Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008893.1 Hibiscus syriacus cultivar Beakdansim tig00112159_pilon, whole genome shotgun sequence
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: 2797279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 13
Found at i:429741 original size:15 final size:15
Alignment explanation
Indices: 429689--429741 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
429679 TTTAATAATA
*
429689 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
429704 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
* *
429719 TAAAAAAACCGATTTTT
1 T--TAAAACCGGTTTTT
429736 TTAAAA
1 TTAAAA
429742 TCGAAACCGG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 18 0.60
17 12 0.40
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:429861 original size:15 final size:17
Alignment explanation
Indices: 429835--429866 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
429825 TTCTATGGGA
429835 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
429851 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
429867 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:434095 original size:7 final size:7
Alignment explanation
Indices: 434083--434114 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
434073 CGAAACCAAG
434083 AAAAAAC
1 AAAAAAC
434090 AAAAAAC
1 AAAAAAC
434097 AAAAAAC
1 AAAAAAC
434104 AAAAAAC
1 AAAAAAC
434111 AAAA
1 AAAA
434115 GAAGAAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:434738 original size:9 final size:9
Alignment explanation
Indices: 434724--434750 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
434714 ATATTTTTAA
434724 ATTTTATTT
1 ATTTTATTT
434733 ATTTTATTT
1 ATTTTATTT
434742 ATTTTATTT
1 ATTTTATTT
434751 TATATCCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
ATTTTATTT
Found at i:435777 original size:15 final size:16
Alignment explanation
Indices: 435746--435778 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
435736 TTTTAATGAT
435746 TATATATAAAGAAATTA
1 TATATATAAAG-AATTA
435763 TATATATAAAG-ATTA
1 TATATATAAAGAATTA
435778 T
1 T
435779 TAATTATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
17 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
TATATATAAAGAATTA
Found at i:439405 original size:4 final size:4
Alignment explanation
Indices: 439398--439432 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
439388 CTTTAAATAA
439398 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
439433 AGAAAGGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:439904 original size:30 final size:30
Alignment explanation
Indices: 439829--439904 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
439819 AATACATTTT
439829 AAAGCGCTGCTAAAAACCATTTTGACAAAAA
1 AAAG-GCTGCTAAAAACCATTTTGACAAAAA
* ** *
439860 AAAGGCCGCTAAAAACCATTTTGGTGAGAAA
1 AAAGGCTGCTAAAAACCATTTT-GACAAAAA
439891 AAAGGCTGC-AAAAA
1 AAAGGCTGCTAAAAA
439905 GCACCGCTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 22 0.56
31 17 0.44
ACGTcount: A:0.47, C:0.17, G:0.18, T:0.17
Consensus pattern (30 bp):
AAAGGCTGCTAAAAACCATTTTGACAAAAA
Found at i:443645 original size:2 final size:2
Alignment explanation
Indices: 443640--443689 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
443630 ATATACACAC
443640 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
443682 AT AT AT AT
1 AT AT AT AT
443690 TTACTTACAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:445667 original size:3 final size:3
Alignment explanation
Indices: 445659--445696 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
445649 TAAATTTCAA
445659 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
445697 ATTAAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:446093 original size:40 final size:39
Alignment explanation
Indices: 446033--446108 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
446023 TGGTTATCTA
* * *
446033 GGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCG
1 GGGGTGACACGACTCATACGTGATGAAGAGATCTGGTCG
*
446072 GGGGATGACACGACTCATACGTGATGAAGAGTTCTGG
1 GGGG-TGACACGACTCATACGTGATGAAGAGATCTGG
446109 CCATCTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 4 0.12
40 28 0.88
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.21
Consensus pattern (39 bp):
GGGGTGACACGACTCATACGTGATGAAGAGATCTGGTCG
Found at i:446117 original size:134 final size:134
Alignment explanation
Indices: 445900--446252 Score: 510
Period size: 134 Copynumber: 2.6 Consensus size: 134
445890 AGTCGTTTAA
* * * *
445900 GGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGGGGGATGACACGGCTCATACGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGA
* * * * * *
445965 CGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTGGTTAT
66 AGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACACAATGAGGACGGCTGGTTAT
446030 CTAG
131 CTAG
446034 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGA
* *
446099 AGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACATAATGAGGACGTCTGGTTAT
66 AGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACACAATGAGGACGGCTGGTTAT
446164 CTAG
131 CTAG
* * * * * * * *
446168 GGGTGACACGACTCCTAAGTGATGAGGAGGTTTGTTCGGTGGATGAAACGACTCATACTTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGA
446233 AGAGTT-TAGGCCATCTTTAG
66 AGAGTTCT-GGCCATCTTTAG
446253 TGATTATGGT
Statistics
Matches: 198, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
133 1 0.01
134 197 0.99
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.25
Consensus pattern (134 bp):
GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGA
AGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACACAATGAGGACGGCTGGTTAT
CTAG
Found at i:446301 original size:28 final size:28
Alignment explanation
Indices: 446277--446340 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
446267 AGGGAAACCG
446277 ACTCAAAGATTTGTTTCAAAAGAAACAA
1 ACTCAAAGATTTGTTTCAAAAGAAACAA
446305 ACTCAAAGATTTGTTTCAAGAA-AAACAA
1 ACTCAAAGATTTGTTTCAA-AAGAAACAA
446333 ACTCAAAG
1 ACTCAAAG
446341 GCGATGTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (28 bp):
ACTCAAAGATTTGTTTCAAAAGAAACAA
Found at i:446354 original size:31 final size:28
Alignment explanation
Indices: 446277--446357 Score: 101
Period size: 28 Copynumber: 2.8 Consensus size: 28
446267 AGGGAAACCG
*
446277 ACTCAAAGATTTGTTTCAAAAGAAACAA
1 ACTCAAAGATGTGTTTCAAAAGAAACAA
*
446305 ACTCAAAGATTTGTTTCAAGAA-AAACAA
1 ACTCAAAGATGTGTTTCAA-AAGAAACAA
446333 ACTCAAAGGCGATGTGTTTCAAAAG
1 ACTCAAA---GATGTGTTTCAAAAG
446358 CAATTGTATC
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
28 32 0.68
29 2 0.04
30 2 0.04
31 11 0.23
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (28 bp):
ACTCAAAGATGTGTTTCAAAAGAAACAA
Found at i:446524 original size:32 final size:33
Alignment explanation
Indices: 446477--446546 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 33
446467 CAAAGATCGG
* *
446477 TGTTTCGAGAGAAACAAACTCAAAGATGTT-TT
1 TGTTTCAAGAAAAACAAACTCAAAGATGTTGTT
* *
446509 TGTTTCAAGAAAAACATACTCAAAGATTTTGTT
1 TGTTTCAAGAAAAACAAACTCAAAGATGTTGTT
446542 TGTTT
1 TGTTT
446547 TTGTTTCAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 26 0.79
33 7 0.21
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (33 bp):
TGTTTCAAGAAAAACAAACTCAAAGATGTTGTT
Found at i:446552 original size:71 final size:73
Alignment explanation
Indices: 446477--446613 Score: 190
Period size: 75 Copynumber: 1.9 Consensus size: 73
446467 CAAAGATCGG
* *
446477 TGTTTCGAGAGAAACAAACTCAAAGATG-T-TTTTGTTT-CAAGAAAAACATACTCAAAGATTTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGATATTTTGTTTCCAA-AAAAACAGACTCAAAGATTTT
446539 GTTTGTTTT
65 GTTTGTTTT
* *
446548 TGTTTCAAGGGAAACAAACTCAAAGATGATAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGAT--ATTTTGTTTCCAAAAAAACAGACTCAAAGATTT
446613 T
64 T
446614 TCTCAAAGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
71 26 0.46
72 1 0.02
75 27 0.47
76 3 0.05
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (73 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGATATTTTGTTTCCAAAAAAACAGACTCAAAGATTTTG
TTTGTTTT
Found at i:446946 original size:31 final size:30
Alignment explanation
Indices: 446882--446955 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
446872 AAAAAATTCG
* *
446882 TTTCAAGGGAAACGACTCAAAGATAGTTTTA
1 TTTCAAGAGAAACAACTCAAAGATA-TTTTA
446913 TTTCAAGAGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGAGAAAC-AACTCAAAGATATTT-TA
**
446944 TTTTTAGAGAAA
1 TTTCAAGAGAAA
446956 TTGCCTTAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 24 0.65
32 10 0.27
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (30 bp):
TTTCAAGAGAAACAACTCAAAGATATTTTA
Found at i:447452 original size:30 final size:30
Alignment explanation
Indices: 447416--447473 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
447406 TCTCAAAAGA
447416 AACAAAATTTTGTTTCCAAAGAAACATAGG
1 AACAAAATTTTGTTTCCAAAGAAACATAGG
*
447446 AACAAAATTTTGTTTCCAAATAAACATA
1 AACAAAATTTTGTTTCCAAAGAAACATA
447474 CTCAATGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (30 bp):
AACAAAATTTTGTTTCCAAAGAAACATAGG
Found at i:447558 original size:38 final size:38
Alignment explanation
Indices: 447516--447588 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
447506 AAGAGACAAA
*
447516 ATTTTGTTATCAA-AGAAACATACTCAAAGATTTTTTTC
1 ATTTTGTT-TCAAGAGAAACAAACTCAAAGATTTTTTTC
* *
447554 ATTTTGTTTTAAGTGAAACAAACTCAAAGATTTTT
1 ATTTTGTTTCAAGAGAAACAAACTCAAAGATTTTT
447589 CAAGAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (38 bp):
ATTTTGTTTCAAGAGAAACAAACTCAAAGATTTTTTTC
Found at i:447673 original size:30 final size:31
Alignment explanation
Indices: 447619--447677 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
447609 GAGAAAAAGT
447619 TTTGTTTCAAAAGAAATAGACTCAAAGATCA
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCA
*
447650 TTTGTTTCAAAAGAAA-CGACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
447678 GATGTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCA
Found at i:447729 original size:34 final size:35
Alignment explanation
Indices: 447691--447806 Score: 85
Period size: 36 Copynumber: 3.3 Consensus size: 35
447681 GTTTGTTTCC
*
447691 AGTGAAACAA-ATTCTAATTTGGA-AAATTGTCTCA
1 AGTGAAACAACATT-TAATTTAGAGAAATTGTCTCA
* **
447725 AGTGAGACAACATTTGTTTTAGAGAAATTGTCTCA
1 AGTGAAACAACATTTAATTTAGAGAAATTGTCTCA
** * * *
447760 AACGACACAAAAATTGT-TTTTAGAGAAATTGTCTCA
1 AGTGAAAC-AACATT-TAATTTAGAGAAATTGTCTCA
* *
447796 AGCGAGACAAC
1 AGTGAAACAAC
447807 GTTTGTTTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
34 15 0.22
35 21 0.31
36 30 0.45
37 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (35 bp):
AGTGAAACAACATTTAATTTAGAGAAATTGTCTCA
Found at i:447788 original size:36 final size:36
Alignment explanation
Indices: 447714--448036 Score: 160
Period size: 36 Copynumber: 9.1 Consensus size: 36
447704 CTAATTTGGA
*
