Multiple sequence alignment - TraesCS2B01G048400

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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 TraesCS2B01G048400 chr2B 100.000 3299 0 0 1 3299 24088537 24091835 0.000000e+00 6093.0
1 TraesCS2B01G048400 chr2B 87.619 1785 156 39 987 2734 17874042 17872286 0.000000e+00 2012.0
2 TraesCS2B01G048400 chr2B 80.608 691 68 32 609 1270 17883694 17883041 1.070000e-129 473.0
3 TraesCS2B01G048400 chr2D 92.151 2064 103 28 589 2612 13421009 13423053 0.000000e+00 2859.0
4 TraesCS2B01G048400 chr2D 86.636 1766 175 43 961 2714 11509941 11508225 0.000000e+00 1897.0
5 TraesCS2B01G048400 chr2D 92.733 1032 75 0 1299 2330 617052674 617053705 0.000000e+00 1491.0
6 TraesCS2B01G048400 chr2D 91.816 1063 87 0 1297 2359 11477722 11476660 0.000000e+00 1482.0
7 TraesCS2B01G048400 chr2D 93.254 252 13 4 960 1209 11478088 11477839 5.200000e-98 368.0
8 TraesCS2B01G048400 chr2D 78.369 282 24 18 3027 3299 13424242 13424495 7.380000e-32 148.0
9 TraesCS2B01G048400 chr2A 91.714 1750 97 18 686 2405 15394541 15396272 0.000000e+00 2385.0
10 TraesCS2B01G048400 chr2A 90.755 1417 99 20 960 2375 12073521 12072136 0.000000e+00 1862.0
11 TraesCS2B01G048400 chr2A 87.393 1642 147 34 748 2366 12048848 12047244 0.000000e+00 1831.0
12 TraesCS2B01G048400 chr2A 91.820 1308 87 8 995 2300 12103307 12102018 0.000000e+00 1805.0
13 TraesCS2B01G048400 chr2A 90.652 353 17 6 2264 2612 15398761 15399101 3.880000e-124 455.0
14 TraesCS2B01G048400 chr2A 92.419 277 21 0 3023 3299 15399775 15400051 2.390000e-106 396.0
15 TraesCS2B01G048400 chr7B 92.338 509 9 15 1 495 12274257 12274749 0.000000e+00 697.0
16 TraesCS2B01G048400 chr7B 93.632 424 13 1 1 410 12267783 12267360 3.620000e-174 621.0
17 TraesCS2B01G048400 chr7B 93.372 347 9 1 1 333 12289065 12289411 4.910000e-138 501.0
18 TraesCS2B01G048400 chr7B 88.972 399 19 7 1 399 93446408 93446035 1.390000e-128 470.0
19 TraesCS2B01G048400 chr7B 88.636 396 20 7 1 396 93467434 93467804 3.000000e-125 459.0
20 TraesCS2B01G048400 chr7B 87.535 361 17 10 1 361 93460231 93460563 3.090000e-105 392.0
21 TraesCS2B01G048400 chr7B 86.835 357 21 8 1 357 93445157 93444827 3.110000e-100 375.0
22 TraesCS2B01G048400 chr7B 87.387 333 14 7 1 330 652115425 652115732 1.130000e-94 357.0
23 TraesCS2B01G048400 chr7B 86.667 330 19 7 1 330 93461457 93461761 3.150000e-90 342.0
24 TraesCS2B01G048400 chr7B 87.302 315 14 5 1 315 652129514 652129802 1.470000e-88 337.0
25 TraesCS2B01G048400 chr7B 86.420 324 19 3 1 324 652089854 652090152 6.820000e-87 331.0
26 TraesCS2B01G048400 chr7B 87.826 115 13 1 382 495 12289379 12289493 2.070000e-27 134.0
27 TraesCS2B01G048400 chr7B 91.892 74 6 0 422 495 652121718 652121791 1.620000e-18 104.0
28 TraesCS2B01G048400 chr7A 79.762 252 30 12 2486 2734 352181624 352181857 2.630000e-36 163.0
29 TraesCS2B01G048400 chr6B 90.099 101 5 5 394 491 31025266 31025168 3.460000e-25 126.0
30 TraesCS2B01G048400 chr3B 80.000 140 24 4 358 495 778255486 778255349 2.090000e-17 100.0
31 TraesCS2B01G048400 chrUn 90.411 73 7 0 2739 2811 93409620 93409692 2.710000e-16 97.1
32 TraesCS2B01G048400 chrUn 90.411 73 7 0 2739 2811 216518591 216518663 2.710000e-16 97.1
33 TraesCS2B01G048400 chrUn 90.411 73 7 0 2739 2811 216521979 216522051 2.710000e-16 97.1
34 TraesCS2B01G048400 chrUn 90.411 73 7 0 2739 2811 372771642 372771714 2.710000e-16 97.1
35 TraesCS2B01G048400 chr6D 90.411 73 7 0 2739 2811 168254937 168254865 2.710000e-16 97.1
36 TraesCS2B01G048400 chr6D 90.411 73 7 0 2739 2811 212227583 212227655 2.710000e-16 97.1
37 TraesCS2B01G048400 chr4D 90.411 73 7 0 2739 2811 78739260 78739332 2.710000e-16 97.1
38 TraesCS2B01G048400 chr3D 87.952 83 9 1 2730 2811 571591979 571592061 2.710000e-16 97.1
39 TraesCS2B01G048400 chr1D 90.411 73 7 0 2739 2811 397088920 397088992 2.710000e-16 97.1
40 TraesCS2B01G048400 chr5D 93.548 62 4 0 431 492 414065186 414065247 3.510000e-15 93.5


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 TraesCS2B01G048400 chr2B 24088537 24091835 3298 False 6093.000000 6093 100.0000 1 3299 1 chr2B.!!$F1 3298
1 TraesCS2B01G048400 chr2B 17872286 17874042 1756 True 2012.000000 2012 87.6190 987 2734 1 chr2B.!!$R1 1747
2 TraesCS2B01G048400 chr2B 17883041 17883694 653 True 473.000000 473 80.6080 609 1270 1 chr2B.!!$R2 661
3 TraesCS2B01G048400 chr2D 11508225 11509941 1716 True 1897.000000 1897 86.6360 961 2714 1 chr2D.!!$R1 1753
4 TraesCS2B01G048400 chr2D 13421009 13424495 3486 False 1503.500000 2859 85.2600 589 3299 2 chr2D.!!$F2 2710
