Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 199 of 226
Found at i:63116049 original size:3 final size:3
Alignment explanation
Indices: 63116035--63116066 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
63116025 GCACCGCCCT
*
63116035 CTC CTT CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
63116067 TCTTATTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (3 bp):
CTC
Found at i:63116243 original size:39 final size:39
Alignment explanation
Indices: 63116131--63116266 Score: 146
Period size: 40 Copynumber: 3.4 Consensus size: 39
63116121 CGTTTGGACA
* * *
63116131 AAAAACGCCGGTAAAAATAGAGCATTAGCGGCGCTTTATG
1 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGTTTTTTG
* * * * *
63116171 GAAATCACCACTAAAGATTGAGCATTAGCGGCGTTTTTTG
1 AAAAACGCCGCTAAA-AATGAGCATTAGCGGCGTTTTTTG
* * *
63116211 AAAATCGCCGCTAAAAATGAGAATTAGCGGCGTTTTTCG
1 AAAAACGCCGCTAAAAATGAGCATTAGCGGCGTTTTTTG
*
63116250 AAAAACGCCGCAAAAAA
1 AAAAACGCCGCTAAAAA
63116267 CCTAAGCCCA
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
39 36 0.46
40 41 0.52
41 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCGGCGTTTTTTG
Found at i:63117765 original size:14 final size:13
Alignment explanation
Indices: 63117761--63117795 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
63117751 GGAGTTAGGG
63117761 GTTAGGGGTTAGA
1 GTTAGGGGTTAGA
63117774 CGTTAGGGGTTAAGA
1 -GTTAGGGGTT-AGA
63117789 GTTAGGG
1 GTTAGGG
63117796 ATTTAAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.23, C:0.03, G:0.46, T:0.29
Consensus pattern (13 bp):
GTTAGGGGTTAGA
Found at i:63117772 original size:21 final size:22
Alignment explanation
Indices: 63117748--63117794 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
63117738 GATTTAAGGT
* *
63117748 TTAGGA-GTTAGGGGTTAGGGG
1 TTAGGACGTTAGGGGTTAAGAG
63117769 TTA-GACGTTAGGGGTTAAGAG
1 TTAGGACGTTAGGGGTTAAGAG
63117790 TTAGG
1 TTAGG
63117795 GATTTAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 19 0.86
22 1 0.05
ACGTcount: A:0.23, C:0.02, G:0.45, T:0.30
Consensus pattern (22 bp):
TTAGGACGTTAGGGGTTAAGAG
Found at i:63118109 original size:27 final size:27
Alignment explanation
Indices: 63118041--63118124 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 27
63118031 AAACCATTTG
*
63118041 ATATATTTAAATATTAGTTTAAATAGA
1 ATATATTTAAATATTAGTTTAAATAAA
*
63118068 AT-TA-ATAAATA--AGTTTAAATAAA
1 ATATATTTAAATATTAGTTTAAATAAA
63118091 ATATATTTAAATATTAGTTTAAATAAA
1 ATATATTTAAATATTAGTTTAAATAAA
63118118 ATA-ATTT
1 ATATATTT
63118125 TTGTTCAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
23 13 0.26
24 2 0.04
25 12 0.24
26 6 0.12
27 17 0.34
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (27 bp):
ATATATTTAAATATTAGTTTAAATAAA
Found at i:63118642 original size:12 final size:12
Alignment explanation
Indices: 63118625--63118649 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63118615 ACCAAAACAG
63118625 GCTTTTAGCGGC
1 GCTTTTAGCGGC
63118637 GCTTTTAGCGGC
1 GCTTTTAGCGGC
63118649 G
1 G
63118650 TTTGGACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.36, T:0.32
Consensus pattern (12 bp):
GCTTTTAGCGGC
Found at i:63118901 original size:41 final size:41
Alignment explanation
Indices: 63118845--63119109 Score: 329
Period size: 41 Copynumber: 6.5 Consensus size: 41
63118835 TTAACGGCGC
* * * * *
63118845 TTTTACATAATCGCCGCTAATGTTGCGGTCTCTCGCGGCGTT
1 TTTTACA-AAGCGCCGCTAATGCTACGGTCTTTAGCGGCGTT
* *
63118887 TTATA-ATATGCGCCGCTAATGCTACGGTCTTTAGCGGCGTT
1 TTTTACA-AAGCGCCGCTAATGCTACGGTCTTTAGCGGCGTT
* *
63118928 TTTTACAAAGCGCCGCTGATTCTACGGTCTTTAGCGGCGTT
1 TTTTACAAAGCGCCGCTAATGCTACGGTCTTTAGCGGCGTT
*
63118969 TTTTACAAAGCGCCGCTGATGCTACGGTCTTTAGCGGCGTT
1 TTTTACAAAGCGCCGCTAATGCTACGGTCTTTAGCGGCGTT
*
63119010 TTTTACAAAGCGCCGCTAATGCTATGGTCTTTAGCGGCGTT
1 TTTTACAAAGCGCCGCTAATGCTACGGTCTTTAGCGGCGTT
* * *
63119051 TTTTACAAAGTG-CGCTAATGCT-CAAGTCTTTAGCTGCGTT
1 TTTTACAAAGCGCCGCTAATGCTAC-GGTCTTTAGCGGCGTT
* * *
63119091 TCTTAAAAAGCACCGCTAA
1 TTTTACAAAGCGCCGCTAA
63119110 AAACCGCAGC
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
40 32 0.16
41 161 0.81
42 5 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (41 bp):
TTTTACAAAGCGCCGCTAATGCTACGGTCTTTAGCGGCGTT
Found at i:63119125 original size:41 final size:41
Alignment explanation
Indices: 63119080--63119173 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
63119070 GCTCAAGTCT
* * *
63119080 TTAGCTGCGTTTCTTA-AAAAGCACCGCTAAAAACCGCAGCA
1 TTAGCGGCGTTTATTAGAAAA-CACCGCTAAAAACCGAAGCA
** * *
63119121 TTAGCGGCGCATATTAGAAAACGCCGCTAAAGACCGAAGCA
1 TTAGCGGCGTTTATTAGAAAACACCGCTAAAAACCGAAGCA
63119162 TTAGCGGCGTTT
1 TTAGCGGCGTTT
63119174 TGTAGCTAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
41 39 0.91
42 4 0.09
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGTTTATTAGAAAACACCGCTAAAAACCGAAGCA
Found at i:63119146 original size:122 final size:123
Alignment explanation
Indices: 63118897--63119150 Score: 280
Period size: 122 Copynumber: 2.1 Consensus size: 123
63118887 TTATAATATG
* * *
63118897 CGCCGCTAATGCTACGGTCTTTAGCGGCGTTTTTTACAAAGCGCCGCTGATTCTACGGTCTTTAG
1 CGCCGCTAATGCTACGGTCTTTAGCGGCGTTTTTTACAAAGCGCCGCTAATGCTACAGTCTTTAG
* * * * ** * * * ** * *
63118962 CGGCGTTTTTTACAAAGCGCCGCTGATGCTACGGTCTTTAGCGGCGTTTTTTACAAAG
66 CGGCGTTTCTTAAAAAGCACCGCTAAAACCACAGTCATTAGCGGCGCATATTACAAAA
* *
63119020 CGCCGCTAATGCTATGGTCTTTAGCGGCGTTTTTTACAAAGTG-CGCTAATGCT-CAAGTCTTTA
1 CGCCGCTAATGCTACGGTCTTTAGCGGCGTTTTTTACAAAGCGCCGCTAATGCTAC-AGTCTTTA
* * *
63119083 GCTGCGTTTCTTAAAAAGCACCGCTAAAAACCGCAG-CATTAGCGGCGCATATTAGAAAA
65 GCGGCGTTTCTTAAAAAGCACCGCT-AAAACCACAGTCATTAGCGGCGCATATTACAAAA
63119142 CGCCGCTAA
1 CGCCGCTAA
63119151 AGACCGAAGC
Statistics
Matches: 108, Mismatches: 21, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
121 1 0.01
122 62 0.57
123 45 0.42
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (123 bp):
CGCCGCTAATGCTACGGTCTTTAGCGGCGTTTTTTACAAAGCGCCGCTAATGCTACAGTCTTTAG
CGGCGTTTCTTAAAAAGCACCGCTAAAACCACAGTCATTAGCGGCGCATATTACAAAA
Found at i:63123068 original size:95 final size:95
Alignment explanation
Indices: 63122926--63123234 Score: 361
Period size: 109 Copynumber: 3.1 Consensus size: 95
63122916 TACATACATT
*
63122926 ACATAACTTATTAATATATATATATATTTTTTAAAATGATACGTAACTTACATAACTTATTAATA
1 ACATAACTTATT-A-ATATATATATA--TTTTAAAATGATACATAACTTACATAACTTATTAATA
63122991 CATAACATTTTTAATACATAACTTATATAATACG
62 CATAACATTTTTAATACATAACTTATATAATACG
*
63123025 ACATAACTTATTAATATATATATATTTTAAAGTGATACATAACTTACATAACTTATTAATACATA
1 ACATAACTTATTAATATATATATATTTTAAAATGATACATAACTTACATAACTTATTAATACATA
* *
63123090 AC-TTATATAATACATAACTTATATAATACATAACTT
66 ACATT-TTTAATACATAAC-T-TAT-ATA-AT-AC-G
* *
63123126 ACATAA-TACAACATAACTTATTAATATATATATTTTAAAATGATACATAACTTACATAACTTAT
1 ACATAACT--TA-TTAA--TA-T-A--TATATATTTTAAAATGATACATAACTTACATAACTTAT
*
63123190 TAATACATAACATTTTTAATACATAACTTACATAATACG
57 TAATACATAACATTTTTAATACATAACTTATATAATACG
63123229 ACATAA
1 ACATAA
63123235 TAACATAAAT
Statistics
Matches: 183, Mismatches: 10, Indels: 30
0.82 0.04 0.13
Matches are distributed among these distances:
94 2 0.01
95 53 0.29
96 1 0.01
97 14 0.08
98 4 0.02
99 14 0.08
100 3 0.02
101 6 0.03
102 1 0.01
103 9 0.05
104 2 0.01
105 4 0.02
106 4 0.02
107 3 0.02
108 1 0.01
109 60 0.33
110 2 0.01
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (95 bp):
ACATAACTTATTAATATATATATATTTTAAAATGATACATAACTTACATAACTTATTAATACATA
ACATTTTTAATACATAACTTATATAATACG
Found at i:63123074 original size:9 final size:9
Alignment explanation
Indices: 63123060--63123131 Score: 68
Period size: 9 Copynumber: 8.8 Consensus size: 9
63123050 TTTAAAGTGA
63123060 TACATAACT
1 TACATAACT
63123069 TACATAACT
1 TACATAACT
*
63123078 TA-TTAA--
1 TACATAACT
63123084 TACATAACT
1 TACATAACT
*
63123093 TATATAA--
1 TACATAACT
63123100 TACATAACT
1 TACATAACT
*
63123109 TATATAA--
1 TACATAACT
63123116 TACATAACT
1 TACATAACT
63123125 TACATAA
1 TACATAA
63123132 TACAACATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
6 2 0.04
7 15 0.30
8 3 0.06
9 30 0.60
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (9 bp):
TACATAACT
Found at i:63123210 original size:109 final size:110
Alignment explanation
Indices: 63122974--63123227 Score: 397
Period size: 109 Copynumber: 2.3 Consensus size: 110
63122964 ATACGTAACT
* * * *
63122974 TACATAACTTATTAATACATAACATT-TTTAATACATAACTTATATAATACGACATAACTTATTA
1 TACATAACTTTTTAATACATAAC-TTATATAATACATAACTTACATAATACAACATAACTTATTA
*
63123038 ATATATATATATTTTAAAGTGATACATAACTTACATAACTTATTAA
65 ATATATATATATTTTAAAATGATACATAACTTACATAACTTATTAA
*
63123084 TACATAACTTATATAATACATAACTTATATAATACATAACTTACATAATACAACATAACTTATT-
1 TACATAACTT-TTTAATACATAACTTATATAATACATAACTTACATAATACAACATAACTTATTA
63123148 A-ATATATATATTTTAAAATGATACATAACTTACATAACTTATTAA
65 ATATATATATATTTTAAAATGATACATAACTTACATAACTTATTAA
*
63123193 TACATAACATTTTTAATACATAACTTACATAATAC
1 TACATAAC-TTTTTAATACATAACTTATATAATAC
63123228 GACATAATAA
Statistics
Matches: 133, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
109 73 0.55
110 15 0.11
111 45 0.34
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.39
Consensus pattern (110 bp):
TACATAACTTTTTAATACATAACTTATATAATACATAACTTACATAATACAACATAACTTATTAA
TATATATATATTTTAAAATGATACATAACTTACATAACTTATTAA
Found at i:63123227 original size:16 final size:15
Alignment explanation
Indices: 63122974--63123219 Score: 131
Period size: 16 Copynumber: 15.7 Consensus size: 15
63122964 ATACGTAACT
63122974 TACATAACTTATTAA
1 TACATAACTTATTAA
*
63122989 TACATAACATTTTTAA
