Multiple sequence alignment - TraesCS7D01G069900

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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 TraesCS7D01G069900 chr7D 100.000 4716 0 0 1 4716 40857731 40853016 0.000000e+00 8709.0
1 TraesCS7D01G069900 chr7D 87.727 440 39 8 2038 2473 40874491 40874063 2.530000e-137 499.0
2 TraesCS7D01G069900 chr7D 92.466 146 10 1 1025 1170 40878093 40877949 1.720000e-49 207.0
3 TraesCS7D01G069900 chr7A 92.648 2285 88 26 1710 3974 40400166 40397942 0.000000e+00 3216.0
4 TraesCS7D01G069900 chr7A 86.786 1506 93 49 3 1471 40401862 40400426 0.000000e+00 1581.0
5 TraesCS7D01G069900 chr7A 88.939 443 37 4 2038 2476 40437049 40436615 1.930000e-148 536.0
6 TraesCS7D01G069900 chr7A 82.150 493 68 15 4228 4708 40397304 40396820 5.680000e-109 405.0
7 TraesCS7D01G069900 chr7A 95.652 184 6 2 1527 1709 40400396 40400214 1.280000e-75 294.0
8 TraesCS7D01G069900 chr7A 78.346 508 45 41 1025 1520 40441027 40440573 7.780000e-68 268.0
9 TraesCS7D01G069900 chr4A 92.065 1550 61 20 2733 4271 647278779 647280277 0.000000e+00 2124.0
10 TraesCS7D01G069900 chr4A 94.937 790 33 4 1710 2493 647277582 647278370 0.000000e+00 1230.0
11 TraesCS7D01G069900 chr4A 90.353 539 25 16 679 1197 647276512 647277043 0.000000e+00 682.0
12 TraesCS7D01G069900 chr4A 92.258 310 17 3 1401 1709 647277224 647277527 2.610000e-117 433.0
13 TraesCS7D01G069900 chr4A 100.000 29 0 0 1867 1895 294787098 294787070 2.000000e-03 54.7
14 TraesCS7D01G069900 chr3D 87.016 439 41 5 2035 2467 560883696 560884124 9.180000e-132 481.0
15 TraesCS7D01G069900 chr3D 87.500 192 9 3 980 1170 560881167 560881344 1.720000e-49 207.0
16 TraesCS7D01G069900 chr3A 86.168 441 47 4 2031 2467 696884875 696885305 9.240000e-127 464.0
17 TraesCS7D01G069900 chr3A 89.583 192 17 2 980 1170 696877895 696878084 1.700000e-59 241.0
18 TraesCS7D01G069900 chr2D 87.688 333 26 9 2040 2366 618090589 618090912 1.600000e-99 374.0
19 TraesCS7D01G069900 chr1A 85.207 338 30 8 2040 2366 586506934 586507262 3.520000e-86 329.0
20 TraesCS7D01G069900 chr1A 89.189 148 11 3 2541 2683 579384242 579384095 3.750000e-41 180.0
21 TraesCS7D01G069900 chr5A 87.156 218 19 6 2040 2250 143733997 143734212 6.100000e-59 239.0
22 TraesCS7D01G069900 chr2A 87.383 214 19 5 2040 2247 73145967 73146178 6.100000e-59 239.0
23 TraesCS7D01G069900 chr4B 86.486 222 19 5 2148 2366 79531952 79531739 2.840000e-57 233.0
24 TraesCS7D01G069900 chr1B 86.486 222 19 6 2148 2366 51236066 51235853 2.840000e-57 233.0
25 TraesCS7D01G069900 chr1B 76.087 138 25 8 4383 4517 489516439 489516307 1.100000e-06 65.8
26 TraesCS7D01G069900 chr6A 92.105 38 3 0 4470 4507 482357595 482357558 2.000000e-03 54.7


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 TraesCS7D01G069900 chr7D 40853016 40857731 4715 True 8709.00 8709 100.00000 1 4716 1 chr7D.!!$R1 4715
1 TraesCS7D01G069900 chr7D 40874063 40878093 4030 True 353.00 499 90.09650 1025 2473 2 chr7D.!!$R2 1448
2 TraesCS7D01G069900 chr7A 40396820 40401862 5042 True 1374.00 3216 89.30900 3 4708 4 chr7A.!!$R1 4705
3 TraesCS7D01G069900 chr7A 40436615 40441027 4412 True 402.00 536 83.64250 1025 2476 2 chr7A.!!$R2 1451
4 TraesCS7D01G069900 chr4A 647276512 647280277 3765 False 1117.25 2124 92.40325 679 4271 4 chr4A.!!$F1 3592
5 TraesCS7D01G069900 chr3D 560881167 560884124 2957 False 344.00 481 87.25800 980 2467 2 chr3D.!!$F1 1487

