Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003805.1 Hibiscus syriacus cultivar Beakdansim tig00008145_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: 2300233
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1838825 original size:77 final size:74
Alignment explanation
Indices: 1838640--1838859 Score: 210
Period size: 77 Copynumber: 2.9 Consensus size: 74
1838630 AATTGCAAGC
* * * ** * * * *
1838640 CAAAACATAAATTTTATCTCAATTGAGATTTTTTTCTTAAAATAAATTTCGTCTCACTTGAGACA
1 CAAAACAGAAATTTCATCTCACTCAAGATTTTTTTCTTAAAACAAATTTCATCTCGCTTGAGAAA
1838705 G-TTTCACT
66 GTTTTCACT
* ** *
1838713 CAAAACAGAAATTTTATCTCACTTGAGATTGTTTTTCTCAAAACAAGA-TTCATCTCGCTTGAGA
1 CAAAACAGAAATTTCATCTCACTCAAGATT-TTTTTCTTAAAACAA-ATTTCATCTCGCTTGAGA
1838777 TAAGTTTTCACT
64 -AAGTTTTCACT
* * * * * *
1838789 CGAAACAATAAATTTCATTTCACTCAAGATTATTTTTCTTAAAGCAAATTTCATCTCGTTTAAGA
1 CAAAAC-AGAAATTTCATCTCACTCAAGATT-TTTTTCTTAAAACAAATTTCATCTCGCTTGAGA
1838854 AAGTTT
64 AAGTTT
1838860 CCCATGAAAT
Statistics
Matches: 123, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
73 28 0.23
74 27 0.22
75 3 0.02
76 19 0.15
77 46 0.37
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (74 bp):
CAAAACAGAAATTTCATCTCACTCAAGATTTTTTTCTTAAAACAAATTTCATCTCGCTTGAGAAA
GTTTTCACT
Found at i:1839011 original size:179 final size:179
Alignment explanation
Indices: 1838705--1839312 Score: 957
Period size: 179 Copynumber: 3.4 Consensus size: 179
1838695 ACTTGAGACA
** * * * *
1838705 GTTTCACTCAAAAC-AGAAATTTTATCTCACTTGAGATTGTTTTTCTCAAAACAAGATTCATCTC
1 GTTTCACTTGAAACAAG-AATTTTATCTCACTTGAGATTGCTTTTCTTAAAACAAAATTCGTCTC
* *** * * * *
1838769 GCTTGAGATAAGTTTTCACTCGAAACAATAAATTTCATTTCACTCAAGATTATTTTTCTTAAAGC
65 GCTT-AAACCGGTTTTTACTCGAAACAAGAAATTTCATTTCACTCAAGATTGTTTTTCTTAAAGA
* * *
1838834 AAATTTCATCTCGTTTAAGAAAGTTTCCCATGAAATATAAAATTTGAAATT
129 AAATTTCATCTCGCTTGAGAAAGTTTCTCATGAAATATAAAATTTGAAATT
*
1838885 GTTTCACTTGAAACAAGAATTTTATCTCACTTGAGATTGCTTTTCTTAAAACAAAATTTGTCTCG
1 GTTTCACTTGAAACAAGAATTTTATCTCACTTGAGATTGCTTTTCTTAAAACAAAATTCGTCTCG
*
1838950 CTTAAACCGGTTTTTACTCGAAACAAGAAATTTCATTTCACTCAAGATTGTTTTTCTTAAAGTAA
66 CTTAAACCGGTTTTTACTCGAAACAAGAAATTTCATTTCACTCAAGATTGTTTTTCTTAAAGAAA
*
1839015 ATTTCATCTCGCTTGAGAAAGTTTATCATGAAATATAAAATTTGAAATT
131 ATTTCATCTCGCTTGAGAAAGTTTCTCATGAAATATAAAATTTGAAATT
* *
1839064 GTTTCACTTGAAACAAGAATTTTATCTCACTTGAGATTGCTTTTCTTAAAACAAAATTTGCCTCG
1 GTTTCACTTGAAACAAGAATTTTATCTCACTTGAGATTGCTTTTCTTAAAACAAAATTCGTCTCG
1839129 CTTAAACCGGTTTTTACTCGAAACAAGAAATTTCATTTCACTCAAGATTGTTTTTCTTAAAGAAA
66 CTTAAACCGGTTTTTACTCGAAACAAGAAATTTCATTTCACTCAAGATTGTTTTTCTTAAAGAAA
1839194 ATTTCATCTCGCTTGAGAAAGTTTCTCATGAAATATAAAATTTGAAATT
131 ATTTCATCTCGCTTGAGAAAGTTTCTCATGAAATATAAAATTTGAAATT
* * * *
1839243 GTTTCACTTGAAACAAGAATTTTATCTCTCTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCA
1 GTTTCACTTGAAACAAGAATTTTATCTCACTTGAGATTGCTTTTCTTAAAACAAAATTCGTCTCG
1839308 CTTAA
66 CTTAA
1839313 GACAATTTTC
Statistics
Matches: 399, Mismatches: 28, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
179 339 0.85
180 58 0.15
181 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (179 bp):
GTTTCACTTGAAACAAGAATTTTATCTCACTTGAGATTGCTTTTCTTAAAACAAAATTCGTCTCG
CTTAAACCGGTTTTTACTCGAAACAAGAAATTTCATTTCACTCAAGATTGTTTTTCTTAAAGAAA
ATTTCATCTCGCTTGAGAAAGTTTCTCATGAAATATAAAATTTGAAATT
Found at i:1839745 original size:93 final size:93
Alignment explanation
Indices: 1839573--1839751 Score: 261
Period size: 93 Copynumber: 1.9 Consensus size: 93
1839563 AATAAGTTCG
* * *
1839573 TAATGAAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCAGCGACGCCTCACTTGA
1 TAATGAAGAACTTGTTCAACCTTTGCACGATTCACGACATTTCGAATCAGCAACGCCTCACTTGA
**
1839638 GGGATTAACATTTCCAGTAGAGCACTCA
66 GGGACCAACATTTCCAGTAGAGCACTCA
* *
1839666 TAATGAAGAACTTGTTCAACCTTTGCACGATTCACGACATTTCTAATCAGCAACGCCTCGCTCT-
1 TAATGAAGAACTTGTTCAACCTTTGCACGATTCACGACATTTCGAATCAGCAACGCCTCACT-TG
**
1839730 AGGGACCAATGTTTCCAGTAGA
65 AGGGACCAACATTTCCAGTAGA
1839752 AAGATCACGA
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
93 75 0.99
94 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (93 bp):
TAATGAAGAACTTGTTCAACCTTTGCACGATTCACGACATTTCGAATCAGCAACGCCTCACTTGA
GGGACCAACATTTCCAGTAGAGCACTCA
Found at i:1840079 original size:38 final size:37
Alignment explanation
Indices: 1839977--1840103 Score: 116
Period size: 36 Copynumber: 3.5 Consensus size: 37
1839967 CAAATTTTTT
* * *
1839977 TTTATCTCACTTGAGATTATTTTTCT--TAACATAAA
1 TTTATCTCACTTGAGATTGTTTTTCTCAAAACAGAAA
* ** **
1840012 TTCCATCTCACTTGAGACAGTTTCACTCAAAACAGAAA
1 TT-TATCTCACTTGAGATTGTTTTTCTCAAAACAGAAA
*
1840050 GTTTATCTCACTTGAGATTGTTTTTCTCAAAACA-AGA
1 -TTTATCTCACTTGAGATTGTTTTTCTCAAAACAGAAA
* *
1840087 TTCATCTCGCTTGAGAT
1 TTTATCTCACTTGAGAT
1840104 AAGTTTTCAC
Statistics
Matches: 72, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
35 2 0.03
36 33 0.46
37 2 0.03
38 33 0.46
39 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.39
Consensus pattern (37 bp):
TTTATCTCACTTGAGATTGTTTTTCTCAAAACAGAAA
Found at i:1840347 original size:179 final size:178
Alignment explanation
Indices: 1840051--1840619 Score: 858
Period size: 179 Copynumber: 3.2 Consensus size: 178
1840041 AAACAGAAAG
* ** *
1840051 TTTATCTCACTTGAGATTGTTTTTCTCAAAACAAGATTCATCTCGCTTGAGATAAGTTTTCACTC
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAA-ATTTGTCTCGCTTGAGAT-AGTTTTTACTC
* * * *
1840116 GAAACAAGAAATTTTATTTTAGTCAAGATTGTTTTTCTTAAAGAAAATTTCATCTCGCTTGAGAA
64 GAAACAAGAAATTTCATTTCACTCAAGATTGTTTTTCTTAAAGCAAATTTCATCTCGCTTGAGAA
1840181 AGTTTCCCATGAAATATAAAATTTGAAATTGTTTCACTTGAAACAAGAAT
129 AGTTTCCCATGAAATATAAAATTTGAAATTGTTTCACTTGAAACAAGAAT
*
1840231 TTTATCTCACTTGAGATTGTTTTTCTTAAATCAAACTTTGTCTCGCTTGAGATAGTTTTTACTCG
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-TTTGTCTCGCTTGAGATAGTTTTTACTCG
*
1840296 AAACAAGAAATTTCATTTCACTCAAGATTGTTTTTCTTAAAGCAAATTTCATCTCACTTGAGAAA
65 AAACAAGAAATTTCATTTCACTCAAGATTGTTTTTCTTAAAGCAAATTTCATCTCGCTTGAGAAA
* *
1840361 GTTTCCCATGAAATATAAAATTTGAATTTGTTTCACTTGAAACAATAAT
130 GTTTCCCATGAAATATAAAATTTGAAATTGTTTCACTTGAAACAAGAAT
* * * *
1840410 TTTATCTCACTTGAGATTGATTTTCTTAAAACAAAATTTGTCTAGCTTGAGACAGTTTTTACTCA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AAATTTGTCTCGCTTGAGATAGTTTTTACTCG
* * *
1840475 AAACAAGAAATTTCATTTCACTCAAAATTGTTTTTTCTTAAAGC----GTCATCTCGCTTGAGAT
65 AAACAAGAAATTTCATTTCACTCAAGATTG-TTTTTCTTAAAGCAAATTTCATCTCGCTTGAGAA
* *
1840536 AGTTTCTCACGAAATATAAAATTTGAAATTGTTTCACTTGAAACAAGAAT
129 AGTTTCCCATGAAATATAAAATTTGAAATTGTTTCACTTGAAACAAGAAT
* *
1840586 TTTATCTCACTTGAGATTGTTTTCCCTAAAACAA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1840620 TTCACCTCAC
Statistics
Matches: 358, Mismatches: 28, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
175 2 0.01
176 89 0.25
179 204 0.57
180 63 0.18
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (178 bp):
TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGATAGTTTTTACTCGA
AACAAGAAATTTCATTTCACTCAAGATTGTTTTTCTTAAAGCAAATTTCATCTCGCTTGAGAAAG
TTTCCCATGAAATATAAAATTTGAAATTGTTTCACTTGAAACAAGAAT
Found at i:1840356 original size:76 final size:75
Alignment explanation
Indices: 1840220--1840364 Score: 193
Period size: 76 Copynumber: 1.9 Consensus size: 75
1840210 TGTTTCACTT
* ** * * * *
1840220 GAAACAAGAATTTTATCTCACTTGAGATTGTTTTTCTTAAATCAAACTTTGTCTCGCTTGAGATA
1 GAAACAAGAATTTCATCTCACTCAAGATTGTTTTTCTTAAAGCAAACTTTATCTCACTTGAGAAA
1840285 GTTTTTACTC
66 GTTTTTACTC
*
1840295 GAAACAAGAAATTTCATTTCACTCAAGATTGTTTTTCTTAAAGCAAA-TTTCATCTCACTTGAGA
1 GAAACAAG-AATTTCATCTCACTCAAGATTGTTTTTCTTAAAGCAAACTTT-ATCTCACTTGAGA
1840359 AAGTTT
64 AAGTTT
1840365 CCCATGAAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
75 11 0.18
76 49 0.82
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (75 bp):
GAAACAAGAATTTCATCTCACTCAAGATTGTTTTTCTTAAAGCAAACTTTATCTCACTTGAGAAA
GTTTTTACTC
Found at i:1841076 original size:93 final size:93
Alignment explanation
Indices: 1840895--1841063 Score: 248
Period size: 93 Copynumber: 1.8 Consensus size: 93
1840885 GAGAAGAAGT
* * * * *
1840895 TCATAATGAAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCAGCGATGCCTTACT
1 TCATAATGAAGAACTTGTTCAACCTTTGCACGATTCACGACATTTCGAATCAGCAACGCCTCACT
* ** *
1840960 TAAGGGATTAGCATTTCCAGTAGAGAAC
66 CAAGGGACCAACATTTCCAGTAGAGAAC
*
1840988 TCATAATGAAGAACTTGTTCAACCTTTGCACGATTCATGACATTTCGAATCAGCAACGCCTCACT
1 TCATAATGAAGAACTTGTTCAACCTTTGCACGATTCACGACATTTCGAATCAGCAACGCCTCACT
1841053 CAAGGGACCAA
66 CAAGGGACCAA
1841064 TGTTTCTAGT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 66 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (93 bp):
TCATAATGAAGAACTTGTTCAACCTTTGCACGATTCACGACATTTCGAATCAGCAACGCCTCACT
CAAGGGACCAACATTTCCAGTAGAGAAC
Found at i:1844426 original size:16 final size:16
Alignment explanation
Indices: 1844405--1844439 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1844395 TGGTTTATAC
1844405 ATTAAAATTCACTTTA
1 ATTAAAATTCACTTTA
1844421 ATTAAAATTCACTTTA
1 ATTAAAATTCACTTTA
1844437 ATT
1 ATT
1844440 TGTAAGTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTAAAATTCACTTTA
Found at i:1846336 original size:17 final size:17
Alignment explanation
Indices: 1846314--1846354 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1846304 TTAATAAACT
1846314 TTCAAAATATTATTTTA
1 TTCAAAATATTATTTTA
*
1846331 TTCAAAATATTGTTTTA
1 TTCAAAATATTATTTTA
*
1846348 ATCAAAA
1 TTCAAAA
1846355 CATTGGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (17 bp):
TTCAAAATATTATTTTA
Found at i:1846359 original size:17 final size:17
Alignment explanation
Indices: 1846315--1846359 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1846305 TAATAAACTT
* *
1846315 TCAAAATATTATTTTAT
1 TCAAAATATTGTTTTAA
1846332 TCAAAATATTGTTTTAA
1 TCAAAATATTGTTTTAA
*
1846349 TCAAAACATTG
1 TCAAAATATTG
1846360 GATATAGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (17 bp):
TCAAAATATTGTTTTAA
Found at i:1852446 original size:16 final size:17
Alignment explanation
Indices: 1852425--1852458 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1852415 AGGTGTCACA
1852425 TTGACT-TTTCAAAACT
1 TTGACTATTTCAAAACT
*
1852441 TTGACTATTTGAAAACT
1 TTGACTATTTCAAAACT
1852458 T
1 T
1852459 ATTAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (17 bp):
TTGACTATTTCAAAACT
Found at i:1853059 original size:23 final size:24
Alignment explanation
Indices: 1853033--1853091 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1853023 CAGTCAAAAC
* * * *
1853033 TGCCACATAGAAT-TGCGCTGATG
1 TGCCACGTAGAATATGCACCGAAG
*
1853056 TGCCGCGTAGAATATGCACCGAAG
1 TGCCACGTAGAATATGCACCGAAG
1853080 TGCCACGTAGAA
1 TGCCACGTAGAA
1853092 ATGTCTCGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (24 bp):
TGCCACGTAGAATATGCACCGAAG
Found at i:1853112 original size:23 final size:23
Alignment explanation
Indices: 1853061--1853183 Score: 97
Period size: 23 Copynumber: 5.3 Consensus size: 23