1 TACATAAC-TTATTAA
63123005 TACATAACTTATATAA
1 TACATAACTTAT-TAA
63123021 TACGACATAACTTATTAA
1 T---ACATAACTTATTAA
* *
63123039 TATATATA-TATTTTAA
1 TACATA-ACT-TATTAA
*
63123055 -A-GTGATAC--A-TAA
1 TACAT-A-ACTTATTAA
63123067 CTTACATAACTTATTAA
1 --TACATAACTTATTAA
63123084 TACATAACTTATATAA
1 TACATAACTTAT-TAA
63123100 TACATAACTTATATAA
1 TACATAACTTAT-TAA
*
63123116 TACATAACTTACATAA
1 TACATAACTTA-TTAA
63123132 TACAACATAACTTATTAA
1 T---ACATAACTTATTAA
*
63123150 TATATATA-TT-TTAA
1 TACATA-ACTTATTAA
63123164 -A-ATGATAC--A-TAA
1 TACAT-A-ACTTATTAA
63123176 CTTACATAACTTATTAA
1 --TACATAACTTATTAA
*
63123193 TACATAACATTTTTAA
1 TACATAAC-TTATTAA
63123209 TACATAACTTA
1 TACATAACTTA
63123220 CATAATACGA
Statistics
Matches: 186, Mismatches: 12, Indels: 66
0.70 0.05 0.25
Matches are distributed among these distances:
12 8 0.04
13 4 0.02
14 9 0.05
15 52 0.28
16 78 0.42
17 6 0.03
18 8 0.04
19 21 0.11
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.39
Consensus pattern (15 bp):
TACATAACTTATTAA
Found at i:63128819 original size:21 final size:21
Alignment explanation
Indices: 63128804--63128843 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
63128794 AGCAGATGTG
63128804 GCAGCGAGAGAAGCAGAGGCA
1 GCAGCGAGAGAAGCAGAGGCA
* *
63128825 GCAGTGAGAGAAGCTGAGG
1 GCAGCGAGAGAAGCAGAGG
63128844 TTCAACGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.45, T:0.05
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGCA
Found at i:63128837 original size:87 final size:87
Alignment explanation
Indices: 63128743--63128910 Score: 250
Period size: 87 Copynumber: 1.9 Consensus size: 87
63128733 AGGCAACATC
*
63128743 GAGAGAAGCTGAGGTT-AAAAAAAGATATGAAAAACTCCAGCTA-CAACTTAAAGCAGATGTGGC
1 GAGAGAAGCTGAGGTTCAAAAAAAG-TATGAAAAACTCCAGC-AGCAACTTAAAGCAGATGAGGC
*
63128806 AGCGAGAGAAGCAGAGGCAGCAGT
64 AGCGAGAGAAACAGAGGCAGCAGT
** * *
63128830 GAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTTAAAGCAGATGAGGCAG
1 GAGAGAAGCTGAGGTTCAAAAAAAGTATGAAAAACTCCAGCAGCAACTTAAAGCAGATGAGGCAG
63128895 CGAGAGAAACAGAGGC
66 CGAGAGAAACAGAGGC
63128911 TGCAACGAGG
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
86 1 0.01
87 66 0.90
88 6 0.08
ACGTcount: A:0.41, C:0.16, G:0.30, T:0.12
Consensus pattern (87 bp):
GAGAGAAGCTGAGGTTCAAAAAAAGTATGAAAAACTCCAGCAGCAACTTAAAGCAGATGAGGCAG
CGAGAGAAACAGAGGCAGCAGT
Found at i:63128919 original size:21 final size:21
Alignment explanation
Indices: 63128895--63128949 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
63128885 GATGAGGCAG
* *
63128895 CGAGAGAAACAGAGGCTGCAA
1 CGAGGGAAGCAGAGGCTGCAA
* *
63128916 CGAGGGAAGTAGAGGCTGCAG
1 CGAGGGAAGCAGAGGCTGCAA
63128937 CGAGGGAAGCAGA
1 CGAGGGAAGCAGA
63128950 ACAGCTTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.42, T:0.05
Consensus pattern (21 bp):
CGAGGGAAGCAGAGGCTGCAA
Found at i:63128951 original size:87 final size:87
Alignment explanation
Indices: 63128732--63128924 Score: 194
Period size: 87 Copynumber: 2.2 Consensus size: 87
63128722 ACTTAAAGCG
* * * * * *
63128732 GAGGCAACATCGAGAGAAGCTGAGGT-TAA-AAAAAGATATGAAAAACTCCAGCTACAACTTAAA
1 GAGGCAGCAACGAGAGAAGCTGAGGTGCAACGAAAGGA-A-GAAGAACTCCAGCTACAACTTAAA
* *
63128795 GCAGATGTGGCAGCGAGAGAAGCA
64 GCAGATGAGGCAGCGAGAGAAACA
** * * * *
63128819 GAGGCAGCAGTGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGC-AGCAGCTTAAAG
1 GAGGCAGCAACGAGAGAAGCTGAGGTGCAACGAAAGGAAGAAGAACTCCAGCTA-CAACTTAAAG
63128883 CAGATGAGGCAGCGAGAGAAACA
65 CAGATGAGGCAGCGAGAGAAACA
* *
63128906 GAGGCTGCAACGAGGGAAG
1 GAGGCAGCAACGAGAGAAG
63128925 TAGAGGCTGC
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
86 1 0.01
87 80 0.92
88 2 0.02
89 4 0.05
ACGTcount: A:0.40, C:0.17, G:0.31, T:0.12
Consensus pattern (87 bp):
GAGGCAGCAACGAGAGAAGCTGAGGTGCAACGAAAGGAAGAAGAACTCCAGCTACAACTTAAAGC
AGATGAGGCAGCGAGAGAAACA
Found at i:63129323 original size:43 final size:43
Alignment explanation
Indices: 63129262--63129555 Score: 373
Period size: 43 Copynumber: 6.8 Consensus size: 43
63129252 GTTTTTCTAA
* *
63129262 AAGCGCCGCTAAAAACCATGAG-CTTTAGCGGCGTTTG-T-GGT
1 AAGCGCCGCTAAAGACCATG-GTCTATAGCGGCGTTTGATGGGT
* * *
63129303 GAAGGCGCCGCTAAAGACCATGGTTTATAGCGGCGTTT-TTCACGGT
1 -AA-GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGAT--GGGT
** * * *
63129349 AAGCGCCGCTAAAGGTCATTGTCTTTCGCGGCGTTT-ATTGGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGA-TGGGT
*
63129392 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGGT
*
63129435 AAGCGCCGCTAAAGACCATGGTCTATAGCGACGTTTGATGGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGGT
*
63129478 AAGCGCCACTAAAGACCATGGTCTATAGCGGCGTTTGATGGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGGT
*
63129521 AAGCGCCGCTAAAGACCATGGTCTATAGCAGCGTT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTT
63129556 GTAAAGAAAA
Statistics
Matches: 221, Mismatches: 23, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
42 3 0.01
43 184 0.83
44 28 0.13
45 3 0.01
46 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (43 bp):
AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGGT
Found at i:63129611 original size:129 final size:129
Alignment explanation
Indices: 63129349--63129620 Score: 298
Period size: 129 Copynumber: 2.1 Consensus size: 129
63129339 TTTTCACGGT
* ** * * *
63129349 AAGCGCCGCTAAAGGTCATTGTCTTTCGCGGCGTTTATTGGGTAAGCGCCGCTAAAGACCATGGT
1 AAGCGCCACTAAAGACCATGGTCTATAGCGGCGTTTATTGGGTAAGCGCCGCTAAAGACCATGGT
* *** * * * * ***
63129414 CTATAGCGGCGTTTGTTGGGTAAGCGCCGCTAAAGACCATGGTCTATAGCGACGTTTGATGGGT
66 CTATAGCAGCGTTTGTAAAGAAAACGCCGCTAAAGACCATGATCTATAGCGACATTTGATGAAA
63129478 AAGCGCCACTAAAGACCATGGTCTATAGCGGCGTTTGA-TGGGTAAGCGCCGCTAAAGACCATGG
1 AAGCGCCACTAAAGACCATGGTCTATAGCGGCGTTT-ATTGGGTAAGCGCCGCTAAAGACCATGG
** * * *
63129542 TCTATAGCAGCG-TTGTAAAGAAAACGCCGCTAAAGGTCTTGATCTTTAGCGGCATTTAGTAT-A
65 TCTATAGCAGCGTTTGTAAAGAAAACGCCGCTAAAGACCATGATCTATAGCGACATTT-G-ATGA
63129605 AA
128 AA
63129607 AAGCGCCACTAAAG
1 AAGCGCCACTAAAG
63129621 TTACCGACGC
Statistics
Matches: 118, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
128 33 0.28
129 82 0.69
130 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (129 bp):
AAGCGCCACTAAAGACCATGGTCTATAGCGGCGTTTATTGGGTAAGCGCCGCTAAAGACCATGGT
CTATAGCAGCGTTTGTAAAGAAAACGCCGCTAAAGACCATGATCTATAGCGACATTTGATGAAA
Found at i:63133517 original size:43 final size:41
Alignment explanation
Indices: 63133420--63133536 Score: 110
Period size: 43 Copynumber: 2.8 Consensus size: 41
63133410 AAGTCATGTT
* * * *
63133420 TTTAGCGGCGTTTGTAA-ATAAGTGCCGCTAAAAGTAATTT
1 TTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAAGTAAATC
* * * *
63133460 TTATAGCGGTGTTTGTAATAGAAGCGCAGCTAAAGGTCATAATC
1 TT-TAGCGGCGTTTGTAATAAAAGCGCCGCTAAAAGT-A-AATC
**
63133504 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAA
1 TTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAA
63133537 TACCATAATG
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
40 2 0.03
41 14 0.23
42 14 0.23
43 27 0.44
44 4 0.07
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAAGTAAATC
Found at i:63134008 original size:21 final size:22
Alignment explanation
Indices: 63133959--63134010 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
63133949 TTTAAATTTT
*
63133959 ATAAAAA-TATTCAAAAAGTTT
1 ATAAAAATTATTCAAAAAGTTC
63133980 A-AATAAATTATT-AAAAAGTTC
1 ATAA-AAATTATTCAAAAAGTTC
63134001 ATAAAAATTA
1 ATAAAAATTA
63134011 AAAAAAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 19 0.70
22 6 0.22
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
ATAAAAATTATTCAAAAAGTTC
Found at i:63134359 original size:19 final size:19
Alignment explanation
Indices: 63134328--63134366 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
63134318 TTATATGGAT
63134328 ATAATTATATAAAATAAAA
1 ATAATTATATAAAATAAAA
*
63134347 ATAATGTAT-TAAATTAAAA
1 ATAAT-TATATAAAATAAAA
63134366 A
1 A
63134367 GTTGGTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAATTATATAAAATAAAA
Found at i:63141550 original size:22 final size:23
Alignment explanation
Indices: 63141507--63141551 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
63141497 TCTCACCGTG
63141507 GGATGAAAATTAACTTTTTTTAAA
1 GGATGAAAATTAAC-TTTTTTAAA
*
63141531 GGATTAAAATTAA-TTTTTTAA
1 GGATGAAAATTAACTTTTTTAA
63141552 TAAAAATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
24 12 0.60
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.44
Consensus pattern (23 bp):
GGATGAAAATTAACTTTTTTAAA
Found at i:63141612 original size:24 final size:24
Alignment explanation
Indices: 63141580--63141628 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
63141570 AAGTTATAAG
63141580 AGAATTTTCTACTCAATGTGGGAT
1 AGAATTTTCTACTCAATGTGGGAT
63141604 AGAATTTTCTACTCAATGTGGGAT
1 AGAATTTTCTACTCAATGTGGGAT
63141628 A
1 A
63141629 AAAATTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (24 bp):
AGAATTTTCTACTCAATGTGGGAT
Found at i:63142565 original size:21 final size:22
Alignment explanation
Indices: 63142524--63142575 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
63142514 TATAAATTAT
*
63142524 TAATATATTT-ATGAATCTTTA
1 TAATATTTTTAATGAATCTTTA
*
63142545 TAATATTTTTAATG-ATGTTTA
1 TAATATTTTTAATGAATCTTTA
*
63142566 TTA-ATTTTTA
1 TAATATTTTTA
63142576 TAATTATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.26
21 17 0.63
22 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (22 bp):
TAATATTTTTAATGAATCTTTA
Found at i:63142576 original size:31 final size:30
Alignment explanation
Indices: 63142511--63142584 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
