Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 131 of 182
Found at i:40289549 original size:29 final size:29
Alignment explanation
Indices: 40289507--40289563 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
40289497 ATAATCTAAA
* *
40289507 TTACCCGCACCAGCTCAACAGACTCGAGG
1 TTACCCACACCAGCTAAACAGACTCGAGG
*
40289536 TTACCCACACCAGCTAAACAGCCTCGAG
1 TTACCCACACCAGCTAAACAGACTCGAG
40289564 TCTCTCCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.39, G:0.18, T:0.14
Consensus pattern (29 bp):
TTACCCACACCAGCTAAACAGACTCGAGG
Found at i:40291007 original size:32 final size:32
Alignment explanation
Indices: 40290966--40291026 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
40290956 TCAACTTAAT
40290966 TTGTTGGTGGAGTATATCCGTCTTGTTTACAA
1 TTGTTGGTGGAGTATATCCGTCTTGTTTACAA
40290998 TTGTTGGTGGAGTATATCCGTCTTGTTTA
1 TTGTTGGTGGAGTATATCCGTCTTGTTTA
40291027 GTGGTATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.16, C:0.11, G:0.26, T:0.46
Consensus pattern (32 bp):
TTGTTGGTGGAGTATATCCGTCTTGTTTACAA
Found at i:40307118 original size:51 final size:50
Alignment explanation
Indices: 40306953--40307124 Score: 220
Period size: 51 Copynumber: 3.4 Consensus size: 50
40306943 AGTGAAAGTG
** *
40306953 ATGGTCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGGT
* * *
40307004 A-GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
* * * *
40307053 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
40307104 AATGGTCACATGTGTAGTACT
1 -ATGGTCACATGTGTAGTACT
40307125 GTGTATCAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
49 3 0.03
50 39 0.38
51 59 0.58
52 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
Found at i:40307129 original size:35 final size:35
Alignment explanation
Indices: 40307090--40307159 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
40307080 AGGCTACTAC
**
40307090 GTGTATCGGATGGTAATGGTCACATGTGTAGTACT
1 GTGTATCAAATGGTAATGGTCACATGTGTAGTACT
40307125 GTGTATCAAATGGTAATGGTCACATGTGTAGTACT
1 GTGTATCAAATGGTAATGGTCACATGTGTAGTACT
40307160 ATGTGTAGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (35 bp):
GTGTATCAAATGGTAATGGTCACATGTGTAGTACT
Found at i:40307249 original size:45 final size:45
Alignment explanation
Indices: 40307185--40307273 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
40307175 TGTGAACTGA
* *
40307185 ACATCATTGATTAGGAAGGTGGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAAGAAGGTGGTTGCTATGTGCTGAATCCACCGG
*
40307230 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
1 ACATCATTGATTAAGAAGGTGGTTGCTATGTGCTGAATCCACCG
40307274 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (45 bp):
ACATCATTGATTAAGAAGGTGGTTGCTATGTGCTGAATCCACCGG
Found at i:40307420 original size:45 final size:45
Alignment explanation
Indices: 40307364--40307455 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
40307354 TACTATGTGA
* *
40307364 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
* *
40307409 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
40307454 AC
1 AC
40307456 TGAGTATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:40307463 original size:184 final size:185
Alignment explanation
Indices: 40307153--40307524 Score: 667
Period size: 184 Copynumber: 2.0 Consensus size: 185
40307143 GTCACATGTG
*
40307153 TAGTACTATGTGTAGGCTACTATGTGAACTGAACATCATTGATTAGGAAGGTGGTTGCTATGTGC
1 TAGTACTATGTGTAGGCTACTATGTGAACCGAACATCATTGATTAGGAAGGTGGTTGCTATGTGC
*
40307218 TGATTCCACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGAGTATCTGT
66 TGATTCCACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGAGTATCTAT
*
40307283 TATTATT-CTAAGTGTTCATC-GGCAAATTGACTAAGTGTAATTGAATAATGAATA
131 TATTATTCCGAAGTGTTCATCTGG-AAATTGACTAAGTGTAATTGAATAATGAATA
*
40307337 TAGTACTATGTGTAGGCTACTATGTGAACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGC
1 TAGTACTATGTGTAGGCTACTATGTGAACCGAACATCATTGATTAGGAAGGTGGTTGCTATGTGC
* *
40307402 TGATTCCACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCCACTGAGTATCTAT
66 TGATTCCACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGAGTATCTAT
40307467 TATTATTCCGAAGTGTTCATCTGGAAATTGACTAAGTGTAATTGAATAATGAATA
131 TATTATTCCGAAGTGTTCATCTGGAAATTGACTAAGTGTAATTGAATAATGAATA
40307522 TAG
1 TAG
40307525 GTGTGGAATT
Statistics
Matches: 180, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
184 132 0.73
185 46 0.26
186 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (185 bp):
TAGTACTATGTGTAGGCTACTATGTGAACCGAACATCATTGATTAGGAAGGTGGTTGCTATGTGC
TGATTCCACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGAGTATCTAT
TATTATTCCGAAGTGTTCATCTGGAAATTGACTAAGTGTAATTGAATAATGAATA
Found at i:40313082 original size:29 final size:29
Alignment explanation
Indices: 40313050--40313241 Score: 167
Period size: 29 Copynumber: 6.6 Consensus size: 29
40313040 AGCTTCGGCT
*
40313050 ATCGATTATGAAAAGGGATGGTGACGACC
1 ATCGAATATGAAAAGGGATGGTGACGACC
* * * *
40313079 ATCGAATATGAAAAGTGATAGCT-TC-AGCT
1 ATCGAATATGAAAAGGGAT-GGTGACGA-CC
* *
40313108 ATCGAATATGAAAAGGGATAGCT-ACGGA-T
1 ATCGAATATGAAAAGGGAT-GGTGAC-GACC
* * *
40313137 ATCGATTATGAAAAGGGATAGTGATGACC
1 ATCGAATATGAAAAGGGATGGTGACGACC
*
40313166 ATCAAATATGAAAAGGGATGGTGACGACC
1 ATCGAATATGAAAAGGGATGGTGACGACC
* ** *
40313195 ATCGATTAATGAAAAGGGATGGTTTCAACC
1 ATCGAAT-ATGAAAAGGGATGGTGACGACC
*
40313225 ATCAAATATGAAAAGGG
1 ATCGAATATGAAAAGGG
40313242 TCGGTTACGA
Statistics
Matches: 133, Mismatches: 23, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
28 4 0.03
29 102 0.77
30 26 0.20
31 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (29 bp):
ATCGAATATGAAAAGGGATGGTGACGACC
Found at i:40313118 original size:58 final size:58
Alignment explanation
Indices: 40313028--40313241 Score: 229
Period size: 58 Copynumber: 3.7 Consensus size: 58
40313018 TCATTGGCCA
* * * * *
40313028 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAAT
1 ATGAAAAGGGATAGCTTCAGCCATCAAATATGAAAAGGGATGGTGACGACCATCGATT
* * * * *
40313086 ATGAAAAGTGATAGCTTCAGCTATCGAATATGAAAAGGGATAGCT-ACGGA-TATCGATT
1 ATGAAAAGGGATAGCTTCAGCCATCAAATATGAAAAGGGAT-GGTGAC-GACCATCGATT
*
40313144 ATGAAAAGGGATAG--TGATGACCATCAAATATGAAAAGGGATGGTGACGACCATCGATT
1 ATGAAAAGGGATAGCTTCA-G-CCATCAAATATGAAAAGGGATGGTGACGACCATCGATT
* * *
40313202 AATGAAAAGGGATGGTTTCAACCATCAAATATGAAAAGGG
1 -ATGAAAAGGGATAGCTTCAGCCATCAAATATGAAAAGGG
40313242 TCGGTTACGA
Statistics
Matches: 132, Mismatches: 15, Indels: 17
0.80 0.09 0.10
Matches are distributed among these distances:
56 2 0.02
57 5 0.04
58 87 0.66
59 36 0.27
61 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (58 bp):
ATGAAAAGGGATAGCTTCAGCCATCAAATATGAAAAGGGATGGTGACGACCATCGATT
Found at i:40313199 original size:87 final size:88
Alignment explanation
Indices: 40313027--40313214 Score: 247
Period size: 87 Copynumber: 2.1 Consensus size: 88
40313017 ATCATTGGCC
* * * *
40313027 AATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAATATGAAA
1 AATGAAAAGGGATAGCTACGGATATCGATTATGAAAAGGGATAGTGACGACCATCAAATATGAAA
* * *
40313092 AGTGATAGCTTCAGCTATCGAAT
66 AGGGATAGCTACAGCCATCGAAT
*
40313115 -ATGAAAAGGGATAGCTACGGATATCGATTATGAAAAGGGATAGTGATGACCATCAAATATGAAA
1 AATGAAAAGGGATAGCTACGGATATCGATTATGAAAAGGGATAGTGACGACCATCAAATATGAAA
* *
40313179 AGGGAT-GGTGAC-GACCATCGATT
66 AGGGATAGCT-ACAG-CCATCGAAT
40313202 AATGAAAAGGGAT
1 AATGAAAAGGGAT
40313215 GGTTTCAACC
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
86 3 0.03
87 72 0.83
88 12 0.14
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (88 bp):
AATGAAAAGGGATAGCTACGGATATCGATTATGAAAAGGGATAGTGACGACCATCAAATATGAAA
AGGGATAGCTACAGCCATCGAAT
Found at i:40317394 original size:49 final size:49
Alignment explanation
Indices: 40317337--40317652 Score: 509
Period size: 49 Copynumber: 6.6 Consensus size: 49
40317327 TTAAACCCAT
40317337 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
40317386 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
40317435 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
40317484 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
*
40317533 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
* * ** * * *
40317580 ATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAATGTGATGG
1 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
*
40317627 ATGTGAAAGTGCATA-A-ATGTGATAAG
1 ATGTGAAAGTGTATATATATGTGATAAG
40317653 TCCCGAAGGG
Statistics
Matches: 256, Mismatches: 9, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
47 95 0.37
48 1 0.00
49 160 0.62
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.31
Consensus pattern (49 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
Found at i:40326793 original size:50 final size:50
Alignment explanation
Indices: 40326714--40326952 Score: 227
Period size: 50 Copynumber: 4.8 Consensus size: 50
40326704 AGGGAATGAA
*
40326714 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGTACCGAGATAAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAG
* *
40326764 GTCCCATGTAAGATCATGTCTGGTG-CATGGCGTTGGCACCGAGATGAGAG
1 GTCCCATGTAAGACCATGTCTGG-GACATGGCGTTGGCACCGAGATAAGAG
* * * * * *
40326814 GTCCCCTGTAAGACCATGTCTGAGACATGGCATGGGCACCGATATAAGAAAC
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATAAG--AG
* * * * * * *
40326866 ATCCCATGTAAGACCATATCTGGGATATGGCATTGGTAGTAC-AGGA-AACA-
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA--CCGA-GATAAGAG
* *
40326916 -TCCCATGTAAGAGCATGTCTGGGACATGGCTTTGGCA
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
40326953 TGTTATTATC
Statistics
Matches: 156, Mismatches: 26, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
49 33 0.21
50 84 0.54
51 2 0.01
52 32 0.21
53 3 0.02
54 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAG
Found at i:40339842 original size:36 final size:36
Alignment explanation
Indices: 40339802--40339874 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
40339792 GAAGTTCAAG
* * * *
40339802 GAAGCCATAACGGGTCTCATTGATCAAGTTTGGGCA
1 GAAGCCATAACGGGACTAATTCATCAAGCTTGGGCA
* * *
40339838 GAAGCTATCACGGGACTAATTCATTAAGCTTGGGCA
1 GAAGCCATAACGGGACTAATTCATCAAGCTTGGGCA
40339874 G
1 G
40339875 GCACTCCGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (36 bp):
