Multiple sequence alignment - TraesCS7D01G408700

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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 TraesCS7D01G408700 chr7D 100.000 4334 0 0 1 4334 526447138 526442805 0.000000e+00 8004.0
1 TraesCS7D01G408700 chr7D 98.753 3529 38 3 1 3528 526499187 526495664 0.000000e+00 6268.0
2 TraesCS7D01G408700 chr7D 95.639 2385 85 7 1270 3640 526528198 526525819 0.000000e+00 3810.0
3 TraesCS7D01G408700 chr7D 93.373 1358 83 5 1270 2625 527196811 527195459 0.000000e+00 2002.0
4 TraesCS7D01G408700 chr7D 93.040 1365 87 6 1270 2632 526804067 526802709 0.000000e+00 1988.0
5 TraesCS7D01G408700 chr7D 93.152 1358 86 5 1270 2625 526975490 526974138 0.000000e+00 1986.0
6 TraesCS7D01G408700 chr7D 94.816 733 33 4 544 1273 526380791 526380061 0.000000e+00 1138.0
7 TraesCS7D01G408700 chr7D 88.318 779 61 21 522 1273 526529039 526528264 0.000000e+00 907.0
8 TraesCS7D01G408700 chr7D 88.165 752 62 13 2736 3466 527195381 527194636 0.000000e+00 870.0
9 TraesCS7D01G408700 chr7D 90.440 659 47 5 2820 3466 526974001 526973347 0.000000e+00 854.0
10 TraesCS7D01G408700 chr7D 85.538 809 71 25 495 1273 526976348 526975556 0.000000e+00 804.0
11 TraesCS7D01G408700 chr7D 84.777 808 77 23 495 1273 527197667 527196877 0.000000e+00 769.0
12 TraesCS7D01G408700 chr7D 88.000 625 59 12 2736 3351 526802635 526802018 0.000000e+00 725.0
13 TraesCS7D01G408700 chr7D 88.352 455 35 8 495 948 526804917 526804480 8.250000e-147 531.0
14 TraesCS7D01G408700 chr7D 87.462 327 27 8 950 1273 526804448 526804133 8.860000e-97 364.0
15 TraesCS7D01G408700 chr7D 80.228 526 59 35 3807 4308 526525816 526525312 1.920000e-93 353.0
16 TraesCS7D01G408700 chr7D 89.147 258 7 3 259 496 526381389 526381133 7.040000e-78 302.0
17 TraesCS7D01G408700 chr7D 93.548 155 7 1 4154 4308 526495235 526495084 1.210000e-55 228.0
18 TraesCS7D01G408700 chr7D 81.863 204 30 5 3807 4007 526495521 526495322 9.640000e-37 165.0
19 TraesCS7D01G408700 chr7D 96.774 93 2 1 3375 3466 526800880 526800788 2.090000e-33 154.0
20 TraesCS7D01G408700 chr7D 92.222 90 6 1 3533 3622 526495714 526495626 4.550000e-25 126.0
21 TraesCS7D01G408700 chr7D 92.754 69 3 1 3524 3592 527464962 527464896 9.920000e-17 99.0
22 TraesCS7D01G408700 chr7D 87.805 82 8 1 3526 3607 526800767 526800688 1.280000e-15 95.3
23 TraesCS7D01G408700 chr7D 92.537 67 3 1 3526 3592 526973326 526973262 1.280000e-15 95.3
24 TraesCS7D01G408700 chr7D 96.078 51 0 2 447 496 526529458 526529409 9.990000e-12 82.4
25 TraesCS7D01G408700 chr7D 94.231 52 2 1 3533 3584 526525981 526525931 1.290000e-10 78.7
26 TraesCS7D01G408700 chr7D 83.529 85 9 4 3829 3909 526377731 526377648 1.670000e-09 75.0
27 TraesCS7D01G408700 chr7D 97.222 36 1 0 3557 3592 526525994 526525959 1.300000e-05 62.1
28 TraesCS7D01G408700 chr7A 95.578 2917 83 9 493 3394 606637922 606635037 0.000000e+00 4630.0
29 TraesCS7D01G408700 chr7A 92.237 1417 99 11 1270 2678 606940924 606939511 0.000000e+00 1997.0
30 TraesCS7D01G408700 chr7A 86.015 808 79 21 495 1273 606941792 606940990 0.000000e+00 835.0
31 TraesCS7D01G408700 chr7A 93.130 262 18 0 3381 3642 606634997 606634736 6.800000e-103 385.0
