Multiple sequence alignment - TraesCS7B01G364500

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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 TraesCS7B01G364500 chr7B 100.000 4613 0 0 1 4613 627447459 627442847 0.000000e+00 8519.0
1 TraesCS7B01G364500 chr7B 89.053 2430 176 35 1359 3767 628452212 628454572 0.000000e+00 2931.0
2 TraesCS7B01G364500 chr7B 87.595 395 36 10 939 1328 628451618 628452004 3.270000e-121 446.0
3 TraesCS7B01G364500 chr7B 82.308 260 27 15 1 253 695807200 695806953 1.680000e-49 207.0
4 TraesCS7B01G364500 chr7A 94.280 2640 91 18 1359 3976 660466343 660463742 0.000000e+00 3984.0
5 TraesCS7B01G364500 chr7A 89.336 1641 130 18 1979 3594 661158083 661159703 0.000000e+00 2019.0
6 TraesCS7B01G364500 chr7A 84.855 931 47 33 428 1328 660467431 660466565 0.000000e+00 852.0
7 TraesCS7B01G364500 chr7A 86.609 463 41 11 1359 1821 661157631 661158072 4.150000e-135 492.0
8 TraesCS7B01G364500 chr7A 89.239 381 30 9 4027 4397 660463590 660463211 2.510000e-127 466.0
9 TraesCS7B01G364500 chr7A 95.305 213 9 1 4390 4602 660463160 660462949 2.060000e-88 337.0
10 TraesCS7B01G364500 chr7A 82.493 377 33 9 2 348 660468088 660467715 2.700000e-77 300.0
11 TraesCS7B01G364500 chr7A 92.500 200 11 3 935 1130 661157066 661157265 2.720000e-72 283.0
12 TraesCS7B01G364500 chr7A 84.699 183 27 1 2 183 552457378 552457196 1.020000e-41 182.0
13 TraesCS7B01G364500 chr7A 84.444 180 14 9 1154 1328 661157253 661157423 1.030000e-36 165.0
14 TraesCS7B01G364500 chr7D 89.324 2426 183 28 1359 3767 571862453 571864819 0.000000e+00 2976.0
15 TraesCS7B01G364500 chr7D 93.804 1388 68 9 1359 2732 571274034 571272651 0.000000e+00 2071.0
16 TraesCS7B01G364500 chr7D 93.744 1087 39 8 2865 3948 571272545 571271485 0.000000e+00 1604.0
17 TraesCS7B01G364500 chr7D 92.290 441 19 11 902 1335 571274681 571274249 3.050000e-171 612.0
18 TraesCS7B01G364500 chr7D 92.840 419 21 7 3986 4397 571271494 571271078 2.380000e-167 599.0
19 TraesCS7B01G364500 chr7D 95.946 222 9 0 4392 4613 571271025 571270804 1.220000e-95 361.0
20 TraesCS7B01G364500 chr7D 82.957 399 33 20 935 1328 571861877 571862245 1.240000e-85 327.0
21 TraesCS7B01G364500 chr7D 96.552 87 3 0 2793 2879 571272652 571272566 1.340000e-30 145.0
22 TraesCS7B01G364500 chr3D 85.634 536 51 9 3251 3778 17702305 17701788 1.460000e-149 540.0
23 TraesCS7B01G364500 chr6B 81.624 234 39 4 1 232 646942782 646942551 1.690000e-44 191.0
24 TraesCS7B01G364500 chr6B 82.266 203 33 3 1 201 693022053 693021852 6.140000e-39 172.0
25 TraesCS7B01G364500 chr4A 85.714 182 24 2 1 180 680367400 680367581 1.690000e-44 191.0
26 TraesCS7B01G364500 chr1B 82.775 209 34 2 2 209 537145751 537145958 7.880000e-43 185.0
27 TraesCS7B01G364500 chr1B 82.381 210 34 3 2 209 503594416 503594208 3.670000e-41 180.0
28 TraesCS7B01G364500 chr1D 84.699 183 27 1 1 183 404244833 404244652 1.020000e-41 182.0
29 TraesCS7B01G364500 chr4D 78.988 257 47 7 1 253 468392780 468393033 7.940000e-38 169.0
30 TraesCS7B01G364500 chr3B 100.000 29 0 0 754 782 436704825 436704853 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 TraesCS7B01G364500 chr7B 627442847 627447459 4612 True 8519.000000 8519 100.00000 1 4613 1 chr7B.!!$R1 4612
1 TraesCS7B01G364500 chr7B 628451618 628454572 2954 False 1688.500000 2931 88.32400 939 3767 2 chr7B.!!$F1 2828
2 TraesCS7B01G364500 chr7A 660462949 660468088 5139 True 1187.800000 3984 89.23440 2 4602 5 chr7A.!!$R2 4600
