Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 91
Found at i:1916141 original size:15 final size:15
Alignment explanation
Indices: 1916121--1916150 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1916111 ATCAATCCAC
*
1916121 ATCATCATCATCAAT
1 ATCATCACCATCAAT
1916136 ATCATCACCATCAAT
1 ATCATCACCATCAAT
1916151 CGGATGAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (15 bp):
ATCATCACCATCAAT
Found at i:1918190 original size:19 final size:20
Alignment explanation
Indices: 1918152--1918190 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1918142 TACTCTAGGA
1918152 GCAGTATCGATACTCCCCTG
1 GCAGTATCGATACTCCCCTG
1918172 GCAGTATCGATAC-CCCCTG
1 GCAGTATCGATACTCCCCTG
1918191 TTATAAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.23
Consensus pattern (20 bp):
GCAGTATCGATACTCCCCTG
Found at i:1930454 original size:20 final size:21
Alignment explanation
Indices: 1930419--1930457 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1930409 GAACTTCGAA
1930419 TTTTCTTTTCTATATTTATTC
1 TTTTCTTTTCTATATTTATTC
*
1930440 TTTTTTTTTCT-TATTTAT
1 TTTTCTTTTCTATATTTAT
1930458 AGTTCCCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTCTTTTCTATATTTATTC
Found at i:1931278 original size:23 final size:24
Alignment explanation
Indices: 1931230--1931281 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1931220 CGAGGCCACG
1931230 GGGCCTACCTGAGAATACATCTCA
1 GGGCCTACCTGAGAATACATCTCA
*
1931254 GGGCCTACCTGAGAAT-GATCTCA
1 GGGCCTACCTGAGAATACATCTCA
1931277 GGGCC
1 GGGCC
1931282 GCAGAGCCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (24 bp):
GGGCCTACCTGAGAATACATCTCA
Found at i:1939802 original size:24 final size:23
Alignment explanation
Indices: 1939774--1939819 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1939764 CAAGCAACAA
* *
1939774 GAAAACGATAATAAGTAAACAAAG
1 GAAAACGAAAATAAAT-AACAAAG
*
1939798 GAAAAGGAAAATAAATAACAAA
1 GAAAACGAAAATAAATAACAAA
1939820 AAAATGCACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.67, C:0.07, G:0.15, T:0.11
Consensus pattern (23 bp):
GAAAACGAAAATAAATAACAAAG
Found at i:1943280 original size:18 final size:16
Alignment explanation
Indices: 1943257--1943300 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
1943247 ACCCATCTTA
1943257 TTTTTCTTTTTTCGTTCT
1 TTTTTCTTTTTTC--TCT
1943275 TTTTTC-TTTTTCTCT
1 TTTTTCTTTTTTCTCT
1943290 TTTTT-TTTTTT
1 TTTTTCTTTTTT
1943301 TAATTTAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.52
17 6 0.24
18 6 0.24
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (16 bp):
TTTTTCTTTTTTCTCT
Found at i:1943301 original size:17 final size:18
Alignment explanation
Indices: 1943252--1943301 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
1943242 CTTGAACCCA
*
1943252 TCTTATTTTTCTTTTTTCG
1 TCTT-TTTTTTTTTTTTCG
* *
1943271 T-TCTTTTTTCTTTTTC-
1 TCTTTTTTTTTTTTTTCG
1943287 TCTTTTTTTTTTTTT
1 TCTTTTTTTTTTTTT
1943302 AATTTAGGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
16 1 0.04
17 22 0.88
18 1 0.04
19 1 0.04
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (18 bp):
TCTTTTTTTTTTTTTTCG
Found at i:1947012 original size:24 final size:24
Alignment explanation
Indices: 1946985--1947038 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1946975 AAAAAATAAA
1946985 AGAAAATTTATTTGCCATGGATAT
1 AGAAAATTTATTTGCCATGGATAT
1947009 AGAAAATTTATTTGCCATGGATAT
1 AGAAAATTTATTTGCCATGGATAT
1947033 AGAAAA
1 AGAAAA
1947039 AAATGCATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (24 bp):
AGAAAATTTATTTGCCATGGATAT
Found at i:1953259 original size:2 final size:2
Alignment explanation
Indices: 1953254--1953278 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1953244 AAAATAAGGA
1953254 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 A
1953279 ATAATACGAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1962612 original size:21 final size:20
Alignment explanation
Indices: 1962574--1962612 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1962564 TTCATTTACG
*
1962574 ATTATGGTTTTTTGTATGAT
1 ATTATGGTTTTTTCTATGAT
*
1962594 ATTATGTTTCTTTTCTATG
1 ATTATGGTT-TTTTCTATG
1962613 CCTTGTATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.18, C:0.05, G:0.15, T:0.62
Consensus pattern (20 bp):
ATTATGGTTTTTTCTATGAT
Found at i:1964759 original size:16 final size:17
Alignment explanation
Indices: 1964729--1964760 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1964719 ATATTTATTT
1964729 ATATAAAATATAATATA
1 ATATAAAATATAATATA
1964746 ATATAAAA-ATAATAT
1 ATATAAAATATAATAT
1964761 TATGATCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:1964867 original size:20 final size:18
Alignment explanation
Indices: 1964825--1964875 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
1964815 AATAACTCAA
*
1964825 AATTAAATATTGTTTTAAGT
1 AATT-AATATT-TTTTAAAT
1964845 AATTACATATTTTTTACAAT
1 AATTA-ATATTTTTTA-AAT
1964865 AA-TAATATTTT
1 AATTAATATTTT
1964876 CACCTCATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 7 0.25
19 8 0.29
20 13 0.46
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (18 bp):
AATTAATATTTTTTAAAT
Found at i:1966783 original size:33 final size:33
Alignment explanation
Indices: 1966741--1966844 Score: 190
Period size: 33 Copynumber: 3.2 Consensus size: 33
1966731 CAATCCTTTG
* *
1966741 TGATGATTGATATAACCATTAAATCTCTTAGTT
1 TGATGATTGATACAACCATTAAATCTCTCAGTT
1966774 TGATGATTGATACAACCATTAAATCTCTCAGTT
1 TGATGATTGATACAACCATTAAATCTCTCAGTT
1966807 TGATGATTGATACAACCATTAAATCTCTCAGTT
1 TGATGATTGATACAACCATTAAATCTCTCAGTT
1966840 TGATG
1 TGATG
1966845 GTCGATATAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (33 bp):
TGATGATTGATACAACCATTAAATCTCTCAGTT
Found at i:1967628 original size:120 final size:121
Alignment explanation
Indices: 1967412--1967639 Score: 334
Period size: 120 Copynumber: 1.9 Consensus size: 121
1967402 AGACATTTTG
* * *
1967412 GATCAACTGAGAAAAAAAATTTACTCAAACTGAAATCTACCCAAATTTTCCTAATATAAACAAAT
1 GATCAACTGAG-AAAAAAATTTACTCAAACTGAAATATACCAAAATTTTCCTAACATAAACAAAT
* * *
1967477 TATATTTCGATTGAAAAGCCATGGAATAACATATATTGAAATAAAGGCCACATTTAA
65 TATATTTCAATTGAAAAGCCATGAAACAACATATATTGAAATAAAGGCCACATTTAA
* ** *
1967534 GATCAACTGAG-AAAAACTTTACTCAAACTGAAATATACCAAAATTTTCCTCAACATACCCATAT
1 GATCAACTGAGAAAAAAATTTACTCAAACTGAAATATACCAAAATTTTCCT-AACATAAACAAAT
1967598 TATATTTCAATTGAAAAG-CATGAAACAACATATATTGAAATA
65 TATATTTCAATTGAAAAGCCATGAAACAACATATATTGAAATA
1967640 TTCACAAAAT
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
120 58 0.61
121 26 0.27
122 11 0.12
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (121 bp):
GATCAACTGAGAAAAAAATTTACTCAAACTGAAATATACCAAAATTTTCCTAACATAAACAAATT
ATATTTCAATTGAAAAGCCATGAAACAACATATATTGAAATAAAGGCCACATTTAA
Found at i:1969222 original size:15 final size:15
Alignment explanation
Indices: 1969202--1969230 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1969192 AGATATATTT
1969202 TAAAATAATTTTAAG
1 TAAAATAATTTTAAG
1969217 TAAAATAATTTTAA
1 TAAAATAATTTTAA
1969231 AATATCTGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TAAAATAATTTTAAG
Found at i:1970696 original size:18 final size:18
Alignment explanation
Indices: 1970673--1970711 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1970663 TATGATGAAA
1970673 CCTTAGGGTTTCTGGAAT
1 CCTTAGGGTTTCTGGAAT
1970691 CCTTAGGGTTTCTGGAAT
1 CCTTAGGGTTTCTGGAAT
1970709 CCT
1 CCT
1970712 CCGGACCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (18 bp):
CCTTAGGGTTTCTGGAAT
Found at i:1970941 original size:3 final size:3
Alignment explanation
Indices: 1970933--1970969 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1970923 ATTTGGCCTG
*
1970933 TAA TAA TAA TAA T-T TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1970970 ATGGGTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 3 0.10
3 27 0.90
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1970952 original size:14 final size:14
Alignment explanation
