Multiple sequence alignment - TraesCS5A01G460600

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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 TraesCS5A01G460600 chr5A 100.000 6495 0 0 1 6495 640937861 640944355 0.000000e+00 11995
1 TraesCS5A01G460600 chr5A 89.623 106 11 0 5937 6042 640943748 640943853 1.140000e-27 135
2 TraesCS5A01G460600 chr5A 89.623 106 11 0 5888 5993 640943797 640943902 1.140000e-27 135
3 TraesCS5A01G460600 chr5B 94.902 1981 82 11 3536 5503 643668424 643670398 0.000000e+00 3081
4 TraesCS5A01G460600 chr5B 89.652 1092 65 18 1651 2701 643666426 643667510 0.000000e+00 1347
5 TraesCS5A01G460600 chr5B 93.246 844 45 8 2696 3534 643667533 643668369 0.000000e+00 1232
6 TraesCS5A01G460600 chr5B 89.384 471 40 7 1279 1745 643665983 643666447 9.380000e-163 584
7 TraesCS5A01G460600 chr5B 82.591 494 45 23 511 969 643664812 643665299 1.310000e-106 398
8 TraesCS5A01G460600 chr5B 89.540 239 20 4 20 257 643664388 643664622 1.370000e-76 298
9 TraesCS5A01G460600 chr5B 86.667 240 11 7 1037 1267 643665703 643665930 5.030000e-61 246
10 TraesCS5A01G460600 chr5D 90.384 2319 144 21 1279 3534 512768637 512770939 0.000000e+00 2974
11 TraesCS5A01G460600 chr5D 93.136 1282 55 15 3536 4803 512770994 512772256 0.000000e+00 1849
12 TraesCS5A01G460600 chr5D 86.889 1289 93 40 14 1267 512767337 512768584 0.000000e+00 1375
13 TraesCS5A01G460600 chr5D 89.299 785 54 16 4915 5678 512772447 512773222 0.000000e+00 957
14 TraesCS5A01G460600 chr7B 93.432 807 49 3 5691 6495 738900149 738900953 0.000000e+00 1194
15 TraesCS5A01G460600 chr7B 92.632 95 7 0 5897 5991 738900404 738900498 3.160000e-28 137
16 TraesCS5A01G460600 chr1B 99.273 550 4 0 5946 6495 6529783 6529234 0.000000e+00 994
17 TraesCS5A01G460600 chr1B 96.721 305 9 1 5692 5996 6529987 6529684 2.090000e-139 507


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 TraesCS5A01G460600 chr5A 640937861 640944355 6494 False 4088.333333 11995 93.082 1 6495 3 chr5A.!!$F1 6494
1 TraesCS5A01G460600 chr5B 643664388 643670398 6010 False 1026.571429 3081 89.426 20 5503 7 chr5B.!!$F1 5483
2 TraesCS5A01G460600 chr5D 512767337 512773222 5885 False 1788.750000 2974 89.927 14 5678 4 chr5D.!!$F1 5664
3 TraesCS5A01G460600 chr7B 738900149 738900953 804 False 665.500000 1194 93.032 5691 6495 2 chr7B.!!$F1 804
4 TraesCS5A01G460600 chr1B 6529234 6529987 753 True 750.500000 994 97.997 5692 6495 2 chr1B.!!$R1 803

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
61 62 0.250166 CTTTGTCGGTTCCCCTCGTT 60.250 55.000 0.00 0.0 0.00 3.85 F
1608 2162 0.114560 AGGGTGAAGAGAGGGTCGAA 59.885 55.000 0.00 0.0 0.00 3.71 F
1855 2497 0.038599 TTGCATCTGTGGGCTGATGT 59.961 50.000 13.29 0.0 46.34 3.06 F
2497 3159 0.524862 GCAAATGCTGGTGACCTGAG 59.475 55.000 13.05 0.0 38.21 3.35 F
3148 3840 0.681175 AAGACAATGCCCAACCAAGC 59.319 50.000 0.00 0.0 0.00 4.01 F
3983 4729 1.562942 TGGCTTCAGGATCAAGATGCT 59.437 47.619 17.82 0.0 40.25 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 2466 0.957395 CACAGGACACACATCAGCCC 60.957 60.0 0.00 0.00 0.00 5.19 R
3180 3872 0.043183 TGAAGAGGGAGGCAGATGGA 59.957 55.0 0.00 0.00 0.00 3.41 R
3534 4227 0.324552 AATGCACCAGGCCATTGCTA 60.325 50.0 20.18 10.03 43.89 3.49 R
4326 5083 0.324943 GCACAGCAAGGGAGGAACTA 59.675 55.0 0.00 0.00 41.55 2.24 R
4328 5085 0.324943 TAGCACAGCAAGGGAGGAAC 59.675 55.0 0.00 0.00 0.00 3.62 R
5686 6562 0.393077 GGCTATCAGCGCCCTTAAGA 59.607 55.0 2.29 0.00 43.62 2.10 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
61 62 0.250166 CTTTGTCGGTTCCCCTCGTT 60.250 55.000 0.00 0.00 0.00 3.85
142 146 2.499693 TGTCCATGTCTTTATCTCGCCA 59.500 45.455 0.00 0.00 0.00 5.69
148 152 2.139118 GTCTTTATCTCGCCATGGAGC 58.861 52.381 18.40 0.00 33.98 4.70
150 154 0.836606 TTTATCTCGCCATGGAGCCA 59.163 50.000 18.40 1.79 33.98 4.75
156 160 1.228033 CGCCATGGAGCCATCATCA 60.228 57.895 18.40 0.00 33.90 3.07
171 175 3.885724 TCATCACGTTATGCTCCAGAA 57.114 42.857 4.81 0.00 0.00 3.02
195 199 3.959478 GTGGTTCTCACGTCTCACA 57.041 52.632 0.00 0.00 36.56 3.58
199 203 2.102420 TGGTTCTCACGTCTCACATGTT 59.898 45.455 0.00 0.00 0.00 2.71
205 209 7.411588 GGTTCTCACGTCTCACATGTTTTATAC 60.412 40.741 0.00 0.00 0.00 1.47
206 210 6.920817 TCTCACGTCTCACATGTTTTATACT 58.079 36.000 0.00 0.00 0.00 2.12
236 241 2.552599 TTCATCACCGTTTGGCTACA 57.447 45.000 0.00 0.00 39.70 2.74
237 242 2.552599 TCATCACCGTTTGGCTACAA 57.447 45.000 0.00 0.00 39.70 2.41
263 268 0.318107 TCGTTCAACGACCCGACTTC 60.318 55.000 9.01 0.00 46.73 3.01
275 280 2.861006 GACTTCGTGAAAGGCGCC 59.139 61.111 21.89 21.89 39.47 6.53
283 288 0.320771 GTGAAAGGCGCCTCTCAAGA 60.321 55.000 33.20 9.30 0.00 3.02
293 298 1.804372 GCCTCTCAAGACGCTATGTGG 60.804 57.143 0.00 0.00 0.00 4.17
299 304 1.390123 CAAGACGCTATGTGGTCAACG 59.610 52.381 0.00 0.00 35.63 4.10
354 359 4.517285 TCCTGATGCACCTCAAAATCTAC 58.483 43.478 0.00 0.00 0.00 2.59
387 392 5.673337 CACCTCGTGGATATGTAATTTGG 57.327 43.478 11.17 0.00 37.04 3.28
