Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 31 of 31
Found at i:5950259 original size:15 final size:15
Alignment explanation
Indices: 5950241--5950302 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
5950231 AATTAAATAA
5950241 AAAATAAATTTAAAT
1 AAAATAAATTTAAAT
*
5950256 AAAATAAATTAAAAT
1 AAAATAAATTTAAAT
* *
5950271 TAAATCATATCTTAAAAT
1 AAAAT-AAAT-TT-AAAT
*
5950289 AAAATAACTTTAAA
1 AAAATAAATTTAAA
5950303 CTACCTAAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
15 21 0.57
16 5 0.14
17 3 0.08
18 8 0.22
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATAAATTTAAAT
Found at i:5951883 original size:16 final size:15
Alignment explanation
Indices: 5951859--5951897 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
5951849 AAACCTACAT
5951859 AATTAAATAAAAAATA
1 AATTAAAT-AAAAATA
*
5951875 AATTTAATAAAAATA
1 AATTAAATAAAAATA
5951890 AATTAAAT
1 AATTAAAT
5951898 TAATTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATTAAATAAAAATA
Found at i:5952822 original size:9 final size:10
Alignment explanation
Indices: 5952805--5952835 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
5952795 CGCACCCAGC
5952805 CCTTTTTTTT
1 CCTTTTTTTT
5952815 CCTTTTTTTT
1 CCTTTTTTTT
5952825 CCTTCTTTTTT
1 CCTT-TTTTTT
5952836 TTTCCTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
CCTTTTTTTT
Found at i:5952834 original size:14 final size:14
Alignment explanation
Indices: 5952817--5952843 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5952807 TTTTTTTTCC
5952817 TTTTTTTTCCTTCT
1 TTTTTTTTCCTTCT
5952831 TTTTTTTTCCTTC
1 TTTTTTTTCCTTC
5952844 ATTCCTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTTTCCTTCT
Found at i:5952852 original size:18 final size:17
Alignment explanation
Indices: 5952813--5952853 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 17
5952803 GCCCTTTTTT
5952813 TTCCTTTTTTTTCCTTC
1 TTCCTTTTTTTTCCTTC
5952830 -T--TTTTTTTTCCTTC
1 TTCCTTTTTTTTCCTTC
5952844 ATTCCTTTTT
1 -TTCCTTTTT
5952854 CAAAATTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 7
0.74 0.00 0.26
Matches are distributed among these distances:
14 13 0.65
16 2 0.10
18 5 0.25
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (17 bp):
TTCCTTTTTTTTCCTTC
Found at i:5953533 original size:15 final size:15
Alignment explanation
Indices: 5953515--5953576 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
5953505 AATTAAATAA
5953515 AAAATAAATTTAAAT
1 AAAATAAATTTAAAT
*
5953530 AAAATAAATTAAAAT
1 AAAATAAATTTAAAT
* *
5953545 TAAATCATATCTTAAAAT
1 AAAAT-AAAT-TT-AAAT
*
5953563 AAAATAACTTTAAA
1 AAAATAAATTTAAA
5953577 CTACCTAAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
15 21 0.57
16 5 0.14
17 3 0.08
18 8 0.22
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATAAATTTAAAT
Found at i:5954743 original size:23 final size:21
Alignment explanation
Indices: 5954717--5954766 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
5954707 AACTCTAATC
*
5954717 AAATTAATCTTATAAATAAAAAT
1 AAATTAACCTTA-AAAT-AAAAT
*
5954740 AAATCAAACCTTAAAATAAAAT
1 AAAT-TAACCTTAAAATAAAAT
5954762 AAATT
1 AAATT
5954767 TTAAACTACC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 9 0.39
23 8 0.35
24 6 0.26
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATTAACCTTAAAATAAAAT
Found at i:5955099 original size:23 final size:22
Alignment explanation
Indices: 5955072--5955115 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5955062 AAAATTTTTA
5955072 ATTTTCAAA-ATATAATAATTAAT
1 ATTTT-AAACATAT-ATAATTAAT
*
5955095 ATTTTAAACCTATATAATTAA
1 ATTTTAAACATATATAATTAA
