Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1500
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: 67516
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:6375 original size:27 final size:27
Alignment explanation
Indices: 6344--6521 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
6334 TAAATTGTAC
*
6344 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
6371 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
6397 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
6425 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
6452 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
6480 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
6507 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6522 GACTTAATAT
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 25 0.19
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:6405 original size:54 final size:55
Alignment explanation
Indices: 6344--6521 Score: 227
Period size: 54 Copynumber: 3.3 Consensus size: 55
6334 TAAATTGTAC
* **
6344 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* * ** *
6399 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* *
6452 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
*
6507 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6522 GACTTAATAT
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.57
55 45 0.42
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:10558 original size:40 final size:41
Alignment explanation
Indices: 10466--10586 Score: 163
Period size: 40 Copynumber: 3.0 Consensus size: 41
10456 TAAAAGCCAC
* * * *
10466 CAGTGGATCCACGGTCTTCAAGTAACCATGCGATCCTTAAT
1 CAGTGGATCCACGGTCATCAAGCAACCATGTGATCCTCAAT
*
10507 CAGTGGGTCCACGGTCATCAAGCAACCAT-TGATCCTCAAT
1 CAGTGGATCCACGGTCATCAAGCAACCATGTGATCCTCAAT
* * *
10547 CGGTGGATCCACGGTCGTCAAGCAACCATGTAATCCTCAA
1 CAGTGGATCCACGGTCATCAAGCAACCATGTGATCCTCAA
10587 ATTCTTCCCC
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
40 35 0.50
41 35 0.50
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (41 bp):
CAGTGGATCCACGGTCATCAAGCAACCATGTGATCCTCAAT
Found at i:10960 original size:27 final size:27
Alignment explanation
Indices: 10884--11079 Score: 106
Period size: 27 Copynumber: 7.2 Consensus size: 27
10874 CAAACCAATA
* ** * *
10884 GTATTTCTATAATTTTTAAAAGTCAAAG
1 GTATTTTTATAATTTTCCAAA-TCGAGG
* ** *
10912 GTATTTTTGTAATTTTGTAAATCGGGG
1 GTATTTTTATAATTTTCCAAATCGAGG
* **
10939 GTATTTTTTTAATTTTCCAAATAAAGG
1 GTATTTTTATAATTTTCCAAATCGAGG
**
10966 GTATTTCGATAATTTTCCAAATCGAGG
1 GTATTTTTATAATTTTCCAAATCGAGG
* * * * *
10993 GTA-TTTCAGAAATTTTACAAGTTGAGG
1 GTATTTTTA-TAATTTTCCAAATCGAGG
* * * **
11020 ATATTTTGATAATTTTACAGGTCGAGG
1 GTATTTTTATAATTTTCCAAATCGAGG
** * * *
11047 GTATTTCAATAATTTTACAAGTCGATG
1 GTATTTTTATAATTTTCCAAATCGAGG
11074 GTATTT
1 GTATTT
11080 CGGTAATTTC
Statistics
Matches: 132, Mismatches: 34, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
26 3 0.02
27 108 0.82
28 21 0.16
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (27 bp):
GTATTTTTATAATTTTCCAAATCGAGG
Found at i:11007 original size:54 final size:54
Alignment explanation
Indices: 10921--11120 Score: 163
Period size: 54 Copynumber: 3.7 Consensus size: 54
10911 GGTATTTTTG
** * *** * * *
10921 TAATTTTGTAAATCGGGGGTATTTTTTTAATTTTCCAAATAAAGGGTATTTCGA
1 TAATTTTCCAAATCGAGGGTATTTCAATAATTTTACAAGTAGAGGGTATTTCGA
* * *
10975 TAATTTTCCAAATCGAGGGTATTTCAGA-AATTTTACAAGTTGAGGATATTTTGA
1 TAATTTTCCAAATCGAGGGTATTTCA-ATAATTTTACAAGTAGAGGGTATTTCGA
* ** * * *
11029 TAATTTTACAGGTCGAGGGTATTTCAATAATTTTACAAGTCGATGGTATTTCGG
1 TAATTTTCCAAATCGAGGGTATTTCAATAATTTTACAAGTAGAGGGTATTTCGA
***
11083 TAA-TTTCTCAAATC-AGGAGTATTTTGGTAATTTTACAA
1 TAATTTTC-CAAATCGAGG-GTATTTCAATAATTTTACAA
11121 ACCAGGGGTA
Statistics
Matches: 116, Mismatches: 26, Indels: 8
0.77 0.17 0.05
Matches are distributed among these distances:
53 7 0.06
54 109 0.94
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (54 bp):
TAATTTTCCAAATCGAGGGTATTTCAATAATTTTACAAGTAGAGGGTATTTCGA
Found at i:11086 original size:27 final size:27
Alignment explanation
Indices: 10963--11120 Score: 160
Period size: 27 Copynumber: 5.9 Consensus size: 27
10953 TTCCAAATAA
* *
10963 AGGGTATTTCGATAATTTTCCAAATCG
1 AGGGTATTTCGATAATTTTACAAGTCG
*
10990 AGGGTATTTCAGA-AATTTTACAAGTTG
1 AGGGTATTTC-GATAATTTTACAAGTCG
* * *
11017 AGGATATTTTGATAATTTTACAGGTCG
1 AGGGTATTTCGATAATTTTACAAGTCG
*
11044 AGGGTATTTCAATAATTTTACAAGTCG
1 AGGGTATTTCGATAATTTTACAAGTCG
* * *
11071 ATGGTATTTCGGTAATTTCT-CAAATC-
1 AGGGTATTTCGATAATTT-TACAAGTCG
* *
11097 AGGAGTATTTTGGTAATTTTACAA
1 AGG-GTATTTCGATAATTTTACAA
11121 ACCAGGGGTA
Statistics
Matches: 109, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
26 5 0.05
27 101 0.93
28 3 0.03
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACAAGTCG
Found at i:11088 original size:81 final size:81
