Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007791.1 Hibiscus syriacus cultivar Beakdansim tig00110077_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 59398
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:14008 original size:15 final size:15
Alignment explanation
Indices: 13973--14009 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
13963 TTAACTGTAT
*
13973 TCATTTATGTTTTTA
1 TCATTTATGTTTTCA
13988 TACATTTATGTTTTCA
1 T-CATTTATGTTTTCA
14004 TCATTT
1 TCATTT
14010 GAGTTAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62
Consensus pattern (15 bp):
TCATTTATGTTTTCA
Found at i:15986 original size:13 final size:13
Alignment explanation
Indices: 15968--16015 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
15958 TGCGTCATAA
*
15968 ATTTATTACACGC
1 ATTTATGACACGC
15981 ATTTATGACACGC
1 ATTTATGACACGC
15994 ATTTATGACGA-GC
1 ATTTATGAC-ACGC
16007 ATTTATGAC
1 ATTTATGAC
16016 GCTCATTGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
13 32 0.97
14 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:16022 original size:13 final size:13
Alignment explanation
Indices: 15968--16022 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
15958 TGCGTCATAA
* *
15968 ATTTATTACACGC
1 ATTTATGACGCGC
*
15981 ATTTATGACACGC
1 ATTTATGACGCGC
*
15994 ATTTATGACGAGC
1 ATTTATGACGCGC
*
16007 ATTTATGACGCTC
1 ATTTATGACGCGC
16020 ATT
1 ATT
16023 GCGCGTCATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:16181 original size:2 final size:2
Alignment explanation
Indices: 16174--16209 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
16164 GTATTTCGTA
16174 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16210 GTAGATTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20874 original size:59 final size:59
Alignment explanation
Indices: 20803--21149 Score: 527
Period size: 59 Copynumber: 5.9 Consensus size: 59
20793 TTCCCATAAA
* * * *
20803 GAAATTCATACACCTAATATGAATTTCTTAACATGTTT-GCACACAAAGTGCCCAACACG
1 GAAATTCATACACTTAGTATGAATTTCTTAACAT-TTTAGCACACATAGTGCCCAATACG
*
20862 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTG-CTAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACG
* * * * *
20920 AAAATTCGTACACTTAGTATGAGTTTCTTAATATTTTAGCACACATAGTGCCCAATATG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACG
* * *
20979 GAAATTCATATACTTAGTATGAAATTCTTAACATTTTAGCACACATAGTGCCCAATATG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACG
*
21038 GAAATTCATACACTCAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACG
*
21097 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTAGCACACTTAGTGCC
1 GAAATTCATACACTTAGTATGAATTTCTTAACA-TTTTAGCACACATAGTGCC
21150 ATTCGGTAAT
Statistics
Matches: 262, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
58 55 0.21
59 189 0.72
60 18 0.07
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (59 bp):
GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACG
Found at i:20947 original size:117 final size:117
Alignment explanation
Indices: 20804--21150 Score: 525
Period size: 117 Copynumber: 2.9 Consensus size: 117
20794 TCCCATAAAG
* * * *
20804 AAATTCATACACCTAATATGAATTTCTTAACATGTTT-GCACACAAAGTGCCCAACACGGAAATT
1 AAATTCATACACTTAGTATGAATTTCTTAACAT-TTTAGCACACATAGTGCCCAATACGGAAATT
*
20868 CATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCTAATACGA
65 CATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCAATACGA
* * * *
20921 AAATTCGTACACTTAGTATGAGTTTCTTAATATTTTAGCACACATAGTGCCCAATATGGAAATTC
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGGAAATTC
* * * *
20986 ATATACTTAGTATGAAATTCTTAACATTTTAGCACACATAGTGCCCAATATGG
66 ATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTG-CCAATACGA
*
21039 AAATTCATACACTCAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGGAAATTC
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGGAAATTC
*
21104 ATACACTTAGTATGAATTTCTTAACATTTTTAGCACACTTAGTGCCA
66 ATACACTTAGTATGAATTTCTTAACA-TTTTAGCACACATAGTGCCA
21151 TTCGGTAATC
Statistics
Matches: 206, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
116 3 0.01
117 94 0.46
118 93 0.45