5955116 ATAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTAAACATATATAATTAAT
Found at i:5955134 original size:16 final size:15
Alignment explanation
Indices: 5955110--5955148 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
5955100 AAACCTATAT
5955110 AATTAAATAAAAAATA
1 AATTAAAT-AAAAATA
*
5955126 AATTTAATAAAAATA
1 AATTAAATAAAAATA
5955141 AATTAAAT
1 AATTAAAT
5955149 TAATTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATTAAATAAAAATA
Found at i:5955185 original size:24 final size:24
Alignment explanation
Indices: 5955132--5955189 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
5955122 AATAAATTTA
*
5955132 ATAAA-AATAAATTAAATTAATTTT
1 ATAAATAA-AAATTAAATTAATCTT
*
5955156 ATAAATAAAAATTAAATTCTATCTT
1 ATAAATAAAAATTAAATT-AATCTT
5955181 A-AAATAAAA
1 ATAAATAAAA
5955190 TAACTTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 23 0.77
25 7 0.23
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAAATAAAAATTAAATTAATCTT
Found at i:5956078 original size:13 final size:13
Alignment explanation
Indices: 5956060--5956093 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
5956050 CACACAACCC
5956060 TTTTTTTT-TTCT
1 TTTTTTTTCTTCT
*
5956072 TTTTTTTCCTTCT
1 TTTTTTTTCTTCT
5956085 TTTTTTTTC
1 TTTTTTTTC
5956094 CTTCATTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTCTTCT
Found at i:5956088 original size:14 final size:13
Alignment explanation
Indices: 5956059--5956097 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
5956049 GCACACAACC
5956059 CTTTTTTTT--TT
1 CTTTTTTTTCCTT
5956070 CTTTTTTTTCCTT
1 CTTTTTTTTCCTT
5956083 CTTTTTTTTTCCTT
1 C-TTTTTTTTCCTT
5956097 C
1 C
5956098 ATTCCTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.36
13 3 0.12
14 13 0.52
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
CTTTTTTTTCCTT
Found at i:5956399 original size:23 final size:21
Alignment explanation
Indices: 5956373--5956422 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
5956363 AACTCTAATC
*
5956373 AAATTAATCTTATAAATAAAAAT
1 AAATTAACCTTA-AAAT-AAAAT
*
5956396 AAATCAAACCTTAAAATAAAAT
1 AAAT-TAACCTTAAAATAAAAT
5956418 AAATT
1 AAATT
5956423 TTAAACTACC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 9 0.39
23 8 0.35
24 6 0.26
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATTAACCTTAAAATAAAAT
Found at i:5956790 original size:16 final size:15
Alignment explanation
Indices: 5956766--5956804 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
5956756 AAACCTACAT
5956766 AATTAAATAAAAAATA
1 AATTAAAT-AAAAATA
*
5956782 AATTTAATAAAAATA
1 AATTAAATAAAAATA
5956797 AATTAAAT
1 AATTAAAT
5956805 TAATTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATTAAATAAAAATA
Found at i:5956841 original size:24 final size:24
Alignment explanation
Indices: 5956788--5956845 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
5956778 AATAAATTTA
* *
5956788 ATAAA-AATAAATTAAATTAATTTT
1 ATAAATAA-AAATTAAATCAATCTT
5956812 ATAAATAAAAATTAAATCATATCTT
1 ATAAATAAAAATTAAATCA-ATCTT
5956837 A-AAATAAAA
1 ATAAATAAAA
5956846 TAACTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 23 0.77
25 7 0.23
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (24 bp):
ATAAATAAAAATTAAATCAATCTT
Found at i:5964294 original size:50 final size:51
Alignment explanation
Indices: 5964201--5964297 Score: 144
Period size: 50 Copynumber: 1.9 Consensus size: 51
5964191 TCATTTATGT
*
5964201 TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCGA
1 TTTTATTTCTAAAACACCGATTTTTCACAATCGGAGATACTCCAACCCCGA
* *
5964252 TTTTATTT-TCAAAACATCGA-TTTTCATAATCGGAGATACTCCAACC
1 TTTTATTTCT-AAAACACCGATTTTTCACAATCGGAGATACTCCAACC