5 TraesCS2B01G048400 chr2D 617052674 617053705 1031 False 1491.000000 1491 92.7330 1299 2330 1 chr2D.!!$F1 1031
6 TraesCS2B01G048400 chr2D 11476660 11478088 1428 True 925.000000 1482 92.5350 960 2359 2 chr2D.!!$R2 1399
7 TraesCS2B01G048400 chr2A 12072136 12073521 1385 True 1862.000000 1862 90.7550 960 2375 1 chr2A.!!$R2 1415
8 TraesCS2B01G048400 chr2A 12047244 12048848 1604 True 1831.000000 1831 87.3930 748 2366 1 chr2A.!!$R1 1618
9 TraesCS2B01G048400 chr2A 12102018 12103307 1289 True 1805.000000 1805 91.8200 995 2300 1 chr2A.!!$R3 1305
10 TraesCS2B01G048400 chr2A 15394541 15400051 5510 False 1078.666667 2385 91.5950 686 3299 3 chr2A.!!$F1 2613
11 TraesCS2B01G048400 chr7B 93444827 93446408 1581 True 422.500000 470 87.9035 1 399 2 chr7B.!!$R2 398
12 TraesCS2B01G048400 chr7B 93460231 93461761 1530 False 367.000000 392 87.1010 1 361 2 chr7B.!!$F8 360

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
562 566 0.035056 ACAATTCTCGGGCCTTCAGG 60.035 55.0 0.84 0.0 38.53 3.86 F
563 567 0.253044 CAATTCTCGGGCCTTCAGGA 59.747 55.0 0.84 0.0 37.39 3.86 F
1992 2399 0.251341 AGGACGCCTTCAAGCCAATT 60.251 50.0 0.00 0.0 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2399 0.904649 AGTTCCAGTCATCGATGCCA 59.095 50.000 20.81 1.1 0.0 4.92 R
2205 2612 2.190578 CAGTCCATTCCCTCGCCC 59.809 66.667 0.00 0.0 0.0 6.13 R
2833 5965 0.038599 TACGACTAGGCCCACACAGA 59.961 55.000 0.00 0.0 0.0 3.41 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
161 162 7.420800 CAACTCTTGCCATGATTTATACTTCC 58.579 38.462 0.00 0.00 0.00 3.46
162 163 6.662755 ACTCTTGCCATGATTTATACTTCCA 58.337 36.000 0.00 0.00 0.00 3.53
163 164 6.543831 ACTCTTGCCATGATTTATACTTCCAC 59.456 38.462 0.00 0.00 0.00 4.02
164 165 5.527214 TCTTGCCATGATTTATACTTCCACG 59.473 40.000 0.00 0.00 0.00 4.94
165 166 3.563808 TGCCATGATTTATACTTCCACGC 59.436 43.478 0.00 0.00 0.00 5.34
170 171 3.625764 TGATTTATACTTCCACGCCTTGC 59.374 43.478 0.00 0.00 0.00 4.01
178 179 4.424566 CACGCCTTGCATGCACCC 62.425 66.667 22.58 10.55 0.00 4.61
181 182 2.677524 GCCTTGCATGCACCCTGA 60.678 61.111 22.58 4.02 0.00 3.86
186 187 1.611977 CTTGCATGCACCCTGATATGG 59.388 52.381 22.58 0.00 0.00 2.74
245 246 3.703001 TGGATGAAGGGTCTTGTCTTC 57.297 47.619 0.00 0.00 39.66 2.87
252 253 6.877611 TGAAGGGTCTTGTCTTCAATTAAC 57.122 37.500 3.63 0.00 44.14 2.01
253 254 6.601332 TGAAGGGTCTTGTCTTCAATTAACT 58.399 36.000 3.63 0.00 44.14 2.24
254 255 6.710744 TGAAGGGTCTTGTCTTCAATTAACTC 59.289 38.462 3.63 0.00 44.14 3.01
255 256 5.561679 AGGGTCTTGTCTTCAATTAACTCC 58.438 41.667 0.00 0.00 32.82 3.85
256 257 5.310857 AGGGTCTTGTCTTCAATTAACTCCT 59.689 40.000 0.00 0.00 32.82 3.69
257 258 6.004574 GGGTCTTGTCTTCAATTAACTCCTT 58.995 40.000 0.00 0.00 32.82 3.36
260 261 7.391833 GGTCTTGTCTTCAATTAACTCCTTGAT 59.608 37.037 0.00 0.00 31.83 2.57
267 268 7.611855 TCTTCAATTAACTCCTTGATCTTTCCC 59.388 37.037 0.00 0.00 31.83 3.97
453 457 4.918588 GGTCTACCCCACCCATATTATTG 58.081 47.826 0.00 0.00 0.00 1.90
454 458 4.600111 GGTCTACCCCACCCATATTATTGA 59.400 45.833 0.00 0.00 0.00 2.57
455 459 5.253096 GGTCTACCCCACCCATATTATTGAT 59.747 44.000 0.00 0.00 0.00 2.57
456 460 6.445786 GGTCTACCCCACCCATATTATTGATA 59.554 42.308 0.00 0.00 0.00 2.15
457 461 7.037153 GGTCTACCCCACCCATATTATTGATAA 60.037 40.741 0.00 0.00 0.00 1.75
458 462 8.557450 GTCTACCCCACCCATATTATTGATAAT 58.443 37.037 2.18 2.18 36.89 1.28
459 463 9.806702 TCTACCCCACCCATATTATTGATAATA 57.193 33.333 6.05 6.05 38.97 0.98
460 464 9.847224 CTACCCCACCCATATTATTGATAATAC 57.153 37.037 5.77 0.00 37.86 1.89
461 465 7.648770 ACCCCACCCATATTATTGATAATACC 58.351 38.462 5.77 0.00 37.86 2.73
462 466 7.467519 ACCCCACCCATATTATTGATAATACCT 59.532 37.037 5.77 0.00 37.86 3.08
463 467 8.343787 CCCCACCCATATTATTGATAATACCTT 58.656 37.037 5.77 0.00 37.86 3.50
495 499 6.721571 TTCGAATTCTATCAATATTCGGGC 57.278 37.500 14.16 0.00 46.34 6.13
498 502 7.289310 TCGAATTCTATCAATATTCGGGCACC 61.289 42.308 14.16 0.00 46.34 5.01
551 555 9.482627 AATTATCGTTCTGGAGATACAATTCTC 57.517 33.333 0.00 0.00 41.21 2.87
552 556 4.921547 TCGTTCTGGAGATACAATTCTCG 58.078 43.478 0.00 0.00 42.57 4.04
553 557 4.045104 CGTTCTGGAGATACAATTCTCGG 58.955 47.826 0.00 0.00 42.57 4.63
554 558 4.372656 GTTCTGGAGATACAATTCTCGGG 58.627 47.826 0.00 0.00 42.57 5.14
555 559 2.365617 TCTGGAGATACAATTCTCGGGC 59.634 50.000 0.00 0.00 42.57 6.13
556 560 1.416401 TGGAGATACAATTCTCGGGCC 59.584 52.381 0.00 0.00 42.57 5.80
