Multiple sequence alignment - TraesCS5D01G462600

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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 TraesCS5D01G462600 chr5D 100.000 3350 0 0 1 3350 506164331 506160982 0.000000e+00 6187.0
1 TraesCS5D01G462600 chr5D 82.684 693 97 18 2671 3350 65900688 65900006 8.000000e-166 593.0
2 TraesCS5D01G462600 chr5D 82.036 334 34 11 276 606 539775736 539775426 9.220000e-66 261.0
3 TraesCS5D01G462600 chr5D 95.161 62 2 1 605 665 213254905 213254966 2.750000e-16 97.1
4 TraesCS5D01G462600 chr5D 73.973 219 40 12 4 218 446139187 446138982 4.640000e-09 73.1
5 TraesCS5D01G462600 chr5B 90.408 2033 116 31 664 2662 636902260 636900273 0.000000e+00 2601.0
6 TraesCS5D01G462600 chr5B 89.592 490 35 9 772 1255 636909903 636909424 2.860000e-170 608.0
7 TraesCS5D01G462600 chr5B 83.179 648 82 16 2708 3350 471139282 471139907 4.850000e-158 568.0
8 TraesCS5D01G462600 chr5B 84.725 563 75 10 2791 3348 65192812 65193368 1.360000e-153 553.0
9 TraesCS5D01G462600 chr5B 94.737 285 11 3 1 285 636911146 636910866 1.100000e-119 440.0
10 TraesCS5D01G462600 chr5B 89.189 333 7 8 284 606 636910772 636910459 4.050000e-104 388.0
11 TraesCS5D01G462600 chr5B 87.755 343 20 9 2341 2662 636897978 636897637 6.780000e-102 381.0
12 TraesCS5D01G462600 chr5B 78.078 333 30 23 276 589 681772275 681771967 1.600000e-38 171.0
13 TraesCS5D01G462600 chr5B 91.111 90 3 2 2574 2662 636899539 636899454 2.110000e-22 117.0
14 TraesCS5D01G462600 chr5B 74.257 303 47 20 6 301 470182397 470182119 7.650000e-17 99.0
15 TraesCS5D01G462600 chr5B 96.226 53 1 1 681 733 636910180 636910129 5.960000e-13 86.1
16 TraesCS5D01G462600 chr3D 84.534 1416 179 23 968 2369 598097581 598096192 0.000000e+00 1365.0
17 TraesCS5D01G462600 chr3D 79.908 1309 218 28 1055 2342 586104592 586103308 0.000000e+00 918.0
18 TraesCS5D01G462600 chr3D 80.142 1128 170 38 1226 2342 551574848 551575932 0.000000e+00 793.0
19 TraesCS5D01G462600 chr3D 78.180 1187 196 41 1026 2195 551624337 551625477 0.000000e+00 699.0
20 TraesCS5D01G462600 chr3D 82.870 683 104 9 2674 3350 452369926 452369251 4.780000e-168 601.0
21 TraesCS5D01G462600 chr3D 81.690 639 96 18 1606 2241 582044725 582045345 2.310000e-141 512.0
22 TraesCS5D01G462600 chr3D 76.838 272 40 11 4 273 23156297 23156547 7.540000e-27 132.0
23 TraesCS5D01G462600 chr3A 83.569 1412 191 23 968 2365 728106998 728105614 0.000000e+00 1284.0
24 TraesCS5D01G462600 chr3A 83.915 889 110 19 968 1847 728256672 728255808 0.000000e+00 819.0