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
885 919 1.602771 GGGTCGGAAGGGGAGAAAG 59.397 63.158 0.00 0.0 0.00 2.62 F
1267 2383 0.322456 TGCTCTGTTTTCCCCGGATG 60.322 55.000 0.73 0.0 0.00 3.51 F
2482 7399 0.620556 ATTCCGCTGGATTGGTCAGT 59.379 50.000 0.00 0.0 34.89 3.41 F
2846 7972 1.539776 CCGCAGCGCTTTGTTGTTTC 61.540 55.000 7.50 0.0 0.00 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2779 7903 0.170339 GGACAAACAGGCATTACCGC 59.830 55.0 0.00 0.0 46.52 5.68 R
2780 7904 0.808755 GGGACAAACAGGCATTACCG 59.191 55.0 0.00 0.0 46.52 4.02 R
3583 8712 0.247460 CGAGCTCCTTGATGGTGTCA 59.753 55.0 8.47 0.0 37.07 3.58 R
3730 8860 0.255604 AACCATCATCACATGGCGGA 59.744 50.0 0.00 0.0 46.71 5.54 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
27 28 4.335082 TGTTCATTCCTAACGAATTGCG 57.665 40.909 0.00 0.00 39.28 4.85
28 29 3.997681 TGTTCATTCCTAACGAATTGCGA 59.002 39.130 0.00 0.00 44.57 5.10
45 46 4.174411 TGCGAGTCTTGGATATATTCGG 57.826 45.455 3.64 0.00 0.00 4.30
65 66 3.139077 GGTACAAGGGATGGCTTAATCG 58.861 50.000 0.00 0.00 0.00 3.34
127 128 6.071952 CCTCTTTGAGTTTTATGCTTGGCTAA 60.072 38.462 0.00 0.00 0.00 3.09
181 182 3.493350 GGTCGATACATGTGCTCATTCCT 60.493 47.826 9.11 0.00 31.15 3.36
193 194 4.883585 GTGCTCATTCCTGATTCCAACATA 59.116 41.667 0.00 0.00 0.00 2.29
236 237 5.596836 ACATTGAAGAAAACCACACACAT 57.403 34.783 0.00 0.00 0.00 3.21
240 241 8.037758 ACATTGAAGAAAACCACACACATTTTA 58.962 29.630 0.00 0.00 0.00 1.52
241 242 7.820044 TTGAAGAAAACCACACACATTTTAC 57.180 32.000 0.00 0.00 0.00 2.01
242 243 6.925211 TGAAGAAAACCACACACATTTTACA 58.075 32.000 0.00 0.00 0.00 2.41
269 279 9.057089 AGGATAATTTCTTCTTATTAGCAACCG 57.943 33.333 0.00 0.00 0.00 4.44
291 301 8.732746 ACCGTCTTAAGTTTAGCAATCATTAT 57.267 30.769 1.63 0.00 0.00 1.28
292 302 8.827677 ACCGTCTTAAGTTTAGCAATCATTATC 58.172 33.333 1.63 0.00 0.00 1.75
302 312 3.070018 GCAATCATTATCACTCCCTCCG 58.930 50.000 0.00 0.00 0.00 4.63
310 320 5.943349 TTATCACTCCCTCCGTTCAATTA 57.057 39.130 0.00 0.00 0.00 1.40
353 363 5.606348 TCAAATAGTGCCCAAAACAGTTT 57.394 34.783 0.00 0.00 0.00 2.66
373 383 4.537135 TTAATCTCAGCTGTCCGAAACT 57.463 40.909 14.67 1.98 0.00 2.66
375 385 4.537135 AATCTCAGCTGTCCGAAACTTA 57.463 40.909 14.67 0.00 0.00 2.24
377 387 5.854010 ATCTCAGCTGTCCGAAACTTATA 57.146 39.130 14.67 0.00 0.00 0.98
379 389 6.032956 TCTCAGCTGTCCGAAACTTATAAA 57.967 37.500 14.67 0.00 0.00 1.40
395 410 4.081050 AAAAACGGAGGGAGCAGC 57.919 55.556 0.00 0.00 0.00 5.25
396 411 1.603739 AAAAACGGAGGGAGCAGCC 60.604 57.895 0.00 0.00 0.00 4.85
403 418 4.075793 AGGGAGCAGCCGGGACTA 62.076 66.667 2.18 0.00 37.63 2.59
416 431 2.607282 CCGGGACTATGTTGCGTCTATC 60.607 54.545 0.00 0.00 0.00 2.08
417 432 2.034179 CGGGACTATGTTGCGTCTATCA 59.966 50.000 0.00 0.00 0.00 2.15
433 452 2.205022 ATCACACCCACTCACATTGG 57.795 50.000 0.00 0.00 0.00 3.16
463 482 7.066645 CAGTCTTTCATCATCAATAAGCAAGGA 59.933 37.037 0.00 0.00 0.00 3.36
465 484 6.319658 TCTTTCATCATCAATAAGCAAGGACC 59.680 38.462 0.00 0.00 0.00 4.46
467 486 3.627395 TCATCAATAAGCAAGGACCGT 57.373 42.857 0.00 0.00 0.00 4.83
470 489 4.764823 TCATCAATAAGCAAGGACCGTTTT 59.235 37.500 0.00 0.00 0.00 2.43
472 491 6.601613 TCATCAATAAGCAAGGACCGTTTTAT 59.398 34.615 0.00 0.00 0.00 1.40
545 564 9.739276 CCTCTAAGCAACATATTATTCCCAATA 57.261 33.333 0.00 0.00 0.00 1.90
