Multiple sequence alignment - TraesCS7A01G259400

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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 TraesCS7A01G259400 chr7A 100.000 4082 0 0 1 4082 251277733 251281814 0.000000e+00 7539.0
1 TraesCS7A01G259400 chr7D 94.164 1662 59 13 1644 3299 236174467 236176096 0.000000e+00 2497.0
2 TraesCS7A01G259400 chr7D 90.811 1393 74 20 297 1661 236173089 236174455 0.000000e+00 1814.0
3 TraesCS7A01G259400 chr7D 84.393 346 30 6 3751 4082 236180307 236180642 6.580000e-83 318.0
4 TraesCS7A01G259400 chr7D 89.524 105 4 3 1 98 236172717 236172821 4.280000e-25 126.0
5 TraesCS7A01G259400 chr7D 92.135 89 7 0 149 237 236173017 236173105 4.280000e-25 126.0
6 TraesCS7A01G259400 chr7D 91.250 80 6 1 3311 3390 236176304 236176382 1.550000e-19 108.0
7 TraesCS7A01G259400 chr7B 93.533 1670 62 20 1734 3384 212472746 212474388 0.000000e+00 2444.0
8 TraesCS7A01G259400 chr7B 88.150 1443 83 24 352 1735 212470927 212472340 0.000000e+00 1637.0
9 TraesCS7A01G259400 chr7B 83.059 425 55 6 3671 4082 212474504 212474924 1.790000e-98 370.0
10 TraesCS7A01G259400 chr7B 76.966 178 25 4 3483 3646 181629876 181629701 2.020000e-13 87.9
11 TraesCS7A01G259400 chr1D 78.218 303 56 6 3654 3952 119005523 119005819 6.970000e-43 185.0
12 TraesCS7A01G259400 chr2D 77.509 289 57 6 3656 3940 390407165 390407449 2.520000e-37 167.0
13 TraesCS7A01G259400 chr3D 80.203 197 37 2 2174 2369 536164254 536164449 3.290000e-31 147.0
14 TraesCS7A01G259400 chr3A 74.631 339 73 12 2174 2509 671661103 671660775 1.980000e-28 137.0
15 TraesCS7A01G259400 chr5A 76.754 228 45 6 3656 3881 54460974 54460753 1.990000e-23 121.0
16 TraesCS7A01G259400 chr3B 77.778 198 42 2 2174 2370 708311103 708310907 1.990000e-23 121.0
17 TraesCS7A01G259400 chr3B 93.478 46 3 0 3521 3566 110231157 110231202 7.320000e-08 69.4
18 TraesCS7A01G259400 chr5D 79.651 172 29 3 3655 3825 379430576 379430410 7.170000e-23 119.0
19 TraesCS7A01G259400 chr5D 76.596 188 29 4 3478 3650 24370206 24370019 5.620000e-14 89.8
20 TraesCS7A01G259400 chr2B 80.435 138 12 10 3521 3643 780901163 780901300 1.560000e-14 91.6
21 TraesCS7A01G259400 chr2B 79.710 138 13 10 3521 3643 780885520 780885657 7.270000e-13 86.1
22 TraesCS7A01G259400 chr2B 79.710 138 13 10 3521 3643 780924666 780924803 7.270000e-13 86.1
23 TraesCS7A01G259400 chr2B 79.710 138 13 10 3521 3643 780948780 780948917 7.270000e-13 86.1
24 TraesCS7A01G259400 chrUn 79.433 141 14 10 3521 3646 350667777 350667637 7.270000e-13 86.1
25 TraesCS7A01G259400 chr6D 82.222 90 9 2 3477 3566 154221787 154221869 2.040000e-08 71.3


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 TraesCS7A01G259400 chr7A 251277733 251281814 4081 False 7539.000000 7539 100.000000 1 4082 1 chr7A.!!$F1 4081
1 TraesCS7A01G259400 chr7D 236172717 236180642 7925 False 831.500000 2497 90.379500 1 4082 6 chr7D.!!$F1 4081
2 TraesCS7A01G259400 chr7B 212470927 212474924 3997 False 1483.666667 2444 88.247333 352 4082 3 chr7B.!!$F1 3730

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
805 965 1.600957 CACAGCCCTTAATCTGCATCG 59.399 52.381 0.0 0.0 33.8 3.84 F
1437 1605 0.459237 TTTTGGCACGGCACAAGTTG 60.459 50.000 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2546 1.003696 GTCAGGTTCAGCTTTAGGGCT 59.996 52.381 0.0 0.0 44.10 5.19 R
3170 3806 0.250989 TCGGGTAAAAACCAGCCAGG 60.251 55.000 0.0 0.0 45.67 4.45 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
43 44 7.201767 GCTTGATCAGCTCTTAATTTGTATGGT 60.202 37.037 9.16 0.00 46.27 3.55
91 97 6.464892 CCCAGCATCTCCTACTAATTTGATGA 60.465 42.308 0.00 0.00 34.86 2.92
93 99 7.500227 CCAGCATCTCCTACTAATTTGATGAAA 59.500 37.037 0.00 0.00 34.86 2.69
120 126 8.599624 AAATCAATACCATCCTGAAGATTTGT 57.400 30.769 0.00 0.00 34.33 2.83
121 127 9.699410 AAATCAATACCATCCTGAAGATTTGTA 57.301 29.630 0.00 0.00 34.33 2.41
122 128 8.682936 ATCAATACCATCCTGAAGATTTGTAC 57.317 34.615 0.00 0.00 30.59 2.90
123 129 7.054124 TCAATACCATCCTGAAGATTTGTACC 58.946 38.462 0.00 0.00 30.59 3.34
124 130 3.873910 ACCATCCTGAAGATTTGTACCG 58.126 45.455 0.00 0.00 30.59 4.02
127 133 4.383118 CCATCCTGAAGATTTGTACCGACT 60.383 45.833 0.00 0.00 30.59 4.18
128 134 4.451629 TCCTGAAGATTTGTACCGACTC 57.548 45.455 0.00 0.00 0.00 3.36
129 135 3.194968 TCCTGAAGATTTGTACCGACTCC 59.805 47.826 0.00 0.00 0.00 3.85
147 265 3.054875 ACTCCTATCATTCAACAGCTGCA 60.055 43.478 15.27 0.00 0.00 4.41
