Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold263
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: 13530
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Found at i:6155 original size:9 final size:9
Alignment explanation
Indices: 6141--6367 Score: 145
Period size: 9 Copynumber: 24.6 Consensus size: 9
6131 TATTTAAGTA
6141 TTATGTAAG
1 TTATGTAAG
*
6150 TTATGTAAT
1 TTATGTAAG
*
6159 TTATGATATG
1 TTATG-TAAG
* * *
6169 ATATAT-AT
1 TTATGTAAG
*
6177 TTATGTAAA
1 TTATGTAAG
* *
6186 TTATAT-AT
1 TTATGTAAG
*
6194 TTATCTAAG
1 TTATGTAAG
*
6203 TTATATAAG
1 TTATGTAAG
6212 TTATGTAAG
1 TTATGTAAG
*
6221 TTATGTAAA
1 TTATGTAAG
*
6230 TTATGATATAAA
1 TTATG---TAAG
*
6242 TATATTTAAG
1 T-TATGTAAG
6252 TATTATGTAAG
1 --TTATGTAAG
6263 TTATGTAAG
1 TTATGTAAG
* *
6272 TTATAT-AT
1 TTATGTAAG
*
6280 TTATCTAAG
1 TTATGTAAG
*
6289 TTATATAAG
1 TTATGTAAG
*
6298 TTATATAAG
1 TTATGTAAG
*
6307 TTATGTAGG
1 TTATGTAAG
*
6316 TTATATAAG
1 TTATGTAAG
6325 TTATGTAAG
1 TTATGTAAG
*
6334 TTATATATATG
1 TTATGTA-A-G
*
6345 TTATATAAG
1 TTATGTAAG
*
6354 TTATGTAAA
1 TTATGTAAG
6363 TTATG
1 TTATG
6368 ATATCAAATA
Statistics
Matches: 173, Mismatches: 33, Indels: 24
0.75 0.14 0.10
Matches are distributed among these distances:
8 16 0.09
9 123 0.71
10 10 0.06
11 15 0.09
12 6 0.03
13 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:6220 original size:18 final size:18
Alignment explanation
Indices: 6141--6367 Score: 163
Period size: 18 Copynumber: 12.3 Consensus size: 18
6131 TATTTAAGTA
* *
6141 TTATGTAAGTTATGTAAT
1 TTATGTAAGTTATATAAG
* * *
6159 TTATGATATGATATAT-AT
1 TTATG-TAAGTTATATAAG
* *
6177 TTATGTAAATTATAT-AT
1 TTATGTAAGTTATATAAG
*
6194 TTATCTAAGTTATATAAG
1 TTATGTAAGTTATATAAG
* *
6212 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
* *
6230 TTATGATATAAATATATTTAAG
1 TTATG---TAAGT-TATATAAG
*
6252 TATTATGTAAGTTATGTAAG
1 --TTATGTAAGTTATATAAG
* * *
6272 TTATAT-ATTTATCTAAG
1 TTATGTAAGTTATATAAG
*
6289 TTATATAAGTTATATAAG
1 TTATGTAAGTTATATAAG
*
6307 TTATGTAGGTTATATAAG
1 TTATGTAAGTTATATAAG
6325 TTATGTAAGTTATATATATG
1 TTATGTAAGTTATATA-A-G
* * *
6345 TTATATAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
6363 TTATG
1 TTATG
6368 ATATCAAATA
Statistics
Matches: 169, Mismatches: 29, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
17 37 0.22
18 82 0.49
19 9 0.05
20 22 0.13
21 8 0.05
22 6 0.04
24 5 0.03
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (18 bp):
TTATGTAAGTTATATAAG
Found at i:6253 original size:113 final size:114
Alignment explanation
Indices: 6117--6337 Score: 313
Period size: 113 Copynumber: 1.9 Consensus size: 114
6107 ACTAGTTATG
* * *
6117 TATGATATGATATATATTTAAGTATTATGTAAGTTATGTAATTTATGATATGATATAT-ATTTAT
1 TATGATATGAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT-ATAT-ATATATAAGTTAT
* *
6181 GTAAATTATAT-ATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
64 ATAAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
* *
6231 TATGATAT-AAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATTTATCTAAGTTATAT
1 TATGATATGAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATATATATAAGTTATAT
* * *
6295 AAGTTATATAAGTTATGTAGGTTATATAAGTTATGTAAGTTAT
66 AAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTAT
6338 ATATATGTTA