32 TraesCS7D01G408700 chr7A 91.525 177 14 1 3633 3808 77440865 77440689 4.330000e-60 243.0
33 TraesCS7D01G408700 chr7A 88.482 191 14 6 3807 3989 606634734 606634544 1.570000e-54 224.0
34 TraesCS7D01G408700 chr7A 94.017 117 7 0 259 375 606638509 606638393 1.240000e-40 178.0
35 TraesCS7D01G408700 chr7A 83.957 187 19 5 4086 4264 606580485 606580302 7.450000e-38 169.0
36 TraesCS7D01G408700 chr7A 89.247 93 10 0 3994 4086 685505160 685505252 2.740000e-22 117.0
37 TraesCS7D01G408700 chr7A 86.538 104 12 2 3988 4091 215184672 215184571 3.540000e-21 113.0
38 TraesCS7D01G408700 chr7A 93.243 74 3 1 3525 3596 606580752 606580679 1.650000e-19 108.0
39 TraesCS7D01G408700 chr7A 97.826 46 0 1 451 496 606638338 606638294 1.290000e-10 78.7
40 TraesCS7D01G408700 chr7A 100.000 33 0 0 366 398 606638391 606638359 1.300000e-05 62.1
41 TraesCS7D01G408700 chr7A 87.273 55 5 2 1 53 606638615 606638561 1.300000e-05 62.1
42 TraesCS7D01G408700 chr7A 94.872 39 1 1 3951 3988 606580544 606580506 4.680000e-05 60.2
43 TraesCS7D01G408700 chr7A 94.444 36 2 0 3557 3592 606634913 606634878 6.050000e-04 56.5
44 TraesCS7D01G408700 chr7B 95.542 2243 77 12 1270 3494 563477439 563475202 0.000000e+00 3567.0
45 TraesCS7D01G408700 chr7B 94.672 2290 94 11 1376 3642 563660353 563658069 0.000000e+00 3528.0
46 TraesCS7D01G408700 chr7B 95.013 782 33 4 493 1273 563478281 563477505 0.000000e+00 1223.0
47 TraesCS7D01G408700 chr7B 96.177 654 18 3 627 1273 562995258 562994605 0.000000e+00 1062.0
48 TraesCS7D01G408700 chr7B 88.158 760 60 15 2727 3466 563735097 563734348 0.000000e+00 878.0
49 TraesCS7D01G408700 chr7B 86.881 808 70 24 495 1273 563737356 563736556 0.000000e+00 872.0
50 TraesCS7D01G408700 chr7B 90.123 324 24 4 950 1273 563666777 563666462 8.670000e-112 414.0
51 TraesCS7D01G408700 chr7B 96.859 191 5 1 259 448 562995530 562995340 6.990000e-83 318.0
52 TraesCS7D01G408700 chr7B 89.516 248 11 5 250 496 563478839 563478606 2.530000e-77 300.0
53 TraesCS7D01G408700 chr7B 90.090 222 12 6 4073 4288 563657775 563657558 3.300000e-71 279.0
54 TraesCS7D01G408700 chr7B 95.070 142 7 0 3501 3642 563475231 563475090 1.570000e-54 224.0
55 TraesCS7D01G408700 chr7B 95.690 116 4 1 3807 3922 563658067 563657953 7.400000e-43 185.0
56 TraesCS7D01G408700 chr7B 94.828 116 5 1 3807 3922 563475088 563474974 3.440000e-41 180.0
57 TraesCS7D01G408700 chr7B 95.522 67 3 0 4152 4218 563462919 563462853 1.650000e-19 108.0
58 TraesCS7D01G408700 chr7B 83.810 105 9 7 3826 3926 562992274 562992174 4.610000e-15 93.5
59 TraesCS7D01G408700 chr7B 94.545 55 1 2 443 496 563672615 563672562 2.780000e-12 84.2
60 TraesCS7D01G408700 chr7B 97.059 34 1 0 3495 3528 563475181 563475148 1.680000e-04 58.4
61 TraesCS7D01G408700 chr6A 93.413 167 11 0 3639 3805 521988240 521988406 9.310000e-62 248.0
62 TraesCS7D01G408700 chr5D 92.486 173 12 1 3634 3805 63786517 63786689 3.350000e-61 246.0
63 TraesCS7D01G408700 chr5D 90.811 185 13 4 3623 3805 322384915 322385097 1.200000e-60 244.0
64 TraesCS7D01G408700 chr3B 92.899 169 12 0 3637 3805 326997373 326997205 3.350000e-61 246.0
65 TraesCS7D01G408700 chr3B 90.761 184 15 2 3641 3822 30684323 30684506 1.200000e-60 244.0
