Multiple sequence alignment - TraesCS4D01G192000

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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 TraesCS4D01G192000 chr4D 100.000 3746 0 0 1 3746 335336854 335333109 0.000000e+00 6918.0
1 TraesCS4D01G192000 chr4D 76.306 823 185 9 2 818 278259242 278260060 7.430000e-117 431.0
2 TraesCS4D01G192000 chr4D 90.722 291 19 4 3463 3746 220356571 220356860 7.590000e-102 381.0
3 TraesCS4D01G192000 chr4B 92.441 1561 103 8 1 1552 413449931 413448377 0.000000e+00 2215.0
4 TraesCS4D01G192000 chr4B 96.233 1168 38 4 1723 2884 413448162 413446995 0.000000e+00 1908.0
5 TraesCS4D01G192000 chr4B 93.636 110 7 0 1595 1704 413448370 413448261 8.320000e-37 165.0
6 TraesCS4D01G192000 chr4A 91.304 1564 103 12 1 1545 137539359 137540908 0.000000e+00 2104.0
7 TraesCS4D01G192000 chr4A 96.048 1164 41 5 1723 2883 137541128 137542289 0.000000e+00 1890.0
8 TraesCS4D01G192000 chr4A 90.647 139 13 0 1585 1723 137540916 137541054 6.390000e-43 185.0
9 TraesCS4D01G192000 chr4A 88.889 99 7 3 3297 3391 625823370 625823468 6.570000e-23 119.0
10 TraesCS4D01G192000 chr7B 91.482 857 70 1 1 854 124326423 124327279 0.000000e+00 1175.0
11 TraesCS4D01G192000 chr7B 75.702 819 190 9 18 830 685746406 685747221 5.830000e-108 401.0
12 TraesCS4D01G192000 chr7A 90.898 857 74 2 1 854 722260837 722261692 0.000000e+00 1147.0
13 TraesCS4D01G192000 chr6A 90.389 822 75 2 36 854 140030592 140031412 0.000000e+00 1077.0
14 TraesCS4D01G192000 chr6A 90.389 822 75 2 36 854 140052734 140053554 0.000000e+00 1077.0
15 TraesCS4D01G192000 chr6A 94.958 238 10 2 3509 3746 30442637 30442872 4.570000e-99 372.0
16 TraesCS4D01G192000 chr5D 87.156 872 79 30 2881 3746 408412641 408411797 0.000000e+00 959.0
17 TraesCS4D01G192000 chr5D 88.028 284 28 4 2885 3164 112947745 112947464 7.760000e-87 331.0
18 TraesCS4D01G192000 chr5D 88.214 280 27 4 2885 3160 394573998 394573721 2.790000e-86 329.0
19 TraesCS4D01G192000 chr5D 100.000 28 0 0 1562 1589 40190810 40190837 7.000000e-03 52.8
20 TraesCS4D01G192000 chr5D 100.000 28 0 0 1562 1589 359859627 359859600 7.000000e-03 52.8
21 TraesCS4D01G192000 chr1D 85.617 737 101 5 1856 2591 203536257 203535525 0.000000e+00 769.0
22 TraesCS4D01G192000 chr1D 100.000 28 0 0 1562 1589 333465301 333465274 7.000000e-03 52.8
23 TraesCS4D01G192000 chr1A 85.517 725 102 3 1856 2579 258180761 258180039 0.000000e+00 754.0
24 TraesCS4D01G192000 chr1A 100.000 29 0 0 1562 1590 566340463 566340435 2.000000e-03 54.7
25 TraesCS4D01G192000 chr1A 100.000 29 0 0 1562 1590 566348890 566348862 2.000000e-03 54.7
26 TraesCS4D01G192000 chr1B 85.789 577 73 5 1856 2431 297477524 297476956 1.490000e-168 603.0
27 TraesCS4D01G192000 chr1B 90.054 372 19 9 3375 3746 555618682 555618329 2.040000e-127 466.0
28 TraesCS4D01G192000 chr2A 88.032 493 58 1 362 854 766044615 766045106 1.940000e-162 582.0
