Multiple sequence alignment - TraesCS2D01G082700

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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 TraesCS2D01G082700 chr2D 100.000 4706 0 0 1 4706 35687488 35682783 0.000000e+00 8691
1 TraesCS2D01G082700 chr2D 80.590 407 34 16 591 962 35711557 35711953 6.000000e-69 272
2 TraesCS2D01G082700 chr2B 86.081 2730 200 74 1 2663 58847771 58845155 0.000000e+00 2771
3 TraesCS2D01G082700 chr2B 89.207 1501 131 13 3190 4679 58844432 58842952 0.000000e+00 1845
4 TraesCS2D01G082700 chr2B 81.794 758 86 21 1957 2707 773749777 773749065 5.250000e-164 588
5 TraesCS2D01G082700 chr2B 81.746 756 85 25 1954 2704 774653973 774654680 2.440000e-162 582
6 TraesCS2D01G082700 chr2B 80.876 753 90 30 1957 2704 774637634 774638337 1.150000e-150 544
7 TraesCS2D01G082700 chr2B 80.611 753 92 31 1957 2704 774612808 774613511 2.490000e-147 532
8 TraesCS2D01G082700 chr2B 83.527 431 40 16 2724 3131 58844879 58844457 1.600000e-99 374
9 TraesCS2D01G082700 chr2A 90.392 1988 141 20 2724 4679 38913707 38911738 0.000000e+00 2567
10 TraesCS2D01G082700 chr2A 91.042 1853 115 29 855 2672 38915685 38913849 0.000000e+00 2455
11 TraesCS2D01G082700 chr2A 83.110 746 80 19 1968 2704 760433105 760433813 5.140000e-179 638
12 TraesCS2D01G082700 chr2A 87.346 569 52 9 1 567 38917290 38916740 6.640000e-178 634
13 TraesCS2D01G082700 chr2A 83.955 268 30 5 2429 2695 760493079 760493334 1.310000e-60 244
14 TraesCS2D01G082700 chr2A 87.421 159 17 3 205 362 38932302 38932146 3.740000e-41 180
15 TraesCS2D01G082700 chr7D 85.267 543 44 20 1152 1685 495138647 495139162 1.160000e-145 527
16 TraesCS2D01G082700 chr4A 80.132 453 75 13 1240 1684 132703144 132702699 1.630000e-84 324
17 TraesCS2D01G082700 chr4A 91.139 79 7 0 1803 1881 132702618 132702540 1.790000e-19 108
18 TraesCS2D01G082700 chr4B 89.121 239 26 0 1240 1478 418752280 418752518 9.900000e-77 298
19 TraesCS2D01G082700 chr4B 92.000 75 6 0 1803 1877 418752808 418752882 6.440000e-19 106
20 TraesCS2D01G082700 chr5A 79.921 254 42 9 1233 1482 332215286 332215534 1.350000e-40 178
21 TraesCS2D01G082700 chr5D 79.447 253 45 7 1233 1482 249523609 249523857 6.260000e-39 172
22 TraesCS2D01G082700 chr5B 79.447 253 45 7 1233 1482 282264880 282265128 6.260000e-39 172
23 TraesCS2D01G082700 chr4D 77.350 234 48 5 1258 1489 116823006 116822776 2.950000e-27 134
24 TraesCS2D01G082700 chr4D 90.667 75 7 0 1803 1877 339227061 339227135 3.000000e-17 100


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 TraesCS2D01G082700 chr2D 35682783 35687488 4705 True 8691.000000 8691 100.000000 1 4706 1 chr2D.!!$R1 4705
1 TraesCS2D01G082700 chr2B 58842952 58847771 4819 True 1663.333333 2771 86.271667 1 4679 3 chr2B.!!$R2 4678
2 TraesCS2D01G082700 chr2B 773749065 773749777 712 True 588.000000 588 81.794000 1957 2707 1 chr2B.!!$R1 750
3 TraesCS2D01G082700 chr2B 774653973 774654680 707 False 582.000000 582 81.746000 1954 2704 1 chr2B.!!$F3 750
4 TraesCS2D01G082700 chr2B 774637634 774638337 703 False 544.000000 544 80.876000 1957 2704 1 chr2B.!!$F2 747
5 TraesCS2D01G082700 chr2B 774612808 774613511 703 False 532.000000 532 80.611000 1957 2704 1 chr2B.!!$F1 747
6 TraesCS2D01G082700 chr2A 38911738 38917290 5552 True 1885.333333 2567 89.593333 1 4679 3 chr2A.!!$R2 4678
7 TraesCS2D01G082700 chr2A 760433105 760433813 708 False 638.000000 638 83.110000 1968 2704 1 chr2A.!!$F1 736
8 TraesCS2D01G082700 chr7D 495138647 495139162 515 False 527.000000 527 85.267000 1152 1685 1 chr7D.!!$F1 533
9 TraesCS2D01G082700 chr4A 132702540 132703144 604 True 216.000000 324 85.635500 1240 1881 2 chr4A.!!$R1 641
10 TraesCS2D01G082700 chr4B 418752280 418752882 602 False 202.000000 298 90.560500 1240 1877 2 chr4B.!!$F1 637

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
43 44 0.109597 GTGATTTGCCGCTGTTCTGG 60.110 55.0 0.0 0.0 0.0 3.86 F
1704 2590 0.166814 GCGCATCAACACCTTCTCAC 59.833 55.0 0.3 0.0 0.0 3.51 F
2937 4101 0.037447 AAGCCACCTTCTCAGCCTTC 59.963 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2891 0.176910 GGCTCCTGTACAGCTTCTCC 59.823 60.0 17.86 9.29 37.05 3.71 R
3431 4602 0.032813 AGGCAGGGAACATCAATGGG 60.033 55.0 0.00 0.00 0.00 4.00 R
4681 5864 0.036294 GGGTCTTGTCACCTGCCTAC 60.036 60.0 0.00 0.00 36.57 3.18 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 0.109597 GTGATTTGCCGCTGTTCTGG 60.110 55.000 0.00 0.00 0.00 3.86
62 63 2.305927 TGGCGAAGGAGAAGGAGAAAAT 59.694 45.455 0.00 0.00 0.00 1.82
72 73 8.386012 AGGAGAAGGAGAAAATGAGAGATTAA 57.614 34.615 0.00 0.00 0.00 1.40
75 76 9.313118 GAGAAGGAGAAAATGAGAGATTAAGAC 57.687 37.037 0.00 0.00 0.00 3.01
113 115 8.409358 AGATAAACAGACTGGTTAAGCAAAAT 57.591 30.769 16.66 0.00 32.68 1.82
124 126 9.601217 ACTGGTTAAGCAAAATGACTATACTAG 57.399 33.333 8.94 0.00 0.00 2.57
125 127 9.601217 CTGGTTAAGCAAAATGACTATACTAGT 57.399 33.333 8.94 0.00 42.86 2.57
172 174 4.021719 ACCACTAACCGATATGGAATACCG 60.022 45.833 0.00 0.00 42.00 4.02
207 209 1.209747 GGGTAGGGGTAGTGAAGCAAG 59.790 57.143 0.00 0.00 0.00 4.01
210 212 1.133809 AGGGGTAGTGAAGCAAGCCA 61.134 55.000 0.00 0.00 32.32 4.75