388 393 5.123227 CACCTCGTGGATATGTAATTTGGT 58.877 41.667 11.17 0.00 37.04 3.67
389 394 5.236478 CACCTCGTGGATATGTAATTTGGTC 59.764 44.000 11.17 0.00 37.04 4.02
390 395 5.104693 ACCTCGTGGATATGTAATTTGGTCA 60.105 40.000 11.17 0.00 37.04 4.02
391 396 5.997746 CCTCGTGGATATGTAATTTGGTCAT 59.002 40.000 0.00 0.00 34.57 3.06
392 397 6.147821 CCTCGTGGATATGTAATTTGGTCATC 59.852 42.308 0.00 0.00 34.57 2.92
393 398 6.587273 TCGTGGATATGTAATTTGGTCATCA 58.413 36.000 0.00 0.00 0.00 3.07
394 399 6.705825 TCGTGGATATGTAATTTGGTCATCAG 59.294 38.462 0.00 0.00 0.00 2.90
395 400 6.073058 CGTGGATATGTAATTTGGTCATCAGG 60.073 42.308 0.00 0.00 0.00 3.86
396 401 6.207417 GTGGATATGTAATTTGGTCATCAGGG 59.793 42.308 0.00 0.00 0.00 4.45
397 402 6.102468 TGGATATGTAATTTGGTCATCAGGGA 59.898 38.462 0.00 0.00 0.00 4.20
398 403 6.656693 GGATATGTAATTTGGTCATCAGGGAG 59.343 42.308 0.00 0.00 0.00 4.30
399 404 3.620488 TGTAATTTGGTCATCAGGGAGC 58.380 45.455 0.00 0.00 35.89 4.70
400 405 1.755179 AATTTGGTCATCAGGGAGCG 58.245 50.000 0.00 0.00 38.10 5.03
401 406 0.749454 ATTTGGTCATCAGGGAGCGC 60.749 55.000 0.00 0.00 38.10 5.92
402 407 2.123248 TTTGGTCATCAGGGAGCGCA 62.123 55.000 11.47 0.00 38.10 6.09
403 408 1.913951 TTGGTCATCAGGGAGCGCAT 61.914 55.000 11.47 0.00 38.10 4.73
404 409 1.048160 TGGTCATCAGGGAGCGCATA 61.048 55.000 11.47 0.00 38.10 3.14
405 410 0.320247 GGTCATCAGGGAGCGCATAG 60.320 60.000 11.47 0.00 0.00 2.23
426 431 7.497249 GCATAGAGAAATACCAAGATGTGAACT 59.503 37.037 0.00 0.00 0.00 3.01
525 630 9.419297 TGAACTTAGTGATCATTGTTAGTACAC 57.581 33.333 0.00 0.00 32.98 2.90
529 634 9.639601 CTTAGTGATCATTGTTAGTACACTTCA 57.360 33.333 0.00 0.00 38.01 3.02
530 635 9.990360 TTAGTGATCATTGTTAGTACACTTCAA 57.010 29.630 0.00 0.00 38.01 2.69
549 654 7.588854 CACTTCAATTTCGGCTATTCATATGTG 59.411 37.037 1.90 0.00 0.00 3.21
556 661 7.503521 TTCGGCTATTCATATGTGCATTTTA 57.496 32.000 1.90 0.00 0.00 1.52
558 663 6.710295 TCGGCTATTCATATGTGCATTTTACT 59.290 34.615 1.90 0.00 0.00 2.24
559 664 7.228507 TCGGCTATTCATATGTGCATTTTACTT 59.771 33.333 1.90 0.00 0.00 2.24
560 665 7.862372 CGGCTATTCATATGTGCATTTTACTTT 59.138 33.333 1.90 0.00 0.00 2.66
561 666 9.185192 GGCTATTCATATGTGCATTTTACTTTC 57.815 33.333 1.90 0.00 0.00 2.62
636 743 9.550811 CGGTTCCTAAAACAAGACAATATAAAC 57.449 33.333 0.00 0.00 0.00 2.01
667 774 5.936956 TGAAGTTGAAAAACAAGGCAAACAT 59.063 32.000 0.00 0.00 39.30 2.71
738 845 3.074281 CCCGCTACCACCCAAAGA 58.926 61.111 0.00 0.00 0.00 2.52
739 846 1.377229 CCCGCTACCACCCAAAGAA 59.623 57.895 0.00 0.00 0.00 2.52
885 1025 1.655959 CGTTTTGTTTCGCACCCCG 60.656 57.895 0.00 0.00 38.61 5.73
932 1074 2.762459 CGTTCCGATCCCCTCCCA 60.762 66.667 0.00 0.00 0.00 4.37
935 1077 2.955859 TTCCGATCCCCTCCCACCT 61.956 63.158 0.00 0.00 0.00 4.00
938 1080 2.844839 GATCCCCTCCCACCTCCG 60.845 72.222 0.00 0.00 0.00 4.63
941 1083 4.400251 CCCCTCCCACCTCCGACT 62.400 72.222 0.00 0.00 0.00 4.18
942 1084 2.760385 CCCTCCCACCTCCGACTC 60.760 72.222 0.00 0.00 0.00 3.36
944 1086 2.360980 CTCCCACCTCCGACTCCT 59.639 66.667 0.00 0.00 0.00 3.69
947 1089 2.361357 CCACCTCCGACTCCTCGT 60.361 66.667 0.00 0.00 38.32 4.18
951 1093 1.078356 CCTCCGACTCCTCGTGAGA 60.078 63.158 10.87 0.00 44.42 3.27
1102 1590 2.355108 CGCCTCAAGAAATCCTTCCAGA 60.355 50.000 0.00 0.00 31.42 3.86
1103 1591 3.013219 GCCTCAAGAAATCCTTCCAGAC 58.987 50.000 0.00 0.00 31.42 3.51
1104 1592 3.615155 CCTCAAGAAATCCTTCCAGACC 58.385 50.000 0.00 0.00 31.42 3.85
1215 1706 2.606519 CCTCCGAACCACTCCCCA 60.607 66.667 0.00 0.00 0.00 4.96
1218 1709 4.388499 CCGAACCACTCCCCACCG 62.388 72.222 0.00 0.00 0.00 4.94
1226 1723 3.003173 CTCCCCACCGCCTTCAGA 61.003 66.667 0.00 0.00 0.00 3.27
1262 1759 2.631580 CGCGCCTAGGATCTCCTCC 61.632 68.421 14.75 0.00 44.77 4.30
1269 1766 2.203714 GGATCTCCTCCTCCCCCG 60.204 72.222 0.00 0.00 41.29 5.73
1270 1767 2.780185 GGATCTCCTCCTCCCCCGA 61.780 68.421 0.00 0.00 41.29 5.14
1272 1769 3.438615 ATCTCCTCCTCCCCCGACG 62.439 68.421 0.00 0.00 0.00 5.12
1273 1770 4.124943 CTCCTCCTCCCCCGACGA 62.125 72.222 0.00 0.00 0.00 4.20
1276 1773 4.790962 CTCCTCCCCCGACGACGA 62.791 72.222 9.28 0.00 42.66 4.20
1277 1774 4.349503 TCCTCCCCCGACGACGAA 62.350 66.667 9.28 0.00 42.66 3.85
1278 1775 4.125695 CCTCCCCCGACGACGAAC 62.126 72.222 9.28 0.00 42.66 3.95
1286 1825 2.883621 GACGACGAACCCCTCTCC 59.116 66.667 0.00 0.00 0.00 3.71
1287 1826 2.679287 ACGACGAACCCCTCTCCC 60.679 66.667 0.00 0.00 0.00 4.30
1395 1946 4.773117 GACACCGCCGAGGACGAC 62.773 72.222 3.89 0.00 45.00 4.34
1401 1952 2.024871 GCCGAGGACGACGATGAG 59.975 66.667 0.00 0.00 42.66 2.90
1404 1955 1.644372 CGAGGACGACGATGAGGAG 59.356 63.158 0.00 0.00 42.66 3.69
1405 1956 1.777030 CGAGGACGACGATGAGGAGG 61.777 65.000 0.00 0.00 42.66 4.30
1406 1957 1.448922 GAGGACGACGATGAGGAGGG 61.449 65.000 0.00 0.00 0.00 4.30
1407 1958 2.491022 GGACGACGATGAGGAGGGG 61.491 68.421 0.00 0.00 0.00 4.79
1487 2038 4.043100 TCTGCCGACGGGAGAGGA 62.043 66.667 31.48 12.71 45.03 3.71
1488 2039 3.827898 CTGCCGACGGGAGAGGAC 61.828 72.222 29.58 3.87 44.17 3.85