Alignment explanation
Indices: 10963--11119 Score: 201
Period size: 81 Copynumber: 1.9 Consensus size: 81
10953 TTCCAAATAA
* * * *
10963 AGGGTATTTCGATAATTTTCCAAATCGAGGGTATTTCAGAAATTT-TACAAGTTGAGGA-TATTT
1 AGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCAGAAATTTCT-CAA-ATCAGGAGTATTT
11026 TGATAATTTTACAGGTCG
64 TGATAATTTTACAGGTCG
* * * *
11044 AGGGTATTTCAATAATTTTACAAGTCGATGGTATTTCGGTAATTTCTCAAATCAGGAGTATTTTG
1 AGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCAGAAATTTCTCAAATCAGGAGTATTTTG
*
11109 GTAATTTTACA
66 ATAATTTTACA
11120 AACCAGGGGT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 5 0.08
81 59 0.91
82 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (81 bp):
AGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCAGAAATTTCTCAAATCAGGAGTATTTTG
ATAATTTTACAGGTCG
Found at i:11121 original size:27 final size:26
Alignment explanation
Indices: 10911--11159 Score: 140
Period size: 27 Copynumber: 9.2 Consensus size: 26
10901 AAAAGTCAAA
* ** *
10911 GGTATTTTTGTAATTTTGTAAATCGGG
1 GGTATTTTGGTAATTTTACAAATC-AG
** * *
10938 GGTATTTTTTTAATTTTCCAAATAAAG
1 GGTATTTTGGTAATTTTACAAAT-CAG
* * *
10965 GGTATTTCGATAATTTTCCAAATCGAG
1 GGTATTTTGGTAATTTTACAAATC-AG
** * * *
10992 GGTATTTCAGAAATTTTACAAGTTGAG
1 GGTATTTTGGTAATTTTACAA-ATCAG
* * **
11019 GATATTTTGATAATTTTACAGGTCGAG
1 GGTATTTTGGTAATTTTACAAATC-AG
*** * *
11046 GGTATTTCAATAATTTTACAAGTCGAT
1 GGTATTTTGGTAATTTTACAAATC-AG
*
11073 GGTATTTCGGTAATTTCT-CAAATCAG
1 GGTATTTTGGTAATTT-TACAAATCAG
*
11099 GAGTATTTTGGTAATTTTACAAACCAGG
1 G-GTATTTTGGTAATTTTACAAATCA-G
* *
11127 GGTATTTTGGTAATTTTATAAACCAAG
1 GGTATTTTGGTAATTTTACAAATC-AG
11154 GGTATT
1 GGTATT
11160 CAGTAATTTC
Statistics
Matches: 178, Mismatches: 35, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
26 4 0.02
27 169 0.95
28 5 0.03
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (26 bp):
GGTATTTTGGTAATTTTACAAATCAG
Found at i:11130 original size:81 final size:81
Alignment explanation
Indices: 10884--11133 Score: 200
Period size: 81 Copynumber: 3.1 Consensus size: 81
10874 CAAACCAATA
* * * ** ** * * **
10884 GTATTTCTATAATTTTTAAAAGTCAAAGGTATTTTTGTAATTTTGTAAATCGGGGGTATTTTTTT
1 GTATTTCAATAA-TTTTACAAGTCGAAGGTATTTCAGTAATTTTACAAATCAGGAGTATTTTGAT
* * *
10949 AATTTTCCAAATAAAGG
65 AATTTTACAAATCAGGG
* * * * * * *
10966 GTATTTCGATAATTTTCCAAATCGAGGGTATTTCAGAAATTTTACAAGTTGAGGA-TATTTTGAT
1 GTATTTCAATAATTTTACAAGTCGAAGGTATTTCAGTAATTTTACAA-ATCAGGAGTATTTTGAT
**
11030 AATTTTACAGGTC-GAGG
65 AATTTTACAAATCAG-GG
* * *
11047 GTATTTCAATAATTTTACAAGTCGATGGTATTTCGGTAATTTCT-CAAATCAGGAGTATTTTGGT
1 GTATTTCAATAATTTTACAAGTCGAAGGTATTTCAGTAATTT-TACAAATCAGGAGTATTTTGAT
*
11111 AATTTTACAAACCAGGG
65 AATTTTACAAATCAGGG
11128 GTATTT
1 GTATTT
11134 TGGTAATTTT
Statistics
Matches: 129, Mismatches: 34, Indels: 11
0.74 0.20 0.06
Matches are distributed among these distances:
80 5 0.04
81 108 0.84
82 16 0.12
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (81 bp):
GTATTTCAATAATTTTACAAGTCGAAGGTATTTCAGTAATTTTACAAATCAGGAGTATTTTGATA
ATTTTACAAATCAGGG
Found at i:11265 original size:27 final size:26
Alignment explanation
Indices: 11188--11268 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 26
11178 TATAAACCAA
*
11188 GGGTATTTCAATAATTCTACCATACAG
1 GGGTATTTCAGTAATTCTACC-TACAG
*
11215 GGGCATTTCAGTAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTA-CCTACAG
* *
11242 TGGTATTTCAGTAATACTAGCCTACAG
1 GGGTATTTCAGTAATTCTA-CCTACAG
11269 ATATGAGATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 45 0.96
28 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (26 bp):
GGGTATTTCAGTAATTCTACCTACAG
Found at i:14795 original size:27 final size:28
Alignment explanation
Indices: 14742--15083 Score: 176
Period size: 27 Copynumber: 12.7 Consensus size: 28
14732 TTACATCTTA
* * * * *
14742 CAAGGGTGTTTTGGTAAATCTATAAACT
1 CAAGGGTATTTCGGTAATTTTACAAACT
*
14770 C-AGGGTATTTCGGTAATTTTGCAAAC-
1 CAAGGGTATTTCGGTAATTTTACAAACT
** * * **
14796 CAATAGCATTTCTGTAATTTTTGAAAGC-
1 CAAGGGTATTTCGGTAATTTTACAAA-CT
* * **
14824 CAAAGG-ATTTCTGTAATTTTGTAAA-T
1 CAAGGGTATTTCGGTAATTTTACAAACT
* * *
14850 CAAGGGTGTTTCTGTAATTTTCCAAA-T
1 CAAGGGTATTTCGGTAATTTTACAAACT
*
14877 CAAGGGTATTTCAGTAATTTTACAAA-T
1 CAAGGGTATTTCGGTAATTTTACAAACT
* * * * *
14904 CGAGTGTTTTTCGATAATTTTAC-AAGT
1 CAAGGGTATTTCGGTAATTTTACAAACT
* * * **
14931 CGAGGGTATTTCAGTAATTTT--TAGGT
1 CAAGGGTATTTCGGTAATTTTACAAACT
** **
14957 CAAGGGTATTTTAGTAATTTTAC-AGGT
1 CAAGGGTATTTCGGTAATTTTACAAACT
* **
14984 CAAGGGTATTTCGGTAATTTTA-TAGGT
1 CAAGGGTATTTCGGTAATTTTACAAACT
* *
15011 CAAGGGTATTTTGGTAATTTTATAAACT
1 CAAGGGTATTTCGGTAATTTTACAAACT
* *
15039 --AGGGATATTTTGGCAATTTTACAAAC-
1 CAAGGG-TATTTCGGTAATTTTACAAACT
*
15065 CAAGGGTA-TTCAGTAATTT
1 CAAGGGTATTTCGGTAATTT
15084 CAGTAAATCT
Statistics
Matches: 255, Mismatches: 46, Indels: 28
0.78 0.14 0.09
