Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 178 of 322
Found at i:58354393 original size:85 final size:82
Alignment explanation
Indices: 58354292--58354459 Score: 212
Period size: 82 Copynumber: 2.0 Consensus size: 82
58354282 AAATTAAGCT
* * ** *
58354292 AGGGAAAGTAACGGAAGTTGATTATCCCTGTTTTCCCTTGAAAGTTTA-ATTTTTATTTATTTAT
1 AGGGAAAGTAACGGAAGTTAAGTATCCCT-CATT---TTGAAAGTTCATATTTTTATTTATTTAT
*
58354356 CCCAATTTGGAGGAAAAGATA
62 CCCAACTTGGAGGAAAAGATA
* * *
58354377 AGGGAAAGTAAGGGAAGTTAAGTATCCCTCATTTTGAAAGTTCATTTTTTTATTTATTTATGCCA
1 AGGGAAAGTAACGGAAGTTAAGTATCCCTCATTTTGAAAGTTCATATTTTTATTTATTTATCCCA
58354442 ACTTGGAGGAAAAGATA
66 ACTTGGAGGAAAAGATA
58354459 A
1 A
58354460 AAGAAAAGAA
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
81 10 0.14
82 35 0.48
84 2 0.03
85 26 0.36
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (82 bp):
AGGGAAAGTAACGGAAGTTAAGTATCCCTCATTTTGAAAGTTCATATTTTTATTTATTTATCCCA
ACTTGGAGGAAAAGATA
Found at i:58355465 original size:16 final size:16
Alignment explanation
Indices: 58355444--58355474 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58355434 GCTTTCCATT
*
58355444 GTTTAATAAGTTTTTA
1 GTTTAAGAAGTTTTTA
58355460 GTTTAAGAAGTTTTT
1 GTTTAAGAAGTTTTT
58355475 GTCTCCTCTT
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:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (16 bp):
GTTTAAGAAGTTTTTA
Found at i:58362931 original size:25 final size:25
Alignment explanation
Indices: 58362880--58362931 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
58362870 CTATAAACTT
* *
58362880 ATATATATTATATAATAAAACCGAC
1 ATATATAATATATAATAAAACCCAC
*
58362905 ATATATAATATAT-ATACAACCCCAC
1 ATATATAATATATAATA-AAACCCAC
58362930 AT
1 AT
58362932 GCTTATTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (25 bp):
ATATATAATATATAATAAAACCCAC
Found at i:58370300 original size:16 final size:17
Alignment explanation
Indices: 58370269--58370311 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
58370259 TTACACATAC
*
58370269 AATCATTTCAATTCAA-A
1 AATCAATTC-ATTCAATA
58370286 AATCAATTCATTCAATA
1 AATCAATTCATTCAATA
58370303 AAT-AATTCA
1 AATCAATTCA
58370312 CTTTTCCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (17 bp):
AATCAATTCATTCAATA
Found at i:58372059 original size:42 final size:43
Alignment explanation
Indices: 58372012--58372094 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 43
58372002 TTTTATATGC
* *
58372012 CACACGGCCTGGACACACGCCCATGTCC-TTGCCCGTGTGGCT
1 CACACGGCCTGGACACACACCCATGTCCTTTGCCCATGTGGCT
* *
58372054 CACACGGCTTGGGCACACACCCATGTCCTTTGCCCATGTGG
1 CACACGGCCTGGACACACACCCATGTCCTTTGCCCATGTGG
58372095 TTCTAAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 25 0.69
43 11 0.31
ACGTcount: A:0.16, C:0.39, G:0.25, T:0.20
Consensus pattern (43 bp):
CACACGGCCTGGACACACACCCATGTCCTTTGCCCATGTGGCT
Found at i:58375190 original size:85 final size:85
Alignment explanation
Indices: 58375047--58375214 Score: 318
Period size: 85 Copynumber: 2.0 Consensus size: 85
58375037 GTAATATCCA
58375047 GCGAGCCCCAGGAAGCTCCGAACTTCGGTAACATTTCTTGGAGGCTTCCAGTTAAGTATGGTTGA
1 GCGAGCCCCAGGAAGCTCCGAACTTCGGTAACATTTCTTGGAGGCTTCCAGTTAAGTATGGTTGA
*
58375112 ATTTTTGCTCGGGTCAACCG
66 AATTTTGCTCGGGTCAACCG
*
58375132 GCGAGCCCCAGGAAGCTCCGAACTTCGGTAATATTTCTTGGAGGCTTCCAGTTAAGTATGGTTGA
1 GCGAGCCCCAGGAAGCTCCGAACTTCGGTAACATTTCTTGGAGGCTTCCAGTTAAGTATGGTTGA
58375197 AATTTTGCTCGGGTCAAC
66 AATTTTGCTCGGGTCAAC
58375215 TCGAATACCC
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.29
Consensus pattern (85 bp):
GCGAGCCCCAGGAAGCTCCGAACTTCGGTAACATTTCTTGGAGGCTTCCAGTTAAGTATGGTTGA
AATTTTGCTCGGGTCAACCG
Found at i:58379423 original size:27 final size:26
Alignment explanation
Indices: 58379393--58379499 Score: 99
Period size: 28 Copynumber: 3.9 Consensus size: 26
58379383 GATTCAAAAG
* *
58379393 TATATATTAAGTCCGCACACTCAGTGC
1 TATATATCAA-TCCGCACACTTAGTGC
58379420 TATATAATCAA-CTCGCACACTTAGTGC
1 TATAT-ATCAATC-CGCACACTTAGTGC
* *
58379447 TATGTACTCAAACTCGCACACTTAGTGC
1 TATATA-TCAATC-CGCACACTTAGTGC
*
58379475 TATATAATCAAACCCGCACACTTAG
1 TATAT-ATC-AATCCGCACACTTAG
58379500 CGCCAATCTC
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
26 2 0.03
27 26 0.38
28 37 0.54
29 4 0.06
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (26 bp):
TATATATCAATCCGCACACTTAGTGC
Found at i:58379468 original size:28 final size:28
Alignment explanation
Indices: 58379406--58379499 Score: 145
Period size: 28 Copynumber: 3.4 Consensus size: 28
58379396 ATATTAAGTC
*
58379406 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
58379433 CGCACACTTAGTGCTATGTACTCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
58379461 CGCACACTTAGTGCTATATAATCAAACC
1 CGCACACTTAGTGCTATATAATCAAACT
58379489 CGCACACTTAG
1 CGCACACTTAG
58379500 CGCCAATCTC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
27 20 0.33
28 40 0.67
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:58387997 original size:27 final size:27
Alignment explanation
Indices: 58387955--58388122 Score: 205
Period size: 27 Copynumber: 6.2 Consensus size: 27
58387945 NNNNNNNNNA
*
58387955 AGGGTAAAAC-AGTAATTCTATAAATCG
1 AGGGTAAAACGA-TAATTCTGTAAATCG
*
58387982 AGGGTAAAACGATAATTCTATAAATCG
1 AGGGTAAAACGATAATTCTGTAAATCG
* * * *
58388009 AGGGTAAAACGGTAATTTTGTAAGTCA
1 AGGGTAAAACGATAATTCTGTAAATCG
*
58388036 AGGGTAAAACGATAATTATGTAAATC-
1 AGGGTAAAACGATAATTCTGTAAATCG
* *
58388062 AGGGGTAAAACGGTAATTATGTAAATCG
1 A-GGGTAAAACGATAATTCTGTAAATCG
* *
58388090 GGGGTAAAACGATAATTCTGTAAATCA
1 AGGGTAAAACGATAATTCTGTAAATCG
58388117 AGGGTA
1 AGGGTA
58388123 CTTTGGTAAT
Statistics
Matches: 124, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
26 1 0.01
27 122 0.98
28 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (27 bp):
AGGGTAAAACGATAATTCTGTAAATCG
Found at i:58388133 original size:54 final size:54
Alignment explanation
Indices: 58387954--58388122 Score: 239
Period size: 54 Copynumber: 3.1 Consensus size: 54
58387944 NNNNNNNNNN
* * * *
58387954 AAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTATAAATC
1 AAGGGTAAAACGGTAATTATGTAAATCGAGGGTAAAACGATAATTCTGTAAATC
* * * * *
58388008 GAGGGTAAAACGGTAATTTTGTAAGTCAAGGGTAAAACGATAATTATGTAAATC
1 AAGGGTAAAACGGTAATTATGTAAATCGAGGGTAAAACGATAATTCTGTAAATC
* *
58388062 AGGGGTAAAACGGTAATTATGTAAATCGGGGGTAAAACGATAATTCTGTAAATC
1 AAGGGTAAAACGGTAATTATGTAAATCGAGGGTAAAACGATAATTCTGTAAATC
58388116 AAGGGTA
1 AAGGGTA
58388123 CTTTGGTAAT
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 99 1.00
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (54 bp):
AAGGGTAAAACGGTAATTATGTAAATCGAGGGTAAAACGATAATTCTGTAAATC
Found at i:58388149 original size:27 final size:27
Alignment explanation
Indices: 58388128--58388194 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
58388118 GGGTACTTTG
*
58388128 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
*
58388155 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
*
58388182 GTATTTTTACAAA
1 GTAATTTTACAAA
58388195 CTNNNNNNNN
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (27 bp):
GTAATTTTACAAATCGAAGGTATTTCA
Found at i:58396113 original size:200 final size:200
Alignment explanation
Indices: 58395765--58396177 Score: 803
Period size: 200 Copynumber: 2.1 Consensus size: 200
58395755 CTTCATAATG
*
58395765 TCATCCTATTGCACCTTCATTTGTTACACCATTTAGAGGCATTCCACACCCATTTCATGCATTAT
1 TCATGCTATTGCACCTTCATTTGTTACACCATTTAGAGGCATTCCACACCCATTTCATGCATTAT
58395830 TAAACTTGTTACCATAACCTCAAATTGTCTACTCATGCACATAGTCATTTTAAGTCATTAGGTCA
66 TAAACTTGTTACCATAACCTCAAATTGTCTACTCATGCACATAGTCATTTTAAGTCATTAGGTCA
58395895 TCCTTTAACCTTTAGCACTTAATCCACTTTTTACCAGACATTCATCAATTAACAACATACCACAT
131 TCCTTTAACCTTTAGCACTTAATCCACTTTTTACCAGACATTCATCAATTAACAACATACCACAT
58395960 CATTA
196 CATTA
58395965 TCATGCTATTGCACCTTCATTTGTTACACCATTTAGAGGCATTCCACACCCATTTCATGCATTAT
1 TCATGCTATTGCACCTTCATTTGTTACACCATTTAGAGGCATTCCACACCCATTTCATGCATTAT
58396030 TAAACTTGTTACCATAACCTCAAATTGTCTACTCATGCACATAGTCATTTTAAGTCATTAGGTCA
66 TAAACTTGTTACCATAACCTCAAATTGTCTACTCATGCACATAGTCATTTTAAGTCATTAGGTCA
58396095 TCCTTTAACCTTTAGCACTTAATCCACTTTTTACCAGACATTCATCAATTAACAACATACCACAT
131 TCCTTTAACCTTTAGCACTTAATCCACTTTTTACCAGACATTCATCAATTAACAACATACCACAT
58396160 CATTA
196 CATTA
58396165 TCATGC-ATT-CACC
1 TCATGCTATTGCACC
58396178 AAGAAATAAC
Statistics
Matches: 212, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
198 4 0.02
199 3 0.01
200 205 0.97
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (200 bp):
TCATGCTATTGCACCTTCATTTGTTACACCATTTAGAGGCATTCCACACCCATTTCATGCATTAT
TAAACTTGTTACCATAACCTCAAATTGTCTACTCATGCACATAGTCATTTTAAGTCATTAGGTCA
TCCTTTAACCTTTAGCACTTAATCCACTTTTTACCAGACATTCATCAATTAACAACATACCACAT
CATTA
Found at i:58402984 original size:43 final size:43
Alignment explanation
Indices: 58402923--58403009 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
58402913 GTTATATGAA
* * * *
58402923 TCGCATCCATCATGAACTC-AGACCTCTCAACGAGTTCGGATGC
1 TCGCAACCATAATGAACTCGA-ACCTCTCAACGAGCTCGAATGC
*
58402966 TCGCAACCATAATGAACTCGAACCTCTCAATGAGCTCGAATGC
1 TCGCAACCATAATGAACTCGAACCTCTCAACGAGCTCGAATGC
58403009 T
1 T
58403010 ACATACCTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
43 37 0.97
44 1 0.03
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (43 bp):
TCGCAACCATAATGAACTCGAACCTCTCAACGAGCTCGAATGC
Found at i:58406157 original size:43 final size:43
Alignment explanation
Indices: 58406095--58406204 Score: 175
Period size: 43 Copynumber: 2.6 Consensus size: 43
58406085 TAAAAGTTTA
* *
58406095 TACTTCGGTTTATCAAATGATGCACTATGTATGCTAGTATATT
1 TACTTTGGTTTATCCAATGATGCACTATGTATGCTAGTATATT
*
58406138 TACTTTGGTTTATCCAATGATGCACTATGTGTGCTAGTATATT
1 TACTTTGGTTTATCCAATGATGCACTATGTATGCTAGTATATT
* *