66 TraesCS7D01G408700 chr3B 91.525 177 12 3 3641 3817 104316917 104316744 1.560000e-59 241.0
67 TraesCS7D01G408700 chr4D 90.659 182 14 3 3639 3819 402433954 402433775 5.600000e-59 239.0
68 TraesCS7D01G408700 chr6D 89.474 190 17 3 3621 3809 352878509 352878322 2.010000e-58 237.0
69 TraesCS7D01G408700 chr2B 89.011 91 10 0 4002 4092 7566832 7566742 3.540000e-21 113.0
70 TraesCS7D01G408700 chr1B 87.629 97 12 0 3988 4084 636858689 636858593 3.540000e-21 113.0
71 TraesCS7D01G408700 chr5B 87.000 100 11 2 3987 4085 560038415 560038513 1.270000e-20 111.0
72 TraesCS7D01G408700 chr5B 84.071 113 17 1 3976 4087 316712592 316712704 1.650000e-19 108.0
73 TraesCS7D01G408700 chr2D 85.714 105 15 0 3988 4092 71761527 71761631 1.270000e-20 111.0
74 TraesCS7D01G408700 chr1D 87.629 97 10 2 3988 4084 453108477 453108571 1.270000e-20 111.0
75 TraesCS7D01G408700 chr6B 85.577 104 15 0 3981 4084 679760498 679760395 4.580000e-20 110.0


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 TraesCS7D01G408700 chr7D 526442805 526447138 4333 True 8004.000000 8004 100.000000 1 4334 1 chr7D.!!$R1 4333
1 TraesCS7D01G408700 chr7D 526495084 526499187 4103 True 1696.750000 6268 91.596500 1 4308 4 chr7D.!!$R4 4307
2 TraesCS7D01G408700 chr7D 527194636 527197667 3031 True 1213.666667 2002 88.771667 495 3466 3 chr7D.!!$R8 2971
3 TraesCS7D01G408700 chr7D 526973262 526976348 3086 True 934.825000 1986 90.416750 495 3592 4 chr7D.!!$R7 3097
4 TraesCS7D01G408700 chr7D 526525312 526529458 4146 True 882.200000 3810 91.952667 447 4308 6 chr7D.!!$R5 3861
5 TraesCS7D01G408700 chr7D 526800688 526804917 4229 True 642.883333 1988 90.238833 495 3607 6 chr7D.!!$R6 3112
6 TraesCS7D01G408700 chr7D 526377648 526381389 3741 True 505.000000 1138 89.164000 259 3909 3 chr7D.!!$R3 3650
7 TraesCS7D01G408700 chr7A 606939511 606941792 2281 True 1416.000000 1997 89.126000 495 2678 2 chr7A.!!$R5 2183
8 TraesCS7D01G408700 chr7A 606634544 606638615 4071 True 709.550000 4630 93.843750 1 3989 8 chr7A.!!$R4 3988
9 TraesCS7D01G408700 chr7B 563657558 563660353 2795 True 1330.666667 3528 93.484000 1376 4288 3 chr7B.!!$R6 2912
10 TraesCS7D01G408700 chr7B 563474974 563478839 3865 True 925.400000 3567 94.504667 250 3922 6 chr7B.!!$R5 3672
11 TraesCS7D01G408700 chr7B 563734348 563737356 3008 True 875.000000 878 87.519500 495 3466 2 chr7B.!!$R7 2971
12 TraesCS7D01G408700 chr7B 562992174 562995530 3356 True 491.166667 1062 92.282000 259 3926 3 chr7B.!!$R4 3667

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
1019 1528 5.633830 TGGATGCTCAGAAAAATGAAGAC 57.366 39.130 0.0 0.0 0.0 3.01 F
1881 2462 2.200067 CAGATGTTCAGCTCGCCTAAG 58.800 52.381 0.0 0.0 0.0 2.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2486 3069 3.177228 ACCTCAGACACTATTCCAGCTT 58.823 45.455 0.00 0.0 0.0 3.74 R
3438 5336 0.977395 GACAGTACCAAGGGAGTGCT 59.023 55.000 6.06 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
1019 1528 5.633830 TGGATGCTCAGAAAAATGAAGAC 57.366 39.130 0.00 0.00 0.00 3.01
1494 2075 3.295093 TGAGGACTTGGATGAGCTAGAG 58.705 50.000 0.00 0.00 0.00 2.43
1881 2462 2.200067 CAGATGTTCAGCTCGCCTAAG 58.800 52.381 0.00 0.00 0.00 2.18