213 215 1.604604 GGTAGTGAAGCAAGCCAACA 58.395 50.000 0.00 0.00 0.00 3.33
226 228 1.017387 GCCAACAGGAGAATAAGCCG 58.983 55.000 0.00 0.00 0.00 5.52
241 243 0.550914 AGCCGCCCTTATGGATTTCA 59.449 50.000 0.00 0.00 35.39 2.69
248 250 5.064707 CCGCCCTTATGGATTTCATAATACG 59.935 44.000 0.00 3.40 44.55 3.06
260 262 2.953648 TCATAATACGTCGGCAGGAGAA 59.046 45.455 0.00 0.00 0.00 2.87
265 267 1.289066 CGTCGGCAGGAGAAACTCA 59.711 57.895 0.00 0.00 31.08 3.41
382 384 3.916061 GAGCAGTCTCGTCAGCTAG 57.084 57.895 0.00 0.00 37.48 3.42
417 419 4.387598 CAGAGAGAGAATAAGCCAATGGG 58.612 47.826 0.00 0.00 37.18 4.00
460 462 5.697473 TTTTGTGTGTTGACAAACAGAGA 57.303 34.783 7.17 0.00 46.79 3.10
461 463 4.678509 TTGTGTGTTGACAAACAGAGAC 57.321 40.909 7.17 0.00 46.79 3.36
469 471 4.238761 TGACAAACAGAGACGAACCTAG 57.761 45.455 0.00 0.00 0.00 3.02
476 478 4.002316 ACAGAGACGAACCTAGTCACTAC 58.998 47.826 0.00 0.00 37.43 2.73
509 512 4.389374 TCTCTTCCGCTGTTCATTCTTTT 58.611 39.130 0.00 0.00 0.00 2.27
510 513 4.452455 TCTCTTCCGCTGTTCATTCTTTTC 59.548 41.667 0.00 0.00 0.00 2.29
511 514 3.502211 TCTTCCGCTGTTCATTCTTTTCC 59.498 43.478 0.00 0.00 0.00 3.13
555 560 8.424133 AGAATTCCTTTTTGAACTGCTTACATT 58.576 29.630 0.65 0.00 0.00 2.71
564 1290 4.278170 TGAACTGCTTACATTGGGAAACAG 59.722 41.667 0.00 0.00 0.00 3.16
602 1328 4.282957 ACATTGTTATGGTTGGTTGCATCA 59.717 37.500 0.00 0.00 36.01 3.07
632 1358 4.319177 ACACCTTCTCTCTAACATGTTGC 58.681 43.478 21.42 0.00 0.00 4.17
638 1364 4.960938 TCTCTCTAACATGTTGCACTGTT 58.039 39.130 21.42 11.81 38.95 3.16
641 1367 2.293122 TCTAACATGTTGCACTGTTGGC 59.707 45.455 21.42 0.00 36.34 4.52
652 1386 1.002033 CACTGTTGGCTCTCAAGTTGC 60.002 52.381 0.00 0.00 35.80 4.17
671 1405 1.013323 GATGCGCATGTCGTCGTTC 60.013 57.895 30.76 6.89 41.07 3.95
699 1458 2.410785 TTCGTCGATCTTCACGTGTT 57.589 45.000 16.51 0.00 37.30 3.32
709 1468 5.444613 CGATCTTCACGTGTTATCAACAAGG 60.445 44.000 16.51 0.00 44.16 3.61
713 1472 4.888917 TCACGTGTTATCAACAAGGATGA 58.111 39.130 16.51 3.14 44.16 2.92
737 1501 4.476628 AGAAAATGCCATGGTTTCCATC 57.523 40.909 14.67 5.61 43.15 3.51
770 1555 4.832266 TGTGTTTGGTCTATTCCATTTGCT 59.168 37.500 0.00 0.00 37.33 3.91
771 1556 5.163513 GTGTTTGGTCTATTCCATTTGCTG 58.836 41.667 0.00 0.00 37.33 4.41
772 1557 4.832266 TGTTTGGTCTATTCCATTTGCTGT 59.168 37.500 0.00 0.00 37.33 4.40
773 1558 5.163513 GTTTGGTCTATTCCATTTGCTGTG 58.836 41.667 0.00 0.00 37.33 3.66
774 1559 4.299586 TGGTCTATTCCATTTGCTGTGA 57.700 40.909 0.00 0.00 31.96 3.58
776 1561 4.263462 TGGTCTATTCCATTTGCTGTGAGT 60.263 41.667 0.00 0.00 31.96 3.41
777 1562 4.095483 GGTCTATTCCATTTGCTGTGAGTG 59.905 45.833 0.00 0.00 0.00 3.51
778 1563 4.095483 GTCTATTCCATTTGCTGTGAGTGG 59.905 45.833 0.00 0.00 0.00 4.00
779 1564 0.961019 TTCCATTTGCTGTGAGTGGC 59.039 50.000 0.00 0.00 0.00 5.01
780 1565 0.895100 TCCATTTGCTGTGAGTGGCC 60.895 55.000 0.00 0.00 0.00 5.36
781 1566 1.588082 CATTTGCTGTGAGTGGCCC 59.412 57.895 0.00 0.00 0.00 5.80
783 1568 0.896940 ATTTGCTGTGAGTGGCCCTG 60.897 55.000 0.00 0.00 0.00 4.45
784 1569 4.648626 TGCTGTGAGTGGCCCTGC 62.649 66.667 0.00 0.00 0.00 4.85
815 1600 9.699410 ATATTTTTGGATTCAGAAGATACCACA 57.301 29.630 0.00 0.00 32.03 4.17
816 1601 6.817765 TTTTGGATTCAGAAGATACCACAC 57.182 37.500 0.00 0.00 32.03 3.82
818 1603 3.843619 TGGATTCAGAAGATACCACACCA 59.156 43.478 0.00 0.00 0.00 4.17
820 1605 4.636206 GGATTCAGAAGATACCACACCAAC 59.364 45.833 0.00 0.00 0.00 3.77
821 1606 4.698201 TTCAGAAGATACCACACCAACA 57.302 40.909 0.00 0.00 0.00 3.33
823 1608 3.074412 CAGAAGATACCACACCAACACC 58.926 50.000 0.00 0.00 0.00 4.16
824 1609 2.708861 AGAAGATACCACACCAACACCA 59.291 45.455 0.00 0.00 0.00 4.17
826 1611 1.073284 AGATACCACACCAACACCACC 59.927 52.381 0.00 0.00 0.00 4.61
828 1613 0.624254 TACCACACCAACACCACCAA 59.376 50.000 0.00 0.00 0.00 3.67
829 1614 0.682855 ACCACACCAACACCACCAAG 60.683 55.000 0.00 0.00 0.00 3.61
830 1615 0.682855 CCACACCAACACCACCAAGT 60.683 55.000 0.00 0.00 0.00 3.16
831 1616 1.181786 CACACCAACACCACCAAGTT 58.818 50.000 0.00 0.00 0.00 2.66
852 1686 3.544772 TGAGCCACACAGACGGAA 58.455 55.556 0.00 0.00 0.00 4.30
853 1687 1.826709 TGAGCCACACAGACGGAAA 59.173 52.632 0.00 0.00 0.00 3.13
854 1688 0.249868 TGAGCCACACAGACGGAAAG 60.250 55.000 0.00 0.00 0.00 2.62
856 1690 1.070786 GCCACACAGACGGAAAGGA 59.929 57.895 0.00 0.00 0.00 3.36
1092 1927 2.776963 CCTCCCCCGGCCCTATTT 60.777 66.667 0.00 0.00 0.00 1.40
1094 1929 2.775219 TCCCCCGGCCCTATTTCC 60.775 66.667 0.00 0.00 0.00 3.13
1096 1931 2.776963 CCCCGGCCCTATTTCCCT 60.777 66.667 0.00 0.00 0.00 4.20
1230 2077 3.706373 CAGGGTGGTGACGAGGGG 61.706 72.222 0.00 0.00 0.00 4.79
1517 2376 4.519213 TCAGTTTCTCCGTCCTTGAAAAA 58.481 39.130 0.00 0.00 32.50 1.94
1524 2383 8.912658 GTTTCTCCGTCCTTGAAAAATTAAATC 58.087 33.333 0.00 0.00 32.50 2.17
1526 2385 8.040716 TCTCCGTCCTTGAAAAATTAAATCTC 57.959 34.615 0.00 0.00 0.00 2.75
1565 2443 3.078837 ACCGTCTCTGTCTCTCTCTTTC 58.921 50.000 0.00 0.00 0.00 2.62
1703 2589 1.291184 CGCGCATCAACACCTTCTCA 61.291 55.000 8.75 0.00 0.00 3.27
1704 2590 0.166814 GCGCATCAACACCTTCTCAC 59.833 55.000 0.30 0.00 0.00 3.51
