Multiple sequence alignment - TraesCS7D01G005300

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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 TraesCS7D01G005300 chr7D 100.000 3469 0 0 1 3469 2568411 2564943 0.000000e+00 6407.0
1 TraesCS7D01G005300 chr7D 88.540 1658 140 21 354 1971 3905052 3906699 0.000000e+00 1964.0
2 TraesCS7D01G005300 chr7D 88.861 1580 139 14 567 2142 3788658 3787112 0.000000e+00 1908.0
3 TraesCS7D01G005300 chr7D 89.403 1406 131 10 567 1965 3634869 3633475 0.000000e+00 1755.0
4 TraesCS7D01G005300 chr7D 91.919 1188 94 2 779 1965 2359150 2357964 0.000000e+00 1661.0
5 TraesCS7D01G005300 chr7D 87.612 1227 113 17 2187 3392 3787115 3785907 0.000000e+00 1387.0
6 TraesCS7D01G005300 chr7D 89.455 1100 81 14 2308 3388 3633199 3632116 0.000000e+00 1356.0
7 TraesCS7D01G005300 chr7D 89.089 1054 80 14 2354 3388 2357659 2356622 0.000000e+00 1277.0
8 TraesCS7D01G005300 chr7D 96.875 32 1 0 705 736 2359199 2359168 2.000000e-03 54.7
9 TraesCS7D01G005300 chr7A 88.983 2723 238 24 690 3392 3311037 3313717 0.000000e+00 3310.0
10 TraesCS7D01G005300 chr7A 90.166 1627 122 15 354 1949 3209911 3208292 0.000000e+00 2084.0
11 TraesCS7D01G005300 chr7A 89.909 1645 127 16 354 1965 1998404 1996766 0.000000e+00 2082.0
12 TraesCS7D01G005300 chr7A 88.018 1519 156 15 448 1953 2119342 2117837 0.000000e+00 1773.0
13 TraesCS7D01G005300 chr7A 89.238 1115 87 17 2296 3392 3631641 3630542 0.000000e+00 1363.0
14 TraesCS7D01G005300 chr7A 88.647 1101 86 20 2308 3388 3208034 3206953 0.000000e+00 1304.0
15 TraesCS7D01G005300 chr7A 89.489 352 35 2 1 351 3309508 3309858 8.830000e-121 444.0
16 TraesCS7D01G005300 chr7A 85.755 351 38 5 1 351 3211001 3210663 9.150000e-96 361.0
17 TraesCS7D01G005300 chr7A 85.623 313 33 6 39 351 1999690 1999390 5.590000e-83 318.0
18 TraesCS7D01G005300 chr4A 89.362 2491 222 19 928 3392 740456804 740454331 0.000000e+00 3092.0
19 TraesCS7D01G005300 chr4A 90.157 2225 173 22 1195 3392 740577922 740580127 0.000000e+00 2854.0
20 TraesCS7D01G005300 chr4A 86.590 2528 226 44 898 3392 741795934 741793487 0.000000e+00 2686.0
21 TraesCS7D01G005300 chr4A 89.701 1806 138 24 354 2123 739865659 739867452 0.000000e+00 2261.0
22 TraesCS7D01G005300 chr4A 87.545 1397 146 15 754 2142 741485751 741484375 0.000000e+00 1591.0
23 TraesCS7D01G005300 chr4A 92.294 1090 32 7 1499 2582 740936878 740937921 0.000000e+00 1500.0
24 TraesCS7D01G005300 chr4A 87.305 1347 117 30 2079 3392 739651802 739653127 0.000000e+00 1491.0
25 TraesCS7D01G005300 chr4A 87.221 1346 118 30 2080 3392 742057082 742058406 0.000000e+00 1483.0
26 TraesCS7D01G005300 chr4A 87.237 1285 102 22 2131 3392 739867427 739868672 0.000000e+00 1408.0
27 TraesCS7D01G005300 chr4A 86.029 1360 132 22 2054 3392 741590157 741591479 0.000000e+00 1406.0
28 TraesCS7D01G005300 chr4A 86.070 1285 105 27 2131 3392 741484419 741483186 0.000000e+00 1314.0
29 TraesCS7D01G005300 chr4A 89.151 1060 78 20 2354 3393 740019075 740018033 0.000000e+00 1286.0
30 TraesCS7D01G005300 chr4A 95.455 792 31 4 354 1142 740930843 740931632 0.000000e+00 1258.0
31 TraesCS7D01G005300 chr4A 83.769 1300 140 39 2131 3392 740270715 740271981 0.000000e+00 1166.0
32 TraesCS7D01G005300 chr4A 83.692 1300 141 39 2131 3392 740304867 740306133 0.000000e+00 1160.0
33 TraesCS7D01G005300 chr4A 84.008 1038 106 33 2131 3141 740348121 740349125 0.000000e+00 942.0
34 TraesCS7D01G005300 chr4A 89.390 754 67 5 2647 3387 740937948 740938701 0.000000e+00 937.0