25 TraesCS5D01G462600 chr3A 74.160 387 60 29 70 438 597966937 597967301 1.260000e-24 124.0
26 TraesCS5D01G462600 chr3B 80.995 1326 203 32 1051 2350 782677381 782678683 0.000000e+00 1007.0
27 TraesCS5D01G462600 chr3B 78.760 1323 223 37 1054 2350 732886259 732884969 0.000000e+00 833.0
28 TraesCS5D01G462600 chr3B 77.584 1316 250 32 1052 2349 734145323 734144035 0.000000e+00 754.0
29 TraesCS5D01G462600 chr3B 82.277 852 133 10 1237 2082 805042042 805041203 0.000000e+00 721.0
30 TraesCS5D01G462600 chr3B 79.672 305 38 14 943 1238 805042375 805042086 7.330000e-47 198.0
31 TraesCS5D01G462600 chr3B 76.900 329 49 18 14 338 59733681 59733376 9.620000e-36 161.0
32 TraesCS5D01G462600 chr7D 82.694 1121 137 26 968 2076 555404631 555403556 0.000000e+00 942.0
33 TraesCS5D01G462600 chr7D 81.214 692 109 17 2671 3350 634808446 634807764 3.800000e-149 538.0
34 TraesCS5D01G462600 chr6A 77.453 1264 182 62 1047 2250 569390425 569391645 0.000000e+00 660.0
35 TraesCS5D01G462600 chr6A 82.533 687 99 17 2674 3350 419744890 419744215 4.820000e-163 584.0
36 TraesCS5D01G462600 chr6A 70.925 1221 278 58 1063 2255 484409989 484408818 2.020000e-52 217.0
37 TraesCS5D01G462600 chr6A 80.608 263 34 8 1 260 22622790 22622542 1.590000e-43 187.0
38 TraesCS5D01G462600 chr4D 84.978 679 68 19 2672 3350 137888516 137889160 0.000000e+00 658.0
39 TraesCS5D01G462600 chr4D 96.970 33 0 1 4 35 386497269 386497237 2.000000e-03 54.7
40 TraesCS5D01G462600 chr1D 83.187 684 102 9 2674 3350 398245640 398244963 6.140000e-172 614.0
41 TraesCS5D01G462600 chr1D 85.000 580 83 3 2772 3350 398244340 398243764 1.340000e-163 586.0
42 TraesCS5D01G462600 chr1D 78.893 289 39 18 153 425 470588601 470588319 3.440000e-40 176.0
43 TraesCS5D01G462600 chr6D 81.331 691 100 24 2675 3350 151496217 151496893 4.920000e-148 534.0
44 TraesCS5D01G462600 chr6D 82.843 204 30 4 1786 1988 424709246 424709047 9.550000e-41 178.0
45 TraesCS5D01G462600 chr6D 76.978 139 26 6 4 140 470760326 470760460 1.290000e-09 75.0
46 TraesCS5D01G462600 chr2A 75.694 432 73 28 185 605 85294012 85293602 1.590000e-43 187.0
47 TraesCS5D01G462600 chr2A 88.710 62 5 2 228 287 759302847 759302786 1.290000e-09 75.0
48 TraesCS5D01G462600 chr5A 77.301 326 53 15 185 496 109934787 109935105 4.440000e-39 172.0
49 TraesCS5D01G462600 chrUn 73.593 231 56 4 1196 1425 324143498 324143724 2.140000e-12 84.2
50 TraesCS5D01G462600 chrUn 97.297 37 1 0 311 347 220716580 220716544 2.790000e-06 63.9
51 TraesCS5D01G462600 chr4B 77.273 132 19 8 4 132 473864586 473864463 2.160000e-07 67.6
