Multiple sequence alignment - TraesCS3B01G209100

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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 TraesCS3B01G209100 chr3B 100.000 1639 0 0 1 1639 245357091 245358729 0.000000e+00 3027.0
1 TraesCS3B01G209100 chr3B 100.000 1506 0 0 1943 3448 245359033 245360538 0.000000e+00 2782.0
2 TraesCS3B01G209100 chr3B 92.800 125 9 0 1481 1605 245508987 245509111 7.600000e-42 182.0
3 TraesCS3B01G209100 chr3A 90.499 1484 69 29 1943 3399 207830712 207832150 0.000000e+00 1893.0
4 TraesCS3B01G209100 chr3A 93.398 1030 24 15 633 1639 207829702 207830710 0.000000e+00 1485.0
5 TraesCS3B01G209100 chr3A 93.548 217 14 0 404 620 207829502 207829718 1.190000e-84 324.0
6 TraesCS3B01G209100 chr3A 92.800 125 9 0 1481 1605 207844396 207844520 7.600000e-42 182.0
7 TraesCS3B01G209100 chr3A 89.474 95 10 0 2327 2421 207844824 207844918 1.680000e-23 121.0
8 TraesCS3B01G209100 chr3D 93.717 1146 28 10 511 1639 170202440 170203558 0.000000e+00 1677.0
9 TraesCS3B01G209100 chr3D 91.983 711 34 10 2286 2982 170203967 170204668 0.000000e+00 976.0
10 TraesCS3B01G209100 chr3D 88.462 520 53 4 10 524 170201905 170202422 3.780000e-174 621.0
11 TraesCS3B01G209100 chr3D 92.000 275 13 4 1943 2210 170203550 170203822 9.030000e-101 377.0
12 TraesCS3B01G209100 chr3D 86.611 239 23 6 3192 3426 170205959 170206192 4.420000e-64 255.0
13 TraesCS3B01G209100 chr3D 90.850 153 13 1 2982 3134 170204782 170204933 1.620000e-48 204.0
14 TraesCS3B01G209100 chr3D 92.000 125 10 0 1481 1605 170237424 170237548 3.540000e-40 176.0
15 TraesCS3B01G209100 chr3D 88.421 95 11 0 2327 2421 170237832 170237926 7.820000e-22 115.0
16 TraesCS3B01G209100 chr3D 97.778 45 1 0 3131 3175 170205822 170205866 1.030000e-10 78.7
17 TraesCS3B01G209100 chr2B 92.975 242 12 2 1402 1638 776315394 776315153 7.080000e-92 348.0
18 TraesCS3B01G209100 chr2B 74.308 253 59 5 40 288 569961474 569961224 6.090000e-18 102.0
19 TraesCS3B01G209100 chr2B 97.368 38 1 0 584 621 303818738 303818701 7.990000e-07 65.8
20 TraesCS3B01G209100 chr4D 80.000 260 40 10 7 257 403420632 403420376 7.600000e-42 182.0
21 TraesCS3B01G209100 chr1A 74.005 427 93 5 2 417 510671683 510672102 1.280000e-34 158.0
22 TraesCS3B01G209100 chr7D 80.488 205 39 1 1 204 559396126 559396330 4.610000e-34 156.0
23 TraesCS3B01G209100 chr2D 73.810 420 89 12 3 416 484972993 484972589 2.770000e-31 147.0
24 TraesCS3B01G209100 chr1D 73.206 418 90 14 2 411 413728675 413729078 7.760000e-27 132.0
25 TraesCS3B01G209100 chr6D 81.176 85 15 1 5 88 395927274 395927190 2.220000e-07 67.6


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 TraesCS3B01G209100 chr3B 245357091 245360538 3447 False 2904.500000 3027 100.000000 1 3448 2 chr3B.!!$F2 3447
1 TraesCS3B01G209100 chr3A 207829502 207832150 2648 False 1234.000000 1893 92.481667 404 3399 3 chr3A.!!$F1 2995
2 TraesCS3B01G209100 chr3D 170201905 170206192 4287 False 598.385714 1677 91.628714 10 3426 7 chr3D.!!$F1 3416

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