35 TraesCS7D01G005300 chr4A 90.909 352 29 3 1 351 739864255 739864604 1.460000e-128 470.0
36 TraesCS7D01G005300 chr4A 88.920 352 10 4 1 351 740929870 740930193 1.160000e-109 407.0
37 TraesCS7D01G005300 chr4A 89.756 205 21 0 1 205 740575336 740575540 2.660000e-66 263.0
38 TraesCS7D01G005300 chr4A 95.146 103 4 1 2021 2123 740270639 740270740 9.960000e-36 161.0
39 TraesCS7D01G005300 chr4A 94.231 104 4 2 2021 2123 740304790 740304892 1.290000e-34 158.0
40 TraesCS7D01G005300 chr4A 94.231 104 4 2 2021 2123 740348044 740348146 1.290000e-34 158.0
41 TraesCS7D01G005300 chr4A 84.906 106 12 3 2169 2272 740020466 740020363 1.700000e-18 104.0
42 TraesCS7D01G005300 chr5D 96.203 79 1 2 3391 3469 325430888 325430964 1.010000e-25 128.0
43 TraesCS7D01G005300 chr2B 96.203 79 1 2 3391 3469 544997342 544997266 1.010000e-25 128.0
44 TraesCS7D01G005300 chrUn 100.000 68 0 0 3402 3469 37082234 37082167 3.630000e-25 126.0
45 TraesCS7D01G005300 chrUn 100.000 68 0 0 3402 3469 68789674 68789607 3.630000e-25 126.0
46 TraesCS7D01G005300 chr6D 100.000 68 0 0 3402 3469 36205976 36206043 3.630000e-25 126.0
47 TraesCS7D01G005300 chr6D 100.000 68 0 0 3402 3469 71539550 71539617 3.630000e-25 126.0
48 TraesCS7D01G005300 chr6D 96.154 78 1 2 3391 3468 472333693 472333618 3.630000e-25 126.0
49 TraesCS7D01G005300 chr4D 94.937 79 2 2 3391 3469 380535552 380535628 4.700000e-24 122.0
50 TraesCS7D01G005300 chr2A 94.937 79 2 2 3391 3469 697117132 697117208 4.700000e-24 122.0


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 TraesCS7D01G005300 chr7D 2564943 2568411 3468 True 6407.000000 6407 100.000000 1 3469 1 chr7D.!!$R1 3468
1 TraesCS7D01G005300 chr7D 3905052 3906699 1647 False 1964.000000 1964 88.540000 354 1971 1 chr7D.!!$F1 1617
2 TraesCS7D01G005300 chr7D 3785907 3788658 2751 True 1647.500000 1908 88.236500 567 3392 2 chr7D.!!$R4 2825
3 TraesCS7D01G005300 chr7D 3632116 3634869 2753 True 1555.500000 1755 89.429000 567 3388 2 chr7D.!!$R3 2821
4 TraesCS7D01G005300 chr7D 2356622 2359199 2577 True 997.566667 1661 92.627667 705 3388 3 chr7D.!!$R2 2683
5 TraesCS7D01G005300 chr7A 3309508 3313717 4209 False 1877.000000 3310 89.236000 1 3392 2 chr7A.!!$F1 3391
6 TraesCS7D01G005300 chr7A 2117837 2119342 1505 True 1773.000000 1773 88.018000 448 1953 1 chr7A.!!$R1 1505
7 TraesCS7D01G005300 chr7A 3630542 3631641 1099 True 1363.000000 1363 89.238000 2296 3392 1 chr7A.!!$R2 1096
8 TraesCS7D01G005300 chr7A 3206953 3211001 4048 True 1249.666667 2084 88.189333 1 3388 3 chr7A.!!$R4 3387
9 TraesCS7D01G005300 chr7A 1996766 1999690 2924 True 1200.000000 2082 87.766000 39 1965 2 chr7A.!!$R3 1926
10 TraesCS7D01G005300 chr4A 740454331 740456804 2473 True 3092.000000 3092 89.362000 928 3392 1 chr4A.!!$R1 2464
11 TraesCS7D01G005300 chr4A 741793487 741795934 2447 True 2686.000000 2686 86.590000 898 3392 1 chr4A.!!$R2 2494
12 TraesCS7D01G005300 chr4A 740575336 740580127 4791 False 1558.500000 2854 89.956500 1 3392 2 chr4A.!!$F8 3391
13 TraesCS7D01G005300 chr4A 739651802 739653127 1325 False 1491.000000 1491 87.305000 2079 3392 1 chr4A.!!$F1 1313
14 TraesCS7D01G005300 chr4A 742057082 742058406 1324 False 1483.000000 1483 87.221000 2080 3392 1 chr4A.!!$F3 1312
15 TraesCS7D01G005300 chr4A 741483186 741485751 2565 True 1452.500000 1591 86.807500 754 3392 2 chr4A.!!$R4 2638
16 TraesCS7D01G005300 chr4A 741590157 741591479 1322 False 1406.000000 1406 86.029000 2054 3392 1 chr4A.!!$F2 1338
17 TraesCS7D01G005300 chr4A 739864255 739868672 4417 False 1379.666667 2261 89.282333 1 3392 3 chr4A.!!$F4 3391
