Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 12 of 161
Found at i:3980451 original size:49 final size:49
Alignment explanation
Indices: 3980378--3980497 Score: 150
Period size: 49 Copynumber: 2.4 Consensus size: 49
3980368 ATTTGGGTAA
* * *
3980378 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCC-TGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGATG
* *
3980428 AGAGGTCCCTGTAAGACCATGTCTAGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCTGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGATG
** *
3980477 AGAACTCTCATGTAAGACCAT
1 AGAGGTC-CCTGTAAGACCAT
3980498 ATCAGGGATA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
49 40 0.66
50 21 0.34
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (49 bp):
AGAGGTCCCTGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGATG
Found at i:3984947 original size:13 final size:12
Alignment explanation
Indices: 3984921--3984958 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
3984911 GGACATATTG
3984921 AAAA-AAAGAAA
1 AAAAGAAAGAAA
3984932 AAAAGAAAGTAAA
1 AAAAGAAAG-AAA
*
3984945 AAAAGTAAGAAA
1 AAAAGAAAGAAA
3984957 AA
1 AA
3984959 CTCATTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 4 0.17
12 9 0.38
13 11 0.46
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (12 bp):
AAAAGAAAGAAA
Found at i:4016608 original size:30 final size:30
Alignment explanation
Indices: 4016574--4016668 Score: 120
Period size: 30 Copynumber: 3.2 Consensus size: 30
4016564 CAGTGGTTTC
* *
4016574 AGTTTCTAGGTACTATGCACTGGTGATTAT
1 AGTTTCTAGGTACTATGTACCGGTGATTAT
* *
4016604 AGTTTTTAGGTACTATGTACCGGTGATTAC
1 AGTTTCTAGGTACTATGTACCGGTGATTAT
* * *
4016634 AGTTTCCAAGAACTATGTACCGGTG-TTAT
1 AGTTTCTAGGTACTATGTACCGGTGATTAT
4016663 AGTTTC
1 AGTTTC
4016669 CAGGCACTCT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
29 9 0.16
30 47 0.84
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (30 bp):
AGTTTCTAGGTACTATGTACCGGTGATTAT
Found at i:4016713 original size:28 final size:29
Alignment explanation
Indices: 4016615--4016715 Score: 87
Period size: 29 Copynumber: 3.5 Consensus size: 29
4016605 GTTTTTAGGT
* * *
4016615 ACTATGTACCGGTGATTACAGTTTCCAAGA
1 ACTATGTACTGGTG-CTATAGTTTCCAAGA
* * * *
4016645 ACTATGTACCGGTGTTATAGTTTCCAGGC
1 ACTATGTACTGGTGCTATAGTTTCCAAGA
* * * *
4016674 ACTCTGTGCTGGTGCTAT-GTTTCCATGT
1 ACTATGTACTGGTGCTATAGTTTCCAAGA
4016702 ACTATGTACTGGTG
1 ACTATGTACTGGTG
4016716 GTGGATACCA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 20 0.33
29 26 0.43
30 14 0.23
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.36
Consensus pattern (29 bp):
ACTATGTACTGGTGCTATAGTTTCCAAGA
Found at i:4026954 original size:50 final size:54
Alignment explanation
Indices: 4026846--4026955 Score: 165
Period size: 56 Copynumber: 2.1 Consensus size: 54
4026836 GGTAAAAAGA
4026846 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGAGA-CATGAGAGG
*
4026902 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GAGA-A-GAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGACATGAGAGG
4026952 TCCC
1 TCCC
4026956 CCGTATGTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
50 10 0.19
51 1 0.02
53 4 0.08
55 2 0.04
56 36 0.68
ACGTcount: A:0.25, C:0.24, G:0.30, T:0.22
Consensus pattern (54 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGACATGAGAGG
Found at i:4028345 original size:40 final size:40
Alignment explanation
Indices: 4028315--4028500 Score: 171
Period size: 40 Copynumber: 4.7 Consensus size: 40
4028305 GCTCCTCGTT
* *
4028315 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATATAGTAACTCGCA
* *
4028355 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATATAGTAACTCGCA
* * * *
4028395 CCAATGCCTTCGGGACTTAACCC-GAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATA-TAGTAACTCGCA
* * ** * * *
4028435 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATATAGTAAC-TCGCA
* *
4028476 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
4028501 CATCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 5 0.04
40 103 0.84
41 14 0.11
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATATAGTAACTCGCA
Found at i:4028460 original size:80 final size:80
Alignment explanation
Indices: 4028317--4028498 Score: 199
Period size: 80 Copynumber: 2.3 Consensus size: 80
4028307 TCCTCGTTCA
* ** *
4028317 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
* *
4028382 TTAGTAAC-TCGCACC
66 ATAGTAACTTAGCA-C
* * **
4028397 AATGCCTTCGGGACTTAACCCGAA-ATTAGTATCTCGCACAAATACCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCCGAATA-TAGTAACTCGCACAAATACCTTCGGGA-CTTAACCCGG
* *
4028460 ATATGGTCACTTAGCAC
64 ATATAGTAACTTAGCAC
*
4028477 AAAGCCTTCGGGACTTAGCCCG
1 AATGCCTTCGGGACTTAGCCCG
4028499 GACATCATTC
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
79 4 0.05
80 77 0.91
81 4 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:4030260 original size:49 final size:49
Alignment explanation
Indices: 4030146--4030275 Score: 174
Period size: 49 Copynumber: 2.6 Consensus size: 49
4030136 CTGTCACACC
* *
4030146 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CGACATGAGAACTCCCAT
* *
4030196 GTAAGACCATATCTGGGATATGGCATTGGCA-GTACATGA-AACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACG-ACATGAGAAC-TCCCAT
*
4030245 GTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
4030276 TGTTATTATC
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
48 4 0.06
49 39 0.55
50 28 0.39
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACGACATGAGAACTCCCAT
Found at i:4034562 original size:32 final size:32
Alignment explanation
Indices: 4034526--4034678 Score: 143
Period size: 32 Copynumber: 4.8 Consensus size: 32
4034516 CCATAAGTAC
* * *
4034526 AGTAATACGATTGGCACAAAGCCATTAGTAGT
1 AGTAATATGATCGGCACAAAGCCATCAGTAGT
* * * *
4034558 AGTAAGATGACCGACACACAGCCATCAGTA--
1 AGTAATATGATCGGCACAAAGCCATCAGTAGT
*
4034588 A-TAATAGTGTAGCCGGCACAAAGCCATCAGTAGT
1 AGTAATA-TG-A-TCGGCACAAAGCCATCAGTAGT
*
4034622 AGTAATATGATCGGCACACAA-CCATCAGTAAT
1 AGTAATATGATCGGCACA-AAGCCATCAGTAGT
* *
4034654 GGTAATATGATCAGCACAAAGCCAT
1 AGTAATATGATCGGCACAAAGCCAT
4034679 TAATAGCATT
Statistics
Matches: 99, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
29 4 0.04
30 3 0.03
31 3 0.03
32 78 0.79
33 3 0.03
34 3 0.03
35 5 0.05
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (32 bp):
AGTAATATGATCGGCACAAAGCCATCAGTAGT
Found at i:4034757 original size:27 final size:26
Alignment explanation
Indices: 4034727--4034791 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
4034717 AGTAAAGCTG
* *
4034727 CCAGTAACAGTATATGTGGCCAAGCCA
1 CCAGTAACAGTAT-TATGGCAAAGCCA
*
4034754 CCAGTAATAGTGATTATGGCAAAGCCA
1 CCAGTAACAGT-ATTATGGCAAAGCCA
4034781 CCAGT-ACAGTA
1 CCAGTAACAGTA
4034792 CTTCCCCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 4 0.12
27 26 0.79
28 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (26 bp):
CCAGTAACAGTATTATGGCAAAGCCA
Found at i:4034888 original size:24 final size:24
Alignment explanation
Indices: 4034867--4034988 Score: 154
Period size: 24 Copynumber: 5.1 Consensus size: 24
4034857 TCAATCATAC
4034867 AAATCACAGACAAATCAGTCATTT
1 AAATCACAGACAAATCAGTCATTT
*
4034891 AAATCACACACAAATCAGTCATTT
1 AAATCACAGACAAATCAGTCATTT
* *
4034915 AAATCATAGACAAATTAGTCATTT
1 AAATCACAGACAAATCAGTCATTT
* * * *
4034939 ACATCTCGGACAAATCAATCATTT
1 AAATCACAGACAAATCAGTCATTT
* * *
4034963 ACATCACAGGCAAATCAATCATTT
1 AAATCACAGACAAATCAGTCATTT
4034987 AA
1 AA
4034989 CTCTGAGAGG
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.27
Consensus pattern (24 bp):
AAATCACAGACAAATCAGTCATTT
Found at i:4035036 original size:27 final size:27
Alignment explanation
Indices: 4035006--4035098 Score: 132
Period size: 27 Copynumber: 3.4 Consensus size: 27
4034996 AGGTAAAATA
* *
4035006 GTCATTTTATCCTACAGGGGCATTACT
1 GTCATTTTACCCTACAGGGGCATTACG
*
4035033 GTCATTTTACCCTACAGGGTCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
4035060 GTCATTTTACCCTACAGAGGCGTTGCG
1 GTCATTTTACCCTACAGGGGCATTACG
4035087 GTCATTTTACCC
1 GTCATTTTACCC
4035099 AACGAGGGTA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.34
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:4035120 original size:54 final size:54
Alignment explanation
Indices: 4035006--4035126 Score: 147
Period size: 54 Copynumber: 2.2 Consensus size: 54
4034996 AGGTAAAATA
* * * *
4035006 GTCATTTTATCCTACAGGGGCATTACTGTCATTTTACCCTACAGGGTCATTACG
1 GTCATTTTACCCTACAGAGGCATTACGGTCATTTTACCCAACAGGGTCATTACG
* * *
4035060 GTCATTTTACCCTACAGAGGCGTTGCGGTCATTTTACCCAACGAGGGT-ATTTC-
1 GTCATTTTACCCTACAGAGGCATTACGGTCATTTTACCCAAC-AGGGTCATTACG
4035113 GTCCATTTTACCCT
1 GT-CATTTTACCCT
4035127 TTGAGGGTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 2 0.03
54 51 0.88
55 5 0.09
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (54 bp):
GTCATTTTACCCTACAGAGGCATTACGGTCATTTTACCCAACAGGGTCATTACG
Found at i:4035182 original size:26 final size:26
Alignment explanation
Indices: 4035143--4035243 Score: 114
Period size: 27 Copynumber: 3.8 Consensus size: 26
4035133 GTATTTTTTT
*
4035143 AGGGTA-TTCTAGTAATTTTACCTTCA
1 AGGGTATTTC-AGTAATTTTACCTTCG
*
4035169 AGGGTATTTCAGTAATATTACCATTCG
1 AGGGTATTTCAGTAATTTTACC-TTCG
* * *
4035196 AGGGTCTTTCGGTAATTTTACTCTTTG
1 AGGGTATTTCAGTAATTTTAC-CTTCG
*
4035223 AGGCTATTTCAGTAATTTTAC
1 AGGGTATTTCAGTAATTTTAC
4035244 AACCTTTTCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
26 17 0.27
27 45 0.71
28 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.43
Consensus pattern (26 bp):
AGGGTATTTCAGTAATTTTACCTTCG
Found at i:4035509 original size:40 final size:39
Alignment explanation
Indices: 4035464--4035568 Score: 120
Period size: 40 Copynumber: 2.6 Consensus size: 39
4035454 ATACACATAT
*
4035464 GTGCCCTTGTTTGTACTTCGGTACCCCTAAATGCAAATAC
1 GTGCCC-TGTTTGTACTTCGGTACCCCAAAATGCAAATAC
* * * *
4035504 GTGCCCCTGTTTGCAGTTCAGTACCCCAAAATGCACATAC
1 GTG-CCCTGTTTGTACTTCGGTACCCCAAAATGCAAATAC
* * *
4035544 ATGCCCCGTTTGTACTTTGGTACCC
1 GTGCCCTGTTTGTACTTCGGTACCC
4035569 TTCAATGTTG
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
39 17 0.32
40 33 0.62
41 3 0.06
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.30
