Multiple sequence alignment - TraesCS4A01G252800

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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 TraesCS4A01G252800 chr4A 100.000 5054 0 0 1 5054 565039539 565044592 0.000000e+00 9334
1 TraesCS4A01G252800 chr4A 83.041 1427 165 42 1465 2832 564971699 564973107 0.000000e+00 1223
2 TraesCS4A01G252800 chr4A 83.003 1212 128 43 2951 4117 564973380 564974558 0.000000e+00 1026
3 TraesCS4A01G252800 chr4A 81.958 521 66 22 3520 4028 565305068 565305572 2.810000e-112 416
4 TraesCS4A01G252800 chr4A 83.898 118 13 5 966 1080 564971239 564971353 1.920000e-19 108
5 TraesCS4A01G252800 chr4D 94.350 3133 123 18 1614 4710 37137427 37134313 0.000000e+00 4756
6 TraesCS4A01G252800 chr4D 84.255 1645 130 53 1 1604 37139022 37137466 0.000000e+00 1483
7 TraesCS4A01G252800 chr4D 83.884 1210 121 39 2949 4117 37254260 37253084 0.000000e+00 1086
8 TraesCS4A01G252800 chr4D 85.414 713 87 11 1619 2317 37262472 37261763 0.000000e+00 725
9 TraesCS4A01G252800 chr4D 90.625 352 13 8 4711 5054 37131275 37130936 2.780000e-122 449
10 TraesCS4A01G252800 chr4D 85.412 425 46 8 3617 4028 37049758 37049337 1.300000e-115 427
11 TraesCS4A01G252800 chr4D 85.593 118 11 5 966 1080 37263350 37263236 8.890000e-23 119
12 TraesCS4A01G252800 chr4B 93.179 2111 83 12 2967 5054 54139026 54136954 0.000000e+00 3044
13 TraesCS4A01G252800 chr4B 89.346 1652 117 33 1191 2797 54140658 54139021 0.000000e+00 2021
14 TraesCS4A01G252800 chr4B 85.858 1195 85 34 1 1185 54141814 54140694 0.000000e+00 1194
15 TraesCS4A01G252800 chr4B 82.073 1428 160 36 1550 2915 54349388 54347995 0.000000e+00 1131
16 TraesCS4A01G252800 chr4B 84.154 1218 124 39 2941 4117 54347366 54346177 0.000000e+00 1116
17 TraesCS4A01G252800 chr4B 83.709 577 65 21 3617 4167 54037054 54036481 7.500000e-143 518
18 TraesCS4A01G252800 chr3A 85.897 234 31 2 2191 2424 145590082 145590313 1.090000e-61 248
19 TraesCS4A01G252800 chr6B 85.124 242 32 4 2183 2424 199578692 199578929 1.410000e-60 244
20 TraesCS4A01G252800 chr7B 85.470 234 32 2 2191 2424 383667616 383667847 5.060000e-60 243
21 TraesCS4A01G252800 chr1A 85.470 234 32 2 2191 2424 424760505 424760736 5.060000e-60 243


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 TraesCS4A01G252800 chr4A 565039539 565044592 5053 False 9334.000000 9334 100.000000 1 5054 1 chr4A.!!$F1 5053
1 TraesCS4A01G252800 chr4A 564971239 564974558 3319 False 785.666667 1223 83.314000 966 4117 3 chr4A.!!$F3 3151
2 TraesCS4A01G252800 chr4A 565305068 565305572 504 False 416.000000 416 81.958000 3520 4028 1 chr4A.!!$F2 508
3 TraesCS4A01G252800 chr4D 37130936 37139022 8086 True 2229.333333 4756 89.743333 1 5054 3 chr4D.!!$R3 5053
4 TraesCS4A01G252800 chr4D 37253084 37254260 1176 True 1086.000000 1086 83.884000 2949 4117 1 chr4D.!!$R2 1168
5 TraesCS4A01G252800 chr4D 37261763 37263350 1587 True 422.000000 725 85.503500 966 2317 2 chr4D.!!$R4 1351
6 TraesCS4A01G252800 chr4B 54136954 54141814 4860 True 2086.333333 3044 89.461000 1 5054 3 chr4B.!!$R2 5053
7 TraesCS4A01G252800 chr4B 54346177 54349388 3211 True 1123.500000 1131 83.113500 1550 4117 2 chr4B.!!$R3 2567
