Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 119 of 213
Found at i:34084894 original size:23 final size:23
Alignment explanation
Indices: 34084847--34084894 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
34084837 GTATGGTTTT
**
34084847 AGGTTAGAAAATAGGGTTTTAAA
1 AGGTTAGAAAATAGGGTTAAAAA
34084870 AGGTTA-AAAATAGGGTTAAACAA
1 AGGTTAGAAAATAGGGTTAAA-AA
34084893 AG
1 AG
34084895 ATTATTCCGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.48, C:0.02, G:0.25, T:0.25
Consensus pattern (23 bp):
AGGTTAGAAAATAGGGTTAAAAA
Found at i:34103199 original size:22 final size:22
Alignment explanation
Indices: 34103173--34103217 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
34103163 ATTATATGTA
34103173 TTAATTCATAACATAA-TTAATT
1 TTAATTCATAAC-TAATTTAATT
* *
34103195 TTAATTTATATCTAATTTAATT
1 TTAATTCATAACTAATTTAATT
34103217 T
1 T
34103218 GGGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTCATAACTAATTTAATT
Found at i:34106747 original size:27 final size:27
Alignment explanation
Indices: 34106717--34106894 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
34106707 ATATTGAGTC
* * * *
34106717 CGCACACTCATTGCTATATAATCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
*
34106744 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
34106771 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAA-T
** ** *
34106799 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
34106826 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
34106853 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
34106880 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
34106895 GTACAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:34106856 original size:82 final size:81
Alignment explanation
Indices: 34106738--34106893 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
34106728 TGCTATATAA
* *
34106738 TCAATTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
34106803 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* **
34106820 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAATTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
34106884 CACTTAGTGC
65 CACTTAGTGC
34106894 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:34111836 original size:40 final size:40
Alignment explanation
Indices: 34111777--34112044 Score: 473
Period size: 40 Copynumber: 6.7 Consensus size: 40
34111767 GAGCATTGGA
*
34111777 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
34111817 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
34111857 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
34111897 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
34111937 ATATATCCGGGCTAAAACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
34111977 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
34112017 ATATGTTCGGGCTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
34112045 ATGTGTTTGC
Statistics
Matches: 219, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 219 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:34126220 original size:24 final size:24
Alignment explanation
Indices: 34126193--34126266 Score: 112
Period size: 24 Copynumber: 3.0 Consensus size: 24
34126183 AAGGCTGTCA
34126193 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* * *
34126217 GGAGAGGATTTAGGAGTTGATAAA
1 GGAGAAGATTTAGGAGCTGATAAG
34126241 GGAGAAGATTTAGGAGCTGATCAAG
1 GGAGAAGATTTAGGAGCTGAT-AAG
34126266 G
1 G
34126267 AGCAGGACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 40 0.93
25 3 0.07
ACGTcount: A:0.36, C:0.04, G:0.38, T:0.22
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:34127930 original size:46 final size:46
Alignment explanation
Indices: 34127863--34128040 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
34127853 TGTAACCCGC
* *
34127863 CCATAAGTGAACTCGGACTCAACTCAACGAGCCCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
* * *
34127909 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG-TTCGCAT
* *** * **
34127955 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
* *
34128002 CTATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG
34128041 CCCAAATATC
Statistics
Matches: 107, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
46 73 0.68
47 34 0.32
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
Found at i:34127983 original size:93 final size:93
Alignment explanation
Indices: 34127871--34128042 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
34127861 GCCCATAAGT
***
34127871 GAACTCGGACTCAACTCAACGAGCCCGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCCCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
34127936 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
** *
34127964 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCTATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCCCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
34128029 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
34128043 CAAATATCCT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCCCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:34130687 original size:27 final size:26
Alignment explanation
Indices: 34130656--34130833 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
34130646 TAAATTGTAC
34130656 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
34130683 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
34130709 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
34130737 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
34130765 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
34130792 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
34130819 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
34130834 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 103 0.80
28 25 0.19
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:34130772 original size:82 final size:81
Alignment explanation
Indices: 34130657--34130812 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
34130647 AAATTGTACA
* *
34130657 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
34130721 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
34130738 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
34130803 TGCGAGTTGA
65 TGCGAATTGA
34130813 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:34130824 original size:82 final size:81
Alignment explanation
Indices: 34130653--34130833 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
34130643 GATTAAATTG
* *
34130653 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
34130718 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
34130734 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
34130798 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
34130816 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
34130834 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:34130844 original size:27 final size:27
Alignment explanation
Indices: 34130738--34130844 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
34130728 TGACCATGCG
* * * *
34130738 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
34130766 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
34130793 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
34130820 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
34130845 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:34135729 original size:40 final size:40
Alignment explanation
Indices: 34135631--34135932 Score: 387
Period size: 40 Copynumber: 7.6 Consensus size: 40
34135621 TCCTCGTTCA
* * * * *
34135631 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
34135670 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
34135710 AATGCCTTCGGGACTTAACCCGGATTTAACAA-TCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
34135749 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
34135789 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
34135829 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
34135869 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
34135909 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
34135933 CAGCATTCAA
Statistics
Matches: 238, Mismatches: 20, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
39 75 0.32
40 155 0.65
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:34135865 original size:80 final size:79
Alignment explanation
Indices: 34135631--34135932 Score: 383
Period size: 79 Copynumber: 3.8 Consensus size: 79
34135621 TCCTCGTTCA
* * * * * *
34135631 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
*
34135696 TAACAACTCGCACG
66 TAATAACTCGCACG
*
34135710 AATGCCTTCGGGACTTAACCCGGATTTAACAA-TCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCGGAT
34135774 TTAATAACTCGCACG
65 TTAATAACTCGCACG
34135789 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCGGAT
* * *
34135854 TTAGTATCTCGCACA
65 TTAATAACTCGCACG
* * * * * * * *
34135869 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACAATGCCTTCGGGACTTAACCCGGA
34135933 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
78 5 0.03
79 99 0.50
80 90 0.45
81 5 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
TAATAACTCGCACG
Found at i:34143718 original size:40 final size:40
Alignment explanation
Indices: 34143615--34143916 Score: 369
Period size: 40 Copynumber: 7.6 Consensus size: 40
34143605 TCCTCGTTCA
* * * * *
34143615 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
34143654 AATGCCTTC-GGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
34143693 AATGCCTTCGGGACTTAACCCGGATTTAACAAATCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
34143733 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