52 TraesCS5D01G462600 chr4B 97.297 37 1 0 311 347 15681438 15681474 2.790000e-06 63.9
53 TraesCS5D01G462600 chr4B 97.297 37 1 0 311 347 15692154 15692190 2.790000e-06 63.9


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 TraesCS5D01G462600 chr5D 506160982 506164331 3349 True 6187.000 6187 100.0000 1 3350 1 chr5D.!!$R3 3349
1 TraesCS5D01G462600 chr5D 65900006 65900688 682 True 593.000 593 82.6840 2671 3350 1 chr5D.!!$R1 679
2 TraesCS5D01G462600 chr5B 636897637 636902260 4623 True 1033.000 2601 89.7580 664 2662 3 chr5B.!!$R3 1998
3 TraesCS5D01G462600 chr5B 471139282 471139907 625 False 568.000 568 83.1790 2708 3350 1 chr5B.!!$F2 642
4 TraesCS5D01G462600 chr5B 65192812 65193368 556 False 553.000 553 84.7250 2791 3348 1 chr5B.!!$F1 557
5 TraesCS5D01G462600 chr5B 636909424 636911146 1722 True 380.525 608 92.4360 1 1255 4 chr5B.!!$R4 1254
6 TraesCS5D01G462600 chr3D 598096192 598097581 1389 True 1365.000 1365 84.5340 968 2369 1 chr3D.!!$R3 1401
7 TraesCS5D01G462600 chr3D 586103308 586104592 1284 True 918.000 918 79.9080 1055 2342 1 chr3D.!!$R2 1287
8 TraesCS5D01G462600 chr3D 551574848 551575932 1084 False 793.000 793 80.1420 1226 2342 1 chr3D.!!$F2 1116
9 TraesCS5D01G462600 chr3D 551624337 551625477 1140 False 699.000 699 78.1800 1026 2195 1 chr3D.!!$F3 1169
10 TraesCS5D01G462600 chr3D 452369251 452369926 675 True 601.000 601 82.8700 2674 3350 1 chr3D.!!$R1 676
11 TraesCS5D01G462600 chr3D 582044725 582045345 620 False 512.000 512 81.6900 1606 2241 1 chr3D.!!$F4 635
12 TraesCS5D01G462600 chr3A 728105614 728106998 1384 True 1284.000 1284 83.5690 968 2365 1 chr3A.!!$R1 1397
13 TraesCS5D01G462600 chr3A 728255808 728256672 864 True 819.000 819 83.9150 968 1847 1 chr3A.!!$R2 879
14 TraesCS5D01G462600 chr3B 782677381 782678683 1302 False 1007.000 1007 80.9950 1051 2350 1 chr3B.!!$F1 1299
15 TraesCS5D01G462600 chr3B 732884969 732886259 1290 True 833.000 833 78.7600 1054 2350 1 chr3B.!!$R2 1296
16 TraesCS5D01G462600 chr3B 734144035 734145323 1288 True 754.000 754 77.5840 1052 2349 1 chr3B.!!$R3 1297
17 TraesCS5D01G462600 chr3B 805041203 805042375 1172 True 459.500 721 80.9745 943 2082 2 chr3B.!!$R4 1139
18 TraesCS5D01G462600 chr7D 555403556 555404631 1075 True 942.000 942 82.6940 968 2076 1 chr7D.!!$R1 1108
19 TraesCS5D01G462600 chr7D 634807764 634808446 682 True 538.000 538 81.2140 2671 3350 1 chr7D.!!$R2 679
20 TraesCS5D01G462600 chr6A 569390425 569391645 1220 False 660.000 660 77.4530 1047 2250 1 chr6A.!!$F1 1203
