Multiple sequence alignment - TraesCS3D01G311400

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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 TraesCS3D01G311400 chr3D 100.000 9013 0 0 1 9013 426079031 426070019 0.000000e+00 16644.0
1 TraesCS3D01G311400 chr3D 80.183 545 78 12 148 664 96128749 96129291 1.840000e-101 381.0
2 TraesCS3D01G311400 chr3D 83.005 406 52 11 2895 3293 105437773 105437378 1.440000e-92 351.0
3 TraesCS3D01G311400 chr3D 75.862 609 112 29 2655 3247 455590398 455590987 2.480000e-70 278.0
4 TraesCS3D01G311400 chr3D 97.143 35 1 0 7699 7733 426071141 426071107 9.770000e-05 60.2
5 TraesCS3D01G311400 chr3D 97.143 35 1 0 7891 7925 426071333 426071299 9.770000e-05 60.2
6 TraesCS3D01G311400 chr3B 95.462 7999 241 53 774 8711 556266690 556274627 0.000000e+00 12648.0
7 TraesCS3D01G311400 chr3B 80.858 653 86 29 2663 3293 157234502 157233867 2.280000e-130 477.0
8 TraesCS3D01G311400 chr3B 92.835 321 15 4 8700 9013 556274742 556275061 8.250000e-125 459.0
9 TraesCS3D01G311400 chr3B 90.278 144 14 0 1 144 556266433 556266576 1.190000e-43 189.0
10 TraesCS3D01G311400 chr3B 88.060 134 10 3 7792 7925 556273639 556273766 4.360000e-33 154.0
11 TraesCS3D01G311400 chr3B 93.878 49 0 2 681 729 466062327 466062282 4.510000e-08 71.3
12 TraesCS3D01G311400 chr3A 96.782 6401 167 20 1546 7925 562201237 562194855 0.000000e+00 10643.0
13 TraesCS3D01G311400 chr3A 93.288 1311 54 15 7710 9013 562194971 562193688 0.000000e+00 1903.0
14 TraesCS3D01G311400 chr3A 91.424 583 28 11 786 1354 562203335 562202761 0.000000e+00 780.0
15 TraesCS3D01G311400 chr3A 82.537 544 68 9 142 658 208078264 208078807 3.840000e-123 453.0
16 TraesCS3D01G311400 chr3A 87.302 126 10 3 7800 7925 562195067 562194948 1.220000e-28 139.0
17 TraesCS3D01G311400 chr3A 91.304 46 4 0 7699 7744 562194790 562194745 7.550000e-06 63.9
18 TraesCS3D01G311400 chr5B 88.068 704 45 12 912 1590 389986557 389987246 0.000000e+00 798.0
19 TraesCS3D01G311400 chr5B 78.431 357 53 8 328 666 641132133 641131783 2.550000e-50 211.0
20 TraesCS3D01G311400 chr5B 77.929 367 50 14 329 666 35516178 35515814 5.520000e-47 200.0
21 TraesCS3D01G311400 chr5B 97.561 41 1 0 681 721 271145841 271145801 4.510000e-08 71.3
22 TraesCS3D01G311400 chr7B 82.362 635 102 9 2662 3290 162096116 162096746 2.210000e-150 544.0
23 TraesCS3D01G311400 chr7B 80.832 553 79 11 141 666 436756450 436757002 8.420000e-110 409.0
24 TraesCS3D01G311400 chr7B 84.286 70 6 4 2664 2732 463635872 463635937 7.550000e-06 63.9
25 TraesCS3D01G311400 chr7B 86.667 60 4 4 681 736 594954387 594954446 7.550000e-06 63.9
26 TraesCS3D01G311400 chr4B 82.188 640 89 16 2662 3287 54030073 54029445 2.230000e-145 527.0
27 TraesCS3D01G311400 chr2A 87.775 409 40 7 1598 2003 710067733 710068134 3.810000e-128 470.0
28 TraesCS3D01G311400 chr2A 87.317 410 41 7 1598 2003 710084955 710085357 8.250000e-125 459.0
29 TraesCS3D01G311400 chr2A 90.253 277 25 2 2176 2451 710085456 710085731 2.390000e-95 361.0
30 TraesCS3D01G311400 chr2A 89.170 277 28 2 2176 2451 710068233 710068508 2.410000e-90 344.0
31 TraesCS3D01G311400 chr2A 91.111 90 8 0 2045 2134 710068134 710068223 1.230000e-23 122.0
32 TraesCS3D01G311400 chr2A 91.111 90 8 0 2045 2134 710085357 710085446 1.230000e-23 122.0
33 TraesCS3D01G311400 chr5D 83.230 483 64 6 2808 3279 351801059 351800583 2.330000e-115 427.0
34 TraesCS3D01G311400 chr5D 80.645 558 78 17 138 666 278143704 278143148 1.090000e-108 405.0
35 TraesCS3D01G311400 chr6A 81.421 549 75 14 144 665 163137182 163136634 3.010000e-114 424.0
36 TraesCS3D01G311400 chr6A 92.361 288 21 1 1716 2003 545750807 545750521 8.420000e-110 409.0
37 TraesCS3D01G311400 chr6A 86.942 291 26 7 2162 2451 545750433 545750154 5.250000e-82 316.0
38 TraesCS3D01G311400 chr6A 90.000 90 9 0 2045 2134 545750521 545750432 5.720000e-22 117.0
39 TraesCS3D01G311400 chr6D 81.204 548 77 12 144 665 128896245 128895698 1.400000e-112 418.0
40 TraesCS3D01G311400 chr6D 88.580 324 36 1 143 465 88773048 88772725 8.480000e-105 392.0
41 TraesCS3D01G311400 chr6D 76.965 369 50 14 328 666 430276009 430276372 2.590000e-40 178.0
42 TraesCS3D01G311400 chr6D 97.561 41 1 0 681 721 104147628 104147588 4.510000e-08 71.3
43 TraesCS3D01G311400 chr6D 97.561 41 1 0 681 721 464673664 464673704 4.510000e-08 71.3
44 TraesCS3D01G311400 chr1B 81.609 522 72 10 1353 1874 458348844 458349341 2.340000e-110 411.0
45 TraesCS3D01G311400 chr1B 79.837 491 76 13 2801 3290 210146385 210145917 4.030000e-88 337.0
46 TraesCS3D01G311400 chr1B 91.057 246 20 1 1891 2134 458349330 458349575 1.880000e-86 331.0
47 TraesCS3D01G311400 chr1B 88.444 225 13 3 2162 2386 458349574 458349785 8.980000e-65 259.0
48 TraesCS3D01G311400 chr7A 80.699 544 79 10 144 661 734297360 734296817 5.070000e-107 399.0
49 TraesCS3D01G311400 chr7A 80.541 555 75 21 143 666 287801021 287801573 6.560000e-106 396.0