29 TraesCS4D01G192000 chr2A 90.566 371 31 4 2884 3252 294234710 294235078 4.350000e-134 488.0
30 TraesCS4D01G192000 chr2A 88.701 354 33 5 2885 3236 503023365 503023713 3.460000e-115 425.0
31 TraesCS4D01G192000 chr2A 92.116 241 15 4 3510 3746 294235354 294235594 1.670000e-88 337.0
32 TraesCS4D01G192000 chr2D 91.272 401 25 8 3355 3745 72196632 72196232 4.260000e-149 538.0
33 TraesCS4D01G192000 chr2D 100.000 28 0 0 1562 1589 508932759 508932786 7.000000e-03 52.8
34 TraesCS4D01G192000 chr2D 100.000 28 0 0 1562 1589 531349866 531349893 7.000000e-03 52.8
35 TraesCS4D01G192000 chr5A 91.214 387 34 0 3360 3746 140472596 140472982 9.220000e-146 527.0
36 TraesCS4D01G192000 chr6B 82.143 588 71 25 2922 3490 515035471 515034899 1.220000e-129 473.0
37 TraesCS4D01G192000 chr5B 89.516 372 21 2 3375 3746 180033483 180033130 4.410000e-124 455.0
38 TraesCS4D01G192000 chr6D 96.218 238 9 0 3509 3746 448079509 448079746 1.260000e-104 390.0
39 TraesCS4D01G192000 chr6D 92.593 81 4 1 3349 3429 448079432 448079510 8.500000e-22 115.0
40 TraesCS4D01G192000 chrUn 88.214 280 27 4 2885 3160 211158254 211157977 2.790000e-86 329.0
41 TraesCS4D01G192000 chrUn 100.000 29 0 0 1562 1590 305480254 305480282 2.000000e-03 54.7
42 TraesCS4D01G192000 chr3D 88.172 279 28 5 2885 3160 276671614 276671890 1.000000e-85 327.0
43 TraesCS4D01G192000 chr3D 100.000 28 0 0 1562 1589 73588961 73588988 7.000000e-03 52.8
44 TraesCS4D01G192000 chr3A 91.026 234 17 4 2885 3114 434849861 434849628 2.810000e-81 313.0


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 TraesCS4D01G192000 chr4D 335333109 335336854 3745 True 6918.000000 6918 100.000000 1 3746 1 chr4D.!!$R1 3745
1 TraesCS4D01G192000 chr4D 278259242 278260060 818 False 431.000000 431 76.306000 2 818 1 chr4D.!!$F2 816
2 TraesCS4D01G192000 chr4B 413446995 413449931 2936 True 1429.333333 2215 94.103333 1 2884 3 chr4B.!!$R1 2883
3 TraesCS4D01G192000 chr4A 137539359 137542289 2930 False 1393.000000 2104 92.666333 1 2883 3 chr4A.!!$F2 2882
4 TraesCS4D01G192000 chr7B 124326423 124327279 856 False 1175.000000 1175 91.482000 1 854 1 chr7B.!!$F1 853
5 TraesCS4D01G192000 chr7B 685746406 685747221 815 False 401.000000 401 75.702000 18 830 1 chr7B.!!$F2 812
6 TraesCS4D01G192000 chr7A 722260837 722261692 855 False 1147.000000 1147 90.898000 1 854 1 chr7A.!!$F1 853
7 TraesCS4D01G192000 chr6A 140030592 140031412 820 False 1077.000000 1077 90.389000 36 854 1 chr6A.!!$F2 818
8 TraesCS4D01G192000 chr6A 140052734 140053554 820 False 1077.000000 1077 90.389000 36 854 1 chr6A.!!$F3 818
9 TraesCS4D01G192000 chr5D 408411797 408412641 844 True 959.000000 959 87.156000 2881 3746 1 chr5D.!!$R4 865
10 TraesCS4D01G192000 chr1D 203535525 203536257 732 True 769.000000 769 85.617000 1856 2591 1 chr1D.!!$R1 735
11 TraesCS4D01G192000 chr1A 258180039 258180761 722 True 754.000000 754 85.517000 1856 2579 1 chr1A.!!$R1 723
