Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold752
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: 44075
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:1321 original size:46 final size:45
Alignment explanation
Indices: 1271--1440 Score: 202
Period size: 46 Copynumber: 3.8 Consensus size: 45
1261 TGGTTGAGCA
1271 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-ATG
* * * * * *
1317 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTA-ACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATGGATGCGATG
1361 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGATG
** *
1408 AGCGAGCTCGTTGAGTTGAGTCCGAGTT-ACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
1441 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 15, Indels: 12
0.79 0.11 0.09
Matches are distributed among these distances:
44 7 0.07
45 27 0.26
46 66 0.63
47 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGATG
Found at i:7948 original size:93 final size:92
Alignment explanation
Indices: 7785--7954 Score: 286
Period size: 93 Copynumber: 1.8 Consensus size: 92
7775 GGATGGTTGA
* * *
7785 GCATCCTAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAATGTCCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAACGCCCGAACTCGTTGAGTT
7850 GAGTCCGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
* *
7877 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAACGCCCGAACTCGTTGAGT
7942 TGAGTCCGAGTTC
65 TGAGTCCGAGTTC
7955 ACTTAGGGCG
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 32 0.44
93 40 0.56
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:7954 original size:46 final size:46
Alignment explanation
Indices: 7792--7959 Score: 193
Period size: 46 Copynumber: 3.7 Consensus size: 46
7782 TGAGCATCCT
* *
7792 AACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
* * *
7837 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC--CCG
*
7884 AACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
*
7930 AGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA
7960 GGGCGGGTTA
Statistics
Matches: 102, Mismatches: 11, Indels: 19
0.77 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 27 0.26
46 31 0.30
47 27 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
Found at i:11470 original size:19 final size:19
Alignment explanation
Indices: 11448--11505 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
11438 AATTTAAGTA
11448 ATATAATGTTATTTATATG
1 ATATAATGTTATTTATATG
* *
11467 ATATGATG--A-TTATTATC
1 ATATAATGTTATTTA-TATG
11484 AT-TAATGTTATTTATATG
1 ATATAATGTTATTTATATG
11502 ATAT
1 ATAT
11506 GAAGATTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 7 0.23
17 6 0.20
18 6 0.20
19 11 0.37
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (19 bp):
ATATAATGTTATTTATATG
Found at i:11490 original size:35 final size:35
Alignment explanation
Indices: 11451--11517 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
11441 TTAAGTAATA
*
11451 TAATGTTATTTATATGATATGATGATTATTATCAT
1 TAATGTTATTTATATGATATGAAGATTATTATCAT
*
11486 TAATGTTATTTATATGATATGAAGATTGTTAT
1 TAATGTTATTTATATGATATGAAGATTATTAT
11518 TATGAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.51
Consensus pattern (35 bp):
TAATGTTATTTATATGATATGAAGATTATTATCAT
Found at i:16453 original size:20 final size:19
Alignment explanation
Indices: 16426--16486 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
16416 AACTCCGACC
16426 AGCTCAATTGAGCTCATTT
1 AGCTCAATTGAGCTCATTT
* *
16445 CATCTCAATCGAGCTCAATTT
1 -AGCTCAATTGAGCTC-ATTT
*
16466 AGCTACAATTCAGCTCATTT
1 AGCT-CAATTGAGCTCATTT
16486 A
1 A
16487 TTTTATTGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 21 0.62
21 13 0.38
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (19 bp):
AGCTCAATTGAGCTCATTT
Found at i:16480 original size:11 final size:10
Alignment explanation
Indices: 16425--16482 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
16415 CAACTCCGAC
16425 CAGCTCAATT
1 CAGCTCAATT
* *
16435 GAGCTCATTT
1 CAGCTCAATT
*
16445 CATCTCAA-T
1 CAGCTCAATT
16454 CGAGCTCAATT
1 C-AGCTCAATT
*
16465 TAGCTACAATT
1 CAGCT-CAATT
16476 CAGCTCA
1 CAGCTCA
16483 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 2 0.05
10 25 0.68
11 10 0.27
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:19003 original size:6 final size:6
Alignment explanation
Indices: 18970--19077 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
18960 AAAGAAATTG
* * * ** *
18970 AAAG-A AAACAA AAAGAA AACGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
19017 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
19068 AAAGAA AAAG
1 AAAGAA AAAG
19078 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:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:19021 original size:27 final size:27
