Multiple sequence alignment - TraesCS2A01G392400

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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 TraesCS2A01G392400 chr2A 100.000 5730 0 0 1 5730 642579159 642573430 0.000000e+00 10582
1 TraesCS2A01G392400 chr2D 91.515 2699 120 47 2820 5431 498034145 498031469 0.000000e+00 3615
2 TraesCS2A01G392400 chr2D 91.456 1463 79 15 834 2278 498036087 498034653 0.000000e+00 1967
3 TraesCS2A01G392400 chr2D 92.308 481 21 8 2263 2732 498034638 498034163 0.000000e+00 669
4 TraesCS2A01G392400 chr2D 92.670 191 8 4 5450 5635 498031232 498031043 2.630000e-68 270
5 TraesCS2A01G392400 chr2D 93.125 160 5 5 661 816 498038253 498038096 4.470000e-56 230
6 TraesCS2A01G392400 chr2B 93.824 1846 85 13 3551 5375 584118591 584116754 0.000000e+00 2750
7 TraesCS2A01G392400 chr2B 89.524 1260 79 16 2332 3552 584119930 584118685 0.000000e+00 1546
8 TraesCS2A01G392400 chr2B 92.337 796 41 11 1567 2355 584120721 584119939 0.000000e+00 1114
9 TraesCS2A01G392400 chr2B 93.149 686 39 5 662 1345 584121507 584120828 0.000000e+00 1000
10 TraesCS2A01G392400 chr2B 93.316 374 19 4 5362 5730 584116736 584116364 1.090000e-151 547
11 TraesCS2A01G392400 chr3A 95.296 659 26 5 1 657 629176479 629177134 0.000000e+00 1040
12 TraesCS2A01G392400 chr3A 93.871 669 38 3 1 666 373325983 373326651 0.000000e+00 1005
13 TraesCS2A01G392400 chr7A 95.144 659 26 4 1 657 136175158 136174504 0.000000e+00 1035
14 TraesCS2A01G392400 chr6A 94.689 659 32 3 9 665 29595517 29596174 0.000000e+00 1020
15 TraesCS2A01G392400 chr7D 93.871 669 34 6 1 667 108365556 108364893 0.000000e+00 1002
16 TraesCS2A01G392400 chr7D 93.124 669 39 6 1 667 108343887 108343224 0.000000e+00 974
17 TraesCS2A01G392400 chr7D 92.273 660 42 7 1 657 591021345 591021998 0.000000e+00 928
18 TraesCS2A01G392400 chr7D 91.933 657 45 6 15 668 586502905 586502254 0.000000e+00 913
19 TraesCS2A01G392400 chr1A 94.655 580 27 4 59 636 404480841 404481418 0.000000e+00 896


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 TraesCS2A01G392400 chr2A 642573430 642579159 5729 True 10582.0 10582 100.0000 1 5730 1 chr2A.!!$R1 5729
1 TraesCS2A01G392400 chr2D 498031043 498038253 7210 True 1350.2 3615 92.2148 661 5635 5 chr2D.!!$R1 4974
2 TraesCS2A01G392400 chr2B 584116364 584121507 5143 True 1391.4 2750 92.4300 662 5730 5 chr2B.!!$R1 5068
3 TraesCS2A01G392400 chr3A 629176479 629177134 655 False 1040.0 1040 95.2960 1 657 1 chr3A.!!$F2 656
4 TraesCS2A01G392400 chr3A 373325983 373326651 668 False 1005.0 1005 93.8710 1 666 1 chr3A.!!$F1 665
5 TraesCS2A01G392400 chr7A 136174504 136175158 654 True 1035.0 1035 95.1440 1 657 1 chr7A.!!$R1 656
6 TraesCS2A01G392400 chr6A 29595517 29596174 657 False 1020.0 1020 94.6890 9 665 1 chr6A.!!$F1 656
7 TraesCS2A01G392400 chr7D 108364893 108365556 663 True 1002.0 1002 93.8710 1 667 1 chr7D.!!$R2 666
8 TraesCS2A01G392400 chr7D 108343224 108343887 663 True 974.0 974 93.1240 1 667 1 chr7D.!!$R1 666
9 TraesCS2A01G392400 chr7D 591021345 591021998 653 False 928.0 928 92.2730 1 657 1 chr7D.!!$F1 656
