Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1075
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: 47562
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Found at i:1399 original size:40 final size:40
Alignment explanation
Indices: 1355--1545 Score: 217
Period size: 40 Copynumber: 4.8 Consensus size: 40
1345 ATAACCACAA
* * *
1355 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
1395 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
1435 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * * * *
1475 GCATAAATGCCTTCGGGACTTAGCCC-GATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
1514 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
1546 CATTCAAATG
Statistics
Matches: 140, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 40 0.29
40 96 0.69
41 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:1516 original size:39 final size:40
Alignment explanation
Indices: 1399--1544 Score: 224
Period size: 40 Copynumber: 3.7 Consensus size: 40
1389 CAACTCGCAC
* * * *
1399 AAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTAGCAT
*
1439 AAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCAT
1 AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
1479 AAATGCCTTCGGGACTTAGCCC-GATAAAATCACTAGCAT
1 AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
1518 AAATGCCTTCGGGACTTAGCCCGGATA
1 AAATGCCTTCGGGACTTAGCCCGGATA
1545 TCATTCAAAT
Statistics
Matches: 100, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
39 39 0.39
40 57 0.57
41 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
Found at i:6126 original size:39 final size:40
Alignment explanation
Indices: 5991--6214 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 40
5981 TTGAATGCTG
* * * * *
5991 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** *
6031 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
6070 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAG-TACTAAA
1 -TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
6110 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
6150 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
6189 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
6215 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
39 67 0.43
40 82 0.52
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:6131 original size:79 final size:78
Alignment explanation
Indices: 5991--6214 Score: 254
Period size: 79 Copynumber: 2.8 Consensus size: 78
5981 TTGAATGCTG
* * * * *
5991 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGC-GAGT-ACTAAATCCGGGCTAAG-TCCCGAAGGCATT
6055 TGTGCGAGATA-CAAA
63 TGTGCGAGATATCAAA
* * *
6070 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 -TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAGTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
* *
6135 GTGCGAGTTATTAAA
64 GTGCGAGATATCAAA
* * * *
6150 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAG-TACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
6215 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
78 10 0.08
79 81 0.66
80 24 0.20
81 8 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGATATCAAA
Found at i:6232 original size:79 final size:79
Alignment explanation
Indices: 6071--6247 Score: 198
Period size: 79 Copynumber: 2.3 Consensus size: 79
6061 AGATACAAAT
* * * *
6071 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
** * *
6136 TGCGAGTTATTAAA
66 AACGAGTGACTAAA
* * *
6150 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAG-TACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
6214 GAACGAG-GAGCTATA
65 GAACGAGTGA-CTAAA
*
6229 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
6248 TACGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 25 0.30
79 58 0.70
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
AACGAGTGACTAAA
Found at i:14018 original size:39 final size:39
Alignment explanation
Indices: 13966--14136 Score: 202
Period size: 39 Copynumber: 4.3 Consensus size: 39
13956 GGACTAAGAT
13966 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
14005 CCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
* * *
14045 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
14085 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
14124 CCGAAGGCATTTG
1 CCGAAGGCATTTG
14137 AACGAGGAGC
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
39 64 0.56
40 51 0.44