1853051 TGATGTGCCG
1853061 CGTAGAATATG-CACCGAAGTG-CCA
1 CGTAGAA-ATGTC-CCGAAG-GACCA
*
1853085 CGTAGAAATGTCTCGAAGGACCA
1 CGTAGAAATGTCCCGAAGGACCA
* * *
1853108 TGTAGAAATATCCCGAATGACCA
1 CGTAGAAATGTCCCGAAGGACCA
* * *
1853131 CATAGGATTGTCCCGAAGGACCA
1 CGTAGAAATGTCCCGAAGGACCA
* * * * *
1853154 CATAGGATTGTCCTGAAGGACCG
1 CGTAGAAATGTCCCGAAGGACCA
1853177 CGTAGAA
1 CGTAGAA
1853184 CCCTCGACTC
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
22 1 0.01
23 73 0.89
24 8 0.10
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGTCCCGAAGGACCA
Found at i:1857076 original size:17 final size:17
Alignment explanation
Indices: 1857054--1857089 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1857044 TCACAAGATG
1857054 AAGACTCAACAAAAAGA
1 AAGACTCAACAAAAAGA
* *
1857071 AAGACTCATCAAAGAGA
1 AAGACTCAACAAAAAGA
1857088 AA
1 AA
1857090 TAAGTAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.17, G:0.14, T:0.08
Consensus pattern (17 bp):
AAGACTCAACAAAAAGA
Found at i:1857525 original size:44 final size:44
Alignment explanation
Indices: 1857457--1857614 Score: 210
Period size: 44 Copynumber: 3.6 Consensus size: 44
1857447 CCTCCACTTG
*
1857457 ATTCCATCACATAAAGAATTGGATCAACATCACCACTTTGCTCA
1 ATTCCATCACATAAAGAATTGGATCAACATAACCACTTTGCTCA
* * * *
1857501 ATTCTATCACATAAAGAGTTGGATCGACATAACCACTTTGCTCG
1 ATTCCATCACATAAAGAATTGGATCAACATAACCACTTTGCTCA
* * * *
1857545 ATTCCATCAAATAAAGAATTGGATCAACATTATCACTTCGCTCA
1 ATTCCATCACATAAAGAATTGGATCAACATAACCACTTTGCTCA
*
1857589 ATTCTATCACAT-AAGAAGTTGGATCA
1 ATTCCATCACATAAAGAA-TTGGATCA
1857615 GTATCATCTT
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 5 0.05
44 93 0.95
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (44 bp):
ATTCCATCACATAAAGAATTGGATCAACATAACCACTTTGCTCA
Found at i:1857987 original size:3 final size:3
Alignment explanation
Indices: 1857979--1858029 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
1857969 AATCACCATT
**
1857979 TTA TTA TTA TTA -TA TTA TTA TTA CCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1858026 TTA T
1 TTA T
1858030 CTTTTATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1859904 original size:30 final size:30
Alignment explanation
Indices: 1859853--1859909 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1859843 TTTATTCTGC
* *
1859853 CCTTTTATAATTCAGCTTTTACGTTTCAAT
1 CCTTTTATAATTCAACATTTACGTTTCAAT
*
1859883 CCTTTTA-AATTCTAACATTTACTTTTC
1 CCTTTTATAATTC-AACATTTACGTTTC
1859910 TGTTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.25, C:0.21, G:0.04, T:0.51
Consensus pattern (30 bp):
CCTTTTATAATTCAACATTTACGTTTCAAT
Found at i:1860914 original size:5 final size:5
Alignment explanation
Indices: 1860904--1860931 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1860894 GCAGTAAATA
1860904 AAGAG AAGAG AAGAG AAGAG AAGAG AAG
1 AAGAG AAGAG AAGAG AAGAG AAGAG AAG
1860932 CAAAAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (5 bp):
AAGAG
Found at i:1861065 original size:7 final size:7
Alignment explanation
Indices: 1861053--1861147 Score: 77
Period size: 7 Copynumber: 13.6 Consensus size: 7
1861043 TGTGATAAGA
1861053 TTTAGGG
1 TTTAGGG
1861060 TTTAGGG
1 TTTAGGG
1861067 TTTAGGG
1 TTTAGGG
1861074 TTTAGGG
1 TTTAGGG
**
1861081 TTTATATG
1 TTTA-GGG
* * *
1861089 ATGA-GA
1 TTTAGGG
* *
1861095 TTTAAGT
1 TTTAGGG
1861102 TTTAGGG
1 TTTAGGG
1861109 TTTAGGG
1 TTTAGGG
*
1861116 TTTA-TG
1 TTTAGGG
1861122 TATTAGGG
1 T-TTAGGG
*
1861130 GTTAGGG
1 TTTAGGG
1861137 TTTAGGG
1 TTTAGGG
1861144 TTTA
1 TTTA
1861148 AGTTATGTAC
Statistics
Matches: 69, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
6 4 0.06
7 61 0.88
8 4 0.06
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:1861109 original size:42 final size:42
Alignment explanation
Indices: 1861040--1861119 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
1861030 TTCCTTCTAA
* *
1861040 TTATGTGATAAGATTTAGGGTTTAGGGTTTAGGGTTTAGGGT
1 TTATATGATAAGATTTAAGGTTTAGGGTTTAGGGTTTAGGGT
* *
1861082 TTATATGATGAGATTTAAGTTTTAGGGTTTAGGGTTTA
1 TTATATGATAAGATTTAAGGTTTAGGGTTTAGGGTTTA
1861120 TGTATTAGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (42 bp):
TTATATGATAAGATTTAAGGTTTAGGGTTTAGGGTTTAGGGT
Found at i:1863119 original size:12 final size:12
Alignment explanation
Indices: 1863102--1863173 Score: 69
Period size: 12 Copynumber: 6.2 Consensus size: 12
1863092 AAACCTGTCT
*
1863102 AGCTCTGAATTG
1 AGCTCTGAATCG
1863114 AGCTCTGAATCG
1 AGCTCTGAATCG
**
1863126 AGCTCAAAATCG
1 AGCTCTGAATCG
1863138 AGCT-TGAATCG
1 AGCTCTGAATCG
*
1863149 AGCT-TAAAATCG
1 AGCTCT-GAATCG
*
1863161 AGCT-TCAATCG
1 AGCTCTGAATCG
1863172 AG
1 AG
1863174 TTCGAGTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
11 17 0.33
12 35 0.67
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (12 bp):
AGCTCTGAATCG
Found at i:1863149 original size:23 final size:23
Alignment explanation
Indices: 1863113--1863173 Score: 95
Period size: 23 Copynumber: 2.6 Consensus size: 23
1863103 GCTCTGAATT
1863113 GAGCTCTGAATCGAGCTCAAAATC
1 GAGCT-TGAATCGAGCTCAAAATC
*
1863137 GAGCTTGAATCGAGCTTAAAATC
1 GAGCTTGAATCGAGCTCAAAATC
*
1863160 GAGCTTCAATCGAG
1 GAGCTTGAATCGAG
1863174 TTCGAGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 30 0.86
24 5 0.14
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (23 bp):
GAGCTTGAATCGAGCTCAAAATC
Found at i:1863349 original size:32 final size:32
Alignment explanation
Indices: 1863267--1863349 Score: 125
Period size: 31 Copynumber: 2.6 Consensus size: 32
1863257 GGCTCGCGAG
* *
1863267 TTTTCGAGTTAAGTCGAGCTTAGATTTATAGT
1 TTTTCGAGTTGAGTCGAGTTTAGATTTATAGT
1863299 TTTT-GAGTTGAGTCGAGTTTAGATTTATA-T
1 TTTTCGAGTTGAGTCGAGTTTAGATTTATAGT
1863329 TTTTCGAGTTCGAGTCGAGTT
1 TTTTCGAGTT-GAGTCGAGTT
1863350 CAGTAATACT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
30 5 0.11
31 28 0.60
32 14 0.30
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.46
Consensus pattern (32 bp):
TTTTCGAGTTGAGTCGAGTTTAGATTTATAGT
Found at i:1869272 original size:29 final size:29
Alignment explanation
Indices: 1869240--1869337 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 29
1869230 TTTGTATATA
1869240 AATTTAAAATATTCAAAATTTTGAGGATC
1 AATTTAAAATATTCAAAATTTTGAGGATC
* * * *
1869269 AATTTAGAATATGTCATAGTTTTGA-GATG
1 AATTTAAAATAT-TCAAAATTTTGAGGATC
* * * * *
1869298 AAATTAGAATATTAAAAAATTTAAGGATC
1 AATTTAAAATATTCAAAATTTTGAGGATC
*
1869327 AATATAAAATA
1 AATTTAAAATA
1869338 AAAGTCATAG
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
28 7 0.13
29 36 0.68
30 10 0.19
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (29 bp):
AATTTAAAATATTCAAAATTTTGAGGATC
Found at i:1869294 original size:30 final size:28
Alignment explanation
Indices: 1869200--1869309 Score: 78
Period size: 29 Copynumber: 3.7 Consensus size: 28
1869190 ATTCAAAAGC
* *
1869200 TTGAGGATCAATTTAGAATGAGGGTCATAAT
1 TTGA-GATCAATTTAGAAT-A-TGTCATATT
* * * *
1869231 TTGTATATAAATTTAAAATAT-TCAAAATT
1 TTG-AGATCAATTTAGAATATGTC-ATATT
1869260 TTGAGGATCAATTTAGAATATGTCATAGTT
1 TTGA-GATCAATTTAGAATATGTCATA-TT
* *
1869290 TTGAGATGAAATTAGAATAT
1 TTGAGATCAATTTAGAATAT
1869310 TAAAAAATTT
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
28 3 0.05
29 35 0.56
30 9 0.15
31 14 0.23
32 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (28 bp):
TTGAGATCAATTTAGAATATGTCATATT
Found at i:1869326 original size:58 final size:58
Alignment explanation
Indices: 1869203--1869355 Score: 148
Period size: 58 Copynumber: 2.6 Consensus size: 58
1869193 CAAAAGCTTG
** * * * * *
1869203 AGGATCAATTTAGAATGAGGGTCATAATTTGTATATAAATTTAAAATATTCAAAATTTTG
1 AGGATCAATTTAGAAT-AAAGTCATAGTTTG-AGATAAATTTAAAATATTAAAAAATTTA
* *
1869263 AGGATCAATTTAGAAT-ATGTCATAGTTTTGAGATGAAA-TTAGAATATTAAAAAATTTA
1 AGGATCAATTTAGAATAAAGTCATAG-TTTGAGAT-AAATTTAAAATATTAAAAAATTTA
* *
1869321 AGGATCAATATAAAATAAAAGTCATAGTTTGAGAT
1 AGGATCAATTTAGAAT-AAAGTCATAGTTTGAGAT
1869356 TTATAGGTCT
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
58 39 0.50
59 15 0.19
60 24 0.31
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (58 bp):
AGGATCAATTTAGAATAAAGTCATAGTTTGAGATAAATTTAAAATATTAAAAAATTTA
Found at i:1870043 original size:182 final size:182
Alignment explanation
Indices: 1869654--1870255 Score: 929
Period size: 182 Copynumber: 3.3 Consensus size: 182
1869644 GATACAAATA
* * * *
1869654 AAAAATGTATCGATCCACATCCATATAATAGGTAAAAATATGACAAAACCGGTTTCAAAATGACA
1 AAAAATGTATCGATCCACAACAATATAATAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
** * * * * *
1869719 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGATTAGATTGAA-ATAAGTATCGGCACT
66 AAACCGGTAAAGCAATACCCGATATGTTGAAAGTGTCGA-TA-CTTTAATATAAGTATCGACACT
* *
1869783 TTTGGAATTTAAAAGAGAAG-AAGTAATATCGCCTATAAAGTGTCGATACTTTAT
129 TTTGGAATTTAAAAGAGAAGCAA-TAATAGCGCCTATAAAGTGTTGATACTTTAT
* * *
1869837 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGATCTCGAAATGACA
1 AAAAATGTATCGATCCACAACAATATAATAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
1869902 AAACCGGTAAAGCAATACCCGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
66 AAACCGGTAAAGCAATACCCGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
** *
1869967 TAAAATTTAAAAGAGAAGCAATAATAGCGCATATAAAGTGTTGATACTTTAT
131 TGGAATTTAAAAGAGAAGCAATAATAGCGCCTATAAAGTGTTGATACTTTAT
* *
1870019 AAAAATGTATCGATCCACAACAATATAAAAGGTAAAAATATGATAAAACCGGTCTCGAAATGACA
1 AAAAATGTATCGATCCACAACAATATAATAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
*
1870084 AAAACGGTAAAGCAATACCCGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
66 AAACCGGTAAAGCAATACCCGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
*
1870149 TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTGTCGATACTTTAT
131 TGGAATTTAAAAGAGAAGCAATAATAGCGCCTATAAAGTGT-T-GATACTTTAT
*
1870203 AAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACCGGT
1 AAAAATGTATCGATCCACAACAATATAATAGGTAAAAATATGACAAAACCGGT
1870256 AAAGCGCTAT
Statistics
Matches: 384, Mismatches: 31, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
181 4 0.01
182 224 0.58
183 96 0.25
184 60 0.16
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCACAACAATATAATAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
AAACCGGTAAAGCAATACCCGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
TGGAATTTAAAAGAGAAGCAATAATAGCGCCTATAAAGTGTTGATACTTTAT
Found at i:1872941 original size:27 final size:27
Alignment explanation
Indices: 1872920--1873004 Score: 145
Period size: 27 Copynumber: 3.2 Consensus size: 27
1872910 AAAAAATATG
1872920 AAGA-AGAAAAGATGGAGGAAAAAGAA
1 AAGATAGAAAAGATGGAGGAAAAAGAA
1872946 AAGATAGAAAAGATGGAGGAAAAAGAA
1 AAGATAGAAAAGATGGAGGAAAAAGAA
* *
1872973 AAGATAGAAAAGATGGAGGAAGAATAA
1 AAGATAGAAAAGATGGAGGAAAAAGAA
1873000 AAGAT
1 AAGAT
1873005 GAAGGAAGTG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
26 4 0.07
27 52 0.93
ACGTcount: A:0.62, C:0.00, G:0.29, T:0.08
Consensus pattern (27 bp):
AAGATAGAAAAGATGGAGGAAAAAGAA