GAAGCCATAACGGGACTAATTCATCAAGCTTGGGCA
Found at i:40339979 original size:9 final size:9
Alignment explanation
Indices: 40339965--40339990 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40339955 TTGAATCCAT
40339965 TTTTAGTTA
1 TTTTAGTTA
40339974 TTTTAGTTA
1 TTTTAGTTA
40339983 TTTTAGTT
1 TTTTAGTT
40339991 TGAACACCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (9 bp):
TTTTAGTTA
Found at i:40340044 original size:39 final size:38
Alignment explanation
Indices: 40339985--40340099 Score: 149
Period size: 39 Copynumber: 3.0 Consensus size: 38
40339975 TTTAGTTATT
* ** *
40339985 TTAGTTTGAACACCGCTAATATGAGTCCTTAATTATGTC
1 TTAGTTTGAACATCATTAATATGAGT-TTTAATTATGTC
*
40340024 TTAGTTTGAACATCATTAATATGCGTTTTTAATTATGTC
1 TTAGTTTGAACATCATTAATATGAG-TTTTAATTATGTC
* *
40340063 TTAGTTTGAATATCATTAATATGTGTTTTAATTATGT
1 TTAGTTTGAACATCATTAATATGAGTTTTAATTATGT
40340100 GTTTTTAATT
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 12 0.18
39 55 0.81
40 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (38 bp):
TTAGTTTGAACATCATTAATATGAGTTTTAATTATGTC
Found at i:40340100 original size:13 final size:14
Alignment explanation
Indices: 40340078--40340109 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40340068 TTGAATATCA
40340078 TTAA-TATGTG-TT
1 TTAATTATGTGTTT
40340090 TTAATTATGTGTTT
1 TTAATTATGTGTTT
40340104 TTAATT
1 TTAATT
40340110 CTGGCATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.22
13 6 0.33
14 8 0.44
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (14 bp):
TTAATTATGTGTTT
Found at i:40342395 original size:29 final size:29
Alignment explanation
Indices: 40342363--40342433 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
40342353 TAGCAGATGC
*
40342363 TATCTCTTTTCATAATCGATAGACGAAGT
1 TATCCCTTTTCATAATCGATAGACGAAGT
* * *
40342392 TATCCCTTTTCATATTTGATAGCCGAAGT
1 TATCCCTTTTCATAATCGATAGACGAAGT
40342421 TATCCCTTTTCAT
1 TATCCCTTTTCAT
40342434 TGGTCGTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.42
Consensus pattern (29 bp):
TATCCCTTTTCATAATCGATAGACGAAGT
Found at i:40344325 original size:20 final size:20
Alignment explanation
Indices: 40344302--40344348 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
40344292 GGGTTAAGAT
*
40344302 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
40344322 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
40344342 TGAGCTG
1 TGAGCTG
40344349 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:40347728 original size:16 final size:16
Alignment explanation
Indices: 40347689--40347728 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
40347679 ATCGGTCTAG
40347689 TTAGTTATTTAGTTAAT
1 TTAGTT-TTTAGTTAAT
**
40347706 TCGGTTTTTAGTTAAT
1 TTAGTTTTTAGTTAAT
40347722 TTAGTTT
1 TTAGTTT
40347729 AATTATGTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.60
Consensus pattern (16 bp):
TTAGTTTTTAGTTAAT
Found at i:40347738 original size:26 final size:24
Alignment explanation
Indices: 40347689--40347739 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
40347679 ATCGGTCTAG
*
40347689 TTAGTTATTTAGTTAATTCGGTTT
1 TTAGTTATTTAGTTAATTAGGTTT
*
40347713 TTAGTTAATTTAGTTTAATTATGTTT
1 TTAGTT-ATTTAG-TTAATTAGGTTT
40347739 T
1 T
40347740 GGTTTGGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 6 0.26
25 6 0.26
26 11 0.48
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.61
Consensus pattern (24 bp):
TTAGTTATTTAGTTAATTAGGTTT
Found at i:40353508 original size:51 final size:51
Alignment explanation
Indices: 40353361--40353497 Score: 175
Period size: 51 Copynumber: 2.7 Consensus size: 51
40353351 CTACCATCAA
* * *
40353361 ATCTCTAAGAATATAATATCATATCTTCTAAGATTCCATATCTTAGATAAG
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
* * ** * * * *
40353412 ATATGTAATCTTATAAAATAATATCTTATAAGATTCCATATCATATCTAAG
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
40353463 ATCTCTAAGATTATAATATCATATCTTCTAAGATT
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATT
40353498 AGTTACCATA
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (51 bp):
ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
Found at i:40356094 original size:51 final size:51
Alignment explanation
Indices: 40355947--40356083 Score: 175
Period size: 51 Copynumber: 2.7 Consensus size: 51
40355937 CTACCATCAA
* * *
40355947 ATCTCTAAGAATATAATATCATATCTTCTAAGATTCCATATCTTAGATAAG
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
* * ** * * * *
40355998 ATATGTAATCTTATAAAATAATATCTTATAAGATTCCATATCATATCTAAG
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
40356049 ATCTCTAAGATTATAATATCATATCTTCTAAGATT
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATT
40356084 AGTTACCATA
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (51 bp):
ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
Found at i:40359613 original size:16 final size:16
Alignment explanation
Indices: 40359574--40359613 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
40359564 ATCGGTCTAG
*
40359574 TTAGTTATTTAGTTAAT
1 TTAGTT-TTTAGTTAAA
*
40359591 TTGGTTTTTAGTTAAA
1 TTAGTTTTTAGTTAAA
40359607 TTAGTTT
1 TTAGTTT
40359614 AAATATGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.60
Consensus pattern (16 bp):
TTAGTTTTTAGTTAAA
Found at i:40369815 original size:29 final size:29
Alignment explanation
Indices: 40369769--40369946 Score: 241
Period size: 29 Copynumber: 6.1 Consensus size: 29
40369759 TGTGCTAAAT
* *
40369769 GATGGTCGTAACCGTCCCTTTTCATATTC
1 GATGGTCGTCACCATCCCTTTTCATATTC
** *
40369798 GATGGTCGAAACCATCCCTTTTCATTAATC
1 GATGGTCGTCACCATCCCTTTTCA-TATTC
* *
40369828 GATAGTTGTCACCATCCCTTTTCATATTC
1 GATGGTCGTCACCATCCCTTTTCATATTC
*
40369857 GATGGTCGTCACCATCCCTTTTCATATTT
1 GATGGTCGTCACCATCCCTTTTCATATTC
40369886 GATGGTCGTCACCATCCCTTTTCATAGTT-
1 GATGGTCGTCACCATCCCTTTTCATA-TTC
* *
40369915 GATGGTCCTCACCATCCCTTTTCATAATC
1 GATGGTCGTCACCATCCCTTTTCATATTC
40369944 GAT
1 GAT
40369947 AGCCGAAGCT
Statistics
Matches: 133, Mismatches: 13, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
28 1 0.01
29 106 0.80
30 26 0.20
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (29 bp):
GATGGTCGTCACCATCCCTTTTCATATTC
Found at i:40374188 original size:21 final size:22
Alignment explanation
Indices: 40374163--40374220 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
40374153 ATGTCCCTGG
40374163 CCCACACGAGCGTGTGCCT-CAT
1 CCCACACGAGCGTGTGCCTAC-T
40374185 -CCACAC-AGCTGTGTGCCTACT
1 CCCACACGAGC-GTGTGCCTACT
*
40374206 CCCACACGGGCGTGT
1 CCCACACGAGCGTGT
40374221 TGACCCCGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 3 0.10
21 15 0.48
22 11 0.35
23 2 0.06
ACGTcount: A:0.17, C:0.40, G:0.24, T:0.19
Consensus pattern (22 bp):
CCCACACGAGCGTGTGCCTACT
Found at i:40374265 original size:21 final size:20
Alignment explanation
Indices: 40374206--40374271 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
40374196 TGTGCCTACT
40374206 CCCACACGGGCGTGTTGACC
1 CCCACACGGGCGTGTTGACC
* * ***
40374226 CCGAAAATTAGCG-GTTGACC
1 CC-CACACGGGCGTGTTGACC
40374246 TCCCACACGGGCGTGTTGACC
1 -CCCACACGGGCGTGTTGACC
40374267 CCCAC
1 CCCAC
40374272 TTGGTCTAAG
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.20, C:0.38, G:0.26, T:0.17
Consensus pattern (20 bp):
CCCACACGGGCGTGTTGACC
Found at i:40380093 original size:16 final size:17
Alignment explanation
Indices: 40380062--40380099 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
40380052 ACAAAATCCA
40380062 AATTTATTTCCCAATTT
1 AATTTATTTCCCAATTT
40380079 AATTTATTT-CCAATTT
1 AATTTATTTCCCAATTT
40380095 -ATTTA
1 AATTTA
40380100 ATTGTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.24
16 7 0.33
17 9 0.43
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTATTTCCCAATTT
Found at i:40388229 original size:40 final size:40
Alignment explanation
Indices: 40388192--40388417 Score: 314
Period size: 40 Copynumber: 5.7 Consensus size: 40
40388182 GCTACTCGTT
* *
40388192 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
40388232 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
40388272 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
40388312 CAAATGCCTTCGGGCCTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
40388352 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
40388393 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
40388418 CATCATTCAA
Statistics
Matches: 171, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
39 2 0.01
40 156 0.91
41 13 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:40396221 original size:40 final size:39
Alignment explanation
Indices: 40396184--40396275 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
40396174 GCTACTCGTT
*
40396184 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
40396224 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
40396263 CAAATGCCTTCGG
1 CAAATGCCTTCGG
40396276 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:40396255 original size:39 final size:40
Alignment explanation
Indices: 40396165--40396328 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
40396155 CGGAATTTAA
** *
40396165 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
40396205 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40396244 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
40396284 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40396324 CCGGA
1 CCGGA
40396329 CATCATTCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.30
40 58 0.55
41 12 0.11
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40398912 original size:44 final size:44
Alignment explanation
Indices: 40398849--40398939 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
40398839 GATCTAAACA
*
40398849 ATATAAACTTAATGAAAAGAATGAACATAAAGAACAATTCAAGG
1 ATATAAACTTAATGAAAAGAATGAACAAAAAGAACAATTCAAGG
40398893 ATATAAACTTAATGAAAAGAATGAACAAAAAGAACAATTCAAGG
1 ATATAAACTTAATGAAAAGAATGAACAAAAAGAACAATTCAAGG
40398937 ATA
1 ATA
40398940 GAGTTTAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.58, C:0.09, G:0.13, T:0.20
Consensus pattern (44 bp):
ATATAAACTTAATGAAAAGAATGAACAAAAAGAACAATTCAAGG