10 TraesCS2A01G392400 chr7D 586502254 586502905 651 True 913.0 913 91.9330 15 668 1 chr7D.!!$R3 653
11 TraesCS2A01G392400 chr1A 404480841 404481418 577 False 896.0 896 94.6550 59 636 1 chr1A.!!$F1 577

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
943 2951 0.672401 TCCGCGAAGTCCAAACCATC 60.672 55.0 8.23 0.0 0.00 3.51 F
1352 3360 0.175760 CAGACCCAGGTACACCGATG 59.824 60.0 0.00 0.0 42.08 3.84 F
1541 3562 0.243636 ATTTAACCAACGCCTGCTGC 59.756 50.0 0.00 0.0 0.00 5.25 F
2817 4917 0.323178 CCATGCAGCTCCTGACCTTT 60.323 55.0 0.00 0.0 32.44 3.11 F
3497 5628 0.185901 TTGGCCTTTTGCTGGAGAGT 59.814 50.0 3.32 0.0 40.92 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2658 4757 1.092921 TTCTTGCGTGGCTCGTTTGT 61.093 50.000 10.87 0.0 42.13 2.83 R
2975 5080 0.314935 ACGAAAAATGCAGTGGCCAG 59.685 50.000 5.11 0.0 40.13 4.85 R
3497 5628 2.265367 TCCCATAACAGTTGGAGCAGA 58.735 47.619 0.00 0.0 36.26 4.26 R
4660 6911 1.151810 AACCTCCCTGAGCTTCCCA 60.152 57.895 0.00 0.0 0.00 4.37 R
4956 7226 0.099436 GCAAGCAAATGCCTAGGTCG 59.901 55.000 11.31 0.0 43.38 4.79 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
55 56 3.397482 AAGTTAGACAACTGAGCAGCAG 58.603 45.455 0.00 5.19 44.41 4.24
124 125 8.275758 TGGTAGGCCAATTTCATAGTATTGTAA 58.724 33.333 5.01 0.00 42.83 2.41
212 213 6.089417 GCCAAGTTGTGATAATGTTAGCAAAC 59.911 38.462 1.45 1.62 36.07 2.93
426 433 6.669278 TCGACGAAACCTATCAATATGAGAG 58.331 40.000 0.00 0.00 35.60 3.20
614 623 4.037327 GCTCCTTTCATATTTGGAAGAGCC 59.963 45.833 5.81 0.00 40.44 4.70
618 627 3.864789 TCATATTTGGAAGAGCCCTCC 57.135 47.619 0.00 0.00 34.97 4.30
625 634 2.626510 GAAGAGCCCTCCTTCCCAT 58.373 57.895 0.00 0.00 35.26 4.00
659 669 2.886124 GCCGCTAGCCACGTCTTC 60.886 66.667 9.66 0.00 34.35 2.87
758 768 5.751990 ACAGATTATTAGGAAGGCGTTTACG 59.248 40.000 0.00 0.00 43.27 3.18
762 772 7.550196 AGATTATTAGGAAGGCGTTTACGAAAA 59.450 33.333 6.44 0.00 43.02 2.29
797 809 7.527457 GTTAAGAAAAGCGTATCAAGTTCCAT 58.473 34.615 0.00 0.00 0.00 3.41
929 2937 3.544167 CTCCGAGGCACTATCCGCG 62.544 68.421 0.00 0.00 46.66 6.46
943 2951 0.672401 TCCGCGAAGTCCAAACCATC 60.672 55.000 8.23 0.00 0.00 3.51
1202 3210 2.300437 AGAAGTCTCGGTCCCAAAAGAG 59.700 50.000 0.00 0.00 0.00 2.85
1203 3211 1.718280 AGTCTCGGTCCCAAAAGAGT 58.282 50.000 0.00 0.00 32.90 3.24
1302 3310 1.609794 GAGGGTTCTGGTCTCCGGT 60.610 63.158 0.00 0.00 0.00 5.28
1351 3359 0.976073 CCAGACCCAGGTACACCGAT 60.976 60.000 0.00 0.00 42.08 4.18
1352 3360 0.175760 CAGACCCAGGTACACCGATG 59.824 60.000 0.00 0.00 42.08 3.84
1353 3361 0.252103 AGACCCAGGTACACCGATGT 60.252 55.000 0.00 0.00 43.30 3.06
1356 3364 2.433239 GACCCAGGTACACCGATGTTAT 59.567 50.000 0.00 0.00 40.48 1.89
1359 3367 3.454375 CCAGGTACACCGATGTTATCAC 58.546 50.000 0.00 0.00 40.48 3.06
1377 3385 9.848710 TGTTATCACTATCTAACTGTAGCTAGT 57.151 33.333 0.00 0.00 39.01 2.57
1383 3391 7.283580 CACTATCTAACTGTAGCTAGTTGGACT 59.716 40.741 15.30 9.08 46.37 3.85
1384 3392 6.702716 ATCTAACTGTAGCTAGTTGGACTC 57.297 41.667 15.30 0.00 46.37 3.36
1385 3393 5.817784 TCTAACTGTAGCTAGTTGGACTCT 58.182 41.667 10.45 0.00 41.38 3.24
