Multiple sequence alignment - TraesCS7A01G303100

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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 TraesCS7A01G303100 chr7A 100.000 6727 0 0 2842 9568 425780116 425773390 0.000000e+00 12423.0
1 TraesCS7A01G303100 chr7A 100.000 2489 0 0 1 2489 425782957 425780469 0.000000e+00 4597.0
2 TraesCS7A01G303100 chr7A 96.660 958 25 5 1537 2489 475966971 475967926 0.000000e+00 1585.0
3 TraesCS7A01G303100 chr7A 95.337 965 36 5 1530 2489 217226636 217227596 0.000000e+00 1524.0
4 TraesCS7A01G303100 chr7A 94.387 962 37 9 1538 2489 727763107 727764061 0.000000e+00 1461.0
5 TraesCS7A01G303100 chr7A 84.427 1021 77 29 1536 2489 5348561 5349566 0.000000e+00 929.0
6 TraesCS7A01G303100 chr7A 96.203 237 7 2 2842 3078 217227726 217227960 4.190000e-103 387.0
7 TraesCS7A01G303100 chr7A 96.170 235 5 4 2842 3072 475968056 475968290 1.950000e-101 381.0
8 TraesCS7A01G303100 chr7A 96.943 229 4 3 2842 3070 727764422 727764647 1.950000e-101 381.0
9 TraesCS7A01G303100 chr7A 94.595 222 6 4 1531 1751 217227961 217227745 1.190000e-88 339.0
10 TraesCS7A01G303100 chr7A 83.983 231 35 2 5210 5439 425790332 425790103 4.500000e-53 220.0
11 TraesCS7A01G303100 chr7A 94.286 105 3 3 588 691 204607944 204608046 3.580000e-34 158.0
12 TraesCS7A01G303100 chr7A 93.396 106 2 2 573 678 689269388 689269288 1.660000e-32 152.0
13 TraesCS7A01G303100 chr7A 83.516 91 13 2 6463 6552 603354839 603354928 6.160000e-12 84.2
14 TraesCS7A01G303100 chr7B 97.941 6509 116 10 3073 9568 372826061 372819558 0.000000e+00 11261.0
15 TraesCS7A01G303100 chr7B 97.578 867 17 3 675 1538 372826918 372826053 0.000000e+00 1482.0
16 TraesCS7A01G303100 chr7B 97.143 595 15 1 1 595 372827507 372826915 0.000000e+00 1003.0
17 TraesCS7A01G303100 chr7B 82.684 231 38 2 5210 5439 372832066 372831837 4.530000e-48 204.0
18 TraesCS7A01G303100 chr7B 96.000 100 3 1 592 691 719465203 719465301 2.770000e-35 161.0
19 TraesCS7A01G303100 chr7D 98.252 6293 92 11 3146 9424 378162116 378155828 0.000000e+00 10996.0
20 TraesCS7A01G303100 chr7D 97.575 866 19 1 675 1538 378162978 378162113 0.000000e+00 1482.0
21 TraesCS7A01G303100 chr7D 95.630 595 18 1 1 595 378163561 378162975 0.000000e+00 948.0
22 TraesCS7A01G303100 chr7D 93.778 225 12 2 2860 3082 240775984 240776208 4.280000e-88 337.0
23 TraesCS7A01G303100 chr7D 83.550 231 36 2 5210 5439 378173273 378173044 2.090000e-51 215.0
24 TraesCS7A01G303100 chr7D 95.192 104 5 0 9465 9568 378155830 378155727 2.140000e-36 165.0
25 TraesCS7A01G303100 chr6B 78.631 2747 477 67 5901 8568 183286651 183289366 0.000000e+00 1720.0
26 TraesCS7A01G303100 chr6B 81.384 607 87 14 4034 4638 183284275 183284857 1.120000e-128 472.0
27 TraesCS7A01G303100 chr6B 84.971 346 49 2 4659 5001 183284918 183285263 1.980000e-91 348.0
28 TraesCS7A01G303100 chr6B 84.472 322 38 11 5211 5524 183286250 183286567 3.360000e-79 307.0