Found at i:40404641 original size:27 final size:26
Alignment explanation
Indices: 40404587--40404709 Score: 133
Period size: 27 Copynumber: 4.7 Consensus size: 26
40404577 AGAGGTCAAT
* * *
40404587 AAATGATCG-AATACCCCCACACGATA
1 AAATGACCGAAATACCCCCATA-GGTA
*
40404613 AAATGATCGAAATACCCCCATAGTGTA
1 AAATGACCGAAATACCCCCATAG-GTA
* *
40404640 AATTGACCGAAATACCCTCATAAGGTA
1 AAATGACCGAAATACCCCCAT-AGGTA
40404667 AAATGACCGAAATA-CCCCATAGGGTA
1 AAATGACCGAAATACCCCCATA-GGTA
*
40404693 GAATGACCGAAATACCC
1 AAATGACCGAAATACCC
40404710 TTATAGGGTA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
25 1 0.01
26 32 0.38
27 49 0.58
28 2 0.02
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.18
Consensus pattern (26 bp):
AAATGACCGAAATACCCCCATAGGTA
Found at i:40404708 original size:53 final size:54
Alignment explanation
Indices: 40404611--40404722 Score: 165
Period size: 53 Copynumber: 2.1 Consensus size: 54
40404601 CCCCACACGA
* *
40404611 TAAAATGATCGAAATACCCCCATAGTGTAAATTGACCGAAATACCCTCATAAGG
1 TAAAATGACCGAAATACCCCCATAGGGTAAATTGACCGAAATACCCTCATAAGG
* *
40404665 TAAAATGACCGAAATA-CCCCATAGGGTAGAA-TGACCGAAATACCCTTATAGGG
1 TAAAATGACCGAAATACCCCCATAGGGTA-AATTGACCGAAATACCCTCATAAGG
40404718 TAAAA
1 TAAAA
40404723 AGATTGTTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
53 36 0.68
54 17 0.32
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (54 bp):
TAAAATGACCGAAATACCCCCATAGGGTAAATTGACCGAAATACCCTCATAAGG
Found at i:40406739 original size:14 final size:12
Alignment explanation
Indices: 40406690--40406731 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
40406680 ACTGGTCATA
40406690 GAGAGATTTGAG
1 GAGAGATTTGAG
* *
40406702 GAGGGATATT-TG
1 GAGAGAT-TTGAG
40406714 GAGAGATTTGAG
1 GAGAGATTTGAG
40406726 GAGAGA
1 GAGAGA
40406732 ATATTGAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (12 bp):
GAGAGATTTGAG
Found at i:40407291 original size:27 final size:27
Alignment explanation
Indices: 40407243--40407347 Score: 106
Period size: 27 Copynumber: 3.9 Consensus size: 27
40407233 GATAAATGAT
* *
40407243 CGAAATACCCCTATACGATAAAATAAC
1 CGAAATACCCCTATAGGGTAAAATAAC
* * *
40407270 CGAAATACCCCTATAGGGTAAATTGAT
1 CGAAATACCCCTATAGGGTAAAATAAC
*
40407297 CAAAATA-CCCTCATAGGG-AAAATTAAC
1 CGAAATACCCCT-ATAGGGTAAAA-TAAC
* *
40407324 CGAAATACCCCCATATGGTAAAAT
1 CGAAATACCCCTATAGGGTAAAAT
40407348 GATCAAAATA
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
26 7 0.11
27 48 0.77
28 7 0.11
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.21
Consensus pattern (27 bp):
CGAAATACCCCTATAGGGTAAAATAAC
Found at i:40407356 original size:27 final size:26
Alignment explanation
Indices: 40407236--40407358 Score: 102
Period size: 27 Copynumber: 4.6 Consensus size: 26
40407226 AGAGGTCGAT
* *
40407236 AAATGATCGAAATACCCCTATACGATA
1 AAATGATCGAAATACCCCCATA-GGTA
* * *
40407263 AAATAACCGAAATACCCCTATAGGGTA
1 AAATGATCGAAATACCCCCATA-GGTA
* * * *
40407290 AATTGATCAAAATACCCTCATAGGGA
1 AAATGATCGAAATACCCCCATAGGTA
* *
40407316 AAATTAACCGAAATACCCCCATATGGTA
1 AAA-TGATCGAAATACCCCCATA-GGTA
*
40407344 AAATGATCAAAATAC
1 AAATGATCGAAATAC
40407359 TTGATACGAG
Statistics
Matches: 74, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
26 5 0.07
27 63 0.85
28 6 0.08
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.21
Consensus pattern (26 bp):
AAATGATCGAAATACCCCCATAGGTA
Found at i:40419959 original size:5 final size:5
Alignment explanation
Indices: 40419951--40419980 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
40419941 AAATAAAAGA
*
40419951 AAATC AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT
40419981 CTAAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:40420219 original size:5 final size:5
Alignment explanation
Indices: 40420209--40420243 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
40420199 AGAAAGGGTA
* *
40420209 AAATC AAATC AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT
40420244 CTAAAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (5 bp):
AAATT
Found at i:40420373 original size:273 final size:267
Alignment explanation
Indices: 40419951--40420507 Score: 726
Period size: 300 Copynumber: 2.0 Consensus size: 267
40419941 AAATAAAAGA
40419951 AAATCAAATTAAATTAAATTAAATTAAATTCTAAAAAGAAAATGTAAATGAAAGCTTACGGGAAA
1 AAATCAAATTAAATTAAATTAAATTAAATTCTAAAAAGAAAATGTAAATGAAAGCTTACGGGAAA
*
40420016 GGAAGCTAAGGTAAGCCAAATCGATTTCAATGTCGCTTGTTTCTACAATAAAACAAAGCAAAAAC
66 GGAAGCTAAGGTAAGCCAAATCGATTTCAATGTCGCTTGTTTCTACAATAAAACAAAGAAAAAAC
40420081 AAAAAAGATGAGATTAAAT-G-AAC--AAATTACAAAGACAGTCAATGACAGTGTTATACTGAGT
131 AAAAAAGATGAGATTAAATAGAAACAAAAATTACAAAGACAGTCAATGACAGTGTTATACTGAGT
40420142 TGGAATTACATATTTCTTACCTGCGGAAAGTGTTGGGATGTATAGCTAACAAGTTGCAGAAAGGG
196 TGGAATTACATATTTCTTACCTGCGGAAAGTGTTGGGATGTATAGCTAACAAGTTGCAGAAAGGG
40420207 TAAAATC
261 TAAAATC
40420214 AAATCAAATTAAATTAAATTAAATTAAATTCTAAAAAGAAAATGTAAATGAAAGCTTACGGGAAA
1 AAATCAAATTAAATTAAATTAAATTAAATTCTAAAAAGAAAATGTAAATGAAAGCTTACGGGAAA
* *
40420279 GGAAGCTAAGGTAAGCCAAGGTAAGCCAAATCGATTTTAATGTCGCTTGTTTCTGCAATAAAACA
66 GGAAGC-----T-----AAGGTAAGCCAAATCGATTTCAATGTCGCTTGTTTCTACAATAAAACA
* *
40420344 AAGAAAAAATAAAAAAGATGAGATTAAATGAAGAAACAAAAAAGATGAGATTAAATGAACAAATT
121 AAGAAAAAACAAAAAAGATGAGATTAAAT--AGAAAC----AA-A--A-A-T---T--ACAAA-G
* *
40420409 ACAAAGACAGTCAATGACAGTGTTATGCTGAGTTGGAATTACATATTTCTTACCTGCGGAAAGTG
169 AC--AGTCA----ATGACAGTGTTATACTGAGTTGGAATTACATATTTCTTACCTGCGGAAAGTG
40420474 TTGGGATGTATAGCTAACAAGTTGCAGAAAGGGT
228 TTGGGATGTATAGCTAACAAGTTGCAGAAAGGGT
40420508 TTTAAGATTT
Statistics
Matches: 250, Mismatches: 7, Indels: 37
0.85 0.02 0.13
Matches are distributed among these distances:
263 71 0.28
268 1 0.00
273 73 0.29
276 1 0.00
277 3 0.01
284 1 0.00
286 1 0.00
287 1 0.00
288 1 0.00
291 1 0.00
293 5 0.02
294 2 0.01
296 4 0.02
300 85 0.34
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (267 bp):
AAATCAAATTAAATTAAATTAAATTAAATTCTAAAAAGAAAATGTAAATGAAAGCTTACGGGAAA
GGAAGCTAAGGTAAGCCAAATCGATTTCAATGTCGCTTGTTTCTACAATAAAACAAAGAAAAAAC
AAAAAAGATGAGATTAAATAGAAACAAAAATTACAAAGACAGTCAATGACAGTGTTATACTGAGT
TGGAATTACATATTTCTTACCTGCGGAAAGTGTTGGGATGTATAGCTAACAAGTTGCAGAAAGGG
TAAAATC
Found at i:40420415 original size:27 final size:27
Alignment explanation
Indices: 40420354--40420406 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
40420344 AAGAAAAAAT
*
40420354 AAAAAAGATGAGATTAAATGAAGAAAC
1 AAAAAAGATGAGATTAAATGAACAAAC
40420381 AAAAAAGATGAGATTAAATGAACAAA
1 AAAAAAGATGAGATTAAATGAACAAA
40420407 TTACAAAGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.64, C:0.04, G:0.17, T:0.15
Consensus pattern (27 bp):
AAAAAAGATGAGATTAAATGAACAAAC
Found at i:40422442 original size:28 final size:28
Alignment explanation
Indices: 40422402--40422477 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 28
40422392 TGACTGATTT
*
40422402 ATTTT-ATATTTTTTATAAGTTTATAT-TA
1 ATTTTAATA-TTTTTATAA-TTTATATAGA
* *
40422430 ATTTTAATATTTTTATGATTTTTATAGA
1 ATTTTAATATTTTTATAATTTATATAGA
40422458 ATTTTAATGCATTTTTATAA
1 ATTTTAAT--ATTTTTATAA
40422478 AATTTTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 6 0.15
28 22 0.55
29 3 0.08
30 9 0.22
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (28 bp):
ATTTTAATATTTTTATAATTTATATAGA
Found at i:40422450 original size:9 final size:9
Alignment explanation
Indices: 40422403--40422517 Score: 74
Period size: 9 Copynumber: 12.2 Consensus size: 9
40422393 GACTGATTTA
*
40422403 TTTTATATT
1 TTTTATAAT
40422412 TTTTATAAGT
1 TTTTATAA-T
*
40422422 TTATATTAAT
1 TTTTA-TAAT
*
40422432 TTTAAT-AT
1 TTTTATAAT
*
40422440 TTTTATGAT
1 TTTTATAAT
40422449 TTTTATAGAAT
1 TTTTAT--AAT
* *
40422460 TTTAATGCAT
1 TTTTAT-AAT
*
40422470 TTTTATAAAA
1 TTTTAT-AAT
40422480 TTTTA-AAT
1 TTTTATAAT
40422488 ATTTTATGAA-
1 -TTTTAT-AAT
40422498 TTTTATAAT
1 TTTTATAAT
40422507 TTTTATAAT
1 TTTTATAAT
40422516 TT
1 TT
40422518 ATTAGAGTTT
Statistics
Matches: 84, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
8 11 0.13
9 38 0.45
10 23 0.27
11 12 0.14
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:40422473 original size:21 final size:20
Alignment explanation
Indices: 40422438--40422514 Score: 72
Period size: 21 Copynumber: 4.0 Consensus size: 20
40422428 TAATTTTAAT
* *
40422438 ATTTTTATGATTTTTATAGA
1 ATTTTAATGATTTTTATAAA
40422458 ATTTTAATGCATTTTTATAAA
1 ATTTTAATG-ATTTTTATAAA
*
40422479 ATTTTAA--ATATTTTAT-GA
1 ATTTTAATGAT-TTTTATAAA
*
40422497 ATTTT-ATAATTTTTATAA
1 ATTTTAATGATTTTTATAA
40422515 TTTATTAGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
17 1 0.02
18 14 0.29
19 8 0.17
20 8 0.17
21 17 0.35
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.57
Consensus pattern (20 bp):
ATTTTAATGATTTTTATAAA
Found at i:40422494 original size:19 final size:19
Alignment explanation
Indices: 40422402--40422514 Score: 74
Period size: 19 Copynumber: 5.9 Consensus size: 19
40422392 TGACTGATTT
*
40422402 ATTTTATATTTTTTAT-AA
1 ATTTTATAATTTTTATAAA
* *
40422420 GTTTATATTAA-TTTTA-ATA
1 ATTT-TA-TAATTTTTATAAA
* * *
40422439 TTTTTATGATTTTTATAGA
1 ATTTTATAATTTTTATAAA
*
40422458 ATTTTAATGCATTTTTATAAA
1 ATTTT-AT-AATTTTTATAAA
*
40422479 ATTTTA-AATATTTTAT-GA
1 ATTTTATAAT-TTTTATAAA
40422497 ATTTTATAATTTTTATAA
1 ATTTTATAATTTTTATAA
40422515 TTTATTAGAG
Statistics
Matches: 73, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
17 2 0.03
18 25 0.34
19 26 0.36
20 5 0.07
21 15 0.21
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.59
Consensus pattern (19 bp):
ATTTTATAATTTTTATAAA
Found at i:40422588 original size:17 final size:18
Alignment explanation
Indices: 40422561--40422607 Score: 80
Period size: 16 Copynumber: 2.7 Consensus size: 18
40422551 ATTTAATAAT
40422561 ATTTATATTTTTTTGATA
1 ATTTATATTTTTTTGATA
40422579 ATTT-TA-TTTTTTGATA
1 ATTTATATTTTTTTGATA
40422595 ATTTATATTTTTT
1 ATTTATATTTTTT
40422608 ATGTGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 14 0.52
17 4 0.15
18 9 0.33
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (18 bp):
ATTTATATTTTTTTGATA
Found at i:40423860 original size:22 final size:21
Alignment explanation
Indices: 40423803--40423860 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