63142501 TTATTTTTTA
63142511 TTTTATAA-ATTATTAATATATTTATGAAT
1 TTTTATAATATTATTAATATATTTATGAAT
* * * *
63142540 CTTTATAATATTTTTAATGATGTTTATTAAT
1 TTTTATAATATTATTAAT-ATATTTATGAAT
63142571 TTTTATAATTATTA
1 TTTTATAA-TATTA
63142585 ATTTTTTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 7 0.19
30 8 0.22
31 17 0.47
32 4 0.11
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (30 bp):
TTTTATAATATTATTAATATATTTATGAAT
Found at i:63145833 original size:13 final size:13
Alignment explanation
Indices: 63145815--63145858 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
63145805 TAAGTATTGA
63145815 AATTATATTATAT
1 AATTATATTATAT
*
63145828 AATTATATTATAC
1 AATTATATTATAT
63145841 AATTAT-TTA-AT
1 AATTATATTATAT
63145852 ATATTAT
1 A-ATTAT
63145859 TAAAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 2 0.07
12 8 0.29
13 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTATATTATAT
Found at i:63155391 original size:19 final size:19
Alignment explanation
Indices: 63155359--63155397 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
63155349 TGTTTTAAAG
* *
63155359 TAAAATAGTGTTATATTAT
1 TAAAATAATATTATATTAT
*
63155378 TAAAATAATATTATTTTAT
1 TAAAATAATATTATATTAT
63155397 T
1 T
63155398 TTAATTTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TAAAATAATATTATATTAT
Found at i:63155496 original size:159 final size:159
Alignment explanation
Indices: 63155245--63155564 Score: 640
Period size: 159 Copynumber: 2.0 Consensus size: 159
63155235 GAATTTATTA
63155245 TTGTCAACCTTTGGGTGCCACCCAAATGGTGGTGTTTGATTTTAATTAAAATCCTTGAAAAGATG
1 TTGTCAACCTTTGGGTGCCACCCAAATGGTGGTGTTTGATTTTAATTAAAATCCTTGAAAAGATG
63155310 ATAACTTATCAGGTTGGAGGTTGGTTAGGATTTTGATTTTGTTTTAAAGTAAAATAGTGTTATAT
66 ATAACTTATCAGGTTGGAGGTTGGTTAGGATTTTGATTTTGTTTTAAAGTAAAATAGTGTTATAT
63155375 TATTAAAATAATATTATTTTATTTTAATT
131 TATTAAAATAATATTATTTTATTTTAATT
63155404 TTGTCAACCTTTGGGTGCCACCCAAATGGTGGTGTTTGATTTTAATTAAAATCCTTGAAAAGATG
1 TTGTCAACCTTTGGGTGCCACCCAAATGGTGGTGTTTGATTTTAATTAAAATCCTTGAAAAGATG
63155469 ATAACTTATCAGGTTGGAGGTTGGTTAGGATTTTGATTTTGTTTTAAAGTAAAATAGTGTTATAT
66 ATAACTTATCAGGTTGGAGGTTGGTTAGGATTTTGATTTTGTTTTAAAGTAAAATAGTGTTATAT
63155534 TATTAAAATAATATTATTTTATTTTAATT
131 TATTAAAATAATATTATTTTATTTTAATT
63155563 TT
1 TT
63155565 ATTTTAATTT
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 161 1.00
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (159 bp):
TTGTCAACCTTTGGGTGCCACCCAAATGGTGGTGTTTGATTTTAATTAAAATCCTTGAAAAGATG
ATAACTTATCAGGTTGGAGGTTGGTTAGGATTTTGATTTTGTTTTAAAGTAAAATAGTGTTATAT
TATTAAAATAATATTATTTTATTTTAATT
Found at i:63155550 original size:19 final size:19
Alignment explanation
Indices: 63155518--63155556 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
63155508 TGTTTTAAAG
* *
63155518 TAAAATAGTGTTATATTAT
1 TAAAATAATATTATATTAT
*
63155537 TAAAATAATATTATTTTAT
1 TAAAATAATATTATATTAT
63155556 T
1 T
63155557 TTAATTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TAAAATAATATTATATTAT
Found at i:63155563 original size:11 final size:11
Alignment explanation
Indices: 63155549--63155575 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
63155539 AAATAATATT
63155549 ATTTTATTTTA
1 ATTTTATTTTA
63155560 ATTTTATTTTA
1 ATTTTATTTTA
63155571 ATTTT
1 ATTTT
63155576 TTCCCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTATTTTA
Found at i:63155566 original size:16 final size:17
Alignment explanation
Indices: 63155542--63155575 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
63155532 ATTATTAAAA
63155542 TAATATTATTTT-ATTT
1 TAATATTATTTTAATTT
*
63155558 TAATTTTATTTTAATTT
1 TAATATTATTTTAATTT
63155575 T
1 T
63155576 TTCCCAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TAATATTATTTTAATTT
Found at i:63156554 original size:40 final size:40
Alignment explanation
Indices: 63156508--63156583 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
63156498 GTTTGGACAA
* *
63156508 AAAACGCCGCTAAAAATCAAGCATTAGCGGTGCTTTAAAT
1 AAAACGCCGCTAAAAACCAAGCATTAGCGGCGCTTTAAAT
* *
63156548 AAAACGCCGCTAAAGACCGAGCATTAGCGGCGCTTT
1 AAAACGCCGCTAAAAACCAAGCATTAGCGGCGCTTT
63156584 CAGGAAAACG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.20
Consensus pattern (40 bp):
AAAACGCCGCTAAAAACCAAGCATTAGCGGCGCTTTAAAT
Found at i:63156592 original size:40 final size:40
Alignment explanation
Indices: 63156508--63156603 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
63156498 GTTTGGACAA
* * *
63156508 AAAACGCCGCTAAAAATCAAGCATTAGCGGTGCTTTAAAT
1 AAAACGCCGCTAAAAACCAAGCATTAGCGGCGCTTTAAAG
* * * *
63156548 AAAACGCCGCTAAAGACCGAGCATTAGCGGCGCTTTCAGG
1 AAAACGCCGCTAAAAACCAAGCATTAGCGGCGCTTTAAAG
* *
63156588 AAAACGCTGCCAAAAA
1 AAAACGCCGCTAAAAA
63156604 TAATAATTAG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.17
Consensus pattern (40 bp):
AAAACGCCGCTAAAAACCAAGCATTAGCGGCGCTTTAAAG
Found at i:63156830 original size:41 final size:41
Alignment explanation
Indices: 63156678--63156830 Score: 202
Period size: 41 Copynumber: 3.7 Consensus size: 41
63156668 GACCTTTCGG
* * **
63156678 GGCTTTTAGCGGCATTTTTTAAAAAGCG-CTGCTAATGCTTG
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCT-CTAATGCTCA
* * *
63156719 GAGC-TTTAGCGGCGTTTTAGAGAAAGCGCCGCTAATGCTCA
1 G-GCTTTTAGCGGCGTTTTTGAAAAAGCGCCTCTAATGCTCA
*
63156760 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCTTTAATGCTCA
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCTCTAATGCTCA
63156801 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCC
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCC
63156831 GCAAAAACAT
Statistics
Matches: 98, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.02
41 93 0.95
42 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (41 bp):
GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCTCTAATGCTCA
Found at i:63157307 original size:20 final size:20
Alignment explanation
Indices: 63157275--63157326 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
63157265 TGTGATTTAG
*
63157275 GGGTTAAGGGTTAGGGGTTA
1 GGGTTTAGGGTTAGGGGTTA
*
63157295 GGGATTT-GGGTTAGGGTTTA
1 GGG-TTTAGGGTTAGGGGTTA
63157315 GGGTTTAGGGTT
1 GGGTTTAGGGTT
63157327 TAGATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 23 0.82
21 2 0.07
ACGTcount: A:0.15, C:0.00, G:0.48, T:0.37
Consensus pattern (20 bp):
GGGTTTAGGGTTAGGGGTTA
Found at i:63157324 original size:14 final size:14
Alignment explanation
Indices: 63157270--63157329 Score: 63
Period size: 13 Copynumber: 4.4 Consensus size: 14
63157260 AGGGTTGTGA
*
63157270 TTTAGGGGTTAAGGG
1 TTTA-GGGTTTAGGG
*
63157285 -TTAGGGGTTAGGG
1 TTTAGGGTTTAGGG
63157298 ATTT-GGG-TTAGGG
1 -TTTAGGGTTTAGGG
63157311 TTTAGGGTTTAGGG
1 TTTAGGGTTTAGGG
63157325 TTTAG
1 TTTAG
63157330 ATTAATTAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 3 0.08
13 17 0.44
14 17 0.44
15 2 0.05
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (14 bp):
TTTAGGGTTTAGGG
Found at i:63157327 original size:7 final size:7
Alignment explanation
Indices: 63157270--63157329 Score: 63
Period size: 7 Copynumber: 8.7 Consensus size: 7
63157260 AGGGTTGTGA
63157270 TTTAGGGG
1 TTTA-GGG
*
63157278 TTAAGGG
1 TTTAGGG
63157285 -TTAGGG
1 TTTAGGG
*
63157291 GTTAGGG
1 TTTAGGG
63157298 ATTT-GGG
1 -TTTAGGG
63157305 -TTAGGG
1 TTTAGGG
63157311 TTTAGGG
1 TTTAGGG
63157318 TTTAGGG
1 TTTAGGG
63157325 TTTAG
1 TTTAG
63157330 ATTAATTAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
5 2 0.04
6 8 0.18
7 30 0.67
8 5 0.11
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (7 bp):
TTTAGGG
Found at i:63157391 original size:7 final size:7
Alignment explanation
Indices: 63157368--63157440 Score: 83
Period size: 7 Copynumber: 10.4 Consensus size: 7
63157358 TAAATAAGGT
63157368 TTAGGGG
1 TTAGGGG
**
63157375 TTAGTAG
1 TTAGGGG
*
63157382 TTACGGG
1 TTAGGGG
63157389 TTAGGGG
1 TTAGGGG
*
63157396 TTTGGGG
1 TTAGGGG
*
63157403 TTAGAGG
1 TTAGGGG
*
63157410 TTTGGGG
1 TTAGGGG
63157417 TTAGGGG
1 TTAGGGG
63157424 TTAGGGG
1 TTAGGGG
*
63157431 TTAGAGG
1 TTAGGGG
63157438 TTA
1 TTA
63157441 AGAGTTAGTG
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 53 1.00
ACGTcount: A:0.16, C:0.01, G:0.48, T:0.34
Consensus pattern (7 bp):
TTAGGGG
Found at i:63157447 original size:28 final size:28
Alignment explanation
Indices: 63157368--63157448 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
63157358 TAAATAAGGT
*
63157368 TTAGGGGTTAGTA-GTTACGGGTTAGGGG
1 TTAGGGGTTAG-AGGTTAAGGGTTAGGGG
* **
63157396 TTTGGGGTTAGAGGTTTGGGGTTAGGGG
1 TTAGGGGTTAGAGGTTAAGGGTTAGGGG
*
63157424 TTAGGGGTTAGAGGTTAAGAGTTAG
1 TTAGGGGTTAGAGGTTAAGGGTTAG
63157449 TGATTTAAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 1 0.02
28 44 0.98
ACGTcount: A:0.19, C:0.01, G:0.47, T:0.33
Consensus pattern (28 bp):
TTAGGGGTTAGAGGTTAAGGGTTAGGGG
Found at i:63157463 original size:15 final size:15
Alignment explanation
Indices: 63157445--63157474 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
63157435 AGGTTAAGAG
*
63157445 TTAGTGATTTAAGGT
1 TTAGAGATTTAAGGT
63157460 TTAGAGATTTAAGGT
1 TTAGAGATTTAAGGT
63157475 CAGATTAGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (15 bp):
TTAGAGATTTAAGGT
Found at i:63158070 original size:27 final size:27
Alignment explanation
Indices: 63158038--63158094 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
63158028 TTACATGTTG
63158038 AAATTAATTAAGGGAATGTAAACAAGA
1 AAATTAATTAAGGGAATGTAAACAAGA
63158065 AAATTAATTAAGGGAATGTAAACAAGA
1 AAATTAATTAAGGGAATGTAAACAAGA
63158092 AAA
1 AAA
