Multiple sequence alignment - TraesCS5A01G451500

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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 TraesCS5A01G451500 chr5A 100.000 3092 0 0 1 3092 633048859 633051950 0.000000e+00 5710
1 TraesCS5A01G451500 chr5A 87.520 1899 166 39 708 2572 633109445 633111306 0.000000e+00 2128
2 TraesCS5A01G451500 chr5A 78.701 1493 248 46 1028 2478 633754613 633753149 0.000000e+00 931
3 TraesCS5A01G451500 chr5D 91.457 2189 104 35 431 2572 505738484 505740636 0.000000e+00 2929
4 TraesCS5A01G451500 chr5D 81.619 1458 221 34 1040 2477 505779701 505781131 0.000000e+00 1164
5 TraesCS5A01G451500 chr5D 78.890 1838 281 55 788 2572 505935818 505934035 0.000000e+00 1146
6 TraesCS5A01G451500 chr5D 86.533 349 24 9 2733 3058 505740619 505740967 2.270000e-96 363
7 TraesCS5A01G451500 chr5D 91.589 214 18 0 226 439 505737904 505738117 2.330000e-76 296
8 TraesCS5A01G451500 chr5D 87.440 207 11 6 37 228 505668919 505669125 1.120000e-54 224
9 TraesCS5A01G451500 chr5D 86.719 128 16 1 2816 2942 505933488 505933361 1.160000e-29 141
10 TraesCS5A01G451500 chr5B 90.709 2045 110 22 465 2448 635767322 635769347 0.000000e+00 2651
11 TraesCS5A01G451500 chr5B 78.921 1798 269 61 824 2572 636349329 636347593 0.000000e+00 1120
12 TraesCS5A01G451500 chr5B 82.938 1137 169 22 989 2113 635776812 635777935 0.000000e+00 1002
13 TraesCS5A01G451500 chr5B 81.052 1293 195 32 1007 2276 636541519 636540254 0.000000e+00 985
14 TraesCS5A01G451500 chr5B 87.042 355 30 5 110 463 635764583 635764922 1.340000e-103 387
15 TraesCS5A01G451500 chr5B 96.648 179 3 3 2558 2735 44640992 44641168 8.390000e-76 294
16 TraesCS5A01G451500 chr5B 87.931 174 7 7 2891 3051 635769350 635769522 3.150000e-45 193
17 TraesCS5A01G451500 chr5B 90.741 108 10 0 3 110 635763442 635763549 8.940000e-31 145
18 TraesCS5A01G451500 chr2A 99.401 167 1 0 2568 2734 469121618 469121784 1.390000e-78 303
19 TraesCS5A01G451500 chr2A 99.398 166 1 0 2568 2733 538368985 538369150 5.010000e-78 302
20 TraesCS5A01G451500 chr1B 98.824 170 2 0 2564 2733 625778102 625778271 1.390000e-78 303
21 TraesCS5A01G451500 chr1B 99.394 165 1 0 2569 2733 550674791 550674955 1.800000e-77 300
22 TraesCS5A01G451500 chr3B 98.817 169 2 0 2566 2734 805827102 805827270 5.010000e-78 302
23 TraesCS5A01G451500 chr3A 99.398 166 1 0 2568 2733 438369603 438369438 5.010000e-78 302
24 TraesCS5A01G451500 chr6A 98.246 171 2 1 2564 2734 3336296 3336465 6.480000e-77 298
25 TraesCS5A01G451500 chr6A 97.688 173 2 1 2570 2742 127190140 127189970 2.330000e-76 296


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 TraesCS5A01G451500 chr5A 633048859 633051950 3091 False 5710.0 5710 100.000000 1 3092 1 chr5A.!!$F1 3091
1 TraesCS5A01G451500 chr5A 633109445 633111306 1861 False 2128.0 2128 87.520000 708 2572 1 chr5A.!!$F2 1864
2 TraesCS5A01G451500 chr5A 633753149 633754613 1464 True 931.0 931 78.701000 1028 2478 1 chr5A.!!$R1 1450
3 TraesCS5A01G451500 chr5D 505737904 505740967 3063 False 1196.0 2929 89.859667 226 3058 3 chr5D.!!$F3 2832
4 TraesCS5A01G451500 chr5D 505779701 505781131 1430 False 1164.0 1164 81.619000 1040 2477 1 chr5D.!!$F2 1437
5 TraesCS5A01G451500 chr5D 505933361 505935818 2457 True 643.5 1146 82.804500 788 2942 2 chr5D.!!$R1 2154
6 TraesCS5A01G451500 chr5B 636347593 636349329 1736 True 1120.0 1120 78.921000 824 2572 1 chr5B.!!$R1 1748
7 TraesCS5A01G451500 chr5B 635776812 635777935 1123 False 1002.0 1002 82.938000 989 2113 1 chr5B.!!$F2 1124
8 TraesCS5A01G451500 chr5B 636540254 636541519 1265 True 985.0 985 81.052000 1007 2276 1 chr5B.!!$R2 1269
9 TraesCS5A01G451500 chr5B 635763442 635769522 6080 False 844.0 2651 89.105750 3 3051 4 chr5B.!!$F3 3048

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
428 1464 0.036105 AGATGAATGTCACAGCGCCA 60.036 50.0 2.29 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2276 6198 0.040958 GGTTGCAGACAAGCGTTCTG 60.041 55.0 7.64 7.64 43.71 3.02 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
27 28 0.460987 CATGAGCCGTCCTCTTCCAC 60.461 60.000 0.00 0.00 41.35 4.02
46 47 3.082579 ATCCACCTTCTCGCTCGCC 62.083 63.158 0.00 0.00 0.00 5.54
66 67 2.351276 GGTCGCCATGGTCCACTT 59.649 61.111 14.67 0.00 0.00 3.16
73 74 2.019984 GCCATGGTCCACTTCAAGATC 58.980 52.381 14.67 0.00 0.00 2.75
102 103 6.037062 TGGTATAAGATGCTGACGTCAAAATG 59.963 38.462 20.49 8.96 33.96 2.32