3 TraesCS7B01G364500 chr7A 661157066 661159703 2637 False 739.750000 2019 88.22225 935 3594 4 chr7A.!!$F1 2659
4 TraesCS7B01G364500 chr7D 571861877 571864819 2942 False 1651.500000 2976 86.14050 935 3767 2 chr7D.!!$F1 2832
5 TraesCS7B01G364500 chr7D 571270804 571274681 3877 True 898.666667 2071 94.19600 902 4613 6 chr7D.!!$R1 3711
6 TraesCS7B01G364500 chr3D 17701788 17702305 517 True 540.000000 540 85.63400 3251 3778 1 chr3D.!!$R1 527

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
352 383 0.031414 TACTAAGTCCAGCCCTCCCC 60.031 60.0 0.00 0.00 0.00 4.81 F
1252 1550 0.318120 TGTAGGGTTCCGTTCCGTTC 59.682 55.0 0.00 0.00 0.00 3.95 F
1253 1551 0.390340 GTAGGGTTCCGTTCCGTTCC 60.390 60.0 0.00 0.00 0.00 3.62 F
1254 1552 0.542702 TAGGGTTCCGTTCCGTTCCT 60.543 55.0 0.00 0.00 0.00 3.36 F
1843 2355 0.872388 CTTACTGTGGTGGCGAAACC 59.128 55.0 0.19 0.19 40.94 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 1552 0.036448 TCCCCGACGGCAATAAACAA 59.964 50.000 8.86 0.0 0.0 2.83 R
3117 3705 0.459489 GCAGTGGAAGGTGTTTTGCA 59.541 50.000 0.00 0.0 0.0 4.08 R
3257 3860 8.603898 TTTCCTTATCTGACTTGGTATACTCA 57.396 34.615 2.25 0.0 0.0 3.41 R
3455 4076 5.451908 GCGTCAAGAACTTCAAATCATCAA 58.548 37.500 0.00 0.0 0.0 2.57 R
3945 4574 1.961277 GAGCGTCACACACTTGGGG 60.961 63.158 0.00 0.0 0.0 4.96 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
85 86 0.744414 CGAGTGGCCCAACGATGAAT 60.744 55.000 0.00 0.00 0.00 2.57
107 108 1.005347 CGGTTCGATATTTGGACGCAC 60.005 52.381 0.00 0.00 0.00 5.34
112 113 1.395608 CGATATTTGGACGCACGGTTT 59.604 47.619 0.00 0.00 0.00 3.27
115 116 4.260456 CGATATTTGGACGCACGGTTTAAT 60.260 41.667 0.00 0.00 0.00 1.40
127 128 8.422973 ACGCACGGTTTAATAGATAAAATGTA 57.577 30.769 0.00 0.00 35.33 2.29
176 177 2.922740 AACTCCTAGGTTGCGACAAA 57.077 45.000 9.08 0.00 0.00 2.83
180 181 1.626321 TCCTAGGTTGCGACAAATGGA 59.374 47.619 9.08 4.97 0.00 3.41
181 182 2.009774 CCTAGGTTGCGACAAATGGAG 58.990 52.381 6.39 0.00 0.00 3.86
182 183 1.398390 CTAGGTTGCGACAAATGGAGC 59.602 52.381 6.39 0.00 0.00 4.70
184 185 0.387239 GGTTGCGACAAATGGAGCAC 60.387 55.000 6.39 2.27 39.51 4.40
185 186 0.310543 GTTGCGACAAATGGAGCACA 59.689 50.000 0.00 0.00 39.51 4.57
186 187 1.068333 GTTGCGACAAATGGAGCACAT 60.068 47.619 0.00 0.00 43.07 3.21
187 188 2.106477 TGCGACAAATGGAGCACATA 57.894 45.000 0.00 0.00 39.40 2.29
188 189 2.642427 TGCGACAAATGGAGCACATAT 58.358 42.857 0.00 0.00 39.40 1.78
204 205 2.029380 ACATATAGCGCGCCACTTATCA 60.029 45.455 30.33 8.32 0.00 2.15
215 216 3.623060 CGCCACTTATCACAACTTAGCAT 59.377 43.478 0.00 0.00 0.00 3.79
219 220 6.112734 CCACTTATCACAACTTAGCATGGTA 58.887 40.000 0.00 0.00 0.00 3.25
224 225 4.253685 TCACAACTTAGCATGGTAAGAGC 58.746 43.478 38.21 6.26 34.58 4.09
238 262 6.525578 TGGTAAGAGCGATCTTTTAGAAGA 57.474 37.500 22.46 0.00 45.45 2.87
240 264 7.383687 TGGTAAGAGCGATCTTTTAGAAGAAA 58.616 34.615 22.46 0.00 44.61 2.52
246 270 8.691797 AGAGCGATCTTTTAGAAGAAATACTCT 58.308 33.333 0.00 7.38 44.61 3.24
261 285 9.981460 AAGAAATACTCTTCAATTTCAGGGTAT 57.019 29.630 9.66 1.62 40.61 2.73
262 286 9.981460 AGAAATACTCTTCAATTTCAGGGTATT 57.019 29.630 11.08 11.08 45.02 1.89
264 288 9.753674 AAATACTCTTCAATTTCAGGGTATTCA 57.246 29.630 15.07 0.00 43.18 2.57
265 289 9.927081 AATACTCTTCAATTTCAGGGTATTCAT 57.073 29.630 11.08 0.00 41.08 2.57
336 367 1.349688 TGATCTTTTGGCCCACGTACT 59.650 47.619 0.00 0.00 0.00 2.73
348 379 1.183549 CACGTACTAAGTCCAGCCCT 58.816 55.000 0.00 0.00 0.00 5.19
349 380 1.134560 CACGTACTAAGTCCAGCCCTC 59.865 57.143 0.00 0.00 0.00 4.30