50 TraesCS3D01G311400 chrUn 79.897 582 82 21 2663 3226 19233580 19233016 2.360000e-105 394.0
51 TraesCS3D01G311400 chrUn 97.561 41 1 0 681 721 316007557 316007517 4.510000e-08 71.3
52 TraesCS3D01G311400 chr1D 80.328 549 81 10 144 666 55773414 55773961 3.050000e-104 390.0
53 TraesCS3D01G311400 chr1D 80.182 550 76 14 144 665 267803499 267802955 1.840000e-101 381.0
54 TraesCS3D01G311400 chr1D 91.509 106 9 0 561 666 31217889 31217994 7.290000e-31 147.0
55 TraesCS3D01G311400 chr6B 80.146 549 81 15 144 666 173799721 173799175 1.420000e-102 385.0
56 TraesCS3D01G311400 chr2D 79.235 549 85 13 144 666 45478716 45479261 1.110000e-93 355.0
57 TraesCS3D01G311400 chr2D 78.114 562 68 29 141 666 627174258 627174800 1.140000e-78 305.0
58 TraesCS3D01G311400 chr2D 96.774 31 1 0 3976 4006 340236648 340236618 1.600000e-02 52.8
59 TraesCS3D01G311400 chr5A 76.892 489 81 23 2669 3149 503769689 503770153 1.940000e-61 248.0
60 TraesCS3D01G311400 chr2B 77.513 378 66 10 2663 3030 690659896 690659528 9.170000e-50 209.0
61 TraesCS3D01G311400 chr2B 80.282 142 22 4 3142 3279 385196618 385196757 1.600000e-17 102.0
62 TraesCS3D01G311400 chr2B 100.000 28 0 0 3976 4003 56161622 56161649 1.600000e-02 52.8
63 TraesCS3D01G311400 chr1A 80.328 183 25 7 2667 2841 167153726 167153905 2.640000e-25 128.0
64 TraesCS3D01G311400 chr1A 93.151 73 4 1 2661 2732 1391298 1391370 1.240000e-18 106.0
65 TraesCS3D01G311400 chr1A 93.151 73 4 1 2661 2732 1512345 1512417 1.240000e-18 106.0
66 TraesCS3D01G311400 chr4D 88.889 72 6 2 2656 2727 499742304 499742373 4.480000e-13 87.9
67 TraesCS3D01G311400 chr7D 100.000 38 0 0 681 718 6009627 6009664 4.510000e-08 71.3
68 TraesCS3D01G311400 chr4A 97.561 41 1 0 681 721 644038522 644038562 4.510000e-08 71.3
69 TraesCS3D01G311400 chr4A 97.561 41 1 0 681 721 644075125 644075165 4.510000e-08 71.3


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 TraesCS3D01G311400 chr3D 426070019 426079031 9012 True 16644.000000 16644 100.000000 1 9013 1 chr3D.!!$R2 9012
1 TraesCS3D01G311400 chr3D 96128749 96129291 542 False 381.000000 381 80.183000 148 664 1 chr3D.!!$F1 516
2 TraesCS3D01G311400 chr3D 455590398 455590987 589 False 278.000000 278 75.862000 2655 3247 1 chr3D.!!$F2 592
3 TraesCS3D01G311400 chr3B 556266433 556275061 8628 False 3362.500000 12648 91.658750 1 9013 4 chr3B.!!$F1 9012
4 TraesCS3D01G311400 chr3B 157233867 157234502 635 True 477.000000 477 80.858000 2663 3293 1 chr3B.!!$R1 630
5 TraesCS3D01G311400 chr3A 562193688 562201237 7549 True 4203.300000 10643 93.791333 1546 9013 3 chr3A.!!$R3 7467
6 TraesCS3D01G311400 chr3A 562202761 562203335 574 True 780.000000 780 91.424000 786 1354 1 chr3A.!!$R2 568
7 TraesCS3D01G311400 chr3A 208078264 208078807 543 False 453.000000 453 82.537000 142 658 1 chr3A.!!$F1 516
8 TraesCS3D01G311400 chr5B 389986557 389987246 689 False 798.000000 798 88.068000 912 1590 1 chr5B.!!$F1 678
9 TraesCS3D01G311400 chr7B 162096116 162096746 630 False 544.000000 544 82.362000 2662 3290 1 chr7B.!!$F1 628
10 TraesCS3D01G311400 chr7B 436756450 436757002 552 False 409.000000 409 80.832000 141 666 1 chr7B.!!$F2 525
11 TraesCS3D01G311400 chr4B 54029445 54030073 628 True 527.000000 527 82.188000 2662 3287 1 chr4B.!!$R1 625
12 TraesCS3D01G311400 chr2A 710084955 710085731 776 False 314.000000 459 89.560333 1598 2451 3 chr2A.!!$F2 853
13 TraesCS3D01G311400 chr2A 710067733 710068508 775 False 312.000000 470 89.352000 1598 2451 3 chr2A.!!$F1 853
14 TraesCS3D01G311400 chr5D 278143148 278143704 556 True 405.000000 405 80.645000 138 666 1 chr5D.!!$R1 528
15 TraesCS3D01G311400 chr6A 163136634 163137182 548 True 424.000000 424 81.421000 144 665 1 chr6A.!!$R1 521
16 TraesCS3D01G311400 chr6A 545750154 545750807 653 True 280.666667 409 89.767667 1716 2451 3 chr6A.!!$R2 735
17 TraesCS3D01G311400 chr6D 128895698 128896245 547 True 418.000000 418 81.204000 144 665 1 chr6D.!!$R3 521
18 TraesCS3D01G311400 chr1B 458348844 458349785 941 False 333.666667 411 87.036667 1353 2386 3 chr1B.!!$F1 1033
19 TraesCS3D01G311400 chr7A 734296817 734297360 543 True 399.000000 399 80.699000 144 661 1 chr7A.!!$R1 517
20 TraesCS3D01G311400 chr7A 287801021 287801573 552 False 396.000000 396 80.541000 143 666 1 chr7A.!!$F1 523
21 TraesCS3D01G311400 chrUn 19233016 19233580 564 True 394.000000 394 79.897000 2663 3226 1 chrUn.!!$R1 563
22 TraesCS3D01G311400 chr1D 55773414 55773961 547 False 390.000000 390 80.328000 144 666 1 chr1D.!!$F2 522
23 TraesCS3D01G311400 chr1D 267802955 267803499 544 True 381.000000 381 80.182000 144 665 1 chr1D.!!$R1 521
24 TraesCS3D01G311400 chr6B 173799175 173799721 546 True 385.000000 385 80.146000 144 666 1 chr6B.!!$R1 522
25 TraesCS3D01G311400 chr2D 45478716 45479261 545 False 355.000000 355 79.235000 144 666 1 chr2D.!!$F1 522