Indices: 1970933--1970959 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1970923 ATTTGGCCTG
1970933 TAATAATAATAATT
1 TAATAATAATAATT
1970947 TAATAATAATAAT
1 TAATAATAATAAT
1970960 AATATAATAA
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):
TAATAATAATAATT
Found at i:1970955 original size:17 final size:17
Alignment explanation
Indices: 1970933--1970969 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1970923 ATTTGGCCTG
*
1970933 TAATAATAATAATTTAA
1 TAATAATAATAATATAA
1970950 TAATAATAATAATATAA
1 TAATAATAATAATATAA
1970967 TAA
1 TAA
1970970 ATGGGTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAATAATATAA
Found at i:1972849 original size:38 final size:38
Alignment explanation
Indices: 1972807--1972903 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 38
1972797 CCATTTTTAA
1972807 AAAAACTATATTATATA-TGTTT-TCAAAAACACGTTCTC
1 AAAAACTATATTATATACT-TTTGT-AAAAACACGTTCTC
* *
1972845 AAAAACTATA-TATTATACTTTTGTAAAAATACGTTTTC
1 AAAAACTATATTA-TATACTTTTGTAAAAACACGTTCTC
1972883 -AAAACATATATTATATACTTT
1 AAAAAC-TATATTATATACTTT
1972904 CAAAAATCAC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
37 7 0.13
38 41 0.79
39 4 0.08
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.40
Consensus pattern (38 bp):
AAAAACTATATTATATACTTTTGTAAAAACACGTTCTC
Found at i:1975127 original size:2 final size:2
Alignment explanation
Indices: 1975120--1975144 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1975110 TTCTTCTTCT
1975120 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1975145 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1983041 original size:40 final size:42
Alignment explanation
Indices: 1982997--1983105 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
1982987 CTATTTATAA
* *
1982997 TTGTGATGA-AAACA-TTTTATCATTAGTCTTAGTTAGTGAT
1 TTGTGACGATAAACATTTTTATCACTAGTCTTAGTTAGTGAT
** * *
1983037 TTGTGACGATAATTATTTTTGTCACTAGTTTTAGTTAGTGAT
1 TTGTGACGATAAACATTTTTATCACTAGTCTTAGTTAGTGAT
* *
1983079 TTATGACGACTATA-ATTTTTATCACTA
1 TTGTGACGA-TAAACATTTTTATCACTA
1983106 TTGAAGTGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
40 8 0.14
41 3 0.05
42 43 0.77
43 2 0.04
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (42 bp):
TTGTGACGATAAACATTTTTATCACTAGTCTTAGTTAGTGAT
Found at i:1983072 original size:42 final size:42
Alignment explanation
Indices: 1983011--1983105 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
1983001 GATGAAAACA
* * *
1983011 TTTTATCATTAGTCTTAGTTAGTGATTTGTGACGA-TAATTAT
1 TTTTATCACTAGTCTTAGTTAGTGATTTATGACGACT-ATAAT
* *
1983053 TTTTGTCACTAGTTTTAGTTAGTGATTTATGACGACTATAAT
1 TTTTATCACTAGTCTTAGTTAGTGATTTATGACGACTATAAT
1983095 TTTTATCACTA
1 TTTTATCACTA
1983106 TTGAAGTGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.49
Consensus pattern (42 bp):
TTTTATCACTAGTCTTAGTTAGTGATTTATGACGACTATAAT
Found at i:1983843 original size:33 final size:33
Alignment explanation
Indices: 1983780--1983845 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1983770 TTAATTCAAT
*
1983780 TCGGTCAATAAATTCGATTAAAACTGAAAAATG
1 TCGGTCAATAAATTCGATTAAAACTAAAAAATG
*
1983813 TCGGTCTATAAATTCGATTAAAA-TCAAAAAATG
1 TCGGTCAATAAATTCGATTAAAACT-AAAAAATG
1983846 AACACCCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (33 bp):
TCGGTCAATAAATTCGATTAAAACTAAAAAATG
Found at i:1985300 original size:43 final size:43
Alignment explanation
Indices: 1985239--1985325 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
1985229 TAAAAATATA
1985239 ATATCTACTATAATTGATTGCATAATAAATTTTTAATTAATTT
1 ATATCTACTATAATTGATTGCATAATAAATTTTTAATTAATTT
1985282 ATATCTACTATAATTGATTGCATAATAAATTTTTAATTAATTT
1 ATATCTACTATAATTGATTGCATAATAAATTTTTAATTAATTT
1985325 A
1 A
1985326 GTTATGTAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (43 bp):
ATATCTACTATAATTGATTGCATAATAAATTTTTAATTAATTT
Found at i:1986972 original size:33 final size:33
Alignment explanation
Indices: 1986901--1986976 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
1986891 AAACCCACGT
* *
1986901 ATTTGAGTCTTATTGAAACACTAAAACCAATGT
1 ATTTGAGTCCTATTGAAACACTAAAACCAATGC
*
1986934 ATTTGAGTCCTATTGAAACACTAAAACGAA-GC
1 ATTTGAGTCCTATTGAAACACTAAAACCAATGC
1986966 ATTTTGAGTCC
1 A-TTTGAGTCC
1986977 AAGTAGGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
32 2 0.05
33 37 0.95
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (33 bp):
ATTTGAGTCCTATTGAAACACTAAAACCAATGC
Found at i:1988835 original size:3 final size:3
Alignment explanation
Indices: 1988827--1988875 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
1988817 TTTGTCCGGG
**
1988827 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
1988873 TTA
1 TTA
1988876 ATTAATTACA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1989496 original size:24 final size:23
Alignment explanation
Indices: 1989453--1989501 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
1989443 CAGAGAATAG
* *
1989453 AAAAAAAAAGAGATACGAAACAA
1 AAAAAAAAAGAGAGAAGAAACAA
*
1989476 AAAAAAAAGAGAGAGAAGAAAGAA
1 AAAAAAAA-AGAGAGAAGAAACAA
1989500 AA
1 AA
1989502 GTTTTACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAGAGAGAAGAAACAA
Found at i:2002407 original size:11 final size:10
Alignment explanation
Indices: 2002387--2002411 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2002377 TATTACACTT
2002387 AAAAATAAAA
1 AAAAATAAAA
2002397 AAAAATAAAA
1 AAAAATAAAA
2002407 AAAAA
1 AAAAA
2002412 GAAAGAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:2002424 original size:23 final size:22
Alignment explanation
Indices: 2002397--2002450 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
2002387 AAAAATAAAA
2002397 AAAAATAAAAAAAAAGAAAGAAG
1 AAAAATAAAAAAAAA-AAAGAAG
**
2002420 AAAAATGAAAAATGAAAAAGAAG
1 AAAAAT-AAAAAAAAAAAAGAAG
2002443 -AAAATAAA
1 AAAAATAAA
2002451 TAAAGGAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.11
22 5 0.18
23 13 0.46
24 7 0.25
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (22 bp):
AAAAATAAAAAAAAAAAAGAAG
Found at i:2003615 original size:141 final size:133
Alignment explanation
Indices: 2003396--2003696 Score: 397
Period size: 141 Copynumber: 2.2 Consensus size: 133
2003386 CAACATCAAC
2003396 TGACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
1 TGACCAGAT-TCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
* ** *
2003461 AGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCAT
65 AGGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCA-
2003526 CTACCCT
129 -T-CCCT
* * *
2003533 TAGACGACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACCTTA-GATAATCAGCCGTCCTCAT
1 T----GACCAGA-TTCCTCATCACGTAGGAG-AGTGTCAACATTAGGATAACCAGCCGTCCTCAT
* * * *
2003597 CACGTAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTATGAGCCGT
60 CACGTAGGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCAT
2003662 GTCATCCCT
125 GTCATCCCT
2003671 TGACCAGATTTCCTCATCACGTAGGA
1 TGACCAGA-TTCCTCATCACGTAGGA
2003697 ACCGAGTTAT
Statistics
Matches: 146, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
134 24 0.16
137 1 0.01
138 5 0.03
139 1 0.01
141 103 0.71
142 12 0.08
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (133 bp):
TGACCAGATTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
CCT
Found at i:2003688 original size:40 final size:40
Alignment explanation
Indices: 2003631--2003784 Score: 110
Period size: 40 Copynumber: 3.6 Consensus size: 40
2003621 TTCTTAAAGA
** *
2003631 TGACCAGAACTCTTCATCGCGTATGAGCCGTGTCATCCCT
1 TGACCAGATTTCTTCATCACGTATGAGCCGTGTCATCCCT
* * * * *
2003671 TGACCAGATTTCCTCATCACGTAGGAACCGAGTTATCACCCTTCTT
1 TGACCAGATTTCTTCATCACGTATGAGCC--G-TGTCATCC--C-T
** *
2003717 AAAGATGACCAGAACTCTTCATCGCGTATGAGCCGTGTCATCCCT
1 -----TGACCAGATTTCTTCATCACGTATGAGCCGTGTCATCCCT
2003762 TGACCAGATTTCTTCATCACGTA
1 TGACCAGATTTCTTCATCACGTA
2003785 GGAATCGTGT
Statistics
Matches: 84, Mismatches: 19, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
40 43 0.51
42 1 0.01
43 6 0.07
45 2 0.02
46 2 0.02
48 6 0.07
49 1 0.01