Consensus pattern (39 bp):
GTGCCCTGTTTGTACTTCGGTACCCCAAAATGCAAATAC
Found at i:4038283 original size:25 final size:25
Alignment explanation
Indices: 4038255--4038310 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
4038245 GTTCTGACCC
* *
4038255 ATAGCTCGTGTA-AGCATACTGATGT
1 ATAGCTCGTG-AGAGCATACCGATCT
4038280 ATAGCTCGTGAGAGCATACCGATCT
1 ATAGCTCGTGAGAGCATACCGATCT
4038305 ATAGCT
1 ATAGCT
4038311 TGAGTTAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (25 bp):
ATAGCTCGTGAGAGCATACCGATCT
Found at i:4038320 original size:25 final size:24
Alignment explanation
Indices: 4038267--4038324 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
4038257 AGCTCGTGTA
* *
4038267 AGCATACTGATGTATAGCTCGTGAG
1 AGCATACCGATCTATAGCTC-TGAG
4038292 AGCATACCGATCTATAGCT-TGAG
1 AGCATACCGATCTATAGCTCTGAG
4038315 TTAGCATACC
1 --AGCATACC
4038325 AATTTACAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 4 0.14
25 25 0.86
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
AGCATACCGATCTATAGCTCTGAG
Found at i:4040190 original size:70 final size:70
Alignment explanation
Indices: 4040032--4040183 Score: 250
Period size: 70 Copynumber: 2.2 Consensus size: 70
4040022 TTTTTATCAG
* *
4040032 AATGCCATAGCCCAACTATATATTACATATAAACACTGCCATAGTCCAACCATGGTCTTACGTTT
1 AATGCCATAGCCCAGCTATATATTACATATAAACACTACCATAGTCCAACCATGGTCTTACGTTT
4040097 GAATA
66 GAATA
* * *
4040102 AATGGCATAGCCCAGCTATATCTTACATATAAACACTACCATGGTCCAACCATGGTCTTACGTTT
1 AATGCCATAGCCCAGCTATATATTACATATAAACACTACCATAGTCCAACCATGGTCTTACGTTT
4040167 GAATA
66 GAATA
*
4040172 ATTGCCATAGCC
1 AATGCCATAGCC
4040184 TCGCTATGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 75 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (70 bp):
AATGCCATAGCCCAGCTATATATTACATATAAACACTACCATAGTCCAACCATGGTCTTACGTTT
GAATA
Found at i:4042554 original size:30 final size:27
Alignment explanation
Indices: 4042518--4042573 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
4042508 TCTTAAATGA
*
4042518 CACACGATCGTGTCGCCAGGCCTTGTGTGT
1 CACACGACCGTGT-GCCA-GCC-TGTGTGT
4042548 CACACGACCGTGTGCCAGCCTGTGTG
1 CACACGACCGTGTGCCAGCCTGTGTG
4042574 AACCTAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 6 0.24
28 3 0.12
29 4 0.16
30 12 0.48
ACGTcount: A:0.14, C:0.32, G:0.30, T:0.23
Consensus pattern (27 bp):
CACACGACCGTGTGCCAGCCTGTGTGT
Found at i:4043289 original size:40 final size:40
Alignment explanation
Indices: 4043223--4043365 Score: 157
Period size: 40 Copynumber: 3.6 Consensus size: 40
4043213 ACCAAAGTAT
** * * *
4043223 AAACA-GGGCACGTATCAGCGTCCAGGGGTATTGAAATAC
1 AAACAGGGGCACGTATGTGCATTCAGGGGTATCGAAATAC
* *
4043262 AAACAGGGGAACGTATGTGCATTCAGGGGTA-CCAAAGTAC
1 AAACAGGGGCACGTATGTGCATTCAGGGGTATCGAAA-TAC
* * *
4043302 AAATAGGGGCACATATGTGCATTCAGAGGTATCGAAATAC
1 AAACAGGGGCACGTATGTGCATTCAGGGGTATCGAAATAC
*
4043342 AAACA-GGGCACGTATGTGCTTTCA
1 AAACAGGGGCACGTATGTGCATTCA
4043366 TTCATTAGTT
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 25 0.29
40 57 0.66
41 4 0.05
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.20
Consensus pattern (40 bp):
AAACAGGGGCACGTATGTGCATTCAGGGGTATCGAAATAC
Found at i:4043358 original size:79 final size:79
Alignment explanation
Indices: 4043203--4043365 Score: 202
Period size: 79 Copynumber: 2.1 Consensus size: 79
4043193 ATACTATTTG
* * * * * *
4043203 ATTCAGGGTTACCAAAGTATAAACAGGGCACGTATCAGCGTCCAGGGGTATTGAAATACAAACAG
1 ATTCAGGGGTACCAAAGTACAAACAGGGCACATATCAGCATCCAGAGGTATCGAAATACAAACAG
4043268 GGGAACGTATGTGC
66 GGGAACGTATGTGC
* ** *
4043282 ATTCAGGGGTACCAAAGTACAAATAGGGGCACATATGTGCATTCAGAGGTATCGAAATACAAACA
1 ATTCAGGGGTACCAAAGTACAAACA-GGGCACATATCAGCATCCAGAGGTATCGAAATACAAACA
*
4043347 -GGGCACGTATGTGC
65 GGGGAACGTATGTGC
*
4043361 TTTCA
1 ATTCA
4043366 TTCATTAGTT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
79 39 0.55
80 32 0.45
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.21
Consensus pattern (79 bp):
ATTCAGGGGTACCAAAGTACAAACAGGGCACATATCAGCATCCAGAGGTATCGAAATACAAACAG
GGGAACGTATGTGC
Found at i:4048519 original size:32 final size:32
Alignment explanation
Indices: 4048483--4048669 Score: 230
Period size: 32 Copynumber: 5.8 Consensus size: 32
4048473 CAATAAGTAC
* *
4048483 AGTAATATGATTGGCACAAAGCCATCAGTAGT
1 AGTAATATGATCGGCACAAAGCCATCAGTAAT
*
4048515 AGTAATATGATCGGCACACAGCCATCAGTAAT
1 AGTAATATGATCGGCACAAAGCCATCAGTAAT
* * *
4048547 AGTAGTATGATCGACACAAAGCCATCAGTAGT
1 AGTAATATGATCGGCACAAAGCCATCAGTAAT
* * *
4048579 AGTAATATGATCGTCATACAGCCATCAGTAAT
1 AGTAATATGATCGGCACAAAGCCATCAGTAAT
* * * *
4048611 GGTAATATGATCGACACACAGCCATCAATAAT
1 AGTAATATGATCGGCACAAAGCCATCAGTAAT
* * *
4048643 GGTAATATGATCAGCACAAAGTCATCA
1 AGTAATATGATCGGCACAAAGCCATCA
4048670 ATAGCATCGC
Statistics
Matches: 135, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 135 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (32 bp):
AGTAATATGATCGGCACAAAGCCATCAGTAAT
Found at i:4048570 original size:64 final size:64
Alignment explanation
Indices: 4048483--4048669 Score: 257
Period size: 64 Copynumber: 2.9 Consensus size: 64
4048473 CAATAAGTAC
* *
4048483 AGTAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAGCCATCAGTAAT
1 AGTAATATGATCGACACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAGCCATCAGTAAT
* * *
4048547 AGTAGTATGATCGACACAAAGCCATCAGTAGTAGTAATATGATCGTCATACAGCCATCAGTAAT
1 AGTAATATGATCGACACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAGCCATCAGTAAT
* * * * * * * *
4048611 GGTAATATGATCGACACACAGCCATCAATAATGGTAATATGATCAGCACAAAGTCATCA
1 AGTAATATGATCGACACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAGCCATCA
4048670 ATAGCATCGC
Statistics
Matches: 107, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 107 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (64 bp):
AGTAATATGATCGACACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAGCCATCAGTAAT
Found at i:4048652 original size:96 final size:96
Alignment explanation
Indices: 4048483--4048669 Score: 259
Period size: 96 Copynumber: 1.9 Consensus size: 96
4048473 CAATAAGTAC
* * * *
4048483 AGTAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAGCCATCAGTAATA
1 AGTAATATGATCGGCACAAAGCCATCAGTAATAGTAATATGATCGACACACAGCCATCAATAATA
*
4048548 GTAGTATGATC-GACACAAAGCCATCAGTAGT
66 GTAATATGATCAG-CACAAAGCCATCAGTAGT
* * * * *
4048579 AGTAATATGATCGTCATACAGCCATCAGTAATGGTAATATGATCGACACACAGCCATCAATAATG
1 AGTAATATGATCGGCACAAAGCCATCAGTAATAGTAATATGATCGACACACAGCCATCAATAATA
*
4048644 GTAATATGATCAGCACAAAGTCATCA
66 GTAATATGATCAGCACAAAGCCATCA
4048670 ATAGCATCGC
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
96 78 0.99
97 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (96 bp):
AGTAATATGATCGGCACAAAGCCATCAGTAATAGTAATATGATCGACACACAGCCATCAATAATA
GTAATATGATCAGCACAAAGCCATCAGTAGT
Found at i:4048748 original size:27 final size:26
Alignment explanation
Indices: 4048718--4048780 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
4048708 GAAATCTACC
*
4048718 AGTAACAGTATATGTGGCCAAGCCACA
1 AGTAACAGTAT-TGTGGCAAAGCCACA
*
4048745 AGTAACAGTGATTGTGGCAAAGCCACC
1 AGTAACAGT-ATTGTGGCAAAGCCACA
4048772 AGT-ACAGTA
1 AGTAACAGTA
4048781 CTTCCTTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 1 0.03
26 5 0.15
27 25 0.76
28 2 0.06
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.19
Consensus pattern (26 bp):
AGTAACAGTATTGTGGCAAAGCCACA
Found at i:4048877 original size:24 final size:24
Alignment explanation
Indices: 4048843--4048901 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
4048833 GCCATGCACG
* *
4048843 AAATCAGTCATACAAACCACAGAG
1 AAATTAGTCATACAAACCACAGAC
* ** *
4048867 AAATTATTCATTTAAATCACAGAC
1 AAATTAGTCATACAAACCACAGAC
4048891 AAATTAGTCAT
1 AAATTAGTCAT
4048902 TTACATCTCG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.25
Consensus pattern (24 bp):
AAATTAGTCATACAAACCACAGAC
Found at i:4048918 original size:24 final size:24
Alignment explanation
Indices: 4048860--4048951 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
4048850 TCATACAAAC
* * *
4048860 CACAGAGAAATTATTCATTTAAAT
1 CACAGACAAATTAATCATTTACAT
*
4048884 CACAGACAAATTAGTCATTTACAT
1 CACAGACAAATTAATCATTTACAT
* * * *
4048908 CTCGGATAAATCAATCATTTACAT
1 CACAGACAAATTAATCATTTACAT
* * *
4048932 CATAGGCAAATCAATCATTT
1 CACAGACAAATTAATCATTT
4048952 TACCCTATTA
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (24 bp):
CACAGACAAATTAATCATTTACAT
Found at i:4049019 original size:27 final size:27
Alignment explanation
Indices: 4048989--4049170 Score: 147
Period size: 27 Copynumber: 6.7 Consensus size: 27
4048979 TACCCTAAAG
* * *
4048989 GGGTGTTACGATCATTTTACCCATCGA
1 GGGTGTTTCGATAATTTTACCCTTCGA
* * * *
4049016 GGGTATTTC-AGTCATTTTATCCTTTGA
1 GGGTGTTTCGA-TAATTTTACCCTTCGA
* ** *
4049043 GGGTATTTAAATAATTTTACCCTT-TA
1 GGGTGTTTCGATAATTTTACCCTTCGA
*
4049069 GGGGTGTTTCGATCATTTTACCCTTCGA
1 -GGGTGTTTCGATAATTTTACCCTTCGA
*
4049097 GGGTG-TTCTAGTAATTTTACCCTTCGA
1 GGGTGTTTCGA-TAATTTTACCCTTCGA
* * *
4049124 GGGTATTTCGGTAATTTTACTCTTCGA
1 GGGTGTTTCGATAATTTTACCCTTCGA
*
4049151 GGGTATTTC-AGTAATTTTAC
1 GGGTGTTTCGA-TAATTTTAC
4049171 AACCTTTTCG
Statistics
Matches: 127, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
26 6 0.05
27 116 0.91
28 5 0.04
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.42
Consensus pattern (27 bp):
GGGTGTTTCGATAATTTTACCCTTCGA
Found at i:4049034 original size:81 final size:81
Alignment explanation
Indices: 4048946--4049131 Score: 216
Period size: 81 Copynumber: 2.3 Consensus size: 81
4048936 GGCAAATCAA
* *
4048946 TCATTTTACCCTATT-AGGGCA-TTACAGTCATTTTACCCTAAAGGGGTGTTACGATCATTTTAC
1 TCATTTTACCCT-TTGAGGGCATTTA-AATAATTTTACCCTAAAGGGGTGTTACGATCATTTTAC
*
4049009 CCATCGAGGGTATT-TCAG
64 CCATCGAGGGTGTTCT-AG
* * ** *
4049027 TCATTTTATCCTTTGAGGGTATTTAAATAATTTTACCCTTTAGGGGTGTTTCGATCATTTTACCC
1 TCATTTTACCCTTTGAGGGCATTTAAATAATTTTACCCTAAAGGGGTGTTACGATCATTTTACCC
*
4049092 TTCGAGGGTGTTCTAG
66 ATCGAGGGTGTTCTAG
* * *
4049108 TAATTTTACCCTTCGAGGGTATTT
1 TCATTTTACCCTTTGAGGGCATTT
4049132 CGGTAATTTT
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
80 2 0.02
81 84 0.93
82 4 0.04
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (81 bp):
TCATTTTACCCTTTGAGGGCATTTAAATAATTTTACCCTAAAGGGGTGTTACGATCATTTTACCC
