Multiple sequence alignment - TraesCS7D01G355000

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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 TraesCS7D01G355000 chr7D 100.000 4213 0 0 1 4213 459082458 459078246 0.000000e+00 7781
1 TraesCS7D01G355000 chr7B 94.031 1843 79 13 1684 3515 481070555 481068733 0.000000e+00 2765
2 TraesCS7D01G355000 chr7B 88.267 750 49 20 1 734 481072675 481071949 0.000000e+00 861
3 TraesCS7D01G355000 chr7B 94.063 539 28 3 3513 4049 481068620 481068084 0.000000e+00 815
4 TraesCS7D01G355000 chr7B 88.073 654 47 17 796 1429 481071725 481071083 0.000000e+00 747
5 TraesCS7D01G355000 chr7B 86.475 244 19 9 1424 1657 481070927 481070688 5.410000e-64 255
6 TraesCS7D01G355000 chr7A 91.644 1843 121 18 1685 3515 540951613 540953434 0.000000e+00 2519
7 TraesCS7D01G355000 chr7A 87.403 643 61 15 3511 4139 540953497 540954133 0.000000e+00 721
8 TraesCS7D01G355000 chr7A 80.483 953 99 47 704 1599 540950644 540951566 0.000000e+00 649
9 TraesCS7D01G355000 chr7A 83.333 222 12 8 418 617 540950065 540950283 9.300000e-42 182


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 TraesCS7D01G355000 chr7D 459078246 459082458 4212 True 7781.00 7781 100.00000 1 4213 1 chr7D.!!$R1 4212
1 TraesCS7D01G355000 chr7B 481068084 481072675 4591 True 1088.60 2765 90.18180 1 4049 5 chr7B.!!$R1 4048
2 TraesCS7D01G355000 chr7A 540950065 540954133 4068 False 1017.75 2519 85.71575 418 4139 4 chr7A.!!$F1 3721

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
358 377 0.539438 AATCGCTTGCCCTCAAACCA 60.539 50.0 0.00 0.0 0.00 3.67 F
1106 1615 0.836400 AAGTCCAGTGGTCGGTGGAT 60.836 55.0 9.54 0.0 44.71 3.41 F
1521 2229 0.320421 AGTTGGATTGACCCGTCACG 60.320 55.0 0.00 0.0 39.66 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1263 1776 0.033796 ACGGGAGGTAAGATGGTCGA 60.034 55.0 0.00 0.00 0.00 4.20 R
2182 3006 0.036577 CAAGGCTGTCTGACCTCCTG 60.037 60.0 15.65 8.61 34.31 3.86 R
3422 4265 0.036010 ATTCAGAAGCTGGACACGGG 60.036 55.0 0.00 0.00 31.51 5.28 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
172 173 8.984891 ATTTGCGATTGAAACTTTCATGAATA 57.015 26.923 9.40 0.00 39.84 1.75
174 175 8.984891 TTGCGATTGAAACTTTCATGAATATT 57.015 26.923 9.40 3.96 39.84 1.28
175 176 8.984891 TGCGATTGAAACTTTCATGAATATTT 57.015 26.923 9.40 12.38 39.84 1.40
225 243 9.491675 AATATTCACAGATTTGATTGTTTTGCA 57.508 25.926 0.00 0.00 0.00 4.08
344 363 4.086199 TGAAACACCCGAATAAAATCGC 57.914 40.909 0.00 0.00 41.40 4.58
345 364 3.754323 TGAAACACCCGAATAAAATCGCT 59.246 39.130 0.00 0.00 41.40 4.93
358 377 0.539438 AATCGCTTGCCCTCAAACCA 60.539 50.000 0.00 0.00 0.00 3.67
373 392 5.224562 TCAAACCAGAAACACAAACTACG 57.775 39.130 0.00 0.00 0.00 3.51
378 397 1.260561 AGAAACACAAACTACGCGCTG 59.739 47.619 5.73 0.62 0.00 5.18
398 417 3.542676 CGTACATGGGCCGGGCTA 61.543 66.667 28.80 23.99 0.00 3.93
399 418 2.879233 CGTACATGGGCCGGGCTAT 61.879 63.158 28.80 25.32 0.00 2.97
425 444 2.993899 CGAACGAAGGGATATATGCCAC 59.006 50.000 23.67 15.77 41.29 5.01
448 467 1.732683 GACCGCGCAACAAAATGGG 60.733 57.895 8.75 0.00 36.42 4.00
449 468 2.432285 CCGCGCAACAAAATGGGG 60.432 61.111 8.75 0.00 34.13 4.96
497 521 3.653078 CCCACGGCCCCTTAACCA 61.653 66.667 0.00 0.00 0.00 3.67