Found at i:1874667 original size:66 final size:66
Alignment explanation
Indices: 1874579--1874756 Score: 286
Period size: 66 Copynumber: 2.7 Consensus size: 66
1874569 TTGTATCTAA
* * *
1874579 ATGTAATTATGTTTGAGGTGAGAAAAGCTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
1874644 G
66 G
* * *
1874645 ATGTAATTATGTATGAGATGAGAAAAATTAACAATAGGTTGTTATACATGTTTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
1874710 G
66 G
1874711 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAAT-GGATTGTTGTA
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGG-TTGTTGTA
1874757 TCTGAATGTA
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
65 2 0.02
66 100 0.98
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (66 bp):
ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
G
Found at i:1875501 original size:201 final size:200
Alignment explanation
Indices: 1875075--1875517 Score: 636
Period size: 201 Copynumber: 2.2 Consensus size: 200
1875065 TTATTGACAC
* * * * *
1875075 ATTATAAAGTAATAGGTAAATTTACAATGTAACCGGTAAAAATATACCGATTTTATGAGAAAATA
1 ATTATAATGTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGATTTAATGAGAAAATA
* **
1875140 GGTCAACATAATGTATCGATATTTTTATAAATTGTGTCGATACTTTTTATCCAGAATGAATGTCA
66 GGTCAACATAATGTATCGACATTTTTATAAATTGTGTCGATACTTTTTATCCAGAATGAATCCCA
* * *
1875205 AACGAAATGCACACATAAAGTGTCGATACATTTATAAAAAGTATCGATCCTAAAAACATCGAAAC
131 AACGAAATGCACACATAAAGGGTCGATACATTTATAAAAAGTAGCGATCCCAAAAACATCGAAAC
1875270 CCATA
196 CCATA
* * * * *
1875275 ATTATAATGTAATAGGTAGTTTTGCAATGTAACTGGTATAAATATATCGGTTTAATTAGAAAATA
1 ATTATAATGTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGATTTAATGAGAAAATA
* * *
1875340 TGTCAACATAATGTATCGACACTTTTTA-AATTTGTGTCGATACTTTTTGTCCAGAATGAATACC
66 GGTCAACATAATGTATCGACA-TTTTTATAAATTGTGTCGATACTTTTTATCCAGAATGAAT-CC
** * *
1875404 CAAACGAGGTGCACGCATAAAGGGTCGATACATTTATAAAAAGTAGCGATCCCAAAAATATCGAA
129 CAAACGAAATGCACACATAAAGGGTCGATACATTTATAAAAAGTAGCGATCCCAAAAACATCGAA
1875469 ACCCATA
194 ACCCATA
* *
1875476 ATTATAATGTAATAGGTAATTTTGCAATATAACCAGTATAAA
1 ATTATAATGTAATAGGTAATTTTGCAATGTAACCGGTATAAA
1875518 CACATCAGTT
Statistics
Matches: 214, Mismatches: 27, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
200 105 0.49
201 109 0.51
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (200 bp):
ATTATAATGTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGATTTAATGAGAAAATA
GGTCAACATAATGTATCGACATTTTTATAAATTGTGTCGATACTTTTTATCCAGAATGAATCCCA
AACGAAATGCACACATAAAGGGTCGATACATTTATAAAAAGTAGCGATCCCAAAAACATCGAAAC
CCATA
Found at i:1875656 original size:129 final size:129
Alignment explanation
Indices: 1875405--1875662 Score: 304
Period size: 129 Copynumber: 2.0 Consensus size: 129
1875395 ATGAATACCC
* * * *
1875405 AAACGAGGTGCACGCATAAAGGGTCGATACATTTATAAAAAGTAGCGATCCCAAAAATATCGAAA
1 AAACAAGGCGCACGCAAAAAGGGTCGATACATTTATAAAAAGTAGCGATCCCAAAAACATCGAAA
* * ** *
1875470 CCCATAATTATAATGTAATAGGTAATTTTGCAATATAACCAGTATAAACACATCAGTTTTATGAG
66 CCCATAATTACAATGTAATAGGTAAATTAACAATATAACCAGTAGAAACACA-CAGTTTTATGAG
* * ** **
1875535 AAACAAGGCGCACGCAAAAAGTGTCGATACATTTA-CAATTGTATTGATCCCAAAAACATCGAAA
1 AAACAAGGCGCACGCAAAAAGGGTCGATACATTTATAAAAAGTAGCGATCCCAAAAACATCGAAA
* * **
1875599 CCGATAATTACAATGTAATAGGTAAATTAACAATGTAACTGGTAGAAATCTAC-CAGTTTTATGA
66 CCCATAATTACAATGTAATAGGTAAATTAACAATATAACCAGTAGAAA-C-ACACAGTTTTATGA
1875663 TAAAATAGGT
Statistics
Matches: 107, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
129 73 0.68
130 32 0.30
131 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (129 bp):
AAACAAGGCGCACGCAAAAAGGGTCGATACATTTATAAAAAGTAGCGATCCCAAAAACATCGAAA
CCCATAATTACAATGTAATAGGTAAATTAACAATATAACCAGTAGAAACACACAGTTTTATGAG
Found at i:1875954 original size:198 final size:197
Alignment explanation
Indices: 1875535--1876089 Score: 688
Period size: 199 Copynumber: 2.8 Consensus size: 197
1875525 GTTTTATGAG
* * * * *
1875535 AAACAAGGCGCACGCAA-AAAGTGTCGATACATTTACAATTGTATTGATCCCAAAAACATCGAAA
1 AAACGAGGTGCACG-AATAAAGTGTCGATACATTTAAAATTGTATCGATCCTAAAAACATCGAAA
* *
1875599 CCGATAATTACAATGTAATAGGTAAA-TTAACAATGTAACTGGTAGAAATCTACCAGTTTTATGA
65 CCGATAATTACAATGTAATAGGTAAATTTAA-AATGTAAC-GGTAGAAATATACCGGTTTTATGA
** *
1875663 TAAAATAGGTCTACATAAAGTATCGACACAAATTTAGAAAGTGTCGATACTTTTAGTCCACAATG
128 -GGAATAGGTCTACATAAAGTATCGACACAAATTTAGAAAGTGTCGATACTTTTAGTCCACAATA
1875728 ATGCCA
192 ATGCCA
* * *
1875734 AAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCTAAAAATATCGAAAC
1 AAACGAGGTGCACGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCTAAAAACATCGAAAC
* * *
1875799 CAATAATTACAATGTAATAGGTAAATTTAAAATGTAACGGTATAAATATACTGGTTTTATGAGGA
66 CGATAATTACAATGTAATAGGTAAATTTAAAATGTAACGGTAGAAATATACCGGTTTTATGAGGA
* * * * *
1875864 AGTAGGTCTACGTAAAGTATCGACACAAATTTATAAAGTGTCGATATTTTTTGTCCAGAATAAAT
131 A-TAGGTCTACATAAAGTATCGACACAAATTTAGAAAGTGTCGATACTTTTAGTCCACAAT-AAT
1875929 GCC-
194 GCCA
* * * *
1875932 CAACGAGGTGCACGAATAAAGTGTCAATACATTTATTAAA-AGTATCGATCCTAAAAACATCAAA
1 AAACGAGGTGCACGAATAAAGTGTCGATACATTTA--AAATTGTATCGATCCTAAAAACATCGAA
* ** * *
1875996 ACCGATAATTAAAATGTAATAGGTAAATTTACGATGTACCCGGTAGAAATATACCGATTTTATGA
64 ACCGATAATTACAATGTAATAGGTAAATTTAAAATGTA-ACGGTAGAAATATACCGGTTTTATGA
* *
1876061 GAGAATAGGTCAACA-AAATATATCGACAC
128 G-GAATAGGTCTACATAAA-GTATCGACAC
1876090 TTTTTAAATT
Statistics
Matches: 309, Mismatches: 38, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
197 2 0.01
198 106 0.34
199 151 0.49
200 47 0.15
201 3 0.01
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (197 bp):
AAACGAGGTGCACGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCTAAAAACATCGAAAC
CGATAATTACAATGTAATAGGTAAATTTAAAATGTAACGGTAGAAATATACCGGTTTTATGAGGA
ATAGGTCTACATAAAGTATCGACACAAATTTAGAAAGTGTCGATACTTTTAGTCCACAATAATGC
CA
Found at i:1879581 original size:18 final size:20
Alignment explanation
Indices: 1879558--1879594 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1879548 TATCGAAACC
1879558 AGAT-AATT-ACAATGTAAT
1 AGATAAATTAACAATGTAAT
1879576 AGATAAATTAACAATGTAA
1 AGATAAATTAACAATGTAA
1879595 CCGGTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.54, C:0.05, G:0.11, T:0.30
Consensus pattern (20 bp):
AGATAAATTAACAATGTAAT
Found at i:1879786 original size:198 final size:199
Alignment explanation
Indices: 1879413--1879872 Score: 642
Period size: 199 Copynumber: 2.3 Consensus size: 199
1879403 CAAATATATT
* * *
1879413 GGTTAATTAGAAAATAGGTCTACATAATATAGCAACACTATTTAAATTTGTGTCGTTACTTTTTT
1 GGTTAATTAGAAAATAGGTCTACATAATGTAGCAACACTATTTAAATTTGTGTCGATACTTTTGT
1879478 CCAGAATGAATGCCAAATGGGGTGCACGCATAAAGTGTCGATACATTTTAAATATTATCGATCCC
66 CCAGAATGAATGCCAAATGGGGTGCACGCATAAAGTGTCGATACATTTTAAATATTATCGATCCC
* *
1879543 AAAAATATCGAAACCAGATAATTACAATGTAATAGATAAATTAACAATGTAACCGGTATAAATTT
131 AAAAATATCGAAACCAGATAAATACAATGTAATAGATAAATTAACAATGTAACCGATATAAATTT
*
1879608 AC-C
196 ACTA
* ** * *
1879611 GGTTAATTAGAAAATAGGTCTGCATAATGTAGTGAGACTTTTTAAATTTGTGTCGATACCTTTTG
1 GGTTAATTAGAAAATAGGTCTACATAATGTAGCAACACTATTTAAATTTGTGTCGATA-CTTTTG
* *
1879676 TCCAGAATGAATGCC-AATCGGGGTGCACGTATAAAGTGTTGATACATTTTAAAT-TGTATCGAT
65 TCCAGAATGAATGCCAAAT-GGGGTGCACGCATAAAGTGTCGATACATTTTAAATAT-TATCGAT
* *
1879739 CCCAAAAATATCTAAACC-GATAAATATAATGTAATAGATAAATTAACAATGTAACCGATATAAA
128 CCCAAAAATATCGAAACCAGATAAATACAATGTAATAGATAAATTAACAATGTAACCGATATAAA
1879803 TTTACTA
193 TTTACTA
* * * * * * * *
1879810 GTTTTATGAGAAAATAAGTCTACATAATGTATCAACA-AATTTTAAATTTGTATCGATATTTTT
1 GGTTAATTAGAAAATAGGTCTACATAATGTAGCAACACTA-TTTAAATTTGTGTCGATACTTTT
1879873 TTAAACTTCA
Statistics
Matches: 229, Mismatches: 28, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
198 107 0.47
199 122 0.53
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (199 bp):
GGTTAATTAGAAAATAGGTCTACATAATGTAGCAACACTATTTAAATTTGTGTCGATACTTTTGT
CCAGAATGAATGCCAAATGGGGTGCACGCATAAAGTGTCGATACATTTTAAATATTATCGATCCC
AAAAATATCGAAACCAGATAAATACAATGTAATAGATAAATTAACAATGTAACCGATATAAATTT
ACTA
Found at i:1884591 original size:198 final size:199
Alignment explanation
Indices: 1884132--1884625 Score: 615
Period size: 198 Copynumber: 2.5 Consensus size: 199
1884122 GTAAACATAT
* * * *
1884132 GTGTCGATACAATTTATAAAAATATCGA-CCC--CAA-ATCGAAACCAATAATTATAATATAATA
1 GTGTCGATAC-ATTTATAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * *
1884193 GGTAAATTAACAATGTAACCGGTATAAATATACCGGTTAATTACAAAACAGATCAACATAATGTA
65 GGTAAATTTACAATGTAACCGATATAAATATACCGGTTAATGACAAAACAGATCAACAAAATGTA
* * * *
1884258 TCGACACTTGTGGAATTTGGGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACAC
130 TCAACACTTGTGAAATTTGGGTCGATACTTATTGTCCAGAATAAATGCCCAAACGAAGTGCACAC
*
1884323 ATGAA
195 ATAAA
*
1884328 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACTGATAATTATAATGTAATA
1 GTGTCGATACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * * *
1884393 GGTAAATTTACAATGTAACCGATATAAATATATCGGTTTTATGAGAGAATAGGTCAACAAAATGT
65 GGTAAATTTACAATGTAACCGATATAAATATACCGG-TTAATGACAAAACAGATCAACAAAATGT
* * * * * *
1884458 ATCAACACTTTTTAAATTTGTGTCGATACTT-TTTTCCAGAATAAATG-CCTAACGAAGTGCACG
129 ATCAACACTTGTGAAATTTGGGTCGATACTTATTGTCCAGAATAAATGCCCAAACGAAGTGCACA
1884521 CATAAA
194 CATAAA
* *
1884527 GTGTCGATACATTTA-AAATTGTATCGATCTCAAAAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * *
1884591 GATAAATTTGCAATGTTACCGATATAAATAAACCG
65 GGTAAATTTACAATGTAACCGATATAAATATACCG
1884626 ATTTAGTTCA
Statistics
Matches: 257, Mismatches: 34, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
195 5 0.02
196 21 0.08
197 6 0.02
198 72 0.28
199 35 0.14
200 71 0.28
201 47 0.18
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (199 bp):
GTGTCGATACATTTATAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGATATAAATATACCGGTTAATGACAAAACAGATCAACAAAATGTAT
CAACACTTGTGAAATTTGGGTCGATACTTATTGTCCAGAATAAATGCCCAAACGAAGTGCACACA
TAAA
Found at i:1884803 original size:23 final size:23
Alignment explanation
Indices: 1884730--1884793 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
1884720 TACATATTTT
1884730 ATTATATAAACGCTACCTATTAC
1 ATTATATAAACGCTACCTATTAC
*
1884753 ATTATATAAACGGTACCTATTAC
1 ATTATATAAACGCTACCTATTAC
*
1884776 ATTATATAAGCGCTACCT
1 ATTATATAAACGCTACCT
1884794 TATATATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (23 bp):
ATTATATAAACGCTACCTATTAC
Found at i:1888351 original size:37 final size:36
Alignment explanation
Indices: 1888282--1888355 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 36
1888272 CATTAAACCT
1888282 TTTTATATTTTCAATTTTGTAAAAAAATTATATAAA
1 TTTTATATTTTCAATTTTGTAAAAAAATTATATAAA
*
1888318 TTTTATGATTTT-AATTTTTTTAAAGAAAA-TATATAAA
1 TTTTAT-ATTTTCAA-TTTTGTAAA-AAAATTATATAAA
1888355 T
1 T
1888356 ATTTTTCAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 8 0.24
37 22 0.65
38 4 0.12
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (36 bp):
TTTTATATTTTCAATTTTGTAAAAAAATTATATAAA
Found at i:1888614 original size:21 final size:20
Alignment explanation