26 TraesCS3D01G311400 chr2D 627174258 627174800 542 False 305.000000 305 78.114000 141 666 1 chr2D.!!$F2 525

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
469 482 0.102481 GGCAATGAGAGCTGCAATGG 59.898 55.000 1.02 0.00 40.46 3.16 F
918 1012 0.106419 CTTCCCGCTCTACCCTCTCT 60.106 60.000 0.00 0.00 0.00 3.10 F
1348 1456 0.739561 GCCTCTCGAATAGTGACCGT 59.260 55.000 0.00 0.00 0.00 4.83 F
1349 1457 1.268640 GCCTCTCGAATAGTGACCGTC 60.269 57.143 0.00 0.00 0.00 4.79 F
3263 3493 1.875514 CCACATGTGAACTCACCACTG 59.124 52.381 27.46 1.63 45.88 3.66 F
3461 3691 2.093921 TCCAGATAACGCGATTGGAACA 60.094 45.455 15.93 0.00 35.13 3.18 F
5103 5352 0.523072 TTGAGATTTCTGCCTTGCGC 59.477 50.000 0.00 0.00 38.31 6.09 F
5674 5924 1.216710 CCGAGCCCTCAGACTGAAC 59.783 63.158 6.61 0.00 0.00 3.18 F
6270 6520 0.396435 TCTCACAACACGGAGCCATT 59.604 50.000 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1457 1589 0.163788 AACAAATGAAGCGCGTCTCG 59.836 50.000 23.50 11.60 42.12 4.04 R
2751 2959 0.592637 CATGAACTGTGCGCAAAGGA 59.407 50.000 30.36 14.83 0.00 3.36 R
3263 3493 4.270008 TCCTGCTTATAAAAGTTGGAGCC 58.730 43.478 0.00 0.00 33.99 4.70 R
3461 3691 3.876309 TTAAGTCCAGCTCCCTGTTTT 57.124 42.857 0.00 0.00 37.38 2.43 R
5100 5349 1.135859 GCCTGCAAGATATGTATGCGC 60.136 52.381 0.00 0.00 42.91 6.09 R
5428 5677 2.304180 CCAAAATATTTGGGGTGGTGCA 59.696 45.455 13.26 0.00 35.96 4.57 R
6050 6300 2.762327 AGCAAGGACTTATTGGCATTGG 59.238 45.455 0.00 0.00 44.87 3.16 R
7553 7808 1.039785 CGCTCAGATCAGGAGGACCA 61.040 60.000 14.11 0.00 38.94 4.02 R
8367 8715 0.593128 GCTAGGTTTGCACACCACAG 59.407 55.000 23.55 19.13 39.62 3.66 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
48 49 1.565759 ACCTATGCATTGGAAGAGGCA 59.434 47.619 30.28 0.00 41.00 4.75
58 59 3.845781 TGGAAGAGGCATAAGACCATC 57.154 47.619 0.00 0.00 0.00 3.51
63 64 5.298026 GGAAGAGGCATAAGACCATCTTTTC 59.702 44.000 0.00 0.00 37.89 2.29
65 66 3.545703 AGGCATAAGACCATCTTTTCCG 58.454 45.455 0.00 0.00 37.89 4.30
75 76 3.260632 ACCATCTTTTCCGATTTTTGGGG 59.739 43.478 0.00 0.00 0.00 4.96
77 78 1.621317 TCTTTTCCGATTTTTGGGGCC 59.379 47.619 0.00 0.00 0.00 5.80
92 93 6.882768 TTTGGGGCCACTTTATTCAATAAT 57.117 33.333 6.53 0.00 0.00 1.28
96 97 8.560124 TGGGGCCACTTTATTCAATAATAATT 57.440 30.769 6.53 0.00 37.40 1.40
134 135 6.509280 AGGATAGGGATAAGAAAATTAGGGGG 59.491 42.308 0.00 0.00 0.00 5.40
260 264 1.270305 GCAGGATACATAGGCGCTGAA 60.270 52.381 7.64 0.00 41.41 3.02
284 288 1.074248 CAACACCACCCCCAGTACC 59.926 63.158 0.00 0.00 0.00 3.34
297 301 2.553028 CCCAGTACCACAAGAGCAACAT 60.553 50.000 0.00 0.00 0.00 2.71
465 478 2.437180 CGGGCAATGAGAGCTGCA 60.437 61.111 1.02 0.00 40.46 4.41
467 480 1.381928 CGGGCAATGAGAGCTGCAAT 61.382 55.000 1.02 0.00 40.46 3.56
469 482 0.102481 GGCAATGAGAGCTGCAATGG 59.898 55.000 1.02 0.00 40.46 3.16
476 497 2.034687 AGCTGCAATGGCGAAGGT 59.965 55.556 1.02 0.00 45.35 3.50
477 498 1.986575 GAGCTGCAATGGCGAAGGTC 61.987 60.000 1.02 0.00 45.35 3.85
479 500 2.031919 TGCAATGGCGAAGGTCGT 59.968 55.556 0.00 0.00 45.35 4.34
480 501 1.577328 CTGCAATGGCGAAGGTCGTT 61.577 55.000 0.00 0.00 45.35 3.85
481 502 1.134694 GCAATGGCGAAGGTCGTTC 59.865 57.895 0.00 0.00 42.81 3.95
482 503 1.794222 CAATGGCGAAGGTCGTTCC 59.206 57.895 0.00 0.00 42.81 3.62
505 526 0.323629 CTTAAAGGCAGGTCCGTCCA 59.676 55.000 5.43 0.00 40.77 4.02
508 529 0.112412 AAAGGCAGGTCCGTCCAAAT 59.888 50.000 5.43 0.00 40.77 2.32
515 536 4.505039 GGCAGGTCCGTCCAAATATAGATT 60.505 45.833 0.00 0.00 39.02 2.40
525 546 9.284968 CCGTCCAAATATAGATTAGGTTTTCAT 57.715 33.333 0.00 0.00 0.00 2.57
552 590 4.293648 CACTCACCGCCACCGACA 62.294 66.667 0.00 0.00 36.29 4.35
558 596 2.266372 CCGCCACCGACAATACCA 59.734 61.111 0.00 0.00 36.29 3.25
570 608 1.077068 AATACCACCCACATGGCCG 60.077 57.895 0.00 0.00 44.33 6.13
669 713 3.126001 TCAAGACCTTGACACCATGAC 57.874 47.619 8.27 0.00 43.90 3.06
670 714 2.437651 TCAAGACCTTGACACCATGACA 59.562 45.455 8.27 0.00 43.90 3.58
671 715 2.549754 CAAGACCTTGACACCATGACAC 59.450 50.000 3.79 0.00 42.93 3.67
672 716 2.050144 AGACCTTGACACCATGACACT 58.950 47.619 0.00 0.00 0.00 3.55
673 717 3.239449 AGACCTTGACACCATGACACTA 58.761 45.455 0.00 0.00 0.00 2.74
674 718 3.840666 AGACCTTGACACCATGACACTAT 59.159 43.478 0.00 0.00 0.00 2.12
675 719 4.287067 AGACCTTGACACCATGACACTATT 59.713 41.667 0.00 0.00 0.00 1.73
676 720 5.483937 AGACCTTGACACCATGACACTATTA 59.516 40.000 0.00 0.00 0.00 0.98
677 721 5.734720 ACCTTGACACCATGACACTATTAG 58.265 41.667 0.00 0.00 0.00 1.73
678 722 4.572389 CCTTGACACCATGACACTATTAGC 59.428 45.833 0.00 0.00 0.00 3.09
679 723 5.420725 TTGACACCATGACACTATTAGCT 57.579 39.130 0.00 0.00 0.00 3.32
680 724 5.420725 TGACACCATGACACTATTAGCTT 57.579 39.130 0.00 0.00 0.00 3.74
681 725 6.538945 TGACACCATGACACTATTAGCTTA 57.461 37.500 0.00 0.00 0.00 3.09
682 726 6.941857 TGACACCATGACACTATTAGCTTAA 58.058 36.000 0.00 0.00 0.00 1.85