34143773 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
34143813 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * * *
34143853 AAGGCCTTC-GGATATTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
34143893 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
34143917 CAGCATTCAA
Statistics
Matches: 234, Mismatches: 24, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
38 24 0.10
39 21 0.09
40 181 0.77
41 8 0.03
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:34148849 original size:27 final size:27
Alignment explanation
Indices: 34148819--34148994 Score: 201
Period size: 27 Copynumber: 6.5 Consensus size: 27
34148809 ATTGAGTCCA
* * * *
34148819 CACACTCAGTGCTATATAATCAACTCG
1 CACACTTAGTGCTACATAGTCAAATCG
* *
34148846 CACACTTAGTGCTACGTAATCAAATCG
1 CACACTTAGTGCTACATAGTCAAATCG
34148873 CACACTTAGTGCTACATAGTCAAACTCG
1 CACACTTAGTGCTACATAGTCAAA-TCG
** * *
34148901 CACACTTAGTGCCGCATGGTCAATTCG
1 CACACTTAGTGCTACATAGTCAAATCG
* **
34148928 CACACTTAGTGC-ATCATATTCATTTCG
1 CACACTTAGTGCTA-CATAGTCAAATCG
*
34148955 CACACTTAGTGCAACATAGTCAAATCG
1 CACACTTAGTGCTACATAGTCAAATCG
34148982 CACACTTAGTGCT
1 CACACTTAGTGCT
34148995 GTACAATTTA
Statistics
Matches: 128, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CACACTTAGTGCTACATAGTCAAATCG
Found at i:34148956 original size:82 final size:81
Alignment explanation
Indices: 34148838--34148993 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
34148828 TGCTATATAA
* *
34148838 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
34148903 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
34148920 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
34148984 CACTTAGTGC
65 CACTTAGTGC
34148994 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:34151454 original size:13 final size:13
Alignment explanation
Indices: 34151436--34151465 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34151426 AAGAAAAAGG
34151436 CATTCATCTTCTA
1 CATTCATCTTCTA
*
34151449 CATTCATCTTCTT
1 CATTCATCTTCTA
34151462 CATT
1 CATT
34151466 TATGAAGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (13 bp):
CATTCATCTTCTA
Found at i:34152932 original size:27 final size:27
Alignment explanation
Indices: 34152894--34152953 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
34152884 TCAGTTGTTG
34152894 TTTTGGTTATAATGACATGTATAGGTA
1 TTTTGGTTATAATGACATGTATAGGTA
* *
34152921 TTTTGGTTATAATGGCATTTATAGGTA
1 TTTTGGTTATAATGACATGTATAGGTA
34152948 TTTTGG
1 TTTTGG
34152954 CTAATGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.23, T:0.48
Consensus pattern (27 bp):
TTTTGGTTATAATGACATGTATAGGTA
Found at i:34155368 original size:31 final size:31
Alignment explanation
Indices: 34155330--34155392 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
34155320 TAGTACAGTA
34155330 TACAAGGTATGAAAATG-AAAATACGAATGAT
1 TACAAGGTATGAAAATGCAAAA-ACGAATGAT
* *
34155361 TACAAGGTATGAATATGCAAAAATGAATGAT
1 TACAAGGTATGAAAATGCAAAAACGAATGAT
34155392 T
1 T
34155393 GATACCCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.25
Consensus pattern (31 bp):
TACAAGGTATGAAAATGCAAAAACGAATGAT
Found at i:34165401 original size:16 final size:17
Alignment explanation
Indices: 34165370--34165404 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
34165360 TATTTCAATC
*
34165370 CAAAATTCATACTTTTG
1 CAAAATTCAGACTTTTG
34165387 CAAAATT-AGACTTTTG
1 CAAAATTCAGACTTTTG
34165403 CA
1 CA
34165405 CTTAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (17 bp):
CAAAATTCAGACTTTTG
Found at i:34171741 original size:59 final size:58
Alignment explanation
Indices: 34171638--34171780 Score: 164
Period size: 59 Copynumber: 2.4 Consensus size: 58
34171628 GTGTGCTAAA
* *
34171638 CGATGGTCATAACCATCCCTTTTCATGTTTGATATTCGAAACCATCCCTTTTCATTAAT
1 CGATGGTCGTAACCATCCCTTTTCATGTTTGATAGTCGAAACCATCCCTTTTCA-TAAT
* * * **
34171697 CGATGGTCGTCACCATCCCTTTTCATAG-TTGGTGGTCGTCACCATCCCTTTTCATAAT
1 CGATGGTCGTAACCATCCCTTTTCAT-GTTTGATAGTCGAAACCATCCCTTTTCATAAT
* *
34171755 CGATAGTCG-AAGCTATCCCTTTTCAT
1 CGATGGTCGTAA-CCATCCCTTTTCAT
34171781 TGTTCGATGA
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
57 1 0.01
58 25 0.35
59 45 0.62
60 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (58 bp):
CGATGGTCGTAACCATCCCTTTTCATGTTTGATAGTCGAAACCATCCCTTTTCATAAT
Found at i:34171742 original size:29 final size:29
Alignment explanation
Indices: 34171678--34171780 Score: 127
Period size: 29 Copynumber: 3.5 Consensus size: 29
34171668 GATATTCGAA
34171678 ACCATCCCTTTTCATTAATCGATGGTCGTC
1 ACCATCCCTTTTCA-TAATCGATGGTCGTC
* * *
34171708 ACCATCCCTTTTCATAGTTGGTGGTCGTC
1 ACCATCCCTTTTCATAATCGATGGTCGTC
* *
34171737 ACCATCCCTTTTCATAATCGATAGTCG-A
1 ACCATCCCTTTTCATAATCGATGGTCGTC
*
34171765 AGCTATCCCTTTTCAT
1 A-CCATCCCTTTTCAT
34171781 TGTTCGATGA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
28 1 0.02
29 48 0.76
30 14 0.22
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.37
Consensus pattern (29 bp):
ACCATCCCTTTTCATAATCGATGGTCGTC
Found at i:34180392 original size:5 final size:5
Alignment explanation
Indices: 34180382--34180475 Score: 188
Period size: 5 Copynumber: 18.8 Consensus size: 5
34180372 AGAACCATGC
34180382 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
34180432 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT
34180476 ATGTAACATC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 89 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:34181089 original size:9 final size:9
Alignment explanation
Indices: 34181077--34181103 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
34181067 ACGTCACTAA
34181077 CGTTTACAG
1 CGTTTACAG
34181086 CGTTTACAG
1 CGTTTACAG
34181095 CGTTTACAG
1 CGTTTACAG
34181104 AAATAAACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (9 bp):
CGTTTACAG
Found at i:34181647 original size:21 final size:21
Alignment explanation
Indices: 34181621--34181692 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
34181611 TTCTTTTAAA
* *
34181621 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCCG
*
34181642 CCTCTGCTTCCCTTGCTGCCG
1 CCTCTGCTTCCCTCGCTGCCG
34181663 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCCG
34181684 CCTCTGCTT
1 CCTCTGCTT
34181693 TTAGTTGTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.01, C:0.47, G:0.18, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCCG
Found at i:34186982 original size:9 final size:9
Alignment explanation
Indices: 34186968--34187427 Score: 338
Period size: 9 Copynumber: 52.2 Consensus size: 9
34186958 TTTTTATGTA
34186968 TTATGTAAG
1 TTATGTAAG
34186977 TTATGTACTAAG
1 TTATG---TAAG
34186989 TTATGT-A-
1 TTATGTAAG
34186996 TTATGTAAG
1 TTATGTAAG
34187005 TTATGTAAG
1 TTATGTAAG
*
34187014 TTGTGT-A-
1 TTATGTAAG
*
34187021 TTATGTGAG
1 TTATGTAAG
*
34187030 TTATGTAGG
1 TTATGTAAG
*
34187039 TTGTGT-A-
1 TTATGTAAG
34187046 TTATGTAAG
1 TTATGTAAG
34187055 TTATGT-A-
1 TTATGTAAG
34187062 TTATGT-A-
1 TTATGTAAG
34187069 TTATGTAAG
1 TTATGTAAG
34187078 -TACTGTAAG
1 TTA-TGTAAG
*
34187087 TAATGTAAG
1 TTATGTAAG
34187096 TTATGTAAG
1 TTATGTAAG
*
34187105 CTATGTAAG
1 TTATGTAAG
*
34187114 TTATGTAGG
1 TTATGTAAG
*
34187123 CTATGT-A-
1 TTATGTAAG
*
34187130 TTATGTAAA
1 TTATGTAAG
*
34187139 TAATGTAAG
1 TTATGTAAG
*
34187148 TTA-GGAAGG
1 TTATGTAA-G
34187157 TTATGT-A-
1 TTATGTAAG
34187164 TTATGTAAG
1 TTATGTAAG
*
34187173 TTATTTAAG
1 TTATGTAAG
34187182 TTATGTAAG
1 TTATGTAAG
34187191 TTATGTAAG
1 TTATGTAAG
* *
34187200 TTATATAAT
1 TTATGTAAG
34187209 TTATGTAAG
1 TTATGTAAG
34187218 TTATGTAAG
1 TTATGTAAG
34187227 TTATGTAAG
1 TTATGTAAG
* *
34187236 TTATTTAGAAAAAA
1 TTA--T-G--TAAG
34187250 TTATGTAAG
1 TTATGTAAG
34187259 TTATGTACTAAG
1 TTATG---TAAG
34187271 TTATGT-A-
1 TTATGTAAG
*
34187278 TTATGTAAA
1 TTATGTAAG
*
34187287 TAATGTAAG
1 TTATGTAAG
*
34187296 TTA-GGAAGG
1 TTATGTAA-G
34187305 TTATGT-A-
1 TTATGTAAG
34187312 TTATGTAAG
1 TTATGTAAG
* *
34187321 TTATTTAAT
1 TTATGTAAG
* *
34187330 TTATGTTAT
1 TTATGTAAG
34187339 TTATGTAAG
1 TTATGTAAG
34187348 TTATGTAAG
1 TTATGTAAG
* *
34187357 TTATTTAAT
1 TTATGTAAG
34187366 TTATGTAAG
1 TTATGTAAG
*
34187375 TTGTGTAAG
1 TTATGTAAG
* *
34187384 CTATGTAGG
1 TTATGTAAG
*
34187393 CTATGT-A-
1 TTATGTAAG
*
34187400 TTATGTTA-
1 TTATGTAAG
*
34187408 TTATATAAG
1 TTATGTAAG
*
34187417 TTATGCAAG
1 TTATGTAAG
34187426 TT
1 TT
34187428 TATATATAAG
Statistics
Matches: 361, Mismatches: 55, Indels: 70
0.74 0.11 0.14
Matches are distributed among these distances:
7 57 0.16
8 27 0.07
9 247 0.68
10 3 0.01
11 2 0.01
12 20 0.06
14 5 0.01
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:34187050 original size:41 final size:40
Alignment explanation
Indices: 34186961--34187239 Score: 190
Period size: 41 Copynumber: 6.9 Consensus size: 40
34186951 TGATATATTT
*
34186961 TTATGTATTATGTAAGTTATGTACTA---AGTTATGTA--
1 TTATGTATTATGTAAGTTATGTATTATGTAGTTATGTAGG
*
34186996 TTATGTAAGTTATGTAAGTTGTGTATTATGTGAGTTATGTAGG
1 TTATGT-A-TTATGTAAGTTATGTATTATGT-AGTTATGTAGG
* *
34187039 TTGTGTATTATGTAAGTTATGTATTATGTA-TTATGTAAG
1 TTATGTATTATGTAAGTTATGTATTATGTAGTTATGTAGG
* *
34187078 -TACTGTAAGTAATGTAAGTTATGTAAGCTATGTAAGTTATGTAGG
1 TTA-TGT-A-TTATGTAAGTTATGT-A-TTATGT-AGTTATGTAGG
* * *
34187123 CTATGTATTATGTAA---A--TA--ATGTAAGTTAGGAAGG
1 TTATGTATTATGTAAGTTATGTATTATGT-AGTTATGTAGG
* *
34187157 TTATGTATTATGTAAGTTATTTAAGTTATGTAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGT-A-TTATGT-AGTTATGTAGG
*
34187200 TTATATAATTTATGTAAGTTATGTAAGTTATGTAAGTTAT
1 TTATGT-A-TTATGTAAGTTATGT-A-TTATGT-AGTTAT
34187240 TTAGAAAAAA
Statistics
Matches: 199, Mismatches: 18, Indels: 44
0.76 0.07 0.17
Matches are distributed among these distances:
34 28 0.14
35 6 0.03
36 1 0.01
37 19 0.10
38 2 0.01
39 12 0.06
40 4 0.02
41 44 0.22
42 2 0.01
43 35 0.18
44 3 0.02
