Multiple sequence alignment - TraesCS4D01G096900

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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 TraesCS4D01G096900 chr4D 100.000 2786 0 0 1 2786 73967890 73965105 0.000000e+00 5145
1 TraesCS4D01G096900 chr4D 89.583 816 70 6 1454 2255 73882315 73881501 0.000000e+00 1022
2 TraesCS4D01G096900 chr4D 89.525 611 63 1 834 1444 73882895 73882286 0.000000e+00 773
3 TraesCS4D01G096900 chr4D 87.633 566 65 5 276 836 73883484 73882919 0.000000e+00 652
4 TraesCS4D01G096900 chr4D 100.000 40 0 0 1405 1444 73966447 73966408 1.070000e-09 75
5 TraesCS4D01G096900 chr4D 100.000 40 0 0 1444 1483 73966486 73966447 1.070000e-09 75
6 TraesCS4D01G096900 chr1B 93.992 1215 49 6 1454 2667 34780475 34779284 0.000000e+00 1818
7 TraesCS4D01G096900 chr1B 93.827 1215 51 6 1454 2667 34797802 34796611 0.000000e+00 1807
8 TraesCS4D01G096900 chr1B 95.085 997 46 3 1441 2436 35453074 35454068 0.000000e+00 1567
9 TraesCS4D01G096900 chr1B 93.341 841 42 8 1 833 35451645 35452479 0.000000e+00 1230
10 TraesCS4D01G096900 chr1B 88.457 823 79 11 22 837 34799219 34798406 0.000000e+00 979
11 TraesCS4D01G096900 chr1B 91.377 719 57 5 1454 2170 35003419 35004134 0.000000e+00 979
12 TraesCS4D01G096900 chr1B 88.335 823 80 11 22 837 34781892 34781079 0.000000e+00 974
13 TraesCS4D01G096900 chr1B 94.599 611 33 0 834 1444 35452506 35453116 0.000000e+00 946
14 TraesCS4D01G096900 chr1B 89.379 612 63 2 834 1444 34781056 34780446 0.000000e+00 769
15 TraesCS4D01G096900 chr1B 88.889 612 66 2 834 1444 34798383 34797773 0.000000e+00 752
16 TraesCS4D01G096900 chr1B 83.836 730 84 20 111 833 35002361 35003063 0.000000e+00 664
17 TraesCS4D01G096900 chr1B 94.000 250 14 1 2187 2436 35006203 35006451 7.280000e-101 377
18 TraesCS4D01G096900 chr1A 95.272 994 46 1 1444 2436 22972459 22971466 0.000000e+00 1574
19 TraesCS4D01G096900 chr1A 96.296 837 28 3 1 836 22973888 22973054 0.000000e+00 1371
20 TraesCS4D01G096900 chr1A 96.890 611 19 0 834 1444 22973030 22972420 0.000000e+00 1024
21 TraesCS4D01G096900 chr1D 95.158 888 39 3 1444 2328 21147402 21146516 0.000000e+00 1399
22 TraesCS4D01G096900 chr1D 95.254 611 29 0 834 1444 21147973 21147363 0.000000e+00 968
23 TraesCS4D01G096900 chr1D 94.505 546 27 2 292 836 21148540 21147997 0.000000e+00 839
24 TraesCS4D01G096900 chr1D 94.553 257 13 1 4 260 21148795 21148540 2.010000e-106 396
25 TraesCS4D01G096900 chrUn 91.377 719 57 5 1454 2170 3001909 3001194 0.000000e+00 979
26 TraesCS4D01G096900 chrUn 83.765 733 85 20 111 836 3002967 3002262 0.000000e+00 664
27 TraesCS4D01G096900 chrUn 94.000 250 14 1 2187 2436 2995701 2995949 7.280000e-101 377
28 TraesCS4D01G096900 chr3B 88.218 348 40 1 2439 2786 435840818 435841164 5.550000e-112 414
29 TraesCS4D01G096900 chr3B 87.966 349 41 1 2438 2786 42911823 42911476 7.180000e-111 411
30 TraesCS4D01G096900 chr4B 87.393 349 43 1 2438 2786 545515093 545514746 1.550000e-107 399
31 TraesCS4D01G096900 chr6D 80.274 365 70 2 915 1278 450344133 450343770 9.830000e-70 274
32 TraesCS4D01G096900 chr6B 80.000 365 68 3 915 1278 683487446 683487806 5.920000e-67 265
33 TraesCS4D01G096900 chr2A 83.616 177 25 4 2438 2613 668447328 668447155 2.220000e-36 163
34 TraesCS4D01G096900 chr4A 83.429 175 25 4 2440 2613 290420610 290420439 2.870000e-35 159
35 TraesCS4D01G096900 chr4A 81.868 182 24 7 2432 2609 333812456 333812280 8.040000e-31 145
36 TraesCS4D01G096900 chr6A 82.857 175 22 7 2438 2609 53983663 53983832 1.730000e-32 150