880 1356 2.146920 TCCAAAACCGAACCCAAACT 57.853 45.000 0.00 0.00 0.00 2.66
883 1359 2.028876 CAAAACCGAACCCAAACTCCT 58.971 47.619 0.00 0.00 0.00 3.69
884 1360 1.977056 AAACCGAACCCAAACTCCTC 58.023 50.000 0.00 0.00 0.00 3.71
889 1365 1.072143 AACCCAAACTCCTCCCCCT 60.072 57.895 0.00 0.00 0.00 4.79
890 1366 1.140772 AACCCAAACTCCTCCCCCTC 61.141 60.000 0.00 0.00 0.00 4.30
891 1367 1.229984 CCCAAACTCCTCCCCCTCT 60.230 63.158 0.00 0.00 0.00 3.69
981 1485 4.918201 CGATTCCTCGCCTGGGCC 62.918 72.222 5.99 0.00 38.20 5.80
1049 1553 2.168054 GCGGTATGCGGAGTTGTTT 58.832 52.632 0.00 0.00 0.00 2.83
1051 1555 1.465187 GCGGTATGCGGAGTTGTTTTC 60.465 52.381 0.00 0.00 0.00 2.29
1080 1585 3.808174 CCGTCGATTTTCTAGGGGATTTC 59.192 47.826 0.00 0.00 0.00 2.17
1088 1593 1.209621 CTAGGGGATTTCGGGTGGAA 58.790 55.000 0.00 0.00 0.00 3.53
1104 1613 1.004918 GAAGTCCAGTGGTCGGTGG 60.005 63.158 9.54 0.00 34.87 4.61
1105 1614 1.458777 AAGTCCAGTGGTCGGTGGA 60.459 57.895 9.54 0.00 40.72 4.02
1106 1615 0.836400 AAGTCCAGTGGTCGGTGGAT 60.836 55.000 9.54 0.00 44.71 3.41
1107 1616 0.836400 AGTCCAGTGGTCGGTGGATT 60.836 55.000 9.54 0.00 44.71 3.01
1285 1798 1.138464 GACCATCTTACCTCCCGTTCC 59.862 57.143 0.00 0.00 0.00 3.62
1290 1803 3.173953 TCTTACCTCCCGTTCCTGTTA 57.826 47.619 0.00 0.00 0.00 2.41
1403 1931 6.422776 TTTCAATTTCCGAATACTCTCAGC 57.577 37.500 0.00 0.00 0.00 4.26
1412 1940 2.738587 ATACTCTCAGCGAGGAAGGA 57.261 50.000 5.87 0.00 44.33 3.36
1419 1947 1.023513 CAGCGAGGAAGGAAAGCAGG 61.024 60.000 0.00 0.00 0.00 4.85
1502 2210 8.807118 TGGTAAAGCCAATGATTATTTACAACA 58.193 29.630 15.54 7.66 45.94 3.33
1504 2212 9.855021 GTAAAGCCAATGATTATTTACAACAGT 57.145 29.630 11.67 0.00 36.69 3.55
1521 2229 0.320421 AGTTGGATTGACCCGTCACG 60.320 55.000 0.00 0.00 39.66 4.35
1603 2313 4.536489 ACCAGACCTGCCTATTTAAAGACT 59.464 41.667 0.00 0.00 0.00 3.24
1621 2337 3.317280 TGGGACAGTAGCTAAGGGG 57.683 57.895 0.00 0.00 0.00 4.79
1623 2339 1.343075 TGGGACAGTAGCTAAGGGGAG 60.343 57.143 0.00 0.00 0.00 4.30
1625 2341 2.091444 GGGACAGTAGCTAAGGGGAGTA 60.091 54.545 0.00 0.00 0.00 2.59
1626 2342 2.957680 GGACAGTAGCTAAGGGGAGTAC 59.042 54.545 0.00 0.00 0.00 2.73
1627 2343 3.372892 GGACAGTAGCTAAGGGGAGTACT 60.373 52.174 0.00 0.00 0.00 2.73
1628 2344 3.633065 GACAGTAGCTAAGGGGAGTACTG 59.367 52.174 0.00 0.00 44.07 2.74
1637 2353 5.832060 GCTAAGGGGAGTACTGTATGACTTA 59.168 44.000 0.00 0.09 0.00 2.24
1650 2399 7.536855 ACTGTATGACTTAGTACTGCAGTTAC 58.463 38.462 27.06 19.46 31.63 2.50
1651 2400 7.176165 ACTGTATGACTTAGTACTGCAGTTACA 59.824 37.037 27.06 20.72 31.63 2.41
1652 2401 7.888424 TGTATGACTTAGTACTGCAGTTACAA 58.112 34.615 27.06 14.64 0.00 2.41
1659 2408 7.817962 ACTTAGTACTGCAGTTACAAATAGGTG 59.182 37.037 27.06 7.21 0.00 4.00
1665 2414 4.069304 GCAGTTACAAATAGGTGACACCA 58.931 43.478 26.30 12.70 41.95 4.17
1726 2549 2.424956 GGAAGCCCAGCAAGTGAATTAG 59.575 50.000 0.00 0.00 0.00 1.73
1844 2668 2.252714 GGGAAAACAATAGGCCACCAA 58.747 47.619 5.01 0.00 0.00 3.67
1874 2698 1.195448 GATGCCCAGATTATTGCGTCG 59.805 52.381 0.00 0.00 30.92 5.12
1886 2710 2.873170 TTGCGTCGAAACTAAGCATG 57.127 45.000 0.00 0.00 37.68 4.06
2065 2889 1.134848 AGCTGTGCTCTCGATCTTTCC 60.135 52.381 0.00 0.00 30.62 3.13