29 TraesCS7A01G303100 chr6B 83.509 285 40 5 3681 3958 183283886 183284170 9.530000e-65 259.0
30 TraesCS7A01G303100 chr6B 95.050 101 3 2 583 682 42774564 42774663 3.580000e-34 158.0
31 TraesCS7A01G303100 chr2A 96.771 960 22 6 1537 2489 724516588 724517545 0.000000e+00 1592.0
32 TraesCS7A01G303100 chr2A 97.021 235 3 2 2842 3072 724517674 724517908 9.010000e-105 392.0
33 TraesCS7A01G303100 chr2A 93.361 241 10 4 2842 3076 659204699 659204459 1.530000e-92 351.0
34 TraesCS7A01G303100 chr2A 93.671 158 9 1 2333 2489 659204990 659204833 1.610000e-57 235.0
35 TraesCS7A01G303100 chr2A 96.000 50 2 0 2288 2337 659205056 659205007 2.210000e-11 82.4
36 TraesCS7A01G303100 chr6A 78.090 2063 393 34 6550 8568 117070372 117072419 0.000000e+00 1251.0
37 TraesCS7A01G303100 chr6A 86.560 439 57 1 6000 6438 117069839 117070275 5.200000e-132 483.0
38 TraesCS7A01G303100 chr6A 81.339 493 65 15 4020 4510 117061524 117061991 9.070000e-100 375.0
39 TraesCS7A01G303100 chr6A 85.260 346 48 2 4659 5001 117062468 117062813 4.250000e-93 353.0
40 TraesCS7A01G303100 chr6A 85.609 271 30 8 5225 5490 117069378 117069644 9.470000e-70 276.0
41 TraesCS7A01G303100 chr6A 94.231 104 2 4 588 688 204478642 204478540 1.290000e-33 156.0
42 TraesCS7A01G303100 chr6A 92.661 109 4 4 590 694 563127998 563127890 4.630000e-33 154.0
43 TraesCS7A01G303100 chr1D 86.382 1006 64 17 1537 2488 486448830 486449816 0.000000e+00 1031.0
44 TraesCS7A01G303100 chr6D 77.900 1543 317 21 7048 8569 98039307 98040846 0.000000e+00 939.0
45 TraesCS7A01G303100 chr6D 87.811 402 47 1 6000 6401 98038256 98038655 4.050000e-128 470.0
46 TraesCS7A01G303100 chr6D 80.998 621 91 15 4020 4638 98035813 98036408 1.450000e-127 468.0
47 TraesCS7A01G303100 chr6D 85.260 346 48 2 4659 5001 98036469 98036814 4.250000e-93 353.0
48 TraesCS7A01G303100 chr6D 85.034 294 33 10 5210 5496 98037783 98038072 1.220000e-73 289.0
49 TraesCS7A01G303100 chr1A 92.746 579 22 11 1522 2089 10500764 10501333 0.000000e+00 819.0
50 TraesCS7A01G303100 chr5D 88.679 583 51 7 1538 2120 391159441 391158874 0.000000e+00 697.0
51 TraesCS7A01G303100 chr5D 94.977 219 9 2 2861 3077 386727947 386727729 9.200000e-90 342.0
52 TraesCS7A01G303100 chr5D 90.435 115 10 1 568 681 322375722 322375836 5.990000e-32 150.0
53 TraesCS7A01G303100 chr5D 93.023 86 6 0 2403 2488 391158705 391158620 1.010000e-24 126.0
54 TraesCS7A01G303100 chr5B 91.315 426 28 6 1541 1966 646379971 646379555 3.000000e-159 573.0
55 TraesCS7A01G303100 chr5B 88.889 99 11 0 2343 2441 646379412 646379314 1.300000e-23 122.0
56 TraesCS7A01G303100 chr3B 85.955 356 40 3 1765 2119 699575649 699575303 1.170000e-98 372.0
57 TraesCS7A01G303100 chr3B 93.644 236 11 3 2842 3073 699575040 699574805 5.500000e-92 350.0
58 TraesCS7A01G303100 chr3B 95.833 216 7 2 2861 3074 699575875 699576090 1.980000e-91 348.0
59 TraesCS7A01G303100 chr3B 92.241 116 8 1 2357 2472 699575312 699575198 7.690000e-36 163.0
