Multiple sequence alignment - TraesCS2B01G477600

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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 TraesCS2B01G477600 chr2B 100.000 3694 0 0 413 4106 675335534 675331841 0.000000e+00 6822.0
1 TraesCS2B01G477600 chr2B 87.510 1241 131 12 1878 3106 675534974 675536202 0.000000e+00 1411.0
2 TraesCS2B01G477600 chr2B 82.314 1210 179 21 1881 3083 675525748 675526929 0.000000e+00 1016.0
3 TraesCS2B01G477600 chr2B 82.353 136 16 4 3315 3446 784522999 784522868 1.210000e-20 111.0
4 TraesCS2B01G477600 chr2B 81.343 134 18 4 3317 3446 783873989 783874119 7.260000e-18 102.0
5 TraesCS2B01G477600 chr2B 100.000 45 0 0 685 729 675335228 675335184 2.630000e-12 84.2
6 TraesCS2B01G477600 chr2B 100.000 45 0 0 719 763 675335262 675335218 2.630000e-12 84.2
7 TraesCS2B01G477600 chr2B 100.000 43 0 0 1 43 675335946 675335904 3.400000e-11 80.5
8 TraesCS2B01G477600 chr2A 95.119 3032 113 16 719 3723 704755846 704752823 0.000000e+00 4747.0
9 TraesCS2B01G477600 chr2A 83.402 1211 164 23 1881 3083 705265526 705266707 0.000000e+00 1088.0
10 TraesCS2B01G477600 chr2A 93.376 619 38 1 2040 2658 705342857 705343472 0.000000e+00 913.0
11 TraesCS2B01G477600 chr2A 83.493 939 122 16 1130 2044 705340964 705341893 0.000000e+00 845.0
12 TraesCS2B01G477600 chr2A 94.194 155 9 0 3952 4106 227393452 227393298 1.910000e-58 237.0
13 TraesCS2B01G477600 chr2A 97.143 140 3 1 3776 3915 704752520 704752382 6.860000e-58 235.0
14 TraesCS2B01G477600 chr2A 91.667 168 12 2 3941 4106 220919836 220919669 8.880000e-57 231.0
15 TraesCS2B01G477600 chr2A 93.651 63 4 0 3717 3779 704752797 704752735 1.220000e-15 95.3
16 TraesCS2B01G477600 chr2A 85.882 85 10 1 567 649 559108286 559108370 5.650000e-14 89.8
17 TraesCS2B01G477600 chr2A 93.617 47 3 0 3406 3452 758927372 758927418 2.050000e-08 71.3
18 TraesCS2B01G477600 chr2D 94.730 3017 120 18 719 3723 564073153 564070164 0.000000e+00 4654.0
19 TraesCS2B01G477600 chr2D 88.935 1211 115 12 1878 3079 564477167 564478367 0.000000e+00 1476.0
20 TraesCS2B01G477600 chr2D 88.396 1241 123 13 1878 3106 564439307 564440538 0.000000e+00 1474.0
21 TraesCS2B01G477600 chr2D 94.839 155 8 0 3952 4106 379784803 379784649 4.100000e-60 243.0
22 TraesCS2B01G477600 chr2D 94.805 154 8 0 3953 4106 602262506 602262353 1.470000e-59 241.0
23 TraesCS2B01G477600 chr2D 90.503 179 15 2 3776 3953 564069852 564069675 6.860000e-58 235.0
24 TraesCS2B01G477600 chr2D 92.929 99 6 1 1488 1586 481595364 481595461 4.280000e-30 143.0
25 TraesCS2B01G477600 chr2D 89.623 106 11 0 1220 1325 481595264 481595369 7.160000e-28 135.0
26 TraesCS2B01G477600 chr2D 82.963 135 15 5 3317 3446 648456195 648456064 9.330000e-22 115.0
27 TraesCS2B01G477600 chr2D 97.015 67 2 0 663 729 564073175 564073109 3.350000e-21 113.0
28 TraesCS2B01G477600 chr2D 92.982 57 4 0 423 479 564073233 564073177 2.630000e-12 84.2
29 TraesCS2B01G477600 chr4B 84.763 1096 132 22 1943 3027 22438650 22437579 0.000000e+00 1066.0
30 TraesCS2B01G477600 chr4B 85.243 1030 129 11 2064 3086 22488508 22487495 0.000000e+00 1038.0
31 TraesCS2B01G477600 chr4B 86.301 73 10 0 475 547 447764816 447764888 3.400000e-11 80.5
32 TraesCS2B01G477600 chr3B 79.363 785 129 13 1876 2660 223963723 223964474 4.700000e-144 521.0
33 TraesCS2B01G477600 chr3B 83.838 99 15 1 559 657 676632082 676631985 4.370000e-15 93.5
34 TraesCS2B01G477600 chr3B 82.796 93 14 2 574 664 801290725 801290817 9.460000e-12 82.4
35 TraesCS2B01G477600 chr3D 79.236 785 130 13 1876 2660 152824032 152824783 2.190000e-142 516.0
36 TraesCS2B01G477600 chr3D 96.364 55 0 2 3544 3596 403106721 403106775 5.650000e-14 89.8
37 TraesCS2B01G477600 chr4D 94.805 154 8 0 3953 4106 367327247 367327094 1.470000e-59 241.0
38 TraesCS2B01G477600 chr4D 92.121 165 12 1 3942 4106 348143299 348143462 8.880000e-57 231.0
39 TraesCS2B01G477600 chr4D 92.073 164 13 0 3943 4106 352939710 352939873 8.880000e-57 231.0
40 TraesCS2B01G477600 chr1A 94.805 154 8 0 3953 4106 291630166 291630319 1.470000e-59 241.0
41 TraesCS2B01G477600 chr1D 94.194 155 9 0 3952 4106 337774431 337774585 1.910000e-58 237.0
42 TraesCS2B01G477600 chr1D 97.500 40 1 0 3415 3454 371704020 371703981 7.360000e-08 69.4
43 TraesCS2B01G477600 chr6D 85.321 109 14 2 551 659 68652319 68652425 1.210000e-20 111.0
44 TraesCS2B01G477600 chr6B 86.667 90 11 1 570 659 566037599 566037687 9.390000e-17 99.0
45 TraesCS2B01G477600 chr6B 83.784 74 8 2 478 547 613584399 613584472 2.650000e-07 67.6
46 TraesCS2B01G477600 chr6B 82.667 75 6 5 478 547 60612936 60612864 4.430000e-05 60.2
47 TraesCS2B01G477600 chr5B 84.158 101 14 2 559 659 90201232 90201330 3.380000e-16 97.1
48 TraesCS2B01G477600 chr5B 84.932 73 10 1 475 547 546098223 546098294 5.690000e-09 73.1
49 TraesCS2B01G477600 chr5B 87.931 58 3 4 468 521 664681578 664681521 9.530000e-07 65.8
50 TraesCS2B01G477600 chr7B 81.982 111 16 4 559 669 378407066 378406960 1.570000e-14 91.6
51 TraesCS2B01G477600 chr7A 88.571 70 8 0 478 547 695850628 695850559 7.310000e-13 86.1