179 332 7.721399 AGAACAGTCAGACATCCTAAATTTTGT 59.279 33.333 2.66 0.00 0.00 2.83
190 343 9.088987 ACATCCTAAATTTTGTCCAACAATACT 57.911 29.630 0.00 0.00 38.00 2.12
573 733 6.642430 TGGATTGAATTTTCCCAATCATGTC 58.358 36.000 15.54 3.68 46.26 3.06
582 742 5.414789 TTCCCAATCATGTCTCTTTACGA 57.585 39.130 0.00 0.00 0.00 3.43
600 760 8.081633 TCTTTACGATTGAACCGAGTAAACTTA 58.918 33.333 0.00 0.00 34.72 2.24
602 762 6.457851 ACGATTGAACCGAGTAAACTTAAC 57.542 37.500 0.00 0.00 0.00 2.01
805 965 1.600957 CACAGCCCTTAATCTGCATCG 59.399 52.381 0.00 0.00 33.80 3.84
875 1035 4.160626 ACTCAGACACCTTAATCTACAGCC 59.839 45.833 0.00 0.00 0.00 4.85
916 1077 2.423538 ACAAACACAGAGCAGAACAACC 59.576 45.455 0.00 0.00 0.00 3.77
930 1091 6.262273 AGCAGAACAACCGAAGAAAGATTAAA 59.738 34.615 0.00 0.00 0.00 1.52
941 1102 6.418057 AAGAAAGATTAAATGTGCCACCAA 57.582 33.333 0.00 0.00 0.00 3.67
956 1121 5.639506 GTGCCACCAAGTGCACTATATATAG 59.360 44.000 22.01 16.73 37.48 1.31
957 1122 5.306937 TGCCACCAAGTGCACTATATATAGT 59.693 40.000 22.01 18.01 44.03 2.12
982 1147 6.171213 GTGGTGCTACTAGTTTTAGAACCAT 58.829 40.000 21.95 0.00 36.39 3.55
985 1150 7.038870 TGGTGCTACTAGTTTTAGAACCATACA 60.039 37.037 17.09 0.00 36.39 2.29
986 1151 7.277319 GGTGCTACTAGTTTTAGAACCATACAC 59.723 40.741 14.35 3.03 36.39 2.90
987 1152 7.277319 GTGCTACTAGTTTTAGAACCATACACC 59.723 40.741 0.00 0.00 36.39 4.16
994 1159 2.425143 AGAACCATACACCTGCCATG 57.575 50.000 0.00 0.00 0.00 3.66
1056 1221 5.573337 ATCAAATTAGGAGCAGCAAGAAC 57.427 39.130 0.00 0.00 0.00 3.01
1069 1234 4.318332 CAGCAAGAACATGACCTACAAGA 58.682 43.478 0.00 0.00 0.00 3.02
1111 1276 1.679898 CTCCCAGTCACCACCTTCC 59.320 63.158 0.00 0.00 0.00 3.46
1116 1281 1.059913 CAGTCACCACCTTCCTCCTT 58.940 55.000 0.00 0.00 0.00 3.36
1156 1321 1.466167 CGTTGGTCTTCCTCAATGCTG 59.534 52.381 0.00 0.00 34.23 4.41
1158 1323 0.694771 TGGTCTTCCTCAATGCTGCT 59.305 50.000 0.00 0.00 34.23 4.24
1215 1380 1.819632 GGGCAATGGTACTCAGCCG 60.820 63.158 11.16 0.00 46.12 5.52
1216 1381 1.220749 GGCAATGGTACTCAGCCGA 59.779 57.895 0.00 0.00 35.42 5.54
1219 1384 0.462047 CAATGGTACTCAGCCGACCC 60.462 60.000 0.00 0.00 31.80 4.46
1245 1410 2.626950 CCCCAAGGTCAGTGATCCTCTA 60.627 54.545 12.78 0.00 33.09 2.43
1247 1412 3.370104 CCAAGGTCAGTGATCCTCTACT 58.630 50.000 12.78 0.00 33.09 2.57
1248 1413 3.772025 CCAAGGTCAGTGATCCTCTACTT 59.228 47.826 12.78 0.96 33.09 2.24
1249 1414 4.142049 CCAAGGTCAGTGATCCTCTACTTC 60.142 50.000 12.78 0.00 33.09 3.01
1250 1415 4.601406 AGGTCAGTGATCCTCTACTTCT 57.399 45.455 0.00 0.00 0.00 2.85
1251 1416 4.941713 AGGTCAGTGATCCTCTACTTCTT 58.058 43.478 0.00 0.00 0.00 2.52
1252 1417 6.080969 AGGTCAGTGATCCTCTACTTCTTA 57.919 41.667 0.00 0.00 0.00 2.10
1253 1418 6.678547 AGGTCAGTGATCCTCTACTTCTTAT 58.321 40.000 0.00 0.00 0.00 1.73
1254 1419 7.129425 AGGTCAGTGATCCTCTACTTCTTATT 58.871 38.462 0.00 0.00 0.00 1.40
1258 1423 8.690884 TCAGTGATCCTCTACTTCTTATTCTTG 58.309 37.037 0.00 0.00 0.00 3.02
1276 1441 5.570262 TCTTGTTGTTCTTGTCGAATACG 57.430 39.130 0.00 0.00 41.26 3.06
1314 1479 3.408634 CACCCTCATTGTTTACCTTCGT 58.591 45.455 0.00 0.00 0.00 3.85
1356 1524 7.067981 AGAGTTTGATCTTGCAAGAAAAGAAGT 59.932 33.333 31.55 23.23 38.77 3.01
1366 1534 4.627035 GCAAGAAAAGAAGTGCAAACTTGT 59.373 37.500 0.00 0.00 36.97 3.16
1369 1537 6.212888 AGAAAAGAAGTGCAAACTTGTGAT 57.787 33.333 0.00 0.00 0.00 3.06
1381 1549 6.922957 TGCAAACTTGTGATCTAATTTTGACC 59.077 34.615 19.90 10.44 32.61 4.02
1383 1551 6.877611 AACTTGTGATCTAATTTTGACCGT 57.122 33.333 0.00 0.00 0.00 4.83
1422 1590 7.803189 GTGTAATCATGTTGTACTGTCCTTTTG 59.197 37.037 0.00 0.00 0.00 2.44
1423 1591 5.964958 ATCATGTTGTACTGTCCTTTTGG 57.035 39.130 0.00 0.00 42.21 3.28
1428 1596 0.872388 GTACTGTCCTTTTGGCACGG 59.128 55.000 0.00 0.00 40.12 4.94
1437 1605 0.459237 TTTTGGCACGGCACAAGTTG 60.459 50.000 0.00 0.00 0.00 3.16
1445 1613 3.553917 GCACGGCACAAGTTGTTTATTTT 59.446 39.130 5.57 0.00 0.00 1.82
1450 1618 4.208253 GGCACAAGTTGTTTATTTTCGGTG 59.792 41.667 5.57 0.00 0.00 4.94
1455 1623 4.472286 AGTTGTTTATTTTCGGTGATGCG 58.528 39.130 0.00 0.00 0.00 4.73
1459 1627 4.023963 TGTTTATTTTCGGTGATGCGTCAA 60.024 37.500 10.93 0.00 35.80 3.18
1537 1723 5.105187 TGGTATGAATGAAGACTGGAGAGTG 60.105 44.000 0.00 0.00 30.16 3.51
1649 1839 2.151202 CAGTTCCTTTTTCGCCTGCTA 58.849 47.619 0.00 0.00 0.00 3.49
1700 1920 2.525368 TGCTGTAGGAGTGTAGAAGCA 58.475 47.619 0.00 0.00 36.88 3.91