1593 2144 1.296715 GCTCAACATGGACGAGGGT 59.703 57.895 0.00 0.00 0.00 4.34
1599 2150 0.898320 ACATGGACGAGGGTGAAGAG 59.102 55.000 0.00 0.00 0.00 2.85
1600 2151 1.186200 CATGGACGAGGGTGAAGAGA 58.814 55.000 0.00 0.00 0.00 3.10
1602 2153 0.612174 TGGACGAGGGTGAAGAGAGG 60.612 60.000 0.00 0.00 0.00 3.69
1604 2155 0.612453 GACGAGGGTGAAGAGAGGGT 60.612 60.000 0.00 0.00 0.00 4.34
1608 2162 0.114560 AGGGTGAAGAGAGGGTCGAA 59.885 55.000 0.00 0.00 0.00 3.71
1613 2167 1.066143 TGAAGAGAGGGTCGAAATGGC 60.066 52.381 0.00 0.00 0.00 4.40
1614 2168 1.208293 GAAGAGAGGGTCGAAATGGCT 59.792 52.381 0.00 0.00 0.00 4.75
1712 2266 2.307392 AGGGGAAGAAGAAGAAGAAGGC 59.693 50.000 0.00 0.00 0.00 4.35
1751 2371 3.592865 AGAAGAGGAAGAAGGACAAGGT 58.407 45.455 0.00 0.00 0.00 3.50
1805 2425 4.365723 GCCGAGAAGGTAACATTTCGATA 58.634 43.478 0.00 0.00 43.70 2.92
1825 2445 8.172352 TCGATAATTTTGTTTCCTTTCCTTCA 57.828 30.769 0.00 0.00 0.00 3.02
1831 2451 4.385358 TGTTTCCTTTCCTTCAGTTTGC 57.615 40.909 0.00 0.00 0.00 3.68
1832 2452 4.023291 TGTTTCCTTTCCTTCAGTTTGCT 58.977 39.130 0.00 0.00 0.00 3.91
1846 2466 3.673338 CAGTTTGCTTGATTGCATCTGTG 59.327 43.478 0.00 0.00 42.96 3.66
1847 2467 2.991190 GTTTGCTTGATTGCATCTGTGG 59.009 45.455 0.00 0.00 42.96 4.17
1848 2468 1.179152 TGCTTGATTGCATCTGTGGG 58.821 50.000 0.00 0.00 38.12 4.61
1849 2469 0.179119 GCTTGATTGCATCTGTGGGC 60.179 55.000 0.00 0.00 0.00 5.36
1855 2497 0.038599 TTGCATCTGTGGGCTGATGT 59.961 50.000 13.29 0.00 46.34 3.06
2009 2651 7.584108 TGTGCATATCTAACTGTTTCTTGTTG 58.416 34.615 0.00 0.00 0.00 3.33
2012 2654 9.013229 TGCATATCTAACTGTTTCTTGTTGATT 57.987 29.630 0.00 0.00 0.00 2.57
2039 2681 0.795085 CTGCAGAGACAAGAAAGGCG 59.205 55.000 8.42 0.00 0.00 5.52
2081 2723 2.346803 CCAGTGTACAAACCCATCTCG 58.653 52.381 0.00 0.00 0.00 4.04
2137 2779 6.064060 TGGAGATTCAGAAAATGTCAGTTGT 58.936 36.000 0.00 0.00 0.00 3.32
2165 2809 5.726980 TGCTTTTCTGAGGTTATGCAAAT 57.273 34.783 0.00 0.00 0.00 2.32
2167 2811 7.408756 TGCTTTTCTGAGGTTATGCAAATAT 57.591 32.000 0.00 0.00 0.00 1.28
2178 2822 8.978874 AGGTTATGCAAATATCACAATGACTA 57.021 30.769 0.00 0.00 0.00 2.59
2194 2838 6.767902 ACAATGACTATCCGCTGATGTTATTT 59.232 34.615 0.20 0.00 32.18 1.40
2204 2848 5.584649 CCGCTGATGTTATTTTTCTCCACTA 59.415 40.000 0.00 0.00 0.00 2.74
2205 2849 6.456988 CCGCTGATGTTATTTTTCTCCACTAC 60.457 42.308 0.00 0.00 0.00 2.73
2305 2967 1.267574 ATGCCTCTTCAGAGCCCGAA 61.268 55.000 0.00 0.00 40.75 4.30
2335 2997 1.106285 CTGAAAAGCCAGCCATACCC 58.894 55.000 0.00 0.00 0.00 3.69
2349 3011 2.484947 CCATACCCGAGGTTAAGGAAGC 60.485 54.545 0.72 0.00 37.09 3.86
2497 3159 0.524862 GCAAATGCTGGTGACCTGAG 59.475 55.000 13.05 0.00 38.21 3.35
2529 3191 1.010795 TCTCCCTGAGGATGAGGTGA 58.989 55.000 0.00 0.00 38.06 4.02
2546 3208 1.728971 GTGATCACTGCTTTCACTCGG 59.271 52.381 18.83 0.00 37.40 4.63
2582 3244 2.350772 GGTGTTTGCACTGTACTGATGC 60.351 50.000 6.77 12.20 44.65 3.91
2585 3247 2.549064 TTGCACTGTACTGATGCTGT 57.451 45.000 19.72 0.00 40.13 4.40
2588 3250 1.728971 GCACTGTACTGATGCTGTGTC 59.271 52.381 6.77 0.00 40.80 3.67
2590 3252 3.657634 CACTGTACTGATGCTGTGTCTT 58.342 45.455 6.77 0.00 36.21 3.01
2632 3294 9.778741 TGATTAGCGACAAGGATCTTAATAAAT 57.221 29.630 0.00 0.00 0.00 1.40
2639 3301 9.104965 CGACAAGGATCTTAATAAATGTGGTAA 57.895 33.333 0.00 0.00 0.00 2.85
2677 3339 0.819666 CAGCGCCCCTTCCCTAATTC 60.820 60.000 2.29 0.00 0.00 2.17
2682 3344 2.171870 CGCCCCTTCCCTAATTCTGTAA 59.828 50.000 0.00 0.00 0.00 2.41
2691 3353 6.499106 TCCCTAATTCTGTAATCATCTGCA 57.501 37.500 0.00 0.00 0.00 4.41
2701 3363 1.095600 ATCATCTGCAGCTGCTGTTG 58.904 50.000 33.76 33.76 42.66 3.33
2703 3365 1.002315 TCATCTGCAGCTGCTGTTGTA 59.998 47.619 35.63 26.14 42.66 2.41
2725 3413 2.234661 CCCATAAGAGCATGCCTCGATA 59.765 50.000 15.66 10.25 45.54 2.92
2761 3450 6.074005 GCGTTGAAGTTTCTATCTCAACTTG 58.926 40.000 10.92 0.15 42.15 3.16
2867 3556 5.540400 ATGGTTGCTGGATTATCAAATGG 57.460 39.130 0.00 0.00 0.00 3.16
3082 3774 8.674263 TTTGTTTAATGATTTGCTTGTTGGAT 57.326 26.923 0.00 0.00 0.00 3.41
3109 3801 3.813724 GGTTCTACCAGGAACTTGTTGAC 59.186 47.826 0.00 0.00 43.43 3.18
3148 3840 0.681175 AAGACAATGCCCAACCAAGC 59.319 50.000 0.00 0.00 0.00 4.01
3160 3852 2.086869 CAACCAAGCGATGACTCCATT 58.913 47.619 0.00 0.00 32.09 3.16
3180 3872 5.821470 CCATTGATGCTGTAGATGAAGAAGT 59.179 40.000 0.00 0.00 0.00 3.01
3252 3944 1.763968 TATCACACCCTCCTCAGTCG 58.236 55.000 0.00 0.00 0.00 4.18
3261 3953 3.394940 ACCCTCCTCAGTCGATGATACTA 59.605 47.826 0.00 0.00 37.28 1.82
3262 3954 4.141228 ACCCTCCTCAGTCGATGATACTAA 60.141 45.833 0.00 0.00 37.28 2.24
3474 4167 9.556030 GCTAAATAACAGAACCATGTAAACTTC 57.444 33.333 0.00 0.00 31.70 3.01
3530 4223 7.002250 TGACATCCTTCTTCTATCCATCATC 57.998 40.000 0.00 0.00 0.00 2.92
3534 4227 7.072202 ACATCCTTCTTCTATCCATCATCTGTT 59.928 37.037 0.00 0.00 0.00 3.16
3540 4286 7.971201 TCTTCTATCCATCATCTGTTAGCAAT 58.029 34.615 0.00 0.00 0.00 3.56
3576 4322 4.653868 TGCATGGAATTTGCCTGATTTTT 58.346 34.783 0.00 0.00 39.39 1.94