379 383 0.038166 TTAGTCCGGACGTACAGGGT 59.962 55.0 28.26 11.32 34.65 4.34 F
1293 1370 0.459237 CATGCACTGACTCCGTCCTC 60.459 60.0 0.00 0.00 0.00 3.71 F
2176 2274 0.322636 TCCGCTCCCTATCGATCTCC 60.323 60.0 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1295 1372 0.038892 GTGCGTACAGGAAGGACGAA 60.039 55.0 3.74 0.0 38.88 3.85 R
2437 2618 0.107508 ATGGATCGGTCACTTGGCAG 60.108 55.0 0.00 0.0 0.00 4.85 R
3039 3349 0.174845 TGGACCAGGTTTCGCTATCG 59.825 55.0 0.00 0.0 0.00 2.92 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
21 22 1.290203 CAATGGATTCCGTCAGGTCG 58.710 55.000 0.00 0.00 39.05 4.79
78 79 1.984026 TGGAGAGCCATGCAGACGA 60.984 57.895 0.00 0.00 39.92 4.20
96 97 1.686428 CGACCATCTCCTCCTCTTCCA 60.686 57.143 0.00 0.00 0.00 3.53
103 104 1.489649 CTCCTCCTCTTCCATGCATGT 59.510 52.381 24.58 0.00 0.00 3.21
105 106 1.211212 CCTCCTCTTCCATGCATGTGA 59.789 52.381 24.58 17.87 0.00 3.58
106 107 2.286872 CTCCTCTTCCATGCATGTGAC 58.713 52.381 24.58 0.00 0.00 3.67
116 117 1.448540 GCATGTGACGAGGTCCCAG 60.449 63.158 0.00 0.00 0.00 4.45
122 123 4.988716 ACGAGGTCCCAGTCGGCA 62.989 66.667 4.26 0.00 40.59 5.69
175 176 1.153289 CCATGTCAGAGAAGGCCGG 60.153 63.158 0.00 0.00 0.00 6.13
180 181 0.827368 GTCAGAGAAGGCCGGAGATT 59.173 55.000 5.05 0.00 0.00 2.40
201 202 3.647771 GGAACGGAGCTTGGGGGT 61.648 66.667 0.00 0.00 0.00 4.95
223 224 1.447314 GTGGCTAGGGTTTCGTCCG 60.447 63.158 0.00 0.00 0.00 4.79
253 257 9.325248 TGTGAATAGGGATGAATATATGTGAGA 57.675 33.333 0.00 0.00 0.00 3.27
257 261 8.774546 ATAGGGATGAATATATGTGAGATCGT 57.225 34.615 0.00 0.00 0.00 3.73
265 269 6.798427 ATATATGTGAGATCGTAATGGGCT 57.202 37.500 0.00 0.00 0.00 5.19
268 272 2.035961 TGTGAGATCGTAATGGGCTAGC 59.964 50.000 6.04 6.04 0.00 3.42
285 289 3.721625 GCGTGTGCTAGATCAGACA 57.278 52.632 0.00 0.00 38.39 3.41
288 292 2.467838 CGTGTGCTAGATCAGACATGG 58.532 52.381 0.00 0.00 31.38 3.66
330 334 0.471211 GGACTCCCCATATCCGTCCA 60.471 60.000 0.00 0.00 42.77 4.02
361 365 2.484742 GGATACAAGGGGTGTCGTTT 57.515 50.000 0.00 0.00 41.98 3.60
364 368 3.055602 GGATACAAGGGGTGTCGTTTAGT 60.056 47.826 0.00 0.00 41.98 2.24
366 370 1.071228 ACAAGGGGTGTCGTTTAGTCC 59.929 52.381 0.00 0.00 34.38 3.85
370 374 0.389037 GGGTGTCGTTTAGTCCGGAC 60.389 60.000 27.67 27.67 0.00 4.79
375 379 1.196808 GTCGTTTAGTCCGGACGTACA 59.803 52.381 28.26 12.59 37.95 2.90
379 383 0.038166 TTAGTCCGGACGTACAGGGT 59.962 55.000 28.26 11.32 34.65 4.34
383 387 3.058160 CGGACGTACAGGGTCGGT 61.058 66.667 0.00 0.00 35.24 4.69
388 392 2.291741 GGACGTACAGGGTCGGTATAAG 59.708 54.545 0.00 0.00 35.24 1.73
420 424 1.250476 GTCGCGATTTTGTGACATGC 58.750 50.000 14.06 0.00 46.15 4.06
430 434 1.078497 GTGACATGCCATGGACCGA 60.078 57.895 18.40 0.00 33.60 4.69
479 485 1.747709 TGAGTAGTCCGGCTGTAGAC 58.252 55.000 0.00 0.00 0.00 2.59
524 530 2.306847 ACCTCCAACAATTGTGTGTCC 58.693 47.619 12.82 0.00 38.27 4.02
652 687 8.622948 AAAGAAGAGTCAGGAACGAATTAATT 57.377 30.769 0.00 0.00 0.00 1.40
685 720 7.455447 GCTTTAAGTGCGCATCAAATTATTTT 58.545 30.769 15.91 0.00 0.00 1.82
686 721 7.956943 GCTTTAAGTGCGCATCAAATTATTTTT 59.043 29.630 15.91 0.00 0.00 1.94
