTACTACTAG 60.048 44.000 0.00 0.00 36.20 2.57
1324 1334 5.279156 CCTTTTTGGGTGACGTACTACTAGT 60.279 44.000 0.00 0.00 0.00 2.57
1325 1335 6.071952 CCTTTTTGGGTGACGTACTACTAGTA 60.072 42.308 1.89 1.89 0.00 1.82
1326 1336 6.500684 TTTTGGGTGACGTACTACTAGTAG 57.499 41.667 25.30 25.30 39.04 2.57
1328 1338 5.932619 TGGGTGACGTACTACTAGTAGTA 57.067 43.478 30.50 30.50 43.98 1.82
1367 1377 7.268586 TCTGAAGAAAGACTTACAGATATGCC 58.731 38.462 0.00 0.00 39.13 4.40
1372 1382 7.856415 AGAAAGACTTACAGATATGCCTCTTT 58.144 34.615 0.00 0.00 31.09 2.52
1373 1383 7.984617 AGAAAGACTTACAGATATGCCTCTTTC 59.015 37.037 15.21 15.21 41.05 2.62
1375 1385 5.361285 AGACTTACAGATATGCCTCTTTCGT 59.639 40.000 0.00 0.00 0.00 3.85
1378 1388 4.207891 ACAGATATGCCTCTTTCGTTGT 57.792 40.909 0.00 0.00 0.00 3.32
1479 1489 0.614979 ACTACGATGGCACCCTGTCT 60.615 55.000 0.00 0.00 0.00 3.41
1536 1546 6.069088 TGTCCCCTGTGGTAAATCAGAATAAT 60.069 38.462 0.00 0.00 34.02 1.28
1602 1612 3.685550 GCACCTGCTTATAGTTGTCCCAT 60.686 47.826 0.00 0.00 38.21 4.00
1605 1615 5.527582 CACCTGCTTATAGTTGTCCCATAAC 59.472 44.000 0.00 0.00 0.00 1.89
1606 1616 5.190925 ACCTGCTTATAGTTGTCCCATAACA 59.809 40.000 0.00 0.00 0.00 2.41
1616 1626 7.839680 AGTTGTCCCATAACATTTTTCTCTT 57.160 32.000 0.00 0.00 0.00 2.85
1633 1643 3.636300 TCTCTTCTTAGATGAGAGCTGCC 59.364 47.826 19.64 0.00 37.74 4.85
1660 1670 1.183676 ACGTCGCCAAGTACTTCCCT 61.184 55.000 4.77 0.00 0.00 4.20
1663 1673 1.192146 TCGCCAAGTACTTCCCTGCT 61.192 55.000 4.77 0.00 0.00 4.24
1697 1707 2.117051 GAAGGTCCCGGAAGAAGGTAT 58.883 52.381 0.73 0.00 0.00 2.73
1702 1712 3.644738 GGTCCCGGAAGAAGGTATTGATA 59.355 47.826 0.73 0.00 0.00 2.15
1707 1717 6.785963 TCCCGGAAGAAGGTATTGATAACTAT 59.214 38.462 0.73 0.00 28.28 2.12
1708 1718 7.951806 TCCCGGAAGAAGGTATTGATAACTATA 59.048 37.037 0.73 0.00 28.28 1.31
1709 1719 8.759782 CCCGGAAGAAGGTATTGATAACTATAT 58.240 37.037 0.73 0.00 28.28 0.86
1710 1720 9.587772 CCGGAAGAAGGTATTGATAACTATATG 57.412 37.037 0.00 0.00 28.28 1.78
1775 1786 2.373169 TCCTCCCCAGTGATATGCAATC 59.627 50.000 0.00 0.00 0.00 2.67
1823 1834 7.649533 TGCATGTTTGATTTCAGAATCCTAT 57.350 32.000 0.00 0.00 40.79 2.57