5964298 TCGTTATTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
50 25 0.60
51 17 0.40
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (51 bp):
TTTTATTTCTAAAACACCGATTTTTCACAATCGGAGATACTCCAACCCCGA
Found at i:5964447 original size:79 final size:80
Alignment explanation
Indices: 5964236--5964456 Score: 263
Period size: 79 Copynumber: 2.8 Consensus size: 80
5964226 CACAATCGGG
* *
5964236 GATACTCCAACCCCGATTTTATTTTCAAAACATCGA-TTTTCATAATCG-GAGATACTCCAA-CC
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTCATAATCGAG-GATACTCCAACCC
* *
5964298 TCGTTATTCTCGAGGG
65 TCATTATTCTCGAGGA
* * *
5964314 GACACTCCAACCCCGATTTTATTTCTAAAATACCGATTTTTCATAATC-AGGGATACTCCAACCC
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTCATAATCGA-GGATACTCCAACCC
*
5964378 T-ATTATTTTCGAGGA
65 TCATTATTCTCGAGGA
* * * ** *
5964393 GATACTCTAACCCCGGTTTTATTTCCAAAACACCAATTTTTCACCATCGAGGATATTCCAACCC
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTCATAATCGAGGATACTCCAACCC
5964457 CGATTTTATT
Statistics
Matches: 121, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
78 31 0.26
79 85 0.70
80 5 0.04
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (80 bp):
GATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTCATAATCGAGGATACTCCAACCCT
CATTATTCTCGAGGA
Found at i:5964483 original size:51 final size:51
Alignment explanation
Indices: 5964394--5964506 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 51
5964384 TTTCGAGGAG
* * * * *
5964394 ATACTCTAACCCCGGTTTTATTTCCAAAACACCAATTTTTCACCATCGAGG
1 ATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGAGA
* * * * * *
5964445 ATATTCCAACCCCGATTTTATTTTCAGAACATCGATTTTCCATAATCGAGA
1 ATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGAGA
5964496 ATACTCCAACC
1 ATACTCCAACC
5964507 TCGTTATTTC
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (51 bp):
ATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGAGA
Found at i:5964489 original size:130 final size:130
Alignment explanation
Indices: 5964319--5964552 Score: 323
Period size: 130 Copynumber: 1.8 Consensus size: 130
5964309 GAGGGGACAC
* * *
5964319 TCCAACCCCGATTTTATTTCTAAAATACCGATTTTTCATAATC-AGGGATACTCCAACC-CTATT
1 TCCAACCCCGATTTTATTTCTAAAACACCGATTTTCCATAATCGA-GAATACTCCAACCTC-ATT
* *
5964382 ATTTTCGAGGAGATACTCTAACCCCGGT-TTTATTTCCAAAACACCAATTTTTCACCATCGAGGA
64 ATTTCCGAGGAGATACTCTAACCCC-GTCTTTATCTCCAAAACACCAATTTTTCACCATCGAGGA
5964446 TAT
128 TAT
* * *
5964449 TCCAACCCCGATTTTATTT-TCAGAACATCGATTTTCCATAATCGAGAATACTCCAACCTCGTTA
1 TCCAACCCCGATTTTATTTCT-AAAACACCGATTTTCCATAATCGAGAATACTCCAACCTCATTA
*
5964513 TTTCCGAGGGGATACTCTAACCCCGTCTTTATCTCCAAAA
65 TTTCCGAGGAGATACTCTAACCCCGTCTTTATCTCCAAAA
5964553 TATTAAATTT
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
129 3 0.03
130 86 0.95
131 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (130 bp):
TCCAACCCCGATTTTATTTCTAAAACACCGATTTTCCATAATCGAGAATACTCCAACCTCATTAT
TTCCGAGGAGATACTCTAACCCCGTCTTTATCTCCAAAACACCAATTTTTCACCATCGAGGATAT
Found at i:5966834 original size:2 final size:2
Alignment explanation
Indices: 5966827--5966868 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5966817 TATCTTTTGT
5966827 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5966868 T
1 T
5966869 TTCAAGTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5967110 original size:2 final size:2
Alignment explanation
Indices: 5967103--5967155 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
5967093 TGGATGAGTG
5967103 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
*
5967145 AT AT AC AT AT A
1 AT AT AT AT AT A