Matches are distributed among these distances:
26 42 0.16
27 201 0.79
28 12 0.05
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (28 bp):
CAAGGGTATTTCGGTAATTTTACAAACT
Found at i:14888 original size:54 final size:54
Alignment explanation
Indices: 14771--15083 Score: 208
Period size: 54 Copynumber: 5.8 Consensus size: 54
14761 CTATAAACTC
* ** * ** * ** *
14771 AGGGTATTTCGGTAATTTTGCAAACCAATAGCATTTCTGTAATTTTTGAAAGCCA
1 AGGGTATTTCAGTAATTTTATAAATCAAGGGTATTTCTGTAATTTTACAAA-TCA
* * * * *
14826 AAGG-ATTTCTGTAATTTTGTAAATCAAGGGTGTTTCTGTAATTTTCCAAATCA
1 AGGGTATTTCAGTAATTTTATAAATCAAGGGTATTTCTGTAATTTTACAAATCA
* * * * * *
14879 AGGGTATTTCAGTAATTTTACAAATCGAGTGTTTTTC-GATAATTTTACAAGTCG
1 AGGGTATTTCAGTAATTTTATAAATCAAGGGTATTTCTG-TAATTTTACAAATCA
** **
14933 AGGGTATTTCAGTAATTTT-TAGGTCAAGGGTATTT-TAGTAATTTTACAGGTCA
1 AGGGTATTTCAGTAATTTTATAAATCAAGGGTATTTCT-GTAATTTTACAAATCA
* ** * *
14986 AGGGTATTTCGGTAATTTTATAGGTCAAGGGTATTT-TGGTAATTTTATAAA-CT
1 AGGGTATTTCAGTAATTTTATAAATCAAGGGTATTTCT-GTAATTTTACAAATCA
** * * * *
15039 AGGGATATTTTGGCAATTTTACAAACCAAGGGTA-TTCAGTAATTT
1 AGGG-TATTTCAGTAATTTTATAAATCAAGGGTATTTCTGTAATTT
15084 CAGTAAATCT
Statistics
Matches: 209, Mismatches: 42, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
53 61 0.29
54 145 0.69
55 3 0.01
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (54 bp):
AGGGTATTTCAGTAATTTTATAAATCAAGGGTATTTCTGTAATTTTACAAATCA
Found at i:14978 original size:80 final size:80
Alignment explanation
Indices: 14849--15031 Score: 204
Period size: 80 Copynumber: 2.3 Consensus size: 80
14839 ATTTTGTAAA
* * * ** * * *
14849 TCAAGGGTGTTTCTGTAATTTTCCAAATCAAGGGTATTTCAGTAATTTTACAAATCGAGTGTTTT
1 TCAAGGGTATTTCAGTAATTTT-TAGGTCAAGGGTATTTCAGTAATTTTACAAATCAAGGGTATT
14914 TCGATAATTTTACAAG
65 TCGATAATTTTACAAG
* * **
14930 TCGAGGGTATTTCAGTAATTTTTAGGTCAAGGGTATTTTAGTAATTTTACAGGTCAAGGGTATTT
1 TCAAGGGTATTTCAGTAATTTTTAGGTCAAGGGTATTTCAGTAATTTTACAAATCAAGGGTATTT
* * *
14995 CGGTAATTTTATAGG
66 CGATAATTTTACAAG
**
15010 TCAAGGGTATTTTGGTAATTTT
1 TCAAGGGTATTTCAGTAATTTT
15032 ATAAACTAGG
Statistics
Matches: 84, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
80 65 0.77
81 19 0.23
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.42
Consensus pattern (80 bp):
TCAAGGGTATTTCAGTAATTTTTAGGTCAAGGGTATTTCAGTAATTTTACAAATCAAGGGTATTT
CGATAATTTTACAAG
Found at i:15191 original size:27 final size:27
Alignment explanation
Indices: 15107--15197 Score: 101
Period size: 27 Copynumber: 3.4 Consensus size: 27
15097 AACCAAGGGT
* *
15107 ATTTTAGTAATTCTACCCTACAGGAGC
1 ATTTCAGTAATTCTACCCTACAGGGGC
* * * *
15134 ATTTCAATAATTCAATCCTACAAGGGC
1 ATTTCAGTAATTCTACCCTACAGGGGC
* *
15161 ATTTCAGTAATTCTACCCTATAGGGGT
1 ATTTCAGTAATTCTACCCTACAGGGGC
*
15188 ATTTTAGTAA
1 ATTTCAGTAA
15198 AACTAGCCTA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (27 bp):
ATTTCAGTAATTCTACCCTACAGGGGC
Found at i:15208 original size:54 final size:54
Alignment explanation
Indices: 15100--15209 Score: 121
Period size: 54 Copynumber: 2.0 Consensus size: 54
15090 ATCTGTAAAC
* * ** *
15100 CAAGGGTATTTTAGTAATTCTACCCTACAGGAGCATTTCAATAATTCAATCCTA
1 CAAGGGCATTTCAGTAATTCTACCCTACAGGAGCATTTCAATAAAACAAGCCTA
* * * * * *
15154 CAAGGGCATTTCAGTAATTCTACCCTATAGGGGTATTTTAGTAAAACTAGCCTA
1 CAAGGGCATTTCAGTAATTCTACCCTACAGGAGCATTTCAATAAAACAAGCCTA
15208 CA
1 CA
15210 GATATGAGAT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (54 bp):
CAAGGGCATTTCAGTAATTCTACCCTACAGGAGCATTTCAATAAAACAAGCCTA
Found at i:19035 original size:24 final size:24
Alignment explanation
Indices: 18986--19072 Score: 122
Period size: 24 Copynumber: 3.6 Consensus size: 24
18976 ATTCAAATCA
* * *
18986 GCACACATAGTGCTA-ATCAACTCC
1 GCACACATAGTGCCATA-CTACACC
19010 GCACACATAGTGCCATACTACACC
1 GCACACATAGTGCCATACTACACC
*
19034 GCACACATAGTGCCATACTACACA
1 GCACACATAGTGCCATACTACACC
19058 GCACACATAGTGCCA
1 GCACACATAGTGCCA
19073 ATGTACACTT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
24 57 0.98
25 1 0.02
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (24 bp):
GCACACATAGTGCCATACTACACC
Found at i:26880 original size:23 final size:23
Alignment explanation
Indices: 26854--26897 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
26844 ATGTTGACAT
26854 TCAAATCAGCACACATAGTGCTA
1 TCAAATCAGCACACATAGTGCTA
* *
26877 TCAACTCCGCACACATAGTGC
1 TCAAATCAGCACACATAGTGC
26898 CATACTACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (23 bp):
TCAAATCAGCACACATAGTGCTA
Found at i:26915 original size:24 final size:24
Alignment explanation
Indices: 26862--26947 Score: 120
Period size: 24 Copynumber: 3.6 Consensus size: 24
26852 ATTCAAATCA
* * *
26862 GCACACATAGTGCTAT-CAACTCC
1 GCACACATAGTGCCATACTACACC
26885 GCACACATAGTGCCATACTACACC
1 GCACACATAGTGCCATACTACACC
*
26909 GCACACATAGTGCCATACTACACA
1 GCACACATAGTGCCATACTACACC
*
26933 GCACACATAATGCCA
1 GCACACATAGTGCCA