1395 3403 4.938226 GCTAGTTGGACTCTTATTTGTGCT 59.062 41.667 0.00 0.00 0.00 4.40
1441 3452 2.040145 CTGCAAATCCATTTTGGGGGTT 59.960 45.455 0.00 0.00 44.10 4.11
1456 3468 2.037381 GGGGGTTATCCTGACGATTCTC 59.963 54.545 0.00 0.00 35.33 2.87
1464 3476 4.551702 TCCTGACGATTCTCCAATTTCA 57.448 40.909 0.00 0.00 0.00 2.69
1483 3495 3.359033 TCATCCTGCAAAATCTTCCCAG 58.641 45.455 0.00 0.00 0.00 4.45
1486 3498 4.380843 TCCTGCAAAATCTTCCCAGTTA 57.619 40.909 0.00 0.00 0.00 2.24
1487 3499 4.934356 TCCTGCAAAATCTTCCCAGTTAT 58.066 39.130 0.00 0.00 0.00 1.89
1488 3500 4.706476 TCCTGCAAAATCTTCCCAGTTATG 59.294 41.667 0.00 0.00 0.00 1.90
1489 3501 4.427312 CTGCAAAATCTTCCCAGTTATGC 58.573 43.478 0.00 0.00 0.00 3.14
1490 3502 3.119531 TGCAAAATCTTCCCAGTTATGCG 60.120 43.478 0.00 0.00 34.16 4.73
1491 3503 3.734902 GCAAAATCTTCCCAGTTATGCGG 60.735 47.826 0.00 0.00 0.00 5.69
1534 3555 7.544217 AGTTCAATTTATCCATTTAACCAACGC 59.456 33.333 0.00 0.00 0.00 4.84
1535 3556 6.334202 TCAATTTATCCATTTAACCAACGCC 58.666 36.000 0.00 0.00 0.00 5.68
1536 3557 6.153680 TCAATTTATCCATTTAACCAACGCCT 59.846 34.615 0.00 0.00 0.00 5.52
1537 3558 4.974368 TTATCCATTTAACCAACGCCTG 57.026 40.909 0.00 0.00 0.00 4.85
1538 3559 0.885196 TCCATTTAACCAACGCCTGC 59.115 50.000 0.00 0.00 0.00 4.85
1539 3560 0.887933 CCATTTAACCAACGCCTGCT 59.112 50.000 0.00 0.00 0.00 4.24
1540 3561 1.402720 CCATTTAACCAACGCCTGCTG 60.403 52.381 0.00 0.00 0.00 4.41
1541 3562 0.243636 ATTTAACCAACGCCTGCTGC 59.756 50.000 0.00 0.00 0.00 5.25
1542 3563 1.801309 TTTAACCAACGCCTGCTGCC 61.801 55.000 0.00 0.00 36.24 4.85
1543 3564 2.967507 TTAACCAACGCCTGCTGCCA 62.968 55.000 0.00 0.00 36.24 4.92
1546 3567 3.730761 CAACGCCTGCTGCCAGTC 61.731 66.667 0.00 0.00 37.38 3.51
1571 3592 0.954449 CTGCTGCAGAGTTGGACCAG 60.954 60.000 24.88 8.63 32.44 4.00
1572 3593 2.331132 GCTGCAGAGTTGGACCAGC 61.331 63.158 20.43 0.00 41.57 4.85
1577 3598 1.002544 GCAGAGTTGGACCAGCTAGTT 59.997 52.381 11.29 0.00 0.00 2.24
1660 3684 5.396213 GCTTCAGAAGTTCAGATAGTGGGAT 60.396 44.000 11.94 0.00 0.00 3.85
2017 4044 1.168714 GGGTGCAACTCAATCCTCAC 58.831 55.000 0.00 0.00 37.19 3.51
2131 4158 7.757097 TGATCTTAAAAAGAGCGATGTACTC 57.243 36.000 0.00 0.00 46.56 2.59
2200 4227 6.044404 AGGTAAGATTCTTTTCTCTTCACCCA 59.956 38.462 3.86 0.00 33.83 4.51
2252 4280 8.400186 CCAATGCTTTTTGAAACATCTTTTCTT 58.600 29.630 0.00 0.00 0.00 2.52
2291 4349 7.559590 AGTTGCAATAGATGATTGACCTTAC 57.440 36.000 0.59 0.00 46.94 2.34
2353 4442 7.854337 ACCAAAAATATGATTGCATTCCTCTT 58.146 30.769 6.16 0.00 35.94 2.85
2366 4458 7.377766 TGCATTCCTCTTTACTGTTGTAATC 57.622 36.000 0.00 0.00 38.31 1.75
2404 4503 3.949754 CAGCCTATTTCCTGATGCTGAAA 59.050 43.478 3.33 0.00 46.88 2.69
2532 4631 1.534595 GTGCCTGCTCACTTTTCAGAG 59.465 52.381 0.00 0.00 34.29 3.35
2537 4636 3.494048 CCTGCTCACTTTTCAGAGTCTGT 60.494 47.826 19.53 0.00 34.39 3.41
2540 4639 3.493350 GCTCACTTTTCAGAGTCTGTGGA 60.493 47.826 19.53 4.95 34.39 4.02
2557 4656 4.158786 TGTGGAAAATCATGAACCATGGT 58.841 39.130 13.00 13.00 41.66 3.55
2559 4658 3.514706 TGGAAAATCATGAACCATGGTGG 59.485 43.478 20.60 8.94 41.66 4.61