63158095 AAGAATGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.58, C:0.04, G:0.18, T:0.21
Consensus pattern (27 bp):
AAATTAATTAAGGGAATGTAAACAAGA
Found at i:63164393 original size:5 final size:5
Alignment explanation
Indices: 63164383--63164409 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
63164373 AAAACCAATC
63164383 AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AA
63164410 AAATAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:63165104 original size:25 final size:24
Alignment explanation
Indices: 63165076--63165125 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
63165066 TTTTAATAAT
* *
63165076 AATAATAAATTAGATAAAAAATTTA
1 AATAACAAATTA-AAAAAAAATTTA
*
63165101 AATACCAAATTAAAAAAAAATTTA
1 AATAACAAATTAAAAAAAAATTTA
63165125 A
1 A
63165126 TATCATTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (24 bp):
AATAACAAATTAAAAAAAAATTTA
Found at i:63180304 original size:21 final size:21
Alignment explanation
Indices: 63180256--63180298 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
63180246 CTTTAAAGAT
63180256 ATATATTTTTTATATTTTTAG
1 ATATATTTTTTATATTTTTAG
63180277 ATATATTTTTTA-ATTTTATAG
1 ATATATTTTTTATATTTT-TAG
63180298 A
1 A
63180299 ATTATTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (21 bp):
ATATATTTTTTATATTTTTAG
Found at i:63180752 original size:21 final size:21
Alignment explanation
Indices: 63180722--63180770 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
63180712 ATAAATGTGT
*
63180722 TAAAATTATTAATTAAAAATAA
1 TAAAAATATT-ATTAAAAATAA
* *
63180744 -AAAAATATTTTTTAAAATAA
1 TAAAAATATTATTAAAAATAA
63180764 TAAAAAT
1 TAAAAAT
63180771 GTGTTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAAATATTATTAAAAATAA
Found at i:63181185 original size:2 final size:2
Alignment explanation
Indices: 63181178--63181216 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
63181168 TACCCTTTAA
63181178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
63181217 TTTAATTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:63188639 original size:16 final size:16
Alignment explanation
Indices: 63188618--63188656 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
63188608 TTTTAATAAA
63188618 ATTAAAACTAATTATT
1 ATTAAAACTAATTATT
* *
63188634 ATTAAAATTAATTGTT
1 ATTAAAACTAATTATT
*
63188650 AGTAAAA
1 ATTAAAA
63188657 TATCAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTAAAACTAATTATT
Found at i:63188642 original size:22 final size:23
Alignment explanation
Indices: 63188589--63188644 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
63188579 CCCGTTTTTA
* *
63188589 ATTAAAATTAAAATTATATTTTT
1 ATTAAAATTAAAACTATATTATT
*
63188612 AATAAAATTAAAACTA-ATTATT
1 ATTAAAATTAAAACTATATTATT
63188634 ATTAAAATTAA
1 ATTAAAATTAA
63188645 TTGTTAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTATT
Found at i:63188932 original size:2 final size:2
Alignment explanation
Indices: 63188925--63188953 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
63188915 ATTGTATTTA
63188925 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
63188954 ACTTTTTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63201589 original size:21 final size:22
Alignment explanation
Indices: 63201552--63201592 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
63201542 GAACATGTTG
63201552 AATTTTAATTAATTTTATATCA
1 AATTTTAATTAATTTTATATCA
*
63201574 AATTTTGATT-ATTTTATAT
1 AATTTTAATTAATTTTATAT
63201593 AGATTTACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
AATTTTAATTAATTTTATATCA
Found at i:63201741 original size:22 final size:22
Alignment explanation
Indices: 63201715--63201759 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
63201705 ATTATGTGTA
*
63201715 TTAATTCATAATATAA-TTAATT
1 TTAATTCA-AATACAATTTAATT
*
63201737 TTAATTTAAATACAATTTAATT
1 TTAATTCAAATACAATTTAATT
63201759 T
1 T
63201760 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAATTCAAATACAATTTAATT
Found at i:63208656 original size:26 final size:25
Alignment explanation
Indices: 63208608--63208656 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
63208598 TGTTTTGGAA
**
63208608 TGAATATTATAATGAAATTGAAATT
1 TGAATATTATAATGAAAGGGAAATT
*
63208633 TGAATCATTATACTGAAAGGGAAA
1 TGAAT-ATTATAATGAAAGGGAAA
63208657 GAGAGGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (25 bp):
TGAATATTATAATGAAAGGGAAATT
Found at i:63209819 original size:18 final size:18
Alignment explanation
Indices: 63209778--63209828 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
63209768 CATGACAAAC
63209778 ATAAATAATTAAAAATAA
1 ATAAATAATTAAAAATAA
* * *
63209796 AAAAATATTTAAAAATAT
1 ATAAATAATTAAAAATAA
63209814 ATAAATTAA-TAAAAA
1 ATAAA-TAATTAAAAA
63209829 AGTATAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAATAATTAAAAATAA
Found at i:63211541 original size:3 final size:3
Alignment explanation
Indices: 63211533--63211563 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
63211523 TGAATGTGGT
*
63211533 GTA GTA GTA GTA GTA GTA GTA CTA GTA GTA G
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA G
63211564 AGTCTAGCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.32
Consensus pattern (3 bp):
GTA
Found at i:63229573 original size:17 final size:16
Alignment explanation
Indices: 63229539--63229569 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63229529 TTTCAAATAT
63229539 ATCGTTATAAGTTTTA
1 ATCGTTATAAGTTTTA
*
63229555 ATCGTTATAAATTTT
1 ATCGTTATAAGTTTT
63229570 TAATTAGCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (16 bp):
ATCGTTATAAGTTTTA
Found at i:63233696 original size:45 final size:45
Alignment explanation
Indices: 63233599--63233724 Score: 112
Period size: 45 Copynumber: 2.8 Consensus size: 45
63233589 TGACGGAAAC
* * ** *
63233599 GAGTAAGACCATAGCCTAAAAACGTTATGGTAA-CATGATGAAAAT
1 GAGTAAGACCATAGCCGAAAGACACTATGG-AATCATGATAAAAAT
* *
63233644 AACTAAGACCATAGCCGAAAGACACTATGGAATCATGA-AAAAAGT
1 GAGTAAGACCATAGCCGAAAGACACTATGGAATCATGATAAAAA-T
* ** * *
63233689 GAGTAAGACCATGGTTGAAAGACACAATGGTATCAT
1 GAGTAAGACCATAGCCGAAAGACACTATGGAATCAT
63233725 TGTAAATAGG
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
44 6 0.09
45 59 0.91
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (45 bp):
GAGTAAGACCATAGCCGAAAGACACTATGGAATCATGATAAAAAT
Found at i:63233741 original size:45 final size:45
Alignment explanation
Indices: 63233645--63233753 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 45
63233635 GATGAAAATA
*
63233645 ACTAAGACCATAGCCGAAAGACACTATGGAATCATGAAAAAAGTG
1 ACTAAGACCATAGCCGAAAGACACAATGGAATCATGAAAAAAGTG
* * ** * * *
63233690 AGTAAGACCATGGTTGAAAGACACAATGGTATCATTGTAAATAG-G
1 ACTAAGACCATAGCCGAAAGACACAATGGAATCA-TGAAAAAAGTG
* *
63233735 ACTAAGATCATAGCTGAAA
1 ACTAAGACCATAGCCGAAA
63233754 TACGCTACGA
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
45 44 0.86
46 7 0.14
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (45 bp):
ACTAAGACCATAGCCGAAAGACACAATGGAATCATGAAAAAAGTG
Found at i:63239687 original size:33 final size:33
Alignment explanation
Indices: 63239650--63239726 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
63239640 TGATCTTATA
63239650 ACACCAACCATTAAGCATCAAAGTGCCAAAAGC
1 ACACCAACCATTAAGCATCAAAGTGCCAAAAGC
*
63239683 ACACCAACCATTAAGCATTAAAGTGCCAAAAGC
1 ACACCAACCATTAAGCATCAAAGTGCCAAAAGC
*
63239716 ACACTAACCAT
1 ACACCAACCAT
63239727 CAAGGAATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.45, C:0.30, G:0.10, T:0.14
Consensus pattern (33 bp):
ACACCAACCATTAAGCATCAAAGTGCCAAAAGC
Found at i:63241017 original size:29 final size:29
Alignment explanation
Indices: 63240975--63241175 Score: 122
Period size: 29 Copynumber: 6.9 Consensus size: 29
63240965 GTGTGCTAAA
*
63240975 CGATGGTC-ATAACCGTCCCTTTTCATATT
1 CGATGGTCGA-AACCATCCCTTTTCATATT
63241004 CGATGGTCGAAACCATCCCTTTTCATTAGTT
1 CGATGGTCGAAACCATCCCTTTTCA-TA-TT
** *
63241035 -GATGGTCGTCACCATCCCTTTTCATAAT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * * *
63241063 CGATAG-CCAAAGCTATCCCTTTTCATAAT
1 CGATGGTCGAAA-CCATCCCTTTTCATATT
* * * * *
63241092 CTATAGCCGAAGCTATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * * * * * *
63241121 CAATAGCCGGAGCTATCCCTTTTCATAAT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * *
63241150 CGATAGAC-AAAGCTATCCCTTTTCAT
1 CGATGGTCGAAA-CCATCCCTTTTCAT
63241176 TGGTTGATGA
Statistics
Matches: 145, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
28 4 0.03
29 111 0.77
30 28 0.19
31 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.34
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCCTTTTCATATT
Found at i:63241041 original size:30 final size:30
Alignment explanation
Indices: 63240975--63241059 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
63240965 GTGTGCTAAA
*
63240975 CGATGGTC-ATAACCGTCCCTTTTCA-TATT
1 CGATGGTCGA-AACCATCCCTTTTCATTATT
63241004 CGATGGTCGAAACCATCCCTTTTCATTAGTT
1 CGATGGTCGAAACCATCCCTTTTCATTA-TT
**
63241035 -GATGGTCGTCACCATCCCTTTTCAT
1 CGATGGTCGAAACCATCCCTTTTCAT
63241060 AATCGATAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
29 22 0.44
30 26 0.52
31 2 0.04
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.36
Consensus pattern (30 bp):
CGATGGTCGAAACCATCCCTTTTCATTATT
Found at i:63241081 original size:59 final size:59
Alignment explanation
Indices: 63240976--63241088 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
63240966 TGTGCTAAAC
* * * *
63240976 GATGGTCATAACCGTCCCTTTTCATATTCGATGGTCGAAACCATCCCTTTTCATTAGTT
1 GATGGTCATAACCATCCCTTTTCATAATCGATAGTCCAAACCATCCCTTTTCATTAGTT