12 TraesCS4D01G192000 chr1B 297476956 297477524 568 True 603.000000 603 85.789000 1856 2431 1 chr1B.!!$R1 575
13 TraesCS4D01G192000 chr2A 294234710 294235594 884 False 412.500000 488 91.341000 2884 3746 2 chr2A.!!$F3 862
14 TraesCS4D01G192000 chr6B 515034899 515035471 572 True 473.000000 473 82.143000 2922 3490 1 chr6B.!!$R1 568

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
830 848 0.037590 TTCTTCACCAACCCGGATGG 59.962 55.000 20.84 20.84 43.84 3.51 F
918 936 0.110238 GCGTACACCACATTGCACAG 60.110 55.000 0.00 0.00 0.00 3.66 F
922 940 1.024271 ACACCACATTGCACAGACAC 58.976 50.000 0.00 0.00 0.00 3.67 F
1806 1920 1.270274 GTTGGCTGTGTGCATCAATGA 59.730 47.619 0.00 0.00 45.15 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1919 0.615331 TCTCCCCAGTGTCTGCATTC 59.385 55.000 0.00 0.0 0.0 2.67 R
1807 1921 0.835941 GATCTCCCCAGTGTCTGCAT 59.164 55.000 0.00 0.0 0.0 3.96 R
2062 2176 4.050852 ACTTGGTCGAATTATCCGTACC 57.949 45.455 0.00 0.0 0.0 3.34 R
3621 3874 0.109827 TGTGAATGCGCATGAAACCG 60.110 50.000 26.09 0.0 0.0 4.44 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
32 33 0.460284 ACGAGCCAGCTCATAAACCG 60.460 55.000 19.08 6.77 42.86 4.44
56 57 6.292865 CGACAAAAGTGCTCTATTCAGTTTGA 60.293 38.462 12.75 0.00 37.22 2.69
62 63 8.430801 AAGTGCTCTATTCAGTTTGATGATAC 57.569 34.615 0.00 0.00 0.00 2.24
118 119 6.719370 ACAGGAATTGCAGGTACAAAAATCTA 59.281 34.615 0.00 0.00 32.27 1.98
126 130 6.150474 TGCAGGTACAAAAATCTAAGTTAGGC 59.850 38.462 10.02 1.74 0.00 3.93
189 193 2.767960 GGGGAAATTCCAGATGTTGCAT 59.232 45.455 14.68 0.00 38.64 3.96
280 284 0.323725 ATCCGTCCTGCAGGCAATTT 60.324 50.000 28.91 9.63 34.44 1.82
306 310 8.723365 TCCACTTATATTATGGGAGTGTTCAAT 58.277 33.333 12.01 0.00 36.79 2.57
332 336 2.031465 TTCGGTTTGCGAGGACCC 59.969 61.111 0.00 0.00 32.14 4.46
336 340 3.047877 GTTTGCGAGGACCCCACG 61.048 66.667 0.00 0.00 40.38 4.94
419 424 6.183360 CGAGCATGGGAGAAAATAATTGAACT 60.183 38.462 0.00 0.00 0.00 3.01
429 434 9.140286 GAGAAAATAATTGAACTAAAGGGCAAC 57.860 33.333 0.00 0.00 0.00 4.17
526 531 6.491745 CACTAGACTGGATTCCTTATGCTCTA 59.508 42.308 3.95 0.00 0.00 2.43
640 657 3.348055 CTCGAGCCGCTCAAGCAGA 62.348 63.158 20.22 7.82 42.21 4.26
775 793 1.880675 GAGTGTCAGAACTCCTCGACA 59.119 52.381 0.00 0.00 40.66 4.35
783 801 0.249741 AACTCCTCGACAACAACGGG 60.250 55.000 0.00 0.00 0.00 5.28
790 808 4.493049 ACAACAACGGGCGGTGGT 62.493 61.111 0.00 0.00 37.09 4.16
801 819 3.077907 CGGTGGTGGGTGGATCTT 58.922 61.111 0.00 0.00 0.00 2.40
830 848 0.037590 TTCTTCACCAACCCGGATGG 59.962 55.000 20.84 20.84 43.84 3.51
887 905 2.978156 ATGGAGGAAAGAGCAAACCA 57.022 45.000 0.00 0.00 0.00 3.67
918 936 0.110238 GCGTACACCACATTGCACAG 60.110 55.000 0.00 0.00 0.00 3.66
922 940 1.024271 ACACCACATTGCACAGACAC 58.976 50.000 0.00 0.00 0.00 3.67
1057 1081 4.681978 GCAGTCCCGCCGTTGTCT 62.682 66.667 0.00 0.00 0.00 3.41