687 722 9.464248 CTTTAAGTGCGCATCAAATTATTTTTC 57.536 29.630 15.91 0.00 0.00 2.29
688 723 8.526218 TTAAGTGCGCATCAAATTATTTTTCA 57.474 26.923 15.91 0.00 0.00 2.69
689 724 6.393720 AGTGCGCATCAAATTATTTTTCAC 57.606 33.333 15.91 0.00 0.00 3.18
690 725 5.925397 AGTGCGCATCAAATTATTTTTCACA 59.075 32.000 15.91 0.00 0.00 3.58
691 726 6.423302 AGTGCGCATCAAATTATTTTTCACAA 59.577 30.769 15.91 0.00 0.00 3.33
692 727 6.733280 GTGCGCATCAAATTATTTTTCACAAG 59.267 34.615 15.91 0.00 0.00 3.16
693 728 6.128607 TGCGCATCAAATTATTTTTCACAAGG 60.129 34.615 5.66 0.00 0.00 3.61
694 729 6.128580 GCGCATCAAATTATTTTTCACAAGGT 60.129 34.615 0.30 0.00 0.00 3.50
695 730 7.062839 GCGCATCAAATTATTTTTCACAAGGTA 59.937 33.333 0.30 0.00 0.00 3.08
696 731 8.372521 CGCATCAAATTATTTTTCACAAGGTAC 58.627 33.333 0.00 0.00 0.00 3.34
697 732 9.202273 GCATCAAATTATTTTTCACAAGGTACA 57.798 29.630 0.00 0.00 0.00 2.90
719 771 2.115291 GCCCAGCGGATTGGAGTTC 61.115 63.158 1.05 0.00 40.87 3.01
741 793 2.062177 CCGTATCCGTCCCCAACCT 61.062 63.158 0.00 0.00 0.00 3.50
771 823 7.230309 CCATTGAAACCTCTTCTTCTTCTCTTT 59.770 37.037 0.00 0.00 0.00 2.52
772 824 7.793927 TTGAAACCTCTTCTTCTTCTCTTTC 57.206 36.000 0.00 0.00 0.00 2.62
773 825 6.292150 TGAAACCTCTTCTTCTTCTCTTTCC 58.708 40.000 0.00 0.00 0.00 3.13
877 932 2.379972 CCTCTGCCCCTATATACTCCG 58.620 57.143 0.00 0.00 0.00 4.63
923 978 1.019805 GTTTCTTCCTCCTTCCGCCG 61.020 60.000 0.00 0.00 0.00 6.46
1060 1125 2.473664 CTTCTGGTCGACGGCGTTCT 62.474 60.000 16.19 0.00 38.98 3.01
1292 1369 1.593787 CATGCACTGACTCCGTCCT 59.406 57.895 0.00 0.00 0.00 3.85
1293 1370 0.459237 CATGCACTGACTCCGTCCTC 60.459 60.000 0.00 0.00 0.00 3.71
1294 1371 1.608717 ATGCACTGACTCCGTCCTCC 61.609 60.000 0.00 0.00 0.00 4.30
1295 1372 1.979693 GCACTGACTCCGTCCTCCT 60.980 63.158 0.00 0.00 0.00 3.69
1296 1373 1.536943 GCACTGACTCCGTCCTCCTT 61.537 60.000 0.00 0.00 0.00 3.36
1297 1374 0.528470 CACTGACTCCGTCCTCCTTC 59.472 60.000 0.00 0.00 0.00 3.46
1298 1375 0.961358 ACTGACTCCGTCCTCCTTCG 60.961 60.000 0.00 0.00 0.00 3.79
1363 1440 1.445238 GTCTCTGGCAGTGACGCTC 60.445 63.158 27.72 10.68 30.44 5.03
1615 1698 2.095415 CGTCGATGTACACAGACCTCAA 60.095 50.000 20.33 0.00 0.00 3.02
1638 1728 4.080299 ACCTCTTCTTCCTCTCTCTCTCTC 60.080 50.000 0.00 0.00 0.00 3.20
2074 2169 0.729690 GACCGTACCTCACCTACGTC 59.270 60.000 0.00 0.00 36.13 4.34
2112 2207 4.228237 ACCCCATCCTCATCAAGGTATA 57.772 45.455 0.00 0.00 46.32 1.47
2113 2208 4.779386 ACCCCATCCTCATCAAGGTATAT 58.221 43.478 0.00 0.00 46.32 0.86
2148 2246 3.138304 GCCCAAAGAACCAAACAAATCC 58.862 45.455 0.00 0.00 0.00 3.01
2156 2254 1.154035 CAAACAAATCCTCCGCCGC 60.154 57.895 0.00 0.00 0.00 6.53
2176 2274 0.322636 TCCGCTCCCTATCGATCTCC 60.323 60.000 0.00 0.00 0.00 3.71
2194 2292 5.576563 TCTCCAACCCAAATCTCAACTTA 57.423 39.130 0.00 0.00 0.00 2.24
2201 2299 5.953571 ACCCAAATCTCAACTTAACCTCTT 58.046 37.500 0.00 0.00 0.00 2.85
2202 2300 6.004574 ACCCAAATCTCAACTTAACCTCTTC 58.995 40.000 0.00 0.00 0.00 2.87
2254 2363 4.705023 ACCTATTTCAAACGCCAGCTATTT 59.295 37.500 0.00 0.00 0.00 1.40
