Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_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: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 29
Found at i:1664103 original size:19 final size:19
Alignment explanation
Indices: 1664079--1664126 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1664069 TTACATTTAC
1664079 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1664098 ATACAAAATTATGAATCGT
1 ATACAAAATTATAAATCGT
1664117 ATACAAAATT
1 ATACAAAATT
1664127 TCCCCTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1665748 original size:20 final size:20
Alignment explanation
Indices: 1665725--1665772 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1665715 TTTCTACCGG
1665725 TTACATTAGAAATTTACCTA
1 TTACATTAGAAATTTACCTA
1665745 TTACATTAGAAATTTACCTA
1 TTACATTAGAAATTTACCTA
1665765 TTACATTA
1 TTACATTA
1665773 TATTTATCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.42
Consensus pattern (20 bp):
TTACATTAGAAATTTACCTA
Found at i:1666084 original size:198 final size:199
Alignment explanation
Indices: 1665745--1666458 Score: 944
Period size: 199 Copynumber: 3.6 Consensus size: 199
1665735 AATTTACCTA
* *
1665745 TTACATTAG-AAATTTACCTATTACATTATATTTATCAGT-TTCGATGTTTATGGGATCGATACT
1 TTACATT-GTAAATTTACCTATTACATTATAATTATCAGTATTCGATGTTTTTGGGATCGATACT
* * * *
1665808 TTTTATAAATGTATCGACACTTTATTCGTACACCACGTTAGGCATTCTTTATGGTCAAAATGTAT
65 TTTTATAAATGTATCGACACTTTATTCGTACACCCCGTTGGGCATTCTTTCTGGTCAAAAAGTAT
* * *
1665873 CGACATAAATTTAAAAAGTGTCGACAAATTATTTAGACCTATTTTCTAATTAACCAGTATATTTC
130 CGACACAAATTTAAAAAGTGTCGATAAATTATGTAGACCTATTTTCTAATTAACC-GTATATTTC
1665938 TACTGG
194 TACTGG
* * * **
1665944 TTACATTGTAAAGTTACCTATTACATTATAATTATCGGT-TTCGATGCTTTTGGGATCGATACAA
1 TTACATTGTAAATTTACCTATTACATTATAATTATCAGTATTCGATGTTTTTGGGATCGATACTT
*
1666008 TTT-TAAATGTATCGACACTTTATTCGTACACCCCGTTGGGCATTCTTTCTGGTCAAAACGTATC
66 TTTATAAATGTATCGACACTTTATTCGTACACCCCGTTGGGCATTCTTTCTGGTCAAAAAGTATC
* *
1666072 GACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTACTTTCTAATTAACCGGTATATTTCT
131 GACACAAATTTAAAAAGTGTCGATAAATTATGTAGACCTATTTTCTAATTAACC-GTATATTTCT
*
1666137 ACCGG
195 ACTGG
* * * * **
1666142 TTACATTGGAAATTGACCTATTACATTATAATTATC-TTATTCGATATTTTTATGATCGATACTT
1 TTACATTGTAAATTTACCTATTACATTATAATTATCAGTATTCGATGTTTTTGGGATCGATACTT
* * * *
1666206 TTTGTAAATGTATCGACACTTTATTCGTGCACCTCAGTTGGTCATT-TATTCTGGAT-AAAAAGT
66 TTTATAAATGTATCGACACTTTATTCGTACACC-CCGTTGGGCATTCT-TTCTGG-TCAAAAAGT
* * *
1666269 ATCGACAC-AATTTAAAAAGTGTTGATATATTATGTAGACCTATTTTCTAATTAACCGATATATA
128 ATCGACACAAATTTAAAAAGTGTCGATAAATTATGTAGACCTATTTTCTAATTAACCG-TATATT
1666333 TCTACTGG
192 TCTACTGG
* *
1666341 TTACATTGTAAATTTACCTATTACATTATAATTAT-ATTATTCGATGTTTTTGAGATCGATA-TT
1 TTACATTGTAAATTTACCTATTACATTATAATTATCAGTATTCGATGTTTTTGGGATCGATACTT
* * * *
1666404 TTTAATAAATATATCGACACTTTATTCGTGCACCTCGATTGGGCATTCATTCTGG
66 TTT-ATAAATGTATCGACACTTTATTCGTACACCCCG-TTGGGCATTCTTTCTGG
1666459 AGATTACTAA
Statistics
Matches: 456, Mismatches: 48, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
197 1 0.00
198 183 0.40
199 241 0.53
200 30 0.07
201 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (199 bp):
TTACATTGTAAATTTACCTATTACATTATAATTATCAGTATTCGATGTTTTTGGGATCGATACTT
TTTATAAATGTATCGACACTTTATTCGTACACCCCGTTGGGCATTCTTTCTGGTCAAAAAGTATC
GACACAAATTTAAAAAGTGTCGATAAATTATGTAGACCTATTTTCTAATTAACCGTATATTTCTA
CTGG
Found at i:1667739 original size:18 final size:18
Alignment explanation
Indices: 1667716--1667752 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1667706 CGAAATTTAT
1667716 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1667734 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1667752 A
1 A
1667753 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1669171 original size:12 final size:12
Alignment explanation
Indices: 1669150--1669183 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1669140 GATCATATCA
* *
1669150 TCATCATCATCT
1 TCATCTTCATCG
1669162 TCATCTTCATCG
1 TCATCTTCATCG
1669174 TCATCTTCAT
1 TCATCTTCAT
1669184 TGACTGCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.32, G:0.03, T:0.44
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:1670329 original size:18 final size:17
Alignment explanation
Indices: 1670308--1670364 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
1670298 TGATTTGATC
1670308 AGAAGAAGCGATTGGTTG
1 AGAAGAAGCG-TTGGTTG
*
1670326 AGAAGGAG-GTTGTCGTTG
1 AGAAGAAGCGTTG--GTTG
1670344 AGAAG-AGC-TTGGTTG
1 AGAAGAAGCGTTGGTTG
1670359 AGAAGA
1 AGAAGA
1670365 GCTTTGAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 9 0.26
16 3 0.09
17 6 0.18
18 16 0.47
ACGTcount: A:0.32, C:0.05, G:0.40, T:0.23
Consensus pattern (17 bp):
AGAAGAAGCGTTGGTTG
Found at i:1670360 original size:15 final size:15
Alignment explanation
Indices: 1670319--1670368 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
1670309 GAAGAAGCGA
*
1670319 TTGGTTGAGAAGGAGG
1 TTGGTTGAGAA-GAGC
1670335 TTGTCGTTGAGAAGAGC
1 TTG--GTTGAGAAGAGC
1670352 TTGGTTGAGAAGAGC
1 TTGGTTGAGAAGAGC
1670367 TT
1 TT
1670369 TGAGAAAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 14 0.45
16 3 0.10
17 6 0.19
18 8 0.26
ACGTcount: A:0.24, C:0.06, G:0.40, T:0.30
Consensus pattern (15 bp):
TTGGTTGAGAAGAGC
Found at i:1671061 original size:201 final size:201
Alignment explanation
Indices: 1670716--1672058 Score: 2005
Period size: 201 Copynumber: 6.7 Consensus size: 201
1670706 CAAGCATAAG
* ** * *
1670716 AAGTGTCGATACATTATATAGACCTATTCTCTTTTAAAACCGGTTTATTTATGCCGGTTACATTG
1 AAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTG
* * * **
1670781 AAAAATTATCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATATATACTTTTTATAAAT
66 AAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGATACTTTTTATAAAT
* * * *
1670846 GTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTTTGGACAAACAGTATCGAAACAAA
131 ATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAA
1670911 ATTAAA
196 ATTAAA
* * *
1670917 AAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATCGATATATTTATACTGGTTACATTG
1 AAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTG
*
1670982 AAAAATTATCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGATACTTTTTATAAAT
66 AAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGATACTTTTTATAAAT
* *
1671047 ATATCGATACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTAGACAAAAAGTATCGACACAAA
131 ATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAA
*
1671112 CTTAAA
196 ATTAAA
**
1671118 AAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACTAGTTACATTG
1 AAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTG
**
1671183 AAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGATACAATTTATAAAT
66 AAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGATACTTTTTATAAAT
*
1671248 ATATCGACACTTTATGCGTGCA-CTAGTTTGGGCATTCATTCTGGA-AGAGAAGTATCGACACAA
131 ATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTGGACA-AAAAGTATCGACACAA
*
1671311 ACTTAAA
195 AATTAAA
* * * * *
1671318 AAGTGTCGATATATTATGTAGACTTATTCTCTCAT-AAACTGATATATTTATACCGGTTACATTT
1 AAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTG
* * * *
1671382 AAAAATTACTTATTACATAATAATTATAGGTTTCGATATTTTTGGGATCGATAATTTTTATAAAT
66 AAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGATACTTTTTATAAAT
* *
1671447 ATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTGGACGAAAAGTATTGACACAAA
131 ATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAA
*
1671512 CTTAAA
196 ATTAAA
* * ** **
1671518 ACGTGTCGATACATTATGTATACCTATTCTCTCATAAAATAGGTATATTTATACATGTTACATTG
1 AAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTG
*
1671583 AAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATTGATACTTTTTATAAAT
66 AAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGATACTTTTTATAAAT
1671648 ATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAA
131 ATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAA
1671713 CA-TAAA
196 -ATTAAA
* *
1671719 AAGTGTCGATACATTATGTAGACCTATTCTCTCTTAAAACCGATATATTTATACCGGTTACATTG
1 AAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTG
* * * *
1671784 AAAAATTACCTATCACATTATAATTATGAGTTTCGATGTTTTTGGGATCGATACTTTTCATAAAT
66 AAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGATACTTTTTATAAAT
* * * * *
1671849 GTATCAAAACTTTATACGTGCA-CTAGTTTGGGCATTCATTCTGGACAAAAAATATCGACAC-AA
131 ATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAA
1671912 ATATAAA
196 AT-TAAA
* * * * **
1671919 AAGTATCGATTCATTATGTAGACCTATTGTCTCATAAAACCGGTATATTTAAACCACTTACATTG
1 AAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTG
* * * *
1671984 AAAAATTATCTATTACATTATAATTGTGGGTTTCGATGTTTTTGGGATCGATACATTTTATAAAT
66 AAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGATACTTTTTATAAAT
*
1672049 GTATCGACAC
131 ATATCGACAC
1672059 ATATGTTTAC
Statistics
Matches: 1039, Mismatches: 96, Indels: 15
0.90 0.08 0.01
Matches are distributed among these distances:
198 1 0.00
199 108 0.10
200 318 0.31
201 612 0.59
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (201 bp):
AAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTG
AAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGATACTTTTTATAAAT
ATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAA
ATTAAA
Found at i:1671907 original size:601 final size:601
Alignment explanation
Indices: 1670698--1672058 Score: 2083
Period size: 601 Copynumber: 2.3 Consensus size: 601
1670688 TTTAAAGAAG
* * * * * * ** *
1670698 TATCAACACAAGCATAAGAAGTGTCGATACATTATATAGACCTATTCTCTTTTAAAACCGGTTTA
1 TATCGACACAAACTTAAAAAGTGTCGATATATTATGTAGACCTATTCTCTCATAAAACCGGTATA
*
1670763 TTTATGCCGGTTACATTGAAAAATTATCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGA
66 TTTATACCGGTTACATTGAAAAATTATCTATTACATTATAATTATG-GTTTCGATGTTTTTGGGA
** * *
1670828 TATATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTTTGGAC
130 TCGATAATTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTGGAC
*
1670893 AAACAGTATCGAAACAAAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATC
195 AAACAGTATCGAAACAAAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATA
*
1670958 GATATATTTATACTGGTTACATTGAAAAATTATCTATTACATTATAATTATGGGTTTCGATATTT
260 GATATATTTATACTGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATATTT
*
1671023 TTGGGATCGATACTTTTTATAAATATATCGATACTTTATGCGTGCACCTAGTTTGGGCATTCATT
325 TTGGGATCGATACTTTTTATAAATATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
*
1671088 CTAGACAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCAT
390 CTAGACAAAAAGTATCGACACAAACATAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCAT
* * * *
1671153 AAAACCGGTATATTTATACTAGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCG
455 AAAACCGATATATTTATACCAGTTACATTGAAAAATTACCTATCACATTATAATTATGAGTTTCG
* * *
1671218 ATATTTTTGGGATCGATACAATTTATAAATATATCGACACTTTATGCGTGCACTAGTTTGGGCAT
520 ATATTTTTGGGATCGATACAATTTATAAATATATCAAAACTTTATACGTGCACTAGTTTGGGCAT
* *
1671283 TCATTCTGGAAGAGAAG
585 TCATTCTGGAAGAAAAA
* * *
1671300 TATCGACACAAACTTAAAAAGTGTCGATATATTATGTAGACTTATTCTCTCAT-AAACTGATATA
1 TATCGACACAAACTTAAAAAGTGTCGATATATTATGTAGACCTATTCTCTCATAAAACCGGTATA
* * *
1671364 TTTATACCGGTTACATTTAAAAATTA-CTTATTACATAATAATTATAGGTTTCGATATTTTTGGG
66 TTTATACCGGTTACATTGAAAAATTATC-TATTACATTATAATTAT-GGTTTCGATGTTTTTGGG
*
1671428 ATCGATAATTTTTATAAATATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTGGA
129 ATCGATAATTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTGGA
* * * * *
1671493 CGAAA-AGTATTGACACAAACTTAAAACGTGTCGATACATTATGTATACCTATTCTCTCATAAAA
194 C-AAACAGTATCGAAACAAAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAA
*
1671557 TAGGTATATTTATACAT-GTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATA
258 TAGATATATTTATAC-TGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATA
*
1671621 TTTTTGGGATTGATACTTTTTATAAATATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTC
322 TTTTTGGGATCGATACTTTTTATAAATATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTC
*
1671686 ATTCTGGACAAAAAGTATCGACACAAACATAAAAAGTGTCGATACATTATGTAGACCTATTCTCT
387 ATTCTAGACAAAAAGTATCGACACAAACATAAAAAGTGTCGATACATTATGTAGACCTATTCTCT
* *
1671751 CTTAAAACCGATATATTTATACCGGTTACATTGAAAAATTACCTATCACATTATAATTATGAGTT
452 CATAAAACCGATATATTTATACCAGTTACATTGAAAAATTACCTATCACATTATAATTATGAGTT
* * *
1671816 TCGATGTTTTTGGGATCGATAC-TTTTCATAAATGTATCAAAACTTTATACGTGCACTAGTTTGG
517 TCGATATTTTTGGGATCGATACAATTT-ATAAATATATCAAAACTTTATACGTGCACTAGTTTGG
1671880 GCATTCATTCTGGACA-AAAAA
581 GCATTCATTCTGGA-AGAAAAA
* *
1671901 TATCGACACAAA-TATAAAAAGTATCGAT-TCATTATGTAGACCTATTGTCTCATAAAACCGGTA
1 TATCGACACAAACT-TAAAAAGTGTCGATAT-ATTATGTAGACCTATTCTCTCATAAAACCGGTA
* ** *
1671964 TATTTAAACCACTTACATTGAAAAATTATCTATTACATTATAATTGTGGGTTTCGATGTTTTTGG
64 TATTTATACCGGTTACATTGAAAAATTATCTATTACATTATAATTAT-GGTTTCGATGTTTTTGG
1672029 GATCGATACA-TTTTATAAATGTATCGACAC
128 GATCGATA-ATTTTTATAAATGTATCGACAC
1672059 ATATGTTTAC
Statistics
Matches: 687, Mismatches: 61, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
600 6 0.01
601 540 0.79
602 139 0.20
603 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (601 bp):
TATCGACACAAACTTAAAAAGTGTCGATATATTATGTAGACCTATTCTCTCATAAAACCGGTATA
TTTATACCGGTTACATTGAAAAATTATCTATTACATTATAATTATGGTTTCGATGTTTTTGGGAT
CGATAATTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTCTGGACA
AACAGTATCGAAACAAAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATAG
ATATATTTATACTGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTT
TGGGATCGATACTTTTTATAAATATATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTC
TAGACAAAAAGTATCGACACAAACATAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATA
AAACCGATATATTTATACCAGTTACATTGAAAAATTACCTATCACATTATAATTATGAGTTTCGA
TATTTTTGGGATCGATACAATTTATAAATATATCAAAACTTTATACGTGCACTAGTTTGGGCATT
CATTCTGGAAGAAAAA
Found at i:1672285 original size:20 final size:20
Alignment explanation
Indices: 1672260--1672324 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
1672250 AAAGTCTATT
*
1672260 TTTACCACCAACATTGTAAA
1 TTTACCACCTACATTGTAAA
* * **
1672280 TTTACCTA-TTAC-TTCTATT
1 TTTACC-ACCTACATTGTAAA
1672299 TTTACCACCTACATTGTAAA
1 TTTACCACCTACATTGTAAA
1672319 TTTACC
1 TTTACC
1672325 TATTACTTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
18 1 0.03
19 13 0.39
20 18 0.55
21 1 0.03
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.42
Consensus pattern (20 bp):
TTTACCACCTACATTGTAAA
Found at i:1672297 original size:39 final size:39
Alignment explanation
Indices: 1672254--1672332 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
1672244 ATTAAAAAAG
1672254 TCTATTTTTACCACCAACATTGTAAATTTACCTATTACT
1 TCTATTTTTACCACCAACATTGTAAATTTACCTATTACT
*
1672293 TCTATTTTTACCACCTACATTGTAAATTTACCTATTACT
1 TCTATTTTTACCACCAACATTGTAAATTTACCTATTACT
1672332 T
1 T
1672333 TAAAGTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.46
Consensus pattern (39 bp):
TCTATTTTTACCACCAACATTGTAAATTTACCTATTACT
Found at i:1674172 original size:14 final size:15
Alignment explanation
Indices: 1674147--1674177 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1674137 CATATTTTTC
1674147 TTCTTCCTTCATATT
1 TTCTTCCTTCATATT
1674162 TTCTT-CTTCATATT
1 TTCTTCCTTCATATT
1674176 TT
1 TT
1674178 TTCAGTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.65
Consensus pattern (15 bp):
TTCTTCCTTCATATT
Found at i:1674391 original size:33 final size:33
Alignment explanation
Indices: 1674354--1674420 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1674344 CCATCTTAAG
*
1674354 TTCACCCCTCAATACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1674387 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1674420 T
1 T
1674421 CCATCTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.46, G:0.00, T:0.30
Consensus pattern (33 bp):
TTCACCCCTCAACACCTCAACTTCTTTCACCAC
Found at i:1674647 original size:18 final size:18
Alignment explanation
Indices: 1674624--1674668 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1674614 TCTCCTCTGC
1674624 CTCCTATGCCTCATCTAT
1 CTCCTATGCCTCATCTAT
*
1674642 CTCCTATGCCTCCTCTAT
1 CTCCTATGCCTCATCTAT
1674660 CTCCT-TGCC
1 CTCCTATGCC
1674669 AACAACCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.11, C:0.44, G:0.07, T:0.38
Consensus pattern (18 bp):
CTCCTATGCCTCATCTAT
Found at i:1674925 original size:22 final size:23
Alignment explanation
Indices: 1674897--1674952 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
1674887 AACCTGCATT
*
1674897 TATAATAAAAT-TTATCATTTTA
1 TATAATAAAATACTATCATTTTA
*
1674919 TATAATAACTATACTATCATTTTA
1 TATAATAA-AATACTATCATTTTA
*
1674943 TATAAAAAAA
1 TATAATAAAA
1674953 ACAAAAATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.29
23 3 0.11
24 17 0.61
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAATAAAATACTATCATTTTA
Found at i:1677181 original size:182 final size:182
Alignment explanation
Indices: 1676874--1677306 Score: 708
Period size: 182 Copynumber: 2.4 Consensus size: 182
1676864 TCTTTCTTTG
** * * * *
1676874 AAAGTATCGACACTTTCAATATATCTAGTAGTGCTTTA-CTGATTTTTTCATTTCAAGACCGGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCAG-TTTTGTCATTTCGAGACCGGTT
*
1676938 TTGTCATATTTTTACCAGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTA
65 TTGTCATAATTTTACCAGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTA
*
1677003 TAGGTGCTATTACTGCTTCTCTTTTAAATTTCC-AAAGTGTCGATACTTATATA
130 TAGGCGCTATTACTGCTTCTCTTTTAAA-TTCCAAAAGTGTCGATACTTATATA
1677056 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCGGTTT
* *
1677121 TGTCATAATTTTACCTGTTATATCGTTATGGATCGATACATTTTTATGAAGTATCGACACTTTAT
66 TGTCATAATTTTACCAGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTAT
* *
1677186 AGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTTGATACTTATATG
131 AGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATA
* *
1677238 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCTTTTCGAGACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCGGTTT
1677303 TGTC
66 TGTC
1677307 TTTTCGATAC
Statistics
Matches: 235, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
181 4 0.02
182 229 0.97
183 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCGGTTT
TGTCATAATTTTACCAGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTAT
AGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATA
Found at i:1677300 original size:20 final size:20
Alignment explanation
Indices: 1677275--1677326 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1677265 GTAGCGCTTT
1677275 ACCGGTTTTGTCTTTTCGAG
1 ACCGGTTTTGTCTTTTCGAG
*
1677295 ACCGGTTTTGTCTTTTCGAT
1 ACCGGTTTTGTCTTTTCGAG
1677315 ACCGGTTTTGTC
1 ACCGGTTTTGTC
1677327 ATATTTTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (20 bp):
ACCGGTTTTGTCTTTTCGAG
Found at i:1677559 original size:21 final size:21
Alignment explanation
Indices: 1677534--1677583 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1677524 TATATCGTTA
*
1677534 TGGATCGATATATTTTTAATC
1 TGGATCGATACATTTTTAATC
* *
1677555 TGGATCGATACATTTTTTATT
1 TGGATCGATACATTTTTAATC
1677576 TGGATCGA
1 TGGATCGA
1677584 CACAAACCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (21 bp):
TGGATCGATACATTTTTAATC
Found at i:1678038 original size:39 final size:39
Alignment explanation
Indices: 1677991--1678095 Score: 169
Period size: 37 Copynumber: 2.7 Consensus size: 39
1677981 TTTTTTATGC
1677991 ATAAGTTGAGGGATATGCAACAATAGTGTGGATTTATAT
1 ATAAGTTGAGGGATATGCAACAATAGTGTGGATTTATAT
* *
1678030 GTAAGTTGAGGG--ATGCAACAATAGTGTGGATTTATGT
1 ATAAGTTGAGGGATATGCAACAATAGTGTGGATTTATAT
*
1678067 ATAAGTTGAGGGATATACAACAATAGTGT
1 ATAAGTTGAGGGATATGCAACAATAGTGT
1678096 AGAGGTAGGA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
37 35 0.58
39 25 0.42
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (39 bp):
ATAAGTTGAGGGATATGCAACAATAGTGTGGATTTATAT
Found at i:1679666 original size:77 final size:77
Alignment explanation
Indices: 1679585--1680031 Score: 513
Period size: 77 Copynumber: 5.8 Consensus size: 77
1679575 TGCGTCTAAA
* *
1679585 AATGTCATGGTTCACTAAGAAATATGTTGTGATTTGGAATGTTAATATTTTTATTAATAAAATGG
1 AATGTCATGGTTCACTAAGAAATAGGTTGTGATCTGGAATGTTAATATTTTTATTAATAAAATGG
1679650 GTTACGCCCAAG
66 GTTACGCCCAAG
* * * * * * * *
1679662 AATGTCATAGTTCATTAAGAAATAGATTGCGATCTAGAATGTTAATATTTTTATTAATCAATTGA
1 AATGTCATGGTTCACTAAGAAATAGGTTGTGATCTGGAATGTTAATATTTTTATTAATAAAATGG
*
1679727 GTTACACCCAAG
66 GTTACGCCCAAG
* * * * * *
1679739 AATGTCATGGTTCACTAATAATTAGGTTGTGATATGGAATGTTAGTACTTTTGTTAATAAAATGG
1 AATGTCATGGTTCACTAAGAAATAGGTTGTGATCTGGAATGTTAATATTTTTATTAATAAAATGG
**
1679804 GTTGTGCCCAAG
66 GTTACGCCCAAG
* * *
1679816 AATGTCATGATTCACTAAGAAATAGGTTGAGATCTGGAATGTTAATATTTTTATTAATAAAATGA
1 AATGTCATGGTTCACTAAGAAATAGGTTGTGATCTGGAATGTTAATATTTTTATTAATAAAATGG
*
1679881 GTTTCGCCCAAG
66 GTTACGCCCAAG
* * * * *
1679893 AATGTCACGGTTCACTAAGAAATAGGTTGAT-ATTTGAAATGTTAATATTTTTATTAGTAAAATA
1 AATGTCATGGTTCACTAAGAAATAGGTTG-TGATCTGGAATGTTAATATTTTTATTAATAAAATG
* * *
1679957 GGTTGCACACAAG
65 GGTTACGCCCAAG
* * * ** *
1679970 AATGTTATAGTTCACTAAGAAAGCAAATTGCGATCTGGAATGTTAAT-TTTTCTATT-ATAAAA
1 AATGTCATGGTTCACTAAGAAA-TAGGTTGTGATCTGGAATGTTAATATTTT-TATTAATAAAA
1680032 AATTCAAAAG
Statistics
Matches: 306, Mismatches: 60, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
77 285 0.93
78 21 0.07
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (77 bp):
AATGTCATGGTTCACTAAGAAATAGGTTGTGATCTGGAATGTTAATATTTTTATTAATAAAATGG
GTTACGCCCAAG
Found at i:1679835 original size:154 final size:154
Alignment explanation
Indices: 1679585--1680031 Score: 596
Period size: 154 Copynumber: 2.9 Consensus size: 154
1679575 TGCGTCTAAA
*
1679585 AATGTCATGGTTCACTAAGAAATATGTTGTGATTTGGAATGTTAATATTTTTATTAATAAAATGG
1 AATGTCATGGTTCACTAAGAAATAGGTTGTGATTTGGAATGTTAATATTTTTATTAATAAAATGG
* * *
1679650 GTTACGCCCAAGAATGTCATAGTTCATTAAGAAATAGATTGCGATCTAGAATGTTAATATTTTTA
66 GTTGCGCCCAAGAATGTCATAGTTCACTAAGAAATAGATTGCGATCTGGAATGTTAATATTTTTA
* *
1679715 TTAATCAATTGAGTTACACCCAAG
131 TTAATAAAATGAGTTACACCCAAG
* * * * * *
1679739 AATGTCATGGTTCACTAATAATTAGGTTGTGATATGGAATGTTAGTACTTTTGTTAATAAAATGG
1 AATGTCATGGTTCACTAAGAAATAGGTTGTGATTTGGAATGTTAATATTTTTATTAATAAAATGG
* * *
1679804 GTTGTGCCCAAGAATGTCAT-GATTCACTAAGAAATAGGTTGAGATCTGGAATGTTAATATTTTT
66 GTTGCGCCCAAGAATGTCATAG-TTCACTAAGAAATAGATTGCGATCTGGAATGTTAATATTTTT
* *
1679868 ATTAATAAAATGAGTTTCGCCCAAG
130 ATTAATAAAATGAGTTACACCCAAG
* * * *
1679893 AATGTCACGGTTCACTAAGAAATAGGTTGAT-ATTTGAAATGTTAATATTTTTATTAGTAAAATA
1 AATGTCATGGTTCACTAAGAAATAGGTTG-TGATTTGGAATGTTAATATTTTTATTAATAAAATG
* * * * *
1679957 GGTTGCACACAAGAATGTTATAGTTCACTAAGAAAGCAAATTGCGATCTGGAATGTTAAT-TTTT
65 GGTTGCGCCCAAGAATGTCATAGTTCACTAAGAAA-TAGATTGCGATCTGGAATGTTAATATTTT
1680021 CTATT-ATAAAA
129 -TATTAATAAAA
1680032 AATTCAAAAG
Statistics
Matches: 253, Mismatches: 35, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
153 1 0.00
154 226 0.89
155 26 0.10
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (154 bp):
AATGTCATGGTTCACTAAGAAATAGGTTGTGATTTGGAATGTTAATATTTTTATTAATAAAATGG
GTTGCGCCCAAGAATGTCATAGTTCACTAAGAAATAGATTGCGATCTGGAATGTTAATATTTTTA
TTAATAAAATGAGTTACACCCAAG
Found at i:1680073 original size:20 final size:20
Alignment explanation
Indices: 1680036--1680073 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1680026 ATAAAAAATT
