Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1617
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: 52485
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Found at i:660 original size:18 final size:18
Alignment explanation
Indices: 625--661 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
615 TTATGAAATC
*
625 TTTTAGACAGTTTGTTTT
1 TTTTAAACAGTTTGTTTT
643 TTTTAAACA-TTT-TTTT
1 TTTTAAACAGTTTGTTTT
659 TTT
1 TTT
662 CCTTTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.19, C:0.05, G:0.08, T:0.68
Consensus pattern (18 bp):
TTTTAAACAGTTTGTTTT
Found at i:4816 original size:66 final size:64
Alignment explanation
Indices: 4688--4870 Score: 210
Period size: 66 Copynumber: 2.8 Consensus size: 64
4678 ATATAGTTCG
* * * * * *
4688 GCTCTCTTGTAC-ACATGGTGAACACTTAGTACCACCCATGGGACCTAGCCA-ATTTATCCCGTA
1 GCTCTCTTGT-CTACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACATATATCCCGTA
* * *
4751 GCTCTCTTGTCTACATGGTGTCCTTCACCTAGAACCACGCATGCGACCTAGCTACATATAT-CCG
1 GCTCTCTTGTCTACATGGTG---TACACATAGAACCACCCATGCGACCTAGCTACATATATCCCG
4815 TA
63 TA
* *
4817 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACAT
1 GCTCTCTTGTCTACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACAT
4871 CATAATGTCT
Statistics
Matches: 102, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
62 1 0.01
63 47 0.46
66 49 0.48
67 5 0.05
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACATATATCCCGTA
Found at i:5296 original size:18 final size:19
Alignment explanation
Indices: 5273--5308 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5263 AACTTGGCAC
*
5273 CATAA-TCATTTAATTTAA
1 CATAATTCAATTAATTTAA
5291 CATAATTCAATTAATTTA
1 CATAATTCAATTAATTTA
5309 CTAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (19 bp):
CATAATTCAATTAATTTAA
Found at i:5634 original size:30 final size:30
Alignment explanation
Indices: 5600--5660 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
5590 TCCTTAACTC
5600 AAACTTTGTG-AAAATTACAATTTTGCCCCT
1 AAACTTT-TGCAAAATTACAATTTTGCCCCT
* * *
5630 AAACTTTTGCATAGTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
5660 A
1 A
5661 GGCTCGGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:14711 original size:3 final size:3
Alignment explanation
Indices: 14703--14731 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
14693 TTGTTTTTAA
14703 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
14732 TACTTACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:18128 original size:31 final size:31
Alignment explanation
Indices: 18052--18125 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 31
18042 TCAAGTTATC
18052 TTAAATATTAAAATAAAAATAAAAATTTAGAA
1 TTAAATA-TAAAATAAAAATAAAAATTTAGAA
18084 TTAAA-ACTAAAATAAATAATAAAAA-TTAG-A
1 TTAAATA-TAAAATAAA-AATAAAAATTTAGAA
18114 TTAAATATAAAA
1 TTAAATATAAAA
18126 ATATCAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
30 11 0.28
31 15 0.38
32 13 0.33
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (31 bp):
TTAAATATAAAATAAAAATAAAAATTTAGAA
Found at i:23009 original size:28 final size:29
Alignment explanation
Indices: 22960--23019 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
22950 CCCCATATTT
* *
22960 ATCCCTAAACGCTAAAAATTAAACCCT-G
1 ATCCCCAAACGCCAAAAATTAAACCCTAG
** *
22988 ATCCCCAAACGCCAAACCTTAAATCCTAG
1 ATCCCCAAACGCCAAAAATTAAACCCTAG
23017 ATC
1 ATC
23020 ATAAATCCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 22 0.85
29 4 0.15
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (29 bp):