447714 AAATTGTCTCAAGTGAGACAACATTTG-TTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * * *
447749 AAATTGTCTCAAACGACACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
*
447785 AAATTGTCTCAAGCGAGACAACGTTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
** * *
447820 AAAACGATCTCAAGTGAGATCAAC-TTTGTTTAATATGA-
1 AAATTG-TCTCAAGCGAGA-CAACATTTGTTT-TTA-GAG
**
447858 AAA------CAA---ATTCGAA-ATTTGTATTTCTA-AGG
1 AAATTGTCTCAAGCGAGAC-AACATTTGT-TTT-TAGA-G
*
447887 AAAAATGTCTCAAGCGAGACGAA-ATTTGTTTTTCA-AG
1 -AAATTGTCTCAAGCGAGAC-AACATTTGTTTTT-AGAG
** * *
447924 AAATTGTCTCAAATGAGACAAAATTTGATTTTAGA-
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * * *
447959 AAACTGTCTCAAGTGAGACAAGATTTGTTTTTCAAAAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTT--AGAG
** * **
447997 AAGCTGTCTCTAGCGAGACAACATTTTGTTTCGAGAG
1 AAATTGTCTCAAGCGAGACAACA-TTTGTTTTTAGAG
448034 AAA
1 AAA
448037 CAACATCAAA
Statistics
Matches: 223, Mismatches: 36, Indels: 56
0.71 0.11 0.18
Matches are distributed among these distances:
27 2 0.01
28 8 0.04
29 4 0.02
30 3 0.01
31 3 0.01
35 60 0.27
36 82 0.37
37 14 0.06
38 27 0.12
39 20 0.09
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:447967 original size:35 final size:36
Alignment explanation
Indices: 447886--448027 Score: 128
Period size: 35 Copynumber: 3.9 Consensus size: 36
447876 TATTTCTAAG
* *
447886 GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTTCA
1 GAAAAATGTCTCAAGTGAGACAAAATTTGTTTTTCA
* * *
447922 -AGAAATTGTCTCAAATGAGACAAAATTTGATTTT-A
1 GA-AAAATGTCTCAAGTGAGACAAAATTTGTTTTTCA
* *
447957 GAAAACTGTCTCAAGTGAGACAAGATTTGTTTTTCA
1 GAAAAATGTCTCAAGTGAGACAAAATTTGTTTTTCA
* * *
447993 -AAAGAAGCTGTCTCTAGCGAGACAACATTTTGTTT
1 GAAA-AA--TGTCTCAAGTGAGACAA-AATTTGTTT
448028 CGAGAGAAAC
Statistics
Matches: 85, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
35 33 0.39
36 30 0.35
38 15 0.18
39 7 0.08
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (36 bp):
GAAAAATGTCTCAAGTGAGACAAAATTTGTTTTTCA
Found at i:448337 original size:4 final size:4
Alignment explanation
Indices: 448337--448423 Score: 129
Period size: 4 Copynumber: 21.8 Consensus size: 4
448327 TGCATGTATG
* * * * *
448337 TGTA TGTA TGCA TGTA TGCA TGTA TGCA TGTA TGCA TGTA TGCA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
448385 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
448424 TTTTCTCGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 73 1.00
ACGTcount: A:0.24, C:0.06, G:0.25, T:0.45
Consensus pattern (4 bp):
TGTA
Found at i:448353 original size:8 final size:8
Alignment explanation
Indices: 448326--448423 Score: 124
Period size: 8 Copynumber: 12.0 Consensus size: 8
448316 TTTATGTATC
448326 ATGCATGT
1 ATGCATGT
*
448334 ATGTGTATGT
1 A--TGCATGT
448344 ATGCATGT
1 ATGCATGT
448352 ATGCATGT
1 ATGCATGT
448360 ATGCATGT
1 ATGCATGT
448368 ATGCATGT
1 ATGCATGT
448376 ATGCATGT
1 ATGCATGT
*
448384 ATGTATGT
1 ATGCATGT
*
448392 ATGTATGT
1 ATGCATGT
*
448400 ATGTATGT
1 ATGCATGT
*
448408 ATGTATGT
1 ATGCATGT
*
448416 ATGTATGT
1 ATGCATGT
448424 TTTTCTCGAT
Statistics
Matches: 85, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
8 78 0.92
10 7 0.08
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (8 bp):
ATGCATGT
Found at i:448361 original size:16 final size:16
Alignment explanation
Indices: 448326--448423 Score: 142
Period size: 16 Copynumber: 6.0 Consensus size: 16
448316 TTTATGTATC
448326 ATGCATGTATGTGTATGT
1 ATGCATGTA--TGTATGT
*
448344 ATGCATGTATGCATGT
1 ATGCATGTATGTATGT
*
448360 ATGCATGTATGCATGT
1 ATGCATGTATGTATGT
448376 ATGCATGTATGTATGT
1 ATGCATGTATGTATGT
*
448392 ATGTATGTATGTATGT
1 ATGCATGTATGTATGT
*
448408 ATGTATGTATGTATGT
1 ATGCATGTATGTATGT
448424 TTTTCTCGAT
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
16 68 0.88
18 9 0.12
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (16 bp):
ATGCATGTATGTATGT
Found at i:449328 original size:236 final size:240
Alignment explanation
Indices: 448875--449352 Score: 837
Period size: 236 Copynumber: 2.0 Consensus size: 240
448865 TTTGATAAAT
448875 GGTTAAGTATGGAAAGGATAAAAAAATCTCAGGTTGTTATGTTTGGTTAAAGGTATGGTGTTCTC
1 GGTTAAGTATGGAAAGGATAAAAAAA-CTCAGGTTGTTATGTTTGGTTAAAGGTATGGTGTTCTC
*
448940 ATTTATTTGAATGTTCAATGATCTGATGGGGTAACGTATCTCTCTTTTGGAAGTTTTCTCTCCGA
65 ATTTATTTGAATGTTCAATGATCTGATGGGGTAACGTATCTATCTTTTGGAAGTTTTCTCTCCGA
*
449005 CTCCCAGCTCTCATGATCTCCTTCAGGTTGGGATGCCTTATCAAGGGACTGTACGATCACCTCAT
130 CTCCCAGCTCTCATGATCTCATTCAGGTTGGGATGCCTTATCAAGGGACTGTACGATCACCTCAT
449070 ATGCAATAGTCTTCATATTCGAGCTGCCTTTTCAGGTTTTCAACTC
195 ATGCAATAGTCTTCATATTCGAGCTGCCTTTTCAGGTTTTCAACTC
449116 GGTTAAGTATGGAAAGGATAAAAAAA-TCAGGTTGTTATGTTTGGTTAAAGGTATGGTG-T-TCA
1 GGTTAAGTATGGAAAGGATAAAAAAACTCAGGTTGTTATGTTTGGTTAAAGGTATGGTGTTCTCA
449178 TTTATTTGAATGTTCAATGATCTGATGGGGTAACGT-TAC-AT-TTTTGGAAG-TTT-TCTCCGA
66 TTTATTTGAATGTTCAATGATCTGATGGGGTAACGTAT-CTATCTTTTGGAAGTTTTCTCTCCGA
449238 CTCCCAGCTCTCATGATCTCATTCAGGTTGTGCGATGCCTTATCAAGGGACTTGTACGATCACCT
130 CTCCCAGCTCTCATGATCTCATTCAGGTTG-G-GATGCCTTATCAAGGGAC-TGTACGATCACCT
449303 CATATGCAATAGTCTTCATATTCGAGCTGCCTTTTCAGGTTTTCAACTC
192 CATATGCAATAGTCTTCATATTCGAGCTGCCTTTTCAGGTTTTCAACTC
449352 G
1 G
449353 TTTGTTATTT
Statistics
Matches: 231, Mismatches: 2, Indels: 13
0.94 0.01 0.05
Matches are distributed among these distances:
233 36 0.16
234 4 0.02
235 27 0.12
236 65 0.28
237 40 0.17
238 1 0.00
239 32 0.14
241 26 0.11
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (240 bp):
GGTTAAGTATGGAAAGGATAAAAAAACTCAGGTTGTTATGTTTGGTTAAAGGTATGGTGTTCTCA
TTTATTTGAATGTTCAATGATCTGATGGGGTAACGTATCTATCTTTTGGAAGTTTTCTCTCCGAC
TCCCAGCTCTCATGATCTCATTCAGGTTGGGATGCCTTATCAAGGGACTGTACGATCACCTCATA
TGCAATAGTCTTCATATTCGAGCTGCCTTTTCAGGTTTTCAACTC
Found at i:452720 original size:19 final size:19
Alignment explanation
Indices: 452670--452731 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
452660 AAAAATTGAA
452670 TATATATATATATATATAAA-
1 TATATA-AT-TATATATAAAC
452690 -ATATAAGTTTATATATAAAC
1 TATATAA--TTATATATAAAC
*
452710 TATATAATTAT-TATAAGC
1 TATATAATTATATATAAAC
452728 TATA
1 TATA
452732 CATATAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
18 11 0.30
19 19 0.51
20 1 0.03
21 6 0.16
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (19 bp):
TATATAATTATATATAAAC
Found at i:452787 original size:15 final size:13
Alignment explanation
Indices: 452753--452778 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
452743 TGTTTATATG
452753 AACTATATATGTA
1 AACTATATATGTA
452766 AACTATATATGTA
1 AACTATATATGTA
452779 TAAACTATAA
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:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
AACTATATATGTA
Found at i:452787 original size:26 final size:26
Alignment explanation
Indices: 452765--452814 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
452755 CTATATATGT
452765 AAACTATATA-TGTATAAACTATAAA
1 AAACTATATAGTGTATAAACTATAAA
* *
452790 AAAGTATATAGTTTATAAACTATAA
1 AAACTATATAGTGTATAAACTATAA
452815 TTTATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (26 bp):
AAACTATATAGTGTATAAACTATAAA
Found at i:452978 original size:19 final size:18
Alignment explanation
Indices: 452942--452991 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 18
452932 TTGGGAAATT
*
452942 TTGAGAATATAG-GAAAA
1 TTGAGAATTTAGAGAAAA
452959 TTGAGAATTTAGAGAGAAA
1 TTGAGAATTTAGAGA-AAA
452978 TTGAGAAATTTAGA
1 TTGAG-AATTTAGA
452992 AGGAATAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 11 0.38
18 2 0.07
19 8 0.28
20 8 0.28
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (18 bp):
TTGAGAATTTAGAGAAAA
Found at i:452987 original size:20 final size:20
Alignment explanation
Indices: 452956--453020 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 20
452946 GAATATAGGA
452956 AAATTGAG-AATTTAGAGAG
1 AAATTGAGAAATTTAGAGAG
452975 AAATTGAGAAATTTAGA-AG
1 AAATTGAGAAATTTAGAGAG
* * * * *
452994 GAATAGAAAAATTTGGAGGG
1 AAATTGAGAAATTTAGAGAG
453014 AAATTGA
1 AAATTGA
453021 TAATTGAGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 23 0.62
20 14 0.38
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.25
Consensus pattern (20 bp):
AAATTGAGAAATTTAGAGAG
Found at i:453005 original size:46 final size:46
Alignment explanation
Indices: 452913--453006 Score: 120
Period size: 46 Copynumber: 2.0 Consensus size: 46
452903 TTGATTTTAT
* * *
452913 TTGAGAATTTAGAAGAAAATTGGGAAATTTTGAGAATATAGGAAAA
1 TTGAGAATTTAGAAGAAAATTGAGAAATTTAGAGAATATAGAAAAA
*
452959 TTGAGAATTTAG-AGAGAAATTGAGAAATTTAGAAGGA-ATAGAAAAA
1 TTGAGAATTTAGAAGA-AAATTGAGAAATTTAG-AGAATATAGAAAAA
453005 TT
1 TT
453007 TGGAGGGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 3 0.07
46 36 0.86
47 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.28
Consensus pattern (46 bp):
TTGAGAATTTAGAAGAAAATTGAGAAATTTAGAGAATATAGAAAAA
Found at i:453306 original size:2 final size:2
Alignment explanation
Indices: 453299--453397 Score: 106
Period size: 2 Copynumber: 52.5 Consensus size: 2
453289 TAATATAGTG
* *
453299 TA TA TA TA TA TA TA TA TA -A CTA -A TA TA -A GTA -A TC CA TA T-
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA
453338 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA T- 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 TA TA
453378 TA TA TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
453398 TAGAAACACT
Statistics
Matches: 83, Mismatches: 4, Indels: 20
0.78 0.04 0.19
Matches are distributed among these distances:
1 8 0.10
2 73 0.88
3 2 0.02
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:453325 original size:30 final size:31
Alignment explanation
Indices: 453284--453399 Score: 125
Period size: 30 Copynumber: 3.7 Consensus size: 31
453274 AATTATAATT
*
453284 TATAT-TAATATAGTGTATA-TATATATATA
1 TATATATAATATAGTATATATTATATATATA
453313 TATA-ACTAATATAAGTAATCCATATTATATATATA
1 TATATA-TAATAT-AGT-AT--ATATTATATATATA
*
453348 TATATATATTATA-TATATATTATATATATA
1 TATATATAATATAGTATATATTATATATATA
*
453378 TATATAT-ATATAATATATATTA
1 TATATATAATATAGTATATATTA
453400 GAAACACTAT
Statistics
Matches: 75, Mismatches: 3, Indels: 17
0.79 0.03 0.18
Matches are distributed among these distances:
29 8 0.11
30 36 0.48
31 3 0.04
32 3 0.04
33 1 0.01
34 4 0.05
35 19 0.25
36 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
TATATATAATATAGTATATATTATATATATA
Found at i:454109 original size:2 final size:2
Alignment explanation
Indices: 454048--454100 Score: 83
Period size: 2 Copynumber: 27.0 Consensus size: 2
454038 TAAAACCATG
454048 TA TA GTA TA TA -A TA TA TA -A 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 TA TA
454089 TA TA TA TA TA TA
1 TA TA TA TA TA TA
454101 AACTATATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.04
2 44 0.92
3 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:454238 original size:14 final size:14
Alignment explanation
