Multiple sequence alignment - TraesCS2D01G560100

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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 TraesCS2D01G560100 chr2D 100.000 3345 0 0 2697 6041 632989830 632986486 0.000000e+00 6178.0
1 TraesCS2D01G560100 chr2D 100.000 2283 0 0 1 2283 632992526 632990244 0.000000e+00 4217.0
2 TraesCS2D01G560100 chr2D 89.953 856 41 18 1 839 633069648 633068821 0.000000e+00 1062.0
3 TraesCS2D01G560100 chr2D 84.644 547 77 5 1736 2280 651684266 651683725 6.890000e-149 538.0
4 TraesCS2D01G560100 chr2D 82.847 548 87 5 1735 2280 651673024 651672482 9.100000e-133 484.0
5 TraesCS2D01G560100 chr2D 81.967 549 92 5 1735 2280 651689143 651688599 5.520000e-125 459.0
6 TraesCS2D01G560100 chr2A 91.291 1975 70 32 333 2282 759451893 759453790 0.000000e+00 2601.0
7 TraesCS2D01G560100 chr2A 92.471 1315 68 14 4050 5352 759455613 759456908 0.000000e+00 1851.0
8 TraesCS2D01G560100 chr2A 90.138 943 63 14 2697 3624 759454062 759454989 0.000000e+00 1199.0
9 TraesCS2D01G560100 chr2A 88.129 556 50 16 5395 5941 759457005 759457553 0.000000e+00 647.0
10 TraesCS2D01G560100 chr2A 91.029 379 18 8 3677 4054 759455171 759455534 1.170000e-136 497.0
11 TraesCS2D01G560100 chr2A 82.847 548 88 4 1735 2280 776014567 776015110 2.530000e-133 486.0
12 TraesCS2D01G560100 chr2A 91.789 341 23 4 1 338 759451334 759451672 2.550000e-128 470.0
13 TraesCS2D01G560100 chr2A 93.640 283 17 1 5760 6041 759457403 759457685 7.240000e-114 422.0
14 TraesCS2D01G560100 chr2A 75.130 386 64 17 3684 4043 20859641 20859262 1.050000e-32 152.0
15 TraesCS2D01G560100 chr2A 87.179 117 13 2 5761 5877 759457500 759457614 1.370000e-26 132.0
16 TraesCS2D01G560100 chr2A 98.000 50 1 0 5337 5386 759456923 759456972 3.000000e-13 87.9
17 TraesCS2D01G560100 chr2B 90.021 1944 119 47 3677 5600 776212745 776214633 0.000000e+00 2446.0
18 TraesCS2D01G560100 chr2B 91.951 1640 76 23 672 2283 776209078 776210689 0.000000e+00 2246.0
19 TraesCS2D01G560100 chr2B 95.021 944 36 6 2697 3632 776211564 776212504 0.000000e+00 1472.0
20 TraesCS2D01G560100 chr2B 90.766 444 35 6 5600 6041 776214687 776215126 6.740000e-164 588.0
21 TraesCS2D01G560100 chr2B 81.536 547 94 6 1736 2280 781363548 781363007 1.550000e-120 444.0
22 TraesCS2D01G560100 chr2B 81.204 548 95 6 1735 2280 781364945 781364404 9.300000e-118 435.0
23 TraesCS2D01G560100 chr2B 80.874 549 97 6 1735 2280 781359372 781358829 5.600000e-115 425.0
24 TraesCS2D01G560100 chr2B 88.060 268 14 9 378 639 776208707 776208962 9.840000e-78 302.0
25 TraesCS2D01G560100 chr4A 77.663 291 49 10 3693 3971 438616015 438615729 4.840000e-36 163.0
26 TraesCS2D01G560100 chr7A 76.190 273 45 12 3685 3944 473668000 473667735 6.360000e-25 126.0


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 TraesCS2D01G560100 chr2D 632986486 632992526 6040 True 5197.500000 6178 100.000000 1 6041 2 chr2D.!!$R5 6040
1 TraesCS2D01G560100 chr2D 633068821 633069648 827 True 1062.000000 1062 89.953000 1 839 1 chr2D.!!$R1 838
2 TraesCS2D01G560100 chr2D 651683725 651684266 541 True 538.000000 538 84.644000 1736 2280 1 chr2D.!!$R3 544