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
111 4 0.04
112 18 0.19
113 65 0.68
114 8 0.08
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (114 bp):
TATGATATGAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATATATATAAGTTATAT
AAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
Found at i:6345 original size:86 final size:88
Alignment explanation
Indices: 6141--6371 Score: 240
Period size: 86 Copynumber: 2.6 Consensus size: 88
6131 TATTTAAGTA
* * * *
6141 TTATGTAAGTTATGTAATTTATGATATGATATATATTTATGTAAATTATATATTTATCTAAGTTA
1 TTATATAAGTTATGTAAGTTAT-ATAT-ATGTATAGTTATGTAAATTATATATTTATCTAAGTTA
* *
6206 TATAAGTTATGTAAGTTATGTAAAT
64 TATAAGTTATATAAGTTATGTAAAG
* * *
6231 TATGATATAAATATATTTAAG---TAT-TATGTA-AGTTATGTAAGTTATATATTTATCTAAGTT
1 T-T-ATATAAGT-TATGTAAGTTATATATATGTATAGTTATGTAAATTATATATTTATCTAAGTT
*
6291 ATATAAGTTATATAAGTTATGT-AGG
63 ATATAAGTTATATAAGTTATGTAAAG
6316 TTATATAAGTTATGTAAGTTATATATATGTTATATAAGTTATGTAAATTATGATAT
1 TTATATAAGTTATGTAAGTTATATATATG---TAT-AGTTATGTAAATTAT-ATAT
6372 CAAATATATT
Statistics
Matches: 115, Mismatches: 13, Indels: 24
0.76 0.09 0.16
Matches are distributed among these distances:
82 7 0.06
83 7 0.06
84 1 0.01
85 5 0.04
86 53 0.46
87 4 0.03
88 1 0.01
89 4 0.03
90 2 0.02
91 15 0.13
92 10 0.09
93 6 0.05
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.48
Consensus pattern (88 bp):
TTATATAAGTTATGTAAGTTATATATATGTATAGTTATGTAAATTATATATTTATCTAAGTTATA
TAAGTTATATAAGTTATGTAAAG
Found at i:6380 original size:86 final size:84
Alignment explanation
Indices: 6141--6380 Score: 211
Period size: 95 Copynumber: 2.8 Consensus size: 84
6131 TATTTAAGTA
* * *
6141 TTATGTAAGTTATGTAATT-TATGATATGATATAT-ATTTATGTAAATTATATAT---TTATCTA
1 TTATGTAAGTTATGTAATTATAT-ATATGTTATATAAGTTATGTAAATTATATATCAATTATATA
6201 AGTTATATAAGTTATGTAAG
65 AGTTATATAAGTTATGTAAG
* * * * * *
6221 TTATGTAAATTATGATATAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATTTATCT
1 TTATGTAAGTTATG---TAATTATATAT-A-TGTTATATAAGTTATGTAA---AT-TATATATC-
*
6286 AAGTTATATAAGTTATATAAGTTATGTAGG
56 AA-TTATATAAGTTATATAAGTTATGTAAG
* *
6316 TTATATAAGTTATGTAAGTTATATATATGTTATATAAGTTATGTAAATTATGATATCAAATATAT
1 TTATGTAAGTTATGTAA-TTATATATATGTTATATAAGTTATGTAAATTAT-ATATCAATTATAT
6381 TTATGTATTA
Statistics
Matches: 124, Mismatches: 18, Indels: 30
0.72 0.10 0.17
Matches are distributed among these distances:
80 13 0.10
83 5 0.04
84 4 0.03
85 5 0.04
86 14 0.11
87 5 0.04
88 6 0.05
89 2 0.02
90 6 0.05
91 17 0.14
92 4 0.03
93 6 0.05
95 37 0.30
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.47
Consensus pattern (84 bp):
TTATGTAAGTTATGTAATTATATATATGTTATATAAGTTATGTAAATTATATATCAATTATATAA
GTTATATAAGTTATGTAAG
Found at i:6492 original size:15 final size:15
Alignment explanation
Indices: 6472--6527 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
6462 AAGTAGCGGG
6472 ATTAAATAATATTTA
1 ATTAAATAATATTTA
6487 ATTAAATAATATTT-
1 ATTAAATAATATTTA
6501 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
6516 ATTAAATAATAT
1 ATTAAATAATAT
6528 ACATGTCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.44
16 6 0.17
17 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:6733 original size:24 final size:24
Alignment explanation