2182 3006 2.047179 GTGTCAGGGGTTCGCTCC 60.047 66.667 0.00 0.00 38.31 4.70
2402 3226 9.053840 ACATCAATTGATCATCTGTGATTAGTC 57.946 33.333 18.16 0.00 44.96 2.59
2406 3230 9.205719 CAATTGATCATCTGTGATTAGTCTAGG 57.794 37.037 0.00 0.00 44.96 3.02
2424 3248 5.527582 GTCTAGGCTGTTCAGTTTCTTTCAA 59.472 40.000 0.00 0.00 0.00 2.69
2431 3255 7.327032 GGCTGTTCAGTTTCTTTCAATGAATAC 59.673 37.037 0.00 0.00 32.93 1.89
2432 3256 8.078596 GCTGTTCAGTTTCTTTCAATGAATACT 58.921 33.333 0.00 0.00 32.93 2.12
2487 3311 7.155442 TCTGGATAGGATGAGAGAAGAACTA 57.845 40.000 0.00 0.00 0.00 2.24
2566 3390 9.163894 AGGAGATTCTTCAGGTTTATGATATCA 57.836 33.333 8.10 8.10 0.00 2.15
2609 3433 2.852449 AGATCTCTCTGGACTCCTCACT 59.148 50.000 0.00 0.00 0.00 3.41
2641 3465 1.155042 GTCTGACAAGGCTGCTCTTG 58.845 55.000 21.45 21.45 46.86 3.02
2825 3649 3.297830 AGAAGTTGCCAAAAATACCGC 57.702 42.857 0.00 0.00 0.00 5.68
2888 3712 2.683211 AATGGAGGCAGTGAGGTTTT 57.317 45.000 0.00 0.00 0.00 2.43
2898 3722 0.030235 GTGAGGTTTTGCCGGTTGAC 59.970 55.000 1.90 0.00 43.70 3.18
3077 3915 3.618690 ATGGACTGTCTTCTAGCAACC 57.381 47.619 7.85 0.00 0.00 3.77
3083 3921 2.490115 CTGTCTTCTAGCAACCGAGAGT 59.510 50.000 0.00 0.00 0.00 3.24
3090 3928 3.937706 TCTAGCAACCGAGAGTACACTAC 59.062 47.826 0.00 0.00 0.00 2.73
3093 3931 4.267536 AGCAACCGAGAGTACACTACATA 58.732 43.478 0.00 0.00 0.00 2.29
3295 4137 1.487482 GTGCTTGTTTTCTTTCGCCC 58.513 50.000 0.00 0.00 0.00 6.13
3355 4197 1.200020 AGCCGCAACATGTCTTTAAGC 59.800 47.619 0.00 0.00 0.00 3.09
3422 4265 2.849880 TGTCAAGTCAGTTTGCTTGC 57.150 45.000 0.00 0.00 41.15 4.01
3550 4515 6.038271 ACAACGGCCATGTTATAATTCTTCTC 59.962 38.462 2.24 0.00 0.00 2.87
3551 4516 5.680619 ACGGCCATGTTATAATTCTTCTCA 58.319 37.500 2.24 0.00 0.00 3.27
3604 4570 5.178061 TCAATTCTATTCACGTGTCTGCAT 58.822 37.500 16.51 4.09 0.00 3.96
3701 4673 4.536765 TCTATCACAGTATCCAGAGCACA 58.463 43.478 0.00 0.00 0.00 4.57
3705 4677 1.480137 ACAGTATCCAGAGCACAGAGC 59.520 52.381 0.00 0.00 46.19 4.09
3732 4705 6.587226 CACATGGATGTTGGTTTGATTAACTG 59.413 38.462 0.00 0.00 39.39 3.16
3825 4799 7.122353 AGTTGCTTTTATCATCTGCATCTCTTT 59.878 33.333 0.00 0.00 30.78 2.52
3851 4826 6.536582 GCTTGTCTGCATTCTCTGTTCTATAA 59.463 38.462 0.00 0.00 0.00 0.98
3934 4909 3.057104 TGCTGAAAAGATGCCATCACTTG 60.057 43.478 7.56 0.00 0.00 3.16
3985 4960 3.367292 GCCAATTGGTTGTAGTGTCATGG 60.367 47.826 25.19 0.00 37.57 3.66
3989 4965 1.024579 GGTTGTAGTGTCATGGCCGG 61.025 60.000 0.00 0.00 0.00 6.13
3994 4970 1.043116 TAGTGTCATGGCCGGAGAGG 61.043 60.000 5.05 0.00 44.97 3.69
4027 5003 5.008217 CGTGGTAGAGAATAGACTTCTGGAG 59.992 48.000 0.00 0.00 0.00 3.86
4037 5013 3.100671 AGACTTCTGGAGGGTACATGAC 58.899 50.000 0.00 0.00 0.00 3.06
4056 5032 6.156949 ACATGACAGGAACACATAAGGTAGAT 59.843 38.462 0.00 0.00 0.00 1.98
4057 5033 6.620877 TGACAGGAACACATAAGGTAGATT 57.379 37.500 0.00 0.00 0.00 2.40
4061 5037 8.147244 ACAGGAACACATAAGGTAGATTACTT 57.853 34.615 0.00 0.00 0.00 2.24
4063 5039 9.751542 CAGGAACACATAAGGTAGATTACTTAG 57.248 37.037 0.00 0.00 33.16 2.18
4108 5085 7.406799 AAAAACACTAAATATGTTGTGCAGC 57.593 32.000 7.31 0.00 40.16 5.25
4109 5086 5.964958 AACACTAAATATGTTGTGCAGCT 57.035 34.783 7.31 0.00 38.84 4.24
