Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 36 of 91
Found at i:12458593 original size:24 final size:23
Alignment explanation
Indices: 12458561--12458682 Score: 172
Period size: 23 Copynumber: 5.2 Consensus size: 23
12458551 CAAATTGGCA
*
12458561 ACAAACAGCTCTAATTTTTCTGC
1 ACAAACAGCTCCAATTTTTCTGC
*
12458584 AGCAAACAGCTCCAATTTTTTTGC
1 A-CAAACAGCTCCAATTTTTCTGC
* *
12458608 ACGAACAGCTCTAATTTTTCTGC
1 ACAAACAGCTCCAATTTTTCTGC
*
12458631 ACAAACAACTCCAATTTTTCTGC
1 ACAAACAGCTCCAATTTTTCTGC
*
12458654 AGCAAACAGCTCCAATTTATCTGC
1 A-CAAACAGCTCCAATTTTTCTGC
12458678 ACAAA
1 ACAAA
12458683 TTGGCAGCAA
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 45 0.52
24 42 0.48
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (23 bp):
ACAAACAGCTCCAATTTTTCTGC
Found at i:12458662 original size:47 final size:46
Alignment explanation
Indices: 12458561--12458682 Score: 181
Period size: 47 Copynumber: 2.6 Consensus size: 46
12458551 CAAATTGGCA
* *
12458561 ACAAACAGCTCTAATTTTTCTGCAGCAAACAGCTCCAATTTTTTTGC
1 ACAAACAGCTCTAATTTTTCTGCA-CAAACAACTCCAATTTTTCTGC
*
12458608 ACGAACAGCTCTAATTTTTCTGCACAAACAACTCCAATTTTTCTGC
1 ACAAACAGCTCTAATTTTTCTGCACAAACAACTCCAATTTTTCTGC
* *
12458654 AGCAAACAGCTCCAATTTATCTGCACAAA
1 A-CAAACAGCTCTAATTTTTCTGCACAAA
12458683 TTGGCAGCAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
46 21 0.31
47 47 0.69
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (46 bp):
ACAAACAGCTCTAATTTTTCTGCACAAACAACTCCAATTTTTCTGC
Found at i:12458893 original size:25 final size:25
Alignment explanation
Indices: 12458865--12458912 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
12458855 AAAAATCAGC
*
12458865 TTTCTTACCT-AAAAAATTTCAACTT
1 TTTCTT-CCTCAAAAAATTACAACTT
*
12458890 TTTCTTCCTCCAAAAATTACAAC
1 TTTCTTCCTCAAAAAATTACAAC
12458913 AAAAAGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (25 bp):
TTTCTTCCTCAAAAAATTACAACTT
Found at i:12463666 original size:60 final size:60
Alignment explanation
Indices: 12463558--12463697 Score: 181
Period size: 60 Copynumber: 2.3 Consensus size: 60
12463548 TAGGAAACCA
* * * ** * * *
12463558 AAACGGAAAGTTTTTCGCTGCAACGAGATTCAATCTCTCTGCAACGAAATTGTAACCCAG
1 AAACAGAAAGTTTCTCGCTGTAGTGAAATTCAATCTCGCTGCAACGAAATTGCAACCCAG
* * *
12463618 AAACAGAATGTTTCTCGCTGTAGTGAAATTCAATCTCGCTGCAGCGAAATTGCAACCTAG
1 AAACAGAAAGTTTCTCGCTGTAGTGAAATTCAATCTCGCTGCAACGAAATTGCAACCCAG
12463678 AAACAGAAAGTTTCTCGCTG
1 AAACAGAAAGTTTCTCGCTG
12463698 CAGCGAGAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 68 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (60 bp):
AAACAGAAAGTTTCTCGCTGTAGTGAAATTCAATCTCGCTGCAACGAAATTGCAACCCAG
Found at i:12463720 original size:60 final size:59
Alignment explanation
Indices: 12463558--12463724 Score: 167
Period size: 60 Copynumber: 2.8 Consensus size: 59
12463548 TAGGAAACCA
* * * * * *
12463558 AAACGGAAAGTTTTTCGCTGCAACGAG-ATTCAATCTCTCTGCAACGAAATTGTAACCCAG
1 AAACAGAAAGTTTCTCGCTGCAGCGAGAATT--ATCTCACTGCAGCGAAATTGCAACCCAG
* * * * *
12463618 AAACAGAATGTTTCTCGCTGTAGTGA-AATTCAATCTCGCTGCAGCGAAATTGCAACCTAG
1 AAACAGAAAGTTTCTCGCTGCAGCGAGAATT--ATCTCACTGCAGCGAAATTGCAACCCAG
*
12463678 AAACAGAAAGTTTCTCGCTGCAGCGAGAATGTATTTCACTGCAGCGA
1 AAACAGAAAGTTTCTCGCTGCAGCGAGAAT-TATCTCACTGCAGCGA
12463725 GAAGCTATAG
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
60 85 0.96
61 3 0.03
62 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.25
Consensus pattern (59 bp):
AAACAGAAAGTTTCTCGCTGCAGCGAGAATTATCTCACTGCAGCGAAATTGCAACCCAG
Found at i:12464133 original size:2 final size:2
Alignment explanation
Indices: 12464126--12464163 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12464116 NNNATATTAC
12464126 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12464164 CCCATCATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12464262 original size:43 final size:43
Alignment explanation
Indices: 12464196--12464319 Score: 162
Period size: 43 Copynumber: 2.9 Consensus size: 43
12464186 CCCATCATCA
* **
12464196 TCATCACCAGCTCATGCGCACTCCCTACTCGCACAT-GGCTGGG
1 TCATCACCAGCTTATGCGCACTCCCTACTCGCACATAATC-GGG
* *
12464239 TCATCACCAGGTTATGCGTACTCCCTACTCGCACATAATCGGG
1 TCATCACCAGCTTATGCGCACTCCCTACTCGCACATAATCGGG
*
12464282 TCATC-CTCAGCTTATGCGCACTCTCTACTCGCACATAA
1 TCATCAC-CAGCTTATGCGCACTCCCTACTCGCACATAA
12464320 CCGAGTCAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
42 1 0.01
43 69 0.97
44 1 0.01
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (43 bp):
TCATCACCAGCTTATGCGCACTCCCTACTCGCACATAATCGGG
Found at i:12468924 original size:22 final size:22
Alignment explanation
Indices: 12468882--12468922 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
12468872 TACCTTTTGT
*
12468882 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
12468904 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
12468923 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:12473760 original size:42 final size:42
Alignment explanation
Indices: 12473601--12473772 Score: 209
Period size: 42 Copynumber: 4.1 Consensus size: 42
12473591 GTTGATGTGG
* * ** * ** * *
12473601 ACCCAGCTATGTGTGAGTACAAGTGCGCATACGTTGATGATG
1 ACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGCTA
* **
12473643 ACCCGGCTATGTGCGAGTAGGAGTGCGTATAAGTTGATGCTA
1 ACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGCTA
*
12473685 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGATGCTA
1 ACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGCTA
* *
12473727 ACCCGGCTATGTGCGAGTAGGAGTGTGCATAAGCCGATGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGCTA
12473769 ACCC
1 ACCC
12473773 AGCCATGTAT
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 115 1.00
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (42 bp):
ACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGCTA
Found at i:12473853 original size:2 final size:2
Alignment explanation
Indices: 12473836--12473879 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
12473826 ATGGTGATGG
* * *
12473836 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12473878 AT
1 AT
12473880 GTTTGCACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:12475603 original size:43 final size:42
Alignment explanation
Indices: 12475485--12475605 Score: 170
Period size: 42 Copynumber: 2.9 Consensus size: 42
12475475 GATATTGACT
* *
12475485 CGGCTATGTGCAAGTGGGAGTGCGCATAAGCCGATGCTGACC
1 CGGCTATGTGCAAGTGGGAGTGCGCATAAGCTGATGCTAACC
*
12475527 CGGCTATGTGCGAGTGGGAGTGCGCATAAGCTGATGCTAACC
1 CGGCTATGTGCAAGTGGGAGTGCGCATAAGCTGATGCTAACC
* * **
12475569 CGGCCATGTGCTAGTGGGGAGTGCATATAAGCTGATG
1 CGGCTATGTGCAAGT-GGGAGTGCGCATAAGCTGATG
12475606 ATGATGGATA
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 52 0.73
43 19 0.27
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.21
Consensus pattern (42 bp):
CGGCTATGTGCAAGTGGGAGTGCGCATAAGCTGATGCTAACC
Found at i:12480019 original size:20 final size:21
Alignment explanation
Indices: 12479996--12480034 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
12479986 AAGTGAGTTA
*
12479996 TTTAATTTTA-TATTATTTCT
1 TTTAATTTGATTATTATTTCT
12480016 TTTAATTTGATTATTATTT
1 TTTAATTTGATTATTATTT
12480035 ATTAGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (21 bp):
TTTAATTTGATTATTATTTCT
Found at i:12486705 original size:46 final size:46
Alignment explanation
Indices: 12486652--12486760 Score: 200
Period size: 46 Copynumber: 2.4 Consensus size: 46
12486642 CTTGCCACAC
12486652 TCAGCTCATGTGCACTCCCTACACACACAATGCAATATCATCATCA
1 TCAGCTCATGTGCACTCCCTACACACACAATGCAATATCATCATCA
**
12486698 TCAGCTCATGTGCACTCCCTACATGCACAATGCAATATCATCATCA
1 TCAGCTCATGTGCACTCCCTACACACACAATGCAATATCATCATCA
12486744 TCAGCTCATGTGCACTC
1 TCAGCTCATGTGCACTC
12486761 ACACACCGCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 61 1.00
ACGTcount: A:0.29, C:0.34, G:0.11, T:0.26
Consensus pattern (46 bp):
TCAGCTCATGTGCACTCCCTACACACACAATGCAATATCATCATCA
Found at i:12486738 original size:40 final size:43
Alignment explanation
Indices: 12486652--12486848 Score: 150
Period size: 46 Copynumber: 4.4 Consensus size: 43
12486642 CTTGCCACAC
12486652 TCAGCTCATGTGCACTCCCTACACACACAATGCAATATCATCATCA
1 TCAGCTCATGTGCACTCCCTACACACACAATGC-A-A-CATCATCA
**
12486698 TCAGCTCATGTGCACTCCCTACATGCACAATGCAATATCATCATCA
1 TCAGCTCATGTGCACTCCCTACACACACAATGC-A-A-CATCATCA
* * ***** *
12486744 TCAGCTCATGTGCACTCAC-ACAC-CGCACATAGTTGGGTCATCC
1 TCAGCTCATGTGCACTCCCTACACACACA-AT-GCAACATCATCA
* * **
12486787 TCAGCTCATGTGCACTCCC-ACAC-CGCATATAGCTAGGTCATCA
1 TCAGCTCATGTGCACTCCCTACACACACA-AT-GCAACATCATCA
12486830 TCAGCTCATGTGCACTCCC
1 TCAGCTCATGTGCACTCCC
12486849 ACATCGCATA
Statistics
Matches: 133, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
43 62 0.47
44 3 0.02
45 5 0.04
46 63 0.47
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (43 bp):
TCAGCTCATGTGCACTCCCTACACACACAATGCAACATCATCA
Found at i:12486772 original size:46 final size:45
Alignment explanation
Indices: 12486652--12486856 Score: 201
Period size: 43 Copynumber: 4.6 Consensus size: 45
12486642 CTTGCCACAC
*
