Multiple sequence alignment - TraesCS7D01G198300

Loading Multiple Alignment...

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 TraesCS7D01G198300 chr7D 100.000 3428 0 0 1 3428 154936822 154933395 0.000000e+00 6331
1 TraesCS7D01G198300 chr7D 92.633 828 26 10 2634 3428 53323616 53324441 0.000000e+00 1158
2 TraesCS7D01G198300 chr7D 91.839 821 33 10 2639 3425 27273231 27274051 0.000000e+00 1114
3 TraesCS7D01G198300 chr7D 91.373 823 35 10 2635 3428 459874444 459875259 0.000000e+00 1094
4 TraesCS7D01G198300 chr7D 93.171 205 14 0 297 501 609178565 609178769 5.560000e-78 302
5 TraesCS7D01G198300 chr7D 88.732 213 21 3 2634 2845 53330151 53329941 1.220000e-64 257
6 TraesCS7D01G198300 chr7D 87.324 213 24 3 297 508 464127202 464127412 1.230000e-59 241
7 TraesCS7D01G198300 chr7D 94.203 138 7 1 2498 2635 573961742 573961606 3.470000e-50 209
8 TraesCS7D01G198300 chr7D 93.617 141 6 1 502 642 154936100 154935963 1.250000e-49 207
9 TraesCS7D01G198300 chr7D 93.617 141 6 1 723 860 154936321 154936181 1.250000e-49 207
10 TraesCS7D01G198300 chr7D 93.571 140 8 1 2496 2635 573954748 573954886 1.250000e-49 207
11 TraesCS7D01G198300 chr7D 76.425 386 47 22 711 1068 154947692 154947323 5.880000e-38 169
12 TraesCS7D01G198300 chr7D 90.291 103 6 3 632 733 154941857 154941758 7.720000e-27 132
13 TraesCS7D01G198300 chr7A 93.444 1861 93 16 633 2477 156548761 156550608 0.000000e+00 2734
14 TraesCS7D01G198300 chr7A 89.865 296 29 1 1 295 580628009 580628304 2.500000e-101 379
15 TraesCS7D01G198300 chr7A 90.909 209 15 4 297 503 580628368 580628574 9.370000e-71 278
16 TraesCS7D01G198300 chr7A 91.429 140 8 3 502 639 156548849 156548986 4.520000e-44 189
17 TraesCS7D01G198300 chr7B 92.329 1786 77 25 708 2451 116752998 116754765 0.000000e+00 2484
18 TraesCS7D01G198300 chr7B 82.565 1583 210 43 888 2434 45052571 45051019 0.000000e+00 1334
19 TraesCS7D01G198300 chr7B 80.842 475 76 7 38 499 644544691 644544219 3.250000e-95 359
20 TraesCS7D01G198300 chr1D 84.402 1513 198 30 940 2435 399394835 399393344 0.000000e+00 1452
21 TraesCS7D01G198300 chr1D 83.505 1455 199 30 999 2431 399415230 399413795 0.000000e+00 1319
22 TraesCS7D01G198300 chr1D 91.677 829 34 12 2634 3428 492587494 492588321 0.000000e+00 1116
23 TraesCS7D01G198300 chr1D 89.202 213 20 3 2634 2845 21341848 21342058 2.620000e-66 263
24 TraesCS7D01G198300 chr1D 93.571 140 8 1 2496 2635 492587468 492587606 1.250000e-49 207
25 TraesCS7D01G198300 chr1D 93.478 138 9 0 2498 2635 21341824 21341961 4.480000e-49 206
26 TraesCS7D01G198300 chr1B 84.341 1488 206 22 962 2435 535799450 535797976 0.000000e+00 1432
27 TraesCS7D01G198300 chr1B 83.033 1497 211 31 969 2442 536122935 536121459 0.000000e+00 1317
28 TraesCS7D01G198300 chr1B 83.322 1463 204 26 991 2442 535940198 535938765 0.000000e+00 1314
29 TraesCS7D01G198300 chr1B 84.593 1032 143 13 991 2009 535915087 535914059 0.000000e+00 1011
30 TraesCS7D01G198300 chr1B 90.102 293 28 1 4 295 270328935 270329227 2.500000e-101 379
31 TraesCS7D01G198300 chr1B 80.690 435 63 13 2007 2435 535908613 535908194 5.520000e-83 318
32 TraesCS7D01G198300 chr1B 93.103 203 12 2 298 499 270329292 270329493 2.590000e-76 296
33 TraesCS7D01G198300 chr1A 84.690 1450 196 22 999 2435 496143383 496141947 0.000000e+00 1424
34 TraesCS7D01G198300 chr2D 93.750 816 19 10 2640 3426 385382933 385382121 0.000000e+00 1195
35 TraesCS7D01G198300 chr2D 91.116 833 35 11 2634 3428 599601169 599600338 0.000000e+00 1092
36 TraesCS7D01G198300 chr2D 96.023 176 7 0 2634 2809 385375220 385375395 1.560000e-73 287
37 TraesCS7D01G198300 chr2D 89.474 209 18 4 2634 2841 588219690 588219485 9.440000e-66 261
38 TraesCS7D01G198300 chr2D 94.203 138 8 0 2498 2635 385375196 385375333 9.640000e-51 211
39 TraesCS7D01G198300 chr3D 91.932 818 41 13 2634 3428 551371939 551372754 0.000000e+00 1122
40 TraesCS7D01G198300 chr3D 91.194 829 39 11 2634 3428 32372704 32371876 0.000000e+00 1096
41 TraesCS7D01G198300 chr3D 93.237 207 11 1 297 503 28585089 28584886 5.560000e-78 302
42 TraesCS7D01G198300 chr3D 92.647 204 14 1 297 500 565243960 565244162 3.350000e-75 292
43 TraesCS7D01G198300 chr3D 88.725 204 21 2 297 500 496350297 496350498 7.350000e-62 248
44 TraesCS7D01G198300 chr3D 93.525 139 9 0 2497 2635 32372729 32372591 1.250000e-49 207
45 TraesCS7D01G198300 chr5D 90.170 824 40 13 2634 3428 494293094 494292283 0.000000e+00 1035
46 TraesCS7D01G198300 chr5D 92.188 704 23 9 2634 3308 489242698 489241998 0.000000e+00 966
47 TraesCS7D01G198300 chr5D 93.237 207 13 1 297 503 7610425 7610220 1.550000e-78 303
48 TraesCS7D01G198300 chr5D 91.346 208 15 3 2634 2840 489235031 489235236 7.240000e-72 281
49 TraesCS7D01G198300 chr5D 94.203 138 8 0 2498 2635 489242722 489242585 9.640000e-51 211
50 TraesCS7D01G198300 chr5D 91.216 148 13 0 2488 2635 348512284 348512137 5.800000e-48 202
51 TraesCS7D01G198300 chr4D 96.284 296 10 1 1 295 486556262 486556557 5.140000e-133 484
52 TraesCS7D01G198300 chr4D 98.049 205 3 1 296 500 486556620 486556823 4.210000e-94 355
