Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 121 of 333
Found at i:39140055 original size:21 final size:22
Alignment explanation
Indices: 39140009--39140055 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
39139999 GAATCCTCCT
*
39140009 TTTTTATTTATTCTTATTTTTA
1 TTTTTATTTATTCTTATTTTAA
39140031 -TTTTATTTATT-TTATTTTAA
1 TTTTTATTTATTCTTATTTTAA
39140051 TTTTT
1 TTTTT
39140056 CTTTTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTATTTATTCTTATTTTAA
Found at i:39140067 original size:7 final size:6
Alignment explanation
Indices: 39140015--39140077 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
39140005 TCCTTTTTTA
* * * * *
39140015 TTTATT CTTATT TTTATT TTATTTAT TTTATT TTAATT TTTCTT TTGATT
1 TTTATT TTTATT TTTATT TT-TAT-T TTTATT TTTATT TTTATT TTTATT
*
39140065 TTTATT TTCATT T
1 TTTATT TTTATT T
39140078 CAATTTTATT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
6 37 0.84
7 4 0.09
8 3 0.07
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:39140077 original size:12 final size:11
Alignment explanation
Indices: 39140009--39140097 Score: 60
Period size: 12 Copynumber: 7.9 Consensus size: 11
39139999 GAATCCTCCT
39140009 TTTTTA-TTTA
1 TTTTTATTTTA
*
39140019 TTCTTATTTT-
1 TTTTTATTTTA
39140029 TATTTTA-TTTA
1 T-TTTTATTTTA
39140040 -TTTTATTTTAA
1 TTTTTATTTT-A
*
39140051 TTTTTCTTTTGA
1 TTTTTATTTT-A
39140063 TTTTTATTTTCA
1 TTTTTATTTT-A
**
39140075 TTTCAATTTTA
1 TTTTTATTTTA
39140086 TTATTTTATTTT
1 -T-TTTTATTTT
39140098 GAAAGACATA
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
9 5 0.08
10 12 0.20
11 9 0.15
12 28 0.46
13 7 0.11
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.75
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:39143023 original size:21 final size:22
Alignment explanation
Indices: 39142989--39143030 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
39142979 TTCTCTCTGC
39142989 TTTAAATAAATTAGTTAATTAG
1 TTTAAATAAATTAGTTAATTAG
39143011 TTTAAAT-AATTAGTTAATTA
1 TTTAAATAAATTAGTTAATTA
39143031 AAACAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTTAAATAAATTAGTTAATTAG
Found at i:39150984 original size:18 final size:18
Alignment explanation
Indices: 39150961--39150998 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
39150951 GTAGGTTTCC
*
39150961 AAAAATGGAAATGGAAAT
1 AAAAATGAAAATGGAAAT
39150979 AAAAATGAAAATGGAAAT
1 AAAAATGAAAATGGAAAT
39150997 AA
1 AA
39150999 TCTATTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (18 bp):
AAAAATGAAAATGGAAAT
Found at i:39152463 original size:38 final size:38
Alignment explanation
Indices: 39152420--39152496 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
39152410 CTTAAGTGGC
*
39152420 ATCATTTTAGTGATGATAGCACTACATGATGCGTTTAT
1 ATCATTTTAGTGATGATAGCACTACATAATGCGTTTAT
39152458 ATCATTTTAGTGATGATAGCACTACATAATGCGTTTAT
1 ATCATTTTAGTGATGATAGCACTACATAATGCGTTTAT
39152496 A
1 A
39152497 CTTATTTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (38 bp):
ATCATTTTAGTGATGATAGCACTACATAATGCGTTTAT
Found at i:39165662 original size:147 final size:147
Alignment explanation
Indices: 39165274--39165716 Score: 654
Period size: 146 Copynumber: 3.0 Consensus size: 147
39165264 TAGGGACGGT
* *
39165274 ATGTATGCATATGTTTTTTTATTATAATTTGTTTATGTTATTGAATGAAGTTAAGTTTAAATGTT
1 ATGTATGCATATG-TTTTGT-TTATAATTTTTTTATGTTATTGAATGAAGTTAAGTTTAAATGTT
* * * * *** *
39165339 TTTGATTGTACGGTAATGCTCTATGACCTTAAATCGGTGATGGATATGGGTTAGAGGTGTTACAA
64 TCTGATTGTACGGTAATGCTCTATGACCCTAAACCGGCGACAAATATGGGTTAGAGGTGTTACAG
39165404 GCCACTTCACTCTTTGCTA
129 GCCACTTCACTCTTTGCTA
* * *
39165423 ATGTACGCATATATTTTGTTTATAA-TTTTTTATGTTATTGAATGAAGTTAAGTTTATATGTTTC
1 ATGTATGCATATGTTTTGTTTATAATTTTTTTATGTTATTGAATGAAGTTAAGTTTAAATGTTTC
*
39165487 TGATTGTACGGTAATGCTCTATGACCCTAAACCGGCGACAAATATGGGTTAGAGGTGTTATAGGC
66 TGATTGTACGGTAATGCTCTATGACCCTAAACCGGCGACAAATATGGGTTAGAGGTGTTACAGGC
*
39165552 CACTTCTCTCTTTGCTA
131 CACTTCACTCTTTGCTA
* *
39165569 ATGTATTCATATGTTTTGTTTATAATTTTTTTATGTTATTGAGTGAAGTTAAGTTTAAATGTTTC
1 ATGTATGCATATGTTTTGTTTATAATTTTTTTATGTTATTGAATGAAGTTAAGTTTAAATGTTTC
* * *
39165634 TGATTGTACGGTAAAGCTCTATGACCCTAAACTGGCGACAAACATGGGTTAGAGGTGTTACAGGC
66 TGATTGTACGGTAATGCTCTATGACCCTAAACCGGCGACAAATATGGGTTAGAGGTGTTACAGGC
* * *
39165699 TACTTCGCTCTTTACTA
131 CACTTCACTCTTTGCTA
39165716 A
1 A
39165717 CTTTTCAGTA
Statistics
Matches: 266, Mismatches: 27, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
146 131 0.49
147 119 0.45
148 5 0.02
149 11 0.04
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (147 bp):
ATGTATGCATATGTTTTGTTTATAATTTTTTTATGTTATTGAATGAAGTTAAGTTTAAATGTTTC
TGATTGTACGGTAATGCTCTATGACCCTAAACCGGCGACAAATATGGGTTAGAGGTGTTACAGGC
CACTTCACTCTTTGCTA
Found at i:39173695 original size:27 final size:27
Alignment explanation
Indices: 39173656--39173940 Score: 342
Period size: 27 Copynumber: 10.6 Consensus size: 27
39173646 CCAAACTGTT
* *
39173656 TAAAATTATCGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACCCTCAATTTG
39173683 TAAAATTACCGAAATACCCTCAATTTG
1 TAAAATTACCGAAATACCCTCAATTTG
* *
39173710 TAAAATTACCAAAATACCCCCAATTTG
1 TAAAATTACCGAAATACCCTCAATTTG
* * *
39173737 TAAAATTACTGAAATACCCTTAGTTTG
1 TAAAATTACCGAAATACCCTCAATTTG
** *
39173764 TAAAATTATTGAAATACCCTCAGTTTG
1 TAAAATTACCGAAATACCCTCAATTTG
* *
39173791 TAAAATTATCGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACCCTCAATTTG
**
39173818 TAAAATTACTAAAATACCC-CAATTTG
1 TAAAATTACCGAAATACCCTCAATTTG
* *
39173844 TAAAATTACTGAAATACCAC-CAGTTTG
1 TAAAATTACCGAAATACC-CTCAATTTG
* * *
39173871 CAAAACTATCGAAATACCC-CAATTTG
1 TAAAATTACCGAAATACCCTCAATTTG
* * *
39173897 TAAAATTACCAAAATAACCTCAGTTTG
1 TAAAATTACCGAAATACCCTCAATTTG
39173924 TAAAATTACCGAAATAC
1 TAAAATTACCGAAATAC
39173941 ATCTATAGGG
Statistics
Matches: 223, Mismatches: 33, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
26 44 0.20
27 179 0.80
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTCAATTTG
Found at i:39174364 original size:27 final size:27
Alignment explanation
Indices: 39174304--39174378 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
39174294 TTGTTTATGG
*
39174304 CTTTGTGCAAATCATATTTACTAGTGG
1 CTTTGTGCAAATCATATTTACTAGTGA
* * *
39174331 CTATGTGCATATCATATTTA-TTGATGA
1 CTTTGTGCAAATCATATTTACTAG-TGA
*
39174358 CTTTGTGTC-GATCATATTTAC
1 CTTTGTG-CAAATCATATTTAC
39174379 CCATGGCTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.05
27 36 0.92
28 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (27 bp):
CTTTGTGCAAATCATATTTACTAGTGA
Found at i:39177896 original size:27 final size:27
Alignment explanation
Indices: 39177859--39178045 Score: 229
Period size: 27 Copynumber: 7.0 Consensus size: 27
39177849 GTAGGGCAAA
*
39177859 TCAGTCATTTTACCTTATAGGGGTATT
1 TCAGTCATTTTACCCTATAGGGGTATT
* * * * *
39177886 ACAATAATTTTACCCTACAGGGATATT
1 TCAGTCATTTTACCCTATAGGGGTATT
*
39177913 ACAGTCATTTTACCCTATAGGGGTATT
1 TCAGTCATTTTACCCTATAGGGGTATT
39177940 TC-GATCATTTTACCCTATAGGGGTATT
1 TCAG-TCATTTTACCCTATAGGGGTATT
* *
39177967 TCGGTCATTTTACCTTAT-GAGGGTATT
1 TCAGTCATTTTACCCTATAG-GGGTATT
39177994 TCAGTCATTTTACCCTAT-GAGGGTATT
1 TCAGTCATTTTACCCTATAG-GGGTATT
*
39178021 TCGGTCATTTTACCCTAT-GGGGTAT
1 TCAGTCATTTTACCCTATAGGGGTAT
39178046 CTCGGTCACC
Statistics
Matches: 142, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
26 8 0.06
27 133 0.94
28 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Consensus pattern (27 bp):
TCAGTCATTTTACCCTATAGGGGTATT
Found at i:39180118 original size:15 final size:15
Alignment explanation
Indices: 39180076--39180119 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
39180066 TGTCAAAATC
*
39180076 AAACAAATGAAAATAT
1 AAACAAAT-AAAATAG
*
39180092 AAA-AATTAAAATAG
1 AAACAAATAAAATAG
39180106 AAACAAATAAAATA
1 AAACAAATAAAATA
39180120 AATGGTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.38
15 12 0.50
16 3 0.12
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.18
Consensus pattern (15 bp):
AAACAAATAAAATAG
Found at i:39183772 original size:52 final size:52
Alignment explanation