1776 2408 6.319405 TCTGTGAATCCATGTCCAATGTAATG 59.681 38.462 0.00 0.00 0.00 1.90
1796 2428 4.301072 TGCCTCATATACCTATTTGGCC 57.699 45.455 0.00 0.00 40.22 5.36
1797 2429 3.916349 TGCCTCATATACCTATTTGGCCT 59.084 43.478 3.32 0.00 40.22 5.19
1914 2546 5.300792 GGCTTGTAATATTCGGATCCCAAAA 59.699 40.000 6.06 0.00 0.00 2.44
1918 2550 2.358322 TATTCGGATCCCAAAAGCCC 57.642 50.000 6.06 0.00 0.00 5.19
1962 2595 2.574322 GCAACGAATATGCGCCTAATG 58.426 47.619 4.18 0.00 33.57 1.90
1992 2625 8.125978 AGAAGGCTTGTGATAAAATGATTTCA 57.874 30.769 3.46 0.00 0.00 2.69
1995 2628 8.937634 AGGCTTGTGATAAAATGATTTCAATC 57.062 30.769 0.00 0.00 35.97 2.67
2015 2648 8.648557 TCAATCACCAGATAAGAGATTTTACG 57.351 34.615 0.00 0.00 33.08 3.18
2023 2656 8.596380 CCAGATAAGAGATTTTACGTGAACTTC 58.404 37.037 0.00 0.00 0.00 3.01
2104 2737 9.888878 AAATCATTTACTATCATCTCATTTGCG 57.111 29.630 0.00 0.00 0.00 4.85
2111 2744 2.216046 TCATCTCATTTGCGGCATCTC 58.784 47.619 2.28 0.00 0.00 2.75
2113 2746 2.112380 TCTCATTTGCGGCATCTCAA 57.888 45.000 2.28 0.00 0.00 3.02
2124 2757 4.072131 GCGGCATCTCAATTATTTCCCTA 58.928 43.478 0.00 0.00 0.00 3.53
2147 2780 2.159734 GCAGACGAAAGCATTGACAGAG 60.160 50.000 0.00 0.00 0.00 3.35
2553 3186 4.778143 GGACCGCCGGTGCAATCT 62.778 66.667 23.60 0.00 43.66 2.40
2555 3188 1.227556 GACCGCCGGTGCAATCTAT 60.228 57.895 16.53 0.00 35.25 1.98
2556 3189 0.032952 GACCGCCGGTGCAATCTATA 59.967 55.000 16.53 0.00 35.25 1.31
2557 3190 0.249741 ACCGCCGGTGCAATCTATAC 60.250 55.000 8.62 0.00 37.32 1.47
2558 3191 0.033504 CCGCCGGTGCAATCTATACT 59.966 55.000 10.27 0.00 37.32 2.12
2559 3192 1.540363 CCGCCGGTGCAATCTATACTT 60.540 52.381 10.27 0.00 37.32 2.24
2560 3193 2.288579 CCGCCGGTGCAATCTATACTTA 60.289 50.000 10.27 0.00 37.32 2.24
2561 3194 2.729882 CGCCGGTGCAATCTATACTTAC 59.270 50.000 0.00 0.00 37.32 2.34
2562 3195 3.064931 GCCGGTGCAATCTATACTTACC 58.935 50.000 1.90 0.00 37.47 2.85
2563 3196 3.493699 GCCGGTGCAATCTATACTTACCA 60.494 47.826 1.90 0.00 37.47 3.25
2565 3198 5.305585 CCGGTGCAATCTATACTTACCATT 58.694 41.667 0.00 0.00 0.00 3.16
2583 3217 5.269505 CCATTTAGGTGTTTGGTGTTTCA 57.730 39.130 0.00 0.00 0.00 2.69
2584 3218 5.852827 CCATTTAGGTGTTTGGTGTTTCAT 58.147 37.500 0.00 0.00 0.00 2.57
2585 3219 6.287525 CCATTTAGGTGTTTGGTGTTTCATT 58.712 36.000 0.00 0.00 0.00 2.57
2586 3220 6.423604 CCATTTAGGTGTTTGGTGTTTCATTC 59.576 38.462 0.00 0.00 0.00 2.67
2587 3221 3.708563 AGGTGTTTGGTGTTTCATTCG 57.291 42.857 0.00 0.00 0.00 3.34
2588 3222 3.020984 AGGTGTTTGGTGTTTCATTCGT 58.979 40.909 0.00 0.00 0.00 3.85
2728 3362 2.652530 GCGGGTTCCTGTACGTGA 59.347 61.111 0.00 0.00 0.00 4.35
3118 3754 3.028969 GCGGCTGCTGGAATGATC 58.971 61.111 11.21 0.00 38.39 2.92
3145 3781 2.124011 TTACACGTCGTGTCCTTGTC 57.876 50.000 32.70 0.00 43.92 3.18
3155 3791 3.385433 TCGTGTCCTTGTCCTTGTTTCTA 59.615 43.478 0.00 0.00 0.00 2.10
3168 3804 0.602905 GTTTCTACGTGGCAGTGGCT 60.603 55.000 18.53 0.00 40.87 4.75
3169 3805 0.602638 TTTCTACGTGGCAGTGGCTG 60.603 55.000 18.53 12.58 40.87 4.85
3205 3841 4.819105 ACCCGAGTTGAGATTGATGTTA 57.181 40.909 0.00 0.00 0.00 2.41
3236 3872 4.216472 TCGCTGCATGTTTGGTGTATTTTA 59.784 37.500 0.00 0.00 0.00 1.52
3252 3888 7.359933 GGTGTATTTTACAACGTCGGATTTACA 60.360 37.037 0.00 0.00 40.93 2.41
3253 3889 8.170553 GTGTATTTTACAACGTCGGATTTACAT 58.829 33.333 0.00 0.00 40.93 2.29
3254 3890 9.363763 TGTATTTTACAACGTCGGATTTACATA 57.636 29.630 0.00 0.00 35.38 2.29
3255 3891 9.623687 GTATTTTACAACGTCGGATTTACATAC 57.376 33.333 0.00 0.00 0.00 2.39
3299 3935 8.725405 TGATAGGCGAATGTAAGAAAAATGTA 57.275 30.769 0.00 0.00 0.00 2.29
3311 3955 9.062524 TGTAAGAAAAATGTATGTACTGTGCTT 57.937 29.630 0.00 0.00 0.00 3.91
3323 4154 9.655769 GTATGTACTGTGCTTGATTAAATCATG 57.344 33.333 0.00 0.00 39.39 3.07
3363 4194 5.099575 CGGTGGATTTTTATGTTAAGGCAC 58.900 41.667 0.00 0.00 0.00 5.01
3369 4200 2.702592 TTATGTTAAGGCACCTCCGG 57.297 50.000 0.00 0.00 40.77 5.14
3385 4216 0.921347 CCGGCTCTAAATCGAACACG 59.079 55.000 0.00 0.00 0.00 4.49
3390 4221 3.251571 GCTCTAAATCGAACACGGTCTT 58.748 45.455 0.00 0.00 0.00 3.01
3395 4226 6.860080 TCTAAATCGAACACGGTCTTTATCT 58.140 36.000 0.00 0.00 0.00 1.98
3396 4227 7.988737 TCTAAATCGAACACGGTCTTTATCTA 58.011 34.615 0.00 0.00 0.00 1.98
3398 4229 4.007282 TCGAACACGGTCTTTATCTACG 57.993 45.455 0.00 0.00 0.00 3.51
3401 4232 2.726821 ACACGGTCTTTATCTACGGGA 58.273 47.619 0.00 0.00 0.00 5.14
3402 4233 3.294214 ACACGGTCTTTATCTACGGGAT 58.706 45.455 0.00 0.00 38.38 3.85