51 23 0.27
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.29
Consensus pattern (40 bp):
TGACCAGATTTCTTCATCACGTATGAGCCGTGTCATCCCT
Found at i:2003703 original size:91 final size:91
Alignment explanation
Indices: 2003590--2003788 Score: 389
Period size: 91 Copynumber: 2.2 Consensus size: 91
2003580 TAATCAGCCG
2003590 TCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTAT
1 TCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTAT
2003655 GAGCCGTGTCATCCCTTGACCAGATT
66 GAGCCGTGTCATCCCTTGACCAGATT
2003681 TCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTAT
1 TCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTAT
2003746 GAGCCGTGTCATCCCTTGACCAGATT
66 GAGCCGTGTCATCCCTTGACCAGATT
*
2003772 TCTTCATCACGTAGGAA
1 TCCTCATCACGTAGGAA
2003789 TCGTGTTTCC
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 107 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.28
Consensus pattern (91 bp):
TCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTAT
GAGCCGTGTCATCCCTTGACCAGATT
Found at i:2003993 original size:3 final size:3
Alignment explanation
Indices: 2003985--2004030 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
2003975 TTTGTTCGGG
**
2003985 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
2004031 ATTAATTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2004618 original size:15 final size:17
Alignment explanation
Indices: 2004600--2004632 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2004590 AAAAAAAACC
2004600 AGAGA-ATA-GAAAAAA
1 AGAGAGATACGAAAAAA
2004615 AGAGAGATACGAAAAAA
1 AGAGAGATACGAAAAAA
2004632 A
1 A
2004633 AACAAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 3 0.19
17 8 0.50
ACGTcount: A:0.70, C:0.03, G:0.21, T:0.06
Consensus pattern (17 bp):
AGAGAGATACGAAAAAA
Found at i:2004651 original size:23 final size:22
Alignment explanation
Indices: 2004609--2004656 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2004599 CAGAGAATAG
* *
2004609 AAAAAAAGAGAGATACGAAAAA
1 AAAAAAAGAGAGAGAAGAAAAA
*
2004631 AAAACAAAGAGAGAGAAGAAAGA
1 AAAA-AAAGAGAGAGAAGAAAAA
2004654 AAA
1 AAA
2004657 GTTTTACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.73, C:0.04, G:0.21, T:0.02
Consensus pattern (22 bp):
AAAAAAAGAGAGAGAAGAAAAA
Found at i:2008652 original size:30 final size:31
Alignment explanation
Indices: 2008616--2008689 Score: 114
Period size: 32 Copynumber: 2.4 Consensus size: 31
2008606 ACTTATATAA
*
2008616 TATATAGTTTTTGAAAAT-GTTTTTGAAAAT
1 TATATAGTTTTTAAAAATAGTTTTTGAAAAT
*
2008646 TATATAGTTTTTAAAAATCATTTTTTGAAAAT
1 TATATAGTTTTTAAAAAT-AGTTTTTGAAAAT
2008678 TATATAGTTTTT
1 TATATAGTTTTT
2008690 TTAAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 17 0.43
32 23 0.57
ACGTcount: A:0.36, C:0.01, G:0.09, T:0.53
Consensus pattern (31 bp):
TATATAGTTTTTAAAAATAGTTTTTGAAAAT
Found at i:2008776 original size:42 final size:41
Alignment explanation
Indices: 2008676--2008791 Score: 144
Period size: 42 Copynumber: 2.8 Consensus size: 41
2008666 TTTTTTGAAA
**
2008676 ATTATATAGTTTTTTTAAAAAAAACATTTTCGAAAATTTAT
1 ATTATATAGTTTTTTTAAAAAAAACATTTTTAAAAATTTAT
**
2008717 A-TATAATACGTAGTTTTAAAAAAAACATTTTTAAAAATTTAT
1 ATTAT-ATA-GTTTTTTTAAAAAAAACATTTTTAAAAATTTAT
*
2008759 ATTATATAGTTTTTTTTAAAAGAAACACTTTTT
1 ATTATATAG-TTTTTTTAAAAAAAACA-TTTTT
2008792 TATATTATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
40 3 0.05
41 5 0.08
42 47 0.75
43 8 0.13
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (41 bp):
ATTATATAGTTTTTTTAAAAAAAACATTTTTAAAAATTTAT
Found at i:2009929 original size:15 final size:14
Alignment explanation
Indices: 2009912--2009953 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
2009902 TTTTTTTGGT
2009912 TTTTATTATTT-TTA
1 TTTTATT-TTTATTA
2009926 TTTTATTTTGTATTA
1 TTTTATTTT-TATTA
2009941 TTTTATTTTTATT
1 TTTTATTTTTATT
2009954 CAATTTAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.08
14 12 0.46
15 12 0.46
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTATTTTTATTA
Found at i:2009953 original size:21 final size:20
Alignment explanation
Indices: 2009911--2009949 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2009901 CTTTTTTTGG
2009911 TTTTTATTATTTTTATTTTA
1 TTTTTATTATTTTTATTTTA
2009931 TTTTGTATTA-TTTTATTTT
1 TTTT-TATTATTTTTATTTT
2009950 TATTCAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTTATTATTTTTATTTTA
Found at i:2009988 original size:20 final size:20
Alignment explanation
Indices: 2009911--2010019 Score: 62
Period size: 21 Copynumber: 5.2 Consensus size: 20
2009901 CTTTTTTTGG
2009911 TTTTTATTATTTTTATTTTAT
1 TTTTTATTATTTTT-TTTTAT
*
2009932 TTTGTATTATTTTATTTTTAT
1 TTTTTATTATTTT-TTTTTAT
* **
2009953 TCAATTTA--ATCCTTTTTTAT
1 T--TTTTATTATTTTTTTTTAT
* *
2009973 TTTTTATCA-TTTTTTTCAT
1 TTTTTATTATTTTTTTTTAT
* *
2009992 TTATGTTATTATTGTTCTTATAT
1 TT-T-TTATTATT-TTTTTTTAT
2010015 TTTTT
1 TTTTT
2010020 CCTAACACAT
Statistics
Matches: 66, Mismatches: 13, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
18 4 0.06
19 9 0.14
20 10 0.15
21 29 0.44
22 3 0.05
23 11 0.17
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTTTATTATTTTTTTTTAT
Found at i:2011703 original size:60 final size:60
Alignment explanation
Indices: 2011639--2011754 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
2011629 ATAGTCAAAT
* * * *
2011639 GATCATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAACAACACTCTATAGTTGAAG
1 GATCATTTTATAACTTTTAATAATCAATGAACTCAACAAAACAACACCCTATAGTTGAAG
* * * *
2011699 GATCATTTTATAACTTTTAATAATCAATGAACTTAATAAAATAATACCCTATAGTT
1 GATCATTTTATAACTTTTAATAATCAATGAACTCAACAAAACAACACCCTATAGTT
2011755 AGGGGGCCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (60 bp):
GATCATTTTATAACTTTTAATAATCAATGAACTCAACAAAACAACACCCTATAGTTGAAG
Found at i:2016388 original size:13 final size:14
Alignment explanation
Indices: 2016365--2016394 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2016355 TTCCCATTAC
2016365 AGACGTGCATATGA
1 AGACGTGCATATGA
2016379 AGAC-TGCATATGA
1 AGACGTGCATATGA
2016392 AGA
1 AGA
2016395 TTGTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:2022563 original size:10 final size:10
Alignment explanation
Indices: 2022550--2022574 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2022540 CAACTATAAC
2022550 CTAAATGCAA
1 CTAAATGCAA
2022560 CTAAATGCAA
1 CTAAATGCAA
2022570 CTAAA
1 CTAAA
2022575 ATGTTGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (10 bp):
CTAAATGCAA
Found at i:2022876 original size:2 final size:2
Alignment explanation
Indices: 2022869--2022895 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2022859 TATATTATTT
2022869 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 T
2022896 CAAGTTTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2029624 original size:21 final size:20
Alignment explanation
Indices: 2029598--2029637 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2029588 TCATCAAGGT
*
2029598 TTTTGTTGAAGCCATGAAATC
1 TTTTGTCGAAGCCAT-AAATC
*
2029619 TTTTGTCGAGGCCATAAAT
1 TTTTGTCGAAGCCATAAAT
2029638 TCATGCAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (20 bp):
TTTTGTCGAAGCCATAAATC
Found at i:2030465 original size:20 final size:20
Alignment explanation
Indices: 2030440--2030492 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
2030430 TATGCCCATG
2030440 ACTCCATTGAGCCTGAAGGA
1 ACTCCATTGAGCCTGAAGGA
2030460 ACTCCATTGAGCCTGAAGGA
1 ACTCCATTGAGCCTGAAGGA
*
2030480 ACTCCACTGAGCC
1 ACTCCATTGAGCC
2030493 AAGCTCTCGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (20 bp):
ACTCCATTGAGCCTGAAGGA
Found at i:2041314 original size:21 final size:21
Alignment explanation
Indices: 2041290--2041352 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
2041280 GTTTCCAGAT
2041290 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGATTTTGGACTA
* ** *
2041311 TCGCAATGCAATAGTCGACTA
1 TCGCAATGCGATTTTGGACTA
2041332 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGATTTTGGACTA
2041353 ACGCCGACCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (21 bp):
TCGCAATGCGATTTTGGACTA
Found at i:2041377 original size:5 final size:5
Alignment explanation
Indices: 2041356--2041391 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
2041346 TGGACTAACG
2041356 CCGACC CCGACC CCGAC CCGAC CCGAC CCGAC CCGA
1 CCGA-C CCGA-C CCGAC CCGAC CCGAC CCGAC CCGA
2041392 GACGAGACGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 20 0.67
6 10 0.33
ACGTcount: A:0.19, C:0.61, G:0.19, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:2041397 original size:5 final size:5
Alignment explanation
Indices: 2041389--2041424 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
2041379 CGACCCGACC
2041389 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
2041425 GCGGTGGCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.36, C:0.22, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:2041927 original size:6 final size:6
Alignment explanation
Indices: 2041911--2041943 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
2041901 TCTCGTCTCG
2041911 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
2041944 TGACATTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.18, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:2043467 original size:21 final size:23
Alignment explanation
Indices: 2043419--2043471 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
2043409 ATAGCCTTCA
*
2043419 AAATCCTAAAAATAAGGTAAAGAT
1 AAATCCT-AAAATAAGATAAAGAT
2043443 -AATCCTAAAATAA-ATAAA-AT
1 AAATCCTAAAATAAGATAAAGAT
2043463 AAATCCTAA
1 AAATCCTAA
2043472 TTAAAATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 12 0.44
22 7 0.26
23 6 0.22
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (23 bp):
AAATCCTAAAATAAGATAAAGAT
Found at i:2044445 original size:28 final size:28
Alignment explanation
Indices: 2044404--2044469 Score: 89
Period size: 27 Copynumber: 2.3 Consensus size: 28
2044394 CCTTTTTTTT
*
2044404 GTTTTTTTCACTATTTCGAAACAATGAACA
1 GTTTTTTT-GCTA-TTCGAAACAATGAACA
*
2044434 -TTTTTTTGCTATTCGAAACAATGAATA
1 GTTTTTTTGCTATTCGAAACAATGAACA
2044461 GTTTTTTTG
1 GTTTTTTTG
2044470 ACTTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 15 0.45
28 11 0.33
29 7 0.21
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (28 bp):
GTTTTTTTGCTATTCGAAACAATGAACA
Found at i:2059355 original size:27 final size:27
Alignment explanation
Indices: 2059317--2059368 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
2059307 TGATGTTCTC
*
2059317 ATTTTATGTTTT-TATTTTTAGAAAATT
1 ATTTTATGTTTTAAATTTTT-GAAAATT
2059344 ATTTTCAT-TTTTAAATTTTTGAAAA
1 ATTTT-ATGTTTTAAATTTTTGAAAA
2059369 CGAGAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.60
Consensus pattern (27 bp):
ATTTTATGTTTTAAATTTTTGAAAATT
Found at i:2074891 original size:22 final size:22
Alignment explanation
Indices: 2074797--2074898 Score: 113
Period size: 23 Copynumber: 4.7 Consensus size: 22
2074787 ATAGGGCAGA
2074797 GGGAATCGATACCCCCTTGAAGG
1 GGGAATCGATACCCCCTTGAA-G
*
2074820 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-TTGAAG
*
2074843 GGGAACCG--ACTCCCCTT--AG
1 GGGAATCGATAC-CCCCTTGAAG
2074862 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* *
2074884 GTGAATCGATTCCCC
1 GGGAATCGATACCCC
2074899 TTCACTCCCC
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
19 9 0.13
20 6 0.09
21 5 0.07
22 19 0.28
23 23 0.34
24 5 0.07
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.21
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:2074898 original size:41 final size:42
Alignment explanation
Indices: 2074819--2074900 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 42
2074809 CCCCTTGAAG
*
2074819 GGGGAATCGATTCCCCCTTTGAAGGGGAACCGACTCCCCTTA
1 GGGGAATCGATACCCCCTTTGAAGGGGAACCGACTCCCCTTA
* * *
2074861 GGGGAATCGATACCCCC-TTGAAGGTGAATCGATTCCCCTT
1 GGGGAATCGATACCCCCTTTGAAGGGGAACCGACTCCCCTT
2074901 CACTCCCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.56
42 16 0.44
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (42 bp):
GGGGAATCGATACCCCCTTTGAAGGGGAACCGACTCCCCTTA
Found at i:2077417 original size:12 final size:13
Alignment explanation
Indices: 2077385--2077422 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
2077375 GATACATATT
2077385 ATAGTTTTTCAAAC
1 ATAG-TTTTCAAAC
*
2077399 TTAGTTTTCAAA-
1 ATAGTTTTCAAAC
2077411 ATAGTTTTCAAA
1 ATAGTTTTCAAA
2077423 TTTGCCCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 8 0.36
14 3 0.14
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (13 bp):
ATAGTTTTCAAAC
Found at i:2078797 original size:12 final size:12
Alignment explanation
Indices: 2078780--2078807 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2078770 TTTCTTTTAA
2078780 TTGATCTCTATT
1 TTGATCTCTATT
2078792 TTGATCTCTATT
1 TTGATCTCTATT
2078804 TTGA
1 TTGA
2078808 ACCTAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.14, G:0.11, T:0.57
Consensus pattern (12 bp):
TTGATCTCTATT
Found at i:2078881 original size:17 final size:17
Alignment explanation
Indices: 2078837--2078881 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
2078827 ATTTTGATAG
2078837 ATTTATGTGT-TTTGGAT
1 ATTT-TGTGTGTTTGGAT
*
2078854 ATTTGGT-TGTTTGGAT
1 ATTTTGTGTGTTTGGAT
2078870 ATTTTGTGTGTT
1 ATTTTGTGTGTT
2078882 GAATGTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 1 0.04
16 15 0.62
17 8 0.33
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (17 bp):
ATTTTGTGTGTTTGGAT
Found at i:2082911 original size:20 final size:21
Alignment explanation
Indices: 2082875--2082925 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
2082865 GGTTGAAATT
2082875 ACTGTAGCAGTGTATCGATACC
1 ACTGTAGCAG-GTATCGATACC
2082897 ACTGTAGCA-GTATCGATACC
1 ACTGTAGCAGGTATCGATACC
2082917 -CATGTAGCA
1 AC-TGTAGCA
2082926 TTCGATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.04
20 18 0.64
22 9 0.32
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGGTATCGATACC
Found at i:2083248 original size:20 final size:20
Alignment explanation
Indices: 2083219--2083258 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2083209 ATGTTTAATG
* *
2083219 AAAAAGATATTATTTGTTAA
1 AAAAAGATATCAATTGTTAA
*
2083239 AAAAATATATCAATTGTTAA
1 AAAAAGATATCAATTGTTAA
2083259 GAAGATACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (20 bp):
AAAAAGATATCAATTGTTAA
Found at i:2083309 original size:33 final size:33
Alignment explanation
Indices: 2083268--2083332 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
2083258 AGAAGATACC
2083268 AATTGTTGGAAAATATATAAAAATGTTAAGCTA
1 AATTGTTGGAAAATATATAAAAATGTTAAGCTA
*
2083301 AATTGTTGGAAAATATATGAAAATGTTAAGCT
1 AATTGTTGGAAAATATATAAAAATGTTAAGCT
2083333 CCCCATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (33 bp):
AATTGTTGGAAAATATATAAAAATGTTAAGCTA
Found at i:2092554 original size:19 final size:19
Alignment explanation
Indices: 2092507--2092555 Score: 75
Period size: 18 Copynumber: 2.6 Consensus size: 19
2092497 CATCATTATT
2092507 GTACTATTCATACATACCA
1 GTACTATTCATACATACCA
2092526 GTAC-ATTCATACATTA-CA
1 GTACTATTCATACA-TACCA
2092544 GTACTATTCATA
1 GTACTATTCATA
2092556 AAAACATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (19 bp):
GTACTATTCATACATACCA
Found at i:2093460 original size:2 final size:2
Alignment explanation
Indices: 2093453--2093477 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2093443 TTTTCTGGTG
2093453 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2093478 GTTTATCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2100563 original size:2 final size:2
Alignment explanation
Indices: 2100558--2100603 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2100548 TATTTTTTAA
2100558 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
2100600 AT AT
1 AT AT
2100604 TTTAAATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2100614 original size:7 final size:7
Alignment explanation
Indices: 2100602--2100630 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2100592 ATATATATAT