12486652 TCAGCTCATGTGCACTCCCTACACACACAATGCAATATCATCATCA
1 TCAGCTCATGTGCACTCCC-ACACGCACAATGCAATATCATCATCA
*
12486698 TCAGCTCATGTGCACTCCCTACATGCACAATGCAATATCATCATCA
1 TCAGCTCATGTGCACTCCC-ACACGCACAATGCAATATCATCATCA
* * ** *
12486744 TCAGCTCATGTGCACTCACACACCGCAC-AT--AGT-TGGGTCATCC
1 TCAGCTCATGTGCACTCCCACA-CGCACAATGCAATAT-CATCATCA
* **
12486787 TCAGCTCATGTGCACTCCCACACCGCA-TATAGC--TA-GGTCATCA
1 TCAGCTCATGTGCACTCCCACA-CGCACAAT-GCAATATCATCATCA
12486830 TCAGCTCATGTGCACTCCCACATCGCA
1 TCAGCTCATGTGCACTCCCACA-CGCA
12486857 TATAGTTGGG
Statistics
Matches: 141, Mismatches: 11, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
42 1 0.01
43 68 0.48
44 1 0.01
45 5 0.04
46 66 0.47
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (45 bp):
TCAGCTCATGTGCACTCCCACACGCACAATGCAATATCATCATCA
Found at i:12486785 original size:43 final size:43
Alignment explanation
Indices: 12486738--12486873 Score: 209
Period size: 43 Copynumber: 3.2 Consensus size: 43
12486728 TGCAATATCA
* *
12486738 TCATCATCAGCTCATGTGCACTCACACACCGCACATAGTTGGG
1 TCATCATCAGCTCATGTGCACTCCCACACCGCATATAGTTGGG
* * *
12486781 TCATCCTCAGCTCATGTGCACTCCCACACCGCATATAGCTAGG
1 TCATCATCAGCTCATGTGCACTCCCACACCGCATATAGTTGGG
*
12486824 TCATCATCAGCTCATGTGCACTCCCACATCGCATATAGTTGGG
1 TCATCATCAGCTCATGTGCACTCCCACACCGCATATAGTTGGG
*
12486867 TCCTCAT
1 TCATCAT
12486874 TATCACACAA
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.26
Consensus pattern (43 bp):
TCATCATCAGCTCATGTGCACTCCCACACCGCATATAGTTGGG
Found at i:12486785 original size:89 final size:86
Alignment explanation
Indices: 12486692--12486873 Score: 224
Period size: 86 Copynumber: 2.1 Consensus size: 86
12486682 TGCAATATCA
*
12486692 TCATCATCAGCTCATGTGCACTCCCTACA-TGCACAAT-GCAATATCATCATCATCAGCTCATGT
1 TCATCATCAGCTCATGTGCACTCCC-ACACCGCA-AATAGC--TA-CATCATCATCAGCTCATGT
12486755 GCACTCACACACCGCACATAGTTGGG
61 GCACTCACACACCGCACATAGTTGGG
* * **
12486781 TCATCCTCAGCTCATGTGCACTCCCACACCGCATATAGCTAGGTCATCATCAGCTCATGTGCACT
1 TCATCATCAGCTCATGTGCACTCCCACACCGCAAATAGCTACATCATCATCAGCTCATGTGCACT
* * *
12486846 CCCACATCGCATATAGTTGGG
66 CACACACCGCACATAGTTGGG
*
12486867 TCCTCAT
1 TCATCAT
12486874 TATCACACAA
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
86 45 0.56
87 2 0.02
88 5 0.06
89 29 0.36
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.26
Consensus pattern (86 bp):
TCATCATCAGCTCATGTGCACTCCCACACCGCAAATAGCTACATCATCATCAGCTCATGTGCACT
CACACACCGCACATAGTTGGG
Found at i:12487282 original size:21 final size:21
Alignment explanation
Indices: 12487249--12487300 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
12487239 TGAGATGGGA
*
12487249 GGAAAAAGAAGAAGAAGCTACT
1 GGAAAATG-AGAAGAAGCTACT
*
12487271 GGAAAATGAGAAGAAGCTATT
1 GGAAAATGAGAAGAAGCTACT
12487292 GGAAAATGA
1 GGAAAATGA
12487301 TATTTATAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.52, C:0.06, G:0.29, T:0.13
Consensus pattern (21 bp):
GGAAAATGAGAAGAAGCTACT
Found at i:12492257 original size:22 final size:22
Alignment explanation
Indices: 12492232--12492280 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12492222 TCGTTGCAGT
12492232 GAGAATCCATTTTCGCTACAGC
1 GAGAATCCATTTTCGCTACAGC
* * * *
12492254 GAGAATTCTTTTTCGCTGCAGT
1 GAGAATCCATTTTCGCTACAGC
12492276 GAGAA
1 GAGAA
12492281 ACAGGGCTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (22 bp):
GAGAATCCATTTTCGCTACAGC
Found at i:12492633 original size:43 final size:43
Alignment explanation
Indices: 12492567--12492659 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
12492557 AGTCGGGTCA
* *
12492567 TCATCATCGACTTATGCGCACTCCCTAC-TAACACATAGCC-GGG
1 TCATCATCAACTCATGCGCACTCCC-ACATAACACATA-CCTGGG
* * *
12492610 TCATCATCAACTCATGTGTACTCCCACATCACACATACCTGGG
1 TCATCATCAACTCATGCGCACTCCCACATAACACATACCTGGG
12492653 TCATCAT
1 TCATCAT
12492660 TATCACACAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.27, C:0.34, G:0.13, T:0.26
Consensus pattern (43 bp):
TCATCATCAACTCATGCGCACTCCCACATAACACATACCTGGG
Found at i:12498740 original size:21 final size:21
Alignment explanation
Indices: 12498716--12498758 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
12498706 AGGAAGAAGA
* * *
12498716 AGAAGAAGTTGCTGGAAAATG
1 AGAAGAAGCTACTGAAAAATG
*
12498737 AGAATAAGCTACTGAAAAATG
1 AGAAGAAGCTACTGAAAAATG
12498758 A
1 A
12498759 TATTTATAGC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.26, T:0.19
Consensus pattern (21 bp):
AGAAGAAGCTACTGAAAAATG
Found at i:12500897 original size:51 final size:49
Alignment explanation
Indices: 12500830--12500997 Score: 151
Period size: 50 Copynumber: 3.3 Consensus size: 49
12500820 CTTGATCTCA
* *
12500830 TTAAAAAGTAAGAATCCCTTGTGTAGATTGTGTAAGAGTTATTGCTTCTAT-
1 TTAAAAAGCAAGAATCCCTT-TGTGGATTGTGTAAG-GTTATTGCTTCT-TG
* * * *
12500881 TTGAAAAGCAATAATCCCTTTGTGGATTATGCAAGGATTATCT-CTTCTTG
1 TTAAAAAGCAAGAATCCCTTTGTGGATTGTGTAAGG-TTAT-TGCTTCTTG
* * * ***
12500931 TTAAAAAGCTAGAATCCTTTTATGGATTGTGTAAGGGTTATTGCTTCCCA
1 TTAAAAAGCAAGAATCCCTTTGTGGATTGTGTAA-GGTTATTGCTTCTTG
*
12500981 TTAAAAAACAAGAATCC
1 TTAAAAAGCAAGAATCC
12500998 TTGATAATGG
Statistics
Matches: 94, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
49 3 0.03
50 71 0.76
51 20 0.21
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (49 bp):
TTAAAAAGCAAGAATCCCTTTGTGGATTGTGTAAGGTTATTGCTTCTTG
Found at i:12509307 original size:19 final size:19
Alignment explanation
Indices: 12509257--12509307 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
12509247 GCTATAAATA
* *
12509257 TCTTTTTCTTCCAGCATCT
1 TCTTCTTCTTCCAGCAGCT
*
12509276 TCTTCATTC-TCCAGTAGCT
1 TCTTC-TTCTTCCAGCAGCT
12509295 TCTTCTTCTTCCA
1 TCTTCTTCTTCCA
12509308 TCTAACGTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.12, C:0.33, G:0.06, T:0.49
Consensus pattern (19 bp):
TCTTCTTCTTCCAGCAGCT
Found at i:12510183 original size:43 final size:43
Alignment explanation
Indices: 12510105--12510186 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
12510095 TTAACTCGGC
* * *
12510105 TATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGACCCGGT
1 TATGTGCGAGTAGAGAGTGCACATAAACCGATGATGACCCGGT
* *
12510148 TATGTGCGAGTAGAGAGTGCACATAAATCGGTGATGACC
1 TATGTGCGAGTAGAGAGTGCACATAAACCGATGATGACC
12510187 TAGCCATGCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.27, C:0.17, G:0.34, T:0.22
Consensus pattern (43 bp):
TATGTGCGAGTAGAGAGTGCACATAAACCGATGATGACCCGGT
Found at i:12513910 original size:17 final size:17
Alignment explanation
Indices: 12513888--12513922 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12513878 GAGCAAAACC
12513888 TTGTTGATTCTCTTGTT
1 TTGTTGATTCTCTTGTT
12513905 TTGTTGATTCTCTTGTT
1 TTGTTGATTCTCTTGTT
12513922 T
1 T
12513923 AAGTTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.11, G:0.17, T:0.66
Consensus pattern (17 bp):
TTGTTGATTCTCTTGTT
Found at i:12518191 original size:25 final size:26
Alignment explanation
Indices: 12518161--12518224 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
12518151 ATATCACTTG
*
12518161 TGGCCTAGCCAC-ATATCATA-ACCAA
1 TGGCCTAGCCACGATATCAAAGACC-A
*
12518186 TGGCCTTGCCACGTATATCAAAGACCA
1 TGGCCTAGCCACG-ATATCAAAGACCA
12518213 TGGCCTCAGCCA
1 TGGCCT-AGCCA
12518225 TGTCTAACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 11 0.34
27 14 0.44
28 7 0.22
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (26 bp):
TGGCCTAGCCACGATATCAAAGACCA
Found at i:12519630 original size:4 final size:4
Alignment explanation
Indices: 12519608--12519666 Score: 54
Period size: 4 Copynumber: 15.2 Consensus size: 4
12519598 CCTTTCCTTC
* *
12519608 CTTT CTCT CTTT -TTT -TTT CTTT CTTT CTTT CCTTT CCTTT CTCT -TTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT -CTTT -CTTT CTTT CTTT
12519655 C-TT CTTT CTTT C
1 CTTT CTTT CTTT C
12519667 CTCTCCTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
3 11 0.23
4 27 0.57
5 9 0.19
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:12519660 original size:28 final size:29
Alignment explanation
Indices: 12519599--12519688 Score: 105
Period size: 28 Copynumber: 3.1 Consensus size: 29
12519589 AAAATCGAGC
* *
12519599 CTTTCCTTCCTTTCTCTCTTT-TTTTTTCTTT
1 CTTTCTTTCCTTTC-C-CTTTCTCTTTTC-TT
12519630 CTTTCTTTCCTTT-CCTTTCTCTTTTCTT
1 CTTTCTTTCCTTTCCCTTTCTCTTTTCTT
*
12519658 CTTTCTTTCCTCT-CCTTTCTCTTTTCTT
1 CTTTCTTTCCTTTCCCTTTCTCTTTTCTT
12519686 CTT
1 CTT
12519689 GGTTATGGGC
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
28 36 0.65
29 7 0.13
31 12 0.22
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (29 bp):
CTTTCTTTCCTTTCCCTTTCTCTTTTCTT
Found at i:12519663 original size:36 final size:35
Alignment explanation
Indices: 12519599--12519666 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
12519589 AAAATCGAGC
*
12519599 CTTTCCTTCCTTTCTCTCTTTTTTTTTCTTTCTTT
1 CTTTCCTTCCTTTCTCTCTTTTTCTTTCTTTCTTT
12519634 CTTTCCTTTCCTTTCTCT-TTTCTTCTTTCTTTC
1 CTTTCC-TTCCTTTCTCTCTTT-TTCTTTCTTTC
12519667 CTCTCCTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 9 0.30
36 21 0.70
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (35 bp):
CTTTCCTTCCTTTCTCTCTTTTTCTTTCTTTCTTT
