Multiple sequence alignment - TraesCS2A01G069300

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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 TraesCS2A01G069300 chr2A 100.000 4384 0 0 1 4384 30332905 30328522 0.000000e+00 8096.0
1 TraesCS2A01G069300 chr2D 90.394 4466 228 95 24 4381 28549814 28554186 0.000000e+00 5685.0
2 TraesCS2A01G069300 chr2B 89.619 4229 227 105 156 4282 45737779 45733661 0.000000e+00 5182.0
3 TraesCS2A01G069300 chr2B 88.571 105 5 3 4284 4381 45733499 45733395 2.140000e-23 121.0
4 TraesCS2A01G069300 chr6A 90.152 132 11 2 1001 1131 578887719 578887589 2.100000e-38 171.0
5 TraesCS2A01G069300 chr6A 90.426 94 9 0 2601 2694 578886311 578886218 1.660000e-24 124.0
6 TraesCS2A01G069300 chr6D 89.394 132 12 2 1001 1131 432710580 432710450 9.750000e-37 165.0
7 TraesCS2A01G069300 chr6D 90.426 94 9 0 2601 2694 432709198 432709105 1.660000e-24 124.0
8 TraesCS2A01G069300 chr6B 88.636 132 13 2 1001 1131 652631344 652631214 4.540000e-35 159.0
9 TraesCS2A01G069300 chr6B 91.489 94 8 0 2601 2694 652629938 652629845 3.560000e-26 130.0
10 TraesCS2A01G069300 chr4A 87.013 77 8 2 2614 2689 468603638 468603713 7.810000e-13 86.1
11 TraesCS2A01G069300 chr4D 85.714 77 9 2 2614 2689 107710347 107710272 3.630000e-11 80.5
12 TraesCS2A01G069300 chr4B 85.714 77 9 2 2614 2689 168985256 168985331 3.630000e-11 80.5


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 TraesCS2A01G069300 chr2A 30328522 30332905 4383 True 8096.0 8096 100.000 1 4384 1 chr2A.!!$R1 4383
1 TraesCS2A01G069300 chr2D 28549814 28554186 4372 False 5685.0 5685 90.394 24 4381 1 chr2D.!!$F1 4357
2 TraesCS2A01G069300 chr2B 45733395 45737779 4384 True 2651.5 5182 89.095 156 4381 2 chr2B.!!$R1 4225

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
700 729 0.107459 CTCCCCTCAAGCTTAGCCAC 60.107 60.0 0.0 0.0 0.00 5.01 F
717 746 0.109153 CACAGCCATAGCCATAGCCA 59.891 55.0 0.0 0.0 41.25 4.75 F
718 747 0.109342 ACAGCCATAGCCATAGCCAC 59.891 55.0 0.0 0.0 41.25 5.01 F
2819 2908 0.180406 ACAGCAACTTCTTCCACGGT 59.820 50.0 0.0 0.0 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2597 2679 0.676184 CGATGATCGACCACCTGGAT 59.324 55.000 9.62 0.00 43.74 3.41 R
2599 2681 1.592669 GCGATGATCGACCACCTGG 60.593 63.158 20.25 0.00 43.74 4.45 R
3059 3151 4.824166 CCGTACTGCGTCCCGTCG 62.824 72.222 0.00 0.00 39.32 5.12 R
3901 4051 0.936764 ATCACATCGAAGCTAGCGCG 60.937 55.000 21.81 21.81 42.32 6.86 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
17 18 2.123597 CCCCCTCGTACATCCGGA 60.124 66.667 6.61 6.61 0.00 5.14
18 19 2.201022 CCCCCTCGTACATCCGGAG 61.201 68.421 11.34 4.72 0.00 4.63
19 20 2.728817 CCCTCGTACATCCGGAGC 59.271 66.667 11.34 0.00 0.00 4.70
20 21 2.331805 CCTCGTACATCCGGAGCG 59.668 66.667 11.34 11.97 0.00 5.03
85 86 0.605589 GTGGCGGCTAGGTTTCTTGT 60.606 55.000 11.43 0.00 0.00 3.16
88 89 1.519408 GCGGCTAGGTTTCTTGTGAA 58.481 50.000 0.00 0.00 0.00 3.18
102 103 0.107831 TGTGAAAGTGGCGGCTTAGT 59.892 50.000 11.43 0.00 0.00 2.24
111 112 3.188786 CGGCTTAGTCGTGCCTGC 61.189 66.667 0.00 0.00 46.42 4.85
203 204 6.127563 TGTTGTGATATTGAACGACCTAGCTA 60.128 38.462 0.00 0.00 30.82 3.32
204 205 6.073327 TGTGATATTGAACGACCTAGCTAG 57.927 41.667 14.20 14.20 0.00 3.42
245 254 7.581476 ACTATGTACAAGTGTGGAAATTTTCG 58.419 34.615 0.00 0.00 0.00 3.46
271 283 6.015519 TGCTGCTAGACCAAAACATACAAATT 60.016 34.615 0.00 0.00 0.00 1.82
308 320 3.851976 ACCTAGCTACAACAACTCTCG 57.148 47.619 0.00 0.00 0.00 4.04
382 400 5.039480 CTGGACAACTAGCACATCAAAAG 57.961 43.478 0.00 0.00 0.00 2.27
383 401 4.460263 TGGACAACTAGCACATCAAAAGT 58.540 39.130 0.00 0.00 0.00 2.66
385 403 6.058833 TGGACAACTAGCACATCAAAAGTAA 58.941 36.000 0.00 0.00 0.00 2.24
390 410 8.076178 ACAACTAGCACATCAAAAGTAATCAAC 58.924 33.333 0.00 0.00 0.00 3.18
391 411 7.744087 ACTAGCACATCAAAAGTAATCAACA 57.256 32.000 0.00 0.00 0.00 3.33
415 436 1.399440 CACGAAGGATTCCATGTGCAG 59.601 52.381 5.29 0.00 43.81 4.41