350 381 0.745468 CGTACTAAGTCCAGCCCTCC 59.255 60.000 0.00 0.00 0.00 4.30
351 382 1.121378 GTACTAAGTCCAGCCCTCCC 58.879 60.000 0.00 0.00 0.00 4.30
352 383 0.031414 TACTAAGTCCAGCCCTCCCC 60.031 60.000 0.00 0.00 0.00 4.81
353 384 1.003573 CTAAGTCCAGCCCTCCCCT 59.996 63.158 0.00 0.00 0.00 4.79
354 385 1.003051 TAAGTCCAGCCCTCCCCTC 59.997 63.158 0.00 0.00 0.00 4.30
355 386 1.821966 TAAGTCCAGCCCTCCCCTCA 61.822 60.000 0.00 0.00 0.00 3.86
356 387 2.610859 GTCCAGCCCTCCCCTCAA 60.611 66.667 0.00 0.00 0.00 3.02
357 388 2.209809 TCCAGCCCTCCCCTCAAA 59.790 61.111 0.00 0.00 0.00 2.69
358 389 1.465188 TCCAGCCCTCCCCTCAAAA 60.465 57.895 0.00 0.00 0.00 2.44
359 390 1.071314 TCCAGCCCTCCCCTCAAAAA 61.071 55.000 0.00 0.00 0.00 1.94
383 414 1.455383 AAAGTCCAGCCCAAACTGCG 61.455 55.000 0.00 0.00 36.29 5.18
413 444 1.594293 ACGCACCAAACCAGACTCG 60.594 57.895 0.00 0.00 0.00 4.18
456 719 0.885196 GTTGTCTGGAGCGAGAGAGT 59.115 55.000 0.00 0.00 0.00 3.24
478 743 1.230017 TTCCCTCCCCCGATTCCAA 60.230 57.895 0.00 0.00 0.00 3.53
533 798 2.796651 CAGCAAGCGATTCCAGGC 59.203 61.111 0.00 0.00 0.00 4.85
567 832 2.835895 GCTCTCCCTCGGTCCCTC 60.836 72.222 0.00 0.00 0.00 4.30
570 835 1.927569 CTCTCCCTCGGTCCCTCTCA 61.928 65.000 0.00 0.00 0.00 3.27
572 837 0.825840 CTCCCTCGGTCCCTCTCATC 60.826 65.000 0.00 0.00 0.00 2.92
593 858 4.824515 CCGGACCTCTCGGCCTCT 62.825 72.222 0.00 0.00 41.07 3.69
594 859 3.213402 CGGACCTCTCGGCCTCTC 61.213 72.222 0.00 0.00 0.00 3.20
595 860 2.277404 GGACCTCTCGGCCTCTCT 59.723 66.667 0.00 0.00 0.00 3.10
596 861 1.826487 GGACCTCTCGGCCTCTCTC 60.826 68.421 0.00 0.00 0.00 3.20
597 862 1.226262 GACCTCTCGGCCTCTCTCT 59.774 63.158 0.00 0.00 0.00 3.10
598 863 0.818040 GACCTCTCGGCCTCTCTCTC 60.818 65.000 0.00 0.00 0.00 3.20
599 864 1.279025 ACCTCTCGGCCTCTCTCTCT 61.279 60.000 0.00 0.00 0.00 3.10
600 865 0.535102 CCTCTCGGCCTCTCTCTCTC 60.535 65.000 0.00 0.00 0.00 3.20
601 866 0.535102 CTCTCGGCCTCTCTCTCTCC 60.535 65.000 0.00 0.00 0.00 3.71
602 867 0.986019 TCTCGGCCTCTCTCTCTCCT 60.986 60.000 0.00 0.00 0.00 3.69
603 868 0.819259 CTCGGCCTCTCTCTCTCCTG 60.819 65.000 0.00 0.00 0.00 3.86
604 869 2.489275 CGGCCTCTCTCTCTCCTGC 61.489 68.421 0.00 0.00 0.00 4.85
605 870 2.133641 GGCCTCTCTCTCTCCTGCC 61.134 68.421 0.00 0.00 0.00 4.85
606 871 2.133641 GCCTCTCTCTCTCCTGCCC 61.134 68.421 0.00 0.00 0.00 5.36
607 872 1.620259 CCTCTCTCTCTCCTGCCCT 59.380 63.158 0.00 0.00 0.00 5.19
656 921 3.532501 CCCTCTCGGCTTCTCCTC 58.467 66.667 0.00 0.00 0.00 3.71
657 922 2.131067 CCCTCTCGGCTTCTCCTCC 61.131 68.421 0.00 0.00 0.00 4.30
658 923 2.485795 CCTCTCGGCTTCTCCTCCG 61.486 68.421 0.00 0.00 46.52 4.63
659 924 3.132481 CTCTCGGCTTCTCCTCCGC 62.132 68.421 0.00 0.00 44.91 5.54
660 925 4.214327 CTCGGCTTCTCCTCCGCC 62.214 72.222 0.00 0.00 44.91 6.13
661 926 4.761058 TCGGCTTCTCCTCCGCCT 62.761 66.667 0.00 0.00 44.91 5.52
662 927 4.214327 CGGCTTCTCCTCCGCCTC 62.214 72.222 0.00 0.00 41.61 4.70
663 928 3.855853 GGCTTCTCCTCCGCCTCC 61.856 72.222 0.00 0.00 40.62 4.30
664 929 4.214327 GCTTCTCCTCCGCCTCCG 62.214 72.222 0.00 0.00 0.00 4.63
712 977 3.043999 GCGCCCTCCACCAAGGTAT 62.044 63.158 0.00 0.00 39.02 2.73
723 988 3.200825 CCACCAAGGTATTCATCCTCTGT 59.799 47.826 0.00 0.00 33.76 3.41
730 995 5.574188 AGGTATTCATCCTCTGTTTGCTTT 58.426 37.500 0.00 0.00 0.00 3.51
734 999 7.755373 GGTATTCATCCTCTGTTTGCTTTTAAC 59.245 37.037 0.00 0.00 0.00 2.01
750 1015 6.770785 TGCTTTTAACATGAACCTGAACTACT 59.229 34.615 0.00 0.00 0.00 2.57