Found at i:12519675 original size:14 final size:14
Alignment explanation
Indices: 12519630--12519677 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
12519620 TTTTTTCTTT
*
12519630 CTTTCTTTCCTTTC
1 CTTTCTTTCCTCTC
* *
12519644 CTTTCTCTT-TTCTT
1 CTTTCT-TTCCTCTC
12519658 CTTTCTTTCCTCTC
1 CTTTCTTTCCTCTC
12519672 CTTTCT
1 CTTTCT
12519678 CTTTTCTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
13 2 0.07
14 23 0.85
15 2 0.07
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (14 bp):
CTTTCTTTCCTCTC
Found at i:12521720 original size:24 final size:24
Alignment explanation
Indices: 12521692--12521741 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
12521682 TTATTCTATC
*
12521692 TATTAACCCATCTTGGCTATCATA
1 TATTAACCCATCTTAGCTATCATA
*
12521716 TATTAACCCCTCTTAGCTATCATA
1 TATTAACCCATCTTAGCTATCATA
12521740 TA
1 TA
12521742 ACTTAGAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (24 bp):
TATTAACCCATCTTAGCTATCATA
Found at i:12525614 original size:52 final size:52
Alignment explanation
Indices: 12525536--12525638 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
12525526 TCCCACATGA
12525536 CACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCACTATCACG
1 CACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCACTATCACG
* *
12525588 CACATGGCATATATCATCAGTGTGTGCACTCACATAGCACACCACTATCAC
1 CACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCACTATCAC
12525639 TGTCATGTGC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (52 bp):
CACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCACTATCACG
Found at i:12526145 original size:17 final size:17
Alignment explanation
Indices: 12526123--12526156 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12526113 ACTAAGAATA
*
12526123 AATAAACAACCCTCAAC
1 AATAAACAACCCACAAC
*
12526140 AATAAATAACCCACAAC
1 AATAAACAACCCACAAC
12526157 TCTAATTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.32, G:0.00, T:0.12
Consensus pattern (17 bp):
AATAAACAACCCACAAC
Found at i:12533258 original size:36 final size:36
Alignment explanation
Indices: 12533211--12533313 Score: 124
Period size: 35 Copynumber: 2.9 Consensus size: 36
12533201 ATGTACATTT
*
12533211 CCACACCGCACATA-GCTAGA-ATCATCTTGTGCACTC
1 CCACACCGCACATAGGC-A-ATATCATCATGTGCACTC
12533247 CCACACCGCACA-AGGCAATATCATCATGTGCACTC
1 CCACACCGCACATAGGCAATATCATCATGTGCACTC
*
12533282 CCACATCGCACAT-GGCATATATCATCAGTGTG
1 CCACACCGCACATAGGCA-ATATCATCA-TGTG
12533314 TGCACTCACA
Statistics
Matches: 60, Mismatches: 2, Indels: 9
0.85 0.03 0.13
Matches are distributed among these distances:
34 1 0.02
35 32 0.53
36 23 0.38
37 4 0.07
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.21
Consensus pattern (36 bp):
CCACACCGCACATAGGCAATATCATCATGTGCACTC
Found at i:12533371 original size:52 final size:52
Alignment explanation
Indices: 12533288--12533399 Score: 197
Period size: 52 Copynumber: 2.2 Consensus size: 52
12533278 ACTCCCACAT
12533288 CGCACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCA
1 CGCACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCA
* * *
12533340 CGCATATGGCATATATCATCAGTGTGTGCACTCGCACAGCACAGCACTATCA
1 CGCACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCA
12533392 CGCACATG
1 CGCACATG
12533400 ATGTCACAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.21
Consensus pattern (52 bp):
CGCACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCA
Found at i:12558964 original size:2 final size:2
Alignment explanation
Indices: 12558946--12558985 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
12558936 GCATGATGAC
* * *
12558946 AT AT GT AT AT GT AT AT AT AT AT AT AT AT AT AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12558986 GTTCCAGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12572088 original size:11 final size:11
Alignment explanation
Indices: 12572074--12572112 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
12572064 AGGCCAAAAC
12572074 AAGAACAAAGG
1 AAGAACAAAGG
12572085 AAGAACAAAGG
1 AAGAACAAAGG
12572096 AAG-A-AAA-G
1 AAGAACAAAGG
12572104 AAGAACAAA
1 AAGAACAAA
12572113 AACCATAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 4 0.15
9 4 0.15
10 4 0.15
11 14 0.54
ACGTcount: A:0.69, C:0.08, G:0.23, T:0.00
Consensus pattern (11 bp):
AAGAACAAAGG
Found at i:12580120 original size:11 final size:11
Alignment explanation
Indices: 12580106--12580144 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
12580096 AGGCCAAAAC
12580106 AAGAACAAAGG
1 AAGAACAAAGG
12580117 AAGAACAAAGG
1 AAGAACAAAGG
12580128 AAG-A-AAA-G
1 AAGAACAAAGG
12580136 AAGAACAAA
1 AAGAACAAA
12580145 AACCATAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 4 0.15
9 4 0.15
10 4 0.15
11 14 0.54
ACGTcount: A:0.69, C:0.08, G:0.23, T:0.00
Consensus pattern (11 bp):
AAGAACAAAGG
Found at i:12585056 original size:43 final size:43
Alignment explanation
Indices: 12584982--12585074 Score: 141
Period size: 43 Copynumber: 2.2 Consensus size: 43
12584972 TTGTATGATA
* * *
12584982 ATGAGGACTCAGCTATGTGCAGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCAGTGTGCGAGTGCACATGAGCTG
**
12585025 ATGATGACCCAGCTATGTGTGGTGTGCGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCAGTGTGCGAGTGCACATGAGCTG
12585068 ATGATGA
1 ATGATGA
12585075 TCTAATGATG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.25
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCAGTGTGCGAGTGCACATGAGCTG
Found at i:12585085 original size:54 final size:54
Alignment explanation
Indices: 12585025--12585129 Score: 183
Period size: 54 Copynumber: 1.9 Consensus size: 54
12585015 ACATGAGCTG
*
12585025 ATGATGACCCAGCTATGTGTGGTGTGCGAGTGCACATGAGCTGATGATGATCTA
1 ATGATGACCCAGCTATGTGCGGTGTGCGAGTGCACATGAGCTGATGATGATCTA
* *
12585079 ATGATGACCCATCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGATGAT
1 ATGATGACCCAGCTATGTGCGGTGTGCGAGTGCACATGAGCTGATGATGAT
12585130 GATATTGCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (54 bp):
ATGATGACCCAGCTATGTGCGGTGTGCGAGTGCACATGAGCTGATGATGATCTA
Found at i:12588397 original size:35 final size:35
Alignment explanation
Indices: 12588347--12588448 Score: 168
Period size: 35 Copynumber: 2.9 Consensus size: 35
12588337 ACCCAGTTCA
* * *
12588347 TGTGCACTCCTTACTCGTACATATCAACATCATCG
1 TGTGCACTCCCTACTCGCACACATCAACATCATCG
*
12588382 TGTGCACTCCCTACTCGCACACATCAACATCATTG
1 TGTGCACTCCCTACTCGCACACATCAACATCATCG
12588417 TGTGCACTCCCTACTCGCACACATCAACATCA
1 TGTGCACTCCCTACTCGCACACATCAACATCA
12588449 CTATCCACAC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.26, C:0.36, G:0.11, T:0.26
Consensus pattern (35 bp):
TGTGCACTCCCTACTCGCACACATCAACATCATCG
Found at i:12590217 original size:21 final size:22
Alignment explanation
Indices: 12590192--12590232 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
12590182 CCTAGGTGGA
12590192 AAAATTCAAGGAAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
12590213 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
12590233 AAAAAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.54, C:0.07, G:0.22, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:12590238 original size:22 final size:21
Alignment explanation
Indices: 12590191--12590238 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
12590181 CCCTAGGTGG
*
12590191 AAAAATTCAAGGAAAAAGTGT
1 AAAAATTCAAGGAAAAAGTGA
*
12590212 GAAAATTCAAGGAAACAAGTGA
1 AAAAATTCAAGGAAA-AAGTGA
12590234 AAAAA
1 AAAAA
12590239 AGGTAAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.60, C:0.06, G:0.19, T:0.15
Consensus pattern (21 bp):
AAAAATTCAAGGAAAAAGTGA
Found at i:12598417 original size:20 final size:20
Alignment explanation
Indices: 12598381--12598418 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12598371 ATATGTCTTG
*
12598381 CATGTTTTATTTATGTTTTA
1 CATGTTTTACTTATGTTTTA
*
12598401 CATGTTTTACTTGTGTTT
1 CATGTTTTACTTATGTTT
12598419 CAAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.08, G:0.13, T:0.63
Consensus pattern (20 bp):
CATGTTTTACTTATGTTTTA
Found at i:12599215 original size:30 final size:30
Alignment explanation
Indices: 12599181--12599241 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
12599171 TGAGCCTAAA
*
12599181 TATATCCTTTATCATACCTAAATCCTAGCC
1 TATATCCTTTATCATACCTAAACCCTAGCC
*
12599211 TATATCCTTTATCATACTTAAACCCTAGCC
1 TATATCCTTTATCATACCTAAACCCTAGCC
12599241 T
1 T
12599242 TACACTACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.30, G:0.03, T:0.38
Consensus pattern (30 bp):
TATATCCTTTATCATACCTAAACCCTAGCC
Found at i:12599772 original size:20 final size:20
Alignment explanation
Indices: 12599744--12599791 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
12599734 TTATAATTTG
*
12599744 TTTATTTTTAAGTTAGTTAC-
1 TTTAATTTTAAGTTA-TTACT
* *
12599764 TTTAATTTTATGTTATTTCT
1 TTTAATTTTAAGTTATTACT
12599784 TTTAATTT
1 TTTAATTT
12599792 GGTTATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67
Consensus pattern (20 bp):
TTTAATTTTAAGTTATTACT
Found at i:12602815 original size:2 final size:2
Alignment explanation