128 1163 2.106332 GGACACCGTATCGCCAGG 59.894 66.667 0.00 0.00 0.00 4.45
131 1166 2.586079 CACCGTATCGCCAGGCAG 60.586 66.667 13.30 4.47 0.00 4.85
135 1170 1.889105 CGTATCGCCAGGCAGCATT 60.889 57.895 13.30 0.00 0.00 3.56
149 1184 2.993471 GCATTGAGGTGGGCCAACG 61.993 63.158 17.48 1.91 37.19 4.10
156 1191 1.826487 GGTGGGCCAACGTTCAAGT 60.826 57.895 8.40 0.00 34.09 3.16
164 1199 0.234884 CAACGTTCAAGTTCTCCCGC 59.765 55.000 0.00 0.00 30.96 6.13
169 1204 4.735132 CAAGTTCTCCCGCGCCGA 62.735 66.667 0.00 0.00 0.00 5.54
184 1219 2.904866 CGAGCTCGGAGGAGGAGG 60.905 72.222 28.40 0.00 40.80 4.30
185 1220 2.277404 GAGCTCGGAGGAGGAGGT 59.723 66.667 7.20 0.00 44.31 3.85
186 1221 2.043450 AGCTCGGAGGAGGAGGTG 60.043 66.667 7.20 0.00 40.47 4.00
187 1222 2.043852 GCTCGGAGGAGGAGGTGA 60.044 66.667 7.20 0.00 40.80 4.02
188 1223 1.682684 GCTCGGAGGAGGAGGTGAA 60.683 63.158 7.20 0.00 40.80 3.18
189 1224 1.671901 GCTCGGAGGAGGAGGTGAAG 61.672 65.000 7.20 0.00 40.80 3.02
202 1237 3.393970 TGAAGGAGGAGGGCAGCG 61.394 66.667 0.00 0.00 0.00 5.18
236 1271 1.231641 CGGAGGTCCAGGAGGAGAT 59.768 63.158 0.00 0.00 46.92 2.75
271 1306 1.758514 GAGTCGCCCATGGAGGAGA 60.759 63.158 15.22 1.19 41.22 3.71
336 1372 2.476320 GCGGGCTCTTCTCCATTGC 61.476 63.158 0.00 0.00 0.00 3.56
410 1446 0.677731 TGCAAATGGAGGCGGAGAAG 60.678 55.000 0.00 0.00 0.00 2.85
422 1458 2.621338 GCGGAGAAGATGAATGTCACA 58.379 47.619 0.00 0.00 0.00 3.58
428 1464 0.036105 AGATGAATGTCACAGCGCCA 60.036 50.000 2.29 0.00 0.00 5.69
465 4273 3.088194 TCGTCAACAAGAACTAAGCGT 57.912 42.857 0.00 0.00 0.00 5.07
466 4274 2.792674 TCGTCAACAAGAACTAAGCGTG 59.207 45.455 0.00 0.00 0.00 5.34
666 4475 4.193090 CGTGTAGGTCTCAGAGTAGTCAT 58.807 47.826 0.00 0.00 0.00 3.06
749 4566 3.035503 CGCCAAAAACGCAAGGGC 61.036 61.111 0.00 0.00 46.39 5.19
778 4595 2.881352 GCTTTCTCTCCGTCCGCG 60.881 66.667 0.00 0.00 37.95 6.46
779 4596 2.875485 CTTTCTCTCCGTCCGCGA 59.125 61.111 8.23 0.00 41.33 5.87
812 4640 2.746277 GCCATCACCGGTCACCAC 60.746 66.667 2.59 0.00 0.00 4.16
1219 5074 7.974675 TCGAGATTACATCACAATTTTTCTCC 58.025 34.615 0.00 0.00 0.00 3.71
1263 5118 1.987855 CCGGGCCTCTTGTGACCTA 60.988 63.158 0.84 0.00 0.00 3.08
1491 5355 2.033448 ACCGAAGCCAAATCGCCA 59.967 55.556 0.00 0.00 38.93 5.69
1500 5364 1.205893 GCCAAATCGCCACCCAAAATA 59.794 47.619 0.00 0.00 0.00 1.40
1797 5665 7.462590 TCGAGGGAGAAGAGAATATTGAGATA 58.537 38.462 0.00 0.00 0.00 1.98
1806 5674 7.962995 AGAGAATATTGAGATAATCCGGCTA 57.037 36.000 0.00 0.00 0.00 3.93
2029 5903 4.281688 CCCAAGGCTTCAAAGATCTCAAAA 59.718 41.667 0.00 0.00 0.00 2.44
2055 5929 2.981921 TGCCCATCTCTCATAGTGGAT 58.018 47.619 0.00 0.00 31.61 3.41
2067 5941 3.713248 TCATAGTGGATGCACTGGAGAAT 59.287 43.478 28.10 11.58 36.68 2.40
2251 6164 7.690454 TGTTCTCCTAAATCATCCCAGAATA 57.310 36.000 0.00 0.00 0.00 1.75
2286 6208 5.095490 GGTTCATTTTATCCAGAACGCTTG 58.905 41.667 0.00 0.00 40.83 4.01
2441 6400 6.148150 ACAAGATTAAACATGCCAAAATGCTG 59.852 34.615 0.00 0.00 0.00 4.41
2557 6526 2.543641 GCAAACAGGGCAATGATTAGC 58.456 47.619 0.00 0.00 0.00 3.09
2572 6541 8.019669 GCAATGATTAGCATTACTACATTGAGG 58.980 37.037 17.17 0.00 45.23 3.86
2573 6542 9.276590 CAATGATTAGCATTACTACATTGAGGA 57.723 33.333 0.00 0.00 45.23 3.71
2574 6543 8.839310 ATGATTAGCATTACTACATTGAGGAC 57.161 34.615 0.00 0.00 31.73 3.85
2575 6544 6.923508 TGATTAGCATTACTACATTGAGGACG 59.076 38.462 0.00 0.00 0.00 4.79
2576 6545 4.737855 AGCATTACTACATTGAGGACGT 57.262 40.909 0.00 0.00 0.00 4.34
2577 6546 4.433615 AGCATTACTACATTGAGGACGTG 58.566 43.478 0.00 0.00 0.00 4.49
2578 6547 3.555956 GCATTACTACATTGAGGACGTGG 59.444 47.826 0.00 0.00 0.00 4.94
2579 6548 3.880047 TTACTACATTGAGGACGTGGG 57.120 47.619 0.00 0.00 0.00 4.61
2580 6549 0.249398 ACTACATTGAGGACGTGGGC 59.751 55.000 0.00 0.00 0.00 5.36
2581 6550 0.249120 CTACATTGAGGACGTGGGCA 59.751 55.000 0.00 0.00 0.00 5.36
2582 6551 0.908910 TACATTGAGGACGTGGGCAT 59.091 50.000 0.00 0.00 0.00 4.40
2583 6552 0.908910 ACATTGAGGACGTGGGCATA 59.091 50.000 0.00 0.00 0.00 3.14
2584 6553 1.134401 ACATTGAGGACGTGGGCATAG 60.134 52.381 0.00 0.00 0.00 2.23
2585 6554 0.179045 ATTGAGGACGTGGGCATAGC 60.179 55.000 0.00 0.00 0.00 2.97
2595 6564 3.924507 GGCATAGCCCAGTGGTTG 58.075 61.111 8.74 1.51 44.06 3.77
2596 6565 1.754234 GGCATAGCCCAGTGGTTGG 60.754 63.158 8.74 0.00 44.06 3.77
2607 6576 4.059304 TGGTTGGGGGCGCATGAT 62.059 61.111 10.83 0.00 0.00 2.45
2608 6577 2.759560 GGTTGGGGGCGCATGATT 60.760 61.111 10.83 0.00 0.00 2.57
