Multiple sequence alignment - TraesCS1D01G199900

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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 TraesCS1D01G199900 chr1D 100.000 3528 0 0 1 3528 282940977 282937450 0.000000e+00 6516
1 TraesCS1D01G199900 chr1D 98.571 630 9 0 2899 3528 234326136 234326765 0.000000e+00 1114
2 TraesCS1D01G199900 chr1D 93.520 571 32 3 241 811 270635048 270635613 0.000000e+00 845
3 TraesCS1D01G199900 chr1D 97.119 243 7 0 1 243 233886855 233887097 9.110000e-111 411
4 TraesCS1D01G199900 chr1D 95.492 244 11 0 1 244 270634777 270635020 1.190000e-104 390
5 TraesCS1D01G199900 chr1B 93.958 811 38 9 1346 2151 384216330 384215526 0.000000e+00 1216
6 TraesCS1D01G199900 chr1B 92.148 433 19 2 2147 2564 384215255 384214823 6.520000e-167 597
7 TraesCS1D01G199900 chr1B 92.201 359 25 3 838 1195 384231037 384230681 4.060000e-139 505
8 TraesCS1D01G199900 chr1B 90.741 216 17 1 2545 2760 384214515 384214303 5.760000e-73 285
9 TraesCS1D01G199900 chr1B 88.462 130 12 2 1231 1358 384230567 384230439 1.700000e-33 154
10 TraesCS1D01G199900 chr1B 96.923 65 2 0 2783 2847 384214305 384214241 3.720000e-20 110
11 TraesCS1D01G199900 chr5D 98.574 631 9 0 2898 3528 493783403 493784033 0.000000e+00 1116
12 TraesCS1D01G199900 chr5D 76.000 1050 195 43 1590 2595 268881063 268880027 1.140000e-134 490
13 TraesCS1D01G199900 chr5D 79.946 369 63 6 1705 2063 486096006 486096373 9.710000e-66 261
14 TraesCS1D01G199900 chr6D 98.571 630 9 0 2899 3528 389736668 389736039 0.000000e+00 1114
15 TraesCS1D01G199900 chr6D 95.563 631 25 3 2899 3528 42227228 42226600 0.000000e+00 1007
16 TraesCS1D01G199900 chr6D 92.548 577 41 2 241 817 441373469 441372895 0.000000e+00 826
17 TraesCS1D01G199900 chr7D 98.254 630 11 0 2899 3528 558010504 558011133 0.000000e+00 1103
18 TraesCS1D01G199900 chr4D 98.254 630 10 1 2899 3528 472187055 472187683 0.000000e+00 1101
19 TraesCS1D01G199900 chr6A 91.007 834 43 15 1 805 419773647 419772817 0.000000e+00 1096
20 TraesCS1D01G199900 chr7A 90.023 852 50 15 1 817 287497084 287496233 0.000000e+00 1070
21 TraesCS1D01G199900 chr7A 92.049 566 37 6 242 805 547108506 547107947 0.000000e+00 789
22 TraesCS1D01G199900 chr7A 91.068 571 45 4 243 811 646084589 646084023 0.000000e+00 767
23 TraesCS1D01G199900 chr7A 95.902 244 10 0 1 244 421747937 421747694 2.550000e-106 396
24 TraesCS1D01G199900 chrUn 96.524 633 20 2 2897 3528 30188868 30188237 0.000000e+00 1046
25 TraesCS1D01G199900 chr7B 95.556 630 27 1 2899 3527 646215391 646214762 0.000000e+00 1007
26 TraesCS1D01G199900 chr1A 95.411 632 28 1 2898 3528 267865971 267865340 0.000000e+00 1005
27 TraesCS1D01G199900 chr1A 92.388 381 19 6 2473 2847 354828929 354828553 5.180000e-148 534
28 TraesCS1D01G199900 chr1A 88.290 427 19 1 1 396 286004722 286004296 1.900000e-132 483
29 TraesCS1D01G199900 chr3A 91.769 571 45 2 241 811 702588132 702587564 0.000000e+00 793
30 TraesCS1D01G199900 chr5B 90.957 575 44 8 241 811 471383172 471383742 0.000000e+00 767
31 TraesCS1D01G199900 chr5B 75.608 1316 216 68 1350 2595 304604260 304602980 3.980000e-154 555
32 TraesCS1D01G199900 chr5B 77.577 553 94 16 1705 2229 597099353 597099903 1.230000e-79 307
33 TraesCS1D01G199900 chr4A 89.831 590 47 10 241 823 702725672 702725089 0.000000e+00 745
34 TraesCS1D01G199900 chr4A 95.082 244 12 0 1 244 712652121 712652364 5.520000e-103 385
35 TraesCS1D01G199900 chr2D 95.902 244 10 0 1 244 558788306 558788549 2.550000e-106 396
36 TraesCS1D01G199900 chr2D 95.082 244 12 0 1 244 534927104 534927347 5.520000e-103 385
37 TraesCS1D01G199900 chr3B 95.492 244 11 0 1 244 662416704 662416461 1.190000e-104 390


