Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold266
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: 372371
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
File 3 of 3
Found at i:300659 original size:174 final size:175
Alignment explanation
Indices: 300355--300704 Score: 630
Period size: 174 Copynumber: 2.0 Consensus size: 175
300345 TTTTCTTAAT
300355 AATTAAATAAATTCATTCATTTTTTATGATTAACAAAAAAAATTAAAATTTTAAAAATAAAGTAA
1 AATTAAATAAATTCATTCATTTTTTATGATTAAC-AAAAAAATTAAAATTTTAAAAATAAAGTAA
* *
300420 ATTAATGTAAATCATAATTCTTTTTATTTATTATTAAATTAAGTTATTTAATAAAAGTTTGTTAA
65 ATTAATGTAAATCATAATTCTTTTTATTTATTATTAAATTAAGTTATTTAACAAAAGTCTGTTAA
300485 TGAAATAAAAATTTTAACATATATTAGACAAATCTTGATAGTAAAA
130 TGAAATAAAAATTTTAACATATATTAGACAAATCTTGATAGTAAAA
* *
300531 AATTAAATAAATTTATTCATTTTTTATGATTAAC-AAAAAATTAGAATTTTAAAAATAAAGTAAA
1 AATTAAATAAATTCATTCATTTTTTATGATTAACAAAAAAATTAAAATTTTAAAAATAAAGTAAA
*
300595 TTAATGTAAATCATAATTCTTTTTATTTATTATTAAATTAATTTATTTAACAAAAGTCTGTTAAT
66 TTAATGTAAATCATAATTCTTTTTATTTATTATTAAATTAAGTTATTTAACAAAAGTCTGTTAAT
*
300660 GAAATAAAAATTTTAACATATATTAGATAAATCTTGATAGTAAAA
131 GAAATAAAAATTTTAACATATATTAGACAAATCTTGATAGTAAAA
300705 TTTACCATAG
Statistics
Matches: 168, Mismatches: 6, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
174 135 0.80
176 33 0.20
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (175 bp):
AATTAAATAAATTCATTCATTTTTTATGATTAACAAAAAAATTAAAATTTTAAAAATAAAGTAAA
TTAATGTAAATCATAATTCTTTTTATTTATTATTAAATTAAGTTATTTAACAAAAGTCTGTTAAT
GAAATAAAAATTTTAACATATATTAGACAAATCTTGATAGTAAAA
Found at i:300888 original size:18 final size:17
Alignment explanation
Indices: 300867--300935 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 17
300857 ATTAAATTTT
300867 TTTTATAAATTAGAT-AAA
1 TTTTATAAA-TA-ATAAAA
*
300885 TTTTATTAATAATAAAA
1 TTTTATAAATAATAAAA
300902 TTTTATCATAATAATTTAAAA
1 TTTTAT-A-AATAA--TAAAA
300923 TTTTAATAAATAA
1 TTTT-ATAAATAA
300936 CAATAATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
16 2 0.05
17 11 0.26
18 8 0.19
19 5 0.12
20 5 0.12
21 10 0.23
22 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (17 bp):
TTTTATAAATAATAAAA
Found at i:300903 original size:197 final size:198
Alignment explanation
Indices: 300534--300935 Score: 431
Period size: 197 Copynumber: 2.0 Consensus size: 198
300524 AGTAAAAAAT
**
300534 TAAATAAATTTATTCATTTTTTATGATTAACAAAAAATTAGAATTTTAAAAATAAAGTAAATTAA
1 TAAATAAATTTATTCATTTTTTATGATTAACAAAAAATTAGAATTTTAAAAATAAAACAAATTAA
* * * * * * *
300599 TGTAAATCATAATTCTTTTTATTTATTATTAAATTAATTTATTTAACAAAAGTCTGTTAATGAAA
66 TGTAAATCATAAATCATTTTATTAATTATAAAATAAATGTATATAACAAAAGTCTGTTAATGAAA
* * * * *
300664 TAAAAATTTTAACATATATTAGATAAATCTTGATAGTAAAA-TTTACCATAGTAATTTAAAAATT
131 TAAAAATTTTAACATAAATTAGATAAATATTAATAATAAAATTTTACCATAATAATTTAAAAATT
*
300728 TAG
196 TAA
* * ** * *
300731 TAAATAAATTTATTTATTTTTTGA-GGTTAATGAAAAATTATAACTTTTAAAAATAAAACAACTT
1 TAAATAAATTTATTCATTTTTT-ATGATTAACAAAAAATTAGAA-TTTTAAAAATAAAACAAATT
* *
300795 AATGTAAA-CTTAAAAT-ATTTTGTTAATTA-AAAATAAATGTATATAACAAAAGT-T-TTAATG
64 AATGTAAATCAT-AAATCATTTTATTAATTATAAAATAAATGTATATAACAAAAGTCTGTTAATG
* * *** *
300855 AAATTAAATTTTTTTTATAAATTAGATAAATTTTATTAATAATAAAATTTTATCATAATAATTTA
128 AAATAAAAATTTTAACATAAATTAGATAAA---TATTAATAATAAAATTTTACCATAATAATTTA
*
300920 AAATTTTAA
190 AAAATTTAA
300929 TAAATAA
1 TAAATAA
300936 CAATAATTAT
Statistics
Matches: 168, Mismatches: 30, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
194 30 0.18
195 1 0.01
196 20 0.12
197 59 0.35
198 58 0.35
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (198 bp):
TAAATAAATTTATTCATTTTTTATGATTAACAAAAAATTAGAATTTTAAAAATAAAACAAATTAA
TGTAAATCATAAATCATTTTATTAATTATAAAATAAATGTATATAACAAAAGTCTGTTAATGAAA
TAAAAATTTTAACATAAATTAGATAAATATTAATAATAAAATTTTACCATAATAATTTAAAAATT
TAA
Found at i:300912 original size:16 final size:17
Alignment explanation
Indices: 300882--300927 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 17
300872 TAAATTAGAT
300882 AAATTTTATTAATAATA
1 AAATTTTATTAATAATA
300899 AAATTTTATCATAATAATTTA
1 AAATTTTAT--TAATAA--TA
300920 AAATTTTA
1 AAATTTTA
300928 ATAAATAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
19 6 0.24
21 10 0.40
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATTTTATTAATAATA
Found at i:300931 original size:19 final size:17
Alignment explanation
Indices: 300882--300931 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
300872 TAAATTAGAT
*
300882 AAATTTTATTAATAATA
1 AAATTTTAATAATAATA
300899 AAATTTTATCATAATAATTTA
1 AAATTTTA--ATAATAA--TA
300920 AAATTTTAATAA
1 AAATTTTAATAA
300932 ATAACAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 8 0.29
19 10 0.36
21 10 0.36
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATTTTAATAATAATA
Found at i:306360 original size:25 final size:25
Alignment explanation
Indices: 306312--306361 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
306302 CTTGGTCTTA
**
306312 AATTAAATAATTTATGACCCAATAT
1 AATTAAATAAAATATGACCCAATAT
306337 AATTAAATAAAATA-GACCCAA-AT
1 AATTAAATAAAATATGACCCAATAT
306360 AA
1 AA
306362 AATAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 7 0.30
25 12 0.52