2609 6578 2.495866 GTTGGGGGCGCATGATTG 59.504 61.111 10.83 0.00 0.00 2.67
2610 6579 2.037049 TTGGGGGCGCATGATTGT 59.963 55.556 10.83 0.00 0.00 2.71
2611 6580 1.034838 GTTGGGGGCGCATGATTGTA 61.035 55.000 10.83 0.00 0.00 2.41
2612 6581 0.323816 TTGGGGGCGCATGATTGTAA 60.324 50.000 10.83 0.00 0.00 2.41
2613 6582 0.323816 TGGGGGCGCATGATTGTAAA 60.324 50.000 10.83 0.00 0.00 2.01
2614 6583 0.102300 GGGGGCGCATGATTGTAAAC 59.898 55.000 10.83 0.00 0.00 2.01
2615 6584 0.102300 GGGGCGCATGATTGTAAACC 59.898 55.000 10.83 0.00 0.00 3.27
2616 6585 1.102978 GGGCGCATGATTGTAAACCT 58.897 50.000 10.83 0.00 0.00 3.50
2617 6586 2.294074 GGGCGCATGATTGTAAACCTA 58.706 47.619 10.83 0.00 0.00 3.08
2618 6587 2.685897 GGGCGCATGATTGTAAACCTAA 59.314 45.455 10.83 0.00 0.00 2.69
2619 6588 3.488553 GGGCGCATGATTGTAAACCTAAC 60.489 47.826 10.83 0.00 0.00 2.34
2620 6589 3.350912 GCGCATGATTGTAAACCTAACG 58.649 45.455 0.30 0.00 0.00 3.18
2621 6590 3.062909 GCGCATGATTGTAAACCTAACGA 59.937 43.478 0.30 0.00 0.00 3.85
2622 6591 4.574759 CGCATGATTGTAAACCTAACGAC 58.425 43.478 0.00 0.00 0.00 4.34
2623 6592 4.493545 CGCATGATTGTAAACCTAACGACC 60.494 45.833 0.00 0.00 0.00 4.79
2624 6593 4.393680 GCATGATTGTAAACCTAACGACCA 59.606 41.667 0.00 0.00 0.00 4.02
2625 6594 5.447279 GCATGATTGTAAACCTAACGACCAG 60.447 44.000 0.00 0.00 0.00 4.00
2626 6595 5.471556 TGATTGTAAACCTAACGACCAGA 57.528 39.130 0.00 0.00 0.00 3.86
2627 6596 5.475719 TGATTGTAAACCTAACGACCAGAG 58.524 41.667 0.00 0.00 0.00 3.35
2628 6597 4.942761 TTGTAAACCTAACGACCAGAGT 57.057 40.909 0.00 0.00 0.00 3.24
2629 6598 4.942761 TGTAAACCTAACGACCAGAGTT 57.057 40.909 0.00 0.00 35.75 3.01
2630 6599 4.874970 TGTAAACCTAACGACCAGAGTTC 58.125 43.478 0.00 0.00 33.42 3.01
2631 6600 2.719426 AACCTAACGACCAGAGTTCG 57.281 50.000 0.00 0.00 33.42 3.95
2632 6601 1.901591 ACCTAACGACCAGAGTTCGA 58.098 50.000 0.00 0.00 33.42 3.71
2633 6602 2.444421 ACCTAACGACCAGAGTTCGAT 58.556 47.619 0.00 0.00 33.42 3.59
2634 6603 2.824341 ACCTAACGACCAGAGTTCGATT 59.176 45.455 0.00 0.00 33.42 3.34
2635 6604 3.119566 ACCTAACGACCAGAGTTCGATTC 60.120 47.826 0.00 0.00 33.42 2.52
2636 6605 3.119602 CCTAACGACCAGAGTTCGATTCA 60.120 47.826 0.00 0.00 33.42 2.57
2637 6606 2.349297 ACGACCAGAGTTCGATTCAC 57.651 50.000 0.00 0.00 0.00 3.18
2638 6607 1.260206 CGACCAGAGTTCGATTCACG 58.740 55.000 0.00 0.00 44.09 4.35
2639 6608 1.401148 CGACCAGAGTTCGATTCACGT 60.401 52.381 0.00 0.00 43.13 4.49
2640 6609 2.251893 GACCAGAGTTCGATTCACGTC 58.748 52.381 0.00 0.00 43.13 4.34
2641 6610 1.260206 CCAGAGTTCGATTCACGTCG 58.740 55.000 0.00 0.00 43.13 5.12
2642 6611 1.260206 CAGAGTTCGATTCACGTCGG 58.740 55.000 0.00 0.00 41.74 4.79
2643 6612 0.170561 AGAGTTCGATTCACGTCGGG 59.829 55.000 0.00 0.00 41.74 5.14
2644 6613 0.801067 GAGTTCGATTCACGTCGGGG 60.801 60.000 0.00 0.00 41.74 5.73
2645 6614 1.213537 GTTCGATTCACGTCGGGGA 59.786 57.895 0.00 0.00 41.74 4.81
2646 6615 1.074872 GTTCGATTCACGTCGGGGAC 61.075 60.000 0.00 0.00 41.74 4.46
2670 6639 6.388435 GAATTTCTGGAATTCTCATGAGGG 57.612 41.667 22.42 0.00 46.59 4.30
2671 6640 5.722172 ATTTCTGGAATTCTCATGAGGGA 57.278 39.130 22.42 12.00 0.00 4.20
2672 6641 5.722172 TTTCTGGAATTCTCATGAGGGAT 57.278 39.130 22.42 13.69 0.00 3.85
2673 6642 4.701651 TCTGGAATTCTCATGAGGGATG 57.298 45.455 22.42 7.14 0.00 3.51
2674 6643 3.147629 CTGGAATTCTCATGAGGGATGC 58.852 50.000 22.42 14.53 31.32 3.91
2675 6644 2.781757 TGGAATTCTCATGAGGGATGCT 59.218 45.455 22.42 3.80 31.32 3.79
2676 6645 3.203710 TGGAATTCTCATGAGGGATGCTT 59.796 43.478 22.42 7.33 31.32 3.91
2677 6646 3.819902 GGAATTCTCATGAGGGATGCTTC 59.180 47.826 22.42 14.34 31.32 3.86
2678 6647 4.446023 GGAATTCTCATGAGGGATGCTTCT 60.446 45.833 22.42 2.49 31.32 2.85
2679 6648 4.792513 ATTCTCATGAGGGATGCTTCTT 57.207 40.909 22.42 0.00 31.32 2.52
2680 6649 3.834489 TCTCATGAGGGATGCTTCTTC 57.166 47.619 22.42 0.00 31.32 2.87
2681 6650 3.382278 TCTCATGAGGGATGCTTCTTCT 58.618 45.455 22.42 0.00 31.32 2.85
2682 6651 4.550669 TCTCATGAGGGATGCTTCTTCTA 58.449 43.478 22.42 0.00 31.32 2.10
2683 6652 5.153675 TCTCATGAGGGATGCTTCTTCTAT 58.846 41.667 22.42 0.00 31.32 1.98
2684 6653 6.318112 TCTCATGAGGGATGCTTCTTCTATA 58.682 40.000 22.42 0.00 31.32 1.31
2685 6654 6.958778 TCTCATGAGGGATGCTTCTTCTATAT 59.041 38.462 22.42 0.00 31.32 0.86
2686 6655 7.123997 TCTCATGAGGGATGCTTCTTCTATATC 59.876 40.741 22.42 0.00 31.32 1.63
2687 6656 6.727697 TCATGAGGGATGCTTCTTCTATATCA 59.272 38.462 0.00 0.00 31.32 2.15
