Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_485
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: 67331
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1119 original size:59 final size:59
Alignment explanation
Indices: 1027--1145 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
1017 TTTGATAACA
1027 TAGATGATGAGATAGTTATTGTATGATCTTTGAGAAAAGCAAAATACAGTCACTAGGGC
1 TAGATGATGAGATAGTTATTGTATGATCTTTGAGAAAAGCAAAATACAGTCACTAGGGC
1086 TAGATGATGAGATAGTTATTGTATGATCTTTGAGAAAAGCAAAATACAGTCACTAGGGC
1 TAGATGATGAGATAGTTATTGTATGATCTTTGAGAAAAGCAAAATACAGTCACTAGGGC
1145 T
1 T
1146 TGGACAGAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (59 bp):
TAGATGATGAGATAGTTATTGTATGATCTTTGAGAAAAGCAAAATACAGTCACTAGGGC
Found at i:5029 original size:23 final size:23
Alignment explanation
Indices: 4966--5041 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
4956 CAACTCATTG
*
4966 GAGCTTACCATTTTAGCTCG-TA
1 GAGCTTACCATTTCAGCTCGATA
*
4988 TGAGTTTA-C-TGTTCAGCTCGATA
1 -GAGCTTACCAT-TTCAGCTCGATA
*
5011 GAGCTTACCATTTCAGCTCAATA
1 GAGCTTACCATTTCAGCTCGATA
5034 GAGCTTAC
1 GAGCTTAC
5042 TGTTCATTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.02
22 15 0.33
23 28 0.62
24 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (23 bp):
GAGCTTACCATTTCAGCTCGATA
Found at i:5077 original size:25 final size:25
Alignment explanation
Indices: 5025--5087 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
5015 TTACCATTTC
*
5025 AGCTCAATAGAGCTTACTGTTCATT
1 AGCTCAATAGAGCTTACTGATCATT
5050 AGCTCAATAGGAGCTTA-TCGATCA-T
1 AGCTCAATA-GAGCTTACT-GATCATT
5075 AGCTCGAA-AGAGC
1 AGCTC-AATAGAGC
5088 ATAAACAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
24 4 0.12
25 17 0.50
26 13 0.38
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (25 bp):
AGCTCAATAGAGCTTACTGATCATT
Found at i:5289 original size:40 final size:41
Alignment explanation
Indices: 5218--5294 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 41
5208 TGTTTATATG
* * **
5218 GATGAAATACTGTTGATACGAATGAGTTACT-GTTATTACT
1 GATGAAATACTATTGATACAAATGAACTACTGGTTATTACT
* *
5258 GATGAACTACTATTTATACAAATGAACTACTGGTTAT
1 GATGAAATACTATTGATACAAATGAACTACTGGTTAT
5295 ATGAATGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
40 25 0.83
41 5 0.17
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (41 bp):
GATGAAATACTATTGATACAAATGAACTACTGGTTATTACT
Found at i:5301 original size:20 final size:19
Alignment explanation
Indices: 5211--5301 Score: 58
Period size: 20 Copynumber: 4.6 Consensus size: 19
5201 GAATATGTGT
* *
5211 TTATATGGATGAAATACTG
1 TTATATGAATGAACTACTG
* **
5230 TTGATACGAATGAGTTACTG
1 TT-ATATGAATGAACTACTG
*
5250 TTATTACTG-ATGAACTACTAT
1 TTA-TA-TGAATGAACTACT-G
**
5271 TTATACAAATGAACTACTGG
1 TTATATGAATGAACTACT-G
5291 TTATATGAATG
1 TTATATGAATG
5302 TATTACAGTT
Statistics
Matches: 53, Mismatches: 14, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
19 3 0.06
20 46 0.87
21 4 0.08
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (19 bp):
TTATATGAATGAACTACTG
Found at i:16844 original size:64 final size:63
Alignment explanation
Indices: 16763--16944 Score: 163
Period size: 67 Copynumber: 2.8 Consensus size: 63
16753 AGACATTATG
* *
16763 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGT-GACAAGAGAGCTACGAGATAA
* * * * * *
16827 ATGTAGCTAGGTCGCATGCGTGGCT-CCAGGTGAAGGACATCATGTTGACAAGAGAGCTACGAGA
1 ATGTAGCTAGGTCGCATGGGT-GATACTA--TG-TGTACACCATG-TGACAAGAGAGCTACGAGA
16891 TAA
61 TAA
* * * *
16894 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGTGTACAAGAGA
1 ATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGTG-ACAAGAGA
16945 TCCGAACTCT
Statistics
Matches: 93, Mismatches: 17, Indels: 17
0.73 0.13 0.13
Matches are distributed among these distances:
62 2 0.02
63 15 0.16
64 23 0.25
65 4 0.04
66 18 0.19
67 30 0.32
68 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (63 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTGACAAGAGAGCTACGAGATAA
Found at i:20924 original size:64 final size:64
Alignment explanation
Indices: 20843--21026 Score: 176
Period size: 67 Copynumber: 2.8 Consensus size: 64
20833 AGACATTATG
* *
20843 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
20907 ATGTAGCTAGGTCGCATGCGTGGCT-CCAGGTGAAGGACATCATGTAGACAAGAGAGCTACGAGA
1 ATGTAGCTAGGTCGCATGGGT-GATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
20971 TAA
62 TAA
* * * * * *
20974 AT-TGGCTAGGTCACGTGGGTGGTACTGA-GTGTTCACCATGTATACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGTAGACAAGAGAGC
21027 CGAACTCTAC
Statistics
Matches: 95, Mismatches: 19, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
63 19 0.20
64 23 0.24
65 4 0.04
66 17 0.18
67 32 0.34