4112 5089 3.696051 ACTAAATATGTTGTGCAGCTGGG 59.304 43.478 17.12 0.00 0.00 4.45
4113 5090 0.819582 AATATGTTGTGCAGCTGGGC 59.180 50.000 17.12 1.74 0.00 5.36
4114 5091 1.378882 ATATGTTGTGCAGCTGGGCG 61.379 55.000 17.12 0.00 36.28 6.13
4134 5111 1.435515 GTGCGCACCTGGTTTTGAA 59.564 52.632 30.12 0.00 0.00 2.69
4139 5116 3.006323 TGCGCACCTGGTTTTGAAATAAT 59.994 39.130 5.66 0.00 0.00 1.28
4140 5117 3.612423 GCGCACCTGGTTTTGAAATAATC 59.388 43.478 0.30 0.00 0.00 1.75
4141 5118 3.851403 CGCACCTGGTTTTGAAATAATCG 59.149 43.478 0.00 0.00 0.00 3.34
4142 5119 4.378978 CGCACCTGGTTTTGAAATAATCGA 60.379 41.667 0.00 0.00 0.00 3.59
4143 5120 5.650543 GCACCTGGTTTTGAAATAATCGAT 58.349 37.500 0.00 0.00 0.00 3.59
4144 5121 6.457663 CGCACCTGGTTTTGAAATAATCGATA 60.458 38.462 0.00 0.00 0.00 2.92
4145 5122 7.425606 GCACCTGGTTTTGAAATAATCGATAT 58.574 34.615 0.00 0.00 0.00 1.63
4146 5123 7.379529 GCACCTGGTTTTGAAATAATCGATATG 59.620 37.037 0.00 0.00 0.00 1.78
4147 5124 8.405531 CACCTGGTTTTGAAATAATCGATATGT 58.594 33.333 0.00 0.00 0.00 2.29
4148 5125 8.405531 ACCTGGTTTTGAAATAATCGATATGTG 58.594 33.333 0.00 0.00 0.00 3.21
4149 5126 7.379529 CCTGGTTTTGAAATAATCGATATGTGC 59.620 37.037 0.00 0.00 0.00 4.57
4150 5127 7.766283 TGGTTTTGAAATAATCGATATGTGCA 58.234 30.769 0.00 0.00 0.00 4.57
4151 5128 8.412456 TGGTTTTGAAATAATCGATATGTGCAT 58.588 29.630 0.00 0.00 0.00 3.96
4152 5129 8.693504 GGTTTTGAAATAATCGATATGTGCATG 58.306 33.333 0.00 0.00 0.00 4.06
4153 5130 9.236691 GTTTTGAAATAATCGATATGTGCATGT 57.763 29.630 0.00 0.00 0.00 3.21
4154 5131 8.785468 TTTGAAATAATCGATATGTGCATGTG 57.215 30.769 0.00 0.00 0.00 3.21
4155 5132 7.495135 TGAAATAATCGATATGTGCATGTGT 57.505 32.000 0.00 0.00 0.00 3.72
4156 5133 8.600449 TGAAATAATCGATATGTGCATGTGTA 57.400 30.769 0.00 0.00 0.00 2.90
4157 5134 9.050601 TGAAATAATCGATATGTGCATGTGTAA 57.949 29.630 0.00 0.00 0.00 2.41
4158 5135 9.533983 GAAATAATCGATATGTGCATGTGTAAG 57.466 33.333 0.00 0.00 0.00 2.34
4159 5136 8.607441 AATAATCGATATGTGCATGTGTAAGT 57.393 30.769 0.00 0.00 0.00 2.24
4160 5137 6.925610 AATCGATATGTGCATGTGTAAGTT 57.074 33.333 0.00 0.00 0.00 2.66
4161 5138 6.925610 ATCGATATGTGCATGTGTAAGTTT 57.074 33.333 0.00 0.00 0.00 2.66
4162 5139 6.735678 TCGATATGTGCATGTGTAAGTTTT 57.264 33.333 0.00 0.00 0.00 2.43
4163 5140 7.139896 TCGATATGTGCATGTGTAAGTTTTT 57.860 32.000 0.00 0.00 0.00 1.94
4164 5141 8.257830 TCGATATGTGCATGTGTAAGTTTTTA 57.742 30.769 0.00 0.00 0.00 1.52
4165 5142 8.722394 TCGATATGTGCATGTGTAAGTTTTTAA 58.278 29.630 0.00 0.00 0.00 1.52
4166 5143 9.335891 CGATATGTGCATGTGTAAGTTTTTAAA 57.664 29.630 0.00 0.00 0.00 1.52
4169 5146 8.940768 ATGTGCATGTGTAAGTTTTTAAAACT 57.059 26.923 16.34 16.34 0.00 2.66
4170 5147 8.764524 TGTGCATGTGTAAGTTTTTAAAACTT 57.235 26.923 30.24 30.24 42.53 2.66
4171 5148 9.209175 TGTGCATGTGTAAGTTTTTAAAACTTT 57.791 25.926 31.82 19.69 40.58 2.66
4189 5166 7.406799 AAACTTTTAGCAATTTGTGGAATCG 57.593 32.000 0.00 0.00 0.00 3.34
4190 5167 6.325919 ACTTTTAGCAATTTGTGGAATCGA 57.674 33.333 0.00 0.00 0.00 3.59
4191 5168 6.744112 ACTTTTAGCAATTTGTGGAATCGAA 58.256 32.000 0.00 0.00 0.00 3.71
4192 5169 7.378181 ACTTTTAGCAATTTGTGGAATCGAAT 58.622 30.769 0.00 0.00 0.00 3.34
4193 5170 7.872483 ACTTTTAGCAATTTGTGGAATCGAATT 59.128 29.630 0.00 0.00 33.29 2.17