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.28
Consensus pattern (25 bp):
AATTAAATAAAATATGACCCAATAT
Found at i:306950 original size:52 final size:51
Alignment explanation
Indices: 306889--307012 Score: 142
Period size: 52 Copynumber: 2.4 Consensus size: 51
306879 GGACTTTGAC
** * *
306889 TTTATAGGACTTGACCTCCTAAAACAGGTGCTAGCTAATATGGCCTTTAGG-T
1 TTTATAGGACTTGACCTCCT-AAACAAATGCCAGCTAATATGGACTTT-GGTT
**
306941 TTTATAGGACTTGACCTCTCTATGCAAATGCCAGCTAATATGGACTTTGGTT
1 TTTATAGGACTTGACCTC-CTAAACAAATGCCAGCTAATATGGACTTTGGTT
* *
306993 TTTATAGGGCTTGACTTCCT
1 TTTATAGGACTTGACCTCCT
307013 TACATCAGTG
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
51 4 0.06
52 56 0.90
53 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.36
Consensus pattern (51 bp):
TTTATAGGACTTGACCTCCTAAACAAATGCCAGCTAATATGGACTTTGGTT
Found at i:307266 original size:53 final size:50
Alignment explanation
Indices: 307060--307368 Score: 177
Period size: 51 Copynumber: 6.0 Consensus size: 50
307050 ATTAGTGTAA
* * * * ** * *
307060 ACTTGGATTCTATAGGGCTTGACCTCTCTATATAGGCACTAGTTAATATGG
1 ACTTGGGTTTTATAGGGCTTGACCTC-CTATACAAGTGCTAGCTAATGTGG
* * * * * * *
307111 ATTTTAGGTTCTATAAGGCTTGATCTGCCTATACAAGTGGTAGCTAGTGTGG
1 A-CTTGGGTTTTATAGGGCTTGACCT-CCTATACAAGTGCTAGCTAATGTGG
* * ** * * * * * *
307163 ACTTAGGTTCTATAGGATTTAACCTTTCTCTATAGGTGCTAGCTAGTGTGG
1 ACTTGGGTTTTATAGGGCTTGACC-TCCTATACAAGTGCTAGCTAATGTGG
*
307214 ACTTGGGGGTTTTATAGGGCTTGACCTCCTTATACAAGTGTTAGCTAATGTGG
1 ACTT--GGGTTTTATAGGGCTTGACCTCC-TATACAAGTGCTAGCTAATGTGG
* ** ** * * * *
307267 ACTTTGACTCCATAAGGTTTGATCTCCCTATACAAGTGCTAGCTAATGTAG
1 ACTTGGGTTTTATAGGGCTTGACCT-CCTATACAAGTGCTAGCTAATGTGG
* * *
307318 ACTTTAGGGTTTTATAGGGCTTGGCCTCACTATATAAGTGCCAGCTAATGT
1 AC-TT-GGGTTTTATAGGGCTTGACCTC-CTATACAAGTGCTAGCTAATGT
307369 AAACTTTGAC
Statistics
Matches: 192, Mismatches: 56, Indels: 18
0.72 0.21 0.07
Matches are distributed among these distances:
51 78 0.41
52 44 0.23
53 70 0.36
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (50 bp):
ACTTGGGTTTTATAGGGCTTGACCTCCTATACAAGTGCTAGCTAATGTGG
Found at i:307307 original size:104 final size:104
Alignment explanation
Indices: 307198--307387 Score: 265
Period size: 104 Copynumber: 1.8 Consensus size: 104
307188 TTCTCTATAG
* * * **
307198 GTGCTAGCTAGTGTGGACTTGGGGGTTTTATAGGGCTTGACCTC-CTTATACAAGTGTTAGCTAA
1 GTGCTAGCTAATGTAGACTTGAGGGTTTTATAGGGCTTGACCTCAC-TATACAAGTGCCAGCTAA
**
307262 TGTGGACTTTGACTCCATAAGGTTTGATCTCCCTATACAA
65 TGTAAACTTTGACTCCATAAGGTTTGATCTCCCTATACAA
* * *
307302 GTGCTAGCTAATGTAGACTTTAGGGTTTTATAGGGCTTGGCCTCACTATATAAGTGCCAGCTAAT
1 GTGCTAGCTAATGTAGACTTGAGGGTTTTATAGGGCTTGACCTCACTATACAAGTGCCAGCTAAT
*
307367 GTAAACTTTGACTCTATAAGG
66 GTAAACTTTGACTCCATAAGG
307388 CTTAACCTCC
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
104 73 0.99
105 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (104 bp):
GTGCTAGCTAATGTAGACTTGAGGGTTTTATAGGGCTTGACCTCACTATACAAGTGCCAGCTAAT
GTAAACTTTGACTCCATAAGGTTTGATCTCCCTATACAA
Found at i:310754 original size:12 final size:12
Alignment explanation
Indices: 310737--310761 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
310727 AGTAAAAATT
310737 TATTCATAATAA
1 TATTCATAATAA
310749 TATTCATAATAA
1 TATTCATAATAA
310761 T
1 T
310762 TAAGCAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TATTCATAATAA
Found at i:312209 original size:17 final size:17
Alignment explanation
Indices: 312189--312234 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
312179 AACACGATAC
312189 AAAAAATAACATGACTT
1 AAAAAATAACATGACTT
* * *
312206 AAAATATTAGATGACTT
1 AAAAAATAACATGACTT
*
312223 GAAAAATAACAT
1 AAAAAATAACAT
312235 AAATACACAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (17 bp):
AAAAAATAACATGACTT
Found at i:312262 original size:54 final size:54
Alignment explanation
Indices: 312187--312308 Score: 145
Period size: 54 Copynumber: 2.2 Consensus size: 54
312177 TAAACACGAT
** * ***
312187 ACAAAAAATAACATGACTTAAAATATTAGATGACTTGAAAAATAACATAAATAC
1 ACAAAAAATAACACAACTTAAAATATTACATGACACAAAAAATAACATAAATAC
* * *
312241 ACAAAAAATAGCACAACTTAAAATATTACTTGACACAAAAAATAACATAAATATA
1 ACAAAAAATAACACAACTTAAAATATTACATGACACAAAAAATAACATAAATA-C
*
312296 ATAAAAAATAACA
1 ACAAAAAATAACA
312309 TAAATATACG
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
54 45 0.80
55 11 0.20
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.22
Consensus pattern (54 bp):
ACAAAAAATAACACAACTTAAAATATTACATGACACAAAAAATAACATAAATAC
Found at i:312309 original size:75 final size:74
Alignment explanation
Indices: 312224--312459 Score: 246
Period size: 75 Copynumber: 3.1 Consensus size: 74
312214 AGATGACTTG
* *
312224 AAAAATAACATAAATACACAAAAAATAGCACAACTTAAAATATTACTTGACACAAAAAATAACAT
1 AAAAATAACATAAATATACAAAAAATAACACAACTTAAAATATTAC-TGACACAAAAAATAACAT
312289 AAATATAATA
65 AAATATAATA
* * * **
312299 AAAAATAACATAAATATACGAAAAATAACACGATTTAAAATATTAC--ACGACATGAAA-AACAT
1 AAAAATAACATAAATATACAAAAAATAACACAACTTAAAATATTACTGAC-ACAAAAAATAACAT
*
312361 AAATATTACACGA
65 AAATA-TA-A-TA
* * * * * *
312374 AAAAATAATACAAATATATGAAAAACTAACACAACTTAAAATACTACATGACACAAAAAATAATA
1 AAAAATAACATAAATATA-CAAAAAATAACACAACTTAAAATATTAC-TGACACAAAAAATAACA
312439 TAAATAT-ATGA
64 TAAATATAAT-A
