Multiple sequence alignment - TraesCS3D01G451100

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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 TraesCS3D01G451100 chr3D 100.000 3753 0 0 1 3753 559119087 559122839 0.000000e+00 6931.0
1 TraesCS3D01G451100 chr3D 83.635 1601 209 33 947 2534 555314670 555313110 0.000000e+00 1456.0
2 TraesCS3D01G451100 chr3D 83.594 1408 212 16 1017 2412 555306224 555304824 0.000000e+00 1303.0
3 TraesCS3D01G451100 chr3D 94.828 58 2 1 1680 1736 554817329 554817386 5.160000e-14 89.8
4 TraesCS3D01G451100 chr3D 82.653 98 8 5 2825 2915 555310723 555310628 1.120000e-10 78.7
5 TraesCS3D01G451100 chr3D 86.207 58 7 1 2732 2788 555304595 555304538 1.130000e-05 62.1
6 TraesCS3D01G451100 chr3A 95.561 2613 91 14 1 2605 695514103 695516698 0.000000e+00 4159.0
7 TraesCS3D01G451100 chr3A 82.491 1405 213 21 1021 2414 692058048 692056666 0.000000e+00 1201.0
8 TraesCS3D01G451100 chr3A 81.884 1380 226 11 1022 2399 692316349 692314992 0.000000e+00 1142.0
9 TraesCS3D01G451100 chr3A 81.719 1373 189 43 1080 2446 692495403 692494087 0.000000e+00 1088.0
10 TraesCS3D01G451100 chr3A 90.328 610 37 11 3144 3749 695517184 695517775 0.000000e+00 780.0
11 TraesCS3D01G451100 chr3A 93.736 447 16 3 2680 3125 695516689 695517124 0.000000e+00 660.0
12 TraesCS3D01G451100 chr3A 83.471 363 37 11 966 1323 692491409 692491065 2.180000e-82 316.0
13 TraesCS3D01G451100 chr3A 93.333 120 7 1 2415 2534 692489026 692488908 3.850000e-40 176.0
14 TraesCS3D01G451100 chr3A 94.000 100 5 1 2603 2702 21405988 21406086 2.340000e-32 150.0
15 TraesCS3D01G451100 chr3A 89.655 58 5 1 2732 2788 692056439 692056382 5.200000e-09 73.1
16 TraesCS3D01G451100 chr3A 89.655 58 5 1 2732 2788 692470351 692470294 5.200000e-09 73.1
17 TraesCS3D01G451100 chr3A 92.000 50 4 0 2867 2916 692488671 692488622 1.870000e-08 71.3
18 TraesCS3D01G451100 chr3B 92.456 1604 96 13 900 2501 742110595 742109015 0.000000e+00 2268.0
19 TraesCS3D01G451100 chr3B 90.222 1667 127 8 947 2605 741968257 741966619 0.000000e+00 2143.0
20 TraesCS3D01G451100 chr3B 82.479 1581 216 36 947 2516 738591967 738590437 0.000000e+00 1328.0
21 TraesCS3D01G451100 chr3B 82.357 1349 186 34 1080 2423 738625876 738624575 0.000000e+00 1125.0
22 TraesCS3D01G451100 chr3B 81.335 1393 224 15 1017 2399 738289890 738288524 0.000000e+00 1099.0
23 TraesCS3D01G451100 chr3B 90.932 783 57 10 900 1680 742081408 742080638 0.000000e+00 1040.0
24 TraesCS3D01G451100 chr3B 80.027 1472 234 36 1080 2534 738156535 738155107 0.000000e+00 1035.0
25 TraesCS3D01G451100 chr3B 90.549 783 60 10 900 1680 742061608 742060838 0.000000e+00 1024.0