* * *
63241035 GATGGTCGTCACCATCCCTTTTCATAATCGATAG-CCAAAGCTATCCCTTTTCAT
1 GATGGTCATAACCATCCCTTTTCATAATCGATAGTCCAAA-CCATCCCTTTTCAT
63241089 AATCTATAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
58 4 0.09
59 42 0.91
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.35
Consensus pattern (59 bp):
GATGGTCATAACCATCCCTTTTCATAATCGATAGTCCAAACCATCCCTTTTCATTAGTT
Found at i:63241127 original size:58 final size:58
Alignment explanation
Indices: 63241048--63241175 Score: 193
Period size: 58 Copynumber: 2.2 Consensus size: 58
63241038 GGTCGTCACC
* * * *
63241048 ATCCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATCTATAGCCGAAGCT
1 ATCCCTTTTCATAATCAATAGCCAAAGCTATCCCTTTTCATAATCGATAGACAAAGCT
* **
63241106 ATCCCTTTTCATATTCAATAGCCGGAGCTATCCCTTTTCATAATCGATAGACAAAGCT
1 ATCCCTTTTCATAATCAATAGCCAAAGCTATCCCTTTTCATAATCGATAGACAAAGCT
63241164 ATCCCTTTTCAT
1 ATCCCTTTTCAT
63241176 TGGTTGATGA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 63 1.00
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.34
Consensus pattern (58 bp):
ATCCCTTTTCATAATCAATAGCCAAAGCTATCCCTTTTCATAATCGATAGACAAAGCT
Found at i:63241685 original size:18 final size:18
Alignment explanation
Indices: 63241662--63241699 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
63241652 AAAAATCACT
63241662 TAACAA-AATACTTTTAAA
1 TAACAACAATA-TTTTAAA
63241680 TAACAACTAATATTTTAAA
1 TAACAAC-AATATTTTAAA
63241699 T
1 T
63241700 TCATAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (18 bp):
TAACAACAATATTTTAAA
Found at i:63249067 original size:23 final size:23
Alignment explanation
Indices: 63249035--63249078 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
63249025 ACTACCATTT
63249035 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
63249058 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
63249079 ATAATTTTTA
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:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:63249071 original size:13 final size:11
Alignment explanation
Indices: 63249039--63249081 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
63249029 CCATTTTCTA
*
63249039 AATAAAATAAT
1 AATAAAATATT
63249050 AAT-AAATATCT
1 AATAAAATAT-T
63249061 AAGTAAAATATT
1 AA-TAAAATATT
63249073 AATAAAATA
1 AATAAAATA
63249082 ATTTTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:63249599 original size:13 final size:13
Alignment explanation
Indices: 63249583--63249608 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63249573 TTTTCTCATT
63249583 CAATTTTGATTCC
1 CAATTTTGATTCC
63249596 CAATTTTGATTCC
1 CAATTTTGATTCC
63249609 TTTGATTTCC
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:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
CAATTTTGATTCC
Found at i:63261294 original size:2 final size:2
Alignment explanation
Indices: 63261287--63261386 Score: 173
Period size: 2 Copynumber: 50.0 Consensus size: 2
63261277 CTGTTCAACA
63261287 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * *
63261329 AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG GG GG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
63261371 AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG
63261387 GGTGTAAATG
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:63262740 original size:26 final size:26
Alignment explanation
Indices: 63262704--63262755 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
63262694 ATAATTGATC
63262704 AACTCAGTAGCAAAAGTCATTCTTAA
1 AACTCAGTAGCAAAAGTCATTCTTAA
63262730 AACTCAGTAGCAAAAGTCATTCTTAA
1 AACTCAGTAGCAAAAGTCATTCTTAA
63262756 TAAGTGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (26 bp):
AACTCAGTAGCAAAAGTCATTCTTAA
Found at i:63265077 original size:14 final size:14
Alignment explanation
Indices: 63265044--63265085 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
63265034 AATGTGTCTT
*
63265044 TTTAATGTT-TATA
1 TTTAATATTATATA
63265057 TTATAATATTATATA
1 TT-TAATATTATATA
*
63265072 TTTAATTTTATATA
1 TTTAATATTATATA
63265086 AATTACATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.08
14 17 0.68
15 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTTAATATTATATA
Found at i:63276896 original size:129 final size:130
Alignment explanation
Indices: 63276687--63276938 Score: 389
Period size: 129 Copynumber: 1.9 Consensus size: 130
63276677 ATTAATTCCG
* * * *
63276687 GAGGTAATCCTTGTCCAACTCCAACACTAATAAAAAAATACACGCTGAGGGGCATTTTGGGCAAA
1 GAGGTAATCCTTGTCCAACTCCAACACCAATAAAAAAATACACACTGAAGGCCATTTTGGGCAAA
63276752 ATTTTTGGGTTGTAATCAGAACAAAAAGCCTTCTTTTGGTTGAGAGAAAGAAAAAATTGAATGTA
66 ATTTTTGGGTTGTAATCAGAACAAAAAGCCTTCTTTTGGTTGAGAGAAAGAAAAAATTGAATGTA
* * * *
63276817 GAGGTAGTTCTTGTCCAACTCCAACACCACT-AAAAAATACACACTGAAGGCCATTTTGGGCACA
1 GAGGTAATCCTTGTCCAACTCCAACACCAATAAAAAAATACACACTGAAGGCCATTTTGGGCAAA
* * * *
63276881 ATTTTTGGGTTGTAATTAGAATAAAAAGGCTTCTTTTGGTTGAGAGAAAGAGAAAATT
66 ATTTTTGGGTTGTAATCAGAACAAAAAGCCTTCTTTTGGTTGAGAGAAAGAAAAAATT
63276939 ACTTTAGATT
Statistics
Matches: 110, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
129 83 0.75
130 27 0.25
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (130 bp):
GAGGTAATCCTTGTCCAACTCCAACACCAATAAAAAAATACACACTGAAGGCCATTTTGGGCAAA
ATTTTTGGGTTGTAATCAGAACAAAAAGCCTTCTTTTGGTTGAGAGAAAGAAAAAATTGAATGTA
Found at i:63279245 original size:14 final size:14
Alignment explanation
Indices: 63279226--63279254 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
63279216 AAAAAATCCC
63279226 TTTTTAGATCATTG
1 TTTTTAGATCATTG
63279240 TTTTTAGATCATTG
1 TTTTTAGATCATTG
63279254 T
1 T
63279255 GGACTACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (14 bp):
TTTTTAGATCATTG
Found at i:63283914 original size:5 final size:5
Alignment explanation
Indices: 63283915--63283940 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
63283905 AATATAATAT
63283915 TAAAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA T
63283941 TTTTTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:63283974 original size:46 final size:46
Alignment explanation
Indices: 63283922--63284011 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
63283912 TATTAAAATA
63283922 AAATAAAATAAAATAAAATTT-TTTATTTATTAAGTGATAAGTAATT
1 AAATAAAAT-AAATAAAATTTGTTTATTTATTAAGTGATAAGTAATT
** * *
63283968 AAATAAAATAAATTGAATTTGTTTTTTTATTAAGTGATACGTAA
1 AAATAAAATAAATAAAATTTGTTTATTTATTAAGTGATAAGTAA
63284012 CTTTTATCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 9 0.23
46 30 0.77
ACGTcount: A:0.48, C:0.01, G:0.09, T:0.42
Consensus pattern (46 bp):
AAATAAAATAAATAAAATTTGTTTATTTATTAAGTGATAAGTAATT
Found at i:63288936 original size:21 final size:22
Alignment explanation
Indices: 63288910--63288953 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
63288900 TACTTTCATG
*
63288910 TTATTTTTATTA-TTACAAAAT
1 TTATTTTTATTATTTAAAAAAT
63288931 TTATTTTTATTATTTAAAAAAT
1 TTATTTTTATTATTTAAAAAAT
63288953 T
1 T
63288954 GAAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATTTTTATTATTTAAAAAAT
Found at i:63290544 original size:6 final size:6
Alignment explanation
Indices: 63290524--63290617 Score: 84
Period size: 6 Copynumber: 15.2 Consensus size: 6
63290514 CAATCACTGA
63290524 TTTA-T TTTAGTT TTTAGTTT TTTATT TTTATT TTTATT TTTATT TTTATT
1 TTTATT TTTA-TT TTTA--TT TTTATT TTTATT TTTATT TTTATT TTTATT
* * * * *
63290574 TTTAGT TGTACT TTTA-T TTTATT GTTAGTT TTTTTAT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT TTTA-TT TTTAT-T TTTATT T
63290618 GTGAGACTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
5 9 0.12
6 45 0.61
7 14 0.19
8 6 0.08
ACGTcount: A:0.16, C:0.01, G:0.06, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:63290628 original size:21 final size:21
Alignment explanation
Indices: 63290585--63290638 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
63290575 TTAGTTGTAC
* **
63290585 TTTTATTTTA-TTGTTAGTTT
1 TTTTATTTTATTTGTGAGACT
63290605 TTTTATTTTATTTGTGAGACT
1 TTTTATTTTATTTGTGAGACT
*
63290626 TTTTGTTTTATTT
1 TTTTATTTTATTT
63290639 TAATTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.15, C:0.02, G:0.11, T:0.72
Consensus pattern (21 bp):
TTTTATTTTATTTGTGAGACT
Found at i:63297325 original size:21 final size:21
Alignment explanation
Indices: 63297299--63297345 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
63297289 ATCAAGAAAG
*
63297299 AAAGAGCTTGAAAGAA-AAGAA
1 AAAGAGATTG-AAGAACAAGAA
*
63297320 AAAGAGATTGAAGAACACGAA
1 AAAGAGATTGAAGAACAAGAA
63297341 AAAGA
1 AAAGA
63297346 AAAAGAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.62, C:0.06, G:0.23, T:0.09
Consensus pattern (21 bp):
AAAGAGATTGAAGAACAAGAA
Found at i:63297349 original size:6 final size:6
Alignment explanation
Indices: 63297338--63297377 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
63297328 TGAAGAACAC
**
63297338 GAAAAA GAAAAA GAAAGT GAGAAAA GAAAAA GAAAAA GAA
1 GAAAAA GAAAAA GAAAAA GA-AAAA GAAAAA GAAAAA GAA
63297378 TTTGAGAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:63297372 original size:25 final size:25
Alignment explanation
Indices: 63297309--63297386 Score: 95
Period size: 25 Copynumber: 3.1 Consensus size: 25
63297299 AAAGAGCTTG
*
63297309 AAAG-AAAAGAAAAAGAGATTGAAGA
1 AAAGAAAAAGAAAAAGAAATTG-AGA
* *
63297334 ACACGAAAAAGAAAAAGAAAGTGAGA
1 A-AAGAAAAAGAAAAAGAAATTGAGA
*
63297360 AAAGAAAAAGAAAAAGAATTTGAGA
1 AAAGAAAAAGAAAAAGAAATTGAGA
63297385 AA
1 AA
63297387 GTGGAAGGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 24 0.53
26 6 0.13
27 15 0.33
ACGTcount: A:0.68, C:0.03, G:0.22, T:0.08