Indices: 12602808--12602835 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12602798 AATTGAAGCT
12602808 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12602836 TTATGGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12606824 original size:76 final size:74
Alignment explanation
Indices: 12606719--12607219 Score: 318
Period size: 76 Copynumber: 6.6 Consensus size: 74
12606709 TTTCGTGGCG
* ** *
12606719 CACTGAGTCGTTGCAATATTATAAAGTGACACGCCACGTTCCAATTGTTAGATGTCGTTGACATC
1 CACTGAGTCGTTGCAGTATTATAGGGTGACACACCACG-T-CAATTGTTAGATGTCGTTGACATC
12606784 TTGTCATGACA
64 TTGTCATGACA
* * * * * * * *
12606795 CACTGAGTCATTGTAGTATTATAAGGTGACACACCACACTCCAATT-TCACCTATGT-TTTTACA
1 CACTGAGTCGTTGCAGTATTATAGGGTGACACACCAC-GT-CAATTGTTA--GATGTCGTTGACA
* * *
12606858 TTTTGCCGTGACA
62 TCTTGTCATGACA
* * * * * * *
12606871 CTCTGAGTCATTGCAGTATTATAGGGTGACACACCATGCTCTAATT-TCACCTATGTCATTGGCA
1 CACTGAGTCGTTGCAGTATTATAGGGTGACACACCACG-TC-AATTGTTA--GATGTCGTTGACA
*
12606935 TCTTGTCGTGACA
62 TCTTGTCATGACA
* * * * * * ** * *
12606948 CATTAAGTCATTGCAGTATTATAGAGAGGCATGCCACGCTTTAATTGTTAGATGTTGTTGACATC
1 CACTGAGTCGTTGCAGTATTATAGGGTGACACACCACG--TCAATTGTTAGATGTCGTTGACATC
*
12607013 TTGCCATGACA
64 TTGTCATGACA
* * * * * *
12607024 TACCGCCATGTCGTTGCAATATTATAGGGTGACACGCCACG-C--TTGTTAGATGTTGTTGATAT
1 CACTG--A-GTCGTTGCAGTATTATAGGGTGACACACCACGTCAATTGTTAGATGTCGTTGACAT
12607086 CTTGTCATGACA
63 CTTGTCATGACA
* * * * *
12607098 CGCCGCCATGTGGTTGTAGTATTATAGGGTGACACACCA---CACTTGTTAGATGTCGTTGACAT
1 CACTG--A-GTCGTTGCAGTATTATAGGGTGACACACCACGTCAATTGTTAGATGTCGTTGACAT
*
12607160 CTTGTCGTGACA
63 CTTGTCATGACA
* * *
12607172 CGCTGAGTTGTTGCAGTATTATAGGGTGACACAACACACTTCAATTGT
1 CACTGAGTCGTTGCAGTATTATAGGGTGACAC-AC-CACGTCAATTGT
12607220 GTGGCGTCAT
Statistics
Matches: 340, Mismatches: 67, Indels: 36
0.77 0.15 0.08
Matches are distributed among these distances:
71 24 0.07
72 4 0.01
73 2 0.01
74 96 0.28
75 3 0.01
76 129 0.38
77 52 0.15
78 4 0.01
79 26 0.08
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (74 bp):
CACTGAGTCGTTGCAGTATTATAGGGTGACACACCACGTCAATTGTTAGATGTCGTTGACATCTT
GTCATGACA
Found at i:12607049 original size:79 final size:74
Alignment explanation
Indices: 12606958--12607172 Score: 223
Period size: 74 Copynumber: 2.8 Consensus size: 74
12606948 CATTAAGTCA
* *
12606958 TTGCAGTATTATAGAGAGGCATGCCACGCTTTAATTGTTAGATGTTGTTGACATCTTGCCATGAC
1 TTGCAGTATTATAGAGAGACACGCCACGC-----TTGTTAGATGTTGTTGACATCTTGCCATGAC
*
12607023 ATACCGCCATGTCG
61 ACACCGCCATGTCG
* * * * * *
12607037 TTGCAATATTATAGGGTGACACGCCACGCTTGTTAGATGTTGTTGATATCTTGTCATGACACGCC
1 TTGCAGTATTATAGAGAGACACGCCACGCTTGTTAGATGTTGTTGACATCTTGCCATGACACACC
*
12607102 GCCATGTGG
66 GCCATGTCG
* * * * * * * *
12607111 TTGTAGTATTATAGGGTGACACACCACACTTGTTAGATGTCGTTGACATCTTGTCGTGACAC
1 TTGCAGTATTATAGAGAGACACGCCACGCTTGTTAGATGTTGTTGACATCTTGCCATGACAC
12607173 GCTGAGTTGT
Statistics
Matches: 119, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
74 95 0.80
79 24 0.20
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (74 bp):
TTGCAGTATTATAGAGAGACACGCCACGCTTGTTAGATGTTGTTGACATCTTGCCATGACACACC
GCCATGTCG
Found at i:12607082 original size:74 final size:74
Alignment explanation
Indices: 12606992--12607212 Score: 268
Period size: 74 Copynumber: 3.0 Consensus size: 74
12606982 CACGCTTTAA
*
12606992 TTGTTAGATGTTGTTGACATCTTGCCATGACATACCGCCATGTCGTTGCAATATTATAGGGTGAC
1 TTGTTAGATGTTGTTGACATCTTGCCATGACACACCGCCATGTCGTTGCAATATTATAGGGTGAC
* *
12607057 ACGCCACGC
66 ACACCACAC
* * * * * *
12607066 TTGTTAGATGTTGTTGATATCTTGTCATGACACGCCGCCATGTGGTTGTAGTATTATAGGGTGAC
1 TTGTTAGATGTTGTTGACATCTTGCCATGACACACCGCCATGTCGTTGCAATATTATAGGGTGAC
12607131 ACACCACAC
66 ACACCACAC
* * * * * * *
12607140 TTGTTAGATGTCGTTGACATCTTGTCGTGACACGCTG--A-GTTGTTGCAGTATTATAGGGTGAC
1 TTGTTAGATGTTGTTGACATCTTGCCATGACACACCGCCATGTCGTTGCAATATTATAGGGTGAC
*
12607202 ACAACACAC
66 ACACCACAC
12607211 TT
1 TT
12607213 CAATTGTGTG
Statistics
Matches: 131, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
71 32 0.24
72 1 0.01
74 98 0.75
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (74 bp):
TTGTTAGATGTTGTTGACATCTTGCCATGACACACCGCCATGTCGTTGCAATATTATAGGGTGAC
ACACCACAC
Found at i:12611553 original size:81 final size:81
Alignment explanation
Indices: 12611409--12611609 Score: 226
Period size: 81 Copynumber: 2.5 Consensus size: 81
12611399 AATCAGTTTT
* * * ** *
12611409 TCCTTCAGCTTGAACTGATTCAAGGTTTCCATCCCCTCCCGCAACTACCTTGATGACCGCATCGG
1 TCCTTCAACTTGAACTGATTCAAGGTTCCCATCCCCTCCAGCAACTACCTCAATAACCGCATCGG
*
12611474 -TCTGAAGAATATGGTC
66 CT-TGAAGAACATGGTC
* * *
12611490 TCCTTCAACTTGAACTGATTCAAGGTTCCCATCCCCTCTAGCAGCTACCTCAATAACCTCATCGG
1 TCCTTCAACTTGAACTGATTCAAGGTTCCCATCCCCTCCAGCAACTACCTCAATAACCGCATCGG
*
12611555 CTTGAGGAACATGGTC
66 CTTGAAGAACATGGTC
* * * **
12611571 TCCTTC-AGTCTCAACTTATTCAAGGCCCCCATCCCCTCC
1 TCCTTCAACT-TGAACTGATTCAAGGTTCCCATCCCCTCC
12611610 CACAGTTGCA
Statistics
Matches: 101, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
80 2 0.02
81 98 0.97
82 1 0.01
ACGTcount: A:0.22, C:0.34, G:0.15, T:0.28
Consensus pattern (81 bp):
TCCTTCAACTTGAACTGATTCAAGGTTCCCATCCCCTCCAGCAACTACCTCAATAACCGCATCGG
CTTGAAGAACATGGTC
Found at i:12614129 original size:31 final size:31
Alignment explanation
Indices: 12614091--12614151 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
12614081 AAATATATGT
* *
12614091 TGTTACACGCTATACAGACTAAGTAAAATGC
1 TGTTACACGCTATACAAACCAAGTAAAATGC
*
12614122 TGTTACACGCTATGCAAACCAAGTAAAATG
1 TGTTACACGCTATACAAACCAAGTAAAATG
12614152 TTGCATGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (31 bp):
TGTTACACGCTATACAAACCAAGTAAAATGC
Found at i:12615143 original size:23 final size:22
Alignment explanation
Indices: 12614918--12615162 Score: 154
Period size: 23 Copynumber: 10.6 Consensus size: 22
12614908 AAATTTATGT
*
12614918 CATGTCACATATTCAAGCCATGG
1 CATGTCACATATTCCA-CCATGG
12614941 CATGTCACATATTCCATCCATGG
1 CATGTCACATATTCCA-CCATGG
** *
12614964 TGTGTCACATATTCCATCTATGG
1 CATGTCACATATTCCA-CCATGG
*
12614987 CATGTCACATATATTCGCACCATGC
1 CATGTCAC--ATATTC-CACCATGG
* * *
12615012 CATGTCATACATTCTCACCATGC
1 CATGTCACATATTC-CACCATGG
* * *
12615035 CGTGTCACACATTCCCACCATAG
1 CATGTCACATATT-CCACCATGG
* * ** * *
12615058 CTTGTCACAAACTCTAAACCCTGC
1 CATGTCACATA-T-TCCACCATGG
*
12615082 CATGTCACATATTCTCACCATGA
1 CATGTCACATATTC-CACCATGG
**
12615105 TGTGTCACATATTCACACCATGG
1 CATGTCACATATTC-CACCATGG
*
12615128 CATGTCAC--ATTCTCA-CATTAG
1 CATGTCACATATTC-CACCA-TGG
12615149 CATGTCACATATTC
1 CATGTCACATATTC
12615163 TCACTATGTA
Statistics
Matches: 175, Mismatches: 37, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.01
21 16 0.09
22 1 0.01
23 121 0.69
24 15 0.09
25 18 0.10
26 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.30
Consensus pattern (22 bp):
CATGTCACATATTCCACCATGG
Found at i:12615201 original size:67 final size:68
Alignment explanation
Indices: 12615081--12615238 Score: 169
Period size: 67 Copynumber: 2.3 Consensus size: 68
12615071 CTAAACCCTG
* *
12615081 CCATGTCACATATTCTCACCATGATGTGTCACATATTCACACCATGGCATGTC-ACATTCTCACA
1 CCATGTCACATATTCTCACCATGATGTCTCACATATTCACACCAGGGCATGTCAACATTCTCAC-
12615145 T-TA
65 TCTA
* * * * ** *
12615148 GCATGTCACATATTCTCACTATG-TAGTCTCACATATTCTCTCCAGGGTGTGTCATATATTCTCA
1 CCATGTCACATATTCTCACCATGAT-GTCTCACATATTCACACCAGGGCATGTCA-ACATTCTCA
12615212 CTCTA
64 CTCTA
* *
12615217 CCGTGTCACATATTCTCTCCAT
1 CCATGTCACATATTCTCACCAT
12615239 AGCGTGTCAT
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
66 1 0.01
67 43 0.58
68 1 0.01
69 29 0.39
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.35
Consensus pattern (68 bp):
CCATGTCACATATTCTCACCATGATGTCTCACATATTCACACCAGGGCATGTCAACATTCTCACT
CTA
Found at i:12615244 original size:23 final size:23
Alignment explanation
Indices: 12614920--12615247 Score: 140
Period size: 23 Copynumber: 14.2 Consensus size: 23
12614910 ATTTATGTCA
* * *
12614920 TGTCACATATTC-AAGCCATGGCA
1 TGTCACATATTCTCA-CCATAGCG
* *
12614943 TGTCACATATTC-CATCCATGGTG
1 TGTCACATATTCTCA-CCATAGCG
* * *
12614966 TGTCACATATTC-CATCTATGGCA
1 TGTCACATATTCTCA-CCATAGCG
* *
12614989 TGTCACATATATTCGCACCAT-GCCA
1 TGTCAC--ATATTCTCACCATAG-CG
* *
12615014 TGTCATACATTCTCACCAT-GCCG
1 TGTCACATATTCTCACCATAG-CG
* * *
12615037 TGTCACACATTCCCACCATAGCT
1 TGTCACATATTCTCACCATAGCG
* * * * *
12615060 TGTCACAAACTCTAAACCCT-GCCA
1 TGTCACATATTCT-CACCATAG-CG
*
12615084 TGTCACATATTCTCACCAT-GATG
1 TGTCACATATTCTCACCATAG-CG
* * *
12615107 TGTCACATATTCACACCATGGCA
1 TGTCACATATTCTCACCATAGCG
*
12615130 TGTCAC--ATTCTCA-CATTAGCA
1 TGTCACATATTCTCACCA-TAGCG
* *
12615151 TGTCACATATTCTCACTAT-GTAG
1 TGTCACATATTCTCACCATAG-CG
* * ** *
12615174 TCTCACATATTCTCTCCAGGGTG
1 TGTCACATATTCTCACCATAGCG
* *
12615197 TGTCATATATTCTCACTC-TACCG
1 TGTCACATATTCTCAC-CATAGCG
*
12615220 TGTCACATATTCTCTCCATAGCG
1 TGTCACATATTCTCACCATAGCG
12615243 TGTCA
1 TGTCA
12615248 TAAACTATTA
Statistics
Matches: 238, Mismatches: 51, Indels: 32
0.74 0.16 0.10
Matches are distributed among these distances:
20 2 0.01
21 16 0.07
22 2 0.01
23 178 0.75
24 22 0.09