3 TraesCS2D01G560100 chr2D 651672482 651673024 542 True 484.000000 484 82.847000 1735 2280 1 chr2D.!!$R2 545
4 TraesCS2D01G560100 chr2D 651688599 651689143 544 True 459.000000 459 81.967000 1735 2280 1 chr2D.!!$R4 545
5 TraesCS2D01G560100 chr2A 759451334 759457685 6351 False 878.544444 2601 91.518444 1 6041 9 chr2A.!!$F2 6040
6 TraesCS2D01G560100 chr2A 776014567 776015110 543 False 486.000000 486 82.847000 1735 2280 1 chr2A.!!$F1 545
7 TraesCS2D01G560100 chr2B 776208707 776215126 6419 False 1410.800000 2446 91.163800 378 6041 5 chr2B.!!$F1 5663
8 TraesCS2D01G560100 chr2B 781358829 781364945 6116 True 434.666667 444 81.204667 1735 2280 3 chr2B.!!$R1 545

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
868 1198 0.324460 TCTTCCTCCCGACCTTCCTC 60.324 60.0 0.00 0.0 0.00 3.71 F
1499 1845 0.107268 TGAGTTGCTTGCTGCTCTGA 59.893 50.0 0.00 0.0 43.37 3.27 F
3126 8209 0.108804 CGCTTCCCGTGTACACTGAT 60.109 55.0 23.01 0.0 0.00 2.90 F
4266 9874 0.109532 TCAACCCCGAAAGCACATGA 59.890 50.0 0.00 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 2141 0.665369 AAATGTGCTCGCTTTGCTGC 60.665 50.0 0.00 0.0 0.0 5.25 R
3463 8786 0.038343 CCAAAACACTCGGGGCATTG 60.038 55.0 0.00 0.0 0.0 2.82 R
4629 10251 0.179097 GAGTGGGCGTCCTTGAGATC 60.179 60.0 7.97 0.0 0.0 2.75 R
5191 10815 0.234625 CAACGTCCACAACACCATCG 59.765 55.0 0.00 0.0 0.0 3.84 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
104 106 2.391389 GCAGCACTAACACCCGCTC 61.391 63.158 0.00 0.00 30.72 5.03
124 126 5.833406 CTCTCTAAGCTCATGAGACAGAA 57.167 43.478 27.04 12.62 33.82 3.02
142 144 0.806868 AAATCGGCTAGACGACACGA 59.193 50.000 25.82 0.00 46.64 4.35
168 170 1.005037 TCTGATTGCGGCAGAACGT 60.005 52.632 1.67 0.00 39.29 3.99
206 208 1.643832 GCCATTGATTCGTCGGCTC 59.356 57.895 0.00 0.00 39.73 4.70
312 315 6.054941 TCATGCGTGAACTTGTTATATGGAT 58.945 36.000 6.04 0.00 0.00 3.41
315 318 5.645929 TGCGTGAACTTGTTATATGGATGTT 59.354 36.000 0.00 0.00 0.00 2.71
391 623 1.321445 CGACACATGCACACATACTCG 59.679 52.381 0.00 0.00 33.67 4.18
399 631 3.624410 ATGCACACATACTCGACGTAGTA 59.376 43.478 0.83 0.83 35.80 1.82
401 633 5.220989 ATGCACACATACTCGACGTAGTAAT 60.221 40.000 2.45 0.00 35.80 1.89
403 635 9.272098 ATGCACACATACTCGACGTAGTAATCA 62.272 40.741 2.45 0.00 35.80 2.57
603 841 4.821589 CCTCGCCCCGCTTGTCTC 62.822 72.222 0.00 0.00 0.00 3.36
606 844 4.394712 CGCCCCGCTTGTCTCCTT 62.395 66.667 0.00 0.00 0.00 3.36
608 846 2.269241 CCCCGCTTGTCTCCTTCC 59.731 66.667 0.00 0.00 0.00 3.46
859 1189 1.972660 AAATCCGCCTCTTCCTCCCG 61.973 60.000 0.00 0.00 0.00 5.14
860 1190 2.873557 AATCCGCCTCTTCCTCCCGA 62.874 60.000 0.00 0.00 0.00 5.14
861 1191 3.839432 CCGCCTCTTCCTCCCGAC 61.839 72.222 0.00 0.00 0.00 4.79
862 1192 3.839432 CGCCTCTTCCTCCCGACC 61.839 72.222 0.00 0.00 0.00 4.79
863 1193 2.364448 GCCTCTTCCTCCCGACCT 60.364 66.667 0.00 0.00 0.00 3.85
864 1194 1.990614 GCCTCTTCCTCCCGACCTT 60.991 63.158 0.00 0.00 0.00 3.50
865 1195 1.962321 GCCTCTTCCTCCCGACCTTC 61.962 65.000 0.00 0.00 0.00 3.46
866 1196 1.331399 CCTCTTCCTCCCGACCTTCC 61.331 65.000 0.00 0.00 0.00 3.46