40423793 AACTAATCAT
* *
40423803 CTCTCAAATTTCATCTCATTTT
1 CTCTCAAA-TTCCTCTCATTTA
40423825 C-CTCAAAATATCCTCTCAATTTA
1 CTCTC-AAAT-TCCTCTC-ATTTA
40423848 CTCTCAAATTCCT
1 CTCTCAAATTCCT
40423861 TCCAAATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
21 4 0.13
22 14 0.47
23 9 0.30
24 3 0.10
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (21 bp):
CTCTCAAATTCCTCTCATTTA
Found at i:40423937 original size:51 final size:51
Alignment explanation
Indices: 40423838--40423937 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
40423828 CAAAATATCC
*
40423838 TCTCAATTTACTCTCAAATTCCTTCCAAATTTCTCTTAAATTCATATTTAA
1 TCTCAATTTACTCTCAAATTCCTTCCAAATTTCTCTTAAATCCATATTTAA
* * * *
40423889 TCTCAATTTGCTCTCAAGTTCC-TCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTACTCTCAAATTCCTTC-CAAATTTCTCTTAAATCCATATTT
40423938 TTAAATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 2 0.05
51 41 0.95
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.46
Consensus pattern (51 bp):
TCTCAATTTACTCTCAAATTCCTTCCAAATTTCTCTTAAATCCATATTTAA
Found at i:40425734 original size:18 final size:18
Alignment explanation
Indices: 40425707--40425746 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40425697 CAGGTGCGTT
* *
40425707 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
40425725 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
40425743 TCCT
1 TCCT
40425747 TTTTCGAGTC
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:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:40426372 original size:22 final size:22
Alignment explanation
Indices: 40426330--40426696 Score: 494
Period size: 22 Copynumber: 17.0 Consensus size: 22
40426320 ACCCTTAATT
* *
40426330 CTTAACCTAAAAATCCT-AACC
1 CTTAACTTAAAAACCCTAAACC
*
40426351 CTCAACTTAAAAACCCTAAACC
1 CTTAACTTAAAAACCCTAAACC
* *
40426373 C--AACTTAAAAACCATAAATC
1 CTTAACTTAAAAACCCTAAACC
40426393 CTTAACTTAAAAACCCTAAACC
1 CTTAACTTAAAAACCCTAAACC
40426415 CTTAACTTAAAAACCCTAAACC
1 CTTAACTTAAAAACCCTAAACC
* ***
40426437 CTTAACCTAAAAATAGT-AACC
1 CTTAACTTAAAAACCCTAAACC
*
40426458 CTTAACTTAAAAACCCTAAACT
1 CTTAACTTAAAAACCCTAAACC
40426480 CTTAACTTAAAAACCCTAAACC
1 CTTAACTTAAAAACCCTAAACC
*
40426502 CTTAACTTAAAAACCATAAACC
1 CTTAACTTAAAAACCCTAAACC
* *
40426524 CTTAACCTAAAACCCCTAAACC
1 CTTAACTTAAAAACCCTAAACC
*
40426546 CTTAACTTAAAAACCATAAACC
1 CTTAACTTAAAAACCCTAAACC
* *
40426568 CTTAACCTAAAAA-CCTTAACC
1 CTTAACTTAAAAACCCTAAACC
*
40426589 CTTAACCTAAAAACCCTAAACC
1 CTTAACTTAAAAACCCTAAACC
*
40426611 CTTAACTTAAAAACCATAAACC
1 CTTAACTTAAAAACCCTAAACC
* * *
40426633 CTTAACCTAAAATCCATAAA-C
1 CTTAACTTAAAAACCCTAAACC
40426654 CTTAACTTAAAAACCCTAAACC
1 CTTAACTTAAAAACCCTAAACC
*
40426676 CTTAACTTAAAAACCATAAAC
1 CTTAACTTAAAAACCCTAAAC
40426697 TCTTTCGAGC
Statistics
Matches: 304, Mismatches: 36, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
20 18 0.06
21 68 0.22
22 218 0.72
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (22 bp):
CTTAACTTAAAAACCCTAAACC
Found at i:40426484 original size:65 final size:64
Alignment explanation
Indices: 40426330--40426696 Score: 497
Period size: 65 Copynumber: 5.7 Consensus size: 64
40426320 ACCCTTAATT
* * * * *
40426330 CTTAACCTAAAAATCCT-AACCCTCAACTTAAAAACCCTAAACCC--AACTTAAAAACCATAAAT
1 CTTAACCTAAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAA-CAT-AAC
40426392 C
64 C
* * *
40426393 CTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACCTAAAAATAGTAACC
1 CTTAACCTAAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAACA-TAACC
* * * *
40426458 CTTAACTTAAAAACCCTAAACTCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCATAAAC
1 CTTAACCTAAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAA-CAT-AAC
40426523 C
64 C
* *
40426524 CTTAACCTAAAACCCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAACCTTAACC
1 CTTAACCTAAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAA-CATAACC
* *
40426589 CTTAACCTAAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAATCCATAAAC
1 CTTAACCTAAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAA-ACATAACC
*
40426654 CTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCATAAAC
1 CTTAACCTAAAAACCCTAAACCCTTAACTTAAAAACCATAAAC
40426697 TCTTTCGAGC
Statistics
Matches: 277, Mismatches: 20, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
63 15 0.05
64 26 0.09
65 166 0.60
66 70 0.25
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (64 bp):
CTTAACCTAAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAACATAACC
Found at i:40426494 original size:87 final size:87
Alignment explanation
Indices: 40426330--40426696 Score: 471
Period size: 87 Copynumber: 4.2 Consensus size: 87
40426320 ACCCTTAATT
* * * *
40426330 CTTAACCTAAAAATCC-T-AACCCTCAACTTAAAAACCCTAAACCC--AACTTAAAAACCATAAA
1 CTTAACTTAAAAA-CCATAAACCCTTAACCTAAAAA-CATAAACCCTTAACTTAAAAACCATAAA
40426391 -TCCTTAACTTAAAAACCCTAAACC
64 CT-CTTAACTTAAAAACCCTAAACC
* * *
40426415 CTTAACTTAAAAACCCTAAACCCTTAACCTAAAAATAGT-AACCCTTAACTTAAAAACCCTAAAC
1 CTTAACTTAAAAACCATAAACCCTTAACCTAAAAACA-TAAACCCTTAACTTAAAAACCATAAAC
40426479 TCTTAACTTAAAAACCCTAAACC
65 TCTTAACTTAAAAACCCTAAACC
* *
40426502 CTTAACTTAAAAACCATAAACCCTTAACCTAAAACCCCTAAACCCTTAACTTAAAAACCATAAAC
1 CTTAACTTAAAAACCATAAACCCTTAACCTAAAA-ACATAAACCCTTAACTTAAAAACCATAAAC
* * *
40426567 CCTTAACCTAAAAA-CCTTAACC
65 TCTTAACTTAAAAACCCTAAACC
* * * * *
40426589 CTTAACCTAAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAATCCATAAAC
1 CTTAACTTAAAAACCATAAACCCTTAACCTAAAAA-CATAAACCCTTAACTTAAAAACCATAAAC
40426654 -CTTAACTTAAAAACCCTAAACC
65 TCTTAACTTAAAAACCCTAAACC
40426676 CTTAACTTAAAAACCATAAAC
1 CTTAACTTAAAAACCATAAAC
40426697 TCTTTCGAGC
Statistics
Matches: 247, Mismatches: 25, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
84 2 0.01
85 18 0.07
86 28 0.11
87 162 0.66
88 37 0.15
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (87 bp):
CTTAACTTAAAAACCATAAACCCTTAACCTAAAAACATAAACCCTTAACTTAAAAACCATAAACT
CTTAACTTAAAAACCCTAAACC
Found at i:40427563 original size:126 final size:126
Alignment explanation
Indices: 40427298--40427723 Score: 669
Period size: 126 Copynumber: 3.4 Consensus size: 126
40427288 CCCAAACATG
* *
40427298 CTACTGTAGCAAAAGCGCGTCCACGTGGGTGCGATTTCACAAATTCTTCTCATAA-AGCATCCTA
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTG
* * * * * * * **
40427362 CTAG-A-AGTGATTTTATACTATTTGCTCAGAAACGTCAAGTCAAAATTATTTTTCCAATAC
65 CTTGCAGCGTTATTTTATACTATTTGCTCAGAAACGTGAACTCGAAATTATTTTTTCAGGAC
*
40427422 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
40427487 TTGCAGCGTTATTTTATACTATTTGCTCAGAAACGTGAACTCGAAATTATTTTTTCAGGAC
66 TTGCAGCGTTATTTTATACTATTTGCTCAGAAACGTGAACTCGAAATTATTTTTTCAGGAC
*
40427548 CTACTGTAGCAAAAGCACGTCCACGTGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
40427613 TTGCAGCGTTATTTTATACTATTTGCTCAGAAACGTGAACTCGAAATTATTTTTTCAGGAC
66 TTGCAGCGTTATTTTATACTATTTGCTCAGAAACGTGAACTCGAAATTATTTTTTCAGGAC
* * * *
40427674 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAAAAATCCTTCT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCT
40427724 GATATTTTAT
Statistics
Matches: 280, Mismatches: 19, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
123 2 0.01
124 61 0.22
125 1 0.00
126 216 0.77
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TTGCAGCGTTATTTTATACTATTTGCTCAGAAACGTGAACTCGAAATTATTTTTTCAGGAC
Found at i:40428386 original size:13 final size:13
Alignment explanation
Indices: 40428368--40428392 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40428358 TTTGGACATG
40428368 AAATATAATAATA
1 AAATATAATAATA
40428381 AAATATAATAAT
1 AAATATAATAAT
40428393 TTAATTAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAATAATA
Found at i:40431190 original size:20 final size:20
Alignment explanation
Indices: 40431167--40431208 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40431157 AGCTCAAATC
40431167 AGCTCATTTGAGCTTAATTT
1 AGCTCATTTGAGCTTAATTT
** *
40431187 AGCTTGTTTGAGCTTGATTT
1 AGCTCATTTGAGCTTAATTT
40431207 AG
1 AG
40431209 TTTCTTTCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.45
Consensus pattern (20 bp):
AGCTCATTTGAGCTTAATTT
Found at i:40433909 original size:98 final size:98
Alignment explanation
Indices: 40433738--40433935 Score: 308
Period size: 98 Copynumber: 2.0 Consensus size: 98
40433728 AGAGTTAGTT
*
40433738 CTTTTGTGCAAGATTGCTTTCTTATGGTTTTTAGAAGCTGTTTTCTTCTTGATTTTCTTTAAGGA
1 CTTTTGTGCAAGATTGCTTTCTTATGATTTTTAGAAGCTGTTTTCTTCTTGATTTTCTTTAAGGA
* *
40433803 GTCATGGGAATTTATTCTTCATCCTTCAAATTG
66 GCCATGGGAATTCATTCTTCATCCTTCAAATTG
* *
40433836 CTTTTGTGCAAGATTGCTTTCTTGTGATTTTTAGAA-TTAGTTTTCTTCTTGATTTTCTTTAAGG
1 CTTTTGTGCAAGATTGCTTTCTTATGATTTTTAGAAGCT-GTTTTCTTCTTGATTTTCTTTAAGG
* * *
40433900 AGCCGTGGGAATTCATTTTTCATCCTTCAATTTG
65 AGCCATGGGAATTCATTCTTCATCCTTCAAATTG
40433934 CT
1 CT
40433936 AAGGATTATT
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
97 1 0.01
98 90 0.99
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (98 bp):
CTTTTGTGCAAGATTGCTTTCTTATGATTTTTAGAAGCTGTTTTCTTCTTGATTTTCTTTAAGGA
GCCATGGGAATTCATTCTTCATCCTTCAAATTG
Found at i:40443350 original size:27 final size:27
Alignment explanation
Indices: 40443296--40443359 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
40443286 ATGTATATTC
* *
40443296 TATATATATGTATTATGTTAAGTATAA
1 TATATATATATATTATGTGAAGTATAA
*
40443323 TATATATATATATATATGTGATGT-TAA
1 TATATATATATAT-TATGTGAAGTATAA
40443350 TACTAT-TATA
1 TA-TATATATA
40443360 ATAAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (27 bp):
TATATATATATATTATGTGAAGTATAA
Found at i:40444424 original size:35 final size:35
Alignment explanation
Indices: 40444379--40444566 Score: 141
Period size: 35 Copynumber: 5.4 Consensus size: 35
40444369 CGATTACTTG
40444379 ACTAGTGCTGGGCACACTTATCGTTGGCTTATCCA
1 ACTAGTGCTGGGCACACTTATCGTTGGCTTATCCA
* * *** * * * *
40444414 ACTAGCGCTGGGCGCAAAACATCG-TCGATTATTCG
1 ACTAGTGCTGGGCAC-ACTTATCGTTGGCTTATCCA
*
40444449 ACTAGTGCTGGGCACACCTATCGTTGGCTTATCCA
1 ACTAGTGCTGGGCACACTTATCGTTGGCTTATCCA
* * * * * * *
40444484 ACTAGCGCTGGGCGCA--AAACATTGGCGATTATTCG
1 ACTAGTGCTGGGCACACTTATCGTTGGC--TTATCCA