768 1033 5.957798 ACTACTTGCCATGTGATTCATTTG 58.042 37.500 0.00 0.00 34.09 2.32
781 1046 6.095720 TGTGATTCATTTGCTGCTTATGATCA 59.904 34.615 14.72 0.00 0.00 2.92
788 1053 4.642445 TGCTGCTTATGATCACAAATGG 57.358 40.909 0.00 0.00 0.00 3.16
809 1074 7.944729 ATGGTTGCTAGACTGATTGTAAATT 57.055 32.000 0.00 0.00 0.00 1.82
827 1092 8.862325 TGTAAATTGATGGACATTGAACTACT 57.138 30.769 0.00 0.00 0.00 2.57
828 1093 8.946085 TGTAAATTGATGGACATTGAACTACTC 58.054 33.333 0.00 0.00 0.00 2.59
829 1094 7.396540 AAATTGATGGACATTGAACTACTCC 57.603 36.000 0.00 0.00 0.00 3.85
830 1095 5.762179 TTGATGGACATTGAACTACTCCT 57.238 39.130 0.00 0.00 0.00 3.69
831 1096 6.867519 TTGATGGACATTGAACTACTCCTA 57.132 37.500 0.00 0.00 0.00 2.94
847 1112 8.006298 ACTACTCCTACTTCTCTTGATCATTG 57.994 38.462 0.00 0.00 0.00 2.82
869 1134 6.951062 TGTCACTGATTGTAAATTGTCCAA 57.049 33.333 0.00 0.00 0.00 3.53
871 1136 7.950512 TGTCACTGATTGTAAATTGTCCAATT 58.049 30.769 0.00 0.00 42.35 2.32
875 1140 8.918658 CACTGATTGTAAATTGTCCAATTTCAG 58.081 33.333 18.45 19.25 44.98 3.02
895 1160 1.968493 GTCAGTAGTGGGTGGAAGTGA 59.032 52.381 0.00 0.00 0.00 3.41
904 1183 0.951040 GGTGGAAGTGAAGTGGAGCG 60.951 60.000 0.00 0.00 0.00 5.03
966 1251 2.703409 CGGCGAGGCGAAATCTTG 59.297 61.111 13.92 0.00 0.00 3.02
1141 1433 3.522553 CCTGTCGATTTACTTCTGTCCC 58.477 50.000 0.00 0.00 0.00 4.46
1249 1547 2.103537 AATTGTAGGGTTCCGTTCCG 57.896 50.000 0.00 0.00 0.00 4.30
1250 1548 0.978907 ATTGTAGGGTTCCGTTCCGT 59.021 50.000 0.00 0.00 0.00 4.69
1251 1549 0.758123 TTGTAGGGTTCCGTTCCGTT 59.242 50.000 0.00 0.00 0.00 4.44
1252 1550 0.318120 TGTAGGGTTCCGTTCCGTTC 59.682 55.000 0.00 0.00 0.00 3.95
1253 1551 0.390340 GTAGGGTTCCGTTCCGTTCC 60.390 60.000 0.00 0.00 0.00 3.62
1254 1552 0.542702 TAGGGTTCCGTTCCGTTCCT 60.543 55.000 0.00 0.00 0.00 3.36
1255 1553 1.071987 GGGTTCCGTTCCGTTCCTT 59.928 57.895 0.00 0.00 0.00 3.36
1267 1565 1.538075 CCGTTCCTTGTTTATTGCCGT 59.462 47.619 0.00 0.00 0.00 5.68
1316 1616 1.077716 GTGCAGCCCCCGAATTAGT 60.078 57.895 0.00 0.00 0.00 2.24
1328 1631 5.186603 CCCCCGAATTAGTACCCTATTACTC 59.813 48.000 0.00 0.00 34.10 2.59
1418 1914 5.837437 ACAGTGCTCTATGTCACTAATAGC 58.163 41.667 0.00 0.00 41.19 2.97
1487 1984 5.900339 TGTGTGCTTCTTAAGTCTTTACG 57.100 39.130 1.63 0.00 0.00 3.18
1554 2051 1.956477 ACAAAAGTGATGACCTGGTGC 59.044 47.619 2.82 0.00 0.00 5.01
1559 2056 2.436646 GATGACCTGGTGCGGGTG 60.437 66.667 2.82 0.00 44.10 4.61
1676 2173 8.691797 ACTGTTTGTATGTTTACACCAATTCTT 58.308 29.630 0.00 0.00 38.05 2.52
1703 2200 6.682611 GCCATGCCAATACTTATGCAGTTTTA 60.683 38.462 0.00 0.00 37.12 1.52
1721 2233 8.752254 GCAGTTTTAGTTTGTTGATTACCTTTC 58.248 33.333 0.00 0.00 0.00 2.62
1793 2305 6.855914 TCGTATTTCATCAGTTTGTTTTGCTC 59.144 34.615 0.00 0.00 0.00 4.26
1811 2323 5.801350 TGCTCTTGTGAATATCCTTTTCG 57.199 39.130 0.00 0.00 0.00 3.46
1843 2355 0.872388 CTTACTGTGGTGGCGAAACC 59.128 55.000 0.19 0.19 40.94 3.27
1910 2422 9.881649 GAGAACATCATGGATAATTAGAGCATA 57.118 33.333 0.00 0.00 0.00 3.14
2084 2598 4.578928 CACACTTGCTGTACCTAGGTTTTT 59.421 41.667 22.11 0.00 0.00 1.94
2141 2659 5.767665 TCTCTAAATGTGCAAGGTTAAAGCA 59.232 36.000 0.00 0.00 35.63 3.91
2283 2813 4.947645 TCAGTTTTCTGGGCTTTTGATTG 58.052 39.130 0.00 0.00 46.94 2.67
2320 2850 8.820933 TCTTCGTTGATCATATTGATGAACTTC 58.179 33.333 14.77 0.00 44.91 3.01
2565 3102 5.876651 TGGCTGCTCCATATACCATATAG 57.123 43.478 0.00 0.00 40.72 1.31
2696 3233 3.610911 CTGAATACCAGGTTGGGTTCTC 58.389 50.000 0.00 0.00 43.37 2.87
