Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008363.1 Corchorus capsularis cultivar CVL-1 contig08384, 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: 70307
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:7134 original size:44 final size:44
Alignment explanation
Indices: 7083--7198 Score: 173
Period size: 44 Copynumber: 2.7 Consensus size: 44
7073 TTATATATAT
7083 GTAATGAAATTATAATTAGGAAATAATATTTAT-AAATTATAAAC
1 GTAATGAAATTATAATTAGGAAATAATATTT-TGAAATTATAAAC
* *
7127 GTAATGAAATTATAATTAGAAAATAATATTTTGAAATTATAAAT
1 GTAATGAAATTATAATTAGGAAATAATATTTTGAAATTATAAAC
* *
7171 GTAATGAAATTATATTTA-GAAATTATAT
1 GTAATGAAATTATAATTAGGAAATAATAT
7199 ATGTAATGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
43 9 0.14
44 57 0.86
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (44 bp):
GTAATGAAATTATAATTAGGAAATAATATTTTGAAATTATAAAC
Found at i:7180 original size:17 final size:16
Alignment explanation
Indices: 7084--7258 Score: 66
Period size: 17 Copynumber: 11.8 Consensus size: 16
7074 TATATATATG
7084 TAATGAAATTAT-AAT
1 TAATGAAATTATAAAT
* *
7099 T-AGGAAA-TA-ATAT
1 TAATGAAATTATAAAT
* *
7112 TTAT-AAATTATAAACG
1 TAATGAAATTATAAA-T
7128 TAATGAAATTAT-AAT
1 TAATGAAATTATAAAT
7143 T-A-GAAA--ATAATAT
1 TAATGAAATTATAA-AT
*
7156 T-TTGAAATTATAAAT
1 TAATGAAATTATAAAT
7171 GTAATGAAATTAT--AT
1 -TAATGAAATTATAAAT
* *
7186 TTA-GAAATTATATAT
1 TAATGAAATTATAAAT
7201 GTAATGAAATTAT--AT
1 -TAATGAAATTATAAAT
*
7216 TTA-GAAA--ATAATAT
1 TAATGAAATTATAA-AT
*
7230 TTA-GAAATTATAAAT
1 TAATGAAATTATAAAT
*
7245 GTGATGAAATTATA
1 -TAATGAAATTATA
7259 TTTAGAAATA
Statistics
Matches: 123, Mismatches: 13, Indels: 46
0.68 0.07 0.25
Matches are distributed among these distances:
11 4 0.03
12 1 0.01
13 27 0.22
14 26 0.21
15 14 0.11
16 18 0.15
17 33 0.27
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.39
Consensus pattern (16 bp):
TAATGAAATTATAAAT
Found at i:7187 original size:74 final size:74
Alignment explanation
Indices: 7102--7340 Score: 354
Period size: 74 Copynumber: 3.2 Consensus size: 74
7092 TTATAATTAG
* * * *
7102 GAAATAATATTTATAAATTATAAACGTAATGAAATTATAATTAGAAAATAATATTTTGAAATTAT
1 GAAATTATATTTAGAAATTATAAATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTAT
7167 AAATGTAAT
66 AAATGTAAT
* *
7176 GAAATTATATTTAGAAATTATATATGTAATGAAATTATATTTAGAAAATAATATTTAGAAATTAT
1 GAAATTATATTTAGAAATTATAAATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTAT
*
7241 AAATGTGAT
66 AAATGTAAT
* * *
7250 GAAATTATATTTAGAAA-TAAACAATGTAATGACATTATAATTACAAAATAATATTTAGAAATTA
1 GAAATTATATTTAGAAATTATA-AATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTA
7314 TAAATGTAAT
65 TAAATGTAAT
* *
7324 GACATTATAATTAGAAA
1 GAAATTATATTTAGAAA
7341 ATAATATTAA
Statistics
Matches: 149, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
73 3 0.02
74 146 0.98
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37
Consensus pattern (74 bp):
GAAATTATATTTAGAAATTATAAATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTAT
AAATGTAAT
Found at i:7193 original size:30 final size:30
Alignment explanation
Indices: 7147--7222 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
7137 TATAATTAGA
* *
7147 AAATAATATTTTGAAATTATAAATGTAATG
1 AAATTATATTTAGAAATTATAAATGTAATG
*
7177 AAATTATATTTAGAAATTATATATGTAATG
1 AAATTATATTTAGAAATTATAAATGTAATG
7207 AAATTATATTTAGAAA
1 AAATTATATTTAGAAA
7223 ATAATATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (30 bp):
AAATTATATTTAGAAATTATAAATGTAATG
Found at i:7225 original size:118 final size:115
Alignment explanation
Indices: 7076--7393 Score: 408
Period size: 118 Copynumber: 2.7 Consensus size: 115
7066 GAAATTATTA
* * *
