Multiple sequence alignment - TraesCS2A01G207900

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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 TraesCS2A01G207900 chr2A 100.000 3075 0 0 1 3075 187954565 187951491 0.000000e+00 5679
1 TraesCS2A01G207900 chr2A 96.633 683 18 1 66 748 562600619 562601296 0.000000e+00 1129
2 TraesCS2A01G207900 chr2A 83.511 564 64 11 62 612 273286941 273287488 1.650000e-137 499
3 TraesCS2A01G207900 chr2D 92.463 1977 76 27 1141 3075 176164124 176162179 0.000000e+00 2758
4 TraesCS2A01G207900 chr2D 89.796 343 17 7 747 1073 176164460 176164120 1.020000e-114 424
5 TraesCS2A01G207900 chr2B 90.759 1515 69 38 1181 2648 233268970 233267480 0.000000e+00 1956
6 TraesCS2A01G207900 chr2B 96.078 357 9 2 2719 3075 233267474 233267123 7.390000e-161 577
7 TraesCS2A01G207900 chr2B 84.330 351 36 10 69 418 277320392 277320060 2.960000e-85 326
8 TraesCS2A01G207900 chr2B 81.868 364 14 9 751 1083 233269317 233268975 3.040000e-65 259
9 TraesCS2A01G207900 chr2B 88.793 116 12 1 635 750 277319559 277319445 1.150000e-29 141
10 TraesCS2A01G207900 chr7D 83.406 1145 117 36 1411 2530 581035091 581036187 0.000000e+00 994
11 TraesCS2A01G207900 chr7A 98.016 504 10 0 245 748 186538625 186539128 0.000000e+00 876
12 TraesCS2A01G207900 chr7A 96.203 158 6 0 66 223 603586519 603586362 3.040000e-65 259
13 TraesCS2A01G207900 chr3D 84.394 487 27 22 2076 2533 604598317 604597851 1.690000e-117 433
14 TraesCS2A01G207900 chr3D 82.736 307 31 5 1736 2042 604598597 604598313 1.420000e-63 254
15 TraesCS2A01G207900 chr6B 96.875 160 3 1 66 223 599852495 599852654 1.820000e-67 267
16 TraesCS2A01G207900 chr6B 96.875 160 3 1 66 223 599866664 599866823 1.820000e-67 267
17 TraesCS2A01G207900 chrUn 95.679 162 3 2 66 223 403531537 403531376 1.090000e-64 257
18 TraesCS2A01G207900 chrUn 97.674 43 1 0 66 108 367844098 367844140 1.180000e-09 75
19 TraesCS2A01G207900 chrUn 97.674 43 1 0 66 108 367883403 367883361 1.180000e-09 75
20 TraesCS2A01G207900 chr5B 87.387 111 13 1 641 750 458576267 458576377 3.220000e-25 126


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 TraesCS2A01G207900 chr2A 187951491 187954565 3074 True 5679.000000 5679 100.000000 1 3075 1 chr2A.!!$R1 3074
1 TraesCS2A01G207900 chr2A 562600619 562601296 677 False 1129.000000 1129 96.633000 66 748 1 chr2A.!!$F2 682
2 TraesCS2A01G207900 chr2A 273286941 273287488 547 False 499.000000 499 83.511000 62 612 1 chr2A.!!$F1 550
3 TraesCS2A01G207900 chr2D 176162179 176164460 2281 True 1591.000000 2758 91.129500 747 3075 2 chr2D.!!$R1 2328
4 TraesCS2A01G207900 chr2B 233267123 233269317 2194 True 930.666667 1956 89.568333 751 3075 3 chr2B.!!$R1 2324
5 TraesCS2A01G207900 chr2B 277319445 277320392 947 True 233.500000 326 86.561500 69 750 2 chr2B.!!$R2 681
6 TraesCS2A01G207900 chr7D 581035091 581036187 1096 False 994.000000 994 83.406000 1411 2530 1 chr7D.!!$F1 1119
7 TraesCS2A01G207900 chr7A 186538625 186539128 503 False 876.000000 876 98.016000 245 748 1 chr7A.!!$F1 503
8 TraesCS2A01G207900 chr3D 604597851 604598597 746 True 343.500000 433 83.565000 1736 2533 2 chr3D.!!$R1 797

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
243 244 0.861837 CGATACAGATCTTTGGGCGC 59.138 55.0 0.00 0.0 0.0 6.53 F
1112 1485 0.041238 TCTCGGTGGATTCCTGGTCT 59.959 55.0 3.95 0.0 0.0 3.85 F
1143 1516 0.031857 TTGCGTCCCATTTTGTGCTG 59.968 50.0 0.00 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1124 1497 0.031857 CAGCACAAAATGGGACGCAA 59.968 50.000 0.00 0.0 0.00 4.85 R
1923 2332 1.002468 CAGCTTGGTTCGGTTCAGTTG 60.002 52.381 0.00 0.0 0.00 3.16 R