2035 2616 9.987272 TGTATAAACTGGAATCTGATATCTGTG 57.013 33.333 3.98 0.00 0.00 3.66
2196 2777 3.191371 GTCAGATGCTAAACCCAAGGTTG 59.809 47.826 0.00 0.00 46.20 3.77
2523 3107 2.040278 TGAGGTCCTCCACAAAATCTGG 59.960 50.000 16.60 0.00 35.89 3.86
2878 3645 2.167487 CTGTACAGGAGCCTTCTCTTCC 59.833 54.545 15.49 0.00 39.31 3.46
2948 3716 6.370453 AGATGATCACCATTTCATTCATCCA 58.630 36.000 0.00 0.00 40.03 3.41
3343 4127 0.667792 GACTGAGTGACGGCCTTCAC 60.668 60.000 29.94 29.94 45.45 3.18
3438 5336 3.277142 TCTGTCGGATGCTCACTAGTA 57.723 47.619 0.00 0.00 0.00 1.82
3471 5370 2.080286 ACTGTCGTGGTCTGTTATGC 57.920 50.000 0.00 0.00 0.00 3.14
3478 5377 2.413112 CGTGGTCTGTTATGCTGTTGAG 59.587 50.000 0.00 0.00 0.00 3.02
3497 5432 3.245371 TGAGACCCTGCTGAATTTCCAAT 60.245 43.478 0.00 0.00 0.00 3.16
3521 5456 5.923733 TTGTTATGTTGTTGAAACCCTGT 57.076 34.783 0.00 0.00 0.00 4.00
3528 5463 5.415221 TGTTGTTGAAACCCTGTTGAATTC 58.585 37.500 0.00 0.00 0.00 2.17
3532 5467 5.894393 TGTTGAAACCCTGTTGAATTCCTTA 59.106 36.000 2.27 0.00 0.00 2.69
3584 5521 4.646945 TGTTGTTGAAACCCTGCTGAATTA 59.353 37.500 0.00 0.00 0.00 1.40
3647 5673 9.884814 AGTATATTCTACTGTGAATTACTCCCT 57.115 33.333 9.58 0.00 37.73 4.20
3649 5675 5.934402 TTCTACTGTGAATTACTCCCTCC 57.066 43.478 0.00 0.00 0.00 4.30
3650 5676 3.952323 TCTACTGTGAATTACTCCCTCCG 59.048 47.826 0.00 0.00 0.00 4.63
3651 5677 2.537143 ACTGTGAATTACTCCCTCCGT 58.463 47.619 0.00 0.00 0.00 4.69
3652 5678 2.904434 ACTGTGAATTACTCCCTCCGTT 59.096 45.455 0.00 0.00 0.00 4.44
3653 5679 3.056035 ACTGTGAATTACTCCCTCCGTTC 60.056 47.826 0.00 0.00 0.00 3.95
3654 5680 2.235402 TGTGAATTACTCCCTCCGTTCC 59.765 50.000 0.00 0.00 0.00 3.62
3655 5681 2.500504 GTGAATTACTCCCTCCGTTCCT 59.499 50.000 0.00 0.00 0.00 3.36
3656 5682 3.703052 GTGAATTACTCCCTCCGTTCCTA 59.297 47.826 0.00 0.00 0.00 2.94
3657 5683 4.161001 GTGAATTACTCCCTCCGTTCCTAA 59.839 45.833 0.00 0.00 0.00 2.69
3658 5684 4.778958 TGAATTACTCCCTCCGTTCCTAAA 59.221 41.667 0.00 0.00 0.00 1.85
3659 5685 5.427481 TGAATTACTCCCTCCGTTCCTAAAT 59.573 40.000 0.00 0.00 0.00 1.40
3660 5686 6.612456 TGAATTACTCCCTCCGTTCCTAAATA 59.388 38.462 0.00 0.00 0.00 1.40
3661 5687 7.291651 TGAATTACTCCCTCCGTTCCTAAATAT 59.708 37.037 0.00 0.00 0.00 1.28
3662 5688 7.628501 ATTACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
3663 5689 5.548181 ACTCCCTCCGTTCCTAAATATTC 57.452 43.478 0.00 0.00 0.00 1.75
3664 5690 4.038883 ACTCCCTCCGTTCCTAAATATTCG 59.961 45.833 0.00 0.00 0.00 3.34
3665 5691 3.064931 CCCTCCGTTCCTAAATATTCGC 58.935 50.000 0.00 0.00 0.00 4.70
3666 5692 3.064931 CCTCCGTTCCTAAATATTCGCC 58.935 50.000 0.00 0.00 0.00 5.54
3667 5693 3.244112 CCTCCGTTCCTAAATATTCGCCT 60.244 47.826 0.00 0.00 0.00 5.52
3668 5694 4.377897 CTCCGTTCCTAAATATTCGCCTT 58.622 43.478 0.00 0.00 0.00 4.35
3669 5695 4.773013 TCCGTTCCTAAATATTCGCCTTT 58.227 39.130 0.00 0.00 0.00 3.11
3670 5696 5.187687 TCCGTTCCTAAATATTCGCCTTTT 58.812 37.500 0.00 0.00 0.00 2.27
3671 5697 5.648960 TCCGTTCCTAAATATTCGCCTTTTT 59.351 36.000 0.00 0.00 0.00 1.94
3672 5698 6.822676 TCCGTTCCTAAATATTCGCCTTTTTA 59.177 34.615 0.00 0.00 0.00 1.52