Indices: 1888590--1888645 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 20
1888580 GTGGCATACA
1888590 ATATTGATGTGGTAATTTATG
1 ATATTGATGT-GTAATTTATG
1888611 ATATT-A----TAATTTATG
1 ATATTGATGTGTAATTTATG
1888626 ATATTGATGTGATAATTTAT
1 ATATTGATGTG-TAATTTAT
1888646 ACTATTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
15 14 0.48
16 1 0.03
20 1 0.03
21 13 0.45
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (20 bp):
ATATTGATGTGTAATTTATG
Found at i:1888663 original size:36 final size:36
Alignment explanation
Indices: 1888590--1888664 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
1888580 GTGGCATACA
* * *
1888590 ATATTGATGTGGTAATTTATGATATTATAATTTATG
1 ATATTGATGTGATAATTTATGATATTATAAATGATG
1888626 ATATTGATGTGATAATTTAT-ACTATT-TAAAATGATG
1 ATATTGATGTGATAATTTATGA-TATTAT-AAATGATG
1888662 ATA
1 ATA
1888665 ATTCATATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 2 0.06
36 32 0.94
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (36 bp):
ATATTGATGTGATAATTTATGATATTATAAATGATG
Found at i:1888733 original size:2 final size:2
Alignment explanation
Indices: 1888726--1888762 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1888716 ATATAATGTT
1888726 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1888763 TGAGAGAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1890180 original size:39 final size:39
Alignment explanation
Indices: 1890123--1890220 Score: 124
Period size: 39 Copynumber: 2.5 Consensus size: 39
1890113 AGGGCCTACA
* * *
1890123 GTAAGAACTTACCTTGTGCACAAAGCAGAGGAGTCTGCG
1 GTAAGGACTTACCCTGTGCACAAAGCAAAGGAGTCTGCG
* *
1890162 GTAAGGGCTTACCCTGTGCACAAAGCAAAGGAGTCTTCG
1 GTAAGGACTTACCCTGTGCACAAAGCAAAGGAGTCTGCG
* * *
1890201 TTAAGGATTTACCCTATGCA
1 GTAAGGACTTACCCTGTGCA
1890221 AGAAATAGAG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (39 bp):
GTAAGGACTTACCCTGTGCACAAAGCAAAGGAGTCTGCG
Found at i:1892188 original size:18 final size:18
Alignment explanation
Indices: 1892165--1892218 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
1892155 GAGGGATTAT
1892165 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
1892183 CAGTGGTTCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
1892201 CAGTGGTCCTACGGGACA
1 CAGTGGTCCTTCGGGACA
1892219 AATTTCTACG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.22
Consensus pattern (18 bp):
CAGTGGTCCTTCGGGACA
Found at i:1899895 original size:18 final size:18
Alignment explanation
Indices: 1899874--1899916 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
1899864 TAATAGCGAA
1899874 TTATTATAAAATATATTT
1 TTATTATAAAATATATTT
*
1899892 TTATTAT-AATTATATTT
1 TTATTATAAAATATATTT
*
1899909 TTTTTATA
1 TTATTATA
1899917 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATTATAAAATATATTT
Found at i:1900868 original size:21 final size:20
Alignment explanation
Indices: 1900832--1900888 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1900822 TTTAATCTAT
*
1900832 AATTTAAAAGCATAAATCATA
1 AATTTAAAA-CTTAAATCATA
* *
1900853 AACTTTAAACCTTAAATTATA
1 AA-TTTAAAACTTAAATCATA
*
1900874 TATTTAAAACTTAAA
1 AATTTAAAACTTAAA
1900889 ATTCAAATCT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 12 0.40
21 12 0.40
22 6 0.20
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.35
Consensus pattern (20 bp):
AATTTAAAACTTAAATCATA
Found at i:1901223 original size:31 final size:29
Alignment explanation
Indices: 1901188--1901251 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 29
1901178 ATTATTTTTG
* *
1901188 TTTTTATTTCATTAAGATGTGATCACGTTTA
1 TTTTTATTTAATTAAAATGTGATCAC--TTA
1901219 TTTTTATTTAATTAAAATGTGATCACTTA
1 TTTTTATTTAATTAAAATGTGATCACTTA
1901248 TTTT
1 TTTT
1901252 ATCGACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 7 0.23
31 24 0.77
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.55
Consensus pattern (29 bp):
TTTTTATTTAATTAAAATGTGATCACTTA
Found at i:1904621 original size:27 final size:27
Alignment explanation
Indices: 1904570--1904685 Score: 157
Period size: 27 Copynumber: 4.4 Consensus size: 27
1904560 CACGAACGTT
* *
1904570 AAACGAACACGTTTGCAAATAATAAAC
1 AAACGAATACGTTTGCAAATGATAAAC
* *
1904597 AAATGAATATGTTTGCAAATGATAAAC
1 AAACGAATACGTTTGCAAATGATAAAC
1904624 AAACGAATACGTTTGCAAATGATAAAC
1 AAACGAATACGTTTGCAAATGATAAAC
* *
1904651 AAACAAATACATTTGCAAAT--T-AAC
1 AAACGAATACGTTTGCAAATGATAAAC
1904675 AAACGAATACG
1 AAACGAATACG
1904686 GTTTCGTTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
24 12 0.15
25 1 0.01
27 66 0.84
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (27 bp):
AAACGAATACGTTTGCAAATGATAAAC
Found at i:1909820 original size:59 final size:59
Alignment explanation
Indices: 1909715--1909847 Score: 153
Period size: 59 Copynumber: 2.3 Consensus size: 59
1909705 GTCGGATGAA
* * * *
1909715 CATTTTGTAACTTTTAATAGTTAGGGACTTCATAAAATAATGTCTTATAATCGAGAGA-
1 CATTTTGTAACTTTTAATAGTCAGAGACTTCATAAAACAATATCTTATAATCGAGAGAT
* * * * *
1909773 CTATTTTGTAACTTTTAATAGTCCGAGAC-TCAATTAAACAATATCTTATAGTTGAGGGAT
1 C-ATTTTGTAACTTTTAATAGTCAGAGACTTC-ATAAAACAATATCTTATAATCGAGAGAT
1909833 CATTTTGTAACTTTT
1 CATTTTGTAACTTTT
1909848 TAAAGTATAA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
58 3 0.05
59 59 0.94
60 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (59 bp):
CATTTTGTAACTTTTAATAGTCAGAGACTTCATAAAACAATATCTTATAATCGAGAGAT
Found at i:1911563 original size:19 final size:20
Alignment explanation
Indices: 1911539--1911589 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1911529 AATGACCAAT
1911539 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* * *
1911558 AAAATCGTAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
1911578 AAAATCGCAACG
1 AAAATCGCAACG
1911590 TTAAAAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:1911583 original size:20 final size:20
Alignment explanation
Indices: 1911539--1911754 Score: 143
Period size: 20 Copynumber: 10.6 Consensus size: 20
1911529 AATGACCAAT
* *
1911539 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
1911558 AAAATCGTAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1911578 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1911598 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
1911618 AAAATCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
*
1911641 AAAATCGCAATG-GATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1911663 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
1911683 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1911703 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
1911723 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
1911743 AAAATCGCAACG
1 AAAATCGCAACG
1911755 TTAAAAAGAA
Statistics
Matches: 163, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.10
20 107 0.66
21 1 0.01
22 23 0.14
23 16 0.10
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1911764 original size:20 final size:20
Alignment explanation
Indices: 1911741--1911784 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1911731 AACGCGATTT
*
1911741 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
1911761 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
1911781 AGAA
1 AGAA
1911785 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:1911870 original size:6 final size:6
Alignment explanation
Indices: 1911859--1911916 Score: 102
Period size: 6 Copynumber: 10.0 Consensus size: 6
1911849 GAAGACACGT
1911859 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
1911907 -CGACC -CGACC
1 ACGACC ACGACC
1911917 CGAGACGAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.19
6 42 0.81
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:1912618 original size:6 final size:6
Alignment explanation
Indices: 1912607--1912699 Score: 186
Period size: 6 Copynumber: 15.5 Consensus size: 6
1912597 TCTCGTCTCG
1912607 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1912655 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1912700 AATACGTGTC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 87 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1912814 original size:20 final size:20
Alignment explanation
Indices: 1912789--1912919 Score: 154
Period size: 20 Copynumber: 6.4 Consensus size: 20
1912779 CTTTTGACCG
1912789 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTATAAATCGCA
* * *
1912809 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATAAATCGCA
* *
1912829 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TATAAATCGCA
* * *
1912852 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTATAAATCGCA
1912872 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTATAAATCGCA
*
1912892 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATAAATCGCA
1912912 TTGCGATT
1 TTGCGATT
1912920 TTCTTCTAAA
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
20 76 0.80
21 2 0.02
22 3 0.03
23 14 0.15
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTATAAATCGCA
Found at i:1912833 original size:40 final size:40
Alignment explanation
Indices: 1912789--1912919 Score: 190
Period size: 40 Copynumber: 3.2 Consensus size: 40
1912779 CTTTTGACCG
*
1912789 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
* * *
1912829 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TTC-TATAAATCGCATTGCGATTCTCTCAATCGCA
*
1912872 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
1912912 TTGCGATT
1 TTGCGATT
1912920 TTCTTCTAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
40 41 0.51
41 3 0.04
42 3 0.04
43 33 0.41
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (40 bp):
TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:1912850 original size:43 final size:43
Alignment explanation
Indices: 1912800--1912940 Score: 207
Period size: 43 Copynumber: 3.3 Consensus size: 43
1912790 TGCGATTCTA
*
1912800 TAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTC
1 TAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTTTCTTC
* * *
1912843 TAAATCGCGTTGCGACTCTCTCAATCGCATTGCGA--TTC-TA
1 TAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTTTCTTC
*
1912883 TAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTC
1 TAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTTTCTTC
*
1912926 TAAATCGCGTTGCGA
1 TAAATCGCATTGCGA
1912941 ACTTGGAAGC
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
40 33 0.38
41 3 0.03
42 3 0.03
43 47 0.55
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (43 bp):
TAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTTTCTTC
Found at i:1912979 original size:20 final size:20
Alignment explanation
Indices: 1912954--1913007 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1912944 TGGAAGCTCG
*
1912954 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
1912974 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
*
1912994 CGTTGTGATTTTCT
1 CGTTGCGATTTTCT
1913008 AAATCGGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.17, G:0.19, T:0.54