21 TraesCS5D01G462600 chr6A 419744215 419744890 675 True 584.000 584 82.5330 2674 3350 1 chr6A.!!$R2 676
22 TraesCS5D01G462600 chr6A 484408818 484409989 1171 True 217.000 217 70.9250 1063 2255 1 chr6A.!!$R3 1192
23 TraesCS5D01G462600 chr4D 137888516 137889160 644 False 658.000 658 84.9780 2672 3350 1 chr4D.!!$F1 678
24 TraesCS5D01G462600 chr1D 398243764 398245640 1876 True 600.000 614 84.0935 2674 3350 2 chr1D.!!$R2 676
25 TraesCS5D01G462600 chr6D 151496217 151496893 676 False 534.000 534 81.3310 2675 3350 1 chr6D.!!$F1 675

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
921 1478 0.3199 ACTGTGTGCGCTGTTCCTAG 60.32 55.0 9.73 0.45 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2700 6105 0.249741 CGCGGGATGTAGGTTAAGGG 60.25 60.0 0.0 0.0 0.0 3.95 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
244 245 1.818060 AGTCTTGCACACAACTTTGCA 59.182 42.857 0.00 0.00 46.93 4.08
247 248 3.717775 TGCACACAACTTTGCACTG 57.282 47.368 0.00 0.00 43.79 3.66
415 511 7.213678 AGGAGAAACACACAAAAACAAAAAGA 58.786 30.769 0.00 0.00 0.00 2.52
505 602 3.482436 AGCAATTCGACTAACCCAAACA 58.518 40.909 0.00 0.00 0.00 2.83
539 643 0.833287 GCTCATAGAACAGCCCAGGA 59.167 55.000 0.00 0.00 0.00 3.86
569 673 3.569548 ACATAGCACGAATCTCATAGCG 58.430 45.455 0.00 0.00 0.00 4.26
596 700 3.495124 CGGGCAACAAATTGACTGG 57.505 52.632 0.00 0.00 45.43 4.00
606 710 3.075884 CAAATTGACTGGCCCAAATTGG 58.924 45.455 4.74 4.74 33.24 3.16
623 991 9.541143 CCCAAATTGGCTATATAATTTCGTTTT 57.459 29.630 6.48 0.00 35.07 2.43
628 996 9.744468 ATTGGCTATATAATTTCGTTTTGTTCC 57.256 29.630 0.00 0.00 0.00 3.62
629 997 7.708998 TGGCTATATAATTTCGTTTTGTTCCC 58.291 34.615 0.00 0.00 0.00 3.97
630 998 7.339721 TGGCTATATAATTTCGTTTTGTTCCCA 59.660 33.333 0.00 0.00 0.00 4.37
631 999 7.860872 GGCTATATAATTTCGTTTTGTTCCCAG 59.139 37.037 0.00 0.00 0.00 4.45
632 1000 8.617809 GCTATATAATTTCGTTTTGTTCCCAGA 58.382 33.333 0.00 0.00 0.00 3.86
636 1004 8.950208 ATAATTTCGTTTTGTTCCCAGAAAAA 57.050 26.923 0.00 0.00 32.44 1.94
744 1276 8.624776 GCTTTAGTTCCATTACTAGCATTCAAT 58.375 33.333 0.00 0.00 32.48 2.57
852 1407 6.042144 CTTCAGGAATTTGAAGCTCGATAC 57.958 41.667 6.89 0.00 45.21 2.24
921 1478 0.319900 ACTGTGTGCGCTGTTCCTAG 60.320 55.000 9.73 0.45 0.00 3.02
953 1510 1.836802 AGGGAAGAAGCTCCACATCTC 59.163 52.381 0.00 0.00 37.20 2.75
960 1518 1.110442 AGCTCCACATCTCCTCTTCG 58.890 55.000 0.00 0.00 0.00 3.79
1021 1579 1.376609 GGGTGCGGTGCTATCAAAGG 61.377 60.000 0.00 0.00 0.00 3.11
1028 1586 3.190535 GCGGTGCTATCAAAGGAAAAGAA 59.809 43.478 0.00 0.00 0.00 2.52