3673 5699 7.011669 TCCGTTCCTAAATATTCGCCTTTTTAG 59.988 37.037 0.00 0.00 33.47 1.85
3674 5700 7.011669 CCGTTCCTAAATATTCGCCTTTTTAGA 59.988 37.037 0.00 0.00 34.90 2.10
3675 5701 8.062448 CGTTCCTAAATATTCGCCTTTTTAGAG 58.938 37.037 0.00 0.00 34.90 2.43
3676 5702 9.106070 GTTCCTAAATATTCGCCTTTTTAGAGA 57.894 33.333 0.00 0.00 34.90 3.10
3677 5703 9.847224 TTCCTAAATATTCGCCTTTTTAGAGAT 57.153 29.630 0.00 0.00 34.90 2.75
3678 5704 9.847224 TCCTAAATATTCGCCTTTTTAGAGATT 57.153 29.630 0.00 0.00 34.90 2.40
3688 5714 9.620660 TCGCCTTTTTAGAGATTTTAAATGAAC 57.379 29.630 0.00 0.00 0.00 3.18
3689 5715 9.626045 CGCCTTTTTAGAGATTTTAAATGAACT 57.374 29.630 0.00 0.00 0.00 3.01
3747 5773 9.988350 AAGTGTATATTTACTCATTTTGCTTCG 57.012 29.630 0.00 0.00 0.00 3.79
3748 5774 9.162764 AGTGTATATTTACTCATTTTGCTTCGT 57.837 29.630 0.00 0.00 0.00 3.85
3755 5781 8.542497 TTTACTCATTTTGCTTCGTATGTAGT 57.458 30.769 0.00 0.00 0.00 2.73
3756 5782 6.648725 ACTCATTTTGCTTCGTATGTAGTC 57.351 37.500 0.00 0.00 0.00 2.59
3757 5783 6.163476 ACTCATTTTGCTTCGTATGTAGTCA 58.837 36.000 0.00 0.00 0.00 3.41
3758 5784 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
3759 5785 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
3760 5786 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
3761 5787 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
3762 5788 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
3763 5789 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
3764 5790 6.016213 TGCTTCGTATGTAGTCACTTGTTA 57.984 37.500 0.00 0.00 0.00 2.41
3765 5791 6.448852 TGCTTCGTATGTAGTCACTTGTTAA 58.551 36.000 0.00 0.00 0.00 2.01
3766 5792 6.924612 TGCTTCGTATGTAGTCACTTGTTAAA 59.075 34.615 0.00 0.00 0.00 1.52
3767 5793 7.438757 TGCTTCGTATGTAGTCACTTGTTAAAA 59.561 33.333 0.00 0.00 0.00 1.52
3768 5794 8.440833 GCTTCGTATGTAGTCACTTGTTAAAAT 58.559 33.333 0.00 0.00 0.00 1.82
3769 5795 9.953825 CTTCGTATGTAGTCACTTGTTAAAATC 57.046 33.333 0.00 0.00 0.00 2.17
3770 5796 9.701098 TTCGTATGTAGTCACTTGTTAAAATCT 57.299 29.630 0.00 0.00 0.00 2.40
3771 5797 9.350357 TCGTATGTAGTCACTTGTTAAAATCTC 57.650 33.333 0.00 0.00 0.00 2.75
3772 5798 9.355215 CGTATGTAGTCACTTGTTAAAATCTCT 57.645 33.333 0.00 0.00 0.00 3.10
3801 5827 9.768215 AAAGACAAATATTTAGGAATGAAGGGA 57.232 29.630 0.00 0.00 0.00 4.20
3802 5828 8.986929 AGACAAATATTTAGGAATGAAGGGAG 57.013 34.615 0.00 0.00 0.00 4.30
3803 5829 8.560903 AGACAAATATTTAGGAATGAAGGGAGT 58.439 33.333 0.00 0.00 0.00 3.85
3804 5830 9.847224 GACAAATATTTAGGAATGAAGGGAGTA 57.153 33.333 0.00 0.00 0.00 2.59
3926 5953 9.552114 GTACAACAATCATCATCTTCTTCTTTG 57.448 33.333 0.00 0.00 0.00 2.77
3927 5954 8.174733 ACAACAATCATCATCTTCTTCTTTGT 57.825 30.769 0.00 0.00 0.00 2.83
3928 5955 8.636213 ACAACAATCATCATCTTCTTCTTTGTT 58.364 29.630 0.00 0.00 35.74 2.83
3929 5956 9.472361 CAACAATCATCATCTTCTTCTTTGTTT 57.528 29.630 0.00 0.00 33.79 2.83
3957 6000 5.869888 TGTTTTTGCGAAAAGGTACAACAAT 59.130 32.000 12.25 0.00 35.53 2.71
3966 6009 3.695830 AGGTACAACAATCATGACGGT 57.304 42.857 0.00 0.00 0.00 4.83
3995 6038 8.315482 GGAGTTCTTGTAATCTCCTACTTTCTT 58.685 37.037 0.00 0.00 42.02 2.52
4000 6043 8.365647 TCTTGTAATCTCCTACTTTCTTCGTTT 58.634 33.333 0.00 0.00 0.00 3.60