2707 3244 3.119495 GGTTGGGTTCTCGATCATTTTGG 60.119 47.826 0.00 0.00 0.00 3.28
2821 3360 5.051891 AGTTTTCTGATTCTTGGCATTCG 57.948 39.130 0.00 0.00 0.00 3.34
2863 3439 2.237392 GGAGAATCTTAGGTGCACCTGT 59.763 50.000 42.35 24.30 40.65 4.00
2887 3464 8.626526 TGTTTAGGTGATTTCTTTACAAAGGAC 58.373 33.333 2.04 0.00 36.67 3.85
2923 3507 4.593597 CGAAGCGCAATTTTTCCTACTA 57.406 40.909 11.47 0.00 0.00 1.82
3100 3688 8.202137 TCCTTCTGGTAATTAAATTAGGAGTCG 58.798 37.037 0.00 0.00 34.23 4.18
3116 3704 4.344390 AGGAGTCGTAGTGAATTTATCCCC 59.656 45.833 0.00 0.00 0.00 4.81
3117 3705 4.344390 GGAGTCGTAGTGAATTTATCCCCT 59.656 45.833 0.00 0.00 0.00 4.79
3257 3860 3.988976 TGGCAGCTCTTTCTTGTCTAT 57.011 42.857 0.00 0.00 0.00 1.98
3260 3863 3.870419 GGCAGCTCTTTCTTGTCTATGAG 59.130 47.826 0.00 0.00 0.00 2.90
3455 4076 3.017581 GACCCCAGGTGGCTCCAT 61.018 66.667 8.51 0.00 35.25 3.41
3480 4101 3.476552 TGATTTGAAGTTCTTGACGCCT 58.523 40.909 4.17 0.00 0.00 5.52
3533 4157 2.668280 GGAAGCAAGTGGACGACGC 61.668 63.158 0.00 0.00 0.00 5.19
3551 4175 1.879380 CGCAAACCCTGAAAGTGATGA 59.121 47.619 0.00 0.00 0.00 2.92
3660 4288 9.177608 ACTCAGCTATTTGCATTCTGTATAAAA 57.822 29.630 0.00 0.00 45.94 1.52
3717 4345 1.001706 GTTTGGTTTCTTCTGGTCGCC 60.002 52.381 0.00 0.00 0.00 5.54
3807 4435 7.121020 TGCACTTCATCTTGCTCATATGTTTTA 59.879 33.333 1.90 0.00 39.62 1.52
3867 4496 9.620259 AGATAACCTTTATCCAGAAATGAAGTC 57.380 33.333 2.88 0.00 0.00 3.01
3911 4540 7.022979 TGCTCATATCTTCAACACAAAAATCG 58.977 34.615 0.00 0.00 0.00 3.34
3942 4571 2.211250 TGTCGCTAGTACCACTCCTT 57.789 50.000 0.00 0.00 0.00 3.36
3945 4574 0.745468 CGCTAGTACCACTCCTTCCC 59.255 60.000 0.00 0.00 0.00 3.97
3968 4597 1.069703 CAAGTGTGTGACGCTCCATTG 60.070 52.381 0.00 0.00 38.11 2.82
4004 4717 2.298158 ATCTTCGCCCGCGTCATCTT 62.298 55.000 4.92 0.00 40.74 2.40
4154 4889 4.199432 TGTGCTTCTCATTCTCTTCTCC 57.801 45.455 0.00 0.00 0.00 3.71
4156 4891 5.019470 TGTGCTTCTCATTCTCTTCTCCTA 58.981 41.667 0.00 0.00 0.00 2.94
4161 4896 4.935578 TCTCATTCTCTTCTCCTACCACA 58.064 43.478 0.00 0.00 0.00 4.17
4243 4983 1.402968 CACCTCCTTTGCATTGGATCG 59.597 52.381 8.39 5.33 0.00 3.69
4262 5002 5.461737 GGATCGACTCATCAATCTTGTCTTC 59.538 44.000 0.00 0.00 0.00 2.87
4325 5065 4.241555 CTTCCTCCCATCGGGCCG 62.242 72.222 22.51 22.51 43.94 6.13
4339 5079 2.742116 GGCCGCCCCTTGATAGACA 61.742 63.158 0.00 0.00 0.00 3.41
4504 5301 8.097038 TGCTTGTATATCTCTTGAGTGAACTTT 58.903 33.333 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.987272 AGATCACATATTGATAGATTTCGACAA 57.013 29.630 0.00 0.00 45.67 3.18
41 42 7.322938 CGCGTCGAGATATTTAAAACTAGATCA 59.677 37.037 0.00 0.00 0.00 2.92
45 46 6.964677 TCGCGTCGAGATATTTAAAACTAG 57.035 37.500 5.77 0.00 0.00 2.57
72 73 1.329599 GAACCGTATTCATCGTTGGGC 59.670 52.381 0.00 0.00 0.00 5.36
85 86 2.159268 TGCGTCCAAATATCGAACCGTA 60.159 45.455 0.00 0.00 0.00 4.02
163 164 1.271108 TGCTCCATTTGTCGCAACCTA 60.271 47.619 0.00 0.00 0.00 3.08
182 183 1.778334 TAAGTGGCGCGCTATATGTG 58.222 50.000 32.29 0.00 0.00 3.21
184 185 2.345641 GTGATAAGTGGCGCGCTATATG 59.654 50.000 32.29 0.00 0.00 1.78
185 186 2.029380 TGTGATAAGTGGCGCGCTATAT 60.029 45.455 32.29 20.26 0.00 0.86
186 187 1.338655 TGTGATAAGTGGCGCGCTATA 59.661 47.619 32.29 15.96 0.00 1.31
187 188 0.104120 TGTGATAAGTGGCGCGCTAT 59.896 50.000 32.29 20.41 0.00 2.97
188 189 0.108567 TTGTGATAAGTGGCGCGCTA 60.109 50.000 32.29 24.64 0.00 4.26
204 205 3.056107 TCGCTCTTACCATGCTAAGTTGT 60.056 43.478 7.50 0.00 0.00 3.32