1705 2591 1.511850 CGCATCAACACCTTCTCACA 58.488 50.000 0.00 0.00 0.00 3.58
1706 2592 1.195448 CGCATCAACACCTTCTCACAC 59.805 52.381 0.00 0.00 0.00 3.82
1707 2593 1.537202 GCATCAACACCTTCTCACACC 59.463 52.381 0.00 0.00 0.00 4.16
1708 2594 2.811873 GCATCAACACCTTCTCACACCT 60.812 50.000 0.00 0.00 0.00 4.00
1732 2618 1.480137 ACCTCGATCCTCTTCTTGCTG 59.520 52.381 0.00 0.00 0.00 4.41
1740 2626 7.726216 TCGATCCTCTTCTTGCTGATAATAAA 58.274 34.615 0.00 0.00 0.00 1.40
1745 2631 9.113838 TCCTCTTCTTGCTGATAATAAATGTTC 57.886 33.333 0.00 0.00 0.00 3.18
1765 2658 9.461312 AATGTTCCAATAGCTGTGAGTTTATTA 57.539 29.630 0.00 0.00 0.00 0.98
1877 2770 1.464376 CGAGTCCTGGCATCCGGTAT 61.464 60.000 0.00 0.00 0.00 2.73
1884 2777 2.510906 GCATCCGGTATGTGGGCT 59.489 61.111 0.00 0.00 37.93 5.19
1885 2778 1.893808 GCATCCGGTATGTGGGCTG 60.894 63.158 0.00 0.00 37.93 4.85
1886 2779 1.893808 CATCCGGTATGTGGGCTGC 60.894 63.158 0.00 0.00 0.00 5.25
1887 2780 2.374525 ATCCGGTATGTGGGCTGCA 61.375 57.895 0.00 0.00 0.00 4.41
1890 2783 0.603707 CCGGTATGTGGGCTGCATAG 60.604 60.000 0.50 0.00 30.45 2.23
1899 2796 0.957362 GGGCTGCATAGATTCCAAGC 59.043 55.000 0.50 0.00 0.00 4.01
1948 2846 4.454728 TGAGCAATTTGATTAACCCTGC 57.545 40.909 0.00 0.00 0.00 4.85
1950 2848 1.926510 GCAATTTGATTAACCCTGCGC 59.073 47.619 0.00 0.00 0.00 6.09
1951 2849 2.673610 GCAATTTGATTAACCCTGCGCA 60.674 45.455 10.98 10.98 0.00 6.09
1955 2853 0.320858 TGATTAACCCTGCGCAACGA 60.321 50.000 13.05 0.00 0.00 3.85
1971 2869 4.440758 CGCAACGATGTCTTGAACAAATTT 59.559 37.500 0.00 0.00 42.37 1.82
2103 3004 4.522789 GGTGAGACCAAATAAGCCAAAAGA 59.477 41.667 0.00 0.00 38.42 2.52
2153 3055 7.988737 TGATTAATTTGCTCATGAGGTAACAG 58.011 34.615 23.89 0.00 41.41 3.16
2168 3070 8.106247 TGAGGTAACAGATGTTTGGTAAAATC 57.894 34.615 3.14 0.00 39.31 2.17
2171 3073 7.176690 AGGTAACAGATGTTTGGTAAAATCTGG 59.823 37.037 17.76 5.17 36.99 3.86
2287 3195 2.159282 GCCGAACGAGAAGAAGGACATA 60.159 50.000 0.00 0.00 0.00 2.29
2288 3196 3.696898 CCGAACGAGAAGAAGGACATAG 58.303 50.000 0.00 0.00 0.00 2.23
2425 3345 3.064545 GTGGTATCTGCTCTTGTTGCATC 59.935 47.826 0.00 0.00 39.86 3.91
2567 3488 3.561143 TGTTATGTGGCTGGACTTTGTT 58.439 40.909 0.00 0.00 0.00 2.83
2615 3536 1.207329 GACAAGCTTCCCTGGTATCGT 59.793 52.381 0.00 0.00 0.00 3.73
2629 3550 5.296035 CCTGGTATCGTGGAAAGGTAAAATC 59.704 44.000 0.00 0.00 0.00 2.17
2644 3571 8.409358 AAGGTAAAATCAACAGAGCTACAATT 57.591 30.769 0.00 0.00 0.00 2.32
2645 3572 8.045176 AGGTAAAATCAACAGAGCTACAATTC 57.955 34.615 0.00 0.00 0.00 2.17
2647 3574 4.606457 AATCAACAGAGCTACAATTCGC 57.394 40.909 0.00 0.00 0.00 4.70
2660 3618 2.262572 AATTCGCGGAATTGCAAGTC 57.737 45.000 18.28 18.28 40.24 3.01
2680 3638 4.747108 AGTCACATCGCTTAATCTGCATAC 59.253 41.667 0.00 0.00 0.00 2.39
2689 3647 4.037208 GCTTAATCTGCATACCATTGTGCT 59.963 41.667 0.00 0.00 40.41 4.40
2700 3685 4.766404 ACCATTGTGCTAAAACTAGTGC 57.234 40.909 0.00 0.00 0.00 4.40
2705 3692 3.459145 TGTGCTAAAACTAGTGCGTTGA 58.541 40.909 0.00 0.00 0.00 3.18
2707 3694 5.231702 TGTGCTAAAACTAGTGCGTTGATA 58.768 37.500 0.00 0.00 0.00 2.15
2708 3695 5.872617 TGTGCTAAAACTAGTGCGTTGATAT 59.127 36.000 0.00 0.00 0.00 1.63
2709 3696 7.036829 TGTGCTAAAACTAGTGCGTTGATATA 58.963 34.615 0.00 0.00 0.00 0.86
2710 3697 7.222031 TGTGCTAAAACTAGTGCGTTGATATAG 59.778 37.037 0.00 0.00 0.00 1.31
2711 3698 7.222224 GTGCTAAAACTAGTGCGTTGATATAGT 59.778 37.037 0.00 0.00 0.00 2.12
2714 3701 6.887376 AAACTAGTGCGTTGATATAGTGTG 57.113 37.500 0.00 0.00 0.00 3.82
2715 3702 5.830000 ACTAGTGCGTTGATATAGTGTGA 57.170 39.130 0.00 0.00 0.00 3.58
2716 3703 6.392625 ACTAGTGCGTTGATATAGTGTGAT 57.607 37.500 0.00 0.00 0.00 3.06
2718 3705 5.011090 AGTGCGTTGATATAGTGTGATGT 57.989 39.130 0.00 0.00 0.00 3.06
2720 3707 5.874810 AGTGCGTTGATATAGTGTGATGTTT 59.125 36.000 0.00 0.00 0.00 2.83
2722 3709 5.872070 TGCGTTGATATAGTGTGATGTTTGA 59.128 36.000 0.00 0.00 0.00 2.69
2733 3877 5.865552 AGTGTGATGTTTGAATAATTGCTGC 59.134 36.000 0.00 0.00 0.00 5.25
2739 3883 7.329962 TGATGTTTGAATAATTGCTGCTTGAAG 59.670 33.333 0.00 0.00 0.00 3.02
2775 3919 1.412710 GTCAGAGTTGACCACAGTCCA 59.587 52.381 0.00 0.00 46.47 4.02
2788 3932 7.629157 TGACCACAGTCCATATCAGATAAAAA 58.371 34.615 0.00 0.00 42.81 1.94
2789 3933 7.552687 TGACCACAGTCCATATCAGATAAAAAC 59.447 37.037 0.00 0.00 42.81 2.43
2821 3965 9.658475 TTGAACAGTCTGAATAAACAATAAACG 57.342 29.630 6.91 0.00 0.00 3.60
2824 3968 7.581476 ACAGTCTGAATAAACAATAAACGTGG 58.419 34.615 6.91 0.00 0.00 4.94
2833 3977 2.817844 ACAATAAACGTGGCCTCCTTTC 59.182 45.455 3.32 0.00 0.00 2.62
2837 3981 0.250770 AACGTGGCCTCCTTTCCTTC 60.251 55.000 3.32 0.00 0.00 3.46
2843 3987 4.086457 GTGGCCTCCTTTCCTTCATAAAA 58.914 43.478 3.32 0.00 0.00 1.52
2845 3989 4.202673 TGGCCTCCTTTCCTTCATAAAAGT 60.203 41.667 3.32 0.00 31.88 2.66
2847 3991 4.158579 GCCTCCTTTCCTTCATAAAAGTGG 59.841 45.833 0.00 0.00 31.88 4.00
2851 3995 7.202001 CCTCCTTTCCTTCATAAAAGTGGTTTT 60.202 37.037 0.00 0.00 39.31 2.43
2903 4064 9.209175 AGTAGTCAAAATAGCAAAGTTACAGAG 57.791 33.333 0.00 0.00 0.00 3.35
2904 4065 8.989980 GTAGTCAAAATAGCAAAGTTACAGAGT 58.010 33.333 0.00 0.00 0.00 3.24