2364 2805 1.467734 GCTGCAGATATGCCATGCTAC 59.532 52.381 20.43 0.0 40.62 3.58 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
36 37 8.126700 AGTGTTGTATTAATATTTAGCAACGCC 58.873 33.333 22.76 14.93 42.93 5.68
37 38 7.911205 GTGTTGTATTAATATTTAGCAACGCCA 59.089 33.333 19.12 5.16 38.88 5.69
38 39 7.911205 TGTTGTATTAATATTTAGCAACGCCAC 59.089 33.333 15.54 0.98 37.95 5.01
39 40 6.651308 TGTATTAATATTTAGCAACGCCACG 58.349 36.000 0.00 0.00 0.00 4.94
40 41 2.468532 AATATTTAGCAACGCCACGC 57.531 45.000 0.00 0.00 0.00 5.34
41 42 1.663695 ATATTTAGCAACGCCACGCT 58.336 45.000 0.00 0.00 42.34 5.07
42 43 1.003851 TATTTAGCAACGCCACGCTC 58.996 50.000 0.00 0.00 39.70 5.03
43 44 1.966493 ATTTAGCAACGCCACGCTCG 61.966 55.000 0.00 0.00 39.70 5.03
44 45 3.561217 TTAGCAACGCCACGCTCGA 62.561 57.895 0.00 0.00 39.70 4.04
45 46 3.561217 TAGCAACGCCACGCTCGAA 62.561 57.895 0.00 0.00 39.70 3.71
46 47 4.007940 GCAACGCCACGCTCGAAA 62.008 61.111 0.00 0.00 0.00 3.46
47 48 2.127758 CAACGCCACGCTCGAAAC 60.128 61.111 0.00 0.00 0.00 2.78
48 49 3.698463 AACGCCACGCTCGAAACG 61.698 61.111 6.00 6.00 0.00 3.60
49 50 4.634133 ACGCCACGCTCGAAACGA 62.634 61.111 13.80 0.00 0.00 3.85
133 134 3.144657 TCCCCTCCGTAAAAGAAAACC 57.855 47.619 0.00 0.00 0.00 3.27
236 237 3.492137 GGCCCGTAAACGATACAGATCTT 60.492 47.826 3.65 0.00 43.02 2.40
243 244 0.861837 CGATACAGATCTTTGGGCGC 59.138 55.000 0.00 0.00 0.00 6.53
277 278 3.514706 ACCTCCTCGCTCGAGACTATATA 59.485 47.826 18.75 0.00 44.53 0.86
652 994 0.968901 TCTGACGGCGGATTACAGGT 60.969 55.000 13.24 0.00 0.00 4.00
654 996 1.252215 TGACGGCGGATTACAGGTGA 61.252 55.000 13.24 0.00 0.00 4.02
704 1046 6.982724 GGTGTACAGTAATATCCAGGTGTAAC 59.017 42.308 0.00 0.00 0.00 2.50
721 1063 9.445786 CAGGTGTAACAATTTACAGTTGTAAAG 57.554 33.333 18.86 11.15 46.63 1.85
773 1115 3.254411 TGGTTTCGTAAATCTGCATTGCA 59.746 39.130 11.50 11.50 36.92 4.08
797 1139 1.070275 CCGATAAGGCCCCCGTAAC 59.930 63.158 0.00 0.00 0.00 2.50
803 1145 4.462280 GGCCCCCGTAACGTCTGG 62.462 72.222 0.00 0.00 0.00 3.86
845 1199 3.216292 ACCCACAAGGCACGCAAC 61.216 61.111 0.00 0.00 40.58 4.17
978 1336 2.794621 CAGTGCTAGCTCGCTCGA 59.205 61.111 17.23 0.00 0.00 4.04
1049 1422 1.722110 AACCCCACCCAGGTAACCAC 61.722 60.000 0.00 0.00 36.27 4.16
1050 1423 1.850755 CCCCACCCAGGTAACCACT 60.851 63.158 0.00 0.00 34.66 4.00
1083 1456 1.590259 GCCGCCGTCTGATCTCTTC 60.590 63.158 0.00 0.00 0.00 2.87
1084 1457 1.809869 CCGCCGTCTGATCTCTTCA 59.190 57.895 0.00 0.00 0.00 3.02
1085 1458 0.387202 CCGCCGTCTGATCTCTTCAT 59.613 55.000 0.00 0.00 32.72 2.57
1086 1459 1.601663 CCGCCGTCTGATCTCTTCATC 60.602 57.143 0.00 0.00 32.72 2.92
1087 1460 1.336440 CGCCGTCTGATCTCTTCATCT 59.664 52.381 0.00 0.00 32.72 2.90
1088 1461 2.223688 CGCCGTCTGATCTCTTCATCTT 60.224 50.000 0.00 0.00 32.72 2.40
1089 1462 3.380142 GCCGTCTGATCTCTTCATCTTC 58.620 50.000 0.00 0.00 32.72 2.87
1090 1463 3.068024 GCCGTCTGATCTCTTCATCTTCT 59.932 47.826 0.00 0.00 32.72 2.85
1091 1464 4.792704 GCCGTCTGATCTCTTCATCTTCTC 60.793 50.000 0.00 0.00 32.72 2.87
1092 1465 4.580167 CCGTCTGATCTCTTCATCTTCTCT 59.420 45.833 0.00 0.00 32.72 3.10
1093 1466 5.067674 CCGTCTGATCTCTTCATCTTCTCTT 59.932 44.000 0.00 0.00 32.72 2.85
1094 1467 6.201517 CGTCTGATCTCTTCATCTTCTCTTC 58.798 44.000 0.00 0.00 32.72 2.87
1095 1468 6.038603 CGTCTGATCTCTTCATCTTCTCTTCT 59.961 42.308 0.00 0.00 32.72 2.85
1096 1469 7.420800 GTCTGATCTCTTCATCTTCTCTTCTC 58.579 42.308 0.00 0.00 32.72 2.87
1097 1470 6.260714 TCTGATCTCTTCATCTTCTCTTCTCG 59.739 42.308 0.00 0.00 32.72 4.04
1098 1471 5.299028 TGATCTCTTCATCTTCTCTTCTCGG 59.701 44.000 0.00 0.00 0.00 4.63