Indices: 454189--454241 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
454179 TATAGGAATC
454189 CTAAACCCTAAACT
1 CTAAACCCTAAACT
* * *
454203 -TCGAACCATAAGCT
1 CT-AAACCCTAAACT
*
454217 TTAAACCCTAAACT
1 CTAAACCCTAAACT
454231 CTAAACCCTAA
1 CTAAACCCTAA
454242 TATAAATGAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 1 0.03
14 28 0.93
15 1 0.03
ACGTcount: A:0.42, C:0.32, G:0.04, T:0.23
Consensus pattern (14 bp):
CTAAACCCTAAACT
Found at i:454691 original size:20 final size:19
Alignment explanation
Indices: 454654--454692 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
454644 GTGAATTAAC
*
454654 CTAATATGCAACTAAAATA
1 CTAATATGCAAATAAAATA
*
454673 CTAATTATGCAAATGAAATA
1 CTAA-TATGCAAATAAAATA
454693 ATATGACATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (19 bp):
CTAATATGCAAATAAAATA
Found at i:454812 original size:11 final size:10
Alignment explanation
Indices: 454781--454829 Score: 57
Period size: 9 Copynumber: 5.0 Consensus size: 10
454771 TATAATTACA
*
454781 TTTAAATAAT
1 TTTATATAAT
454791 TTTAT-TAAT
1 TTTATATAAT
454800 TTTATTATAAT
1 TTTA-TATAAT
454811 TTTATATAA-
1 TTTATATAAT
*
454820 TATATATAAT
1 TTTATATAAT
454830 ATAATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 16 0.47
10 10 0.29
11 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTATATAAT
Found at i:454832 original size:24 final size:23
Alignment explanation
Indices: 454767--454840 Score: 66
Period size: 24 Copynumber: 3.3 Consensus size: 23
454757 ATTAATCATG
*
454767 TTTATATAATTACATTTAA-ATAAT
1 TTTATATAA-TATA-TTAATATAAT
*
454791 TTTAT-TAAT-T-TTATTATAAT
1 TTTATATAATATATTAATATAAT
454811 TTTATATAATATATATAATATAAT
1 TTTATATAATATAT-TAATATAAT
*
454835 TATATA
1 TTTATA
454841 GTTTATAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 3 0.07
20 10 0.24
21 4 0.10
22 2 0.05
23 4 0.10
24 18 0.44
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTATATAATATATTAATATAAT
Found at i:455168 original size:23 final size:23
Alignment explanation
Indices: 455140--455183 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
455130 TTATTTTTTC
455140 TTTATATAAATTAAACTATATAA
1 TTTATATAAATTAAACTATATAA
455163 TTTATATAAATTAAACTATAT
1 TTTATATAAATTAAACTATAT
455184 TAACTTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTATATAAATTAAACTATATAA
Found at i:455508 original size:16 final size:16
Alignment explanation
Indices: 455462--455510 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
455452 GATCATTTAT
*
455462 AGGTCAGGTTAAAAAA
1 AGGTCAGGTTAAAAAC
455478 AGGTCAGGTTAAAAAC
1 AGGTCAGGTTAAAAAC
* *
455494 AGGTCATGTTGAAAAC
1 AGGTCAGGTTAAAAAC
455510 A
1 A
455511 TGTCGGGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.20
Consensus pattern (16 bp):
AGGTCAGGTTAAAAAC
Found at i:456730 original size:3 final size:3
Alignment explanation
Indices: 456717--456774 Score: 107
Period size: 3 Copynumber: 19.0 Consensus size: 3
456707 TATTTTGATA
456717 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
456763 AAT AAT AAT AAT
1 AAT AAT AAT AAT
456775 CCAACGAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:456809 original size:2 final size:2
Alignment explanation
Indices: 456802--456827 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
456792 AACTATTTTG
456802 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
456828 TAGGGTATAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:458844 original size:16 final size:16
Alignment explanation
Indices: 458815--458887 Score: 105
Period size: 16 Copynumber: 4.7 Consensus size: 16
458805 CGTTCAATTA
458815 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
*
458829 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
* *
458845 ATAAAGGAACACGGAC
1 ATAAATGAACACGAAC
458861 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
458877 ATAAATGAACA
1 ATAAATGAACA
458888 TAAACGTTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 45 0.87
ACGTcount: A:0.58, C:0.18, G:0.14, T:0.11
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:460369 original size:7 final size:7
Alignment explanation
Indices: 460357--460454 Score: 79
Period size: 7 Copynumber: 14.0 Consensus size: 7
460347 TAGATTGAGA
460357 GTTTAGG
1 GTTTAGG
460364 GTTTAGG
1 GTTTAGG
* *
460371 GGTTAGA
1 GTTTAGG
*
460378 GTTTAAG
1 GTTTAGG
* *
460385 TTTTATG
1 GTTTAGG
460392 GTTTAGG
1 GTTTAGG
*
460399 GGTTAGG
1 GTTTAGG
*
460406 GTTTAAG
1 GTTTAGG
* *
460413 TTTTATG
1 GTTTAGG
460420 GTTTAGG
1 GTTTAGG
* *
460427 ATTTAGA
1 GTTTAGG
*
460434 GTTTATG
1 GTTTAGG
*
460441 TTTTAGG
1 GTTTAGG
460448 GTTTAGG
1 GTTTAGG
460455 ATTTTAATAA
Statistics
Matches: 67, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 67 1.00
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:460396 original size:28 final size:28
Alignment explanation
Indices: 460358--460454 Score: 140
Period size: 28 Copynumber: 3.5 Consensus size: 28
460348 AGATTGAGAG
460358 TTTAGGGTTTAGGGGTTAGAGTTTAAGT
1 TTTAGGGTTTAGGGGTTAGAGTTTAAGT
* *
460386 TTTATGGTTTAGGGGTTAGGGTTTAAGT
1 TTTAGGGTTTAGGGGTTAGAGTTTAAGT
* ** *
460414 TTTATGGTTTAGGATTTAGAGTTTATGT
1 TTTAGGGTTTAGGGGTTAGAGTTTAAGT
460442 TTTAGGGTTTAGG
1 TTTAGGGTTTAGG
460455 ATTTTAATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (28 bp):
TTTAGGGTTTAGGGGTTAGAGTTTAAGT
Found at i:460621 original size:10 final size:10
Alignment explanation
Indices: 460606--460704 Score: 54
Period size: 10 Copynumber: 8.7 Consensus size: 10
460596 AACATAAATG
460606 AACGAACATA
1 AACGAACATA
460616 AACGAACATAA
1 AACGAACAT-A
*
460627 CCGAACAAACATA
1 ---AACGAACATA
460640 AACGAACATAA
1 AACGAACAT-A
*
460651 TCTAACAAACATA
1 ---AACGAACATA
460664 AACGAACATAA
1 AACGAACAT-A
460675 TCTAACGAACATA
1 ---AACGAACATA
*
460688 ACCGAACATA
1 AACGAACATA
*
460698 ACCGAAC
1 AACGAAC
460705 GTTCACGAAC
Statistics
Matches: 72, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
10 41 0.57
11 3 0.04
13 3 0.04
14 25 0.35
ACGTcount: A:0.56, C:0.24, G:0.08, T:0.12
Consensus pattern (10 bp):
AACGAACATA
Found at i:460632 original size:24 final size:24
Alignment explanation
Indices: 460596--460705 Score: 139
Period size: 24 Copynumber: 4.6 Consensus size: 24
460586 GATTGGGTTA
**
460596 AACATAAATGAACGAACATAAACG
1 AACATAACCGAACGAACATAAACG
*
460620 AACATAACCGAACAAACATAAACG
1 AACATAACCGAACGAACATAAACG
* * *
460644 AACATAATCTAACAAACATAAACG
1 AACATAACCGAACGAACATAAACG
* * *
460668 AACATAATCTAACGAACATAACCG
1 AACATAACCGAACGAACATAAACG
460692 AACATAACCGAACG
1 AACATAACCGAACG
460706 TTCACGAACG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 77 1.00
ACGTcount: A:0.55, C:0.23, G:0.09, T:0.13
Consensus pattern (24 bp):
AACATAACCGAACGAACATAAACG
Found at i:460647 original size:14 final size:14
Alignment explanation
Indices: 460595--460671 Score: 53
Period size: 14 Copynumber: 6.1 Consensus size: 14
460585 AGATTGGGTT
*
460595 AAACATAAATGAAC
1 AAACATAAACGAAC
*
460609 GAACATAAACG---
1 AAACATAAACGAAC
*
460620 -AACATAACCGAAC
1 AAACATAAACGAAC
460633 AAACATAAACG---
1 AAACATAAACGAAC
* *
460644 -AACATAATCTAAC
1 AAACATAAACGAAC
460657 AAACATAAACGAAC
1 AAACATAAACGAAC
460671 A
1 A
460672 TAATCTAACG
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
10 17 0.36
14 30 0.64
ACGTcount: A:0.60, C:0.21, G:0.08, T:0.12
Consensus pattern (14 bp):
AAACATAAACGAAC
Found at i:460681 original size:14 final size:14
Alignment explanation
Indices: 460640--460688 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
460630 AACAAACATA
460640 AACGAACATAATCT
1 AACGAACATAATCT
*
460654 AACAAACAT-A---
1 AACGAACATAATCT
460664 AACGAACATAATCT
1 AACGAACATAATCT
460678 AACGAACATAA
1 AACGAACATAA
460689 CCGAACATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 8 0.28
11 1 0.03
13 1 0.03
14 19 0.66
ACGTcount: A:0.57, C:0.20, G:0.06, T:0.16
Consensus pattern (14 bp):
AACGAACATAATCT
Found at i:466313 original size:36 final size:33
Alignment explanation
Indices: 466267--466333 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 33
466257 AATAGGAATT
*
466267 ACAATTTCTCTCGATTTAACAAGGAGAAAACAATG
1 ACAATTTCTCTCGA--TAAAAAGGAGAAAACAATG
*
466302 ACAATTTTCTCTTGATAAAAAGGAGAAAACAA
1 ACAA-TTTCTCTCGATAAAAAGGAGAAAACAA
466334 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 16 0.55
35 4 0.14
36 9 0.31
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.25
Consensus pattern (33 bp):
ACAATTTCTCTCGATAAAAAGGAGAAAACAATG
Found at i:467369 original size:24 final size:24
Alignment explanation
Indices: 467336--467384 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
467326 TCCTTATCCT
*
467336 TATCCTTATCCATATCCATGTCCA
1 TATCCATATCCATATCCATGTCCA
467360 TATCCATATCCATATCCATGTCCA
1 TATCCATATCCATATCCATGTCCA
467384 T
1 T
467385 GGGATAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.33, G:0.04, T:0.37
Consensus pattern (24 bp):
TATCCATATCCATATCCATGTCCA
Found at i:467385 original size:6 final size:6
Alignment explanation
Indices: 467330--467384 Score: 74
Period size: 6 Copynumber: 9.2 Consensus size: 6
467320 ACATTGTCCT
* * *
467330 TATCCT TATCCT TATCCA TATCCA TGTCCA TATCCA TATCCA TATCCA
1 TATCCA TATCCA TATCCA TATCCA TATCCA TATCCA TATCCA TATCCA
*
467378 TGTCCA T
1 TATCCA T
467385 GGGATAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.38
Consensus pattern (6 bp):
TATCCA
Found at i:469681 original size:32 final size:32
Alignment explanation
Indices: 469640--469703 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
469630 AGGGACAACC
469640 ATTTTATAATAATAGATATTTGTTTATATTTA
1 ATTTTATAATAATAGATATTTGTTTATATTTA
469672 ATTTTATAATAATAGATATTTGTTTATATTTA
1 ATTTTATAATAATAGATATTTGTTTATATTTA
469704 TTTCAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (32 bp):
ATTTTATAATAATAGATATTTGTTTATATTTA
Found at i:483701 original size:38 final size:37
Alignment explanation
Indices: 483570--483731 Score: 138
Period size: 38 Copynumber: 4.5 Consensus size: 37
483560 ATTTTGAATG
* ** *
483570 TATATAATATATGGTTTTTGAAAC-A-TTTTGAAAACT
1 TATATAATATATAGTTTTAAAAACTATTTTTGAAAA-A
* * *
483606 TATATAATAT-T--TTTTAAAATC-ATTTTTCCAAAAC
1 TATATAATATATAGTTTTAAAAACTATTTTT-GAAAAA
* * *
483640 TATATAATATATAGTTTTGAAAACTTTTTTTTAAAAA
1 TATATAATATATAGTTTTAAAAACTATTTTTGAAAAA
*
483677 TATATAATATATAGTTTTAAAAAACTATTTTTGAAATA
1 TATATAATATATAGTTTT-AAAAACTATTTTTGAAAAA
* *
483715 TATATATTTTATAGTTT
1 TATATAATATATAGTTT
483732 ATATTATTTT
Statistics
Matches: 103, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
33 8 0.08
34 14 0.14
35 6 0.06
36 10 0.10
37 30 0.29
38 35 0.34
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (37 bp):
TATATAATATATAGTTTTAAAAACTATTTTTGAAAAA
Found at i:483772 original size:14 final size:14
Alignment explanation
Indices: 483753--483779 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
483743 TTATAAGTAT
483753 ATTTTATTTTATTC
1 ATTTTATTTTATTC
483767 ATTTTATTTTATT
1 ATTTTATTTTATT
483780 TTTGGTCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTTATTTTATTC
Found at i:485008 original size:21 final size:20
Alignment explanation
Indices: 484969--485035 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
484959 TTTTTTCCTT
484969 TTTATTTGTATTATATTTTTTA
1 TTTATTTGT-TT-TATTTTTTA
* *
484991 TTTATTTTGTTTTATTTTATG
1 TTTA-TTTGTTTTATTTTTTA
* *
485012 TTTATTTATTTTACTGTTTTA
1 TTTATTTGTTTTA-TTTTTTA
485033 TTT
1 TTT
485036 TTTATATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
20 8 0.22
21 18 0.49
22 6 0.16
23 5 0.14
ACGTcount: A:0.18, C:0.01, G:0.06, T:0.75
Consensus pattern (20 bp):
TTTATTTGTTTTATTTTTTA
Found at i:485036 original size:5 final size:5
Alignment explanation
Indices: 484941--485024 Score: 64
Period size: 5 Copynumber: 16.0 Consensus size: 5
484931 TATATGCTAT
* * *
484941 TTTTA TTCTTA TTTTA TTTT- TTTTCCT TTTTA TTTGTA TTATA TTTTT
1 TTTTA TT-TTA TTTTA TTTTA TTTT--A TTTTA TTT-TA TTTTA TTTTA
*
484989 TATTTA TTTTG TTTTA TTTTA TGTTTA -TTTA TTTTA
1 T-TTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA
485025 CTGTTTTATT
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
4 8 0.12
5 35 0.55
6 17 0.27
7 4 0.06
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:486789 original size:12 final size:13
Alignment explanation
Indices: 486772--486800 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
486762 CTTAATTGTG
486772 AAAATTAAAA-TT
1 AAAATTAAAATTT
486784 AAAATTAAAATTT
1 AAAATTAAAATTT
486797 AAAA
1 AAAA
486801 ATTCGATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:487094 original size:30 final size:31
Alignment explanation
Indices: 487008--487096 Score: 101
Period size: 30 Copynumber: 2.9 Consensus size: 31
486998 GCTACAAGAG
* * *
487008 AAAAACAGAAACTTAAGGGATT-AAATAGCA
1 AAAAACAGAAATTTAAAGAATTAAAATAGCA
* **
487038 AAAAACAGAAATTTAAAGTACCAAAATAGC-
1 AAAAACAGAAATTTAAAGAATTAAAATAGCA
*
487068 ACAAACAGAAATTTAAAGAATTAAAATAG
1 AAAAACAGAAATTTAAAGAATTAAAATAG
487097 TATTAACAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 42 0.86
31 7 0.14
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.18
Consensus pattern (31 bp):
AAAAACAGAAATTTAAAGAATTAAAATAGCA
Found at i:494691 original size:29 final size:28
Alignment explanation
Indices: 494647--494706 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 28
494637 ACTATTAGTT
494647 TTTTTAATTTAGTCATTG-TTATTTTAA
1 TTTTTAATTTAGTCATTGTTTATTTTAA
* *
494674 TTTTTACATTTGGATCATTGTTTATTTTTA
1 TTTTTA-ATTTAG-TCATTGTTTATTTTAA
494704 TTT
1 TTT
494707 AGCTACCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 6 0.21
28 5 0.18
29 6 0.21
30 11 0.39
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.65
Consensus pattern (28 bp):
TTTTTAATTTAGTCATTGTTTATTTTAA
Found at i:494885 original size:30 final size:30
Alignment explanation
Indices: 494851--494907 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
494841 TCTGTAAATA
* *
494851 CTATTTTAATTCTTTAAATTTTTGTTTGTG
1 CTATTTTAATACTTTAAATTTCTGTTTGTG
**
494881 CTATTTTGGTACTTTAAATTTCTGTTT
1 CTATTTTAATACTTTAAATTTCTGTTT
494908 TTTTCTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.19, C:0.09, G:0.11, T:0.61
Consensus pattern (30 bp):
CTATTTTAATACTTTAAATTTCTGTTTGTG
Found at i:512983 original size:12 final size:12
Alignment explanation
Indices: 512965--512994 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
512955 ATCCTAAGTC
512965 AAAAAAAGAAAAG
1 AAAAAAA-AAAAG
512978 AAAAAAAAAAAG
1 AAAAAAAAAAAG
512990 AAAAA
1 AAAAA
512995 TAAGGTGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:513954 original size:65 final size:64
Alignment explanation
Indices: 513797--514229 Score: 485
Period size: 65 Copynumber: 6.9 Consensus size: 64
513787 CAACGCAACA
* * *
513797 ACACAAGATTGGATTTCAACTTCACAACGAAA-GTTATCTAACTCAAAGCCAATTTAGTGAAA--
1 ACACAAGATTGGATTTCAACTTCACAAC-AAAGGATATCCAACTCAAAGCCAATTTGGTGAAACT
* * *
513859 A-ACAATACTTGGATTTCAACTTCACAACAAAGGATATTCAACTCAAAGCCAATTTAGTGAAACT
1 ACACAAGA-TTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTTGGTGAAAC-
513923 T
64 T
* *
513924 ACACAAGATTGGATTTCAACTTCACAACAAATGATATCCAACTCAAAGTCAATTTGGTGAAA-T
1 ACACAAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTTGGTGAAACT
* * * * * *
513987 A-A-TA-CTTGAATTTTAACTTCACGACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACTT
1 ACACAAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTTGGTGAAAC-T
* * * *
514049 ACACGAGATTGGATTTCAACTTCACAACAAAGGATATTCAACTTAAAGCCGATTTGGTGAAAC-
1 ACACAAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTTGGTGAAACT
* * * * **
514112 ACA-AA-ATTGAATTTCAACTTCACAACGAAGGATATCCAACTGAAAGCCAAATTGGTGAAGTT
1 ACACAAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTTGGTGAAACT
* * *
514174 ATACAAGATTGGATTTCAACTTTACGACGAAA-GATATCCAACTCAAAGCTCAATTT
1 ACACAAGATTGGATTTCAACTTCACAAC-AAAGGATATCCAACTCAAAGC-CAATTT
514230 CACGACGAAT
Statistics
Matches: 313, Mismatches: 42, Indels: 29
0.82 0.11 0.08
Matches are distributed among these distances:
60 48 0.15
61 57 0.18
62 54 0.17
63 8 0.03
64 35 0.11
65 106 0.34
66 5 0.02
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (64 bp):
ACACAAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTTGGTGAAACT
Found at i:514047 original size:125 final size:125
Alignment explanation
Indices: 513797--514229 Score: 584
Period size: 125 Copynumber: 3.4 Consensus size: 125
513787 CAACGCAACA
* * *
513797 ACACAAGATTGGATTTCAACTTCACAACGAAAGTTATCTAACTCAAAGCCAATTTAGTGAAAAAC
1 ACACAAGATTGGATTTCAACTTCACAACGAAAGATATCCAACTCAAAGCCAATTTGGTG--AAAC
* * * *
513862 AATACTTGGATTTCAACTTCACAACAAAGGATATTCAACTCAAAGCCAATTTAGTGAAACTT
64 AATACTTGAATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACTT
* *
513924 ACACAAGATTGGATTTCAACTTCACAAC-AAATGATATCCAACTCAAAGTCAATTTGGTGAAATA
1 ACACAAGATTGGATTTCAACTTCACAACGAAA-GATATCCAACTCAAAGCCAATTTGGTGAAACA
* *
513988 ATACTTGAATTTTAACTTCACGACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACTT
65 ATACTTGAATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACTT
* * * *
514049 ACACGAGATTGGATTTCAACTTCACAAC-AAAGGATATTCAACTTAAAGCCGATTTGGTGAAACA
1 ACACAAGATTGGATTTCAACTTCACAACGAAA-GATATCCAACTCAAAGCCAATTTGGTGAAACA
* * * * *
514113 CAAAATTGAATTTCAACTTCACAACGAAGGATATCCAACTGAAAGCCAAATTGGTG-AAGTT
65 -ATACTTGAATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACTT
* * *
514174 ATACAAGATTGGATTTCAACTTTACGACGAAAGATATCCAACTCAAAGCTCAATTT
1 ACACAAGATTGGATTTCAACTTCACAACGAAAGATATCCAACTCAAAGC-CAATTT
514230 CACGACGAAT
Statistics
Matches: 270, Mismatches: 32, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
125 159 0.59
126 60 0.22
127 51 0.19
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (125 bp):
ACACAAGATTGGATTTCAACTTCACAACGAAAGATATCCAACTCAAAGCCAATTTGGTGAAACAA
TACTTGAATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACTT
Found at i:514080 original size:190 final size:184
Alignment explanation
Indices: 513804--514229 Score: 532
Period size: 190 Copynumber: 2.3 Consensus size: 184
513794 ACAACACAAG
* * * * *
513804 ATTGGATTTCAACTTCACAACGAAAGTTATCTAACTCAAAGCCAATTTAGTGAAAAACAATACTT
1 ATTGAATTTCAACTTCACGACGAAAGATATCCAACTCAAAGCCAATTTAGTGAAAAACAAGACTT
513869 GGATTTCAACTTCACAACAAAGGATATTCAACTCAAAGCCAATTTAGTGAAACTTACACAAGATT
66 GGATTTCAACTTCACAACAAAGGATATTCAACTCAAAGCCAATTTAGTGAAAC--ACA-AA-ATT
* * * *
513934 GGATTTCAACTTCACAACAAATGATATCCAACTCAAAGTCAATTTGGTGAAATAATAC
127 GAATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAAATTGGTGAAATAATAC
* * * *
513992 -TTGAATTTTAACTTCACGACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACTTACACGAG
1 ATTGAATTTCAACTTCACGACGAAAGATATCCAACTCAAAGCCAATTTAGTGAAA---A-ACAAG
* * *
514056 A-TTGGATTTCAACTTCACAACAAAGGATATTCAACTTAAAGCCGATTTGGTGAAACACAAAATT
62 ACTTGGATTTCAACTTCACAACAAAGGATATTCAACTCAAAGCCAATTTAGTGAAACACAAAATT
* * * *
514120 GAATTTCAACTTCACAACGAAGGATATCCAACTGAAAGCCAAATTGGTGAAGTTATAC
127 GAATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAAATTGGTGAAATAATAC
* *
514178 AAGATTGGATTTCAACTTTACGACGAAAGATATCCAACTCAAAGCTCAATTT
1 ---ATTGAATTTCAACTTCACGACGAAAGATATCCAACTCAAAGC-CAATTT
514230 CACGACGAAT
Statistics
Matches: 205, Mismatches: 24, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
186 53 0.26
187 49 0.24
188 3 0.01
190 90 0.44
191 10 0.05
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (184 bp):
ATTGAATTTCAACTTCACGACGAAAGATATCCAACTCAAAGCCAATTTAGTGAAAAACAAGACTT
GGATTTCAACTTCACAACAAAGGATATTCAACTCAAAGCCAATTTAGTGAAACACAAAATTGAAT
TTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAAATTGGTGAAATAATAC
Found at i:520113 original size:85 final size:85
Alignment explanation
Indices: 519983--520139 Score: 201
Period size: 85 Copynumber: 1.8 Consensus size: 85
519973 TTTACGATAA
* *
519983 CAAACACCGCAATAGGTCATACTATTTAACGGTGTTTTGGATACAAACG-T-CAAAATAGGTCAT
1 CAAACACCACAATAGGTCATACTATTTAACGGCGTTTTGGATACAAACGCTGC--AATAGGTCAT
520046 GTTATTTAGCAGTGTTTTAGGT
64 GTTATTTAGCAGTGTTTTAGGT
* ** ** * *
520068 CAAACACCATAATAGGTCATGTTATTTAGTGGCGTTTTGGGTACAAACGCTGCAGTAGGTCATGT
1 CAAACACCACAATAGGTCATACTATTTAACGGCGTTTTGGATACAAACGCTGCAATAGGTCATGT
520133 TATTTAG
66 TATTTAG
520140 TATCGTTTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
85 59 0.97
86 1 0.02
87 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (85 bp):
CAAACACCACAATAGGTCATACTATTTAACGGCGTTTTGGATACAAACGCTGCAATAGGTCATGT
TATTTAGCAGTGTTTTAGGT
Found at i:520244 original size:43 final size:43
Alignment explanation
Indices: 519982--520244 Score: 174
Period size: 43 Copynumber: 6.2 Consensus size: 43
519972 TTTTACGATA
* ** * *
519982 ACAAACACCGCAATAGGTCATACTATTTAACGGTGTTTTGGAT
1 ACAAACGCCGCAATAGGTCATGTTATTTAGCGGTGTTTTTGAT
* ** * * *
520025 ACAAACGTCAAAATAGGTCATGTTATTTAGCAGTGTTTTAGGT
1 ACAAACGCCGCAATAGGTCATGTTATTTAGCGGTGTTTTTGAT
* ** * * * *
520068 -CAAACACCATAATAGGTCATGTTATTTAGTGGCGTTTTGGGT
1 ACAAACGCCGCAATAGGTCATGTTATTTAGCGGTGTTTTTGAT
* * ** *
520110 ACAAACGCTGCAGTAGGTCATGTTATTTAG-TATCGTTTATGAT
1 ACAAACGCCGCAATAGGTCATGTTATTTAGCGGT-GTTTTTGAT
* * * * * * * **
520153 ACAAACGTCGTAATATGTTAGGTTA-ATAGTGGCAATTTTTG-T
1 ACAAACGCCGCAATAGGTCATGTTATTTAGCGG-TGTTTTTGAT
* *
520195 ACAAACGCCGCAATAGGTTATGTTATTTAGCGGTGTTTTTGAA
1 ACAAACGCCGCAATAGGTCATGTTATTTAGCGGTGTTTTTGAT
520238 ACAAACG
1 ACAAACG
520245 ATATAATAAT
Statistics
Matches: 164, Mismatches: 50, Indels: 12
0.73 0.22 0.05
Matches are distributed among these distances:
42 66 0.40
43 98 0.60
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTCATGTTATTTAGCGGTGTTTTTGAT
Found at i:524551 original size:233 final size:235
Alignment explanation
Indices: 524141--524612 Score: 898
Period size: 233 Copynumber: 2.0 Consensus size: 235
524131 TTTTTACACC
524141 TTGACCAGTGAATGCAAAAAGCCCTACACTTTACCTTTTGAAGCAAAGTCGAATCACACAATGAA
1 TTGACCAGTGAATGCAAAAAGCCCTACACTTTACCTTTTGAAGCAAAGTCGAATCACACAATGAA
524206 ATTGGACAGGAAATACATATATCCATTTGGACTTACGCTAAAAAGCTATACTTTTTTTTTTCACT
66 ATTGGACAGGAAATACATATATCCATTTGGACTTACGCTAAAAAGCTATACTTTTTTTTTTCACT