683 727 7.390823 TGACACCATGACACTATTAGCTTAAA 58.609 34.615 0.00 0.00 0.00 1.52
684 728 7.333423 TGACACCATGACACTATTAGCTTAAAC 59.667 37.037 0.00 0.00 0.00 2.01
685 729 6.312918 ACACCATGACACTATTAGCTTAAACG 59.687 38.462 0.00 0.00 0.00 3.60
686 730 5.293569 ACCATGACACTATTAGCTTAAACGC 59.706 40.000 0.00 0.00 0.00 4.84
687 731 5.523916 CCATGACACTATTAGCTTAAACGCT 59.476 40.000 0.00 0.00 43.83 5.07
688 732 6.292381 CCATGACACTATTAGCTTAAACGCTC 60.292 42.308 0.00 0.00 41.30 5.03
689 733 5.962433 TGACACTATTAGCTTAAACGCTCT 58.038 37.500 0.00 0.00 41.30 4.09
690 734 6.395629 TGACACTATTAGCTTAAACGCTCTT 58.604 36.000 0.00 0.00 41.30 2.85
691 735 7.541162 TGACACTATTAGCTTAAACGCTCTTA 58.459 34.615 0.00 0.00 41.30 2.10
692 736 8.195436 TGACACTATTAGCTTAAACGCTCTTAT 58.805 33.333 0.00 0.00 41.30 1.73
693 737 9.674824 GACACTATTAGCTTAAACGCTCTTATA 57.325 33.333 0.00 0.00 41.30 0.98
707 751 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
708 752 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
709 753 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
710 754 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
711 755 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
719 763 9.710818 ATTAGTTTACAGAGGGAGTAGATTACA 57.289 33.333 0.00 0.00 0.00 2.41
720 764 9.537852 TTAGTTTACAGAGGGAGTAGATTACAA 57.462 33.333 0.00 0.00 0.00 2.41
721 765 7.838884 AGTTTACAGAGGGAGTAGATTACAAC 58.161 38.462 0.00 0.00 0.00 3.32
722 766 7.674772 AGTTTACAGAGGGAGTAGATTACAACT 59.325 37.037 0.00 0.00 0.00 3.16
723 767 5.923733 ACAGAGGGAGTAGATTACAACTG 57.076 43.478 0.00 0.00 0.00 3.16
724 768 5.580998 ACAGAGGGAGTAGATTACAACTGA 58.419 41.667 0.00 0.00 0.00 3.41
725 769 5.654650 ACAGAGGGAGTAGATTACAACTGAG 59.345 44.000 0.00 0.00 0.00 3.35
726 770 5.068460 CAGAGGGAGTAGATTACAACTGAGG 59.932 48.000 0.00 0.00 0.00 3.86
727 771 5.044030 AGAGGGAGTAGATTACAACTGAGGA 60.044 44.000 0.00 0.00 0.00 3.71
728 772 5.782925 AGGGAGTAGATTACAACTGAGGAT 58.217 41.667 0.00 0.00 0.00 3.24
729 773 6.206042 AGGGAGTAGATTACAACTGAGGATT 58.794 40.000 0.00 0.00 0.00 3.01
730 774 7.363031 AGGGAGTAGATTACAACTGAGGATTA 58.637 38.462 0.00 0.00 0.00 1.75
731 775 8.013667 AGGGAGTAGATTACAACTGAGGATTAT 58.986 37.037 0.00 0.00 0.00 1.28
732 776 8.308207 GGGAGTAGATTACAACTGAGGATTATC 58.692 40.741 0.00 0.00 0.00 1.75
733 777 8.024285 GGAGTAGATTACAACTGAGGATTATCG 58.976 40.741 0.00 0.00 0.00 2.92
734 778 7.371936 AGTAGATTACAACTGAGGATTATCGC 58.628 38.462 0.00 0.00 0.00 4.58
735 779 6.412362 AGATTACAACTGAGGATTATCGCT 57.588 37.500 0.00 0.00 0.00 4.93
736 780 6.219473 AGATTACAACTGAGGATTATCGCTG 58.781 40.000 0.00 0.00 0.00 5.18
737 781 3.895232 ACAACTGAGGATTATCGCTGT 57.105 42.857 0.00 0.00 0.00 4.40
744 788 4.119862 TGAGGATTATCGCTGTGCTAAAC 58.880 43.478 0.00 0.00 0.00 2.01
749 793 1.076533 ATCGCTGTGCTAAACGGTCG 61.077 55.000 0.00 0.00 37.49 4.79
752 796 1.623973 GCTGTGCTAAACGGTCGGAC 61.624 60.000 0.00 0.00 37.49 4.79
759 803 2.268298 CTAAACGGTCGGACCAGAATG 58.732 52.381 25.80 12.10 38.47 2.67
762 806 0.395312 ACGGTCGGACCAGAATGTTT 59.605 50.000 25.80 0.78 38.47 2.83
831 920 5.456548 TTACGAATCTACCACAACACAGA 57.543 39.130 0.00 0.00 0.00 3.41
856 945 1.947456 GGAAAGAAAAGGCGAGTGTGT 59.053 47.619 0.00 0.00 0.00 3.72
883 977 0.392461 TTCATTTCCCTCCTTCCGCG 60.392 55.000 0.00 0.00 0.00 6.46
884 978 1.819632 CATTTCCCTCCTTCCGCGG 60.820 63.158 22.12 22.12 0.00 6.46
885 979 2.298661 ATTTCCCTCCTTCCGCGGT 61.299 57.895 27.15 0.00 0.00 5.68
888 982 4.468689 CCCTCCTTCCGCGGTTCC 62.469 72.222 27.15 0.00 0.00 3.62
889 983 4.814294 CCTCCTTCCGCGGTTCCG 62.814 72.222 27.15 11.38 0.00 4.30
910 1004 1.511305 CGTCTTGCTTCCCGCTCTA 59.489 57.895 0.00 0.00 40.11 2.43
918 1012 0.106419 CTTCCCGCTCTACCCTCTCT 60.106 60.000 0.00 0.00 0.00 3.10
926 1020 3.677424 CGCTCTACCCTCTCTTTTTCCAG 60.677 52.174 0.00 0.00 0.00 3.86
927 1021 3.515901 GCTCTACCCTCTCTTTTTCCAGA 59.484 47.826 0.00 0.00 0.00 3.86
937 1031 2.360801 TCTTTTTCCAGAAAAGCCCACG 59.639 45.455 5.76 0.00 40.83 4.94
961 1055 4.382040 CCATTTACAAGAGCGGAAGAGAGA 60.382 45.833 0.00 0.00 0.00 3.10
962 1056 4.442375 TTTACAAGAGCGGAAGAGAGAG 57.558 45.455 0.00 0.00 0.00 3.20
984 1078 2.210711 GGGAGGGACAGATAGCGGG 61.211 68.421 0.00 0.00 0.00 6.13
1199 1302 2.361230 GCCCCTTTCTTGGACCGG 60.361 66.667 0.00 0.00 0.00 5.28
1219 1322 3.242804 CGGCGAAAAACTAGTTTTGACCA 60.243 43.478 29.33 0.00 41.45 4.02
1348 1456 0.739561 GCCTCTCGAATAGTGACCGT 59.260 55.000 0.00 0.00 0.00 4.83
1349 1457 1.268640 GCCTCTCGAATAGTGACCGTC 60.269 57.143 0.00 0.00 0.00 4.79
1457 1589 4.036734 TGTTTCTCACAGGATTGCTGAAAC 59.963 41.667 12.54 11.63 39.17 2.78
1489 1621 5.221244 GCTTCATTTGTTCTGTTGTACCCTT 60.221 40.000 0.00 0.00 0.00 3.95
1527 1659 2.815215 TCTGTCCCAGTGCCAAGAATTG 60.815 50.000 0.00 0.00 38.10 2.32
1539 1671 8.892723 CAGTGCCAAGAATTGTTGTATCTATAA 58.107 33.333 13.69 0.00 46.99 0.98