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:1920324 original size:24 final size:24
Alignment explanation
Indices: 1920283--1920328 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1920273 TTATCTTAGC
*
1920283 ACTTTATGTTTATCTATGTTTGGT
1 ACTTTATGTTCATCTATGTTTGGT
1920307 ACTTTATGTTCA-CTTATGTTTG
1 ACTTTATGTTCATC-TATGTTTG
1920329 AACTATTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.17, C:0.11, G:0.15, T:0.57
Consensus pattern (24 bp):
ACTTTATGTTCATCTATGTTTGGT
Found at i:1922114 original size:33 final size:33
Alignment explanation
Indices: 1922065--1922137 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
1922055 TTTTTTAAAA
* *
1922065 AAATTCGGGTTCGGTCGGGTTTTTTTAAGTTTG
1 AAATTCGGGTTCGGTCGAGTTTTTTTAAGTGTG
*
1922098 ATATTCGGG-TCGGGTCGAGTTTTTTTAAGTGTG
1 AAATTCGGGTTC-GGTCGAGTTTTTTTAAGTGTG
1922131 AAATTCG
1 AAATTCG
1922138 TGTAACACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 2 0.06
33 33 0.94
ACGTcount: A:0.18, C:0.10, G:0.30, T:0.42
Consensus pattern (33 bp):
AAATTCGGGTTCGGTCGAGTTTTTTTAAGTGTG
Found at i:1923058 original size:5 final size:5
Alignment explanation
Indices: 1923048--1923790 Score: 1403
Period size: 5 Copynumber: 149.6 Consensus size: 5
1923038 CATGCCTGAA
1923048 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1923098 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT C--AT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1923146 CATAT CATAT CATAT CATAT C--AT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1923194 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1923244 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1923294 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1923344 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1923394 CATAT CATAT CATAT CATAT CATAT CATAT CATAT C--AT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1923442 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1923492 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT C--ATAT CATAT CATAT
1923544 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1923594 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1923644 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1923694 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1923744 CATAT CATAT CATAT CATAT CATAT CATA- -ATAT CATAT CATCAT CAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CAT-AT CAT
1923791 CATTCATGTC
Statistics
Matches: 727, Mismatches: 0, Indels: 21
0.97 0.00 0.03
Matches are distributed among these distances:
3 12 0.02
5 705 0.97
6 5 0.01
7 5 0.01
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
CATAT
Found at i:1928683 original size:16 final size:15
Alignment explanation
Indices: 1928659--1928692 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1928649 TAGCTCATAT
1928659 ATACATCACATAGCAC
1 ATACATCACATAG-AC
*
1928675 ATACTTCACATAGAC
1 ATACATCACATAGAC
1928690 ATA
1 ATA
1928693 TAAAAACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.44, C:0.26, G:0.06, T:0.24
Consensus pattern (15 bp):
ATACATCACATAGAC
Found at i:1931998 original size:24 final size:23
Alignment explanation
Indices: 1931936--1931999 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
1931926 TCCCCTTGAA
*
1931936 GTGCATCGATGCATCC-TACCGT
1 GTGCATCGATGCATCCTTAACGT
1931958 GT--ATCGATGCATCCCTTAACGT
1 GTGCATCGATGCAT-CCTTAACGT
1931980 GTGCATCGATGCACTCCTTA
1 GTGCATCGATGCA-TCCTTA
1932000 TGCATCGATG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 10 0.28
21 2 0.06
22 9 0.25
24 14 0.39
25 1 0.03
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (23 bp):
GTGCATCGATGCATCCTTAACGT
Found at i:1940516 original size:2 final size:2
Alignment explanation
Indices: 1940505--1940540 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1940495 AATGGTTTAC
1940505 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1940541 TTTGAAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1940811 original size:20 final size:20
Alignment explanation
Indices: 1940786--1940823 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1940776 ATTGAGAAGG
1940786 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
*
1940806 GATGCATCGATGCACTCA
1 GATGCACCGATGCACTCA
1940824 CCATATCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:1944679 original size:196 final size:196
Alignment explanation
Indices: 1944345--1944733 Score: 760
Period size: 196 Copynumber: 2.0 Consensus size: 196
1944335 TTTTTGGGCA
1944345 GAAGCCACAAATACCGCTTGTTATGTTATTAATCGAGTAATGATTAGGCCTATTTTGAAGAAAAC
1 GAAGCCACAAATACCGCTTGTTATGTTATTAATCGAGTAATGATTAGGCCTATTTTGAAGAAAAC
*
1944410 TCCATATGAACTTTTTAAAATTAAAAAGCCTAACATCAGTTATTTTCATCCTTTTGGATATAAAT
66 TCCATATGAACATTTTAAAATTAAAAAGCCTAACATCAGTTATTTTCATCCTTTTGGATATAAAT
*
1944475 GTTTTGTTTTAAACAACGGTAAAGACAATCTTGGCAAATTTGATGCTAAAAGTGATGAAGGAAGC
131 GTTTTGTTTTAAACAACGATAAAGACAATCTTGGCAAATTTGATGCTAAAAGTGATGAAGGAAGC
1944540 G
196 G
1944541 GAAGCCACAAATACCGCTTGTTATGTTATTAATCGAGTAATGATTAGGCCTATTTTGAAGAAAAC
1 GAAGCCACAAATACCGCTTGTTATGTTATTAATCGAGTAATGATTAGGCCTATTTTGAAGAAAAC
1944606 TCCATATGAACATTTTAAAATTAAAAAGCCTAACATCAGTTATTTTCATCCTTTTGGATATAAAT
66 TCCATATGAACATTTTAAAATTAAAAAGCCTAACATCAGTTATTTTCATCCTTTTGGATATAAAT
1944671 GTTTTGTTTTAAACAACGATAAAGACAATCTTGGCAAATTTGATGCTAAAAGTGATGAAGGAA
131 GTTTTGTTTTAAACAACGATAAAGACAATCTTGGCAAATTTGATGCTAAAAGTGATGAAGGAA
1944734 TTTTTCTGGG
Statistics
Matches: 191, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
196 191 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (196 bp):
GAAGCCACAAATACCGCTTGTTATGTTATTAATCGAGTAATGATTAGGCCTATTTTGAAGAAAAC
TCCATATGAACATTTTAAAATTAAAAAGCCTAACATCAGTTATTTTCATCCTTTTGGATATAAAT
GTTTTGTTTTAAACAACGATAAAGACAATCTTGGCAAATTTGATGCTAAAAGTGATGAAGGAAGC
G
Found at i:1946984 original size:45 final size:44
Alignment explanation
Indices: 1946908--1947005 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 44
1946898 TTGTGCATAA
* **
1946908 TGCATCGATACATTATGAAAGTGCATTGATGCATC-CCTTTGAATG
1 TGCATCGATACATCATGAAAGTGCACCGATGCA-CGCC-TTGAATG
1946953 TGCATCGATACATCATG-AAGATGCACCGATGCACGCCTTGAATG
1 TGCATCGATACATCATGAAAG-TGCACCGATGCACGCCTTGAATG
1946997 TGCATCGAT
1 TGCATCGAT
1947006 GCACAAGGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
44 20 0.42
45 28 0.58
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
TGCATCGATACATCATGAAAGTGCACCGATGCACGCCTTGAATG
Found at i:1949090 original size:20 final size:20
Alignment explanation
Indices: 1949067--1949117 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1949057 AATGATGGAC
1949067 CGATGCACTCATCGATGCAT
1 CGATGCACTCATCGATGCAT
*
1949087 CGATGCACTCATTGATGCAT
1 CGATGCACTCATCGATGCAT
1949107 CGATGCACTCA
1 CGATGCACTCA
1949118 CCATATCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (20 bp):
CGATGCACTCATCGATGCAT
Found at i:1949266 original size:64 final size:62
Alignment explanation
Indices: 1949122--1949268 Score: 163
Period size: 64 Copynumber: 2.3 Consensus size: 62
1949112 CACTCACCAT
* ** * *
1949122 ATCGAATGCATTTTATGCATCGATGATTACCATCCATCGATGCACTTAGGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCAATGAAGACCATCCATAGATGCACTCAGGTTTTATGAAAAC
* ** *
1949184 ATCGAATGGATTGCATGCATCAATGCACAGACCATGCATAGATGCACTCAGGCTTGTT-T-AAAA
1 ATCGAATGCATTTTATGCATCAATG-A-AGACCATCCATAGATGCACTCAGG-TT-TTATGAAAA
1949247 C
62 C
1949248 ATCGAATGCATTTTATGCATC
1 ATCGAATGCATTTTATGCATC
1949269 GATGGACTCT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
62 21 0.30
63 1 0.01
64 42 0.61
65 3 0.04
66 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (62 bp):
ATCGAATGCATTTTATGCATCAATGAAGACCATCCATAGATGCACTCAGGTTTTATGAAAAC
Found at i:1956560 original size:15 final size:15
Alignment explanation
Indices: 1956540--1956579 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
1956530 TTTGACTGCT
1956540 TTTGGATTGTTTTAC
1 TTTGGATTGTTTTAC
1956555 TTTGGATTGTTTTAC
1 TTTGGATTGTTTTAC
1956570 TTTGG-TTGTT
1 TTTGGATTGTT
1956580 GAATGTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.10, C:0.05, G:0.23, T:0.62
Consensus pattern (15 bp):
TTTGGATTGTTTTAC
Found at i:1957306 original size:18 final size:18
Alignment explanation
Indices: 1957298--1957367 Score: 131
Period size: 18 Copynumber: 3.9 Consensus size: 18
1957288 GAATGCATTT
1957298 TATGCATCGATGCACTAC
1 TATGCATCGATGCACTAC
1957316 TATGCATCGATGCACTAC
1 TATGCATCGATGCACTAC
*
1957334 TACGCATCGATGCACTAC
1 TATGCATCGATGCACTAC
1957352 TATGCATCGATGCACT
1 TATGCATCGATGCACT
1957368 CAGGTTTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (18 bp):
TATGCATCGATGCACTAC
Found at i:1958632 original size:16 final size:16
Alignment explanation
Indices: 1958613--1958644 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1958603 AATTTTACGA
1958613 AATTAGAATTATATTT
1 AATTAGAATTATATTT
1958629 AATTAGAATTATATTT
1 AATTAGAATTATATTT
1958645 TTAAGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
AATTAGAATTATATTT
Found at i:1966109 original size:21 final size:20
Alignment explanation
Indices: 1966080--1966119 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1966070 CCAGGGATAT
*
1966080 AGTATCGATACTCCTCCTTAA
1 AGTAACGATACTCC-CCTTAA
1966101 AGTAACGATACTCCCCTTA
1 AGTAACGATACTCCCCTTA
1966120 TAAAATGCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAACGATACTCCCCTTAA
Found at i:1979147 original size:23 final size:20
Alignment explanation
Indices: 1979073--1979176 Score: 102
Period size: 20 Copynumber: 4.9 Consensus size: 20
1979063 TTTTTGTGCA
1979073 GAGGGAATCGATCCCCCCAT
1 GAGGGAATCGATCCCCCCAT
1979093 GAGGGAATCGATCCCCCCAT
1 GAGGGAATCGATCCCCCCAT
* **
1979113 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGA-TCCCCCCAT
1979134 GAAGGGGAATCGATTCCCCCCCA-
1 G-A-GGGAATCGA-T-CCCCCCAT
*
1979157 CAGGGGAATCGATACCCCCC
1 GA-GGGAATCGAT-CCCCCC
1979177 TGGGGTTCTG
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
20 30 0.42
21 15 0.21
22 12 0.17
23 10 0.14
24 5 0.07
ACGTcount: A:0.24, C:0.36, G:0.25, T:0.15
Consensus pattern (20 bp):
GAGGGAATCGATCCCCCCAT
Found at i:1981764 original size:21 final size:22
Alignment explanation
Indices: 1981740--1981781 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1981730 TTCCAGATTG
1981740 CTCAGA-GGGAACCGATTCCCT
1 CTCAGAGGGGAACCGATTCCCT
* *
1981761 CTCATAGGGGTACCGATTCCC
1 CTCAGAGGGGAACCGATTCCC
1981782 CCCCTTAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.21, C:0.33, G:0.24, T:0.21
Consensus pattern (22 bp):
CTCAGAGGGGAACCGATTCCCT
Found at i:1993302 original size:19 final size:19
Alignment explanation
Indices: 1993278--1993330 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1993268 ATAATGTTTA
*
1993278 AAAGTATCGATACTTGTAG
1 AAAGTATCGATACTTGTAC
* *
1993297 AAAGTATCGAAACTTTTAC
1 AAAGTATCGATACTTGTAC
*
1993316 AAGAGTATTGATACT
1 AA-AGTATCGATACT
1993331 CTTGGGCTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (19 bp):