867 1197 0.324830 CTCTTCCTCCCGACCTTCCT 60.325 60.000 0.00 0.00 0.00 3.36
868 1198 0.324460 TCTTCCTCCCGACCTTCCTC 60.324 60.000 0.00 0.00 0.00 3.71
869 1199 1.305887 TTCCTCCCGACCTTCCTCC 60.306 63.158 0.00 0.00 0.00 4.30
870 1200 2.764547 CCTCCCGACCTTCCTCCC 60.765 72.222 0.00 0.00 0.00 4.30
1459 1805 2.358322 TCCTGCCTTCCTTCGTTTTT 57.642 45.000 0.00 0.00 0.00 1.94
1476 1822 1.585297 TTTCCTTCCGTTGACCGAAC 58.415 50.000 0.00 0.00 39.56 3.95
1499 1845 0.107268 TGAGTTGCTTGCTGCTCTGA 59.893 50.000 0.00 0.00 43.37 3.27
1500 1846 1.271217 TGAGTTGCTTGCTGCTCTGAT 60.271 47.619 0.00 0.00 43.37 2.90
1503 1849 1.538512 GTTGCTTGCTGCTCTGATTGA 59.461 47.619 0.00 0.00 43.37 2.57
1504 1850 2.124277 TGCTTGCTGCTCTGATTGAT 57.876 45.000 0.00 0.00 43.37 2.57
1505 1851 2.443416 TGCTTGCTGCTCTGATTGATT 58.557 42.857 0.00 0.00 43.37 2.57
1506 1852 2.823747 TGCTTGCTGCTCTGATTGATTT 59.176 40.909 0.00 0.00 43.37 2.17
1515 1861 7.704899 TGCTGCTCTGATTGATTTGATTAATTG 59.295 33.333 0.00 0.00 0.00 2.32
1584 1942 6.014012 TGATCCGTGTAATGGTCCTATGATA 58.986 40.000 0.00 0.00 45.66 2.15
1585 1943 5.717078 TCCGTGTAATGGTCCTATGATAC 57.283 43.478 0.00 0.00 45.66 2.24
1586 1944 5.391256 TCCGTGTAATGGTCCTATGATACT 58.609 41.667 0.00 0.00 45.66 2.12
1660 2020 3.118956 GGTACTGGTCTGAGTGGAATCAG 60.119 52.174 0.00 0.00 46.70 2.90
1684 2044 3.456280 GAGCTTCTTACCTGCTCTCATG 58.544 50.000 6.92 0.00 46.69 3.07
1691 2051 1.198713 ACCTGCTCTCATGGTACTGG 58.801 55.000 0.00 0.00 31.50 4.00
1701 2061 1.066143 CATGGTACTGGGGTGTGAGTC 60.066 57.143 0.00 0.00 0.00 3.36
1702 2062 1.183030 TGGTACTGGGGTGTGAGTCG 61.183 60.000 0.00 0.00 0.00 4.18
1728 2088 4.284550 AGCTCCCTTTTGCGGCCA 62.285 61.111 2.24 0.00 0.00 5.36
1733 2093 2.262292 CCTTTTGCGGCCATGTGG 59.738 61.111 2.24 0.00 38.53 4.17
1781 2141 3.058983 TGCAATGAACTTTAGTGTCTGCG 60.059 43.478 0.00 0.00 0.00 5.18
2134 3897 4.444733 CCCGATTTATTACCCTAAACCCGT 60.445 45.833 0.00 0.00 0.00 5.28
2772 7852 0.618680 CCATGGTGACTGAGGAGGGA 60.619 60.000 2.57 0.00 0.00 4.20
2776 7856 0.325671 GGTGACTGAGGAGGGATCCA 60.326 60.000 15.23 0.00 0.00 3.41
2851 7931 1.596934 GCGTTGGTGGATCTGGAGA 59.403 57.895 0.00 0.00 0.00 3.71
3126 8209 0.108804 CGCTTCCCGTGTACACTGAT 60.109 55.000 23.01 0.00 0.00 2.90
3294 8377 1.648467 GGTTCGTGCATCCAGCCTTC 61.648 60.000 0.00 0.00 44.83 3.46
3317 8623 2.698855 TTATTGTCTGCAGAGGAGCC 57.301 50.000 18.89 5.39 0.00 4.70
3405 8728 2.601240 TGATTGATTGGGTTGCCTCA 57.399 45.000 0.00 0.00 0.00 3.86
3448 8771 1.756538 TGACTGGCGATTCTGCTGATA 59.243 47.619 0.00 0.00 34.52 2.15
3452 8775 1.221414 GGCGATTCTGCTGATACACC 58.779 55.000 0.00 0.00 34.52 4.16
3471 8797 1.506262 CGTGTAGTTGCAATGCCCC 59.494 57.895 0.59 0.00 0.00 5.80
3549 8875 0.530744 TGGAGACTGGATGCGTGTAC 59.469 55.000 0.00 0.00 0.00 2.90
3632 8958 4.473196 TCAGTGCCTCTATTGGTGGATTAA 59.527 41.667 0.00 0.00 0.00 1.40
3633 8959 4.576463 CAGTGCCTCTATTGGTGGATTAAC 59.424 45.833 0.00 0.00 0.00 2.01
3636 8962 5.758784 GTGCCTCTATTGGTGGATTAACTAC 59.241 44.000 0.00 0.00 0.00 2.73
3637 8963 5.665812 TGCCTCTATTGGTGGATTAACTACT 59.334 40.000 0.00 0.00 0.00 2.57
3638 8964 6.157994 TGCCTCTATTGGTGGATTAACTACTT 59.842 38.462 0.00 0.00 0.00 2.24