8 TraesCS4A01G252800 chr4B 54036481 54037054 573 True 518.000000 518 83.709000 3617 4167 1 chr4B.!!$R1 550

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
963 981 0.038526 TCTTCTTGCTTCCCGTCGAC 60.039 55.000 5.18 5.18 0.00 4.20 F
1120 1148 0.392461 ATCGCCGCCTCTGCTTTTTA 60.392 50.000 0.00 0.00 34.43 1.52 F
1271 1331 0.454600 TACTGTAGCTGTAGTGCCGC 59.545 55.000 13.18 0.00 0.00 6.53 F
1956 2657 0.693049 AGCTCCCAAAGGTGTTCGAT 59.307 50.000 0.00 0.00 33.44 3.59 F
2453 3167 1.669795 GCTTGCTGTGGGTTTATGTGC 60.670 52.381 0.00 0.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2222 2933 0.399949 AGGAACCACAGTGACCCTGA 60.400 55.000 0.62 0.0 44.49 3.86 R
2453 3167 1.431488 CTCCATCACAACCATCGCCG 61.431 60.000 0.00 0.0 0.00 6.46 R
2569 3290 4.429854 AATAGGATTGCTCTTGGAGGAC 57.570 45.455 0.00 0.0 27.75 3.85 R
3303 4703 2.102925 CCAACATTTTGACAGCCTTGGT 59.897 45.455 0.00 0.0 34.24 3.67 R
4359 5818 0.174845 TTTAGTCCCACATCGGAGCG 59.825 55.000 0.00 0.0 36.56 5.03 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
44 45 2.144730 CCGTGAACGACCATACCAAAA 58.855 47.619 4.03 0.00 43.02 2.44
128 130 0.777446 CCTCCTCCCACCCAAGAAAA 59.223 55.000 0.00 0.00 0.00 2.29
129 131 1.146982 CCTCCTCCCACCCAAGAAAAA 59.853 52.381 0.00 0.00 0.00 1.94
130 132 2.225369 CCTCCTCCCACCCAAGAAAAAT 60.225 50.000 0.00 0.00 0.00 1.82
131 133 3.011257 CCTCCTCCCACCCAAGAAAAATA 59.989 47.826 0.00 0.00 0.00 1.40
132 134 4.273318 CTCCTCCCACCCAAGAAAAATAG 58.727 47.826 0.00 0.00 0.00 1.73
133 135 3.660669 TCCTCCCACCCAAGAAAAATAGT 59.339 43.478 0.00 0.00 0.00 2.12
162 164 1.229177 AAATGTTGCCAGGGTCCCC 60.229 57.895 3.51 0.00 0.00 4.81
164 166 2.155197 AATGTTGCCAGGGTCCCCTC 62.155 60.000 3.51 0.00 46.28 4.30
165 167 4.048470 GTTGCCAGGGTCCCCTCC 62.048 72.222 3.51 0.00 46.28 4.30
216 219 2.798680 CGTGAGATCGGGTAGTTGAAG 58.201 52.381 0.00 0.00 0.00 3.02
234 237 1.523938 GGATTGTAGAGTGGCGGGC 60.524 63.158 0.00 0.00 0.00 6.13
249 252 2.324860 GCGGGCTGTAACATTCAAAAC 58.675 47.619 0.00 0.00 0.00 2.43
332 339 7.319646 TCGTTTCAAAAATAAATATGCAGGCT 58.680 30.769 0.00 0.00 0.00 4.58
333 340 7.275341 TCGTTTCAAAAATAAATATGCAGGCTG 59.725 33.333 10.94 10.94 0.00 4.85
334 341 6.907206 TTCAAAAATAAATATGCAGGCTGC 57.093 33.333 31.91 31.91 45.29 5.25
335 342 6.224665 TCAAAAATAAATATGCAGGCTGCT 57.775 33.333 36.50 24.67 45.31 4.24
336 343 6.044046 TCAAAAATAAATATGCAGGCTGCTG 58.956 36.000 36.50 22.50 45.31 4.41
343 350 3.207669 GCAGGCTGCTGCGCTTAT 61.208 61.111 31.37 1.63 40.96 1.73
344 351 1.889105 GCAGGCTGCTGCGCTTATA 60.889 57.895 31.37 0.00 40.96 0.98
345 352 1.439353 GCAGGCTGCTGCGCTTATAA 61.439 55.000 31.37 0.00 40.96 0.98
346 353 1.016627 CAGGCTGCTGCGCTTATAAA 58.983 50.000 9.73 0.00 40.82 1.40
347 354 1.003116 CAGGCTGCTGCGCTTATAAAG 60.003 52.381 9.73 0.00 40.82 1.85
348 355 0.308993 GGCTGCTGCGCTTATAAAGG 59.691 55.000 9.73 0.00 40.82 3.11
349 356 1.017387 GCTGCTGCGCTTATAAAGGT 58.983 50.000 9.73 0.00 0.00 3.50
350 357 1.268234 GCTGCTGCGCTTATAAAGGTG 60.268 52.381 9.73 0.00 0.00 4.00
351 358 2.009774 CTGCTGCGCTTATAAAGGTGT 58.990 47.619 9.73 0.00 0.00 4.16