1599 1737 6.385649 TTTGGTCCTGCTTTAGTTACAAAG 57.614 37.500 0.00 3.94 38.34 2.77
1603 1741 5.306394 GTCCTGCTTTAGTTACAAAGTCCT 58.694 41.667 8.31 0.00 37.74 3.85
1608 1746 5.705441 TGCTTTAGTTACAAAGTCCTCCATG 59.295 40.000 8.31 0.00 37.74 3.66
1610 1748 6.206829 GCTTTAGTTACAAAGTCCTCCATGTT 59.793 38.462 0.00 0.00 37.74 2.71
1636 1774 6.928979 TTCGTAGAAATTTTGTTGGTGAGA 57.071 33.333 0.00 0.00 45.90 3.27
1713 1853 3.123621 CGTAGTTTCCTGATGCAGTTGAC 59.876 47.826 0.00 0.00 0.00 3.18
1714 1854 3.498774 AGTTTCCTGATGCAGTTGACT 57.501 42.857 0.00 0.00 0.00 3.41
1775 1915 6.149474 AGAGTTATGTACAACTGCAATTCACC 59.851 38.462 4.93 0.00 38.86 4.02
1803 1943 2.025981 TCCTGAGTGCAGCACCATAAAT 60.026 45.455 22.41 1.64 40.91 1.40
1816 1956 5.070313 AGCACCATAAATTCACCTGTGTTTT 59.930 36.000 0.00 2.54 0.00 2.43
1817 1957 5.177327 GCACCATAAATTCACCTGTGTTTTG 59.823 40.000 0.00 0.00 0.00 2.44
1819 1959 5.163364 ACCATAAATTCACCTGTGTTTTGCA 60.163 36.000 0.00 0.00 0.00 4.08
1864 2005 2.103094 TGAGTACTGCATGCATAGGGTC 59.897 50.000 22.97 14.47 0.00 4.46
1943 2086 3.329386 CCAATGAAGAGCGAACAAGAGA 58.671 45.455 0.00 0.00 0.00 3.10
2066 2255 7.551035 AGAAGTTTCTTTGCATATGAGCTAG 57.449 36.000 6.97 0.00 32.55 3.42
2350 2539 4.113354 GCTTTAGAACTGATCCAGGTACG 58.887 47.826 0.00 0.00 35.51 3.67
2402 2591 9.511272 AACTTGTTACCACCTATTTAAAGTAGG 57.489 33.333 16.12 16.12 43.54 3.18
2621 2811 9.804758 GTTCTAGAGTAAGCACACTATTACAAT 57.195 33.333 0.00 0.00 34.91 2.71
2751 2959 7.826690 AGAAAACCGTTAATATTGTTCTGCAT 58.173 30.769 0.00 0.00 0.00 3.96
3263 3493 1.875514 CCACATGTGAACTCACCACTG 59.124 52.381 27.46 1.63 45.88 3.66
3461 3691 2.093921 TCCAGATAACGCGATTGGAACA 60.094 45.455 15.93 0.00 35.13 3.18
3972 4208 5.657745 TGATGGAAGTTAATGGAATGCATGT 59.342 36.000 0.00 0.00 0.00 3.21
3976 4212 7.222872 TGGAAGTTAATGGAATGCATGTTTTT 58.777 30.769 0.00 0.00 0.00 1.94
4232 4470 9.265901 AGCTGATGTTTATACACTTCATACATC 57.734 33.333 7.76 0.00 40.28 3.06
4280 4518 9.699410 ATTCCTTCTAATGACCATTGAATACAA 57.301 29.630 5.56 0.00 40.42 2.41
4838 5079 3.575687 GCATGGAAGATATGAAAAGGGGG 59.424 47.826 0.00 0.00 0.00 5.40
4971 5220 8.908903 ACTACCATCATCTTACAGAAGTAGAAG 58.091 37.037 0.00 0.00 32.95 2.85
5103 5352 0.523072 TTGAGATTTCTGCCTTGCGC 59.477 50.000 0.00 0.00 38.31 6.09
5132 5381 1.252904 TTGCAGGCCAGCATTCCTTC 61.253 55.000 24.71 0.00 45.19 3.46
5674 5924 1.216710 CCGAGCCCTCAGACTGAAC 59.783 63.158 6.61 0.00 0.00 3.18
5829 6079 3.411517 CGTGCCTTCCCCTGGGAT 61.412 66.667 16.20 0.00 44.74 3.85
5850 6100 6.115446 GGATGATTCAGATAGTGTTTCACCA 58.885 40.000 0.00 0.00 34.49 4.17
5900 6150 3.181474 GGTCCTCTTTCTAGGGATCAACG 60.181 52.174 0.00 0.00 37.24 4.10
5982 6232 3.083122 AGTCCTACCTTCTTACTGCGA 57.917 47.619 0.00 0.00 0.00 5.10
6050 6300 4.275936 AGGTCAGTTATTGCAACACAAGTC 59.724 41.667 0.00 0.00 42.87 3.01
6108 6358 7.834068 TCTCTAATTTCTGTAGTTGATGTGC 57.166 36.000 0.00 0.00 0.00 4.57
6109 6359 7.386059 TCTCTAATTTCTGTAGTTGATGTGCA 58.614 34.615 0.00 0.00 0.00 4.57
6270 6520 0.396435 TCTCACAACACGGAGCCATT 59.604 50.000 0.00 0.00 0.00 3.16
6337 6587 8.091449 ACTGTAAGGAGTTCATACTTCAAGAAG 58.909 37.037 8.22 8.22 40.79 2.85
6363 6613 4.590850 AGAGGGTTTTCACAAATCAAGC 57.409 40.909 0.00 0.00 0.00 4.01
6368 6618 5.104982 AGGGTTTTCACAAATCAAGCAGAAA 60.105 36.000 0.00 0.00 0.00 2.52
6376 6626 5.581874 CACAAATCAAGCAGAAAACCAGTTT 59.418 36.000 0.00 0.00 0.00 2.66
6397 6650 5.868043 TTGATGATGATGATGATAACGCC 57.132 39.130 0.00 0.00 0.00 5.68
6842 7095 3.900971 TGGCAGCTTGATTATCATTCCA 58.099 40.909 0.00 0.00 0.00 3.53
7436 7691 9.555727 AGTGAATATATAACGGCACAGTTATTT 57.444 29.630 10.67 6.66 42.68 1.40
7553 7808 2.049063 GCCTCGAATAGCGCCGAT 60.049 61.111 2.29 0.00 40.61 4.18
7858 8206 0.962855 ACTGCTAGTCGCTCTGAGCA 60.963 55.000 27.46 13.12 42.58 4.26
7976 8324 2.284754 TTGCAGGGACAACATTAGCA 57.715 45.000 0.00 0.00 0.00 3.49
8025 8373 3.885724 TCACATAGAACTGCCGATGAA 57.114 42.857 0.00 0.00 0.00 2.57
8165 8513 2.753043 CACCCATGGACCTGCAGC 60.753 66.667 15.22 0.00 0.00 5.25
8185 8533 0.107456 CCCGATGAACCCCTGATCTG 59.893 60.000 0.00 0.00 0.00 2.90
8189 8537 2.035704 CGATGAACCCCTGATCTGAGAG 59.964 54.545 0.38 0.00 0.00 3.20
8195 8543 1.440893 CCTGATCTGAGAGCACCCG 59.559 63.158 0.00 0.00 0.00 5.28
8279 8627 8.842358 TCGGTACTTGACTTCATTTTTATCTT 57.158 30.769 0.00 0.00 0.00 2.40
8363 8711 5.690464 ATAGCTTCAGTTTCAGAGACCAT 57.310 39.130 0.00 0.00 0.00 3.55
8367 8715 3.577649 TCAGTTTCAGAGACCATCGTC 57.422 47.619 0.00 0.00 39.50 4.20
8439 8787 7.744087 ACTGTTGTCATTTGAGCATTAGTAA 57.256 32.000 0.00 0.00 0.00 2.24
8476 8824 6.151648 TCTGTCAATTCCCAATCAAGATGAAC 59.848 38.462 0.00 0.00 0.00 3.18
8518 8866 5.596361 TGTTGTATTGTGGTTTGTGGATTCT 59.404 36.000 0.00 0.00 0.00 2.40
8597 8945 9.898152 TGAATGTACTATTTGTGTATGGAATGA 57.102 29.630 0.00 0.00 0.00 2.57
8604 8952 9.685276 ACTATTTGTGTATGGAATGATCTTGAA 57.315 29.630 0.00 0.00 0.00 2.69