60 TraesCS7A01G303100 chr1B 96.939 98 2 1 582 679 172000868 172000772 7.690000e-36 163.0
61 TraesCS7A01G303100 chr2D 94.231 104 4 2 586 687 650861486 650861383 3.580000e-34 158.0


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 TraesCS7A01G303100 chr7A 425773390 425782957 9567 True 8510.00 12423 100.000000 1 9568 2 chr7A.!!$R4 9567
1 TraesCS7A01G303100 chr7A 475966971 475968290 1319 False 983.00 1585 96.415000 1537 3072 2 chr7A.!!$F5 1535
2 TraesCS7A01G303100 chr7A 217226636 217227960 1324 False 955.50 1524 95.770000 1530 3078 2 chr7A.!!$F4 1548
3 TraesCS7A01G303100 chr7A 5348561 5349566 1005 False 929.00 929 84.427000 1536 2489 1 chr7A.!!$F1 953
4 TraesCS7A01G303100 chr7A 727763107 727764647 1540 False 921.00 1461 95.665000 1538 3070 2 chr7A.!!$F6 1532
5 TraesCS7A01G303100 chr7B 372819558 372827507 7949 True 4582.00 11261 97.554000 1 9568 3 chr7B.!!$R2 9567
6 TraesCS7A01G303100 chr7D 378155727 378163561 7834 True 3397.75 10996 96.662250 1 9568 4 chr7D.!!$R2 9567
7 TraesCS7A01G303100 chr6B 183283886 183289366 5480 False 621.20 1720 82.593400 3681 8568 5 chr6B.!!$F2 4887
8 TraesCS7A01G303100 chr2A 724516588 724517908 1320 False 992.00 1592 96.896000 1537 3072 2 chr2A.!!$F1 1535
9 TraesCS7A01G303100 chr2A 659204459 659205056 597 True 222.80 351 94.344000 2288 3076 3 chr2A.!!$R1 788
10 TraesCS7A01G303100 chr6A 117069378 117072419 3041 False 670.00 1251 83.419667 5225 8568 3 chr6A.!!$F2 3343
11 TraesCS7A01G303100 chr6A 117061524 117062813 1289 False 364.00 375 83.299500 4020 5001 2 chr6A.!!$F1 981
12 TraesCS7A01G303100 chr1D 486448830 486449816 986 False 1031.00 1031 86.382000 1537 2488 1 chr1D.!!$F1 951
13 TraesCS7A01G303100 chr6D 98035813 98040846 5033 False 503.80 939 83.400600 4020 8569 5 chr6D.!!$F1 4549
14 TraesCS7A01G303100 chr1A 10500764 10501333 569 False 819.00 819 92.746000 1522 2089 1 chr1A.!!$F1 567
15 TraesCS7A01G303100 chr5D 391158620 391159441 821 True 411.50 697 90.851000 1538 2488 2 chr5D.!!$R2 950
16 TraesCS7A01G303100 chr5B 646379314 646379971 657 True 347.50 573 90.102000 1541 2441 2 chr5B.!!$R1 900
17 TraesCS7A01G303100 chr3B 699574805 699575649 844 True 295.00 372 90.613333 1765 3073 3 chr3B.!!$R1 1308

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
796 797 1.559219 TCATGCCAGCAGCCTAGTTTA 59.441 47.619 0.00 0.00 42.71 2.01 F
1697 1716 2.026915 TGCTGATGTGGCACTAGTCAAT 60.027 45.455 19.83 2.01 34.56 2.57 F
2939 3077 0.392060 CTAGTGCCACATCAGCAGCA 60.392 55.000 0.00 0.00 41.87 4.41 F
3293 3434 0.940126 CCTGACGGCATACATTCAGC 59.060 55.000 0.00 0.00 35.18 4.26 F
4149 4330 1.112113 GGTAGTTCCGATGCTCCTCA 58.888 55.000 0.00 0.00 0.00 3.86 F
4391 4573 2.045561 TTGTTGGAGAAAACTCGGCA 57.954 45.000 0.00 0.00 0.00 5.69 F
4966 5479 2.106338 TGGGAAGAGCACTGTGATTTCA 59.894 45.455 12.86 3.58 0.00 2.69 F
4967 5480 3.149196 GGGAAGAGCACTGTGATTTCAA 58.851 45.455 12.86 0.00 0.00 2.69 F