25 16 0.07
26 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.32
Consensus pattern (23 bp):
TGTCACATATTCTCACCATAGCG
Found at i:12615302 original size:23 final size:23
Alignment explanation
Indices: 12615276--12615388 Score: 120
Period size: 23 Copynumber: 4.9 Consensus size: 23
12615266 ATGTCACAAT
* *
12615276 CGTGTCACATATTCTCACCATGG
1 CGTGTCACACATTCTCACCATGC
*
12615299 CGTGTCACATATTCTCACCATGC
1 CGTGTCACACATTCTCACCATGC
* * *
12615322 CATGTCATAGATTCTCACCATGC
1 CGTGTCACACATTCTCACCATGC
* * * *
12615345 CATTTAAGACATTCTCACCATGC
1 CGTGTCACACATTCTCACCATGC
12615368 CGTGTCACACATT-TCCACCAT
1 CGTGTCACACATTCT-CACCAT
12615389 TGTGTGTCAC
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
22 1 0.01
23 76 0.99
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.30
Consensus pattern (23 bp):
CGTGTCACACATTCTCACCATGC
Found at i:12616473 original size:32 final size:32
Alignment explanation
Indices: 12616398--12616460 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
12616388 TCAGTTTTTT
12616398 ACAAATAGCTATCTTTTTTTTTTTGTTAAGTA
1 ACAAATAGCTATCTTTTTTTTTTTGTTAAGTA
12616430 ACAAATAGCTATCTTTTTTTTTTTGTTAAGT
1 ACAAATAGCTATCTTTTTTTTTTTGTTAAGT
12616461 TATAGATAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (32 bp):
ACAAATAGCTATCTTTTTTTTTTTGTTAAGTA
Found at i:12626656 original size:14 final size:15
Alignment explanation
Indices: 12626630--12626658 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12626620 TAAATTACAC
12626630 ATTAATCTTATTTAA
1 ATTAATCTTATTTAA
12626645 ATTAAT-TTATTTAA
1 ATTAATCTTATTTAA
12626659 CTATAAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTAATCTTATTTAA
Found at i:12629859 original size:2 final size:2
Alignment explanation
Indices: 12629852--12629881 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12629842 ATTTTTAGTA
12629852 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12629882 GTAGTTTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:12641118 original size:2 final size:2
Alignment explanation
Indices: 12641111--12641154 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12641101 TTTTACGCCA
12641111 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12641153 AT
1 AT
12641155 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12641159 original size:2 final size:2
Alignment explanation
Indices: 12641154--12641184 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12641144 TATATATATA
12641154 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
12641185 ACACACATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:12641220 original size:26 final size:26
Alignment explanation
Indices: 12641191--12641245 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
12641181 GTGTACACAC
* **
12641191 ATACATATGTATGTGTATATGTATAT
1 ATACATATGTATGTATATACATATAT
12641217 ATACATATGTATGTATATACATATAT
1 ATACATATGTATGTATATACATATAT
12641243 ATA
1 ATA
12641246 ACAACATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (26 bp):
ATACATATGTATGTATATACATATAT
Found at i:12641242 original size:18 final size:18
Alignment explanation
Indices: 12641208--12641242 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12641198 TGTATGTGTA
*
12641208 TATGTATATATACATATG
1 TATGTATATACACATATG
*
12641226 TATGTATATACATATAT
1 TATGTATATACACATAT
12641243 ATAACAACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (18 bp):
TATGTATATACACATATG
Found at i:12654163 original size:4 final size:4
Alignment explanation
Indices: 12654156--12654186 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
12654146 TTCTTTCTGT
12654156 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
12654187 TCTTATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:12655709 original size:2 final size:2
Alignment explanation
Indices: 12655702--12655728 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12655692 TGCCATTCAA
12655702 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12655729 GTTATGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12661133 original size:3 final size:3
Alignment explanation
Indices: 12661125--12661153 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12661115 TAAATAAATA
12661125 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12661154 AAAAAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12664127 original size:7 final size:7
Alignment explanation
Indices: 12664115--12664140 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12664105 AATTACTTGA
12664115 TTAAAAT
1 TTAAAAT
12664122 TTAAAAT
1 TTAAAAT
12664129 TTAAAAT
1 TTAAAAT
12664136 TTAAA
1 TTAAA
12664141 CACTATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAAAT
Found at i:12666057 original size:2 final size:2
Alignment explanation
Indices: 12666052--12666077 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12666042 AATAATAAAT
12666052 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
12666078 GAGGAAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12666141 original size:2 final size:2
Alignment explanation
Indices: 12666136--12666161 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12666126 AAAATAAATA
12666136 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
12666162 GAGGAGGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12673947 original size:13 final size:13
Alignment explanation
Indices: 12673929--12673953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12673919 TTTTAGAAAA
12673929 TTTATAAAATCAT
1 TTTATAAAATCAT
12673942 TTTATAAAATCA
1 TTTATAAAATCA
12673954 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:12677328 original size:42 final size:42
Alignment explanation
Indices: 12677255--12677380 Score: 146
Period size: 42 Copynumber: 3.0 Consensus size: 42
12677245 CAGCTCATAT
* * *
12677255 GCAACGGCTTATGCGTACTTCTACTCGCACATAGTCGGGTCA
1 GCAACGGCTTATGCGCACTCCTACTCTCACATAGTCGGGTCA
* * *
12677297 GCAATGGCTTATGCGCACTCCCACTCTCACATAGTCGGGTTA
1 GCAACGGCTTATGCGCACTCCTACTCTCACATAGTCGGGTCA
* * * *
12677339 GTAACGGCTTAAGCGCACTCTTACT-TGCACATAGCCGGGTCA
1 GCAACGGCTTATGCGCACTCCTACTCT-CACATAGTCGGGTCA
12677381 ATATCATTAC
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
41 1 0.01
42 69 0.99
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.25
Consensus pattern (42 bp):
GCAACGGCTTATGCGCACTCCTACTCTCACATAGTCGGGTCA
Found at i:12681398 original size:38 final size:40
Alignment explanation
Indices: 12681356--12681458 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 40
12681346 ATAGTGCTCG
*
12681356 TGTGCACGATGTGGGGGGATGTACACGATGAC-ACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGACGACGGATA
* * * *
12681394 TGTGCATGATGTGGGGGGATGCACACGATGACGTCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGACGACGGATA
*
12681434 TGTGCACTATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
12681459 TGAGCCGGGT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 30 0.55
39 3 0.05
40 22 0.40
ACGTcount: A:0.21, C:0.16, G:0.39, T:0.24
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGACGACGGATA
Found at i:12687610 original size:2 final size:2
Alignment explanation
Indices: 12687605--12687643 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12687595 ATATTTAGAT
12687605 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
12687644 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12688138 original size:20 final size:21
Alignment explanation
Indices: 12688104--12688143 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12688094 AGGAGAAGAA
*
12688104 GAAGAAGTTGCTGG-AGAAAT
1 GAAGAAGCTGCTGGAAGAAAT
*
12688124 GAAGAAGCTGTTGGAAGAAA
1 GAAGAAGCTGCTGGAAGAAA
12688144 ATGATATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.42, C:0.05, G:0.35, T:0.17
Consensus pattern (21 bp):
GAAGAAGCTGCTGGAAGAAAT
Found at i:12690517 original size:77 final size:81
Alignment explanation
Indices: 12690353--12690519 Score: 218
Period size: 77 Copynumber: 2.1 Consensus size: 81
12690343 AAATACCATC
* *
12690353 TATTTTAATTTTGGGTGATTCGAAAAAAAAAAGAAGGGAAATTGTTTCCTACTTTAAAAGCAATT
1 TATTTTAATTTTGGGTGATTC--AAAAAAAAAGAAGGGAAATTCTTTCCTACTTTAAAAGAAATT
*
12690418 CCTAAAATTAAGGATAGA
64 CCTAAAATTAAGAATAGA
* * *
12690436 -ATTTTAATTTTGGGTGATTC-ATAAAAAA-TA-GGAAATTCTTTCCTACTTTAAAAGAAATTCT
1 TATTTTAATTTTGGGTGATTCAAAAAAAAAGAAGGGAAATTCTTTCCTACTTTAAAAGAAATTCC
*
12690497 TAAAATTTAGAATA-A
66 TAAAATTAAGAATAGA
12690512 TATTTTAA
1 TATTTTAA
12690520 ATTAGGAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
76 1 0.01
77 47 0.62
78 1 0.01
79 7 0.09
82 20 0.26
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (81 bp):
TATTTTAATTTTGGGTGATTCAAAAAAAAAGAAGGGAAATTCTTTCCTACTTTAAAAGAAATTCC
TAAAATTAAGAATAGA
Found at i:12695560 original size:43 final size:42
Alignment explanation
Indices: 12695490--12695623 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 42
12695480 CTGGGTCATT
* **
12695490 ATCATCGGCTTTTGCGCACTTTGTACTCGCACATAGTCGGGTC
1 ATCATCGGCTTATGCGCAC-TCCTACTCGCACATAGTCGGGTC
* * * *
12695533 ATCATCGGCTTATGCACACTCCCTACTCACACATAGTTGGATC
