Multiple sequence alignment - TraesCS2B01G218300

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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 TraesCS2B01G218300 chr2B 100.000 3666 0 0 1 3666 207099458 207103123 0.000000e+00 6770.0
1 TraesCS2B01G218300 chr2B 91.017 2015 130 27 661 2674 207470905 207472869 0.000000e+00 2671.0
2 TraesCS2B01G218300 chr2B 80.365 1589 277 25 1000 2573 207482067 207483635 0.000000e+00 1173.0
3 TraesCS2B01G218300 chr2B 91.626 203 15 1 194 394 207470691 207470893 2.790000e-71 279.0
4 TraesCS2B01G218300 chr2A 95.926 1988 75 4 651 2636 155075234 155073251 0.000000e+00 3217.0
5 TraesCS2B01G218300 chr2A 91.971 1669 116 8 1000 2667 154849656 154848005 0.000000e+00 2324.0
6 TraesCS2B01G218300 chr2A 82.138 1366 236 7 1213 2574 154422566 154421205 0.000000e+00 1164.0
7 TraesCS2B01G218300 chr2A 93.103 261 12 3 397 652 362286520 362286779 9.610000e-101 377.0
8 TraesCS2B01G218300 chr2A 91.667 264 16 3 397 655 27092417 27092679 9.680000e-96 361.0
9 TraesCS2B01G218300 chr2A 91.985 262 12 4 397 653 602718868 602719125 3.480000e-95 359.0
10 TraesCS2B01G218300 chr2A 90.943 265 19 2 396 655 5765330 5765066 5.820000e-93 351.0
11 TraesCS2B01G218300 chr2A 90.637 267 20 2 391 652 48493614 48493880 2.090000e-92 350.0
12 TraesCS2B01G218300 chr2A 83.729 295 27 10 107 394 154850219 154849939 3.630000e-65 259.0
13 TraesCS2B01G218300 chr2A 86.243 189 10 6 661 849 154849928 154849756 1.340000e-44 191.0
14 TraesCS2B01G218300 chr2D 97.864 1732 37 0 954 2685 147425991 147427722 0.000000e+00 2994.0
15 TraesCS2B01G218300 chr2D 90.316 2024 143 23 661 2674 147937612 147939592 0.000000e+00 2603.0
16 TraesCS2B01G218300 chr2D 82.185 1364 239 4 1213 2574 147953717 147955078 0.000000e+00 1170.0
17 TraesCS2B01G218300 chr2D 93.985 399 14 4 1 399 147424345 147424733 2.440000e-166 595.0
18 TraesCS2B01G218300 chr2D 98.077 312 6 0 651 962 147424731 147425042 8.950000e-151 544.0
19 TraesCS2B01G218300 chr2D 87.560 209 16 6 194 394 147937394 147937600 2.200000e-57 233.0
20 TraesCS2B01G218300 chr2D 97.143 35 1 0 2778 2812 147427899 147427933 3.950000e-05 60.2
21 TraesCS2B01G218300 chr1D 81.785 1356 241 6 1213 2565 483972824 483974176 0.000000e+00 1131.0
22 TraesCS2B01G218300 chr7B 80.674 771 127 17 2904 3666 425223044 425222288 2.450000e-161 579.0
23 TraesCS2B01G218300 chr7B 81.470 653 121 0 3014 3666 728936361 728937013 1.500000e-148 536.0
24 TraesCS2B01G218300 chr5B 93.889 360 21 1 3307 3666 703176095 703176453 3.220000e-150 542.0
25 TraesCS2B01G218300 chr5B 89.731 409 38 4 2904 3311 703174968 703175373 1.510000e-143 520.0
26 TraesCS2B01G218300 chr7D 81.402 656 116 4 3014 3666 508346867 508346215 6.970000e-147 531.0
27 TraesCS2B01G218300 chr6A 93.561 264 12 2 397 655 326629976 326629713 4.440000e-104 388.0
28 TraesCS2B01G218300 chr6A 92.803 264 12 4 396 653 399204616 399204354 3.460000e-100 375.0
29 TraesCS2B01G218300 chr3A 93.233 266 12 3 392 652 339745683 339745419 1.600000e-103 387.0
30 TraesCS2B01G218300 chr1A 93.333 255 11 3 403 652 147451190 147450937 4.470000e-99 372.0
31 TraesCS2B01G218300 chr6D 82.946 387 66 0 3280 3666 385459975 385460361 2.090000e-92 350.0


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 TraesCS2B01G218300 chr2B 207099458 207103123 3665 False 6770.000000 6770 100.000000 1 3666 1 chr2B.!!$F1 3665
1 TraesCS2B01G218300 chr2B 207470691 207472869 2178 False 1475.000000 2671 91.321500 194 2674 2 chr2B.!!$F3 2480
2 TraesCS2B01G218300 chr2B 207482067 207483635 1568 False 1173.000000 1173 80.365000 1000 2573 1 chr2B.!!$F2 1573
3 TraesCS2B01G218300 chr2A 155073251 155075234 1983 True 3217.000000 3217 95.926000 651 2636 1 chr2A.!!$R3 1985
4 TraesCS2B01G218300 chr2A 154421205 154422566 1361 True 1164.000000 1164 82.138000 1213 2574 1 chr2A.!!$R2 1361
5 TraesCS2B01G218300 chr2A 154848005 154850219 2214 True 924.666667 2324 87.314333 107 2667 3 chr2A.!!$R4 2560
6 TraesCS2B01G218300 chr2D 147937394 147939592 2198 False 1418.000000 2603 88.938000 194 2674 2 chr2D.!!$F3 2480
7 TraesCS2B01G218300 chr2D 147953717 147955078 1361 False 1170.000000 1170 82.185000 1213 2574 1 chr2D.!!$F1 1361
8 TraesCS2B01G218300 chr2D 147424345 147427933 3588 False 1048.300000 2994 96.767250 1 2812 4 chr2D.!!$F2 2811
9 TraesCS2B01G218300 chr1D 483972824 483974176 1352 False 1131.000000 1131 81.785000 1213 2565 1 chr1D.!!$F1 1352
10 TraesCS2B01G218300 chr7B 425222288 425223044 756 True 579.000000 579 80.674000 2904 3666 1 chr7B.!!$R1 762
11 TraesCS2B01G218300 chr7B 728936361 728937013 652 False 536.000000 536 81.470000 3014 3666 1 chr7B.!!$F1 652
12 TraesCS2B01G218300 chr5B 703174968 703176453 1485 False 531.000000 542 91.810000 2904 3666 2 chr5B.!!$F1 762