52 TraesCS2B01G477600 chr4A 82.178 101 16 2 559 659 508273205 508273303 7.310000e-13 86.1
53 TraesCS2B01G477600 chr4A 84.615 65 6 2 478 538 66146186 66146122 1.230000e-05 62.1
54 TraesCS2B01G477600 chr7D 81.188 101 18 1 559 659 618176564 618176663 3.400000e-11 80.5
55 TraesCS2B01G477600 chr5D 90.385 52 3 2 462 513 214329115 214329066 2.650000e-07 67.6
56 TraesCS2B01G477600 chrUn 82.857 70 6 4 480 547 31599568 31599633 1.590000e-04 58.4


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 TraesCS2B01G477600 chr2B 675331841 675335946 4105 True 1767.725000 6822 100.000000 1 4106 4 chr2B.!!$R2 4105
1 TraesCS2B01G477600 chr2B 675534974 675536202 1228 False 1411.000000 1411 87.510000 1878 3106 1 chr2B.!!$F2 1228
2 TraesCS2B01G477600 chr2B 675525748 675526929 1181 False 1016.000000 1016 82.314000 1881 3083 1 chr2B.!!$F1 1202
3 TraesCS2B01G477600 chr2A 704752382 704755846 3464 True 1692.433333 4747 95.304333 719 3915 3 chr2A.!!$R3 3196
4 TraesCS2B01G477600 chr2A 705265526 705266707 1181 False 1088.000000 1088 83.402000 1881 3083 1 chr2A.!!$F2 1202
5 TraesCS2B01G477600 chr2A 705340964 705343472 2508 False 879.000000 913 88.434500 1130 2658 2 chr2A.!!$F4 1528
6 TraesCS2B01G477600 chr2D 564477167 564478367 1200 False 1476.000000 1476 88.935000 1878 3079 1 chr2D.!!$F2 1201
7 TraesCS2B01G477600 chr2D 564439307 564440538 1231 False 1474.000000 1474 88.396000 1878 3106 1 chr2D.!!$F1 1228
8 TraesCS2B01G477600 chr2D 564069675 564073233 3558 True 1271.550000 4654 93.807500 423 3953 4 chr2D.!!$R4 3530
9 TraesCS2B01G477600 chr4B 22437579 22438650 1071 True 1066.000000 1066 84.763000 1943 3027 1 chr4B.!!$R1 1084
10 TraesCS2B01G477600 chr4B 22487495 22488508 1013 True 1038.000000 1038 85.243000 2064 3086 1 chr4B.!!$R2 1022
11 TraesCS2B01G477600 chr3B 223963723 223964474 751 False 521.000000 521 79.363000 1876 2660 1 chr3B.!!$F1 784
12 TraesCS2B01G477600 chr3D 152824032 152824783 751 False 516.000000 516 79.236000 1876 2660 1 chr3D.!!$F1 784

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
703 704 0.599466 CTCCATCATCGAGCATGCGT 60.599 55.0 13.01 0.0 31.70 5.24 F
1773 1800 0.179029 CCTGGAACTTCACCACGGTT 60.179 55.0 0.00 0.0 33.57 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 3215 1.369839 CGTAGACGAGGAGCAGCTCA 61.370 60.000 24.09 0.0 43.02 4.26 R
3743 4811 1.150536 GTGTTGTCCCCTTCTGGCA 59.849 57.895 0.00 0.0 0.00 4.92 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
22 23 5.784750 TGCTTAACAAGATCAAGATGACG 57.215 39.130 0.00 0.00 0.00 4.35
23 24 4.093408 TGCTTAACAAGATCAAGATGACGC 59.907 41.667 0.00 0.00 0.00 5.19
24 25 4.494855 GCTTAACAAGATCAAGATGACGCC 60.495 45.833 0.00 0.00 0.00 5.68
25 26 3.340814 AACAAGATCAAGATGACGCCT 57.659 42.857 0.00 0.00 0.00 5.52
26 27 4.471904 AACAAGATCAAGATGACGCCTA 57.528 40.909 0.00 0.00 0.00 3.93
27 28 3.786635 ACAAGATCAAGATGACGCCTAC 58.213 45.455 0.00 0.00 0.00 3.18
28 29 3.449018 ACAAGATCAAGATGACGCCTACT 59.551 43.478 0.00 0.00 0.00 2.57
29 30 4.645136 ACAAGATCAAGATGACGCCTACTA 59.355 41.667 0.00 0.00 0.00 1.82
30 31 4.839668 AGATCAAGATGACGCCTACTAC 57.160 45.455 0.00 0.00 0.00 2.73
31 32 4.465886 AGATCAAGATGACGCCTACTACT 58.534 43.478 0.00 0.00 0.00 2.57
32 33 4.517453 AGATCAAGATGACGCCTACTACTC 59.483 45.833 0.00 0.00 0.00 2.59
33 34 3.887352 TCAAGATGACGCCTACTACTCT 58.113 45.455 0.00 0.00 0.00 3.24
34 35 4.270834 TCAAGATGACGCCTACTACTCTT 58.729 43.478 0.00 0.00 0.00 2.85
35 36 4.705507 TCAAGATGACGCCTACTACTCTTT 59.294 41.667 0.00 0.00 0.00 2.52
36 37 5.185249 TCAAGATGACGCCTACTACTCTTTT 59.815 40.000 0.00 0.00 0.00 2.27
37 38 5.662674 AGATGACGCCTACTACTCTTTTT 57.337 39.130 0.00 0.00 0.00 1.94
450 451 3.634397 ACTCATTGATCCCACGACATT 57.366 42.857 0.00 0.00 0.00 2.71
461 462 3.759618 TCCCACGACATTGTAAATTTCCC 59.240 43.478 0.00 0.00 0.00 3.97
467 468 5.095490 CGACATTGTAAATTTCCCTCAAGC 58.905 41.667 0.00 0.00 0.00 4.01
471 472 6.494835 ACATTGTAAATTTCCCTCAAGCTTCT 59.505 34.615 0.00 0.00 0.00 2.85
479 480 5.662674 TTCCCTCAAGCTTCTACTTCTAC 57.337 43.478 0.00 0.00 0.00 2.59
480 481 4.936802 TCCCTCAAGCTTCTACTTCTACT 58.063 43.478 0.00 0.00 0.00 2.57
481 482 4.951094 TCCCTCAAGCTTCTACTTCTACTC 59.049 45.833 0.00 0.00 0.00 2.59
482 483 4.098807 CCCTCAAGCTTCTACTTCTACTCC 59.901 50.000 0.00 0.00 0.00 3.85
483 484 4.098807 CCTCAAGCTTCTACTTCTACTCCC 59.901 50.000 0.00 0.00 0.00 4.30
484 485 4.936802 TCAAGCTTCTACTTCTACTCCCT 58.063 43.478 0.00 0.00 0.00 4.20
485 486 4.951094 TCAAGCTTCTACTTCTACTCCCTC 59.049 45.833 0.00 0.00 0.00 4.30
486 487 3.905968 AGCTTCTACTTCTACTCCCTCC 58.094 50.000 0.00 0.00 0.00 4.30
487 488 2.619646 GCTTCTACTTCTACTCCCTCCG 59.380 54.545 0.00 0.00 0.00 4.63
488 489 3.888583 CTTCTACTTCTACTCCCTCCGT 58.111 50.000 0.00 0.00 0.00 4.69
489 490 4.271661 CTTCTACTTCTACTCCCTCCGTT 58.728 47.826 0.00 0.00 0.00 4.44
490 491 3.883669 TCTACTTCTACTCCCTCCGTTC 58.116 50.000 0.00 0.00 0.00 3.95
491 492 1.849977 ACTTCTACTCCCTCCGTTCC 58.150 55.000 0.00 0.00 0.00 3.62
492 493 1.358445 ACTTCTACTCCCTCCGTTCCT 59.642 52.381 0.00 0.00 0.00 3.36