26 TraesCS3D01G451100 chr3B 91.556 450 23 3 2687 3129 742108826 742108385 1.150000e-169 606.0
27 TraesCS3D01G451100 chr3B 81.759 762 104 23 985 1740 738295542 738294810 4.150000e-169 604.0
28 TraesCS3D01G451100 chr3B 86.923 520 53 8 3143 3657 742108330 742107821 1.510000e-158 569.0
29 TraesCS3D01G451100 chr3B 84.177 474 43 16 2680 3129 741966628 741966163 7.450000e-117 431.0
30 TraesCS3D01G451100 chr3B 92.424 132 10 0 3144 3275 741966079 741965948 4.950000e-44 189.0
31 TraesCS3D01G451100 chr3B 95.370 108 5 0 2498 2605 742108935 742108828 4.980000e-39 172.0
32 TraesCS3D01G451100 chr3B 97.778 90 2 0 2603 2692 512457420 512457509 5.020000e-34 156.0
33 TraesCS3D01G451100 chr3B 89.706 68 6 1 1680 1746 738105965 738105898 6.680000e-13 86.1
34 TraesCS3D01G451100 chr3B 81.633 98 13 4 2825 2917 738588021 738587924 4.020000e-10 76.8
35 TraesCS3D01G451100 chr3B 92.157 51 4 0 2867 2917 738590186 738590136 5.200000e-09 73.1
36 TraesCS3D01G451100 chr3B 87.931 58 6 1 2732 2788 738288282 738288225 2.420000e-07 67.6
37 TraesCS3D01G451100 chr4B 81.529 471 60 14 379 832 85435606 85435146 2.760000e-96 363.0
38 TraesCS3D01G451100 chrUn 72.871 1139 252 40 1264 2369 272482922 272481808 4.640000e-89 339.0
39 TraesCS3D01G451100 chr4A 97.778 90 2 0 2603 2692 723335652 723335563 5.020000e-34 156.0
40 TraesCS3D01G451100 chr4A 97.619 42 1 0 342 383 572830241 572830200 5.200000e-09 73.1
41 TraesCS3D01G451100 chr7A 95.789 95 4 0 2597 2691 942240 942334 1.810000e-33 154.0
42 TraesCS3D01G451100 chr7A 100.000 41 0 0 342 382 667343185 667343225 4.020000e-10 76.8
43 TraesCS3D01G451100 chr5B 96.739 92 3 0 2604 2695 79817782 79817691 1.810000e-33 154.0
44 TraesCS3D01G451100 chr5B 97.753 89 2 0 2603 2691 135750648 135750736 1.810000e-33 154.0
45 TraesCS3D01G451100 chr5A 97.753 89 2 0 2601 2689 657182858 657182946 1.810000e-33 154.0
46 TraesCS3D01G451100 chr5A 95.745 94 4 0 2602 2695 535678520 535678427 6.490000e-33 152.0
47 TraesCS3D01G451100 chr1D 93.939 99 3 3 2594 2692 225701727 225701822 3.020000e-31 147.0
48 TraesCS3D01G451100 chr2A 100.000 43 0 0 342 384 53078512 53078470 3.110000e-11 80.5
49 TraesCS3D01G451100 chr4D 97.674 43 1 0 342 384 341396729 341396687 1.450000e-09 75.0
50 TraesCS3D01G451100 chr4D 93.478 46 3 0 338 383 509434136 509434181 6.730000e-08 69.4
51 TraesCS3D01G451100 chr2D 97.674 43 1 0 342 384 51940852 51940810 1.450000e-09 75.0
52 TraesCS3D01G451100 chr2B 97.674 43 1 0 342 384 387071351 387071309 1.450000e-09 75.0
53 TraesCS3D01G451100 chr1A 90.196 51 5 0 332 382 547258247 547258297 2.420000e-07 67.6


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 TraesCS3D01G451100 chr3D 559119087 559122839 3752 False 6931.000000 6931 100.000000 1 3753 1 chr3D.!!$F2 3752