7076 TATATATGTAATGAAATTATAATTAGGAAATAATATTTATAAATTATAAACGTAATGAAATTATA
1 TATATATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTATAAATGTAATGAAATTATA
* *
7141 ATTAGAAAATAATATTTTGAAATTATAAATGTA-ATGAAATTATATTTAGAAAT
66 TTTAGAAAATAATATTTTGAAATTAT-AAT-TACA--AAATAATATTTAGAAAT
* *
7194 TATATATGTAATGAAATTATATTTAGAAAATAATATTTAGAAATTATAAATGTGATGAAATTATA
1 TATATATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTATAAATGTAATGAAATTATA
* * *
7259 TTTAG-AAATAAACAATGTAATGACATTATAATTACAAAATAATATTTAGAAAT
66 TTTAGAAAAT-AA-TAT-T-TTGAAATTATAATTACAAAATAATATTTAGAAAT
* * *
7312 TATAAATGTAATGACATTATAATTAGAAAATAATATTAAGAAATTA-AATATGTAATGAAATTAT
1 TATATATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTATAA-ATGTAATGAAATTAT
*
7376 ATTTAGAAAAAAATATTT
65 ATTTAGAAAATAATATTT
7394 AAAAACATAA
Statistics
Matches: 175, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
116 1 0.01
117 8 0.05
118 146 0.83
119 7 0.04
120 5 0.03
121 8 0.05
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (115 bp):
TATATATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTATAAATGTAATGAAATTATA
TTTAGAAAATAATATTTTGAAATTATAATTACAAAATAATATTTAGAAAT
Found at i:7230 original size:44 final size:44
Alignment explanation
Indices: 7177--7266 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
7167 AAATGTAATG
* *
7177 AAATTATATTTAGAAATTATATATGTAATGAAATTATATTTAGA
1 AAATAATATTTAGAAATTATAAATGTAATGAAATTATATTTAGA
*
7221 AAATAATATTTAGAAATTATAAATGTGATGAAATTATATTTAGA
1 AAATAATATTTAGAAATTATAAATGTAATGAAATTATATTTAGA
7265 AA
1 AA
7267 TAAACAATGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (44 bp):
AAATAATATTTAGAAATTATAAATGTAATGAAATTATATTTAGA
Found at i:7276 original size:30 final size:30
Alignment explanation
Indices: 7221--7288 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
7211 TATATTTAGA
* * *
7221 AAATAATATTTAGAAATTATAAATGTGATG
1 AAATTATATTTAGAAATTAAAAATGTAATG
7251 AAATTATATTTAGAAA-TAAACAATGTAATG
1 AAATTATATTTAGAAATTAAA-AATGTAATG
*
7281 ACATTATA
1 AAATTATA
7289 ATTACAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATTATATTTAGAAATTAAAAATGTAATG
Found at i:7304 original size:44 final size:44
Alignment explanation
Indices: 7251--7394 Score: 200
Period size: 44 Copynumber: 3.3 Consensus size: 44
7241 AAATGTGATG
* *
7251 AAATTATATTTAGAAA-TAAACAATGTAATGACATTATAATTACA
1 AAATAATATTTAGAAATTAAA-AATGTAATGACATTATAATTAGA
*
7295 AAATAATATTTAGAAATTATAAATGTAATGACATTATAATTAGA
1 AAATAATATTTAGAAATTAAAAATGTAATGACATTATAATTAGA
* * * *
7339 AAATAATATTAAGAAATTAAATATGTAATGAAATTATATTTAGA
1 AAATAATATTTAGAAATTAAAAATGTAATGACATTATAATTAGA
*
7383 AAAAAATATTTA
1 AAATAATATTTA
7395 AAAACATAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
44 86 0.97
45 3 0.03
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (44 bp):
AAATAATATTTAGAAATTAAAAATGTAATGACATTATAATTAGA
Found at i:7378 original size:74 final size:73
Alignment explanation
Indices: 7127--7384 Score: 280
Period size: 74 Copynumber: 3.5 Consensus size: 73
7117 AATTATAAAC
*
7127 GTAATGAAATT-ATAATT-AGAAAATAATATTTTGAAATTATAAATGTAATGAAATTATATTTAG
1 GTAATGAAATTAAT-ATTAAG-AAATAATATTTAGAAATTATAAATGTAATGAAATTATATTTAG
*
7190 AAATTATATAT
64 AAAATA-ATAT
* *
7201 GTAATGAAATT-ATATTTAGAAAATAATATTTAGAAATTATAAATGTGATGAAATTATATTTAG-
1 GTAATGAAATTAATATTAAG-AAATAATATTTAGAAATTATAAATGTAATGAAATTATATTTAGA
*
7264 AAATAAACAAT
65 AAAT-AA-TAT
* * *
7275 GTAATGACATT-ATAATTACA-AAATAATATTTAGAAATTATAAATGTAATGACATTATAATTAG
1 GTAATGAAATTAAT-ATTA-AGAAATAATATTTAGAAATTATAAATGTAATGAAATTATATTTAG
7338 AAAATAATAT
64 AAAATAATAT
*
7348 -TAA-GAAATTAAATATGTAATGAAATTATATTTAGAAA
1 GTAATGAAATT-AATAT-TAA-GAAATAATATTTAGAAA
7385 AAAATATTTA
Statistics
Matches: 161, Mismatches: 12, Indels: 22