576 595 7.253750 GCAGTACTTGACATTGTTGAAAAGTTG 60.254 37.037 0.00 7.56 35.33 3.16
580 599 7.826690 ACTTGACATTGTTGAAAAGTTGTACT 58.173 30.769 0.00 0.00 32.13 2.73
581 600 7.754924 ACTTGACATTGTTGAAAAGTTGTACTG 59.245 33.333 0.00 0.00 32.13 2.74
582 601 7.151999 TGACATTGTTGAAAAGTTGTACTGT 57.848 32.000 0.00 0.00 0.00 3.55
583 602 8.270080 TGACATTGTTGAAAAGTTGTACTGTA 57.730 30.769 0.00 0.00 0.00 2.74
584 603 8.178964 TGACATTGTTGAAAAGTTGTACTGTAC 58.821 33.333 10.98 10.98 0.00 2.90
585 604 8.276252 ACATTGTTGAAAAGTTGTACTGTACT 57.724 30.769 17.98 0.00 0.00 2.73
586 605 8.736244 ACATTGTTGAAAAGTTGTACTGTACTT 58.264 29.630 17.98 4.23 36.20 2.24
587 606 9.009327 CATTGTTGAAAAGTTGTACTGTACTTG 57.991 33.333 17.98 0.00 34.95 3.16
588 607 7.675962 TGTTGAAAAGTTGTACTGTACTTGT 57.324 32.000 17.98 2.16 34.95 3.16
589 608 7.745015 TGTTGAAAAGTTGTACTGTACTTGTC 58.255 34.615 17.98 11.26 38.52 3.18
590 609 7.388224 TGTTGAAAAGTTGTACTGTACTTGTCA 59.612 33.333 17.98 17.52 43.43 3.58
641 660 8.985805 ACTCTACTATTTTTCACCGTTGTTTAG 58.014 33.333 0.00 0.00 0.00 1.85
664 683 3.536956 TCTACGGAGCTTTTACCATGG 57.463 47.619 11.19 11.19 0.00 3.66
686 705 4.281657 GCTCCCTTTCCACCAGATATTTT 58.718 43.478 0.00 0.00 0.00 1.82
696 715 7.834881 TCCACCAGATATTTTATCGAGTAGT 57.165 36.000 0.00 0.00 0.00 2.73
861 895 6.709846 TGCATAAAACAAATCAGAAAAAGGGG 59.290 34.615 0.00 0.00 0.00 4.79
885 919 1.602771 GGGTCGGAAGGGGAGAAAG 59.397 63.158 0.00 0.00 0.00 2.62
890 924 2.303890 GTCGGAAGGGGAGAAAGGTAAA 59.696 50.000 0.00 0.00 0.00 2.01
1197 1246 1.891150 GTCGAGACCAAGACCAAGGTA 59.109 52.381 0.00 0.00 38.50 3.08
1198 1247 2.496470 GTCGAGACCAAGACCAAGGTAT 59.504 50.000 0.00 0.00 38.50 2.73
1205 1254 4.663334 ACCAAGACCAAGGTATTTTCCTC 58.337 43.478 0.00 0.00 36.74 3.71
1206 1255 4.354087 ACCAAGACCAAGGTATTTTCCTCT 59.646 41.667 0.00 0.00 36.74 3.69
1207 1256 5.162980 ACCAAGACCAAGGTATTTTCCTCTT 60.163 40.000 0.00 0.00 36.74 2.85
1208 1257 5.416013 CCAAGACCAAGGTATTTTCCTCTTC 59.584 44.000 0.00 0.00 36.74 2.87
1209 1258 5.180810 AGACCAAGGTATTTTCCTCTTCC 57.819 43.478 0.00 0.00 36.74 3.46
1210 1259 4.852697 AGACCAAGGTATTTTCCTCTTCCT 59.147 41.667 0.00 0.00 36.74 3.36
1211 1260 5.313506 AGACCAAGGTATTTTCCTCTTCCTT 59.686 40.000 0.00 0.00 36.74 3.36
1212 1261 5.571285 ACCAAGGTATTTTCCTCTTCCTTC 58.429 41.667 0.00 0.00 36.74 3.46
1213 1262 5.313506 ACCAAGGTATTTTCCTCTTCCTTCT 59.686 40.000 0.00 0.00 36.74 2.85
1214 1263 6.183361 ACCAAGGTATTTTCCTCTTCCTTCTT 60.183 38.462 0.00 0.00 36.74 2.52
1215 1264 6.375736 CCAAGGTATTTTCCTCTTCCTTCTTC 59.624 42.308 0.00 0.00 36.74 2.87
1216 1265 6.068461 AGGTATTTTCCTCTTCCTTCTTCC 57.932 41.667 0.00 0.00 31.32 3.46
1217 1266 5.044772 AGGTATTTTCCTCTTCCTTCTTCCC 60.045 44.000 0.00 0.00 31.32 3.97
1218 1267 3.808834 TTTTCCTCTTCCTTCTTCCCC 57.191 47.619 0.00 0.00 0.00 4.81
1219 1268 1.670059 TTCCTCTTCCTTCTTCCCCC 58.330 55.000 0.00 0.00 0.00 5.40
1257 1324 1.526887 CACGTCACGATTGCTCTGTTT 59.473 47.619 2.91 0.00 0.00 2.83
1262 2378 1.200020 CACGATTGCTCTGTTTTCCCC 59.800 52.381 0.00 0.00 0.00 4.81
1267 2383 0.322456 TGCTCTGTTTTCCCCGGATG 60.322 55.000 0.73 0.00 0.00 3.51
1301 2959 7.124901 GCCTACCCTAGATTCATTGATCATCTA 59.875 40.741 0.00 0.00 0.00 1.98
1341 3013 5.582439 AGATTCGCGATTAATAACTGCTG 57.418 39.130 10.88 0.00 0.00 4.41
1378 3050 1.342819 CTCCTGCTGGGATGCTAGTAC 59.657 57.143 10.07 0.00 44.15 2.73