3582 4328 9.116067 CATGGAATTTGCCTGATTTTTCATATT 57.884 29.630 0.00 0.00 0.00 1.28
3612 4358 8.417273 TTGATGCACTATACTACTGGCTATTA 57.583 34.615 0.00 0.00 0.00 0.98
3818 4564 2.694213 GTTGAAGCTGAGGAAGAGGAC 58.306 52.381 0.00 0.00 0.00 3.85
3837 4583 3.515630 GACGACAGTGATGATGACATGT 58.484 45.455 0.00 0.00 36.82 3.21
3983 4729 1.562942 TGGCTTCAGGATCAAGATGCT 59.437 47.619 17.82 0.00 40.25 3.79
4043 4789 3.188048 GTCATCAGGAGCAGAAAGTGTTG 59.812 47.826 0.00 0.00 0.00 3.33
4196 4942 7.614494 TCACAGATGAGAATGACACTTATGAA 58.386 34.615 0.00 0.00 0.00 2.57
4275 5021 3.877508 AGAAGTAAGCGCTGACACTTTTT 59.122 39.130 26.70 11.71 31.57 1.94
4276 5022 3.609103 AGTAAGCGCTGACACTTTTTG 57.391 42.857 26.70 0.00 0.00 2.44
4282 5028 3.058224 AGCGCTGACACTTTTTGAATACC 60.058 43.478 10.39 0.00 0.00 2.73
4287 5033 5.666969 TGACACTTTTTGAATACCGAGTG 57.333 39.130 0.00 0.00 40.11 3.51
4336 5093 7.933215 TTTTTAAAGTGCTATAGTTCCTCCC 57.067 36.000 0.84 0.00 0.00 4.30
4381 5138 2.710096 TCCACCCTATGTGCTTTAGC 57.290 50.000 0.00 0.00 44.01 3.09
4427 5186 8.752766 TTCTTTGTTAGGTTCATAGTACTTCG 57.247 34.615 0.00 0.00 0.00 3.79
4503 5262 5.124645 AGAAGCTCAATATTGCTCCTCAAG 58.875 41.667 10.76 2.44 38.75 3.02
4562 5321 8.149631 AGGATTCCCAAAATTTCAATACATGT 57.850 30.769 2.69 2.69 33.88 3.21
4692 5451 4.495422 AGGTAAATGCTTACTGACACTCG 58.505 43.478 0.00 0.00 38.01 4.18
4731 5490 5.163550 CGTACTTCTCACCTGGATGTTGATA 60.164 44.000 0.00 0.00 0.00 2.15
4748 5507 9.118236 GATGTTGATAAGCTGAAAGTTTGTAAC 57.882 33.333 0.00 0.00 38.11 2.50
4855 5709 8.598916 TGTACTATCCCTCATTGTTTTGTTAGA 58.401 33.333 0.00 0.00 0.00 2.10
4860 5714 5.468746 TCCCTCATTGTTTTGTTAGAGAACG 59.531 40.000 0.00 0.00 38.51 3.95
4882 5736 4.036262 CGTTTTGTGGTTCTCTTCCATTGA 59.964 41.667 0.00 0.00 37.30 2.57
4911 5765 4.421948 CAAGGCATTGCTGAGATTTTCTC 58.578 43.478 8.82 0.00 43.65 2.87
4971 5829 9.319143 GACAGTATTGTATATTCTTTGCAGTCT 57.681 33.333 0.00 0.00 37.76 3.24
5130 5988 4.681483 GTGGTAAGCTTGATGAAAACTTGC 59.319 41.667 9.86 0.00 0.00 4.01
5156 6014 7.268199 TCTGATCTTGTCATAATTCCAATGC 57.732 36.000 0.00 0.00 35.97 3.56
5184 6042 1.364626 GCAGAGTCGCACATTCCCTG 61.365 60.000 2.68 0.00 0.00 4.45
5207 6065 7.381766 TGTATTCAGAAACATTCTCATGTGG 57.618 36.000 0.00 0.00 43.34 4.17
5220 6078 0.105862 CATGTGGCCCCTCATTCCAT 60.106 55.000 0.00 0.00 31.83 3.41
5238 6096 2.439507 CCATTATACAGCAGGACCAGGT 59.560 50.000 0.00 0.00 0.00 4.00
5252 6110 1.604593 CAGGTGAACCCCAGCCAAG 60.605 63.158 0.00 0.00 44.01 3.61
5317 6175 4.021925 GGCACAAGCTCCGAGGGT 62.022 66.667 0.00 0.00 41.70 4.34
5431 6289 1.220206 CATCACGGAGAGCCAAGCT 59.780 57.895 0.00 0.00 43.88 3.74
5512 6370 1.833630 TGACTCACATAGCCTCCCTTG 59.166 52.381 0.00 0.00 0.00 3.61
5513 6371 2.111384 GACTCACATAGCCTCCCTTGA 58.889 52.381 0.00 0.00 0.00 3.02
5516 6374 1.207791 CACATAGCCTCCCTTGACCT 58.792 55.000 0.00 0.00 0.00 3.85
5519 6377 2.022918 ACATAGCCTCCCTTGACCTACT 60.023 50.000 0.00 0.00 0.00 2.57
5520 6378 2.456073 TAGCCTCCCTTGACCTACTC 57.544 55.000 0.00 0.00 0.00 2.59
5523 6381 1.938585 CCTCCCTTGACCTACTCACA 58.061 55.000 0.00 0.00 0.00 3.58
5530 6388 3.686726 CCTTGACCTACTCACAATTGCTC 59.313 47.826 5.05 0.00 0.00 4.26
5533 6391 2.237392 GACCTACTCACAATTGCTCCCT 59.763 50.000 5.05 0.00 0.00 4.20
5546 6406 0.881796 GCTCCCTTGCACCTGTTTAC 59.118 55.000 0.00 0.00 0.00 2.01
5550 6410 1.588674 CCTTGCACCTGTTTACGTCA 58.411 50.000 0.00 0.00 0.00 4.35
5551 6411 1.944024 CCTTGCACCTGTTTACGTCAA 59.056 47.619 0.00 0.00 0.00 3.18
5552 6412 2.356382 CCTTGCACCTGTTTACGTCAAA 59.644 45.455 0.00 0.00 0.00 2.69
5553 6413 3.181495 CCTTGCACCTGTTTACGTCAAAA 60.181 43.478 0.00 0.00 0.00 2.44
5555 6415 2.356382 TGCACCTGTTTACGTCAAAAGG 59.644 45.455 15.83 15.83 33.82 3.11
5556 6416 2.857104 GCACCTGTTTACGTCAAAAGGC 60.857 50.000 17.10 2.43 32.23 4.35
5558 6418 3.018149 ACCTGTTTACGTCAAAAGGCAA 58.982 40.909 17.10 0.00 32.23 4.52
5559 6419 3.444388 ACCTGTTTACGTCAAAAGGCAAA 59.556 39.130 17.10 0.00 32.23 3.68
5560 6420 4.041723 CCTGTTTACGTCAAAAGGCAAAG 58.958 43.478 5.76 0.00 0.00 2.77
5561 6421 3.440228 TGTTTACGTCAAAAGGCAAAGC 58.560 40.909 0.00 0.00 0.00 3.51
5564 6424 1.102978 ACGTCAAAAGGCAAAGCACT 58.897 45.000 0.00 0.00 0.00 4.40
5592 6468 3.245284 CGCGGTATTTTCAGATGTACCTG 59.755 47.826 0.00 0.00 35.53 4.00
5593 6469 4.189231 GCGGTATTTTCAGATGTACCTGT 58.811 43.478 0.00 0.00 35.53 4.00
5605 6481 1.257743 GTACCTGTCTGTGCTCTGGA 58.742 55.000 0.00 0.00 0.00 3.86
5612 6488 2.294233 TGTCTGTGCTCTGGAAAAATGC 59.706 45.455 0.00 0.00 0.00 3.56
5613 6489 2.294233 GTCTGTGCTCTGGAAAAATGCA 59.706 45.455 0.00 0.00 0.00 3.96
5618 6494 3.655486 TGCTCTGGAAAAATGCACATTG 58.345 40.909 0.00 0.00 0.00 2.82
5622 6498 5.394443 GCTCTGGAAAAATGCACATTGGATA 60.394 40.000 0.00 0.00 0.00 2.59
5623 6499 6.684613 GCTCTGGAAAAATGCACATTGGATAT 60.685 38.462 0.00 0.00 0.00 1.63
5624 6500 7.470424 GCTCTGGAAAAATGCACATTGGATATA 60.470 37.037 0.00 0.00 0.00 0.86
5625 6501 8.303780 TCTGGAAAAATGCACATTGGATATAA 57.696 30.769 0.00 0.00 0.00 0.98