*
40444519 ACTAGTACTGGGCACACTTATCGTTGG-TATATCCA
1 ACTAGTGCTGGGCACACTTATCGTTGGCT-TATCCA
*
40444554 ACTAGTACTGGGC
1 ACTAGTGCTGGGC
40444567 GCAAAAAGAT
Statistics
Matches: 113, Mismatches: 33, Indels: 14
0.71 0.21 0.09
Matches are distributed among these distances:
33 7 0.06
34 6 0.05
35 89 0.79
36 5 0.04
37 6 0.05
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.27
Consensus pattern (35 bp):
ACTAGTGCTGGGCACACTTATCGTTGGCTTATCCA
Found at i:40444458 original size:70 final size:70
Alignment explanation
Indices: 40444338--40444572 Score: 350
Period size: 70 Copynumber: 3.3 Consensus size: 70
40444328 TTGTCGGTTA
*
40444338 ATCCGACTAGCGCTGGGCGCAAAA-ATCTTGTCGATTACTT-GACTAGTGCTGGGCACACTTATC
1 ATCCAACTAGCGCTGGGCGCAAAACATC--GTCGATTA-TTCGACTAGTGCTGGGCACACTTATC
40444401 GTTGGCTT
63 GTTGGCTT
*
40444409 ATCCAACTAGCGCTGGGCGCAAAACATCGTCGATTATTCGACTAGTGCTGGGCACACCTATCGTT
1 ATCCAACTAGCGCTGGGCGCAAAACATCGTCGATTATTCGACTAGTGCTGGGCACACTTATCGTT
40444474 GGCTT
66 GGCTT
* * *
40444479 ATCCAACTAGCGCTGGGCGCAAAACATTGGCGATTATTCGACTAGTACTGGGCACACTTATCGTT
1 ATCCAACTAGCGCTGGGCGCAAAACATCGTCGATTATTCGACTAGTGCTGGGCACACTTATCGTT
40444544 GG-TAT
66 GGCT-T
**
40444549 ATCCAACTAGTACTGGGCGCAAAA
1 ATCCAACTAGCGCTGGGCGCAAAA
40444573 AGATTATTTT
Statistics
Matches: 153, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
69 3 0.02
70 124 0.81
71 23 0.15
72 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (70 bp):
ATCCAACTAGCGCTGGGCGCAAAACATCGTCGATTATTCGACTAGTGCTGGGCACACTTATCGTT
GGCTT
Found at i:40447172 original size:15 final size:15
Alignment explanation
Indices: 40447152--40447197 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
40447142 ACAACATGTT
40447152 AACATAAGTGACTTA
1 AACATAAGTGACTTA
*
40447167 AACATAA-T-ATTTA
1 AACATAAGTGACTTA
40447180 AACATAAGTGACTTA
1 AACATAAGTGACTTA
40447195 AAC
1 AAC
40447198 GTAATTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.41
14 2 0.07
15 14 0.52
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (15 bp):
AACATAAGTGACTTA
Found at i:40451004 original size:24 final size:24
Alignment explanation
Indices: 40450972--40451018 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
40450962 TAACAAACTG
40450972 GCACACCAAAACTAAAGTATTCAT
1 GCACACCAAAACTAAAGTATTCAT
40450996 GCACACCAAAACTAAAGTATTCA
1 GCACACCAAAACTAAAGTATTCA
40451019 CACAAGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.26, G:0.09, T:0.19
Consensus pattern (24 bp):
GCACACCAAAACTAAAGTATTCAT
Found at i:40451996 original size:24 final size:22
Alignment explanation
Indices: 40451969--40452012 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
40451959 TGTTTGGAGC
40451969 GATTTCAAGAATTAAGAAAATCAA
1 GATTTCAA-AATT-AGAAAATCAA
*
40451993 GATTTCAAAATTTGAAAATC
1 GATTTCAAAATTAGAAAATC
40452013 TTGGTCCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 4 0.21
24 8 0.42
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (22 bp):
GATTTCAAAATTAGAAAATCAA
Found at i:40461624 original size:23 final size:23
Alignment explanation
Indices: 40461598--40461653 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
40461588 TTCGTTTCCT
* *
40461598 ATTTAGTTTTATTTTTACTTGTA
1 ATTTAGTTTTATTTTCAATTGTA
*
40461621 ATTTAGGTTTATTTTCAATTGTA
1 ATTTAGTTTTATTTTCAATTGTA
40461644 ATTATAGTTT
1 ATT-TAGTTT
40461654 AATATTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.25, C:0.04, G:0.11, T:0.61
Consensus pattern (23 bp):
ATTTAGTTTTATTTTCAATTGTA
Found at i:40475580 original size:31 final size:31
Alignment explanation
Indices: 40475542--40475606 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
40475532 TAACGCAAGA
40475542 TTTGGGTTGATATTGCATATAATATCGGTTC
1 TTTGGGTTGATATTGCATATAATATCGGTTC
*
40475573 TTTGGGTTGATATTGCATATAATATCTGTTC
1 TTTGGGTTGATATTGCATATAATATCGGTTC
40475604 TTT
1 TTT
40475607 CTTCAGCCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.49
Consensus pattern (31 bp):
TTTGGGTTGATATTGCATATAATATCGGTTC
Found at i:40475858 original size:10 final size:10
Alignment explanation
Indices: 40475842--40475897 Score: 64
Period size: 10 Copynumber: 5.8 Consensus size: 10
40475832 CGATATTGTA
40475842 AAAAAAATTTC
1 AAAAAAA-TTC
**
40475853 AAAAAAATAA
1 AAAAAAATTC
40475863 AAAAAAATTC
1 AAAAAAATTC
40475873 AAAAAAA-T-
1 AAAAAAATTC
40475881 AAAAAAATT-
1 AAAAAAATTC
40475890 AAAAAAAT
1 AAAAAAAT
40475898 CATAGAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
8 7 0.17
9 10 0.25
10 16 0.40
11 7 0.17
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:40475865 original size:9 final size:9
Alignment explanation
Indices: 40475853--40475896 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
40475843 AAAAAATTTC
40475853 AAAAAAATAA
1 AAAAAAAT-A
*
40475863 AAAAAAATTC
1 AAAAAAA-TA
40475873 AAAAAAATA
1 AAAAAAATA
*
40475882 AAAAAATTA
1 AAAAAAATA
40475891 AAAAAA
1 AAAAAA
40475897 TCATAGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
9 15 0.50
10 14 0.47
11 1 0.03
ACGTcount: A:0.84, C:0.02, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAAAATA
Found at i:40475867 original size:21 final size:20
Alignment explanation
Indices: 40475840--40475887 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
40475830 TACGATATTG
*
40475840 TAAAAAAAATTTCAAAAAAA
1 TAAAAAAAAATTCAAAAAAA
40475860 TAAAAAAAAATTCAAAAAAA
1 TAAAAAAAAATTCAAAAAAA
40475880 TAAAAAAA
1 TAAAAAAA
40475888 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (20 bp):
TAAAAAAAAATTCAAAAAAA
Found at i:40475896 original size:20 final size:19
Alignment explanation
Indices: 40475841--40475896 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
40475831 ACGATATTGT
* *
40475841 AAAAAAAATTTCAAAAAAAT
1 AAAAAAAAATT-AAAAAAAA
*
40475861 AAAAAAAAATT-CAAAAAA
1 AAAAAAAAATTAAAAAAAA
*
40475879 ATAAAAAAATTAAAAAAA
1 AAAAAAAAATTAAAAAAA
40475897 TCATAGAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 15 0.50
19 5 0.17
20 10 0.33
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAAAAAATTAAAAAAAA
Found at i:40475907 original size:18 final size:18
Alignment explanation
Indices: 40475842--40475897 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 18
40475832 CGATATTGTA
40475842 AAAAAAATTTCAAAAAAAT
1 AAAAAAA-TTCAAAAAAAT
40475861 AAAAAAAAATTCAAAAAAAT
1 --AAAAAAATTCAAAAAAAT
40475881 AAAAAAATT-AAAAAAAT
1 AAAAAAATTCAAAAAAAT
40475898 CATAGAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.23
18 9 0.26
20 11 0.31
21 7 0.20
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAAAAATTCAAAAAAAT
Found at i:40477059 original size:12 final size:12
Alignment explanation
Indices: 40477042--40477076 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
40477032 GACGAGAAGA
40477042 GAAAAATGAAAGT
1 GAAAAA-GAAAGT
*
40477055 GAAAAAGAAATT
1 GAAAAAGAAAGT
40477067 GAAAAAGAAA
1 GAAAAAGAAA
40477077 AAAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (12 bp):
GAAAAAGAAAGT
Found at i:40477080 original size:21 final size:21
Alignment explanation
Indices: 40477056--40477116 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
40477046 AATGAAAGTG
40477056 AAAAAGAAATTGAAAAAGAAA
1 AAAAAGAAATTGAAAAAGAAA
**
40477077 AAAAAGAAAAAGAAGAAA-AAA
1 AAAAAGAAATTGAA-AAAGAAA
*
40477098 AGAAAGAAATTGAAAAAGA
1 AAAAAGAAATTGAAAAAGA
40477117 GAGTGAGACT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 3 0.09
21 27 0.82
22 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (21 bp):
AAAAAGAAATTGAAAAAGAAA
Found at i:40477082 original size:9 final size:9
Alignment explanation
Indices: 40477068--40477102 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
40477058 AAAGAAATTG
40477068 AAAAAGAAA
1 AAAAAGAAA
40477077 AAAAAGAAA
1 AAAAAGAAA
*
40477086 AAGAAG-AA
1 AAAAAGAAA
40477094 AAAAAGAAA
1 AAAAAGAAA
40477103 GAAATTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:40477087 original size:15 final size:15
Alignment explanation
Indices: 40477067--40477106 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
40477057 AAAAGAAATT
40477067 GAAAAAGAAAAAAAA
1 GAAAAAGAAAAAAAA
40477082 GAAAAAGAAGAAAAAA
1 GAAAAAGAA-AAAAAA
*
40477098 -AGAAAGAAA
1 GAAAAAGAAA
40477107 TTGAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 16 0.70
16 6 0.26
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAAAAAAA
Found at i:40479009 original size:22 final size:21
Alignment explanation
Indices: 40478984--40479025 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
40478974 TTAAATAAAT
*
40478984 TTTAGTTAATTTAGTTTAAGTA
1 TTTAATTAATTTAG-TTAAGTA
40479006 TTTAATTAATTTAGTTAAGT
1 TTTAATTAATTTAGTTAAGT
40479026 GTTAAATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTAATTAATTTAGTTAAGTA
Found at i:40483330 original size:20 final size:20
Alignment explanation
Indices: 40483292--40483341 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
40483282 ACTTCAAGCT
40483292 CATTCAGCTCAACCATAGCC
1 CATTCAGCTCAACCATAGCC
* * * *
40483312 CATTGAGCTCATCCTTAGCT
1 CATTCAGCTCAACCATAGCC
*
40483332 TATTCAGCTC
1 CATTCAGCTC
40483342 GTTCTTAGTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.34, G:0.12, T:0.30
Consensus pattern (20 bp):
CATTCAGCTCAACCATAGCC
Found at i:40489134 original size:14 final size:15
Alignment explanation
Indices: 40489098--40489138 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
40489088 GAATATTTAC
40489098 ATAAAAATTAAACTAA
1 ATAAAAA-TAAACTAA
*
40489114 GTAAAAATAAA-TAA
1 ATAAAAATAAACTAA
40489128 ATAAAAATAAA
1 ATAAAAATAAA
40489139 ACTTTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 4 0.17
16 6 0.26
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
ATAAAAATAAACTAA
Found at i:40490087 original size:45 final size:45
Alignment explanation
Indices: 40490030--40490119 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
40490020 GGACCTCACT
40490030 AAAAAAATCCTCATAATCCTGCGAAAAATATTGAAACACACTAGG
1 AAAAAAATCCTCATAATCCTGCGAAAAATATTGAAACACACTAGG
* *
40490075 AAAAACATCCTCATAATCCTGCGAAAAATATTGAAACACATTAGG
1 AAAAAAATCCTCATAATCCTGCGAAAAATATTGAAACACACTAGG
40490120 CAAATTTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.21
Consensus pattern (45 bp):
AAAAAAATCCTCATAATCCTGCGAAAAATATTGAAACACACTAGG