Indices: 39183694--39183797 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
39183684 ATATGTATGC
*
39183694 GGCATCCGAGCTTATTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
1 GGCATCCGAGCTCATTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
*
39183746 GGCATCTGAGCTCATTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
1 GGCATCCGAGCTCATTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
39183798 AATTGGGTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (52 bp):
GGCATCCGAGCTCATTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
Found at i:39185858 original size:43 final size:43
Alignment explanation
Indices: 39185761--39185926 Score: 156
Period size: 43 Copynumber: 3.9 Consensus size: 43
39185751 ATCGAGATGA
* * *
39185761 GATTACATGTAAGACCATGTCTAGCACATTGGCATTG-TATTGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTTA-TAT
* * *
39185804 GTTTACGTGTAAGACAATGTCTGGGACATTGGCATTGTTATAT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTTATAT
* * * *** * *
39185847 GATTTCATGTAAGGCCACGTCTGGGTTGTTGGCATCGATATAT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTTATAT
* * *
39185890 GATGACATGTAAGACCATATCTGGGATA-TGGCATTGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGT
39185927 ACGAGCTCTA
Statistics
Matches: 96, Mismatches: 26, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
42 7 0.07
43 87 0.91
44 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.34
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTTATAT
Found at i:39188729 original size:27 final size:27
Alignment explanation
Indices: 39188699--39188875 Score: 169
Period size: 27 Copynumber: 6.5 Consensus size: 27
39188689 ATATTGAGCC
* *
39188699 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
39188726 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
39188753 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
39188781 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
39188808 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
39188835 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
39188862 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39188876 CGCACAATTT
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
27 102 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:39188838 original size:82 final size:81
Alignment explanation
Indices: 39188720--39188879 Score: 232
Period size: 82 Copynumber: 2.0 Consensus size: 81
39188710 TGCTATATAA
* * *
39188720 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTC-GAATCGCA
39188785 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39188802 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA
39188866 CACTTAGTGCCGCA
65 CACTTAGTGCCGCA
39188880 CAATTTAATC
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
81 23 0.33
82 47 0.67
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39203146 original size:40 final size:40
Alignment explanation
Indices: 39203109--39203294 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
39203099 GCTACTCGTT
* *
39203109 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
39203149 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
39203189 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
39203229 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
39203270 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
39203295 CATCATTCAA
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 3 0.02
40 117 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:39211151 original size:79 final size:81
Alignment explanation
Indices: 39211049--39211233 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
39211039 GCTACTCATT
* *
39211049 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
39211112 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
39211129 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
39211193 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
39211209 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39211234 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:39211233 original size:40 final size:40
Alignment explanation
Indices: 39211049--39211233 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
39211039 GCTACTCATT
* *
39211049 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
39211089 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
39211129 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
39211168 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
39211209 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39211234 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:39213165 original size:21 final size:20
Alignment explanation
Indices: 39213135--39213174 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
39213125 GCTTTTTCAA
*
39213135 TCTCATTCTCGTTTTGCTTTC
1 TCTCACTCTC-TTTTGCTTTC
*
39213156 TCTCACTCTCTTTTTCTTT
1 TCTCACTCTCTTTTGCTTT
39213175 TTCAAGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.05, C:0.30, G:0.05, T:0.60
Consensus pattern (20 bp):
TCTCACTCTCTTTTGCTTTC
Found at i:39215606 original size:22 final size:22
Alignment explanation
Indices: 39215576--39215617 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
39215566 TTTATGAATT
39215576 AGGGACTAAATTGTTAAAATGTG
1 AGGGACTAAATTG-TAAAATGTG
*
39215599 AGGG-CTAATTTGTAAAATG
1 AGGGACTAAATTGTAAAATG
39215618 CCCTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (22 bp):
AGGGACTAAATTGTAAAATGTG
Found at i:39216136 original size:43 final size:43
Alignment explanation
Indices: 39215980--39216136 Score: 149
Period size: 43 Copynumber: 3.7 Consensus size: 43
39215970 TGTGTTATCT
** *
39215980 TGTAAGACCACGTCCGGGACATTGGCATCGACT-TATGATTTACG
1 TGTAAGACCACGTCTAGGACATTGGCATCGA-TATTTGA-TTACG
* * **
39216024 TGTAAGACTATGTCTAGGACATTGGCATCG-TATTTGATTTTG
1 TGTAAGACCACGTCTAGGACATTGGCATCGATATTTGATTACG
* * ** *
39216066 TGTAAGACC-CTATCTGGGACAGAGGCATCGATATTTGATTACA
1 TGTAAGACCAC-GTCTAGGACATTGGCATCGATATTTGATTACG
*
39216109 TGTAAGACCACGTCTAGGACGTTGGCAT
1 TGTAAGACCACGTCTAGGACATTGGCAT
39216137 TGTATGAGCT
Statistics
Matches: 88, Mismatches: 21, Indels: 9
0.75 0.18 0.08
Matches are distributed among these distances:
42 27 0.31
43 34 0.39
44 27 0.31
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTAGGACATTGGCATCGATATTTGATTACG
Found at i:39219671 original size:49 final size:49
Alignment explanation
Indices: 39219563--39219695 Score: 135
Period size: 49 Copynumber: 2.7 Consensus size: 49
39219553 TGGGTTAAGA
* * *
39219563 TGTTGATGCCATGTCCCGGACATGGTCTTACACTAGCTTTCATATAGCGAG
1 TGTTGATGCCATGT-CCAGACA-GGTCTTACACTGGCTCTCATATAGCGAG
*** * *
39219614 -GCCAATGCCATGTCCTAGACAGGTCTTACACTGGCTCTCATCTATCG-G
1 TGTTGATGCCATGTCC-AGACAGGTCTTACACTGGCTCTCATATAGCGAG
*
39219662 TGTTGATGCCATGTACCAGATAGGTCTTACACTG
1 TGTTGATGCCATGT-CCAGACAGGTCTTACACTG
39219696 ACACACCACA
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
48 1 0.01
49 50 0.75
50 16 0.24
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.30
Consensus pattern (49 bp):
TGTTGATGCCATGTCCAGACAGGTCTTACACTGGCTCTCATATAGCGAG
Found at i:39219785 original size:48 final size:46
Alignment explanation
Indices: 39219707--39219879 Score: 170
Period size: 48 Copynumber: 3.7 Consensus size: 46
39219697 CACACCACAA
* *
39219707 GCTGATGCCATGTCCCAGATAGGTCTTACACTAGCTTGTATATCGCAAG
1 GCTGATG-CATGTCCCAGACATGTCTTACACTAGCTT-TATATC-CAAG
* * * *
39219756 GCTGATGCATGTCCCAGATATGTCCTACACTAGCTCTTGTAT-CAAT
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCT-TTATATCCAAG
* * **
39219802 G-TCGATGCATGTCCCAGACATGTCTTACACTGGCTTAAATATCTTGAG
1 GCT-GATGCATGTCCCAGACATGTCTTACACTAGCTT-TATATC-CAAG
*
39219850 GCTGATGCATGTCCTAGACATGTCTTACAC
1 GCTGATGCATGTCCCAGACATGTCTTACAC
39219880 CGTGATACGA
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
45 2 0.02
46 36 0.34
48 58 0.55
49 9 0.09
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (46 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTAGCTTTATATCCAAG
Found at i:39220083 original size:30 final size:30
Alignment explanation