13 TraesCS2B01G218300 chr7D 508346215 508346867 652 True 531.000000 531 81.402000 3014 3666 1 chr7D.!!$R1 652

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
448 459 1.745232 TGGTCAAAGTCAAGCGTTGT 58.255 45.000 0.00 0.0 37.72 3.32 F
1187 2217 1.069668 AGCGATGATGACTGCTGCATA 59.930 47.619 1.31 0.0 36.09 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1291 2321 0.110678 AGATGCTCAGGATGCCCATG 59.889 55.0 0.0 0.0 34.76 3.66 R
2827 3979 0.105709 GAGAGAGGAGAGGGGAAGGG 60.106 65.0 0.0 0.0 0.00 3.95 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
73 74 3.246416 AGTCCCAGAGTACAGAGTTGT 57.754 47.619 0.00 0.00 41.39 3.32
133 136 8.415950 TTGGATTACTTCAGCCTCAAAATTTA 57.584 30.769 0.00 0.00 0.00 1.40
233 238 2.359900 CGGCAGGAGCTCAAAGTTAAT 58.640 47.619 17.19 0.00 41.70 1.40
287 292 6.310956 GCTCAGCATATTATGTCATCAGAGAC 59.689 42.308 5.60 0.00 38.99 3.36
396 407 2.093869 GGCCATGTGCTGAAACAATCAT 60.094 45.455 0.00 0.00 40.92 2.45
398 409 4.107622 GCCATGTGCTGAAACAATCATAC 58.892 43.478 0.00 0.00 37.44 2.39
399 410 4.142315 GCCATGTGCTGAAACAATCATACT 60.142 41.667 0.00 0.00 37.44 2.12
400 411 5.575957 CCATGTGCTGAAACAATCATACTC 58.424 41.667 0.00 0.00 37.44 2.59
401 412 4.926860 TGTGCTGAAACAATCATACTCG 57.073 40.909 0.00 0.00 37.44 4.18
402 413 3.125146 TGTGCTGAAACAATCATACTCGC 59.875 43.478 0.00 0.00 37.44 5.03
404 415 3.618594 TGCTGAAACAATCATACTCGCTC 59.381 43.478 0.00 0.00 37.44 5.03
405 416 3.302092 GCTGAAACAATCATACTCGCTCG 60.302 47.826 0.00 0.00 37.44 5.03
406 417 3.186909 TGAAACAATCATACTCGCTCGG 58.813 45.455 0.00 0.00 31.50 4.63
407 418 2.961526 AACAATCATACTCGCTCGGT 57.038 45.000 0.00 0.00 0.00 4.69
408 419 2.961526 ACAATCATACTCGCTCGGTT 57.038 45.000 0.00 0.00 0.00 4.44
409 420 3.247006 ACAATCATACTCGCTCGGTTT 57.753 42.857 0.00 0.00 0.00 3.27
410 421 3.187700 ACAATCATACTCGCTCGGTTTC 58.812 45.455 0.00 0.00 0.00 2.78
411 422 3.119101 ACAATCATACTCGCTCGGTTTCT 60.119 43.478 0.00 0.00 0.00 2.52
412 423 3.802948 ATCATACTCGCTCGGTTTCTT 57.197 42.857 0.00 0.00 0.00 2.52
413 424 3.587797 TCATACTCGCTCGGTTTCTTT 57.412 42.857 0.00 0.00 0.00 2.52
414 425 3.921677 TCATACTCGCTCGGTTTCTTTT 58.078 40.909 0.00 0.00 0.00 2.27
415 426 4.312443 TCATACTCGCTCGGTTTCTTTTT 58.688 39.130 0.00 0.00 0.00 1.94
416 427 5.472148 TCATACTCGCTCGGTTTCTTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
417 428 5.575606 TCATACTCGCTCGGTTTCTTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
418 429 3.725490 ACTCGCTCGGTTTCTTTTTAGT 58.275 40.909 0.00 0.00 0.00 2.24
419 430 3.739810 ACTCGCTCGGTTTCTTTTTAGTC 59.260 43.478 0.00 0.00 0.00 2.59
420 431 3.986277 TCGCTCGGTTTCTTTTTAGTCT 58.014 40.909 0.00 0.00 0.00 3.24
421 432 3.739300 TCGCTCGGTTTCTTTTTAGTCTG 59.261 43.478 0.00 0.00 0.00 3.51
422 433 3.664537 CGCTCGGTTTCTTTTTAGTCTGC 60.665 47.826 0.00 0.00 0.00 4.26
423 434 3.250040 GCTCGGTTTCTTTTTAGTCTGCA 59.750 43.478 0.00 0.00 0.00 4.41
424 435 4.261031 GCTCGGTTTCTTTTTAGTCTGCAA 60.261 41.667 0.00 0.00 0.00 4.08
425 436 5.418310 TCGGTTTCTTTTTAGTCTGCAAG 57.582 39.130 0.00 0.00 0.00 4.01
426 437 5.120399 TCGGTTTCTTTTTAGTCTGCAAGA 58.880 37.500 0.00 0.00 43.69 3.02
439 450 4.836125 TCTGCAAGATTTGGTCAAAGTC 57.164 40.909 2.55 1.51 38.67 3.01
440 451 4.206375 TCTGCAAGATTTGGTCAAAGTCA 58.794 39.130 2.55 0.00 38.67 3.41
441 452 4.644234 TCTGCAAGATTTGGTCAAAGTCAA 59.356 37.500 2.55 0.00 38.67 3.18
442 453 4.935702 TGCAAGATTTGGTCAAAGTCAAG 58.064 39.130 2.55 0.50 33.32 3.02
443 454 3.737774 GCAAGATTTGGTCAAAGTCAAGC 59.262 43.478 2.55 5.23 33.32 4.01
444 455 3.904136 AGATTTGGTCAAAGTCAAGCG 57.096 42.857 2.55 0.00 33.32 4.68
445 456 3.214328 AGATTTGGTCAAAGTCAAGCGT 58.786 40.909 2.55 0.00 33.32 5.07
446 457 3.632145 AGATTTGGTCAAAGTCAAGCGTT 59.368 39.130 2.55 0.00 33.32 4.84
447 458 2.842208 TTGGTCAAAGTCAAGCGTTG 57.158 45.000 0.00 0.00 37.80 4.10
448 459 1.745232 TGGTCAAAGTCAAGCGTTGT 58.255 45.000 0.00 0.00 37.72 3.32
449 460 2.907634 TGGTCAAAGTCAAGCGTTGTA 58.092 42.857 0.00 0.00 37.72 2.41
450 461 3.271729 TGGTCAAAGTCAAGCGTTGTAA 58.728 40.909 0.00 0.00 37.72 2.41
451 462 3.690139 TGGTCAAAGTCAAGCGTTGTAAA 59.310 39.130 0.00 0.00 37.72 2.01
452 463 4.201871 TGGTCAAAGTCAAGCGTTGTAAAG 60.202 41.667 0.00 0.00 37.72 1.85
453 464 4.201881 GGTCAAAGTCAAGCGTTGTAAAGT 60.202 41.667 0.00 0.00 37.72 2.66
454 465 5.329493 GTCAAAGTCAAGCGTTGTAAAGTT 58.671 37.500 0.00 0.00 37.72 2.66
455 466 5.798434 GTCAAAGTCAAGCGTTGTAAAGTTT 59.202 36.000 0.00 0.00 37.72 2.66
456 467 5.797934 TCAAAGTCAAGCGTTGTAAAGTTTG 59.202 36.000 0.00 1.90 37.72 2.93
457 468 5.554822 AAGTCAAGCGTTGTAAAGTTTGA 57.445 34.783 0.00 5.92 35.72 2.69
459 470 4.033019 GTCAAGCGTTGTAAAGTTTGACC 58.967 43.478 20.65 9.62 46.03 4.02
460 471 3.690139 TCAAGCGTTGTAAAGTTTGACCA 59.310 39.130 0.00 0.00 33.73 4.02