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:22756 original size:27 final size:27
Alignment explanation
Indices: 22726--22903 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
22716 ATATTGAGTC
* * * *
22726 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
22753 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
22780 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
22808 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
22835 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
22862 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
22889 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
22904 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:22865 original size:82 final size:81
Alignment explanation
Indices: 22747--22902 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
22737 TGCTATATAA
* *
22747 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
22812 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
22829 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
22893 CACTTAGTGC
65 CACTTAGTGC
22903 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:30947 original size:27 final size:27
Alignment explanation
Indices: 30917--31094 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
30907 ATATTGAGTC
* * * *
30917 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
30944 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
30971 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
30999 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
31026 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
31053 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31080 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31095 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:31056 original size:82 final size:81
Alignment explanation
Indices: 30938--31093 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
30928 TGCTATATAA
* *
30938 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31003 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
31020 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31084 CACTTAGTGC
65 CACTTAGTGC
31094 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:36776 original size:11 final size:11
Alignment explanation
Indices: 36760--36787 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
36750 ATTAACGTTC
36760 TGAAATATGAA
1 TGAAATATGAA
36771 TGAAATATGAA
1 TGAAATATGAA
36782 TGAAAT
1 TGAAAT
36788 TTTATGGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.29
Consensus pattern (11 bp):
TGAAATATGAA
Found at i:38049 original size:84 final size:83
Alignment explanation
Indices: 37908--38075 Score: 318
Period size: 84 Copynumber: 2.0 Consensus size: 83
37898 TAACCCTCAA
37908 TATGTATGGTCAAACATATATAATCATGCAATACAGGACCAAATAAAAGGGTAAGCACAAATGAT
1 TATGTATGGTCAAACATATATAATCATGCAATACAGGACCAAATAAAAGGGTAAGCACAAATGAT
37973 TGTTTTTTAGCTCAGGTAT
66 T-TTTTTTAGCTCAGGTAT
*
37992 TATGTATGGTCAAACGTATATAATCATGCAATACAGGACCAAATAAAAGGGTAAGCACAAATGAT
1 TATGTATGGTCAAACATATATAATCATGCAATACAGGACCAAATAAAAGGGTAAGCACAAATGAT
38057 TTTTTTTAGCTCAGGTAT
66 TTTTTTTAGCTCAGGTAT
38075 T
1 T
38076 GTATAGAGGT
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
83 18 0.22
84 65 0.78
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (83 bp):
TATGTATGGTCAAACATATATAATCATGCAATACAGGACCAAATAAAAGGGTAAGCACAAATGAT
TTTTTTTAGCTCAGGTAT
Found at i:42852 original size:19 final size:20
Alignment explanation
Indices: 42828--42877 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
42818 GGAATTTTTA
*
42828 AAATAAATAATAATAA-GAG
1 AAATAAATAATAATAACAAG
42847 AAATAAAT-A-AATAACAAG
1 AAATAAATAATAATAACAAG
42865 AAATCAAATAATA
1 AAAT-AAATAATA
42878 GAATCTGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.19
18 7 0.27
19 12 0.46
20 1 0.04
21 1 0.04
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.20
Consensus pattern (20 bp):
AAATAAATAATAATAACAAG
Found at i:51052 original size:39 final size:40
Alignment explanation
Indices: 50935--51119 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
50925 GCTACTCGTT
*
50935 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* * *
50975 CAATTGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
51015 CAAATGTCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
51054 CAAATGCCTTC-GGATCTTAGTCCGGATAT-GATCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAG-TAAC-TCGCA
51095 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
51120 CATCATTCAA
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 73 0.60
41 13 0.11
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:51079 original size:79 final size:82
Alignment explanation
Indices: 50935--51119 Score: 204