312450 AAAAATAACA
1 AAAAATAACA
312460 CAATATTCGT
Statistics
Matches: 130, Mismatches: 21, Indels: 19
0.76 0.12 0.11
Matches are distributed among these distances:
72 12 0.09
73 8 0.06
74 1 0.01
75 58 0.45
76 33 0.25
78 7 0.05
79 11 0.08
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.21
Consensus pattern (74 bp):
AAAAATAACATAAATATACAAAAAATAACACAACTTAAAATATTACTGACACAAAAAATAACATA
AATATAATA
Found at i:312324 original size:20 final size:21
Alignment explanation
Indices: 312275--312328 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
312265 ATTACTTGAC
312275 ACAAAAAATAACATAAATATA
1 ACAAAAAATAACATAAATATA
*
312296 ATAAAAAATAACATAAATAT-
1 ACAAAAAATAACATAAATATA
*
312316 ACGAAAAATAACA
1 ACAAAAAATAACA
312329 CGATTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 11 0.37
21 19 0.63
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (21 bp):
ACAAAAAATAACATAAATATA
Found at i:312553 original size:17 final size:17
Alignment explanation
Indices: 312533--312588 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
312523 TTGTATTGTA
312533 TTTTAGGTCATGTTATT
1 TTTTAGGTCATGTTATT
** * *
312550 TTTTCATTTCATGTAATA
1 TTTT-AGGTCATGTTATT
312568 TTTTAGGTCATGTTATT
1 TTTTAGGTCATGTTATT
312585 TTTT
1 TTTT
312589 CGTATATTTG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.20, C:0.07, G:0.12, T:0.61
Consensus pattern (17 bp):
TTTTAGGTCATGTTATT
Found at i:312795 original size:107 final size:104
Alignment explanation
Indices: 312548--312842 Score: 276
Period size: 106 Copynumber: 2.8 Consensus size: 104
312538 GGTCATGTTA
* * *
312548 TTTTTTCATTTCATGTAATATTTTAGGTCATGTTATTTTTTCGTATA-TTTG-TATTTTT-TTAG
1 TTTTTTAATGTCATGTAATATTTTA-GTCATGTTA-TTTTTCATATATTTTGCTATTTTTCTT-G
* * * *
312610 TATCATATTCATTTTATTTTTATGTCTTGTTCATGTTTCATTAG
63 T-T-ATATTTATTTTATTTTTATATCGTGTTCATGTTTAATTAG
** *
312654 TTTTTTCGTGTCATGTAGTATTTTAAGTCATGTTATTTTTCATATATTTGTGCTATTTTTCTTGT
1 TTTTTTAATGTCATGTAATATTTT-AGTCATGTTATTTTTCATATATTT-TGCTATTTTTCTTGT
*
312719 TATGTTTATTTTATTTTTCATATCGTGTTCATGTTTTAATT-G
64 TATATTTATTTTATTTTT-ATATCGTGTTCATG-TTTAATTAG
** * * * *
312761 TTTTTTAATGTTGTGTAATATTTTCAGTTATGTTATTTTT-TTATATTTATACTATTTTTTTCAT
1 TTTTTTAATGTCATGTAATATTTT-AGTCATGTTATTTTTCATATATTT-TGCTA--TTTTTCTT
*
312825 ATTATATTTATTTTATTT
62 GTTATATTTATTTTATTT
312843 ATTTTAAATA
Statistics
Matches: 158, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
105 10 0.06
106 58 0.37
107 50 0.32
108 38 0.24
109 2 0.01
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (104 bp):
TTTTTTAATGTCATGTAATATTTTAGTCATGTTATTTTTCATATATTTTGCTATTTTTCTTGTTA
TATTTATTTTATTTTTATATCGTGTTCATGTTTAATTAG
Found at i:312821 original size:20 final size:21
Alignment explanation
Indices: 312796--312848 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
312786 AGTTATGTTA
312796 TTTTTTTATATTTATA-CTAT
1 TTTTTTTATATTTATATCTAT
* *
312816 TTTTTTCATA-TTATATTTAT
1 TTTTTTTATATTTATATCTAT
*
312836 TTTATTTAT-TTTA
1 TTTTTTTATATTTA
312849 AATAATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTTTATATTTATATCTAT
Found at i:313052 original size:28 final size:28
Alignment explanation
Indices: 313021--313075 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
313011 CTGACGTGGG
313021 AAAAACAAAAATA-TTTGATAATATGTT
1 AAAAACAAAAATATTTTGATAATATGTT
* *
313048 AAAAACAACATTATTTTGATAATATGTT
1 AAAAACAAAAATATTTTGATAATATGTT
313076 TCAAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.36
Consensus pattern (28 bp):
AAAAACAAAAATATTTTGATAATATGTT
Found at i:313091 original size:29 final size:28
Alignment explanation
Indices: 313021--313099 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
313011 CTGACGTGGG
* *
313021 AAAAACAAAAATA-TTTGATAATATGTT
1 AAAAACAACATTATTTTGATAATATGTT
313048 AAAAACAACATTATTTTGATAATATGTTT
1 AAAAACAACATTATTTTGATAATATG-TT
* * * *
313077 CAAAATAATATTATTTTAATAAT
1 AAAAACAACATTATTTTGATAAT
313100 TAATTTCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.25
28 12 0.27
29 21 0.48
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (28 bp):
AAAAACAACATTATTTTGATAATATGTT
Found at i:314059 original size:19 final size:19
Alignment explanation
Indices: 314024--314063 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
314014 GAAATGAAGC
*
314024 TTTAATAAAAAATTAAAAA
1 TTTAATAAAAAAGTAAAAA
314043 TTTAA-AAATAAAGTAAAAA
1 TTTAATAAA-AAAGTAAAAA
314062 TT
1 TT
314064 ATTATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
TTTAATAAAAAAGTAAAAA
Found at i:315031 original size:15 final size:15
Alignment explanation
Indices: 314963--315079 Score: 76
Period size: 16 Copynumber: 7.3 Consensus size: 15
314953 AACTTGTATC
*
314963 TAAAATGATTTAAACT
1 TAAAAT-ATTCAAACT
* *
314979 TGAAATAACTCAAACT
1 TAAAAT-ATTCAAACT
* *
314995 TAAAAAATTTCAAATT
1 TAAAATA-TTCAAACT
315011 TGAAAATATTCAAA-T
1 T-AAAATATTCAAACT
*
315026 TCAAAATGAGT-AAACT
1 T-AAAAT-ATTCAAACT
315042 TAAAATAAATTCAAACT
1 TAAAAT--ATTCAAACT
*
315059 TAAAATATTTCAAATT
1 TAAAATA-TTCAAACT
315075 TAAAA
1 TAAAA
315080 ATAATCTAAT
Statistics
Matches: 80, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
15 17 0.21
16 47 0.59
17 16 0.20
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.32
Consensus pattern (15 bp):