ATCGAGGGTGTTCTAG
Found at i:4049060 original size:54 final size:50
Alignment explanation
Indices: 4049002--4049170 Score: 167
Period size: 54 Copynumber: 3.1 Consensus size: 50
4048992 TGTTACGATC
* *
4049002 ATTTTACCCATCGAGGGTATTTCAGTCATTTTATCCTTTGAGGGTATTTAAATA
1 ATTTTACCC-TCGAGGGTATTTC-GTCATTTTA-CCTTCGAGGGTATTT-AGTA
** * *
4049056 ATTTTACCCTTTAGGGGTGTTTCGATCATTTTACCCTTCGAGGGTGTTCTAGTA
1 ATTTTACCCTCGA-GGGTATTTCG-TCATTTTA-CCTTCGAGGGTATT-TAGTA
*
4049110 ATTTTACCCTTCGAGGGTATTTCGGTAATTTTACTCTTCGAGGGTATTTCAGTA
1 ATTTTACCC-TCGAGGGTATTTC-GTCATTTTAC-CTTCGAGGGTATTT-AGTA
4049164 ATTTTAC
1 ATTTTAC
4049171 AACCTTTTCG
Statistics
Matches: 96, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
53 5 0.05
54 87 0.91
55 4 0.04
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (50 bp):
ATTTTACCCTCGAGGGTATTTCGTCATTTTACCTTCGAGGGTATTTAGTA
Found at i:4049143 original size:81 final size:81
Alignment explanation
Indices: 4048975--4049131 Score: 226
Period size: 81 Copynumber: 1.9 Consensus size: 81
4048965 CATTACAGTC
* *
4048975 ATTTTACCCTAAAGGGGTGTTACGATCATTTTACCCATCGAGGGTATTTCAGTCATTTTATCCTT
1 ATTTTACCCTAAAGGGGTGTTACGATCATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCTT
*
4049040 TGAGGGTATTTAAATA
66 CGAGGGTATTTAAATA
** * * *
4049056 ATTTTACCCTTTAGGGGTGTTTCGATCATTTTACCCTTCGAGGGT-GTTCTAGTAATTTTACCCT
1 ATTTTACCCTAAAGGGGTGTTACGATCATTTTACCCATCGAGGGTATTTC-AGTAATTTTACCCT
4049120 TCGAGGGTATTT
65 TCGAGGGTATTT
4049132 CGGTAATTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 3 0.04
81 64 0.96
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (81 bp):
ATTTTACCCTAAAGGGGTGTTACGATCATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCTT
CGAGGGTATTTAAATA
Found at i:4049168 original size:81 final size:81
Alignment explanation
Indices: 4048975--4049170 Score: 191
Period size: 81 Copynumber: 2.4 Consensus size: 81
4048965 CATTACAGTC
** * * * * *
4048975 ATTTTACCCTAAAGGGGTGTTACGATCATTTTACCCATCGAGGGTATTTCAGTCATTTTATCCTT
1 ATTTTACCCTTGAGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCTT
*
4049040 TGAGGGTATTTAAATA
66 CGAGGGTATTTAAATA
* * * * *
4049056 ATTTTACCCTTTAGGGGTGTTTCGATCATTTTACCCTTCGAGGGT-GTTCTAGTAATTTTACCCT
1 ATTTTACCCTTGAGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTC-AGTAATTTTACCCT
***
4049120 TCGAGGGTATTTCGGTA
65 TCGAGGGTATTTAAATA
*
4049137 ATTTTACTCTTCGA-GGGTATTTC-AGTAATTTTAC
1 ATTTTACCCTT-GAGGGGTATTTCGA-TAATTTTAC
4049171 AACCTTTTCG
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
80 4 0.04
81 92 0.95
82 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (81 bp):
ATTTTACCCTTGAGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCTT
CGAGGGTATTTAAATA
Found at i:4059277 original size:28 final size:28
Alignment explanation
Indices: 4059237--4059344 Score: 155
Period size: 28 Copynumber: 3.9 Consensus size: 28
4059227 GCGAATTGAA
4059237 TTGACTATGTAGCACTAAGTGTGCGAGT
1 TTGACTATGTAGCACTAAGTGTGCGAGT
4059265 TTGACTATGTAGCACTAAGTGTGCGAGT
1 TTGACTATGTAGCACTAAGTGTGCGAGT
* * *
4059293 ATGATTATGTAGCGCTAAGTGTGCGAG-
1 TTGACTATGTAGCACTAAGTGTGCGAGT
* * *
4059320 TTGATTATATAGCACTGAGTGTGCG
1 TTGACTATGTAGCACTAAGTGTGCG
4059345 GACTTAATAA
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
27 21 0.29
28 52 0.71
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (28 bp):
TTGACTATGTAGCACTAAGTGTGCGAGT
Found at i:4059314 original size:56 final size:58
Alignment explanation
Indices: 4059215--4059344 Score: 167
Period size: 56 Copynumber: 2.3 Consensus size: 58
4059205 TAAATTGTGC
*
4059215 AGCACTAAGTGTGCGAATTGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAA-TGAATTGACTATGTAGCACTAAGTGTGCGAG-TTGACTATAT
* * * *
4059275 AGCACTAAGTGTGCG-A-GTA-TGATTATGTAGCGCTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATGAATTGACTATGTAGCACTAAGTGTGCGAGTTGACTATAT
*
4059330 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
4059345 GACTTAATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
55 22 0.34
56 24 0.38
57 2 0.03
59 1 0.02
60 15 0.23
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (58 bp):
AGCACTAAGTGTGCGAATGAATTGACTATGTAGCACTAAGTGTGCGAGTTGACTATAT
Found at i:4062148 original size:35 final size:35
Alignment explanation
Indices: 4062102--4062262 Score: 107
Period size: 35 Copynumber: 4.6 Consensus size: 35
4062092 TATCCATTGC
*
4062102 CTCTACGGAGTGACACCATGGAAACAGTATATAAG
1 CTCTACAGAGTGACACCATGGAAACAGTATATAAG
* ** *
4062137 CTCTACAGAGTGACACCATGAAAATTGTTATCTACAAG
1 CTCTACAGAGTGACACCATGGAAACAG-TA--TATAAG
* * *
4062175 CT-TTCTAGAGTGTA-ATCATGGAAACGGTATA-AAGG
1 CTCTAC-AGAGTG-ACACCATGGAAACAGTATATAA-G
** *
4062210 CTCTAGGGAGTGACACCATGGAAA-A-TATATAGG
1 CTCTACAGAGTGACACCATGGAAACAGTATATAAG
* * *
4062243 CTTTACATAGTAACACCATG
1 CTCTACAGAGTGACACCATG
4062263 AAAATGGTTA
Statistics
Matches: 96, Mismatches: 21, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
33 20 0.21
34 4 0.04
35 42 0.44
36 3 0.03
37 4 0.04
38 22 0.23
39 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (35 bp):
CTCTACAGAGTGACACCATGGAAACAGTATATAAG
Found at i:4072761 original size:27 final size:27
Alignment explanation
Indices: 4072726--4072782 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
4072716 TTTTAACCAT
4072726 TATGTTCCATTCCTTCAAAGTTTGCCA
1 TATGTTCCATTCCTTCAAAGTTTGCCA
* *
4072753 TATGTTCCATTCCTTTAGAGTTTGCCA
1 TATGTTCCATTCCTTCAAAGTTTGCCA
4072780 TAT
1 TAT
4072783 ATATATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (27 bp):
TATGTTCCATTCCTTCAAAGTTTGCCA
Found at i:4074503 original size:230 final size:231
Alignment explanation
Indices: 4074088--4074528 Score: 627
Period size: 230 Copynumber: 1.9 Consensus size: 231
4074078 TATTTGGAGC
* *
4074088 ATCTAGTGTTGTGAAATACAGTAAGGATTTTCTTATAAATGAGAAGTACACCTTATACAATCTAA
1 ATCTAGTGTTGTAAAATACAGTAAGGATTTTCTTATAAATGAAAAGTACACCTTATACAATCTAA
* *
4074153 AGATGAGATAGTTCGCCAAGGATTATCCACCTCTAGAAATATCAATTCAAACTACCTTATGGAAG
66 AGATGAGATAGTTCGCCAAGGACTATCCACCTCTAGAAATATCAATTCAAACTACCTGATGGAAG
* * * *
4074218 AAGGTTCAGTTGAAATATCTTACAAGAGTAATCCAACAATAAGGGTGATTGGTGTTCA-TCCATT
131 AAGGTTCAGTCGAAATATCTTACAAGAGTAATCCAACAATAACGGTGAGTGGTGTTCACT-CATC
4074282 CGTC-AAATCTCTAATTGAAGGCCTAATACGTCAAAT
195 CGTCAAAATCTCTAATTGAAGGCCTAATACGTCAAAT
* * * *
4074318 ATCTAGTGTTGTAAAATCCATTAAGGATTTTCTTATAAATGAAAAGTATACCTTATACAATCTAG
1 ATCTAGTGTTGTAAAATACAGTAAGGATTTTCTTATAAATGAAAAGTACACCTTATACAATCTAA
* * * * * * * * *
4074383 GGGTTAGATAGTTCGTCAGGGACTATCTACCTCTAGAAGTATCCATTCAAACTACCTGAT-GAGG
66 AGATGAGATAGTTCGCCAAGGACTATCCACCTCTAGAAATATCAATTCAAACTACCTGATGGA-A
* *
4074447 GAAGGTTCAGTCGAACTATCTTACAAGAGTAATCCTACAATAACGGTGAGTGGTGTTCACTCATC
130 GAAGGTTCAGTCGAAATATCTTACAAGAGTAATCCAACAATAACGGTGAGTGGTGTTCACTCATC
4074512 CGTCAAAAATCTCTAAT
195 CGTC-AAAATCTCTAAT
4074529 CGAGGGTCTA
Statistics
Matches: 184, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
229 2 0.01
230 170 0.92
231 1 0.01
232 11 0.06
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (231 bp):
ATCTAGTGTTGTAAAATACAGTAAGGATTTTCTTATAAATGAAAAGTACACCTTATACAATCTAA
AGATGAGATAGTTCGCCAAGGACTATCCACCTCTAGAAATATCAATTCAAACTACCTGATGGAAG
AAGGTTCAGTCGAAATATCTTACAAGAGTAATCCAACAATAACGGTGAGTGGTGTTCACTCATCC
GTCAAAATCTCTAATTGAAGGCCTAATACGTCAAAT
Found at i:4081162 original size:19 final size:19
Alignment explanation
Indices: 4081138--4081179 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
4081128 AAAATGAGAT
4081138 CACGTCCCGTAAGTTAGAA
1 CACGTCCCGTAAGTTAGAA
4081157 CACGTCCCGTAAGTTAGAA
1 CACGTCCCGTAAGTTAGAA
4081176 CACG
1 CACG
4081180 ATCTTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (19 bp):
CACGTCCCGTAAGTTAGAA
Found at i:4081736 original size:25 final size:25
Alignment explanation
Indices: 4081708--4081755 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
4081698 ACTAATGAAA
4081708 ATACAAATAAAA-AGAAAAGAAAATT
1 ATACAAATAAAACA-AAAAGAAAATT
*
4081733 ATACTAATAAAACAAAAAGAAAA
1 ATACAAATAAAACAAAAAGAAAA
4081756 AAAATAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (25 bp):
ATACAAATAAAACAAAAAGAAAATT
Found at i:4081771 original size:29 final size:30
Alignment explanation
Indices: 4081707--4081764 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
4081697 TACTAATGAA
* *
4081707 AATACAAATAAAAAGAAAAGAAAATTATACT
1 AATA-AAACAAAAAGAAAAGAAAATAATACT
4081738 AATAAAACAAAAAGAAAA-AAAATAATA
1 AATAAAACAAAAAGAAAAGAAAATAATA
4081765 GCAATAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 13 0.52
31 4 0.16
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (30 bp):
AATAAAACAAAAAGAAAAGAAAATAATACT
Found at i:4085695 original size:19 final size:20
Alignment explanation
Indices: 4085671--4085708 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4085661 TGTGAAAGTG
4085671 TATATATGT-AATAAGGCCA
1 TATATATGTGAATAAGGCCA
*
4085690 TATATATGTGGATAAGGCC
1 TATATATGTGAATAAGGCC
4085709 TAATAGCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
TATATATGTGAATAAGGCCA
Found at i:4085731 original size:67 final size:67
Alignment explanation
Indices: 4085624--4085756 Score: 223
Period size: 67 Copynumber: 2.0 Consensus size: 67
4085614 TGTGAAAGTG
*
4085624 TATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT-AATAAGGC
1 TATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATAAGGC
4085688 CA
66 CA
* *
4085690 TATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGGATAAGG
1 TATATATGT-AATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATAAGG
4085755 CC
65 CC
4085757 TAATAGCCGA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 9 0.15
67 45 0.73
68 8 0.13
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (67 bp):
TATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATAAGGC
CA
Found at i:4085742 original size:48 final size:48
Alignment explanation
Indices: 4085689--4086607 Score: 1693
Period size: 48 Copynumber: 19.2 Consensus size: 48
4085679 TAATAAGGCC
4085689 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
*
4085737 GTATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
4085785 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
4085833 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
4085881 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