352 359 2.420022 CTGCTGCGCTTATAAAGGTGTT 59.580 45.455 9.73 0.00 0.00 3.32
355 362 3.006940 CTGCGCTTATAAAGGTGTTCCA 58.993 45.455 9.73 0.00 35.89 3.53
358 365 5.186942 TGCGCTTATAAAGGTGTTCCAATA 58.813 37.500 9.73 0.00 35.89 1.90
382 389 2.295909 TGGAGCACGGAATTTCCAAAAG 59.704 45.455 15.58 1.73 36.81 2.27
459 471 0.179045 ATGCAACCCTCTATCCGCAC 60.179 55.000 0.00 0.00 31.22 5.34
474 486 2.812591 TCCGCACTCGATATCTTCTACC 59.187 50.000 0.34 0.00 38.10 3.18
492 504 7.510685 TCTTCTACCAATACTTGCATATCCTCT 59.489 37.037 0.00 0.00 0.00 3.69
493 505 8.721133 TTCTACCAATACTTGCATATCCTCTA 57.279 34.615 0.00 0.00 0.00 2.43
494 506 8.721133 TCTACCAATACTTGCATATCCTCTAA 57.279 34.615 0.00 0.00 0.00 2.10
495 507 8.807118 TCTACCAATACTTGCATATCCTCTAAG 58.193 37.037 0.00 0.00 0.00 2.18
523 535 2.978156 TGCACCCCTCAGAAAGAATT 57.022 45.000 0.00 0.00 0.00 2.17
559 571 4.728608 CGCTTATAAATGTCTTGCGTTTCC 59.271 41.667 5.21 0.00 37.48 3.13
560 572 5.447279 CGCTTATAAATGTCTTGCGTTTCCT 60.447 40.000 5.21 0.00 37.48 3.36
561 573 6.322491 GCTTATAAATGTCTTGCGTTTCCTT 58.678 36.000 0.00 0.00 37.48 3.36
562 574 6.469275 GCTTATAAATGTCTTGCGTTTCCTTC 59.531 38.462 0.00 0.00 37.48 3.46
563 575 7.626452 GCTTATAAATGTCTTGCGTTTCCTTCT 60.626 37.037 0.00 0.00 37.48 2.85
564 576 4.918810 AAATGTCTTGCGTTTCCTTCTT 57.081 36.364 0.00 0.00 31.04 2.52
565 577 4.918810 AATGTCTTGCGTTTCCTTCTTT 57.081 36.364 0.00 0.00 0.00 2.52
566 578 3.963383 TGTCTTGCGTTTCCTTCTTTC 57.037 42.857 0.00 0.00 0.00 2.62
579 591 8.893727 CGTTTCCTTCTTTCAATAATGGAGTAT 58.106 33.333 0.00 0.00 0.00 2.12
582 594 8.964476 TCCTTCTTTCAATAATGGAGTATCAC 57.036 34.615 0.00 0.00 36.25 3.06
583 595 8.548025 TCCTTCTTTCAATAATGGAGTATCACA 58.452 33.333 0.00 0.00 36.25 3.58
798 816 2.158325 TCACTCCCAAGGCTGGAAAAAT 60.158 45.455 4.77 0.00 46.92 1.82
818 836 0.894184 ATCGGCGGTCTCCATCGTAT 60.894 55.000 7.21 0.00 0.00 3.06
860 878 3.217743 GCGTCTACCCCCTCGGAG 61.218 72.222 0.00 0.00 34.64 4.63
963 981 0.038526 TCTTCTTGCTTCCCGTCGAC 60.039 55.000 5.18 5.18 0.00 4.20
970 988 1.596895 GCTTCCCGTCGACTTCCTCT 61.597 60.000 14.70 0.00 0.00 3.69
971 989 0.889306 CTTCCCGTCGACTTCCTCTT 59.111 55.000 14.70 0.00 0.00 2.85
972 990 0.886563 TTCCCGTCGACTTCCTCTTC 59.113 55.000 14.70 0.00 0.00 2.87
974 992 0.966370 CCCGTCGACTTCCTCTTCCT 60.966 60.000 14.70 0.00 0.00 3.36
1005 1026 3.935024 TCGAGGACGAAGATGGGG 58.065 61.111 0.00 0.00 45.74 4.96
1006 1027 1.305287 TCGAGGACGAAGATGGGGA 59.695 57.895 0.00 0.00 45.74 4.81
1014 1035 1.835693 GAAGATGGGGAGGAGCCTG 59.164 63.158 0.00 0.00 36.66 4.85
1085 1113 2.052690 TTCGGCTCTTCTCCTCCGG 61.053 63.158 0.00 0.00 41.98 5.14
1087 1115 2.776913 CGGCTCTTCTCCTCCGGTC 61.777 68.421 0.00 0.00 38.35 4.79
1107 1135 2.049985 GTCGAGATCCCATCGCCG 60.050 66.667 0.00 0.00 39.98 6.46
1116 1144 4.845580 CCATCGCCGCCTCTGCTT 62.846 66.667 0.00 0.00 34.43 3.91
1120 1148 0.392461 ATCGCCGCCTCTGCTTTTTA 60.392 50.000 0.00 0.00 34.43 1.52
1159 1187 4.889409 TGCTCTGAGAAGTCAAACCAAAAT 59.111 37.500 9.28 0.00 30.14 1.82
1167 1195 7.773224 TGAGAAGTCAAACCAAAATAACTCTCA 59.227 33.333 0.00 0.00 0.00 3.27
