Multiple sequence alignment - TraesCS6D01G005100

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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 TraesCS6D01G005100 chr6D 100.000 3477 0 0 1 3477 2271826 2275302 0.000000e+00 6421.0
1 TraesCS6D01G005100 chr6D 95.488 820 20 13 2660 3477 2244595 2243791 0.000000e+00 1293.0
2 TraesCS6D01G005100 chr3B 83.766 1965 119 72 653 2526 772894889 772896744 0.000000e+00 1677.0
3 TraesCS6D01G005100 chr3B 88.864 449 23 12 3055 3477 772897434 772897881 8.550000e-146 527.0
4 TraesCS6D01G005100 chr3B 83.817 482 45 21 2575 3033 772896846 772897317 8.920000e-116 427.0
5 TraesCS6D01G005100 chr3B 82.424 165 11 9 256 418 772894371 772894519 1.010000e-25 128.0
6 TraesCS6D01G005100 chr6A 86.507 1549 90 51 1042 2531 637726 639214 0.000000e+00 1592.0
7 TraesCS6D01G005100 chr6A 86.364 638 45 31 1 620 636601 637214 0.000000e+00 658.0
8 TraesCS6D01G005100 chr6A 84.134 479 40 19 2580 3033 639299 639766 6.890000e-117 431.0
9 TraesCS6D01G005100 chr6A 83.791 364 35 15 2584 2942 615339 614995 1.200000e-84 324.0
10 TraesCS6D01G005100 chr6A 96.703 182 5 1 3158 3339 639954 640134 5.640000e-78 302.0
11 TraesCS6D01G005100 chr6A 88.757 169 12 6 646 813 637417 637579 2.120000e-47 200.0
12 TraesCS6D01G005100 chr6A 92.701 137 9 1 3341 3477 640169 640304 2.740000e-46 196.0
13 TraesCS6D01G005100 chr6A 92.424 132 9 1 880 1010 637594 637725 1.650000e-43 187.0
14 TraesCS6D01G005100 chr6A 91.209 91 2 2 3220 3309 614593 614508 6.100000e-23 119.0
15 TraesCS6D01G005100 chr6B 86.390 1036 71 21 1539 2531 3882320 3881312 0.000000e+00 1068.0
16 TraesCS6D01G005100 chr6B 85.573 707 55 20 830 1506 3883158 3882469 0.000000e+00 697.0
17 TraesCS6D01G005100 chr6B 83.308 647 40 26 1 614 3883945 3883334 5.110000e-148 534.0
18 TraesCS6D01G005100 chr6B 87.783 442 27 5 3063 3477 4138586 4139027 3.120000e-135 492.0
19 TraesCS6D01G005100 chr6B 87.010 408 39 9 2623 3017 3881175 3880769 6.850000e-122 448.0
20 TraesCS6D01G005100 chr6B 89.439 303 31 1 2726 3028 4138175 4138476 7.040000e-102 381.0
21 TraesCS6D01G005100 chr6B 80.465 215 24 11 3123 3325 139853199 139852991 7.780000e-32 148.0
22 TraesCS6D01G005100 chr6B 80.769 208 21 12 3150 3345 420517071 420517271 1.010000e-30 145.0
23 TraesCS6D01G005100 chr5A 88.722 133 13 2 2858 2989 486768426 486768557 9.990000e-36 161.0
24 TraesCS6D01G005100 chr5B 78.723 235 31 12 3123 3345 678552397 678552624 4.680000e-29 139.0
25 TraesCS6D01G005100 chr2A 80.556 144 26 2 1831 1973 16419810 16419952 3.670000e-20 110.0
26 TraesCS6D01G005100 chr2A 97.500 40 1 0 1739 1778 16419751 16419790 6.230000e-08 69.4
27 TraesCS6D01G005100 chr2D 79.861 144 27 2 1831 1973 13896802 13896660 1.710000e-18 104.0
28 TraesCS6D01G005100 chr2D 83.696 92 9 4 3220 3310 633491555 633491641 8.000000e-12 82.4
29 TraesCS6D01G005100 chr2D 97.500 40 1 0 1739 1778 13896861 13896822 6.230000e-08 69.4
30 TraesCS6D01G005100 chr2B 97.500 40 1 0 1739 1778 25258536 25258497 6.230000e-08 69.4


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 TraesCS6D01G005100 chr6D 2271826 2275302 3476 False 6421.000000 6421 100.000000 1 3477 1 chr6D.!!$F1 3476
1 TraesCS6D01G005100 chr6D 2243791 2244595 804 True 1293.000000 1293 95.488000 2660 3477 1 chr6D.!!$R1 817