Alignment explanation
Indices: 18991--19099 Score: 87
Period size: 27 Copynumber: 3.9 Consensus size: 27
18981 AAAGAAAACG
*
18991 AAGAAGAAAAAGAAATTGCAAAAGAAA
1 AAGAAGAAAAAGAAATTGAAAAAGAAA
** **
19018 AAGAAATCGAAAAAGTGAGAGAAAAAGAAA
1 AAG-AA--GAAAAAGAAATTGAAAAAGAAA
*
19048 ATGAAG-AAAAGAAAATTGAAAAAGAAA
1 AAGAAGAAAAAG-AAATTGAAAAAGAAA
* *
19075 AAG-CGAAAAAAGAATTTGAAAAAGA
1 AAGAAG-AAAAAGAAATTGAAAAAGA
19100 GTTTGAAAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
26 6 0.10
27 29 0.46
28 7 0.11
29 2 0.03
30 19 0.30
ACGTcount: A:0.68, C:0.03, G:0.20, T:0.09
Consensus pattern (27 bp):
AAGAAGAAAAAGAAATTGAAAAAGAAA
Found at i:19031 original size:18 final size:18
Alignment explanation
Indices: 18974--19032 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
18964 AAATTGAAAG
* *
18974 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* * *
18992 AGAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
19010 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
19028 AAAAG
1 AAAAG
19033 TGAGAGAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.71, C:0.07, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:19059 original size:14 final size:13
Alignment explanation
Indices: 19038--19075 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
19028 AAAAGTGAGA
19038 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
19050 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
19065 GAAAAAGAAAA
1 GAAAAAGAAAA
19076 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:19072 original size:13 final size:12
Alignment explanation
Indices: 18956--19075 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
18946 AGAAAGAGAT
*
18956 TGAAAAAGAAAT
1 TGAAAAAGAAAA
18968 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
18978 -CAAAAAGAAAA
1 TGAAAAAGAAAA
* *
18989 CGAAGAAGAAAA
1 TGAAAAAGAAAA
* **
19001 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
19014 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* *
19024 TCGAAAAAGTGAGA
1 T-GAAAAAG-AAAA
19038 -GAAAAAGAAAA
1 TGAAAAAGAAAA
19049 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
19063 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
19076 AGCGAAAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
10 10 0.12
11 10 0.12
12 35 0.42
13 14 0.17
14 12 0.14
15 2 0.02
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:19112 original size:12 final size:12
Alignment explanation
Indices: 19081--19112 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
19071 GAAAAAGCGA
*
19081 AAAAAGAATTTG
1 AAAAAGAGTTTG
19093 AAAAAGAGTTTG
1 AAAAAGAGTTTG
19105 AAAAAGAG
1 AAAAAGAG
19113 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:20777 original size:10 final size:10
Alignment explanation
Indices: 20761--20818 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
20751 CAACTCCGAC
20761 CAGCTCAATT
1 CAGCTCAATT
* *
20771 GAGCTCATTT
1 CAGCTCAATT
20781 CAGCTCAA-T
1 CAGCTCAATT
20790 CGAGCTCAATT
1 C-AGCTCAATT
*
20801 TAGCTACAATT
1 CAGCT-CAATT
20812 CAGCTCA
1 CAGCTCA
20819 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:20784 original size:20 final size:20
Alignment explanation
Indices: 20761--20821 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
20751 CAACTCCGAC
20761 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
20781 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
20802 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
20822 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:23132 original size:49 final size:49
Alignment explanation
Indices: 23066--23297 Score: 286
Period size: 49 Copynumber: 4.7 Consensus size: 49
23056 GCTATTGTGA
*
23066 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTT
* * * *
23115 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACT-TT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACC--A-AATTGTT
* * * *
23166 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTT
* ** **
23215 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTT
*
23265 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
23298 TGCGTACTAG
Statistics
Matches: 157, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
48 2 0.01
49 71 0.45
50 43 0.27
51 38 0.24
52 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTT
Found at i:25801 original size:30 final size:31
Alignment explanation
Indices: 25743--25801 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
25733 ATGGAAAAAG
* *
25743 AAATGAGCTGGAAAGAAGCTAAATTGAGCTC
1 AAATGAGCTGGAAACAAGCTAAAGTGAGCTC
*
25774 AAATGAGCT-GAAACAAGCTCAAGTGAGC
1 AAATGAGCTGGAAACAAGCTAAAGTGAGC
25802 AGATTGGAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.17
Consensus pattern (31 bp):
AAATGAGCTGGAAACAAGCTAAAGTGAGCTC