493 494 2.579860 ACTTCTACTCCCTCCGTTCCTA 59.420 50.000 0.00 0.00 0.00 2.94
494 495 3.011032 ACTTCTACTCCCTCCGTTCCTAA 59.989 47.826 0.00 0.00 0.00 2.69
495 496 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
496 497 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
497 498 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
498 499 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
499 500 7.095183 TCTACTCCCTCCGTTCCTAAATATA 57.905 40.000 0.00 0.00 0.00 0.86
500 501 7.529555 TCTACTCCCTCCGTTCCTAAATATAA 58.470 38.462 0.00 0.00 0.00 0.98
501 502 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
502 503 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
503 504 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
504 505 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
505 506 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
506 507 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
507 508 7.656542 CCCTCCGTTCCTAAATATAAGTCTTTC 59.343 40.741 0.00 0.00 0.00 2.62
508 509 8.422566 CCTCCGTTCCTAAATATAAGTCTTTCT 58.577 37.037 0.00 0.00 0.00 2.52
509 510 9.250624 CTCCGTTCCTAAATATAAGTCTTTCTG 57.749 37.037 0.00 0.00 0.00 3.02
510 511 8.202137 TCCGTTCCTAAATATAAGTCTTTCTGG 58.798 37.037 0.00 0.00 0.00 3.86
511 512 8.202137 CCGTTCCTAAATATAAGTCTTTCTGGA 58.798 37.037 0.00 0.00 0.00 3.86
512 513 9.032420 CGTTCCTAAATATAAGTCTTTCTGGAC 57.968 37.037 0.00 0.00 36.56 4.02
522 523 5.939764 AGTCTTTCTGGACTACATATGCA 57.060 39.130 1.58 0.00 43.76 3.96
523 524 5.911752 AGTCTTTCTGGACTACATATGCAG 58.088 41.667 1.58 1.32 43.76 4.41
524 525 5.423610 AGTCTTTCTGGACTACATATGCAGT 59.576 40.000 8.38 8.38 43.76 4.40
525 526 6.607600 AGTCTTTCTGGACTACATATGCAGTA 59.392 38.462 8.62 0.00 43.76 2.74
526 527 7.124298 AGTCTTTCTGGACTACATATGCAGTAA 59.876 37.037 8.62 4.36 43.76 2.24
527 528 7.764443 GTCTTTCTGGACTACATATGCAGTAAA 59.236 37.037 8.62 5.33 36.90 2.01
528 529 8.486210 TCTTTCTGGACTACATATGCAGTAAAT 58.514 33.333 8.62 0.00 36.90 1.40
529 530 9.113838 CTTTCTGGACTACATATGCAGTAAATT 57.886 33.333 8.62 0.00 36.90 1.82
532 533 9.764363 TCTGGACTACATATGCAGTAAATTAAG 57.236 33.333 8.62 1.89 36.90 1.85
533 534 9.547753 CTGGACTACATATGCAGTAAATTAAGT 57.452 33.333 8.62 0.00 31.37 2.24
534 535 9.325198 TGGACTACATATGCAGTAAATTAAGTG 57.675 33.333 8.62 0.00 0.00 3.16
535 536 9.542462 GGACTACATATGCAGTAAATTAAGTGA 57.458 33.333 8.62 0.00 0.00 3.41
554 555 9.642327 TTAAGTGAATTTATACTCTTACACGCA 57.358 29.630 0.00 0.00 33.18 5.24
555 556 8.542497 AAGTGAATTTATACTCTTACACGCAA 57.458 30.769 0.00 0.00 33.18 4.85
556 557 8.542497 AGTGAATTTATACTCTTACACGCAAA 57.458 30.769 0.00 0.00 33.18 3.68
557 558 8.995220 AGTGAATTTATACTCTTACACGCAAAA 58.005 29.630 0.00 0.00 33.18 2.44
558 559 9.601971 GTGAATTTATACTCTTACACGCAAAAA 57.398 29.630 0.00 0.00 0.00 1.94
601 602 8.624367 ACTCTAAACTACGTCTATATGCATCT 57.376 34.615 0.19 0.00 0.00 2.90
602 603 8.508062 ACTCTAAACTACGTCTATATGCATCTG 58.492 37.037 0.19 0.00 0.00 2.90
603 604 8.392372 TCTAAACTACGTCTATATGCATCTGT 57.608 34.615 0.19 0.00 0.00 3.41
604 605 9.498176 TCTAAACTACGTCTATATGCATCTGTA 57.502 33.333 0.19 0.00 0.00 2.74
606 607 8.972262 AAACTACGTCTATATGCATCTGTATG 57.028 34.615 0.19 0.00 36.09 2.39
607 608 7.689446 ACTACGTCTATATGCATCTGTATGT 57.311 36.000 0.19 2.36 35.38 2.29
608 609 8.788325 ACTACGTCTATATGCATCTGTATGTA 57.212 34.615 0.19 3.45 35.38 2.29
609 610 8.884726 ACTACGTCTATATGCATCTGTATGTAG 58.115 37.037 19.61 19.61 34.74 2.74
610 611 7.689446 ACGTCTATATGCATCTGTATGTAGT 57.311 36.000 0.19 0.00 34.91 2.73
611 612 8.112016 ACGTCTATATGCATCTGTATGTAGTT 57.888 34.615 0.19 0.00 34.91 2.24
612 613 9.227777 ACGTCTATATGCATCTGTATGTAGTTA 57.772 33.333 0.19 0.00 34.91 2.24
702 703 2.151295 CTCCATCATCGAGCATGCG 58.849 57.895 13.01 0.00 31.70 4.73
703 704 0.599466 CTCCATCATCGAGCATGCGT 60.599 55.000 13.01 0.00 31.70 5.24
704 705 0.877213 TCCATCATCGAGCATGCGTG 60.877 55.000 13.01 9.05 31.70 5.34
724 725 3.934962 GCTCCGCTCCCCTCCATC 61.935 72.222 0.00 0.00 0.00 3.51
782 783 4.126437 TCGCAAGTCAAAGTCTCATTTGA 58.874 39.130 0.00 0.00 44.72 2.69
978 984 1.418334 CTCGTCTTCCATCCCATCCT 58.582 55.000 0.00 0.00 0.00 3.24
979 985 1.342819 CTCGTCTTCCATCCCATCCTC 59.657 57.143 0.00 0.00 0.00 3.71
1003 1009 0.873743 GCAGAGACGAGTAGCCATGC 60.874 60.000 0.00 0.00 0.00 4.06
1031 1037 2.903357 CATGACCCTGCGGCTAGT 59.097 61.111 0.00 0.00 0.00 2.57
1035 1041 1.142097 GACCCTGCGGCTAGTCTTC 59.858 63.158 0.00 0.00 0.00 2.87
1043 1049 2.886124 GCTAGTCTTCGCGGCCAC 60.886 66.667 6.13 0.00 0.00 5.01
1066 1072 3.002583 TCCTCATCCTGTGCGGCA 61.003 61.111 0.00 0.00 32.54 5.69
1309 1318 1.079503 GGAGTTCGTGCTCAACATCC 58.920 55.000 10.17 0.99 37.24 3.51
1364 1391 1.764571 CTCCTCACCAACAACCCGGA 61.765 60.000 0.73 0.00 0.00 5.14
1374 1401 3.966543 AACCCGGACTTGCCCAGG 61.967 66.667 0.73 0.00 33.64 4.45
1410 1437 1.675641 GCTCGGCCTGACCAACAAT 60.676 57.895 0.00 0.00 39.03 2.71
1621 1648 0.248215 CGACGGCAAAATGATGAGCC 60.248 55.000 0.00 0.00 43.61 4.70
1773 1800 0.179029 CCTGGAACTTCACCACGGTT 60.179 55.000 0.00 0.00 33.57 4.44