2 TraesCS6D01G005100 chr3B 772894371 772897881 3510 False 689.750000 1677 84.717750 256 3477 4 chr3B.!!$F1 3221
3 TraesCS6D01G005100 chr6A 636601 640304 3703 False 509.428571 1592 89.655714 1 3477 7 chr6A.!!$F1 3476
4 TraesCS6D01G005100 chr6A 614508 615339 831 True 221.500000 324 87.500000 2584 3309 2 chr6A.!!$R1 725
5 TraesCS6D01G005100 chr6B 3880769 3883945 3176 True 686.750000 1068 85.570250 1 3017 4 chr6B.!!$R2 3016
6 TraesCS6D01G005100 chr6B 4138175 4139027 852 False 436.500000 492 88.611000 2726 3477 2 chr6B.!!$F2 751

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
459 508 0.098905 CTCCACGTGACGTCGATGAT 59.901 55.0 19.30 0.0 38.32 2.45 F
1080 1378 0.040058 TGTTTGCCATGGCTCCTCAT 59.960 50.0 35.53 0.0 42.51 2.90 F
1111 1416 0.105709 TCTCCCCATCCTCATGCGTA 60.106 55.0 0.00 0.0 0.00 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2560 0.389817 TCTGTTGAATCCTCGCCGTG 60.390 55.0 0.00 0.00 0.00 4.94 R
2049 2563 0.462759 CCCTCTGTTGAATCCTCGCC 60.463 60.0 0.00 0.00 0.00 5.54 R
2650 3274 0.609131 ATCAACTTGGGCCGTTGGAG 60.609 55.0 19.85 6.76 41.47 3.86 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
313 336 2.436109 GGGAGGGAAGCAACAGCA 59.564 61.111 0.00 0.00 0.00 4.41
428 477 7.061789 GCTTTTGCAACCACACTTGTTATATAC 59.938 37.037 0.00 0.00 46.58 1.47
434 483 5.666462 ACCACACTTGTTATATACATGCGA 58.334 37.500 0.00 0.00 36.44 5.10
435 484 6.288294 ACCACACTTGTTATATACATGCGAT 58.712 36.000 0.00 0.00 36.44 4.58
438 487 7.003648 CACACTTGTTATATACATGCGATTCG 58.996 38.462 0.62 0.62 36.44 3.34
439 488 6.009474 CACTTGTTATATACATGCGATTCGC 58.991 40.000 23.58 23.58 42.30 4.70
440 489 5.120208 ACTTGTTATATACATGCGATTCGCC 59.880 40.000 26.71 10.60 41.69 5.54
441 490 5.234752 TTGTTATATACATGCGATTCGCCT 58.765 37.500 26.71 15.60 41.69 5.52
442 491 5.347635 TTGTTATATACATGCGATTCGCCTC 59.652 40.000 26.71 4.77 41.69 4.70
443 492 7.556006 TTGTTATATACATGCGATTCGCCTCC 61.556 42.308 26.71 1.54 41.69 4.30
444 493 9.821062 TTGTTATATACATGCGATTCGCCTCCA 62.821 40.741 26.71 9.85 41.69 3.86
449 498 2.180769 CGATTCGCCTCCACGTGA 59.819 61.111 19.30 2.03 0.00 4.35
450 499 2.158959 CGATTCGCCTCCACGTGAC 61.159 63.158 19.30 2.31 0.00 3.67
451 500 2.126071 ATTCGCCTCCACGTGACG 60.126 61.111 19.30 14.84 0.00 4.35
452 501 2.814183 GATTCGCCTCCACGTGACGT 62.814 60.000 19.30 4.10 42.36 4.34
453 502 2.814183 ATTCGCCTCCACGTGACGTC 62.814 60.000 19.30 9.11 38.32 4.34
455 504 4.034258 GCCTCCACGTGACGTCGA 62.034 66.667 19.30 6.43 38.32 4.20
456 505 2.875485 CCTCCACGTGACGTCGAT 59.125 61.111 19.30 0.00 38.32 3.59
457 506 1.514228 CCTCCACGTGACGTCGATG 60.514 63.158 19.30 0.00 38.32 3.84
458 507 1.500396 CTCCACGTGACGTCGATGA 59.500 57.895 19.30 1.75 38.32 2.92
459 508 0.098905 CTCCACGTGACGTCGATGAT 59.901 55.000 19.30 0.00 38.32 2.45
471 520 2.681706 GTCGATGATGATTCGCTCCAT 58.318 47.619 0.00 0.00 36.56 3.41
482 531 1.226688 CGCTCCATGTGACGTCGAT 60.227 57.895 11.62 2.34 0.00 3.59
485 534 1.536922 GCTCCATGTGACGTCGATGAT 60.537 52.381 22.55 5.93 0.00 2.45
486 535 2.287608 GCTCCATGTGACGTCGATGATA 60.288 50.000 22.55 12.62 0.00 2.15
553 610 5.106317 GCTCATTTTCCAGTTAACCGATCAA 60.106 40.000 0.88 0.00 0.00 2.57
560 621 4.525487 TCCAGTTAACCGATCAACAGTACT 59.475 41.667 0.88 0.00 0.00 2.73