2688 6657 7.236225 TCATGAGGGATGCTTCTTCTATATCAA 59.764 37.037 0.00 0.00 31.32 2.57
2689 6658 7.565190 TGAGGGATGCTTCTTCTATATCAAT 57.435 36.000 0.00 0.00 0.00 2.57
2690 6659 8.670521 TGAGGGATGCTTCTTCTATATCAATA 57.329 34.615 0.00 0.00 0.00 1.90
2691 6660 9.104713 TGAGGGATGCTTCTTCTATATCAATAA 57.895 33.333 0.00 0.00 0.00 1.40
2692 6661 9.950496 GAGGGATGCTTCTTCTATATCAATAAA 57.050 33.333 0.00 0.00 0.00 1.40
2697 6666 8.958119 TGCTTCTTCTATATCAATAAAACCGT 57.042 30.769 0.00 0.00 0.00 4.83
2698 6667 8.826710 TGCTTCTTCTATATCAATAAAACCGTG 58.173 33.333 0.00 0.00 0.00 4.94
2699 6668 8.283291 GCTTCTTCTATATCAATAAAACCGTGG 58.717 37.037 0.00 0.00 0.00 4.94
2700 6669 8.671384 TTCTTCTATATCAATAAAACCGTGGG 57.329 34.615 0.00 0.00 0.00 4.61
2701 6670 7.798071 TCTTCTATATCAATAAAACCGTGGGT 58.202 34.615 0.00 0.00 37.65 4.51
2702 6671 7.713507 TCTTCTATATCAATAAAACCGTGGGTG 59.286 37.037 0.00 0.00 35.34 4.61
2703 6672 4.911514 ATATCAATAAAACCGTGGGTGC 57.088 40.909 0.00 0.00 35.34 5.01
2704 6673 2.279935 TCAATAAAACCGTGGGTGCT 57.720 45.000 0.00 0.00 35.34 4.40
2705 6674 3.420300 TCAATAAAACCGTGGGTGCTA 57.580 42.857 0.00 0.00 35.34 3.49
2706 6675 3.340034 TCAATAAAACCGTGGGTGCTAG 58.660 45.455 0.00 0.00 35.34 3.42
2707 6676 3.078837 CAATAAAACCGTGGGTGCTAGT 58.921 45.455 0.00 0.00 35.34 2.57
2708 6677 2.172851 TAAAACCGTGGGTGCTAGTG 57.827 50.000 0.00 0.00 35.34 2.74
2709 6678 1.170290 AAAACCGTGGGTGCTAGTGC 61.170 55.000 0.00 0.00 35.34 4.40
2710 6679 3.546714 AACCGTGGGTGCTAGTGCC 62.547 63.158 0.00 0.00 35.34 5.01
2711 6680 4.778143 CCGTGGGTGCTAGTGCCC 62.778 72.222 14.48 14.48 45.04 5.36
2715 6684 2.124151 GGGTGCTAGTGCCCATGG 60.124 66.667 15.91 4.14 44.23 3.66
2716 6685 2.679342 GGGTGCTAGTGCCCATGGA 61.679 63.158 15.22 0.00 44.23 3.41
2717 6686 1.153086 GGTGCTAGTGCCCATGGAG 60.153 63.158 15.22 2.70 38.71 3.86
2718 6687 1.604378 GTGCTAGTGCCCATGGAGT 59.396 57.895 15.22 0.00 38.71 3.85
2719 6688 0.035056 GTGCTAGTGCCCATGGAGTT 60.035 55.000 15.22 0.00 38.71 3.01
2720 6689 0.698238 TGCTAGTGCCCATGGAGTTT 59.302 50.000 15.22 0.00 38.71 2.66
2721 6690 1.340017 TGCTAGTGCCCATGGAGTTTC 60.340 52.381 15.22 0.00 38.71 2.78
2722 6691 1.340017 GCTAGTGCCCATGGAGTTTCA 60.340 52.381 15.22 0.00 0.00 2.69
2723 6692 2.684927 GCTAGTGCCCATGGAGTTTCAT 60.685 50.000 15.22 0.00 0.00 2.57
2724 6693 2.610438 AGTGCCCATGGAGTTTCATT 57.390 45.000 15.22 0.00 0.00 2.57
2725 6694 2.893424 AGTGCCCATGGAGTTTCATTT 58.107 42.857 15.22 0.00 0.00 2.32
2726 6695 3.242011 AGTGCCCATGGAGTTTCATTTT 58.758 40.909 15.22 0.00 0.00 1.82
2727 6696 3.647590 AGTGCCCATGGAGTTTCATTTTT 59.352 39.130 15.22 0.00 0.00 1.94
2791 6764 1.610624 CCGGTACTGCCTCATGTGTTT 60.611 52.381 0.00 0.00 34.25 2.83
2806 6779 2.817258 TGTGTTTCCTCGGCCAAATTAG 59.183 45.455 2.24 0.00 0.00 1.73
2812 6785 4.764050 TCCTCGGCCAAATTAGTGAATA 57.236 40.909 2.24 0.00 0.00 1.75
2821 7277 6.208204 GGCCAAATTAGTGAATATCATCTGCT 59.792 38.462 0.00 0.00 0.00 4.24
2871 7327 1.077429 GCCCCCAGTCCATGTTCTC 60.077 63.158 0.00 0.00 0.00 2.87
2886 7342 4.695217 TGTTCTCGTTGCTTCTTTGTTT 57.305 36.364 0.00 0.00 0.00 2.83
2901 7357 3.658757 TTGTTTGGCATTAAGGCTGTC 57.341 42.857 12.41 0.00 44.55 3.51
2986 7450 5.749109 CAGTCTATAGGCGTTTCTTTACCTG 59.251 44.000 0.00 0.00 33.60 4.00
3013 7477 1.494721 TCTGGGTGTTTCTTGCCTTCT 59.505 47.619 0.00 0.00 0.00 2.85
3022 7486 4.826733 TGTTTCTTGCCTTCTAAATCTGCA 59.173 37.500 0.00 0.00 0.00 4.41
3027 7491 4.789012 TGCCTTCTAAATCTGCAAAAGG 57.211 40.909 0.00 0.00 37.04 3.11
3051 7520 3.634910 TGTTAGACTAGTGTCAGTGTGCA 59.365 43.478 0.00 0.00 45.20 4.57
3054 7523 0.597637 ACTAGTGTCAGTGTGCACGC 60.598 55.000 22.76 22.76 40.26 5.34
3058 7527 3.261951 GTCAGTGTGCACGCGTGT 61.262 61.111 36.80 17.11 36.20 4.49
3059 7528 2.959599 TCAGTGTGCACGCGTGTC 60.960 61.111 36.80 28.50 36.20 3.67
3060 7529 2.961721 CAGTGTGCACGCGTGTCT 60.962 61.111 36.80 25.75 36.20 3.41
3061 7530 2.658593 AGTGTGCACGCGTGTCTC 60.659 61.111 36.80 27.56 36.20 3.36
3062 7531 3.702555 GTGTGCACGCGTGTCTCC 61.703 66.667 36.80 22.29 0.00 3.71
3063 7532 4.961511 TGTGCACGCGTGTCTCCC 62.962 66.667 36.80 21.93 0.00 4.30
3066 7535 3.755628 GCACGCGTGTCTCCCCTA 61.756 66.667 36.80 0.00 0.00 3.53
3067 7536 2.490217 CACGCGTGTCTCCCCTAG 59.510 66.667 30.50 0.71 0.00 3.02
3068 7537 2.044555 CACGCGTGTCTCCCCTAGA 61.045 63.158 30.50 0.00 0.00 2.43
3069 7538 1.076923 ACGCGTGTCTCCCCTAGAT 60.077 57.895 12.93 0.00 36.36 1.98