45 41 0.21
46 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.46
Consensus pattern (40 bp):
TTATGTATTATGTAAGTTATGTATTATGTAGTTATGTAGG
Found at i:34187476 original size:157 final size:156
Alignment explanation
Indices: 34187132--34187479 Score: 387
Period size: 157 Copynumber: 2.3 Consensus size: 156
34187122 GCTATGTATT
34187132 ATGTAAATAATGTAAGTTAGGAAGGTTATGTATTATGTAAGTTATTT-A---A-G----TTATGT
1 ATGTAAATAATGTAAGTTAGGAAGGTTATGTATTATGTAAGTTATTTAATTTATGTTATTTATGT
* * *
34187188 AAGTTATGTAAGTTATATAATTTATGTAAGTTATGTAAGTTATGTAAGTTATTTAGAAAAAATTA
66 AAGTTATGTAAGTTATATAATTTATGTAAGTTATGTAAGCTATGTAAGCTATGTAGAAAAAATTA
* * *
34187253 TGTAAGTTATGTACTAAGTTATGTATT
131 TATAAGTTATG-ACTAAGTTATATATA
34187280 ATGTAAATAATGTAAGTTAGGAAGGTTATGTATTATGTAAGTTATTTAATTTATGTTATTTATGT
1 ATGTAAATAATGTAAGTTAGGAAGGTTATGTATTATGTAAGTTATTTAATTTATGTTATTTATGT
* * * * ****
34187345 AAGTTATGTAAGTTATTTAATTTATGTAAGTTGTGTAAGCTATGTAGGCTATGTATTATGTTATT
66 AAGTTATGTAAGTTATATAATTTATGTAAGTTATGTAAGCTATGTAAGCTATGTA-GAAAAAATT
34187410 ATATAAGTTATG-C-AAGTTTATATATA
130 ATATAAGTTATGACTAAG-TTATATATA
* * * * **
34187436 AGTTTATATATTGTATGTTATTTAA-GTTATGTATTATGTAAGTT
1 A-TGTAAATAATGTAAGTTA-GGAAGGTTATGTATTATGTAAGTT
34187480 TATATATAAG
Statistics
Matches: 167, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
148 47 0.28
149 1 0.01
152 1 0.01
153 1 0.01
155 3 0.02
156 9 0.05
157 88 0.53
158 17 0.10
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (156 bp):
ATGTAAATAATGTAAGTTAGGAAGGTTATGTATTATGTAAGTTATTTAATTTATGTTATTTATGT
AAGTTATGTAAGTTATATAATTTATGTAAGTTATGTAAGCTATGTAAGCTATGTAGAAAAAATTA
TATAAGTTATGACTAAGTTATATATA
Found at i:34187500 original size:14 final size:14
Alignment explanation
Indices: 34187429--34187501 Score: 50
Period size: 12 Copynumber: 5.5 Consensus size: 14
34187419 ATGCAAGTTT
34187429 ATATATAAGTT-T-
1 ATATATAAGTTATG
*
34187441 ATATAT-TG-TATG
1 ATATATAAGTTATG
* *
34187453 TTATTTAAGTTATG
1 ATATATAAGTTATG
*
34187467 TATTATGTAAGTT-T-
1 -A-TATATAAGTTATG
34187481 ATATATAAGTTATG
1 ATATATAAGTTATG
34187495 ATATATA
1 ATATATA
34187502 TTATTGATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
10 1 0.02
11 2 0.04
12 19 0.41
13 3 0.07
14 11 0.24
15 1 0.02
16 9 0.20
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (14 bp):
ATATATAAGTTATG
Found at i:34187585 original size:15 final size:15
Alignment explanation
Indices: 34187554--34187596 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
34187544 AAATTTTGAA
* *
34187554 AAAAATATAGATTTT
1 AAAAATATATATATT
*
34187569 AAATATATATATATT
1 AAAAATATATATATT
*
34187584 AAAAATGTATATA
1 AAAAATATATATA
34187597 AATATGTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (15 bp):
AAAAATATATATATT
Found at i:34187625 original size:23 final size:23
Alignment explanation
Indices: 34187599--34187689 Score: 94
Period size: 23 Copynumber: 3.8 Consensus size: 23
34187589 TGTATATAAA
*
34187599 TATGTAAGTTATTATAAGTGAGT
1 TATGAAAGTTATTATAAGTGAGT
*
34187622 TATGAAAGTTATTAAATAAATGTA-T
1 TATGAAAGTTATT--ATAAGTG-AGT
* *
34187647 TGTGTAAGTTATTATAAGTGAGT
1 TATGAAAGTTATTATAAGTGAGT
*
34187670 TATGAAAGTCATATATAAGT
1 TATGAAAGTTAT-TATAAGT
34187690 TTATATATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
22 1 0.02
23 28 0.51
24 7 0.13
25 18 0.33
26 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.41
Consensus pattern (23 bp):
TATGAAAGTTATTATAAGTGAGT
Found at i:34187697 original size:12 final size:12
Alignment explanation
Indices: 34187680--34187707 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
34187670 TATGAAAGTC
34187680 ATATATAAGTTT
1 ATATATAAGTTT
34187692 ATATATAAGTTT
1 ATATATAAGTTT
34187704 ATAT
1 ATAT
34187708 TAAATTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
ATATATAAGTTT
Found at i:34187747 original size:23 final size:22
Alignment explanation
Indices: 34187706--34187793 Score: 110
Period size: 23 Copynumber: 4.0 Consensus size: 22
34187696 ATAAGTTTAT
34187706 ATTAAATTTTCAAAATATATATAA
1 ATTAAATTTT-AAAATATATAT-A
*
34187730 ATTAAATTTTAAAATATATACA
1 ATTAAATTTTAAAATATATATA
34187752 TATTAAATTTTAAAGATATATAT-
1 -ATTAAATTTTAAA-ATATATATA
34187775 A-T-AATTTTAAAATATATAT
1 ATTAAATTTTAAAATATATAT
34187794 TAATAAGTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 9
0.85 0.03 0.13
Matches are distributed among these distances:
19 8 0.13
20 9 0.15
21 1 0.02
22 2 0.03
23 23 0.38
24 17 0.28
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (22 bp):
ATTAAATTTTAAAATATATATA
Found at i:34187758 original size:47 final size:43
Alignment explanation
Indices: 34187704--34187792 Score: 126
Period size: 47 Copynumber: 2.0 Consensus size: 43
34187694 ATATAAGTTT
34187704 ATATTAAATTTTCAAA-ATATATATAAATTAAATTTTAAAATATATAC
1 ATATTAAATTTT-AAAGATATATAT--A-T-AATTTTAAAATATATAC
34187751 ATATTAAATTTTAAAGATATATATATAATTTTAAAATATATA
1 ATATTAAATTTTAAAGATATATATATAATTTTAAAATATATA
34187793 TTAATAAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
43 16 0.39
44 1 0.02
45 1 0.02
46 3 0.07
47 20 0.49
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (43 bp):
ATATTAAATTTTAAAGATATATATATAATTTTAAAATATATAC
Found at i:34190342 original size:14 final size:14
Alignment explanation
Indices: 34190318--34190359 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
34190308 ATTTATTAGA
34190318 CCTTAAACCCTAAAC
1 CCTT-AACCCTAAAC
*
34190333 TCTTAACCCTAAAC
1 CCTTAACCCTAAAC
34190347 CCTTAACCCTAAA
1 CCTTAACCCTAAA
34190360 TTGACTTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 22 0.88
15 3 0.12
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (14 bp):
CCTTAACCCTAAAC
Found at i:34190347 original size:7 final size:7
Alignment explanation
Indices: 34190321--34190359 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
34190311 TATTAGACCT
34190321 TAAACCC
1 TAAACCC
*
34190328 TAAACTC
1 TAAACCC
*
34190335 TTAACCC
1 TAAACCC
34190342 TAAACCC
1 TAAACCC
*
34190349 TTAACCC
1 TAAACCC
34190356 TAAA
1 TAAA
34190360 TTGACTTGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.41, C:0.36, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:34190553 original size:21 final size:21
Alignment explanation
Indices: 34190529--34190591 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
34190519 AACCCCTAAC
34190529 CCTTAACCCTAAACACTTAAA
1 CCTTAACCCTAAACACTTAAA
* * *
34190550 CCTTAAACCCCAAATA-TTACA
1 CCTT-AACCCTAAACACTTAAA
* *
34190571 CCATAATCCCTAAACCCTTAA
1 CCTTAA-CCCTAAACACTTAA
34190592 CTCGGCAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
20 2 0.06
21 17 0.55
22 12 0.39
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (21 bp):
CCTTAACCCTAAACACTTAAA
Found at i:34190639 original size:25 final size:25
Alignment explanation
Indices: 34190607--34190661 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
34190597 CAATATTCCT
* *
34190607 TAAACCCTAAATTATAGAACATATA
1 TAAACCCTAAATCATAAAACATATA
34190632 TAAACCCTAAATCATAAAACATATA
1 TAAACCCTAAATCATAAAACATATA
34190657 TAAAC
1 TAAAC
34190662 TATAAAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (25 bp):
TAAACCCTAAATCATAAAACATATA
Found at i:34190674 original size:25 final size:25
Alignment explanation
Indices: 34190624--34190674 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
34190614 TAAATTATAG
* *
34190624 AACATATATAAACCCTAAATCATAA
1 AACATATATAAACCATAAAACATAA
* *
34190649 AACATATATAAACTATAAAACTTAA
1 AACATATATAAACCATAAAACATAA
34190674 A
1 A
34190675 CCTCAACCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.25
Consensus pattern (25 bp):
AACATATATAAACCATAAAACATAA
Found at i:34195380 original size:27 final size:27
Alignment explanation
Indices: 34195349--34195526 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
34195339 TAAATTGTAC
34195349 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
34195376 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
34195402 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
34195430 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
34195458 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
34195485 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
34195512 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
34195527 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:34195463 original size:82 final size:81
Alignment explanation
Indices: 34195350--34195505 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
34195340 AAATTGTACA
* *
34195350 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
34195414 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
34195431 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
34195496 TGCGAGTTGA
65 TGCGAATTGA
34195506 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:34195517 original size:82 final size:81
Alignment explanation
Indices: 34195346--34195526 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
34195336 GATTAAATTG
* *
34195346 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
34195411 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
34195427 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
34195491 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
34195509 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
34195527 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:34203426 original size:27 final size:27
Alignment explanation
Indices: 34203395--34203572 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
34203385 TAAATTGTAC
34203395 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
34203422 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
34203448 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
34203476 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
34203504 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