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 TraesCS4D01G096900 chr4D 73965105 73967890 2785 True 1765.000000 5145 100.000000 1 2786 3 chr4D.!!$R2 2785
1 TraesCS4D01G096900 chr4D 73881501 73883484 1983 True 815.666667 1022 88.913667 276 2255 3 chr4D.!!$R1 1979
2 TraesCS4D01G096900 chr1B 35451645 35454068 2423 False 1247.666667 1567 94.341667 1 2436 3 chr1B.!!$F2 2435
3 TraesCS4D01G096900 chr1B 34779284 34781892 2608 True 1187.000000 1818 90.568667 22 2667 3 chr1B.!!$R1 2645
4 TraesCS4D01G096900 chr1B 34796611 34799219 2608 True 1179.333333 1807 90.391000 22 2667 3 chr1B.!!$R2 2645
5 TraesCS4D01G096900 chr1B 35002361 35006451 4090 False 673.333333 979 89.737667 111 2436 3 chr1B.!!$F1 2325
6 TraesCS4D01G096900 chr1A 22971466 22973888 2422 True 1323.000000 1574 96.152667 1 2436 3 chr1A.!!$R1 2435
7 TraesCS4D01G096900 chr1D 21146516 21148795 2279 True 900.500000 1399 94.867500 4 2328 4 chr1D.!!$R1 2324
8 TraesCS4D01G096900 chrUn 3001194 3002967 1773 True 821.500000 979 87.571000 111 2170 2 chrUn.!!$R1 2059

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
997 1045 0.108186 CACCAAGCTCATCCTGCGTA 60.108 55.0 0.0 0.0 35.28 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2750 4867 0.031917 TTCCGTCAGGTAGGCCCATA 60.032 55.0 0.0 0.0 39.05 2.74 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
27 28 6.360681 GCTGTTCATATGTGCGATATTTTTCC 59.639 38.462 1.90 0.00 0.00 3.13
360 376 2.066340 TGGCACAGGAACTCCGAAT 58.934 52.632 0.00 0.00 42.08 3.34
405 423 1.142314 GCCATGCCGATGTTGCATT 59.858 52.632 0.00 0.00 46.91 3.56
578 596 0.827925 TGCTCGACTTCAGGGTGAGT 60.828 55.000 0.00 0.00 0.00 3.41
729 751 1.672881 CCAATGGAATCACGAGCTTCC 59.327 52.381 8.33 8.33 39.85 3.46
731 753 3.432186 CCAATGGAATCACGAGCTTCCTA 60.432 47.826 15.02 4.20 40.05 2.94
771 793 4.070552 GGCGCGTGAAGACCCTCT 62.071 66.667 8.43 0.00 0.00 3.69
882 930 3.016736 TGATCAGACGCAGACATACAGA 58.983 45.455 0.00 0.00 0.00 3.41
997 1045 0.108186 CACCAAGCTCATCCTGCGTA 60.108 55.000 0.00 0.00 35.28 4.42
1042 1090 2.826428 CCATGTATGAGAGGGTGTTCG 58.174 52.381 0.00 0.00 0.00 3.95
1183 1231 3.815396 TGATCGAGCTGCGCGACT 61.815 61.111 29.35 18.30 38.60 4.18
1265 1313 0.179000 GTTCCGAGCCTCATGGACAT 59.821 55.000 0.00 0.00 34.57 3.06
1356 1404 2.131854 CTTGGTATGTCCCCCACCATA 58.868 52.381 0.00 0.00 41.80 2.74
1413 1461 1.048601 GGATTCGGCCCAGTCATCTA 58.951 55.000 0.00 0.00 0.00 1.98
1414 1462 1.001406 GGATTCGGCCCAGTCATCTAG 59.999 57.143 0.00 0.00 0.00 2.43
1415 1463 1.964223 GATTCGGCCCAGTCATCTAGA 59.036 52.381 0.00 0.00 0.00 2.43
1416 1464 1.403814 TTCGGCCCAGTCATCTAGAG 58.596 55.000 0.00 0.00 0.00 2.43
1417 1465 0.551396 TCGGCCCAGTCATCTAGAGA 59.449 55.000 0.00 0.00 0.00 3.10
1418 1466 0.958091 CGGCCCAGTCATCTAGAGAG 59.042 60.000 0.00 0.00 0.00 3.20
1419 1467 1.337118 GGCCCAGTCATCTAGAGAGG 58.663 60.000 0.00 0.00 0.00 3.69
1420 1468 1.133325 GGCCCAGTCATCTAGAGAGGA 60.133 57.143 0.00 0.00 31.89 3.71
1421 1469 2.672098 GCCCAGTCATCTAGAGAGGAA 58.328 52.381 0.00 0.00 36.56 3.36
1422 1470 2.627699 GCCCAGTCATCTAGAGAGGAAG 59.372 54.545 0.00 0.00 36.56 3.46
1423 1471 3.909732 CCCAGTCATCTAGAGAGGAAGT 58.090 50.000 0.00 0.00 36.56 3.01
1424 1472 4.285863 CCCAGTCATCTAGAGAGGAAGTT 58.714 47.826 0.00 0.00 36.56 2.66
1425 1473 4.099266 CCCAGTCATCTAGAGAGGAAGTTG 59.901 50.000 0.00 0.00 36.56 3.16
1426 1474 4.441356 CCAGTCATCTAGAGAGGAAGTTGC 60.441 50.000 0.00 0.00 36.56 4.17
1427 1475 3.704061 AGTCATCTAGAGAGGAAGTTGCC 59.296 47.826 0.00 0.00 36.56 4.52