3070 7539 0.683504 ACGCGTGTCTCCCCTAGATT 60.684 55.000 12.93 0.00 36.36 2.40
3071 7540 0.249073 CGCGTGTCTCCCCTAGATTG 60.249 60.000 0.00 0.00 36.36 2.67
3072 7541 0.105039 GCGTGTCTCCCCTAGATTGG 59.895 60.000 0.00 0.00 36.36 3.16
3073 7542 1.486211 CGTGTCTCCCCTAGATTGGT 58.514 55.000 0.00 0.00 36.36 3.67
3074 7543 2.662866 CGTGTCTCCCCTAGATTGGTA 58.337 52.381 0.00 0.00 36.36 3.25
3075 7544 3.028850 CGTGTCTCCCCTAGATTGGTAA 58.971 50.000 0.00 0.00 36.36 2.85
3076 7545 3.641906 CGTGTCTCCCCTAGATTGGTAAT 59.358 47.826 0.00 0.00 36.36 1.89
3077 7546 4.101119 CGTGTCTCCCCTAGATTGGTAATT 59.899 45.833 0.00 0.00 36.36 1.40
3078 7547 5.396436 CGTGTCTCCCCTAGATTGGTAATTT 60.396 44.000 0.00 0.00 36.36 1.82
3079 7548 6.056236 GTGTCTCCCCTAGATTGGTAATTTC 58.944 44.000 0.00 0.00 36.36 2.17
3080 7549 5.970640 TGTCTCCCCTAGATTGGTAATTTCT 59.029 40.000 0.00 0.00 36.36 2.52
3081 7550 6.447084 TGTCTCCCCTAGATTGGTAATTTCTT 59.553 38.462 0.00 0.00 36.36 2.52
3082 7551 7.036863 TGTCTCCCCTAGATTGGTAATTTCTTT 60.037 37.037 0.00 0.00 36.36 2.52
3083 7552 7.834681 GTCTCCCCTAGATTGGTAATTTCTTTT 59.165 37.037 0.00 0.00 36.36 2.27
3084 7553 7.834181 TCTCCCCTAGATTGGTAATTTCTTTTG 59.166 37.037 0.00 0.00 0.00 2.44
3085 7554 7.475299 TCCCCTAGATTGGTAATTTCTTTTGT 58.525 34.615 0.00 0.00 0.00 2.83
3086 7555 7.953493 TCCCCTAGATTGGTAATTTCTTTTGTT 59.047 33.333 0.00 0.00 0.00 2.83
3087 7556 8.034804 CCCCTAGATTGGTAATTTCTTTTGTTG 58.965 37.037 0.00 0.00 0.00 3.33
3088 7557 7.545615 CCCTAGATTGGTAATTTCTTTTGTTGC 59.454 37.037 0.00 0.00 0.00 4.17
3089 7558 7.545615 CCTAGATTGGTAATTTCTTTTGTTGCC 59.454 37.037 0.00 0.00 0.00 4.52
3090 7559 5.925969 AGATTGGTAATTTCTTTTGTTGCCG 59.074 36.000 0.00 0.00 31.26 5.69
3091 7560 3.385577 TGGTAATTTCTTTTGTTGCCGC 58.614 40.909 0.00 0.00 31.26 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.904865 ATGTGGAAGAGGACGGCTCA 60.905 55.000 0.00 0.00 0.00 4.26
16 17 1.280457 AGGTGGATGTGGAAGAGGAC 58.720 55.000 0.00 0.00 0.00 3.85
27 28 1.880340 GCGAGCGAGAAGGTGGATG 60.880 63.158 0.00 0.00 0.00 3.51
49 50 1.745489 GAAGTGGACCATGGCGACC 60.745 63.158 13.04 13.66 0.00 4.79
53 54 2.019984 GATCTTGAAGTGGACCATGGC 58.980 52.381 13.04 4.47 0.00 4.40
73 74 4.433615 ACGTCAGCATCTTATACCAAGTG 58.566 43.478 0.00 0.00 0.00 3.16
125 1160 2.050350 CCCACCTCAATGCTGCCTG 61.050 63.158 0.00 0.00 0.00 4.85
126 1161 2.357836 CCCACCTCAATGCTGCCT 59.642 61.111 0.00 0.00 0.00 4.75
128 1163 3.455469 GGCCCACCTCAATGCTGC 61.455 66.667 0.00 0.00 0.00 5.25
131 1166 2.973082 GTTGGCCCACCTCAATGC 59.027 61.111 0.00 0.00 36.63 3.56
135 1170 2.112297 GAACGTTGGCCCACCTCA 59.888 61.111 5.00 0.00 36.63 3.86
141 1176 0.591659 GAGAACTTGAACGTTGGCCC 59.408 55.000 5.00 0.00 0.00 5.80
149 1184 2.677979 GGCGCGGGAGAACTTGAAC 61.678 63.158 8.83 0.00 0.00 3.18
169 1204 2.043450 CACCTCCTCCTCCGAGCT 60.043 66.667 0.00 0.00 34.49 4.09
171 1206 1.040339 CCTTCACCTCCTCCTCCGAG 61.040 65.000 0.00 0.00 35.72 4.63
178 1213 0.689412 CCCTCCTCCTTCACCTCCTC 60.689 65.000 0.00 0.00 0.00 3.71
179 1214 1.394151 CCCTCCTCCTTCACCTCCT 59.606 63.158 0.00 0.00 0.00 3.69
180 1215 2.371259 GCCCTCCTCCTTCACCTCC 61.371 68.421 0.00 0.00 0.00 4.30
181 1216 1.613630 TGCCCTCCTCCTTCACCTC 60.614 63.158 0.00 0.00 0.00 3.85
182 1217 1.614824 CTGCCCTCCTCCTTCACCT 60.615 63.158 0.00 0.00 0.00 4.00
183 1218 2.993853 CTGCCCTCCTCCTTCACC 59.006 66.667 0.00 0.00 0.00 4.02
184 1219 2.270527 GCTGCCCTCCTCCTTCAC 59.729 66.667 0.00 0.00 0.00 3.18
185 1220 3.393970 CGCTGCCCTCCTCCTTCA 61.394 66.667 0.00 0.00 0.00 3.02
186 1221 3.077556 TCGCTGCCCTCCTCCTTC 61.078 66.667 0.00 0.00 0.00 3.46
187 1222 3.394836 GTCGCTGCCCTCCTCCTT 61.395 66.667 0.00 0.00 0.00 3.36
213 1248 2.764128 TCCTGGACCTCCGCCATC 60.764 66.667 0.00 0.00 39.43 3.51
271 1306 3.083997 GTGACCATCGCCTCCCCT 61.084 66.667 0.00 0.00 0.00 4.79
336 1372 0.035458 AACTTGTTCCTCTGCCTCCG 59.965 55.000 0.00 0.00 0.00 4.63
391 1427 0.677731 CTTCTCCGCCTCCATTTGCA 60.678 55.000 0.00 0.00 0.00 4.08
410 1446 0.097674 GTGGCGCTGTGACATTCATC 59.902 55.000 7.64 0.00 38.42 2.92
428 1464 1.654954 CGATCTTCGGGTCCGTGAGT 61.655 60.000 9.36 1.30 40.74 3.41
465 4273 1.354155 CTATGTACGGACGCGAGCA 59.646 57.895 15.93 2.11 0.00 4.26
466 4274 2.009755 GCTATGTACGGACGCGAGC 61.010 63.158 15.93 3.49 0.00 5.03
552 4361 0.614979 TCCTCCGGTTCCTCCAAGAG 60.615 60.000 0.00 0.00 36.54 2.85
553 4362 0.903454 GTCCTCCGGTTCCTCCAAGA 60.903 60.000 0.00 0.00 35.57 3.02
691 4500 3.461773 CTGGTCGCCCCTCACGAT 61.462 66.667 0.00 0.00 42.26 3.73