0.83 0.06 0.11
Matches are distributed among these distances:
71 5 0.03
72 6 0.04
73 13 0.08
74 129 0.80
75 7 0.04
76 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.37
Consensus pattern (73 bp):
GTAATGAAATTAATATTAAGAAATAATATTTAGAAATTATAAATGTAATGAAATTATATTTAGAA
AATAATAT
Found at i:7451 original size:32 final size:32
Alignment explanation
Indices: 7414--7489 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
7404 AATTTAGTCG
*
7414 TTTCTT-AATGAAACGCCGCTATTTAGGGGCGT
1 TTTCTTCAAT-AAACGCCGCTATTTAGGGACGT
* *
7446 TTTCTTCGATAGACGCCGCTATTTAGGGACGT
1 TTTCTTCAATAAACGCCGCTATTTAGGGACGT
7478 TTTCTTCAATAA
1 TTTCTTCAATAA
7490 GAGCCCCTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
32 36 0.95
33 2 0.05
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (32 bp):
TTTCTTCAATAAACGCCGCTATTTAGGGACGT
Found at i:7500 original size:32 final size:32
Alignment explanation
Indices: 7426--7501 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
7416 TCTTAATGAA
* * *
7426 ACGCCGCTATTTAGGGGCGTTTTCTTCGATAG
1 ACGCCCCTATTTAGGGACGTTTTCTTCAATAG
*
7458 ACGCCGCTATTTAGGGACGTTTTCTTCAATAAG
1 ACGCCCCTATTTAGGGACGTTTTCTTCAAT-AG
7491 A-GCCCCTATTT
1 ACGCCCCTATTT
7502 TGCAGAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 37 0.93
33 3 0.08
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (32 bp):
ACGCCCCTATTTAGGGACGTTTTCTTCAATAG
Found at i:11800 original size:10 final size:10
Alignment explanation
Indices: 11785--11817 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
11775 TCCCAACTAC
11785 CTTCATTAAT
1 CTTCATTAAT
11795 CTTCATTAAT
1 CTTCATTAAT
11805 C-TCTATTAAT
1 CTTC-ATTAAT
11815 CTT
1 CTT
11818 TATCTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.10
10 18 0.86
11 1 0.05
ACGTcount: A:0.27, C:0.21, G:0.00, T:0.52
Consensus pattern (10 bp):
CTTCATTAAT
Found at i:13418 original size:39 final size:39
Alignment explanation
Indices: 13339--13506 Score: 164
Period size: 39 Copynumber: 4.4 Consensus size: 39
13329 GTACCTCAAA
* * *
13339 GGTTAAACTGA-TGGTAAGAGTGGACC-AATGCATCATGG
1 GGTTAAACTGATTGGTAAGAGTGGACCTGA-GCCTCAGGG
* **
13377 GGTTAAACTGATTGGTAAGAGTAGACCTGAGTTTCAGGG
1 GGTTAAACTGATTGGTAAGAGTGGACCTGAGCCTCAGGG
* * *
13416 GGTTAAACTGATTGGTAAAAGTGGAACTGTGCCTCAGGG
1 GGTTAAACTGATTGGTAAGAGTGGACCTGAGCCTCAGGG
* ** * * *
13455 GGTTAAACGGATTAATAAGAGTGGACCCGTGTCTCAGGG
1 GGTTAAACTGATTGGTAAGAGTGGACCTGAGCCTCAGGG
13494 GGTT-AACTG-TTGG
1 GGTTAAACTGATTGG
13507 CTAGATTCAA
Statistics
Matches: 107, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
37 2 0.02
38 15 0.14
39 89 0.83
40 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.33, T:0.26
Consensus pattern (39 bp):
GGTTAAACTGATTGGTAAGAGTGGACCTGAGCCTCAGGG
Found at i:13457 original size:78 final size:78
Alignment explanation
Indices: 13339--13506 Score: 198
Period size: 78 Copynumber: 2.2 Consensus size: 78
13329 GTACCTCAAA
* * * * **
13339 GGTTAAACTGA-TGGTAAGAGTGGACCAATGCATCATGGGGTTAAACTGATTGGTAAGAGTAGAC
1 GGTTAAACTGATTGGTAAAAGTGGAACAATGCATCAGGGGGTTAAACGGATTAATAAGAGTAGAC
* *
13403 CTGAGTTTCAGGG
66 CCGAGTCTCAGGG
** * *
13416 GGTTAAACTGATTGGTAAAAGTGGAACTGTGCCTCAGGGGGTTAAACGGATTAATAAGAGTGGAC
1 GGTTAAACTGATTGGTAAAAGTGGAACAATGCATCAGGGGGTTAAACGGATTAATAAGAGTAGAC
*
13481 CCGTGTCTCAGGG
66 CCGAGTCTCAGGG
13494 GGTT-AACTG-TTGG
1 GGTTAAACTGATTGG
13507 CTAGATTCAA
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
76 4 0.05
77 16 0.21
78 57 0.74
ACGTcount: A:0.28, C:0.12, G:0.33, T:0.26
Consensus pattern (78 bp):
GGTTAAACTGATTGGTAAAAGTGGAACAATGCATCAGGGGGTTAAACGGATTAATAAGAGTAGAC
CCGAGTCTCAGGG
Found at i:14016 original size:2 final size:2
Alignment explanation