1 TraesCS3D01G451100 chr3D 555310628 555314670 4042 True 767.350000 1456 83.144000 947 2915 2 chr3D.!!$R2 1968
2 TraesCS3D01G451100 chr3D 555304538 555306224 1686 True 682.550000 1303 84.900500 1017 2788 2 chr3D.!!$R1 1771
3 TraesCS3D01G451100 chr3A 695514103 695517775 3672 False 1866.333333 4159 93.208333 1 3749 3 chr3A.!!$F2 3748
4 TraesCS3D01G451100 chr3A 692314992 692316349 1357 True 1142.000000 1142 81.884000 1022 2399 1 chr3A.!!$R1 1377
5 TraesCS3D01G451100 chr3A 692056382 692058048 1666 True 637.050000 1201 86.073000 1021 2788 2 chr3A.!!$R3 1767
6 TraesCS3D01G451100 chr3A 692488622 692495403 6781 True 412.825000 1088 87.630750 966 2916 4 chr3A.!!$R4 1950
7 TraesCS3D01G451100 chr3B 738624575 738625876 1301 True 1125.000000 1125 82.357000 1080 2423 1 chr3B.!!$R4 1343
8 TraesCS3D01G451100 chr3B 742080638 742081408 770 True 1040.000000 1040 90.932000 900 1680 1 chr3B.!!$R6 780
9 TraesCS3D01G451100 chr3B 738155107 738156535 1428 True 1035.000000 1035 80.027000 1080 2534 1 chr3B.!!$R2 1454
10 TraesCS3D01G451100 chr3B 742060838 742061608 770 True 1024.000000 1024 90.549000 900 1680 1 chr3B.!!$R5 780
11 TraesCS3D01G451100 chr3B 741965948 741968257 2309 True 921.000000 2143 88.941000 947 3275 3 chr3B.!!$R9 2328
12 TraesCS3D01G451100 chr3B 742107821 742110595 2774 True 903.750000 2268 91.576250 900 3657 4 chr3B.!!$R10 2757
13 TraesCS3D01G451100 chr3B 738294810 738295542 732 True 604.000000 604 81.759000 985 1740 1 chr3B.!!$R3 755
14 TraesCS3D01G451100 chr3B 738288225 738289890 1665 True 583.300000 1099 84.633000 1017 2788 2 chr3B.!!$R7 1771
15 TraesCS3D01G451100 chr3B 738587924 738591967 4043 True 492.633333 1328 85.423000 947 2917 3 chr3B.!!$R8 1970
16 TraesCS3D01G451100 chrUn 272481808 272482922 1114 True 339.000000 339 72.871000 1264 2369 1 chrUn.!!$R1 1105

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
578 581 0.182537 TGTAGGCAAACACCAGCACT 59.817 50.0 0.0 0.0 0.00 4.40 F
666 669 0.527565 GCATCCGCCAACAAATGAGT 59.472 50.0 0.0 0.0 0.00 3.41 F
876 882 0.796312 AAAATGGCGTGCGTGTCTAG 59.204 50.0 0.0 0.0 0.00 2.43 F
1073 1086 0.959553 CTCGCCGCTTATCCCTAAGA 59.040 55.0 0.0 0.0 37.16 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1845 0.982852 ATCCCCACCTCTTCGATGCA 60.983 55.000 0.00 0.0 0.00 3.96 R
2282 2375 4.693283 TCCGTCCAAGATCACATATGAAC 58.307 43.478 10.38 0.0 38.69 3.18 R
2687 10094 3.958798 ACACGGGCAGAGTACTGTTATAT 59.041 43.478 0.00 0.0 45.04 0.86 R
3068 10731 0.586802 GAACCGTGCTTTGAGACCAC 59.413 55.000 0.00 0.0 0.00 4.16 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
145 146 3.072330 TCACCTTCAGCCATGTAGTTCAA 59.928 43.478 0.00 0.00 0.00 2.69
