Multiple sequence alignment - TraesCS2D01G046500

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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 TraesCS2D01G046500 chr2D 100.000 4534 0 0 1 4534 17009880 17014413 0.000000e+00 8373
1 TraesCS2D01G046500 chr2D 84.992 2452 293 43 1155 3576 16765264 16762858 0.000000e+00 2420
2 TraesCS2D01G046500 chr2A 95.216 3595 97 16 957 4534 18425182 18421646 0.000000e+00 5616
3 TraesCS2D01G046500 chr2A 85.086 2454 291 41 1155 3584 18544619 18547021 0.000000e+00 2435
4 TraesCS2D01G046500 chr2A 91.317 357 22 4 1 351 18461101 18460748 3.170000e-131 479
5 TraesCS2D01G046500 chr2A 94.239 243 14 0 712 954 18448094 18447852 5.540000e-99 372
6 TraesCS2D01G046500 chr2A 95.980 199 3 1 347 545 18448434 18448241 7.320000e-83 318
7 TraesCS2D01G046500 chr2A 96.104 77 3 0 543 619 18448168 18448092 4.760000e-25 126
8 TraesCS2D01G046500 chr2B 93.351 3414 176 19 747 4124 28882685 28886083 0.000000e+00 5000
9 TraesCS2D01G046500 chr2B 88.095 672 28 14 1 650 28881998 28882639 0.000000e+00 750
10 TraesCS2D01G046500 chr2B 92.135 267 16 2 4109 4375 28886096 28886357 5.540000e-99 372
11 TraesCS2D01G046500 chr6A 87.245 2642 264 35 982 3582 28410320 28412929 0.000000e+00 2944
12 TraesCS2D01G046500 chr6A 79.005 2453 439 61 1157 3565 22953048 22955468 0.000000e+00 1607
13 TraesCS2D01G046500 chr6D 88.388 2463 233 32 1155 3582 27056851 27059295 0.000000e+00 2915
14 TraesCS2D01G046500 chr6D 79.295 2468 437 59 1157 3580 24377883 24375446 0.000000e+00 1659
15 TraesCS2D01G046500 chr6B 86.970 2594 267 33 1030 3582 49437949 49435386 0.000000e+00 2852
16 TraesCS2D01G046500 chr6B 87.293 2471 252 35 1155 3582 49733991 49736442 0.000000e+00 2767
17 TraesCS2D01G046500 chr6B 88.707 1709 184 8 1682 3384 49306006 49307711 0.000000e+00 2078
18 TraesCS2D01G046500 chr6B 90.115 1305 123 6 2280 3582 49537635 49538935 0.000000e+00 1690
19 TraesCS2D01G046500 chr6B 76.244 985 193 32 1160 2116 39367149 39368120 6.820000e-133 484
20 TraesCS2D01G046500 chrUn 75.930 1022 203 27 1246 2242 35132788 35133791 6.820000e-133 484


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 TraesCS2D01G046500 chr2D 17009880 17014413 4533 False 8373.000000 8373 100.000000 1 4534 1 chr2D.!!$F1 4533
1 TraesCS2D01G046500 chr2D 16762858 16765264 2406 True 2420.000000 2420 84.992000 1155 3576 1 chr2D.!!$R1 2421
2 TraesCS2D01G046500 chr2A 18421646 18425182 3536 True 5616.000000 5616 95.216000 957 4534 1 chr2A.!!$R1 3577
3 TraesCS2D01G046500 chr2A 18544619 18547021 2402 False 2435.000000 2435 85.086000 1155 3584 1 chr2A.!!$F1 2429
4 TraesCS2D01G046500 chr2A 18447852 18448434 582 True 272.000000 372 95.441000 347 954 3 chr2A.!!$R3 607
5 TraesCS2D01G046500 chr2B 28881998 28886357 4359 False 2040.666667 5000 91.193667 1 4375 3 chr2B.!!$F1 4374
