Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008425.1 Hibiscus syriacus cultivar Beakdansim tig00111208_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: 2340112
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 12
Found at i:1785296 original size:64 final size:63
Alignment explanation
Indices: 1785143--1785302 Score: 196
Period size: 64 Copynumber: 2.5 Consensus size: 63
1785133 TGGAACACTT
** * *
1785143 AGTGCATCGGTGCACCAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTG
1 AGTGCATCGGTGCATGAA-TGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAACCCTG
* ** *
1785207 AGTGCATCGATGCATGTCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAAACCCT
1 AGTGCATCGGTGCATG-AATGTGCATCGATGCATAAAATGCATTCGATGTTTTCA--AAAACCCT
1785272 G
63 G
1785273 AGTGCATCGGTGCATGAAT-TGCATTCGATG
1 AGTGCATCGGTGCATGAATGTGCA-TCGATG
1785303 TTCAATTTAT
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
64 51 0.63
65 7 0.09
66 23 0.28
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (63 bp):
AGTGCATCGGTGCATGAATGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAACCCTG
Found at i:1785340 original size:20 final size:20
Alignment explanation
Indices: 1785315--1785353 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1785305 CAATTTATTC
1785315 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
1785335 ATTGGTGCATCGGTGCATG
1 ATTGGTGCATCGATGCATG
1785354 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.36, T:0.31
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:1791279 original size:22 final size:21
Alignment explanation
Indices: 1791237--1791276 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1791227 GAGTTTATTT
*
1791237 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
1791258 TCATTTTT-ACATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1791277 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:1793336 original size:19 final size:19
Alignment explanation
Indices: 1793312--1793348 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1793302 TTTCATTAAA
1793312 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1793331 AGAGTGCATCGGTGCATG
1 AGAGTGCATCGATGCATG
1793349 AATTGCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1793356 original size:62 final size:61
Alignment explanation
Indices: 1793208--1793364 Score: 172
Period size: 62 Copynumber: 2.5 Consensus size: 61
1793198 TGCACCAAGT
* ****
1793208 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGTCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAA--C-GAGTGCATCGATGCATGGAGA
*
1793272 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAAA-GAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA--AAAACGAGTGCATCGATGCATGGAGA
* * * *
1793334 GTGCATCGGTGCATGAATTGCATTTGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
1793365 CAATTTATTC
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
62 44 0.54
64 33 0.41
66 4 0.05
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (61 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAACGAGTGCATCGATGCATGGAGA
Found at i:1793411 original size:20 final size:20
Alignment explanation
Indices: 1793375--1793413 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1793365 CAATTTATTC
*
1793375 ATTGGTGCATTGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
1793395 ATTGGTGCATCGGTGCATG
1 ATTGGTGCATCGATGCATG
1793414 CCTTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.13, G:0.36, T:0.33
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:1794923 original size:20 final size:20
Alignment explanation
Indices: 1794898--1794937 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1794888 TAACTCAGGC
1794898 AAAATAATGTCTCATTCCAT
1 AAAATAATGTCTCATTCCAT
1794918 AAAATAATGTCTCATTCCAT
1 AAAATAATGTCTCATTCCAT
1794938 CTATTTTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (20 bp):
AAAATAATGTCTCATTCCAT
Found at i:1796076 original size:17 final size:18
Alignment explanation
Indices: 1796044--1796077 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1796034 ATAATCTCAA
*
1796044 AAAAATAATATTTTTAAT
1 AAAAATAATATATTTAAT
1796062 AAAAAT-ATATATTTAA
1 AAAAATAATATATTTAA
1796078 ACATTCGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAATAATATATTTAAT
Found at i:1799612 original size:31 final size:32
Alignment explanation
Indices: 1799569--1799645 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
1799559 GTCAAGTTTG
* *
1799569 CATTCAGATAATGCACAATATT-TCAG-GTACA
1 CATTTAGATAATGCACAAGATTATCAGTGT-CA
* *
1799600 CTTTTAGATAATGCACAGGATTATCAGTGTCA
1 CATTTAGATAATGCACAAGATTATCAGTGTCA
1799632 CATTTAGATAATGC
1 CATTTAGATAATGC
1799646 GTAGCAGTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 18 0.46
32 19 0.49
33 2 0.05
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (32 bp):
CATTTAGATAATGCACAAGATTATCAGTGTCA
Found at i:1805300 original size:12 final size:12
Alignment explanation
Indices: 1805283--1805307 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1805273 AAGATATAAA
1805283 TGATAATTATAT
1 TGATAATTATAT
1805295 TGATAATTATAT
1 TGATAATTATAT
1805307 T
1 T
1805308 TTTTAGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TGATAATTATAT
Found at i:1805403 original size:21 final size:20
Alignment explanation
Indices: 1805365--1805403 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1805355 ACAAATTATT
* *
1805365 TTCATAAAATATTTTAACTA
1 TTCATAAAAGATTCTAACTA
1805385 TTCATAAAAAGATTCTAAC
1 TTCAT-AAAAGATTCTAAC
1805404 CTTTTGATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (20 bp):
TTCATAAAAGATTCTAACTA
Found at i:1806787 original size:44 final size:44
Alignment explanation
Indices: 1806737--1806830 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 44
1806727 ACCTATTGCG
*
1806737 GCGTTTGTAGT-CTAAAACGCCGC-AATATAACATGACCTTTAGCA
1 GCGTTTGTA-TACTAAAACGCCACTAA-ATAACATGACCTTTAGCA
* * *
1806781 GCGTTTGTATACTCAAACGCCACTAAATAACATGACTTTTAGCG
1 GCGTTTGTATACTAAAACGCCACTAAATAACATGACCTTTAGCA
1806825 GCGTTT
1 GCGTTT
1806831 ATTAGTAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 41 0.93
45 2 0.05
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (44 bp):
GCGTTTGTATACTAAAACGCCACTAAATAACATGACCTTTAGCA
Found at i:1813240 original size:30 final size:28
Alignment explanation
Indices: 1813206--1813262 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
1813196 TTTAATATCA
1813206 AAATAAGTG-CTCAAATTATATTGTTTTTTC
1 AAATAAGTGTCT-AAATTAT-TT-TTTTTTC
*
1813236 AAATAGGTGTCTAAATTATTTTTTTTT
1 AAATAAGTGTCTAAATTATTTTTTTTT
1813263 GACTCATCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 6 0.24
29 2 0.08
30 15 0.60
31 2 0.08
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.51
Consensus pattern (28 bp):
AAATAAGTGTCTAAATTATTTTTTTTTC
Found at i:1813406 original size:2 final size:2
Alignment explanation
Indices: 1813401--1813433 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1813391 AAATTACAAT
1813401 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 T
1813434 TTGGTTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1814040 original size:14 final size:14
Alignment explanation
Indices: 1813993--1814042 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
1813983 CAACCTGATA
* *
1813993 ATTTAAAATTTTTT
1 ATTTAAAATTATAT
* *
1814007 ATTTAAAATTAAAA
1 ATTTAAAATTATAT
*
1814021 AATTAAAATTATAT
1 ATTTAAAATTATAT
1814035 ATTTAAAA
1 ATTTAAAA
1814043 AAACCAGAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTTAAAATTATAT
Found at i:1825070 original size:15 final size:16
Alignment explanation
Indices: 1825045--1825082 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1825035 ACGAAAAAGA
* *
1825045 AATATAAATAATATAT
1 AATATACATAAAATAT
1825061 -ATATACATAAAATAT
1 AATATACATAAAATAT
1825076 AATATAC
1 AATATAC
1825083 TATAGCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
AATATACATAAAATAT
Found at i:1826303 original size:17 final size:17
Alignment explanation
Indices: 1826278--1826310 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1826268 TTTAAAAAAA
*
1826278 TAATTTATATATATATG
1 TAATATATATATATATG
1826295 TAATATATATATATAT
1 TAATATATATATATAT
1826311 ATGTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TAATATATATATATATG
Found at i:1826766 original size:105 final size:105
Alignment explanation
Indices: 1826584--1826903 Score: 577
Period size: 105 Copynumber: 3.0 Consensus size: 105
1826574 CAATATCCTT
* *
1826584 CTCTGAAATTGAGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
1 CTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
* *
1826649 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGACACTGG
66 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
*
1826689 CTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATT
1 CTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
1826754 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
66 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
* *
1826794 CTTTGAATTTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
1 CTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
1826859 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
66 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
1826899 CTCTG
1 CTCTG
1826904 GGTAAAACCT
Statistics
Matches: 206, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 206 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
CTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
Found at i:1827758 original size:46 final size:48
Alignment explanation
Indices: 1827687--1827777 Score: 132
Period size: 46 Copynumber: 1.9 Consensus size: 48
1827677 CTCTTTTTCT
* * *
1827687 TTTTCTTTTCTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTCTTTTCTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
*
1827735 TTTT-TTTT-TCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTCTTTTCTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
1827778 GCGAAGTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 31 0.79
47 4 0.10
48 4 0.10