155 156 5.416952 AGCCATGTAGTTCAAGAAGGATTTG 59.583 40.000 0.00 0.00 0.00 2.32
199 202 3.510719 CCACTCGGCAAACATAATTTGG 58.489 45.455 1.89 0.00 0.00 3.28
259 262 7.101054 GTGAACACACACATACTTTATCCCTA 58.899 38.462 0.00 0.00 40.11 3.53
284 287 4.378774 AGCACATCTGAGATTGCACTATC 58.621 43.478 22.29 0.00 37.44 2.08
285 288 4.124970 GCACATCTGAGATTGCACTATCA 58.875 43.478 18.24 1.21 34.97 2.15
326 329 7.502561 GCCTATGTAAGTAATGGTTGGAAGAAT 59.497 37.037 0.00 0.00 0.00 2.40
395 398 2.288825 TGAACTAAGGCCGTGTTCTGAG 60.289 50.000 26.52 10.18 40.27 3.35
407 410 3.366396 GTGTTCTGAGTGGAGGGATAGA 58.634 50.000 0.00 0.00 0.00 1.98
436 439 8.980481 AACATAGGAATATAAACCTGTGAAGG 57.020 34.615 22.31 6.03 44.38 3.46
439 442 9.799106 CATAGGAATATAAACCTGTGAAGGAAT 57.201 33.333 15.23 0.00 44.38 3.01
449 452 2.564062 CTGTGAAGGAATTGGGTTGCAT 59.436 45.455 0.00 0.00 0.00 3.96
547 550 6.883744 TCCAAAGAAAAAGCTAATTGTTGGT 58.116 32.000 15.83 0.00 0.00 3.67
578 581 0.182537 TGTAGGCAAACACCAGCACT 59.817 50.000 0.00 0.00 0.00 4.40
584 587 1.302511 AAACACCAGCACTAGGGCG 60.303 57.895 12.24 6.58 39.27 6.13
611 614 7.489757 CAGCTAGTACCTTTCTTTCTCACATAC 59.510 40.741 0.00 0.00 0.00 2.39
666 669 0.527565 GCATCCGCCAACAAATGAGT 59.472 50.000 0.00 0.00 0.00 3.41
741 747 4.848562 TGGAATACTGTACTGCTATCCG 57.151 45.455 0.00 0.00 0.00 4.18
775 781 4.446719 CACTTCAAAGGAAAAGCATTCAGC 59.553 41.667 4.87 0.00 36.55 4.26
836 842 1.197812 ACGAACGGGCCTAAGGTTAT 58.802 50.000 0.84 0.00 0.00 1.89
837 843 2.387757 ACGAACGGGCCTAAGGTTATA 58.612 47.619 0.84 0.00 0.00 0.98
838 844 2.967887 ACGAACGGGCCTAAGGTTATAT 59.032 45.455 0.84 0.00 0.00 0.86
839 845 4.151883 ACGAACGGGCCTAAGGTTATATA 58.848 43.478 0.84 0.00 0.00 0.86
876 882 0.796312 AAAATGGCGTGCGTGTCTAG 59.204 50.000 0.00 0.00 0.00 2.43
882 888 1.081442 CGTGCGTGTCTAGCAGTGA 60.081 57.895 0.00 0.00 46.10 3.41
1073 1086 0.959553 CTCGCCGCTTATCCCTAAGA 59.040 55.000 0.00 0.00 37.16 2.10
1157 1187 6.542574 ACGTAGTATCATTCTAACCTCTCG 57.457 41.667 0.00 0.00 41.94 4.04
1162 1192 5.766174 AGTATCATTCTAACCTCTCGTCCTC 59.234 44.000 0.00 0.00 0.00 3.71
1201 1233 4.388499 GCCGCTCGTTTCCTCCCA 62.388 66.667 0.00 0.00 0.00 4.37
1319 1351 1.228063 CAAGTCCACCTGCTGCTGT 60.228 57.895 0.00 0.00 0.00 4.40
1395 1429 1.609501 CTTCCCCAGTCGACCCTCA 60.610 63.158 13.01 0.00 0.00 3.86
1445 1480 4.429212 CGCGATCCACGGTGTCCA 62.429 66.667 0.00 0.00 42.83 4.02
2201 2285 2.751259 CCACCCAGAAGACAATGTGATG 59.249 50.000 0.00 0.00 0.00 3.07
2282 2375 4.951963 GATTCGAGGGAGCCGCGG 62.952 72.222 24.05 24.05 46.27 6.46
2407 2501 4.922206 AGCCTTCACAATTGTCCATCTTA 58.078 39.130 8.48 0.00 0.00 2.10