26948 ATGTACACTT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 15 0.26
24 42 0.74
ACGTcount: A:0.35, C:0.35, G:0.13, T:0.17
Consensus pattern (24 bp):
GCACACATAGTGCCATACTACACC
Found at i:30275 original size:26 final size:27
Alignment explanation
Indices: 30221--30275 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
30211 ATTCAACACC
* * *
30221 TAGGGGTATTTTGGTCATTTTTTCCCT
1 TAGGGGCATTTCGGTCAATTTTTCCCT
*
30248 TAGGGGCATTTCGGT-AATTTTTCTCT
1 TAGGGGCATTTCGGTCAATTTTTCCCT
30274 TA
1 TA
30276 TTATGGTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.49
Consensus pattern (27 bp):
TAGGGGCATTTCGGTCAATTTTTCCCT
Found at i:30646 original size:59 final size:57
Alignment explanation
Indices: 30535--30648 Score: 131
Period size: 59 Copynumber: 2.0 Consensus size: 57
30525 CATACATGAA
* * * * **
30535 TATGGCCCACTAGGTCCAATCTTATTCAAATGGCCCATCTAGCCCAGTTCATATTCT
1 TATGGCCCACCAGGCCCAATCTCATTCAAATGGCCCATATAGCCCAAATCATATTCT
*
30592 TATGGCCCCACCAGGCCCAATTCTCATTCATATGGCCCA-ATAGCCTCAAATCATATT
1 TATGG-CCCACCAGGCCCAA-TCTCATTCAAATGGCCCATATAGCC-CAAATCATATT
30649 ATATTCATAC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
57 5 0.11
58 17 0.36
59 25 0.53
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29
Consensus pattern (57 bp):
TATGGCCCACCAGGCCCAATCTCATTCAAATGGCCCATATAGCCCAAATCATATTCT
Found at i:32725 original size:101 final size:100
Alignment explanation
Indices: 32595--32937 Score: 300
Period size: 101 Copynumber: 3.4 Consensus size: 100
32585 ATCAATCTGG
* * * *
32595 TACACGTAGTAGCCTGCA-TTCAGTACTACACATGTGACTTATCCATTTGATACACGTAGTAGCC
1 TACACATAGTAGCCTGCACTT-AGTACTACACATGTGACCTATCAATTAGATACACGTAGTAGCC
** * ** *
32659 TGCACTTAGTACTACCCACATGATCGAAGTTAACGGG
65 TGCACTTAGTACTACAAACATGACCGAA-CCAACGGA
** * **
32696 TACGTATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCCGATACACGTAGTAGCCT
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATTAGATACACGTAGTAGCCT
* * * *
32761 ACACTTAGTACTACAAACATGACCTAACCATCTGA
66 GCACTTAGTACTACAAACATGACCGAACCAACGGA
* ** * * * **
32796 TACACATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAACTATTAGGTATGCGTAGTAGCC
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTATCAATTAGATACACGTAGTAGCC
*
32861 TGCACTTAGTACTAC--ACATGCGACCTAA-CAATCTGG-
65 TGCACTTAGTACTACAAACAT--GACCGAACCAA-C-GGA
* * **
32897 TACACGTAGTATCCTGCACTTAGTACTACACACATGACCTA
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTA
32938 AAACTGTCTT
Statistics
Matches: 197, Mismatches: 39, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
99 4 0.02
100 40 0.20
101 150 0.76
102 3 0.02
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (100 bp):
TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATTAGATACACGTAGTAGCCT
GCACTTAGTACTACAAACATGACCGAACCAACGGA
Found at i:32806 original size:151 final size:151
Alignment explanation
Indices: 32543--32980 Score: 590
Period size: 151 Copynumber: 2.9 Consensus size: 151
32533 GAAGCTCTCT
*
32543 GGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
** * * * *
32608 CTGCA-TTCAGTACTACACATGTGACTTATCCATTTGATACACGTAGTAGCCTGCACTTAGTACT
66 CTGCACTT-AGTACTACACACATGACCTAACCATCTGATACACATAGTAGCCTGCACTTAGTACT
* ** *
32672 ACCCACATGATCGAAGTTAACG
130 ACACACATGATCGAAACTAACA
* * *
32694 GGTACGTATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCCGATACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
* *
32759 CTACACTTAGTACTACAAACATGACCTAACCATCTGATACACATAGTAGCCTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACATGACCTAACCATCTGATACACATAGTAGCCTGCACTTAGTACTA
* **
32824 CACACGTGATCGAAACTATTA
131 CACACATGATCGAAACTAACA
* * * *
32845 GGTATGCGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTATC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
** * * *
32910 CTGCACTTAGTACTACACACATGACCTAAAACTGTCTTAAACACATAGTAGCCTGCACATAGTAC
66 CTGCACTTAGTACTACACACATGACCT--AACCATCTGATACACATAGTAGCCTGCACTTAGTAC
32975 TACACA
129 TACACA
32981 TGTGTTCTCA
Statistics
Matches: 251, Mismatches: 33, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
151 212 0.84
152 2 0.01
153 37 0.15
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
CTGCACTTAGTACTACACACATGACCTAACCATCTGATACACATAGTAGCCTGCACTTAGTACTA
CACACATGATCGAAACTAACA
Found at i:32936 original size:50 final size:50
Alignment explanation
Indices: 32540--32980 Score: 370
Period size: 50 Copynumber: 8.7 Consensus size: 50
32530 ACCGAAGCTC
* * * * * *
32540 TCTGGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
* * * *
32590 TCTGGTACACGTAGTAGCCTGCA-TTCAGTACTACACATGTGACTTATCCA
1 TCTGGTACACGTAGTAGCCTGCACTT-AGTACTACACACGTGACCTAACAA
* * * * * * *
32640 TTTGATACACGTAGTAGCCTGCACTTAGTACTACCCACATGATCGAAGTTAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA--CAA
* *** * * *
32692 -CGGGTACGTATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
* * * * * *