58406181 TACTTTGGCTTATCCAATAATGCA
1 TACTTTGGTTTATCCAATGATGCA
58406205 TTGAGGTGTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.42
Consensus pattern (43 bp):
TACTTTGGTTTATCCAATGATGCACTATGTATGCTAGTATATT
Found at i:58407606 original size:17 final size:17
Alignment explanation
Indices: 58407581--58407616 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
58407571 GAATATAAGT
*
58407581 ATGCGTATAAATGAAGC
1 ATGCATATAAATGAAGC
58407598 ATGCATATAAATGAAGC
1 ATGCATATAAATGAAGC
58407615 AT
1 AT
58407617 TTGGCACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.25
Consensus pattern (17 bp):
ATGCATATAAATGAAGC
Found at i:58416958 original size:12 final size:13
Alignment explanation
Indices: 58416932--58416971 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
58416922 TTATATTTTT
*
58416932 TAAAAAATTTTATA
1 TAAAAAA-TTAATA
58416946 TAAAAAA-TAATA
1 TAAAAAATTAATA
58416958 TAAAAAATTAATA
1 TAAAAAATTAATA
58416971 T
1 T
58416972 GGGCAGGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 11 0.46
13 6 0.25
14 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAAAAATTAATA
Found at i:58417928 original size:89 final size:89
Alignment explanation
Indices: 58417812--58417974 Score: 308
Period size: 89 Copynumber: 1.8 Consensus size: 89
58417802 ATTATAGTTC
58417812 ATGAGGCTAAATGGTTAAAGTTAAAATAAACTAATTTATTTGATATTGTATATTGTGATTGGAAT
1 ATGAGGCTAAATGGTTAAAGTTAAAATAAACTAATTTATTTGATATTGTATATTGTGATTGGAAT
58417877 TGGAATTGGAATTGGTTATTTGAA
66 TGGAATTGGAATTGGTTATTTGAA
* *
58417901 ATGAGGCTAAATGGTTAAAGTTAAAATAAATTAATTTATTTGATATTGTATATTGTGATTGTAAT
1 ATGAGGCTAAATGGTTAAAGTTAAAATAAACTAATTTATTTGATATTGTATATTGTGATTGGAAT
58417966 TGGAATTGG
66 TGGAATTGG
58417975 TTATTTGAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 72 1.00
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.41
Consensus pattern (89 bp):
ATGAGGCTAAATGGTTAAAGTTAAAATAAACTAATTTATTTGATATTGTATATTGTGATTGGAAT
TGGAATTGGAATTGGTTATTTGAA
Found at i:58420959 original size:25 final size:25
Alignment explanation
Indices: 58420926--58421022 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 25
58420916 GAAGCCCTCT
*
58420926 TTCGAGCCATATAACAGGAAGCTTA
1 TTCGAGCCATATAACGGGAAGCTTA
* *
58420951 TGT-GAGCCATGTAATGGGAAGCTTA
1 T-TCGAGCCATATAACGGGAAGCTTA
* * *
58420976 TTCGGGCTATATAACGGGAAGCTCA
1 TTCGAGCCATATAACGGGAAGCTTA
** *
58421001 TAAGAGCCATA-ATCGGGAAGCT
1 TTCGAGCCATATAACGGGAAGCT
58421023 CTTACAAGCC
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
24 11 0.19
25 45 0.79
26 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.24
Consensus pattern (25 bp):
TTCGAGCCATATAACGGGAAGCTTA
Found at i:58421032 original size:24 final size:24
Alignment explanation
Indices: 58420986--58421071 Score: 77
Period size: 24 Copynumber: 3.6 Consensus size: 24
58420976 TTCGGGCTAT
58420986 ATAACGGGAAGCTCATAAGAGCC-
1 ATAACGGGAAGCTCATAAGAGCCA
*
58421009 ATAATCGGGAAGCTCTTACA-AGCCA
1 ATAA-CGGGAAGCTCATA-AGAGCCA
* * ** *
58421034 ATAACGGGTAGTTCCGAAGAGCTA
1 ATAACGGGAAGCTCATAAGAGCCA
*
58421058 TTAACGGGAAGCTC
1 ATAACGGGAAGCTC
58421072 TAGATAACCA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
23 5 0.10
24 40 0.80
25 5 0.10
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.19
Consensus pattern (24 bp):
ATAACGGGAAGCTCATAAGAGCCA
Found at i:58421255 original size:24 final size:25
Alignment explanation
Indices: 58421228--58421275 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
58421218 GGATGCTCCG
*
58421228 AAGAACTAT-TAACGAAAAGCTCGC
1 AAGAACCATATAACGAAAAGCTCGC
**
58421252 AAGAACCATATAACGGGAAGCTCG
1 AAGAACCATATAACGAAAAGCTCG
58421276 AGAGGGCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.15
Consensus pattern (25 bp):
AAGAACCATATAACGAAAAGCTCGC
Found at i:58422217 original size:14 final size:14
Alignment explanation
Indices: 58422181--58422217 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
58422171 TGATATTAGA
58422181 TATTTA-TTTTATT
1 TATTTACTTTTATT
58422194 TA-TTATCTTTTATT
1 TATTTA-CTTTTATT
58422208 TATTTACTTT
1 TATTTACTTT
58422218 CCAATTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 2 0.10
14 13 0.62
15 3 0.14
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTACTTTTATT
Found at i:58422579 original size:11 final size:11
Alignment explanation
Indices: 58422563--58422587 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58422553 ATCTATTATT
58422563 ACATAAATTTC
1 ACATAAATTTC
58422574 ACATAAATTTC
1 ACATAAATTTC
58422585 ACA
1 ACA
58422588 ATTTATTCAC
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:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (11 bp):
ACATAAATTTC
Found at i:58425185 original size:15 final size:15
Alignment explanation
Indices: 58425165--58425195 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
58425155 CGAGGCGTGG
58425165 TTGAAACGATTTAAT
1 TTGAAACGATTTAAT
*
58425180 TTGAAATGATTTAAT
1 TTGAAACGATTTAAT
58425195 T
1 T
58425196 AAGTTTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (15 bp):
TTGAAACGATTTAAT
Found at i:58433206 original size:17 final size:17
Alignment explanation
Indices: 58433184--58433219 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
58433174 TGATAAATAA
58433184 AAGATAAAACTAGGTAG
1 AAGATAAAACTAGGTAG
58433201 AAGATAAAACTAGGTAG
1 AAGATAAAACTAGGTAG
58433218 AA
1 AA
58433220 TCACTAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.22, T:0.17
Consensus pattern (17 bp):
AAGATAAAACTAGGTAG
Found at i:58440253 original size:39 final size:40
Alignment explanation
Indices: 58440149--58440253 Score: 185
Period size: 40 Copynumber: 2.6 Consensus size: 40
58440139 GATGCTAGTG
58440149 ACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
1 ACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
58440189 ACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
1 ACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
* *
58440229 GCTATATCC-GGCTAAATCCCGAAGG
1 ACTATATCCGGGCTAAGTCCCGAAGG
58440254 TACTTGGGTT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
39 15 0.24
40 48 0.76
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.26
Consensus pattern (40 bp):
ACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
Found at i:58455607 original size:40 final size:41
Alignment explanation
Indices: 58455544--58455669 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 41
58455534 AACCCAAGTA
58455544 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGATATAGTCAACTCGCACAAATG
* * * *
58455583 CCTTTGGGTTTTAGCCCAGATATAGTCAA-TAC-CACAAAAG
1 CCTTCGGGATTTAGCCCGGATATAGTCAACT-CGCACAAATG
* *
58455623 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGATTTAGCCCGGATATAGTCAACTCGCACAAATG
58455663 CCTTCGG
1 CCTTCGG
58455670 NNNNNNNNNN
Statistics
Matches: 72, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
39 13 0.18
40 55 0.76
41 4 0.06
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (41 bp):
CCTTCGGGATTTAGCCCGGATATAGTCAACTCGCACAAATG
Found at i:58462665 original size:22 final size:23
Alignment explanation
Indices: 58462632--58462675 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
58462622 CAATTTATAT
58462632 TTTATTTTATATATAAATATTTA
1 TTTATTTTATATATAAATATTTA
* *
58462655 TTTA-TTTATATTTATATATTT
1 TTTATTTTATATATAAATATTT
58462676 TGTGCGCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTTTATATATAAATATTTA
Found at i:58462674 original size:14 final size:14
Alignment explanation
Indices: 58462624--58462675 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
58462614 AAATTATTCA
58462624 ATTTATAT-TTTAT
1 ATTTATATATTTAT
**
58462637 -TTTATATATAAAT
1 ATTTATATATTTAT
*
58462650 ATTTATTTATTTAT
1 ATTTATATATTTAT
58462664 ATTTATATATTT
1 ATTTATATATTT
58462676 TGTGCGCTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 21 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTATATATTTAT
Found at i:58462674 original size:18 final size:18
Alignment explanation
Indices: 58462624--58462675 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
58462614 AAATTATTCA
58462624 ATTTATATTT-TAT-TTT
1 ATTTATATTTATATATTT
* ** *
58462640 ATATATAAATATTTATTT
1 ATTTATATTTATATATTT
58462658 ATTTATATTTATATATTT
1 ATTTATATTTATATATTT
58462676 TGTGCGCTAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
16 7 0.27
17 2 0.08
18 17 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTATATTTATATATTT
Found at i:58469006 original size:11 final size:10
Alignment explanation
Indices: 58468976--58469009 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
58468966 ATTTCATATG
58468976 TTATTATTAA
1 TTATTATTAA
*
58468986 TTATTTTTAA
1 TTATTATTAA
58468996 TATATTATTAA
1 T-TATTATTAA
58469007 TTA
1 TTA
58469010 GTTTCAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATTATTAA
Found at i:58469021 original size:21 final size:21
Alignment explanation
Indices: 58468977--58469021 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
58468967 TTTCATATGT
* * *
58468977 TATTATTAATTATTTTTAATA
1 TATTATTAATTAGTTTCAAAA
58468998 TATTATTAATTAGTTTCAAAA
1 TATTATTAATTAGTTTCAAAA
58469019 TAT
1 TAT
58469022 ACGTTTCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TATTATTAATTAGTTTCAAAA
Found at i:58472133 original size:21 final size:21
Alignment explanation
Indices: 58472107--58472146 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
58472097 ACCCTTCAGT
**
58472107 GGTATTGTGATATCCTCTTTG
1 GGTATTGCAATATCCTCTTTG
58472128 GGTATTGCAATATCCTCTT
1 GGTATTGCAATATCCTCTT
58472147 CTGGATATCA
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:0.17, C:0.17, G:0.20, T:0.45
Consensus pattern (21 bp):
GGTATTGCAATATCCTCTTTG
Found at i:58478023 original size:34 final size:34
Alignment explanation
Indices: 58477984--58478051 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