461 472 4.156190 TCAAGCGTTGTAAAGTTTGACCAA 59.844 37.500 0.00 0.00 33.73 3.67
462 473 4.023739 AGCGTTGTAAAGTTTGACCAAC 57.976 40.909 13.40 13.40 35.32 3.77
588 599 9.601217 TTGATATTTTCTCCTACAAAGCTAGTC 57.399 33.333 0.00 0.00 0.00 2.59
589 600 8.758829 TGATATTTTCTCCTACAAAGCTAGTCA 58.241 33.333 0.00 0.00 0.00 3.41
590 601 9.255304 GATATTTTCTCCTACAAAGCTAGTCAG 57.745 37.037 0.00 0.00 0.00 3.51
591 602 6.665992 TTTTCTCCTACAAAGCTAGTCAGA 57.334 37.500 0.00 0.00 0.00 3.27
592 603 5.646577 TTCTCCTACAAAGCTAGTCAGAC 57.353 43.478 0.00 0.00 0.00 3.51
593 604 4.924625 TCTCCTACAAAGCTAGTCAGACT 58.075 43.478 8.50 8.50 0.00 3.24
594 605 5.326069 TCTCCTACAAAGCTAGTCAGACTT 58.674 41.667 8.80 0.00 0.00 3.01
595 606 5.775701 TCTCCTACAAAGCTAGTCAGACTTT 59.224 40.000 8.80 0.00 34.03 2.66
596 607 6.946583 TCTCCTACAAAGCTAGTCAGACTTTA 59.053 38.462 8.80 0.00 32.54 1.85
597 608 6.921914 TCCTACAAAGCTAGTCAGACTTTAC 58.078 40.000 8.80 0.00 32.54 2.01
598 609 6.492429 TCCTACAAAGCTAGTCAGACTTTACA 59.508 38.462 8.80 0.00 32.54 2.41
599 610 7.178628 TCCTACAAAGCTAGTCAGACTTTACAT 59.821 37.037 8.80 0.00 32.54 2.29
600 611 8.467598 CCTACAAAGCTAGTCAGACTTTACATA 58.532 37.037 8.80 0.00 32.54 2.29
601 612 9.509855 CTACAAAGCTAGTCAGACTTTACATAG 57.490 37.037 8.80 0.00 32.54 2.23
602 613 7.897864 ACAAAGCTAGTCAGACTTTACATAGT 58.102 34.615 8.80 0.00 32.54 2.12
603 614 8.368668 ACAAAGCTAGTCAGACTTTACATAGTT 58.631 33.333 8.80 0.00 32.54 2.24
604 615 8.651588 CAAAGCTAGTCAGACTTTACATAGTTG 58.348 37.037 8.80 0.00 32.54 3.16
605 616 7.704578 AGCTAGTCAGACTTTACATAGTTGA 57.295 36.000 8.80 0.00 0.00 3.18
606 617 7.540299 AGCTAGTCAGACTTTACATAGTTGAC 58.460 38.462 8.80 0.00 36.95 3.18
607 618 7.394923 AGCTAGTCAGACTTTACATAGTTGACT 59.605 37.037 8.80 17.31 42.40 3.41
608 619 8.030106 GCTAGTCAGACTTTACATAGTTGACTT 58.970 37.037 8.80 9.24 41.38 3.01
609 620 9.915629 CTAGTCAGACTTTACATAGTTGACTTT 57.084 33.333 8.80 6.55 41.38 2.66
610 621 8.594881 AGTCAGACTTTACATAGTTGACTTTG 57.405 34.615 0.00 0.87 40.03 2.77
611 622 8.421784 AGTCAGACTTTACATAGTTGACTTTGA 58.578 33.333 0.00 0.00 40.03 2.69
612 623 9.209175 GTCAGACTTTACATAGTTGACTTTGAT 57.791 33.333 8.29 0.00 35.57 2.57
613 624 9.424319 TCAGACTTTACATAGTTGACTTTGATC 57.576 33.333 8.29 0.00 0.00 2.92
614 625 9.208022 CAGACTTTACATAGTTGACTTTGATCA 57.792 33.333 8.29 0.00 0.00 2.92
615 626 9.778741 AGACTTTACATAGTTGACTTTGATCAA 57.221 29.630 3.38 3.38 36.23 2.57
627 638 9.162793 GTTGACTTTGATCAAATCTTATATGCG 57.837 33.333 20.76 8.05 40.22 4.73
628 639 8.661352 TGACTTTGATCAAATCTTATATGCGA 57.339 30.769 20.76 0.00 0.00 5.10
629 640 9.108284 TGACTTTGATCAAATCTTATATGCGAA 57.892 29.630 20.76 0.00 0.00 4.70
630 641 9.374960 GACTTTGATCAAATCTTATATGCGAAC 57.625 33.333 20.76 3.21 0.00 3.95
631 642 9.113838 ACTTTGATCAAATCTTATATGCGAACT 57.886 29.630 20.76 0.00 0.00 3.01
642 653 9.916397 ATCTTATATGCGAACTAAAAAGAAACG 57.084 29.630 0.00 0.00 0.00 3.60
643 654 8.385111 TCTTATATGCGAACTAAAAAGAAACGG 58.615 33.333 0.00 0.00 0.00 4.44
644 655 6.730960 ATATGCGAACTAAAAAGAAACGGA 57.269 33.333 0.00 0.00 0.00 4.69
645 656 4.461992 TGCGAACTAAAAAGAAACGGAG 57.538 40.909 0.00 0.00 0.00 4.63
646 657 3.249080 TGCGAACTAAAAAGAAACGGAGG 59.751 43.478 0.00 0.00 0.00 4.30
647 658 3.364664 GCGAACTAAAAAGAAACGGAGGG 60.365 47.826 0.00 0.00 0.00 4.30
648 659 4.060205 CGAACTAAAAAGAAACGGAGGGA 58.940 43.478 0.00 0.00 0.00 4.20
649 660 4.151867 CGAACTAAAAAGAAACGGAGGGAG 59.848 45.833 0.00 0.00 0.00 4.30
701 714 9.113838 ACAATAATCAGATAGTTGGTTGATCAC 57.886 33.333 0.00 0.00 30.39 3.06
786 801 8.024145 AGTATAAAAAGGTCCTGGAGATAGTG 57.976 38.462 0.00 0.00 0.00 2.74
964 1952 1.820906 CATGGTCAGTGGCATCCCG 60.821 63.158 0.00 0.00 0.00 5.14
972 1960 3.321648 TGGCATCCCGCTGTGAGT 61.322 61.111 0.00 0.00 41.91 3.41
1187 2217 1.069668 AGCGATGATGACTGCTGCATA 59.930 47.619 1.31 0.00 36.09 3.14
1291 2321 1.142748 CGTGCAGGTGGAGATCCTC 59.857 63.158 0.00 0.00 36.82 3.71
1428 2458 2.819595 GCTCATGGGCTTCGCGAA 60.820 61.111 22.01 22.01 0.00 4.70
2005 3035 2.915659 TCCGACTCCGTGGTGCTT 60.916 61.111 0.00 0.00 0.00 3.91
2110 3140 3.069980 GCTCGTCATCCTGGTCGCT 62.070 63.158 0.00 0.00 0.00 4.93
2515 3545 0.178891 TCTTCTTCACCTGCCTCCCT 60.179 55.000 0.00 0.00 0.00 4.20
2667 3697 4.444876 GCCTGGAGCCAGAGTTGATTAATA 60.445 45.833 17.88 0.00 46.30 0.98
2669 3699 6.122277 CCTGGAGCCAGAGTTGATTAATAAA 58.878 40.000 17.88 0.00 46.30 1.40
2688 3718 7.688918 AATAAAATGAATATTTGGGGCTGGA 57.311 32.000 0.00 0.00 36.65 3.86
2689 3719 7.876978 ATAAAATGAATATTTGGGGCTGGAT 57.123 32.000 0.00 0.00 36.65 3.41
2690 3720 6.579850 AAAATGAATATTTGGGGCTGGATT 57.420 33.333 0.00 0.00 36.65 3.01
2691 3721 5.556006 AATGAATATTTGGGGCTGGATTG 57.444 39.130 0.00 0.00 0.00 2.67