1099 1472 4.594970 TCTCTTCATCTTCTCTTCTCGGT 58.405 43.478 0.00 0.00 0.00 4.69
1100 1473 4.397730 TCTCTTCATCTTCTCTTCTCGGTG 59.602 45.833 0.00 0.00 0.00 4.94
1101 1474 3.445450 TCTTCATCTTCTCTTCTCGGTGG 59.555 47.826 0.00 0.00 0.00 4.61
1102 1475 3.087370 TCATCTTCTCTTCTCGGTGGA 57.913 47.619 0.00 0.00 0.00 4.02
1103 1476 3.636679 TCATCTTCTCTTCTCGGTGGAT 58.363 45.455 0.00 0.00 0.00 3.41
1104 1477 4.026744 TCATCTTCTCTTCTCGGTGGATT 58.973 43.478 0.00 0.00 0.00 3.01
1105 1478 4.098654 TCATCTTCTCTTCTCGGTGGATTC 59.901 45.833 0.00 0.00 0.00 2.52
1106 1479 2.761208 TCTTCTCTTCTCGGTGGATTCC 59.239 50.000 0.00 0.00 0.00 3.01
1107 1480 2.534042 TCTCTTCTCGGTGGATTCCT 57.466 50.000 3.95 0.00 0.00 3.36
1108 1481 2.103373 TCTCTTCTCGGTGGATTCCTG 58.897 52.381 3.95 0.00 0.00 3.86
1109 1482 1.137872 CTCTTCTCGGTGGATTCCTGG 59.862 57.143 3.95 0.00 0.00 4.45
1110 1483 0.905357 CTTCTCGGTGGATTCCTGGT 59.095 55.000 3.95 0.00 0.00 4.00
1111 1484 0.902531 TTCTCGGTGGATTCCTGGTC 59.097 55.000 3.95 0.00 0.00 4.02
1112 1485 0.041238 TCTCGGTGGATTCCTGGTCT 59.959 55.000 3.95 0.00 0.00 3.85
1113 1486 0.905357 CTCGGTGGATTCCTGGTCTT 59.095 55.000 3.95 0.00 0.00 3.01
1114 1487 1.279271 CTCGGTGGATTCCTGGTCTTT 59.721 52.381 3.95 0.00 0.00 2.52
1115 1488 1.702957 TCGGTGGATTCCTGGTCTTTT 59.297 47.619 3.95 0.00 0.00 2.27
1116 1489 2.084546 CGGTGGATTCCTGGTCTTTTC 58.915 52.381 3.95 0.00 0.00 2.29
1117 1490 2.552155 CGGTGGATTCCTGGTCTTTTCA 60.552 50.000 3.95 0.00 0.00 2.69
1118 1491 3.701664 GGTGGATTCCTGGTCTTTTCAT 58.298 45.455 3.95 0.00 0.00 2.57
1119 1492 4.089361 GGTGGATTCCTGGTCTTTTCATT 58.911 43.478 3.95 0.00 0.00 2.57
1120 1493 4.158579 GGTGGATTCCTGGTCTTTTCATTC 59.841 45.833 3.95 0.00 0.00 2.67
1121 1494 5.012893 GTGGATTCCTGGTCTTTTCATTCT 58.987 41.667 3.95 0.00 0.00 2.40
1122 1495 5.478332 GTGGATTCCTGGTCTTTTCATTCTT 59.522 40.000 3.95 0.00 0.00 2.52
1123 1496 5.711976 TGGATTCCTGGTCTTTTCATTCTTC 59.288 40.000 3.95 0.00 0.00 2.87
1124 1497 5.948758 GGATTCCTGGTCTTTTCATTCTTCT 59.051 40.000 0.00 0.00 0.00 2.85
1125 1498 6.435591 GGATTCCTGGTCTTTTCATTCTTCTT 59.564 38.462 0.00 0.00 0.00 2.52
1126 1499 6.639632 TTCCTGGTCTTTTCATTCTTCTTG 57.360 37.500 0.00 0.00 0.00 3.02
1127 1500 4.520492 TCCTGGTCTTTTCATTCTTCTTGC 59.480 41.667 0.00 0.00 0.00 4.01
1128 1501 4.470462 CTGGTCTTTTCATTCTTCTTGCG 58.530 43.478 0.00 0.00 0.00 4.85
1129 1502 3.882888 TGGTCTTTTCATTCTTCTTGCGT 59.117 39.130 0.00 0.00 0.00 5.24
1130 1503 4.024048 TGGTCTTTTCATTCTTCTTGCGTC 60.024 41.667 0.00 0.00 0.00 5.19
1131 1504 4.467735 GTCTTTTCATTCTTCTTGCGTCC 58.532 43.478 0.00 0.00 0.00 4.79
1132 1505 3.502211 TCTTTTCATTCTTCTTGCGTCCC 59.498 43.478 0.00 0.00 0.00 4.46
1133 1506 2.559698 TTCATTCTTCTTGCGTCCCA 57.440 45.000 0.00 0.00 0.00 4.37
1134 1507 2.787473 TCATTCTTCTTGCGTCCCAT 57.213 45.000 0.00 0.00 0.00 4.00
1135 1508 3.071874 TCATTCTTCTTGCGTCCCATT 57.928 42.857 0.00 0.00 0.00 3.16
1136 1509 3.420893 TCATTCTTCTTGCGTCCCATTT 58.579 40.909 0.00 0.00 0.00 2.32
1137 1510 3.826157 TCATTCTTCTTGCGTCCCATTTT 59.174 39.130 0.00 0.00 0.00 1.82
1138 1511 3.641437 TTCTTCTTGCGTCCCATTTTG 57.359 42.857 0.00 0.00 0.00 2.44
1139 1512 2.582052 TCTTCTTGCGTCCCATTTTGT 58.418 42.857 0.00 0.00 0.00 2.83
1140 1513 2.293122 TCTTCTTGCGTCCCATTTTGTG 59.707 45.455 0.00 0.00 0.00 3.33
1141 1514 0.313672 TCTTGCGTCCCATTTTGTGC 59.686 50.000 0.00 0.00 0.00 4.57
1142 1515 0.314935 CTTGCGTCCCATTTTGTGCT 59.685 50.000 0.00 0.00 0.00 4.40
1143 1516 0.031857 TTGCGTCCCATTTTGTGCTG 59.968 50.000 0.00 0.00 0.00 4.41
1144 1517 1.106351 TGCGTCCCATTTTGTGCTGT 61.106 50.000 0.00 0.00 0.00 4.40
