Multiple sequence alignment - TraesCS5D01G472300

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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 TraesCS5D01G472300 chr5D 100.000 6712 0 0 1 6712 512767318 512774029 0.000000e+00 12395
1 TraesCS5D01G472300 chr5B 93.371 3228 153 28 1699 4891 643666426 643669627 0.000000e+00 4719
2 TraesCS5D01G472300 chr5B 90.904 1682 72 17 5056 6712 643669722 643671347 0.000000e+00 2183
3 TraesCS5D01G472300 chr5B 92.950 766 24 12 1037 1793 643665703 643666447 0.000000e+00 1088
4 TraesCS5D01G472300 chr5B 90.543 497 24 10 496 971 643664812 643665306 2.640000e-178 636
5 TraesCS5D01G472300 chr5B 90.164 244 18 5 26 269 643664388 643664625 5.050000e-81 313
6 TraesCS5D01G472300 chr5A 90.384 2319 144 21 1320 3622 640939139 640941394 0.000000e+00 2974
7 TraesCS5D01G472300 chr5A 93.136 1282 55 15 3677 4939 640941396 640942663 0.000000e+00 1849
8 TraesCS5D01G472300 chr5A 86.879 1288 95 38 20 1267 640937874 640939127 0.000000e+00 1375
9 TraesCS5D01G472300 chr5A 97.266 695 19 0 6018 6712 640945696 640946390 0.000000e+00 1179
10 TraesCS5D01G472300 chr5A 89.299 785 54 16 5130 5905 640942775 640943538 0.000000e+00 957


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 TraesCS5D01G472300 chr5D 512767318 512774029 6711 False 12395.0 12395 100.0000 1 6712 1 chr5D.!!$F1 6711
1 TraesCS5D01G472300 chr5B 643664388 643671347 6959 False 1787.8 4719 91.5864 26 6712 5 chr5B.!!$F1 6686
2 TraesCS5D01G472300 chr5A 640937874 640946390 8516 False 1666.8 2974 91.3928 20 6712 5 chr5A.!!$F1 6692

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
308 311 0.036010 AAGGCGCTATGTGCTCAACT 60.036 50.0 7.64 0.0 39.23 3.16 F
984 1150 0.396060 GAGATCCCTAGGCAGGCAAG 59.604 60.0 2.05 0.0 41.08 4.01 F
1937 2518 0.400213 GTTGATGGGTGTCCTGTGGA 59.600 55.0 0.00 0.0 0.00 4.02 F
1974 2555 0.465278 GGAGGGCTCAGCTTGAATCC 60.465 60.0 0.00 0.0 0.00 3.01 F
3501 4115 0.659123 GTTTTGGTTGTAGCACCGCG 60.659 55.0 0.00 0.0 40.09 6.46 F
4404 5019 2.433868 TCAAAGCGAGAAGTAAGCGT 57.566 45.0 0.00 0.0 35.78 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1432 1938 0.256464 TCTTCCTCCTCCTCCTCGTC 59.744 60.0 0.00 0.0 0.00 4.20 R
2402 3004 0.107459 CCCACTTCCTTAGCCTCAGC 60.107 60.0 0.00 0.0 40.32 4.26 R
3665 4279 0.109597 GCCGTTGCTTGTTCTCCATG 60.110 55.0 0.00 0.0 33.53 3.66 R
3666 4280 1.244019 GGCCGTTGCTTGTTCTCCAT 61.244 55.0 0.00 0.0 37.74 3.41 R
4480 5096 1.103803 TACTAGCACAGCGAAGGGAG 58.896 55.0 0.00 0.0 0.00 4.30 R
5934 6593 0.320683 CAGGCTGTCGACCATCAACA 60.321 55.0 14.12 0.0 0.00 3.33 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
24 25 2.009774 CTAGTTTGCATCCAAGACCGG 58.990 52.381 0.00 0.00 31.52 5.28
112 113 0.317160 TGTCTTTGGCGACGACATCT 59.683 50.000 3.10 0.00 36.71 2.90
116 117 2.230508 TCTTTGGCGACGACATCTAGTT 59.769 45.455 3.10 0.00 0.00 2.24
139 140 3.251004 GCGGGATAAATGTCCATGTCTTC 59.749 47.826 0.00 0.00 40.17 2.87
140 141 4.708177 CGGGATAAATGTCCATGTCTTCT 58.292 43.478 0.00 0.00 40.17 2.85
141 142 5.126067 CGGGATAAATGTCCATGTCTTCTT 58.874 41.667 0.00 0.00 40.17 2.52
222 224 7.682865 CGTCTCGTGTGTCTTATAAATTTGTTC 59.317 37.037 0.00 0.00 0.00 3.18
223 225 8.492748 GTCTCGTGTGTCTTATAAATTTGTTCA 58.507 33.333 0.00 0.00 0.00 3.18
224 226 9.214957 TCTCGTGTGTCTTATAAATTTGTTCAT 57.785 29.630 0.00 0.00 0.00 2.57
272 275 2.589798 TCGTTCAACGACCTGACTTT 57.410 45.000 9.01 0.00 46.73 2.66
284 287 4.515107 GACTTTGTGAAAGGCGCG 57.485 55.556 0.00 0.00 42.82 6.86
292 295 1.667830 TGAAAGGCGCGTCTCAAGG 60.668 57.895 16.36 0.00 0.00 3.61
302 305 1.756375 CGTCTCAAGGCGCTATGTGC 61.756 60.000 7.64 3.91 38.45 4.57
308 311 0.036010 AAGGCGCTATGTGCTCAACT 60.036 50.000 7.64 0.00 39.23 3.16
363 366 5.104193 ACTCCTGATGCACCTCAAAATCTAT 60.104 40.000 0.00 0.00 0.00 1.98
415 442 6.406370 AGAAATACCAAGATGTGAACGATCA 58.594 36.000 0.00 0.00 0.00 2.92
419 446 5.598416 ACCAAGATGTGAACGATCATAGA 57.402 39.130 0.00 0.00 38.01 1.98
519 646 3.641437 TTGCTAGCACATTTCGCTTTT 57.359 38.095 19.17 0.00 40.96 2.27
543 670 9.729023 TTTGGCTATTCATATGTACATTTTTCG 57.271 29.630 14.77 0.00 0.00 3.46
615 745 6.027749 GCGGTTCCTAAAACAAGACAATATG 58.972 40.000 0.00 0.00 0.00 1.78
665 799 0.983378 ACGGAGGAGAAATGGAGGGG 60.983 60.000 0.00 0.00 0.00 4.79
677 811 1.152673 GGAGGGGCCCATGTTGATC 60.153 63.158 27.72 11.55 0.00 2.92
745 886 2.052782 AAACACGCCAACTTTCTCCT 57.947 45.000 0.00 0.00 0.00 3.69
896 1050 0.480252 CCCCTCCTTCCATTCCATCC 59.520 60.000 0.00 0.00 0.00 3.51
914 1068 2.721167 CCCGAGATCTGCCGTTCCA 61.721 63.158 0.00 0.00 0.00 3.53
