Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold871
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: 32430
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3881 original size:25 final size:26
Alignment explanation
Indices: 3848--3899 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
3838 ATCATTCATG
*
3848 CATAGTTGCAAATTAACATTACATAT
1 CATAGTTGCAAATTAACATAACATAT
3874 CATA-TTGCAAATTAACATAACATAT
1 CATAGTTGCAAATTAACATAACATAT
3899 C
1 C
3900 GTAAACCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (26 bp):
CATAGTTGCAAATTAACATAACATAT
Found at i:4519 original size:29 final size:30
Alignment explanation
Indices: 4485--4548 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
4475 CAAGTAGTTG
*
4485 AAGCTAG-TTAAATC-GCACACTTAGTGCCA
1 AAGCTAGTTTAAATCAAC-CACTTAGTGCCA
4514 AAGCTAGTTTAAATCAACCACTTAGTGCCA
1 AAGCTAGTTTAAATCAACCACTTAGTGCCA
4544 AAGCT
1 AAGCT
4549 TCCGAATCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 7 0.22
30 24 0.75
31 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (30 bp):
AAGCTAGTTTAAATCAACCACTTAGTGCCA
Found at i:8247 original size:4 final size:4
Alignment explanation
Indices: 8238--8269 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
8228 AGGAGATGAA
8238 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
8270 TGTTCCATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:9400 original size:30 final size:30
Alignment explanation
Indices: 9375--9473 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
9365 TGAGCTCACT
9375 CTTAGCTCATA-TTCAGCTCACGAGCTAAAC
1 CTTAGCTCA-ACTTCAGCTCACGAGCTAAAC
* * * * *
9405 CTTAGCTCAACTTCAGCTTAGGAGTTTAAT
1 CTTAGCTCAACTTCAGCTCACGAGCTAAAC
* * *
9435 CTCAGCTCAACTTTAGCTCACGAGCTAAAG
1 CTTAGCTCAACTTCAGCTCACGAGCTAAAC
9465 CTTAGCTCA
1 CTTAGCTCA
9474 TTTTAGTTTA
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 54 0.98
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
CTTAGCTCAACTTCAGCTCACGAGCTAAAC
Found at i:11159 original size:12 final size:12
Alignment explanation
Indices: 11142--11172 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
11132 TATACAAGTT
11142 AAAAAAAATTCG
1 AAAAAAAATTCG
11154 AAAAAAAATTCG
1 AAAAAAAATTCG
11166 AAAAAAA
1 AAAAAAA
11173 TCTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:11182 original size:10 final size:11
Alignment explanation
Indices: 11143--11182 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
11133 ATACAAGTTA
11143 AAAAAAATTCG
1 AAAAAAATTCG
11154 AAAAAAAATTCG
1 -AAAAAAATTCG
*
11166 AAAAAAA-TCT
1 AAAAAAATTCG
11176 AAAAAAA
1 AAAAAAA
11183 AAAGTGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 9 0.33
11 7 0.26
12 11 0.41
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:12107 original size:9 final size:10
Alignment explanation
Indices: 12100--12156 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
12090 AAGAGAAAAC
12100 AAAGAAAAGA
1 AAAGAAAAGA
12110 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
12122 AAAGAAGA-A
1 AAAGAAAAGA
12131 AAAGAAAATGA
1 AAAGAAAA-GA
12142 AATA-AAAAGA
1 AA-AGAAAAGA
12152 AAAGA
1 AAAGA
12157 GGGACAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:12123 original size:21 final size:20
Alignment explanation
Indices: 12089--12156 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
12079 ACATTCTTGT
12089 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
12110 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
12131 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
12152 AAAGA
1 AAAGA
12157 GGGACAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:12124 original size:6 final size:5
Alignment explanation