1145 1518 0.878416 GCGTCCCATTTTGTGCTGTA 59.122 50.000 0.00 0.00 0.00 2.74
1146 1519 1.401018 GCGTCCCATTTTGTGCTGTAC 60.401 52.381 0.00 0.00 0.00 2.90
1155 1528 0.941542 TTGTGCTGTACTTTCGGTGC 59.058 50.000 0.00 0.00 0.00 5.01
1554 1927 0.175073 CAGGGGCTCAAGGTACGTAC 59.825 60.000 17.56 17.56 0.00 3.67
1567 1950 3.432782 GGTACGTACCTTCAGATTCACG 58.567 50.000 32.93 0.00 43.10 4.35
1583 1976 3.257561 CGCGGTCATTCTGAGGCG 61.258 66.667 0.00 7.74 41.67 5.52
1632 2033 1.454976 CTGATGGATCAGCCCAGGG 59.545 63.158 0.00 0.00 46.63 4.45
1659 2065 5.922544 AGATAAACTTGCTGAAATTGTGTGC 59.077 36.000 0.00 0.00 0.00 4.57
1734 2140 1.588139 CTACGGGATCAACGCCGTC 60.588 63.158 15.73 0.00 42.34 4.79
1830 2236 0.755327 ACAACAACCAGGGCAAGGTC 60.755 55.000 0.31 0.00 38.76 3.85
1872 2281 1.972075 GTAAGATGCCCTCCTAGTCCC 59.028 57.143 0.00 0.00 0.00 4.46
1874 2283 0.570218 AGATGCCCTCCTAGTCCCAT 59.430 55.000 0.00 0.00 0.00 4.00
1875 2284 0.980423 GATGCCCTCCTAGTCCCATC 59.020 60.000 0.00 0.00 0.00 3.51
1876 2285 0.570218 ATGCCCTCCTAGTCCCATCT 59.430 55.000 0.00 0.00 0.00 2.90
1877 2286 0.105453 TGCCCTCCTAGTCCCATCTC 60.105 60.000 0.00 0.00 0.00 2.75
1878 2287 0.105453 GCCCTCCTAGTCCCATCTCA 60.105 60.000 0.00 0.00 0.00 3.27
1879 2288 1.692762 GCCCTCCTAGTCCCATCTCAA 60.693 57.143 0.00 0.00 0.00 3.02
1880 2289 2.324541 CCCTCCTAGTCCCATCTCAAG 58.675 57.143 0.00 0.00 0.00 3.02
1881 2290 2.359781 CCCTCCTAGTCCCATCTCAAGT 60.360 54.545 0.00 0.00 0.00 3.16
1920 2329 5.775686 TCTGAAGAATCCATTGTTTGCTTG 58.224 37.500 0.00 0.00 0.00 4.01
1921 2330 4.309099 TGAAGAATCCATTGTTTGCTTGC 58.691 39.130 0.00 0.00 0.00 4.01
1923 2332 4.184079 AGAATCCATTGTTTGCTTGCTC 57.816 40.909 0.00 0.00 0.00 4.26
1924 2333 3.575256 AGAATCCATTGTTTGCTTGCTCA 59.425 39.130 0.00 0.00 0.00 4.26
2221 2634 8.008513 TGTATACAGTCTATGGAAGGAGAAAC 57.991 38.462 0.08 0.00 0.00 2.78
2275 2694 2.392662 TGAGGGCTCTGAATCTGGTAG 58.607 52.381 0.00 0.00 0.00 3.18
2279 2698 2.365941 GGGCTCTGAATCTGGTAGTACC 59.634 54.545 12.80 12.80 39.22 3.34
2280 2699 3.301274 GGCTCTGAATCTGGTAGTACCT 58.699 50.000 20.07 0.00 39.58 3.08
2281 2700 4.471548 GGCTCTGAATCTGGTAGTACCTA 58.528 47.826 20.07 8.94 39.58 3.08
2282 2701 4.278919 GGCTCTGAATCTGGTAGTACCTAC 59.721 50.000 20.07 7.62 39.58 3.18
2309 2728 7.387119 TGTAGACGACTCTTTTTCTATAGCA 57.613 36.000 0.00 0.00 0.00 3.49
2364 2805 9.995003 AGATAGCAATCTGAATAGTTAAAGAGG 57.005 33.333 0.00 0.00 41.08 3.69
2368 2809 7.713073 AGCAATCTGAATAGTTAAAGAGGTAGC 59.287 37.037 0.00 0.00 0.00 3.58
2414 2864 1.123077 AGGGCAATGCAGAGTCGATA 58.877 50.000 7.79 0.00 0.00 2.92
2423 2873 2.101415 TGCAGAGTCGATATGTTCTGGG 59.899 50.000 12.50 0.00 37.97 4.45
2495 2945 4.201666 GCATAGCTTCTCTGTTCAGAAACG 60.202 45.833 0.00 0.00 38.28 3.60
2537 2988 9.739276 ATCAAGTCAACAATGGAACTCTAATTA 57.261 29.630 0.00 0.00 0.00 1.40
2563 3014 6.003859 TCTCCCTAGTTCTACTCGAAGATT 57.996 41.667 0.00 0.00 33.89 2.40
2564 3015 6.056884 TCTCCCTAGTTCTACTCGAAGATTC 58.943 44.000 0.00 0.00 33.89 2.52
2603 3062 7.164230 AGTAGAGAATCATCCGGATATGTTC 57.836 40.000 18.63 19.50 37.82 3.18
2609 3068 9.219603 GAGAATCATCCGGATATGTTCAAATTA 57.780 33.333 25.24 1.39 34.28 1.40
2610 3069 9.224267 AGAATCATCCGGATATGTTCAAATTAG 57.776 33.333 25.24 9.71 34.28 1.73
2614 3073 6.241882 TCCGGATATGTTCAAATTAGTCCA 57.758 37.500 0.00 0.00 0.00 4.02
2650 3109 4.159377 TGTTAATGCCAGAAAAAGAGCG 57.841 40.909 0.00 0.00 0.00 5.03
2652 3111 0.890683 AATGCCAGAAAAAGAGCGGG 59.109 50.000 0.00 0.00 0.00 6.13
2665 3124 1.482593 AGAGCGGGTCAGGATAAACAG 59.517 52.381 10.15 0.00 0.00 3.16