2211 3215 1.151450 CTGGTGCCACAAGAAGGGT 59.849 57.895 0.00 0.00 0.00 4.34
2442 3453 2.542907 CGTCAAGGCCAGCAACGTT 61.543 57.895 5.01 0.00 0.00 3.99
2844 3858 4.443266 GGCGAGTTCGAGCAGGCT 62.443 66.667 5.60 0.00 43.02 4.58
3193 4212 8.455903 ACCAGAATCAAATGTACATTGATAGG 57.544 34.615 21.46 22.90 0.00 2.57
3360 4385 4.349930 GGGTGTATACACTTGATATGGGGT 59.650 45.833 29.89 0.00 45.73 4.95
3363 4388 7.256908 GGGTGTATACACTTGATATGGGGTAAT 60.257 40.741 29.89 0.00 45.73 1.89
3496 4524 6.723298 TTGTTCACACTATTTTGACCCAAT 57.277 33.333 0.00 0.00 0.00 3.16
3497 4525 6.723298 TGTTCACACTATTTTGACCCAATT 57.277 33.333 0.00 0.00 0.00 2.32
3597 4629 7.678207 TGTATATACACCCATAGACCAAACA 57.322 36.000 11.62 0.00 0.00 2.83
3598 4630 7.732025 TGTATATACACCCATAGACCAAACAG 58.268 38.462 11.62 0.00 0.00 3.16
3600 4632 3.876309 ACACCCATAGACCAAACAGTT 57.124 42.857 0.00 0.00 0.00 3.16
3601 4633 3.486383 ACACCCATAGACCAAACAGTTG 58.514 45.455 0.00 0.00 34.25 3.16
3602 4634 3.137544 ACACCCATAGACCAAACAGTTGA 59.862 43.478 0.00 0.00 36.83 3.18
3703 4738 0.821517 TGCGTGACTCAATATCCCGT 59.178 50.000 0.00 0.00 0.00 5.28
3729 4797 3.382832 CCGGAGACAAGGCGAGGT 61.383 66.667 0.00 0.00 0.00 3.85
3743 4811 1.689273 GCGAGGTGAGTAGGGAATGAT 59.311 52.381 0.00 0.00 0.00 2.45
3744 4812 2.546795 GCGAGGTGAGTAGGGAATGATG 60.547 54.545 0.00 0.00 0.00 3.07
3786 4854 3.918220 CGCGGCATCAACGAGCTC 61.918 66.667 2.73 2.73 0.00 4.09
3923 5220 8.548721 AGTTCTGTGTTATAAAACGAAGACAAG 58.451 33.333 11.09 0.00 38.53 3.16
3954 5251 8.940768 ATTTTGTTGTGCATTTAGTAAACACT 57.059 26.923 14.17 0.00 32.49 3.55
3956 5253 9.509855 TTTTGTTGTGCATTTAGTAAACACTAG 57.490 29.630 14.17 0.00 32.49 2.57
3957 5254 6.664515 TGTTGTGCATTTAGTAAACACTAGC 58.335 36.000 14.17 7.84 32.49 3.42
3958 5255 6.261158 TGTTGTGCATTTAGTAAACACTAGCA 59.739 34.615 14.17 9.70 32.49 3.49
3959 5256 6.869315 TGTGCATTTAGTAAACACTAGCAA 57.131 33.333 14.17 3.96 32.49 3.91
3960 5257 6.664515 TGTGCATTTAGTAAACACTAGCAAC 58.335 36.000 14.17 8.40 32.49 4.17
3961 5258 6.261158 TGTGCATTTAGTAAACACTAGCAACA 59.739 34.615 14.17 9.99 32.49 3.33
3962 5259 7.040755 TGTGCATTTAGTAAACACTAGCAACAT 60.041 33.333 14.17 0.00 32.49 2.71
3963 5260 7.271223 GTGCATTTAGTAAACACTAGCAACATG 59.729 37.037 0.00 0.00 0.00 3.21
3964 5261 6.251376 GCATTTAGTAAACACTAGCAACATGC 59.749 38.462 0.00 0.00 45.46 4.06
3965 5262 5.873179 TTAGTAAACACTAGCAACATGCC 57.127 39.130 0.00 0.00 46.52 4.40
3966 5263 3.081804 AGTAAACACTAGCAACATGCCC 58.918 45.455 0.00 0.00 46.52 5.36
3967 5264 0.881118 AAACACTAGCAACATGCCCG 59.119 50.000 0.00 0.00 46.52 6.13
3968 5265 0.250727 AACACTAGCAACATGCCCGT 60.251 50.000 0.00 0.00 46.52 5.28
3969 5266 0.955428 ACACTAGCAACATGCCCGTG 60.955 55.000 15.58 15.58 46.52 4.94
3970 5267 2.040544 ACTAGCAACATGCCCGTGC 61.041 57.895 0.00 0.00 46.52 5.34
3971 5268 3.099619 CTAGCAACATGCCCGTGCG 62.100 63.158 0.00 0.00 46.52 5.34
3972 5269 3.892740 TAGCAACATGCCCGTGCGT 62.893 57.895 0.00 0.00 46.52 5.24
3973 5270 4.341502 GCAACATGCCCGTGCGTT 62.342 61.111 0.00 0.00 41.78 4.84
3974 5271 2.428902 CAACATGCCCGTGCGTTG 60.429 61.111 0.00 0.00 41.78 4.10
3975 5272 4.341502 AACATGCCCGTGCGTTGC 62.342 61.111 0.00 0.00 41.78 4.17
3977 5274 4.118995 CATGCCCGTGCGTTGCAT 62.119 61.111 11.29 11.29 46.09 3.96
3978 5275 4.118995 ATGCCCGTGCGTTGCATG 62.119 61.111 14.78 4.04 43.66 4.06
3994 5291 3.449377 TTGCATGGAACATCAAGATGCAT 59.551 39.130 9.85 0.00 46.44 3.96
3995 5292 4.081365 TTGCATGGAACATCAAGATGCATT 60.081 37.500 9.85 0.00 46.44 3.56
3996 5293 5.569832 TTGCATGGAACATCAAGATGCATTT 60.570 36.000 9.85 0.00 46.44 2.32
3997 5294 7.562138 TTGCATGGAACATCAAGATGCATTTG 61.562 38.462 9.85 7.88 46.44 2.32
3998 5295 9.833813 TTGCATGGAACATCAAGATGCATTTGT 62.834 37.037 9.85 0.00 46.44 2.83
4000 5297 6.778834 TGGAACATCAAGATGCATTTGTAT 57.221 33.333 9.85 1.80 42.39 2.29
4001 5298 6.566141 TGGAACATCAAGATGCATTTGTATG 58.434 36.000 9.85 13.57 42.39 2.39
4002 5299 6.377712 TGGAACATCAAGATGCATTTGTATGA 59.622 34.615 22.17 15.31 42.39 2.15
4003 5300 6.916387 GGAACATCAAGATGCATTTGTATGAG 59.084 38.462 22.17 12.56 42.39 2.90
4004 5301 7.400599 AACATCAAGATGCATTTGTATGAGT 57.599 32.000 22.17 12.92 42.39 3.41
4005 5302 8.510243 AACATCAAGATGCATTTGTATGAGTA 57.490 30.769 22.17 8.59 42.39 2.59
4006 5303 8.151141 ACATCAAGATGCATTTGTATGAGTAG 57.849 34.615 22.17 12.72 42.39 2.57
4007 5304 7.772292 ACATCAAGATGCATTTGTATGAGTAGT 59.228 33.333 22.17 13.08 42.39 2.73
4008 5305 8.618677 CATCAAGATGCATTTGTATGAGTAGTT 58.381 33.333 0.00 0.00 33.37 2.24
4009 5306 8.565896 TCAAGATGCATTTGTATGAGTAGTTT 57.434 30.769 0.00 0.00 33.37 2.66
4010 5307 9.665719 TCAAGATGCATTTGTATGAGTAGTTTA 57.334 29.630 0.00 0.00 33.37 2.01
4020 5317 9.575868 TTTGTATGAGTAGTTTATTTTGTGGGA 57.424 29.630 0.00 0.00 0.00 4.37
4021 5318 8.786826 TGTATGAGTAGTTTATTTTGTGGGAG 57.213 34.615 0.00 0.00 0.00 4.30
4022 5319 8.598916 TGTATGAGTAGTTTATTTTGTGGGAGA 58.401 33.333 0.00 0.00 0.00 3.71
4023 5320 9.444600 GTATGAGTAGTTTATTTTGTGGGAGAA 57.555 33.333 0.00 0.00 0.00 2.87
4024 5321 8.934023 ATGAGTAGTTTATTTTGTGGGAGAAA 57.066 30.769 0.00 0.00 0.00 2.52