Indices: 12100--12156 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
12090 AAGAGAAAAC
*
12100 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
12147 AAAGA AAAGA
1 AAAGA AAAGA
12157 GGGACAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:12131 original size:15 final size:14
Alignment explanation
Indices: 12100--12156 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
12090 AAGAGAAAAC
12100 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
12116 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
12131 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
12147 AAAGAAAAGA
1 AAAGAAAAGA
12157 GGGACAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:12236 original size:11 final size:12
Alignment explanation
Indices: 12204--12234 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
12194 TTGAGAGAAC
12204 TTGAAAAAGCCT
1 TTGAAAAAGCCT
12216 TTGAAAAAGCCT
1 TTGAAAAAGCCT
12228 TTGAAAA
1 TTGAAAA
12235 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:12245 original size:12 final size:12
Alignment explanation
Indices: 12237--12261 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12227 TTTGAAAAGC
12237 AAAAAGAAAATG
1 AAAAAGAAAATG
12249 AAAAAGAAAATG
1 AAAAAGAAAATG
12261 A
1 A
12262 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:12258 original size:18 final size:18
Alignment explanation
Indices: 12231--12286 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
12221 AAAGCCTTTG
*
12231 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAATGAAAATGA
* *
12250 AAAAGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
*
12268 AAAAGAGAATGAAAA-GA
1 AAAAGAAAATGAAAATGA
12285 AA
1 AA
12287 TTTGAGAGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 4 0.13
18 22 0.71
19 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09
Consensus pattern (18 bp):
AAAAGAAAATGAAAATGA
Found at i:12271 original size:30 final size:31
Alignment explanation
Indices: 12237--12318 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 31
12227 TTTGAAAAGC
*
12237 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* *
12267 AAAAAGAGAATG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
12297 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
12319 TGAAACAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.18
30 28 0.62
31 9 0.20
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:14501 original size:47 final size:47
Alignment explanation
Indices: 14447--14688 Score: 281
Period size: 47 Copynumber: 5.1 Consensus size: 47
14437 TTAGGATTTT
** *
14447 ATGTGATGAATGTGAATGTGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
14494 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
14541 ATGTGATGAATGTGAGCACGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
14588 ATATGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
** * * * *
14635 ATGTGAAAAATGTATGATAAATG--TATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATG--TGA-ACATGCATATATGTGATAAGGCCGAATGGCCA
14683 ATGTGA
1 ATGTGA
14689 AATATGTATG
Statistics
Matches: 171, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
47 133 0.78
48 31 0.18
49 3 0.02
50 4 0.02
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:14547 original size:22 final size:22
Alignment explanation
Indices: 14476--14547 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
14466 GCATATATGA
14476 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
14498 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
14523 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
14545 GAT
1 GAT