1918 1929 1.577736 AGGAACTCTGCTATGCTGGT 58.422 50.000 0.00 0.00 0.00 4.00
1965 1976 5.784750 TCTTCTTCAGCACATTATGAACG 57.215 39.130 0.00 0.00 32.25 3.95
2041 2052 5.090652 TCACTGTCTTTTCGCATAAACAC 57.909 39.130 0.00 0.00 0.00 3.32
2049 2060 8.293157 TGTCTTTTCGCATAAACACAAATATGA 58.707 29.630 0.00 0.00 32.43 2.15
2065 2076 7.269724 CACAAATATGATATGCGTGCAATACTG 59.730 37.037 0.00 0.00 0.00 2.74
2155 2166 0.108186 TGATCGATGAGGTGCGCTTT 60.108 50.000 9.73 0.00 0.00 3.51
2205 2216 7.324375 TGACAAACTGTAATACTTTAGTCGACG 59.676 37.037 10.46 0.00 0.00 5.12
2266 2277 3.256383 TCCATTCATGCAAAGTTCAGTGG 59.744 43.478 0.00 0.00 0.00 4.00
2313 2332 0.106918 TCGCAACAGGTTTCCAAGGT 60.107 50.000 0.00 0.00 0.00 3.50
2333 2352 0.390472 CCTCTTGGAAGTCACGAGCC 60.390 60.000 0.00 0.00 39.57 4.70
2380 2399 2.863740 CAACAAGTTCTGCGTGTCTGTA 59.136 45.455 0.00 0.00 38.82 2.74
2395 2414 2.091588 GTCTGTACATTACCGCAACGTG 59.908 50.000 0.00 0.00 0.00 4.49
2434 2458 2.345244 CGCCTCAAGCACTGGACT 59.655 61.111 0.00 0.00 44.04 3.85
2435 2459 2.031516 CGCCTCAAGCACTGGACTG 61.032 63.158 0.00 0.00 44.04 3.51
2436 2460 1.372683 GCCTCAAGCACTGGACTGA 59.627 57.895 0.00 0.00 42.97 3.41
2437 2461 0.035630 GCCTCAAGCACTGGACTGAT 60.036 55.000 0.00 0.00 42.97 2.90
2442 2466 1.601171 AGCACTGGACTGATGCTCC 59.399 57.895 0.00 0.00 46.68 4.70
2443 2467 1.451028 GCACTGGACTGATGCTCCC 60.451 63.158 0.00 0.00 36.40 4.30
2459 2483 2.709213 CTCCCTTTTGCCTCTTCTCTG 58.291 52.381 0.00 0.00 0.00 3.35
2478 2502 1.010046 TGGGTCTCTCCTTCCATGGAT 59.990 52.381 17.06 0.00 35.30 3.41
2520 2556 2.146342 CTGACAGTTTTGCCTGATCGT 58.854 47.619 0.00 0.00 36.30 3.73
2574 2610 2.610859 TGCTGGAGGACTTCCCCC 60.611 66.667 0.38 0.00 46.19 5.40
2575 2611 3.787001 GCTGGAGGACTTCCCCCG 61.787 72.222 0.38 0.00 46.19 5.73
2594 2630 1.537348 CGTCTCAAAGTGACCAACGGA 60.537 52.381 0.00 0.00 0.00 4.69
2618 2654 4.320870 GAATGGTTTTAGAGGTTCGTCCA 58.679 43.478 2.77 0.00 39.02 4.02
2690 2726 1.213013 GCTGAGCGACTCCGAGAAA 59.787 57.895 1.33 0.00 38.22 2.52
2699 2735 2.104170 GACTCCGAGAAAGTGATCCCT 58.896 52.381 1.33 0.00 0.00 4.20
2759 2795 5.324832 TCAAGGTTCCCATTTCTTTCTCT 57.675 39.130 0.00 0.00 0.00 3.10
2780 2816 1.792301 CAGCTGTGCAGTCCATTCG 59.208 57.895 5.25 0.00 0.00 3.34