6 TraesCS2D01G046500 chr6A 28410320 28412929 2609 False 2944.000000 2944 87.245000 982 3582 1 chr6A.!!$F2 2600
7 TraesCS2D01G046500 chr6A 22953048 22955468 2420 False 1607.000000 1607 79.005000 1157 3565 1 chr6A.!!$F1 2408
8 TraesCS2D01G046500 chr6D 27056851 27059295 2444 False 2915.000000 2915 88.388000 1155 3582 1 chr6D.!!$F1 2427
9 TraesCS2D01G046500 chr6D 24375446 24377883 2437 True 1659.000000 1659 79.295000 1157 3580 1 chr6D.!!$R1 2423
10 TraesCS2D01G046500 chr6B 49435386 49437949 2563 True 2852.000000 2852 86.970000 1030 3582 1 chr6B.!!$R1 2552
11 TraesCS2D01G046500 chr6B 49733991 49736442 2451 False 2767.000000 2767 87.293000 1155 3582 1 chr6B.!!$F4 2427
12 TraesCS2D01G046500 chr6B 49306006 49307711 1705 False 2078.000000 2078 88.707000 1682 3384 1 chr6B.!!$F2 1702
13 TraesCS2D01G046500 chr6B 49537635 49538935 1300 False 1690.000000 1690 90.115000 2280 3582 1 chr6B.!!$F3 1302
14 TraesCS2D01G046500 chr6B 39367149 39368120 971 False 484.000000 484 76.244000 1160 2116 1 chr6B.!!$F1 956
15 TraesCS2D01G046500 chrUn 35132788 35133791 1003 False 484.000000 484 75.930000 1246 2242 1 chrUn.!!$F1 996

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
710 795 0.175760 CCGGTCCTCACCTGTACATG 59.824 60.0 0.0 0.0 41.17 3.21 F
2086 2271 0.331278 CCAAGGCAACCCATACCTCA 59.669 55.0 0.0 0.0 31.86 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2360 2574 0.749454 CACTGCCAACTCCTATGCCC 60.749 60.0 0.0 0.0 0.0 5.36 R
3959 4189 0.541392 TTGCATCCATGTACGCCTCT 59.459 50.0 0.0 0.0 0.0 3.69 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 2.860735 GCATCTTGCAGTAGGTTAGACG 59.139 50.000 0.00 0.00 44.26 4.18
62 63 7.450074 AGGTTAGACGGCATCATATATGAAAA 58.550 34.615 19.03 0.00 40.69 2.29
63 64 7.936847 AGGTTAGACGGCATCATATATGAAAAA 59.063 33.333 19.03 0.00 40.69 1.94
64 65 8.730680 GGTTAGACGGCATCATATATGAAAAAT 58.269 33.333 19.03 4.78 40.69 1.82
100 101 8.416329 GGATGGACATTATTACAAAGCAGAAAT 58.584 33.333 0.00 0.00 0.00 2.17
102 103 8.347004 TGGACATTATTACAAAGCAGAAATGA 57.653 30.769 0.00 0.00 0.00 2.57
103 104 8.461222 TGGACATTATTACAAAGCAGAAATGAG 58.539 33.333 0.00 0.00 0.00 2.90
126 127 2.335316 TGTTCCACTACCAACACCAC 57.665 50.000 0.00 0.00 0.00 4.16
132 133 0.179067 ACTACCAACACCACCACACG 60.179 55.000 0.00 0.00 0.00 4.49
155 157 2.632028 TGCATTACAATTTGTGTGGCCT 59.368 40.909 12.30 0.00 41.89 5.19
182 184 0.901827 TCTTCAGGATGCAGCCGTAA 59.098 50.000 16.75 12.85 34.76 3.18
185 187 0.392461 TCAGGATGCAGCCGTAAACC 60.392 55.000 16.75 0.00 34.76 3.27
186 188 0.676466 CAGGATGCAGCCGTAAACCA 60.676 55.000 16.75 0.00 0.00 3.67
201 203 5.105917 CCGTAAACCAAGAGTGCCAATAATT 60.106 40.000 0.00 0.00 0.00 1.40
244 246 7.403231 AGGAAGGAATTCTACATGGTTAGAAGA 59.597 37.037 5.23 0.00 35.99 2.87
253 255 3.818773 ACATGGTTAGAAGAACGGGTTTG 59.181 43.478 0.00 0.00 0.00 2.93
279 281 4.336433 CGTCAAGGTATGGCTGAAAATCAT 59.664 41.667 0.00 0.00 0.00 2.45