Indices: 39220049--39220145 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
39220039 AGCTCACTCC
39220049 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
39220079 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
39220109 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
39220139 TAGCTCA
1 TAGCTCA
39220146 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:39224683 original size:24 final size:26
Alignment explanation
Indices: 39224651--39224699 Score: 75
Period size: 24 Copynumber: 1.9 Consensus size: 26
39224641 AGTTCATGCA
39224651 ATATTAAAGC-ATTTAA-ATACGATT
1 ATATTAAAGCTATTTAACATACGATT
39224675 ATATTAAAGCTTATTTAACATACGA
1 ATATTAAAGC-TATTTAACATACGA
39224700 ACTTACCTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.45
26 6 0.27
27 6 0.27
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (26 bp):
ATATTAAAGCTATTTAACATACGATT
Found at i:39226675 original size:40 final size:40
Alignment explanation
Indices: 39226626--39226758 Score: 144
Period size: 40 Copynumber: 3.3 Consensus size: 40
39226616 ACTCGATATC
* *
39226626 TTGCACACTAAGTGTCGTACATAGCTGAA-TATATCTCGAA
1 TTGCACACTAAGTGCCATACATAGCTGAAGT-TATCTCGAA
* *
39226666 TTGCACACTAAGTGCCATATATAGCTGAAGTTATGTCGAA
1 TTGCACACTAAGTGCCATACATAGCTGAAGTTATCTCGAA
* * * *
39226706 TAT-CACACTAAGTGCCATATATAGCCGAAGCTATGTCGAA
1 T-TGCACACTAAGTGCCATACATAGCTGAAGTTATCTCGAA
* *
39226746 TCGTACACTAAGT
1 TTGCACACTAAGT
39226759 ACCACAAATA
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
40 80 0.98
41 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (40 bp):
TTGCACACTAAGTGCCATACATAGCTGAAGTTATCTCGAA
Found at i:39226770 original size:40 final size:39
Alignment explanation
Indices: 39226661--39226773 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 39
39226651 TGAATATATC
* * *
39226661 TCGAATTGCACACTAAGTGCCATATATAGCTGAAGTTATG
1 TCGAA-TGTACACTAAGTGCCATATATAGCCGAAGCTATG
*
39226701 TCGAATATCACACTAAGTGCCATATATAGCCGAAGCTATG
1 TCGAATGT-ACACTAAGTGCCATATATAGCCGAAGCTATG
* * *
39226741 TCGAATCGTACACTAAGTACCACAAATAGCCGA
1 TCGAAT-GTACACTAAGTGCCATATATAGCCGA
39226774 TTTGTCGTCA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.02
40 61 0.97
41 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (39 bp):
TCGAATGTACACTAAGTGCCATATATAGCCGAAGCTATG
Found at i:39231249 original size:40 final size:40
Alignment explanation
Indices: 39231097--39231242 Score: 181
Period size: 40 Copynumber: 3.6 Consensus size: 40
39231087 TTGAATGATG
* * * *
39231097 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
39231137 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39231177 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
39231218 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39231243 AACGAGTAGC
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
39 1 0.01
40 82 0.88
41 10 0.11
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:39231249 original size:80 final size:80
Alignment explanation
Indices: 39231097--39231275 Score: 195
Period size: 80 Copynumber: 2.2 Consensus size: 80
39231087 TTGAATGATG
* *
39231097 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
39231162 GTGCGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
* * * * *
39231177 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
*
39231240 TTGAACGAGTAGCTATA
64 TTGAACGAGTAGCTAAA
* *
39231257 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
39231276 TACGTGATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
79 17 0.20
80 60 0.71
81 7 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTAGCTAAA
Found at i:39244375 original size:16 final size:16
Alignment explanation
Indices: 39244350--39244392 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
39244340 ACAGATCTTG
*
39244350 AAAAGCTGAAATGCCA
1 AAAAGTTGAAATGCCA
*
39244366 AAAAGTTGAAATGCCG
1 AAAAGTTGAAATGCCA
*
39244382 AAAAGTCGAAA
1 AAAAGTTGAAA
39244393 GTTTAGCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.51, C:0.14, G:0.21, T:0.14
Consensus pattern (16 bp):
AAAAGTTGAAATGCCA
Found at i:39244534 original size:18 final size:19
Alignment explanation
Indices: 39244499--39244535 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39244489 TGAATTGGAC
39244499 AAATGGGCCAGAATGGGCT
1 AAATGGGCCAGAATGGGCT
*
39244518 AAATGGGCCCG-ATGGGCT
1 AAATGGGCCAGAATGGGCT
39244536 GTTGGGCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.27, C:0.19, G:0.38, T:0.16
Consensus pattern (19 bp):
AAATGGGCCAGAATGGGCT
Found at i:39244656 original size:28 final size:27
Alignment explanation
Indices: 39244609--39244711 Score: 134
Period size: 28 Copynumber: 3.7 Consensus size: 27
39244599 CATGACTGTA
* *
39244609 AATGTGATTAGGCCAAATGGCCATATG
1 AATGTGATTGGGCCTAATGGCCATATG
* *
39244636 AATGTGATTTGGGCCTAATGGCCACATA
1 AATGTGA-TTGGGCCTAATGGCCATATG
39244664 AATGTGATTGGGCCTAATGGGCCATATG
1 AATGTGATTGGGCCTAAT-GGCCATATG
* *
39244692 AAAGAGATTGGGCCTAATGG
1 AATGTGATTGGGCCTAATGG
39244712 GCTATATACA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
27 20 0.30
28 46 0.70
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (27 bp):
AATGTGATTGGGCCTAATGGCCATATG
Found at i:39244703 original size:55 final size:55
Alignment explanation
Indices: 39244607--39244711 Score: 158
Period size: 55 Copynumber: 1.9 Consensus size: 55
39244597 AGCATGACTG
* *
39244607 TAAATGTGATTAGGCCAAATGGCCATATGAATGTGATTTGGGCCTAATGGCCACA
1 TAAATGTGATTAGGCCAAATGGCCATATGAAAGAGATTTGGGCCTAATGGCCACA
* *
39244662 TAAATGTGATTGGGCCTAATGGGCCATATGAAAGAGA-TTGGGCCTAATGG
1 TAAATGTGATTAGGCCAAAT-GGCCATATGAAAGAGATTTGGGCCTAATGG
39244712 GCTATATACA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
55 31 0.69
56 14 0.31
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (55 bp):
TAAATGTGATTAGGCCAAATGGCCATATGAAAGAGATTTGGGCCTAATGGCCACA
Found at i:39248864 original size:19 final size:20
Alignment explanation
Indices: 39248840--39248877 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39248830 GGTACCACCA
39248840 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
39248859 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
39248878 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:39249191 original size:46 final size:46
Alignment explanation
Indices: 39249106--39249227 Score: 156
Period size: 46 Copynumber: 2.7 Consensus size: 46
39249096 CGCCCCTAAG
* * * *
39249106 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCTGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
* * *
39249152 TGAACTCTGACTCAACTCAACAAGTTCGGACATTTGCATCCATAAG
1 TGAACTCTGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
*
39249198 TGAACT-TGAACTCCACTCAACGAGTTCGGA
1 TGAACTCTG-ACTCAACTCAACGAGTTCGGA
39249228 TGCTCGACCA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
45 2 0.03
46 64 0.97
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
TGAACTCTGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
Found at i:39249684 original size:30 final size:30
Alignment explanation
Indices: 39249650--39249709 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
39249640 ATTTAATATG
39249650 AACTTTAAAAAAATTACACTTTTGCACCTA
1 AACTTTAAAAAAATTACACTTTTGCACCTA
*** * *
39249680 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCACCTA
39249710 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCACCTA
Found at i:39256395 original size:19 final size:20
Alignment explanation
Indices: 39256371--39256408 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39256361 GGTACCACCA
39256371 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
39256390 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
39256409 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:39256703 original size:46 final size:46
Alignment explanation
Indices: 39256636--39256757 Score: 174
Period size: 46 Copynumber: 2.7 Consensus size: 46
39256626 CGCCCCTAAG
* * * *
39256636 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCTGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
* *
39256682 TGAACTCTGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG
1 TGAACTCTGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
39256728 TGAACT-TGAACTCAACTCAACGAGTTCGGA
1 TGAACTCTG-ACTCAACTCAACGAGTTCGGA
39256758 TGCTCGACCA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
45 2 0.03
46 67 0.97
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TGAACTCTGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
Found at i:39264237 original size:44 final size:46
Alignment explanation
Indices: 39264132--39264254 Score: 198
Period size: 45 Copynumber: 2.7 Consensus size: 46
39264122 AACCCGCCCC
* * *
39264132 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
39264178 TAA-TGAACTCGGACTCAACTCAACGAGTTCGGACATT-GCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
39264222 TAAGTGAACTC-GACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39264255 TGCTCAACCA
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
44 32 0.44
45 38 0.52
46 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:39264273 original size:45 final size:45
Alignment explanation
Indices: 39264134--39264273 Score: 144
Period size: 45 Copynumber: 3.1 Consensus size: 45
39264124 CCCGCCCCTA
* * *
39264134 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACCATCC-T
* * *
39264179 AATGAACTCGGACTCAACTCAACGAGTTCGGACATTGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGACGTT-CA-CCATCCT
* *
39264224 AGTGAACTC-GACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTC-ACCATCCT
39264269 AGTGA
1 AGTGA
39264274 CATGTCACTT
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
43 5 0.06
44 24 0.31
45 45 0.58
46 1 0.01
48 3 0.04
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACCATCCT
Found at i:39271369 original size:41 final size:42
Alignment explanation
Indices: 39271226--39271389 Score: 147
Period size: 44 Copynumber: 3.8 Consensus size: 42
39271216 AACCCGCCCC
* *
39271226 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC--GCATT--CATCCA
* * *
39271272 T--GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGCAT-TC-A--TCCA
* *
39271316 TTTCA-CGAACTCGGACTCAACTCAACGAGTTC-CATTCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGCATTCATCCA
39271358 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
39271390 GATGCTCAAC
Statistics
Matches: 97, Mismatches: 11, Indels: 24
0.73 0.08 0.18
Matches are distributed among these distances:
40 2 0.02
41 27 0.28
42 6 0.06
44 31 0.32
45 1 0.01
46 4 0.04
47 26 0.27
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (42 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGCATTCATCCA
Found at i:39271383 original size:88 final size:88
Alignment explanation
Indices: 39271231--39271394 Score: 251
Period size: 88 Copynumber: 1.8 Consensus size: 88
39271221 GCCCCTAAGT
*
39271231 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGTGAACTCGGACTCAACTCAACG
1 GAACTCGGACTCAACTCAACGAGCTC--GCATTC-CATCCATGTGAACTCGGACTCAACTCAACG
39271296 AGTTCGGATGCCTAGTTACATTTCAC
63 AGTTCGGATGCCTAGTTACATTTCAC
*
39271322 GAACTCGGACTCAACTCAACGAGTTC-CATT-CATCCATAAGTGAACTCGGACTCAACTCAACGA
1 GAACTCGGACTCAACTCAACGAGCTCGCATTCCATCCAT--GTGAACTCGGACTCAACTCAACGA
39271385 GTTCGGATGC
64 GTTCGGATGC
39271395 TCAACCATCC
Statistics
Matches: 69, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
86 7 0.10
88 37 0.54
91 25 0.36
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (88 bp):
GAACTCGGACTCAACTCAACGAGCTCGCATTCCATCCATGTGAACTCGGACTCAACTCAACGAGT
TCGGATGCCTAGTTACATTTCAC
Found at i:39271827 original size:30 final size:30
Alignment explanation
Indices: 39271793--39271852 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
39271783 ATTTAATACG
39271793 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
39271823 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
39271853 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:39283803 original size:14 final size:14
Alignment explanation
Indices: 39283784--39283810 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39283774 CTAGACCGTA
39283784 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
39283798 TGCAATTTTTTTT
1 TGCAATTTTTTTT
39283811 CCTTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:39283808 original size:12 final size:13
Alignment explanation
Indices: 39283785--39283846 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
39283775 TAGACCGTAT
*
39283785 GCAATTTTTTTTTT
1 GCAA-TTTTTTTTC
39283799 GCAATTTTTTTTC
1 GCAATTTTTTTTC
39283812 -C--TTTTTTTTC
1 GCAATTTTTTTTC
* *
39283822 GGATTTTTTTTTC
1 GCAATTTTTTTTC
*
39283835 GAAATTTTTTTT
1 GCAATTTTTTTT
39283847 AACTTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 9 0.22
12 1 0.02
13 27 0.66
14 4 0.10
ACGTcount: A:0.13, C:0.10, G:0.08, T:0.69
Consensus pattern (13 bp):
GCAATTTTTTTTC
Found at i:39283820 original size:23 final size:23
Alignment explanation
Indices: 39283790--39283834 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
39283780 CGTATGCAAT
*
39283790 TTTTTTTTTGCAATTTTTTTTCC
1 TTTTTTTTCGCAATTTTTTTTCC
* *
39283813 TTTTTTTTCGGATTTTTTTTTC
1 TTTTTTTTCGCAATTTTTTTTC
39283835 GAAATTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.07, C:0.11, G:0.07, T:0.76
Consensus pattern (23 bp):
TTTTTTTTCGCAATTTTTTTTCC
Found at i:39283841 original size:36 final size:37
Alignment explanation
Indices: 39283788--39283857 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
39283778 ACCGTATGCA
* * *
39283788 ATTTTTTTTTTGCAATTTTTTTT-CCTTTTTTTTCGG
1 ATTTTTTTTTCGAAATTTTTTTTAACTTTTTTTTCGG
39283824 ATTTTTTTTTCGAAATTTTTTTTAACTTTTTTTT
1 ATTTTTTTTTCGAAATTTTTTTTAACTTTTTTTT
39283858 TTCGAAGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 21 0.70
37 9 0.30
ACGTcount: A:0.13, C:0.09, G:0.06, T:0.73
Consensus pattern (37 bp):
ATTTTTTTTTCGAAATTTTTTTTAACTTTTTTTTCGG
Found at i:39288208 original size:24 final size:25
Alignment explanation
Indices: 39288155--39288208 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
39288145 AACAAATTCT
* *
39288155 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
39288180 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
39288203 TTTTTT
1 TTTTTT
39288209 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:39290483 original size:15 final size:14
Alignment explanation
Indices: 39290454--39290482 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39290444 CTAGACCGTA
39290454 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
39290468 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
39290482 T
1 T
39290483 TTTTTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:39290483 original size:19 final size:18
Alignment explanation
Indices: 39290459--39290499 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
39290449 CCGTATGCAA
39290459 TTTTTTTTTTGCAATTTTT
1 TTTTTTTTTTGC-ATTTTT
*
39290478 TTTTTTTTTTTCATTTTT
1 TTTTTTTTTTGCATTTTT
39290496 TTTT
1 TTTT
39290500 CGAAACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.07, C:0.05, G:0.02, T:0.85
Consensus pattern (18 bp):
TTTTTTTTTTGCATTTTT
Found at i:39290509 original size:14 final size:15
Alignment explanation
Indices: 39290491--39290529 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
39290481 TTTTTTTTCA
39290491 TTTTTTTTTCGAAAC
1 TTTTTTTTTCGAAAC
39290506 -TTTTTTTT---AAC
1 TTTTTTTTTCGAAAC
39290517 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
39290530 GCTACGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 8
0.71 0.00 0.29
Matches are distributed among these distances:
11 3 0.15
12 8 0.40
14 8 0.40
15 1 0.05
ACGTcount: A:0.18, C:0.10, G:0.05, T:0.67
Consensus pattern (15 bp):
TTTTTTTTTCGAAAC
Found at i:39290509 original size:26 final size:26
Alignment explanation
Indices: 39290481--39290529 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
39290471 AATTTTTTTT
*
39290481 TTTTTTTTCA-TTTTTTTTTCGAAAC
1 TTTTTTTTAACTTTTTTTTTCGAAAC
39290506 TTTTTTTTAACTTTTTTTTTCGAA
1 TTTTTTTTAACTTTTTTTTTCGAA
39290530 GCTACGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.16, C:0.10, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTTTTTTAACTTTTTTTTTCGAAAC