58477974 TTAAGAACCA
* *
58477984 AAGAAAATGGAATTAGACTGGGGAAAGTCGAAAG
1 AAGAAAATGGAATTAGACCGGGAAAAGTCGAAAG
58478018 AAGAAAATGGAATTAGACCGGGAAAAGTCGAAAG
1 AAGAAAATGGAATTAGACCGGGAAAAGTCGAAAG
58478052 TCGTCGAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.49, C:0.07, G:0.31, T:0.13
Consensus pattern (34 bp):
AAGAAAATGGAATTAGACCGGGAAAAGTCGAAAG
Found at i:58478374 original size:43 final size:43
Alignment explanation
Indices: 58478310--58478430 Score: 147
Period size: 43 Copynumber: 2.8 Consensus size: 43
58478300 TCCGATATGT
* *
58478310 GATATCGTGTAAGACCTTGTCTGGGACTTTGGCATCGACTT-GA
1 GATATCGTGTAAGACCCTGTCTGGGACATTGGCATCGA-TTAGA
* * *
58478353 GATATCATGTAAGACCGTGTCTGAGACATTGGCATCGATTAGA
1 GATATCGTGTAAGACCCTGTCTGGGACATTGGCATCGATTAGA
* *
58478396 GAT-TACGTGTAAGGCCCTGTCTGGGACAGTGGCAT
1 GATAT-CGTGTAAGACCCTGTCTGGGACATTGGCAT
58478431 TGATATTTGA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 3 0.04
43 64 0.96
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (43 bp):
GATATCGTGTAAGACCCTGTCTGGGACATTGGCATCGATTAGA
Found at i:58479589 original size:42 final size:42
Alignment explanation
Indices: 58479542--58479628 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
58479532 ATGCCTATGT
58479542 GTTAGGTTCTTGAATGGCCAAATGAATTGGTCAAATTGGTAA
1 GTTAGGTTCTTGAATGGCCAAATGAATTGGTCAAATTGGTAA
58479584 GTTAGGTTCTTGAATGGCCAAATGAATTGGTCAAATTGGTAA
1 GTTAGGTTCTTGAATGGCCAAATGAATTGGTCAAATTGGTAA
58479626 GTT
1 GTT
58479629 TTTGGTATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.34
Consensus pattern (42 bp):
GTTAGGTTCTTGAATGGCCAAATGAATTGGTCAAATTGGTAA
Found at i:58485933 original size:40 final size:40
Alignment explanation
Indices: 58485877--58486077 Score: 156
Period size: 40 Copynumber: 5.0 Consensus size: 40
58485867 ATATGCATTC
* *
58485877 AGGGTACTGAATTACAAATAGGGGCATGTATGTGCAATCA
1 AGGGTACTGAAGTACAAATAGGGGCACGTATGTGCAATCA
* * * * * *
58485917 AGGGTACTGAAGTACAAACAAGGGCATGTATGTGTAGTTA
1 AGGGTACTGAAGTACAAATAGGGGCACGTATGTGCAATCA
* * * *
58485957 GGGGTACCGAAGTACAAA-ATGGGACACGTATGTGCAAACA
1 AGGGTACTGAAGTACAAATA-GGGGCACGTATGTGCAATCA
* * * * *
58485997 GGGGTA-TCGAAGTACAAATAGAGGCACATATATGCAAT-T
1 AGGGTACT-GAAGTACAAATAGGGGCACGTATGTGCAATCA
** * * *
58486036 AGAGGTACCAAAGTACAAATAGAGGTACATATGTGCAATCA
1 AG-GGTACTGAAGTACAAATAGGGGCACGTATGTGCAATCA
58486077 A
1 A
58486078 ACAATAATCA
Statistics
Matches: 127, Mismatches: 28, Indels: 11
0.77 0.17 0.07
Matches are distributed among these distances:
39 2 0.02
40 123 0.97
41 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.21
Consensus pattern (40 bp):
AGGGTACTGAAGTACAAATAGGGGCACGTATGTGCAATCA
Found at i:58488742 original size:23 final size:24
Alignment explanation
Indices: 58488665--58488757 Score: 75
Period size: 23 Copynumber: 3.8 Consensus size: 24
58488655 AGACTCACCA
*
58488665 CAGCTCGTATGAGATTACTGATAT
1 CAGCTCGTATGAGCTTACTGATAT
* * * * *
58488689 AACACCTTGTAAGACCTTACT-ATTCT
1 --CAGCTCGTATGAGCTTACTGA-TAT
58488715 CAGCTCGTATGAGCTTACTGAT-T
1 CAGCTCGTATGAGCTTACTGATAT
58488738 CAGCTCGTCA-GAGCTTACTG
1 CAGCTCGT-ATGAGCTTACTG
58488758 TTTTAGTTCA
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
23 19 0.35
24 17 0.31
25 2 0.04
26 16 0.30
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (24 bp):
CAGCTCGTATGAGCTTACTGATAT
Found at i:58490367 original size:46 final size:44
Alignment explanation
Indices: 58490314--58490427 Score: 122
Period size: 46 Copynumber: 2.5 Consensus size: 44
58490304 AGCTAATTTT
58490314 AGACATGTTTGGGACATGCGTCAACCT-CAAGATGTAAGCCAGTGTA
1 AGACATGTTTGGGACATGCGTC-ACCTACAAGATGT--GCCAGTGTA
* * ** * *
58490360 AGACATGTCTGGGACATGCATCGGCTACGAGATGTGTCAGTGTA
1 AGACATGTTTGGGACATGCGTCACCTACAAGATGTGCCAGTGTA
58490404 AGACCATGTTTGGGACATGGCGTC
1 AGA-CATGTTTGGGACAT-GCGTC
58490428 GGCCTCGATT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
44 11 0.19
45 15 0.26
46 31 0.54
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (44 bp):
AGACATGTTTGGGACATGCGTCACCTACAAGATGTGCCAGTGTA
Found at i:58490502 original size:96 final size:93
Alignment explanation
Indices: 58490353--58490526 Score: 231
Period size: 96 Copynumber: 1.8 Consensus size: 93
58490343 AGATGTAAGC
* * * * * * *
58490353 CAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGTCAGTGTAAGACCATGTTTGGG
1 CAGTGTAAGACATGTCTAGGACATGCATCGACTAAGAGATGAGCCAGTGTAAGACCATGTCTGAG
*
58490418 ACATGGCGTCGGCCTCGATTTCGATAGT
66 ACATGGCATCGGCCTCGATTTCGATAGT
* *
58490446 CAGTGTAAGACCATGTTTAGGACATGGCATCGACTTAATAGATGAGCCAGTGTAAGACCATGTCT
1 CAGTGTAAGA-CATGTCTAGGACAT-GCATCGAC-TAAGAGATGAGCCAGTGTAAGACCATGTCT
58490511 GAGACATGGCATCGGC
63 GAGACATGGCATCGGC
58490527 AATATACCCT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
93 10 0.15
94 12 0.18
95 7 0.10
96 39 0.57
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (93 bp):
CAGTGTAAGACATGTCTAGGACATGCATCGACTAAGAGATGAGCCAGTGTAAGACCATGTCTGAG
ACATGGCATCGGCCTCGATTTCGATAGT
Found at i:58490517 original size:47 final size:47
Alignment explanation
Indices: 58490350--58490524 Score: 144
Period size: 47 Copynumber: 3.7 Consensus size: 47
58490340 TCAAGATGTA
* * **
58490350 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TACGAGATG
1 AGCCAGTGTAAGACCATGTCTGAGACATGGCATCGACTTAATAGATG
* * * * * * * * *
58490394 TGTCAGTGTAAGACCATGTTTGGGACATGGCGTCGGCCTCGATTTCGAT-
1 AGCCAGTGTAAGACCATGTCTGAGACATGGCATC-GACT-TA-ATAGATG
* *
58490443 AGTCAGTGTAAGACCATGT-TTAGGACATGGCATCGACTTAATAGATG
1 AGCCAGTGTAAGACCATGTCTGA-GACATGGCATCGACTTAATAGATG
58490490 AGCCAGTGTAAGACCATGTCTGAGACATGGCATCG
1 AGCCAGTGTAAGACCATGTCTGAGACATGGCATCG
58490525 GCAATATACC
Statistics
Matches: 103, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
44 11 0.11
45 13 0.13
46 8 0.08
47 33 0.32
48 6 0.06
49 29 0.28
50 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (47 bp):
AGCCAGTGTAAGACCATGTCTGAGACATGGCATCGACTTAATAGATG
Found at i:58492834 original size:13 final size:13
Alignment explanation
Indices: 58492816--58492842 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58492806 TTGTGACTTG
58492816 GCTGTATTGATAA
1 GCTGTATTGATAA
58492829 GCTGTATTGATAA
1 GCTGTATTGATAA
58492842 G
1 G
58492843 TCAGTATACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (13 bp):
GCTGTATTGATAA
Found at i:58497398 original size:12 final size:13
Alignment explanation
Indices: 58497381--58497409 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
58497371 ATGTCAAAGT
58497381 ACAAAAAAAAAA-
1 ACAAAAAAAAAAC
58497393 ACAAAAAAAAAAC
1 ACAAAAAAAAAAC
58497406 ACAA
1 ACAA
58497410 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (13 bp):
ACAAAAAAAAAAC
Found at i:58499727 original size:26 final size:26
Alignment explanation
Indices: 58499689--58499824 Score: 121
Period size: 26 Copynumber: 5.3 Consensus size: 26
58499679 CTGGCTTAAA
* * * *
58499689 GCCTACTAGATAACCACTGGCTCAAG
1 GCCTGCTAAATAAACACCGGCTCAAG
* * *
58499715 GCTTGCTAAATAAAGACCAGCTCAAG
1 GCCTGCTAAATAAACACCGGCTCAAG
* * *
58499741 GCCTACTAAATAAACACTGGCTTAAG
1 GCCTGCTAAATAAACACCGGCTCAAG
* *
58499767 GCCTGCTAAATCAACACCAGCTCAAG
1 GCCTGCTAAATAAACACCGGCTCAAG
* * * *
58499793 TCATGCTAAATAACCACAGG-TCAAG
1 GCCTGCTAAATAAACACCGGCTCAAG
58499818 GCCTGCT
1 GCCTGCT
58499825 TTTCTTGTAT
Statistics
Matches: 84, Mismatches: 26, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
25 10 0.12
26 74 0.88
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.20
Consensus pattern (26 bp):
GCCTGCTAAATAAACACCGGCTCAAG
Found at i:58499768 original size:52 final size:52
Alignment explanation
Indices: 58499689--58499824 Score: 166
Period size: 52 Copynumber: 2.6 Consensus size: 52
58499679 CTGGCTTAAA
* * * *
58499689 GCCTACTAGATAACCACTGGCTCAAGGCTTGCTAAATAAAGACCAGCTCAAG
1 GCCTACTAAATAAACACTGGCTCAAGGCCTGCTAAATAAACACCAGCTCAAG
* *
58499741 GCCTACTAAATAAACACTGGCTTAAGGCCTGCTAAATCAACACCAGCTCAAG
1 GCCTACTAAATAAACACTGGCTCAAGGCCTGCTAAATAAACACCAGCTCAAG
* * * * *
58499793 TCATGCTAAATAACCACAGG-TCAAGGCCTGCT
1 GCCTACTAAATAAACACTGGCTCAAGGCCTGCT
58499825 TTTCTTGTAT
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
51 11 0.15
52 61 0.85
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.20
Consensus pattern (52 bp):
GCCTACTAAATAAACACTGGCTCAAGGCCTGCTAAATAAACACCAGCTCAAG
Found at i:58506769 original size:43 final size:43
Alignment explanation
Indices: 58506718--58506800 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
58506708 GAGATATGTG
* *
58506718 GCATCCGAGCTCATTGAGAGGTCTGAGTTCATTATGGATGCGA
1 GCATCCGAGCTCATTGAGAGGTCCGAGTTCATAATGGATGCGA
*
58506761 GCATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGGATG
1 GCATCCGAGCTCATTGAGAGGTCCGAGTTCATAATGGATG
58506801 GGATTCATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (43 bp):
GCATCCGAGCTCATTGAGAGGTCCGAGTTCATAATGGATGCGA
Found at i:58518332 original size:26 final size:26
Alignment explanation
Indices: 58518251--58518374 Score: 81
Period size: 26 Copynumber: 4.8 Consensus size: 26
58518241 ATAGTACCTG
* * ** *
58518251 CTAAATATACACTAGCTCAAAACCTG
1 CTAAATAAACACCAGCTCAAGTCCTA
** * *
58518277 CTAAATAAACACTGGCTTAAGGT-CTG
1 CTAAATAAACACCAGCTCAA-GTCCTA
* *
58518303 CTAAATAATCACCGGCTCAAGTCCTA
1 CTAAATAAACACCAGCTCAAGTCCTA
* *
58518329 CTAAAAAAACATCAGCTCAAAG-CCTA
1 CTAAATAAACACCAGCTC-AAGTCCTA
* *
58518355 CCAAATAACCACCAGCTCAA
1 CTAAATAAACACCAGCTCAA
58518375 TGCTTGCATT
Statistics
Matches: 78, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
25 4 0.05
26 71 0.91
27 3 0.04
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.20
Consensus pattern (26 bp):
CTAAATAAACACCAGCTCAAGTCCTA
Found at i:58522927 original size:47 final size:47
Alignment explanation
Indices: 58522858--58522988 Score: 217
Period size: 47 Copynumber: 2.8 Consensus size: 47
58522848 CACAATCGAT