524271 TTGTTAGACAAACGATTGGTGCATCCAACAATAATTTGACAAAATCGATCATGTCTTTGT-TGTT
131 TTGTTAGACAAACGATTGGTGCATCCAACAATAATTTGACAAAATCGATCATGTCTTTGTCTGTT
524335 TC-AACAATAATTTCTTGATTCCTTTACAAATATTTAAAG
196 TCAAACAATAATTTCTTGATTCCTTTACAAATATTTAAAG
524374 TTGACCAGTGAATGCAAAAAGCCCTACACTTTACCTTTTGAAGCAAAGTCGAATCACACAATGAA
1 TTGACCAGTGAATGCAAAAAGCCCTACACTTTACCTTTTGAAGCAAAGTCGAATCACACAATGAA
524439 ATTGGACAGGAAATACATAGATATCCATTTGGACTTACGCT-AAAAGCTATACTTTTTTTTTTCA
66 ATTGGACAGGAAATACAT--ATATCCATTTGGACTTACGCTAAAAAGCTATACTTTTTTTTTTCA
524503 CTTTGTTAGACAAACGATTGGTGCATCCAACAATAATTTGAC-AAATCGATCATGTCTTTGTCTG
129 CTTTGTTAGACAAACGATTGGTGCATCCAACAATAATTTGACAAAATCGATCATGTCTTTGTCTG
524567 TTTCAAACAATAATTTCTTGATTCCTTTACAAATATTTAAAG
194 TTTCAAACAATAATTTCTTGATTCCTTTACAAATATTTAAAG
524609 TTGA
1 TTGA
524613 AAAAAAAATT
Statistics
Matches: 235, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
233 102 0.43
234 71 0.30
235 62 0.26
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (235 bp):
TTGACCAGTGAATGCAAAAAGCCCTACACTTTACCTTTTGAAGCAAAGTCGAATCACACAATGAA
ATTGGACAGGAAATACATATATCCATTTGGACTTACGCTAAAAAGCTATACTTTTTTTTTTCACT
TTGTTAGACAAACGATTGGTGCATCCAACAATAATTTGACAAAATCGATCATGTCTTTGTCTGTT
TCAAACAATAATTTCTTGATTCCTTTACAAATATTTAAAG
Found at i:526442 original size:65 final size:64
Alignment explanation
Indices: 526315--526448 Score: 153
Period size: 65 Copynumber: 2.1 Consensus size: 64
526305 ACCCCATTTT
* * * * * * * *
526315 GAATGCATTTTAGGCACCGATGCATATCCATGCATTGATGCACTCTGGATTTTATTGGAACATC
1 GAATGCATTTGAGGCACCAAAGCACATCCATGCATCGATGCACTCTGGATTGTATTGAAACATA
* *
526379 GAATGCATTTGATGCACCAAAGCACATACCATGCATCGATGCACTCCTGGCTTGT-TTGAAACAT
1 GAATGCATTTGAGGCACCAAAGCACAT-CCATGCATCGATGCACT-CTGGATTGTATTGAAACAT
526443 A
64 A
526444 GAATG
1 GAATG
526449 TAACTAGTGC
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
64 22 0.38
65 29 0.50
66 7 0.12
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (64 bp):
GAATGCATTTGAGGCACCAAAGCACATCCATGCATCGATGCACTCTGGATTGTATTGAAACATA
Found at i:528778 original size:54 final size:54
Alignment explanation
Indices: 528641--529035 Score: 506
Period size: 54 Copynumber: 7.3 Consensus size: 54
528631 ACTCTATGGT
* * * * * * **
528641 TTGCACACGTAGTGCCAATACTG-TAATTCACAAACTCATTATGAATTACGTGGG
1 TTGCACACATAGTGCCAATAC-GAAAATTCATAAACTTATTATGAATTTCTTAAG
* * * *
528695 TTTGCACACATAATGTCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
1 -TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
* *
528750 TTGCACATATAGTGCCAATACGAAAATTCATAAACTTATTATAAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
* *
528804 TTGCACACACAGTGCCAATAC-AGAAATTCATAAACTCATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAAG
* * *
528858 TTGCACAAATAGTGCCAATGCGGAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
* * * * * *
528912 TTACACATACAGTGCCAATATGGAAATTCATAAACTTATTACGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
* *
528966 TTGCATACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
529020 TTGCACACATAGTGCC
1 TTGCACACATAGTGCC
529036 CATTTGGTAA
Statistics
Matches: 299, Mismatches: 38, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
53 1 0.00
54 255 0.85
55 43 0.14
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (54 bp):
TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
Found at i:528909 original size:162 final size:161
Alignment explanation
Indices: 528641--529035 Score: 565
Period size: 162 Copynumber: 2.4 Consensus size: 161
528631 ACTCTATGGT
** * * * * **
528641 TTGCACACGTAGTGCCAATACTGTAATTCACAAACTCATTATGAATTACGTGGGTTTGCACACAT
1 TTGCACACACAGTGCCAATAC-GAAATTCATAAACTCATTATGAATTTCTTAAG-TTGCACACAT
* * * *
528706 AATGTCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACATATAGTGCCAATAC
64 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTACACATACAGTGCCAATAC
*
528771 GAAAATTCATAAACTTATTATAAATTTCTTAAG
129 GAAAATTCATAAACTTATTACAAATTTCTTAAG
*
528804 TTGCACACACAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACAAATA
1 TTGCACACACAGTGCCAATAC-GAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATA
* * *
528869 GTGCCAATGCGGAAATTCATAAACTTATTATGAATTTCTTAAGTTACACATACAGTGCCAATATG
65 GTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTACACATACAGTGCCAATACG
* *
528934 GAAATTCATAAACTTATTACGAATTTCTTAAG
130 AAAATTCATAAACTTATTACAAATTTCTTAAG
* *
528966 TTGCATACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACATA
1 TTGCACACACAGTGCCAATACG-AAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATA
529031 GTGCC
65 GTGCC
529036 CATTTGGTAA
Statistics
Matches: 208, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
161 1 0.00
162 162 0.78
163 45 0.22
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (161 bp):
TTGCACACACAGTGCCAATACGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTACACATACAGTGCCAATACGA
AAATTCATAAACTTATTACAAATTTCTTAAG
Found at i:532715 original size:35 final size:36
Alignment explanation
Indices: 532653--532720 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
532643 TGGAAAATGC
**
532653 ATCATGAGGTATCGATATTGAATTGGTAGTATCAGT
1 ATCATGAGGTATCGATATCCAATTGGTAGTATCAGT
532689 ATCATG-GGTATCGATA-CCAATGTGGTAGTATC
1 ATCATGAGGTATCGATATCCAAT-TGGTAGTATC
532721 GGTACCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 3 0.10
35 20 0.69
36 6 0.21
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (36 bp):
ATCATGAGGTATCGATATCCAATTGGTAGTATCAGT
Found at i:533617 original size:42 final size:42
Alignment explanation
Indices: 533558--533711 Score: 157
Period size: 42 Copynumber: 3.6 Consensus size: 42
533548 GTTCTACGCA
* *
533558 GTCCTTCGGGACATATATGTGATCATTGGGAACATATATGTG
1 GTCCTTTGGGACATATATGTGGTCATTGGGAACATATATGTG
* *
533600 GTCCTTTGGGACATATATTTGGTCATTTGGAACATATATGTG
1 GTCCTTTGGGACATATATGTGGTCATTGGGAACATATATGTG
* * ** * *
533642 GT-CTTTAGGGACAATTCTATGTGGTCTTTCGGGATATTTCTACGTG
1 GTCCTTT-GGGAC-A-TATATGTGGTCATT-GGGA-ACATATATGTG
*
533688 GTCCTTAGGGACATATATGTGGTC
1 GTCCTTTGGGACATATATGTGGTC
533712 CTTCGGGATA
Statistics
Matches: 92, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
41 4 0.04
42 45 0.49
43 1 0.01
44 21 0.23
45 4 0.04
46 14 0.15
47 3 0.03
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (42 bp):
GTCCTTTGGGACATATATGTGGTCATTGGGAACATATATGTG
Found at i:533711 original size:21 final size:21
Alignment explanation
Indices: 533558--533719 Score: 137
Period size: 21 Copynumber: 7.5 Consensus size: 21
533548 GTTCTACGCA
533558 GTCCTTCGGGACATATATGTG
1 GTCCTTCGGGACATATATGTG
* *
533579 ATCATT-GGGAACATATATGTG
1 GTCCTTCGGG-ACATATATGTG
* *
533600 GTCCTTTGGGACATATATTTG
1 GTCCTTCGGGACATATATGTG
* * *
533621 GTCATTTGGAACATATATGTG
1 GTCCTTCGGGACATATATGTG
* * *
533642 GTCTTTAGGGACAATTCTATGTG
1 GTCCTTCGGGAC-A-TATATGTG
* * * *
533665 GTCTTTCGGGATATTTCTACGTG
1 GTCCTTCGGGACA--TATATGTG
*
533688 GTCCTTAGGGACATATATGTG
1 GTCCTTCGGGACATATATGTG
533709 GTCCTTCGGGA
1 GTCCTTCGGGA
533720 TAATTTTATA
Statistics
Matches: 115, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.03
21 72 0.63
22 5 0.04
23 35 0.30
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.37
Consensus pattern (21 bp):
GTCCTTCGGGACATATATGTG
Found at i:538605 original size:54 final size:54
Alignment explanation
Indices: 538125--538626 Score: 707
Period size: 54 Copynumber: 9.3 Consensus size: 54
538115 ACTCTATGGT
* * * * * * * **
538125 TTGCACACATAGTGCTAATACGGTAATTCACAAACTCATTATGAATTACGTGGG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
* * * * *
538179 TTGCACACATAATGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAT
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
*
538233 TTGCACACACAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
* * *
538287 TTGAACACATAGTGTCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
* * *
538341 TTGCACACACAGTGTCAATACGGAAATTCATAAACTAATTGTGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
* *
538395 TTGCACACACAGTCCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
* * * *
538449 TTGCACACGCAATGCTAATACAGAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
* * * **
538503 TTGCACACGCAGTGCTAATACGGAAACTCATAAACTTATTATTTATTTCTTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
538557 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
*
538611 TTGCACACATAGTGCC
1 TTGCACACACAGTGCC
538627 CATTTTGTAA
Statistics
Matches: 404, Mismatches: 44, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 404 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (54 bp):
TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
Found at i:547687 original size:20 final size:20
Alignment explanation
Indices: 547658--547696 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
547648 AGAATGCTCG
547658 GAGGGAACCGATTCCCCCCA
1 GAGGGAACCGATTCCCCCCA
*
547678 GAGGGTACCGATTCCCCCC
1 GAGGGAACCGATTCCCCCC
547697 TGTTTAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.41, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCCA
Found at i:549980 original size:21 final size:21
Alignment explanation
Indices: 549951--550025 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
549941 ATATATATTA
* * *
549951 TGTATCGATGTATTGCTACAG
1 TGTACCGATGCATTGTTACAG
*
549972 TGTACCGATGCACTGTTACAG
1 TGTACCGATGCATTGTTACAG
549993 TGTACCGATGCATTGTTACAG
1 TGTACCGATGCATTGTTACAG
550014 TGTACCGATGCA
1 TGTACCGATGCA
550026 CTACTATAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (21 bp):
TGTACCGATGCATTGTTACAG
Found at i:550015 original size:42 final size:42
Alignment explanation
Indices: 549951--550056 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 42
549941 ATATATATTA
* * **
549951 TGTATCGATGTATTGCTACAGTGTACCGATGCACTGTTACAG
1 TGTATCGATGCATTGATACAGTGTACCGATGCACTACTACAG
* * *
549993 TGTACCGATGCATTGTTACAGTGTACCGATGCACTACTATAG
1 TGTATCGATGCATTGATACAGTGTACCGATGCACTACTACAG
*
550035 TGTATCGATGCACTGATACAGT
1 TGTATCGATGCATTGATACAGT
550057 AACTTCGGCA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (42 bp):
TGTATCGATGCATTGATACAGTGTACCGATGCACTACTACAG
Found at i:550036 original size:21 final size:21
Alignment explanation
Indices: 549967--550056 Score: 126
Period size: 21 Copynumber: 4.3 Consensus size: 21
549957 GATGTATTGC
549967 TACAGTGTACCGATGCACTGT
1 TACAGTGTACCGATGCACTGT
*
549988 TACAGTGTACCGATGCATTGT
1 TACAGTGTACCGATGCACTGT
**
550009 TACAGTGTACCGATGCACTAC
1 TACAGTGTACCGATGCACTGT
* * *
550030 TATAGTGTATCGATGCACTGA
1 TACAGTGTACCGATGCACTGT
550051 TACAGT
1 TACAGT
550057 AACTTCGGCA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (21 bp):
TACAGTGTACCGATGCACTGT
Found at i:553663 original size:32 final size:32
Alignment explanation
Indices: 553620--553682 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
553610 AATTAAAACC
553620 TTTTAAAACAAATAAAAC-TTCATATATTAATT
1 TTTTAAAACAAATAAAACATT-ATATATTAATT
* **
553652 TTTTTAAACAAATATTACATTATATATTAAT
1 TTTTAAAACAAATAAAACATTATATATTAAT