*
1680036 CAAAAGTATGAATGCTTTTC
1 CAAAAGTATGAATACTTTTC
1680056 CAAAAGTATTG-ATACTTT
1 CAAAAGTA-TGAATACTTT
1680074 CGAATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (20 bp):
CAAAAGTATGAATACTTTTC
Found at i:1680255 original size:77 final size:79
Alignment explanation
Indices: 1680155--1680315 Score: 215
Period size: 78 Copynumber: 2.1 Consensus size: 79
1680145 TTTAAATTTG
*
1680155 AAATTTGAAAATTAAAATATCATTTT-CA-TTTTTT-AAATTCGAAAGTATCAATACTTTTT-CA
1 AAATTCGAAAATTAAAATATCATTTTCCATTTTTTTAAAATTCGAAAG--TCAATA-TTTTTCCA
*
1680216 AAAGTATCGATACTTTT
63 AAAGTATCGATACTTTC
* * *
1680233 AAATTCGAAAGTT-AAATATCATTTTCCATTTTTTTAAAATTTGAAAGTGAATATTTTTCCAAAA
1 AAATTCGAAAATTAAAATATCATTTTCCATTTTTTTAAAATTCGAAAGTCAATATTTTTCCAAAA
1680297 GTATCGATACTTTC
66 GTATCGATACTTTC
1680311 AAATT
1 AAATT
1680316 TAAAGAAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
77 17 0.23
78 41 0.55
79 6 0.08
80 10 0.14
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (79 bp):
AAATTCGAAAATTAAAATATCATTTTCCATTTTTTTAAAATTCGAAAGTCAATATTTTTCCAAAA
GTATCGATACTTTC
Found at i:1680286 original size:35 final size:33
Alignment explanation
Indices: 1680229--1680293 Score: 78
Period size: 35 Copynumber: 1.9 Consensus size: 33
1680219 GTATCGATAC
1680229 TTTTAAATTCGAAAGTTAAATATCATTTTCCATTT
1 TTTTAAATTCGAAAGTTAAATAT--TTTTCCATTT
* *
1680264 TTTTAAAATTTGAAAG-TGAATATTTTTCCA
1 TTTT-AAATTCGAAAGTTAAATATTTTTCCA
1680294 AAAGTATCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 7 0.26
35 10 0.37
36 10 0.37
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.48
Consensus pattern (33 bp):
TTTTAAATTCGAAAGTTAAATATTTTTCCATTT
Found at i:1680624 original size:99 final size:99
Alignment explanation
Indices: 1680473--1680686 Score: 313
Period size: 99 Copynumber: 2.2 Consensus size: 99
1680463 ACATTTTTTC
* * * *
1680473 TTTAATGTTAAACGTTTAAGTTATAAGTATGAAACCGTTTATATGATGCAAAAGTAAAACAAAAC
1 TTTAATGTCAACCGTTTAAGTTATAAGTATGAAACCATTTATATGATACAAAAGTAAAACAAAAC
* * *
1680538 ATTTTACTCATGATAACATAGTAGGTAGTGTCTTT
66 ATGTTACTCATGATAACATACTAGGTAGCG-CTTT
* *
1680573 TTT-ATGTCAACCGTTTAAGTTATAAGTATGAAACCATTTATATTATACAAAAGTAAGACAAAAC
1 TTTAATGTCAACCGTTTAAGTTATAAGTATGAAACCATTTATATGATACAAAAGTAAAACAAAAC
* *
1680637 ATGTTGCTCATGATAACGTACTAGGTAGCGCTTT
66 ATGTTACTCATGATAACATACTAGGTAGCGCTTT
1680671 TTTAATGTCAACCGTT
1 TTTAATGTCAACCGTT
1680687 AATATTATGT
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
98 7 0.07
99 92 0.90
100 3 0.03
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (99 bp):
TTTAATGTCAACCGTTTAAGTTATAAGTATGAAACCATTTATATGATACAAAAGTAAAACAAAAC
ATGTTACTCATGATAACATACTAGGTAGCGCTTT
Found at i:1681244 original size:70 final size:70
Alignment explanation
Indices: 1681090--1681290 Score: 197
Period size: 70 Copynumber: 2.8 Consensus size: 70
1681080 CATAATATAT
* * * * * * * * *
1681090 GTATCGATATTTTAAGTATCAATCATATCCATCAACTTGTTCAATATCTAAAAGTATCGATCATC
1 GTATCGATATTTTAAATTTCAATCTTAT-CTTCAACTTTTTTAATATTTAAAAATATC-A--ATT
*
1681155 ATCGCATAA
62 ACCGCATAA
* * *
1681164 GTATCTATATTTTAAATTTCAATCTT-TTTATCAACTTTTTTAATTTTTAAAAATATCAATTACC
1 GTATCGATATTTTAAATTTCAATCTTATCT-TCAACTTTTTTAATATTTAAAAATATCAATTACC
1681228 GCATAA
65 GCATAA
** * *
1681234 GTATCGATATTTTAAATTTTGATCTTATCTTCATCTTTTTTAATATTTAAAAGTATC
1 GTATCGATATTTTAAATTTCAATCTTATCTTCAACTTTTTTAATATTTAAAAATATC
1681291 GATATTCAAA
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
70 57 0.54
71 2 0.02
72 1 0.01
73 23 0.22
74 22 0.21
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.45
Consensus pattern (70 bp):
GTATCGATATTTTAAATTTCAATCTTATCTTCAACTTTTTTAATATTTAAAAATATCAATTACCG
CATAA
Found at i:1681327 original size:10 final size:11
Alignment explanation
Indices: 1681301--1681326 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1681291 GATATTCAAA
1681301 TTTTTGAATTT
1 TTTTTGAATTT
1681312 TTTTTGAATTT
1 TTTTTGAATTT
1681323 TTTT
1 TTTT
1681327 GTGCGACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTTGAATTT
Found at i:1681417 original size:77 final size:77
Alignment explanation
Indices: 1681332--1681547 Score: 227
Period size: 82 Copynumber: 2.7 Consensus size: 77
1681322 TTTTTGTGCG
* * * * *
1681332 ACCTATTTTATTAATAAAAATATTAATATAACATATCGCAACCTATTTCTTAGTGAACCATGACA
1 ACCTATTTTATTAATAAAAATATTAATATTACAAATCACAACATATTTCTTAGTGAACCATAACA
*
1681397 TTCTTGGATGCA
66 TTCTGGGATGCA
* * * * * *
1681409 ACCTATTTTATTTA-AAAAATATCAAAATTACATTACAGATCACAACATACTTTCTTAATTAATC
1 ACCTATTTTATTAATAAAAATAT--TAA-T--ATTACAAATCACAACATA-TTTCTTAGTGAACC
* *
1681473 ATAATATTCTGGGGTGCA
60 ATAACATTCTGGGATGCA
* *
1681491 ACGTATTTTATTAATAAAAATATTAATATTACAAATCACAACATGTTTCTTAGTGAA
1 ACCTATTTTATTAATAAAAATATTAATATTACAAATCACAACATATTTCTTAGTGAA
1681548 TACATTATTG
Statistics
Matches: 112, Mismatches: 20, Indels: 14
0.77 0.14 0.10
Matches are distributed among these distances:
76 8 0.07
77 23 0.21
78 18 0.16
79 1 0.01
80 1 0.01
81 16 0.14
82 37 0.33
83 8 0.07
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (77 bp):
ACCTATTTTATTAATAAAAATATTAATATTACAAATCACAACATATTTCTTAGTGAACCATAACA
TTCTGGGATGCA
Found at i:1692278 original size:21 final size:21
Alignment explanation
Indices: 1692253--1692295 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1692243 GAATATGAAA
1692253 ATTACCC-CTAATATCGATACT
1 ATTACCCTC-AATATCGATACT
*
1692274 ATTACCCTCAATATTGATACT
1 ATTACCCTCAATATCGATACT
1692295 A
1 A
1692296 GGGCTACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.35
Consensus pattern (21 bp):
ATTACCCTCAATATCGATACT
Found at i:1694984 original size:23 final size:26
Alignment explanation
Indices: 1694925--1694984 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
1694915 ATTTTACTTA
1694925 TATGCTATATTATATATATATGTATATGT
1 TATG-TAT-TTATATATATATGTATA-GT
*
1694954 TTTGTATTTATATATATAT-TATA-T
1 TATGTATTTATATATATATGTATAGT
1694978 TAT-TATT
1 TATGTATT
1694985 AGTTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 4 0.14
24 3 0.10
26 4 0.14
27 12 0.41
28 3 0.10
29 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (26 bp):
TATGTATTTATATATATATGTATAGT
Found at i:1695011 original size:121 final size:120
Alignment explanation
Indices: 1694844--1695085 Score: 434
Period size: 121 Copynumber: 2.0 Consensus size: 120
1694834 AATATATATA
*
1694844 TATATATATTTTATATTATTATTAGTTTTTTATTTTTCAGTTTCGTATATATGTATTATTAATAT
1 TATATATATATTATATTATTATTAGTTTTTTATTTTTCAGTTTCGTATATATGTATTATTAATAT
1694909 TTTATCATTTTACTTATATGCTATA-T-TATATATATATGTATATGTTTTGTATT
66 TTTATCATTTTACTTATATGCTATATTATATATATATATGTATATGTTTTGTATT
1694962 TATATATATATTATATTATTATTAGTTTTTTTTTATTTTTCAGTTTCGTATATATGTATTATTAA
1 TATATATATATTATATTATTATTAG---TTTTTTATTTTTCAGTTTCGTATATATGTATTATTAA
1695027 TATTTTATCATTTTACTTATATGCTATATTATATATATATATGTATATGTTTTGTATT
63 TATTTTATCATTTTACTTATATGCTATATTATATATATATATGTATATGTTTTGTATT
1695085 T
1 T
1695086 TATCTTATTA
Statistics
Matches: 118, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
118 24 0.20
121 65 0.55
122 1 0.01
123 28 0.24
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (120 bp):
TATATATATATTATATTATTATTAGTTTTTTATTTTTCAGTTTCGTATATATGTATTATTAATAT
TTTATCATTTTACTTATATGCTATATTATATATATATATGTATATGTTTTGTATT
Found at i:1696531 original size:10 final size:10
Alignment explanation
Indices: 1696510--1696544 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1696500 TTCCTCTACC
1696510 ATTTATTTTTT
1 ATTTA-TTTTT
1696521 ATTTATTTTT
1 ATTTATTTTT
*
1696531 ATTTATTTCT
1 ATTTATTTTT
1696541 ATTT
1 ATTT
1696545 TACTAACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.78
11 5 0.22
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:1706400 original size:105 final size:105
Alignment explanation
Indices: 1706126--1706690 Score: 943
Period size: 105 Copynumber: 5.4 Consensus size: 105
1706116 AGGTTTTACC
*
1706126 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1706191 ACGAAGGGACCGCTAGTTGTCAACAAACATCTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
1706231 CAGAGCCAATTT-AACTTCACAACGAAGGTTATTGGATTCCAGACAACGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1706295 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
1706335 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1706400 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1706440 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1706505 ACGAAGGGACCGCTAGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1706545 CAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
1706610 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAGTTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * * *
1706651 CATAACCAATTTCAACTTCACGACGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1706691 GGAACAGTAC
Statistics
Matches: 433, Mismatches: 25, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
104 97 0.22
105 292 0.67
106 44 0.10
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:1708312 original size:23 final size:26
Alignment explanation
Indices: 1708253--1708312 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
1708243 ATTTTACTTA
1708253 TATGCTATATTATATATATATGTATATGT
1 TATG-TAT-TTATATATATATGTATA-GT
*
1708282 TTTGTATTTATATATATAT-TATA-T
1 TATGTATTTATATATATATGTATAGT
1708306 TAT-TATT
1 TATGTATT
1708313 AGTTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 4 0.14
24 3 0.10
26 4 0.14
27 12 0.41
28 3 0.10
29 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (26 bp):
TATGTATTTATATATATATGTATAGT
Found at i:1708343 original size:122 final size:121
Alignment explanation
Indices: 1708166--1708402 Score: 404
Period size: 122 Copynumber: 2.0 Consensus size: 121
1708156 ACATATATAA
* *
1708166 TATTTATATATATATTTTATATTATTATTAGTTTTTTATTTTTCAGTTTCGTATATATGTATTAT
1 TATTTATATATATATTATATATTATTATTAGTTTTTTATTTTTCAGTTTCATATATATGTATTAT
*
1708231 TAATATTTTATCATTTTACTTATATGCTATAT-TATATATATATGTATATGTTTTG
66 TAATATTTTATCATTTTACTTATATGCTATATATATATATATATATATATGTTTTG
**
1708286 TATTTATATATATATTATATTATTATTAGTTTTTTTTTTATTTTTCAGTTTCATATATATGTATT
1 TATTTATATATATATTATA-TATTATTA-TTAGTTTTTTATTTTTCAGTTTCATATATATGTATT
1708351 ATTAATATTTTATCATTTTACTTATATGCTATATATATATATATATATATAT
64 ATTAATATTTTATCATTTTACTTATATGCTATATATATATATATATATATAT
1708403 ATATGTATAT
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
120 18 0.17
121 8 0.07
122 67 0.61
123 16 0.15
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (121 bp):
TATTTATATATATATTATATATTATTATTAGTTTTTTATTTTTCAGTTTCATATATATGTATTAT
TAATATTTTATCATTTTACTTATATGCTATATATATATATATATATATATGTTTTG
Found at i:1708387 original size:2 final size:2
Alignment explanation
Indices: 1708380--1708412 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1708370 ACTTATATGC
*
1708380 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1708413 GTTTTGTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1710678 original size:7 final size:7
Alignment explanation
Indices: 1710668--1710737 Score: 51
Period size: 7 Copynumber: 10.7 Consensus size: 7
1710658 TCGGTTACAG
*
1710668 TTATTAG
1 TTATTAA
1710675 TTATTAA
1 TTATTAA
*
1710682 TTATT-C
1 TTATTAA
*
1710688 TTTTTAA
1 TTATTAA
1710695 TTATT-A
1 TTATTAA
*
1710701 TTATTAT
1 TTATTAA
1710708 TTATT-A
1 TTATTAA
*
1710714 TTA-CAA
1 TTATTAA
*
1710720 TTATT-G
1 TTATTAA
1710726 TTATTAA
1 TTATTAA
1710733 TTATT
1 TTATT
1710738 GTAGTTGAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
6 22 0.47
7 25 0.53
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (7 bp):
TTATTAA
Found at i:1710702 original size:3 final size:3
Alignment explanation
Indices: 1710668--1710737 Score: 50
Period size: 3 Copynumber: 21.7 Consensus size: 3