1381 3053 2.560542 CCTGCTGGGATGCTAGTACTAG 59.439 54.545 23.25 23.25 37.23 2.57
1383 3055 4.399219 CTGCTGGGATGCTAGTACTAGTA 58.601 47.826 26.76 24.00 35.65 1.82
1385 3057 4.583489 TGCTGGGATGCTAGTACTAGTAAC 59.417 45.833 26.76 21.57 35.65 2.50
1387 3059 6.002704 GCTGGGATGCTAGTACTAGTAACTA 58.997 44.000 26.76 17.52 35.65 2.24
1389 3061 7.177041 GCTGGGATGCTAGTACTAGTAACTAAT 59.823 40.741 26.76 10.61 35.65 1.73
1423 3096 3.123620 CCCAACTCTCTGCAGCGC 61.124 66.667 9.47 0.00 0.00 5.92
1435 3670 3.741476 CAGCGCTGGGAAGGTTGC 61.741 66.667 29.88 0.00 0.00 4.17
1437 3672 3.435186 GCGCTGGGAAGGTTGCTC 61.435 66.667 0.00 0.00 0.00 4.26
1450 3685 3.944087 AGGTTGCTCCTATGAGTTGAAC 58.056 45.455 0.00 0.00 46.10 3.18
1681 3937 1.476110 CCGTTCCAAACCAGTTCTGGA 60.476 52.381 23.45 9.13 37.47 3.86
1706 6527 1.005924 CCTTTGGGAGGTGCTTGGTAT 59.994 52.381 0.00 0.00 40.95 2.73
1708 6529 2.507407 TTGGGAGGTGCTTGGTATTC 57.493 50.000 0.00 0.00 0.00 1.75
1713 6613 3.908103 GGGAGGTGCTTGGTATTCCTATA 59.092 47.826 0.00 0.00 34.23 1.31
1727 6627 7.235606 TGGTATTCCTATAGCTGCTCAAGTATT 59.764 37.037 4.91 0.00 36.06 1.89
1742 6644 7.029563 GCTCAAGTATTTCCGAATGTGAAAAT 58.970 34.615 0.00 0.00 35.52 1.82
1784 6689 6.491403 GTCTTGGGATGATGTTAATATTGGCT 59.509 38.462 0.00 0.00 0.00 4.75
1804 6711 4.697352 GGCTGAGAAATTATGTGACAGTGT 59.303 41.667 0.00 0.00 0.00 3.55
1855 6762 7.277760 GGTTATCTGCAATTCAATTGGGTTTAC 59.722 37.037 12.14 0.00 40.57 2.01
1932 6840 4.099419 GGAAACTTGGCCATAATAACCCAG 59.901 45.833 6.09 0.00 0.00 4.45
2437 7354 8.601845 TGTTACATGTATTACATACTGCCATC 57.398 34.615 6.36 0.00 36.53 3.51
2482 7399 0.620556 ATTCCGCTGGATTGGTCAGT 59.379 50.000 0.00 0.00 34.89 3.41
2513 7431 3.751479 ATTCAGTTTCTTTGCCCCAAC 57.249 42.857 0.00 0.00 0.00 3.77
2527 7445 2.942306 GCCCCAACGTGTACCATTACAT 60.942 50.000 0.00 0.00 40.40 2.29
2650 7572 3.930336 TCAACTTATGTCACTGCTCAGG 58.070 45.455 1.66 0.00 0.00 3.86
2761 7885 4.864916 ACAATGCTATCTGTTGCTTACG 57.135 40.909 0.00 0.00 0.00 3.18
2779 7903 6.966632 TGCTTACGCTTATTTTTATTGCTGAG 59.033 34.615 0.00 0.00 36.97 3.35
2780 7904 6.075362 GCTTACGCTTATTTTTATTGCTGAGC 60.075 38.462 0.00 0.00 0.00 4.26
2846 7972 1.539776 CCGCAGCGCTTTGTTGTTTC 61.540 55.000 7.50 0.00 0.00 2.78
2894 8020 8.103305 AGAAAGTGATCCTGTGTTATGTACATT 58.897 33.333 14.77 0.00 39.39 2.71
2937 8063 2.103373 GATGGGTCTGCTGAGTACTGA 58.897 52.381 0.00 0.00 0.00 3.41
2962 8088 1.817357 TCTGTCTTGCATGGAAGCTG 58.183 50.000 21.14 18.00 34.99 4.24
2971 8097 4.027674 TGCATGGAAGCTGGTTAACTTA 57.972 40.909 5.42 0.00 34.99 2.24
3011 8137 4.471904 TGTCCAGGTGATGTCAGATTAC 57.528 45.455 0.00 0.00 0.00 1.89
3127 8253 5.696270 TGTTTTGAGCAGTAGTGTATCTGTG 59.304 40.000 0.00 0.00 34.57 3.66
3129 8255 6.584185 TTTGAGCAGTAGTGTATCTGTGTA 57.416 37.500 0.00 0.00 34.57 2.90
3130 8256 6.775594 TTGAGCAGTAGTGTATCTGTGTAT 57.224 37.500 0.00 0.00 34.57 2.29
3131 8257 6.775594 TGAGCAGTAGTGTATCTGTGTATT 57.224 37.500 0.00 0.00 34.57 1.89
3132 8258 7.170393 TGAGCAGTAGTGTATCTGTGTATTT 57.830 36.000 0.00 0.00 34.57 1.40
3133 8259 7.035612 TGAGCAGTAGTGTATCTGTGTATTTG 58.964 38.462 0.00 0.00 34.57 2.32
3134 8260 6.936279 AGCAGTAGTGTATCTGTGTATTTGT 58.064 36.000 0.00 0.00 34.57 2.83
3135 8261 8.063200 AGCAGTAGTGTATCTGTGTATTTGTA 57.937 34.615 0.00 0.00 34.57 2.41
3136 8262 8.696374 AGCAGTAGTGTATCTGTGTATTTGTAT 58.304 33.333 0.00 0.00 34.57 2.29
