Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3549
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: 67938
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:3179 original size:46 final size:47
Alignment explanation
Indices: 2971--3297 Score: 469
Period size: 46 Copynumber: 7.0 Consensus size: 47
2961 GAAATGATAG
2971 TAAGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATTATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA-TATGTGA
*
3018 TAAGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
3064 TAAGGCCTAAT-GCCGATGT--TGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3108 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3155 TAA-GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGCA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG-A
*
3202 AAAGGCCTAATGGCCGATGTGATGAATGTTGTGAAAGTGTAATATATGTG-
1 TAAGGCCTAATGGCCGATGTGATGAA---TGTGAAAGTGT-ATATATGTGA
3252 --AGGCCTAATGGCCCGAATGTGATG-ATGTGAAAGTGTA-ATTATGTGA
1 TAAGGCCTAATGG-CCG-ATGTGATGAATGTGAAAGTGTATA-TATGTGA
3298 CGGGGCCGGA
Statistics
Matches: 263, Mismatches: 3, Indels: 29
0.89 0.01 0.10
Matches are distributed among these distances:
43 8 0.03
44 28 0.11
45 23 0.09
46 70 0.27
47 69 0.26
48 33 0.13
49 4 0.02
50 8 0.03
51 11 0.04
52 9 0.03
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.30
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:5262 original size:41 final size:42
Alignment explanation
Indices: 5171--5270 Score: 177
Period size: 42 Copynumber: 2.4 Consensus size: 42
5161 TTGGTTTTCA
5171 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGTTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGTTG
5213 GCACTAAGTGTGCGGGCAATAAGT-TTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAG-TTG
5255 GCA-TAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
5271 TTGAAATGCA
Statistics
Matches: 57, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
41 27 0.47
42 30 0.53
ACGTcount: A:0.22, C:0.15, G:0.36, T:0.27
Consensus pattern (42 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGTTG
Found at i:5734 original size:40 final size:38
Alignment explanation
Indices: 5636--5810 Score: 178
Period size: 40 Copynumber: 4.5 Consensus size: 38
5626 CGAATGATGT
* *
5636 CGGCTAAGTCCGAAG-GC-TTTGTGCTAGTGACCATATC
1 CGGCTAAGTCCGAAGAGCATTCGTGCTAGTGA-TATATC
* * * *
5673 CGGACTAAGATCCGAAG-GCATTGGTGCGAGTTACTAAATC
1 CGG-CTAAG-TCCGAAGAGCATTCGTGCTAGTGA-TATATC
* *
5713 CGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGCTAAGT-CCGAAGAGCATTCGTGCTAGTGATATATC
5752 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATC
1 C-GGCTAAG-TCCGAAGAGCATTCGTGCTAGTGATATATC
5792 CGGCTAA-TCCCGAAGAGCA
1 CGGCTAAGT-CCGAAGAGCA
5811 ATCATGCTGG
Statistics
Matches: 117, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
37 4 0.03
38 16 0.14
39 31 0.26
40 65 0.56
41 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (38 bp):
CGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATATATC
Found at i:5766 original size:79 final size:80
Alignment explanation
Indices: 5636--5824 Score: 219
Period size: 79 Copynumber: 2.4 Consensus size: 80
5626 CGAATGATGT
** *
5636 CGGCTAAGT-CCGAAG-GC-TTTGTGCTAGTGACCATATCCGGACTAAGATCCGAAG-GCATTGG
1 CGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACCATATCCGGACTAAGATCCGAAGAGCATTCG
*
5697 TGCGAGTTACTAAATC
66 TGCGAGTGA-TAAATC
** * *
5713 CGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TGTATCCGGGCTAAGTTCCGAAGAGCATTCG
1 CGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACCATATCCGGACTAAGATCCGAAGAGCATTCG
* *
5777 TGCTAGTGATATATC
66 TGCGAGTGATAAATC
* *
5792 CGGCTAA-TCCCGAAGAGCAATCATGCTGGTGAC
1 CGGCTAAGTCCCGAAGAGCATTCATGCTAGTGAC
5825 GTGTATTCGG
Statistics
Matches: 95, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
77 9 0.09
78 29 0.31
79 33 0.35
80 24 0.25
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
CGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACCATATCCGGACTAAGATCCGAAGAGCATTCG
TGCGAGTGATAAATC
Found at i:9149 original size:47 final size:47
Alignment explanation
Indices: 9042--9463 Score: 678
Period size: 47 Copynumber: 9.1 Consensus size: 47
9032 GAAATGATAG
9042 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
9091 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
9138 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
9183 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