Period size: 79 Copynumber: 2.3 Consensus size: 82
50925 GCTACTCGTT
* * * *
50935 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTTGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTTCGGACTTAACCCG
* *
50999 GAT-TTAGTAAC-TCGCA
66 GATATGA-TAACTTAGCA
* * **
51015 CAAATGTCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCC-TTCGGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTTCGGA-CTTAACCC
*
51077 GGATATGATCACTTAGCA
65 GGATATGATAACTTAGCA
51095 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
51120 CATCATTCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
78 5 0.06
79 48 0.55
80 35 0.40
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTTCGGACTTAACCCG
GATATGATAACTTAGCA
Found at i:57983 original size:42 final size:42
Alignment explanation
Indices: 57899--58018 Score: 116
Period size: 42 Copynumber: 2.9 Consensus size: 42
57889 ATGTGGGTGC
* * * * *
57899 CGATGCCATGTCCTAGACATGGTCTTATAC-AGGACCTTATAT
1 CGATGCCATGTCCCAGACATGGTCTTACACGA-AATCTCATAT
57941 CGATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAT
1 CGATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAT
* ** * * * *
57983 CAACACCATATCCCAGATATGGTCTAACATGAAATC
1 CGATGCCATGTCCCAGACATGGTCTTACACGAAATC
58019 ACATTCTGAG
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 64 0.98
43 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (42 bp):
CGATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAT
Found at i:58105 original size:48 final size:48
Alignment explanation
Indices: 58049--58156 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
58039 TATCTTAGAT
** * *
58049 ATGGTCTTACACTGGCACAT-ATATCAATGCTGATGTCATGTCCCAAAC
1 ATGGTCTTACACTGGCAC-TCATATCAACACCGATGACATGTCCCAAAC
* * * *
58097 ATGTTCTTACATTGGCTCTCATATCAACACCGATGACATGTCCCAGAC
1 ATGGTCTTACACTGGCACTCATATCAACACCGATGACATGTCCCAAAC
58145 ATGGTCTTACAC
1 ATGGTCTTACAC
58157 CGAATCTCAT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
47 1 0.02
48 48 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (48 bp):
ATGGTCTTACACTGGCACTCATATCAACACCGATGACATGTCCCAAAC
Found at i:64856 original size:79 final size:78
Alignment explanation
Indices: 64745--64967 Score: 242
Period size: 79 Copynumber: 2.8 Consensus size: 78
64735 GCTCCTCGTT
* ** *
64745 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGAAT-TAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
64810 ATTTAGTAAT-TCGCA
64 AATTAGT-ATCTCGCA
64825 CAAATGCCTTCGGGCTTAGCCCAGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCC-GAATTAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
64888 AATTAGTATCTCGCA
64 AATTAGTATCTCGCA
* * * *
64903 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGG-GCTTAG-CCCGA-ATTAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCC
64965 GGA
62 GGA
64968 CATCATTCAA
Statistics
Matches: 125, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
77 2 0.02
78 44 0.35
79 52 0.42
80 26 0.21
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGAATTAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTATCTCGCA
Found at i:64866 original size:39 final size:40
Alignment explanation
Indices: 64745--64967 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
64735 GCTCCTCGTT
* *
64745 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATTCGCA
* *
64785 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATTCGCA
*
64825 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAAT-TCGCA
64864 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAAT-TCGCA
* * *
64903 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-AATTCGCA
64944 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
64968 CATCATTCAA
Statistics
Matches: 165, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 4 0.02
39 84 0.51
40 66 0.40
41 10 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATTCGCA
Found at i:64928 original size:118 final size:119
Alignment explanation
Indices: 64745--64964 Score: 283
Period size: 118 Copynumber: 1.9 Consensus size: 119
64735 GCTCCTCGTT
*
64745 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
*
64810 AT-TTAGT-AATTCGCACAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
66 ATATT-GTCAATTAGCAC-AA-GCCTTCGGGACTTAGCCCAGAATTAGTATCTCGCA
* **
64864 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
*
64925 CGGATATTGTCACTTAGCACAAGCCTTCGGGACTTAGCCC
63 CGGATATTGTCAATTAGCACAAGCCTTCGGGACTTAGCCC
64965 GGACATCATT
Statistics
Matches: 89, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
117 15 0.17
118 51 0.57
119 23 0.26
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (119 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATTGTCAATTAGCACAAGCCTTCGGGACTTAGCCCAGAATTAGTATCTCGCA
Done.