53 TraesCS7D01G198300 chr2A 90.190 316 25 2 2634 2949 36746554 36746863 1.150000e-109 407
54 TraesCS7D01G198300 chr3A 92.157 204 14 1 297 500 112923814 112924015 1.560000e-73 287
55 TraesCS7D01G198300 chr3A 92.708 192 14 0 297 488 21353053 21352862 9.370000e-71 278
56 TraesCS7D01G198300 chr3A 94.203 138 7 1 2498 2635 71577925 71577789 3.470000e-50 209
57 TraesCS7D01G198300 chr5B 81.407 199 32 3 301 499 530975286 530975093 1.270000e-34 158


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 TraesCS7D01G198300 chr7D 154933395 154936822 3427 True 2248.333333 6331 95.744667 1 3428 3 chr7D.!!$R5 3427
1 TraesCS7D01G198300 chr7D 53323616 53324441 825 False 1158.000000 1158 92.633000 2634 3428 1 chr7D.!!$F2 794
2 TraesCS7D01G198300 chr7D 27273231 27274051 820 False 1114.000000 1114 91.839000 2639 3425 1 chr7D.!!$F1 786
3 TraesCS7D01G198300 chr7D 459874444 459875259 815 False 1094.000000 1094 91.373000 2635 3428 1 chr7D.!!$F3 793
4 TraesCS7D01G198300 chr7A 156548761 156550608 1847 False 1461.500000 2734 92.436500 502 2477 2 chr7A.!!$F1 1975
5 TraesCS7D01G198300 chr7A 580628009 580628574 565 False 328.500000 379 90.387000 1 503 2 chr7A.!!$F2 502
6 TraesCS7D01G198300 chr7B 116752998 116754765 1767 False 2484.000000 2484 92.329000 708 2451 1 chr7B.!!$F1 1743
7 TraesCS7D01G198300 chr7B 45051019 45052571 1552 True 1334.000000 1334 82.565000 888 2434 1 chr7B.!!$R1 1546
8 TraesCS7D01G198300 chr1D 399393344 399394835 1491 True 1452.000000 1452 84.402000 940 2435 1 chr1D.!!$R1 1495
9 TraesCS7D01G198300 chr1D 399413795 399415230 1435 True 1319.000000 1319 83.505000 999 2431 1 chr1D.!!$R2 1432
10 TraesCS7D01G198300 chr1D 492587468 492588321 853 False 661.500000 1116 92.624000 2496 3428 2 chr1D.!!$F2 932
11 TraesCS7D01G198300 chr1B 535797976 535799450 1474 True 1432.000000 1432 84.341000 962 2435 1 chr1B.!!$R1 1473
12 TraesCS7D01G198300 chr1B 536121459 536122935 1476 True 1317.000000 1317 83.033000 969 2442 1 chr1B.!!$R5 1473
13 TraesCS7D01G198300 chr1B 535938765 535940198 1433 True 1314.000000 1314 83.322000 991 2442 1 chr1B.!!$R4 1451
14 TraesCS7D01G198300 chr1B 535914059 535915087 1028 True 1011.000000 1011 84.593000 991 2009 1 chr1B.!!$R3 1018
15 TraesCS7D01G198300 chr1B 270328935 270329493 558 False 337.500000 379 91.602500 4 499 2 chr1B.!!$F1 495
16 TraesCS7D01G198300 chr1A 496141947 496143383 1436 True 1424.000000 1424 84.690000 999 2435 1 chr1A.!!$R1 1436
17 TraesCS7D01G198300 chr2D 385382121 385382933 812 True 1195.000000 1195 93.750000 2640 3426 1 chr2D.!!$R1 786
18 TraesCS7D01G198300 chr2D 599600338 599601169 831 True 1092.000000 1092 91.116000 2634 3428 1 chr2D.!!$R3 794
19 TraesCS7D01G198300 chr3D 551371939 551372754 815 False 1122.000000 1122 91.932000 2634 3428 1 chr3D.!!$F2 794
20 TraesCS7D01G198300 chr3D 32371876 32372729 853 True 651.500000 1096 92.359500 2497 3428 2 chr3D.!!$R2 931
21 TraesCS7D01G198300 chr5D 494292283 494293094 811 True 1035.000000 1035 90.170000 2634 3428 1 chr5D.!!$R3 794
22 TraesCS7D01G198300 chr5D 489241998 489242722 724 True 588.500000 966 93.195500 2498 3308 2 chr5D.!!$R4 810
23 TraesCS7D01G198300 chr4D 486556262 486556823 561 False 419.500000 484 97.166500 1 500 2 chr4D.!!$F1 499

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
693 758 0.036483 TGACGTATGCATGCCAGTGT 60.036 50.0 16.68 8.88 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2599 2757 0.099791 ACGCCTGTCAAACCGTTTTG 59.9 50.0 0.0 0.0 43.17 2.44 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
88 89 1.407437 GCACTTTCGGTGGATGGATCT 60.407 52.381 0.00 0.00 45.44 2.75
113 114 0.457853 GCAAGATGACGGTACTGCGA 60.458 55.000 0.23 0.00 0.00 5.10
189 191 5.150683 TCGTTTTATTTTCCATGCAACGAG 58.849 37.500 0.00 0.00 39.52 4.18
232 234 0.381801 GTTGATGCAAGGTATGGCGG 59.618 55.000 0.00 0.00 0.00 6.13
518 583 5.613358 AAAAAGATCTTGGTGCTAAGACG 57.387 39.130 9.17 0.00 39.33 4.18
519 584 4.537135 AAAGATCTTGGTGCTAAGACGA 57.463 40.909 9.17 0.00 39.33 4.20
520 585 4.537135 AAGATCTTGGTGCTAAGACGAA 57.463 40.909 7.30 0.00 39.33 3.85
521 586 3.851098 AGATCTTGGTGCTAAGACGAAC 58.149 45.455 0.13 0.00 39.33 3.95
522 587 2.060326 TCTTGGTGCTAAGACGAACG 57.940 50.000 0.00 0.00 32.02 3.95
523 588 1.068474 CTTGGTGCTAAGACGAACGG 58.932 55.000 0.00 0.00 0.00 4.44
524 589 0.390124 TTGGTGCTAAGACGAACGGT 59.610 50.000 0.00 0.00 0.00 4.83
525 590 1.246649 TGGTGCTAAGACGAACGGTA 58.753 50.000 0.00 0.00 0.00 4.02
526 591 1.068333 TGGTGCTAAGACGAACGGTAC 60.068 52.381 0.00 0.00 0.00 3.34
527 592 1.622232 GTGCTAAGACGAACGGTACC 58.378 55.000 0.16 0.16 0.00 3.34
528 593 1.068333 GTGCTAAGACGAACGGTACCA 60.068 52.381 13.54 0.00 0.00 3.25
529 594 1.200716 TGCTAAGACGAACGGTACCAG 59.799 52.381 13.54 7.45 0.00 4.00
530 595 1.470098 GCTAAGACGAACGGTACCAGA 59.530 52.381 13.54 0.00 0.00 3.86
531 596 2.098770 GCTAAGACGAACGGTACCAGAT 59.901 50.000 13.54 0.00 0.00 2.90
532 597 2.649331 AAGACGAACGGTACCAGATG 57.351 50.000 13.54 0.98 0.00 2.90
533 598 1.542492 AGACGAACGGTACCAGATGT 58.458 50.000 13.54 4.56 0.00 3.06
534 599 2.715046 AGACGAACGGTACCAGATGTA 58.285 47.619 13.54 0.00 0.00 2.29