9229 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
9275 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA--TGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
9320 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
9367 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
** * * * * * * *
9414 -CGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
9460 TAAG
1 TAAG
9464 TCCCGAAGGG
Statistics
Matches: 352, Mismatches: 15, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
44 24 0.07
45 64 0.18
46 101 0.29
47 127 0.36
49 36 0.10
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:9279 original size:92 final size:94
Alignment explanation
Indices: 9042--9463 Score: 678
Period size: 92 Copynumber: 4.5 Consensus size: 94
9032 GAAATGATAG
9042 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
9107 ATGTGATGAATGTGAAAGTGTATATGTGTGA
64 ATGTGATGAATGTGAAAGTGTATATGTGTGA
9138 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATGTGATAAGGCCTAAT-GCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
9200 GTGATGAATGTGAAAGTGTATATGTGTGA
66 GTGATGAATGTGAAAGTGTATATGTGTGA
9229 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
*
9293 GTGATGAATGTGAAAGTGTATA--TATGA
66 GTGATGAATGTGAAAGTGTATATGTGTGA
9320 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
*
9385 GTGATGAATGTGAAAGTGTATATATGTGA
66 GTGATGAATGTGAAAGTGTATATGTGTGA
** * * * * * * *
9414 -CGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGATAAG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
9464 TCCCGAAGGG
Statistics
Matches: 309, Mismatches: 11, Indels: 15
0.92 0.03 0.04
Matches are distributed among these distances:
90 24 0.08
91 61 0.20
92 115 0.37
93 69 0.22
94 4 0.01
96 36 0.12
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.29
Consensus pattern (94 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATGTGTGA
Found at i:9638 original size:37 final size:37
Alignment explanation
Indices: 9582--9660 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
9572 CCGAGCTCTA
* *
9582 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
9619 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
9656 AAGAC
1 AAGAC
9661 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:12900 original size:30 final size:28
Alignment explanation
Indices: 12866--12921 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
12856 GTGATTAAAT
12866 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
12896 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
12922 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:18358 original size:25 final size:25
Alignment explanation
Indices: 18330--18377 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
18320 CAACTTCTAA
18330 AGAAAA-CTCAAGAGAGAATTCTTGG
1 AGAAAAGCTCAAG-GAGAATTCTTGG
18355 AGAAAAGCTCAAGGAGAATTCTT
1 AGAAAAGCTCAAGGAGAATTCTT
18378 CACTTAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (25 bp):
AGAAAAGCTCAAGGAGAATTCTTGG
Found at i:21983 original size:40 final size:40
Alignment explanation
Indices: 21899--22082 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
21889 TTGAATGCTG
* * * *
21899 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
21938 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
21979 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
22019 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
*
22059 TCCGGGTTAAGTCCTGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
22083 GAATGAGTTA
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 110 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:22036 original size:80 final size:81
Alignment explanation
Indices: 21899--22079 Score: 212
Period size: 80 Copynumber: 2.3 Consensus size: 81
21889 TTGAATGCTG
* * *
21899 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
21963 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
21979 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
22040 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
*
22059 TCCGGGTTAAGTCCTGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
22080 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
79 4 0.05
80 75 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:22103 original size:39 final size:39
Alignment explanation
Indices: 21979--22129 Score: 126
Period size: 40 Copynumber: 3.8 Consensus size: 39