119 16 0.08
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (117 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGGAAATTC
ATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCAATACGA
Found at i:23146 original size:29 final size:28
Alignment explanation
Indices: 23102--23235 Score: 169
Period size: 29 Copynumber: 4.6 Consensus size: 28
23092 GGAAAATTAT
** * *
23102 TTTATAAATTTTAATAAAGGACAAAATT
1 TTTATAAATTACAATAAAGTACAAAATA
* *
23130 TGTTATAAATTACAATAACGTACACAACTA
1 T-TTATAAATTACAATAAAGTACA-AAATA
23160 TTTATAAATTACAATAAAGTACAAAATAA
1 TTTATAAATTACAATAAAGTACAAAAT-A
*
23189 TTTATAAATTACAATAAAATACAAAACTA
1 TTTATAAATTACAATAAAGTACAAAA-TA
23218 TTTATAAATTACAATAAA
1 TTTATAAATTACAATAAA
23236 AGATAAAACC
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
28 4 0.04
29 84 0.90
30 5 0.05
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.34
Consensus pattern (28 bp):
TTTATAAATTACAATAAAGTACAAAATA
Found at i:23165 original size:58 final size:58
Alignment explanation
Indices: 23102--23235 Score: 189
Period size: 58 Copynumber: 2.3 Consensus size: 58
23092 GGAAAATTAT
** * ** *
23102 TTTATAAATTTTAATAAAGGACAAAAT-TTGTTATAAATTACAATAACGTACACAACTA
1 TTTATAAATTACAATAAAGGACAAAATAAT-TTATAAATTACAATAAAATACAAAACTA
*
23160 TTTATAAATTACAATAAAGTACAAAATAATTTATAAATTACAATAAAATACAAAACTA
1 TTTATAAATTACAATAAAGGACAAAATAATTTATAAATTACAATAAAATACAAAACTA
23218 TTTATAAATTACAATAAA
1 TTTATAAATTACAATAAA
23236 AGATAAAACC
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 67 0.99
59 1 0.01
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.34
Consensus pattern (58 bp):
TTTATAAATTACAATAAAGGACAAAATAATTTATAAATTACAATAAAATACAAAACTA
Found at i:23236 original size:29 final size:29
Alignment explanation
Indices: 23132--23265 Score: 164
Period size: 29 Copynumber: 4.6 Consensus size: 29
23122 ACAAAATTTG
** *
23132 TTATAAATTACAATAACGTACACAACTAT
1 TTATAAATTACAATAAAATACAAAACTAT
*
23161 TTATAAATTACAATAAAGTACAAAA-TAAT
1 TTATAAATTACAATAAAATACAAAACT-AT
23190 TTATAAATTACAATAAAATACAAAACTAT
1 TTATAAATTACAATAAAATACAAAACTAT
* *
23219 TTATAAATTACAATAAAAGATAAAACCT-T
1 TTATAAATTACAATAAAATACAAAA-CTAT
* *
23248 TTATAAATCATAATAAAA
1 TTATAAATTACAATAAAA
23266 GGAGACAATT
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
28 1 0.01
29 91 0.96
30 3 0.03
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (29 bp):
TTATAAATTACAATAAAATACAAAACTAT
Found at i:23251 original size:87 final size:84
Alignment explanation
Indices: 23021--23264 Score: 206
Period size: 87 Copynumber: 2.8 Consensus size: 84
23011 AAAAATCATC
* ** * * * *
23021 AAATTACAATAAAAGACAAAATGTTT-TAAAATTTGTAATAAAAGTTTAAACTTTTTAGAATTTA
1 AAATTACAATAAAAGACAAAATATTTAT-AAA-TTACAATAAAAG-TAAAACCTTTTATAAATTA
* * *
23085 CAGTAAAGGAAAATTATTTTAT
63 CAATAAAGGAAAAATAATTTAT
** * * *
23107 AAATTTTAATAAAGGACAAAATTTGTTATAAATTACAAT-AACGTACACAA-CTATTTATAAATT
1 AAATTACAATAAAAGACAAAATAT-TTATAAATTACAATAAAAGTA-A-AACCT-TTTATAAATT
*
23170 ACAATAAAGTACAAAATAATTTAT
62 ACAATAAAGGA-AAAATAATTTAT
* * *
23194 AAATTACAATAAAATACAAAACTATTTATAAATTACAATAAAAGATAAAACCTTTTATAAATCAT
1 AAATTACAATAAAAGACAAAA-TATTTATAAATTACAATAAAAG-TAAAACCTTTTATAAATTAC
23259 AATAAA
64 AATAAA
23265 AGGAGACAAT
Statistics
Matches: 125, Mismatches: 23, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
84 1 0.01
85 5 0.04
86 44 0.35
87 64 0.51
88 9 0.07
89 2 0.02
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.34
Consensus pattern (84 bp):
AAATTACAATAAAAGACAAAATATTTATAAATTACAATAAAAGTAAAACCTTTTATAAATTACAA
TAAAGGAAAAATAATTTAT
Found at i:23266 original size:29 final size:29
Alignment explanation
Indices: 23102--23266 Score: 160
Period size: 29 Copynumber: 5.7 Consensus size: 29
23092 GGAAAATTAT
** * *
23102 TTTATAAATTTTAATAAAGGACAAAA-TT
1 TTTATAAATTACAATAAAAGACAAAACTA
* *
23130 TGTTATAAATTACAAT-AACGTACACAACTA
1 T-TTATAAATTACAATAAAAG-ACAAAACTA
23160 TTTATAAATTACAAT-AAAGTACAAAA-TAA
1 TTTATAAATTACAATAAAAG-ACAAAACT-A
*
23189 TTTATAAATTACAATAAAATACAAAACTA
1 TTTATAAATTACAATAAAAGACAAAACTA
*
23218 TTTATAAATTACAATAAAAGATAAAACCT-
1 TTTATAAATTACAATAAAAGACAAAA-CTA
* *
