Multiple sequence alignment - TraesCS4A01G499000

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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 TraesCS4A01G499000 chr4A 100.000 3950 0 0 1 3950 744033331 744029382 0.000000e+00 7295
1 TraesCS4A01G499000 chr4A 90.901 3275 222 37 697 3950 744380587 744377368 0.000000e+00 4327
2 TraesCS4A01G499000 chr4A 87.636 1844 193 23 936 2765 744415967 744417789 0.000000e+00 2109
3 TraesCS4A01G499000 chr4A 85.263 1995 256 28 664 2635 743674506 743676485 0.000000e+00 2021
4 TraesCS4A01G499000 chr4A 86.697 1526 177 15 1201 2710 743345791 743347306 0.000000e+00 1670
5 TraesCS4A01G499000 chr4A 86.521 1417 179 7 1201 2611 744013729 744012319 0.000000e+00 1548
6 TraesCS4A01G499000 chr4A 86.570 484 46 5 1 478 744382493 744382023 2.100000e-142 516
7 TraesCS4A01G499000 chr4A 78.421 380 72 5 75 447 744415072 744415448 5.100000e-59 239
8 TraesCS4A01G499000 chr7A 94.196 2550 126 13 924 3462 330661 333199 0.000000e+00 3869
9 TraesCS4A01G499000 chr7A 87.802 1492 163 12 1201 2684 634009 635489 0.000000e+00 1729
10 TraesCS4A01G499000 chr7A 87.832 452 43 2 3 451 329547 329989 1.630000e-143 520
11 TraesCS4A01G499000 chr7A 90.503 179 11 5 487 663 330236 330410 8.540000e-57 231
12 TraesCS4A01G499000 chr7A 88.500 200 12 4 697 885 330464 330663 8.540000e-57 231
13 TraesCS4A01G499000 chr7D 87.780 1383 148 12 1315 2684 1236143 1234769 0.000000e+00 1598
14 TraesCS4A01G499000 chr7D 77.332 922 164 22 3054 3944 526005969 526006876 1.640000e-138 503
15 TraesCS4A01G499000 chr7D 79.254 429 67 20 3532 3950 243787243 243787659 3.010000e-71 279
16 TraesCS4A01G499000 chr7D 75.758 363 55 15 3613 3950 378973748 378974102 6.840000e-33 152
17 TraesCS4A01G499000 chr3D 81.873 1986 277 52 784 2743 18908122 18910050 0.000000e+00 1596
18 TraesCS4A01G499000 chr3D 81.991 1788 273 31 876 2645 18800837 18802593 0.000000e+00 1472
19 TraesCS4A01G499000 chr3D 78.641 927 153 37 3040 3950 342696491 342695594 1.230000e-159 573
20 TraesCS4A01G499000 chr3D 76.580 807 150 28 3040 3827 279208169 279207383 1.320000e-109 407
21 TraesCS4A01G499000 chr3D 75.738 305 48 13 872 1158 18951795 18952091 3.200000e-26 130
22 TraesCS4A01G499000 chr3D 80.952 105 11 4 2674 2772 18953899 18954000 1.520000e-09 75
23 TraesCS4A01G499000 chrUn 88.784 1275 134 6 1349 2619 51384670 51385939 0.000000e+00 1554
24 TraesCS4A01G499000 chrUn 77.222 360 65 13 19 368 122222364 122222012 1.120000e-45 195
25 TraesCS4A01G499000 chr3B 85.313 1389 183 13 1357 2743 29781964 29783333 0.000000e+00 1415
26 TraesCS4A01G499000 chr3B 84.490 1412 181 25 1222 2629 29734386 29735763 0.000000e+00 1360