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 TraesCS1D01G199900 chr1D 282937450 282940977 3527 True 6516.0 6516 100.0000 1 3528 1 chr1D.!!$R1 3527
1 TraesCS1D01G199900 chr1D 234326136 234326765 629 False 1114.0 1114 98.5710 2899 3528 1 chr1D.!!$F2 629
2 TraesCS1D01G199900 chr1D 270634777 270635613 836 False 617.5 845 94.5060 1 811 2 chr1D.!!$F3 810
3 TraesCS1D01G199900 chr1B 384214241 384216330 2089 True 552.0 1216 93.4425 1346 2847 4 chr1B.!!$R1 1501
4 TraesCS1D01G199900 chr1B 384230439 384231037 598 True 329.5 505 90.3315 838 1358 2 chr1B.!!$R2 520
5 TraesCS1D01G199900 chr5D 493783403 493784033 630 False 1116.0 1116 98.5740 2898 3528 1 chr5D.!!$F2 630
6 TraesCS1D01G199900 chr5D 268880027 268881063 1036 True 490.0 490 76.0000 1590 2595 1 chr5D.!!$R1 1005
7 TraesCS1D01G199900 chr6D 389736039 389736668 629 True 1114.0 1114 98.5710 2899 3528 1 chr6D.!!$R2 629
8 TraesCS1D01G199900 chr6D 42226600 42227228 628 True 1007.0 1007 95.5630 2899 3528 1 chr6D.!!$R1 629
9 TraesCS1D01G199900 chr6D 441372895 441373469 574 True 826.0 826 92.5480 241 817 1 chr6D.!!$R3 576
10 TraesCS1D01G199900 chr7D 558010504 558011133 629 False 1103.0 1103 98.2540 2899 3528 1 chr7D.!!$F1 629
11 TraesCS1D01G199900 chr4D 472187055 472187683 628 False 1101.0 1101 98.2540 2899 3528 1 chr4D.!!$F1 629
12 TraesCS1D01G199900 chr6A 419772817 419773647 830 True 1096.0 1096 91.0070 1 805 1 chr6A.!!$R1 804
13 TraesCS1D01G199900 chr7A 287496233 287497084 851 True 1070.0 1070 90.0230 1 817 1 chr7A.!!$R1 816
14 TraesCS1D01G199900 chr7A 547107947 547108506 559 True 789.0 789 92.0490 242 805 1 chr7A.!!$R3 563
15 TraesCS1D01G199900 chr7A 646084023 646084589 566 True 767.0 767 91.0680 243 811 1 chr7A.!!$R4 568
16 TraesCS1D01G199900 chrUn 30188237 30188868 631 True 1046.0 1046 96.5240 2897 3528 1 chrUn.!!$R1 631
17 TraesCS1D01G199900 chr7B 646214762 646215391 629 True 1007.0 1007 95.5560 2899 3527 1 chr7B.!!$R1 628
18 TraesCS1D01G199900 chr1A 267865340 267865971 631 True 1005.0 1005 95.4110 2898 3528 1 chr1A.!!$R1 630
19 TraesCS1D01G199900 chr3A 702587564 702588132 568 True 793.0 793 91.7690 241 811 1 chr3A.!!$R1 570
20 TraesCS1D01G199900 chr5B 471383172 471383742 570 False 767.0 767 90.9570 241 811 1 chr5B.!!$F1 570
21 TraesCS1D01G199900 chr5B 304602980 304604260 1280 True 555.0 555 75.6080 1350 2595 1 chr5B.!!$R1 1245
22 TraesCS1D01G199900 chr5B 597099353 597099903 550 False 307.0 307 77.5770 1705 2229 1 chr5B.!!$F2 524
23 TraesCS1D01G199900 chr4A 702725089 702725672 583 True 745.0 745 89.8310 241 823 1 chr4A.!!$R1 582

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
840 886 1.683629 CGGCTCCTAGAGGAAGACTGT 60.684 57.143 0.0 0.0 44.91 3.55 F
1079 1126 0.978907 ACATACCCGGTCGAGGTTTT 59.021 50.000 0.0 0.0 38.89 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 2127 0.035439 ACACCGGGCTGTTTATCCAG 60.035 55.0 6.32 0.00 35.49 3.86 R
2860 3690 0.031449 GGCGAGTGGAGATGCTCTAC 59.969 60.0 3.11 3.11 41.33 2.59 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
60 61 2.279851 CGTCTCACCACGGCACAA 60.280 61.111 0.00 0.00 36.07 3.33
123 124 4.002506 ATCAGCACCGTCGGCACA 62.003 61.111 12.28 0.00 0.00 4.57
829 875 4.577246 GCAGGTCGCGGCTCCTAG 62.577 72.222 11.94 9.99 32.26 3.02
830 876 2.829003 CAGGTCGCGGCTCCTAGA 60.829 66.667 11.94 0.00 32.26 2.43
831 877 2.517402 AGGTCGCGGCTCCTAGAG 60.517 66.667 11.94 0.00 31.66 2.43
832 878 3.597728 GGTCGCGGCTCCTAGAGG 61.598 72.222 11.94 0.00 0.00 3.69
833 879 2.516460 GTCGCGGCTCCTAGAGGA 60.516 66.667 1.90 0.00 43.08 3.71
834 880 2.119655 GTCGCGGCTCCTAGAGGAA 61.120 63.158 1.90 0.00 44.91 3.36