Indices: 6705--6771 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
6695 ACTTAAATGG
6705 TAAAACGGACGATAATATTTGTAA
1 TAAAACGGACGATAATATTTGTAA
*
6729 TAAAACGGA-GAATAATATTTGTGA
1 TAAAACGGACG-ATAATATTTGTAA
6753 TAAAACGGACGA-AATATTT
1 TAAAACGGACGATAATATTT
6772 CAATAATAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
23 8 0.20
24 31 0.77
25 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.28
Consensus pattern (24 bp):
TAAAACGGACGATAATATTTGTAA
Found at i:6994 original size:22 final size:22
Alignment explanation
Indices: 6969--7013 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
6959 CTATATACTT
6969 TGAATCTTTAAAATATTTAAAA
1 TGAATCTTTAAAATATTTAAAA
6991 TGAATCTTTAAAATATTTAAAA
1 TGAATCTTTAAAATATTTAAAA
7013 T
1 T
7014 AAGGTTGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (22 bp):
TGAATCTTTAAAATATTTAAAA
Found at i:7095 original size:7 final size:7
Alignment explanation
Indices: 7083--7142 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
7073 AGAAATTTAA
7083 AAATATT
1 AAATATT
7090 AAATATT
1 AAATATT
*
7097 AAA-ATA
1 AAATATT
*
7103 AAACATT
1 AAATATT
*
7110 ATTAATATA
1 A--AATATT
7119 AAAT-TT
1 AAATATT
7125 AAAATATT
1 -AAATATT
7133 AAATATT
1 AAATATT
7140 AAA
1 AAA
7143 ATAAAACATT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
6 6 0.14
7 30 0.70
8 2 0.05
9 5 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (7 bp):
AAATATT
Found at i:7100 original size:15 final size:15
Alignment explanation
Indices: 7082--7145 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 15
7072 AAGAAATTTA
7082 AAAATATTAAATATT
1 AAAATATTAAATATT
*
7097 AAAATA--AAACATT
1 AAAATATTAAATATT
* *
7110 ATTAATATAAAAT-TT
1 A-AAATATTAAATATT
7125 AAAATATTAAATATT
1 AAAATATTAAATATT
7140 AAAATA
1 AAAATA
7146 AAACATTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
13 7 0.17
14 13 0.32
15 17 0.43
16 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATATTAAATATT
Found at i:7100 original size:16 final size:15
Alignment explanation
Indices: 7075--7143 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
7065 ACTTTTAAAG
7075 AAAT-TTAAAAATATT
1 AAATATTAAAAATA-T
7090 AAATATT-AAAATA-
1 AAATATTAAAAATAT
* **
7103 AAACATTATTAATAT
1 AAATATTAAAAATAT
*
7118 AAA-ATTTAAAATATT
1 AAATATTAAAAATA-T
7133 AAATATTAAAA
1 AAATATTAAAA
7144 TAAAACATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 6 0.14
14 11 0.26
15 17 0.40
16 8 0.19
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATATTAAAAATAT
Found at i:7110 original size:20 final size:20
Alignment explanation
Indices: 7082--7153 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
7072 AAGAAATTTA
*
7082 AAAATATTAAATATTAAAAT
1 AAAACATTAAATATTAAAAT
7102 AAAACATTATTAATA-TAAAATTT
1 AAAACATTA--AATATTAAAA--T
*
7125 AAAATATTAAATATTAAAAT
1 AAAACATTAAATATTAAAAT
7145 AAAACATTA
1 AAAACATTA
7154 TTAATATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
20 17 0.39
21 9 0.20
22 9 0.20
23 9 0.20
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAACATTAAATATTAAAAT
Found at i:7134 original size:43 final size:44
Alignment explanation
Indices: 7075--7164 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 44
7065 ACTTTTAAAG
7075 AAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATA
1 AAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATA
7119 AAATTT-AAAATATTAAATATTAAAATAAAACATTATTAATATA
1 AAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATA
7162 AAA
1 AAA
7165 AATAGTAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 40 0.87
44 6 0.13
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (44 bp):
AAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATA
Found at i:7157 original size:16 final size:14
Alignment explanation
Indices: 7090--7165 Score: 66
Period size: 16 Copynumber: 5.2 Consensus size: 14
7080 TAAAAATATT
7090 AAATATTAAAATAA
1 AAATATTAAAATAA
*
7104 AACATTATTAATAT-A
1 AA-A-TATTAAAATAA
*
7119 AAAT-TTAAAATATT
1 AAATATTAAAATA-A
7133 AAATATTAAAATAA
1 AAATATTAAAATAA
*
7147 AACATTATTAATATAA
1 AA-A-TATTAAAATAA
7163 AAA
1 AAA
7166 ATAGTAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
12 6 0.12
13 1 0.02
14 9 0.18
15 14 0.28
16 20 0.40
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATATTAAAATAA
Found at i:11934 original size:10 final size:10
Alignment explanation
Indices: 11919--11963 Score: 63
Period size: 10 Copynumber: 4.3 Consensus size: 10
11909 CCACTTTCCA
11919 TATATATATT
1 TATATATATT
11929 TATATATATT
1 TATATATATT
*
11939 TAAATAATATTT
1 TATAT-ATA-TT
11951 TATATATATT
1 TATATATATT
11961 TAT
1 TAT
11964 CTTATATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 19 0.61
11 6 0.19
12 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TATATATATT
Found at i:11970 original size:15 final size:15
Alignment explanation
Indices: 11950--11981 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11940 AAATAATATT
*
11950 TTATATATATTTATC
1 TTATATACATTTATC
11965 TTATATACATTTATC
1 TTATATACATTTATC
11980 TT
1 TT
11982 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:11970 original size:22 final size:23
Alignment explanation
Indices: 11921--11971 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
11911 ACTTTCCATA
11921 TATATATTTATATATATTTAAAT
1 TATATATTTATATATATTTAAAT
* **
11944 AATAT-TTTATATATATTTATCT
1 TATATATTTATATATATTTAAAT
11966 TATATA
1 TATATA
11972 CATTTATCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TATATATTTATATATATTTAAAT
Found at i:12859 original size:14 final size:14
Alignment explanation
Indices: 12840--12873 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
12830 ATTGAACCTG
12840 CTTAAACCATATAT-
1 CTTAAACCATA-ATC
12854 CTTAAACCATAATC
1 CTTAAACCATAATC
12868 CTTAAA
1 CTTAAA
12874 ATATAATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 17 0.89
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (14 bp):
CTTAAACCATAATC
Found at i:13172 original size:81 final size:80
Alignment explanation
Indices: 13029--13205 Score: 327
Period size: 81 Copynumber: 2.2 Consensus size: 80
13019 GTTTAGGGGT
13029 TTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGGTTTTAGCGGCGTTTTACCTAAAGCG
1 TTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGGTTTTAGCGGCGTTTTACCTAAAGCG
13094 CCGCTAATGCTCTGG
66 CCGCTAATGCTCTGG
*
13109 TTTTAGCGGCGTTTTACCTAAAGCGCTGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCTAAAGC
1 TTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGG-TTTTAGCGGCGTTTTACCTAAAGC
*
13174 GCCGCTAATGCTCTGT
65 GCCGCTAATGCTCTGG
13190 TTTTAGCGGCGTTTTA
1 TTTTAGCGGCGTTTTA
13206 GTAAAAAACG