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.43
Consensus pattern (48 bp):
TTTTCTTTTCTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
Found at i:1838429 original size:15 final size:16
Alignment explanation
Indices: 1838404--1838441 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1838394 ACGAAAAAGA
* *
1838404 AATATAAATAATATAT
1 AATATACATAAAATAT
1838420 -ATATACATAAAATAT
1 AATATACATAAAATAT
1838435 AATATAC
1 AATATAC
1838442 TATAGCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
AATATACATAAAATAT
Found at i:1839646 original size:2 final size:2
Alignment explanation
Indices: 1839641--1839674 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1839631 AAAAATAATT
*
1839641 TA TA TA TA TA TG TA -A 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 T
1839675 GTTAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1839661 original size:17 final size:17
Alignment explanation
Indices: 1839636--1839668 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1839626 TTAAAAAAAA
*
1839636 TAATTTATATATATATG
1 TAATATATATATATATG
1839653 TAATATATATATATAT
1 TAATATATATATATAT
1839669 ATATATGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TAATATATATATATATG
Found at i:1842100 original size:12 final size:12
Alignment explanation
Indices: 1842053--1842101 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
1842043 ATTGGAGGAT
1842053 ATTTTTTTATTA
1 ATTTTTTTATTA
*
1842065 A--TTTTAATTA
1 ATTTTTTTATTA
1842075 ATTTTTTTATTTA
1 ATTTTTTTA-TTA
*
1842088 ATTTTTCTATTA
1 ATTTTTTTATTA
1842100 AT
1 AT
1842102 ACATGATTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 9 0.29
12 11 0.35
13 11 0.35
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (12 bp):
ATTTTTTTATTA
Found at i:1842172 original size:64 final size:61
Alignment explanation
Indices: 1842035--1842159 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 61
1842025 GACAAATGGC
*
1842035 AATACATGATTGGAGGATATTTTTTTATTAATTTTAATTAATTTTTTTATTTAATTTTTCTATT
1 AATACATGATTGGAGGATATTTTTTTATTAATTTTAATTAA---TTTAATTTAATTTTTCTATT
1842099 AATACATGATTGGAGGATA-TTTTTTATTAATTTTAATTAA-TTAATTTAATTTTTCTATT
1 AATACATGATTGGAGGATATTTTTTTATTAATTTTAATTAATTTAATTTAATTTTTCTATT
1842158 AA
1 AA
1842160 ATTAGAAGAT
Statistics
Matches: 60, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
59 20 0.33
63 21 0.35
64 19 0.32
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (61 bp):
AATACATGATTGGAGGATATTTTTTTATTAATTTTAATTAATTTAATTTAATTTTTCTATT
Found at i:1851008 original size:27 final size:27
Alignment explanation
Indices: 1850978--1851048 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
1850968 ACTCAACAAT
1850978 TTTAAAAATAAATTTAAGA-TTTTTATA
1 TTTAAAAATAAATTTAAGACTTTTT-TA
* *
1851005 TTTAAAACA-AAAGTTAATACTTTTTTA
1 TTTAAAA-ATAAATTTAAGACTTTTTTA
*
1851032 TTTTAAAATAAATTTAA
1 TTTAAAAATAAATTTAA
1851049 TATATTTCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
26 1 0.03
27 30 0.81
28 6 0.16
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (27 bp):
TTTAAAAATAAATTTAAGACTTTTTTA
Found at i:1851049 original size:27 final size:25
Alignment explanation
Indices: 1850976--1851079 Score: 84
Period size: 26 Copynumber: 3.9 Consensus size: 25
1850966 TAACTCAACA
*
1850976 ATTTTAAAAATAAATTTAAGATTTTT
1 ATTTT-AAAATAAATTTAATATTTTT
* *
1851002 ATATTTAAAACAAAAGTTAATACTTTTTT
1 AT-TTTAAAA-TAAATTTAATA--TTTTT
1851031 ATTTTAAAATAAATTTAATATATTTCT
1 ATTTTAAAATAAATTTAATAT-TTT-T
* * *
1851058 A-GTTATATTAAATTTAATATTT
1 ATTTTAAAATAAATTTAATATTT
1851080 ATAATAATAT
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
25 3 0.05
26 25 0.39
27 22 0.34
28 7 0.11
29 7 0.11
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (25 bp):
ATTTTAAAATAAATTTAATATTTTT
Found at i:1858799 original size:14 final size:14
Alignment explanation
Indices: 1858780--1858809 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1858770 GGTAATTAAC
1858780 AATCAATGGACATA
1 AATCAATGGACATA
1858794 AATCAATGGACATA
1 AATCAATGGACATA
1858808 AA
1 AA
1858810 AATGATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (14 bp):
AATCAATGGACATA
Found at i:1860773 original size:117 final size:117
Alignment explanation
Indices: 1860567--1860905 Score: 450
Period size: 117 Copynumber: 2.9 Consensus size: 117
1860557 TCTTGAGCTC
* * * *
1860567 CAAGTTCTTCTTATTATGAACTTTTTTTGCCTCATCGGATGAGTTT-TTCTTATTATGTACTCTC
1 CAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGA-TTTCTTCTTATTATGAACTCTC
* * *
1860631 TGTTGGAAATGTTAATACATCTCATTCTATGATGAAATCGAGCAAA-GGTTGAA
65 TGCTGGAAATGTTAATCCATCTCATTCTGTGATGAAATCGAG-AAAGGGTTGAA
* *
1860684 CAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGAATGATTTCTTCTTATTATGAACTCTCT
1 CAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGATTTCTTCTTATTATGAACTCTCT
* * *
1860749 GCTAGAAATGTCAATCCATCTCATTCTGTGATGGAATCGAGAAAGGGTTGAA
66 GCTGGAAATGTTAATCCATCTCATTCTGTGATGAAATCGAGAAAGGGTTGAA
* ** * *
1860801 CAAGTTCTTCTCATTATGAACTTTTTCTCCCTAATCGGATGAGCTCTTCTCATTATGAACTCTCC
1 CAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGATTTCTTCTTATTATGAACTCTCT
* * *
1860866 ACTGGAAATGTTGATCCACCTTC-TTCTGTGATGAAATCGA
66 GCTGGAAATGTTAATCCATC-TCATTCTGTGATGAAATCGA
1860906 TAAAATGTGA
Statistics
Matches: 194, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
116 6 0.03
117 186 0.96
118 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (117 bp):
CAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGATTTCTTCTTATTATGAACTCTCT
GCTGGAAATGTTAATCCATCTCATTCTGTGATGAAATCGAGAAAGGGTTGAA
Found at i:1861306 original size:36 final size:36
Alignment explanation
Indices: 1861249--1861449 Score: 120
Period size: 36 Copynumber: 5.6 Consensus size: 36
1861239 TGAGTGAGGA
* * * *
1861249 AAAATTTGTTTCAA-GATAAACATTTTTAACTGAGAT
1 AAAATTTGTTTTAAGGA-AAACAATCTTAACTGAGAC
*
1861285 AAAATTTGTTTTAAGGAAAACAATCTTAAGTGAGAC
1 AAAATTTGTTTTAAGGAAAACAATCTTAACTGAGAC
* * * * * *
1861321 GAATTTTTTTTTAAGAAAAACAATCTCAAGTGAGA-
1 AAAATTTGTTTTAAGGAAAACAATCTTAACTGAGAC
* ** * ** *
1861356 TAAATATCATTTTGA-GAAGAACAATCTCGAGTGAGAC
1 AAAAT-TTGTTTTAAGGAA-AACAATCTTAACTGAGAC
* * * * **
1861393 AAAATTTGTTTTAAGAAAAACAATATCAATTGAGTT
1 AAAATTTGTTTTAAGGAAAACAATCTTAACTGAGAC
*
1861429 AAAATTTGTTTTTAAGAAAAA
1 AAAATTTG-TTTTAAGGAAAA
1861450 AAACTCTCAA
Statistics
Matches: 132, Mismatches: 27, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
35 5 0.04
36 107 0.81
37 20 0.15
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (36 bp):
AAAATTTGTTTTAAGGAAAACAATCTTAACTGAGAC
Found at i:1861342 original size:72 final size:72
Alignment explanation
Indices: 1861241--1861465 Score: 213
Period size: 72 Copynumber: 3.1 Consensus size: 72
1861231 AATTTCCCTG
* * * * *
1861241 AGTGAGGA-AAAATTTGTTTCAAGATAAACATTTTTAACTGAGATAAAATTTGTTTTAAGGAAAA
1 AGTGA-GACAAAATTTGTTTTAAGAAAAACAATATCAACTGAGATAAAATTTGTTTTAAGGAAAA
*
1861305 CAATCTTA
65 CAATCTCA
* * * * * ** *
1861313 AGTGAGACGAATTTTTTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATATCATTTTGA-GAAGA
1 AGTGAGACAAAATTTGTTTTAAGAAAAACAATATCAACTGAGATAAAAT-TTGTTTTAAGGAA-A
*
1861376 ACAATCTCG
64 ACAATCTCA
* * *
1861385 AGTGAGACAAAATTTGTTTTAAGAAAAACAATATCAATTGAGTTAAAATTTGTTTTTAAGAAAAA
1 AGTGAGACAAAATTTGTTTTAAGAAAAACAATATCAACTGAGATAAAATTTG-TTTTAAGGAAAA
*
1861450 AAACTCTCA
65 CAA-TCTCA
1861459 AGTGAGA
1 AGTGAGA
1861466 TAACATCTTA
Statistics
Matches: 120, Mismatches: 26, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
71 9 0.08
72 85 0.71
73 13 0.11
74 13 0.11
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (72 bp):
AGTGAGACAAAATTTGTTTTAAGAAAAACAATATCAACTGAGATAAAATTTGTTTTAAGGAAAAC
AATCTCA
Found at i:1862137 original size:17 final size:17
Alignment explanation
Indices: 1862111--1862152 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
1862101 GTTTTGTCCG
*
1862111 CTTTGTTGAGTCTT-CAT
1 CTTTGATGAG-CTTCCAT
1862128 CTTTGATGAGCTTCCAT
1 CTTTGATGAGCTTCCAT
1862145 CTTATGAT
1 CTT-TGAT
1862153 AAATTGTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 15 0.68
18 4 0.18
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.48
Consensus pattern (17 bp):
CTTTGATGAGCTTCCAT
Found at i:1863258 original size:6 final size:6
Alignment explanation
Indices: 1863247--1863340 Score: 80
Period size: 6 Copynumber: 16.8 Consensus size: 6
1863237 CTTTTTCCCT
*
1863247 TTTTTC TTTTTC -TTTTC TTTTTC -TTTTC -TTTTC -TTTTC TTTAT-
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* *
1863290 TTTTTC TTTTTC TTTTT- TATTTTC --TTCC ATTTTC TTCTTT- TTTTTC
1 TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TT-TTTC TTTTTC
1863336 TTTTT
1 TTTTT
1863341 ATTTCATGAA
Statistics
Matches: 74, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
4 3 0.04
5 28 0.38
6 40 0.54
7 3 0.04
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:1863262 original size:5 final size:5
Alignment explanation
Indices: 1863248--1863305 Score: 71
Period size: 5 Copynumber: 10.8 Consensus size: 5
1863238 TTTTTCCCTT
*
1863248 TTTTC TTTTTC TTTTC TTTTTC TTTTC TTTTC TTTTC TTTATT TTTTC
1 TTTTC -TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTT-TC TTTTC
1863296 TTTTTC TTTT
1 -TTTTC TTTT
1863306 TTATTTTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
5 28 0.60
6 19 0.40
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:1863272 original size:32 final size:33
Alignment explanation
Indices: 1863218--1863306 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 33
1863208 TCATCTCATG
* * *
1863218 TTTCTTTCTC-TTTCTCTATCTTTTTCCCTT-T
1 TTTCTTTTTCTTTTCTTTTTCTTTTTCCCTTCT
**
1863249 TTTCTTTTTCTTTTCTTTTTC-TTTTCTTTTCT
1 TTTCTTTTTCTTTTCTTTTTCTTTTTCCCTTCT
1863281 TTTCTTTATT-TTTTCTTTTTCTTTTT
1 TTTCTTT-TTCTTTTCTTTTTCTTTTT
1863307 TATTTTCTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
31 16 0.33
32 27 0.55
33 6 0.12
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (33 bp):
TTTCTTTTTCTTTTCTTTTTCTTTTTCCCTTCT
Found at i:1863276 original size:22 final size:22
Alignment explanation
Indices: 1863248--1863339 Score: 100
Period size: 22 Copynumber: 4.2 Consensus size: 22