1 ATCATCGGCTTATGCGCACT-CCTACTCGCACATAGTCGGGTC
* * * *
12695576 ATCATCAGCTCATGTGCACTCTTACATCGCACATAG-CTGGGTC
1 ATCATCGGCTTATGCGCACTCCTAC-TCGCACATAGTC-GGGTC
12695619 ATCAT
1 ATCAT
12695624 TATCACACAA
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
42 5 0.07
43 68 0.93
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (42 bp):
ATCATCGGCTTATGCGCACTCCTACTCGCACATAGTCGGGTC
Found at i:12699507 original size:35 final size:34
Alignment explanation
Indices: 12699441--12699510 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
12699431 TTTCACCAAG
* * *
12699441 CTTTACAATGGCTTTTACTAGGCTCAGCCAAAAC
1 CTTTACAATGGCTTTTACCAGGATCAACCAAAAC
* *
12699475 CTTTCACAATGGTTTTTACCGGGATCAACCAAAAC
1 CTTT-ACAATGGCTTTTACCAGGATCAACCAAAAC
12699510 C
1 C
12699511 CAACAACTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 4 0.13
35 26 0.87
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (34 bp):
CTTTACAATGGCTTTTACCAGGATCAACCAAAAC
Found at i:12728033 original size:35 final size:36
Alignment explanation
Indices: 12727967--12728058 Score: 98
Period size: 35 Copynumber: 2.6 Consensus size: 36
12727957 TCAAGTGAAA
** *
12727967 CCTTCACAATAGCTTTTTAATGGGATTAAGCAAAAC
1 CCTTCACAATAGCTTTTTAACAGGATCAAGCAAAAC
* *
12728003 CCTT-ACAATAGCTTTTTCACAGGATCAAGCATAAC
1 CCTTCACAATAGCTTTTTAACAGGATCAAGCAAAAC
* *
12728038 CTTTCAACAAT-GGTTTTTAAC
1 CCTTC-ACAATAGCTTTTTAAC
12728059 GGGCTTAACC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 29 0.63
36 12 0.26
37 5 0.11
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.33
Consensus pattern (36 bp):
CCTTCACAATAGCTTTTTAACAGGATCAAGCAAAAC
Found at i:12735271 original size:39 final size:39
Alignment explanation
Indices: 12735136--12735312 Score: 132
Period size: 39 Copynumber: 4.6 Consensus size: 39
12735126 TTCCCCTGGC
**
12735136 TCATGTGCACTCCCACACCGCACATTACAATATCATC-A
1 TCATGTGCACTCCCACACCGCACACGACAATATCATCGA
* ** ** *
12735174 TCAGGTGCACTCCCACA-C-CACACCTCACCATCA-CTA
1 TCATGTGCACTCCCACACCGCACACGACAATATCATCGA
* *
12735210 TCAAGTGCACTCCTACACCGCACACGACAAATATCATC-A
1 TCATGTGCACTCCCACACCGCACACGAC-AATATCATCGA
* * * * * *
12735249 TCATGTGCTCTCCCACAACGCACATGGCGTATATCATCGG
1 TCATGTGCACTCCCACACCGCACACGAC-AATATCATCGA
* *
12735289 T-GTGTGCTCTCCCACACCGCACAC
1 TCATGTGCACTCCCACACCGCACAC
12735313 TACCGACACC
Statistics
Matches: 109, Mismatches: 24, Indels: 11
0.76 0.17 0.08
Matches are distributed among these distances:
35 1 0.01
36 26 0.24
37 2 0.02
38 22 0.20
39 56 0.51
40 2 0.02
ACGTcount: A:0.28, C:0.39, G:0.12, T:0.21
Consensus pattern (39 bp):
TCATGTGCACTCCCACACCGCACACGACAATATCATCGA
Found at i:12737302 original size:27 final size:27
Alignment explanation
Indices: 12737271--12737330 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
12737261 TCAAATAAGA
* * *
12737271 AATTTTACTATCTCG-GGGTAAAATGGT
1 AATTTTACCA-CTCGAGGATAAAATGGG
*
12737298 AATTTTGCCACTCGAGGATAAAATGGG
1 AATTTTACCACTCGAGGATAAAATGGG
12737325 AATTTT
1 AATTTT
12737331 TTTAAACAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.35
Consensus pattern (27 bp):
AATTTTACCACTCGAGGATAAAATGGG
Found at i:12745683 original size:22 final size:22
Alignment explanation
Indices: 12745640--12745683 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12745630 GGTGAAGAAT
*
12745640 TTCAAGAGAAAAAGTATGAAAA
1 TTCAAGAGAAAAAGTATCAAAA
*
12745662 TTCAAG-GAAACAAGTGTCAAAA
1 TTCAAGAGAAA-AAGTATCAAAA
12745684 GGTAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.55, C:0.09, G:0.18, T:0.18
Consensus pattern (22 bp):
TTCAAGAGAAAAAGTATCAAAA
Found at i:12748618 original size:20 final size:18
Alignment explanation
Indices: 12748575--12748622 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
12748565 AGCCGACCCC
12748575 TTTTTCT-TTTTCTCCTT
1 TTTTTCTCTTTTCTCCTT
*
12748592 TCCTTTCTCTTTTCTTCTCTT
1 T-TTTTCTCTTTTC-TC-CTT
12748613 TTTTTCTCTT
1 TTTTTCTCTT
12748623 CTCGAGTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 1 0.04
18 5 0.20
19 5 0.20
20 10 0.40
21 4 0.16
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTCTCTTTTCTCCTT
Found at i:12751519 original size:2 final size:2
Alignment explanation
Indices: 12751512--12751559 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
12751502 AAAGAAGGAA
12751512 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12751554 AT AT AT
1 AT AT AT
12751560 GAAAGCATAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12753807 original size:25 final size:28
Alignment explanation
Indices: 12753744--12753813 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
12753734 TCGACGTTCT
*
12753744 ATTAGATGTGGCTAAGCCACGGTTTGTG
1 ATTATATGTGGCTAAGCCACGGTTTGTG
*
12753772 ATTATATGTGGCAAAGCCACGG-TT-TG
1 ATTATATGTGGCTAAGCCACGGTTTGTG
12753798 -TTATATGTGGCTAAGC
1 ATTATATGTGGCTAAGC
12753814 TATGAGTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
25 15 0.38
26 2 0.05
27 2 0.05
28 20 0.51
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (28 bp):
ATTATATGTGGCTAAGCCACGGTTTGTG
Found at i:12755964 original size:34 final size:34
Alignment explanation
Indices: 12755921--12755989 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 34
12755911 CTTGCCCAAC
12755921 AACATTTAGGTTGCAAAGAG-TTCAATTAAACCT
1 AACATTTAGGTTGCAAAGAGTTTCAATTAAACCT
12755954 NAACATTTAGGTTGCAAAGAGTTTCAATTAAACCT
1 -AACATTTAGGTTGCAAAGAGTTTCAATTAAACCT
12755989 A
1 A
12755990 GCCCTGACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 21 0.62
35 13 0.38
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.30
Consensus pattern (34 bp):
AACATTTAGGTTGCAAAGAGTTTCAATTAAACCT
Found at i:12773102 original size:35 final size:35
Alignment explanation
Indices: 12772986--12773103 Score: 94
Period size: 35 Copynumber: 3.4 Consensus size: 35
12772976 GTGAGAAAGA
*
12772986 GAGGTTGTGTTGCTGCTGGTTTGTGCAGGAAAAATG
1 GAGGTTGTG-TGCTGCTGGTTTGTGAAGGAAAAATG
* * ** * * ** * * *
12773022 GAGGCTGTTTTTTACCGAATTGTGAAAGATAAAGG
1 GAGGTTGTGTGCTGCTGGTTTGTGAAGGAAAAATG
* *
12773057 GAGCTT-TGTGCTGCTGGTTTGTGTAGGAAAAATG
1 GAGGTTGTGTGCTGCTGGTTTGTGAAGGAAAAATG
12773091 GAGGTTGTGTGCT
1 GAGGTTGTGTGCT
12773104 ACCACTTAGA
Statistics
Matches: 55, Mismatches: 26, Indels: 3
0.65 0.31 0.04
Matches are distributed among these distances:
34 22 0.40
35 26 0.47
36 7 0.13
ACGTcount: A:0.22, C:0.08, G:0.36, T:0.34
Consensus pattern (35 bp):
GAGGTTGTGTGCTGCTGGTTTGTGAAGGAAAAATG
Found at i:12773351 original size:4 final size:4
Alignment explanation
Indices: 12773344--12773394 Score: 54
Period size: 4 Copynumber: 13.2 Consensus size: 4
12773334 AGAAAGGGGA
* *
12773344 AAAG AAAG AAAG AAAG AAA- AAAA AAAG AAAG -AAG AAAAG AAA- AAAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG
12773390 AAAG A
1 AAAG A
12773395 GTGGGCATGG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 9 0.22
4 29 0.71
5 3 0.07
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:12773370 original size:19 final size:19
Alignment explanation
Indices: 12773343--12773394 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
12773333 AAGAAAGGGG
*
12773343 AAAAGAAAGAAAGAAAGAA
1 AAAAAAAAGAAAGAAAGAA
12773362 AAAAAAAAGAAAG-AAGAA
1 AAAAAAAAGAAAGAAAGAA
*
12773380 AAGAAAAAAAAAAGA
1 AA-AAAAAAGAAAGA
12773395 GTGGGCATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 7 0.24
19 22 0.76
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGAAAGAAAGAA
Found at i:12773373 original size:23 final size:23
Alignment explanation
Indices: 12773343--12773394 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
12773333 AAGAAAGGGG
12773343 AAAAGAAAGAA-AGAAAGAAAAAA
1 AAAAGAAAGAAGA-AAAGAAAAAA
12773366 AAAAGAAAGAAGAAAAGAAAAAA
1 AAAAGAAAGAAGAAAAGAAAAAA
12773389 AAAAGA
1 AAAAGA
12773395 GTGGGCATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAGAAAGAAGAAAAGAAAAAA
Found at i:12784732 original size:27 final size:28
Alignment explanation
Indices: 12784695--12784752 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
12784685 CCCGAACTTC
12784695 TTTCTATTGGGCCATGCCCA-T-TTTTT
1 TTTCTATTGGGCCATGCCCACTCTTTTT
12784721 TTTCTTATTGGGCCATGCCCACTCTTTTT
1 TTTC-TATTGGGCCATGCCCACTCTTTTT
12784750 TTT
1 TTT
12784753 TCTTTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 4 0.14
27 16 0.55
28 1 0.03
29 8 0.28
ACGTcount: A:0.10, C:0.24, G:0.14, T:0.52
Consensus pattern (28 bp):
TTTCTATTGGGCCATGCCCACTCTTTTT
Found at i:12784792 original size:4 final size:5
Alignment explanation
Indices: 12784743--12784791 Score: 66
Period size: 5 Copynumber: 10.0 Consensus size: 5
12784733 CCATGCCCAC
*
12784743 TCTTT TTTTT TCTTTT TCTTT TCTTT TCTTT TCTTT TC-TT TC-TT TCTTT
1 TCTTT TCTTT TC-TTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT
12784792 CACCGCTCAG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 8 0.20
5 27 0.68
6 5 0.12
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TCTTT
Found at i:12785100 original size:34 final size:35
Alignment explanation
Indices: 12785062--12785158 Score: 151
Period size: 35 Copynumber: 2.8 Consensus size: 35
12785052 AAATCGCACC
*
12785062 TTTCAGCCTTCAAAATCAGCAGCAAAGA-TACACT