14548 GAATGTGAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:14768 original size:50 final size:49
Alignment explanation
Indices: 14610--14794 Score: 261
Period size: 48 Copynumber: 3.8 Consensus size: 49
14600 TGAACATGCA
* *
14610 TATATGTGGTAAAGCCGAATGGCTAATGTGAAAA-ATGTATGATAAATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAAATATGTATGAGATATG
14658 TATATGTGGTAAAGCCGAATGGCTAATGTG-AAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAAATATGTATGAGATATG
* * *
14706 CATATGTGGTAAAGCTGAATGG-TCAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTGAAA-ATATGTATGAGATATG
* *
14756 TATATGTGGTAAAGCTGAATGGCTAGTGTG-AAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAAATATGTA
14795 GGCGATGTGC
Statistics
Matches: 124, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
47 4 0.03
48 74 0.60
49 4 0.03
50 41 0.33
51 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (49 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAAATATGTATGAGATATG
Found at i:14768 original size:98 final size:96
Alignment explanation
Indices: 14611--14794 Score: 280
Period size: 98 Copynumber: 1.9 Consensus size: 96
14601 GAACATGCAT
* *
14611 ATATGTGGTAAAGCCGAATGGCTAATGTGAAAAATGTATGATAAATGTATATGTGGTAAAGCCGA
1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAAAATATATGAGAAATGTATATGTGGTAAAGCCGA
14676 ATGGCTAATGTGAAATATGTATGAGATATGC
66 ATGGCTAATGTGAAATATGTATGAGATATGC
* *
14707 ATATGTGGTAAAGCTGAATGG-TCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGC
1 ATATGTGGTAAAGCCGAATGGCT-AATGTGAAA-A-ATATATGAGAAATGTATATGTGGTAAAGC
* *
14771 TGAATGGCTAGTGTGAAATATGTA
63 CGAATGGCTAATGTGAAATATGTA
14795 GGCGATGTGC
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
95 1 0.01
96 29 0.37
97 1 0.01
98 48 0.61
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (96 bp):
ATATGTGGTAAAGCCGAATGGCTAATGTGAAAAATATATGAGAAATGTATATGTGGTAAAGCCGA
ATGGCTAATGTGAAATATGTATGAGATATGC
Found at i:14809 original size:50 final size:50
Alignment explanation
Indices: 14605--14815 Score: 238
Period size: 48 Copynumber: 4.3 Consensus size: 50
14595 GAATATGAAC
* * * *
14605 ATGCATATATGTGGTAAAGCCGAATGGCTAATGTGAAAAATGTATGATAA
1 ATGCGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
14655 AT--GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
1 ATGCGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
* *
14703 ATGC--ATATGTGGTAAAGCTGAATGG-TCAATGTGAAATATATATATGAGAT
1 ATGCGTATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGAT
* * * *
14753 AT--GTATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTAGGCGAT
1 ATGCGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
*
14801 GTGCGTATATTGTGG
1 ATGCGTATA-TGTGG
14816 CCGAACGACC
Statistics
Matches: 139, Mismatches: 11, Indels: 21
0.81 0.06 0.12
Matches are distributed among these distances:
47 1 0.01
48 81 0.58
49 4 0.03
50 47 0.34
51 6 0.04
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (50 bp):
ATGCGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
Found at i:14990 original size:37 final size:37
Alignment explanation
Indices: 14940--15047 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
14930 GGAAATATAT
14940 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
14977 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * * * *
15014 TCTGGGTAAGACTCGATAACTTCATGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
15048 TCGTCTGAGC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:20318 original size:63 final size:63
Alignment explanation
Indices: 20271--20540 Score: 237
Period size: 63 Copynumber: 4.3 Consensus size: 63
20261 TTGAGCCTCT
* * *
20271 ACAAAGCCATGATTTATTTATCAATTTTTAGTTTTGATTCCTGTATTCATCCACCAAACCTTC