749 4566 1.355066 GAGAAAGCCGCCTCGACTTG 61.355 60.000 0.00 0.00 28.87 3.16
766 4583 2.638154 GGTATCGCGGACGGAGAG 59.362 66.667 6.13 0.00 40.63 3.20
812 4640 1.433534 GCGAACCTTCAGAACTCAGG 58.566 55.000 0.00 0.00 0.00 3.86
893 4731 7.502120 TCTGATGGTTTGAAAGAAGAAGAAG 57.498 36.000 0.00 0.00 0.00 2.85
894 4732 8.469309 AATCTGATGGTTTGAAAGAAGAAGAA 57.531 30.769 0.00 0.00 0.00 2.52
895 4733 9.224267 CTAATCTGATGGTTTGAAAGAAGAAGA 57.776 33.333 0.00 0.00 0.00 2.87
896 4734 7.967303 GCTAATCTGATGGTTTGAAAGAAGAAG 59.033 37.037 0.00 0.00 0.00 2.85
935 4783 3.633609 ATCGTCGGGACTCGGGACA 62.634 63.158 0.00 0.00 39.77 4.02
945 4793 2.541556 GGAGAAGAAAGAATCGTCGGG 58.458 52.381 0.00 0.00 40.93 5.14
946 4794 2.186076 CGGAGAAGAAAGAATCGTCGG 58.814 52.381 0.00 0.00 40.93 4.79
947 4795 2.186076 CCGGAGAAGAAAGAATCGTCG 58.814 52.381 0.00 0.00 40.93 5.12
1299 5154 2.009774 CTAGGCCCTGTTTTGATCACG 58.990 52.381 0.00 0.00 0.00 4.35
1491 5355 2.714250 TGGTGGTCTGTCTATTTTGGGT 59.286 45.455 0.00 0.00 0.00 4.51
1500 5364 2.015456 TGTCAGATGGTGGTCTGTCT 57.985 50.000 4.07 0.00 44.66 3.41
1797 5665 1.202770 GCCACCAGTAATAGCCGGATT 60.203 52.381 5.05 0.00 0.00 3.01
1806 5674 1.078426 GTCCGCAGCCACCAGTAAT 60.078 57.895 0.00 0.00 0.00 1.89
1883 5751 2.515057 TTGCCACGGTGTCCACAC 60.515 61.111 7.45 0.85 45.72 3.82
1947 5815 6.651755 ATTTTGATAAATTCAAGGCAAGCG 57.348 33.333 0.00 0.00 44.90 4.68
2029 5903 3.972638 ACTATGAGAGATGGGCAAGTCAT 59.027 43.478 0.00 0.00 0.00 3.06
2055 5929 4.019860 AGCTTTCTTCTATTCTCCAGTGCA 60.020 41.667 0.00 0.00 0.00 4.57
2150 6025 9.551734 TCATCCATCTAACATTGAGTAGAAATG 57.448 33.333 6.12 0.00 40.23 2.32
2157 6032 6.505048 TCCATCATCCATCTAACATTGAGT 57.495 37.500 0.00 0.00 0.00 3.41
2267 6186 5.327091 CAGACAAGCGTTCTGGATAAAATG 58.673 41.667 4.77 0.00 0.00 2.32
2276 6198 0.040958 GGTTGCAGACAAGCGTTCTG 60.041 55.000 7.64 7.64 43.71 3.02
2286 6208 1.578583 AGTGTTACACGGTTGCAGAC 58.421 50.000 10.00 0.00 39.64 3.51
2521 6490 4.917385 TGTTTGCCCACTCTTACATATGT 58.083 39.130 13.93 13.93 0.00 2.29
2557 6526 4.119862 CCCACGTCCTCAATGTAGTAATG 58.880 47.826 0.00 0.00 0.00 1.90
2579 6548 3.924507 CCAACCACTGGGCTATGC 58.075 61.111 0.00 0.00 42.17 3.14
2590 6559 3.598747 AATCATGCGCCCCCAACCA 62.599 57.895 4.18 0.00 0.00 3.67
2591 6560 2.759560 AATCATGCGCCCCCAACC 60.760 61.111 4.18 0.00 0.00 3.77
2592 6561 1.034838 TACAATCATGCGCCCCCAAC 61.035 55.000 4.18 0.00 0.00 3.77
2593 6562 0.323816 TTACAATCATGCGCCCCCAA 60.324 50.000 4.18 0.00 0.00 4.12
2594 6563 0.323816 TTTACAATCATGCGCCCCCA 60.324 50.000 4.18 0.00 0.00 4.96
2595 6564 0.102300 GTTTACAATCATGCGCCCCC 59.898 55.000 4.18 0.00 0.00 5.40
2596 6565 0.102300 GGTTTACAATCATGCGCCCC 59.898 55.000 4.18 0.00 0.00 5.80
2597 6566 1.102978 AGGTTTACAATCATGCGCCC 58.897 50.000 4.18 0.00 0.00 6.13
2598 6567 3.691498 GTTAGGTTTACAATCATGCGCC 58.309 45.455 4.18 0.00 0.00 6.53
2599 6568 3.062909 TCGTTAGGTTTACAATCATGCGC 59.937 43.478 0.00 0.00 0.00 6.09
2600 6569 4.493545 GGTCGTTAGGTTTACAATCATGCG 60.494 45.833 0.00 0.00 0.00 4.73
2601 6570 4.393680 TGGTCGTTAGGTTTACAATCATGC 59.606 41.667 0.00 0.00 0.00 4.06
2602 6571 5.872617 TCTGGTCGTTAGGTTTACAATCATG 59.127 40.000 0.00 0.00 0.00 3.07
2603 6572 6.045072 TCTGGTCGTTAGGTTTACAATCAT 57.955 37.500 0.00 0.00 0.00 2.45
2604 6573 5.011329 ACTCTGGTCGTTAGGTTTACAATCA 59.989 40.000 0.00 0.00 0.00 2.57
2605 6574 5.476614 ACTCTGGTCGTTAGGTTTACAATC 58.523 41.667 0.00 0.00 0.00 2.67
2606 6575 5.479124 ACTCTGGTCGTTAGGTTTACAAT 57.521 39.130 0.00 0.00 0.00 2.71
2607 6576 4.942761 ACTCTGGTCGTTAGGTTTACAA 57.057 40.909 0.00 0.00 0.00 2.41
2608 6577 4.557296 CGAACTCTGGTCGTTAGGTTTACA 60.557 45.833 0.00 0.00 0.00 2.41
2609 6578 3.916776 CGAACTCTGGTCGTTAGGTTTAC 59.083 47.826 0.00 0.00 0.00 2.01
2610 6579 3.820467 TCGAACTCTGGTCGTTAGGTTTA 59.180 43.478 4.93 0.00 0.00 2.01
2611 6580 2.624838 TCGAACTCTGGTCGTTAGGTTT 59.375 45.455 4.93 0.00 0.00 3.27
2612 6581 2.233271 TCGAACTCTGGTCGTTAGGTT 58.767 47.619 4.93 0.00 0.00 3.50
2613 6582 1.901591 TCGAACTCTGGTCGTTAGGT 58.098 50.000 4.93 0.00 0.00 3.08
2614 6583 3.119602 TGAATCGAACTCTGGTCGTTAGG 60.120 47.826 4.93 0.00 0.00 2.69
2615 6584 3.852536 GTGAATCGAACTCTGGTCGTTAG 59.147 47.826 4.93 0.00 0.00 2.34
2616 6585 3.668757 CGTGAATCGAACTCTGGTCGTTA 60.669 47.826 4.93 0.00 42.86 3.18
2617 6586 2.673833 GTGAATCGAACTCTGGTCGTT 58.326 47.619 4.93 0.00 0.00 3.85
