Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2284
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: 42491
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Found at i:190 original size:81 final size:81
Alignment explanation
Indices: 47--201 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 81
37 AAATTGTACA
* * *
47 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGGCAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGGCAAATGAATACGATACACTAAGTGT
112 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
** *
128 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGT-GCGATTTGATTACG-TACACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGGC-AAATGAATACGATACACTAAGT
*
191 GTGCGAGTTGA
64 GTGCGAATTGA
202 TTATATAGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
81 36 0.55
82 29 0.45
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGGCAAATGAATACGATACACTAAGTGT
GCGAATTGACCATGCG
Found at i:193 original size:26 final size:27
Alignment explanation
Indices: 46--222 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
36 TAAATTGTAC
*
46 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
73 TGCACTAAGTGTG-GCAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTTGATTATGT
* ** *
99 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* *
127 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGATTATGT
*
155 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* *
182 A-CACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
208 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
223 GACTCAATAA
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
26 24 0.19
27 77 0.62
28 24 0.19
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:213 original size:81 final size:81
Alignment explanation
Indices: 43--222 Score: 211
Period size: 81 Copynumber: 2.2 Consensus size: 81
33 GATTAAATTG
* * *
43 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGGCAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGGCAAATGAATACGATACACTAA
108 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
124 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGT-GCGATTTGATTACG-TACACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGGC-AAATGAATACGATACACT
* **
187 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
205 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
223 GACTCAATAA
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
81 53 0.65
82 29 0.35
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGGCAAATGAATACGATACACTAA
GTGTGCGAATTGACCA
Found at i:8162 original size:27 final size:27
Alignment explanation
Indices: 8131--8308 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
8121 TAAATTGTAC
8131 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
8158 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
8184 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
8212 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
8240 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
8267 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
8294 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
8309 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:8245 original size:82 final size:81
Alignment explanation
Indices: 8132--8287 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
8122 AAATTGTACA
* *
8132 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
8196 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
8213 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
8278 TGCGAGTTGA
65 TGCGAATTGA
8288 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:8299 original size:82 final size:81
Alignment explanation
Indices: 8128--8308 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
8118 GATTAAATTG
* *
8128 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
8193 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
8209 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
8273 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
8291 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
8309 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:20371 original size:28 final size:28
Alignment explanation
Indices: 20331--20394 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
20321 TGGGAAGTAG
* *
20331 TTGGGCCTGATGGGCCATATGAATGTGA
1 TTGGGCCTGATGGGCCATATGAACGAGA
* *
20359 TTGGGCTTGATGGGCCATGTGAACGAGA
1 TTGGGCCTGATGGGCCATATGAACGAGA
20387 TTGGGCCT
1 TTGGGCCT
20395 AAAGGGGCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.19, C:0.16, G:0.38, T:0.28
Consensus pattern (28 bp):
TTGGGCCTGATGGGCCATATGAACGAGA
Found at i:20805 original size:53 final size:52
Alignment explanation
Indices: 20711--21168 Score: 594
Period size: 53 Copynumber: 8.6 Consensus size: 52
20701 TAATAAAGAG
* *
20711 AAATTACTGAAATACCCTCGAATTGTAAAATTATTGAAATACCCTCGATTTGTA