3137 8263 8.969267 GCAGTAGTGTATCTGTGTATTTGTATC 58.031 37.037 0.00 0.00 34.57 2.24
3172 8298 2.565834 TCAGGTTGTACAGCCTAGGAAC 59.434 50.000 28.43 6.59 40.24 3.62
3583 8712 3.587061 TGATCATGGTCACCCAGTACTTT 59.413 43.478 4.01 0.00 46.15 2.66
3694 8823 1.750018 CCGCACAGGCATGATGGAA 60.750 57.895 4.84 0.00 41.24 3.53
3715 8844 3.378602 TCGAGCAGCGGCCTGTAA 61.379 61.111 4.82 0.00 42.56 2.41
3730 8860 1.078426 GTAAGCCATGGCCGTCTGT 60.078 57.895 33.14 10.96 43.17 3.41
3732 8862 2.252072 TAAGCCATGGCCGTCTGTCC 62.252 60.000 33.14 2.26 43.17 4.02
3739 8869 4.760047 GCCGTCTGTCCGCCATGT 62.760 66.667 0.00 0.00 0.00 3.21
3740 8870 2.815211 CCGTCTGTCCGCCATGTG 60.815 66.667 0.00 0.00 0.00 3.21
3741 8871 2.261361 CGTCTGTCCGCCATGTGA 59.739 61.111 0.00 0.00 0.00 3.58
3742 8872 1.153568 CGTCTGTCCGCCATGTGAT 60.154 57.895 0.00 0.00 0.00 3.06
3743 8873 1.423721 CGTCTGTCCGCCATGTGATG 61.424 60.000 0.00 0.00 0.00 3.07
3894 9026 4.826733 ACTTGGTTGTGCATGAAGATTGTA 59.173 37.500 0.00 0.00 0.00 2.41
3897 9029 4.696877 TGGTTGTGCATGAAGATTGTAGAG 59.303 41.667 0.00 0.00 0.00 2.43
3974 9113 4.582656 TGGGTTTACTTGTTTGAGATGTGG 59.417 41.667 0.00 0.00 0.00 4.17
4026 9165 7.584987 TGAAGTTCTAGCTTTGCACTAATTTC 58.415 34.615 4.17 0.00 0.00 2.17
4079 9777 1.674057 CGCTCCTGGGTCAAGAGTT 59.326 57.895 0.00 0.00 0.00 3.01
4080 9778 0.671781 CGCTCCTGGGTCAAGAGTTG 60.672 60.000 0.00 0.00 0.00 3.16
4081 9779 0.398318 GCTCCTGGGTCAAGAGTTGT 59.602 55.000 0.00 0.00 0.00 3.32
4082 9780 1.623811 GCTCCTGGGTCAAGAGTTGTA 59.376 52.381 0.00 0.00 0.00 2.41
4083 9781 2.354203 GCTCCTGGGTCAAGAGTTGTAG 60.354 54.545 0.00 0.00 0.00 2.74
4084 9782 2.234908 CTCCTGGGTCAAGAGTTGTAGG 59.765 54.545 0.00 0.00 0.00 3.18
4085 9783 1.339151 CCTGGGTCAAGAGTTGTAGGC 60.339 57.143 0.00 0.00 0.00 3.93
4086 9784 1.625818 CTGGGTCAAGAGTTGTAGGCT 59.374 52.381 0.00 0.00 0.00 4.58
4201 9899 2.527100 CACGTCGACCTAAATGGACTC 58.473 52.381 10.58 0.00 39.71 3.36
4206 9904 3.087031 TCGACCTAAATGGACTCGAAGT 58.913 45.455 0.00 0.00 39.41 3.01
4426 10156 8.502161 AAATGTTCAACGTGTATTTAAGAAGC 57.498 30.769 0.00 0.00 0.00 3.86
4427 10157 5.672051 TGTTCAACGTGTATTTAAGAAGCG 58.328 37.500 0.00 0.00 0.00 4.68
4430 10160 5.908106 TCAACGTGTATTTAAGAAGCGTTC 58.092 37.500 0.00 0.00 38.71 3.95
4431 10161 5.462729 TCAACGTGTATTTAAGAAGCGTTCA 59.537 36.000 0.00 0.00 38.71 3.18
4432 10162 5.260027 ACGTGTATTTAAGAAGCGTTCAC 57.740 39.130 0.00 0.00 0.00 3.18
4433 10163 4.151157 ACGTGTATTTAAGAAGCGTTCACC 59.849 41.667 0.00 0.00 0.00 4.02
4435 10165 5.163893 CGTGTATTTAAGAAGCGTTCACCAT 60.164 40.000 1.58 0.00 0.00 3.55
4436 10166 6.035220 CGTGTATTTAAGAAGCGTTCACCATA 59.965 38.462 1.58 0.00 0.00 2.74
4437 10167 7.254319 CGTGTATTTAAGAAGCGTTCACCATAT 60.254 37.037 1.58 0.00 0.00 1.78
4438 10168 9.037737 GTGTATTTAAGAAGCGTTCACCATATA 57.962 33.333 1.58 0.00 0.00 0.86
4439 10169 9.772973 TGTATTTAAGAAGCGTTCACCATATAT 57.227 29.630 1.58 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.542130 GCAATTCGTTAGGAATGAACAAATTCT 59.458 33.333 0.71 0.00 44.59 2.40
27 28 7.091443 CCTTGTACCGAATATATCCAAGACTC 58.909 42.308 0.00 0.00 29.88 3.36
28 29 6.014499 CCCTTGTACCGAATATATCCAAGACT 60.014 42.308 0.00 0.00 29.88 3.24
45 46 4.067972 TCGATTAAGCCATCCCTTGTAC 57.932 45.455 0.00 0.00 0.00 2.90
65 66 4.535116 CAGCTTTGCTCTCTTTCTTGTTC 58.465 43.478 0.00 0.00 36.40 3.18