553683 ATATATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 25 0.93
33 2 0.07
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (32 bp):
TTTTAAAACAAATAAAACATTATATATTAATT
Found at i:557029 original size:16 final size:18
Alignment explanation
Indices: 557010--557042 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
557000 ATAAACTCTT
557010 TATTT-TATTTT-TTGTC
1 TATTTATATTTTATTGTC
557026 TATTTATATTTTATTGT
1 TATTTATATTTTATTGT
557043 AATATCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (18 bp):
TATTTATATTTTATTGTC
Found at i:558319 original size:7 final size:7
Alignment explanation
Indices: 558307--558333 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
558297 TTCTACTTTT
558307 ACTCTCA
1 ACTCTCA
558314 ACTCTCA
1 ACTCTCA
558321 ACTCTCA
1 ACTCTCA
558328 ACTCTC
1 ACTCTC
558334 CCCTGATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.44, G:0.00, T:0.30
Consensus pattern (7 bp):
ACTCTCA
Found at i:562996 original size:31 final size:33
Alignment explanation
Indices: 562960--563027 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
562950 GTAATTTTAA
562960 AGTATTTGAA-TTATTAATTTTGA-TCTATTTT
1 AGTATTTGAATTTATTAATTTTGATTCTATTTT
* * *
562991 AGTATTTGAATTTTTTAATTTTTATTTTATTTT
1 AGTATTTGAATTTATTAATTTTGATTCTATTTT
563024 AGTA
1 AGTA
563028 AATCGTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 10 0.31
32 11 0.34
33 11 0.34
ACGTcount: A:0.28, C:0.01, G:0.09, T:0.62
Consensus pattern (33 bp):
AGTATTTGAATTTATTAATTTTGATTCTATTTT
Found at i:564313 original size:20 final size:18
Alignment explanation
Indices: 564248--564382 Score: 81
Period size: 21 Copynumber: 6.8 Consensus size: 18
564238 AATAACCAAC
**
564248 GAATTCGCAAGTCAATTT
1 GAATTCGCAACACAATTT
**
564266 CGAATTCGCAACACGAAAGT
1 -GAATTCGCAACAC-AATTT
*
564286 CAATTTCGCAACACAATTTCT
1 GAA-TTCGCAACACAA-TT-T
**
564307 GAATTCGCAACTTGAATTT
1 GAATTCGCAAC-ACAATTT
564326 GGAATTCGCAACACAGAATTT
1 -GAATTCGCAACAC--AATTT
*
564347 AAAATTCGCAACACGGAATTT
1 -GAATTCGCAACAC--AATTT
564368 AGAATTCGCAACACA
1 -GAATTCGCAACACA
564383 GAAGTCTAAT
Statistics
Matches: 92, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
19 17 0.18
20 34 0.37
21 41 0.45
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (18 bp):
GAATTCGCAACACAATTT
Found at i:564344 original size:21 final size:21
Alignment explanation
Indices: 564290--564385 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 21
564280 GAAAGTCAAT
*
564290 TTCGCAACAC--AATTTCTGAA
1 TTCGCAACACAGAATTT-AGAA
** *
564310 TTCGCAAC-TTGAATTTGGAA
1 TTCGCAACACAGAATTTAGAA
*
564330 TTCGCAACACAGAATTTAAAA
1 TTCGCAACACAGAATTTAGAA
*
564351 TTCGCAACACGGAATTTAGAA
1 TTCGCAACACAGAATTTAGAA
564372 TTCGCAACACAGAA
1 TTCGCAACACAGAA
564386 GTCTAATTCG
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
20 19 0.30
21 45 0.70
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.26
Consensus pattern (21 bp):
TTCGCAACACAGAATTTAGAA
Found at i:564438 original size:20 final size:20
Alignment explanation
Indices: 564413--564543 Score: 79
Period size: 20 Copynumber: 6.5 Consensus size: 20
564403 AATTTGACAA
564413 TTTCGCAACACGAATTTCTT
1 TTTCGCAACACGAATTTCTT
*
564433 TTTCGCAACTCG-ATTT-TT
1 TTTCGCAACACGAATTTCTT
* * *
564451 AAATTCGCAACACGAGTTTCCT
1 --TTTCGCAACACGAATTTCTT
* * * *
564473 TTTCGCAAAAAGATTTTTTT
1 TTTCGCAACACGAATTTCTT
* * **
564493 TAATTCGCAACGCGAGTTTCAA
1 T--TTCGCAACACGAATTTCTT
*
564515 TTTCGCAACATGAATTT-TAT
1 TTTCGCAACACGAATTTCT-T
564535 TTTCGCAAC
1 TTTCGCAAC
564544 TCGATTTTCG
Statistics
Matches: 81, Mismatches: 23, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
18 2 0.02
19 4 0.05
20 58 0.72
21 3 0.04
22 14 0.17
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (20 bp):
TTTCGCAACACGAATTTCTT
Found at i:564438 original size:42 final size:41
Alignment explanation
Indices: 564290--564470 Score: 165
Period size: 42 Copynumber: 4.4 Consensus size: 41
564280 GAAAGTCAAT
* *
564290 TTCGCAACAC-AATTTCTGAATTCGCAACTTGAATTTG-GAA
1 TTCGCAACACGAATTTCT-AATTCGCAACTCGAATTTGACAA
** * *
564330 TTCGCAACACAGAATTTAAAATTCGCAACACGGAATTT-AGAA
1 TTCGCAACAC-GAATTTCTAATTCGCAACTC-GAATTTGACAA
* *
564372 TTCGCAACACAGAA-GTCTAATTCGCAATTCGAATTTGACAA
1 TTCGCAACAC-GAATTTCTAATTCGCAACTCGAATTTGACAA
** * *
564413 TTTCGCAACACGAATTTCTTTTTCGCAACTCGATTTTTA-AA
1 -TTCGCAACACGAATTTCTAATTCGCAACTCGAATTTGACAA
*
564454 TTCGCAACACGAGTTTC
1 TTCGCAACACGAATTTC
564471 CTTTTCGCAA
Statistics
Matches: 117, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
40 32 0.27
41 29 0.25
42 56 0.48
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.31
Consensus pattern (41 bp):
TTCGCAACACGAATTTCTAATTCGCAACTCGAATTTGACAA
Found at i:564488 original size:40 final size:41
Alignment explanation
Indices: 564414--564522 Score: 121
Period size: 42 Copynumber: 2.7 Consensus size: 41
564404 ATTTGACAAT
* * ***
564414 TTCGCAACACGAATTTCTTTTTCGCAACTCGA-TTTTTAAA
1 TTCGCAACACGAGTTTCATTTTCGCAAAAAGATTTTTTAAA
* *
564454 TTCGCAACACGAGTTTCCTTTTCGCAAAAAGATTTTTTTTAA
1 TTCGCAACACGAGTTTCATTTTCGCAAAAAGA-TTTTTTAAA
* *
564496 TTCGCAACGCGAGTTTCAATTTCGCAA
1 TTCGCAACACGAGTTTCATTTTCGCAA
564523 CATGAATTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 27 0.47
42 31 0.53
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (41 bp):
TTCGCAACACGAGTTTCATTTTCGCAAAAAGATTTTTTAAA
Found at i:564550 original size:62 final size:60
Alignment explanation
Indices: 564390--564566 Score: 147
Period size: 62 Copynumber: 2.9 Consensus size: 60
564380 ACAGAAGTCT
** * * * * *
564390 AATTCGCAATTCGAATTTGACAATTTCGCAACACGAATTTCTTTTTCGCAACTCGATTTTTA
1 AATTCGCAACACGAATTT--CATTTTCGCAACACGATTTTCTTTTTCGCAACGCGAGTTTCA
* * * * *
564452 AATTCGCAACACGAGTTTCCTTTTCGCAAAAAGATTTTTTTTAATTCGCAACGCGAGTTTCA
1 AATTCGCAACACGAATTTCATTTTCGCAACACGATTTTCTTT--TTCGCAACGCGAGTTTCA
* * * * ***
564514 ATTTCGCAACATGAATTTTATTTTCGCAACTCGATTTTCGAATTCGCAACGCG
1 AATTCGCAACACGAATTTCATTTTCGCAACACGATTTTCTTTTTCGCAACGCG
564567 GATTTAAATT
Statistics
Matches: 89, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
60 29 0.33
62 60 0.67
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (60 bp):
AATTCGCAACACGAATTTCATTTTCGCAACACGATTTTCTTTTTCGCAACGCGAGTTTCA
Found at i:564720 original size:22 final size:22
Alignment explanation
Indices: 564695--564743 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
564685 TCTCTCACTC
*
564695 TCTCTGGCGACATCCGTCCCCA
1 TCTCTGACGACATCCGTCCCCA
* *
564717 TCTCCGACGACATCCTTCCCCA
1 TCTCTGACGACATCCGTCCCCA
564739 TCTCT
1 TCTCT
564744 AATCTTTTCA
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:0.14, C:0.47, G:0.12, T:0.27
Consensus pattern (22 bp):
TCTCTGACGACATCCGTCCCCA
Found at i:565397 original size:12 final size:12
Alignment explanation
Indices: 565376--565409 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
565366 ACCACATTTC
*
565376 CAATACCAAACA
1 CAATATCAAACA
565388 CAATATCAAACA
1 CAATATCAAACA
565400 CAATATCAAA
1 CAATATCAAA
565410 ATCCACAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:565551 original size:24 final size:24
Alignment explanation
Indices: 565519--565571 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
565509 GTGAGTACTA
565519 GTCAATACCCAGACTTTGATCTTG
1 GTCAATACCCAGACTTTGATCTTG
565543 GTCAATACCCAGACTTTGATCTTG
1 GTCAATACCCAGACTTTGATCTTG
565567 GTCAA
1 GTCAA
565572 GACTCGGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (24 bp):
GTCAATACCCAGACTTTGATCTTG
Found at i:565848 original size:3 final size:3
Alignment explanation
Indices: 565840--565870 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
565830 ATATAACCCT
*
565840 GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
565871 TCCCTGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:569160 original size:2 final size:2
Alignment explanation
Indices: 569153--569177 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
569143 TTCGACAATG
569153 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 T
569178 GTAAGTGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:570841 original size:40 final size:40
Alignment explanation
Indices: 570796--570875 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
570786 GCTGTTATCG
570796 GTACGAGAGATATGCATGAATTGCAGATGCCAAGGAAAGT
1 GTACGAGAGATATGCATGAATTGCAGATGCCAAGGAAAGT
*
570836 GTACGAGAGATATGCATGAATTGCAGATGCGAAGGAAAGT
1 GTACGAGAGATATGCATGAATTGCAGATGCCAAGGAAAGT
570876 TGGTGAAGGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.31, T:0.20
Consensus pattern (40 bp):
GTACGAGAGATATGCATGAATTGCAGATGCCAAGGAAAGT
Found at i:574565 original size:108 final size:107
Alignment explanation
Indices: 574442--575367 Score: 1218
Period size: 108 Copynumber: 8.6 Consensus size: 107
574432 GAACTCGAAT
* *
574442 AATCTTTAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAA
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAA
*
574507 TCGCGTCTGCCCTCTATTTCTTCAGAGAGTATAAGACTCAAAC
66 TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AAC
* * *
574550 AATCTTCAACGATCGTGTCTGCCCCCTATATT-TTCAGAGAGTATAAGACTCGAACAATCTTCAA
1 AATCTTCAACAATCGCGTCTGCCCCCTAT-TTCTTCAGAGAGTATAAGAC-C-CACAATCTTC-A
* ** * * * *
574614 T-GATCATGTCTCCCCCCTATATCTTTAGAGAGTATAAGAC-CCAC
62 TCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAC
* *
574658 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAA
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAA
* * *
574723 TCGTGTTTGCCCCCTATTTTTTCAGAGAGTATAAGACTCGAAC
66 TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AAC
** * ** *
574766 AATCTTCAATGATCGTGTCTGCCCCCTAAATCTTTAGAGAGTATAAGACCCACAATCTTCATCAA
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAA
* *
574831 TCGCGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTC-AC
66 TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAC
* *
574872 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAT
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTC-AT
* * * * *
574937 -GATCGTGTCTGCCCCCTATATCTTTAGAGAGTATAAGACCCGAAC
63 CAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AAC
* *
574982 AATCTTCAACTATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAA
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAA
575047 TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
66 TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AAC
* * *
575090 AATCTTCAATAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATC
* * *
575155 GATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-CCAC
64 AATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAC
* * *
575198 AATCTTCATCAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAAC
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCC--ACAATCTTCATC
* * *
575263 GATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-CCAC
64 AATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAC
*
575306 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTC
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCC--ACAATCTTC
575368 TTTTACTTCA
Statistics
Matches: 726, Mismatches: 74, Indels: 36
0.87 0.09 0.04
Matches are distributed among these distances:
105 2 0.00
106 85 0.12
107 7 0.01
108 484 0.67
109 9 0.01
110 137 0.19
111 2 0.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (107 bp):
AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAA
TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAC
Found at i:574652 original size:163 final size:161
Alignment explanation
Indices: 574434--575354 Score: 1430
Period size: 163 Copynumber: 5.7 Consensus size: 161
574424 GGAGTATGGA
* * ** *
574434 ACTCGAATAATCTTTAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
* * *
574499 TTCATCAATCGCGTCTGCCCTCTATTTCTTCAGAGAGTATAAGACTCAAACAATCTTCAACGATC
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATC
*
574564 GTGTCTGCCCCCTATATT-TTCAGAGAGTATAAG
129 GCGTCTGCCCCCTAT-TTCTTCAGAGAGTATAAG
* * *
574597 ACTCGAACAATCTTCAATGATCATGTCTCCCCCCTATATCTTTAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
*
574662 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGT
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGC
* *
574727 GTTTGCCCCCTATTTTTTCAGAGAGTATAAG
131 GTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
574758 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTAAATCTTTAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
* *
574823 TTCATCAATCGCGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCACAATCTTCATCAATCGC
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGC
574888 GTCTGCCCCCTATTTCTTCAGAGAGTATAAG
131 GTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
574919 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTTAGAGAGTATAAGACCCGAACAA
1 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCC--ACAA
* * * *
574984 TCTTCAACTATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATC
64 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATC
575049 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
129 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
575082 ACTCGAACAATCTTCAATAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGAC-C-CACAA
* * * *
575147 TCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATC
64 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATC
*
575212 GCGTATGCCCCCTATTTCTTCAGAGAGTATAAG
129 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * *
575245 ACCCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
575310 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC
575355 CCGAACAATC
Statistics
Matches: 711, Mismatches: 42, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
160 2 0.00
161 302 0.42
162 1 0.00
163 405 0.57
164 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (161 bp):
ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGC
GTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:576422 original size:128 final size:127
Alignment explanation
Indices: 576141--576549 Score: 590
Period size: 128 Copynumber: 3.2 Consensus size: 127
576131 TCTCATCATG
* *
576141 ATGTGTGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTTCAAAATGCCCCTATT
1 ATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCC-TTCAAAATGCCCC-ATC
* * ** * *
576206 ACCTCAAATTATAAGGCTCATTCTTCATGCC-TC--CTTGGTCTGAATCTTTTCATCTCAACATG
64 ACCTCAGATTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAAT-TTTTCATCTCAACCTA
576268 ATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCAC
1 ATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCAC
* *
576333 CTTAGTTTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAATTTTATCATCTCAACCTA
66 CTCAGATTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAATTTT-TCATCTCAACCTA
* * * *
576396 ATGTGGGTTCAGTCATGCCCCAACATTATCTTGTACTGGTACGAGCCTTCAAAATGTCCCATCAC
1 ATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCAC
* *
576461 CTCAGATTGTAAGGCTTATTCTTCATGCCTTCTTCTTCTTCTGAATCTTGTCATCTCAACCTA
66 CTCAGATTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAAT-TTTTCATCTCAACCTA
* *
576524 ATGTGGGTTCAGCCGTGCCACAACAT
1 ATGTGGGTTCAGTCGTGCCCCAACAT
576550 ATCGCAACTT
Statistics
Matches: 256, Mismatches: 21, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
125 29 0.11
126 15 0.06
127 49 0.19
128 161 0.63
129 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (127 bp):
ATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCAC
CTCAGATTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAATTTTTCATCTCAACCTA
Found at i:577825 original size:16 final size:16
Alignment explanation
Indices: 577807--577836 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
577797 TTCATTCTTT
577807 TTTTC-ATTTTTCTCA
1 TTTTCAATTTTTCTCA
577822 TTTTCAATTTTTCTC
1 TTTTCAATTTTTCTC
577837 TTTCTTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTCAATTTTTCTCA
Found at i:577863 original size:6 final size:6
Alignment explanation
Indices: 577806--577920 Score: 60
Period size: 6 Copynumber: 18.5 Consensus size: 6
577796 TTTCATTCTT
* *
577806 TTTTTC ATTTTTC TCATTTTC AATTTTTC TCTTTC TTTTCC TTTTT- TATTTTC
1 TTTTTC -TTTTTC T--TTTTC --TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC
* * *
577859 TTTTTC -ATTTC ATTTTT- TTTATC -TTTTC TTTTTC TCTTTC TATATTTC
1 TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T-T-TTTC
*
577907 -TTTTC TTTCTC TTT
1 TTTTTC TTTTTC TTT
577921 ATGATGTCAA
Statistics
Matches: 84, Mismatches: 11, Indels: 27
0.69 0.09 0.22
Matches are distributed among these distances:
5 17 0.20
6 42 0.50
7 10 0.12
8 14 0.17
10 1 0.01
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTTC
Found at i:581408 original size:12 final size:12
Alignment explanation
Indices: 581391--581416 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
581381 TTTATTTGTT
581391 AATTAAAATGCA
1 AATTAAAATGCA
581403 AATTAAAATGCA
1 AATTAAAATGCA
581415 AA
1 AA
581417 CAACAATTTA
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:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (12 bp):
AATTAAAATGCA
Found at i:583983 original size:95 final size:94
Alignment explanation
Indices: 583821--584008 Score: 358
Period size: 95 Copynumber: 2.0 Consensus size: 94
583811 TTTTTGCTTC
*
583821 CTCGTGTTCTGTTGTTTGTGTGCAGGGGCCCCGGTTGGGCATGGTGATCACGAGCGACGATAATG
1 CTCGTGTTCTGTTGTTTGTGTGCAGGGCCCCCGGTTGGGCATGGTGATCACGAGCGACGATAATG
583886 GTGGCCTGGTATCGGATGGGTGGCCGACT
66 GTGGCCTGGTATCGGATGGGTGGCCGACT
583915 CTCGTGTTCTGTTGTTTGTGTGCAGGGCCCCCCGGTTGGGCATGGTGATCACGAGCGACGATAAT
1 CTCGTGTTCTGTTGTTTGTGTGCAGGG-CCCCCGGTTGGGCATGGTGATCACGAGCGACGATAAT
583980 GGTGGCCTGGTATCGGATGGGTGGCCGAC
65 GGTGGCCTGGTATCGGATGGGTGGCCGAC
584009 CAACACGGGT
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 27 0.29
95 65 0.71
ACGTcount: A:0.13, C:0.21, G:0.39, T:0.27
Consensus pattern (94 bp):
CTCGTGTTCTGTTGTTTGTGTGCAGGGCCCCCGGTTGGGCATGGTGATCACGAGCGACGATAATG
GTGGCCTGGTATCGGATGGGTGGCCGACT
Found at i:585515 original size:3 final size:3
Alignment explanation
Indices: 585501--585575 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
585491 TTGGCCCGTT
* * * * * * *
585501 TTA TTT TTA TTA TTA TAA TTT TTA TAA TAA TAA TTA TTA TTA -TA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
585548 TTA TTA TTA TTAA TAA ATA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA
585576 CATATTACAG
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
2 2 0.04
3 52 0.93
4 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:585568 original size:27 final size:27
Alignment explanation
Indices: 585511--585570 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
585501 TTATTTTTAT
* *
585511 TATTATAATTTTTATAATAATAATTAT
1 TATTATAATTTTTATAATAATAATAAA
* *
585538 TATTAT-ATTTTTATTATTATTAATAAA
1 TATTATAATTTTTA-TAATAATAATAAA
585565 TATTAT
1 TATTAT
585571 TATTACATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TATTATAATTTTTATAATAATAATAAA
Found at i:587553 original size:136 final size:136
Alignment explanation
Indices: 587373--587701 Score: 525
Period size: 136 Copynumber: 2.4 Consensus size: 136
587363 TATTTTAATA
* * * *
587373 TTTATATATATATTTTTTAATATTAAGAAATGAGCTGTCATAAAGCACTTAGAAATCATTTTCTT
1 TTTATATATTTATTTTTTAATATTAAGAAATGAGATGTCTTAAAGCACCTAGAAATCATTTTCTT
587438 CTTAAATAAATAAAATATCCTAATTTTAAATTATATATTAACCTATTGTTTTAATTATTTTTAGA
66 CTTAAATAAATAAAATATCCTAATTTTAAATTATATATTAACCTATT-TTTTAATTATTTTTAGA
587503 TAAATGT
130 TAAATGT
* *
587510 TTTA-ATATTTATTTTTTAATATTAAGAAATGGGATGTCTTAAAGCACCTAGAAGTCATTTTCTT
1 TTTATATATTTATTTTTTAATATTAAGAAATGAGATGTCTTAAAGCACCTAGAAATCATTTTCTT
* *
587574 CTTAAATAAATAAAATATCCTACTTTTAAATTATATATTAATCTATTTTTTAATTATTTTTAGAT
66 CTTAAATAAATAAAATATCCTAATTTTAAATTATATATTAACCTATTTTTTAATTATTTTTAGAT
587639 AAATGT
131 AAATGT
* *
587645 TTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGTTGTCTTAAAGCACCTAGAA
1 TTT-ATA--TATTTATTTTTTAATATTAAGAAATGAGATGTCTTAAAGCACCTAGAA
587702 GTTCTGTTCT
Statistics
Matches: 177, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
135 27 0.15
136 100 0.56
137 5 0.03
139 45 0.25
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (136 bp):
TTTATATATTTATTTTTTAATATTAAGAAATGAGATGTCTTAAAGCACCTAGAAATCATTTTCTT
CTTAAATAAATAAAATATCCTAATTTTAAATTATATATTAACCTATTTTTTAATTATTTTTAGAT
AAATGT
Found at i:588224 original size:24 final size:26
Alignment explanation
Indices: 588193--588252 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
588183 TTCATATATT
588193 ATATTTATA-A-TTATTTCTTTTCAAA
1 ATATTTATATACTTATTT-TTTTCAAA
*
588218 AT-TTTATATACTTATTTTTTTCATA
1 ATATTTATATACTTATTTTTTTCAAA
588243 ATATTTATAT
1 ATATTTATAT
588253 GTATATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 6 0.19
25 12 0.39
26 13 0.42
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (26 bp):
ATATTTATATACTTATTTTTTTCAAA
Found at i:588232 original size:26 final size:26
Alignment explanation
Indices: 588198--588266 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 26
588188 ATATTATATT
588198 TATAATTATTTCTTTTCAAAAT-TTTA
1 TATAATTATTT-TTTTCAAAATATTTA
* *
588224 TATACTTATTTTTTTCATAATATTTA
1 TATAATTATTTTTTTCAAAATATTTA
588250 TATGTATATTATTTTTT
1 TA--TA-ATTATTTTTT
588267 AATATTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.25
26 16 0.44
28 2 0.06
29 9 0.25
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.62
Consensus pattern (26 bp):
TATAATTATTTTTTTCAAAATATTTA
Found at i:589966 original size:22 final size:21
Alignment explanation
Indices: 589938--589981 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
589928 CATATTTACA
589938 TTTGCATTTGCATTTTACATTT
1 TTTGCATTTGCA-TTTACATTT
*
589960 TTTGCATTTGTATTTACATTT
1 TTTGCATTTGCATTTACATTT
589981 T
1 T
589982 CATTTTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.61
Consensus pattern (21 bp):
TTTGCATTTGCATTTACATTT
Found at i:589967 original size:28 final size:28
Alignment explanation