Found at i:39297134 original size:14 final size:14
Alignment explanation
Indices: 39297115--39297141 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39297105 CTAGACCGTA
39297115 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
39297129 TGCAATTTTTTTT
1 TGCAATTTTTTTT
39297142 CTTTTTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:39297149 original size:22 final size:22
Alignment explanation
Indices: 39297121--39297164 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39297111 CGTATGCAAT
*
39297121 TTTTTTTTTGCAATTTTTTTTC
1 TTTTTTTTCGCAATTTTTTTTC
* *
39297143 TTTTTTTTCGGATTTTTTTTTC
1 TTTTTTTTCGCAATTTTTTTTC
39297165 GAACTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.77
Consensus pattern (22 bp):
TTTTTTTTCGCAATTTTTTTTC
Found at i:39297159 original size:13 final size:14
Alignment explanation
Indices: 39297143--39297192 Score: 63
Period size: 13 Copynumber: 3.9 Consensus size: 14
39297133 ATTTTTTTTC
*
39297143 TTTTTTTTCGGA-T
1 TTTTTTTTCGAACT
39297156 TTTTTTTTCGAAC-
1 TTTTTTTTCGAACT
39297169 TTTTTTTT--AACT
1 TTTTTTTTCGAACT
39297181 TTTTTTTTCGAA
1 TTTTTTTTCGAA
39297193 GCTACGATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
11 3 0.09
12 8 0.25
13 19 0.59
14 2 0.06
ACGTcount: A:0.14, C:0.10, G:0.08, T:0.68
Consensus pattern (14 bp):
TTTTTTTTCGAACT
Found at i:39297186 original size:11 final size:12
Alignment explanation
Indices: 39297122--39297187 Score: 52
Period size: 13 Copynumber: 5.7 Consensus size: 12
39297112 GTATGCAATT
39297122 TTTTTTTTGCAA-
1 TTTTTTTT-CAAC
39297134 TTTTTTTT---C
1 TTTTTTTTCAAC
* *
39297143 TTTTTTTTCGGAT
1 TTTTTTTTC-AAC
39297156 TTTTTTTTCGAAC
1 TTTTTTTTC-AAC
39297169 TTTTTTTT-AAC
1 TTTTTTTTCAAC
39297180 TTTTTTTT
1 TTTTTTTT
39297188 TCGAAGCTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
9 8 0.17
11 11 0.24
12 8 0.17
13 19 0.41
ACGTcount: A:0.11, C:0.09, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCAAC
Found at i:39305256 original size:30 final size:30
Alignment explanation
Indices: 39305222--39305318 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
39305212 TAAACTAAAA
*
39305222 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
39305252 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
39305282 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
39305311 ATGAGCTA
1 -TGAGCTA
39305319 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:39310398 original size:30 final size:31
Alignment explanation
Indices: 39310303--39310400 Score: 94
Period size: 30 Copynumber: 3.2 Consensus size: 31
39310293 TAAACTAAAA
*
39310303 TGAGCTAAGCTTTTAGCTCGTGAGCT-AAAGT
1 TGAGCTAAG-GTTTAGCTCGTGAGCTGAAAGT
* * * * * *
39310334 TGAGCTGAGGCTAAACTCTTAAGCTG-AAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
*
39310364 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
39310394 TGAGCTA
1 TGAGCTA
39310401 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
30 40 0.78
31 11 0.22
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.30
Consensus pattern (31 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
Found at i:39315565 original size:22 final size:22
Alignment explanation
Indices: 39315537--39315580 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39315527 TTTTGAACCA
39315537 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
39315559 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
39315581 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:39315913 original size:10 final size:11
Alignment explanation
Indices: 39315897--39315928 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
39315887 AGAGTTCGAA
39315897 AAAAAAAATTG
1 AAAAAAAATTG
39315908 AAAAAAAATT-
1 AAAAAAAATTG
39315918 AAAAAAAATTG
1 AAAAAAAATTG
39315929 CATACGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:39318161 original size:17 final size:17
Alignment explanation
Indices: 39318116--39318169 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
39318106 AGAAAAGAGC
* *
39318116 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
39318133 GAAAAATGAAAAAAAAA
1 GAAAATTCAAAAAAAAA
*
39318150 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
39318167 GAA
1 GAA
39318170 TGAAAAGAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:39318874 original size:30 final size:30
Alignment explanation
Indices: 39318840--39318944 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 30
39318830 AGCTCACTCC
39318840 TAGCTCATATTTAGCTCACGAGCTAAACCT
1 TAGCTCATATTTAGCTCACGAGCTAAACCT
* * * * * *
39318870 TAGCTCA-ACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
* * *
39318900 CAGCTCAACTTTTTAGCTCACGAGCTAAAACT
1 TAGCTC-A-TATTTAGCTCACGAGCTAAACCT
39318932 TAGCTCAT-TTTAG
1 TAGCTCATATTTAG
39318945 TTTAAACTCG
Statistics
Matches: 55, Mismatches: 16, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
29 6 0.11
30 28 0.51
31 2 0.04
32 19 0.35
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (30 bp):
TAGCTCATATTTAGCTCACGAGCTAAACCT
Found at i:39324952 original size:15 final size:16
Alignment explanation
Indices: 39324913--39324953 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
39324903 AACAACACTC
39324913 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
39324929 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
39324943 CTTTCTTTTTC
1 CTTTCTTTTTC
39324954 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:39326087 original size:26 final size:27
Alignment explanation
Indices: 39326048--39326110 Score: 92
Period size: 26 Copynumber: 2.3 Consensus size: 27
39326038 CAATCACTCT
* *
39326048 TTTTTTTTTCAATTTCGATTTTTTTTC
1 TTTTTTTTTCAATTCCGAATTTTTTTC
39326075 TTTTTTTTT-AATTCCGAATTTTTTTC
1 TTTTTTTTTCAATTCCGAATTTTTTTC
39326101 TTCTTTTTTT
1 TT-TTTTTTT
39326111 TCTTCAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 17 0.52
27 16 0.48
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.75
Consensus pattern (27 bp):
TTTTTTTTTCAATTCCGAATTTTTTTC
Found at i:39326095 original size:27 final size:29
Alignment explanation
Indices: 39326048--39326111 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
39326038 CAATCACTCT
*
39326048 TTTTTTTTTCAATTTCGA-TTTTTT-TTC
1 TTTTTTTTTCAATTCCGATTTTTTTCTTC
39326075 TTTTTTTTT-AATTCCGAATTTTTTTCTTC
1 TTTTTTTTTCAATTCCG-ATTTTTTTCTTC
39326104 TTTTTTTT
1 TTTTTTTT
39326112 CTTCAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 6 0.18
27 10 0.30
28 6 0.18
29 11 0.33
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.75
Consensus pattern (29 bp):
TTTTTTTTTCAATTCCGATTTTTTTCTTC
Found at i:39326173 original size:11 final size:11
Alignment explanation
Indices: 39326157--39326210 Score: 90
Period size: 11 Copynumber: 4.7 Consensus size: 11
39326147 AATACAAACT
39326157 TTTTTTTTGAA
1 TTTTTTTTGAA
39326168 TTTTTTTTGAA
1 TTTTTTTTGAA
39326179 TTTTTTTTCGAA
1 TTTTTTTT-GAA
39326191 TTTTTTTTTGAA
1 -TTTTTTTTGAA
39326203 TTTTTTTT
1 TTTTTTTT
39326211 TACAATACCG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
11 27 0.66
12 6 0.15
13 8 0.20
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:39326173 original size:12 final size:12
Alignment explanation
Indices: 39326156--39326211 Score: 96
Period size: 12 Copynumber: 4.8 Consensus size: 12
39326146 GAATACAAAC
39326156 TTTTTTTTTGAA
1 TTTTTTTTTGAA
39326168 -TTTTTTTTGAA
1 TTTTTTTTTGAA
*
39326179 TTTTTTTTCGAA
1 TTTTTTTTTGAA
39326191 TTTTTTTTTGAA
1 TTTTTTTTTGAA
39326203 TTTTTTTTT
1 TTTTTTTTT
39326212 ACAATACCGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.27
12 30 0.73
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:39331255 original size:30 final size:30
Alignment explanation
Indices: 39331184--39331266 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
39331174 CTTTTGTTTC
* *
39331184 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
39331215 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
39331244 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
39331267 GATTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:39331257 original size:12 final size:12