Found at i:40495891 original size:14 final size:15
Alignment explanation
Indices: 40495855--40495895 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
40495845 GAATATTTAC
40495855 ATAAAAATTAAACTAA
1 ATAAAAA-TAAACTAA
*
40495871 GTAAAAATAAA-TAA
1 ATAAAAATAAACTAA
40495885 ATAAAAATAAA
1 ATAAAAATAAA
40495896 ACTTTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 4 0.17
16 6 0.26
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
ATAAAAATAAACTAA
Found at i:40496242 original size:20 final size:20
Alignment explanation
Indices: 40496181--40496234 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
40496171 CTCTACTTCA
* *
40496181 AGCTCATTCAGCTCAACCAT
1 AGCTCATTCAGCTCATCCTT
*
40496201 AGCTCATTGAGCTCATCCTT
1 AGCTCATTCAGCTCATCCTT
40496221 AGCTCATTCAGCTC
1 AGCTCATTCAGCTC
40496235 GTTCTTAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.33, G:0.13, T:0.30
Consensus pattern (20 bp):
AGCTCATTCAGCTCATCCTT
Found at i:40499835 original size:22 final size:22
Alignment explanation
Indices: 40499807--40499852 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
40499797 CTCTATCCTT
40499807 AAAAAAACTCAGTCTAGCAAAA
1 AAAAAAACTCAGTCTAGCAAAA
40499829 AAAAAAACTCAGTCTAGCAAAA
1 AAAAAAACTCAGTCTAGCAAAA
40499851 AA
1 AA
40499853 TGTTCTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.61, C:0.17, G:0.09, T:0.13
Consensus pattern (22 bp):
AAAAAAACTCAGTCTAGCAAAA
Found at i:40506207 original size:31 final size:31
Alignment explanation
Indices: 40506171--40506240 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
40506161 ACCGTTTCTA
* *
40506171 TGTGTGAACTAAAGGAAA-TGATCAGGCCTT-G
1 TGTGTGAAC-AAACGAAATTGA-AAGGCCTTAG
*
40506202 TGTGTGAACACACGAAATTGAAAGGCCTTAG
1 TGTGTGAACAAACGAAATTGAAAGGCCTTAG
40506233 TGTGTGAA
1 TGTGTGAA
40506241 GGGAACATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.38
31 21 0.62
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.26
Consensus pattern (31 bp):
TGTGTGAACAAACGAAATTGAAAGGCCTTAG
Found at i:40510729 original size:86 final size:86
Alignment explanation
Indices: 40510584--40510756 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
40510574 CCAAAGTGTT
40510584 TAAACTTACTTTCATAAATAATTCTTTTATAGTCTCTGTGGGTACGATAGCTCGACATTTACTTG
1 TAAACTTACTTTCATAAATAATTCTTTTATAGTCTCTGTGGGTACGATAGCTCGACATTTACTTG
40510649 TCACTTTATTACTTGTTGCGA
66 TCACTTTATTACTTGTTGCGA
40510670 TAAACTTACTTTCATAAATAATTCTTTTATAGTCTCTGTGGGTACGATAGCTCGACATTTACTTG
1 TAAACTTACTTTCATAAATAATTCTTTTATAGTCTCTGTGGGTACGATAGCTCGACATTTACTTG
40510735 TCACTTTATTACTTGTTGCGA
66 TCACTTTATTACTTGTTGCGA
40510756 T
1 T
40510757 TATGTACACT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.43
Consensus pattern (86 bp):
TAAACTTACTTTCATAAATAATTCTTTTATAGTCTCTGTGGGTACGATAGCTCGACATTTACTTG
TCACTTTATTACTTGTTGCGA
Found at i:40512110 original size:23 final size:23
Alignment explanation
Indices: 40512084--40512136 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
40512074 ATAAGTGCCA
40512084 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
*
40512107 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
40512130 CACTGAT
1 CACTGAT
40512137 CAATAACACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCAAAGCTAC
Found at i:40519306 original size:101 final size:101
Alignment explanation
Indices: 40519198--40519409 Score: 334
Period size: 101 Copynumber: 2.1 Consensus size: 101
40519188 ACACGGTAAA
* * *
40519198 GCTCACACAAAGTGTGGTAAACATATAGTCATAGCTTATACGAGCTGTAAAATGGGCCTGCTCAC
1 GCTCACACAAAGTGTGGTAAACATATAGTCATAGCTCATACGAGCAGTAAAATGGGCCTGCTAAC
* * *
40519263 ATAAGCTGACGGTCAGAATGGAAGCTACACAATGTT
66 AAAAGCTGACAGTCAGAATGGAAGCTACACAATGCT
* *
40519299 GCTCACACAAAGTGTGGTAAACATATAGTCGTAGCTCATATGAGCAGTAAAATGGGCCTGCTAAC
1 GCTCACACAAAGTGTGGTAAACATATAGTCATAGCTCATACGAGCAGTAAAATGGGCCTGCTAAC
*
40519364 AAAAGCTGACAGTCAGAATGGAGGCTACACAATGCT
66 AAAAGCTGACAGTCAGAATGGAAGCTACACAATGCT
*
40519400 GCTCATACAA
1 GCTCACACAA
40519410 GTTGTCGAGT
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (101 bp):
GCTCACACAAAGTGTGGTAAACATATAGTCATAGCTCATACGAGCAGTAAAATGGGCCTGCTAAC
AAAAGCTGACAGTCAGAATGGAAGCTACACAATGCT
Found at i:40520851 original size:21 final size:22
Alignment explanation
Indices: 40520827--40520870 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
40520817 TATTCAACCA
*
40520827 ATCCAGAATAA-GAAAAAAATC
1 ATCCAAAATAATGAAAAAAATC
*
40520848 ATCCAAAATAATTAAAAAAATC
1 ATCCAAAATAATGAAAAAAATC
40520870 A
1 A
40520871 AAGCACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.64, C:0.14, G:0.05, T:0.18
Consensus pattern (22 bp):
ATCCAAAATAATGAAAAAAATC
Found at i:40523891 original size:24 final size:23
Alignment explanation
Indices: 40523842--40523891 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
40523832 TAAAGTAGGT
* *
40523842 TATATATTATTTTTATAATATTA
1 TATATATGATTTTTATAATATCA
40523865 TATATTATGATTTTTATTAAT-TCA
1 TATA-TATGATTTTTA-TAATATCA
40523889 TAT
1 TAT
40523892 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 15 0.65
25 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TATATATGATTTTTATAATATCA
Found at i:40524025 original size:58 final size:57
Alignment explanation
Indices: 40523869--40524027 Score: 182
Period size: 58 Copynumber: 2.8 Consensus size: 57
40523859 ATATTATATA
* *
40523869 TTATGATTTTTATT-AATTCATATTTTAATAATAA--TATTAAGAATATTATTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATTTATTAA-AATATGATTAAATTAT
* * * * *
40523926 ATATTA-TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATGATTAATTTTT
1 TTATTATTTTTATTAAATTATATTTAATAATAATT-TATTAAAATATGATTAAATTAT
40523983 TTATTATTTTTATTAAATTATATTTAATAATAATCTTATTAAAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAAT-TTATTAAAAT
40524028 TTAATAACAA
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
55 11 0.13
56 9 0.10
57 26 0.30
58 39 0.45
59 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (57 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATTTATTAAAATATGATTAAATTAT
Found at i:40550574 original size:30 final size:30
Alignment explanation
Indices: 40550518--40550574 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
40550508 AAAAGATACC
* *
40550518 AACTCAGGAGCATACTGGCTCAACAGAACA
1 AACTCAGGAGCATACTCGATCAACAGAACA
* *
40550548 AACTCAGGAGCATACTCTATCGACAGA
1 AACTCAGGAGCATACTCGATCAACAGA
40550575 GCACCCTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (30 bp):
AACTCAGGAGCATACTCGATCAACAGAACA
Found at i:40552756 original size:23 final size:23
Alignment explanation
Indices: 40552729--40552792 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
40552719 TTATTAACAT
40552729 TGTTCATGAACATGTTC-ATTTAA
1 TGTTCATGAACATGTTCGA-TTAA
*
40552752 TGTTCGTGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCGATTAA
*
40552775 -GTTAAATGAACATGTTCG
1 TGTT-CATGAACATGTTCG
40552793 TGAACATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 3 0.08
23 32 0.89
24 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (23 bp):
TGTTCATGAACATGTTCGATTAA
Found at i:40552802 original size:23 final size:23
Alignment explanation
Indices: 40552758--40552809 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
40552748 TTAATGTTCG
* *
40552758 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
40552781 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
*
40552804 TAAACA
1 TGAACA
40552810 AACATGAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:40553833 original size:22 final size:22
Alignment explanation
Indices: 40553807--40553848 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
40553797 AAGTTTAAAC
40553807 TAACCACTAACGTTTGTTTAGT
1 TAACCACTAACGTTTGTTTAGT
40553829 TAACCACTAACGTTTGTTTA
1 TAACCACTAACGTTTGTTTA
40553849 TTTTAGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (22 bp):
TAACCACTAACGTTTGTTTAGT
Found at i:40556185 original size:72 final size:72
Alignment explanation
Indices: 40556099--40556233 Score: 207
Period size: 72 Copynumber: 1.9 Consensus size: 72
40556089 GGTTTTGGGA
* *
40556099 GTATAGCAGTAAACAGTCTGTCTGACGTGGTGTTATCCACCCAAATGATTATTTTGGCGTATAAG
1 GTATAGCAGTAAACAGTCTATCTGACGTGGTGTTATCCACCAAAATGATTATTTTGGCGTATAAG
40556164 CGTTGAC
66 CGTTGAC
* ** * *
40556171 GTATAGCAGTAAACAGTCTATTTGGTGTGGTGTTATCCTCCAAAATTATTATTTTGGCGTATA
1 GTATAGCAGTAAACAGTCTATCTGACGTGGTGTTATCCACCAAAATGATTATTTTGGCGTATA
40556234 CGTGTAGGTG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (72 bp):
GTATAGCAGTAAACAGTCTATCTGACGTGGTGTTATCCACCAAAATGATTATTTTGGCGTATAAG
CGTTGAC
Found at i:40566432 original size:25 final size:25
Alignment explanation
Indices: 40566402--40566482 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
40566392 TTTGACCTAC
*
40566402 AGCTCGTGTGAGCATACTGATTCAT
1 AGCTCGAGTGAGCATACTGATTCAT
* * *
40566427 AGCTCGAGAGAGCATA-TCAATCTAT
1 AGCTCGAGTGAGCATACTGATTC-AT
* * * *
40566452 AGCTCAAGTAACCATACCGATTCAT
1 AGCTCGAGTGAGCATACTGATTCAT
40566477 AGCTCG
1 AGCTCG
40566483 TACGAGCATA
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
24 4 0.10
25 35 0.83
26 3 0.07
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (25 bp):
AGCTCGAGTGAGCATACTGATTCAT
Found at i:40573212 original size:52 final size:50
Alignment explanation
Indices: 40573116--40573259 Score: 175
Period size: 52 Copynumber: 2.8 Consensus size: 50
40573106 TCATGTATAT
* * * *
40573116 GTATGCTCAT-ACGAGCTGTGAATCGGTATGCTCTCTCGAGCTGTAAATCC
1 GTATGCTC-TCACGAGCTATAAATTGGTATGCTCTCACGAGCTGTAAATCC
**
40573166 GTATGCTCTCACGAGCTATATAAATTGGTATGCTCTCACGAGCTGTAAATTG
1 GTATGCTCTCACGAGC--TATAAATTGGTATGCTCTCACGAGCTGTAAATCC
*
40573218 GTATGCTCTCACGAGCTATAAATTGGTAAGCTCAT-ACGAGCT
1 GTATGCTCTCACGAGCTATAAATTGGTATGCTC-TCACGAGCT
40573260 ATTGTGTGTC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
49 1 0.01
50 37 0.45
51 1 0.01
52 44 0.53
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (50 bp):
GTATGCTCTCACGAGCTATAAATTGGTATGCTCTCACGAGCTGTAAATCC
Found at i:40573257 original size:77 final size:77
Alignment explanation
Indices: 40573116--40573261 Score: 197
Period size: 77 Copynumber: 1.9 Consensus size: 77
40573106 TCATGTATAT
* * * *
40573116 GTATGCTCATACGAGCTGTGAATCGGTATGCTCTCTCGAGCTGTAAATCCGTATGCTCTCACGAG