922 1076 1.452108 CTGCCGTTCCAATCCCCTC 60.452 63.158 0.00 0.00 0.00 4.30
923 1077 2.196997 CTGCCGTTCCAATCCCCTCA 62.197 60.000 0.00 0.00 0.00 3.86
978 1144 1.075226 AAGCGGAGATCCCTAGGCA 60.075 57.895 2.05 0.00 0.00 4.75
979 1145 1.118356 AAGCGGAGATCCCTAGGCAG 61.118 60.000 2.05 0.00 0.00 4.85
980 1146 2.578714 GCGGAGATCCCTAGGCAGG 61.579 68.421 2.05 0.00 42.22 4.85
981 1147 2.578714 CGGAGATCCCTAGGCAGGC 61.579 68.421 2.05 0.00 41.08 4.85
982 1148 1.460305 GGAGATCCCTAGGCAGGCA 60.460 63.158 2.05 0.00 41.08 4.75
983 1149 1.056700 GGAGATCCCTAGGCAGGCAA 61.057 60.000 2.05 0.00 41.08 4.52
984 1150 0.396060 GAGATCCCTAGGCAGGCAAG 59.604 60.000 2.05 0.00 41.08 4.01
985 1151 1.228094 GATCCCTAGGCAGGCAAGC 60.228 63.158 2.05 0.00 41.08 4.01
986 1152 1.987807 GATCCCTAGGCAGGCAAGCA 61.988 60.000 2.05 0.00 41.08 3.91
987 1153 1.992519 ATCCCTAGGCAGGCAAGCAG 61.993 60.000 2.05 0.00 41.08 4.24
988 1154 2.124403 CCTAGGCAGGCAAGCAGG 60.124 66.667 0.00 0.00 34.35 4.85
989 1155 2.827642 CTAGGCAGGCAAGCAGGC 60.828 66.667 0.00 0.00 44.61 4.85
1044 1541 4.467107 GACCTCCTCGCCCTCCCT 62.467 72.222 0.00 0.00 0.00 4.20
1131 1631 1.527370 CGTCTCCCCTCCCAAATCC 59.473 63.158 0.00 0.00 0.00 3.01
1270 1776 1.490574 AGGATCTCCTCTTCCCAACG 58.509 55.000 0.00 0.00 44.77 4.10
1297 1803 3.043713 CGCCGTCAGAGCAGCAAA 61.044 61.111 0.00 0.00 0.00 3.68
1338 1844 1.045911 CCCCTCTTCTTCCTCCTCCG 61.046 65.000 0.00 0.00 0.00 4.63
1458 1964 2.632512 GGAGGAGGAGGAAGATGATGAC 59.367 54.545 0.00 0.00 0.00 3.06
1473 1982 1.456196 ATGACGATGACGGGCTCGAT 61.456 55.000 15.95 0.00 44.46 3.59
1728 2243 1.208293 AGGAAGAAGAAGGATGCGGAC 59.792 52.381 0.00 0.00 0.00 4.79
1730 2245 0.608640 AAGAAGAAGGATGCGGACGT 59.391 50.000 0.00 0.00 0.00 4.34
1821 2402 1.874019 CAAGGAGTCGGTCGCATCG 60.874 63.158 0.00 0.00 0.00 3.84
1833 2414 2.100631 CGCATCGAAGAAACGGGCT 61.101 57.895 0.00 0.00 43.58 5.19
1843 2424 1.550976 AGAAACGGGCTGAGAAGGTAG 59.449 52.381 0.00 0.00 0.00 3.18
1853 2434 3.247173 GCTGAGAAGGTAGCATTTCGATG 59.753 47.826 0.00 0.00 39.67 3.84
1898 2479 3.871006 TCGTATGATTGCATCTGTTCCAC 59.129 43.478 0.00 0.00 35.94 4.02
1937 2518 0.400213 GTTGATGGGTGTCCTGTGGA 59.600 55.000 0.00 0.00 0.00 4.02
1974 2555 0.465278 GGAGGGCTCAGCTTGAATCC 60.465 60.000 0.00 0.00 0.00 3.01
2025 2606 5.646793 GCGAGGTATATATCCTGACAGTGTA 59.353 44.000 0.00 0.00 35.20 2.90
2157 2738 3.650942 TGTACAAACCCATCTCCTCAGTT 59.349 43.478 0.00 0.00 0.00 3.16
2224 2805 4.278170 CAGTTGCCTGACTTGGTTTTATGA 59.722 41.667 0.00 0.00 41.50 2.15
2308 2889 4.527038 AGGTCAAATACTCCTGTCGAAGAA 59.473 41.667 0.00 0.00 39.69 2.52
2320 2913 4.021894 CCTGTCGAAGAAGAAGAGGAAGAA 60.022 45.833 0.00 0.00 39.69 2.52
2326 2919 5.861787 CGAAGAAGAAGAGGAAGAAGAAGAC 59.138 44.000 0.00 0.00 0.00 3.01
2327 2920 5.738619 AGAAGAAGAGGAAGAAGAAGACC 57.261 43.478 0.00 0.00 0.00 3.85
2332 2925 4.882842 AGAGGAAGAAGAAGACCAAGAC 57.117 45.455 0.00 0.00 0.00 3.01
2341 2934 4.513198 AGAAGACCAAGACGAAGAAGAG 57.487 45.455 0.00 0.00 0.00 2.85
2344 2937 2.823154 AGACCAAGACGAAGAAGAGGAG 59.177 50.000 0.00 0.00 0.00 3.69
2377 2979 0.682855 CCTCTTCAGAGCCCGAGAGT 60.683 60.000 0.00 0.00 40.75 3.24
2456 3058 9.657419 ACAAAAATTTGAAGAATGTGAGTCTTT 57.343 25.926 12.54 0.00 40.55 2.52
2491 3093 6.314896 GCTTGATTTGAGCTCAGTATAGTGTT 59.685 38.462 17.43 0.00 37.18 3.32
2527 3129 3.181510 GGTTGTGAATCGTTGTAGGATGC 60.182 47.826 0.00 0.00 0.00 3.91
2553 3155 3.073798 TGACAAGGAGGTTGGAGCAAATA 59.926 43.478 0.00 0.00 40.90 1.40
2791 3393 8.065473 TGTTTTGCAACAGAATATATGATGGT 57.935 30.769 0.00 0.00 38.03 3.55
2846 3449 6.908284 TGTGTTATTTGCGTTGAAGTTTCTAC 59.092 34.615 0.00 0.00 0.00 2.59
2956 3560 5.302568 TGAATCAATGGTTGCTGGATTATCC 59.697 40.000 3.91 3.91 36.96 2.59
2979 3593 7.931578 CCAATGTTTGGTACTATGGTTAGAA 57.068 36.000 0.00 0.00 45.93 2.10
3131 3745 9.817809 TGCATCTACGATTTTAAAGTCTAAGAT 57.182 29.630 13.96 13.96 0.00 2.40
3238 3852 1.000274 GACAATGCCCAACCAAGTGAC 60.000 52.381 0.00 0.00 0.00 3.67
3432 4046 7.201487 GCCCCTTTAAAAACTTATTTATGCACG 60.201 37.037 0.00 0.00 0.00 5.34
3501 4115 0.659123 GTTTTGGTTGTAGCACCGCG 60.659 55.000 0.00 0.00 40.09 6.46
3740 4354 8.601845 TTACATATGTATATTGGTGCACTGTC 57.398 34.615 17.98 0.00 0.00 3.51
3845 4460 7.017551 ACAAGGAGAACATATATCCAGGCATTA 59.982 37.037 0.00 0.00 35.45 1.90
3847 4462 7.988937 AGGAGAACATATATCCAGGCATTAAA 58.011 34.615 0.00 0.00 35.45 1.52
3902 4517 3.248602 ACGAACTCTTGCAAGTGATTCAC 59.751 43.478 29.78 8.82 34.10 3.18
4222 4837 4.902443 TGATATCGAAGACTGTGAGGAC 57.098 45.455 0.00 0.00 42.51 3.85