2692 3722 3.992999 TGAATATTTGGGGCTGGATTGT 58.007 40.909 0.00 0.00 0.00 2.71
2693 3723 3.960102 TGAATATTTGGGGCTGGATTGTC 59.040 43.478 0.00 0.00 0.00 3.18
2694 3724 3.686227 ATATTTGGGGCTGGATTGTCA 57.314 42.857 0.00 0.00 0.00 3.58
2695 3725 1.560505 ATTTGGGGCTGGATTGTCAC 58.439 50.000 0.00 0.00 0.00 3.67
2696 3726 0.187117 TTTGGGGCTGGATTGTCACA 59.813 50.000 0.00 0.00 0.00 3.58
2697 3727 0.409092 TTGGGGCTGGATTGTCACAT 59.591 50.000 0.00 0.00 0.00 3.21
2698 3728 0.034186 TGGGGCTGGATTGTCACATC 60.034 55.000 0.00 0.00 0.00 3.06
2699 3729 0.034186 GGGGCTGGATTGTCACATCA 60.034 55.000 0.00 0.00 0.00 3.07
2700 3730 1.098050 GGGCTGGATTGTCACATCAC 58.902 55.000 0.00 0.00 0.00 3.06
2701 3731 1.098050 GGCTGGATTGTCACATCACC 58.902 55.000 0.00 0.00 0.00 4.02
2702 3732 1.614051 GGCTGGATTGTCACATCACCA 60.614 52.381 0.00 0.00 0.00 4.17
2703 3733 1.470098 GCTGGATTGTCACATCACCAC 59.530 52.381 0.00 0.00 0.00 4.16
2704 3734 2.781923 CTGGATTGTCACATCACCACA 58.218 47.619 0.00 0.00 0.00 4.17
2705 3735 3.349927 CTGGATTGTCACATCACCACAT 58.650 45.455 0.00 0.00 0.00 3.21
2706 3736 3.346315 TGGATTGTCACATCACCACATC 58.654 45.455 0.00 0.00 0.00 3.06
2707 3737 3.244840 TGGATTGTCACATCACCACATCA 60.245 43.478 0.00 0.00 0.00 3.07
2708 3738 3.376234 GGATTGTCACATCACCACATCAG 59.624 47.826 0.00 0.00 0.00 2.90
2709 3739 3.767902 TTGTCACATCACCACATCAGA 57.232 42.857 0.00 0.00 0.00 3.27
2710 3740 3.044235 TGTCACATCACCACATCAGAC 57.956 47.619 0.00 0.00 0.00 3.51
2711 3741 2.634453 TGTCACATCACCACATCAGACT 59.366 45.455 0.00 0.00 0.00 3.24
2712 3742 3.071457 TGTCACATCACCACATCAGACTT 59.929 43.478 0.00 0.00 0.00 3.01
2713 3743 4.067896 GTCACATCACCACATCAGACTTT 58.932 43.478 0.00 0.00 0.00 2.66
2714 3744 5.221621 TGTCACATCACCACATCAGACTTTA 60.222 40.000 0.00 0.00 0.00 1.85
2715 3745 5.120830 GTCACATCACCACATCAGACTTTAC 59.879 44.000 0.00 0.00 0.00 2.01
2716 3746 4.996758 CACATCACCACATCAGACTTTACA 59.003 41.667 0.00 0.00 0.00 2.41
2717 3747 5.121298 CACATCACCACATCAGACTTTACAG 59.879 44.000 0.00 0.00 0.00 2.74
2718 3748 5.012046 ACATCACCACATCAGACTTTACAGA 59.988 40.000 0.00 0.00 0.00 3.41
2719 3749 4.883083 TCACCACATCAGACTTTACAGAC 58.117 43.478 0.00 0.00 0.00 3.51
2720 3750 4.588951 TCACCACATCAGACTTTACAGACT 59.411 41.667 0.00 0.00 0.00 3.24
2721 3751 5.070446 TCACCACATCAGACTTTACAGACTT 59.930 40.000 0.00 0.00 0.00 3.01
2722 3752 5.178252 CACCACATCAGACTTTACAGACTTG 59.822 44.000 0.00 0.00 0.00 3.16
2723 3753 4.692625 CCACATCAGACTTTACAGACTTGG 59.307 45.833 0.00 0.00 0.00 3.61
2724 3754 5.511373 CCACATCAGACTTTACAGACTTGGA 60.511 44.000 0.00 0.00 0.00 3.53
2725 3755 5.636965 CACATCAGACTTTACAGACTTGGAG 59.363 44.000 0.00 0.00 0.00 3.86
2726 3756 5.540337 ACATCAGACTTTACAGACTTGGAGA 59.460 40.000 0.00 0.00 0.00 3.71
2732 3762 9.689976 CAGACTTTACAGACTTGGAGATATATG 57.310 37.037 0.00 0.00 0.00 1.78
2747 3777 7.555195 TGGAGATATATGAAAATATGCTGCCAG 59.445 37.037 0.00 0.00 0.00 4.85
2750 3780 1.113788 TGAAAATATGCTGCCAGGGC 58.886 50.000 2.62 2.62 42.35 5.19
2751 3781 1.342275 TGAAAATATGCTGCCAGGGCT 60.342 47.619 12.19 0.00 42.51 5.19
2752 3782 2.091939 TGAAAATATGCTGCCAGGGCTA 60.092 45.455 12.19 0.00 42.51 3.93
2754 3784 2.986534 AATATGCTGCCAGGGCTAAT 57.013 45.000 12.19 5.20 42.51 1.73
2756 3786 2.276732 TATGCTGCCAGGGCTAATTC 57.723 50.000 12.19 0.00 42.51 2.17
2757 3787 0.554792 ATGCTGCCAGGGCTAATTCT 59.445 50.000 12.19 0.00 42.51 2.40
2758 3788 0.394762 TGCTGCCAGGGCTAATTCTG 60.395 55.000 12.19 0.00 42.51 3.02
2759 3789 1.732417 GCTGCCAGGGCTAATTCTGC 61.732 60.000 12.19 1.47 42.51 4.26
2769 3799 2.622436 GCTAATTCTGCTTGGTCTCGT 58.378 47.619 0.00 0.00 0.00 4.18
2812 3964 5.843673 TGCTTCTTACATTTTGGAACACA 57.156 34.783 0.00 0.00 39.29 3.72
2813 3965 6.214191 TGCTTCTTACATTTTGGAACACAA 57.786 33.333 0.00 0.00 39.29 3.33
2814 3966 6.634805 TGCTTCTTACATTTTGGAACACAAA 58.365 32.000 0.00 0.00 46.82 2.83
2826 3978 6.870971 TTGGAACACAAACTAGTGGTTATC 57.129 37.500 0.00 0.00 40.09 1.75
2827 3979 5.310451 TGGAACACAAACTAGTGGTTATCC 58.690 41.667 15.34 15.34 40.09 2.59
2828 3980 4.698780 GGAACACAAACTAGTGGTTATCCC 59.301 45.833 0.00 0.00 40.09 3.85
2829 3981 4.296621 ACACAAACTAGTGGTTATCCCC 57.703 45.455 0.00 0.00 43.72 4.81
2830 3982 3.914435 ACACAAACTAGTGGTTATCCCCT 59.086 43.478 0.00 0.00 43.72 4.79
2831 3983 4.352893 ACACAAACTAGTGGTTATCCCCTT 59.647 41.667 0.00 0.00 43.72 3.95
2832 3984 4.941873 CACAAACTAGTGGTTATCCCCTTC 59.058 45.833 0.00 0.00 37.12 3.46
2833 3985 4.018688 ACAAACTAGTGGTTATCCCCTTCC 60.019 45.833 0.00 0.00 37.12 3.46
2834 3986 2.772930 ACTAGTGGTTATCCCCTTCCC 58.227 52.381 0.00 0.00 0.00 3.97
2835 3987 2.055579 CTAGTGGTTATCCCCTTCCCC 58.944 57.143 0.00 0.00 0.00 4.81
2836 3988 0.426022 AGTGGTTATCCCCTTCCCCT 59.574 55.000 0.00 0.00 0.00 4.79