32741 TCCGATACACGTAGTAGCCTACACTTAGTACTACAAACATGACCTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
* * ** *
32791 TCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAACTA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCTAACAA
** * *
32842 T-TAGGTATGCGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
1 TCT-GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
* *
32892 TCTGGTACACGTAGTATCCTGCACTTAGTACTACACACATGACCTAA-AA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
* * *
32941 -CTGTCTTAAACACATAGTAGCCTGCACATAGTACTACACA
1 TCTG--GT--ACACGTAGTAGCCTGCACTTAGTACTACACA
32981 TGTGTTCTCA
Statistics
Matches: 309, Mismatches: 70, Indels: 22
0.77 0.17 0.05
Matches are distributed among these distances:
48 3 0.01
49 6 0.02
50 196 0.63
51 75 0.24
52 29 0.09
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
Found at i:35021 original size:25 final size:25
Alignment explanation
Indices: 34950--35002 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
34940 TGAATCAATA
34950 AACTCATGAGTAAAATATCAAACAT
1 AACTCATGAGTAAAATATCAAACAT
34975 AACTCATGAGTAAAATATCAAACAT
1 AACTCATGAGTAAAATATCAAACAT
35000 AAC
1 AAC
35003 CATACTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.23
Consensus pattern (25 bp):
AACTCATGAGTAAAATATCAAACAT
Found at i:35038 original size:15 final size:16
Alignment explanation
Indices: 35018--35047 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35008 TTATATATAT
35018 CAAAACCA-AATCAAC
1 CAAAACCATAATCAAC
35033 CAAAACCATAATCAA
1 CAAAACCATAATCAA
35048 ATATAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.30, G:0.00, T:0.10
Consensus pattern (16 bp):
CAAAACCATAATCAAC
Found at i:36440 original size:43 final size:42
Alignment explanation
Indices: 36267--36443 Score: 164
Period size: 43 Copynumber: 4.1 Consensus size: 42
36257 TAACGCATAT
* * *
36267 CATA-CAATGCCAACGTCCCATACGTGGTCTTACATGTAATCA
1 CATATCAATGCCAACGTCCCAGACGTGGTCTTACACG-AAACA
* * *
36309 CATGTCGATGCC-ACTGTCCCAGACAG-GGTCTTACACGAATCA
1 CATATCAATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAACA
* * * * *
36351 CA-ATTACGATGCCGATGTCCAAGACGTGGTCTTACTCGAAATCA
1 CATA-T-CAATGCCAACGTCCCAGACGTGGTCTTACACGAAA-CA
36395 CATATCAATGCCAACGTCCCAGACGTGGTCTTACACGAGAACA
1 CATATCAATGCCAACGTCCCAGACGTGGTCTTACACGA-AACA
36438 CATATC
1 CATATC
36444 GGAAATCCTA
Statistics
Matches: 111, Mismatches: 14, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
42 14 0.13
43 87 0.78
44 9 0.08
45 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (42 bp):
CATATCAATGCCAACGTCCCAGACGTGGTCTTACACGAAACA
Found at i:37539 original size:51 final size:51
Alignment explanation
Indices: 37463--37565 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
37453 AAACTCTAGT
37463 GATGGAGGGATCCCACATCGGGAAGCTAACATAAGAGTAGATAGGGAGCTG
1 GATGGAGGGATCCCACATCGGGAAGCTAACATAAGAGTAGATAGGGAGCTG
37514 GATGGAGGGATCCCACATCGGGAAGCTAACATAAGAGTAGATAGGGAGCTG
1 GATGGAGGGATCCCACATCGGGAAGCTAACATAAGAGTAGATAGGGAGCTG
37565 G
1 G
37566 CTTTAAATAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.33, C:0.16, G:0.36, T:0.16
Consensus pattern (51 bp):
GATGGAGGGATCCCACATCGGGAAGCTAACATAAGAGTAGATAGGGAGCTG
Found at i:37884 original size:27 final size:27
Alignment explanation
Indices: 37854--37960 Score: 119
Period size: 27 Copynumber: 4.0 Consensus size: 27
37844 AATCTCATAT
*
37854 CTGTAGGCTAGCATTACTGAAATACCC
1 CTGTAGGCTAGAATTACTGAAATACCC
37881 CTGTAGGGC-AGAATTACTGAAATACCC
1 CTGTA-GGCTAGAATTACTGAAATACCC
* *
37908 TTGTAGTG-TAGAATTACTGAAATGCCC
1 CTGTAG-GCTAGAATTACTGAAATACCC
* * **
37935 CTATAGGGTAGAATTACAAAAATACC
1 CTGTAGGCTAGAATTACTGAAATACC
37961 ATTGGTTTAC
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
26 2 0.03
27 63 0.93
28 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (27 bp):
CTGTAGGCTAGAATTACTGAAATACCC
Found at i:37976 original size:27 final size:27
Alignment explanation
Indices: 37946--38113 Score: 185
Period size: 27 Copynumber: 6.2 Consensus size: 27
37936 TATAGGGTAG
* * *
37946 AATTACAAAAATACCATTGGTTTACAA
1 AATTACCAAAATACCCTTGGTTTATAA
*
37973 AATTACCAAAATACCCCTGGTTTATAA
1 AATTACCAAAATACCCTTGGTTTATAA
*
38000 AATTACCAAAATACCCTTGGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTATAA
* * *
38027 AATTACCAAAATACCCCTGATTTATGA
1 AATTACCAAAATACCCTTGGTTTATAA
* * *
38054 AATTACCGAAATACCCTCGACTTGTA-AA
1 AATTACCAAAATACCCTTG-GTT-TATAA
* * *
38082 AATTACCAAAATACCCCTGATTTATAG
1 AATTACCAAAATACCCTTGGTTTATAA
38109 AATTA
1 AATTA
38114 ATATTTTACC
Statistics
Matches: 118, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
26 2 0.02
27 95 0.81
28 19 0.16
29 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGGTTTATAA
Found at i:37977 original size:54 final size:53
Alignment explanation
Indices: 37866--37990 Score: 126
Period size: 54 Copynumber: 2.3 Consensus size: 53
37856 GTAGGCTAGC
* ** * *
37866 ATTACTGAAATACCCCTGTAGGGCAGAATTACTGAAATACCCTTGTAGTGTAGA