Consensus pattern (25 bp):
AAAGAAAAAGAAAAAGAAATTGAGA
Found at i:63305320 original size:17 final size:19
Alignment explanation
Indices: 63305298--63305332 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
63305288 CTAAAATAGT
63305298 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
63305315 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
63305333 TTCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:63305368 original size:22 final size:22
Alignment explanation
Indices: 63305343--63305387 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
63305333 TTCAAATAAT
63305343 AACAACAAAATAGTGAG-AAAAC
1 AACAACAAAATAGT-AGTAAAAC
*
63305365 AACAAGAAAATAGTAGTAAAAC
1 AACAACAAAATAGTAGTAAAAC
63305387 A
1 A
63305388 GTAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.64, C:0.11, G:0.13, T:0.11
Consensus pattern (22 bp):
AACAACAAAATAGTAGTAAAAC
Found at i:63305396 original size:22 final size:22
Alignment explanation
Indices: 63305343--63305401 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
63305333 TTCAAATAAT
*
63305343 AACAACAAAATAGTGAGAAAAC
1 AACAAAAAAATAGTGAGAAAAC
*
63305365 AACAAGAAAATAGT-AGTAAAAC
1 AACAAAAAAATAGTGAG-AAAAC
*
63305387 AGTAAAAAAAAATAG
1 A--ACAAAAAAATAG
63305402 CAAGAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 2 0.06
22 19 0.61
24 10 0.32
ACGTcount: A:0.66, C:0.08, G:0.14, T:0.12
Consensus pattern (22 bp):
AACAAAAAAATAGTGAGAAAAC
Found at i:63306707 original size:16 final size:17
Alignment explanation
Indices: 63306665--63306707 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
63306655 TATTTATGGG
*
63306665 AAATTAACTCTCAAGAA
1 AAATTAAATCTCAAGAA
*
63306682 AAAGTTAAATTTCAAG-A
1 AAA-TTAAATCTCAAGAA
63306699 AAATTAAAT
1 AAATTAAAT
63306708 AAAATTTAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 7 0.30
18 10 0.43
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (17 bp):
AAATTAAATCTCAAGAA
Found at i:63307729 original size:29 final size:29
Alignment explanation
Indices: 63307685--63307763 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 29
63307675 AATGATAAAA
63307685 AATAAAAATCAATAAAAAAT-TATTAAATTTT
1 AATAAAAAT--ATAAAAAATAT-TTAAATTTT
63307716 AATAAAAATATAAAAAATATTTAAATTTT
1 AATAAAAATATAAAAAATATTTAAATTTT
* *
63307745 ATTTAAAAATTTTAAAAAA
1 A-ATAAAAA-TATAAAAAA
63307764 GTTTAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 19 0.44
30 7 0.16
31 17 0.40
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (29 bp):
AATAAAAATATAAAAAATATTTAAATTTT
Found at i:63308072 original size:19 final size:19
Alignment explanation
Indices: 63308044--63308117 Score: 112
Period size: 19 Copynumber: 3.9 Consensus size: 19
63308034 ATTTTATATT
*
63308044 TTTTATGATTTTTATAAAA
1 TTTTACGATTTTTATAAAA
63308063 TTTTACGATTTTTATAAAA
1 TTTTACGATTTTTATAAAA
* * *
63308082 TTTTACAATTTTTATATAT
1 TTTTACGATTTTTATAAAA
63308101 TTTTACGATTTTTATAA
1 TTTTACGATTTTTATAA
63308118 TTTTTTTCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTTACGATTTTTATAAAA
Found at i:63308093 original size:38 final size:39
Alignment explanation
Indices: 63308051--63308143 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 39
63308041 ATTTTTTATG
63308051 ATTTTTATAAAATTTTACGATTTTTATAAAATTTTAC-A
1 ATTTTTATAAAATTTTACGATTTTTATAAAATTTTACTA
* * ** *
63308089 ATTTTTATATATTTTTACGATTTTTATAATTTTTTTCTA
1 ATTTTTATAAAATTTTACGATTTTTATAAAATTTTACTA
63308128 ATTTTTAATAAAATTT
1 ATTTTT-ATAAAATTT
63308144 ATTATTTATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
38 32 0.70
39 7 0.15
40 7 0.15
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.59
Consensus pattern (39 bp):
ATTTTTATAAAATTTTACGATTTTTATAAAATTTTACTA
Found at i:63308122 original size:19 final size:19
Alignment explanation
Indices: 63308035--63308123 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
63308025 CTTTGATGCA
*
63308035 TTTTAT-ATTTTTTATGAT
1 TTTTATAATTTTTTACGAT
**
63308053 TTTTATAAAATTTTACGAT
1 TTTTATAATTTTTTACGAT
** *
63308072 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTACGAT
63308091 TTTTAT-ATATTTTTACGAT
1 TTTTATAAT-TTTTTACGAT
63308110 TTTTATAATTTTTT
1 TTTTATAATTTTTT
63308124 TCTAATTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
18 7 0.11
19 52 0.85
20 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTTACGAT
Found at i:63308194 original size:9 final size:9
Alignment explanation
Indices: 63308035--63308122 Score: 68
Period size: 9 Copynumber: 9.4 Consensus size: 9
63308025 CTTTGATGCA
*
63308035 TTTTATATT
1 TTTTATAAT
*
63308044 TTTTATGAT
1 TTTTATAAT
*
63308053 TTTTATAAAA
1 TTTTAT-AAT
**
63308063 TTTTACGAT
1 TTTTATAAT
*
63308072 TTTTATAAAA
1 TTTTAT-AAT
*
63308082 TTTTACAAT
1 TTTTATAAT
63308091 TTTTATATAT
1 TTTTATA-AT
**
63308101 TTTTACGAT
1 TTTTATAAT
63308110 TTTTATAAT
1 TTTTATAAT
63308119 TTTT
1 TTTT
63308123 TTCTAATTTT
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
9 40 0.68
10 19 0.32
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:63310748 original size:41 final size:40
Alignment explanation
Indices: 63310642--63310748 Score: 103
Period size: 37 Copynumber: 2.7 Consensus size: 40
63310632 AGATAATTCG
* ** *
63310642 AAGTAATAATTTGACATCCAGTGTCTCATCGGCTAAATTG
1 AAGTAATAATTTGACACCCAGTGTCTCATCGAATAAATTA
** * *
63310682 AAG---TAATTTGGTACCCAGTGCCTCATCGAATATATCTA
1 AAGTAATAATTTGACACCCAGTGTCTCATCGAATAAAT-TA
*
63310720 AAGTAATAATTTGACACCCAGTATCTCAT
1 AAGTAATAATTTGACACCCAGTGTCTCAT
63310749 TGACTCGAAG
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
37 25 0.49
38 4 0.08
40 3 0.06
41 19 0.37
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (40 bp):
AAGTAATAATTTGACACCCAGTGTCTCATCGAATAAATTA
Found at i:63310901 original size:11 final size:11
Alignment explanation
Indices: 63310885--63310909 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
63310875 TTCAATTCAA
63310885 ATAATCAATAT
1 ATAATCAATAT
63310896 ATAATCAATAT
1 ATAATCAATAT
63310907 ATA
1 ATA
63310910 TACCAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATCAATAT
Found at i:63310934 original size:15 final size:16
Alignment explanation
Indices: 63310860--63310936 Score: 58
Period size: 15 Copynumber: 5.0 Consensus size: 16
63310850 CAAATACAAC
*
63310860 CAATATTCAATTCAATT
1 CAATATACAATTCAA-T
*
63310877 CAAT-T-CAAAT-AAT
1 CAATATACAATTCAAT
*
63310890 CAATATATAA-TCAAT
1 CAATATACAATTCAAT
63310905 -ATATATACCAATTCAAT
1 CA-ATATA-CAATTCAAT
63310922 CAATATA-AATTCAAT
1 CAATATACAATTCAAT
63310937 AAATTCATCA
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 22 0.44
16 3 0.06
17 14 0.28
18 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (16 bp):
CAATATACAATTCAAT
Found at i:63310959 original size:24 final size:24
Alignment explanation
Indices: 63310914--63310960 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
63310904 TATATATACC
63310914 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
63310938 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
63310961 TCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:63312660 original size:21 final size:21
Alignment explanation
Indices: 63312636--63312675 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
63312626 ATTATATACT
63312636 ATTTTGATAAT-TTTTTAAATA
1 ATTTT-ATAATATTTTTAAATA
*
63312657 ATTTTATTATATTTTTAAA
1 ATTTTATAATATTTTTAAA
63312676 AATCCTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
ATTTTATAATATTTTTAAATA
Found at i:63312755 original size:29 final size:29
Alignment explanation
Indices: 63312723--63312781 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
63312713 TTAATGATTA
*
63312723 TTATTATTTAT-ATAAATTTAAATATTTTT
1 TTATCATTTATAATAAATTTAAA-ATTTTT
* *
63312752 TTATCATTTTTAATAAATTTATAATTTTT
1 TTATCATTTATAATAAATTTAAAATTTTT
63312781 T
1 T
63312782 CAACAATTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (29 bp):
TTATCATTTATAATAAATTTAAAATTTTT
Found at i:63312770 original size:30 final size:31
Alignment explanation
Indices: 63312720--63312781 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
63312710 TTATTAATGA
*
63312720 TTATTATTATTTATATAAATTTAAATATTTTT
1 TTATCATTATTTATATAAATTTAAA-ATTTTT
*
63312752 TTATCATT-TTTA-ATAAATTTATAATTTTT
1 TTATCATTATTTATATAAATTTAAAATTTTT
63312781 T
1 T
63312782 CAACAATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 7 0.25
30 10 0.36
31 4 0.14
32 7 0.25
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (31 bp):
TTATCATTATTTATATAAATTTAAAATTTTT
Found at i:63313420 original size:27 final size:27
Alignment explanation
Indices: 63313390--63313442 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
63313380 AATACTAATA
63313390 TAAAATATAAAATTTTTAT-TATTTTTT
1 TAAAATAT-AAATTTTTATATATTTTTT
* **
63313417 TAAATTATTTATTTTTATATATTTTT
1 TAAAATATAAATTTTTATATATTTTT
63313443 AAATTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TAAAATATAAATTTTTATATATTTTTT
Found at i:63313456 original size:27 final size:25
Alignment explanation
Indices: 63313401--63313453 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
63313391 AAAATATAAA
* *
63313401 ATTTTTATTATTTTTTTAAATTATTT
1 ATTTTTA-TATATTTTTAAATTATAT
*
63313427 ATTTTTATATATTTTTAAATTTTAT
1 ATTTTTATATATTTTTAAATTATAT
63313452 AT
1 AT
63313454 ATTATTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (25 bp):
ATTTTTATATATTTTTAAATTATAT
Found at i:63313461 original size:27 final size:25
Alignment explanation
Indices: 63313404--63313463 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 25
63313394 ATATAAAATT
63313404 TTTATTATT-TTTTTAAATTATTTA