835 881 1.824329 TCGCGGCTCCTAGAGGAAG 60.824 63.158 6.13 0.00 44.91 3.46
836 882 1.824329 CGCGGCTCCTAGAGGAAGA 60.824 63.158 0.00 0.00 44.91 2.87
840 886 1.683629 CGGCTCCTAGAGGAAGACTGT 60.684 57.143 0.00 0.00 44.91 3.55
847 893 5.502079 TCCTAGAGGAAGACTGTAGTTCTG 58.498 45.833 0.00 0.00 40.51 3.02
849 895 6.215023 TCCTAGAGGAAGACTGTAGTTCTGTA 59.785 42.308 0.00 0.00 40.51 2.74
868 914 6.061441 TCTGTATTCACAAGTCACAACCATT 58.939 36.000 0.00 0.00 33.22 3.16
870 916 7.717436 TCTGTATTCACAAGTCACAACCATTAA 59.283 33.333 0.00 0.00 33.22 1.40
891 937 8.749354 CATTAACTTCCTTTTAGGTTTGGCTAT 58.251 33.333 0.00 0.00 36.53 2.97
987 1034 2.991713 ACTTGGGCCATCATATGATCCT 59.008 45.455 15.49 0.00 31.21 3.24
995 1042 4.836825 CCATCATATGATCCTGGTGTACC 58.163 47.826 15.49 0.00 31.21 3.34
999 1046 7.256655 CCATCATATGATCCTGGTGTACCTAAA 60.257 40.741 15.49 0.00 32.48 1.85
1005 1052 2.645297 TCCTGGTGTACCTAAAATGGCA 59.355 45.455 2.32 0.00 36.82 4.92
1012 1059 5.594317 GGTGTACCTAAAATGGCAGATTCAT 59.406 40.000 0.00 0.00 0.00 2.57
1050 1097 3.366985 CCTTGAGGATTGTTAAAACCGGC 60.367 47.826 0.00 0.00 37.39 6.13
1051 1098 2.164338 TGAGGATTGTTAAAACCGGCC 58.836 47.619 0.00 0.00 33.54 6.13
1055 1102 2.164338 GATTGTTAAAACCGGCCCTGA 58.836 47.619 0.00 0.00 0.00 3.86
1079 1126 0.978907 ACATACCCGGTCGAGGTTTT 59.021 50.000 0.00 0.00 38.89 2.43
1083 1130 2.622962 CCCGGTCGAGGTTTTTGGC 61.623 63.158 0.00 0.00 0.00 4.52
1090 1137 3.135994 GTCGAGGTTTTTGGCAGAGTTA 58.864 45.455 0.00 0.00 0.00 2.24
1095 1142 5.507315 CGAGGTTTTTGGCAGAGTTATTGTT 60.507 40.000 0.00 0.00 0.00 2.83
1124 1171 4.102524 TGAGGTTGACTACAAATGTGTCCT 59.897 41.667 0.00 0.00 39.30 3.85
1156 1203 3.320541 TCGTGAAAAGAACAATGCCCAAT 59.679 39.130 0.00 0.00 0.00 3.16
1167 1214 4.435425 ACAATGCCCAATTCATCAATTCG 58.565 39.130 0.00 0.00 28.97 3.34
1175 1222 6.237901 CCCAATTCATCAATTCGGAGGTATA 58.762 40.000 0.00 0.00 33.22 1.47
1275 1400 2.597578 ATCCACCCCACTGTAAAACC 57.402 50.000 0.00 0.00 0.00 3.27
1276 1401 1.223501 TCCACCCCACTGTAAAACCA 58.776 50.000 0.00 0.00 0.00 3.67
1278 1403 1.324383 CACCCCACTGTAAAACCACC 58.676 55.000 0.00 0.00 0.00 4.61
1282 1407 2.225017 CCCCACTGTAAAACCACCATCT 60.225 50.000 0.00 0.00 0.00 2.90
1286 1411 5.048294 CCCACTGTAAAACCACCATCTTAAC 60.048 44.000 0.00 0.00 0.00 2.01
1287 1412 5.048294 CCACTGTAAAACCACCATCTTAACC 60.048 44.000 0.00 0.00 0.00 2.85
1291 1416 7.343574 ACTGTAAAACCACCATCTTAACCTTTT 59.656 33.333 0.00 0.00 0.00 2.27
1337 1464 4.022849 GCAGCTTGTTATCATATCCAACCC 60.023 45.833 0.00 0.00 0.00 4.11
1365 1492 7.999679 TGTTTCATCTTCTTGTCAGAAACAAT 58.000 30.769 14.00 0.00 46.59 2.71
1396 1524 8.454570 TTTCATCAATTCTGCTGCATTCTATA 57.545 30.769 1.31 0.00 0.00 1.31
1423 1551 4.533707 TGTGAGATTTCTCCATTGAGGTCT 59.466 41.667 5.17 0.00 42.20 3.85
1427 1555 5.885465 AGATTTCTCCATTGAGGTCTTGTT 58.115 37.500 0.00 0.00 39.23 2.83
1441 1569 8.603242 TGAGGTCTTGTTACTTGTTTAATCTC 57.397 34.615 0.00 0.00 0.00 2.75
1459 1587 4.351874 TCTCTTTCTGTGTAAAGGTGGG 57.648 45.455 0.00 0.00 37.13 4.61
1465 1593 3.292460 TCTGTGTAAAGGTGGGTTTTGG 58.708 45.455 0.00 0.00 0.00 3.28
1467 1595 2.292323 TGTGTAAAGGTGGGTTTTGGGT 60.292 45.455 0.00 0.00 0.00 4.51
1468 1596 2.767394 GTGTAAAGGTGGGTTTTGGGTT 59.233 45.455 0.00 0.00 0.00 4.11
1469 1597 3.198200 GTGTAAAGGTGGGTTTTGGGTTT 59.802 43.478 0.00 0.00 0.00 3.27
1471 1599 3.358111 AAAGGTGGGTTTTGGGTTTTG 57.642 42.857 0.00 0.00 0.00 2.44
1472 1600 2.255770 AGGTGGGTTTTGGGTTTTGA 57.744 45.000 0.00 0.00 0.00 2.69
1473 1601 2.770447 AGGTGGGTTTTGGGTTTTGAT 58.230 42.857 0.00 0.00 0.00 2.57
1518 1646 9.373603 ATGTTGACATGTTTTAATCATGGAATG 57.626 29.630 17.09 0.00 44.57 2.67