626 693 3.157932 GCTTTTGCAACCACACTGTTA 57.842 42.857 0.00 0.00 46.58 2.41
627 694 3.716601 GCTTTTGCAACCACACTGTTAT 58.283 40.909 0.00 0.00 46.58 1.89
628 695 4.865776 GCTTTTGCAACCACACTGTTATA 58.134 39.130 0.00 0.00 46.58 0.98
630 697 6.616947 GCTTTTGCAACCACACTGTTATATA 58.383 36.000 0.00 0.00 46.58 0.86
631 698 7.257722 GCTTTTGCAACCACACTGTTATATAT 58.742 34.615 0.00 0.00 46.58 0.86
633 700 6.935741 TTGCAACCACACTGTTATATATCC 57.064 37.500 0.00 0.00 0.00 2.59
634 701 5.995446 TGCAACCACACTGTTATATATCCA 58.005 37.500 0.00 0.00 0.00 3.41
695 969 1.682323 GAACGGAGGAACCCTAGCTAG 59.318 57.143 14.20 14.20 31.76 3.42
696 970 0.756070 ACGGAGGAACCCTAGCTAGC 60.756 60.000 15.74 6.62 31.76 3.42
697 971 1.465200 CGGAGGAACCCTAGCTAGCC 61.465 65.000 15.74 10.85 31.76 3.93
701 975 1.448069 GAACCCTAGCTAGCCAGGC 59.552 63.158 22.49 1.84 0.00 4.85
706 980 1.699634 CCCTAGCTAGCCAGGCAATTA 59.300 52.381 22.49 0.00 0.00 1.40
760 1034 0.960861 GGAGTGGTTGCAGTTAGGCC 60.961 60.000 0.00 0.00 0.00 5.19
761 1035 0.250727 GAGTGGTTGCAGTTAGGCCA 60.251 55.000 5.01 0.00 0.00 5.36
802 1076 5.287674 AGTCCATCACTCACTATCAATGG 57.712 43.478 0.00 0.00 35.95 3.16
810 1084 3.713764 ACTCACTATCAATGGAAGGGGAG 59.286 47.826 4.08 4.08 36.12 4.30
813 1087 1.074566 CTATCAATGGAAGGGGAGGGC 59.925 57.143 0.00 0.00 0.00 5.19
814 1088 0.925720 ATCAATGGAAGGGGAGGGCA 60.926 55.000 0.00 0.00 0.00 5.36
815 1089 1.380380 CAATGGAAGGGGAGGGCAC 60.380 63.158 0.00 0.00 0.00 5.01
830 1104 1.265236 GGCACCCACCAATTCAATCA 58.735 50.000 0.00 0.00 0.00 2.57
831 1105 1.622811 GGCACCCACCAATTCAATCAA 59.377 47.619 0.00 0.00 0.00 2.57
832 1106 2.236893 GGCACCCACCAATTCAATCAAT 59.763 45.455 0.00 0.00 0.00 2.57
833 1107 3.524541 GCACCCACCAATTCAATCAATC 58.475 45.455 0.00 0.00 0.00 2.67
834 1108 3.055963 GCACCCACCAATTCAATCAATCA 60.056 43.478 0.00 0.00 0.00 2.57
835 1109 4.563168 GCACCCACCAATTCAATCAATCAA 60.563 41.667 0.00 0.00 0.00 2.57
836 1110 5.172934 CACCCACCAATTCAATCAATCAAG 58.827 41.667 0.00 0.00 0.00 3.02
878 1155 2.006888 GTGTGTGTGTGTAGCTTGTGT 58.993 47.619 0.00 0.00 0.00 3.72
887 1164 1.202687 TGTAGCTTGTGTGCTGCTTCT 60.203 47.619 0.00 0.00 44.19 2.85
890 1167 0.664761 GCTTGTGTGCTGCTTCTTCA 59.335 50.000 0.00 0.00 0.00 3.02
892 1169 2.667724 GCTTGTGTGCTGCTTCTTCATC 60.668 50.000 0.00 0.00 0.00 2.92
1003 1284 8.447787 AATTGTTATCTCGTTGTTACAAATGC 57.552 30.769 0.00 0.00 0.00 3.56
1051 1332 6.183361 TGTTAATCATCCATCCATCCATCCTT 60.183 38.462 0.00 0.00 0.00 3.36
1080 1378 0.040058 TGTTTGCCATGGCTCCTCAT 59.960 50.000 35.53 0.00 42.51 2.90
1082 1380 0.627451 TTTGCCATGGCTCCTCATCT 59.373 50.000 35.53 0.00 42.51 2.90
1095 1393 4.692228 CTCCTCATCTGGTAAAGCTTCTC 58.308 47.826 0.00 0.00 0.00 2.87
1102 1407 1.564348 TGGTAAAGCTTCTCCCCATCC 59.436 52.381 14.57 4.21 0.00 3.51
1109 1414 0.250209 CTTCTCCCCATCCTCATGCG 60.250 60.000 0.00 0.00 0.00 4.73
1111 1416 0.105709 TCTCCCCATCCTCATGCGTA 60.106 55.000 0.00 0.00 0.00 4.42
1116 1421 2.487086 CCCCATCCTCATGCGTATTCAA 60.487 50.000 0.00 0.00 0.00 2.69
1123 1428 5.052481 TCCTCATGCGTATTCAATGAAGAG 58.948 41.667 1.10 0.93 0.00 2.85
1126 1431 6.145209 CCTCATGCGTATTCAATGAAGAGTAG 59.855 42.308 1.10 0.00 0.00 2.57