23247 TTTATAAATCATAATAAAAG
1 TTTATAAATTACAATAAAAG
23267 GAGACAATTT
Statistics
Matches: 118, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
28 5 0.04
29 105 0.89
30 8 0.07
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (29 bp):
TTTATAAATTACAATAAAAGACAAAACTA
Found at i:34947 original size:13 final size:13
Alignment explanation
Indices: 34929--34953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34919 AATGAATTTT
34929 AAGATTTTCTAAA
1 AAGATTTTCTAAA
34942 AAGATTTTCTAA
1 AAGATTTTCTAA
34954 GTATATTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Found at i:38111 original size:33 final size:34
Alignment explanation
Indices: 38074--38144 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
38064 CCTTTACAAC
*
38074 TCCCTAG-TTTT-TCACGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTAT-ACGGGATAAACTAGAACATT
* * *
38107 TCCCTAGCTTTTATACGGGTTTAGCTAGAACATT
1 TCCCTAGCTTTTATACGGGATAAACTAGAACATT
38141 TCCC
1 TCCC
38145 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 7 0.22
34 24 0.75
35 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.35
Consensus pattern (34 bp):
TCCCTAGCTTTTATACGGGATAAACTAGAACATT
Found at i:38680 original size:36 final size:37
Alignment explanation
Indices: 38611--38680 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
38601 CAATCATAGA
* * *
38611 TGTATGGATACACCTGCTGGGGGTATCGGTACACCAG
1 TGTATGGATACACCTGATAGGGGTATCGATACACCAG
*
38648 TGTATGGATACA-CTTATAGGGGTATCGATACAC
1 TGTATGGATACACCTGATAGGGGTATCGATACAC
38681 ATTTGCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 17 0.59
37 12 0.41
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27
Consensus pattern (37 bp):
TGTATGGATACACCTGATAGGGGTATCGATACACCAG
Found at i:43189 original size:59 final size:59
Alignment explanation
Indices: 43117--43638 Score: 726
Period size: 59 Copynumber: 9.0 Consensus size: 59
43107 TATATTTCCC
* * * *
43117 ATACGGAAATTCATACACCTAGTATGAATTTCTTAACATGTTT-GCAAACAAAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACAT-TTTAGCACACATAGTGCCCA
* * * *
43176 ATACGAAAATTCATGCACTTAATATGAATTTCTTAACATTTTTAGCACACTTACTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACA-TTTTAGCACACATAGTGCCCA
* *
43236 ATAC-AGAAATTCATACACTTAGTATGAATTTCTTAACATTTTATCACACATAGTTCCCA
1 ATACGA-AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* *
43295 ATACGAAAATTCATATATTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* *
43354 ATACGGAAATTCATATACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
43413 ATACGAAAATTCAT--AC------TGAATTTCTTAACATTTTAGCACACATAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* ** *
43464 ATACGAAAATTCATACCCTTAGTATGAATTTCTTTTCATTTTAGCATACATAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
*
43523 ATAC-AGAAATTCATACACTTAGTATGAATTTATTAACATTTTAGCACACATAGTGCCCA
1 ATACGA-AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* *
43582 ATACTG-AAATCCATACACTTAGTATGAATTTCTTAACATTTTAGCACACTTAGTGCC
1 ATAC-GAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCC
43639 ATTTGGTAAT
Statistics
Matches: 415, Mismatches: 33, Indels: 30
0.87 0.07 0.06
Matches are distributed among these distances:
51 49 0.12
53 1 0.00
57 2 0.00
58 1 0.00
59 314 0.76
60 48 0.12
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (59 bp):
ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
Found at i:43517 original size:228 final size:231
Alignment explanation
Indices: 43117--43638 Score: 759
Period size: 228 Copynumber: 2.2 Consensus size: 231
43107 TATATTTCCC
* * *
43117 ATACGGAAATTCATACACCTAGTATGAATTTCTTAACATGTTT-GCAAACAAAGTGCCCAATACG
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACAT-TTTAGCACACATAGTGCCCAATACG
*
43181 AAAATTCATGCACTTAATATGAATTTCTTAACATTTTTAGCACACTTACTGCCCAATACAGAAAT
65 AAAATTCAT-CAC-----ATGAATTTCTTAACATTTTTAGCACACATACTGCCCAATACAGAAAT
* *
43246 TCATACACTTAGTATGAATTTCTTAACATTTTATCACACATAGTTCCCAATAC-GAAAATTCATA
124 TCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACAG-AAATTCATA
* * *
43310 TATTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
188 CACTTAGTATGAATTTATTAACATTTTAGCACACATAGTGCCCA