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:14049 original size:79 final size:79
Alignment explanation
Indices: 13913--14136 Score: 256
Period size: 79 Copynumber: 2.8 Consensus size: 79
13903 TTGAATGCTG
* * * * * *
13913 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGT-ACTAAATCCGGGCTAAG-TCCCGAAGGCATT
13977 TGTGCGAGATA-CAAA
64 TGTGCGAGATATCAAA
*
13992 TTCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATT
* * *
14056 CGTGCGAGTTATTAAA
64 TGTGCGAGATATCAAA
* * * * *
14072 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
14137 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
78 1 0.01
79 90 0.73
80 32 0.26
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:14154 original size:79 final size:80
Alignment explanation
Indices: 13993--14169 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
13983 AGATACAAAT
* * *
13993 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
14057 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
14072 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
14136 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
14151 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
14170 TACGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 16 0.19
79 59 0.71
80 8 0.10
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:17866 original size:22 final size:23
Alignment explanation
Indices: 17829--17871 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
17819 TATTTAGGAA
17829 TTGGTACGAAATGGT-ATGGTAT
1 TTGGTACGAAATGGTAATGGTAT
17851 TTGGTACG-AATAGGTAATGGT
1 TTGGTACGAAAT-GGTAATGGT
17872 TCAAAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 11 0.58
23 5 0.26
ACGTcount: A:0.28, C:0.05, G:0.33, T:0.35
Consensus pattern (23 bp):
TTGGTACGAAATGGTAATGGTAT
Found at i:28167 original size:30 final size:30
Alignment explanation
Indices: 28132--28205 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
28122 AGTTTTTCCC
*
28132 AGCTCGATTT-AGCTCACA-TGAGCTTAGTTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTACTTT
*
28162 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTACTTT
28192 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
28206 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTACTTT
Found at i:30896 original size:19 final size:19
Alignment explanation
Indices: 30872--30909 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
30862 TAAGCATGTG
30872 TGGA-CTTCTTGATTGGGCT
1 TGGACCTTCTT-ATTGGGCT
30891 TGGACTCTTCTTATTGGGC
1 TGGAC-CTTCTTATTGGGC
30910 CTTGCCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.11, C:0.18, G:0.29, T:0.42
Consensus pattern (19 bp):
TGGACCTTCTTATTGGGCT
Found at i:34117 original size:20 final size:20
Alignment explanation
Indices: 34071--34117 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
34061 AGCTCGTTTC
*
34071 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
34091 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
34111 CAGCTCA
1 CAGCTCA
34118 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:35621 original size:13 final size:13
Alignment explanation
Indices: 35603--35663 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 13
35593 ACAAAAAAAT
35603 AAAAAAAATTTGA
1 AAAAAAAATTTGA
35616 AAAAAAAATTGATTGA
1 AAAAAAAA-T--TTGA
*
35632 AAAAAAAA-TTCA
1 AAAAAAAATTTGA
**
35644 AAAAAAAAAGTGA
1 AAAAAAAATTTGA
35657 AAAAAAA
1 AAAAAAA
35664 TCGAGCAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 11 0.27
13 17 0.41
14 1 0.02
16 12 0.29
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAAAAATTTGA
Found at i:35676 original size:17 final size:17
Alignment explanation
Indices: 35656--35694 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
35646 AAAAAAAGTG
35656 AAAAAAA-ATCGAGCAAA
1 AAAAAAAGAT-GAGCAAA
*
35673 AAAAAAAGGTGAGCAAA
1 AAAAAAAGATGAGCAAA
35690 AAAAA
1 AAAAA
35695 TCAAGTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.72, C:0.08, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAAAAAGATGAGCAAA
Found at i:36760 original size:6 final size:6
Alignment explanation
Indices: 36727--36834 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
36717 AAAGAAATTG
* * * ** *
36727 AAAG-A AAACAA AAAGAA AATGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
36774 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
36825 AAAGAA AAAG
1 AAAGAA AAAG
36835 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 26, Indels: 7
0.69 0.25 0.07
Matches are distributed among these distances:
5 3 0.04