4008 6051 9.550406 TCTCCTACTTTCTTCGTTTCAAAATAA 57.450 29.630 0.00 0.00 0.00 1.40
4009 6052 9.813080 CTCCTACTTTCTTCGTTTCAAAATAAG 57.187 33.333 0.00 0.00 0.00 1.73
4014 6057 8.674607 ACTTTCTTCGTTTCAAAATAAGTGTCT 58.325 29.630 0.00 0.00 0.00 3.41
4015 6058 9.159470 CTTTCTTCGTTTCAAAATAAGTGTCTC 57.841 33.333 0.00 0.00 0.00 3.36
4016 6059 7.780008 TCTTCGTTTCAAAATAAGTGTCTCA 57.220 32.000 0.00 0.00 0.00 3.27
4018 6061 8.120465 TCTTCGTTTCAAAATAAGTGTCTCAAC 58.880 33.333 0.00 0.00 0.00 3.18
4020 6063 7.981142 TCGTTTCAAAATAAGTGTCTCAACTT 58.019 30.769 0.00 0.00 42.89 2.66
4021 6064 8.455682 TCGTTTCAAAATAAGTGTCTCAACTTT 58.544 29.630 0.00 0.00 40.77 2.66
4093 6166 5.927281 AACGGAGGAAGTACTAATTAGCA 57.073 39.130 12.54 0.00 0.00 3.49
4137 6211 2.351738 GGAACACATAGCTGCACCAAAC 60.352 50.000 1.02 0.00 0.00 2.93
4184 6258 0.888285 GCAAGCTTCCAGCAGACAGT 60.888 55.000 0.00 0.00 45.56 3.55
4222 6296 4.493547 CCAAGCTGTCAAAACACAAAGAA 58.506 39.130 0.00 0.00 0.00 2.52
4234 6308 8.792633 TCAAAACACAAAGAAAGAGAGAGAAAA 58.207 29.630 0.00 0.00 0.00 2.29
4238 6329 8.286191 ACACAAAGAAAGAGAGAGAAAAATGT 57.714 30.769 0.00 0.00 0.00 2.71
4244 6335 8.472683 AGAAAGAGAGAGAAAAATGTATGTCG 57.527 34.615 0.00 0.00 0.00 4.35
4264 6361 1.021390 GCAAGCTGGTGTCGCTACAT 61.021 55.000 0.00 0.00 38.08 2.29
4283 6380 4.957971 ACATTCGTATTTCTGCAAGTTCG 58.042 39.130 0.00 0.00 33.76 3.95
4300 6397 5.435820 AGTTCGATATACTTCCTCCGTTC 57.564 43.478 0.00 0.00 0.00 3.95
4308 6405 7.309012 CGATATACTTCCTCCGTTCCTAAATGA 60.309 40.741 0.00 0.00 0.00 2.57
4309 6406 6.749036 ATACTTCCTCCGTTCCTAAATGAT 57.251 37.500 0.00 0.00 0.00 2.45
4310 6407 7.850935 ATACTTCCTCCGTTCCTAAATGATA 57.149 36.000 0.00 0.00 0.00 2.15
4311 6408 6.749036 ACTTCCTCCGTTCCTAAATGATAT 57.251 37.500 0.00 0.00 0.00 1.63
4312 6409 6.525629 ACTTCCTCCGTTCCTAAATGATATG 58.474 40.000 0.00 0.00 0.00 1.78
4313 6410 6.326583 ACTTCCTCCGTTCCTAAATGATATGA 59.673 38.462 0.00 0.00 0.00 2.15
4314 6411 6.346477 TCCTCCGTTCCTAAATGATATGAG 57.654 41.667 0.00 0.00 0.00 2.90
4315 6412 5.839063 TCCTCCGTTCCTAAATGATATGAGT 59.161 40.000 0.00 0.00 0.00 3.41
4316 6413 6.326583 TCCTCCGTTCCTAAATGATATGAGTT 59.673 38.462 0.00 0.00 0.00 3.01
4317 6414 7.507956 TCCTCCGTTCCTAAATGATATGAGTTA 59.492 37.037 0.00 0.00 0.00 2.24
4318 6415 8.314751 CCTCCGTTCCTAAATGATATGAGTTAT 58.685 37.037 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1019 1528 2.679336 TCATCATGTTCATGCTTCCGTG 59.321 45.455 7.80 1.67 0.00 4.94
1494 2075 0.179215 CCACGCGAGAAAGCATTGAC 60.179 55.000 15.93 0.00 36.85 3.18
2035 2616 3.433615 GCTTCATACAAGATACCCATCGC 59.566 47.826 0.00 0.00 36.20 4.58
2196 2777 4.425577 CTGGAATCCAGCTGTGTAAAAC 57.574 45.455 17.25 0.00 45.13 2.43
2486 3069 3.177228 ACCTCAGACACTATTCCAGCTT 58.823 45.455 0.00 0.00 0.00 3.74
2878 3645 7.010460 GGTTTGAAAGTTGAAGTGAAAATGGAG 59.990 37.037 0.00 0.00 0.00 3.86
3093 3871 2.289444 CCAGTCGATGTTGTACCTGGTT 60.289 50.000 3.84 0.00 0.00 3.67
3228 4006 3.071206 GAGGAGCCGTGCAGGAGA 61.071 66.667 8.24 0.00 45.00 3.71
3438 5336 0.977395 GACAGTACCAAGGGAGTGCT 59.023 55.000 6.06 0.00 0.00 4.40
3471 5370 2.486472 ATTCAGCAGGGTCTCAACAG 57.514 50.000 0.00 0.00 0.00 3.16