4025 5322 8.754991 TGAGTAGTTTATTTTGTGGGAGAAAA 57.245 30.769 0.00 0.00 0.00 2.29
4026 5323 9.362151 TGAGTAGTTTATTTTGTGGGAGAAAAT 57.638 29.630 0.00 0.00 36.98 1.82
4027 5324 9.626045 GAGTAGTTTATTTTGTGGGAGAAAATG 57.374 33.333 0.00 0.00 35.25 2.32
4028 5325 9.362151 AGTAGTTTATTTTGTGGGAGAAAATGA 57.638 29.630 0.00 0.00 35.25 2.57
4031 5328 8.869109 AGTTTATTTTGTGGGAGAAAATGATGA 58.131 29.630 0.00 0.00 35.25 2.92
4032 5329 9.487790 GTTTATTTTGTGGGAGAAAATGATGAA 57.512 29.630 0.00 0.00 35.25 2.57
4033 5330 9.487790 TTTATTTTGTGGGAGAAAATGATGAAC 57.512 29.630 0.00 0.00 35.25 3.18
4034 5331 4.764679 TTGTGGGAGAAAATGATGAACG 57.235 40.909 0.00 0.00 0.00 3.95
4035 5332 4.014569 TGTGGGAGAAAATGATGAACGA 57.985 40.909 0.00 0.00 0.00 3.85
4036 5333 4.393834 TGTGGGAGAAAATGATGAACGAA 58.606 39.130 0.00 0.00 0.00 3.85
4037 5334 4.824537 TGTGGGAGAAAATGATGAACGAAA 59.175 37.500 0.00 0.00 0.00 3.46
4038 5335 5.300539 TGTGGGAGAAAATGATGAACGAAAA 59.699 36.000 0.00 0.00 0.00 2.29
4039 5336 6.183360 TGTGGGAGAAAATGATGAACGAAAAA 60.183 34.615 0.00 0.00 0.00 1.94
4058 5355 3.531934 AAAGGCCTTATCTGCAAATGC 57.468 42.857 20.84 0.00 42.50 3.56
4059 5356 1.027357 AGGCCTTATCTGCAAATGCG 58.973 50.000 0.00 0.00 45.83 4.73
4067 5364 4.623814 TGCAAATGCGGAGAGGAG 57.376 55.556 0.35 0.00 45.83 3.69
4068 5365 1.679311 TGCAAATGCGGAGAGGAGT 59.321 52.632 0.35 0.00 45.83 3.85
4069 5366 0.674581 TGCAAATGCGGAGAGGAGTG 60.675 55.000 0.35 0.00 45.83 3.51
4070 5367 1.986575 GCAAATGCGGAGAGGAGTGC 61.987 60.000 0.00 0.00 0.00 4.40
4071 5368 1.448540 AAATGCGGAGAGGAGTGCG 60.449 57.895 0.00 0.00 0.00 5.34
4072 5369 2.859273 AAATGCGGAGAGGAGTGCGG 62.859 60.000 0.00 0.00 0.00 5.69
4075 5372 2.439701 CGGAGAGGAGTGCGGGTA 60.440 66.667 0.00 0.00 0.00 3.69
4076 5373 2.050350 CGGAGAGGAGTGCGGGTAA 61.050 63.158 0.00 0.00 0.00 2.85
4077 5374 1.601419 CGGAGAGGAGTGCGGGTAAA 61.601 60.000 0.00 0.00 0.00 2.01
4078 5375 0.831307 GGAGAGGAGTGCGGGTAAAT 59.169 55.000 0.00 0.00 0.00 1.40
4079 5376 1.209747 GGAGAGGAGTGCGGGTAAATT 59.790 52.381 0.00 0.00 0.00 1.82
4080 5377 2.280628 GAGAGGAGTGCGGGTAAATTG 58.719 52.381 0.00 0.00 0.00 2.32
4081 5378 1.628846 AGAGGAGTGCGGGTAAATTGT 59.371 47.619 0.00 0.00 0.00 2.71
4082 5379 2.007608 GAGGAGTGCGGGTAAATTGTC 58.992 52.381 0.00 0.00 0.00 3.18
4083 5380 1.349688 AGGAGTGCGGGTAAATTGTCA 59.650 47.619 0.00 0.00 0.00 3.58
4084 5381 2.026262 AGGAGTGCGGGTAAATTGTCAT 60.026 45.455 0.00 0.00 0.00 3.06
4085 5382 3.199071 AGGAGTGCGGGTAAATTGTCATA 59.801 43.478 0.00 0.00 0.00 2.15
4086 5383 3.560068 GGAGTGCGGGTAAATTGTCATAG 59.440 47.826 0.00 0.00 0.00 2.23
4087 5384 4.189231 GAGTGCGGGTAAATTGTCATAGT 58.811 43.478 0.00 0.00 0.00 2.12
4088 5385 4.585879 AGTGCGGGTAAATTGTCATAGTT 58.414 39.130 0.00 0.00 0.00 2.24
4089 5386 5.007682 AGTGCGGGTAAATTGTCATAGTTT 58.992 37.500 0.00 0.00 0.00 2.66
4090 5387 5.123344 AGTGCGGGTAAATTGTCATAGTTTC 59.877 40.000 0.00 0.00 0.00 2.78
4091 5388 4.396790 TGCGGGTAAATTGTCATAGTTTCC 59.603 41.667 0.00 0.00 0.00 3.13
4092 5389 4.638865 GCGGGTAAATTGTCATAGTTTCCT 59.361 41.667 0.00 0.00 0.00 3.36
4093 5390 5.124936 GCGGGTAAATTGTCATAGTTTCCTT 59.875 40.000 0.00 0.00 0.00 3.36
4094 5391 6.677187 GCGGGTAAATTGTCATAGTTTCCTTC 60.677 42.308 0.00 0.00 0.00 3.46
4095 5392 6.183360 CGGGTAAATTGTCATAGTTTCCTTCC 60.183 42.308 0.00 0.00 0.00 3.46
4096 5393 6.890268 GGGTAAATTGTCATAGTTTCCTTCCT 59.110 38.462 0.00 0.00 0.00 3.36
4097 5394 8.050930 GGGTAAATTGTCATAGTTTCCTTCCTA 58.949 37.037 0.00 0.00 0.00 2.94
4098 5395 9.628500 GGTAAATTGTCATAGTTTCCTTCCTAT 57.372 33.333 0.00 0.00 0.00 2.57
4100 5397 8.753497 AAATTGTCATAGTTTCCTTCCTATCC 57.247 34.615 0.00 0.00 0.00 2.59
4101 5398 5.531122 TGTCATAGTTTCCTTCCTATCCG 57.469 43.478 0.00 0.00 0.00 4.18
4102 5399 4.960469 TGTCATAGTTTCCTTCCTATCCGT 59.040 41.667 0.00 0.00 0.00 4.69
4103 5400 5.424252 TGTCATAGTTTCCTTCCTATCCGTT 59.576 40.000 0.00 0.00 0.00 4.44
4104 5401 6.608405 TGTCATAGTTTCCTTCCTATCCGTTA 59.392 38.462 0.00 0.00 0.00 3.18
4105 5402 7.146648 GTCATAGTTTCCTTCCTATCCGTTAG 58.853 42.308 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.093408 GCGTCATCTTGATCTTGTTAAGCA 59.907 41.667 0.00 0.00 0.00 3.91
1 2 4.494855 GGCGTCATCTTGATCTTGTTAAGC 60.495 45.833 0.00 0.00 0.00 3.09
2 3 4.872691 AGGCGTCATCTTGATCTTGTTAAG 59.127 41.667 0.00 0.00 0.00 1.85
3 4 4.832248 AGGCGTCATCTTGATCTTGTTAA 58.168 39.130 0.00 0.00 0.00 2.01
4 5 4.471904 AGGCGTCATCTTGATCTTGTTA 57.528 40.909 0.00 0.00 0.00 2.41
5 6 3.340814 AGGCGTCATCTTGATCTTGTT 57.659 42.857 0.00 0.00 0.00 2.83
6 7 3.449018 AGTAGGCGTCATCTTGATCTTGT 59.551 43.478 0.00 0.00 0.00 3.16
7 8 4.052159 AGTAGGCGTCATCTTGATCTTG 57.948 45.455 0.00 0.00 0.00 3.02
8 9 4.890581 AGTAGTAGGCGTCATCTTGATCTT 59.109 41.667 0.00 0.00 0.00 2.40
9 10 4.465886 AGTAGTAGGCGTCATCTTGATCT 58.534 43.478 0.00 0.00 0.00 2.75
10 11 4.517453 AGAGTAGTAGGCGTCATCTTGATC 59.483 45.833 0.00 0.00 0.00 2.92
11 12 4.465886 AGAGTAGTAGGCGTCATCTTGAT 58.534 43.478 0.00 0.00 0.00 2.57
12 13 3.887352 AGAGTAGTAGGCGTCATCTTGA 58.113 45.455 0.00 0.00 0.00 3.02