215 216 6.525578 TCTTCTAAAAGATCGCTCTTACCA 57.474 37.500 1.27 0.00 40.93 3.25
219 220 9.308318 GAGTATTTCTTCTAAAAGATCGCTCTT 57.692 33.333 0.00 0.00 43.71 2.85
238 262 9.753674 TGAATACCCTGAAATTGAAGAGTATTT 57.246 29.630 8.19 0.00 31.27 1.40
240 264 9.347240 CATGAATACCCTGAAATTGAAGAGTAT 57.653 33.333 0.00 0.00 0.00 2.12
246 270 8.827832 ATTCTCATGAATACCCTGAAATTGAA 57.172 30.769 0.00 0.00 40.77 2.69
253 277 4.977739 AGGGAATTCTCATGAATACCCTGA 59.022 41.667 18.44 0.77 43.80 3.86
254 278 5.316158 AGGGAATTCTCATGAATACCCTG 57.684 43.478 18.44 0.00 43.80 4.45
255 279 4.977739 TCAGGGAATTCTCATGAATACCCT 59.022 41.667 8.33 15.35 45.98 4.34
257 281 7.830099 ATTTCAGGGAATTCTCATGAATACC 57.170 36.000 18.27 4.73 41.62 2.73
258 282 8.787852 GGTATTTCAGGGAATTCTCATGAATAC 58.212 37.037 18.27 18.79 41.62 1.89
259 283 8.501904 TGGTATTTCAGGGAATTCTCATGAATA 58.498 33.333 18.27 11.54 41.62 1.75
260 284 7.356680 TGGTATTTCAGGGAATTCTCATGAAT 58.643 34.615 18.27 12.28 44.08 2.57
261 285 6.730447 TGGTATTTCAGGGAATTCTCATGAA 58.270 36.000 8.33 12.85 36.54 2.57
262 286 6.325993 TGGTATTTCAGGGAATTCTCATGA 57.674 37.500 8.33 7.56 0.00 3.07
263 287 7.408756 TTTGGTATTTCAGGGAATTCTCATG 57.591 36.000 8.33 5.26 0.00 3.07
264 288 8.434589 TTTTTGGTATTTCAGGGAATTCTCAT 57.565 30.769 8.33 0.00 0.00 2.90
265 289 7.847711 TTTTTGGTATTTCAGGGAATTCTCA 57.152 32.000 8.33 0.00 0.00 3.27
296 327 6.490040 AGATCAACGAATAAACATTATGGGGG 59.510 38.462 0.00 0.00 0.00 5.40
307 338 4.524714 TGGGCCAAAAGATCAACGAATAAA 59.475 37.500 2.13 0.00 0.00 1.40
312 343 1.243902 GTGGGCCAAAAGATCAACGA 58.756 50.000 8.40 0.00 0.00 3.85
336 367 1.003051 GAGGGGAGGGCTGGACTTA 59.997 63.158 0.00 0.00 0.00 2.24
362 393 1.138859 GCAGTTTGGGCTGGACTTTTT 59.861 47.619 0.00 0.00 37.00 1.94
363 394 0.752658 GCAGTTTGGGCTGGACTTTT 59.247 50.000 0.00 0.00 37.00 2.27
364 395 1.455383 CGCAGTTTGGGCTGGACTTT 61.455 55.000 0.00 0.00 37.00 2.66
365 396 1.898574 CGCAGTTTGGGCTGGACTT 60.899 57.895 0.00 0.00 37.00 3.01
366 397 2.281761 CGCAGTTTGGGCTGGACT 60.282 61.111 0.00 0.00 37.00 3.85
367 398 3.365265 CCGCAGTTTGGGCTGGAC 61.365 66.667 0.00 0.00 37.00 4.02
368 399 4.659172 CCCGCAGTTTGGGCTGGA 62.659 66.667 0.00 0.00 40.47 3.86
374 405 2.666862 TACGTGCCCGCAGTTTGG 60.667 61.111 0.00 0.00 37.70 3.28
375 406 2.860293 CTACGTGCCCGCAGTTTG 59.140 61.111 0.00 0.00 37.70 2.93
397 428 1.305201 TTTCGAGTCTGGTTTGGTGC 58.695 50.000 0.00 0.00 0.00 5.01
419 450 1.972223 CCAGTCGGTCGAGTCTGGT 60.972 63.158 16.87 0.00 41.51 4.00
421 452 3.669686 ACCAGTCGGTCGAGTCTG 58.330 61.111 0.00 1.45 44.71 3.51
456 719 1.484446 GGAATCGGGGGAGGGAAGATA 60.484 57.143 0.00 0.00 0.00 1.98
461 724 0.626277 ATTTGGAATCGGGGGAGGGA 60.626 55.000 0.00 0.00 0.00 4.20
464 727 2.435372 TTGATTTGGAATCGGGGGAG 57.565 50.000 0.00 0.00 0.00 4.30
465 728 2.424234 GGATTGATTTGGAATCGGGGGA 60.424 50.000 0.00 0.00 31.59 4.81
478 743 1.413517 GCTGGGGAATGGGGATTGATT 60.414 52.381 0.00 0.00 0.00 2.57
586 851 2.489275 GCAGGAGAGAGAGAGGCCG 61.489 68.421 0.00 0.00 0.00 6.13
587 852 2.133641 GGCAGGAGAGAGAGAGGCC 61.134 68.421 0.00 0.00 0.00 5.19
588 853 2.133641 GGGCAGGAGAGAGAGAGGC 61.134 68.421 0.00 0.00 0.00 4.70
589 854 0.468029 GAGGGCAGGAGAGAGAGAGG 60.468 65.000 0.00 0.00 0.00 3.69
590 855 0.819259 CGAGGGCAGGAGAGAGAGAG 60.819 65.000 0.00 0.00 0.00 3.20
591 856 1.225983 CGAGGGCAGGAGAGAGAGA 59.774 63.158 0.00 0.00 0.00 3.10
592 857 1.827789 CCGAGGGCAGGAGAGAGAG 60.828 68.421 0.00 0.00 0.00 3.20