1034 1592 7.087007 GTGCTATCAAAGGAAAAGAAAAGGAG 58.913 38.462 0.00 0.00 0.00 3.69
1143 1707 2.279120 CCGCTCGACCTCATGCTC 60.279 66.667 0.00 0.00 0.00 4.26
1212 1788 1.487231 CGACTTCTTTGACGTGGCG 59.513 57.895 0.00 0.00 0.00 5.69
1302 1923 3.041940 CGTGACGGCAGGTTGGTC 61.042 66.667 1.88 0.00 0.00 4.02
1305 1926 0.036765 GTGACGGCAGGTTGGTCATA 60.037 55.000 0.00 0.00 42.10 2.15
1548 2170 1.349357 GCCTTCCACTTCTTCCAGACT 59.651 52.381 0.00 0.00 0.00 3.24
1583 2220 4.796231 GGACGATGACGCGGCAGT 62.796 66.667 23.88 14.91 42.26 4.40
1998 2697 3.210528 GACGTCGCCTCCTCGGAT 61.211 66.667 0.00 0.00 33.16 4.18
2004 2727 3.934962 GCCTCCTCGGATGGCCTC 61.935 72.222 3.32 0.00 40.71 4.70
2148 2889 1.076923 GGAGACGGAGCTGAGGGTA 60.077 63.158 0.00 0.00 0.00 3.69
2325 3072 0.173481 CGATCCTCAGCGACTTCCAA 59.827 55.000 0.00 0.00 31.13 3.53
2358 3105 1.482593 GCCAAGTTCTAGCTCTAGGCA 59.517 52.381 0.00 0.00 44.79 4.75
2359 3106 2.482839 GCCAAGTTCTAGCTCTAGGCAG 60.483 54.545 0.00 2.57 44.79 4.85
2405 5789 0.861837 GACGCTGAGGTGTTCAACAG 59.138 55.000 0.00 0.00 36.19 3.16
2409 5793 2.411904 GCTGAGGTGTTCAACAGAGAG 58.588 52.381 0.00 0.00 34.81 3.20
2415 5801 5.304357 TGAGGTGTTCAACAGAGAGATTACA 59.696 40.000 0.00 0.00 31.34 2.41
2418 5804 5.163814 GGTGTTCAACAGAGAGATTACATGC 60.164 44.000 0.00 0.00 0.00 4.06
2479 5865 6.691508 ACATTAGCAAAAGATTCCTGGTTTC 58.308 36.000 0.00 0.00 0.00 2.78
2485 5871 5.578336 GCAAAAGATTCCTGGTTTCATTAGC 59.422 40.000 0.00 0.00 0.00 3.09
2515 5901 2.223971 ACGGCCATTACAGGAGAATACG 60.224 50.000 2.24 0.00 0.00 3.06
2546 5932 8.059798 AGTAGCATGCAACAAGAATAGAAATT 57.940 30.769 21.98 0.00 0.00 1.82
2547 5933 7.972277 AGTAGCATGCAACAAGAATAGAAATTG 59.028 33.333 21.98 0.00 0.00 2.32
2553 5954 8.801715 TGCAACAAGAATAGAAATTGTCTTTC 57.198 30.769 0.00 0.00 36.18 2.62
2571 5975 0.463654 TCAGCCTGTTGAAAGCGTGT 60.464 50.000 0.00 0.00 0.00 4.49
2572 5976 0.381801 CAGCCTGTTGAAAGCGTGTT 59.618 50.000 0.00 0.00 0.00 3.32
2578 5982 4.219033 CCTGTTGAAAGCGTGTTGTATTC 58.781 43.478 0.00 0.00 0.00 1.75
2641 6045 7.392673 AGAAACTCTTGTGATCATGCAACTTAT 59.607 33.333 0.00 0.00 0.00 1.73
2650 6054 8.763356 TGTGATCATGCAACTTATTTTTGTTTC 58.237 29.630 0.00 0.00 0.00 2.78
2656 6060 5.752955 TGCAACTTATTTTTGTTTCTCTGCC 59.247 36.000 0.00 0.00 0.00 4.85
2658 6062 6.074142 GCAACTTATTTTTGTTTCTCTGCCTG 60.074 38.462 0.00 0.00 0.00 4.85
2662 6066 1.593196 TTTGTTTCTCTGCCTGGTCG 58.407 50.000 0.00 0.00 0.00 4.79
2663 6067 0.468226 TTGTTTCTCTGCCTGGTCGT 59.532 50.000 0.00 0.00 0.00 4.34