*
58522858 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTTATCCCG
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACATATCCCG
58522905 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACATATCCCG
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACATATCCCG
* * * *
58522952 GAGTACCTATACCATGGCTCGTAACCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTA
58522989 TTTACTCGAA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 79 1.00
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (47 bp):
AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACATATCCCG
Found at i:58525773 original size:3 final size:3
Alignment explanation
Indices: 58525765--58525814 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
58525755 CTGAGTCAAA
* * *
58525765 AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT AAAT AAA AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
58525811 AAT A
1 AAT A
58525815 TTTTTTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:58527253 original size:329 final size:331
Alignment explanation
Indices: 58526651--58527310 Score: 1225
Period size: 329 Copynumber: 2.0 Consensus size: 331
58526641 ATAAAGGGGG
58526651 CTGTTATGCGAATTAATTTTAAGTTGTGTTATTTTATATATATATATAATATAATCTATGGGGTA
1 CTGTTATGCGAATTAATTTTAAGTTGTGTTA--TTATATATATATATAATATAATCTATGGGGTA
58526716 ATGTTAAGTGGATCAATTGATCGATTAAATAGTTGCTTTACTTTAATTCAAGCTCAAGACCCAAA
64 ATGTTAAGTGGATCAATTGATCGATTAAATAGTTGCTTTACTTTAATTCAAGCTCAAGACCCAAA
58526781 GAACCGAGATTTGGATCGGGAAAGGCGAAGTTAGCCGAGTAGTCGACACTATTGTACGAAGTTGT
129 GAACCGAGATTTGGATCGGGAAAGGCGAAGTTAGCCGAGTAGTCGACACTATTGTACGAAGTTGT
*
58526846 CGAGGTAAGTTCTTAAGTAATTTAAATTCAATTCGGCATGTTTAGAATTTAAATAAACATAGTAA
194 CGAGGTAAGTTCTTAAGTAATTTAAATTCAATTCGGCATGCTTAGAATTTAAATAAACATAGTAA
*
58526911 GGTAAAATGCTTGATTATATAGATGTATAAATATAATGTGATGGATATATGTTTGGAGAAATGAT
259 GGTAAAATGCTTGATTATATAGATGTATAAATATAATCTGATGGATATATGTTTGGAGAAATGAT
58526976 TAGAGCCA
324 TAGAGCCA
*
58526984 CTGTTATGCGAATTATTTTTAAGTTGTGTTA-T-TATATATATATAATATAATCTATGGGGTAAT
1 CTGTTATGCGAATTAATTTTAAGTTGTGTTATTATATATATATATAATATAATCTATGGGGTAAT
* *
58527047 GTTAAGTGGATCAATTGATCGATTAAATAGTTTCTTTGCTTTAATTCAAGCTCAAGACCCAAAGA
66 GTTAAGTGGATCAATTGATCGATTAAATAGTTGCTTTACTTTAATTCAAGCTCAAGACCCAAAGA
58527112 ACCGAGATTTGGATCGGGAAAGGCGAAGTTAGCCGAGTAGTCGACACTATTGTACGAAGTTGTCG
131 ACCGAGATTTGGATCGGGAAAGGCGAAGTTAGCCGAGTAGTCGACACTATTGTACGAAGTTGTCG
*
58527177 AGGTAAGTTCTTAAGTAATTTAAATTCAATTCGGTATGCTTAGAATTTAAATAAACATAGTAAGG
196 AGGTAAGTTCTTAAGTAATTTAAATTCAATTCGGCATGCTTAGAATTTAAATAAACATAGTAAGG
*
58527242 TAAAATGCTTGATTATATAGATGTATAAATATAATCTGATGGATATATGTTTGGAGAAATTATTA
261 TAAAATGCTTGATTATATAGATGTATAAATATAATCTGATGGATATATGTTTGGAGAAATGATTA
58527307 GAGC
326 GAGC
58527311 TAAATGTTGC
Statistics
Matches: 320, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
329 289 0.90
330 1 0.00
333 30 0.09
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (331 bp):
CTGTTATGCGAATTAATTTTAAGTTGTGTTATTATATATATATATAATATAATCTATGGGGTAAT
GTTAAGTGGATCAATTGATCGATTAAATAGTTGCTTTACTTTAATTCAAGCTCAAGACCCAAAGA
ACCGAGATTTGGATCGGGAAAGGCGAAGTTAGCCGAGTAGTCGACACTATTGTACGAAGTTGTCG
AGGTAAGTTCTTAAGTAATTTAAATTCAATTCGGCATGCTTAGAATTTAAATAAACATAGTAAGG
TAAAATGCTTGATTATATAGATGTATAAATATAATCTGATGGATATATGTTTGGAGAAATGATTA
GAGCCA
Found at i:58531657 original size:43 final size:44
Alignment explanation
Indices: 58531595--58531702 Score: 166
Period size: 43 Copynumber: 2.5 Consensus size: 44
58531585 TATCCTAGAT
* * * *
58531595 ATGGTCTTACATGTTATCACATAT-CGATGCCACTGTCCCAGAC
1 ATGGTCTTACACGTAATCACATATACAATGCCAATGTCCCAGAC
58531638 ATGGTCTTACACGTAATCACA-ATACAATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACATATACAATGCCAATGTCCCAGAC
58531681 ATGGTCTTACACGTAATCACAT
1 ATGGTCTTACACGTAATCACAT
58531703 CTCAGTAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
42 2 0.03
43 57 0.97
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (44 bp):
ATGGTCTTACACGTAATCACATATACAATGCCAATGTCCCAGAC
Found at i:58535309 original size:27 final size:26
Alignment explanation
Indices: 58535262--58535419 Score: 176
Period size: 27 Copynumber: 5.9 Consensus size: 26
58535252 CAAGGCTGCT
* *
58535262 AGATATTGTGAC-GAAGTCACCAGACAC
1 AGATATTGTGGCAG-AGCCACCAGA-AC
58535289 AGATATTGTGGCAGAGCCACCAGAAC
1 AGATATTGTGGCAGAGCCACCAGAAC
*
58535315 AGATATATGTGGCAGAGCCACCAGATC
1 AGATAT-TGTGGCAGAGCCACCAGAAC
* *
58535342 AGATAATTGTGGCATAGCCACCAGGAC
1 AGAT-ATTGTGGCAGAGCCACCAGAAC
*
58535369 AGATATATGTGGTAGAGCCACCA-AATC
1 AGATAT-TGTGGCAGAGCCACCAGAA-C
*
58535396 AGATAATTGTGGCATAGCCACCAG
1 AGAT-ATTGTGGCAGAGCCACCAG
58535420 GACGTTTCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
26 11 0.10
27 97 0.86
28 5 0.04
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (26 bp):
AGATATTGTGGCAGAGCCACCAGAAC
Found at i:58535420 original size:54 final size:54
Alignment explanation
Indices: 58535288--58535422 Score: 227
Period size: 54 Copynumber: 2.5 Consensus size: 54
58535278 TCACCAGACA
* * *
58535288 CAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAAAT
*
58535341 CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGTAGAGCCACCAAAT
1 CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAAAT
58535395 CAGATAATTGTGGCATAGCCACCAGGAC
1 CAGATAATTGTGGCATAGCCACCAGGAC
58535423 GTTTCCTCCA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 5 0.06
54 72 0.94
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (54 bp):
CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAAAT
Found at i:58541808 original size:26 final size:26
Alignment explanation
Indices: 58541777--58541884 Score: 207
Period size: 26 Copynumber: 4.2 Consensus size: 26
58541767 TGAAATTTCC
58541777 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
58541803 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
58541829 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
58541855 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
58541881 ATCA
1 ATCA
58541885 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:58542856 original size:18 final size:17
Alignment explanation
Indices: 58542816--58542857 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
58542806 ACTTATTGCC
58542816 TATT-TTTTTATATTAT
1 TATTATTTTTATATTAT
* *
58542832 AAATATTTTTATTATTAT
1 TATTATTTTTA-TATTAT
58542850 TATTATTT
1 TATTATTT
58542858 ACCCGTATGG
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 2 0.10
17 6 0.30
18 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTATTTTTATATTAT
Found at i:58544929 original size:30 final size:30
Alignment explanation
Indices: 58544895--58544952 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
58544885 CTGGGCATTT
*
58544895 CCACACAGGCTA-AGCACACGCCCATGTGAG
1 CCACACAGGCTAGA-CACAAGCCCATGTGAG
* *
58544925 CCACACGGGCTGGACACAAGCCCATGTG
1 CCACACAGGCTAGACACAAGCCCATGTG
58544953 TCAGCCCGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.36, G:0.26, T:0.10
Consensus pattern (30 bp):
CCACACAGGCTAGACACAAGCCCATGTGAG
Found at i:58549207 original size:7 final size:7
Alignment explanation
Indices: 58549177--58549214 Score: 55
Period size: 6 Copynumber: 5.9 Consensus size: 7
58549167 GGTGTTCTCA
58549177 AAATG-G
1 AAATGAG
58549183 AAATG-G
1 AAATGAG
58549189 AAATGA-
1 AAATGAG
58549195 AAATGAG
1 AAATGAG
58549202 AAATGAG
1 AAATGAG
58549209 AAATGA
1 AAATGA
58549215 TTCATTTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.58, C:0.00, G:0.26, T:0.16
Consensus pattern (7 bp):
AAATGAG
Found at i:58561633 original size:13 final size:13
Alignment explanation
Indices: 58561615--58561640 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58561605 ATGAAATAAC
58561615 TTAATTCTCTGTA
1 TTAATTCTCTGTA
58561628 TTAATTCTCTGTA
1 TTAATTCTCTGTA
58561641 AAAACTTAAG
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:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
TTAATTCTCTGTA
Found at i:58566361 original size:18 final size:18
Alignment explanation
Indices: 58566334--58566374 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
58566324 AGCAATTTAA
*
58566334 TTTTTTACTTTTATGTTC
1 TTTTTAACTTTTATGTTC
* *
58566352 TTTTTAACTTTTTTTTTC
1 TTTTTAACTTTTATGTTC
58566370 TTTTT
1 TTTTT
58566375 CTTTTTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTAACTTTTATGTTC
Found at i:58570802 original size:39 final size:39
Alignment explanation
Indices: 58570740--58570879 Score: 199
Period size: 39 Copynumber: 3.6 Consensus size: 39
58570730 ATCGTGATTT
* ** *
58570740 GAAGCCCGAAGTCTAGTTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
* *
58570779 GAAGCCCGAAGGCTAACTAAAGCACACAAGTGTTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
*
58570818 GAAGCCCGAAGGTTAACTGAAGCACACAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
* *
58570857 GAAGGCCGGAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
58570880 TCATCAGAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
Found at i:58576646 original size:24 final size:24
Alignment explanation
Indices: 58576609--58576707 Score: 103
Period size: 24 Copynumber: 4.0 Consensus size: 24
58576599 ATGATTTTCT
58576609 TTTTATATACATTATTTATTTTAAAC
1 TTTTATAT--ATTATTTATTTTAAAC
*
58576635 TTTTACATATTATTTATTTTAAA-
1 TTTTATATATTATTTATTTTAAAC
* * *
58576658 TTTATATACATTATGTA-GTTAAAC
1 TTT-TATATATTATTTATTTTAAAC
58576682 TATTTTATATATTATTTATTTTAAAC
1 --TTTTATATATTATTTATTTTAAAC
58576708 CCTCTTTATT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
23 8 0.13
24 25 0.42
25 11 0.18
26 16 0.27
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTATATATTATTTATTTTAAAC
Found at i:58576702 original size:49 final size:48
Alignment explanation
Indices: 58576610--58576706 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 48
