Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold534
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: 83246
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.32
Warning! 3467 characters in sequence are not A, C, G, or T
Found at i:1717 original size:15 final size:15
Alignment explanation
Indices: 1697--1727 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1687 AAACCTTTGC
1697 GAACAATCACAACTT
1 GAACAATCACAACTT
1712 GAACAATCACAACTT
1 GAACAATCACAACTT
1727 G
1 G
1728 TAGCCTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.19
Consensus pattern (15 bp):
GAACAATCACAACTT
Found at i:3815 original size:21 final size:21
Alignment explanation
Indices: 3777--3817 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3767 AATCTCGAAG
**
3777 GCTAAATAGAATTACATAAGT
1 GCTAAATAGAAACACATAAGT
*
3798 GCTAAATAGAAACCCATAAG
1 GCTAAATAGAAACACATAAG
3818 GGTTGAACAG
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:0.49, C:0.15, G:0.15, T:0.22
Consensus pattern (21 bp):
GCTAAATAGAAACACATAAGT
Found at i:4903 original size:3 final size:3
Alignment explanation
Indices: 4844--4884 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
4834 AGATAAAAAA
*
4844 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG GA- AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
4885 GAAAACAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.09
3 31 0.91
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5048 original size:2 final size:2
Alignment explanation
Indices: 5041--5068 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5031 CTTTTTATCA
5041 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5069 TAATTGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6745 original size:20 final size:20
Alignment explanation
Indices: 6706--6745 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6696 TTCAAATATC
* *
6706 AAAAATAACATTTTAGAAGA
1 AAAAATAACATATTAAAAGA
*
6726 AAAAATATCATATTAAAAGA
1 AAAAATAACATATTAAAAGA
6746 TTTGATAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (20 bp):
AAAAATAACATATTAAAAGA
Found at i:11873 original size:15 final size:15
Alignment explanation
Indices: 11853--11883 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11843 AAACCTTTGC
11853 GAACAATCACAACTT
1 GAACAATCACAACTT
11868 GAACAATCACAACTT
1 GAACAATCACAACTT
11883 G
1 G
11884 TAGCCTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.19
Consensus pattern (15 bp):
GAACAATCACAACTT
Found at i:13411 original size:21 final size:21
Alignment explanation
Indices: 13373--13413 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13363 AATCTCGAAG
**
13373 GCTAAATAGAATTACATAAGT
1 GCTAAATAGAAACACATAAGT
*
13394 GCTAAATAGAAACCCATAAG
1 GCTAAATAGAAACACATAAG
13414 GGTTGAACAG
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:0.49, C:0.15, G:0.15, T:0.22
Consensus pattern (21 bp):
GCTAAATAGAAACACATAAGT
Found at i:14499 original size:3 final size:3
Alignment explanation
Indices: 14440--14480 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
14430 AGATAAAAAA
*
14440 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG GA- AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
14481 GAAAACAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.09
3 31 0.91
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:14644 original size:2 final size:2
Alignment explanation
Indices: 14637--14664 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14627 CTTTTTATCA
14637 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14665 TAATTGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16341 original size:20 final size:20
Alignment explanation
Indices: 16302--16341 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16292 TTCAAATATC
* *
16302 AAAAATAACATTTTAGAAGA
1 AAAAATAACATATTAAAAGA
*
16322 AAAAATATCATATTAAAAGA