535 600 3.285484 AGACGAACGGTACCAGATGTAT 58.715 45.455 13.54 0.00 0.00 2.29
536 601 4.454678 AGACGAACGGTACCAGATGTATA 58.545 43.478 13.54 0.00 0.00 1.47
537 602 4.514441 AGACGAACGGTACCAGATGTATAG 59.486 45.833 13.54 0.00 0.00 1.31
538 603 3.567164 ACGAACGGTACCAGATGTATAGG 59.433 47.826 13.54 0.00 0.00 2.57
539 604 3.567164 CGAACGGTACCAGATGTATAGGT 59.433 47.826 13.54 0.00 39.41 3.08
540 605 4.756642 CGAACGGTACCAGATGTATAGGTA 59.243 45.833 13.54 0.00 36.87 3.08
541 606 5.106791 CGAACGGTACCAGATGTATAGGTAG 60.107 48.000 13.54 0.00 38.49 3.18
542 607 4.660168 ACGGTACCAGATGTATAGGTAGG 58.340 47.826 13.54 0.00 38.49 3.18
543 608 4.105377 ACGGTACCAGATGTATAGGTAGGT 59.895 45.833 13.54 0.00 38.49 3.08
544 609 5.310594 ACGGTACCAGATGTATAGGTAGGTA 59.689 44.000 13.54 0.00 38.49 3.08
545 610 5.645497 CGGTACCAGATGTATAGGTAGGTAC 59.355 48.000 13.54 9.69 45.65 3.34
570 635 7.158243 CGTTAACGGTAGATTATCCACTTTC 57.842 40.000 20.24 0.00 35.37 2.62
571 636 6.075205 CGTTAACGGTAGATTATCCACTTTCG 60.075 42.308 20.24 0.00 35.37 3.46
572 637 3.714391 ACGGTAGATTATCCACTTTCGC 58.286 45.455 0.00 0.00 0.00 4.70
573 638 2.724690 CGGTAGATTATCCACTTTCGCG 59.275 50.000 0.00 0.00 0.00 5.87
574 639 3.714391 GGTAGATTATCCACTTTCGCGT 58.286 45.455 5.77 0.00 0.00 6.01
575 640 4.555313 CGGTAGATTATCCACTTTCGCGTA 60.555 45.833 5.77 0.00 0.00 4.42
576 641 4.678742 GGTAGATTATCCACTTTCGCGTAC 59.321 45.833 5.77 0.00 0.00 3.67
577 642 4.650754 AGATTATCCACTTTCGCGTACT 57.349 40.909 5.77 0.00 0.00 2.73
578 643 4.608951 AGATTATCCACTTTCGCGTACTC 58.391 43.478 5.77 0.00 0.00 2.59
579 644 4.338682 AGATTATCCACTTTCGCGTACTCT 59.661 41.667 5.77 0.00 0.00 3.24
580 645 2.279582 ATCCACTTTCGCGTACTCTG 57.720 50.000 5.77 0.00 0.00 3.35
581 646 0.242825 TCCACTTTCGCGTACTCTGG 59.757 55.000 5.77 6.14 0.00 3.86
582 647 0.038526 CCACTTTCGCGTACTCTGGT 60.039 55.000 5.77 0.00 0.00 4.00
583 648 1.060713 CACTTTCGCGTACTCTGGTG 58.939 55.000 5.77 3.58 0.00 4.17
584 649 0.672342 ACTTTCGCGTACTCTGGTGT 59.328 50.000 5.77 0.00 0.00 4.16
585 650 1.335689 ACTTTCGCGTACTCTGGTGTC 60.336 52.381 5.77 0.00 0.00 3.67
586 651 0.386352 TTTCGCGTACTCTGGTGTCG 60.386 55.000 5.77 0.00 0.00 4.35
587 652 2.791396 TTCGCGTACTCTGGTGTCGC 62.791 60.000 5.77 0.00 42.04 5.19
588 653 2.257371 GCGTACTCTGGTGTCGCA 59.743 61.111 0.00 0.00 43.49 5.10
589 654 2.087009 GCGTACTCTGGTGTCGCAC 61.087 63.158 0.00 1.92 43.49 5.34
590 655 1.284715 CGTACTCTGGTGTCGCACA 59.715 57.895 11.20 0.00 35.86 4.57
591 656 0.109272 CGTACTCTGGTGTCGCACAT 60.109 55.000 11.20 0.00 35.86 3.21
592 657 1.350193 GTACTCTGGTGTCGCACATG 58.650 55.000 11.20 0.00 35.86 3.21
593 658 0.389817 TACTCTGGTGTCGCACATGC 60.390 55.000 11.20 0.00 35.86 4.06
594 659 1.668793 CTCTGGTGTCGCACATGCA 60.669 57.895 4.49 0.00 42.21 3.96
595 660 1.227793 TCTGGTGTCGCACATGCAA 60.228 52.632 4.49 0.00 42.21 4.08
596 661 0.817229 TCTGGTGTCGCACATGCAAA 60.817 50.000 4.49 0.00 42.21 3.68
597 662 0.386352 CTGGTGTCGCACATGCAAAG 60.386 55.000 4.49 0.00 42.21 2.77
598 663 1.730547 GGTGTCGCACATGCAAAGC 60.731 57.895 4.49 0.00 42.21 3.51
599 664 1.008652 GTGTCGCACATGCAAAGCA 60.009 52.632 4.49 0.00 44.86 3.91
600 665 1.000233 GTGTCGCACATGCAAAGCAG 61.000 55.000 4.49 2.75 43.65 4.24
601 666 1.443194 GTCGCACATGCAAAGCAGG 60.443 57.895 4.49 1.77 46.22 4.85
602 667 2.807895 CGCACATGCAAAGCAGGC 60.808 61.111 3.34 3.64 44.57 4.85
603 668 2.433664 GCACATGCAAAGCAGGCC 60.434 61.111 3.34 0.00 44.57 5.19
604 669 2.263540 CACATGCAAAGCAGGCCC 59.736 61.111 0.00 0.00 44.57 5.80
605 670 3.376078 ACATGCAAAGCAGGCCCG 61.376 61.111 0.00 0.00 44.57 6.13
606 671 3.063704 CATGCAAAGCAGGCCCGA 61.064 61.111 0.00 0.00 43.65 5.14
607 672 3.064324 ATGCAAAGCAGGCCCGAC 61.064 61.111 0.00 0.00 43.65 4.79
626 691 3.353029 CACGTGCCGACCATGCAA 61.353 61.111 0.82 0.00 41.06 4.08
627 692 3.049674 ACGTGCCGACCATGCAAG 61.050 61.111 0.00 0.00 41.06 4.01
628 693 4.465512 CGTGCCGACCATGCAAGC 62.466 66.667 0.00 0.00 41.06 4.01
629 694 4.465512 GTGCCGACCATGCAAGCG 62.466 66.667 0.00 0.00 41.06 4.68
631 696 3.737172 GCCGACCATGCAAGCGTT 61.737 61.111 0.00 0.00 0.00 4.84
632 697 2.480555 CCGACCATGCAAGCGTTC 59.519 61.111 0.00 0.00 0.00 3.95
633 698 2.096406 CGACCATGCAAGCGTTCG 59.904 61.111 0.00 0.00 0.00 3.95
634 699 2.202349 GACCATGCAAGCGTTCGC 60.202 61.111 9.24 9.24 0.00 4.70
635 700 3.667429 GACCATGCAAGCGTTCGCC 62.667 63.158 13.54 0.00 0.00 5.54
636 701 4.481112 CCATGCAAGCGTTCGCCC 62.481 66.667 13.54 3.71 0.00 6.13
648 713 1.750018 TTCGCCCATCCATGCACTG 60.750 57.895 0.00 0.00 0.00 3.66
649 714 2.438975 CGCCCATCCATGCACTGT 60.439 61.111 0.00 0.00 0.00 3.55
654 719 2.173519 CCCATCCATGCACTGTTCTTT 58.826 47.619 0.00 0.00 0.00 2.52
663 728 5.452356 CCATGCACTGTTCTTTTCTTTCCTT 60.452 40.000 0.00 0.00 0.00 3.36
668 733 7.033185 GCACTGTTCTTTTCTTTCCTTACAAA 58.967 34.615 0.00 0.00 0.00 2.83
669 734 7.544217 GCACTGTTCTTTTCTTTCCTTACAAAA 59.456 33.333 0.00 0.00 0.00 2.44
678 743 6.539649 TCTTTCCTTACAAAACATCTGACG 57.460 37.500 0.00 0.00 0.00 4.35
693 758 0.036483 TGACGTATGCATGCCAGTGT 60.036 50.000 16.68 8.88 0.00 3.55