Indices: 589936--590017 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
589926 CACATATTTA
589936 CATTTGCATTTGCATTTTACATTTTTTG
1 CATTTGCATTTGCATTTTACATTTTTTG
* *
589964 CATTTGTATTTACATTTT-CA-TTTTTG
1 CATTTGCATTTGCATTTTACATTTTTTG
*
589990 CATTTGCATCTTGGCATAATTACATTTT
1 CATTTGCAT-TT-GCAT-TTTACATTTT
590018 ATTTCAAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 14 0.32
27 4 0.09
28 19 0.43
29 2 0.05
30 2 0.05
31 3 0.07
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.55
Consensus pattern (28 bp):
CATTTGCATTTGCATTTTACATTTTTTG
Found at i:592761 original size:10 final size:9
Alignment explanation
Indices: 592742--592789 Score: 71
Period size: 9 Copynumber: 5.3 Consensus size: 9
592732 CTTGAAGATG
*
592742 AAAAGAAAA
1 AAAAGGAAA
592751 AAAAGGAAA
1 AAAAGGAAA
592760 AAAAGGGAAA
1 AAAA-GGAAA
592770 AAAAGG-AA
1 AAAAGGAAA
592778 AAAAGGAAA
1 AAAAGGAAA
592787 AAA
1 AAA
592790 TTGAACCAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 8 0.22
9 19 0.53
10 9 0.25
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAGGAAA
Found at i:592779 original size:7 final size:8
Alignment explanation
Indices: 592749--592789 Score: 55
Period size: 8 Copynumber: 4.8 Consensus size: 8
592739 ATGAAAAGAA
592749 AAAAAAGG
1 AAAAAAGG
592757 AAAAAAAGGG
1 -AAAAAA-GG
592767 AAAAAAAGG
1 -AAAAAAGG
592776 AAAAAAGG
1 AAAAAAGG
592784 AAAAAA
1 AAAAAA
592790 TTGAACCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 14 0.45
9 8 0.26
10 9 0.29
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:597118 original size:22 final size:22
Alignment explanation
Indices: 597090--597146 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
597080 ACATCTACAT
597090 TCTTCAAAGATGATAGATTCCC
1 TCTTCAAAGATGATAGATTCCC
* *
597112 TCTTCAAAAATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCCC
*
597134 TTTTCAAAGATGA
1 TCTTCAAAGATGA
597147 AAGCTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCCC
Found at i:598184 original size:113 final size:113
Alignment explanation
Indices: 597986--598749 Score: 1135
Period size: 113 Copynumber: 6.7 Consensus size: 113
597976 CATTTACAGA
597986 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* *
598051 TCAACCTTTTGCTTGAATTCATCACTCGATGGATCATCAATT-CCAAGT
66 TCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGC-ATTGCCAGGT
* * *
598099 AGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAATAAGTTCATAATGAGAAGAACTTTT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * *
598164 TTAACTTTTTGCTCGAATTCATCACTCGATGGATCAGAATTGCCAGGT
66 TCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAGGT
598212 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
598277 TCAACCTTTTGCTCGAATTCATCACTCGATGAATCAACATTGCCAGGT
66 TCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAGGT
* *
598325 AGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAATAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
*
598390 TCAACATTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAGGT
66 TCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAGGT
* *
598438 AGAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAATAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
598503 TCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAGGT
66 TCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAGGT
598551 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * *
598615 TCAACCTTTTG-TATG-ACTCTATCACAGATGGAGATAGATCAGCATCAACTTTTCCAGAG-
66 TCAACCTTTTGCT-TGAATTC-ATCAC---T--CGATGGATCAG---C-A--TTGCCAG-GT
* * *
598674 AAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
598738 TCAACCTTTTGC
66 TCAACCTTTTGC
598750 ATGACTCTAT
Statistics
Matches: 597, Mismatches: 37, Indels: 23
0.91 0.06 0.04
Matches are distributed among these distances:
111 4 0.01
112 49 0.08
113 454 0.76
115 1 0.00
117 9 0.02
120 1 0.00
121 1 0.00
122 3 0.01
123 74 0.12
124 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (113 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAGGT
Found at i:598695 original size:123 final size:122
Alignment explanation
Indices: 598553--598856 Score: 475
Period size: 123 Copynumber: 2.5 Consensus size: 122
598543 TGCCAGGTAG
598553 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* ** * *
598618 ACCTTTTGTATGACTCTATCACAGATGGAGATAGATCAGCATCAACTTTTCCAGAGAA
66 ACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAGA-AA
* *
598676 AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
598740 AACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAGAAG
65 AACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAGAAA
* * * *
598798 TGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATAATAAGAACT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACT
598857 CATCTGAAGA
Statistics
Matches: 165, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
122 53 0.32
123 112 0.68
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (122 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAGAAA
Found at i:598846 original size:39 final size:40
Alignment explanation
Indices: 598799--598896 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 40
598789 TTCCAGAAGT
598799 GTTCATAATAAGAAGAACTCATCTGAAGAAGG-AGAAGAA
1 GTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAA
*
598838 GTTCATAATAATAAGAACTCATCTGAAGAAGGAAGAAGAA
1 GTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAA
*
598878 GTTCAGAATAAGAAGAACT
1 GTTCATAATAAGAAGAACT
598897 TGTTCAACCT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.56
40 24 0.44
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.19
Consensus pattern (40 bp):
GTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAA
Found at i:598876 original size:162 final size:161
Alignment explanation
Indices: 598675--599018 Score: 467
Period size: 162 Copynumber: 2.1 Consensus size: 161
598665 TTTCCAGAGA
* * * *
598675 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAGAATAAGAAGAACTTGTTC
* * *
598740 AACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAGAAG-TGTTCA
66 AACCTTTTGCATGACTCTATC-CAGAAAGAGATAAATCAACACCAACATTTCCAGAAGAAGTTCA
598804 TAATAAGAAGAACTCATCTGAAGAAGG-AGAAG
130 TAATAAGAAGAACTCATCTGAAG-AGGAAGAAG
* *
598836 AAGTTCATAATAATAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAGAATAAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCAGAATAAGAAGAACTTGTT
** * * * * * *
598901 CAACCTTTTGTTTGATTTTATCCAGATAGAGATAAATCAGCACCTACATTTCCAGAGGAAGTTCA
65 CAACCTTTTGCATGACTCTATCCAGAAAGAGATAAATCAACACCAACATTTCCAGAAGAAGTTCA
* * *
598966 TAATGAGAAGAACTTATCTGAAGAGGAATAAG
130 TAATAAGAAGAACTCATCTGAAGAGGAAGAAG
598998 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
599019 TGTTCAACCT
Statistics
Matches: 158, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
161 60 0.38
162 98 0.62
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (161 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAGAATAAGAAGAACTTGTTC
AACCTTTTGCATGACTCTATCCAGAAAGAGATAAATCAACACCAACATTTCCAGAAGAAGTTCAT
AATAAGAAGAACTCATCTGAAGAGGAAGAAG
Found at i:598942 original size:284 final size:284
Alignment explanation
Indices: 598553--599135 Score: 943
Period size: 284 Copynumber: 2.1 Consensus size: 284
598543 TGCCAGGTAG
* * *
598553 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCAGAATAAGAAGAACTTGTTCA
* * * *
598618 ACCTTTTGTATGACTCTATCACAGATGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCAT
66 ACCTTTTGTATGACTCTATCACAGATAGAGATAAATCAGCACCAACATTTCCAGAGAAAGTTCAT
*
598683 AATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTT
131 AATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
* * *
598748 GCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAGAAGTGTTCATAATAAGAA
196 GCATGACGCTATCACAGAAAGAGATAGACCAACATAAACATTTCCAGAAGTGTTCATAATAAGAA
598813 GAACTCATCTGAAGAAGGAGAAGA
261 GAACTCATCTGAAGAAGGAGAAGA
*
598837 AGTTCATAATAATAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAGAATAAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCAGAATAAGAAGAACTTGTTC
* * * * *
598902 AACCTTTTGTTTGATTTTATC-CAGATAGAGATAAATCAGCACCTACATTTCCAGAGGAAGTTCA
65 AACCTTTTGTATGACTCTATCACAGATAGAGATAAATCAGCACCAACATTTCCAGAGAAAGTTCA
*
598966 TAATGAGAAGAACTTATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
130 TAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
* * *
599031 TGCTTGACGCTATCACAGAATGAGATAGACCAGCATAAACATTTCCAGAAGTGTTCATAATAAGA
195 TGCATGACGCTATCACAGAAAGAGATAGACCAACATAAACATTTCCAGAAGTGTTCATAATAAGA
599096 AGAACTCATCTGAAGAAGGAGAAGA
260 AGAACTCATCTGAAGAAGGAGAAGA
* *
599121 AATTCATAATGAGAA
1 AGTTCATAATAAGAA
599136 TAATTTGTTC
Statistics
Matches: 274, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
284 227 0.83
285 47 0.17
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (284 bp):
AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCAGAATAAGAAGAACTTGTTCA
ACCTTTTGTATGACTCTATCACAGATAGAGATAAATCAGCACCAACATTTCCAGAGAAAGTTCAT
AATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
GCATGACGCTATCACAGAAAGAGATAGACCAACATAAACATTTCCAGAAGTGTTCATAATAAGAA
GAACTCATCTGAAGAAGGAGAAGA
Found at i:599097 original size:122 final size:123
Alignment explanation
Indices: 598831--599151 Score: 416
Period size: 122 Copynumber: 2.6 Consensus size: 123
598821 CTGAAGAAGG
* * *
598831 AGAAGAAGTTCATAATAATAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAGAATAAGAAGAAC
1 AGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* *** * **
598896 TTGTTCAACCTTTTGTTTGATTTTATCCAGATAGAGATAAATCAGCACCTACATTTCC
66 TTGTTCAACCTTTTGCTTGACGCTATCCAGATAGAGATAAACCAGCACAAACATTTCC
* * * *
598954 AGAGGAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAATAAGAAGTTCATAATGAGAAGAAC
1 AGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* *
599018 TTGTTCAACCTTTTGCTTGACGCTATCACAGA-ATGAGATAGACCAGCATAAACATTTCC
66 TTGTTCAACCTTTTGCTTGACGCTATC-CAGATA-GAGATAAACCAGCACAAACATTTCC
* * * *
599077 AGAAG-TGTTCATAATAAGAAGAACTCATCTGAAGAAGG-AGAAGAAATTCATAATGAGAATAAT
1 AGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
599140 TTGTTCAACCTT
66 TTGTTCAACCTT
599152 AATTTAATTC
Statistics
Matches: 171, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
122 109 0.64
123 62 0.36
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (123 bp):
AGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACCTTTTGCTTGACGCTATCCAGATAGAGATAAACCAGCACAAACATTTCC
Found at i:599493 original size:3 final size:3
Alignment explanation
Indices: 599479--599553 Score: 71
Period size: 3 Copynumber: 25.0 Consensus size: 3
599469 TTGGCCCGTT
* * * * *
599479 TTA TTT TTA TTA TTA TAA TTG TTA TAA TTA TTA TTA TTA TTA -TA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
599526 TTA TTA TTA TTAA TAA ATA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA
599554 CTACATATTA
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
2 2 0.04
3 52 0.93
4 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Done.