2618 6587 1.401148 CGTGAATCGAACTCTGGTCGT 60.401 52.381 4.93 0.00 42.86 4.34
2619 6588 1.260206 CGTGAATCGAACTCTGGTCG 58.740 55.000 0.00 0.00 42.86 4.79
2620 6589 2.251893 GACGTGAATCGAACTCTGGTC 58.748 52.381 0.00 0.00 42.86 4.02
2621 6590 1.401148 CGACGTGAATCGAACTCTGGT 60.401 52.381 0.00 0.00 45.13 4.00
2622 6591 1.260206 CGACGTGAATCGAACTCTGG 58.740 55.000 0.00 0.00 45.13 3.86
2623 6592 1.260206 CCGACGTGAATCGAACTCTG 58.740 55.000 0.00 0.00 45.13 3.35
2624 6593 0.170561 CCCGACGTGAATCGAACTCT 59.829 55.000 0.00 0.00 45.13 3.24
2625 6594 0.801067 CCCCGACGTGAATCGAACTC 60.801 60.000 0.00 0.00 45.13 3.01
2626 6595 1.214589 CCCCGACGTGAATCGAACT 59.785 57.895 0.00 0.00 45.13 3.01
2627 6596 1.074872 GTCCCCGACGTGAATCGAAC 61.075 60.000 0.00 0.00 45.13 3.95
2628 6597 1.213537 GTCCCCGACGTGAATCGAA 59.786 57.895 0.00 0.00 45.13 3.71
2629 6598 2.879907 GTCCCCGACGTGAATCGA 59.120 61.111 0.00 0.00 45.13 3.59
2638 6607 0.248289 TCCAGAAATTCGTCCCCGAC 59.752 55.000 0.00 0.00 44.13 4.79
2639 6608 0.978151 TTCCAGAAATTCGTCCCCGA 59.022 50.000 0.00 0.00 42.41 5.14
2640 6609 2.038387 ATTCCAGAAATTCGTCCCCG 57.962 50.000 0.00 0.00 0.00 5.73
2648 6617 6.083487 TCCCTCATGAGAATTCCAGAAATT 57.917 37.500 24.62 0.00 40.34 1.82
2649 6618 5.722172 TCCCTCATGAGAATTCCAGAAAT 57.278 39.130 24.62 0.00 0.00 2.17
2650 6619 5.443283 CATCCCTCATGAGAATTCCAGAAA 58.557 41.667 24.62 0.00 33.80 2.52
2651 6620 4.688045 GCATCCCTCATGAGAATTCCAGAA 60.688 45.833 24.62 0.00 33.80 3.02
2652 6621 3.181447 GCATCCCTCATGAGAATTCCAGA 60.181 47.826 24.62 8.82 33.80 3.86
2653 6622 3.147629 GCATCCCTCATGAGAATTCCAG 58.852 50.000 24.62 5.13 33.80 3.86
2654 6623 2.781757 AGCATCCCTCATGAGAATTCCA 59.218 45.455 24.62 0.28 33.80 3.53
2655 6624 3.505480 AGCATCCCTCATGAGAATTCC 57.495 47.619 24.62 9.10 33.80 3.01
2656 6625 4.716794 AGAAGCATCCCTCATGAGAATTC 58.283 43.478 24.62 15.91 33.80 2.17
2657 6626 4.792513 AGAAGCATCCCTCATGAGAATT 57.207 40.909 24.62 8.69 33.80 2.17
2658 6627 4.412858 AGAAGAAGCATCCCTCATGAGAAT 59.587 41.667 24.62 13.73 33.80 2.40
2659 6628 3.779183 AGAAGAAGCATCCCTCATGAGAA 59.221 43.478 24.62 11.97 33.80 2.87
2660 6629 3.382278 AGAAGAAGCATCCCTCATGAGA 58.618 45.455 24.62 5.64 33.80 3.27
2661 6630 3.842007 AGAAGAAGCATCCCTCATGAG 57.158 47.619 16.24 16.24 33.80 2.90
2662 6631 6.727697 TGATATAGAAGAAGCATCCCTCATGA 59.272 38.462 0.00 0.00 33.80 3.07
2663 6632 6.944096 TGATATAGAAGAAGCATCCCTCATG 58.056 40.000 0.00 0.00 35.29 3.07
2664 6633 7.565190 TTGATATAGAAGAAGCATCCCTCAT 57.435 36.000 0.00 0.00 0.00 2.90
2665 6634 7.565190 ATTGATATAGAAGAAGCATCCCTCA 57.435 36.000 0.00 0.00 0.00 3.86
2666 6635 9.950496 TTTATTGATATAGAAGAAGCATCCCTC 57.050 33.333 0.00 0.00 0.00 4.30
2671 6640 9.561069 ACGGTTTTATTGATATAGAAGAAGCAT 57.439 29.630 0.00 0.00 0.00 3.79
2672 6641 8.826710 CACGGTTTTATTGATATAGAAGAAGCA 58.173 33.333 0.00 0.00 0.00 3.91
2673 6642 8.283291 CCACGGTTTTATTGATATAGAAGAAGC 58.717 37.037 0.00 0.00 0.00 3.86
2674 6643 8.774586 CCCACGGTTTTATTGATATAGAAGAAG 58.225 37.037 0.00 0.00 0.00 2.85
2675 6644 8.269317 ACCCACGGTTTTATTGATATAGAAGAA 58.731 33.333 0.00 0.00 27.29 2.52
2676 6645 7.713507 CACCCACGGTTTTATTGATATAGAAGA 59.286 37.037 0.00 0.00 31.02 2.87
2677 6646 7.519970 GCACCCACGGTTTTATTGATATAGAAG 60.520 40.741 0.00 0.00 31.02 2.85
2678 6647 6.261381 GCACCCACGGTTTTATTGATATAGAA 59.739 38.462 0.00 0.00 31.02 2.10
2679 6648 5.761234 GCACCCACGGTTTTATTGATATAGA 59.239 40.000 0.00 0.00 31.02 1.98
2680 6649 5.763204 AGCACCCACGGTTTTATTGATATAG 59.237 40.000 0.00 0.00 31.02 1.31
2681 6650 5.686753 AGCACCCACGGTTTTATTGATATA 58.313 37.500 0.00 0.00 31.02 0.86
2682 6651 4.532834 AGCACCCACGGTTTTATTGATAT 58.467 39.130 0.00 0.00 31.02 1.63
2683 6652 3.958018 AGCACCCACGGTTTTATTGATA 58.042 40.909 0.00 0.00 31.02 2.15
2684 6653 2.802719 AGCACCCACGGTTTTATTGAT 58.197 42.857 0.00 0.00 31.02 2.57
2685 6654 2.279935 AGCACCCACGGTTTTATTGA 57.720 45.000 0.00 0.00 31.02 2.57
2686 6655 3.078837 ACTAGCACCCACGGTTTTATTG 58.921 45.455 0.00 0.00 31.02 1.90
2687 6656 3.078837 CACTAGCACCCACGGTTTTATT 58.921 45.455 0.00 0.00 31.02 1.40
2688 6657 2.706890 CACTAGCACCCACGGTTTTAT 58.293 47.619 0.00 0.00 31.02 1.40
2689 6658 1.878948 GCACTAGCACCCACGGTTTTA 60.879 52.381 0.00 0.00 41.58 1.52
2690 6659 1.170290 GCACTAGCACCCACGGTTTT 61.170 55.000 0.00 0.00 41.58 2.43
2691 6660 1.599797 GCACTAGCACCCACGGTTT 60.600 57.895 0.00 0.00 41.58 3.27
2692 6661 2.032071 GCACTAGCACCCACGGTT 59.968 61.111 0.00 0.00 41.58 4.44