2837 3989 0.844660 GTGGTTATCCCCTTCCCCTC 59.155 60.000 0.00 0.00 0.00 4.30
2838 3990 0.728843 TGGTTATCCCCTTCCCCTCT 59.271 55.000 0.00 0.00 0.00 3.69
2839 3991 1.345112 TGGTTATCCCCTTCCCCTCTC 60.345 57.143 0.00 0.00 0.00 3.20
2840 3992 1.436326 GTTATCCCCTTCCCCTCTCC 58.564 60.000 0.00 0.00 0.00 3.71
2841 3993 1.061268 GTTATCCCCTTCCCCTCTCCT 60.061 57.143 0.00 0.00 0.00 3.69
2842 3994 0.868186 TATCCCCTTCCCCTCTCCTC 59.132 60.000 0.00 0.00 0.00 3.71
2843 3995 0.938926 ATCCCCTTCCCCTCTCCTCT 60.939 60.000 0.00 0.00 0.00 3.69
2844 3996 1.074850 CCCCTTCCCCTCTCCTCTC 60.075 68.421 0.00 0.00 0.00 3.20
2845 3997 1.598856 CCCCTTCCCCTCTCCTCTCT 61.599 65.000 0.00 0.00 0.00 3.10
2846 3998 0.105709 CCCTTCCCCTCTCCTCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
2847 3999 0.105709 CCTTCCCCTCTCCTCTCTCC 60.106 65.000 0.00 0.00 0.00 3.71
2848 4000 0.105709 CTTCCCCTCTCCTCTCTCCC 60.106 65.000 0.00 0.00 0.00 4.30
2849 4001 1.595058 TTCCCCTCTCCTCTCTCCCC 61.595 65.000 0.00 0.00 0.00 4.81
2850 4002 2.018086 CCCCTCTCCTCTCTCCCCT 61.018 68.421 0.00 0.00 0.00 4.79
2851 4003 1.598856 CCCCTCTCCTCTCTCCCCTT 61.599 65.000 0.00 0.00 0.00 3.95
2852 4004 0.105709 CCCTCTCCTCTCTCCCCTTC 60.106 65.000 0.00 0.00 0.00 3.46
2853 4005 0.105709 CCTCTCCTCTCTCCCCTTCC 60.106 65.000 0.00 0.00 0.00 3.46
2854 4006 0.105709 CTCTCCTCTCTCCCCTTCCC 60.106 65.000 0.00 0.00 0.00 3.97
2855 4007 1.074850 CTCCTCTCTCCCCTTCCCC 60.075 68.421 0.00 0.00 0.00 4.81
2856 4008 2.040359 CCTCTCTCCCCTTCCCCC 60.040 72.222 0.00 0.00 0.00 5.40
2857 4009 2.444895 CTCTCTCCCCTTCCCCCG 60.445 72.222 0.00 0.00 0.00 5.73
2858 4010 4.798682 TCTCTCCCCTTCCCCCGC 62.799 72.222 0.00 0.00 0.00 6.13
2947 4099 1.599047 CATCCACTCCGCCTTCAGT 59.401 57.895 0.00 0.00 0.00 3.41
2948 4100 0.036010 CATCCACTCCGCCTTCAGTT 60.036 55.000 0.00 0.00 0.00 3.16
2992 4145 2.685380 CGCCCACTCCTCTCCCTT 60.685 66.667 0.00 0.00 0.00 3.95
2997 4150 1.690985 CACTCCTCTCCCTTCCCCC 60.691 68.421 0.00 0.00 0.00 5.40
2998 4151 1.869452 ACTCCTCTCCCTTCCCCCT 60.869 63.158 0.00 0.00 0.00 4.79
3012 4165 1.302285 CCCCTGTGCAAGCAGATCT 59.698 57.895 5.92 0.00 38.70 2.75
3323 5202 2.562876 GGTCCCGGCCGATCTCTAC 61.563 68.421 30.73 14.24 0.00 2.59
3410 5289 2.583441 CCGCTGTGGACTTGAGGGA 61.583 63.158 0.00 0.00 42.00 4.20
3433 5312 1.135717 CATTTCGTCGGATTGCAAGCA 60.136 47.619 17.68 0.00 0.00 3.91
3434 5313 1.164411 TTTCGTCGGATTGCAAGCAT 58.836 45.000 17.68 0.00 0.00 3.79
3437 5316 1.368345 CGTCGGATTGCAAGCATCCA 61.368 55.000 17.68 1.81 34.22 3.41
3654 5533 3.215245 GAGGCGTCTGCATCCTCT 58.785 61.111 0.00 0.00 45.85 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 5.420739 GCAGGGGAATTCTAACATAAAACCA 59.579 40.000 5.23 0.00 0.00 3.67
133 136 8.674263 TTTTCAAGGAAATTACACAAATGCAT 57.326 26.923 0.00 0.00 31.34 3.96
183 186 5.912149 TTGCCAAAGAGGGAGTATGATAT 57.088 39.130 0.00 0.00 39.73 1.63
186 189 3.587061 TCTTTGCCAAAGAGGGAGTATGA 59.413 43.478 15.70 0.00 42.31 2.15
187 190 3.955471 TCTTTGCCAAAGAGGGAGTATG 58.045 45.455 15.70 0.00 42.31 2.39
233 238 0.474614 TTCCCGGTGAAACATCCACA 59.525 50.000 0.00 0.00 39.98 4.17
260 265 6.527423 TCTGATGACATAATATGCTGAGCAA 58.473 36.000 12.69 0.97 43.62 3.91
261 266 6.014840 TCTCTGATGACATAATATGCTGAGCA 60.015 38.462 10.59 10.59 44.86 4.26
287 292 4.434593 GCTGCAACAAATTTTCTATTGCCG 60.435 41.667 17.20 13.88 43.97 5.69
396 407 4.874970 ACTAAAAAGAAACCGAGCGAGTA 58.125 39.130 0.00 0.00 0.00 2.59
398 409 3.988517 AGACTAAAAAGAAACCGAGCGAG 59.011 43.478 0.00 0.00 0.00 5.03
399 410 3.739300 CAGACTAAAAAGAAACCGAGCGA 59.261 43.478 0.00 0.00 0.00 4.93
400 411 3.664537 GCAGACTAAAAAGAAACCGAGCG 60.665 47.826 0.00 0.00 0.00 5.03
401 412 3.250040 TGCAGACTAAAAAGAAACCGAGC 59.750 43.478 0.00 0.00 0.00 5.03
402 413 5.236478 TCTTGCAGACTAAAAAGAAACCGAG 59.764 40.000 0.00 0.00 0.00 4.63
404 415 5.418310 TCTTGCAGACTAAAAAGAAACCG 57.582 39.130 0.00 0.00 0.00 4.44
405 416 7.169813 CCAAATCTTGCAGACTAAAAAGAAACC 59.830 37.037 0.00 0.00 32.72 3.27
406 417 7.706607 ACCAAATCTTGCAGACTAAAAAGAAAC 59.293 33.333 0.00 0.00 32.72 2.78
407 418 7.781056 ACCAAATCTTGCAGACTAAAAAGAAA 58.219 30.769 0.00 0.00 32.72 2.52
408 419 7.068103 TGACCAAATCTTGCAGACTAAAAAGAA 59.932 33.333 0.00 0.00 32.72 2.52
409 420 6.545666 TGACCAAATCTTGCAGACTAAAAAGA 59.454 34.615 0.00 0.00 33.45 2.52
410 421 6.738114 TGACCAAATCTTGCAGACTAAAAAG 58.262 36.000 0.00 0.00 0.00 2.27
411 422 6.707440 TGACCAAATCTTGCAGACTAAAAA 57.293 33.333 0.00 0.00 0.00 1.94
412 423 6.707440 TTGACCAAATCTTGCAGACTAAAA 57.293 33.333 0.00 0.00 0.00 1.52
413 424 6.321181 ACTTTGACCAAATCTTGCAGACTAAA 59.679 34.615 0.00 0.00 0.00 1.85
414 425 5.827797 ACTTTGACCAAATCTTGCAGACTAA 59.172 36.000 0.00 0.00 0.00 2.24
415 426 5.376625 ACTTTGACCAAATCTTGCAGACTA 58.623 37.500 0.00 0.00 0.00 2.59