34203531 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
34203558 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
34203573 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:34203509 original size:82 final size:81
Alignment explanation
Indices: 34203396--34203551 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
34203386 AAATTGTACA
* *
34203396 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
34203460 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
34203477 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
34203542 TGCGAGTTGA
65 TGCGAATTGA
34203552 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:34203563 original size:82 final size:81
Alignment explanation
Indices: 34203392--34203572 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
34203382 GATTAAATTG
* *
34203392 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
34203457 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
34203473 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
34203537 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
34203555 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
34203573 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:34207038 original size:19 final size:19
Alignment explanation
Indices: 34207011--34207056 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
34207001 TAATATGTTG
*
34207011 TTTATTTAATTCCTAATCA
1 TTTAATTAATTCCTAATCA
34207030 TTTAATTAATTCCTAATCA
1 TTTAATTAATTCCTAATCA
34207049 TTTAATTA
1 TTTAATTA
34207057 TATAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAATTAATTCCTAATCA
Found at i:34207990 original size:13 final size:13
Alignment explanation
Indices: 34207972--34207998 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34207962 TCACTCCATG
34207972 AAGATTAAACACA
1 AAGATTAAACACA
34207985 AAGATTAAACACA
1 AAGATTAAACACA
34207998 A
1 A
34207999 GAACATGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.15, G:0.07, T:0.15
Consensus pattern (13 bp):
AAGATTAAACACA
Found at i:34210693 original size:89 final size:89
Alignment explanation
Indices: 34210542--34210709 Score: 309
Period size: 89 Copynumber: 1.9 Consensus size: 89
34210532 GCATATCAAC
*
34210542 CATATCAACTTATTTGAGCATGGCCATTCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATAT
1 CATATCAACTTATTTGAGCATGGCCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATAT
*
34210607 TACTCCTATTATGTTCAATCATCT
66 TACTCCCATTATGTTCAATCATCT
*
34210631 CATATCAACTTATTTGAGCATGGCCATGCATTTCTAGTCTCACTCAATCAAGTGGCTTAAGATAT
1 CATATCAACTTATTTGAGCATGGCCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATAT
34210696 TACTCCCATTATGT
66 TACTCCCATTATGT
34210710 AGGAGGGACT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 76 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (89 bp):
CATATCAACTTATTTGAGCATGGCCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATAT
TACTCCCATTATGTTCAATCATCT
Found at i:34213823 original size:22 final size:22
Alignment explanation
Indices: 34213796--34213869 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
34213786 AAATCTAATT
34213796 TTTTATAGTTATCGGAATTTTA
1 TTTTATAGTTATCGGAATTTTA
* *
34213818 TTTTATAATAACTATATC-TAA-TTT-
1 -TTT-T-AT-AGT-TATCGGAATTTTA
34213842 TTTTATAGTTATCGGAATTTTA
1 TTTTATAGTTATCGGAATTTTA
34213864 TTTTAT
1 TTTTAT
34213870 TATAACTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 15
0.68 0.07 0.25
Matches are distributed among these distances:
19 4 0.10
20 4 0.10
21 5 0.12
22 7 0.17
23 6 0.15
24 1 0.03
25 5 0.12
26 4 0.10
27 4 0.10
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (22 bp):
TTTTATAGTTATCGGAATTTTA
Found at i:34213838 original size:45 final size:46
Alignment explanation
Indices: 34213788--34213878 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
34213778 CAACTAATAA
34213788 ATCTAA-TTTTTTATAGTTATCGGAATTTTATTTTATAATAACTAT
1 ATCTAATTTTTTTATAGTTATCGGAATTTTATTTTATAATAACTAT
*
34213833 ATCTAATTTTTTTATAGTTATCGGAATTTTATTTTATTATAACTAT
1 ATCTAATTTTTTTATAGTTATCGGAATTTTATTTTATAATAACTAT
34213879 CATATGCTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 6 0.14
46 38 0.86
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.55
Consensus pattern (46 bp):
ATCTAATTTTTTTATAGTTATCGGAATTTTATTTTATAATAACTAT
Found at i:34213872 original size:25 final size:25
Alignment explanation
Indices: 34213793--34213873 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
34213783 AATAAATCTA
34213793 ATTTT-TTATAGTTATCGGAATTTT
1 ATTTTATTATAGTTATCGGAATTTT
* ** * *
34213817 ATTTTATAATAACTAT----ATCTA
1 ATTTTATTATAGTTATCGGAATTTT
*
34213838 ATTTTTTTATAGTTATCGGAATTTT
1 ATTTTATTATAGTTATCGGAATTTT
34213863 ATTTTATTATA
1 ATTTTATTATA
34213874 ACTATCATAT
Statistics
Matches: 40, Mismatches: 12, Indels: 9
0.66 0.20 0.15
Matches are distributed among these distances:
21 15 0.38
24 5 0.12
25 20 0.50
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (25 bp):
ATTTTATTATAGTTATCGGAATTTT
Found at i:34217950 original size:23 final size:23
Alignment explanation
Indices: 34217920--34217974 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
34217910 TTTGTGCCCA
34217920 TGTAACTCAGGGTCACACAGCCG
1 TGTAACTCAGGGTCACACAGCCG
**
34217943 TGTAACTCAGGGTCACATGGCCG
1 TGTAACTCAGGGTCACACAGCCG
34217966 TGTAACTCA
1 TGTAACTCA
34217975 CTGTGGCCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.22
Consensus pattern (23 bp):
TGTAACTCAGGGTCACACAGCCG
Found at i:34218076 original size:89 final size:89
Alignment explanation
Indices: 34217963--34218146 Score: 305
Period size: 89 Copynumber: 2.1 Consensus size: 89
34217953 GGTCACATGG
34217963 CCGTGTAACTCACTGTGGCCGTGTGAACTAAAAATCACCCTGAACGATAGCACACATGGCCATGT
1 CCGTGTAACTCACTGTGGCCGTGTGAACTAAAAATCACCCTGAACGATAGCACACATGGCCATGT
* *
34218028 CAACCACCCGTGTGTGGCACACGA
66 CAACCACCCATGTGTGACACACGA
* * * *
34218052 CCGTGTAACTCATTGTGGCTGTGTGAACTAAAAATCACCCTGAATGGTAGCACACATGGCCATGT
1 CCGTGTAACTCACTGTGGCCGTGTGAACTAAAAATCACCCTGAACGATAGCACACATGGCCATGT
*
34218117 CAATCACCCATGTGTGACACACGA
66 CAACCACCCATGTGTGACACACGA
34218141 CCGTGT
1 CCGTGT
34218147 GGTAGCCCGT
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (89 bp):
CCGTGTAACTCACTGTGGCCGTGTGAACTAAAAATCACCCTGAACGATAGCACACATGGCCATGT
CAACCACCCATGTGTGACACACGA
Found at i:34218384 original size:23 final size:23
Alignment explanation
Indices: 34218354--34218412 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
34218344 TCAAATACAA
34218354 TTCATACTAAAACGTTTAACCAT
1 TTCATACTAAAACGTTTAACCAT
* *
34218377 TTCATACTAAAGCTTTTAACCAT
1 TTCATACTAAAACGTTTAACCAT
*
34218400 TTCATACCAAAAC
1 TTCATACTAAAAC
34218413 ACTCAACTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (23 bp):
TTCATACTAAAACGTTTAACCAT
Found at i:34221216 original size:42 final size:41
Alignment explanation
Indices: 34221139--34221369 Score: 191
Period size: 43 Copynumber: 5.5 Consensus size: 41
34221129 CTCGATAGAT
* **
34221139 TCAGCACTTGGCAACCACC-TTA-AATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACC-CCTTTACAA-TCAAAGATACGGGGAA
* *
34221180 TCAACACATAGCAACCCCTTTCACAATCAAAGATACGGTGGAA
1 TCAGCACTTAGCAACCCCTTT-ACAATCAAAGATACGG-GGAA
* * * **
34221223 TCAGCACTTAACAACCACCTTTATATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACC-CCTTTACAATCAAAGATACGGGGAA
* *
34221265 TCAGCA-TATAGCAACCCCTTTCACAATCAAATATATGGTGGAA
1 TCAGCACT-TAGCAACCCCTTT-ACAATCAAAGATACGG-GGAA
* * ** *
34221308 TCAACACTTAGCAACCACCTTTAAAATCAATA-ATTTGAGGAA
1 TCAGCACTTAGCAACC-CCTTTACAATCAA-AGATACGGGGAA
34221350 TCAGCACTTAGCAACCCCTT
1 TCAGCACTTAGCAACCCCTT
34221370 GGGGAATCTG
Statistics
Matches: 155, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
40 2 0.01
41 25 0.16
42 57 0.37
43 59 0.38
44 12 0.08
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (41 bp):
TCAGCACTTAGCAACCCCTTTACAATCAAAGATACGGGGAA
Found at i:34221281 original size:85 final size:85
Alignment explanation
Indices: 34221139--34221369 Score: 311
Period size: 85 Copynumber: 2.7 Consensus size: 85
34221129 CTCGATAGAT
*
34221139 TCAGCACTTGGCAACCACC-TTAAATTCAGTGATACGGGGAATCAACACATAGCAACCCCTTTCA
1 TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAACACATAGCAACCCCTTTCA
34221203 CAATCAAAGATACGGTGGAA
66 CAATCAAAGATACGGTGGAA
* * * *
34221223 TCAGCACTTAACAACCACCTTTATATTCAGTGATACGGGGAATCAGCATATAGCAACCCCTTTCA
1 TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAACACATAGCAACCCCTTTCA
* *
34221288 CAATCAAATATATGGTGGAA
66 CAATCAAAGATACGGTGGAA
* * * * ** * * *
34221308 TCAACACTTAGCAACCACCTTTAAAATCAATAATTTGAGGAATCAGCACTTAGCAACCCCTT
1 TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAACACATAGCAACCCCTT
34221370 GGGGAATCTG
Statistics
Matches: 128, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 17 0.13
85 111 0.87
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (85 bp):
TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAACACATAGCAACCCCTTTCA
CAATCAAAGATACGGTGGAA
Found at i:34221382 original size:26 final size:26
Alignment explanation
Indices: 34221346--34221395 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
34221336 AATAATTTGA
34221346 GGAATCAGCACTTAGCAACCCCTTGG
1 GGAATCAGCACTTAGCAACCCCTTGG
* *
34221372 GGAATCTGCACTTAGCGACCCCTT
1 GGAATCAGCACTTAGCAACCCCTT
34221396 TCTATCCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (26 bp):
GGAATCAGCACTTAGCAACCCCTTGG
Found at i:34221522 original size:30 final size:31
Alignment explanation
Indices: 34221480--34221539 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
34221470 TCAAACTTAG
34221480 CCACATTTTTTTTATAATCTACATCAAATAA
1 CCACATTTTTTTTATAATCTACATCAAATAA
*
34221511 CCACA-TTTTTTTATAATCTACATGAAATA
1 CCACATTTTTTTTATAATCTACATCAAATA
34221540 TTTAATCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (31 bp):