1058 1082 2.432628 CAGTCCCGCCGTTGTCTC 60.433 66.667 0.00 0.00 0.00 3.36
1063 1087 4.796231 CCGCCGTTGTCTCCTCCG 62.796 72.222 0.00 0.00 0.00 4.63
1066 1090 3.382832 CCGTTGTCTCCTCCGCCT 61.383 66.667 0.00 0.00 0.00 5.52
1067 1091 2.182030 CGTTGTCTCCTCCGCCTC 59.818 66.667 0.00 0.00 0.00 4.70
1068 1092 2.579738 GTTGTCTCCTCCGCCTCC 59.420 66.667 0.00 0.00 0.00 4.30
1069 1093 3.068691 TTGTCTCCTCCGCCTCCG 61.069 66.667 0.00 0.00 0.00 4.63
1482 1514 1.350684 TGGCAGTTGCACTGGAGAATA 59.649 47.619 15.16 0.00 46.01 1.75
1493 1525 4.752101 GCACTGGAGAATAGCGTTAATGAT 59.248 41.667 0.00 0.00 0.00 2.45
1552 1584 6.019762 GCTGCTCGGTTATTTTGTTAGTTAC 58.980 40.000 0.00 0.00 0.00 2.50
1553 1585 6.128363 GCTGCTCGGTTATTTTGTTAGTTACT 60.128 38.462 0.00 0.00 0.00 2.24
1554 1586 7.355332 TGCTCGGTTATTTTGTTAGTTACTC 57.645 36.000 0.00 0.00 0.00 2.59
1555 1587 6.369615 TGCTCGGTTATTTTGTTAGTTACTCC 59.630 38.462 0.00 0.00 0.00 3.85
1556 1588 6.183360 GCTCGGTTATTTTGTTAGTTACTCCC 60.183 42.308 0.00 0.00 0.00 4.30
1557 1589 7.008021 TCGGTTATTTTGTTAGTTACTCCCT 57.992 36.000 0.00 0.00 0.00 4.20
1558 1590 7.099120 TCGGTTATTTTGTTAGTTACTCCCTC 58.901 38.462 0.00 0.00 0.00 4.30
1559 1591 6.314648 CGGTTATTTTGTTAGTTACTCCCTCC 59.685 42.308 0.00 0.00 0.00 4.30
1560 1592 6.314648 GGTTATTTTGTTAGTTACTCCCTCCG 59.685 42.308 0.00 0.00 0.00 4.63
1561 1593 3.323751 TTTGTTAGTTACTCCCTCCGC 57.676 47.619 0.00 0.00 0.00 5.54
1562 1594 2.226962 TGTTAGTTACTCCCTCCGCT 57.773 50.000 0.00 0.00 0.00 5.52
1563 1595 2.532843 TGTTAGTTACTCCCTCCGCTT 58.467 47.619 0.00 0.00 0.00 4.68
1564 1596 3.700538 TGTTAGTTACTCCCTCCGCTTA 58.299 45.455 0.00 0.00 0.00 3.09
1565 1597 4.284178 TGTTAGTTACTCCCTCCGCTTAT 58.716 43.478 0.00 0.00 0.00 1.73
1566 1598 5.448654 TGTTAGTTACTCCCTCCGCTTATA 58.551 41.667 0.00 0.00 0.00 0.98
1567 1599 6.073314 TGTTAGTTACTCCCTCCGCTTATAT 58.927 40.000 0.00 0.00 0.00 0.86
1568 1600 6.552350 TGTTAGTTACTCCCTCCGCTTATATT 59.448 38.462 0.00 0.00 0.00 1.28
1569 1601 7.725397 TGTTAGTTACTCCCTCCGCTTATATTA 59.275 37.037 0.00 0.00 0.00 0.98
1570 1602 8.747471 GTTAGTTACTCCCTCCGCTTATATTAT 58.253 37.037 0.00 0.00 0.00 1.28
1571 1603 7.171630 AGTTACTCCCTCCGCTTATATTATG 57.828 40.000 0.00 0.00 0.00 1.90
1572 1604 6.154706 AGTTACTCCCTCCGCTTATATTATGG 59.845 42.308 0.00 0.00 0.00 2.74
1573 1605 3.775316 ACTCCCTCCGCTTATATTATGGG 59.225 47.826 0.00 0.00 34.98 4.00
1574 1606 4.030913 CTCCCTCCGCTTATATTATGGGA 58.969 47.826 0.00 0.00 39.87 4.37
1575 1607 3.773119 TCCCTCCGCTTATATTATGGGAC 59.227 47.826 0.00 0.00 37.56 4.46
1576 1608 3.775316 CCCTCCGCTTATATTATGGGACT 59.225 47.826 0.00 0.00 35.64 3.85
1577 1609 4.383118 CCCTCCGCTTATATTATGGGACTG 60.383 50.000 0.00 0.00 35.64 3.51
1578 1610 4.466370 CCTCCGCTTATATTATGGGACTGA 59.534 45.833 0.00 0.00 0.00 3.41
1579 1611 5.394663 CCTCCGCTTATATTATGGGACTGAG 60.395 48.000 0.00 0.00 0.00 3.35
1580 1612 4.466370 TCCGCTTATATTATGGGACTGAGG 59.534 45.833 0.00 0.00 0.00 3.86