733 798 3.317608 GCACATTGATCTTGGTGCG 57.682 52.632 16.37 0.00 45.84 5.34
735 800 1.466360 GCACATTGATCTTGGTGCGAC 60.466 52.381 16.37 0.00 45.84 5.19
791 859 3.956199 ACGGTAGATTATCCACTTTCGGA 59.044 43.478 0.00 0.00 40.07 4.55
804 872 2.163815 ACTTTCGGATACTCTGGTGTCG 59.836 50.000 0.00 0.00 34.94 4.35
807 875 0.385751 CGGATACTCTGGTGTCGCAT 59.614 55.000 0.00 0.00 34.94 4.73
907 1011 1.000060 CCCGCTATAAATCGAACCGGA 60.000 52.381 9.46 0.00 36.55 5.14
924 1028 1.589716 GGACGCTGATTGCTTTGCCT 61.590 55.000 0.00 0.00 40.11 4.75
932 1039 2.097825 GATTGCTTTGCCTCACTCCAT 58.902 47.619 0.00 0.00 0.00 3.41
945 1052 2.492088 TCACTCCATACGAGACACCAAG 59.508 50.000 0.00 0.00 41.63 3.61
965 1072 3.699894 CTCGCCAGTGCCCACTCT 61.700 66.667 0.00 0.00 40.20 3.24
1008 1118 1.555075 GACTACCTGCCAATGTCTCCA 59.445 52.381 0.00 0.00 0.00 3.86
1530 1652 3.823330 GACCACCTCGTCGGCGAT 61.823 66.667 14.65 0.00 46.80 4.58
1731 1854 0.958876 GCAAGGTCGTTCCCGGATTT 60.959 55.000 0.73 0.00 36.75 2.17
1771 1897 4.421479 CGCTCAAGTCGACGCCCT 62.421 66.667 10.46 0.00 0.00 5.19
2250 2408 2.686835 AGCTGGCAGGAGGAGGAC 60.687 66.667 17.64 0.00 0.00 3.85
2292 2450 2.305607 CGGGGTGGAGATTGGGGAA 61.306 63.158 0.00 0.00 0.00 3.97
2296 2454 1.186200 GGTGGAGATTGGGGAAAAGC 58.814 55.000 0.00 0.00 0.00 3.51
2451 2609 4.806330 TGTTCTAGCGACCACTTTCTAAG 58.194 43.478 0.00 0.00 0.00 2.18
2452 2610 4.174762 GTTCTAGCGACCACTTTCTAAGG 58.825 47.826 0.00 0.00 0.00 2.69
2457 2615 1.270625 CGACCACTTTCTAAGGGCACA 60.271 52.381 0.00 0.00 0.00 4.57
2458 2616 2.808933 CGACCACTTTCTAAGGGCACAA 60.809 50.000 0.00 0.00 0.00 3.33
2463 2621 3.751698 CACTTTCTAAGGGCACAACTACC 59.248 47.826 0.00 0.00 0.00 3.18
2474 2632 0.815734 ACAACTACCTGACGATCCCG 59.184 55.000 0.00 0.00 42.50 5.14
2476 2634 1.673808 AACTACCTGACGATCCCGGC 61.674 60.000 0.00 0.00 46.00 6.13
2480 2638 3.470888 CTGACGATCCCGGCCCTT 61.471 66.667 0.00 0.00 44.97 3.95
2481 2639 2.042741 TGACGATCCCGGCCCTTA 60.043 61.111 0.00 0.00 44.97 2.69
2482 2640 2.088674 CTGACGATCCCGGCCCTTAG 62.089 65.000 0.00 0.00 44.97 2.18
2483 2641 2.042230 ACGATCCCGGCCCTTAGT 60.042 61.111 0.00 0.00 40.78 2.24
2484 2642 0.825010 GACGATCCCGGCCCTTAGTA 60.825 60.000 0.00 0.00 38.01 1.82
2485 2643 0.178941 ACGATCCCGGCCCTTAGTAT 60.179 55.000 0.00 0.00 40.78 2.12
2486 2644 0.531200 CGATCCCGGCCCTTAGTATC 59.469 60.000 0.00 0.00 0.00 2.24
2487 2645 1.640917 GATCCCGGCCCTTAGTATCA 58.359 55.000 0.00 0.00 0.00 2.15
2488 2646 1.550976 GATCCCGGCCCTTAGTATCAG 59.449 57.143 0.00 0.00 0.00 2.90
2489 2647 0.471211 TCCCGGCCCTTAGTATCAGG 60.471 60.000 0.00 0.00 0.00 3.86
2490 2648 0.763223 CCCGGCCCTTAGTATCAGGT 60.763 60.000 0.00 0.00 0.00 4.00
2491 2649 1.129058 CCGGCCCTTAGTATCAGGTT 58.871 55.000 0.00 0.00 0.00 3.50
2492 2650 1.202651 CCGGCCCTTAGTATCAGGTTG 60.203 57.143 0.00 0.00 0.00 3.77
2493 2651 1.202651 CGGCCCTTAGTATCAGGTTGG 60.203 57.143 0.00 0.00 0.00 3.77
2494 2652 2.124411 GGCCCTTAGTATCAGGTTGGA 58.876 52.381 0.00 0.00 0.00 3.53
2516 2674 2.414559 CGGAGTTAATTGCAAGGCACTG 60.415 50.000 4.94 0.00 40.86 3.66
2552 2710 4.842139 GTTGTGACGAATCAGTATCACC 57.158 45.455 0.00 0.00 40.63 4.02
2553 2711 4.242475 GTTGTGACGAATCAGTATCACCA 58.758 43.478 0.00 0.00 40.63 4.17
2554 2712 4.110036 TGTGACGAATCAGTATCACCAG 57.890 45.455 0.00 0.00 40.63 4.00
2555 2713 3.509967 TGTGACGAATCAGTATCACCAGT 59.490 43.478 0.00 0.00 40.63 4.00
2556 2714 4.021456 TGTGACGAATCAGTATCACCAGTT 60.021 41.667 0.00 0.00 40.63 3.16
2557 2715 5.184287 TGTGACGAATCAGTATCACCAGTTA 59.816 40.000 0.00 0.00 40.63 2.24
2558 2716 5.515626 GTGACGAATCAGTATCACCAGTTAC 59.484 44.000 0.00 0.00 36.31 2.50
2559 2717 5.417894 TGACGAATCAGTATCACCAGTTACT 59.582 40.000 0.00 0.00 31.94 2.24
2560 2718 6.071560 TGACGAATCAGTATCACCAGTTACTT 60.072 38.462 0.00 0.00 29.87 2.24
2561 2719 6.698380 ACGAATCAGTATCACCAGTTACTTT 58.302 36.000 0.00 0.00 29.87 2.66
2562 2720 7.159372 ACGAATCAGTATCACCAGTTACTTTT 58.841 34.615 0.00 0.00 29.87 2.27
2563 2721 7.660208 ACGAATCAGTATCACCAGTTACTTTTT 59.340 33.333 0.00 0.00 29.87 1.94
2581 2739 2.810439 TTTTGCCATGTAGTGCCAAC 57.190 45.000 0.00 0.00 0.00 3.77
2582 2740 1.993956 TTTGCCATGTAGTGCCAACT 58.006 45.000 0.00 0.00 40.67 3.16
2583 2741 1.533625 TTGCCATGTAGTGCCAACTC 58.466 50.000 0.00 0.00 37.88 3.01
2584 2742 0.692476 TGCCATGTAGTGCCAACTCT 59.308 50.000 0.00 0.00 37.88 3.24
2585 2743 1.905894 TGCCATGTAGTGCCAACTCTA 59.094 47.619 0.00 0.00 37.88 2.43
2586 2744 2.304470 TGCCATGTAGTGCCAACTCTAA 59.696 45.455 0.00 0.00 37.88 2.10
2587 2745 2.939103 GCCATGTAGTGCCAACTCTAAG 59.061 50.000 0.00 0.00 37.88 2.18
2588 2746 2.939103 CCATGTAGTGCCAACTCTAAGC 59.061 50.000 0.00 0.00 37.88 3.09
2589 2747 2.762535 TGTAGTGCCAACTCTAAGCC 57.237 50.000 0.00 0.00 37.88 4.35
2590 2748 2.257207 TGTAGTGCCAACTCTAAGCCT 58.743 47.619 0.00 0.00 37.88 4.58
2591 2749 3.437213 TGTAGTGCCAACTCTAAGCCTA 58.563 45.455 0.00 0.00 37.88 3.93
2592 2750 3.835978 TGTAGTGCCAACTCTAAGCCTAA 59.164 43.478 0.00 0.00 37.88 2.69
2593 2751 3.618690 AGTGCCAACTCTAAGCCTAAG 57.381 47.619 0.00 0.00 26.77 2.18
2594 2752 2.907042 AGTGCCAACTCTAAGCCTAAGT 59.093 45.455 0.00 0.00 26.77 2.24