5657 6959 5.163622 CGTTACTCCCTCCGTTTGACTATTA 60.164 44.000 0.00 0.00 0.00 0.98 F
5902 7204 5.533528 ACCACCAAATTACTTAGGACAACAC 59.466 40.000 0.00 0.00 0.00 3.32 F
6188 7492 5.843019 TGAAAGGGAGGACTGTTATCTTT 57.157 39.130 0.00 0.00 0.00 2.52 F
7823 9197 6.231211 AGGTAATGTTGAGTTCGAAGATGTT 58.769 36.000 0.00 0.00 35.04 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1777 1.005394 GTCGCCTTCGGTTGGAGAA 60.005 57.895 0.00 0.00 35.30 2.87 R
3483 3625 0.037590 CCCCGATCCACACTTTTCCA 59.962 55.000 0.00 0.00 0.00 3.53 R
4627 5097 6.694844 CGACATCACATGGTATATGCTAGATC 59.305 42.308 0.00 0.00 33.60 2.75 R
5059 5574 5.335949 CGTGAACATAATCGAACACAACAAC 59.664 40.000 0.00 0.00 0.00 3.32 R
5902 7204 4.083908 GCTATGTTTGGTGCAACAAATTGG 60.084 41.667 31.08 22.84 41.80 3.16 R
6188 7492 3.760738 TGTTGACATTCTGTGGGCAATA 58.239 40.909 0.00 0.00 31.80 1.90 R
6448 7754 5.651172 TGTATGGCATCGAATAGTTTTCG 57.349 39.130 1.65 9.16 42.74 3.46 R
6986 8324 1.666189 GCGAGATACCTGAAAACAGGC 59.334 52.381 15.02 1.07 46.05 4.85 R
7514 8879 1.046472 TCCCCTGTACCGCACCATAG 61.046 60.000 0.00 0.00 0.00 2.23 R
7823 9197 3.884091 GTCTCGAGGGATAGCTGAAACTA 59.116 47.826 13.56 0.00 0.00 2.24 R
8198 9572 1.346479 TTCCTTTGTCCCCGACCACA 61.346 55.000 0.00 0.00 0.00 4.17 R
8824 10209 2.489329 CTCCATTGCACGTTGAAGGATT 59.511 45.455 0.00 0.00 0.00 3.01 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
105 106 5.361857 AGCAGAAACTACCGCCTATTACTAA 59.638 40.000 0.00 0.00 0.00 2.24
110 111 7.763071 AGAAACTACCGCCTATTACTAAAACTG 59.237 37.037 0.00 0.00 0.00 3.16
240 241 9.740239 CAAGGTATCCATCATTTTGATTTACTG 57.260 33.333 0.00 0.00 34.28 2.74
249 250 7.214467 TCATTTTGATTTACTGGACAACTCC 57.786 36.000 0.00 0.00 37.04 3.85
255 256 6.356556 TGATTTACTGGACAACTCCATATGG 58.643 40.000 16.25 16.25 46.18 2.74
308 309 7.821846 ACAGAAACTGGAAAAATGTTTTAGCAA 59.178 29.630 0.00 0.00 35.51 3.91
384 385 4.023291 AGGAAACAAGAAACCTGCAAAGA 58.977 39.130 0.00 0.00 0.00 2.52
400 401 7.123247 ACCTGCAAAGAAATATCAAAGTATGCT 59.877 33.333 0.00 0.00 0.00 3.79
405 406 9.875675 CAAAGAAATATCAAAGTATGCTAGAGC 57.124 33.333 0.00 0.00 42.50 4.09
595 596 9.121517 CAACAACAAAAGATTCATGCTTAGTAG 57.878 33.333 0.00 0.00 0.00 2.57
596 597 8.396272 ACAACAAAAGATTCATGCTTAGTAGT 57.604 30.769 0.00 0.00 0.00 2.73
597 598 8.507249 ACAACAAAAGATTCATGCTTAGTAGTC 58.493 33.333 0.00 0.00 0.00 2.59
598 599 7.617041 ACAAAAGATTCATGCTTAGTAGTCC 57.383 36.000 0.00 0.00 0.00 3.85
599 600 6.599638 ACAAAAGATTCATGCTTAGTAGTCCC 59.400 38.462 0.00 0.00 0.00 4.46
600 601 6.567602 AAAGATTCATGCTTAGTAGTCCCT 57.432 37.500 0.00 0.00 0.00 4.20
601 602 5.799827 AGATTCATGCTTAGTAGTCCCTC 57.200 43.478 0.00 0.00 0.00 4.30
602 603 5.463154 AGATTCATGCTTAGTAGTCCCTCT 58.537 41.667 0.00 0.00 0.00 3.69
603 604 5.304101 AGATTCATGCTTAGTAGTCCCTCTG 59.696 44.000 0.00 0.00 0.00 3.35
604 605 3.982516 TCATGCTTAGTAGTCCCTCTGT 58.017 45.455 0.00 0.00 0.00 3.41