1128 1433 4.693283 TGCGTATTCAATGAAGAGTAGGG 58.307 43.478 1.10 0.00 0.00 3.53
1129 1434 4.161565 TGCGTATTCAATGAAGAGTAGGGT 59.838 41.667 1.10 0.00 0.00 4.34
1130 1435 4.508124 GCGTATTCAATGAAGAGTAGGGTG 59.492 45.833 1.10 0.00 0.00 4.61
1131 1436 5.661458 CGTATTCAATGAAGAGTAGGGTGT 58.339 41.667 1.10 0.00 0.00 4.16
1132 1437 5.520288 CGTATTCAATGAAGAGTAGGGTGTG 59.480 44.000 1.10 0.00 0.00 3.82
1133 1438 4.974645 TTCAATGAAGAGTAGGGTGTGT 57.025 40.909 0.00 0.00 0.00 3.72
1134 1439 4.537135 TCAATGAAGAGTAGGGTGTGTC 57.463 45.455 0.00 0.00 0.00 3.67
1136 1441 4.593206 TCAATGAAGAGTAGGGTGTGTCTT 59.407 41.667 0.00 0.00 31.85 3.01
1139 1446 3.964688 TGAAGAGTAGGGTGTGTCTTGAA 59.035 43.478 0.00 0.00 29.28 2.69
1209 1541 0.327000 ACCATGGAGGAGGAAGAGGG 60.327 60.000 21.47 0.00 41.22 4.30
1220 1561 0.849417 GGAAGAGGGGGAGCATCATT 59.151 55.000 0.00 0.00 36.25 2.57
1231 1572 1.003116 GAGCATCATTGTCATGGCGAC 60.003 52.381 0.00 0.00 39.31 5.19
1265 1606 3.117171 CGTGTGAGCAGGAGCAGC 61.117 66.667 0.00 0.00 45.49 5.25
1271 1612 4.411981 AGCAGGAGCAGCAGCAGG 62.412 66.667 3.17 0.00 45.49 4.85
1273 1614 2.350134 CAGGAGCAGCAGCAGGAA 59.650 61.111 3.17 0.00 45.49 3.36
1446 1811 2.224821 TCAGGATGATGGCCACCTC 58.775 57.895 8.16 2.62 42.56 3.85
1447 1812 1.150081 CAGGATGATGGCCACCTCC 59.850 63.158 8.16 15.00 39.69 4.30
1448 1813 1.308128 AGGATGATGGCCACCTCCA 60.308 57.895 24.61 14.69 40.97 3.86
1451 1816 1.925285 GATGATGGCCACCTCCACCA 61.925 60.000 8.16 0.00 39.25 4.17
1576 2057 4.863707 ATGCCGATGACGAGCATT 57.136 50.000 0.00 0.00 45.93 3.56
1656 2137 4.353437 GTTCCGGGTGTCGTCGCT 62.353 66.667 0.00 0.00 37.11 4.93
1657 2138 4.351938 TTCCGGGTGTCGTCGCTG 62.352 66.667 0.00 0.00 37.11 5.18
1661 2142 4.338539 GGGTGTCGTCGCTGTCGT 62.339 66.667 0.00 0.00 36.96 4.34
1662 2143 2.799916 GGTGTCGTCGCTGTCGTC 60.800 66.667 0.00 0.00 36.96 4.20
1663 2144 3.157523 GTGTCGTCGCTGTCGTCG 61.158 66.667 0.00 5.26 45.67 5.12
1798 2303 0.855855 TGGAGGAGGAGGAGGAGGAA 60.856 60.000 0.00 0.00 0.00 3.36
1799 2304 0.105709 GGAGGAGGAGGAGGAGGAAG 60.106 65.000 0.00 0.00 0.00 3.46
1800 2305 0.105709 GAGGAGGAGGAGGAGGAAGG 60.106 65.000 0.00 0.00 0.00 3.46
1801 2306 0.556380 AGGAGGAGGAGGAGGAAGGA 60.556 60.000 0.00 0.00 0.00 3.36
1802 2307 0.105709 GGAGGAGGAGGAGGAAGGAG 60.106 65.000 0.00 0.00 0.00 3.69
1803 2308 0.105709 GAGGAGGAGGAGGAAGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
1806 2311 2.770475 GGAGGAGGAAGGAGGGGC 60.770 72.222 0.00 0.00 0.00 5.80
1809 2314 3.803162 GGAGGAAGGAGGGGCAGC 61.803 72.222 0.00 0.00 0.00 5.25
1997 2508 4.548513 CTCCCCCTCCTCCTCCCG 62.549 77.778 0.00 0.00 0.00 5.14
2040 2554 0.679321 GGCAGCCAAGAAGAAGGAGG 60.679 60.000 6.55 0.00 0.00 4.30
2043 2557 2.431454 CAGCCAAGAAGAAGGAGGAAC 58.569 52.381 0.00 0.00 0.00 3.62
2046 2560 2.431454 CCAAGAAGAAGGAGGAACAGC 58.569 52.381 0.00 0.00 0.00 4.40
2048 2562 2.810852 CAAGAAGAAGGAGGAACAGCAC 59.189 50.000 0.00 0.00 0.00 4.40
2049 2563 1.001406 AGAAGAAGGAGGAACAGCACG 59.999 52.381 0.00 0.00 0.00 5.34
2050 2564 0.035458 AAGAAGGAGGAACAGCACGG 59.965 55.000 0.00 0.00 0.00 4.94
2051 2565 2.032681 AAGGAGGAACAGCACGGC 59.967 61.111 0.00 0.00 0.00 5.68
2055 2569 4.379243 AGGAACAGCACGGCGAGG 62.379 66.667 16.62 6.41 0.00 4.63
2057 2571 2.125512 GAACAGCACGGCGAGGAT 60.126 61.111 16.62 0.00 0.00 3.24