13 14 4.640789 AAGAGTAGTAGGCGTCATCTTG 57.359 45.455 0.00 0.00 0.00 3.02
14 15 5.662674 AAAAGAGTAGTAGGCGTCATCTT 57.337 39.130 0.00 0.00 0.00 2.40
15 16 5.662674 AAAAAGAGTAGTAGGCGTCATCT 57.337 39.130 0.00 0.00 0.00 2.90
417 418 1.408453 AATGAGTAGTAGGCGCCCCC 61.408 60.000 26.15 14.55 0.00 5.40
418 419 0.249911 CAATGAGTAGTAGGCGCCCC 60.250 60.000 26.15 14.99 0.00 5.80
419 420 0.750850 TCAATGAGTAGTAGGCGCCC 59.249 55.000 26.15 9.10 0.00 6.13
420 421 2.610727 GGATCAATGAGTAGTAGGCGCC 60.611 54.545 21.89 21.89 0.00 6.53
421 422 2.610727 GGGATCAATGAGTAGTAGGCGC 60.611 54.545 0.00 0.00 0.00 6.53
450 451 6.779860 AGTAGAAGCTTGAGGGAAATTTACA 58.220 36.000 2.10 0.00 0.00 2.41
461 462 4.953579 AGGGAGTAGAAGTAGAAGCTTGAG 59.046 45.833 2.10 0.00 0.00 3.02
467 468 3.888583 ACGGAGGGAGTAGAAGTAGAAG 58.111 50.000 0.00 0.00 0.00 2.85
471 472 2.579860 AGGAACGGAGGGAGTAGAAGTA 59.420 50.000 0.00 0.00 0.00 2.24
479 480 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
480 481 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
481 482 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
482 483 8.422566 AGAAAGACTTATATTTAGGAACGGAGG 58.577 37.037 0.00 0.00 0.00 4.30
483 484 9.250624 CAGAAAGACTTATATTTAGGAACGGAG 57.749 37.037 0.00 0.00 0.00 4.63
484 485 8.202137 CCAGAAAGACTTATATTTAGGAACGGA 58.798 37.037 0.00 0.00 0.00 4.69
485 486 8.202137 TCCAGAAAGACTTATATTTAGGAACGG 58.798 37.037 0.00 0.00 0.00 4.44
486 487 9.032420 GTCCAGAAAGACTTATATTTAGGAACG 57.968 37.037 0.00 0.00 29.85 3.95
496 497 9.143155 TGCATATGTAGTCCAGAAAGACTTATA 57.857 33.333 4.29 1.25 44.83 0.98
497 498 8.023021 TGCATATGTAGTCCAGAAAGACTTAT 57.977 34.615 4.29 0.00 44.83 1.73
498 499 7.124298 ACTGCATATGTAGTCCAGAAAGACTTA 59.876 37.037 19.46 0.00 44.83 2.24
499 500 6.070538 ACTGCATATGTAGTCCAGAAAGACTT 60.071 38.462 19.46 0.00 44.83 3.01
501 502 5.665459 ACTGCATATGTAGTCCAGAAAGAC 58.335 41.667 19.46 0.00 36.19 3.01
502 503 5.939764 ACTGCATATGTAGTCCAGAAAGA 57.060 39.130 19.46 0.00 36.19 2.52
503 504 8.668510 ATTTACTGCATATGTAGTCCAGAAAG 57.331 34.615 26.98 0.00 41.24 2.62
506 507 9.764363 CTTAATTTACTGCATATGTAGTCCAGA 57.236 33.333 26.98 9.59 41.24 3.86
507 508 9.547753 ACTTAATTTACTGCATATGTAGTCCAG 57.452 33.333 26.98 15.86 41.24 3.86
508 509 9.325198 CACTTAATTTACTGCATATGTAGTCCA 57.675 33.333 26.98 16.36 41.24 4.02
509 510 9.542462 TCACTTAATTTACTGCATATGTAGTCC 57.458 33.333 26.98 0.01 41.24 3.85
528 529 9.642327 TGCGTGTAAGAGTATAAATTCACTTAA 57.358 29.630 0.00 0.00 0.00 1.85
529 530 9.642327 TTGCGTGTAAGAGTATAAATTCACTTA 57.358 29.630 0.00 0.00 0.00 2.24
530 531 8.542497 TTGCGTGTAAGAGTATAAATTCACTT 57.458 30.769 0.00 0.00 0.00 3.16
531 532 8.542497 TTTGCGTGTAAGAGTATAAATTCACT 57.458 30.769 0.00 0.00 0.00 3.41
532 533 9.601971 TTTTTGCGTGTAAGAGTATAAATTCAC 57.398 29.630 0.00 0.00 0.00 3.18
581 582 8.577296 ACATACAGATGCATATAGACGTAGTTT 58.423 33.333 0.00 0.00 37.48 2.66
582 583 8.112016 ACATACAGATGCATATAGACGTAGTT 57.888 34.615 0.00 0.00 37.48 2.24
583 584 7.689446 ACATACAGATGCATATAGACGTAGT 57.311 36.000 0.00 0.00 39.62 2.73
584 585 8.884726 ACTACATACAGATGCATATAGACGTAG 58.115 37.037 0.00 9.81 36.43 3.51
585 586 8.788325 ACTACATACAGATGCATATAGACGTA 57.212 34.615 0.00 0.00 36.43 3.57
586 587 7.689446 ACTACATACAGATGCATATAGACGT 57.311 36.000 0.00 0.00 36.43 4.34
639 640 7.650504 GCAAAAGTACTCCCTTCGTTTTTAAAT 59.349 33.333 0.00 0.00 0.00 1.40
640 641 6.974048 GCAAAAGTACTCCCTTCGTTTTTAAA 59.026 34.615 0.00 0.00 0.00 1.52
641 642 6.319405 AGCAAAAGTACTCCCTTCGTTTTTAA 59.681 34.615 0.00 0.00 0.00 1.52
642 643 5.824097 AGCAAAAGTACTCCCTTCGTTTTTA 59.176 36.000 0.00 0.00 0.00 1.52
643 644 4.643334 AGCAAAAGTACTCCCTTCGTTTTT 59.357 37.500 0.00 0.00 0.00 1.94
644 645 4.204799 AGCAAAAGTACTCCCTTCGTTTT 58.795 39.130 0.00 0.00 0.00 2.43
645 646 3.816994 AGCAAAAGTACTCCCTTCGTTT 58.183 40.909 0.00 0.00 0.00 3.60
646 647 3.487120 AGCAAAAGTACTCCCTTCGTT 57.513 42.857 0.00 0.00 0.00 3.85
647 648 3.139077 CAAGCAAAAGTACTCCCTTCGT 58.861 45.455 0.00 0.00 0.00 3.85
648 649 2.095718 GCAAGCAAAAGTACTCCCTTCG 60.096 50.000 0.00 0.00 0.00 3.79
649 650 3.149981 AGCAAGCAAAAGTACTCCCTTC 58.850 45.455 0.00 0.00 0.00 3.46
650 651 3.229697 AGCAAGCAAAAGTACTCCCTT 57.770 42.857 0.00 0.00 0.00 3.95
651 652 2.959465 AGCAAGCAAAAGTACTCCCT 57.041 45.000 0.00 0.00 0.00 4.20
652 653 4.277423 TGTTAAGCAAGCAAAAGTACTCCC 59.723 41.667 0.00 0.00 0.00 4.30
653 654 5.432885 TGTTAAGCAAGCAAAAGTACTCC 57.567 39.130 0.00 0.00 0.00 3.85
654 655 6.976350 CTTGTTAAGCAAGCAAAAGTACTC 57.024 37.500 0.00 0.00 46.68 2.59
708 709 1.825281 GATGATGGAGGGGAGCGGAG 61.825 65.000 0.00 0.00 0.00 4.63
709 710 1.838846 GATGATGGAGGGGAGCGGA 60.839 63.158 0.00 0.00 0.00 5.54
710 711 2.746359 GATGATGGAGGGGAGCGG 59.254 66.667 0.00 0.00 0.00 5.52
711 712 2.152297 CTCGATGATGGAGGGGAGCG 62.152 65.000 0.00 0.00 0.00 5.03
712 713 1.670590 CTCGATGATGGAGGGGAGC 59.329 63.158 0.00 0.00 0.00 4.70
713 714 1.117749 TGCTCGATGATGGAGGGGAG 61.118 60.000 6.59 0.00 32.10 4.30
714 715 0.472543 ATGCTCGATGATGGAGGGGA 60.473 55.000 6.59 0.00 32.10 4.81