4271 4886 3.342377 TGACTCCAAATATTGTGCGGA 57.658 42.857 0.00 0.00 0.00 5.54
4318 4933 4.619973 TGATTGCCAAAATGTTCACAGAC 58.380 39.130 0.00 0.00 0.00 3.51
4404 5019 2.433868 TCAAAGCGAGAAGTAAGCGT 57.566 45.000 0.00 0.00 35.78 5.07
4439 5055 6.917217 AATACTGAGTATCTTCAGCTTTGC 57.083 37.500 5.45 0.00 46.77 3.68
4440 5056 4.550076 ACTGAGTATCTTCAGCTTTGCT 57.450 40.909 3.10 0.00 46.77 3.91
4441 5057 4.904241 ACTGAGTATCTTCAGCTTTGCTT 58.096 39.130 3.10 0.00 46.77 3.91
4442 5058 4.694509 ACTGAGTATCTTCAGCTTTGCTTG 59.305 41.667 3.10 0.00 46.77 4.01
4443 5059 4.898320 TGAGTATCTTCAGCTTTGCTTGA 58.102 39.130 0.00 0.00 33.47 3.02
4444 5060 5.494724 TGAGTATCTTCAGCTTTGCTTGAT 58.505 37.500 0.00 0.00 33.47 2.57
4445 5061 6.643388 TGAGTATCTTCAGCTTTGCTTGATA 58.357 36.000 0.00 0.00 33.47 2.15
4446 5062 7.105588 TGAGTATCTTCAGCTTTGCTTGATAA 58.894 34.615 0.00 0.00 33.47 1.75
4487 5104 2.904434 TGGACTGTTAGTTCCTCCCTTC 59.096 50.000 0.00 0.00 0.00 3.46
4516 5133 7.097834 GTGCTAGTACAGACTTTTTATCCACT 58.902 38.462 6.04 0.00 37.10 4.00
4583 5200 8.997621 TGTTAGGTTCATAGTACTTCATTCAC 57.002 34.615 0.00 0.00 0.00 3.18
4694 5311 4.235079 AGCAAGCCACATGTAAGGATTA 57.765 40.909 5.48 0.00 31.26 1.75
4714 5331 6.822676 GGATTACCAAAATTTCAATCCATGCA 59.177 34.615 19.13 0.00 42.72 3.96
4748 5365 5.220710 ACATGGCTGGTCATCTACTAATC 57.779 43.478 0.00 0.00 0.00 1.75
4750 5367 5.309020 ACATGGCTGGTCATCTACTAATCAT 59.691 40.000 0.00 0.00 0.00 2.45
4755 5372 9.100197 TGGCTGGTCATCTACTAATCATTATTA 57.900 33.333 0.00 0.00 0.00 0.98
4816 5433 3.258372 TCGGAAGTAACAGCAACTCATCT 59.742 43.478 0.00 0.00 0.00 2.90
4830 5447 6.716628 AGCAACTCATCTTCAAAGGTAAATGA 59.283 34.615 0.00 0.00 0.00 2.57
4854 5471 7.552687 TGATTACTGACACTCTTTTCTGTTTGT 59.447 33.333 0.00 0.00 0.00 2.83
4859 5476 5.471797 TGACACTCTTTTCTGTTTGTTGTCA 59.528 36.000 0.00 0.00 0.00 3.58
4863 5480 7.120579 ACACTCTTTTCTGTTTGTTGTCATACA 59.879 33.333 0.00 0.00 35.11 2.29
4870 5487 6.287525 TCTGTTTGTTGTCATACATCTCACA 58.712 36.000 0.00 0.00 35.64 3.58
4895 5527 4.333926 GGATGTTGACTAGCTGAAATGACC 59.666 45.833 0.00 0.00 0.00 4.02
4915 5547 3.079578 CCTCATATGGCAAATCATCGCT 58.920 45.455 2.13 0.00 0.00 4.93
4917 5549 4.473199 CTCATATGGCAAATCATCGCTTG 58.527 43.478 2.13 0.00 0.00 4.01
4931 5563 1.001487 TCGCTTGTGTTGCTCCAAATG 60.001 47.619 0.00 0.00 0.00 2.32
4939 5571 6.166984 TGTGTTGCTCCAAATGGAAAATTA 57.833 33.333 3.35 0.00 44.91 1.40
4940 5572 5.988561 TGTGTTGCTCCAAATGGAAAATTAC 59.011 36.000 3.35 6.00 44.91 1.89
4941 5573 6.183360 TGTGTTGCTCCAAATGGAAAATTACT 60.183 34.615 3.35 0.00 44.91 2.24
4942 5574 6.146021 GTGTTGCTCCAAATGGAAAATTACTG 59.854 38.462 3.35 0.00 44.91 2.74
4943 5575 4.819769 TGCTCCAAATGGAAAATTACTGC 58.180 39.130 3.35 1.76 44.91 4.40
4944 5576 4.527816 TGCTCCAAATGGAAAATTACTGCT 59.472 37.500 3.35 0.00 44.91 4.24
4945 5577 5.011943 TGCTCCAAATGGAAAATTACTGCTT 59.988 36.000 3.35 0.00 44.91 3.91
4946 5578 6.210385 TGCTCCAAATGGAAAATTACTGCTTA 59.790 34.615 3.35 0.00 44.91 3.09
4947 5579 6.531594 GCTCCAAATGGAAAATTACTGCTTAC 59.468 38.462 3.35 0.00 44.91 2.34
4948 5580 7.577616 GCTCCAAATGGAAAATTACTGCTTACT 60.578 37.037 3.35 0.00 44.91 2.24
4949 5581 8.871629 TCCAAATGGAAAATTACTGCTTACTA 57.128 30.769 0.00 0.00 42.18 1.82
4950 5582 9.303116 TCCAAATGGAAAATTACTGCTTACTAA 57.697 29.630 0.00 0.00 42.18 2.24
4951 5583 9.921637 CCAAATGGAAAATTACTGCTTACTAAA 57.078 29.630 0.00 0.00 37.39 1.85
4960 5592 9.749340 AAATTACTGCTTACTAAACATTACCCT 57.251 29.630 0.00 0.00 0.00 4.34
4961 5593 8.959705 ATTACTGCTTACTAAACATTACCCTC 57.040 34.615 0.00 0.00 0.00 4.30
4962 5594 6.622427 ACTGCTTACTAAACATTACCCTCT 57.378 37.500 0.00 0.00 0.00 3.69
4963 5595 6.407202 ACTGCTTACTAAACATTACCCTCTG 58.593 40.000 0.00 0.00 0.00 3.35
4964 5596 6.013639 ACTGCTTACTAAACATTACCCTCTGT 60.014 38.462 0.00 0.00 0.00 3.41
4979 5611 5.022122 ACCCTCTGTACCTAGTAAAACCTC 58.978 45.833 0.00 0.00 0.00 3.85
4990 5622 7.150640 ACCTAGTAAAACCTCGACTTAAACAG 58.849 38.462 0.00 0.00 0.00 3.16
4991 5623 7.014615 ACCTAGTAAAACCTCGACTTAAACAGA 59.985 37.037 0.00 0.00 0.00 3.41
4992 5624 7.869429 CCTAGTAAAACCTCGACTTAAACAGAA 59.131 37.037 0.00 0.00 0.00 3.02
4993 5625 9.420551 CTAGTAAAACCTCGACTTAAACAGAAT 57.579 33.333 0.00 0.00 0.00 2.40
4994 5626 8.672823 AGTAAAACCTCGACTTAAACAGAATT 57.327 30.769 0.00 0.00 0.00 2.17
4995 5627 9.117183 AGTAAAACCTCGACTTAAACAGAATTT 57.883 29.630 0.00 0.00 0.00 1.82
4996 5628 9.726232 GTAAAACCTCGACTTAAACAGAATTTT 57.274 29.630 0.00 0.00 0.00 1.82
4997 5629 8.628882 AAAACCTCGACTTAAACAGAATTTTG 57.371 30.769 0.00 0.00 0.00 2.44