2670 3129 2.615493 CGGGTCAGGATAAACAGCAAGT 60.615 50.000 0.00 0.00 0.00 3.16
2673 3132 4.564821 GGGTCAGGATAAACAGCAAGTGTA 60.565 45.833 0.00 0.00 39.03 2.90
2777 3236 7.518161 CGAATTCAGTACATTAAGCTTTCACA 58.482 34.615 3.20 0.00 0.00 3.58
2836 3295 9.653516 AGAGTAGATATATAGGACATTCATGGG 57.346 37.037 0.00 0.00 0.00 4.00
2952 3416 6.601613 TGAATCCAATCCCACATTACAGTAAC 59.398 38.462 0.00 0.00 0.00 2.50
2955 3419 4.640201 CCAATCCCACATTACAGTAACCTG 59.360 45.833 0.00 0.00 44.68 4.00
2956 3420 3.343941 TCCCACATTACAGTAACCTGC 57.656 47.619 0.00 0.00 42.81 4.85
2957 3421 2.910319 TCCCACATTACAGTAACCTGCT 59.090 45.455 0.00 0.00 42.81 4.24
2958 3422 4.098155 TCCCACATTACAGTAACCTGCTA 58.902 43.478 0.00 0.00 42.81 3.49
3065 3529 1.341156 CCATCCTCCACCTCCCTCAC 61.341 65.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.126700 GGCGTTGCTAAATATTAATACAACACT 58.873 33.333 18.48 0.00 36.58 3.55
13 14 7.111041 CGTGGCGTTGCTAAATATTAATACAAC 59.889 37.037 12.54 12.54 34.15 3.32
14 15 7.127042 CGTGGCGTTGCTAAATATTAATACAA 58.873 34.615 0.00 0.00 0.00 2.41
15 16 6.651308 CGTGGCGTTGCTAAATATTAATACA 58.349 36.000 0.00 0.00 0.00 2.29
16 17 5.562623 GCGTGGCGTTGCTAAATATTAATAC 59.437 40.000 0.00 0.00 0.00 1.89
17 18 5.467399 AGCGTGGCGTTGCTAAATATTAATA 59.533 36.000 0.00 0.00 40.28 0.98
18 19 4.274950 AGCGTGGCGTTGCTAAATATTAAT 59.725 37.500 0.00 0.00 40.28 1.40
19 20 3.623960 AGCGTGGCGTTGCTAAATATTAA 59.376 39.130 0.00 0.00 40.28 1.40
20 21 3.199677 AGCGTGGCGTTGCTAAATATTA 58.800 40.909 0.00 0.00 40.28 0.98
21 22 2.014128 AGCGTGGCGTTGCTAAATATT 58.986 42.857 0.00 0.00 40.28 1.28
22 23 1.597663 GAGCGTGGCGTTGCTAAATAT 59.402 47.619 0.00 0.00 42.60 1.28
23 24 1.003851 GAGCGTGGCGTTGCTAAATA 58.996 50.000 0.00 0.00 42.60 1.40
24 25 1.794222 GAGCGTGGCGTTGCTAAAT 59.206 52.632 0.00 0.00 42.60 1.40
25 26 2.663478 CGAGCGTGGCGTTGCTAAA 61.663 57.895 0.00 0.00 42.60 1.85
26 27 3.109547 CGAGCGTGGCGTTGCTAA 61.110 61.111 0.00 0.00 42.60 3.09
27 28 3.561217 TTCGAGCGTGGCGTTGCTA 62.561 57.895 0.00 0.00 42.60 3.49
28 29 4.961511 TTCGAGCGTGGCGTTGCT 62.962 61.111 0.00 0.00 45.90 3.91
29 30 4.007940 TTTCGAGCGTGGCGTTGC 62.008 61.111 0.00 0.00 0.00 4.17
30 31 2.127758 GTTTCGAGCGTGGCGTTG 60.128 61.111 0.00 0.00 0.00 4.10
31 32 3.698463 CGTTTCGAGCGTGGCGTT 61.698 61.111 3.73 0.00 0.00 4.84
32 33 4.634133 TCGTTTCGAGCGTGGCGT 62.634 61.111 10.44 0.00 0.00 5.68
33 34 3.827784 CTCGTTTCGAGCGTGGCG 61.828 66.667 6.24 0.00 46.75 5.69
41 42 6.974932 AAGATGTAGTACTACTCGTTTCGA 57.025 37.500 28.56 10.53 37.00 3.71
42 43 7.343691 CCTAAGATGTAGTACTACTCGTTTCG 58.656 42.308 28.56 15.26 37.00 3.46
43 44 7.131565 GCCTAAGATGTAGTACTACTCGTTTC 58.868 42.308 28.56 18.09 37.00 2.78
44 45 6.039159 GGCCTAAGATGTAGTACTACTCGTTT 59.961 42.308 28.56 19.84 37.00 3.60
45 46 5.530543 GGCCTAAGATGTAGTACTACTCGTT 59.469 44.000 28.56 20.74 37.00 3.85
46 47 5.062528 GGCCTAAGATGTAGTACTACTCGT 58.937 45.833 28.56 22.25 37.00 4.18
47 48 4.455190 GGGCCTAAGATGTAGTACTACTCG 59.545 50.000 28.56 13.97 37.00 4.18
48 49 5.474189 CAGGGCCTAAGATGTAGTACTACTC 59.526 48.000 28.56 22.51 37.00 2.59
49 50 5.386924 CAGGGCCTAAGATGTAGTACTACT 58.613 45.833 28.56 16.82 37.00 2.57
50 51 4.022155 GCAGGGCCTAAGATGTAGTACTAC 60.022 50.000 23.58 23.58 36.63 2.73
51 52 4.140994 AGCAGGGCCTAAGATGTAGTACTA 60.141 45.833 5.28 0.00 0.00 1.82
52 53 2.966516 GCAGGGCCTAAGATGTAGTACT 59.033 50.000 5.28 0.00 0.00 2.73
53 54 2.966516 AGCAGGGCCTAAGATGTAGTAC 59.033 50.000 5.28 0.00 0.00 2.73
54 55 3.330126 AGCAGGGCCTAAGATGTAGTA 57.670 47.619 5.28 0.00 0.00 1.82
55 56 2.171448 CAAGCAGGGCCTAAGATGTAGT 59.829 50.000 5.28 0.00 0.00 2.73