1428 1476 3.449018 GTCATCTAGAGAGGAAGTTGCCA 59.551 47.826 0.00 0.00 36.56 4.92
1429 1477 3.449018 TCATCTAGAGAGGAAGTTGCCAC 59.551 47.826 0.00 0.00 31.35 5.01
1430 1478 2.889512 TCTAGAGAGGAAGTTGCCACA 58.110 47.619 0.00 0.00 0.00 4.17
1431 1479 2.563179 TCTAGAGAGGAAGTTGCCACAC 59.437 50.000 0.00 0.00 0.00 3.82
1432 1480 0.398318 AGAGAGGAAGTTGCCACACC 59.602 55.000 0.00 0.00 0.00 4.16
1433 1481 0.398318 GAGAGGAAGTTGCCACACCT 59.602 55.000 6.43 6.43 35.52 4.00
1434 1482 0.109342 AGAGGAAGTTGCCACACCTG 59.891 55.000 10.48 0.00 33.77 4.00
1435 1483 0.108585 GAGGAAGTTGCCACACCTGA 59.891 55.000 10.48 0.00 33.77 3.86
1436 1484 0.550914 AGGAAGTTGCCACACCTGAA 59.449 50.000 6.03 0.00 32.82 3.02
1437 1485 1.064017 AGGAAGTTGCCACACCTGAAA 60.064 47.619 6.03 0.00 32.82 2.69
1438 1486 1.754226 GGAAGTTGCCACACCTGAAAA 59.246 47.619 0.00 0.00 0.00 2.29
1439 1487 2.167487 GGAAGTTGCCACACCTGAAAAA 59.833 45.455 0.00 0.00 0.00 1.94
1440 1488 3.447742 GAAGTTGCCACACCTGAAAAAG 58.552 45.455 0.00 0.00 0.00 2.27
1441 1489 1.136891 AGTTGCCACACCTGAAAAAGC 59.863 47.619 0.00 0.00 0.00 3.51
1442 1490 1.136891 GTTGCCACACCTGAAAAAGCT 59.863 47.619 0.00 0.00 0.00 3.74
1443 1491 1.032014 TGCCACACCTGAAAAAGCTC 58.968 50.000 0.00 0.00 0.00 4.09
1444 1492 1.032014 GCCACACCTGAAAAAGCTCA 58.968 50.000 0.00 0.00 0.00 4.26
1445 1493 1.000938 GCCACACCTGAAAAAGCTCAG 60.001 52.381 0.00 0.00 42.19 3.35
1446 1494 2.301346 CCACACCTGAAAAAGCTCAGT 58.699 47.619 0.00 0.00 41.15 3.41
1447 1495 2.291741 CCACACCTGAAAAAGCTCAGTC 59.708 50.000 0.00 0.00 41.15 3.51
1448 1496 2.945008 CACACCTGAAAAAGCTCAGTCA 59.055 45.455 0.00 0.00 41.15 3.41
1449 1497 3.567164 CACACCTGAAAAAGCTCAGTCAT 59.433 43.478 0.00 0.00 41.15 3.06
1450 1498 3.817647 ACACCTGAAAAAGCTCAGTCATC 59.182 43.478 0.00 0.00 41.15 2.92
1451 1499 4.070716 CACCTGAAAAAGCTCAGTCATCT 58.929 43.478 0.00 0.00 41.15 2.90
1467 1515 3.449018 GTCATCTAGAGAGGAAGTTGCCA 59.551 47.826 0.00 0.00 36.56 4.92
1535 1583 2.927856 ATGGACACGTGGCCTCCA 60.928 61.111 38.95 30.75 45.91 3.86
1589 1637 0.606401 CACGTGCCCCACTCAGAAAT 60.606 55.000 0.82 0.00 31.34 2.17
1603 1651 2.097036 CAGAAATGGAGCCAGATTGCA 58.903 47.619 0.00 0.00 0.00 4.08
1669 1717 0.471780 TCACCTCAAGGAGCTGGTCA 60.472 55.000 9.30 0.00 38.94 4.02
1762 1810 1.702182 TGTTTTGCTGAAGGATGGCA 58.298 45.000 0.00 0.00 0.00 4.92
1784 1832 2.989909 TGTTCGGTACATCGGACTCTA 58.010 47.619 4.84 0.00 39.26 2.43
1896 1944 3.452627 GGCCTCTTCCTGAACTGATCTTA 59.547 47.826 0.00 0.00 0.00 2.10
2003 2058 5.243060 TCCTCAGTTTAGTTTCACTCGATCA 59.757 40.000 0.00 0.00 0.00 2.92
2062 2117 2.108250 AGTTTGTGGGAGTAGCACCAAT 59.892 45.455 0.00 0.00 38.73 3.16
2080 2137 6.061441 CACCAATAGTATGCCAACATCCTTA 58.939 40.000 0.00 0.00 37.74 2.69
2086 2143 0.323302 TGCCAACATCCTTAGACGCA 59.677 50.000 0.00 0.00 0.00 5.24
2298 4415 6.436738 TGGGTGTACATAGACCAGTAAAAA 57.563 37.500 0.00 0.00 41.12 1.94
2405 4522 1.804151 CATTTGTACACCCACGTCCTG 59.196 52.381 0.00 0.00 0.00 3.86
2442 4559 0.252330 TCAACCGGTCCATGTAGGGA 60.252 55.000 8.04 0.00 38.24 4.20
2479 4596 1.005804 GAACCGAAGACCGAACCGAC 61.006 60.000 0.00 0.00 41.76 4.79
2482 4599 2.808321 GAAGACCGAACCGACGCC 60.808 66.667 0.00 0.00 0.00 5.68
2485 4602 4.705519 GACCGAACCGACGCCGAA 62.706 66.667 0.00 0.00 38.22 4.30
2486 4603 4.283403 ACCGAACCGACGCCGAAA 62.283 61.111 0.00 0.00 38.22 3.46
2487 4604 3.770424 CCGAACCGACGCCGAAAC 61.770 66.667 0.00 0.00 38.22 2.78
2488 4605 2.732094 CGAACCGACGCCGAAACT 60.732 61.111 0.00 0.00 38.22 2.66