27 TraesCS4A01G499000 chr3B 84.472 1391 191 13 1357 2743 30207352 30208721 0.000000e+00 1349
28 TraesCS4A01G499000 chr3B 80.732 519 79 15 1 509 809483482 809482975 6.190000e-103 385
29 TraesCS4A01G499000 chr3B 76.176 319 58 13 809 1123 29853025 29853329 6.840000e-33 152
30 TraesCS4A01G499000 chr3A 82.868 1611 231 36 957 2556 26489108 26490684 0.000000e+00 1404
31 TraesCS4A01G499000 chr3A 84.713 1413 176 26 1222 2629 26427525 26428902 0.000000e+00 1376
32 TraesCS4A01G499000 chr1B 79.937 947 144 22 3042 3950 387937954 387938892 0.000000e+00 654
33 TraesCS4A01G499000 chr5A 78.869 937 159 25 3040 3950 275139975 275140898 7.310000e-167 597
34 TraesCS4A01G499000 chr6D 79.097 775 132 25 3065 3825 192012739 192011981 1.270000e-139 507
35 TraesCS4A01G499000 chr4D 77.134 949 166 33 3039 3950 323899091 323898157 1.640000e-138 503
36 TraesCS4A01G499000 chr4D 86.029 136 19 0 3815 3950 293828096 293827961 3.180000e-31 147
37 TraesCS4A01G499000 chr2D 77.819 807 140 34 3040 3827 324175402 324174616 2.780000e-126 462
38 TraesCS4A01G499000 chr2D 75.866 953 142 41 3037 3950 474681719 474682622 4.750000e-109 405
39 TraesCS4A01G499000 chr5D 75.168 745 134 37 3232 3950 328004530 328005249 1.780000e-78 303
40 TraesCS4A01G499000 chr1D 77.077 349 63 9 3616 3950 275711652 275711307 6.740000e-43 185
41 TraesCS4A01G499000 chr7B 84.496 129 20 0 3815 3943 522974211 522974083 1.150000e-25 128


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 TraesCS4A01G499000 chr4A 744029382 744033331 3949 True 7295.00 7295 100.00000 1 3950 1 chr4A.!!$R2 3949
1 TraesCS4A01G499000 chr4A 744377368 744382493 5125 True 2421.50 4327 88.73550 1 3950 2 chr4A.!!$R3 3949
2 TraesCS4A01G499000 chr4A 743674506 743676485 1979 False 2021.00 2021 85.26300 664 2635 1 chr4A.!!$F2 1971
3 TraesCS4A01G499000 chr4A 743345791 743347306 1515 False 1670.00 1670 86.69700 1201 2710 1 chr4A.!!$F1 1509
4 TraesCS4A01G499000 chr4A 744012319 744013729 1410 True 1548.00 1548 86.52100 1201 2611 1 chr4A.!!$R1 1410
5 TraesCS4A01G499000 chr4A 744415072 744417789 2717 False 1174.00 2109 83.02850 75 2765 2 chr4A.!!$F3 2690
6 TraesCS4A01G499000 chr7A 634009 635489 1480 False 1729.00 1729 87.80200 1201 2684 1 chr7A.!!$F1 1483
7 TraesCS4A01G499000 chr7A 329547 333199 3652 False 1212.75 3869 90.25775 3 3462 4 chr7A.!!$F2 3459
8 TraesCS4A01G499000 chr7D 1234769 1236143 1374 True 1598.00 1598 87.78000 1315 2684 1 chr7D.!!$R1 1369
9 TraesCS4A01G499000 chr7D 526005969 526006876 907 False 503.00 503 77.33200 3054 3944 1 chr7D.!!$F3 890
10 TraesCS4A01G499000 chr3D 18908122 18910050 1928 False 1596.00 1596 81.87300 784 2743 1 chr3D.!!$F2 1959