TAAAATATTCAAACT
Found at i:317312 original size:18 final size:18
Alignment explanation
Indices: 317289--317328 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
317279 AGAAAAAAAG
**
317289 AAGAACGAAAGACTAGGA
1 AAGAACGAAAGAAGAGGA
317307 AAGAACGAAAGAAGAGGA
1 AAGAACGAAAGAAGAGGA
317325 AAGA
1 AAGA
317329 GAAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.60, C:0.07, G:0.30, T:0.03
Consensus pattern (18 bp):
AAGAACGAAAGAAGAGGA
Found at i:320889 original size:11 final size:12
Alignment explanation
Indices: 320868--320897 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
320858 CTCATTGTTT
320868 TTTTCTTTCTTC
1 TTTTCTTTCTTC
320880 TTTT-TTTCTTC
1 TTTTCTTTCTTC
320891 TTTTCTT
1 TTTTCTT
320898 CAATTATTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTCTTTCTTC
Found at i:330019 original size:110 final size:110
Alignment explanation
Indices: 329811--330031 Score: 266
Period size: 110 Copynumber: 2.0 Consensus size: 110
329801 GAAAGCCTAT
* * *
329811 ATTAGTTAGCATTCATGTTAAATCCCACATTAGCTATCACATGAATCGAAGCCTATATTAGTTGG
1 ATTAGCTAGCATTCATGTTAAAACCCACATTAGCTATCACATGAATCGAAGCCTACATTAGTTGG
* * *
329876 CCTTTAAGTTTAAGCCCACACTCGCTGAAACCTAAGTAAGCCCAC
66 CATTTAAGTCTAAGCCCACACTAGCTGAAACCTAAGTAAGCCCAC
* * * * *
329921 ATTAGCTAGCATTCATGTTAAAACCCATATTAG-TTTGTACATGAATTGAAG-CTCGCATTAGTT
1 ATTAGCTAGCATTCATGTTAAAACCCACATTAGCTAT-CACATGAATCGAAGCCT-ACATTAGTT
* * ** *
329984 GGCATTTAAGTCTAAGCCCACATTAGTTGGCACCTAAGTAAGCTCAC
64 GGCATTTAAGTCTAAGCCCACACTAGCTGAAACCTAAGTAAGCCCAC
330031 A
1 A
330032 CTAGTTGGCA
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
109 4 0.04
110 89 0.96
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (110 bp):
ATTAGCTAGCATTCATGTTAAAACCCACATTAGCTATCACATGAATCGAAGCCTACATTAGTTGG
CATTTAAGTCTAAGCCCACACTAGCTGAAACCTAAGTAAGCCCAC
Found at i:330082 original size:28 final size:28
Alignment explanation
Indices: 329969--330115 Score: 113
Period size: 28 Copynumber: 5.3 Consensus size: 28
329959 ACATGAATTG
* * * *
329969 AAGCTCGCATTAGTTGGCATTTAAGTCT
1 AAGCTCACATTAGTTGGCATATGAGTCA
* ** *
329997 AAGCCCACATTAGTTGGCACCTAAGT--
1 AAGCTCACATTAGTTGGCATATGAGTCA
* *
330023 AAGCTCACACTAGTTGGCATATGAGTCG
1 AAGCTCACATTAGTTGGCATATGAGTCA
* *
330051 AAGCTTACATTAGTTGGCATATGCA-TTA
1 AAGCTCACATTAGTTGGCATATG-AGTCA
**
330079 AAGCTCATGTTAGTTGGCACT-TGAGTCA
1 AAGCTCACATTAGTTGGCA-TATGAGTCA
*
330107 AAGCCCACA
1 AAGCTCACA
330116 CAAGTTGGAA
Statistics
Matches: 94, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
26 21 0.22
27 1 0.01
28 70 0.74
29 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (28 bp):
AAGCTCACATTAGTTGGCATATGAGTCA
Found at i:332634 original size:78 final size:78
Alignment explanation
Indices: 332445--332764 Score: 308
Period size: 78 Copynumber: 4.1 Consensus size: 78
332435 TATTTTGGAG
* * * * * **
332445 ATAAAATCGGGG-TTGAAGTATCCCCTAAAAAATAATGGTGTTGGAGTATCCCCAGTGGTGAAAA
1 ATAAAATCGGGGTTTG-AGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAA
332509 TCGATGTTTT-GAA
65 TCGATGTTTTAGAA
* * *
332522 ATAAAACCGGGGTTGGAGTATCCCCTC-GAAAATAATGGGGTTGGAGTATCCCCAATTATGAAAA
1 ATAAAATCGGGGTTTGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCAATTATGAAAA
*
332586 TTTGATGTTTTAGAA
65 -TCGATGTTTTAGAA
* * * ***
332601 AT-AAATTGGGGTTTGAGTATCCCCTCAGAAATAACGAGGTTAGAGTATCCTTGATTATAGAAAA
1 ATAAAATCGGGGTTTGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATTAT-GAAAA
* *
332665 TTGGTGTTTTAGAA
65 TCGATGTTTTAGAA
* * * * * * *
332679 ATAAAAATCGAGGTTAGAGTATGCCTTTAGAAATAACGGGGTTGGAGTTTCCCCGA-TAGTGAAA
1 AT-AAAATCGGGGTTTGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATTA-TG-AA
332743 AATCGATGTTTTAGAA
63 AATCGATGTTTTAGAA
332759 ATAAAA
1 ATAAAA
332765 CCAAGGTTGG
Statistics
Matches: 201, Mismatches: 32, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
77 52 0.26
78 71 0.35
79 18 0.09
80 60 0.30
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.30
Consensus pattern (78 bp):
ATAAAATCGGGGTTTGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAT
CGATGTTTTAGAA
Found at i:332871 original size:130 final size:131
Alignment explanation
Indices: 332637--332894 Score: 367
Period size: 130 Copynumber: 2.0 Consensus size: 131
332627 AGAAATAACG
* * *
332637 AGGTTAGAGTATCCTTGATTATAGAAAATTGGTGTTTTAGAAATAAAAATCGAGGTTAGAGTATG
1 AGGTTAGAGTATCCTCGATTATAGAAAATTGGTGTTTTAGAAATAAAAACCGAGGTTAGAGTATC
* * * *
332702 CCTTTAGAAATAACGGGGTTGGAGTTTCCCCGATAGTGAAAAATCGATGTTTTAGAAATAAAACC
66 CCCTCAGAAATAACGGGGTTGGAGTATCCCCGATAGTGAAAAATCGATATTTTAGAAATAAAACC
332767 A
131 A
* * * * *
332768 AGGTTGGAGTATCCTCGATTGTGGACAATTGGTGTTTTGGAAAT-AAAACC-AGGGTTAGAGTAT
1 AGGTTAGAGTATCCTCGATTATAGAAAATTGGTGTTTTAGAAATAAAAACCGA-GGTTAGAGTAT
* *
332831 CCCCTCAGAAATAGCGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATATTTTAGAAATAAAA
65 CCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATAGTGAAAAATCGATATTTTAGAAATAAAA
332895 ACATGAATGA
Statistics
Matches: 112, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
129 1 0.01
130 73 0.65
131 38 0.34
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (131 bp):
AGGTTAGAGTATCCTCGATTATAGAAAATTGGTGTTTTAGAAATAAAAACCGAGGTTAGAGTATC