*
43354 ATACGGAAATTCATATACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGA
*
43419 AAATTCAT-AC-TGAATTTCTTAACA-TTTTAGCACACATAGTGCCCAATAC-GAAAATTCATAC
66 AAATTCATCACATGAATTTCTTAACATTTTTAGCACACATACTGCCCAATACAG-AAATTCATAC
* ** *
43480 CCTTAGTATGAATTTCTTTTCATTTTAGCATACATAGTGCCCAATACAGAAATTCATACACTTAG
130 ACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACAGAAATTCATACACTTAG
43545 TATGAATTTATTAACATTTTAGCACACATAGTGCCCA
195 TATGAATTTATTAACATTTTAGCACACATAGTGCCCA
* * *
43582 ATACTGAAATCCATACACTTAGTATGAATTTCTTAACATTTTAGCACACTTAGTGCC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCC
43639 ATTTGGTAAT
Statistics
Matches: 263, Mismatches: 19, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
227 1 0.00
228 177 0.67
229 15 0.06
235 2 0.01
236 3 0.01
237 65 0.25
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (231 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGA
AAATTCATCACATGAATTTCTTAACATTTTTAGCACACATACTGCCCAATACAGAAATTCATACA
CTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACAGAAATTCATACACTTAGT
ATGAATTTATTAACATTTTAGCACACATAGTGCCCA
Found at i:46221 original size:21 final size:21
Alignment explanation
Indices: 46197--46250 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
46187 TATCGCAAAT
46197 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGGAAA
46218 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGGAAA
46239 TCGCGTTGCGAT
1 TCGCGTTGCGAT
46251 GGTCTACAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGGAAA
Found at i:46306 original size:20 final size:21
Alignment explanation
Indices: 46281--46332 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
46271 TTTTCCCAAT
*
46281 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
46301 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGAAAAA
46322 TCGCAATGCGA
1 TCGCAATGCGA
46333 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:46394 original size:20 final size:20
Alignment explanation
Indices: 46322--46393 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
46312 ATTGGAAAAA
* *
46322 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
*
46342 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
46362 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
46382 TCGCAACGCGAT
1 TCGCAACGCGAT
46394 TTACATAGCG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:46948 original size:19 final size:19
Alignment explanation
Indices: 46910--46976 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
46900 TTCGAGAATG
46910 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
46930 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* *
46949 AAAAACGCAACGCGAAACA
1 AAAATCGCAACGCGAAATA
46968 AAAATCGCA
1 AAAATCGCA
46977 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.51, C:0.24, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:46994 original size:19 final size:19
Alignment explanation
Indices: 46972--47136 Score: 125
Period size: 19 Copynumber: 9.1 Consensus size: 19
46962 GAAACAAAAA
*
46972 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
46991 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
47010 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
47029 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
47043 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
47062 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* ** **
47076 TCTCAATGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
47095 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
47115 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
47135 TC
1 TC
47137 AACCAAAAGA
Statistics
Matches: 114, Mismatches: 20, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
14 17 0.15
16 4 0.04
17 5 0.04
19 58 0.51
20 29 0.25
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:47061 original size:33 final size:33
Alignment explanation
Indices: 47024--47111 Score: 142
Period size: 33 Copynumber: 2.6 Consensus size: 33
47014 GTTGCGATTT
*
47024 TCATTTCGCGTTGCGATTCTCTC-GTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCAAT-GCGATAG