Indices: 14009--14038 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13999 GGGGCGTGAC
*
14009 AT AT AT AT AC 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
14039 CCCTATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17897 original size:14 final size:15
Alignment explanation
Indices: 17878--17910 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
17868 TTATTTCTAA
17878 ATTAGTAAATAT-TT
1 ATTAGTAAATATATT
*
17892 ATTAGTATATATATT
1 ATTAGTAAATATATT
17907 ATTA
1 ATTA
17911 TTTATTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
ATTAGTAAATATATT
Found at i:17923 original size:44 final size:40
Alignment explanation
Indices: 17846--17925 Score: 97
Period size: 44 Copynumber: 1.9 Consensus size: 40
17836 TTAAAAATAT
*
17846 ATATTTTTAATATATATTTATATTATTTCTAAATTAGTAA
1 ATATTTTTAATATATATTTATATTATTACTAAATTAGTAA
* *
17886 ATATTTATTAGTATATATATTATTATTTATTAGTAAATTA
1 ATATTT-TTAATATATAT-TTA-TA-TTATTACTAAATTA
17926 TCAAAACATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 6 0.18
41 10 0.30
42 3 0.09
43 2 0.06
44 12 0.36
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (40 bp):
ATATTTTTAATATATATTTATATTATTACTAAATTAGTAA
Found at i:24213 original size:56 final size:56
Alignment explanation
Indices: 24077--24444 Score: 632
Period size: 56 Copynumber: 6.6 Consensus size: 56
24067 TCCTACATAC
* * * **
24077 TTTTTAGGATCTGTCTTCAGAACCCATTTGTGAGTTGTCTTCATACTCATTCTTAA
1 TTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCATACTCATTCTTAA
24133 -TTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCATACTCATTCTTAA
1 TTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCATACTCATTCTTAA
*
24188 TTTTTAGGAACTGTCTTCAGAACCCATCTGTGAGCAGTCTTCATACTCATTCTTAA
1 TTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCATACTCATTCTTAA
*
24244 TTTTTTAAGAACTGTCTTCAGAA-CCATCTATGAGCAGTCTTCATACTCATTCTTAA
1 -TTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCATACTCATTCTTAA
24300 TTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCATACTCATTCTTAA
1 TTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCATACTCATTCTTAA
*
24356 TATTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCATACTCATTCTTAA
1 TTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCATACTCATTCTTAA
*
24412 TTTTTAGGAACTGTCTTCAAAACCCATCTATGA
1 TTTTTAGGAACTGTCTTCAGAACCCATCTATGA
24445 ATCTGTCTAT
Statistics
Matches: 297, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
55 71 0.24
56 205 0.69
57 21 0.07
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (56 bp):
TTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCATACTCATTCTTAA
Found at i:25075 original size:14 final size:15
Alignment explanation
Indices: 25058--25090 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
25048 AATATTTTTA
25058 ATTAGTAATTTAG-C
1 ATTAGTAATTTAGTC
*
25072 ATTAGTACTTTAGTC
1 ATTAGTAATTTAGTC
25087 ATTA
1 ATTA
25091 TCTTAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (15 bp):
ATTAGTAATTTAGTC
Found at i:35876 original size:2 final size:2
Alignment explanation
Indices: 35869--35899 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35859 TAGATTCTTG
35869 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35900 GTAATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36753 original size:48 final size:48
Alignment explanation
Indices: 36697--37358 Score: 649
Period size: 48 Copynumber: 13.8 Consensus size: 48
36687 AGGTCAGCAA
* *
36697 TGTCTATTTCCAATTTTGCCCTTCCTGGTTGGAAGGTGCTGTTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCTGGTCGGAAGGTGCTGTTTTCAG
* * *
36745 TGTCTATTT-CAGTTTCGCCCTTCCAGGTCGGAAGGTGCTGTCTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCTGGTCGGAAGGTGCTGTTTTCAG
* * * * *