280 282 5.585390 GTCAAGGTATGGCTGAAAATCATG 58.415 41.667 0.00 0.00 0.00 3.07
281 283 5.357878 GTCAAGGTATGGCTGAAAATCATGA 59.642 40.000 0.00 0.00 0.00 3.07
283 285 4.467769 AGGTATGGCTGAAAATCATGAGG 58.532 43.478 0.09 0.00 0.00 3.86
284 286 3.571401 GGTATGGCTGAAAATCATGAGGG 59.429 47.826 0.09 0.00 0.00 4.30
285 287 3.675348 ATGGCTGAAAATCATGAGGGA 57.325 42.857 0.09 0.00 0.00 4.20
286 288 3.008835 TGGCTGAAAATCATGAGGGAG 57.991 47.619 0.09 0.00 0.00 4.30
287 289 2.305009 GGCTGAAAATCATGAGGGAGG 58.695 52.381 0.09 0.00 0.00 4.30
288 290 1.680207 GCTGAAAATCATGAGGGAGGC 59.320 52.381 0.09 0.00 0.00 4.70
289 291 2.947243 GCTGAAAATCATGAGGGAGGCA 60.947 50.000 0.09 0.00 0.00 4.75
290 292 2.686915 CTGAAAATCATGAGGGAGGCAC 59.313 50.000 0.09 0.00 0.00 5.01
291 293 2.041485 TGAAAATCATGAGGGAGGCACA 59.959 45.455 0.09 0.00 0.00 4.57
292 294 2.134789 AAATCATGAGGGAGGCACAC 57.865 50.000 0.09 0.00 0.00 3.82
293 295 0.994247 AATCATGAGGGAGGCACACA 59.006 50.000 0.09 0.00 0.00 3.72
294 296 0.254178 ATCATGAGGGAGGCACACAC 59.746 55.000 0.09 0.00 0.00 3.82
295 297 1.126948 TCATGAGGGAGGCACACACA 61.127 55.000 0.00 0.00 0.00 3.72
296 298 0.675837 CATGAGGGAGGCACACACAG 60.676 60.000 0.00 0.00 0.00 3.66
297 299 1.130054 ATGAGGGAGGCACACACAGT 61.130 55.000 0.00 0.00 0.00 3.55
320 322 5.657302 GTGAGAGTCAAAGGAGGGATTAGTA 59.343 44.000 0.00 0.00 0.00 1.82
325 327 5.250774 AGTCAAAGGAGGGATTAGTAAAGCA 59.749 40.000 0.00 0.00 0.00 3.91
633 710 3.508402 TGTACTGTCGCTCACCTTCATTA 59.492 43.478 0.00 0.00 0.00 1.90
650 727 4.836825 TCATTAGGGACTTGAAGCTTCAG 58.163 43.478 27.02 22.15 41.75 3.02
651 728 4.287067 TCATTAGGGACTTGAAGCTTCAGT 59.713 41.667 27.02 24.76 41.75 3.41
652 729 5.483937 TCATTAGGGACTTGAAGCTTCAGTA 59.516 40.000 27.02 14.26 41.75 2.74
653 730 6.156949 TCATTAGGGACTTGAAGCTTCAGTAT 59.843 38.462 27.02 17.23 41.75 2.12
654 731 4.479786 AGGGACTTGAAGCTTCAGTATC 57.520 45.455 27.02 23.11 38.61 2.24
655 732 4.100373 AGGGACTTGAAGCTTCAGTATCT 58.900 43.478 27.02 20.96 38.61 1.98
656 733 4.161377 AGGGACTTGAAGCTTCAGTATCTC 59.839 45.833 27.02 23.36 38.61 2.75
657 734 4.109050 GGACTTGAAGCTTCAGTATCTCG 58.891 47.826 27.02 13.62 38.61 4.04
658 735 4.381079 GGACTTGAAGCTTCAGTATCTCGT 60.381 45.833 27.02 16.19 38.61 4.18
659 736 4.739195 ACTTGAAGCTTCAGTATCTCGTC 58.261 43.478 27.02 0.00 38.61 4.20
660 737 4.461081 ACTTGAAGCTTCAGTATCTCGTCT 59.539 41.667 27.02 2.57 38.61 4.18
661 738 5.047660 ACTTGAAGCTTCAGTATCTCGTCTT 60.048 40.000 27.02 1.96 38.61 3.01
662 739 4.987832 TGAAGCTTCAGTATCTCGTCTTC 58.012 43.478 25.16 0.00 32.50 2.87
663 740 4.459337 TGAAGCTTCAGTATCTCGTCTTCA 59.541 41.667 25.16 0.00 37.09 3.02
667 744 2.014857 TCAGTATCTCGTCTTCACCCG 58.985 52.381 0.00 0.00 0.00 5.28
668 745 2.014857 CAGTATCTCGTCTTCACCCGA 58.985 52.381 0.00 0.00 0.00 5.14
701 786 1.079750 GAGCTGAACCGGTCCTCAC 60.080 63.158 8.04 4.25 0.00 3.51