1 ATTACTGAAATACCCCTATAGGGCAGAATTACAAAAATACCATTG-AGTGTAAA
* * *
37920 ATTACTGAAATGCCCCTATAGGGTAGAATTACAAAAATACCATTG-GTTTACAAA
1 ATTACTGAAATACCCCTATAGGGCAGAATTACAAAAATACCATTGAGTGT--AAA
**
37974 ATTACCAAAATACCCCT
1 ATTACTGAAATACCCCT
37991 GGTTTATAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
52 3 0.05
54 55 0.95
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (53 bp):
ATTACTGAAATACCCCTATAGGGCAGAATTACAAAAATACCATTGAGTGTAAA
Found at i:38004 original size:54 final size:53
Alignment explanation
Indices: 37946--38113 Score: 219
Period size: 54 Copynumber: 3.1 Consensus size: 53
37936 TATAGGGTAG
* * *
37946 AATTACAAAAATACCATTGGTTTACAAAATTACCAAAATACCCCTGGTTTATAA
1 AATTACCAAAATACCCTTGGTTTA-AAAATTACCAAAATACCCCTGATTTATAA
* *
38000 AATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTGATTTATGA
1 AATTACCAAAATACCCTTGGTTT-AAAAATTACCAAAATACCCCTGATTTATAA
* * * *
38054 AATTACCGAAATACCCTCGACTTGTAAAAATTACCAAAATACCCCTGATTTATAG
1 AATTACCAAAATACCCTTG-GTT-TAAAAATTACCAAAATACCCCTGATTTATAA
38109 AATTA
1 AATTA
38114 ATATTTTACC
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
54 65 0.65
55 34 0.34
56 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (53 bp):
AATTACCAAAATACCCTTGGTTTAAAAATTACCAAAATACCCCTGATTTATAA
Found at i:38166 original size:27 final size:27
Alignment explanation
Indices: 38143--38215 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
38133 CAAAATTATT
*
38143 GAAATACCCTTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
38170 GAAATACCCCTGTAGGGTAGGACTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
** *
38197 GATTTACCCCTGGAGGGTA
1 GAAATACCCCTGTAGGGTA
38216 AAATGACTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACC
Found at i:38243 original size:27 final size:26
Alignment explanation
Indices: 38199--38250 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
38189 GGACTACCGA
*
38199 TTTACCCCTGGAGGGTAAAATGACTAT
1 TTTACCCCTGGAGCGT-AAATGACTAT
* *
38226 TTTACCCCTTGTGCGTAAATGACTA
1 TTTACCCCTGGAGCGTAAATGACTA
38251 ACTTGTGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (26 bp):
TTTACCCCTGGAGCGTAAATGACTAT
Found at i:38967 original size:73 final size:67
Alignment explanation
Indices: 38833--38967 Score: 162
Period size: 73 Copynumber: 1.9 Consensus size: 67
38823 GCGTTCTGGC
* * *
38833 AGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTCAAAATATTTG
1 AGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACCTAGCCAAAATATTTG
38898 GT
66 GT
* * *
38900 AGCCTCGCTGCAATCTGGTGGCTTCGCTACACATATATATATCTGTTCTGGTGGCCTAGCCACAA
1 AGCCTCGCTGCAATCTGGTGGCCTCGC--CAC----ATATATCTGTTCTGGTGACCTAGCCAAAA
38965 TAT
60 TAT
38968 CTGTATCTGG
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
67 26 0.46
69 3 0.05
73 27 0.48
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (67 bp):
AGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACCTAGCCAAAATATTTG
GT
Found at i:38989 original size:26 final size:26
Alignment explanation
Indices: 38938--38996 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
38928 ACACATATAT
*
38938 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGGACTAGCCACA
* *
38964 ATATCTGTATCTGGT-GACTTGTCACA
1 ATATCTGT-TCTGGTGGACTAGCCACA
38990 ATATCTG
1 ATATCTG
38997 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 23 0.79
27 6 0.21
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (26 bp):
ATATCTGTTCTGGTGGACTAGCCACA
Found at i:43652 original size:27 final size:27
Alignment explanation
Indices: 43610--43716 Score: 142
Period size: 27 Copynumber: 4.0 Consensus size: 27
43600 AATCTCATAT
* *
43610 CTGTAGGCTAGCATTACTGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* *
43637 CTGTTGGGTAGAATTATTGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
*
43664 CTGTAGGGTAGAATTACTGAAATGCCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* **
43691 CTATAGGGTAGAATTACCAAAATACC
1 CTGTAGGGTAGAATTACTGAAATACC
43717 ATTGGTTTAC
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (27 bp):
CTGTAGGGTAGAATTACTGAAATACCC
Found at i:43732 original size:27 final size:27
Alignment explanation
Indices: 43702--43854 Score: 180
Period size: 27 Copynumber: 5.6 Consensus size: 27
43692 TATAGGGTAG
* **
43702 AATTACCAAAATACCATTGGTTTACAA
1 AATTACCAAAATACCCTTGGTTTGTAA
* *
43729 AATTTCCAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTGTAA
43756 AATTACCAAAATACCCTTGGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTGTAA
* *
43783 AATTACCAAAATACCCTTGATTTGTGA
1 AATTACCAAAATACCCTTGGTTTGTAA
* * * **
43810 AATTACCGAAATAACCTCGACTTGTAAA
1 AATTACCAAAATACCCTTGGTTTGT-AA
*
43838 AATTACCAAAGTACCCT
1 AATTACCAAAATACCCT
43855 CGATTTACAG
Statistics
Matches: 108, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
27 93 0.86
28 15 0.14
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGGTTTGTAA
Found at i:43746 original size:54 final size:54
Alignment explanation
Indices: 43683--43822 Score: 138
Period size: 54 Copynumber: 2.6 Consensus size: 54
43673 AGAATTACTG
* * *
43683 AAATGCCCCT-ATAGGGTAGAATTACCAAAATACCATTGGTTTACAAAATTTCCA
1 AAATACCCCTGAT-GGGTAAAATTACCAAAATACCATTGGTTTACAAAATTACCA
* ** * **
43737 AAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCA
1 AAATACCCCTGATGGGTAAAATTACCAAAATACCATTGGTTTACAAAATTACCA
* ** * *
43791 AAATACCCTTGATTTGTGAAATTACCGAAATA
1 AAATACCCCTGATGGGTAAAATTACCAAAATA
43823 ACCTCGACTT
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
54 71 0.99
55 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (54 bp):
AAATACCCCTGATGGGTAAAATTACCAAAATACCATTGGTTTACAAAATTACCA
Found at i:43906 original size:27 final size:27
Alignment explanation
Indices: 43702--43907 Score: 112
Period size: 27 Copynumber: 7.6 Consensus size: 27
43692 TATAGGGTAG
* * * *
43702 AATTACCAAAATACCATTGGTTTACAA
1 AATTATCAAAATACCCTCGATTTACAA
* **
43729 AATT-TCCAAAATACCC-CTGGTTTGTAA
1 AATTAT-CAAAATACCCTC-GATTTACAA
* * * **
43756 AATTACCAAAATACCCTTGGTTTGTAA
1 AATTATCAAAATACCCTCGATTTACAA
* * ***
43783 AATTACCAAAATACCCTTGATTTGTGA
1 AATTATCAAAATACCCTCGATTTACAA
* * *
43810 AATTACCGAAATAACCTCGACTTGTA-AA
1 AATTATCAAAATACCCTCGA-TT-TACAA
* * *
43838 AATTACCAAAGTACCCTCGATTTACAG
1 AATTATCAAAATACCCTCGATTTACAA
***
43865 AATTATCATTTTACCCTCGATTTACAA
1 AATTATCAAAATACCCTCGATTTACAA
*
43892 AATTATTAAAATACCC
1 AATTATCAAAATACCC
43908 CTGTAGGGTA
Statistics
Matches: 145, Mismatches: 27, Indels: 14
0.78 0.15 0.08
Matches are distributed among these distances:
26 2 0.01
27 122 0.84
28 20 0.14
29 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.32
Consensus pattern (27 bp):
AATTATCAAAATACCCTCGATTTACAA
Found at i:44721 original size:26 final size:26
Alignment explanation
Indices: 44670--44728 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
44660 ACATATATAT
*
44670 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGGACTAGCCACA
* *
44696 ATATCTGTATCTGGT-GACTTGTCACA
1 ATATCTGT-TCTGGTGGACTAGCCACA
44722 ATATCTG
1 ATATCTG
44729 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 23 0.79
27 6 0.21
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (26 bp):
ATATCTGTTCTGGTGGACTAGCCACA
Found at i:47404 original size:43 final size:44
Alignment explanation
Indices: 47257--47413 Score: 130
Period size: 43 Copynumber: 3.7 Consensus size: 44
47247 TGTGTTATCG
* * * * *
47257 TGTAAGACCACGTTTGGGA-TGTTGGCATCGAT-TTGTAATTTACG
1 TGTAAAACCACGTCTGGGACAGTTGGCATCGATATT-TGA-TTACA
* * * * *
47301 TGTAAGACCATGTCTGGGACA-TTAGCATCG-TATATGATTTCA
1 TGTAAAACCACGTCTGGGACAGTTGGCATCGATATTTGATTACA
*
47343 TGTAAAACC-CTATCTGGGACAG-TGGCATCGATATTTGATTACA
1 TGTAAAACCAC-GTCTGGGACAGTTGGCATCGATATTTGATTACA
*
47386 TGTAAAACCACGTGTGGGAC-GTTGGCAT
1 TGTAAAACCACGTCTGGGACAGTTGGCAT
47414 TGTACGAGCT
Statistics
Matches: 90, Mismatches: 16, Indels: 15
0.74 0.13 0.12
Matches are distributed among these distances:
42 28 0.31
43 35 0.39
44 27 0.30
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (44 bp):
TGTAAAACCACGTCTGGGACAGTTGGCATCGATATTTGATTACA
Found at i:52143 original size:56 final size:56
Alignment explanation
Indices: 52057--52176 Score: 240
Period size: 56 Copynumber: 2.1 Consensus size: 56
52047 ACAAGGGATG
52057 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
52113 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
52169 ATGGGCAA
1 ATGGGCAA
52177 TAAACTAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:52266 original size:10 final size:10
Alignment explanation
Indices: 52251--52275 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
52241 TGACCAAAAA
52251 AAAAGAAGAG
1 AAAAGAAGAG
52261 AAAAGAAGAG
1 AAAAGAAGAG
52271 AAAAG
1 AAAAG
52276 CTCTCATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AAAAGAAGAG
Found at i:53396 original size:40 final size:39
Alignment explanation
Indices: 53312--53496 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
53302 TCGAATGATG
* * * *
53312 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
53352 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
53392 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
53431 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
53472 -CCGGGCTATGTCCAGAAGGCATTTG
1 TCCGGGCTAAGTCC-GAAGGCATTTG
53497 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 36 0.29
40 77 0.63
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53448 original size:79 final size:81
Alignment explanation
Indices: 53312--53494 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
53302 TCGAATGATG
* *
53312 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
53376 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
53391 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
53453 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* * *
53471 ACCGGGCTATGTCCAGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
53495 TGAACGAGTA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.66
80 29 0.33
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:53518 original size:79 final size:79
Alignment explanation
Indices: 53365--53519 Score: 190
Period size: 79 Copynumber: 2.0 Consensus size: 79
53355 GGACTAAGAT
* * **
53365 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCAGAAGGCATTGGAACGAGTTACTAA
53430 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
53444 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCAGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCAGAAGGCATTGGAACGAGTTA-C
*
53507 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
53520 ATTCTGAAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 2 0.03
79 40 0.62
80 23 0.35
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCAGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:60019 original size:56 final size:56
Alignment explanation
Indices: 59933--60052 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
59923 ACAAGGGATG
59933 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
59989 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
60045 ATGGGCAA
1 ATGGGCAA
60053 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:61338 original size:79 final size:79
Alignment explanation
Indices: 61146--61369 Score: 292
Period size: 79 Copynumber: 2.8 Consensus size: 79
61136 TCGAATGATG
* * * * *
61146 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCGAAGGCATT
*
61210 TGTGCGAGATACTAAT
64 TGTGCGAGATACTAAA
* *
61226 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
*
61290 TGCGAGTTACTAAA
66 TGCGAGATACTAAA
* *
61304 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATT
61368 TG
64 TG
61370 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
78 36 0.28
79 59 0.46
80 32 0.25
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:61383 original size:40 final size:40
Alignment explanation
Indices: 61146--61369 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
61136 TCGAATGATG
* * * *
61146 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
61186 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
61226 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
61265 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
61304 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
61345 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
61370 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
39 72 0.44
40 81 0.50
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:61400 original size:79 final size:79
Alignment explanation
Indices: 61185--61402 Score: 237
Period size: 79 Copynumber: 2.8 Consensus size: 79
61175 AAGTGACCAT
* ** * * * *
61185 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCT-AAGCCCGAAGGCATT
1 ATCCGGGCTAAG-TCCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATT
61249 GGTGCGAGTTACTAA
65 GGTGCGAGTTACTAA
* ** * *
61264 ATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 ATCCGGGCTAAGTCCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTG
61329 GTGCGAGTTACTATA
66 GTGCGAGTTACTA-A
* * *
61344 A-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 ATCCGGGCTAAGT-CCGAAGGCATTTGAACGAGTTA-CTAAATCCGGGTTAAATCCCGAAGG
61403 TACGTGATTT
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
78 33 0.28
79 61 0.51
80 26 0.22
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
ATCCGGGCTAAGTCCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTG
GTGCGAGTTACTAA
Found at i:65489 original size:84 final size:81
Alignment explanation
Indices: 65267--65555 Score: 304
Period size: 84 Copynumber: 3.5 Consensus size: 81
65257 CCCGTCATTT
* *
65267 AACAAATTTTATTCCATTCTTTATTGTTTCCAAACGAAGAATT-AAAATTGAATAAAATTTGTTT
1 AACATATTTTATTCCATT-TTTTTTGTTTCCAAAC-AAGAATTAAAAATTGAAT-AAATTTGTTT
* *
65331 CGAGATTTATTCCTACCATTC
63 AG-GATTTATTCCT-CCGTTC
* * * *
65352 AACAGATTTTATTCCATTTTTTTT-TTCTCCAAACGAGATTTAAAATTTGAATAAATTTGTTTAG
1 AACATATTTTATTCCATTTTTTTTGTT-TCCAAACAAGAATTAAAAATTGAATAAATTTGTTTAG
65416 GATTTATTACCTCCGTTC
65 GATTTATT-CCTCCGTTC
65434 AACATATTTTATTCCATTTTAATTTTGTTTCCAAACAAGAATTAAAAATTGAAT-AATTCTGTTT
1 AACATATTTTATTCCATTTT--TTTTGTTTCCAAACAAGAATTAAAAATTGAATAAATT-TGTTT
* *
65498 CGGGATTTATTCCCACCGTTC
63 -AGGATTTATT-CCTCCGTTC
* *
65519 -A-ATGA-TTTATTCAATTTTTTTTG-TTCCAAATAAGAAT
1 AACAT-ATTTTATTCCATTTTTTTTGTTTCCAAACAAGAAT
65556 AATTGTTGAA
Statistics
Matches: 179, Mismatches: 16, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
80 13 0.07
81 5 0.03
82 32 0.18
83 39 0.22
84 54 0.30
85 36 0.20
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.44
Consensus pattern (81 bp):
AACATATTTTATTCCATTTTTTTTGTTTCCAAACAAGAATTAAAAATTGAATAAATTTGTTTAGG
ATTTATTCCTCCGTTC
Done.