2058 2572 1.741770 GAACAGCACGGCGAGGATT 60.742 57.895 16.62 0.24 0.00 3.01
2059 2573 1.696832 GAACAGCACGGCGAGGATTC 61.697 60.000 16.62 6.90 0.00 2.52
2061 2575 1.741401 CAGCACGGCGAGGATTCAA 60.741 57.895 16.62 0.00 0.00 2.69
2062 2576 1.741770 AGCACGGCGAGGATTCAAC 60.742 57.895 16.62 0.00 0.00 3.18
2063 2577 2.032634 GCACGGCGAGGATTCAACA 61.033 57.895 16.62 0.00 0.00 3.33
2065 2579 0.389817 CACGGCGAGGATTCAACAGA 60.390 55.000 16.62 0.00 0.00 3.41
2104 2624 1.218316 GGTGATCCTGGTGACGGTC 59.782 63.158 0.00 0.00 33.66 4.79
2485 3030 3.643320 TCCCTCAGCCATAGACAACATAG 59.357 47.826 0.00 0.00 0.00 2.23
2505 3054 7.573916 CATAGTACATATGTAACTCTGCTGC 57.426 40.000 17.07 2.09 37.15 5.25
2506 3055 5.598416 AGTACATATGTAACTCTGCTGCA 57.402 39.130 17.07 0.88 31.52 4.41
2613 3229 8.777865 AAAAGGGCTTCTTGCTTTTATTTATC 57.222 30.769 0.00 0.00 42.39 1.75
2615 3231 5.885912 AGGGCTTCTTGCTTTTATTTATCGA 59.114 36.000 0.00 0.00 42.39 3.59
2617 3233 7.033185 GGGCTTCTTGCTTTTATTTATCGAAA 58.967 34.615 0.00 0.00 42.39 3.46
2619 3235 9.087424 GGCTTCTTGCTTTTATTTATCGAAATT 57.913 29.630 0.00 0.00 42.39 1.82
2650 3274 6.683974 ATATTTGTGTTCTCAGCATACACC 57.316 37.500 0.00 0.00 41.03 4.16
2655 3279 2.637382 TGTTCTCAGCATACACCTCCAA 59.363 45.455 0.00 0.00 0.00 3.53
2683 3311 5.053145 CCAAGTTGATACCTAGCTTAGCTG 58.947 45.833 17.97 3.26 40.10 4.24
2685 3313 5.523438 AGTTGATACCTAGCTTAGCTGTC 57.477 43.478 17.97 7.56 40.10 3.51
2692 3320 2.102252 CCTAGCTTAGCTGTCCCTTCTG 59.898 54.545 17.97 0.00 40.10 3.02
2697 3325 0.833287 TAGCTGTCCCTTCTGCATCC 59.167 55.000 0.00 0.00 35.31 3.51
2702 3330 2.002977 TCCCTTCTGCATCCCCTGG 61.003 63.158 0.00 0.00 0.00 4.45
2710 3340 2.824041 CATCCCCTGGTTTCGGCG 60.824 66.667 0.00 0.00 0.00 6.46
2763 3403 1.263356 TCCCCTACAACTCGTCCTTG 58.737 55.000 0.00 0.00 0.00 3.61
2769 3409 0.549469 ACAACTCGTCCTTGGGGTTT 59.451 50.000 0.00 0.00 0.00 3.27
2811 3451 4.047059 GTCGTCGAACCCGAGCCA 62.047 66.667 0.00 0.00 46.52 4.75
2814 3454 2.582498 GTCGAACCCGAGCCATCG 60.582 66.667 0.00 0.00 46.52 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.807622 CCTCTCGAGCAAAACAAGTGTTA 59.192 43.478 7.81 0.00 37.25 2.41
13 14 0.250727 CCCCCTCTCGAGCAAAACAA 60.251 55.000 7.81 0.00 0.00 2.83
434 483 2.126071 CGTCACGTGGAGGCGAAT 60.126 61.111 17.00 0.00 35.59 3.34
435 484 3.547249 GACGTCACGTGGAGGCGAA 62.547 63.158 8.08 0.00 41.37 4.70
438 487 3.338126 ATCGACGTCACGTGGAGGC 62.338 63.158 20.07 11.28 46.21 4.70
439 488 1.514228 CATCGACGTCACGTGGAGG 60.514 63.158 20.07 16.44 46.21 4.30
440 489 0.098905 ATCATCGACGTCACGTGGAG 59.901 55.000 20.07 12.13 46.21 3.86
441 490 0.179174 CATCATCGACGTCACGTGGA 60.179 55.000 17.81 17.81 46.93 4.02
442 491 0.179174 TCATCATCGACGTCACGTGG 60.179 55.000 8.08 6.85 41.37 4.94
443 492 1.827578 ATCATCATCGACGTCACGTG 58.172 50.000 8.08 9.94 41.37 4.49
444 493 2.451132 GAATCATCATCGACGTCACGT 58.549 47.619 17.16 0.09 45.10 4.49
445 494 1.444634 CGAATCATCATCGACGTCACG 59.555 52.381 17.16 2.92 42.76 4.35
446 495 1.188138 GCGAATCATCATCGACGTCAC 59.812 52.381 17.16 0.00 42.76 3.67
447 496 1.065551 AGCGAATCATCATCGACGTCA 59.934 47.619 17.16 3.13 42.76 4.35
448 497 1.711298 GAGCGAATCATCATCGACGTC 59.289 52.381 5.18 5.18 42.76 4.34