2595 2753 3.003480 GTGCCAACTCTAAGCCTAAGTG 58.997 50.000 0.00 0.00 0.00 3.16
2596 2754 2.637872 TGCCAACTCTAAGCCTAAGTGT 59.362 45.455 0.00 0.00 0.00 3.55
2597 2755 3.072476 TGCCAACTCTAAGCCTAAGTGTT 59.928 43.478 0.00 0.00 32.46 3.32
2598 2756 3.437049 GCCAACTCTAAGCCTAAGTGTTG 59.563 47.826 14.06 14.06 43.24 3.33
2599 2757 3.437049 CCAACTCTAAGCCTAAGTGTTGC 59.563 47.826 14.96 0.00 42.71 4.17
2600 2758 4.065088 CAACTCTAAGCCTAAGTGTTGCA 58.935 43.478 10.59 0.00 39.88 4.08
2601 2759 4.351874 ACTCTAAGCCTAAGTGTTGCAA 57.648 40.909 0.00 0.00 0.00 4.08
2602 2760 4.714632 ACTCTAAGCCTAAGTGTTGCAAA 58.285 39.130 0.00 0.00 0.00 3.68
2603 2761 5.130350 ACTCTAAGCCTAAGTGTTGCAAAA 58.870 37.500 0.00 0.00 0.00 2.44
2604 2762 5.008712 ACTCTAAGCCTAAGTGTTGCAAAAC 59.991 40.000 12.10 12.10 0.00 2.43
2605 2763 2.774439 AGCCTAAGTGTTGCAAAACG 57.226 45.000 14.06 1.20 0.00 3.60
2606 2764 1.336755 AGCCTAAGTGTTGCAAAACGG 59.663 47.619 14.06 10.52 0.00 4.44
2607 2765 1.066454 GCCTAAGTGTTGCAAAACGGT 59.934 47.619 14.06 8.92 0.00 4.83
2608 2766 2.480587 GCCTAAGTGTTGCAAAACGGTT 60.481 45.455 14.06 6.78 0.00 4.44
2609 2767 3.776340 CCTAAGTGTTGCAAAACGGTTT 58.224 40.909 14.06 6.08 0.00 3.27
2610 2768 3.549873 CCTAAGTGTTGCAAAACGGTTTG 59.450 43.478 21.60 21.60 45.88 2.93
2611 2769 3.305398 AAGTGTTGCAAAACGGTTTGA 57.695 38.095 29.42 11.66 45.99 2.69
2612 2770 2.601804 AGTGTTGCAAAACGGTTTGAC 58.398 42.857 29.42 18.93 45.99 3.18
2613 2771 2.029828 AGTGTTGCAAAACGGTTTGACA 60.030 40.909 29.42 21.25 45.99 3.58
2614 2772 2.344142 GTGTTGCAAAACGGTTTGACAG 59.656 45.455 29.42 3.13 45.99 3.51
2615 2773 1.923864 GTTGCAAAACGGTTTGACAGG 59.076 47.619 29.42 2.72 45.99 4.00
2616 2774 0.179124 TGCAAAACGGTTTGACAGGC 60.179 50.000 29.42 13.89 45.99 4.85
2617 2775 1.206115 GCAAAACGGTTTGACAGGCG 61.206 55.000 29.42 1.13 45.99 5.52
2618 2776 0.099791 CAAAACGGTTTGACAGGCGT 59.900 50.000 21.39 0.00 45.99 5.68
2619 2777 1.331138 CAAAACGGTTTGACAGGCGTA 59.669 47.619 21.39 0.00 45.99 4.42
2620 2778 1.886886 AAACGGTTTGACAGGCGTAT 58.113 45.000 5.12 0.00 0.00 3.06
2621 2779 2.747396 AACGGTTTGACAGGCGTATA 57.253 45.000 0.00 0.00 0.00 1.47
2622 2780 2.747396 ACGGTTTGACAGGCGTATAA 57.253 45.000 0.00 0.00 0.00 0.98
2623 2781 2.613691 ACGGTTTGACAGGCGTATAAG 58.386 47.619 0.00 0.00 0.00 1.73
2624 2782 1.326548 CGGTTTGACAGGCGTATAAGC 59.673 52.381 1.57 1.57 0.00 3.09
2625 2783 2.629051 GGTTTGACAGGCGTATAAGCT 58.371 47.619 10.52 0.00 37.29 3.74
2626 2784 2.608090 GGTTTGACAGGCGTATAAGCTC 59.392 50.000 10.52 1.45 37.29 4.09
2627 2785 2.203800 TTGACAGGCGTATAAGCTCG 57.796 50.000 10.52 4.72 37.29 5.03
2628 2786 1.100510 TGACAGGCGTATAAGCTCGT 58.899 50.000 10.52 7.74 37.29 4.18
2629 2787 2.291365 TGACAGGCGTATAAGCTCGTA 58.709 47.619 10.52 0.00 37.29 3.43
2630 2788 2.882761 TGACAGGCGTATAAGCTCGTAT 59.117 45.455 10.52 0.00 37.29 3.06
2631 2789 3.317149 TGACAGGCGTATAAGCTCGTATT 59.683 43.478 10.52 0.00 37.29 1.89
2632 2790 3.639538 ACAGGCGTATAAGCTCGTATTG 58.360 45.455 10.52 3.36 37.29 1.90
2668 2826 6.510879 TGTGACGAATCAGTATCACTAGTT 57.489 37.500 0.00 0.00 41.65 2.24
2728 2887 0.107410 TGCAAAACGGTCTGACAGGT 60.107 50.000 12.43 2.49 0.00 4.00
3052 3234 0.614979 GGTCAGTGGTGGAGCTAGGA 60.615 60.000 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 2.301870 AGTACCGTCATCTTGCTGGAAA 59.698 45.455 0.00 0.00 0.00 3.13
113 114 3.450904 TCCTTAGAACCATACCAGCTGT 58.549 45.455 13.81 3.45 0.00 4.40
142 143 1.324736 GCTGCGAAGAGAATTGTACCG 59.675 52.381 0.00 0.00 0.00 4.02
232 234 3.631227 AGGTCCGAGTGTTGTATAGCTAC 59.369 47.826 0.00 0.00 0.00 3.58
259 261 2.172483 GAGTCCGACTGCACCACCAT 62.172 60.000 5.57 0.00 0.00 3.55
500 565 3.673594 CGTTCGTCTTAGCACCAAGATCT 60.674 47.826 0.00 0.00 36.93 2.75
501 566 2.599082 CGTTCGTCTTAGCACCAAGATC 59.401 50.000 0.00 0.00 36.93 2.75
502 567 2.607187 CGTTCGTCTTAGCACCAAGAT 58.393 47.619 0.00 0.00 36.93 2.40
503 568 1.336517 CCGTTCGTCTTAGCACCAAGA 60.337 52.381 0.00 0.00 32.11 3.02
504 569 1.068474 CCGTTCGTCTTAGCACCAAG 58.932 55.000 0.00 0.00 0.00 3.61
505 570 0.390124 ACCGTTCGTCTTAGCACCAA 59.610 50.000 0.00 0.00 0.00 3.67
506 571 1.068333 GTACCGTTCGTCTTAGCACCA 60.068 52.381 0.00 0.00 0.00 4.17
507 572 1.622232 GTACCGTTCGTCTTAGCACC 58.378 55.000 0.00 0.00 0.00 5.01
508 573 1.068333 TGGTACCGTTCGTCTTAGCAC 60.068 52.381 7.57 0.00 0.00 4.40
509 574 1.200716 CTGGTACCGTTCGTCTTAGCA 59.799 52.381 7.57 0.00 0.00 3.49
510 575 1.470098 TCTGGTACCGTTCGTCTTAGC 59.530 52.381 7.57 0.00 0.00 3.09
511 576 3.128242 ACATCTGGTACCGTTCGTCTTAG 59.872 47.826 7.57 0.00 0.00 2.18
512 577 3.084039 ACATCTGGTACCGTTCGTCTTA 58.916 45.455 7.57 0.00 0.00 2.10
513 578 1.891150 ACATCTGGTACCGTTCGTCTT 59.109 47.619 7.57 0.00 0.00 3.01
514 579 1.542492 ACATCTGGTACCGTTCGTCT 58.458 50.000 7.57 0.00 0.00 4.18
515 580 3.705043 ATACATCTGGTACCGTTCGTC 57.295 47.619 7.57 0.00 34.07 4.20
516 581 3.567164 CCTATACATCTGGTACCGTTCGT 59.433 47.826 7.57 4.80 34.07 3.85
517 582 3.567164 ACCTATACATCTGGTACCGTTCG 59.433 47.826 7.57 0.00 34.07 3.95
518 583 5.182760 CCTACCTATACATCTGGTACCGTTC 59.817 48.000 7.57 0.00 34.07 3.95