2907 4068 9.595357 GTCAAAATAGCAAAGTTACAGAGTTAC 57.405 33.333 0.00 0.00 0.00 2.50
2908 4069 9.332502 TCAAAATAGCAAAGTTACAGAGTTACA 57.667 29.630 0.00 0.00 0.00 2.41
2909 4070 9.944663 CAAAATAGCAAAGTTACAGAGTTACAA 57.055 29.630 0.00 0.00 0.00 2.41
2912 4073 8.904099 ATAGCAAAGTTACAGAGTTACAAAGT 57.096 30.769 0.00 0.00 0.00 2.66
2913 4074 7.625828 AGCAAAGTTACAGAGTTACAAAGTT 57.374 32.000 0.00 0.00 0.00 2.66
2928 4092 3.381590 ACAAAGTTTCAGAAGCCACCTTC 59.618 43.478 0.00 0.00 46.29 3.46
2937 4101 0.037447 AAGCCACCTTCTCAGCCTTC 59.963 55.000 0.00 0.00 0.00 3.46
2946 4113 3.618351 CTTCTCAGCCTTCCATGACAAT 58.382 45.455 0.00 0.00 0.00 2.71
3028 4197 2.490903 GCTGCATCTTTCACTGTCCATT 59.509 45.455 0.00 0.00 0.00 3.16
3224 4394 4.828939 TGTCATTGCTCAAATCCTTCAACT 59.171 37.500 0.00 0.00 0.00 3.16
3343 4514 0.470766 ACTACGGGTGGCTCAACAAA 59.529 50.000 0.00 0.00 0.00 2.83
3358 4529 3.252215 TCAACAAAATCCACCACGACATC 59.748 43.478 0.00 0.00 0.00 3.06
3431 4602 1.134907 TGGAGGCGGTAAGAATCGAAC 60.135 52.381 0.00 0.00 0.00 3.95
3434 4605 0.108041 GGCGGTAAGAATCGAACCCA 60.108 55.000 0.00 0.00 0.00 4.51
3519 4690 1.024271 TTGTGCTTGTCTTGCAGACC 58.976 50.000 11.99 0.98 44.44 3.85
3633 4804 0.956633 TGAAGAGCGACCACTACGTT 59.043 50.000 0.00 0.00 0.00 3.99
3715 4886 6.150976 ACACACATCCGATTAACAACATCAAT 59.849 34.615 0.00 0.00 0.00 2.57
3801 4973 0.694771 TGCCAAGTTCCTCAGCATCT 59.305 50.000 0.00 0.00 0.00 2.90
3802 4974 1.908619 TGCCAAGTTCCTCAGCATCTA 59.091 47.619 0.00 0.00 0.00 1.98
3902 5074 6.923508 CACGGTAGAATAGATTATGTGCTTGA 59.076 38.462 0.00 0.00 0.00 3.02
3921 5093 6.974622 TGCTTGAAAGAAACAAGTGATTCTTC 59.025 34.615 14.59 10.03 43.38 2.87
3926 5098 4.703897 AGAAACAAGTGATTCTTCGGACA 58.296 39.130 0.00 0.00 34.12 4.02
3934 5106 2.038426 TGATTCTTCGGACAAGAGCCAA 59.962 45.455 0.00 0.00 0.00 4.52
3935 5107 2.631160 TTCTTCGGACAAGAGCCAAA 57.369 45.000 0.00 0.00 0.00 3.28
3956 5130 2.746362 AGCAGCTCGAAAGATTGGAAAG 59.254 45.455 0.00 0.00 40.84 2.62
3962 5136 4.214332 GCTCGAAAGATTGGAAAGACTTGT 59.786 41.667 0.00 0.00 40.84 3.16
3967 5141 6.148480 CGAAAGATTGGAAAGACTTGTCTGAT 59.852 38.462 3.87 0.00 0.00 2.90
3991 5165 2.738743 AGGGGCATTCATTGTTCGATT 58.261 42.857 0.00 0.00 0.00 3.34
3997 5171 5.009010 GGGCATTCATTGTTCGATTCTACAT 59.991 40.000 0.00 0.00 0.00 2.29
4006 5181 8.820933 CATTGTTCGATTCTACATCACTGTTAT 58.179 33.333 0.00 0.00 36.79 1.89
4012 5187 9.297586 TCGATTCTACATCACTGTTATTACAAC 57.702 33.333 0.00 0.00 36.79 3.32
4042 5217 4.074970 CAGTATTTGTTTCAGCTGGTCCT 58.925 43.478 15.13 0.00 0.00 3.85
4070 5245 5.570973 GCATATACTACTGCAGTGAAGATCG 59.429 44.000 29.57 13.47 38.24 3.69
4095 5273 4.142622 TGCTTAATTCCAGATCTTTGCACG 60.143 41.667 0.00 0.00 0.00 5.34
4096 5274 4.731773 GCTTAATTCCAGATCTTTGCACGG 60.732 45.833 0.00 0.00 0.00 4.94
4146 5324 4.092816 GTCGTTGTCGTGAATTTTGTTGT 58.907 39.130 0.00 0.00 38.33 3.32
4160 5338 8.154203 TGAATTTTGTTGTATCTGTCCTAGTGA 58.846 33.333 0.00 0.00 0.00 3.41
4211 5389 3.142838 GCTCATTGCCGCCCACAT 61.143 61.111 0.00 0.00 35.15 3.21
4213 5395 2.755064 TCATTGCCGCCCACATGG 60.755 61.111 0.00 0.00 37.09 3.66
4263 5445 5.370584 TCATATGGGTTCTGTGATCCTTGAT 59.629 40.000 2.13 0.00 0.00 2.57
4267 5449 3.944015 GGGTTCTGTGATCCTTGATCTTG 59.056 47.826 5.74 0.00 39.56 3.02
4278 5460 4.899502 TCCTTGATCTTGGTTCTTGACTC 58.100 43.478 0.00 0.00 0.00 3.36
4291 5473 2.109128 TCTTGACTCTCTGTGGTCCTCT 59.891 50.000 0.00 0.00 0.00 3.69
4309 5491 7.715686 TGGTCCTCTTTTTCTTCTTCTTAGAAC 59.284 37.037 0.00 0.00 35.49 3.01
4332 5514 9.430838 GAACGATCATCAGATTTATGTTGAAAG 57.569 33.333 0.00 0.00 33.76 2.62
4344 5526 1.881973 TGTTGAAAGCTCACCATGCTC 59.118 47.619 0.00 0.00 40.22 4.26
4355 5538 3.025978 TCACCATGCTCCCATTGAAATC 58.974 45.455 0.00 0.00 0.00 2.17
4371 5554 3.517100 TGAAATCCTAGCTGAGCTCTGTT 59.483 43.478 11.68 17.19 40.44 3.16
4375 5558 5.885449 ATCCTAGCTGAGCTCTGTTTTAT 57.115 39.130 11.68 7.50 40.44 1.40
4378 5561 5.049167 CCTAGCTGAGCTCTGTTTTATCAG 58.951 45.833 11.68 9.22 40.44 2.90
4425 5608 4.361783 TCCAGATCTTGTAATGGTGGAGA 58.638 43.478 0.00 0.00 34.32 3.71
4431 5614 3.054434 TCTTGTAATGGTGGAGATGGTGG 60.054 47.826 0.00 0.00 0.00 4.61
4434 5617 0.033796 AATGGTGGAGATGGTGGCAG 60.034 55.000 0.00 0.00 0.00 4.85
4435 5618 0.915872 ATGGTGGAGATGGTGGCAGA 60.916 55.000 0.00 0.00 0.00 4.26
4438 5621 2.300967 TGGAGATGGTGGCAGACCC 61.301 63.158 1.87 0.00 45.45 4.46
4451 5634 3.017442 GGCAGACCCAATAAAAGTCTCC 58.983 50.000 0.00 0.00 38.80 3.71
4459 5642 3.127030 CCAATAAAAGTCTCCTGCGGTTC 59.873 47.826 0.00 0.00 0.00 3.62
4465 5648 1.416401 AGTCTCCTGCGGTTCTTTTGA 59.584 47.619 0.00 0.00 0.00 2.69
4468 5651 1.740025 CTCCTGCGGTTCTTTTGATCC 59.260 52.381 0.00 0.00 35.48 3.36
4485 5668 2.660189 TCCCGTCGGTTGTAGATTTC 57.340 50.000 11.06 0.00 0.00 2.17
4486 5669 1.894466 TCCCGTCGGTTGTAGATTTCA 59.106 47.619 11.06 0.00 0.00 2.69
4490 5673 2.669113 CGTCGGTTGTAGATTTCACGGA 60.669 50.000 0.00 0.00 0.00 4.69
4491 5674 2.665052 GTCGGTTGTAGATTTCACGGAC 59.335 50.000 0.00 0.00 0.00 4.79
4499 5682 1.887198 AGATTTCACGGACTGTCGTCT 59.113 47.619 1.07 0.00 41.86 4.18