1 TTTATTATTATTTTTAAATTATTTA
63313428 TTT-TTATATATTTTTAAA-T-TTTA
1 TTTATTAT-TATTTTTAAATTATTTA
*
63313451 TATATTATTATTT
1 TTTATTATTATTT
63313464 ATTGCCAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
23 15 0.47
24 9 0.28
25 8 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTATTATTATTTTTAAATTATTTA
Found at i:63318128 original size:22 final size:22
Alignment explanation
Indices: 63318098--63318175 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
63318088 TTAAGGAAAG
*
63318098 GAACCGTATTGTAGAATACTGC
1 GAACTGTATTGTAGAATACTGC
* *
63318120 GAACTGTATGTTTA-AA-AATGTC
1 GAACTGTAT-TGTAGAATACTG-C
*
63318142 GCAAACTGTATTGTAGAATACTAC
1 G--AACTGTATTGTAGAATACTGC
63318166 GAACTGTATT
1 GAACTGTATT
63318176 CCTCGTAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
21 3 0.07
22 21 0.48
23 6 0.14
24 12 0.27
25 2 0.05
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (22 bp):
GAACTGTATTGTAGAATACTGC
Found at i:63318263 original size:39 final size:39
Alignment explanation
Indices: 63318201--63318283 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
63318191 TTTGCGATCA
* * *
63318201 TAAATCAGCGAACCATGAGAAAGCTAAAGGTCGTGATAG
1 TAAATCAGCGAACCATAAGAAAGCCAAAGGTCATGATAG
* * *
63318240 TAAATCAGCGAACCGTAATAAAGCCAAAGGTCATGATCG
1 TAAATCAGCGAACCATAAGAAAGCCAAAGGTCATGATAG
63318279 TAAAT
1 TAAAT
63318284 TAGTGAACTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (39 bp):
TAAATCAGCGAACCATAAGAAAGCCAAAGGTCATGATAG
Found at i:63318393 original size:93 final size:93
Alignment explanation
Indices: 63318226--63318830 Score: 424
Period size: 93 Copynumber: 6.2 Consensus size: 93
63318216 TGAGAAAGCT
* * * *
63318226 AAAGGTCGTGATAGTAAATCAGCGAACCGTAATAAAGCCAAAGGTCATGATCGTAAATTAGT-GA
1 AAAGGTCGTGATCGTAAATCAACGGACCGTAATAAAGCCAAAGGTCATGATCGTAAATCAGTAG-
* * *
63318290 ACTGCGAGATTCATTAAATCCCGTAAGTA
65 ACCGCGAGATTCGTAAAATCCCGTAAGTA
* * *
63318319 AAAGGTCGTGATTGTAAATCAACGGATCGTAAGAAAGCCAAAGGTCATGATCGTAAATCAGTAGA
1 AAAGGTCGTGATCGTAAATCAACGGACCGTAATAAAGCCAAAGGTCATGATCGTAAATCAGTAGA
*
63318384 CCGCAAGATTCGTAAAATCCCGTAAGTA
66 CCGCGAGATTCGTAAAATCCCGTAAGTA
* ** *
63318412 AAAGGTCGTGATCGTAAATCAACGGACCGTAATAAAGCTAAAGGTTGTGATCGTAAATCAGCAGA
1 AAAGGTCGTGATCGTAAATCAACGGACCGTAATAAAGCCAAAGGTCATGATCGTAAATCAGTAGA
* *
63318477 CCACGAGATTCGTAAAATCCCATAAGTA
66 CCGCGAGATTCGTAAAATCCCGTAAGTA
* * **
63318505 AAAGGTCGTGATCATAAATCAGCTAACGCGAGATTCGTAAAATCCAATAAGTAAAAGGTCATGAT
1 AAAGGTCGTGATCGTAAAT---C-AA--CG-GA-CCGT--AAT---A-AAGCCAAAGGTCATGAT
* ** * *
63318570 CATAAATCAACAGACCGCGAGATTCATAAAATCTCGTAAGTA
52 CGTAAATCAGTAGACCGCGAGATTCGTAAAATCCCGTAAGTA
* * * * * *
63318612 AAAGGTTGTGATCATAAATCAGA-AGACCGCGAGATTCATTAAATCCCATAA-GTAAAAGGTTGT
1 AAAGGTCGTGATCGTAAATCA-ACGGA-C-C--G--T-AATAAA-GCCA-AAGGT--CA---TG-
* * * ** * *
63318675 AATCTTAAATTAGCGGACTGCGAGATTTGTAAAATCCCGTAAGTA
50 AT-CGTAAATCAGTAGACCGCGAGATTCGTAAAATCCCGTAAGTA
** * * * * *
63318720 AAACATCGTGATCGTAAATCAGCGGACCGTAAGAAAGCCAAATGTCGTGATCGTAAATCAGCAGA
1 AAAGGTCGTGATCGTAAATCAACGGACCGTAATAAAGCCAAAGGTCATGATCGTAAATCAGTAGA
** * **
63318785 CCATGAGATTCGTAAAATTCTATAAGTA
66 CCGCGAGATTCGTAAAATCCCGTAAGTA
* *
63318813 AAAGGTCTTAATCGTAAA
1 AAAGGTCGTGATCGTAAA
63318831 AAAGTCAAAG
Statistics
Matches: 403, Mismatches: 77, Indels: 64
0.74 0.14 0.12
Matches are distributed among these distances:
93 228 0.57
94 2 0.00
95 2 0.00
96 1 0.00
97 2 0.00
99 4 0.01
100 11 0.03
101 12 0.03
102 3 0.01
103 6 0.01
104 5 0.01
105 1 0.00
106 4 0.01
107 69 0.17
108 53 0.13
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.23
Consensus pattern (93 bp):
AAAGGTCGTGATCGTAAATCAACGGACCGTAATAAAGCCAAAGGTCATGATCGTAAATCAGTAGA
CCGCGAGATTCGTAAAATCCCGTAAGTA
Found at i:63318510 original size:54 final size:54
Alignment explanation
Indices: 63318451--63318748 Score: 348
Period size: 54 Copynumber: 5.5 Consensus size: 54
63318441 TAATAAAGCT
* * *
63318451 AAAGGTTGTGATCGTAAATCAGCAGACCACGAGATTCGTAAAATCCCATAAGTA
1 AAAGGTCGTGATCATAAATCAGCAGACCGCGAGATTCGTAAAATCCCATAAGTA
*
63318505 AAAGGTCGTGATCATAAATCAGCTA-A-CGCGAGATTCGTAAAATCCAATAAGTA
1 AAAGGTCGTGATCATAAATCAGC-AGACCGCGAGATTCGTAAAATCCCATAAGTA
* * * * *
63318558 AAAGGTCATGATCATAAATCAACAGACCGCGAGATTCATAAAATCTCGTAAGTA
1 AAAGGTCGTGATCATAAATCAGCAGACCGCGAGATTCGTAAAATCCCATAAGTA
* * * *
63318612 AAAGGTTGTGATCATAAATCAGAAGACCGCGAGATTCATTAAATCCCATAAGTA
1 AAAGGTCGTGATCATAAATCAGCAGACCGCGAGATTCGTAAAATCCCATAAGTA
* * * * * * * *
63318666 AAAGGTTGTAATCTTAAATTAGCGGACTGCGAGATTTGTAAAATCCCGTAAGTA
1 AAAGGTCGTGATCATAAATCAGCAGACCGCGAGATTCGTAAAATCCCATAAGTA
** * *
63318720 AAACATCGTGATCGTAAATCAGCGGACCG
1 AAAGGTCGTGATCATAAATCAGCAGACCG
63318749 TAAGAAAGCC
Statistics
Matches: 207, Mismatches: 34, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
52 1 0.00
53 47 0.23
54 158 0.76
55 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.23
Consensus pattern (54 bp):
AAAGGTCGTGATCATAAATCAGCAGACCGCGAGATTCGTAAAATCCCATAAGTA
Found at i:63318847 original size:78 final size:78
Alignment explanation
Indices: 63318747--63318908 Score: 200
Period size: 78 Copynumber: 2.1 Consensus size: 78
63318737 ATCAGCGGAC
* * * *
63318747 CGTAAGAAAGCCAAATGTCGTGA-TCGTAAATCAGCAGACCATGAGATTCGTAAAATTCTATAAG
1 CGTAAAAAAGCCAAAGGTCGTGACT-GTAAATCAGCAGACCATGAGATTCGTAAAATCCCATAAG
*
63318811 TAAAAGGTCTTAAT
65 TAAAAGGTCGTAAT
* ** * * * *
63318825 CGTAAAAAAGTCAAAGGTCGTGACTGTAAATCAGTGGATCGTGAGATTTGTAAAATCCCGTAAGT
1 CGTAAAAAAGCCAAAGGTCGTGACTGTAAATCAGCAGACCATGAGATTCGTAAAATCCCATAAGT
63318890 AAAAGGTCGTAAT
66 AAAAGGTCGTAAT
63318903 CGTAAA
1 CGTAAA
63318909 TCAACAGACC
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 70 0.99
79 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (78 bp):
CGTAAAAAAGCCAAAGGTCGTGACTGTAAATCAGCAGACCATGAGATTCGTAAAATCCCATAAGT
AAAAGGTCGTAAT
Found at i:63319028 original size:54 final size:54
Alignment explanation
Indices: 63318941--63319066 Score: 153
Period size: 54 Copynumber: 2.3 Consensus size: 54
63318931 AAAGTAGTCA
* *
63318941 TGATCATAAATCAGCGGACCATGAAATTCGTAAAATCCCATATGTAAAAAATCG
1 TGATCATAAATCAACGGACCACGAAATTCGTAAAATCCCATATGTAAAAAATCG
* * * * * ** *
63318995 TGATCGTAAATCAACGGGCCACGAGATTTGTAAAATCCCATTTGTAAAAGGTTG
1 TGATCATAAATCAACGGACCACGAAATTCGTAAAATCCCATATGTAAAAAATCG
*
63319049 TGACCATAAATCAACGGA
1 TGATCATAAATCAACGGA
63319067 TGGTAAGAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (54 bp):
TGATCATAAATCAACGGACCACGAAATTCGTAAAATCCCATATGTAAAAAATCG
Found at i:63319142 original size:42 final size:42
Alignment explanation
Indices: 63319088--63319234 Score: 138
Period size: 42 Copynumber: 3.5 Consensus size: 42
63319078 CAGAAGGTCA
* * *
63319088 TGATTGTAAATTAGTGGACCATAAGAAAGTCAAATGTGGTTG
1 TGATCGTAAATTAGCGGACCATAAGAAAGCCAAATGTGGTTG
* ** * * *
63319130 TGGTCGTAAATTAGCAAACCATAA-AAAACCGAAGGTGGTCT-
1 TGATCGTAAATTAGCGGACCATAAGAAAGCCAAATGTGGT-TG
* *
63319171 TGATCATAAATTAGCGGACCATAAGAAAGCCGAAAT-TAGTTG
1 TGATCGTAAATTAGCGGACCATAAGAAAGCC-AAATGTGGTTG
**
63319213 TGATCGTAAATTAAAGGACCAT
1 TGATCGTAAATTAGCGGACCAT
63319235 GAGATTCATA
Statistics
Matches: 81, Mismatches: 20, Indels: 8
0.74 0.18 0.07
Matches are distributed among these distances:
41 32 0.40
42 47 0.58
43 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (42 bp):
TGATCGTAAATTAGCGGACCATAAGAAAGCCAAATGTGGTTG
Found at i:63319411 original size:54 final size:54
Alignment explanation
Indices: 63319352--63319481 Score: 179
Period size: 54 Copynumber: 2.4 Consensus size: 54
63319342 TAAGAAAGCC
* * * * *
63319352 AAAGGTTGTGACCGTAAATCAACAAACTGCGAGATTCGTAAAATCCCGTAAGTA
1 AAAGGTCGTGATCGTAAATCAACAAACCGCGAGATCCATAAAATCCCGTAAGTA
* * *
63319406 AAAGGTCGTGATCGTAAATCAACGAACCGTGAGATCCATAAAATCTCGTAAGTA
1 AAAGGTCGTGATCGTAAATCAACAAACCGCGAGATCCATAAAATCCCGTAAGTA
*
63319460 AAAGGTCATGATCGTAAATCAA
1 AAAGGTCGTGATCGTAAATCAA
63319482 TGGGCCATAA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (54 bp):
AAAGGTCGTGATCGTAAATCAACAAACCGCGAGATCCATAAAATCCCGTAAGTA
Found at i:63319493 original size:147 final size:147
Alignment explanation
Indices: 63319235--63319501 Score: 333
Period size: 147 Copynumber: 1.8 Consensus size: 147
63319225 AAAGGACCAT
* * * **
63319235 GAGATTCATAAAATCTCATATGTAAAAGGCCATGATCGTAAATCAACAGACTGCGAGATTTATAA
1 GAGATTCATAAAATCCCATAAGTAAAAGGCCATGATCGTAAATCAACAGACCGCGAGATCCATAA
* * *
63319300 AATCCTGTAAGTAAAAGGTCGTGATAATAAATCAGTGAATAGTAAGAAAGCCAAAGGTTGTGACC
66 AATCCTGTAAGTAAAAGGTCATGATAATAAATCAATGAACAGTAAGAAAGCCAAAGGTTGTGACC
63319365 GTAAATCAACAAACTGC
131 GTAAATCAACAAACTGC
* * * * *
63319382 GAGATTCGTAAAATCCCGTAAGTAAAAGGTCGTGATCGTAAATCAAC-GAACCGTGAGATCCATA
1 GAGATTCATAAAATCCCATAAGTAAAAGGCCATGATCGTAAATCAACAG-ACCGCGAGATCCATA
** **
63319446 AAAT-CTCGTAAGTAAAAGGTCATGATCGTAAATCAATGGGCCA-TAAGAAAGCCAAA
65 AAATCCT-GTAAGTAAAAGGTCATGATAATAAATCAAT-GAACAGTAAGAAAGCCAAA
63319502 AGTAGTTTTG
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
146 3 0.03
147 95 0.95
148 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (147 bp):
GAGATTCATAAAATCCCATAAGTAAAAGGCCATGATCGTAAATCAACAGACCGCGAGATCCATAA
AATCCTGTAAGTAAAAGGTCATGATAATAAATCAATGAACAGTAAGAAAGCCAAAGGTTGTGACC
GTAAATCAACAAACTGC
Found at i:63319632 original size:39 final size:40
Alignment explanation
Indices: 63319584--63319697 Score: 124
Period size: 42 Copynumber: 2.8 Consensus size: 40
63319574 TCAGTAGACG
*
63319584 TAAGAAAGCCGAA-AGTCGTGATCATAAATT-AGCAAACCA
1 TAAGAAAGCCGAAGAGTCATGATCATAAATTGA-CAAACCA
* *
63319623 TAAGAAAGCCGAAGGTGGTCATGATCGTAAATTGACAAACCA
1 TAAGAAAGCCGAA-G-AGTCATGATCATAAATTGACAAACCA
* *