47057 TCATTTCGCGTTGCGATTCTCTCAATGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCAATGCGATAG
47090 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
47112 ATTATCTCGT
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
33 36 0.69
34 16 0.31
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.38
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCAATGCGATAG
Found at i:47113 original size:20 final size:20
Alignment explanation
Indices: 47090--47136 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
47080 AATGCGATAG
47090 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
47110 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
47130 TCATTTC
1 TCATTTC
47137 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:49123 original size:41 final size:42
Alignment explanation
Indices: 49046--49133 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
49036 GACTCGCCTG
* *
49046 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCATCGTTCAAGAGGCCCCTA
* * * * *
49088 TCATTCCTCGAGAGTCCCCTCCCA-CGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCATCGTTCAAGAGGCCCCTA
49129 TCATC
1 TCATC
49134 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 18 0.47
42 20 0.53
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCATCGTTCAAGAGGCCCCTA
Found at i:50531 original size:14 final size:14
Alignment explanation
Indices: 50512--50547 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
50502 ATTGTTTAAT
50512 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
50526 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
50540 TGATTTGT
1 TGATTTGT
50548 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:50678 original size:19 final size:18
Alignment explanation
Indices: 50654--50712 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
50644 AAAAAGTACT
50654 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
50673 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
50687 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
50706 CTCGCAA
1 ATCGCAA
50713 CGAGAGAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.50
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:50699 original size:33 final size:33
Alignment explanation
Indices: 50654--50743 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
50644 AAAAAGTACT
*
50654 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
50687 ATCGCAACGCGAAATGAAACTCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
50720 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
50744 GTTGCGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:50713 original size:19 final size:18
Alignment explanation
Indices: 50654--50739 Score: 62
Period size: 14 Copynumber: 5.1 Consensus size: 18
50644 AAAAAGTACT
*
50654 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATG-AA
*
50673 ATCGCAA--CGAGA-G-A
1 ATCGCAACGCGAAATGAA
50687 ATCGCAACGCGAAATGAA
1 ATCGCAACGCGAAATGAA
*
50705 ACTCGCAA--CGAGA-G-A
1 A-TCGCAACGCGAAATGAA
*
50720 ATCGCAACGCGAAATTAA
1 ATCGCAACGCGAAATGAA
50738 AT
1 AT
50740 TCGCGTTGCG
Statistics
Matches: 53, Mismatches: 5, Indels: 19
0.69 0.06 0.25
Matches are distributed among these distances:
14 14 0.26
15 2 0.04
16 10 0.19
17 9 0.17
18 5 0.09
19 13 0.25
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (18 bp):
ATCGCAACGCGAAATGAA
Found at i:50785 original size:33 final size:32
Alignment explanation
Indices: 50743--50867 Score: 162
Period size: 33 Copynumber: 3.8 Consensus size: 32
50733 ATTAAATTCG
50743 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
50776 CGTTGCGATTTTCATTTTGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
**
50809 CGTTGCGATTTTCATTTCGCATTATGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
50842 CGTTGCGATTTTCATTTCGCATTGCG
1 CGTTGCGATTTTCATTTCGCATTGCG
50868 GTAGTAATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
31 3 0.04
33 72 0.92
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:50816 original size:66 final size:66
Alignment explanation
Indices: 50736--50867 Score: 219
Period size: 66 Copynumber: 2.0 Consensus size: 66