585 611 2.611751 CACATCGTCGTCTCTCTCATCT 59.388 50.000 0.00 0.00 0.00 2.90
586 612 2.869801 ACATCGTCGTCTCTCTCATCTC 59.130 50.000 0.00 0.00 0.00 2.75
675 701 0.389025 GCTTAGCTCTGGCCTCTCTC 59.611 60.000 3.32 0.00 39.73 3.20
676 702 2.028996 GCTTAGCTCTGGCCTCTCTCT 61.029 57.143 3.32 0.00 39.73 3.10
700 729 0.107459 CTCCCCTCAAGCTTAGCCAC 60.107 60.000 0.00 0.00 0.00 5.01
706 735 0.329261 TCAAGCTTAGCCACAGCCAT 59.671 50.000 0.00 0.00 41.25 4.40
717 746 0.109153 CACAGCCATAGCCATAGCCA 59.891 55.000 0.00 0.00 41.25 4.75
718 747 0.109342 ACAGCCATAGCCATAGCCAC 59.891 55.000 0.00 0.00 41.25 5.01
719 748 0.399454 CAGCCATAGCCATAGCCACT 59.601 55.000 0.00 0.00 41.25 4.00
942 995 6.534934 CGTTGTATCTAGCTTTGTTTCTTCC 58.465 40.000 0.00 0.00 0.00 3.46
943 996 6.369065 CGTTGTATCTAGCTTTGTTTCTTCCT 59.631 38.462 0.00 0.00 0.00 3.36
944 997 7.412020 CGTTGTATCTAGCTTTGTTTCTTCCTC 60.412 40.741 0.00 0.00 0.00 3.71
945 998 6.407202 TGTATCTAGCTTTGTTTCTTCCTCC 58.593 40.000 0.00 0.00 0.00 4.30
946 999 5.770685 ATCTAGCTTTGTTTCTTCCTCCT 57.229 39.130 0.00 0.00 0.00 3.69
947 1000 5.568620 TCTAGCTTTGTTTCTTCCTCCTT 57.431 39.130 0.00 0.00 0.00 3.36
966 1022 4.714308 TCCTTCTCCTCATCTTCTTCTTCC 59.286 45.833 0.00 0.00 0.00 3.46
967 1023 4.716287 CCTTCTCCTCATCTTCTTCTTCCT 59.284 45.833 0.00 0.00 0.00 3.36
968 1024 5.163416 CCTTCTCCTCATCTTCTTCTTCCTC 60.163 48.000 0.00 0.00 0.00 3.71
969 1025 3.951037 TCTCCTCATCTTCTTCTTCCTCG 59.049 47.826 0.00 0.00 0.00 4.63
970 1026 2.428890 TCCTCATCTTCTTCTTCCTCGC 59.571 50.000 0.00 0.00 0.00 5.03
971 1027 2.458951 CTCATCTTCTTCTTCCTCGCG 58.541 52.381 0.00 0.00 0.00 5.87
972 1028 1.819288 TCATCTTCTTCTTCCTCGCGT 59.181 47.619 5.77 0.00 0.00 6.01
973 1029 2.159366 TCATCTTCTTCTTCCTCGCGTC 60.159 50.000 5.77 0.00 0.00 5.19
986 1042 3.064958 TCCTCGCGTCGATATATCAATCC 59.935 47.826 13.11 0.00 34.61 3.01
988 1044 4.498177 CCTCGCGTCGATATATCAATCCAT 60.498 45.833 13.11 0.00 34.61 3.41
989 1045 4.598062 TCGCGTCGATATATCAATCCATC 58.402 43.478 13.11 0.00 0.00 3.51
990 1046 4.335594 TCGCGTCGATATATCAATCCATCT 59.664 41.667 13.11 0.00 0.00 2.90
1170 1226 3.615155 AGCTTCCTGCCTTGTAGATTTC 58.385 45.455 0.00 0.00 44.23 2.17
1215 1271 4.857679 TGGTACTTTGGTTTGTGTAAGGT 58.142 39.130 0.00 0.00 0.00 3.50
1227 1283 2.306512 TGTGTAAGGTTATGGGTCACCC 59.693 50.000 5.63 5.63 45.71 4.61
1310 1366 6.409524 TGAATTTGTCCTTGATTTGCTTCT 57.590 33.333 0.00 0.00 0.00 2.85
1315 1371 4.464008 TGTCCTTGATTTGCTTCTGTCTT 58.536 39.130 0.00 0.00 0.00 3.01
1318 1374 5.917447 GTCCTTGATTTGCTTCTGTCTTTTC 59.083 40.000 0.00 0.00 0.00 2.29
1356 1412 7.201974 GGGATGATCAGTTGAAATTTGGATGAT 60.202 37.037 0.09 0.05 0.00 2.45
1357 1413 8.202137 GGATGATCAGTTGAAATTTGGATGATT 58.798 33.333 0.09 0.00 0.00 2.57
1519 1575 6.116126 ACTTCTTCTTTTCCAATCTATCCGG 58.884 40.000 0.00 0.00 0.00 5.14
1597 1655 5.411053 CACCAAACACTTGTTCCATGTTTTT 59.589 36.000 0.00 0.00 42.43 1.94
1598 1656 6.591834 CACCAAACACTTGTTCCATGTTTTTA 59.408 34.615 0.00 0.00 42.43 1.52
1600 1658 6.257630 CCAAACACTTGTTCCATGTTTTTAGG 59.742 38.462 0.00 0.00 42.43 2.69
1602 1660 6.783708 ACACTTGTTCCATGTTTTTAGGAA 57.216 33.333 0.00 0.00 39.01 3.36
1612 1674 5.238432 CCATGTTTTTAGGAACCAAAAAGGC 59.762 40.000 11.24 0.00 43.14 4.35
1613 1675 5.422214 TGTTTTTAGGAACCAAAAAGGCA 57.578 34.783 11.24 7.01 43.14 4.75
1633 1695 5.189736 AGGCACTTGTGGTTAATCATCTCTA 59.810 40.000 2.81 0.00 27.25 2.43
1634 1696 5.294552 GGCACTTGTGGTTAATCATCTCTAC 59.705 44.000 2.81 0.00 0.00 2.59
1635 1697 6.109359 GCACTTGTGGTTAATCATCTCTACT 58.891 40.000 2.81 0.00 0.00 2.57
1685 1749 2.819348 GCACCCATTTCTCCTTGGACTT 60.819 50.000 0.00 0.00 34.81 3.01
1686 1750 3.500343 CACCCATTTCTCCTTGGACTTT 58.500 45.455 0.00 0.00 34.81 2.66
1687 1751 4.662278 CACCCATTTCTCCTTGGACTTTA 58.338 43.478 0.00 0.00 34.81 1.85
1688 1752 4.459337 CACCCATTTCTCCTTGGACTTTAC 59.541 45.833 0.00 0.00 34.81 2.01
1689 1753 4.354087 ACCCATTTCTCCTTGGACTTTACT 59.646 41.667 0.00 0.00 34.81 2.24
1690 1754 5.550403 ACCCATTTCTCCTTGGACTTTACTA 59.450 40.000 0.00 0.00 34.81 1.82