449 498 1.600663 GGAGCGAATCATCATCGACGT 60.601 52.381 0.00 0.00 42.76 4.34
450 499 1.056103 GGAGCGAATCATCATCGACG 58.944 55.000 0.00 0.00 42.76 5.12
451 500 2.140065 TGGAGCGAATCATCATCGAC 57.860 50.000 0.00 0.00 42.76 4.20
452 501 2.036346 ACATGGAGCGAATCATCATCGA 59.964 45.455 0.00 0.00 42.76 3.59
453 502 2.157085 CACATGGAGCGAATCATCATCG 59.843 50.000 0.00 0.00 42.99 3.84
454 503 3.186001 GTCACATGGAGCGAATCATCATC 59.814 47.826 0.00 0.00 0.00 2.92
455 504 3.136763 GTCACATGGAGCGAATCATCAT 58.863 45.455 0.00 0.00 0.00 2.45
456 505 2.554142 GTCACATGGAGCGAATCATCA 58.446 47.619 0.00 0.00 0.00 3.07
457 506 1.524355 CGTCACATGGAGCGAATCATC 59.476 52.381 0.00 0.00 0.00 2.92
458 507 1.134699 ACGTCACATGGAGCGAATCAT 60.135 47.619 11.02 0.00 0.00 2.45
459 508 0.246360 ACGTCACATGGAGCGAATCA 59.754 50.000 11.02 0.00 0.00 2.57
471 520 4.537015 GTCATCATATCATCGACGTCACA 58.463 43.478 17.16 0.88 0.00 3.58
482 531 3.123050 CAAACGCTCGGTCATCATATCA 58.877 45.455 0.00 0.00 0.00 2.15
485 534 2.951457 TCAAACGCTCGGTCATCATA 57.049 45.000 0.00 0.00 0.00 2.15
486 535 2.205074 GATCAAACGCTCGGTCATCAT 58.795 47.619 0.00 0.00 0.00 2.45
553 610 9.436957 CAATTCTTGTAGACCAAATAGTACTGT 57.563 33.333 5.39 0.00 31.20 3.55
560 621 8.458573 ACAACACAATTCTTGTAGACCAAATA 57.541 30.769 0.00 0.00 43.23 1.40
584 645 4.618489 GCAACACAGAGATGCATAACAAAC 59.382 41.667 0.00 0.00 44.62 2.93
695 969 1.322538 CCCACTGGTAATTGCCTGGC 61.323 60.000 20.60 12.87 32.57 4.85
696 970 0.039618 ACCCACTGGTAATTGCCTGG 59.960 55.000 20.60 16.49 45.45 4.45
697 971 1.176527 CACCCACTGGTAATTGCCTG 58.823 55.000 16.21 16.21 45.57 4.85
701 975 2.754552 CACCATCACCCACTGGTAATTG 59.245 50.000 0.00 0.00 45.57 2.32
760 1034 6.999272 TGGACTTCTACTACCTATCTAGCTTG 59.001 42.308 0.00 0.00 0.00 4.01
761 1035 7.151694 TGGACTTCTACTACCTATCTAGCTT 57.848 40.000 0.00 0.00 0.00 3.74
802 1076 4.048470 GTGGGTGCCCTCCCCTTC 62.048 72.222 8.91 0.00 46.48 3.46
810 1084 0.536724 GATTGAATTGGTGGGTGCCC 59.463 55.000 0.00 0.00 0.00 5.36
813 1087 4.804868 TGATTGATTGAATTGGTGGGTG 57.195 40.909 0.00 0.00 0.00 4.61
814 1088 4.322953 GCTTGATTGATTGAATTGGTGGGT 60.323 41.667 0.00 0.00 0.00 4.51
815 1089 4.081309 AGCTTGATTGATTGAATTGGTGGG 60.081 41.667 0.00 0.00 0.00 4.61
816 1090 5.080969 AGCTTGATTGATTGAATTGGTGG 57.919 39.130 0.00 0.00 0.00 4.61
817 1091 5.575606 GTGAGCTTGATTGATTGAATTGGTG 59.424 40.000 0.00 0.00 0.00 4.17
818 1092 5.479375 AGTGAGCTTGATTGATTGAATTGGT 59.521 36.000 0.00 0.00 0.00 3.67
819 1093 5.962433 AGTGAGCTTGATTGATTGAATTGG 58.038 37.500 0.00 0.00 0.00 3.16
820 1094 6.527023 GTGAGTGAGCTTGATTGATTGAATTG 59.473 38.462 0.00 0.00 0.00 2.32
823 1097 5.180680 CAGTGAGTGAGCTTGATTGATTGAA 59.819 40.000 0.00 0.00 0.00 2.69
824 1098 4.694037 CAGTGAGTGAGCTTGATTGATTGA 59.306 41.667 0.00 0.00 0.00 2.57
825 1099 4.694037 TCAGTGAGTGAGCTTGATTGATTG 59.306 41.667 0.00 0.00 0.00 2.67
828 1102 3.323115 AGTCAGTGAGTGAGCTTGATTGA 59.677 43.478 0.00 0.00 35.13 2.57
829 1103 3.661944 AGTCAGTGAGTGAGCTTGATTG 58.338 45.455 0.00 0.00 35.13 2.67
830 1104 4.348863 AAGTCAGTGAGTGAGCTTGATT 57.651 40.909 0.00 0.00 35.13 2.57
831 1105 5.011533 ACTTAAGTCAGTGAGTGAGCTTGAT 59.988 40.000 1.12 0.00 35.13 2.57
832 1106 4.342378 ACTTAAGTCAGTGAGTGAGCTTGA 59.658 41.667 1.12 6.30 35.13 3.02