1581 1613 4.383118 CCGCTTATATTATGGGACTGAGGG 60.383 50.000 0.00 0.00 0.00 4.30
1582 1614 4.466370 CGCTTATATTATGGGACTGAGGGA 59.534 45.833 0.00 0.00 0.00 4.20
1583 1615 5.394663 CGCTTATATTATGGGACTGAGGGAG 60.395 48.000 0.00 0.00 0.00 4.30
1592 1624 3.289836 GGGACTGAGGGAGTAGTTAGTC 58.710 54.545 0.00 0.00 33.83 2.59
1597 1629 3.957497 CTGAGGGAGTAGTTAGTCAGCAT 59.043 47.826 0.00 0.00 0.00 3.79
1677 1709 7.006210 CAGCAAATTTCGTAGTTTAATGTCGTC 59.994 37.037 0.00 0.00 0.00 4.20
1697 1729 5.934043 TCGTCATTATTTCCATCCATAGCTG 59.066 40.000 0.00 0.00 0.00 4.24
1747 1859 9.976511 AATATGCAAAATCCTGTTCATAAGATG 57.023 29.630 0.00 0.00 0.00 2.90
1748 1860 5.653507 TGCAAAATCCTGTTCATAAGATGC 58.346 37.500 0.00 0.00 0.00 3.91
1749 1861 5.185442 TGCAAAATCCTGTTCATAAGATGCA 59.815 36.000 0.00 0.00 36.65 3.96
1750 1862 6.127281 TGCAAAATCCTGTTCATAAGATGCAT 60.127 34.615 0.00 0.00 34.36 3.96
1751 1863 6.200286 GCAAAATCCTGTTCATAAGATGCATG 59.800 38.462 2.46 0.00 0.00 4.06
1787 1901 9.146984 TCGAATGATTGAAACTTCGTAATAAGT 57.853 29.630 0.00 0.00 41.46 2.24
1805 1919 1.271379 AGTTGGCTGTGTGCATCAATG 59.729 47.619 0.00 0.00 45.15 2.82
1806 1920 1.270274 GTTGGCTGTGTGCATCAATGA 59.730 47.619 0.00 0.00 45.15 2.57
1807 1921 1.618487 TGGCTGTGTGCATCAATGAA 58.382 45.000 0.00 0.00 45.15 2.57
1846 1960 8.350722 GGAGATCCCCTTTTCGAATAAATAAAC 58.649 37.037 0.00 0.00 0.00 2.01
2198 2312 1.336755 GTTAACACAACACAGCCAGGG 59.663 52.381 0.00 0.00 0.00 4.45
2228 2342 6.773638 AGGAGTTATAGTTATGCAGATTGGG 58.226 40.000 0.00 0.00 0.00 4.12
2243 2357 5.010282 CAGATTGGGGCTTACTTGTTAGTT 58.990 41.667 0.00 0.00 35.78 2.24
2334 2449 6.706716 GCCTTCTTTAGTATACATCTTGGACC 59.293 42.308 5.50 0.00 0.00 4.46
2643 2759 8.388484 AGATCAGTTTCTATGTATCCAATTGC 57.612 34.615 0.00 0.00 0.00 3.56
2662 2778 4.519540 TGCTTGCTTAGATTTTGGGAAC 57.480 40.909 0.00 0.00 0.00 3.62
2775 2891 9.796120 TTAATTAGAAATGGTAAATCAAAGCGG 57.204 29.630 0.00 0.00 0.00 5.52
2800 2916 6.304624 CCTTTTGAAGTTCTTTAGTAGGGGT 58.695 40.000 4.17 0.00 0.00 4.95
2802 2918 5.899631 TTGAAGTTCTTTAGTAGGGGTGT 57.100 39.130 4.17 0.00 0.00 4.16
2986 3105 8.803235 CACACCTGTACATGTATATATACTGGT 58.197 37.037 20.80 19.16 45.44 4.00
3028 3147 8.978874 ATACAAGTTGCATATTCCTAACATGA 57.021 30.769 1.81 0.00 0.00 3.07
3142 3263 2.040278 CTGCTCCTCTCCCCCTGT 59.960 66.667 0.00 0.00 0.00 4.00
3151 3272 0.490017 TCTCCCCCTGTAGGTCAACA 59.510 55.000 0.00 0.00 0.00 3.33
3194 3315 1.172812 GCCGCCAGTTCCTTCTTGTT 61.173 55.000 0.00 0.00 0.00 2.83
3198 3319 1.691196 CCAGTTCCTTCTTGTTGCCA 58.309 50.000 0.00 0.00 0.00 4.92
3202 3323 2.554032 AGTTCCTTCTTGTTGCCAATCG 59.446 45.455 0.00 0.00 0.00 3.34
3204 3325 0.883833 CCTTCTTGTTGCCAATCGCT 59.116 50.000 0.00 0.00 38.78 4.93
3207 3328 0.890542 TCTTGTTGCCAATCGCTGCT 60.891 50.000 0.00 0.00 38.78 4.24
3222 3343 3.532155 GCTGTCCTCGCCGGATCT 61.532 66.667 5.05 0.00 45.44 2.75