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
80 39 0.41
81 55 0.59
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (80 bp):
TTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGGTTTTAGCGGCGTTTTACCTAAAGCG
CCGCTAATGCTCTGG
Found at i:13233 original size:81 final size:80
Alignment explanation
Indices: 13027--13233 Score: 326
Period size: 81 Copynumber: 2.6 Consensus size: 80
13017 AGGTTTAGGG
* *
13027 GTTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGGTTTTAGCGGCGTTTTACCTAAAG
1 GTTTTTAGCGGCGTTTTACCTAAAGCGCTGCTAATGCTCTGTTTTTAGCGGCGTTTTACCTAAAG
13092 CGCCGCTAATGCTCT
66 CGCCGCTAATGCTCT
*
13107 GGTTTTAGCGGCGTTTTACCTAAAGCGCTGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCTAAA
1 GTTTTTAGCGGCGTTTTACCTAAAGCGCTGCTAATGCTCT-GTTTTTAGCGGCGTTTTACCTAAA
13172 GCGCCGCTAATGCTCT
65 GCGCCGCTAATGCTCT
* * *
13188 GTTTTTAGCGGCGTTTTA-GTAAAAAACGCTGCGAATGCTCTGTTTT
1 GTTTTTAGCGGCGTTTTACCT--AAAGCGCTGCTAATGCTCTGTTTT
13234 ACCAGCGTTT
Statistics
Matches: 117, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
80 39 0.33
81 61 0.52
82 17 0.15
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.35
Consensus pattern (80 bp):
GTTTTTAGCGGCGTTTTACCTAAAGCGCTGCTAATGCTCTGTTTTTAGCGGCGTTTTACCTAAAG
CGCCGCTAATGCTCT
Found at i:13234 original size:40 final size:40
Alignment explanation
Indices: 13029--13205 Score: 327
Period size: 40 Copynumber: 4.4 Consensus size: 40
13019 GTTTAGGGGT
13029 TTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGG
1 TTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGG
13069 TTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGG
1 TTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGG
*
13109 TTTTAGCGGCGTTTTACCTAAAGCGCTGCTAATGCTCTGG
1 TTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGG
*
13149 TTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGT
1 -TTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGG
13190 TTTTAGCGGCGTTTTA
1 TTTTAGCGGCGTTTTA
13206 GTAAAAAACG
Statistics
Matches: 133, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
40 95 0.71
41 38 0.29
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGG
Found at i:13242 original size:121 final size:121
Alignment explanation
Indices: 13026--13244 Score: 343
Period size: 121 Copynumber: 1.8 Consensus size: 121
13016 GAGGTTTAGG
13026 GGTTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGGTTTTAGCGGCGTTTTACCTAAA
1 GGTTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGGTTTTAGCGGCGTTTTACCTAAA
* * * *
13091 GCGCCGCTAATGCTCTGGTTTTAGCGGCGTTTTACCTAAAGCGCTGCTAATGCTCT
66 ACGCCGCGAATGCTCTGGTTTTACCAGCGTTTTACCTAAAGCGCTGCTAATGCTCT
* *
13147 GGTTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGTTTTTAGCGGCGTTTTA-GTAAA
1 GGTTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGGTTTTAGCGGCGTTTTACCT--A
*
13211 AAACGCTGCGAATGCTCT-GTTTTACCAGCGTTTT
64 AAACGCCGCGAATGCTCTGGTTTTACCAGCGTTTT
13245 TTTAACGCCG
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
120 1 0.01
121 72 0.81
122 16 0.18
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.35
Consensus pattern (121 bp):
GGTTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGGTTTTAGCGGCGTTTTACCTAAA
ACGCCGCGAATGCTCTGGTTTTACCAGCGTTTTACCTAAAGCGCTGCTAATGCTCT
Done.