1522 1650 8.028354 TGACATGTTTTAATCATGGAATGTGTC 58.972 33.333 17.09 8.19 46.80 3.67
1563 1695 4.216042 CCATACAACTCACAAATGTGCAGA 59.784 41.667 8.67 0.00 45.25 4.26
1567 1700 2.653726 ACTCACAAATGTGCAGAACCA 58.346 42.857 8.67 0.00 45.25 3.67
1644 1806 7.252612 TGGTTTTCATCTCCAACTGTAGATA 57.747 36.000 0.00 0.00 31.25 1.98
1685 1849 6.785076 TGGGGAGTCATGTTTTGTCTAATTA 58.215 36.000 0.00 0.00 0.00 1.40
1859 2025 3.884091 ACTGTACCATCTCGACCAGTATC 59.116 47.826 0.00 0.00 31.80 2.24
1961 2127 5.062809 GCAGCTAGTGTTCAAGTCTATGTTC 59.937 44.000 0.00 0.00 0.00 3.18
2015 2193 6.938030 TGGTAAAATAACAGTTGGGACTACTG 59.062 38.462 8.83 8.83 46.56 2.74
2111 2309 5.353123 TCCCTTGTGTTAAATCGTAATCTGC 59.647 40.000 0.00 0.00 0.00 4.26
2155 2628 0.874607 ACACTGCGTTCAAGGACGAC 60.875 55.000 4.84 0.00 45.47 4.34
2262 2735 3.432326 GCGGATTATATTAGGGCTGGAGG 60.432 52.174 0.00 0.00 0.00 4.30
2263 2736 3.775316 CGGATTATATTAGGGCTGGAGGT 59.225 47.826 0.00 0.00 0.00 3.85
2266 2739 5.338463 GGATTATATTAGGGCTGGAGGTGAC 60.338 48.000 0.00 0.00 0.00 3.67
2311 2793 3.815962 GTGAAGGGGAAACTGAAGAAGAC 59.184 47.826 0.00 0.00 0.00 3.01
2455 2958 1.209128 CTCCGCATGGTGAATACGTC 58.791 55.000 0.00 0.00 36.30 4.34
2503 3006 6.938507 TGGTTACAAGTCACCTAATTATCGT 58.061 36.000 5.28 0.00 33.76 3.73
2531 3034 4.193021 TCGTTCTTCGATCGATAGTGAC 57.807 45.455 20.18 17.53 44.01 3.67
2535 3038 5.276726 CGTTCTTCGATCGATAGTGACTGTA 60.277 44.000 20.18 0.00 42.86 2.74
2550 3053 7.182817 AGTGACTGTATTATCTTGGTTGCTA 57.817 36.000 0.00 0.00 0.00 3.49
2564 3067 8.158169 TCTTGGTTGCTATGCTTATTCTATTG 57.842 34.615 0.00 0.00 0.00 1.90
2565 3068 6.882610 TGGTTGCTATGCTTATTCTATTGG 57.117 37.500 0.00 0.00 0.00 3.16
2566 3069 6.600388 TGGTTGCTATGCTTATTCTATTGGA 58.400 36.000 0.00 0.00 0.00 3.53
2571 3401 9.578576 TTGCTATGCTTATTCTATTGGAAGAAT 57.421 29.630 4.65 4.65 45.79 2.40
2593 3423 8.890472 AGAATACTAATGTAATATTGGAGGGCA 58.110 33.333 0.00 0.00 31.80 5.36
2615 3445 1.846782 CTGCGTAACTATGTCGTGCTC 59.153 52.381 0.00 0.00 0.00 4.26
2640 3470 5.180271 TCACGTTGGGAACACCTAATTATC 58.820 41.667 0.00 0.00 42.67 1.75
2673 3503 6.149633 CACTAATTGTGCTCTTTTGGGTTAC 58.850 40.000 0.00 0.00 40.06 2.50
2679 3509 3.818773 GTGCTCTTTTGGGTTACTTAGCA 59.181 43.478 0.00 0.00 36.45 3.49
2681 3511 3.119814 GCTCTTTTGGGTTACTTAGCAGC 60.120 47.826 0.00 0.00 0.00 5.25
2695 3525 4.335594 ACTTAGCAGCGGATGTATTTTTCC 59.664 41.667 0.00 0.00 0.00 3.13
2727 3557 7.710676 ATATCAGAGTACACACTGAAGAAGT 57.289 36.000 12.48 0.69 44.42 3.01
2728 3558 8.809468 ATATCAGAGTACACACTGAAGAAGTA 57.191 34.615 12.48 2.63 44.42 2.24
2729 3559 6.315091 TCAGAGTACACACTGAAGAAGTAC 57.685 41.667 6.99 0.00 39.88 2.73
2760 3590 5.738619 TGTGCAGTGATCTAAGTAAGGAA 57.261 39.130 0.00 0.00 0.00 3.36
2761 3591 6.109156 TGTGCAGTGATCTAAGTAAGGAAA 57.891 37.500 0.00 0.00 0.00 3.13
2762 3592 6.711277 TGTGCAGTGATCTAAGTAAGGAAAT 58.289 36.000 0.00 0.00 0.00 2.17
2763 3593 6.818644 TGTGCAGTGATCTAAGTAAGGAAATC 59.181 38.462 0.00 0.00 0.00 2.17
2764 3594 6.258947 GTGCAGTGATCTAAGTAAGGAAATCC 59.741 42.308 0.00 0.00 0.00 3.01
2765 3595 5.760743 GCAGTGATCTAAGTAAGGAAATCCC 59.239 44.000 0.00 0.00 36.42 3.85
2766 3596 6.632672 GCAGTGATCTAAGTAAGGAAATCCCA 60.633 42.308 0.00 0.00 37.41 4.37
2767 3597 7.338710 CAGTGATCTAAGTAAGGAAATCCCAA 58.661 38.462 0.00 0.00 37.41 4.12
2768 3598 7.497249 CAGTGATCTAAGTAAGGAAATCCCAAG 59.503 40.741 0.00 0.00 37.41 3.61
2769 3599 6.261158 GTGATCTAAGTAAGGAAATCCCAAGC 59.739 42.308 0.00 0.00 37.41 4.01
2770 3600 4.766375 TCTAAGTAAGGAAATCCCAAGCG 58.234 43.478 0.00 0.00 37.41 4.68
2771 3601 3.434940 AAGTAAGGAAATCCCAAGCGT 57.565 42.857 0.00 0.00 37.41 5.07