4998 5630 5.758924 ACCTCGACTTAAACAGAATTTTGC 58.241 37.500 0.00 0.00 0.00 3.68
4999 5631 5.298276 ACCTCGACTTAAACAGAATTTTGCA 59.702 36.000 0.00 0.00 0.00 4.08
5000 5632 6.016276 ACCTCGACTTAAACAGAATTTTGCAT 60.016 34.615 0.00 0.00 0.00 3.96
5001 5633 6.863126 CCTCGACTTAAACAGAATTTTGCATT 59.137 34.615 0.00 0.00 0.00 3.56
5002 5634 7.061094 CCTCGACTTAAACAGAATTTTGCATTC 59.939 37.037 0.00 0.00 0.00 2.67
5003 5635 7.648142 TCGACTTAAACAGAATTTTGCATTCT 58.352 30.769 0.00 0.00 38.78 2.40
5004 5636 8.134895 TCGACTTAAACAGAATTTTGCATTCTT 58.865 29.630 0.00 0.00 36.32 2.52
5005 5637 8.755018 CGACTTAAACAGAATTTTGCATTCTTT 58.245 29.630 0.00 0.00 36.32 2.52
5012 5644 8.947055 ACAGAATTTTGCATTCTTTTTGTAGT 57.053 26.923 0.00 0.00 36.32 2.73
5013 5645 9.382275 ACAGAATTTTGCATTCTTTTTGTAGTT 57.618 25.926 0.00 0.00 36.32 2.24
5070 5702 7.553881 CAGGTAATTACATGTACTTTCCCTG 57.446 40.000 24.21 24.21 33.68 4.45
5071 5703 6.038271 CAGGTAATTACATGTACTTTCCCTGC 59.962 42.308 24.97 8.65 33.68 4.85
5079 5711 3.153919 TGTACTTTCCCTGCCATTGTTC 58.846 45.455 0.00 0.00 0.00 3.18
5089 5721 3.624777 CTGCCATTGTTCTGTTAGGGAT 58.375 45.455 0.00 0.00 0.00 3.85
5095 5727 6.681368 GCCATTGTTCTGTTAGGGATCATTTC 60.681 42.308 0.00 0.00 0.00 2.17
5096 5728 6.377996 CCATTGTTCTGTTAGGGATCATTTCA 59.622 38.462 0.00 0.00 0.00 2.69
5104 5736 6.493166 TGTTAGGGATCATTTCATGGTTCTT 58.507 36.000 0.00 0.00 0.00 2.52
5116 5748 4.885413 TCATGGTTCTTTTCCATTGCAAG 58.115 39.130 4.94 0.00 42.92 4.01
5117 5749 3.110447 TGGTTCTTTTCCATTGCAAGC 57.890 42.857 4.94 0.00 0.00 4.01
5118 5750 2.224257 TGGTTCTTTTCCATTGCAAGCC 60.224 45.455 4.94 0.00 0.00 4.35
5119 5751 2.224257 GGTTCTTTTCCATTGCAAGCCA 60.224 45.455 4.94 0.00 0.00 4.75
5120 5752 3.557686 GGTTCTTTTCCATTGCAAGCCAT 60.558 43.478 4.94 0.00 0.00 4.40
5125 5774 4.659111 TTTCCATTGCAAGCCATATCTG 57.341 40.909 4.94 0.00 0.00 2.90
5127 5776 3.483421 TCCATTGCAAGCCATATCTGAG 58.517 45.455 4.94 0.00 0.00 3.35
5134 5783 3.950395 GCAAGCCATATCTGAGAAAACCT 59.050 43.478 0.00 0.00 0.00 3.50
5135 5784 4.201990 GCAAGCCATATCTGAGAAAACCTG 60.202 45.833 0.00 0.00 0.00 4.00
5143 5792 2.783510 TCTGAGAAAACCTGTTTCCCCT 59.216 45.455 0.00 0.00 31.45 4.79
5148 5797 4.556697 AGAAAACCTGTTTCCCCTTCATT 58.443 39.130 0.00 0.00 31.45 2.57
5152 5801 6.816616 AAACCTGTTTCCCCTTCATTTTTA 57.183 33.333 0.00 0.00 0.00 1.52
5160 5809 6.530019 TTCCCCTTCATTTTTATCTCTTGC 57.470 37.500 0.00 0.00 0.00 4.01
5161 5810 5.579047 TCCCCTTCATTTTTATCTCTTGCA 58.421 37.500 0.00 0.00 0.00 4.08
5162 5811 6.197168 TCCCCTTCATTTTTATCTCTTGCAT 58.803 36.000 0.00 0.00 0.00 3.96
5163 5812 6.322201 TCCCCTTCATTTTTATCTCTTGCATC 59.678 38.462 0.00 0.00 0.00 3.91
5267 5916 2.467566 AAGGCTACATTTTCGGTCGT 57.532 45.000 0.00 0.00 0.00 4.34
5334 5983 2.829720 AGTAACTCGGATGTGGTAAGCA 59.170 45.455 0.00 0.00 0.00 3.91
5405 6054 3.643763 CAGAGTCGCACATTCCCTATAC 58.356 50.000 0.00 0.00 0.00 1.47
5428 6077 3.087031 CAGAAACATTCTCATGTGCCCT 58.913 45.455 0.00 0.00 43.34 5.19
5514 6164 2.980233 AGACAAAGCCAGCCGCAC 60.980 61.111 0.00 0.00 41.38 5.34
5594 6244 4.302509 TCAACTTCCGCCGCCGAA 62.303 61.111 0.00 0.00 36.29 4.30
5729 6379 3.300388 CTGACTCACATAGCCTCCCTTA 58.700 50.000 0.00 0.00 0.00 2.69
5730 6380 3.031736 TGACTCACATAGCCTCCCTTAC 58.968 50.000 0.00 0.00 0.00 2.34
5733 6383 0.765510 CACATAGCCTCCCTTACCCC 59.234 60.000 0.00 0.00 0.00 4.95
5736 6386 0.345502 ATAGCCTCCCTTACCCCACA 59.654 55.000 0.00 0.00 0.00 4.17
5737 6387 0.345502 TAGCCTCCCTTACCCCACAT 59.654 55.000 0.00 0.00 0.00 3.21
5776 6429 3.142951 CACCTGTTTATGTCGGTGGAAA 58.857 45.455 0.00 0.00 42.40 3.13
5787 6440 6.582677 ATGTCGGTGGAAATACATTTTTCA 57.417 33.333 0.00 0.00 37.34 2.69
5793 6446 6.750039 CGGTGGAAATACATTTTTCATGGTAC 59.250 38.462 0.00 0.00 37.34 3.34
5813 6466 4.323553 ACTTTCAGTGTAGCTCGTTTCT 57.676 40.909 0.00 0.00 0.00 2.52
5814 6467 4.051922 ACTTTCAGTGTAGCTCGTTTCTG 58.948 43.478 0.00 0.00 0.00 3.02
5815 6468 3.728076 TTCAGTGTAGCTCGTTTCTGT 57.272 42.857 0.00 0.00 0.00 3.41
5825 6478 4.304939 AGCTCGTTTCTGTTGTTACCTAC 58.695 43.478 0.00 0.00 0.00 3.18
5850 6503 3.193267 GTGCTCTGGGAAAATGTGCATTA 59.807 43.478 0.00 0.00 33.76 1.90
5928 6587 7.565323 ACATATGGATCTTTTTCTTCTGAGC 57.435 36.000 7.80 0.00 0.00 4.26
5929 6588 7.114754 ACATATGGATCTTTTTCTTCTGAGCA 58.885 34.615 7.80 0.00 0.00 4.26
5930 6589 7.613022 ACATATGGATCTTTTTCTTCTGAGCAA 59.387 33.333 7.80 0.00 0.00 3.91
5931 6590 6.906157 ATGGATCTTTTTCTTCTGAGCAAA 57.094 33.333 0.00 0.00 0.00 3.68
5932 6591 6.076981 TGGATCTTTTTCTTCTGAGCAAAC 57.923 37.500 0.00 0.00 0.00 2.93