18 TraesCS7D01G005300 chr4A 740936878 740938701 1823 False 1218.500000 1500 90.842000 1499 3387 2 chr4A.!!$F10 1888
19 TraesCS7D01G005300 chr4A 740929870 740931632 1762 False 832.500000 1258 92.187500 1 1142 2 chr4A.!!$F9 1141
20 TraesCS7D01G005300 chr4A 740018033 740020466 2433 True 695.000000 1286 87.028500 2169 3393 2 chr4A.!!$R3 1224
21 TraesCS7D01G005300 chr4A 740270639 740271981 1342 False 663.500000 1166 89.457500 2021 3392 2 chr4A.!!$F5 1371
22 TraesCS7D01G005300 chr4A 740304790 740306133 1343 False 659.000000 1160 88.961500 2021 3392 2 chr4A.!!$F6 1371
23 TraesCS7D01G005300 chr4A 740348044 740349125 1081 False 550.000000 942 89.119500 2021 3141 2 chr4A.!!$F7 1120

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
313 317 0.178995 TGTCATGGAAGGCAGCACAA 60.179 50.000 0.0 0.0 0.00 3.33 F
571 2616 0.670546 CGAGTGGTCGTCTGCCAAAT 60.671 55.000 0.0 0.0 41.57 2.32 F
1819 4186 1.002430 AGAGGCTTTTCTGCGACATGA 59.998 47.619 0.0 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 3948 1.263217 CCGGAACAAGTTTTCTCACGG 59.737 52.381 0.00 0.0 0.00 4.94 R
2457 6141 1.135859 GCAACGTCTTCAATGCTGAGG 60.136 52.381 0.48 0.0 35.93 3.86 R
3439 7169 0.178831 AGGGGTTGAGACAAGGGGAT 60.179 55.000 0.00 0.0 0.00 3.85 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
217 220 0.811616 GATTACCACCTGCCTCTGCG 60.812 60.000 0.00 0.00 41.78 5.18
313 317 0.178995 TGTCATGGAAGGCAGCACAA 60.179 50.000 0.00 0.00 0.00 3.33
352 356 5.895928 TCAGAATGACTAGAATGAACTCCG 58.104 41.667 0.00 0.00 42.56 4.63
571 2616 0.670546 CGAGTGGTCGTCTGCCAAAT 60.671 55.000 0.00 0.00 41.57 2.32
601 2646 6.321181 TGAATAAACAAGGTTGAGCTTCTGTT 59.679 34.615 0.00 0.00 0.00 3.16
811 3042 3.904800 TGTGTTGGTGGATATGACGAT 57.095 42.857 0.00 0.00 0.00 3.73
1113 3350 2.509548 CAAGGGGGTCAATGATAGGTCA 59.490 50.000 0.00 0.00 39.04 4.02
1135 3372 7.099764 GTCACAACTCCTCAAAGATGATCTTA 58.900 38.462 8.30 0.00 35.27 2.10
1165 3402 2.168313 TGCGCATACCTTGAAGATCTGA 59.832 45.455 5.66 0.00 0.00 3.27
1281 3645 1.694048 CCCCCTGAGTCTCTTGGCTAT 60.694 57.143 0.65 0.00 0.00 2.97
1341 3705 1.202976 AGGCTCAAGTGGCAGAAACAT 60.203 47.619 0.00 0.00 34.73 2.71
1397 3761 7.173047 ACATTTTATCTCCAAAACCATTTGTGC 59.827 33.333 1.17 0.00 43.59 4.57
1477 3841 4.263018 TCAGAATTCAGGATCTATGCCG 57.737 45.455 8.44 0.00 0.00 5.69
1584 3948 3.766691 CCAATGCTGCCACTGCCC 61.767 66.667 0.00 0.00 36.33 5.36
1585 3949 3.766691 CAATGCTGCCACTGCCCC 61.767 66.667 0.00 0.00 36.33 5.80
1649 4016 7.333528 TGAGCAACTTTATCAACTCTTTGTT 57.666 32.000 0.00 0.00 39.92 2.83
1677 4044 1.405526 GCGGATCAACAGCTCAAGGTA 60.406 52.381 0.00 0.00 36.79 3.08
1698 4065 4.970860 AGTGTCTATTCATGGATCTGGG 57.029 45.455 0.00 0.00 0.00 4.45
1714 4081 1.956477 CTGGGTGTCTTGGGAAAACAG 59.044 52.381 0.00 0.00 0.00 3.16
1819 4186 1.002430 AGAGGCTTTTCTGCGACATGA 59.998 47.619 0.00 0.00 0.00 3.07
2457 6141 7.982354 AGTGTAGTCAAGGAAGCAGAATAATAC 59.018 37.037 0.00 0.00 0.00 1.89
2459 6143 6.567602 AGTCAAGGAAGCAGAATAATACCT 57.432 37.500 0.00 0.00 0.00 3.08
2460 6144 6.587273 AGTCAAGGAAGCAGAATAATACCTC 58.413 40.000 0.00 0.00 0.00 3.85
2461 6145 6.156949 AGTCAAGGAAGCAGAATAATACCTCA 59.843 38.462 0.00 0.00 0.00 3.86
2462 6146 6.481644 GTCAAGGAAGCAGAATAATACCTCAG 59.518 42.308 0.00 0.00 0.00 3.35
2463 6147 4.967036 AGGAAGCAGAATAATACCTCAGC 58.033 43.478 0.00 0.00 0.00 4.26
2518 6207 3.699038 TGACCCAGAACAAGTTTTTGAGG 59.301 43.478 0.00 0.00 37.73 3.86