1169 1197 7.556275 AGAAGTCAAACCAAAATAACTCTCACA 59.444 33.333 0.00 0.00 0.00 3.58
1227 1287 4.775058 AGCTGCGGAGATATTAGTAGTG 57.225 45.455 8.65 0.00 0.00 2.74
1259 1319 2.543238 GCGAATCCCGGAAGTACTGTAG 60.543 54.545 0.73 0.00 39.04 2.74
1261 1321 2.456073 ATCCCGGAAGTACTGTAGCT 57.544 50.000 0.73 0.00 0.00 3.32
1266 1326 3.015327 CCGGAAGTACTGTAGCTGTAGT 58.985 50.000 0.00 2.93 0.00 2.73
1267 1327 3.181499 CCGGAAGTACTGTAGCTGTAGTG 60.181 52.174 13.18 0.00 0.00 2.74
1268 1328 3.731264 CGGAAGTACTGTAGCTGTAGTGC 60.731 52.174 13.18 11.94 0.00 4.40
1269 1329 3.429135 GGAAGTACTGTAGCTGTAGTGCC 60.429 52.174 13.18 6.82 32.38 5.01
1270 1330 1.743958 AGTACTGTAGCTGTAGTGCCG 59.256 52.381 13.18 0.00 31.00 5.69
1271 1331 0.454600 TACTGTAGCTGTAGTGCCGC 59.545 55.000 13.18 0.00 0.00 6.53
1272 1332 1.874019 CTGTAGCTGTAGTGCCGCG 60.874 63.158 0.00 0.00 0.00 6.46
1273 1333 2.266376 CTGTAGCTGTAGTGCCGCGA 62.266 60.000 8.23 0.00 0.00 5.87
1274 1334 1.872679 GTAGCTGTAGTGCCGCGAC 60.873 63.158 8.23 0.00 0.00 5.19
1275 1335 3.060020 TAGCTGTAGTGCCGCGACC 62.060 63.158 8.23 0.00 0.00 4.79
1404 1513 3.249559 GCTGATACTAAGCTTGATGCCAC 59.750 47.826 9.86 0.00 44.23 5.01
1415 1524 3.555586 GCTTGATGCCACCACTGAAAATT 60.556 43.478 0.00 0.00 35.15 1.82
1432 1541 4.843220 AAATTGAACAGCTCTGAACCAG 57.157 40.909 3.60 0.00 0.00 4.00
1451 1560 4.202472 ACCAGAGTTCGATCCCTTTCTTTT 60.202 41.667 0.00 0.00 0.00 2.27
1533 1749 8.709386 TTGCTTTAACATGTGTTTGTACAATT 57.291 26.923 9.56 1.37 39.31 2.32
1593 1809 4.464262 GGAATCATCCAGGTCGGC 57.536 61.111 0.00 0.00 45.79 5.54
1611 1827 2.880890 CGGCTTTTTATCCCCATCTGAG 59.119 50.000 0.00 0.00 0.00 3.35
1626 2302 5.396548 CCCATCTGAGTGACATCATCTTCTT 60.397 44.000 0.00 0.00 0.00 2.52
1769 2464 5.523916 CACTGTACATATAACACCCTCTTGC 59.476 44.000 0.00 0.00 0.00 4.01
1796 2491 2.503331 TGTTGTCATCGAAGCACCATT 58.497 42.857 0.00 0.00 0.00 3.16
1797 2492 2.884012 TGTTGTCATCGAAGCACCATTT 59.116 40.909 0.00 0.00 0.00 2.32
1903 2598 1.221021 CCTCCAGGTTTACGGGCTC 59.779 63.158 0.00 0.00 34.03 4.70
1932 2633 4.488879 GCACCAAAACTCATTCAAGATCC 58.511 43.478 0.00 0.00 0.00 3.36
1956 2657 0.693049 AGCTCCCAAAGGTGTTCGAT 59.307 50.000 0.00 0.00 33.44 3.59
2055 2760 7.272515 CCATGAATCGGTTGTACATTGTTTTAC 59.727 37.037 0.00 0.00 0.00 2.01
2080 2785 3.117512 ACACTGACCCACTTCATTTCCTT 60.118 43.478 0.00 0.00 0.00 3.36
2088 2799 5.302823 ACCCACTTCATTTCCTTCTCTTTTG 59.697 40.000 0.00 0.00 0.00 2.44
2093 2804 5.200368 TCATTTCCTTCTCTTTTGCCAAC 57.800 39.130 0.00 0.00 0.00 3.77
2147 2858 7.976175 CAGATCAAGTAAGTCTATGCACACTAA 59.024 37.037 0.00 0.00 0.00 2.24
2317 3028 2.224606 CATGGTGAGTGCATATGGACC 58.775 52.381 22.20 14.53 37.04 4.46
2360 3072 9.758651 GTCTATTTTTAAACAGGAATGTTTGGT 57.241 29.630 14.83 0.00 41.49 3.67
2392 3106 1.896220 TAACCAGCCTGCTGTTTCTG 58.104 50.000 17.23 4.81 42.15 3.02
2453 3167 1.669795 GCTTGCTGTGGGTTTATGTGC 60.670 52.381 0.00 0.00 0.00 4.57
2569 3290 9.698309 CTACTTACTACCACTTCAATATCATGG 57.302 37.037 0.00 0.00 36.46 3.66
2673 3412 8.993121 CAATGGGTATTACTGAATCTGTCATAC 58.007 37.037 13.02 13.02 35.07 2.39
2786 3553 4.899502 ACAGCTCAGTTAGTGCTTGTATT 58.100 39.130 0.00 0.00 44.16 1.89