559 563 3.394719 GAGATACAATTCTCGGGCCTTC 58.605 50.000 0.84 0.00 33.35 3.46
560 564 2.771943 AGATACAATTCTCGGGCCTTCA 59.228 45.455 0.84 0.00 0.00 3.02
562 566 0.035056 ACAATTCTCGGGCCTTCAGG 60.035 55.000 0.84 0.00 38.53 3.86
563 567 0.253044 CAATTCTCGGGCCTTCAGGA 59.747 55.000 0.84 0.00 37.39 3.86
564 568 0.543749 AATTCTCGGGCCTTCAGGAG 59.456 55.000 0.84 0.00 37.39 3.69
566 570 0.325671 TTCTCGGGCCTTCAGGAGAT 60.326 55.000 0.84 0.00 35.63 2.75
567 571 0.556258 TCTCGGGCCTTCAGGAGATA 59.444 55.000 0.84 0.00 37.39 1.98
568 572 0.676736 CTCGGGCCTTCAGGAGATAC 59.323 60.000 0.84 0.00 37.39 2.24
570 574 0.830648 CGGGCCTTCAGGAGATACAA 59.169 55.000 0.84 0.00 37.39 2.41
573 577 3.217626 GGGCCTTCAGGAGATACAATTG 58.782 50.000 0.84 3.24 37.39 2.32
574 578 3.372025 GGGCCTTCAGGAGATACAATTGT 60.372 47.826 16.68 16.68 37.39 2.71
575 579 3.879892 GGCCTTCAGGAGATACAATTGTC 59.120 47.826 15.85 1.24 37.39 3.18
576 580 3.557595 GCCTTCAGGAGATACAATTGTCG 59.442 47.826 15.85 0.00 37.39 4.35
577 581 4.759782 CCTTCAGGAGATACAATTGTCGT 58.240 43.478 15.85 5.15 37.39 4.34
578 582 5.178797 CCTTCAGGAGATACAATTGTCGTT 58.821 41.667 15.85 0.99 37.39 3.85
581 585 5.410924 TCAGGAGATACAATTGTCGTTCTG 58.589 41.667 15.85 14.29 0.00 3.02
582 586 4.033358 CAGGAGATACAATTGTCGTTCTGC 59.967 45.833 15.85 18.91 0.00 4.26
584 588 4.033358 GGAGATACAATTGTCGTTCTGCTG 59.967 45.833 15.85 0.00 0.00 4.41
585 589 3.935203 AGATACAATTGTCGTTCTGCTGG 59.065 43.478 15.85 0.00 0.00 4.85
587 591 1.603802 ACAATTGTCGTTCTGCTGGTG 59.396 47.619 4.92 0.00 0.00 4.17
627 631 5.623169 GAGTCCTACTATAGCTGTGGTAGT 58.377 45.833 25.26 16.40 32.33 2.73
629 633 6.771573 AGTCCTACTATAGCTGTGGTAGTAG 58.228 44.000 25.26 22.17 43.62 2.57
637 641 1.960471 GCTGTGGTAGTAGCTGAGGGA 60.960 57.143 0.00 0.00 36.99 4.20
638 642 2.457598 CTGTGGTAGTAGCTGAGGGAA 58.542 52.381 0.00 0.00 0.00 3.97
651 659 1.338105 TGAGGGAATCAAGCACGAGTG 60.338 52.381 0.00 0.00 34.02 3.51
675 683 1.681166 GCAACTGTCTGGGCAGATGAT 60.681 52.381 14.87 0.00 40.34 2.45
736 744 0.327259 GACCCAACTAACCCCCACTC 59.673 60.000 0.00 0.00 0.00 3.51
738 746 1.196104 CCCAACTAACCCCCACTCGA 61.196 60.000 0.00 0.00 0.00 4.04
820 1028 1.690219 CCCTCCATCTTCCCGTCCAG 61.690 65.000 0.00 0.00 0.00 3.86
840 1061 1.734465 GCTGACCAAATCACTTCTCCG 59.266 52.381 0.00 0.00 32.37 4.63
870 1091 2.590092 CAACCCTTCCCGCCTAGG 59.410 66.667 3.67 3.67 40.63 3.02
872 1093 1.689582 AACCCTTCCCGCCTAGGAG 60.690 63.158 14.75 9.83 45.00 3.69
894 1186 4.850386 AGTATATATCCCTTTCCCCACACC 59.150 45.833 0.00 0.00 0.00 4.16
980 1289 1.066587 GCTAGTCGATCAGCCGCTT 59.933 57.895 9.44 0.00 0.00 4.68
984 1293 0.530744 AGTCGATCAGCCGCTTGTAA 59.469 50.000 0.00 0.00 0.00 2.41
993 1314 1.277495 GCCGCTTGTAACGTACGTGT 61.277 55.000 23.57 14.24 0.00 4.49
1200 1531 5.426689 AGAGGATGTGTAAGCTCAATCAA 57.573 39.130 0.00 0.00 0.00 2.57
1201 1532 5.999044 AGAGGATGTGTAAGCTCAATCAAT 58.001 37.500 0.00 0.00 0.00 2.57
1202 1533 6.421485 AGAGGATGTGTAAGCTCAATCAATT 58.579 36.000 0.00 0.00 0.00 2.32
1203 1534 6.541641 AGAGGATGTGTAAGCTCAATCAATTC 59.458 38.462 0.00 0.00 0.00 2.17
1204 1535 5.591877 AGGATGTGTAAGCTCAATCAATTCC 59.408 40.000 0.00 0.00 0.00 3.01
1205 1536 5.357878 GGATGTGTAAGCTCAATCAATTCCA 59.642 40.000 0.00 0.00 0.00 3.53
1206 1537 6.040166 GGATGTGTAAGCTCAATCAATTCCAT 59.960 38.462 0.00 0.00 0.00 3.41
1207 1538 6.839124 TGTGTAAGCTCAATCAATTCCATT 57.161 33.333 0.00 0.00 0.00 3.16
1208 1539 6.855836 TGTGTAAGCTCAATCAATTCCATTC 58.144 36.000 0.00 0.00 0.00 2.67
1209 1540 6.127647 TGTGTAAGCTCAATCAATTCCATTCC 60.128 38.462 0.00 0.00 0.00 3.01
1240 1587 5.547465 TCTTCTTTGCCGTCTCTTTTATGA 58.453 37.500 0.00 0.00 0.00 2.15
1272 1619 1.138047 GATGGACACGCGACCTAACG 61.138 60.000 15.93 0.00 0.00 3.18
1280 1677 1.134226 CGCGACCTAACGAACAAACT 58.866 50.000 0.00 0.00 35.09 2.66
1295 1702 6.803320 ACGAACAAACTATGCTTCATTTCATG 59.197 34.615 0.00 0.00 0.00 3.07
1863 2270 0.382158 CTGCGAGCCAGACGATTCTA 59.618 55.000 0.00 0.00 44.64 2.10
1990 2397 1.302511 GAGGACGCCTTCAAGCCAA 60.303 57.895 0.00 0.00 31.76 4.52
1992 2399 0.251341 AGGACGCCTTCAAGCCAATT 60.251 50.000 0.00 0.00 0.00 2.32
2067 2474 1.746615 CCTTGACATGGTGGAGGCG 60.747 63.158 0.00 0.00 0.00 5.52
2331 2738 7.696872 GCATGATCATTCATTCTCCATTTATCG 59.303 37.037 5.16 0.00 40.70 2.92
2448 5506 5.062308 CGTTTCTTTCCTCTGTGCTACATAC 59.938 44.000 0.00 0.00 0.00 2.39
2489 5553 8.082242 TGAGATCGTTGTGGTATATATGAACTG 58.918 37.037 0.00 0.00 0.00 3.16
2495 5559 8.487970 CGTTGTGGTATATATGAACTGTTGATC 58.512 37.037 0.00 0.00 0.00 2.92