11 TraesCS4A01G499000 chr3D 18800837 18802593 1756 False 1472.00 1472 81.99100 876 2645 1 chr3D.!!$F1 1769
12 TraesCS4A01G499000 chr3D 342695594 342696491 897 True 573.00 573 78.64100 3040 3950 1 chr3D.!!$R2 910
13 TraesCS4A01G499000 chr3D 279207383 279208169 786 True 407.00 407 76.58000 3040 3827 1 chr3D.!!$R1 787
14 TraesCS4A01G499000 chrUn 51384670 51385939 1269 False 1554.00 1554 88.78400 1349 2619 1 chrUn.!!$F1 1270
15 TraesCS4A01G499000 chr3B 29781964 29783333 1369 False 1415.00 1415 85.31300 1357 2743 1 chr3B.!!$F2 1386
16 TraesCS4A01G499000 chr3B 29734386 29735763 1377 False 1360.00 1360 84.49000 1222 2629 1 chr3B.!!$F1 1407
17 TraesCS4A01G499000 chr3B 30207352 30208721 1369 False 1349.00 1349 84.47200 1357 2743 1 chr3B.!!$F4 1386
18 TraesCS4A01G499000 chr3B 809482975 809483482 507 True 385.00 385 80.73200 1 509 1 chr3B.!!$R1 508
19 TraesCS4A01G499000 chr3A 26489108 26490684 1576 False 1404.00 1404 82.86800 957 2556 1 chr3A.!!$F2 1599
20 TraesCS4A01G499000 chr3A 26427525 26428902 1377 False 1376.00 1376 84.71300 1222 2629 1 chr3A.!!$F1 1407
21 TraesCS4A01G499000 chr1B 387937954 387938892 938 False 654.00 654 79.93700 3042 3950 1 chr1B.!!$F1 908
22 TraesCS4A01G499000 chr5A 275139975 275140898 923 False 597.00 597 78.86900 3040 3950 1 chr5A.!!$F1 910
23 TraesCS4A01G499000 chr6D 192011981 192012739 758 True 507.00 507 79.09700 3065 3825 1 chr6D.!!$R1 760
24 TraesCS4A01G499000 chr4D 323898157 323899091 934 True 503.00 503 77.13400 3039 3950 1 chr4D.!!$R2 911
25 TraesCS4A01G499000 chr2D 324174616 324175402 786 True 462.00 462 77.81900 3040 3827 1 chr2D.!!$R1 787
26 TraesCS4A01G499000 chr2D 474681719 474682622 903 False 405.00 405 75.86600 3037 3950 1 chr2D.!!$F1 913
27 TraesCS4A01G499000 chr5D 328004530 328005249 719 False 303.00 303 75.16800 3232 3950 1 chr5D.!!$F1 718

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
464 916 0.036671 TGCTACGAGAGGTCAGTCGA 60.037 55.000 0.00 0.00 39.53 4.20 F
485 939 1.223763 GGCTAGCTACCAACCCCAC 59.776 63.158 15.72 0.00 0.00 4.61 F
1582 3468 1.268625 CTTGGAAAAGGTGGTTACGGC 59.731 52.381 0.00 0.00 0.00 5.68 F
2689 4609 1.746991 CTCTTTGAGAAGGCGGCCC 60.747 63.158 17.02 0.38 33.56 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 3534 0.965439 CAAACTCGCCCCCATTTTCA 59.035 50.000 0.0 0.0 0.0 2.69 R
2348 4234 6.998074 TCTAAGCTTCTCTCAAACATTTCCAA 59.002 34.615 0.0 0.0 0.0 3.53 R
2780 4700 0.392706 ACTTGTGGACGCTGACATCA 59.607 50.000 0.0 0.0 0.0 3.07 R
3518 5471 0.744281 CCTTTCCGTTTTGTGGTGCT 59.256 50.000 0.0 0.0 0.0 4.40 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