2823 3595 4.647853 TGCTAACGGTGTATATCTGAACCT 59.352 41.667 0.00 0.00 0.00 3.50
2905 3699 5.063312 GCACAACATTACAATACAAATGGCC 59.937 40.000 0.00 0.00 37.40 5.36
2923 3717 4.532834 TGGCCCTGTTTCAAATATAGGTC 58.467 43.478 0.00 0.00 0.00 3.85
2940 4285 9.594936 AATATAGGTCATCTTTGTCTAGCTAGT 57.405 33.333 20.10 0.00 0.00 2.57
3303 4703 5.508573 CGTTTGATGTTTGACGTGTGTTTTA 59.491 36.000 0.00 0.00 0.00 1.52
3330 4730 2.863704 GCTGTCAAAATGTTGGTGGAGC 60.864 50.000 0.00 0.00 35.29 4.70
3336 4736 2.307496 AATGTTGGTGGAGCATGGAA 57.693 45.000 0.00 0.00 0.00 3.53
3429 4829 9.063615 ACTGAATAAAACCGTAGAAAGAACATT 57.936 29.630 0.00 0.00 0.00 2.71
3452 4856 9.370126 CATTACAGTAGAAAGAGAAACAAAACG 57.630 33.333 0.00 0.00 0.00 3.60
3464 4868 6.366332 AGAGAAACAAAACGTACATGCTCTAG 59.634 38.462 0.00 0.00 0.00 2.43
3465 4869 5.989777 AGAAACAAAACGTACATGCTCTAGT 59.010 36.000 0.00 0.00 0.00 2.57
3466 4870 6.482308 AGAAACAAAACGTACATGCTCTAGTT 59.518 34.615 0.00 0.00 0.00 2.24
3467 4871 7.654520 AGAAACAAAACGTACATGCTCTAGTTA 59.345 33.333 0.00 0.00 0.00 2.24
3468 4872 6.946229 ACAAAACGTACATGCTCTAGTTAG 57.054 37.500 0.00 0.00 0.00 2.34
3469 4873 6.453092 ACAAAACGTACATGCTCTAGTTAGT 58.547 36.000 0.00 0.00 0.00 2.24
3470 4874 7.596494 ACAAAACGTACATGCTCTAGTTAGTA 58.404 34.615 0.00 0.00 0.00 1.82
3591 5023 7.435068 AGAAAATATTTGTTACTCGCTGTGT 57.565 32.000 0.39 0.00 0.00 3.72
3861 5297 1.524002 CTGGGGCGATGTGAGTGAT 59.476 57.895 0.00 0.00 0.00 3.06
3905 5350 2.159531 GCAAGAGTGAATGCATGCGTTA 60.160 45.455 24.64 10.77 42.12 3.18
4158 5617 4.141711 TGGTACCAGGATTCTGTATTCTGC 60.142 45.833 11.60 0.00 38.39 4.26
4227 5686 2.175878 AGGCATCTGTGAGTGACAAC 57.824 50.000 0.00 0.00 32.80 3.32
4275 5734 6.882610 AATGAAGCTGAGTTGTGTTCATTA 57.117 33.333 6.79 0.00 42.97 1.90
4276 5735 5.673337 TGAAGCTGAGTTGTGTTCATTAC 57.327 39.130 0.00 0.00 0.00 1.89
4298 5757 1.683790 AAATACGACGCGTGCAGAGC 61.684 55.000 20.70 0.00 41.39 4.09
4309 5768 1.451067 GTGCAGAGCTCTCATGCTTT 58.549 50.000 22.48 0.00 44.17 3.51
4341 5800 3.769300 AGAAAAACAACCCCTCATATGCC 59.231 43.478 0.00 0.00 0.00 4.40
4359 5818 2.671682 GGGCTCAACACCCTCTCC 59.328 66.667 0.00 0.00 44.68 3.71
4365 5824 3.382832 AACACCCTCTCCGCTCCG 61.383 66.667 0.00 0.00 0.00 4.63
4421 5880 6.146347 GCAATACTAATGGACCTTCGAGATTC 59.854 42.308 0.00 0.00 0.00 2.52
4482 5941 5.886960 ACTTCAACAGAAACCTATGCATC 57.113 39.130 0.19 0.00 0.00 3.91
4533 5992 6.445475 CAACATGAACCATGACAACAATACA 58.555 36.000 13.22 0.00 43.81 2.29
4633 6092 6.507900 TCATCTTCGATAGCTTACCTGAAAG 58.492 40.000 0.00 0.00 0.00 2.62
4678 6137 5.059161 GCCTATATCTCTCATGTTGTGCAA 58.941 41.667 0.00 0.00 0.00 4.08
4693 6152 6.713520 TGTTGTGCAAATTTCAAGCAAATAC 58.286 32.000 3.48 3.84 40.35 1.89
4695 6154 6.915544 TGTGCAAATTTCAAGCAAATACAA 57.084 29.167 3.48 0.00 40.35 2.41
4750 9246 3.788227 AGGGTTGCTCACATACTCAAA 57.212 42.857 0.00 0.00 0.00 2.69
4781 9277 6.882656 TCAAAGTCACAAATTTTGGGATTCA 58.117 32.000 16.65 0.00 46.25 2.57
4844 9340 3.685139 TCCAACAAAACCAACAAGCAA 57.315 38.095 0.00 0.00 0.00 3.91
4891 9393 0.538584 TACTCATGGCACCTGAGCTG 59.461 55.000 16.11 0.00 43.18 4.24