2100602 ATTTTAA
1 ATTTTAA
2100609 ATTTTAA
1 ATTTTAA
2100616 ATTTTAA
1 ATTTTAA
2100623 ATTTTAA
1 ATTTTAA
2100630 A
1 A
2100631 AGTTTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATTTTAA
Found at i:2102589 original size:22 final size:22
Alignment explanation
Indices: 2102550--2102591 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2102540 AGTCATGGGT
**
2102550 TTCATAGGTCATTCGGGACATA
1 TTCATAGGTCATAAGGGACATA
*
2102572 TTCATAGGTCCTAAGGGACA
1 TTCATAGGTCATAAGGGACA
2102592 AATTTCACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (22 bp):
TTCATAGGTCATAAGGGACATA
Found at i:2103657 original size:2 final size:2
Alignment explanation
Indices: 2103650--2103682 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2103640 TAGATCATTA
2103650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2103683 AACTTTAATC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2108486 original size:101 final size:100
Alignment explanation
Indices: 2108377--2108626 Score: 234
Period size: 101 Copynumber: 2.5 Consensus size: 100
2108367 CTACACTTTG
* * * * *
2108377 TTTTATTCACTTACACTGGTGTAAGTATGTGTTAAGTTTTATATTTTTTTATTTAATTCAATTAC
1 TTTTATTCAC-TACATTGGTATAAGTATGTGTTAAGTCTTATAATTTTTTATTTAATTC-ACTAC
** * **
2108442 ATAAATGTAAGTATATGTT-AGTGTTATGTTTTTTTA
64 ATAAACATAAGTATATGTTAAGTGCTATACTTTTTTA
* * * * *
2108478 TTTTATTCACATACATTGATATAAATTTGTGTTAAGTGC-TACAATTTTTTATTTTATTCACTAC
1 TTTTATTCAC-TACATTGGTATAAGTATGTGTTAAGT-CTTATAATTTTTTATTTAATTCACTAC
** *
2108542 ATCGACATAAGTATGTGTTAAGTGCTATACTTTTTTA
64 ATAAACATAAGTATATGTTAAGTGCTATACTTTTTTA
* * * * * *
2108579 TTTGATTCACTATATTGGTCTAAGAATATGTTAAGTCTTATACTTTTT
1 TTTTATTCACTACATTGGTATAAGTATGTGTTAAGTCTTATAATTTTT
2108627 CGTAGTATGA
Statistics
Matches: 117, Mismatches: 29, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
99 1 0.01
100 45 0.38
101 71 0.61
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.50
Consensus pattern (100 bp):
TTTTATTCACTACATTGGTATAAGTATGTGTTAAGTCTTATAATTTTTTATTTAATTCACTACAT
AAACATAAGTATATGTTAAGTGCTATACTTTTTTA
Found at i:2108588 original size:50 final size:50
Alignment explanation
Indices: 2108398--2108590 Score: 199
Period size: 50 Copynumber: 3.8 Consensus size: 50
2108388 TACACTGGTG
** * * * *
2108398 TAAGTATGTGTTAAGTTTTATATTTTTTTATTTAATTCAATTACATAAATG
1 TAAGTATGTGTTAAGTGCTATATTTTTTTATTTTATTC-ACTACATAGATA
* * * *
2108449 TAAGTATATGTT-AGTGTTATGTTTTTTTATTTTATTCACATACATTGATA
1 TAAGTATGTGTTAAGTGCTATATTTTTTTATTTTATTCAC-TACATAGATA
* * * * * *
2108499 TAAATTTGTGTTAAGTGCTACAATTTTTTATTTTATTCACTACATCGACA
1 TAAGTATGTGTTAAGTGCTATATTTTTTTATTTTATTCACTACATAGATA
* *
2108549 TAAGTATGTGTTAAGTGCTATACTTTTTTATTTGATTCACTA
1 TAAGTATGTGTTAAGTGCTATATTTTTTTATTTTATTCACTA
2108591 TATTGGTCTA
Statistics
Matches: 118, Mismatches: 22, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
49 1 0.01
50 83 0.70
51 34 0.29
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (50 bp):
TAAGTATGTGTTAAGTGCTATATTTTTTTATTTTATTCACTACATAGATA
Found at i:2108611 original size:50 final size:50
Alignment explanation
Indices: 2108449--2108626 Score: 139
Period size: 50 Copynumber: 3.6 Consensus size: 50
2108439 TACATAAATG
* * ** * * *
2108449 TAAGTATATGTT-AGTGTTATGTTTTTTTATTTTATTCACATACATTGATA
1 TAAGAATATGTTAAGTGCTATACTTTTTTATTTGATTCAC-TACATCGACA
* * * * *
2108499 TAA-ATTTGTGTTAAGTGCTACAATTTTTTATTTTATTCACTACATCGACA
1 TAAGA-ATATGTTAAGTGCTATACTTTTTTATTTGATTCACTACATCGACA
* * * * *
2108549 TAAGTATGTGTTAAGTGCTATACTTTTTTATTTGATTCACTATATTGGTC-
1 TAAGAATATGTTAAGTGCTATACTTTTTTATTTGATTCACTACA-TCGACA
2108599 TAAGAATATGTTAAGT-CTTATACTTTTT
1 TAAGAATATGTTAAGTGC-TATACTTTTT
2108627 CGTAGTATGA
Statistics
Matches: 104, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
49 1 0.01
50 77 0.74
51 26 0.25
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (50 bp):
TAAGAATATGTTAAGTGCTATACTTTTTTATTTGATTCACTACATCGACA
Found at i:2108810 original size:17 final size:20
Alignment explanation
Indices: 2108757--2108799 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2108747 AAATCTCACA
*
2108757 ACCGTTATAACGGTTAACCG
1 ACCGTTATAATGGTTAACCG
2108777 ACCGTTATAATGGTTAACCG
1 ACCGTTATAATGGTTAACCG
2108797 ACC
1 ACC
2108800 TTTTAGGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (20 bp):
ACCGTTATAATGGTTAACCG
Found at i:2109152 original size:2 final size:2
Alignment explanation
Indices: 2109145--2109176 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2109135 ATGTGCCTAA
2109145 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
2109177 TTTTGATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2126862 original size:205 final size:206
Alignment explanation
Indices: 2126426--2126876 Score: 513
Period size: 206 Copynumber: 2.2 Consensus size: 206
2126416 CAAAATGAGG
* * *
2126426 ATAGAACAACATTTCCAGT-AAAGAGTTCATAATGAGAAGAACTCGTCCAATGAGGGAGAAAAAG
1 ATAGATCAACATTTCTAGTGAAAGAGTTCATAATGAG--GAACTCCTCCAATGAGGGAGAAAAAG
* * ** * * *
2126490 TCCATAATTAGAAGAACTTATTCAACATTGGCTTGTCTATCACATAAGAAGTTAGATCAGTATCA
64 TCCATAATGAGAAAAACTTATTCAACATTGGCTCATCCATCACATAAGAAGTTAGACCAGCATCA
** * **
2126555 TCATTTCATTCGATTCCATCACATAAAGAGTTTGGATCAGAATCATCTCGTTCGAGTTCAAACTC
129 TCATTTCACCCAATTCCATCACATAAAGAGTTTGGATCAGAATCATCTCACTCGAGTTCAAACTC
2126620 ATCACAGAAGGCA
194 ATCACAGAAGGCA
* * *
2126633 ATAGATCATCATTTCTAGTGAAAGAGTTCATAATGAGGAACTCCTCCAATGAGGGAGAAGAAGTT
1 ATAGATCAACATTTCTAGTGAAAGAGTTCATAATGAGGAACTCCTCCAATGAGGGAGAAAAAGTC
* * *
2126698 CATAATGAGAAAAACTTGTTCAACCTTGGCTCATCCATCACTTAA-AGAGTTAGACCAGCATCAT
66 CATAATGAGAAAAACTTATTCAACATTGGCTCATCCATCACATAAGA-AGTTAGACCAGCATCAT
* * * * *
2126762 CTTTTCGCCCAATTCCATCACATAAGGAG-TTGGATCA-ACATCATCTCACTCTATTTCAAACTC
130 CATTTCACCCAATTCCATCACATAAAGAGTTTGGATCAGA-ATCATCTCACTCGAGTTCAAACTC
* *
2126825 AT-ATCGGAATG-A
194 ATCA-CAGAAGGCA
* *
2126837 GGTA-AGTCAACATTTCTAATGAAAGAGTTCATAATG-GGAA
1 -ATAGA-TCAACATTTCTAGTGAAAGAGTTCATAATGAGGAA
2126877 GAACTTATAC
Statistics
Matches: 207, Mismatches: 31, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
204 8 0.04
205 66 0.32
206 100 0.48
207 16 0.08
208 17 0.08
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (206 bp):
ATAGATCAACATTTCTAGTGAAAGAGTTCATAATGAGGAACTCCTCCAATGAGGGAGAAAAAGTC
CATAATGAGAAAAACTTATTCAACATTGGCTCATCCATCACATAAGAAGTTAGACCAGCATCATC
ATTTCACCCAATTCCATCACATAAAGAGTTTGGATCAGAATCATCTCACTCGAGTTCAAACTCAT
CACAGAAGGCA
Found at i:2127711 original size:25 final size:25
Alignment explanation
Indices: 2127675--2127731 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
2127665 AAAGGGGAGA
*
2127675 TGTTTTTATATATCAAAGAAAGTGG
1 TGTTTTTATATATAAAAGAAAGTGG
*
2127700 TGTTTTTTTATATAAAAGAAAGTGG
1 TGTTTTTATATATAAAAGAAAGTGG
2127725 TGTTTTT
1 TGTTTTT
2127732 CGAAGGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (25 bp):
TGTTTTTATATATAAAAGAAAGTGG
Found at i:2129116 original size:24 final size:24
Alignment explanation
Indices: 2129089--2129137 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2129079 AATACAAATC
2129089 AATTTGTATTTAAAA-ATGATTTTT
1 AATTTGTATTTAAAAGAT-ATTTTT
* *
2129113 AATTTTTTTTTAAAAGATATTTTT
1 AATTTGTATTTAAAAGATATTTTT
2129137 A
1 A
2129138 GGTATTCGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (24 bp):
AATTTGTATTTAAAAGATATTTTT
Found at i:2130377 original size:32 final size:32
Alignment explanation
Indices: 2130331--2130416 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
2130321 AGGAAAGTAC
2130331 TTAGTGTTCGAGAGAAACTAAGTAGCTCATAT
1 TTAGTGTTCGAGAGAAACTAAGTAGCTCATAT
** * *
2130363 TTAGTGTTTAAGAGAAACTAAGTAGCTTATCT
1 TTAGTGTTCGAGAGAAACTAAGTAGCTCATAT
2130395 TTAGTGTTCGAGAGAAACTAAG
1 TTAGTGTTCGAGAGAAACTAAG
2130417 GAGGATCAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (32 bp):
TTAGTGTTCGAGAGAAACTAAGTAGCTCATAT
Found at i:2138038 original size:22 final size:22
Alignment explanation
Indices: 2138013--2138054 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2138003 AACAGTACCA