5626 6502 8.756927 TCTGGAAAAATGCACATTGGATATAAA 58.243 29.630 0.00 0.00 0.00 1.40
5627 6503 8.715191 TGGAAAAATGCACATTGGATATAAAC 57.285 30.769 0.00 0.00 0.00 2.01
5638 6514 9.770097 CACATTGGATATAAACTCTGTATCACT 57.230 33.333 0.00 0.00 0.00 3.41
5660 6536 6.742718 CACTTTAGGTTCAAGATAAATGTGCG 59.257 38.462 0.00 0.00 0.00 5.34
5668 6544 4.754618 TCAAGATAAATGTGCGTCTGTGTT 59.245 37.500 0.00 0.00 0.00 3.32
5670 6546 5.034554 AGATAAATGTGCGTCTGTGTTTG 57.965 39.130 0.00 0.00 0.00 2.93
5671 6547 1.838913 AAATGTGCGTCTGTGTTTGC 58.161 45.000 0.00 0.00 0.00 3.68
5672 6548 1.024271 AATGTGCGTCTGTGTTTGCT 58.976 45.000 0.00 0.00 0.00 3.91
5673 6549 0.308684 ATGTGCGTCTGTGTTTGCTG 59.691 50.000 0.00 0.00 0.00 4.41
5674 6550 1.024046 TGTGCGTCTGTGTTTGCTGT 61.024 50.000 0.00 0.00 0.00 4.40
5676 6552 1.531149 GTGCGTCTGTGTTTGCTGTAT 59.469 47.619 0.00 0.00 0.00 2.29
5677 6553 2.734606 GTGCGTCTGTGTTTGCTGTATA 59.265 45.455 0.00 0.00 0.00 1.47
5678 6554 3.370978 GTGCGTCTGTGTTTGCTGTATAT 59.629 43.478 0.00 0.00 0.00 0.86
5679 6555 3.616821 TGCGTCTGTGTTTGCTGTATATC 59.383 43.478 0.00 0.00 0.00 1.63
5680 6556 3.301835 GCGTCTGTGTTTGCTGTATATCG 60.302 47.826 0.00 0.00 0.00 2.92
5681 6557 3.242944 CGTCTGTGTTTGCTGTATATCGG 59.757 47.826 0.00 0.00 0.00 4.18
5682 6558 4.181578 GTCTGTGTTTGCTGTATATCGGT 58.818 43.478 0.00 0.00 0.00 4.69
5683 6559 4.630069 GTCTGTGTTTGCTGTATATCGGTT 59.370 41.667 0.00 0.00 0.00 4.44
5684 6560 5.121768 GTCTGTGTTTGCTGTATATCGGTTT 59.878 40.000 0.00 0.00 0.00 3.27
5685 6561 5.703592 TCTGTGTTTGCTGTATATCGGTTTT 59.296 36.000 0.00 0.00 0.00 2.43
5686 6562 6.205853 TCTGTGTTTGCTGTATATCGGTTTTT 59.794 34.615 0.00 0.00 0.00 1.94
5687 6563 6.375377 TGTGTTTGCTGTATATCGGTTTTTC 58.625 36.000 0.00 0.00 0.00 2.29
5688 6564 6.205853 TGTGTTTGCTGTATATCGGTTTTTCT 59.794 34.615 0.00 0.00 0.00 2.52
5689 6565 7.081976 GTGTTTGCTGTATATCGGTTTTTCTT 58.918 34.615 0.00 0.00 0.00 2.52
5729 6605 2.435234 CGACCGGCCCAAATTCGA 60.435 61.111 0.00 0.00 0.00 3.71
5801 6677 2.548480 GTCCGTCTTTCCTTTTCACCTG 59.452 50.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.460284 ACTTCGGTCCGATGTGCATC 60.460 55.000 26.87 2.26 41.41 3.91
3 4 0.036388 AACTTCGGTCCGATGTGCAT 60.036 50.000 27.80 13.70 41.95 3.96
6 7 0.796312 CCAAACTTCGGTCCGATGTG 59.204 55.000 27.80 18.19 41.95 3.21
8 9 0.036765 TCCCAAACTTCGGTCCGATG 60.037 55.000 22.05 22.05 35.23 3.84
9 10 0.909623 ATCCCAAACTTCGGTCCGAT 59.090 50.000 16.23 0.00 35.23 4.18
10 11 0.248289 GATCCCAAACTTCGGTCCGA 59.752 55.000 10.71 10.71 0.00 4.55
11 12 0.743345 GGATCCCAAACTTCGGTCCG 60.743 60.000 4.39 4.39 0.00 4.79
12 13 0.393944 GGGATCCCAAACTTCGGTCC 60.394 60.000 26.95 0.00 35.81 4.46
142 146 3.405831 CATAACGTGATGATGGCTCCAT 58.594 45.455 7.14 0.14 39.69 3.41
148 152 2.804527 CTGGAGCATAACGTGATGATGG 59.195 50.000 17.56 0.00 0.00 3.51
150 154 4.406648 TTCTGGAGCATAACGTGATGAT 57.593 40.909 17.56 10.74 0.00 2.45
156 160 2.622436 GAGCTTTCTGGAGCATAACGT 58.378 47.619 0.00 0.00 45.12 3.99
205 209 6.885735 AACGGTGATGAAAAGAAACAAAAG 57.114 33.333 0.00 0.00 0.00 2.27
206 210 6.091441 CCAAACGGTGATGAAAAGAAACAAAA 59.909 34.615 0.00 0.00 0.00 2.44
257 262 2.470286 GCGCCTTTCACGAAGTCG 59.530 61.111 0.00 0.00 41.61 4.18
263 268 1.630244 CTTGAGAGGCGCCTTTCACG 61.630 60.000 40.49 35.33 36.99 4.35
275 280 2.164422 TGACCACATAGCGTCTTGAGAG 59.836 50.000 0.00 0.00 0.00 3.20
283 288 3.117589 GTCGTTGACCACATAGCGT 57.882 52.632 0.00 0.00 0.00 5.07
293 298 4.929808 AGATGAACACATAAGGTCGTTGAC 59.070 41.667 0.00 0.00 0.00 3.18
299 304 6.699642 GCTCTAAGAGATGAACACATAAGGTC 59.300 42.308 0.00 0.00 0.00 3.85
379 384 2.614057 CGCTCCCTGATGACCAAATTAC 59.386 50.000 0.00 0.00 0.00 1.89
382 387 0.749454 GCGCTCCCTGATGACCAAAT 60.749 55.000 0.00 0.00 0.00 2.32
383 388 1.377202 GCGCTCCCTGATGACCAAA 60.377 57.895 0.00 0.00 0.00 3.28
384 389 1.913951 ATGCGCTCCCTGATGACCAA 61.914 55.000 9.73 0.00 0.00 3.67
385 390 1.048160 TATGCGCTCCCTGATGACCA 61.048 55.000 9.73 0.00 0.00 4.02
386 391 0.320247 CTATGCGCTCCCTGATGACC 60.320 60.000 9.73 0.00 0.00 4.02
387 392 0.676184 TCTATGCGCTCCCTGATGAC 59.324 55.000 9.73 0.00 0.00 3.06
388 393 0.964700 CTCTATGCGCTCCCTGATGA 59.035 55.000 9.73 0.00 0.00 2.92
389 394 0.964700 TCTCTATGCGCTCCCTGATG 59.035 55.000 9.73 0.00 0.00 3.07
390 395 1.709578 TTCTCTATGCGCTCCCTGAT 58.290 50.000 9.73 0.00 0.00 2.90
391 396 1.485124 TTTCTCTATGCGCTCCCTGA 58.515 50.000 9.73 0.00 0.00 3.86
392 397 2.540265 ATTTCTCTATGCGCTCCCTG 57.460 50.000 9.73 0.00 0.00 4.45
393 398 2.300437 GGTATTTCTCTATGCGCTCCCT 59.700 50.000 9.73 0.00 0.00 4.20
394 399 2.037251 TGGTATTTCTCTATGCGCTCCC 59.963 50.000 9.73 0.00 0.00 4.30
395 400 3.386768 TGGTATTTCTCTATGCGCTCC 57.613 47.619 9.73 0.00 0.00 4.70
396 401 4.621991 TCTTGGTATTTCTCTATGCGCTC 58.378 43.478 9.73 0.00 0.00 5.03
397 402 4.672587 TCTTGGTATTTCTCTATGCGCT 57.327 40.909 9.73 0.00 0.00 5.92
398 403 4.752101 ACATCTTGGTATTTCTCTATGCGC 59.248 41.667 0.00 0.00 0.00 6.09
399 404 5.985530 TCACATCTTGGTATTTCTCTATGCG 59.014 40.000 0.00 0.00 0.00 4.73