2693 6662 4.016706 GGCACTAGCACCCACGGT 62.017 66.667 0.00 0.00 44.61 4.83
2694 6663 4.778143 GGGCACTAGCACCCACGG 62.778 72.222 14.48 0.00 46.22 4.94
2698 6667 2.124151 CCATGGGCACTAGCACCC 60.124 66.667 12.83 12.83 46.13 4.61
2699 6668 1.153086 CTCCATGGGCACTAGCACC 60.153 63.158 13.02 0.00 46.13 5.01
2701 6670 0.698238 AAACTCCATGGGCACTAGCA 59.302 50.000 13.02 0.00 44.61 3.49
2702 6671 1.340017 TGAAACTCCATGGGCACTAGC 60.340 52.381 13.02 0.00 41.10 3.42
2703 6672 2.787473 TGAAACTCCATGGGCACTAG 57.213 50.000 13.02 3.62 0.00 2.57
2704 6673 3.737559 AATGAAACTCCATGGGCACTA 57.262 42.857 13.02 0.00 0.00 2.74
2705 6674 2.610438 AATGAAACTCCATGGGCACT 57.390 45.000 13.02 0.00 0.00 4.40
2706 6675 3.683365 AAAATGAAACTCCATGGGCAC 57.317 42.857 13.02 0.33 0.00 5.01
2729 6698 9.109393 CCTAAGCTCAATGTAGTAATGCTAAAA 57.891 33.333 0.00 0.00 0.00 1.52
2730 6699 8.482943 TCCTAAGCTCAATGTAGTAATGCTAAA 58.517 33.333 0.00 0.00 0.00 1.85
2731 6700 8.018537 TCCTAAGCTCAATGTAGTAATGCTAA 57.981 34.615 0.00 0.00 0.00 3.09
2732 6701 7.597288 TCCTAAGCTCAATGTAGTAATGCTA 57.403 36.000 0.00 0.00 0.00 3.49
2733 6702 6.485830 TCCTAAGCTCAATGTAGTAATGCT 57.514 37.500 0.00 0.00 0.00 3.79
2734 6703 7.579726 CATTCCTAAGCTCAATGTAGTAATGC 58.420 38.462 0.00 0.00 0.00 3.56
2735 6704 7.227314 TGCATTCCTAAGCTCAATGTAGTAATG 59.773 37.037 4.24 4.24 31.29 1.90
2736 6705 7.282585 TGCATTCCTAAGCTCAATGTAGTAAT 58.717 34.615 0.00 0.00 31.29 1.89
2737 6706 6.649155 TGCATTCCTAAGCTCAATGTAGTAA 58.351 36.000 0.00 0.00 31.29 2.24
2738 6707 6.233905 TGCATTCCTAAGCTCAATGTAGTA 57.766 37.500 0.00 0.00 31.29 1.82
2739 6708 5.102953 TGCATTCCTAAGCTCAATGTAGT 57.897 39.130 0.00 0.00 31.29 2.73
2740 6709 5.587844 ACTTGCATTCCTAAGCTCAATGTAG 59.412 40.000 0.00 0.00 31.29 2.74
2741 6710 5.355071 CACTTGCATTCCTAAGCTCAATGTA 59.645 40.000 0.00 0.00 31.29 2.29
2742 6711 4.157289 CACTTGCATTCCTAAGCTCAATGT 59.843 41.667 0.00 0.00 31.29 2.71
2743 6712 4.439700 CCACTTGCATTCCTAAGCTCAATG 60.440 45.833 0.00 0.00 0.00 2.82
2744 6713 3.698040 CCACTTGCATTCCTAAGCTCAAT 59.302 43.478 0.00 0.00 0.00 2.57
2745 6714 3.084039 CCACTTGCATTCCTAAGCTCAA 58.916 45.455 0.00 0.00 0.00 3.02
2746 6715 2.715046 CCACTTGCATTCCTAAGCTCA 58.285 47.619 0.00 0.00 0.00 4.26
2747 6716 1.403323 GCCACTTGCATTCCTAAGCTC 59.597 52.381 0.00 0.00 40.77 4.09
2748 6717 1.467920 GCCACTTGCATTCCTAAGCT 58.532 50.000 0.00 0.00 40.77 3.74
2749 6718 0.099436 CGCCACTTGCATTCCTAAGC 59.901 55.000 0.00 0.00 41.33 3.09
2752 6721 2.106074 CGCGCCACTTGCATTCCTA 61.106 57.895 0.00 0.00 41.33 2.94
2774 6743 3.003480 GAGGAAACACATGAGGCAGTAC 58.997 50.000 0.00 0.00 0.00 2.73
2791 6764 3.644966 ATTCACTAATTTGGCCGAGGA 57.355 42.857 0.00 0.00 0.00 3.71
2871 7327 1.919918 TGCCAAACAAAGAAGCAACG 58.080 45.000 0.00 0.00 0.00 4.10
2886 7342 0.323302 TGTCGACAGCCTTAATGCCA 59.677 50.000 15.76 0.00 0.00 4.92
2986 7450 3.057245 GCAAGAAACACCCAGAGATTTCC 60.057 47.826 0.00 0.00 32.56 3.13
3013 7477 9.383519 CTAGTCTAACATCCTTTTGCAGATTTA 57.616 33.333 0.00 0.00 0.00 1.40
3022 7486 7.155328 CACTGACACTAGTCTAACATCCTTTT 58.845 38.462 0.00 0.00 45.20 2.27
3027 7491 4.859798 GCACACTGACACTAGTCTAACATC 59.140 45.833 0.00 0.00 45.20 3.06
3051 7520 0.683504 AATCTAGGGGAGACACGCGT 60.684 55.000 5.58 5.58 40.46 6.01
3054 7523 1.486211 ACCAATCTAGGGGAGACACG 58.514 55.000 3.46 0.00 40.46 4.49
3058 7527 7.525158 AAAGAAATTACCAATCTAGGGGAGA 57.475 36.000 3.46 0.00 39.01 3.71
3059 7528 7.615757 ACAAAAGAAATTACCAATCTAGGGGAG 59.384 37.037 3.46 0.00 0.00 4.30
3060 7529 7.475299 ACAAAAGAAATTACCAATCTAGGGGA 58.525 34.615 3.46 0.00 0.00 4.81
3061 7530 7.718334 ACAAAAGAAATTACCAATCTAGGGG 57.282 36.000 0.00 0.00 0.00 4.79
3062 7531 7.545615 GCAACAAAAGAAATTACCAATCTAGGG 59.454 37.037 0.00 0.00 0.00 3.53
3063 7532 7.545615 GGCAACAAAAGAAATTACCAATCTAGG 59.454 37.037 0.00 0.00 0.00 3.02
3064 7533 7.273381 CGGCAACAAAAGAAATTACCAATCTAG 59.727 37.037 0.00 0.00 0.00 2.43
3065 7534 7.087639 CGGCAACAAAAGAAATTACCAATCTA 58.912 34.615 0.00 0.00 0.00 1.98
3066 7535 5.925969 CGGCAACAAAAGAAATTACCAATCT 59.074 36.000 0.00 0.00 0.00 2.40
3067 7536 5.389411 GCGGCAACAAAAGAAATTACCAATC 60.389 40.000 0.00 0.00 0.00 2.67
3068 7537 4.450757 GCGGCAACAAAAGAAATTACCAAT 59.549 37.500 0.00 0.00 0.00 3.16
3069 7538 3.804873 GCGGCAACAAAAGAAATTACCAA 59.195 39.130 0.00 0.00 0.00 3.67
3070 7539 3.385577 GCGGCAACAAAAGAAATTACCA 58.614 40.909 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.