AAAGTATCGATACTTGTAC
Found at i:2004934 original size:47 final size:45
Alignment explanation
Indices: 2004859--2004984 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
2004849 TATAAAATCT
* *
2004859 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
* * *
2004904 CTTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
* * *
2004951 CTTGCCA-TTATTTCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTT
2004985 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
Found at i:2005144 original size:40 final size:40
Alignment explanation
Indices: 2005089--2005210 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
2005079 ACTGTAGTGC
2005089 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2005129 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2005169 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2005209 TA
1 TA
2005211 TAAACCTGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2011919 original size:47 final size:45
Alignment explanation
Indices: 2011844--2011969 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
2011834 TATAAAATCT
* *
2011844 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
* * *
2011889 CTTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
* *
2011936 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTT
2011970 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 24 0.33
45 10 0.14
46 2 0.03
47 36 0.50
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
Found at i:2012129 original size:40 final size:40
Alignment explanation
Indices: 2012074--2012195 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
2012064 ACTGTAGTGC
2012074 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2012114 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2012154 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2012194 TA
1 TA
2012196 TAAATCTGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2018407 original size:23 final size:23
Alignment explanation
Indices: 2018371--2018426 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
2018361 CAGAGGGAAT
*
2018371 CGATACCCCC-TTGAAGGAGAAC
1 CGATTCCCCCTTTGAAGGAGAAC
** *
2018393 TTATTCCCCCTTTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGAGAAC
2018416 CGATTCCCCCT
1 CGATTCCCCCT
2018427 GTAGGGGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (23 bp):
CGATTCCCCCTTTGAAGGAGAAC
Found at i:2020801 original size:18 final size:18
Alignment explanation
Indices: 2020778--2020818 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2020768 AAACTTGATT
2020778 TCAAAATCTTAAAATTAC
1 TCAAAATCTTAAAATTAC
2020796 TCAAAATCTTAAAATTAC
1 TCAAAATCTTAAAATTAC
2020814 T-AAAA
1 TCAAAA
2020819 CGTTTTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.32
Consensus pattern (18 bp):
TCAAAATCTTAAAATTAC
Found at i:2024385 original size:2 final size:2
Alignment explanation
Indices: 2024378--2024406 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2024368 GGGTGTTACA
2024378 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 A
2024407 CATGAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2031094 original size:21 final size:20
Alignment explanation
Indices: 2031040--2031100 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
2031030 TTATAGGGCA
*
2031040 GAGGGAATCGATACCCCCTT
1 GAGGGAATCAATACCCCCTT
* *
2031060 GAAGGGGAACCAATTCCCTCCTT
1 G-A-GGGAATCAATACCC-CCTT
2031083 GAGGGAATCAATACCCCC
1 GAGGGAATCAATACCCCC
2031101 CACGGGTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
20 3 0.09
21 13 0.39
22 12 0.36
23 5 0.15
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (20 bp):
GAGGGAATCAATACCCCCTT
Found at i:2036089 original size:44 final size:43
Alignment explanation
Indices: 2036026--2036132 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 43
2036016 CATTTATCCG
*
2036026 ATAAGCTCGTAAGCTTATTTATCAATATACT-TACCAATTATTCC
1 ATAAGCTCGTAAGCTTATTTACCAATATA-TATACC-ATTATTCC
* *
2036070 ATAAGCTCGTAAGCTTATTTTACCAATATATATGCCATTTTTCC
1 ATAAGCTCGTAAGCTTA-TTTACCAATATATATACCATTATTCC
*
2036114 AT-AGCTCATAAGCTTATTT
1 ATAAGCTCGTAAGCTTATTT
2036133 GCACGGTTAC
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
42 3 0.05
43 13 0.23
44 27 0.47
45 14 0.25
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (43 bp):
ATAAGCTCGTAAGCTTATTTACCAATATATATACCATTATTCC
Found at i:2040385 original size:30 final size:27
Alignment explanation
Indices: 2040328--2040385 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
2040318 CTCAAAACAT
**
2040328 TATTATTTTATATATTTAATATTAATA
1 TATTATTTTATATATTTAATAAAAATA
2040355 TATTATTTTATTATCATTTTAATAAAAATA
1 TATTATTTTA-TAT-A-TTTAATAAAAATA
2040385 T
1 T
2040386 TACTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 3 0.12
29 1 0.04
30 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TATTATTTTATATATTTAATAAAAATA
Found at i:2040461 original size:42 final size:43
Alignment explanation
Indices: 2040415--2040495 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
2040405 ATTGATAATT
*
2040415 TTAATAATATAATATAATA-TTTTATTTTTATAAT-TAAATTAA
1 TTAAT-ATATAATATAATACTTTTATTTTAATAATATAAATTAA
*
2040457 TTAATATATAATATTATACTTTTATTTTAATAATATAAA
1 TTAATATATAATATAATACTTTTATTTTAATAATATAAA
2040496 ATAAATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 12 0.34
42 19 0.54
43 4 0.11
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (43 bp):
TTAATATATAATATAATACTTTTATTTTAATAATATAAATTAA
Found at i:2040616 original size:17 final size:17
Alignment explanation
Indices: 2040594--2040652 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
2040584 TATTTTTTTA
2040594 TATTTTAATAATATTAT
1 TATTTTAATAATATTAT
*
2040611 TATTTTAATAAGTAATTAA
1 TATTTTAATAA-T-ATTAT
* *
2040630 TATAATTAATAAT-GTAT
1 TAT-TTTAATAATATTAT
2040647 TATTTT
1 TATTTT
2040653 TATTTTAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 2 0.06
17 16 0.47
18 1 0.03
19 8 0.24
20 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TATTTTAATAATATTAT
Found at i:2040639 original size:37 final size:38
Alignment explanation
Indices: 2040598--2040701 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 38
2040588 TTTTTATATT
* *
2040598 TTAATAATATTATTATTTTAATAAGTAATTAATAT-AA
1 TTAATAATATTATTATTTTAATAAATAACTAATATAAA
2040635 TTAATAATGTATTATTTTTATTTTAATAAATAACTAATATAAA
1 TTAATAA--TATTA---TTATTTTAATAAATAACTAATATAAA
2040678 TT-ATAATAGTT-TTATTTTAATAAA
1 TTAATAATA-TTATTATTTTAATAAA
2040702 ATATAATAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
37 20 0.34
39 5 0.09
40 2 0.03
41 2 0.03
42 25 0.43
43 4 0.07
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (38 bp):
TTAATAATATTATTATTTTAATAAATAACTAATATAAA
Found at i:2040658 original size:42 final size:43
Alignment explanation
Indices: 2040605--2040695 Score: 123
Period size: 42 Copynumber: 2.1 Consensus size: 43
2040595 ATTTTAATAA
* * *
2040605 TATTATTATTTTAATAAGTAATTAATAT-AATTAATAAT-GTAT
1 TATTTTTATTTTAATAAATAACTAATATAAATT-ATAATAGTAT
*
2040647 TATTTTTATTTTAATAAATAACTAATATAAATTATAATAGTTT
1 TATTTTTATTTTAATAAATAACTAATATAAATTATAATAGTAT
2040690 TATTTT
1 TATTTT
2040696 AATAAAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 30 0.70
43 13 0.30
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (43 bp):
TATTTTTATTTTAATAAATAACTAATATAAATTATAATAGTAT
Found at i:2049910 original size:77 final size:76
Alignment explanation
Indices: 2049799--2050203 Score: 333
Period size: 77 Copynumber: 5.3 Consensus size: 76
2049789 CACGCCTAAA
* * *
2049799 AATGTCATGGTTCACTAAAAATAGGTTACAATCTGAAATGTTAATTTTTTTATTAATAAAAT-AT
1 AATGTCATGGTTCACTAAAAATAGGTTACGATCTGAAATGTTAATATTTTTATTAATAAAATGAG
*
2049863 GT-TACGCTCAAG
66 GTGCAC-C-CAAG
* * ** *
2049875 AATGTCATGATTCACTAATAAATATGTTTTGATCTGAAATGTTAATATTTTTATTAATAAAGTGA
1 AATGTCATGGTTCACTAA-AAATAGGTTACGATCTGAAATGTTAATATTTTTATTAATAAAATGA
2049940 GGTGCACCCAAG
65 GGTGCACCCAAG
* * *
2049952 AATATCATGGTTCACTAAGAAATGGGTTACGATCTAAAATGTTAATATTTTTATTAATAAAATGA
1 AATGTCATGGTTCACTAA-AAATAGGTTACGATCTGAAATGTTAATATTTTTATTAATAAAATGA
* ** *
2050017 GTTGCACAAAAA
65 GGTGCACCCAAG
* * *
2050029 AATGTCACT-GTTTACTAAGAAATAGGTTGTA-AAT-TGGAATGTTAATATTTTTATTAATAAAA
1 AATGTCA-TGGTTCACTAA-AAATAGG-T-TACGATCTGAAATGTTAATATTTTTATTAATAAAA
*
2050091 TG-GGTTG-AGCCCAAA
62 TGAGG-TGCA-CCCAAG
* * * * ** *
2050106 AATATTATGGTTCACTAAGAAATAGATTGCGAT-AAAGAATGTTAATATTTGTATTAATAAAAT-
1 AATGTCATGGTTCACTAA-AAATAGGTTACGATCTGA-AATGTTAATATTTTTATTAATAAAATG
* **
2050169 AGTTTGCACAAAAG
64 AG-GTGCACCCAAG
* * *
2050183 AATATTATGATTCACTAAAAA
1 AATGTCATGGTTCACTAAAAA
2050204 AGCAAGTCGC
Statistics
Matches: 269, Mismatches: 46, Indels: 28
0.78 0.13 0.08
Matches are distributed among these distances:
75 1 0.00
76 26 0.10
77 229 0.85
78 9 0.03
79 4 0.01
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (76 bp):
AATGTCATGGTTCACTAAAAATAGGTTACGATCTGAAATGTTAATATTTTTATTAATAAAATGAG
GTGCACCCAAG
Found at i:2050200 original size:154 final size:154
Alignment explanation
Indices: 2049796--2050200 Score: 450
Period size: 154 Copynumber: 2.6 Consensus size: 154
2049786 AGGCACGCCT
* * * ** *
2049796 AAAAATGTCATGGTTCACTAA-AAATAGGTTACAATCTGAAATGTTAATTTTTTTATTAATAAAA
1 AAAAATATCATGGTTCACTAAGAAATAGATTACGATCAAAAATGTTAATATTTTTATTAATAAAA
* * * * **
2049860 TATGTTACGCTC--AAGAATGTCATGATTCACTAATAAATATGTTTTGATCTGAAATGTTAATAT
66 TA-GTT-TGCACAAAAGAATGTCATGATTCACTAAGAAATAGGTTTAAATCTGAAATGTTAATAT
*
2049923 TTTTATTAATAAAGTGAGGTGCACCC
129 TTTTATTAATAAAATGAGGTGCACCC
* * * *
2049949 AAGAATATCATGGTTCACTAAGAAATGGGTTACGATCTAAAATGTTAATATTTTTATTAATAAAA
1 AAAAATATCATGGTTCACTAAGAAATAGATTACGATCAAAAATGTTAATATTTTTATTAATAAAA
* * *
2050014 TGAG-TTGCACAAAAAAATGTCACTG-TTTACTAAGAAATAGGTTGTAAAT-TGGAATGTTAATA
66 T-AGTTTGCACAAAAGAATGTCA-TGATTCACTAAGAAATAGGTT-TAAATCTGAAATGTTAATA
2050076 TTTTTATTAATAAAATG-GGTTG-AGCCC
128 TTTTTATTAATAAAATGAGG-TGCA-CCC
* * *
2050103 AAAAATATTATGGTTCACTAAGAAATAGATTGCGAT-AAAGAATGTTAATATTTGTATTAATAAA
1 AAAAATATCATGGTTCACTAAGAAATAGATTACGATCAAA-AATGTTAATATTTTTATTAATAAA
* *
2050167 ATAGTTTGCACAAAAGAATATTATGATTCACTAA
65 ATAGTTTGCACAAAAGAATGTCATGATTCACTAA
2050201 AAAAGCAAGT
Statistics
Matches: 214, Mismatches: 27, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
152 3 0.01
153 29 0.14
154 176 0.82
155 6 0.03
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (154 bp):
AAAAATATCATGGTTCACTAAGAAATAGATTACGATCAAAAATGTTAATATTTTTATTAATAAAA
TAGTTTGCACAAAAGAATGTCATGATTCACTAAGAAATAGGTTTAAATCTGAAATGTTAATATTT
TTATTAATAAAATGAGGTGCACCC
Found at i:2050243 original size:154 final size:154
Alignment explanation
Indices: 2049909--2050244 Score: 371
Period size: 154 Copynumber: 2.2 Consensus size: 154
2049899 TGTTTTGATC
* *
2049909 TGAAATGTTAATATTTTTATTAATAAAGTGAGG-TGCA-CCCAAGAATATCATGGTTCACTAAGA
1 TGAAATGTTAATATTTTTATTAATAAAATG-GGTTG-AGCCCAAAAATATCATGGTTCACTAAGA
* * * * *
2049972 AATGGGTTACGATCTAAAATGTTAATATTTTTATTAATAAAATGAGTTGCACAAAAAAATGTCAC