1 GTATGCTCATACGAGCTGTAAATCGGTATGCTCTCACGAGCTATAAATCCGTAAGCTCTCACGAG
40573181 CTATATAAATTG
66 CTATATAAATTG
* **
40573193 GTATGCTC-TCACGAGCTGTAAATTGGTATGCTCTCACGAGCTATAAATTGGTAAGCTCAT-ACG
1 GTATGCTCAT-ACGAGCTGTAAATCGGTATGCTCTCACGAGCTATAAATCCGTAAGCTC-TCACG
40573256 AGCTAT
64 AGCTAT
40573262 TGTGTGTCCG
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
76 1 0.02
77 58 0.97
78 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (77 bp):
GTATGCTCATACGAGCTGTAAATCGGTATGCTCTCACGAGCTATAAATCCGTAAGCTCTCACGAG
CTATATAAATTG
Found at i:40573260 original size:25 final size:25
Alignment explanation
Indices: 40573116--40573261 Score: 161
Period size: 25 Copynumber: 5.8 Consensus size: 25
40573106 TCATGTATAT
* * *
40573116 GTATGCTCAT-ACGAGCTGTGAATCG
1 GTATGCTC-TCACGAGCTATAAATTG
* * **
40573141 GTATGCTCTCTCGAGCTGTAAATCC
1 GTATGCTCTCACGAGCTATAAATTG
40573166 GTATGCTCTCACGAGCTATATAAATTG
1 GTATGCTCTCACGAGC--TATAAATTG
*
40573193 GTATGCTCTCACGAGCTGTAAATTG
1 GTATGCTCTCACGAGCTATAAATTG
40573218 GTATGCTCTCACGAGCTATAAATTG
1 GTATGCTCTCACGAGCTATAAATTG
*
40573243 GTAAGCTCAT-ACGAGCTAT
1 GTATGCTC-TCACGAGCTAT
40573262 TGTGTGTCCG
Statistics
Matches: 107, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
24 1 0.01
25 83 0.78
26 1 0.01
27 22 0.21
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (25 bp):
GTATGCTCTCACGAGCTATAAATTG
Found at i:40576991 original size:21 final size:21
Alignment explanation
Indices: 40576962--40577011 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
40576952 ATGTTAATTG
*
40576962 AATAATATTTATATTTATGAT
1 AATATTATTTATATTTATGAT
*
40576983 AATATTATTTATCTTTATGAT
1 AATATTATTTATATTTATGAT
*
40577004 AATTTTAT
1 AATATTAT
40577012 ATATTTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (21 bp):
AATATTATTTATATTTATGAT
Found at i:40581582 original size:31 final size:31
Alignment explanation
Indices: 40581539--40581622 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
40581529 ACCATGTTTG
40581539 CACTTTCGTTTTGGTCACCCAACTCGC-AAGT
1 CACTTTCGTTTTGGTCACCCAACTC-CTAAGT
* * *
40581570 GACTTTCATTTTGGTCACCCAACTCCTAGGT
1 CACTTTCGTTTTGGTCACCCAACTCCTAAGT
*
40581601 CACTTTCGTTTTAGTCACCCAA
1 CACTTTCGTTTTGGTCACCCAA
40581623 TAATATATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 1 0.02
31 45 0.98
ACGTcount: A:0.20, C:0.31, G:0.14, T:0.35
Consensus pattern (31 bp):
CACTTTCGTTTTGGTCACCCAACTCCTAAGT
Found at i:40581777 original size:7 final size:7
Alignment explanation
Indices: 40581765--40581791 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
40581755 TTTTTTTATA
40581765 TTTAAAT
1 TTTAAAT
40581772 TTTAAAT
1 TTTAAAT
40581779 TTTAAAT
1 TTTAAAT
40581786 TTTAAA
1 TTTAAA
40581792 ATATCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTTAAAT
Found at i:40598293 original size:43 final size:43
Alignment explanation
Indices: 40598246--40598505 Score: 213
Period size: 43 Copynumber: 6.1 Consensus size: 43
40598236 ATCATTTTTA
* * * *
40598246 TAGCGGCATTTGTAATAGAAGCACCACTAAAGGTCATGATCTT
1 TAGCGGCATTTGTGATAGAAGCGCCGCTAAAGGCCATGATCTT
** * * * *
40598289 TAGCGGCATTTGTG-TAGAAATGTCGCCAAAGGTCAT-ATTTT
1 TAGCGGCATTTGTGATAGAAGCGCCGCTAAAGGCCATGATCTT
* * * * * *
40598330 TAGTGACATTTGTGGTAAAAGCACCGCTAAAGACCATGATCTT
1 TAGCGGCATTTGTGATAGAAGCGCCGCTAAAGGCCATGATCTT
* * *
40598373 TAGTGGCGTTTGTGGTAGAAGCGCCGCTAAA-GCTCATGATCTT
1 TAGCGGCATTTGTGATAGAAGCGCCGCTAAAGGC-CATGATCTT
* * ** * * * *
40598416 TAACGGCGTTTGCAAAAGAAGTGCTGCTAAAGGCCATGATATT
1 TAGCGGCATTTGTGATAGAAGCGCCGCTAAAGGCCATGATCTT
* *
40598459 TAGCGGCATTTGTGGA-AGAAGCGCCACTAAAGACCATGATCTT
1 TAGCGGCATTTGT-GATAGAAGCGCCGCTAAAGGCCATGATCTT
40598502 TAGC
1 TAGC
40598506 AGCAGTTTTT
Statistics
Matches: 170, Mismatches: 42, Indels: 10
0.77 0.19 0.05
Matches are distributed among these distances:
41 16 0.09
42 31 0.18
43 120 0.71
44 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (43 bp):
TAGCGGCATTTGTGATAGAAGCGCCGCTAAAGGCCATGATCTT
Found at i:40612404 original size:37 final size:37
Alignment explanation
Indices: 40612349--40612425 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
40612339 TGAAATATGC
* * *
40612349 AAGATCAAATTAGGGTCGCATCGCTGTGCTCGAAAGA
1 AAGATCAAATTAGGGTCGCATCACCGTGCTCCAAAGA
40612386 AAGATCAAATT-GGCGTCGCATCACCGTGCTCCAAAGA
1 AAGATCAAATTAGG-GTCGCATCACCGTGCTCCAAAGA
40612423 AAG
1 AAG
40612426 TATGCATCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 2 0.06
37 34 0.94
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (37 bp):
AAGATCAAATTAGGGTCGCATCACCGTGCTCCAAAGA
Found at i:40613401 original size:3 final size:3
Alignment explanation
Indices: 40613393--40613468 Score: 50
Period size: 3 Copynumber: 25.7 Consensus size: 3
40613383 TAACTAAACA
* * * * *
40613393 AAT AAT AAT AAC AAC ATAT AAT AA- ACAG AAT AAT AAT ATT AGT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* *
40613439 AAT AGT AAT AAT AA- AAA AAT -AT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40613469 ATAAGGGGAG
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
2 5 0.08
3 51 0.86
4 3 0.05
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:40613936 original size:27 final size:26
Alignment explanation
Indices: 40613880--40613939 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
40613870 CGTAAAGGAC
* *
40613880 TGGTGAGGTGAAAAACAAGAACGGCTG
1 TGGTG-GGTAAAAAACAAGAACGACTG
* *
40613907 TGGTGGGTAAAAAAGAAGAACGATTGG
1 TGGTGGGTAAAAAACAAGAACGACT-G
40613934 TGGTGG
1 TGGTGG
40613940 TTTTTTGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.35, C:0.07, G:0.40, T:0.18
Consensus pattern (26 bp):
TGGTGGGTAAAAAACAAGAACGACTG
Found at i:40614498 original size:9 final size:10
Alignment explanation
Indices: 40614475--40614499 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40614465 GTACAATTTT
40614475 TTTTTGCATA
1 TTTTTGCATA
40614485 TTTTTGCATA
1 TTTTTGCATA
40614495 TTTTT
1 TTTTT
40614500 TAAAAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (10 bp):
TTTTTGCATA
Found at i:40620365 original size:17 final size:16
Alignment explanation
Indices: 40620339--40620379 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
40620329 ATTAGCATAT
*
40620339 AAAAAAATTAAATTAA
1 AAAAAAATTAAAATAA
40620355 AAAAAATATTAAAATAA
1 AAAAAA-ATTAAAATAA
40620372 AAATAAAA
1 AAA-AAAA
40620380 AATGGCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 13 0.59
18 3 0.14
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAAAATTAAAATAA
Found at i:40629264 original size:30 final size:30
Alignment explanation
Indices: 40629228--40629289 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
40629218 TGAATTATTT
* * *
40629228 TTAAAAATTTGGTTACTCTTTTTGTAAATA
1 TTAAAAATTAGATGACTCTTTTTGTAAATA
*
40629258 TTAAAAATTAGATGCCTCTTTTTGTAAATA
1 TTAAAAATTAGATGACTCTTTTTGTAAATA
40629288 TT
1 TT
40629290 TTCAAAAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (30 bp):
TTAAAAATTAGATGACTCTTTTTGTAAATA
Found at i:40641253 original size:25 final size:25
Alignment explanation
Indices: 40641217--40641277 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
40641207 CTCCTAAATT
*
40641217 TTAATTTAATTATCTAAT-TTTTCA-A
1 TTAATTAAATTAT-TAATATTTT-ATA
*
40641242 TTTATTAAATTATTAATATTTTATA
1 TTAATTAAATTATTAATATTTTATA
40641267 TTAATTAAATT
1 TTAATTAAATT
40641278 TTTGAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATTAATATTTTATA
Found at i:40658853 original size:13 final size:13
Alignment explanation
Indices: 40658835--40658870 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
40658825 TGAAAAATGA
*
40658835 TTTGGTGGCAAAG
1 TTTGGTGACAAAG
40658848 TTTGGTGACAAAG
1 TTTGGTGACAAAG
*
40658861 TATGGTGACA
1 TTTGGTGACA
40658871 TAACAAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.28, C:0.08, G:0.33, T:0.31
Consensus pattern (13 bp):
TTTGGTGACAAAG
Found at i:40662240 original size:29 final size:28
Alignment explanation
Indices: 40662207--40662268 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
40662197 TTGGACATGT
40662207 ATTTTT-AAATAAAAAAGTAGAGAGACTAA
1 ATTTTTCAAA-AAAAAAGTAG-GAGACTAA
* *
40662236 ATTTTTCGAAAATAAAAGTAGGGGACTAA
1 ATTTTTC-AAAAAAAAAGTAGGAGACTAA
40662265 ATTT
1 ATTT
40662269 CAAATGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 17 0.59
30 9 0.31
31 3 0.10
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.31
Consensus pattern (28 bp):
ATTTTTCAAAAAAAAAGTAGGAGACTAA
Found at i:40665167 original size:40 final size:40
Alignment explanation
Indices: 40665119--40665385 Score: 507
Period size: 40 Copynumber: 6.7 Consensus size: 40
40665109 GCAAACACCT
* * *
40665119 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40665159 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40665199 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40665239 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40665279 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40665319 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40665359 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
40665386 ATCCAATGCT
Statistics
Matches: 224, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 224 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:40673965 original size:27 final size:27
Alignment explanation
Indices: 40673926--40674094 Score: 196
Period size: 27 Copynumber: 6.2 Consensus size: 27
40673916 NNNNNNNNNC
* * *
40673926 AGTGCTATATAATCAACTCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
* *
40673953 AGTGCTACGTAATCAAATCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
40673980 AGTGCTACATAGTCAAACTCGCACACTT
1 AGTGCTACATAGTCAAA-TCGCACACTT
** * *
40674008 AGTGCCGCATGGTCAATTCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
* **
40674035 AGTGC-ATCATATTCATTTCGCACACTT
1 AGTGCTA-CATAGTCAAATCGCACACTT
*
40674062 AGTGCAACATAGTCAAATCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
40674089 AGTGCT
1 AGTGCT
40674095 GTACAATTTA
Statistics
Matches: 122, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 98 0.80
28 24 0.20
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
AGTGCTACATAGTCAAATCGCACACTT
Found at i:40674063 original size:82 final size:81