2525 5589 9.620660 ATGATTGAAAGTAACCAATTACGTTTC 57.379 29.630 0.00 7.19 44.69 2.78
2635 5702 6.817140 ACGGAGTGAATGAGTTTAGTAATTCC 59.183 38.462 0.00 0.00 42.51 3.01
2638 5705 7.610305 GGAGTGAATGAGTTTAGTAATTCCCAA 59.390 37.037 0.00 0.00 0.00 4.12
2673 5745 9.610705 TGACTCTATAGATACGGTAATATGGAC 57.389 37.037 2.11 0.00 0.00 4.02
2696 5768 6.970484 ACAAGATAAAATTGTTCGAAGCACT 58.030 32.000 0.00 0.00 37.61 4.40
2698 5770 8.040518 ACAAGATAAAATTGTTCGAAGCACTCG 61.041 37.037 0.00 2.03 39.93 4.18
2735 5807 4.324641 GCCCCTTATTTCAAAGAGAGGACT 60.325 45.833 0.00 0.00 0.00 3.85
2736 5808 5.432645 CCCCTTATTTCAAAGAGAGGACTC 58.567 45.833 0.00 0.00 42.90 3.36
2739 5811 3.685139 ATTTCAAAGAGAGGACTCGCA 57.315 42.857 5.88 0.00 46.64 5.10
2740 5812 2.732412 TTCAAAGAGAGGACTCGCAG 57.268 50.000 5.88 0.00 46.64 5.18
2743 5815 2.230025 TCAAAGAGAGGACTCGCAGAAG 59.770 50.000 5.88 0.00 46.64 2.85
2744 5816 0.530288 AAGAGAGGACTCGCAGAAGC 59.470 55.000 5.88 0.00 46.64 3.86
2761 5893 2.112815 GCGGAGGCGCCACTTATTT 61.113 57.895 31.54 5.22 35.94 1.40
2762 5894 2.014594 CGGAGGCGCCACTTATTTC 58.985 57.895 31.54 15.47 35.94 2.17
2771 5903 3.181506 GCGCCACTTATTTCAAAGAGAGG 60.182 47.826 0.00 0.00 0.00 3.69
2776 5908 6.183360 GCCACTTATTTCAAAGAGAGGATGAC 60.183 42.308 4.56 0.00 0.00 3.06
2777 5909 6.036517 CCACTTATTTCAAAGAGAGGATGACG 59.963 42.308 0.00 0.00 0.00 4.35
2778 5910 6.036517 CACTTATTTCAAAGAGAGGATGACGG 59.963 42.308 0.00 0.00 0.00 4.79
2779 5911 3.334583 TTTCAAAGAGAGGATGACGGG 57.665 47.619 0.00 0.00 0.00 5.28
2780 5912 1.938585 TCAAAGAGAGGATGACGGGT 58.061 50.000 0.00 0.00 0.00 5.28
2781 5913 2.257207 TCAAAGAGAGGATGACGGGTT 58.743 47.619 0.00 0.00 0.00 4.11
2782 5914 3.437213 TCAAAGAGAGGATGACGGGTTA 58.563 45.455 0.00 0.00 0.00 2.85
2783 5915 4.030913 TCAAAGAGAGGATGACGGGTTAT 58.969 43.478 0.00 0.00 0.00 1.89
2784 5916 4.469945 TCAAAGAGAGGATGACGGGTTATT 59.530 41.667 0.00 0.00 0.00 1.40
2785 5917 4.674281 AAGAGAGGATGACGGGTTATTC 57.326 45.455 0.00 0.00 0.00 1.75
2787 5919 3.385111 AGAGAGGATGACGGGTTATTCAC 59.615 47.826 0.00 0.00 0.00 3.18
2788 5920 3.104512 AGAGGATGACGGGTTATTCACA 58.895 45.455 0.00 0.00 0.00 3.58
2789 5921 3.711704 AGAGGATGACGGGTTATTCACAT 59.288 43.478 0.00 0.00 0.00 3.21
2790 5922 4.164221 AGAGGATGACGGGTTATTCACATT 59.836 41.667 0.00 0.00 0.00 2.71
2791 5923 4.855340 AGGATGACGGGTTATTCACATTT 58.145 39.130 0.00 0.00 0.00 2.32
2792 5924 5.996644 AGGATGACGGGTTATTCACATTTA 58.003 37.500 0.00 0.00 0.00 1.40
2793 5925 6.419791 AGGATGACGGGTTATTCACATTTAA 58.580 36.000 0.00 0.00 0.00 1.52
2794 5926 7.060421 AGGATGACGGGTTATTCACATTTAAT 58.940 34.615 0.00 0.00 0.00 1.40
2795 5927 7.559897 AGGATGACGGGTTATTCACATTTAATT 59.440 33.333 0.00 0.00 0.00 1.40
2796 5928 8.194769 GGATGACGGGTTATTCACATTTAATTT 58.805 33.333 0.00 0.00 0.00 1.82
2797 5929 8.925161 ATGACGGGTTATTCACATTTAATTTG 57.075 30.769 0.00 0.00 0.00 2.32
2798 5930 8.112016 TGACGGGTTATTCACATTTAATTTGA 57.888 30.769 0.00 0.00 0.00 2.69
2799 5931 8.744652 TGACGGGTTATTCACATTTAATTTGAT 58.255 29.630 0.00 0.00 0.00 2.57
2800 5932 8.925161 ACGGGTTATTCACATTTAATTTGATG 57.075 30.769 0.00 0.00 0.00 3.07
2801 5933 7.978975 ACGGGTTATTCACATTTAATTTGATGG 59.021 33.333 0.00 0.00 0.00 3.51
2802 5934 7.042791 CGGGTTATTCACATTTAATTTGATGGC 60.043 37.037 0.00 0.00 0.00 4.40
2804 5936 7.768120 GGTTATTCACATTTAATTTGATGGCCA 59.232 33.333 8.56 8.56 0.00 5.36
2806 5938 5.735285 TCACATTTAATTTGATGGCCACA 57.265 34.783 8.16 5.62 0.00 4.17
2807 5939 5.722263 TCACATTTAATTTGATGGCCACAG 58.278 37.500 8.16 0.00 0.00 3.66
2808 5940 4.871557 CACATTTAATTTGATGGCCACAGG 59.128 41.667 8.16 0.00 0.00 4.00
2821 5953 1.582968 CACAGGCAGTGGTTGATGC 59.417 57.895 1.52 0.00 44.69 3.91
2823 5955 1.968017 CAGGCAGTGGTTGATGCGT 60.968 57.895 0.00 0.00 43.49 5.24
2825 5957 1.081242 GGCAGTGGTTGATGCGTTG 60.081 57.895 0.00 0.00 43.49 4.10
2826 5958 1.081242 GCAGTGGTTGATGCGTTGG 60.081 57.895 0.00 0.00 31.87 3.77
2827 5959 1.514678 GCAGTGGTTGATGCGTTGGA 61.515 55.000 0.00 0.00 31.87 3.53
2828 5960 0.238289 CAGTGGTTGATGCGTTGGAC 59.762 55.000 0.00 0.00 0.00 4.02
2829 5961 1.206578 GTGGTTGATGCGTTGGACG 59.793 57.895 0.00 0.00 45.88 4.79
2830 5962 1.227704 TGGTTGATGCGTTGGACGT 60.228 52.632 0.00 0.00 44.73 4.34
2831 5963 0.816018 TGGTTGATGCGTTGGACGTT 60.816 50.000 2.27 0.00 44.73 3.99
2832 5964 0.110373 GGTTGATGCGTTGGACGTTC 60.110 55.000 2.27 0.00 44.73 3.95
2833 5965 0.865769 GTTGATGCGTTGGACGTTCT 59.134 50.000 0.00 0.00 44.73 3.01
2834 5966 1.136336 GTTGATGCGTTGGACGTTCTC 60.136 52.381 0.00 0.00 44.73 2.87