58576600 TGATTTTCTT
* *
58576610 TTTATATACATTATTTATTTTAAACTTTTACATATTATTTATTTTAAA
1 TTTATATACATTATGTATGTTAAACTTTTACATATTATTTATTTTAAA
*
58576658 TTTATATACATTATGTA-GTTAAACTATTTTATATATTATTTATTTTAAA
1 TTTATATACATTATGTATGTTAAAC--TTTTACATATTATTTATTTTAAA
58576707 CCCTCTTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 6 0.14
48 16 0.36
49 22 0.50
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (48 bp):
TTTATATACATTATGTATGTTAAACTTTTACATATTATTTATTTTAAA
Found at i:58580754 original size:54 final size:54
Alignment explanation
Indices: 58580682--58580788 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
58580672 TCGATGAAAA
*
58580682 CTACCACGAATCGGTCCAAGTAAGGTTGGAACACTCGATTCATCAGATCCATGG
1 CTACCACGAATCGCTCCAAGTAAGGTTGGAACACTCGATTCATCAGATCCATGG
58580736 CTACCACGAATCGCTCCAAGTAAGGTTGGAACACTCGATTCATCAGATCCATG
1 CTACCACGAATCGCTCCAAGTAAGGTTGGAACACTCGATTCATCAGATCCATG
58580789 AAAGCGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (54 bp):
CTACCACGAATCGCTCCAAGTAAGGTTGGAACACTCGATTCATCAGATCCATGG
Found at i:58582971 original size:12 final size:12
Alignment explanation
Indices: 58582954--58582996 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
58582944 AGTACTACCT
58582954 CGGCCTCGACCA
1 CGGCCTCGACCA
*
58582966 CGGCCTCAACCA
1 CGGCCTCGACCA
* *
58582978 CAGCCTCGACGA
1 CGGCCTCGACCA
58582990 CGGCCTC
1 CGGCCTC
58582997 TTCCCCGAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:58584467 original size:25 final size:27
Alignment explanation
Indices: 58584430--58584482 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
58584420 TCAAACATGC
58584430 ATTTAGGTCAATTTAACT-CTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
58584456 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
58584482 A
1 A
58584483 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.40
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:58585982 original size:26 final size:26
Alignment explanation
Indices: 58585946--58586002 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
58585936 ATGAAATGCC
58585946 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
58585972 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
58585998 TATCA
1 TATCA
58586003 ATTTTTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.32
Consensus pattern (26 bp):
TATCATGGAACATTTACCTAACCCAT
Found at i:58588638 original size:42 final size:42
Alignment explanation
Indices: 58588592--58588675 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
58588582 CCAACCCAAA
58588592 GCTACAATATTTATGATAGGAGTGGTGAGAATGAGGACCACT
1 GCTACAATATTTATGATAGGAGTGGTGAGAATGAGGACCACT
58588634 GCTACAATATTTATGATAGGAGTGGTGAGAATGAGGACCACT
1 GCTACAATATTTATGATAGGAGTGGTGAGAATGAGGACCACT
58588676 TGCTTTCTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (42 bp):
GCTACAATATTTATGATAGGAGTGGTGAGAATGAGGACCACT
Found at i:58602855 original size:18 final size:18
Alignment explanation
Indices: 58602834--58602887 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
58602824 TCTAGCTGTG
*
58602834 GCTCAGGCTCTGGCTCTA
1 GCTCAGGCTCAGGCTCTA
* * **
58602852 GCTCGGGCTCGGGAGCTA
1 GCTCAGGCTCAGGCTCTA
*
58602870 GCTCTGGCTCAGGCTCTA
1 GCTCAGGCTCAGGCTCTA
58602888 TATTGGCTAC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.11, C:0.31, G:0.33, T:0.24
Consensus pattern (18 bp):
GCTCAGGCTCAGGCTCTA
Found at i:58606129 original size:150 final size:150
Alignment explanation
Indices: 58605669--58606563 Score: 1403
Period size: 150 Copynumber: 6.0 Consensus size: 150
58605659 TTTCGATGAT
* * ** *
58605669 TTTTG-CCATTTGTTGGTATTTTTT-AATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGT
1 TTTTGACCATTTATTTGTATTTTTTAAATTTTTAGATTTTATTTTTTAAAATATACAATTTTCGT
58605732 -ATT--TTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATT
66 AATTAATTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATT
* *
58605794 AATTTAATAAATAACCTTGA
131 AATTTAGTAAATAACCCTGA
* * * *
58605814 TTTTGGCCATTTGTTTGTTTTTTTTAAAATTTTT-GAATTTTATTTTTTAAAATATACTATTTTC
1 TTTTGACCATTTATTTGTATTTTTT-AAATTTTTAG-ATTTTATTTTTTAAAATATACAATTTTC
* * * *
58605878 GTATTTTATTTTTTTATATTATTTTAATACATATTGTTTCAAATGTATTATTTTAAT-TTTTTTA
64 GTA-ATTA-ATTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTA
58605942 TATTAATTTAGTAAATAACCCTGA
127 TATTAATTTAGTAAATAACCCTGA
58605966 TTTTGACCATTTATTTGTATTTTTTAAATTTTTAGATTTTATTTTTTAAAATATACAATTTTCGT
1 TTTTGACCATTTATTTGTATTTTTTAAATTTTTAGATTTTATTTTTTAAAATATACAATTTTCGT
*
58606031 AATTAATTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATT
66 AATTAATTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATT
58606096 AATTTAGTAAATAACCCTGA
131 AATTTAGTAAATAACCCTGA
58606116 TTTTGACCATTTATTTGTATTTTTTAAATTTTTAGATTTTATTTTTTAAAATATACAATTTTCGT
1 TTTTGACCATTTATTTGTATTTTTTAAATTTTTAGATTTTATTTTTTAAAATATACAATTTTCGT
*
58606181 AATTAATTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATT
66 AATTAATTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATT
* *
58606246 AATTTAATAAATAACCTTGA
131 AATTTAGTAAATAACCCTGA
* * * *
58606266 TTTTGGCCATTTGTTTGTTTTTTTTAAAATTTTT-GAATTTTATTTTTTAAAATATACTATTTTC
1 TTTTGACCATTTATTTGTATTTTTT-AAATTTTTAG-ATTTTATTTTTTAAAATATACAATTTTC
* * * *
58606330 GTATTTTATTTTTTTATATTATTTTAATACATATTGTTTCAAATGTATTATTTTAAT-TTTTTTA
64 GTA-ATTA-ATTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTA
58606394 TATTAATTTAGTAAATAACCCTGA
127 TATTAATTTAGTAAATAACCCTGA
58606418 TTTTGACCATTTATTTGTATTTTTTAAATTTTTAGATTTTATTTTTTAAAATATACAATTTTCGT
1 TTTTGACCATTTATTTGTATTTTTTAAATTTTTAGATTTTATTTTTTAAAATATACAATTTTCGT
*
58606483 AATTAATTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATT
66 AATTAATTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATT
58606548 AATTTAGTAAATAACC
131 AATTTAGTAAATAACC
58606564 TTTTTTAAAT
Statistics
Matches: 694, Mismatches: 39, Indels: 29
0.91 0.05 0.04
Matches are distributed among these distances:
145 5 0.01
146 17 0.02
147 1 0.00
148 36 0.05
149 88 0.13
150 237 0.34
151 114 0.16
152 107 0.15
153 89 0.13
ACGTcount: A:0.30, C:0.06, G:0.07, T:0.57
Consensus pattern (150 bp):
TTTTGACCATTTATTTGTATTTTTTAAATTTTTAGATTTTATTTTTTAAAATATACAATTTTCGT
AATTAATTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATT
AATTTAGTAAATAACCCTGA
Found at i:58606393 original size:302 final size:300
Alignment explanation
Indices: 58605665--58606565 Score: 1433
Period size: 302 Copynumber: 3.0 Consensus size: 300
58605655 TTTTTTTCGA
* * * *
58605665 TGATTTTTGCCATTTGTTGGTATTTTTT-AATTTTCGGATTTTATTTTTTAAAATATACTATTTT
1 TGATTTTGGCCATTTGTTTGTATTTTTTAAATTTTTGAATTTTATTTTTTAAAATATACTATTTT
58605729 CG---TATTTTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAT
66 CGTATTATTTTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAT
* * * * *
58605791 ATTAATTTAATAAATAACCTTGATTTTGGCCATTTGTTTGTTTTTTTTAAAATTTTT-GAATTTT
131 ATTAATTTAGTAAATAACCCTGATTTTGACCATTTATTTGTATTTTTT-AAATTTTTAG-ATTTT
* * * * *
58605855 ATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTTATATTATTTTAATACATATTGTTTCAA
194 ATTTTTTAAAATATACAATTTTCGTA-ATTA-ATTTTTATATTATTTTAGTACATAATGTTTCAA
* *
58605920 ATGTATTATTTTAAT-TTTTTTATATTAATTTAGTAAATAACCC
257 ATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCT
* * *
58605963 TGATTTTGACCATTTATTTGTATTTTTTAAATTTTT-AGATTTTATTTTTTAAAATATACAATTT
1 TGATTTTGGCCATTTGTTTGTATTTTTTAAATTTTTGA-ATTTTATTTTTTAAAATATACTATTT
* *
58606027 TCGTAATTA-ATTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTT
65 TCGT-ATTATTTTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTGTTTTTT
58606091 ATATTAATTTAGTAAATAACCCTGATTTTGACCATTTATTTGTATTTTTTAAATTTTTAGATTTT
129 ATATTAATTTAGTAAATAACCCTGATTTTGACCATTTATTTGTATTTTTTAAATTTTTAGATTTT
58606156 ATTTTTTAAAATATACAATTTTCGTAATTAATTTTTATATTATTTTAGTACATAATGTTTCAAAT
194 ATTTTTTAAAATATACAATTTTCGTAATTAATTTTTATATTATTTTAGTACATAATGTTTCAAAT
*
58606221 GTATTATTTTAGTGTTTTTTATATTAATTTAATAAATAACCT
259 GTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCT
*
58606263 TGATTTTGGCCATTTGTTTGTTTTTTTTAAAATTTTTGAATTTTATTTTTTAAAATATACTATTT
1 TGATTTTGGCCATTTGTTTGTATTTTTT-AAATTTTTGAATTTTATTTTTTAAAATATACTATTT
* *
58606328 TCGTATTTTATTTTTTTATATTATTTTAATACATATTGTTTCAAATGTATTATTTTAAT-TTTTT
65 TCGTA--TTATTTTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTGTTTTT
58606392 TATATTAATTTAGTAAATAACCCTGATTTTGACCATTTATTTGTATTTTTTAAATTTTTAGATTT
128 TATATTAATTTAGTAAATAACCCTGATTTTGACCATTTATTTGTATTTTTTAAATTTTTAGATTT
58606457 TATTTTTTAAAATATACAATTTTCGTAATTAATTTTTATATTATTTTAGTACATAATGTTTCAAA
193 TATTTTTTAAAATATACAATTTTCGTAATTAATTTTTATATTATTTTAGTACATAATGTTTCAAA
58606522 TGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCT
258 TGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCT
58606565 T
1 T
58606566 TTTTAAATTT
Statistics
Matches: 559, Mismatches: 31, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
298 24 0.04
299 78 0.14
300 55 0.10
301 75 0.13
302 281 0.50
303 46 0.08
ACGTcount: A:0.30, C:0.06, G:0.07, T:0.57
Consensus pattern (300 bp):
TGATTTTGGCCATTTGTTTGTATTTTTTAAATTTTTGAATTTTATTTTTTAAAATATACTATTTT
CGTATTATTTTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAT
ATTAATTTAGTAAATAACCCTGATTTTGACCATTTATTTGTATTTTTTAAATTTTTAGATTTTAT
TTTTTAAAATATACAATTTTCGTAATTAATTTTTATATTATTTTAGTACATAATGTTTCAAATGT
ATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCT
Found at i:58606691 original size:17 final size:17
Alignment explanation
Indices: 58606671--58606704 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
58606661 TTTGATTAAG
* *
58606671 ATTTTTTTTAGTATTTT
1 ATTTTTTATACTATTTT
58606688 ATTTTTTATACTATTTT
1 ATTTTTTATACTATTTT
58606705 TGTAAAAGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTTATACTATTTT
Found at i:58607132 original size:9 final size:10
Alignment explanation