64 AATAGATTACGATCAAAAATGTTAATATTTGTATTAATAAAATGAGTTGCACAAAAAAATATCAC
* * * * * *
2050037 TGTTTACTAAGAAATAGGTTGTAAAT
129 TGTTCACTAAAAAACAAGTCGCAAAT
* *
2050063 TGGAATGTTAATATTTTTATTAATAAAATGGGTTGAGCCCAAAAATATTATGGTTCACTAAGAAA
1 TGAAATGTTAATATTTTTATTAATAAAATGGGTTGAGCCCAAAAATATCATGGTTCACTAAGAAA
* * *
2050128 TAGATTGCGAT-AAAGAATGTTAATATTTGTATTAATAAAAT-AGTTTGCACAAAAGAATATTA-
66 TAGATTACGATCAAA-AATGTTAATATTTGTATTAATAAAATGAG-TTGCACAAAAAAATATCAC
*
2050190 TGATTCACTAAAAAAGCAAGTCGCAATT
129 TG-TTCACTAAAAAA-CAAGTCGCAAAT
* *
2050218 TTAAATGTTACT-TTTTCTATT-ATAAAA
1 TGAAATGTTAATATTTT-TATTAATAAAA
2050245 AATTTCAAAA
Statistics
Matches: 153, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
153 9 0.06
154 124 0.81
155 20 0.13
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (154 bp):
TGAAATGTTAATATTTTTATTAATAAAATGGGTTGAGCCCAAAAATATCATGGTTCACTAAGAAA
TAGATTACGATCAAAAATGTTAATATTTGTATTAATAAAATGAGTTGCACAAAAAAATATCACTG
TTCACTAAAAAACAAGTCGCAAAT
Found at i:2051988 original size:14 final size:14
Alignment explanation
Indices: 2051969--2052003 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2051959 GCGGATTCAA
*
2051969 AAATTTAAGATTAT
1 AAATTTAAAATTAT
2051983 AAATTTAAAATTAT
1 AAATTTAAAATTAT
*
2051997 AATTTTA
1 AAATTTA
2052004 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
AAATTTAAAATTAT
Found at i:2053185 original size:23 final size:24
Alignment explanation
Indices: 2053158--2053208 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
2053148 ACTACATTAT
2053158 TTAATATTTTTAAAAT-AATAATA
1 TTAATATTTTTAAAATGAATAATA
* *
2053181 TTAATCTTTTTACAATGAATAATA
1 TTAATATTTTTAAAATGAATAATA
2053205 TTAA
1 TTAA
2053209 ATCTTGCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
TTAATATTTTTAAAATGAATAATA
Found at i:2053191 original size:24 final size:25
Alignment explanation
Indices: 2053155--2053213 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
2053145 TTAACTACAT
* *
2053155 TATTTAATATTTTTAAAAT-AATAA
1 TATTAAATCTTTTTAAAATGAATAA
*
2053179 TATT-AATCTTTTTACAATGAATAA
1 TATTAAATCTTTTTAAAATGAATAA
2053203 TATTAAATCTT
1 TATTAAATCTT
2053214 GCAGTAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 12 0.39
24 13 0.42
25 6 0.19
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (25 bp):
TATTAAATCTTTTTAAAATGAATAA
Found at i:2053361 original size:14 final size:14
Alignment explanation
Indices: 2053342--2053368 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2053332 AAACCCAGAT
2053342 CTTCCGTCCAACAG
1 CTTCCGTCCAACAG
2053356 CTTCCGTCCAACA
1 CTTCCGTCCAACA
2053369 CCAGTCATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.44, G:0.11, T:0.22
Consensus pattern (14 bp):
CTTCCGTCCAACAG
Found at i:2054950 original size:23 final size:23
Alignment explanation
Indices: 2054924--2054971 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2054914 ATAAAGTACA
*
2054924 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
2054947 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
2054970 AT
1 AT
2054972 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2055754 original size:23 final size:23
Alignment explanation
Indices: 2055728--2055790 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2055718 ATATAACTAC
2055728 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2055751 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2055774 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2055791 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2056244 original size:39 final size:39
Alignment explanation
Indices: 2056190--2056276 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
2056180 TCAAGTTGTA
*
2056190 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
2056229 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
2056268 GATTTTGAT
1 GATTTTGAT
2056277 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:2056557 original size:18 final size:18
Alignment explanation
Indices: 2056534--2056570 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2056524 CGAAATATAT
2056534 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2056552 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2056570 A
1 A
2056571 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:2056989 original size:25 final size:25
Alignment explanation
Indices: 2056955--2057005 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
2056945 TTTTTCCAAA
*
2056955 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
2056980 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
2057005 T
1 T
2057006 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:2057215 original size:21 final size:22
Alignment explanation
Indices: 2057190--2057241 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
2057180 ACACTTTACA
*
2057190 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
2057213 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
2057236 ATATAA
1 ATATAA
2057242 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:2057226 original size:23 final size:23
Alignment explanation
Indices: 2057200--2057262 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2057190 ATATAACCAC
2057200 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
2057223 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
2057246 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2057263 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2057606 original size:25 final size:25
Alignment explanation
Indices: 2057549--2057614 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
2057539 CACTCAAAAG
*
2057549 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
2057574 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
2057599 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
2057615 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:2058785 original size:183 final size:183
Alignment explanation
Indices: 2058473--2059544 Score: 1970
Period size: 183 Copynumber: 5.9 Consensus size: 183
2058463 TTAAAATTAC
*
2058473 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
2058538 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACTGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
2058603 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
2058656 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
2058721 ATTATAAAGTGTCGAGATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * *
2058786 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATATGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* *
2058839 CGATACTTTTTTAAATCGTATCGACATATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
2058904 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
2058969 ATATTACAAAATTATCTATTACATTAT-ATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
2059021 CGACAC-TTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
2059085 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
2059150 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
2059203 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
2059268 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
2059333 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
2059386 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
2059451 ATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * * **
2059515 ATATTGCAAATTTACCTATTTTATTATAAT
131 ATATTACAAAATTATCTATTACATTATAAT
2059545 ATGTTGAAAG
Statistics
Matches: 868, Mismatches: 19, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
181 149 0.17
182 144 0.17
183 575 0.66
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:2059188 original size:364 final size:366
Alignment explanation
Indices: 2058473--2059544 Score: 1970
Period size: 364 Copynumber: 2.9 Consensus size: 366
2058463 TTAAAATTAC
*
2058473 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
2058538 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACTGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * *
2058603 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACTTTTTT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
*
2058668 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTATAAAGTGT
196 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
*
2058733 CGAGATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
261 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
* *
2058798 TATCTATTACATTATAAATCTGGGTTCCGATATGTAAATGT
326 TATCTATTACATTATAATTATGGGTTCCGATATGTAAATGT
* *
2058839 CGATACTTTTTTAAATCGTATCGACATATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
2058904 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
2058969 ATATTACAAAATTATCTATTACATTAT-ATTATGGGTTCCGATGTGTAAATGTCGACAC-TTTTT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
2059032 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
196 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
2059097 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
261 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
*
2059162 TATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
326 TATCTATTACATTATAATTATGGGTTCCGATATGTAAATGT
2059203 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
2059268 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
2059333 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
2059398 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATT-AAAAGTGT
196 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
* *
2059462 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTGCAAATT
261 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
* **
2059527 TACCTATTTTATTATAAT
326 TATCTATTACATTATAAT
2059545 ATGTTGAAAG
Statistics
Matches: 685, Mismatches: 19, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
364 326 0.48
365 145 0.21
366 214 0.31
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (366 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
TATCTATTACATTATAATTATGGGTTCCGATATGTAAATGT
Found at i:2060969 original size:3 final size:3
Alignment explanation
Indices: 2060961--2061002 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
2060951 ACTTGTTTGG
* * *
2060961 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
2061003 GTCAGCTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.26, C:0.33, G:0.02, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:2060978 original size:12 final size:12
Alignment explanation
Indices: 2060961--2061014 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
2060951 ACTTGTTTGG
2060961 ATCATCATCTTC
1 ATCATCATCTTC
2060973 ATCATCATCATCATC
1 ATCATCATC-T--TC
*
2060988 ATCGTCATCTTC
1 ATCATCATCTTC
* *
2061000 ATCGTCAGCTTC
1 ATCATCATCTTC
2061012 ATC
1 ATC
2061015 TTCTGCGACC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
12 25 0.68
13 1 0.03
14 1 0.03
15 10 0.27
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:2063119 original size:197 final size:199