96 97 8.394121 CAAGCATAAAACTCAAAGAGGATAGTC 58.606 37.037 0.00 0.00 33.35 2.59
148 149 6.250819 CACATGTATCGACCTTTCATTTGAC 58.749 40.000 0.00 0.00 0.00 3.18
255 265 9.362539 CTAAACTTAAGACGGTTGCTAATAAGA 57.637 33.333 10.09 0.00 0.00 2.10
291 301 7.507956 TCTTATATAATTGAACGGAGGGAGTGA 59.492 37.037 0.00 0.00 0.00 3.41
292 302 7.667557 TCTTATATAATTGAACGGAGGGAGTG 58.332 38.462 0.00 0.00 0.00 3.51
328 338 6.173427 ACTGTTTTGGGCACTATTTGAAAT 57.827 33.333 0.00 0.00 0.00 2.17
353 363 4.537135 AAGTTTCGGACAGCTGAGATTA 57.463 40.909 23.35 5.46 0.00 1.75
379 389 2.034221 GGCTGCTCCCTCCGTTTT 59.966 61.111 0.00 0.00 0.00 2.43
392 407 2.173669 CGCAACATAGTCCCGGCTG 61.174 63.158 0.00 0.00 0.00 4.85
395 410 0.742505 TAGACGCAACATAGTCCCGG 59.257 55.000 0.00 0.00 38.08 5.73
396 411 2.034179 TGATAGACGCAACATAGTCCCG 59.966 50.000 0.00 0.00 38.08 5.14
397 412 3.181479 TGTGATAGACGCAACATAGTCCC 60.181 47.826 0.00 0.00 38.08 4.46
416 431 2.205022 ATCCAATGTGAGTGGGTGTG 57.795 50.000 0.00 0.00 36.73 3.82
417 432 2.642311 TGTATCCAATGTGAGTGGGTGT 59.358 45.455 0.00 0.00 36.73 4.16
433 452 9.049523 TGCTTATTGATGATGAAAGACTGTATC 57.950 33.333 0.00 0.00 0.00 2.24
452 471 6.350696 GGGAAATAAAACGGTCCTTGCTTATT 60.351 38.462 0.00 0.00 0.00 1.40
463 482 9.100554 CTTTGTTTTTAAGGGAAATAAAACGGT 57.899 29.630 0.00 0.00 41.18 4.83
465 484 9.315525 TCCTTTGTTTTTAAGGGAAATAAAACG 57.684 29.630 0.00 0.00 42.02 3.60
472 491 8.544622 ACATTCTTCCTTTGTTTTTAAGGGAAA 58.455 29.630 0.00 0.00 42.81 3.13
545 564 7.744087 TCAACAATGTCAAGTACTGCTAAAT 57.256 32.000 0.00 0.00 0.00 1.40
552 571 7.826690 ACAACTTTTCAACAATGTCAAGTACT 58.173 30.769 0.00 0.00 32.87 2.73
576 595 6.539649 TCTTTTGCATGACAAGTACAGTAC 57.460 37.500 2.05 2.05 40.06 2.73
580 599 7.935520 TGTTATTCTTTTGCATGACAAGTACA 58.064 30.769 0.00 0.00 40.06 2.90
581 600 8.970691 ATGTTATTCTTTTGCATGACAAGTAC 57.029 30.769 0.00 0.00 40.06 2.73
583 602 9.630098 CTTATGTTATTCTTTTGCATGACAAGT 57.370 29.630 0.00 0.00 40.06 3.16
584 603 9.630098 ACTTATGTTATTCTTTTGCATGACAAG 57.370 29.630 0.00 0.00 40.06 3.16
611 630 9.498176 ACAACGGTGAAAAATAGTAGAGTATTT 57.502 29.630 7.88 0.00 34.67 1.40
623 642 7.641020 CGTAGAAACTAAACAACGGTGAAAAAT 59.359 33.333 7.88 0.00 0.00 1.82
641 660 4.094442 CCATGGTAAAAGCTCCGTAGAAAC 59.906 45.833 2.57 0.00 0.00 2.78
664 683 3.584733 AATATCTGGTGGAAAGGGAGC 57.415 47.619 0.00 0.00 0.00 4.70
686 705 9.660180 TCGAGATACTACTACTACTACTCGATA 57.340 37.037 0.00 0.00 44.95 2.92
837 861 6.934083 TCCCCTTTTTCTGATTTGTTTTATGC 59.066 34.615 0.00 0.00 0.00 3.14
861 895 2.436115 CCCTTCCGACCCGCTTTC 60.436 66.667 0.00 0.00 0.00 2.62
1197 1246 3.011821 GGGGGAAGAAGGAAGAGGAAAAT 59.988 47.826 0.00 0.00 0.00 1.82
1198 1247 2.378886 GGGGGAAGAAGGAAGAGGAAAA 59.621 50.000 0.00 0.00 0.00 2.29
1216 1265 0.679960 CGGTAAAGAAGCCAAGGGGG 60.680 60.000 0.00 0.00 40.85 5.40
1217 1266 1.313091 GCGGTAAAGAAGCCAAGGGG 61.313 60.000 0.00 0.00 37.18 4.79
1218 1267 2.180674 GCGGTAAAGAAGCCAAGGG 58.819 57.895 0.00 0.00 0.00 3.95
1224 1273 0.947180 TGACGTGGCGGTAAAGAAGC 60.947 55.000 0.00 0.00 0.00 3.86
1229 1278 0.319727 AATCGTGACGTGGCGGTAAA 60.320 50.000 4.40 0.00 0.00 2.01
1232 1281 2.736995 CAATCGTGACGTGGCGGT 60.737 61.111 4.40 0.00 0.00 5.68
1257 1324 1.415672 GCTACCATCCATCCGGGGAA 61.416 60.000 0.00 0.00 41.12 3.97
1292 2950 4.129380 CCGGCAAGTGAAATAGATGATCA 58.871 43.478 0.00 0.00 0.00 2.92