* * *
2138013 TGAATAGTATTGAGCAGTATTG
1 TGAACAGTAATGAACAGTATTG
2138035 TGAACAGTAATGAACAGTAT
1 TGAACAGTAATGAACAGTAT
2138055 CAAATGCTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (22 bp):
TGAACAGTAATGAACAGTATTG
Found at i:2144567 original size:13 final size:13
Alignment explanation
Indices: 2144551--2144605 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
2144541 GACGACACGC
*
2144551 AATGAGCGTCATA
1 AATGCGCGTCATA
*
2144564 AATGCGTGTCATA
1 AATGCGCGTCATA
* *
2144577 AATGTGTGTCATA
1 AATGCGCGTCATA
2144590 AATGCGCGTCATA
1 AATGCGCGTCATA
2144603 AAT
1 AAT
2144606 TCATAACGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:2150806 original size:9 final size:9
Alignment explanation
Indices: 2150792--2150816 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2150782 TTTATCGTAA
2150792 CGTCATCCT
1 CGTCATCCT
2150801 CGTCATCCT
1 CGTCATCCT
2150810 CGTCATC
1 CGTCATC
2150817 ATCATAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.44, G:0.12, T:0.32
Consensus pattern (9 bp):
CGTCATCCT
Found at i:2151437 original size:34 final size:34
Alignment explanation
Indices: 2151399--2151499 Score: 157
Period size: 34 Copynumber: 3.0 Consensus size: 34
2151389 GAATTTAATG
*
2151399 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
* * * *
2151433 TTAAATTTTGAATAATATTATTTGTATTTTAATT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
2151467 TTAAATTTCGAATACTATAATTTGTATTTTAAA
1 TTAAATTTCGAATACTATAATTTGTATTTTAAA
2151500 AACATTTATT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (34 bp):
TTAAATTTCGAATACTATAATTTGTATTTTAAAT
Found at i:2152051 original size:21 final size:20
Alignment explanation
Indices: 2152024--2152093 Score: 104
Period size: 21 Copynumber: 3.4 Consensus size: 20
2152014 GGTATAAAAC
*
2152024 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
2152044 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
2152065 CCCTGCGGGCTAGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
2152086 CCCTGCGG
1 -CCTGCGG
2152094 AGATGACATA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
20 3 0.06
21 41 0.87
22 3 0.06
ACGTcount: A:0.20, C:0.26, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:2153908 original size:27 final size:27
Alignment explanation
Indices: 2153878--2153930 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
2153868 TAAAAAAATT
*
2153878 AATA-AATTTAAATAAAATAATTATATA
1 AATATAATTTAAATAAAA-AAATATATA
* *
2153905 AATATTATTTTAATAAAAAAATATAT
1 AATATAATTTAAATAAAAAAATATAT
2153931 TTATATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AATATAATTTAAATAAAAAAATATATA
Found at i:2153964 original size:25 final size:24
Alignment explanation
Indices: 2153900--2153964 Score: 58
Period size: 25 Copynumber: 2.6 Consensus size: 24
2153890 TAAAATAATT
** *
2153900 ATATAAATATTATTTTAATAAAAAA
1 ATATAAATATT-TAATAATATAAAA
**
2153925 ATATATTTATATTAATAATATAAAA
1 ATATAAATAT-TTAATAATATAAAA
2153950 ATAATAAATATTTAA
1 AT-ATAAATATTTAA
2153965 AAAATAATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
25 24 0.77
26 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATAAATATTTAATAATATAAAA
Found at i:2154300 original size:61 final size:60
Alignment explanation
Indices: 2154173--2154303 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
2154163 GACGCGTCTT
* * *
2154173 CGGGGATGTGTCTTTCACACGTGGCAACTGAATCAGTAAAATAAAGGTAAAGCGCGTCCC
1 CGGGGATGCGCCTTTCACACGTGGCAACTCAATCAGTAAAATAAAGGTAAAGCGCGTCCC
* *
2154233 CGGGGATGCGCCTTTCACACGTGGCATC-CAACTCAGCGTAAAACT-AA-GTAAAGCGTGTCCC
1 CGGGGATGCGCCTTTCACACGTGGCAACTCAA-TCA--GTAAAA-TAAAGGTAAAGCGCGTCCC
2154294 CGGGGATGCG
1 CGGGGATGCG
2154304 TTTTTCGCCA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
59 2 0.03
60 28 0.45
61 23 0.37
62 8 0.13
63 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (60 bp):
CGGGGATGCGCCTTTCACACGTGGCAACTCAATCAGTAAAATAAAGGTAAAGCGCGTCCC
Found at i:2161039 original size:30 final size:32
Alignment explanation
Indices: 2160976--2161046 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 32
2160966 TATAGTTTTA
* *
2160976 ATATTTAATATTATAATAGTACTGTTATGATTT
1 ATATTAAATATTATAATAGTAC-GTTATAATTT
*
2161009 ATATTAAATATTATTA-AGTA-GTTATAATTT
1 ATATTAAATATTATAATAGTACGTTATAATTT
*
2161039 AAATTAAA
1 ATATTAAA
2161047 AACAAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 16 0.47
32 4 0.12
33 14 0.41
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (32 bp):
ATATTAAATATTATAATAGTACGTTATAATTT
Found at i:2169691 original size:65 final size:64
Alignment explanation
Indices: 2169620--2169772 Score: 175
Period size: 65 Copynumber: 2.4 Consensus size: 64
2169610 TACACCTTAG
* * * *
2169620 GTGCATCTGTACACT-AATTACATTCGATATTTTAA-AAGAGCCAGGAGTGCATCGATGCATGGT
1 GTGCATCGGTACA-TAAAATACATTCGATATTTCAATAA-AGCCAAGAGTGCATCGATGCATGGT
2169683 CT
64 -T
* * * **
2169685 GTGCATCGGTGCATAAAATGCATTCGATGTTTCAATAAATTCAAGAGTGCATCGATGCATGGTT
1 GTGCATCGGTACATAAAATACATTCGATATTTCAATAAAGCCAAGAGTGCATCGATGCATGGTT
*
2169749 GTGCATCGGTACATAAAATGCATT
1 GTGCATCGGTACATAAAATACATT
2169773 TGAAATAGGG
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 25 0.33
65 49 0.64
66 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATACATTCGATATTTCAATAAAGCCAAGAGTGCATCGATGCATGGTT
Found at i:2171895 original size:13 final size:13
Alignment explanation
Indices: 2171861--2171908 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
2171851 CCCTAATGAG
*
2171861 CAATCTTTGAAAA
1 CAATATTTGAAAA
2171874 CTAA-ATTTGAAAA
1 C-AATATTTGAAAA
*
2171887 CAATGTTTGAAAA
1 CAATATTTGAAAA
2171900 TCAATATTT
1 -CAATATTT
2171909 AGTTTTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 2 0.07
13 18 0.62
14 9 0.31
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.35
Consensus pattern (13 bp):
CAATATTTGAAAA
Found at i:2172439 original size:21 final size:21
Alignment explanation
Indices: 2172377--2172440 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 21
2172367 AACCCGACGG
2172377 GTGTATCGATGCATATTCAAA
1 GTGTATCGATGCATATTCAAA
* * *
2172398 GAATGCATC-AGTGCATCTTCATA
1 G--TGTATCGA-TGCATATTCAAA
2172421 GTGTATCGATGCATATTCAA
1 GTGTATCGATGCATATTCAA
2172441 GGGATGCATC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
21 15 0.45
22 2 0.06
23 16 0.48
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (21 bp):
GTGTATCGATGCATATTCAAA
Found at i:2172440 original size:44 final size:44
Alignment explanation
Indices: 2172377--2172471 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 44
2172367 AACCCGACGG
*
2172377 GTGTATCGATGCATATTCAAAGAATGCATCAGTGCA-TCTTCATA
1 GTGTATCGATGCATATTCAAAGAATGCATCAGTACACT-TTCATA
* * *
2172421 GTGTATCGATGCATATTCAAGGGATGCATCGGTACACTTTCATA
1 GTGTATCGATGCATATTCAAAGAATGCATCAGTACACTTTCATA
2172465 GTGTATC
1 GTGTATC
2172472 CATACATAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 45 0.98
45 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (44 bp):
GTGTATCGATGCATATTCAAAGAATGCATCAGTACACTTTCATA
Found at i:2176808 original size:21 final size:18
Alignment explanation
Indices: 2176768--2176810 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 18
2176758 AACTCCCACG
*
2176768 TTCTTCTTTTTCTCATTC
1 TTCTTCTTTTTCTCAATC
2176786 TTCTTCTTTGTCTCGTCAATC
1 TTCTTCTTT-T-TC-TCAATC
2176807 TTCT
1 TTCT
2176811 CGAGGTCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 1 0.05
20 2 0.10
21 9 0.43
ACGTcount: A:0.07, C:0.28, G:0.05, T:0.60
Consensus pattern (18 bp):
TTCTTCTTTTTCTCAATC
Found at i:2178892 original size:28 final size:28
Alignment explanation
Indices: 2178861--2178918 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
2178851 TTTTGAGATT
* *
2178861 AAATCTAATATTTATATAATAATAAATA
1 AAATCTAATATTAATAGAATAATAAATA
2178889 AAATCTAATATTAATAGAATAATAAATA
1 AAATCTAATATTAATAGAATAATAAATA
2178917 AA
1 AA
2178919 TTTAGTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (28 bp):
AAATCTAATATTAATAGAATAATAAATA
Found at i:2185643 original size:14 final size:14