400 405 7.497249 AGTTCACATCTTGGTATTTCTCTATGC 59.503 37.037 0.00 0.00 0.00 3.14
401 406 8.954950 AGTTCACATCTTGGTATTTCTCTATG 57.045 34.615 0.00 0.00 0.00 2.23
404 409 7.923344 CGATAGTTCACATCTTGGTATTTCTCT 59.077 37.037 0.00 0.00 0.00 3.10
405 410 8.066668 CGATAGTTCACATCTTGGTATTTCTC 57.933 38.462 0.00 0.00 0.00 2.87
513 618 6.430000 AGCCGAAATTGAAGTGTACTAACAAT 59.570 34.615 9.78 9.78 37.36 2.71
517 622 7.820386 TGAATAGCCGAAATTGAAGTGTACTAA 59.180 33.333 0.00 0.00 0.00 2.24
521 626 8.773645 CATATGAATAGCCGAAATTGAAGTGTA 58.226 33.333 0.00 0.00 0.00 2.90
525 630 6.580041 GCACATATGAATAGCCGAAATTGAAG 59.420 38.462 10.38 0.00 0.00 3.02
529 634 6.579666 ATGCACATATGAATAGCCGAAATT 57.420 33.333 10.38 0.00 0.00 1.82
530 635 6.579666 AATGCACATATGAATAGCCGAAAT 57.420 33.333 10.38 0.00 0.00 2.17
583 688 7.222611 CCTTGCCGTCCTTAAAATAAATGAATG 59.777 37.037 0.00 0.00 0.00 2.67
641 748 6.429385 TGTTTGCCTTGTTTTTCAACTTCATT 59.571 30.769 0.00 0.00 33.58 2.57
642 749 5.936956 TGTTTGCCTTGTTTTTCAACTTCAT 59.063 32.000 0.00 0.00 33.58 2.57
667 774 1.281925 GGCCCTCCATTTCTCCTCCA 61.282 60.000 0.00 0.00 0.00 3.86
688 795 1.303317 GTCCGGCCCAATGAACACT 60.303 57.895 0.00 0.00 0.00 3.55
689 796 2.340328 GGTCCGGCCCAATGAACAC 61.340 63.158 0.00 0.00 0.00 3.32
739 846 5.561339 CGGCCGTGTATTTCACTTACTTTTT 60.561 40.000 19.50 0.00 44.16 1.94
745 852 1.361793 GCGGCCGTGTATTTCACTTA 58.638 50.000 28.70 0.00 44.16 2.24
771 900 3.062466 CGGGGAGAGTGACGCTGA 61.062 66.667 0.00 0.00 0.00 4.26
773 902 3.063084 GTCGGGGAGAGTGACGCT 61.063 66.667 0.00 0.00 0.00 5.07
776 905 1.316706 CCAGAGTCGGGGAGAGTGAC 61.317 65.000 0.58 0.00 31.40 3.67
885 1025 1.587547 GAGATGGAATGGAAGGACGC 58.412 55.000 0.00 0.00 0.00 5.19
887 1027 1.762957 TCGGAGATGGAATGGAAGGAC 59.237 52.381 0.00 0.00 0.00 3.85
938 1080 1.679153 GGAGGATTCTCACGAGGAGTC 59.321 57.143 2.72 1.42 44.40 3.36
941 1083 0.397254 GGGGAGGATTCTCACGAGGA 60.397 60.000 2.72 0.00 44.22 3.71
942 1084 1.739338 CGGGGAGGATTCTCACGAGG 61.739 65.000 10.85 0.00 44.22 4.63
944 1086 1.756950 CCGGGGAGGATTCTCACGA 60.757 63.158 16.37 0.00 44.22 4.35
947 1089 3.154473 CGCCGGGGAGGATTCTCA 61.154 66.667 14.46 0.00 45.00 3.27
951 1093 4.176752 GCTTCGCCGGGGAGGATT 62.177 66.667 31.14 0.00 45.00 3.01
969 1111 2.279784 GGATCTCCGCTCCGCTTG 60.280 66.667 0.00 0.00 0.00 4.01
970 1112 2.642183 TAGGGATCTCCGCTCCGCTT 62.642 60.000 0.00 0.00 41.52 4.68
971 1113 3.134703 TAGGGATCTCCGCTCCGCT 62.135 63.158 0.00 0.00 41.52 5.52
972 1114 2.597805 TAGGGATCTCCGCTCCGC 60.598 66.667 0.00 0.00 41.52 5.54
973 1115 1.974343 CCTAGGGATCTCCGCTCCG 60.974 68.421 0.00 0.00 41.52 4.63
974 1116 2.279810 GCCTAGGGATCTCCGCTCC 61.280 68.421 11.72 0.00 41.52 4.70
975 1117 2.279810 GGCCTAGGGATCTCCGCTC 61.280 68.421 11.72 0.00 41.52 5.03
976 1118 2.203714 GGCCTAGGGATCTCCGCT 60.204 66.667 11.72 0.00 41.52 5.52
977 1119 3.686045 CGGCCTAGGGATCTCCGC 61.686 72.222 11.72 0.00 41.52 5.54
978 1120 2.992114 CCGGCCTAGGGATCTCCG 60.992 72.222 11.72 14.04 41.52 4.63
1005 1162 2.046023 TCGTCGAAGGGCTCCGTA 60.046 61.111 0.00 0.00 0.00 4.02
1125 1613 2.317609 CGGCGGCGGAGATTTATGG 61.318 63.158 25.36 0.00 0.00 2.74
1127 1615 2.665185 GCGGCGGCGGAGATTTAT 60.665 61.111 33.02 0.00 0.00 1.40
1128 1616 4.150203 TGCGGCGGCGGAGATTTA 62.150 61.111 33.02 0.00 44.10 1.40
1215 1706 1.684049 CTCCTCCTCTGAAGGCGGT 60.684 63.158 0.69 0.00 46.22 5.68
1218 1709 2.741055 GGCCTCCTCCTCTGAAGGC 61.741 68.421 8.49 8.49 43.02 4.35
1219 1710 2.430610 CGGCCTCCTCCTCTGAAGG 61.431 68.421 0.00 0.00 44.89 3.46
1221 1712 1.984570 CACGGCCTCCTCCTCTGAA 60.985 63.158 0.00 0.00 0.00 3.02
1262 1759 4.125695 GGTTCGTCGTCGGGGGAG 62.126 72.222 1.55 0.00 37.69 4.30
1267 1764 3.048941 GAGAGGGGTTCGTCGTCGG 62.049 68.421 1.55 0.00 37.69 4.79
1268 1765 2.484203 GAGAGGGGTTCGTCGTCG 59.516 66.667 0.00 0.00 38.55 5.12
1269 1766 2.708865 GGGAGAGGGGTTCGTCGTC 61.709 68.421 0.00 0.00 33.41 4.20
1270 1767 2.679287 GGGAGAGGGGTTCGTCGT 60.679 66.667 0.00 0.00 33.41 4.34
1272 1769 3.082055 GGGGGAGAGGGGTTCGTC 61.082 72.222 0.00 0.00 0.00 4.20
1386 1937 1.644372 CTCCTCATCGTCGTCCTCG 59.356 63.158 0.00 0.00 38.55 4.63
1392 1943 1.531840 ATCCCCCTCCTCATCGTCG 60.532 63.158 0.00 0.00 0.00 5.12
1395 1946 1.810606 CGTCATCCCCCTCCTCATCG 61.811 65.000 0.00 0.00 0.00 3.84
1405 1956 4.222847 GTCGAGCCCGTCATCCCC 62.223 72.222 0.00 0.00 37.05 4.81
1406 1957 4.222847 GGTCGAGCCCGTCATCCC 62.223 72.222 2.39 0.00 37.05 3.85
1486 2037 2.462782 CCTCCTCCTCGTCGTCGTC 61.463 68.421 1.33 0.00 38.33 4.20
1487 2038 2.436292 CCTCCTCCTCGTCGTCGT 60.436 66.667 1.33 0.00 38.33 4.34
1488 2039 2.125229 TCCTCCTCCTCGTCGTCG 60.125 66.667 0.00 0.00 38.55 5.12
1593 2144 1.066143 GCCATTTCGACCCTCTCTTCA 60.066 52.381 0.00 0.00 0.00 3.02
1599 2150 1.084370 CGACAGCCATTTCGACCCTC 61.084 60.000 0.00 0.00 37.43 4.30
1600 2151 1.079127 CGACAGCCATTTCGACCCT 60.079 57.895 0.00 0.00 37.43 4.34
1602 2153 1.696832 GCTCGACAGCCATTTCGACC 61.697 60.000 0.00 0.00 39.29 4.79
1604 2155 4.185413 GCTCGACAGCCATTTCGA 57.815 55.556 0.00 0.00 41.83 3.71