CCACATTTTTTTTATAATCTACATCAAATAA
Found at i:34223893 original size:13 final size:13
Alignment explanation
Indices: 34223875--34223921 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
34223865 ATATTTCTGT
34223875 AAATATTTAATAA
1 AAATATTTAATAA
34223888 AAATATTT-ATAA
1 AAATATTTAATAA
**
34223900 ACTTGATTTAATAA
1 AAAT-ATTTAATAA
34223914 AAATATTT
1 AAATATTT
34223922 CAGACCGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.21
13 16 0.57
14 6 0.21
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (13 bp):
AAATATTTAATAA
Found at i:34224632 original size:24 final size:25
Alignment explanation
Indices: 34224584--34224634 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
34224574 CCTCCTCAAA
* *
34224584 TCCAAATATTCTCTCCTCAAATCTC
1 TCCAAATATTCCCTCATCAAATCTC
*
34224609 TCCAAATA-TCCCTCATCAATTCTC
1 TCCAAATATTCCCTCATCAAATCTC
34224633 TC
1 TC
34224635 TATGACAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.35
Consensus pattern (25 bp):
TCCAAATATTCCCTCATCAAATCTC
Found at i:34228005 original size:17 final size:18
Alignment explanation
Indices: 34227973--34228006 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
34227963 ATAAACATAA
*
34227973 AAATAAACACCTAAAAAG
1 AAATAAACAACTAAAAAG
34227991 AAATAAA-AACTAAAAA
1 AAATAAACAACTAAAAA
34228007 AAAAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.74, C:0.12, G:0.03, T:0.12
Consensus pattern (18 bp):
AAATAAACAACTAAAAAG
Found at i:34235655 original size:29 final size:29
Alignment explanation
Indices: 34235613--34235809 Score: 234
Period size: 29 Copynumber: 6.8 Consensus size: 29
34235603 GATAGTCGAA
*
34235613 ACCATCCCTTTTCATATTCGATGGTCATC
1 ACCATCCCTTTTCATATTCGATAGTCATC
* * *
34235642 ACCATCCCCTTTCATATTTGATAGTCGTC
1 ACCATCCCTTTTCATATTCGATAGTCATC
* * * *
34235671 ACCATTCATTTTCATATTCGATGGTCGA-A
1 ACCATCCCTTTTCATATTCGATAGTC-ATC
* * **
34235700 ACCATCCCTTTTCATATCCGACAGTTGTC
1 ACCATCCCTTTTCATATTCGATAGTCATC
* *
34235729 ACCATCCCTTTTCATATTTGATGGTCATC
1 ACCATCCCTTTTCATATTCGATAGTCATC
* *
34235758 ACCATCCCTTTTCATATTTGATAGTCGTC
1 ACCATCCCTTTTCATATTCGATAGTCATC
34235787 ACCATCCCTTTTCATATTCGATA
1 ACCATCCCTTTTCATATTCGATA
34235810 AGGGTCGATA
Statistics
Matches: 138, Mismatches: 28, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
29 138 1.00
ACGTcount: A:0.22, C:0.29, G:0.10, T:0.39
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTCGATAGTCATC
Found at i:34235675 original size:58 final size:58
Alignment explanation
Indices: 34235602--34235808 Score: 299
Period size: 58 Copynumber: 3.6 Consensus size: 58
34235592 GTGTTCTAAA
** *
34235602 TGATAGTCGAAACCATCCCTTTTCATATTCGATGGTCATCACCATCCCCTTTCATATT
1 TGATAGTCGTCACCATCCCTTTTCATATTCGATGGTCATCACCATCCCTTTTCATATT
* * * *
34235660 TGATAGTCGTCACCATTCATTTTCATATTCGATGGTCGA-AACCATCCCTTTTCATATC
1 TGATAGTCGTCACCATCCCTTTTCATATTCGATGGTC-ATCACCATCCCTTTTCATATT
* * * *
34235718 CGACAGTTGTCACCATCCCTTTTCATATTTGATGGTCATCACCATCCCTTTTCATATT
1 TGATAGTCGTCACCATCCCTTTTCATATTCGATGGTCATCACCATCCCTTTTCATATT
34235776 TGATAGTCGTCACCATCCCTTTTCATATTCGAT
1 TGATAGTCGTCACCATCCCTTTTCATATTCGAT
34235809 AAGGGTCGAT
Statistics
Matches: 128, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
57 1 0.01
58 126 0.98
59 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.38
Consensus pattern (58 bp):
TGATAGTCGTCACCATCCCTTTTCATATTCGATGGTCATCACCATCCCTTTTCATATT
Found at i:34235760 original size:87 final size:87
Alignment explanation
Indices: 34235603--34235803 Score: 276
Period size: 87 Copynumber: 2.3 Consensus size: 87
34235593 TGTTCTAAAT
* **
34235603 GATAGTCGAAACCATCCCTTTTCATATTCGATGGTCATCACCATCCCCTTTCATATTTGATAGTC
1 GATAGTCGAAACCATCCCTTTTCATATCCGACAGTCATCACCATCCCCTTTCATATTTGATAGTC
* *
34235668 GTCACCATTCATTTTCATATTC
66 ATCACCATCCATTTTCATATTC
* ** * *
34235690 GATGGTCGAAACCATCCCTTTTCATATCCGACAGTTGTCACCATCCCTTTTCATATTTGATGGTC
1 GATAGTCGAAACCATCCCTTTTCATATCCGACAGTCATCACCATCCCCTTTCATATTTGATAGTC
* *
34235755 ATCACCATCCCTTTTCATATTT
66 ATCACCATCCATTTTCATATTC
**
34235777 GATAGTCGTCACCATCCCTTTTCATAT
1 GATAGTCGAAACCATCCCTTTTCATAT
34235804 TCGATAAGGG
Statistics
Matches: 99, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 99 1.00
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.38
Consensus pattern (87 bp):
GATAGTCGAAACCATCCCTTTTCATATCCGACAGTCATCACCATCCCCTTTCATATTTGATAGTC
ATCACCATCCATTTTCATATTC
Found at i:34243380 original size:25 final size:25
Alignment explanation
Indices: 34243352--34243418 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
34243342 TTTCGATTTT
* *
34243352 AGCTCTTATGTGCTTACCGATACTC
1 AGCTCATATGAGCTTACCGATACTC
* *
34243377 AGCTCATATGAGCTTACCGTTATTC
1 AGCTCATATGAGCTTACCGATACTC
* *
34243402 AGCTCAGAGGAGCTTAC
1 AGCTCATATGAGCTTAC
34243419 TGTTTACAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.31
Consensus pattern (25 bp):
AGCTCATATGAGCTTACCGATACTC
Found at i:34266396 original size:25 final size:25
Alignment explanation
Indices: 34266368--34266464 Score: 85
Period size: 25 Copynumber: 3.9 Consensus size: 25
34266358 ACGAGCTATG
*
34266368 AATCGGTATGCTC-TCACAAGCTGGA
1 AATCGGTAAGCTCAT-ACAAGCTGGA
** *
34266393 AATCGGTAAGCTCATATGAG-TTGA
1 AATCGGTAAGCTCATACAAGCTGGA
* *
34266417 GAATCAGTAAGATC-TCACAAGCT-GA
1 -AATCGGTAAGCTCAT-ACAAGCTGGA
34266442 AATCGGTAAGCTCATACAAGCTG
1 AATCGGTAAGCTCATACAAGCTG
34266465 TGGTGTATCT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
24 22 0.39
25 32 0.57
26 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (25 bp):
AATCGGTAAGCTCATACAAGCTGGA
Found at i:34268621 original size:11 final size:12
Alignment explanation
Indices: 34268594--34268626 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
34268584 TCTTACGAAA
34268594 TTTATTTTGTAAT
1 TTTATTTT-TAAT
34268607 TTTATTTTT-AT
1 TTTATTTTTAAT
34268618 TTTATTTTT
1 TTTATTTTT
34268627 GTTTCTGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 1 0.05
13 8 0.40
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTATTTTTAAT
Found at i:34272533 original size:14 final size:14
Alignment explanation
Indices: 34272514--34272546 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
34272504 GGCTGGTTCA
34272514 GTTCACTAGATTCG
1 GTTCACTAGATTCG
34272528 GTTCACTAGATTCG
1 GTTCACTAGATTCG
34272542 GTTCA
1 GTTCA
34272547 ACCAATGCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
GTTCACTAGATTCG
Found at i:34278396 original size:91 final size:91
Alignment explanation
Indices: 34278241--34278423 Score: 341
Period size: 91 Copynumber: 2.0 Consensus size: 91
34278231 CTTAATCTTA
*
34278241 TATGTGCCTATGAAGGTTGATTAATTGTTTGAATTAGCATTGAGAAATTTTCAAGTGATTTGTTA
1 TATGTGCCTACGAAGGTTGATTAATTGTTTGAATTAGCATTGAGAAATTTTCAAGTGATTTGTTA
34278306 ATTTAGTAAGTATGTATATGCAATAG
66 ATTTAGTAAGTATGTATATGCAATAG
34278332 TATGTGCCTACGAAGGTTGATTAATTGTTTGAATT-GACATTGAGAAATTTTCAAGTGATTTGTT
1 TATGTGCCTACGAAGGTTGATTAATTGTTTGAATTAG-CATTGAGAAATTTTCAAGTGATTTGTT
34278396 AATTTAGTAAGTATGTATATGCAATAG
65 AATTTAGTAAGTATGTATATGCAATAG
34278423 T
1 T
34278424 TAGCAAATTA
Statistics
Matches: 90, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
90 1 0.01
91 89 0.99
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.42
Consensus pattern (91 bp):
TATGTGCCTACGAAGGTTGATTAATTGTTTGAATTAGCATTGAGAAATTTTCAAGTGATTTGTTA
ATTTAGTAAGTATGTATATGCAATAG
Found at i:34278914 original size:32 final size:32
Alignment explanation
Indices: 34278868--34278929 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 32
34278858 TTTAACTTAG
34278868 TTAATTTTTCTGTGTTTATTTAGGTGTTTAAA
1 TTAATTTTTCTGTGTTTATTTAGGTGTTTAAA
34278900 TTAATTTCTT-TGTGTTTATTTAGGTGTTTA
1 TTAATTT-TTCTGTGTTTATTTAGGTGTTTA
34278930 TGAGTATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 27 0.93
33 2 0.07
ACGTcount: A:0.19, C:0.03, G:0.16, T:0.61
Consensus pattern (32 bp):
TTAATTTTTCTGTGTTTATTTAGGTGTTTAAA
Found at i:34283460 original size:54 final size:54
Alignment explanation
Indices: 34283378--34283640 Score: 296
Period size: 54 Copynumber: 4.9 Consensus size: 54
34283368 AATAGGCCTC
* ** * * * *
34283378 TAAAATTACTGAAATACCCTTAATGGGTAAAATTACTAAACTACCCTTGATGGG
1 TAAAATTACCGAAATACCCTCGATGGGTAAAATTACCAAAATACCCCTGAAGGG
34283432 TAAAATTACCGAAATACCCTCGATGGGTAAAATTACCAAAATACCCCTGAAGGG
1 TAAAATTACCGAAATACCCTCGATGGGTAAAATTACCAAAATACCCCTGAAGGG
* ** * * * *
34283486 TAAAATGACTAAAATACCCTCGAAGGGTAAAATGACCAAAAGA-CCCTCGATGGG
1 TAAAATTACCGAAATACCCTCGATGGGTAAAATTACCAAAATACCCCT-GAAGGG
* * *
34283540 TAAAATTATCGAAATACCCT-AATGGGTAAAATTACTAAAATACCCCTGAAGGG
1 TAAAATTACCGAAATACCCTCGATGGGTAAAATTACCAAAATACCCCTGAAGGG
* * * * * *
34283593 TAAAATGACCGAAATACCATCGATAGGTAAAGTTATCGAAATACCCCT
1 TAAAATTACCGAAATACCCTCGATGGGTAAAATTACCAAAATACCCCT
34283641 ATATGGTAAA
Statistics
Matches: 173, Mismatches: 33, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
53 43 0.25
54 130 0.75
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.23
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCTCGATGGGTAAAATTACCAAAATACCCCTGAAGGG
Found at i:34283514 original size:81 final size:80
Alignment explanation
Indices: 34283378--34283652 Score: 349
Period size: 81 Copynumber: 3.4 Consensus size: 80
34283368 AATAGGCCTC
* * * * *
34283378 TAAAATTACTGAAATACCCTTAATGGGTAAAATTACTAAACTACCCTTGATGGGTAAAATTACCG
1 TAAAATTACCGAAATACCC-TAATGGGTAAAATTACTAAAATACCCTCGAAGGGTAAAATGACCG
34283443 AAATACCCTCGATGGG
65 AAATACCCTCGATGGG
* *
34283459 TAAAATTACCAAAATACCCCTGAA-GGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACC
1 TAAAATTACCGAAATA-CCCT-AATGGGTAAAATTACTAAAATACCCTCGAAGGGTAAAATGACC
* *
34283523 AAAAGACCCTCGATGGG
64 GAAATACCCTCGATGGG
*
34283540 TAAAATTATCGAAATACCCTAATGGGTAAAATTACTAAAATACCC-CTGAAGGGTAAAATGACCG
1 TAAAATTACCGAAATACCCTAATGGGTAAAATTACTAAAATACCCTC-GAAGGGTAAAATGACCG
* *
34283604 AAATACCATCGATAGG