4506 5689 1.080434 GGACTGTCGTCTGGTGCTC 60.080 63.158 1.07 0.00 40.10 4.26
4618 5801 7.606456 AGCAAGCAAGATGAAAATGAAAATCAT 59.394 29.630 0.00 0.00 39.09 2.45
4642 5825 5.911752 TGACATTAGGTTTTGCACAATGTT 58.088 33.333 0.00 0.00 39.31 2.71
4666 5849 7.686438 TCTGCAAATTAAGCAATCTAACTCA 57.314 32.000 6.90 0.00 42.17 3.41
4668 5851 6.314018 TGCAAATTAAGCAATCTAACTCACG 58.686 36.000 3.25 0.00 39.39 4.35
4669 5852 5.739161 GCAAATTAAGCAATCTAACTCACGG 59.261 40.000 0.00 0.00 0.00 4.94
4674 5857 1.659098 GCAATCTAACTCACGGTTCCG 59.341 52.381 9.81 9.81 39.17 4.30
4679 5862 3.087031 TCTAACTCACGGTTCCGAAGAT 58.913 45.455 18.28 11.12 39.17 2.40
4680 5863 2.833631 AACTCACGGTTCCGAAGATT 57.166 45.000 18.28 6.83 31.69 2.40
4681 5864 2.080286 ACTCACGGTTCCGAAGATTG 57.920 50.000 18.28 5.44 0.00 2.67
4682 5865 1.343465 ACTCACGGTTCCGAAGATTGT 59.657 47.619 18.28 7.61 0.00 2.71
4683 5866 2.559668 ACTCACGGTTCCGAAGATTGTA 59.440 45.455 18.28 0.00 0.00 2.41
4684 5867 3.179830 CTCACGGTTCCGAAGATTGTAG 58.820 50.000 18.28 2.23 0.00 2.74
4685 5868 2.094390 TCACGGTTCCGAAGATTGTAGG 60.094 50.000 18.28 0.00 0.00 3.18
4686 5869 1.287425 CGGTTCCGAAGATTGTAGGC 58.713 55.000 5.19 0.00 0.00 3.93
4687 5870 1.404986 CGGTTCCGAAGATTGTAGGCA 60.405 52.381 5.19 0.00 0.00 4.75
4688 5871 2.280628 GGTTCCGAAGATTGTAGGCAG 58.719 52.381 0.00 0.00 0.00 4.85
4689 5872 2.280628 GTTCCGAAGATTGTAGGCAGG 58.719 52.381 0.00 0.00 0.00 4.85
4690 5873 1.568504 TCCGAAGATTGTAGGCAGGT 58.431 50.000 0.00 0.00 0.00 4.00
4691 5874 1.207089 TCCGAAGATTGTAGGCAGGTG 59.793 52.381 0.00 0.00 0.00 4.00
4692 5875 1.207089 CCGAAGATTGTAGGCAGGTGA 59.793 52.381 0.00 0.00 0.00 4.02
4693 5876 2.271800 CGAAGATTGTAGGCAGGTGAC 58.728 52.381 0.00 0.00 0.00 3.67
4694 5877 2.353704 CGAAGATTGTAGGCAGGTGACA 60.354 50.000 0.00 0.00 0.00 3.58
4695 5878 3.674997 GAAGATTGTAGGCAGGTGACAA 58.325 45.455 0.00 0.00 37.47 3.18
4696 5879 3.340814 AGATTGTAGGCAGGTGACAAG 57.659 47.619 0.00 0.00 36.57 3.16
4697 5880 2.906389 AGATTGTAGGCAGGTGACAAGA 59.094 45.455 0.00 0.00 36.57 3.02
4698 5881 2.543777 TTGTAGGCAGGTGACAAGAC 57.456 50.000 0.00 0.00 0.00 3.01
4699 5882 0.685097 TGTAGGCAGGTGACAAGACC 59.315 55.000 0.00 0.00 36.09 3.85
4700 5883 0.036294 GTAGGCAGGTGACAAGACCC 60.036 60.000 0.00 0.00 36.56 4.46
4701 5884 1.198759 TAGGCAGGTGACAAGACCCC 61.199 60.000 0.00 0.00 36.56 4.95
4702 5885 2.829384 GGCAGGTGACAAGACCCCA 61.829 63.158 0.00 0.00 36.56 4.96
4703 5886 1.302832 GCAGGTGACAAGACCCCAG 60.303 63.158 0.00 0.00 36.56 4.45
4704 5887 1.302832 CAGGTGACAAGACCCCAGC 60.303 63.158 0.00 0.00 36.56 4.85
4705 5888 2.034221 GGTGACAAGACCCCAGCC 59.966 66.667 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.600388 TCATTTTCTCCTTCTCCTTCGC 58.400 45.455 0.00 0.00 0.00 4.70
62 63 8.490311 TCTGTCTATCTCTGTCTTAATCTCTCA 58.510 37.037 0.00 0.00 0.00 3.27
72 73 8.271458 TCTGTTTATCTCTGTCTATCTCTGTCT 58.729 37.037 0.00 0.00 0.00 3.41
75 76 8.344831 CAGTCTGTTTATCTCTGTCTATCTCTG 58.655 40.741 0.00 0.00 0.00 3.35
81 82 8.645814 TTAACCAGTCTGTTTATCTCTGTCTA 57.354 34.615 0.00 0.00 0.00 2.59
83 84 6.311690 GCTTAACCAGTCTGTTTATCTCTGTC 59.688 42.308 0.00 0.00 0.00 3.51
84 85 6.166982 GCTTAACCAGTCTGTTTATCTCTGT 58.833 40.000 0.00 0.00 0.00 3.41
85 86 6.166279 TGCTTAACCAGTCTGTTTATCTCTG 58.834 40.000 0.00 0.00 0.00 3.35
129 131 8.921353 AGTGGTCGACATAAGAGTAGTATAAT 57.079 34.615 18.91 0.00 0.00 1.28
130 132 9.836864 TTAGTGGTCGACATAAGAGTAGTATAA 57.163 33.333 18.91 0.00 0.00 0.98
131 133 9.265901 GTTAGTGGTCGACATAAGAGTAGTATA 57.734 37.037 18.91 0.00 0.00 1.47
132 134 7.228308 GGTTAGTGGTCGACATAAGAGTAGTAT 59.772 40.741 18.91 0.00 0.00 2.12
133 135 6.540189 GGTTAGTGGTCGACATAAGAGTAGTA 59.460 42.308 18.91 0.00 0.00 1.82
134 136 5.356470 GGTTAGTGGTCGACATAAGAGTAGT 59.644 44.000 18.91 0.00 0.00 2.73
135 137 5.503683 CGGTTAGTGGTCGACATAAGAGTAG 60.504 48.000 18.91 0.00 0.00 2.57
136 138 4.333649 CGGTTAGTGGTCGACATAAGAGTA 59.666 45.833 18.91 0.07 0.00 2.59
137 139 3.128242 CGGTTAGTGGTCGACATAAGAGT 59.872 47.826 18.91 1.01 0.00 3.24
138 140 3.376234 TCGGTTAGTGGTCGACATAAGAG 59.624 47.826 18.91 9.48 0.00 2.85
139 141 3.346315 TCGGTTAGTGGTCGACATAAGA 58.654 45.455 18.91 5.33 0.00 2.10
150 152 4.021719 ACGGTATTCCATATCGGTTAGTGG 60.022 45.833 1.76 0.00 43.38 4.00
153 155 6.309737 GCTTTACGGTATTCCATATCGGTTAG 59.690 42.308 1.76 0.00 43.38 2.34
172 174 4.267536 CCCTACCCCACTAAAAGCTTTAC 58.732 47.826 13.10 0.00 0.00 2.01
207 209 1.017387 CGGCTTATTCTCCTGTTGGC 58.983 55.000 0.00 0.00 0.00 4.52
210 212 0.107165 GGGCGGCTTATTCTCCTGTT 60.107 55.000 9.56 0.00 0.00 3.16
213 215 1.802553 TAAGGGCGGCTTATTCTCCT 58.197 50.000 9.56 0.00 0.00 3.69
241 243 3.383825 AGTTTCTCCTGCCGACGTATTAT 59.616 43.478 0.00 0.00 0.00 1.28
248 250 1.433534 CTTGAGTTTCTCCTGCCGAC 58.566 55.000 0.00 0.00 0.00 4.79
260 262 7.992008 TGAAATTCGTTCTTTTACCTTGAGTT 58.008 30.769 0.00 0.00 37.13 3.01
265 267 9.353999 GCATTATGAAATTCGTTCTTTTACCTT 57.646 29.630 0.00 0.00 37.13 3.50
382 384 3.119459 TCTCTCTCTGGTACAAATGCGAC 60.119 47.826 0.00 0.00 38.70 5.19
417 419 0.543749 AGAGCAGGTTCACCTATGGC 59.456 55.000 0.00 0.00 46.65 4.40