3478 5377 4.541973 AAATTGGAAATTCAGCAGGGTC 57.458 40.909 0.00 0.00 0.00 4.46
3497 5432 6.702329 ACAGGGTTTCAACAACATAACAAAA 58.298 32.000 0.00 0.00 0.00 2.44
3521 5456 4.766891 CCAGCAGGAGTTTAAGGAATTCAA 59.233 41.667 7.93 0.00 36.89 2.69
3642 5668 4.557205 CGAATATTTAGGAACGGAGGGAG 58.443 47.826 0.00 0.00 0.00 4.30
3643 5669 3.243975 GCGAATATTTAGGAACGGAGGGA 60.244 47.826 0.00 0.00 0.00 4.20
3644 5670 3.064931 GCGAATATTTAGGAACGGAGGG 58.935 50.000 0.00 0.00 0.00 4.30
3645 5671 3.064931 GGCGAATATTTAGGAACGGAGG 58.935 50.000 0.00 0.00 0.00 4.30
3646 5672 3.991367 AGGCGAATATTTAGGAACGGAG 58.009 45.455 0.00 0.00 0.00 4.63
3647 5673 4.411256 AAGGCGAATATTTAGGAACGGA 57.589 40.909 0.00 0.00 0.00 4.69
3648 5674 5.494632 AAAAGGCGAATATTTAGGAACGG 57.505 39.130 0.00 0.00 0.00 4.44
3649 5675 7.912383 TCTAAAAAGGCGAATATTTAGGAACG 58.088 34.615 0.00 0.00 36.48 3.95
3650 5676 9.106070 TCTCTAAAAAGGCGAATATTTAGGAAC 57.894 33.333 0.00 0.00 36.48 3.62
3651 5677 9.847224 ATCTCTAAAAAGGCGAATATTTAGGAA 57.153 29.630 0.00 0.00 36.48 3.36
3652 5678 9.847224 AATCTCTAAAAAGGCGAATATTTAGGA 57.153 29.630 0.00 0.00 36.48 2.94
3662 5688 9.620660 GTTCATTTAAAATCTCTAAAAAGGCGA 57.379 29.630 0.00 0.00 0.00 5.54
3663 5689 9.626045 AGTTCATTTAAAATCTCTAAAAAGGCG 57.374 29.630 0.00 0.00 0.00 5.52
3721 5747 9.988350 CGAAGCAAAATGAGTAAATATACACTT 57.012 29.630 0.00 0.00 34.29 3.16
3722 5748 9.162764 ACGAAGCAAAATGAGTAAATATACACT 57.837 29.630 0.00 0.00 34.29 3.55
3729 5755 9.162764 ACTACATACGAAGCAAAATGAGTAAAT 57.837 29.630 0.00 0.00 0.00 1.40
3730 5756 8.542497 ACTACATACGAAGCAAAATGAGTAAA 57.458 30.769 0.00 0.00 0.00 2.01
3731 5757 7.815549 TGACTACATACGAAGCAAAATGAGTAA 59.184 33.333 0.00 0.00 0.00 2.24
3732 5758 7.274904 GTGACTACATACGAAGCAAAATGAGTA 59.725 37.037 0.00 0.00 0.00 2.59
3733 5759 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
3734 5760 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
3735 5761 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
3736 5762 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
3737 5763 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
3738 5764 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
3739 5765 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
3740 5766 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
3741 5767 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
3742 5768 6.939551 TTAACAAGTGACTACATACGAAGC 57.060 37.500 0.00 0.00 0.00 3.86
3743 5769 9.953825 GATTTTAACAAGTGACTACATACGAAG 57.046 33.333 0.00 0.00 0.00 3.79
3744 5770 9.701098 AGATTTTAACAAGTGACTACATACGAA 57.299 29.630 0.00 0.00 0.00 3.85
3745 5771 9.350357 GAGATTTTAACAAGTGACTACATACGA 57.650 33.333 0.00 0.00 0.00 3.43
3746 5772 9.355215 AGAGATTTTAACAAGTGACTACATACG 57.645 33.333 0.00 0.00 0.00 3.06
3775 5801 9.768215 TCCCTTCATTCCTAAATATTTGTCTTT 57.232 29.630 11.05 0.00 0.00 2.52
3776 5802 9.413734 CTCCCTTCATTCCTAAATATTTGTCTT 57.586 33.333 11.05 0.00 0.00 3.01
3777 5803 8.560903 ACTCCCTTCATTCCTAAATATTTGTCT 58.439 33.333 11.05 0.00 0.00 3.41
3778 5804 8.753497 ACTCCCTTCATTCCTAAATATTTGTC 57.247 34.615 11.05 0.00 0.00 3.18