2772 3602 2.711542 AGTAAGGAAATCCCAAGCGTG 58.288 47.619 0.00 0.00 37.41 5.34
2773 3603 2.039879 AGTAAGGAAATCCCAAGCGTGT 59.960 45.455 0.00 0.00 37.41 4.49
2774 3604 1.995376 AAGGAAATCCCAAGCGTGTT 58.005 45.000 0.00 0.00 37.41 3.32
2775 3605 1.995376 AGGAAATCCCAAGCGTGTTT 58.005 45.000 0.00 0.00 37.41 2.83
2776 3606 3.149005 AGGAAATCCCAAGCGTGTTTA 57.851 42.857 0.00 0.00 37.41 2.01
2777 3607 3.492337 AGGAAATCCCAAGCGTGTTTAA 58.508 40.909 0.00 0.00 37.41 1.52
2778 3608 3.506067 AGGAAATCCCAAGCGTGTTTAAG 59.494 43.478 0.00 0.00 37.41 1.85
2779 3609 3.254903 GGAAATCCCAAGCGTGTTTAAGT 59.745 43.478 0.00 0.00 34.14 2.24
2780 3610 4.261867 GGAAATCCCAAGCGTGTTTAAGTT 60.262 41.667 0.00 0.00 34.14 2.66
2781 3611 4.499037 AATCCCAAGCGTGTTTAAGTTC 57.501 40.909 0.00 0.00 0.00 3.01
2782 3612 1.868498 TCCCAAGCGTGTTTAAGTTCG 59.132 47.619 0.00 0.00 0.00 3.95
2783 3613 1.069500 CCCAAGCGTGTTTAAGTTCGG 60.069 52.381 0.00 0.00 0.00 4.30
2784 3614 1.868498 CCAAGCGTGTTTAAGTTCGGA 59.132 47.619 0.00 0.00 0.00 4.55
2795 3625 7.508134 GTGTTTAAGTTCGGAGCTTTTACTAG 58.492 38.462 12.38 0.00 0.00 2.57
2836 3666 8.829514 TCTATTTTATTTTCCGTGCAAATACG 57.170 30.769 0.00 0.00 43.35 3.06
2847 3677 3.124466 CGTGCAAATACGATGGTGAGAAA 59.876 43.478 0.00 0.00 46.46 2.52
2848 3678 4.403453 GTGCAAATACGATGGTGAGAAAC 58.597 43.478 0.00 0.00 0.00 2.78
2849 3679 4.154195 GTGCAAATACGATGGTGAGAAACT 59.846 41.667 0.00 0.00 0.00 2.66
2850 3680 4.154015 TGCAAATACGATGGTGAGAAACTG 59.846 41.667 0.00 0.00 0.00 3.16
2851 3681 4.437390 GCAAATACGATGGTGAGAAACTGG 60.437 45.833 0.00 0.00 0.00 4.00
2852 3682 2.380084 TACGATGGTGAGAAACTGGC 57.620 50.000 0.00 0.00 0.00 4.85
2853 3683 0.687354 ACGATGGTGAGAAACTGGCT 59.313 50.000 0.00 0.00 0.00 4.75
2854 3684 1.081892 CGATGGTGAGAAACTGGCTG 58.918 55.000 0.00 0.00 0.00 4.85
2855 3685 1.338105 CGATGGTGAGAAACTGGCTGA 60.338 52.381 0.00 0.00 0.00 4.26
2856 3686 2.354259 GATGGTGAGAAACTGGCTGAG 58.646 52.381 0.00 0.00 0.00 3.35
2857 3687 1.423584 TGGTGAGAAACTGGCTGAGA 58.576 50.000 0.00 0.00 0.00 3.27
2858 3688 1.768275 TGGTGAGAAACTGGCTGAGAA 59.232 47.619 0.00 0.00 0.00 2.87
2859 3689 2.147150 GGTGAGAAACTGGCTGAGAAC 58.853 52.381 0.00 0.00 0.00 3.01
2860 3690 1.795286 GTGAGAAACTGGCTGAGAACG 59.205 52.381 0.00 0.00 0.00 3.95
2861 3691 1.412710 TGAGAAACTGGCTGAGAACGT 59.587 47.619 0.00 0.00 0.00 3.99
2862 3692 2.626266 TGAGAAACTGGCTGAGAACGTA 59.374 45.455 0.00 0.00 0.00 3.57
2863 3693 3.246619 GAGAAACTGGCTGAGAACGTAG 58.753 50.000 0.00 0.00 0.00 3.51
2864 3694 2.891580 AGAAACTGGCTGAGAACGTAGA 59.108 45.455 0.00 0.00 0.00 2.59
2865 3695 3.057174 AGAAACTGGCTGAGAACGTAGAG 60.057 47.826 0.00 0.00 0.00 2.43
2866 3696 0.528470 ACTGGCTGAGAACGTAGAGC 59.472 55.000 0.00 0.00 0.00 4.09
2867 3697 0.528017 CTGGCTGAGAACGTAGAGCA 59.472 55.000 9.41 0.00 32.83 4.26
2868 3698 1.135915 CTGGCTGAGAACGTAGAGCAT 59.864 52.381 9.41 0.00 32.83 3.79
2869 3699 1.135139 TGGCTGAGAACGTAGAGCATC 59.865 52.381 9.41 0.00 32.83 3.91
2880 3710 2.107953 GAGCATCTCCACTCGCCC 59.892 66.667 0.00 0.00 0.00 6.13
2881 3711 3.453070 GAGCATCTCCACTCGCCCC 62.453 68.421 0.00 0.00 0.00 5.80
2882 3712 4.554036 GCATCTCCACTCGCCCCC 62.554 72.222 0.00 0.00 0.00 5.40
3029 3860 2.210711 CCCATCGGGTAGAGAGGGC 61.211 68.421 0.00 0.00 40.03 5.19
3040 3871 1.760875 GAGAGGGCACGGGTATGGA 60.761 63.158 0.00 0.00 0.00 3.41
3502 4335 1.766496 CCTTGACGGGTATGGGTATGT 59.234 52.381 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 1.664965 GCGCTGTCCTCACTTCGTT 60.665 57.895 0.00 0.00 0.00 3.85
60 61 2.049063 GCGCTGTCCTCACTTCGT 60.049 61.111 0.00 0.00 0.00 3.85
81 82 1.280457 AGTCCCGGCTCTGATTCTTT 58.720 50.000 0.00 0.00 0.00 2.52