4085929 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
4085977 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
4086025 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
4086073 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
4086121 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
4086169 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
4086217 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
4086265 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
4086313 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
4086361 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
* * *
4086409 GTATATATGT-AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
* * *
4086456 GTATATATGT-AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
* * *
4086503 GTATATATGT-AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
* *
4086550 GTATATATGT-GATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
1 ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
*
4086597 GTATATATGTG
1 ATATATATGTG
4086608 ACAGGGCCGA
Statistics
Matches: 864, Mismatches: 6, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
47 185 0.21
48 679 0.79
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.29
Consensus pattern (48 bp):
ATATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
Found at i:4085790 original size:115 final size:114
Alignment explanation
Indices: 4085577--4085804 Score: 377
Period size: 114 Copynumber: 2.0 Consensus size: 114
4085567 TGTGAAAGTG
*
4085577 TATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCC
1 TATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCC
* *
4085642 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT-AATAAGGCCA
66 TAATAGCCGATGTGATGAATGTGAAAGTATATATATGTGAATAAGGCCA
* *
4085690 TATATATGTGGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGGATAAGG
1 TATATATGT-AATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT-AATAAGG
*
4085755 CCTAATAGCCGATGTGATGAATGTGAAAGTATATATATGTGGATAAGGCC
64 CCTAATAGCCGATGTGATGAATGTGAAAGTATATATATGTGAATAAGGCC
4085805 TAATAGCCGA
Statistics
Matches: 106, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
113 9 0.08
114 45 0.42
115 44 0.42
116 8 0.08
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.30
Consensus pattern (114 bp):
TATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCC
TAATAGCCGATGTGATGAATGTGAAAGTATATATATGTGAATAAGGCCA
Found at i:4086834 original size:37 final size:37
Alignment explanation
Indices: 4086778--4086856 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
4086768 CCGAGCTCTA
* *
4086778 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
4086815 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
4086852 AAGAC
1 AAGAC
4086857 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:4094429 original size:12 final size:12
Alignment explanation
Indices: 4094412--4094437 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4094402 ATTAATATTA
4094412 CACATAAAATTT
1 CACATAAAATTT
4094424 CACATAAAATTT
1 CACATAAAATTT
4094436 CA
1 CA
4094438 ATTTTCACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (12 bp):
CACATAAAATTT
Found at i:4094889 original size:15 final size:16
Alignment explanation
Indices: 4094871--4094905 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4094861 CTTCTTCTCA
4094871 TTTTATTTC-TTTCTT
1 TTTTATTTCTTTTCTT
*
4094886 TTTTCTTTCTTTTCTT
1 TTTTATTTCTTTTCTT
4094902 TTTT
1 TTTT
4094906 TAATTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTATTTCTTTTCTT
Found at i:4094933 original size:32 final size:32
Alignment explanation
Indices: 4094897--4094994 Score: 95
Period size: 32 Copynumber: 3.3 Consensus size: 32
4094887 TTTCTTTCTT
4094897 TTCTTTTTTTAATTTGTATGCATCCACTATCA
1 TTCTTTTTTTAATTTGTATGCATCCACTATCA
*** **
4094929 TTCTTTTTTTCCCTT-T-T-C-T-TTCT-T--
1 TTCTTTTTTTAATTTGTATGCATCCACTATCA
4094953 TTCTTTTTTTAATTTGTATGCATCCACTATCA
1 TTCTTTTTTTAATTTGTATGCATCCACTATCA
4094985 TTCTTTTTTT
1 TTCTTTTTTT
4094995 TCCCTTTCTT
Statistics
Matches: 48, Mismatches: 10, Indels: 16
0.65 0.14 0.22
Matches are distributed among these distances:
24 12 0.25
25 1 0.02
26 2 0.04
27 3 0.06
28 2 0.04
29 3 0.06
30 2 0.04
31 1 0.02
32 22 0.46
ACGTcount: A:0.14, C:0.19, G:0.04, T:0.62
Consensus pattern (32 bp):
TTCTTTTTTTAATTTGTATGCATCCACTATCA
Found at i:4094956 original size:56 final size:57
Alignment explanation
Indices: 4094886--4095005 Score: 226
Period size: 56 Copynumber: 2.1 Consensus size: 57
4094876 TTTCTTTCTT
4094886 TTTTCTTTCTTTTCTTTTTTTAATTTGTATGCATCCACTATCATTC-TTTTTTTCCC
1 TTTTCTTTCTTTTCTTTTTTTAATTTGTATGCATCCACTATCATTCTTTTTTTTCCC
4094942 TTTTCTTTCTTTTCTTTTTTTAATTTGTATGCATCCACTATCATTCTTTTTTTTCCC
1 TTTTCTTTCTTTTCTTTTTTTAATTTGTATGCATCCACTATCATTCTTTTTTTTCCC
4094999 -TTTCTTT
1 TTTTCTTT
4095006 TATTATAAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
56 53 0.84
57 10 0.16
ACGTcount: A:0.12, C:0.21, G:0.03, T:0.64
Consensus pattern (57 bp):
TTTTCTTTCTTTTCTTTTTTTAATTTGTATGCATCCACTATCATTCTTTTTTTTCCC
Found at i:4095966 original size:13 final size:13
Alignment explanation
Indices: 4095948--4095973 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4095938 TTAAGTTATA
4095948 TGTGTGAAAATTT
1 TGTGTGAAAATTT
4095961 TGTGTGAAAATTT
1 TGTGTGAAAATTT
4095974 GATAGTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:4097375 original size:41 final size:41
Alignment explanation
Indices: 4097311--4097428 Score: 164
Period size: 41 Copynumber: 2.9 Consensus size: 41
4097301 TATAATTGGT
* * *
4097311 TTTCAGGCTTAGTGCCTAACAGGCTTGATGCTGGTGAATTA
1 TTTCAGACTTAATGTCTAACAGGCTTGATGCTGGTGAATTA
* *
4097352 TTTCAGACTTAATGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTAATGTCTAACAGGCTTGATGCTGGTGAATTA
* * *
4097393 CTTCAGACTTATTGTCTAACAGGCTTCATGCTGGTG
1 TTTCAGACTTAATGTCTAACAGGCTTGATGCTGGTG
4097429 TACTTTAGTA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (41 bp):
TTTCAGACTTAATGTCTAACAGGCTTGATGCTGGTGAATTA
Found at i:4106740 original size:9 final size:9
Alignment explanation
Indices: 4106720--4106750 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
4106710 TAAAAATAAC
4106720 ATTAATTTTA
1 ATTAA-TTTA
4106730 ATTAATTTA
1 ATTAATTTA
4106739 ATTAATTTA
1 ATTAATTTA
4106748 ATT
1 ATT
4106751 TTACTTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTAATTTA
Found at i:4113314 original size:71 final size:71
Alignment explanation
Indices: 4113226--4113466 Score: 482
Period size: 71 Copynumber: 3.4 Consensus size: 71
4113216 GGAGTAATGC
4113226 TATGAATTGGATATAGACTGAAAAGCAATTTATTATCAACATTAATAGTAGATTAAACTGGAAAT
1 TATGAATTGGATATAGACTGAAAAGCAATTTATTATCAACATTAATAGTAGATTAAACTGGAAAT
4113291 TATTGG
66 TATTGG
4113297 TATGAATTGGATATAGACTGAAAAGCAATTTATTATCAACATTAATAGTAGATTAAACTGGAAAT
1 TATGAATTGGATATAGACTGAAAAGCAATTTATTATCAACATTAATAGTAGATTAAACTGGAAAT
4113362 TATTGG
66 TATTGG
4113368 TATGAATTGGATATAGACTGAAAAGCAATTTATTATCAACATTAATAGTAGATTAAACTGGAAAT
1 TATGAATTGGATATAGACTGAAAAGCAATTTATTATCAACATTAATAGTAGATTAAACTGGAAAT
4113433 TATTGG
66 TATTGG
4113439 TATGAATTGGATATAGACTGAAAAGCAA
1 TATGAATTGGATATAGACTGAAAAGCAA
4113467 GGTACCAAAC
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 170 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (71 bp):
TATGAATTGGATATAGACTGAAAAGCAATTTATTATCAACATTAATAGTAGATTAAACTGGAAAT
TATTGG
Found at i:4116777 original size:17 final size:18
Alignment explanation
Indices: 4116745--4116780 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4116735 AGATCGATTC
*
4116745 AATTAAAAAATTATTAAA
1 AATTAAAAAATAATTAAA
4116763 AATTAAAAAA-AATTAAA
1 AATTAAAAAATAATTAAA
4116780 A
1 A
4116781 GATTCAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AATTAAAAAATAATTAAA
Found at i:4119511 original size:1 final size:1
Alignment explanation
Indices: 4119495--4119532 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
4119485 CCTCCGTGTG
* *
4119495 TTTTGTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4119533 GCAAAGATGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.05, T:0.95
Consensus pattern (1 bp):
T
Found at i:4122201 original size:20 final size:20
Alignment explanation
Indices: 4122176--4122213 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4122166 TAATTTTATT
4122176 CATGCATTACAATAATAATC
1 CATGCATTACAATAATAATC
4122196 CATGCATTACAATAATAA
1 CATGCATTACAATAATAA
4122214 ATTTTATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29
Consensus pattern (20 bp):
CATGCATTACAATAATAATC
Found at i:4122274 original size:17 final size:17
Alignment explanation
Indices: 4122248--4122299 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
4122238 TTTATTAAAA
4122248 ATATAAAATAATTTAAT
1 ATATAAAATAATTTAAT
**
4122265 ATATTTAATAATTTAA-
1 ATATAAAATAATTTAAT
4122281 ATATAAAATAATTTGAAT
1 ATATAAAATAATTT-AAT
4122299 A
1 A
4122300 ACTCGATTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 12 0.41
17 16 0.55
18 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
ATATAAAATAATTTAAT
Found at i:4122290 original size:16 final size:16
Alignment explanation
Indices: 4122246--4122299 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
4122236 AATTTATTAA
4122246 AAATATAAAATAATTT
1 AAATATAAAATAATTT
**
4122262 AATATATTTAATAATTT
1 AA-ATATAAAATAATTT
4122279 AAATATAAAATAATTT
1 AAATATAAAATAATTT
*
4122295 GAATA
1 AAATA
4122300 ACTCGATTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 18 0.56
17 14 0.44
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
AAATATAAAATAATTT
Found at i:4123889 original size:20 final size:20
Alignment explanation
Indices: 4123856--4123913 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
4123846 TTACTTTTAA
*
4123856 ATTTTTAAAT-ATT-AAAAT
1 ATTTTAAAATAATTAAAAAT
4123874 ATATTTAAAATAATTATAAAAT
1 AT-TTTAAAATAATTA-AAAAT
*
4123896 ATTTTAAGA-AATTAAAAA
1 ATTTTAAAATAATTAAAAA
4123914 ATTAGAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 2 0.06
19 11 0.32
20 8 0.24
21 6 0.18
22 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTTAAAATAATTAAAAAT
Found at i:4123914 original size:20 final size:22
Alignment explanation