2840 6049 0.852777 CGTTGGACGTTCTCTGTGTG 59.147 55.000 0.00 0.00 36.74 3.82
2844 6053 1.668151 GACGTTCTCTGTGTGGGCC 60.668 63.158 0.00 0.00 0.00 5.80
2846 6055 0.830444 ACGTTCTCTGTGTGGGCCTA 60.830 55.000 4.53 0.00 0.00 3.93
2850 6059 0.965866 TCTCTGTGTGGGCCTAGTCG 60.966 60.000 4.53 0.00 0.00 4.18
2852 6061 0.038599 TCTGTGTGGGCCTAGTCGTA 59.961 55.000 4.53 0.00 0.00 3.43
2856 6065 1.108776 TGTGGGCCTAGTCGTATGAC 58.891 55.000 4.53 7.01 45.86 3.06
2865 6074 3.132863 GTCGTATGACAACGGCCTT 57.867 52.632 10.30 0.00 44.82 4.35
2866 6075 0.997196 GTCGTATGACAACGGCCTTC 59.003 55.000 10.30 0.00 44.82 3.46
2877 6086 1.281656 CGGCCTTCGTGAAAACACC 59.718 57.895 0.00 0.00 0.00 4.16
2879 6088 1.281656 GCCTTCGTGAAAACACCCG 59.718 57.895 0.00 0.00 0.00 5.28
2882 6091 0.306533 CTTCGTGAAAACACCCGTGG 59.693 55.000 0.00 0.00 34.19 4.94
2892 6101 2.518426 ACCCGTGGTGGCATTTCA 59.482 55.556 0.00 0.00 32.98 2.69
2895 6104 0.607620 CCCGTGGTGGCATTTCATTT 59.392 50.000 0.00 0.00 35.87 2.32
2906 6115 5.469421 GTGGCATTTCATTTCCACATTTGAA 59.531 36.000 5.47 0.00 46.09 2.69
2910 6119 7.293018 GCATTTCATTTCCACATTTGAAGAAC 58.707 34.615 0.00 0.00 30.45 3.01
2916 6125 8.369424 TCATTTCCACATTTGAAGAACAATCAT 58.631 29.630 0.00 0.00 38.36 2.45
2917 6126 8.653338 CATTTCCACATTTGAAGAACAATCATC 58.347 33.333 0.00 0.00 38.36 2.92
2931 6226 9.860898 AAGAACAATCATCAAATAGGCTAAAAC 57.139 29.630 0.00 0.00 0.00 2.43
2949 6244 8.352942 GGCTAAAACAGTGAGATATTTATTGGG 58.647 37.037 0.00 0.00 0.00 4.12
2957 6252 9.305555 CAGTGAGATATTTATTGGGATGGAAAT 57.694 33.333 0.00 0.00 0.00 2.17
2996 6291 3.374745 CTTTTTGTCAAGCAATCGCACT 58.625 40.909 0.00 0.00 42.27 4.40
3062 6398 2.607750 TTCTTCGCAGGGGAGCCT 60.608 61.111 0.00 0.00 0.00 4.58
3103 6439 2.886523 TCTGAAACAAGAGCACCATTGG 59.113 45.455 0.00 0.00 0.00 3.16
3128 6464 4.946772 TGATTGGATAAAATTGGTCTGCGA 59.053 37.500 0.00 0.00 0.00 5.10
3138 6474 0.461548 TGGTCTGCGATCATCCACTC 59.538 55.000 0.00 0.00 0.00 3.51
3154 6490 2.740981 CCACTCTTGTGCTCTTGTGATC 59.259 50.000 0.00 0.00 42.54 2.92
3204 7090 8.229253 TGCAGAAATAATATGCTCATGACTTT 57.771 30.769 0.00 0.00 40.62 2.66
3214 7100 3.072330 TGCTCATGACTTTACCAACCAGA 59.928 43.478 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.178996 CAGTCTGGACAAAATTCTCAGTCTG 59.821 44.000 3.51 0.00 36.15 3.51
145 146 4.389374 AGGCGTGGAAGTATAAATCATGG 58.611 43.478 0.00 0.00 0.00 3.66
146 147 5.751680 CAAGGCGTGGAAGTATAAATCATG 58.248 41.667 0.00 0.00 0.00 3.07
147 148 4.275936 GCAAGGCGTGGAAGTATAAATCAT 59.724 41.667 1.91 0.00 0.00 2.45
148 149 3.625764 GCAAGGCGTGGAAGTATAAATCA 59.374 43.478 1.91 0.00 0.00 2.57
149 150 3.625764 TGCAAGGCGTGGAAGTATAAATC 59.374 43.478 1.91 0.00 0.00 2.17
150 151 3.616219 TGCAAGGCGTGGAAGTATAAAT 58.384 40.909 1.91 0.00 0.00 1.40
151 152 3.060736 TGCAAGGCGTGGAAGTATAAA 57.939 42.857 1.91 0.00 0.00 1.40
152 153 2.772077 TGCAAGGCGTGGAAGTATAA 57.228 45.000 1.91 0.00 0.00 0.98
153 154 2.560504 CATGCAAGGCGTGGAAGTATA 58.439 47.619 0.00 0.00 41.34 1.47
154 155 1.382522 CATGCAAGGCGTGGAAGTAT 58.617 50.000 0.00 0.00 41.34 2.12
155 156 1.305219 GCATGCAAGGCGTGGAAGTA 61.305 55.000 14.21 0.00 44.72 2.24
156 157 2.629656 GCATGCAAGGCGTGGAAGT 61.630 57.895 14.21 0.00 44.72 3.01
157 158 2.180017 GCATGCAAGGCGTGGAAG 59.820 61.111 14.21 0.00 44.72 3.46
165 166 1.611977 CATATCAGGGTGCATGCAAGG 59.388 52.381 24.58 12.16 0.00 3.61
199 200 4.271661 TGCATGAAGACAATATTCAGCCA 58.728 39.130 0.00 0.00 39.86 4.75
202 203 6.750501 CCAAGTTGCATGAAGACAATATTCAG 59.249 38.462 0.00 0.00 39.86 3.02
245 246 5.880332 TCGGGAAAGATCAAGGAGTTAATTG 59.120 40.000 0.00 0.00 0.00 2.32
249 250 5.221185 CGTATCGGGAAAGATCAAGGAGTTA 60.221 44.000 0.00 0.00 32.39 2.24
252 253 3.553096 CCGTATCGGGAAAGATCAAGGAG 60.553 52.174 0.00 0.00 44.15 3.69
253 254 2.364324 CCGTATCGGGAAAGATCAAGGA 59.636 50.000 0.00 0.00 44.15 3.36
254 255 2.755650 CCGTATCGGGAAAGATCAAGG 58.244 52.381 0.00 0.00 44.15 3.61
267 268 0.235665 GCCATGCAACATCCGTATCG 59.764 55.000 0.00 0.00 0.00 2.92
431 435 4.600111 TCAATAATATGGGTGGGGTAGACC 59.400 45.833 0.00 0.00 39.11 3.85
432 436 5.836024 TCAATAATATGGGTGGGGTAGAC 57.164 43.478 0.00 0.00 0.00 2.59
433 437 8.709153 ATTATCAATAATATGGGTGGGGTAGA 57.291 34.615 0.00 0.00 31.54 2.59
434 438 9.847224 GTATTATCAATAATATGGGTGGGGTAG 57.153 37.037 5.90 0.00 37.50 3.18
435 439 8.783903 GGTATTATCAATAATATGGGTGGGGTA 58.216 37.037 5.90 0.00 37.50 3.69
436 440 7.467519 AGGTATTATCAATAATATGGGTGGGGT 59.532 37.037 5.90 0.00 37.50 4.95