1 AAATTAC-GAAATACCCTCG-ATTGTGAAATTACTGAAATACCCTCGATTTGTA
20765 AAATTATCGAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTA
1 AAATTA-CGAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTA
20818 AAATTATCGAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTA
1 AAATTA-CGAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTA
* * * * *
20871 AAATTGTCGAAATACCCTCAATTGTAAAATTACTAAAATACCCTCAATTTGTA
1 AAATT-ACGAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTA
* * * * * *
20924 AAATTACCAAAATACCCTCGATTATGAAATTACCGAAGTACCCTCAATTTTTA
1 AAATTA-CGAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTA
*
20977 AAATTACTAAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTA
1 AAATTAC-GAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTA
* * **
21030 AAATTATCAAAATACCCTCGATTGTGAAATTACTAAAATACAATCGATTTGTA
1 AAATTA-CGAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTA
* * * * *
21083 AAATTACTGAAATACGCTCGAGTCTAAAATTACTGAAATACCCTCAATTTGTA
1 AAATTAC-GAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTA
21136 AAATTACTGAAATATCCC-CGATTTGTGAAATTA
1 AAATTAC-GAAATA-CCCTCGA-TTGTGAAATTA
21169 TCGAAACACC
Statistics
Matches: 359, Mismatches: 37, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
52 2 0.01
53 327 0.91
54 29 0.08
55 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (52 bp):
AAATTACGAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTA
Found at i:20901 original size:106 final size:105
Alignment explanation
Indices: 20711--21259 Score: 606
Period size: 106 Copynumber: 5.2 Consensus size: 105
20701 TAATAAAGAG
* *
20711 AAATTA-CTGAAATACCCTCGAATTGTAAAATTATTGAAATACCCTCGATTTGTAAAATTATCGA
1 AAATTATC-GAAATACCCTCG-ATTGTGAAATTACTGAAATACCCTCGATTTGTAAAATTA-CGA
*
20775 AATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTA
63 AATACCCTCGATTGTAAAATTACTGAAATACCCTCGATTTGTA
*
20818 AAATTATCGAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTAAAATTGTCGAAA
1 AAATTATCGAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTAAAATT-ACGAAA
* * *
20883 TACCCTCAATTGTAAAATTACTAAAATACCCTCAATTTGTA
65 TACCCTCGATTGTAAAATTACTGAAATACCCTCGATTTGTA
* * * * * * * *
20924 AAATTACCAAAATACCCTCGATTATGAAATTACCGAAGTACCCTCAATTTTTAAAATTACTAAAA
1 AAATTATCGAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTAAAATTAC-GAAA
*
20989 TACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTA
65 TACCCTCGATTGTAAAATTACTGAAATACCCTCGATTTGTA
* * **
21030 AAATTATCAAAATACCCTCGATTGTGAAATTACTAAAATACAATCGATTTGTAAAATTACTGAAA
1 AAATTATCGAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTAAAATTAC-GAAA
* * * *
21095 TACGCTCGAGTCTAAAATTACTGAAATACCCTCAATTTGTA
65 TACCCTCGATTGTAAAATTACTGAAATACCCTCGATTTGTA
* * ** *
21136 AAATTA-CTGAAATATCCC-CGATTTGTGAAATTA-TCGAAACACCTTTAATTTATAAAATTACC
1 AAATTATC-GAAATA-CCCTCGA-TTGTGAAATTACT-GAAATACCCTCGATTTGTAAAATTA-C
* * * * * *
21198 AAAACACCCCCAATTTGTAAAATTA-TCGAAATACCCTTG-TAGTGTA
61 GAAATACCCTCGA-TTGTAAAATTACT-GAAATACCCTCGAT-TTGTA
*
21244 AAACTATCGAAATACC
1 AAATTATCGAAATACC
21260 GTTGTCGTGT
Statistics
Matches: 376, Mismatches: 54, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
105 2 0.01
106 275 0.73
107 62 0.16
108 36 0.10
109 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (105 bp):
AAATTATCGAAATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTAAAATTACGAAAT
ACCCTCGATTGTAAAATTACTGAAATACCCTCGATTTGTA
Found at i:21020 original size:159 final size:159
Alignment explanation
Indices: 20711--21222 Score: 654
Period size: 159 Copynumber: 3.2 Consensus size: 159
20701 TAATAAAGAG
* * *
20711 AAATTA-CTGAAATACCCTCGAATTGTAAAATTATTGAAATACCCTCGATTTGTAAAATTATCGA
1 AAATTATC-GAAATACCCTC-AATTGTAAAATTACTAAAATACCCTCGATTTGTAAAATTACCGA
* *
20775 AATACCCTCGATTGTGAAATTACTGAAATACCCTCGATTTGTAAAATTA-TCGAAATACCCTCGA
64 AATACCCTCGATTATGAAATTACTGAAATACCCTCAATTTGTAAAATTACT-GAAATACCCTCGA
20839 TTGTGAAATTACTGAAATACCCTCGATTTGTA
128 TTGTGAAATTACTGAAATACCCTCGATTTGTA
* * *
20871 AAATTGTCGAAATACCCTCAATTGTAAAATTACTAAAATACCCTCAATTTGTAAAATTACCAAAA
1 AAATTATCGAAATACCCTCAATTGTAAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAA
* * * *
20936 TACCCTCGATTATGAAATTACCGAAGTACCCTCAATTTTTAAAATTACTAAAATACCCTCGATTG
66 TACCCTCGATTATGAAATTACTGAAATACCCTCAATTTGTAAAATTACTGAAATACCCTCGATTG
21001 TGAAATTACTGAAATACCCTCGATTTGTA
131 TGAAATTACTGAAATACCCTCGATTTGTA
* * * ** *
21030 AAATTATCAAAATACCCTCGATTGTGAAATTACTAAAATACAATCGATTTGTAAAATTACTGAAA
1 AAATTATCGAAATACCCTCAATTGTAAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAA
* * * *
21095 TACGCTCGAGTCTAAAATTACTGAAATACCCTCAATTTGTAAAATTACTGAAATATCCC-CGATT
66 TACCCTCGATTATGAAATTACTGAAATACCCTCAATTTGTAAAATTACTGAAATA-CCCTCGA-T
* * ** *
21159 TGTGAAATTA-TCGAAACACCTTTAATTTATA
129 TGTGAAATTACT-GAAATACCCTCGATTTGTA
* * * *
21190 AAATTACCAAAACACCCCCAATTTGTAAAATTA
1 AAATTATCGAAATACCCTCAA-TTGTAAAATTA
21223 TCGAAATACC
Statistics