Indices: 4123869--4123915 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
4123859 TTTAAATATT
*
4123869 AAAATATATTTAAAATAATTAT
1 AAAATATATTTAAAATAATTAA
*
4123891 AAAATAT-TTTAAGA-AATTAA
1 AAAATATATTTAAAATAATTAA
4123911 AAAAT
1 AAAAT
4123916 TAGAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 6 0.26
22 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATATATTTAAAATAATTAA
Found at i:4124781 original size:10 final size:10
Alignment explanation
Indices: 4124766--4124813 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
4124756 TAACGTGTTG
4124766 AATTTTAATT
1 AATTTTAATT
*
4124776 AATTTTATAATA
1 AA-TTT-TAATT
*
4124788 AATTTTGATT
1 AATTTTAATT
4124798 AATTTTAATT
1 AATTTTAATT
*
4124808 TATTTT
1 AATTTT
4124814 CGACAGATTC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 19 0.61
11 6 0.19
12 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (10 bp):
AATTTTAATT
Found at i:4127067 original size:81 final size:81
Alignment explanation
Indices: 4126977--4127127 Score: 302
Period size: 81 Copynumber: 1.9 Consensus size: 81
4126967 TTAAGTACAA
4126977 TTTAATTATTTTATAATTATTATATATTTTTCGACAAGAATTACTATGAAATTACATGAAATTGA
1 TTTAATTATTTTATAATTATTATATATTTTTCGACAAGAATTACTATGAAATTACATGAAATTGA
4127042 GTTAACCGAACTCATT
66 GTTAACCGAACTCATT
4127058 TTTAATTATTTTATAATTATTATATATTTTTCGACAAGAATTACTATGAAATTACATGAAATTGA
1 TTTAATTATTTTATAATTATTATATATTTTTCGACAAGAATTACTATGAAATTACATGAAATTGA
4127123 GTTAA
66 GTTAA
4127128 AAGTGTGTAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (81 bp):
TTTAATTATTTTATAATTATTATATATTTTTCGACAAGAATTACTATGAAATTACATGAAATTGA
GTTAACCGAACTCATT
Found at i:4129966 original size:25 final size:26
Alignment explanation
Indices: 4129938--4129991 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
4129928 TAATTAGTAT
*
4129938 AAAATATT-AATAATTCAAT-AAATTG
1 AAAA-ATTAAATAATTAAATAAAATTG
4129963 AAAAATTAAATAATTAAATAAAATTG
1 AAAAATTAAATAATTAAATAAAATTG
4129989 AAA
1 AAA
4129992 TTTAGGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 3 0.12
25 14 0.54
26 9 0.35
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (26 bp):
AAAAATTAAATAATTAAATAAAATTG
Found at i:4130840 original size:30 final size:30
Alignment explanation
Indices: 4130783--4130841 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
4130773 TGCCTTTGAA
* * *
4130783 AATATTTACAAAGAGAGATATCTAATTTTT
1 AATATTTACAAAAAGAGATACCAAATTTTT
4130813 AATATTTACAAAAAGAG-TAACCAAATTTT
1 AATATTTACAAAAAGAGAT-ACCAAATTTT
4130842 GAAAATAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (30 bp):
AATATTTACAAAAAGAGATACCAAATTTTT
Found at i:4139230 original size:4 final size:4
Alignment explanation
Indices: 4139221--4139320 Score: 173
Period size: 4 Copynumber: 25.0 Consensus size: 4
4139211 GTTACATATT
* *
4139221 TACA TACA TACA TACA TACG TACA TACC TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
4139269 TATA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
4139317 TACA
1 TACA
4139321 CTATAATAAA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 90 1.00
ACGTcount: A:0.48, C:0.25, G:0.01, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:4140487 original size:12 final size:12
Alignment explanation
Indices: 4140470--4140507 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
4140460 TTTTATTATA
4140470 TTTTAACTTTAC
1 TTTTAACTTTAC
*
4140482 TTTTAAC-TTAA
1 TTTTAACTTTAC
4140493 TTTTAACATTTAC
1 TTTTAAC-TTTAC
4140506 TT
1 TT
4140508 AATTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
12 7 0.32
13 5 0.23
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTAACTTTAC
Found at i:4144105 original size:85 final size:85
Alignment explanation
Indices: 4143870--4144119 Score: 322
Period size: 85 Copynumber: 2.9 Consensus size: 85
4143860 AAACAGTGTG
* *
4143870 GTTCGATCACAAACCAAGTGACAGTTCATTTAATCTT-CAAATATGTTGTGCACCCATAACAAGT
1 GTTCGATCACAAACCAAGTGGCAGTTCATTTAAT-TTACAAATATGTTGTGCACCCACAACAAGT
** * *** *
4143934 GATAGTAACAAAAAATATACG
65 GGCAATAACTGCAAATATACA
** * * *
4143955 GTTCGATCATGAACCAAGTAGCAGTTCGTTTAATTTACAAATTTGTTGTGCACCCACAACAAGTG
1 GTTCGATCACAAACCAAGTGGCAGTTCATTTAATTTACAAATATGTTGTGCACCCACAACAAGTG
* * *
4144020 GCACTAATTGCAAATATGCA
66 GCAATAACTGCAAATATACA
*
4144040 GTTCGATCACAAACCAAGTGGCAGTTCATTTAATTTACAAATATGTTGTGCACCTACAACAAGTG
1 GTTCGATCACAAACCAAGTGGCAGTTCATTTAATTTACAAATATGTTGTGCACCCACAACAAGTG
4144105 GCAATAACTGCAAAT
66 GCAATAACTGCAAAT
4144120 CAGCGATGGT
Statistics
Matches: 140, Mismatches: 24, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
84 2 0.01
85 138 0.99
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (85 bp):
GTTCGATCACAAACCAAGTGGCAGTTCATTTAATTTACAAATATGTTGTGCACCCACAACAAGTG
GCAATAACTGCAAATATACA
Found at i:4147925 original size:27 final size:27
Alignment explanation
Indices: 4147895--4147950 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
4147885 GTAAAATCGA
4147895 AACGTTTTATTAAAACAATTGAATTGT
1 AACGTTTTATTAAAACAATTGAATTGT
4147922 AACGTTTTATTAAAACAATTGAATTGT
1 AACGTTTTATTAAAACAATTGAATTGT
4147949 AA
1 AA
4147951 GGTGATTCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (27 bp):
AACGTTTTATTAAAACAATTGAATTGT
Found at i:4157315 original size:21 final size:21
Alignment explanation
Indices: 4157273--4157315 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4157263 AAACTAACAG
*
4157273 TTTAAAATAATAATATAATAT
1 TTTAAAATAATAAAATAATAT
*
4157294 TTTATAATAA-AAAATAACTAT
1 TTTAAAATAATAAAATAA-TAT
4157315 T
1 T
4157316 ATAATGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAAAATAATAAAATAATAT
Found at i:4168151 original size:16 final size:15
Alignment explanation
Indices: 4168124--4168155 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
4168114 TTTCACTTTA
4168124 TTTCTTATTATTATT
1 TTTCTTATTATTATT
4168139 TTTCTTCATTATTATT
1 TTTCTT-ATTATTATT
4168155 T
1 T
4168156 CTTAGTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTCTTATTATTATT
Found at i:4169631 original size:16 final size:16
Alignment explanation
Indices: 4169610--4169679 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 16
4169600 GACCATTAAG
4169610 TTTATTTTTTTTATTT
1 TTTATTTTTTTTATTT
*
4169626 TTTATTTATTTTACGTTT
1 TTTATTTTTTTTA--TTT
*
4169644 ATTT-TTATTTTTATTT
1 -TTTATTTTTTTTATTT
* *
4169660 TTAATTCTTTTTATTAT
1 TTTATTTTTTTTATT-T
4169677 TTT
1 TTT
4169680 CTTAGCCTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
15 2 0.05
16 25 0.58
17 3 0.07
18 10 0.23
19 3 0.07
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.79
Consensus pattern (16 bp):
TTTATTTTTTTTATTT
Found at i:4169650 original size:6 final size:6
Alignment explanation
Indices: 4169617--4169662 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
4169607 AAGTTTATTT
* **
4169617 TTTTTA TTTTT- TATTTA -TTTTA CGTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
4169663 ATTCTTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
5 8 0.24
6 25 0.76
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:4175384 original size:8 final size:8
Alignment explanation
Indices: 4175367--4175398 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
4175357 ATTGGACTTA
*
4175367 TTGGGGAT
1 TTGGGTAT
4175375 TTGGGTAT
1 TTGGGTAT
4175383 TTGGGTAT
1 TTGGGTAT
4175391 TTGGGTAT
1 TTGGGTAT
4175399 ATTTTTAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.41, T:0.47
Consensus pattern (8 bp):
TTGGGTAT
Found at i:4185181 original size:3 final size:3
Alignment explanation
Indices: 4185173--4185200 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4185163 GTTTTATTCA
4185173 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4185201 TATTGTCAAC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4186337 original size:18 final size:18
Alignment explanation
Indices: 4186314--4186350 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4186304 ATAATGTATT
*
4186314 TTTTATCCTTTATATTTA
1 TTTTATCCTTCATATTTA
*
4186332 TTTTATCGTTCATATTTA
1 TTTTATCCTTCATATTTA
4186350 T
1 T
4186351 ATGTTGGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTATCCTTCATATTTA
Found at i:4192953 original size:22 final size:21
Alignment explanation
Indices: 4192928--4192971 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
4192918 GGTCTTTACC
*
4192928 ATTTTTGAACTTGAGTATCGAT
1 ATTTTGGAACTTG-GTATCGAT
* *
4192950 ATTTTGGCATTTGGTATCGAT
1 ATTTTGGAACTTGGTATCGAT
4192971 A
1 A
4192972 CTTGATCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.25, C:0.09, G:0.20, T:0.45
Consensus pattern (21 bp):
ATTTTGGAACTTGGTATCGAT
Found at i:4194215 original size:2 final size:2
Alignment explanation
Indices: 4194210--4194261 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
4194200 GGCTTTCTTT
* *
4194210 TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
4194251 TC TC TT TC TC T
1 TC TC TC TC TC T
4194262 TTCGTAGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:4194262 original size:6 final size:6
Alignment explanation
Indices: 4194202--4194264 Score: 67
Period size: 6 Copynumber: 10.8 Consensus size: 6
4194192 TTTTTTTGGG
* * * * *
4194202 CTTTCT -TTTCT CTCTC- CTCTCT CTCTCT CTCTCT CTCTCT CTTTCT
1 CTTTCT CTTTCT CTTTCT CTTTCT CTTTCT CTTTCT CTTTCT CTTTCT
4194248 CTTTCT CTTTCT CTTTC
1 CTTTCT CTTTCT CTTTC
4194265 GTAGTTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
5 10 0.19
6 43 0.81
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (6 bp):
CTTTCT
Found at i:4198151 original size:5 final size:6
Alignment explanation
Indices: 4198135--4198160 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4198125 AAATCAATTC
4198135 ATTTTT ATTTTT ATTTTT ATTTTT AT
1 ATTTTT ATTTTT ATTTTT ATTTTT AT
4198161 GTAGAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:4200222 original size:11 final size:11
Alignment explanation
Indices: 4200208--4200232 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4200198 AAAAAAATGT
4200208 AAATAAAAATA
1 AAATAAAAATA
4200219 AAATAAAAATA
1 AAATAAAAATA
4200230 AAA
1 AAA
4200233 ACGGCACTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:4202051 original size:19 final size:19
Alignment explanation
Indices: 4201998--4202052 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
4201988 TTTTTTTATA
* * *
4201998 TATAAATTTTAATACTTTT