3264 3460 4.101790 GCATCAACGCCCGTGGTG 62.102 66.667 0.00 2.39 39.41 4.17
3334 3578 4.873129 CCACGATCCAGCCGACCG 62.873 72.222 0.00 0.00 0.00 4.79
3347 3591 4.047059 GACCGGTTCCGCTCGTGA 62.047 66.667 9.42 0.00 0.00 4.35
3491 3739 2.044806 ATTCCTTCGGCCTGATCCCG 62.045 60.000 0.00 2.76 46.88 5.14
3519 3767 1.562942 TGCAGATTGAGGCTCCTGATT 59.437 47.619 19.41 0.00 0.00 2.57
3520 3768 1.948145 GCAGATTGAGGCTCCTGATTG 59.052 52.381 19.41 10.05 0.00 2.67
3528 3776 3.027412 GAGGCTCCTGATTGTCTGTCTA 58.973 50.000 2.15 0.00 0.00 2.59
3569 3822 0.811616 CTGTCCTCCGGCTATGTTGC 60.812 60.000 0.00 0.00 0.00 4.17
3621 3874 5.761234 TGGTACCAACTACATTGAGTTTGTC 59.239 40.000 13.60 3.75 41.23 3.18
3624 3877 3.813166 CCAACTACATTGAGTTTGTCGGT 59.187 43.478 0.00 0.00 41.23 4.69
3712 3965 1.048601 GTGTCCAGTTCCTCCTGTGA 58.951 55.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.613260 TGTCGGTTTATGAGCTGGCT 59.387 50.000 0.00 0.00 0.00 4.75
32 33 6.959361 TCAAACTGAATAGAGCACTTTTGTC 58.041 36.000 0.00 0.00 0.00 3.18
56 57 1.922447 TCACCAAGGGGCAAGTATCAT 59.078 47.619 0.00 0.00 37.90 2.45
62 63 1.601419 CTGCATCACCAAGGGGCAAG 61.601 60.000 0.00 0.00 37.90 4.01
189 193 2.613026 TTCTTCTGGTCAAACTCGCA 57.387 45.000 0.00 0.00 0.00 5.10
280 284 7.684317 TGAACACTCCCATAATATAAGTGGA 57.316 36.000 11.65 0.00 41.23 4.02
306 310 0.247735 CGCAAACCGAACACGACAAA 60.248 50.000 0.00 0.00 40.02 2.83
310 314 1.952133 CCTCGCAAACCGAACACGA 60.952 57.895 0.00 0.00 46.81 4.35
332 336 1.080093 TTCCTCACTAAGCGCGTGG 60.080 57.895 8.43 5.43 33.31 4.94
336 340 2.095718 CCAAAAGTTCCTCACTAAGCGC 60.096 50.000 0.00 0.00 32.94 5.92
419 424 1.428718 AAGTCCCCCGTTGCCCTTTA 61.429 55.000 0.00 0.00 0.00 1.85
429 434 2.746277 CGAAAGCCAAGTCCCCCG 60.746 66.667 0.00 0.00 0.00 5.73
492 497 4.511786 ATCCAGTCTAGTGAGTAGCTGA 57.488 45.455 15.58 6.75 36.08 4.26
494 499 4.079443 AGGAATCCAGTCTAGTGAGTAGCT 60.079 45.833 0.61 0.00 0.00 3.32
783 801 3.268103 AAGATCCACCCACCACCGC 62.268 63.158 0.00 0.00 0.00 5.68
790 808 3.874383 TTGTTGAAGAAGATCCACCCA 57.126 42.857 0.00 0.00 0.00 4.51
801 819 4.340950 GGGTTGGTGAAGAATTGTTGAAGA 59.659 41.667 0.00 0.00 0.00 2.87
870 888 4.400529 TTTTTGGTTTGCTCTTTCCTCC 57.599 40.909 0.00 0.00 0.00 4.30
949 967 2.693074 GGGCTTTCTTCCAAAGACACAA 59.307 45.455 2.47 0.00 37.01 3.33
951 969 2.294512 CTGGGCTTTCTTCCAAAGACAC 59.705 50.000 2.47 0.00 37.01 3.67
1315 1339 3.061848 GGTCCGGTCGGGTCGTAA 61.062 66.667 9.68 0.00 37.00 3.18
1392 1416 0.857675 TGACCGAGGAGATCCCCATA 59.142 55.000 0.00 0.00 36.42 2.74
1552 1584 4.030913 TCCCATAATATAAGCGGAGGGAG 58.969 47.826 0.00 0.00 39.06 4.30
1553 1585 3.773119 GTCCCATAATATAAGCGGAGGGA 59.227 47.826 0.00 0.00 41.55 4.20
1554 1586 3.775316 AGTCCCATAATATAAGCGGAGGG 59.225 47.826 0.00 0.00 36.38 4.30
1555 1587 4.466370 TCAGTCCCATAATATAAGCGGAGG 59.534 45.833 0.00 0.00 0.00 4.30
1556 1588 5.394663 CCTCAGTCCCATAATATAAGCGGAG 60.395 48.000 0.00 0.00 0.00 4.63