443 445 3.239587 TCGTCTCTGTTTGTCAACACA 57.760 42.857 0.00 0.00 38.03 3.72
456 458 4.020396 TCTGTAGTGACTAGGTTCGTCTCT 60.020 45.833 0.00 0.00 38.39 3.10
457 459 4.252073 TCTGTAGTGACTAGGTTCGTCTC 58.748 47.826 0.00 0.00 32.70 3.36
460 462 3.695060 CCATCTGTAGTGACTAGGTTCGT 59.305 47.826 0.00 0.00 0.00 3.85
461 463 3.066900 CCCATCTGTAGTGACTAGGTTCG 59.933 52.174 0.00 0.00 0.00 3.95
469 471 3.196685 AGAGAAAGCCCATCTGTAGTGAC 59.803 47.826 0.00 0.00 0.00 3.67
476 478 1.661341 CGGAAGAGAAAGCCCATCTG 58.339 55.000 0.00 0.00 0.00 2.90
509 512 8.561738 AATTCTTCTTTTATCTTTACAGCGGA 57.438 30.769 0.00 0.00 0.00 5.54
510 513 7.910683 GGAATTCTTCTTTTATCTTTACAGCGG 59.089 37.037 5.23 0.00 0.00 5.52
511 514 8.669243 AGGAATTCTTCTTTTATCTTTACAGCG 58.331 33.333 5.23 0.00 0.00 5.18
555 560 1.172180 CCGCTCTTTGCTGTTTCCCA 61.172 55.000 0.00 0.00 40.11 4.37
564 1290 0.593128 AATGTCACACCGCTCTTTGC 59.407 50.000 0.00 0.00 38.57 3.68
573 1299 3.572255 ACCAACCATAACAATGTCACACC 59.428 43.478 0.00 0.00 0.00 4.16
577 1303 3.638627 TGCAACCAACCATAACAATGTCA 59.361 39.130 0.00 0.00 0.00 3.58
579 1305 4.282957 TGATGCAACCAACCATAACAATGT 59.717 37.500 0.00 0.00 0.00 2.71
602 1328 5.540337 TGTTAGAGAGAAGGTGTCAACATCT 59.460 40.000 0.00 0.00 39.39 2.90
632 1358 1.002033 GCAACTTGAGAGCCAACAGTG 60.002 52.381 0.00 0.00 0.00 3.66
638 1364 1.300971 GCATCGCAACTTGAGAGCCA 61.301 55.000 1.59 0.00 27.73 4.75
652 1386 2.650408 GAACGACGACATGCGCATCG 62.650 60.000 26.83 26.83 46.04 3.84
699 1458 7.818930 GGCATTTTCTTTTCATCCTTGTTGATA 59.181 33.333 0.00 0.00 0.00 2.15
709 1468 6.128200 GGAAACCATGGCATTTTCTTTTCATC 60.128 38.462 19.97 4.41 31.21 2.92
713 1472 5.046288 TGGAAACCATGGCATTTTCTTTT 57.954 34.783 19.97 8.79 31.21 2.27
737 1501 0.823460 ACCAAACACAACTGCTTGGG 59.177 50.000 7.58 0.00 44.85 4.12
758 1528 2.754552 GCCACTCACAGCAAATGGAATA 59.245 45.455 0.00 0.00 31.69 1.75
778 1563 2.235898 TCCAAAAATATTGTGGCAGGGC 59.764 45.455 11.89 0.00 32.10 5.19
779 1564 4.758773 ATCCAAAAATATTGTGGCAGGG 57.241 40.909 11.89 0.00 32.10 4.45
780 1565 5.732633 TGAATCCAAAAATATTGTGGCAGG 58.267 37.500 11.89 0.00 32.10 4.85
781 1566 6.632909 TCTGAATCCAAAAATATTGTGGCAG 58.367 36.000 11.89 12.62 32.10 4.85
783 1568 7.322664 TCTTCTGAATCCAAAAATATTGTGGC 58.677 34.615 11.89 2.18 32.10 5.01
791 1576 7.093771 GGTGTGGTATCTTCTGAATCCAAAAAT 60.094 37.037 0.00 0.00 33.41 1.82
792 1577 6.208599 GGTGTGGTATCTTCTGAATCCAAAAA 59.791 38.462 0.00 0.00 33.41 1.94
793 1578 5.710099 GGTGTGGTATCTTCTGAATCCAAAA 59.290 40.000 0.00 0.00 33.41 2.44
794 1579 5.222027 TGGTGTGGTATCTTCTGAATCCAAA 60.222 40.000 0.00 0.00 33.41 3.28
811 1596 0.682855 ACTTGGTGGTGTTGGTGTGG 60.683 55.000 0.00 0.00 0.00 4.17
814 1599 1.135141 CACAACTTGGTGGTGTTGGTG 60.135 52.381 10.03 3.52 45.79 4.17
815 1600 1.181786 CACAACTTGGTGGTGTTGGT 58.818 50.000 10.03 0.00 45.79 3.67
820 1605 0.381801 GCTCACACAACTTGGTGGTG 59.618 55.000 3.90 3.90 42.66 4.17
821 1606 0.751643 GGCTCACACAACTTGGTGGT 60.752 55.000 9.28 0.00 43.08 4.16
823 1608 2.792500 TGGCTCACACAACTTGGTG 58.208 52.632 0.00 0.00 44.35 4.17
848 1682 2.125512 CACGAGGGCTCCTTTCCG 60.126 66.667 0.00 0.00 31.76 4.30
849 1683 1.079057 GACACGAGGGCTCCTTTCC 60.079 63.158 0.00 0.00 31.76 3.13
851 1685 2.943978 CGGACACGAGGGCTCCTTT 61.944 63.158 0.00 0.00 44.60 3.11
852 1686 3.382832 CGGACACGAGGGCTCCTT 61.383 66.667 0.00 0.00 44.60 3.36
1084 1919 1.060729 GAGGAGGAGGGAAATAGGGC 58.939 60.000 0.00 0.00 0.00 5.19
1086 1921 1.343069 CGGAGGAGGAGGGAAATAGG 58.657 60.000 0.00 0.00 0.00 2.57
1494 2353 3.830744 TTCAAGGACGGAGAAACTGAA 57.169 42.857 0.00 0.00 0.00 3.02
1517 2376 3.706594 TCCTCTGGACAGCGAGATTTAAT 59.293 43.478 0.00 0.00 0.00 1.40
1524 2383 2.003658 GAGCTCCTCTGGACAGCGAG 62.004 65.000 0.87 10.21 29.72 5.03
1526 2385 2.346541 TGAGCTCCTCTGGACAGCG 61.347 63.158 12.15 0.00 29.72 5.18
1565 2443 2.934570 GCAGCAACCACCACCATGG 61.935 63.158 11.19 11.19 46.10 3.66
1634 2520 2.592308 GAGTGGAGGATGTGGCCC 59.408 66.667 0.00 0.00 0.00 5.80
1703 2589 2.100989 GAGGATCGAGGTGTAAGGTGT 58.899 52.381 0.00 0.00 0.00 4.16
1704 2590 2.379972 AGAGGATCGAGGTGTAAGGTG 58.620 52.381 0.00 0.00 42.67 4.00
1705 2591 2.830651 AGAGGATCGAGGTGTAAGGT 57.169 50.000 0.00 0.00 42.67 3.50
1706 2592 3.292460 AGAAGAGGATCGAGGTGTAAGG 58.708 50.000 0.00 0.00 42.67 2.69
1707 2593 4.677584 CAAGAAGAGGATCGAGGTGTAAG 58.322 47.826 0.00 0.00 42.67 2.34
1708 2594 3.119101 GCAAGAAGAGGATCGAGGTGTAA 60.119 47.826 0.00 0.00 42.67 2.41
1740 2626 7.944729 AATAAACTCACAGCTATTGGAACAT 57.055 32.000 0.00 0.00 39.30 2.71
1745 2631 7.283127 ACACCATAATAAACTCACAGCTATTGG 59.717 37.037 0.00 0.00 0.00 3.16
1765 2658 7.823745 AAAGAGACATTTTTACTGACACCAT 57.176 32.000 0.00 0.00 0.00 3.55
1781 2674 4.037923 GCAGGTTTGATTGGAAAAGAGACA 59.962 41.667 0.00 0.00 0.00 3.41
1782 2675 4.037923 TGCAGGTTTGATTGGAAAAGAGAC 59.962 41.667 0.00 0.00 0.00 3.36
1877 2770 0.918258 TGGAATCTATGCAGCCCACA 59.082 50.000 0.00 0.00 0.00 4.17
1884 2777 2.424601 GCAACAGCTTGGAATCTATGCA 59.575 45.455 7.19 0.00 0.00 3.96
1885 2778 2.686915 AGCAACAGCTTGGAATCTATGC 59.313 45.455 0.00 0.00 34.18 3.14