2308 2483 9.733556 TGCTTACTAATTTCCTTTTCTGTGATA 57.266 29.630 0.00 0.00 0.00 2.15
2325 2500 6.929049 TCTGTGATATTATTTTCCGATTCGCT 59.071 34.615 0.00 0.00 0.00 4.93
2569 2756 0.391130 TTGCGCGATTCTGGCTAAGT 60.391 50.000 12.10 0.00 0.00 2.24
2652 2839 9.803315 AAAGGATGCATATATACATACTGTACG 57.197 33.333 10.90 0.00 36.41 3.67
2653 2840 8.521170 AGGATGCATATATACATACTGTACGT 57.479 34.615 9.56 0.00 36.08 3.57
2655 2842 9.880064 GGATGCATATATACATACTGTACGTAG 57.120 37.037 0.00 0.00 35.42 3.51
2656 2843 9.383462 GATGCATATATACATACTGTACGTAGC 57.617 37.037 0.00 0.00 35.42 3.58
2657 2844 8.271312 TGCATATATACATACTGTACGTAGCA 57.729 34.615 0.00 1.32 35.42 3.49
2659 2846 9.731819 GCATATATACATACTGTACGTAGCAAT 57.268 33.333 0.00 0.00 35.42 3.56
2665 2852 7.843490 ACATACTGTACGTAGCAATTCAATT 57.157 32.000 0.00 0.00 0.00 2.32
2666 2853 8.263940 ACATACTGTACGTAGCAATTCAATTT 57.736 30.769 0.00 0.00 0.00 1.82
2667 2854 8.175069 ACATACTGTACGTAGCAATTCAATTTG 58.825 33.333 0.00 0.00 0.00 2.32
2706 2893 0.892755 TTCCGATCACTACCGCTTGT 59.107 50.000 0.00 0.00 0.00 3.16
2712 2899 0.888619 TCACTACCGCTTGTCTCCTG 59.111 55.000 0.00 0.00 0.00 3.86
2713 2900 0.108615 CACTACCGCTTGTCTCCTGG 60.109 60.000 0.00 0.00 0.00 4.45
2739 2933 7.625185 GCTGTTGTAGAGGATTTTAAGCTTCTG 60.625 40.741 0.00 0.00 32.77 3.02
2777 2971 8.682936 ATACAGTTGTTAGATTGGATCATTCC 57.317 34.615 0.00 0.00 42.94 3.01
2930 3125 5.584649 TGAACTCCTAGTTTTGTTGTCAGTG 59.415 40.000 0.00 0.00 38.80 3.66
3039 3349 6.651755 TGTCGTTCGGTTATTAGAAATTCC 57.348 37.500 0.00 0.00 0.00 3.01
3045 3355 7.508134 GTTCGGTTATTAGAAATTCCGATAGC 58.492 38.462 14.54 8.35 44.73 2.97
3089 3399 9.922305 GGATACTATGAAAAAGAAAGTTCATCG 57.078 33.333 2.34 0.21 42.18 3.84
3100 3410 0.107017 AGTTCATCGATGGGCAAGGG 60.107 55.000 24.61 0.00 0.00 3.95
3122 3432 0.614697 AAATAGGTGCACCAAGGGCC 60.615 55.000 36.39 9.07 38.89 5.80
3124 3434 1.799157 ATAGGTGCACCAAGGGCCAA 61.799 55.000 36.39 11.93 38.89 4.52
3126 3436 2.521708 GTGCACCAAGGGCCAAGT 60.522 61.111 5.22 0.00 0.00 3.16
3127 3437 2.203480 TGCACCAAGGGCCAAGTC 60.203 61.111 6.18 0.00 0.00 3.01
3128 3438 2.203480 GCACCAAGGGCCAAGTCA 60.203 61.111 6.18 0.00 0.00 3.41
3249 4535 1.470098 GCTCAATCCAACTCGCATGTT 59.530 47.619 0.00 0.00 0.00 2.71
3250 4536 2.095059 GCTCAATCCAACTCGCATGTTT 60.095 45.455 0.00 0.00 0.00 2.83
3298 4584 2.504367 CCAGTGGGTGAACAGGTTAAG 58.496 52.381 0.00 0.00 0.00 1.85
3300 4586 1.493022 AGTGGGTGAACAGGTTAAGCA 59.507 47.619 7.52 0.00 0.00 3.91
3301 4587 2.092103 AGTGGGTGAACAGGTTAAGCAA 60.092 45.455 7.52 0.00 0.00 3.91
3302 4588 2.890945 GTGGGTGAACAGGTTAAGCAAT 59.109 45.455 7.52 0.00 0.00 3.56
3303 4589 4.076394 GTGGGTGAACAGGTTAAGCAATA 58.924 43.478 7.52 0.00 0.00 1.90
3335 4621 8.871686 ACAAGAAGATTTGCTAACGAATTTTT 57.128 26.923 0.00 0.00 29.49 1.94
3415 4704 4.426416 TCGTCACAATAATTACAGGGACG 58.574 43.478 26.01 26.01 45.73 4.79
3426 4715 2.474410 ACAGGGACGGACAAAAGATC 57.526 50.000 0.00 0.00 0.00 2.75
3427 4716 1.003233 ACAGGGACGGACAAAAGATCC 59.997 52.381 0.00 0.00 0.00 3.36
3428 4717 1.279271 CAGGGACGGACAAAAGATCCT 59.721 52.381 0.00 0.00 33.70 3.24