2605 10012 3.138304 TGTTGGTGCTTGAGTGATGTAC 58.862 45.455 0.00 0.00 0.00 2.90
2616 10023 3.377253 AGTGATGTACTCCCTCCGTAA 57.623 47.619 0.00 0.00 33.17 3.18
2617 10024 3.705051 AGTGATGTACTCCCTCCGTAAA 58.295 45.455 0.00 0.00 33.17 2.01
2618 10025 3.446516 AGTGATGTACTCCCTCCGTAAAC 59.553 47.826 0.00 0.00 33.17 2.01
2619 10026 3.446516 GTGATGTACTCCCTCCGTAAACT 59.553 47.826 0.00 0.00 0.00 2.66
2620 10027 4.641989 GTGATGTACTCCCTCCGTAAACTA 59.358 45.833 0.00 0.00 0.00 2.24
2621 10028 5.126061 GTGATGTACTCCCTCCGTAAACTAA 59.874 44.000 0.00 0.00 0.00 2.24
2622 10029 5.895534 TGATGTACTCCCTCCGTAAACTAAT 59.104 40.000 0.00 0.00 0.00 1.73
2623 10030 7.013655 GTGATGTACTCCCTCCGTAAACTAATA 59.986 40.741 0.00 0.00 0.00 0.98
2624 10031 7.727186 TGATGTACTCCCTCCGTAAACTAATAT 59.273 37.037 0.00 0.00 0.00 1.28
2625 10032 9.236006 GATGTACTCCCTCCGTAAACTAATATA 57.764 37.037 0.00 0.00 0.00 0.86
2626 10033 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
2627 10034 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
2628 10035 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2629 10036 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2630 10037 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2631 10038 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2634 10041 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2635 10042 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2637 10044 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2649 10056 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
2650 10057 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
2651 10058 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
2652 10059 8.614346 AGAGCGTTTAGATCACTACTTTAGTAG 58.386 37.037 13.92 13.92 42.10 2.57
2682 10089 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2683 10090 8.461249 ACGCTCTTATATTAGTTTACAGAGGA 57.539 34.615 0.00 0.00 0.00 3.71
2684 10091 8.910944 ACGCTCTTATATTAGTTTACAGAGGAA 58.089 33.333 0.00 0.00 0.00 3.36
2685 10092 9.400638 CGCTCTTATATTAGTTTACAGAGGAAG 57.599 37.037 0.00 0.00 0.00 3.46
2705 10115 6.494146 AGGAAGTATATAACAGTACTCTGCCC 59.506 42.308 0.00 0.00 44.77 5.36
2788 10225 9.829507 ATTCTGGTCTCTGTTATTTCTCTATTG 57.170 33.333 0.00 0.00 0.00 1.90
2956 10455 7.890515 TGTCTTTGGTATTTCATTTATGTGCA 58.109 30.769 0.00 0.00 0.00 4.57
2957 10456 7.812191 TGTCTTTGGTATTTCATTTATGTGCAC 59.188 33.333 10.75 10.75 0.00 4.57
3015 10667 7.792374 TTCTGATATATGAACTGCTGTTTCC 57.208 36.000 10.54 0.00 36.39 3.13
3068 10731 1.934589 TGTGTTCGTGTCACCTTCAG 58.065 50.000 0.00 0.00 35.25 3.02
3125 10788 1.961277 CAGACGAGTTGCCCGCTTT 60.961 57.895 0.00 0.00 0.00 3.51