1 ACAAAGCCATAATTTATTTATCAATTTTCAATTTTGATTCCTGTATTCATCCACCAAACCTTC
* ** * * *
20334 GCAAAGCCATAATTTATTTATCAATTTTCAATTTTGATCTCC-GTAAACGTACACCAAATC-TC
1 ACAAAGCCATAATTTATTTATCAATTTTCAATTTTGAT-TCCTGTATTCATCCACCAAACCTTC
** * ** * * * **
20396 TGTAAAGCCATAATTTATTCATTGA-TTTAAATTTTGATTACTGTACTCATCCACCAAAATTTC
1 -ACAAAGCCATAATTTATTTATCAATTTTCAATTTTGATTCCTGTATTCATCCACCAAACCTTC
* * * * *
20459 A-AAAGCCATAATTTATTTATCGATTTTCAATTCTGATTCTTGTACTCATCCACCGAACC-TC
1 ACAAAGCCATAATTTATTTATCAATTTTCAATTTTGATTCCTGTATTCATCCACCAAACCTTC
*
20520 TGC-AAGTCCATAATTTATTTA
1 -ACAAAG-CCATAATTTATTTA
20541 CATGTAACAT
Statistics
Matches: 167, Mismatches: 32, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
61 24 0.14
62 57 0.34
63 83 0.50
64 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.39
Consensus pattern (63 bp):
ACAAAGCCATAATTTATTTATCAATTTTCAATTTTGATTCCTGTATTCATCCACCAAACCTTC
Found at i:20521 original size:124 final size:125
Alignment explanation
Indices: 20302--20538 Score: 300
Period size: 124 Copynumber: 1.9 Consensus size: 125
20292 CAATTTTTAG
* * * *
20302 TTTTGATTCCTGTATTCATCCACCAAACCTTCGCAAAGCCATAATTTATTTATCAATTTTCAATT
1 TTTTGATTACTGTACTCATCCACCAAAACTTCGAAAAGCCATAATTTATTTATCAATTTTCAATT
* * *
20367 TTGATCTCCGTAAACGTACACCAAATCTCTGTAAAG-CCATAATTTATTCATTGATTTAAA
66 CTGATCTCCGTAAACATACACCAAACCTCTG-AAAGTCCATAATTTATTCATTGATTTAAA
* *
20427 TTTTGATTACTGTACTCATCCACCAAAATTTC-AAAAGCCATAATTTATTTATCGATTTTCAATT
1 TTTTGATTACTGTACTCATCCACCAAAACTTCGAAAAGCCATAATTTATTTATCAATTTTCAATT
* ** * * *
20491 CTGAT-TCTTGTACTCATCCACCGAACCTCTGCAAGTCCATAATTTATT
66 CTGATCTC-CGTAAACATACACCAAACCTCTGAAAGTCCATAATTTATT
20539 TACATGTAAC
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
123 5 0.05
124 62 0.65
125 28 0.29
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (125 bp):
TTTTGATTACTGTACTCATCCACCAAAACTTCGAAAAGCCATAATTTATTTATCAATTTTCAATT
CTGATCTCCGTAAACATACACCAAACCTCTGAAAGTCCATAATTTATTCATTGATTTAAA
Found at i:23693 original size:27 final size:27
Alignment explanation
Indices: 23663--23739 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
23653 CCTATAGGGG
* *
23663 AAAATGACCGAAATACCCTTGTAGTGT
1 AAAATGACCGAAATACCCTTGTAGAGC
* *
23690 AAAATTATCGAAATACCCTTGTAGAGC
1 AAAATGACCGAAATACCCTTGTAGAGC
* *
23717 AAAATGACCGTAATACCCCTGTA
1 AAAATGACCGAAATACCCTTGTA
23740 TGGTAATATG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.25
Consensus pattern (27 bp):
AAAATGACCGAAATACCCTTGTAGAGC
Found at i:23750 original size:27 final size:27
Alignment explanation
Indices: 23634--23739 Score: 95
Period size: 27 Copynumber: 3.9 Consensus size: 27
23624 ACCATAGTTT
* * * * *
23634 GTAAATTGACCGTAATGCCCCTATAGG
1 GTAAAATGACCGAAATACCCCTGTAGA
* * *
23661 GGAAAATGACCGAAATACCCTTGTAGT
1 GTAAAATGACCGAAATACCCCTGTAGA
* * *
23688 GTAAAATTATCGAAATACCCTTGTAGA
1 GTAAAATGACCGAAATACCCCTGTAGA
* *
23715 GCAAAATGACCGTAATACCCCTGTA
1 GTAAAATGACCGAAATACCCCTGTA
23740 TGGTAATATG
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (27 bp):
GTAAAATGACCGAAATACCCCTGTAGA
Found at i:26999 original size:28 final size:28
Alignment explanation
Indices: 26936--27058 Score: 167
Period size: 28 Copynumber: 4.4 Consensus size: 28
26926 ATATTAAGTC
*
26936 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
26963 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
26991 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
27019 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
27048 CGCACACTTAG
1 CGCACACTTAG
27059 CGCCAATCTC
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 21 0.25
28 48 0.56
29 16 0.19
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Done.