3429 4718 1.985895 AGGGACGGACAAAAGATCCTT 59.014 47.619 0.00 0.00 33.70 3.36
3430 4719 2.084546 GGGACGGACAAAAGATCCTTG 58.915 52.381 4.06 4.06 33.70 3.61
3431 4720 2.084546 GGACGGACAAAAGATCCTTGG 58.915 52.381 9.34 0.00 33.70 3.61
3432 4721 2.084546 GACGGACAAAAGATCCTTGGG 58.915 52.381 9.34 2.42 33.70 4.12
3433 4722 1.423921 ACGGACAAAAGATCCTTGGGT 59.576 47.619 9.34 0.00 33.70 4.51
3434 4723 2.158519 ACGGACAAAAGATCCTTGGGTT 60.159 45.455 9.34 0.00 33.70 4.11
3435 4724 2.228822 CGGACAAAAGATCCTTGGGTTG 59.771 50.000 9.34 0.00 33.70 3.77
3436 4725 3.230976 GGACAAAAGATCCTTGGGTTGT 58.769 45.455 9.34 2.61 33.03 3.32
3437 4726 3.005791 GGACAAAAGATCCTTGGGTTGTG 59.994 47.826 9.34 0.00 33.03 3.33
3438 4727 3.888930 GACAAAAGATCCTTGGGTTGTGA 59.111 43.478 9.34 0.00 29.75 3.58
3439 4728 3.891366 ACAAAAGATCCTTGGGTTGTGAG 59.109 43.478 9.34 0.00 0.00 3.51
3440 4729 2.887151 AAGATCCTTGGGTTGTGAGG 57.113 50.000 0.00 0.00 0.00 3.86
3441 4730 1.747444 AGATCCTTGGGTTGTGAGGT 58.253 50.000 0.00 0.00 32.33 3.85
3442 4731 2.065799 AGATCCTTGGGTTGTGAGGTT 58.934 47.619 0.00 0.00 32.33 3.50
3443 4732 2.162681 GATCCTTGGGTTGTGAGGTTG 58.837 52.381 0.00 0.00 32.33 3.77
3444 4733 0.923358 TCCTTGGGTTGTGAGGTTGT 59.077 50.000 0.00 0.00 32.33 3.32
3445 4734 1.032014 CCTTGGGTTGTGAGGTTGTG 58.968 55.000 0.00 0.00 0.00 3.33
3446 4735 1.409521 CCTTGGGTTGTGAGGTTGTGA 60.410 52.381 0.00 0.00 0.00 3.58
3447 4736 1.949525 CTTGGGTTGTGAGGTTGTGAG 59.050 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.017387 GACCTGACGGAATCCATTGC 58.983 55.000 0.00 0.00 0.00 3.56
2 3 1.134818 TCGACCTGACGGAATCCATTG 60.135 52.381 0.00 0.00 0.00 2.82
3 4 1.134788 GTCGACCTGACGGAATCCATT 60.135 52.381 3.51 0.00 37.96 3.16
4 5 0.460311 GTCGACCTGACGGAATCCAT 59.540 55.000 3.51 0.00 37.96 3.41
5 6 1.888018 GTCGACCTGACGGAATCCA 59.112 57.895 3.51 0.00 37.96 3.41
6 7 4.808649 GTCGACCTGACGGAATCC 57.191 61.111 3.51 0.00 37.96 3.01
53 54 3.474570 ATGGCTCTCCACCGCTCC 61.475 66.667 0.00 0.00 46.92 4.70
57 58 2.513204 CTGCATGGCTCTCCACCG 60.513 66.667 0.00 0.00 46.92 4.94
73 74 0.923358 AGAGGAGGAGATGGTCGTCT 59.077 55.000 0.00 0.00 39.60 4.18
78 79 2.406559 CATGGAAGAGGAGGAGATGGT 58.593 52.381 0.00 0.00 0.00 3.55
96 97 1.221840 GGGACCTCGTCACATGCAT 59.778 57.895 0.00 0.00 35.79 3.96
103 104 2.675423 CCGACTGGGACCTCGTCA 60.675 66.667 12.18 0.00 38.47 4.35
105 106 4.988716 TGCCGACTGGGACCTCGT 62.989 66.667 1.47 0.00 38.47 4.18
106 107 4.135153 CTGCCGACTGGGACCTCG 62.135 72.222 0.00 0.00 38.47 4.63
116 117 3.883997 GATCTCCTGATCTGCCGAC 57.116 57.895 0.00 0.00 44.19 4.79
143 144 0.034863 ACATGGCGGGTAACGGATTT 60.035 50.000 0.00 0.00 44.51 2.17
188 189 4.101448 CTCCACCCCCAAGCTCCG 62.101 72.222 0.00 0.00 0.00 4.63
189 190 2.936032 ACTCCACCCCCAAGCTCC 60.936 66.667 0.00 0.00 0.00 4.70
201 202 0.834687 ACGAAACCCTAGCCACTCCA 60.835 55.000 0.00 0.00 0.00 3.86
209 210 0.104304 CATCCCGGACGAAACCCTAG 59.896 60.000 0.73 0.00 0.00 3.02
223 224 8.497745 ACATATATTCATCCCTATTCACATCCC 58.502 37.037 0.00 0.00 0.00 3.85
251 255 1.000163 CACGCTAGCCCATTACGATCT 60.000 52.381 9.66 0.00 0.00 2.75