1 AAAAATAACATATTAAAAGA
16342 TTTGATAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (20 bp):
AAAAATAACATATTAAAAGA
Found at i:50323 original size:51 final size:51
Alignment explanation
Indices: 50267--50371 Score: 122
Period size: 51 Copynumber: 2.1 Consensus size: 51
50257 TGTGGCACGG
* * ** *
50267 ACTGTGTGTAGGCCACTATATGAAAGTGA-AAATGTTGGTCACGTGTGTAGT
1 ACTGTGTGAAGGCCACTACATGAAAG-GATAAATAATGGTCACATGTGTAGT
* * *
50318 ACTGTGTGAAGGCTACTACGTGAATGGATAAATAATGGTCACATGTGTAGT
1 ACTGTGTGAAGGCCACTACATGAAAGGATAAATAATGGTCACATGTGTAGT
50369 ACT
1 ACT
50372 AAGTGAATGC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
50 2 0.04
51 43 0.96
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (51 bp):
ACTGTGTGAAGGCCACTACATGAAAGGATAAATAATGGTCACATGTGTAGT
Found at i:50474 original size:50 final size:50
Alignment explanation
Indices: 50305--50541 Score: 280
Period size: 50 Copynumber: 4.7 Consensus size: 50
50295 AAAATGTTGG
* ** * *
50305 TCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATGGATAAATA-ATGG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGA
* * * * ** * * *
50356 TCACATGTGTAGTACTAAGTGAATGCTACAATATGTACCG-AGAAGCTTTGG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGA
50407 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGA
* *
50457 TCACGTGTGTAGTACTATGTGAAGGCTATTACGTGAACCGTAAAAATTGA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGA
50507 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
50542 NNNNNNNNNN
Statistics
Matches: 158, Mismatches: 24, Indels: 9
0.83 0.13 0.05
Matches are distributed among these distances:
49 1 0.01
50 87 0.55
51 69 0.44
52 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGA
Found at i:50526 original size:100 final size:102
Alignment explanation
Indices: 50305--50541 Score: 284
Period size: 101 Copynumber: 2.3 Consensus size: 102
50295 AAAATGTTGG
* ** *
50305 TCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATGGATAAATAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAATGATCACATGTGTAGTA
* * * ** *
50370 CTAAGTGAATGCTACAATATGTACCGAGAAGCTTTGG
66 CTAAGTGAAGGCTACAACATGAACCGAGAAGAATTGA
* *
50407 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTGTAGT
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATA-ATGATCACATGTGTAGT
* ** *
50470 ACTATGTGAAGGCTATTACGTGAACCGTA-AA-AATTGA
65 ACTAAGTGAAGGCTACAACATGAACCG-AGAAGAATTGA
50507 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
50542 NNNNNNNNNN
Statistics
Matches: 117, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
100 39 0.33
101 40 0.34
102 38 0.32
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAATGATCACATGTGTAGTA
CTAAGTGAAGGCTACAACATGAACCGAGAAGAATTGA
Found at i:51159 original size:51 final size:50
Alignment explanation
Indices: 51061--51239 Score: 171
Period size: 51 Copynumber: 3.5 Consensus size: 50
51051 TTTTGATACA
* * * * * * *
51061 TGTGTAGTACTAAGTGAAGGCTACAATATGTATCGAGAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACATGAACCGAAAAGC-ATGGTCACG
* ** *
51112 TGTGTAGTACTATGTGAAGGCTACTACGTGAATTGATAAATG-ATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACATGAACCGA-AAA-GCATGGTCACG
* * * * *
51163 TGTGTAGTACTAAGTGAAGGTTACTATATGTACCGAAAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACATGAACCGAAAAGC-ATGGTCACG
51214 TGTGTAGTACTATGTGAAGGCTACTA
1 TGTGTAGTACTATGTGAAGGCTACTA
51240 NNNNNNNNNN
Statistics
Matches: 104, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
49 1 0.01
50 3 0.03
51 97 0.93
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGAAGGCTACTACATGAACCGAAAAGCATGGTCACG
Found at i:52209 original size:5 final size:5
Alignment explanation
Indices: 52199--52257 Score: 73
Period size: 5 Copynumber: 11.8 Consensus size: 5
52189 TGCTTGATGA
* * * *
52199 AATGG AATGG AATGG AATGG TATGA AATGG AATAG TATGG AATGG AATGG
1 AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG
*
52249 TATGG AATG
1 AATGG AATG
52258 AAATATATAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.39, C:0.00, G:0.36, T:0.25
Consensus pattern (5 bp):
AATGG
Found at i:52227 original size:15 final size:15
Alignment explanation
Indices: 52199--52257 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
52189 TGCTTGATGA
*
52199 AATGGAATGGAATGG
1 AATGGTATGGAATGG
*
52214 AATGGTATGAAATGG
1 AATGGTATGGAATGG
*
52229 AATAGTATGGAATGG
1 AATGGTATGGAATGG
52244 AATGGTATGGAATG
1 AATGGTATGGAATG
52258 AAATATATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.39, C:0.00, G:0.36, T:0.25
Consensus pattern (15 bp):
AATGGTATGGAATGG
Found at i:54481 original size:20 final size:20
Alignment explanation
Indices: 54456--54495 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54446 AATATTTTCC
*
54456 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
54476 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
54496 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:56413 original size:21 final size:21
Alignment explanation
Indices: 56389--56430 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
56379 ATTTTTTCTT
*
56389 AATTAACTATCTAAATATTAA
1 AATTAACTAACTAAATATTAA
* *
56410 AATTACCTAACTAAATTTTAA
1 AATTAACTAACTAAATATTAA
56431 TATGGCACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTAACTAACTAAATATTAA
Found at i:57877 original size:17 final size:18
Alignment explanation
Indices: 57855--57891 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
57845 CAATTAATTA
57855 TAACATCAATAT-TATTT
1 TAACATCAATATATATTT
*
57872 TAACATCAGTATATATTT
1 TAACATCAATATATATTT
57890 TA
1 TA
57892 TTGGTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.46
Consensus pattern (18 bp):
TAACATCAATATATATTT
Found at i:57992 original size:20 final size:19
Alignment explanation
Indices: 57959--58007 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
57949 AAAAAATATA
*
57959 TAAATATTACGACTAAATTTG
1 TAAA-ATTAAGACTAAA-TTG
* *
57980 TTAAATTAAGACTCAATTG
1 TAAAATTAAGACTAAATTG
57999 TAAAATTAA
1 TAAAATTAA
58008 TTCTCAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 11 0.46
20 10 0.42
21 3 0.12
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (19 bp):
TAAAATTAAGACTAAATTG
Found at i:63677 original size:2 final size:2
Alignment explanation
Indices: 63670--63694 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63660 ACTAGGCTGC
63670 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
63695 TTATTTNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63773 original size:2 final size:2
Alignment explanation
Indices: 63766--63798 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
63756 TCTAGGGTGC
63766 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
63799 TAAATTCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:67576 original size:91 final size:91
Alignment explanation
Indices: 67421--67694 Score: 512
Period size: 91 Copynumber: 3.0 Consensus size: 91
67411 TAATTTTTAA
67421 AACAAAATCTTTGAGTTTTGAAGGATGCTAATGTTGTGGAAGTATAAAAGCCAATATCAATTCAT
1 AACAAAATCTTTGAGTTTTGAAGGATGCTAATGTTGTGGAAGTATAAAAGCCAATATCAATTCAT
67486 TTGAAACAACTTATCTTGAAGATTAG
66 TTGAAACAACTTATCTTGAAGATTAG
* * *
67512 AACAAAATCTTTAAGTTTTGAAGGATGCTAATGTTGTGAAAGTATTAAAGCCAATATCAATTCAT
1 AACAAAATCTTTGAGTTTTGAAGGATGCTAATGTTGTGGAAGTATAAAAGCCAATATCAATTCAT
67577 TTGAAACAACTTATCTTGAAGATTAG
66 TTGAAACAACTTATCTTGAAGATTAG
67603 AACAAAATCTTTGAGTTTTGAAGGATGCTAATGTTGTGGAAGTATAAAAGCCAATATCAATTCAT
1 AACAAAATCTTTGAGTTTTGAAGGATGCTAATGTTGTGGAAGTATAAAAGCCAATATCAATTCAT
*
67668 TTTAAACAACTTATCTTGAAGATTAG
66 TTGAAACAACTTATCTTGAAGATTAG
67694 A
1 A
67695 TTAGATCGGC
Statistics
Matches: 176, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 176 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (91 bp):