416 427 4.210331 ACTTTGACCAAATCTTGCAGACT 58.790 39.130 0.00 0.00 0.00 3.24
417 428 4.036734 TGACTTTGACCAAATCTTGCAGAC 59.963 41.667 0.00 0.00 0.00 3.51
418 429 4.206375 TGACTTTGACCAAATCTTGCAGA 58.794 39.130 0.00 0.00 0.00 4.26
419 430 4.572985 TGACTTTGACCAAATCTTGCAG 57.427 40.909 0.00 0.00 0.00 4.41
420 431 4.737352 GCTTGACTTTGACCAAATCTTGCA 60.737 41.667 0.00 0.00 0.00 4.08
421 432 3.737774 GCTTGACTTTGACCAAATCTTGC 59.262 43.478 0.00 3.00 0.00 4.01
422 433 3.976942 CGCTTGACTTTGACCAAATCTTG 59.023 43.478 0.00 0.00 0.00 3.02
423 434 3.632145 ACGCTTGACTTTGACCAAATCTT 59.368 39.130 0.00 0.00 0.00 2.40
424 435 3.214328 ACGCTTGACTTTGACCAAATCT 58.786 40.909 0.00 0.00 0.00 2.40
425 436 3.626028 ACGCTTGACTTTGACCAAATC 57.374 42.857 0.00 0.00 0.00 2.17
426 437 3.130340 ACAACGCTTGACTTTGACCAAAT 59.870 39.130 5.01 0.00 32.10 2.32
427 438 2.490115 ACAACGCTTGACTTTGACCAAA 59.510 40.909 5.01 0.00 32.10 3.28
428 439 2.088423 ACAACGCTTGACTTTGACCAA 58.912 42.857 5.01 0.00 32.10 3.67
429 440 1.745232 ACAACGCTTGACTTTGACCA 58.255 45.000 5.01 0.00 32.10 4.02
430 441 3.955771 TTACAACGCTTGACTTTGACC 57.044 42.857 5.01 0.00 32.10 4.02
431 442 4.905269 ACTTTACAACGCTTGACTTTGAC 58.095 39.130 5.01 0.00 32.10 3.18
432 443 5.554822 AACTTTACAACGCTTGACTTTGA 57.445 34.783 5.01 0.00 32.10 2.69
433 444 5.797934 TCAAACTTTACAACGCTTGACTTTG 59.202 36.000 5.01 0.00 33.85 2.77
434 445 5.798434 GTCAAACTTTACAACGCTTGACTTT 59.202 36.000 7.21 0.00 39.54 2.66
435 446 5.329493 GTCAAACTTTACAACGCTTGACTT 58.671 37.500 7.21 0.00 39.54 3.01
436 447 4.201881 GGTCAAACTTTACAACGCTTGACT 60.202 41.667 11.89 0.00 41.40 3.41
437 448 4.033019 GGTCAAACTTTACAACGCTTGAC 58.967 43.478 6.30 6.30 41.09 3.18
438 449 3.690139 TGGTCAAACTTTACAACGCTTGA 59.310 39.130 5.01 0.00 0.00 3.02
439 450 4.022464 TGGTCAAACTTTACAACGCTTG 57.978 40.909 0.00 0.00 0.00 4.01
440 451 4.417506 GTTGGTCAAACTTTACAACGCTT 58.582 39.130 0.00 0.00 35.75 4.68
441 452 4.023739 GTTGGTCAAACTTTACAACGCT 57.976 40.909 0.00 0.00 35.75 5.07
562 573 9.601217 GACTAGCTTTGTAGGAGAAAATATCAA 57.399 33.333 0.00 0.00 0.00 2.57
563 574 8.758829 TGACTAGCTTTGTAGGAGAAAATATCA 58.241 33.333 0.00 0.00 0.00 2.15
564 575 9.255304 CTGACTAGCTTTGTAGGAGAAAATATC 57.745 37.037 0.00 0.00 0.00 1.63
565 576 8.982723 TCTGACTAGCTTTGTAGGAGAAAATAT 58.017 33.333 0.00 0.00 0.00 1.28
566 577 8.251721 GTCTGACTAGCTTTGTAGGAGAAAATA 58.748 37.037 0.00 0.00 0.00 1.40
567 578 7.038658 AGTCTGACTAGCTTTGTAGGAGAAAAT 60.039 37.037 8.91 0.00 0.00 1.82
568 579 6.267928 AGTCTGACTAGCTTTGTAGGAGAAAA 59.732 38.462 8.91 0.00 0.00 2.29
569 580 5.775701 AGTCTGACTAGCTTTGTAGGAGAAA 59.224 40.000 8.91 0.00 0.00 2.52
570 581 5.326069 AGTCTGACTAGCTTTGTAGGAGAA 58.674 41.667 8.91 0.00 0.00 2.87
571 582 4.924625 AGTCTGACTAGCTTTGTAGGAGA 58.075 43.478 8.91 0.00 0.00 3.71
572 583 5.652994 AAGTCTGACTAGCTTTGTAGGAG 57.347 43.478 11.30 0.00 0.00 3.69
573 584 6.492429 TGTAAAGTCTGACTAGCTTTGTAGGA 59.508 38.462 11.30 0.00 34.45 2.94
574 585 6.688578 TGTAAAGTCTGACTAGCTTTGTAGG 58.311 40.000 11.30 0.00 34.45 3.18
575 586 9.509855 CTATGTAAAGTCTGACTAGCTTTGTAG 57.490 37.037 11.30 4.85 34.45 2.74
576 587 9.021807 ACTATGTAAAGTCTGACTAGCTTTGTA 57.978 33.333 11.30 0.00 34.45 2.41
577 588 7.897864 ACTATGTAAAGTCTGACTAGCTTTGT 58.102 34.615 11.30 6.94 34.45 2.83
578 589 8.651588 CAACTATGTAAAGTCTGACTAGCTTTG 58.348 37.037 11.30 2.15 34.45 2.77
579 590 8.585881 TCAACTATGTAAAGTCTGACTAGCTTT 58.414 33.333 11.30 4.28 35.72 3.51
580 591 8.030106 GTCAACTATGTAAAGTCTGACTAGCTT 58.970 37.037 11.30 4.65 36.13 3.74
581 592 7.394923 AGTCAACTATGTAAAGTCTGACTAGCT 59.605 37.037 11.30 1.69 41.15 3.32
582 593 7.540299 AGTCAACTATGTAAAGTCTGACTAGC 58.460 38.462 11.30 5.14 41.15 3.42
583 594 9.915629 AAAGTCAACTATGTAAAGTCTGACTAG 57.084 33.333 11.30 6.13 41.56 2.57
584 595 9.692749 CAAAGTCAACTATGTAAAGTCTGACTA 57.307 33.333 11.30 0.00 41.56 2.59
585 596 8.421784 TCAAAGTCAACTATGTAAAGTCTGACT 58.578 33.333 4.06 4.06 42.71 3.41
586 597 8.589335 TCAAAGTCAACTATGTAAAGTCTGAC 57.411 34.615 0.00 0.00 37.55 3.51
587 598 9.424319 GATCAAAGTCAACTATGTAAAGTCTGA 57.576 33.333 0.00 0.00 0.00 3.27
588 599 9.208022 TGATCAAAGTCAACTATGTAAAGTCTG 57.792 33.333 0.00 0.00 0.00 3.51
589 600 9.778741 TTGATCAAAGTCAACTATGTAAAGTCT 57.221 29.630 5.45 0.00 33.41 3.24
601 612 9.162793 CGCATATAAGATTTGATCAAAGTCAAC 57.837 33.333 24.17 13.22 37.80 3.18
602 613 9.108284 TCGCATATAAGATTTGATCAAAGTCAA 57.892 29.630 24.17 11.64 36.38 3.18
603 614 8.661352 TCGCATATAAGATTTGATCAAAGTCA 57.339 30.769 24.17 11.02 33.32 3.41
604 615 9.374960 GTTCGCATATAAGATTTGATCAAAGTC 57.625 33.333 24.17 19.70 33.32 3.01
605 616 9.113838 AGTTCGCATATAAGATTTGATCAAAGT 57.886 29.630 24.17 14.86 33.32 2.66
616 627 9.916397 CGTTTCTTTTTAGTTCGCATATAAGAT 57.084 29.630 0.00 0.00 0.00 2.40