56 57 2.435805 TCAAGCAGGGCCTAAGATGTAG 59.564 50.000 5.28 0.00 0.00 2.74
57 58 2.477245 TCAAGCAGGGCCTAAGATGTA 58.523 47.619 5.28 0.00 0.00 2.29
58 59 1.289160 TCAAGCAGGGCCTAAGATGT 58.711 50.000 5.28 0.00 0.00 3.06
59 60 2.425143 TTCAAGCAGGGCCTAAGATG 57.575 50.000 5.28 3.40 0.00 2.90
60 61 3.294214 CATTTCAAGCAGGGCCTAAGAT 58.706 45.455 5.28 0.00 0.00 2.40
133 134 2.105128 CCTAGTCGAAGCCCAGCG 59.895 66.667 0.00 0.00 0.00 5.18
236 237 1.379309 GGGGAAATACAGCGCCCAA 60.379 57.895 2.29 0.00 42.52 4.12
243 244 1.139058 CGAGGAGGTGGGGAAATACAG 59.861 57.143 0.00 0.00 0.00 2.74
342 356 0.539518 TGTAAATAGCCAGCGCCTCA 59.460 50.000 2.29 0.00 34.57 3.86
487 771 2.354401 CGCTTGGAGCAGGAGGAGA 61.354 63.158 0.50 0.00 42.58 3.71
654 996 9.849166 CCAGTAAAATACAACCGAATACATTTT 57.151 29.630 0.00 0.00 32.21 1.82
704 1046 9.781834 TCTGTGAAACTTTACAACTGTAAATTG 57.218 29.630 13.86 7.50 45.88 2.32
721 1063 2.350772 CCGCTTGGAATGTCTGTGAAAC 60.351 50.000 0.00 0.00 33.02 2.78
792 1134 2.180017 CCCCGACCAGACGTTACG 59.820 66.667 2.19 2.19 0.00 3.18
793 1135 2.575461 CCCCCGACCAGACGTTAC 59.425 66.667 0.00 0.00 0.00 2.50
794 1136 3.384532 GCCCCCGACCAGACGTTA 61.385 66.667 0.00 0.00 0.00 3.18
845 1199 1.811266 CGGCTCCGAGAACCACATG 60.811 63.158 1.35 0.00 42.83 3.21
978 1336 1.405821 GTGGTTGAGAGGACGATCGAT 59.594 52.381 24.34 7.06 0.00 3.59
993 1351 2.440599 GTGGAGGCCATGGTGGTT 59.559 61.111 14.67 0.00 40.46 3.67
994 1352 3.661648 GGTGGAGGCCATGGTGGT 61.662 66.667 14.67 0.00 40.46 4.16
1035 1408 0.613777 GAGGAGTGGTTACCTGGGTG 59.386 60.000 2.07 0.00 36.57 4.61
1049 1422 1.911471 GGCAGGAAGAAGGGAGGAG 59.089 63.158 0.00 0.00 0.00 3.69
1050 1423 1.990060 CGGCAGGAAGAAGGGAGGA 60.990 63.158 0.00 0.00 0.00 3.71
1083 1456 4.367450 GAATCCACCGAGAAGAGAAGATG 58.633 47.826 0.00 0.00 0.00 2.90
1084 1457 3.386402 GGAATCCACCGAGAAGAGAAGAT 59.614 47.826 0.00 0.00 0.00 2.40
1085 1458 2.761208 GGAATCCACCGAGAAGAGAAGA 59.239 50.000 0.00 0.00 0.00 2.87
1086 1459 2.763448 AGGAATCCACCGAGAAGAGAAG 59.237 50.000 0.61 0.00 34.73 2.85
1087 1460 2.497675 CAGGAATCCACCGAGAAGAGAA 59.502 50.000 0.61 0.00 34.73 2.87
1088 1461 2.103373 CAGGAATCCACCGAGAAGAGA 58.897 52.381 0.61 0.00 34.73 3.10
1089 1462 1.137872 CCAGGAATCCACCGAGAAGAG 59.862 57.143 0.61 0.00 34.73 2.85
1090 1463 1.195115 CCAGGAATCCACCGAGAAGA 58.805 55.000 0.61 0.00 34.73 2.87
1091 1464 0.905357 ACCAGGAATCCACCGAGAAG 59.095 55.000 0.61 0.00 34.73 2.85
1092 1465 0.902531 GACCAGGAATCCACCGAGAA 59.097 55.000 0.61 0.00 34.73 2.87
1093 1466 0.041238 AGACCAGGAATCCACCGAGA 59.959 55.000 0.61 0.00 34.73 4.04
1094 1467 0.905357 AAGACCAGGAATCCACCGAG 59.095 55.000 0.61 0.00 34.73 4.63
1095 1468 1.358152 AAAGACCAGGAATCCACCGA 58.642 50.000 0.61 0.00 34.73 4.69
1096 1469 2.084546 GAAAAGACCAGGAATCCACCG 58.915 52.381 0.61 0.00 34.73 4.94
1097 1470 3.154827 TGAAAAGACCAGGAATCCACC 57.845 47.619 0.61 0.00 0.00 4.61
1098 1471 5.012893 AGAATGAAAAGACCAGGAATCCAC 58.987 41.667 0.61 0.00 0.00 4.02
1099 1472 5.261040 AGAATGAAAAGACCAGGAATCCA 57.739 39.130 0.61 0.00 0.00 3.41
1100 1473 5.948758 AGAAGAATGAAAAGACCAGGAATCC 59.051 40.000 0.00 0.00 0.00 3.01
1101 1474 7.311408 CAAGAAGAATGAAAAGACCAGGAATC 58.689 38.462 0.00 0.00 0.00 2.52
1102 1475 6.294955 GCAAGAAGAATGAAAAGACCAGGAAT 60.295 38.462 0.00 0.00 0.00 3.01
1103 1476 5.010012 GCAAGAAGAATGAAAAGACCAGGAA 59.990 40.000 0.00 0.00 0.00 3.36
1104 1477 4.520492 GCAAGAAGAATGAAAAGACCAGGA 59.480 41.667 0.00 0.00 0.00 3.86
1105 1478 4.614535 CGCAAGAAGAATGAAAAGACCAGG 60.615 45.833 0.00 0.00 43.02 4.45