36792 TGTCTATTTTCAGTTTTGCCCTTCCCGGTCAGAAGGCGCCGTTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCTGGTCGGAAGGTGCTGTTTTCAG
* * *
36840 TGTCTATTT-CAGTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCTG
1 TGTCTATTTCCAGTTTTGCCCTTCCTGGTCGGAAGGTGCTGTTTTCAG
* * * * * *
36887 TGTCTGTTTCCAGTTTTTCCCTT-CTCGGTCGGAAGGGGCAGTCTTCGG
1 TGTCTATTTCCAGTTTTGCCCTTCCT-GGTCGGAAGGTGCTGTTTTCAG
* * * *
36935 TGTTTATTTCCAGTTTTGCCCTT-CTCGGTCGGAAGGTGCAGTCTTCGG
1 TGTCTATTTCCAGTTTTGCCCTTCCT-GGTCGGAAGGTGCTGTTTTCAG
* * * * * *
36983 TGTTTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGGGCAGTCTTCGG
1 TGTCTATTTCCAGTTTTGCCCTTCCTGGTCGGAAGGTGCTGTTTTCAG
* * *
37031 TGTTTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCTGGTCGGAAGGTGCTGTTTTCAG
* * * * * *
37079 TGTTTATTTCCTGTTTTGCCCTTCTTGATCGGAATGTGCTATTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCTGGTCGGAAGGTGCTGTTTTCAG
* * * *
37127 TGTCTATTTCCAGTTTTACCCTT-TTCGGTCGGAAGG-GGTAGTCTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCT-GGTCGGAAGGTGCT-GTTTTCAG
* * * *
37175 TGTTTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCGG
1 TGTCTATTTCCAGTTTTGCCCTTCCTGGTCGGAAGGTGCTGTTTTCAG
* * ** * *
37223 TGTCTCTTTCCTGTTTCACCATT-CTCGGTCGGAAGGTGCTGTTTTCAA
1 TGTCTATTTCCAGTTTTGCCCTTCCT-GGTCGGAAGGTGCTGTTTTCAG
* * * * * * *
37271 TGTTTACTTCCTA-TGTTGCCTTTCCTGATCGGAAGGTGCAGTCTTCAG
1 TGTCTATTTCC-AGTTTTGCCCTTCCTGGTCGGAAGGTGCTGTTTTCAG
* *
37319 TGTCTCTTTCCTGTTTTGCCCTT-CTCGGTCGGAAGGTGCT
1 TGTCTATTTCCAGTTTTGCCCTTCCT-GGTCGGAAGGTGCT
37359 TAGATTTGTC
Statistics
Matches: 516, Mismatches: 85, Indels: 26
0.82 0.14 0.04
Matches are distributed among these distances:
47 91 0.18
48 420 0.81
49 5 0.01
ACGTcount: A:0.11, C:0.23, G:0.25, T:0.41
Consensus pattern (48 bp):
TGTCTATTTCCAGTTTTGCCCTTCCTGGTCGGAAGGTGCTGTTTTCAG
Found at i:36993 original size:96 final size:96
Alignment explanation
Indices: 36701--37357 Score: 723
Period size: 96 Copynumber: 6.9 Consensus size: 96
36691 CAGCAATGTC
* * * * *
36701 TATTTCCAATTTTGCCCTTCCTGGTTGGAAGGTGCTGTTTTCAGTGTCTATTT-CAGTTTCGCCC
1 TATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTCTATTTCCAGTTTTGCCC
* *
36765 TTC-CAGGTCGGAAGGTGCTGTCTTCAGTGTC
66 TTCTC-GGTCGGAAGGTGCAGTCTTCAGTGTT
* * * *
36796 TATTTTCAGTTTTGCCCTTCCCGGTCAGAAGGCGCCGTTTTCAGTGTCTATTT-CAGTTTTGCCC
1 TATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTCTATTTCCAGTTTTGCCC
* * * *
36860 TTCCCGGTCGGAAGGTGCTA-TTTTCTGTGTC
66 TTCTCGGTCGGAAGGTGC-AGTCTTCAGTGTT
* * * * * * *
36891 TGTTTCCAGTTTTTCCCTTCTCGGTCGGAAGGGGCAGTCTTCGGTGTTTATTTCCAGTTTTGCCC
1 TATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTCTATTTCCAGTTTTGCCC
*
36956 TTCTCGGTCGGAAGGTGCAGTCTTCGGTGTT
66 TTCTCGGTCGGAAGGTGCAGTCTTCAGTGTT
* * * *
36987 TATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGGGCAGTCTTCGGTGTTTATTTCCAGTTTTGCCC
1 TATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTCTATTTCCAGTTTTGCCC
* *
37052 TTCCCGGTCGGAAGGTGCAGTTTTCAGTGTT
66 TTCTCGGTCGGAAGGTGCAGTCTTCAGTGTT
* ** * * *
37083 TATTTCCTGTTTTGCCCTTCTTGATCGGAATGTGCTA-TTTTCAGTGTCTATTTCCAGTTTTACC
1 TATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGC-AGTTTTCAGTGTCTATTTCCAGTTTTGCC
* * *
37147 CTTTTCGGTCGGAAGGGGTAGTCTTCAGTGTT
65 CTTCTCGGTCGGAAGGTGCAGTCTTCAGTGTT
** * * * ** *
37179 TATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCGGTGTCTCTTTCCTGTTTCACCA
1 TATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTCTATTTCCAGTTTTGCCC
* * *
37244 TTCTCGGTCGGAAGGTGCTGTTTTCAATGTT
66 TTCTCGGTCGGAAGGTGCAGTCTTCAGTGTT
* * * * * * * *
37275 TACTTCCTA-TGTTGCCTTTCCTGATCGGAAGGTGCAGTCTTCAGTGTCTCTTTCCTGTTTTGCC
1 TATTTCC-AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTCTATTTCCAGTTTTGCC
37339 CTTCTCGGTCGGAAGGTGC
65 CTTCTCGGTCGGAAGGTGC
37358 TTAGATTTGT
Statistics
Matches: 479, Mismatches: 76, Indels: 13
0.84 0.13 0.02
Matches are distributed among these distances:
95 125 0.26
96 352 0.73
97 2 0.00
ACGTcount: A:0.11, C:0.23, G:0.25, T:0.40
Consensus pattern (96 bp):
TATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTCTATTTCCAGTTTTGCCC
TTCTCGGTCGGAAGGTGCAGTCTTCAGTGTT
Found at i:37063 original size:144 final size:144
Alignment explanation
Indices: 36697--37357 Score: 729
Period size: 144 Copynumber: 4.6 Consensus size: 144
36687 AGGTCAGCAA
* * * * * *
36697 TGTCTATTTCCAATTTTGCCCTTCCTGGTTGGAAGGTGCTGTTTTCAGTGTCTATTT-CAGTTTC
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAGTGTCTATTTCCAGTTTT
* * * * *
36761 GCCCTTCCAGGTCGGAAGGTGCTGTCTTCAGTGTCTATTTTCAGTTTTGCCCTTCCCGGTCAGAA
66 GCCCTTCCCGGTCGGAAGGTGCAGTCTTCAGTGTCTATTTCCAGTTTTGCCCTTCTCGGTCGGAA
* *
36826 GGCGCCGTTTTCAG
131 GGTGCAGTTTTCAG
* * *
36840 TGTCTATTT-CAGTTTTGCCCTTCCCGGTCGGAAGGTGCTA-TTTTCTGTGTCTGTTTCCAGTTT
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGC-AGTCTTCAGTGTCTATTTCCAGTTT
* * * * *
36903 TTCCCTTCTCGGTCGGAAGGGGCAGTCTTCGGTGTTTATTTCCAGTTTTGCCCTTCTCGGTCGGA
65 TGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAGTGTCTATTTCCAGTTTTGCCCTTCTCGGTCGGA
* *
36968 AGGTGCAGTCTTCGG
130 AGGTGCAGTTTTCAG
* * * *
36983 TGTTTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGGGCAGTCTTCGGTGTTTATTTCCAGTTTT
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAGTGTCTATTTCCAGTTTT
* * * * *
37048 GCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTTATTTCCTGTTTTGCCCTTCTTGATCGGAA
66 GCCCTTCCCGGTCGGAAGGTGCAGTCTTCAGTGTCTATTTCCAGTTTTGCCCTTCTCGGTCGGAA
*
37113 TGTGCTA-TTTTCAG
131 GGTGC-AGTTTTCAG
* ** * * *
37127 TGTCTATTTCCAGTTTTACCCTTTTCGGTCGGAAGGGGTAGTCTTCAGTGTTTATTTCCAGTTTT
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAGTGTCTATTTCCAGTTTT
** * * * * ** *
37192 GCCCTTCCCGGTCGGAAGGTGTTGTTTTCGGTGTCTCTTTCCTGTTTCACCATTCTCGGTCGGAA
66 GCCCTTCCCGGTCGGAAGGTGCAGTCTTCAGTGTCTATTTCCAGTTTTGCCCTTCTCGGTCGGAA
* *
37257 GGTGCTGTTTTCAA
131 GGTGCAGTTTTCAG
* * * * * * * *
37271 TGTTTACTTCCTA-TGTTGCCTTTCCTGATCGGAAGGTGCAGTCTTCAGTGTCTCTTTCCTGTTT
1 TGTCTATTTCC-AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAGTGTCTATTTCCAGTTT
*
37335 TGCCCTTCTCGGTCGGAAGGTGC
65 TGCCCTTCCCGGTCGGAAGGTGC
37358 TTAGATTTGT
Statistics
Matches: 438, Mismatches: 73, Indels: 13
0.84 0.14 0.02
Matches are distributed among these distances:
142 40 0.09
143 89 0.20
144 307 0.70
145 2 0.00
ACGTcount: A:0.11, C:0.23, G:0.25, T:0.41
Consensus pattern (144 bp):
TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAGTGTCTATTTCCAGTTTT
GCCCTTCCCGGTCGGAAGGTGCAGTCTTCAGTGTCTATTTCCAGTTTTGCCCTTCTCGGTCGGAA
GGTGCAGTTTTCAG
Found at i:49978 original size:35 final size:34
Alignment explanation
Indices: 49927--50025 Score: 135
Period size: 35 Copynumber: 2.8 Consensus size: 34
49917 GTTCGGTGAA
*
49927 TCAGATGACTCGGTGTAGCATCTTCAAAGATGGAT
1 TCAGATGACTC-GTGTAACATCTTCAAAGATGGAT
*
49962 TCAGATGACTCAGTGTAACATCTTCAAAGTTGGAT
1 TCAGATGACTC-GTGTAACATCTTCAAAGATGGAT
* *
49997 TCAGATGACTCGATGTATCATCTGCAAAG
1 TCAGATGACTCG-TGTAACATCTTCAAAG
50026 GTGAAATTCG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
34 1 0.02
35 57 0.98
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (34 bp):
TCAGATGACTCGTGTAACATCTTCAAAGATGGAT
Found at i:50190 original size:90 final size:92
Alignment explanation
Indices: 50058--50262 Score: 288
Period size: 90 Copynumber: 2.2 Consensus size: 92
50048 CAGCAAATTT
** * *
50058 TCAGGGTGATTCGGTGAATCAAGGTAATGCGGTGCATTATTTCTACAAAG-CTGGGTTCGGTGAG