1 TATAAATTTTTATAATTCT
*
4202017 TGATAAA-TTTTGTAATTCT
1 T-ATAAATTTTTATAATTCT
4202036 TATAAATTTTTATAATT
1 TATAAATTTTTATAATT
4202053 ATATATTATG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 5 0.17
19 19 0.66
20 5 0.17
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (19 bp):
TATAAATTTTTATAATTCT
Found at i:4205238 original size:60 final size:60
Alignment explanation
Indices: 4205163--4205281 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 60
4205153 ATTTTTTTTA
*
4205163 TAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTG
*
4205223 TAATTATTTTAAAATTAATTTATTAGTCATTTAGGATTATGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTT
4205282 AGTTTAGTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTG
Found at i:4205484 original size:36 final size:36
Alignment explanation
Indices: 4205443--4205553 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 36
4205433 AGGTTACAAA
4205443 TTGTTAGTGTTTTGTGTTTTGTTATAGTTATTTATT
1 TTGTTAGTGTTTTGTGTTTTGTTATAGTTATTTATT
** * * * **
4205479 TTGTTAGTAATTTGTG---GGATTA-GGTTA--CAAA
1 TTGTTAGTGTTTTGTGTTTTG-TTATAGTTATTTATT
4205510 TTGTTAGTGTTTTGTGTTTTGTTATAGTTATTTATT
1 TTGTTAGTGTTTTGTGTTTTGTTATAGTTATTTATT
4205546 TTGTTAGT
1 TTGTTAGT
4205554 AATTTGTGGG
Statistics
Matches: 54, Mismatches: 14, Indels: 14
0.66 0.17 0.17
Matches are distributed among these distances:
31 15 0.28
33 8 0.15
34 8 0.15
36 23 0.43
ACGTcount: A:0.18, C:0.01, G:0.22, T:0.59
Consensus pattern (36 bp):
TTGTTAGTGTTTTGTGTTTTGTTATAGTTATTTATT
Found at i:4205514 original size:31 final size:31
Alignment explanation
Indices: 4205479--4205584 Score: 88
Period size: 31 Copynumber: 3.3 Consensus size: 31
4205469 GTTATTTATT
4205479 TTGTTAGTAATTTGTGGGATTAGGTTACAAA
1 TTGTTAGTAATTTGTGGGATTAGGTTACAAA
** * * * **
4205510 TTGTTAGTGTTTTGTGTTTTG-TTATAGTTATTTATT
1 TTGTTAGTAATTTGTG---GGATTA-GGTTA--CAAA
4205546 TTGTTAGTAATTTGTGGGATTAGGTTACAAA
1 TTGTTAGTAATTTGTGGGATTAGGTTACAAA
4205577 TTGTTAGT
1 TTGTTAGT
4205585 GTTTAGTATA
Statistics
Matches: 54, Mismatches: 14, Indels: 14
0.66 0.17 0.17
Matches are distributed among these distances:
31 23 0.43
33 8 0.15
34 8 0.15
36 15 0.28
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.52
Consensus pattern (31 bp):
TTGTTAGTAATTTGTGGGATTAGGTTACAAA
Found at i:4205515 original size:67 final size:67
Alignment explanation
Indices: 4205409--4205588 Score: 328
Period size: 67 Copynumber: 2.7 Consensus size: 67
4205399 AAAATTATAG
* *
4205409 TTATTTTGTTAGTAGTTTAT--GATTAGGTTACAAATTGTTAGTGTTTTGTGTTTTGTTATAGTT
1 TTATTTTGTTAGTAATTTGTGGGATTAGGTTACAAATTGTTAGTGTTTTGTGTTTTGTTATAGTT
4205472 AT
66 AT
4205474 TTATTTTGTTAGTAATTTGTGGGATTAGGTTACAAATTGTTAGTGTTTTGTGTTTTGTTATAGTT
1 TTATTTTGTTAGTAATTTGTGGGATTAGGTTACAAATTGTTAGTGTTTTGTGTTTTGTTATAGTT
4205539 AT
66 AT
4205541 TTATTTTGTTAGTAATTTGTGGGATTAGGTTACAAATTGTTAGTGTTT
1 TTATTTTGTTAGTAATTTGTGGGATTAGGTTACAAATTGTTAGTGTTT
4205589 AGTATAGGGT
Statistics
Matches: 111, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
65 18 0.16
67 93 0.84
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.55
Consensus pattern (67 bp):
TTATTTTGTTAGTAATTTGTGGGATTAGGTTACAAATTGTTAGTGTTTTGTGTTTTGTTATAGTT
AT
Found at i:4205695 original size:77 final size:77
Alignment explanation
Indices: 4205574--4205725 Score: 236
Period size: 77 Copynumber: 2.0 Consensus size: 77
4205564 ATTAGGTTAC
4205574 AAATTGTTAGTGTTTAGTATAGGGTTTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAAATTAA
1 AAATTGTTAGTGTTTAGTATAGGGTTTTTGTGATTTTTTAGTAATGT-ATTTTAAAAAAAA-TAA
4205639 ATTTATAGTTATAT
64 ATTTATAGTTATAT
* * * *
4205653 AAATTTTTAGTGTTTAGT-TA-TGTTTTTGTGATTTTTTAGTAATGTATTTTAAAAATAATAATT
1 AAATTGTTAGTGTTTAGTATAGGGTTTTTGTGATTTTTTAGTAATGTATTTTAAAAAAAATAAAT
4205716 TTATAGTTAT
66 TTATAGTTAT
4205726 TTTGTTAGTA
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
75 14 0.20
76 12 0.17
77 24 0.35
78 2 0.03
79 17 0.25
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (77 bp):
AAATTGTTAGTGTTTAGTATAGGGTTTTTGTGATTTTTTAGTAATGTATTTTAAAAAAAATAAAT
TTATAGTTATAT
Found at i:4207878 original size:33 final size:33
Alignment explanation
Indices: 4207836--4207970 Score: 130
Period size: 33 Copynumber: 4.1 Consensus size: 33
4207826 CAGCCCACTA
* *
4207836 CCACCTCAGTACTCCAGTCATCCTGGCTCGTAT
1 CCACCTCAGTACTCCACTCATCCTGGCCCGTAT
* * * *
4207869 CCACCTCAGTACTCCGCTCCT-TTCGGCTCGTAT
1 CCACCTCAGTACTCCACTCATCCT-GGCCCGTAT
* * * *
4207902 CTA-CTACCGTACTCCACTCTTCCCGGCCCGTAT
1 CCACCT-CAGTACTCCACTCATCCTGGCCCGTAT
* *
4207935 CCACCGCTGTACTCCACTCATCCTGGCCCGTAT
1 CCACCTCAGTACTCCACTCATCCTGGCCCGTAT
4207968 CCA
1 CCA
4207971 TTGTCGTACT
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
32 3 0.04
33 78 0.95
34 1 0.01
ACGTcount: A:0.16, C:0.44, G:0.14, T:0.27
Consensus pattern (33 bp):
CCACCTCAGTACTCCACTCATCCTGGCCCGTAT
Found at i:4207967 original size:66 final size:66
Alignment explanation
Indices: 4207844--4207991 Score: 145
Period size: 66 Copynumber: 2.2 Consensus size: 66
4207834 TACCACCTCA
* * * * * * * * *
4207844 GTACTCCAGTCATCCTGGCTCGTATCCACCTCAGTACTCCGCTCCTTTCGGCTCGTATCTACTAC
1 GTACTCCACTCATCCCGGCCCGTATCCACCGCAGTACTCCACTCATCTCGGCCCGTATCCACTAC
4207909 C
66 C
* * * *
4207910 GTACTCCACTCTTCCCGGCCCGTATCCACCGCTGTACTCCACTCATC-CTGGCCCGTATCCATTG
1 GTACTCCACTCATCCCGGCCCGTATCCACCGCAGTACTCCACTCATCTC-GGCCCGTATCCACTA
*
4207974 TC
65 CC
*
4207976 GTACTCCACTCCTCCC
1 GTACTCCACTCATCCC
4207992 AGCTCAAGTT
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
65 1 0.02
66 65 0.98
ACGTcount: A:0.14, C:0.43, G:0.14, T:0.28
Consensus pattern (66 bp):
GTACTCCACTCATCCCGGCCCGTATCCACCGCAGTACTCCACTCATCTCGGCCCGTATCCACTAC
C
Found at i:4207980 original size:33 final size:32
Alignment explanation
Indices: 4207844--4207991 Score: 109
Period size: 33 Copynumber: 4.5 Consensus size: 32
4207834 TACCACCTCA
* * * *
4207844 GTACTCCAGTCATCCTGGCTCGTATCCACCTC
1 GTACTCCACTCATCCCGGCCCGTATCCACCGC
* * ** * *
4207876 AGTACTCCGCTCCTTTCGGCTCGTATCTACTAC-C
1 -GTACTCCACTCATCCCGGCCCGTATCCAC--CGC
*
4207910 GTACTCCACTCTTCCCGGCCCGTATCCACCGC
1 GTACTCCACTCATCCCGGCCCGTATCCACCGC
* **
4207942 TGTACTCCACTCATCCTGGCCCGTATCCATTGTC
1 -GTACTCCACTCATCCCGGCCCGTATCCACCG-C
*
4207976 GTACTCCACTCCTCCC
1 GTACTCCACTCATCCC
4207992 AGCTCAAGTT
Statistics
Matches: 91, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
31 1 0.01
32 1 0.01
33 86 0.95
34 2 0.02
35 1 0.01
ACGTcount: A:0.14, C:0.43, G:0.14, T:0.28
Consensus pattern (32 bp):
GTACTCCACTCATCCCGGCCCGTATCCACCGC
Found at i:4208386 original size:76 final size:77
Alignment explanation
Indices: 4208181--4208528 Score: 517
Period size: 75 Copynumber: 4.5 Consensus size: 77
4208171 AATAACTTCA
*
4208181 TATTTATGTAATGGATTTTTTTCCATTTTATTTATCAATTTTATGGATTTTTTTTTGCAATTTAA
1 TATTTATGTAATGAATTTTTTTCCATTTTATTTATCAATTTTATGG-TTTTTTTTTGCAATTTAA
**
4208246 ATAGTCAACTTCA
65 ATAGTCAACTTTG
* * * *
4208259 TATTTATGTAATGAATTTGTTGCCATTTTATTTATCAATTTTATGG-GTTTTTTTGCAATTTTAA
1 TATTTATGTAATGAATTTTTTTCCATTTTATTTATCAATTTTATGGTTTTTTTTTGCAATTTAAA
4208323 TAGTCAACTTTG
66 TAGTCAACTTTG
4208335 TATTTATGTAAT-AATTTTTTTCCATTTTATTTATCAATTTTATGG-TTTTTTTTGCAATTTAAA
1 TATTTATGTAATGAATTTTTTTCCATTTTATTTATCAATTTTATGGTTTTTTTTTGCAATTTAAA
4208398 TAGTCAACTTTG
66 TAGTCAACTTTG
* *
4208410 TATTAATGTAATGAATTTTTTGT-CATTTTATTTATCAATCTTATGAGTTTTTTTTTTTGCAATT
1 TATTTATGTAATGAATTTTTT-TCCATTTTATTTATCAATTTTATG-G--TTTTTTTTTGCAATT
4208474 TAAATAGTCAACTTTG
62 TAAATAGTCAACTTTG
*
4208490 TATTTATGTAAT-AATTTTTTTACCATTTTAATTATCAAT
1 TATTTATGTAATGAATTTTTTT-CCATTTTATTTATCAAT
4208529 GTTGACACCA
Statistics
Matches: 247, Mismatches: 15, Indels: 14
0.89 0.05 0.05
Matches are distributed among these distances:
75 70 0.28
76 67 0.27
77 2 0.01
78 44 0.18
79 8 0.03
80 56 0.23
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.55
Consensus pattern (77 bp):
TATTTATGTAATGAATTTTTTTCCATTTTATTTATCAATTTTATGGTTTTTTTTTGCAATTTAAA
TAGTCAACTTTG
Found at i:4208425 original size:151 final size:154
Alignment explanation
Indices: 4208181--4208528 Score: 540
Period size: 151 Copynumber: 2.2 Consensus size: 154
4208171 AATAACTTCA
*
4208181 TATTTATGTAATGGATTTTTTTCCATTTTATTTATCAATTTTATGGATTTTTTTTTGCAATTTAA
1 TATTTATGTAAT-AATTTTTTTCCATTTTATTTATCAATTTTATGGA-TTTTTTTTGCAATTTAA
* *
4208246 ATAGTCAACTTCATATTTATGTAATGAATTTGTTGCCATTTTATTTATCAATTTTATG-G-GTTT
64 ATAGTCAACTTCATATTAATGTAATGAATTTGTTGCCATTTTATTTATCAATCTTATGAGTGTTT
*
4208309 TTTTGCAATTTTAATAGTCAACTTTG
129 TTTTGCAATTTAAATAGTCAACTTTG
4208335 TATTTATGTAATAATTTTTTTCCATTTTATTTATCAATTTTATGG-TTTTTTTTGCAATTTAAAT
1 TATTTATGTAATAATTTTTTTCCATTTTATTTATCAATTTTATGGATTTTTTTTGCAATTTAAAT
** * * *
4208399 AGTCAACTTTGTATTAATGTAATGAATTTTTTGTCATTTTATTTATCAATCTTATGAGTTTTTTT
66 AGTCAACTTCATATTAATGTAATGAATTTGTTGCCATTTTATTTATCAATCTTATGAG--TGTTT
4208464 TTTTGCAATTTAAATAGTCAACTTTG
129 TTTTGCAATTTAAATAGTCAACTTTG
*
4208490 TATTTATGTAATAATTTTTTTACCATTTTAATTATCAAT
1 TATTTATGTAATAATTTTTTT-CCATTTTATTTATCAAT
4208529 GTTGACACCA
Statistics
Matches: 179, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
151 69 0.39
152 1 0.01
153 32 0.18
154 12 0.07
155 49 0.27
156 16 0.09
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.55
Consensus pattern (154 bp):
TATTTATGTAATAATTTTTTTCCATTTTATTTATCAATTTTATGGATTTTTTTTGCAATTTAAAT
AGTCAACTTCATATTAATGTAATGAATTTGTTGCCATTTTATTTATCAATCTTATGAGTGTTTTT
TTGCAATTTAAATAGTCAACTTTG
Found at i:4211540 original size:44 final size:43
Alignment explanation
Indices: 4211490--4212062 Score: 116
Period size: 44 Copynumber: 13.2 Consensus size: 43
4211480 GTACTTAGGA
4211490 AGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACTGATGG
1 AGGCAAGATCTG-TATCTTTAACCAGCTCCACTGCAACTGATGG
* * ** * * * * *
4211534 AGGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAAC-GCA-GG
1 AGGCAA-GATCTGTATCTTTAACCAGCTCCACTG-CAACTG-ATGG
4211576 AAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACTGATGG
1 -AGGCAAGATCTG-TATCTTTAACCAGCTCCACTGCAACTGATGG
* * ** * * * * *
4211621 AGGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAAC-GCA-GG
1 AGGCAA-GATCTGTATCTTTAACCAGCTCCACTG-CAACTG-ATGG
*
4211663 AAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGG
1 -AGGCAAGATCTG-TATCTTTAACCAGCTCCACTGCAACTGATGG