1710658 TCGGTTACAG
* *
1710668 TTA TTA GTTA TTAA TTA TTC TTT TTAA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TT-A TTA TTA TTA TT-A TTA TTA TTA TTA -TTA TTA TTA
** *
1710717 CAA TTA TTG TTA TTAA TTA TT
1 TTA TTA TTA TTA TT-A TTA TT
1710738 GTAGTTGAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
3 39 0.74
4 14 0.26
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1710702 original size:16 final size:16
Alignment explanation
Indices: 1710668--1710716 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1710658 TCGGTTACAG
*
1710668 TTATTAGTTATTAATTA
1 TTATTATTTATT-ATTA
*
1710685 TTCTT-TTTAATTATTA
1 TTATTATTT-ATTATTA
1710701 TTATTATTTATTATTA
1 TTATTATTTATTATTA
1710717 CAATTATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTATTTATTATTA
Found at i:1710711 original size:13 final size:13
Alignment explanation
Indices: 1710668--1710737 Score: 79
Period size: 13 Copynumber: 5.4 Consensus size: 13
1710658 TCGGTTACAG
1710668 TTATTAGTTATTAA
1 TTATTA-TTATTAA
* *
1710682 TTATTCTTTTTAA
1 TTATTATTATTAA
*
1710695 TTATTATTATTAT
1 TTATTATTATTAA
*
1710708 TTATTATTA-CAA
1 TTATTATTATTAA
*
1710720 TTATTGTTATTAA
1 TTATTATTATTAA
1710733 TTATT
1 TTATT
1710738 GTAGTTGAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
12 9 0.20
13 32 0.70
14 5 0.11
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:1714414 original size:41 final size:41
Alignment explanation
Indices: 1714357--1714450 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
1714347 TATAGGTAGA
*
1714357 ACACAATAACACTATACTAGGTATAGGGATGGTAGTTCATG
1 ACACAATAACACTATACTAGGTATAGGGATGGTAGTTCACG
*
1714398 ACACAATAACACTATACTAGGTATCGGGATGGTAGTTCACG
1 ACACAATAACACTATACTAGGTATAGGGATGGTAGTTCACG
1714439 ACATCAA-AACAC
1 ACA-CAATAACAC
1714451 CATGAACCCC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
41 47 0.94
42 3 0.06
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (41 bp):
ACACAATAACACTATACTAGGTATAGGGATGGTAGTTCACG
Found at i:1714588 original size:24 final size:23
Alignment explanation
Indices: 1714543--1714602 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 23
1714533 AGTGCATAAA
1714543 GCACTAAACTAGAGCGCACGAAT
1 GCACTAAACTAGAGCGCACGAAT
* *
1714566 GCACTAACACTTGAGTGCACGAAT
1 GCACTAA-ACTAGAGCGCACGAAT
*
1714590 GCACTAATCTAGA
1 GCACTAAACTAGA
1714603 TCGATCTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 11 0.34
24 21 0.66
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (23 bp):
GCACTAAACTAGAGCGCACGAAT
Found at i:1716225 original size:120 final size:120
Alignment explanation
Indices: 1716081--1716318 Score: 458
Period size: 120 Copynumber: 2.0 Consensus size: 120
1716071 ATTTCACACT
1716081 TTAGTCCAAATTCTCACTAAAATTGATCAAAAATGAAAATGAAAATCAAACTAACCTTGGCTATG
1 TTAGTCCAAATTCTCACTAAAATTGATCAAAAATGAAAATGAAAATCAAACTAACCTTGGCTATG
*
1716146 GTGTTTTGGTAGAATGGAGAAGAAGAGAGAAACATTTATTGAAATTTCTTGTACA
66 GTGTTTTGGTAGAATGGAGAAGAAGAAAGAAACATTTATTGAAATTTCTTGTACA
*
1716201 TTAGTCCAAATTCTCACTAAAATTGATCAAAAATGAAAATGAAAATCAAATTAACCTTGGCTATG
1 TTAGTCCAAATTCTCACTAAAATTGATCAAAAATGAAAATGAAAATCAAACTAACCTTGGCTATG
1716266 GTGTTTTGGTAGAATGGAGAAGAAGAAAGAAACATTTATTGAAATTTCTTGTA
66 GTGTTTTGGTAGAATGGAGAAGAAGAAAGAAACATTTATTGAAATTTCTTGTA
1716319 AAAAATCTCC
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (120 bp):
TTAGTCCAAATTCTCACTAAAATTGATCAAAAATGAAAATGAAAATCAAACTAACCTTGGCTATG
GTGTTTTGGTAGAATGGAGAAGAAGAAAGAAACATTTATTGAAATTTCTTGTACA
Found at i:1719530 original size:36 final size:35
Alignment explanation
Indices: 1719461--1719589 Score: 152
Period size: 35 Copynumber: 3.6 Consensus size: 35
1719451 ACTTTAGGTC
* * * * *
1719461 TATAAAGAATTACTAGCTGATTGGTGCTGAACCTA
1 TATAAGGAATTACCAGTTGATCGGTGCTAAACCTA
* *
1719496 CAATAAGGAATTACCAGTTGATCGATGCTAAACCTA
1 -TATAAGGAATTACCAGTTGATCGGTGCTAAACCTA
*
1719532 TATAGGGAATTACCAGTTGATCGGTGCTAAACCTA
1 TATAAGGAATTACCAGTTGATCGGTGCTAAACCTA
1719567 TAT-AGAGAATTACCAGCTTGATC
1 TATAAG-GAATTACCAG-TTGATC
1719590 AGAACTGAAC
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
34 1 0.01
35 45 0.56
36 34 0.43
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (35 bp):
TATAAGGAATTACCAGTTGATCGGTGCTAAACCTA
Found at i:1724095 original size:20 final size:20
Alignment explanation
Indices: 1724072--1724135 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
1724062 TAGTATTTAG
1724072 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
1724092 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
1724112 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
1724131 TTAAA
1 ATAAA
1724136 CTTTATTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:1724105 original size:19 final size:20
Alignment explanation
Indices: 1724081--1724130 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1724071 GATAAATTTA
*
1724081 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
1724100 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
1724121 TT-ATAATTTT
1 TTAATAATTTT
1724131 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:1724133 original size:31 final size:30
Alignment explanation
Indices: 1724048--1724134 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
1724038 TTCAATAATA
* *
1724048 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
1724079 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
1724110 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
1724135 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:1724893 original size:31 final size:30
Alignment explanation
Indices: 1724858--1724944 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
1724848 TCAATAAAGT
1724858 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
1724889 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
1724920 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
1724945 TATTATTGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:1724920 original size:20 final size:20
Alignment explanation
Indices: 1724853--1724920 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
1724843 TTTCGTCAAT
*
1724853 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
1724871 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
1724892 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
1724911 ATAA-ATTTAT
1 A-AAGATTTAT
1724921 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:1737772 original size:16 final size:16
Alignment explanation
Indices: 1737743--1737781 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1737733 ATCATCATAA
*
1737743 GATGTATCAAATTAGT
1 GATGTGTCAAATTAGT
*
1737759 GATGTGTCACATTAGT
1 GATGTGTCAAATTAGT
1737775 GATGTGT
1 GATGTGT
1737782 TTCAGTGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (16 bp):
GATGTGTCAAATTAGT
Found at i:1738875 original size:16 final size:16
Alignment explanation
Indices: 1738850--1738888 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1738840 ATCATCATAA
* *
1738850 GATGTATCACATTAGT
1 GATGTGTCACAATAGT
1738866 GATGTGTCACAATAGT
1 GATGTGTCACAATAGT
1738882 GATGTGT
1 GATGTGT
1738889 TTCGGTGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (16 bp):
GATGTGTCACAATAGT
Found at i:1739118 original size:736 final size:735
Alignment explanation
Indices: 1737397--1739161 Score: 2183
Period size: 736 Copynumber: 2.4 Consensus size: 735
1737387 TGTCATCATA
* *
1737397 AGATGTATCACATTAGTGATGTATTTCAGTGTGCAACATTCACTATAAAATTTTCCTCCTTATTA
1 AGATGTGTCACATTAGTGATGT-TTTCAGTGTGCGACATTCACTATAAAATTTTCCTCCTTATTA
* * * * *
1737462 ATGGTTTTTCCTTTAAAA-TAAAAATGGGTATAATTAATTTAAGATCCATTGATTTGTCAACTTA
65 ATGGTTTTTCCTTTAAAATTAAAATTGGGTATAATTAGTTTAAGATCCCTTGACTTGACAACTTA
* *
1737526 GTTTTTTCCTAATAAAAAATGTCATGTGGCAGCCTGTGATTGAGCCATGTATTAAGTAACTTAAA
130 GTTTTTTCCTAATAAACAATGTCATGTGGCAGCCTGTGATTGAGCCATGTATTAAGTAACTTTAA
** * * * * *
1737591 TATTATGGTAAACTACACATTTAATCACTCAATTATTCTCGTGATTATGTTTTCGTCACTTAACT
195 TATTAAAGTAAACTACAAATTTAATCACTCAATTATTCTCGTTATTATGTTTTGGTCACTCAAAT
* * *
1737656 A-TTTTTTAAAGAAACACTAAACTTTTTTTTCTATTTTAATCATTCGTCATTAAAAAAATTAACA
260 ATTTTTTTAAAGCAACACTAAACTTTTTTTTCTATTTTAATCATTAGGCATTAAAAAAATTAACA
** * *
1737720 ATGATGCTGATTTATCATCATAAGATGTATCAAATTAGTGATGTGTCACATTAGTGATGTGTTTC
325 ATGATGCTGACATATCATCATAAGATGTATCAAATCAATGATGTGTCACATTAGTGATGTGTTTC
* * *
1737785 AGTGTGCGACGCTCACTATATAATTTTCCTTCTTATTAATGGTTTTTCCTTTAAAATTAAAATTG
390 AGTGTGCGACGCTCACTATAGAATTTTCCTCCTTATTAATGGTTTTTCCTTTAAAATTAAAACTG
*
1737850 AGTATAATTAGTTTAAAATCCCTTAACTCGAACGATTAGCTTTTTGTCTCCAAATAAACAACATC
455 AGTATAATTAGTTTAAAATCCCTTAACTCGAACGATTAGCTTTTTGTCCCCAAATAAACAACATC
* * ** *
1737915 ATATGACAGCCTGTGATTGGGATATGTATTATGTAACATTTAATTTTAAGGTGGACTACATATTT
520 ATATGACAGCCTGTGATTGGGACATGTATTAAGTAACATTTAATTTTAAGGTAAACTACATATTG
* * *
1737980 AATTATTTAATTATTCTCGTGATTCTATTTTGGTCACTCAATTATTATTTTTAAATCAACACTAA
585 AATCATTTAATTATTCTCATGATTCTATATTGGTCACTCAATTATTATTTTTAAATCAACACTAA
* * * *
1738045 ACTTTCATTTTTTTCTATTTTAATCATTTGTAGTTAAACAAATTAACAATTATGCTGACATACCA
650 ACTTTCATTTTTTTCTATTTTAATCATTTGCAGTTAAAAAAATTAACAATGATGCTAACATACCA
1738110 TCATAAGATGTATCACAATAG
715 TCATAAGATGTATCACAATAG
** * * ** * *
1738131 AGATGTGTTGCATTAGTGATGTATTCAGTGTGTGATGTTCACTCTAGAATTTTCCTCCTTATTAA
1 AGATGTGTCACATTAGTGATGTTTTCAGTGTGCGACATTCACTATAAAATTTTCCTCCTTATTAA
* * * **
1738196 TGATTTTTTCTTTAAAATTAAAATTGGGTATAATTAGTTTAAGATCTCTTGACTTGACTGCTTAG
66 TGGTTTTTCCTTTAAAATTAAAATTGGGTATAATTAGTTTAAGATCCCTTGACTTGACAACTTAG
* * **
1738261 TTTTTTTCCTAAAAAACAATGTCATGTGACAGCCTGTGATTGAATCATGTATTAAGTAACATTTA
131 -TTTTTTCCTAATAAACAATGTCATGTGGCAGCCTGTGATTGAGCCATGTATTAAGTAAC-TTTA
* * ** *
1738326 ATATT-AAGATAAACTACAAATATCATCGTTCAATTATTCTCGTTATTTTGTTTTGGTCACTCAA
194 ATATTAAAG-TAAACTACAAATTTAATCACTCAATTATTCTCGTTATTATGTTTTGGTCACTCAA
* * ** *
1738390 TTATTTTTTTAAAGCAACTCT-AGTTTTGTTTTTCTGTTTTAATCATTAGGC-TCT-AAAAAATT
258 ATATTTTTTTAAAGCAACACTAAACTTT-TTTTTCTATTTTAATCATTAGGCAT-TAAAAAAATT
* **
1738452 AACGATGATGCTGACATATCATCATAAGATGTATCAAATCAATGATGTGTCGTATTAGTGATGTG
321 AACAATGATGCTGACATATCATCATAAGATGTATCAAATCAATGATGTGTCACATTAGTGATGTG
** * * *
1738517 TTTTGGTGTGTGACGTTCAGTATAGAATTTTCCTCCTTATTAATGG-TTTTCCTTTAAAATTAAA
386 TTTCAGTGTGCGACGCTCACTATAGAATTTTCCTCCTTATTAATGGTTTTTCCTTTAAAATTAAA
* * ** * * * * * * * *
1738581 ACTGGGTATAATTTGTTTATGATCCCTTGACTTGACCGCTTAG-TTTTTTTCCCCTAATAAAGAT
451 ACTGAGTATAATTAGTTTAAAATCCCTTAACTCGAACGATTAGCTTTTTGTCCCCAAATAAACAA
** * * * * *
1738645 TGTCATGTTG-CATCTTGTGATTGGGCCATGTATTAAGTAA-ATTTTAGTTTTAA-GTAAACTAC
516 CATCAT-ATGACAGCCTGTGATTGGGACATGTATTAAGTAACA-TTTAATTTTAAGGTAAACTAC
*
1738707 ATATTGAATCATTTAATTATTCTCATGATTCTGTATTGGTCACTCAATTATT-TTTTCTAAATCA
579 ATATTGAATCATTTAATTATTCTCATGATTCTATATTGGTCACTCAATTATTATTTT-TAAATCA
* * * *
1738771 ACAGTAAACTTTCATTTTTGCTT-TGTTTTAATCATTAT-CCGTTAAAAAAATTAACGATGATGC
643 ACACTAAACTTTCATTTTT--TTCTATTTTAATCATT-TGCAGTTAAAAAAATTAACAATGATGC
* *
1738834 TAACATATCATCATAAGATGTATCACATTAG
705 TAACATACCATCATAAGATGTATCACAATAG
* * * *
1738865 TGATGTGTCACAATAGTGATGTGTTTCGGTGTGCGACATTCACTGTAAAATTTTCCTCCTTATTA
1 AGATGTGTCACATTAGTGATGT-TTTCAGTGTGCGACATTCACTATAAAATTTTCCTCCTTATTA
* *
1738930 ATGGTTTTTCCTTTAAAATTAAAATTGGGTATAGTTAGTTTTAAGATCCCTTGACTTGACCACTT
65 ATGGTTTTTCCTTTAAAATTAAAATTGGGTATAATTAG-TTTAAGATCCCTTGACTTGACAACTT
* * * * * *
1738995 AGTTCTTTTCCCAATAAACAATATCATGTGGCAACATGTGATTGGGCCATGAATTAAGTAACTTT
129 AGTT-TTTTCCTAATAAACAATGTCATGTGGCAGCCTGTGATTGAGCCATGTATTAAGTAAC-TT
* * * * *
1739060 TAATTTTAAAGTAAACTACATATTTAATCACTCAATTATTCTCGTTAGTCTATTTTGGT-AGCTC
192 TAATATTAAAGTAAACTACAAATTTAATCACTCAATTATTCTCGTTATTATGTTTTGGTCA-CTC
*
1739124 AAATATTTGTTTTTAAATCAACACTAAACTTTTATTTT