702 787 2.047179 GCTGAACCGGTCCTCACC 60.047 66.667 8.04 0.00 39.69 4.02
703 788 2.584391 GCTGAACCGGTCCTCACCT 61.584 63.158 8.04 0.00 41.17 4.00
704 789 1.293498 CTGAACCGGTCCTCACCTG 59.707 63.158 8.04 0.00 41.17 4.00
705 790 1.458777 TGAACCGGTCCTCACCTGT 60.459 57.895 8.04 0.00 41.69 4.00
706 791 0.178955 TGAACCGGTCCTCACCTGTA 60.179 55.000 8.04 0.00 39.11 2.74
707 792 0.245813 GAACCGGTCCTCACCTGTAC 59.754 60.000 8.04 0.00 39.11 2.90
708 793 0.470456 AACCGGTCCTCACCTGTACA 60.470 55.000 8.04 0.00 39.11 2.90
709 794 0.252103 ACCGGTCCTCACCTGTACAT 60.252 55.000 0.00 0.00 38.30 2.29
710 795 0.175760 CCGGTCCTCACCTGTACATG 59.824 60.000 0.00 0.00 41.17 3.21
711 796 0.895530 CGGTCCTCACCTGTACATGT 59.104 55.000 2.69 2.69 41.17 3.21
712 797 1.404181 CGGTCCTCACCTGTACATGTG 60.404 57.143 21.32 21.32 41.17 3.21
713 798 1.623811 GGTCCTCACCTGTACATGTGT 59.376 52.381 24.71 8.68 40.00 3.72
714 799 2.829720 GGTCCTCACCTGTACATGTGTA 59.170 50.000 24.71 14.01 40.00 2.90
715 800 3.119101 GGTCCTCACCTGTACATGTGTAG 60.119 52.174 24.71 20.05 40.00 2.74
734 819 5.590259 GTGTAGATTCACCACAAGGCAATAT 59.410 40.000 0.00 0.00 39.06 1.28
737 822 7.998383 TGTAGATTCACCACAAGGCAATATAAT 59.002 33.333 0.00 0.00 39.06 1.28
742 827 6.862209 TCACCACAAGGCAATATAATCAAAC 58.138 36.000 0.00 0.00 39.06 2.93
811 896 9.713740 CTAAACAGCATTCTCAGTTATTTGATC 57.286 33.333 0.00 0.00 0.00 2.92
889 974 5.106277 GCTCTCACCCAAACTATAAACCAAC 60.106 44.000 0.00 0.00 0.00 3.77
891 976 5.766174 TCTCACCCAAACTATAAACCAACAC 59.234 40.000 0.00 0.00 0.00 3.32
913 998 4.870106 CAAAATTATTTGCGAGGCGTTTC 58.130 39.130 0.00 0.00 39.50 2.78
1110 1233 9.920946 AGAAAGCTTTATAGTAATGGATTGGAA 57.079 29.630 12.68 0.00 0.00 3.53
1122 1245 3.955471 TGGATTGGAAAGACAGTCATCC 58.045 45.455 15.40 15.40 0.00 3.51
1443 1577 1.276421 ACGGTGAGAATCTTGGACAGG 59.724 52.381 0.00 0.00 34.92 4.00
1472 1606 0.603569 GTCAAGCTCACCTTCTCCGA 59.396 55.000 0.00 0.00 0.00 4.55
1494 1634 2.264480 CTCGATGGCAACGGGACA 59.736 61.111 12.06 0.00 40.35 4.02
2086 2271 0.331278 CCAAGGCAACCCATACCTCA 59.669 55.000 0.00 0.00 31.86 3.86
2088 2273 1.072266 AAGGCAACCCATACCTCACA 58.928 50.000 0.00 0.00 31.86 3.58
2268 2456 7.436080 CACCAAAACCAATAATACATGCAGATC 59.564 37.037 0.00 0.00 0.00 2.75
2317 2527 5.721000 AGATGTCAGAGACTCTTCCTTCATT 59.279 40.000 0.98 0.00 33.15 2.57
2360 2574 5.215160 GCACATTCTTCAGGTTTAAGTGTG 58.785 41.667 0.00 0.00 35.58 3.82
3221 3435 2.633488 GAGGAAGCCCTTGTCACATAC 58.367 52.381 0.00 0.00 44.53 2.39
3224 3438 3.074538 AGGAAGCCCTTGTCACATACTTT 59.925 43.478 0.00 0.00 40.78 2.66
3225 3439 3.191371 GGAAGCCCTTGTCACATACTTTG 59.809 47.826 0.00 0.00 0.00 2.77
3350 3564 4.021104 TGTGTGAGGATTGAAGTAGACCAG 60.021 45.833 0.00 0.00 0.00 4.00
3426 3640 5.756195 TGATAGCTTTGTAATGCATGACC 57.244 39.130 11.88 0.00 0.00 4.02
3921 4151 9.689976 AGAGATGATCACAGTTTCGAATATAAG 57.310 33.333 0.00 0.00 0.00 1.73