2610 4709 7.360522 GCTTAAGCTCTGTCCTTTTCTAAAGAC 60.361 40.741 20.38 0.00 38.21 3.01
2658 4757 8.994429 TTGTATTCAAGCAAACTTTCTTTTCA 57.006 26.923 0.00 0.00 32.29 2.69
2732 4832 7.947282 ACAATCTGTAGAGTTATCTCCTTAGC 58.053 38.462 0.00 0.00 41.26 3.09
2754 4854 5.881923 CCTTACCCTACAACTATAAGGCA 57.118 43.478 0.00 0.00 36.49 4.75
2785 4885 2.422479 GCTCAGAAAATACGTTTCCCCC 59.578 50.000 0.00 0.00 45.91 5.40
2817 4917 0.323178 CCATGCAGCTCCTGACCTTT 60.323 55.000 0.00 0.00 32.44 3.11
2895 4995 5.008118 TGTTCAATCACATTTGTTCGCTGTA 59.992 36.000 0.00 0.00 0.00 2.74
2904 5004 1.045407 TGTTCGCTGTAAGACTGGGT 58.955 50.000 1.56 0.00 34.07 4.51
2955 5055 8.964150 GTAATGTTACACATTTCCTGTTTTGTC 58.036 33.333 7.40 0.00 45.80 3.18
3027 5132 5.007682 GGATCATACTCTAGAGGTCCACTC 58.992 50.000 23.50 12.00 46.98 3.51
3102 5207 7.041372 ACGTATCAGTTTGAGCAAGTATGTTTT 60.041 33.333 0.00 0.00 0.00 2.43
3189 5295 5.869579 TGACTGAGAATTAGTCTTTTGCCT 58.130 37.500 8.05 0.00 43.79 4.75
3202 5308 3.642848 TCTTTTGCCTGATGCTTTCCTTT 59.357 39.130 0.00 0.00 42.00 3.11
3252 5358 6.235231 ACAAGAGGAACAAAACTAGACTCA 57.765 37.500 0.00 0.00 0.00 3.41
3311 5417 9.031360 TCTTATGAATCATACAGACGCTTAAAC 57.969 33.333 1.88 0.00 0.00 2.01
3346 5452 5.595542 ACATTGATGCTGGTATACATGCTTT 59.404 36.000 16.57 7.56 0.00 3.51
3401 5507 6.639671 TTGTTTTGTAACAACAATCTGTGC 57.360 33.333 0.00 0.00 46.46 4.57
3423 5529 7.038373 TGTGCCAGCTAGTATTATGGAATCATA 60.038 37.037 0.00 0.00 34.60 2.15
3497 5628 0.185901 TTGGCCTTTTGCTGGAGAGT 59.814 50.000 3.32 0.00 40.92 3.24
3530 5661 9.740239 CAACTGTTATGGGAATGAATTATTGAG 57.260 33.333 0.00 0.00 0.00 3.02
3625 5873 3.025322 TGTCTGTGGGTTTGGATTTGT 57.975 42.857 0.00 0.00 0.00 2.83
3667 5915 5.758296 TGACATCGAGCTTTGTTTTAGAGTT 59.242 36.000 0.00 0.00 0.00 3.01
3719 5967 6.634035 CGTATTGTGCATACCATTGAATTCAG 59.366 38.462 8.41 0.00 35.15 3.02
3818 6066 7.414873 CCATGTTGAAGAGTATGATTCCTGTTG 60.415 40.741 0.00 0.00 0.00 3.33
3819 6067 5.412594 TGTTGAAGAGTATGATTCCTGTTGC 59.587 40.000 0.00 0.00 0.00 4.17
3822 6070 2.173569 AGAGTATGATTCCTGTTGCCCC 59.826 50.000 0.00 0.00 0.00 5.80
3823 6071 1.134098 AGTATGATTCCTGTTGCCCCG 60.134 52.381 0.00 0.00 0.00 5.73
3841 6089 4.382362 GCCCCGTACTACAAGTTTATCTGT 60.382 45.833 0.00 0.00 0.00 3.41
3977 6225 6.176183 CACCAATCTAGAAAGGACACAGAAT 58.824 40.000 17.89 0.00 0.00 2.40
4006 6254 3.063452 ACACAGACTGTAGTTTGTTTGCG 59.937 43.478 8.02 0.00 40.77 4.85
4064 6312 3.830755 ACTGCTGCTTGATTTCATCCTTT 59.169 39.130 0.00 0.00 0.00 3.11
4116 6364 5.929058 AGACATTCTCATCTACAGCTTGA 57.071 39.130 0.00 0.00 0.00 3.02
4125 6373 3.063510 TCTACAGCTTGAGCATGCTTT 57.936 42.857 23.61 0.00 45.16 3.51
4142 6390 5.633830 TGCTTTTTCCTCATGATCTGAAC 57.366 39.130 0.00 0.00 32.14 3.18
4231 6482 2.036346 GCACAAGAACCATCAGCCTTTT 59.964 45.455 0.00 0.00 0.00 2.27
4232 6483 3.493176 GCACAAGAACCATCAGCCTTTTT 60.493 43.478 0.00 0.00 0.00 1.94
4276 6527 3.314635 GCTTGGTCTTCCTGAATAGCATG 59.685 47.826 0.00 0.00 34.23 4.06
4277 6528 4.521146 CTTGGTCTTCCTGAATAGCATGT 58.479 43.478 0.00 0.00 34.23 3.21
4281 6532 5.415701 TGGTCTTCCTGAATAGCATGTTTTC 59.584 40.000 0.00 0.00 34.23 2.29