519 584 5.075493 CCTACCTATACATCTGGTACCGTT 58.925 45.833 7.57 0.00 34.07 4.44
520 585 4.105377 ACCTACCTATACATCTGGTACCGT 59.895 45.833 7.57 1.09 34.07 4.83
521 586 4.660168 ACCTACCTATACATCTGGTACCG 58.340 47.826 7.57 2.25 34.07 4.02
523 588 5.645497 CGGTACCTACCTATACATCTGGTAC 59.355 48.000 10.90 10.00 44.25 3.34
524 589 5.310594 ACGGTACCTACCTATACATCTGGTA 59.689 44.000 10.90 0.00 44.25 3.25
525 590 4.105377 ACGGTACCTACCTATACATCTGGT 59.895 45.833 10.90 0.00 44.25 4.00
526 591 4.660168 ACGGTACCTACCTATACATCTGG 58.340 47.826 10.90 0.00 44.25 3.86
527 592 7.571983 CGTTAACGGTACCTACCTATACATCTG 60.572 44.444 20.24 0.00 44.25 2.90
528 593 6.428159 CGTTAACGGTACCTACCTATACATCT 59.572 42.308 20.24 0.00 44.25 2.90
529 594 6.603095 CGTTAACGGTACCTACCTATACATC 58.397 44.000 20.24 0.00 44.25 3.06
530 595 6.560253 CGTTAACGGTACCTACCTATACAT 57.440 41.667 20.24 0.00 44.25 2.29
546 611 6.075205 CGAAAGTGGATAATCTACCGTTAACG 60.075 42.308 20.99 20.99 39.44 3.18
547 612 6.292008 GCGAAAGTGGATAATCTACCGTTAAC 60.292 42.308 0.00 0.00 0.00 2.01
548 613 5.750067 GCGAAAGTGGATAATCTACCGTTAA 59.250 40.000 0.00 0.00 0.00 2.01
549 614 5.284079 GCGAAAGTGGATAATCTACCGTTA 58.716 41.667 0.00 0.00 0.00 3.18
550 615 4.117685 GCGAAAGTGGATAATCTACCGTT 58.882 43.478 0.00 0.00 0.00 4.44
551 616 3.714391 GCGAAAGTGGATAATCTACCGT 58.286 45.455 0.00 0.00 0.00 4.83
552 617 2.724690 CGCGAAAGTGGATAATCTACCG 59.275 50.000 0.00 0.00 38.12 4.02
565 630 0.672342 ACACCAGAGTACGCGAAAGT 59.328 50.000 15.93 2.55 0.00 2.66
566 631 1.337821 GACACCAGAGTACGCGAAAG 58.662 55.000 15.93 0.00 0.00 2.62
567 632 0.386352 CGACACCAGAGTACGCGAAA 60.386 55.000 15.93 0.00 0.00 3.46
568 633 1.208358 CGACACCAGAGTACGCGAA 59.792 57.895 15.93 0.00 0.00 4.70
569 634 2.865308 CGACACCAGAGTACGCGA 59.135 61.111 15.93 0.00 0.00 5.87
570 635 2.874780 GCGACACCAGAGTACGCG 60.875 66.667 3.53 3.53 39.68 6.01
571 636 2.087009 GTGCGACACCAGAGTACGC 61.087 63.158 0.00 0.00 45.07 4.42
572 637 0.109272 ATGTGCGACACCAGAGTACG 60.109 55.000 7.38 0.00 32.73 3.67
573 638 1.350193 CATGTGCGACACCAGAGTAC 58.650 55.000 7.38 0.00 32.73 2.73
574 639 0.389817 GCATGTGCGACACCAGAGTA 60.390 55.000 7.38 0.00 32.73 2.59
575 640 1.669115 GCATGTGCGACACCAGAGT 60.669 57.895 7.38 0.00 32.73 3.24
576 641 1.229975 TTGCATGTGCGACACCAGAG 61.230 55.000 7.38 0.00 45.83 3.35
577 642 0.817229 TTTGCATGTGCGACACCAGA 60.817 50.000 7.38 0.00 45.83 3.86
578 643 0.386352 CTTTGCATGTGCGACACCAG 60.386 55.000 7.38 2.23 45.83 4.00
579 644 1.653667 CTTTGCATGTGCGACACCA 59.346 52.632 7.38 0.00 45.83 4.17
580 645 1.730547 GCTTTGCATGTGCGACACC 60.731 57.895 7.38 0.00 45.83 4.16
581 646 1.000233 CTGCTTTGCATGTGCGACAC 61.000 55.000 0.01 3.44 45.83 3.67
582 647 1.283487 CTGCTTTGCATGTGCGACA 59.717 52.632 0.01 0.00 45.83 4.35
583 648 1.443194 CCTGCTTTGCATGTGCGAC 60.443 57.895 0.01 0.00 45.83 5.19
584 649 2.956194 CCTGCTTTGCATGTGCGA 59.044 55.556 0.01 0.00 45.83 5.10
585 650 2.807895 GCCTGCTTTGCATGTGCG 60.808 61.111 0.01 0.00 45.83 5.34
586 651 2.433664 GGCCTGCTTTGCATGTGC 60.434 61.111 0.00 0.00 38.13 4.57
587 652 2.263540 GGGCCTGCTTTGCATGTG 59.736 61.111 0.84 0.00 38.13 3.21
588 653 3.376078 CGGGCCTGCTTTGCATGT 61.376 61.111 0.84 0.00 38.13 3.21
589 654 3.063704 TCGGGCCTGCTTTGCATG 61.064 61.111 6.73 0.00 38.13 4.06
590 655 3.064324 GTCGGGCCTGCTTTGCAT 61.064 61.111 6.73 0.00 38.13 3.96
612 677 4.465512 CGCTTGCATGGTCGGCAC 62.466 66.667 1.34 0.00 41.75 5.01
614 679 3.667429 GAACGCTTGCATGGTCGGC 62.667 63.158 1.34 0.00 0.00 5.54
615 680 2.480555 GAACGCTTGCATGGTCGG 59.519 61.111 1.34 0.00 0.00 4.79
616 681 2.096406 CGAACGCTTGCATGGTCG 59.904 61.111 7.09 7.09 0.00 4.79
617 682 2.202349 GCGAACGCTTGCATGGTC 60.202 61.111 11.97 0.00 38.26 4.02
618 683 3.737172 GGCGAACGCTTGCATGGT 61.737 61.111 18.14 0.00 41.60 3.55
619 684 4.481112 GGGCGAACGCTTGCATGG 62.481 66.667 18.14 0.00 41.60 3.66
620 685 2.924922 GATGGGCGAACGCTTGCATG 62.925 60.000 18.14 0.00 41.60 4.06
621 686 2.751436 ATGGGCGAACGCTTGCAT 60.751 55.556 18.14 0.00 41.60 3.96
622 687 3.430862 GATGGGCGAACGCTTGCA 61.431 61.111 18.14 0.00 41.60 4.08
623 688 4.179579 GGATGGGCGAACGCTTGC 62.180 66.667 18.14 6.20 41.60 4.01
624 689 2.114670 ATGGATGGGCGAACGCTTG 61.115 57.895 18.14 0.00 41.60 4.01
625 690 2.114670 CATGGATGGGCGAACGCTT 61.115 57.895 18.14 4.60 41.60 4.68
626 691 2.514592 CATGGATGGGCGAACGCT 60.515 61.111 18.14 0.00 41.60 5.07
627 692 4.256090 GCATGGATGGGCGAACGC 62.256 66.667 10.81 10.81 41.06 4.84
628 693 2.823593 TGCATGGATGGGCGAACG 60.824 61.111 0.00 0.00 0.00 3.95
629 694 1.750399 AGTGCATGGATGGGCGAAC 60.750 57.895 0.00 0.00 0.00 3.95
630 695 1.750018 CAGTGCATGGATGGGCGAA 60.750 57.895 0.00 0.00 0.00 4.70
631 696 2.124612 CAGTGCATGGATGGGCGA 60.125 61.111 0.00 0.00 0.00 5.54
632 697 1.996786 GAACAGTGCATGGATGGGCG 61.997 60.000 0.00 0.00 0.00 6.13
633 698 0.682209 AGAACAGTGCATGGATGGGC 60.682 55.000 0.00 0.00 0.00 5.36
634 699 1.843368 AAGAACAGTGCATGGATGGG 58.157 50.000 0.00 0.00 0.00 4.00
635 700 3.508793 AGAAAAGAACAGTGCATGGATGG 59.491 43.478 0.00 0.00 0.00 3.51