4194 5171 9.352784 CTTTTAGCAATTTGTGGAATCGAATTA 57.647 29.630 0.00 0.00 32.25 1.40
4195 5172 9.868277 TTTTAGCAATTTGTGGAATCGAATTAT 57.132 25.926 0.00 0.00 32.25 1.28
4196 5173 9.868277 TTTAGCAATTTGTGGAATCGAATTATT 57.132 25.926 0.00 0.00 32.25 1.40
4197 5174 7.760131 AGCAATTTGTGGAATCGAATTATTG 57.240 32.000 0.00 0.00 32.25 1.90
4198 5175 6.757947 AGCAATTTGTGGAATCGAATTATTGG 59.242 34.615 0.00 0.00 32.25 3.16
4199 5176 6.756074 GCAATTTGTGGAATCGAATTATTGGA 59.244 34.615 0.00 0.00 32.25 3.53
4200 5177 7.439056 GCAATTTGTGGAATCGAATTATTGGAT 59.561 33.333 0.00 0.00 32.25 3.41
4201 5178 8.757789 CAATTTGTGGAATCGAATTATTGGATG 58.242 33.333 3.32 0.00 32.25 3.51
4202 5179 5.437289 TGTGGAATCGAATTATTGGATGC 57.563 39.130 3.32 1.60 0.00 3.91
4203 5180 4.886489 TGTGGAATCGAATTATTGGATGCA 59.114 37.500 9.59 0.00 0.00 3.96
4204 5181 5.008911 TGTGGAATCGAATTATTGGATGCAG 59.991 40.000 9.59 0.00 0.00 4.41
4205 5182 5.009010 GTGGAATCGAATTATTGGATGCAGT 59.991 40.000 9.59 0.00 0.00 4.40
4206 5183 5.008911 TGGAATCGAATTATTGGATGCAGTG 59.991 40.000 9.59 0.00 0.00 3.66
4207 5184 5.009010 GGAATCGAATTATTGGATGCAGTGT 59.991 40.000 9.59 0.00 0.00 3.55
4208 5185 4.880886 TCGAATTATTGGATGCAGTGTG 57.119 40.909 0.00 0.00 0.00 3.82
4209 5186 4.512484 TCGAATTATTGGATGCAGTGTGA 58.488 39.130 0.00 0.00 0.00 3.58
4210 5187 5.125356 TCGAATTATTGGATGCAGTGTGAT 58.875 37.500 0.00 0.00 0.00 3.06
4211 5188 5.237127 TCGAATTATTGGATGCAGTGTGATC 59.763 40.000 0.00 0.00 0.00 2.92
4212 5189 5.007921 CGAATTATTGGATGCAGTGTGATCA 59.992 40.000 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.766277 TTTTCTAAAATGCACAAAAATGTTGAC 57.234 25.926 0.00 0.00 0.00 3.18
139 140 9.346725 GAAAGTTTCAATCGCAAATATTCTCTT 57.653 29.630 10.81 0.00 0.00 2.85
141 142 8.673626 TGAAAGTTTCAATCGCAAATATTCTC 57.326 30.769 15.92 0.00 36.59 2.87
142 143 9.079833 CATGAAAGTTTCAATCGCAAATATTCT 57.920 29.630 21.57 0.00 43.95 2.40
143 144 9.075519 TCATGAAAGTTTCAATCGCAAATATTC 57.924 29.630 21.57 0.00 43.95 1.75
146 147 8.984891 ATTCATGAAAGTTTCAATCGCAAATA 57.015 26.923 21.57 0.00 43.95 1.40
222 240 9.862371 AAACCGTGTAAATTATTCATATTTGCA 57.138 25.926 0.00 0.00 0.00 4.08
328 347 2.450160 GCAAGCGATTTTATTCGGGTG 58.550 47.619 0.00 0.00 39.49 4.61
341 360 1.600636 CTGGTTTGAGGGCAAGCGA 60.601 57.895 0.00 0.00 36.24 4.93
344 363 2.031120 TGTTTCTGGTTTGAGGGCAAG 58.969 47.619 0.00 0.00 35.04 4.01
345 364 1.754226 GTGTTTCTGGTTTGAGGGCAA 59.246 47.619 0.00 0.00 0.00 4.52
358 377 1.260561 CAGCGCGTAGTTTGTGTTTCT 59.739 47.619 8.43 0.00 0.00 2.52
373 392 2.890474 CCCATGTACGGACAGCGC 60.890 66.667 6.62 0.00 39.50 5.92
409 428 1.003118 TGGCGTGGCATATATCCCTTC 59.997 52.381 0.00 0.00 0.00 3.46
414 433 1.726853 GGTCTGGCGTGGCATATATC 58.273 55.000 0.00 0.00 0.00 1.63
415 434 0.037326 CGGTCTGGCGTGGCATATAT 60.037 55.000 0.00 0.00 0.00 0.86
416 435 1.365999 CGGTCTGGCGTGGCATATA 59.634 57.895 0.00 0.00 0.00 0.86
448 467 0.460811 TGTCTGCGATGTGATCTGCC 60.461 55.000 0.00 0.00 0.00 4.85
449 468 1.362768 TTGTCTGCGATGTGATCTGC 58.637 50.000 0.00 0.00 0.00 4.26
497 521 4.309950 GGGAGGTTGGTGACGCGT 62.310 66.667 13.85 13.85 0.00 6.01
544 576 1.612199 CGGGGGAAATTTCGAACTGGA 60.612 52.381 11.95 0.00 0.00 3.86