833 1107 4.447054 CACTTAAGTCAGTGAGTGAGCTTG 59.553 45.833 4.77 0.00 46.29 4.01
834 1108 4.100189 ACACTTAAGTCAGTGAGTGAGCTT 59.900 41.667 14.42 7.19 46.29 3.74
835 1109 3.639094 ACACTTAAGTCAGTGAGTGAGCT 59.361 43.478 14.42 0.00 46.29 4.09
836 1110 3.738282 CACACTTAAGTCAGTGAGTGAGC 59.262 47.826 17.13 0.00 46.29 4.26
878 1155 3.755378 GGAGAAAAGATGAAGAAGCAGCA 59.245 43.478 0.00 0.00 0.00 4.41
887 1164 4.407365 GTGGGAAAGGGAGAAAAGATGAA 58.593 43.478 0.00 0.00 0.00 2.57
890 1167 2.290960 CCGTGGGAAAGGGAGAAAAGAT 60.291 50.000 0.00 0.00 35.72 2.40
892 1169 1.534729 CCGTGGGAAAGGGAGAAAAG 58.465 55.000 0.00 0.00 35.72 2.27
989 1270 2.579541 TGCATCGCATTTGTAACAACG 58.420 42.857 0.00 0.00 31.71 4.10
1051 1332 1.053264 ATGGCAAACAAGCACCCCAA 61.053 50.000 0.00 0.00 35.83 4.12
1080 1378 2.038863 TGGGGAGAAGCTTTACCAGA 57.961 50.000 19.47 6.94 0.00 3.86
1082 1380 1.564348 GGATGGGGAGAAGCTTTACCA 59.436 52.381 19.47 16.16 0.00 3.25
1095 1393 1.072173 TGAATACGCATGAGGATGGGG 59.928 52.381 0.00 0.00 44.84 4.96
1102 1407 5.980698 ACTCTTCATTGAATACGCATGAG 57.019 39.130 0.00 0.00 0.00 2.90
1109 1414 6.407202 ACACACCCTACTCTTCATTGAATAC 58.593 40.000 0.00 0.00 0.00 1.89
1111 1416 5.249393 AGACACACCCTACTCTTCATTGAAT 59.751 40.000 0.00 0.00 0.00 2.57
1116 1421 4.160329 TCAAGACACACCCTACTCTTCAT 58.840 43.478 0.00 0.00 0.00 2.57
1123 1428 3.008049 ACCATCTTCAAGACACACCCTAC 59.992 47.826 0.00 0.00 0.00 3.18
1126 1431 2.568623 ACCATCTTCAAGACACACCC 57.431 50.000 0.00 0.00 0.00 4.61
1128 1433 3.744660 AGGAACCATCTTCAAGACACAC 58.255 45.455 0.00 0.00 0.00 3.82
1129 1434 4.136796 CAAGGAACCATCTTCAAGACACA 58.863 43.478 0.00 0.00 0.00 3.72
1130 1435 4.023707 CACAAGGAACCATCTTCAAGACAC 60.024 45.833 0.00 0.00 0.00 3.67
1131 1436 4.136796 CACAAGGAACCATCTTCAAGACA 58.863 43.478 0.00 0.00 0.00 3.41
1132 1437 3.057946 GCACAAGGAACCATCTTCAAGAC 60.058 47.826 0.00 0.00 0.00 3.01
1133 1438 3.149196 GCACAAGGAACCATCTTCAAGA 58.851 45.455 0.00 0.00 0.00 3.02
1134 1439 2.886523 TGCACAAGGAACCATCTTCAAG 59.113 45.455 0.00 0.00 0.00 3.02
1136 1441 2.507484 CTGCACAAGGAACCATCTTCA 58.493 47.619 0.00 0.00 0.00 3.02
1161 1481 2.049433 CGGCGTCGTCCTTGTTCT 60.049 61.111 0.00 0.00 0.00 3.01
1162 1482 3.774702 GCGGCGTCGTCCTTGTTC 61.775 66.667 12.58 0.00 38.89 3.18
1192 1515 1.059006 CCCCCTCTTCCTCCTCCATG 61.059 65.000 0.00 0.00 0.00 3.66
1209 1541 0.672342 GCCATGACAATGATGCTCCC 59.328 55.000 0.00 0.00 35.67 4.30
1265 1606 2.110967 CGGCATCCTGTTCCTGCTG 61.111 63.158 0.00 0.00 36.18 4.41
1271 1612 1.648467 GGCTTGTCGGCATCCTGTTC 61.648 60.000 0.00 0.00 38.25 3.18
1273 1614 2.045926 GGCTTGTCGGCATCCTGT 60.046 61.111 0.00 0.00 38.25 4.00
1446 1811 2.460853 AAGGTGGTGGAGGTGGTGG 61.461 63.158 0.00 0.00 0.00 4.61
1447 1812 1.228245 CAAGGTGGTGGAGGTGGTG 60.228 63.158 0.00 0.00 0.00 4.17
1448 1813 2.460853 CCAAGGTGGTGGAGGTGGT 61.461 63.158 0.00 0.00 41.65 4.16
2008 2519 3.803082 CTGCCGGTGCCATTGTCG 61.803 66.667 1.90 0.00 36.33 4.35
2009 2520 4.120331 GCTGCCGGTGCCATTGTC 62.120 66.667 1.90 0.00 36.33 3.18
2019 2530 2.042831 CCTTCTTCTTGGCTGCCGG 61.043 63.158 14.98 9.61 0.00 6.13
2020 2531 1.003355 TCCTTCTTCTTGGCTGCCG 60.003 57.895 14.98 0.00 0.00 5.69
2029 2540 1.001406 CGTGCTGTTCCTCCTTCTTCT 59.999 52.381 0.00 0.00 0.00 2.85