3639 8965 7.054751 GCCTCTATTGGTGGATTAACTACTTT 58.945 38.462 0.00 0.00 0.00 2.66
3641 8967 9.765795 CCTCTATTGGTGGATTAACTACTTTAG 57.234 37.037 0.00 0.00 0.00 1.85
3647 8973 8.611654 TGGTGGATTAACTACTTTAGTTTGTC 57.388 34.615 4.00 3.73 46.27 3.18
3649 8975 8.501580 GGTGGATTAACTACTTTAGTTTGTCAC 58.498 37.037 4.00 7.88 46.27 3.67
3650 8976 9.048446 GTGGATTAACTACTTTAGTTTGTCACA 57.952 33.333 4.00 2.56 46.27 3.58
3651 8977 9.787435 TGGATTAACTACTTTAGTTTGTCACAT 57.213 29.630 4.00 0.00 46.27 3.21
3654 8980 9.787435 ATTAACTACTTTAGTTTGTCACATGGA 57.213 29.630 4.00 0.00 46.27 3.41
3655 8981 7.492352 AACTACTTTAGTTTGTCACATGGAC 57.508 36.000 0.00 2.43 46.27 4.02
3656 8982 7.051623 AACTACTTTAGTTTGTCACATGGACA 58.948 34.615 11.56 11.56 46.27 4.02
3663 8989 1.293498 GTCACATGGACAGCTCCGT 59.707 57.895 0.00 0.00 46.19 4.69
3664 8990 0.737715 GTCACATGGACAGCTCCGTC 60.738 60.000 0.00 0.00 46.19 4.79
3665 8991 1.184970 TCACATGGACAGCTCCGTCA 61.185 55.000 6.54 0.00 39.88 4.35
3666 8992 1.016130 CACATGGACAGCTCCGTCAC 61.016 60.000 6.54 0.00 39.88 3.67
3668 8994 0.738762 CATGGACAGCTCCGTCACTG 60.739 60.000 6.54 0.00 39.88 3.66
3670 8996 0.538746 TGGACAGCTCCGTCACTGTA 60.539 55.000 6.54 0.00 46.82 2.74
3671 8997 0.601558 GGACAGCTCCGTCACTGTAA 59.398 55.000 6.54 0.00 46.82 2.41
3674 9000 2.731976 GACAGCTCCGTCACTGTAAAAG 59.268 50.000 0.00 0.00 46.82 2.27
3745 9268 8.729756 TGTCACATGTTACCTTATCATGAAAAG 58.270 33.333 7.68 0.00 40.64 2.27
3784 9307 4.511826 CAGAAACTCAGAACTGTGGTTACC 59.488 45.833 7.07 0.00 34.57 2.85
3792 9315 5.046591 TCAGAACTGTGGTTACCTATGGAAG 60.047 44.000 2.07 0.00 35.58 3.46
3795 9318 5.836024 ACTGTGGTTACCTATGGAAGAAA 57.164 39.130 2.07 0.00 0.00 2.52
3797 9320 5.546499 ACTGTGGTTACCTATGGAAGAAAGA 59.454 40.000 2.07 0.00 0.00 2.52
3818 9341 9.750125 GAAAGATTTTTCAAATGTGTTCTAGGT 57.250 29.630 3.93 0.00 41.86 3.08
4004 9527 2.215196 TGTGGCAAGTAAAACTCGACC 58.785 47.619 0.00 0.00 0.00 4.79
4026 9549 7.169982 CGACCTCCATTTAGTTGAGTGAATATC 59.830 40.741 0.00 0.00 0.00 1.63
4031 9554 9.396022 TCCATTTAGTTGAGTGAATATCTTTCC 57.604 33.333 0.00 0.00 0.00 3.13
4055 9661 6.257193 CCGATATGGAACCTTTTACAGTACAC 59.743 42.308 0.00 0.00 42.00 2.90
4108 9714 9.188588 GTATATCATCAAGCATTTCACATTTGG 57.811 33.333 0.00 0.00 0.00 3.28
4228 9836 7.102993 ACACCTTTTGGGCAATAATTATTCAC 58.897 34.615 7.76 5.55 46.08 3.18
4254 9862 3.634910 TCTGTGTTAAAGCTTTCAACCCC 59.365 43.478 16.57 11.41 0.00 4.95
4258 9866 3.700038 TGTTAAAGCTTTCAACCCCGAAA 59.300 39.130 16.57 0.00 33.89 3.46
4262 9870 3.865700 CTTTCAACCCCGAAAGCAC 57.134 52.632 0.86 0.00 43.84 4.40
4263 9871 1.028905 CTTTCAACCCCGAAAGCACA 58.971 50.000 0.86 0.00 43.84 4.57
4264 9872 1.613437 CTTTCAACCCCGAAAGCACAT 59.387 47.619 0.86 0.00 43.84 3.21
4265 9873 0.958091 TTCAACCCCGAAAGCACATG 59.042 50.000 0.00 0.00 0.00 3.21
4266 9874 0.109532 TCAACCCCGAAAGCACATGA 59.890 50.000 0.00 0.00 0.00 3.07
4267 9875 0.240945 CAACCCCGAAAGCACATGAC 59.759 55.000 0.00 0.00 0.00 3.06
4268 9876 0.893727 AACCCCGAAAGCACATGACC 60.894 55.000 0.00 0.00 0.00 4.02
4271 9879 0.606401 CCCGAAAGCACATGACCAGT 60.606 55.000 0.00 0.00 0.00 4.00