4907 9409 1.676635 CTGCCACCATGGTCACCAG 60.677 63.158 16.53 16.83 40.46 4.00
4942 9444 3.055719 CCACGGTCACCACCATGC 61.056 66.667 0.00 0.00 44.02 4.06
5004 9506 4.501229 GGATGCCAAAACTTGATCACACAA 60.501 41.667 0.00 0.00 0.00 3.33
5006 9508 4.180057 TGCCAAAACTTGATCACACAAAC 58.820 39.130 0.00 0.00 0.00 2.93
5007 9509 4.081752 TGCCAAAACTTGATCACACAAACT 60.082 37.500 0.00 0.00 0.00 2.66
5008 9510 4.869861 GCCAAAACTTGATCACACAAACTT 59.130 37.500 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.671716 ACTCCTTTTGGTATGGTCGTTC 58.328 45.455 0.00 0.00 41.38 3.95
166 168 1.656441 GATATGCCGCCTTGCCAAG 59.344 57.895 0.00 0.00 0.00 3.61
192 194 1.102222 ACTACCCGATCTCACGCTCC 61.102 60.000 0.00 0.00 0.00 4.70
193 195 0.739561 AACTACCCGATCTCACGCTC 59.260 55.000 0.00 0.00 0.00 5.03
216 219 1.523938 GCCCGCCACTCTACAATCC 60.524 63.158 0.00 0.00 0.00 3.01
291 297 8.420374 TTTGAAACGAGCATTTACTATAGAGG 57.580 34.615 6.78 0.00 0.00 3.69
307 313 7.275341 CAGCCTGCATATTTATTTTTGAAACGA 59.725 33.333 0.00 0.00 0.00 3.85
334 341 3.006940 TGGAACACCTTTATAAGCGCAG 58.993 45.455 11.47 0.00 0.00 5.18
335 342 3.060736 TGGAACACCTTTATAAGCGCA 57.939 42.857 11.47 0.00 0.00 6.09
336 343 4.632538 ATTGGAACACCTTTATAAGCGC 57.367 40.909 0.00 0.00 39.29 5.92
337 344 8.560576 CATTTATTGGAACACCTTTATAAGCG 57.439 34.615 0.00 0.00 39.29 4.68
355 362 4.709397 TGGAAATTCCGTGCTCCATTTATT 59.291 37.500 7.60 0.00 40.17 1.40
358 365 2.524306 TGGAAATTCCGTGCTCCATTT 58.476 42.857 7.60 0.00 40.17 2.32
382 389 4.493220 CGATGTTTCTTCTTGCGAGAATCC 60.493 45.833 16.86 6.08 40.93 3.01
404 411 0.458889 CATGGGTTGCCATTGCTTCG 60.459 55.000 0.00 0.00 38.71 3.79
425 436 0.867746 TGCATATCGGCTTGATTCGC 59.132 50.000 0.00 2.69 38.57 4.70
492 504 4.730966 TGAGGGGTGCATTTTTGTACTTA 58.269 39.130 0.00 0.00 0.00 2.24
493 505 3.571590 TGAGGGGTGCATTTTTGTACTT 58.428 40.909 0.00 0.00 0.00 2.24
494 506 3.157087 CTGAGGGGTGCATTTTTGTACT 58.843 45.455 0.00 0.00 0.00 2.73
495 507 3.153919 TCTGAGGGGTGCATTTTTGTAC 58.846 45.455 0.00 0.00 0.00 2.90
579 591 7.563906 AGAATCCTTTTGTGGAAAATTTGTGA 58.436 30.769 0.00 0.00 39.85 3.58
582 594 6.346838 GCGAGAATCCTTTTGTGGAAAATTTG 60.347 38.462 0.00 0.00 39.85 2.32
583 595 5.696270 GCGAGAATCCTTTTGTGGAAAATTT 59.304 36.000 0.00 0.00 39.85 1.82
585 597 4.280677 TGCGAGAATCCTTTTGTGGAAAAT 59.719 37.500 0.00 0.00 39.85 1.82
616 632 1.608093 CGTTGCCGTTGCTTCAATGC 61.608 55.000 0.00 0.00 38.71 3.56
798 816 0.250424 TACGATGGAGACCGCCGATA 60.250 55.000 0.00 0.00 0.00 2.92
860 878 1.601914 CGCCGCCCTTTTATAATTGGC 60.602 52.381 9.32 9.32 38.74 4.52
887 905 1.988982 GATGCTTCTCCTCCCACCCC 61.989 65.000 0.00 0.00 0.00 4.95
888 906 1.274703 TGATGCTTCTCCTCCCACCC 61.275 60.000 0.88 0.00 0.00 4.61
889 907 0.620556 TTGATGCTTCTCCTCCCACC 59.379 55.000 0.88 0.00 0.00 4.61
890 908 2.016096 GCTTGATGCTTCTCCTCCCAC 61.016 57.143 0.88 0.00 38.95 4.61
891 909 0.254178 GCTTGATGCTTCTCCTCCCA 59.746 55.000 0.88 0.00 38.95 4.37
892 910 0.254178 TGCTTGATGCTTCTCCTCCC 59.746 55.000 0.88 0.00 43.37 4.30
941 959 0.608640 GACGGGAAGCAAGAAGAGGA 59.391 55.000 0.00 0.00 0.00 3.71
963 981 1.306226 ACGGGGGAGGAAGAGGAAG 60.306 63.158 0.00 0.00 0.00 3.46