AACAAAATCTTTGAGTTTTGAAGGATGCTAATGTTGTGGAAGTATAAAAGCCAATATCAATTCAT
TTGAAACAACTTATCTTGAAGATTAG
Found at i:74198 original size:9 final size:9
Alignment explanation
Indices: 74184--74214 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
74174 GTTAAACGAA
74184 TCGAGTTAT
1 TCGAGTTAT
*
74193 TCGAGTTAA
1 TCGAGTTAT
74202 TCGAGTTAT
1 TCGAGTTAT
74211 TCGA
1 TCGA
74215 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:74286 original size:9 final size:9
Alignment explanation
Indices: 74269--74305 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
74259 TGAGTTTTCG
74269 AATTCGAAT
1 AATTCGAAT
*
74278 AACTCGAAT
1 AATTCGAAT
74287 AATTCGAAT
1 AATTCGAAT
74296 AATTCGAAT
1 AATTCGAAT
74305 A
1 A
74306 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:75198 original size:5 final size:5
Alignment explanation
Indices: 75188--75213 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
75178 CTCGAAAATT
75188 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
75214 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:79290 original size:11 final size:13
Alignment explanation
Indices: 79274--79306 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
79264 ATTTTACGGG
79274 AAAATTTCG-T-A
1 AAAATTTCGTTCA
79285 AAAATTTCGTTCA
1 AAAATTTCGTTCA
79298 AAAATTTCG
1 AAAATTTCG
79307 ACGTTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 1 0.05
13 10 0.50
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (13 bp):
AAAATTTCGTTCA
Found at i:80427 original size:33 final size:33
Alignment explanation
Indices: 80377--80592 Score: 150
Period size: 33 Copynumber: 6.6 Consensus size: 33
80367 AATATGAAGG
* *
80377 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATAGGT
* *
80410 GGTTACTAAGTGCTGATTCCACCGTATCTTTAACTATAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A---TT--C-AT--AGGT
*
80453 GGTTGTTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATAGGT
*
80480 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATAGGT
*
80513 GGTTGCTAAGTGCTAATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATAGGT
* * * * *
80540 GATTGCTAAGTGCTGATTCCCTGAATGATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATAGGT
80573 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
80593 ACCATATCTT
Statistics
Matches: 145, Mismatches: 16, Indels: 44
0.71 0.08 0.21
Matches are distributed among these distances:
27 40 0.28
28 5 0.03
29 2 0.01
31 4 0.03
32 5 0.03
33 58 0.40
34 3 0.02
35 1 0.01
38 2 0.01
40 1 0.01
41 2 0.01
42 2 0.01
43 20 0.14
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATAGGT
Found at i:80489 original size:27 final size:27
Alignment explanation
Indices: 80451--80560 Score: 130
Period size: 27 Copynumber: 3.9 Consensus size: 27
80441 AACTATAAAG
*
80451 GGGGTTGTTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
*
80478 GGGGTTGCTAAGTGCTGATTCCCCGATTCATT
1 GGGGTTGCTAAGTGCTGATTCCCC----CA-A
*
80510 GGTGGTTGCTAAGTGCTAATTCCCCCAA
1 GG-GGTTGCTAAGTGCTGATTCCCCCAA
*
80538 GGGATTGCTAAGTGCTGATTCCC
1 GGGGTTGCTAAGTGCTGATTCCC
80561 TGAATGATTG
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
27 42 0.59
28 2 0.03
29 2 0.03
31 2 0.03
32 2 0.03
33 21 0.30
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:80546 original size:60 final size:60
Alignment explanation
Indices: 80453--80592 Score: 226
Period size: 60 Copynumber: 2.3 Consensus size: 60
80443 CTATAAAGGG
* * *
80453 GGTTGTTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
80513 GGTTGCTAAGTGCTAATTCCCCCAAGGGATTGCTAAGTGCTGATTCCCTGAATGATTGGT
1 GGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGTGCTGATTCCCCGAATCATTGGT
80573 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
80593 ACCATATCTT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.33
Consensus pattern (60 bp):
GGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGTGCTGATTCCCCGAATCATTGGT
Done.