1863238 TTTTTCCCTT
1863248 TTTTCTTTTTCTTTTCTTTTTC
1 TTTTCTTTTTCTTTTCTTTTTC
1863270 TTTTC-TTTTCTTTTCTTTATT-
1 TTTTCTTTTTCTTTTCTTT-TTC
*
1863291 TTTTCTTTTTCTTTTTTATTTTC
1 TTTTCTTTTTCTTTTCT-TTTTC
* * *
1863314 -TTCCATTTTCTTCTTTTTTTTC
1 TTTTCTTTTTCTT-TTCTTTTTC
1863336 TTTT
1 TTTT
1863340 TATTTCATGA
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
21 18 0.30
22 34 0.57
23 8 0.13
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTCTTTTTCTTTTCTTTTTC
Found at i:1863323 original size:39 final size:39
Alignment explanation
Indices: 1863253--1863340 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 39
1863243 CCCTTTTTTC
* *
1863253 TTTTTC-TTTTCTTTTTCTTTTCTTTTCTTTTCTT-TAT
1 TTTTTCTTTTTCTTTTTATTTTCTTTCCTTTTCTTCTAT
*
1863290 TTTTTCTTTTTCTTTTTTATTTTC-TTCCATTTTCTTCTTT
1 TTTTTCTTTTTC-TTTTTATTTTCTTTCC-TTTTCTTCTAT
1863330 TTTTTCTTTTT
1 TTTTTCTTTTT
1863341 ATTTCATGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
37 6 0.14
38 8 0.18
39 17 0.39
40 13 0.30
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (39 bp):
TTTTTCTTTTTCTTTTTATTTTCTTTCCTTTTCTTCTAT
Found at i:1863332 original size:10 final size:10
Alignment explanation
Indices: 1863245--1863340 Score: 58
Period size: 10 Copynumber: 9.6 Consensus size: 10
1863235 ATCTTTTTCC
1863245 CTTTTTTCTT
1 CTTTTTTCTT
*
1863255 TTTCTTTTCTT
1 CTT-TTTTCTT
*
1863266 TTTCTTTTCTT
1 CTT-TTTTCTT
1863277 -TTCTTTTCTTT
1 CTT-TTTTC-TT
*
1863288 ATTTTTTCTT
1 CTTTTTTCTT
1863298 -TTTCTTT-TT
1 CTTT-TTTCTT
*
1863307 -TATTTTCTT
1 CTTTTTTCTT
**
1863316 CCATTTTCTT
1 CTTTTTTCTT
1863326 CTTTTTT-TT
1 CTTTTTTCTT
1863335 CTTTTT
1 CTTTTT
1863341 ATTTCATGAA
Statistics
Matches: 75, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
8 3 0.04
9 17 0.23
10 28 0.37
11 25 0.33
12 2 0.03
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTTTTCTT
Found at i:1863345 original size:10 final size:9
Alignment explanation
Indices: 1863246--1863345 Score: 67
Period size: 9 Copynumber: 10.8 Consensus size: 9
1863236 TCTTTTTCCC
1863246 TTTTTTCTT
1 TTTTTTCTT
*
1863255 TTTCTT-TT
1 TTTTTTCTT
*
1863263 CTTTTTCTT
1 TTTTTTCTT
1863272 TTCTTTTCTT
1 TT-TTTTCTT
* *
1863282 TTCTTTATT
1 TTTTTTCTT
*
1863291 TTTTCTTTTT
1 TTTT-TTCTT
*
1863301 CTTTTTTATT
1 -TTTTTTCTT
* * *
1863311 TTCTTCCAT
1 TTTTTTCTT
*
1863320 TTTCTTCTT
1 TTTTTTCTT
1863329 TTTTTTCTT
1 TTTTTTCTT
1863338 TTTATTTC
1 TTT-TTTC
1863346 ATGAACTCAA
Statistics
Matches: 68, Mismatches: 18, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
8 6 0.09
9 37 0.54
10 21 0.31
11 4 0.06
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:1864681 original size:14 final size:14
Alignment explanation
Indices: 1864664--1864737 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
1864654 AAATGCACAT
1864664 ATGCAAAGATGTGA
1 ATGCAAAGATGTGA
*
1864678 ATGC-AA-ATGTAAA
1 ATGCAAAGATGT-GA
* *
1864691 ATGAAAATATGTGA
1 ATGCAAAGATGTGA
**
1864705 ATGCAAAGATGCAA
1 ATGCAAAGATGTGA
* *
1864719 ATG-AAAAATATGA
1 ATGCAAAGATGTGA
1864732 ATGCAA
1 ATGCAA
1864738 CAAAGGTATT
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
12 4 0.09
13 15 0.33
14 22 0.49
15 4 0.09
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.22
Consensus pattern (14 bp):
ATGCAAAGATGTGA
Found at i:1864704 original size:27 final size:27
Alignment explanation
Indices: 1864672--1864737 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
1864662 ATATGCAAAG
1864672 ATGTGAATGC-AA-ATGTAAAATGAAAA
1 ATGTGAATGCAAAGATG-AAAATGAAAA
*
1864698 TATGTGAATGCAAAGATGCAAATGAAAA
1 -ATGTGAATGCAAAGATGAAAATGAAAA
*
1864726 ATATGAATGCAA
1 ATGTGAATGCAA
1864738 CAAAGGTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 21 0.60
28 11 0.31
29 3 0.09
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.23
Consensus pattern (27 bp):
ATGTGAATGCAAAGATGAAAATGAAAA
Found at i:1869595 original size:2 final size:2
Alignment explanation
Indices: 1869588--1869684 Score: 194
Period size: 2 Copynumber: 48.5 Consensus size: 2
1869578 AGTACCTAGT
1869588 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1869630 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1869672 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1869685 GAATTATTTA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 95 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1869701 original size:16 final size:17
Alignment explanation
Indices: 1869587--1869708 Score: 60
Period size: 18 Copynumber: 7.1 Consensus size: 17
1869577 GAGTACCTAG
1869587 TTATATATAT--ATATAT
1 TTATATATATGAAT-TAT
*
1869603 ATATATATAT-ATATATAT
1 TTATATATATGA-AT-TAT
*
1869621 ATATATATAT-ATATATAT
1 TTATATATATGA-AT-TAT
*
1869639 ATATATATAT-ATATATAT
1 TTATATATATGA-AT-TAT
*
1869657 ATATATATAT-ATATATAT
1 TTATATATATGA-AT-TAT
*
1869675 ATATATATATGAATTAT
1 TTATATATATGAATTAT
*
1869692 TTATAT-TATGGATTAT
1 TTATATATATGAATTAT
1869708 T
1 T
1869709 AGATTTTGTA
Statistics
Matches: 100, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
16 19 0.19
17 8 0.08
18 72 0.72
19 1 0.01
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTATATATATGAATTAT
Found at i:1873406 original size:21 final size:21
Alignment explanation
Indices: 1873377--1873416 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1873367 GAGAAATTAT
1873377 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
*
1873398 TTTTGAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
1873417 AAATAATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:1877320 original size:23 final size:23
Alignment explanation
Indices: 1877241--1877329 Score: 85
Period size: 23 Copynumber: 3.9 Consensus size: 23
1877231 TATTGATACA
*
1877241 TTGAATAGTGCATCGATGCACCCC
1 TTGAAT-GTGCATCGATGCACTCC
* *
1877265 TTTGAATATGCATCGATACA-T-C
1 -TTGAATGTGCATCGATGCACTCC
* *
1877287 ATGAA-GATGCACCGATGCACTCC
1 TTGAATG-TGCATCGATGCACTCC
1877310 TTGAATGTGCATCGATGCAC
1 TTGAATGTGCATCGATGCAC
1877330 AAGGTCATGC
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
21 14 0.27
22 2 0.04
23 17 0.33
24 12 0.24
25 6 0.12
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (23 bp):
TTGAATGTGCATCGATGCACTCC
Found at i:1877986 original size:24 final size:24
Alignment explanation
Indices: 1877959--1878009 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
1877949 CTAACCGACT
1877959 TCCTAATTC-TATTCCTCCTCAACC
1 TCCTAA-TCATATTCCTCCTCAACC
*
1877983 TCCTAATCATATTCCTCCTTAACC
1 TCCTAATCATATTCCTCCTCAACC
1878007 TCC
1 TCC
1878010 ACATCCAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (24 bp):
TCCTAATCATATTCCTCCTCAACC
Found at i:1881254 original size:22 final size:21
Alignment explanation
Indices: 1881229--1881270 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1881219 ACTTTTTATA
* *
1881229 AATATATATATATAATTAAATT
1 AATATACAAATAT-ATTAAATT
1881251 AATATACAAATATATTAAAT
1 AATATACAAATATATTAAAT
1881271 GATGTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATACAAATATATTAAATT
Found at i:1881435 original size:9 final size:9
Alignment explanation
Indices: 1881421--1881453 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1881411 GGATTAAATT
1881421 TAAAATTTG
1 TAAAATTTG
1881430 TAAAA-TT-
1 TAAAATTTG
1881437 TAAAATTTG
1 TAAAATTTG
1881446 TAAAATTT
1 TAAAATTT
1881454 AAATGAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 5 0.23
8 4 0.18
9 13 0.59
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (9 bp):
TAAAATTTG
Found at i:1881437 original size:16 final size:16
Alignment explanation
Indices: 1881416--1881456 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
1881406 AATTAGGATT
1881416 AAATTTAAAATTTGTA
1 AAATTTAAAATTTGTA
1881432 AAATTTAAAATTTGTA
1 AAATTTAAAATTTGTA
1881448 AAATTTAAA
1 AAATTTAAA
1881457 TGAATGGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (16 bp):
AAATTTAAAATTTGTA
Found at i:1882832 original size:25 final size:25
Alignment explanation
Indices: 1882803--1882888 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 25
1882793 GAATATGTCA
*
1882803 ATATTTTTAAAATAATCAAAATAAT
1 ATATTTTTAAAATAATTAAAATAAT
* *
1882828 ATATTTTATAATAATATATTTATAATTAT
1 ATATTTT-TAA-AATA-A-TTAAAATAAT
* * * *
1882857 TTGTTTTTTAAATTATTAAAATAAT
1 ATATTTTTAAAATAATTAAAATAAT
1882882 ATATTTT
1 ATATTTT
1882889 AACATTAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
25 20 0.43
26 4 0.09
27 7 0.15
28 3 0.07
29 12 0.26
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (25 bp):
ATATTTTTAAAATAATTAAAATAAT
Found at i:1882851 original size:14 final size:15
Alignment explanation
Indices: 1882822--1882853 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1882812 AAATAATCAA
1882822 AATAATATATTTTAT
1 AATAATATATTTTAT
1882837 AATAATATA-TTTAT
1 AATAATATATTTTAT
1882851 AAT
1 AAT
1882854 TATTTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:1882878 original size:54 final size:56
Alignment explanation
Indices: 1882804--1882969 Score: 185
Period size: 62 Copynumber: 2.9 Consensus size: 56
1882794 AATATGTCAA
* * *
1882804 TATTTTTAAAATAATCAAAATAATATATTTTATAATAATATATTTATAATTA-T-T
1 TATTTTTTAAATTATTAAAATAATATATTTTATAATAATATATTTATAATTATTAT
*
1882858 TGTTTTTTAAATTATTAAAATAATATATTTTAACATTAAATAATATATTTATAATTATTTAT
1 TATTTTTTAAATTATTAAAATAATATATTTT---A-T-AATAATATATTTATAATTA-TTAT
* * * *
1882920 TATTTTTTAAATTGTTAAAACAATATATTTTATATTAATTTA-TTATAATT
1 TATTTTTTAAATTATTAAAATAATATATTTTATAATAATATATTTATAATT
1882970 TTAGTAATTA
Statistics
Matches: 95, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
54 27 0.28
56 8 0.08
57 8 0.08
58 2 0.02
59 20 0.21
61 1 0.01
62 29 0.31
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (56 bp):
TATTTTTTAAATTATTAAAATAATATATTTTATAATAATATATTTATAATTATTAT
Found at i:1882987 original size:42 final size:42
Alignment explanation
Indices: 1882892--1882993 Score: 111
Period size: 42 Copynumber: 2.4 Consensus size: 42
1882882 ATATTTTAAC
* *
1882892 ATTAAATAATATA-TTTATAATTATTTATTATTTTTTAAATT
1 ATTAAATAATATATTTTATAATTATTTATTATATTTTAAATA
* * *
1882933 GTTAAAACAATATATTTTAT-ATTAATTTATTATAATTTT-AGTA
1 ATT-AAATAATATATTTTATAATT-ATTTATTAT-ATTTTAAATA