3403 4234 3.317430 ACACGGTCTTTATCTACGGGATC 59.683 47.826 0.00 0.00 35.98 3.36
3404 4235 3.568853 CACGGTCTTTATCTACGGGATCT 59.431 47.826 0.00 0.00 35.98 2.75
3405 4236 4.037684 CACGGTCTTTATCTACGGGATCTT 59.962 45.833 0.00 0.00 35.98 2.40
3407 4238 5.128335 ACGGTCTTTATCTACGGGATCTTTT 59.872 40.000 0.00 0.00 35.98 2.27
3408 4239 5.462398 CGGTCTTTATCTACGGGATCTTTTG 59.538 44.000 0.00 0.00 35.98 2.44
3409 4240 5.236695 GGTCTTTATCTACGGGATCTTTTGC 59.763 44.000 0.00 0.00 35.98 3.68
3410 4241 5.236695 GTCTTTATCTACGGGATCTTTTGCC 59.763 44.000 0.00 0.00 35.98 4.52
3413 6878 1.209504 TCTACGGGATCTTTTGCCCTG 59.790 52.381 0.00 0.00 42.40 4.45
3422 6887 4.565652 GGATCTTTTGCCCTGTAAGACTGA 60.566 45.833 0.00 0.00 34.07 3.41
3427 6892 5.692115 TTTGCCCTGTAAGACTGATATCA 57.308 39.130 5.07 5.07 34.07 2.15
3428 6893 5.692115 TTGCCCTGTAAGACTGATATCAA 57.308 39.130 6.90 0.00 34.07 2.57
3438 6903 3.126831 GACTGATATCAAAGCCTCCACG 58.873 50.000 6.90 0.00 0.00 4.94
3443 6908 0.254178 ATCAAAGCCTCCACGCTCAT 59.746 50.000 0.00 0.00 38.44 2.90
3451 6916 1.066573 CCTCCACGCTCATTCTGTCTT 60.067 52.381 0.00 0.00 0.00 3.01
3452 6917 2.266554 CTCCACGCTCATTCTGTCTTC 58.733 52.381 0.00 0.00 0.00 2.87
3463 6928 1.178276 TCTGTCTTCGCCTCCTTCTC 58.822 55.000 0.00 0.00 0.00 2.87
3469 6934 4.856607 CGCCTCCTTCTCGTCCGC 62.857 72.222 0.00 0.00 0.00 5.54
3471 6936 3.007973 GCCTCCTTCTCGTCCGCTT 62.008 63.158 0.00 0.00 0.00 4.68
3473 6938 1.595993 CCTCCTTCTCGTCCGCTTCA 61.596 60.000 0.00 0.00 0.00 3.02
3475 6940 1.176619 TCCTTCTCGTCCGCTTCACA 61.177 55.000 0.00 0.00 0.00 3.58
3497 6962 3.582208 AGTCTCCAGCTGATTCTTCAAGT 59.418 43.478 17.39 0.00 0.00 3.16
3513 6978 7.566760 TCTTCAAGTGCTTCAACATTCTAAA 57.433 32.000 0.00 0.00 0.00 1.85
3516 6981 7.094508 TCAAGTGCTTCAACATTCTAAAACA 57.905 32.000 0.00 0.00 0.00 2.83
3518 6983 6.076981 AGTGCTTCAACATTCTAAAACAGG 57.923 37.500 0.00 0.00 0.00 4.00
3519 6984 5.594317 AGTGCTTCAACATTCTAAAACAGGT 59.406 36.000 0.00 0.00 0.00 4.00
3530 6995 1.034838 AAAACAGGTGGCTTGCACGA 61.035 50.000 0.00 0.00 0.00 4.35
3544 7009 1.302366 GCACGATCATCCTTGCATCA 58.698 50.000 1.63 0.00 34.97 3.07
3558 7023 3.657398 TGCATCATCATCCAACTCCTT 57.343 42.857 0.00 0.00 0.00 3.36
3565 7045 5.678583 TCATCATCCAACTCCTTCATCTTC 58.321 41.667 0.00 0.00 0.00 2.87
3571 7051 3.873952 CCAACTCCTTCATCTTCGAATCC 59.126 47.826 0.00 0.00 0.00 3.01
3573 7053 5.181748 CAACTCCTTCATCTTCGAATCCTT 58.818 41.667 0.00 0.00 0.00 3.36
3574 7054 4.764172 ACTCCTTCATCTTCGAATCCTTG 58.236 43.478 0.00 0.00 0.00 3.61
3582 7062 3.173965 TCTTCGAATCCTTGGAAGAGGT 58.826 45.455 9.40 0.00 45.53 3.85
3585 7065 2.637872 TCGAATCCTTGGAAGAGGTTGT 59.362 45.455 0.00 0.00 38.04 3.32
3586 7066 2.744202 CGAATCCTTGGAAGAGGTTGTG 59.256 50.000 0.00 0.00 38.04 3.33
3591 7071 3.652869 TCCTTGGAAGAGGTTGTGATCTT 59.347 43.478 0.00 0.00 38.46 2.40
3606 7086 7.445707 GGTTGTGATCTTAACCTTCTTCTCTTT 59.554 37.037 18.60 0.00 42.37 2.52
3619 7099 2.191128 TCTCTTTGAGCTTGGCCTTC 57.809 50.000 3.32 0.00 0.00 3.46
3627 7107 2.906389 TGAGCTTGGCCTTCTTCTCTTA 59.094 45.455 3.32 0.00 0.00 2.10
3629 7109 4.202461 TGAGCTTGGCCTTCTTCTCTTAAA 60.202 41.667 3.32 0.00 0.00 1.52
3644 7124 8.592809 TCTTCTCTTAAATCTTGAGCTTCTTCT 58.407 33.333 0.00 0.00 0.00 2.85
3647 7127 7.009179 TCTTAAATCTTGAGCTTCTTCTCCA 57.991 36.000 0.00 0.00 32.22 3.86
3650 7130 3.516981 TCTTGAGCTTCTTCTCCATCG 57.483 47.619 0.00 0.00 32.22 3.84
3652 7132 4.017126 TCTTGAGCTTCTTCTCCATCGTA 58.983 43.478 0.00 0.00 32.22 3.43
3669 7149 0.108756 GTAGACACGGCCTCTTGGAC 60.109 60.000 0.00 0.00 38.25 4.02
3678 7158 0.527817 GCCTCTTGGACGATGTACCG 60.528 60.000 0.00 0.00 34.57 4.02
3696 7176 2.755655 ACCGTCGATGATTGAGAGACTT 59.244 45.455 6.11 0.00 0.00 3.01
3697 7177 3.945921 ACCGTCGATGATTGAGAGACTTA 59.054 43.478 6.11 0.00 0.00 2.24
3698 7178 4.398358 ACCGTCGATGATTGAGAGACTTAA 59.602 41.667 6.11 0.00 0.00 1.85
3699 7179 5.067936 ACCGTCGATGATTGAGAGACTTAAT 59.932 40.000 6.11 0.00 0.00 1.40
3713 7193 5.484998 AGAGACTTAATTTACCCCACGGTTA 59.515 40.000 0.00 0.00 40.58 2.85
3724 7204 1.338389 CCCACGGTTACGGATGAGTTT 60.338 52.381 0.00 0.00 46.48 2.66
3736 7216 2.353803 GGATGAGTTTGTCAGCGTAGGT 60.354 50.000 0.00 0.00 42.99 3.08
3751 7231 4.401519 AGCGTAGGTCTCTAAATGCTTGTA 59.598 41.667 0.00 0.00 31.13 2.41
3754 7234 6.331061 CGTAGGTCTCTAAATGCTTGTACTT 58.669 40.000 0.00 0.00 0.00 2.24
3787 8190 2.181954 TGAATGTTGGCCCAAAATGC 57.818 45.000 0.00 0.00 0.00 3.56