437 441 7.882755 AGGTATTATCAATAATATGGGTGGGG 58.117 38.462 5.90 0.00 37.50 4.96
475 479 5.123979 GGGTGCCCGAATATTGATAGAATTC 59.876 44.000 0.00 0.00 0.00 2.17
476 480 5.010282 GGGTGCCCGAATATTGATAGAATT 58.990 41.667 0.00 0.00 0.00 2.17
477 481 4.042809 TGGGTGCCCGAATATTGATAGAAT 59.957 41.667 2.44 0.00 39.42 2.40
478 482 3.392947 TGGGTGCCCGAATATTGATAGAA 59.607 43.478 2.44 0.00 39.42 2.10
479 483 2.976185 TGGGTGCCCGAATATTGATAGA 59.024 45.455 2.44 0.00 39.42 1.98
480 484 3.417069 TGGGTGCCCGAATATTGATAG 57.583 47.619 2.44 0.00 39.42 2.08
481 485 5.506730 TTATGGGTGCCCGAATATTGATA 57.493 39.130 2.44 0.00 39.42 2.15
482 486 2.978156 ATGGGTGCCCGAATATTGAT 57.022 45.000 2.44 0.00 39.42 2.57
483 487 3.866703 TTATGGGTGCCCGAATATTGA 57.133 42.857 2.44 0.00 39.42 2.57
484 488 4.927978 TTTTATGGGTGCCCGAATATTG 57.072 40.909 2.44 0.00 39.42 1.90
485 489 7.604657 TTATTTTTATGGGTGCCCGAATATT 57.395 32.000 2.44 0.00 39.42 1.28
486 490 7.604657 TTTATTTTTATGGGTGCCCGAATAT 57.395 32.000 2.44 2.05 39.42 1.28
487 491 7.419711 TTTTATTTTTATGGGTGCCCGAATA 57.580 32.000 2.44 0.00 39.42 1.75
488 492 5.941555 TTTATTTTTATGGGTGCCCGAAT 57.058 34.783 2.44 0.00 39.42 3.34
489 493 5.740290 TTTTATTTTTATGGGTGCCCGAA 57.260 34.783 2.44 0.00 39.42 4.30
490 494 5.740290 TTTTTATTTTTATGGGTGCCCGA 57.260 34.783 2.44 0.00 39.42 5.14
491 495 8.494016 TTTATTTTTATTTTTATGGGTGCCCG 57.506 30.769 2.44 0.00 39.42 6.13
527 531 7.139392 CGAGAATTGTATCTCCAGAACGATAA 58.861 38.462 0.00 0.00 42.34 1.75
528 532 6.294010 CCGAGAATTGTATCTCCAGAACGATA 60.294 42.308 0.00 0.00 42.34 2.92
529 533 5.508153 CCGAGAATTGTATCTCCAGAACGAT 60.508 44.000 0.00 0.00 42.34 3.73
530 534 4.202020 CCGAGAATTGTATCTCCAGAACGA 60.202 45.833 0.00 0.00 42.34 3.85
532 536 4.372656 CCCGAGAATTGTATCTCCAGAAC 58.627 47.826 0.00 0.00 42.34 3.01
534 538 2.365617 GCCCGAGAATTGTATCTCCAGA 59.634 50.000 0.00 0.00 42.34 3.86
535 539 2.548920 GGCCCGAGAATTGTATCTCCAG 60.549 54.545 0.00 0.00 42.34 3.86
537 541 1.694696 AGGCCCGAGAATTGTATCTCC 59.305 52.381 0.00 0.00 42.34 3.71
538 542 3.181465 TGAAGGCCCGAGAATTGTATCTC 60.181 47.826 0.00 0.00 41.99 2.75
539 543 2.771943 TGAAGGCCCGAGAATTGTATCT 59.228 45.455 0.00 0.00 0.00 1.98
540 544 3.134458 CTGAAGGCCCGAGAATTGTATC 58.866 50.000 0.00 0.00 0.00 2.24
541 545 2.158755 CCTGAAGGCCCGAGAATTGTAT 60.159 50.000 0.00 0.00 0.00 2.29
542 546 1.209504 CCTGAAGGCCCGAGAATTGTA 59.790 52.381 0.00 0.00 0.00 2.41
543 547 0.035056 CCTGAAGGCCCGAGAATTGT 60.035 55.000 0.00 0.00 0.00 2.71
544 548 0.253044 TCCTGAAGGCCCGAGAATTG 59.747 55.000 0.00 0.00 34.44 2.32
546 550 0.325671 TCTCCTGAAGGCCCGAGAAT 60.326 55.000 0.00 0.00 34.44 2.40
547 551 0.325671 ATCTCCTGAAGGCCCGAGAA 60.326 55.000 0.00 0.00 35.15 2.87
549 553 0.676736 GTATCTCCTGAAGGCCCGAG 59.323 60.000 0.00 0.00 34.44 4.63
550 554 0.032515 TGTATCTCCTGAAGGCCCGA 60.033 55.000 0.00 0.00 34.44 5.14
551 555 0.830648 TTGTATCTCCTGAAGGCCCG 59.169 55.000 0.00 0.00 34.44 6.13
552 556 3.217626 CAATTGTATCTCCTGAAGGCCC 58.782 50.000 0.00 0.00 34.44 5.80
553 557 3.879892 GACAATTGTATCTCCTGAAGGCC 59.120 47.826 11.95 0.00 34.44 5.19
554 558 3.557595 CGACAATTGTATCTCCTGAAGGC 59.442 47.826 11.95 0.00 34.44 4.35
555 559 4.759782 ACGACAATTGTATCTCCTGAAGG 58.240 43.478 11.95 0.00 0.00 3.46
556 560 6.035435 CAGAACGACAATTGTATCTCCTGAAG 59.965 42.308 11.95 0.07 0.00 3.02
559 563 4.033358 GCAGAACGACAATTGTATCTCCTG 59.967 45.833 11.95 15.01 0.00 3.86
560 564 4.081420 AGCAGAACGACAATTGTATCTCCT 60.081 41.667 11.95 8.42 0.00 3.69
562 566 4.033358 CCAGCAGAACGACAATTGTATCTC 59.967 45.833 11.95 8.00 0.00 2.75
563 567 3.935203 CCAGCAGAACGACAATTGTATCT 59.065 43.478 11.95 12.45 0.00 1.98
564 568 3.684788 ACCAGCAGAACGACAATTGTATC 59.315 43.478 11.95 10.37 0.00 2.24
566 570 2.805671 CACCAGCAGAACGACAATTGTA 59.194 45.455 11.95 0.00 0.00 2.41
567 571 1.603802 CACCAGCAGAACGACAATTGT 59.396 47.619 11.78 11.78 0.00 2.71
568 572 1.872952 TCACCAGCAGAACGACAATTG 59.127 47.619 3.24 3.24 0.00 2.32
570 574 2.079158 CATCACCAGCAGAACGACAAT 58.921 47.619 0.00 0.00 0.00 2.71
573 577 1.790387 GCATCACCAGCAGAACGAC 59.210 57.895 0.00 0.00 0.00 4.34
574 578 1.737735 CGCATCACCAGCAGAACGA 60.738 57.895 0.00 0.00 0.00 3.85
575 579 2.743752 CCGCATCACCAGCAGAACG 61.744 63.158 0.00 0.00 0.00 3.95
576 580 1.375908 TCCGCATCACCAGCAGAAC 60.376 57.895 0.00 0.00 0.00 3.01
577 581 1.375908 GTCCGCATCACCAGCAGAA 60.376 57.895 0.00 0.00 0.00 3.02
578 582 2.265739 GTCCGCATCACCAGCAGA 59.734 61.111 0.00 0.00 0.00 4.26