5934 6593 5.242615 GGATCTTTTTCTTCTGAGCAAACCT 59.757 40.000 0.00 0.00 0.00 3.50
5936 6595 4.949856 TCTTTTTCTTCTGAGCAAACCTGT 59.050 37.500 0.00 0.00 0.00 4.00
5938 6597 4.637483 TTTCTTCTGAGCAAACCTGTTG 57.363 40.909 0.00 0.00 0.00 3.33
5939 6598 3.558931 TCTTCTGAGCAAACCTGTTGA 57.441 42.857 0.00 0.00 0.00 3.18
6011 8702 3.790223 GGCTTGAATGGCCCAACA 58.210 55.556 0.00 0.00 43.49 3.33
6012 8703 2.289840 GGCTTGAATGGCCCAACAT 58.710 52.632 0.00 0.00 43.49 2.71
6098 8801 3.089284 AGGGTTCAAATCAAATCGACCC 58.911 45.455 0.00 0.00 44.39 4.46
6407 9118 1.148759 GCGTTCTGAGCTCCGGATTC 61.149 60.000 12.15 6.91 0.00 2.52
6410 9121 2.545731 GTTCTGAGCTCCGGATTCTTC 58.454 52.381 12.15 0.87 0.00 2.87
6519 9230 3.946201 AGCAACAGAGGCGGCAGT 61.946 61.111 13.08 3.52 36.08 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.935828 GGTCTTGGATGCAAACTAGAGAC 59.064 47.826 0.00 3.60 33.37 3.36
1 2 3.368427 CGGTCTTGGATGCAAACTAGAGA 60.368 47.826 0.00 0.00 0.00 3.10
2 3 2.932614 CGGTCTTGGATGCAAACTAGAG 59.067 50.000 0.00 0.00 0.00 2.43
4 5 2.009774 CCGGTCTTGGATGCAAACTAG 58.990 52.381 0.00 0.00 0.00 2.57
5 6 1.626321 TCCGGTCTTGGATGCAAACTA 59.374 47.619 0.00 0.00 31.53 2.24
6 7 0.400213 TCCGGTCTTGGATGCAAACT 59.600 50.000 0.00 0.00 31.53 2.66
7 8 0.804989 CTCCGGTCTTGGATGCAAAC 59.195 55.000 0.00 2.77 37.41 2.93
9 10 0.400213 AACTCCGGTCTTGGATGCAA 59.600 50.000 0.00 0.00 37.41 4.08
10 11 0.400213 AAACTCCGGTCTTGGATGCA 59.600 50.000 0.00 0.00 37.41 3.96
11 12 0.804989 CAAACTCCGGTCTTGGATGC 59.195 55.000 0.00 0.00 37.41 3.91
12 13 1.453155 CCAAACTCCGGTCTTGGATG 58.547 55.000 20.49 5.54 41.88 3.51
13 14 0.328258 CCCAAACTCCGGTCTTGGAT 59.672 55.000 24.41 0.00 41.88 3.41
14 15 0.765135 TCCCAAACTCCGGTCTTGGA 60.765 55.000 24.41 12.70 41.88 3.53
15 16 0.328258 ATCCCAAACTCCGGTCTTGG 59.672 55.000 19.03 19.03 39.51 3.61
16 17 1.679032 GGATCCCAAACTCCGGTCTTG 60.679 57.143 0.00 3.61 0.00 3.02
17 18 0.618981 GGATCCCAAACTCCGGTCTT 59.381 55.000 0.00 0.00 0.00 3.01
18 19 1.272554 GGGATCCCAAACTCCGGTCT 61.273 60.000 26.95 0.00 35.81 3.85
112 113 3.916359 TGGACATTTATCCCGCAACTA 57.084 42.857 0.00 0.00 38.06 2.24
116 117 2.172505 AGACATGGACATTTATCCCGCA 59.827 45.455 0.00 0.00 38.06 5.69
139 140 2.517650 GACTCCAGGGCGAGATAAAG 57.482 55.000 0.00 0.00 33.83 1.85
214 216 5.115480 ACGGTGCTGAAAAATGAACAAATT 58.885 33.333 0.00 0.00 0.00 1.82
215 217 4.692228 ACGGTGCTGAAAAATGAACAAAT 58.308 34.783 0.00 0.00 0.00 2.32
222 224 1.526464 GCCAAACGGTGCTGAAAAATG 59.474 47.619 0.00 0.00 0.00 2.32
223 225 1.412343 AGCCAAACGGTGCTGAAAAAT 59.588 42.857 0.00 0.00 36.23 1.82
224 226 0.820871 AGCCAAACGGTGCTGAAAAA 59.179 45.000 0.00 0.00 36.23 1.94
231 233 0.110373 CTTTCGTAGCCAAACGGTGC 60.110 55.000 4.30 0.00 43.05 5.01
266 269 1.092921 ACGCGCCTTTCACAAAGTCA 61.093 50.000 5.73 0.00 36.77 3.41
272 275 1.221466 CTTGAGACGCGCCTTTCACA 61.221 55.000 5.73 0.00 0.00 3.58
284 287 2.009888 GCACATAGCGCCTTGAGAC 58.990 57.895 13.54 0.00 0.00 3.36
302 305 7.551585 AGAGATGAACACATAAGGTAGTTGAG 58.448 38.462 0.00 0.00 0.00 3.02
308 311 7.561722 AGCTCTAAGAGATGAACACATAAGGTA 59.438 37.037 0.00 0.00 0.00 3.08
388 391 8.964476 ATCGTTCACATCTTGGTATTTCTTAT 57.036 30.769 0.00 0.00 0.00 1.73
450 477 9.678260 AAGAGCACTCATAAACTTAAAGATCAT 57.322 29.630 0.00 0.00 0.00 2.45
478 505 7.771183 AGCAAAGATCACTAAGTTCAACAAAA 58.229 30.769 0.00 0.00 0.00 2.44
519 646 8.445275 ACGAAAAATGTACATATGAATAGCCA 57.555 30.769 9.21 0.00 0.00 4.75
735 876 1.889530 CGGCCTCGGAGGAGAAAGTT 61.890 60.000 27.95 0.00 43.27 2.66
896 1050 2.107141 GGAACGGCAGATCTCGGG 59.893 66.667 8.50 0.00 0.00 5.14
914 1068 2.044620 GGGGAGGGTGAGGGGATT 59.955 66.667 0.00 0.00 0.00 3.01
1005 1171 3.685214 CTCGTCGAAGGGCTCCGTG 62.685 68.421 0.00 0.00 0.00 4.94
1422 1928 4.100084 TCCTCGTCCTCCGCCGTA 62.100 66.667 0.00 0.00 36.19 4.02
1425 1931 4.816984 TCCTCCTCGTCCTCCGCC 62.817 72.222 0.00 0.00 36.19 6.13
1426 1932 3.213402 CTCCTCCTCGTCCTCCGC 61.213 72.222 0.00 0.00 36.19 5.54
1427 1933 2.517402 CCTCCTCCTCGTCCTCCG 60.517 72.222 0.00 0.00 38.13 4.63
1428 1934 1.152839 CTCCTCCTCCTCGTCCTCC 60.153 68.421 0.00 0.00 0.00 4.30
1429 1935 1.152839 CCTCCTCCTCCTCGTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
1430 1936 1.215679 TTCCTCCTCCTCCTCGTCCT 61.216 60.000 0.00 0.00 0.00 3.85
1431 1937 0.753848 CTTCCTCCTCCTCCTCGTCC 60.754 65.000 0.00 0.00 0.00 4.79
1432 1938 0.256464 TCTTCCTCCTCCTCCTCGTC 59.744 60.000 0.00 0.00 0.00 4.20
1433 1939 0.930726 ATCTTCCTCCTCCTCCTCGT 59.069 55.000 0.00 0.00 0.00 4.18