253 257 0.750850 ACACGCTAGCCCATTACGAT 59.249 50.000 9.66 0.00 0.00 3.73
257 261 4.532490 GCACACGCTAGCCCATTA 57.468 55.556 9.66 0.00 34.30 1.90
268 272 2.467838 CCATGTCTGATCTAGCACACG 58.532 52.381 0.00 0.00 0.00 4.49
279 283 4.794439 CGCGTCCGCCATGTCTGA 62.794 66.667 6.04 0.00 37.98 3.27
327 331 5.455183 CCTTGTATCCAGCACATATCTTGGA 60.455 44.000 0.00 0.00 0.00 3.53
330 334 4.202503 CCCCTTGTATCCAGCACATATCTT 60.203 45.833 0.00 0.00 0.00 2.40
356 360 1.464608 CTGTACGTCCGGACTAAACGA 59.535 52.381 30.92 14.78 39.59 3.85
358 362 1.135286 CCCTGTACGTCCGGACTAAAC 60.135 57.143 30.92 23.92 0.00 2.01
359 363 1.176527 CCCTGTACGTCCGGACTAAA 58.823 55.000 30.92 16.28 0.00 1.85
361 365 0.392998 GACCCTGTACGTCCGGACTA 60.393 60.000 30.92 19.07 0.00 2.59
364 368 2.747460 CGACCCTGTACGTCCGGA 60.747 66.667 0.00 0.00 0.00 5.14
366 370 1.097547 ATACCGACCCTGTACGTCCG 61.098 60.000 0.00 0.00 0.00 4.79
370 374 1.610522 CCCTTATACCGACCCTGTACG 59.389 57.143 0.00 0.00 0.00 3.67
375 379 1.052694 GCACCCCTTATACCGACCCT 61.053 60.000 0.00 0.00 0.00 4.34
379 383 2.799452 GCCGCACCCCTTATACCGA 61.799 63.158 0.00 0.00 0.00 4.69
383 387 2.448582 CCCAGCCGCACCCCTTATA 61.449 63.158 0.00 0.00 0.00 0.98
420 424 1.447838 CAGACGGTTCGGTCCATGG 60.448 63.158 4.97 4.97 37.66 3.66
497 503 6.094719 CACACAATTGTTGGAGGTATCATTG 58.905 40.000 8.77 0.00 31.66 2.82
498 504 5.774690 ACACACAATTGTTGGAGGTATCATT 59.225 36.000 8.77 0.00 31.66 2.57
524 530 6.208644 CAACCAGTTTTGACATGTTTCCTAG 58.791 40.000 0.00 0.00 0.00 3.02
652 687 2.104253 GCACTTAAAGCGCCGCCTA 61.104 57.895 4.98 0.00 0.00 3.93
685 720 3.884895 CTGGGCATATGTACCTTGTGAA 58.115 45.455 16.28 0.00 0.00 3.18
686 721 2.421388 GCTGGGCATATGTACCTTGTGA 60.421 50.000 16.28 0.00 0.00 3.58
687 722 1.949525 GCTGGGCATATGTACCTTGTG 59.050 52.381 16.28 7.90 0.00 3.33
688 723 1.475034 CGCTGGGCATATGTACCTTGT 60.475 52.381 16.28 0.00 0.00 3.16
689 724 1.229428 CGCTGGGCATATGTACCTTG 58.771 55.000 16.28 11.42 0.00 3.61
690 725 0.108585 CCGCTGGGCATATGTACCTT 59.891 55.000 16.28 0.00 0.00 3.50
691 726 0.762842 TCCGCTGGGCATATGTACCT 60.763 55.000 16.28 0.00 0.00 3.08
692 727 0.324943 ATCCGCTGGGCATATGTACC 59.675 55.000 4.29 8.00 0.00 3.34
693 728 1.806542 CAATCCGCTGGGCATATGTAC 59.193 52.381 4.29 0.00 0.00 2.90
694 729 1.271325 CCAATCCGCTGGGCATATGTA 60.271 52.381 4.29 0.00 32.32 2.29
695 730 0.538057 CCAATCCGCTGGGCATATGT 60.538 55.000 4.29 0.00 32.32 2.29
696 731 0.250858 TCCAATCCGCTGGGCATATG 60.251 55.000 0.00 0.00 37.06 1.78
697 732 0.037303 CTCCAATCCGCTGGGCATAT 59.963 55.000 0.00 0.00 37.06 1.78
698 733 1.344953 ACTCCAATCCGCTGGGCATA 61.345 55.000 0.00 0.00 37.06 3.14
699 734 2.194056 CTCCAATCCGCTGGGCAT 59.806 61.111 0.00 0.00 37.06 4.40
700 735 2.819984 GAACTCCAATCCGCTGGGCA 62.820 60.000 0.00 0.00 37.06 5.36
701 736 2.044946 AACTCCAATCCGCTGGGC 60.045 61.111 0.00 0.00 37.06 5.36
741 793 2.358258 AGAAGAGGTTTCAATGGGGGA 58.642 47.619 0.00 0.00 0.00 4.81
773 825 8.550359 TGCGATTGAGCTTTTTCGTTTATTACG 61.550 37.037 12.64 0.00 43.87 3.18
877 932 4.298763 GTCGAGTAATCGGCGACC 57.701 61.111 13.76 2.91 46.15 4.79