65 AAATACCCTCGATGGG
* *
34283620 TAAAGTTATCGAAATACCCCTATAT-GGTAAAAT
1 TAAAATTACCGAAATA-CCCTA-ATGGGTAAAAT
34283653 AACTGTTATA
Statistics
Matches: 171, Mismatches: 17, Indels: 12
0.86 0.09 0.06
Matches are distributed among these distances:
79 3 0.02
80 69 0.40
81 92 0.54
82 7 0.04
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (80 bp):
TAAAATTACCGAAATACCCTAATGGGTAAAATTACTAAAATACCCTCGAAGGGTAAAATGACCGA
AATACCCTCGATGGG
Found at i:34283607 original size:27 final size:26
Alignment explanation
Indices: 34283378--34283610 Score: 225
Period size: 27 Copynumber: 8.7 Consensus size: 26
34283368 AATAGGCCTC
** *
34283378 TAAAATTACTGAAATACCCTTAATGGG
1 TAAAATTACCAAAATACCCTGAA-GGG
* * *
34283405 TAAAATTACTAAACTACCCTTGATGGG
1 TAAAATTACCAAAATACCC-TGAAGGG
* *
34283432 TAAAATTACCGAAATACCCTCGATGGG
1 TAAAATTACCAAAATACCCT-GAAGGG
34283459 TAAAATTACCAAAATACCCCTGAAGGG
1 TAAAATTACCAAAATA-CCCTGAAGGG
* *
34283486 TAAAATGACTAAAATACCCTCGAAGGG
1 TAAAATTACCAAAATACCCT-GAAGGG
* * *
34283513 TAAAATGACCAAAAGACCCTCGATGGG
1 TAAAATTACCAAAATACCCT-GAAGGG
* *
34283540 TAAAATTATCGAAATACCCT-AATGGG
1 TAAAATTACCAAAATACCCTGAA-GGG
*
34283566 TAAAATTACTAAAATACCCCTGAAGGG
1 TAAAATTACCAAAATA-CCCTGAAGGG
* *
34283593 TAAAATGACCGAAATACC
1 TAAAATTACCAAAATACC
34283611 ATCGATAGGT
Statistics
Matches: 174, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
25 1 0.01
26 23 0.13
27 142 0.82
28 8 0.05
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.22
Consensus pattern (26 bp):
TAAAATTACCAAAATACCCTGAAGGG
Found at i:34283621 original size:27 final size:27
Alignment explanation
Indices: 34283378--34283652 Score: 195
Period size: 27 Copynumber: 10.2 Consensus size: 27
34283368 AATAGGCCTC
** ** *
34283378 TAAAATTACTGAAATACCCTTAATGGG
1 TAAAATTACCAAAATACCCTCGATAGG
* * * *
34283405 TAAAATTACTAAACTACCCTTGATGGG
1 TAAAATTACCAAAATACCCTCGATAGG
* *
34283432 TAAAATTACCGAAATACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATAGG
34283459 TAAAATTACCAAAATACCC-CTGA-AGGG
1 TAAAATTACCAAAATACCCTC-GATA-GG
* *
34283486 TAAAATGACTAAAATACCCTCGA-AGGG
1 TAAAATTACCAAAATACCCTCGATA-GG
* * *
34283513 TAAAATGACCAAAAGACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATAGG
* * * *
34283540 TAAAATTATCGAAATACCCT-AATGGG
1 TAAAATTACCAAAATACCCTCGATAGG
*
34283566 TAAAATTACTAAAATACCC-CTGA-AGGG
1 TAAAATTACCAAAATACCCTC-GATA-GG
* * *
34283593 TAAAATGACCGAAATACCATCGATAGG
1 TAAAATTACCAAAATACCCTCGATAGG
* * * *
34283620 TAAAGTTATCGAAATACCC-CTATATGG
1 TAAAATTACCAAAATACCCTCGATA-GG
34283647 TAAAAT
1 TAAAAT
34283653 AACTGTTATA
Statistics
Matches: 204, Mismatches: 34, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
26 26 0.13
27 175 0.86
28 3 0.01
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTCGATAGG
Found at i:34283883 original size:26 final size:26
Alignment explanation
Indices: 34283853--34283927 Score: 96
Period size: 26 Copynumber: 2.9 Consensus size: 26
34283843 CAAATACTAT
*
34283853 TATTGGTAGCTTTGCTGCGTTACTGA
1 TATTGGCAGCTTTGCTGCGTTACTGA
* * *
34283879 TATTGGCAGCTCTGCTGCATTACTGT
1 TATTGGCAGCTTTGCTGCGTTACTGA
* *
34283905 TATTGGCAGCTTTTCTCCGTTAC
1 TATTGGCAGCTTTGCTGCGTTAC
34283928 AATTACTGGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (26 bp):
TATTGGCAGCTTTGCTGCGTTACTGA
Found at i:34292378 original size:7 final size:7
Alignment explanation
Indices: 34292368--34292395 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
34292358 ATATACCTTA
34292368 TATTATT
1 TATTATT
34292375 TATTATT
1 TATTATT
34292382 TATTATT
1 TATTATT
34292389 TATTATT
1 TATTATT
34292396 AACTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TATTATT
Found at i:34294377 original size:28 final size:28
Alignment explanation
Indices: 34294314--34294521 Score: 350
Period size: 28 Copynumber: 7.5 Consensus size: 28
34294304 ATATTAAGTC
* * *
34294314 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAGTCAAACT
*
34294341 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
34294369 CGCACACTTAGTGCTACATAGTC-AACT
1 CGCACACTTAGTGCTACATAGTCAAACT
34294396 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
34294424 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
34294452 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
*
34294480 CGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAGTCAAACT
34294507 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
34294522 GCACAATTTA
Statistics
Matches: 175, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
27 66 0.38
28 109 0.62
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAGTCAAACT
Found at i:34294398 original size:55 final size:55
Alignment explanation
Indices: 34294314--34294546 Score: 358
Period size: 55 Copynumber: 4.2 Consensus size: 55
34294304 ATATTAAGTC
* * *
34294314 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
34294369 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
34294424 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAATCAAACT
* * * * *
34294480 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAA-TCAAACT
34294536 CGCACACTTAG
1 CGCACACTTAG
34294547 CGCCAATCTC
Statistics
Matches: 166, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
55 95 0.57
56 71 0.43
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:34294510 original size:111 final size:110
Alignment explanation
Indices: 34294314--34294521 Score: 362
Period size: 111 Copynumber: 1.9 Consensus size: 110
34294304 ATATTAAGTC
*
34294314 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
1 CGCACACTCAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
34294379 GTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
66 GTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
* * *
34294424 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 CGCACACTCAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
*
34294489 AGTGCTACATAGTCAATTCGCACACTTAGTGCT
65 AGTGCTACATAGTCAACTCGCACACTTAGTGCT
34294522 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 20 0.22
111 72 0.78
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (110 bp):
CGCACACTCAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
Found at i:34296323 original size:8 final size:8
Alignment explanation
Indices: 34296310--34296357 Score: 57
Period size: 8 Copynumber: 6.1 Consensus size: 8
34296300 AATTTCAATG
34296310 TTATTTAA
1 TTATTTAA
34296318 TTATTTAA
1 TTATTTAA
34296326 TT-TTTCAAA
1 TTATTT--AA
34296335 TTATTTAA
1 TTATTTAA
34296343 TTA-TTAA
1 TTATTTAA
34296350 -TATTTAA
1 TTATTTAA
34296357 T
1 T
34296358 GCAAATTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
6 2 0.06
7 11 0.31
8 15 0.43
9 4 0.11
10 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (8 bp):
TTATTTAA
Found at i:34304190 original size:16 final size:16
Alignment explanation
Indices: 34304146--34304218 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 16
34304136 CTTTATCGTC
* *
34304146 TTCATAGTCTAGAGTT
1 TTCAAAGTCTATAGTT
34304162 TTCAAAGTCTATAGTT
1 TTCAAAGTCTATAGTT
34304178 TTCACAATTTATAGTCTATAGTT
1 TT--C-A---A-AGTCTATAGTT
*
34304201 TTCACAGTCTATAGTT
1 TTCAAAGTCTATAGTT
34304217 TT
1 TT
34304219 GAATCTAAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
16 29 0.62
18 1 0.02
19 1 0.02
20 1 0.02
21 1 0.02
22 1 0.02
23 13 0.28
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (16 bp):
TTCAAAGTCTATAGTT
Found at i:34304193 original size:23 final size:23
Alignment explanation
Indices: 34304167--34304215 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
34304157 GAGTTTTCAA
*
34304167 AGTCTATAGTTTTCACAATTTAT
1 AGTCTATAGTTTTCACAATCTAT
*
34304190 AGTCTATAGTTTTCACAGTCTAT
1 AGTCTATAGTTTTCACAATCTAT
34304213 AGT
1 AGT
34304216 TTTGAATCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (23 bp):
AGTCTATAGTTTTCACAATCTAT
Found at i:34307295 original size:32 final size:32
Alignment explanation
Indices: 34307254--34307331 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 32
34307244 TCTAAAAAGT
* *
34307254 CCTT-GGTGTGAACAT-ATGTACTTGGACGGTC
1 CCTTGGGTGTGAACATCA-GGACTTGGACAGTC
*
34307285 CCTTGGGTGTGAACATCAGGAGTTGGACAGTC
1 CCTTGGGTGTGAACATCAGGACTTGGACAGTC
34307317 CCTTGGGTGTGAACA
1 CCTTGGGTGTGAACA
34307332 AAACAGTTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.10
32 37 0.88
33 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (32 bp):
CCTTGGGTGTGAACATCAGGACTTGGACAGTC
Found at i:34308912 original size:20 final size:21
Alignment explanation
Indices: 34308884--34308925 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
34308874 TGAATGTTTA
34308884 TATTGTATA-AGCTTACT-ATG
1 TATTGTATATA-CTTACTCATG
*
34308904 TATTTTATATACTTACTCATG
1 TATTGTATATACTTACTCATG
34308925 T
1 T
34308926 TAATACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.50
Consensus pattern (21 bp):
TATTGTATATACTTACTCATG
Found at i:34310793 original size:50 final size:49
Alignment explanation
Indices: 34310658--34310802 Score: 152
Period size: 50 Copynumber: 2.9 Consensus size: 49
34310648 GATAATAACA
* *
34310658 TGCCAAAGCCATGTCCTAGATATTGTCTTACATGGGATGTT-TCATATAC
1 TGCCAAAGCCATATCCTAGATATGGTCTTACATGGGA-GTTCTCATATAC
* *
34310707 TGCCAATGTCATATCCTAGATATGG-CATTACATGGGAGTTCTCATAT-C
1 TGCCAAAGCCATATCCTAGATATGGTC-TTACATGGGAGTTCTCATATAC
* * * **
34310755 GGTGCCAACGCCATATCCTAGACATGGTCTTACGTGGGACCTCTCATA
1 --TGCCAAAGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATA
34310803 ACCTCAATCA
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
48 5 0.06
49 37 0.46
50 38 0.47
51 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (49 bp):
TGCCAAAGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATAC
Found at i:34316113 original size:23 final size:19
Alignment explanation
Indices: 34316071--34316116 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