ATCCCCAAACGCCAAAAATTAAACCCTAG
Found at i:23215 original size:494 final size:494
Alignment explanation
Indices: 22272--23396 Score: 2106
Period size: 494 Copynumber: 2.3 Consensus size: 494
22262 TTTTAAGTTT
* *
22272 TTTATTTTTGATTTAATCATAGACATTTTAAAAAATAAATACATCAATATATTTTTATATTGAAT
1 TTTAATTTTGATTTAATCATACACATTTTAAAAAATAAATACATCAATATATTTTTATATTGAAT
*
22337 AAATATAAATATTTATGTATGCAATAAATAAATATAAAATGATGTTATATCAATAATTGTGTTAA
66 AAATATAAATATTTATGTATGCAATATATAAATATAAAATGATGTTATATCAATAATTGTGTTAA
*
22402 TAATTTACAAGAACTAGATCAAATTAAAGTTCATATATACAATTTTACCCTGATCCCCATATTTA
131 TAATTTACAAGAACTAGATCAAATTAAAGTTCATATATACAATTGTACCCTGATCCCCATATTTA
*
22467 TCCCTAAAAGCTAAAAATTAAACCTTGATCCCCAAACACCAAACCTTAAATCCTAGATCATAAAT
196 TCCCTAAAAGCTAAAAATTAAACCCTGATCCCCAAACACCAAACCTTAAATCCTAGATCATAAAT
*
22532 TCTAAACCCCAAAATAATGAACATTATATCATAACCCCTATCCCCTAAACTCTAAACCATAAAAC
261 CCTAAACCCCAAAATAATGAACATTATATCATAACCCCTATCCCCTAAACTCTAAACCATAAAAC
22597 ATAAACCATAAACCCTTAACCCCAACCCTTAAACCATAATTAGATATTTAATTATATGTACACAC
326 ATAAACCATAAACCCTTAACCCCAACCCTTAAACCATAATTAGATATTTAATTATATGTACACAC
22662 CTAAATTTTGATAGAGATACATCTCAGAATTATATATGAATTTCGATTTAATATGTAATTGTAGA
391 CTAAATTTTGATAGAGATACATCTCAGAATTATATATGAATTTCGATTTAATATGTAATTGTAGA
*
22727 TGTGAAATTCTAATTGTGGTTTAAATGTATAATTGAAAC
456 TGTAAAATTCTAATTGTGGTTTAAATGTATAATTGAAAC
22766 TTTAATTTTGATTTAATCATACACATTTTAAAAAATAAATACATCAATATATTTTTATATTGAAT
1 TTTAATTTTGATTTAATCATACACATTTTAAAAAATAAATACATCAATATATTTTTATATTGAAT
22831 AAATATAAATATTTATGTATGCAATATATAAATATAAAATGATGTTATATCAATAATTGTGTTAA
66 AAATATAAATATTTATGTATGCAATATATAAATATAAAATGATGTTATATCAATAATTGTGTTAA
* *
22896 TAATTTACAAGAACTAGATCCAATTAAAGTTTATATATACAATTGTACCCTGATCCCCATATTTA
131 TAATTTACAAGAACTAGATCAAATTAAAGTTCATATATACAATTGTACCCTGATCCCCATATTTA
* *
22961 TCCCTAAACGCTAAAAATTAAACCCTGATCCCCAAACGCCAAACCTTAAATCCTAGATCATAAAT
196 TCCCTAAAAGCTAAAAATTAAACCCTGATCCCCAAACACCAAACCTTAAATCCTAGATCATAAAT
*
23026 CCTAAACCCCAAAATAATGAACATTATATCATAACCCCTATCCCTTAAACTCTAAACCATAAAAC
261 CCTAAACCCCAAAATAATGAACATTATATCATAACCCCTATCCCCTAAACTCTAAACCATAAAAC
*
23091 ATAAACCATAAATCCTTAACCCCAACCCTTAAACCATAATTAGATATTTAATTATATGTACACAC
326 ATAAACCATAAACCCTTAACCCCAACCCTTAAACCATAATTAGATATTTAATTATATGTACACAC
* *
23156 CTAAATTTTGATAGAGATACATCTCAGAATTATATATGAATTTCGGTTTAATGTGTAATTGTAGA
391 CTAAATTTTGATAGAGATACATCTCAGAATTATATATGAATTTCGATTTAATATGTAATTGTAGA
23221 TGTAAAATTCTAATTGTGGTTTAAATGTATAATTGAAAC
456 TGTAAAATTCTAATTGTGGTTTAAATGTATAATTGAAAC
23260 TTTAATTTTGATTTAATCATACACATTTTAAAAAATAAATACATCAATATATTTTTATATTGAAT
1 TTTAATTTTGATTTAATCATACACATTTTAAAAAATAAATACATCAATATATTTTTATATTGAAT
*
23325 AAATATAAATATTTATGTATGCAATATATAAATATAAAATGATGTTATATCAATAATTGTGTTCA
66 AAATATAAATATTTATGTATGCAATATATAAATATAAAATGATGTTATATCAATAATTGTGTTAA
23390 TAATTTA
131 TAATTTA
23397 TGCTTTTGGG
Statistics
Matches: 615, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
494 615 1.00
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (494 bp):
TTTAATTTTGATTTAATCATACACATTTTAAAAAATAAATACATCAATATATTTTTATATTGAAT
AAATATAAATATTTATGTATGCAATATATAAATATAAAATGATGTTATATCAATAATTGTGTTAA
TAATTTACAAGAACTAGATCAAATTAAAGTTCATATATACAATTGTACCCTGATCCCCATATTTA
TCCCTAAAAGCTAAAAATTAAACCCTGATCCCCAAACACCAAACCTTAAATCCTAGATCATAAAT
CCTAAACCCCAAAATAATGAACATTATATCATAACCCCTATCCCCTAAACTCTAAACCATAAAAC
ATAAACCATAAACCCTTAACCCCAACCCTTAAACCATAATTAGATATTTAATTATATGTACACAC
CTAAATTTTGATAGAGATACATCTCAGAATTATATATGAATTTCGATTTAATATGTAATTGTAGA
TGTAAAATTCTAATTGTGGTTTAAATGTATAATTGAAAC