1301 2959 1.003118 TCTAGCACCGGCAAGTGAAAT 59.997 47.619 0.00 0.00 44.61 2.17
1303 2961 0.613260 ATCTAGCACCGGCAAGTGAA 59.387 50.000 0.00 0.00 44.61 3.18
1309 2967 2.202878 GCGAATCTAGCACCGGCA 60.203 61.111 0.00 0.00 44.61 5.69
1341 3013 0.593773 GAGCGATCTCGTCAGCTTCC 60.594 60.000 0.00 0.00 42.22 3.46
1347 3019 2.801421 GCAGGAGCGATCTCGTCA 59.199 61.111 0.00 0.00 40.26 4.35
1381 3053 7.642586 GGCAACCACGATGAATTAATTAGTTAC 59.357 37.037 0.00 0.00 0.00 2.50
1383 3055 6.560711 GGCAACCACGATGAATTAATTAGTT 58.439 36.000 0.00 0.00 0.00 2.24
1435 3670 6.073003 GGTGTTTCAAGTTCAACTCATAGGAG 60.073 42.308 2.12 2.12 46.96 3.69
1437 3672 5.048713 GGGTGTTTCAAGTTCAACTCATAGG 60.049 44.000 0.00 0.00 0.00 2.57
1445 3680 2.383855 CCAGGGGTGTTTCAAGTTCAA 58.616 47.619 0.00 0.00 0.00 2.69
1446 3681 2.026905 GCCAGGGGTGTTTCAAGTTCA 61.027 52.381 0.00 0.00 0.00 3.18
1447 3682 0.673985 GCCAGGGGTGTTTCAAGTTC 59.326 55.000 0.00 0.00 0.00 3.01
1448 3683 0.759060 GGCCAGGGGTGTTTCAAGTT 60.759 55.000 0.00 0.00 0.00 2.66
1449 3684 1.152546 GGCCAGGGGTGTTTCAAGT 60.153 57.895 0.00 0.00 0.00 3.16
1450 3685 0.758685 TTGGCCAGGGGTGTTTCAAG 60.759 55.000 5.11 0.00 0.00 3.02
1475 3710 8.023706 AGAGAGTTCTTAATTTGGCGATTTTTC 58.976 33.333 0.00 0.00 0.00 2.29
1706 6527 6.525629 GGAAATACTTGAGCAGCTATAGGAA 58.474 40.000 0.00 0.00 0.00 3.36
1708 6529 4.926238 CGGAAATACTTGAGCAGCTATAGG 59.074 45.833 0.00 0.00 0.00 2.57
1713 6613 3.334583 TTCGGAAATACTTGAGCAGCT 57.665 42.857 0.00 0.00 0.00 4.24
1742 6644 7.112122 TCCCAAGACGTAACACTACTCTATTA 58.888 38.462 0.00 0.00 0.00 0.98
1784 6689 6.758254 TCTCACACTGTCACATAATTTCTCA 58.242 36.000 0.00 0.00 0.00 3.27
1804 6711 2.541383 CGTTGTGCAAGCAATGTTCTCA 60.541 45.455 0.00 0.00 32.39 3.27
1855 6762 0.251077 AGGAAGGTTTGCTCCAGCTG 60.251 55.000 6.78 6.78 42.66 4.24
1932 6840 4.508124 AGAAACTCAGAATGTGTGAACGAC 59.492 41.667 0.00 0.00 42.75 4.34
2437 7354 9.283420 TGATTTAAATACATGTAACAATGTGCG 57.717 29.630 10.14 0.00 40.93 5.34
2467 7384 6.377327 AATAAATTACTGACCAATCCAGCG 57.623 37.500 0.00 0.00 35.14 5.18
2527 7445 4.686191 AGCATGTTTGACCAAAATCCAA 57.314 36.364 0.00 0.00 31.33 3.53
2725 7658 5.633830 AGCATTGTACAAATCAGACAAGG 57.366 39.130 13.23 0.00 36.57 3.61
2761 7885 4.672409 ACCGCTCAGCAATAAAAATAAGC 58.328 39.130 0.00 0.00 0.00 3.09
2779 7903 0.170339 GGACAAACAGGCATTACCGC 59.830 55.000 0.00 0.00 46.52 5.68
2780 7904 0.808755 GGGACAAACAGGCATTACCG 59.191 55.000 0.00 0.00 46.52 4.02
2832 7958 6.635239 TGTAATAAGAAGAAACAACAAAGCGC 59.365 34.615 0.00 0.00 0.00 5.92
2846 7972 9.658799 TTTCTCAAGAGATGGTGTAATAAGAAG 57.341 33.333 0.00 0.00 37.29 2.85
2907 8033 3.135348 CAGCAGACCCATCCAAGAAGATA 59.865 47.826 0.00 0.00 0.00 1.98
2908 8034 2.092538 CAGCAGACCCATCCAAGAAGAT 60.093 50.000 0.00 0.00 0.00 2.40
2909 8035 1.280133 CAGCAGACCCATCCAAGAAGA 59.720 52.381 0.00 0.00 0.00 2.87
2910 8036 1.280133 TCAGCAGACCCATCCAAGAAG 59.720 52.381 0.00 0.00 0.00 2.85
2911 8037 1.280133 CTCAGCAGACCCATCCAAGAA 59.720 52.381 0.00 0.00 0.00 2.52
2912 8038 0.907486 CTCAGCAGACCCATCCAAGA 59.093 55.000 0.00 0.00 0.00 3.02
2959 8085 7.054751 AGGTAGGATTCATTAAGTTAACCAGC 58.945 38.462 0.88 0.00 0.00 4.85
2962 8088 8.265764 ACAGAGGTAGGATTCATTAAGTTAACC 58.734 37.037 0.88 0.00 0.00 2.85
2971 8097 5.014123 TGGACAAACAGAGGTAGGATTCATT 59.986 40.000 0.00 0.00 0.00 2.57
3011 8137 1.155889 TGTGCTCAATGCTGTAACCG 58.844 50.000 0.00 0.00 43.37 4.44