2664 6068 1.334160 TGTTTCTCTGCCTGGTCGTA 58.666 50.000 0.00 0.00 0.00 3.43
2665 6069 1.272490 TGTTTCTCTGCCTGGTCGTAG 59.728 52.381 0.00 0.00 0.00 3.51
2666 6070 0.895530 TTTCTCTGCCTGGTCGTAGG 59.104 55.000 0.00 0.00 40.95 3.18
2667 6071 0.039180 TTCTCTGCCTGGTCGTAGGA 59.961 55.000 7.20 0.00 40.42 2.94
2668 6072 0.394488 TCTCTGCCTGGTCGTAGGAG 60.394 60.000 7.20 0.00 40.42 3.69
2669 6073 1.379977 TCTGCCTGGTCGTAGGAGG 60.380 63.158 7.20 0.00 40.42 4.30
2740 6145 2.279408 GCCTCCTACGACCTCCCT 59.721 66.667 0.00 0.00 0.00 4.20
2744 6149 0.259356 CTCCTACGACCTCCCTTCCT 59.741 60.000 0.00 0.00 0.00 3.36
2755 6160 3.441290 CCTTCCTCTCGCCGTCGT 61.441 66.667 0.00 0.00 36.96 4.34
2770 6179 4.367023 CGTCAGAACCGCCGGGAA 62.367 66.667 8.57 0.00 36.97 3.97
2812 6222 2.042435 CGGGGCCTCTCTCTCCTT 60.042 66.667 0.00 0.00 0.00 3.36
2870 6898 1.375908 GAGGAGTGGCGTTCATGCA 60.376 57.895 0.00 0.00 36.28 3.96
2877 6905 2.747460 GCGTTCATGCAGGGCAGA 60.747 61.111 0.00 0.00 43.65 4.26
2880 6908 1.375908 GTTCATGCAGGGCAGACGA 60.376 57.895 0.00 0.00 43.65 4.20
3028 7056 4.426313 CTTGGCCTCCCCGGGTTC 62.426 72.222 21.85 4.79 35.87 3.62
3057 7087 2.066393 TCTGGATGGGGGCTTCTCG 61.066 63.158 0.00 0.00 0.00 4.04
3147 7178 3.067461 CGAGAGATGGAGGTTCTTCGAAT 59.933 47.826 0.00 0.00 31.45 3.34
3172 7203 0.187117 TGGGTGAAAACCTGCCATCA 59.813 50.000 0.00 0.00 0.00 3.07
3173 7204 1.337118 GGGTGAAAACCTGCCATCAA 58.663 50.000 0.00 0.00 0.00 2.57
3260 7872 2.301583 AGAAGTTCAAGGCCACTCTCTC 59.698 50.000 5.01 0.00 0.00 3.20
3273 7885 1.308481 TCTCTCCTACCTCCGGGGA 60.308 63.158 0.37 0.00 38.76 4.81
3318 7931 1.608717 ATGACGGCTCTCTGGTGTCC 61.609 60.000 0.00 0.00 0.00 4.02
3343 7956 1.890174 CCTTGGGGGCGTCATTTTC 59.110 57.895 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 5.354234 GGGTAATATCCATGCCACTAATTCG 59.646 44.000 0.00 0.00 0.00 3.34
215 216 8.546597 AAGTTGTGTGCAAGACTTTTTAATTT 57.453 26.923 0.00 0.00 34.94 1.82
216 217 8.442384 CAAAGTTGTGTGCAAGACTTTTTAATT 58.558 29.630 12.53 0.00 32.25 1.40
217 218 7.412891 GCAAAGTTGTGTGCAAGACTTTTTAAT 60.413 33.333 12.53 0.00 40.58 1.40
219 220 5.347364 GCAAAGTTGTGTGCAAGACTTTTTA 59.653 36.000 12.53 0.00 40.58 1.52
237 238 7.096551 ACAAAAGTGTAATTTCAGTGCAAAGT 58.903 30.769 0.00 0.00 35.72 2.66
244 245 9.062524 TGCATACTACAAAAGTGTAATTTCAGT 57.937 29.630 0.00 0.00 39.75 3.41
441 538 1.354705 GTACCTCTCAGCCCCCTTTTT 59.645 52.381 0.00 0.00 0.00 1.94
442 539 0.992695 GTACCTCTCAGCCCCCTTTT 59.007 55.000 0.00 0.00 0.00 2.27
443 540 0.178873 TGTACCTCTCAGCCCCCTTT 60.179 55.000 0.00 0.00 0.00 3.11