617 628 8.385111 CCGTTTCTTTTTAGTTCGCATATAAGA 58.615 33.333 0.00 0.00 0.00 2.10
618 629 8.385111 TCCGTTTCTTTTTAGTTCGCATATAAG 58.615 33.333 0.00 0.00 0.00 1.73
619 630 8.254178 TCCGTTTCTTTTTAGTTCGCATATAA 57.746 30.769 0.00 0.00 0.00 0.98
620 631 7.010738 CCTCCGTTTCTTTTTAGTTCGCATATA 59.989 37.037 0.00 0.00 0.00 0.86
621 632 6.183360 CCTCCGTTTCTTTTTAGTTCGCATAT 60.183 38.462 0.00 0.00 0.00 1.78
622 633 5.121142 CCTCCGTTTCTTTTTAGTTCGCATA 59.879 40.000 0.00 0.00 0.00 3.14
623 634 4.083484 CCTCCGTTTCTTTTTAGTTCGCAT 60.083 41.667 0.00 0.00 0.00 4.73
624 635 3.249080 CCTCCGTTTCTTTTTAGTTCGCA 59.751 43.478 0.00 0.00 0.00 5.10
625 636 3.364664 CCCTCCGTTTCTTTTTAGTTCGC 60.365 47.826 0.00 0.00 0.00 4.70
626 637 4.060205 TCCCTCCGTTTCTTTTTAGTTCG 58.940 43.478 0.00 0.00 0.00 3.95
627 638 5.061853 ACTCCCTCCGTTTCTTTTTAGTTC 58.938 41.667 0.00 0.00 0.00 3.01
628 639 5.045012 ACTCCCTCCGTTTCTTTTTAGTT 57.955 39.130 0.00 0.00 0.00 2.24
629 640 4.701651 ACTCCCTCCGTTTCTTTTTAGT 57.298 40.909 0.00 0.00 0.00 2.24
630 641 5.544650 TGTACTCCCTCCGTTTCTTTTTAG 58.455 41.667 0.00 0.00 0.00 1.85
631 642 5.549742 TGTACTCCCTCCGTTTCTTTTTA 57.450 39.130 0.00 0.00 0.00 1.52
632 643 4.426736 TGTACTCCCTCCGTTTCTTTTT 57.573 40.909 0.00 0.00 0.00 1.94
633 644 4.635699 ATGTACTCCCTCCGTTTCTTTT 57.364 40.909 0.00 0.00 0.00 2.27
634 645 4.635699 AATGTACTCCCTCCGTTTCTTT 57.364 40.909 0.00 0.00 0.00 2.52
635 646 4.041198 TCAAATGTACTCCCTCCGTTTCTT 59.959 41.667 0.00 0.00 0.00 2.52
636 647 3.581332 TCAAATGTACTCCCTCCGTTTCT 59.419 43.478 0.00 0.00 0.00 2.52
637 648 3.933332 CTCAAATGTACTCCCTCCGTTTC 59.067 47.826 0.00 0.00 0.00 2.78
638 649 3.868754 GCTCAAATGTACTCCCTCCGTTT 60.869 47.826 0.00 0.00 0.00 3.60
639 650 2.354805 GCTCAAATGTACTCCCTCCGTT 60.355 50.000 0.00 0.00 0.00 4.44
640 651 1.207329 GCTCAAATGTACTCCCTCCGT 59.793 52.381 0.00 0.00 0.00 4.69
641 652 1.473434 GGCTCAAATGTACTCCCTCCG 60.473 57.143 0.00 0.00 0.00 4.63
642 653 1.840635 AGGCTCAAATGTACTCCCTCC 59.159 52.381 0.00 0.00 0.00 4.30
643 654 4.965200 ATAGGCTCAAATGTACTCCCTC 57.035 45.455 0.00 0.00 0.00 4.30
644 655 5.191722 TCAAATAGGCTCAAATGTACTCCCT 59.808 40.000 0.00 0.00 0.00 4.20
645 656 5.437060 TCAAATAGGCTCAAATGTACTCCC 58.563 41.667 0.00 0.00 0.00 4.30
646 657 7.391148 TTTCAAATAGGCTCAAATGTACTCC 57.609 36.000 0.00 0.00 0.00 3.85
647 658 9.860898 ATTTTTCAAATAGGCTCAAATGTACTC 57.139 29.630 0.00 0.00 0.00 2.59
701 714 5.477510 GCTCTAGTCATCCTATTGACCATG 58.522 45.833 1.19 0.00 45.80 3.66
786 801 9.143631 CTTGTTGGATTTCTTAATTTCCATGAC 57.856 33.333 0.00 0.00 0.00 3.06
927 958 5.061853 CCATGGTCTACTGATTGATGAAGG 58.938 45.833 2.57 0.00 0.00 3.46
969 1957 4.035208 GCTACTCTTCTCTGCTCTGTACTC 59.965 50.000 0.00 0.00 0.00 2.59
972 1960 2.939756 CGCTACTCTTCTCTGCTCTGTA 59.060 50.000 0.00 0.00 0.00 2.74
1187 2217 1.613437 CGGCCATGAAAGGAACAGTTT 59.387 47.619 2.24 0.00 0.00 2.66
1291 2321 0.110678 AGATGCTCAGGATGCCCATG 59.889 55.000 0.00 0.00 34.76 3.66
1428 2458 0.462581 CATGAGCATGGTGTAGCCGT 60.463 55.000 0.00 0.00 41.21 5.68
1498 2528 1.982395 CTCAGCCGTGTACAGGGGA 60.982 63.158 30.37 20.52 36.88 4.81
1664 2694 0.749454 GCAAGAAGGACGGATGGCAT 60.749 55.000 0.00 0.00 0.00 4.40
1858 2888 2.232298 CTCTCTTCCTGGGCACGACC 62.232 65.000 0.00 0.00 37.93 4.79
1927 2957 1.835483 GCAGTATTCGCCGCATGGAG 61.835 60.000 0.00 0.00 37.49 3.86
2005 3035 4.973055 AACACGCGCGGGCTGTAA 62.973 61.111 35.17 0.00 36.88 2.41
2110 3140 1.721664 CGCGGTCGAGGAGGAACATA 61.722 60.000 0.00 0.00 38.10 2.29
2625 3655 0.318441 CGAGTTGCCCAAGAGTCTCA 59.682 55.000 1.94 0.00 0.00 3.27
2667 3697 6.069498 ACAATCCAGCCCCAAATATTCATTTT 60.069 34.615 0.00 0.00 31.82 1.82
2669 3699 4.970640 ACAATCCAGCCCCAAATATTCATT 59.029 37.500 0.00 0.00 0.00 2.57
2685 3715 2.947127 TGTGGTGATGTGACAATCCA 57.053 45.000 0.00 0.00 0.00 3.41
2687 3717 4.093998 GTCTGATGTGGTGATGTGACAATC 59.906 45.833 0.00 0.00 0.00 2.67
2688 3718 4.005650 GTCTGATGTGGTGATGTGACAAT 58.994 43.478 0.00 0.00 0.00 2.71
2689 3719 3.071457 AGTCTGATGTGGTGATGTGACAA 59.929 43.478 0.00 0.00 0.00 3.18
2690 3720 2.634453 AGTCTGATGTGGTGATGTGACA 59.366 45.455 0.00 0.00 0.00 3.58
2691 3721 3.325293 AGTCTGATGTGGTGATGTGAC 57.675 47.619 0.00 0.00 0.00 3.67
2692 3722 4.356405 AAAGTCTGATGTGGTGATGTGA 57.644 40.909 0.00 0.00 0.00 3.58
2693 3723 4.996758 TGTAAAGTCTGATGTGGTGATGTG 59.003 41.667 0.00 0.00 0.00 3.21
2694 3724 5.012046 TCTGTAAAGTCTGATGTGGTGATGT 59.988 40.000 0.00 0.00 0.00 3.06
2695 3725 5.349817 GTCTGTAAAGTCTGATGTGGTGATG 59.650 44.000 0.00 0.00 0.00 3.07
2696 3726 5.247110 AGTCTGTAAAGTCTGATGTGGTGAT 59.753 40.000 0.00 0.00 0.00 3.06
2697 3727 4.588951 AGTCTGTAAAGTCTGATGTGGTGA 59.411 41.667 0.00 0.00 0.00 4.02
2698 3728 4.887748 AGTCTGTAAAGTCTGATGTGGTG 58.112 43.478 0.00 0.00 0.00 4.17
