Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2673
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: 59544
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Found at i:6507 original size:31 final size:29
Alignment explanation
Indices: 6456--6522 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
6446 CAAATTTTCG
* *
6456 TATATAAAATTACACAAAATCGAAATTCA
1 TATATAAAATTACACAAAATCAAAATTAA
* *
6485 TATATAAAATTATATATTAAATCAAAATTAA
1 TATATAAAATTACACA--AAATCAAAATTAA
*
6516 TGTATAA
1 TATATAA
6523 TTTTCTTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 14 0.45
31 17 0.55
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.34
Consensus pattern (29 bp):
TATATAAAATTACACAAAATCAAAATTAA
Found at i:7995 original size:21 final size:21
Alignment explanation
Indices: 7955--7995 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
7945 TAGCTTTATA
*
7955 CAAGTAATTTTTATATATATT
1 CAAGTAATTTTTACATATATT
7976 CAAGTAA-TTTTACATGATAT
1 CAAGTAATTTTTACAT-ATAT
7996 ATAAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (21 bp):
CAAGTAATTTTTACATATATT
Found at i:10817 original size:31 final size:32
Alignment explanation
Indices: 10758--10817 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
10748 TTATATGAAA
*
10758 TGGGTCGCAGGGCGGGTATAGCGAGGATTAGG
1 TGGGTCGCAGGGCGGGTATAGAGAGGATTAGG
*
10790 TGGGTCGCA-GGCGGGTATAGAGGGGATT
1 TGGGTCGCAGGGCGGGTATAGAGAGGATT
10818 TTAGTATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.18, C:0.12, G:0.50, T:0.20
Consensus pattern (32 bp):
TGGGTCGCAGGGCGGGTATAGAGAGGATTAGG
Found at i:12025 original size:10 final size:9
Alignment explanation
Indices: 11867--12041 Score: 72
Period size: 9 Copynumber: 18.9 Consensus size: 9
11857 ATTTAAAATT
*
11867 ATTATAGAA
1 ATTATAAAA
*
11876 ATCATAAAA
1 ATTATAAAA
*
11885 AATATAAAA
1 ATTATAAAA
11894 ATT-TAAAA
1 ATTATAAAA
*
11902 AATATATAAA
1 ATTATA-AAA
* **
11912 AGTGCACAAA
1 ATTATA-AAA
11922 A-TATAGAAA
1 ATTATA-AAA
11931 ATTATAAATGA
1 ATTATAAA--A
* *
11942 CAATATATAA
1 -ATTATAAAA
11952 ATTATAAAA
1 ATTATAAAA
*
11961 TTTATTTAAAA
1 ATTA--TAAAA
*
11972 GTTGA-AAAA
1 ATT-ATAAAA
* *
11981 AATATTAAA
1 ATTATAAAA
11990 A-TA-AAAA
1 ATTATAAAA
* *
11997 ATTATTAGA
1 ATTATAAAA
12006 ATTATTAAAA
1 ATTA-TAAAA
*
12016 ATTGTAAAA
1 ATTATAAAA
12025 ATTATAAAA
1 ATTATAAAA
*
12034 ATAATAAA
1 ATTATAAA
12042 GTTTTAAAAA
Statistics
Matches: 123, Mismatches: 30, Indels: 26
0.69 0.17 0.15
Matches are distributed among these distances:
7 4 0.03
8 12 0.10
9 71 0.58
10 21 0.17
11 8 0.07
12 7 0.06
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (9 bp):
ATTATAAAA
Found at i:12148 original size:13 final size:11
Alignment explanation
Indices: 12122--12167 Score: 51
Period size: 10 Copynumber: 4.2 Consensus size: 11
12112 GAAATTTATT
12122 AAAAATATTAA
1 AAAAATATTAA
12133 AAAAATATATAGA
1 AAAAATAT-TA-A
*
12146 AAAAAT-GTAA
1 AAAAATATTAA
12156 AAAAATA-TAA
1 AAAAATATTAA
12166 AA
1 AA
12168 TATAGGAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 12 0.39
11 10 0.32
12 2 0.06
13 7 0.23
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (11 bp):
AAAAATATTAA
Found at i:12249 original size:8 final size:7
Alignment explanation
Indices: 12218--12246 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
12208 ATATAAAATT
12218 ACAAAAA
1 ACAAAAA
12225 ACAAAAA
1 ACAAAAA
12232 ACAAAAA
1 ACAAAAA
12239 ACAAAAA
1 ACAAAAA
12246 A
1 A
12247 ACATACAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (7 bp):
ACAAAAA
Found at i:12660 original size:38 final size:37
Alignment explanation
Indices: 12618--12703 Score: 100
Period size: 38 Copynumber: 2.3 Consensus size: 37
12608 CTTATATTTT
* **
12618 TTTATAATTTTTCATAAACTATACAATTTTTTTTGTAA
1 TTTATAATTTTTAATAAA-TATACAATTTTTAATGTAA
* * *
12656 TTTATATATTTTTAATAAATTTTCAATTTTTAATGTAT
1 TTTATA-ATTTTTAATAAATATACAATTTTTAATGTAA
12694 TTTATAATTT
1 TTTATAATTT
12704 ATATAAAACT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
37 4 0.10
38 26 0.63
39 11 0.27
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (37 bp):
TTTATAATTTTTAATAAATATACAATTTTTAATGTAA
Found at i:12702 original size:19 final size:19
Alignment explanation
Indices: 12651--12703 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
12641 CAATTTTTTT
*
12651 TGTAATTTATATATTTTTAA
1 TGTATTTTATA-ATTTTTAA
** *
12671 TAAATTTT-CAATTTTTAA
1 TGTATTTTATAATTTTTAA
12689 TGTATTTTATAATTT
1 TGTATTTTATAATTT
12704 ATATAAAACT
Statistics
Matches: 25, Mismatches: 7, Indels: 3
0.71 0.20 0.09
Matches are distributed among these distances:
18 14 0.56
19 6 0.24
20 5 0.20
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (19 bp):
TGTATTTTATAATTTTTAA
Found at i:13788 original size:6 final size:6
Alignment explanation
Indices: 13777--13815 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
13767 GGAAAATTTT
* *
13777 CCTTTC CCTTTC CCTTCC CCTTCC CCTTCC CCTTCC CCT
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCT
13816 ATCCTTGACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
CCTTCC
Found at i:19485 original size:21 final size:21
Alignment explanation
Indices: 19459--19499 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19449 AGACGAGCAA
* *
19459 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
19480 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
19500 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:22943 original size:24 final size:24
Alignment explanation
Indices: 22916--22963 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
22906 AAAGCAGAAG
* *
22916 AGAATAAAAAAGAAAAAGATTAAA
1 AGAACAAAAAAGAAAAAAATTAAA
*
22940 AGAACATAAAAGAAAAAAATTAAA
1 AGAACAAAAAAGAAAAAAATTAAA
22964 TTATTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.12
Consensus pattern (24 bp):
AGAACAAAAAAGAAAAAAATTAAA
Found at i:29273 original size:67 final size:67
Alignment explanation
Indices: 29165--29299 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
29155 GTAATTGTCA
29165 TTGCAGGGGATTTAGCCTGGACTAGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1 TTGCAGGGGATTTAGCCTGGACTAGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
29230 TC
66 TC
*