2040 2554 1.696832 GAATCCTCGCCGTGCTGTTC 61.697 60.000 0.00 0.00 0.00 3.18
2043 2557 1.741401 TTGAATCCTCGCCGTGCTG 60.741 57.895 0.00 0.00 0.00 4.41
2046 2560 0.389817 TCTGTTGAATCCTCGCCGTG 60.390 55.000 0.00 0.00 0.00 4.94
2048 2562 0.807667 CCTCTGTTGAATCCTCGCCG 60.808 60.000 0.00 0.00 0.00 6.46
2049 2563 0.462759 CCCTCTGTTGAATCCTCGCC 60.463 60.000 0.00 0.00 0.00 5.54
2050 2564 0.462759 CCCCTCTGTTGAATCCTCGC 60.463 60.000 0.00 0.00 0.00 5.03
2051 2565 0.905357 ACCCCTCTGTTGAATCCTCG 59.095 55.000 0.00 0.00 0.00 4.63
2055 2569 1.826385 CCACACCCCTCTGTTGAATC 58.174 55.000 0.00 0.00 0.00 2.52
2057 2571 1.150536 GCCACACCCCTCTGTTGAA 59.849 57.895 0.00 0.00 0.00 2.69
2058 2572 2.836154 GCCACACCCCTCTGTTGA 59.164 61.111 0.00 0.00 0.00 3.18
2059 2573 2.669569 CGCCACACCCCTCTGTTG 60.670 66.667 0.00 0.00 0.00 3.33
2104 2624 1.333931 CAGAAGTATGCCAGCATGCTG 59.666 52.381 35.88 35.88 46.01 4.41
2116 2636 2.191400 TGCTCCAGGAAGCAGAAGTAT 58.809 47.619 8.95 0.00 47.00 2.12
2252 2773 1.601419 GAGTAGGCCCACACGTAGCA 61.601 60.000 3.54 0.00 0.00 3.49
2266 2787 2.125912 AACTGCAGCGCCGAGTAG 60.126 61.111 15.27 6.19 0.00 2.57
2485 3030 5.352284 AGTGCAGCAGAGTTACATATGTAC 58.648 41.667 15.20 10.44 0.00 2.90
2571 3168 6.153340 AGCCCTTTTCTTACTACACATACGTA 59.847 38.462 0.00 0.00 0.00 3.57
2572 3169 5.046807 AGCCCTTTTCTTACTACACATACGT 60.047 40.000 0.00 0.00 0.00 3.57
2573 3170 5.416947 AGCCCTTTTCTTACTACACATACG 58.583 41.667 0.00 0.00 0.00 3.06
2574 3171 7.104290 AGAAGCCCTTTTCTTACTACACATAC 58.896 38.462 0.00 0.00 33.74 2.39
2575 3172 7.253905 AGAAGCCCTTTTCTTACTACACATA 57.746 36.000 0.00 0.00 33.74 2.29
2577 3174 5.562298 AGAAGCCCTTTTCTTACTACACA 57.438 39.130 0.00 0.00 33.74 3.72
2578 3175 5.334957 GCAAGAAGCCCTTTTCTTACTACAC 60.335 44.000 1.13 0.00 43.62 2.90
2579 3176 4.760204 GCAAGAAGCCCTTTTCTTACTACA 59.240 41.667 1.13 0.00 43.62 2.74
2581 3178 5.242795 AGCAAGAAGCCCTTTTCTTACTA 57.757 39.130 1.13 0.00 43.62 1.82
2617 3233 8.887717 GCTGAGAACACAAATATTGACTAGAAT 58.112 33.333 0.00 0.00 0.00 2.40
2619 3235 7.386059 TGCTGAGAACACAAATATTGACTAGA 58.614 34.615 0.00 0.00 0.00 2.43
2620 3236 7.601073 TGCTGAGAACACAAATATTGACTAG 57.399 36.000 0.00 0.00 0.00 2.57
2621 3237 9.098355 GTATGCTGAGAACACAAATATTGACTA 57.902 33.333 0.00 0.00 0.00 2.59
2625 3245 6.968904 GGTGTATGCTGAGAACACAAATATTG 59.031 38.462 12.86 0.00 44.18 1.90
2650 3274 0.609131 ATCAACTTGGGCCGTTGGAG 60.609 55.000 19.85 6.76 41.47 3.86
2655 3279 1.485066 CTAGGTATCAACTTGGGCCGT 59.515 52.381 0.00 0.00 0.00 5.68
2683 3311 1.225704 CAGGGGATGCAGAAGGGAC 59.774 63.158 0.00 0.00 0.00 4.46
2685 3313 1.867595 AACCAGGGGATGCAGAAGGG 61.868 60.000 0.00 0.00 0.00 3.95
2692 3320 3.140814 GCCGAAACCAGGGGATGC 61.141 66.667 0.00 0.00 0.00 3.91
2702 3330 3.346631 TAGGAGCCGACGCCGAAAC 62.347 63.158 0.00 0.00 41.37 2.78
2710 3340 1.000506 TGACAACAAGTAGGAGCCGAC 59.999 52.381 0.00 0.00 0.00 4.79
2713 3343 2.749621 CCATTGACAACAAGTAGGAGCC 59.250 50.000 0.00 0.00 39.46 4.70
2763 3403 1.674651 GAGCTCCGGTTCAAACCCC 60.675 63.158 0.87 0.00 46.53 4.95
2769 3409 1.883732 CGAGAAGAGCTCCGGTTCA 59.116 57.895 10.93 0.00 40.70 3.18


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

AutoCloner maintained by Alex Coulton.