284 317 2.738521 CGTGGCCTCGTTGTCTGG 60.739 66.667 18.86 0.00 0.00 3.86
462 497 4.980805 GTGTCGCTCGGTTGGGCA 62.981 66.667 0.00 0.00 0.00 5.36
593 630 1.190643 CTTCGCCTCCTCTTCCTCTT 58.809 55.000 0.00 0.00 0.00 2.85
814 860 2.517402 CTCTAGGAGCCGCGACCT 60.517 66.667 8.23 15.84 39.95 3.85
823 869 5.588648 CAGAACTACAGTCTTCCTCTAGGAG 59.411 48.000 0.00 0.00 46.36 3.69
824 870 5.014333 ACAGAACTACAGTCTTCCTCTAGGA 59.986 44.000 0.00 0.00 43.73 2.94
825 871 5.258051 ACAGAACTACAGTCTTCCTCTAGG 58.742 45.833 0.00 0.00 0.00 3.02
826 872 8.514330 AATACAGAACTACAGTCTTCCTCTAG 57.486 38.462 0.00 0.00 0.00 2.43
827 873 8.107729 TGAATACAGAACTACAGTCTTCCTCTA 58.892 37.037 0.00 0.00 0.00 2.43
828 874 6.948886 TGAATACAGAACTACAGTCTTCCTCT 59.051 38.462 0.00 0.00 0.00 3.69
829 875 7.030768 GTGAATACAGAACTACAGTCTTCCTC 58.969 42.308 0.00 0.00 0.00 3.71
830 876 6.493802 TGTGAATACAGAACTACAGTCTTCCT 59.506 38.462 0.00 0.00 31.91 3.36
831 877 6.688578 TGTGAATACAGAACTACAGTCTTCC 58.311 40.000 0.00 0.00 31.91 3.46
832 878 7.868415 ACTTGTGAATACAGAACTACAGTCTTC 59.132 37.037 0.00 0.00 38.23 2.87
833 879 7.727181 ACTTGTGAATACAGAACTACAGTCTT 58.273 34.615 0.00 0.00 38.23 3.01
834 880 7.014326 TGACTTGTGAATACAGAACTACAGTCT 59.986 37.037 0.00 0.00 36.43 3.24
835 881 7.115095 GTGACTTGTGAATACAGAACTACAGTC 59.885 40.741 0.00 0.00 38.23 3.51
836 882 6.924060 GTGACTTGTGAATACAGAACTACAGT 59.076 38.462 0.00 0.00 38.23 3.55
840 886 6.704493 GGTTGTGACTTGTGAATACAGAACTA 59.296 38.462 0.00 0.00 38.23 2.24
847 893 7.871853 AGTTAATGGTTGTGACTTGTGAATAC 58.128 34.615 0.00 0.00 0.00 1.89
849 895 6.959639 AGTTAATGGTTGTGACTTGTGAAT 57.040 33.333 0.00 0.00 0.00 2.57
868 914 7.945664 TCAATAGCCAAACCTAAAAGGAAGTTA 59.054 33.333 0.00 0.00 37.67 2.24
870 916 6.311735 TCAATAGCCAAACCTAAAAGGAAGT 58.688 36.000 0.00 0.00 37.67 3.01
891 937 5.369409 AGAGGATGAATGCTTCTGATCAA 57.631 39.130 0.00 0.00 0.00 2.57
914 960 6.712095 AGCAGAGATACAAATCAGAACAAACA 59.288 34.615 0.00 0.00 34.28 2.83
946 993 7.041508 CCCAAGTTTTGCATTTGCTGTAAATTA 60.042 33.333 3.94 0.00 38.91 1.40
948 995 5.239087 CCCAAGTTTTGCATTTGCTGTAAAT 59.761 36.000 3.94 0.00 38.91 1.40
951 998 3.726607 CCCAAGTTTTGCATTTGCTGTA 58.273 40.909 3.94 0.00 42.66 2.74
952 999 2.563702 CCCAAGTTTTGCATTTGCTGT 58.436 42.857 3.94 0.00 42.66 4.40
987 1034 4.584638 ATCTGCCATTTTAGGTACACCA 57.415 40.909 0.38 0.00 38.89 4.17
995 1042 6.644248 TGATGGATGAATCTGCCATTTTAG 57.356 37.500 8.41 0.00 42.22 1.85
999 1046 4.899457 ACATTGATGGATGAATCTGCCATT 59.101 37.500 8.41 0.00 42.22 3.16
1005 1052 9.430399 AAGGAAATAACATTGATGGATGAATCT 57.570 29.630 0.00 0.00 0.00 2.40
1012 1059 6.730447 TCCTCAAGGAAATAACATTGATGGA 58.270 36.000 0.00 0.00 42.18 3.41
1045 1092 1.140252 GTATGTGTAATCAGGGCCGGT 59.860 52.381 1.90 0.00 0.00 5.28
1050 1097 1.766496 ACCGGGTATGTGTAATCAGGG 59.234 52.381 6.32 0.00 0.00 4.45
1051 1098 2.545113 CGACCGGGTATGTGTAATCAGG 60.545 54.545 6.32 0.00 0.00 3.86
1055 1102 1.684983 CCTCGACCGGGTATGTGTAAT 59.315 52.381 6.32 0.00 0.00 1.89
1079 1126 4.919774 TCCCTAACAATAACTCTGCCAA 57.080 40.909 0.00 0.00 0.00 4.52
1083 1130 6.240549 ACCTCATCCCTAACAATAACTCTG 57.759 41.667 0.00 0.00 0.00 3.35
1090 1137 5.487488 TGTAGTCAACCTCATCCCTAACAAT 59.513 40.000 0.00 0.00 0.00 2.71
1095 1142 5.487488 ACATTTGTAGTCAACCTCATCCCTA 59.513 40.000 0.00 0.00 32.93 3.53
1124 1171 4.806775 TGTTCTTTTCACGATCGAACAGAA 59.193 37.500 24.34 16.58 38.65 3.02
1167 1214 6.954352 AGGAAGGGACAAATATATACCTCC 57.046 41.667 0.00 0.00 0.00 4.30
1181 1228 8.430431 AGCAAATAGTAGTATTAAGGAAGGGAC 58.570 37.037 3.21 0.00 0.00 4.46
1275 1400 6.991938 TCCAATTGAAAAGGTTAAGATGGTG 58.008 36.000 7.12 0.00 0.00 4.17