2789 2825 1.672881 GCAGTCCATTCGGATCTTTGG 59.327 52.381 0.00 0.00 45.33 3.28
2790 2826 1.672881 CAGTCCATTCGGATCTTTGGC 59.327 52.381 0.00 0.00 45.33 4.52
2793 2829 1.447317 CCATTCGGATCTTTGGCCCG 61.447 60.000 0.00 0.00 44.22 6.13
2794 2830 1.152963 ATTCGGATCTTTGGCCCGG 60.153 57.895 0.00 0.00 43.16 5.73
2795 2831 3.987954 TTCGGATCTTTGGCCCGGC 62.988 63.158 0.00 0.00 43.16 6.13
2805 2841 3.440415 GGCCCGGCTGTAAACTGC 61.440 66.667 9.86 3.60 39.66 4.40
2902 2939 3.431725 GCGCCCAAGGAAACCGAG 61.432 66.667 0.00 0.00 0.00 4.63
2938 2975 2.038033 CAGGGACCCGTCTGAAGTAAAA 59.962 50.000 4.40 0.00 33.11 1.52
2984 3021 0.473755 TCCTGCTGGCTCTGTTCAAA 59.526 50.000 4.42 0.00 0.00 2.69
3047 3088 2.368875 GTTCCTGAACTCCTTGGTGAGA 59.631 50.000 2.80 0.00 38.25 3.27
3086 3129 5.064452 GCTATGAACAAACAGGAGATGACTG 59.936 44.000 0.00 0.00 41.64 3.51
3115 3158 2.327940 GCGACAGTTTTGCAGCGT 59.672 55.556 0.00 0.00 34.24 5.07
3124 3167 0.532573 TTTTGCAGCGTTGGAAACCA 59.467 45.000 17.90 2.58 46.28 3.67
3212 3255 3.077359 GCTAGTCATGTTCTTTGCCACT 58.923 45.455 0.00 0.00 0.00 4.00
3331 3374 2.396601 CGGTAGCGTGTGAACTTACAA 58.603 47.619 6.07 0.00 31.36 2.41
3335 3378 3.173668 AGCGTGTGAACTTACAAGTGA 57.826 42.857 0.00 0.00 39.66 3.41
3455 3498 2.314647 GCGTGAACGTAGCCAGCAA 61.315 57.895 4.59 0.00 42.22 3.91
3701 3763 9.823647 CTCCTCTTTTTATACTTGATGCTAAGA 57.176 33.333 0.00 0.00 0.00 2.10
3799 3865 4.931661 TTTCTCTTGGTCTGTTACGACT 57.068 40.909 0.00 0.00 34.38 4.18
3853 4055 5.605564 TCGTAAGGTCAACAAACATCATG 57.394 39.130 0.00 0.00 38.47 3.07
4035 5852 3.542969 AAAGGCTTTCCTAACCCATGT 57.457 42.857 6.68 0.00 43.40 3.21
4063 6489 2.542595 CGTAATCAGAAATACGGGTGGC 59.457 50.000 10.03 0.00 40.78 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 192 3.689161 TGGTGAGTGTTTCTGTTTCTGTG 59.311 43.478 0.00 0.00 0.00 3.66
192 193 3.950397 TGGTGAGTGTTTCTGTTTCTGT 58.050 40.909 0.00 0.00 0.00 3.41
257 258 1.577328 GATATGCCGGCCCAATCACG 61.577 60.000 26.77 0.00 0.00 4.35
388 393 8.947055 AATGTCAAAGTAAAAACTTGCAGATT 57.053 26.923 0.00 0.00 0.00 2.40
422 427 3.160269 ACATCCAGAAAAAGCAGAAGGG 58.840 45.455 0.00 0.00 0.00 3.95