1434 1940 1.133637 TCATCTTCCTCCTCCTCCTCG 60.134 57.143 0.00 0.00 0.00 4.63
1435 1941 2.765689 TCATCTTCCTCCTCCTCCTC 57.234 55.000 0.00 0.00 0.00 3.71
1436 1942 2.521841 TCATCATCTTCCTCCTCCTCCT 59.478 50.000 0.00 0.00 0.00 3.69
1439 1945 2.091610 TCGTCATCATCTTCCTCCTCCT 60.092 50.000 0.00 0.00 0.00 3.69
1458 1964 2.049985 GGATCGAGCCCGTCATCG 60.050 66.667 9.02 0.00 40.26 3.84
1651 2166 2.351322 CTCGACGTCCATCTCGCG 60.351 66.667 10.58 0.00 0.00 5.87
1652 2167 2.652496 GCTCGACGTCCATCTCGC 60.652 66.667 10.58 0.00 0.00 5.03
1728 2243 1.198759 TCTTCCCCTTCCCTTCCACG 61.199 60.000 0.00 0.00 0.00 4.94
1730 2245 1.132201 TCTTCTTCCCCTTCCCTTCCA 60.132 52.381 0.00 0.00 0.00 3.53
1814 2395 2.098233 GCCCGTTTCTTCGATGCGA 61.098 57.895 0.00 0.00 0.00 5.10
1821 2402 1.270893 ACCTTCTCAGCCCGTTTCTTC 60.271 52.381 0.00 0.00 0.00 2.87
1833 2414 4.736126 TCATCGAAATGCTACCTTCTCA 57.264 40.909 0.00 0.00 32.58 3.27
1843 2424 6.710692 AAGGAAACAAAATCATCGAAATGC 57.289 33.333 0.00 0.00 32.58 3.56
1898 2479 2.624838 ACAAAAGCCACAGACCATTCAG 59.375 45.455 0.00 0.00 0.00 3.02
1908 2489 1.411977 CACCCATCAACAAAAGCCACA 59.588 47.619 0.00 0.00 0.00 4.17
1909 2490 1.412343 ACACCCATCAACAAAAGCCAC 59.588 47.619 0.00 0.00 0.00 5.01
1911 2492 1.000843 GGACACCCATCAACAAAAGCC 59.999 52.381 0.00 0.00 0.00 4.35
1913 2494 2.958355 ACAGGACACCCATCAACAAAAG 59.042 45.455 0.00 0.00 33.88 2.27
1937 2518 0.612229 CCTCTCCTGCACACATCAGT 59.388 55.000 0.00 0.00 0.00 3.41
1946 2527 2.364842 GAGCCCTCCTCTCCTGCA 60.365 66.667 0.00 0.00 37.60 4.41
1974 2555 2.202919 TGCGACTCGGCATGGATG 60.203 61.111 0.00 0.00 38.17 3.51
2025 2606 1.076024 ACCATCTGCTTCCAACCATGT 59.924 47.619 0.00 0.00 0.00 3.21
2157 2738 1.115467 GAAGGCGGATCTTCTCCAGA 58.885 55.000 0.00 0.00 45.24 3.86
2216 2797 8.699749 GTGTTCTTTGCATAACCTTCATAAAAC 58.300 33.333 0.00 0.00 0.00 2.43
2224 2805 6.040842 AGTCATTGTGTTCTTTGCATAACCTT 59.959 34.615 0.00 0.00 0.00 3.50
2308 2889 5.011635 GTCTTGGTCTTCTTCTTCCTCTTCT 59.988 44.000 0.00 0.00 0.00 2.85
2320 2913 3.257127 CCTCTTCTTCGTCTTGGTCTTCT 59.743 47.826 0.00 0.00 0.00 2.85
2326 2919 2.171840 TCCTCCTCTTCTTCGTCTTGG 58.828 52.381 0.00 0.00 0.00 3.61
2327 2920 3.508012 TCTTCCTCCTCTTCTTCGTCTTG 59.492 47.826 0.00 0.00 0.00 3.02
2332 2925 4.461081 TCTTCTTCTTCCTCCTCTTCTTCG 59.539 45.833 0.00 0.00 0.00 3.79
2341 2934 2.771372 AGAGGCATCTTCTTCTTCCTCC 59.229 50.000 0.00 0.00 40.60 4.30
2377 2979 2.268920 GGCTGTTCAGCGGGATCA 59.731 61.111 16.84 0.00 35.24 2.92
2402 3004 0.107459 CCCACTTCCTTAGCCTCAGC 60.107 60.000 0.00 0.00 40.32 4.26
2409 3011 4.020218 TGTCATCTGAACCCACTTCCTTAG 60.020 45.833 0.00 0.00 0.00 2.18
2491 3093 9.005777 ACGATTCACAACCTTTTAGCTTTATAA 57.994 29.630 0.00 0.00 0.00 0.98
2498 3100 4.855531 ACAACGATTCACAACCTTTTAGC 58.144 39.130 0.00 0.00 0.00 3.09
2507 3109 3.684305 CAGCATCCTACAACGATTCACAA 59.316 43.478 0.00 0.00 0.00 3.33
2527 3129 0.397941 TCCAACCTCCTTGTCAGCAG 59.602 55.000 0.00 0.00 0.00 4.24
2553 3155 1.072331 GTGGTCATTCAGGTCACCAGT 59.928 52.381 0.00 0.00 39.64 4.00
2682 3284 6.469410 ACCACGTTTATTAAGATCCTTGTCA 58.531 36.000 0.00 0.00 0.00 3.58
2791 3393 3.381272 GGCATGCTCTTATGGTAAAAGCA 59.619 43.478 18.92 0.74 46.04 3.91
2846 3449 5.527214 TGACATTGTGACACTTAAGTTGAGG 59.473 40.000 5.07 0.00 0.00 3.86
2956 3560 9.010029 ACTTTCTAACCATAGTACCAAACATTG 57.990 33.333 0.00 0.00 0.00 2.82
2991 3605 8.890410 ATTTTGAATCTATGATAATCCTGGGG 57.110 34.615 0.00 0.00 0.00 4.96
3055 3669 7.605449 ACTTTATGAGAATTGACAACCATTGG 58.395 34.615 0.00 0.00 34.12 3.16
3153 3767 3.674753 CCAATAGTCCAAAAAGCAAAGCG 59.325 43.478 0.00 0.00 0.00 4.68
3214 3828 0.958091 TTGGTTGGGCATTGTCTTCG 59.042 50.000 0.00 0.00 0.00 3.79
3474 4088 5.344884 GTGCTACAACCAAAACAAGCTTTA 58.655 37.500 0.00 0.00 0.00 1.85
3501 4115 7.149307 GTCAAGGCTACAGGAAGAGATAATAC 58.851 42.308 0.00 0.00 0.00 1.89
3654 4268 5.984926 GCTTGTTCTCCATGAAAATTTGTCA 59.015 36.000 0.00 0.00 36.30 3.58
3660 4274 4.549458 CGTTGCTTGTTCTCCATGAAAAT 58.451 39.130 0.00 0.00 36.30 1.82
3665 4279 0.109597 GCCGTTGCTTGTTCTCCATG 60.110 55.000 0.00 0.00 33.53 3.66
3666 4280 1.244019 GGCCGTTGCTTGTTCTCCAT 61.244 55.000 0.00 0.00 37.74 3.41
3740 4354 9.868277 TTCAACAAAATGTTAATAGCCAATAGG 57.132 29.630 0.00 0.00 38.77 2.57
3902 4517 1.812922 GGACAGCAGCATCTGGACG 60.813 63.158 9.55 0.00 38.36 4.79
4222 4837 6.000891 TGTGACCTTTCATTTTCTGATTCG 57.999 37.500 0.00 0.00 33.11 3.34
4271 4886 6.469782 TTGTTTTGCCTTCTCAGAATTCTT 57.530 33.333 4.86 0.00 0.00 2.52
4318 4933 4.428209 AGTGCTCATAAGTGTCATTCTCG 58.572 43.478 0.00 0.00 0.00 4.04