35 36 1.812686 CGACTTTCTCGACCCCACCA 61.813 60.000 0.00 0.00 46.14 4.17
36 37 0.320508 GACTTTCTCGACCCCACCAC 60.321 60.000 0.00 0.00 0.00 4.16
53 54 1.684734 ACCAACTCCGGCGAGGTAT 60.685 57.895 9.30 0.00 40.77 2.73
60 61 0.402887 TCCGGCGAGGTATATCTCCA 59.597 55.000 9.30 0.00 41.99 3.86
63 64 3.021695 CCGGCGAGGTATATCTCCATAA 58.978 50.000 9.30 0.00 34.51 1.90
65 66 3.442625 CGGCGAGGTATATCTCCATAACA 59.557 47.826 0.00 0.00 0.00 2.41
71 72 2.770164 ATATCTCCATAACAGCGCCC 57.230 50.000 2.29 0.00 0.00 6.13
81 82 2.438975 CAGCGCCCACATCACCAT 60.439 61.111 2.29 0.00 0.00 3.55
97 98 1.515487 CATCACCGACGTCCATGGA 59.485 57.895 11.44 11.44 0.00 3.41
116 117 1.485294 ATACCAACAGGCGGTCACCA 61.485 55.000 0.00 0.00 37.99 4.17
124 125 2.032681 GCGGTCACCAGCCTTCTT 59.967 61.111 0.00 0.00 0.00 2.52
222 227 2.035576 GGTTCCGCAATATCTACTCGGT 59.964 50.000 0.00 0.00 40.81 4.69
229 234 1.037493 ATATCTACTCGGTGGCGCAA 58.963 50.000 10.83 0.00 0.00 4.85
311 316 2.823587 TGGACCACGTTCCACTACA 58.176 52.632 4.82 0.00 41.00 2.74
314 319 1.274167 GGACCACGTTCCACTACATGA 59.726 52.381 0.00 0.00 35.49 3.07
325 330 2.355756 CCACTACATGAATTTGGAGGCG 59.644 50.000 0.00 0.00 31.31 5.52
329 334 2.120909 ATGAATTTGGAGGCGGCGG 61.121 57.895 9.78 0.00 0.00 6.13
391 396 1.634757 CGTTCTACATTGGCAGCGCA 61.635 55.000 11.47 0.00 0.00 6.09
395 400 0.248743 CTACATTGGCAGCGCAATGG 60.249 55.000 26.93 14.77 41.60 3.16
464 916 0.036671 TGCTACGAGAGGTCAGTCGA 60.037 55.000 0.00 0.00 39.53 4.20
465 917 1.301423 GCTACGAGAGGTCAGTCGAT 58.699 55.000 0.00 0.00 39.53 3.59
466 918 1.262151 GCTACGAGAGGTCAGTCGATC 59.738 57.143 0.00 0.00 39.53 3.69
467 919 1.523515 CTACGAGAGGTCAGTCGATCG 59.476 57.143 9.36 9.36 39.53 3.69
485 939 1.223763 GGCTAGCTACCAACCCCAC 59.776 63.158 15.72 0.00 0.00 4.61
511 965 5.531122 AGAGTTTAAGCCTTGAAAAACCC 57.469 39.130 0.00 0.00 33.33 4.11
516 970 7.172342 AGTTTAAGCCTTGAAAAACCCTTTTT 58.828 30.769 0.00 0.00 44.93 1.94
556 1010 1.356494 GGAGGATTAGCCCCTGCCTT 61.356 60.000 0.00 0.00 36.30 4.35
588 1042 6.576551 ACGCGTCAACAAAACAATTTTATT 57.423 29.167 5.58 0.00 0.00 1.40
589 1043 6.406820 ACGCGTCAACAAAACAATTTTATTG 58.593 32.000 5.58 0.00 0.00 1.90
605 1059 6.755461 TTTTATTGTGGTTGTTTATGCACG 57.245 33.333 0.00 0.00 0.00 5.34
649 2375 4.026145 CCAAATCAAACGCGTCAACAAAAT 60.026 37.500 14.44 0.00 0.00 1.82
665 2442 8.699749 GTCAACAAAATAATTTTACTCACTGCC 58.300 33.333 0.00 0.00 0.00 4.85
682 2459 1.277273 TGCCTCAGACAAGATGGAGTG 59.723 52.381 0.00 0.00 0.00 3.51
685 2462 3.133721 GCCTCAGACAAGATGGAGTGTAT 59.866 47.826 0.00 0.00 0.00 2.29
686 2463 4.383552 GCCTCAGACAAGATGGAGTGTATT 60.384 45.833 0.00 0.00 0.00 1.89