1882976 ATTAAATAATATATTTTA
1 ATTAAATAATATATTTTA
1882994 ACATTATAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
41 2 0.04
42 26 0.52
43 18 0.36
44 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (42 bp):
ATTAAATAATATATTTTATAATTATTTATTATATTTTAAATA
Found at i:1883022 original size:2 final size:2
Alignment explanation
Indices: 1883017--1883051 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1883007 TAAAAAATCT
1883017 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1883052 ATTTGGTCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1893166 original size:2 final size:2
Alignment explanation
Indices: 1893159--1893185 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1893149 ATAAACTTTA
1893159 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1893186 AACTAACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1902341 original size:59 final size:59
Alignment explanation
Indices: 1902239--1902374 Score: 148
Period size: 59 Copynumber: 2.3 Consensus size: 59
1902229 AAATGTGTCT
* * ***
1902239 ATTTCATCCCTAAACTATGATATCATTCTAAACCAATCCTCAAACTTTTT-AATATTTTA
1 ATTTCA-CCCCAAACTATGACATCATTCTAAACCAATCCTCAAACTTTTTGAATATCCCA
*** * *
1902298 ATTTCACCCCAAACTATGACATCCATTCTAAATTGATCTTCAAACTTTTTGGATATCCCA
1 ATTTCACCCCAAACTATGACAT-CATTCTAAACCAATCCTCAAACTTTTTGAATATCCCA
*
1902358 ATTTCATCCCAAACTAT
1 ATTTCACCCCAAACTAT
1902375 ACGTAAATAC
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
58 14 0.22
59 29 0.45
60 21 0.33
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (59 bp):
ATTTCACCCCAAACTATGACATCATTCTAAACCAATCCTCAAACTTTTTGAATATCCCA
Found at i:1917328 original size:18 final size:19
Alignment explanation
Indices: 1917288--1917334 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1917278 ATTTTATTTA
*
1917288 TTTATAATTTACACTAATT
1 TTTATAATTTACACTAATG
*
1917307 TTTATAATTTA-ATTAATG
1 TTTATAATTTACACTAATG
*
1917325 TTTACAATTT
1 TTTATAATTT
1917335 TGTTAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTATAATTTACACTAATG
Found at i:1918027 original size:21 final size:21
Alignment explanation
Indices: 1918002--1918083 Score: 121
Period size: 21 Copynumber: 4.0 Consensus size: 21
1917992 CCGTTAGACA
*
1918002 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
*
1918023 GGGGGAATCTGTTCCCCCT-G
1 GGGGGAATCTGTACCCCCTGG
* *
1918043 GGGGAAATCTGTACCCCCTAG
1 GGGGGAATCTGTACCCCCTGG
1918064 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
1918084 AGCAATCTGT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 18 0.33
21 36 0.67
ACGTcount: A:0.16, C:0.29, G:0.35, T:0.20
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:1918059 original size:41 final size:40
Alignment explanation
Indices: 1918002--1918083 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 40
1917992 CCGTTAGACA
* *
1918002 GGGGGAATCGGTACCCCCTGGGGGGGAATCTGTTCCCCCT
1 GGGGGAATCGGTACCCCCTAGGGGGGAATCTGTACCCCCT
*
1918042 GGGGGAAATCTGTACCCCCTAGGGGGGAATCTGTACCCCCT
1 GGGGG-AATCGGTACCCCCTAGGGGGGAATCTGTACCCCCT
1918083 G
1 G
1918084 AGCAATCTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
40 5 0.13
41 33 0.87
ACGTcount: A:0.16, C:0.29, G:0.35, T:0.20
Consensus pattern (40 bp):
GGGGGAATCGGTACCCCCTAGGGGGGAATCTGTACCCCCT
Found at i:1918459 original size:26 final size:26
Alignment explanation
Indices: 1918423--1918480 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
1918413 TGAAAAATTA
1918423 CTCCCCTTTAAAACACTTTAACACTT
1 CTCCCCTTTAAAACACTTTAACACTT
1918449 CTCCCCTTTAAAACACTTTAACACTT
1 CTCCCCTTTAAAACACTTTAACACTT
1918475 CTCCCC
1 CTCCCC
1918481 CTTTTTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.33
Consensus pattern (26 bp):
CTCCCCTTTAAAACACTTTAACACTT
Found at i:1919587 original size:19 final size:20
Alignment explanation
Indices: 1919544--1919591 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1919534 TCTAAATCAT
*
1919544 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1919564 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1919583 TTTTCAAAA
1 TTTTCAAAA
1919592 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1920495 original size:32 final size:33
Alignment explanation
Indices: 1920453--1920517 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
1920443 TTACAAACTC
*
1920453 CCTAG-TTTTTACGGGCTAAACTAGAACCTTTA
1 CCTAGCTTTTAACGGGCTAAACTAGAACCTTTA
*
1920485 CCTAGCTTTTACACGGGCTAAGCTAGAACCTTT
1 CCTAGCTTTTA-ACGGGCTAAACTAGAACCTTT
1920518 CCCCTTTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 5 0.17
33 4 0.14
34 20 0.69
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (33 bp):
CCTAGCTTTTAACGGGCTAAACTAGAACCTTTA
Found at i:1920894 original size:21 final size:21
Alignment explanation
Indices: 1920869--1920929 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 21
1920859 CCGTTAGACA
*
1920869 GGGGGAATCAGTATCCCCTGG
1 GGGGGAATCAGTACCCCCTGG
*
1920890 GGGGGAATCGGTACCCCCT-G
1 GGGGGAATCAGTACCCCCTGG
*
1920910 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCAGTACCCCCTG
1920930 AGCAATCTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.16, C:0.28, G:0.38, T:0.18
Consensus pattern (21 bp):
GGGGGAATCAGTACCCCCTGG
Found at i:1921648 original size:19 final size:20
Alignment explanation
Indices: 1921624--1921675 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1921614 AAATAACCAA
*
1921624 CGAATTCGCAACTCA-ATTT
1 CGAATTCGCAACACAGATTT
* *
1921643 CGAATTTGCAACACAGTTTT
1 CGAATTCGCAACACAGATTT
*
1921663 CGAATTCGTAACA
1 CGAATTCGCAACA
1921676 AGAATTTACA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (20 bp):
CGAATTCGCAACACAGATTT
Found at i:1922022 original size:18 final size:17
Alignment explanation
Indices: 1921999--1922032 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1921989 TGGGTCCATT
*
1921999 AATAAATACATGAATCAC
1 AATAAACACAT-AATCAC
1922017 AATAAACACATAATCA
1 AATAAACACATAATCA
1922033 TATTGATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.59, C:0.18, G:0.03, T:0.21
Consensus pattern (17 bp):
AATAAACACATAATCAC
Found at i:1922762 original size:62 final size:62
Alignment explanation
Indices: 1922658--1922776 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 62
1922648 GCGGTAAAAT
* * *
1922658 TGAGTTGTGAAATTGGCGAATTCGAGTTGCGAAATCCGAATTCGAGTTGCGAATTTGAAACA
1 TGAGTTGCGAAATTGGCAAATTCGAGTTGCGAAATCCAAATTCGAGTTGCGAATTTGAAACA
* * * ** **
1922720 TGAGTTGCGAATTTGGCAAATTTGTGTTGCGAAATGTAAATTCTTGTTGCGAATTTG
1 TGAGTTGCGAAATTGGCAAATTCGAGTTGCGAAATCCAAATTCGAGTTGCGAATTTG
1922777 GCTTTCGTGT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
62 47 1.00
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.34
Consensus pattern (62 bp):
TGAGTTGCGAAATTGGCAAATTCGAGTTGCGAAATCCAAATTCGAGTTGCGAATTTGAAACA
Found at i:1929102 original size:30 final size:30
Alignment explanation
Indices: 1929032--1929109 Score: 122
Period size: 29 Copynumber: 2.6 Consensus size: 30
1929022 CATATAAACA
1929032 TTAAAAATATATATTTTATTCTTATCTTAAC
1 TTAAAAA-ATATATTTTATTCTTATCTTAAC
* *
1929063 TT-TAAAATATATTTTATTCTTATTTTAAC
1 TTAAAAAATATATTTTATTCTTATCTTAAC
1929092 TTAAAAAATATATTTTAT
1 TTAAAAAATATATTTTAT
1929110 ATATCTTATA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 24 0.56
30 17 0.40
31 2 0.05
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (30 bp):
TTAAAAAATATATTTTATTCTTATCTTAAC
Found at i:1930200 original size:26 final size:26
Alignment explanation
Indices: 1930171--1930251 Score: 60
Period size: 26 Copynumber: 3.0 Consensus size: 26
1930161 TATACCTAAT
1930171 TGTTAGAATGTCATAAATGCTACATG
1 TGTTAGAATGTCATAAATGCTACATG
* *
1930197 TGTTCACCGAGATTTCATGATAAAGCTA-AT-
1 TGTT-A--GA-ATGTCAT-A-AATGCTACATG
*
1930227 TGTTAGAATGTCAT-AATGCCACATG
1 TGTTAGAATGTCATAAATGCTACATG
1930252 CGTTCACCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 17
0.66 0.08 0.27
Matches are distributed among these distances:
23 5 0.12
24 2 0.05
26 10 0.24
27 3 0.07
29 3 0.07
30 10 0.24
31 3 0.07
32 6 0.14
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (26 bp):
TGTTAGAATGTCATAAATGCTACATG
Found at i:1932232 original size:21 final size:20
Alignment explanation
Indices: 1932208--1932246 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1932198 AAATCTTTGG
*
1932208 AAATAAAGATTTTGAAAAACA
1 AAATAAA-ACTTTGAAAAACA
*
1932229 AAATGAAACTTTGAAAAA
1 AAATAAAACTTTGAAAAA
1932247 TGATTTAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (20 bp):
AAATAAAACTTTGAAAAACA
Found at i:1937050 original size:60 final size:60
Alignment explanation
Indices: 1936957--1937077 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
1936947 TATCCGCCAA
* *
1936957 AGATTTTAGGTATTCATATTTGATGAATCATTGTCGATTGTGATGCTTTTGAAACAAAAT
1 AGATTTTAAGTATTCATATTTGATGAATCATTGTCAATTGTGATGCTTTTGAAACAAAAT
1937017 AGATTTTAAGTATTCATATTTGATGAATCATTGTCAATTGTGATGCTTTTGAAACAAAAT
1 AGATTTTAAGTATTCATATTTGATGAATCATTGTCAATTGTGATGCTTTTGAAACAAAAT
1937077 A
1 A
1937078 CAATGTTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (60 bp):
AGATTTTAAGTATTCATATTTGATGAATCATTGTCAATTGTGATGCTTTTGAAACAAAAT
Found at i:1937130 original size:31 final size:31
Alignment explanation
Indices: 1937088--1937150 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
1937078 CAATGTTAAT
* *
1937088 TTTTTATTTTTACAAGACTGATGAGTGAAAA
1 TTTTTAGTTTTACAAGACTAATGAGTGAAAA
1937119 TTTTTAGTTTTACAAGACTAATGAGTGAAAA
1 TTTTTAGTTTTACAAGACTAATGAGTGAAAA
1937150 T
1 T
1937151 AGACTGAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (31 bp):
TTTTTAGTTTTACAAGACTAATGAGTGAAAA
Found at i:1941574 original size:2 final size:2
Alignment explanation
Indices: 1941569--1941593 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1941559 ACACACACAC
1941569 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1941594 TCCATACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1950058 original size:24 final size:24
Alignment explanation
Indices: 1950026--1950074 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1950016 TATTCTATAA
1950026 TGGGTGAAGCACCACTTTCCCCAT
1 TGGGTGAAGCACCACTTTCCCCAT