256 AAATA-TT-TTTTTAAAGCAACACTAAACTTTT-TTTT
1739162 TGTTCAACTT
Statistics
Matches: 868, Mismatches: 141, Indels: 39
0.83 0.13 0.04
Matches are distributed among these distances:
732 4 0.00
733 131 0.15
734 191 0.22
735 185 0.21
736 293 0.34
737 41 0.05
738 15 0.02
739 8 0.01
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (735 bp):
AGATGTGTCACATTAGTGATGTTTTCAGTGTGCGACATTCACTATAAAATTTTCCTCCTTATTAA
TGGTTTTTCCTTTAAAATTAAAATTGGGTATAATTAGTTTAAGATCCCTTGACTTGACAACTTAG
TTTTTTCCTAATAAACAATGTCATGTGGCAGCCTGTGATTGAGCCATGTATTAAGTAACTTTAAT
ATTAAAGTAAACTACAAATTTAATCACTCAATTATTCTCGTTATTATGTTTTGGTCACTCAAATA
TTTTTTTAAAGCAACACTAAACTTTTTTTTCTATTTTAATCATTAGGCATTAAAAAAATTAACAA
TGATGCTGACATATCATCATAAGATGTATCAAATCAATGATGTGTCACATTAGTGATGTGTTTCA
GTGTGCGACGCTCACTATAGAATTTTCCTCCTTATTAATGGTTTTTCCTTTAAAATTAAAACTGA
GTATAATTAGTTTAAAATCCCTTAACTCGAACGATTAGCTTTTTGTCCCCAAATAAACAACATCA
TATGACAGCCTGTGATTGGGACATGTATTAAGTAACATTTAATTTTAAGGTAAACTACATATTGA
ATCATTTAATTATTCTCATGATTCTATATTGGTCACTCAATTATTATTTTTAAATCAACACTAAA
CTTTCATTTTTTTCTATTTTAATCATTTGCAGTTAAAAAAATTAACAATGATGCTAACATACCAT
CATAAGATGTATCACAATAG
Found at i:1739220 original size:371 final size:367
Alignment explanation
Indices: 1737398--1739205 Score: 1963
Period size: 372 Copynumber: 4.9 Consensus size: 367
1737388 GTCATCATAA
* * * *
1737398 GATGTATCACATTAGTGATGTATTTCAGTGTGCAACATTCACTATAAAATTTTCCTCCTTATTAA
1 GATGTGTCACATTAGTGATGTGTTTCAGTGTGCGACGTTCACTATAAAATTTTCCTCCTTATTAA
* * * * * *
1737463 TGGTTTTTCCTTTAAAA-TAAAAATGGGTATAATTAATTTAAGATCCATTGATTTGTCAACTTAG
66 TGGTTTTTCCTTTAAAATTAAAATTGGGTATAATTAGTTTAAGATCCCTTGACTTGACCACTTAG
* * * *
1737527 TTTTTTCCTAATAAAAAATGTCATGTGGCAGCCTGTGATTGAGCCATGTATTAAGTAAC-TTAAA
131 TTTTTTCCCAATAAACAATGTCATGTGGCAGCCTGTGATTGGGCCATGTATTAAGTAACATTTAA
* ** * * * * * *
1737591 TATTATGGTAAACTACACATTTAATCACTCAATTATTCTCGTGATTATGTTTTCGTCACTTAACT
196 TTTTAAAGTAAACTACATATTTAATCATTCAATTATTCTCGTGATTCTGTTTTGGTCACTCAATT
** * *
1737656 A-TTTTTTAAAGAAACACTAAAC---T-TTTTTTTCTATTTTAATCATTCGTCATTAAAAAAATT
261 ATTTTTTTAAATCAACACTAAACTTTTATTTTTTTCTATTTTAATCATTCCTCGTT-AAAAAATT
**
1737716 AACAATGATGCTGATTTATCATCATAAGATGTATCAAATTAGT
325 AACAATGATGCTGACATATCATCATAAGATGTATCAAATTAGT
* * *
1737759 GATGTGTCACATTAGTGATGTGTTTCAGTGTGCGACGCTCACTATATAATTTTCCTTCTTATTAA
1 GATGTGTCACATTAGTGATGTGTTTCAGTGTGCGACGTTCACTATAAAATTTTCCTCCTTATTAA
* * * * *
1737824 TGGTTTTTCCTTTAAAATTAAAATTGAGTATAATTAGTTTAAAATCCCTTAACTCGAACGA-TTA
66 TGGTTTTTCCTTTAAAATTAAAATTGGGTATAATTAGTTTAAGATCCCTTGACTTG-ACCACTTA
** * * ** *
1737888 GCTTTTTGTCTCCAAATAAACAACATCATATGACAGCCTGTGATTGGGATATGTATTATGTAACA
130 G-TTTTT-TC-CC-AATAAACAATGTCATGTGGCAGCCTGTGATTGGGCCATGTATTAAGTAACA
* ** * * *
1737953 TTTAATTTTAAGGTGGACTACATATTTAATTATTTAATTATTCTCGTGATTCTATTTTGGTCACT
191 TTTAATTTTAAAGTAAACTACATATTTAATCATTCAATTATTCTCGTGATTCTGTTTTGGTCACT
* ** *
1738018 CAATTATTATTTTTAAATCAACACTAAACTTTCATTTTTTTCTATTTTAATCATTTGTAGTTAAA
256 CAATTATT-TTTTTAAATCAACACTAAACTTTTATTTTTTTCTATTTTAATCATTCCTCGTTAAA
* * *
1738083 CAAATTAACAATTATGCTGACATACCATCATAAGATGTATCACAA-TAGA
320 -AAATTAACAATGATGCTGACATATCATCATAAGATGTATCA-AATTAGT
** * * * * *
1738132 GATGTGTTGCATTAGTGATGT-ATTCAGTGTGTGATGTTCACTCTAGAATTTTCCTCCTTATTAA
1 GATGTGTCACATTAGTGATGTGTTTCAGTGTGCGACGTTCACTATAAAATTTTCCTCCTTATTAA
* * * **
1738196 TGATTTTTTCTTTAAAATTAAAATTGGGTATAATTAGTTTAAGATCTCTTGACTTGACTGCTTAG
66 TGGTTTTTCCTTTAAAATTAAAATTGGGTATAATTAGTTTAAGATCCCTTGACTTGACCACTTAG
* * * ***
1738261 TTTTTTTCCTAAAAAACAATGTCATGTGACAGCCTGTGATTGAATCATGTATTAAGTAACATTTA
131 -TTTTTTCCCAATAAACAATGTCATGTGGCAGCCTGTGATTGGGCCATGTATTAAGTAACATTTA
* * * * * * *
1738326 ATATT-AAGATAAACTACAAATATCATCGTTCAATTATTCTCGTTATTTTGTTTTGGTCACTCAA
195 ATTTTAAAG-TAAACTACATATTTAATCATTCAATTATTCTCGTGATTCTGTTTTGGTCACTCAA
* * * * * *
1738390 TTATTTTTTTAAAGCAACTCT--A-GTTT-TGTTTTTCTGTTTTAATCATTAGGCTC--TAAAAA
259 TTATTTTTTTAAATCAACACTAAACTTTTATTTTTTTCTATTTTAATCATT--CCTCGTTAAAAA
* * *
1738449 ATTAACGATGATGCTGACATATCATCATAAGATGTATCAAATCAAT
322 ATTAACAATGATGCTGACATATCATCATAAGATGTATCAAATTAGT
** ** * * *
1738495 GATGTGTCGTATTAGTGATGTGTTTTGGTGTGTGACGTTCAGTATAGAATTTTCCTCCTTATTAA
1 GATGTGTCACATTAGTGATGTGTTTCAGTGTGCGACGTTCACTATAAAATTTTCCTCCTTATTAA
* * * *
1738560 TGG-TTTTCCTTTAAAATTAAAACTGGGTATAATTTGTTTATGATCCCTTGACTTGACCGCTTAG
66 TGGTTTTTCCTTTAAAATTAAAATTGGGTATAATTAGTTTAAGATCCCTTGACTTGACCACTTAG
* * * * *
1738624 TTTTTTTCCCCTAATAAAGATTGTCATGTTGCATCTTGTGATTGGGCCATGTATTAAGTAA-ATT
131 -TTTTTT-CCC-AATAAACAATGTCATGTGGCAGCCTGTGATTGGGCCATGTATTAAGTAACA-T
* * * * *
1738688 TTAGTTTT-AAGTAAACTACATATTGAATCATTTAATTATTCTCATGATTCTGTATTGGTCACTC
192 TTAATTTTAAAGTAAACTACATATTTAATCATTCAATTATTCTCGTGATTCTGTTTTGGTCACTC
* * * *
1738752 AATTATTTTTTCTAAATCAACAGTAAACTTTCATTTTTGCTT-TGTTTTAATCATT-ATCCGTTA
257 AATTATTTTTT-TAAATCAACACTAAACTTTTATTTTT--TTCTATTTTAATCATTCCT-CGTT-
* * *
1738815 AAAAAATTAACGATGATGCTAACATATCATCATAAGATGTATCACATTAGT
317 AAAAAATTAACAATGATGCTGACATATCATCATAAGATGTATCAAATTAGT
* * * *
1738866 GATGTGTCACAATAGTGATGTGTTTCGGTGTGCGACATTCACTGTAAAATTTTCCTCCTTATTAA
1 GATGTGTCACATTAGTGATGTGTTTCAGTGTGCGACGTTCACTATAAAATTTTCCTCCTTATTAA
*
1738931 TGGTTTTTCCTTTAAAATTAAAATTGGGTATAGTTAGTTTTAAGATCCCTTGACTTGACCACTTA
66 TGGTTTTTCCTTTAAAATTAAAATTGGGTATAATTAG-TTTAAGATCCCTTGACTTGACCACTTA
* * * * *
1738996 GTTCTTTTCCCAATAAACAATATCATGTGGCAACATGTGATTGGGCCATGAATTAAGTAACTTTT
130 GTT-TTTTCCCAATAAACAATGTCATGTGGCAGCCTGTGATTGGGCCATGTATTAAGTAACATTT
* * * *
1739061 AATTTTAAAGTAAACTACATATTTAATCACTCAATTATTCTCGTTAGTCTATTTTGGT-AGCTCA
194 AATTTTAAAGTAAACTACATATTTAATCATTCAATTATTCTCGTGATTCTGTTTTGGTCA-CTCA
* * * *
1739125 AATATTTGTTTTTAAATCAACACTAAACTTTTATTTTTGTTCAACTTTCATCATTCCTCGTTAAA
258 ATTA-TT-TTTTTAAATCAACACTAAACTTTTATTTTT-TTCTATTTTAATCATTCCTCGTTAAA
1739190 AAA-TAACAATGATGCT
320 AAATTAACAATGATGCT
1739206 AATGTGTCAT
Statistics
Matches: 1203, Mismatches: 199, Indels: 80
0.81 0.13 0.05
Matches are distributed among these distances:
361 75 0.06
362 36 0.03
363 127 0.11
364 121 0.10
365 61 0.05
366 43 0.04
367 59 0.05
368 20 0.02
369 121 0.10
370 15 0.01
371 175 0.15
372 190 0.16
373 153 0.13
374 7 0.01
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (367 bp):
GATGTGTCACATTAGTGATGTGTTTCAGTGTGCGACGTTCACTATAAAATTTTCCTCCTTATTAA
TGGTTTTTCCTTTAAAATTAAAATTGGGTATAATTAGTTTAAGATCCCTTGACTTGACCACTTAG
TTTTTTCCCAATAAACAATGTCATGTGGCAGCCTGTGATTGGGCCATGTATTAAGTAACATTTAA
TTTTAAAGTAAACTACATATTTAATCATTCAATTATTCTCGTGATTCTGTTTTGGTCACTCAATT
ATTTTTTTAAATCAACACTAAACTTTTATTTTTTTCTATTTTAATCATTCCTCGTTAAAAAATTA
ACAATGATGCTGACATATCATCATAAGATGTATCAAATTAGT
Found at i:1740230 original size:22 final size:23
Alignment explanation
Indices: 1740187--1740234 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
1740177 AAATTCAGAT
1740187 TTTTTAAATATCAAAATAATTTA
1 TTTTTAAATATCAAAATAATTTA
1740210 TTTTTAAA-AT-AAAATATATTTA
1 TTTTTAAATATCAAAATA-ATTTA
1740232 TTT
1 TTT
1740235 AAAAATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 6 0.25
22 10 0.42
23 8 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTAAATATCAAAATAATTTA
Found at i:1740239 original size:21 final size:21
Alignment explanation
Indices: 1740185--1740240 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1740175 TAAAATTCAG
*
1740185 ATTT-TTTAAATATCAAAATA
1 ATTTATTTAAAAATCAAAATA
*
1740205 ATTTATTTTTAAAAT-AAAATA
1 ATTTA-TTTAAAAATCAAAATA
1740226 TATTTATTTAAAAAT
1 -ATTTATTTAAAAAT
1740241 TATAATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 4 0.13
21 14 0.47
22 12 0.40
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTATTTAAAAATCAAAATA
Found at i:1742664 original size:21 final size:24
Alignment explanation
Indices: 1742622--1742664 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1742612 TCTCATAAAC
1742622 ATAAGCATGCTAGAAGACATGCTA
1 ATAAGCATGCTAGAAGACATGCTA
1742646 ATAAGCA-G-TAGAA-ACATGC
1 ATAAGCATGCTAGAAGACATGC
1742665 ATGAACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 1 0.05
24 7 0.37
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (24 bp):
ATAAGCATGCTAGAAGACATGCTA
Found at i:1746360 original size:45 final size:45
Alignment explanation
Indices: 1746309--1746485 Score: 302
Period size: 45 Copynumber: 3.9 Consensus size: 45
1746299 AATTTCTTAT
*
1746309 CAATATACTTACCATTCATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1746354 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1746399 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTA-TTTTAC
* * *
1746445 AAATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
1746486 ACATGGTTAT
Statistics
Matches: 127, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
44 3 0.02
45 106 0.83
46 18 0.14
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (45 bp):
CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
Found at i:1746395 original size:25 final size:25
Alignment explanation
Indices: 1746367--1746440 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
1746357 TATACTTACC
1746367 ATTTATCCCATAAGCTCGTAAGCTT
1 ATTTATCCCATAAGCTCGTAAGCTT
* *
1746392 ATTT-TACCAATATA-CT--T-A-C-C
1 ATTTAT-CCCATA-AGCTCGTAAGCTT
1746412 ATTTATCCCATAAGCTCGTAAGCTT
1 ATTTATCCCATAAGCTCGTAAGCTT
1746437 ATTT
1 ATTT
1746441 TTACAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 2 0.06
22 2 0.06
23 2 0.06
24 2 0.06
25 15 0.42
26 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (25 bp):
ATTTATCCCATAAGCTCGTAAGCTT
Found at i:1746642 original size:22 final size:22
Alignment explanation
Indices: 1746614--1746679 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
1746604 TGCCCACCAT
1746614 ATACACCGAAGTGTATTACACA
1 ATACACCGAAGTGTATTACACA
1746636 ATACACCGAAGTGTATTACACA
1 ATACACCGAAGTGTATTACACA
1746658 ATACACCGAAGTGTATTACACA
1 ATACACCGAAGTGTATTACACA
1746680 TAAGGTCATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.23
Consensus pattern (22 bp):
ATACACCGAAGTGTATTACACA
Found at i:1747051 original size:24 final size:24
Alignment explanation
Indices: 1747019--1747067 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1747009 AGTATTCCTG
1747019 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
1747043 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
1747067 A
1 A
1747068 ATGTCATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:1749013 original size:24 final size:24
Alignment explanation
Indices: 1748920--1749029 Score: 116
Period size: 24 Copynumber: 4.6 Consensus size: 24
1748910 AAACGGAGAT
*
1748920 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
1748944 ATAAGATATCAAAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
1748968 ATCATAAATCAGAACAGAATTCAT
1 ATCAGAAATCAGAACAGAATTCAG
*
1748992 ATCAGAAATCAGAACATG-ATTCAA
1 ATCAGAAATCAGAACA-GAATTCAG
1749016 ATC-GTAAATCAGAA
1 ATCAG-AAATCAGAA
1749030 AAAACATTCC
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
23 1 0.01
24 71 0.97
25 1 0.01
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:1751368 original size:20 final size:20
Alignment explanation
Indices: 1751343--1751383 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1751333 GGGTCGGGTC
*
1751343 GGTCAGGTCGGGTCGGACCG
1 GGTCAGGTCAGGTCGGACCG
*
1751363 GGTCAGGTCAGGTTGGACCG
1 GGTCAGGTCAGGTCGGACCG
1751383 G
1 G
1751384 TCAAACTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (20 bp):
GGTCAGGTCAGGTCGGACCG
Found at i:1753249 original size:13 final size:13
Alignment explanation
Indices: 1753231--1753257 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1753221 GAAAACATAC
1753231 ATATATTTTTAAA
1 ATATATTTTTAAA
1753244 ATATATTTTTAAA
1 ATATATTTTTAAA
1753257 A
1 A
1753258 CATAACACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATATTTTTAAA
Found at i:1753460 original size:24 final size:24
Alignment explanation
Indices: 1753426--1753476 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1753416 AAACGGAATT
*
1753426 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATCCAG
* * *
1753450 ATCAGATATCAGAATAGAATCCAG
1 ATCAGAAATCAAAACAGAATCCAG
1753474 ATC
1 ATC
1753477 GGGCATAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAG
Found at i:1758033 original size:17 final size:17
Alignment explanation
Indices: 1758011--1758045 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1758001 TTCTTTAATA
1758011 AAGCATGCATTGCATTT
1 AAGCATGCATTGCATTT
* *
1758028 AAGCATGTATTTCATTT
1 AAGCATGCATTGCATTT
1758045 A
1 A
1758046 GGGAAGTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (17 bp):
AAGCATGCATTGCATTT
Found at i:1758072 original size:17 final size:17
Alignment explanation
Indices: 1758052--1758110 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
1758042 TTTAGGGAAG
1758052 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
1758069 TAG-TCATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
1758085 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
1758102 TAGTTCATT
1 TAGTTCATT
1758111 AATAAAGTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:1758140 original size:34 final size:34
Alignment explanation
Indices: 1758068--1758171 Score: 97
Period size: 34 Copynumber: 3.1 Consensus size: 34
1758058 ATTTATGCAT
* * * *
1758068 CTAG-TCATTTAATAAACTACTTCATTCATGC-AT
1 CTAGTTCATTTAATAAACTAGTGCATTAAT-CAAA
* * *
1758101 TTAGTTCA-TTAATAAAGTTAGTTCATTAATCAAA
1 CTAGTTCATTTAATAAA-CTAGTGCATTAATCAAA
*
1758135 CTAGTTCATTTATTAAACTAGTGCATTAATCAAA
1 CTAGTTCATTTAATAAACTAGTGCATTAATCAAA
1758169 CTA
1 CTA
1758172 ACTCTTAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
33 12 0.21
34 39 0.67
35 7 0.12
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (34 bp):
CTAGTTCATTTAATAAACTAGTGCATTAATCAAA
Found at i:1758169 original size:17 final size:17
Alignment explanation
Indices: 1758102--1758171 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
1758092 TTCATGCATT
*
1758102 TAGTTCATTAAT-AAAGT
1 TAGTTCATTAATCAAA-C
1758119 TAGTTCATTAATCAAAC
1 TAGTTCATTAATCAAAC
* *
1758136 TAGTTCATTTATTAAAC
1 TAGTTCATTAATCAAAC
*
1758153 TAGTGCATTAATCAAAC
1 TAGTTCATTAATCAAAC
1758170 TA
1 TA
1758172 ACTCTTAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
17 43 0.93
18 3 0.07
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.39
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:1765416 original size:2 final size:2
Alignment explanation
Indices: 1765409--1765449 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1765399 AAATTGGTTC
1765409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1765450 ATTAAAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1767256 original size:78 final size:78
Alignment explanation
Indices: 1767167--1767328 Score: 308
Period size: 78 Copynumber: 2.1 Consensus size: 78
1767157 CACGTAGATA
1767167 TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTTATATACTAATA
1 TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTT-TATACTAATA
1767232 TCTTGTTTAAACG-
65 TCTTGTTTAAACGT
1767245 TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTTTATACTAATAT
1 TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTTTATACTAATAT
1767310 CTTGTTTAAACGT
66 CTTGTTTAAACGT
1767323 TATTAT
1 TATTAT
1767329 ATATATATAT
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
77 23 0.28
78 60 0.72
ACGTcount: A:0.20, C:0.12, G:0.07, T:0.60
Consensus pattern (78 bp):
TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTTTATACTAATAT
CTTGTTTAAACGT
Found at i:1778138 original size:1 final size:1
Alignment explanation
Indices: 1778132--1778159 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1778122 TCCTAAGTTG
1778132 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1778160 CGTTTGGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1779210 original size:106 final size:106
Alignment explanation
Indices: 1778958--1779524 Score: 915
Period size: 106 Copynumber: 5.4 Consensus size: 106
1778948 GTTTTACCCA
*
1778958 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
* * * *
1779023 GAAGGGACCGCTGGTTGTCAACGAA-CATTTCTCAATTTCA
66 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
1779063 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
1779128 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
66 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
* *
1779169 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGGC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
1779234 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
66 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
*
1779275 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
1779340 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
66 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
* * *
1779381 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCAC--AAGCTCAACTTCACG
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC-G-ACGTAAGTTCAACTTCACG
* * ** * * * *
1779444 ACGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTCCA
64 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
*
1779487 GAACCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1779525 TGAACAATAC
Statistics
Matches: 439, Mismatches: 20, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
105 88 0.20
106 348 0.79
107 1 0.00
108 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (106 bp):
GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
Found at i:1781378 original size:75 final size:76
Alignment explanation
Indices: 1781299--1781450 Score: 265
Period size: 75 Copynumber: 2.0 Consensus size: 76
1781289 CACGTAGATA
1781299 TATTATCGTTCGTACTTCTTTTCGTTTA-TTTCATTTCA-TTTGT-TTTTTTTTATATACTAATA
1 TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTT-TATACTAATA
1781361 TCTTGTTTAAACG
65 TC-TGTTTAAACG
1781374 TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTTTATACTAATAT
1 TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTTTATACTAATAT
1781439 CTGTTTAAACG
66 CTGTTTAAACG
1781450 T
1 T
1781451 TATATATATA
Statistics
Matches: 74, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
75 28 0.38
76 21 0.28
77 17 0.23
78 8 0.11
ACGTcount: A:0.20, C:0.13, G:0.08, T:0.59
Consensus pattern (76 bp):
TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTTTATACTAATAT
CTGTTTAAACG
Found at i:1783581 original size:16 final size:16
Alignment explanation
Indices: 1783560--1783592 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1783550 GATGATCATG
1783560 GATTTAAATTGCGGTT
1 GATTTAAATTGCGGTT
1783576 GATTTAAATTGCGGTT
1 GATTTAAATTGCGGTT
1783592 G
1 G
1783593 TGGTCCTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.27, T:0.42
Consensus pattern (16 bp):
GATTTAAATTGCGGTT
Found at i:1793194 original size:45 final size:45
Alignment explanation
Indices: 1793103--1793285 Score: 244
Period size: 45 Copynumber: 4.1 Consensus size: 45
1793093 GTAACCATAC
* *
1793103 AAATAAGCTTACCAGCTTATGGAAT-AATGGAAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
1793147 AAATAAGCTTACGAACTTATGGAACAAATGGTAAGTATATTGTTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* ** * *
1793192 AAAT-AGCTTATGAGCTTATGGGTTAAATGATAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
1793236 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATGTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1793281 AAATA
1 AAATA
1793286 TTGGATATAT
Statistics
Matches: 120, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
44 58 0.48
45 62 0.52
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:1798521 original size:60 final size:60
Alignment explanation
Indices: 1798419--1798536 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
1798409 TCGAGTAACC
* * * * *
1798419 ATTTTGTAACTTTTACTAGTCGAGGGACTCAATAAATAAACATCCTATAGTTGAGGGATT
1 ATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGAAACATCCTATAGTGGAGGGATT
* * *
1798479 ATTTTGTAACTTTTAATAGTC-AGAAGACTTAACAAAGCAACATCTTATAGTGGAGGGA
1 ATTTTGTAACTTTTAATAGTCGAG-AGACTCAACAAAGAAACATCCTATAGTGGAGGGA
1798537 CAATTTCTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 2 0.04
60 47 0.96
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGAAACATCCTATAGTGGAGGGATT
Found at i:1798725 original size:18 final size:18
Alignment explanation
Indices: 1798689--1798726 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1798679 TTTAGTAATA
*
1798689 AACAAAAATAATATTACT
1 AACAAAAATAATATAACT
1798707 AACAATAAATAA-ATAACT
1 AACAA-AAATAATATAACT
1798725 AA
1 AA
1798727 AATGAGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.24
Consensus pattern (18 bp):
AACAAAAATAATATAACT
Found at i:1798981 original size:31 final size:31
Alignment explanation
Indices: 1798943--1799033 Score: 91
Period size: 31 Copynumber: 2.9 Consensus size: 31
1798933 TATATATATA
*
1798943 ATATATTTTTATTTTCAAAACTATAATATGT
1 ATATATTTTTATTTTCAAAACTATAATATCT
*
1798974 ATATATTTTTA--AT--AAACTATATATACTCT
1 ATATATTTTTATTTTCAAAACTATA-ATA-TCT
*
1799003 ATATAATATTTTATTTTCAAAACCATAATAT
1 ATAT-AT-TTTTATTTTCAAAACTATAATAT
1799034 ACTCTCTCTC
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
27 8 0.17
28 3 0.06
29 7 0.15
30 2 0.04
31 16 0.33
33 2 0.04
34 3 0.06
35 7 0.15
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (31 bp):
ATATATTTTTATTTTCAAAACTATAATATCT
Found at i:1801338 original size:23 final size:23
Alignment explanation
Indices: 1801312--1801365 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
1801302 ACATCGGTTG
*
1801312 ATGGTCAAATTC-AGTGCCAATCA
1 ATGGTCAAAGTCAAG-GCCAATCA
*
1801335 ATGGTCAAAGTCAAGGCTAATCA
1 ATGGTCAAAGTCAAGGCCAATCA
1801358 ATGGTCAA
1 ATGGTCAA
1801366 CGTTAATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (23 bp):
ATGGTCAAAGTCAAGGCCAATCA
Found at i:1802475 original size:29 final size:29
Alignment explanation
Indices: 1802420--1802475 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
1802410 CAAATTTTGG
** *
1802420 TTAGTGACCAAAATATAAGTGTTGAAAGT
1 TTAGTGACCAAAATATAAAAGTGGAAAGT
* *
1802449 TTAGTGGCCAAAGTATAAAAGTGGAAA
1 TTAGTGACCAAAATATAAAAGTGGAAA
1802476 AAGTTTAGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (29 bp):
TTAGTGACCAAAATATAAAAGTGGAAAGT
Found at i:1803546 original size:596 final size:599
Alignment explanation
Indices: 1802411--1803591 Score: 1836
Period size: 596 Copynumber: 2.0 Consensus size: 599
1802401 GAAATACCCC
*
1802411 AAATTTTGGTTAGTGACCAAAATATAAGTGTTGAAAGTTTAGTGGCCAAAGTATAAAAGTGGAAA
1 AAATTTTGGTTAGTGACCAAAATATAAGTGTTGAAAGTTTAATGGCCAAAGTATAAAAGTGGAAA
* * * * *
1802476 AAGTTTAGGGATTTAATTGGTAATTTTCCCAAAATAATTTTTATTCCATAAATAAATAGTTTACT
66 AAGTTTAGAGATCTAAGTGGTAATTTTCCCAAAATAATATCTATTCCATAAATAAATAGTTTACT
** * * *
1802541 CTTGAGAGTGGGGTTTTATTAAAATCATATTCTTGATTCGGAATTTAGGTTGAAAATTAGAAAGG
131 CTCAAGAGTGGGGTTTAATTAAAATCAGATTCTTGATTCGGAATTTAGGTTGAAAACTAGAAAGG
*
1802606 ATTAAAGTCCAGTAAGAAATCGGTAAATCAGATCGAATAGAAATTTCAGGAAAAAATGAAGGATG
196 ATTAAAGTCCAGTAAGAAATAGGTAAATCAGATCGAATAGAAATTTCAGGAAAAAATGAAGGATG
* * * *
1802671 GTAAATTAGGCTTAAAAATATTATTTCCACATGTTAAAATGATGAAAAACAATATGTATCATTGG
261 ATAAATTAGGCTTAAAAATATTATTTACACATGTTAAAATGAGGAAAAACAATATGTATCATTCG
*
1802736 ATTTGAAAATTTATTTCCATGTTAAATTTTGGACTCCTGGATTAAAGTGACAATATTACAATTTT
326 ATTTGAAAATTTATTTCCATGTTAAATTTTGGACTCCTGGATTAAAGTGACAAGATTACAATTTT
* *
1802801 TGGAAAATTGCTTGGTAAAATTGGAAAAGGGGTAAAATAATTTGTTCATCTTTGACTTTGAAAGA
391 TGGAAAATTGCTTGGTAAAATTGGAAAAAGGGTAAAATAATTTGTTCATCTTTGAATTTGAAAGA