722 2502 8.609176 TGGAATACATTTTAAATGACTAGCGAC 58.391 33.333 22.53 6.93 0.00 5.19
759 2545 2.663826 AAGAAGTGAGAGATGCGACC 57.336 50.000 0.00 0.00 0.00 4.79
792 2586 6.466308 TGTCAACACTGTATTCGATCAAAG 57.534 37.500 0.00 0.00 0.00 2.77
802 2596 4.928661 ATTCGATCAAAGGAAAGTCACG 57.071 40.909 0.00 0.00 0.00 4.35
823 2649 9.084164 GTCACGTATGTAGTTCATGTTCTATTT 57.916 33.333 0.00 0.00 37.91 1.40
824 2650 9.297586 TCACGTATGTAGTTCATGTTCTATTTC 57.702 33.333 0.00 0.00 37.91 2.17
835 2661 6.189859 TCATGTTCTATTTCCCTTCAATGCT 58.810 36.000 0.00 0.00 0.00 3.79
900 2726 5.591643 AATGAACATTCATATACGACGCC 57.408 39.130 7.52 0.00 46.60 5.68
930 2758 9.377312 CTCTTTCTTTTGGAAAAACAACCAATA 57.623 29.630 0.00 0.00 44.10 1.90
973 2801 7.530010 ACAGTGTTTACTCATAAATGTGATGC 58.470 34.615 0.00 0.00 34.07 3.91
1041 2873 9.908152 AATAGGTATGCTAAAAACTTTTGTCAC 57.092 29.630 0.00 0.00 0.00 3.67
1420 3299 3.652057 TGGCATAGAAAAGGGAGAAGG 57.348 47.619 0.00 0.00 0.00 3.46
1435 3314 4.505742 GGGAGAAGGCTATGGTTTATCCTG 60.506 50.000 8.30 0.00 33.74 3.86
1582 3468 1.268625 CTTGGAAAAGGTGGTTACGGC 59.731 52.381 0.00 0.00 0.00 5.68
1648 3534 5.244402 TGTGAAATTCTTGCATGACTCCAAT 59.756 36.000 1.02 0.00 0.00 3.16
2299 4185 7.445402 GCTAGAAAGATGACATTAATTGGCCTA 59.555 37.037 3.32 0.00 29.16 3.93
2348 4234 3.696051 TCGCCCTACTATAACACGAGTTT 59.304 43.478 2.93 0.00 39.15 2.66
2495 4384 6.998802 AGCACTAACTTGATCTACTCACTTT 58.001 36.000 0.00 0.00 32.17 2.66
2543 4436 4.035675 GCTCACAATATGGAGGTACAAAGC 59.964 45.833 0.00 0.00 0.00 3.51
2598 4498 3.030291 AGCCATGTGAACTCAAAAACCA 58.970 40.909 0.00 0.00 0.00 3.67
2645 4546 8.531982 TCAGCAGATATATAAGCCTCGTTAATT 58.468 33.333 5.50 0.00 0.00 1.40
2684 4603 4.074970 TGATTTCCACTCTTTGAGAAGGC 58.925 43.478 1.25 0.00 33.56 4.35
2689 4609 1.746991 CTCTTTGAGAAGGCGGCCC 60.747 63.158 17.02 0.38 33.56 5.80
2780 4700 1.134580 CATGAACTGGAGCATCGGTCT 60.135 52.381 0.00 0.00 34.37 3.85
2804 4724 2.624364 TGTCAGCGTCCACAAGTTACTA 59.376 45.455 0.00 0.00 0.00 1.82
2871 4793 2.294233 TGCAAGCTCCAACTGCTAAAAG 59.706 45.455 8.68 0.00 40.22 2.27
2990 4912 8.904712 CACATAAACATTGTGGCGATATATTTG 58.095 33.333 0.00 0.00 40.60 2.32
2995 4917 9.598517 AAACATTGTGGCGATATATTTGAATTT 57.401 25.926 0.00 0.00 0.00 1.82
3112 5041 5.858581 GGAACACTACAAAGATGCAATGAAC 59.141 40.000 0.00 0.00 0.00 3.18
3119 5048 5.992729 ACAAAGATGCAATGAACAATTTGC 58.007 33.333 0.00 6.28 34.02 3.68
3245 5178 0.249155 AACAGTCGCTCGAACGGAAA 60.249 50.000 8.55 0.00 0.00 3.13
3297 5234 2.623416 AGCATACGATCTTCACGATCCA 59.377 45.455 0.00 0.00 44.66 3.41
3302 5239 2.035193 ACGATCTTCACGATCCATCAGG 59.965 50.000 0.00 0.00 44.66 3.86