715 716 0.321387 CATGCTCGATGATGGAGGGG 60.321 60.000 6.59 0.00 33.31 4.79
716 717 0.954449 GCATGCTCGATGATGGAGGG 60.954 60.000 11.37 0.00 33.31 4.30
717 718 1.289800 CGCATGCTCGATGATGGAGG 61.290 60.000 17.13 0.00 33.31 4.30
751 752 2.028420 TTGACTTGCGATGATGGAGG 57.972 50.000 0.00 0.00 0.00 4.30
794 795 0.912486 CCAGAGAAGTCCGGGGATTT 59.088 55.000 0.00 0.00 0.00 2.17
978 984 1.200252 GCTACTCGTCTCTGCAACAGA 59.800 52.381 0.00 0.00 38.25 3.41
979 985 1.623359 GCTACTCGTCTCTGCAACAG 58.377 55.000 0.00 0.00 0.00 3.16
994 1000 3.044305 GCGATCGGGCATGGCTAC 61.044 66.667 19.78 2.07 33.51 3.58
996 1002 4.923942 CTGCGATCGGGCATGGCT 62.924 66.667 19.78 0.00 42.99 4.75
1003 1009 2.969238 GGTCATGCTGCGATCGGG 60.969 66.667 18.30 0.00 0.00 5.14
1025 1031 4.143333 TGGCCGCGAAGACTAGCC 62.143 66.667 8.23 10.97 44.13 3.93
1043 1049 1.694133 GCACAGGATGAGGAGGAGGG 61.694 65.000 0.00 0.00 39.69 4.30
1127 1136 1.671742 GGGGTGAAGCTGAAGTCGA 59.328 57.895 0.00 0.00 0.00 4.20
1242 1251 0.110192 CGCCGTTTTTCCAGAGCTTC 60.110 55.000 0.00 0.00 0.00 3.86
1269 1278 2.720758 CTTGAACGAGGTGAGCGCG 61.721 63.158 6.18 6.18 0.00 6.86
1309 1318 4.410400 GGTGCCGTTCTGGGGGAG 62.410 72.222 0.00 0.00 38.63 4.30
1345 1372 1.302511 CCGGGTTGTTGGTGAGGAG 60.303 63.158 0.00 0.00 0.00 3.69
1364 1391 3.177884 TGCTGTCCCTGGGCAAGT 61.178 61.111 8.22 0.00 32.79 3.16
1483 1510 3.343421 GACGTGGTTGCCGTCCAC 61.343 66.667 0.00 10.67 46.73 4.02
1794 1821 1.517694 CAACCGATACCCACCGTCG 60.518 63.158 0.00 0.00 35.29 5.12
1957 1984 3.258971 CTCCCTGAGCTTAAACCTGAG 57.741 52.381 0.00 0.00 0.00 3.35
2211 3215 1.369839 CGTAGACGAGGAGCAGCTCA 61.370 60.000 24.09 0.00 43.02 4.26
2442 3453 2.426024 GTTGTACTCCTCGTCCAGCATA 59.574 50.000 0.00 0.00 0.00 3.14
2544 3555 4.230002 GCCATGTAGCCGCGGGTA 62.230 66.667 31.91 31.91 0.00 3.69
3054 4070 1.197430 AGAAGCTACTGTGCTGCCCT 61.197 55.000 0.00 2.55 43.24 5.19
3292 4317 2.028748 ACAACGCAATACTACCTCCGTT 60.029 45.455 0.00 0.00 39.17 4.44
3597 4629 3.454371 AAGACTACAACGCAGTCAACT 57.546 42.857 5.38 0.00 45.00 3.16
3598 4630 5.840940 ATAAAGACTACAACGCAGTCAAC 57.159 39.130 5.38 0.00 45.00 3.18
3600 4632 5.294356 ACAATAAAGACTACAACGCAGTCA 58.706 37.500 5.38 0.00 45.00 3.41
3601 4633 5.840940 ACAATAAAGACTACAACGCAGTC 57.159 39.130 0.00 0.00 45.00 3.51
3729 4797 2.763039 TCTGGCATCATTCCCTACTCA 58.237 47.619 0.00 0.00 0.00 3.41
3743 4811 1.150536 GTGTTGTCCCCTTCTGGCA 59.849 57.895 0.00 0.00 0.00 4.92
3744 4812 1.603739 GGTGTTGTCCCCTTCTGGC 60.604 63.158 0.00 0.00 0.00 4.85
3937 5234 6.664515 TGTTGCTAGTGTTTACTAAATGCAC 58.335 36.000 0.00 0.00 37.63 4.57
3938 5235 6.869315 TGTTGCTAGTGTTTACTAAATGCA 57.131 33.333 0.00 0.00 38.85 3.96
3945 5242 3.081804 GGGCATGTTGCTAGTGTTTACT 58.918 45.455 0.00 0.00 44.28 2.24
3950 5247 0.955428 CACGGGCATGTTGCTAGTGT 60.955 55.000 14.78 2.05 44.28 3.55
3953 5250 2.793946 GCACGGGCATGTTGCTAG 59.206 61.111 3.77 0.00 44.28 3.42
3954 5251 3.124270 CGCACGGGCATGTTGCTA 61.124 61.111 11.77 0.00 44.28 3.49
3956 5253 4.341502 AACGCACGGGCATGTTGC 62.342 61.111 11.77 0.00 44.08 4.17
3957 5254 2.428902 CAACGCACGGGCATGTTG 60.429 61.111 11.77 13.50 41.24 3.33
3958 5255 4.341502 GCAACGCACGGGCATGTT 62.342 61.111 11.77 3.22 41.24 2.71
3960 5257 4.118995 ATGCAACGCACGGGCATG 62.119 61.111 11.77 9.58 45.80 4.06
3964 5261 3.361158 TTCCATGCAACGCACGGG 61.361 61.111 0.72 1.92 42.60 5.28
3965 5262 2.126888 GTTCCATGCAACGCACGG 60.127 61.111 0.00 0.00 43.82 4.94
3966 5263 0.794229 GATGTTCCATGCAACGCACG 60.794 55.000 0.00 0.00 43.04 5.34
3967 5264 0.240678 TGATGTTCCATGCAACGCAC 59.759 50.000 0.00 0.00 43.04 5.34
3968 5265 0.957362 TTGATGTTCCATGCAACGCA 59.043 45.000 0.00 0.00 44.86 5.24
3969 5266 1.199789 TCTTGATGTTCCATGCAACGC 59.800 47.619 0.00 0.00 0.00 4.84
3970 5267 3.431856 CATCTTGATGTTCCATGCAACG 58.568 45.455 0.00 0.00 0.00 4.10
3971 5268 3.184541 GCATCTTGATGTTCCATGCAAC 58.815 45.455 11.61 0.00 39.76 4.17
3972 5269 2.826725 TGCATCTTGATGTTCCATGCAA 59.173 40.909 11.61 0.00 45.22 4.08
3973 5270 2.448453 TGCATCTTGATGTTCCATGCA 58.552 42.857 11.61 0.81 45.83 3.96
3974 5271 3.728076 ATGCATCTTGATGTTCCATGC 57.272 42.857 11.61 0.00 40.29 4.06
3975 5272 5.416083 ACAAATGCATCTTGATGTTCCATG 58.584 37.500 20.96 7.77 0.00 3.66
3976 5273 5.670792 ACAAATGCATCTTGATGTTCCAT 57.329 34.783 20.96 4.88 0.00 3.41
3977 5274 6.377712 TCATACAAATGCATCTTGATGTTCCA 59.622 34.615 20.96 2.92 32.76 3.53
3978 5275 6.798482 TCATACAAATGCATCTTGATGTTCC 58.202 36.000 20.96 0.00 32.76 3.62
3979 5276 7.478322 ACTCATACAAATGCATCTTGATGTTC 58.522 34.615 20.96 0.00 32.76 3.18
3980 5277 7.400599 ACTCATACAAATGCATCTTGATGTT 57.599 32.000 20.96 1.04 32.76 2.71
3981 5278 7.772292 ACTACTCATACAAATGCATCTTGATGT 59.228 33.333 20.96 14.21 32.76 3.06
3982 5279 8.151141 ACTACTCATACAAATGCATCTTGATG 57.849 34.615 20.96 18.39 32.76 3.07
3983 5280 8.743085 AACTACTCATACAAATGCATCTTGAT 57.257 30.769 20.96 11.48 32.76 2.57
3984 5281 8.565896 AAACTACTCATACAAATGCATCTTGA 57.434 30.769 20.96 10.81 32.76 3.02
3994 5291 9.575868 TCCCACAAAATAAACTACTCATACAAA 57.424 29.630 0.00 0.00 0.00 2.83