507 512 2.987213 TTCCACGACGTCGACAACCG 62.987 60.000 41.52 21.19 43.02 4.44
580 585 2.806244 AGGTGTCACTGCACGAATTAAC 59.194 45.455 2.35 0.00 40.08 2.01
836 846 2.675348 GCAGAATACCTGTGAACTGAGC 59.325 50.000 0.00 0.00 44.71 4.26
852 862 4.520492 GGAGGAAGTTCATCAAAAGCAGAA 59.480 41.667 18.46 0.00 0.00 3.02
946 956 1.000163 GTGGTCGTCTCTCTTTCAGCA 60.000 52.381 0.00 0.00 0.00 4.41
965 975 2.994186 AAAAGTGTGGTCAGTACGGT 57.006 45.000 0.00 0.00 0.00 4.83
1146 1156 1.456196 CCTCCTCGATCTTGCGCCTA 61.456 60.000 4.18 0.00 0.00 3.93
1191 1201 2.218953 GTGGCGACGAGGATTTCATA 57.781 50.000 0.00 0.00 0.00 2.15
1237 1247 4.137543 TCTTCTTCAGGCAAGTTTTCCTC 58.862 43.478 0.00 0.00 33.27 3.71
1246 1256 1.340405 GGCAGGATCTTCTTCAGGCAA 60.340 52.381 0.00 0.00 0.00 4.52
1273 1283 7.959658 TCATGAAAAATCTTACCATCCATGT 57.040 32.000 0.00 0.00 32.95 3.21
1288 1298 6.765512 GTCACCCAAAAAGGAATCATGAAAAA 59.234 34.615 0.00 0.00 41.22 1.94
1289 1299 6.287525 GTCACCCAAAAAGGAATCATGAAAA 58.712 36.000 0.00 0.00 41.22 2.29
1290 1300 5.508825 CGTCACCCAAAAAGGAATCATGAAA 60.509 40.000 0.00 0.00 41.22 2.69
1293 1303 3.255642 ACGTCACCCAAAAAGGAATCATG 59.744 43.478 0.00 0.00 41.22 3.07
1295 1305 2.938838 ACGTCACCCAAAAAGGAATCA 58.061 42.857 0.00 0.00 41.22 2.57
1296 1306 4.070009 AGTACGTCACCCAAAAAGGAATC 58.930 43.478 0.00 0.00 41.22 2.52
1297 1307 4.094830 AGTACGTCACCCAAAAAGGAAT 57.905 40.909 0.00 0.00 41.22 3.01
1298 1308 3.564053 AGTACGTCACCCAAAAAGGAA 57.436 42.857 0.00 0.00 41.22 3.36
1300 1310 3.999046 AGTAGTACGTCACCCAAAAAGG 58.001 45.455 0.00 0.00 37.03 3.11
1301 1311 5.776744 ACTAGTAGTACGTCACCCAAAAAG 58.223 41.667 0.00 0.00 0.00 2.27
1302 1312 5.789643 ACTAGTAGTACGTCACCCAAAAA 57.210 39.130 0.00 0.00 0.00 1.94
1303 1313 6.003950 ACTACTAGTAGTACGTCACCCAAAA 58.996 40.000 29.96 0.00 43.98 2.44
1304 1314 5.560724 ACTACTAGTAGTACGTCACCCAAA 58.439 41.667 29.96 0.00 43.98 3.28
1305 1315 5.165961 ACTACTAGTAGTACGTCACCCAA 57.834 43.478 29.96 0.00 43.98 4.12
1306 1316 4.826274 ACTACTAGTAGTACGTCACCCA 57.174 45.455 29.96 0.00 43.98 4.51
1321 1331 8.260099 TCAGAAGAGGCATACTAGTACTACTA 57.740 38.462 4.31 0.00 0.00 1.82
1322 1332 7.139287 TCAGAAGAGGCATACTAGTACTACT 57.861 40.000 4.31 3.32 0.00 2.57