2627 6339 9.689075 GAAACAAGTTTCAATCTTTTAGCAAAC 57.311 29.630 18.09 0.00 46.03 2.93
2628 6340 7.770801 ACAAGTTTCAATCTTTTAGCAAACC 57.229 32.000 0.00 0.00 0.00 3.27
2630 6342 7.986889 ACAAGTTTCAATCTTTTAGCAAACCAT 59.013 29.630 0.00 0.00 0.00 3.55
2631 6343 8.490355 CAAGTTTCAATCTTTTAGCAAACCATC 58.510 33.333 0.00 0.00 0.00 3.51
2632 6344 7.725251 AGTTTCAATCTTTTAGCAAACCATCA 58.275 30.769 0.00 0.00 0.00 3.07
2633 6345 7.869429 AGTTTCAATCTTTTAGCAAACCATCAG 59.131 33.333 0.00 0.00 0.00 2.90
2634 6346 5.713025 TCAATCTTTTAGCAAACCATCAGC 58.287 37.500 0.00 0.00 0.00 4.26
2635 6347 5.477984 TCAATCTTTTAGCAAACCATCAGCT 59.522 36.000 0.00 0.00 42.14 4.24
2636 6348 6.658816 TCAATCTTTTAGCAAACCATCAGCTA 59.341 34.615 0.00 0.00 39.68 3.32
2637 6349 7.340232 TCAATCTTTTAGCAAACCATCAGCTAT 59.660 33.333 0.00 0.00 40.23 2.97
2638 6350 7.651027 ATCTTTTAGCAAACCATCAGCTATT 57.349 32.000 0.00 0.00 40.23 1.73
2639 6351 7.088589 TCTTTTAGCAAACCATCAGCTATTC 57.911 36.000 0.00 0.00 40.23 1.75
2640 6352 6.886459 TCTTTTAGCAAACCATCAGCTATTCT 59.114 34.615 0.00 0.00 40.23 2.40
2641 6353 7.394359 TCTTTTAGCAAACCATCAGCTATTCTT 59.606 33.333 0.00 0.00 40.23 2.52
2642 6354 7.466746 TTTAGCAAACCATCAGCTATTCTTT 57.533 32.000 0.00 0.00 40.23 2.52
2643 6355 5.320549 AGCAAACCATCAGCTATTCTTTG 57.679 39.130 0.00 0.00 36.73 2.77
2644 6356 4.159135 AGCAAACCATCAGCTATTCTTTGG 59.841 41.667 0.00 0.00 36.73 3.28
2649 6361 3.552273 CCATCAGCTATTCTTTGGCATGC 60.552 47.826 9.90 9.90 0.00 4.06
2722 6434 5.525378 CAGCCTTCTGTATCAGTGGATTTAC 59.475 44.000 12.50 0.00 35.61 2.01
2757 6469 7.259290 ACATGATTCGTTAGTGTCTTGTTTT 57.741 32.000 0.00 0.00 0.00 2.43
2830 6542 1.482593 ACAGCCTTCCTCATTACCTCG 59.517 52.381 0.00 0.00 0.00 4.63
2832 6544 1.757699 AGCCTTCCTCATTACCTCGAC 59.242 52.381 0.00 0.00 0.00 4.20
2931 6644 1.000171 GAAGGGTTTCTTGCTGCAAGG 60.000 52.381 34.49 20.04 41.33 3.61
2989 6702 9.087424 TGTATTTCGATGAACTTGTTGATAGAG 57.913 33.333 0.00 0.00 0.00 2.43
3075 6788 6.322969 ACATGGTTCATGATCTTATTGCACAT 59.677 34.615 13.96 0.00 43.81 3.21
3109 6822 7.545965 CAGAAGAGAATTTCGTTGTGGTAGTAT 59.454 37.037 4.67 0.00 32.33 2.12
3178 6893 2.886523 TCTCCAACTTGGTGATGCAAAG 59.113 45.455 7.72 0.00 39.03 2.77
3202 6917 3.961849 TGCCAAGATACCAGCAAACATA 58.038 40.909 0.00 0.00 30.97 2.29
3393 7123 7.712205 TGAAGATTGTATGTGATGTCTACATGG 59.288 37.037 0.00 0.00 39.03 3.66
3394 7124 5.994054 AGATTGTATGTGATGTCTACATGGC 59.006 40.000 0.00 0.00 39.03 4.40
3395 7125 4.071961 TGTATGTGATGTCTACATGGCC 57.928 45.455 0.00 0.00 39.03 5.36
3396 7126 3.454082 TGTATGTGATGTCTACATGGCCA 59.546 43.478 8.56 8.56 39.03 5.36
3397 7127 3.870538 ATGTGATGTCTACATGGCCAT 57.129 42.857 14.09 14.09 37.38 4.40
3398 7128 3.198409 TGTGATGTCTACATGGCCATC 57.802 47.619 17.61 4.62 36.57 3.51
3399 7129 2.158769 TGTGATGTCTACATGGCCATCC 60.159 50.000 17.61 2.03 36.57 3.51
3409 7139 3.751767 TGGCCATCCAATATCTGCC 57.248 52.632 0.00 0.00 39.99 4.85
3410 7140 0.852155 TGGCCATCCAATATCTGCCA 59.148 50.000 0.00 0.00 45.96 4.92
3411 7141 1.251251 GGCCATCCAATATCTGCCAC 58.749 55.000 0.00 0.00 38.73 5.01
3412 7142 1.479205 GGCCATCCAATATCTGCCACA 60.479 52.381 0.00 0.00 38.73 4.17
3413 7143 2.309613 GCCATCCAATATCTGCCACAA 58.690 47.619 0.00 0.00 0.00 3.33
3414 7144 2.895404 GCCATCCAATATCTGCCACAAT 59.105 45.455 0.00 0.00 0.00 2.71
3415 7145 4.081406 GCCATCCAATATCTGCCACAATA 58.919 43.478 0.00 0.00 0.00 1.90
3416 7146 4.708421 GCCATCCAATATCTGCCACAATAT 59.292 41.667 0.00 0.00 0.00 1.28
3417 7147 5.186409 GCCATCCAATATCTGCCACAATATT 59.814 40.000 0.00 0.00 0.00 1.28