* * * * * **** * * *
4211708 AGACAAGGCTTTGT-T-TTTGATCTA-CTTTGGTGTTAAC-GCAAGA
1 AGGCAA-GATCTGTATCTTT-AACCAGCTCCACTG-CAACTG-ATGG
4211751 AGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACTGATGG
1 AGGCAAGATCTG-TATCTTTAACCAGCTCCACTGCAACTGATGG
* * * * * ** * * **
4211795 AGGTAAG-GCTTTTTTTTTTGTCTA-CTTCACTATTAAC-G-TAGG
1 AGGCAAGATC-TGTATCTTTAACCAGCTCCACT-GCAACTGAT-GG
* *
4211837 AAGGCAAGATCTGCTATCTTTAACCAGCTCCATTGCAACCGATGG
1 -AGGCAAGATCTG-TATCTTTAACCAGCTCCACTGCAACTGATGG
* * * * * * * *
4211882 AGGCAAGGCTTTGT-T-TTCGATCTA-CTTCGCTGTTAAC-GCA-GG
1 AGGCAA-GATCTGTATCTT-TAACCAGCTCCACTG-CAACTG-ATGG
*
4211924 AAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGG
1 -AGGCAAGATCTG-TATCTTTAACCAGCTCCACTGCAACTGATGG
* * *** * * * *
4211969 AGGCAATGCTTTGT-T-TTTGGTCTGCTTCGCTGTTAAC-GCA-GG
1 AGGCAA-GATCTGTATCTTTAACCAGCTCCACTG-CAACTG-ATGG
*
4212011 AAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGG
1 -AGGCAAGATCTG-TATCTTTAACCAGCTCCACTGCAACTGATGG
4212056 AGGCAAG
1 AGGCAAG
4212063 GCTTTGTTTT
Statistics
Matches: 355, Mismatches: 118, Indels: 112
0.61 0.20 0.19
Matches are distributed among these distances:
41 1 0.00
42 89 0.25
43 84 0.24
44 91 0.26
45 89 0.25
46 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (43 bp):
AGGCAAGATCTGTATCTTTAACCAGCTCCACTGCAACTGATGG
Found at i:4211583 original size:43 final size:43
Alignment explanation
Indices: 4211534--4211670 Score: 129
Period size: 43 Copynumber: 3.2 Consensus size: 43
4211524 CAACTGATGG
4211534 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGA
* * * * * * * *
4211577 AGGCAAGATCTGTTATCTTT-AACCAGCTCCACTG-CAACTG-ATGG-
1 AGGCAAG-GCT-TTGT-TTTCGATCTGCTTCGCTGTTAAC-GCA-GGA
4211621 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGA
4211664 AGGCAAG
1 AGGCAAG
4211671 ATCTGTTATC
Statistics
Matches: 69, Mismatches: 16, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
41 3 0.04
42 15 0.22
43 20 0.29
44 13 0.19
45 15 0.22
46 3 0.04
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (43 bp):
AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGA
Found at i:4211588 original size:87 final size:87
Alignment explanation
Indices: 4211486--4212078 Score: 954
Period size: 87 Copynumber: 6.8 Consensus size: 87
4211476 GCTAGTACTT
* *
4211486 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACTGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
4211551 CGATCTGCTTCGCTGTTAACGC
66 CGATCTACTTCGCTGTTAACGC
*
4211573 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACTGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
4211638 CGATCTGCTTCGCTGTTAACGC
66 CGATCTACTTCGCTGTTAACGC
*
4211660 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGACAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* * *
4211725 TGATCTACTTTGGTGTTAACGC
66 CGATCTACTTCGCTGTTAACGC
* * * *
4211747 AAGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACTGATGGAGGTAAGGCTTTTTTTT
1 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGC-TTTGTTT
* * * *
4211812 TTG-TCTACTTCACTATTAACGT
65 TCGATCTACTTCGCTGTTAACGC
* *
4211834 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCATTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
4211899 CGATCTACTTCGCTGTTAACGC
66 CGATCTACTTCGCTGTTAACGC
*
4211921 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAATGCTTTGTTTT
1 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* * *
4211986 TGGTCTGCTTCGCTGTTAACGC
66 CGATCTACTTCGCTGTTAACGC
*
4212008 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
4212073 CGATCT
66 CGATCT
4212079 TCACTGATCT
Statistics
Matches: 467, Mismatches: 37, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
86 8 0.02
87 450 0.96
88 9 0.02
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (87 bp):
AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
CGATCTACTTCGCTGTTAACGC
Found at i:4213317 original size:7 final size:7
Alignment explanation
Indices: 4213305--4213337 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
4213295 TCCATTTTAC
4213305 TTTTCAT
1 TTTTCAT
4213312 TTTTCA-
1 TTTTCAT
4213318 TTTTCA-
1 TTTTCAT
4213324 TTTTCAT
1 TTTTCAT
4213331 TTTTCAT
1 TTTTCAT
4213338 CACTCCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTCAT
Found at i:4213777 original size:46 final size:47
Alignment explanation
Indices: 4213720--4213813 Score: 127
Period size: 46 Copynumber: 2.0 Consensus size: 47
4213710 GCTTTTCATA
* *
4213720 TTTTTATTTTGACTTTGATTGATTTCTCT-TTTTATTTTTTCTTTTT
1 TTTTTATTTTGACTTTGATTGATTTCTCTCTTTTACTTTTCCTTTTT
* ** *
4213766 TTTTTATTTTGATTTTGATTTTTTTCTCTCTTTTCCTTTTCCTTTTT
1 TTTTTATTTTGACTTTGATTGATTTCTCTCTTTTACTTTTCCTTTTT
4213813 T
1 T
4213814 CGAATCGGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
46 26 0.63
47 15 0.37
ACGTcount: A:0.09, C:0.12, G:0.05, T:0.74
Consensus pattern (47 bp):
TTTTTATTTTGACTTTGATTGATTTCTCTCTTTTACTTTTCCTTTTT
Found at i:4219285 original size:33 final size:33
Alignment explanation
Indices: 4219243--4219497 Score: 216
Period size: 33 Copynumber: 7.7 Consensus size: 33
4219233 AATACATGTG
* *
4219243 TAAGACCATAGCTGAGCTATGACATTCTGATGA
1 TAAGACCATAACTGAGCTATGGCATTCTGATGA
* * * **
4219276 TAAGACCATAACTGGGTTATGGCACTACAAATG-
1 TAAGACCATAACTGAGCTATGGCA-TTCTGATGA
*
4219309 TAAGACCATATCT-AGGCTATGGCATTCTGATGA
1 TAAGACCATAACTGA-GCTATGGCATTCTGATGA
* * * **
4219342 TAAGACCATAACTGGGTTATGGCACTACAAATG-
1 TAAGACCATAACTGAGCTATGGCA-TTCTGATGA
*
4219375 TAAGACCATATCT-AGGCTATGGCATTCTGATGA
1 TAAGACCATAACTGA-GCTATGGCATTCTGATGA
* * * **
4219408 TAAGACCATAACTGGGTTATGGCACTACAAATG-
1 TAAGACCATAACTGAGCTATGGCA-TTCTGATGA
*
4219441 TAAGACCATATCT-AGGCTATGGCATTCTGATGA
1 TAAGACCATAACTGA-GCTATGGCATTCTGATGA
* *
4219474 TAAGACCATAACTGGGTTATGGCA
1 TAAGACCATAACTGAGCTATGGCA
4219498 CTACAAATGG
Statistics
Matches: 170, Mismatches: 40, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
32 15 0.09
33 140 0.82
34 15 0.09
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (33 bp):
TAAGACCATAACTGAGCTATGGCATTCTGATGA
Found at i:4219512 original size:33 final size:33
Alignment explanation
Indices: 4219276--4219515 Score: 261
Period size: 33 Copynumber: 7.3 Consensus size: 33
4219266 ATTCTGATGA
4219276 TAAGACCATAACTGGGTTATGGCACTACAAATG
1 TAAGACCATAACTGGGTTATGGCACTACAAATG
* * * * **
4219309 TAAGACCATATCTAGGCTATGGCA-TTCTGATG
1 TAAGACCATAACTGGGTTATGGCACTACAAATG
4219341 ATAAGACCATAACTGGGTTATGGCACTACAAATG
1 -TAAGACCATAACTGGGTTATGGCACTACAAATG
* * * * **
4219375 TAAGACCATATCTAGGCTATGGCA-TTCTGATG
1 TAAGACCATAACTGGGTTATGGCACTACAAATG
4219407 ATAAGACCATAACTGGGTTATGGCACTACAAATG
1 -TAAGACCATAACTGGGTTATGGCACTACAAATG
* * * * **
4219441 TAAGACCATATCTAGGCTATGGCA-TTCTGATG
1 TAAGACCATAACTGGGTTATGGCACTACAAATG
4219473 ATAAGACCATAACTGGGTTATGGCACTACAAATG
1 -TAAGACCATAACTGGGTTATGGCACTACAAATG
*
4219507 GAAGACCAT
1 TAAGACCAT
4219516 GGCAGGGCCA
Statistics
Matches: 164, Mismatches: 37, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
32 15 0.09
33 134 0.82
34 15 0.09
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (33 bp):
TAAGACCATAACTGGGTTATGGCACTACAAATG
Found at i:4219544 original size:132 final size:132
Alignment explanation
Indices: 4219244--4219549 Score: 476
Period size: 132 Copynumber: 2.3 Consensus size: 132
4219234 ATACATGTGT
* * *
4219244 AAGACCATAGCT-GAGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAAAT
1 AAGACCATAGCTAG-GCCATGGCATGCTGATGATAAGACCATAACTGGGTTATGGCACTACAAAT
4219308 GTAAGACCATATCTAGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAAA
65 GTAAGACCATATCTAGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAAA
*
4219373 TGT
130 TGG
* * *
4219376 AAGACCATATCTAGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAAATG
1 AAGACCATAGCTAGGCCATGGCATGCTGATGATAAGACCATAACTGGGTTATGGCACTACAAATG
4219441 TAAGACCATATCTAGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAAAT
66 TAAGACCATATCTAGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAAAT
4219506 GG
131 GG
*
4219508 AAGACCATGGC-AGGGCCATGGCAATGCATG-TG-TAAGACCATA
1 AAGACCATAGCTA-GGCCATGGC-ATGC-TGATGATAAGACCATA
4219550 GTTGGACTAT
Statistics
Matches: 163, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
131 1 0.01
132 154 0.94
133 6 0.04
134 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.25
Consensus pattern (132 bp):
AAGACCATAGCTAGGCCATGGCATGCTGATGATAAGACCATAACTGGGTTATGGCACTACAAATG
TAAGACCATATCTAGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAAAT
GG
Found at i:4219563 original size:66 final size:66
Alignment explanation
Indices: 4219241--4219515 Score: 507
Period size: 66 Copynumber: 4.2 Consensus size: 66
4219231 TAAATACATG
* *
4219241 TGTAAGACCATAGCT-GAGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGGCACTACA
1 TGTAAGACCATATCTAG-GCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACA
4219305 AA
65 AA
4219307 TGTAAGACCATATCTAGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAA
1 TGTAAGACCATATCTAGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAA
4219372 A
66 A
4219373 TGTAAGACCATATCTAGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAA
1 TGTAAGACCATATCTAGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAA
4219438 A
66 A
4219439 TGTAAGACCATATCTAGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAA
1 TGTAAGACCATATCTAGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAA
4219504 A
66 A
*
4219505 TGGAAGACCAT
1 TGTAAGACCAT
4219516 GGCAGGGCCA
Statistics
Matches: 205, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
66 204 1.00
67 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (66 bp):
TGTAAGACCATATCTAGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAA
A
Found at i:4221114 original size:30 final size:28
Alignment explanation
Indices: 4221073--4221154 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
4221063 ATGAAAAAAA
*
4221073 ATATTAGATTTTTATGTTTTAAATATATT
1 ATATTATATTTTTAT-TTTTAAATATATT
* *
4221102 A-A-TATATTATTTTATTATAAAATATATT
1 ATATTATA-T-TTTTATTTTTAAATATATT
*
4221130 ATATTATATTATTATATTTTAAATA
1 ATATTATATTTTTAT-TTTTAAATA
4221155 AACAAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
27 3 0.07
28 19 0.45
29 16 0.38