605 606 5.125367 TCATGCTTAGTAGTCCCTCTGTA 57.875 43.478 0.00 0.00 0.00 2.74
606 607 5.516044 TCATGCTTAGTAGTCCCTCTGTAA 58.484 41.667 0.00 0.00 0.00 2.41
607 608 5.955959 TCATGCTTAGTAGTCCCTCTGTAAA 59.044 40.000 0.00 0.00 0.00 2.01
608 609 5.656213 TGCTTAGTAGTCCCTCTGTAAAC 57.344 43.478 0.00 0.00 0.00 2.01
609 610 5.331069 TGCTTAGTAGTCCCTCTGTAAACT 58.669 41.667 0.00 0.00 0.00 2.66
610 611 6.487828 TGCTTAGTAGTCCCTCTGTAAACTA 58.512 40.000 0.00 0.00 0.00 2.24
611 612 6.950041 TGCTTAGTAGTCCCTCTGTAAACTAA 59.050 38.462 0.00 0.00 0.00 2.24
612 613 7.618512 TGCTTAGTAGTCCCTCTGTAAACTAAT 59.381 37.037 0.00 0.00 29.05 1.73
613 614 9.129532 GCTTAGTAGTCCCTCTGTAAACTAATA 57.870 37.037 0.00 0.00 29.05 0.98
620 621 8.862085 AGTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
621 622 7.808856 GTCCCTCTGTAAACTAATATAAGAGCG 59.191 40.741 0.00 0.00 0.00 5.03
622 623 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
623 624 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
624 625 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
669 670 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
670 671 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
671 672 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
672 673 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
673 674 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
674 675 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
675 676 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
676 677 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
677 678 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
715 716 8.143193 TGTGACATCAAGCAAATAATTGAGTTT 58.857 29.630 0.00 0.00 38.72 2.66
719 720 7.599998 ACATCAAGCAAATAATTGAGTTTCACC 59.400 33.333 0.00 0.00 38.72 4.02
726 727 1.892209 ATTGAGTTTCACCCGTCACC 58.108 50.000 0.00 0.00 0.00 4.02
787 788 1.746470 TGATCTGTTCATGCCAGCAG 58.254 50.000 0.00 0.57 0.00 4.24
796 797 1.559219 TCATGCCAGCAGCCTAGTTTA 59.441 47.619 0.00 0.00 42.71 2.01
951 952 7.124298 ACTCCTGTTACTCTACATATTTGCTCA 59.876 37.037 0.00 0.00 0.00 4.26
1324 1325 6.364568 TTTCTAAGGTTACCTTCTACCCAC 57.635 41.667 21.00 0.00 43.57 4.61
1581 1584 4.766891 CCCTGAATAAAGTGTGTGGTTCAT 59.233 41.667 0.00 0.00 0.00 2.57
1697 1716 2.026915 TGCTGATGTGGCACTAGTCAAT 60.027 45.455 19.83 2.01 34.56 2.57
2180 2237 2.031012 CGCTGCTGTTGACTCCCA 59.969 61.111 0.00 0.00 0.00 4.37
2939 3077 0.392060 CTAGTGCCACATCAGCAGCA 60.392 55.000 0.00 0.00 41.87 4.41
3036 3176 2.136863 TCAGGGGGTAAAGTGAACCAA 58.863 47.619 0.00 0.00 38.87 3.67
3062 3202 8.387813 ACCACTTTATTCAGGGTAGTAAAATGA 58.612 33.333 0.00 0.00 0.00 2.57
3204 3344 9.474249 CTAAAGTAGTATTTAAAAAGCACGAGC 57.526 33.333 0.00 0.00 42.56 5.03
3247 3388 4.908601 TTTCAAGTATTCAGGCTGGAGA 57.091 40.909 15.73 0.00 0.00 3.71
3280 3421 3.650139 ACAGCACTAGTAAAACCTGACG 58.350 45.455 0.00 0.00 0.00 4.35