Found at i:23891 original size:12 final size:12
Alignment explanation
Indices: 23874--23899 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23864 TTTTTTACCC
23874 AAACGCCACTAA
1 AAACGCCACTAA
23886 AAACGCCACTAA
1 AAACGCCACTAA
23898 AA
1 AA
23900 CCCTATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.31, G:0.08, T:0.08
Consensus pattern (12 bp):
AAACGCCACTAA
Found at i:26563 original size:36 final size:36
Alignment explanation
Indices: 26523--26595 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
26513 CTAAAACAAC
26523 TAACAAATTAGCCATTCATGAAATAACTTCTTGTAT
1 TAACAAATTAGCCATTCATGAAATAACTTCTTGTAT
26559 TAACAAATTAGCCATTCATGAAATAACTTCTTGTAT
1 TAACAAATTAGCCATTCATGAAATAACTTCTTGTAT
26595 T
1 T
26596 CATATAACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.37
Consensus pattern (36 bp):
TAACAAATTAGCCATTCATGAAATAACTTCTTGTAT
Found at i:27279 original size:46 final size:46
Alignment explanation
Indices: 27184--27399 Score: 195
Period size: 46 Copynumber: 4.6 Consensus size: 46
27174 CCATTAAGTT
* * **
27184 GATGCCATGTCCCAAACATGGTCTTACACTGAC--ACCTCTATATGTGCC
1 GATG-CATGTCCCAAACAT-GTCTTACACTGGCTTACATCTCGA-G-GCC
**
27232 GATGCATGTCCCAGGCATGTCTTACACTGGCTTACATCTCGAGGCC
1 GATGCATGTCCCAAACATGTCTTACACTGGCTTACATCTCGAGGCC
* * * * * *
27278 GATACGTGTCCCAAACATGTCTTACACTAGCTCT-CGTCTCAATGCC
1 GATGCATGTCCCAAACATGTCTTACACTGGCT-TACATCTCGAGGCC
* * *
27324 GATGCCATGTCCCAAACATGGTCTTACACTGGGTCACATCTTGAGGCC
1 GATG-CATGTCCCAAACAT-GTCTTACACTGGCTTACATCTCGAGGCC
* *
27372 AATGCATGTCCCAGACATGTCTTACACT
1 GATGCATGTCCCAAACATGTCTTACACT
27400 AGCGCACAAA
Statistics
Matches: 137, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
46 64 0.47
47 40 0.29
48 33 0.24
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (46 bp):
GATGCATGTCCCAAACATGTCTTACACTGGCTTACATCTCGAGGCC
Found at i:27370 original size:94 final size:92
Alignment explanation
Indices: 27228--27402 Score: 251
Period size: 94 Copynumber: 1.9 Consensus size: 92
27218 CCTCTATATG
** * * *
27228 TGCCGATGCATGTCCCAGGCATGTCTTACACTGGCTTACATCTCGAGGCCGATACGTGTCCCAAA
1 TGCCGATGCATGTCCCAAACATGTCTTACACTGGCTCACATCTCGAGGCCAATACATGTCCCAAA
27293 CATGTCTTACACTAGCTCTCGTCTCAA
66 CATGTCTTACACTAGCTCTCGTCTCAA
* * *
27320 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGGGTCACATCTTGAGGCCAATGCATGTCCCA
1 TGCCGATG-CATGTCCCAAACAT-GTCTTACACTGGCTCACATCTCGAGGCCAATACATGTCCCA
*
27385 GACATGTCTTACACTAGC
64 AACATGTCTTACACTAGC
27403 GCACAAATGA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
92 8 0.11
93 12 0.17
94 52 0.72
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (92 bp):
TGCCGATGCATGTCCCAAACATGTCTTACACTGGCTCACATCTCGAGGCCAATACATGTCCCAAA
CATGTCTTACACTAGCTCTCGTCTCAA
Found at i:34253 original size:49 final size:50
Alignment explanation
Indices: 34196--34324 Score: 158
Period size: 50 Copynumber: 2.6 Consensus size: 50
34186 TTAAGTCGAT
*
34196 GCCATGTCCCAAACATGGTCTTACACTGACTATTGA-A-ATC-GAGGCCGAC
1 GCCATGTCCCAAACATGGTCTTACACTGACT-TTCACATATCTG-GGCCGAC
* * *
34245 GCCATGTCCCAGACATGGTCTTACACT-AGCTTTCACATATCTGTGCCGAT
1 GCCATGTCCCAAACATGGTCTTACACTGA-CTTTCACATATCTGGGCCGAC
*
34295 GCCAGGTCCCAAACATGGTCTTACACTGAC
1 GCCATGTCCCAAACATGGTCTTACACTGAC
34325 ACCTCTATAT
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
48 4 0.06
49 29 0.42
50 34 0.49
51 2 0.03
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (50 bp):
GCCATGTCCCAAACATGGTCTTACACTGACTTTCACATATCTGGGCCGAC
Found at i:34387 original size:46 final size:46