Indices: 58607109--58607138 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
58607099 AAAATTATAT
58607109 TTTTTCCTTC
1 TTTTTCCTTC
*
58607119 TTTTTCTTTC
1 TTTTTCCTTC
58607129 TTTTTCCTTC
1 TTTTTCCTTC
58607139 CCTCCCTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTCCTTC
Found at i:58607221 original size:3 final size:3
Alignment explanation
Indices: 58607207--58607254 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
58607197 GTGCCGCCTC
* *
58607207 CTT CTC CTT CTT CTT CTT C-T CTT CTT -TT CTT CTT CTC CTT CTTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT
58607251 CTT C
1 CTT C
58607255 CCATAATGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:58607236 original size:25 final size:24
Alignment explanation
Indices: 58607208--58607254 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
58607198 TGCCGCCTCC
*
58607208 TTCTCCTTCTTCTTCTTCTCTTCTT
1 TTCTCCTTCTCCTTCTT-TCTTCTT
*
58607233 TTCTTCTTCTCCTTCTTTCTTC
1 TTCTCCTTCTCCTTCTTTCTTC
58607255 CCATAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (24 bp):
TTCTCCTTCTCCTTCTTTCTTCTT
Found at i:58607238 original size:19 final size:16
Alignment explanation
Indices: 58607207--58607254 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
58607197 GTGCCGCCTC
58607207 CTTCTCCTTC-TTCTT
1 CTTCTCCTTCTTTCTT
58607222 CTTCT-CTTCTTTTCTT
1 CTTCTCCTTC-TTTCTT
58607238 CTTCTCCTTCTTTCTT
1 CTTCTCCTTCTTTCTT
58607254 C
1 C
58607255 CCATAATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.13
15 5 0.17
16 17 0.57
17 4 0.13
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTCTCCTTCTTTCTT
Found at i:58607241 original size:22 final size:21
Alignment explanation
Indices: 58607213--58607253 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
58607203 CCTCCTTCTC
*
58607213 CTTCTTCTTCTTCTCTTCTTTT
1 CTTCTTCTCCTTCT-TTCTTTT
58607235 CTTCTTCTCCTTCTTTCTT
1 CTTCTTCTCCTTCTTTCTT
58607254 CCCATAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (21 bp):
CTTCTTCTCCTTCTTTCTTTT
Found at i:58610825 original size:45 final size:45
Alignment explanation
Indices: 58610761--58610852 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
58610751 ACGAGGATCA
58610761 TAGCAGAAACCCTATTGCATTTATTCCTTTTTAAGTTTGAACAAT
1 TAGCAGAAACCCTATTGCATTTATTCCTTTTTAAGTTTGAACAAT
58610806 TAGCAGAAACCCTATTGCATTTATTCCTTTTTAAGTTTGAACAAT
1 TAGCAGAAACCCTATTGCATTTATTCCTTTTTAAGTTTGAACAAT
58610851 TA
1 TA
58610853 TTCTCTTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (45 bp):
TAGCAGAAACCCTATTGCATTTATTCCTTTTTAAGTTTGAACAAT
Found at i:58613037 original size:22 final size:23
Alignment explanation
Indices: 58613012--58613067 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
58613002 TAATATTAAA
58613012 TTATTTTAAATTATTTT-ATTTT
1 TTATTTTAAATTATTTTAATTTT
* *
58613034 TTATTTTTAATTTTTTTAATTTT
1 TTATTTTAAATTATTTTAATTTT
*
58613057 TAATTTTAAAT
1 TTATTTTAAAT
58613068 AACTTTAGTA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
TTATTTTAAATTATTTTAATTTT
Found at i:58613041 original size:23 final size:23
Alignment explanation
Indices: 58613014--58613067 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
58613004 ATATTAAATT
*
58613014 ATTTTAAATTATTTT-ATTTTTT
1 ATTTTAAATTATTTTAATTTTTA
* *
58613036 ATTTTTAATTTTTTTAATTTTTA
1 ATTTTAAATTATTTTAATTTTTA
58613059 ATTTTAAAT
1 ATTTTAAAT
58613068 AACTTTAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTTAAATTATTTTAATTTTTA
Found at i:58613049 original size:16 final size:16
Alignment explanation
Indices: 58612999--58613063 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
58612989 CCCGGCTCGA
* *
58612999 TTTTAATATTAAATTAT
1 TTTTAATTTTTAATT-T
* *
58613016 TTTAAATTATTTTA-TT
1 TTTTAATT-TTTAATTT
58613032 TTTT-ATTTTTAATTT
1 TTTTAATTTTTAATTT
58613047 TTTTAATTTTTAATTT
1 TTTTAATTTTTAATTT
58613063 T
1 T
58613064 AAATAACTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
14 4 0.10
15 9 0.23
16 16 0.41
17 7 0.18
18 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAATTTTTAATTT
Found at i:58613288 original size:19 final size:20
Alignment explanation
Indices: 58613260--58613298 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
58613250 TCCCATTATT
58613260 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
*
58613279 TATTTGTTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
58613299 ATGTATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:58613316 original size:25 final size:23
Alignment explanation
Indices: 58613279--58613324 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
58613269 TTTGTTTTAA
*
58613279 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
58613302 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
58613325 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:58617917 original size:47 final size:48
Alignment explanation
Indices: 58617859--58617955 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 48
58617849 TATAAAATAG
* * **
58617859 GGAAAGTACACATAAAGTAA-TTACGAGCTTAGTAAGCCATATACAAA
1 GGAAAGAACACACAAAGTAACTTAAAAGCTTAGTAAGCCATATACAAA
58617906 GGAAAGAACACACAAAGTAAGCTTTAAAAGCTTAGTAAGCCATATACAAA
1 GGAAAGAACACACAAAGTAA-C-TTAAAAGCTTAGTAAGCCATATACAAA
58617956 TAAAGTCATC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 18 0.42
50 25 0.58
ACGTcount: A:0.48, C:0.15, G:0.16, T:0.20
Consensus pattern (48 bp):
GGAAAGAACACACAAAGTAACTTAAAAGCTTAGTAAGCCATATACAAA
Found at i:58624124 original size:42 final size:42
Alignment explanation
Indices: 58624040--58624129 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 42
58624030 TGTGACTAGC
*
58624040 CCGTGTACCATTCGAAATGGCCTTACACACCTGTGTGCCAGA
1 CCGTGTACCATTCGAAATGGCCTTACACACCTGTATGCCAGA
* *
58624082 CCGTGTACCCTTCGAAATGGCC-T-CACACGCTCGTATGTCAGA
1 CCGTGTACCATTCGAAATGGCCTTACACAC-CT-GTATGCCAGA
58624124 CCGTGT
1 CCGTGT
58624130 GCTAGGTCGT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 5 0.12
41 3 0.07
42 35 0.81
ACGTcount: A:0.21, C:0.32, G:0.22, T:0.24
Consensus pattern (42 bp):
CCGTGTACCATTCGAAATGGCCTTACACACCTGTATGCCAGA
Found at i:58635090 original size:3 final size:3
Alignment explanation
Indices: 58635082--58635130 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
58635072 TGGGCTACCA
* *
58635082 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
58635130 A
1 A
58635131 TTCTCAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:58639018 original size:31 final size:31
Alignment explanation
Indices: 58638983--58639046 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
58638973 TGAGCTTTGT
58638983 TTGGAATGGAAGATAAAATTAATTAATTTAA
1 TTGGAATGGAAGATAAAATTAATTAATTTAA
*
58639014 TTGGAATGGAAGATAAAATTATTTAATTTAA
1 TTGGAATGGAAGATAAAATTAATTAATTTAA
58639045 TT
1 TT
58639047 AATTGAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (31 bp):
TTGGAATGGAAGATAAAATTAATTAATTTAA
Found at i:58639591 original size:31 final size:31
Alignment explanation
Indices: 58639523--58639583 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
58639513 AACGTTTAGG
* *
58639523 TAACTAAAATGAAAGCATCCTAAAAATTGGA
1 TAACCAAAATGAAAACATCCTAAAAATTGGA
*
58639554 TAACCAAAATGAAAACA-CCTTAAAAGTTGG
1 TAACCAAAATGAAAACATCC-TAAAAATTGG
58639584 GTGACCAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (31 bp):
TAACCAAAATGAAAACATCCTAAAAATTGGA
Found at i:58639939 original size:21 final size:21
Alignment explanation
Indices: 58639913--58639961 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
58639903 ATTCTTATTA
58639913 TTTTTTAATTTTC-AAACAATT
1 TTTTTTAATTTTCTAAA-AATT
58639934 TTTTTT-ATTTTCTAAAAATT
1 TTTTTTAATTTTCTAAAAATT
*
58639954 ATTTTTAA
1 TTTTTTAA
58639962 AATTTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTTAATTTTCTAAAAATT
Found at i:58643906 original size:52 final size:52
Alignment explanation
Indices: 58643828--58643932 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
58643818 ATCAAGAGAG
58643828 TTAGTGGAATTATCTAATTTTTCACTAATCCTTGTCTCCAAGCTTAAGTATA
1 TTAGTGGAATTATCTAATTTTTCACTAATCCTTGTCTCCAAGCTTAAGTATA
**
58643880 TTAGTGGAATTATCTAATTTTTCACTAATCCTTGTCTCTGAGCTTAAGTATA
1 TTAGTGGAATTATCTAATTTTTCACTAATCCTTGTCTCCAAGCTTAAGTATA
58643932 T
1 T
58643933 AAGTATAGCG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (52 bp):
TTAGTGGAATTATCTAATTTTTCACTAATCCTTGTCTCCAAGCTTAAGTATA
Found at i:58645976 original size:42 final size:42
Alignment explanation
Indices: 58645917--58646000 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
58645907 AATCTTAATT
58645917 GGGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA
1 GGGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA
* *
58645959 GGGAAAATAGTTCCCTTATTTTAATAAACTACTAAAAGATAA
1 GGGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA
58646001 AATAAAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (42 bp):
GGGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA
Found at i:58646008 original size:42 final size:42
Alignment explanation
Indices: 58645919--58646013 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 42
58645909 TCTTAATTGG
**
58645919 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAGG
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
* *
58645961 GAAAATAGTTCCCTTATTTTAATAAACTACTAAAAGATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
*
58646003 TAAAATA-TTCC
1 GAAAATAGTTCC
58646014 TAGAATATGA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
Found at i:58646051 original size:19 final size:18
Alignment explanation
Indices: 58646027--58646070 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
58646017 AATATGAATA
*
58646027 AAATTTTTCTATCTAAAT
1 AAATTTATCTATCTAAAT
58646045 AAGATTTATCTATCTAAAT
1 AA-ATTTATCTATCTAAAT
58646064 AAATTTA
1 AAATTTA
58646071 AAATATATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (18 bp):