1 TCAGGGTGATTCGGTGAATCAAGCAAATGCGGTGCATCATTTCTACAAAGACTGGATTCGGTGAG
* ** *
50122 CTCGGTGCAGCACATTTTCAAA-GAGA
66 CTCGATGCAGCACATTCGCAAACAAGA
* *
50148 TCAGGGTGATTCGGTGAATCAAGCAAATGCGGTGCATCATTTCTTCAAAGATTGGATTCGGTGAG
1 TCAGGGTGATTCGGTGAATCAAGCAAATGCGGTGCATCATTTCTACAAAGACTGGATTCGGTGAG
*
50213 CTCGATGCAGCACATTCGCAAACAAGT
66 CTCGATGCAGCACATTCGCAAACAAGA
*
50240 TCAGAGTGATTCGGTGAATCAAG
1 TCAGGGTGATTCGGTGAATCAAG
50263 GATTATTCTG
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 46 0.46
91 31 0.31
92 24 0.24
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (92 bp):
TCAGGGTGATTCGGTGAATCAAGCAAATGCGGTGCATCATTTCTACAAAGACTGGATTCGGTGAG
CTCGATGCAGCACATTCGCAAACAAGA
Found at i:53050 original size:10 final size:10
Alignment explanation
Indices: 53035--53059 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53025 GTTGCTGCTC
53035 AATTCCAGAA
1 AATTCCAGAA
53045 AATTCCAGAA
1 AATTCCAGAA
53055 AATTC
1 AATTC
53060 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:53205 original size:14 final size:15
Alignment explanation
Indices: 53186--53223 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
53176 TATCACAAAT
53186 CACACACA-TAGATA
1 CACACACATTAGATA
53200 CACACACATTAGATA
1 CACACACATTAGATA
53215 CACATCACA
1 CACA-CACA
53224 AATTTTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 10 0.45
16 4 0.18
ACGTcount: A:0.47, C:0.32, G:0.05, T:0.16
Consensus pattern (15 bp):
CACACACATTAGATA
Found at i:54005 original size:13 final size:13
Alignment explanation
Indices: 53987--54021 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
53977 TTAATTATTG
53987 TTTGCTTTATTAA
1 TTTGCTTTATTAA
54000 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
54013 TCTGCTTTA
1 TTTGCTTTA
54022 GATTTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:54397 original size:38 final size:39
Alignment explanation
Indices: 54341--54437 Score: 124
Period size: 39 Copynumber: 2.5 Consensus size: 39
54331 TCCGAAAATT
** *
54341 AGTTTTTTGTTTTTGTTTTTCCGTTTTTTCT-AAAAAAAA
1 AGTTTTTT-TTTCCGTTTTTCCGATTTTTCTAAAAAAAAA
54380 AGTTTTTTTTTCCGTTTTTCCGATTTTTCTAAAAAAAAA
1 AGTTTTTTTTTCCGTTTTTCCGATTTTTCTAAAAAAAAA
** *
54419 AAATTATTTTTCCGTTTTT
1 AGTTTTTTTTTCCGTTTTT
54438 AAAATTAGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
38 19 0.37
39 32 0.63
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.57
Consensus pattern (39 bp):
AGTTTTTTTTTCCGTTTTTCCGATTTTTCTAAAAAAAAA
Found at i:60803 original size:10 final size:10
Alignment explanation
Indices: 60788--60812 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
60778 GTTGCTGCTC
60788 AATTCCAGAA
1 AATTCCAGAA
60798 AATTCCAGAA
1 AATTCCAGAA
60808 AATTC
1 AATTC
60813 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:60958 original size:14 final size:15
Alignment explanation
Indices: 60939--60976 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
60929 TATCACAAAT
60939 CACACACA-TAGATA
1 CACACACATTAGATA
60953 CACACACATTAGATA
1 CACACACATTAGATA
60968 CACATCACA
1 CACA-CACA
60977 AATTTTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 10 0.45
16 4 0.18
ACGTcount: A:0.47, C:0.32, G:0.05, T:0.16
Consensus pattern (15 bp):
CACACACATTAGATA
Found at i:61758 original size:13 final size:13
Alignment explanation
Indices: 61740--61774 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
61730 TTAATTATTG
61740 TTTGCTTTATTAA
1 TTTGCTTTATTAA
61753 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
61766 TCTGCTTTA
1 TTTGCTTTA
61775 GATTTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:61782 original size:6 final size:6
Alignment explanation
Indices: 61771--61797 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
61761 ATTAATCTGC