3418 7148 6.627243 CCATCCAATATCTGCCACAATATTG 58.373 40.000 14.01 14.01 41.96 1.90
3419 7149 6.434965 CCATCCAATATCTGCCACAATATTGA 59.565 38.462 22.16 0.00 43.68 2.57
3420 7150 7.039574 CCATCCAATATCTGCCACAATATTGAA 60.040 37.037 22.16 3.97 43.68 2.69
3421 7151 7.275888 TCCAATATCTGCCACAATATTGAAC 57.724 36.000 22.16 10.61 43.68 3.18
3422 7152 6.832900 TCCAATATCTGCCACAATATTGAACA 59.167 34.615 22.16 14.21 43.68 3.18
3423 7153 7.013559 TCCAATATCTGCCACAATATTGAACAG 59.986 37.037 22.16 21.39 43.68 3.16
3424 7154 7.013559 CCAATATCTGCCACAATATTGAACAGA 59.986 37.037 26.48 26.48 43.68 3.41
3425 7155 8.407832 CAATATCTGCCACAATATTGAACAGAA 58.592 33.333 27.28 20.74 43.68 3.02
3426 7156 5.885230 TCTGCCACAATATTGAACAGAAG 57.115 39.130 22.16 10.52 34.56 2.85
3427 7157 5.559770 TCTGCCACAATATTGAACAGAAGA 58.440 37.500 22.16 12.42 34.56 2.87
3428 7158 5.645067 TCTGCCACAATATTGAACAGAAGAG 59.355 40.000 22.16 6.60 34.56 2.85
3429 7159 4.701651 TGCCACAATATTGAACAGAAGAGG 59.298 41.667 22.16 9.46 0.00 3.69
3430 7160 4.702131 GCCACAATATTGAACAGAAGAGGT 59.298 41.667 22.16 0.00 0.00 3.85
3431 7161 5.392380 GCCACAATATTGAACAGAAGAGGTG 60.392 44.000 22.16 5.06 0.00 4.00
3432 7162 5.939883 CCACAATATTGAACAGAAGAGGTGA 59.060 40.000 22.16 0.00 0.00 4.02
3433 7163 6.128172 CCACAATATTGAACAGAAGAGGTGAC 60.128 42.308 22.16 0.00 0.00 3.67
3434 7164 6.427853 CACAATATTGAACAGAAGAGGTGACA 59.572 38.462 22.16 0.00 0.00 3.58
3435 7165 7.120285 CACAATATTGAACAGAAGAGGTGACAT 59.880 37.037 22.16 0.00 0.00 3.06
3436 7166 7.120285 ACAATATTGAACAGAAGAGGTGACATG 59.880 37.037 22.16 0.00 0.00 3.21
3437 7167 3.407424 TGAACAGAAGAGGTGACATGG 57.593 47.619 0.00 0.00 0.00 3.66
3438 7168 2.972021 TGAACAGAAGAGGTGACATGGA 59.028 45.455 0.00 0.00 0.00 3.41
3439 7169 3.390967 TGAACAGAAGAGGTGACATGGAA 59.609 43.478 0.00 0.00 0.00 3.53
3440 7170 4.042062 TGAACAGAAGAGGTGACATGGAAT 59.958 41.667 0.00 0.00 0.00 3.01
3441 7171 4.213564 ACAGAAGAGGTGACATGGAATC 57.786 45.455 0.00 0.00 0.00 2.52
3442 7172 3.054802 ACAGAAGAGGTGACATGGAATCC 60.055 47.826 0.00 0.00 0.00 3.01
3443 7173 2.507471 AGAAGAGGTGACATGGAATCCC 59.493 50.000 0.00 0.00 0.00 3.85
3444 7174 1.216990 AGAGGTGACATGGAATCCCC 58.783 55.000 0.00 0.00 0.00 4.81
3445 7175 1.216990 GAGGTGACATGGAATCCCCT 58.783 55.000 0.00 0.00 35.38 4.79
3446 7176 1.566231 GAGGTGACATGGAATCCCCTT 59.434 52.381 0.00 0.00 35.38 3.95
3447 7177 1.285962 AGGTGACATGGAATCCCCTTG 59.714 52.381 0.00 0.00 43.61 3.61
3452 7182 2.278245 ACATGGAATCCCCTTGTCTCA 58.722 47.619 0.00 0.00 46.76 3.27
3453 7183 2.649312 ACATGGAATCCCCTTGTCTCAA 59.351 45.455 0.00 0.00 46.76 3.02
3454 7184 2.879103 TGGAATCCCCTTGTCTCAAC 57.121 50.000 0.00 0.00 35.38 3.18
3455 7185 1.354368 TGGAATCCCCTTGTCTCAACC 59.646 52.381 0.00 0.00 35.38 3.77
3456 7186 1.341089 GGAATCCCCTTGTCTCAACCC 60.341 57.143 0.00 0.00 0.00 4.11
3457 7187 0.704664 AATCCCCTTGTCTCAACCCC 59.295 55.000 0.00 0.00 0.00 4.95
3458 7188 0.178831 ATCCCCTTGTCTCAACCCCT 60.179 55.000 0.00 0.00 0.00 4.79
3459 7189 0.402861 TCCCCTTGTCTCAACCCCTT 60.403 55.000 0.00 0.00 0.00 3.95
3460 7190 1.132332 TCCCCTTGTCTCAACCCCTTA 60.132 52.381 0.00 0.00 0.00 2.69
3461 7191 1.923148 CCCCTTGTCTCAACCCCTTAT 59.077 52.381 0.00 0.00 0.00 1.73
3462 7192 2.357154 CCCCTTGTCTCAACCCCTTATG 60.357 54.545 0.00 0.00 0.00 1.90
3463 7193 2.369394 CCTTGTCTCAACCCCTTATGC 58.631 52.381 0.00 0.00 0.00 3.14
3464 7194 2.009774 CTTGTCTCAACCCCTTATGCG 58.990 52.381 0.00 0.00 0.00 4.73
3465 7195 0.981183 TGTCTCAACCCCTTATGCGT 59.019 50.000 0.00 0.00 0.00 5.24