3293 3434 0.940126 CCTGACGGCATACATTCAGC 59.060 55.000 0.00 0.00 35.18 4.26
3347 3489 3.211865 AGCTGCATACAATCATGGTCAG 58.788 45.455 1.02 0.00 0.00 3.51
3401 3543 3.064900 ACCTTCTGCCTGACATTCTTC 57.935 47.619 0.00 0.00 0.00 2.87
3483 3625 3.299503 AGTGAATTTGGGTTGAGCTTGT 58.700 40.909 0.00 0.00 0.00 3.16
3510 3652 1.526917 GTGGATCGGGGGCTCATTG 60.527 63.158 0.00 0.00 0.00 2.82
3546 3688 6.884280 AGTTACAAAGAGAATGGTTCAAGG 57.116 37.500 0.00 0.00 0.00 3.61
3566 3708 8.281212 TCAAGGTGGCTAGAATTTTATCTTTC 57.719 34.615 0.00 0.00 0.00 2.62
3666 3808 4.141251 ACCAGTCCTCATTTGGTTACTTGT 60.141 41.667 0.00 0.00 42.36 3.16
3690 3832 7.039011 TGTCCTCATGTACAGTAACAAGAGAAT 60.039 37.037 9.99 0.00 44.21 2.40
3730 3872 8.316946 AGCACTAGCAATATGAATAGCATTAGA 58.683 33.333 0.00 0.00 45.49 2.10
3985 4162 5.113502 GTTTCAGCAAGTGAAGCACTAAT 57.886 39.130 0.00 0.00 44.62 1.73
4149 4330 1.112113 GGTAGTTCCGATGCTCCTCA 58.888 55.000 0.00 0.00 0.00 3.86
4391 4573 2.045561 TTGTTGGAGAAAACTCGGCA 57.954 45.000 0.00 0.00 0.00 5.69
4966 5479 2.106338 TGGGAAGAGCACTGTGATTTCA 59.894 45.455 12.86 3.58 0.00 2.69
4967 5480 3.149196 GGGAAGAGCACTGTGATTTCAA 58.851 45.455 12.86 0.00 0.00 2.69
5452 6745 6.866770 TCGACTGAGGTAAGACTTTATGTTTG 59.133 38.462 0.00 0.00 0.00 2.93
5657 6959 5.163622 CGTTACTCCCTCCGTTTGACTATTA 60.164 44.000 0.00 0.00 0.00 0.98
5743 7045 5.826601 TGTTGCAATGTTTTCACTCTGTA 57.173 34.783 0.59 0.00 0.00 2.74
5902 7204 5.533528 ACCACCAAATTACTTAGGACAACAC 59.466 40.000 0.00 0.00 0.00 3.32
6188 7492 5.843019 TGAAAGGGAGGACTGTTATCTTT 57.157 39.130 0.00 0.00 0.00 2.52
6448 7754 8.503196 TCGCATTGTATATGTGGAATTATGAAC 58.497 33.333 0.00 0.00 0.00 3.18
7823 9197 6.231211 AGGTAATGTTGAGTTCGAAGATGTT 58.769 36.000 0.00 0.00 35.04 2.71
8198 9572 4.475016 AGCCTGTCAAAAGGGTATGATACT 59.525 41.667 2.24 0.00 46.21 2.12
8594 9977 3.674997 TGATCAGTCCTTTTGCTGGTAC 58.325 45.455 0.00 0.00 33.81 3.34
8909 10294 4.351192 CGCCAGTGCCATAAAACTATTTC 58.649 43.478 0.00 0.00 0.00 2.17
8935 10320 7.362142 CCCAGTTCTTTTACCAATCTTAGCTTC 60.362 40.741 0.00 0.00 0.00 3.86
9161 10546 8.576442 CCTATAATCCATAGCCACGAAAATTTT 58.424 33.333 2.28 2.28 36.09 1.82
9245 10631 1.610038 TGAGTTTGCGAGGAACTACGA 59.390 47.619 0.00 0.00 41.55 3.43
9252 10638 0.879765 CGAGGAACTACGACCAGTGT 59.120 55.000 0.00 0.00 41.55 3.55
9305 10691 5.949354 ACCAAATCGAAGGGAAATGATTGTA 59.051 36.000 7.30 0.00 31.79 2.41
9428 10814 4.146788 CCGGTGCGTTATAAACAAACAAAC 59.853 41.667 0.00 0.00 0.00 2.93
9429 10815 4.733887 CGGTGCGTTATAAACAAACAAACA 59.266 37.500 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 2.832129 TCGCTTCCTGATCCTACAGTTT 59.168 45.455 0.00 0.00 36.30 2.66
110 111 2.365617 TCCATTCGCTTCCTGATCCTAC 59.634 50.000 0.00 0.00 0.00 3.18
240 241 2.505819 AGGTCACCATATGGAGTTGTCC 59.494 50.000 28.77 20.67 44.24 4.02
255 256 8.726988 TGCAAAGTATTTTACAGATTAGGTCAC 58.273 33.333 0.00 0.00 35.03 3.67