Alignment explanation
Indices: 34337--34507 Score: 191
Period size: 46 Copynumber: 3.7 Consensus size: 46
34327 CTCTATATGT
* *
34337 GCCGATGCATGTCCTAGACATGTCTTACACTGGCTTACATCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAC
* * * * * * *
34383 GCCGATGCGTGTCCCAGACATATCTTACACTAGCTCT-CGTTTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCT-TACATCTCGAC
* * *
34429 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATCTTGAC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGAC
*
34477 ACCGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
34508 AGCGTACAAA
Statistics
Matches: 101, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
46 53 0.52
47 26 0.26
48 22 0.22
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAC
Found at i:34461 original size:94 final size:92
Alignment explanation
Indices: 34336--34510 Score: 260
Period size: 94 Copynumber: 1.9 Consensus size: 92
34326 CCTCTATATG
* * * ** *
34336 TGCCGATGCATGTCCTAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATGCGTGTCCCAGA
1 TGCCGATGCATGTCCCAAACATGTCTTACACTGGCTCACATCTCGACACCGATGCATGTCCCAGA
34401 CATATCTTACACTAGCTCTCGTTTCAA
66 CATATCTTACACTAGCTCTCGTTTCAA
*
34428 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATCTTGACACCGATGCATGTCCCA
1 TGCCGATG-CATGTCCCAAACAT-GTCTTACACTGGCTCACATCTCGACACCGATGCATGTCCCA
*
34493 GACATGTCTTACACTAGC
64 GACATATCTTACACTAGC
34511 GTACAAATGA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
92 8 0.11
93 12 0.16
94 53 0.73
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (92 bp):
TGCCGATGCATGTCCCAAACATGTCTTACACTGGCTCACATCTCGACACCGATGCATGTCCCAGA
CATATCTTACACTAGCTCTCGTTTCAA
Found at i:38615 original size:23 final size:22
Alignment explanation
Indices: 38589--38633 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
38579 CATTTCATAT
*
38589 ACCAAAATCAAACCATAATCACA
1 ACCAAAACCAAACCAT-ATCACA
*
38612 ACCAAAACCAAGCCATATCACA
1 ACCAAAACCAAACCATATCACA
38634 TGGCTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.53, C:0.33, G:0.02, T:0.11
Consensus pattern (22 bp):
ACCAAAACCAAACCATATCACA
Found at i:43448 original size:39 final size:40
Alignment explanation
Indices: 43378--43585 Score: 280
Period size: 39 Copynumber: 5.3 Consensus size: 40
43368 GGACTAAGAT
* * * * *
43378 CCGAAGGCATTTGTGCGAGATA-CAAGTTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGTTATTAA-ATCCGGGTTAAGTC
*
43418 CCGAAGGCCTT-GTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
43457 CCGAAGGCATTCGTGCGAGTTA-TAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
43496 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* * * * *
43536 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
43575 CCGAAGGCATT
1 CCGAAGGCATT
43586 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 104 0.68
40 50 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
Found at i:43461 original size:79 final size:79
Alignment explanation
Indices: 43378--43585 Score: 276
Period size: 79 Copynumber: 2.6 Consensus size: 79
43368 GGACTAAGAT
* *
43378 CCGAAGGCATTTGTGCGAGATACAAGTTCCGGGTTAAGCCCCGAAGGCCTT-GTGCGAGTTATTA
1 CCGAAGGCATTTGTGCGAGATACAA-ATCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGTTATTA
43442 AATCCGGGTTAAGTC
65 AATCCGGGTTAAGTC
* * * *
43457 CCGAAGGCATTCGTGCGAGTTATAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGTTATTAA
43522 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * * * * *
43536 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGCCCCGAAGGCATT
43586 TGAACGAGGA