1085 1113 0.236187 CGATGGGATCTCGACTCGAC 59.764 60.000 6.24 0.00 38.38 4.20
1087 1115 1.081774 GCGATGGGATCTCGACTCG 60.082 63.158 7.00 7.24 38.38 4.18
1107 1135 1.156736 TGCGAGTAAAAAGCAGAGGC 58.843 50.000 0.00 0.00 35.81 4.70
1128 1156 3.056962 TGACTTCTCAGAGCAGCTGTTAG 60.057 47.826 16.64 3.92 45.14 2.34
1140 1168 8.159344 AGAGTTATTTTGGTTTGACTTCTCAG 57.841 34.615 0.00 0.00 0.00 3.35
1186 1214 6.698766 GCAGCTTACCAAATTGGATTCTATTG 59.301 38.462 20.25 8.76 40.96 1.90
1187 1215 6.460123 CGCAGCTTACCAAATTGGATTCTATT 60.460 38.462 20.25 0.00 40.96 1.73
1188 1216 5.009010 CGCAGCTTACCAAATTGGATTCTAT 59.991 40.000 20.25 0.00 40.96 1.98
1189 1217 4.335315 CGCAGCTTACCAAATTGGATTCTA 59.665 41.667 20.25 0.00 40.96 2.10
1227 1287 1.291132 GGGATTCGCAGAACTACAGC 58.709 55.000 0.00 0.00 45.90 4.40
1274 1334 4.351938 TTCGCAGTGGACGACGGG 62.352 66.667 0.00 0.00 39.67 5.28
1275 1335 2.805353 CTTCGCAGTGGACGACGG 60.805 66.667 0.00 0.00 39.67 4.79
1276 1336 3.470567 GCTTCGCAGTGGACGACG 61.471 66.667 0.00 0.00 39.67 5.12
1277 1337 3.470567 CGCTTCGCAGTGGACGAC 61.471 66.667 0.00 0.00 39.67 4.34
1379 1486 2.225068 TCAAGCTTAGTATCAGCGGC 57.775 50.000 0.00 0.00 42.55 6.53
1382 1489 3.249559 GTGGCATCAAGCTTAGTATCAGC 59.750 47.826 0.00 0.00 44.79 4.26
1404 1513 4.276678 TCAGAGCTGTTCAATTTTCAGTGG 59.723 41.667 0.00 0.00 0.00 4.00
1432 1541 6.183360 CCCATAAAAAGAAAGGGATCGAACTC 60.183 42.308 0.00 0.00 42.25 3.01
1533 1749 2.631418 CTCCGACGAGCTGAAAGTAA 57.369 50.000 0.00 0.00 35.30 2.24
1593 1809 5.500234 TGTCACTCAGATGGGGATAAAAAG 58.500 41.667 0.00 0.00 0.00 2.27
1611 1827 8.345565 ACTACAAACAAAAGAAGATGATGTCAC 58.654 33.333 0.00 0.00 0.00 3.67
1722 2417 0.611618 TTCGCGAGGTAGGGGTTGTA 60.612 55.000 9.59 0.00 0.00 2.41
1769 2464 3.248363 TGCTTCGATGACAACAACAAGAG 59.752 43.478 1.89 0.00 0.00 2.85
1932 2633 2.037136 CACCTTTGGGAGCTGCTCG 61.037 63.158 22.25 10.54 36.25 5.03
1956 2657 1.002624 GGACCATTTCGACCTGGCA 60.003 57.895 11.48 0.00 35.88 4.92
2055 2760 4.455877 GGAAATGAAGTGGGTCAGTGTAAG 59.544 45.833 0.00 0.00 0.00 2.34
2080 2785 2.031120 CCAAGGTGTTGGCAAAAGAGA 58.969 47.619 0.00 0.00 46.99 3.10
2093 2804 3.369546 AAATCAGCGTTTTCCAAGGTG 57.630 42.857 0.00 0.00 35.00 4.00
2147 2858 4.021368 ACTCGTGGAGCTAACAATGTAAGT 60.021 41.667 0.00 0.00 32.04 2.24
2222 2933 0.399949 AGGAACCACAGTGACCCTGA 60.400 55.000 0.62 0.00 44.49 3.86
2317 3028 7.581213 AAATAGACCAGAGAGTAGACAGATG 57.419 40.000 0.00 0.00 0.00 2.90
2360 3072 5.253330 CAGGCTGGTTATGTAAGAAAGGAA 58.747 41.667 6.61 0.00 0.00 3.36
2392 3106 2.484264 AGCGTAATGTTCTGCAAGGAAC 59.516 45.455 10.98 10.98 43.97 3.62
2411 3125 2.421424 CACTAGGTCATTGGCAGAAAGC 59.579 50.000 0.00 0.00 44.65 3.51
2453 3167 1.431488 CTCCATCACAACCATCGCCG 61.431 60.000 0.00 0.00 0.00 6.46
2569 3290 4.429854 AATAGGATTGCTCTTGGAGGAC 57.570 45.455 0.00 0.00 27.75 3.85
2576 3297 9.584008 AATGATGACAATAATAGGATTGCTCTT 57.416 29.630 0.00 0.00 39.94 2.85
2723 3488 8.859090 ACAAACCAATCAATTCATTTACAGAGA 58.141 29.630 0.00 0.00 0.00 3.10
2807 3579 8.562892 CATGATTTTCAGGTTCAGATATACACC 58.437 37.037 0.00 0.00 0.00 4.16