3794 8197 2.347322 GGCCCAAAATGCTACGCCA 61.347 57.895 0.00 0.00 36.38 5.69
3818 8221 2.231215 ACTTCGTGCCATAGATCTGC 57.769 50.000 5.18 0.38 0.00 4.26
3850 8253 3.436704 GTGACCAACCATGTATCACACAG 59.563 47.826 0.00 0.00 41.51 3.66
3856 8259 3.754965 ACCATGTATCACACAGCAACTT 58.245 40.909 0.00 0.00 41.51 2.66
3857 8260 3.503363 ACCATGTATCACACAGCAACTTG 59.497 43.478 0.00 0.00 41.51 3.16
3906 8312 9.376075 CTTCTCTACTCTTATTTGAATCAGCAA 57.624 33.333 0.00 0.00 0.00 3.91
3914 8320 9.850628 CTCTTATTTGAATCAGCAAGAAATTCA 57.149 29.630 0.00 0.00 37.57 2.57
3917 8323 7.751047 ATTTGAATCAGCAAGAAATTCATCG 57.249 32.000 0.00 0.00 38.72 3.84
3922 8328 4.272489 TCAGCAAGAAATTCATCGGGATT 58.728 39.130 0.00 0.00 0.00 3.01
3951 8357 4.406173 CGTCGTGCTCCTCGTGCT 62.406 66.667 0.00 0.00 0.00 4.40
3956 8362 2.601666 TGCTCCTCGTGCTCCTGT 60.602 61.111 0.00 0.00 0.00 4.00
3962 8368 3.535629 CTCGTGCTCCTGTTGGCCA 62.536 63.158 0.00 0.00 0.00 5.36
3975 8381 4.188462 CTGTTGGCCAGTATACGAATTCA 58.812 43.478 5.11 0.00 36.37 2.57
3989 8395 3.130693 ACGAATTCAGCTCTAGGGTGTAC 59.869 47.826 6.22 0.00 43.26 2.90
4022 8438 3.057337 GGACTGGGTGTACGTGCT 58.943 61.111 4.97 0.00 0.00 4.40
4030 8446 2.668212 TGTACGTGCTTGGCTGCC 60.668 61.111 12.87 12.87 0.00 4.85
4069 8485 1.480954 CATACCCGTCCTTGTAGCAGT 59.519 52.381 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 8.121305 TGTCAATCTTGCTTACCATACAAATT 57.879 30.769 0.00 0.00 0.00 1.82
37 38 7.320443 TGAATGTCAATCTTGCTTACCATAC 57.680 36.000 0.00 0.00 0.00 2.39
43 44 7.395772 TGGGTATTTGAATGTCAATCTTGCTTA 59.604 33.333 0.00 0.00 36.11 3.09
53 54 4.858850 AGATGCTGGGTATTTGAATGTCA 58.141 39.130 0.00 0.00 0.00 3.58
93 99 9.880157 CAAATCTTCAGGATGGTATTGATTTTT 57.120 29.630 0.00 0.00 36.16 1.94
98 104 7.054124 GGTACAAATCTTCAGGATGGTATTGA 58.946 38.462 0.00 0.00 36.16 2.57
99 105 6.017934 CGGTACAAATCTTCAGGATGGTATTG 60.018 42.308 0.00 0.00 36.16 1.90
101 107 5.365605 TCGGTACAAATCTTCAGGATGGTAT 59.634 40.000 0.00 0.00 36.16 2.73
102 108 4.712829 TCGGTACAAATCTTCAGGATGGTA 59.287 41.667 0.00 0.00 36.16 3.25
103 109 3.517901 TCGGTACAAATCTTCAGGATGGT 59.482 43.478 0.00 0.00 36.16 3.55
104 110 3.871594 GTCGGTACAAATCTTCAGGATGG 59.128 47.826 0.00 0.00 36.16 3.51
105 111 4.759782 AGTCGGTACAAATCTTCAGGATG 58.240 43.478 0.00 0.00 34.45 3.51
106 112 4.141914 GGAGTCGGTACAAATCTTCAGGAT 60.142 45.833 0.00 0.00 35.97 3.24
107 113 3.194968 GGAGTCGGTACAAATCTTCAGGA 59.805 47.826 0.00 0.00 0.00 3.86
111 117 6.145338 TGATAGGAGTCGGTACAAATCTTC 57.855 41.667 0.00 0.00 0.00 2.87
112 118 6.732896 ATGATAGGAGTCGGTACAAATCTT 57.267 37.500 0.00 0.00 0.00 2.40
113 119 6.323996 TGAATGATAGGAGTCGGTACAAATCT 59.676 38.462 0.00 0.00 0.00 2.40
114 120 6.513180 TGAATGATAGGAGTCGGTACAAATC 58.487 40.000 0.00 0.00 0.00 2.17
115 121 6.479972 TGAATGATAGGAGTCGGTACAAAT 57.520 37.500 0.00 0.00 0.00 2.32
116 122 5.925506 TGAATGATAGGAGTCGGTACAAA 57.074 39.130 0.00 0.00 0.00 2.83
117 123 5.186215 TGTTGAATGATAGGAGTCGGTACAA 59.814 40.000 0.00 0.00 0.00 2.41
118 124 4.707934 TGTTGAATGATAGGAGTCGGTACA 59.292 41.667 0.00 0.00 0.00 2.90
120 126 4.202121 GCTGTTGAATGATAGGAGTCGGTA 60.202 45.833 0.00 0.00 0.00 4.02
121 127 3.430929 GCTGTTGAATGATAGGAGTCGGT 60.431 47.826 0.00 0.00 0.00 4.69
122 128 3.126831 GCTGTTGAATGATAGGAGTCGG 58.873 50.000 0.00 0.00 0.00 4.79
123 129 3.801050 CAGCTGTTGAATGATAGGAGTCG 59.199 47.826 5.25 0.00 0.00 4.18
124 130 3.559242 GCAGCTGTTGAATGATAGGAGTC 59.441 47.826 16.64 0.00 0.00 3.36
127 133 3.054875 AGTGCAGCTGTTGAATGATAGGA 60.055 43.478 16.64 0.00 0.00 2.94
128 134 3.276857 AGTGCAGCTGTTGAATGATAGG 58.723 45.455 16.64 0.00 0.00 2.57
129 135 6.426980 TTTAGTGCAGCTGTTGAATGATAG 57.573 37.500 16.64 0.00 0.00 2.08
147 265 6.426646 AGGATGTCTGACTGTTCTTTTAGT 57.573 37.500 9.51 0.00 0.00 2.24
283 436 9.620660 CGTATACATACATACATACACACACAT 57.379 33.333 3.32 0.00 31.96 3.21
284 437 8.623030 ACGTATACATACATACATACACACACA 58.377 33.333 3.32 0.00 31.96 3.72
516 676 2.143122 CATGTGGCAACGTGTCTAGTT 58.857 47.619 5.17 0.00 38.33 2.24
519 679 3.225272 CCATGTGGCAACGTGTCTA 57.775 52.632 12.50 0.00 41.06 2.59
573 733 6.585322 AGTTTACTCGGTTCAATCGTAAAGAG 59.415 38.462 0.00 0.00 32.61 2.85
582 742 7.713942 ACTTCTGTTAAGTTTACTCGGTTCAAT 59.286 33.333 0.00 0.00 0.00 2.57
600 760 6.706270 CACACCTATCAAAGTACACTTCTGTT 59.294 38.462 0.00 0.00 34.61 3.16