8633 8981 1.340697 GGACCTGGCGGAACCTTTATT 60.341 52.381 0.00 0.00 40.22 1.40
8813 9290 7.064134 TCCTATGCTTTATTTTACTCGTGTGTG 59.936 37.037 0.00 0.00 0.00 3.82
8937 9415 0.249868 CAGTTTCAGAGACCACCGCA 60.250 55.000 0.00 0.00 0.00 5.69
9006 9488 5.840940 AGTTTCTTTAGAATTCGTGTCGG 57.159 39.130 0.00 0.00 33.54 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.036733 GGTGCATGCTACGGGATAGTAA 59.963 50.000 20.33 0.00 32.90 2.24
48 49 7.363793 CCCAAAAATCGGAAAAGATGGTCTTAT 60.364 37.037 0.00 0.00 35.27 1.73
58 59 1.346068 TGGCCCCAAAAATCGGAAAAG 59.654 47.619 0.00 0.00 0.00 2.27
63 64 0.684535 AAAGTGGCCCCAAAAATCGG 59.315 50.000 0.00 0.00 0.00 4.18
65 66 5.159273 TGAATAAAGTGGCCCCAAAAATC 57.841 39.130 0.00 0.00 0.00 2.17
107 108 9.124104 CCCCTAATTTTCTTATCCCTATCCTTA 57.876 37.037 0.00 0.00 0.00 2.69
112 113 5.281037 CGCCCCCTAATTTTCTTATCCCTAT 60.281 44.000 0.00 0.00 0.00 2.57
123 124 0.626916 TAGTGCCGCCCCCTAATTTT 59.373 50.000 0.00 0.00 0.00 1.82
278 282 3.402110 TCATGTTGCTCTTGTGGTACTG 58.598 45.455 0.00 0.00 0.00 2.74
284 288 2.740981 GAGGACTCATGTTGCTCTTGTG 59.259 50.000 10.06 0.00 0.00 3.33
297 301 1.116308 TGTTCACGGTTGAGGACTCA 58.884 50.000 0.00 0.00 37.91 3.41
325 329 2.799562 CGTATGCGGCTTCATCTCTTCA 60.800 50.000 0.00 0.00 0.00 3.02
410 423 1.835494 AACTCTGATTCTCGGGTCGA 58.165 50.000 0.00 0.00 0.00 4.20
465 478 1.376812 GGGAACGACCTTCGCCATT 60.377 57.895 0.00 0.00 45.12 3.16
467 480 2.920912 AGGGAACGACCTTCGCCA 60.921 61.111 0.00 0.00 45.12 5.69
487 508 0.766131 TTGGACGGACCTGCCTTTAA 59.234 50.000 0.00 0.00 39.86 1.52
489 510 0.112412 ATTTGGACGGACCTGCCTTT 59.888 50.000 0.00 0.00 39.86 3.11
491 512 1.213296 ATATTTGGACGGACCTGCCT 58.787 50.000 0.00 0.00 39.86 4.75
492 513 2.367567 TCTATATTTGGACGGACCTGCC 59.632 50.000 0.00 0.00 39.86 4.85
495 516 6.082707 ACCTAATCTATATTTGGACGGACCT 58.917 40.000 8.04 0.00 39.52 3.85
508 529 8.108378 TGGTTGGGATGAAAACCTAATCTATA 57.892 34.615 6.18 0.00 45.12 1.31
515 536 3.892588 GTGTTGGTTGGGATGAAAACCTA 59.107 43.478 6.18 0.00 45.12 3.08
525 546 1.147376 CGGTGAGTGTTGGTTGGGA 59.853 57.895 0.00 0.00 0.00 4.37
530 551 2.203153 GTGGCGGTGAGTGTTGGT 60.203 61.111 0.00 0.00 0.00 3.67
552 590 1.077068 CGGCCATGTGGGTGGTATT 60.077 57.895 2.24 0.00 41.47 1.89
681 725 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
682 726 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
683 727 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
684 728 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
685 729 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
693 737 9.710818 TGTAATCTACTCCCTCTGTAAACTAAT 57.289 33.333 0.00 0.00 0.00 1.73
694 738 9.537852 TTGTAATCTACTCCCTCTGTAAACTAA 57.462 33.333 0.00 0.00 0.00 2.24
695 739 8.964772 GTTGTAATCTACTCCCTCTGTAAACTA 58.035 37.037 0.00 0.00 0.00 2.24
696 740 7.674772 AGTTGTAATCTACTCCCTCTGTAAACT 59.325 37.037 0.00 0.00 0.00 2.66
697 741 7.760340 CAGTTGTAATCTACTCCCTCTGTAAAC 59.240 40.741 0.00 0.00 0.00 2.01
698 742 7.672660 TCAGTTGTAATCTACTCCCTCTGTAAA 59.327 37.037 0.00 0.00 0.00 2.01
699 743 7.179966 TCAGTTGTAATCTACTCCCTCTGTAA 58.820 38.462 0.00 0.00 0.00 2.41
700 744 6.728411 TCAGTTGTAATCTACTCCCTCTGTA 58.272 40.000 0.00 0.00 0.00 2.74
701 745 5.580998 TCAGTTGTAATCTACTCCCTCTGT 58.419 41.667 0.00 0.00 0.00 3.41
702 746 5.068460 CCTCAGTTGTAATCTACTCCCTCTG 59.932 48.000 0.00 0.00 0.00 3.35
703 747 5.044030 TCCTCAGTTGTAATCTACTCCCTCT 60.044 44.000 0.00 0.00 0.00 3.69
704 748 5.202004 TCCTCAGTTGTAATCTACTCCCTC 58.798 45.833 0.00 0.00 0.00 4.30
705 749 5.208294 TCCTCAGTTGTAATCTACTCCCT 57.792 43.478 0.00 0.00 0.00 4.20
706 750 6.487299 AATCCTCAGTTGTAATCTACTCCC 57.513 41.667 0.00 0.00 0.00 4.30
707 751 8.024285 CGATAATCCTCAGTTGTAATCTACTCC 58.976 40.741 0.00 0.00 0.00 3.85
708 752 7.539366 GCGATAATCCTCAGTTGTAATCTACTC 59.461 40.741 0.00 0.00 0.00 2.59
709 753 7.231722 AGCGATAATCCTCAGTTGTAATCTACT 59.768 37.037 0.00 0.00 0.00 2.57
710 754 7.327275 CAGCGATAATCCTCAGTTGTAATCTAC 59.673 40.741 0.00 0.00 0.00 2.59
711 755 7.014326 ACAGCGATAATCCTCAGTTGTAATCTA 59.986 37.037 0.00 0.00 0.00 1.98
712 756 6.183360 ACAGCGATAATCCTCAGTTGTAATCT 60.183 38.462 0.00 0.00 0.00 2.40
713 757 5.986135 ACAGCGATAATCCTCAGTTGTAATC 59.014 40.000 0.00 0.00 0.00 1.75
714 758 5.755375 CACAGCGATAATCCTCAGTTGTAAT 59.245 40.000 0.00 0.00 0.00 1.89
715 759 5.109210 CACAGCGATAATCCTCAGTTGTAA 58.891 41.667 0.00 0.00 0.00 2.41
716 760 4.682787 CACAGCGATAATCCTCAGTTGTA 58.317 43.478 0.00 0.00 0.00 2.41
717 761 3.525537 CACAGCGATAATCCTCAGTTGT 58.474 45.455 0.00 0.00 0.00 3.32
718 762 2.286294 GCACAGCGATAATCCTCAGTTG 59.714 50.000 0.00 0.00 0.00 3.16
719 763 2.169352 AGCACAGCGATAATCCTCAGTT 59.831 45.455 0.00 0.00 0.00 3.16
720 764 1.759445 AGCACAGCGATAATCCTCAGT 59.241 47.619 0.00 0.00 0.00 3.41
721 765 2.522836 AGCACAGCGATAATCCTCAG 57.477 50.000 0.00 0.00 0.00 3.35