2823 3595 6.427853 CAGGACACACTAAGACATGATTTTCA 59.572 38.462 0.00 0.00 0.00 2.69
2905 3699 8.960591 ACAAAGATGACCTATATTTGAAACAGG 58.039 33.333 12.31 1.70 46.09 4.00
3303 4703 2.102925 CCAACATTTTGACAGCCTTGGT 59.897 45.455 0.00 0.00 34.24 3.67
3330 4730 9.643693 AGTAATTAGCAGAAATTTTGTTCCATG 57.356 29.630 0.00 0.00 31.63 3.66
3429 4829 9.023967 GTACGTTTTGTTTCTCTTTCTACTGTA 57.976 33.333 0.00 0.00 0.00 2.74
3452 4856 7.928103 TGCTAACTACTAACTAGAGCATGTAC 58.072 38.462 0.00 0.00 30.77 2.90
3567 4999 7.435068 ACACAGCGAGTAACAAATATTTTCT 57.565 32.000 0.00 0.00 0.00 2.52
3591 5023 7.443477 TGGAGAAAATTGCAGAATGAAATCAA 58.557 30.769 0.00 0.00 41.74 2.57
3719 5151 7.989947 TTAACAAGATACCCAGTAATCCTCT 57.010 36.000 0.00 0.00 0.00 3.69
3861 5297 6.943146 TGCAAGTCAACAATACAGGGTATTTA 59.057 34.615 0.00 0.00 0.00 1.40
3905 5350 9.705290 CACAAACCAAAACTTATTAATTAGCCT 57.295 29.630 1.40 0.00 0.00 4.58
4096 5555 4.380867 CCGCTTAAATTTGACAGGCAGATT 60.381 41.667 0.00 0.00 33.13 2.40
4099 5558 2.415893 CCCGCTTAAATTTGACAGGCAG 60.416 50.000 0.00 0.00 0.00 4.85
4158 5617 3.425525 CGGACACATTAATAGCTAGTGCG 59.574 47.826 3.45 5.31 45.42 5.34
4264 5723 5.164070 CGTCGTATTTCGGTAATGAACACAA 60.164 40.000 0.00 0.00 40.32 3.33
4275 5734 2.438954 GCACGCGTCGTATTTCGGT 61.439 57.895 9.86 0.00 38.32 4.69
4276 5735 2.315356 GCACGCGTCGTATTTCGG 59.685 61.111 9.86 0.00 38.32 4.30
4298 5757 2.768527 TCACCTCCCTAAAGCATGAGAG 59.231 50.000 0.00 0.00 0.00 3.20
4309 5768 3.181437 GGGTTGTTTTTCTCACCTCCCTA 60.181 47.826 0.00 0.00 0.00 3.53
4355 5814 3.147595 CCCACATCGGAGCGGAGA 61.148 66.667 0.00 0.00 36.56 3.71
4359 5818 0.174845 TTTAGTCCCACATCGGAGCG 59.825 55.000 0.00 0.00 36.56 5.03
4365 5824 3.058224 GGCGCAATATTTAGTCCCACATC 60.058 47.826 10.83 0.00 0.00 3.06
4435 5894 1.680338 GGGCTCTCGGCACATTAAAT 58.320 50.000 0.00 0.00 45.23 1.40
4482 5941 0.902531 AGTTCACACCCCCTATGTCG 59.097 55.000 0.00 0.00 0.00 4.35
4533 5992 9.565090 TGAAGATGCTCTAACATATTGCTAATT 57.435 29.630 0.00 0.00 31.88 1.40
4584 6043 7.290061 AGCAAAATTCTCCTATACCTAATGCA 58.710 34.615 0.00 0.00 0.00 3.96
4633 6092 6.712547 AGGCAATTAGAAGATGGTATAAGCAC 59.287 38.462 0.00 0.00 0.00 4.40
4731 9227 4.941263 TGTATTTGAGTATGTGAGCAACCC 59.059 41.667 0.00 0.00 0.00 4.11
4732 9228 6.683974 ATGTATTTGAGTATGTGAGCAACC 57.316 37.500 0.00 0.00 0.00 3.77
4750 9246 9.054922 CCCAAAATTTGTGACTTTGAAATGTAT 57.945 29.630 4.92 0.00 32.87 2.29
4781 9277 7.391833 GTGAGACCTATCTTTTGGATGAACTTT 59.608 37.037 0.00 0.00 34.34 2.66
4891 9393 2.361610 CCTGGTGACCATGGTGGC 60.362 66.667 25.52 14.39 42.67 5.01
4907 9409 4.365111 TGGGCATGGTGGTGAGCC 62.365 66.667 0.00 0.00 46.28 4.70
4942 9444 1.418334 TCATGGGTGGTTTTGGTTGG 58.582 50.000 0.00 0.00 0.00 3.77
5004 9506 4.936685 AGGGAAGAGCCTATTTCAAGTT 57.063 40.909 0.00 0.00 36.66 2.66
5006 9508 3.873952 CGAAGGGAAGAGCCTATTTCAAG 59.126 47.826 0.00 0.00 36.66 3.02
5007 9509 3.873910 CGAAGGGAAGAGCCTATTTCAA 58.126 45.455 0.00 0.00 36.66 2.69
5008 9510 3.543680 CGAAGGGAAGAGCCTATTTCA 57.456 47.619 0.00 0.00 36.66 2.69


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

AutoCloner maintained by Alex Coulton.