1 TTTCAGCCTTCAAAATTAGCAGCAAAGACTACACT
* *
12785096 TTTCAGCCTTCAAAATTAGTAGCAAAAACTACACT
1 TTTCAGCCTTCAAAATTAGCAGCAAAGACTACACT
12785131 TTTCAGCCTTCAAAATTAGCAGCTAAAG
1 TTTCAGCCTTCAAAATTAGCAGC-AAAG
12785159 CTGTTCCTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
34 25 0.45
35 28 0.50
36 3 0.05
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (35 bp):
TTTCAGCCTTCAAAATTAGCAGCAAAGACTACACT
Found at i:12788943 original size:11 final size:11
Alignment explanation
Indices: 12788927--12788954 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12788917 CACTGTAAAT
12788927 TTTAAAACAAC
1 TTTAAAACAAC
12788938 TTTAAAACAAC
1 TTTAAAACAAC
12788949 TTTAAA
1 TTTAAA
12788955 CTCAAAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (11 bp):
TTTAAAACAAC
Found at i:12791147 original size:27 final size:27
Alignment explanation
Indices: 12791105--12791165 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 27
12791095 TCTCCCCAAC
*
12791105 TTTTTTCTATTGGGCCATGCCCATT-T
1 TTTTTTCTATTAGGCCATGCCCATTCT
12791131 TTTTTTCTTATTAGGCCATGCCCATTCT
1 TTTTTTC-TATTAGGCCATGCCCATTCT
12791159 TTCTTTT
1 TT-TTTT
12791166 TCTTTTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 7 0.23
27 17 0.55
28 3 0.10
29 4 0.13
ACGTcount: A:0.11, C:0.23, G:0.11, T:0.54
Consensus pattern (27 bp):
TTTTTTCTATTAGGCCATGCCCATTCT
Found at i:12791170 original size:10 final size:10
Alignment explanation
Indices: 12791155--12791214 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 10
12791145 GCCATGCCCA
12791155 TTCTTTCTT-T
1 TTCTTT-TTCT
12791165 TTCTTTTTCT
1 TTCTTTTTCT
12791175 TT-TCTTTTCTT
1 TTCT-TTTTC-T
12791186 TTCTTTTCTCT
1 TTCTTTT-TCT
12791197 TCTCTTATTTCT
1 T-TCTT-TTTCT
12791209 TTCTTT
1 TTCTTT
12791215 CACCGATCAG
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
9 3 0.07
10 15 0.35
11 12 0.28
12 11 0.26
13 2 0.05
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.77
Consensus pattern (10 bp):
TTCTTTTTCT
Found at i:12791176 original size:16 final size:17
Alignment explanation
Indices: 12791155--12791212 Score: 68
Period size: 16 Copynumber: 3.5 Consensus size: 17
12791145 GCCATGCCCA
12791155 TTCTTTCT-TTTTCTTT
1 TTCTTTCTCTTTTCTTT
12791171 TTCTTT-TCTTTTC-TT
1 TTCTTTCTCTTTTCTTT
*
12791186 TTCTTTTCTCTTCTCTTAT
1 TTC-TTTCTCTTTTCTT-T
12791205 TTCTTTCT
1 TTCTTTCT
12791213 TTCACCGATC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 6 0.17
16 14 0.39
17 6 0.17
18 6 0.17
19 4 0.11
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTTTCTCTTTTCTTT
Found at i:12791185 original size:22 final size:22
Alignment explanation
Indices: 12791158--12791202 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
12791148 ATGCCCATTC
*
12791158 TTTCTTTTTCTTTT-TCTTTTCT
1 TTTC-TTTTCTTTTCTCTTCTCT
12791180 TTTCTTTTCTTTTCTCTTCTCT
1 TTTCTTTTCTTTTCTCTTCTCT
12791202 T
1 T
12791203 ATTTCTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTCTTTTCTTTTCTCTTCTCT
Found at i:12791202 original size:5 final size:5
Alignment explanation
Indices: 12791158--12791199 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
12791148 ATGCCCATTC
*
12791158 TTTCTT TTTCTT TTTCT TTTCT TTTCT TTTCT TTTCT CTTCT
1 TTTC-T TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
12791200 CTTATTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 25 0.71
6 10 0.29
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:12791560 original size:35 final size:34
Alignment explanation
Indices: 12791484--12791567 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 34
12791474 AACCGCACCC
* ** * *
12791484 TTCAGCCTTTAAAATCAGTAGCAAAATTGCACTT
1 TTCAGCCTTCAAAATCAGTAAAAAAACTACACTT
*
12791518 TTAAGCCTTCAAAATCAGTAAAAAAAACTACACTT
1 TTCAGCCTTCAAAATCAGT-AAAAAAACTACACTT
12791553 TTCAGCCTTCAAAAT
1 TTCAGCCTTCAAAAT
12791568 TAGCAGCTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 17 0.40
35 25 0.60
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.30
Consensus pattern (34 bp):
TTCAGCCTTCAAAATCAGTAAAAAAACTACACTT
Found at i:12793933 original size:54 final size:54
Alignment explanation
Indices: 12793867--12794045 Score: 270
Period size: 54 Copynumber: 3.3 Consensus size: 54
12793857 TGTAACCGTG
* *
12793867 CATGAGCTGGGTGAGATGTGGTGTCCGGTTATGTGCACAATGTGGTGGGATGCA
1 CATGAGCTGGGTGAGATGTGGTGTCCGGCTATGTGCACGATGTGGTGGGATGCA
* * *
12793921 CATGAGTTGGGTGAGATGTGGTGTTCAGCTATGTGCACGATGTGGTGGGATGCA
1 CATGAGCTGGGTGAGATGTGGTGTCCGGCTATGTGCACGATGTGGTGGGATGCA
*
12793975 CATGAGCTGGGT-AGGATATGGTGTCCGGCTATGTGCACGATGTGGTGGGATGCA
1 CATGAGCTGGGTGA-GATGTGGTGTCCGGCTATGTGCACGATGTGGTGGGATGCA
* *
12794029 CATGAGTTAGGTGAGAT
1 CATGAGCTGGGTGAGAT
12794046 AAAATGTTTT
Statistics
Matches: 112, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.01
54 110 0.98
55 1 0.01
ACGTcount: A:0.20, C:0.12, G:0.40, T:0.28
Consensus pattern (54 bp):
CATGAGCTGGGTGAGATGTGGTGTCCGGCTATGTGCACGATGTGGTGGGATGCA
Found at i:12796755 original size:19 final size:20
Alignment explanation
Indices: 12796720--12796765 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
12796710 ATTTTTTTTG
*
12796720 AAACACAAATAAAACATGCA
1 AAACATAAATAAAACATGCA
12796740 AAACATAAAT-AAACATGCA
1 AAACATAAATAAAACATGCA
*
12796759 AGACATA
1 AAACATA
12796766 TCTTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.63, C:0.17, G:0.07, T:0.13
Consensus pattern (20 bp):
AAACATAAATAAAACATGCA
Found at i:12799065 original size:16 final size:17
Alignment explanation
Indices: 12799041--12799076 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
12799031 CGCTGAACTC
*
12799041 TTTTGTTTTT-CTTTTT
1 TTTTCTTTTTCCTTTTT
12799057 TTTTCTTTTTCCTTTTT
1 TTTTCTTTTTCCTTTTT
12799074 TTT
1 TTT
12799077 GAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (17 bp):
TTTTCTTTTTCCTTTTT
Found at i:12800841 original size:54 final size:54
Alignment explanation
Indices: 12800776--12800935 Score: 250
Period size: 54 Copynumber: 3.0 Consensus size: 54
12800766 ATGGTGATAC
*
12800776 TGTTTGGCTATGTGCACGATGTGGTGGGATGCACATGAGCACGGTGAGATGGGA
1 TGTTTGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTCGGTGAGATGGGA
*
12800830 TGTTTGGCTATGTGCACGTTGTGGTGGGATGCACATGAG-TCGAGTGAGATGGGA
1 TGTTTGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTCG-GTGAGATGGGA
** * *
12800884 TGTCCGGCTATGTGCACGATGTGATGGGATGCACATGAGCTGGGTGAGATGG
1 TGTTTGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTCGGTGAGATGG
12800936 AATGATTACT
Statistics
Matches: 97, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
53 2 0.02
54 93 0.96
55 2 0.02
ACGTcount: A:0.19, C:0.13, G:0.41, T:0.27
Consensus pattern (54 bp):
TGTTTGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTCGGTGAGATGGGA
Found at i:12800857 original size:29 final size:29
Alignment explanation
Indices: 12800776--12800860 Score: 79
Period size: 29 Copynumber: 3.1 Consensus size: 29
12800766 ATGGTGATAC
12800776 TGTTTGGCTATGTGCACGATGTGGTGGGA
1 TGTTTGGCTATGTGCACGATGTGGTGGGA
** * * * *
12800805 TG---CAC-ATGAGCACGGTGAGATGGGA
1 TGTTTGGCTATGTGCACGATGTGGTGGGA
*
12800830 TGTTTGGCTATGTGCACGTTGTGGTGGGA
1 TGTTTGGCTATGTGCACGATGTGGTGGGA
12800859 TG
1 TG
12800861 CACATGAGTC
Statistics
Matches: 40, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
25 18 0.45
26 1 0.03
28 1 0.03
29 20 0.50
ACGTcount: A:0.16, C:0.12, G:0.41, T:0.31
Consensus pattern (29 bp):
TGTTTGGCTATGTGCACGATGTGGTGGGA
Found at i:12802229 original size:200 final size:204
Alignment explanation
Indices: 12801858--12802267 Score: 603
Period size: 200 Copynumber: 2.0 Consensus size: 204
12801848 AGATGGATGG
*
12801858 GGGAGCAAGATGGTCCTAATGAGATGACAGATAGGCCACAAGCATCCACTCTTAGGGGGCGAGGT
1 GGGAGCAAGATGCTCCTAATGAGATGACAGATAGGCCACAAGCATCCACTCTTAGGGGGCGAGGT
* *
12801923 AGACTTGGCGGGGCCACTAGGCCGGTGAGGGCAGATACGCTTATGGGTAAGCGAGAGGAAGGACA
66 AGACATGGCGGGG---CT--G-CGCTGAGGGCAGATACGCTTATGGGTAAGCGAGAGGAAGGACA
* *
12801988 ATCTTCGGGTGATGTGGATAGACAACCAATTGGGGGCATTACCATTGAGGACTTGACGGCAGGCC
125 ACCTTCGGGTGATGTGGATAGACAACCAATTGGGGGCATTACCATTAAGGACTTGACGGCAGGCC
*
12802053 TGCAGGGAGTTAATC
190 TGCAAGGAGTTAATC
** *
12802068 GGGAGCAAGATGCTCCTAATGAGATGACAGATAGGCCACGGGCATCCACTCTTAGGGGTCGAGGT
1 GGGAGCAAGATGCTCCTAATGAGATGACAGATAGGCCACAAGCATCCACTCTTAGGGGGCGAGGT
* * * * *
12802133 AGACATGGTGGGG-T-CGCT-AGGTC-GATATGTTTATGGGTAGGCGAGAGGAAGGACAACCTTC
66 AGACATGGCGGGGCTGCGCTGAGGGCAGATACGCTTATGGGTAAGCGAGAGGAAGGACAACCTTC
*
12802194 GGGTGATGTGGATAGACAACCAATTGGGGGCATTACCATTAAGGACTTGGCGGCAGGCCTGCAAG
131 GGGTGATGTGGATAGACAACCAATTGGGGGCATTACCATTAAGGACTTGACGGCAGGCCTGCAAG
12802259 GAGTTAATC
196 GAGTTAATC
12802268 AGGTTGTAGA
Statistics
Matches: 185, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
200 105 0.57
201 4 0.02
202 3 0.02
206 1 0.01
210 72 0.39
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.20
Consensus pattern (204 bp):
GGGAGCAAGATGCTCCTAATGAGATGACAGATAGGCCACAAGCATCCACTCTTAGGGGGCGAGGT
AGACATGGCGGGGCTGCGCTGAGGGCAGATACGCTTATGGGTAAGCGAGAGGAAGGACAACCTTC
GGGTGATGTGGATAGACAACCAATTGGGGGCATTACCATTAAGGACTTGACGGCAGGCCTGCAAG
GAGTTAATC
Found at i:12819020 original size:21 final size:21