617 657 2.202427 CGTTTTGAATCGCGGGGC 60.202 61.111 6.13 0.00 0.00 5.80
670 710 3.053896 GCGTTTCGGGTTGAGGGG 61.054 66.667 0.00 0.00 0.00 4.79
810 1285 0.390603 TGATAACGTTGGCCTGGACG 60.391 55.000 20.17 20.17 44.34 4.79
813 1288 2.104111 TCCTATGATAACGTTGGCCTGG 59.896 50.000 11.99 6.40 0.00 4.45
850 1326 1.818674 CGGTTTTGGAATGGAAGGAGG 59.181 52.381 0.00 0.00 0.00 4.30
880 1356 1.349542 CGAGAGAGAGAGGGGGAGGA 61.350 65.000 0.00 0.00 0.00 3.71
883 1359 4.502106 TCGAGAGAGAGAGGGGGA 57.498 61.111 0.00 0.00 34.84 4.81
921 1397 2.822701 GAACCGGCGATGGGGAAC 60.823 66.667 9.30 0.00 0.00 3.62
981 1485 2.202272 GACTCGAACGACGGACCG 60.202 66.667 13.61 13.61 42.82 4.79
1080 1585 2.347490 CCACTGGACTTCCACCCG 59.653 66.667 0.00 0.00 42.01 5.28
1088 1593 0.836400 AATCCACCGACCACTGGACT 60.836 55.000 0.71 0.00 39.44 3.85
1092 1597 0.250727 AACCAATCCACCGACCACTG 60.251 55.000 0.00 0.00 0.00 3.66
1104 1613 5.358160 CCAAAACCCTAGATCAGAACCAATC 59.642 44.000 0.00 0.00 0.00 2.67
1105 1614 5.222337 ACCAAAACCCTAGATCAGAACCAAT 60.222 40.000 0.00 0.00 0.00 3.16
1106 1615 4.105697 ACCAAAACCCTAGATCAGAACCAA 59.894 41.667 0.00 0.00 0.00 3.67
1107 1616 3.655777 ACCAAAACCCTAGATCAGAACCA 59.344 43.478 0.00 0.00 0.00 3.67
1147 1657 2.032071 AGTTTGGACCCCTTCGCG 59.968 61.111 0.00 0.00 0.00 5.87
1219 1732 3.136750 CCGCTAGGAGCAGCATCT 58.863 61.111 0.00 0.00 42.58 2.90
1263 1776 0.033796 ACGGGAGGTAAGATGGTCGA 60.034 55.000 0.00 0.00 0.00 4.20
1378 1902 7.305474 GCTGAGAGTATTCGGAAATTGAAAAA 58.695 34.615 0.00 0.00 0.00 1.94
1379 1903 6.402118 CGCTGAGAGTATTCGGAAATTGAAAA 60.402 38.462 0.00 0.00 0.00 2.29
1389 1913 1.309950 TCCTCGCTGAGAGTATTCGG 58.690 55.000 7.63 0.00 45.44 4.30
1391 1915 2.952978 TCCTTCCTCGCTGAGAGTATTC 59.047 50.000 7.63 0.00 45.44 1.75
1403 1931 0.321671 TGTCCTGCTTTCCTTCCTCG 59.678 55.000 0.00 0.00 0.00 4.63
1412 1940 4.351874 TGCTAAGTACTTGTCCTGCTTT 57.648 40.909 18.56 0.00 0.00 3.51
1419 1947 3.372206 CAGTGGCATGCTAAGTACTTGTC 59.628 47.826 18.92 9.78 0.00 3.18
1482 2172 7.178274 TCCAACTGTTGTAAATAATCATTGGCT 59.822 33.333 18.38 0.00 34.23 4.75
1502 2210 0.320421 CGTGACGGGTCAATCCAACT 60.320 55.000 2.58 0.00 41.85 3.16
1504 2212 0.107081 AACGTGACGGGTCAATCCAA 59.893 50.000 10.66 0.00 41.85 3.53
1521 2229 7.278868 ACAAGACAATGTCTAGCAGCTATAAAC 59.721 37.037 17.04 2.94 42.59 2.01
1603 2313 0.714180 TCCCCTTAGCTACTGTCCCA 59.286 55.000 0.00 0.00 0.00 4.37
1613 2329 4.216708 AGTCATACAGTACTCCCCTTAGC 58.783 47.826 0.00 0.00 0.00 3.09
1615 2331 6.978261 ACTAAGTCATACAGTACTCCCCTTA 58.022 40.000 0.00 0.00 0.00 2.69
1623 2339 7.086230 ACTGCAGTACTAAGTCATACAGTAC 57.914 40.000 20.16 3.49 43.18 2.73
1625 2341 6.591750 AACTGCAGTACTAAGTCATACAGT 57.408 37.500 22.01 0.00 37.44 3.55
1626 2342 7.535997 TGTAACTGCAGTACTAAGTCATACAG 58.464 38.462 22.01 4.56 0.00 2.74
1627 2343 7.457024 TGTAACTGCAGTACTAAGTCATACA 57.543 36.000 22.01 17.66 0.00 2.29
1628 2344 8.752766 TTTGTAACTGCAGTACTAAGTCATAC 57.247 34.615 22.01 15.27 0.00 2.39
1637 2353 6.164176 GTCACCTATTTGTAACTGCAGTACT 58.836 40.000 22.01 8.20 0.00 2.73
1650 2399 4.701651 ACATGTCATGGTGTCACCTATTTG 59.298 41.667 22.56 14.11 39.58 2.32
1651 2400 4.701651 CACATGTCATGGTGTCACCTATTT 59.298 41.667 22.56 2.84 39.58 1.40