1691 1755 6.116126 CCCATTTCTCCTTGGACTTTACTAG 58.884 44.000 0.00 0.00 34.81 2.57
1692 1756 5.586643 CCATTTCTCCTTGGACTTTACTAGC 59.413 44.000 0.00 0.00 34.81 3.42
1693 1757 5.818678 TTTCTCCTTGGACTTTACTAGCA 57.181 39.130 0.00 0.00 0.00 3.49
1694 1758 5.407407 TTCTCCTTGGACTTTACTAGCAG 57.593 43.478 0.00 0.00 0.00 4.24
1697 1761 3.519510 TCCTTGGACTTTACTAGCAGCAT 59.480 43.478 0.00 0.00 0.00 3.79
1698 1762 4.714802 TCCTTGGACTTTACTAGCAGCATA 59.285 41.667 0.00 0.00 0.00 3.14
1699 1763 4.811557 CCTTGGACTTTACTAGCAGCATAC 59.188 45.833 0.00 0.00 0.00 2.39
1700 1764 5.414789 TTGGACTTTACTAGCAGCATACA 57.585 39.130 0.00 0.00 0.00 2.29
1702 1766 4.466370 TGGACTTTACTAGCAGCATACAGT 59.534 41.667 0.00 0.00 0.00 3.55
1703 1767 5.046591 TGGACTTTACTAGCAGCATACAGTT 60.047 40.000 0.00 0.00 0.00 3.16
1704 1768 5.875359 GGACTTTACTAGCAGCATACAGTTT 59.125 40.000 0.00 0.00 0.00 2.66
1705 1769 6.371825 GGACTTTACTAGCAGCATACAGTTTT 59.628 38.462 0.00 0.00 0.00 2.43
1709 1773 4.256920 ACTAGCAGCATACAGTTTTCCAG 58.743 43.478 0.00 0.00 0.00 3.86
1753 1818 5.378230 AATGCTATGACTCCTGAATTCCA 57.622 39.130 2.27 0.00 0.00 3.53
1761 1826 5.494724 TGACTCCTGAATTCCATTTCTCAG 58.505 41.667 2.27 0.00 35.99 3.35
1774 1839 7.364522 TCCATTTCTCAGACGTCTAATTTTG 57.635 36.000 19.57 11.47 0.00 2.44
1779 1844 7.548196 TTCTCAGACGTCTAATTTTGTGTTT 57.452 32.000 19.57 0.00 0.00 2.83
1833 1899 7.660030 ACCTATTGTTTCTATTCCCCATTTG 57.340 36.000 0.00 0.00 0.00 2.32
1836 1902 8.197439 CCTATTGTTTCTATTCCCCATTTGTTC 58.803 37.037 0.00 0.00 0.00 3.18
1860 1926 8.256611 TCAGTATTGAACAATGAACTTCTAGC 57.743 34.615 9.87 0.00 32.50 3.42
1894 1961 9.435688 GACATTTCTAATGGCCTTAATTTGTTT 57.564 29.630 3.32 0.00 0.00 2.83
1984 2051 2.507407 TTAAGCATGGGGAGTTCACC 57.493 50.000 0.00 0.00 40.76 4.02
2093 2160 5.466819 CATGCATGTTCTCTCACATTGTTT 58.533 37.500 18.91 0.00 35.03 2.83
2097 2164 5.978919 GCATGTTCTCTCACATTGTTTTGAA 59.021 36.000 0.00 0.00 35.03 2.69
2176 2244 1.740025 GTCCTCAAATTTCCAGCCGAG 59.260 52.381 0.00 0.00 0.00 4.63
2184 2252 5.296780 TCAAATTTCCAGCCGAGAATATGAC 59.703 40.000 0.00 0.00 0.00 3.06
2189 2257 4.667573 TCCAGCCGAGAATATGACTATCT 58.332 43.478 0.00 0.00 0.00 1.98
2190 2258 4.460731 TCCAGCCGAGAATATGACTATCTG 59.539 45.833 0.00 0.00 0.00 2.90
2198 2266 4.904251 AGAATATGACTATCTGTGGCCTGT 59.096 41.667 3.32 0.00 0.00 4.00
2202 2270 3.024547 TGACTATCTGTGGCCTGTCTAC 58.975 50.000 3.32 0.00 0.00 2.59
2209 2278 4.072131 TCTGTGGCCTGTCTACAAAATTC 58.928 43.478 3.32 0.00 35.68 2.17
2210 2279 3.153919 TGTGGCCTGTCTACAAAATTCC 58.846 45.455 3.32 0.00 32.96 3.01
2229 2298 6.581171 ATTCCTCCTGTCAATGTTTTCTTC 57.419 37.500 0.00 0.00 0.00 2.87
2230 2299 4.398319 TCCTCCTGTCAATGTTTTCTTCC 58.602 43.478 0.00 0.00 0.00 3.46
2231 2300 4.141274 TCCTCCTGTCAATGTTTTCTTCCA 60.141 41.667 0.00 0.00 0.00 3.53
2390 2464 2.170187 CCCTATCTTGTGCTCAGAGCTT 59.830 50.000 23.15 4.27 42.97 3.74
2505 2587 4.967084 ACATTACCCCCAAAAAGGAAAC 57.033 40.909 0.00 0.00 41.22 2.78
2558 2640 6.199908 GCACAACTATGAACTATCTACTGCAG 59.800 42.308 13.48 13.48 0.00 4.41
2559 2641 7.484140 CACAACTATGAACTATCTACTGCAGA 58.516 38.462 23.35 0.00 37.79 4.26
2560 2642 8.140628 CACAACTATGAACTATCTACTGCAGAT 58.859 37.037 23.35 6.43 46.19 2.90
2561 2643 8.356657 ACAACTATGAACTATCTACTGCAGATC 58.643 37.037 23.35 5.76 43.27 2.75
2562 2644 7.139896 ACTATGAACTATCTACTGCAGATCG 57.860 40.000 23.35 8.02 43.27 3.69
2563 2645 6.937465 ACTATGAACTATCTACTGCAGATCGA 59.063 38.462 23.35 13.39 43.27 3.59
2564 2646 6.832520 ATGAACTATCTACTGCAGATCGAT 57.167 37.500 23.35 19.09 43.27 3.59
2565 2647 6.641169 TGAACTATCTACTGCAGATCGATT 57.359 37.500 23.35 5.44 43.27 3.34
2566 2648 7.745620 TGAACTATCTACTGCAGATCGATTA 57.254 36.000 23.35 0.00 43.27 1.75
2567 2649 7.811653 TGAACTATCTACTGCAGATCGATTAG 58.188 38.462 23.35 10.56 43.27 1.73
2568 2650 6.189677 ACTATCTACTGCAGATCGATTAGC 57.810 41.667 23.35 14.03 43.27 3.09
2569 2651 3.924918 TCTACTGCAGATCGATTAGCC 57.075 47.619 23.35 0.00 0.00 3.93