888 943 5.049405 GGAAGAAACAACAATGATGTCGAGT 60.049 40.000 0.00 0.00 39.40 4.18
923 978 7.201487 CGATATGATATAGAGGGACGATCGATC 60.201 44.444 24.34 15.68 35.64 3.69
1292 1369 1.171308 CGTACAGGAAGGACGAAGGA 58.829 55.000 0.00 0.00 38.88 3.36
1293 1370 0.458025 GCGTACAGGAAGGACGAAGG 60.458 60.000 3.74 0.00 38.88 3.46
1294 1371 0.242825 TGCGTACAGGAAGGACGAAG 59.757 55.000 3.74 0.00 38.88 3.79
1295 1372 0.038892 GTGCGTACAGGAAGGACGAA 60.039 55.000 3.74 0.00 38.88 3.85
1296 1373 1.582968 GTGCGTACAGGAAGGACGA 59.417 57.895 3.74 0.00 38.88 4.20
1297 1374 1.800315 CGTGCGTACAGGAAGGACG 60.800 63.158 4.09 0.00 43.85 4.79
1298 1375 0.319297 AACGTGCGTACAGGAAGGAC 60.319 55.000 4.09 0.00 35.62 3.85
1615 1698 3.852578 AGAGAGAGAGAGGAAGAAGAGGT 59.147 47.826 0.00 0.00 0.00 3.85
2074 2169 2.550208 GGGGTAGTCTGTTGTCAAGGTG 60.550 54.545 0.00 0.00 0.00 4.00
2112 2207 4.767928 TCTTTGGGCGTATGGTTACAAAAT 59.232 37.500 0.00 0.00 0.00 1.82
2113 2208 4.142790 TCTTTGGGCGTATGGTTACAAAA 58.857 39.130 0.00 0.00 0.00 2.44
2156 2254 1.091537 GAGATCGATAGGGAGCGGAG 58.908 60.000 0.00 0.00 34.49 4.63
2176 2274 5.770162 AGAGGTTAAGTTGAGATTTGGGTTG 59.230 40.000 0.00 0.00 0.00 3.77
2228 2337 3.007635 GCTGGCGTTTGAAATAGGTACT 58.992 45.455 0.00 0.00 46.37 2.73
2265 2374 5.968582 AGTAAGCACGCATATGCATACAGAA 60.969 40.000 26.52 4.17 46.96 3.02
2266 2375 4.501400 AGTAAGCACGCATATGCATACAGA 60.501 41.667 26.52 5.43 46.96 3.41
2267 2376 3.742882 AGTAAGCACGCATATGCATACAG 59.257 43.478 26.52 12.64 46.96 2.74
2273 2382 5.049405 AGGAAATTAGTAAGCACGCATATGC 60.049 40.000 18.08 18.08 46.50 3.14
2274 2383 6.545504 AGGAAATTAGTAAGCACGCATATG 57.454 37.500 0.00 0.00 0.00 1.78
2275 2384 7.568199 AAAGGAAATTAGTAAGCACGCATAT 57.432 32.000 0.00 0.00 0.00 1.78
2276 2385 6.995511 AAAGGAAATTAGTAAGCACGCATA 57.004 33.333 0.00 0.00 0.00 3.14
2277 2386 5.897377 AAAGGAAATTAGTAAGCACGCAT 57.103 34.783 0.00 0.00 0.00 4.73
2278 2387 5.472137 AGAAAAGGAAATTAGTAAGCACGCA 59.528 36.000 0.00 0.00 0.00 5.24
2279 2388 5.795441 CAGAAAAGGAAATTAGTAAGCACGC 59.205 40.000 0.00 0.00 0.00 5.34
2280 2389 6.797033 CACAGAAAAGGAAATTAGTAAGCACG 59.203 38.462 0.00 0.00 0.00 5.34
2437 2618 0.107508 ATGGATCGGTCACTTGGCAG 60.108 55.000 0.00 0.00 0.00 4.85
2448 2629 6.256539 GCAAGATATGTATGTACATGGATCGG 59.743 42.308 18.81 12.42 45.77 4.18
2450 2631 8.663025 CAAGCAAGATATGTATGTACATGGATC 58.337 37.037 18.81 13.81 45.77 3.36
2527 2713 1.422950 CGGCGGGTTTGTACATACGG 61.423 60.000 9.88 6.18 0.00 4.02
2528 2714 0.737019 ACGGCGGGTTTGTACATACG 60.737 55.000 13.24 7.34 0.00 3.06
2554 2741 4.634443 TCCTTTTTACTTAGCCAGAATCGC 59.366 41.667 0.00 0.00 0.00 4.58
2651 2838 6.303970 CACAAGAGTCAAATTGAATTGCTACG 59.696 38.462 13.39 0.00 0.00 3.51
2652 2839 6.088616 GCACAAGAGTCAAATTGAATTGCTAC 59.911 38.462 9.64 0.00 0.00 3.58
2653 2840 6.151691 GCACAAGAGTCAAATTGAATTGCTA 58.848 36.000 9.64 0.00 0.00 3.49
2655 2842 4.746115 TGCACAAGAGTCAAATTGAATTGC 59.254 37.500 9.89 9.89 0.00 3.56
2656 2843 6.210796 TCTGCACAAGAGTCAAATTGAATTG 58.789 36.000 12.41 12.41 0.00 2.32
2657 2844 6.395426 TCTGCACAAGAGTCAAATTGAATT 57.605 33.333 0.00 0.00 0.00 2.17