** * * *
1802866 TGATAGGGTTTATATAGCTTGGTATTAAGGTAGTTATCAAGTTTCATTAATGGCAAAATGGATAT
456 TGATAAAGTTTATATAGCTTGGTATTAAGGTAATTATCAAGTTTCATTAATGGCAAAATAGACAT
*
1802931 TTGTCATTAAATGAATATTTTATTCATTTAAGA-TTAAATTAAAGATAAATTAACATGAAAATAA
521 TTGTCATTAAATGAATATTTCATTCATTTAA-ACTTAAATTAAAGATAAATTAACATGAAAATAA
1802995 ATTTTAAAATAGCTT
585 ATTTTAAAATAGCTT
* * *
1803010 AAATTTTGGTTAGTGACCAAAATGTAAGTTTTGAAAGTTTAATGGCCAAAGTATAAAAGTGGGAA
1 AAATTTTGGTTAGTGACCAAAATATAAGTGTTGAAAGTTTAATGGCCAAAGTATAAAAGTGGAAA
**
1803075 AAGTTTAGAGATCTAAGTGGTAATTTTCCCAAAA-AA-ATCTATTCCATAAATGGATAGTTTACT
66 AAGTTTAGAGATCTAAGTGGTAATTTTCCCAAAATAATATCTATTCCATAAATAAATAGTTTACT
*
1803138 CTCAAGAGTGGGGTTTAATTAAAATCAGATTCTTGA-TCTGGAATTTATGTTGAAAACTAGATAA
131 CTCAAGAGTGGGGTTTAATTAAAATCAGATTCTTGATTC-GGAATTTAGGTTGAAAACTAGA-AA
* ** * *
1803202 GG-TTAAAGTCCGGTAAGAAATAGGTAAATTGGATCGAATAGAAATTTC-GGGAAAATTGAAGGA
194 GGATTAAAGTCCAGTAAGAAATAGGTAAATCAGATCGAATAGAAATTTCAGGAAAAAATGAAGGA
* * **
1803265 TGATAAATTAGGCTTAAAAATTTTATTTACACATGTTAAAATGAGGGAAAATGATATGTATCATT
259 TGATAAATTAGGCTTAAAAATATTATTTACACATGTTAAAATGAGGAAAAACAATATGTATCATT
* **
1803330 CGATTTGAAAATTTATTTCCATGTTAAATTTTGGAC-CTTTGGATTAAAGTGGTAAGATTACAAT
324 CGATTTGAAAATTTATTTCCATGTTAAATTTTGGACTC-CTGGATTAAAGTGACAAGATTACAAT
* * *
1803394 TTTTGGAAAATTGCTTGGTAAAGTTGGAAAAATGGTAAAATAATTTGTTCATCTTTGAATTTGGA
388 TTTTGGAAAATTGCTTGGTAAAATTGGAAAAAGGGTAAAATAATTTGTTCATCTTTGAATTTGAA
* *
1803459 AGATGATAAAGTTTATGTGGCTTGGTATTAAGGTAATTATCAAGTTTCATTAATGGCAAAATAGA
453 AGATGATAAAGTTTATATAGCTTGGTATTAAGGTAATTATCAAGTTTCATTAATGGCAAAATAGA
*
1803524 CATTTGTCATTAAATGAATATTTCATTCATTTAAACTTAAATTAAAGATAAATTAACATGAAATT
518 CATTTGTCATTAAATGAATATTTCATTCATTTAAACTTAAATTAAAGATAAATTAACATGAAAAT
1803589 AAA
583 AAA
1803592 GGAAAATTTC
Statistics
Matches: 529, Mismatches: 49, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
595 2 0.00
596 312 0.59
597 117 0.22
598 6 0.01
599 92 0.17
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (599 bp):
AAATTTTGGTTAGTGACCAAAATATAAGTGTTGAAAGTTTAATGGCCAAAGTATAAAAGTGGAAA
AAGTTTAGAGATCTAAGTGGTAATTTTCCCAAAATAATATCTATTCCATAAATAAATAGTTTACT
CTCAAGAGTGGGGTTTAATTAAAATCAGATTCTTGATTCGGAATTTAGGTTGAAAACTAGAAAGG
ATTAAAGTCCAGTAAGAAATAGGTAAATCAGATCGAATAGAAATTTCAGGAAAAAATGAAGGATG
ATAAATTAGGCTTAAAAATATTATTTACACATGTTAAAATGAGGAAAAACAATATGTATCATTCG
ATTTGAAAATTTATTTCCATGTTAAATTTTGGACTCCTGGATTAAAGTGACAAGATTACAATTTT
TGGAAAATTGCTTGGTAAAATTGGAAAAAGGGTAAAATAATTTGTTCATCTTTGAATTTGAAAGA
TGATAAAGTTTATATAGCTTGGTATTAAGGTAATTATCAAGTTTCATTAATGGCAAAATAGACAT
TTGTCATTAAATGAATATTTCATTCATTTAAACTTAAATTAAAGATAAATTAACATGAAAATAAA
TTTTAAAATAGCTT
Found at i:1805021 original size:121 final size:121
Alignment explanation
Indices: 1804878--1805119 Score: 430
Period size: 121 Copynumber: 2.0 Consensus size: 121
1804868 AACGAATGAA
*
1804878 TGCCTTTCATACAAATTATTATTTATTAATGGTTTGGAATAAATGTTTAACTTGCTAATTGGATT
1 TGCCTTTCATACAAATTATTATTTATTAATGGTTTGGAATAAATGTTTAACATGCTAATTGGATT
* *
1804943 TTAAAGCCTATTGTATGTACATGGAGAGTTATAGGAGTAATAATAATACCATAAAT
66 TTAAAGCCTATTATATGTACATGGAGAGTTATAGGAGCAATAATAATACCATAAAT
* *
1804999 TGCCTTTCATACAAATTATTATTTATTGATGGTTTGGAATAAATGTTTAACATGCTATTTGGATT
1 TGCCTTTCATACAAATTATTATTTATTAATGGTTTGGAATAAATGTTTAACATGCTAATTGGATT
*
1805064 TTAAAGCCTATTATATGTACATGGAGAGTTATAGGTGCAATAATAATACCATAAAT
66 TTAAAGCCTATTATATGTACATGGAGAGTTATAGGAGCAATAATAATACCATAAAT
1805120 AATATGGTAT
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 115 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.40
Consensus pattern (121 bp):
TGCCTTTCATACAAATTATTATTTATTAATGGTTTGGAATAAATGTTTAACATGCTAATTGGATT
TTAAAGCCTATTATATGTACATGGAGAGTTATAGGAGCAATAATAATACCATAAAT
Found at i:1805257 original size:21 final size:21
Alignment explanation
Indices: 1805233--1805312 Score: 90
Period size: 21 Copynumber: 3.7 Consensus size: 21
1805223 TTTTCGTAAG
1805233 AGTACTTTGTGTACTTGAAGT
1 AGTACTTTGTGTACTTGAAGT
*
1805254 AGTACTTGGTGTACTATGGCAAG-
1 AGTACTTTGTGTACT-T-G-AAGT
* * *
1805277 AATACTTTGTGCACTTGGAGT
1 AGTACTTTGTGTACTTGAAGT
1805298 AGTACTTTGTGTACT
1 AGTACTTTGTGTACT
1805313 ATGGCACTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
20 2 0.04
21 28 0.58
22 2 0.04
23 13 0.27
24 3 0.06
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGAAGT
Found at i:1805299 original size:44 final size:44
Alignment explanation
Indices: 1805230--1805318 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
1805220 GCATTTTCGT
* *
1805230 AAGAGTACTTTGTGTACTTGAAGTAGTACTTGGTGTACTATGGC
1 AAGAATACTTTGTGCACTTGAAGTAGTACTTGGTGTACTATGGC
* *
1805274 AAGAATACTTTGTGCACTTGGAGTAGTACTTTGTGTACTATGGC
1 AAGAATACTTTGTGCACTTGAAGTAGTACTTGGTGTACTATGGC
1805318 A
1 A
1805319 CTTTGTGTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (44 bp):
AAGAATACTTTGTGCACTTGAAGTAGTACTTGGTGTACTATGGC
Found at i:1807237 original size:24 final size:24
Alignment explanation
Indices: 1807164--1807242 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 24
1807154 ACATCCAAGG
1807164 AGTATCGATACTACTATGTATAGT
1 AGTATCGATACTACTATGTATAGT
* * ** *
1807188 AGTATTGGTAC--C-ATCCA-AGG
1 AGTATCGATACTACTATGTATAGT
1807208 AGTATCGATACTACTATGTATAGT
1 AGTATCGATACTACTATGTATAGT
1807232 AGTATCGATAC
1 AGTATCGATAC
1807243 CGAAACATGG
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
20 11 0.27
21 3 0.07
22 2 0.05
23 3 0.07
24 22 0.54
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (24 bp):
AGTATCGATACTACTATGTATAGT
Found at i:1809357 original size:20 final size:21
Alignment explanation
Indices: 1809328--1809379 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
1809318 ATTCATGTAG
*
1809328 TATCGGTACTG-CAAGAACAA
1 TATCGATACTGACAAGAACAA
*
1809348 TATCGATACTTGATAAGAACAA
1 TATCGATAC-TGACAAGAACAA
1809370 TATCGATACT
1 TATCGATACT
1809380 AGGTTAGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.29
21 3 0.11
22 17 0.61
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (21 bp):
TATCGATACTGACAAGAACAA
Found at i:1815368 original size:20 final size:21
Alignment explanation
Indices: 1815329--1815368 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1815319 GATACTACTA
1815329 TAAGGCATAGTATCGATACTGC
1 TAAGGCATA-TATCGATACTGC
*
1815351 TAAGGCAT-TATCGGTACT
1 TAAGGCATATATCGATACT
1815369 ACCTCTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (21 bp):
TAAGGCATATATCGATACTGC
Found at i:1815534 original size:18 final size:18
Alignment explanation
Indices: 1815511--1815551 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1815501 GAGTAATATT
*
1815511 TATAATAATTGAATCGAA
1 TATAATAATTAAATCGAA
* *
1815529 TATAATATTTAAATTGAA
1 TATAATAATTAAATCGAA
1815547 TATAA
1 TATAA
1815552 AATCTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (18 bp):
TATAATAATTAAATCGAA
Found at i:1822104 original size:20 final size:22
Alignment explanation
Indices: 1822072--1822116 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
1822062 GTTGTTTCCT
1822072 TTTAATGGAAAAA-TTTATTTA
1 TTTAATGGAAAAATTTTATTTA
1822093 TTTAAT-GAAAAATTTTATTTA
1 TTTAATGGAAAAATTTTATTTA
1822114 TTT
1 TTT
1822117 TTAATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (22 bp):
TTTAATGGAAAAATTTTATTTA
Found at i:1825076 original size:2 final size:2
Alignment explanation
Indices: 1825029--1825061 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
1825019 CTATACGAAA
1825029 AT AT CAT 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
1825062 TAACATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1837257 original size:13 final size:14
Alignment explanation
Indices: 1837239--1837277 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1837229 ATCTTCAGTG
1837239 TTCTTATTATTTT-
1 TTCTTATTATTTTA
*
1837252 TTCTTATTGTTTTA
1 TTCTTATTATTTTA
*
1837266 TTCTTTTTATTT
1 TTCTTATTATTT
1837278 CATAACACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.77
Consensus pattern (14 bp):
TTCTTATTATTTTA
Found at i:1838926 original size:6 final size:6
Alignment explanation
Indices: 1838911--1838957 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
1838901 TTCTCAAATA
* *
1838911 TTTA-T TTTATT TTTATT TTTACT TTTACT TTTACT TTTACT TTTACT
1 TTTACT TTTACT TTTACT TTTACT TTTACT TTTACT TTTACT TTTACT
1838958 GAATTTTTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
5 4 0.10
6 36 0.90
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTACT
Found at i:1841396 original size:17 final size:17
Alignment explanation
Indices: 1841369--1841402 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1841359 TATTTGAATT
1841369 AAAGTGCATGA-TAGTG
1 AAAGTGCATGATTAGTG
1841385 AAAGTAGCATGATTAGTG
1 AAAGT-GCATGATTAGTG
1841403 TTTTCATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.38, C:0.06, G:0.29, T:0.26
Consensus pattern (17 bp):
AAAGTGCATGATTAGTG
Found at i:1850539 original size:2 final size:2
Alignment explanation
Indices: 1850532--1850562 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1850522 ATATTCTCTA
1850532 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1850563 ATAATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1850713 original size:59 final size:54
Alignment explanation
Indices: 1850625--1850872 Score: 202
Period size: 53 Copynumber: 4.6 Consensus size: 54
1850615 AAAATACAAA
* * * *
1850625 ACATACTTACACCAATATAATTACT-TGTTATTTTTAGGAACTAAGATATTAAGAGATGT
1 ACATACTTACACTAATATAAGTA-TGTGTTA-TTTT--G--CTAAGATATTGAGAGATAT
* *
1850684 ACATACTTACACTAATGTAAGTATGTGTTA-ATTGCTAAGATATTGAGAGATAT
1 ACATACTTACACTAATATAAGTATGTGTTATTTTGCTAAGATATTGAGAGATAT
* * *
1850737 ACGTACTTAAACGT-ATATAAGTACGTGTTAATTTT--TAAGATATTGAGAGATAT
1 ACATACTTACAC-TAATATAAGTATGTGTT-ATTTTGCTAAGATATTGAGAGATAT
* * * * * **
1850790 ACATACTTACACTAGTGTAAGTATGTGTTA-ATTGTTAAGATATTGAGAAACGT
1 ACATACTTACACTAATATAAGTATGTGTTATTTTGCTAAGATATTGAGAGATAT
* * * *
1850843 ACATAATTACACCAATGTAAGTATATGTTA
1 ACATACTTACACTAATATAAGTATGTGTTA
1850873 ATTGATACAC
Statistics
Matches: 158, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
51 2 0.01
52 2 0.01
53 121 0.77
54 2 0.01
55 3 0.02
57 2 0.01
58 1 0.01
59 25 0.16
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (54 bp):
ACATACTTACACTAATATAAGTATGTGTTATTTTGCTAAGATATTGAGAGATAT
Found at i:1850745 original size:53 final size:53
Alignment explanation
Indices: 1850665--1850876 Score: 264
Period size: 53 Copynumber: 4.0 Consensus size: 53
1850655 TTTTTAGGAA
* *
1850665 CTAAGATATTAAGAGATGTACATACTTACACTAATGTAAGTATGTGTTAATTG
1 CTAAGATATTGAGAGATATACATACTTACACTAATGTAAGTATGTGTTAATTG
* * * * *
1850718 CTAAGATATTGAGAGATATACGTACTTAAACGT-ATATAAGTACGTGTTAATTT
1 CTAAGATATTGAGAGATATACATACTTACAC-TAATGTAAGTATGTGTTAATTG
* *
1850771 TTAAGATATTGAGAGATATACATACTTACACTAGTGTAAGTATGTGTTAATTG
1 CTAAGATATTGAGAGATATACATACTTACACTAATGTAAGTATGTGTTAATTG
* * ** * * *
1850824 TTAAGATATTGAGAAACGTACATAATTACACCAATGTAAGTATATGTTAATTG
1 CTAAGATATTGAGAGATATACATACTTACACTAATGTAAGTATGTGTTAATTG
1850877 ATACACTTTT
Statistics
Matches: 136, Mismatches: 21, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
52 1 0.01
53 134 0.99
54 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (53 bp):
CTAAGATATTGAGAGATATACATACTTACACTAATGTAAGTATGTGTTAATTG
Found at i:1864135 original size:12 final size:12
Alignment explanation
Indices: 1864118--1864161 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
1864108 GGTGCGTTTA
1864118 GTGGACTGATTG
1 GTGGACTGATTG
* *
1864130 GTGGACTGTTTA
1 GTGGACTGATTG
*
1864142 GTGGACTTATTG
1 GTGGACTGATTG
1864154 GTGGACTG
1 GTGGACTG
1864162 TTCGCTGAGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.16, C:0.09, G:0.39, T:0.36
Consensus pattern (12 bp):
GTGGACTGATTG