2570 2652 2.226674 TCTACTGCAGATCGATTAGCCG 59.773 50.000 23.35 14.01 0.00 5.52
2592 2674 5.178252 CCGATTAGCATTACTCATTCTGTGG 59.822 44.000 0.00 0.00 0.00 4.17
2593 2675 5.755375 CGATTAGCATTACTCATTCTGTGGT 59.245 40.000 0.00 0.00 0.00 4.16
2595 2677 7.096023 CGATTAGCATTACTCATTCTGTGGTAC 60.096 40.741 0.00 0.00 0.00 3.34
2597 2679 5.804639 AGCATTACTCATTCTGTGGTACAA 58.195 37.500 0.00 0.00 44.16 2.41
2598 2680 6.418101 AGCATTACTCATTCTGTGGTACAAT 58.582 36.000 0.00 0.00 44.16 2.71
2599 2681 6.540189 AGCATTACTCATTCTGTGGTACAATC 59.460 38.462 0.00 0.00 44.16 2.67
2815 2904 3.135712 TCCAACTACAGCAACTTCTTCCA 59.864 43.478 0.00 0.00 0.00 3.53
2819 2908 0.180406 ACAGCAACTTCTTCCACGGT 59.820 50.000 0.00 0.00 0.00 4.83
2888 2977 1.204704 CAAGACCACTACATGCTCGGA 59.795 52.381 0.00 0.00 0.00 4.55
2891 2980 1.204941 GACCACTACATGCTCGGAAGT 59.795 52.381 0.00 0.00 0.00 3.01
3032 3124 2.167219 CATGATCGCGTTCGGCTGT 61.167 57.895 5.77 0.00 40.44 4.40
3169 3261 1.885157 CCTACGGAGTGTACGGCAA 59.115 57.895 0.00 0.00 45.73 4.52
3278 3373 0.459489 ACGAGGAGATCAAGCAGCTC 59.541 55.000 0.00 0.00 0.00 4.09
3281 3376 3.383092 GGAGATCAAGCAGCTCCTG 57.617 57.895 0.00 0.00 43.79 3.86
3324 3428 2.680352 ACGGCCTGATCCACGACT 60.680 61.111 0.00 0.00 0.00 4.18
3398 3511 8.450964 ACGATGATGTAAAAACCAGAGTAATTG 58.549 33.333 0.00 0.00 0.00 2.32
3444 3557 3.994392 GCACGTAAAGAAGGTCATCAAGA 59.006 43.478 0.00 0.00 0.00 3.02
3445 3558 4.092091 GCACGTAAAGAAGGTCATCAAGAG 59.908 45.833 0.00 0.00 0.00 2.85
3659 3782 4.222336 TGGGATCAAGATTCTCTCTCTCC 58.778 47.826 0.00 0.00 31.03 3.71
3660 3783 4.078688 TGGGATCAAGATTCTCTCTCTCCT 60.079 45.833 0.00 0.00 31.03 3.69
3661 3784 4.524328 GGGATCAAGATTCTCTCTCTCCTC 59.476 50.000 0.00 0.00 31.03 3.71
3662 3785 5.388654 GGATCAAGATTCTCTCTCTCCTCT 58.611 45.833 0.00 0.00 31.03 3.69
3663 3786 5.474876 GGATCAAGATTCTCTCTCTCCTCTC 59.525 48.000 0.00 0.00 31.03 3.20
3664 3787 5.715439 TCAAGATTCTCTCTCTCCTCTCT 57.285 43.478 0.00 0.00 31.03 3.10
3665 3788 5.684704 TCAAGATTCTCTCTCTCCTCTCTC 58.315 45.833 0.00 0.00 31.03 3.20
3666 3789 4.713792 AGATTCTCTCTCTCCTCTCTCC 57.286 50.000 0.00 0.00 0.00 3.71
3814 3960 1.476488 GACAGTGTTTGTTTGGCCAGT 59.524 47.619 5.11 0.00 41.05 4.00
3839 3985 3.165071 TGACTCTCATAGCTTGGTGTGA 58.835 45.455 0.00 0.00 0.00 3.58
3860 4010 1.511613 ACCACCCTACTCCATCATGG 58.488 55.000 0.00 0.00 39.43 3.66
3886 4036 4.883585 GTGTCCATTTCTTCTCCATGCATA 59.116 41.667 0.00 0.00 0.00 3.14
3901 4051 1.580893 CATACATGTGTGTGCGCGC 60.581 57.895 27.26 27.26 39.39 6.86
3950 4100 7.730332 TCTGACACCCTGAATGTACTATATGAT 59.270 37.037 0.00 0.00 0.00 2.45
3991 4141 3.256879 TCTCATTCACTCACTCACTCACC 59.743 47.826 0.00 0.00 0.00 4.02
3992 4142 3.234353 TCATTCACTCACTCACTCACCT 58.766 45.455 0.00 0.00 0.00 4.00
4069 4230 2.320215 TGAAGGCTCACAAGTTGCG 58.680 52.632 1.81 0.00 0.00 4.85
4088 4249 2.887733 CGAAGCATACGCGGATTAAAC 58.112 47.619 12.47 0.00 45.49 2.01
4200 4362 4.203226 TGTGGCAGTGATTACTTGTTTCA 58.797 39.130 0.00 0.00 34.07 2.69
4207 4369 7.141363 GCAGTGATTACTTGTTTCATTTCACT 58.859 34.615 0.00 0.00 42.27 3.41
4282 4446 7.670140 TCTCTGACCTAGACATGTTTTCTCTAA 59.330 37.037 0.00 0.00 0.00 2.10
4346 4671 2.457366 GGATTAGGTCCACCGCATAG 57.543 55.000 0.00 0.00 46.96 2.23
4348 4673 2.028930 GGATTAGGTCCACCGCATAGAG 60.029 54.545 0.00 0.00 46.96 2.43
4349 4674 2.154567 TTAGGTCCACCGCATAGAGT 57.845 50.000 0.00 0.00 42.08 3.24
4350 4675 2.154567 TAGGTCCACCGCATAGAGTT 57.845 50.000 0.00 0.00 42.08 3.01
4370 4701 5.783111 AGTTTACACAAGATTTTGGGATGC 58.217 37.500 5.04 0.00 40.26 3.91
4377 4708 1.669999 GATTTTGGGATGCTGCCGCT 61.670 55.000 0.70 0.00 36.97 5.52
4381 4712 2.280457 GGGATGCTGCCGCTAGAC 60.280 66.667 0.70 0.00 36.97 2.59
4382 4713 2.501128 GGATGCTGCCGCTAGACA 59.499 61.111 0.70 0.00 36.97 3.41
4383 4714 1.070445 GGATGCTGCCGCTAGACAT 59.930 57.895 0.70 0.00 36.97 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.123597 TCCGGATGTACGAGGGGG 60.124 66.667 0.00 0.00 35.47 5.40