3210 12497 9.751542 ATACCGTAATTTTGATTGTTTGTCAAA 57.248 25.926 0.00 0.00 42.14 2.69
3265 12552 4.357142 GCAATATGGTCTGCACATTTGAG 58.643 43.478 11.37 0.00 38.48 3.02
3287 12574 6.374053 TGAGTCAGTTCTAGATGAAGAGTGAG 59.626 42.308 0.00 0.00 35.01 3.51
3288 12575 6.480763 AGTCAGTTCTAGATGAAGAGTGAGA 58.519 40.000 0.00 0.00 35.01 3.27
3411 12698 1.739466 TGCTGCGATCCAATCTTCAAC 59.261 47.619 0.00 0.00 0.00 3.18
3414 12701 1.009829 GCGATCCAATCTTCAACGCT 58.990 50.000 0.00 0.00 41.07 5.07
3423 12710 3.678056 ATCTTCAACGCTTGTACCTGA 57.322 42.857 0.00 0.00 0.00 3.86
3424 12711 3.462483 TCTTCAACGCTTGTACCTGAA 57.538 42.857 0.00 0.00 0.00 3.02
3425 12712 3.128349 TCTTCAACGCTTGTACCTGAAC 58.872 45.455 0.00 0.00 0.00 3.18
3684 12987 9.767684 GAAACAAAAAGGGAAAAACTAAACATG 57.232 29.630 0.00 0.00 0.00 3.21
3692 12995 6.613679 AGGGAAAAACTAAACATGGAAAGGAA 59.386 34.615 0.00 0.00 0.00 3.36
3694 12997 7.441157 GGGAAAAACTAAACATGGAAAGGAAAG 59.559 37.037 0.00 0.00 0.00 2.62
3723 13026 9.508642 AAGGAAGAGAAAACCTACTTTTGATAG 57.491 33.333 0.00 0.00 31.81 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.189910 GCTGATGAGCACTTCACAAATCA 59.810 43.478 0.00 0.00 45.46 2.57
69 70 3.261580 CATAGGCGATGAACAACTCACA 58.738 45.455 0.79 0.00 37.82 3.58
145 146 2.354403 GCAAAGCATGGCAAATCCTTCT 60.354 45.455 0.00 0.00 35.26 2.85
155 156 4.714851 CAATTTTAGTTGCAAAGCATGGC 58.285 39.130 0.00 0.00 38.76 4.40
213 216 9.371136 GTTCACAGAGATGAGTATGACAAATTA 57.629 33.333 0.00 0.00 0.00 1.40
234 237 5.938125 AGGGATAAAGTATGTGTGTGTTCAC 59.062 40.000 0.00 0.00 44.08 3.18
253 256 6.709281 CAATCTCAGATGTGCTAATAGGGAT 58.291 40.000 0.00 0.00 0.00 3.85
254 257 5.512060 GCAATCTCAGATGTGCTAATAGGGA 60.512 44.000 12.15 0.00 34.13 4.20
259 262 4.778579 AGTGCAATCTCAGATGTGCTAAT 58.221 39.130 17.40 6.15 37.87 1.73
285 288 1.337384 TAGGCCGTCATGCAGGACAT 61.337 55.000 28.84 14.80 38.23 3.06
326 329 9.734984 ATCGAAGGGAGTCTTAATTAAAGAAAA 57.265 29.630 0.00 0.00 45.78 2.29
347 350 4.939271 TGCGACACTTATTATGGATCGAA 58.061 39.130 0.00 0.00 0.00 3.71
436 439 3.193267 TCAAGCTACATGCAACCCAATTC 59.807 43.478 0.00 0.00 45.94 2.17
439 442 2.284754 TCAAGCTACATGCAACCCAA 57.715 45.000 0.00 0.00 45.94 4.12
449 452 6.770785 AGTATCACAAAGGTTTTCAAGCTACA 59.229 34.615 0.00 0.00 38.49 2.74
481 484 2.168728 ACCTCAGTTTTAGCCGATCCTC 59.831 50.000 0.00 0.00 0.00 3.71
547 550 1.436326 TGCCTACAACTTGGTGGGTA 58.564 50.000 0.00 0.00 41.15 3.69
560 563 2.076863 CTAGTGCTGGTGTTTGCCTAC 58.923 52.381 0.00 0.00 0.00 3.18
578 581 0.396695 AAGGTACTAGCTGCGCCCTA 60.397 55.000 4.18 4.71 38.49 3.53
584 587 4.627900 GTGAGAAAGAAAGGTACTAGCTGC 59.372 45.833 0.00 0.00 38.49 5.25
601 604 8.310382 CCCCAAATAAAATGTTGTATGTGAGAA 58.690 33.333 0.00 0.00 0.00 2.87