AAATTTATCTATCTAAAT
Found at i:58649904 original size:42 final size:42
Alignment explanation
Indices: 58649849--58649928 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
58649839 ATAATTGGGG
58649849 AAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAGGGA
1 AAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAGGGA
* *
58649891 AAATAGTTTCCTTATTCTAATAAACTACTAAAATATAA
1 AAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA
58649929 AATAAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (42 bp):
AAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAGGGA
Found at i:58649980 original size:19 final size:18
Alignment explanation
Indices: 58649956--58649999 Score: 79
Period size: 19 Copynumber: 2.4 Consensus size: 18
58649946 AATATGAATA
58649956 AAATTTATCTACCTAAAT
1 AAATTTATCTACCTAAAT
58649974 AAGATTTATCTACCTAAAT
1 AA-ATTTATCTACCTAAAT
58649993 AAATTTA
1 AAATTTA
58650000 AAATATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATTTATCTACCTAAAT
Found at i:58657732 original size:39 final size:40
Alignment explanation
Indices: 58657635--58657732 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 40
58657625 NNNNNNNNNN
* * *
58657635 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
1 CCGGGCTAAATCCCGAAGGCATGTGTGCGAGTGACTATAT
58657675 CCGGGCTAAGA-CCCGAAGGCATGTGTGCGAGTTG-CTATAT
1 CCGGGCTAA-ATCCCGAAGGCATGTGTGCGAG-TGACTATAT
58657715 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAATCCCGAAGG
58657733 TACTTGGGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
38 1 0.02
39 14 0.27
40 35 0.67
41 2 0.04
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.22
Consensus pattern (40 bp):
CCGGGCTAAATCCCGAAGGCATGTGTGCGAGTGACTATAT
Found at i:58663517 original size:23 final size:22
Alignment explanation
Indices: 58663472--58663517 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
58663462 TTTTTCATGT
* *
58663472 TTCGATGCTTCGACGTTACAAA
1 TTCGATCCTTCGACGTAACAAA
*
58663494 TTCGATCCTTCGCACGTAATAAA
1 TTCGATCCTTCG-ACGTAACAAA
58663517 T
1 T
58663518 CCCTCCGAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (22 bp):
TTCGATCCTTCGACGTAACAAA
Found at i:58667475 original size:17 final size:17
Alignment explanation
Indices: 58667453--58667495 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
58667443 TTTTGGTTAA
58667453 AAATTACCAAAGTAACC
1 AAATTACCAAAGTAACC
* *
58667470 AAATTAACCAAATTACCC
1 AAATT-ACCAAAGTAACC
*
58667488 GAATTACC
1 AAATTACC
58667496 CGAATTACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.49, C:0.26, G:0.05, T:0.21
Consensus pattern (17 bp):
AAATTACCAAAGTAACC
Found at i:58667492 original size:9 final size:9
Alignment explanation
Indices: 58667480--58667510 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
58667470 AAATTAACCA
58667480 AATTACCCG
1 AATTACCCG
58667489 AATTACCCG
1 AATTACCCG
*
58667498 AATTACCTG
1 AATTACCCG
58667507 AATT
1 AATT
58667511 GAATCACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTACCCG
Found at i:58667492 original size:18 final size:18
Alignment explanation
Indices: 58667471--58667510 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
58667461 AAAGTAACCA
58667471 AATTAACCAAATTACCCG
1 AATTAACCAAATTACCCG
* * *
58667489 AATTACCCGAATTACCTG
1 AATTAACCAAATTACCCG
58667507 AATT
1 AATT
58667511 GAATCACTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (18 bp):
AATTAACCAAATTACCCG
Found at i:58669076 original size:46 final size:47
Alignment explanation
Indices: 58669009--58669183 Score: 177
Period size: 46 Copynumber: 3.8 Consensus size: 47
58668999 TGTAACCTAC
*
58669009 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCAGG-TGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCAGGCTGTTCGCAT
* *
58669055 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCAGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCAG--G-CT-GTTCGCAT
* * * *
58669105 -C-TCA-CGAACTCGGACTCAACTCAACGAGCTC-GGAC-ATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCAGG-CTGTTCGCAT
58669148 CCATAAGTGAACTC-GAACTCAACTCAACGAGCTCAG
1 CCATAAGTGAACTCAG-ACTCAACTCAACGAGCTCAG
58669184 ATGCCCAAAT
Statistics
Matches: 108, Mismatches: 10, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 3 0.03
46 61 0.56
47 25 0.23
48 3 0.03
49 1 0.01
50 4 0.04
51 3 0.03
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (47 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGCTCAGGCTGTTCGCAT
Found at i:58669176 original size:93 final size:93
Alignment explanation
Indices: 58669017--58669188 Score: 267
Period size: 93 Copynumber: 1.8 Consensus size: 93
58669007 ACCCATAAGT
* **
58669017 GAACTCAGACTCAACTCAACGAGTTCAGGTGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
58669082 CGAGTTCAGATGCCTAGTTACATCTCAC
66 CGAGCTCAGATGCCTAGTTACATCTCAC
*
58669110 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTC-GAACTCAACTC
1 GAACTCAGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACTCAG-ACTCAACTC
58669173 AACGAGCTCAGATGCC
64 AACGAGCTCAGATGCC
58669189 CAAATATCCT
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
92 3 0.04
93 69 0.96
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCAGATGCCTAGTTACATCTCAC
Found at i:58670937 original size:41 final size:41
Alignment explanation
Indices: 58670891--58670991 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 41
58670881 TCGACCTCGA
*
58670891 GTCGATGAGACACTGGGTGTCACTAAATTT-CTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACGAAATTTACTTCGGATAG
* ** * *
58670931 ATTCGATGAGGTACT-GG-GT-ACGAACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACGAAATTTACTTCGGATAG
*
58670970 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
58670992 ACTATTACTT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
38 17 0.37
39 13 0.28
40 4 0.09
41 12 0.26
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (41 bp):
GTCGATGAGACACTGGGTGTCACGAAATTTACTTCGGATAG
Found at i:58671000 original size:39 final size:40
Alignment explanation
Indices: 58670893--58671003 Score: 104
Period size: 39 Copynumber: 2.8 Consensus size: 40
58670883 GACCTCGAGT
* **
58670893 CGATGAGACACTGGGTGTC-ACTAAATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAACT--ATTACTTCGGATAGAGC
** * *
58670934 CGATGAGGTACTGGGT-ACGAACT-TTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTC-AACTATTACTTCGGATAGAGC
58670972 CGATGAGACACTGGGTGTCAACTATTACTTCG
1 CGATGAGACACTGGGTGTCAACTATTACTTCG
58671004 AACGATCCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
38 18 0.32
39 20 0.36
40 1 0.02
41 14 0.25
42 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAGC
Found at i:58671157 original size:18 final size:18
Alignment explanation
Indices: 58671136--58671176 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
58671126 ATATAAAAAA
58671136 AGAAATT-GAATTATGAAT
1 AGAAATTGGAATTATG-AT
*
58671154 AGAAATTGGAATTGTGAT
1 AGAAATTGGAATTATGAT
58671172 AGAAA
1 AGAAA
58671177 GAGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (18 bp):
AGAAATTGGAATTATGAT
Found at i:58673403 original size:41 final size:41
Alignment explanation
Indices: 58673346--58673428 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
58673336 GAAAAGTCTA
58673346 AACATTGAGTCAATTAAATAAGTAGGAAAAAAATTGAAACT
1 AACATTGAGTCAATTAAATAAGTAGGAAAAAAATTGAAACT
58673387 AACATTGAGTCAATTAAATAAGTAGGAAAAAAATTGAAACT
1 AACATTGAGTCAATTAAATAAGTAGGAAAAAAATTGAAACT
58673428 A
1 A
58673429 TTAAAATAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.24
Consensus pattern (41 bp):
AACATTGAGTCAATTAAATAAGTAGGAAAAAAATTGAAACT
Found at i:58691162 original size:43 final size:42
Alignment explanation
Indices: 58691000--58691167 Score: 160
Period size: 43 Copynumber: 4.0 Consensus size: 42
58690990 TCGTACAATT
*
58691000 CCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATG
1 CCAATGTCCCAGACGTGGTCTTACATG-AATCACATATCGATG
* * * * * *
58691043 TCACTGCCCCAGATAG-GGTCTTACACGAATCAAATA-CGATG
1 CCAATGTCCCAGA-CGTGGTCTTACATGAATCACATATCGATG
** * * *
58691084 CTGATGTCCCCGACATGGTCTTACACTTAATCACATATCGATG
1 CCAATGTCCCAGACGTGGTCTTACA-TGAATCACATATCGATG
* *
58691127 CCAAAGTCCCAGACGTGGTCTTACATGAGAACACATATCGA
1 CCAATGTCCCAGACGTGGTCTTACATGA-ATCACATATCGA
58691168 AAATCCTATG
Statistics
Matches: 95, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
41 21 0.22
42 18 0.19
43 55 0.58
44 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (42 bp):
CCAATGTCCCAGACGTGGTCTTACATGAATCACATATCGATG
Found at i:58700023 original size:17 final size:17
Alignment explanation
Indices: 58700001--58700036 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
58699991 TTACGAGGTC
* *
58700001 ATTAGTGTTATATTAAA
1 ATTAGTGTCATATCAAA
58700018 ATTAGTGTCATATCAAA
1 ATTAGTGTCATATCAAA
58700035 AT
1 AT
58700037 ATTTAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (17 bp):
ATTAGTGTCATATCAAA
Found at i:58702639 original size:18 final size:18
Alignment explanation
Indices: 58702605--58702639 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58702595 TATGCCAAAA
**
58702605 TGGTATCGATATTTAATT
1 TGGTATCGATACCTAATT
58702623 TGGTATCGATACCTAAT
1 TGGTATCGATACCTAAT
58702640 AACAAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (18 bp):
TGGTATCGATACCTAATT
Found at i:58702652 original size:21 final size:21
Alignment explanation
Indices: 58702626--58702676 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
58702616 TTTAATTTGG
58702626 TATCGATACCTAATAACAAA-A
1 TATCGATACCT-ATAACAAAGA
*
58702647 TATCGATACCTATTACAAAGA
1 TATCGATACCTATAACAAAGA
*
58702668 TATTGATAC
1 TATCGATAC
58702677 TTTGTGCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (21 bp):
TATCGATACCTATAACAAAGA
Found at i:58704867 original size:48 final size:49
Alignment explanation