Alignment explanation
Indices: 39331242--39331273 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39331232 TTTTTCAATC
39331242 TCATTTTCTTTT
1 TCATTTTCTTTT
39331254 TCATTTTCTTTT
1 TCATTTTCTTTT
*
39331266 TGATTTTC
1 TCATTTTC
39331274 AAAGGCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.16, G:0.03, T:0.72
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:39331361 original size:5 final size:5
Alignment explanation
Indices: 39331337--39331391 Score: 51
Period size: 5 Copynumber: 10.6 Consensus size: 5
39331327 TTTTCCTCTT
*
39331337 TTTTC TTTT- TATTTC GTTTTC TTTT- TCTTC TTTTGC TTTTTC TTTTC
1 TTTTC TTTTC T-TTTC -TTTTC TTTTC TTTTC TTTT-C -TTTTC TTTTC
39331384 TTTTC TTT
1 TTTTC TTT
39331392 GTTTTCTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
4 4 0.10
5 27 0.64
6 6 0.14
7 5 0.12
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:39331388 original size:31 final size:32
Alignment explanation
Indices: 39331325--39331391 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
39331315 TCTTACTTGC
*
39331325 CTTTTTCCTCTTTTTTCTTTTTATTTCGTTTT
1 CTTTTTCCTCTTTTTGCTTTTTATTTCGTTTT
* *
39331357 CTTTTTCTTC-TTTTGCTTTTTCTTTTC-TTTT
1 CTTTTTCCTCTTTTTGCTTTTT-ATTTCGTTTT
39331388 CTTT
1 CTTT
39331392 GTTTTCTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.76
Consensus pattern (32 bp):
CTTTTTCCTCTTTTTGCTTTTTATTTCGTTTT
Found at i:39331392 original size:21 final size:20
Alignment explanation
Indices: 39331353--39331402 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
39331343 TTTTATTTCG
39331353 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTCTTCTTTTG-T
*
39331374 TTTTC-TTTTCTTTTCTTTGT
1 TTTTCTTTTTCTTCT-TTTGT
39331394 TTTCTCTTT
1 TTT-TCTTT
39331403 ACAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 12 0.48
21 11 0.44
22 2 0.08
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTTCTTCTTTTGT
Found at i:39332408 original size:17 final size:16
Alignment explanation
Indices: 39332373--39332408 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
39332363 ATTACAACTT
*
39332373 GAATTTTTTTTAATTC
1 GAATTTTTTTTAATAC
39332389 GAATTTTTTTTAACTAC
1 GAATTTTTTTTAA-TAC
39332406 GAA
1 GAA
39332409 CCTATTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (16 bp):
GAATTTTTTTTAATAC
Found at i:39335002 original size:21 final size:22
Alignment explanation
Indices: 39334976--39335019 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
39334966 AAACGAGCTC
39334976 GTTGAGCTAAGTTAAG-TTGAA
1 GTTGAGCTAAGTTAAGCTTGAA
* *
39334997 GTTGAGCTGATTTAAGCTTGAA
1 GTTGAGCTAAGTTAAGCTTGAA
39335019 G
1 G
39335020 GAGTATGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.34
Consensus pattern (22 bp):
GTTGAGCTAAGTTAAGCTTGAA
Found at i:39338353 original size:23 final size:22
Alignment explanation
Indices: 39338302--39338353 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
39338292 CCTCGTCTTT
*
39338302 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
39338324 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
39338347 TTCTTTT
1 TTCTTTT
39338354 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:39340763 original size:4 final size:4
Alignment explanation
Indices: 39340754--39340781 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
39340744 TTAAACTAAG
39340754 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
39340782 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:39342481 original size:4 final size:4
Alignment explanation
Indices: 39342468--39342497 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
39342458 ATATTTGAAC
39342468 TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
39342498 TACACCAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:39345396 original size:29 final size:29
Alignment explanation
Indices: 39345330--39345419 Score: 110
Period size: 29 Copynumber: 3.1 Consensus size: 29
39345320 CACATACCTA
* * *
39345330 TATATGGCCCACTAGGCCC-AATCATATT
1 TATATGGCCCATTAGGCCCAAATAACATT
*
39345358 TATATGGCCCATTAGGCCCAAATAACGTT
1 TATATGGCCCATTAGGCCCAAATAACATT
* * *
39345387 TATATGGCCCATCAGGCCCAATTCACATT
1 TATATGGCCCATTAGGCCCAAATAACATT
39345416 TATA
1 TATA
39345420 GTCATGCTCA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 18 0.34
29 35 0.66
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (29 bp):
TATATGGCCCATTAGGCCCAAATAACATT
Found at i:39347449 original size:21 final size:21
Alignment explanation
Indices: 39347425--39347473 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
39347415 TGAGCTAGAT
* *
39347425 CGAGCTGAATTCTAGCTCAAA
1 CGAGCTGAAATCGAGCTCAAA
*
39347446 CGAGCT-AAATCGAGCTCAAG
1 CGAGCTGAAATCGAGCTCAAA
*
39347466 TGAGCTGA
1 CGAGCTGA
39347474 TGGGAGCTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (21 bp):
CGAGCTGAAATCGAGCTCAAA
Found at i:39354029 original size:20 final size:20
Alignment explanation
Indices: 39353982--39354029 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
39353972 AGTAAGCTCG
39353982 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
39354002 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
39354022 GTTGAGCT
1 GTTGAGCT
39354030 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:39355307 original size:22 final size:22
Alignment explanation
Indices: 39355277--39355320 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39355267 TTTGGTATTT
39355277 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
39355299 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
39355321 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:39361230 original size:12 final size:12
Alignment explanation
Indices: 39361213--39361251 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 12
39361203 AAACCGTATG
39361213 CAATTTTTTTTT
1 CAATTTTTTTTT
39361225 CAATTTTTTTTT
1 CAATTTTTTTTT
39361237 CGAACTCTTTTTTTT
1 C-AA-T-TTTTTTTT
39361252 TACGTACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 13 0.54
13 2 0.08
14 1 0.04
15 8 0.33
ACGTcount: A:0.15, C:0.13, G:0.03, T:0.69
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:39361581 original size:22 final size:22
Alignment explanation
Indices: 39361551--39361594 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39361541 TTTGGTATTT
39361551 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
39361573 GGGAGTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
39361595 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.39, T:0.23
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:39363633 original size:20 final size:19
Alignment explanation
Indices: 39363610--39363674 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
39363600 AAGCTCAAAC
39363610 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
39363630 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
39363650 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
39363670 GAGCT
1 GAGCT
39363675 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:39366440 original size:11 final size:12
Alignment explanation
Indices: 39366410--39366441 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39366400 TTTCACTCTT
39366410 CTCTTTTTCAAA
1 CTCTTTTTCAAA
39366422 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
39366434 TTCTTTTT
1 CTCTTTTT
39366442 TCGCTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:39366453 original size:27 final size:27
Alignment explanation
Indices: 39366423--39366484 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
39366413 TTTTTCAAAC
*
39366423 TCTTTTTCAAATTCTT-TTTTC-GCTTTT
1 TCTTTTTC-AATT-TTCTTTTCTGCATTT
*
39366450 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATTTTCTTTTCTGCATTT
39366477 TCTTTTTC
1 TCTTTTTC
39366485 TCTCACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 9 0.29
27 20 0.65
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (27 bp):
TCTTTTTCAATTTTCTTTTCTGCATTT
Found at i:39366463 original size:13 final size:12
Alignment explanation
Indices: 39366447--39366566 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