444 541 0.618968 CTGTACCTCTCAGCCCCCTT 60.619 60.000 0.00 0.00 0.00 3.95
445 542 1.002274 CTGTACCTCTCAGCCCCCT 59.998 63.158 0.00 0.00 0.00 4.79
446 543 2.066999 CCTGTACCTCTCAGCCCCC 61.067 68.421 0.00 0.00 0.00 5.40
447 544 0.032416 TACCTGTACCTCTCAGCCCC 60.032 60.000 0.00 0.00 0.00 5.80
448 545 1.861982 TTACCTGTACCTCTCAGCCC 58.138 55.000 0.00 0.00 0.00 5.19
449 546 2.103263 CCATTACCTGTACCTCTCAGCC 59.897 54.545 0.00 0.00 0.00 4.85
450 547 2.103263 CCCATTACCTGTACCTCTCAGC 59.897 54.545 0.00 0.00 0.00 4.26
451 548 2.103263 GCCCATTACCTGTACCTCTCAG 59.897 54.545 0.00 0.00 0.00 3.35
452 549 2.116238 GCCCATTACCTGTACCTCTCA 58.884 52.381 0.00 0.00 0.00 3.27
453 550 2.399580 AGCCCATTACCTGTACCTCTC 58.600 52.381 0.00 0.00 0.00 3.20
454 551 2.570386 AGCCCATTACCTGTACCTCT 57.430 50.000 0.00 0.00 0.00 3.69
455 552 2.504175 TGAAGCCCATTACCTGTACCTC 59.496 50.000 0.00 0.00 0.00 3.85
505 602 2.603075 TGAGCTGGTTTGGGCTATTT 57.397 45.000 0.00 0.00 39.05 1.40
569 673 3.575965 ATTTGTTGCCCGTTGATTCTC 57.424 42.857 0.00 0.00 0.00 2.87
606 710 8.617809 TCTGGGAACAAAACGAAATTATATAGC 58.382 33.333 0.00 0.00 42.06 2.97
713 1081 4.236527 AGTAATGGAACTAAAGCAGGGG 57.763 45.455 0.00 0.00 0.00 4.79
744 1276 1.067669 CCGGAGAATCAGATGCTCGAA 59.932 52.381 11.81 0.00 36.25 3.71
921 1478 5.795972 AGCTTCTTCCCTTTTGTAGTCTAC 58.204 41.667 2.81 2.81 0.00 2.59
953 1510 1.137825 GTGAGGTCGAGCGAAGAGG 59.862 63.158 9.28 0.00 0.00 3.69
960 1518 2.183046 GCTGAGGTGAGGTCGAGC 59.817 66.667 6.48 6.48 0.00 5.03
994 1552 1.555967 AGCACCGCACCCATTTTAAT 58.444 45.000 0.00 0.00 0.00 1.40
995 1553 2.201921 TAGCACCGCACCCATTTTAA 57.798 45.000 0.00 0.00 0.00 1.52
996 1554 2.294074 GATAGCACCGCACCCATTTTA 58.706 47.619 0.00 0.00 0.00 1.52
997 1555 1.102978 GATAGCACCGCACCCATTTT 58.897 50.000 0.00 0.00 0.00 1.82
1021 1579 4.499865 GGCACCACTTCTCCTTTTCTTTTC 60.500 45.833 0.00 0.00 0.00 2.29
1028 1586 0.535102 CACGGCACCACTTCTCCTTT 60.535 55.000 0.00 0.00 0.00 3.11
1034 1592 3.660111 GCACCACGGCACCACTTC 61.660 66.667 0.00 0.00 0.00 3.01
1143 1707 1.961277 GGTGTGGCCTCTGTTGACG 60.961 63.158 3.32 0.00 0.00 4.35
1203 1779 3.573772 CTTGAGCCTCGCCACGTCA 62.574 63.158 0.00 0.00 0.00 4.35
1212 1788 4.537433 ATCGCCGCCTTGAGCCTC 62.537 66.667 0.00 0.00 38.78 4.70
1297 1918 1.153647 CGGCGCAGTCTATGACCAA 60.154 57.895 10.83 0.00 32.18 3.67
1302 1923 1.589993 CTGACCGGCGCAGTCTATG 60.590 63.158 24.62 14.10 35.21 2.23
1460 2081 2.174349 CGCCGCACTTCAAGAAGC 59.826 61.111 9.62 0.00 41.99 3.86
1548 2170 3.702048 CGGGAGAAGGCGGACCAA 61.702 66.667 0.00 0.00 39.06 3.67