3959 4189 7.380065 GCGTTAGGAATGTTTCAACAACAATTA 59.620 33.333 0.00 0.00 43.03 1.40
4005 4247 6.216569 TCACCATCGAATACTTCTCTTATGC 58.783 40.000 0.00 0.00 0.00 3.14
4010 4252 5.833082 TCGAATACTTCTCTTATGCACCTC 58.167 41.667 0.00 0.00 0.00 3.85
4011 4253 5.594725 TCGAATACTTCTCTTATGCACCTCT 59.405 40.000 0.00 0.00 0.00 3.69
4012 4254 5.918011 CGAATACTTCTCTTATGCACCTCTC 59.082 44.000 0.00 0.00 0.00 3.20
4013 4255 6.238897 CGAATACTTCTCTTATGCACCTCTCT 60.239 42.308 0.00 0.00 0.00 3.10
4014 4256 7.041030 CGAATACTTCTCTTATGCACCTCTCTA 60.041 40.741 0.00 0.00 0.00 2.43
4015 4257 8.719645 AATACTTCTCTTATGCACCTCTCTAT 57.280 34.615 0.00 0.00 0.00 1.98
4016 4258 9.815306 AATACTTCTCTTATGCACCTCTCTATA 57.185 33.333 0.00 0.00 0.00 1.31
4017 4259 9.989296 ATACTTCTCTTATGCACCTCTCTATAT 57.011 33.333 0.00 0.00 0.00 0.86
4019 4261 9.815306 ACTTCTCTTATGCACCTCTCTATATAA 57.185 33.333 0.00 0.00 0.00 0.98
4021 4263 9.815306 TTCTCTTATGCACCTCTCTATATAACT 57.185 33.333 0.00 0.00 0.00 2.24
4032 4274 9.892130 ACCTCTCTATATAACTCTTGGTTTTTG 57.108 33.333 0.00 0.00 39.17 2.44
4097 4339 1.612950 TCACCACACCAATGCATTGTC 59.387 47.619 31.87 0.00 36.06 3.18
4222 4492 7.966753 CCTGTTGATGAGTTCATAAGTGAAATG 59.033 37.037 0.00 0.00 45.38 2.32
4295 4565 6.883744 TGTTCACTACACATTATGCAGGATA 58.116 36.000 0.00 0.00 0.00 2.59
4296 4566 7.508687 TGTTCACTACACATTATGCAGGATAT 58.491 34.615 0.00 0.00 0.00 1.63
4297 4567 8.646900 TGTTCACTACACATTATGCAGGATATA 58.353 33.333 0.00 0.00 0.00 0.86
4298 4568 9.658799 GTTCACTACACATTATGCAGGATATAT 57.341 33.333 0.00 0.00 0.00 0.86
4330 4600 6.204882 CCCTTTTACACTTTGAGTTAGACAGG 59.795 42.308 0.00 0.00 0.00 4.00
4385 4655 4.910195 ACAAGATTTGGCTGAGTACATGA 58.090 39.130 0.00 0.00 34.12 3.07
4393 4663 3.055385 TGGCTGAGTACATGACCCTAAAC 60.055 47.826 0.00 0.00 0.00 2.01
4440 4710 3.315191 TCTTTGCAAGTTAAGGACACTGC 59.685 43.478 0.00 0.00 38.89 4.40
4448 4718 5.078411 AGTTAAGGACACTGCACTCTATG 57.922 43.478 0.00 0.00 0.00 2.23
4449 4719 4.081420 AGTTAAGGACACTGCACTCTATGG 60.081 45.833 0.00 0.00 0.00 2.74
4450 4720 1.944177 AGGACACTGCACTCTATGGT 58.056 50.000 0.00 0.00 0.00 3.55
4451 4721 3.101643 AGGACACTGCACTCTATGGTA 57.898 47.619 0.00 0.00 0.00 3.25
4452 4722 2.761208 AGGACACTGCACTCTATGGTAC 59.239 50.000 0.00 0.00 0.00 3.34
4471 4741 7.966339 TGGTACACATATACCTCATATACCC 57.034 40.000 3.76 0.00 44.43 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.010314 TGCAAGATGCCAGGATTCATAAATC 59.990 40.000 0.00 0.00 44.23 2.17
12 13 4.279982 TGCAAGATGCCAGGATTCATAAA 58.720 39.130 0.00 0.00 44.23 1.40
15 16 2.307768 CTGCAAGATGCCAGGATTCAT 58.692 47.619 0.00 0.00 44.23 2.57
105 106 3.219281 GTGGTGTTGGTAGTGGAACAAT 58.781 45.455 0.00 0.00 44.16 2.71
126 127 4.047822 ACAAATTGTAATGCAACGTGTGG 58.952 39.130 0.00 0.00 40.28 4.17
132 133 3.186205 GGCCACACAAATTGTAATGCAAC 59.814 43.478 0.00 0.00 40.28 4.17