63319665 TAAGAAAGCCGAAGATGGCCATGATCGTAAATT
1 TAAGAAAGCCGAAGA--GTCATGATCATAAATT
63319698 AACAGATTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
39 13 0.20
41 1 0.02
42 49 0.77
43 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (40 bp):
TAAGAAAGCCGAAGAGTCATGATCATAAATTGACAAACCA
Found at i:63319662 original size:42 final size:42
Alignment explanation
Indices: 63319602--63319821 Score: 181
Period size: 42 Copynumber: 5.2 Consensus size: 42
63319592 CCGAAAGTCG
* *
63319602 TGATCATAAATTAGCAAACCATAAGAAAGCCGAAGGTGGTCA
1 TGATCGTAAATTAACAAACCATAAGAAAGCCGAAGGTGGTCA
* * *
63319644 TGATCGTAAATTGACAAACCATAAGAAAGCCGAAGATGGCCA
1 TGATCGTAAATTAACAAACCATAAGAAAGCCGAAGGTGGTCA
* ** * * *
63319686 TGATCGTAAATTAACAGATTATACA-AAAGTCAAAGGTGGTCG
1 TGATCGTAAATTAACAAACCATA-AGAAAGCCGAAGGTGGTCA
* * * * * *
63319728 TGGTCGTAAATCAACAGACCATAAAAAAGTCGAAAGTGGTCA
1 TGATCGTAAATTAACAAACCATAAGAAAGCCGAAGGTGGTCA
* ** *** * * * *
63319770 TGATCATAAACCAATGGACCATAAGAAAGCTGAAAGTAGTCG
1 TGATCGTAAATTAACAAACCATAAGAAAGCCGAAGGTGGTCA
63319812 TGATCGTAAA
1 TGATCGTAAA
63319822 GCAGCGGACC
Statistics
Matches: 144, Mismatches: 32, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
41 1 0.01
42 142 0.99
43 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.20
Consensus pattern (42 bp):
TGATCGTAAATTAACAAACCATAAGAAAGCCGAAGGTGGTCA
Found at i:63319891 original size:54 final size:54
Alignment explanation
Indices: 63319808--63319988 Score: 254
Period size: 54 Copynumber: 3.4 Consensus size: 54
63319798 GCTGAAAGTA
* * **
63319808 GTCGTGATCGTAAAGCAGCGGACCGCGAGATTTGTAAAATCCCGTCTGTAAAAG
1 GTCGTGATCGTAAATCAACGGACCGCGAGATTTGTAAAATCCCGTAAGTAAAAG
* * *
63319862 GTCGTGATCGTAAATCAATGGACCACGAGATTTGTAAAATCCCATAAGTAAAAG
1 GTCGTGATCGTAAATCAACGGACCGCGAGATTTGTAAAATCCCGTAAGTAAAAG
* * * *
63319916 GTCGTGATCGTAAATTAGCGGACCGCGATATTCGTAAAATCCCGTAAGTAAAAG
1 GTCGTGATCGTAAATCAACGGACCGCGAGATTTGTAAAATCCCGTAAGTAAAAG
*
63319970 GTCGTGATCCTAAATCAAC
1 GTCGTGATCGTAAATCAAC
63319989 AGATCATAAG
Statistics
Matches: 110, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 110 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (54 bp):
GTCGTGATCGTAAATCAACGGACCGCGAGATTTGTAAAATCCCGTAAGTAAAAG
Found at i:63320321 original size:42 final size:42
Alignment explanation
Indices: 63320275--63320519 Score: 220
Period size: 42 Copynumber: 5.8 Consensus size: 42
63320265 AATCAGCAGA
* * * **
63320275 CCATAAAAAAGTCGAAGGTAGTAATGATCGTAAATTAATGGG
1 CCATAAGAAAGCCGAAGGTGGTCGTGATCGTAAATTAATGGG
* * * *
63320317 CCATAAGAAAGCCGAAGGTGGTCGTGATCGTAAATCAGTAGA
1 CCATAAGAAAGCCGAAGGTGGTCGTGATCGTAAATTAATGGG
* * * *
63320359 CTATAAGAAAGTCAAAGGTGGTCGTGATCATAAATTAATGGG
1 CCATAAGAAAGCCGAAGGTGGTCGTGATCGTAAATTAATGGG
* * *
63320401 CCATAAGAAAGCCGAAGGTGGTCGTGATCGTAAATCAGTGGA
1 CCATAAGAAAGCCGAAGGTGGTCGTGATCGTAAATTAATGGG
* * * * * ** * * *
63320443 CAATAAGAAAGTCAAAGGTCGTCGTGATCATAAACCAGTAGA
1 CCATAAGAAAGCCGAAGGTGGTCGTGATCGTAAATTAATGGG
* * * *
63320485 CCATAAGAAAGTCAAAAGTAGTCGTGATCGTAAAT
1 CCATAAGAAAGCCGAAGGTGGTCGTGATCGTAAAT
63320520 CAGCGGATTG
Statistics
Matches: 167, Mismatches: 36, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 167 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (42 bp):
CCATAAGAAAGCCGAAGGTGGTCGTGATCGTAAATTAATGGG
Found at i:63320377 original size:84 final size:84
Alignment explanation
Indices: 63320239--63320522 Score: 358
Period size: 84 Copynumber: 3.4 Consensus size: 84
63320229 CAGCAAACTG
* * * * * **
63320239 TAAGAAAGCCGAA---GGTCGTGATCATAAATCAGCAGACCATAAAAAAGTCGAAGGTAGTAATG
1 TAAGAAAGCCGAAGGTGGTCGTGATCGTAAATCAGTAGACAATAAGAAAGTCAAAGGTAGTCGTG
*
63320301 ATCGTAAATTAATGGGCCA
66 ATCATAAATTAATGGGCCA
* *
63320320 TAAGAAAGCCGAAGGTGGTCGTGATCGTAAATCAGTAGACTATAAGAAAGTCAAAGGTGGTCGTG
1 TAAGAAAGCCGAAGGTGGTCGTGATCGTAAATCAGTAGACAATAAGAAAGTCAAAGGTAGTCGTG
63320385 ATCATAAATTAATGGGCCA
66 ATCATAAATTAATGGGCCA
* *
63320404 TAAGAAAGCCGAAGGTGGTCGTGATCGTAAATCAGTGGACAATAAGAAAGTCAAAGGTCGTCGTG
1 TAAGAAAGCCGAAGGTGGTCGTGATCGTAAATCAGTAGACAATAAGAAAGTCAAAGGTAGTCGTG
** * * *
63320469 ATCATAAACCAGTAGACCA
66 ATCATAAATTAATGGGCCA
* * * *
63320488 TAAGAAAGTCAAAAGTAGTCGTGATCGTAAATCAG
1 TAAGAAAGCCGAAGGTGGTCGTGATCGTAAATCAG
63320523 CGGATTGCAA
Statistics
Matches: 179, Mismatches: 21, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
81 13 0.07
84 166 0.93
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (84 bp):
TAAGAAAGCCGAAGGTGGTCGTGATCGTAAATCAGTAGACAATAAGAAAGTCAAAGGTAGTCGTG
ATCATAAATTAATGGGCCA
Found at i:63320449 original size:126 final size:126
Alignment explanation
Indices: 63320252--63320521 Score: 333
Period size: 126 Copynumber: 2.1 Consensus size: 126
63320242 GAAAGCCGAA
* * * *
63320252 GGTCGTGATCATAAATCAGCAGACCATAAAAAAGTCGAAGGTAGTAATGATCGTAAATTAATGGG
1 GGTCGTGATCATAAATCAACAGACCATAAAAAAGCCGAAGGTAGTAATGATCGTAAATCAATGGA
* * * * * * *
63320317 CCATAAGAAAGCCGAAGGTGGTCGTGATCGTAAATCAGTAGACTATAAGAAAGTCAAAGGT
66 CAATAAGAAAGCCAAAGGTCGTCGTGATCATAAACCAGTAGACCATAAGAAAGTCAAAAGT
* ** * * * ** *
63320378 GGTCGTGATCATAAATTAATGGGCCATAAGAAAGCCGAAGGTGGTCGTGATCGTAAATCAGTGGA
1 GGTCGTGATCATAAATCAACAGACCATAAAAAAGCCGAAGGTAGTAATGATCGTAAATCAATGGA
*
63320443 CAATAAGAAAGTCAAAGGTCGTCGTGATCATAAACCAGTAGACCATAAGAAAGTCAAAAGT
66 CAATAAGAAAGCCAAAGGTCGTCGTGATCATAAACCAGTAGACCATAAGAAAGTCAAAAGT
* *
63320504 AGTCGTGATCGTAAATCA
1 GGTCGTGATCATAAATCA
63320522 GCGGATTGCA
Statistics
Matches: 120, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
126 120 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (126 bp):
GGTCGTGATCATAAATCAACAGACCATAAAAAAGCCGAAGGTAGTAATGATCGTAAATCAATGGA
CAATAAGAAAGCCAAAGGTCGTCGTGATCATAAACCAGTAGACCATAAGAAAGTCAAAAGT
Found at i:63320720 original size:54 final size:55
Alignment explanation
Indices: 63320662--63320782 Score: 131
Period size: 54 Copynumber: 2.2 Consensus size: 55
63320652 GTTGTGACCA
* * * * *
63320662 TAAATCAGCAGACAACG-AGATTTATAAAATCACGTAAGTAAAGGGTTGTGATTG
1 TAAATCAGCAGACAACGAAGATTCATAAAATCACATAAGTAAAAGGTCGTGATCG
* * *
63320716 TAAATCAAC-GA-ACCGTAAGATTCATAAAATCTCATAAGTAAAAGGTCGTGATCG
1 TAAATCAGCAGACAACG-AAGATTCATAAAATCACATAAGTAAAAGGTCGTGATCG
*
63320770 TAAATCAGTAGAC
1 TAAATCAGCAGAC
63320783 TATAAAAAAG
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
52 3 0.06
53 2 0.04
54 46 0.87
55 2 0.04
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (55 bp):
TAAATCAGCAGACAACGAAGATTCATAAAATCACATAAGTAAAAGGTCGTGATCG
Found at i:63323401 original size:20 final size:20
Alignment explanation
Indices: 63323378--63323419 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
63323368 AACTATTTAA
**
63323378 ATAATATTATTTGAATAATT
1 ATAATATTAAATGAATAATT
63323398 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
63323418 AT
1 AT
63323420 GTGTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:63327288 original size:24 final size:24
Alignment explanation
Indices: 63327255--63327306 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
63327245 TTTCTAGGTC
* *
63327255 AAATAAATTATGCTAATAAATACT
1 AAATAAATTATACTAATAAATACA
*
63327279 AAATATATTATACTAATAAATACA
1 AAATAAATTATACTAATAAATACA
63327303 AAAT
1 AAAT
63327307 CTTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:63345009 original size:69 final size:67
Alignment explanation
Indices: 63344887--63345018 Score: 192
Period size: 69 Copynumber: 1.9 Consensus size: 67
63344877 ATAAACAATA
* *** *
63344887 TAATGGTTTTGCCTTTTAACTTAATGGGTAAACATTTTTCAAAACGACGTAGTTTTGCCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACGACGTAGTTTTGCCTTTTAA
63344952 CT
66 CT
*
63344954 TAATGGTTTTGACTTTTAACTTTAAAAAAGTAAACATTTATCAAAACGACTTAGTTTTGCCTTTT
1 TAATGGTTTTGACTTTTAAC-TT-AAAAAGTAAACATTTATCAAAACGACGTAGTTTTGCCTTTT
63345019 CTTATTTGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 19 0.33
68 2 0.04
69 36 0.63
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACGACGTAGTTTTGCCTTTTAA
CT
Found at i:63355871 original size:26 final size:26
Alignment explanation
Indices: 63355834--63355891 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
63355824 TGTCTCTGTT
*
63355834 TGCTGTTG-GGTAGGTCGTTTAGTTTC
1 TGCT-TTGTGGTAGGTCGTTTAGCTTC
* * *
63355860 TTCTTTGTGGTAGTTTGTTTAGCTTC
1 TGCTTTGTGGTAGGTCGTTTAGCTTC
63355886 TGCTTT
1 TGCTTT
63355892 TTACTTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 3 0.12
26 23 0.88
ACGTcount: A:0.07, C:0.12, G:0.28, T:0.53
Consensus pattern (26 bp):
TGCTTTGTGGTAGGTCGTTTAGCTTC
Found at i:63359908 original size:44 final size:44
Alignment explanation
Indices: 63359882--63360118 Score: 368
Period size: 44 Copynumber: 5.4 Consensus size: 44
63359872 TTCTTATTCC
*
63359882 TAATTTAAAACACGTTAAATTATAATACAATATACATGCATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATGCATATT
63359926 TAATTTAAAACACATTAAATTATAATACAATATACATGCATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATGCATATT
* *
63359970 TAATTTAAAACACAATAAATTATAATACAATATACATACATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATGCATATT
* * * *
63360014 TGAA-TTAAAGCACATTAAATTATAATACAATAGACATACATGTT
1 T-AATTTAAAACACATTAAATTATAATACAATATACATGCATATT
* *
63360058 TATTTTAAAACACATTAAATTATAATACAATATACATACATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATGCATATT
*
63360102 TATTTTAAAACACATTA
1 TAATTTAAAACACATTA
63360119 TATATATTAA
Statistics
Matches: 180, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
43 1 0.01
44 177 0.98
45 2 0.01
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.36
Consensus pattern (44 bp):
TAATTTAAAACACATTAAATTATAATACAATATACATGCATATT
Done.