34316061 TTAAAGATTG
34316071 ATTAATTAAGATTTTATTA
1 ATTAATTAAGATTTTATTA
*
34316090 ATTAATTAAGA-TTAATTA
1 ATTAATTAAGATTTTATTA
34316108 ATTTAATTA
1 A-TTAATTA
34316117 TAAGTATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (19 bp):
ATTAATTAAGATTTTATTA
Found at i:34319526 original size:79 final size:82
Alignment explanation
Indices: 34319415--34319599 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
34319405 GCTACTCGTT
* * *
34319415 CAAATGCCTTCGGGTCATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
34319478 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
34319495 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
34319558 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
34319575 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
34319600 CATCATTCGA
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:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:34319599 original size:40 final size:40
Alignment explanation
Indices: 34319396--34319599 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
34319386 CGGAATTTAA
** * *
34319396 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGTCATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
34319436 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
34319476 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
34319515 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
34319555 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
34319595 CCGGA
1 CCGGA
34319600 CATCATTCGA
Statistics
Matches: 140, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 93 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:34320789 original size:56 final size:56
Alignment explanation
Indices: 34320727--34320902 Score: 334
Period size: 56 Copynumber: 3.1 Consensus size: 56
34320717 TATTAGTTTA
* *
34320727 TTGCCCATGATTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
34320783 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
34320839 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
34320895 TTGCCCAT
1 TTGCCCAT
34320903 CATCCCTTGT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 118 1.00
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:34325178 original size:51 final size:51
Alignment explanation
Indices: 34325102--34325251 Score: 273
Period size: 51 Copynumber: 2.9 Consensus size: 51
34325092 AAAAAAGTAC
*
34325102 GAGTATAGGTATTTCATAGAATTACTTAATAAGAAGGGTAGTGAGAGATAA
1 GAGTATAGGTATTTCGTAGAATTACTTAATAAGAAGGGTAGTGAGAGATAA
* *
34325153 GAGTATAGGTATATCGTAGAATTACTTAATAAGAAGAGTAGTGAGAGATAA
1 GAGTATAGGTATTTCGTAGAATTACTTAATAAGAAGGGTAGTGAGAGATAA
34325204 GAGTATAGGTATTTCGTAGAATTACTTAATAAGAAGGGTAGTGAGAGA
1 GAGTATAGGTATTTCGTAGAATTACTTAATAAGAAGGGTAGTGAGAGA
34325252 GTTGTAGATG
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 94 1.00
ACGTcount: A:0.41, C:0.04, G:0.27, T:0.29
Consensus pattern (51 bp):
GAGTATAGGTATTTCGTAGAATTACTTAATAAGAAGGGTAGTGAGAGATAA
Found at i:34330855 original size:24 final size:25
Alignment explanation
Indices: 34330820--34330868 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
34330810 TTTAATTTTC
34330820 TAAATAATATTA-ATTTATTTTAAA
1 TAAATAATATTACATTTATTTTAAA
34330844 TAAA-AATGATTACATTTATTTTAAA
1 TAAATAAT-ATTACATTTATTTTAAA
34330869 ATTAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.13
24 8 0.35
25 12 0.52
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
TAAATAATATTACATTTATTTTAAA
Found at i:34331565 original size:3 final size:3
Alignment explanation
Indices: 34331557--34331584 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
34331547 AAAAATCCCC
34331557 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
34331585 ATAACCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:34335904 original size:15 final size:15
Alignment explanation
Indices: 34335884--34335912 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34335874 CAAAATTTCA
34335884 AAAAAATAAAAATTT
1 AAAAAATAAAAATTT
34335899 AAAAAATAAAAATT
1 AAAAAATAAAAATT
34335913 GCATTTTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAAATAAAAATTT
Found at i:34335948 original size:30 final size:29
Alignment explanation
Indices: 34335908--34336027 Score: 129
Period size: 30 Copynumber: 4.1 Consensus size: 29
34335898 TAAAAAATAA
*
34335908 AAATTGCATTTTGACCCCTAAACTTTTACT
1 AAATTTCATTTTGACCCCTAAACTTTT-CT
* *
34335938 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTT-TCT
* *
34335968 AAATTTCACTTAGACCCCTAAAC-TTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTTC--T
*
34335998 AAATTTCATTTT-AACCCTAAA-TTTTCT
1 AAATTTCATTTTGACCCCTAAACTTTTCT
34336025 AAA
1 AAA
34336028 AATTACATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
27 4 0.05
28 1 0.01
29 14 0.18
30 56 0.74
31 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (29 bp):
AAATTTCATTTTGACCCCTAAACTTTTCT
Found at i:34336301 original size:14 final size:15
Alignment explanation
Indices: 34336282--34336313 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
34336272 GAAAAGAGAA
34336282 GAGAAAAGA-AAGAG
1 GAGAAAAGAGAAGAG
34336296 GAG-AAAGAGAAGAG
1 GAGAAAAGAGAAGAG
34336310 GAGA
1 GAGA
34336314 GCCCGACCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (15 bp):
GAGAAAAGAGAAGAG
Found at i:34336313 original size:28 final size:28
Alignment explanation
Indices: 34336257--34336309 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 28
34336247 AGTTTCGAAA
34336257 AAAAGAAAAAGGAAGGAAAAGAGAAGAG
1 AAAAGAAAAAGGAAGGAAAAGAGAAGAG
*
34336285 AAAAGAAAGAGG-A-G-AAAGAGAAGAG
1 AAAAGAAAAAGGAAGGAAAAGAGAAGAG
34336310 GAGAGCCCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 11 0.46
26 1 0.04
27 1 0.04
28 11 0.46
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (28 bp):
AAAAGAAAAAGGAAGGAAAAGAGAAGAG
Found at i:34336425 original size:14 final size:14
Alignment explanation
Indices: 34336407--34336459 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
34336397 AAGAAGAAGA
34336407 AAAGAAAGAAAAAA-
1 AAAGAAA-AAAAAAG
***
34336421 AAAGAAAAAAGGGG
1 AAAGAAAAAAAAAG
34336435 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAAG
34336449 AAAGAAAAAAA
1 AAAGAAAAAAA
34336460 TAAAAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 3 0.09
14 29 0.91
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:34336561 original size:12 final size:12
Alignment explanation
Indices: 34336543--34336590 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 12
34336533 GGCTAGCCCA
34336543 AAAAAAACAAAGC
1 AAAAAAA-AAAGC
34336556 AAAAAAAAAAGC
1 AAAAAAAAAAGC
34336568 AGCAAAAAAAGAAGC
1 A--AAAAAAA-AAGC
34336583 AGAAAAAA
1 A-AAAAAA
34336591 GAAGAAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 6 0.19
13 7 0.23
14 13 0.42
15 5 0.16
ACGTcount: A:0.77, C:0.10, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGC
Found at i:34336591 original size:13 final size:13
Alignment explanation
Indices: 34336560--34336600 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
34336550 CAAAGCAAAA
*
34336560 AAAAAAGCAGCA-
1 AAAAAAGAAGCAG
34336572 AAAAAAGAAGCAG
1 AAAAAAGAAGCAG
*
34336585 AAAAAAGAAGAAG
1 AAAAAAGAAGCAG
34336598 AAA
1 AAA
34336601 GAAGCAGCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAGCAG
Found at i:34337236 original size:17 final size:17
Alignment explanation
Indices: 34337193--34337240 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
34337183 AGAAAAAAAT
34337193 CGTGTTTCAAAAATTTTCA
1 CGTGTTTC-AAAA-TTTCA
34337212 --TGTCTTCAAAATTTCA
1 CGTGT-TTCAAAATTTCA
34337228 CGTGTTTCAAAAT
1 CGTGTTTCAAAAT
34337241 AATAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (17 bp):
CGTGTTTCAAAATTTCA
Found at i:34337323 original size:17 final size:18
Alignment explanation
Indices: 34337303--34337367 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 18
34337293 TAAAAAAATC
34337303 CGTG-TTTCAAAAATTCT
1 CGTGATTTCAAAAATTCT
* **
34337320 CGTGAATAAAAAAATT-T
1 CGTGATTTCAAAAATTCT
* *
34337337 CGTGTTTTCAAAAATTCC
1 CGTGATTTCAAAAATTCT
*
34337355 CGTG-TTTTAAAAA
1 CGTGATTTCAAAAA
34337368 AAATTTTCGT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
17 25 0.68
18 12 0.32
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (18 bp):
CGTGATTTCAAAAATTCT
Found at i:34337387 original size:28 final size:28
Alignment explanation
Indices: 34337355--34337409 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
34337345 CAAAAATTCC
*
34337355 CGTGTTTTAAAAAAAATTTTCGTGTTTT
1 CGTGTTTTAAAAAAAATTCTCGTGTTTT
34337383 CGTGTTTTAAAAAAAATTCTCGTGTTT
1 CGTGTTTTAAAAAAAATTCTCGTGTTT
34337410 CAAAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (28 bp):
CGTGTTTTAAAAAAAATTCTCGTGTTTT
Found at i:34337428 original size:18 final size:18
Alignment explanation
Indices: 34337394--34337445 Score: 72
Period size: 17 Copynumber: 3.0 Consensus size: 18
34337384 GTGTTTTAAA
* *
34337394 AAAAATTCTCGTG-TTTC
1 AAAAATTTTCATGTTTTC
34337411 AAAAATTTTCATGTTTTC
1 AAAAATTTTCATGTTTTC
34337429 -AAAATTTTCATGTTTTC
1 AAAAATTTTCATGTTTTC
34337446 GTGTTTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 28 0.88
18 4 0.12
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (18 bp):
AAAAATTTTCATGTTTTC
Found at i:34337542 original size:18 final size:17
Alignment explanation
Indices: 34337505--34337638 Score: 78
Period size: 17 Copynumber: 7.6 Consensus size: 17
34337495 AAAAAATTCA
*
34337505 TGTTTTCGAAATTTTCG
1 TGTTTTCAAAATTTTCG
*
34337522 TGTTTTCAAAATTTT-T
1 TGTTTTCAAAATTTTCG
* *
34337538 TG-TGTCAAAAATTTCTCA
1 TGTTTTC-AAAATTT-TCG
* * *
34337556 TG-TATCGAAAATTTCCT
1 TGTTTTC-AAAATTTTCG
* *
34337573 TGTTTTCAAAAAAATTCCG
1 TGTTTTC--AAAATTTTCG
34337592 TGTTTTCAAAAAATTTTCG
1 TGTTTTC--AAAATTTTCG
*
34337611 TG-TTTCAAAAATCTTCG