4445 5061 9.729281 AGTCCAAAAATGAAATATCAAGCATTT 57.271 25.926 0.00 0.00 41.27 2.32
4446 5062 9.158233 CAGTCCAAAAATGAAATATCAAGCATT 57.842 29.630 0.00 0.00 39.49 3.56
4470 5086 1.550976 AGCGAAGGGAGGAACTAACAG 59.449 52.381 0.00 0.00 41.55 3.16
4480 5096 1.103803 TACTAGCACAGCGAAGGGAG 58.896 55.000 0.00 0.00 0.00 4.30
4487 5104 2.638556 AAGTCTGTACTAGCACAGCG 57.361 50.000 17.03 0.00 44.62 5.18
4583 5200 4.778579 ACTGTCATCTTCCAATGGAGATG 58.221 43.478 23.67 23.67 38.00 2.90
4694 5311 7.566569 TCATATGCATGGATTGAAATTTTGGT 58.433 30.769 10.16 0.00 32.61 3.67
4708 5325 6.779115 CCATGTTTTCAATCATATGCATGG 57.221 37.500 10.16 15.71 43.72 3.66
4714 5331 5.657745 TGACCAGCCATGTTTTCAATCATAT 59.342 36.000 0.00 0.00 0.00 1.78
4762 5379 7.874016 AGCATTTCAAGATTTGCTGAAAACATA 59.126 29.630 6.50 0.00 43.44 2.29
4816 5433 8.918202 AGTGTCAGTAATCATTTACCTTTGAA 57.082 30.769 0.00 0.00 38.81 2.69
4830 5447 7.865706 ACAAACAGAAAAGAGTGTCAGTAAT 57.134 32.000 0.00 0.00 0.00 1.89
4863 5480 4.408270 AGCTAGTCAACATCCATGTGAGAT 59.592 41.667 0.00 0.00 41.61 2.75
4870 5487 5.587844 GTCATTTCAGCTAGTCAACATCCAT 59.412 40.000 0.00 0.00 0.00 3.41
4881 5498 4.694509 GCCATATGAGGTCATTTCAGCTAG 59.305 45.833 3.65 0.00 37.76 3.42
4895 5527 4.023450 ACAAGCGATGATTTGCCATATGAG 60.023 41.667 3.65 0.00 32.06 2.90
4915 5547 4.478206 TTTTCCATTTGGAGCAACACAA 57.522 36.364 0.00 0.00 46.36 3.33
4917 5549 6.146021 CAGTAATTTTCCATTTGGAGCAACAC 59.854 38.462 0.00 0.00 46.36 3.32
4939 5571 6.013639 ACAGAGGGTAATGTTTAGTAAGCAGT 60.014 38.462 5.64 5.35 0.00 4.40
4940 5572 6.407202 ACAGAGGGTAATGTTTAGTAAGCAG 58.593 40.000 5.64 0.00 0.00 4.24
4941 5573 6.368779 ACAGAGGGTAATGTTTAGTAAGCA 57.631 37.500 1.63 1.63 0.00 3.91
4942 5574 6.760298 GGTACAGAGGGTAATGTTTAGTAAGC 59.240 42.308 0.00 0.00 32.72 3.09
4943 5575 8.075761 AGGTACAGAGGGTAATGTTTAGTAAG 57.924 38.462 0.00 0.00 32.72 2.34
4944 5576 9.193806 CTAGGTACAGAGGGTAATGTTTAGTAA 57.806 37.037 0.00 0.00 32.72 2.24
4945 5577 8.339247 ACTAGGTACAGAGGGTAATGTTTAGTA 58.661 37.037 0.00 0.00 32.72 1.82
4946 5578 7.187676 ACTAGGTACAGAGGGTAATGTTTAGT 58.812 38.462 0.00 0.00 32.72 2.24
4947 5579 7.657023 ACTAGGTACAGAGGGTAATGTTTAG 57.343 40.000 0.00 0.00 32.72 1.85
4948 5580 9.545928 TTTACTAGGTACAGAGGGTAATGTTTA 57.454 33.333 0.00 0.00 32.72 2.01
4949 5581 8.439964 TTTACTAGGTACAGAGGGTAATGTTT 57.560 34.615 0.00 0.00 32.72 2.83
4950 5582 8.316946 GTTTTACTAGGTACAGAGGGTAATGTT 58.683 37.037 0.00 0.00 32.72 2.71
4951 5583 7.093156 GGTTTTACTAGGTACAGAGGGTAATGT 60.093 40.741 0.00 0.00 32.72 2.71
4952 5584 7.125356 AGGTTTTACTAGGTACAGAGGGTAATG 59.875 40.741 0.00 0.00 32.72 1.90
4953 5585 7.194761 AGGTTTTACTAGGTACAGAGGGTAAT 58.805 38.462 0.00 0.00 32.72 1.89
4954 5586 6.565036 AGGTTTTACTAGGTACAGAGGGTAA 58.435 40.000 0.00 0.00 32.72 2.85
4955 5587 6.157862 AGGTTTTACTAGGTACAGAGGGTA 57.842 41.667 0.00 0.00 0.00 3.69
4956 5588 5.020941 AGGTTTTACTAGGTACAGAGGGT 57.979 43.478 0.00 0.00 0.00 4.34
4957 5589 4.097589 CGAGGTTTTACTAGGTACAGAGGG 59.902 50.000 0.00 0.00 0.00 4.30
4958 5590 4.946157 TCGAGGTTTTACTAGGTACAGAGG 59.054 45.833 0.00 0.00 0.00 3.69
4959 5591 5.647225 AGTCGAGGTTTTACTAGGTACAGAG 59.353 44.000 0.00 0.00 0.00 3.35
4960 5592 5.564550 AGTCGAGGTTTTACTAGGTACAGA 58.435 41.667 0.00 0.00 0.00 3.41
4961 5593 5.893897 AGTCGAGGTTTTACTAGGTACAG 57.106 43.478 0.00 0.00 0.00 2.74
4962 5594 7.759489 TTAAGTCGAGGTTTTACTAGGTACA 57.241 36.000 0.00 0.00 0.00 2.90
4963 5595 8.082242 TGTTTAAGTCGAGGTTTTACTAGGTAC 58.918 37.037 0.00 0.00 0.00 3.34
4964 5596 8.177119 TGTTTAAGTCGAGGTTTTACTAGGTA 57.823 34.615 0.00 0.00 0.00 3.08
4979 5611 7.858052 AGAATGCAAAATTCTGTTTAAGTCG 57.142 32.000 0.24 0.00 37.03 4.18
5042 5674 9.623000 GGGAAAGTACATGTAATTACCTGTATT 57.377 33.333 26.37 21.95 38.76 1.89
5043 5675 8.999895 AGGGAAAGTACATGTAATTACCTGTAT 58.000 33.333 27.51 16.37 38.76 2.29
5044 5676 8.262227 CAGGGAAAGTACATGTAATTACCTGTA 58.738 37.037 34.04 22.40 40.06 2.74
5045 5677 7.110155 CAGGGAAAGTACATGTAATTACCTGT 58.890 38.462 34.04 24.05 40.06 4.00
5046 5678 6.038271 GCAGGGAAAGTACATGTAATTACCTG 59.962 42.308 35.83 35.83 43.43 4.00
5047 5679 6.120220 GCAGGGAAAGTACATGTAATTACCT 58.880 40.000 24.83 24.83 33.74 3.08
5048 5680 5.298527 GGCAGGGAAAGTACATGTAATTACC 59.701 44.000 22.28 22.28 0.00 2.85
5049 5681 5.883673 TGGCAGGGAAAGTACATGTAATTAC 59.116 40.000 18.08 13.74 0.00 1.89
5050 5682 6.068461 TGGCAGGGAAAGTACATGTAATTA 57.932 37.500 18.08 0.00 0.00 1.40
5051 5683 4.929479 TGGCAGGGAAAGTACATGTAATT 58.071 39.130 12.58 12.58 0.00 1.40