1950050 TGGGTGAAGCACCACTTTCCCCAT
1 TGGGTGAAGCACCACTTTCCCCAT
1950074 T
1 T
1950075 TAGAGAAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (24 bp):
TGGGTGAAGCACCACTTTCCCCAT
Found at i:1950082 original size:24 final size:24
Alignment explanation
Indices: 1950031--1950087 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
1950021 TATAATGGGT
* *
1950031 GAAGCACCACTTTCCCCATTGGGT
1 GAAGCACCACTTTCCCCATTGAGA
*
1950055 GAAGCACCACTTTCCCCATTTAGA
1 GAAGCACCACTTTCCCCATTGAGA
*
1950079 GAAGGACCA
1 GAAGCACCA
1950088 GTGATAGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (24 bp):
GAAGCACCACTTTCCCCATTGAGA
Found at i:1952692 original size:14 final size:14
Alignment explanation
Indices: 1952673--1952699 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1952663 CAATACTGAA
1952673 ATTTAAAATAAATT
1 ATTTAAAATAAATT
1952687 ATTTAAAATAAAT
1 ATTTAAAATAAAT
1952700 CAATCCATAC
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTTAAAATAAATT
Found at i:1952775 original size:32 final size:31
Alignment explanation
Indices: 1952736--1953036 Score: 256
Period size: 32 Copynumber: 10.5 Consensus size: 31
1952726 CAATCCATAT
1952736 TTTAAAATAAATCAATCTATACAGATAAATTA
1 TTTAAAATAAATCAATCTATACA-ATAAATTA
1952768 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATAC-AATAAATTA
1952800 TTTAAAATAAATC-A---AT-CAAT--A-T-
1 TTTAAAATAAATCAATCTATACAATAAATTA
*
1952822 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCTATAC-AATAAATTA
1952854 TTTAAAATAAATCAATC----C-AT--A-T-
1 TTTAAAATAAATCAATCTATACAATAAATTA
1952876 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATAC-AATAAATTA
* * *
1952908 TTTAAAATAAATTAATCCATACAACTACA--A
1 TTTAAAATAAATCAATCTATACAA-TAAATTA
1952938 --T--AATAAATCAATCTAT---AT------
1 TTTAAAATAAATCAATCTATACAATAAATTA
1952956 TTTAAAATAAATCAATCTATACAAATAAATTA
1 TTTAAAATAAATCAATCTATAC-AATAAATTA
1952988 TTTAAAATAAATCAAT-TCATACTAATAAATTA
1 TTTAAAATAAATCAATCT-ATAC-AATAAATTA
1953020 TTTAAAATAAATCAATC
1 TTTAAAATAAATCAATC
1953037 CATATTTTAA
Statistics
Matches: 225, Mismatches: 6, Indels: 75
0.74 0.02 0.25
Matches are distributed among these distances:
20 1 0.00
22 46 0.20
23 4 0.02
24 2 0.01
26 23 0.10
27 2 0.01
28 9 0.04
30 3 0.01
31 6 0.03
32 128 0.57
33 1 0.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (31 bp):
TTTAAAATAAATCAATCTATACAATAAATTA
Found at i:1952779 original size:14 final size:14
Alignment explanation
Indices: 1952760--1952811 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
1952750 ATCTATACAG
1952760 ATAAATTATTTAAA
1 ATAAATTATTTAAA
* *
1952774 ATAAATCAATCTATACTA
1 ATAAAT-TAT-T-TA-AA
1952792 ATAAATTATTTAAA
1 ATAAATTATTTAAA
1952806 ATAAAT
1 ATAAAT
1952812 CAATCAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 13 0.43
15 4 0.13
16 2 0.07
17 4 0.13
18 7 0.23
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAAATTATTTAAA
Found at i:1952830 original size:86 final size:80
Alignment explanation
Indices: 1952679--1953084 Score: 286
Period size: 80 Copynumber: 5.0 Consensus size: 80
1952669 TGAAATTTAA
* *
1952679 AATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAAT
1 AATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCAATATTTTAAAAT
*
1952744 AAATCAATCTATAC-
66 AAATCAATCCATACT
*
1952758 AGATAAATTATTTAAAATAAATCAATCTATACTAA-TAAATTATTTAAAATAAATCAATCAATAT
1 A-ATAAATTATTTAAAATAAATCAATCCATAC-AACTAAA--A--T--AATAAATCAATCAATAT
1952822 TTTAAAATAAATCAATCCATACT
58 TTTAAAATAAATCAATCCATACT
*** * *
1952845 AATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCTATACTAATAAATTAT
1 AATAAATTATTTAAAATAAATCAATCCATACAACTAAAAT-AATAAATCAAT-C-AAT--A-T-T
*
1952909 TTAAAATAAATTAATCCATAC-
59 TTAAAATAAATCAATCCATACT
* * *** * *
1952930 AACTACA--A--T--AATAAATCAATCTATA-TTTTAAAATAAATCAATCTATACAAATAAATTA
1 AA-TAAATTATTTAAAATAAATCAATCCATACAACTAAAAT-AATAAATCAAT-C-AAT--A-T-
*
1952988 TTTAAAATAAATCAATTCATACT
58 TTTAAAATAAATCAATCCATACT
* ** *
1953011 AATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATTAATTC-ATATTTTAAAA
1 AATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAA-TCAATATTTTAAAA
1953071 TAAATCAATCCATA
65 TAAATCAATCCATA
1953085 TTTTAAAATA
Statistics
Matches: 278, Mismatches: 24, Indels: 53
0.78 0.07 0.15
Matches are distributed among these distances:
76 20 0.07
77 1 0.00
78 1 0.00
79 1 0.00
80 114 0.41
81 6 0.02
82 14 0.05
83 2 0.01
84 8 0.03
85 7 0.03
86 103 0.37
87 1 0.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (80 bp):
AATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCAATATTTTAAAAT
AAATCAATCCATACT
Found at i:1952851 original size:22 final size:22
Alignment explanation
Indices: 1952802--1952850 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1952792 ATAAATTATT
**
1952802 TAAAATAAATCAATCAATATTT
1 TAAAATAAATCAATCAATATAA
*
1952824 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCAATA-TAA
1952847 TAAA
1 TAAA
1952851 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCAATATAA
Found at i:1952905 original size:22 final size:22
Alignment explanation
Indices: 1952856--1952904 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1952846 ATAAATTATT
**
1952856 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
1952878 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
1952901 TAAA
1 TAAA
1952905 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1952960 original size:80 final size:83
Alignment explanation
Indices: 1952822--1953053 Score: 328
Period size: 80 Copynumber: 2.8 Consensus size: 83
1952812 CAATCAATAT
1952822 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAA
*
1952887 TCAATCTATACTAATAAATTA
63 TCAATCTATACAAATAAATTA
* * *
1952908 TTTAAAATAAATTAATCCATAC-AACTACA-A-T-AATAAATCAATCTATATTTTAAAATAAATC
1 TTTAAAATAAATCAATCCATACTAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATC
1952969 AATCTATACAAATAAATTA
65 AATCTATACAAATAAATTA
*
1952988 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAA
1953053 T
63 T
1953054 TAATTCATAT
Statistics
Matches: 130, Mismatches: 8, Indels: 16
0.84 0.05 0.10
Matches are distributed among these distances:
80 70 0.54
81 2 0.02
82 2 0.02
84 2 0.02
85 2 0.02
86 52 0.40
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (83 bp):
TTTAAAATAAATCAATCCATACTAATAAATATTAAATAAATCAATCCATATTTTAAAATAAATCA
ATCTATACAAATAAATTA
Found at i:1952981 original size:18 final size:15
Alignment explanation
Indices: 1952956--1953035 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 15
1952946 CAATCTATAT
1952956 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
*
1952971 TCTATACAAATAAAT-TA
1 T-T-TA-AAATAAATCAA
1952988 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
* *
1953003 TTCATACTAATAAAT-TA
1 TT--TA-AAATAAATCAA
1953020 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
1953035 T
1 T
1953036 CCATATTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
14 15 0.29
15 10 0.20
16 2 0.04
17 9 0.18
18 15 0.29
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (15 bp):
TTTAAAATAAATCAA
Found at i:1953046 original size:22 final size:22
Alignment explanation
Indices: 1953020--1953095 Score: 134
Period size: 22 Copynumber: 3.5 Consensus size: 22
1953010 TAATAAATTA
1953020 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
* *
1953042 TTTAAAATAAATTAATTCATAT
1 TTTAAAATAAATCAATCCATAT
1953064 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1953086 TTTAAAATAA
1 TTTAAAATAA
1953096 TATATTTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1953062 original size:54 final size:54
Alignment explanation
Indices: 1952768--1952928 Score: 295
Period size: 54 Copynumber: 3.0 Consensus size: 54
1952758 AGATAAATTA
*
1952768 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCAATAT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
1952822 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
1952876 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATTAATCCATA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA
1952929 CAACTACAAT
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 103 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (54 bp):
TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:1953102 original size:15 final size:15
Alignment explanation
Indices: 1953083--1953292 Score: 332
Period size: 15 Copynumber: 14.0 Consensus size: 15
1953073 AATCAATCCA
1953083 TATTTTAAAAT-AAT
1 TATTTTAAAATAAAT
1953097 ATATTTTAAAATAAAT
1 -TATTTTAAAATAAAT
*
1953113 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
1953128 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
1953143 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
1953158 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
*
1953173 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
*
1953188 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
*
1953203 TGTTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
1953218 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
*
1953233 TATTTGAAAATAAAT
1 TATTTTAAAATAAAT
*
1953248 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
1953263 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
1953278 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
1953293 AACCTTATTA
Statistics
Matches: 182, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
15 179 0.98
16 3 0.02
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:1957088 original size:14 final size:14
Alignment explanation
Indices: 1957069--1957104 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1957059 GCCTGAAATA
1957069 TTCATAAATGATTG
1 TTCATAAATGATTG
*
1957083 TTCATAAGTGATTG
1 TTCATAAATGATTG
*
1957097 ATCATAAA
1 TTCATAAA
1957105 GATCAAGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (14 bp):
TTCATAAATGATTG
Found at i:1957141 original size:2 final size:2
Alignment explanation
Indices: 1957134--1957180 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1957124 ACATTCATGC
1957134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1957176 AT AT A
1 AT AT A