4336 6587 3.469008 TTCTCTCAAAGAAAGCGGACA 57.531 42.857 0.00 0.00 41.10 4.02
4399 6650 2.540931 CAGTGCAACACCAATTTTCAGC 59.459 45.455 0.00 0.00 41.43 4.26
4648 6899 6.213195 GGATTAATCTGGTGATGGAGAGAGAT 59.787 42.308 14.95 0.00 32.44 2.75
4657 6908 5.512232 GGTGATGGAGAGAGATTATGGAACC 60.512 48.000 0.00 0.00 0.00 3.62
4660 6911 4.483950 TGGAGAGAGATTATGGAACCGAT 58.516 43.478 0.00 0.00 0.00 4.18
4684 6935 2.283529 GCTCAGGGAGGTTCGGACA 61.284 63.158 0.00 0.00 0.00 4.02
4922 7192 1.945819 GCAGGCTTCGGTTTCATCAGA 60.946 52.381 0.00 0.00 0.00 3.27
4924 7194 2.417933 CAGGCTTCGGTTTCATCAGAAG 59.582 50.000 0.00 0.21 40.62 2.85
4926 7196 2.615493 GGCTTCGGTTTCATCAGAAGGA 60.615 50.000 6.25 0.00 39.04 3.36
4941 7211 4.281688 TCAGAAGGAAAAATGGGCTGAAAG 59.718 41.667 0.00 0.00 0.00 2.62
4956 7226 4.899048 CTGAAAGAGAGCCCAGGAAGGC 62.899 59.091 0.00 0.00 46.57 4.35
5006 7276 7.093245 TGCATGGCCATATTTTATGCATAGAAT 60.093 33.333 20.30 21.99 46.31 2.40
5009 7279 9.705103 ATGGCCATATTTTATGCATAGAATAGT 57.295 29.630 25.30 15.48 0.00 2.12
5177 7448 9.868389 GTATAACCGTATACAAAAATGTTAGCC 57.132 33.333 3.32 0.00 41.21 3.93
5279 7598 2.900122 TGTTTGCTTAGCTTGATCGC 57.100 45.000 5.60 0.00 0.00 4.58
5317 7638 1.407851 CCTGGACCATGGTCATGACTG 60.408 57.143 38.83 25.72 46.20 3.51
5335 7656 1.411977 CTGGTGGAGCAGATGTAGGAG 59.588 57.143 0.00 0.00 0.00 3.69
5337 7658 0.105778 GTGGAGCAGATGTAGGAGGC 59.894 60.000 0.00 0.00 0.00 4.70
5405 7758 6.428159 AGACGATGAAGAACATTGCTACTTTT 59.572 34.615 0.00 0.00 42.47 2.27
5462 8033 9.060347 TGATAAAGAAGAGATGCATATGGTTTC 57.940 33.333 0.00 0.24 0.00 2.78
5529 8105 6.265577 AGTACCATTCGCATTGCTTTATTTC 58.734 36.000 7.12 0.00 0.00 2.17
5540 8116 5.743026 TTGCTTTATTTCGCCGAATATCA 57.257 34.783 0.00 0.00 0.00 2.15
5541 8117 5.090652 TGCTTTATTTCGCCGAATATCAC 57.909 39.130 0.00 0.00 0.00 3.06
5648 8224 3.260632 TGGCAGTACAAGCTAGATGTTCA 59.739 43.478 9.72 0.00 32.27 3.18
5665 8244 7.506114 AGATGTTCAAAGTTTACACAGTAGGA 58.494 34.615 5.53 0.00 0.00 2.94
5688 8267 3.546020 GGGAATTATCGTGTTGATGTGCG 60.546 47.826 0.00 0.00 37.99 5.34
5689 8268 2.737467 ATTATCGTGTTGATGTGCGC 57.263 45.000 0.00 0.00 37.99 6.09
5691 8270 2.570442 TATCGTGTTGATGTGCGCTA 57.430 45.000 9.73 0.00 37.99 4.26
5727 8306 3.200165 GCTCTACCCCATTCTAAACTGGT 59.800 47.826 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 5.606749 TGGCCTACCATTGATGTCTAGTTAT 59.393 40.000 3.32 0.00 42.67 1.89
124 125 3.881688 GCTATCATTGATGTCCAGTTGCT 59.118 43.478 9.46 0.00 0.00 3.91
212 213 5.778161 TTGCACTACGTGTATCAATGAAG 57.222 39.130 0.00 0.00 35.75 3.02
262 263 7.844009 AGAAAATCACACAAAATATGAGGCAT 58.156 30.769 0.00 0.00 0.00 4.40
426 433 3.421955 GCGACGAGTTCTTCAAAACTAGC 60.422 47.826 0.00 0.00 39.55 3.42
598 607 3.397527 AGGAGGGCTCTTCCAAATATGA 58.602 45.455 5.08 0.00 36.21 2.15
614 623 2.507944 CCGCTGATGGGAAGGAGG 59.492 66.667 0.00 0.00 0.00 4.30
657 667 7.179338 TGCATTAGGGCCAGTAATTAAAAAGAA 59.821 33.333 6.18 0.00 0.00 2.52
659 669 6.872920 TGCATTAGGGCCAGTAATTAAAAAG 58.127 36.000 6.18 0.00 0.00 2.27
690 700 4.585955 AAGTGTGACTACAGTAGTGTGG 57.414 45.455 18.41 12.88 39.52 4.17