1557 1589 4.466370 CCTCAGTCCCATAATATAAGCGGA 59.534 45.833 0.00 0.00 0.00 5.54
1558 1590 4.383118 CCCTCAGTCCCATAATATAAGCGG 60.383 50.000 0.00 0.00 0.00 5.52
1559 1591 4.466370 TCCCTCAGTCCCATAATATAAGCG 59.534 45.833 0.00 0.00 0.00 4.68
1560 1592 5.485708 ACTCCCTCAGTCCCATAATATAAGC 59.514 44.000 0.00 0.00 0.00 3.09
1561 1593 7.896496 ACTACTCCCTCAGTCCCATAATATAAG 59.104 40.741 0.00 0.00 36.43 1.73
1562 1594 7.776745 ACTACTCCCTCAGTCCCATAATATAA 58.223 38.462 0.00 0.00 36.43 0.98
1563 1595 7.358255 ACTACTCCCTCAGTCCCATAATATA 57.642 40.000 0.00 0.00 36.43 0.86
1564 1596 6.234404 ACTACTCCCTCAGTCCCATAATAT 57.766 41.667 0.00 0.00 36.43 1.28
1565 1597 5.681494 ACTACTCCCTCAGTCCCATAATA 57.319 43.478 0.00 0.00 36.43 0.98
1566 1598 4.561254 ACTACTCCCTCAGTCCCATAAT 57.439 45.455 0.00 0.00 36.43 1.28
1567 1599 4.348020 AACTACTCCCTCAGTCCCATAA 57.652 45.455 0.00 0.00 36.43 1.90
1568 1600 4.481280 ACTAACTACTCCCTCAGTCCCATA 59.519 45.833 0.00 0.00 36.43 2.74
1569 1601 2.950990 AACTACTCCCTCAGTCCCAT 57.049 50.000 0.00 0.00 36.43 4.00
1570 1602 2.653366 ACTAACTACTCCCTCAGTCCCA 59.347 50.000 0.00 0.00 36.43 4.37
1571 1603 3.289836 GACTAACTACTCCCTCAGTCCC 58.710 54.545 0.00 0.00 36.43 4.46
1572 1604 3.949113 CTGACTAACTACTCCCTCAGTCC 59.051 52.174 0.00 0.00 36.43 3.85
1573 1605 3.379057 GCTGACTAACTACTCCCTCAGTC 59.621 52.174 0.00 0.00 36.43 3.51
1574 1606 3.245300 TGCTGACTAACTACTCCCTCAGT 60.245 47.826 0.00 0.00 39.41 3.41
1575 1607 3.357203 TGCTGACTAACTACTCCCTCAG 58.643 50.000 0.00 0.00 0.00 3.35
1576 1608 3.451402 TGCTGACTAACTACTCCCTCA 57.549 47.619 0.00 0.00 0.00 3.86
1577 1609 3.702045 ACATGCTGACTAACTACTCCCTC 59.298 47.826 0.00 0.00 0.00 4.30
1578 1610 3.714144 ACATGCTGACTAACTACTCCCT 58.286 45.455 0.00 0.00 0.00 4.20
1579 1611 4.473477 AACATGCTGACTAACTACTCCC 57.527 45.455 0.00 0.00 0.00 4.30
1580 1612 5.962433 TGTAACATGCTGACTAACTACTCC 58.038 41.667 0.00 0.00 0.00 3.85
1581 1613 7.221067 GTCATGTAACATGCTGACTAACTACTC 59.779 40.741 0.00 0.00 36.07 2.59
1582 1614 7.036220 GTCATGTAACATGCTGACTAACTACT 58.964 38.462 0.00 0.00 36.07 2.57
1583 1615 7.036220 AGTCATGTAACATGCTGACTAACTAC 58.964 38.462 11.47 0.00 44.80 2.73
1592 1624 4.847757 CGAACAAAGTCATGTAACATGCTG 59.152 41.667 0.00 0.00 32.02 4.41
1597 1629 6.220201 TCAGATCGAACAAAGTCATGTAACA 58.780 36.000 0.00 0.00 32.02 2.41
1677 1709 4.142534 CGGCAGCTATGGATGGAAATAATG 60.143 45.833 0.00 0.00 0.00 1.90
1697 1729 4.275936 AGTTTATCCAATGTATCTTGCGGC 59.724 41.667 0.00 0.00 0.00 6.53
1734 1846 7.260558 AGAACATCATGCATCTTATGAACAG 57.739 36.000 16.32 2.93 38.01 3.16
1742 1854 7.443272 TCATTCGAATAGAACATCATGCATCTT 59.557 33.333 10.97 0.00 42.39 2.40
1744 1856 7.125536 TCATTCGAATAGAACATCATGCATC 57.874 36.000 10.97 0.00 42.39 3.91
1745 1857 7.683437 ATCATTCGAATAGAACATCATGCAT 57.317 32.000 10.97 0.00 42.39 3.96
1746 1858 7.227116 TCAATCATTCGAATAGAACATCATGCA 59.773 33.333 10.97 0.00 42.39 3.96