1 2 2.857744 GCTCCGGATGTACGAGGGG 61.858 68.421 3.57 0.00 35.47 4.79
2 3 2.728817 GCTCCGGATGTACGAGGG 59.271 66.667 3.57 0.00 35.47 4.30
3 4 2.331805 CGCTCCGGATGTACGAGG 59.668 66.667 3.57 0.00 35.47 4.63
14 15 4.647615 CCTCCGCATACCGCTCCG 62.648 72.222 0.00 0.00 39.08 4.63
15 16 3.214250 CTCCTCCGCATACCGCTCC 62.214 68.421 0.00 0.00 39.08 4.70
16 17 1.170919 TACTCCTCCGCATACCGCTC 61.171 60.000 0.00 0.00 39.08 5.03
17 18 1.152819 TACTCCTCCGCATACCGCT 60.153 57.895 0.00 0.00 39.08 5.52
18 19 1.286260 CTACTCCTCCGCATACCGC 59.714 63.158 0.00 0.00 35.03 5.68
19 20 1.524863 CCCTACTCCTCCGCATACCG 61.525 65.000 0.00 0.00 0.00 4.02
20 21 1.186267 CCCCTACTCCTCCGCATACC 61.186 65.000 0.00 0.00 0.00 2.73
21 22 0.178970 TCCCCTACTCCTCCGCATAC 60.179 60.000 0.00 0.00 0.00 2.39
22 23 0.178970 GTCCCCTACTCCTCCGCATA 60.179 60.000 0.00 0.00 0.00 3.14
27 28 2.123382 CGGGTCCCCTACTCCTCC 60.123 72.222 1.00 0.00 0.00 4.30
34 35 4.791069 GAGGCCACGGGTCCCCTA 62.791 72.222 5.01 0.00 0.00 3.53
85 86 0.669318 CGACTAAGCCGCCACTTTCA 60.669 55.000 0.00 0.00 0.00 2.69
88 89 1.374252 CACGACTAAGCCGCCACTT 60.374 57.895 0.00 0.00 0.00 3.16
111 112 2.636830 CTGAACTAATGCAGTCCCAGG 58.363 52.381 0.00 0.00 36.04 4.45
121 122 8.341173 GGATAAAGTCAATCTGCTGAACTAATG 58.659 37.037 0.00 0.00 0.00 1.90
203 204 6.793505 ACATAGTAAATTCCGGAGAAGACT 57.206 37.500 3.34 10.11 34.86 3.24
204 205 7.486647 TGTACATAGTAAATTCCGGAGAAGAC 58.513 38.462 3.34 2.20 34.86 3.01
243 252 1.202592 TGTTTTGGTCTAGCAGCACGA 60.203 47.619 0.00 0.00 30.04 4.35
245 254 3.751175 TGTATGTTTTGGTCTAGCAGCAC 59.249 43.478 0.00 0.00 30.04 4.40
271 283 3.746045 AGGTAGCTTCTTCGTGACAAA 57.254 42.857 0.00 0.00 0.00 2.83
366 384 8.165239 TGTTGATTACTTTTGATGTGCTAGTT 57.835 30.769 0.00 0.00 0.00 2.24
367 385 7.744087 TGTTGATTACTTTTGATGTGCTAGT 57.256 32.000 0.00 0.00 0.00 2.57
368 386 7.752239 CCTTGTTGATTACTTTTGATGTGCTAG 59.248 37.037 0.00 0.00 0.00 3.42
381 399 3.074412 CCTTCGTGCCTTGTTGATTACT 58.926 45.455 0.00 0.00 0.00 2.24
382 400 3.071479 TCCTTCGTGCCTTGTTGATTAC 58.929 45.455 0.00 0.00 0.00 1.89
383 401 3.410631 TCCTTCGTGCCTTGTTGATTA 57.589 42.857 0.00 0.00 0.00 1.75
385 403 2.496899 ATCCTTCGTGCCTTGTTGAT 57.503 45.000 0.00 0.00 0.00 2.57
390 410 1.402968 CATGGAATCCTTCGTGCCTTG 59.597 52.381 0.00 0.00 0.00 3.61
391 411 1.004745 ACATGGAATCCTTCGTGCCTT 59.995 47.619 0.00 0.00 0.00 4.35
415 436 5.824097 TCCCTTTCTGTAAACAAAGTACACC 59.176 40.000 0.00 0.00 0.00 4.16
464 488 2.905260 CGAAATTTCGTAGCCTAGCG 57.095 50.000 28.21 3.54 45.09 4.26
585 611 4.335037 CAGACAGTTGATCGATCAGAGAGA 59.665 45.833 25.95 10.24 38.19 3.10
586 612 4.600032 CAGACAGTTGATCGATCAGAGAG 58.400 47.826 25.95 19.05 38.19 3.20
675 701 1.210885 AAGCTTGAGGGGAGGGGAAG 61.211 60.000 0.00 0.00 0.00 3.46
676 702 0.120377 TAAGCTTGAGGGGAGGGGAA 59.880 55.000 9.86 0.00 0.00 3.97
700 729 0.399454 AGTGGCTATGGCTATGGCTG 59.601 55.000 17.60 0.00 40.33 4.85
706 735 0.563173 AGGAGGAGTGGCTATGGCTA 59.437 55.000 0.00 0.00 38.73 3.93
717 746 1.627834 CAGAAAGCAAGGAGGAGGAGT 59.372 52.381 0.00 0.00 0.00 3.85
718 747 1.627834 ACAGAAAGCAAGGAGGAGGAG 59.372 52.381 0.00 0.00 0.00 3.69
719 748 1.349026 CACAGAAAGCAAGGAGGAGGA 59.651 52.381 0.00 0.00 0.00 3.71
919 972 7.148390 GGAGGAAGAAACAAAGCTAGATACAAC 60.148 40.741 0.00 0.00 0.00 3.32
942 995 5.163416 GGAAGAAGAAGATGAGGAGAAGGAG 60.163 48.000 0.00 0.00 0.00 3.69
943 996 4.714308 GGAAGAAGAAGATGAGGAGAAGGA 59.286 45.833 0.00 0.00 0.00 3.36
944 997 4.716287 AGGAAGAAGAAGATGAGGAGAAGG 59.284 45.833 0.00 0.00 0.00 3.46
945 998 5.450412 CGAGGAAGAAGAAGATGAGGAGAAG 60.450 48.000 0.00 0.00 0.00 2.85
946 999 4.400884 CGAGGAAGAAGAAGATGAGGAGAA 59.599 45.833 0.00 0.00 0.00 2.87
947 1000 3.951037 CGAGGAAGAAGAAGATGAGGAGA 59.049 47.826 0.00 0.00 0.00 3.71
966 1022 4.016113 TGGATTGATATATCGACGCGAG 57.984 45.455 15.93 6.55 39.91 5.03
967 1023 4.335594 AGATGGATTGATATATCGACGCGA 59.664 41.667 15.93 4.51 41.13 5.87