2489 4606 2.851104 GAACCGACGCCGAAACTG 59.149 61.111 0.00 0.00 38.22 3.16
2490 4607 1.662446 GAACCGACGCCGAAACTGA 60.662 57.895 0.00 0.00 38.22 3.41
2491 4608 1.216941 GAACCGACGCCGAAACTGAA 61.217 55.000 0.00 0.00 38.22 3.02
2492 4609 0.601841 AACCGACGCCGAAACTGAAT 60.602 50.000 0.00 0.00 38.22 2.57
2493 4610 0.601841 ACCGACGCCGAAACTGAATT 60.602 50.000 0.00 0.00 38.22 2.17
2560 4677 5.687166 TTTCAGGTCCACTAACCGAATAT 57.313 39.130 0.00 0.00 44.49 1.28
2566 4683 6.365247 CAGGTCCACTAACCGAATATAATTCG 59.635 42.308 13.64 13.64 44.49 3.34
2602 4719 4.312443 TCATCTCGGTTAACTGAACAACC 58.688 43.478 17.63 0.00 40.09 3.77
2603 4720 3.823281 TCTCGGTTAACTGAACAACCA 57.177 42.857 17.63 0.00 43.70 3.67
2604 4721 4.139859 TCTCGGTTAACTGAACAACCAA 57.860 40.909 17.63 0.00 43.70 3.67
2605 4722 3.872771 TCTCGGTTAACTGAACAACCAAC 59.127 43.478 17.63 0.00 43.70 3.77
2606 4723 2.944349 TCGGTTAACTGAACAACCAACC 59.056 45.455 14.85 0.00 43.70 3.77
2607 4724 3.343380 GGTTAACTGAACAACCAACCG 57.657 47.619 5.42 0.00 43.13 4.44
2608 4725 2.944349 GGTTAACTGAACAACCAACCGA 59.056 45.455 5.42 0.00 43.13 4.69
2609 4726 3.377798 GGTTAACTGAACAACCAACCGAA 59.622 43.478 5.42 0.00 43.13 4.30
2610 4727 4.345288 GTTAACTGAACAACCAACCGAAC 58.655 43.478 0.00 0.00 38.02 3.95
2611 4728 2.116827 ACTGAACAACCAACCGAACA 57.883 45.000 0.00 0.00 0.00 3.18
2612 4729 2.438411 ACTGAACAACCAACCGAACAA 58.562 42.857 0.00 0.00 0.00 2.83
2613 4730 2.162809 ACTGAACAACCAACCGAACAAC 59.837 45.455 0.00 0.00 0.00 3.32
2655 4772 2.099098 AGAGAACCAACGCAAAAACAGG 59.901 45.455 0.00 0.00 0.00 4.00
2660 4777 0.922717 CAACGCAAAAACAGGCACAG 59.077 50.000 0.00 0.00 0.00 3.66
2667 4784 2.662091 AAAACAGGCACAGCGAACGC 62.662 55.000 11.31 11.31 42.33 4.84
2677 4794 4.719369 GCGAACGCTCCCGACAGT 62.719 66.667 11.97 0.00 38.26 3.55
2678 4795 2.872557 CGAACGCTCCCGACAGTA 59.127 61.111 0.00 0.00 38.29 2.74
2679 4796 1.226323 CGAACGCTCCCGACAGTAG 60.226 63.158 0.00 0.00 38.29 2.57
2680 4797 1.516603 GAACGCTCCCGACAGTAGC 60.517 63.158 0.00 0.00 38.29 3.58
2683 4800 3.827898 GCTCCCGACAGTAGCGCT 61.828 66.667 17.26 17.26 0.00 5.92
2684 4801 2.409651 CTCCCGACAGTAGCGCTC 59.590 66.667 16.34 5.88 0.00 5.03
2685 4802 2.360726 TCCCGACAGTAGCGCTCA 60.361 61.111 16.34 0.00 0.00 4.26
2686 4803 2.202623 CCCGACAGTAGCGCTCAC 60.203 66.667 16.34 11.18 0.00 3.51
2687 4804 2.577112 CCGACAGTAGCGCTCACG 60.577 66.667 16.34 13.54 44.07 4.35
2688 4805 2.479198 CGACAGTAGCGCTCACGA 59.521 61.111 16.34 0.00 43.93 4.35
2689 4806 1.863880 CGACAGTAGCGCTCACGAC 60.864 63.158 16.34 6.55 43.93 4.34
2690 4807 1.514443 GACAGTAGCGCTCACGACC 60.514 63.158 16.34 0.00 43.93 4.79
2691 4808 2.202623 CAGTAGCGCTCACGACCC 60.203 66.667 16.34 0.00 43.93 4.46
2692 4809 3.450115 AGTAGCGCTCACGACCCC 61.450 66.667 16.34 0.00 43.93 4.95
2693 4810 3.450115 GTAGCGCTCACGACCCCT 61.450 66.667 16.34 0.00 43.93 4.79
2694 4811 2.678934 TAGCGCTCACGACCCCTT 60.679 61.111 16.34 0.00 43.93 3.95
2695 4812 2.280552 TAGCGCTCACGACCCCTTT 61.281 57.895 16.34 0.00 43.93 3.11
2696 4813 1.823169 TAGCGCTCACGACCCCTTTT 61.823 55.000 16.34 0.00 43.93 2.27
2697 4814 2.258726 GCGCTCACGACCCCTTTTT 61.259 57.895 0.00 0.00 43.93 1.94
2727 4844 3.186047 CCGACGATCGCCACCAAC 61.186 66.667 16.60 0.00 38.82 3.77
2728 4845 2.431771 CGACGATCGCCACCAACA 60.432 61.111 16.60 0.00 31.14 3.33
2729 4846 2.726691 CGACGATCGCCACCAACAC 61.727 63.158 16.60 0.00 31.14 3.32
2730 4847 1.666553 GACGATCGCCACCAACACA 60.667 57.895 16.60 0.00 0.00 3.72