1652 2401 4.019411 TCACATGTCATGGTGTCACCTATT 60.019 41.667 22.56 5.31 39.58 1.73
1659 2408 3.141398 ACTGTTCACATGTCATGGTGTC 58.859 45.455 17.08 5.76 36.43 3.67
1665 2414 4.774726 AGGACTCTACTGTTCACATGTCAT 59.225 41.667 0.00 0.00 0.00 3.06
1706 2529 3.084786 ACTAATTCACTTGCTGGGCTTC 58.915 45.455 0.00 0.00 0.00 3.86
1715 2538 2.369394 GGGCCTCCACTAATTCACTTG 58.631 52.381 0.84 0.00 0.00 3.16
1719 2542 0.251916 CACGGGCCTCCACTAATTCA 59.748 55.000 0.84 0.00 0.00 2.57
1813 2637 2.727123 TGTTTTCCCAGAGACTTGCA 57.273 45.000 0.00 0.00 0.00 4.08
1874 2698 3.005791 ACCAAACAGGCATGCTTAGTTTC 59.994 43.478 23.08 6.30 43.14 2.78
1886 2710 1.470098 CTGACATAGCACCAAACAGGC 59.530 52.381 0.00 0.00 43.14 4.85
2065 2889 1.261619 GCTGATTTATCCTTCACGGCG 59.738 52.381 4.80 4.80 0.00 6.46
2182 3006 0.036577 CAAGGCTGTCTGACCTCCTG 60.037 60.000 15.65 8.61 34.31 3.86
2402 3226 6.205464 TCATTGAAAGAAACTGAACAGCCTAG 59.795 38.462 1.46 0.00 0.00 3.02
2406 3230 8.078596 AGTATTCATTGAAAGAAACTGAACAGC 58.921 33.333 2.68 0.00 0.00 4.40
2487 3311 1.075374 TGCCTGGCCACATAAGTCTTT 59.925 47.619 17.53 0.00 0.00 2.52
2566 3390 8.820153 ATCTTTAGCTTCTCAAAATCTTCCAT 57.180 30.769 0.00 0.00 0.00 3.41
2641 3465 1.589716 GGAGTCACATTGGCAGCACC 61.590 60.000 0.00 0.00 39.84 5.01
2784 3608 3.204418 GCAGGAGCATTCTTGGCC 58.796 61.111 0.00 0.00 41.58 5.36
2810 3634 1.964223 TCTTGGCGGTATTTTTGGCAA 59.036 42.857 0.00 0.00 44.54 4.52
2825 3649 2.546584 GCCTGCTTCTTGGTTTTCTTGG 60.547 50.000 0.00 0.00 0.00 3.61
2888 3712 2.434185 GATCTGCGTCAACCGGCA 60.434 61.111 0.00 0.00 36.94 5.69
2954 3779 6.423182 AGGCTATAAATTGCAGAAACAGGTA 58.577 36.000 0.00 0.00 0.00 3.08
2996 3825 5.009911 TCCTTCACCACATCAACTGAAAATG 59.990 40.000 0.00 0.00 0.00 2.32
3057 3895 2.093973 CGGTTGCTAGAAGACAGTCCAT 60.094 50.000 0.00 0.00 0.00 3.41
3059 3897 1.544691 TCGGTTGCTAGAAGACAGTCC 59.455 52.381 0.00 0.00 0.00 3.85
3077 3915 7.479897 AGTGTACATATGTAGTGTACTCTCG 57.520 40.000 15.93 0.00 45.97 4.04
3106 3944 4.612264 ACGAAACAGTAACCTGGTACAT 57.388 40.909 0.00 0.00 37.77 2.29
3295 4137 7.755591 ACAAGTGCTAATGACATATCAACAAG 58.244 34.615 0.00 0.00 38.69 3.16
3355 4197 3.181501 CCCAGCAAACCATAATACACACG 60.182 47.826 0.00 0.00 0.00 4.49
3422 4265 0.036010 ATTCAGAAGCTGGACACGGG 60.036 55.000 0.00 0.00 31.51 5.28
3529 4488 6.605849 CATGAGAAGAATTATAACATGGCCG 58.394 40.000 0.00 0.00 32.79 6.13
3530 4489 6.385033 GCATGAGAAGAATTATAACATGGCC 58.615 40.000 0.00 0.00 35.63 5.36
3550 4515 2.600420 CACAGACTACTAAGCACGCATG 59.400 50.000 0.00 0.00 0.00 4.06
3551 4516 2.492088 TCACAGACTACTAAGCACGCAT 59.508 45.455 0.00 0.00 0.00 4.73
3701 4673 1.074405 ACCAACATCCATGTGTGCTCT 59.926 47.619 0.00 0.00 41.61 4.09
3705 4677 4.524316 ATCAAACCAACATCCATGTGTG 57.476 40.909 0.00 0.00 41.61 3.82
3706 4678 6.267471 AGTTAATCAAACCAACATCCATGTGT 59.733 34.615 0.00 0.00 38.84 3.72
3732 4705 4.243007 AGAAATGTGGCTTACAAGTTGC 57.757 40.909 1.81 0.00 43.77 4.17
3851 4826 4.657436 TTGGCCGTAAACTCAAAAACAT 57.343 36.364 0.00 0.00 0.00 2.71
3891 4866 3.696281 TCATGTGCTGTTGAAACACAG 57.304 42.857 0.00 0.00 46.55 3.66
3934 4909 1.639534 GCGCATTTGGCATTGCATC 59.360 52.632 19.07 9.12 45.17 3.91
4027 5003 2.851263 TGTGTTCCTGTCATGTACCC 57.149 50.000 0.00 0.00 0.00 3.69