182 184 5.324409 TCTCAATTATTGGCACTCTTGGTT 58.676 37.500 5.02 0.00 0.00 3.67
185 187 5.220548 CGTCTCTCAATTATTGGCACTCTTG 60.221 44.000 5.02 0.00 0.00 3.02
186 188 4.872691 CGTCTCTCAATTATTGGCACTCTT 59.127 41.667 5.02 0.00 0.00 2.85
201 203 1.558294 TCCTAGGTGTAGCGTCTCTCA 59.442 52.381 9.08 0.00 0.00 3.27
229 231 4.467198 ACCCGTTCTTCTAACCATGTAG 57.533 45.455 0.00 0.00 0.00 2.74
234 236 2.438763 TCCAAACCCGTTCTTCTAACCA 59.561 45.455 0.00 0.00 0.00 3.67
244 246 0.816421 CCTTGACGTCCAAACCCGTT 60.816 55.000 14.12 0.00 37.44 4.44
253 255 0.535335 TCAGCCATACCTTGACGTCC 59.465 55.000 14.12 0.00 0.00 4.79
279 281 1.766059 ACTGTGTGTGCCTCCCTCA 60.766 57.895 0.00 0.00 0.00 3.86
280 282 1.302033 CACTGTGTGTGCCTCCCTC 60.302 63.158 0.00 0.00 40.06 4.30
281 283 1.762522 CTCACTGTGTGTGCCTCCCT 61.763 60.000 7.79 0.00 45.81 4.20
283 285 0.320247 CTCTCACTGTGTGTGCCTCC 60.320 60.000 7.79 0.00 45.81 4.30
284 286 0.390860 ACTCTCACTGTGTGTGCCTC 59.609 55.000 7.79 0.00 45.81 4.70
285 287 0.390860 GACTCTCACTGTGTGTGCCT 59.609 55.000 7.79 0.00 45.81 4.75
286 288 0.104855 TGACTCTCACTGTGTGTGCC 59.895 55.000 7.79 0.00 45.81 5.01
287 289 1.939974 TTGACTCTCACTGTGTGTGC 58.060 50.000 7.79 4.14 45.81 4.57
289 291 2.766263 TCCTTTGACTCTCACTGTGTGT 59.234 45.455 7.79 5.72 34.79 3.72
290 292 3.388308 CTCCTTTGACTCTCACTGTGTG 58.612 50.000 7.79 5.56 34.45 3.82
291 293 2.366916 CCTCCTTTGACTCTCACTGTGT 59.633 50.000 7.79 0.00 0.00 3.72
292 294 2.289320 CCCTCCTTTGACTCTCACTGTG 60.289 54.545 0.17 0.17 0.00 3.66
293 295 1.974236 CCCTCCTTTGACTCTCACTGT 59.026 52.381 0.00 0.00 0.00 3.55
294 296 2.251818 TCCCTCCTTTGACTCTCACTG 58.748 52.381 0.00 0.00 0.00 3.66
295 297 2.704190 TCCCTCCTTTGACTCTCACT 57.296 50.000 0.00 0.00 0.00 3.41
296 298 3.990959 AATCCCTCCTTTGACTCTCAC 57.009 47.619 0.00 0.00 0.00 3.51
297 299 4.689062 ACTAATCCCTCCTTTGACTCTCA 58.311 43.478 0.00 0.00 0.00 3.27
298 300 6.793505 TTACTAATCCCTCCTTTGACTCTC 57.206 41.667 0.00 0.00 0.00 3.20
299 301 6.352308 GCTTTACTAATCCCTCCTTTGACTCT 60.352 42.308 0.00 0.00 0.00 3.24
300 302 5.818336 GCTTTACTAATCCCTCCTTTGACTC 59.182 44.000 0.00 0.00 0.00 3.36
301 303 5.250774 TGCTTTACTAATCCCTCCTTTGACT 59.749 40.000 0.00 0.00 0.00 3.41
302 304 5.497474 TGCTTTACTAATCCCTCCTTTGAC 58.503 41.667 0.00 0.00 0.00 3.18
303 305 5.772393 TGCTTTACTAATCCCTCCTTTGA 57.228 39.130 0.00 0.00 0.00 2.69
304 306 6.659242 TCTTTGCTTTACTAATCCCTCCTTTG 59.341 38.462 0.00 0.00 0.00 2.77
305 307 6.790319 TCTTTGCTTTACTAATCCCTCCTTT 58.210 36.000 0.00 0.00 0.00 3.11
306 308 6.215636 TCTCTTTGCTTTACTAATCCCTCCTT 59.784 38.462 0.00 0.00 0.00 3.36
320 322 6.012745 ACTTATTGACCCATCTCTTTGCTTT 58.987 36.000 0.00 0.00 0.00 3.51
501 503 1.002921 TCAGGGTCCGGTGATGGAT 59.997 57.895 0.00 0.00 40.91 3.41
633 710 4.100373 AGATACTGAAGCTTCAAGTCCCT 58.900 43.478 28.16 21.24 36.64 4.20
650 727 2.015587 AGTCGGGTGAAGACGAGATAC 58.984 52.381 0.00 0.00 42.97 2.24