4284 9892 5.356882 CATGACCAGTACATGTTCGTTTT 57.643 39.130 2.30 0.00 39.84 2.43
4296 9904 2.287308 TGTTCGTTTTGGCATGTGCTAC 60.287 45.455 4.84 0.00 41.70 3.58
4325 9935 9.817809 GTCATTAGAAGTAGTCCACATATTTCA 57.182 33.333 0.00 0.00 0.00 2.69
4359 9969 6.238648 CCGTTCTTGTGAAATTCCAAAGTAGT 60.239 38.462 5.16 0.00 33.52 2.73
4364 9974 8.567948 TCTTGTGAAATTCCAAAGTAGTTGATC 58.432 33.333 5.16 0.00 39.87 2.92
4365 9975 7.815840 TGTGAAATTCCAAAGTAGTTGATCA 57.184 32.000 0.00 0.00 39.87 2.92
4402 10023 7.149569 TCATTTCTGTGGCTGAATAAGAAAG 57.850 36.000 0.00 0.00 39.48 2.62
4475 10097 7.984617 TGCATTTAAATATTTTAGGGGAAGTGC 59.015 33.333 5.91 11.65 0.00 4.40
4511 10133 0.399233 GGATACTGCCTCCTCCAGGT 60.399 60.000 0.00 0.00 45.61 4.00
4552 10174 6.725369 ACTGATCTATGCTATGACCTGATTCT 59.275 38.462 0.00 0.00 0.00 2.40
4553 10175 7.235193 ACTGATCTATGCTATGACCTGATTCTT 59.765 37.037 0.00 0.00 0.00 2.52
4629 10251 4.471344 GGAGCATCTCAAGGAACTTCGTG 61.471 52.174 0.00 0.00 41.31 4.35
4722 10344 2.124570 AGGCGGCGATCAAGCATT 60.125 55.556 12.98 0.00 39.27 3.56
4758 10380 1.260538 TGAACGGAGAGGCATCAGCT 61.261 55.000 0.00 0.00 41.70 4.24
5053 10675 3.792736 GGTGATGGGCCCGTGCTA 61.793 66.667 25.05 0.00 37.74 3.49
5191 10815 6.990341 AACGATAAACCCTTGTACATTACC 57.010 37.500 0.00 0.00 0.00 2.85
5211 10835 1.305201 GATGGTGTTGTGGACGTTGT 58.695 50.000 0.00 0.00 0.00 3.32
5230 10854 7.204604 ACGTTGTGGATTATATGTAATCGTGA 58.795 34.615 13.99 1.15 44.65 4.35
5269 10900 2.165301 CGATGTTCGCCTTCGGGTC 61.165 63.158 3.38 0.00 37.15 4.46
5312 10943 6.700081 GTGTGTTTCTGTTAGTGATCTGTGTA 59.300 38.462 0.00 0.00 0.00 2.90
5450 11135 9.933723 CAAAGATTTGTCCAGGAAAATTTATCT 57.066 29.630 0.00 0.00 33.59 1.98
5548 11236 6.867662 AGCTGTACTGATTTAATATGCACC 57.132 37.500 3.61 0.00 0.00 5.01
5651 11398 4.024556 CCTTGCGCAATTAATCACTAGAGG 60.025 45.833 25.26 12.50 0.00 3.69
5718 11466 0.882042 GAGCGTGTATGGCCTCATGG 60.882 60.000 3.32 0.00 34.96 3.66
5819 11601 1.378911 GCCACATGTCATGAGGGCA 60.379 57.895 30.83 2.82 46.14 5.36
5883 11665 4.386951 CACATGTCACGGGGGCGA 62.387 66.667 0.00 0.00 0.00 5.54
5953 11735 3.731728 TCATGGGACCTGGGCTGC 61.732 66.667 0.00 0.00 0.00 5.25
6001 11783 0.846015 TGGGCTTATCATGAGTGGGG 59.154 55.000 0.09 0.00 0.00 4.96
6005 11787 1.490490 GCTTATCATGAGTGGGGTCCA 59.510 52.381 0.09 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.558554 AAAGACCCGCTCGATGACCG 62.559 60.000 0.00 0.00 40.25 4.79
104 106 5.686841 CGATTTCTGTCTCATGAGCTTAGAG 59.313 44.000 18.36 9.08 0.00 2.43
112 114 3.954258 TCTAGCCGATTTCTGTCTCATGA 59.046 43.478 0.00 0.00 0.00 3.07
113 115 4.047822 GTCTAGCCGATTTCTGTCTCATG 58.952 47.826 0.00 0.00 0.00 3.07
124 126 0.098376 GTCGTGTCGTCTAGCCGATT 59.902 55.000 0.00 0.00 39.34 3.34
142 144 0.811616 GCCGCAATCAGAGAATCCGT 60.812 55.000 0.00 0.00 33.66 4.69
168 170 1.743958 CTAGGAGGCGAAGAAAGTCGA 59.256 52.381 0.00 0.00 43.86 4.20
371 603 1.321445 CGAGTATGTGTGCATGTGTCG 59.679 52.381 0.00 0.00 36.58 4.35
391 623 8.438513 GTTTTAGAAAAGGGTGATTACTACGTC 58.561 37.037 0.00 0.00 0.00 4.34
399 631 4.732065 TCCGGTTTTAGAAAAGGGTGATT 58.268 39.130 0.00 0.00 0.00 2.57