1323 1333 7.716123 TCTTCAGAAGAGGCATACTAGTACTAC 59.284 40.741 8.95 0.00 32.71 2.73
1324 1334 7.803131 TCTTCAGAAGAGGCATACTAGTACTA 58.197 38.462 8.95 1.89 32.71 1.82
1325 1335 6.664714 TCTTCAGAAGAGGCATACTAGTACT 58.335 40.000 8.95 0.00 32.71 2.73
1326 1336 6.945938 TCTTCAGAAGAGGCATACTAGTAC 57.054 41.667 8.95 0.00 32.71 2.73
1327 1337 7.834681 TCTTTCTTCAGAAGAGGCATACTAGTA 59.165 37.037 12.74 4.77 39.03 1.82
1328 1338 6.665680 TCTTTCTTCAGAAGAGGCATACTAGT 59.334 38.462 12.74 0.00 39.03 2.57
1329 1339 6.978080 GTCTTTCTTCAGAAGAGGCATACTAG 59.022 42.308 12.74 0.00 39.03 2.57
1330 1340 6.665680 AGTCTTTCTTCAGAAGAGGCATACTA 59.334 38.462 12.74 0.00 39.03 1.82
1331 1341 5.483583 AGTCTTTCTTCAGAAGAGGCATACT 59.516 40.000 12.74 10.30 39.03 2.12
1332 1342 5.729510 AGTCTTTCTTCAGAAGAGGCATAC 58.270 41.667 12.74 8.49 39.03 2.39
1367 1377 3.914364 GCATTTTGCCTACAACGAAAGAG 59.086 43.478 0.00 0.00 37.42 2.85
1392 1402 1.059098 TGAAGGAAGCCAGAGCAGAA 58.941 50.000 0.00 0.00 43.56 3.02
1536 1546 8.750298 AGAATTGCTACTAGTAGTTTAAGCAGA 58.250 33.333 26.76 14.23 38.23 4.26
1555 1565 7.412237 GCTCATTTGTTGATAACCAAGAATTGC 60.412 37.037 0.00 0.00 38.13 3.56
1558 1568 7.092716 GTGCTCATTTGTTGATAACCAAGAAT 58.907 34.615 0.00 0.00 37.77 2.40
1605 1615 8.605746 CAGCTCTCATCTAAGAAGAGAAAAATG 58.394 37.037 6.55 1.02 36.26 2.32
1606 1616 7.280652 GCAGCTCTCATCTAAGAAGAGAAAAAT 59.719 37.037 6.55 0.00 36.26 1.82
1615 1625 2.103373 ACGGCAGCTCTCATCTAAGAA 58.897 47.619 0.00 0.00 0.00 2.52
1616 1626 1.406898 CACGGCAGCTCTCATCTAAGA 59.593 52.381 0.00 0.00 0.00 2.10
1663 1673 2.125552 CTTCCGCTGACGATGGCA 60.126 61.111 0.00 0.00 43.93 4.92
1707 1717 8.935844 CATGTGCAAAGAGTTAGTAACTTCATA 58.064 33.333 16.56 8.77 43.03 2.15
1708 1718 7.445402 ACATGTGCAAAGAGTTAGTAACTTCAT 59.555 33.333 16.56 9.76 43.03 2.57
1709 1719 6.765989 ACATGTGCAAAGAGTTAGTAACTTCA 59.234 34.615 16.56 7.61 43.03 3.02
1710 1720 7.042051 TGACATGTGCAAAGAGTTAGTAACTTC 60.042 37.037 16.56 9.94 43.03 3.01
1711 1721 6.765989 TGACATGTGCAAAGAGTTAGTAACTT 59.234 34.615 16.56 4.74 43.03 2.66
1712 1722 6.202954 GTGACATGTGCAAAGAGTTAGTAACT 59.797 38.462 15.48 15.48 46.38 2.24