2731 4848 1.225376 GACGATCGCCACCAACACAA 61.225 55.000 16.60 0.00 0.00 3.33
2732 4849 0.605319 ACGATCGCCACCAACACAAT 60.605 50.000 16.60 0.00 0.00 2.71
2733 4850 0.179192 CGATCGCCACCAACACAATG 60.179 55.000 0.26 0.00 0.00 2.82
2734 4851 0.456653 GATCGCCACCAACACAATGC 60.457 55.000 0.00 0.00 0.00 3.56
2735 4852 2.198906 ATCGCCACCAACACAATGCG 62.199 55.000 0.00 0.00 43.05 4.73
2736 4853 2.734346 GCCACCAACACAATGCGC 60.734 61.111 0.00 0.00 0.00 6.09
2737 4854 2.428902 CCACCAACACAATGCGCG 60.429 61.111 0.00 0.00 0.00 6.86
2738 4855 3.098958 CACCAACACAATGCGCGC 61.099 61.111 27.26 27.26 0.00 6.86
2739 4856 4.681643 ACCAACACAATGCGCGCG 62.682 61.111 28.44 28.44 0.00 6.86
2740 4857 4.681643 CCAACACAATGCGCGCGT 62.682 61.111 32.35 25.30 0.00 6.01
2741 4858 3.158813 CAACACAATGCGCGCGTC 61.159 61.111 32.35 23.18 0.00 5.19
2742 4859 3.345808 AACACAATGCGCGCGTCT 61.346 55.556 32.35 16.28 0.00 4.18
2743 4860 3.295228 AACACAATGCGCGCGTCTC 62.295 57.895 32.35 15.65 0.00 3.36
2744 4861 4.833561 CACAATGCGCGCGTCTCG 62.834 66.667 32.35 19.78 42.12 4.04
2755 4872 4.343581 CGTCTCGCATGGTATGGG 57.656 61.111 0.00 0.00 43.79 4.00
2756 4873 1.956170 CGTCTCGCATGGTATGGGC 60.956 63.158 0.00 0.00 42.34 5.36
2757 4874 1.598130 GTCTCGCATGGTATGGGCC 60.598 63.158 0.00 0.00 42.34 5.80
2758 4875 1.766059 TCTCGCATGGTATGGGCCT 60.766 57.895 4.53 0.00 42.34 5.19
2759 4876 0.471022 TCTCGCATGGTATGGGCCTA 60.471 55.000 4.53 0.00 42.34 3.93
2760 4877 0.320771 CTCGCATGGTATGGGCCTAC 60.321 60.000 4.53 4.83 42.34 3.18
2761 4878 1.302511 CGCATGGTATGGGCCTACC 60.303 63.158 19.42 19.42 41.39 3.18
2762 4879 1.768684 CGCATGGTATGGGCCTACCT 61.769 60.000 23.77 12.59 41.54 3.08
2763 4880 0.250901 GCATGGTATGGGCCTACCTG 60.251 60.000 23.77 20.16 41.54 4.00
2764 4881 1.434188 CATGGTATGGGCCTACCTGA 58.566 55.000 23.77 11.76 41.54 3.86
2765 4882 1.072331 CATGGTATGGGCCTACCTGAC 59.928 57.143 23.77 3.72 41.54 3.51
2766 4883 1.046472 TGGTATGGGCCTACCTGACG 61.046 60.000 23.77 0.00 41.54 4.35
2767 4884 1.746517 GTATGGGCCTACCTGACGG 59.253 63.158 4.53 0.00 41.11 4.79
2768 4885 0.757935 GTATGGGCCTACCTGACGGA 60.758 60.000 4.53 0.00 41.11 4.69
2769 4886 0.031917 TATGGGCCTACCTGACGGAA 60.032 55.000 4.53 0.00 41.11 4.30
2770 4887 1.623542 ATGGGCCTACCTGACGGAAC 61.624 60.000 4.53 0.00 41.11 3.62
2771 4888 1.988406 GGGCCTACCTGACGGAACT 60.988 63.158 0.84 0.00 35.85 3.01
2772 4889 1.218316 GGCCTACCTGACGGAACTG 59.782 63.158 0.00 0.00 0.00 3.16
2773 4890 1.448013 GCCTACCTGACGGAACTGC 60.448 63.158 0.00 0.00 0.00 4.40
2774 4891 1.972198 CCTACCTGACGGAACTGCA 59.028 57.895 0.00 0.00 0.00 4.41
2775 4892 0.537188 CCTACCTGACGGAACTGCAT 59.463 55.000 0.00 0.00 0.00 3.96
2776 4893 1.645034 CTACCTGACGGAACTGCATG 58.355 55.000 0.00 0.00 0.00 4.06
2777 4894 0.391130 TACCTGACGGAACTGCATGC 60.391 55.000 11.82 11.82 0.00 4.06
2778 4895 1.672030 CCTGACGGAACTGCATGCA 60.672 57.895 21.29 21.29 0.00 3.96
2779 4896 1.236616 CCTGACGGAACTGCATGCAA 61.237 55.000 22.88 5.74 0.00 4.08
2780 4897 0.167470 CTGACGGAACTGCATGCAAG 59.833 55.000 22.88 17.38 0.00 4.01
2781 4898 1.154150 GACGGAACTGCATGCAAGC 60.154 57.895 22.88 13.19 0.00 4.01
2782 4899 1.855213 GACGGAACTGCATGCAAGCA 61.855 55.000 22.88 16.74 43.35 3.91
2783 4900 1.246056 ACGGAACTGCATGCAAGCAT 61.246 50.000 22.88 2.95 44.68 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.594796 GTGGGCGCACTTGTCAAAAG 60.595 55.000 25.28 0.00 0.00 2.27
188 189 7.281549 GGAAGAAACAACAGTCTTAGGTAAACA 59.718 37.037 0.00 0.00 34.23 2.83