21969 AGTTATTAAT
* ** * *
21979 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACT-AAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAG-TTCTAAAA
** *
22019 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* * *
22059 TCCGGGTTAAGTCCTGAAGGCATTGAATGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
22099 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
22130 GAGCTATATC
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
39 29 0.31
40 64 0.69
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:24401 original size:17 final size:18
Alignment explanation
Indices: 24364--24402 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
24354 GAGACTTTGG
*
24364 AAAAAGAAAATGAGTTAA
1 AAAAAGAAAATGAGTGAA
*
24382 AAAAAG-AAATGAGTGGA
1 AAAAAGAAAATGAGTGAA
24399 AAAA
1 AAAA
24403 TGAGAGAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.13
Consensus pattern (18 bp):
AAAAAGAAAATGAGTGAA
Found at i:24401 original size:18 final size:18
Alignment explanation
Indices: 24364--24402 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
24354 GAGACTTTGG
*
24364 AAAAAGAAAATGAGTTAA
1 AAAAAGAAAATGAGTGAA
24382 AAAAAG-AAATGAGTGGAA
1 AAAAAGAAAATGAGT-GAA
24400 AAA
1 AAA
24403 TGAGAGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.13
Consensus pattern (18 bp):
AAAAAGAAAATGAGTGAA
Found at i:26923 original size:21 final size:21
Alignment explanation
Indices: 26894--26934 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
26884 TCTCTCTCGC
*
26894 TTTCCTTTTCACCTTTTTCAT
1 TTTCATTTTCACCTTTTTCAT
**
26915 TTTCATTTTCTTCTTTTTCA
1 TTTCATTTTCACCTTTTTCA
26935 CTTGTATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.24, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTCATTTTCACCTTTTTCAT
Found at i:30913 original size:21 final size:21
Alignment explanation
Indices: 30889--30938 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
30879 TCTCTCTCGC
*
30889 TTTCCTTTTCGCCTTTTTCAT
1 TTTCATTTTCGCCTTTTTCAT
** *
30910 TTTCATTTTCTTCTTTTTCAC
1 TTTCATTTTCGCCTTTTTCAT
30931 TTT-ATTTT
1 TTTCATTTT
30939 TCTCTTCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTCATTTTCGCCTTTTTCAT
Found at i:30939 original size:21 final size:23
Alignment explanation
Indices: 30901--30951 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
30891 TCCTTTTCGC
*
30901 CTTTTTCATTTTCA-TTT-TCTT
1 CTTTTTCACTTTCATTTTCTCTT
30922 CTTTTTCACTTT-ATTTTTCTCTT
1 CTTTTTCACTTTCA-TTTTCTCTT
30945 CTTTTTC
1 CTTTTTC
30952 TTTTTCCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 11 0.42
22 3 0.12
23 11 0.42
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.71
Consensus pattern (23 bp):
CTTTTTCACTTTCATTTTCTCTT
Found at i:39024 original size:14 final size:13
Alignment explanation
Indices: 38993--39026 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
38983 ACTACTAGCC
*
38993 TCTTTTCTATTTG
1 TCTTTTTTATTTG
39006 TCTTTTTTATTTG
1 TCTTTTTTATTTG
39019 TCCTTTTT
1 T-CTTTTT
39027 CCCTCACCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.74
Consensus pattern (13 bp):
TCTTTTTTATTTG
Found at i:42665 original size:50 final size:50
Alignment explanation
Indices: 42607--42797 Score: 242
Period size: 50 Copynumber: 3.8 Consensus size: 50
42597 TTAATAAAGT
42607 CATGCATTATGTAACTCTTATGTTAGTTAAGTTTGCATCATAAATTATGA
1 CATGCATTATGTAACTCTTATGTTAGTTAAGTTTGCATCATAAATTATGA
42657 CATGCATTATGTAACTCTTATGTTAGTTAAGTTTGCATCATAAATTATGA
1 CATGCATTATGTAACTCTTATGTTAGTTAAGTTTGCATCATAAATTATGA
** * * * * *
42707 CATGCATTATGTAACTCCCATGTTAGTTTAAGTCTACATCATTATATTAAGT
1 CATGCATTATGTAACTCTTATGTTAG-TTAAGTTTGCATCA-TAAATTATGA
* * *
42759 CATGCAATAAGTAACTCATT-TGTTCA-TTTAGTTTGCATC
1 CATGCATTATGTAACTC-TTATGTT-AGTTAAGTTTGCATC
42798 TTAATTAAAT
Statistics
Matches: 123, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
50 74 0.60
51 22 0.18
52 26 0.21
53 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (50 bp):
CATGCATTATGTAACTCTTATGTTAGTTAAGTTTGCATCATAAATTATGA
Found at i:62309 original size:24 final size:24
Alignment explanation
Indices: 62264--62309 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
62254 GCAAAAAAAT
* *
62264 GAAAAGAATAAAGAAAAGAATGTA
1 GAAAAGAAGAAAGAAAAAAATGTA
62288 GAAAAGAAGAAA-ATAAAAAATG
1 GAAAAGAAGAAAGA-AAAAAATG
62310 AGTGATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.11
Consensus pattern (24 bp):
GAAAAGAAGAAAGAAAAAAATGTA
Done.