1886 2779 3.488721 GCAGCAACAGCTTGGAATCTATG 60.489 47.826 0.00 0.00 36.19 2.23
1887 2780 2.686915 GCAGCAACAGCTTGGAATCTAT 59.313 45.455 0.00 0.00 36.19 1.98
1890 2783 0.886563 AGCAGCAACAGCTTGGAATC 59.113 50.000 0.00 0.00 39.87 2.52
1899 2796 2.291465 TGAGCAAAGTAAGCAGCAACAG 59.709 45.455 0.00 0.00 0.00 3.16
1931 2828 3.229276 TGCGCAGGGTTAATCAAATTG 57.771 42.857 5.66 0.00 0.00 2.32
1948 2846 2.661504 TTGTTCAAGACATCGTTGCG 57.338 45.000 0.00 0.00 38.26 4.85
1950 2848 6.624526 GCAAAAATTTGTTCAAGACATCGTTG 59.375 34.615 7.64 0.00 40.24 4.10
1951 2849 6.534793 AGCAAAAATTTGTTCAAGACATCGTT 59.465 30.769 7.64 0.00 40.24 3.85
1955 2853 5.585445 TGCAGCAAAAATTTGTTCAAGACAT 59.415 32.000 7.64 0.00 40.24 3.06
1993 2891 0.176910 GGCTCCTGTACAGCTTCTCC 59.823 60.000 17.86 9.29 37.05 3.71
2126 3028 7.828717 TGTTACCTCATGAGCAAATTAATCAGA 59.171 33.333 17.76 0.00 0.00 3.27
2153 3055 5.634859 CAGCAACCAGATTTTACCAAACATC 59.365 40.000 0.00 0.00 0.00 3.06
2168 3070 4.036734 ACAAACAATACAGTCAGCAACCAG 59.963 41.667 0.00 0.00 0.00 4.00
2171 3073 4.920376 ACACAAACAATACAGTCAGCAAC 58.080 39.130 0.00 0.00 0.00 4.17
2272 3180 3.127203 ACGTCACTATGTCCTTCTTCTCG 59.873 47.826 0.00 0.00 0.00 4.04
2287 3195 1.442184 GCATGTCGTCGACGTCACT 60.442 57.895 33.56 21.64 39.83 3.41
2288 3196 1.442184 AGCATGTCGTCGACGTCAC 60.442 57.895 33.56 26.48 39.83 3.67
2425 3345 1.555075 TGGCAGGAAGTAAGGCTACAG 59.445 52.381 0.00 0.00 0.00 2.74
2567 3488 1.537814 CGTGGTGGTGCAGGTAGGTA 61.538 60.000 0.00 0.00 0.00 3.08
2615 3536 5.385198 AGCTCTGTTGATTTTACCTTTCCA 58.615 37.500 0.00 0.00 0.00 3.53
2629 3550 1.061131 CCGCGAATTGTAGCTCTGTTG 59.939 52.381 8.23 0.00 0.00 3.33
2644 3571 0.882484 TGTGACTTGCAATTCCGCGA 60.882 50.000 8.23 0.00 33.35 5.87
2645 3572 0.168788 ATGTGACTTGCAATTCCGCG 59.831 50.000 13.60 0.00 33.35 6.46
2647 3574 1.791555 GCGATGTGACTTGCAATTCCG 60.792 52.381 13.60 10.62 0.00 4.30
2660 3618 3.809279 TGGTATGCAGATTAAGCGATGTG 59.191 43.478 0.00 0.00 33.85 3.21
2680 3638 3.188460 ACGCACTAGTTTTAGCACAATGG 59.812 43.478 0.00 0.00 0.00 3.16
2689 3647 8.245491 TCACACTATATCAACGCACTAGTTTTA 58.755 33.333 0.00 0.00 30.96 1.52
2707 3694 7.703621 GCAGCAATTATTCAAACATCACACTAT 59.296 33.333 0.00 0.00 0.00 2.12
2708 3695 7.028962 GCAGCAATTATTCAAACATCACACTA 58.971 34.615 0.00 0.00 0.00 2.74
2709 3696 5.865552 GCAGCAATTATTCAAACATCACACT 59.134 36.000 0.00 0.00 0.00 3.55
2710 3697 5.865552 AGCAGCAATTATTCAAACATCACAC 59.134 36.000 0.00 0.00 0.00 3.82
2711 3698 6.028146 AGCAGCAATTATTCAAACATCACA 57.972 33.333 0.00 0.00 0.00 3.58
2714 3701 7.543172 TCTTCAAGCAGCAATTATTCAAACATC 59.457 33.333 0.00 0.00 0.00 3.06
2715 3702 7.380536 TCTTCAAGCAGCAATTATTCAAACAT 58.619 30.769 0.00 0.00 0.00 2.71
2716 3703 6.747125 TCTTCAAGCAGCAATTATTCAAACA 58.253 32.000 0.00 0.00 0.00 2.83
2718 3705 9.357652 GTTATCTTCAAGCAGCAATTATTCAAA 57.642 29.630 0.00 0.00 0.00 2.69
2720 3707 8.284945 AGTTATCTTCAAGCAGCAATTATTCA 57.715 30.769 0.00 0.00 0.00 2.57
2722 3709 8.517062 AGAGTTATCTTCAAGCAGCAATTATT 57.483 30.769 0.00 0.00 28.57 1.40
2733 3877 8.539770 TGACAGCTTAAAGAGTTATCTTCAAG 57.460 34.615 0.00 0.00 45.25 3.02
2788 3932 8.375506 TGTTTATTCAGACTGTTCAATCCTAGT 58.624 33.333 1.59 0.00 0.00 2.57
2789 3933 8.777865 TGTTTATTCAGACTGTTCAATCCTAG 57.222 34.615 1.59 0.00 0.00 3.02
2821 3965 3.366052 TTATGAAGGAAAGGAGGCCAC 57.634 47.619 5.01 0.00 0.00 5.01
2824 3968 4.158579 CCACTTTTATGAAGGAAAGGAGGC 59.841 45.833 0.00 0.00 37.22 4.70
2851 3995 3.831911 CCTCTTTTATGCTTGTCCCCAAA 59.168 43.478 0.00 0.00 0.00 3.28
2854 3998 2.755103 CACCTCTTTTATGCTTGTCCCC 59.245 50.000 0.00 0.00 0.00 4.81
2857 4001 5.948992 ACTTCACCTCTTTTATGCTTGTC 57.051 39.130 0.00 0.00 0.00 3.18
2858 4002 6.534634 ACTACTTCACCTCTTTTATGCTTGT 58.465 36.000 0.00 0.00 0.00 3.16
2903 4064 4.338400 AGGTGGCTTCTGAAACTTTGTAAC 59.662 41.667 0.00 0.00 0.00 2.50
2904 4065 4.532834 AGGTGGCTTCTGAAACTTTGTAA 58.467 39.130 0.00 0.00 0.00 2.41
2907 4068 3.633986 AGAAGGTGGCTTCTGAAACTTTG 59.366 43.478 0.00 0.00 41.61 2.77
2908 4069 3.885901 GAGAAGGTGGCTTCTGAAACTTT 59.114 43.478 0.00 0.00 43.03 2.66
2909 4070 3.117888 TGAGAAGGTGGCTTCTGAAACTT 60.118 43.478 0.00 0.00 43.03 2.66
2911 4072 2.810852 CTGAGAAGGTGGCTTCTGAAAC 59.189 50.000 0.00 0.00 43.03 2.78
2912 4073 2.811873 GCTGAGAAGGTGGCTTCTGAAA 60.812 50.000 0.00 0.00 43.03 2.69
2913 4074 1.271054 GCTGAGAAGGTGGCTTCTGAA 60.271 52.381 0.00 0.00 43.03 3.02
2928 4092 2.426024 CCAATTGTCATGGAAGGCTGAG 59.574 50.000 4.43 0.00 40.56 3.35
2937 4101 5.818136 ACGTTATCTTCCAATTGTCATGG 57.182 39.130 4.43 0.00 39.41 3.66
2946 4113 7.062749 AGATATGCCTTACGTTATCTTCCAA 57.937 36.000 0.00 0.00 0.00 3.53
3198 4368 6.349243 TGAAGGATTTGAGCAATGACAAAT 57.651 33.333 14.73 14.73 45.37 2.32
3224 4394 6.551227 AGTGATCACATACAGGAGCAGTAATA 59.449 38.462 27.02 0.00 31.82 0.98
3343 4514 1.220749 CCCGATGTCGTGGTGGATT 59.779 57.895 1.44 0.00 37.74 3.01
3431 4602 0.032813 AGGCAGGGAACATCAATGGG 60.033 55.000 0.00 0.00 0.00 4.00
3434 4605 0.685458 GGCAGGCAGGGAACATCAAT 60.685 55.000 0.00 0.00 0.00 2.57
3633 4804 1.753930 TTATGTCTCCGGTGTCGCTA 58.246 50.000 0.00 0.00 34.56 4.26