Found at i:28639 original size:40 final size:40
Alignment explanation
Indices: 28546--28809 Score: 295
Period size: 40 Copynumber: 6.7 Consensus size: 40
28536 GCTCCTCGTT
* * * * *
28546 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
28586 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
*
28625 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
*
28665 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * * *
28705 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAATAACTCGCA
** * * * *
28745 CAAATGCCTTC-GGATCTT-AGTCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCA
*
28785 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
28810 CAGCATTCAA
Statistics
Matches: 194, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.01
39 52 0.27
40 137 0.71
41 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:28793 original size:119 final size:118
Alignment explanation
Indices: 28546--28809 Score: 291
Period size: 119 Copynumber: 2.2 Consensus size: 118
28536 GCTCCTCGTT
* * * *
28546 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAAGGCCTTCGGGACTTAACCCGGA
* * * *
28611 TTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
65 CTTAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
* * * *
28665 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACAC-AAGGCCTTCGGGACTTAACCCGG
* * ** * *
28730 AACTT-GTATCTCGCACAAATGCCTTC-GGATCTT-AGTCGGATATAGTCACTTAGCA
64 -ACTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAAC-TAGCA
28785 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
28810 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
119 68 0.57
120 49 0.41
121 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (118 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAAGGCCTTCGGGACTTAACCCGGAC
TTAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
Found at i:32775 original size:17 final size:17
Alignment explanation
Indices: 32755--32787 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
32745 CTATAAGCAC
32755 AATTAAACAAGTTAAAT
1 AATTAAACAAGTTAAAT
32772 AATTAAACAAGTTAAA
1 AATTAAACAAGTTAAA
32788 CGGCTGTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (17 bp):
AATTAAACAAGTTAAAT
Found at i:36204 original size:14 final size:14
Alignment explanation
Indices: 36157--36204 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
36147 GTACAAATTG
*
36157 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
36171 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
36185 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
36199 ATTGGT
1 AATGGT
36205 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:38955 original size:39 final size:39
Alignment explanation
Indices: 38763--39013 Score: 295
Period size: 38 Copynumber: 6.5 Consensus size: 39
38753 TGGATGATAA
* *
38763 CCGGGCTAAGTCCCGAAGGCATTTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTGTGCG--AGTTACTA-TAT
* *
38804 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATAT
*
38844 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTAT-T
1 CCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATAT
38883 CCGGGCTAAGT-CC-AAGG-ATTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAT
38919 CCGGGCTAAGTCCC-AAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATT-GTGCGAGTTACTATAT
* *
38958 CC-GGCTATGTCCCGAAGGCATTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTA-CTATAT
* *
38996 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
39014 TACTTGGCTT
Statistics
Matches: 189, Mismatches: 13, Indels: 19
0.86 0.06 0.09
Matches are distributed among these distances:
35 15 0.08
36 13 0.07
37 12 0.06
38 42 0.22
39 38 0.20
40 42 0.22
41 21 0.11
42 6 0.03
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAT
Found at i:38986 original size:38 final size:40
Alignment explanation
Indices: 38763--39013 Score: 301
Period size: 40 Copynumber: 6.5 Consensus size: 40
38753 TGGATGATAA
*
38763 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* *
38804 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
38844 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTAT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
38883 CCGGGCTAAGT-CC-AAGG-A-TTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
38919 CCGGGCTAAGTCCC-AAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
38958 CC-GGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
38996 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
39014 TACTTGGCTT
Statistics
Matches: 188, Mismatches: 14, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
35 15 0.08
36 13 0.07
37 12 0.06
38 41 0.22
39 37 0.20
40 42 0.22
41 24 0.13
42 4 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Done.