4037 5013 9.751542 CTAAGTAATCTACCTTATGTGTTCCTG 57.248 37.037 0.00 0.00 0.00 3.86
4089 5066 4.439153 CCCAGCTGCACAACATATTTAGTG 60.439 45.833 8.66 0.00 35.19 2.74
4114 5091 4.264638 AAAACCAGGTGCGCACGC 62.265 61.111 32.35 24.53 42.35 5.34
4115 5092 2.329678 TTCAAAACCAGGTGCGCACG 62.330 55.000 32.35 21.76 0.00 5.34
4116 5093 0.179124 TTTCAAAACCAGGTGCGCAC 60.179 50.000 32.15 32.15 0.00 5.34
4117 5094 0.749649 ATTTCAAAACCAGGTGCGCA 59.250 45.000 5.66 5.66 0.00 6.09
4120 5097 5.054390 TCGATTATTTCAAAACCAGGTGC 57.946 39.130 0.00 0.00 0.00 5.01
4134 5111 8.607441 ACTTACACATGCACATATCGATTATT 57.393 30.769 1.71 0.00 0.00 1.40
4139 5116 6.735678 AAAACTTACACATGCACATATCGA 57.264 33.333 0.00 0.00 0.00 3.59
4140 5117 8.888332 TTAAAAACTTACACATGCACATATCG 57.112 30.769 0.00 0.00 0.00 2.92
4144 5121 8.940768 AGTTTTAAAAACTTACACATGCACAT 57.059 26.923 1.31 0.00 0.00 3.21
4145 5122 8.764524 AAGTTTTAAAAACTTACACATGCACA 57.235 26.923 0.00 0.00 38.58 4.57
4163 5140 8.973378 CGATTCCACAAATTGCTAAAAGTTTTA 58.027 29.630 7.80 7.80 0.00 1.52
4164 5141 7.708752 TCGATTCCACAAATTGCTAAAAGTTTT 59.291 29.630 6.06 6.06 0.00 2.43
4165 5142 7.206687 TCGATTCCACAAATTGCTAAAAGTTT 58.793 30.769 0.00 0.00 0.00 2.66
4166 5143 6.744112 TCGATTCCACAAATTGCTAAAAGTT 58.256 32.000 0.00 0.00 0.00 2.66
4167 5144 6.325919 TCGATTCCACAAATTGCTAAAAGT 57.674 33.333 0.00 0.00 0.00 2.66
4168 5145 7.816945 ATTCGATTCCACAAATTGCTAAAAG 57.183 32.000 0.00 0.00 0.00 2.27
4169 5146 9.868277 ATAATTCGATTCCACAAATTGCTAAAA 57.132 25.926 0.00 0.00 0.00 1.52
4170 5147 9.868277 AATAATTCGATTCCACAAATTGCTAAA 57.132 25.926 0.00 0.00 0.00 1.85
4171 5148 9.299963 CAATAATTCGATTCCACAAATTGCTAA 57.700 29.630 0.00 0.00 0.00 3.09
4172 5149 7.920151 CCAATAATTCGATTCCACAAATTGCTA 59.080 33.333 0.00 0.00 0.00 3.49
4173 5150 6.757947 CCAATAATTCGATTCCACAAATTGCT 59.242 34.615 0.00 0.00 0.00 3.91
4174 5151 6.756074 TCCAATAATTCGATTCCACAAATTGC 59.244 34.615 0.00 0.00 0.00 3.56
4175 5152 8.757789 CATCCAATAATTCGATTCCACAAATTG 58.242 33.333 0.00 0.00 0.00 2.32
4176 5153 7.439056 GCATCCAATAATTCGATTCCACAAATT 59.561 33.333 0.00 0.00 0.00 1.82
4177 5154 6.925165 GCATCCAATAATTCGATTCCACAAAT 59.075 34.615 0.00 0.00 0.00 2.32
4178 5155 6.127507 TGCATCCAATAATTCGATTCCACAAA 60.128 34.615 0.00 0.00 0.00 2.83
4179 5156 5.359292 TGCATCCAATAATTCGATTCCACAA 59.641 36.000 0.00 0.00 0.00 3.33
4180 5157 4.886489 TGCATCCAATAATTCGATTCCACA 59.114 37.500 0.00 0.00 0.00 4.17
4181 5158 5.009010 ACTGCATCCAATAATTCGATTCCAC 59.991 40.000 0.00 0.00 0.00 4.02
4182 5159 5.008911 CACTGCATCCAATAATTCGATTCCA 59.991 40.000 0.00 0.00 0.00 3.53
4183 5160 5.009010 ACACTGCATCCAATAATTCGATTCC 59.991 40.000 0.00 0.00 0.00 3.01
4184 5161 5.911280 CACACTGCATCCAATAATTCGATTC 59.089 40.000 0.00 0.00 0.00 2.52
4185 5162 5.589855 TCACACTGCATCCAATAATTCGATT 59.410 36.000 0.00 0.00 0.00 3.34
4186 5163 5.125356 TCACACTGCATCCAATAATTCGAT 58.875 37.500 0.00 0.00 0.00 3.59
4187 5164 4.512484 TCACACTGCATCCAATAATTCGA 58.488 39.130 0.00 0.00 0.00 3.71
4188 5165 4.880886 TCACACTGCATCCAATAATTCG 57.119 40.909 0.00 0.00 0.00 3.34
4189 5166 6.381481 TGATCACACTGCATCCAATAATTC 57.619 37.500 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.