1601 2241 4.309950 GGGTGCGGTCGTGGAACT 62.310 66.667 0.00 0.00 31.75 3.01
1926 2613 1.671054 GTTGCCGAAGTAGCCTGCA 60.671 57.895 0.00 0.00 0.00 4.41
2148 2889 1.756950 CATGCCCAGCCAGCTGATT 60.757 57.895 21.01 0.00 46.30 2.57
2282 3029 0.725686 CTCCGTACAGATGACGACGT 59.274 55.000 0.00 0.00 42.98 4.34
2358 3105 2.117156 GCCATTCATGTCAGGCGCT 61.117 57.895 7.64 0.00 37.41 5.92
2359 3106 2.410469 GCCATTCATGTCAGGCGC 59.590 61.111 0.00 0.00 37.41 6.53
2405 5789 7.010552 ACAGTACAATTTCGCATGTAATCTCTC 59.989 37.037 0.00 0.00 34.08 3.20
2409 5793 9.716507 AATTACAGTACAATTTCGCATGTAATC 57.283 29.630 10.13 0.00 39.93 1.75
2449 5835 7.820872 CCAGGAATCTTTTGCTAATGTCAAAAT 59.179 33.333 2.01 0.00 41.03 1.82
2451 5837 6.267471 ACCAGGAATCTTTTGCTAATGTCAAA 59.733 34.615 0.00 0.00 31.53 2.69
2453 5839 5.324409 ACCAGGAATCTTTTGCTAATGTCA 58.676 37.500 0.00 0.00 31.53 3.58
2467 5853 5.220796 GGTTACGCTAATGAAACCAGGAATC 60.221 44.000 0.00 0.00 40.89 2.52
2468 5854 4.638865 GGTTACGCTAATGAAACCAGGAAT 59.361 41.667 0.00 0.00 40.89 3.01
2515 5901 2.437200 TGTTGCATGCTACTTTTGCC 57.563 45.000 28.07 5.43 35.51 4.52
2553 5954 0.381801 AACACGCTTTCAACAGGCTG 59.618 50.000 14.16 14.16 0.00 4.85
2641 6045 2.357637 CGACCAGGCAGAGAAACAAAAA 59.642 45.455 0.00 0.00 0.00 1.94
2650 6054 1.388065 CCTCCTACGACCAGGCAGAG 61.388 65.000 0.00 0.00 35.49 3.35
2656 6060 4.554363 CGCGCCTCCTACGACCAG 62.554 72.222 0.00 0.00 0.00 4.00
2658 6062 4.549516 GACGCGCCTCCTACGACC 62.550 72.222 5.73 0.00 0.00 4.79
2698 6103 1.211212 GCGGGATGTAGGTTAAGGGTT 59.789 52.381 0.00 0.00 0.00 4.11
2700 6105 0.249741 CGCGGGATGTAGGTTAAGGG 60.250 60.000 0.00 0.00 0.00 3.95
2732 6137 2.428085 GGCGAGAGGAAGGGAGGTC 61.428 68.421 0.00 0.00 0.00 3.85
2733 6138 2.364448 GGCGAGAGGAAGGGAGGT 60.364 66.667 0.00 0.00 0.00 3.85
2740 6145 2.670592 TGACGACGGCGAGAGGAA 60.671 61.111 22.49 0.00 41.64 3.36
2744 6149 2.559840 GTTCTGACGACGGCGAGA 59.440 61.111 22.49 8.16 41.64 4.04
2755 6160 1.302192 CTTTTCCCGGCGGTTCTGA 60.302 57.895 26.32 12.14 0.00 3.27
2856 6266 2.360350 CCCTGCATGAACGCCACT 60.360 61.111 0.00 0.00 0.00 4.00
3042 7070 1.452108 CAACGAGAAGCCCCCATCC 60.452 63.158 0.00 0.00 0.00 3.51
3057 7087 1.885871 GCTGCCAGATCCCAACAAC 59.114 57.895 0.00 0.00 0.00 3.32
3147 7178 2.026262 GGCAGGTTTTCACCCAGATCTA 60.026 50.000 0.00 0.00 45.63 1.98
3172 7203 4.337013 CCGGCCTTGGCAATAGTT 57.663 55.556 14.04 0.00 0.00 2.24
3300 7913 2.276116 GGACACCAGAGAGCCGTCA 61.276 63.158 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.