1957181 GTGTCGCCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1958837 original size:25 final size:23
Alignment explanation
Indices: 1958785--1958866 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 23
1958775 GTATTTTATG
*
1958785 TATTTA-TTTCTTTTTATTATTT
1 TATTTATTTTCTTTTTATTATTC
*
1958807 TA-TTATTTTCTTTTTTTCTCATTC
1 TATTTATTTTCTTTTTAT-T-ATTC
*
1958831 TATTTATTTTATTTATGT-TTA-TC
1 TATTTATTTTCTTT-T-TATTATTC
1958854 T-TTTATTTTCTTT
1 TATTTATTTTCTTT
1958867 ATTTCATTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.06
22 23 0.46
23 4 0.08
24 6 0.12
25 11 0.22
26 2 0.04
27 1 0.02
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.74
Consensus pattern (23 bp):
TATTTATTTTCTTTTTATTATTC
Found at i:1958845 original size:9 final size:9
Alignment explanation
Indices: 1958769--1958875 Score: 53
Period size: 9 Copynumber: 11.9 Consensus size: 9
1958759 TTCTTCTTTG
*
1958769 TTTTATGTA
1 TTTTATTTA
*
1958778 TTTTATGTA
1 TTTTATTTA
*
1958787 -TTTATTTC
1 TTTTATTTA
1958795 TTTT-TATTA
1 TTTTAT-TTA
1958804 TTTTA-TTA
1 TTTTATTTA
*
1958812 TTTTCTTT-
1 TTTTATTTA
* *
1958820 TTTT-CTCA
1 TTTTATTTA
*
1958828 TTCTATTTA
1 TTTTATTTA
1958837 TTTTATTTA
1 TTTTATTTA
1958846 TGTTTATCTTTTA
1 T-TTTA---TTTA
*
1958859 TTTTCTTTA
1 TTTTATTTA
*
1958868 TTTCATTT
1 TTTTATTT
1958876 GTTTCTCCAT
Statistics
Matches: 75, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
7 1 0.01
8 21 0.28
9 41 0.55
10 4 0.05
12 3 0.04
13 5 0.07
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1959721 original size:21 final size:21
Alignment explanation
Indices: 1959697--1959750 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
1959687 TCTTCTTTGT
1959697 TTTATGTATTTTATT-TATTTA
1 TTTAT-TATTTTATTATATTTA
*
1959718 TTTATTTATTTCTATTATTTTTA
1 TTTA-TTATTT-TATTATATTTA
1959741 TTT-TTATTTT
1 TTTATTATTTT
1959751 CTTTTTTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.03
21 15 0.52
22 5 0.17
23 8 0.28
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTATTATTTTATTATATTTA
Found at i:1959751 original size:22 final size:22
Alignment explanation
Indices: 1959722--1959806 Score: 86
Period size: 22 Copynumber: 3.7 Consensus size: 22
1959712 TATTTATTTA
1959722 TTTA-TTTCTATTATTTTTAT-T
1 TTTATTTTCT-TTATTTTTATCT
1959743 TTTATTTTCTTT-TTTTCCTCATTCT
1 TTTATTTTCTTTATTTT--T-A-TCT
*
1959768 ATTTATTTTATTTATTTTTATCT
1 -TTTATTTTCTTTATTTTTATCT
1959791 TTTATTTTCTTTATTT
1 TTTATTTTCTTTATTT
1959807 CATTTGTTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
20 4 0.07
21 6 0.11
22 21 0.39
23 4 0.07
24 2 0.04
25 2 0.04
26 11 0.20
27 4 0.07
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTATTTTCTTTATTTTTATCT
Found at i:1959781 original size:9 final size:9
Alignment explanation
Indices: 1959696--1959811 Score: 66
Period size: 9 Copynumber: 13.3 Consensus size: 9
1959686 TTCTTCTTTG
*
1959696 TTTTATGTA
1 TTTTATTTA
1959705 TTTTATTTA
1 TTTTATTTA
1959714 -TTTATTTA
1 TTTTATTTA
*
1959722 -TTTATTTC
1 TTTTATTTA
*
1959730 TATTATTT-
1 TTTTATTTA
1959738 TTATT-TTTA
1 TT-TTATTTA
*
1959747 TTTTCTTT-
1 TTTTATTTA
** *
1959755 TTTTCCTCA
1 TTTTATTTA
*
1959764 TTCTATTTA
1 TTTTATTTA
1959773 TTTTATTTA
1 TTTTATTTA
* *
1959782 TTTT-TATC
1 TTTTATTTA
1959790 TTTTATTT-
1 TTTTATTTA
1959798 TCTTTATTTCA
1 T-TTTATTT-A
1959809 TTT
1 TTT
1959812 GTTTCTCCAT
Statistics
Matches: 84, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
8 34 0.40
9 47 0.56
10 2 0.02
11 1 0.01
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1959845 original size:37 final size:38
Alignment explanation
Indices: 1959783--1959854 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
1959773 TTTTATTTAT
*
1959783 TTTTATCTTTTATTTTCTTTATTTCATTTGTTTCTCCA
1 TTTTATCTTTTATTTACTTTATTTCATTTGTTTCTCCA
*
1959821 TTTTA-CTTTT-TTTACTTTATTTTCATTTTTTTCT
1 TTTTATCTTTTATTTACTTTA-TTTCATTTGTTTCT
1959855 AATACGTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 8 0.26
37 18 0.58
38 5 0.16
ACGTcount: A:0.12, C:0.14, G:0.01, T:0.72
Consensus pattern (38 bp):
TTTTATCTTTTATTTACTTTATTTCATTTGTTTCTCCA
Found at i:1962645 original size:20 final size:20
Alignment explanation
Indices: 1962620--1962663 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1962610 GAGCTCATAT
1962620 AGGATCATATAGATGCATTC
1 AGGATCATATAGATGCATTC
* *
1962640 AGGATCATATAGTTGCATTT
1 AGGATCATATAGATGCATTC
1962660 AGGA
1 AGGA
1962664 GCTCATACAG
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:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (20 bp):
AGGATCATATAGATGCATTC
Found at i:1965003 original size:19 final size:18
Alignment explanation
Indices: 1964981--1965038 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
1964971 GTCATAGCAC
1964981 TTTTATTTTACTTGTTTAT
1 TTTTATTTTACTT-TTTAT
*
1965000 TTTTCTTTT-CTTTTT-T
1 TTTTATTTTACTTTTTAT
*
1965016 TATATAATTTTACTTTTTAT
1 T-T-TTATTTTACTTTTTAT
1965036 TTT
1 TTT
1965039 CCTTATCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
16 2 0.06
17 4 0.12
18 9 0.28
19 15 0.47
20 2 0.06
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTATTTTACTTTTTAT
Found at i:1971738 original size:20 final size:20
Alignment explanation
Indices: 1971709--1971747 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1971699 AGAGCTCATA
*
1971709 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1971729 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1971748 GTGGTGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1974895 original size:124 final size:124
Alignment explanation
Indices: 1974709--1975438 Score: 1082
Period size: 124 Copynumber: 5.9 Consensus size: 124
1974699 TTGGACTCAA
*
1974709 AGCAACATTCATCTTTAGATTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAGGCTCAAC
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCATGATGAAGGATATCCAATTCAAGGCTCAAC
* * *
1974774 TTCACAACGAATGGACCATCCACGGTTTCAACTTCACGACGAAGGGAATTGTGCTCACC
66 TTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACC
* *
1974833 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGATATCCAATTTAAGGCTCAAC
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCATGATGAAGGATATCCAATTCAAGGCTCAAC
* * *
1974898 TTCACAACGAAGGGGCCATCAACGGTTTTAACTTCACGATGAAGGGAATCGTGCTCACC
66 TTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACC
* * *
1974957 AGCAATATTCATCTTTAGATTGAATTTCAACTTCATGATAAAGGATATCCAATTCAAGGCTCAAC
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCATGATGAAGGATATCCAATTCAAGGCTCAAC
* *
1975022 TTCACAACGAAGAGGCCATCCACAGTTTCAACTTCACGACGAAGGGAATCGTGCTCACC
66 TTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACC
* * * *
1975081 AGCAACATTCATCTTTAGATTGGATTTTAACTTCATGACGAAGGATATCTAATTCAATGCTCAAC
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCATGATGAAGGATATCCAATTCAAGGCTCAAC
* *
1975146 TTCACAACGAAAGAGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACC
66 TTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACC
* * * ** * * *
1975205 AACAACATTCATCTTTAGATTGGATTTCAAATTCACGATGAAATACATCCAATTTAAGGCTCAAT
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCATGATGAAGGATATCCAATTCAAGGCTCAAC
* * * * *
1975270 TTCATAACGAAGGGGCCATCCACGATTTCAACTTCATGACGAAGAGAACCGTGCTCACC
66 TTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACC
* * *
1975329 AGAAACATTCATATTTAGATTGGATTTCAACTTCAAGATGAAGGATATCCAATTCAAGGCTCAAC
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCATGATGAAGGATATCCAATTCAAGGCTCAAC
* * * * **
1975394 TTCATAATGAAGGGGTCATCCACGATTTCAACTTCATTACGAAGG
66 TTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACGAAGG
1975439 ATATCGAGCT
Statistics
Matches: 543, Mismatches: 63, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
124 543 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (124 bp):
AGCAACATTCATCTTTAGATTGGATTTCAACTTCATGATGAAGGATATCCAATTCAAGGCTCAAC
TTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACC
Found at i:1975658 original size:84 final size:84
Alignment explanation
Indices: 1975512--1976471 Score: 925
Period size: 84 Copynumber: 11.4 Consensus size: 84
1975502 TAATTTACAA
* ** * * * * *
1975512 CATAGCTCAAGGCAAGAAAGACTATTTTCCAATAAAAGACCTTCGAGTTTGACTACGCTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTC
1975577 CAAGGCACATCATTTGCAG
66 CAAGGCACATCATTTGCAG
* * * * *
1975596 CATAACTCAAGGCTAGAAGGGTTATCCGCCAACAAAGGACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTC
* ** *
1975661 TAAGGCACATCATTTATAA
66 CAAGGCACATCATTTGCAG
* * * *
1975680 CATAGCTCAAGGCAAGAAGTGTTATTTTCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTC
* ** *
1975745 AAAGAAACAAT-ATTTACAG
66 CAAGGCAC-ATCATTTGCAG
* ** * * *
1975764 CATAGCTCAAGGCGAGAAGGCCTATCTACCAACAAAAGACCTTCGAGTTCAACTACGCTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTC
* * *
1975829 CAAGACACATAATTTGCAA
66 CAAGGCACATCATTTGCAG
* * *
1975848 TATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTC
*
1975913 AAAGGCACAAT-ATTTGCAG
66 CAAGGCAC-ATCATTTGCAG
* * * * * * * *
1975932 CATAGCTCAAGGCGATAAGGGCTATCTGCCAACAAAAAACCTTTGAGTTTGACTACGCTC-GATT
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAG-CT
*
1975996 CCAAGGCACATCTTTTGCAG
65 CCAAGGCACATCATTTGCAG
** * * * * *
1976016 CATAAATCAAGGCTAGAAGAGTTATCTGACAACAAAATACCTTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTC
* *
1976081 AAAGACACATCATTTGCAG
66 CAAGGCACATCATTTGCAG
* * * * * * * *
1976100 TATAGCTCAAGG-AGAAAAGGGCTATCTGTCAAC-CAAGACCTTTGAGTTCGACTACGCTTAGCT
1 CATAGCTCAAGGCA-AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCT
1976163 CCAAGGCACATCATTTGCAG
65 CCAAGGCACATCATTTGCAG
* * * * *
1976183 CATAACTCAAGGCTAGAAGGGTTATCTGCCAAAAAAAGACCTTCGAGTTCAATTACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTC
*
1976248 AAAGGCACATCATTTG-A-
66 CAAGGCACATCATTTGCAG
* * * * *
1976265 TATATGGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTTAGC
1 CATA--GCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGC
* * * *
1976330 TTCGAGGCATATCATTTGTAG
64 TCCAAGGCACATCATTTGCAG
* ** * *
1976351 CATAGCTCAAGGCAAGAA-AGTCTATCTATCAATC--AATACCTTCGAGTTC-AGTTACACTCAG
1 CATAGCTCAAGGCAAGAAGGGT-TATCTGCCAA-CAAAAGACCTTCGAGTTCGA-CTACACTCAG