602 762 6.455647 TCACACCTATCAAAGTACACTTCTG 58.544 40.000 0.00 0.00 34.61 3.02
619 779 7.936847 TCACTCACTTTACAAAATATCACACCT 59.063 33.333 0.00 0.00 0.00 4.00
805 965 5.183140 TGCTCTAATGCCTACTTTTTCCAAC 59.817 40.000 0.00 0.00 0.00 3.77
875 1035 4.571919 TGTGGAGGTTTATGGAACGTTAG 58.428 43.478 0.00 0.00 39.22 2.34
916 1077 5.095490 GGTGGCACATTTAATCTTTCTTCG 58.905 41.667 20.82 0.00 44.52 3.79
956 1121 5.407691 GGTTCTAAAACTAGTAGCACCACAC 59.592 44.000 7.77 0.00 35.62 3.82
957 1122 5.070714 TGGTTCTAAAACTAGTAGCACCACA 59.929 40.000 10.51 0.00 39.15 4.17
960 1125 7.277319 GTGTATGGTTCTAAAACTAGTAGCACC 59.723 40.741 6.13 6.13 35.97 5.01
969 1134 4.202524 TGGCAGGTGTATGGTTCTAAAACT 60.203 41.667 0.00 0.00 35.61 2.66
972 1137 4.269183 CATGGCAGGTGTATGGTTCTAAA 58.731 43.478 0.00 0.00 0.00 1.85
982 1147 1.545136 CATGTTTGCATGGCAGGTGTA 59.455 47.619 0.00 0.00 46.47 2.90
994 1159 1.537202 AGAGAAGAACGCCATGTTTGC 59.463 47.619 0.00 0.00 42.09 3.68
1006 1171 4.366586 GACGCATCATCATCAGAGAAGAA 58.633 43.478 0.00 0.00 0.00 2.52
1056 1221 3.070734 CCCCTCTCATCTTGTAGGTCATG 59.929 52.174 0.00 0.00 0.00 3.07
1069 1234 2.172293 GCTTCTTCATGTCCCCTCTCAT 59.828 50.000 0.00 0.00 0.00 2.90
1134 1299 1.522668 CATTGAGGAAGACCAACGCA 58.477 50.000 0.00 0.00 38.94 5.24
1156 1321 1.364626 CGCCAGTTCACATCCAGAGC 61.365 60.000 0.00 0.00 0.00 4.09
1158 1323 1.296392 CCGCCAGTTCACATCCAGA 59.704 57.895 0.00 0.00 0.00 3.86
1193 1358 1.142870 GCTGAGTACCATTGCCCCATA 59.857 52.381 0.00 0.00 0.00 2.74
1202 1367 2.064581 GGGGTCGGCTGAGTACCAT 61.065 63.158 11.70 0.00 34.83 3.55
1215 1380 3.190391 ACCTTGGGGTTGGGGGTC 61.190 66.667 0.00 0.00 44.73 4.46
1245 1410 7.494625 TCGACAAGAACAACAAGAATAAGAAGT 59.505 33.333 0.00 0.00 0.00 3.01
1247 1412 7.780008 TCGACAAGAACAACAAGAATAAGAA 57.220 32.000 0.00 0.00 0.00 2.52
1248 1413 7.780008 TTCGACAAGAACAACAAGAATAAGA 57.220 32.000 0.00 0.00 33.14 2.10
1249 1414 9.530129 GTATTCGACAAGAACAACAAGAATAAG 57.470 33.333 0.00 0.00 42.39 1.73
1250 1415 8.218441 CGTATTCGACAAGAACAACAAGAATAA 58.782 33.333 0.00 0.00 42.39 1.40
1251 1416 7.383029 ACGTATTCGACAAGAACAACAAGAATA 59.617 33.333 0.00 0.00 42.39 1.75
1252 1417 6.202188 ACGTATTCGACAAGAACAACAAGAAT 59.798 34.615 0.00 0.00 42.39 2.40
1253 1418 5.521010 ACGTATTCGACAAGAACAACAAGAA 59.479 36.000 0.00 0.00 42.39 2.52
1254 1419 5.045215 ACGTATTCGACAAGAACAACAAGA 58.955 37.500 0.00 0.00 42.39 3.02
1258 1423 4.374828 GCAAACGTATTCGACAAGAACAAC 59.625 41.667 0.00 0.00 42.39 3.32
1269 1434 5.060446 GGAAAAATGGAAGCAAACGTATTCG 59.940 40.000 0.00 0.00 43.34 3.34
1276 1441 3.138304 GGGTGGAAAAATGGAAGCAAAC 58.862 45.455 0.00 0.00 0.00 2.93
1331 1497 7.167136 CACTTCTTTTCTTGCAAGATCAAACTC 59.833 37.037 28.89 0.00 34.49 3.01
1356 1524 6.922957 GGTCAAAATTAGATCACAAGTTTGCA 59.077 34.615 19.72 11.28 39.52 4.08
1366 1534 7.162761 TGTTTCCTACGGTCAAAATTAGATCA 58.837 34.615 0.00 0.00 0.00 2.92
1369 1537 6.938030 ACATGTTTCCTACGGTCAAAATTAGA 59.062 34.615 0.00 0.00 0.00 2.10
1381 1549 7.841486 CATGATTACACTACATGTTTCCTACG 58.159 38.462 2.30 0.00 43.19 3.51
1412 1580 2.192861 TGCCGTGCCAAAAGGACAG 61.193 57.895 0.00 0.00 36.40 3.51
1422 1590 0.382515 TAAACAACTTGTGCCGTGCC 59.617 50.000 0.00 0.00 0.00 5.01
1423 1591 2.415697 ATAAACAACTTGTGCCGTGC 57.584 45.000 0.00 0.00 0.00 5.34
1428 1596 5.038033 TCACCGAAAATAAACAACTTGTGC 58.962 37.500 0.00 0.00 0.00 4.57
1437 1605 4.073169 TGACGCATCACCGAAAATAAAC 57.927 40.909 0.00 0.00 0.00 2.01
1445 1613 1.206132 ACCTTATTGACGCATCACCGA 59.794 47.619 0.00 0.00 33.38 4.69
1493 1661 5.974108 ACCACGTAGTTACTCAATTAGCAT 58.026 37.500 0.00 0.00 41.61 3.79
1509 1695 4.707934 TCCAGTCTTCATTCATACCACGTA 59.292 41.667 0.00 0.00 0.00 3.57
1511 1697 4.115516 CTCCAGTCTTCATTCATACCACG 58.884 47.826 0.00 0.00 0.00 4.94
1562 1751 9.358872 AGTTTTCTCTTCTGTTCAATTTTGTTC 57.641 29.630 0.00 0.00 0.00 3.18
1649 1839 8.752187 ACATAGCCAAATTTGATCATGTAACTT 58.248 29.630 19.86 1.24 0.00 2.66
1700 1920 7.637511 AGAAAATCAAGGGAGTCAATAGATGT 58.362 34.615 0.00 0.00 0.00 3.06
1776 2408 4.576330 AGGCCAAATAGGTATATGAGGC 57.424 45.455 5.01 0.00 39.60 4.70
1914 2546 1.003696 GTCAGGTTCAGCTTTAGGGCT 59.996 52.381 0.00 0.00 44.10 5.19
1918 2550 2.079925 GCAGGTCAGGTTCAGCTTTAG 58.920 52.381 0.00 0.00 0.00 1.85
1992 2625 8.258007 TCACGTAAAATCTCTTATCTGGTGATT 58.742 33.333 0.00 0.00 34.32 2.57
1995 2628 7.545965 AGTTCACGTAAAATCTCTTATCTGGTG 59.454 37.037 0.00 0.00 0.00 4.17
2005 2638 7.583860 AGCTTAGAAGTTCACGTAAAATCTC 57.416 36.000 5.50 0.00 0.00 2.75