3466 7196 1.066430 TGTCTCAACCCCTTATGCGTC 60.066 52.381 0.00 0.00 0.00 5.19
3467 7197 1.207329 GTCTCAACCCCTTATGCGTCT 59.793 52.381 0.00 0.00 0.00 4.18
3468 7198 1.207089 TCTCAACCCCTTATGCGTCTG 59.793 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 146 3.814842 AGTTGAATGCAATGTCGACAAGA 59.185 39.130 24.13 6.98 36.22 3.02
208 211 0.323087 TCACCTAGTACGCAGAGGCA 60.323 55.000 6.19 0.00 41.24 4.75
264 268 0.173935 CACCCGCACCGACAAGTATA 59.826 55.000 0.00 0.00 0.00 1.47
313 317 1.903877 CTGAATGGGAGGCCGACACT 61.904 60.000 0.00 0.00 0.00 3.55
344 348 2.489938 AATTAGCTTGCCGGAGTTCA 57.510 45.000 5.05 0.00 0.00 3.18
351 355 3.751698 GGGATTACCTAATTAGCTTGCCG 59.248 47.826 6.99 0.00 35.85 5.69
352 356 4.725490 TGGGATTACCTAATTAGCTTGCC 58.275 43.478 6.99 6.42 41.11 4.52
488 2532 6.075467 CGGTTGTGGTCGTGTTTTATTTTTAC 60.075 38.462 0.00 0.00 0.00 2.01
571 2616 5.362430 AGCTCAACCTTGTTTATTCAACCAA 59.638 36.000 0.00 0.00 33.97 3.67
601 2646 6.323739 ACAGGCAAGGAGAAAGTTCATAAAAA 59.676 34.615 0.00 0.00 0.00 1.94
645 2855 0.108585 AGGACGCTCACAACCAACAT 59.891 50.000 0.00 0.00 0.00 2.71
1057 3294 3.400255 CATCAGGACCTAGCATCATGTG 58.600 50.000 0.00 0.00 0.00 3.21
1113 3350 8.378565 TCTTTAAGATCATCTTTGAGGAGTTGT 58.621 33.333 4.90 0.00 37.89 3.32
1135 3372 6.318648 TCTTCAAGGTATGCGCATATTTCTTT 59.681 34.615 31.14 18.39 0.00 2.52
1144 3381 2.168313 TCAGATCTTCAAGGTATGCGCA 59.832 45.455 14.96 14.96 0.00 6.09
1281 3645 6.358974 TGAGTCATCTTGTGGTCAGATTTA 57.641 37.500 0.00 0.00 0.00 1.40
1341 3705 5.704053 CACATCAGGAGCTGCATATTCAATA 59.296 40.000 8.35 0.00 0.00 1.90
1397 3761 1.293924 GGGAGCACGAATGACATCAG 58.706 55.000 0.00 0.00 0.00 2.90
1477 3841 1.917336 TACCGTTGGATTGCCTCCCC 61.917 60.000 0.30 0.00 44.23 4.81
1485 3849 3.387050 GGTACCTCTCATACCGTTGGATT 59.613 47.826 4.06 0.00 33.11 3.01
1490 3854 1.755380 GCTGGTACCTCTCATACCGTT 59.245 52.381 14.36 0.00 44.46 4.44
1584 3948 1.263217 CCGGAACAAGTTTTCTCACGG 59.737 52.381 0.00 0.00 0.00 4.94
1585 3949 1.333791 GCCGGAACAAGTTTTCTCACG 60.334 52.381 5.05 0.00 0.00 4.35
1649 4016 1.342555 CTGTTGATCCGCGTCGTTAA 58.657 50.000 4.92 0.00 0.00 2.01
1677 4044 4.102210 CACCCAGATCCATGAATAGACACT 59.898 45.833 0.00 0.00 0.00 3.55
1698 4065 2.024414 AGCACTGTTTTCCCAAGACAC 58.976 47.619 0.00 0.00 0.00 3.67
1714 4081 2.159310 TGTACAACACTTTGGCAAGCAC 60.159 45.455 0.00 0.00 37.00 4.40
1819 4186 2.880890 GCTTCCGCTGGAATTGTGATAT 59.119 45.455 9.88 0.00 41.23 1.63
1842 4209 1.531602 GTCTTGGCTTGCTTGGGGT 60.532 57.895 0.00 0.00 0.00 4.95
2457 6141 1.135859 GCAACGTCTTCAATGCTGAGG 60.136 52.381 0.48 0.00 35.93 3.86
2459 6143 1.592064 TGCAACGTCTTCAATGCTGA 58.408 45.000 8.91 0.00 39.49 4.26
2460 6144 2.624316 ATGCAACGTCTTCAATGCTG 57.376 45.000 8.91 0.00 39.49 4.41
2461 6145 3.426695 GCTAATGCAACGTCTTCAATGCT 60.427 43.478 8.91 0.00 39.49 3.79
2462 6146 2.848302 GCTAATGCAACGTCTTCAATGC 59.152 45.455 0.71 0.71 39.41 3.56
2518 6207 5.826737 AGTGATCATCATCCAAAGGATTCAC 59.173 40.000 15.17 15.17 39.79 3.18
2617 6329 7.466746 AAGAATAGCTGATGGTTTGCTAAAA 57.533 32.000 0.00 0.00 41.71 1.52
2618 6330 7.315142 CAAAGAATAGCTGATGGTTTGCTAAA 58.685 34.615 0.00 0.00 41.71 1.85
2619 6331 6.127647 CCAAAGAATAGCTGATGGTTTGCTAA 60.128 38.462 0.00 0.00 41.71 3.09
2620 6332 5.357878 CCAAAGAATAGCTGATGGTTTGCTA 59.642 40.000 0.00 0.00 42.44 3.49
2621 6333 4.159135 CCAAAGAATAGCTGATGGTTTGCT 59.841 41.667 0.00 0.00 40.43 3.91
2622 6334 4.427312 CCAAAGAATAGCTGATGGTTTGC 58.573 43.478 0.00 0.00 32.45 3.68