Alignment explanation
Indices: 2185599--2185645 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
2185589 GACTTGGATC
2185599 AGTTGACTCAAATG
1 AGTTGACTCAAATG
*
2185613 AATTGACTCAAATG
1 AGTTGACTCAAATG
* *
2185627 AGTTGACTCGAACG
1 AGTTGACTCAAATG
2185641 AGTTG
1 AGTTG
2185646 GCTCGGTCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (14 bp):
AGTTGACTCAAATG
Found at i:2201491 original size:64 final size:65
Alignment explanation
Indices: 2201423--2201545 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 65
2201413 TTGGAACACT
** *
2201423 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCC
1 TGATGCATCAATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCC
*****
2201487 TGATGCATCAATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAA
1 TGATGCATCAATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAA
2201546 TATTCATAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
64 42 0.84
65 8 0.16
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (65 bp):
TGATGCATCAATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCC
Found at i:2201577 original size:19 final size:19
Alignment explanation
Indices: 2201553--2201620 Score: 104
Period size: 19 Copynumber: 3.6 Consensus size: 19
2201543 AAATATTCAT
2201553 AGTGCATCGATGCATGGAG
1 AGTGCATCGATGCATGGAG
2201572 AGTGCATCGATGCATGGAG
1 AGTGCATCGATGCATGGAG
*
2201591 AGTGCATCGGTGCATGGA-
1 AGTGCATCGATGCATGGAG
2201609 A-TGCATTCGATG
1 AGTGCA-TCGATG
2201621 TTCAATTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
17 4 0.09
18 6 0.13
19 36 0.78
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCATGGAG
Found at i:2201577 original size:65 final size:64
Alignment explanation
Indices: 2201444--2201586 Score: 182
Period size: 64 Copynumber: 2.2 Consensus size: 64
2201434 TGCACCAAGT
* * ***
2201444 GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCAATGCATGGCTT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAGCATGATGCATCAATGCATGGAGA
* *
2201508 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAT-AGTGCATCGATGCATGGA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTGAAAAATA-GCATGA-TGCATCAATGCATGGA
2201571 GA
63 GA
2201573 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2201587 GGAGAGTGCA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 35 0.51
65 34 0.49
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAGCATGATGCATCAATGCATGGAGA
Found at i:2201662 original size:84 final size:84
Alignment explanation
Indices: 2201481--2201671 Score: 201
Period size: 84 Copynumber: 2.3 Consensus size: 84
2201471 TGTTTGAAAA
* * *** *
2201481 ATAGCCTGATGCATCAATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAA
1 ATAGACTGATGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATG-TTTCAAAA
2201546 TATTCATAGTGCATCGATGC
65 TATTCATAGTGCATCGATGC
* * ** *
2201566 ATGGA--GAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATG-TTC-AAT
1 ATAGACTGA-TGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAA
*
2201627 TAATTCATCGATGCATCGATGC
65 T-ATTCATAG-TGCATCGATGC
*
2201649 ATAGACTGATGCATCGGTGCATG
1 ATAGACTGATGCATCGATGCATG
2201672 CCTTTGAATA
Statistics
Matches: 87, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
81 3 0.03
82 9 0.10
83 17 0.20
84 53 0.61
85 5 0.06
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (84 bp):
ATAGACTGATGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT
ATTCATAGTGCATCGATGC
Found at i:2207826 original size:15 final size:15
Alignment explanation
Indices: 2207806--2207838 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2207796 CTGGCCTGTT
*
2207806 CGACCCGATCTAACC
1 CGACCCGATCCAACC
2207821 CGACCCGATCCAACC
1 CGACCCGATCCAACC
2207836 CGA
1 CGA
2207839 ACCAAACAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.48, G:0.15, T:0.09
Consensus pattern (15 bp):
CGACCCGATCCAACC
Found at i:2208464 original size:23 final size:23
Alignment explanation
Indices: 2208437--2208481 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2208427 ATTTTATGAA
*
2208437 TATTGTGTATCTTAT-ATATGATT
1 TATTGTATAT-TTATGATATGATT
2208460 TATTGTATATTTATGATATGAT
1 TATTGTATATTTATGATATGAT
2208482 ATCTGGTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.56
Consensus pattern (23 bp):
TATTGTATATTTATGATATGATT
Found at i:2210796 original size:18 final size:18
Alignment explanation
Indices: 2210773--2210807 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2210763 GATAATATTG
2210773 AGAGTTCAGTGATAGTTA
1 AGAGTTCAGTGATAGTTA
2210791 AGAGTTCAGTGATAGTT
1 AGAGTTCAGTGATAGTT
2210808 CAGATTCTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (18 bp):
AGAGTTCAGTGATAGTTA
Found at i:2213884 original size:65 final size:65
Alignment explanation
Indices: 2213763--2213906 Score: 229
Period size: 65 Copynumber: 2.2 Consensus size: 65
2213753 AATACTATGG
* *
2213763 GTGGCACC-TTTATGCTATAATGCACTGTTATACATTTAACAAAAATCGATTGATACTTTTATTA
1 GTGGCACCTTTTATGCTATAATGCACCGTTATACATTTAACAAAAATCGATCGATACTTTTATTA
*
2213827 GTGGCACCTTTTATGCCTATAATGCACCGTTATGCATTTAAC-AAAATCGATCGATACTTTTATT
1 GTGGCACCTTTTATG-CTATAATGCACCGTTATACATTTAACAAAAATCGATCGATACTTTTATT
2213891 A
65 A
*
2213892 GTGGTACCTTTTATG
1 GTGGCACCTTTTATG
2213907 TCAAATATGA
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
64 8 0.11
65 42 0.57
66 24 0.32
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (65 bp):
GTGGCACCTTTTATGCTATAATGCACCGTTATACATTTAACAAAAATCGATCGATACTTTTATTA
Found at i:2218224 original size:2 final size:2
Alignment explanation
Indices: 2218217--2218249 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2218207 ACGATTTTCT
2218217 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
2218250 CGTATAAACC
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:2220636 original size:2 final size:2
Alignment explanation
Indices: 2220629--2220653 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2220619 TTTAGAATCA
2220629 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2220654 CTGTTTGATG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2232825 original size:12 final size:12
Alignment explanation
Indices: 2232808--2232839 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
2232798 TAGAGCTTCT
2232808 TCAAGGATCGTC
1 TCAAGGATCGTC
2232820 TCAAGGATCGTC
1 TCAAGGATCGTC
2232832 TCAAGGAT
1 TCAAGGAT
2232840 GTGAAGCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (12 bp):
TCAAGGATCGTC
Found at i:2235539 original size:13 final size:13
Alignment explanation
Indices: 2235521--2235545 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2235511 TTTCATTTCT
2235521 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
2235534 AAAAAAAAAAGA
1 AAAAAAAAAAGA
2235546 AAACAGAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:2235548 original size:18 final size:17
Alignment explanation
Indices: 2235521--2235554 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2235511 TTTCATTTCT
*
2235521 AAAAAAAAAAGAGAAAA
1 AAAAAAAAAACAGAAAA
2235538 AAAAAAGAAAACAGAAA
1 AAAAAA-AAAACAGAAA
2235555 GAGACATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAACAGAAAA
Found at i:2236790 original size:17 final size:17
Alignment explanation
Indices: 2236767--2236808 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2236757 TATTTTCTTT
2236767 ATTTTTACT-TTAAATC
1 ATTTTTACTATTAAATC
* *
2236783 ACTTTTTATTATTTAATC
1 A-TTTTTACTATTAAATC
2236801 ATTTTTAC
1 ATTTTTAC
2236809 CAAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 7 0.33
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTACTATTAAATC
Found at i:2237249 original size:21 final size:21
Alignment explanation
Indices: 2237205--2237249 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2237195 TGTTTCTGAC
*
2237205 TTGAGAGCTAGCTTTGATGAT
1 TTGAGAGCTAGCTTTAATGAT
* * *
2237226 TTGAGATCTAGTTTTAATGCT
1 TTGAGAGCTAGCTTTAATGAT
2237247 TTG
1 TTG
2237250 GAGGCTCACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.44