1713 1723 6.202954 AGTGACATGTGCAAAGAGTTAGTAAC 59.797 38.462 1.15 4.78 0.00 2.50
1714 1724 6.202762 CAGTGACATGTGCAAAGAGTTAGTAA 59.797 38.462 1.15 0.00 0.00 2.24
1859 1870 8.292444 TCAAGAACCTACATAAATTGGAATGG 57.708 34.615 0.00 0.00 0.00 3.16
1874 1885 8.665643 TTCAGTTTTACGAATTCAAGAACCTA 57.334 30.769 6.22 0.00 0.00 3.08
1918 1929 5.606329 TGTCATTATGTCCATCCCATGACTA 59.394 40.000 18.46 9.47 40.70 2.59
1965 1976 1.000060 TGCTCACCTTTTCAGCATTGC 60.000 47.619 0.00 0.00 38.25 3.56
2041 2052 7.479603 GTCAGTATTGCACGCATATCATATTTG 59.520 37.037 0.00 0.00 0.00 2.32
2049 2060 2.135139 CCGTCAGTATTGCACGCATAT 58.865 47.619 0.00 0.00 32.03 1.78
2155 2166 9.725019 TCAGCTTCATCAGAGTTAAATAAGAAA 57.275 29.630 0.00 0.00 0.00 2.52
2205 2216 4.398044 TGAAGTTTCAGTTTCAGTTGTCCC 59.602 41.667 0.00 0.00 32.50 4.46
2313 2332 0.603569 GCTCGTGACTTCCAAGAGGA 59.396 55.000 9.33 0.00 46.84 3.71
2333 2352 2.021931 GCTTGCGCCTTCGATTCG 59.978 61.111 4.18 0.00 38.10 3.34
2380 2399 1.286354 CGTCCACGTTGCGGTAATGT 61.286 55.000 0.00 0.00 39.06 2.71
2395 2414 3.072211 CAGGGTTTTTACCTTCTCGTCC 58.928 50.000 0.00 0.00 35.78 4.79
2434 2458 0.700564 AGAGGCAAAAGGGAGCATCA 59.299 50.000 0.00 0.00 43.39 3.07
2435 2459 1.747924 GAAGAGGCAAAAGGGAGCATC 59.252 52.381 0.00 0.00 41.46 3.91
2436 2460 1.357079 AGAAGAGGCAAAAGGGAGCAT 59.643 47.619 0.00 0.00 0.00 3.79
2437 2461 0.773644 AGAAGAGGCAAAAGGGAGCA 59.226 50.000 0.00 0.00 0.00 4.26
2442 2466 1.074566 ACCCAGAGAAGAGGCAAAAGG 59.925 52.381 0.00 0.00 0.00 3.11
2443 2467 2.039613 AGACCCAGAGAAGAGGCAAAAG 59.960 50.000 0.00 0.00 0.00 2.27
2459 2483 1.419387 CATCCATGGAAGGAGAGACCC 59.581 57.143 20.67 0.00 41.90 4.46
2520 2556 1.379977 CGACCAGCTCCCAGTCCTA 60.380 63.158 0.00 0.00 0.00 2.94
2574 2610 0.859232 CCGTTGGTCACTTTGAGACG 59.141 55.000 0.00 0.00 36.87 4.18
2575 2611 1.865340 GTCCGTTGGTCACTTTGAGAC 59.135 52.381 0.00 0.00 35.29 3.36
2594 2630 3.999046 ACGAACCTCTAAAACCATTCGT 58.001 40.909 4.15 4.15 45.15 3.85
2618 2654 0.898320 CCTTGTCCCAGTCGATCACT 59.102 55.000 0.00 0.00 34.67 3.41
2690 2726 3.093057 GCCGATGTAGATAGGGATCACT 58.907 50.000 1.44 1.44 34.17 3.41
2699 2735 0.870393 GGTCGTCGCCGATGTAGATA 59.130 55.000 6.17 0.00 46.30 1.98