2013 2646 6.708949 TGGAATTTTAGCTTAGAAGTTCACGT 59.291 34.615 5.50 0.00 0.00 4.49
2015 2648 9.346725 CATTGGAATTTTAGCTTAGAAGTTCAC 57.653 33.333 5.50 0.00 0.00 3.18
2085 2718 4.702831 TGCCGCAAATGAGATGATAGTAA 58.297 39.130 0.00 0.00 0.00 2.24
2086 2719 4.335400 TGCCGCAAATGAGATGATAGTA 57.665 40.909 0.00 0.00 0.00 1.82
2104 2737 5.477984 TGCATAGGGAAATAATTGAGATGCC 59.522 40.000 0.00 0.00 37.05 4.40
2111 2744 6.618287 TTCGTCTGCATAGGGAAATAATTG 57.382 37.500 0.00 0.00 0.00 2.32
2113 2746 5.239525 GCTTTCGTCTGCATAGGGAAATAAT 59.760 40.000 0.00 0.00 31.32 1.28
2147 2780 2.033141 TTCAGCACCTCTGCCAGC 59.967 61.111 0.00 0.00 45.53 4.85
2360 2993 1.751927 GGAGCGACGGAGGAGGTAA 60.752 63.158 0.00 0.00 0.00 2.85
2561 3194 5.269505 TGAAACACCAAACACCTAAATGG 57.730 39.130 0.00 0.00 42.93 3.16
2562 3195 6.143758 CGAATGAAACACCAAACACCTAAATG 59.856 38.462 0.00 0.00 0.00 2.32
2563 3196 6.183360 ACGAATGAAACACCAAACACCTAAAT 60.183 34.615 0.00 0.00 0.00 1.40
2565 3198 4.641094 ACGAATGAAACACCAAACACCTAA 59.359 37.500 0.00 0.00 0.00 2.69
2581 3215 2.230266 TGTCGATGTCCTGAACGAATGA 59.770 45.455 0.00 0.00 36.57 2.57
2582 3216 2.606108 TGTCGATGTCCTGAACGAATG 58.394 47.619 0.00 0.00 36.57 2.67
2583 3217 3.119137 TGATGTCGATGTCCTGAACGAAT 60.119 43.478 0.00 0.00 36.57 3.34
2584 3218 2.230266 TGATGTCGATGTCCTGAACGAA 59.770 45.455 0.00 0.00 36.57 3.85
2585 3219 1.816224 TGATGTCGATGTCCTGAACGA 59.184 47.619 0.00 0.00 0.00 3.85
2586 3220 2.278026 TGATGTCGATGTCCTGAACG 57.722 50.000 0.00 0.00 0.00 3.95
2587 3221 3.308053 CACATGATGTCGATGTCCTGAAC 59.692 47.826 0.00 0.00 31.46 3.18
2588 3222 3.524541 CACATGATGTCGATGTCCTGAA 58.475 45.455 0.00 0.00 31.46 3.02
2746 3380 2.348888 ACCGCCGGTAGAACTCCAG 61.349 63.158 7.20 0.00 32.11 3.86
3118 3754 2.256174 ACACGACGTGTAATTCGATGG 58.744 47.619 30.95 1.79 45.56 3.51
3145 3781 1.531149 CACTGCCACGTAGAAACAAGG 59.469 52.381 0.00 0.00 0.00 3.61
3168 3804 0.830023 GGGTAAAAACCAGCCAGGCA 60.830 55.000 15.80 0.00 43.14 4.75
3169 3805 1.873270 CGGGTAAAAACCAGCCAGGC 61.873 60.000 1.84 1.84 43.14 4.85
3170 3806 0.250989 TCGGGTAAAAACCAGCCAGG 60.251 55.000 0.00 0.00 45.67 4.45
3171 3807 1.165270 CTCGGGTAAAAACCAGCCAG 58.835 55.000 0.00 0.00 32.95 4.85
3172 3808 0.475044 ACTCGGGTAAAAACCAGCCA 59.525 50.000 0.00 0.00 32.95 4.75
3173 3809 1.268625 CAACTCGGGTAAAAACCAGCC 59.731 52.381 0.00 0.00 0.00 4.85
3174 3810 2.223745 TCAACTCGGGTAAAAACCAGC 58.776 47.619 0.00 0.00 0.00 4.85
3175 3811 3.735591 TCTCAACTCGGGTAAAAACCAG 58.264 45.455 0.00 0.00 0.00 4.00
3205 3841 2.679837 CAAACATGCAGCGAACTCCTAT 59.320 45.455 0.00 0.00 0.00 2.57
3236 3872 5.030295 CGTAGTATGTAAATCCGACGTTGT 58.970 41.667 1.30 0.00 0.00 3.32
3311 3955 8.250143 TCCACTCTACTAGCATGATTTAATCA 57.750 34.615 10.23 10.23 44.55 2.57
3320 3964 3.055591 CGCAATCCACTCTACTAGCATG 58.944 50.000 0.00 0.00 0.00 4.06
3323 4154 1.409427 ACCGCAATCCACTCTACTAGC 59.591 52.381 0.00 0.00 0.00 3.42
3369 4200 2.877335 AGACCGTGTTCGATTTAGAGC 58.123 47.619 0.00 0.00 39.71 4.09
3385 4216 5.236695 GCAAAAGATCCCGTAGATAAAGACC 59.763 44.000 0.00 0.00 34.42 3.85
3390 4221 4.081322 GGGCAAAAGATCCCGTAGATAA 57.919 45.455 0.00 0.00 34.42 1.75
3398 4229 3.017442 GTCTTACAGGGCAAAAGATCCC 58.983 50.000 0.00 0.00 42.94 3.85
3401 4232 4.640771 TCAGTCTTACAGGGCAAAAGAT 57.359 40.909 0.00 0.00 32.26 2.40
3402 4233 4.640771 ATCAGTCTTACAGGGCAAAAGA 57.359 40.909 0.00 0.00 0.00 2.52
3403 4234 6.115446 TGATATCAGTCTTACAGGGCAAAAG 58.885 40.000 0.00 0.00 0.00 2.27
3404 4235 6.061022 TGATATCAGTCTTACAGGGCAAAA 57.939 37.500 0.00 0.00 0.00 2.44
3405 4236 5.692115 TGATATCAGTCTTACAGGGCAAA 57.308 39.130 0.00 0.00 0.00 3.68
3407 4238 5.674525 CTTTGATATCAGTCTTACAGGGCA 58.325 41.667 5.39 0.00 0.00 5.36
3408 4239 4.513318 GCTTTGATATCAGTCTTACAGGGC 59.487 45.833 5.39 0.00 0.00 5.19
3409 4240 5.059833 GGCTTTGATATCAGTCTTACAGGG 58.940 45.833 5.39 0.00 0.00 4.45
3410 4241 5.923204 AGGCTTTGATATCAGTCTTACAGG 58.077 41.667 5.39 0.00 0.00 4.00
3413 6878 5.755861 GTGGAGGCTTTGATATCAGTCTTAC 59.244 44.000 5.39 3.11 0.00 2.34
3422 6887 1.486310 TGAGCGTGGAGGCTTTGATAT 59.514 47.619 0.00 0.00 44.93 1.63
3427 6892 0.326264 AGAATGAGCGTGGAGGCTTT 59.674 50.000 0.00 0.00 44.93 3.51
3428 6893 0.392193 CAGAATGAGCGTGGAGGCTT 60.392 55.000 0.00 0.00 44.93 4.35
3438 6903 1.285578 GAGGCGAAGACAGAATGAGC 58.714 55.000 0.00 0.00 39.87 4.26