* ** *
1976412 CTCAAAGGCATGTCATTTTACAG
63 CTCCAAGGCACATCA-TTTGCAG
* * * *
1976435 CATAGCTCAAGTCAAGAAGGGATATATGTCAACAAAA
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAA
1976472 TTGTCGAGTT
Statistics
Matches: 712, Mismatches: 144, Indels: 39
0.80 0.16 0.04
Matches are distributed among these distances:
82 4 0.01
83 109 0.15
84 586 0.82
85 10 0.01
86 3 0.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (84 bp):
CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTC
CAAGGCACATCATTTGCAG
Found at i:1975798 original size:168 final size:168
Alignment explanation
Indices: 1975504--1976471 Score: 1056
Period size: 168 Copynumber: 5.8 Consensus size: 168
1975494 TATCGTGTTA
* * ** * * * * *
1975504 ATTTACAACATAGCTCAAGGCAAGAAAGACTATTTTCCAATAAAAGACCTTCGAGTTTGACTACG
1 ATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACA
* * * * * *
1975569 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCCGCCAACAAAGG
66 CTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAG
*
1975634 ACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATC
131 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
** * *
1975672 ATTTATAACATAGCTCAAGGCAAGAAGTGTTATTTTCCAACAAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACA
** * * *
1975737 CTCAGCTCAAAGAAACAAT-ATTTACAGCATAGCTCAAGGCGAGAAGGCCTATCTACCAACAAAA
66 CTCAGCTCAAAGGCAC-ATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAA
* * *
1975801 GACCTTCGAGTTCAACTACGCTCAGCTCCAAGACACATA
130 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
1975840 ATTTGCAATATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACA
*
1975905 CTCAGCTCAAAGGCACAAT-ATTTGCAGCATAGCTCAAGGCGATAAGGGCTATCTGCCAACAAAA
66 CTCAGCTCAAAGGCAC-ATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAA
* * * *
1975969 AACCTTTGAGTTTGACTACGCTC-GATTCCAAGGCACATC
130 GACCTTCGAGTTCGACTACGCTCAG-CTCCAAGGCACATC
* * ** * * * * *
1976008 TTTTGCAGCATAAATCAAGGCTAGAAGAGTTATCTGACAACAAAATACCTTCGAGTTCGATTACA
1 ATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACA
* * * * * *
1976073 CTCAGCTCAAAGACACATCATTTGCAGTATAGCTCAAGGAGAAAAGGGCTATCTGTCAAC-CAAG
66 CTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAG
* *
1976137 ACCTTTGAGTTCGACTACGCTTAGCTCCAAGGCACATC
131 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * * * * *
1976175 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAAAAAAGACCTTCGAGTTCAATTACA
1 ATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACA
* * *
1976240 CTCAGCTCAAAGGCACATCATTTG-A-TATATGGCTCAAGGCAAGAAGGGCTATTTGCCAACAAA
66 CTCAGCTCAAAGGCACATCATTTGCAGCATA--GCTCAAGGCGAGAAGGGCTATCTGCCAACAAA
* * * * * *
1976303 AGACCTTCGAGTTCGATTACACTTAGCTTCGAGGCATATC
129 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * * * ** *
1976343 ATTTGTAGCATAGCTCAAGGCAAGAA-AGTCTATCTATCAATC--AATACCTTCGAGTTC-AGTT
1 ATTTGCAACATAGCTCAAGGCAAGAAGGGT-TATTTGCCAA-CAAAAGACCTTCGAGTTCGA-TT
** * * * * * *
1976404 ACACTCAGCTCAAAGGCATGTCATTTTACAGCATAGCTCAAGTCAAGAAGGGATATATGTCAACA
63 ACACTCAGCTCAAAGGCACATCA-TTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACA
1976469 AAA
127 AAA
1976472 TTGTCGAGTT
Statistics
Matches: 689, Mismatches: 98, Indels: 26
0.85 0.12 0.03
Matches are distributed among these distances:
165 4 0.01
166 2 0.00
167 182 0.26
168 495 0.72
169 3 0.00
170 3 0.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (168 bp):
ATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACA
CTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAG
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:1980206 original size:9 final size:9
Alignment explanation
Indices: 1980192--1980232 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
1980182 TTCTTCTTTG
1980192 TTTTATGTA
1 TTTTATGTA
1980201 TTTTATGTA
1 TTTTATGTA
*
1980210 -TTTATTTA
1 TTTTATGTA
1980218 TTTTTAT-TA
1 -TTTTATGTA
1980227 TTTTAT
1 TTTTAT
1980233 TTTTATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 13 0.45
9 11 0.38
10 5 0.17
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (9 bp):
TTTTATGTA
Found at i:1980219 original size:17 final size:18
Alignment explanation
Indices: 1980192--1980248 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
1980182 TTCTTCTTTG
*
1980192 TTTTATGTA-TTTTATGTA
1 TTTTATTTATTTTTAT-TA
1980210 -TTTATTTATTTTTATTA
1 TTTTATTTATTTTTATTA
*
1980227 TTTTATTTTTATTTTATT-
1 TTTTATTTAT-TTTTATTA
1980245 TTTT
1 TTTT
1980249 CTCATTCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 9 0.26
18 18 0.53
19 7 0.21
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTTATTTATTTTTATTA
Found at i:1980247 original size:26 final size:26
Alignment explanation
Indices: 1980192--1980276 Score: 77
Period size: 26 Copynumber: 3.3 Consensus size: 26
1980182 TTCTTCTTTG
1980192 TTTTATGTATTTTATGTATTTA-TTTA-T
1 TTTTAT-TATTTTAT-T-TTTATTTTATT
1980219 TTTTATTATTTTATTTTTATTTTATT
1 TTTTATTATTTTATTTTTATTTTATT
* * * * *
1980245 TTTTCTCATTCTATTTAT-TTTTATC
1 TTTTATTATTTTATTTTTATTTTATT
1980270 TTTTATT
1 TTTTATT
1980277 TTCCTTATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
24 4 0.08
25 16 0.33
26 23 0.47
27 6 0.12
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTTATTATTTTATTTTTATTTTATT
Found at i:1980248 original size:18 final size:19
Alignment explanation
Indices: 1980214--1980278 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 19
1980204 TATGTATTTA
1980214 TTTATTTTTATTATTTTAT-T
1 TTTA-TTTTATT-TTTTATCT
*
1980234 TTTATTTTATTTTTTCTCAT
1 TTTATTTTATTTTTTATC-T
*
1980254 TCTA-TTTA-TTTTTATCT
1 TTTATTTTATTTTTTATCT
1980271 TTTATTTT
1 TTTATTTT
1980279 CCTTATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 4 0.11
18 15 0.39
19 11 0.29
20 8 0.21
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTATTTTATTTTTTATCT
Found at i:1980321 original size:9 final size:9
Alignment explanation
Indices: 1980309--1980334 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1980299 CATTTTACTT
1980309 TTTTTTTCA
1 TTTTTTTCA
1980318 TTTTTTTCA
1 TTTTTTTCA
1980327 TTTTTTTC
1 TTTTTTTC
1980335 GTAATATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:1980325 original size:46 final size:46
Alignment explanation
Indices: 1980212--1980325 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 46
1980202 TTTATGTATT
*
1980212 TATTTATTTTTATTATTT-TATTT--TTATTTTATTTTTTCTCATTC
1 TATTTATTTTTATCATTTAT-TTTCCTTATTTTATTTTTTCTCATTC
* *
1980256 TATTTATTTTTATCTTTTATTTTCCTTATTTTATTTGTTTCTCCATTT
1 TATTTATTTTTATCATTTATTTTCCTTATTTTATTT-TTTCT-CATTC
1980304 TACTTT-TTTTT-TCATTT-TTTTC
1 TA-TTTATTTTTATCATTTATTTTC
1980326 ATTTTTTTCG
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
44 19 0.32
45 1 0.02
46 16 0.27
47 10 0.17
48 11 0.18
49 3 0.05
ACGTcount: A:0.15, C:0.11, G:0.01, T:0.74
Consensus pattern (46 bp):
TATTTATTTTTATCATTTATTTTCCTTATTTTATTTTTTCTCATTC
Found at i:1982345 original size:4 final size:4
Alignment explanation
Indices: 1982328--1983556 Score: 2377
Period size: 4 Copynumber: 309.5 Consensus size: 4
1982318 TAGCAATATG
*
1982328 CATA CATG CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982376 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982424 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982472 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982520 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982568 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982616 CATA CATA CATA C--A CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982662 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982710 CATA C--A CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982756 CAT- -ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982802 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982850 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982898 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982946 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1982994 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1983042 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1983090 CATA CATA C-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1983137 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1983185 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT- -ATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1983231 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1983279 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1983327 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1983375 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1983423 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1983471 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1983519 CATA CATA CATA CATA CATA CATA CACA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
1983557 CACACACACA
Statistics
Matches: 1212, Mismatches: 4, Indels: 18
0.98 0.00 0.01
Matches are distributed among these distances:
2 8 0.01
3 3 0.00
4 1201 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:1983559 original size:2 final size:2
Alignment explanation
Indices: 1983542--1984209 Score: 1288
Period size: 2 Copynumber: 335.5 Consensus size: 2
1983532 ATACATACAT
* *
1983542 AC AC AC AT AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1983584 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC -C AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1983625 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1983667 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
1983709 AC AC CC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1983751 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1983793 AC AC AC AC AC AC AC AC AC AC AC -C AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1983834 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1983876 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1983918 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1983960 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1984002 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1984044 AC AC AC AC -C AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1984085 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1984127 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1984169 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1984210 TACATACATA