636 701 4.778534 AGAAAAGAACAGTGCATGGATG 57.221 40.909 0.00 0.00 0.00 3.51
648 713 9.803315 AGATGTTTTGTAAGGAAAGAAAAGAAC 57.197 29.630 0.00 0.00 0.00 3.01
649 714 9.801873 CAGATGTTTTGTAAGGAAAGAAAAGAA 57.198 29.630 0.00 0.00 0.00 2.52
654 719 6.540914 ACGTCAGATGTTTTGTAAGGAAAGAA 59.459 34.615 0.00 0.00 0.00 2.52
663 728 5.447144 GCATGCATACGTCAGATGTTTTGTA 60.447 40.000 14.21 0.08 0.00 2.41
668 733 1.942657 GGCATGCATACGTCAGATGTT 59.057 47.619 21.36 0.00 0.00 2.71
669 734 1.134431 TGGCATGCATACGTCAGATGT 60.134 47.619 21.36 0.00 0.00 3.06
678 743 1.203052 AGCAAACACTGGCATGCATAC 59.797 47.619 21.36 2.31 41.18 2.39
733 798 3.705043 ATACATCTGGTACCGTTCGTC 57.295 47.619 7.57 0.00 34.07 4.20
735 800 3.567164 ACCTATACATCTGGTACCGTTCG 59.433 47.826 7.57 0.00 34.07 3.95
791 859 2.365293 TGCATATGCGACACCAGAGTAT 59.635 45.455 22.21 0.00 45.83 2.12
804 872 1.068585 GGGCCTGCTTTGCATATGC 59.931 57.895 21.09 21.09 38.13 3.14
807 875 1.102809 CATCGGGCCTGCTTTGCATA 61.103 55.000 6.73 0.00 38.13 3.14
924 1028 2.209690 TGGTGTCTCGTATGGAGTGA 57.790 50.000 0.00 0.00 43.60 3.41
932 1039 0.240145 CGAGTGCTTGGTGTCTCGTA 59.760 55.000 0.00 0.00 42.83 3.43
965 1072 2.158813 GGTTTGTGACTGAGAGTGGGAA 60.159 50.000 0.00 0.00 0.00 3.97
1562 1684 2.507102 CACGCGGGCAGTAGTCTG 60.507 66.667 12.47 0.00 43.87 3.51
1771 1897 2.223595 CCTTATCGCTTCTTCTCGCTGA 60.224 50.000 0.00 0.00 0.00 4.26
2022 2177 2.855014 TTGGTTACCAGGCCCCGT 60.855 61.111 3.65 0.00 33.81 5.28
2034 2189 1.716028 GGTCCACCCACTCCTTGGTT 61.716 60.000 0.00 0.00 45.25 3.67
2211 2369 2.531428 TGCTCCATCCACACCCCA 60.531 61.111 0.00 0.00 0.00 4.96
2250 2408 1.658686 CCACCGAACTCTCCTCCGAG 61.659 65.000 0.00 0.00 37.48 4.63
2279 2437 1.710244 TCAGCTTTTCCCCAATCTCCA 59.290 47.619 0.00 0.00 0.00 3.86
2292 2450 1.005215 CCCATCACCTCCTTCAGCTTT 59.995 52.381 0.00 0.00 0.00 3.51
2296 2454 1.153289 CGCCCATCACCTCCTTCAG 60.153 63.158 0.00 0.00 0.00 3.02
2451 2609 0.249398 ATCGTCAGGTAGTTGTGCCC 59.751 55.000 0.00 0.00 0.00 5.36
2452 2610 1.641577 GATCGTCAGGTAGTTGTGCC 58.358 55.000 0.00 0.00 0.00 5.01
2457 2615 1.673808 GCCGGGATCGTCAGGTAGTT 61.674 60.000 2.18 0.00 33.95 2.24
2458 2616 2.125961 GCCGGGATCGTCAGGTAGT 61.126 63.158 2.18 0.00 33.95 2.73
2463 2621 2.088674 CTAAGGGCCGGGATCGTCAG 62.089 65.000 2.18 0.00 33.95 3.51
2474 2632 2.124411 TCCAACCTGATACTAAGGGCC 58.876 52.381 0.00 0.00 39.30 5.80
2476 2634 2.102588 CCGTCCAACCTGATACTAAGGG 59.897 54.545 0.00 0.00 39.30 3.95
2478 2636 3.700038 ACTCCGTCCAACCTGATACTAAG 59.300 47.826 0.00 0.00 0.00 2.18
2479 2637 3.705051 ACTCCGTCCAACCTGATACTAA 58.295 45.455 0.00 0.00 0.00 2.24
2480 2638 3.377253 ACTCCGTCCAACCTGATACTA 57.623 47.619 0.00 0.00 0.00 1.82
2481 2639 2.233305 ACTCCGTCCAACCTGATACT 57.767 50.000 0.00 0.00 0.00 2.12
2482 2640 4.460948 TTAACTCCGTCCAACCTGATAC 57.539 45.455 0.00 0.00 0.00 2.24
2483 2641 5.424757 CAATTAACTCCGTCCAACCTGATA 58.575 41.667 0.00 0.00 0.00 2.15
2484 2642 4.261801 CAATTAACTCCGTCCAACCTGAT 58.738 43.478 0.00 0.00 0.00 2.90
2485 2643 3.670625 CAATTAACTCCGTCCAACCTGA 58.329 45.455 0.00 0.00 0.00 3.86
2486 2644 2.161609 GCAATTAACTCCGTCCAACCTG 59.838 50.000 0.00 0.00 0.00 4.00
2487 2645 2.224670 TGCAATTAACTCCGTCCAACCT 60.225 45.455 0.00 0.00 0.00 3.50
2488 2646 2.156098 TGCAATTAACTCCGTCCAACC 58.844 47.619 0.00 0.00 0.00 3.77
2489 2647 3.365969 CCTTGCAATTAACTCCGTCCAAC 60.366 47.826 0.00 0.00 0.00 3.77
2490 2648 2.817258 CCTTGCAATTAACTCCGTCCAA 59.183 45.455 0.00 0.00 0.00 3.53
2491 2649 2.432444 CCTTGCAATTAACTCCGTCCA 58.568 47.619 0.00 0.00 0.00 4.02
2492 2650 1.132453 GCCTTGCAATTAACTCCGTCC 59.868 52.381 0.00 0.00 0.00 4.79
2493 2651 1.810151 TGCCTTGCAATTAACTCCGTC 59.190 47.619 0.00 0.00 34.76 4.79
2494 2652 1.539827 GTGCCTTGCAATTAACTCCGT 59.460 47.619 0.00 0.00 41.47 4.69
2521 2679 2.235016 CGTCACAACGTGCCGAAGT 61.235 57.895 0.00 0.00 43.94 3.01
2522 2680 1.484227 TTCGTCACAACGTGCCGAAG 61.484 55.000 8.70 0.00 46.14 3.79
2523 2681 2.104530 TCGTCACAACGTGCCGAA 59.895 55.556 0.00 0.00 40.80 4.30
2531 2689 4.242475 TGGTGATACTGATTCGTCACAAC 58.758 43.478 6.68 0.00 42.00 3.32
2532 2690 4.021456 ACTGGTGATACTGATTCGTCACAA 60.021 41.667 6.68 0.00 42.00 3.33
2533 2691 3.509967 ACTGGTGATACTGATTCGTCACA 59.490 43.478 6.68 0.00 42.00 3.58
2534 2692 4.111375 ACTGGTGATACTGATTCGTCAC 57.889 45.455 0.00 0.00 40.07 3.67
2535 2693 4.801330 AACTGGTGATACTGATTCGTCA 57.199 40.909 0.00 0.00 0.00 4.35
2536 2694 5.892568 AGTAACTGGTGATACTGATTCGTC 58.107 41.667 0.00 0.00 31.81 4.20
2537 2695 5.916661 AGTAACTGGTGATACTGATTCGT 57.083 39.130 0.00 0.00 31.81 3.85
2538 2696 7.596749 AAAAGTAACTGGTGATACTGATTCG 57.403 36.000 0.00 0.00 33.06 3.34
2567 2725 2.939103 GCTTAGAGTTGGCACTACATGG 59.061 50.000 0.00 0.00 31.22 3.66
2568 2726 2.939103 GGCTTAGAGTTGGCACTACATG 59.061 50.000 0.00 0.00 31.22 3.21
2569 2727 2.840651 AGGCTTAGAGTTGGCACTACAT 59.159 45.455 0.00 0.00 31.22 2.29
2570 2728 2.257207 AGGCTTAGAGTTGGCACTACA 58.743 47.619 0.00 0.00 31.22 2.74
2571 2729 4.081586 ACTTAGGCTTAGAGTTGGCACTAC 60.082 45.833 7.64 0.00 31.22 2.73
2572 2730 4.081642 CACTTAGGCTTAGAGTTGGCACTA 60.082 45.833 7.64 0.00 31.22 2.74