299 307 9.751542 GCATCAAATATAGTACACAGTCTTACT 57.248 33.333 0.00 0.00 33.11 2.24
338 354 2.673258 TCGGAGTTCCTGTGCCATATA 58.327 47.619 0.00 0.00 0.00 0.86
360 376 1.001181 GGCAATGGCAGAGCAGAAAAA 59.999 47.619 14.66 0.00 43.71 1.94
449 467 3.153130 GAGGATCAGATCGTCATGGAGA 58.847 50.000 22.85 0.00 42.21 3.71
578 596 4.776965 TCCAGCGGGAGTATGTCA 57.223 55.556 0.00 0.00 38.64 3.58
592 610 1.577328 GACGGTCCGTTCGTACTCCA 61.577 60.000 19.95 0.00 41.37 3.86
654 672 0.536687 TTGAGACCGTCGAGTGTCCT 60.537 55.000 9.92 0.03 31.76 3.85
729 751 0.610174 TGGCCACTGTCTGCTTCTAG 59.390 55.000 0.00 0.00 0.00 2.43
731 753 0.322277 CATGGCCACTGTCTGCTTCT 60.322 55.000 8.16 0.00 0.00 2.85
788 810 5.007039 GTCCACACAGATGCTATTGTATGTG 59.993 44.000 1.45 1.45 42.78 3.21
882 930 1.444933 TGAGACAGTTGTGGGGGAAT 58.555 50.000 0.00 0.00 0.00 3.01
933 981 0.886490 GCAGTGCACAGTACTTGCCT 60.886 55.000 21.04 15.53 39.39 4.75
997 1045 1.237285 GGCGTGGAAGCAGACATGTT 61.237 55.000 0.00 0.00 39.27 2.71
1042 1090 2.743928 CAGCCCGGTGCAGTCTTC 60.744 66.667 15.92 0.00 44.83 2.87
1356 1404 2.762535 ATCGGATGACAAGGTTCGTT 57.237 45.000 0.00 0.00 0.00 3.85
1413 1461 0.398318 GGTGTGGCAACTTCCTCTCT 59.602 55.000 0.00 0.00 37.61 3.10
1414 1462 0.398318 AGGTGTGGCAACTTCCTCTC 59.602 55.000 3.28 0.00 37.61 3.20
1415 1463 0.109342 CAGGTGTGGCAACTTCCTCT 59.891 55.000 5.73 0.00 32.04 3.69
1416 1464 0.108585 TCAGGTGTGGCAACTTCCTC 59.891 55.000 5.73 0.00 32.04 3.71
1417 1465 0.550914 TTCAGGTGTGGCAACTTCCT 59.449 50.000 3.28 3.28 33.71 3.36
1418 1466 1.398692 TTTCAGGTGTGGCAACTTCC 58.601 50.000 0.00 0.00 37.61 3.46
1419 1467 3.447742 CTTTTTCAGGTGTGGCAACTTC 58.552 45.455 0.00 0.00 37.61 3.01
1420 1468 2.418609 GCTTTTTCAGGTGTGGCAACTT 60.419 45.455 0.00 0.00 37.61 2.66
1421 1469 1.136891 GCTTTTTCAGGTGTGGCAACT 59.863 47.619 0.00 0.00 37.61 3.16
1422 1470 1.136891 AGCTTTTTCAGGTGTGGCAAC 59.863 47.619 0.00 0.00 0.00 4.17
1423 1471 1.408702 GAGCTTTTTCAGGTGTGGCAA 59.591 47.619 0.00 0.00 31.44 4.52
1424 1472 1.032014 GAGCTTTTTCAGGTGTGGCA 58.968 50.000 0.00 0.00 31.44 4.92
1425 1473 1.000938 CTGAGCTTTTTCAGGTGTGGC 60.001 52.381 0.00 0.00 40.69 5.01
1433 1481 6.350864 CCTCTCTAGATGACTGAGCTTTTTCA 60.351 42.308 0.00 0.00 0.00 2.69
1434 1482 6.042143 CCTCTCTAGATGACTGAGCTTTTTC 58.958 44.000 0.00 0.00 0.00 2.29
1435 1483 5.719085 TCCTCTCTAGATGACTGAGCTTTTT 59.281 40.000 0.00 0.00 0.00 1.94
1436 1484 5.268387 TCCTCTCTAGATGACTGAGCTTTT 58.732 41.667 0.00 0.00 0.00 2.27
1437 1485 4.865905 TCCTCTCTAGATGACTGAGCTTT 58.134 43.478 0.00 0.00 0.00 3.51
1438 1486 4.518278 TCCTCTCTAGATGACTGAGCTT 57.482 45.455 0.00 0.00 0.00 3.74
1439 1487 4.079787 ACTTCCTCTCTAGATGACTGAGCT 60.080 45.833 0.00 0.00 0.00 4.09
1440 1488 4.207165 ACTTCCTCTCTAGATGACTGAGC 58.793 47.826 0.00 0.00 0.00 4.26
1441 1489 5.450412 GCAACTTCCTCTCTAGATGACTGAG 60.450 48.000 0.00 0.00 0.00 3.35
1442 1490 4.400884 GCAACTTCCTCTCTAGATGACTGA 59.599 45.833 0.00 0.00 0.00 3.41
1443 1491 4.441356 GGCAACTTCCTCTCTAGATGACTG 60.441 50.000 0.00 0.00 0.00 3.51
1444 1492 3.704061 GGCAACTTCCTCTCTAGATGACT 59.296 47.826 0.00 0.00 0.00 3.41
1445 1493 3.449018 TGGCAACTTCCTCTCTAGATGAC 59.551 47.826 0.00 0.00 37.61 3.06
1446 1494 3.449018 GTGGCAACTTCCTCTCTAGATGA 59.551 47.826 0.00 0.00 37.61 2.92
1447 1495 3.196469 TGTGGCAACTTCCTCTCTAGATG 59.804 47.826 0.00 0.00 37.61 2.90
1448 1496 3.196685 GTGTGGCAACTTCCTCTCTAGAT 59.803 47.826 0.00 0.00 37.61 1.98
1449 1497 2.563179 GTGTGGCAACTTCCTCTCTAGA 59.437 50.000 0.00 0.00 37.61 2.43