2623 6335 4.082081 TGCCAAAGAATAGCTGATGGTTTG 60.082 41.667 0.00 0.02 36.98 2.93
2624 6336 4.088634 TGCCAAAGAATAGCTGATGGTTT 58.911 39.130 0.00 0.00 36.98 3.27
2626 6338 3.370840 TGCCAAAGAATAGCTGATGGT 57.629 42.857 0.00 0.00 36.98 3.55
2627 6339 3.552273 GCATGCCAAAGAATAGCTGATGG 60.552 47.826 6.36 0.00 37.43 3.51
2628 6340 3.639538 GCATGCCAAAGAATAGCTGATG 58.360 45.455 6.36 0.00 0.00 3.07
2630 6342 1.672363 CGCATGCCAAAGAATAGCTGA 59.328 47.619 13.15 0.00 0.00 4.26
2631 6343 1.268896 CCGCATGCCAAAGAATAGCTG 60.269 52.381 13.15 0.00 0.00 4.24
2632 6344 1.027357 CCGCATGCCAAAGAATAGCT 58.973 50.000 13.15 0.00 0.00 3.32
2633 6345 0.740737 ACCGCATGCCAAAGAATAGC 59.259 50.000 13.15 0.00 0.00 2.97
2634 6346 1.066002 CCACCGCATGCCAAAGAATAG 59.934 52.381 13.15 0.00 0.00 1.73
2635 6347 1.102154 CCACCGCATGCCAAAGAATA 58.898 50.000 13.15 0.00 0.00 1.75
2636 6348 0.899717 ACCACCGCATGCCAAAGAAT 60.900 50.000 13.15 0.00 0.00 2.40
2637 6349 1.112315 AACCACCGCATGCCAAAGAA 61.112 50.000 13.15 0.00 0.00 2.52
2638 6350 1.112315 AAACCACCGCATGCCAAAGA 61.112 50.000 13.15 0.00 0.00 2.52
2639 6351 0.945265 CAAACCACCGCATGCCAAAG 60.945 55.000 13.15 1.21 0.00 2.77
2640 6352 1.068753 CAAACCACCGCATGCCAAA 59.931 52.632 13.15 0.00 0.00 3.28
2641 6353 2.733301 CAAACCACCGCATGCCAA 59.267 55.556 13.15 0.00 0.00 4.52
2642 6354 3.988525 GCAAACCACCGCATGCCA 61.989 61.111 13.15 0.00 32.73 4.92
2722 6434 6.975197 ACTAACGAATCATGTATCTGTGTCAG 59.025 38.462 0.00 0.00 0.00 3.51
2730 6442 7.757097 ACAAGACACTAACGAATCATGTATC 57.243 36.000 0.00 0.00 0.00 2.24
2807 6519 2.912956 AGGTAATGAGGAAGGCTGTTGA 59.087 45.455 0.00 0.00 0.00 3.18
2830 6542 0.959372 AGCTGGAGCAAGCATGTGTC 60.959 55.000 8.52 0.00 46.08 3.67
2832 6544 0.677098 AGAGCTGGAGCAAGCATGTG 60.677 55.000 0.00 0.00 46.08 3.21
2931 6644 7.323420 CAACTTCTTCCATATTTTTCCCTTCC 58.677 38.462 0.00 0.00 0.00 3.46
3043 6756 8.812513 ATAAGATCATGAACCATGTTCTGAAA 57.187 30.769 16.61 9.29 44.86 2.69
3075 6788 5.784177 ACGAAATTCTCTTCTGCAGACTTA 58.216 37.500 18.03 0.20 0.00 2.24
3109 6822 6.899393 AGTGCCAAAATCTTTCTTGTGATA 57.101 33.333 0.00 0.00 0.00 2.15
3178 6893 3.694072 TGTTTGCTGGTATCTTGGCATAC 59.306 43.478 0.00 0.00 37.24 2.39
3202 6917 5.416947 AGTGAACGTACTTGTGACTTTCTT 58.583 37.500 0.00 0.00 0.00 2.52
3228 6943 5.324409 TGCACTCTGATAATCCAAAAACCT 58.676 37.500 0.00 0.00 0.00 3.50
3229 6944 5.643379 TGCACTCTGATAATCCAAAAACC 57.357 39.130 0.00 0.00 0.00 3.27
3388 7118 2.522185 GCAGATATTGGATGGCCATGT 58.478 47.619 26.56 0.00 45.46 3.21
3393 7123 1.985473 TGTGGCAGATATTGGATGGC 58.015 50.000 0.00 0.00 39.75 4.40
3394 7124 6.434965 TCAATATTGTGGCAGATATTGGATGG 59.565 38.462 26.80 13.03 42.42 3.51
3395 7125 7.457024 TCAATATTGTGGCAGATATTGGATG 57.543 36.000 26.80 13.85 42.42 3.51
3396 7126 7.506599 TGTTCAATATTGTGGCAGATATTGGAT 59.493 33.333 26.80 6.59 42.42 3.41
3397 7127 6.832900 TGTTCAATATTGTGGCAGATATTGGA 59.167 34.615 26.80 21.62 42.42 3.53
3398 7128 7.013559 TCTGTTCAATATTGTGGCAGATATTGG 59.986 37.037 26.80 17.95 42.42 3.16
3399 7129 7.933396 TCTGTTCAATATTGTGGCAGATATTG 58.067 34.615 24.17 24.17 43.03 1.90
3400 7130 8.523915 TTCTGTTCAATATTGTGGCAGATATT 57.476 30.769 24.75 9.20 34.38 1.28
3401 7131 7.994911 TCTTCTGTTCAATATTGTGGCAGATAT 59.005 33.333 24.75 0.00 34.38 1.63
3402 7132 7.337938 TCTTCTGTTCAATATTGTGGCAGATA 58.662 34.615 24.75 18.30 34.38 1.98
3403 7133 6.182627 TCTTCTGTTCAATATTGTGGCAGAT 58.817 36.000 24.75 0.00 34.38 2.90
3404 7134 5.559770 TCTTCTGTTCAATATTGTGGCAGA 58.440 37.500 22.56 22.56 33.44 4.26