CCCTCAGAAATAACGGGGTTGGAGTATCCCCGATAGTGAAAAATCGATATTTTAGAAATAAAACC
A
Found at i:334834 original size:17 final size:18
Alignment explanation
Indices: 334809--334842 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
334799 GAGTACTAAG
334809 GGGA-TTTTTTTGCTGCA
1 GGGACTTTTTTTGCTGCA
334826 GGGACTTTTTTTGCTGC
1 GGGACTTTTTTTGCTGC
334843 CAAAAAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.09, C:0.15, G:0.29, T:0.47
Consensus pattern (18 bp):
GGGACTTTTTTTGCTGCA
Found at i:338918 original size:691 final size:688
Alignment explanation
Indices: 338019--339377 Score: 2425
Period size: 690 Copynumber: 2.0 Consensus size: 688
338009 AAACCTTTAA
*
338019 TTTAAAGCTCATGTATGCATTGTCATGTAGTTAAGCAAGGTTAATTACAACATGTGATTATCATA
1 TTTAAAGCTCATGTATGCATTGTCATGCAGTTAAGCAAGGTTAATTACAACATGTGATTATCATA
338084 TCTCATGAAATAATAATAAAGCATGAAAAAACGATTAATTCATAATATATCTTTTAATTATCTTT
66 TCTCATGAAATAATAATAAAGCATGAAAAAACGATTAATTCATAATATATCTTTTAATTATCTTT
338149 GATTATTTAAAGAAATAATTAATTGATAGTTTAAAAACAAACTTAGACTCAAACAGTAGTTAAGG
131 GATTATTTAAAGAAATAATTAATTGATAGTTTAAAAACAAACTTAGACTCAAACAGTAGTTAAGG
*
338214 TATAAAACTAAGTAAAAATTGGATAAAATCTAG-AAAAACTAGTAGAAAAAAAAACTTATAATTT
196 TATAAAACTAAGTAAAAAATGGATAAAATCTAGAAAAAACTAGTAGAAAAAAAAAC-T-TAATTT
338278 TTTTAGAGACTTTAAAAATGAGGTTGACAAATCAAAATGAGTGAAAATCGGTGTGAAATTCATTA
259 TTTTAGAGACTTTAAAAATGAGGTTGACAAATCAAAATGAGTGAAAATCGGTGTGAAATTCATTA
338343 ATTATTATAAAACAAGACATTTTGTGGAATTTTTGAAGGAAATGATGAAATTTGAGATTTAAATC
324 ATTATTATAAAACAAGACATTTTGTGGAATTTTTGAAGGAAATGATGAAATTTGAGATTTAAATC
** *
338408 AAGAAGGAATTTGTAAAACTTGAATTAAAATCTACAAAATTCATAGAGATTTGGATCGAGCCTTA
389 AAGAAGGAATTTGTAAAACTTGAATTAAAATCTACAAAAGCCATAGAGATTTAGATCGAGCCTTA
338473 GATGACCTCTATATGCCTTAAAACCATTAAATGAAGCAAATCAGACTCATTAC-AAGACATTCGA
454 GATGACCTCTATATGCCTTAAAACCATTAAATGAAGCAAATCAGACTCATT-CTAAGACATTCGA
* *
338537 ACACCTTAGAAGAGTAGTAAGATAAAAATCATGCATTGTGCTCTATTTTGGAAAATAAGGGAAAG
518 ACACCTTAAAAGAGTAGTAAGATAAAAATCATGCATTGCGCTCTATTTTGGAAAATAAGGGAAAG
* * *
338602 CTTGCGTTAATAGATTTCTTGAAGTTATTCCCAACTTAAACAAACCCCAAATGAGACAAATATAT
583 CCTGCATTAATAGATTTCTTGAAGTTATTCCCAACTTAAA-AAA-CCCAAATGAAACAAATATAT
338667 GTGGTTAAAGTTTATCTAAAAATATATGTGGTTGAAGTTTTTC
646 GTGGTTAAAGTTTATCTAAAAATATATGTGGTTGAAGTTTTTC
338710 TTTAAAGCTCATGTATGCATTGTCATGCAGTTAAGCAAGGTTAATTACAACATGTGATTATCATA
1 TTTAAAGCTCATGTATGCATTGTCATGCAGTTAAGCAAGGTTAATTACAACATGTGATTATCATA
* *
338775 TCTCATGAAATAATAATAAAGCATGAAAAAATGATTAATTCATAATATATCTTTTAATTGTCTTT
66 TCTCATGAAATAATAATAAAGCATGAAAAAACGATTAATTCATAATATATCTTTTAATTATCTTT
338840 GATTATTTAAAGAAATAATTAATTGATAGTTTAAAAACAAACTTAGACTCAAACAGTAGTTAAGG
131 GATTATTTAAAGAAATAATTAATTGATAGTTTAAAAACAAACTTAGACTCAAACAGTAGTTAAGG
*
338905 TGTAAAACTAAGTAAAAAATGGATAAAATCTAGAAAAAACTAGTAGAAAAAAAAACTTAATTTTT
196 TATAAAACTAAGTAAAAAATGGATAAAATCTAGAAAAAACTAGTAGAAAAAAAAACTTAATTTTT
* *
338970 TTAGGGACTTTAAAAATGAGGTTGACAAATCAAAATGAGTGAAAATTGGTGTGAAATTCATTAAT
261 TTAGAGACTTTAAAAATGAGGTTGACAAATCAAAATGAGTGAAAATCGGTGTGAAATTCATTAAT
* *
339035 TATTATAAAACAGGACATTTTGTGGAATTTTTGAAGGAATTGATGAAATTTGAGATTTAAATCAA
326 TATTATAAAACAAGACATTTTGTGGAATTTTTGAAGGAAATGATGAAATTTGAGATTTAAATCAA
** *
339100 GAAGGAATTTGTAAAACTTGAATTAAAATCTTTAAAAGCCATAGAGATTTAGATTGAGCCTTAGA
391 GAAGGAATTTGTAAAACTTGAATTAAAATCTACAAAAGCCATAGAGATTTAGATCGAGCCTTAGA
*
339165 TGACCTCTATATGCCTTAAAACCATTAAATGAAGCAAATCAGACTCATTCTAAGACGTTCGAACA
456 TGACCTCTATATGCCTTAAAACCATTAAATGAAGCAAATCAGACTCATTCTAAGACATTCGAACA
*
339230 CCTTAAAAGAGTAGTAAGATAAAAATCATGCATTGCGCTCTATTTTGGAAAATAGGGGAAAGCCT
521 CCTTAAAAGAGTAGTAAGATAAAAATCATGCATTGCGCTCTATTTTGGAAAATAAGGGAAAGCCT
* * *
339295 GCATTAATGGATTTCTTGAATTTATTCCCAACTTAAAGAACCCAAATGAAACAAATATATGTGGT
586 GCATTAATAGATTTCTTGAAGTTATTCCCAACTTAAAAAACCCAAATGAAACAAATATATGTGGT
*
339360 TGAAGTTTATCTAAAAAT
651 TAAAGTTTATCTAAAAAT
339378 GTGAGAAATT
Statistics
Matches: 640, Mismatches: 26, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
688 41 0.06
689 3 0.00
690 350 0.55
691 224 0.35
692 22 0.03
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (688 bp):
TTTAAAGCTCATGTATGCATTGTCATGCAGTTAAGCAAGGTTAATTACAACATGTGATTATCATA
TCTCATGAAATAATAATAAAGCATGAAAAAACGATTAATTCATAATATATCTTTTAATTATCTTT
GATTATTTAAAGAAATAATTAATTGATAGTTTAAAAACAAACTTAGACTCAAACAGTAGTTAAGG
TATAAAACTAAGTAAAAAATGGATAAAATCTAGAAAAAACTAGTAGAAAAAAAAACTTAATTTTT
TTAGAGACTTTAAAAATGAGGTTGACAAATCAAAATGAGTGAAAATCGGTGTGAAATTCATTAAT
TATTATAAAACAAGACATTTTGTGGAATTTTTGAAGGAAATGATGAAATTTGAGATTTAAATCAA
GAAGGAATTTGTAAAACTTGAATTAAAATCTACAAAAGCCATAGAGATTTAGATCGAGCCTTAGA
TGACCTCTATATGCCTTAAAACCATTAAATGAAGCAAATCAGACTCATTCTAAGACATTCGAACA
CCTTAAAAGAGTAGTAAGATAAAAATCATGCATTGCGCTCTATTTTGGAAAATAAGGGAAAGCCT
GCATTAATAGATTTCTTGAAGTTATTCCCAACTTAAAAAACCCAAATGAAACAAATATATGTGGT
TAAAGTTTATCTAAAAATATATGTGGTTGAAGTTTTTC
Found at i:345337 original size:13 final size:13
Alignment explanation
Indices: 345319--345343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
345309 CATAAAGTGT
345319 TGTATCGATACAA
1 TGTATCGATACAA
345332 TGTATCGATACA
1 TGTATCGATACA
345344 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:345355 original size:33 final size:33
Alignment explanation
Indices: 345299--345365 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