29232 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1 TTGCAGGGGATTTAGCCTGGACTAGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
29297 TC
66 TC
29299 T
1 T
29300 GAATTGGAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.27
Consensus pattern (67 bp):
TTGCAGGGGATTTAGCCTGGACTAGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
TC
Found at i:30986 original size:125 final size:124
Alignment explanation
Indices: 30763--31041 Score: 450
Period size: 125 Copynumber: 2.2 Consensus size: 124
30753 TTCCTCTCAA
* * * *
30763 TTTCCAGGACCTACTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAAT
1 TTTCCAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTATCAAAC
* * *
30828 AGCATCCTATTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATT
66 AGCATCCTACTAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAACTAGAAATTATT
30887 TCTTCCAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTATCAAA
1 T-TTCCAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTATCAAA
*
30952 CAGCATCCTGCTAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAACTAGAAATTATT
65 CAGCATCCTACTAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAACTAGAAATTATT
* * *
31012 TTTTCAGGACCTACAGTAGCAAAAGTGCGT
1 TTTCCAGGACCTACTGTAGCAAAAGCGCGT
31042 AAACGTGGGC
Statistics
Matches: 143, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
124 27 0.19
125 116 0.81
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (124 bp):
TTTCCAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTATCAAAC
AGCATCCTACTAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAACTAGAAATTATT
Found at i:35512 original size:29 final size:30
Alignment explanation
Indices: 35453--35510 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
35443 TCCGAGCCTT
*
35453 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
35483 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
35511 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:35740 original size:13 final size:13
Alignment explanation
Indices: 35722--35753 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
35712 TTTCCAGCAA
35722 TTATGAATTTATT
1 TTATGAATTTATT
35735 TTATGAATTTATT
1 TTATGAATTTATT
*
35748 TGATGA
1 TTATGA
35754 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:35961 original size:50 final size:50
Alignment explanation
Indices: 35848--36089 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
35838 ATTTGGGTAA
* * *
35848 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
35904 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
35954 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
36004 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
36054 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
36090 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:36037 original size:100 final size:103
Alignment explanation
Indices: 35848--36097 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
35838 ATTTGGGTAA
35848 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
35913 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
35954 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
36016 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
36054 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
36098 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:43103 original size:29 final size:30
Alignment explanation
Indices: 43044--43101 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
43034 TCCGAGCCTT
*
43044 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
43074 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
43102 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:43331 original size:13 final size:13
Alignment explanation
Indices: 43313--43344 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
43303 TTTCCAGCAA
43313 TTATGAATTTATT
1 TTATGAATTTATT
43326 TTATGAATTTATT
1 TTATGAATTTATT
*
43339 TGATGA
1 TTATGA
43345 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:43552 original size:50 final size:50
Alignment explanation
Indices: 43439--43680 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
43429 ATTTGGGTAA
* * *
43439 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
43495 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
43545 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
43595 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
43645 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
43681 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:43628 original size:100 final size:103
Alignment explanation
Indices: 43439--43688 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
43429 ATTTGGGTAA
43439 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
43504 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
43545 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
43607 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
43645 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
43689 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:46162 original size:23 final size:23
Alignment explanation
Indices: 46136--46211 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
46126 ATAAGTGCCA
46136 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
46159 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
46182 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
46205 CACTGAT
1 CACTGAT
46212 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:46311 original size:8 final size:8
Alignment explanation
Indices: 46298--46326 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
46288 ACCCGGGACT
46298 CACTGTAA
1 CACTGTAA
46306 CACTGTAA
1 CACTGTAA
46314 CACTGTAA
1 CACTGTAA
46322 CACTG
1 CACTG
46327 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:46457 original size:18 final size:17
Alignment explanation
Indices: 46431--46469 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
46421 ATTTTCCTTC
46431 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
46448 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
46466 CACA
1 CACA
46470 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Done.