2659 2846 5.833406 TTCTGCACAAGAGTCAAATTGAA 57.167 34.783 0.00 0.00 35.91 2.69
2660 2847 5.125257 TGTTTCTGCACAAGAGTCAAATTGA 59.875 36.000 0.00 0.00 35.91 2.57
2661 2848 5.230726 GTGTTTCTGCACAAGAGTCAAATTG 59.769 40.000 0.00 0.00 39.07 2.32
2662 2849 5.126061 AGTGTTTCTGCACAAGAGTCAAATT 59.874 36.000 0.00 0.00 41.52 1.82
2663 2850 4.641989 AGTGTTTCTGCACAAGAGTCAAAT 59.358 37.500 0.00 0.00 41.52 2.32
2664 2851 4.009675 AGTGTTTCTGCACAAGAGTCAAA 58.990 39.130 0.00 0.00 41.52 2.69
2665 2852 3.609853 AGTGTTTCTGCACAAGAGTCAA 58.390 40.909 0.00 0.00 41.52 3.18
2666 2853 3.266510 AGTGTTTCTGCACAAGAGTCA 57.733 42.857 0.00 0.00 41.52 3.41
2667 2854 4.496507 GGAAAGTGTTTCTGCACAAGAGTC 60.497 45.833 0.00 0.00 41.52 3.36
2706 2893 1.077169 TCCTCTACAACAGCCAGGAGA 59.923 52.381 0.00 0.00 0.00 3.71
2712 2899 4.944317 AGCTTAAAATCCTCTACAACAGCC 59.056 41.667 0.00 0.00 0.00 4.85
2713 2900 6.372937 AGAAGCTTAAAATCCTCTACAACAGC 59.627 38.462 0.00 0.00 0.00 4.40
2739 2933 5.613358 ACAACTGTATAAGCAGCAAGAAC 57.387 39.130 0.00 0.00 39.96 3.01
2777 2971 5.054390 ACACCAAAACGGCATTATAACAG 57.946 39.130 0.00 0.00 39.03 3.16
2930 3125 1.074752 GCGCCTATTGCTAGCAGATC 58.925 55.000 18.45 6.05 38.05 2.75
3039 3349 0.174845 TGGACCAGGTTTCGCTATCG 59.825 55.000 0.00 0.00 0.00 2.92
3045 3355 0.881118 CCAACATGGACCAGGTTTCG 59.119 55.000 21.47 11.53 40.96 3.46
3067 3377 8.454106 CCATCGATGAACTTTCTTTTTCATAGT 58.546 33.333 26.86 0.00 41.52 2.12
3068 3378 7.912250 CCCATCGATGAACTTTCTTTTTCATAG 59.088 37.037 26.86 3.02 41.52 2.23
3086 3396 0.614415 TTTTGCCCTTGCCCATCGAT 60.614 50.000 0.00 0.00 36.33 3.59
3089 3399 1.413812 CCTATTTTGCCCTTGCCCATC 59.586 52.381 0.00 0.00 36.33 3.51
3100 3410 1.066929 CCCTTGGTGCACCTATTTTGC 60.067 52.381 34.75 7.98 40.63 3.68
3122 3432 1.000283 AGTGAAGACGAGCCTGACTTG 60.000 52.381 0.00 0.00 35.67 3.16
3124 3434 0.600557 CAGTGAAGACGAGCCTGACT 59.399 55.000 0.00 0.00 0.00 3.41
3126 3436 1.290324 GCAGTGAAGACGAGCCTGA 59.710 57.895 0.00 0.00 0.00 3.86
3127 3437 0.601046 TTGCAGTGAAGACGAGCCTG 60.601 55.000 0.00 0.00 0.00 4.85
3128 3438 0.601311 GTTGCAGTGAAGACGAGCCT 60.601 55.000 0.00 0.00 0.00 4.58
3303 4589 9.959749 TCGTTAGCAAATCTTCTTGTTTTATTT 57.040 25.926 0.00 0.00 0.00 1.40
3335 4621 9.930158 AAAGGCTAAACCCAACATATAGATTTA 57.070 29.630 0.00 0.00 40.58 1.40
3388 4677 7.280205 GTCCCTGTAATTATTGTGACGATTTCT 59.720 37.037 0.00 0.00 0.00 2.52
3389 4678 7.407337 GTCCCTGTAATTATTGTGACGATTTC 58.593 38.462 0.00 0.00 0.00 2.17
3404 4693 4.514401 GATCTTTTGTCCGTCCCTGTAAT 58.486 43.478 0.00 0.00 0.00 1.89
3408 4697 1.279271 AGGATCTTTTGTCCGTCCCTG 59.721 52.381 0.00 0.00 40.76 4.45
3415 4704 3.005791 CACAACCCAAGGATCTTTTGTCC 59.994 47.826 8.85 0.00 35.94 4.02
3426 4715 1.032014 CACAACCTCACAACCCAAGG 58.968 55.000 0.00 0.00 36.21 3.61
3427 4716 1.949525 CTCACAACCTCACAACCCAAG 59.050 52.381 0.00 0.00 0.00 3.61
3428 4717 2.051334 CTCACAACCTCACAACCCAA 57.949 50.000 0.00 0.00 0.00 4.12
3429 4718 3.798794 CTCACAACCTCACAACCCA 57.201 52.632 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.