50726 ACGCGAAATT
* * *
50736 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTTGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
50801 G
66 G
* *
50802 AAATTAGCGTTGCGATTTTCATTTCGCATTATGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
50867 G
66 G
50868 GTAGTAATTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:53145 original size:11 final size:11
Alignment explanation
Indices: 53129--53163 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
53119 TCTTCGGGGA
53129 CTTTTCTTCTT
1 CTTTTCTTCTT
53140 CTTTTCTTCTT
1 CTTTTCTTCTT
53151 CATTTTCTTCTT
1 C-TTTTCTTCTT
53163 C
1 C
53164 AGGATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.69
Consensus pattern (11 bp):
CTTTTCTTCTT
Found at i:53158 original size:12 final size:12
Alignment explanation
Indices: 53130--53164 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
53120 CTTCGGGGAC
53130 TTTTCTTCTTC-
1 TTTTCTTCTTCA
53141 TTTTCTTCTTCA
1 TTTTCTTCTTCA
53153 TTTTCTTCTTCA
1 TTTTCTTCTTCA
53165 GGATTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 11 0.48
12 12 0.52
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTCTTCTTCA
Found at i:54406 original size:20 final size:20
Alignment explanation
Indices: 54381--54418 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
54371 ATTTATTTGA
*
54381 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
54401 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
54419 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:54459 original size:14 final size:14
Alignment explanation
Indices: 54440--54466 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54430 ATGAAAATCG
54440 CATTGCGATTTTCT
1 CATTGCGATTTTCT
54454 CATTGCGATTTTC
1 CATTGCGATTTTC
54467 ATTTCGCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (14 bp):
CATTGCGATTTTCT
Found at i:54476 original size:19 final size:19
Alignment explanation
Indices: 54449--54503 Score: 94
Period size: 18 Copynumber: 2.9 Consensus size: 19
54439 GCATTGCGAT
*
54449 TTTCTCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
54468 TTTCGCATTGCGA-TTTCA
1 TTTCGCATTGCGATTTTCA
54486 TTTCGCATTGCGATTTTC
1 TTTCGCATTGCGATTTTC
54504 TCGTTGCGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 18 0.53
19 16 0.47
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.49
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:56528 original size:20 final size:20
Alignment explanation
Indices: 56505--56558 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
56495 GAAACTTAAA
56505 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
56525 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
56545 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
56559 TAAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:56606 original size:31 final size:33
Alignment explanation
Indices: 56545--56633 Score: 119
Period size: 31 Copynumber: 2.8 Consensus size: 33
56535 GGAAATGGCT
* *
56545 ATCGCAATGCGAAATAAAAATCTCAACGACAAA
1 ATCGCAACGCGAAATAAAAATCGCAACGACAAA
*
56578 ATCGCAACGCGAAAT-GAAA-CGCAACGACAAA
1 ATCGCAACGCGAAATAAAAATCGCAACGACAAA
* *
56609 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAACGCGAAATAAAAATCGCA
56634 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 25 0.51
32 6 0.12
33 18 0.37
ACGTcount: A:0.48, C:0.26, G:0.16, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATAAAAATCGCAACGACAAA
Found at i:56616 original size:14 final size:14
Alignment explanation
Indices: 56561--56617 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
56551 ATGCGAAATA
*
56561 AAAATCTCAACGAC
1 AAAATCGCAACGAC
56575 AAAATCGCAACG-C
1 AAAATCGCAACGAC
*
56588 GAAATGAAACGCAACGAC
1 --AA--AATCGCAACGAC
56606 AAAATCGCAACG
1 AAAATCGCAACG
56618 CGAAACACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
13 1 0.03
14 20 0.57
15 2 0.06
16 2 0.06
17 9 0.26
18 1 0.03
ACGTcount: A:0.49, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:56699 original size:32 final size:32
Alignment explanation
Indices: 56634--56719 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
56624 ACAAATCGCA