3344 5281 3.178865 TCGTCCCCAAAGAATTAGAGGT 58.821 45.455 0.00 0.00 0.00 3.85
3349 5286 5.191124 GTCCCCAAAGAATTAGAGGTAGGAA 59.809 44.000 0.00 0.00 0.00 3.36
3451 5398 7.931046 ACTAGAACTAGAAAGGACTAGAGGAA 58.069 38.462 14.64 0.00 41.42 3.36
3518 5471 1.229853 GTTGAGGGGGAAGGAGGGA 60.230 63.158 0.00 0.00 0.00 4.20
3530 5483 0.178990 AGGAGGGAGCACCACAAAAC 60.179 55.000 1.58 0.00 43.89 2.43
3556 5512 1.544917 AATCCCCTCCCCTTGTGCT 60.545 57.895 0.00 0.00 0.00 4.40
3562 5518 3.391665 CTCCCCTTGTGCTAGCCCG 62.392 68.421 13.29 0.00 0.00 6.13
3609 5580 1.425428 CAATTCGGTCTCGCCAAGC 59.575 57.895 0.00 0.00 36.97 4.01
3644 5617 2.113243 CTCCCCTATACGGCCCTTGC 62.113 65.000 0.00 0.00 0.00 4.01
3680 5653 1.874872 CCACCGTTTCGCCTTTTAAGA 59.125 47.619 0.00 0.00 0.00 2.10
3681 5654 2.291190 CCACCGTTTCGCCTTTTAAGAA 59.709 45.455 0.00 0.00 0.00 2.52
3847 5864 5.062308 CGGTTCCTCTCGAAACTATTTCAAG 59.938 44.000 2.50 0.00 39.63 3.02
3915 5932 4.399004 ACTAACACTCAGGAGATCATGC 57.601 45.455 2.79 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.396139 TATACCTCGCCGGAGTTGGT 60.396 55.000 22.78 22.78 38.70 3.67
36 37 0.966920 ATATACCTCGCCGGAGTTGG 59.033 55.000 5.05 12.15 38.70 3.77
53 54 1.070134 GTGGGCGCTGTTATGGAGATA 59.930 52.381 7.64 0.00 0.00 1.98
60 61 0.748005 GGTGATGTGGGCGCTGTTAT 60.748 55.000 7.64 0.00 0.00 1.89
63 64 3.272364 ATGGTGATGTGGGCGCTGT 62.272 57.895 7.64 0.00 0.00 4.40
65 66 2.124570 GATGGTGATGTGGGCGCT 60.125 61.111 7.64 0.00 0.00 5.92
71 72 0.389817 ACGTCGGTGATGGTGATGTG 60.390 55.000 0.00 0.00 31.01 3.21
81 82 0.742505 GTATCCATGGACGTCGGTGA 59.257 55.000 18.99 8.77 0.00 4.02
97 98 1.298667 GGTGACCGCCTGTTGGTAT 59.701 57.895 0.00 0.00 40.63 2.73
116 117 2.125512 CGTGGCGCTAAGAAGGCT 60.126 61.111 7.64 0.00 0.00 4.58
124 125 2.717044 ATACTGCACCGTGGCGCTA 61.717 57.895 7.64 0.00 36.28 4.26
199 204 2.296471 CGAGTAGATATTGCGGAACCCT 59.704 50.000 0.00 0.00 0.00 4.34
229 234 4.760047 GACAGGTCCGGTGCGCAT 62.760 66.667 15.91 0.00 0.00 4.73
268 273 4.020617 CCCACGAGGCCTTGCAGA 62.021 66.667 20.81 0.00 0.00 4.26
308 313 1.388547 GCCGCCTCCAAATTCATGTA 58.611 50.000 0.00 0.00 0.00 2.29
311 316 2.120909 CCGCCGCCTCCAAATTCAT 61.121 57.895 0.00 0.00 0.00 2.57
329 334 4.899239 CCTCGGACCAGCGATGCC 62.899 72.222 0.00 0.00 0.00 4.40
391 396 1.331214 CCTTGGTCTGTTGCACCATT 58.669 50.000 0.00 0.00 43.66 3.16
395 400 2.639286 CGCCTTGGTCTGTTGCAC 59.361 61.111 0.00 0.00 0.00 4.57
464 916 1.408453 GGGGTTGGTAGCTAGCCGAT 61.408 60.000 19.78 0.00 32.72 4.18
465 917 2.062177 GGGGTTGGTAGCTAGCCGA 61.062 63.158 19.78 9.01 32.72 5.54
466 918 2.363975 TGGGGTTGGTAGCTAGCCG 61.364 63.158 19.78 0.00 32.72 5.52