5967156 CACCTTACTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5972652 original size:13 final size:13
Alignment explanation
Indices: 5972634--5972659 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5972624 GGCTTATTCT
5972634 TCTTTATGGTTCA
1 TCTTTATGGTTCA
5972647 TCTTTATGGTTCA
1 TCTTTATGGTTCA
5972660 ACAATGAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
TCTTTATGGTTCA
Found at i:5974566 original size:16 final size:14
Alignment explanation
Indices: 5974528--5974590 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 14
5974518 ATTTAAATTG
5974528 ATTTAAAATGTTAAAA
1 ATTT-AAAT-TTAAAA
5974544 ATTTAAATTTAAAA
1 ATTTAAATTTAAAA
*
5974558 ATATCTAAATTCAAAAA
1 AT-T-TAAATT-TAAAA
*
5974575 AGTTTAAAATTAAAA
1 A-TTTAAATTTAAAA
5974590 A
1 A
5974591 GGCCCAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
14 8 0.20
15 10 0.25
16 15 0.38
17 6 0.15
18 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (14 bp):
ATTTAAATTTAAAA
Found at i:5975967 original size:35 final size:36
Alignment explanation
Indices: 5975891--5975967 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 36
5975881 TTTAAAATTT
* * *
5975891 TAATTTTAGTATTTTTATCATTACGTAAAAGTAAAAT
1 TAATTTTAGTATTTATAGCATTAC-TAAAAGTAAAAA
*
5975928 TAATTTTAGTATTTATAGC-TTA-TAAAATTAAAAAA
1 TAATTTTAGTATTTATAGCATTACTAAAAGT-AAAAA
5975963 TAATT
1 TAATT
5975968 CAAATCTATC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 6 0.17
35 9 0.26
36 3 0.09
37 17 0.49
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TAATTTTAGTATTTATAGCATTACTAAAAGTAAAAA
Found at i:5976076 original size:16 final size:16
Alignment explanation
Indices: 5976057--5976097 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
5976047 AGATCTAAAT
5976057 TTAAAATAATTCAAAC
1 TTAAAATAATTCAAAC
*
5976073 TTAAAAAAATTCAAAC
1 TTAAAATAATTCAAAC
*
5976089 TCAAAATAA
1 TTAAAATAA
5976098 ATTTGAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (16 bp):
TTAAAATAATTCAAAC
Found at i:5979897 original size:35 final size:36
Alignment explanation
Indices: 5979858--5979934 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 36
5979848 ACGTGTTATG
*
5979858 TAATTATATCATATAAAATATCATACTATCTTGTA-
1 TAATTATATCATATAAAATATCATACTATCTTATAC
5979893 TAATTATATCATATAAAATATCATACTATCTTATAC
1 TAATTATATCATATAAAATATCATACTATCTTATAC
5979929 TAATTA
1 TAATTA
5979935 GTCATTACTG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 34 0.85
36 6 0.15
ACGTcount: A:0.44, C:0.12, G:0.01, T:0.43
Consensus pattern (36 bp):
TAATTATATCATATAAAATATCATACTATCTTATAC
Found at i:5979927 original size:20 final size:20
Alignment explanation
Indices: 5979864--5979927 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 20
5979854 TATGTAATTA
5979864 TATCATATAAAATATCATAC
1 TATCATATAAAATATCATAC
* * *
5979884 TATCTTGT-ATA-AT--TA-
1 TATCATATAAAATATCATAC
5979899 TATCATATAAAATATCATAC
1 TATCATATAAAATATCATAC
*
5979919 TATCTTATA
1 TATCATATA
5979928 CTAATTAGTC
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
15 6 0.19
16 4 0.12
17 2 0.06
18 2 0.06
19 4 0.12
20 14 0.44
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (20 bp):
TATCATATAAAATATCATAC
Found at i:5980584 original size:32 final size:33
Alignment explanation
Indices: 5980524--5980588 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
5980514 CACACCCAGA
* *
5980524 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCAATACATGCTGCATTGTATCGATACAT
*
5980557 TGTATCAATACATG-TTCATTGTATCGATACAT
1 TGTATCAATACATGCTGCATTGTATCGATACAT
5980589 GGACAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCAATACATGCTGCATTGTATCGATACAT
Done.