1450 1498 2.354203 GGTGTGGCAACTTCCTCTCTAG 60.354 54.545 0.00 0.00 37.61 2.43
1451 1499 1.623811 GGTGTGGCAACTTCCTCTCTA 59.376 52.381 0.00 0.00 37.61 2.43
1467 1515 2.952310 GACAAGGAGCTTTTTCAGGTGT 59.048 45.455 0.00 0.00 31.44 4.16
1535 1583 2.086869 CAAGAAATGTCGAGGCCATGT 58.913 47.619 5.01 0.00 0.00 3.21
1589 1637 2.116533 CGCATGCAATCTGGCTCCA 61.117 57.895 19.57 0.00 34.04 3.86
1603 1651 1.447317 GACCAATTCATCCCGCGCAT 61.447 55.000 8.75 0.00 0.00 4.73
1669 1717 1.220529 CGCTGCGTGTATCCAATCAT 58.779 50.000 14.93 0.00 0.00 2.45
1784 1832 2.505982 CGACCATCCGCCAATCCT 59.494 61.111 0.00 0.00 0.00 3.24
2003 2058 5.839517 TTGGGAATTGGAAAATGGACATT 57.160 34.783 0.00 0.00 0.00 2.71
2062 2117 4.500887 GCGTCTAAGGATGTTGGCATACTA 60.501 45.833 0.00 0.00 45.20 1.82
2080 2137 0.731417 GCTTGAGATTGCATGCGTCT 59.269 50.000 21.22 21.22 30.80 4.18
2086 2143 3.767673 ACCATTGAAGCTTGAGATTGCAT 59.232 39.130 2.10 0.00 0.00 3.96
2231 4348 0.739462 TGCCGGTTGATGATCACGAC 60.739 55.000 1.90 2.41 0.00 4.34
2442 4559 3.132111 GGTTCATCGGTTTTTATGCCCAT 59.868 43.478 0.00 0.00 0.00 4.00
2479 4596 1.727880 TCGGTTAATTCAGTTTCGGCG 59.272 47.619 0.00 0.00 0.00 6.46
2482 4599 6.952403 CGAAAATTCGGTTAATTCAGTTTCG 58.048 36.000 7.64 0.00 46.30 3.46
2533 4650 2.486013 GGTTAGTGGACCTGAAAACCGT 60.486 50.000 0.00 0.00 36.73 4.83
2560 4677 6.819649 AGATGAAAACCGAACATACCGAATTA 59.180 34.615 0.00 0.00 0.00 1.40
2566 4683 3.308866 CCGAGATGAAAACCGAACATACC 59.691 47.826 0.00 0.00 0.00 2.73
2602 4719 0.042188 CAGCTCGTGTTGTTCGGTTG 60.042 55.000 0.00 0.00 0.00 3.77
2603 4720 1.157870 CCAGCTCGTGTTGTTCGGTT 61.158 55.000 0.72 0.00 0.00 4.44
2604 4721 1.594293 CCAGCTCGTGTTGTTCGGT 60.594 57.895 0.72 0.00 0.00 4.69
2605 4722 2.954753 GCCAGCTCGTGTTGTTCGG 61.955 63.158 0.72 0.00 0.00 4.30
2606 4723 2.551270 GCCAGCTCGTGTTGTTCG 59.449 61.111 0.72 0.00 0.00 3.95
2607 4724 0.942410 TACGCCAGCTCGTGTTGTTC 60.942 55.000 10.46 0.00 43.21 3.18
2608 4725 0.531090 TTACGCCAGCTCGTGTTGTT 60.531 50.000 10.46 0.00 43.21 2.83
2609 4726 0.531090 TTTACGCCAGCTCGTGTTGT 60.531 50.000 10.46 0.00 43.21 3.32
2610 4727 0.163788 CTTTACGCCAGCTCGTGTTG 59.836 55.000 10.46 0.00 43.21 3.33
2611 4728 0.949105 CCTTTACGCCAGCTCGTGTT 60.949 55.000 10.46 0.00 43.21 3.32
2612 4729 1.374252 CCTTTACGCCAGCTCGTGT 60.374 57.895 10.46 6.74 43.21 4.49
2613 4730 2.100631 CCCTTTACGCCAGCTCGTG 61.101 63.158 10.46 0.00 43.21 4.35
2660 4777 3.332493 TACTGTCGGGAGCGTTCGC 62.332 63.158 9.24 9.24 0.00 4.70
2667 4784 2.407428 TGAGCGCTACTGTCGGGAG 61.407 63.158 11.50 0.00 0.00 4.30
2668 4785 2.360726 TGAGCGCTACTGTCGGGA 60.361 61.111 11.50 0.00 0.00 5.14
2669 4786 2.202623 GTGAGCGCTACTGTCGGG 60.203 66.667 11.50 0.00 0.00 5.14
2670 4787 2.577112 CGTGAGCGCTACTGTCGG 60.577 66.667 11.50 0.00 0.00 4.79
2671 4788 1.863880 GTCGTGAGCGCTACTGTCG 60.864 63.158 11.50 11.21 38.14 4.35
2672 4789 1.514443 GGTCGTGAGCGCTACTGTC 60.514 63.158 11.50 0.00 38.14 3.51
2673 4790 2.567049 GGTCGTGAGCGCTACTGT 59.433 61.111 11.50 0.00 38.14 3.55
2674 4791 2.202623 GGGTCGTGAGCGCTACTG 60.203 66.667 11.50 2.25 38.14 2.74
2675 4792 3.450115 GGGGTCGTGAGCGCTACT 61.450 66.667 11.50 0.00 38.50 2.57
2679 4796 2.258726 AAAAAGGGGTCGTGAGCGC 61.259 57.895 0.00 0.00 41.32 5.92
2680 4797 4.058797 AAAAAGGGGTCGTGAGCG 57.941 55.556 0.00 0.00 39.92 5.03
2710 4827 3.186047 GTTGGTGGCGATCGTCGG 61.186 66.667 15.94 0.00 40.84 4.79
2711 4828 2.431771 TGTTGGTGGCGATCGTCG 60.432 61.111 15.94 0.00 43.89 5.12