*
56634 TTGCGATTTTCATTTCGCGTTGCGATTTATCG
1 TTGCGATTTTCATTTCGCATTGCGATTTATCG
*
56666 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGA-TTTATCG
56698 TTGCGATTTTCATTTCGCATTG
1 TTGCGATTTTCATTTCGCATTG
56720 TGATAGCCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
31 17 0.34
32 18 0.36
33 15 0.30
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.48
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCATTGCGATTTATCG
Found at i:56732 original size:19 final size:20
Alignment explanation
Indices: 56708--56751 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
56698 TTGCGATTTT
*
56708 CATTT-CGCATTGTGATAGC
1 CATTTCCGCATTGCGATAGC
* *
56727 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
56747 CATTT
1 CATTT
56752 TGTGTTGCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:56750 original size:20 final size:19
Alignment explanation
Indices: 56696--56761 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
56686 GCGATTTTGT
**
56696 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
56715 CATTGTGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
56735 CGTTGCGATAGTCATTTTG
1 CGTTGCGATAGTCATTTCG
*
56754 TGTTGCGA
1 CGTTGCGA
56762 AAGTAAACTA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:57264 original size:18 final size:18
Alignment explanation
Indices: 57238--57282 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
57228 GTCGATCAGA
*
57238 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
57256 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
57274 TGATGGCTC
1 TGATGGCTC
57283 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:58613 original size:20 final size:20
Alignment explanation
Indices: 58590--58662 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 20
58580 AATAGTTTCT
58590 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
58610 GAAAATGACTATCGCAA-AC
1 GAAAATGAAAATCGCAACAC
** * *
58629 GAATTTGACAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
58649 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
58663 GTTGCGATTT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
19 23 0.53
20 20 0.47
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.15
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:58637 original size:19 final size:20
Alignment explanation
Indices: 58590--58652 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
58580 AATAGTTTCT
*
58590 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACAC
*
58610 GAAAATGACTATCGCAA-AC
1 GAAAATGACAATCGCAACAC
** *
58629 GAATTTGACAATCGCAACGC
1 GAAAATGACAATCGCAACAC
58649 GAAA
1 GAAA
58653 CTAAAATCGC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (20 bp):
GAAAATGACAATCGCAACAC
Found at i:59141 original size:20 final size:20
Alignment explanation
Indices: 59116--59183 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
59106 GATATTATAT
*
59116 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
59136 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
* *
59156 CGTTGCGAAAGTAAGTATCT
1 CGTTGCGAAAGTCAGTATCG
59176 CGTTGCGA
1 CGTTGCGA
59184 TTTTGTATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGTATCG
Found at i:59238 original size:20 final size:20
Alignment explanation
Indices: 59194--59286 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
59184 TTTTGTATTA
* **
59194 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
59215 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
59235 TCGCATTGCGATTTTTCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
59256 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
59276 TCGCATTGCGA
1 TCGCATTGCGA
59287 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:59239 original size:41 final size:41
Alignment explanation
Indices: 59194--59286 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
59184 TTTTGTATTA
59194 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
59235 TCGCATTGCGATTTTTCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
59276 TCGCATTGCGA
1 TCGCATTGCGA
59287 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Done.