467 919 1.223763 GTGGGGTTGGTAGCTAGCC 59.776 63.158 19.78 14.97 0.00 3.93
485 939 7.201609 GGGTTTTTCAAGGCTTAAACTCTTTTG 60.202 37.037 18.51 0.00 32.53 2.44
516 970 7.039270 CCTCCTTTTCTTTTCCTTTTTCGAAA 58.961 34.615 6.47 6.47 0.00 3.46
520 974 9.698309 CTAATCCTCCTTTTCTTTTCCTTTTTC 57.302 33.333 0.00 0.00 0.00 2.29
521 975 8.150945 GCTAATCCTCCTTTTCTTTTCCTTTTT 58.849 33.333 0.00 0.00 0.00 1.94
522 976 7.256332 GGCTAATCCTCCTTTTCTTTTCCTTTT 60.256 37.037 0.00 0.00 0.00 2.27
524 978 5.717178 GGCTAATCCTCCTTTTCTTTTCCTT 59.283 40.000 0.00 0.00 0.00 3.36
525 979 5.265191 GGCTAATCCTCCTTTTCTTTTCCT 58.735 41.667 0.00 0.00 0.00 3.36
526 980 4.402793 GGGCTAATCCTCCTTTTCTTTTCC 59.597 45.833 0.00 0.00 34.39 3.13
527 981 4.402793 GGGGCTAATCCTCCTTTTCTTTTC 59.597 45.833 0.00 0.00 34.39 2.29
532 986 2.937519 CAGGGGCTAATCCTCCTTTTC 58.062 52.381 0.00 0.00 35.19 2.29
556 1010 0.378610 TGTTGACGCGTTTGATGCAA 59.621 45.000 15.53 9.17 0.00 4.08
562 1016 3.898005 ATTGTTTTGTTGACGCGTTTG 57.102 38.095 15.53 0.00 0.00 2.93
588 1042 1.261885 CGACGTGCATAAACAACCACA 59.738 47.619 0.00 0.00 0.00 4.17
589 1043 1.527736 TCGACGTGCATAAACAACCAC 59.472 47.619 0.00 0.00 0.00 4.16
605 1059 6.243811 TGGTAACACAACCAATAAATCGAC 57.756 37.500 0.00 0.00 46.55 4.20
649 2375 6.109156 TGTCTGAGGCAGTGAGTAAAATTA 57.891 37.500 0.00 0.00 32.61 1.40
665 2442 6.875726 TCAAAATACACTCCATCTTGTCTGAG 59.124 38.462 0.00 0.00 0.00 3.35
775 2569 6.368791 TGACTTTCCTTTGATCGAATACAGTG 59.631 38.462 0.00 0.00 0.00 3.66
792 2586 5.867716 ACATGAACTACATACGTGACTTTCC 59.132 40.000 0.00 0.00 37.46 3.13
802 2596 9.614792 AAGGGAAATAGAACATGAACTACATAC 57.385 33.333 0.00 0.00 37.46 2.39
823 2649 2.633967 ACATTGCAAAGCATTGAAGGGA 59.366 40.909 17.54 0.00 40.83 4.20
824 2650 3.048337 ACATTGCAAAGCATTGAAGGG 57.952 42.857 17.54 0.00 40.83 3.95
835 2661 9.979578 ATACAGAAGAAACAAATACATTGCAAA 57.020 25.926 1.71 0.00 43.13 3.68
900 2726 7.011389 GGTTGTTTTTCCAAAAGAAAGAGATGG 59.989 37.037 0.00 0.00 45.11 3.51
930 2758 8.540507 AACACTGTCTCATCCAATAGTACTAT 57.459 34.615 9.71 9.71 0.00 2.12
947 2775 7.693951 GCATCACATTTATGAGTAAACACTGTC 59.306 37.037 0.00 0.00 32.91 3.51
973 2801 4.455606 CCCTCTTGCTACCTGGAATAAAG 58.544 47.826 0.00 0.00 0.00 1.85
1058 2890 5.465724 GTGGACCATTGGTATCTAAATCGTC 59.534 44.000 8.70 0.00 35.25 4.20
1060 2892 5.611374 AGTGGACCATTGGTATCTAAATCG 58.389 41.667 8.70 0.00 35.25 3.34
1120 2958 7.473735 TTCAATGATTACAGGCATGGTAAAA 57.526 32.000 2.31 0.00 34.67 1.52
1420 3299 3.694072 TGTTGCACAGGATAAACCATAGC 59.306 43.478 0.00 0.00 42.04 2.97
1435 3314 6.598753 TTGTTTCTACTAGACTTGTTGCAC 57.401 37.500 0.00 0.00 0.00 4.57