3405 7135 5.163683 CCTCTTCTGTTCAATATTGTGGCAG 60.164 44.000 14.97 18.21 0.00 4.85
3406 7136 4.701651 CCTCTTCTGTTCAATATTGTGGCA 59.298 41.667 14.97 11.00 0.00 4.92
3407 7137 4.702131 ACCTCTTCTGTTCAATATTGTGGC 59.298 41.667 14.97 7.36 0.00 5.01
3408 7138 5.939883 TCACCTCTTCTGTTCAATATTGTGG 59.060 40.000 14.97 4.78 0.00 4.17
3409 7139 6.427853 TGTCACCTCTTCTGTTCAATATTGTG 59.572 38.462 14.97 2.18 0.00 3.33
3410 7140 6.533730 TGTCACCTCTTCTGTTCAATATTGT 58.466 36.000 14.97 0.00 0.00 2.71
3411 7141 7.414873 CCATGTCACCTCTTCTGTTCAATATTG 60.415 40.741 9.29 9.29 0.00 1.90
3412 7142 6.600822 CCATGTCACCTCTTCTGTTCAATATT 59.399 38.462 0.00 0.00 0.00 1.28
3413 7143 6.070021 TCCATGTCACCTCTTCTGTTCAATAT 60.070 38.462 0.00 0.00 0.00 1.28
3414 7144 5.248248 TCCATGTCACCTCTTCTGTTCAATA 59.752 40.000 0.00 0.00 0.00 1.90
3415 7145 4.042062 TCCATGTCACCTCTTCTGTTCAAT 59.958 41.667 0.00 0.00 0.00 2.57
3416 7146 3.390967 TCCATGTCACCTCTTCTGTTCAA 59.609 43.478 0.00 0.00 0.00 2.69
3417 7147 2.972021 TCCATGTCACCTCTTCTGTTCA 59.028 45.455 0.00 0.00 0.00 3.18
3418 7148 3.685139 TCCATGTCACCTCTTCTGTTC 57.315 47.619 0.00 0.00 0.00 3.18
3419 7149 4.566488 GGATTCCATGTCACCTCTTCTGTT 60.566 45.833 0.00 0.00 0.00 3.16
3420 7150 3.054802 GGATTCCATGTCACCTCTTCTGT 60.055 47.826 0.00 0.00 0.00 3.41
3421 7151 3.539604 GGATTCCATGTCACCTCTTCTG 58.460 50.000 0.00 0.00 0.00 3.02
3422 7152 2.507471 GGGATTCCATGTCACCTCTTCT 59.493 50.000 4.80 0.00 0.00 2.85
3423 7153 2.422093 GGGGATTCCATGTCACCTCTTC 60.422 54.545 4.80 0.00 36.20 2.87
3424 7154 1.566231 GGGGATTCCATGTCACCTCTT 59.434 52.381 4.80 0.00 36.20 2.85
3425 7155 1.216990 GGGGATTCCATGTCACCTCT 58.783 55.000 4.80 0.00 36.20 3.69
3426 7156 1.216990 AGGGGATTCCATGTCACCTC 58.783 55.000 4.80 0.00 46.53 3.85
3427 7157 3.443095 AGGGGATTCCATGTCACCT 57.557 52.632 4.80 0.00 44.66 4.00
3428 7158 1.005924 ACAAGGGGATTCCATGTCACC 59.994 52.381 4.80 0.00 43.26 4.02
3429 7159 2.514458 ACAAGGGGATTCCATGTCAC 57.486 50.000 4.80 0.00 43.26 3.67
3433 7163 3.019564 GTTGAGACAAGGGGATTCCATG 58.980 50.000 4.80 3.15 39.94 3.66
3434 7164 2.024941 GGTTGAGACAAGGGGATTCCAT 60.025 50.000 4.80 0.00 38.24 3.41
3435 7165 1.354368 GGTTGAGACAAGGGGATTCCA 59.646 52.381 4.80 0.00 38.24 3.53
3436 7166 1.341089 GGGTTGAGACAAGGGGATTCC 60.341 57.143 0.00 0.00 0.00 3.01
3437 7167 1.341089 GGGGTTGAGACAAGGGGATTC 60.341 57.143 0.00 0.00 0.00 2.52
3438 7168 0.704664 GGGGTTGAGACAAGGGGATT 59.295 55.000 0.00 0.00 0.00 3.01
3439 7169 0.178831 AGGGGTTGAGACAAGGGGAT 60.179 55.000 0.00 0.00 0.00 3.85
3440 7170 0.402861 AAGGGGTTGAGACAAGGGGA 60.403 55.000 0.00 0.00 0.00 4.81
3441 7171 1.368374 TAAGGGGTTGAGACAAGGGG 58.632 55.000 0.00 0.00 0.00 4.79
3442 7172 2.945890 GCATAAGGGGTTGAGACAAGGG 60.946 54.545 0.00 0.00 0.00 3.95
3443 7173 2.369394 GCATAAGGGGTTGAGACAAGG 58.631 52.381 0.00 0.00 0.00 3.61
3444 7174 2.009774 CGCATAAGGGGTTGAGACAAG 58.990 52.381 0.00 0.00 0.00 3.16
3445 7175 1.349688 ACGCATAAGGGGTTGAGACAA 59.650 47.619 0.00 0.00 40.15 3.18
3446 7176 0.981183 ACGCATAAGGGGTTGAGACA 59.019 50.000 0.00 0.00 40.15 3.41
3447 7177 1.207329 AGACGCATAAGGGGTTGAGAC 59.793 52.381 0.00 0.00 43.60 3.36
3448 7178 1.207089 CAGACGCATAAGGGGTTGAGA 59.793 52.381 0.00 0.00 43.60 3.27
3449 7179 1.656652 CAGACGCATAAGGGGTTGAG 58.343 55.000 0.00 0.00 43.60 3.02
3450 7180 3.853104 CAGACGCATAAGGGGTTGA 57.147 52.632 0.00 0.00 43.60 3.18


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

AutoCloner maintained by Alex Coulton.