39366437 TTTTTTCGCT
39366447 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
39366460 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
39366474 TTTTCTTTTTC-
1 TTTTCTTTTTCA
** *
39366485 TCTCACTTTTTTGA
1 T-TTTC-TTTTTCA
39366499 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
39366509 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
39366522 TTTTCTTTTTCG
1 TTTTCTTTTTCA
*
39366534 TTTTCTTTTT-G
1 TTTTCTTTTTCA
39366545 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
39366555 ATTTCTTTTTCA
1 TTTTCTTTTTCA
39366567 ATCTCTTTCT
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 15 0.18
12 32 0.39
13 17 0.20
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:39366476 original size:14 final size:14
Alignment explanation
Indices: 39366425--39366483 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
39366415 TTTCAAACTC
*
39366425 TTTTTCAA-ATTCT
1 TTTTTCAATTTTCT
**
39366438 TTTTTCGCTTTT-T
1 TTTTTCAATTTTCT
39366451 CTTTTTCAATTTTCT
1 -TTTTTCAATTTTCT
39366466 TTTCTTC-ATTTTCT
1 TTT-TTCAATTTTCT
39366480 TTTT
1 TTTT
39366484 CTCTCACTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 8 0.22
14 25 0.68
15 4 0.11
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTCAATTTTCT
Found at i:39366565 original size:6 final size:6
Alignment explanation
Indices: 39366445--39366552 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
39366435 TCTTTTTTCG
* * * **
39366445 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
39366496 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
39366544 -GTTTT CTTT
1 CTTTTT CTTT
39366553 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 23, Indels: 10
0.69 0.21 0.09
Matches are distributed among these distances:
5 5 0.07
6 56 0.76
7 10 0.14
8 3 0.04
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:39367637 original size:21 final size:21
Alignment explanation
Indices: 39367613--39367671 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
39367603 TTGTCACTTC
*
39367613 TTTTTTCTCTTTTTTTTCGAT
1 TTTTTTCTCTTTTTTTTCGAA
*** *
39367634 TTTTTTGAATTTTTTTTTGAA
1 TTTTTTCTCTTTTTTTTCGAA
*
39367655 TTTCTTCTCTTTTTTTT
1 TTTTTTCTCTTTTTTTT
39367672 TAAAATCCAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.08, C:0.10, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTTTTCTCTTTTTTTTCGAA
Found at i:39367648 original size:12 final size:12
Alignment explanation
Indices: 39367633--39367657 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39367623 TTTTTTTCGA
39367633 TTTTTTTGAATT
1 TTTTTTTGAATT
39367645 TTTTTTTGAATT
1 TTTTTTTGAATT
39367657 T
1 T
39367658 CTTCTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:39367787 original size:20 final size:21
Alignment explanation
Indices: 39367736--39367786 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
39367726 CCAACTCAAA
39367736 TTTTTTTTTTATTTTTTTGAC
1 TTTTTTTTTTATTTTTTTGAC
39367757 TTTTTTTTTTATTTTTTTGAC
1 TTTTTTTTTTATTTTTTTGAC
39367778 TTTTTTTTT
1 TTTTTTTTT
39367787 ACATTACGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.08, C:0.04, G:0.04, T:0.84
Consensus pattern (21 bp):
TTTTTTTTTTATTTTTTTGAC
Found at i:39369077 original size:30 final size:30
Alignment explanation
Indices: 39369043--39369139 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
39369033 AGCTCACTCC
39369043 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * * *
39369073 TAGCTCAACTTCAACTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
39369103 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
39369133 TAGCTCA
1 TAGCTCA
39369140 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
29 1 0.02
30 48 0.98
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:39370879 original size:10 final size:11
Alignment explanation
Indices: 39370856--39370892 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
39370846 AAAGGAGAAG
39370856 AAATTCAGAAAA
1 AAATTCA-AAAA
39370868 AAATTCAAAAA
1 AAATTCAAAAA
*
39370879 AAATTGAAAAA
1 AAATTCAAAAA
39370890 AAA
1 AAA
39370893 GGAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 17 0.71
12 7 0.29
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.16
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:39370898 original size:21 final size:21
Alignment explanation
Indices: 39370841--39370914 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
39370831 TATTGGATTT
* *
39370841 AAAAAAAAGGAGAAGAAATTCAG
1 AAAAAAAAGGAAAAAAAATT--G
***
39370864 AAAAAAATTCAAAAAAAATTG
1 AAAAAAAAGGAAAAAAAATTG
*
39370885 AAAAAAAAGGAAAAAAAAGTG
1 AAAAAAAAGGAAAAAAAATTG
39370906 ACAAAAAAA
1 A-AAAAAAA
39370915 TCGAGTTAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
21 19 0.46
22 7 0.17
23 15 0.37
ACGTcount: A:0.73, C:0.04, G:0.14, T:0.09
Consensus pattern (21 bp):
AAAAAAAAGGAAAAAAAATTG
Found at i:39370911 original size:11 final size:11
Alignment explanation
Indices: 39370864--39370914 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
39370854 AGAAATTCAG
* *
39370864 AAAAAAATTCA
1 AAAAAAAGTGA
*
39370875 AAAAAAATTGA
1 AAAAAAAGTGA
39370886 AAAAAAAG-GA
1 AAAAAAAGTGA
39370896 AAAAAAAGTGA
1 AAAAAAAGTGA
39370907 CAAAAAAA
1 -AAAAAAA
39370915 TCGAGTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
10 10 0.28
11 19 0.53
12 7 0.19
ACGTcount: A:0.76, C:0.04, G:0.10, T:0.10
Consensus pattern (11 bp):
AAAAAAAGTGA
Found at i:39371878 original size:37 final size:37
Alignment explanation
Indices: 39371827--39371897 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
39371817 CATTCTTGTA
39371827 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
39371864 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
39371898 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:39371897 original size:6 final size:6
Alignment explanation
Indices: 39371837--39371886 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
39371827 AAGAGAAAAC
*
39371837 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
39371886 A
1 A
39371887 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:39371979 original size:11 final size:12
Alignment explanation
Indices: 39371947--39371977 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
39371937 TTGAGAGAAC
39371947 TTGAAAAAGCCT
1 TTGAAAAAGCCT
39371959 TTGAAAAAGCCT
1 TTGAAAAAGCCT
39371971 TTGAAAA
1 TTGAAAA
39371978 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:39374192 original size:30 final size:30
Alignment explanation
Indices: 39374158--39374254 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
39374148 AGCTCACTCC
39374158 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
39374188 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
39374218 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
39374248 TAGCTCA
1 TAGCTCA
39374255 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:39377211 original size:10 final size:10
Alignment explanation
Indices: 39377196--39377257 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
39377186 TTTGAACCAT
*
39377196 TACCAATTCG
1 TACCAATTCA
*
39377206 TACCAAATACCA
1 TACC-AAT-TCA
*
39377218 TACCATTTCA
1 TACCAATTCA
39377228 TACCAATTCCA
1 TACCAATT-CA
* *
39377239 TACCATTTCG
1 TACCAATTCA
39377249 TACCAATTC
1 TACCAATTC
39377258 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:39377241 original size:21 final size:21
Alignment explanation
Indices: 39377196--39377258 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
39377186 TTTGAACCAT
* *
39377196 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
39377218 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
39377239 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
39377259 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:39390796 original size:15 final size:15
Alignment explanation
Indices: 39390776--39390823 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
39390766 TCAAAGATGG
39390776 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
39390791 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