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
78 32 0.28
79 83 0.72
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGTTATTAA
ATCCGGGTTAAGTC
Found at i:43605 original size:79 final size:79
Alignment explanation
Indices: 43355--43620 Score: 227
Period size: 79 Copynumber: 3.4 Consensus size: 79
43345 CTTTGTGCTA
* ** * * * ** * *
43355 AGTGACTATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACAAGTTCCGGGTTAAGCCC
1 AGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATAA-AACCGGGCTAAGTCC
* **
43419 CGAAGGCCTT-GTGCG
64 CGAAGGCATTCGAACG
* * * *
43434 AGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATAAATCCGGGTTAAGTCCCG
1 AGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATAAAACCGGGCTAAGTCCCG
**
43499 AAGGCATTCGTGCG
66 AAGGCATTCGAACG
* * * *
43513 AGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCC
1 AGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTA-TAAAACCGGGCTAAGTCCC
*
43577 GAAGGCATTTGAACG
65 GAAGGCATTCGAACG
* *
43592 AG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 AGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
43621 TACGTGATTT
Statistics
Matches: 161, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
78 48 0.30
79 113 0.70
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
AGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATAAAACCGGGCTAAGTCCCG
AAGGCATTCGAACG
Found at i:43609 original size:118 final size:118
Alignment explanation
Indices: 43355--43620 Score: 297
Period size: 118 Copynumber: 2.2 Consensus size: 118
43345 CTTTGTGCTA
* * *
43355 AGTGACTATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACAAGTTCCGGGTTAAGCCC
1 AGTGACTATATCCGG-TTAAG-TCCCGAAGGCATTCGTGCGAGATACAAGATCCGGGTTAAGCCC
* * * * **
43419 CGAAGGCCTTGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCG
64 CGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACG
* * * * *
43474 AGTTA-TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA-ATCCGGGTTAAGTCC
1 AGTGACTATATCC-GGTTAAGTCCCGAAGGCATTCGTGCGAGATA-CAAGATCCGGGTTAAGCCC
* * *
43537 CGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACG
64 CGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACG
*
43592 AG-GAGCTATATCCGGTTAAATCCCGAAGG
1 AGTGA-CTATATCCGGTTAAGTCCCGAAGG
43621 TACGTGATTT
Statistics
Matches: 122, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
117 2 0.02
118 106 0.87
119 14 0.11
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (118 bp):
AGTGACTATATCCGGTTAAGTCCCGAAGGCATTCGTGCGAGATACAAGATCCGGGTTAAGCCCCG
AAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACG
Found at i:50805 original size:39 final size:40
Alignment explanation
Indices: 50678--50890 Score: 261
Period size: 40 Copynumber: 5.3 Consensus size: 40
50668 AGTCCTCGTT
* * * * *
50678 CAAATGCCTTCGGGACAATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGAC-TTAACCCGGATTTAATAACTCGCA
50719 C-AATGCCTTCGGGACTTAACCCGGATTTAATAAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAAT-AACTCGCA
*
50759 CGAATGCCTTCGGGACTTAA-CCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* *
50798 CGAATGCCTTCGGGACTTAACCCGGATTAAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * * *
50838 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAATAACTCGCA
50878 CAAATGCCTTCGG
1 CAAATGCCTTCGG
50891 ATCTTAGTCG
Statistics
Matches: 154, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 40 0.26
40 93 0.60
41 21 0.14
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Done.