611 614 6.589907 GCAGAAGTACCCCAAATAAAATGTTG 59.410 38.462 0.00 0.00 0.00 3.33
620 623 3.832490 GGAAAAGCAGAAGTACCCCAAAT 59.168 43.478 0.00 0.00 0.00 2.32
622 625 2.445525 AGGAAAAGCAGAAGTACCCCAA 59.554 45.455 0.00 0.00 0.00 4.12
696 701 2.961062 AGAAATGCTGGCTTCTTGTGTT 59.039 40.909 0.00 0.00 0.00 3.32
741 747 3.003275 TCCTTTGAAGTGTTCGCATTGTC 59.997 43.478 0.00 0.00 0.00 3.18
775 781 5.572896 GGATTTTTACACGCAAGAATTCCTG 59.427 40.000 0.65 0.00 43.62 3.86
897 903 4.079443 TGGGCTTTTTACTGGGCTGTATAT 60.079 41.667 0.00 0.00 0.00 0.86
945 953 1.970114 GGATGATGGATGCTGCGGG 60.970 63.158 0.00 0.00 0.00 6.13
1157 1187 3.607661 GAGATCGGGGCGGAGGAC 61.608 72.222 0.00 0.00 0.00 3.85
1162 1192 4.598894 CTGCAGAGATCGGGGCGG 62.599 72.222 8.42 1.00 0.00 6.13
1170 1200 3.603144 GCGGCTAATCTGCAGAGAT 57.397 52.632 22.96 15.57 46.35 2.75
1201 1233 2.123251 ATCCCGTCGCCATCTCCT 60.123 61.111 0.00 0.00 0.00 3.69
1395 1429 2.105993 AGGTTTTGTAGAAGAAGCCGGT 59.894 45.455 1.90 0.00 32.16 5.28
1441 1476 2.292292 ACGCTTTGGTAAACATGTGGAC 59.708 45.455 0.00 0.00 0.00 4.02
1445 1480 2.478894 CGAGACGCTTTGGTAAACATGT 59.521 45.455 0.00 0.00 0.00 3.21
1653 1704 2.007608 GAACAAGGAATACTCGGTGGC 58.992 52.381 0.00 0.00 0.00 5.01
1654 1705 2.268298 CGAACAAGGAATACTCGGTGG 58.732 52.381 0.00 0.00 0.00 4.61
1655 1706 2.666508 CACGAACAAGGAATACTCGGTG 59.333 50.000 0.00 0.00 33.89 4.94
1656 1707 2.559668 TCACGAACAAGGAATACTCGGT 59.440 45.455 0.00 0.00 33.89 4.69
1657 1708 3.226346 TCACGAACAAGGAATACTCGG 57.774 47.619 0.00 0.00 33.89 4.63
1658 1709 3.059044 CGTTCACGAACAAGGAATACTCG 59.941 47.826 10.35 0.00 43.02 4.18
1779 1845 0.982852 ATCCCCACCTCTTCGATGCA 60.983 55.000 0.00 0.00 0.00 3.96
2201 2285 6.697455 TCGATGCAGATTCTACAGTTATGAAC 59.303 38.462 0.00 0.00 0.00 3.18
2282 2375 4.693283 TCCGTCCAAGATCACATATGAAC 58.307 43.478 10.38 0.00 38.69 3.18
2407 2501 9.365906 AGATCTAAGTTCACTATCATCATCAGT 57.634 33.333 0.00 0.00 0.00 3.41
2516 7800 5.719173 ACAGAGAAGTTGACTGAATAGCTC 58.281 41.667 11.33 0.00 35.85 4.09
2605 10012 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
2607 10014 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2608 10015 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2609 10016 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2610 10017 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2623 10030 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
2624 10031 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
2625 10032 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
2626 10033 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
2627 10034 8.770850 CTACTAAAGTAGTGATCTAAACGCTC 57.229 38.462 8.69 0.00 42.22 5.03