Indices: 58704796--58705073 Score: 229
Period size: 48 Copynumber: 5.9 Consensus size: 49
58704786 GTAAGATGCT
* *
58704796 GATGCCATGTCCCGGACATGGTCTTACACTAGCTCAT-ATGTCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATATCGAGGCC
* * * *
58704844 GATGCCATGTCCCAGACATGGTCTTACACTAGCTC-TCGTCTCCATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATATCGAGGCC
* * * * * *
58704892 GATACCATGT-CCA-ACATGGTCTTCCATTGGCTCA-CA-ATCAACGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATATCGAGGCC
* * * **
58704937 GATGCCATGT-CCA-ACATGGTCTTACACTGGCTC-TCATAAC-ATTGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATATCGA-GGCC
* * * * * * * *
58704983 GATGCCATGTTCCAAACATGGTCTTACACTGGCACATGAAAT-GTGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATATCGAGGCC
*
58705031 GATGCCATGTCCCAGACATGGTCTTACACTAGCACA-CATATCG
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATATCG
58705074 CCCTAGTACC
Statistics
Matches: 188, Mismatches: 32, Indels: 20
0.78 0.13 0.08
Matches are distributed among these distances:
45 39 0.21
46 31 0.16
47 10 0.05
48 105 0.56
49 3 0.02
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATATCGAGGCC
Found at i:58709507 original size:16 final size:15
Alignment explanation
Indices: 58709466--58709510 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
58709456 CAAAGATAAC
58709466 AAGAAATCCAAG-TA
1 AAGAAATCCAAGATA
58709480 AAGAAATCCAAGATA
1 AAGAAATCCAAGATA
*
58709495 GAGAAATTCCAAGATA
1 AAGAAA-TCCAAGATA
58709511 CGATACTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 12 0.43
15 7 0.25
16 9 0.32
ACGTcount: A:0.56, C:0.13, G:0.16, T:0.16
Consensus pattern (15 bp):
AAGAAATCCAAGATA
Found at i:58713037 original size:48 final size:45
Alignment explanation
Indices: 58712972--58713175 Score: 212
Period size: 45 Copynumber: 4.4 Consensus size: 45
58712962 CATGTCTTAG
* * * *
58712972 ACATGGAT-TTACACTAGCTCACATGTCGAGGTCGATGCCATGTCCCA
1 ACATGG-TCTTACACTAGCTCACA-ATCAACGCCGATGCCATGT-CCA
* * ** * * *
58713019 GACATGGTCTTACGCTAGCTCTCGTCTCCACGCAGATGCCGTGTCCA
1 -ACATGGTCTTACACTAGCTCAC-AATCAACGCCGATGCCATGTCCA
*
58713066 ACATGGTCTTACACTGGCTCACAATCAACGCCGATGCCATGTCCA
1 ACATGGTCTTACACTAGCTCACAATCAACGCCGATGCCATGTCCA
* * *
58713111 ACATGGTCTTACACTGGCTCTCAATCAATGCCGATGCCATGTCCA
1 ACATGGTCTTACACTAGCTCACAATCAACGCCGATGCCATGTCCA
*
58713156 ACATGGTCTTACACTGGCTC
1 ACATGGTCTTACACTAGCTC
58713176 TCATAACATT
Statistics
Matches: 135, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
45 81 0.60
46 19 0.14
47 4 0.03
48 31 0.23
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.25
Consensus pattern (45 bp):
ACATGGTCTTACACTAGCTCACAATCAACGCCGATGCCATGTCCA
Found at i:58713110 original size:45 final size:45
Alignment explanation
Indices: 58713004--58713178 Score: 242
Period size: 45 Copynumber: 3.8 Consensus size: 45
58712994 ATGTCGAGGT
* * ** *
58713004 CGATGCCATGTCCCAGACATGGTCTTACGCTAGCTCTCGTCTCCACGC
1 CGATGCCATGT-CCA-ACATGGTCTTACACTGGCTCTC-AATCAACGC
* * *
58713052 AGATGCCGTGTCCAACATGGTCTTACACTGGCTCACAATCAACGC
1 CGATGCCATGTCCAACATGGTCTTACACTGGCTCTCAATCAACGC
*
58713097 CGATGCCATGTCCAACATGGTCTTACACTGGCTCTCAATCAATGC
1 CGATGCCATGTCCAACATGGTCTTACACTGGCTCTCAATCAACGC
58713142 CGATGCCATGTCCAACATGGTCTTACACTGGCTCTCA
1 CGATGCCATGTCCAACATGGTCTTACACTGGCTCTCA
58713179 TAACATTGTC
Statistics
Matches: 115, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
45 84 0.73
46 19 0.17
47 3 0.03
48 9 0.08
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (45 bp):
CGATGCCATGTCCAACATGGTCTTACACTGGCTCTCAATCAACGC
Found at i:58713508 original size:26 final size:25
Alignment explanation
Indices: 58713469--58713552 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 25
58713459 TGATACAAAT
*
58713469 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAAT-GGTTAGGTAAATGTTTCA
58713495 TGATAATGGATTAGGTAAATGTTTCA
1 TGATAATGG-TTAGGTAAATGTTTCA
58713521 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAAT-GGTTAGGTAAATGTTTCA
58713547 TGATAA
1 TGATAA
58713553 GAATTTCATG
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
25 2 0.04
26 51 0.93
27 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (25 bp):
TGATAATGGTTAGGTAAATGTTTCA
Found at i:58721623 original size:26 final size:26
Alignment explanation
Indices: 58721584--58721641 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
58721574 TGATACAAAT
*
58721584 TGATAATAGTTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
58721610 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
58721636 TGATAA
1 TGATAA
58721642 GAATTTCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:58723159 original size:26 final size:26
Alignment explanation
Indices: 58723130--58723179 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
58723120 TACAGTTTTA
58723130 CCCTAGGAGATAAATT-ACCGAAATAC
1 CCCTAGG-GATAAATTGACCGAAATAC
* *
58723156 CCCTAGGGTTAAATTGACCTAAAT
1 CCCTAGGGATAAATTGACCGAAAT
58723180 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (26 bp):
CCCTAGGGATAAATTGACCGAAATAC
Found at i:58724020 original size:48 final size:48
Alignment explanation
Indices: 58723949--58724169 Score: 164
Period size: 50 Copynumber: 4.6 Consensus size: 48
58723939 GTAAGGTGTC
* * * *
58723949 GATGCCATGTCCCGGACATGGTCTTTCAGTGGCTCACACATC-AAAGTT
1 GATGCCATGTCCCAGACATGGTCTTACAATGGCTCACACATCGAAA-CT
* * * * *
58723997 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGACACT
1 GATGCCATGTCCCAGACATGGTCTTACAATG--GCTCACACATCGAAACT
* ***
58724047 GATGCCATGTCCCAGACATGGTCTTACAATGGCTCTCATCTATCGGTGGC-
1 GATGCCATGTCCCAGACATGGTCTTACAATGGCTCACA-C-ATC-GAAACT
* * ** * * * *
58724097 GATGCTATGCCCCAGACATGGTCTTACGCT-G-ACACATATC-AAGCC
1 GATGCCATGTCCCAGACATGGTCTTACAATGGCTCACACATCGAAACT
58724142 GATGCCATGTCCCAGACATGGTCTTACA
1 GATGCCATGTCCCAGACATGGTCTTACA
58724170 CTAGCGCACA
Statistics
Matches: 138, Mismatches: 28, Indels: 17
0.75 0.15 0.09
Matches are distributed among these distances:
44 2 0.01
45 25 0.18
46 3 0.02
48 35 0.25
49 1 0.01
50 68 0.49
51 4 0.03
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACAATGGCTCACACATCGAAACT
Found at i:58724057 original size:50 final size:49
Alignment explanation
Indices: 58723996--58724171 Score: 184
Period size: 50 Copynumber: 3.6 Consensus size: 49
58723986 ACATCAAAGT
58723996 TGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGACAC
1 TGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGA-AC
* * * **
58724046 TGATGCCATGTCCCAGACATGGTCTTACAATGGCTCTCATCTATCGGTGGC
1 TGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATC-G-AAC
* * * *
58724097 -GATGCTATGCCCCAGACATGGTCTTACGCTGA----CACATATC-AAGC
1 TGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAA-C
*
58724141 CGATGCCATGTCCCAGACATGGTCTTACACT
1 TGATGCCATGTCCCAGACATGGTCTTACACT
58724172 AGCGCACATA
Statistics
Matches: 105, Mismatches: 17, Indels: 13
0.78 0.13 0.10
Matches are distributed among these distances:
44 1 0.01
45 27 0.26
46 6 0.06
50 69 0.66
51 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.27
Consensus pattern (49 bp):
TGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAAC
Found at i:58724135 original size:98 final size:94
Alignment explanation
Indices: 58723948--58724169 Score: 241
Period size: 98 Copynumber: 2.3 Consensus size: 94
58723938 GGTAAGGTGT
* * * ** *
58723948 CGATGCCATGTCCCGGACATGGTCTTTCAGTGGCTCACACATCAAAGTTGATGCCATGTCCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACAATGGCTCACACATCAAAGGCGATGCCATGCCCCAGA
*
58724013 CATGGTCTTACACTGACTCTCATATATCGACA-C
66 CATGGTCTTACACTGA--C-CACATATC-A-AGC
* * *** *
58724046 TGATGCCATGTCCCAGACATGGTCTTACAATGGCTCTCATCTATCGGTGGCGATGCTATGCCCCA
1 CGATGCCATGTCCCAGACATGGTCTTACAATGGCTCACA-C-ATCAAAGGCGATGCCATGCCCCA
*
58724111 GACATGGTCTTACGCTGA-CACATATCAAGC
64 GACATGGTCTTACACTGACCACATATCAAGC
58724141 CGATGCCATGTCCCAGACATGGTCTTACA
1 CGATGCCATGTCCCAGACATGGTCTTACA
58724170 CTAGCGCACA
Statistics
Matches: 106, Mismatches: 15, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
94 1 0.01
95 30 0.28
96 7 0.07
98 34 0.32
99 1 0.01
100 33 0.31
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (94 bp):
CGATGCCATGTCCCAGACATGGTCTTACAATGGCTCACACATCAAAGGCGATGCCATGCCCCAGA
CATGGTCTTACACTGACCACATATCAAGC
Found at i:58727300 original size:32 final size:29
Alignment explanation
Indices: 58727264--58727335 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 29
58727254 TTATATATTT
*
58727264 TATTAATAAATTAAATAATTGAATTAATAAAA
1 TATTAATAAATTAAATAATT--ATGAA-AAAA
58727296 TATTAAT-AA-TAAATAATTATGAAAAAA
1 TATTAATAAATTAAATAATTATGAAAAAA
58727323 TATATAATAAATT
1 TAT-TAATAAATT
58727336 TCATTTTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
27 7 0.19
28 8 0.22
29 2 0.06
30 10 0.28
31 2 0.06
32 7 0.19
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
TATTAATAAATTAAATAATTATGAAAAAA
Found at i:58732939 original size:61 final size:60
Alignment explanation
Indices: 58732797--58732968 Score: 154
Period size: 60 Copynumber: 2.8 Consensus size: 60
58732787 TCAAGCTTTA
* * *
58732797 CTGGGCC-TAAGCTCTATTCAGAAATCAGAGT-TAACTGGGCCTTAGCCCATATTAATATTAAT
1 CTGGGCCAT-AGCTCTATT-ACAAATCAGAGTAT-ACTGGGCC-TAGCCCATATCAATATCAAT
** * *
58732859 CTGGGCCATAGC-CCCTTACAATATCAGAGTATACTGGGCCTAGCCCATGTCAGTATCAAT
1 CTGGGCCATAGCTCTATTACAA-ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAAT
* * * * *
58732919 CTGGGTCGTAGCTCTATTACAAGTC-GAGATATATTGGGCCTTGCCCATAT
1 CTGGGCCATAGCTCTATTACAAATCAGAG-TATACTGGGCCTAGCCCATAT
58732969 TAACACAGTT
Statistics
Matches: 90, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
59 3 0.03
60 49 0.54
61 26 0.29
62 11 0.12
63 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (60 bp):
CTGGGCCATAGCTCTATTACAAATCAGAGTATACTGGGCCTAGCCCATATCAATATCAAT
Done.