345289 TCAACTGATT
*
345299 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCAATACAA
*** *
345332 TGTATCGATACATATTTTTTTGTATCAATACAA
1 TGTATCGATACATAAAGTGTTGTATCAATACAA
345365 T
1 T
345366 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCAATACAA
Found at i:345423 original size:34 final size:34
Alignment explanation
Indices: 345385--345464 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
345375 TGCCAAAAAA
345385 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCGATACATTACTCAAATGTATCGATACAT
345419 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCGATACATTACTCAAATGTATCGATACAT
345453 TGTATCGATACA
1 TGTATCGATACA
345465 CTGATCTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (34 bp):
TGTATCGATACATTACTCAAATGTATCGATACAT
Found at i:345424 original size:13 final size:12
Alignment explanation
Indices: 345384--345464 Score: 70
Period size: 13 Copynumber: 7.1 Consensus size: 12
345374 CTGCCAAAAA
345384 ATGTATCGATAC
1 ATGTATCGATAC
345396 AT-TACTC-A-A-
1 ATGTA-TCGATAC
345405 ATGTATCGATAC
1 ATGTATCGATAC
345417 ATTGTATCGATAC
1 A-TGTATCGATAC
345430 AT-TACTC-A-A-
1 ATGTA-TCGATAC
345439 ATGTATCGATAC
1 ATGTATCGATAC
345451 ATTGTATCGATAC
1 A-TGTATCGATAC
345464 A
1 A
345465 CTGATCTTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 23
0.71 0.00 0.29
Matches are distributed among these distances:
9 8 0.14
10 8 0.14
11 8 0.14
12 9 0.16
13 24 0.42
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:345529 original size:52 final size:52
Alignment explanation
Indices: 345473--345601 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
345463 CACTGATCTT
*
345473 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
345525 TGTATCGATACGTGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
345577 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
345602 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:353264 original size:19 final size:20
Alignment explanation
Indices: 353220--353273 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
353210 CTGCCAGTTT
**
353220 CATGTATCGATACAATTATC
1 CATGTATCGATACAATTAAA
353240 CATGTATCGATACAA-TAAA
1 CATGTATCGATACAATTAAA
353259 CATGTATCGATACAA
1 CATGTATCGATACAA
353274 AGCATAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTAAA
Found at i:358462 original size:19 final size:19
Alignment explanation
Indices: 358425--358464 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
358415 ATGAATTTAT
*
358425 ATAACTTTAACTATAAAAA
1 ATAACTTTAACAATAAAAA
358444 ATAACTTTAA-AATACAAAA
1 ATAACTTTAACAATA-AAAA
358463 AT
1 AT
358465 TAAATAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAACTTTAACAATAAAAA
Found at i:361605 original size:25 final size:25
Alignment explanation
Indices: 361569--361658 Score: 94
Period size: 25 Copynumber: 3.6 Consensus size: 25
361559 TCATATTTAG
*
361569 ACTAATAAAATTGAAATTAATCATT
1 ACTAATACAATTGAAATTAATCATT
* * * *
361594 ACTAGTACAATTG-AATATACTTA-A
1 ACTAATACAATTGAAAT-TAATCATT
*
361618 ACTAATTAAAATTGAAATTAATCATT
1 ACTAA-TACAATTGAAATTAATCATT
361644 ACTAATACAATTGAA
1 ACTAATACAATTGAA
361659 TATATATTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
24 7 0.14
25 35 0.70
26 8 0.16
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (25 bp):
ACTAATACAATTGAAATTAATCATT
Found at i:361682 original size:122 final size:121
Alignment explanation
Indices: 361379--361682 Score: 343
Period size: 125 Copynumber: 2.5 Consensus size: 121
361369 ATCATAGTTG
*
361379 AAATTGAAATTGATCATTACTAGTACAATTGAATATATACTTAATATTATTACATTCCTATTTAG
1 AAATTGAAATTGATCATTACTAGTACAATTGAATATATACTTAATATTATTACATTCATATTTAG
* * *
361444 ATTAATGGAAACTGAAATTGAAATGGGTCAGTACTAGTACAGGTGAATATGTACCTAAACT
66 ACTAATGAAAACTGAAATT-AAA---GTCAGTACTAGTACAAGTGAATA-GTACCTAAACT
* *
361505 -AATTGAAATTGATCATTACTAGTACAATTAAATATATACTTAATATTATTGCATTCATATTTAG
1 AAATTGAAATTGATCATTACTAGTACAATTGAATATATACTTAATATTATTACATTCATATTTAG
* * * *
361569 ACTAAT-AAAATTGAAATT-AA-TCATTACTAGTACAATTGAATA-TACTTAAACTAATT
66 ACTAATGAAAACTGAAATTAAAGTCAGTACTAGTACAAGTGAATAGTACCTAAAC----T
* *
361625 AAAATTGAAATTAATCATTACTAATACAATTGAATATATA-TTAA-ATGCTATTACATTC
1 -AAATTGAAATTGATCATTACTAGTACAATTGAATATATACTTAATAT--TATTACATTC
361683 TTTAAACTAA
Statistics
Matches: 156, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
116 8 0.05
118 19 0.12
120 3 0.02
121 4 0.03
122 46 0.29
124 10 0.06
125 66 0.42
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.37
Consensus pattern (121 bp):
AAATTGAAATTGATCATTACTAGTACAATTGAATATATACTTAATATTATTACATTCATATTTAG
ACTAATGAAAACTGAAATTAAAGTCAGTACTAGTACAAGTGAATAGTACCTAAACT
Found at i:361852 original size:73 final size:73
Alignment explanation
Indices: 361610--361955 Score: 333
Period size: 73 Copynumber: 4.8 Consensus size: 73
361600 ACAATTGAAT
* * ** *
361610 ATACTTAAACTAATTAAAATTGAAATTAATCATTACTAATACAATTGAATATATA-TTAA-ATGC
1 ATACTTAGACTAATTGAAATTGAAATTGGTCATTACTAGTACAATTGAATATATACTTAATAT--
361673 TATTACATTC
64 TATTACATTC
* * * * * ** ** *
361683 -T--TTAAACTAAATGAAATTGGAATTGGTTATTACTATTATGATTGTGTATGTACTTAATATTT
1 ATACTTAGACTAATTGAAATTGAAATTGGTCATTACTAGTACAATTGAATATATACTTAATA-TT
* *
361745 TTTATATTC
65 ATTACATTC
* * * *