651 728 2.014857 CAGTCGGGTGAAGACGAGATA 58.985 52.381 0.00 0.00 42.97 1.98
652 729 0.811915 CAGTCGGGTGAAGACGAGAT 59.188 55.000 0.00 0.00 42.97 2.75
653 730 1.241990 CCAGTCGGGTGAAGACGAGA 61.242 60.000 0.00 0.00 42.97 4.04
654 731 1.213013 CCAGTCGGGTGAAGACGAG 59.787 63.158 0.00 0.00 42.97 4.18
655 732 3.362262 CCAGTCGGGTGAAGACGA 58.638 61.111 0.00 0.00 42.97 4.20
667 744 6.128254 GGTTCAGCTCAACTAATAAACCAGTC 60.128 42.308 0.00 0.00 0.00 3.51
668 745 5.705905 GGTTCAGCTCAACTAATAAACCAGT 59.294 40.000 0.00 0.00 0.00 4.00
678 755 0.606604 GGACCGGTTCAGCTCAACTA 59.393 55.000 9.42 0.00 0.00 2.24
679 756 1.122019 AGGACCGGTTCAGCTCAACT 61.122 55.000 17.22 0.00 0.00 3.16
683 768 1.079750 GTGAGGACCGGTTCAGCTC 60.080 63.158 17.22 4.47 0.00 4.09
701 786 4.870426 GTGGTGAATCTACACATGTACAGG 59.130 45.833 5.87 5.87 41.88 4.00
702 787 5.478407 TGTGGTGAATCTACACATGTACAG 58.522 41.667 0.00 0.00 39.92 2.74
703 788 5.476091 TGTGGTGAATCTACACATGTACA 57.524 39.130 0.00 0.00 39.92 2.90
704 789 5.351465 CCTTGTGGTGAATCTACACATGTAC 59.649 44.000 0.00 0.00 43.75 2.90
705 790 5.487433 CCTTGTGGTGAATCTACACATGTA 58.513 41.667 0.00 0.00 43.75 2.29
706 791 4.326826 CCTTGTGGTGAATCTACACATGT 58.673 43.478 10.33 0.00 43.75 3.21
707 792 3.127548 GCCTTGTGGTGAATCTACACATG 59.872 47.826 10.33 11.74 43.75 3.21
708 793 3.244875 TGCCTTGTGGTGAATCTACACAT 60.245 43.478 10.33 0.00 43.75 3.21
709 794 2.105649 TGCCTTGTGGTGAATCTACACA 59.894 45.455 6.51 6.51 42.77 3.72
710 795 2.778299 TGCCTTGTGGTGAATCTACAC 58.222 47.619 0.00 0.00 37.26 2.90
711 796 3.500448 TTGCCTTGTGGTGAATCTACA 57.500 42.857 0.00 0.00 35.78 2.74
712 797 7.801716 TTATATTGCCTTGTGGTGAATCTAC 57.198 36.000 0.00 0.00 35.27 2.59
713 798 8.217111 TGATTATATTGCCTTGTGGTGAATCTA 58.783 33.333 0.00 0.00 35.27 1.98
714 799 7.062322 TGATTATATTGCCTTGTGGTGAATCT 58.938 34.615 0.00 0.00 35.27 2.40
715 800 7.275888 TGATTATATTGCCTTGTGGTGAATC 57.724 36.000 0.00 0.00 35.27 2.52
852 937 2.421424 GGTGAGAGCAAAGCATAACCAG 59.579 50.000 0.00 0.00 0.00 4.00
891 976 4.201580 GGAAACGCCTCGCAAATAATTTTG 60.202 41.667 0.00 0.00 44.18 2.44
904 989 2.791927 GCGATTGGGAAACGCCTC 59.208 61.111 0.00 0.00 45.35 4.70
913 998 5.247507 TGTGAATTTTCTATGCGATTGGG 57.752 39.130 0.00 0.00 0.00 4.12
1110 1233 2.494059 CGGTTGTTGGATGACTGTCTT 58.506 47.619 9.51 2.27 0.00 3.01
1122 1245 0.960364 ATACCAGCCAGCGGTTGTTG 60.960 55.000 10.56 0.00 37.99 3.33
2287 2490 5.802956 GGAAGAGTCTCTGACATCTAAAACG 59.197 44.000 2.28 0.00 34.60 3.60
2360 2574 0.749454 CACTGCCAACTCCTATGCCC 60.749 60.000 0.00 0.00 0.00 5.36
3207 3421 1.202348 GGCAAAGTATGTGACAAGGGC 59.798 52.381 0.00 0.00 24.68 5.19
3244 3458 2.709125 TAGCACGCGAACCAGCTTGT 62.709 55.000 15.93 0.00 38.45 3.16
3426 3640 1.212688 TGGATACTTGGGCACATCCAG 59.787 52.381 4.85 0.00 41.52 3.86
3601 3816 6.833933 AGACCACAAAAACCATTATATCCCTC 59.166 38.462 0.00 0.00 0.00 4.30