Found at i:1864140 original size:24 final size:24
Alignment explanation
Indices: 1864113--1864163 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1864103 TGTTTGGTGC
1864113 GTTTAGTGGACTGATTGGTGGACT
1 GTTTAGTGGACTGATTGGTGGACT
*
1864137 GTTTAGTGGACTTATTGGTGGACT
1 GTTTAGTGGACTGATTGGTGGACT
1864161 GTT
1 GTT
1864164 CGCTGAGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.35, T:0.41
Consensus pattern (24 bp):
GTTTAGTGGACTGATTGGTGGACT
Found at i:1869490 original size:18 final size:18
Alignment explanation
Indices: 1869467--1869513 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
1869457 TGGTTAGGCT
1869467 AGCTAAAAATAGGGTAGA
1 AGCTAAAAATAGGGTAGA
1869485 AGCTAAAAATAGGGTAGA
1 AGCTAAAAATAGGGTAGA
*
1869503 AACTAAAAATA
1 AGCTAAAAATA
1869514 ATGTAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.55, C:0.06, G:0.21, T:0.17
Consensus pattern (18 bp):
AGCTAAAAATAGGGTAGA
Found at i:1872860 original size:19 final size:20
Alignment explanation
Indices: 1872812--1872860 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1872802 GGGCAAGGAA
1872812 TTCACTATTTTTAGTGACAC
1 TTCACTATTTTTAGTGACAC
*
1872832 TTCACTATTTTTAGTGATAC
1 TTCACTATTTTTAGTGACAC
1872852 TTCAC-ATTT
1 TTCACTATTT
1872861 GTGACTTGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.49
Consensus pattern (20 bp):
TTCACTATTTTTAGTGACAC
Found at i:1874140 original size:2 final size:2
Alignment explanation
Indices: 1874133--1874160 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1874123 TGTTGTTAAC
1874133 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
1874161 TAAATTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1880887 original size:6 final size:6
Alignment explanation
Indices: 1880876--1880900 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1880866 AAATGTGTCG
1880876 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
1880901 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:1880904 original size:2 final size:2
Alignment explanation
Indices: 1880897--1880952 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1880887 ATTAATATTA
1880897 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
1880939 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1880953 GCACATGTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1882354 original size:29 final size:28
Alignment explanation
Indices: 1882318--1882374 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
1882308 TATTATATAG
*
1882318 TATAAACATAC-TATATGATTATATTTAT
1 TATAAACATACATATA-CATTATATTTAT
*
1882346 TATATAACATGCATATACATTATATTTAT
1 TATA-AACATACATATACATTATATTTAT
1882375 ATTATATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.16
29 17 0.68
30 4 0.16
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.46
Consensus pattern (28 bp):
TATAAACATACATATACATTATATTTAT
Found at i:1894338 original size:16 final size:16
Alignment explanation
Indices: 1894317--1894352 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1894307 TGAAAGTTGA
1894317 AAAAAGAAAAAAAATG
1 AAAAAGAAAAAAAATG
1894333 AAAAAGAAAAAAAATG
1 AAAAAGAAAAAAAATG
1894349 AAAA
1 AAAA
1894353 TCGAGAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAAGAAAAAAAATG
Found at i:1894503 original size:45 final size:45
Alignment explanation
Indices: 1894433--1894550 Score: 157
Period size: 45 Copynumber: 2.6 Consensus size: 45
1894423 AAAAATAAGT
*** *
1894433 TGGGTCTAAGATGAAAACGTACAAAGGGTGGCTTGAAACCAAAGA
1 TGGGTCTAAGATGAAAACCCGCAAAGGGCGGCTTGAAACCAAAGA
* *
1894478 TGGGTCTAAGATGAAAACCCGCAAAGGGCGTCTTGAAACCAATGA
1 TGGGTCTAAGATGAAAACCCGCAAAGGGCGGCTTGAAACCAAAGA
* *
1894523 TGGGTCCAAGTTGAAAACCCG-AAAGGGC
1 TGGGTCTAAGATGAAAACCCGCAAAGGGC
1894551 AATTGGGATA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 7 0.11
45 58 0.89
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.17
Consensus pattern (45 bp):
TGGGTCTAAGATGAAAACCCGCAAAGGGCGGCTTGAAACCAAAGA
Found at i:1895863 original size:14 final size:14
Alignment explanation
Indices: 1895832--1895869 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1895822 GTCCGATTTT
1895832 ATATAGTAT-TATC
1 ATATAGTATATATC
*
1895845 ATATATTATATATC
1 ATATAGTATATATC
*
1895859 TTATAGTATAT
1 ATATAGTATAT
1895870 TTATATTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (14 bp):
ATATAGTATATATC
Found at i:1896059 original size:14 final size:14
Alignment explanation
Indices: 1896028--1896065 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1896018 GACCCTTTGT
1896028 ATATAGTAT-TATC
1 ATATAGTATATATC
*
1896041 ATATATTATATATC
1 ATATAGTATATATC
*
1896055 TTATAGTATAT
1 ATATAGTATAT
1896066 TTATATTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (14 bp):
ATATAGTATATATC
Found at i:1896119 original size:16 final size:17
Alignment explanation
Indices: 1896098--1896131 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1896088 ACAATATGAT
1896098 TATATTT-ATTATATAG
1 TATATTTAATTATATAG
1896114 TATATTTACATTATATAG
1 TATATTTA-ATTATATAG
1896132 CATGAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (17 bp):
TATATTTAATTATATAG
Found at i:1896143 original size:53 final size:53
Alignment explanation
Indices: 1896056--1896156 Score: 132
Period size: 53 Copynumber: 1.9 Consensus size: 53
1896046 TTATATATCT
* *
1896056 TATAGTATATTTATATTACATAGTATAAACATACAATATGA-TTATATTTATTA
1 TATAGTATATTTACATTACATAGCATAAACATACAATAT-ATTTATATTTATTA
* * * *
1896109 TATAGTATATTTACATTATATAGCATGAATATACATTATATTTATATT
1 TATAGTATATTTACATTACATAGCATAAACATACAATATATTTATATT
1896157 ATATGATACA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 1 0.02
53 40 0.98
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (53 bp):
TATAGTATATTTACATTACATAGCATAAACATACAATATATTTATATTTATTA
Found at i:1896171 original size:53 final size:53
Alignment explanation
Indices: 1896059--1896172 Score: 124
Period size: 53 Copynumber: 2.2 Consensus size: 53
1896049 TATATCTTAT
* * * *
1896059 AGTATATTTATATTACATAGTATAAACATACAATATGATTATATTTATTATAT
1 AGTATATTTACATTACATAGCATAAACATACAATATGATTATATTTATGATAC
* * * *
1896112 AGTATATTTACATTATATAGCATGAATATACATTAT-ATTTATATTATATGATAC
1 AGTATATTTACATTACATAGCATAAACATACAATATGA-TTATATT-TATGATAC
1896166 A-TATATT
1 AGTATATT
1896173 ATTTATATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
52 1 0.02
53 43 0.84
54 7 0.14
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (53 bp):
AGTATATTTACATTACATAGCATAAACATACAATATGATTATATTTATGATAC
Found at i:1898834 original size:24 final size:24
Alignment explanation
Indices: 1898799--1898901 Score: 109
Period size: 24 Copynumber: 4.3 Consensus size: 24
1898789 ATCGATCGCT
* *
1898799 TGTATTAGTGCATTTGTACACTCC
1 TGTATTAATGCATTTGTACACTCA
1898823 TGTATTAATGCATTTGTACACTCA
1 TGTATTAATGCATTTGTACACTCA
** * *
1898847 TGTATTAATGCATTCATGCATTCA
1 TGTATTAATGCATTTGTACACTCA
* * *
1898871 TGTATTAGTGCAATTG-AGCACTCT
1 TGTATTAATGCATTTGTA-CACTCA
1898895 TGTATTA
1 TGTATTA
1898902 CTGTGTACTC
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.42
Consensus pattern (24 bp):
TGTATTAATGCATTTGTACACTCA
Found at i:1900047 original size:23 final size:23
Alignment explanation
Indices: 1900017--1900069 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
1900007 TGGCATTACT
1900017 TGAAGCTGCAGATAATGTTGTGA
1 TGAAGCTGCAGATAATGTTGTGA
1900040 TGAAGCTGCAGATAATGTTGTGA
1 TGAAGCTGCAGATAATGTTGTGA
1900063 TGAAGCT
1 TGAAGCT
1900070 ACAGCAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (23 bp):
TGAAGCTGCAGATAATGTTGTGA
Found at i:1908720 original size:15 final size:15
Alignment explanation
Indices: 1908702--1908737 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1908692 ATGTTTATGT
1908702 TATTTGTGTTGTCTA
1 TATTTGTGTTGTCTA
*
1908717 TATTTTTGTTGTCTA
1 TATTTGTGTTGTCTA
1908732 TATTTG
1 TATTTG
1908738 CTTGCATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.06, G:0.17, T:0.64
Consensus pattern (15 bp):
TATTTGTGTTGTCTA
Found at i:1913114 original size:20 final size:20
Alignment explanation
Indices: 1913045--1913289 Score: 131
Period size: 20 Copynumber: 12.2 Consensus size: 20
1913035 TTCACAACTC
*
1913045 AATTTCGAATTCGCAACACG
1 AATTTCGAATTCGCAACGCG
** * *
1913065 AA-AGCCAATTTCGCAAC-AG
1 AATTTCGAA-TTCGCAACGCG
* *
1913084 AGTTTCCGAATTCGCAACTCG
1 AATTT-CGAATTCGCAACGCG
* *
1913105 AATTTGGAATTCGCAACACAG
1 AATTTCGAATTCGCAACGC-G
* *
1913126 AA-GTCGAATTCGCAACTCG
1 AATTTCGAATTCGCAACGCG
*
1913145 AATTT-GACATTTTCGCAACACG
1 AATTTCGA-A--TTCGCAACGCG
*** *
1913167 AATTTCTTTTTCGCAACTCG
1 AATTTCGAATTCGCAACGCG
* ** * *
1913187 ATTTTTAAATTTGCAACACG
1 AATTTCGAATTCGCAACGCG
* **
1913207 AGTTTCGTTTTCGCAACGCG
1 AATTTCGAATTCGCAACGCG
** **
1913227 AATTTAAAACCCGCAACGCG
1 AATTTCGAATTCGCAACGCG
*
1913247 AATTTCGAACTCGCAACGCG
1 AATTTCGAATTCGCAACGCG
1913267 AATTTCGAACTT-GCAACGCG
1 AATTTCGAA-TTCGCAACGCG
1913287 AAT
1 AAT
1913290 CCTGCTATGT
Statistics
Matches: 168, Mismatches: 46, Indels: 22
0.71 0.19 0.09
Matches are distributed among these distances:
19 10 0.06
20 131 0.78
21 12 0.07
22 15 0.09
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (20 bp):
AATTTCGAATTCGCAACGCG
Found at i:1913218 original size:40 final size:42
Alignment explanation
Indices: 1913070--1913231 Score: 147
Period size: 40 Copynumber: 4.0 Consensus size: 42
1913060 ACACGAAAGC
* **
1913070 CAATTTCGCAACA-GAGTTTCCGAATTCGCAACTCGAATTTG-
1 CAATTTCGCAACACGAATTT-CGTTTTCGCAACTCGAATTTGA
* * **
1913111 GAA-TTCGCAACACAGAA-GTCGAATTCGCAACTCGAATTTGA
1 CAATTTCGCAACAC-GAATTTCGTTTTCGCAACTCGAATTTGA
* * * *
1913152 CATTTTCGCAACACGAATTTCTTTTTCGCAACTCGATTTTTA
1 CAATTTCGCAACACGAATTTCGTTTTCGCAACTCGAATTTGA
* *
1913194 -AATTT-GCAACACGAGTTTCGTTTTCGCAACGCGAATTT
1 CAATTTCGCAACACGAATTTCGTTTTCGCAACTCGAATTT
1913232 AAAACCCGCA
Statistics
Matches: 100, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
40 59 0.59
41 11 0.11
42 30 0.30
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (42 bp):
CAATTTCGCAACACGAATTTCGTTTTCGCAACTCGAATTTGA
Found at i:1913888 original size:20 final size:20
Alignment explanation
Indices: 1913828--1913882 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1913818 ACATAGCAGG
*
1913828 ATTCGCGTTGCGAAAACGAA
1 ATTCGAGTTGCGAAAACGAA
*
1913848 ATTCGAGTTGTGAAAACGAA
1 ATTCGAGTTGCGAAAACGAA
1913868 ATTCGAGTTGCGAAA
1 ATTCGAGTTGCGAAA
1913883 TTGAAACTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (20 bp):
ATTCGAGTTGCGAAAACGAA
Found at i:1915089 original size:21 final size:20
Alignment explanation
Indices: 1915052--1915090 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1915042 TTGTTTAATA
*
1915052 AAAGTTTTCATTTTTTTTTC
1 AAAGTTTTCATTGTTTTTTC
*
1915072 AAAGTTTTTCCTTGTTTTT
1 AAAG-TTTTCATTGTTTTT
1915091 ATTTTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.18, C:0.10, G:0.08, T:0.64
Consensus pattern (20 bp):
AAAGTTTTCATTGTTTTTTC
Found at i:1922867 original size:21 final size:20
Alignment explanation
Indices: 1922837--1922875 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1922827 TTGTTTAATA
*
1922837 AAAGTTTTCCTTTTTTTTTC
1 AAAGTTTTCCTTGTTTTTTC
1922857 AAAGTTTTTCCTTGTTTTT
1 AAAG-TTTTCCTTGTTTTT
1922876 ATTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.13, G:0.08, T:0.64
Consensus pattern (20 bp):
AAAGTTTTCCTTGTTTTTTC
Found at i:1924601 original size:21 final size:20
Alignment explanation
Indices: 1924571--1924609 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1924561 TTGTTTAATA
*
1924571 AAAGTTTTCCTTTTTTTTTC
1 AAAGTTTTCCTTGTTTTTTC
1924591 AAAGTTTTTCCTTGTTTTT
1 AAAG-TTTTCCTTGTTTTT
1924610 ATTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.13, G:0.08, T:0.64
Consensus pattern (20 bp):
AAAGTTTTCCTTGTTTTTTC
Done.