361754 GTATTTAGACTAATGGAAATTGAAATAGGTCATTACTAGTACAATTGAATATATACTTAATATTA
1 ATACTTAGACTAATTGAAATTGAAATTGGTCATTACTAGTACAATTGAATATATACTTAATATTA
*
361819 TTACGTTC
66 TTACATTC
* * **
361827 ATACTTAGACTAATTGATATTGAAATTGGTCATTACTTGTATGATTGAATATATACTTAATATTA
1 ATACTTAGACTAATTGAAATTGAAATTGGTCATTACTAGTACAATTGAATATATACTTAATATTA
*
361892 TTACACTC
66 TTACATTC
* * * * * *
361900 ATATTTGGTCTAATAGAAATTGAAATTGGTCATTACTAGTACACTTGAATACATAC
1 ATACTTAGACTAATTGAAATTGAAATTGGTCATTACTAGTACAATTGAATATATAC
361956 ATAAACTAAT
Statistics
Matches: 218, Mismatches: 49, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
70 39 0.18
71 12 0.06
72 3 0.01
73 118 0.54
74 46 0.21
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (73 bp):
ATACTTAGACTAATTGAAATTGAAATTGGTCATTACTAGTACAATTGAATATATACTTAATATTA
TTACATTC
Found at i:361937 original size:146 final size:144
Alignment explanation
Indices: 361618--361960 Score: 381
Period size: 146 Copynumber: 2.4 Consensus size: 144
361608 ATATACTTAA
** *
361618 ACTAATTA-AAATTGAAATTAATCATTACTAATACAATTGAATATATA-TTAAATGCTATTACAT
1 ACTAA-TAGAAATTGAAATTGGTCATTACTAGTACAATTGAATATATACTTAAAT-CTATTACAT
* * ** * *
361681 TCTTTAAACTAAATGAAATTGGAATTGGTTATTACTATTATGATTGTGTATGTACTTAATATTTT
64 TCTTTAAACTAAATGAAATTGAAATTGGTCATTACTATTATGATTGAATATATACTTAATATTTA
* * *
361746 TTATATTCGTATTTAG
129 TTACACTCATATTTAG
* * *
361762 ACTAATGGAAATTGAAATAGGTCATTACTAGTACAATTGAATATATACTTAATAT-TATTACGTT
1 ACTAATAGAAATTGAAATTGGTCATTACTAGTACAATTGAATATATACTTAA-ATCTATTACATT
* * *
361826 CATACTTAGACTAATTGATATTGAAATTGGTCATTACT-TGTATGATTGAATATATACTTAATA-
65 C-T--TTAAACTAAATGAAATTGAAATTGGTCATTACTAT-TATGATTGAATATATACTTAATAT
*
361889 TTATTACACTCATATTTGG
126 TTATTACACTCATATTTAG
* * * *
361908 TCTAATAGAAATTGAAATTGGTCATTACTAGTACACTTGAATACATACATAAA
1 ACTAATAGAAATTGAAATTGGTCATTACTAGTACAATTGAATATATACTTAAA
361961 CTAATTGAAA
Statistics
Matches: 167, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
143 1 0.01
144 49 0.29
145 6 0.04
146 63 0.38
147 48 0.29
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (144 bp):
ACTAATAGAAATTGAAATTGGTCATTACTAGTACAATTGAATATATACTTAAATCTATTACATTC
TTTAAACTAAATGAAATTGAAATTGGTCATTACTATTATGATTGAATATATACTTAATATTTATT
ACACTCATATTTAG
Found at i:362001 original size:52 final size:52
Alignment explanation
Indices: 361909--362007 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 52
361899 CATATTTGGT
** * ** *
361909 CTAATAGAAATTGAAATTGGTCATTACTAGTACACTTGAATACATACATAAA
1 CTAATAGAAATTGAAATTAATCAGTACTAGTACAAGTGAATAAATACATAAA
*
361961 CTAATTGAAATTGAAATTAATCAGTACTAGTACAAGTGAATAAATAC
1 CTAATAGAAATTGAAATTAATCAGTACTAGTACAAGTGAATAAATAC
362008 TTAATGTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 40 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (52 bp):
CTAATAGAAATTGAAATTAATCAGTACTAGTACAAGTGAATAAATACATAAA
Found at i:363060 original size:28 final size:28
Alignment explanation
Indices: 362979--363060 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
362969 TTTTGGAGAT
*
362979 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
363007 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
363035 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
363061 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:363203 original size:51 final size:51
Alignment explanation
Indices: 363043--363213 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
363033 GAAATAACGA
* * * *
363043 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATCGGTA-TTTTGAAAATAAAATCGG
** * * * * * *
363095 AATTGGAGTATCCCCGATTAAAGGAGAAATGGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATCGGTATTTTGAAAATAAAATCGG
* *
363148 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATCGGTATTTTGAAAATAAAATCGG
363199 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
363214 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 39 0.41
52 16 0.17
53 32 0.33
54 9 0.09
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATCGGTATTTTGAAAATAAAATCGG
Found at i:363259 original size:27 final size:28
Alignment explanation
Indices: 363196--363271 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
363186 AAAATAAAGT
*
363196 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
363224 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
363251 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
363272 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:365702 original size:13 final size:13
Alignment explanation
Indices: 365684--365709 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
365674 ACAAAGATCC
365684 ATGTATCGATACA
1 ATGTATCGATACA
365697 ATGTATCGATACA
1 ATGTATCGATACA
365710 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:365705 original size:33 final size:33
Alignment explanation
Indices: 365663--365727 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
365653 AAAATTTCCA
***
365663 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
365696 AATGTATCGATACACAGAAAAATGTATCGATA
1 AATGTATCGATACAAAGAAAAATGTATCGATA
365728 TATTTCCTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:365773 original size:19 final size:18
Alignment explanation
Indices: 365749--365816 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