758 768 7.111139 GCTTTTCTTAACGAAAGCAACTTTTC 58.889 34.615 18.84 0.00 42.22 2.29
762 772 4.201881 ACGCTTTTCTTAACGAAAGCAACT 60.202 37.500 21.49 8.21 42.22 3.16
797 809 0.391927 CCGGGATACGCTTTTGGTGA 60.392 55.000 0.00 0.00 42.52 4.02
929 2937 0.322546 AGGCGGATGGTTTGGACTTC 60.323 55.000 0.00 0.00 0.00 3.01
1068 3076 3.851128 GTAGAGGTGGAGGGGCGC 61.851 72.222 0.00 0.00 0.00 6.53
1131 3139 0.905337 AGACGTTCTCCTTCCCCCTG 60.905 60.000 0.00 0.00 0.00 4.45
1186 3194 1.343465 GTGACTCTTTTGGGACCGAGA 59.657 52.381 0.85 0.00 0.00 4.04
1255 3263 2.758130 GTCATTCTCCTTCCTCCTCCT 58.242 52.381 0.00 0.00 0.00 3.69
1359 3367 7.717875 AGAGTCCAACTAGCTACAGTTAGATAG 59.282 40.741 7.07 3.05 45.97 2.08
1376 3384 5.880332 TCCATAGCACAAATAAGAGTCCAAC 59.120 40.000 0.00 0.00 0.00 3.77
1377 3385 5.880332 GTCCATAGCACAAATAAGAGTCCAA 59.120 40.000 0.00 0.00 0.00 3.53
1383 3391 4.199310 GCCTGTCCATAGCACAAATAAGA 58.801 43.478 0.00 0.00 0.00 2.10
1384 3392 3.002656 CGCCTGTCCATAGCACAAATAAG 59.997 47.826 0.00 0.00 0.00 1.73
1385 3393 2.942376 CGCCTGTCCATAGCACAAATAA 59.058 45.455 0.00 0.00 0.00 1.40
1395 3403 1.552578 ACTACACACGCCTGTCCATA 58.447 50.000 0.00 0.00 0.00 2.74
1441 3452 6.233905 TGAAATTGGAGAATCGTCAGGATA 57.766 37.500 0.00 0.00 34.08 2.59
1456 3468 5.583457 GGAAGATTTTGCAGGATGAAATTGG 59.417 40.000 0.00 0.00 39.69 3.16
1464 3476 3.463048 ACTGGGAAGATTTTGCAGGAT 57.537 42.857 0.00 0.00 0.00 3.24
1483 3495 2.922740 TCCCTATCAACCCGCATAAC 57.077 50.000 0.00 0.00 0.00 1.89
1486 3498 3.587061 TCATAATCCCTATCAACCCGCAT 59.413 43.478 0.00 0.00 0.00 4.73
1487 3499 2.976185 TCATAATCCCTATCAACCCGCA 59.024 45.455 0.00 0.00 0.00 5.69
1488 3500 3.008049 ACTCATAATCCCTATCAACCCGC 59.992 47.826 0.00 0.00 0.00 6.13
1489 3501 4.891992 ACTCATAATCCCTATCAACCCG 57.108 45.455 0.00 0.00 0.00 5.28
1490 3502 6.187727 TGAACTCATAATCCCTATCAACCC 57.812 41.667 0.00 0.00 0.00 4.11
1491 3503 8.697507 AATTGAACTCATAATCCCTATCAACC 57.302 34.615 0.00 0.00 0.00 3.77
1563 3584 3.007614 GGACTACAAACTAGCTGGTCCAA 59.992 47.826 2.06 0.00 40.73 3.53
1571 3592 2.737252 GCACAGTGGACTACAAACTAGC 59.263 50.000 1.84 0.00 0.00 3.42
1572 3593 3.990092 TGCACAGTGGACTACAAACTAG 58.010 45.455 1.84 0.00 0.00 2.57
1602 3623 1.136141 GTGAGTGACATGCTTTGCGAG 60.136 52.381 0.00 0.00 0.00 5.03
1660 3684 3.622206 GCCACAAGTCATTCTCCATGGTA 60.622 47.826 12.58 0.00 33.07 3.25
1663 3687 1.399440 CGCCACAAGTCATTCTCCATG 59.601 52.381 0.00 0.00 0.00 3.66
1675 3699 1.480205 CAAGTTTGCTTCGCCACAAG 58.520 50.000 0.00 0.00 31.49 3.16
2131 4158 8.066595 GGTTCTTCAATCATAACATCTTCATCG 58.933 37.037 0.00 0.00 0.00 3.84
2179 4206 7.846101 AAATGGGTGAAGAGAAAAGAATCTT 57.154 32.000 0.00 0.00 38.46 2.40
2225 4253 6.622833 AAAGATGTTTCAAAAAGCATTGGG 57.377 33.333 0.00 0.00 36.57 4.12
2252 4280 3.016031 TGCAACTTTCAAGAGCTGAACA 58.984 40.909 0.00 0.00 43.90 3.18
2366 4458 9.262358 GAAATAGGCTGTGGTTATAACTTCTAG 57.738 37.037 15.05 9.58 0.00 2.43
2380 4472 2.617308 CAGCATCAGGAAATAGGCTGTG 59.383 50.000 0.00 0.00 42.69 3.66
2404 4503 8.038944 TCTAAAACACCATCTAAGCGTTCTATT 58.961 33.333 0.00 0.00 0.00 1.73