1106 1479 4.023707 ACGCAAGAAGAATGAAAAGACCAG 60.024 41.667 0.00 0.00 43.62 4.00
1107 1480 3.882888 ACGCAAGAAGAATGAAAAGACCA 59.117 39.130 0.00 0.00 43.62 4.02
1108 1481 4.467735 GACGCAAGAAGAATGAAAAGACC 58.532 43.478 0.00 0.00 43.62 3.85
1109 1482 4.467735 GGACGCAAGAAGAATGAAAAGAC 58.532 43.478 0.00 0.00 43.62 3.01
1110 1483 3.502211 GGGACGCAAGAAGAATGAAAAGA 59.498 43.478 0.00 0.00 43.62 2.52
1111 1484 3.253188 TGGGACGCAAGAAGAATGAAAAG 59.747 43.478 0.00 0.00 43.62 2.27
1112 1485 3.218453 TGGGACGCAAGAAGAATGAAAA 58.782 40.909 0.00 0.00 43.62 2.29
1113 1486 2.857483 TGGGACGCAAGAAGAATGAAA 58.143 42.857 0.00 0.00 43.62 2.69
1114 1487 2.559698 TGGGACGCAAGAAGAATGAA 57.440 45.000 0.00 0.00 43.62 2.57
1115 1488 2.787473 ATGGGACGCAAGAAGAATGA 57.213 45.000 0.00 0.00 43.62 2.57
1116 1489 3.855689 AAATGGGACGCAAGAAGAATG 57.144 42.857 0.00 0.00 43.62 2.67
1117 1490 3.573967 ACAAAATGGGACGCAAGAAGAAT 59.426 39.130 0.00 0.00 43.62 2.40
1118 1491 2.955660 ACAAAATGGGACGCAAGAAGAA 59.044 40.909 0.00 0.00 43.62 2.52
1119 1492 2.293122 CACAAAATGGGACGCAAGAAGA 59.707 45.455 0.00 0.00 43.62 2.87
1120 1493 2.664916 CACAAAATGGGACGCAAGAAG 58.335 47.619 0.00 0.00 43.62 2.85
1121 1494 1.269517 GCACAAAATGGGACGCAAGAA 60.270 47.619 0.00 0.00 43.62 2.52
1122 1495 0.313672 GCACAAAATGGGACGCAAGA 59.686 50.000 0.00 0.00 43.62 3.02
1124 1497 0.031857 CAGCACAAAATGGGACGCAA 59.968 50.000 0.00 0.00 0.00 4.85
1125 1498 1.106351 ACAGCACAAAATGGGACGCA 61.106 50.000 0.00 0.00 0.00 5.24
1126 1499 0.878416 TACAGCACAAAATGGGACGC 59.122 50.000 0.00 0.00 0.00 5.19
1127 1500 2.151202 AGTACAGCACAAAATGGGACG 58.849 47.619 0.00 0.00 0.00 4.79
1128 1501 4.546570 GAAAGTACAGCACAAAATGGGAC 58.453 43.478 0.00 0.00 0.00 4.46
1129 1502 3.252215 CGAAAGTACAGCACAAAATGGGA 59.748 43.478 0.00 0.00 0.00 4.37
1130 1503 3.564511 CGAAAGTACAGCACAAAATGGG 58.435 45.455 0.00 0.00 0.00 4.00
1131 1504 3.004315 ACCGAAAGTACAGCACAAAATGG 59.996 43.478 0.00 0.00 0.00 3.16
1132 1505 3.974401 CACCGAAAGTACAGCACAAAATG 59.026 43.478 0.00 0.00 0.00 2.32
1133 1506 3.550030 GCACCGAAAGTACAGCACAAAAT 60.550 43.478 0.00 0.00 0.00 1.82
1134 1507 2.223386 GCACCGAAAGTACAGCACAAAA 60.223 45.455 0.00 0.00 0.00 2.44
1135 1508 1.332375 GCACCGAAAGTACAGCACAAA 59.668 47.619 0.00 0.00 0.00 2.83
1136 1509 0.941542 GCACCGAAAGTACAGCACAA 59.058 50.000 0.00 0.00 0.00 3.33
1137 1510 1.218875 CGCACCGAAAGTACAGCACA 61.219 55.000 0.00 0.00 0.00 4.57
1138 1511 1.491563 CGCACCGAAAGTACAGCAC 59.508 57.895 0.00 0.00 0.00 4.40
1139 1512 2.314647 GCGCACCGAAAGTACAGCA 61.315 57.895 0.30 0.00 0.00 4.41
1140 1513 2.474712 GCGCACCGAAAGTACAGC 59.525 61.111 0.30 0.00 0.00 4.40
1141 1514 1.674611 CTCGCGCACCGAAAGTACAG 61.675 60.000 8.75 0.00 46.81 2.74
1142 1515 1.731613 CTCGCGCACCGAAAGTACA 60.732 57.895 8.75 0.00 46.81 2.90
1143 1516 1.403972 CTCTCGCGCACCGAAAGTAC 61.404 60.000 8.75 0.00 46.81 2.73
1144 1517 1.154093 CTCTCGCGCACCGAAAGTA 60.154 57.895 8.75 0.00 46.81 2.24
1145 1518 2.430921 CTCTCGCGCACCGAAAGT 60.431 61.111 8.75 0.00 46.81 2.66
1146 1519 2.126463 TCTCTCGCGCACCGAAAG 60.126 61.111 8.75 0.00 46.81 2.62
1155 1528 2.202676 GAACCTGGCTCTCTCGCG 60.203 66.667 0.00 0.00 0.00 5.87
1167 1540 2.028112 TCTCAGCAAGCATAACGAACCT 60.028 45.455 0.00 0.00 0.00 3.50
1554 1927 0.389817 TGACCGCGTGAATCTGAAGG 60.390 55.000 4.92 0.00 0.00 3.46
1567 1950 1.696832 GAACGCCTCAGAATGACCGC 61.697 60.000 0.00 0.00 42.56 5.68
1583 1976 4.333649 TCTGCTTGCATATAGCTTGTGAAC 59.666 41.667 10.10 0.00 45.94 3.18
1634 2035 6.421801 GCACACAATTTCAGCAAGTTTATCTT 59.578 34.615 0.00 0.00 36.75 2.40
1638 2039 5.003692 TGCACACAATTTCAGCAAGTTTA 57.996 34.783 0.00 0.00 31.42 2.01