968 1024 4.602006 AGATGGATTGATATATCGACGCG 58.398 43.478 3.53 3.53 0.00 6.01
969 1025 6.269315 AGAAGATGGATTGATATATCGACGC 58.731 40.000 4.71 1.13 0.00 5.19
970 1026 7.430793 GTGAGAAGATGGATTGATATATCGACG 59.569 40.741 4.71 0.00 0.00 5.12
971 1027 7.704472 GGTGAGAAGATGGATTGATATATCGAC 59.296 40.741 4.71 0.69 0.00 4.20
972 1028 7.617329 AGGTGAGAAGATGGATTGATATATCGA 59.383 37.037 5.09 5.09 0.00 3.59
973 1029 7.705752 CAGGTGAGAAGATGGATTGATATATCG 59.294 40.741 8.19 0.00 0.00 2.92
986 1042 2.104451 CTCCCCATCAGGTGAGAAGATG 59.896 54.545 0.00 0.00 39.02 2.90
988 1044 1.623557 CCTCCCCATCAGGTGAGAAGA 60.624 57.143 0.00 0.00 35.85 2.87
989 1045 0.835941 CCTCCCCATCAGGTGAGAAG 59.164 60.000 0.00 0.00 35.85 2.85
990 1046 0.621571 CCCTCCCCATCAGGTGAGAA 60.622 60.000 0.00 0.00 35.85 2.87
1227 1283 2.079925 GAAGTTAAGACAGGCCAGCAG 58.920 52.381 5.01 0.00 0.00 4.24
1310 1366 4.080015 TCCCCAAGTCAAGAAGAAAAGACA 60.080 41.667 0.00 0.00 33.56 3.41
1315 1371 4.722526 TCATCCCCAAGTCAAGAAGAAA 57.277 40.909 0.00 0.00 0.00 2.52
1318 1374 4.197750 CTGATCATCCCCAAGTCAAGAAG 58.802 47.826 0.00 0.00 0.00 2.85
1356 1412 4.114073 TCTAGACGCGTGAGAAACAAAAA 58.886 39.130 20.70 0.00 0.00 1.94
1357 1413 3.708890 TCTAGACGCGTGAGAAACAAAA 58.291 40.909 20.70 0.00 0.00 2.44
1361 1417 2.658285 TGTTCTAGACGCGTGAGAAAC 58.342 47.619 26.31 20.12 31.26 2.78
1465 1521 0.788391 GACGACGGCATTTCGACTTT 59.212 50.000 0.00 0.00 39.83 2.66
1519 1575 7.544804 AATTGATTAGGGGGAAATGATAAGC 57.455 36.000 0.00 0.00 0.00 3.09
1546 1604 7.997482 TCCTGTTATGTAGAGTGAATGTACTC 58.003 38.462 0.00 0.00 45.83 2.59
1550 1608 7.268586 GTGATCCTGTTATGTAGAGTGAATGT 58.731 38.462 0.00 0.00 0.00 2.71
1557 1615 6.313905 GTGTTTGGTGATCCTGTTATGTAGAG 59.686 42.308 0.00 0.00 34.23 2.43
1558 1616 6.013725 AGTGTTTGGTGATCCTGTTATGTAGA 60.014 38.462 0.00 0.00 34.23 2.59
1597 1655 3.383185 CACAAGTGCCTTTTTGGTTCCTA 59.617 43.478 0.00 0.00 38.35 2.94
1598 1656 2.168313 CACAAGTGCCTTTTTGGTTCCT 59.832 45.455 0.00 0.00 38.35 3.36
1600 1658 2.093711 ACCACAAGTGCCTTTTTGGTTC 60.094 45.455 10.13 0.00 35.11 3.62
1602 1660 1.567357 ACCACAAGTGCCTTTTTGGT 58.433 45.000 10.13 10.13 34.34 3.67
1604 1662 5.355596 TGATTAACCACAAGTGCCTTTTTG 58.644 37.500 0.00 0.00 0.00 2.44
1612 1674 8.037758 AGAAGTAGAGATGATTAACCACAAGTG 58.962 37.037 0.00 0.00 0.00 3.16
1613 1675 8.140112 AGAAGTAGAGATGATTAACCACAAGT 57.860 34.615 0.00 0.00 0.00 3.16
1628 1690 9.132923 TGAGAGAAACAAACTAAGAAGTAGAGA 57.867 33.333 0.00 0.00 33.75 3.10
1629 1691 9.187455 GTGAGAGAAACAAACTAAGAAGTAGAG 57.813 37.037 0.00 0.00 33.75 2.43
1633 1695 8.561738 TTTGTGAGAGAAACAAACTAAGAAGT 57.438 30.769 0.00 0.00 41.37 3.01
1647 1711 2.938823 GCGCGCGTTTGTGAGAGAA 61.939 57.895 32.35 0.00 0.00 2.87
1659 1723 4.520846 GAGAAATGGGTGCGCGCG 62.521 66.667 28.44 28.44 0.00 6.86
1669 1733 6.173339 TGCTAGTAAAGTCCAAGGAGAAATG 58.827 40.000 0.00 0.00 0.00 2.32
1671 1735 5.794894 CTGCTAGTAAAGTCCAAGGAGAAA 58.205 41.667 0.00 0.00 0.00 2.52
1685 1749 5.800296 TGGAAAACTGTATGCTGCTAGTAA 58.200 37.500 0.00 0.00 0.00 2.24
1686 1750 5.046591 ACTGGAAAACTGTATGCTGCTAGTA 60.047 40.000 0.00 0.00 0.00 1.82
1687 1751 4.256920 CTGGAAAACTGTATGCTGCTAGT 58.743 43.478 0.00 0.00 0.00 2.57
1688 1752 4.256920 ACTGGAAAACTGTATGCTGCTAG 58.743 43.478 0.00 0.00 0.00 3.42
1689 1753 4.286297 ACTGGAAAACTGTATGCTGCTA 57.714 40.909 0.00 0.00 0.00 3.49
1690 1754 3.146104 ACTGGAAAACTGTATGCTGCT 57.854 42.857 0.00 0.00 0.00 4.24
1691 1755 3.923017 AACTGGAAAACTGTATGCTGC 57.077 42.857 0.00 0.00 0.00 5.25
1692 1756 5.437289 TCAAACTGGAAAACTGTATGCTG 57.563 39.130 0.00 0.00 0.00 4.41
1693 1757 5.565439 GCATCAAACTGGAAAACTGTATGCT 60.565 40.000 0.00 0.00 37.45 3.79
1694 1758 4.622740 GCATCAAACTGGAAAACTGTATGC 59.377 41.667 0.00 0.00 35.12 3.14
1697 1761 4.037446 GGTGCATCAAACTGGAAAACTGTA 59.963 41.667 0.00 0.00 0.00 2.74
1698 1762 3.181476 GGTGCATCAAACTGGAAAACTGT 60.181 43.478 0.00 0.00 0.00 3.55
1699 1763 3.068590 AGGTGCATCAAACTGGAAAACTG 59.931 43.478 0.00 0.00 0.00 3.16