1276 1401 7.070571 TGTTCCAATTGAAAAGGTTAAGATGGT 59.929 33.333 7.12 0.00 33.94 3.55
1278 1403 9.492973 AATGTTCCAATTGAAAAGGTTAAGATG 57.507 29.630 7.12 0.00 33.94 2.90
1291 1416 9.368674 CTGCAAACAATATAATGTTCCAATTGA 57.631 29.630 7.12 0.00 42.49 2.57
1308 1433 6.152492 TGGATATGATAACAAGCTGCAAACAA 59.848 34.615 1.02 0.00 0.00 2.83
1309 1434 5.651576 TGGATATGATAACAAGCTGCAAACA 59.348 36.000 1.02 0.00 0.00 2.83
1313 1438 4.580167 GGTTGGATATGATAACAAGCTGCA 59.420 41.667 1.02 0.00 38.06 4.41
1329 1454 5.336102 AGAAGATGAAACAATGGGTTGGAT 58.664 37.500 0.00 0.00 40.35 3.41
1337 1464 7.916977 TGTTTCTGACAAGAAGATGAAACAATG 59.083 33.333 14.12 0.00 45.31 2.82
1365 1492 7.160547 TGCAGCAGAATTGATGAAAAGAATA 57.839 32.000 0.00 0.00 43.30 1.75
1396 1524 7.580910 ACCTCAATGGAGAAATCTCACATAAT 58.419 34.615 12.21 0.00 44.26 1.28
1441 1569 5.348164 CAAAACCCACCTTTACACAGAAAG 58.652 41.667 0.00 0.00 36.38 2.62
1459 1587 8.669946 TTTCCTGATTAATCAAAACCCAAAAC 57.330 30.769 18.47 0.00 36.18 2.43
1518 1646 4.470462 GTCAAATGAGCAAGACATGACAC 58.530 43.478 0.00 0.00 0.00 3.67
1563 1695 2.908351 ACTACCGTTCCTACCAATGGTT 59.092 45.455 11.41 0.00 42.13 3.67
1567 1700 1.903860 TGCACTACCGTTCCTACCAAT 59.096 47.619 0.00 0.00 0.00 3.16
1644 1806 2.440409 CCCAGATAGTTGTGCAAGCTT 58.560 47.619 0.00 0.00 0.00 3.74
1685 1849 5.047092 CCTCCTGCATAGGTTTCACAAAAAT 60.047 40.000 7.02 0.00 44.88 1.82
1859 2025 4.389576 GCGGGTGAAGCGCTTGTG 62.390 66.667 30.47 12.94 0.00 3.33
1930 2096 0.674895 GAACACTAGCTGCCACTGGG 60.675 60.000 0.00 0.00 37.18 4.45
1961 2127 0.035439 ACACCGGGCTGTTTATCCAG 60.035 55.000 6.32 0.00 35.49 3.86
2111 2309 0.463620 GAAGGCTCCTGGACAGCTAG 59.536 60.000 7.73 0.00 37.05 3.42
2155 2628 5.153513 CAAACATAGACCACCATTTGTTCG 58.846 41.667 0.00 0.00 0.00 3.95
2262 2735 3.914312 TCTTCACTGATTTCCTCGTCAC 58.086 45.455 0.00 0.00 0.00 3.67
2263 2736 3.056536 CCTCTTCACTGATTTCCTCGTCA 60.057 47.826 0.00 0.00 0.00 4.35
2266 2739 3.876274 TCCTCTTCACTGATTTCCTCG 57.124 47.619 0.00 0.00 0.00 4.63
2311 2793 1.517832 GTCCACAGACCCATCCTCG 59.482 63.158 0.00 0.00 37.00 4.63
2365 2868 2.254459 CCGAATTCACAGACAGTCTCG 58.746 52.381 0.00 0.00 0.00 4.04
2455 2958 3.221771 TGGAAGGACACCAAATCTTGTG 58.778 45.455 0.00 0.00 34.25 3.33
2527 3030 7.519008 GCATAGCAACCAAGATAATACAGTCAC 60.519 40.741 0.00 0.00 0.00 3.67
2531 3034 7.502120 AAGCATAGCAACCAAGATAATACAG 57.498 36.000 0.00 0.00 0.00 2.74
2535 3038 8.930846 AGAATAAGCATAGCAACCAAGATAAT 57.069 30.769 0.00 0.00 0.00 1.28
2566 3069 9.740710 GCCCTCCAATATTACATTAGTATTCTT 57.259 33.333 0.00 0.00 0.00 2.52
2571 3401 8.321353 CAGATGCCCTCCAATATTACATTAGTA 58.679 37.037 0.00 0.00 0.00 1.82
2593 3423 2.099263 AGCACGACATAGTTACGCAGAT 59.901 45.455 0.00 0.00 0.00 2.90
2615 3445 2.536761 TAGGTGTTCCCAACGTGAAG 57.463 50.000 0.00 0.00 31.82 3.02
2621 3451 5.163693 CCAACGATAATTAGGTGTTCCCAAC 60.164 44.000 0.00 0.00 34.66 3.77
2673 3503 4.576463 AGGAAAAATACATCCGCTGCTAAG 59.424 41.667 0.00 0.00 40.78 2.18
2679 3509 2.722094 TGCAGGAAAAATACATCCGCT 58.278 42.857 0.00 0.00 40.78 5.52
2695 3525 8.734386 TCAGTGTGTACTCTGATATATATGCAG 58.266 37.037 11.51 7.69 40.34 4.41
2713 3543 7.768807 AGATTCTAGTACTTCTTCAGTGTGT 57.231 36.000 0.00 0.00 35.97 3.72
2715 3545 8.085296 CACAAGATTCTAGTACTTCTTCAGTGT 58.915 37.037 0.00 0.00 35.97 3.55
2727 3557 6.782082 AGATCACTGCACAAGATTCTAGTA 57.218 37.500 0.00 0.00 0.00 1.82
2728 3558 5.674052 AGATCACTGCACAAGATTCTAGT 57.326 39.130 0.00 0.00 0.00 2.57
2729 3559 7.264221 ACTTAGATCACTGCACAAGATTCTAG 58.736 38.462 0.00 0.00 0.00 2.43
2760 3590 3.058501 CGAACTTAAACACGCTTGGGATT 60.059 43.478 0.00 0.00 0.00 3.01