593 858 2.277072 CCGAGGGCAGGAGAGAGA 59.723 66.667 0.00 0.00 0.00 3.10
703 968 5.256474 CAAACAGAGGATGAATACCTTGGT 58.744 41.667 0.00 0.00 37.93 3.67
704 969 4.096984 GCAAACAGAGGATGAATACCTTGG 59.903 45.833 0.00 0.00 37.93 3.61
712 977 6.707440 TGTTAAAAGCAAACAGAGGATGAA 57.293 33.333 0.00 0.00 33.13 2.57
723 988 6.872920 AGTTCAGGTTCATGTTAAAAGCAAA 58.127 32.000 0.00 0.00 0.00 3.68
730 995 5.472137 GGCAAGTAGTTCAGGTTCATGTTAA 59.528 40.000 0.00 0.00 0.00 2.01
734 999 3.411446 TGGCAAGTAGTTCAGGTTCATG 58.589 45.455 0.00 0.00 0.00 3.07
750 1015 3.591023 CAGCAAATGAATCACATGGCAA 58.409 40.909 0.00 0.00 40.33 4.52
768 1033 4.644103 ACCATTTGTGATCATAAGCAGC 57.356 40.909 4.99 0.00 0.00 5.25
781 1046 5.072741 ACAATCAGTCTAGCAACCATTTGT 58.927 37.500 0.00 0.00 34.90 2.83
788 1053 7.912250 CCATCAATTTACAATCAGTCTAGCAAC 59.088 37.037 0.00 0.00 0.00 4.17
809 1074 5.958380 AGTAGGAGTAGTTCAATGTCCATCA 59.042 40.000 0.00 0.00 0.00 3.07
825 1090 6.438741 TGACAATGATCAAGAGAAGTAGGAGT 59.561 38.462 0.00 0.00 0.00 3.85
826 1091 6.756074 GTGACAATGATCAAGAGAAGTAGGAG 59.244 42.308 0.00 0.00 0.00 3.69
827 1092 6.438741 AGTGACAATGATCAAGAGAAGTAGGA 59.561 38.462 0.00 0.00 0.00 2.94
828 1093 6.534436 CAGTGACAATGATCAAGAGAAGTAGG 59.466 42.308 0.00 0.00 0.00 3.18
829 1094 7.318893 TCAGTGACAATGATCAAGAGAAGTAG 58.681 38.462 0.51 0.00 0.00 2.57
830 1095 7.232118 TCAGTGACAATGATCAAGAGAAGTA 57.768 36.000 0.51 0.00 0.00 2.24
831 1096 6.106648 TCAGTGACAATGATCAAGAGAAGT 57.893 37.500 0.51 0.00 0.00 3.01
847 1112 8.816640 AAATTGGACAATTTACAATCAGTGAC 57.183 30.769 18.48 0.00 45.93 3.67
869 1134 3.248024 TCCACCCACTACTGACTGAAAT 58.752 45.455 0.00 0.00 0.00 2.17
871 1136 2.391926 TCCACCCACTACTGACTGAA 57.608 50.000 0.00 0.00 0.00 3.02
875 1140 1.968493 TCACTTCCACCCACTACTGAC 59.032 52.381 0.00 0.00 0.00 3.51
895 1160 1.536073 TACTGCTCAGCGCTCCACTT 61.536 55.000 7.13 0.00 40.11 3.16
904 1183 2.231215 ATGTCCGATTACTGCTCAGC 57.769 50.000 0.00 0.00 0.00 4.26
964 1246 2.112297 GGAGTTGGTGGGCGTCAA 59.888 61.111 0.00 0.00 0.00 3.18
966 1251 3.485346 TTGGGAGTTGGTGGGCGTC 62.485 63.158 0.00 0.00 0.00 5.19
1141 1433 1.492599 GAGAGGAGAAGGATTTGGGGG 59.507 57.143 0.00 0.00 0.00 5.40
1159 1453 0.179189 GCGGAAGGCACGAAATTGAG 60.179 55.000 0.00 0.00 42.87 3.02
1249 1547 2.413634 CCGACGGCAATAAACAAGGAAC 60.414 50.000 0.00 0.00 0.00 3.62
1250 1548 1.807742 CCGACGGCAATAAACAAGGAA 59.192 47.619 0.00 0.00 0.00 3.36
1251 1549 1.444836 CCGACGGCAATAAACAAGGA 58.555 50.000 0.00 0.00 0.00 3.36
1252 1550 0.450184 CCCGACGGCAATAAACAAGG 59.550 55.000 8.86 0.00 0.00 3.61
1253 1551 0.450184 CCCCGACGGCAATAAACAAG 59.550 55.000 8.86 0.00 0.00 3.16
1254 1552 0.036448 TCCCCGACGGCAATAAACAA 59.964 50.000 8.86 0.00 0.00 2.83
1255 1553 0.253610 ATCCCCGACGGCAATAAACA 59.746 50.000 8.86 0.00 0.00 2.83
1267 1565 2.574369 ACCTACATTTCACAATCCCCGA 59.426 45.455 0.00 0.00 0.00 5.14
1418 1914 6.127810 AGAACAATCATTTCATCACCATCG 57.872 37.500 0.00 0.00 0.00 3.84
1487 1984 2.159254 TGGCAAGTGACAACAAAGAAGC 60.159 45.455 0.00 0.00 0.00 3.86
1554 2051 0.391263 GTCAGCTCCCTTAACACCCG 60.391 60.000 0.00 0.00 0.00 5.28
1559 2056 0.458025 CGACCGTCAGCTCCCTTAAC 60.458 60.000 0.00 0.00 0.00 2.01
1607 2104 1.699634 ACCTTTCTGCCTTGTAGCTCA 59.300 47.619 0.00 0.00 0.00 4.26
1676 2173 3.029570 TGCATAAGTATTGGCATGGCAA 58.970 40.909 33.51 33.51 35.32 4.52
1703 2200 4.721132 TCGGGAAAGGTAATCAACAAACT 58.279 39.130 0.00 0.00 0.00 2.66
1721 2233 1.683943 TCGTGTAGTAAGGGATCGGG 58.316 55.000 0.00 0.00 0.00 5.14