5052 5684 4.584638 TGGCAGGGAAAGTACATGTAAT 57.415 40.909 7.25 2.94 0.00 1.89
5053 5685 4.584638 ATGGCAGGGAAAGTACATGTAA 57.415 40.909 7.25 0.00 0.00 2.41
5054 5686 4.263727 ACAATGGCAGGGAAAGTACATGTA 60.264 41.667 0.08 0.08 0.00 2.29
5064 5696 2.380064 AACAGAACAATGGCAGGGAA 57.620 45.000 0.00 0.00 0.00 3.97
5070 5702 3.620488 TGATCCCTAACAGAACAATGGC 58.380 45.455 0.00 0.00 0.00 4.40
5071 5703 6.377996 TGAAATGATCCCTAACAGAACAATGG 59.622 38.462 0.00 0.00 0.00 3.16
5095 5727 3.434299 GCTTGCAATGGAAAAGAACCATG 59.566 43.478 0.00 0.00 45.89 3.66
5104 5736 4.279982 TCAGATATGGCTTGCAATGGAAA 58.720 39.130 0.00 0.00 0.00 3.13
5116 5748 5.163612 GGAAACAGGTTTTCTCAGATATGGC 60.164 44.000 0.00 0.00 32.11 4.40
5117 5749 5.358160 GGGAAACAGGTTTTCTCAGATATGG 59.642 44.000 3.39 0.00 32.11 2.74
5118 5750 5.358160 GGGGAAACAGGTTTTCTCAGATATG 59.642 44.000 3.39 0.00 28.85 1.78
5119 5751 5.254032 AGGGGAAACAGGTTTTCTCAGATAT 59.746 40.000 5.88 0.00 30.81 1.63
5120 5752 4.601857 AGGGGAAACAGGTTTTCTCAGATA 59.398 41.667 5.88 0.00 30.81 1.98
5125 5774 3.562182 TGAAGGGGAAACAGGTTTTCTC 58.438 45.455 3.39 0.00 32.11 2.87
5127 5776 4.955811 AATGAAGGGGAAACAGGTTTTC 57.044 40.909 0.00 0.00 32.11 2.29
5134 5783 7.525360 GCAAGAGATAAAAATGAAGGGGAAACA 60.525 37.037 0.00 0.00 0.00 2.83
5135 5784 6.813649 GCAAGAGATAAAAATGAAGGGGAAAC 59.186 38.462 0.00 0.00 0.00 2.78
5143 5792 8.114331 ACTGTGATGCAAGAGATAAAAATGAA 57.886 30.769 0.00 0.00 0.00 2.57
5148 5797 8.565896 ACAATACTGTGATGCAAGAGATAAAA 57.434 30.769 0.00 0.00 33.30 1.52
5160 5809 9.874215 CTGCAAAGAATATACAATACTGTGATG 57.126 33.333 0.00 0.00 36.96 3.07
5161 5810 9.618890 ACTGCAAAGAATATACAATACTGTGAT 57.381 29.630 0.00 0.00 36.96 3.06
5162 5811 9.098355 GACTGCAAAGAATATACAATACTGTGA 57.902 33.333 0.00 0.00 36.96 3.58
5163 5812 8.058328 CGACTGCAAAGAATATACAATACTGTG 58.942 37.037 0.00 0.00 36.96 3.66
5225 5874 9.092876 CCTTTGTAAGTTGATCTATGAGAAGAC 57.907 37.037 0.00 0.00 0.00 3.01
5267 5916 2.421073 GCTGTTGCTATTGCTGTCATCA 59.579 45.455 0.00 0.00 40.48 3.07
5334 5983 7.664731 ACAAGATCAGAGACAAGTTTTCATCAT 59.335 33.333 0.00 0.00 0.00 2.45
5405 6054 3.128242 GGGCACATGAGAATGTTTCTGAG 59.872 47.826 0.00 0.00 40.87 3.35
5428 6077 4.141711 GGTCCTGCTGTATAGTGGAATGAA 60.142 45.833 5.29 0.00 33.07 2.57
5514 6164 2.435586 CTCGGAGCTTGTGCCTGG 60.436 66.667 0.00 0.00 40.80 4.45
5542 6192 1.004440 AACAGAGAGGCGCCTGAAC 60.004 57.895 38.41 23.67 34.65 3.18
5594 6244 1.008079 GCGCTTGTGCTCTTGCTTT 60.008 52.632 0.00 0.00 40.48 3.51
5615 6265 1.739466 GTGATGATGCCGAAGCTTTCA 59.261 47.619 0.00 0.00 40.80 2.69
5729 6379 1.214424 GGTAGCAATGGTATGTGGGGT 59.786 52.381 0.00 0.00 0.00 4.95
5730 6380 1.214175 TGGTAGCAATGGTATGTGGGG 59.786 52.381 0.00 0.00 0.00 4.96
5733 6383 5.007626 GTGTACATGGTAGCAATGGTATGTG 59.992 44.000 0.00 5.30 31.84 3.21
5736 6386 4.412199 AGGTGTACATGGTAGCAATGGTAT 59.588 41.667 0.00 0.00 0.00 2.73
5737 6387 3.778075 AGGTGTACATGGTAGCAATGGTA 59.222 43.478 0.00 0.00 0.00 3.25
5793 6446 4.051922 ACAGAAACGAGCTACACTGAAAG 58.948 43.478 0.00 0.00 42.29 2.62
5813 6466 2.969950 AGAGCACAGGTAGGTAACAACA 59.030 45.455 0.00 0.00 41.41 3.33
5814 6467 3.326747 CAGAGCACAGGTAGGTAACAAC 58.673 50.000 0.00 0.00 41.41 3.32
5815 6468 2.301870 CCAGAGCACAGGTAGGTAACAA 59.698 50.000 0.00 0.00 41.41 2.83
5825 6478 1.542915 CACATTTTCCCAGAGCACAGG 59.457 52.381 0.00 0.00 0.00 4.00
5850 6503 9.268282 TCTTAAACCTAAGGTGATACAGAATCT 57.732 33.333 0.00 0.00 35.34 2.40
5927 6586 1.069227 GTCGACCATCAACAGGTTTGC 60.069 52.381 3.51 0.00 40.09 3.68
5928 6587 2.217750 TGTCGACCATCAACAGGTTTG 58.782 47.619 14.12 0.00 40.09 2.93
5929 6588 2.494059 CTGTCGACCATCAACAGGTTT 58.506 47.619 14.12 0.00 40.09 3.27
5930 6589 1.878102 GCTGTCGACCATCAACAGGTT 60.878 52.381 14.12 0.00 40.09 3.50
5931 6590 0.320771 GCTGTCGACCATCAACAGGT 60.321 55.000 14.12 0.00 43.46 4.00
5932 6591 1.021390 GGCTGTCGACCATCAACAGG 61.021 60.000 14.12 0.00 40.57 4.00
5934 6593 0.320683 CAGGCTGTCGACCATCAACA 60.321 55.000 14.12 0.00 0.00 3.33
5936 6595 1.296392 CCAGGCTGTCGACCATCAA 59.704 57.895 14.12 0.00 0.00 2.57
5938 6597 2.187946 CCCAGGCTGTCGACCATC 59.812 66.667 14.12 1.97 0.00 3.51
5939 6598 4.101448 GCCCAGGCTGTCGACCAT 62.101 66.667 14.12 0.00 38.26 3.55
6098 8801 1.182385 GGATAGGGCGAGGAGGACAG 61.182 65.000 0.00 0.00 0.00 3.51
6407 9118 2.641305 CTGCCATGGGAGAGAAAGAAG 58.359 52.381 28.19 0.00 35.50 2.85
6410 9121 0.750911 GGCTGCCATGGGAGAGAAAG 60.751 60.000 35.08 10.52 35.50 2.62
6519 9230 1.238896 AGGGGGAGGAGAGATGGGAA 61.239 60.000 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.