1639 2040 3.859443 TGCACACAATTTCAGCAAGTTT 58.141 36.364 0.00 0.00 31.42 2.66
1659 2065 3.583054 AGGATCACCCTGCAACATG 57.417 52.632 0.00 0.00 45.61 3.21
1734 2140 1.063649 GCATCCAAGATGCGTGCAG 59.936 57.895 13.32 0.00 35.17 4.41
1872 2281 5.303971 AGGTTCAGTTGAGAACTTGAGATG 58.696 41.667 6.77 0.00 45.52 2.90
1874 2283 5.359194 AAGGTTCAGTTGAGAACTTGAGA 57.641 39.130 6.77 0.00 45.52 3.27
1875 2284 5.819901 AGAAAGGTTCAGTTGAGAACTTGAG 59.180 40.000 6.77 0.00 45.52 3.02
1876 2285 5.586243 CAGAAAGGTTCAGTTGAGAACTTGA 59.414 40.000 6.77 0.00 45.52 3.02
1877 2286 5.586243 TCAGAAAGGTTCAGTTGAGAACTTG 59.414 40.000 6.77 0.45 45.52 3.16
1878 2287 5.745227 TCAGAAAGGTTCAGTTGAGAACTT 58.255 37.500 6.77 0.00 45.52 2.66
1879 2288 5.359194 TCAGAAAGGTTCAGTTGAGAACT 57.641 39.130 6.77 0.00 45.52 3.01
1880 2289 5.817816 TCTTCAGAAAGGTTCAGTTGAGAAC 59.182 40.000 0.00 0.00 45.50 3.01
1881 2290 5.989477 TCTTCAGAAAGGTTCAGTTGAGAA 58.011 37.500 0.00 0.00 33.03 2.87
1920 2329 1.264288 CTTGGTTCGGTTCAGTTGAGC 59.736 52.381 0.00 0.00 0.00 4.26
1921 2330 1.264288 GCTTGGTTCGGTTCAGTTGAG 59.736 52.381 0.00 0.00 0.00 3.02
1923 2332 1.002468 CAGCTTGGTTCGGTTCAGTTG 60.002 52.381 0.00 0.00 0.00 3.16
1924 2333 1.134220 TCAGCTTGGTTCGGTTCAGTT 60.134 47.619 0.00 0.00 0.00 3.16
2239 2652 6.611642 AGAGCCCTCAAAATGTGATACTACTA 59.388 38.462 0.00 0.00 35.07 1.82
2240 2653 5.426833 AGAGCCCTCAAAATGTGATACTACT 59.573 40.000 0.00 0.00 35.07 2.57
2241 2654 5.525378 CAGAGCCCTCAAAATGTGATACTAC 59.475 44.000 0.00 0.00 35.07 2.73
2244 2657 4.517285 TCAGAGCCCTCAAAATGTGATAC 58.483 43.478 0.00 0.00 35.07 2.24
2275 2694 4.367450 AGAGTCGTCTACATCGTAGGTAC 58.633 47.826 1.53 0.00 0.00 3.34
2279 2698 6.544622 AGAAAAAGAGTCGTCTACATCGTAG 58.455 40.000 0.00 0.00 30.45 3.51
2280 2699 6.492007 AGAAAAAGAGTCGTCTACATCGTA 57.508 37.500 0.00 0.00 30.45 3.43
2281 2700 5.373981 AGAAAAAGAGTCGTCTACATCGT 57.626 39.130 0.00 0.00 30.45 3.73
2282 2701 7.321746 GCTATAGAAAAAGAGTCGTCTACATCG 59.678 40.741 3.21 0.00 30.45 3.84
2309 2728 5.511386 AGATTCAGGTTCAGGTTTGATCT 57.489 39.130 0.00 0.00 32.27 2.75
2364 2805 1.467734 GCTGCAGATATGCCATGCTAC 59.532 52.381 20.43 0.00 40.62 3.58
2368 2809 2.296190 ACAATGCTGCAGATATGCCATG 59.704 45.455 20.43 8.35 0.00 3.66
2414 2864 4.210331 GGCTTGTATCATTCCCAGAACAT 58.790 43.478 0.00 0.00 0.00 2.71
2423 2873 4.764172 AGAGACAGTGGCTTGTATCATTC 58.236 43.478 0.00 0.00 40.76 2.67
2495 2945 3.823304 ACTTGATTCAAGAGGAAAGTGCC 59.177 43.478 28.60 0.00 43.42 5.01
2537 2988 6.424883 TCTTCGAGTAGAACTAGGGAGAAAT 58.575 40.000 0.00 0.00 34.66 2.17
2563 3014 7.818997 TTCTCTACTTATTAGAATGGCTCGA 57.181 36.000 0.00 0.00 36.32 4.04
2564 3015 8.300286 TGATTCTCTACTTATTAGAATGGCTCG 58.700 37.037 0.00 0.00 39.46 5.03
2641 3100 3.713826 TTATCCTGACCCGCTCTTTTT 57.286 42.857 0.00 0.00 0.00 1.94
2650 3109 2.749621 CACTTGCTGTTTATCCTGACCC 59.250 50.000 0.00 0.00 0.00 4.46
2652 3111 6.554334 TTTACACTTGCTGTTTATCCTGAC 57.446 37.500 0.00 0.00 33.91 3.51
2691 3150 3.034635 TGCTTTTGGTAACCCACATTGT 58.965 40.909 0.00 0.00 41.67 2.71
2777 3236 5.925397 TGCGAATGTTTGCATATTTGTTCTT 59.075 32.000 3.58 0.00 42.41 2.52
2836 3295 2.786777 TGATGCTGGATGTATCATGGC 58.213 47.619 0.00 0.00 41.66 4.40
2952 3416 5.593095 TGGTGTGATTAGTACTAGTAGCAGG 59.407 44.000 1.87 0.00 0.00 4.85
2955 3419 7.980099 ACATTTGGTGTGATTAGTACTAGTAGC 59.020 37.037 1.87 0.00 40.28 3.58
2958 3422 9.032624 AGTACATTTGGTGTGATTAGTACTAGT 57.967 33.333 0.00 0.00 42.24 2.57


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

AutoCloner maintained by Alex Coulton.