2759 2795 2.702040 AATGGACTGCACAGCTGCCA 62.702 55.000 15.27 12.42 43.51 4.92
2780 2816 2.265467 TACAGCCGGGCCAAAGATCC 62.265 60.000 17.02 0.00 0.00 3.36
2789 2825 2.200170 CTTGCAGTTTACAGCCGGGC 62.200 60.000 12.11 12.11 0.00 6.13
2790 2826 1.875963 CTTGCAGTTTACAGCCGGG 59.124 57.895 2.18 0.00 0.00 5.73
2793 2829 1.238439 TGAGCTTGCAGTTTACAGCC 58.762 50.000 2.23 0.00 0.00 4.85
2794 2830 2.415090 CCATGAGCTTGCAGTTTACAGC 60.415 50.000 0.00 0.00 0.00 4.40
2795 2831 2.816087 ACCATGAGCTTGCAGTTTACAG 59.184 45.455 0.00 0.00 0.00 2.74
2805 2841 2.363683 GGGAAGAAGACCATGAGCTTG 58.636 52.381 0.00 0.00 0.00 4.01
2902 2939 1.439644 CCTGAGCGAGTAGAAGGCC 59.560 63.158 0.00 0.00 0.00 5.19
2938 2975 6.037610 CAGAGCACACAAAAACTAGAAAGAGT 59.962 38.462 0.00 0.00 0.00 3.24
2953 2990 2.031616 GCAGGAGCAGAGCACACA 59.968 61.111 0.00 0.00 41.58 3.72
2954 2991 2.033755 CAGCAGGAGCAGAGCACAC 61.034 63.158 0.00 0.00 45.49 3.82
2984 3021 4.202441 CCAAACGATCAGGAATCCATTCT 58.798 43.478 0.61 0.00 37.00 2.40
3086 3129 0.243095 ACTGTCGCCTCGGAAACTAC 59.757 55.000 0.00 0.00 0.00 2.73
3087 3130 0.963962 AACTGTCGCCTCGGAAACTA 59.036 50.000 0.00 0.00 0.00 2.24
3115 3158 2.169769 CGACCCTAGCTATGGTTTCCAA 59.830 50.000 20.20 0.00 36.95 3.53
3124 3167 4.800914 GCAACATCATTCGACCCTAGCTAT 60.801 45.833 0.00 0.00 0.00 2.97
3212 3255 2.749076 CAGCCACCGATCAAATTTCTCA 59.251 45.455 0.00 0.00 0.00 3.27
3331 3374 5.129485 AGAGTATGGGATTTCGTCAATCACT 59.871 40.000 11.84 7.02 44.78 3.41
3335 3378 5.989477 TCAAGAGTATGGGATTTCGTCAAT 58.011 37.500 0.00 0.00 0.00 2.57
3455 3498 2.750141 TCTGGGCGTCTTCTACCTAT 57.250 50.000 0.00 0.00 0.00 2.57
3701 3763 2.838637 TTTGGTTTTGGTCCCTGTCT 57.161 45.000 0.00 0.00 0.00 3.41
3799 3865 6.153340 GGGAGAATGTTGGAATTTGATCTCAA 59.847 38.462 0.00 0.00 35.04 3.02
3967 5554 8.265055 TCTTGTAAACCATCTCCCATAAAGTAG 58.735 37.037 0.00 0.00 0.00 2.57
4035 5852 3.548668 CGTATTTCTGATTACGTTGCCGA 59.451 43.478 0.00 0.00 37.13 5.54
4043 5860 2.542595 CGCCACCCGTATTTCTGATTAC 59.457 50.000 0.00 0.00 0.00 1.89
4050 6476 2.178235 GGCTCGCCACCCGTATTTC 61.178 63.158 2.41 0.00 38.35 2.17


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

AutoCloner maintained by Alex Coulton.