1629 2183 4.778415 CCCGTCACAGCGACCTCG 62.778 72.222 0.00 0.00 42.07 4.63
1712 2266 3.714078 TTCCCCTCCCCATCCTCCG 62.714 68.421 0.00 0.00 0.00 4.63
1805 2425 7.148255 GCAAACTGAAGGAAAGGAAACAAAATT 60.148 33.333 0.00 0.00 0.00 1.82
1846 2466 0.957395 CACAGGACACACATCAGCCC 60.957 60.000 0.00 0.00 0.00 5.19
1847 2467 0.957395 CCACAGGACACACATCAGCC 60.957 60.000 0.00 0.00 0.00 4.85
1848 2468 0.957395 CCCACAGGACACACATCAGC 60.957 60.000 0.00 0.00 33.47 4.26
1849 2469 0.957395 GCCCACAGGACACACATCAG 60.957 60.000 0.00 0.00 33.47 2.90
1855 2497 1.376086 CATCAGCCCACAGGACACA 59.624 57.895 0.00 0.00 33.47 3.72
1931 2573 5.473846 CACACTGTCAGGATATATACCTCGT 59.526 44.000 4.53 0.00 35.35 4.18
2039 2681 3.861689 GCTCTGCAATTGGCTTAAATGAC 59.138 43.478 7.72 0.00 45.15 3.06
2081 2723 1.407258 CGGATCTTCTCCAGGACTGAC 59.593 57.143 0.00 0.00 45.24 3.51
2102 2744 2.167281 CTGAATCTCCAGCTTCCGAAGA 59.833 50.000 12.54 0.00 0.00 2.87
2137 2779 5.124457 GCATAACCTCAGAAAAGCAATCAGA 59.876 40.000 0.00 0.00 0.00 3.27
2150 2793 7.859377 GTCATTGTGATATTTGCATAACCTCAG 59.141 37.037 0.00 0.00 0.00 3.35
2165 2809 5.011023 ACATCAGCGGATAGTCATTGTGATA 59.989 40.000 0.00 0.00 30.87 2.15
2167 2811 3.132824 ACATCAGCGGATAGTCATTGTGA 59.867 43.478 0.00 0.00 30.87 3.58
2178 2822 5.066505 GTGGAGAAAAATAACATCAGCGGAT 59.933 40.000 0.00 0.00 0.00 4.18
2194 2838 2.489971 CTGCAAACCGTAGTGGAGAAA 58.510 47.619 0.00 0.00 42.00 2.52
2321 2983 2.746375 CCTCGGGTATGGCTGGCTT 61.746 63.158 2.00 0.00 0.00 4.35
2332 2994 1.595357 CGCTTCCTTAACCTCGGGT 59.405 57.895 0.00 0.00 37.65 5.28
2335 2997 0.036671 AACCCGCTTCCTTAACCTCG 60.037 55.000 0.00 0.00 0.00 4.63
2349 3011 5.527951 TCAAATTTTTGTCATCTGAACCCG 58.472 37.500 3.18 0.00 39.18 5.28
2418 3080 8.911918 TCACAGCCTTTTAGTTTTATAGACAA 57.088 30.769 0.00 0.00 0.00 3.18
2497 3159 1.122019 AGGGAGACTGGTGTGGTCAC 61.122 60.000 0.00 0.00 43.19 3.67
2529 3191 0.322975 AGCCGAGTGAAAGCAGTGAT 59.677 50.000 0.00 0.00 0.00 3.06
2546 3208 4.475944 CAAACACCAAACAGCATACTAGC 58.524 43.478 0.00 0.00 0.00 3.42
2582 3244 2.606308 GCATCCTGCAAACAAGACACAG 60.606 50.000 0.00 0.00 44.26 3.66
2632 3294 5.068460 CCTTGTTTGGAGATTTGTTACCACA 59.932 40.000 0.00 0.00 31.87 4.17
2639 3301 3.319122 GCTGACCTTGTTTGGAGATTTGT 59.681 43.478 0.00 0.00 0.00 2.83
2677 3339 2.288186 CAGCAGCTGCAGATGATTACAG 59.712 50.000 38.24 13.47 45.16 2.74
2682 3344 1.095600 CAACAGCAGCTGCAGATGAT 58.904 50.000 38.24 27.35 45.16 2.45
2691 3353 2.571653 TCTTATGGGTACAACAGCAGCT 59.428 45.455 0.00 0.00 0.00 4.24
2701 3363 2.772287 GAGGCATGCTCTTATGGGTAC 58.228 52.381 18.92 0.00 0.00 3.34
2703 3365 0.107456 CGAGGCATGCTCTTATGGGT 59.893 55.000 18.92 0.00 0.00 4.51
2725 3413 6.978080 AGAAACTTCAACGCAAATAACACAAT 59.022 30.769 0.00 0.00 0.00 2.71
2761 3450 4.913924 GCTTTCATTGACATTGTGACACTC 59.086 41.667 7.20 0.00 0.00 3.51
2867 3556 9.347240 TGACTAACCATAGTAGATAGTACCAAC 57.653 37.037 0.00 0.00 42.47 3.77
3068 3760 7.008021 AGAACCAATAATCCAACAAGCAAAT 57.992 32.000 0.00 0.00 0.00 2.32
3148 3840 2.558378 ACAGCATCAATGGAGTCATCG 58.442 47.619 0.00 0.00 32.24 3.84
3160 3852 4.467438 TGGACTTCTTCATCTACAGCATCA 59.533 41.667 0.00 0.00 0.00 3.07
3180 3872 0.043183 TGAAGAGGGAGGCAGATGGA 59.957 55.000 0.00 0.00 0.00 3.41
3295 3988 5.538118 CAAGGGGGTGAATTTTCTTTACAC 58.462 41.667 0.00 0.00 0.00 2.90
3530 4223 0.813184 CACCAGGCCATTGCTAACAG 59.187 55.000 5.01 0.00 37.74 3.16
3534 4227 0.324552 AATGCACCAGGCCATTGCTA 60.325 50.000 20.18 10.03 43.89 3.49
3582 4328 9.035890 AGCCAGTAGTATAGTGCATCAATATAA 57.964 33.333 0.00 0.00 40.69 0.98
3590 4336 8.647796 TGTTTAATAGCCAGTAGTATAGTGCAT 58.352 33.333 0.00 0.00 40.69 3.96
3612 4358 9.480053 CCAGACAGATAATTCAACAAAATGTTT 57.520 29.630 0.00 0.00 38.77 2.83
3818 4564 2.533129 CGACATGTCATCATCACTGTCG 59.467 50.000 24.93 8.27 38.95 4.35
3837 4583 3.318839 TCTTCGTTGTCCTTAAACCTCGA 59.681 43.478 0.00 0.00 0.00 4.04
4043 4789 4.599047 ATCATCTTCGTCTTCCTCCATC 57.401 45.455 0.00 0.00 0.00 3.51
4196 4942 6.041865 CCTCTATTTCCTCATCATCAGAGTGT 59.958 42.308 0.00 0.00 0.00 3.55
4276 5022 5.232414 GCATAACTGAAGACACTCGGTATTC 59.768 44.000 0.00 0.00 45.70 1.75
4282 5028 4.237724 TCAAGCATAACTGAAGACACTCG 58.762 43.478 0.00 0.00 0.00 4.18
4317 5074 4.626529 GCAAGGGAGGAACTATAGCACTTT 60.627 45.833 0.00 0.00 41.55 2.66
4318 5075 3.118223 GCAAGGGAGGAACTATAGCACTT 60.118 47.826 0.00 0.00 41.55 3.16
4323 5080 3.742640 GCACAGCAAGGGAGGAACTATAG 60.743 52.174 0.00 0.00 41.55 1.31
4326 5083 0.324943 GCACAGCAAGGGAGGAACTA 59.675 55.000 0.00 0.00 41.55 2.24
4328 5085 0.324943 TAGCACAGCAAGGGAGGAAC 59.675 55.000 0.00 0.00 0.00 3.62
4329 5086 0.615331 CTAGCACAGCAAGGGAGGAA 59.385 55.000 0.00 0.00 0.00 3.36
4331 5088 1.134670 GTACTAGCACAGCAAGGGAGG 60.135 57.143 0.00 0.00 0.00 4.30
4333 5090 1.550524 CTGTACTAGCACAGCAAGGGA 59.449 52.381 10.17 0.00 39.54 4.20
4336 5093 3.919216 AGTTCTGTACTAGCACAGCAAG 58.081 45.455 17.03 0.00 44.62 4.01
4427 5186 6.994496 TGTCATCTTCCAATGGAGATATGAAC 59.006 38.462 18.52 14.56 32.16 3.18