1582 3468 4.095782 TGAAGTCTTCCTTTGAAAACCACG 59.904 41.667 10.12 0.00 32.03 4.94
1648 3534 0.965439 CAAACTCGCCCCCATTTTCA 59.035 50.000 0.00 0.00 0.00 2.69
2348 4234 6.998074 TCTAAGCTTCTCTCAAACATTTCCAA 59.002 34.615 0.00 0.00 0.00 3.53
2495 4384 9.102757 GCTGAACTTTCACTGAAATGATAGATA 57.897 33.333 4.65 0.00 33.38 1.98
2500 4389 5.766670 TGAGCTGAACTTTCACTGAAATGAT 59.233 36.000 4.65 0.00 30.85 2.45
2543 4436 2.230508 TCTGGTACTGGTAGAACTTGCG 59.769 50.000 0.00 0.00 0.00 4.85
2645 4546 8.522830 GTGGAAATCATTGTAGGATCTTTTTGA 58.477 33.333 0.00 0.00 0.00 2.69
2684 4603 2.895372 GTACTCCAATGCGGGCCG 60.895 66.667 24.35 24.35 34.36 6.13
2689 4609 4.944962 TTTCTGAATGTACTCCAATGCG 57.055 40.909 0.00 0.00 0.00 4.73
2765 4685 0.463204 CATCAGACCGATGCTCCAGT 59.537 55.000 0.00 0.00 44.95 4.00
2780 4700 0.392706 ACTTGTGGACGCTGACATCA 59.607 50.000 0.00 0.00 0.00 3.07
2804 4724 7.725251 TGAACTAATTTTGTTCTTGCTTGGAT 58.275 30.769 19.53 0.00 42.86 3.41
2871 4793 8.560374 GTGTTTATACTCTTAAAGATCCATGCC 58.440 37.037 0.00 0.00 0.00 4.40
2965 4887 8.845227 TCAAATATATCGCCACAATGTTTATGT 58.155 29.630 0.00 0.00 0.00 2.29
2966 4888 9.676195 TTCAAATATATCGCCACAATGTTTATG 57.324 29.630 0.00 0.00 0.00 1.90
3112 5041 5.911280 GTCGGTAATGATCTGATGCAAATTG 59.089 40.000 0.00 0.00 0.00 2.32
3119 5048 4.860072 TCGAAGTCGGTAATGATCTGATG 58.140 43.478 0.00 0.00 40.29 3.07
3233 5166 2.478547 TTTTGGTTTTCCGTTCGAGC 57.521 45.000 0.00 0.00 44.36 5.03
3245 5178 1.029681 GAGAGGCCGTGTTTTTGGTT 58.970 50.000 0.00 0.00 0.00 3.67
3297 5234 0.549950 CTGGATGGTGAAGCCCTGAT 59.450 55.000 0.00 0.00 36.04 2.90
3302 5239 0.833287 TAGCTCTGGATGGTGAAGCC 59.167 55.000 0.00 0.00 37.90 4.35
3407 5346 9.535878 GTTCTAGTTGGTCCTAATTGATCTTAG 57.464 37.037 0.00 0.00 0.00 2.18
3409 5348 8.152023 AGTTCTAGTTGGTCCTAATTGATCTT 57.848 34.615 0.00 0.00 0.00 2.40
3451 5398 6.536224 CACTTTTGAATTGAAGTTTTGGAGCT 59.464 34.615 0.00 0.00 34.04 4.09
3482 5432 5.419471 CCTCAACCTGTATATACTAGAGGGC 59.581 48.000 17.63 0.00 37.16 5.19
3497 5448 1.566298 CCTCCTTCCCCCTCAACCTG 61.566 65.000 0.00 0.00 0.00 4.00
3518 5471 0.744281 CCTTTCCGTTTTGTGGTGCT 59.256 50.000 0.00 0.00 0.00 4.40
3562 5518 1.700985 AGGACTCCTCCTCCCACTC 59.299 63.158 0.00 0.00 44.59 3.51
3644 5617 1.689233 TGGAGGGAGGATTGGACCG 60.689 63.158 0.00 0.00 34.73 4.79
3747 5721 8.893563 ATAGGTGAAAAATGTTTCCCAAGATA 57.106 30.769 14.68 3.42 42.20 1.98
3877 5894 8.694581 AGTGTTAGTAGGATAGGAGTAATGAC 57.305 38.462 0.00 0.00 0.00 3.06
3915 5932 5.010282 ACAGGGTCAAATGCTTAAGGTAAG 58.990 41.667 4.29 0.00 38.80 2.34


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

AutoCloner maintained by Alex Coulton.