Matches: 307, Mismatches: 39, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
159 234 0.76
160 62 0.20
161 11 0.04
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.32
Consensus pattern (159 bp):
AAATTATCGAAATACCCTCAATTGTAAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAA
TACCCTCGATTATGAAATTACTGAAATACCCTCAATTTGTAAAATTACTGAAATACCCTCGATTG
TGAAATTACTGAAATACCCTCGATTTGTA
Found at i:21186 original size:27 final size:27
Alignment explanation
Indices: 21107--21233 Score: 105
Period size: 27 Copynumber: 4.7 Consensus size: 27
21097 CGCTCGAGTC
* *
21107 TAAAATTA-CTGAAATACCCTCAATTTG
1 TAAAATTATC-GAAACACCCCCAATTTG
* * *
21134 TAAAATTA-CTGAAATATCCCCGATTTG
1 TAAAATTATC-GAAACACCCCCAATTTG
* *** *
21161 TGAAATTATCGAAACACCTTTAATTTA
1 TAAAATTATCGAAACACCCCCAATTTG
* *
21188 TAAAATTACCAAAACACCCCCAATTTG
1 TAAAATTATCGAAACACCCCCAATTTG
*
21215 TAAAATTATCGAAATACCC
1 TAAAATTATCGAAACACCC
21234 TTGTAGTGTA
Statistics
Matches: 78, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
27 77 0.99
28 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
TAAAATTATCGAAACACCCCCAATTTG
Found at i:21243 original size:27 final size:27
Alignment explanation
Indices: 21213--21301 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
21203 ACCCCCAATT
21213 TGTAAAATTATCGAAATACCCTTGTAG
1 TGTAAAATTATCGAAATACCCTTGTAG
* * *
21240 TGTAAAACTATCGAAATACCGTTGTCG
1 TGTAAAATTATCGAAATACCCTTGTAG
* * *
21267 TGTAAAATGA-CTAACATACCCCTGTAG
1 TGTAAAATTATCGAA-ATACCCTTGTAG
*
21294 GGTAAAAT
1 TGTAAAAT
21302 GACTATTTTG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
26 3 0.06
27 48 0.94
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (27 bp):
TGTAAAATTATCGAAATACCCTTGTAG
Found at i:21252 original size:81 final size:81
Alignment explanation
Indices: 21107--21255 Score: 178
Period size: 81 Copynumber: 1.8 Consensus size: 81
21097 CGCTCGAGTC
** * * * * *
21107 TAAAATTACTGAAATACCCTCAATTTGTAAAATTACTGAAATATCCCCGATTTGTGAAATTATCG
1 TAAAATTACCAAAACACCCCCAATTTGTAAAATTACTGAAATATCCCCGATGTGTAAAACTATCG
21172 AAACACCTTTAATTTA
66 AAACACCTTTAATTTA
*
21188 TAAAATTACCAAAACACCCCCAATTTGTAAAATTA-TCGAAATA-CCCTTG-TAGTGTAAAACTA
1 TAAAATTACCAAAACACCCCCAATTTGTAAAATTACT-GAAATATCCC-CGAT-GTGTAAAACTA
21250 TCGAAA
63 TCGAAA
21256 TACCGTTGTC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
80 5 0.09
81 52 0.91
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.31
Consensus pattern (81 bp):
TAAAATTACCAAAACACCCCCAATTTGTAAAATTACTGAAATATCCCCGATGTGTAAAACTATCG
AAACACCTTTAATTTA
Found at i:28759 original size:13 final size:12
Alignment explanation
Indices: 28741--28771 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
28731 TTCTATTATG
28741 ATTTTCAATTTC
1 ATTTTCAATTTC
28753 ATCTTTCAATTTC
1 AT-TTTCAATTTC
28766 ATTTTC
1 ATTTTC
28772 CCCAGTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTTCAATTTC
Found at i:29943 original size:12 final size:13
Alignment explanation
Indices: 29916--29944 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
29906 TTATTTATTA
29916 TTTAACATAAAAT
1 TTTAACATAAAAT
29929 TTTAAC-TAAAAT
1 TTTAACATAAAAT
29941 TTTA
1 TTTA
29945 TAATATACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTAACATAAAAT
Found at i:34458 original size:85 final size:85
Alignment explanation
Indices: 34354--34532 Score: 358
Period size: 85 Copynumber: 2.1 Consensus size: 85
34344 GGCCGGCCAT
34354 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
34419 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
34439 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
34504 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
34524 GAGCATGGG
1 GAGCATGGG
34533 CAATAAAATA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:35897 original size:40 final size:40
Alignment explanation
Indices: 35702--35883 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 40
35692 AATGATGTCT
* * * * *
35702 GGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACC
* *
35742 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-ACC
*
35782 GGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
*
35821 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
*
35861 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
35884 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
39 35 0.28
40 78 0.63
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
Found at i:35905 original size:79 final size:79
Alignment explanation
Indices: 35752--35906 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
35742 GGACTAAGAT
* **
35752 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
35817 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
35831 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
35894 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
35907 ATTTCGAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 41 0.61
80 24 0.36
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Done.