1700 1764 3.299503 AGGTGCATCAAACTGGAAAACT 58.700 40.909 0.00 0.00 0.00 2.66
1702 1766 4.211125 TGTAGGTGCATCAAACTGGAAAA 58.789 39.130 0.00 0.00 0.00 2.29
1703 1767 3.826524 TGTAGGTGCATCAAACTGGAAA 58.173 40.909 0.00 0.00 0.00 3.13
1704 1768 3.500448 TGTAGGTGCATCAAACTGGAA 57.500 42.857 0.00 0.00 0.00 3.53
1705 1769 3.500448 TTGTAGGTGCATCAAACTGGA 57.500 42.857 0.00 0.00 0.00 3.86
1709 1773 7.432252 GCATTAGTTATTGTAGGTGCATCAAAC 59.568 37.037 0.00 0.00 0.00 2.93
1753 1818 7.730364 ACACAAAATTAGACGTCTGAGAAAT 57.270 32.000 28.12 16.11 0.00 2.17
1782 1847 8.874156 AGCATATGATTAACCAGAGATAACAGA 58.126 33.333 6.97 0.00 0.00 3.41
1836 1902 8.261492 AGCTAGAAGTTCATTGTTCAATACTG 57.739 34.615 5.50 0.00 0.00 2.74
1894 1961 6.430925 CACATCTTCTCAACCCTAATTGTGAA 59.569 38.462 0.00 0.00 38.87 3.18
1930 1997 4.101741 AGGTAGTTTAGCCATCTAAGCCTG 59.898 45.833 0.00 0.00 36.88 4.85
1984 2051 3.257873 AGATGACCCTATCTTCATGCTCG 59.742 47.826 0.00 0.00 33.74 5.03
2093 2160 2.136298 TCAACTTGGGTGTGCTTCAA 57.864 45.000 0.00 0.00 0.00 2.69
2097 2164 2.175202 TGTTTTCAACTTGGGTGTGCT 58.825 42.857 0.00 0.00 0.00 4.40
2146 2214 8.470002 GCTGGAAATTTGAGGACTAACATAAAT 58.530 33.333 0.00 0.00 0.00 1.40
2147 2215 7.093945 GGCTGGAAATTTGAGGACTAACATAAA 60.094 37.037 0.00 0.00 0.00 1.40
2148 2216 6.377146 GGCTGGAAATTTGAGGACTAACATAA 59.623 38.462 0.00 0.00 0.00 1.90
2153 2221 3.008594 TCGGCTGGAAATTTGAGGACTAA 59.991 43.478 0.00 0.00 0.00 2.24
2168 2236 4.219507 ACAGATAGTCATATTCTCGGCTGG 59.780 45.833 0.00 0.00 0.00 4.85
2176 2244 5.011533 AGACAGGCCACAGATAGTCATATTC 59.988 44.000 5.01 0.00 0.00 1.75
2184 2252 4.471904 TTTGTAGACAGGCCACAGATAG 57.528 45.455 5.01 0.00 0.00 2.08
2189 2257 3.153919 GGAATTTTGTAGACAGGCCACA 58.846 45.455 5.01 0.00 0.00 4.17
2190 2258 3.421844 AGGAATTTTGTAGACAGGCCAC 58.578 45.455 5.01 0.00 0.00 5.01
2198 2266 6.542821 ACATTGACAGGAGGAATTTTGTAGA 58.457 36.000 0.00 0.00 0.00 2.59
2202 2270 7.212274 AGAAAACATTGACAGGAGGAATTTTG 58.788 34.615 0.00 0.00 0.00 2.44
2209 2278 4.144297 TGGAAGAAAACATTGACAGGAGG 58.856 43.478 0.00 0.00 0.00 4.30
2210 2279 5.706916 CATGGAAGAAAACATTGACAGGAG 58.293 41.667 0.00 0.00 0.00 3.69
2255 2324 9.504708 ACATGAAAATCTGCAAATTTTATCCAA 57.495 25.926 10.64 0.00 38.59 3.53
2295 2367 7.147983 TGCATGTGTTAGGGATATTTTGGTAAC 60.148 37.037 0.00 0.00 0.00 2.50
2476 2554 6.406512 CCTTTTTGGGGGTAATGTAACTATGC 60.407 42.308 0.00 0.00 0.00 3.14
2536 2618 7.536964 CGATCTGCAGTAGATAGTTCATAGTTG 59.463 40.741 14.67 0.00 46.12 3.16
2537 2619 7.445707 TCGATCTGCAGTAGATAGTTCATAGTT 59.554 37.037 14.67 0.00 46.12 2.24
2540 2622 7.929941 ATCGATCTGCAGTAGATAGTTCATA 57.070 36.000 14.67 0.00 46.12 2.15
2541 2623 6.832520 ATCGATCTGCAGTAGATAGTTCAT 57.167 37.500 14.67 0.00 46.12 2.57
2542 2624 6.641169 AATCGATCTGCAGTAGATAGTTCA 57.359 37.500 14.67 0.00 46.12 3.18
2543 2625 6.745450 GCTAATCGATCTGCAGTAGATAGTTC 59.255 42.308 14.67 4.69 46.12 3.01
2560 2642 5.048294 TGAGTAATGCTAATCGGCTAATCGA 60.048 40.000 0.00 0.00 43.61 3.59
2561 2643 5.161358 TGAGTAATGCTAATCGGCTAATCG 58.839 41.667 0.00 0.00 0.00 3.34
2562 2644 7.547370 AGAATGAGTAATGCTAATCGGCTAATC 59.453 37.037 0.00 0.00 0.00 1.75
2563 2645 7.332926 CAGAATGAGTAATGCTAATCGGCTAAT 59.667 37.037 0.00 0.00 39.69 1.73
2564 2646 6.646653 CAGAATGAGTAATGCTAATCGGCTAA 59.353 38.462 0.00 0.00 39.69 3.09
2565 2647 6.159293 CAGAATGAGTAATGCTAATCGGCTA 58.841 40.000 0.00 0.00 39.69 3.93
2566 2648 4.993584 CAGAATGAGTAATGCTAATCGGCT 59.006 41.667 0.00 0.00 39.69 5.52
2567 2649 4.752101 ACAGAATGAGTAATGCTAATCGGC 59.248 41.667 0.00 0.00 39.69 5.54
2568 2650 5.178252 CCACAGAATGAGTAATGCTAATCGG 59.822 44.000 0.00 0.00 39.69 4.18
2569 2651 5.755375 ACCACAGAATGAGTAATGCTAATCG 59.245 40.000 0.00 0.00 39.69 3.34
2570 2652 7.710907 TGTACCACAGAATGAGTAATGCTAATC 59.289 37.037 0.00 0.00 39.69 1.75
2592 2674 2.167693 TGATCGACCACCTGGATTGTAC 59.832 50.000 0.00 0.00 38.94 2.90
2593 2675 2.462723 TGATCGACCACCTGGATTGTA 58.537 47.619 0.00 0.00 38.94 2.41