401 633 3.860968 TCCGGTTTTAGAAAAGGGTGA 57.139 42.857 0.00 0.00 0.00 4.02
403 635 5.141910 TCATTTCCGGTTTTAGAAAAGGGT 58.858 37.500 0.00 0.00 35.72 4.34
404 636 5.715434 TCATTTCCGGTTTTAGAAAAGGG 57.285 39.130 0.00 0.00 35.72 3.95
405 637 9.869757 ATAAATCATTTCCGGTTTTAGAAAAGG 57.130 29.630 0.00 0.00 35.72 3.11
601 839 3.157949 GCGGGGAGGAGGAAGGAG 61.158 72.222 0.00 0.00 0.00 3.69
870 1200 2.909292 ATAAGGAGTGGGGGACGGGG 62.909 65.000 0.00 0.00 0.00 5.73
974 1314 4.452733 GCGGACCTGTTCCCCGAG 62.453 72.222 0.00 0.00 45.58 4.63
1125 1471 4.369591 TCCCACATGGCCTCCCCT 62.370 66.667 3.32 0.00 0.00 4.79
1439 1785 2.358322 AAAACGAAGGAAGGCAGGAA 57.642 45.000 0.00 0.00 0.00 3.36
1459 1805 0.464870 TTGTTCGGTCAACGGAAGGA 59.535 50.000 3.67 0.00 44.45 3.36
1506 1852 9.589111 CAATCAATCAATCACACCAATTAATCA 57.411 29.630 0.00 0.00 0.00 2.57
1515 1861 4.707030 TCAGCAATCAATCAATCACACC 57.293 40.909 0.00 0.00 0.00 4.16
1584 1942 2.694397 TCCAGCATGCTCCCTAATAGT 58.306 47.619 19.68 0.00 31.97 2.12
1585 1943 3.777106 TTCCAGCATGCTCCCTAATAG 57.223 47.619 19.68 3.58 31.97 1.73
1586 1944 4.352001 AGATTTCCAGCATGCTCCCTAATA 59.648 41.667 19.68 0.00 31.97 0.98
1684 2044 0.896940 TCGACTCACACCCCAGTACC 60.897 60.000 0.00 0.00 0.00 3.34
1691 2051 2.356382 CTCTACTGATCGACTCACACCC 59.644 54.545 0.00 0.00 0.00 4.61
1701 2061 3.452474 CAAAAGGGAGCTCTACTGATCG 58.548 50.000 14.64 0.00 0.00 3.69
1702 2062 3.202097 GCAAAAGGGAGCTCTACTGATC 58.798 50.000 14.64 0.00 0.00 2.92
1728 2088 4.653801 GCCCTAATTTCCAAATACCCACAT 59.346 41.667 0.00 0.00 0.00 3.21
1733 2093 5.775195 AGCATAGCCCTAATTTCCAAATACC 59.225 40.000 0.00 0.00 0.00 2.73
1781 2141 0.665369 AAATGTGCTCGCTTTGCTGC 60.665 50.000 0.00 0.00 0.00 5.25
2114 3877 6.290605 TGCTACGGGTTTAGGGTAATAAATC 58.709 40.000 0.00 0.00 0.00 2.17
2134 3897 1.645402 GGAGGGGGCTGGAATTGCTA 61.645 60.000 0.00 0.00 0.00 3.49
2722 7800 2.656069 CCGGCCCCGAAGAAGAGAA 61.656 63.158 8.54 0.00 42.83 2.87
2772 7852 3.081409 CCGGACCCGAACCTGGAT 61.081 66.667 10.42 0.00 42.83 3.41
2831 7911 2.819595 CCAGATCCACCAACGCCG 60.820 66.667 0.00 0.00 0.00 6.46
2851 7931 4.335647 CCACACAGCCTCGCCCTT 62.336 66.667 0.00 0.00 0.00 3.95
2934 8017 0.250901 ACGCTTTGTTCTGCTCCCAT 60.251 50.000 0.00 0.00 0.00 4.00
2964 8047 2.045926 AGATCCACCAACGCCAGC 60.046 61.111 0.00 0.00 0.00 4.85
3126 8209 3.965026 CTCCTCAGGACTCCCGCCA 62.965 68.421 0.00 0.00 37.58 5.69
3213 8296 0.039437 GCTCGACAGACTTGGACGAA 60.039 55.000 0.00 0.00 37.02 3.85
3294 8377 3.181516 GCTCCTCTGCAGACAATAAAACG 60.182 47.826 13.74 0.00 0.00 3.60
3317 8623 1.901591 AGTGGAGGAAACATGTGCTG 58.098 50.000 0.00 0.00 0.00 4.41
3342 8648 8.680903 CAAAATTGCTCTATGAACAGATAAGGT 58.319 33.333 0.00 0.00 0.00 3.50
3344 8650 9.932699 CTCAAAATTGCTCTATGAACAGATAAG 57.067 33.333 0.00 0.00 0.00 1.73
3448 8771 1.234821 CATTGCAACTACACGGGTGT 58.765 50.000 0.00 9.66 46.87 4.16
3452 8775 1.506262 GGGCATTGCAACTACACGG 59.494 57.895 11.39 0.00 0.00 4.94
3463 8786 0.038343 CCAAAACACTCGGGGCATTG 60.038 55.000 0.00 0.00 0.00 2.82
3471 8797 4.610945 AGAGCAAATTTCCAAAACACTCG 58.389 39.130 0.00 0.00 0.00 4.18