Statistics
Matches: 657, Mismatches: 6, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
1 3 0.00
2 654 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1984214 original size:4 final size:4
Alignment explanation
Indices: 1984207--1984311 Score: 165
Period size: 4 Copynumber: 26.2 Consensus size: 4
1984197 ACACACACAC
* * * *
1984207 ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT GCAT GCAT GCAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1984255 GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1984303 ACAT ACAT A
1 ACAT ACAT A
1984312 TGACCTATGA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 97 1.00
ACGTcount: A:0.46, C:0.25, G:0.05, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:1986037 original size:26 final size:26
Alignment explanation
Indices: 1986007--1986081 Score: 150
Period size: 26 Copynumber: 2.9 Consensus size: 26
1985997 AATATATAAA
1986007 GAATAATTGCAATATTATCTCAATTC
1 GAATAATTGCAATATTATCTCAATTC
1986033 GAATAATTGCAATATTATCTCAATTC
1 GAATAATTGCAATATTATCTCAATTC
1986059 GAATAATTGCAATATTATCTCAA
1 GAATAATTGCAATATTATCTCAA
1986082 CAGCTCTTAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (26 bp):
GAATAATTGCAATATTATCTCAATTC
Found at i:1987264 original size:2 final size:2
Alignment explanation
Indices: 1987257--1987287 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1987247 TCCATTGTAA
1987257 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1987288 ATTGTATCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:1992660 original size:21 final size:21
Alignment explanation
Indices: 1992636--1992692 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
1992626 AGATAAGCTA
1992636 TGACTTTGCAATAAAGT-TGC-T
1 TGACTTTGC-A-AAAGTGTGCAT
1992657 TGACTTTGCAAAAGTGTGCAT
1 TGACTTTGCAAAAGTGTGCAT
*
1992678 TGACTTTACAAAAGT
1 TGACTTTGCAAAAGT
1992693 ATGCCTTGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 5 0.15
20 4 0.12
21 24 0.73
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (21 bp):
TGACTTTGCAAAAGTGTGCAT
Found at i:1992705 original size:21 final size:20
Alignment explanation
Indices: 1992648--1992705 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
1992638 ACTTTGCAAT
*
1992648 AAAGTTG-CTTGACTTTGCA
1 AAAGTTGCCTTGACTTTACA
*
1992667 AAAGTGTGCATTGACTTTACA
1 AAAGT-TGCCTTGACTTTACA
*
1992688 AAAGTATGCCTTGGCTTT
1 AAAGT-TGCCTTGACTTT
1992706 TAATTATTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 5 0.16
20 2 0.06
21 25 0.78
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (20 bp):
AAAGTTGCCTTGACTTTACA
Found at i:1992780 original size:21 final size:21
Alignment explanation
Indices: 1992738--1992776 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1992728 CATCAAAGCC
1992738 TTAGTTGAAGCCATGAAATCT
1 TTAGTTGAAGCCATGAAATCT
*
1992759 TTAGTTGAAGTCAT-AAAT
1 TTAGTTGAAGCCATGAAAT
1992777 TCTTACAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (21 bp):
TTAGTTGAAGCCATGAAATCT
Found at i:2005029 original size:45 final size:45
Alignment explanation
Indices: 2004980--2005256 Score: 410
Period size: 45 Copynumber: 6.2 Consensus size: 45
2004970 CACCCATATG
* *
2004980 CATTTCATTTATGGCATCCTTTCATGCCTTTTATACTCTATTATA
1 CATTTCATTTATGGCGTCCTTTCATGCCTTTTATACACTATTATA
* * * * *
2005025 CATTTCATTGATGACGTCATTCCATGCCTTTTATACATTATTATA
1 CATTTCATTTATGGCGTCCTTTCATGCCTTTTATACACTATTATA
* *
2005070 CATTTCATTTATGCCGTCCCTTCATGCCTTTTATACACTATTATA
1 CATTTCATTTATGGCGTCCTTTCATGCCTTTTATACACTATTATA
* * *
2005115 CATTTCATTTATGGCGTCCATTCATGCCTTTTACACACAATTATA
1 CATTTCATTTATGGCGTCCTTTCATGCCTTTTATACACTATTATA
*
2005160 CATTTCATTTATGGCGTCATTTCATGCCTTTTATACACTATTATA
1 CATTTCATTTATGGCGTCCTTTCATGCCTTTTATACACTATTATA
* * *
2005205 CATTTAATTTATGGCATCCTTTCATGCATTTTATACACTATTATA
1 CATTTCATTTATGGCGTCCTTTCATGCCTTTTATACACTATTATA
2005250 CATTTCA
1 CATTTCA
2005257 AAACCCATTT
Statistics
Matches: 206, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 206 1.00
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.45
Consensus pattern (45 bp):
CATTTCATTTATGGCGTCCTTTCATGCCTTTTATACACTATTATA
Found at i:2008289 original size:45 final size:45
Alignment explanation
Indices: 2008188--2008426 Score: 273
Period size: 45 Copynumber: 5.3 Consensus size: 45
2008178 ATAATGCACC
* * * ** * *
2008188 ATTATGCATTTTCAATTATGGCATCATTTCGTGCCAATAATACACCC
1 ATTATACA-TTTCATTTATGGCATCATTTCATGCCTTTTATACA-CT
* * * * *
2008235 A-TATGCATTTTATTTATGGCATCCTTTCATGTCTTTTATACGCT
1 ATTATACATTTCATTTATGGCATCATTTCATGCCTTTTATACACT
* * * *
2008279 ATTATACATTTCATTGATGACGTCATTTCATGCCTTTTATACATT
1 ATTATACATTTCATTTATGGCATCATTTCATGCCTTTTATACACT
* *
2008324 ATTATACATTTCATTTATGGCGTCATTTCATGCCTTTTATACAAT
1 ATTATACATTTCATTTATGGCATCATTTCATGCCTTTTATACACT
*
2008369 ATTATGCATTTCATTTATGGCATCATTTCATGCCTTTTATACACT
1 ATTATACATTTCATTTATGGCATCATTTCATGCCTTTTATACACT
*
2008414 ATTAGACATTTCA
1 ATTATACATTTCA
2008427 AAACCTATTT
Statistics
Matches: 164, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
44 2 0.01
45 155 0.95
46 6 0.04
47 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (45 bp):
ATTATACATTTCATTTATGGCATCATTTCATGCCTTTTATACACT
Found at i:2012933 original size:6 final size:6
Alignment explanation
Indices: 2012910--2012944 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
2012900 TTTTCATTTG
2012910 AAACAA AACACAAA AAACAA AAACAA AAACAA AAA
1 AAACAA AA-AC-AA AAACAA AAACAA AAACAA AAA
2012945 AATGGACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACAA
Found at i:2015619 original size:34 final size:34
Alignment explanation
Indices: 2015548--2015654 Score: 180
Period size: 34 Copynumber: 3.2 Consensus size: 34
2015538 TCTTTTTCTA
* *
2015548 TTTTTTCACTCTTACTATAATGGTAAAATTCA-T
1 TTTTTTCACTCTTACTATAATGGTAAAACTCACC
*
2015581 TTTTTTCATTCTTACTATAATGGTAAAACTCACC
1 TTTTTTCACTCTTACTATAATGGTAAAACTCACC
2015615 TTTTTTCACTCTTACTATAATGGTAAAACTCACC
1 TTTTTTCACTCTTACTATAATGGTAAAACTCACC
2015649 TTTTTT
1 TTTTTT
2015655 TTTAAAGATG
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
33 30 0.43
34 39 0.57
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.48
Consensus pattern (34 bp):
TTTTTTCACTCTTACTATAATGGTAAAACTCACC
Found at i:2024130 original size:31 final size:31
Alignment explanation
Indices: 2024095--2024170 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
2024085 TTTTATTATT
* *
2024095 TCGGGTCGGGTTTCTAATTCAT-ATATTCGGG
1 TCGGGTCGGGTTTCTAAAT-ATGATATTCAGG
* *
2024126 TCGGGTCGGGTTTTTTAAATGTGATATTCAGG
1 TCGGGTCGGG-TTTCTAAATATGATATTCAGG
2024158 TCGGGTCGGGTTT
1 TCGGGTCGGGTTT
2024171 GGGTTTAGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 14 0.36
32 25 0.64
ACGTcount: A:0.14, C:0.13, G:0.33, T:0.39
Consensus pattern (31 bp):
TCGGGTCGGGTTTCTAAATATGATATTCAGG
Found at i:2024378 original size:27 final size:27
Alignment explanation
Indices: 2024348--2024410 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
2024338 TGTTCGGGTC
*
2024348 GGGTCGGGTTTTTTAAGTGTGATATTT
1 GGGTCGAGTTTTTTAAGTGTGATATTT
2024375 GGGTCGAGTTTTTTAAGTGTGATATTT
1 GGGTCGAGTTTTTTAAGTGTGATATTT
2024402 GGGTCGAGT
1 GGGTCGAGT
2024411 CGAGTCGGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.16, C:0.05, G:0.35, T:0.44
Consensus pattern (27 bp):
GGGTCGAGTTTTTTAAGTGTGATATTT
Found at i:2024413 original size:32 final size:31
Alignment explanation
Indices: 2024343--2024415 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 31
2024333 TATTTTGTTC
*
2024343 GGGTCGGGTCGGGTTTTTTAAGTGTGATATTT
1 GGGTC-GGTCGAGTTTTTTAAGTGTGATATTT
2024375 --G--GGTCGAGTTTTTTAAGTGTGATATTT
1 GGGTCGGTCGAGTTTTTTAAGTGTGATATTT
2024402 GGGTCGAGTCGAGT
1 GGGTCG-GTCGAGT
2024416 CGGGTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
27 25 0.71
29 1 0.03
30 1 0.03
31 1 0.03
32 7 0.20
ACGTcount: A:0.15, C:0.07, G:0.37, T:0.41
Consensus pattern (31 bp):
GGGTCGGTCGAGTTTTTTAAGTGTGATATTT
Found at i:2024725 original size:216 final size:210
Alignment explanation
Indices: 2024459--2024890 Score: 722
Period size: 216 Copynumber: 2.0 Consensus size: 210
2024449 CGGCTCAGGT
* *
2024459 TCGGGTTTAGGGTGAAAAAAATCGGACCAACCCGAAAATATATATAATTCGGGTCGGGTCGGATT
1 TCGGGTTTAGGGTGAAAAAAATCGGACCAACCCAAAAATATATATAATTCGGGTCAGGTCGGATT
*
2024524 AAGTCACTGTTTGTATTAAATAAAAATAATTTTTTATTATTTTGGGTCGGGTCGGATTTCTAATT
66 AAGTCACTGTTTGTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATT
* *
2024589 CATATATTCGGGTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGACGGGTTTTTTT
131 CATATATT----T-GAGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGACGGG-TGTTTT
*
2024654 AAGTGTGATATTCGGGTCGGGG
190 AAGTGTGATATTCGGGTC-GAG
*
2024676 TCGGGTTTAGGGTG-AAAAAATCGGACCGACCCAAAAATATATATAATTCGGGTCAGGTCGGATT
1 TCGGGTTTAGGGTGAAAAAAATCGGACCAACCCAAAAATATATATAATTCGGGTCAGGTCGGATT
2024740 AAGTCACTGTTTGTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATT
66 AAGTCACTGTTTGTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATT
*
2024805 CATATATTTGAGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTGTTTTAAGTGT
131 CATATATTTGAGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGACGGGTGTTTTAAGTGT
2024870 GATATTCGGGTCGAG
196 GATATTCGGGTCGAG
2024885 TCGGGT
1 TCGGGT
2024891 CAGGTTTTTT
Statistics
Matches: 207, Mismatches: 8, Indels: 8
0.93 0.04 0.04
Matches are distributed among these distances:
209 8 0.04
210 23 0.11
211 42 0.20
212 1 0.00
216 119 0.57
217 14 0.07
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.36
Consensus pattern (210 bp):
TCGGGTTTAGGGTGAAAAAAATCGGACCAACCCAAAAATATATATAATTCGGGTCAGGTCGGATT
AAGTCACTGTTTGTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATT
CATATATTTGAGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGACGGGTGTTTTAAGTGT
GATATTCGGGTCGAG
Done.