3127 8253 7.606456 TGAAAACAGGACTCCAGATACAAATAC 59.394 37.037 0.00 0.00 0.00 1.89
3129 8255 6.542821 TGAAAACAGGACTCCAGATACAAAT 58.457 36.000 0.00 0.00 0.00 2.32
3130 8256 5.935945 TGAAAACAGGACTCCAGATACAAA 58.064 37.500 0.00 0.00 0.00 2.83
3131 8257 5.513094 CCTGAAAACAGGACTCCAGATACAA 60.513 44.000 10.33 0.00 45.00 2.41
3132 8258 4.020218 CCTGAAAACAGGACTCCAGATACA 60.020 45.833 10.33 0.00 45.00 2.29
3133 8259 4.020128 ACCTGAAAACAGGACTCCAGATAC 60.020 45.833 20.85 0.00 45.00 2.24
3134 8260 4.168101 ACCTGAAAACAGGACTCCAGATA 58.832 43.478 20.85 0.00 45.00 1.98
3135 8261 2.982488 ACCTGAAAACAGGACTCCAGAT 59.018 45.455 20.85 0.00 45.00 2.90
3136 8262 2.408565 ACCTGAAAACAGGACTCCAGA 58.591 47.619 20.85 0.00 45.00 3.86
3137 8263 2.880890 CAACCTGAAAACAGGACTCCAG 59.119 50.000 20.85 0.00 45.00 3.86
3138 8264 2.241176 ACAACCTGAAAACAGGACTCCA 59.759 45.455 20.85 0.00 45.00 3.86
3160 8286 6.368779 TGTAATAAACAGTTCCTAGGCTGT 57.631 37.500 14.42 14.42 46.61 4.40
3172 8298 7.325660 AGACAATCCAGCATGTAATAAACAG 57.674 36.000 0.00 0.00 42.70 3.16
3583 8712 0.247460 CGAGCTCCTTGATGGTGTCA 59.753 55.000 8.47 0.00 37.07 3.58
3682 8811 1.522355 CGACGCTTCCATCATGCCT 60.522 57.895 0.00 0.00 0.00 4.75
3715 8844 4.101448 GGACAGACGGCCATGGCT 62.101 66.667 34.70 17.99 41.60 4.75
3730 8860 0.255604 AACCATCATCACATGGCGGA 59.744 50.000 0.00 0.00 46.71 5.54
3732 8862 1.202325 CCAAACCATCATCACATGGCG 60.202 52.381 0.00 0.00 46.71 5.69
3733 8863 1.472026 GCCAAACCATCATCACATGGC 60.472 52.381 0.00 0.00 46.71 4.40
3735 8865 2.159156 CCAGCCAAACCATCATCACATG 60.159 50.000 0.00 0.00 0.00 3.21
3736 8866 2.104967 CCAGCCAAACCATCATCACAT 58.895 47.619 0.00 0.00 0.00 3.21
3738 8868 1.838112 TCCAGCCAAACCATCATCAC 58.162 50.000 0.00 0.00 0.00 3.06
3739 8869 2.380941 CATCCAGCCAAACCATCATCA 58.619 47.619 0.00 0.00 0.00 3.07
3740 8870 1.684983 CCATCCAGCCAAACCATCATC 59.315 52.381 0.00 0.00 0.00 2.92
3741 8871 1.690209 CCCATCCAGCCAAACCATCAT 60.690 52.381 0.00 0.00 0.00 2.45
3742 8872 0.324552 CCCATCCAGCCAAACCATCA 60.325 55.000 0.00 0.00 0.00 3.07
3743 8873 0.324645 ACCCATCCAGCCAAACCATC 60.325 55.000 0.00 0.00 0.00 3.51
3861 8993 3.570212 AACCAAGTCCCTGCGCCT 61.570 61.111 4.18 0.00 0.00 5.52
3943 9079 8.750298 TCTCAAACAAGTAAACCCAATGTAAAA 58.250 29.630 0.00 0.00 0.00 1.52
4084 9782 2.111582 GCTCCTGGCAGCTACAAGC 61.112 63.158 9.56 8.46 42.84 4.01
4085 9783 1.812922 CGCTCCTGGCAGCTACAAG 60.813 63.158 9.56 2.09 41.91 3.16
4086 9784 2.265739 CGCTCCTGGCAGCTACAA 59.734 61.111 9.56 0.00 41.91 2.41
4201 9899 0.673437 AAATGGGCCACAACACTTCG 59.327 50.000 9.28 0.00 0.00 3.79
4206 9904 1.338337 CAACGTAAATGGGCCACAACA 59.662 47.619 9.28 0.00 0.00 3.33
4400 10130 8.964150 GCTTCTTAAATACACGTTGAACATTTT 58.036 29.630 0.00 0.00 0.00 1.82
4411 10141 4.150980 TGGTGAACGCTTCTTAAATACACG 59.849 41.667 0.00 0.00 0.00 4.49
4442 10172 9.921637 TCTTAAACACAAACTGAACATTTCTTT 57.078 25.926 0.00 0.00 0.00 2.52
4444 10174 9.921637 TTTCTTAAACACAAACTGAACATTTCT 57.078 25.926 0.00 0.00 0.00 2.52
4447 10177 9.651913 ACATTTCTTAAACACAAACTGAACATT 57.348 25.926 0.00 0.00 0.00 2.71
4448 10178 9.651913 AACATTTCTTAAACACAAACTGAACAT 57.348 25.926 0.00 0.00 0.00 2.71
4449 10179 9.482627 AAACATTTCTTAAACACAAACTGAACA 57.517 25.926 0.00 0.00 0.00 3.18
4456 10186 9.915629 ACACACTAAACATTTCTTAAACACAAA 57.084 25.926 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.