3789 5815 9.634021 GAAGATAAAATTACTCCCTTCATTCCT 57.366 33.333 0.00 0.00 31.59 3.36
3790 5816 9.408648 TGAAGATAAAATTACTCCCTTCATTCC 57.591 33.333 0.00 0.00 35.18 3.01
3794 5820 9.581289 TGTTTGAAGATAAAATTACTCCCTTCA 57.419 29.630 0.00 0.00 37.38 3.02
3796 5822 8.523658 GCTGTTTGAAGATAAAATTACTCCCTT 58.476 33.333 0.00 0.00 0.00 3.95
3797 5823 7.669722 TGCTGTTTGAAGATAAAATTACTCCCT 59.330 33.333 0.00 0.00 0.00 4.20
3798 5824 7.826690 TGCTGTTTGAAGATAAAATTACTCCC 58.173 34.615 0.00 0.00 0.00 4.30
3799 5825 9.294030 CATGCTGTTTGAAGATAAAATTACTCC 57.706 33.333 0.00 0.00 0.00 3.85
3800 5826 9.846248 ACATGCTGTTTGAAGATAAAATTACTC 57.154 29.630 0.00 0.00 0.00 2.59
3801 5827 9.846248 GACATGCTGTTTGAAGATAAAATTACT 57.154 29.630 0.00 0.00 0.00 2.24
3802 5828 8.788813 CGACATGCTGTTTGAAGATAAAATTAC 58.211 33.333 0.00 0.00 0.00 1.89
3803 5829 8.511321 ACGACATGCTGTTTGAAGATAAAATTA 58.489 29.630 0.00 0.00 0.00 1.40
3804 5830 7.326789 CACGACATGCTGTTTGAAGATAAAATT 59.673 33.333 0.00 0.00 0.00 1.82
3805 5831 6.803320 CACGACATGCTGTTTGAAGATAAAAT 59.197 34.615 0.00 0.00 0.00 1.82
3817 5843 2.009774 GCTAATCCACGACATGCTGTT 58.990 47.619 0.00 0.00 0.00 3.16
3926 5953 5.444983 ACCTTTTCGCAAAAACACAAAAAC 58.555 33.333 0.00 0.00 31.23 2.43
3927 5954 5.674933 ACCTTTTCGCAAAAACACAAAAA 57.325 30.435 0.00 0.00 31.23 1.94
3928 5955 5.694910 TGTACCTTTTCGCAAAAACACAAAA 59.305 32.000 0.00 0.00 31.23 2.44
3929 5956 5.227908 TGTACCTTTTCGCAAAAACACAAA 58.772 33.333 0.00 0.00 31.23 2.83
3930 5957 4.806330 TGTACCTTTTCGCAAAAACACAA 58.194 34.783 0.00 0.00 31.23 3.33
3931 5958 4.436242 TGTACCTTTTCGCAAAAACACA 57.564 36.364 0.00 0.00 31.23 3.72
3932 5959 4.621886 TGTTGTACCTTTTCGCAAAAACAC 59.378 37.500 0.00 0.00 31.23 3.32
3957 6000 3.576982 ACAAGAACTCCTTACCGTCATGA 59.423 43.478 0.00 0.00 32.86 3.07
3991 6034 8.203937 TGAGACACTTATTTTGAAACGAAGAA 57.796 30.769 5.32 0.00 0.00 2.52
3992 6035 7.780008 TGAGACACTTATTTTGAAACGAAGA 57.220 32.000 5.32 0.00 0.00 2.87
3995 6038 7.548196 AGTTGAGACACTTATTTTGAAACGA 57.452 32.000 0.00 0.00 0.00 3.85
4056 6099 9.074576 ACTTCCTCCGTTTTAAAATAAATGTCT 57.925 29.630 3.52 0.00 0.00 3.41
4069 6142 6.704310 TGCTAATTAGTACTTCCTCCGTTTT 58.296 36.000 13.91 0.00 0.00 2.43
4070 6143 6.290294 TGCTAATTAGTACTTCCTCCGTTT 57.710 37.500 13.91 0.00 0.00 3.60
4071 6144 5.927281 TGCTAATTAGTACTTCCTCCGTT 57.073 39.130 13.91 0.00 0.00 4.44
4079 6152 8.630054 TGTGATTGGTTTGCTAATTAGTACTT 57.370 30.769 13.91 0.00 0.00 2.24
4093 6166 9.790344 TTCCATATTGAAAATTGTGATTGGTTT 57.210 25.926 0.00 0.00 0.00 3.27
4137 6211 0.395862 TCTAAGCGAGAGGGGACAGG 60.396 60.000 0.00 0.00 0.00 4.00
4184 6258 2.675075 GGCCGCCCTTTGTTGCTA 60.675 61.111 0.00 0.00 0.00 3.49
4222 6296 5.582665 GCCGACATACATTTTTCTCTCTCTT 59.417 40.000 0.00 0.00 0.00 2.85
4234 6308 1.340017 ACCAGCTTGCCGACATACATT 60.340 47.619 0.00 0.00 0.00 2.71
4238 6329 0.391130 GACACCAGCTTGCCGACATA 60.391 55.000 0.00 0.00 0.00 2.29
4244 6335 2.047274 TAGCGACACCAGCTTGCC 60.047 61.111 0.00 0.00 43.24 4.52
4264 6361 7.919091 AGTATATCGAACTTGCAGAAATACGAA 59.081 33.333 0.00 0.00 32.69 3.85
4283 6380 7.893658 TCATTTAGGAACGGAGGAAGTATATC 58.106 38.462 0.00 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.