2595 2677 2.487934 GATGATCGACCACCTGGATTG 58.512 52.381 0.00 0.00 38.94 2.67
2597 2679 0.676184 CGATGATCGACCACCTGGAT 59.324 55.000 9.62 0.00 43.74 3.41
2598 2680 2.016393 GCGATGATCGACCACCTGGA 62.016 60.000 20.25 0.00 43.74 3.86
2599 2681 1.592669 GCGATGATCGACCACCTGG 60.593 63.158 20.25 0.00 43.74 4.45
3059 3151 4.824166 CCGTACTGCGTCCCGTCG 62.824 72.222 0.00 0.00 39.32 5.12
3080 3172 4.373116 CCGTGCACGTACTGGCCT 62.373 66.667 34.81 0.00 37.74 5.19
3182 3274 1.673665 CTTGTGCTCCTGCTCCACC 60.674 63.158 0.00 0.00 40.48 4.61
3365 3475 5.240623 TGGTTTTTACATCATCGTCAGCTTT 59.759 36.000 0.00 0.00 0.00 3.51
3398 3511 1.260033 CGTACGTACGTCCTGATCCTC 59.740 57.143 33.95 4.61 44.13 3.71
3423 3536 4.627467 CCTCTTGATGACCTTCTTTACGTG 59.373 45.833 0.00 0.00 0.00 4.49
3424 3537 4.283722 ACCTCTTGATGACCTTCTTTACGT 59.716 41.667 0.00 0.00 0.00 3.57
3425 3538 4.822026 ACCTCTTGATGACCTTCTTTACG 58.178 43.478 0.00 0.00 0.00 3.18
3426 3539 4.865365 CGACCTCTTGATGACCTTCTTTAC 59.135 45.833 0.00 0.00 0.00 2.01
3444 3557 3.181454 ACACACCTTCTTCAATTCGACCT 60.181 43.478 0.00 0.00 0.00 3.85
3445 3558 3.058914 CACACACCTTCTTCAATTCGACC 60.059 47.826 0.00 0.00 0.00 4.79
3659 3782 3.312890 AGAGAGAGAGAGAGGGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
3660 3783 3.051803 AGAGAGAGAGAGAGAGGGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
3661 3784 3.312890 AGAGAGAGAGAGAGAGGGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
3662 3785 3.051803 AGAGAGAGAGAGAGAGAGGGAGA 60.052 52.174 0.00 0.00 0.00 3.71
3663 3786 3.312890 AGAGAGAGAGAGAGAGAGGGAG 58.687 54.545 0.00 0.00 0.00 4.30
3664 3787 3.051803 AGAGAGAGAGAGAGAGAGAGGGA 60.052 52.174 0.00 0.00 0.00 4.20
3665 3788 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
3666 3789 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
3814 3960 3.196469 CACCAAGCTATGAGAGTCAAGGA 59.804 47.826 0.00 0.00 0.00 3.36
3839 3985 3.251484 CCATGATGGAGTAGGGTGGTAT 58.749 50.000 5.27 0.00 40.96 2.73
3845 3991 1.141657 CACACCCATGATGGAGTAGGG 59.858 57.143 14.26 0.00 40.96 3.53
3860 4010 3.140325 TGGAGAAGAAATGGACACACC 57.860 47.619 0.00 0.00 39.54 4.16
3899 4049 4.039601 CATCGAAGCTAGCGCGCG 62.040 66.667 28.44 28.44 42.32 6.86
3901 4051 0.936764 ATCACATCGAAGCTAGCGCG 60.937 55.000 21.81 21.81 42.32 6.86
3903 4053 1.520174 CACATCACATCGAAGCTAGCG 59.480 52.381 9.55 2.74 0.00 4.26
3904 4054 2.537625 GACACATCACATCGAAGCTAGC 59.462 50.000 6.62 6.62 0.00 3.42
3905 4055 3.795639 CAGACACATCACATCGAAGCTAG 59.204 47.826 0.00 0.00 0.00 3.42
3950 4100 1.070445 GAGAGACCGGGAGAGATCGTA 59.930 57.143 6.32 0.00 0.00 3.43
3959 4109 1.006043 AGTGAATGAGAGAGACCGGGA 59.994 52.381 6.32 0.00 0.00 5.14
3991 4141 2.073117 TTGCATTGCAGCATCAACAG 57.927 45.000 11.76 0.00 45.19 3.16
3992 4142 2.342179 CATTGCATTGCAGCATCAACA 58.658 42.857 11.76 0.00 45.19 3.33
4069 4230 4.531659 AAGTTTAATCCGCGTATGCTTC 57.468 40.909 4.92 0.00 39.65 3.86
4078 4239 4.392216 GTTCTCGACAAAGTTTAATCCGC 58.608 43.478 0.00 0.00 0.00 5.54
4080 4241 5.587033 ACGTTCTCGACAAAGTTTAATCC 57.413 39.130 0.00 0.00 40.62 3.01
4105 4266 6.656693 AGAAGAAAAATCCACGAGACATGAAT 59.343 34.615 0.00 0.00 0.00 2.57
4108 4269 5.409520 TGAGAAGAAAAATCCACGAGACATG 59.590 40.000 0.00 0.00 0.00 3.21
4109 4270 5.551233 TGAGAAGAAAAATCCACGAGACAT 58.449 37.500 0.00 0.00 0.00 3.06
4200 4362 3.055530 TGGCCAAACAAACACAGTGAAAT 60.056 39.130 0.61 0.00 0.00 2.17
4207 4369 3.834489 ATTCATGGCCAAACAAACACA 57.166 38.095 10.96 0.00 0.00 3.72
4315 4639 0.939577 CCTAATCCACCGATCGCGTG 60.940 60.000 22.24 22.24 35.23 5.34
4318 4642 3.196613 GACCTAATCCACCGATCGC 57.803 57.895 10.32 0.00 0.00 4.58
4346 4671 5.863935 GCATCCCAAAATCTTGTGTAAACTC 59.136 40.000 0.00 0.00 0.00 3.01
4348 4673 5.634859 CAGCATCCCAAAATCTTGTGTAAAC 59.365 40.000 0.00 0.00 0.00 2.01
4349 4674 5.782047 CAGCATCCCAAAATCTTGTGTAAA 58.218 37.500 0.00 0.00 0.00 2.01
4350 4675 4.321899 GCAGCATCCCAAAATCTTGTGTAA 60.322 41.667 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.