4520 5279 2.161855 TCCTTACATGTGGCTTGCTTG 58.838 47.619 9.11 0.00 0.00 4.01
4562 5321 4.164796 ACCAGCCATGTTCTCAATCATAGA 59.835 41.667 0.00 0.00 0.00 1.98
4573 5332 3.550437 AGTAGATGACCAGCCATGTTC 57.450 47.619 0.00 0.00 0.00 3.18
4611 5370 7.013529 GCATTTCAAGATTTGCTGAAAACATC 58.986 34.615 1.74 0.00 34.54 3.06
4692 5451 4.270325 AGAAGTACGACAGCAAACAGAAAC 59.730 41.667 0.00 0.00 0.00 2.78
4731 5490 8.196771 TCAATTCATGTTACAAACTTTCAGCTT 58.803 29.630 0.00 0.00 0.00 3.74
4860 5714 5.514274 TCAATGGAAGAGAACCACAAAAC 57.486 39.130 0.00 0.00 40.36 2.43
4971 5829 1.600485 GTTGTTCGGCCGAGAAAAGAA 59.400 47.619 29.20 15.50 0.00 2.52
5130 5988 7.521748 GCATTGGAATTATGACAAGATCAGAGG 60.522 40.741 0.00 0.00 41.91 3.69
5156 6014 2.101965 CGACTCTGCCTCTGAGCG 59.898 66.667 0.00 0.00 33.65 5.03
5184 6042 6.261118 GCCACATGAGAATGTTTCTGAATAC 58.739 40.000 0.00 0.00 40.87 1.89
5207 6065 3.084786 GCTGTATAATGGAATGAGGGGC 58.915 50.000 0.00 0.00 0.00 5.80
5220 6078 2.827755 TCACCTGGTCCTGCTGTATAA 58.172 47.619 0.00 0.00 0.00 0.98
5238 6096 3.080158 TTGGCTTGGCTGGGGTTCA 62.080 57.895 0.00 0.00 0.00 3.18
5252 6110 1.664302 GCTGAACTTCGCTTTCTTGGC 60.664 52.381 0.00 0.00 0.00 4.52
5317 6175 4.742201 GCGCCTGAAGTCGAGCCA 62.742 66.667 0.00 0.00 0.00 4.75
5431 6289 2.280797 GCCGAGAACTGGTGCACA 60.281 61.111 20.43 3.92 0.00 4.57
5512 6370 2.237392 AGGGAGCAATTGTGAGTAGGTC 59.763 50.000 7.40 0.00 0.00 3.85
5513 6371 2.269940 AGGGAGCAATTGTGAGTAGGT 58.730 47.619 7.40 0.00 0.00 3.08
5516 6374 2.224744 TGCAAGGGAGCAATTGTGAGTA 60.225 45.455 7.40 0.00 42.46 2.59
5519 6377 3.435846 TGCAAGGGAGCAATTGTGA 57.564 47.368 7.40 0.00 42.46 3.58
5530 6388 0.872388 GACGTAAACAGGTGCAAGGG 59.128 55.000 0.00 0.00 0.00 3.95
5533 6391 3.181495 CCTTTTGACGTAAACAGGTGCAA 60.181 43.478 9.43 0.00 0.00 4.08
5546 6406 2.208326 AAGTGCTTTGCCTTTTGACG 57.792 45.000 0.00 0.00 0.00 4.35
5571 6431 4.189231 ACAGGTACATCTGAAAATACCGC 58.811 43.478 6.18 0.00 41.71 5.68
5572 6432 5.520288 CAGACAGGTACATCTGAAAATACCG 59.480 44.000 13.16 7.28 43.69 4.02
5577 6437 4.065088 GCACAGACAGGTACATCTGAAAA 58.935 43.478 21.35 0.00 43.69 2.29
5584 6444 1.552337 CCAGAGCACAGACAGGTACAT 59.448 52.381 0.00 0.00 0.00 2.29
5585 6445 0.969149 CCAGAGCACAGACAGGTACA 59.031 55.000 0.00 0.00 0.00 2.90
5586 6446 1.257743 TCCAGAGCACAGACAGGTAC 58.742 55.000 0.00 0.00 0.00 3.34
5592 6468 2.294233 TGCATTTTTCCAGAGCACAGAC 59.706 45.455 0.00 0.00 0.00 3.51
5593 6469 2.585330 TGCATTTTTCCAGAGCACAGA 58.415 42.857 0.00 0.00 0.00 3.41
5605 6481 9.590451 CAGAGTTTATATCCAATGTGCATTTTT 57.410 29.630 0.00 0.00 0.00 1.94
5612 6488 9.770097 AGTGATACAGAGTTTATATCCAATGTG 57.230 33.333 0.00 0.00 0.00 3.21
5623 6499 9.706691 CTTGAACCTAAAGTGATACAGAGTTTA 57.293 33.333 0.00 0.00 0.00 2.01
5624 6500 8.429641 TCTTGAACCTAAAGTGATACAGAGTTT 58.570 33.333 0.00 0.00 0.00 2.66
5625 6501 7.963532 TCTTGAACCTAAAGTGATACAGAGTT 58.036 34.615 0.00 0.00 0.00 3.01
5626 6502 7.540474 TCTTGAACCTAAAGTGATACAGAGT 57.460 36.000 0.00 0.00 0.00 3.24
5638 6514 6.653320 AGACGCACATTTATCTTGAACCTAAA 59.347 34.615 0.00 0.00 0.00 1.85
5646 6522 4.668576 ACACAGACGCACATTTATCTTG 57.331 40.909 0.00 0.00 0.00 3.02
5660 6536 4.181578 ACCGATATACAGCAAACACAGAC 58.818 43.478 0.00 0.00 0.00 3.51
5668 6544 7.066525 CCCTTAAGAAAAACCGATATACAGCAA 59.933 37.037 3.36 0.00 0.00 3.91
5670 6546 6.512903 GCCCTTAAGAAAAACCGATATACAGC 60.513 42.308 3.36 0.00 0.00 4.40
5671 6547 6.292703 CGCCCTTAAGAAAAACCGATATACAG 60.293 42.308 3.36 0.00 0.00 2.74
5672 6548 5.524646 CGCCCTTAAGAAAAACCGATATACA 59.475 40.000 3.36 0.00 0.00 2.29
5673 6549 5.559608 GCGCCCTTAAGAAAAACCGATATAC 60.560 44.000 3.36 0.00 0.00 1.47
5674 6550 4.512571 GCGCCCTTAAGAAAAACCGATATA 59.487 41.667 3.36 0.00 0.00 0.86
5676 6552 2.679336 GCGCCCTTAAGAAAAACCGATA 59.321 45.455 3.36 0.00 0.00 2.92
5677 6553 1.471287 GCGCCCTTAAGAAAAACCGAT 59.529 47.619 3.36 0.00 0.00 4.18
5678 6554 0.876399 GCGCCCTTAAGAAAAACCGA 59.124 50.000 3.36 0.00 0.00 4.69
5679 6555 0.879090 AGCGCCCTTAAGAAAAACCG 59.121 50.000 2.29 0.00 0.00 4.44
5680 6556 1.883926 TCAGCGCCCTTAAGAAAAACC 59.116 47.619 2.29 0.00 0.00 3.27
5681 6557 3.850122 ATCAGCGCCCTTAAGAAAAAC 57.150 42.857 2.29 0.00 0.00 2.43
5682 6558 3.377172 GCTATCAGCGCCCTTAAGAAAAA 59.623 43.478 2.29 0.00 0.00 1.94
5683 6559 2.943033 GCTATCAGCGCCCTTAAGAAAA 59.057 45.455 2.29 0.00 0.00 2.29
5684 6560 2.561569 GCTATCAGCGCCCTTAAGAAA 58.438 47.619 2.29 0.00 0.00 2.52
5685 6561 1.202651 GGCTATCAGCGCCCTTAAGAA 60.203 52.381 2.29 0.00 43.62 2.52
5686 6562 0.393077 GGCTATCAGCGCCCTTAAGA 59.607 55.000 2.29 0.00 43.62 2.10
5687 6563 0.946221 CGGCTATCAGCGCCCTTAAG 60.946 60.000 2.29 0.00 43.62 1.85
5688 6564 1.069090 CGGCTATCAGCGCCCTTAA 59.931 57.895 2.29 0.00 43.62 1.85
5689 6565 2.734591 CGGCTATCAGCGCCCTTA 59.265 61.111 2.29 0.00 43.62 2.69
5801 6677 1.662026 GGATCAAAACGTTCGTGTGCC 60.662 52.381 0.00 5.80 0.00 5.01


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

AutoCloner maintained by Alex Coulton.