Alignment explanation
Indices: 2062785--2063339 Score: 984
Period size: 197 Copynumber: 2.8 Consensus size: 199
2062775 GATGATTTTG
2062785 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA-AAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAAC
***
2062849 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
2062914 GATTG-AAAATTACATATTACATTATACTTTTGGTTCGATGA-TTTTGGGATCGACACTTTTTAT
131 GATTGAAAAATTACATATTACATTATACTTTTGGTTCGATGATTTTTGGGATCGACACTTTTTAT
2062977 ATAT
196 ATAT
2062981 GGATCGACAC-TTATGGGTGCAACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAA
1 GGATCGACACTTTATGGGTGC-ACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAA
*
2063045 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACTGGTT
65 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
2063110 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTTGGGATCGACACTTTTT
130 AGATTGAAAAATTACATATTACATTATACTTTT-GGTTCGATGATTTTTGGGATCGACACTTTTT
2063175 ATATAT
194 ATATAT
2063181 GGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAACAAATATCGACACAAA-
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAAC
*
2063244 -ATATTAGTGTCG--ACATTATTTATACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
2063306 GATTGAAAAATTACATATTACATTATACTTTTGG
131 GATTGAAAAATTACATATTACATTATACTTTTGG
2063340 GATCGACACT
Statistics
Matches: 347, Mismatches: 6, Indels: 14
0.95 0.02 0.04
Matches are distributed among these distances:
194 2 0.01
195 90 0.26
196 37 0.11
197 94 0.27
198 26 0.07
199 46 0.13
200 42 0.12
201 10 0.03
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (199 bp):
GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAAC
TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
GATTGAAAAATTACATATTACATTATACTTTTGGTTCGATGATTTTTGGGATCGACACTTTTTAT
ATAT
Found at i:2063307 original size:195 final size:197
Alignment explanation
Indices: 2062785--2063345 Score: 965
Period size: 195 Copynumber: 2.9 Consensus size: 197
2062775 GATGATTTTG
2062785 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA-AAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAAC
***
2062849 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATAATTGTACCGGTTA
66 -ATATTAGTGTCGA-ACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
2062914 GATTG-AAAATTACATATTACATTATACTTTT-GGTTCGATGATTTTGGGATCGACACTTTTTAT
129 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
2062977 ATAT
194 ATAT
2062981 GGATCGACAC-TTATGGGTGCAACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAA
1 GGATCGACACTTTATGGGTGC-ACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAA
*
2063045 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACTGGTT
65 C-ATATTAGTGTCGA-ACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
2063110 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTTGGGATCGACACTTTTT
128 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTTGGGATCGACACTTTTT
2063175 ATATAT
192 ATATAT
2063181 GGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAACAAATATCGACACAAA-
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAAC
*
2063244 ATATTAGTGTCG-ACATTATTTATACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGA
66 ATATTAGTGTCGAACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGA
*
2063308 TTGAAAAATTACATATTACATTATACTTTTGGGATCGA
131 TTGAAAAATTACATATTACATTATACTTTTGGGTTCGA
2063346 CACTTTTTTA
Statistics
Matches: 352, Mismatches: 7, Indels: 13
0.95 0.02 0.03
Matches are distributed among these distances:
195 97 0.28
196 37 0.11
197 94 0.27
198 26 0.07
199 46 0.13
200 42 0.12
201 10 0.03
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (197 bp):
GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAAC
ATATTAGTGTCGAACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGA
TTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
AT
Found at i:2063482 original size:176 final size:178
Alignment explanation
Indices: 2063155--2063520 Score: 602
Period size: 176 Copynumber: 2.1 Consensus size: 178
2063145 GTTCGATGAT
*
2063155 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATT
1 TTTTGGGATCGACACTTTTTATATAT-GATCGACACTTTATGGGTGCACCCTGTTGCCATTCATT
*
2063220 CTGGAAAACAAATATCGACACAAAATATTAGTGTCGACATTATTTATACATATTCTCTCATAAAA
65 CTGGAAAACAAATATCGACACAAAATATTAGTGTCGACATTATTTAGACATATTCTCTCATAAAA
2063285 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
130 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
2063334 TTTTGGGATCGACACTTTTT-TATAT-ATCGACAC-TT-TGGGTGCACCCTGTTGGCCATTCATT
1 TTTTGGGATCGACACTTTTTATATATGATCGACACTTTATGGGTGCACCCTGTT-GCCATTCATT
*
2063395 CTGGAAAA-AAATATCGACACAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
65 CTGGAAAACAAATATCGACACAA-AATATTAGTGTCG--ACATTATTTAGACATATTCTCTCATA
2063459 AAA-CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
127 AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
*
2063510 -TTTGGGTTCGA
1 TTTTGGGATCGA
2063521 TGATTTGGGA
Statistics
Matches: 179, Mismatches: 4, Indels: 12
0.92 0.02 0.06
Matches are distributed among these distances:
174 29 0.16
175 41 0.23
176 56 0.31
177 28 0.16
178 5 0.03
179 20 0.11
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (178 bp):
TTTTGGGATCGACACTTTTTATATATGATCGACACTTTATGGGTGCACCCTGTTGCCATTCATTC
TGGAAAACAAATATCGACACAAAATATTAGTGTCGACATTATTTAGACATATTCTCTCATAAAAC
CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
Found at i:2063718 original size:19 final size:17
Alignment explanation
Indices: 2063694--2063740 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 17
2063684 ATTATTTCAC
2063694 ATACAAAATTATAAATCAT
1 ATACAAAATTAT-AATC-T
2063713 ATACAAAATTATAATCT
1 ATACAAAATTATAATCT
2063730 ATACAAAATTA
1 ATACAAAATTA
2063741 ACCCTACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 12 0.43
18 4 0.14
19 12 0.43
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (17 bp):
ATACAAAATTATAATCT
Found at i:2065533 original size:33 final size:33
Alignment explanation
Indices: 2065496--2065561 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2065486 CATCTTAATA
* *
2065496 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
* *
2065529 TCACCCCTCAACACCTCTACTTCATTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
2065562 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.27
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCATTCACCACT
Found at i:2065635 original size:21 final size:21
Alignment explanation
Indices: 2065595--2065659 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2065585 CCCCTTATGC
* *
2065595 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
2065616 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
2065637 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
2065658 CT
1 CT
2065660 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:2067917 original size:19 final size:19
Alignment explanation
Indices: 2067862--2067908 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
2067852 ATCCGGTATC
2067862 ATTTTACCGGTTTTATCAT
1 ATTTTACCGGTTTTATCAT
2067881 -TTTGATACCGGTTTTATCAT
1 ATTT--TACCGGTTTTATCAT
2067901 ATTTTACC
1 ATTTTACC
2067909 TGTTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 4 0.16
20 15 0.60
21 3 0.12
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.51
Consensus pattern (19 bp):
ATTTTACCGGTTTTATCAT
Found at i:2068056 original size:20 final size:19
Alignment explanation
Indices: 2068030--2068074 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
2068020 CACTTTTAAA
2068030 TTTACCGGTTTTATCAT-TT
1 TTTACCGG-TTTATCATATT
2068049 TGTTACCGGTTTATCATATT
1 T-TTACCGGTTTATCATATT
2068069 TTTACC
1 TTTACC
2068075 TGGTATATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTACCGGTTTATCATATT
Found at i:2068063 original size:19 final size:19
Alignment explanation
Indices: 2068031--2068089 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
2068021 ACTTTTAAAT
2068031 TTACCGGTTTTATCATTTTG
1 TTACCGG-TTTATCATTTTG
2068051 TTACCGGTTTATCATATTT-
1 TTACCGGTTTATCAT-TTTG
* *
2068070 TTACCTGGTATATCGTTTTG
1 TTACC-GGTTTATCATTTTG
2068090 GATCGATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (19 bp):
TTACCGGTTTATCATTTTG
Found at i:2073488 original size:40 final size:39
Alignment explanation
Indices: 2073367--2073499 Score: 119
Period size: 40 Copynumber: 3.3 Consensus size: 39
2073357 TCAACTTCAA
*
2073367 AATTTAATTTAGTATAAACCTTAATAATAAATATTAACCT
1 AATTTAA-TTAATATAAACCTTAATAATAAATATTAACCT
* ** * * *
2073407 AATTTAATT-ATTTAAATATTTTAACATATAAA-AAT-ATCT
1 AATTTAATTAATAT-AA-ACCTTAATA-ATAAATATTAACCT
2073446 AATCTTAATTAATATAAACCTTAATAATAAATATTAACCT
1 AAT-TTAATTAATATAAACCTTAATAATAAATATTAACCT
*
2073486 AATGTAATTTAATA
1 AATTTAA-TTAATA
2073500 ATATTGTATA
Statistics
Matches: 71, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
38 7 0.10
39 21 0.30
40 35 0.49
41 8 0.11
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (39 bp):
AATTTAATTAATATAAACCTTAATAATAAATATTAACCT
Found at i:2074847 original size:10 final size:10
Alignment explanation
Indices: 2074832--2074864 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
2074822 GTCTCTATAG
2074832 TTTTTTATTT
1 TTTTTTATTT
2074842 TTTTTTATTT
1 TTTTTTATTT
2074852 TTTTTTATTT
1 TTTTTTATTT
2074862 TTT
1 TTT
2074865 AAAGCATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:2077170 original size:22 final size:23
Alignment explanation
Indices: 2077126--2077171 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
2077116 TCTTACATGT
*
2077126 TAAAAGCAGAACACAAAATGTTA
1 TAAAAGCAGAACACAAAAAGTTA
2077149 TAAAA-CAGAAC-CGAAAAAGTTA
1 TAAAAGCAGAACAC-AAAAAGTTA
2077171 T
1 T
2077172 CAATGTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 15 0.71
23 5 0.24
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (23 bp):
TAAAAGCAGAACACAAAAAGTTA
Found at i:2077506 original size:77 final size:77
Alignment explanation
Indices: 2077360--2077588 Score: 262
Period size: 77 Copynumber: 3.0 Consensus size: 77
2077350 TATATATAAG
* * * * * * *
2077360 AAATACGTTGCGCCTAAAAATGTCACGGCTT-ACTAAGAAATATGTTGCGATCTGGAACGTTAAT
1 AAATAAGTTGCACCTAAGAATGTCATGG-TTCACTAAGAAATAGGTTGCGATCTAGAATGTTAAT
2077424 ATTTTTATTAATA
65 ATTTTTATTAATA
** *** * *
2077437 AAATGGGTTGTGGCTAAGAATGTCATGGTTCACTAAGAAATAGGTTGCGATCTAAAATGTTAATG
1 AAATAAGTTGCACCTAAGAATGTCATGGTTCACTAAGAAATAGGTTGCGATCTAGAATGTTAATA
2077502 TTTTTATTAATA
66 TTTTTATTAATA
* * * * *
2077514 AAATAAGTTGCACCCAAGAATATTATGGTTCACTAAGAAAGTAGGTTACGATATAGAATGTTAAT
1 AAATAAGTTGCACCTAAGAATGTCATGGTTCACTAAGAAA-TAGGTTGCGATCTAGAATGTTAAT
2077579 ATTTTTATTA
65 ATTTTTATTA
2077589 CAAAAAATTC
Statistics
Matches: 127, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
76 2 0.02
77 95 0.75
78 30 0.24
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.35
Consensus pattern (77 bp):
AAATAAGTTGCACCTAAGAATGTCATGGTTCACTAAGAAATAGGTTGCGATCTAGAATGTTAATA
TTTTTATTAATA
Done.