3645 8971 0.737715 GACGGAGCTGTCCATGTGAC 60.738 60.000 0.00 7.22 44.18 3.67
3647 8973 1.016130 GTGACGGAGCTGTCCATGTG 61.016 60.000 6.97 0.00 44.18 3.21
3649 8975 0.738762 CAGTGACGGAGCTGTCCATG 60.739 60.000 6.97 2.55 44.18 3.66
3650 8976 1.188219 ACAGTGACGGAGCTGTCCAT 61.188 55.000 6.97 0.00 44.18 3.41
3651 8977 0.538746 TACAGTGACGGAGCTGTCCA 60.539 55.000 10.46 0.00 44.18 4.02
3652 8978 0.601558 TTACAGTGACGGAGCTGTCC 59.398 55.000 10.46 0.00 43.91 4.02
3653 8979 2.433868 TTTACAGTGACGGAGCTGTC 57.566 50.000 10.46 2.51 43.91 3.51
3654 8980 2.548067 CCTTTTACAGTGACGGAGCTGT 60.548 50.000 0.00 11.56 46.33 4.40
3655 8981 2.069273 CCTTTTACAGTGACGGAGCTG 58.931 52.381 0.00 0.00 38.58 4.24
3656 8982 1.968493 TCCTTTTACAGTGACGGAGCT 59.032 47.619 0.00 0.00 0.00 4.09
3657 8983 2.450609 TCCTTTTACAGTGACGGAGC 57.549 50.000 0.00 0.00 0.00 4.70
3658 8984 4.152402 CACAATCCTTTTACAGTGACGGAG 59.848 45.833 0.00 0.00 0.00 4.63
3659 8985 4.062293 CACAATCCTTTTACAGTGACGGA 58.938 43.478 0.00 0.00 0.00 4.69
3660 8986 3.813166 ACACAATCCTTTTACAGTGACGG 59.187 43.478 0.00 0.00 0.00 4.79
3661 8987 6.147164 ACATACACAATCCTTTTACAGTGACG 59.853 38.462 0.00 0.00 0.00 4.35
3663 8989 7.936847 AGAACATACACAATCCTTTTACAGTGA 59.063 33.333 0.00 0.00 0.00 3.41
3664 8990 8.017373 CAGAACATACACAATCCTTTTACAGTG 58.983 37.037 0.00 0.00 0.00 3.66
3665 8991 7.936847 TCAGAACATACACAATCCTTTTACAGT 59.063 33.333 0.00 0.00 0.00 3.55
3666 8992 8.230486 GTCAGAACATACACAATCCTTTTACAG 58.770 37.037 0.00 0.00 0.00 2.74
3668 8994 8.094798 TGTCAGAACATACACAATCCTTTTAC 57.905 34.615 0.00 0.00 0.00 2.01
3670 8996 7.765695 ATGTCAGAACATACACAATCCTTTT 57.234 32.000 0.00 0.00 44.38 2.27
3671 8997 7.765695 AATGTCAGAACATACACAATCCTTT 57.234 32.000 0.00 0.00 45.48 3.11
3674 9000 7.370383 ACAAAATGTCAGAACATACACAATCC 58.630 34.615 0.00 0.00 45.48 3.01
3745 9268 7.148641 TGAGTTTCTGACATCTGAGTAAAGAC 58.851 38.462 0.00 0.00 0.00 3.01
3792 9315 9.750125 ACCTAGAACACATTTGAAAAATCTTTC 57.250 29.630 0.00 0.00 41.25 2.62
3795 9318 9.574516 AGTACCTAGAACACATTTGAAAAATCT 57.425 29.630 0.00 0.00 0.00 2.40
3844 9367 4.317530 AATAGTCCAAAGGGTTCCTTCC 57.682 45.455 0.00 0.00 43.92 3.46
3979 9502 5.849604 GTCGAGTTTTACTTGCCACAATAAC 59.150 40.000 0.00 0.00 29.55 1.89
4031 9554 7.039882 AGTGTACTGTAAAAGGTTCCATATCG 58.960 38.462 0.00 0.00 0.00 2.92
4085 9691 7.172868 ACCAAATGTGAAATGCTTGATGATA 57.827 32.000 0.00 0.00 0.00 2.15
4108 9714 3.009723 ACACCATTACATAGTGCTGCAC 58.990 45.455 24.59 24.59 34.83 4.57
4111 9717 6.341316 AGAAGTACACCATTACATAGTGCTG 58.659 40.000 0.00 0.00 34.83 4.41
4203 9809 7.038373 AGTGAATAATTATTGCCCAAAAGGTGT 60.038 33.333 15.39 0.00 38.26 4.16
4228 9836 5.743872 GGTTGAAAGCTTTAACACAGAACAG 59.256 40.000 12.68 0.00 0.00 3.16
4254 9862 2.412870 TGTACTGGTCATGTGCTTTCG 58.587 47.619 0.00 0.00 0.00 3.46
4262 9870 5.146460 CAAAACGAACATGTACTGGTCATG 58.854 41.667 0.00 10.98 42.09 3.07
4263 9871 4.215399 CCAAAACGAACATGTACTGGTCAT 59.785 41.667 0.00 0.00 42.09 3.06
4264 9872 3.562141 CCAAAACGAACATGTACTGGTCA 59.438 43.478 0.00 0.00 42.09 4.02
4265 9873 3.608474 GCCAAAACGAACATGTACTGGTC 60.608 47.826 0.00 0.00 38.29 4.02