1 TGTTTTC-AAAATTTTCG
34337628 TGTTTTCAAAA
1 TGTTTTCAAAA
34337639 ATTATTATTG
Statistics
Matches: 96, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
15 3 0.03
16 9 0.09
17 34 0.35
18 23 0.24
19 27 0.28
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (17 bp):
TGTTTTCAAAATTTTCG
Found at i:34337602 original size:17 final size:18
Alignment explanation
Indices: 34337563--34337639 Score: 77
Period size: 19 Copynumber: 4.2 Consensus size: 18
34337553 TCATGTATCG
* *
34337563 AAAATTTCCTTGTTTTCAA
1 AAAAATTCCGTGTTTTC-A
34337582 AAAAATTCCGTGTTTTCA
1 AAAAATTCCGTGTTTTCA
*
34337600 AAAAATTTTCGTG-TTTC-
1 AAAAA-TTCCGTGTTTTCA
*
34337617 AAAAATCTTCGTGTTTTCA
1 AAAAAT-TCCGTGTTTTCA
34337636 AAAA
1 AAAA
34337640 TTATTATTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
16 1 0.02
17 11 0.22
18 14 0.27
19 25 0.49
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (18 bp):
AAAAATTCCGTGTTTTCA
Found at i:34337630 original size:36 final size:38
Alignment explanation
Indices: 34337572--34337657 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 38
34337562 GAAAATTTCC
34337572 TTGT-TTTCAAAAAAATTCCGTGTTTTCAAAAA-ATT-
1 TTGTGTTTCAAAAAAATTCCGTGTTTTCAAAAATATTA
**
34337607 TTCGTGTTTCAAAAATCTT-CGTGTTTTCAAAAATTATTA
1 TT-GTGTTTCAAAAAAATTCCGTGTTTTCAAAAA-TATTA
34337646 TTGTGTTTCAAA
1 TTGTGTTTCAAA
34337658 GTTCTCGTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 2 0.05
36 16 0.36
37 11 0.25
38 13 0.30
39 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (38 bp):
TTGTGTTTCAAAAAAATTCCGTGTTTTCAAAAATATTA
Found at i:34337639 original size:18 final size:18
Alignment explanation
Indices: 34337443--34337640 Score: 88
Period size: 18 Copynumber: 10.9 Consensus size: 18
34337433 TTTTCATGTT
34337443 TTCGTGTTTTCAAAAA-A
1 TTCGTGTTTTCAAAAATA
* *
34337460 TTCTCGTGTTTTTTTAAAAAAAA
1 -T-TCGTG---TTTTCAAAAATA
* * *
34337483 TTCATGTTTTAAAAAAAA
1 TTCGTGTTTTCAAAAATA
* * *
34337501 TTCATGTTTTC-GAAATT
1 TTCGTGTTTTCAAAAATA
34337518 TTCGTGTTTTC-AAAAT-
1 TTCGTGTTTTCAAAAATA
** * *
34337534 TTTTTG-TGTCAAAAATT
1 TTCGTGTTTTCAAAAATA
* * *
34337551 TCTCATG-TATCGAAAAT-
1 T-TCGTGTTTTCAAAAATA
* *
34337568 TTCCTTGTTTTCAAAAAAA
1 TT-CGTGTTTTCAAAAATA
*
34337587 TTCCGTGTTTTCAAAAAATT
1 TT-CGTGTTTTC-AAAAATA
*
34337607 TTCGTG-TTTCAAAAATC
1 TTCGTGTTTTCAAAAATA
34337624 TTCGTGTTTTCAAAAAT
1 TTCGTGTTTTCAAAAAT
34337641 TATTATTGTG
Statistics
Matches: 144, Mismatches: 23, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
15 3 0.02
16 10 0.07
17 34 0.24
18 55 0.38
19 20 0.14
20 7 0.05
21 4 0.03
22 10 0.07
23 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (18 bp):
TTCGTGTTTTCAAAAATA
Found at i:34338249 original size:34 final size:35
Alignment explanation
Indices: 34338204--34338271 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
34338194 CCAGTAAAAT
* *
34338204 ATTTTCCGTAAAATGA-TTTCGGGAAAATGTTTTA
1 ATTTTCCGTAAAATGACTTACGGGAAAATATTTTA
* *
34338238 ATTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 ATTTTCCGTAAAATGACTTACGGGAAAATATTTT
34338272 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 15 0.52
35 14 0.48
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.43
Consensus pattern (35 bp):
ATTTTCCGTAAAATGACTTACGGGAAAATATTTTA
Found at i:34340448 original size:43 final size:43
Alignment explanation
Indices: 34340345--34340454 Score: 172
Period size: 44 Copynumber: 2.6 Consensus size: 43
34340335 TTTTATCTTA
* *
34340345 GAAAAAA-AATTT-AAAA-AGGAGAAGGTAATCTTGGGTTGTT
1 GAAAAAAGAATTTAAAAAGAGGAGAAGATAATCTCGGGTTGTT
34340385 GAAAAAAGAATTTAAAAAAGAGGAGAAGATAATCTCGGGTTGTT
1 GAAAAAAGAATTT-AAAAAGAGGAGAAGATAATCTCGGGTTGTT
34340429 GAAAAAAGAATTTAAAAAGAGGAGAA
1 GAAAAAAGAATTTAAAAAGAGGAGAA
34340455 AGTAAACATG
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
40 7 0.11
41 5 0.08
43 17 0.27
44 35 0.55
ACGTcount: A:0.51, C:0.03, G:0.25, T:0.22
Consensus pattern (43 bp):
GAAAAAAGAATTTAAAAAGAGGAGAAGATAATCTCGGGTTGTT
Found at i:34340468 original size:43 final size:42
Alignment explanation
Indices: 34340345--34340472 Score: 165
Period size: 44 Copynumber: 3.0 Consensus size: 42
34340335 TTTTATCTTA
*
34340345 GAAAAAA-AATTT-AAAA-AGGAGAAGGTAATCTTGGGTTGTT
1 GAAAAAAGAATTTAAAAAGAGGAGAAAGTAATC-TGGGTTGTT
34340385 GAAAAAAGAATTTAAAAAAGAGGAG-AAGATAATCTCGGGTTGTT
1 GAAAAAAGAATTT-AAAAAGAGGAGAAAG-TAATCT-GGGTTGTT
*
34340429 GAAAAAAGAATTTAAAAAGAGGAGAAAGTAAACATGGGTTGTT
1 GAAAAAAGAATTTAAAAAGAGGAGAAAGTAATC-TGGGTTGTT
34340472 G
1 G
34340473 GTTTTACCTT
Statistics
Matches: 78, Mismatches: 2, Indels: 13
0.84 0.02 0.14
Matches are distributed among these distances:
40 7 0.09
41 5 0.06
43 31 0.40
44 35 0.45
ACGTcount: A:0.48, C:0.03, G:0.26, T:0.23
Consensus pattern (42 bp):
GAAAAAAGAATTTAAAAAGAGGAGAAAGTAATCTGGGTTGTT
Found at i:34362885 original size:17 final size:17
Alignment explanation
Indices: 34362841--34362887 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
34362831 TACTCTCCTC
*
34362841 CTCTTCTTCTTCTTTTT
1 CTCTTCTTCTTCTTCTT
* **
34362858 ATCTTAGTCTTCTTCTT
1 CTCTTCTTCTTCTTCTT
34362875 CTCTTCTTCTTCT
1 CTCTTCTTCTTCT
34362888 ACTACCTAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.04, C:0.30, G:0.02, T:0.64
Consensus pattern (17 bp):
CTCTTCTTCTTCTTCTT
Found at i:34362885 original size:23 final size:23
Alignment explanation
Indices: 34362842--34362885 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
34362832 ACTCTCCTCC
*
34362842 TCTTCTTCTTCTTTTTATCTTAG
1 TCTTCTTCTTCTTTCTATCTTAG
34362865 TCTTCTTCTTCTCTTCT-TCTT
1 TCTTCTTCTTCT-TTCTATCTT
34362886 CTACTACCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.05, C:0.27, G:0.02, T:0.66
Consensus pattern (23 bp):
TCTTCTTCTTCTTTCTATCTTAG
Found at i:34376583 original size:21 final size:22
Alignment explanation
Indices: 34376548--34376606 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
34376538 GGTAGCCATT
34376548 AAATGATTAAGATTAA-TGAATAAA
1 AAATGATT-A-ATTAATTGAAT-AA
*
34376572 AAATG-TTAATTAATTTAATAA
1 AAATGATTAATTAATTGAATAA
34376593 AAATGATTAATTAA
1 AAATGATTAATTAA
34376607 AATTTGATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 12 0.38
22 13 0.41
23 2 0.06
24 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (22 bp):
AAATGATTAATTAATTGAATAA
Found at i:34379271 original size:20 final size:20
Alignment explanation
Indices: 34379246--34379284 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
34379236 TACTTTCTTC
34379246 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
34379266 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
34379285 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:34379646 original size:49 final size:50
Alignment explanation
Indices: 34379487--34379680 Score: 178
Period size: 49 Copynumber: 3.9 Consensus size: 50
34379477 GATAATAACA
* * ** * *
34379487 TGCCAAAGCCATGTCCCAGATATGGTCTTACATGGGATGTTTCCTATAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* ** ** * **
34379536 TACCAATACCATACCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
34379586 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
34379635 TGCTAACGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
34379681 ACCTTAATAA
Statistics
Matches: 117, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
48 1 0.01
49 80 0.68
50 36 0.31
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:34381728 original size:13 final size:12
Alignment explanation
Indices: 34381701--34381735 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
34381691 ATTGAATAGT
34381701 AACTTGAAT-CA
1 AACTTGAATGCA
34381712 AACTTGAATGACA
1 AACTTGAATG-CA
34381725 AACTTGAATGC
1 AACTTGAATGC
34381736 CTTCTTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.41
12 1 0.05
13 12 0.55
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (12 bp):
AACTTGAATGCA
Found at i:34381841 original size:25 final size:26
Alignment explanation
Indices: 34381813--34381865 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
34381803 TTCGCATAGT
*
34381813 TTTTTGATAAGGATGACATATTT-TC
1 TTTTGGATAAGGATGACATATTTGTC
*
34381838 TTTTGGATAAGGATGACATCTTTGTC
1 TTTTGGATAAGGATGACATATTTGTC
34381864 TT
1 TT
34381866 GTTGTGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.47
Consensus pattern (26 bp):
TTTTGGATAAGGATGACATATTTGTC
Found at i:34381962 original size:112 final size:108
Alignment explanation
Indices: 34381820--34382040 Score: 316
Period size: 112 Copynumber: 2.0 Consensus size: 108
34381810 AGTTTTTTGA
* * * * *
34381820 TAAGGATGACATATTTTCTTTTGGATAAGGATGACATCTTTGTCTTGTTGTGGTTTCTTCCACGT
1 TAAGGATAACATATTTTCTTTTAGATAAGGATGACATCTTTGTCTTGTTAT--TGT-TTCCACAT
* **
34381885 TGCTTCTTTTTTTTTCATTTCTTGGTAGTGATTTTTTCCATGTAGCT
63 TGCTTCCTTTTTTTTCATTTCTTGGTAGTG-GCTTTTCCATGTAGCT
34381932 TAAGGATAACATATTTTCTTTTAGATAAGGATGACATCTTTGTCTTGTTATTGTTTCCACATTGC
1 TAAGGATAACATATTTTCTTTTAGATAAGGATGACATCTTTGTCTTGTTATTGTTTCCACATTGC
* *
34381997 TTCCTTTTTTTTCGTTTCTTGGTAGTGGCTTTTCTATGTAGCT
66 TTCCTTTTTTTTCATTTCTTGGTAGTGGCTTTTCCATGTAGCT
34382040 T
1 T
34382041 CCTTTATCTT
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
108 14 0.14
109 35 0.35
110 2 0.02
112 48 0.48
ACGTcount: A:0.17, C:0.14, G:0.18, T:0.51
Consensus pattern (108 bp):
TAAGGATAACATATTTTCTTTTAGATAAGGATGACATCTTTGTCTTGTTATTGTTTCCACATTGC
TTCCTTTTTTTTCATTTCTTGGTAGTGGCTTTTCCATGTAGCT
Found at i:34384207 original size:27 final size:27
Alignment explanation
Indices: 34384167--34384222 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
34384157 CAGTAACAAA
* *
34384167 ACAGAACAATGTGGGCTTTAGCCCAAT
1 ACAGAACAAGGTGGGCCTTAGCCCAAT
34384194 ACAGAACAAGGTGGGCCTTAGCCCAAT
1 ACAGAACAAGGTGGGCCTTAGCCCAAT
34384221 AC
1 AC
34384223 CATATCAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (27 bp):
ACAGAACAAGGTGGGCCTTAGCCCAAT
Done.