2712 4829 1.225376 TTGTGTTGGTGGCGATCGTC 61.225 55.000 13.98 13.98 0.00 4.20
2713 4830 0.605319 ATTGTGTTGGTGGCGATCGT 60.605 50.000 17.81 0.00 0.00 3.73
2714 4831 0.179192 CATTGTGTTGGTGGCGATCG 60.179 55.000 11.69 11.69 0.00 3.69
2715 4832 0.456653 GCATTGTGTTGGTGGCGATC 60.457 55.000 0.00 0.00 0.00 3.69
2716 4833 1.586028 GCATTGTGTTGGTGGCGAT 59.414 52.632 0.00 0.00 0.00 4.58
2717 4834 2.902419 CGCATTGTGTTGGTGGCGA 61.902 57.895 0.00 0.00 46.65 5.54
2718 4835 2.428902 CGCATTGTGTTGGTGGCG 60.429 61.111 0.00 0.00 38.45 5.69
2719 4836 2.734346 GCGCATTGTGTTGGTGGC 60.734 61.111 0.30 0.00 0.00 5.01
2720 4837 2.428902 CGCGCATTGTGTTGGTGG 60.429 61.111 8.75 0.00 0.00 4.61
2721 4838 3.098958 GCGCGCATTGTGTTGGTG 61.099 61.111 29.10 0.00 0.00 4.17
2722 4839 4.681643 CGCGCGCATTGTGTTGGT 62.682 61.111 32.61 0.00 0.00 3.67
2723 4840 4.681643 ACGCGCGCATTGTGTTGG 62.682 61.111 32.58 13.71 0.00 3.77
2724 4841 3.158813 GACGCGCGCATTGTGTTG 61.159 61.111 32.58 14.51 0.00 3.33
2725 4842 3.295228 GAGACGCGCGCATTGTGTT 62.295 57.895 32.58 7.51 0.00 3.32
2726 4843 3.777925 GAGACGCGCGCATTGTGT 61.778 61.111 32.58 20.43 0.00 3.72
2727 4844 4.833561 CGAGACGCGCGCATTGTG 62.834 66.667 32.58 16.92 0.00 3.33
2738 4855 1.956170 GCCCATACCATGCGAGACG 60.956 63.158 0.00 0.00 0.00 4.18
2739 4856 1.598130 GGCCCATACCATGCGAGAC 60.598 63.158 0.00 0.00 0.00 3.36
2740 4857 0.471022 TAGGCCCATACCATGCGAGA 60.471 55.000 0.00 0.00 0.00 4.04
2741 4858 0.320771 GTAGGCCCATACCATGCGAG 60.321 60.000 0.00 0.00 0.00 5.03
2742 4859 1.752198 GTAGGCCCATACCATGCGA 59.248 57.895 0.00 0.00 0.00 5.10
2743 4860 1.302511 GGTAGGCCCATACCATGCG 60.303 63.158 14.84 0.00 44.04 4.73
2744 4861 0.250901 CAGGTAGGCCCATACCATGC 60.251 60.000 20.33 0.00 46.56 4.06
2745 4862 1.072331 GTCAGGTAGGCCCATACCATG 59.928 57.143 20.33 15.28 46.56 3.66
2746 4863 1.435256 GTCAGGTAGGCCCATACCAT 58.565 55.000 20.33 5.85 46.56 3.55
2747 4864 1.046472 CGTCAGGTAGGCCCATACCA 61.046 60.000 20.33 1.27 46.56 3.25
2748 4865 1.746517 CGTCAGGTAGGCCCATACC 59.253 63.158 12.37 12.37 44.81 2.73
2749 4866 0.757935 TCCGTCAGGTAGGCCCATAC 60.758 60.000 0.00 0.00 39.05 2.39
2750 4867 0.031917 TTCCGTCAGGTAGGCCCATA 60.032 55.000 0.00 0.00 39.05 2.74
2751 4868 1.306654 TTCCGTCAGGTAGGCCCAT 60.307 57.895 0.00 0.00 39.05 4.00
2752 4869 2.120940 TTCCGTCAGGTAGGCCCA 59.879 61.111 0.00 0.00 39.05 5.36
2753 4870 1.988406 AGTTCCGTCAGGTAGGCCC 60.988 63.158 0.00 0.00 39.05 5.80
2754 4871 1.218316 CAGTTCCGTCAGGTAGGCC 59.782 63.158 0.00 0.00 39.05 5.19
2755 4872 1.448013 GCAGTTCCGTCAGGTAGGC 60.448 63.158 0.00 0.00 39.05 3.93
2756 4873 0.537188 ATGCAGTTCCGTCAGGTAGG 59.463 55.000 0.00 0.00 39.05 3.18
2757 4874 1.645034 CATGCAGTTCCGTCAGGTAG 58.355 55.000 0.00 0.00 39.05 3.18
2758 4875 0.391130 GCATGCAGTTCCGTCAGGTA 60.391 55.000 14.21 0.00 39.05 3.08
2759 4876 1.672356 GCATGCAGTTCCGTCAGGT 60.672 57.895 14.21 0.00 39.05 4.00
2760 4877 1.236616 TTGCATGCAGTTCCGTCAGG 61.237 55.000 21.50 0.00 39.46 3.86
2761 4878 0.167470 CTTGCATGCAGTTCCGTCAG 59.833 55.000 21.50 8.94 0.00 3.51
2762 4879 1.855213 GCTTGCATGCAGTTCCGTCA 61.855 55.000 21.50 2.04 0.00 4.35
2763 4880 1.154150 GCTTGCATGCAGTTCCGTC 60.154 57.895 21.50 2.64 0.00 4.79
2764 4881 1.246056 ATGCTTGCATGCAGTTCCGT 61.246 50.000 28.23 11.19 46.71 4.69
2765 4882 0.800683 CATGCTTGCATGCAGTTCCG 60.801 55.000 28.23 12.92 46.71 4.30
2766 4883 3.044809 CATGCTTGCATGCAGTTCC 57.955 52.632 28.23 10.77 46.71 3.62


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

AutoCloner maintained by Alex Coulton.