30 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATTATATTTTTATTTTTAAATATATT
Found at i:4221127 original size:20 final size:22
Alignment explanation
Indices: 4221102--4221141 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
4221092 TAAATATATT
4221102 AATATATTAT-TT-TATTATAA
1 AATATATTATATTATATTATAA
4221122 AATATATTATATTATATTAT
1 AATATATTATATTATATTAT
4221142 TATATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATATTATATTATATTATAA
Found at i:4221134 original size:22 final size:20
Alignment explanation
Indices: 4221102--4221141 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
4221092 TAAATATATT
*
4221102 AATATATTATTTTATTATAA
1 AATATATTATTATATTATAA
4221122 AATATATTATATTATATTAT
1 AATATA-T-TATTATATTAT
4221142 TATATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATATATTATTATATTATAA
Found at i:4221397 original size:16 final size:16
Alignment explanation
Indices: 4221376--4221411 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4221366 AGACGAAAAA
* *
4221376 GAAAGAAAGGAAAGGG
1 GAAAGAAAAGAAAAGG
4221392 GAAAGAAAAGAAAAGG
1 GAAAGAAAAGAAAAGG
4221408 GAAA
1 GAAA
4221412 AACTAGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAGAAAAGG
Found at i:4222408 original size:27 final size:23
Alignment explanation
Indices: 4222363--4222417 Score: 56
Period size: 27 Copynumber: 2.2 Consensus size: 23
4222353 TTTAAAATTG
*
4222363 ATTGAAAAGTGGAAAATGATTCA
1 ATTGAAAAGTGGAAAATGACTCA
*
4222386 ATTGAAAATGTGAGAAATTATGACTGA
1 ATTGAAAA-GTG-GAAA--ATGACTCA
4222413 ATTGA
1 ATTGA
4222418 GTTTTAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 8 0.31
24 3 0.12
25 4 0.15
27 11 0.42
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (23 bp):
ATTGAAAAGTGGAAAATGACTCA
Found at i:4222575 original size:23 final size:23
Alignment explanation
Indices: 4222522--4222576 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
4222512 AGCTTTACCG
*
4222522 ATCAGGCATTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
*
4222545 ATCGGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
* *
4222568 TTTAGGCAC
1 ATCAGGCAC
4222577 CTCGTGTGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAT
Found at i:4228422 original size:30 final size:30
Alignment explanation
Indices: 4228388--4228460 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
4228378 AATAAACACC
4228388 AAAAATTTATTTTACAAA-TAAAAAAGTAAA
1 AAAAATTTATTTTA-AAATTAAAAAAGTAAA
** *
4228418 AAAAAAGTATTTTAAAATTAAAAAATTAAA
1 AAAAATTTATTTTAAAATTAAAAAAGTAAA
4228448 AAATATATTTATT
1 AAA-A-ATTTATT
4228461 ATATATTCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 3 0.09
30 26 0.74
31 1 0.03
32 5 0.14
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAAATTTATTTTAAAATTAAAAAAGTAAA
Found at i:4234126 original size:48 final size:48
Alignment explanation
Indices: 4234029--4234127 Score: 119
Period size: 48 Copynumber: 2.1 Consensus size: 48
4234019 ACACTCTAGT
* *
4234029 TTGTGGATGAACCACCAATACTTGCAAATAAACTATTAGTACAAAAAA
1 TTGTGGAGGAACCACCAATACTTGCAAATAAAATATTAGTACAAAAAA
* * * * *
4234077 TTGTGGAGGAACCACCAGTATTTTCAAATAAAAATATTTGTA-AATAAA
1 TTGTGGAGGAACCACCAATACTTGCAAAT-AAAATATTAGTACAAAAAA
4234125 TTG
1 TTG
4234128 CCACTTGTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 33 0.77
49 10 0.23
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.29
Consensus pattern (48 bp):
TTGTGGAGGAACCACCAATACTTGCAAATAAAATATTAGTACAAAAAA
Found at i:4240673 original size:125 final size:125
Alignment explanation
Indices: 4240236--4240672 Score: 705
Period size: 125 Copynumber: 3.5 Consensus size: 125
4240226 TTTATGGTTT
* ** *
4240236 AGGATGCTTTATCAGAAGAATTTCTGAAATGGCATCCACGTGGACGCGCTTTTGCTACAGTTGGT
1 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTAGT
* * *
4240301 CCTGAAAAAATAATTTCGAGTTGACGTTTGTGAGAAAATAGTATAAAAAAACGCTTCAAGT
66 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAAACGCTTCAAGC
*
4240362 AGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTAGT
1 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTAGT
*
4240427 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTATAAAAAACGCTTCAAGC
66 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
* * *
4240487 AGGATGCTTTATTAGAAGAATTTCTGAAATTGCCCCCACGTGGACGCGCTTTTGCTACAG-TATG
1 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTA-G
*
4240551 TCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGAATAAAAAACGCTTCAAGC
65 TCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
* * *
4240612 AGGATGCTTTATCAGAAGAATTTATGAAATCGCGCCCTCGTGGATGCGCTTTTGCTACAGT
1 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
4240673 AGCATGTTTG
Statistics
Matches: 288, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
124 2 0.01
125 185 0.64
126 101 0.35
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (125 bp):
AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTAGT
CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
Found at i:4242794 original size:22 final size:22
Alignment explanation
Indices: 4242769--4242831 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 22
4242759 AAATATGGAT
4242769 TTGAGAGAAATTTG-GAAGGAAA
1 TTGAGAGAAATTTGAG-AGGAAA
4242791 TTGAGAGCAAA-TTGAGAGGAAA
1 TTGAGAG-AAATTTGAGAGGAAA
4242813 TTGAGA-AAATAATTGAGAG
1 TTGAGAGAAAT--TTGAGAG
4242832 AGTATTAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.08
22 22 0.61
23 11 0.31
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:4242804 original size:11 final size:11
Alignment explanation
Indices: 4242788--4242818 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4242778 ATTTGGAAGG
4242788 AAATTGAGAGC
1 AAATTGAGAGC
*
4242799 AAATTGAGAGG
1 AAATTGAGAGC
4242810 AAATTGAGA
1 AAATTGAGA
4242819 AAATAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.48, C:0.03, G:0.29, T:0.19
Consensus pattern (11 bp):
AAATTGAGAGC
Found at i:4244859 original size:29 final size:31
Alignment explanation
Indices: 4244809--4244866 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
4244799 GAATCTTTAG
*
4244809 TTTTTAGGATTTTTAAGCTTTTTTTTTTGTC
1 TTTTTAGGATTTTTAAGATTTTTTTTTTGTC
*
4244840 TTTTT-GGA-TTTTATGATTTTTTTTTTG
1 TTTTTAGGATTTTTAAGATTTTTTTTTTG
4244867 AATTTATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.68
30 3 0.12
31 5 0.20
ACGTcount: A:0.12, C:0.03, G:0.14, T:0.71
Consensus pattern (31 bp):
TTTTTAGGATTTTTAAGATTTTTTTTTTGTC
Found at i:4244881 original size:28 final size:29
Alignment explanation
Indices: 4244827--4244881 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
4244817 ATTTTTAAGC
** * *
4244827 TTTTTTTTTTGTCTTTTTGGATTTTATGA
1 TTTTTTTTTTGAATTTATGGATATTATGA
4244856 TTTTTTTTTTGAATTTAT-GATATTAT
1 TTTTTTTTTTGAATTTATGGATATTAT
4244882 TTTGAAGTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 7 0.32
29 15 0.68
ACGTcount: A:0.16, C:0.02, G:0.11, T:0.71
Consensus pattern (29 bp):
TTTTTTTTTTGAATTTATGGATATTATGA
Found at i:4244884 original size:21 final size:20
Alignment explanation
Indices: 4244840--4244884 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4244830 TTTTTTTGTC
* *
4244840 TTTTTGGATTTTATGATTTT
1 TTTTTGGAATTTATGATTTA
*
4244860 TTTTTTGAATTTATGATATTA
1 TTTTTGGAATTTATGAT-TTA
4244881 TTTT
1 TTTT
4244885 GAAGTGGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (20 bp):
TTTTTGGAATTTATGATTTA
Found at i:4259703 original size:20 final size:20
Alignment explanation
Indices: 4259672--4259727 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
4259662 GGAACCTGCA
*
4259672 AATTGATGTTTAGTTGATGT
1 AATTAATGTTTAGTTGATGT
*
4259692 AATTAATTTTTAGTTGATGT
1 AATTAATGTTTAGTTGATGT
*
4259712 AATTGATGTTTAGTTG
1 AATTAATGTTTAGTTG
4259728 TCACTTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (20 bp):
AATTAATGTTTAGTTGATGT
Found at i:4268289 original size:23 final size:23
Alignment explanation
Indices: 4268262--4268323 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
4268252 ATATTAATGG
*
4268262 TAGTGATAATATTTAGAATTCTT
1 TAGTGATAATATTTAGAATTATT
**
4268285 TAGTGATAATATTTAGGGTTATT
1 TAGTGATAATATTTAGAATTATT
*
4268308 TAGAGATAATATTTAG
1 TAGTGATAATATTTAG
4268324 GAAAAGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.45
Consensus pattern (23 bp):
TAGTGATAATATTTAGAATTATT
Found at i:4273601 original size:23 final size:23
Alignment explanation
Indices: 4273575--4273651 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
4273565 TAATTTTTAA
*
4273575 ATTTTGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
* *
4273598 ATTTAGAAGTATTTAGTAATAAT
1 ATTTAGAATTATTTAGTGATAAT
** *
4273621 ATTTAGGGTTATTTAGGGATAAT
1 ATTTAGAATTATTTAGTGATAAT
4273644 ATTTAGAA
1 ATTTAGAA
4273652 AAAAATTTAG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:4273602 original size:13 final size:12
Alignment explanation
Indices: 4273584--4273649 Score: 50
Period size: 13 Copynumber: 5.6 Consensus size: 12
4273574 AATTTTGAAT
4273584 TATTTAGTGATAA
1 TATTTAG-GATAA
*
4273597 TATTTA-GA-AG
1 TATTTAGGATAA
*
4273607 TATTTAGTAATAA
1 TATTTAG-GATAA
*
4273620 TATTTAGGGT--
1 TATTTAGGATAA
4273630 TATTTAGGGATAA
1 TATTTA-GGATAA
4273643 TATTTAG
1 TATTTAG
4273650 AAAAAAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
10 13 0.32
11 5 0.12
12 3 0.07
13 20 0.49
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (12 bp):
TATTTAGGATAA
Found at i:4274924 original size:19 final size:19
Alignment explanation
Indices: 4274897--4274938 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
4274887 TGAAAATTAA
4274897 TATTAATATATTTATAGAT
1 TATTAATATATTTATAGAT
*
4274916 TATTCATATATTTATAGAT
1 TATTAATATATTTATAGAT
4274935 TATT
1 TATT
4274939 TAATTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
TATTAATATATTTATAGAT
Found at i:4274959 original size:16 final size:16
Alignment explanation
Indices: 4274906--4274959 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
4274896 ATATTAATAT
4274906 ATTTATAGATTATTCATA
1 ATTTATAGATTATT-A-A
*
4274924 TATTTATAGATTATTTA
1 -ATTTATAGATTATTAA
* *
4274941 ATTTATATATTGTTAA
1 ATTTATAGATTATTAA
4274957 ATT
1 ATT
4274960 AATTTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 16 0.52
17 1 0.03
19 14 0.45
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (16 bp):
ATTTATAGATTATTAA
Done.