Alignment explanation
Indices: 12818996--12819035 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12818986 TTCCTCCCCT
*
12818996 TTCTCTTTTCT-TTATTCTTTC
1 TTCTCCTTTCTCTT-TTCTTTC
12819017 TTCTCCTTTCTCTTTTCTT
1 TTCTCCTTTCTCTTTTCTT
12819036 CTTGGTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.70
Consensus pattern (21 bp):
TTCTCCTTTCTCTTTTCTTTC
Found at i:12819024 original size:28 final size:29
Alignment explanation
Indices: 12818965--12819035 Score: 108
Period size: 28 Copynumber: 2.4 Consensus size: 29
12818955 TTCCTTCCTT
12818965 TTTCTCTTTTTCTTTATTTCTTTCCTCCCC
1 TTTCTC-TTTTCTTTATTTCTTTCCTCCCC
* *
12818995 TTTCTCTTTTCTTTA-TTCTTTCTTCTCC
1 TTTCTCTTTTCTTTATTTCTTTCCTCCCC
12819023 TTTCTCTTTTCTT
1 TTTCTCTTTTCTT
12819036 CTTGGTTATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 24 0.62
29 9 0.23
30 6 0.15
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.68
Consensus pattern (29 bp):
TTTCTCTTTTCTTTATTTCTTTCCTCCCC
Found at i:12824111 original size:20 final size:21
Alignment explanation
Indices: 12824075--12824114 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12824065 AAAAACTAAT
*
12824075 AAATAACAATCAAATTAAAAG
1 AAATAACAATAAAATTAAAAG
12824096 AAATAAC-ATAAAATTAAAA
1 AAATAACAATAAAATTAAAA
12824115 TAACTCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (21 bp):
AAATAACAATAAAATTAAAAG
Found at i:12827491 original size:38 final size:40
Alignment explanation
Indices: 12827405--12827507 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 40
12827395 ATCCAGCTCA
*
12827405 TGTACATCCCCCCACATCATGCAC-ATAGCCGGAGTCATCG
1 TGTACATCCCCCCACATCGTGCACAATAG-CGGAGTCATCG
* *
12827445 TGTGCATCCCCCCACATCGTGCACAATTAG-TG-G-CATCG
1 TGTACATCCCCCCACATCGTGCACAA-TAGCGGAGTCATCG
12827483 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
12827508 CAGGCACTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
38 29 0.51
39 1 0.02
40 23 0.40
41 1 0.02
42 3 0.05
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (40 bp):
TGTACATCCCCCCACATCGTGCACAATAGCGGAGTCATCG
Found at i:12831924 original size:2 final size:2
Alignment explanation
Indices: 12831917--12831953 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12831907 TATGACATAG
12831917 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12831954 CAACATTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12832970 original size:20 final size:20
Alignment explanation
Indices: 12832933--12832971 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12832923 AAAACCAAGC
* *
12832933 TTTTCTTCCTTTTTCTCTTT
1 TTTTCTTCCTTCTCCTCTTT
*
12832953 TTTTCTTGCTTCTCCTCTT
1 TTTTCTTCCTTCTCCTCTT
12832972 AGGGTTTATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTCTTCCTTCTCCTCTTT
Found at i:12838528 original size:37 final size:37
Alignment explanation
Indices: 12838487--12838593 Score: 196
Period size: 37 Copynumber: 2.9 Consensus size: 37
12838477 AGGTTGTTGA
*
12838487 AGTGTGCGAGTAAGGAGTGCACACATGATGATGTTAG
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGTTAG
12838524 AGTGTGCGAGTAGGGAGTGCACACATGATGATGTTAG
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGTTAG
*
12838561 AGTGTACGAGTAGGGAGTGCACACATGATGATG
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATG
12838594 AATGCATATG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.29, C:0.11, G:0.36, T:0.23
Consensus pattern (37 bp):
AGTGTGCGAGTAGGGAGTGCACACATGATGATGTTAG
Found at i:12858668 original size:18 final size:18
Alignment explanation
Indices: 12858637--12858671 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12858627 AAATCAAGAT
12858637 TTTTCATTTTTTTCCTTG
1 TTTTCATTTTTTTCCTTG
12858655 TTTTC-TTTTCTTTCCTT
1 TTTTCATTTT-TTTCCTT
12858672 TTCTCTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTCATTTTTTTCCTTG
Found at i:12859554 original size:39 final size:37
Alignment explanation
Indices: 12859506--12859736 Score: 107
Period size: 37 Copynumber: 6.4 Consensus size: 37
12859496 AGTGGTGTGC
*
12859506 TGTGTGAGTGCACACATTGATGATATATGCCATGTCCGA
1 TGTGGGAGTGCACACA-TGATGATATATGCCATGT-CGA
* *
12859545 TGTGGGAGTG--CACATGACGATGATAGTG--GTGT--A
1 TGTGGGAGTGCACACATGATGAT-ATA-TGCCATGTCGA
* *
12859578 TTGTGTGAGTGCACACACTGATGATATATGCCATGTGCGG
1 -TGTGGGAGTGCACACA-TGATGATATATGCCATGT-CGA
* * * *
12859618 TGTGGGAGTG--CACATGACGGTGATA-G-TAGTGT-GT
1 TGTGGGAGTGCACACATGATGAT-ATATGCCA-TGTCGA
**
12859652 TGTGTTAGTGCACACACTGATG--ATATGCCATGTGCGA
1 TGTGGGAGTGCACACA-TGATGATATATGCCATGT-CGA
* * * *
12859689 TGTGAGAGTG--CACATGATGATAT-TGCCTTGTGTGG
1 TGTGGGAGTGCACACATGATGATATATGCCATGT-CGA
12859724 TGTGGGAGTGCAC
1 TGTGGGAGTGCAC
12859737 GAGGTGATTT
Statistics
Matches: 145, Mismatches: 23, Indels: 50
0.67 0.11 0.23
Matches are distributed among these distances:
33 1 0.01
34 26 0.18
35 29 0.20
36 32 0.22
37 37 0.26
38 2 0.01
39 18 0.12
ACGTcount: A:0.23, C:0.14, G:0.33, T:0.30
Consensus pattern (37 bp):
TGTGGGAGTGCACACATGATGATATATGCCATGTCGA
Found at i:12859591 original size:73 final size:73
Alignment explanation
Indices: 12859472--12859705 Score: 348
Period size: 73 Copynumber: 3.2 Consensus size: 73
12859462 GCGTGTGTGG
* * *
12859472 TGTGGGAGAGCACATGAC-AGTGATAGTGGTGTGCTGTGTGAGTGCACACATTGATGATATATGC
1 TGTGGGAGTGCACATGACGA-TGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGC
*
12859536 CATGTCCGA
65 CATGTGCGA
*
12859545 TGTGGGAGTGCACATGACGATGATAGTGGTGTATTGTGTGAGTGCACACACTGATGATATATGCC
1 TGTGGGAGTGCACATGACGATGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCC
*
12859610 ATGTGCGG
66 ATGTGCGA
* * *
12859618 TGTGGGAGTGCACATGACGGTGATAGTAGTGTGTTGTGTTAGTGCACACACTGATG--ATATGCC
1 TGTGGGAGTGCACATGACGATGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCC
12859681 ATGTGCGA
66 ATGTGCGA
*
12859689 TGTGAGAGTGCACATGA
1 TGTGGGAGTGCACATGA
12859706 TGATATTGCC
Statistics
Matches: 148, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
71 30 0.20
73 117 0.79
74 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.34, T:0.28
Consensus pattern (73 bp):
TGTGGGAGTGCACATGACGATGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCC
ATGTGCGA
Found at i:12859699 original size:37 final size:37
Alignment explanation
Indices: 12859506--12859736 Score: 128
Period size: 34 Copynumber: 6.4 Consensus size: 37
12859496 AGTGGTGTGC
* * *
12859506 TGTGTGAGTGCACACATTGATGATATATGCCATGTCCGA
1 TGTGGGAGTGCACACACTGATG--ATATGCCATGTGCGA
* *
12859545 TGTGGGAGTGCACATGAC-GATGATA-G---TGGTG-TA
1 TGTGGGAGTGCACA-CACTGATGATATGCCAT-GTGCGA
* *
12859578 TTGTGTGAGTGCACACACTGATGATATATGCCATGTGCGG
1 -TGTGGGAGTGCACACACTGATG--ATATGCCATGTGCGA
* * * * *
12859618 TGTGGGAGTGCACATGAC-GGTGATA-G-TA-GTGTGT
1 TGTGGGAGTGCACA-CACTGATGATATGCCATGTGCGA
**
12859652 TGTGTTAGTGCACACACTGATGATATGCCATGTGCGA
1 TGTGGGAGTGCACACACTGATGATATGCCATGTGCGA
* * * *
12859689 TGTGAGAGTG--CACA-TGATGATATTGCCTTGTGTGG
1 TGTGGGAGTGCACACACTGATGATA-TGCCATGTGCGA
12859724 TGTGGGAGTGCAC
1 TGTGGGAGTGCAC
12859737 GAGGTGATTT
Statistics
Matches: 145, Mismatches: 28, Indels: 40
0.68 0.13 0.19
Matches are distributed among these distances:
33 6 0.04
34 49 0.34
35 24 0.17
36 6 0.04
37 20 0.14
39 36 0.25
40 4 0.03
ACGTcount: A:0.23, C:0.14, G:0.33, T:0.30
Consensus pattern (37 bp):
TGTGGGAGTGCACACACTGATGATATGCCATGTGCGA
Found at i:12862357 original size:43 final size:43
Alignment explanation
Indices: 12862264--12862367 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 43
12862254 GGACTCGGCT
* * * * **
12862264 ATGTGCGAGT-AGTGAGTACGCATAAGCCGATGATGACCCGGTT
1 ATGTGCGAGTAAG-GAGTGCACATAAACCGATGATGACCCAGCC
* *
12862307 ATATGCGAGTAAGGAGTGCACATAAACCGGTGATGACCCAGCC
1 ATGTGCGAGTAAGGAGTGCACATAAACCGATGATGACCCAGCC
*
12862350 ATGTGCGAGTAGGGAGTG
1 ATGTGCGAGTAAGGAGTG
12862368 TGCATGAGCT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 48 0.96
44 2 0.04
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAAGGAGTGCACATAAACCGATGATGACCCAGCC
Found at i:12866180 original size:19 final size:19
Alignment explanation
Indices: 12866146--12866183 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12866136 CCATTTCACT
*
12866146 TATTGGAGTACGATTTGAG
1 TATTGGAGTACAATTTGAG
*
12866165 TATTGGAGTATAATTTGAG
1 TATTGGAGTACAATTTGAG
12866184 GGTTTGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.39
Consensus pattern (19 bp):
TATTGGAGTACAATTTGAG
Found at i:12871704 original size:19 final size:19
Alignment explanation
Indices: 12871680--12871717 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12871670 CTGCCAAACC
*
12871680 CTCAAATTATACTCCAATA
1 CTCAAATAATACTCCAATA
12871699 CTCAAATAATACTCCAATA
1 CTCAAATAATACTCCAATA
12871718 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATAATACTCCAATA
Found at i:12872881 original size:19 final size:20
Alignment explanation
Indices: 12872854--12872899 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
12872844 AGGAGACAAG
*
12872854 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
12872873 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
12872892 ATAATATT
1 ATAATATT
12872900 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Done.