4266 9874 2.292292 GCCAAAACGAACATGTACTGGT 59.708 45.455 0.00 0.00 0.00 4.00
4267 9875 2.292016 TGCCAAAACGAACATGTACTGG 59.708 45.455 0.00 1.27 0.00 4.00
4268 9876 3.617540 TGCCAAAACGAACATGTACTG 57.382 42.857 0.00 0.00 0.00 2.74
4296 9904 9.770097 AATATGTGGACTACTTCTAATGACATG 57.230 33.333 0.00 0.00 0.00 3.21
4325 9935 2.571212 TCACAAGAACGGCAAATGACT 58.429 42.857 0.00 0.00 0.00 3.41
4365 9975 4.276678 CACAGAAATGATCACAACCACTGT 59.723 41.667 0.00 5.84 39.56 3.55
4385 10006 8.579850 AACATTATCTTTCTTATTCAGCCACA 57.420 30.769 0.00 0.00 0.00 4.17
4464 10085 0.251165 GCAACCAAGCACTTCCCCTA 60.251 55.000 0.00 0.00 0.00 3.53
4475 10097 3.947910 ATCCATCAGTTTGCAACCAAG 57.052 42.857 0.00 0.00 31.52 3.61
4629 10251 0.179097 GAGTGGGCGTCCTTGAGATC 60.179 60.000 7.97 0.00 0.00 2.75
4665 10287 1.482593 AGGCGGATGAAGTACTTCTGG 59.517 52.381 30.47 19.23 40.14 3.86
4722 10344 3.047735 ACGCTGGTGATGTCGTGA 58.952 55.556 0.00 0.00 33.59 4.35
4758 10380 2.356278 GTGATTGGGCCCTGAGCA 59.644 61.111 25.70 17.91 46.50 4.26
4803 10425 2.384933 ATTGCTTGGGGGACTTGCCA 62.385 55.000 0.00 0.00 38.95 4.92
4944 10566 1.071471 GTATCCCATGTGAGGCGGG 59.929 63.158 0.00 0.00 41.76 6.13
5001 10623 1.006102 CATCGGGTACATCGGAGCC 60.006 63.158 7.77 0.00 0.00 4.70
5044 10666 1.326548 CGTCTATTTTGTAGCACGGGC 59.673 52.381 0.00 0.00 41.61 6.13
5053 10675 5.910637 TCGCTTAACAACGTCTATTTTGT 57.089 34.783 0.00 0.00 37.55 2.83
5178 10802 3.869065 ACACCATCGGTAATGTACAAGG 58.131 45.455 0.00 0.00 32.11 3.61
5191 10815 0.234625 CAACGTCCACAACACCATCG 59.765 55.000 0.00 0.00 0.00 3.84
5269 10900 1.054406 ACCCAGTATCCATCCACCCG 61.054 60.000 0.00 0.00 0.00 5.28
5272 10903 1.559682 ACACACCCAGTATCCATCCAC 59.440 52.381 0.00 0.00 0.00 4.02
5312 10943 1.304713 CTTCCCCTGTGCCTGCATT 60.305 57.895 0.00 0.00 0.00 3.56
5386 11047 7.129457 ACACAGATACACCACAGATGATAAT 57.871 36.000 0.00 0.00 0.00 1.28
5387 11048 6.544928 ACACAGATACACCACAGATGATAA 57.455 37.500 0.00 0.00 0.00 1.75
5388 11049 7.123547 TGTTACACAGATACACCACAGATGATA 59.876 37.037 0.00 0.00 0.00 2.15
5389 11050 6.070824 TGTTACACAGATACACCACAGATGAT 60.071 38.462 0.00 0.00 0.00 2.45
5390 11051 5.245075 TGTTACACAGATACACCACAGATGA 59.755 40.000 0.00 0.00 0.00 2.92
5391 11052 5.478407 TGTTACACAGATACACCACAGATG 58.522 41.667 0.00 0.00 0.00 2.90
5442 11127 8.648557 TCGAAATGAGAACATCGAGATAAATT 57.351 30.769 0.00 0.00 35.50 1.82
5447 11132 5.957910 GTTCGAAATGAGAACATCGAGAT 57.042 39.130 0.00 0.00 45.21 2.75
5548 11236 4.718858 TGTCCGTTTTCACTTTATCGTG 57.281 40.909 0.00 0.00 36.25 4.35
5651 11398 1.477105 GTCAAGCTTTGGCGTTCAAC 58.523 50.000 0.00 0.00 44.37 3.18
5825 11607 3.936203 GACACCTGTCCACCGCCA 61.936 66.667 0.00 0.00 39.07 5.69
5932 11714 2.606587 GCCCAGGTCCCATGACACT 61.607 63.158 0.00 0.00 43.65 3.55
5953 11735 3.041940 GCGTGACAAGTGTCCCCG 61.042 66.667 8.91 11.46 44.15 5.73
6001 11783 0.730265 TCGTTTGTTGTGCTGTGGAC 59.270 50.000 0.00 0.00 0.00 4.02
6005 11787 0.732571 CACCTCGTTTGTTGTGCTGT 59.267 50.000 0.00 0.00 0.00 4.40
6007 11789 1.014352 GTCACCTCGTTTGTTGTGCT 58.986 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.