2532 4631 5.404946 CATGGTTCATGATTTTCCACAGAC 58.595 41.667 0.00 0.00 43.81 3.51
2537 4636 3.514706 CCACCATGGTTCATGATTTTCCA 59.485 43.478 16.84 4.15 43.81 3.53
2610 4709 6.526566 AACTAGCTGTTCAAGTTAAACTCG 57.473 37.500 0.00 0.00 32.63 4.18
2655 4754 1.369839 TTGCGTGGCTCGTTTGTGAA 61.370 50.000 10.87 0.00 42.13 3.18
2656 4755 1.771073 CTTGCGTGGCTCGTTTGTGA 61.771 55.000 10.87 0.00 42.13 3.58
2658 4757 1.092921 TTCTTGCGTGGCTCGTTTGT 61.093 50.000 10.87 0.00 42.13 2.83
2732 4832 5.601313 TCTGCCTTATAGTTGTAGGGTAAGG 59.399 44.000 5.36 5.36 42.63 2.69
2817 4917 1.946984 ACTTACATGGGGAGGAACGA 58.053 50.000 0.00 0.00 0.00 3.85
2895 4995 3.049344 GGGGAGATGATAACCCAGTCTT 58.951 50.000 0.00 0.00 44.87 3.01
2955 5055 5.346281 GCCAGAGGAATAAGTCGATAATTCG 59.654 44.000 9.73 0.00 46.87 3.34
2975 5080 0.314935 ACGAAAAATGCAGTGGCCAG 59.685 50.000 5.11 0.00 40.13 4.85
3027 5132 7.432252 TCATCATATTCACCGATTTCGATATCG 59.568 37.037 25.38 25.38 45.27 2.92
3033 5138 7.356641 AGATTCATCATATTCACCGATTTCG 57.643 36.000 0.00 0.00 39.44 3.46
3102 5207 6.321690 GGGCAGATAGTAAAGTTCAGTAGAGA 59.678 42.308 0.00 0.00 0.00 3.10
3151 5257 6.882610 TCTCAGTCAACATTGCAGTATTTT 57.117 33.333 0.00 0.00 0.00 1.82
3152 5258 6.882610 TTCTCAGTCAACATTGCAGTATTT 57.117 33.333 0.00 0.00 0.00 1.40
3189 5295 4.914983 ACAGATCTCAAAGGAAAGCATCA 58.085 39.130 0.00 0.00 0.00 3.07
3217 5323 8.608844 TTTGTTCCTCTTGTAAAAAGCAAAAA 57.391 26.923 0.00 0.00 0.00 1.94
3218 5324 8.499967 GTTTTGTTCCTCTTGTAAAAAGCAAAA 58.500 29.630 0.00 0.00 32.18 2.44
3219 5325 7.875554 AGTTTTGTTCCTCTTGTAAAAAGCAAA 59.124 29.630 0.00 0.00 0.00 3.68
3220 5326 7.382898 AGTTTTGTTCCTCTTGTAAAAAGCAA 58.617 30.769 0.00 0.00 0.00 3.91
3221 5327 6.930731 AGTTTTGTTCCTCTTGTAAAAAGCA 58.069 32.000 0.00 0.00 0.00 3.91
3252 5358 8.996271 CACATGTCTATGCAATAGTTATCACAT 58.004 33.333 0.00 0.00 46.98 3.21
3311 5417 3.909430 AGCATCAATGTTGAGTTTGCTG 58.091 40.909 17.02 4.98 44.68 4.41
3318 5424 6.665465 CATGTATACCAGCATCAATGTTGAG 58.335 40.000 8.23 2.19 40.86 3.02
3325 5431 5.651576 TCAAAAGCATGTATACCAGCATCAA 59.348 36.000 16.11 0.00 0.00 2.57
3346 5452 2.435805 GGAGTCCCTAGCACATCATCAA 59.564 50.000 0.00 0.00 0.00 2.57
3401 5507 8.834465 GCAATATGATTCCATAATACTAGCTGG 58.166 37.037 0.00 0.00 38.62 4.85
3423 5529 6.098982 AGTTGATTAGTAGCTACCTCTGCAAT 59.901 38.462 20.31 9.96 0.00 3.56
3497 5628 2.265367 TCCCATAACAGTTGGAGCAGA 58.735 47.619 0.00 0.00 36.26 4.26
3570 5815 4.515567 CGAAAGGAGAAAGTTAAAGGCAGT 59.484 41.667 0.00 0.00 0.00 4.40
3625 5873 6.258507 CGATGTCATTGTCAGTTATGGATTGA 59.741 38.462 0.00 0.00 0.00 2.57
3645 5893 6.430451 CAAACTCTAAAACAAAGCTCGATGT 58.570 36.000 0.00 0.00 0.00 3.06
3667 5915 2.079170 TTGTGGCATCCTTTGACCAA 57.921 45.000 0.00 0.00 34.63 3.67
3719 5967 4.585955 TGTATATTCGCTCCTCCTTCAC 57.414 45.455 0.00 0.00 0.00 3.18
3818 6066 4.117685 CAGATAAACTTGTAGTACGGGGC 58.882 47.826 0.00 0.00 0.00 5.80
3819 6067 5.334724 ACAGATAAACTTGTAGTACGGGG 57.665 43.478 0.00 0.00 0.00 5.73
3822 6070 9.793245 CAGAAAAACAGATAAACTTGTAGTACG 57.207 33.333 0.00 0.00 0.00 3.67
3823 6071 9.595357 GCAGAAAAACAGATAAACTTGTAGTAC 57.405 33.333 0.00 0.00 0.00 2.73