3443 6908 1.546476 GAGAAGGAGGCGAAGACAGAA 59.454 52.381 0.00 0.00 39.87 3.02
3451 6916 3.132139 CGGACGAGAAGGAGGCGA 61.132 66.667 0.00 0.00 0.00 5.54
3452 6917 4.856607 GCGGACGAGAAGGAGGCG 62.857 72.222 0.00 0.00 0.00 5.52
3463 6928 1.444553 GGAGACTGTGAAGCGGACG 60.445 63.158 0.00 0.00 0.00 4.79
3469 6934 3.055963 AGAATCAGCTGGAGACTGTGAAG 60.056 47.826 15.13 0.00 36.50 3.02
3471 6936 2.533916 AGAATCAGCTGGAGACTGTGA 58.466 47.619 15.13 0.00 36.50 3.58
3473 6938 2.902486 TGAAGAATCAGCTGGAGACTGT 59.098 45.455 15.13 0.00 36.50 3.55
3475 6940 3.582208 ACTTGAAGAATCAGCTGGAGACT 59.418 43.478 15.13 5.88 36.78 3.24
3497 6962 5.221224 CCACCTGTTTTAGAATGTTGAAGCA 60.221 40.000 0.00 0.00 0.00 3.91
3513 6978 1.228245 ATCGTGCAAGCCACCTGTT 60.228 52.632 0.00 0.00 41.53 3.16
3516 6981 0.745845 GATGATCGTGCAAGCCACCT 60.746 55.000 0.00 0.00 41.53 4.00
3518 6983 0.745845 AGGATGATCGTGCAAGCCAC 60.746 55.000 9.29 0.00 41.15 5.01
3519 6984 0.035152 AAGGATGATCGTGCAAGCCA 60.035 50.000 9.29 0.00 0.00 4.75
3530 6995 4.382386 TGGATGATGATGCAAGGATGAT 57.618 40.909 0.00 0.00 0.00 2.45
3544 7009 4.406972 TCGAAGATGAAGGAGTTGGATGAT 59.593 41.667 0.00 0.00 0.00 2.45
3558 7023 4.141846 CCTCTTCCAAGGATTCGAAGATGA 60.142 45.833 3.35 1.61 40.77 2.92
3565 7045 2.744202 CACAACCTCTTCCAAGGATTCG 59.256 50.000 0.00 0.00 38.87 3.34
3571 7051 5.412904 GGTTAAGATCACAACCTCTTCCAAG 59.587 44.000 17.09 0.00 40.90 3.61
3573 7053 4.906618 GGTTAAGATCACAACCTCTTCCA 58.093 43.478 17.09 0.00 40.90 3.53
3582 7062 8.210946 TCAAAGAGAAGAAGGTTAAGATCACAA 58.789 33.333 0.00 0.00 0.00 3.33
3585 7065 6.876257 GCTCAAAGAGAAGAAGGTTAAGATCA 59.124 38.462 0.00 0.00 0.00 2.92
3586 7066 7.102993 AGCTCAAAGAGAAGAAGGTTAAGATC 58.897 38.462 0.00 0.00 0.00 2.75
3591 7071 5.308825 CCAAGCTCAAAGAGAAGAAGGTTA 58.691 41.667 0.00 0.00 0.00 2.85
3598 7078 2.197283 AGGCCAAGCTCAAAGAGAAG 57.803 50.000 5.01 0.00 0.00 2.85
3601 7081 2.197283 AGAAGGCCAAGCTCAAAGAG 57.803 50.000 5.01 0.00 0.00 2.85
3606 7086 1.356124 AGAGAAGAAGGCCAAGCTCA 58.644 50.000 5.01 0.00 0.00 4.26
3619 7099 8.776376 AGAAGAAGCTCAAGATTTAAGAGAAG 57.224 34.615 0.00 0.00 0.00 2.85
3627 7107 4.874966 CGATGGAGAAGAAGCTCAAGATTT 59.125 41.667 0.00 0.00 36.62 2.17
3629 7109 3.450457 ACGATGGAGAAGAAGCTCAAGAT 59.550 43.478 0.00 0.00 36.62 2.40
3650 7130 0.108756 GTCCAAGAGGCCGTGTCTAC 60.109 60.000 0.00 0.00 33.74 2.59
3652 7132 2.932234 CGTCCAAGAGGCCGTGTCT 61.932 63.158 0.00 0.00 33.74 3.41
3658 7138 0.179081 GGTACATCGTCCAAGAGGCC 60.179 60.000 0.00 0.00 33.74 5.19
3659 7139 0.527817 CGGTACATCGTCCAAGAGGC 60.528 60.000 0.00 0.00 33.74 4.70
3678 7158 8.756864 GGTAAATTAAGTCTCTCAATCATCGAC 58.243 37.037 0.00 0.00 0.00 4.20
3685 7165 6.113411 CGTGGGGTAAATTAAGTCTCTCAAT 58.887 40.000 0.00 0.00 0.00 2.57
3713 7193 0.033504 ACGCTGACAAACTCATCCGT 59.966 50.000 0.00 0.00 34.00 4.69
3724 7204 3.428999 GCATTTAGAGACCTACGCTGACA 60.429 47.826 0.00 0.00 0.00 3.58
3736 7216 7.769044 GGTTCCATAAGTACAAGCATTTAGAGA 59.231 37.037 0.00 0.00 0.00 3.10
3751 7231 8.477256 CCAACATTCATATTTGGTTCCATAAGT 58.523 33.333 0.00 0.00 35.91 2.24
3754 7234 6.183360 GGCCAACATTCATATTTGGTTCCATA 60.183 38.462 0.00 0.00 41.69 2.74
3787 8190 2.222953 GGCACGAAGTAAAATGGCGTAG 60.223 50.000 0.00 0.00 41.61 3.51
3794 8197 5.237344 GCAGATCTATGGCACGAAGTAAAAT 59.763 40.000 0.00 0.00 41.61 1.82
3802 8205 0.312102 CGAGCAGATCTATGGCACGA 59.688 55.000 15.12 0.00 42.76 4.35
3818 8221 1.204704 TGGTTGGTCACTAGCATCGAG 59.795 52.381 0.00 0.00 32.06 4.04
3850 8253 4.036734 TCAACATGAAGAAGGACAAGTTGC 59.963 41.667 1.81 0.00 41.91 4.17
3893 8296 6.755141 CCGATGAATTTCTTGCTGATTCAAAT 59.245 34.615 2.58 0.00 41.51 2.32
3906 8312 5.057149 CGACCTTAATCCCGATGAATTTCT 58.943 41.667 0.00 0.00 0.00 2.52
3914 8320 1.336125 GACGACGACCTTAATCCCGAT 59.664 52.381 0.00 0.00 0.00 4.18
3917 8323 0.453390 ACGACGACGACCTTAATCCC 59.547 55.000 15.32 0.00 42.66 3.85
3922 8328 1.492873 CACGACGACGACGACCTTA 59.507 57.895 25.15 0.00 42.66 2.69
3956 8362 3.118408 AGCTGAATTCGTATACTGGCCAA 60.118 43.478 7.01 0.00 0.00 4.52
3962 8368 5.241949 CACCCTAGAGCTGAATTCGTATACT 59.758 44.000 0.00 0.00 0.00 2.12
3975 8381 1.321074 GGCACGTACACCCTAGAGCT 61.321 60.000 0.00 0.00 0.00 4.09
4022 8438 1.834856 CTCAGAGTCCAGGCAGCCAA 61.835 60.000 15.80 0.00 0.00 4.52
4030 8446 2.174360 TGTGGATGACTCAGAGTCCAG 58.826 52.381 25.11 0.00 44.44 3.86


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

AutoCloner maintained by Alex Coulton.