3921 4151 2.456989 TCCTAACGCGATCGAAATGTC 58.543 47.619 21.57 0.00 39.41 3.06
3959 4189 0.541392 TTGCATCCATGTACGCCTCT 59.459 50.000 0.00 0.00 0.00 3.69
4005 4247 9.892130 AAAAACCAAGAGTTATATAGAGAGGTG 57.108 33.333 0.00 0.00 37.88 4.00
4011 4253 9.162764 GCAGTCAAAAACCAAGAGTTATATAGA 57.837 33.333 0.00 0.00 37.88 1.98
4012 4254 8.946085 TGCAGTCAAAAACCAAGAGTTATATAG 58.054 33.333 0.00 0.00 37.88 1.31
4013 4255 8.726988 GTGCAGTCAAAAACCAAGAGTTATATA 58.273 33.333 0.00 0.00 37.88 0.86
4014 4256 7.309194 GGTGCAGTCAAAAACCAAGAGTTATAT 60.309 37.037 0.00 0.00 37.88 0.86
4015 4257 6.016610 GGTGCAGTCAAAAACCAAGAGTTATA 60.017 38.462 0.00 0.00 37.88 0.98
4016 4258 5.221244 GGTGCAGTCAAAAACCAAGAGTTAT 60.221 40.000 0.00 0.00 37.88 1.89
4017 4259 4.097286 GGTGCAGTCAAAAACCAAGAGTTA 59.903 41.667 0.00 0.00 37.88 2.24
4018 4260 3.119137 GGTGCAGTCAAAAACCAAGAGTT 60.119 43.478 0.00 0.00 41.81 3.01
4019 4261 2.427095 GGTGCAGTCAAAAACCAAGAGT 59.573 45.455 0.00 0.00 32.69 3.24
4020 4262 2.689983 AGGTGCAGTCAAAAACCAAGAG 59.310 45.455 0.00 0.00 35.01 2.85
4021 4263 2.733956 AGGTGCAGTCAAAAACCAAGA 58.266 42.857 0.00 0.00 35.01 3.02
4032 4274 1.732259 CATCGTGGTAAAGGTGCAGTC 59.268 52.381 0.00 0.00 0.00 3.51
4097 4339 7.465513 GCCTCAGTAAATGATTAACCAACTACG 60.466 40.741 0.00 0.00 37.28 3.51
4295 4565 8.877864 TCAAAGTGTAAAAGGGATGTGAATAT 57.122 30.769 0.00 0.00 0.00 1.28
4296 4566 7.942341 ACTCAAAGTGTAAAAGGGATGTGAATA 59.058 33.333 0.00 0.00 0.00 1.75
4297 4567 6.777580 ACTCAAAGTGTAAAAGGGATGTGAAT 59.222 34.615 0.00 0.00 0.00 2.57
4298 4568 6.126409 ACTCAAAGTGTAAAAGGGATGTGAA 58.874 36.000 0.00 0.00 0.00 3.18
4440 4710 7.761038 TGAGGTATATGTGTACCATAGAGTG 57.239 40.000 8.41 0.00 45.35 3.51
4448 4718 7.618512 ACAGGGTATATGAGGTATATGTGTACC 59.381 40.741 0.00 0.00 43.65 3.34
4449 4719 8.591114 ACAGGGTATATGAGGTATATGTGTAC 57.409 38.462 0.00 0.00 33.96 2.90
4451 4721 9.201989 CATACAGGGTATATGAGGTATATGTGT 57.798 37.037 0.00 0.00 33.96 3.72
4452 4722 9.421399 TCATACAGGGTATATGAGGTATATGTG 57.579 37.037 0.00 0.00 34.77 3.21
4457 4727 8.974292 ACTTTCATACAGGGTATATGAGGTAT 57.026 34.615 0.00 0.00 39.57 2.73
4459 4729 8.974292 ATACTTTCATACAGGGTATATGAGGT 57.026 34.615 0.00 0.00 39.57 3.85
4460 4730 9.035890 TGATACTTTCATACAGGGTATATGAGG 57.964 37.037 0.00 0.00 39.57 3.86
4463 4733 9.605275 CCATGATACTTTCATACAGGGTATATG 57.395 37.037 0.00 0.00 43.40 1.78
4464 4734 9.560860 TCCATGATACTTTCATACAGGGTATAT 57.439 33.333 0.00 0.00 43.40 0.86
4465 4735 8.812972 GTCCATGATACTTTCATACAGGGTATA 58.187 37.037 0.00 0.00 43.40 1.47
4466 4736 7.292356 TGTCCATGATACTTTCATACAGGGTAT 59.708 37.037 0.00 0.00 43.40 2.73
4467 4737 6.613679 TGTCCATGATACTTTCATACAGGGTA 59.386 38.462 0.00 0.00 43.40 3.69
4471 4741 7.466455 GCTGTTGTCCATGATACTTTCATACAG 60.466 40.741 0.00 9.50 43.40 2.74


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

AutoCloner maintained by Alex Coulton.