2656 10063 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2657 10064 8.910944 TCCTCTGTAAACTAATATAAGAGCGTT 58.089 33.333 0.00 0.00 0.00 4.84
2658 10065 8.461249 TCCTCTGTAAACTAATATAAGAGCGT 57.539 34.615 0.00 0.00 0.00 5.07
2659 10066 9.400638 CTTCCTCTGTAAACTAATATAAGAGCG 57.599 37.037 0.00 0.00 0.00 5.03
2676 10083 9.344772 CAGAGTACTGTTATATACTTCCTCTGT 57.655 37.037 0.00 0.00 38.12 3.41
2677 10084 8.293867 GCAGAGTACTGTTATATACTTCCTCTG 58.706 40.741 0.00 0.00 45.04 3.35
2678 10085 7.449086 GGCAGAGTACTGTTATATACTTCCTCT 59.551 40.741 0.00 0.00 45.04 3.69
2679 10086 7.309316 GGGCAGAGTACTGTTATATACTTCCTC 60.309 44.444 0.00 0.00 45.04 3.71
2680 10087 6.494146 GGGCAGAGTACTGTTATATACTTCCT 59.506 42.308 0.00 0.00 45.04 3.36
2681 10088 6.569994 CGGGCAGAGTACTGTTATATACTTCC 60.570 46.154 0.00 0.00 45.04 3.46
2682 10089 6.016443 ACGGGCAGAGTACTGTTATATACTTC 60.016 42.308 0.00 0.00 45.04 3.01
2683 10090 5.832060 ACGGGCAGAGTACTGTTATATACTT 59.168 40.000 0.00 0.00 45.04 2.24
2684 10091 5.241064 CACGGGCAGAGTACTGTTATATACT 59.759 44.000 0.00 0.00 45.04 2.12
2685 10092 5.009410 ACACGGGCAGAGTACTGTTATATAC 59.991 44.000 0.00 0.00 45.04 1.47
2686 10093 5.135383 ACACGGGCAGAGTACTGTTATATA 58.865 41.667 0.00 0.00 45.04 0.86
2687 10094 3.958798 ACACGGGCAGAGTACTGTTATAT 59.041 43.478 0.00 0.00 45.04 0.86
2788 10225 5.584442 CCGCAAATAAAAGTTGGTATACCC 58.416 41.667 19.42 4.75 34.29 3.69
2956 10455 5.106555 CGGTTTCAGCAGACATGAAAATAGT 60.107 40.000 0.00 0.00 45.48 2.12
2957 10456 5.122239 TCGGTTTCAGCAGACATGAAAATAG 59.878 40.000 0.00 0.00 45.48 1.73
3068 10731 0.586802 GAACCGTGCTTTGAGACCAC 59.413 55.000 0.00 0.00 0.00 4.16
3125 10788 1.568597 CAACCCCAGTCCCCATGAATA 59.431 52.381 0.00 0.00 0.00 1.75
3210 12497 9.467796 TCTGAACGTTCTCCAGATATATATCAT 57.532 33.333 27.32 7.07 35.17 2.45
3265 12552 6.751514 TCTCACTCTTCATCTAGAACTGAC 57.248 41.667 0.00 0.00 31.61 3.51
3287 12574 2.072490 GCACAACGCATGCCAAATC 58.928 52.632 13.15 0.00 41.79 2.17
3288 12575 4.265282 GCACAACGCATGCCAAAT 57.735 50.000 13.15 0.00 41.79 2.32
3441 12731 9.790389 TCAACGAACACTGTTTTTAATTACATT 57.210 25.926 0.00 0.00 0.00 2.71
3675 12978 7.563556 TCCTTTTCTTTCCTTTCCATGTTTAGT 59.436 33.333 0.00 0.00 0.00 2.24
3678 12981 6.806668 TCCTTTTCTTTCCTTTCCATGTTT 57.193 33.333 0.00 0.00 0.00 2.83
3684 12987 6.961360 TTCTCTTCCTTTTCTTTCCTTTCC 57.039 37.500 0.00 0.00 0.00 3.13
3692 12995 8.824756 AAAGTAGGTTTTCTCTTCCTTTTCTT 57.175 30.769 0.00 0.00 33.34 2.52
3694 12997 8.683615 TCAAAAGTAGGTTTTCTCTTCCTTTTC 58.316 33.333 0.00 0.00 36.11 2.29


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

AutoCloner maintained by Alex Coulton.