39390806 -TTTATGGATATAAA
1 GTTTATGGATATGAA
39390820 GTTT
1 GTTT
39390824 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:39390803 original size:29 final size:29
Alignment explanation
Indices: 39390770--39390829 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
39390760 AAGGATTCAA
* *
39390770 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
39390799 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
39390828 AG
1 AG
39390830 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:39390877 original size:6 final size:6
Alignment explanation
Indices: 39390863--39390897 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
39390853 GATGGAATGG
*
39390863 AATGGA AATGAA AATGAA AATGAA AATGAA AATGA
1 AATGAA AATGAA AATGAA AATGAA AATGAA AATGA
39390898 TCTAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (6 bp):
AATGAA
Found at i:39391965 original size:19 final size:19
Alignment explanation
Indices: 39391941--39391980 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39391931 AGCTCCCATG
39391941 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
39391960 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
39391979 TA
1 TA
39391981 TCAACTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:39395858 original size:30 final size:28
Alignment explanation
Indices: 39395805--39395860 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
39395795 TTCTTCCACG
* *
39395805 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
39395833 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
39395861 TTTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:39397700 original size:16 final size:16
Alignment explanation
Indices: 39397679--39397715 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
39397669 AAAGATTGTT
39397679 AAAACAACTTCTAAAG
1 AAAACAACTTCTAAAG
39397695 AAAACAACTTCTAAAG
1 AAAACAACTTCTAAAG
39397711 AAAAC
1 AAAAC
39397716 TCAAGAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.59, C:0.19, G:0.05, T:0.16
Consensus pattern (16 bp):
AAAACAACTTCTAAAG
Found at i:39399833 original size:12 final size:11
Alignment explanation
Indices: 39399816--39399844 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
39399806 ATTCGGAATT
39399816 AAAAAAAAAAG
1 AAAAAAAAAAG
39399827 AAAAAAAAAAG
1 AAAAAAAAAAG
39399838 AAAAAAA
1 AAAAAAA
39399845 GAGAAGTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:39401903 original size:15 final size:14
Alignment explanation
Indices: 39401867--39401908 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
39401857 TCTATTGATC
39401867 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
39401881 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
39401895 GAGTGAAAAGAAAA
1 GAG-AAAAAGAAAA
39401909 TGAAAGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:39406256 original size:30 final size:30
Alignment explanation
Indices: 39406222--39406318 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
39406212 TAAACTAAAA
*
39406222 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
39406252 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
39406282 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
39406311 ATGAGCTA
1 -TGAGCTA
39406319 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:39408708 original size:15 final size:15
Alignment explanation
Indices: 39408688--39408735 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
39408678 TCAAAGATGG
39408688 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
39408703 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
39408718 -TTTATGGATATAAA
1 GTTTATGGATATGAA
39408732 GTTT
1 GTTT
39408736 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:39408715 original size:29 final size:29
Alignment explanation
Indices: 39408682--39408741 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
39408672 AAGGATTCAA
* *
39408682 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
39408711 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
39408740 AG
1 AG
39408742 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:39411910 original size:27 final size:27
Alignment explanation
Indices: 39411848--39411910 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
39411838 GCCGAATTTC
*
39411848 ATGTGTCTTAGTTCCAGCATGATTTTA
1 ATGTGTCTTAGTTCCAGCATGATTTAA
* * **
39411875 ATTTCTCTTAGTTATTA-CATGATTTAA
1 ATGTGTCTTAGTT-CCAGCATGATTTAA
39411902 ATGTGTCTT
1 ATGTGTCTT
39411911 TGAGCCGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.49
Consensus pattern (27 bp):
ATGTGTCTTAGTTCCAGCATGATTTAA
Found at i:39413011 original size:30 final size:30
Alignment explanation
Indices: 39412977--39413073 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
39412967 AGCTCACTCC
*
39412977 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * *
39413007 TAGCTCAACTTTAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
39413037 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
39413067 TAGCTCA
1 TAGCTCA
39413074 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 47 0.90
31 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:39415971 original size:63 final size:65
Alignment explanation
Indices: 39415904--39416038 Score: 154
Period size: 67 Copynumber: 2.1 Consensus size: 65
39415894 CTAACTTAAA
*
39415904 TAAATGAAC-TAACACTTATGCATCA-T-TTAATCC-AGAAACTAGTTTAATTAATAGAAGCAT-
1 TAAATGAACTTAA-ACTCATGCATCACTATT-ATCCTAGAAACTAGTTTAATTAA-AGAAGCATC
39415964 TAT
63 TAT
* * *
39415967 TAAATGAACTTTAACTCATGCATCACTAAATTATCCTAGTAACTAGTTTATTTAAAGAAGCATCT
1 TAAATGAACTTAAACTCATGCATCACT--ATTATCCTAGAAACTAGTTTAATTAAAGAAGCATCT
39416032 AT
64 AT
39416034 TAAAT
1 TAAAT
39416039 CAAGTTCATA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
63 20 0.33
64 3 0.05
66 12 0.20
67 26 0.43
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (65 bp):
TAAATGAACTTAAACTCATGCATCACTATTATCCTAGAAACTAGTTTAATTAAAGAAGCATCTAT
Found at i:39427134 original size:15 final size:15
Alignment explanation
Indices: 39427114--39427168 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
39427104 ACTCTCCTCA
*
39427114 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
39427129 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
39427144 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
39427158 TTCTTTT-TCTC
1 TTCTTTTCTCTC
39427169 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:39432946 original size:18 final size:18
Alignment explanation
Indices: 39432923--39433011 Score: 56
Period size: 18 Copynumber: 4.8 Consensus size: 18
39432913 AACAAGTGAG
39432923 GAAAAAGAAAAAGAGAAT
1 GAAAAAGAAAAAGAGAAT
*
39432941 GAAAAAGAGCAAAAAGAGATT
1 G-AAAA-AG-AAAAAGAGAAT
* *
39432962 GAGAATGAAAAAGA-AATT
1 GAAAAAGAAAAAGAGAA-T
* *
39432980 GAAGAAAG-AAGAGAAAAT
1 GAA-AAAGAAAAAGAGAAT
**
39432998 GAATTAGAAAAAGA
1 GAAAAAGAAAAAGA
39433012 AACAAAAGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
17 3 0.06
18 25 0.46
19 10 0.19
20 5 0.09
21 11 0.20
ACGTcount: A:0.65, C:0.01, G:0.24, T:0.10
Consensus pattern (18 bp):
GAAAAAGAAAAAGAGAAT
Found at i:39432996 original size:23 final size:22
Alignment explanation
Indices: 39432970--39433022 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
39432960 TTGAGAATGA
*
39432970 AAAAGAAATT-GAAGAAAGAAGAG
1 AAAAGAAATTAGAA-AAAGAA-AC
39432993 AAAATG-AATTAGAAAAAGAAAC
1 AAAA-GAAATTAGAAAAAGAAAC
39433015 AAAAGAAA
1 AAAAGAAA
39433023 AAGACGTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 14 0.54
24 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAGAAATTAGAAAAAGAAAC
Found at i:39435236 original size:20 final size:20
Alignment explanation
Indices: 39435190--39435236 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
39435180 AGCTTGTTTC
*
39435190 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
39435210 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
39435230 CAGCTCA
1 CAGCTCA
39435237 ATCTTAACCT
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:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Done.