3995 5292 9.226606 CTCCCACAAAATAAACTACTCATACAA 57.773 33.333 0.00 0.00 0.00 2.41
3996 5293 8.598916 TCTCCCACAAAATAAACTACTCATACA 58.401 33.333 0.00 0.00 0.00 2.29
3997 5294 9.444600 TTCTCCCACAAAATAAACTACTCATAC 57.555 33.333 0.00 0.00 0.00 2.39
3999 5296 8.934023 TTTCTCCCACAAAATAAACTACTCAT 57.066 30.769 0.00 0.00 0.00 2.90
4000 5297 8.754991 TTTTCTCCCACAAAATAAACTACTCA 57.245 30.769 0.00 0.00 0.00 3.41
4001 5298 9.626045 CATTTTCTCCCACAAAATAAACTACTC 57.374 33.333 0.00 0.00 32.74 2.59
4002 5299 9.362151 TCATTTTCTCCCACAAAATAAACTACT 57.638 29.630 0.00 0.00 32.74 2.57
4005 5302 8.869109 TCATCATTTTCTCCCACAAAATAAACT 58.131 29.630 0.00 0.00 32.74 2.66
4006 5303 9.487790 TTCATCATTTTCTCCCACAAAATAAAC 57.512 29.630 0.00 0.00 32.74 2.01
4007 5304 9.487790 GTTCATCATTTTCTCCCACAAAATAAA 57.512 29.630 0.00 0.00 32.74 1.40
4008 5305 7.812191 CGTTCATCATTTTCTCCCACAAAATAA 59.188 33.333 0.00 0.00 32.74 1.40
4009 5306 7.175816 TCGTTCATCATTTTCTCCCACAAAATA 59.824 33.333 0.00 0.00 32.74 1.40
4010 5307 6.015519 TCGTTCATCATTTTCTCCCACAAAAT 60.016 34.615 0.00 0.00 34.42 1.82
4011 5308 5.300539 TCGTTCATCATTTTCTCCCACAAAA 59.699 36.000 0.00 0.00 0.00 2.44
4012 5309 4.824537 TCGTTCATCATTTTCTCCCACAAA 59.175 37.500 0.00 0.00 0.00 2.83
4013 5310 4.393834 TCGTTCATCATTTTCTCCCACAA 58.606 39.130 0.00 0.00 0.00 3.33
4014 5311 4.014569 TCGTTCATCATTTTCTCCCACA 57.985 40.909 0.00 0.00 0.00 4.17
4015 5312 5.371115 TTTCGTTCATCATTTTCTCCCAC 57.629 39.130 0.00 0.00 0.00 4.61
4016 5313 6.398234 TTTTTCGTTCATCATTTTCTCCCA 57.602 33.333 0.00 0.00 0.00 4.37
4036 5333 4.256110 GCATTTGCAGATAAGGCCTTTTT 58.744 39.130 26.08 12.16 41.59 1.94
4037 5334 3.676873 CGCATTTGCAGATAAGGCCTTTT 60.677 43.478 26.08 16.99 42.21 2.27
4038 5335 2.159198 CGCATTTGCAGATAAGGCCTTT 60.159 45.455 26.08 11.72 42.21 3.11
4039 5336 1.406539 CGCATTTGCAGATAAGGCCTT 59.593 47.619 24.18 24.18 42.21 4.35
4040 5337 1.027357 CGCATTTGCAGATAAGGCCT 58.973 50.000 0.00 0.00 42.21 5.19
4041 5338 0.031178 CCGCATTTGCAGATAAGGCC 59.969 55.000 0.00 0.00 42.21 5.19
4042 5339 1.002033 CTCCGCATTTGCAGATAAGGC 60.002 52.381 3.13 1.46 42.21 4.35
4043 5340 2.547211 CTCTCCGCATTTGCAGATAAGG 59.453 50.000 3.13 4.38 42.21 2.69
4044 5341 2.547211 CCTCTCCGCATTTGCAGATAAG 59.453 50.000 3.13 0.00 42.21 1.73
4045 5342 2.170397 TCCTCTCCGCATTTGCAGATAA 59.830 45.455 3.13 0.00 42.21 1.75
4046 5343 1.762370 TCCTCTCCGCATTTGCAGATA 59.238 47.619 3.13 0.00 42.21 1.98
4047 5344 0.543277 TCCTCTCCGCATTTGCAGAT 59.457 50.000 3.13 0.00 42.21 2.90
4048 5345 0.107993 CTCCTCTCCGCATTTGCAGA 60.108 55.000 3.13 0.00 42.21 4.26
4049 5346 0.392193 ACTCCTCTCCGCATTTGCAG 60.392 55.000 3.13 0.00 42.21 4.41
4050 5347 0.674581 CACTCCTCTCCGCATTTGCA 60.675 55.000 3.13 0.00 42.21 4.08
4051 5348 1.986575 GCACTCCTCTCCGCATTTGC 61.987 60.000 0.00 0.00 37.78 3.68
4052 5349 1.699656 CGCACTCCTCTCCGCATTTG 61.700 60.000 0.00 0.00 0.00 2.32
4053 5350 1.448540 CGCACTCCTCTCCGCATTT 60.449 57.895 0.00 0.00 0.00 2.32
4054 5351 2.185350 CGCACTCCTCTCCGCATT 59.815 61.111 0.00 0.00 0.00 3.56
4055 5352 3.842923 CCGCACTCCTCTCCGCAT 61.843 66.667 0.00 0.00 0.00 4.73
4058 5355 1.601419 TTTACCCGCACTCCTCTCCG 61.601 60.000 0.00 0.00 0.00 4.63
4059 5356 0.831307 ATTTACCCGCACTCCTCTCC 59.169 55.000 0.00 0.00 0.00 3.71
4060 5357 2.280628 CAATTTACCCGCACTCCTCTC 58.719 52.381 0.00 0.00 0.00 3.20
4061 5358 1.628846 ACAATTTACCCGCACTCCTCT 59.371 47.619 0.00 0.00 0.00 3.69
4062 5359 2.007608 GACAATTTACCCGCACTCCTC 58.992 52.381 0.00 0.00 0.00 3.71
4063 5360 1.349688 TGACAATTTACCCGCACTCCT 59.650 47.619 0.00 0.00 0.00 3.69
4064 5361 1.816074 TGACAATTTACCCGCACTCC 58.184 50.000 0.00 0.00 0.00 3.85
4065 5362 4.189231 ACTATGACAATTTACCCGCACTC 58.811 43.478 0.00 0.00 0.00 3.51
4066 5363 4.216411 ACTATGACAATTTACCCGCACT 57.784 40.909 0.00 0.00 0.00 4.40
4067 5364 4.957759 AACTATGACAATTTACCCGCAC 57.042 40.909 0.00 0.00 0.00 5.34
4068 5365 4.396790 GGAAACTATGACAATTTACCCGCA 59.603 41.667 0.00 0.00 0.00 5.69
4069 5366 4.638865 AGGAAACTATGACAATTTACCCGC 59.361 41.667 0.00 0.00 40.61 6.13
4070 5367 6.183360 GGAAGGAAACTATGACAATTTACCCG 60.183 42.308 0.00 0.00 42.68 5.28
4071 5368 6.890268 AGGAAGGAAACTATGACAATTTACCC 59.110 38.462 0.00 0.00 42.68 3.69
4072 5369 7.939784 AGGAAGGAAACTATGACAATTTACC 57.060 36.000 0.00 0.00 42.68 2.85
4074 5371 9.847224 GGATAGGAAGGAAACTATGACAATTTA 57.153 33.333 0.00 0.00 42.68 1.40
4075 5372 7.499232 CGGATAGGAAGGAAACTATGACAATTT 59.501 37.037 0.00 0.00 42.68 1.82
4076 5373 6.992715 CGGATAGGAAGGAAACTATGACAATT 59.007 38.462 0.00 0.00 42.68 2.32
4077 5374 6.099845 ACGGATAGGAAGGAAACTATGACAAT 59.900 38.462 0.00 0.00 42.68 2.71
4078 5375 5.424252 ACGGATAGGAAGGAAACTATGACAA 59.576 40.000 0.00 0.00 42.68 3.18
4079 5376 4.960469 ACGGATAGGAAGGAAACTATGACA 59.040 41.667 0.00 0.00 42.68 3.58
4080 5377 5.532664 ACGGATAGGAAGGAAACTATGAC 57.467 43.478 0.00 0.00 42.68 3.06
4081 5378 7.286215 CTAACGGATAGGAAGGAAACTATGA 57.714 40.000 0.00 0.00 42.68 2.15


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

AutoCloner maintained by Alex Coulton.