Consensus pattern (21 bp):
TTGAGAGCTAGCTTTAATGAT
Found at i:2244914 original size:31 final size:31
Alignment explanation
Indices: 2244876--2244998 Score: 201
Period size: 31 Copynumber: 4.0 Consensus size: 31
2244866 GAGTCAAAGG
* * *
2244876 TTACCTATGTTCTTCGGGATATATGGATTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGA
2244907 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGA
2244938 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGA
* *
2244969 TTACCTATGTTCTTCGGAACATATGAACTG
1 TTACCTATGTTCTTCGGGACATATGGACTG
2244999 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 87 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGA
Found at i:2246417 original size:22 final size:22
Alignment explanation
Indices: 2246389--2246437 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
2246379 ACCGTACGGT
*
2246389 ATGAATAGTGTCGTGAACAATA
1 ATGAATAGTGCCGTGAACAATA
*
2246411 ATGAATAGTGCCGTGAACAGTA
1 ATGAATAGTGCCGTGAACAATA
2246433 ATGAA
1 ATGAA
2246438 CAGTCAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (22 bp):
ATGAATAGTGCCGTGAACAATA
Found at i:2248229 original size:22 final size:22
Alignment explanation
Indices: 2248203--2248255 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
2248193 ATCTAACGGT
* *
2248203 ATGAACAGTATCGTGAACAGTA
1 ATGAACAATACCGTGAACAGTA
2248225 ATGAACAATACCGTGAACAGTA
1 ATGAACAATACCGTGAACAGTA
*
2248247 TTGAACAAT
1 ATGAACAAT
2248256 GCTACAGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (22 bp):
ATGAACAATACCGTGAACAGTA
Found at i:2248861 original size:18 final size:18
Alignment explanation
Indices: 2248838--2248912 Score: 87
Period size: 18 Copynumber: 3.9 Consensus size: 18
2248828 ACTATATATT
*
2248838 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
2248856 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCAC----TA
2248878 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
2248896 TATCTCGAAGGACCACT
1 TGTCCCGAAGGACCACT
2248913 CCTTAAGAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
18 32 0.64
22 18 0.36
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2252854 original size:22 final size:22
Alignment explanation
Indices: 2252819--2252869 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2252809 AAGAGAATTT
* *
2252819 ATATACATAGTTTATATATACA
1 ATATATATACTTTATATATACA
2252841 ATATATATACTTTATATATACA
1 ATATATATACTTTATATATACA
*
2252863 CTATATA
1 ATATATA
2252870 GTTTATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATATATACTTTATATATACA
Found at i:2252878 original size:11 final size:11
Alignment explanation
Indices: 2252820--2253052 Score: 64
Period size: 11 Copynumber: 22.0 Consensus size: 11
2252810 AGAGAATTTA
*
2252820 TATACATAGTT
1 TATATATAGTT
***
2252831 TATATATACAA
1 TATATATAGTT
*
2252842 TATATATACTT
1 TATATATAGTT
2252853 TATATATA---
1 TATATATAGTT
*
2252861 CACTATATAGTT
1 TA-TATATAGTT
2252873 TATATATAGTT
1 TATATATAGTT
* *
2252884 TATAT-TAATA
1 TATATATAGTT
*
2252894 AACTATATAGTT
1 TA-TATATAGTT
* *
2252906 TATACATA--A
1 TATATATAGTT
2252915 TATATATCA-TT
1 TATATAT-AGTT
*
2252926 TATATATAGTA
1 TATATATAGTT
* *
2252937 TATA-ATAATA
1 TATATATAGTT
* ***
2252947 TAAATATAAAC
1 TATATATAGTT
* *
2252958 TATA-AAATTT
1 TATATATAGTT
2252968 ATATATATAGTT
1 -TATATATAGTT
*
2252980 TATATATA-TAA
1 TATATATAGT-T
*
2252991 TATATATACTT
1 TATATATAGTT
*
2253002 TATACATA---
1 TATATATAGTT
*
2253010 AACTATATAGTT
1 TA-TATATAGTT
* *
2253022 TATACATA--A
1 TATATATAGTT
2253031 TATATATAGTT
1 TATATATAGTT
*
2253042 CATATATAGTT
1 TATATATAGTT
2253053 GTTTCAATTT
Statistics
Matches: 161, Mismatches: 41, Indels: 40
0.67 0.17 0.17
Matches are distributed among these distances:
8 2 0.01
9 24 0.15
10 17 0.11
11 107 0.66
12 11 0.07
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (11 bp):
TATATATAGTT
Found at i:2252878 original size:22 final size:21
Alignment explanation
Indices: 2252819--2252880 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
2252809 AAGAGAATTT
*
2252819 ATATACATAGTTTATATATACA
1 ATATATATA-TTTATATATACA
2252841 ATATATATACTTTATATATACA
1 ATATATATA-TTTATATATACA
* *
2252863 CTATATA-GTTTATATATA
1 ATATATATATTTATATATA
2252881 GTTTATATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.28
22 26 0.72
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (21 bp):
ATATATATATTTATATATACA
Found at i:2252887 original size:20 final size:20
Alignment explanation
Indices: 2252819--2253049 Score: 127
Period size: 20 Copynumber: 12.0 Consensus size: 20
2252809 AAGAGAATTT
*
2252819 ATATACATAGTTTATATATACA
1 ATATATATAGTTTATATAT--A
*
2252841 ATATATATACTTTATATATA
1 ATATATATAGTTTATATATA
*
2252861 CA-CTATATAGTTTATATATA
1 -ATATATATAGTTTATATATA
*
2252881 GT-T-TATA--TTA-ATA-A
1 ATATATATAGTTTATATATA
* *
2252895 A-CTATATAGTTTATACATA
1 ATATATATAGTTTATATATA
2252914 ATATATATCA-TTTATATATA
1 ATATATAT-AGTTTATATATA
*
2252934 GTATATA-A---TA-ATATA
1 ATATATATAGTTTATATATA
* * * * *
2252949 A-ATATAAACTATA-AAATTT
1 ATATATATAGTTTATATA-TA
2252968 ATATATATAGTTTATATATATA
1 ATATATATAG-TT-TATATATA
* *
2252990 ATATATATACTTTATACATA
1 ATATATATAGTTTATATATA
*
2253010 A-ACTATATAGTTTATACATA
1 ATA-TATATAGTTTATATATA
*
2253030 ATATATATAGTTCATATATA
1 ATATATATAGTTTATATATA
2253050 GTTGTTTCAA
Statistics
Matches: 165, Mismatches: 23, Indels: 44
0.71 0.10 0.19
Matches are distributed among these distances:
14 7 0.04
15 13 0.08
16 5 0.03
17 3 0.02
18 11 0.07
19 6 0.04
20 83 0.50
21 6 0.04
22 29 0.18
23 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (20 bp):
ATATATATAGTTTATATATA
Found at i:2252974 original size:13 final size:13
Alignment explanation
Indices: 2252958--2252998 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2252948 AAATATAAAC
*
2252958 TATAAAATTTATA
1 TATATAATTTATA
*
2252971 TATATAGTTTATA
1 TATATAATTTATA
*
2252984 TATATAATATATA
1 TATATAATTTATA
2252997 TA
1 TA
2252999 CTTTATACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
TATATAATTTATA
Found at i:2255992 original size:3 final size:3
Alignment explanation
Indices: 2255984--2256016 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2255974 TTAATTTTAT
2255984 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2256017 TTTTGATCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2257914 original size:138 final size:138
Alignment explanation
Indices: 2257740--2257995 Score: 363
Period size: 138 Copynumber: 1.9 Consensus size: 138
2257730 ACCCTGAACT
* * *
2257740 TTTTAAATTAGGTAATATTTGATTTGGCCCTCACCTTAATGCCCTAGGGTCCATTTCAATTATTT
1 TTTTAAATTAGGTAATATTCGATTTGGCCCTCACCTTAATGCCCAAGGGTCCATTTCAATTATTC
* * * *
2257805 GATTCAATATTTGGTTAAAATCAATTAGGATTAACATTATAGCATCCATCTTATGTTTAATTTTA
66 CATTCAATAATTGATTAAAATCAATTAGGATTAACATTAGAGCATCCAT-TTATGTTTAATTTTA
2257870 CTTTATTCC
130 CTTTATTCC
* * * *
2257879 TTTT-AATTAGAG-AATATTCGATTTGGCCCTCACCTTATTGCTCAAGGGTCTATTTCGATTATT
1 TTTTAAATTAG-GTAATATTCGATTTGGCCCTCACCTTAATGCCCAAGGGTCCATTTCAATTATT
* *
2257942 CCATTCAATAATTGATTAAAATCAATTAGGATTAATATTAGAGCCTCCATTTAT
65 CCATTCAATAATTGATTAAAATCAATTAGGATTAACATTAGAGCATCCATTTAT
2257996 AGGTTTATCC
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
137 4 0.04
138 94 0.91
139 5 0.05
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (138 bp):
TTTTAAATTAGGTAATATTCGATTTGGCCCTCACCTTAATGCCCAAGGGTCCATTTCAATTATTC
CATTCAATAATTGATTAAAATCAATTAGGATTAACATTAGAGCATCCATTTATGTTTAATTTTAC
TTTATTCC
Found at i:2258926 original size:24 final size:24
Alignment explanation
Indices: 2258870--2258945 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
2258860 CTGCTCATAT
*
2258870 AATTTG-CACCGAAGTG-CCACATAG
1 AATTTGTC-CCGAAG-GACCACGTAG
*
2258894 -ATTTGTCCCGAAGGACCGCGTAG
1 AATTTGTCCCGAAGGACCACGTAG
2258917 AATTTGTCCCGAAGGACCACGTAG
1 AATTTGTCCCGAAGGACCACGTAG
2258941 AATTT
1 AATTT
2258946 ATTCAACATT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
22 1 0.02
23 17 0.37
24 28 0.61
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (24 bp):
AATTTGTCCCGAAGGACCACGTAG
Done.