61771 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
61798 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:62923 original size:50 final size:51
Alignment explanation
Indices: 62869--62964 Score: 126
Period size: 50 Copynumber: 1.9 Consensus size: 51
62859 AAAAAAGTAA
* * *
62869 GTTTTCATTCATGAT-GTGT-TCAAAGTTGGGTC-TTTTAGCTTTAAACTTAG
1 GTTTTCATTCAT-ATAGTATAT-AAAGTTGAGTCTTTTTAGCATTAAACTTAG
62919 GTTTTCATTCATATAGTATATAAAGTTGAGTCTTTTTAGCATTAAA
1 GTTTTCATTCATATAGTATATAAAGTTGAGTCTTTTTAGCATTAAA
62965 TTTAACCTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
49 2 0.05
50 25 0.62
51 13 0.32
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (51 bp):
GTTTTCATTCATATAGTATATAAAGTTGAGTCTTTTTAGCATTAAACTTAG
Found at i:62979 original size:50 final size:50
Alignment explanation
Indices: 62890--62991 Score: 118
Period size: 50 Copynumber: 2.0 Consensus size: 50
62880 TGATGTGTTC
* * ***
62890 AAAGTTGGGTCTTTTAGCTTTAAACTTAGGTTTTCATTCAT-ATAGTATAT
1 AAAGTTGAGTCTTTTAGCATTAAACTTAACCTTTCATTCATAATA-TATAT
*
62940 AAAGTTGAGTCTTTTTAGCATTAAATTTAACCTTT-ATTCATAATATATAT
1 AAAGTTGAGTC-TTTTAGCATTAAACTTAACCTTTCATTCATAATATATAT
62990 AA
1 AA
62992 TATATATAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
50 23 0.52
51 21 0.48
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (50 bp):
AAAGTTGAGTCTTTTAGCATTAAACTTAACCTTTCATTCATAATATATAT
Found at i:63228 original size:2 final size:2
Alignment explanation
Indices: 63221--63245 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63211 TAGATTCTTG
63221 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
63246 GTAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64169 original size:48 final size:48
Alignment explanation
Indices: 64044--64654 Score: 627
Period size: 48 Copynumber: 12.8 Consensus size: 48
64034 AGGTCAGCAA
*
64044 TGTCTATTTCCAATTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * * *
64092 TGCCTATTT-CAGTTTCGCCCTTCCAGGTCGGAAGGTGCTGTCTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * * *
64139 TGTCTATTTTCAGTTTTGCCCTTCCCGGTCGGAAGGCGCCGTTTTCAA
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
*
64187 TGTCTATTT-CAGTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * * * *
64234 TGTCTTTTTCCAGTTTTGCCCTTCCCGGTCGGAAGGGGCAGTCTTCGG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * * * *
64282 TGTTTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGGGCAGTCTTCGG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * **
64330 TGTTTATTTCCAGTTTTGCCCTTCTCGGTCGGAAGGTGCAATTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * ** * * *
64378 TGTTTATTTCCTGTTTTGCCCTTCTTGATCGGAAGGTGCTATTCTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * * * * * *
64426 TGTCTATTTCTAGTTTTACCTTTCTCGGTCGGAAGG-GGTAGTCTTCGG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCT-GTTTTCAG
* * *
64474 TGTTTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCGG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * ** * * *
64522 TGTCTCTTTCCTGTTTCACCCTTCCCGGTCAGAAGGTGCTATTTTCAA
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * ** * * * * *
64570 TGTTTACTTCCTA-TGATGCCTTTCCTGATCGGAAGGTGCAGTCTTCAG
1 TGTCTATTTCC-AGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
* * * *
64618 TGTCTCTTTCCTGTTTTGCCCTTCTCGGTCGAAAGGT
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGT
64655 CCTAGATTTG
Statistics
Matches: 467, Mismatches: 90, Indels: 12
0.82 0.16 0.02
Matches are distributed among these distances:
47 86 0.18
48 379 0.81
49 2 0.00
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.40
Consensus pattern (48 bp):
TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTGTTTTCAG
Done.