2699 3729 5.300752 CAAGTCTGTAAAGTCTGATGTGGT 58.699 41.667 0.00 0.00 0.00 4.16
2700 3730 4.692625 CCAAGTCTGTAAAGTCTGATGTGG 59.307 45.833 0.00 0.00 0.00 4.17
2701 3731 5.541845 TCCAAGTCTGTAAAGTCTGATGTG 58.458 41.667 0.00 0.00 0.00 3.21
2702 3732 5.540337 TCTCCAAGTCTGTAAAGTCTGATGT 59.460 40.000 0.00 0.00 0.00 3.06
2703 3733 6.030548 TCTCCAAGTCTGTAAAGTCTGATG 57.969 41.667 0.00 0.00 0.00 3.07
2704 3734 6.865834 ATCTCCAAGTCTGTAAAGTCTGAT 57.134 37.500 0.00 0.00 0.00 2.90
2705 3735 7.962995 ATATCTCCAAGTCTGTAAAGTCTGA 57.037 36.000 0.00 0.00 0.00 3.27
2706 3736 9.689976 CATATATCTCCAAGTCTGTAAAGTCTG 57.310 37.037 0.00 0.00 0.00 3.51
2707 3737 9.647918 TCATATATCTCCAAGTCTGTAAAGTCT 57.352 33.333 0.00 0.00 0.00 3.24
2718 3748 8.954350 GCAGCATATTTTCATATATCTCCAAGT 58.046 33.333 0.00 0.00 0.00 3.16
2719 3749 8.404000 GGCAGCATATTTTCATATATCTCCAAG 58.596 37.037 0.00 0.00 0.00 3.61
2720 3750 7.889600 TGGCAGCATATTTTCATATATCTCCAA 59.110 33.333 0.00 0.00 0.00 3.53
2721 3751 7.404481 TGGCAGCATATTTTCATATATCTCCA 58.596 34.615 0.00 0.00 0.00 3.86
2722 3752 7.013083 CCTGGCAGCATATTTTCATATATCTCC 59.987 40.741 9.56 0.00 0.00 3.71
2723 3753 7.013083 CCCTGGCAGCATATTTTCATATATCTC 59.987 40.741 9.56 0.00 0.00 2.75
2724 3754 6.832384 CCCTGGCAGCATATTTTCATATATCT 59.168 38.462 9.56 0.00 0.00 1.98
2725 3755 6.460676 GCCCTGGCAGCATATTTTCATATATC 60.461 42.308 9.56 0.00 41.49 1.63
2726 3756 5.361857 GCCCTGGCAGCATATTTTCATATAT 59.638 40.000 9.56 0.00 41.49 0.86
2732 3762 1.406903 AGCCCTGGCAGCATATTTTC 58.593 50.000 9.56 0.00 44.88 2.29
2747 3777 2.293170 GAGACCAAGCAGAATTAGCCC 58.707 52.381 0.00 0.00 0.00 5.19
2750 3780 5.613358 AAAACGAGACCAAGCAGAATTAG 57.387 39.130 0.00 0.00 0.00 1.73
2752 3782 4.918810 AAAAACGAGACCAAGCAGAATT 57.081 36.364 0.00 0.00 0.00 2.17
2774 3804 8.952278 TGTAAGAAGCAAAAGTCTACAAAGAAA 58.048 29.630 0.00 0.00 32.16 2.52
2782 3934 8.458573 TCCAAAATGTAAGAAGCAAAAGTCTA 57.541 30.769 0.00 0.00 0.00 2.59
2818 3970 0.844660 GAGGGGAAGGGGATAACCAC 59.155 60.000 0.00 0.00 42.91 4.16
2819 3971 0.728843 AGAGGGGAAGGGGATAACCA 59.271 55.000 0.00 0.00 42.91 3.67
2820 3972 1.436326 GAGAGGGGAAGGGGATAACC 58.564 60.000 0.00 0.00 39.11 2.85
2821 3973 1.061268 AGGAGAGGGGAAGGGGATAAC 60.061 57.143 0.00 0.00 0.00 1.89
2822 3974 1.223337 GAGGAGAGGGGAAGGGGATAA 59.777 57.143 0.00 0.00 0.00 1.75
2823 3975 0.868186 GAGGAGAGGGGAAGGGGATA 59.132 60.000 0.00 0.00 0.00 2.59
2824 3976 0.938926 AGAGGAGAGGGGAAGGGGAT 60.939 60.000 0.00 0.00 0.00 3.85
2825 3977 1.550374 AGAGGAGAGGGGAAGGGGA 60.550 63.158 0.00 0.00 0.00 4.81
2826 3978 1.074850 GAGAGGAGAGGGGAAGGGG 60.075 68.421 0.00 0.00 0.00 4.79
2827 3979 0.105709 GAGAGAGGAGAGGGGAAGGG 60.106 65.000 0.00 0.00 0.00 3.95
2828 3980 0.105709 GGAGAGAGGAGAGGGGAAGG 60.106 65.000 0.00 0.00 0.00 3.46
2829 3981 0.105709 GGGAGAGAGGAGAGGGGAAG 60.106 65.000 0.00 0.00 0.00 3.46
2830 3982 1.595058 GGGGAGAGAGGAGAGGGGAA 61.595 65.000 0.00 0.00 0.00 3.97
2831 3983 2.015726 GGGGAGAGAGGAGAGGGGA 61.016 68.421 0.00 0.00 0.00 4.81
2832 3984 1.598856 AAGGGGAGAGAGGAGAGGGG 61.599 65.000 0.00 0.00 0.00 4.79
2833 3985 0.105709 GAAGGGGAGAGAGGAGAGGG 60.106 65.000 0.00 0.00 0.00 4.30
2834 3986 0.105709 GGAAGGGGAGAGAGGAGAGG 60.106 65.000 0.00 0.00 0.00 3.69
2835 3987 0.105709 GGGAAGGGGAGAGAGGAGAG 60.106 65.000 0.00 0.00 0.00 3.20
2836 3988 1.595058 GGGGAAGGGGAGAGAGGAGA 61.595 65.000 0.00 0.00 0.00 3.71
2837 3989 1.074850 GGGGAAGGGGAGAGAGGAG 60.075 68.421 0.00 0.00 0.00 3.69
2838 3990 2.647949 GGGGGAAGGGGAGAGAGGA 61.648 68.421 0.00 0.00 0.00 3.71
2839 3991 2.040359 GGGGGAAGGGGAGAGAGG 60.040 72.222 0.00 0.00 0.00 3.69
2840 3992 2.444895 CGGGGGAAGGGGAGAGAG 60.445 72.222 0.00 0.00 0.00 3.20
2841 3993 4.798682 GCGGGGGAAGGGGAGAGA 62.799 72.222 0.00 0.00 0.00 3.10
2888 4040 3.408853 GGGAACGGGAAGAGGGGG 61.409 72.222 0.00 0.00 0.00 5.40
2930 4082 0.250513 GAACTGAAGGCGGAGTGGAT 59.749 55.000 0.00 0.00 0.00 3.41
2936 4088 4.388499 GCGGGAACTGAAGGCGGA 62.388 66.667 0.00 0.00 36.31 5.54
2980 4133 1.869452 AGGGGGAAGGGAGAGGAGT 60.869 63.158 0.00 0.00 0.00 3.85
2992 4145 2.202236 GATCTGCTTGCACAGGGGGA 62.202 60.000 4.64 0.00 38.26 4.81
2997 4150 1.671328 CATGGAGATCTGCTTGCACAG 59.329 52.381 15.82 0.00 39.12 3.66
2998 4151 1.680860 CCATGGAGATCTGCTTGCACA 60.681 52.381 20.56 0.00 0.00 4.57
3050 4203 1.358051 TGATGGGCTGCATCCTGGAT 61.358 55.000 6.53 2.57 0.00 3.41
3069 4222 3.090532 GAGCCCCAACCCCGAGAT 61.091 66.667 0.00 0.00 0.00 2.75
3314 4467 1.299468 GCACAGGCCGTAGAGATCG 60.299 63.158 0.00 0.00 0.00 3.69
3323 5202 1.447317 AACACTTGAAGCACAGGCCG 61.447 55.000 0.00 0.00 42.56 6.13
3410 5289 1.518325 TGCAATCCGACGAAATGTGT 58.482 45.000 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.