722 766 4.119862 GTTTAGCACAGCGATAATCCTCA 58.880 43.478 0.00 0.00 0.00 3.86
723 767 3.182572 CGTTTAGCACAGCGATAATCCTC 59.817 47.826 0.00 0.00 0.00 3.71
724 768 3.123804 CGTTTAGCACAGCGATAATCCT 58.876 45.455 0.00 0.00 0.00 3.24
725 769 2.221055 CCGTTTAGCACAGCGATAATCC 59.779 50.000 0.00 0.00 0.00 3.01
726 770 2.864343 ACCGTTTAGCACAGCGATAATC 59.136 45.455 0.00 0.00 0.00 1.75
727 771 2.864343 GACCGTTTAGCACAGCGATAAT 59.136 45.455 0.00 0.00 0.00 1.28
728 772 2.264813 GACCGTTTAGCACAGCGATAA 58.735 47.619 0.00 0.00 0.00 1.75
729 773 1.796253 CGACCGTTTAGCACAGCGATA 60.796 52.381 0.00 0.00 0.00 2.92
730 774 1.076533 CGACCGTTTAGCACAGCGAT 61.077 55.000 0.00 0.00 0.00 4.58
731 775 1.731613 CGACCGTTTAGCACAGCGA 60.732 57.895 0.00 0.00 0.00 4.93
732 776 2.726691 CCGACCGTTTAGCACAGCG 61.727 63.158 0.00 0.00 0.00 5.18
733 777 1.373748 TCCGACCGTTTAGCACAGC 60.374 57.895 0.00 0.00 0.00 4.40
734 778 1.012486 GGTCCGACCGTTTAGCACAG 61.012 60.000 0.65 0.00 0.00 3.66
735 779 1.005867 GGTCCGACCGTTTAGCACA 60.006 57.895 0.65 0.00 0.00 4.57
736 780 1.005867 TGGTCCGACCGTTTAGCAC 60.006 57.895 13.02 0.00 42.58 4.40
737 781 1.180456 TCTGGTCCGACCGTTTAGCA 61.180 55.000 13.02 0.00 42.58 3.49
744 788 1.519408 AAAACATTCTGGTCCGACCG 58.481 50.000 13.02 7.91 42.58 4.79
831 920 4.159693 ACACTCGCCTTTTCTTTCCTTTTT 59.840 37.500 0.00 0.00 0.00 1.94
856 945 0.965363 GAGGGAAATGAAGCGCCCAA 60.965 55.000 2.29 0.00 43.20 4.12
883 977 4.699522 AGCAAGACGGGCGGAACC 62.700 66.667 0.00 0.00 36.08 3.62
884 978 2.668550 AAGCAAGACGGGCGGAAC 60.669 61.111 0.00 0.00 36.08 3.62
885 979 2.358247 GAAGCAAGACGGGCGGAA 60.358 61.111 0.00 0.00 36.08 4.30
910 1004 3.891977 GCTTTTCTGGAAAAAGAGAGGGT 59.108 43.478 13.02 0.00 39.49 4.34
918 1012 1.202475 GCGTGGGCTTTTCTGGAAAAA 60.202 47.619 9.35 0.00 39.49 1.94
926 1020 1.271102 TGTAAATGGCGTGGGCTTTTC 59.729 47.619 6.36 1.71 36.93 2.29
927 1021 1.333177 TGTAAATGGCGTGGGCTTTT 58.667 45.000 7.87 7.87 38.53 2.27
937 1031 2.352960 CTCTTCCGCTCTTGTAAATGGC 59.647 50.000 0.00 0.00 0.00 4.40
961 1055 0.178975 CTATCTGTCCCTCCCTCGCT 60.179 60.000 0.00 0.00 0.00 4.93
962 1056 1.811645 GCTATCTGTCCCTCCCTCGC 61.812 65.000 0.00 0.00 0.00 5.03
1199 1302 3.722289 CGTGGTCAAAACTAGTTTTTCGC 59.278 43.478 27.12 22.33 40.45 4.70
1219 1322 1.545875 CGGATCAGGAGACCCTATCGT 60.546 57.143 0.00 0.00 42.02 3.73
1348 1456 2.689471 CAATCAAGAAATCATGGCGGGA 59.311 45.455 0.00 0.00 0.00 5.14
1349 1457 2.223876 CCAATCAAGAAATCATGGCGGG 60.224 50.000 0.00 0.00 0.00 6.13
1388 1520 2.205074 CTTCATCTGGAACGGGATTCG 58.795 52.381 0.00 0.00 45.88 3.34
1396 1528 4.829492 CCCCATTTATCCTTCATCTGGAAC 59.171 45.833 0.00 0.00 37.13 3.62
1421 1553 3.612423 GTGAGAAACAACACAAACAAGGC 59.388 43.478 0.00 0.00 37.05 4.35
1457 1589 0.163788 AACAAATGAAGCGCGTCTCG 59.836 50.000 23.50 11.60 42.12 4.04
1489 1621 5.261216 GGACAGATGGGGAAATTCAGTTTA 58.739 41.667 0.00 0.00 0.00 2.01
1571 1709 5.966742 AACTAAAGCAGGACCAAATCTTC 57.033 39.130 0.00 0.00 0.00 2.87
1599 1737 7.787725 ATTTCTACGAATTAACATGGAGGAC 57.212 36.000 0.00 0.00 0.00 3.85
1608 1746 9.453325 TCACCAACAAAATTTCTACGAATTAAC 57.547 29.630 0.00 0.00 0.00 2.01
1610 1748 9.058174 TCTCACCAACAAAATTTCTACGAATTA 57.942 29.630 0.00 0.00 0.00 1.40
1713 1853 6.963242 CACTATGATTCGGTGACAAATGAAAG 59.037 38.462 0.00 0.00 33.32 2.62
1714 1854 6.622679 GCACTATGATTCGGTGACAAATGAAA 60.623 38.462 7.94 0.00 33.32 2.69
1775 1915 1.015109 GCTGCACTCAGGATGTGATG 58.985 55.000 0.00 0.00 40.65 3.07
1816 1956 2.364970 CCTGGTTCAAATTCAAGGTGCA 59.635 45.455 0.00 0.00 0.00 4.57
1817 1957 2.867647 GCCTGGTTCAAATTCAAGGTGC 60.868 50.000 0.00 0.00 0.00 5.01
1819 1959 2.676748 TGCCTGGTTCAAATTCAAGGT 58.323 42.857 0.00 0.00 0.00 3.50
1864 2005 0.940519 CATGGTGCCGCAACAAGTTG 60.941 55.000 16.56 5.59 43.14 3.16
2066 2255 1.244019 GCCCCAGATGACCACAACAC 61.244 60.000 0.00 0.00 0.00 3.32
2402 2591 6.483640 ACCAAACATTCTCACTCTGTTAGAAC 59.516 38.462 0.00 0.00 30.20 3.01
2621 2811 2.880612 TTGAGGGCTGAGGAGGGGA 61.881 63.158 0.00 0.00 0.00 4.81
2702 2895 1.134280 CCAGTGGCCTAACTCCTCATG 60.134 57.143 3.32 0.00 0.00 3.07
2732 2928 6.377327 AAGGATGCAGAACAATATTAACGG 57.623 37.500 0.00 0.00 0.00 4.44
2751 2959 0.592637 CATGAACTGTGCGCAAAGGA 59.407 50.000 30.36 14.83 0.00 3.36
2808 3022 4.697514 TCTCTTAAGATTCTCCAATGCCG 58.302 43.478 5.44 0.00 0.00 5.69
2847 3061 4.389374 ACATCCGAAATGTTGTGTCTTCT 58.611 39.130 0.00 0.00 0.00 2.85
3263 3493 4.270008 TCCTGCTTATAAAAGTTGGAGCC 58.730 43.478 0.00 0.00 33.99 4.70
3461 3691 3.876309 TTAAGTCCAGCTCCCTGTTTT 57.124 42.857 0.00 0.00 37.38 2.43
3745 3976 3.114809 GCTTGCGCATTATGCACATTTA 58.885 40.909 12.75 0.00 45.36 1.40
4232 4470 5.469373 TGGACGAATGATGAAAAAGATCG 57.531 39.130 0.00 0.00 35.16 3.69
4241 4479 4.760530 AGAAGGAATGGACGAATGATGA 57.239 40.909 0.00 0.00 0.00 2.92