1781 2293 7.147976 AGGATATTCACAAGAGCAAAACAAAC 58.852 34.615 0.00 0.00 0.00 2.93
1793 2305 7.133891 ACAGAACGAAAAGGATATTCACAAG 57.866 36.000 0.00 0.00 0.00 3.16
1811 2323 5.462398 CACCACAGTAAGTCAGTAACAGAAC 59.538 44.000 0.00 0.00 0.00 3.01
1843 2355 7.350744 TGAATAACCTCATGGGAATTTCATG 57.649 36.000 13.37 13.37 42.28 3.07
1869 2381 7.672983 TGATGTTCTCATTTCTACCAAGAAC 57.327 36.000 6.61 6.61 41.48 3.01
1934 2446 9.996554 CACCATAATAGTCAAAGTGGACATATA 57.003 33.333 0.00 0.00 40.29 0.86
2044 2558 2.531912 GTGTGAGCACGTATCAGATTCG 59.468 50.000 7.82 7.82 35.75 3.34
2084 2598 8.325421 ACATTGCAATTCATTTTTCAAGCATA 57.675 26.923 9.83 0.00 0.00 3.14
2283 2813 5.168569 TGATCAACGAAGATAACTGACACC 58.831 41.667 0.00 0.00 0.00 4.16
2320 2850 7.471721 TGTTTTTATCATCCTGCGATAAACAG 58.528 34.615 5.14 0.00 42.26 3.16
2484 3014 2.067365 AACAGGTGGTCCCAAGAAAC 57.933 50.000 0.00 0.00 34.66 2.78
2517 3051 2.032549 CACAGGCAGAACTTTCTTCACG 60.033 50.000 0.00 0.00 34.74 4.35
2754 3293 2.622942 ACCATTTTCAGTTCGCATGTGT 59.377 40.909 6.09 0.00 0.00 3.72
2755 3294 2.981805 CACCATTTTCAGTTCGCATGTG 59.018 45.455 0.00 0.00 0.00 3.21
2756 3295 2.622942 ACACCATTTTCAGTTCGCATGT 59.377 40.909 0.00 0.00 0.00 3.21
2821 3360 7.047891 TCTCCTCCACATCAATACATTGTAAC 58.952 38.462 0.00 0.00 38.84 2.50
2863 3439 8.846211 CAGTCCTTTGTAAAGAAATCACCTAAA 58.154 33.333 5.95 0.00 38.28 1.85
2887 3464 1.069636 GCTTCGCTCAAGAAACCACAG 60.070 52.381 0.00 0.00 33.29 3.66
2923 3507 3.898123 TCTGAGGAGAAGCAAGTACAGTT 59.102 43.478 0.00 0.00 0.00 3.16
3100 3688 6.071616 TGTTTTGCAGGGGATAAATTCACTAC 60.072 38.462 0.00 0.00 0.00 2.73
3116 3704 1.536709 GCAGTGGAAGGTGTTTTGCAG 60.537 52.381 0.00 0.00 0.00 4.41
3117 3705 0.459489 GCAGTGGAAGGTGTTTTGCA 59.541 50.000 0.00 0.00 0.00 4.08
3257 3860 8.603898 TTTCCTTATCTGACTTGGTATACTCA 57.396 34.615 2.25 0.00 0.00 3.41
3455 4076 5.451908 GCGTCAAGAACTTCAAATCATCAA 58.548 37.500 0.00 0.00 0.00 2.57
3533 4157 4.319766 CGAGTTCATCACTTTCAGGGTTTG 60.320 45.833 0.00 0.00 35.01 2.93
3551 4175 4.466370 TCCTCTGGTTGATATTGTCGAGTT 59.534 41.667 0.00 0.00 0.00 3.01
3717 4345 7.547019 TCTGATATTTCATAATAGCTCTTGCCG 59.453 37.037 0.00 0.00 40.80 5.69
3849 4478 9.581289 TTTGGTTAGACTTCATTTCTGGATAAA 57.419 29.630 0.00 0.00 0.00 1.40
3911 4540 3.692576 ACTAGCGACATCGACATGTAAC 58.307 45.455 5.26 0.00 43.79 2.50
3945 4574 1.961277 GAGCGTCACACACTTGGGG 60.961 63.158 0.00 0.00 0.00 4.96
3968 4597 3.699411 AGATCTTGGCATCTAGGATGC 57.301 47.619 20.23 20.23 43.85 3.91
4043 4773 7.502060 AGGAGAATCAACTGATTAAAGAGGA 57.498 36.000 4.94 0.00 44.14 3.71
4045 4775 7.414984 GCCAAGGAGAATCAACTGATTAAAGAG 60.415 40.741 4.94 0.00 44.14 2.85
4115 4845 3.861131 GCACAAGGACGACACAGATAAGT 60.861 47.826 0.00 0.00 0.00 2.24
4154 4889 4.909696 AGAGAAGATGACGATGTGGTAG 57.090 45.455 0.00 0.00 0.00 3.18
4156 4891 3.259374 ACAAGAGAAGATGACGATGTGGT 59.741 43.478 0.00 0.00 0.00 4.16
4161 4896 4.199432 AGCAACAAGAGAAGATGACGAT 57.801 40.909 0.00 0.00 0.00 3.73
4243 4983 6.373774 ACAATGGAAGACAAGATTGATGAGTC 59.626 38.462 0.00 0.00 31.53 3.36
4262 5002 0.103026 TGGAGAGATCGCGACAATGG 59.897 55.000 12.93 0.00 0.00 3.16
4325 5065 2.290960 ACTTTGGTGTCTATCAAGGGGC 60.291 50.000 0.00 0.00 28.92 5.80
4339 5079 4.445879 GGAAACAAGGAGTCCTACTTTGGT 60.446 45.833 13.43 2.12 29.53 3.67
4487 5284 7.067496 TGTAGGAAAAGTTCACTCAAGAGAT 57.933 36.000 3.73 0.00 0.00 2.75
4504 5301 6.932400 CACCTTGTAGTTGTATGTTGTAGGAA 59.068 38.462 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.