365739 CAGTAGCTAA
365749 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
365768 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
365783 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
365800 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
365817 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:365789 original size:13 final size:13
Alignment explanation
Indices: 365771--365795 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
365761 ACAATACTTA
365771 TGTATCGATACAT
1 TGTATCGATACAT
365784 TGTATCGATACA
1 TGTATCGATACA
365796 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:365793 original size:32 final size:32
Alignment explanation
Indices: 365752--365814 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
365742 TAGCTAATTA
*
365752 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
365784 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
365815 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:365896 original size:21 final size:21
Alignment explanation
Indices: 365872--365924 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
365862 CATTTGTAGG
365872 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
365893 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
365914 ATGTATCGATA
1 ATGTATCGATA
365925 TATTTAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:366629 original size:55 final size:54
Alignment explanation
Indices: 366545--367057 Score: 764
Period size: 55 Copynumber: 9.3 Consensus size: 54
366535 ATAAATTGTA
* * * * *
366545 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT-AAAGGTG
366600 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAGGTG
*
366655 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAA-AGGTG
* *
366710 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
366765 TCCTGCTCGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAGGTG
366820 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAGGTG
366875 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAGGTG
* *
366930 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
366985 TCCTGCTCGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
367040 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
367058 AAAAAGCGGA
Statistics
Matches: 430, Mismatches: 20, Indels: 16
0.92 0.04 0.03
Matches are distributed among these distances:
54 12 0.03
55 404 0.94
56 14 0.03
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTG
Found at i:366675 original size:26 final size:26
Alignment explanation
Indices: 366646--366735 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
366636 GTGTGGGCTT
366646 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGAGGAC
** * * *
366672 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGTGTCCTGC-TCTT-TGAGGAC
* *
366699 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGAGGAC
366727 TGAAAGGTG
1 TGAAAGGTG
366736 CCACCAACTT
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 17 0.36
27 8 0.17
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGAGGAC
Found at i:366764 original size:29 final size:29
Alignment explanation
Indices: 366676--366764 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
366666 GAGGACTGAA
366676 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
** * *
366705 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA-
1 AGGTG-CCACCAACTTGTGTGGG-CTTTAAG
366731 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
366760 AGGTG
1 AGGTG
366765 TCCTGCTCGT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (29 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAG
Found at i:368065 original size:13 final size:12
Alignment explanation
Indices: 368041--368102 Score: 61
Period size: 14 Copynumber: 4.8 Consensus size: 12
368031 CTTTTCTCTC
*
368041 TTTTTCTTTGTT
1 TTTTTTTTTGTT
368053 TTGTTTTTTTGTT
1 TT-TTTTTTTGTT
*
368066 TTTTTTTTTCCTTT
1 TTTTTTTTT--GTT
368080 TTTTTTTTTGCTCT
1 TTTTTTTTTG-T-T
368094 TTTTTTTTT
1 TTTTTTTTT
368103 TTGAAGAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.21
13 12 0.29
14 21 0.50
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:368071 original size:17 final size:16
Alignment explanation
Indices: 368041--368105 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
368031 CTTTTCTCTC
* *
368041 TTTTTCTTTGTTTTGT
1 TTTTTTTTTTTTTTGT
368057 TTTTTTGTTTTTTTT-T
1 TTTTTT-TTTTTTTTGT
*
368073 TTCCTTTTTTTTTTTTGC
1 TT--TTTTTTTTTTTTGT
*
368091 TCTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTG
368106 AAGAGAAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 21 0.51
17 15 0.37
18 5 0.12
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTTTTTTGT
Found at i:368095 original size:16 final size:15
Alignment explanation
Indices: 368064--368105 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 15
368054 TGTTTTTTTG
368064 TTTTTTTTTTT-CCT
1 TTTTTTTTTTTGCCT
368078 TTTTTTTTTTTGCTCT
1 TTTTTTTTTTTGC-CT
368094 TTTTTTTTTTTG
1 TTTTTTTTTTTG
368106 AAGAGAAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 11 0.42
15 1 0.04
16 14 0.54
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTTGCCT
Done.