2573 2731 2.907042 ACTTAGGCTTAGAGTTGGCACT 59.093 45.455 7.64 0.00 35.17 4.40
2574 2732 3.003480 CACTTAGGCTTAGAGTTGGCAC 58.997 50.000 7.64 0.00 0.00 5.01
2575 2733 2.637872 ACACTTAGGCTTAGAGTTGGCA 59.362 45.455 7.64 0.00 0.00 4.92
2576 2734 3.336138 ACACTTAGGCTTAGAGTTGGC 57.664 47.619 7.64 0.00 0.00 4.52
2577 2735 3.437049 GCAACACTTAGGCTTAGAGTTGG 59.563 47.826 30.64 19.27 41.49 3.77
2578 2736 4.065088 TGCAACACTTAGGCTTAGAGTTG 58.935 43.478 27.91 27.91 42.97 3.16
2579 2737 4.351874 TGCAACACTTAGGCTTAGAGTT 57.648 40.909 7.64 8.95 0.00 3.01
2580 2738 4.351874 TTGCAACACTTAGGCTTAGAGT 57.648 40.909 7.64 2.36 0.00 3.24
2581 2739 5.452777 GTTTTGCAACACTTAGGCTTAGAG 58.547 41.667 7.64 1.65 32.54 2.43
2582 2740 4.024387 CGTTTTGCAACACTTAGGCTTAGA 60.024 41.667 13.50 0.00 32.54 2.10
2583 2741 4.219033 CGTTTTGCAACACTTAGGCTTAG 58.781 43.478 13.50 0.00 32.54 2.18
2584 2742 3.003897 CCGTTTTGCAACACTTAGGCTTA 59.996 43.478 13.50 0.00 32.54 3.09
2585 2743 2.223711 CCGTTTTGCAACACTTAGGCTT 60.224 45.455 13.50 0.00 32.54 4.35
2586 2744 1.336755 CCGTTTTGCAACACTTAGGCT 59.663 47.619 13.50 0.00 32.54 4.58
2587 2745 1.066454 ACCGTTTTGCAACACTTAGGC 59.934 47.619 13.50 0.00 32.54 3.93
2588 2746 3.430333 AACCGTTTTGCAACACTTAGG 57.570 42.857 13.50 9.79 32.54 2.69
2589 2747 4.264380 GTCAAACCGTTTTGCAACACTTAG 59.736 41.667 13.50 5.21 41.78 2.18
2590 2748 4.167268 GTCAAACCGTTTTGCAACACTTA 58.833 39.130 13.50 0.00 41.78 2.24
2591 2749 2.990514 GTCAAACCGTTTTGCAACACTT 59.009 40.909 13.50 0.00 41.78 3.16
2592 2750 2.029828 TGTCAAACCGTTTTGCAACACT 60.030 40.909 13.50 0.00 41.78 3.55
2593 2751 2.329379 TGTCAAACCGTTTTGCAACAC 58.671 42.857 5.63 5.63 41.78 3.32
2594 2752 2.600731 CTGTCAAACCGTTTTGCAACA 58.399 42.857 0.00 0.56 41.78 3.33
2595 2753 1.923864 CCTGTCAAACCGTTTTGCAAC 59.076 47.619 0.00 0.00 41.78 4.17
2596 2754 1.737363 GCCTGTCAAACCGTTTTGCAA 60.737 47.619 0.00 0.00 41.78 4.08
2597 2755 0.179124 GCCTGTCAAACCGTTTTGCA 60.179 50.000 0.00 1.99 41.78 4.08
2598 2756 1.206115 CGCCTGTCAAACCGTTTTGC 61.206 55.000 0.00 0.00 41.78 3.68
2599 2757 0.099791 ACGCCTGTCAAACCGTTTTG 59.900 50.000 0.00 0.00 43.17 2.44
2600 2758 1.666054 TACGCCTGTCAAACCGTTTT 58.334 45.000 0.00 0.00 35.36 2.43
2601 2759 1.886886 ATACGCCTGTCAAACCGTTT 58.113 45.000 0.00 0.00 35.36 3.60
2602 2760 2.747396 TATACGCCTGTCAAACCGTT 57.253 45.000 0.00 0.00 35.36 4.44
2603 2761 2.613691 CTTATACGCCTGTCAAACCGT 58.386 47.619 0.00 0.00 37.68 4.83
2604 2762 1.326548 GCTTATACGCCTGTCAAACCG 59.673 52.381 0.00 0.00 0.00 4.44
2605 2763 2.608090 GAGCTTATACGCCTGTCAAACC 59.392 50.000 0.00 0.00 0.00 3.27
2606 2764 2.281762 CGAGCTTATACGCCTGTCAAAC 59.718 50.000 0.00 0.00 0.00 2.93
2607 2765 2.094390 ACGAGCTTATACGCCTGTCAAA 60.094 45.455 0.00 0.00 0.00 2.69
2608 2766 1.475280 ACGAGCTTATACGCCTGTCAA 59.525 47.619 0.00 0.00 0.00 3.18
2609 2767 1.100510 ACGAGCTTATACGCCTGTCA 58.899 50.000 0.00 0.00 0.00 3.58
2610 2768 3.555917 ATACGAGCTTATACGCCTGTC 57.444 47.619 0.00 0.00 0.00 3.51
2611 2769 3.317149 TCAATACGAGCTTATACGCCTGT 59.683 43.478 0.00 0.00 0.00 4.00
2612 2770 3.669122 GTCAATACGAGCTTATACGCCTG 59.331 47.826 0.00 0.00 0.00 4.85
2613 2771 3.568853 AGTCAATACGAGCTTATACGCCT 59.431 43.478 0.00 0.00 0.00 5.52
2614 2772 3.898529 AGTCAATACGAGCTTATACGCC 58.101 45.455 0.00 0.00 0.00 5.68
2615 2773 4.086804 CGAAGTCAATACGAGCTTATACGC 59.913 45.833 0.00 0.00 0.00 4.42
2616 2774 4.611782 CCGAAGTCAATACGAGCTTATACG 59.388 45.833 0.00 0.00 0.00 3.06
2617 2775 4.382160 GCCGAAGTCAATACGAGCTTATAC 59.618 45.833 0.00 0.00 0.00 1.47
2618 2776 4.037089 TGCCGAAGTCAATACGAGCTTATA 59.963 41.667 0.00 0.00 0.00 0.98
2619 2777 3.181479 TGCCGAAGTCAATACGAGCTTAT 60.181 43.478 0.00 0.00 0.00 1.73
2620 2778 2.164827 TGCCGAAGTCAATACGAGCTTA 59.835 45.455 0.00 0.00 0.00 3.09
2621 2779 1.067142 TGCCGAAGTCAATACGAGCTT 60.067 47.619 0.00 0.00 0.00 3.74
2622 2780 0.530744 TGCCGAAGTCAATACGAGCT 59.469 50.000 0.00 0.00 0.00 4.09
2623 2781 0.645868 GTGCCGAAGTCAATACGAGC 59.354 55.000 0.00 0.00 0.00 5.03
2624 2782 0.914551 CGTGCCGAAGTCAATACGAG 59.085 55.000 0.00 0.00 33.78 4.18
2625 2783 0.241749 ACGTGCCGAAGTCAATACGA 59.758 50.000 0.00 0.00 35.69 3.43
2626 2784 1.065358 AACGTGCCGAAGTCAATACG 58.935 50.000 0.00 0.00 37.54 3.06
2627 2785 1.796459 ACAACGTGCCGAAGTCAATAC 59.204 47.619 0.00 0.00 0.00 1.89
2628 2786 1.795872 CACAACGTGCCGAAGTCAATA 59.204 47.619 0.00 0.00 0.00 1.90
2629 2787 0.586319 CACAACGTGCCGAAGTCAAT 59.414 50.000 0.00 0.00 0.00 2.57
2630 2788 0.460459 TCACAACGTGCCGAAGTCAA 60.460 50.000 0.00 0.00 32.98 3.18
2631 2789 1.142097 TCACAACGTGCCGAAGTCA 59.858 52.632 0.00 0.00 32.98 3.41
2632 2790 1.563173 GTCACAACGTGCCGAAGTC 59.437 57.895 0.00 0.00 32.98 3.01
2728 2887 4.096833 ACGTGGTCAATACGAGCTTATACA 59.903 41.667 4.43 0.00 43.82 2.29
2949 3131 2.434185 TCGAAGACCATGGCACGC 60.434 61.111 13.04 0.00 0.00 5.34
2952 3134 0.178767 CATCCTCGAAGACCATGGCA 59.821 55.000 13.04 0.00 0.00 4.92
3052 3234 4.123745 TCCCCAAATCACCTAACCCTAAT 58.876 43.478 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.