608 612 5.413213 CAGCTACTACCACAGCTATAGTAGG 59.587 48.000 22.49 10.47 46.26 3.18
627 631 1.134699 CGTGCTTGATTCCCTCAGCTA 60.135 52.381 0.00 0.00 34.68 3.32
629 633 0.391661 TCGTGCTTGATTCCCTCAGC 60.392 55.000 0.00 0.00 34.68 4.26
631 635 0.976641 ACTCGTGCTTGATTCCCTCA 59.023 50.000 0.00 0.00 0.00 3.86
651 659 4.030452 GCCCAGACAGTTGCACGC 62.030 66.667 0.00 0.00 0.00 5.34
759 774 4.541482 CATGGATGGCGCGTGTGC 62.541 66.667 8.43 0.00 37.91 4.57
820 1028 1.734465 CGGAGAAGTGATTTGGTCAGC 59.266 52.381 0.00 0.00 37.56 4.26
840 1061 0.335019 AGGGTTGGTAGGGGAAATGC 59.665 55.000 0.00 0.00 0.00 3.56
870 1091 5.045797 GGTGTGGGGAAAGGGATATATACTC 60.046 48.000 0.00 0.00 0.00 2.59
872 1093 4.018688 GGGTGTGGGGAAAGGGATATATAC 60.019 50.000 0.00 0.00 0.00 1.47
894 1186 2.098233 GTGCGGTGTGGTGATACGG 61.098 63.158 0.00 0.00 0.00 4.02
980 1289 5.334319 CCATTGATCTACACGTACGTTACA 58.666 41.667 20.23 9.62 0.00 2.41
984 1293 2.793585 CGCCATTGATCTACACGTACGT 60.794 50.000 16.72 16.72 0.00 3.57
993 1314 1.299850 CGTCGCCGCCATTGATCTA 60.300 57.895 0.00 0.00 0.00 1.98
1101 1432 2.487532 CGGGTAGTCGGCCTGGTAG 61.488 68.421 0.00 0.00 0.00 3.18
1200 1531 7.562135 CAAAGAAGAATGGAATGGAATGGAAT 58.438 34.615 0.00 0.00 0.00 3.01
1201 1532 6.574859 GCAAAGAAGAATGGAATGGAATGGAA 60.575 38.462 0.00 0.00 0.00 3.53
1202 1533 5.105228 GCAAAGAAGAATGGAATGGAATGGA 60.105 40.000 0.00 0.00 0.00 3.41
1203 1534 5.114081 GCAAAGAAGAATGGAATGGAATGG 58.886 41.667 0.00 0.00 0.00 3.16
1204 1535 5.114081 GGCAAAGAAGAATGGAATGGAATG 58.886 41.667 0.00 0.00 0.00 2.67
1205 1536 4.142093 CGGCAAAGAAGAATGGAATGGAAT 60.142 41.667 0.00 0.00 0.00 3.01
1206 1537 3.193267 CGGCAAAGAAGAATGGAATGGAA 59.807 43.478 0.00 0.00 0.00 3.53
1207 1538 2.754552 CGGCAAAGAAGAATGGAATGGA 59.245 45.455 0.00 0.00 0.00 3.41
1208 1539 2.493278 ACGGCAAAGAAGAATGGAATGG 59.507 45.455 0.00 0.00 0.00 3.16
1209 1540 3.441572 AGACGGCAAAGAAGAATGGAATG 59.558 43.478 0.00 0.00 0.00 2.67
1240 1587 1.096416 GTCCATCGTCCGAGAGAAGT 58.904 55.000 0.00 0.00 0.00 3.01
1295 1702 1.416401 TCTGGGACTTGTCACCTGAAC 59.584 52.381 0.17 0.00 30.62 3.18
1485 1892 1.352352 ACAAGGTGGGTGATCTTGGAG 59.648 52.381 0.00 0.00 45.92 3.86
1785 2192 4.470170 TCCGCACCGACGATCACG 62.470 66.667 0.00 0.00 45.75 4.35
1830 2237 1.376424 CGCAGACACCAGCTGGAAT 60.376 57.895 39.19 25.20 38.94 3.01
1990 2397 2.092753 AGTTCCAGTCATCGATGCCAAT 60.093 45.455 20.81 0.44 0.00 3.16
1992 2399 0.904649 AGTTCCAGTCATCGATGCCA 59.095 50.000 20.81 1.10 0.00 4.92
2067 2474 4.024302 CGTTCCTTGTTCAGGTTTACCTTC 60.024 45.833 0.00 0.00 46.09 3.46
2205 2612 2.190578 CAGTCCATTCCCTCGCCC 59.809 66.667 0.00 0.00 0.00 6.13
2331 2738 9.517609 AACAGTAGTAGATTATTTCATGACGAC 57.482 33.333 0.00 0.00 0.00 4.34
2377 5433 7.819900 ACAAACCTCATACAACAGAATAGAGTC 59.180 37.037 0.00 0.00 0.00 3.36
2381 5437 9.436957 ACTTACAAACCTCATACAACAGAATAG 57.563 33.333 0.00 0.00 0.00 1.73
2448 5506 4.695455 ACGATCTCAACAATAAACAGGGTG 59.305 41.667 0.00 0.00 0.00 4.61
2489 5553 8.946085 TGGTTACTTTCAATCATGTAGATCAAC 58.054 33.333 0.00 0.00 35.39 3.18
2495 5559 9.702726 CGTAATTGGTTACTTTCAATCATGTAG 57.297 33.333 0.00 0.00 38.41 2.74
2525 5589 6.748333 TGCTTGATTCTTAGGTTTCATCAG 57.252 37.500 0.00 0.00 0.00 2.90
2612 5676 7.110155 TGGGAATTACTAAACTCATTCACTCC 58.890 38.462 0.00 0.00 31.40 3.85
2613 5677 8.561738 TTGGGAATTACTAAACTCATTCACTC 57.438 34.615 0.00 0.00 31.40 3.51
2615 5679 8.561738 TCTTGGGAATTACTAAACTCATTCAC 57.438 34.615 0.00 0.00 30.84 3.18
2660 5727 9.403583 ACAATTTTATCTTGTCCATATTACCGT 57.596 29.630 0.00 0.00 31.29 4.83
2673 5745 7.484471 GAGTGCTTCGAACAATTTTATCTTG 57.516 36.000 0.00 0.00 0.00 3.02
2719 5791 3.259374 TCTGCGAGTCCTCTCTTTGAAAT 59.741 43.478 0.00 0.00 38.45 2.17
2744 5816 0.742990 TGAAATAAGTGGCGCCTCCG 60.743 55.000 29.70 0.00 37.80 4.63
2746 5818 2.747446 TCTTTGAAATAAGTGGCGCCTC 59.253 45.455 29.70 25.08 0.00 4.70
2749 5821 3.181506 CCTCTCTTTGAAATAAGTGGCGC 60.182 47.826 0.00 0.00 0.00 6.53
2750 5822 4.253685 TCCTCTCTTTGAAATAAGTGGCG 58.746 43.478 4.57 0.00 0.00 5.69
2751 5823 5.882557 TCATCCTCTCTTTGAAATAAGTGGC 59.117 40.000 4.57 0.00 0.00 5.01
2752 5824 6.036517 CGTCATCCTCTCTTTGAAATAAGTGG 59.963 42.308 3.50 3.50 0.00 4.00
2753 5825 6.036517 CCGTCATCCTCTCTTTGAAATAAGTG 59.963 42.308 0.00 0.00 0.00 3.16
2754 5826 6.109359 CCGTCATCCTCTCTTTGAAATAAGT 58.891 40.000 0.00 0.00 0.00 2.24
2757 5829 4.469945 ACCCGTCATCCTCTCTTTGAAATA 59.530 41.667 0.00 0.00 0.00 1.40
2761 5893 1.938585 ACCCGTCATCCTCTCTTTGA 58.061 50.000 0.00 0.00 0.00 2.69