3927 6175 7.201617 GGCACCAATCTGACACTATTAGTAAAC 60.202 40.741 0.00 0.00 0.00 2.01
3977 6225 9.772973 AAACAAACTACAGTCTGTGTTATGATA 57.227 29.630 16.03 0.00 40.94 2.15
4006 6254 8.736751 TTCAATTAGCCTTGTTTTAATTCGTC 57.263 30.769 0.00 0.00 0.00 4.20
4064 6312 5.180117 GCTGTGAAAGTAGAAAGCATCTTCA 59.820 40.000 0.00 0.00 39.71 3.02
4116 6364 4.098044 CAGATCATGAGGAAAAAGCATGCT 59.902 41.667 16.30 16.30 39.30 3.79
4125 6373 5.752036 AGACAGTTCAGATCATGAGGAAA 57.248 39.130 0.09 0.00 39.68 3.13
4142 6390 7.940137 ACTATAGGAGGCCGATATATAAGACAG 59.060 40.741 4.43 0.00 0.00 3.51
4276 6527 6.645003 CAGGGGTATTACTGCAAAAAGAAAAC 59.355 38.462 0.00 0.00 0.00 2.43
4277 6528 6.325286 ACAGGGGTATTACTGCAAAAAGAAAA 59.675 34.615 0.00 0.00 38.25 2.29
4281 6532 5.242838 TCAACAGGGGTATTACTGCAAAAAG 59.757 40.000 0.00 0.00 38.25 2.27
4336 6587 2.887152 GCCTGTCAGTTCTGATGGTTTT 59.113 45.455 18.33 0.00 0.00 2.43
4399 6650 6.091441 CACCCTCTATTTCTTTCACTTTCTCG 59.909 42.308 0.00 0.00 0.00 4.04
4648 6899 1.843851 AGCTTCCCATCGGTTCCATAA 59.156 47.619 0.00 0.00 0.00 1.90
4657 6908 1.445095 CTCCCTGAGCTTCCCATCG 59.555 63.158 0.00 0.00 0.00 3.84
4660 6911 1.151810 AACCTCCCTGAGCTTCCCA 60.152 57.895 0.00 0.00 0.00 4.37
4684 6935 3.181476 ACCTGCGCTTGATTTCAGTTTTT 60.181 39.130 9.73 0.00 0.00 1.94
4718 6969 5.945784 TGATTTCTTTGAACTATGGTGGGAG 59.054 40.000 0.00 0.00 0.00 4.30
4922 7192 4.482990 TCTCTTTCAGCCCATTTTTCCTT 58.517 39.130 0.00 0.00 0.00 3.36
4924 7194 3.367806 GCTCTCTTTCAGCCCATTTTTCC 60.368 47.826 0.00 0.00 0.00 3.13
4926 7196 3.949842 GCTCTCTTTCAGCCCATTTTT 57.050 42.857 0.00 0.00 0.00 1.94
4956 7226 0.099436 GCAAGCAAATGCCTAGGTCG 59.901 55.000 11.31 0.00 43.38 4.79
5107 7377 9.595823 GTAGTTCAGGCTATTTTATACTCACAA 57.404 33.333 0.00 0.00 0.00 3.33
5185 7456 2.290705 GGGTTACCTTGCACATGGTAGT 60.291 50.000 13.31 0.00 40.67 2.73
5248 7544 7.413475 AGCTAAGCAAACATTATATCGACAG 57.587 36.000 0.00 0.00 0.00 3.51
5251 7547 8.607441 ATCAAGCTAAGCAAACATTATATCGA 57.393 30.769 0.00 0.00 0.00 3.59
5279 7598 1.679898 GTCCACCCCTGTTCTCCAG 59.320 63.158 0.00 0.00 41.15 3.86
5317 7638 0.755686 CCTCCTACATCTGCTCCACC 59.244 60.000 0.00 0.00 0.00 4.61
5335 7656 1.953231 GCATCTTCCAAAGCTGGGCC 61.953 60.000 0.00 0.00 43.71 5.80
5337 7658 1.067354 GTTGCATCTTCCAAAGCTGGG 60.067 52.381 0.00 0.00 43.71 4.45
5379 7731 5.105752 AGTAGCAATGTTCTTCATCGTCTC 58.894 41.667 0.00 0.00 35.48 3.36
5405 7758 5.636965 TCGACGGTTTCAAATTTTATACGGA 59.363 36.000 0.00 0.00 0.00 4.69
5462 8033 8.066595 CCTTTCTAGCATCAATCTTTAATCACG 58.933 37.037 0.00 0.00 0.00 4.35
5529 8105 2.028476 TCCCCATTAGTGATATTCGGCG 60.028 50.000 0.00 0.00 0.00 6.46
5540 8116 4.687219 GCAAGCACTAGATTCCCCATTAGT 60.687 45.833 0.00 0.00 0.00 2.24
5541 8117 3.817647 GCAAGCACTAGATTCCCCATTAG 59.182 47.826 0.00 0.00 0.00 1.73
5648 8224 5.899631 TTCCCTCCTACTGTGTAAACTTT 57.100 39.130 0.00 0.00 0.00 2.66
5665 8244 3.627577 GCACATCAACACGATAATTCCCT 59.372 43.478 0.00 0.00 31.20 4.20
5700 8279 1.883084 GAATGGGGTAGAGCGCACG 60.883 63.158 11.47 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.