1747 1859 7.578852 TCAATCATTCGAATAGAACATCATGC 58.421 34.615 10.97 0.00 42.39 4.06
1748 1860 9.940166 TTTCAATCATTCGAATAGAACATCATG 57.060 29.630 10.97 0.00 42.39 3.07
1749 1861 9.941664 GTTTCAATCATTCGAATAGAACATCAT 57.058 29.630 10.97 0.00 42.39 2.45
1750 1862 9.166173 AGTTTCAATCATTCGAATAGAACATCA 57.834 29.630 10.97 0.00 42.39 3.07
1751 1863 9.994432 AAGTTTCAATCATTCGAATAGAACATC 57.006 29.630 10.97 6.55 42.39 3.06
1787 1901 1.618487 TCATTGATGCACACAGCCAA 58.382 45.000 0.00 0.00 44.83 4.52
1805 1919 0.615331 TCTCCCCAGTGTCTGCATTC 59.385 55.000 0.00 0.00 0.00 2.67
1806 1920 1.211457 GATCTCCCCAGTGTCTGCATT 59.789 52.381 0.00 0.00 0.00 3.56
1807 1921 0.835941 GATCTCCCCAGTGTCTGCAT 59.164 55.000 0.00 0.00 0.00 3.96
2062 2176 4.050852 ACTTGGTCGAATTATCCGTACC 57.949 45.455 0.00 0.00 0.00 3.34
2198 2312 5.925509 TGCATAACTATAACTCCTTCACCC 58.074 41.667 0.00 0.00 0.00 4.61
2228 2342 7.543520 ACGTACATAGAAACTAACAAGTAAGCC 59.456 37.037 0.00 0.00 0.00 4.35
2243 2357 5.599242 TCAACATGGGGATACGTACATAGAA 59.401 40.000 0.00 0.00 37.60 2.10
2643 2759 6.331369 TGAAGTTCCCAAAATCTAAGCAAG 57.669 37.500 0.00 0.00 0.00 4.01
2662 2778 8.438513 CAACTAGTGTGAAGTTCATACATGAAG 58.561 37.037 27.93 21.19 46.44 3.02
2751 2867 6.756542 GCCGCTTTGATTTACCATTTCTAATT 59.243 34.615 0.00 0.00 0.00 1.40
2775 2891 5.183331 CCCCTACTAAAGAACTTCAAAAGGC 59.817 44.000 0.00 0.00 0.00 4.35
2901 3020 9.480053 GTAAATACGAAAGGTTACATGGCTATA 57.520 33.333 0.00 0.00 31.43 1.31
2986 3105 3.119319 TGTATTTCCAGGTGGCCATAGA 58.881 45.455 9.72 0.00 34.44 1.98
3028 3147 7.779798 TGCCAAAAATTGACCTAGCTCTAATAT 59.220 33.333 0.00 0.00 0.00 1.28
3051 3170 3.730761 CAGGAGTTGCAGCGTGCC 61.731 66.667 7.38 0.00 44.23 5.01
3066 3185 0.798776 GCGAGGTGGATCAACAACAG 59.201 55.000 1.86 0.00 0.00 3.16
3142 3263 0.677288 CACGTCCTGGTGTTGACCTA 59.323 55.000 0.00 0.00 43.58 3.08
3151 3272 2.413310 AAAGAACAACACGTCCTGGT 57.587 45.000 0.00 0.00 0.00 4.00
3198 3319 2.510238 GCGAGGACAGCAGCGATT 60.510 61.111 0.00 0.00 34.19 3.34
3245 3441 3.133464 CCACGGGCGTTGATGCAT 61.133 61.111 0.00 0.00 36.28 3.96
3281 3525 2.827715 GATCCTCCCACTGGATCGT 58.172 57.895 6.96 0.00 46.88 3.73
3309 3553 3.723235 CTGGATCGTGGGCAGGACG 62.723 68.421 0.00 0.00 38.20 4.79
3334 3578 3.310860 ATGGGTCACGAGCGGAACC 62.311 63.158 8.03 8.03 42.69 3.62
3370 3614 4.899239 GACCTGGCGGCTGGATCG 62.899 72.222 36.16 14.07 0.00 3.69
3491 3739 3.109612 CTCAATCTGCAGCAGCGGC 62.110 63.158 18.43 11.05 46.95 6.53
3569 3822 0.803768 CATCGGACAGCGAGGAACAG 60.804 60.000 0.00 0.00 0.00 3.16
3595 3848 7.455058 ACAAACTCAATGTAGTTGGTACCATA 58.545 34.615 17.17 2.84 40.99 2.74
3621 3874 0.109827 TGTGAATGCGCATGAAACCG 60.110 50.000 26.09 0.00 0.00 4.44
3647 3900 4.821589 CGCCCCAGAGACGAAGGC 62.822 72.222 0.00 0.00 40.33 4.35
3712 3965 2.045131 GCGTCGGTGGAGTAGGAGT 61.045 63.158 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.