2761 3591 2.482721 CGAACTTAAACACGCTTGGGAT 59.517 45.455 0.00 0.00 0.00 3.85
2762 3592 1.868498 CGAACTTAAACACGCTTGGGA 59.132 47.619 0.00 0.00 0.00 4.37
2763 3593 1.069500 CCGAACTTAAACACGCTTGGG 60.069 52.381 0.00 0.00 0.00 4.12
2764 3594 1.868498 TCCGAACTTAAACACGCTTGG 59.132 47.619 0.00 0.00 0.00 3.61
2765 3595 2.661979 GCTCCGAACTTAAACACGCTTG 60.662 50.000 0.00 0.00 0.00 4.01
2766 3596 1.529865 GCTCCGAACTTAAACACGCTT 59.470 47.619 0.00 0.00 0.00 4.68
2767 3597 1.145803 GCTCCGAACTTAAACACGCT 58.854 50.000 0.00 0.00 0.00 5.07
2768 3598 1.145803 AGCTCCGAACTTAAACACGC 58.854 50.000 0.00 0.00 0.00 5.34
2769 3599 3.872560 AAAGCTCCGAACTTAAACACG 57.127 42.857 0.00 0.00 0.00 4.49
2770 3600 6.296365 AGTAAAAGCTCCGAACTTAAACAC 57.704 37.500 0.00 0.00 0.00 3.32
2771 3601 6.146673 GCTAGTAAAAGCTCCGAACTTAAACA 59.853 38.462 0.00 0.00 39.50 2.83
2772 3602 6.532311 GCTAGTAAAAGCTCCGAACTTAAAC 58.468 40.000 0.00 0.00 39.50 2.01
2773 3603 6.716898 GCTAGTAAAAGCTCCGAACTTAAA 57.283 37.500 0.00 0.00 39.50 1.52
2795 3625 2.057137 TAGAATTGACCCATGGCAGC 57.943 50.000 6.09 0.00 0.00 5.25
2836 3666 2.027745 TCTCAGCCAGTTTCTCACCATC 60.028 50.000 0.00 0.00 0.00 3.51
2847 3677 0.528470 GCTCTACGTTCTCAGCCAGT 59.472 55.000 0.00 0.00 0.00 4.00
2848 3678 0.528017 TGCTCTACGTTCTCAGCCAG 59.472 55.000 0.00 0.00 0.00 4.85
2849 3679 1.135139 GATGCTCTACGTTCTCAGCCA 59.865 52.381 0.00 0.00 0.00 4.75
2850 3680 1.407258 AGATGCTCTACGTTCTCAGCC 59.593 52.381 0.00 0.00 0.00 4.85
2851 3681 2.542824 GGAGATGCTCTACGTTCTCAGC 60.543 54.545 13.19 7.63 0.00 4.26
2852 3682 2.685388 TGGAGATGCTCTACGTTCTCAG 59.315 50.000 13.19 0.00 26.79 3.35
2853 3683 2.423892 GTGGAGATGCTCTACGTTCTCA 59.576 50.000 13.19 0.00 32.76 3.27
2854 3684 2.685897 AGTGGAGATGCTCTACGTTCTC 59.314 50.000 0.00 0.00 44.77 2.87
2855 3685 2.685897 GAGTGGAGATGCTCTACGTTCT 59.314 50.000 0.00 0.00 44.77 3.01
2856 3686 2.539953 CGAGTGGAGATGCTCTACGTTC 60.540 54.545 0.00 0.00 44.77 3.95
2857 3687 1.402259 CGAGTGGAGATGCTCTACGTT 59.598 52.381 0.00 0.00 44.77 3.99
2858 3688 1.018148 CGAGTGGAGATGCTCTACGT 58.982 55.000 5.48 0.00 44.77 3.57
2859 3689 0.317436 GCGAGTGGAGATGCTCTACG 60.317 60.000 5.48 0.00 44.77 3.51
2860 3690 0.031449 GGCGAGTGGAGATGCTCTAC 59.969 60.000 3.11 3.11 41.33 2.59
2861 3691 1.109920 GGGCGAGTGGAGATGCTCTA 61.110 60.000 0.00 0.00 0.00 2.43
2862 3692 2.430610 GGGCGAGTGGAGATGCTCT 61.431 63.158 0.00 0.00 0.00 4.09
2863 3693 2.107953 GGGCGAGTGGAGATGCTC 59.892 66.667 0.00 0.00 0.00 4.26
2864 3694 3.474570 GGGGCGAGTGGAGATGCT 61.475 66.667 0.00 0.00 0.00 3.79
2865 3695 4.554036 GGGGGCGAGTGGAGATGC 62.554 72.222 0.00 0.00 0.00 3.91
2881 3711 2.333695 CTAAGGGGAGGGGGAGAGGG 62.334 70.000 0.00 0.00 0.00 4.30
2882 3712 1.237458 CTAAGGGGAGGGGGAGAGG 59.763 68.421 0.00 0.00 0.00 3.69
2883 3713 1.237458 CCTAAGGGGAGGGGGAGAG 59.763 68.421 0.00 0.00 37.23 3.20
2884 3714 3.464405 CCTAAGGGGAGGGGGAGA 58.536 66.667 0.00 0.00 37.23 3.71
2894 3724 0.852842 TCCATTGCCATCCCTAAGGG 59.147 55.000 0.00 0.00 46.11 3.95
2895 3725 2.986534 ATCCATTGCCATCCCTAAGG 57.013 50.000 0.00 0.00 0.00 2.69
2913 3743 0.681175 GGTACGCGGGTAATGGGTAT 59.319 55.000 14.50 0.00 37.15 2.73
2987 3818 9.990868 GGGTATGATATTTCCCCATTTAAGTAT 57.009 33.333 0.00 0.00 35.32 2.12
3029 3860 4.240096 GGTTATACGATTCCATACCCGTG 58.760 47.826 0.00 0.00 36.58 4.94
3040 3871 1.880646 GCGGGCATGGGTTATACGATT 60.881 52.381 0.00 0.00 0.00 3.34
3126 3957 7.127339 AGTTTTTACCTAGCATGATTAGGAGGA 59.873 37.037 23.18 10.29 40.12 3.71
3502 4335 1.609580 GCCGTGAGTTTACCCATCACA 60.610 52.381 5.52 0.00 42.76 3.58


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

AutoCloner maintained by Alex Coulton.