308 309 4.331443 TCGTTGCATAAATACACGATGCTT 59.669 37.500 3.56 0.00 45.04 3.91
384 385 6.226787 AGCGCTCTAGCATACTTTGATATTT 58.773 36.000 2.64 0.00 42.21 1.40
405 406 5.434423 CACTTGGTGAAAGCTACTCTAGCG 61.434 50.000 0.00 0.00 45.57 4.26
565 566 6.804677 AGCATGAATCTTTTGTTGTTGTGTA 58.195 32.000 0.00 0.00 0.00 2.90
595 596 7.808856 CGCTCTTATATTAGTTTACAGAGGGAC 59.191 40.741 4.76 0.00 40.49 4.46
596 597 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
597 598 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
598 599 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
643 644 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
644 645 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
645 646 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
646 647 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
647 648 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
648 649 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
649 650 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
650 651 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
651 652 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
656 657 9.151177 TGAAATACTCCCTCCGTAAACTAATAT 57.849 33.333 0.00 0.00 0.00 1.28
657 658 8.416329 GTGAAATACTCCCTCCGTAAACTAATA 58.584 37.037 0.00 0.00 0.00 0.98
658 659 7.093201 TGTGAAATACTCCCTCCGTAAACTAAT 60.093 37.037 0.00 0.00 0.00 1.73
659 660 6.211184 TGTGAAATACTCCCTCCGTAAACTAA 59.789 38.462 0.00 0.00 0.00 2.24
660 661 5.716228 TGTGAAATACTCCCTCCGTAAACTA 59.284 40.000 0.00 0.00 0.00 2.24
661 662 4.529377 TGTGAAATACTCCCTCCGTAAACT 59.471 41.667 0.00 0.00 0.00 2.66
662 663 4.824289 TGTGAAATACTCCCTCCGTAAAC 58.176 43.478 0.00 0.00 0.00 2.01
663 664 5.486735 TTGTGAAATACTCCCTCCGTAAA 57.513 39.130 0.00 0.00 0.00 2.01
664 665 5.188163 TCATTGTGAAATACTCCCTCCGTAA 59.812 40.000 0.00 0.00 0.00 3.18
665 666 4.712829 TCATTGTGAAATACTCCCTCCGTA 59.287 41.667 0.00 0.00 0.00 4.02
666 667 3.517901 TCATTGTGAAATACTCCCTCCGT 59.482 43.478 0.00 0.00 0.00 4.69
667 668 4.137116 TCATTGTGAAATACTCCCTCCG 57.863 45.455 0.00 0.00 0.00 4.63
668 669 5.440610 ACATCATTGTGAAATACTCCCTCC 58.559 41.667 0.00 0.00 33.85 4.30
700 701 4.805219 ACGGGTGAAACTCAATTATTTGC 58.195 39.130 0.00 0.00 36.87 3.68
702 703 5.048294 GGTGACGGGTGAAACTCAATTATTT 60.048 40.000 0.00 0.00 36.87 1.40
715 716 1.835494 TTGTTTTTGGTGACGGGTGA 58.165 45.000 0.00 0.00 0.00 4.02
787 788 8.693504 GGTTGACGTTTTAAATTTAAACTAGGC 58.306 33.333 20.35 16.59 34.20 3.93
796 797 5.239087 TCCTAGCGGTTGACGTTTTAAATTT 59.761 36.000 0.00 0.00 46.52 1.82
1437 1440 6.260936 ACATATATGGAACTAACTGCAACAGC 59.739 38.462 16.96 0.00 34.37 4.40
1740 1759 2.563179 CGGTTGGAGAAAGAGAGAGGAA 59.437 50.000 0.00 0.00 0.00 3.36
1741 1760 2.171840 CGGTTGGAGAAAGAGAGAGGA 58.828 52.381 0.00 0.00 0.00 3.71
1751 1777 1.005394 GTCGCCTTCGGTTGGAGAA 60.005 57.895 0.00 0.00 35.30 2.87