Alignment explanation
Indices: 40673938--40674093 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40673928 TGCTATATAA
* *
40673938 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40674003 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40674020 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40674084 CACTTAGTGC
65 CACTTAGTGC
40674094 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40688326 original size:50 final size:49
Alignment explanation
Indices: 40688220--40688400 Score: 154
Period size: 50 Copynumber: 3.7 Consensus size: 49
40688210 AGAGGTCCCC
* * * * *
40688220 TGTAAGACCATGTCTGGGACATGGCGTTGGAACCGAGATGAGAGGTCCCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACC-AAATGAGA--ACACCCA
* *
40688272 --TAAGATCATGTCTGGGACATGGCATGGGCACCAATATGAGAACACCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCAA-ATGAGAACACCCA
* * * **
40688320 TGTAAGACCATATCTGGGATATGACATTGGCAGTACAA-GA-AACATCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCA-AATGAGAACA-CCCA
* *
40688369 TGTAAGACCATGTCTGGGACATGACTTTGGCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA
40688401 TGTTATTATC
Statistics
Matches: 107, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
48 9 0.08
49 36 0.34
50 61 0.57
51 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (49 bp):
TGTAAGACCATGTCTGGGACATGGCATTGGCACCAAATGAGAACACCCA
Found at i:40702234 original size:27 final size:26
Alignment explanation
Indices: 40702205--40702521 Score: 289
Period size: 27 Copynumber: 11.7 Consensus size: 26
40702195 TACCCTATAG
*
40702205 GGGTATTCTGATAATTTTACCCATCGGG
1 GGGTATT-TGATAATTTTACCCATC-GA
* *
40702233 GGGTATTTTGAAAATTTTACCCATTGA
1 GGGTA-TTTGATAATTTTACCCATCGA
* *
40702260 GGGTATTTCAGTAATTTTACCCTTCGA
1 GGGTATTTGA-TAATTTTACCCATCGA
* *
40702287 GGGTATTTCAGTAATTTTACCCTTCGA
1 GGGTATTTGA-TAATTTTACCCATCGA
* *
40702314 GGGTATTTCAGTAATTTTACCCTTCGA
1 GGGTATTTGA-TAATTTTACCCATCGA
*
40702341 GGGTATTTCGATAATTTTACCCAT-TA
1 GGGTATTT-GATAATTTTACCCATCGA
*
40702367 GGGGTATTTCGATAATTTTACCCATTGA
1 -GGGTATTT-GATAATTTTACCCATCGA
*
40702395 GGGTATTATGGTAATTTTACCCATC-A
1 GGGTATT-TGATAATTTTACCCATCGA
* * *
40702421 GGGTATTTTAGTAATTTTACCCTTCGG
1 GGGTATTTGA-TAATTTTACCCATCGA
* *
40702448 GGGTATTTCGATAATATTACCCAT-TA
1 GGGTATTT-GATAATTTTACCCATCGA
* * *
40702474 GGGGTATTTTGGTAATATTACCCATTGA
1 -GGGTA-TTTGATAATTTTACCCATCGA
*
40702502 GGGTATTTTAATAATTTTAC
1 GGGTA-TTTGATAATTTTAC
40702522 GCTCGTGTGA
Statistics
Matches: 250, Mismatches: 27, Indels: 25
0.83 0.09 0.08
Matches are distributed among these distances:
25 1 0.00
26 26 0.10
27 193 0.77
28 28 0.11
29 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.41
Consensus pattern (26 bp):
GGGTATTTGATAATTTTACCCATCGA
Found at i:40702516 original size:54 final size:54
Alignment explanation
Indices: 40702193--40702521 Score: 336
Period size: 54 Copynumber: 6.1 Consensus size: 54
40702183 TAACAATCAG
* * * *
40702193 TTTACCC-TATAGGGGTA-TTCTGATAATTTTACCCATCGGGGGGTATTTTGAA-AAT
1 TTTACCCAT-TAGGGGTATTTCAG-TAATTTTACCCTTC-GAGGGTA-TTTCAATAAT
*
40702248 TTTACCCATT-GAGGGTATTTCAGTAATTTTACCCTTCGAGGGTATTTCAGTAAT
1 TTTACCCATTAG-GGGTATTTCAGTAATTTTACCCTTCGAGGGTATTTCAATAAT
* *
40702302 TTTACCC-TTCGAGGGTATTTCAGTAATTTTACCCTTCGAGGGTATTTCGATAAT
1 TTTACCCATTAG-GGGTATTTCAGTAATTTTACCCTTCGAGGGTATTTCAATAAT
**
40702356 TTTACCCATTAGGGGTATTTC-GATAATTTTACCCATT-GAGGGTATTAT-GGTAAT
1 TTTACCCATTAGGGGTATTTCAG-TAATTTTACCC-TTCGAGGGTATT-TCAATAAT
* * * *
40702410 TTTACCCATCA-GGGTATTTTAGTAATTTTACCCTTCGGGGGTATTTCGATAAT
1 TTTACCCATTAGGGGTATTTCAGTAATTTTACCCTTCGAGGGTATTTCAATAAT
* ** * *
40702463 ATTACCCATTAGGGGTATTTTGGTAATATTACCCATT-GAGGGTATTTTAATAAT
1 TTTACCCATTAGGGGTATTTCAGTAATTTTACCC-TTCGAGGGTATTTCAATAAT
40702517 TTTAC
1 TTTAC
40702522 GCTCGTGTGA
Statistics
Matches: 239, Mismatches: 21, Indels: 29
0.83 0.07 0.10
Matches are distributed among these distances:
52 3 0.01
53 48 0.20
54 149 0.62
55 34 0.14
56 5 0.02
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (54 bp):
TTTACCCATTAGGGGTATTTCAGTAATTTTACCCTTCGAGGGTATTTCAATAAT
Found at i:40705491 original size:27 final size:27
Alignment explanation
Indices: 40705461--40705986 Score: 432
Period size: 27 Copynumber: 19.7 Consensus size: 27
40705451 TACCCTATGG
*
40705461 GGGTATTTCGATAATTTTACCCTTCGA
1 GGGTATTTCGATAATTTTACCCATCGA
*
40705488 GGGTGTTTCGATAATTTTACCCATC--
1 GGGTATTTCGATAATTTTACCCATCGA
* *
40705513 GGGTATTTTGGTAATTTTACCCATCGA
1 GGGTATTTCGATAATTTTACCCATCGA
* * *
40705540 GAGTATTT-GGTAATTTTACCCCTCGA
1 GGGTATTTCGATAATTTTACCCATCGA
40705566 GGGTATTTCGATAATTTTACCCATC-A
1 GGGTATTTCGATAATTTTACCCATCGA
* * *
40705592 AGGCATTTCAATAATTTTACCCATCGA
1 GGGTATTTCGATAATTTTACCCATCGA
* * * * *
40705619 GGGTATTTTGGTAAGTTTACCAATCAA
1 GGGTATTTCGATAATTTTACCCATCGA
* *
40705646 GGGTATTTC-AGTAATTTTACCCTTTGTA
1 GGGTATTTCGA-TAATTTTACCCATCG-A
* *
40705674 -GGTATTTCAATAATTTTACCCTTC-A
1 GGGTATTTCGATAATTTTACCCATCGA
* *
40705699 GGGGTATTTCGATAATATTACCCAT-TA
1 -GGGTATTTCGATAATTTTACCCATCGA
* * ** *
40705726 GGGGTATTTTGGTAATTTTATGCTTC-A
1 -GGGTATTTCGATAATTTTACCCATCGA
* * *
40705753 GGGGTATTT-TAGTAATTTTACGCTTC-A
1 -GGGTATTTCGA-TAATTTTACCCATCGA
** * **
40705780 GGGTATTTTAATAATTTTACCTATTAA
1 GGGTATTTCGATAATTTTACCCATCGA
40705807 GGGTATTTC-AGTAATTTTACCCATCGA
1 GGGTATTTCGA-TAATTTTACCCATCGA
* *
40705834 GGGTATTT-TAGTAATTTTACCCATCGG
1 GGGTATTTCGA-TAATTTTACCCATCGA
* * * * *
40705861 GGGTATTTCAATAGTTTTACCCTTTGG
1 GGGTATTTCGATAATTTTACCCATCGA
* *
40705888 GGGTATTTCAATAATTTTACCCTTCG-
1 GGGTATTTCGATAATTTTACCCATCGA
* * *
40705914 GGGTATTTCGGTAATATTACCCATCGG
1 GGGTATTTCGATAATTTTACCCATCGA
*
40705941 GGGTATTTTGATAATTTTACCCATCGA
1 GGGTATTTCGATAATTTTACCCATCGA
* * *
40705968 GGGTGTTTCGGTAAGTTTA
1 GGGTATTTCGATAATTTTA
40705987 ACTACCTTTT
Statistics
Matches: 412, Mismatches: 69, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
25 23 0.06
26 88 0.21
27 298 0.72
28 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.41
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACCCATCGA
Found at i:40705783 original size:134 final size:132
Alignment explanation
Indices: 40705460--40705986 Score: 472
Period size: 134 Copynumber: 3.9 Consensus size: 132
40705450 TTACCCTATG
* * * **
40705460 GGGGTATTTCGATAATTTTACCCTTCGAGGGT-GTTTCGATAATTTTACCCATC-GGGTATTTTG
1 GGGGTATTTCAATAATTTTACCCTTCG-GGGTATTTTAG-TAATTTTACCCATCAGGGTATTTCA
** *
40705523 GTAATTTTACCCATCGAGAGTATTT-GGTAATTTTACCCCTCGAGGGTATTTCGATAATTTTACC
64 GTAATTTTACCCATCGAG-GTATTTCAATAATTTTACCCATCGAGGGTATTTCGATAATTTTACC
40705587 CATCA
128 CATCA
* * * * * *
40705592 -AGGCATTTCAATAATTTTACCCATCGAGGGTATTTTGGTAAGTTTACCAATCAAGGGTATTTCA
1 GGGGTATTTCAATAATTTTACCCTTCG-GGGTATTTTAGTAATTTTACCCATC-AGGGTATTTCA
* * * *
40705656 GTAATTTTACCCTTTGTAGGTATTTCAATAATTTTACCCTTC-AGGGGTATTTCGATAATATTAC
64 GTAATTTTACCCATCG-AGGTATTTCAATAATTTTACCCATCGA-GGGTATTTCGATAATTTTAC
*
40705720 CCATTA
127 CCATCA
*** ** * * * *
40705726 GGGGTATTTTGGTAATTTTATGCTTCAGGGGTATTTTAGTAATTTTACGCTTCAGGGTATTTTAA
1 GGGGTATTTCAATAATTTTACCCTTC-GGGGTATTTTAGTAATTTTACCCATCAGGGTATTTCAG
* ** * *
40705791 TAATTTTACCTATTAAGGGTATTTCAGTAATTTTACCCATCGAGGGTATTT-TAGTAATTTTACC
65 TAATTTTACCCATCGA-GGTATTTCAATAATTTTACCCATCGAGGGTATTTCGA-TAATTTTACC
*
40705855 CATCG
128 CATCA
* * * * * * *
40705860 GGGGTATTTCAATAGTTTTACCCTTTGGGGGTATTTCAATAATTTTACCCTTCGGGGTATTTCGG
1 GGGGTATTTCAATAATTTTACCC-TTCGGGGTATTTTAGTAATTTTACCCATCAGGGTATTTCAG
* * ** * * *
40705925 TAATATTACCCATCGGGGGTATTTTGATAATTTTACCCATCGAGGGTGTTTCGGTAAGTTTA
65 TAATTTTACCCATC-GAGGTATTTCAATAATTTTACCCATCGAGGGTATTTCGATAATTTTA
40705987 ACTACCTTTT
Statistics
Matches: 314, Mismatches: 67, Indels: 26
0.77 0.16 0.06
Matches are distributed among these distances:
131 39 0.12
132 4 0.01
133 31 0.10
134 199 0.63
135 40 0.13
136 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (132 bp):
GGGGTATTTCAATAATTTTACCCTTCGGGGTATTTTAGTAATTTTACCCATCAGGGTATTTCAGT
AATTTTACCCATCGAGGTATTTCAATAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCAT
CA
Found at i:40711844 original size:17 final size:18
Alignment explanation
Indices: 40711809--40711845 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
40711799 GTTGAGACAA
40711809 ATGAGAGAGGAGAGAATG
1 ATGAGAGAGGAGAGAATG
40711827 ATGAGA-AGTGAG-GAATG
1 ATGAGAGAG-GAGAGAATG
40711844 AT
1 AT
40711846 AGATGAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.43, C:0.00, G:0.41, T:0.16
Consensus pattern (18 bp):
ATGAGAGAGGAGAGAATG
Found at i:40718615 original size:45 final size:45
Alignment explanation
Indices: 40718551--40718637 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
40718541 TATAGATACT
* *
40718551 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATATC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATATC
40718596 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGAT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGAT
40718638 GTTCGGTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATATC
Found at i:40734185 original size:55 final size:54
Alignment explanation
Indices: 40734090--40734239 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
40734080 CTACTTTGTT
* ** * *
40734090 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
40734144 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
40734199 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
40734240 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:40734202 original size:27 final size:27
Alignment explanation
Indices: 40734062--40734239 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
40734052 TAAATTGTAC
40734062 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
40734089 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
40734115 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
40734143 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
40734171 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
40734198 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
40734225 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40734240 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Done.