4280 4518 6.152831 ACCCTTAGCTTATTTTCAAATTCGCT 59.847 34.615 0.00 10.79 36.92 4.93
4332 4570 4.627284 TCAGGAGGTAAAACGATTTGGA 57.373 40.909 0.28 0.00 0.00 3.53
4551 4789 6.015940 AGAGAAAACAAGCATAACTTTCCCAG 60.016 38.462 0.00 0.00 36.04 4.45
5100 5349 1.135859 GCCTGCAAGATATGTATGCGC 60.136 52.381 0.00 0.00 42.91 6.09
5103 5352 2.486982 GCTGGCCTGCAAGATATGTATG 59.513 50.000 27.96 0.00 34.07 2.39
5298 5547 6.699642 GCATCTAGGAGCTCACTTTAGTAAAG 59.300 42.308 19.07 19.07 44.10 1.85
5428 5677 2.304180 CCAAAATATTTGGGGTGGTGCA 59.696 45.455 13.26 0.00 35.96 4.57
5429 5678 2.939198 GCCAAAATATTTGGGGTGGTGC 60.939 50.000 21.05 4.00 39.90 5.01
5674 5924 0.393537 GAATCAGGGGTGCCAGAGTG 60.394 60.000 0.00 0.00 0.00 3.51
5829 6079 5.700832 GTGTGGTGAAACACTATCTGAATCA 59.299 40.000 0.00 0.00 45.69 2.57
5850 6100 5.651530 CCAATATCACGAGAACTACAGTGT 58.348 41.667 0.00 0.00 36.16 3.55
5900 6150 5.298777 AGAAATACCTCTGCATCTTCAATGC 59.701 40.000 3.10 3.10 44.76 3.56
5982 6232 7.227156 AGACACAAGGACAAGAGAAATATGTT 58.773 34.615 0.00 0.00 0.00 2.71
6050 6300 2.762327 AGCAAGGACTTATTGGCATTGG 59.238 45.455 0.00 0.00 44.87 3.16
6108 6358 7.621428 ATCACATGACTTCTGGATTAAGTTG 57.379 36.000 0.00 0.00 37.31 3.16
6109 6359 8.543774 ACTATCACATGACTTCTGGATTAAGTT 58.456 33.333 0.00 0.00 37.31 2.66
6196 6446 4.094442 GTCCCTAGAAACATAAAACAGGCG 59.906 45.833 0.00 0.00 0.00 5.52
6270 6520 2.940971 GCATAATGTGGCACTGGTCTCA 60.941 50.000 19.83 0.00 0.00 3.27
6337 6587 6.834168 TGATTTGTGAAAACCCTCTTATCC 57.166 37.500 0.00 0.00 0.00 2.59
6363 6613 6.916440 TCATCATCATCAAACTGGTTTTCTG 58.084 36.000 0.00 0.00 0.00 3.02
6368 6618 8.627403 GTTATCATCATCATCATCAAACTGGTT 58.373 33.333 0.00 0.00 0.00 3.67
6376 6626 3.928375 CGGCGTTATCATCATCATCATCA 59.072 43.478 0.00 0.00 0.00 3.07
7436 7691 5.127845 GGGTCTGAGAATAGATCTGTGACAA 59.872 44.000 5.18 0.00 38.96 3.18
7553 7808 1.039785 CGCTCAGATCAGGAGGACCA 61.040 60.000 14.11 0.00 38.94 4.02
7858 8206 3.262915 AGCTGTAGGAGACAATTTGCTCT 59.737 43.478 15.58 9.65 37.70 4.09
7929 8277 2.178580 GCCATCCAAAGGTTTCATGGA 58.821 47.619 11.76 0.00 46.60 3.41
7976 8324 2.611518 CGAGAATTTCGTCCAGAAGCT 58.388 47.619 0.00 0.00 44.27 3.74
8025 8373 6.655003 CGCCCATATCATAAAAGGTAACAGAT 59.345 38.462 0.00 0.00 41.41 2.90
8068 8416 0.964700 GAAGGCTGGCAGAAGCTTTT 59.035 50.000 20.86 3.10 41.99 2.27
8165 8513 1.056700 AGATCAGGGGTTCATCGGGG 61.057 60.000 0.00 0.00 0.00 5.73
8185 8533 2.954611 GCCAAAACGGGTGCTCTC 59.045 61.111 0.00 0.00 34.06 3.20
8195 8543 1.139163 CATTCTGTTGGCGCCAAAAC 58.861 50.000 41.60 31.25 37.70 2.43
8253 8601 8.842358 AGATAAAAATGAAGTCAAGTACCGAA 57.158 30.769 0.00 0.00 0.00 4.30
8279 8627 2.231721 TGCTTCAGCTTGCATTTGCATA 59.768 40.909 6.00 0.00 44.44 3.14
8363 8711 1.092921 GGTTTGCACACCACAGACGA 61.093 55.000 17.27 0.00 36.73 4.20
8367 8715 0.593128 GCTAGGTTTGCACACCACAG 59.407 55.000 23.55 19.13 39.62 3.66
8581 8929 7.924412 GCATTCAAGATCATTCCATACACAAAT 59.076 33.333 0.00 0.00 0.00 2.32
8582 8930 7.123098 AGCATTCAAGATCATTCCATACACAAA 59.877 33.333 0.00 0.00 0.00 2.83
8583 8931 6.604396 AGCATTCAAGATCATTCCATACACAA 59.396 34.615 0.00 0.00 0.00 3.33
8585 8933 6.485984 AGAGCATTCAAGATCATTCCATACAC 59.514 38.462 0.00 0.00 0.00 2.90
8587 8935 6.149142 GGAGAGCATTCAAGATCATTCCATAC 59.851 42.308 0.00 0.00 0.00 2.39
8589 8937 5.071370 GGAGAGCATTCAAGATCATTCCAT 58.929 41.667 0.00 0.00 0.00 3.41
8591 8939 3.497640 CGGAGAGCATTCAAGATCATTCC 59.502 47.826 0.00 0.00 0.00 3.01
8592 8940 3.497640 CCGGAGAGCATTCAAGATCATTC 59.502 47.826 0.00 0.00 0.00 2.67
8593 8941 3.135348 TCCGGAGAGCATTCAAGATCATT 59.865 43.478 0.00 0.00 0.00 2.57
8594 8942 2.702478 TCCGGAGAGCATTCAAGATCAT 59.298 45.455 0.00 0.00 0.00 2.45
8595 8943 2.110578 TCCGGAGAGCATTCAAGATCA 58.889 47.619 0.00 0.00 0.00 2.92
8596 8944 2.478831 GTCCGGAGAGCATTCAAGATC 58.521 52.381 3.06 0.00 0.00 2.75
8597 8945 1.139853 GGTCCGGAGAGCATTCAAGAT 59.860 52.381 3.06 0.00 40.37 2.40
8598 8946 0.537188 GGTCCGGAGAGCATTCAAGA 59.463 55.000 3.06 0.00 40.37 3.02
8599 8947 0.539051 AGGTCCGGAGAGCATTCAAG 59.461 55.000 3.06 0.00 43.21 3.02
8600 8948 0.250234 CAGGTCCGGAGAGCATTCAA 59.750 55.000 3.06 0.00 43.21 2.69
8601 8949 1.617018 CCAGGTCCGGAGAGCATTCA 61.617 60.000 3.06 0.00 43.21 2.57
8602 8950 1.144936 CCAGGTCCGGAGAGCATTC 59.855 63.158 3.06 0.00 43.21 2.67
8603 8951 3.036429 GCCAGGTCCGGAGAGCATT 62.036 63.158 3.06 0.00 43.21 3.56
8604 8952 3.474570 GCCAGGTCCGGAGAGCAT 61.475 66.667 3.06 0.00 43.21 3.79
8623 8971 9.896263 TTTAACAAACGGTATCAATAAAGGTTC 57.104 29.630 0.00 0.00 0.00 3.62
8633 8981 5.366460 TGAGGTGTTTAACAAACGGTATCA 58.634 37.500 0.00 0.00 44.28 2.15
8813 9290 7.148820 ACGCACATGTAAAATAATTTCAACTGC 60.149 33.333 0.00 0.00 0.00 4.40
8937 9415 3.743714 TGCTAGGTTTGCACACCAT 57.256 47.368 23.55 11.25 39.62 3.55


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

AutoCloner maintained by Alex Coulton.