1926 1952 2.030562 CGTGAGGCGGTGGAGTTT 59.969 61.111 0.00 0.00 36.85 2.66
2219 2276 4.115199 GCGAGGCCATGGAAGGGT 62.115 66.667 18.40 0.00 42.11 4.34
2939 3077 0.537371 CGGCTGGTTTTTCTCCACCT 60.537 55.000 0.00 0.00 33.76 4.00
3036 3176 8.387813 TCATTTTACTACCCTGAATAAAGTGGT 58.612 33.333 0.00 0.00 29.86 4.16
3183 3323 6.086319 TCGCTCGTGCTTTTTAAATACTAC 57.914 37.500 7.97 0.00 36.97 2.73
3247 3388 7.801716 TTACTAGTGCTGTTGTTCTCATTTT 57.198 32.000 5.39 0.00 0.00 1.82
3378 3520 3.445008 AGAATGTCAGGCAGAAGGTAGA 58.555 45.455 0.00 0.00 0.00 2.59
3401 3543 0.515127 TGGTTTACATGCAACTCGCG 59.485 50.000 0.00 0.00 46.97 5.87
3483 3625 0.037590 CCCCGATCCACACTTTTCCA 59.962 55.000 0.00 0.00 0.00 3.53
3546 3688 7.277981 TCGACAGAAAGATAAAATTCTAGCCAC 59.722 37.037 0.00 0.00 34.24 5.01
3566 3708 5.682943 TGTTTGGTTAAGGAATTCGACAG 57.317 39.130 0.00 0.00 0.00 3.51
3634 3776 9.574516 AACCAAATGAGGACTGGTATTATTATC 57.425 33.333 0.00 0.00 42.72 1.75
3642 3784 5.072600 ACAAGTAACCAAATGAGGACTGGTA 59.927 40.000 0.00 0.00 42.72 3.25
3666 3808 6.911250 TTCTCTTGTTACTGTACATGAGGA 57.089 37.500 20.08 14.82 44.32 3.71
3690 3832 1.146041 GTGCTCCCATCATGCGGTA 59.854 57.895 0.00 0.00 0.00 4.02
3985 4162 8.731605 TGCGGTTTGTTATCATAAAAAGACATA 58.268 29.630 0.00 0.00 0.00 2.29
4268 4449 8.305046 ACAAATTTAATATGGCAGAGGCTTAA 57.695 30.769 0.00 0.00 40.87 1.85
4627 5097 6.694844 CGACATCACATGGTATATGCTAGATC 59.305 42.308 0.00 0.00 33.60 2.75
5059 5574 5.335949 CGTGAACATAATCGAACACAACAAC 59.664 40.000 0.00 0.00 0.00 3.32
5533 6835 9.343539 GACCACATTTCTTAAGGCTATTTAGAT 57.656 33.333 1.85 0.00 0.00 1.98
5672 6974 7.441157 TGGACGGATATATTAAAACAGAGCTTG 59.559 37.037 0.00 0.00 0.00 4.01
5743 7045 8.679344 AATTCCTGAAACAATTTAATAGGGGT 57.321 30.769 0.00 0.00 0.00 4.95
5902 7204 4.083908 GCTATGTTTGGTGCAACAAATTGG 60.084 41.667 31.08 22.84 41.80 3.16
6188 7492 3.760738 TGTTGACATTCTGTGGGCAATA 58.239 40.909 0.00 0.00 31.80 1.90
6448 7754 5.651172 TGTATGGCATCGAATAGTTTTCG 57.349 39.130 1.65 9.16 42.74 3.46
6986 8324 1.666189 GCGAGATACCTGAAAACAGGC 59.334 52.381 15.02 1.07 46.05 4.85
7514 8879 1.046472 TCCCCTGTACCGCACCATAG 61.046 60.000 0.00 0.00 0.00 2.23
7823 9197 3.884091 GTCTCGAGGGATAGCTGAAACTA 59.116 47.826 13.56 0.00 0.00 2.24
7982 9356 6.488006 TGATGTCCTTACCGTCTATAAGTACC 59.512 42.308 0.00 0.00 0.00 3.34
8198 9572 1.346479 TTCCTTTGTCCCCGACCACA 61.346 55.000 0.00 0.00 0.00 4.17
8352 9726 2.569404 TGTTTTTCCACCCTTTTGCACT 59.431 40.909 0.00 0.00 0.00 4.40
8824 10209 2.489329 CTCCATTGCACGTTGAAGGATT 59.511 45.455 0.00 0.00 0.00 3.01
8909 10294 5.946377 AGCTAAGATTGGTAAAAGAACTGGG 59.054 40.000 0.00 0.00 0.00 4.45
9245 10631 9.474313 AATTATGGACAATAATAACACACTGGT 57.526 29.630 0.00 0.00 40.00 4.00
9324 10710 6.401394 TGGATTGTATCTGCTATATGTCAGC 58.599 40.000 2.27 0.00 39.56 4.26
9446 10832 9.778741 AACGAATTTAAGATGCTAGGATTGATA 57.221 29.630 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.