6 59 0.81
7 7 0.10
8 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:36775 original size:57 final size:55
Alignment explanation
Indices: 36714--36834 Score: 138
Period size: 57 Copynumber: 2.1 Consensus size: 55
36704 GAAAGAGATT
* *
36714 GAAAAAGAAATTGAAAGAA-A-ACAAAAAGAAAATGAAGAAGAAAAAGAAATTGCAAAA
1 GAAAAAGAAATCGAAA-AAGAGACAAAAAGAAAATGAAG-A-AAAAA-AAATTGAAAAA
* *
36771 GAAAAAGAAATCGAAAAAGTGAGAGAAAAAGAAAATGAAGAAAAGAAAATTGAAAAA
1 GAAAAAGAAATCGAAAAA--GAGACAAAAAGAAAATGAAGAAAAAAAAATTGAAAAA
36828 GAAAAAG
1 GAAAAAG
36835 CGAAAAAAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
56 2 0.04
57 32 0.57
58 4 0.07
59 2 0.04
60 16 0.29
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.08
Consensus pattern (55 bp):
GAAAAAGAAATCGAAAAAGAGACAAAAAGAAAATGAAGAAAAAAAAATTGAAAAA
Found at i:36788 original size:18 final size:17
Alignment explanation
Indices: 36713--36789 Score: 68
Period size: 18 Copynumber: 4.5 Consensus size: 17
36703 AGAAAGAGAT
**
36713 TGAAAAAGAAATTGAAA
1 TGAAAAAGAAAAAGAAA
*
36730 -G-AAAACAAAAAGAAAA
1 TGAAAAAGAAAAAG-AAA
*
36746 TGAAGAAGAAAAAGAAA
1 TGAAAAAGAAAAAGAAA
*
36763 TTGCAAAAGAAAAAGAAA
1 -TGAAAAAGAAAAAGAAA
36781 TCGAAAAAG
1 T-GAAAAAG
36790 TGAGAGAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
15 8 0.17
16 4 0.09
17 5 0.11
18 30 0.64
ACGTcount: A:0.69, C:0.04, G:0.18, T:0.09
Consensus pattern (17 bp):
TGAAAAAGAAAAAGAAA
Found at i:36816 original size:14 final size:13
Alignment explanation
Indices: 36795--36832 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
36785 AAAAGTGAGA
36795 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
36807 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
36822 GAAAAAGAAAA
1 GAAAAAGAAAA
36833 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:36846 original size:21 final size:21
Alignment explanation
Indices: 36796--36846 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
36786 AAAGTGAGAG
*
36796 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
36817 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
36838 AAAAAGAAA
1 AAAAAGAAA
36847 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:36850 original size:27 final size:27
Alignment explanation
Indices: 36748--36852 Score: 77
Period size: 27 Copynumber: 3.8 Consensus size: 27
36738 AAAGAAAATG
* *
36748 AAGAAGAAAAAGAAATTGCAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*** **
36775 AAGAAATCGAAAAAGTGAGAGAAAAAGAAA
1 AAG-AA--GAAAAAAAAATTGAAAAAGAAA
* *
36805 ATGAAGAAAAGAAAATTGAAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*
36832 AAG-CGAAAAAAGAAATTGAAA
1 AAGAAGAAAAAA-AAATTGAAA
36853 GAGAGCTTGA
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
26 6 0.10
27 30 0.51
28 2 0.03
29 2 0.03
30 19 0.32
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.09
Consensus pattern (27 bp):
AAGAAGAAAAAAAAATTGAAAAAGAAA
Found at i:36994 original size:48 final size:47
Alignment explanation
Indices: 36915--37020 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
36905 GAGTGTCATG
*
36915 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
36963 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
37011 GAAAAAGAAA
1 GAAAAAGAAA
37021 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:42074 original size:15 final size:15
Alignment explanation
Indices: 42054--42108 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
42044 ACTCTCCTCA
*
42054 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
42069 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
42084 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
42098 TTCTTTT-TCTC
1 TTCTTTTCTCTC
42109 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:44130 original size:17 final size:17
Alignment explanation
Indices: 44110--44144 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
44100 TCACTTCTCT
*
44110 TTTTTTTTAATTCTGAA
1 TTTTTTTTAATACTGAA
44127 TTTTTTTTAATACTGAA
1 TTTTTTTTAATACTGAA
44144 T
1 T
44145 ACACAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.63
Consensus pattern (17 bp):
TTTTTTTTAATACTGAA
Found at i:46891 original size:20 final size:20
Alignment explanation
Indices: 46845--46891 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46835 AGCTCGTTTC
*
46845 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
46865 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
46885 CAGCTCA
1 CAGCTCA
46892 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Done.