3715 4886 2.846206 AGCATCCCCACAAAGAGTATGA 59.154 45.455 0.00 0.00 0.00 2.15
3779 4951 1.174712 TGCTGAGGAACTTGGCAAGC 61.175 55.000 26.45 11.73 41.55 4.01
3801 4973 2.436417 GTCCACCTGCTTGATTTGCTA 58.564 47.619 0.00 0.00 0.00 3.49
3802 4974 1.251251 GTCCACCTGCTTGATTTGCT 58.749 50.000 0.00 0.00 0.00 3.91
3843 5015 7.090173 CCTATTGTACAACCAAAAATCCAGTG 58.910 38.462 11.22 0.00 0.00 3.66
3902 5074 5.588648 TGTCCGAAGAATCACTTGTTTCTTT 59.411 36.000 13.85 2.37 41.51 2.52
3921 5093 1.871772 CTGCTTTGGCTCTTGTCCG 59.128 57.895 0.00 0.00 39.59 4.79
3934 5106 2.479566 TCCAATCTTTCGAGCTGCTT 57.520 45.000 2.53 0.00 0.00 3.91
3935 5107 2.479566 TTCCAATCTTTCGAGCTGCT 57.520 45.000 0.00 0.00 0.00 4.24
3943 5115 6.867662 TCAGACAAGTCTTTCCAATCTTTC 57.132 37.500 0.00 0.00 37.98 2.62
3956 5130 2.087646 GCCCCTTGAATCAGACAAGTC 58.912 52.381 0.00 0.00 41.88 3.01
3962 5136 3.675348 ATGAATGCCCCTTGAATCAGA 57.325 42.857 0.00 0.00 0.00 3.27
3967 5141 2.230992 CGAACAATGAATGCCCCTTGAA 59.769 45.455 0.00 0.00 0.00 2.69
3997 5171 8.967918 ACTGCTCTATAGTTGTAATAACAGTGA 58.032 33.333 0.00 0.00 36.83 3.41
4012 5187 7.042187 CCAGCTGAAACAAATACTGCTCTATAG 60.042 40.741 17.39 0.00 36.88 1.31
4028 5203 2.436417 TGCATAAGGACCAGCTGAAAC 58.564 47.619 17.39 4.21 0.00 2.78
4030 5205 4.712051 ATATGCATAAGGACCAGCTGAA 57.288 40.909 17.39 0.00 0.00 3.02
4060 5235 3.873952 GGAATTAAGCAGCGATCTTCACT 59.126 43.478 0.00 0.00 0.00 3.41
4070 5245 4.142315 TGCAAAGATCTGGAATTAAGCAGC 60.142 41.667 0.00 0.00 0.00 5.25
4079 5254 1.071542 TGTCCGTGCAAAGATCTGGAA 59.928 47.619 0.00 0.00 0.00 3.53
4095 5273 5.901884 CGCGTAAATTCTATTTCACATGTCC 59.098 40.000 0.00 0.00 0.00 4.02
4096 5274 6.408039 CACGCGTAAATTCTATTTCACATGTC 59.592 38.462 13.44 0.00 0.00 3.06
4146 5324 5.519808 ACTGACCAATCACTAGGACAGATA 58.480 41.667 15.65 0.00 46.12 1.98
4160 5338 3.648067 TCTGAAGAGGACAACTGACCAAT 59.352 43.478 1.16 0.00 32.26 3.16
4234 5416 3.181329 TCACAGAACCCATATGACCACT 58.819 45.455 3.65 0.00 0.00 4.00
4236 5418 3.136443 GGATCACAGAACCCATATGACCA 59.864 47.826 3.65 0.00 0.00 4.02
4263 5445 3.070159 CCACAGAGAGTCAAGAACCAAGA 59.930 47.826 0.00 0.00 0.00 3.02
4267 5449 2.289133 GGACCACAGAGAGTCAAGAACC 60.289 54.545 0.00 0.00 34.58 3.62
4278 5460 4.967036 AGAAGAAAAAGAGGACCACAGAG 58.033 43.478 0.00 0.00 0.00 3.35
4291 5473 9.489084 TGATGATCGTTCTAAGAAGAAGAAAAA 57.511 29.630 0.00 0.00 42.40 1.94
4309 5491 7.637229 AGCTTTCAACATAAATCTGATGATCG 58.363 34.615 0.00 0.00 29.47 3.69
4332 5514 0.394762 TCAATGGGAGCATGGTGAGC 60.395 55.000 0.00 0.00 0.00 4.26
4344 5526 2.883386 GCTCAGCTAGGATTTCAATGGG 59.117 50.000 0.00 0.00 0.00 4.00
4355 5538 5.016051 TGATAAAACAGAGCTCAGCTAGG 57.984 43.478 17.77 0.00 39.88 3.02
4371 5554 7.465379 CGACAATAATTCGGCTTCACTGATAAA 60.465 37.037 0.00 0.00 32.28 1.40
4375 5558 3.616821 CGACAATAATTCGGCTTCACTGA 59.383 43.478 0.00 0.00 32.66 3.41
4431 5614 3.691609 CAGGAGACTTTTATTGGGTCTGC 59.308 47.826 5.87 5.87 44.74 4.26
4434 5617 2.678336 CGCAGGAGACTTTTATTGGGTC 59.322 50.000 0.00 0.00 40.21 4.46
4435 5618 2.711542 CGCAGGAGACTTTTATTGGGT 58.288 47.619 0.00 0.00 40.21 4.51
4451 5634 0.447801 CGGGATCAAAAGAACCGCAG 59.552 55.000 0.00 0.00 37.93 5.18
4459 5642 1.519408 ACAACCGACGGGATCAAAAG 58.481 50.000 20.00 1.02 36.97 2.27
4465 5648 2.498481 TGAAATCTACAACCGACGGGAT 59.502 45.455 20.00 7.80 36.97 3.85
4468 5651 1.652124 CGTGAAATCTACAACCGACGG 59.348 52.381 13.61 13.61 0.00 4.79
4490 5673 0.823769 TCTGAGCACCAGACGACAGT 60.824 55.000 4.92 0.00 46.38 3.55
4491 5674 1.959848 TCTGAGCACCAGACGACAG 59.040 57.895 4.92 0.00 46.38 3.51
4499 5682 2.092429 ACCAAAGAAAGTCTGAGCACCA 60.092 45.455 0.00 0.00 0.00 4.17
4506 5689 0.593128 CCGCCACCAAAGAAAGTCTG 59.407 55.000 0.00 0.00 0.00 3.51
4509 5692 1.454847 TGCCGCCACCAAAGAAAGT 60.455 52.632 0.00 0.00 0.00 2.66
4618 5801 5.911752 ACATTGTGCAAAACCTAATGTCAA 58.088 33.333 0.00 0.00 0.00 3.18
4642 5825 7.530010 GTGAGTTAGATTGCTTAATTTGCAGA 58.470 34.615 6.05 0.00 41.71 4.26
4666 5849 1.405121 GCCTACAATCTTCGGAACCGT 60.405 52.381 12.93 0.00 40.74 4.83
4668 5851 2.280628 CTGCCTACAATCTTCGGAACC 58.719 52.381 0.00 0.00 0.00 3.62
4669 5852 2.280628 CCTGCCTACAATCTTCGGAAC 58.719 52.381 0.00 0.00 0.00 3.62
4674 5857 3.334583 TGTCACCTGCCTACAATCTTC 57.665 47.619 0.00 0.00 0.00 2.87
4679 5862 1.071699 GGTCTTGTCACCTGCCTACAA 59.928 52.381 0.00 0.00 33.08 2.41
4680 5863 0.685097 GGTCTTGTCACCTGCCTACA 59.315 55.000 0.00 0.00 33.08 2.74
4681 5864 0.036294 GGGTCTTGTCACCTGCCTAC 60.036 60.000 0.00 0.00 36.57 3.18
4682 5865 1.198759 GGGGTCTTGTCACCTGCCTA 61.199 60.000 0.00 0.00 36.57 3.93
4683 5866 2.529744 GGGGTCTTGTCACCTGCCT 61.530 63.158 0.00 0.00 36.57 4.75
4684 5867 2.034221 GGGGTCTTGTCACCTGCC 59.966 66.667 0.00 0.00 36.57 4.85
4685 5868 1.302832 CTGGGGTCTTGTCACCTGC 60.303 63.158 0.00 0.00 36.57 4.85
4686 5869 1.302832 GCTGGGGTCTTGTCACCTG 60.303 63.158 0.00 0.00 36.57 4.00
4687 5870 2.529744 GGCTGGGGTCTTGTCACCT 61.530 63.158 0.00 0.00 36.57 4.00
4688 5871 2.034221 GGCTGGGGTCTTGTCACC 59.966 66.667 0.00 0.00 35.42 4.02


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

AutoCloner maintained by Alex Coulton.