2762 5894 2.770164 AACCCGTCATCCTCTCTTTG 57.230 50.000 0.00 0.00 0.00 2.77
2771 5903 9.019764 CAAATTAAATGTGAATAACCCGTCATC 57.980 33.333 0.00 0.00 0.00 2.92
2776 5908 7.042791 GCCATCAAATTAAATGTGAATAACCCG 60.043 37.037 0.00 0.00 0.00 5.28
2777 5909 7.226523 GGCCATCAAATTAAATGTGAATAACCC 59.773 37.037 0.00 0.00 0.00 4.11
2778 5910 7.768120 TGGCCATCAAATTAAATGTGAATAACC 59.232 33.333 0.00 0.00 0.00 2.85
2779 5911 8.603181 GTGGCCATCAAATTAAATGTGAATAAC 58.397 33.333 9.72 0.00 0.00 1.89
2780 5912 8.316946 TGTGGCCATCAAATTAAATGTGAATAA 58.683 29.630 9.72 0.00 0.00 1.40
2781 5913 7.845037 TGTGGCCATCAAATTAAATGTGAATA 58.155 30.769 9.72 0.00 0.00 1.75
2782 5914 6.709281 TGTGGCCATCAAATTAAATGTGAAT 58.291 32.000 9.72 0.00 0.00 2.57
2783 5915 6.106648 TGTGGCCATCAAATTAAATGTGAA 57.893 33.333 9.72 0.00 0.00 3.18
2784 5916 5.337410 CCTGTGGCCATCAAATTAAATGTGA 60.337 40.000 9.72 0.00 0.00 3.58
2785 5917 4.871557 CCTGTGGCCATCAAATTAAATGTG 59.128 41.667 9.72 0.00 0.00 3.21
2787 5919 3.872771 GCCTGTGGCCATCAAATTAAATG 59.127 43.478 9.72 0.00 44.06 2.32
2788 5920 4.141233 GCCTGTGGCCATCAAATTAAAT 57.859 40.909 9.72 0.00 44.06 1.40
2789 5921 3.608316 GCCTGTGGCCATCAAATTAAA 57.392 42.857 9.72 0.00 44.06 1.52
2804 5936 1.968017 CGCATCAACCACTGCCTGT 60.968 57.895 0.00 0.00 34.89 4.00
2806 5938 1.228245 AACGCATCAACCACTGCCT 60.228 52.632 0.00 0.00 34.89 4.75
2807 5939 1.081242 CAACGCATCAACCACTGCC 60.081 57.895 0.00 0.00 34.89 4.85
2808 5940 1.081242 CCAACGCATCAACCACTGC 60.081 57.895 0.00 0.00 35.02 4.40
2810 5942 1.227999 CGTCCAACGCATCAACCACT 61.228 55.000 0.00 0.00 33.65 4.00
2811 5943 1.206578 CGTCCAACGCATCAACCAC 59.793 57.895 0.00 0.00 33.65 4.16
2812 5944 3.649096 CGTCCAACGCATCAACCA 58.351 55.556 0.00 0.00 33.65 3.67
2823 5955 0.105964 CCCACACAGAGAACGTCCAA 59.894 55.000 0.00 0.00 0.00 3.53
2825 5957 1.668151 GCCCACACAGAGAACGTCC 60.668 63.158 0.00 0.00 0.00 4.79
2826 5958 1.668151 GGCCCACACAGAGAACGTC 60.668 63.158 0.00 0.00 0.00 4.34
2827 5959 0.830444 TAGGCCCACACAGAGAACGT 60.830 55.000 0.00 0.00 0.00 3.99
2828 5960 0.108615 CTAGGCCCACACAGAGAACG 60.109 60.000 0.00 0.00 0.00 3.95
2829 5961 0.977395 ACTAGGCCCACACAGAGAAC 59.023 55.000 0.00 0.00 0.00 3.01
2830 5962 1.267121 GACTAGGCCCACACAGAGAA 58.733 55.000 0.00 0.00 0.00 2.87
2831 5963 0.965866 CGACTAGGCCCACACAGAGA 60.966 60.000 0.00 0.00 0.00 3.10
2832 5964 1.251527 ACGACTAGGCCCACACAGAG 61.252 60.000 0.00 0.00 0.00 3.35
2833 5965 0.038599 TACGACTAGGCCCACACAGA 59.961 55.000 0.00 0.00 0.00 3.41
2834 5966 1.112113 ATACGACTAGGCCCACACAG 58.888 55.000 0.00 0.00 0.00 3.66
2840 6049 1.535437 CGTTGTCATACGACTAGGCCC 60.535 57.143 0.00 0.00 43.99 5.80
2844 6053 1.404391 AGGCCGTTGTCATACGACTAG 59.596 52.381 0.00 0.00 43.99 2.57
2846 6055 0.606604 AAGGCCGTTGTCATACGACT 59.393 50.000 0.00 4.85 43.99 4.18
2877 6086 1.404047 GGAAATGAAATGCCACCACGG 60.404 52.381 0.00 0.00 38.11 4.94
2879 6088 2.036992 TGTGGAAATGAAATGCCACCAC 59.963 45.455 0.00 0.00 46.30 4.16
2882 6091 4.996122 TCAAATGTGGAAATGAAATGCCAC 59.004 37.500 0.00 0.00 46.74 5.01
2892 6101 8.369424 TGATGATTGTTCTTCAAATGTGGAAAT 58.631 29.630 0.00 0.00 39.62 2.17
2895 6104 6.897706 TGATGATTGTTCTTCAAATGTGGA 57.102 33.333 0.00 0.00 39.62 4.02
2906 6115 9.023962 TGTTTTAGCCTATTTGATGATTGTTCT 57.976 29.630 0.00 0.00 0.00 3.01
2910 6119 8.461222 TCACTGTTTTAGCCTATTTGATGATTG 58.539 33.333 0.00 0.00 0.00 2.67
2916 6125 9.905713 AATATCTCACTGTTTTAGCCTATTTGA 57.094 29.630 0.00 0.00 0.00 2.69
2931 6226 8.696043 TTTCCATCCCAATAAATATCTCACTG 57.304 34.615 0.00 0.00 0.00 3.66
2975 6270 3.374745 AGTGCGATTGCTTGACAAAAAG 58.625 40.909 6.47 0.00 42.86 2.27
2976 6271 3.435105 AGTGCGATTGCTTGACAAAAA 57.565 38.095 6.47 0.00 42.86 1.94
2985 6280 0.801251 GCTCTCAAAGTGCGATTGCT 59.199 50.000 6.47 0.00 43.34 3.91
2996 6291 2.565391 TGGACGTTGATAGGCTCTCAAA 59.435 45.455 15.84 0.00 34.59 2.69
3103 6439 5.516339 CGCAGACCAATTTTATCCAATCAAC 59.484 40.000 0.00 0.00 0.00 3.18
3128 6464 3.008813 ACAAGAGCACAAGAGTGGATGAT 59.991 43.478 0.00 0.00 45.98 2.45
3138 6474 3.181513 CCGATTGATCACAAGAGCACAAG 60.182 47.826 0.00 0.00 40.39 3.16
3154 6490 1.202222 GCACTTCATTCAGGCCGATTG 60.202 52.381 0.00 5.20 0.00 2.67
3204 7090 1.340017 GCAGCATTCCTCTGGTTGGTA 60.340 52.381 0.00 0.00 32.41 3.25
3214 7100 2.419667 GCAAATTTGTGCAGCATTCCT 58.580 42.857 19.03 0.00 44.29 3.36
3267 7161 2.295909 GCCTTCTGTTGCCATTGTACAA 59.704 45.455 11.41 11.41 0.00 2.41
3275 7169 2.158682 TCTGTTTAGCCTTCTGTTGCCA 60.159 45.455 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.